Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 130 of 335
Found at i:38733063 original size:25 final size:26
Alignment explanation
Indices: 38733029--38733136 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
38733019 TGGTACAAAT
38733029 TGATAAT-GGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
38733054 TGATAAT-GGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
38733079 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
38733105 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
38733131 TGATAA
1 TGATAA
38733137 GAATTTCATG
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
25 31 0.39
26 48 0.61
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:38733091 original size:51 final size:51
Alignment explanation
Indices: 38733029--38733136 Score: 173
Period size: 51 Copynumber: 2.1 Consensus size: 51
38733019 TGGTACAAAT
38733029 TGATAATGGTTAGGTAAATGTTCCATGATAAT-GGTTAGGTAAATATTCCA
1 TGATAATGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATATTCCA
* * *
38733079 TGATAATGGGTTAGGTAAATGTTTCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAAT-GGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATATTCCA
38733131 TGATAA
1 TGATAA
38733137 GAATTTCATG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
50 7 0.13
51 24 0.45
52 22 0.42
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (51 bp):
TGATAATGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATATTCCA
Found at i:38742423 original size:33 final size:33
Alignment explanation
Indices: 38742361--38742423 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
38742351 ACACAATATG
* * *
38742361 GTATTTAAAATATATATATATGTATATATAATA
1 GTATTTAAAATATATACATAAGTAAATATAATA
38742394 GTATTTAAGAATATATACATAAG-AAATATA
1 GTATTTAA-AATATATACATAAGTAAATATA
38742424 TAACTAATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 14 0.54
34 12 0.46
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40
Consensus pattern (33 bp):
GTATTTAAAATATATACATAAGTAAATATAATA
Found at i:38742980 original size:23 final size:22
Alignment explanation
Indices: 38742949--38742998 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
38742939 GGTTTCTTGG
38742949 TTTTTTTTTGGGGGTTAGGTTT
1 TTTTTTTTTGGGGGTTAGGTTT
**
38742971 TCTTTTTTTTTTGGGTTAGGTTT
1 T-TTTTTTTTGGGGGTTAGGTTT
38742994 TTTTT
1 TTTTT
38742999 GGGGGGCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.04, C:0.02, G:0.24, T:0.70
Consensus pattern (22 bp):
TTTTTTTTTGGGGGTTAGGTTT
Found at i:38743943 original size:72 final size:73
Alignment explanation
Indices: 38743731--38744726 Score: 1191
Period size: 72 Copynumber: 13.5 Consensus size: 73
38743721 GTGATCTGAA
38743731 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGACAGAAATTGAAAATACCTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTGAAA-ACAGAAATTGAAAATACCTCA
* *
38743796 GCATGTGAAC-CGAG
62 GC--GTG-TCTTGAG
* * *
38743810 GCTCAACTCACCTATCGCAATATAAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAACG
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATTGAAAATACCTCAGCG
*
38743875 TGACTTGAG
65 TGTCTTGAG
** * *
38743884 GCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGT
*
38743948 GTC-CGAG
66 GTCTTGAG
* *
38743955 TCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACCTCAGC
*
38744020 ATGTCTTGAG
64 GTGTCTTGAG
** * *
38744030 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTTTGACAACAGAAATTGAAATTACCTC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTTGAAAACAGAAATTGAAAATACCTC
* *
38744095 AGCATGTCCTGAG
61 AGCGTGTCTTGAG
* * *
38744108 GCTCAACTCACCTCTCGCAATATAATTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAACGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGT
38744173 GTCTTGAG
66 GTCTTGAG
** * * *
38744181 GCTCAACTCATTTCTTGCAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAAATACCTCAACGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGT
38744245 GTCTTGAG
66 GTCTTGAG
** * * * *
38744253 GCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAATAGAAATTGAAATTACCTCAGCAT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGT
**
38744317 GTCCCGAG
66 GTCTTGAG
*
38744325 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAA-ACAGAAATTGAAAATACCTCAGC
*
38744390 ATGTCTTGAG
64 GTGTCTTGAG
** * *
38744400 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTTGACAACAGAAATTGAAATTACCTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTTGAAAACAGAAATTGAAAATACCTCA
*
38744465 GCGTGTCCTGAG
62 GCGTGTCTTGAG
* *
38744477 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTGAAAACAGAAATTG-AAATACCTCAACGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGT
38744541 GTCTTGAG
66 GTCTTGAG
** * * *
38744549 GCTCAACTCATTTCTCACAATATGAGTTGA-ATTTTGAAAACAGAAATTGAAATTACCTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGT
**
38744613 GTCCCGAG
66 GTCTTGAG
** * *
38744621 GCTCAACTCACCTCTCGCAATATGAGTTGA--AATTAAAACACAAAAATTGAAAATACCTCAGCG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAA-ACAGAAATTGAAAATACCTCAGCG
* *
38744684 TGACCTGAG
65 TGTCTTGAG
* *
38744693 GCTCGACTCACCTCTAGCAATATGAGTTGATTTT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTT
38744727 GAAAAACAAA
Statistics
Matches: 803, Mismatches: 95, Indels: 43
0.85 0.10 0.05
Matches are distributed among these distances:
71 53 0.07
72 314 0.39
73 92 0.11
74 65 0.08
75 86 0.11
76 22 0.03
77 67 0.08
78 66 0.08
79 38 0.05
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (73 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGT
GTCTTGAG
Found at i:38744126 original size:224 final size:220
Alignment explanation
Indices: 38743731--38744726 Score: 1222
Period size: 224 Copynumber: 4.5 Consensus size: 220
38743721 GTGATCTGAA
38743731 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGACAGAAATTGAAAATACCTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAA-ACAGAAATTGAAAATACCTCA
* * *
38743796 GCATGTGAACC-GAGGCTCAACTCACCTATCGCAATATAAGTTGATTTTTTTGAAAACAGAAATT
63 GC--GTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAACAGAAATT
* * * * **
38743860 GAAAATACCTCAACGTGACTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAA
124 GAAATTACCTCAACATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATATTTTGAAAA
*
38743924 CAGAAATTGAAATTACCTCAGCGTGTC-CGAG
189 CAGAAATTGAAAATACCTCAGCGTGTCTCGAG
* *
38743955 TCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAAATTGAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-ACAGAAATTGAAAATACCTCAGC
* * ** *
38744020 ATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTTTGACAACAGAAATTG
65 GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-----TTTTTTGAAAACAGAAATTG
* * * *
38744085 AAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATAATTTGATTTTTTGAAAAC
125 AAATTACCTCAACATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATATTTTGAAAAC
* *
38744150 AGAAATTGAAAATACCTCAACGTGTCTTGAG
190 AGAAATTGAAAATACCTCAGCGTGTCTCGAG
** * * *
38744181 GCTCAACTCATTTCTTGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAAATACCTCAACG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAGCG
* ** * *
38744244 TGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-ATTTTGAAAATAGAAATTGAAATTA
66 TGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAATTA
* * * *
38744308 CCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAAAA
131 CCTCAACATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TATTTTGAAA-ACAGAA
* *
38744373 ATTGAAAATACCTCAGCATGTCTTGAG
194 ATTGAAAATACCTCAGCGTGTCTCGAG
** * *
38744400 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTTGACAACAGAAATTGAAATTACCTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTTGAAAACAGAAATTGAAAATACCTCA
*
38744465 GCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTGAAAACAGAAATTGAAA
63 GCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAA
* * ** *
38744530 -TACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGA-ATTTTGAAAACAGA
128 TTACCTCAACATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATATTTTGAAAACAGA
* *
38744593 AATTGAAATTACCTCAGCGTGTCCCGAG
193 AATTGAAAATACCTCAGCGTGTCTCGAG
** * *
38744621 GCTCAACTCACCTCTCGCAATATGAGTTGA---AATTAAAACACAAAAATTGAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAA-ACAGAAATTGAAAATACCTCAGC
* * *
38744683 GTGACCTGAGGCTCGACTCACCTCTAGCAATATGAGTTGATTTT
65 GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
38744727 GAAAAACAAA
Statistics
Matches: 680, Mismatches: 76, Indels: 40
0.85 0.10 0.05
Matches are distributed among these distances:
215 4 0.01
216 61 0.09
217 66 0.10
218 10 0.01
219 60 0.09
220 31 0.05
221 56 0.08
222 42 0.06
223 60 0.09
224 207 0.30
225 54 0.08
226 29 0.04
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (220 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAGCG
TGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAATTA
CCTCAACATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATATTTTGAAAACAGAAAT
TGAAAATACCTCAGCGTGTCTCGAG
Found at i:38744522 original size:369 final size:370
Alignment explanation
Indices: 38743726--38744726 Score: 1589
Period size: 369 Copynumber: 2.7 Consensus size: 370
38743716 AGTGTGTGAT
* *
38743726 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGACAGAAATTGAAAATA
1 CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGA---TTTTTTGAAA-ACAGAAATTGAAAATA
* * * ** * * *
38743791 CCTCAGCATGTGAAC-CGAGGCTCAACTCACCTATCGCAATATAAGTTGATTTTTTTGAAAACAG
62 CCTCA--ACGTG-TCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA--ATTTTGAAAACAG
*
38743855 AAATTGAAAATACCTCAACGTGACTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
122 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTG
*
38743920 AAAACAGAAATTGAAATTACCTCAGCGTGT-CCGAGTCTCAACTCACCTCTCGCAATATGAGTTG
187 AAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
38743984 ATTTTTTTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCA
252 ATTTTTTTGAAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCA
38744049 ATATGAGTTGATTTTTTTTTTTGACAACAGAAATTGAAATTACCTCAGCATGTC
317 ATATGAGTTGATTTTTTTTTTTGACAACAGAAATTGAAATTACCTCAGCATGTC
*
38744103 CTGAGGCTCAACTCACCTCTCGCAATATAATTTGATTTTTTGAAAACAGAAATTGAAAATACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTC
*
38744168 AACGTGTCTTGAGGCTCAACTCATTTCTTGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAA
66 AACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAA
*
38744233 ATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAATAGAA
131 ATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAA
*
38744298 ATTGAAATTACCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
196 ATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
38744363 AAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
261 AAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
*
38744428 GA-TTTTTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTC
326 GATTTTTTTTTTTGACAACAGAAATTGAAATTACCTCAGCATGTC
38744472 CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTGAAAACAGAAATTG-AAATACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTC
*
38744536 AACGTGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGAATTTTGAAAACAGAAATTGAAA
66 AACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAA
* * ** ** * * *
38744601 TTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAA-ATTAAAACACAAA
131 ATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAA-ACAGA
* * * * *
38744665 AATTGAAAATACCTCAGCGTGACCTGAGGCTCGACTCACCTCTAGCAATATGAGTTGATTTT
195 AATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
38744727 GAAAAACAAA
Statistics
Matches: 585, Mismatches: 36, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
367 5 0.01
368 176 0.30
369 199 0.34
370 110 0.19
371 32 0.05
373 21 0.04
374 10 0.02
377 32 0.05
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (370 bp):
CTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTC
AACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAA
ATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAGAA
ATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
AAAGACAAAAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
GATTTTTTTTTTTGACAACAGAAATTGAAATTACCTCAGCATGTC
Found at i:38749728 original size:12 final size:12
Alignment explanation
Indices: 38749708--38749743 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
38749698 TGGGATATGC
*
38749708 AATGTATGAATG
1 AATGCATGAATG
38749720 AATGCATGAATG
1 AATGCATGAATG
38749732 AATGCATGAATG
1 AATGCATGAATG
38749744 TCAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:38751663 original size:15 final size:15
Alignment explanation
Indices: 38751641--38751695 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
38751631 AAATATACAC
38751641 TAAT-ATAATAATAG
1 TAATAATAATAATAG
* *
38751655 TTATAATAATACTAG
1 TAATAATAATAATAG
* * *
38751670 CAATAGTAATAATTG
1 TAATAATAATAATAG
38751685 TAATAATAATA
1 TAATAATAATA
38751696 TATACACAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
14 3 0.10
15 28 0.90
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (15 bp):
TAATAATAATAATAG
Found at i:38752357 original size:28 final size:27
Alignment explanation
Indices: 38752304--38752356 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
38752294 GGTTTCTTGG
38752304 TTTTTTTTTTGGGGGGTTAGGTTTTTC
1 TTTTTTTTTTGGGGGGTTAGGTTTTTC
*
38752331 TTTTTTTTTTTGGGGGTTAGGTTTTT
1 TTTTTTTTTTGGGGGGTTAGGTTTTT
38752357 TGGGGGGGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.04, C:0.02, G:0.28, T:0.66
Consensus pattern (27 bp):
TTTTTTTTTTGGGGGGTTAGGTTTTTC
Found at i:38753804 original size:19 final size:16
Alignment explanation
Indices: 38753774--38753821 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 16
38753764 ACAAATAGGC
*
38753774 AAGAAAAATAAATAGAT
1 AAGAAAACTAAATA-AT
38753791 AAATGAAAACTAAATAAT
1 -AA-GAAAACTAAATAAT
38753809 AAGAAAAC-AAATA
1 AAGAAAACTAAATA
38753822 TAGGTGAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.18
16 6 0.21
17 2 0.07
18 4 0.14
19 11 0.39
ACGTcount: A:0.71, C:0.04, G:0.08, T:0.17
Consensus pattern (16 bp):
AAGAAAACTAAATAAT
Found at i:38753942 original size:3 final size:3
Alignment explanation
Indices: 38753934--38754216 Score: 156
Period size: 3 Copynumber: 93.3 Consensus size: 3
38753924 TTAAAAAATG
38753934 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * ** *
38753982 ATA ATA ATA ATA GA-A ATTA AGGA ATA ATA ATT AT- ATCA ACC AT- ATT
1 ATA ATA ATA ATA -ATA A-TA A-TA ATA ATA ATA ATA AT-A ATA ATA ATA
* * * * *
38754028 ATAA ATA ATAA ATA AAA ACA AAA ATC ATA ACA ATA A-A AT- ATA AGTA
1 AT-A ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
* * * * ** * *
38754074 ATA GTA ATG ATA ATG GTA ATA ACG ATA ATAA ATA ATA GTA GTA GATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA -ATA
* *
38754121 ATGA A-A ATA ATA ATA GTA ATA ATA ATA ATGA A-A ATA GTGA A-A ATA
1 AT-A ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA AT-A ATA ATA
* * *
38754166 ATA ATA GTA A-G ATA ATA A-A TATA AGTA ATA GTA A-A ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA A-TA ATA ATA ATA ATA ATA ATA
38754210 ATA ATA A
1 ATA ATA A
38754217 ATAAACTAAT
Statistics
Matches: 216, Mismatches: 40, Indels: 48
0.71 0.13 0.16
Matches are distributed among these distances:
2 19 0.09
3 169 0.78
4 28 0.13
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:38754128 original size:22 final size:21
Alignment explanation
Indices: 38754103--38754215 Score: 82
Period size: 22 Copynumber: 5.5 Consensus size: 21
38754093 TAACGATAAT
*
38754103 AAATAATAGTAGTAGATAATGA
1 AAATAATAATAGTA-ATAATGA
38754125 AAATAATAATAGTAATAAT--
1 AAATAATAATAGTAATAATGA
* *
38754144 -AATAATGA-A--AATAGTGA
1 AAATAATAATAGTAATAATGA
38754161 AAATAATAATAGTAAGATAAT-A
1 AAATAATAATAGT-A-ATAATGA
38754183 AATATAAGTAATAGTAA-AAT-A
1 AA-ATAA-TAATAGTAATAATGA
38754204 ATAATAATAATA
1 A-AATAATAATA
38754216 AATAAACTAA
Statistics
Matches: 75, Mismatches: 5, Indels: 24
0.72 0.05 0.23
Matches are distributed among these distances:
15 5 0.07
17 1 0.01
18 14 0.19
19 1 0.01
20 5 0.07
21 14 0.19
22 19 0.25
23 9 0.12
24 7 0.09
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (21 bp):
AAATAATAATAGTAATAATGA
Found at i:38755301 original size:17 final size:17
Alignment explanation
Indices: 38755275--38755307 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38755265 TGGGCTGATA
38755275 GTTGGGTTTAGGTTTGG
1 GTTGGGTTTAGGTTTGG
*
38755292 GTTGGTTTTAGGTTTG
1 GTTGGGTTTAGGTTTG
38755308 TATTGGTTTG
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:0.06, C:0.00, G:0.42, T:0.52
Consensus pattern (17 bp):
GTTGGGTTTAGGTTTGG
Found at i:38755313 original size:17 final size:17
Alignment explanation
Indices: 38755276--38755316 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
38755266 GGGCTGATAG
* *
38755276 TTGGGTTTAGGTTTGGG
1 TTGGTTTTAGGTTTGGA
*
38755293 TTGGTTTTAGGTTTGTA
1 TTGGTTTTAGGTTTGGA
38755310 TTGGTTT
1 TTGGTTT
38755317 GTTTTAGCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.07, C:0.00, G:0.37, T:0.56
Consensus pattern (17 bp):
TTGGTTTTAGGTTTGGA
Found at i:38755859 original size:181 final size:181
Alignment explanation
Indices: 38755536--38756185 Score: 930
Period size: 181 Copynumber: 3.6 Consensus size: 181
38755526 AGGACTTGTT
* * * * *
38755536 GCTTTAATCTGCTT-CACTGCAACTTCAGGAAAATAAGATTTGCTATCTTTACTCTGCTACACTG
1 GCTTCAATCTG-TTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTG
* * * * *
38755600 CAACTTTAGGGAGATAAGACTAGTGACTTCAACCTACTCCACTGCAACTTAATGA-AGATAAGGT
65 CAACTTCAGGGAGATAAGACTAGTGATTTCAACCTGCTCCACTGCAACTTCA-GAGAGATAAAGT
* ** * *
38755664 TTGTTTTGATCTGCTCTACTAAAACTTTAGAGAGATAAGATCTGCGATTTGTA
129 TTGTTTTGATCTGCTCTATTGCAACTTTAGAGAGATAAGATCTGTGATTTATA
* * * * *
38755717 GCTTCAATTTGTTCCACTACAACTTCAGGGAAATAAGATTTTCTACCTTCAGTGC-ACTCCACTG
1 GCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGT-CTGCTCCACTG
38755781 CAACTTCAGGGAGATAAGACTAGTGATTTCAACCTGCTCCACTGCAACTTCAGAGAGATAAAGTT
65 CAACTTCAGGGAGATAAGACTAGTGATTTCAACCTGCTCCACTGCAACTTCAGAGAGATAAAGTT
* *
38755846 TGTTTTGATCTGCTCTATTGCAACTTCAGAGACATAAGATCTGTGATTTATA
130 TGTTTTGATCTGCTCTATTGCAACTTTAGAGAGATAAGATCTGTGATTTATA
* *
38755898 GCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGGTCTACTGC
1 GCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGC
* *
38755963 AACTTCAGGGAGATAAGACTAGTGATTTCAACTTGCTCCACTGCAACTTCAGGGAGAT-AAGTTT
66 AACTTCAGGGAGATAAGACTAGTGATTTCAACCTGCTCCACTGCAACTTCAGAGAGATAAAGTTT
* *
38756027 TTTTTGATCTGCTCTATTGCAACTTTAGAGAGATAAGATCTATGATTTATA
131 GTTTTGATCTGCTCTATTGCAACTTTAGAGAGATAAGATCTGTGATTTATA
* * *
38756078 GCTTCAATCTGTTCCACTGCAACTTCAAGGAAATAAGATTTGCTATCTTTAGTCTGCTCCACTAC
1 GCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGC
* * *
38756143 AACTTCAGGGAGATAAGACTCGTAATTTTCAGCCTGCTCCACT
66 AACTTCAGGGAGATAAGACTAGTGA-TTTCAACCTGCTCCACT
38756186 ACTGCTTAGG
Statistics
Matches: 420, Mismatches: 44, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
180 141 0.34
181 278 0.66
182 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (181 bp):
GCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGC
AACTTCAGGGAGATAAGACTAGTGATTTCAACCTGCTCCACTGCAACTTCAGAGAGATAAAGTTT
GTTTTGATCTGCTCTATTGCAACTTTAGAGAGATAAGATCTGTGATTTATA
Found at i:38755962 original size:45 final size:43
Alignment explanation
Indices: 38755542--38756160 Score: 299
Period size: 45 Copynumber: 13.7 Consensus size: 43
38755532 TGTTGCTTTA
* * * *
38755542 ATCTGCTTCACTGCAACTTCAGGAAAATAAGATTTGCTATCTTT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTC
* * * *
38755586 ACTCTGCTACACTGCAACTTTAGGGAGATAAGACTAGTGA-CTTC
1 A-TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT-ATCTTC
* * * * * * *
38755630 AACCTACTCCACTGCAACTTAATGAAGATAAGGTTTGT-T-TTG
1 -ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTC
* ** * * *
38755672 ATCTGCTCTACTAAAACTTTAGAGAGATAAGATCTGCGATTTGTAGCTTC
1 ATCTGCTCCACTGCAACTTCAGGGAGAT-A-A-----GATTTGTATCTTC
* * * * * *
38755722 AATTTGTTCCACTACAACTTCAGGGAAATAAGATTTTCTACCTTC
1 -ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTTGTATCTTC
* * *
38755767 AGTGC-ACTCCACTGCAACTTCAGGGAGATAAGACTAGTGAT-TTC
1 A-T-CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT-ATCTTC
* * *
38755811 AACCTGCTCCACTGCAACTTCAGAGAGATAA-AGTTTGT-T-TTG
1 -ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTTGTATCTTC
* * * *
38755853 ATCTGCTCTATTGCAACTTCAGAGACATAAGATCTGTGATTTATAGCTTC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T-TG---TAT--CTTC
* *
38755903 AATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTC
1 -ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTC
* * * *
38755948 AGTCTGGTCTACTGCAACTTCAGGGAGATAAGACTAGTGAT-TTC
1 A-TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT-ATCTTC
* * *
38755992 AACTTGCTCCACTGCAACTTCAGGGAGATAAG-TTT-T-TTTTG
1 ATC-TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTC
* * * *
38756033 ATCTGCTCTATTGCAACTTTAGAGAGATAAGATCTATGATTTATAGCTTC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T-TG---TAT--CTTC
* * * *
38756083 AATCTGTTCCACTGCAACTTCAAGGAAATAAGATTTGCTATCTTT
1 -ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TATCTTC
*
38756128 AGTCTGCTCCACTACAACTTCAGGGAGATAAGA
1 A-TCTGCTCCACTGCAACTTCAGGGAGATAAGA
38756161 CTCGTAATTT
Statistics
Matches: 432, Mismatches: 95, Indels: 95
0.69 0.15 0.15
Matches are distributed among these distances:
40 25 0.06
41 51 0.12
42 10 0.02
43 8 0.02
44 100 0.23
45 133 0.31
46 1 0.00
47 8 0.02
48 7 0.02
49 5 0.01
50 9 0.02
51 75 0.17
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (43 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTC
Found at i:38756260 original size:88 final size:88
Alignment explanation
Indices: 38756133--38756579 Score: 519
Period size: 88 Copynumber: 5.1 Consensus size: 88
38756123 TCTTTAGTCT
** * *
38756133 GCTCCACTACAACTTCAGGGAGATAAGA-CTCGTAATTTTCAGCCTGCT-CCACTACTGCTTAGG
1 GCTCCACTACTGCTT-AGGGAGATAAGATCT-GTAATCTTCAGCCTGTTACC-CTACTGCTTAGG
* * * *
38756196 GAGATAAGGCT-TACTGTCTGCTATCT
63 GAGTTAAGGCTCT-CTGTCTTCGATCC
* * * * *
38756222 GCTCCACTATTGTTTAGGGAGATTAA-ATCTGTAATTTTCAGTCTGTTACCCTACTGCTTAGGGG
1 GCTCCACTACTGCTTAGGGAGA-TAAGATCTGTAATCTTCAGCCTGTTACCCTACTGCTTAGGGA
* ** *
38756286 GTTAAGGCTCACCATCTTCGATCT
65 GTTAAGGCTCTCTGTCTTCGATCC
* *
38756310 GCTCCACTACTGCTTAAGGAGATAAGATCTGTAATCTTCAGCCTGTTA-CCTCACTGCTTAGGAA
1 GCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACCCT-ACTGCTTAGGGA
* *
38756374 GTTAAGGCTCTTTGTCTTCGTTCC
65 GTTAAGGCTCTCTGTCTTCGATCC
*
38756398 GCTCAACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACCCTACTGCTTAGAGG-
1 GCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACCCTACTGCTTAG-GGA
38756462 GTTAAGGCTCTCTGTCTTCGATCC
65 GTTAAGGCTCTCTGTCTTCGATCC
* * * *
38756486 GCTCCGCTATTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACCCTACTACTTAGGGGG
1 GCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACCCTACTGCTTAGGGAG
* * * *
38756551 TTAAGGCTCACCGTATTCGATCT
66 TTAAGGCTCTCTGTCTTCGATCC
38756574 GCTCCA
1 GCTCCA
38756580 TTGCTATCTT
Statistics
Matches: 309, Mismatches: 40, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
87 8 0.03
88 279 0.90
89 22 0.07
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (88 bp):
GCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAGCCTGTTACCCTACTGCTTAGGGAG
TTAAGGCTCTCTGTCTTCGATCC
Found at i:38756347 original size:44 final size:44
Alignment explanation
Indices: 38756122--38756548 Score: 222
Period size: 44 Copynumber: 9.7 Consensus size: 44
38756112 AAGATTTGCT
* **
38756122 ATCTTTAGTCTGCTCCACTACAACTTCAGGGAGATAAGA-CTCGTA
1 ATCTTCAGTCTGCTCCACTACTGCTT-AGGGAGATAAGATCT-GTA
* * *
38756167 ATTTTCAGCCTGCTCCACTACTGCTTAGGGAGATAAG-GCT-TA
1 ATCTTCAGTCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
* * * *
38756209 CTGTCTGCTA-TCTGCTCCACTATTGTTTAGGGAGATTAA-ATCTGTA
1 --ATCTTC-AGTCTGCTCCACTACTGCTTAGGGAGA-TAAGATCTGTA
* * * * * *
38756255 ATTTTCAGTCTGTTACC-CTACTGCTTAGGGGGTTAAG-GCT-CA
1 ATCTTCAGTCTGCT-CCACTACTGCTTAGGGAGATAAGATCTGTA
*
38756297 CCATCTTC-GATCTGCTCCACTACTGCTTAAGGAGATAAGATCTGTA
1 --ATCTTCAG-TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
* * * * * * *
38756343 ATCTTCAGCCTGTTAC-CTCACTGCTTAGGAAGTTAAGGCTCT-TT
1 ATCTTCAGTCTGCTCCACT-ACTGCTTAGGGAGATAA-GATCTGTA
* * *
38756387 GTCTTC-GTTCCGCTCAACTACTGCTTAGGGAGATAAGATCTGTA
1 ATCTTCAG-TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
* * * * *
38756431 ATCTTCAGCCTGTTACC-CTACTGCTTAGAGG-GTTAAGGCTCTCT-
1 ATCTTCAGTCTGCT-CCACTACTGCTTAG-GGAGATAA-GATCTGTA
* * * *
38756475 GTCTTC-GATCCGCTCCGCTATTGCTTAGGGAGATAAGATCTGTA
1 ATCTTCAG-TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
* * *
38756519 ATCTTCAGCCTGTTACC-CTACTACTTAGGG
1 ATCTTCAGTCTGCT-CCACTACTGCTTAGGG
38756549 GGTTAAGGCT
Statistics
Matches: 281, Mismatches: 69, Indels: 65
0.68 0.17 0.16
Matches are distributed among these distances:
42 3 0.01
43 26 0.09
44 199 0.71
45 50 0.18
46 3 0.01
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.33
Consensus pattern (44 bp):
ATCTTCAGTCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
Found at i:38758315 original size:10 final size:10
Alignment explanation
Indices: 38758309--38758344 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
38758299 GTCTTTTTTA
38758309 CTTTTTTCTT
1 CTTTTTTCTT
38758319 CTTTTTT-TT
1 CTTTTTTCTT
*
38758328 ATTTTTTCTT
1 CTTTTTTCTT
38758338 CTTTTTT
1 CTTTTTT
38758345 GTATGTGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (10 bp):
CTTTTTTCTT
Found at i:38758325 original size:20 final size:19
Alignment explanation
Indices: 38758302--38758344 Score: 77
Period size: 19 Copynumber: 2.2 Consensus size: 19
38758292 TTTTGTTGTC
38758302 TTTTTTACTTTTTTCTTCTT
1 TTTTTTA-TTTTTTCTTCTT
38758322 TTTTTTATTTTTTCTTCTT
1 TTTTTTATTTTTTCTTCTT
38758341 TTTT
1 TTTT
38758345 GTATGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTATTTTTTCTTCTT
Found at i:38759106 original size:16 final size:16
Alignment explanation
Indices: 38759085--38759115 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38759075 ATGGTATGAT
*
38759085 CATGAATAAAAGAATA
1 CATGAAAAAAAGAATA
38759101 CATGAAAAAAAGAAT
1 CATGAAAAAAAGAAT
38759116 CTAAGAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.06, G:0.13, T:0.16
Consensus pattern (16 bp):
CATGAAAAAAAGAATA
Found at i:38760110 original size:15 final size:16
Alignment explanation
Indices: 38760076--38760112 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
38760066 ACCCAACCTA
*
38760076 ACCCAAAACCCAGAAG
1 ACCCAAAACCCACAAG
38760092 -CCCAAAACCC-CAAG
1 ACCCAAAACCCACAAG
38760106 ACCCAAA
1 ACCCAAA
38760113 TCAGAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 3 0.16
15 16 0.84
ACGTcount: A:0.49, C:0.43, G:0.08, T:0.00
Consensus pattern (16 bp):
ACCCAAAACCCACAAG
Found at i:38760537 original size:26 final size:26
Alignment explanation
Indices: 38760500--38760635 Score: 245
Period size: 26 Copynumber: 5.2 Consensus size: 26
38760490 TGATACAAAT
* *
38760500 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
38760526 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
38760552 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
38760578 TGATAATGGGTTAGGTAAATGTTTAA
1 TGATAATGGGTTAGGTAAATGTTTCA
38760604 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
38760630 TGATAA
1 TGATAA
38760636 GAATATCATG
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 106 1.00
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:38762145 original size:25 final size:25
Alignment explanation
Indices: 38762116--38762164 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
38762106 GCAGTTTTAC
38762116 CCCTAGGAGATAAATT-ACCGAAATA
1 CCCTAGG-GATAAATTGACCGAAATA
* *
38762141 CCCTAGGGTTAAATTGACCTAAAT
1 CCCTAGGGATAAATTGACCGAAAT
38762165 GCATGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
CCCTAGGGATAAATTGACCGAAATA
Found at i:38762658 original size:137 final size:137
Alignment explanation
Indices: 38762412--38762698 Score: 538
Period size: 137 Copynumber: 2.1 Consensus size: 137
38762402 GAGTAGTCTC
38762412 CCCAAATGGGCTTGCATATGTTTACTAATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTAATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
38762477 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
38762542 ACTGTTA
131 ACTGTTA
*
38762549 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTAATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
38762614 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGTTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
38762679 ACTGTTA
131 ACTGTTA
**
38762686 CCTGAATGGGCTT
1 CCCAAATGGGCTT
38762699 AGGCCCAATA
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 146 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTAATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:38764412 original size:16 final size:18
Alignment explanation
Indices: 38764391--38764437 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
38764381 ATTAAATTTG
38764391 TAATATTAAT-TT-TATT
1 TAATATTAATATTATATT
38764407 TAATATTAATATTATATT
1 TAATATTAATATTATATT
* *
38764425 TACTATTATTATT
1 TAATATTAATATT
38764438 TTTAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 10 0.37
17 2 0.07
18 15 0.56
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TAATATTAATATTATATT
Found at i:38764424 original size:18 final size:17
Alignment explanation
Indices: 38764391--38764448 Score: 66
Period size: 16 Copynumber: 3.5 Consensus size: 17
38764381 ATTAAATTTG
38764391 TAATATTAAT-TTTATT
1 TAATATTAATATTTATT
38764407 TAATATTAATATTATATT
1 TAATATTAATATT-TATT
* *
38764425 TACTATTATTATTT-TT
1 TAATATTAATATTTATT
*
38764441 AAATATTA
1 TAATATTA
38764449 GTGTACTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
16 18 0.50
17 3 0.08
18 15 0.42
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATATTAATATTTATT
Found at i:38764826 original size:2 final size:2
Alignment explanation
Indices: 38764821--38764852 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
38764811 TTATTACACG
38764821 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38764853 AAACTTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38768486 original size:19 final size:16
Alignment explanation
Indices: 38768456--38768503 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 16
38768446 ACAAGTAGGC
*
38768456 AAGAAAAATAAATAGAT
1 AAGAAAACTAAATA-AT
38768473 AAATGAAAACTAAATAAT
1 -AA-GAAAACTAAATAAT
38768491 AAGAAAAC-AAATA
1 AAGAAAACTAAATA
38768504 TAGGTGAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.18
16 6 0.21
17 2 0.07
18 4 0.14
19 11 0.39
ACGTcount: A:0.71, C:0.04, G:0.08, T:0.17
Consensus pattern (16 bp):
AAGAAAACTAAATAAT
Found at i:38768629 original size:3 final size:3
Alignment explanation
Indices: 38768616--38768906 Score: 156
Period size: 3 Copynumber: 96.7 Consensus size: 3
38768606 TTAAAAAATG
* **
38768616 ATA AGA ATA ATA ATA ATA ACG ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
38768664 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA A-A TTA AGGA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
** * * * * *
38768708 ATA A-A ATCA ACC AT- ATT ATAA ATA ATAA ATA AAA ACA AAA ATC ATA
1 ATA ATA AT-A ATA ATA ATA AT-A ATA AT-A ATA ATA ATA ATA ATA ATA
* * * * *
38768754 ATA ATA A-A AT- ATA AGTA ATA GTA ATG ATA ATG GTA AT- ATCG ATA
1 ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
* * * *
38768798 ATAA ATA ATA GTA GTA GATA ATGA A-A ATT ATA ATA GTA ATA ATA ATA
1 AT-A ATA ATA ATA ATA -ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
* * *
38768845 ATGA A-A ATA GTGA A-A ATA ATA ATA GTA ATG ATA ATA A-A TATA AGTA
1 AT-A ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA A-TA
*
38768891 ATA GTA A-A ATA ATA AT
1 ATA ATA ATA ATA ATA AT
38768907 TAATTAATTA
Statistics
Matches: 220, Mismatches: 43, Indels: 50
0.70 0.14 0.16
Matches are distributed among these distances:
2 22 0.10
3 170 0.77
4 28 0.13
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:38768912 original size:4 final size:4
Alignment explanation
Indices: 38768903--38768931 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
38768893 AGTAAAATAA
38768903 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT T
38768932 TAATAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TAAT
Found at i:38771322 original size:15 final size:15
Alignment explanation
Indices: 38771302--38771331 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38771292 CATTTTATTT
*
38771302 ATATTAGGATAATTA
1 ATATTAAGATAATTA
38771317 ATATTAAGATAATTA
1 ATATTAAGATAATTA
38771332 TTAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:38771359 original size:27 final size:26
Alignment explanation
Indices: 38771298--38771360 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
38771288 ACTCCATTTT
38771298 ATTTATATTAGGATAATTAATATTAAG
1 ATTT-TATTAGGATAATTAATATTAAG
* * *
38771325 ATAATTATTAGGATTATTTAATTTTAAG
1 AT-TTTATTAGGA-TAATTAATATTAAG
38771353 ATTTTATT
1 ATTTTATT
38771361 TTAATAATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 15 0.50
28 15 0.50
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.51
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:38772625 original size:21 final size:22
Alignment explanation
Indices: 38772599--38772652 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 22
38772589 GGTGATGATA
38772599 TTTCTTTAAA-CTCAATTTTCC
1 TTTCTTTAAATCTCAATTTTCC
38772620 TTTCTTTGTAAATTGCTCAATTTTCC
1 TTTC-TT-TAAA-T-CTCAATTTTCC
38772646 TTTCTTT
1 TTTCTTT
38772653 GTAAAATTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
21 4 0.14
22 2 0.07
23 4 0.14
24 1 0.04
25 2 0.07
26 15 0.54
ACGTcount: A:0.19, C:0.20, G:0.04, T:0.57
Consensus pattern (22 bp):
TTTCTTTAAATCTCAATTTTCC
Found at i:38772639 original size:26 final size:27
Alignment explanation
Indices: 38772609--38772662 Score: 101
Period size: 26 Copynumber: 2.0 Consensus size: 27
38772599 TTTCTTTAAA
38772609 CTCAATTTTCCTTTCTTTGT-AAATTG
1 CTCAATTTTCCTTTCTTTGTAAAATTG
38772635 CTCAATTTTCCTTTCTTTGTAAAATTG
1 CTCAATTTTCCTTTCTTTGTAAAATTG
38772662 C
1 C
38772663 ATGATTTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 20 0.74
27 7 0.26
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.52
Consensus pattern (27 bp):
CTCAATTTTCCTTTCTTTGTAAAATTG
Found at i:38782811 original size:17 final size:17
Alignment explanation
Indices: 38782791--38782825 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
38782781 TTATTGATTG
38782791 TATTATTTTAT-TAAAAT
1 TATTA-TTTATGTAAAAT
38782808 TATTATTTATGTAAAAT
1 TATTATTTATGTAAAAT
38782825 T
1 T
38782826 GTTTTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TATTATTTATGTAAAAT
Found at i:38786340 original size:26 final size:26
Alignment explanation
Indices: 38786303--38786386 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
38786293 TGATACAAAT
* *
38786303 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
38786329 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
38786355 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
38786381 TGATAA
1 TGATAA
38786387 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:38787915 original size:25 final size:25
Alignment explanation
Indices: 38787867--38787915 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
38787857 ACAGTTTTAC
38787867 CCCTAGGAGATAAATTACCGAAATA
1 CCCTAGGAGATAAATTACCGAAATA
* *
38787892 CCCTAGG-GTTAAATTGACCTAAAT
1 CCCTAGGAGATAAATT-ACCGAAAT
38787916 GCATGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
CCCTAGGAGATAAATTACCGAAATA
Found at i:38792119 original size:26 final size:26
Alignment explanation
Indices: 38792082--38792139 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
38792072 TGATACAAAT
38792082 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
38792108 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
38792134 TGATAA
1 TGATAA
38792140 GAATTTCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:38793662 original size:25 final size:25
Alignment explanation
Indices: 38793614--38793662 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
38793604 ACAGTTTTAC
38793614 CCCTAGGAGATAAATTACCGAAATA
1 CCCTAGGAGATAAATTACCGAAATA
* *
38793639 CCCTAGG-GTTAAATTGACCTAAAT
1 CCCTAGGAGATAAATT-ACCGAAAT
38793663 GCATGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
CCCTAGGAGATAAATTACCGAAATA
Found at i:38796104 original size:12 final size:12
Alignment explanation
Indices: 38796087--38796111 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38796077 TCGAGTCACC
38796087 TCAAATTAATCA
1 TCAAATTAATCA
38796099 TCAAATTAATCA
1 TCAAATTAATCA
38796111 T
1 T
38796112 TTTAATAAGA
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (12 bp):
TCAAATTAATCA
Found at i:38797464 original size:15 final size:17
Alignment explanation
Indices: 38797444--38797475 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
38797434 AAAGATACAT
38797444 ATGTATA-GT-ATAAAA
1 ATGTATACGTAATAAAA
38797459 ATGTATACGTAATAAAA
1 ATGTATACGTAATAAAA
38797476 TTACATAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.31
Consensus pattern (17 bp):
ATGTATACGTAATAAAA
Found at i:38797898 original size:21 final size:21
Alignment explanation
Indices: 38797865--38797904 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38797855 AATACAGAAC
*
38797865 AAAATATACACATAATATATT
1 AAAACATACACATAATATATT
*
38797886 AAAACATATACATAATATA
1 AAAACATACACATAATATA
38797905 CATGGTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAACATACACATAATATATT
Found at i:38798263 original size:18 final size:18
Alignment explanation
Indices: 38798242--38798281 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
38798232 ATATAATGGT
*
38798242 AATAGTGATAATAATAAA
1 AATAGTGACAATAATAAA
* *
38798260 AATAGTGACAATGATAAT
1 AATAGTGACAATAATAAA
38798278 AATA
1 AATA
38798282 ACGGTGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.03, G:0.12, T:0.28
Consensus pattern (18 bp):
AATAGTGACAATAATAAA
Found at i:38802337 original size:44 final size:44
Alignment explanation
Indices: 38802274--38802634 Score: 589
Period size: 44 Copynumber: 8.2 Consensus size: 44
38802264 GGTGAATCCT
38802274 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * *
38802318 GCAGATTTGGCATCTCTGTATTGGCGGAGAGTAGATCAAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
*
38802362 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAAATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* *
38802406 GCAGATTTGGCGTCTTTGTATTGGCGGAGAGCAGATCAAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* *
38802450 GCAGATTTAGCGTCTCTGTATTGGCGGAAAGCAGATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
*
38802494 GCAGATTTGTCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * *
38802538 GCAGATTTGGCATCTCTGTATTGGCGGAAAGTAGATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* *
38802582 GCAGATTTGGCGTTTCTGTATT-GCGGAGATCAGATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
38802625 GCAGATTTGG
1 GCAGATTTGG
38802635 AGTTCTTGAG
Statistics
Matches: 291, Mismatches: 26, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
43 28 0.10
44 263 0.90
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (44 bp):
GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
Found at i:38804357 original size:2 final size:2
Alignment explanation
Indices: 38804350--38804379 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
38804340 TACATGTAAC
*
38804350 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38804380 CATCTATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:38804676 original size:2 final size:2
Alignment explanation
Indices: 38804669--38804699 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38804659 TAGTTTTCTT
38804669 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38804700 GAGCATGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38806628 original size:22 final size:20
Alignment explanation
Indices: 38806590--38806630 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
38806580 TCTTTTTTTT
*
38806590 TTAAGTTTTTAAAATAATAA
1 TTAAGTTTGTAAAATAATAA
38806610 TTAAGCTTTGTAACAATAATA
1 TTAAG-TTTGTAA-AATAATA
38806631 TCATCATCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (20 bp):
TTAAGTTTGTAAAATAATAA
Found at i:38810180 original size:18 final size:19
Alignment explanation
Indices: 38810145--38810181 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
38810135 TGAATAAAAG
*
38810145 TGAAAATAGTGTAAATTGA
1 TGAAAATAGTGAAAATTGA
38810164 TGAAAAT-GTGAAAATTGA
1 TGAAAATAGTGAAAATTGA
38810182 ATTGGATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.30
Consensus pattern (19 bp):
TGAAAATAGTGAAAATTGA
Found at i:38813252 original size:33 final size:33
Alignment explanation
Indices: 38813196--38813260 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
38813186 TATTACAATT
38813196 ATATGAATGAAATTGTAATTTGATTGATTAATTGA
1 ATATGAATGAAATTGTAATTTGATT-A-TAATTGA
38813231 ATATG-AT-AAATTGTGAA-TTGATTATAATTG
1 ATATGAATGAAATTGT-AATTTGATTATAATTG
38813261 TAAATTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
31 6 0.21
32 1 0.03
33 13 0.45
34 4 0.14
35 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (33 bp):
ATATGAATGAAATTGTAATTTGATTATAATTGA
Found at i:38816710 original size:21 final size:20
Alignment explanation
Indices: 38816682--38816723 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
38816672 GTCAATAACG
38816682 AGAAGTTCACACAAACAGAC
1 AGAAGTTCACACAAACAGAC
**
38816702 AGAATGTTCTGACAAACAGAC
1 AGAA-GTTCACACAAACAGAC
38816723 A
1 A
38816724 TATATTCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.14
Consensus pattern (20 bp):
AGAAGTTCACACAAACAGAC
Found at i:38817366 original size:19 final size:19
Alignment explanation
Indices: 38817342--38817379 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
38817332 CCACATGGCC
*
38817342 ATGTGCCCTGACCGTGTGG
1 ATGTGCCCAGACCGTGTGG
*
38817361 ATGTGCCCAGACTGTGTGG
1 ATGTGCCCAGACCGTGTGG
38817380 GGTCTACATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.13, C:0.24, G:0.37, T:0.26
Consensus pattern (19 bp):
ATGTGCCCAGACCGTGTGG
Found at i:38829693 original size:2 final size:2
Alignment explanation
Indices: 38829676--38829717 Score: 59
Period size: 2 Copynumber: 20.5 Consensus size: 2
38829666 TAACATTATG
38829676 AT AT GAT AT GAT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT A
1 AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38829718 AATTTCTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 1 0.03
2 32 0.86
3 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38832550 original size:26 final size:26
Alignment explanation
Indices: 38832513--38832596 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
38832503 TGATACAAAT
* *
38832513 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
38832539 TGATAATGGGTTAGTTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
38832565 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
38832591 TGATAA
1 TGATAA
38832597 GAATTTCATG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:38836863 original size:14 final size:15
Alignment explanation
Indices: 38836837--38836865 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
38836827 TGTTAAGTTG
38836837 TTAGGTGTAATAAAC
1 TTAGGTGTAATAAAC
38836852 TTAGGT-TAATAAAC
1 TTAGGTGTAATAAAC
38836866 ATATATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (15 bp):
TTAGGTGTAATAAAC
Found at i:38838181 original size:22 final size:22
Alignment explanation
Indices: 38838155--38838200 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
38838145 GCAAATCAAT
*
38838155 TTAATAAATATTTATTTTCCTC
1 TTAATAAATATGTATTTTCCTC
*
38838177 TTAATAAATATGTATTTTTCTC
1 TTAATAAATATGTATTTTCCTC
38838199 TT
1 TT
38838201 TTTCCCCACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (22 bp):
TTAATAAATATGTATTTTCCTC
Found at i:38840281 original size:19 final size:21
Alignment explanation
Indices: 38840253--38840294 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
38840243 TGATTGTGTT
*
38840253 TACATGTGTA-AAAATAA-AA
1 TACATATGTATAAAATAATAA
38840272 TACATATGTATAAAATAATAA
1 TACATATGTATAAAATAATAA
38840293 TA
1 TA
38840295 TATGAAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 7 0.35
21 4 0.20
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (21 bp):
TACATATGTATAAAATAATAA
Found at i:38842015 original size:69 final size:69
Alignment explanation
Indices: 38841899--38842052 Score: 193
Period size: 69 Copynumber: 2.2 Consensus size: 69
38841889 TGGATAAACG
* * * *
38841899 AGAAAGAGAGGGAGGGAGCATGTTTGGCGGCATGGATTGGAGCTTGGGGCAATTGTAGATTGACA
1 AGAAAGAGAGGGAGGAAGCATGTTTGGCGGCATGGATTGGAGCTTGGGACAATTGGAGATAGACA
38841964 AATA
66 AATA
* * * * *
38841968 AGAAAGAGAGTGTGGAAGCATGTTTGGGGGCATGGATTGGAGGTTGGGACAGTTGGAGATAGACA
1 AGAAAGAGAGGGAGGAAGCATGTTTGGCGGCATGGATTGGAGCTTGGGACAATTGGAGATAGACA
38842033 AAT-
66 AATA
*
38842036 TGCAAAGAGAGGTGAGG
1 AG-AAAGAGAGG-GAGG
38842053 TGTTGAAACC
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
68 1 0.01
69 67 0.94
70 3 0.04
ACGTcount: A:0.31, C:0.07, G:0.41, T:0.21
Consensus pattern (69 bp):
AGAAAGAGAGGGAGGAAGCATGTTTGGCGGCATGGATTGGAGCTTGGGACAATTGGAGATAGACA
AATA
Found at i:38848228 original size:28 final size:28
Alignment explanation
Indices: 38848188--38848243 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
38848178 AGAAACAAAG
*
38848188 TTAGTCTTGGTTTAGGGACTAAATTGAA
1 TTAGTCTCGGTTTAGGGACTAAATTGAA
38848216 TTAGTCTCGGTTTAGGGACTAAATTGAA
1 TTAGTCTCGGTTTAGGGACTAAATTGAA
38848244 ATTTAGACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.09, G:0.25, T:0.38
Consensus pattern (28 bp):
TTAGTCTCGGTTTAGGGACTAAATTGAA
Found at i:38850238 original size:18 final size:18
Alignment explanation
Indices: 38850217--38850271 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 18
38850207 ATGTAAAATA
38850217 TTTCAAATATCATTGTTT
1 TTTCAAATATCATTGTTT
**
38850235 TTTCATCTA-CA-T-TTT
1 TTTCAAATATCATTGTTT
38850250 TTT-AAATATCATTGTTT
1 TTTCAAATATCATTGTTT
38850267 TTTCA
1 TTTCA
38850272 TCTACATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 2 0.07
17 8 0.28
18 8 0.28
ACGTcount: A:0.25, C:0.13, G:0.04, T:0.58
Consensus pattern (18 bp):
TTTCAAATATCATTGTTT
Found at i:38850252 original size:17 final size:17
Alignment explanation
Indices: 38850227--38850279 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 17
38850217 TTTCAAATAT
38850227 CATTGTTTTTTCATCTA
1 CATTGTTTTTTCATCTA
** *
38850244 CATT-TTTTTAAATAT-
1 CATTGTTTTTTCATCTA
38850259 CATTGTTTTTTCATCTA
1 CATTGTTTTTTCATCTA
38850276 CATT
1 CATT
38850280 TACATTGTGG
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 4 0.14
16 16 0.57
17 8 0.29
ACGTcount: A:0.23, C:0.15, G:0.04, T:0.58
Consensus pattern (17 bp):
CATTGTTTTTTCATCTA
Found at i:38850566 original size:19 final size:18
Alignment explanation
Indices: 38850515--38850566 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
38850505 AATAAATGAG
38850515 TTATTAATTAAAAATATT
1 TTATTAATTAAAAATATT
* *
38850533 TTTTTGAA--AACAATATAT
1 TTATT-AATTAAAAATAT-T
38850551 TTATTAATTAAAAATA
1 TTATTAATTAAAAATA
38850567 AAAAAGCTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
17 9 0.35
18 9 0.35
19 8 0.31
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
TTATTAATTAAAAATATT
Found at i:38853899 original size:61 final size:62
Alignment explanation
Indices: 38853739--38853917 Score: 216
Period size: 62 Copynumber: 2.9 Consensus size: 62
38853729 TGCGAACGGC
* * * * * *
38853739 CGTGTAACTTACTGTTCATGGTATAAAACCACATGGCCAGGGACACGGGTGTGTGCCCAGGT
1 CGTGTAACTCACTATTCATAGTATAAAACCACACGACCAGGGACACGGGCGTGTGCCCAGGT
* * * ** *
38853801 CGTGTAACTCACTTTTTATAGTGTAAAACCATGCGACCAGGGACATGGGCGTGTGCCCAGG-
1 CGTGTAACTCACTATTCATAGTATAAAACCACACGACCAGGGACACGGGCGTGTGCCCAGGT
* * *
38853862 CGTGTAACTCACTATTCATTGTATAAAACCACACGACCAGGGACACGAGCATGTGC
1 CGTGTAACTCACTATTCATAGTATAAAACCACACGACCAGGGACACGGGCGTGTGC
38853918 ATCACTGTTG
Statistics
Matches: 97, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
61 47 0.48
62 50 0.52
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (62 bp):
CGTGTAACTCACTATTCATAGTATAAAACCACACGACCAGGGACACGGGCGTGTGCCCAGGT
Found at i:38861577 original size:30 final size:30
Alignment explanation
Indices: 38861541--38861648 Score: 117
Period size: 30 Copynumber: 3.6 Consensus size: 30
38861531 TGGCCATGTC
** **
38861541 TATAATGCTGGTCAATCTGATGGTTAAGTT
1 TATAATGCTGGTCAAAATGATGGTTAAAAT
*
38861571 TATAATGCTGGTCAAAATGCTGGTTAAAAT
1 TATAATGCTGGTCAAAATGATGGTTAAAAT
* * * *
38861601 TATAATCCTGGTTAAAATGCTGGTCAAAAT
1 TATAATGCTGGTCAAAATGATGGTTAAAAT
* *
38861631 TATCATACTGGTCAAAAT
1 TATAATGCTGGTCAAAAT
38861649 TGGTCTCTGC
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (30 bp):
TATAATGCTGGTCAAAATGATGGTTAAAAT
Found at i:38866403 original size:26 final size:27
Alignment explanation
Indices: 38866366--38866435 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 27
38866356 ATAAATATTT
38866366 AATTATCT-ATATTTAATCA-TATAATA
1 AATTAT-TAATATTTAATCATTATAATA
* *
38866392 AATTATTAATATAGTTTATCATTTTAATA
1 AATTATTAATAT--TTAATCATTATAATA
*
38866421 AATTTCTTAATATTT
1 AA-TTATTAATATTT
38866436 TAATTTTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
25 1 0.03
26 10 0.28
28 8 0.22
29 8 0.22
30 9 0.25
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.51
Consensus pattern (27 bp):
AATTATTAATATTTAATCATTATAATA
Found at i:38866404 original size:28 final size:30
Alignment explanation
Indices: 38866373--38866439 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
38866363 TTTAATTATC
38866373 TATATTTAATCA-TATAATAAA-TTATTAA
1 TATATTTAATCATTATAATAAATTTATTAA
* *
38866401 TATAGTTT-ATCATTTTAATAAATTTCTTAA
1 TATA-TTTAATCATTATAATAAATTTATTAA
38866431 TAT-TTTAAT
1 TATATTTAAT
38866440 TTTATTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
28 11 0.33
29 13 0.39
30 9 0.27
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (30 bp):
TATATTTAATCATTATAATAAATTTATTAA
Found at i:38872221 original size:34 final size:34
Alignment explanation
Indices: 38872181--38872291 Score: 134
Period size: 34 Copynumber: 3.3 Consensus size: 34
38872171 GAAGTACATA
*
38872181 AATATATATGTATGGCTTGGCATAATCGAAGATG
1 AATATATATGTATGGCTTGGTATAATCGAAGATG
* * *
38872215 ATTATATATGTATAGCTTGGTATAATC-AAAAGTG
1 AATATATATGTATGGCTTGGTATAATCGAAGA-TG
* * * *
38872249 AATATATATGTATGGTTTGATATAACCGAAGGTG
1 AATATATATGTATGGCTTGGTATAATCGAAGATG
38872283 AATATATAT
1 AATATATAT
38872292 ATACATCTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
33 3 0.05
34 59 0.92
35 2 0.03
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (34 bp):
AATATATATGTATGGCTTGGTATAATCGAAGATG
Found at i:38872491 original size:59 final size:61
Alignment explanation
Indices: 38872364--38872501 Score: 167
Period size: 59 Copynumber: 2.3 Consensus size: 61
38872354 TAAGCTTGAG
* * *
38872364 ATGAGCACTAAGTGTGCGAAATGAAATTGGTACTGAGTACTAAGTGTACGAAATTGGTCAT
1 ATGAGCACTAAGTGTGCGAAATGAAATTGATACCGAGTACTAAGTGTACGAAATCGGTCAT
* * * * *
38872425 TTG-GCACTAAGGGTGC-AAATTG-AATTTATACCGAGTACTAAGTGTACGAGATCGGTTA-
1 ATGAGCACTAAGTGTGCGAAA-TGAAATTGATACCGAGTACTAAGTGTACGAAATCGGTCAT
38872483 ATGAGCACTAAGTGTGCGA
1 ATGAGCACTAAGTGTGCGA
38872502 GTTTATCTTT
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
58 2 0.03
59 45 0.70
60 15 0.23
61 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.28
Consensus pattern (61 bp):
ATGAGCACTAAGTGTGCGAAATGAAATTGATACCGAGTACTAAGTGTACGAAATCGGTCAT
Found at i:38877122 original size:15 final size:15
Alignment explanation
Indices: 38877083--38877162 Score: 76
Period size: 15 Copynumber: 5.4 Consensus size: 15
38877073 ATAATTTGGG
*
38877083 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
38877098 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
38877113 TTTCTTTATTCCAGG-
1 TTTCTTTATT-CTGGA
*
38877128 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
38877143 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
38877157 TTTCTT
1 TTTCTT
38877163 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
13 1 0.02
14 11 0.21
15 36 0.68
16 5 0.09
ACGTcount: A:0.11, C:0.19, G:0.12, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:38890022 original size:34 final size:34
Alignment explanation
Indices: 38889982--38890097 Score: 144
Period size: 34 Copynumber: 3.4 Consensus size: 34
38889972 GAAGTACATA
* *
38889982 AATATATATGTATAGCTTGGCATAATCGAAGGTG
1 AATATATATGTATAGTTTGGTATAATCGAAGGTG
* * *
38890016 ATTATATATGTATAGTTTGGTATAATCAAAAGTG
1 AATATATATGTATAGTTTGGTATAATCGAAGGTG
* *
38890050 AATATATATGTATGGTTTGATATAA-CTGAAGGTG
1 AATATATATGTATAGTTTGGTATAATC-GAAGGTG
*
38890084 AATATATATATATA
1 AATATATATGTATA
38890098 CATTTATTTG
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
33 1 0.01
34 68 0.99
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.38
Consensus pattern (34 bp):
AATATATATGTATAGTTTGGTATAATCGAAGGTG
Found at i:38890294 original size:59 final size:61
Alignment explanation
Indices: 38890167--38890297 Score: 144
Period size: 59 Copynumber: 2.2 Consensus size: 61
38890157 TAAGCTTGAG
* * ** *
38890167 ATGAGCACTAAGTGTGCGAAATGAAATTGGTACTGAGTACTAAGTGTACGAAATTGGTCAT
1 ATGAGCACTAAGGGTGCGAAATGAAATTGATACCAAGTACTAAGTGTACGAAATCGGTCAT
* * * *
38890228 TTG-GCACTAAGGGTGC-AAATTG-AATTTATACCAAGTACTAAGTGTACGAGATCGGTTA-
1 ATGAGCACTAAGGGTGCGAAA-TGAAATTGATACCAAGTACTAAGTGTACGAAATCGGTCAT
38890286 ATGAGCACTAAG
1 ATGAGCACTAAG
38890298 TGTACGAGTT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
58 2 0.03
59 40 0.69
60 14 0.24
61 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.27
Consensus pattern (61 bp):
ATGAGCACTAAGGGTGCGAAATGAAATTGATACCAAGTACTAAGTGTACGAAATCGGTCAT
Found at i:38893811 original size:18 final size:18
Alignment explanation
Indices: 38893788--38893822 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38893778 ATGCGAATAT
*
38893788 ATAAAAACAATAAATAAC
1 ATAAAAACAACAAATAAC
*
38893806 ATAAAAATAACAAATAA
1 ATAAAAACAACAAATAA
38893823 TTTATGAGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (18 bp):
ATAAAAACAACAAATAAC
Found at i:38894219 original size:12 final size:12
Alignment explanation
Indices: 38894204--38894262 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 12
38894194 TAATATAAGG
38894204 AATAATATATAT
1 AATAATATATAT
38894216 AATAA-A-ATAT
1 AATAATATATAT
*
38894226 AAT-ATGTA-AT
1 AATAATATATAT
38894236 AA-AATATATA-
1 AATAATATATAT
*
38894246 AATAAAATATAT
1 AATAATATATAT
38894258 AATAA
1 AATAA
38894263 AATACAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
9 1 0.03
10 17 0.45
11 10 0.26
12 10 0.26
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (12 bp):
AATAATATATAT
Found at i:38894226 original size:42 final size:42
Alignment explanation
Indices: 38894155--38894266 Score: 115
Period size: 42 Copynumber: 2.7 Consensus size: 42
38894145 ATGTACTAAT
* **
38894155 AAATA-ATAAATAATAGA-ATAATATGATATAAAATG-AAGA
1 AAATATATAAATAATATATATAATAAAATATAAAATGTAAGA
* * *
38894194 TAATATA-AGGAATAATATATATAATAAAATATAATATGTAATA
1 AAATATATA--AATAATATATATAATAAAATATAAAATGTAAGA
*
38894237 AAATATATAAATAAAATATATAATAAAATA
1 AAATATATAAATAATATATATAATAAAATA
38894267 CAAATAACCT
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
39 5 0.08
40 1 0.02
41 8 0.14
42 35 0.59
43 9 0.15
44 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.30
Consensus pattern (42 bp):
AAATATATAAATAATATATATAATAAAATATAAAATGTAAGA
Found at i:38894263 original size:12 final size:12
Alignment explanation
Indices: 38894221--38894266 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
38894211 TATATAATAA
* *
38894221 AATATAATATGT
1 AATAAAATATAT
38894233 AATAAAATATAT
1 AATAAAATATAT
38894245 AAATAAAATATAT
1 -AATAAAATATAT
38894258 AATAAAATA
1 AATAAAATA
38894267 CAAATAACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
12 19 0.61
13 12 0.39
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
AATAAAATATAT
Found at i:38894355 original size:18 final size:18
Alignment explanation
Indices: 38894328--38894370 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
38894318 AAATAATGTT
*
38894328 TATA-AAAATAATTAATA
1 TATATAAAATAATTAAAA
*
38894345 TATATAAAATATTTAAAA
1 TATATAAAATAATTAAAA
*
38894363 TAAATAAA
1 TATATAAA
38894371 TTGTATGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TATATAAAATAATTAAAA
Found at i:38898568 original size:3 final size:3
Alignment explanation
Indices: 38898544--38898642 Score: 80
Period size: 3 Copynumber: 34.0 Consensus size: 3
38898534 AATGAAAACG
* * * * * * **
38898544 ATA ATA TTA ATA ATA TTG ATA ATA AAA ATA GTG ATA A-A AGG ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
38898590 ATA A-A GATA ATA ATA ATA ATG ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
38898635 AT- ATA ATA
1 ATA ATA ATA
38898643 CCTATGATAA
Statistics
Matches: 74, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
2 7 0.09
3 66 0.89
4 1 0.01
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:38898995 original size:11 final size:11
Alignment explanation
Indices: 38898947--38899050 Score: 50
Period size: 11 Copynumber: 8.9 Consensus size: 11
38898937 ATATATATTA
38898947 ATAAGTATATAC
1 ATAA-TATATAC
*
38898959 ATAATAATGATATT
1 ATAAT-AT-ATA-C
*
38898973 AAAATATATAC
1 ATAATATATAC
*
38898984 ATAATATGTAC
1 ATAATATATAC
*
38898995 ATGATATATATAA
1 AT-A-ATATATAC
* *
38899008 AGAAAAATATAC
1 A-TAATATATAC
*
38899020 ATAGTATATTA-
1 ATAATATA-TAC
*
38899031 A-AATATAGAC
1 ATAATATATAC
38899041 ATAATATATA
1 ATAATATATA
38899051 TAAAAATATA
Statistics
Matches: 67, Mismatches: 16, Indels: 19
0.66 0.16 0.19
Matches are distributed among these distances:
9 1 0.01
10 6 0.09
11 24 0.36
12 19 0.28
13 13 0.19
14 4 0.06
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.34
Consensus pattern (11 bp):
ATAATATATAC
Found at i:38899042 original size:21 final size:23
Alignment explanation
Indices: 38898976--38899060 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 23
38898966 TGATATTAAA
* *
38898976 ATATATACATAATAT-GTACATGAT
1 ATATATA-AAAATATAG-ACATAAT
* * *
38899000 ATATATAAAGAAAAATATACATAGT
1 ATATAT-AA-AAATATAGACATAAT
38899025 ATAT-T-AAAATATAGACATAAT
1 ATATATAAAAATATAGACATAAT
38899046 ATATATAAAAATATA
1 ATATATAAAAATATA
38899061 TATATACATA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
21 16 0.33
22 2 0.04
23 8 0.17
24 8 0.17
25 14 0.29
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (23 bp):
ATATATAAAAATATAGACATAAT
Found at i:38899061 original size:25 final size:24
Alignment explanation
Indices: 38898976--38899062 Score: 65
Period size: 25 Copynumber: 3.7 Consensus size: 24
38898966 TGATATTAAA
* * *
38898976 ATATATACATAATAT-GTACATGAT
1 ATATATAAAAAATATAG-ACATAAT
* * *
38899000 ATATATAAAGAAAAATATACATAGT
1 ATATATAAA-AAATATAGACATAAT
38899025 ATAT-T--AAAATATAGACATAAT
1 ATATATAAAAAATATAGACATAAT
38899046 ATATATAAAAATATATA
1 ATATATAAAAA-ATATA
38899063 TATACATATA
Statistics
Matches: 48, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
21 16 0.33
22 2 0.04
24 12 0.25
25 18 0.38
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (24 bp):
ATATATAAAAAATATAGACATAAT
Found at i:38900193 original size:64 final size:64
Alignment explanation
Indices: 38900120--38900330 Score: 151
Period size: 64 Copynumber: 3.2 Consensus size: 64
38900110 ATGGGCCAGA
*
38900120 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * *** * ** *
38900184 GCCCATTTCAAAATAC-ATGCAACATCAGTAAACATATGCAAGCCC--ATTTGGGTAACAGTGGT
1 GCCCATTTCAGATTACAAT--AA-A-CTG-GGCCTTA-GC---CCCTTATTCAGATAACA---GT
* *
38900246 ACTGGGCCAGA-
54 A-TGGCCCATAG
*
38900257 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
38900321 GCCCATTTCA
1 GCCCATTTCA
38900331 AAATACATGC
Statistics
Matches: 103, Mismatches: 27, Indels: 34
0.63 0.16 0.21
Matches are distributed among these distances:
63 9 0.09
64 25 0.24
65 5 0.05
66 1 0.01
67 11 0.11
68 5 0.05
69 5 0.05
70 11 0.11
71 1 0.01
72 5 0.05
73 16 0.16
74 9 0.09
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:38900332 original size:137 final size:137
Alignment explanation
Indices: 38900086--38900372 Score: 547
Period size: 137 Copynumber: 2.1 Consensus size: 137
38900076 TATTGGGCCT
**
38900086 AAGCCCATTCAGGTAACAGTGGTAATGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTAATGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
38900151 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
38900216 CATATGC
131 CATATGC
*
38900223 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTAATGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
38900288 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
38900353 CATATGC
131 CATATGC
38900360 AAGCCCATTTGGG
1 AAGCCCATTTGGG
38900373 GAGACTACTC
Statistics
Matches: 147, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
137 147 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTAATGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:38902201 original size:26 final size:26
Alignment explanation
Indices: 38902165--38902300 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
38902155 CATGATATTC
38902165 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
38902191 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
38902217 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
38902243 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
38902269 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
38902295 TTATCA
1 TTATCA
38902301 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:38906131 original size:64 final size:64
Alignment explanation
Indices: 38906058--38906268 Score: 151
Period size: 64 Copynumber: 3.2 Consensus size: 64
38906048 ATGGGCCAGA
*
38906058 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * *** * ** *
38906122 GCCCATTTCAAAATAC-ATGCAACATCAGTAAACATATGCAAGCCC--ATTTGGGTAACAGTGGT
1 GCCCATTTCAGATTACAAT--AA-A-CTG-GGCCTTA-GC---CCCTTATTCAGATAACA---GT
* *
38906184 ACTGGGCCAGA-
54 A-TGGCCCATAG
*
38906195 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
38906259 GCCCATTTCA
1 GCCCATTTCA
38906269 AAATACATGC
Statistics
Matches: 103, Mismatches: 27, Indels: 34
0.63 0.16 0.21
Matches are distributed among these distances:
63 9 0.09
64 25 0.24
65 5 0.05
66 1 0.01
67 11 0.11
68 5 0.05
69 5 0.05
70 11 0.11
71 1 0.01
72 5 0.05
73 16 0.16
74 9 0.09
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:38906270 original size:137 final size:137
Alignment explanation
Indices: 38906024--38906310 Score: 547
Period size: 137 Copynumber: 2.1 Consensus size: 137
38906014 TATTGGGCCT
**
38906024 AAGCCCATTCAGGTAACAGTGGTAATGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTAATGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
38906089 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
38906154 CATATGC
131 CATATGC
*
38906161 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTAATGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
38906226 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
38906291 CATATGC
131 CATATGC
38906298 AAGCCCATTTGGG
1 AAGCCCATTTGGG
38906311 GAGACTACTC
Statistics
Matches: 147, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
137 147 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTAATGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:38906595 original size:25 final size:27
Alignment explanation
Indices: 38906558--38906611 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
38906548 TCAAACATGC
38906558 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
* **
38906584 ATTTCGGT-AATTTTGCACCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
38906610 AT
1 AT
38906612 AACAGTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACACCTAGGGGT
Found at i:38906619 original size:26 final size:27
Alignment explanation
Indices: 38906575--38906650 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 27
38906565 TCAATTTAAC
* * *
38906575 CCTAGGGGTATTTCGGTAATTTTGC-A
1 CCTAGGGGTATTACAGTAATTTTCCAA
*
38906601 CCTAGGGGTATAACAGTAATTTTCCATA
1 CCTAGGGGTATTACAGTAATTTTCCA-A
* *
38906629 CATAGGGGTATTATAGTAATTT
1 CCTAGGGGTATTACAGTAATTT
38906651 AGTTACTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 21 0.51
28 20 0.49
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (27 bp):
CCTAGGGGTATTACAGTAATTTTCCAA
Found at i:38908132 original size:26 final size:26
Alignment explanation
Indices: 38908096--38908231 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
38908086 CATGATATTC
38908096 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
38908122 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
38908148 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
38908174 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
38908200 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
38908226 TTATCA
1 TTATCA
38908232 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:38910579 original size:44 final size:42
Alignment explanation
Indices: 38910523--38910890 Score: 171
Period size: 44 Copynumber: 8.5 Consensus size: 42
38910513 AATCTTCAGC
* * *
38910523 CTGTTACCCTACTGCTTAGGAGGTTAACGCTTGTTACCTTTGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAA-G-TTGTAATCTTTGAT
* * * * **
38910567 CTGTTTCCCTACTGCTTAGGGGGATAAGATCTATAATCTTCGGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAG-T-TGTAATCTTTGAT
*
38910611 CTGTTACCCTACTGCTTAGGGGGTTAAG--GTCCATCTTTGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGTTGT-AATCTTTGAT
* * * * *
38910652 CTGTTTCCCTACTGCTTAGGGGGTTAAGAGCTGGAAATC-TTCAGC
1 CTGTTACCCTACTGCTTAGGGGGTT-A-AG-TTGTAATCTTTGA-T
* * ** *
38910697 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCT-TCGTCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAA-G--TTGTAATCTTTGAT
* * * * *
38910741 CTGCT-CCACTACTACTTAGGGAGATAAGATCTGTAA--TTCGAT
1 CTGTTACC-CTACTGCTTAGGGGGTTAAG-T-TGTAATCTTTGAT
* * ** *
38910783 CTGTTACCCTACTGCTTAGGGGTTTAAGACCCT-TCGTCTTCGAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAG---TTGTAATCTTTGAT
* * * *
38910827 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAA--ATTCAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAG-T-TGTAATCTTTGA-T
38910870 CTGTTACCCTACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGG
38910891 AGATAAGGCT
Statistics
Matches: 241, Mismatches: 61, Indels: 45
0.69 0.18 0.13
Matches are distributed among these distances:
40 1 0.00
41 30 0.12
42 30 0.12
43 33 0.14
44 117 0.49
45 29 0.12
46 1 0.00
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.35
Consensus pattern (42 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGTTGTAATCTTTGAT
Found at i:38910665 original size:174 final size:172
Alignment explanation
Indices: 38910472--38910890 Score: 519
Period size: 174 Copynumber: 2.4 Consensus size: 172
38910462 TTCGTCGTCT
* * * * * *
38910472 TTTGATCTGCTTCCCTACTGCTTATGGTGATGAGATCTATAAATCTTCAGCCTGTTACCCTACTG
1 TTTGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTG
* * * * *
38910537 CTTAGGAGG-TTAA-CGCTT-GTTACCTTTGATCTGTTTCC-CTACTGCTTAGGGGGATAAGATC
66 CTTAGG-GGTTTAAGCCCTTCG-T--CTTCGATCTG-CTCCACTACTACTTAGGGAGATAAGATC
* **
38910598 TATAATCTTCGGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTCCATC-
126 TATAA--TTCGACCTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCG
* *
38910646 TTTGATCTGTTTCCCTACTGCTTAGGGGGTTAAGAGCTGGAAATCTTCAGCCTGTTACCCTACTG
1 TTTGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTG
*
38910711 CTTAGGGGTTTAAGGCCCTTCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTA
66 CTTAGGGGTTTAA-GCCCTTCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTATA
* * *
38910776 ATTCGATCTGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCG
130 ATTCGACCTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCG
38910819 TCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAA--TTCAGCCTGTTACCCTAC
1 T-TT-GATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTAC
38910882 TGCTTAGGG
64 TGCTTAGGG
38910891 AGATAAGGCT
Statistics
Matches: 215, Mismatches: 22, Indels: 17
0.85 0.09 0.07
Matches are distributed among these distances:
172 35 0.16
173 33 0.15
174 103 0.48
175 38 0.18
176 5 0.02
177 1 0.00
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.35
Consensus pattern (172 bp):
TTTGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATCTTCAGCCTGTTACCCTACTG
CTTAGGGGTTTAAGCCCTTCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTATAA
TTCGACCTGTTACCCTACTGCTTAGGGGGTTAAGACCCATCG
Found at i:38910787 original size:86 final size:87
Alignment explanation
Indices: 38910466--38910890 Score: 465
Period size: 86 Copynumber: 4.9 Consensus size: 87
38910456 GCAAGATTCG
* * * * * *
38910466 TCGTCTTTTGATCTGCTTCCCTACTGCTTATGGTGATGAGATCTATAAATCTTCAGCCTGTTACC
1 TCGTC-TTCGATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTGT-AA-CTTCAGCCTGTTACC
*
38910531 CTACTGCTTAGGAGG-TTAA--CGCT
63 CTACTGCTTAGG-GGTTTAAGGCCCT
* * *
38910554 T-GTTACCTTTGATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTATAATCTTCGGCCTGTTAC
1 TCG-T--CTTCGATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTGTAA-CTTCAGCCTGTTAC
* * *
38910618 CCTACTGCTTAGGGGGTTAAGGTCCA
62 CCTACTGCTTAGGGGTTTAAGGCCCT
* * *
38910644 TC-T-TT-GATCTGTTTCCCTACTGCTTAGGGGGTTAAGAGCTGGAAATCTTCAGCCTGTTACCC
1 TCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGATAAGATCT-GTAA-CTTCAGCCTGTTACCC
38910706 TACTGCTTAGGGGTTTAAGGCCCT
64 TACTGCTTAGGGGTTTAAGGCCCT
* * * *
38910730 TCGTCTTCGATCTG-CTCCACTACTACTTAGGGAGATAAGATCTGTAA-TTC-GATCTGTTACCC
1 TCGTCTTCGATCTGTTTCC-CTACTGCTTAGGGGGATAAGATCTGTAACTTCAG-CCTGTTACCC
*
38910792 TACTGCTTAGGGGTTTAAGACCCT
64 TACTGCTTAGGGGTTTAAGGCCCT
* *
38910816 TCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTACCCTA
1 TCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTGTAACTTCAGCCTGTTACCCTA
38910881 CTGCTTAGGG
66 CTGCTTAGGG
38910891 AGATAAGGCT
Statistics
Matches: 292, Mismatches: 29, Indels: 33
0.82 0.08 0.09
Matches are distributed among these distances:
85 34 0.12
86 117 0.40
87 31 0.11
88 44 0.15
89 63 0.22
90 3 0.01
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.36
Consensus pattern (87 bp):
TCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGATAAGATCTGTAACTTCAGCCTGTTACCCTA
CTGCTTAGGGGTTTAAGGCCCT
Found at i:38910909 original size:130 final size:127
Alignment explanation
Indices: 38910523--38910909 Score: 312
Period size: 130 Copynumber: 3.0 Consensus size: 127
38910513 AATCTTCAGC
* *
38910523 CTGTTACCCTACTGCTTAGGAGGTT-A-ACGCTTGTTACCTTTGATCTGTTTCCCTACTGCTTAG
1 CTGTTACCCTACTGCTTAGG-GGTTAAGACGCTTG--ATCTTCGATCTGTTTCCCTACTGCTTAG
* * * * * *
38910586 GGGGATAAGATCTATAATCTTCGGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTCCATCT--TT
63 GGGGTTAAGATCTGTAA-CTTC-GCCTGTTACCCTACTGCTTAGGGAGATAAGG--CTTGTAATT
38910649 -GAT
124 CGAT
* * * *
38910652 CTGTTTCCCTACTGCTTAGGGGGTTAAGA-GCTGGAAATCTTC-AGCCTGTTACCCTACTGCTTA
1 CTGTTACCCTACTGCTTA-GGGGTTAAGACGCTTG--ATCTTCGA-TCTGTTTCCCTACTGCTTA
* ** * * * *
38910715 GGGGTTTAAGGCCCTTCGT--CTTCGATCTGCT-CCACTACTACTTAGGGAGATAA-GATCTGTA
62 GGGGGTTAA-GATC-T-GTAACTTCG-CCTGTTACC-CTACTGCTTAGGGAGATAAGGCT-TGTA
38910776 ATTCGAT
121 ATTCGAT
*
38910783 CTGTTACCCTACTGCTTAGGGGTTTAAGACCCTTCG-TCTTCGATCTGTTTCCCTACTGCTTAGG
1 CTGTTACCCTACTGCTTAGGGG-TTAAGACGCTT-GATCTTCGATCTGTTTCCCTACTGCTTAGG
*
38910847 GGGTTAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGAGATAAGGCTTGTGAATTC
64 GGGTTAAGATCTGTAACTTC-GCCTGTTACCCTACTGCTTAGGGAGATAAGGCTTGT-AATTC
38910910 ACCGATTCCA
Statistics
Matches: 201, Mismatches: 34, Indels: 45
0.72 0.12 0.16
Matches are distributed among these distances:
127 2 0.01
128 3 0.01
129 56 0.28
130 105 0.52
131 30 0.15
132 3 0.01
133 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (127 bp):
CTGTTACCCTACTGCTTAGGGGTTAAGACGCTTGATCTTCGATCTGTTTCCCTACTGCTTAGGGG
GTTAAGATCTGTAACTTCGCCTGTTACCCTACTGCTTAGGGAGATAAGGCTTGTAATTCGAT
Found at i:38910910 original size:43 final size:43
Alignment explanation
Indices: 38910484--38910897 Score: 131
Period size: 44 Copynumber: 9.5 Consensus size: 43
38910474 TGATCTGCTT
* * * *
38910484 CCCTACTGCTTATGGTGATGAGATCTATAAATCTTCAGCCTGTTA
1 CCCTACTGCTTAGGGAGATAAGATCTGTAAA--TTCAGCCTGTTA
* * ** * * *
38910529 CCCTACTGCTTA-GGAGGTTAACGCT-TGTTACCTT-TGATCTGTTT
1 CCCTACTGCTTAGGGA-GATAA-GATCTG-TAAATTCAG-CCTGTTA
* * * *
38910573 CCCTACTGCTTAGGGGGATAAGATCTATAATCTTCGGCCTGTTA
1 CCCTACTGCTTAGGGAGATAAGATCTGTAA-ATTCAGCCTGTTA
* * * ** ** * * *
38910617 CCCTACTGCTTAGGGGGTTAAGGTCCAT-CTTTGA-TCTGTTT
1 CCCTACTGCTTAGGGAGATAAGATCTGTAAATTCAGCCTGTTA
* * * *
38910658 CCCTACTGCTTAGGGGGTTAAGAGCTGGAAATCTTCAGCCTGTTA
1 CCCTACTGCTTAGGGAGATAAGATCTGTAAA--TTCAGCCTGTTA
* ** * * *
38910703 CCCTACTGCTTAGGG-GTTTAAGGCCCTTCGT--CTTC-GATCTGCT-
1 CCCTACTGCTTAGGGAG-ATAA-GATC-T-GTAAATTCAG-CCTGTTA
* *
38910746 CCACTACTACTTAGGGAGATAAGATCTGT-AATTC-GATCTGTTA
1 CC-CTACTGCTTAGGGAGATAAGATCTGTAAATTCAG-CCTGTTA
* * * * *
38910789 CCCTACTGCTTAGGG-GTTTAAGACCCTTCGT--CTTC-GATCTGTTT
1 CCCTACTGCTTAGGGAG-ATAAGA-TC-T-GTAAATTCAG-CCTGTTA
* *
38910833 CCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTGTTA
1 CCCTACTGCTTAGGGAGATAAGATCTGTAAATTCAGCCTGTTA
38910876 CCCTACTGCTTAGGGAGATAAG
1 CCCTACTGCTTAGGGAGATAAG
38910898 GCTTGTGAAT
Statistics
Matches: 280, Mismatches: 60, Indels: 60
0.70 0.15 0.15
Matches are distributed among these distances:
41 33 0.12
42 31 0.11
43 42 0.15
44 119 0.43
45 47 0.17
46 6 0.02
47 1 0.00
48 1 0.00
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.34
Consensus pattern (43 bp):
CCCTACTGCTTAGGGAGATAAGATCTGTAAATTCAGCCTGTTA
Found at i:38911075 original size:64 final size:64
Alignment explanation
Indices: 38910974--38911097 Score: 194
Period size: 64 Copynumber: 1.9 Consensus size: 64
38910964 GTATCTATGT
*
38910974 TTATGCCAAATAATTAGGATGATATGATTGAAATGAATCAAATGCTCCTAACTAAATGTGATGC
1 TTATGCCAAATAATTAGGATGATATGATCGAAATGAATCAAATGCTCCTAACTAAATGTGATGC
* * * * *
38911038 TTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAACTGCTCCTAATTAGATGTG
1 TTATGCCAAATAATTAGGATGATATGATCGAAATGAATCAAATGCTCCTAACTAAATGTG
38911098 TTATGAATGC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (64 bp):
TTATGCCAAATAATTAGGATGATATGATCGAAATGAATCAAATGCTCCTAACTAAATGTGATGC
Found at i:38922535 original size:46 final size:46
Alignment explanation
Indices: 38922482--38922657 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
38922472 CGGTTGAGCA
38922482 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
38922528 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
38922573 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
38922621 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
38922658 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.04
45 3 0.03
46 63 0.56
47 29 0.26
48 3 0.03
50 5 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:38922638 original size:93 final size:93
Alignment explanation
Indices: 38922479--38922650 Score: 326
Period size: 93 Copynumber: 1.8 Consensus size: 93
38922469 GGACGGTTGA
*
38922479 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
38922544 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
38922572 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
38922637 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
38922651 CTTATGGGCG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:38926169 original size:24 final size:24
Alignment explanation
Indices: 38926137--38926184 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
38926127 CAAAACCTAA
38926137 GGTGATTTTAAGTTTATTTTCGTT
1 GGTGATTTTAAGTTTATTTTCGTT
38926161 GGTGATTTTAAGTTTATTTTCGTT
1 GGTGATTTTAAGTTTATTTTCGTT
38926185 ATACTTTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.04, G:0.21, T:0.58
Consensus pattern (24 bp):
GGTGATTTTAAGTTTATTTTCGTT
Found at i:38926483 original size:3 final size:3
Alignment explanation
Indices: 38926475--38926570 Score: 56
Period size: 3 Copynumber: 32.7 Consensus size: 3
38926465 TCCTTATGAC
* * * *
38926475 TAT TAT TAT TAA TAT TCT TAT TAT CAT TAT TAT TTT TAT TCAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT
* * * * *
38926520 TAT CAA TA- TAT TAT TAC TA- CAGT TAC TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
*
38926563 CAT TAT TA
1 TAT TAT TA
38926571 CCATTATTCT
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
2 7 0.10
3 58 0.84
4 4 0.06
ACGTcount: A:0.33, C:0.08, G:0.01, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:38926514 original size:24 final size:25
Alignment explanation
Indices: 38926476--38926535 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
38926466 CCTTATGACT
38926476 ATTATTATTAATATTC-TTATTATC-
1 ATTATTATTAATATTCATT-TTATCA
**
38926500 ATTATTATTTTTATTCATTTTATCA
1 ATTATTATTAATATTCATTTTATCA
38926525 ATATATTATTA
1 AT-TATTATTA
38926536 CTACAGTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 19 0.63
25 4 0.13
26 7 0.23
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTATTATTAATATTCATTTTATCA
Found at i:38926777 original size:3 final size:3
Alignment explanation
Indices: 38926763--38926848 Score: 59
Period size: 3 Copynumber: 28.7 Consensus size: 3
38926753 ACAGTATTCA
* * * * *
38926763 TAT TAT TTT TAT TAT TAT TAT TAT T-G TATT TAT TTT TAC TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
* * * *
38926808 TA- TATT TAT TAT TAG TAT TAA TAT TAT AAT TAC TAT TAT TA
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
38926849 CACTTATATG
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
2 3 0.05
3 56 0.89
4 4 0.06
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:38926781 original size:21 final size:21
Alignment explanation
Indices: 38926763--38926857 Score: 75
Period size: 21 Copynumber: 4.4 Consensus size: 21
38926753 ACAGTATTCA
* *
38926763 TATTATTTTTATTATTATTAT
1 TATTATATTTATTATTATTAC
* * *
38926784 TATTGTATTTATTTTTACTAC
1 TATTATATTTATTATTATTAC
*
38926805 TATTATATTTATTATTAGTATTAA
1 TATTATATTTATTA-T--TATTAC
* *
38926829 TATTATAATTACTATTATTAC
1 TATTATATTTATTATTATTAC
38926850 -ACTTATAT
1 TA-TTATAT
38926858 GTATATATAT
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.02
21 38 0.67
22 1 0.02
23 1 0.02
24 16 0.28
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTATATTTATTATTATTAC
Found at i:38926938 original size:23 final size:25
Alignment explanation
Indices: 38926912--38926969 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 25
38926902 TATCATCATC
*
38926912 TTAATATTA-ATATTTATATATTT-
1 TTAATATTATATATGTATATATTTA
*
38926935 TTAACA-TATATATGTATATATTTA
1 TTAATATTATATATGTATATATTTA
38926959 TGTAATATTAT
1 T-TAATATTAT
38926970 TAATATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 2 0.07
23 18 0.64
24 1 0.04
25 4 0.14
26 3 0.11
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (25 bp):
TTAATATTATATATGTATATATTTA
Found at i:38926977 original size:20 final size:20
Alignment explanation
Indices: 38926952--38926997 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
38926942 ATATATGTAT
*
38926952 ATATTTATGTAATATTATTA
1 ATATTTATGTAACATTATTA
* *
38926972 ATATTTTTTTAACATTATTA
1 ATATTTATGTAACATTATTA
*
38926992 TTATTT
1 ATATTT
38926998 CTTAGATGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
ATATTTATGTAACATTATTA
Found at i:38927037 original size:14 final size:14
Alignment explanation
Indices: 38927018--38927047 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
38927008 TACATCATGT
*
38927018 TTTTTACTACTATA
1 TTTTTAATACTATA
38927032 TTTTTAATACTATA
1 TTTTTAATACTATA
38927046 TT
1 TT
38927048 ATGTATATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTTAATACTATA
Found at i:38927137 original size:23 final size:23
Alignment explanation
Indices: 38927105--38927162 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
38927095 TCATATGTAT
38927105 ATATT-TTATGTACATACTTTTA
1 ATATTATTATGTACATACTTTTA
** *
38927127 ATATTATTATGTATTTATTTTTA
1 ATATTATTATGTACATACTTTTA
38927150 ATA-TATATATGTA
1 ATATTAT-TATGTA
38927163 TATATTTATG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.26
23 23 0.74
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (23 bp):
ATATTATTATGTACATACTTTTA
Found at i:38927203 original size:58 final size:59
Alignment explanation
Indices: 38927091--38927217 Score: 143
Period size: 58 Copynumber: 2.2 Consensus size: 59
38927081 TTTCAATAAC
* *
38927091 TATATCATATGTATATATTTTATGTACATACTTTTAATATTATTATGTATTTATTTTTAA
1 TATAT-ATATGTATATATTTTATGTACATACTTTTAATATCATTATGTATTTATTTCTAA
* * * *
38927151 TATATATATGTATATA-TTTATGTA-GTA-TTATTAATAGTCATTTTTTTTTTATTTCTAA
1 TATATATATGTATATATTTTATGTACATACTT-TTAATA-TCATTATGTATTTATTTCTAA
*
38927209 TATGTATAT
1 TATATATAT
38927218 ACTATGTAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
56 2 0.03
57 8 0.14
58 32 0.55
59 11 0.19
60 5 0.09
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.57
Consensus pattern (59 bp):
TATATATATGTATATATTTTATGTACATACTTTTAATATCATTATGTATTTATTTCTAA
Found at i:38927256 original size:24 final size:22
Alignment explanation
Indices: 38927213--38927288 Score: 62
Period size: 24 Copynumber: 3.3 Consensus size: 22
38927203 TTCTAATATG
* * *
38927213 TATATACTATGTAAATATTTTAA
1 TATATATTATGTATACATTTT-A
*
38927236 TACTATATTATGTATACATTTTT
1 TA-TATATTATGTATACATTTTA
* * *
38927259 TATATATTACGTATATATATATA
1 TATATATTATGTATACAT-TTTA
38927282 TATATAT
1 TATATAT
38927289 ATATCTCTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 14 0.33
23 13 0.30
24 16 0.37
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.51
Consensus pattern (22 bp):
TATATATTATGTATACATTTTA
Found at i:38927398 original size:29 final size:29
Alignment explanation
Indices: 38927349--38927410 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
38927339 ACTATATTAC
* *
38927349 TTTTTTTACATATTATCTTATGTATATAT
1 TTTTTTTACATACTATATTATGTATATAT
*
38927378 TTTTTTTA-ATAACTATATTATGTATGTAT
1 TTTTTTTACAT-ACTATATTATGTATATAT
38927407 TTTT
1 TTTT
38927411 AACGCTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (29 bp):
TTTTTTTACATACTATATTATGTATATAT
Found at i:38927443 original size:25 final size:25
Alignment explanation
Indices: 38927380--38927443 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
38927370 GTATATATTT
**
38927380 TTTTTAATAACTATATTATGTATGTA
1 TTTTTAAT-ACTATATTATGTACATA
**
38927406 TTTTTAACGCTATATTATGTACATA
1 TTTTTAATACTATATTATGTACATA
38927431 TTTTTAATACTAT
1 TTTTTAATACTAT
38927444 GTATATACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 25 0.78
26 7 0.22
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (25 bp):
TTTTTAATACTATATTATGTACATA
Found at i:38939575 original size:12 final size:12
Alignment explanation
Indices: 38939549--38939585 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
38939539 ACATGTGCAT
*
38939549 ATCATG-ATAAC
1 ATCATGCATGAC
38939560 ATCATGCATGAC
1 ATCATGCATGAC
38939572 ATCATGCATGAC
1 ATCATGCATGAC
38939584 AT
1 AT
38939586 ATACAGGTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 6 0.25
12 18 0.75
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.27
Consensus pattern (12 bp):
ATCATGCATGAC
Found at i:38940073 original size:85 final size:84
Alignment explanation
Indices: 38939872--38940119 Score: 347
Period size: 85 Copynumber: 2.9 Consensus size: 84
38939862 TGTTCATCAA
* *
38939872 AAAAATCAACTCATATTGCGAGAGGTCAGTTGAGCCTCGGCTCACATGCTGAGGTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG---ACACGCTGAGGTATTTTCAATT
*
38939937 TCTGTTTTTCAATTTCTATTCG
63 TCTGTTTTTCAATTTATATTCG
* *
38939959 TTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTAAGGTATTTTCAATTT
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTCAATTT
*
38940024 -TCGTTTTTCAATTTATGTTTC-
64 CT-GTTTTTCAATTTAT-ATTCG
*
38940045 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACACTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTCAATTTC
38940110 TGTTTTTCAA
65 TGTTTTTCAA
38940120 AAAAATCAAG
Statistics
Matches: 146, Mismatches: 10, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
85 70 0.48
86 35 0.24
87 3 0.02
88 36 0.25
89 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (84 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACGCTGAGGTATTTTCAATTTCT
GTTTTTCAATTTATATTCG
Found at i:38940393 original size:19 final size:19
Alignment explanation
Indices: 38940355--38940393 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
38940345 AGTCTTATCT
**
38940355 CCCTGAAGTTGTAGTAGAG
1 CCCTGAAGTTACAGTAGAG
*
38940374 CCCTGAAGTTACAGTGGAG
1 CCCTGAAGTTACAGTAGAG
38940393 C
1 C
38940394 TGATCGCAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.23
Consensus pattern (19 bp):
CCCTGAAGTTACAGTAGAG
Found at i:38940425 original size:21 final size:21
Alignment explanation
Indices: 38940377--38940426 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
38940367 AGTAGAGCCC
* **
38940377 TGAAGTTACAGTGGAGCTGAT
1 TGAAGTTGCAGTGGAGCACAT
* *
38940398 CGCAGTTGCAGTGGAGCACAT
1 TGAAGTTGCAGTGGAGCACAT
38940419 TGAAGTTG
1 TGAAGTTG
38940427 TAGATCTTAT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.14, G:0.34, T:0.26
Consensus pattern (21 bp):
TGAAGTTGCAGTGGAGCACAT
Found at i:38941961 original size:24 final size:26
Alignment explanation
Indices: 38941898--38941982 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 26
38941888 ATATTTTAAA
* *
38941898 TATTATTTATATT-ATCCTTATGACTAT
1 TATTA-TTATATTCAT-TTTATCACTAT
38941925 TATTATTAATATTC-TTATTATCACTAT
1 TATTATT-ATATTCATT-TTATCACTAT
*
38941952 TATT-TT-TATTCATTTTATCAATA-
1 TATTATTATATTCATTTTATCACTAT
38941975 TATTATTA
1 TATTATTA
38941983 CTACAGTTAC
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
23 4 0.08
24 15 0.31
25 2 0.04
26 4 0.08
27 24 0.49
ACGTcount: A:0.32, C:0.09, G:0.01, T:0.58
Consensus pattern (26 bp):
TATTATTATATTCATTTTATCACTAT
Found at i:38941969 original size:27 final size:27
Alignment explanation
Indices: 38941915--38941982 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 27
38941905 TATATTATCC
*
38941915 TTATGACTATTATTATTAATATTCTTA
1 TTATCACTATTATTATTAATATTCTTA
38941942 TTATCACTATTATT-TT--TATTCATT-
1 TTATCACTATTATTATTAATATTC-TTA
*
38941966 TTATCAATA-TATTATTA
1 TTATCACTATTATTATTA
38941983 CTACAGTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
23 4 0.11
24 15 0.42
25 2 0.06
26 2 0.06
27 13 0.36
ACGTcount: A:0.32, C:0.09, G:0.01, T:0.57
Consensus pattern (27 bp):
TTATCACTATTATTATTAATATTCTTA
Found at i:38942168 original size:3 final size:3
Alignment explanation
Indices: 38942162--38942295 Score: 51
Period size: 3 Copynumber: 44.0 Consensus size: 3
38942152 TTTTGTTTTT
* * * **
38942162 TTA TTA TCA TTA TTA -TA TCA TTA TTA TTT TTCA TGTA CACA TTA TTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A T-TA -TTA TTA TT-A
* * * * * *
38942210 -TA TTA TTT TTA TGA TTA TTA TTA TT- GTA TTTA TTC TTA CTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* * * *
38942254 TTA -TA TTTA TTA TTA GTA TTA ATA TTA TGA TTA CTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
38942296 CACTTATATG
Statistics
Matches: 93, Mismatches: 28, Indels: 20
0.66 0.20 0.14
Matches are distributed among these distances:
2 6 0.06
3 78 0.84
4 8 0.09
5 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:38942488 original size:14 final size:14
Alignment explanation
Indices: 38942469--38942498 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
38942459 TACATCATGT
38942469 TTTTTAATACTATA
1 TTTTTAATACTATA
38942483 TTTTTAATACTATA
1 TTTTTAATACTATA
38942497 TT
1 TT
38942499 ATGTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTTAATACTATA
Found at i:38942577 original size:64 final size:60
Alignment explanation
Indices: 38942493--38942627 Score: 148
Period size: 64 Copynumber: 2.2 Consensus size: 60
38942483 TTTTTAATAC
* *
38942493 TATA-TTATGTATATATTTTTACAT-GCATTATGTACATATTTTCAATAACTATATCATATGTA
1 TATATTTATGTACATACTTTTA-ATAGCATTATGTACATATTTTCAAT-A-TATAT-ATATGTA
** ** *
38942555 TATATTTTATGTACATACTTTTAATATTATTATGTATTTATTTTTAATATATATATATGTA
1 TATA-TTTATGTACATACTTTTAATAGCATTATGTACATATTTTCAATATATATATATGTA
38942616 TATATTTATGTA
1 TATATTTATGTA
38942628 GTATTATTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
60 8 0.13
61 11 0.17
62 9 0.14
63 3 0.05
64 32 0.51
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (60 bp):
TATATTTATGTACATACTTTTAATAGCATTATGTACATATTTTCAATATATATATATGTA
Found at i:38942588 original size:23 final size:23
Alignment explanation
Indices: 38942556--38942615 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
38942546 TCATATGTAT
38942556 ATATT-TTATGTACATACTTTTA
1 ATATTATTATGTACATACTTTTA
** *
38942578 ATATTATTATGTATTTATTTTTA
1 ATATTATTATGTACATACTTTTA
38942601 ATATATATATATGTA
1 ATAT-TAT-TATGTA
38942616 TATATTTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.16
23 18 0.56
24 3 0.09
25 6 0.19
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (23 bp):
ATATTATTATGTACATACTTTTA
Done.