Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007718.1 Hibiscus syriacus cultivar Beakdansim tig00109949_pilon, whole genome shotgun sequence
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: 1062497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:348297 original size:12 final size:12
Alignment explanation
Indices: 348280--348313 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
348270 GATTGTTAAC
348280 TTTGACTTTGAA
1 TTTGACTTTGAA
*
348292 TTTGACTTTGAT
1 TTTGACTTTGAA
348304 TGTTGACTTT
1 T-TTGACTTT
348314 TTTAAGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.56
Consensus pattern (12 bp):
TTTGACTTTGAA
Found at i:348973 original size:46 final size:46
Alignment explanation
Indices: 348828--348974 Score: 136
Period size: 46 Copynumber: 3.2 Consensus size: 46
348818 CGAAATAGGC
* * * * * * *
348828 TGGTGCATCTTTATCGGATGGTTAAATCTAATTACCGAACTACATGT
1 TGGTGCATCCTTATCGGATTGATAATTCCAATTATC-AATTACATGT
* * * *
348875 TGATGCATCCTTATCGGA-TGATAATTTCAATTATCAATTTACAAGC
1 TGGTGCATCCTTATCGGATTGATAATTCCAATTATCAA-TTACATGT
* *
348921 TAGTGCATCGTTATCGGATTG-TAATTCCAATTATCTAATTACATGT
1 TGGTGCATCCTTATCGGATTGATAATTCCAATTATC-AATTACATGT
348967 TGGTGCAT
1 TGGTGCAT
348975 ACTTCTAGAA
Statistics
Matches: 79, Mismatches: 18, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
45 2 0.03
46 57 0.72
47 20 0.25
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (46 bp):
TGGTGCATCCTTATCGGATTGATAATTCCAATTATCAATTACATGT
Found at i:355700 original size:46 final size:46
Alignment explanation
Indices: 355598--355760 Score: 157
Period size: 46 Copynumber: 3.5 Consensus size: 46
355588 AGGAAGGATA
* * * *
355598 ACTGAATTACAGGCTGGTGCATCCTCATCGGATGGCTAAATATAA-T
1 ACTGAATTACAGGCTGGTGCATCCTTATCGGAT-GATAATTTTAATT
* * *
355644 ACTAAATTACATGCGGGTGCATCCTTATCGGATGATAATTTTAATT
1 ACTGAATTACAGGCTGGTGCATCCTTATCGGATGATAATTTTAATT
* * * * * *
355690 ACTGATTTACAGGATGGTGCACCCTTATCGGAAGGTAATTTCAATT
1 ACTGAATTACAGGCTGGTGCATCCTTATCGGATGATAATTTTAATT
* * * *
355736 ACCGAATTATAGGTTGGTGGATCCT
1 ACTGAATTACAGGCTGGTGCATCCT
355761 CGTAGGATGG
Statistics
Matches: 94, Mismatches: 22, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
45 8 0.09
46 86 0.91
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (46 bp):
ACTGAATTACAGGCTGGTGCATCCTTATCGGATGATAATTTTAATT
Found at i:356693 original size:54 final size:55
Alignment explanation
Indices: 356580--356697 Score: 141
Period size: 55 Copynumber: 2.2 Consensus size: 55
356570 CCTAAAAAGT
** * *
356580 TAAGAAATTCATAATCTGTTTAGAATTTCCGTATGGGCACTTCAGGTGCAAAAAG
1 TAAGAAATTCATAATCTGTTTAGAATTTCCGTATAAGAACTTCAGGTGCAAAAAC
* * * *
356635 TAAGAATTTCATAAT-TGTTTATGAATTTCTGTATAAGAACTTTATGT-CAAAAAC
1 TAAGAAATTCATAATCTGTTTA-GAATTTCCGTATAAGAACTTCAGGTGCAAAAAC
356689 TAAGAAATT
1 TAAGAAATT
356698 ATATGAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
54 20 0.38
55 33 0.62
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (55 bp):
TAAGAAATTCATAATCTGTTTAGAATTTCCGTATAAGAACTTCAGGTGCAAAAAC
Found at i:356957 original size:67 final size:68
Alignment explanation
Indices: 356872--357257 Score: 558
Period size: 67 Copynumber: 5.8 Consensus size: 68
356862 AAAGATTAAT
* *
356872 GGCCTAGTTGTGGC-TTTGACA-AAAGGGTGTTAATTATTCCAGTTAGATGAAAGGCTAA-TGCC
1 GGCCTAGTTGT-GCATTTGACAGAAA-GGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
356934 TTTGA
64 TTTGA
* * *
356939 GGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCAAGTTAGATGAAA-GCTAAGTGCCTT
1 GGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
357003 TGA
66 TGA
*
357006 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1 GGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
357071 TGA
66 TGA
* * * * *
357074 GGCCTAGTTATGCATTTGAAAGAAAGTTGTCAATTATGCCAGTTAGATGAAA-TCTAATTGCCTT
1 GGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
357138 TG-
66 TGA
* *
357140 GGCCTAGTTGTGCATTTGATACAAAGGTGTC-ATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1 GGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
357204 TGA
66 TGA
*
357207 GGCCTAGTTGTGCA-TTGACAGAAATGTG-CAATTATG-CAGTTAGATGAAAGG
1 GGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
357258 TTAAATACAT
Statistics
Matches: 290, Mismatches: 22, Indels: 16
0.88 0.07 0.05
Matches are distributed among these distances:
65 36 0.12
66 63 0.22
67 125 0.43
68 66 0.23
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (68 bp):
GGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
TGA
Found at i:357799 original size:45 final size:45
Alignment explanation
Indices: 357446--357787 Score: 449
Period size: 45 Copynumber: 7.7 Consensus size: 45
357436 GAATAAAAAA
* *
357446 GCATGAAAGGATGCCATAAATG-AATACATATGGTTGCATTATCG
1 GCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCG
* * *
357490 GCATGAAAGGATGCCATAAATGAAATGTATAT-GGTGTATAAT-G
1 GCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCG
* * *
357533 CCATAAAAGGATGCCATTAATGAAATGCATATGGGTGCATTATCG
1 GCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCG
* * *
357578 GCATGAAAGGAGGCCATAATTGAAATGGATATGGGTGCATTATCG
1 GCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCG
* * * *
357623 ACATGAAAGGATGTCATAATTGAAATGCATATGGTTGCATTATCG
1 GCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCG
* * * *
357668 GAATGAAATGATGCCATAATTGAAATACATATGGGTGCATTATCG
1 GCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCG
* *
357713 GCATGAAAGGATGCCAT-AATGAAATGCATATGGGTACATTATTG
1 GCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCG
* *
357757 GCATGAAAGAATGTCATAAATGAAATGCATA
1 GCATGAAAGGATGCCATAAATGAAATGCATA
357788 ATTGTGCATT
Statistics
Matches: 258, Mismatches: 36, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
43 29 0.11
44 75 0.29
45 154 0.60
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.27
Consensus pattern (45 bp):
GCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCG
Found at i:357870 original size:27 final size:29
Alignment explanation
Indices: 357817--357871 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
357807 GGATGTTATC
*
357817 AATGAAAATAAGAAAATTACTAAAGAGAT
1 AATGAAAATAAGAAAAGTACTAAAGAGAT
*
357846 AATGGAAA-AAGAAAAGTA-TAAAGAGA
1 AATGAAAATAAGAAAAGTACTAAAGAGA
357872 GATAGTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 8 0.33
28 9 0.38
29 7 0.29
ACGTcount: A:0.64, C:0.02, G:0.18, T:0.16
Consensus pattern (29 bp):
AATGAAAATAAGAAAAGTACTAAAGAGAT
Found at i:358249 original size:68 final size:67
Alignment explanation
Indices: 358108--358497 Score: 568
Period size: 68 Copynumber: 5.8 Consensus size: 67
358098 AGATTAATTT
* * * * *
358108 CCTAGCTATGGATTTGACA-AAAGGATGTTAATTATTCCAGTTAAATGAAAGGCTAA-TGCCTTT
1 CCTAGCTGTGCATTTGACAGAAAGG-TGTCAATTA-TGCAGTTAGATGAAAGGCTAAGTGCCTTT
358171 GAGG
64 GAGG
358175 CCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCTTTG
1 CCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATG-CAGTTAGATGAAAGGCTAAGTGCCTTTG
358240 AGG
65 AGG
358243 CCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1 CCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATG-CAGTTAGATGAAAGGCTAAGTGCCTTTG
358308 AGG
65 AGG
* * * * *
358311 CCTAGTTATGCATTTGAAAGAAAGTTGTCAATTATGCCAGTTAGATGAAAGGCTAATTGCCTTTG
1 CCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATG-CAGTTAGATGAAAGGCTAAGTGCCTTTG
358376 AGG
65 AGG
* * * *
358379 CCTAGTTGTGCATTTGACAGAAAGATGTCAATTATGCAAGTTAGATGAAAGGCTAAATTCCTTTG
1 CCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGC-AGTTAGATGAAAGGCTAAGTGCCTTTG
358444 AGG
65 AGG
* *
358447 CCTAGCTGTGCATTTGATAGAAATGTGTCAATTATGCAGTTAGATGAAAGG
1 CCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCAGTTAGATGAAAGG
358498 TTAAATACAT
Statistics
Matches: 299, Mismatches: 20, Indels: 8
0.91 0.06 0.02
Matches are distributed among these distances:
66 1 0.00
67 58 0.19
68 240 0.80
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (67 bp):
CCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCAGTTAGATGAAAGGCTAAGTGCCTTTGA
GG
Found at i:358735 original size:45 final size:45
Alignment explanation
Indices: 358686--359032 Score: 469
Period size: 45 Copynumber: 7.7 Consensus size: 45
358676 GAATAAAAAA
358686 GCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCG
1 GCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCG
* * * *
358731 GCATGAAAAGATGCCATAAATGAAATGTATATGGGTGAATTATTG
1 GCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCG
* * *
358776 CCATAAAAGGATGCCATTAATGAAATGCATATGGGTGCATTATCG
1 GCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCG
* * *
358821 GCATGAAAGGATGCCATAATTGAAATGGATATGAGTGCATTATCG
1 GCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCG
* * * *
358866 ACATGAAAGGATGTCATAATTGAAATGCATATGGTTGCATTATCG
1 GCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCG
* * * * *
358911 GTATGAAAGGATCCCATAATTGAAATACATATGGGTGCATCATCG
1 GCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCG
* * *
358956 GCATGAAAGGATGCCATAATTGAAATGCATATGGGTACATTATTG
1 GCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCG
* *
359001 GCATGAAAGAATGTCATAAATGAAAATGCATA
1 GCATGAAAGGATGCCATAAATG-AAATGCATA
359033 ATTGTGCATT
Statistics
Matches: 263, Mismatches: 38, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
45 254 0.97
46 9 0.03
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (45 bp):
GCATGAAAGGATGCCATAAATGAAATGCATATGGGTGCATTATCG
Found at i:358750 original size:90 final size:89
Alignment explanation
Indices: 358640--359024 Score: 380
Period size: 90 Copynumber: 4.3 Consensus size: 89
358630 AATGTTAAAA
* *
358640 GGCATGAAAGGGTGCCATAAATGAATGTATAAT-AGCGAATAAAAAAGCATGAAAGGATGCCATA
1 GGCATGAAAGGATGCCATAAATGAATGTAT-ATGAGTGAAT-AAAAAGCATGAAAGGATGCCATA
358704 AATGAAATGCATATGGGTGCATTATC
64 AATGAAATGCATATGGGTGCATTATC
* * * ** * *
358730 GGCATGAAAAGATGCCATAAATGAAATGTATATGGGTGAAT-TATTGCCATAAAAGGATGCCATT
1 GGCATGAAAGGATGCCATAAATG-AATGTATATGAGTGAATAAAAAG-CATGAAAGGATGCCATA
358794 AATGAAATGCATATGGGTGCATTATC
64 AATGAAATGCATATGGGTGCATTATC
* * * * ** *
358820 GGCATGAAAGGATGCCATAATTGAAATGGATATGAGTGCAT-TATCGACATGAAAGGATGTCATA
1 GGCATGAAAGGATGCCATAAATG-AATGTATATGAGTGAATAAAAAG-CATGAAAGGATGCCATA
* *
358884 ATTGAAATGCATATGGTTGCATTATC
64 AATGAAATGCATATGGGTGCATTATC
* * * ** * * * ***
358910 GGTATGAAAGGATCCCATAATTGAAATACATATGGGTGCATCATCGGCATGAAAGGATGCCATAA
1 GGCATGAAAGGATGCCATAAATG-AATGTATATGAGTGAATAAAAAGCATGAAAGGATGCCATAA
* * *
358975 TTGAAATGCATATGGGTACATTATT
65 ATGAAATGCATATGGGTGCATTATC
* *
359000 GGCATGAAAGAATGTCATAAATGAA
1 GGCATGAAAGGATGCCATAAATGAA
359025 AATGCATAAT
Statistics
Matches: 252, Mismatches: 39, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
89 4 0.02
90 235 0.93
91 13 0.05
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.26
Consensus pattern (89 bp):
GGCATGAAAGGATGCCATAAATGAATGTATATGAGTGAATAAAAAGCATGAAAGGATGCCATAAA
TGAAATGCATATGGGTGCATTATC
Found at i:360642 original size:19 final size:19
Alignment explanation
Indices: 360618--360654 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
360608 TATAAGACTT
360618 AGTGCATCGGTACACTAAG
1 AGTGCATCGGTACACTAAG
360637 AGTGCATCGGTACACTAA
1 AGTGCATCGGTACACTAA
360655 TTACATTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.22
Consensus pattern (19 bp):
AGTGCATCGGTACACTAAG
Found at i:360771 original size:65 final size:64
Alignment explanation
Indices: 360638--360793 Score: 213
Period size: 65 Copynumber: 2.4 Consensus size: 64
360628 TACACTAAGA
* * * ** *
360638 GTGCATCGGTACACTAATTACATTCGATGTTCCAAAGAGTCAGGAGTGCATCGATGCATGGTTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTCCAAAGAGTCAAAAGTGCATCGATGCATGGCTT
* * * *
360702 GTGCATCCGTACACAAAATGCATTCGATGTTTCAAATTATTCAAAAGTGCATCGATGCATGGCTT
1 GTGCATCGGTACACAAAATGCATTCGATGTTCCAAA-GAGTCAAAAGTGCATCGATGCATGGCTT
360767 GTGCATCGGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
360794 AATGGGTTGC
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
64 31 0.39
65 49 0.61
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATGCATTCGATGTTCCAAAGAGTCAAAAGTGCATCGATGCATGGCTT
Found at i:363872 original size:9 final size:9
Alignment explanation
Indices: 363858--363900 Score: 59
Period size: 9 Copynumber: 4.4 Consensus size: 9
363848 CTATTTTTTT
363858 AAAAAAACAA
1 AAAAAAAC-A
363868 AAAAAAAGGCA
1 AAAAAAA--CA
363879 AAAAAAACA
1 AAAAAAACA
363888 AAAAAAACA
1 AAAAAAACA
363897 AAAA
1 AAAA
363901 TTTCAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 15 0.48
10 7 0.23
11 8 0.26
12 1 0.03
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:375267 original size:19 final size:19
Alignment explanation
Indices: 375231--375267 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
375221 TATAAGACTT
* *
375231 AGTGCATCGGTTCCCTAAG
1 AGTGCATCGGTACACTAAG
375250 AGTGCATCGGTACACTAA
1 AGTGCATCGGTACACTAA
375268 TTACATTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (19 bp):
AGTGCATCGGTACACTAAG
Found at i:375383 original size:65 final size:64
Alignment explanation
Indices: 375251--375406 Score: 206
Period size: 65 Copynumber: 2.4 Consensus size: 64
375241 TTCCCTAAGA
* * * * *
375251 GTGCATCGGTACACTAATTACATTCGATTTTCCAAAGAGTCAGGAGTGCATCGATGCATGGTCT
1 GTGCATCGGTACACAAAATGCATTCGATTTTCAAAAGAGTCAAGAGTGCATCGATGCATGGTCT
* * *
375315 GTGCATCGGTACACAAAATGCATTCGATGTTTTAAAATATTCAAGAGTGCATCGATGCAT-GTCT
1 GTGCATCGGTACACAAAATGCATTCGAT-TTTCAAAAGAGTCAAGAGTGCATCGATGCATGGTC-
375379 T
64 T
*
375380 GTGCATCAGTACACAAAATGCATTCGA
1 GTGCATCGGTACACAAAATGCATTCGA
375407 AATGGTGTGC
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 28 0.35
65 53 0.65
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATGCATTCGATTTTCAAAAGAGTCAAGAGTGCATCGATGCATGGTCT
Found at i:380766 original size:131 final size:130
Alignment explanation
Indices: 380580--381074 Score: 527
Period size: 131 Copynumber: 3.8 Consensus size: 130
380570 TTTTAAGAGA
* * * *
380580 GAAAACGATAATATTTAATTA-TTTCTAATCGATAATAAATGATCTTTTATGTCTTAAAACAATC
1 GAAAACGATAATATCTAATTATTTTC-AATCGAGAATAAATGATCTCTCATGTCTTAAAACAATC
* * * * * *
380644 ATTTATTATTCCAATCAAAATGAAGAGATATTACTGTTTCGTCTTAAAATTCAATATCGATTCGA
65 ATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAA-TCAATATTGATTCGA
380709 GT
129 GT
* * * * * ** *
380711 GAAAATGATAATATCTAATGATTTTCATTCGAGAATAAATGATCTATCATATCTT-AAAGTAGCT
1 GAAAACGATAATATCTAATTATTTTCAATCGAGAATAAATGATCTCTCATGTCTTAAAACAATC-
* * *
380775 ATTTATTGCTCCAATCGAAATGAAGAGATATCACAATTCCGTCTTAAAAATCAATATTGATT-AA
65 ATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTT-AAAATCAATATTGATTCGA
*
380839 GGA
129 -GT
* * *
380842 GAAAAC-AGTAATAT-TGAATTATTTTCAATCGAGAATAAATGACCTCTCATG-CTTTAAAGCAT
1 GAAAACGA-TAATATCT-AATTATTTTCAATCGAGAATAAATGATCTCTCATGTC-TTAAAACAA
* * * *
380904 TCATTTATTACTTCAATCGAAATAAAGAGATATCATTATTCCATCTTAAAATCAATATTGATTCG
63 TCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAATCAATATTGATTCG
*
380969 CGAT
128 AG-T
* * * * *
380973 -AAAACGGTAATATCTAATTATTTTCAATCGAGAATAAATGATCTCTTATGCCTTAAAGCAGTCA
1 GAAAACGATAATATCTAATTATTTTCAATCGAGAATAAATGATCTCTCATGTCTTAAAACAATCA
* *
381037 TTTATTACTCCAATCGAAATGAAAAGATATTACTATTC
66 TTTATTACTCCAATCGAAATGAAGAGATATCACTATTC
381075 TTAATATCGA
Statistics
Matches: 301, Mismatches: 50, Indels: 27
0.80 0.13 0.07
Matches are distributed among these distances:
130 114 0.38
131 176 0.58
132 11 0.04
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (130 bp):
GAAAACGATAATATCTAATTATTTTCAATCGAGAATAAATGATCTCTCATGTCTTAAAACAATCA
TTTATTACTCCAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAATCAATATTGATTCGAGT
Found at i:381050 original size:261 final size:263
Alignment explanation
Indices: 380572--381066 Score: 637
Period size: 261 Copynumber: 1.9 Consensus size: 263
380562 CAAAATAATT
* * * * *
380572 TTAAGAGAGAAAACGATAATATTTAATTATTTCTAATCGATAATAAATGATCTTTTATGTCTTAA
1 TTAAGAGAGAAAACGATAATATTGAATTATTTCTAATCGAGAATAAATGACCTCTCATGTCTTAA
* * * * *
380637 AACAATCATTTATTATTCCAATCAAAATGAAGAGATATTACTGTTTCGTCTTAAAATTCAATATC
66 AACAATCATTTATTATTCCAATCAAAATAAAGAGATATCACTATTCCATCTTAAAATTCAATATC
* * *
380702 GATTCGAGTGAAAATGATAATATCTAATGATTTTCATTCGAGAATAAATGATCTATCATATCTTA
131 GATTCGAGTGAAAACGATAATATCTAATGATTTTCAATCGAGAATAAATGATCTATCATACCTTA
* * *
380767 AAGTAGCTATTTATTGCTCCAATCGAAATGAAGAGATATCACAATTCCGTCTTAAAAATCAATAT
196 AAGCAGCTATTTATTACTCCAATCGAAATGAAAAGATATCACAATTCCGTCTTAAAAATCAATAT
380832 TGA
261 TGA
380835 TTAAG-GAGAAAAC-AGTAATATTGAATTATTT-TCAATCGAGAATAAATGACCTCTCATG-CTT
1 TTAAGAGAGAAAACGA-TAATATTGAATTATTTCT-AATCGAGAATAAATGACCTCTCATGTC-T
* * * *
380896 TAAAGCATTCATTTATTACTT-CAATCGAAATAAAGAGATATCATTATTCCATCTTAAAA-TCAA
63 TAAAACAATCATTTATTA-TTCCAATCAAAATAAAGAGATATCACTATTCCATCTTAAAATTCAA
* * * * * * *
380959 TATTGATTCGCGAT-AAAACGGTAATATCTAATTATTTTCAATCGAGAATAAATGATCTCTTATG
127 TATCGATTCGAG-TGAAAACGATAATATCTAATGATTTTCAATCGAGAATAAATGATCTATCATA
381023 CCTTAAAGCAG-TCATTTATTACTCCAATCGAAATGAAAAGATAT
191 CCTTAAAGCAGCT-ATTTATTACTCCAATCGAAATGAAAAGATAT
381067 TACTATTCTT
Statistics
Matches: 199, Mismatches: 27, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
260 1 0.01
261 98 0.49
262 93 0.47
263 7 0.04
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.35
Consensus pattern (263 bp):
TTAAGAGAGAAAACGATAATATTGAATTATTTCTAATCGAGAATAAATGACCTCTCATGTCTTAA
AACAATCATTTATTATTCCAATCAAAATAAAGAGATATCACTATTCCATCTTAAAATTCAATATC
GATTCGAGTGAAAACGATAATATCTAATGATTTTCAATCGAGAATAAATGATCTATCATACCTTA
AAGCAGCTATTTATTACTCCAATCGAAATGAAAAGATATCACAATTCCGTCTTAAAAATCAATAT
TGA
Found at i:383174 original size:13 final size:12
Alignment explanation
Indices: 383149--383180 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
383139 AACCAAAAAT
383149 AAAATAATAATA
1 AAAATAATAATA
383161 AAAATAATTAATA
1 AAAATAA-TAATA
383174 AAAATAA
1 AAAATAA
383181 AAACATCGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:383179 original size:19 final size:17
Alignment explanation
Indices: 383143--383183 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
383133 ACCTGTAACC
*
383143 AAAAATAAAATAATAAT
1 AAAAATAAAATAAAAAT
383160 AAAAATAATTAATAAAAAT
1 AAAAATAA--AATAAAAAT
383179 AAAAA
1 AAAAA
383184 CATCGAGACG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
19 13 0.62
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAAATAAAATAAAAAT
Found at i:383655 original size:134 final size:134
Alignment explanation
Indices: 383350--383923 Score: 680
Period size: 134 Copynumber: 4.3 Consensus size: 134
383340 ATCATATTGA
* ** * * * * * *
383350 GAAACGTTGATTCATTTTACTGTTCTTCAGGGAAGATTGAATCAAGGCAGGCTTGTTCAATTGCT
1 GAAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGACAGACTTGTTCCACTGTT
* * * *
383415 ACTCATGGAATATCAAATCTTGAAAGAGATGGATTTG-TTC-C-ACTTCTTAAGGGAAAATCAGA
66 ACTCAGGGAATATCAAATCTTGAAAGAGATGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGA
383477 TCTG
131 TCTG
* *
383481 GAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGACAGACTTGTTCCATTGTT
1 GAAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGACAGACTTGTTCCACTGTT
* * *
383546 ACTCAGGGAATATCAAGTCTTGAAAGAGA-GTTATATGTTTTGCTTCTTCTTGAGGGAAAATCAG
66 ACTCAGGGAATATCAAATCTTGAAAGAGATG-GATATGTTTCGCTTCTTCTTGAGGGAAAATCAG
383610 ATCTG
130 ATCTG
* * *
383615 GAAATATTGATTCATTGCACTGTTCTTCAGGGAAGGTTGAATCGAGGA-AGACTTGTTCCACTGT
1 GAAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGA-GACAGACTTGTTCCACTGT
* * * * * * *
383679 TTCTTAGGGAATATTAAATCTTGAAAGATATGGATCTATTTCG-TTGCTTCTTGAGGGAAAATCG
65 TACTCAGGGAATATCAAATCTTGAAAGAGATGGATATGTTTCGCTT-CTTCTTGAGGGAAAATCA
*
383743 GATCTA
129 GATCTG
* *
383749 AAAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAAT-GAGACAGACTTGTTCCACCGTT
1 GAAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGACAGACTTGTTCCACTGTT
* * * * * * * *
383813 CCTCA-GAAAGATCAAATC-TGAGAAAAGAGGGATATGTTCCGCTGCTTCTTGAGGGAAAATCAT
66 ACTCAGGGAATATCAAATCTTGA-AAGAGATGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAG
*
383876 ATTTG
130 ATCTG
*
383881 GAAATGTTGATTCATTCCACTGTTCTTCAGGCAAGATTGAATC
1 GAAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATC
383924 CAGTTCAATT
Statistics
Matches: 377, Mismatches: 55, Indels: 20
0.83 0.12 0.04
Matches are distributed among these distances:
130 1 0.00
131 90 0.24
132 87 0.23
133 25 0.07
134 171 0.45
135 3 0.01
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (134 bp):
GAAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGACAGACTTGTTCCACTGTT
ACTCAGGGAATATCAAATCTTGAAAGAGATGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGA
TCTG
Found at i:389713 original size:907 final size:907
Alignment explanation
Indices: 387467--390183 Score: 3970
Period size: 907 Copynumber: 3.0 Consensus size: 907
387457 TCCACCATGA
*
387467 ACTAGCTTTATTTGGTGGGAGTTCATTTTGGATGCTTAAGTTTTTCTTTAATAGATGGTTGTTCT
1 ACTAGCTTTATTTGGTGGGAGTTCATTTTGGATGCTTAAGTTTTTCTTTAATGGATGGTTGTTCT
* * *
387532 TTTTCTATGTGTTTATTTGTTTTGTTTTTGGTGCTTAATAACTTAAGG-T-T-GGAGCTATGAGA
66 TTTTTTATGTGTTTATTTGTTTTGTTTATGGTGCTTAATGACTTAAGGTTGTAGGAGCTATGAGA
*
387594 GTAATCATTCCTTAGGAAAATACTTAGTGTTCGAGAGAAACTAAGTAACTCATCTTTAATGTTCG
131 GTAA-CATTCCTTAGGAAAATACTTAGTGTTCGAGAGAAACTAAGTAACTCATCTTTAGTGTTCG
* * * * *
387659 AGATAAACAAAGAAGGATTAAAATAAACAATGGGTTTTAGATAGTAACTAGACTTAATCCATCAT
195 AGA-GAACAAAGGAGGATTAACATAAAAAATGGGTTTTAGATAGTAACTAGACTTAATCCACCAT
*
387724 TAG--ATAAGGCTAGGATTTCAATCAATTAAAAG-GGAGT--TCGGTCGAGAGGTTAGATGCTAG
259 TAGACATAAGGCTAGGATTTCAATCAATTAAAAGAGTAGTGCTCGGTCGAGAGGTTAGATGCTAG
* *
387784 TGCTAACACTGAGTGGTATTAATGTCACATATTATGTTGATTTGAACTGATGGGATCCCTGCACC
324 TGCTAACATTGAGTGGTATT-ATG--ACATATTCTGTTGATTTGAACTGATGGGATCCCTGCACC
* *
387849 TACTAACGCCGAGAGGT-ATACCATGGCATTTTCAACCTGTCGAGTCCCTTGACTAGAGATAGCA
386 TGCTAACG-CGAGAGGTAATACCATGGAATTTTCAACCTGTCGAGTCCCTTGACTAGAGATAGCA
*
387913 TAGGGCACCTTTGGTAAACTCTTTCGGGCAAGTAAGGCATAGAAGTAAAACCATCTTGAG-AGAT
450 TAGGGCACCTTTGGTAAACTCTGTCGGGCAAGTAAGGCATAGAAGTAAAACCATCTTGAGAAGAT
* * *
387977 AAACTTAAGTTTCCTAATTTACTCCTATCATTCATTCCCATAGTATATTGTTGTGTGAGGATTAT
515 AAACTTAAGTTTCCTAAGTGACTCCTATCATTCATTCCCATAGTATCTT-TTGTGTGAGGATTAT
*
388042 CAAGTTATTCTATTCAAATCCAGTGTTTAAATTTTGTTTTGCCTTTACATTTTCATTTGATTTCA
579 CAAGTTATTCTATTCAAATCCAGTGTTTACATTTTGTTTTGCCTTTACATTTTCATTTGATTTCA
* * * * *
388107 C--TACAC-ATTTTAT--TATGCAACATCACCATTTATTACCATATCACACTATCATTCAATCCG
644 CTATACACAATTTTCTGCAATG--ACATCACCATTTACTACCATATCACACTATCATTC-CT-CA
*
388167 CCAATATACATTTCACATTGCCTCAGCGTTCTCATTAGTACATACCAT--CACTAA-TACAGTTA
705 CCAA-ATACATTTCACATTGCCTCAGCGTTCTCATTAGTACATACCATCACACTAACTACACTTA
**
388229 AAT-AAGTAGATATTTGCTTTAACTGAACCTATAAATTTCCTTTAATCCTTGGAGATGATACTCA
769 AATAAAGTAGATATTTGCTTTAACTGAACCTATAAATTTCCTCCAATCCTTGGAGATGATACTCA
*
388293 CTCATCACTGTATTACTTGTTCGATTGTGTACTCTTGCACATATTTCGCGTCCATATTAAGTACT
834 CTCATCACTATATTACTTGTTCGATTGTGTA-TCTTGCACATATTTCGCGTCCATATTAAGTACT
388358 CAC-AAAAGT
898 CACAAAAAGT
**
388367 ACTAGCTTTATTTGGTAAGAGTTTCA-TTTGGATGCTTAAGTTTTTCTTTAATGGATGGTTGTTC
1 ACTAGCTTTATTTGGTGGGAG-TTCATTTTGGATGCTTAAGTTTTTCTTTAATGGATGGTTGTTC
* *
388431 --TTTTTCTGTGTCTATTTGTTTTGTTTATGGTGCTTAATGACTTAAGGTTGTAGGAGCTATGAG
65 TTTTTTTATGTGTTTATTTGTTTTGTTTATGGTGCTTAATGACTTAAGGTTGTAGGAGCTATGAG
*
388494 AGTAACCATTCCTTAGGAAAATACTTAGTGTTCGAGAGAAACTAAGTAACTCATCTTTAGTGGTC
130 AGTAA-CATTCCTTAGGAAAATACTTAGTGTTCGAGAGAAACTAAGTAACTCATCTTTAGTGTTC
*
388559 GAGAGAAACAAAGGAGGATTAACATAAATAATGGGTTTTTAGATAGTAACTAGACTTAATCCACC
194 GAGAG-AACAAAGGAGGATTAACATAAAAAATGGG-TTTTAGATAGTAACTAGACTTAATCCACC
* *
388624 ATTAGACATAAGGCTAGGATTTCAATCGATTAAAAGGAGTAGTGCTCGGT--AGAGGTTAAATGC
257 ATTAGACATAAGGCTAGGATTTCAATCAATTAAAA-GAGTAGTGCTCGGTCGAGAGGTTAGATGC
* * * *
388687 TAGTGCTAACATTGAGTGGTATTACCGTCACATATTC---TGATTTGAAATGATGAGATCCCTGT
321 TAGTGCTAACATTGAGTGGTATTA---TGACATATTCTGTTGATTTGAACTGATGGGATCCCTGC
* *
388749 ACCTGCTAACGCTGAGAGGTATTACCATGGAATTTTCAACCTGTCGAGTCTCTTGACTAGAGATA
383 ACCTGCTAACGC-GAGAGGTAATACCATGGAATTTTCAACCTGTCGAGTCCCTTGACTAGAGATA
* * *
388814 GCATAGGGTACCTTTGGTAAACTCTGTCGGGCAAGTAAGGCATAGAATTAAAACCTTCTTGAGAA
447 GCATAGGGCACCTTTGGTAAACTCTGTCGGGCAAGTAAGGCATAGAAGTAAAACCATCTTGAGAA
* *
388879 GATAAACTTAAG-TTCCTAAGTGACTGCTATCATTCATTCCCATAATATCTTATTGTGTGAGGAT
512 GATAAACTTAAGTTTCCTAAGTGACTCCTATCATTCATTCCCATAGTATCTT-TTGTGTGAGGAT
388943 TATCAAGTTATTCTATTCAAATCCAGTGTTTACATTTTGTTTTGCCTTTACATTTTCATTTGATT
576 TATCAAGTTATTCTATTCAAATCCAGTGTTTACATTTTGTTTTGCCTTTACATTTTCATTTGATT
*
389008 TCACTATATACAATTTTCTGCAATGACATCACCATTTACTACCATATCACACTATCATTCCTCAA
641 TCACTATACACAATTTTCTGCAATGACATCACCATTTACTACCATATCACACTATCATTCCTC-A
389073 CCAACATACA-TTCACATTGCCTCAGCGTTCTCATTAGTACATACCATCACACTAACTACACTTA
705 CCAA-ATACATTTCACATTGCCTCAGCGTTCTCATTAGTACATACCATCACACTAACTACACTTA
389137 AATAAAGTAGATATTTGCTTTAACTGAACCTATAAATTTCCTCCAATCCTTGTGGAGATGATACT
769 AATAAAGTAGATATTTGCTTTAACTGAACCTATAAATTTCCTCCAATCC-T-TGGAGATGATACT
* * *
389202 CACTCATCATTCTATTACTTGTTCGATTGTGTATGCTTGCACATATGTCGCGT-CATA-TAAGTA
832 CACTCATCACTATATTACTTGTTCGATTGTGTAT-CTTGCACATATTTCGCGTCCATATTAAGTA
389265 CTCACAAAAAGT
896 CTCACAAAAAGT
*
389277 ACTAGCTTTA-TTGGTGGGAGTTCATTTTGGATGCTTAAGTTTTTCTTTAATGGATGGTTATTCT
1 ACTAGCTTTATTTGGTGGGAGTTCATTTTGGATGCTTAAGTTTTTCTTTAATGGATGGTTGTTCT
* * *
389341 TTTTTTATGTGTTTATTTGTTTTGTGTATAGTGCTAAATGACTTAAGGTTGTAGGAGCTATGAGA
66 TTTTTTATGTGTTTATTTGTTTTGTTTATGGTGCTTAATGACTTAAGGTTGTAGGAGCTATGAGA
* *
389406 -T-A-ATTCCTTAGGAAAATACTTAGTGTTCGAGAGAAACTAAGTAACTCATATTTAGTGTTCAA
131 GTAACATTCCTTAGGAAAATACTTAGTGTTCGAGAGAAACTAAGTAACTCATCTTTAGTGTTCGA
** * * *
389468 GAGAACTGAGGAGGATTATCATAAAAAATGGGTTTTAGATAATAA-TTGTACTTAATCCACCATT
196 GAGAACAAAGGAGGATTAACATAAAAAATGGGTTTTAGATAGTAACTAG-ACTTAATCCACCATT
* *
389532 AGACATAAGGCTAGGATTTCAATCAACTAAAAGAAGTAGTGCTCAGTCGAGAGGTTAGATGCTAG
260 AGACATAAGGCTAGGATTTCAATCAATTAAAAG-AGTAGTGCTCGGTCGAGAGGTTAGATGCTAG
* *
389597 TGCTAACGTTGAGTGGTATTATGACATATTCTGTTGATTTGAACTGGTGGGATCCCTGCACCTGC
324 TGCTAACATTGAGTGGTATTATGACATATTCTGTTGATTTGAACTGATGGGATCCCTGCACCTGC
*
389662 TAACGTCGAGAGGTAATACCATGGTATTTTCAACCTGTCGAGTCCCTTGACTAGAGATAGCATAG
389 TAACG-CGAGAGGTAATACCATGGAATTTTCAACCTGTCGAGTCCCTTGACTAGAGATAGCATAG
* *
389727 GGCACCTTTGGTAAACTCTGT-AGGCAAGTAAGGCATAGAAGT-AGACCATCTTGAGAAGATAAA
453 GGCACCTTTGGTAAACTCTGTCGGGCAAGTAAGGCATAGAAGTAAAACCATCTTGAGAAGATAAA
* * * * *
389790 CATAAGTTTCCTAAGTGACTCCTATCATTCATTCCCATAGTAGCTTGTGTGTGAAGATTAT--AT
518 CTTAAGTTTCCTAAGTGACTCCTATCATTCATTCCCATAGTATCTTTTGTGTGAGGATTATCAAG
* * * *
389853 TTATTATATTCAAATCCAATGTTTACATTTTGTTTTGCCTTTACTTTTTCATTTGATTTCACTAC
583 TTATTCTATTCAAATCCAGTGTTTACATTTTGTTTTGCCTTTACATTTTCATTTGATTTCACTAT
* * * * * *
389918 AGACAATTTATTCTGCCATGACATCTCCATTTAGTGCCACATCACACTATCATTCAATCCTCACC
648 ACACAA-TT-TTCTGCAATGACATCACCATTTACTACCATATCACACTATCA-T---TCCTCACC
** **
389983 AAATACATTTCACATTGCCTCATTGTTCTCATTAGTACATAATATCACACTAACTACACTTAAAT
707 AAATACATTTCACATTGCCTCAGCGTTCTCATTAGTACATACCATCACACTAACTACACTTAAAT
*
390048 AAAGTAGATATTTGCTTTAACTGAACCTATAAATTTCCTCCAATACTATGGAGATGATACTCACT
772 AAAGTAGATATTTGCTTTAACTGAACCTATAAATTTCCTCCAATCCT-TGGAGATGATACTCACT
*
390113 CATCACTATATTACTTGTTCGATTGTGTATACTT-CACATATTTCGCATCCATATTAAGTACTCA
836 CATCACTATATTACTTGTTCGATTGTGTAT-CTTGCACATATTTCGCGTCCATATTAAGTACTCA
390177 CAAAAAG
900 CAAAAAG
390184 CCAACAATTT
Statistics
Matches: 1648, Mismatches: 116, Indels: 98
0.89 0.06 0.05
Matches are distributed among these distances:
898 42 0.03
899 1 0.00
900 57 0.03
901 107 0.06
902 34 0.02
903 106 0.06
904 255 0.15
905 196 0.12
906 152 0.09
907 306 0.19
908 141 0.09
909 108 0.07
910 23 0.01
911 120 0.07
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (907 bp):
ACTAGCTTTATTTGGTGGGAGTTCATTTTGGATGCTTAAGTTTTTCTTTAATGGATGGTTGTTCT
TTTTTTATGTGTTTATTTGTTTTGTTTATGGTGCTTAATGACTTAAGGTTGTAGGAGCTATGAGA
GTAACATTCCTTAGGAAAATACTTAGTGTTCGAGAGAAACTAAGTAACTCATCTTTAGTGTTCGA
GAGAACAAAGGAGGATTAACATAAAAAATGGGTTTTAGATAGTAACTAGACTTAATCCACCATTA
GACATAAGGCTAGGATTTCAATCAATTAAAAGAGTAGTGCTCGGTCGAGAGGTTAGATGCTAGTG
CTAACATTGAGTGGTATTATGACATATTCTGTTGATTTGAACTGATGGGATCCCTGCACCTGCTA
ACGCGAGAGGTAATACCATGGAATTTTCAACCTGTCGAGTCCCTTGACTAGAGATAGCATAGGGC
ACCTTTGGTAAACTCTGTCGGGCAAGTAAGGCATAGAAGTAAAACCATCTTGAGAAGATAAACTT
AAGTTTCCTAAGTGACTCCTATCATTCATTCCCATAGTATCTTTTGTGTGAGGATTATCAAGTTA
TTCTATTCAAATCCAGTGTTTACATTTTGTTTTGCCTTTACATTTTCATTTGATTTCACTATACA
CAATTTTCTGCAATGACATCACCATTTACTACCATATCACACTATCATTCCTCACCAAATACATT
TCACATTGCCTCAGCGTTCTCATTAGTACATACCATCACACTAACTACACTTAAATAAAGTAGAT
ATTTGCTTTAACTGAACCTATAAATTTCCTCCAATCCTTGGAGATGATACTCACTCATCACTATA
TTACTTGTTCGATTGTGTATCTTGCACATATTTCGCGTCCATATTAAGTACTCACAAAAAGT
Found at i:391976 original size:12 final size:12
Alignment explanation
Indices: 391959--391983 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
391949 AACTTGAGAG
391959 GCTTACTGAAGA
1 GCTTACTGAAGA
391971 GCTTACTGAAGA
1 GCTTACTGAAGA
391983 G
1 G
391984 GAAAGCGTCG
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:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (12 bp):
GCTTACTGAAGA
Found at i:395503 original size:13 final size:13
Alignment explanation
Indices: 395484--395531 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
395474 ATCTATGACG
395484 CACATTTATAACA
1 CACATTTATAACA
* * *
395497 AACATTTATGACG
1 CACATTTATAACA
*
395510 CGCATTTATAACA
1 CACATTTATAACA
395523 CACATTTAT
1 CACATTTAT
395532 GATGCTCATT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (13 bp):
CACATTTATAACA
Found at i:395554 original size:26 final size:26
Alignment explanation
Indices: 395477--395544 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
395467 GTCATAAATC
* *
395477 TATGACGCACATTTATAACAAACATT
1 TATGACGCGCATTTATAACACACATT
395503 TATGACGCGCATTTATAACACACATT
1 TATGACGCGCATTTATAACACACATT
* *
395529 TATGATGCTCATTTAT
1 TATGACGCGCATTTAT
395545 GACATGCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (26 bp):
TATGACGCGCATTTATAACACACATT
Found at i:395720 original size:2 final size:2
Alignment explanation
Indices: 395713--395755 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
395703 TCGTAAATTT
395713 TA TA TA TA TA 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 TA TA TA TA TA
395755 T
1 T
395756 TAGATTGACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:403075 original size:20 final size:20
Alignment explanation
Indices: 403050--403102 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
403040 TTTTCAAGGG
403050 GTATCGATACCAAAAGGGTA
1 GTATCGATACCAAAAGGGTA
*
403070 GTATCGATACCTAAAGGGTA
1 GTATCGATACCAAAAGGGTA
403090 GTATCGATACCAA
1 GTATCGATACCAA
403103 GGGTACCGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (20 bp):
GTATCGATACCAAAAGGGTA
Found at i:410877 original size:20 final size:20
Alignment explanation
Indices: 410849--410888 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
410839 AGAATGATGC
410849 ATGTAAGTGGTTTGTTGAGG
1 ATGTAAGTGGTTTGTTGAGG
*
410869 ATGTGAGTGGTTTGTTGAGG
1 ATGTAAGTGGTTTGTTGAGG
410889 GCTTACGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.40
Consensus pattern (20 bp):
ATGTAAGTGGTTTGTTGAGG
Found at i:415708 original size:18 final size:20
Alignment explanation
Indices: 415674--415711 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
415664 TATTCAAGGG
415674 GTATCGATACCTAAAGGGTA
1 GTATCGATACCTAAAGGGTA
415694 GTATCGATA-CT-AAGGGTA
1 GTATCGATACCTAAAGGGTA
415712 CCGATACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.26
Consensus pattern (20 bp):
GTATCGATACCTAAAGGGTA
Found at i:415995 original size:18 final size:18
Alignment explanation
Indices: 415969--416006 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
415959 AACATAAGCA
415969 AGTTCAGGAACGATCGAAG
1 AGTTCAGGAACGATC-AAG
*
415988 AGTT-AGGATCGATCAAG
1 AGTTCAGGAACGATCAAG
416005 AG
1 AG
416007 AGATAAAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 9 0.50
19 4 0.22
ACGTcount: A:0.37, C:0.13, G:0.32, T:0.18
Consensus pattern (18 bp):
AGTTCAGGAACGATCAAG
Found at i:426048 original size:19 final size:20
Alignment explanation
Indices: 426012--426053 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
426002 AGGATGCAAT
426012 ATTTTTCAAAATTCTTGAAA
1 ATTTTTCAAAATTCTTGAAA
426032 ATTTTTCAAAATT-TTGAAA
1 ATTTTTCAAAATTCTTGAAA
426051 ATT
1 ATT
426054 CAAAAGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (20 bp):
ATTTTTCAAAATTCTTGAAA
Found at i:426717 original size:36 final size:36
Alignment explanation
Indices: 426584--427416 Score: 815
Period size: 36 Copynumber: 23.2 Consensus size: 36
426574 ATTTATCTCA
* * * *
426584 AAACAAACTTTGTCTCGCTTAAGACACTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
426620 AAATAAA--TTGTCTCTCTTGAGACAATTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
426654 AAAAAAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
** * * *
426691 AAACAAACGTTATCTCCCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
426727 AAACAAATTTTGTCTCTCTTAAGACACTTTCCTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
426763 AAATAAATTTTGTCTCTCTTGAGACAGTTTCCTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
426799 AAACAAATTTTATCTCTCTTGAGACAGTTTCCTTTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
426835 AAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
426871 AAACAAGTTTTGTCTCCCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
426907 AAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
426943 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
426979 AAACAAGTTTTGTCTCCCTTGAGACATTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * *
427015 AAACAAATTTCGTCACCCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
*
427051 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* ** *
427087 AAATATAA-----AATCT-TTGA-ATATGTTTCCCTTGG
1 AAACA-AATTTTGTCTCTCTTGAGACA-GTTTCCCTT-G
* * * * *
427119 AAAAAAAATTTGTCTCCCTTGAGACAGTTTCTCTGG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* ** *
427155 AAACAAAGTTTTGTCTCT-TTAAAGACAGTTTTACTCG
1 AAACAAA-TTTTGTCTCTCTT-GAGACAGTTTCCCTTG
* * * *
427192 AAACAAAATTTTGTCTCTCTTGAGATTATTTTTCC-TA
1 AAAC-AAATTTTGTCTCTCTTGAGA-CAGTTTCCCTTG
* *
427229 AAACAAATTTTATCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* ** * ** *
427265 AAACAAATTTTGTCTCCCTCAAGATAGTTTTTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * *
427301 AAACCAACTTCGTCTCACTTGAGACAGTTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAG-TTTCCCTTG
* * * * ** ** *
427338 AAACAAAATGTATCTCACTTGAGATGGTTTTTCTTA
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * *
427374 AAACCAACTTTGTCTCGCTTGAGACAGTTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAG-TTTCCCTTG
427411 AAACAA
1 AAACAA
427417 GAAATTTTAT
Statistics
Matches: 655, Mismatches: 121, Indels: 41
0.80 0.15 0.05
Matches are distributed among these distances:
30 2 0.00
31 14 0.02
32 8 0.01
34 29 0.04
35 5 0.01
36 462 0.71
37 122 0.19
38 13 0.02
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:428103 original size:139 final size:140
Alignment explanation
Indices: 427728--428235 Score: 629
Period size: 139 Copynumber: 3.7 Consensus size: 140
427718 TATTTCAAAA
* * *
427728 GGAGAGTTCGTAATGAGAATAACTCATAC-GATAAAGGGAGAAGAAGTTCATAATGAGAAGAGCT
1 GGAGAGTTCATAATGAGAATAACTCAT-CTAATAAAGGGAGAAGAAGTTCATAATGAGAAGAACT
* * * ** ** * **
427792 TATTCGACCTATCACTCGATTCAT--GGTATT---TTGAATCAGTGACACCTCGCTTTAGGGATC
65 TGTTCAACCT-TAACTCGATTCATCACATATTGAGTTGAATCAGCAACACCTCACTCGAGGGATC
* *
427852 AACATTTCAAAT
129 AACATTTCCAGT
* *
427864 GGAGAGTTCATAATGAGAATAACTCAT-TCAACAAAGGGAGAAGAAGTTCATAATGAGAAAAACT
1 GGAGAGTTCATAATGAGAATAACTCATCT-AATAAAGGGAGAAGAAGTTCATAATGAGAAGAACT
* * *
427928 TGTTCAACCTTAGCTCGATTAATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCA
65 TGTTCAACCTTAACTCGATTCATCACATATTGAGTTGAATCAGCAACACCTCACTCGAGGGATCA
427993 ACATTTCCAGT
130 ACATTTCCAGT
* * * *
428004 GGAGAGCTCATAATGAGAATAACTCATCTGATGAA-GGAGAAGAAATTCATAATGAGAAGAACTT
1 GGAGAGTTCATAATGAGAATAACTCATCTAATAAAGGGAGAAGAAGTTCATAATGAGAAGAACTT
* * *
428068 GTTCAACCTCAACTCGATTCATCACATATTGAGTTGAATCAACAACACCTCACTCGAGGAATCAA
66 GTTCAACCTTAACTCGATTCATCACATATTGAGTTGAATCAGCAACACCTCACTCGAGGGATCAA
*
428133 TATTTCCAGT
131 CATTTCCAGT
* *
428143 GGAGAGTTCATAATGAGAAGAACTCATCTAAT-GAGGGAGAAGAAGTTCATAATGAGAAGAACTT
1 GGAGAGTTCATAATGAGAATAACTCATCTAATAAAGGGAGAAGAAGTTCATAATGAGAAGAACTT
* *
428207 GTTCAACCTTAGCTCGTTTCCATCACATA
66 GTTCAACCTTAACTCGATT-CATCACATA
428236 AGGAGTTGGA
Statistics
Matches: 321, Mismatches: 41, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
135 10 0.03
136 65 0.20
137 3 0.01
138 1 0.00
139 168 0.52
140 73 0.23
141 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.26
Consensus pattern (140 bp):
GGAGAGTTCATAATGAGAATAACTCATCTAATAAAGGGAGAAGAAGTTCATAATGAGAAGAACTT
GTTCAACCTTAACTCGATTCATCACATATTGAGTTGAATCAGCAACACCTCACTCGAGGGATCAA
CATTTCCAGT
Found at i:428235 original size:279 final size:275
Alignment explanation
Indices: 427728--428243 Score: 673
Period size: 279 Copynumber: 1.9 Consensus size: 275
427718 TATTTCAAAA
* * * *
427728 GGAGAGTTCGTAATGAGAATAACTCATACGATAAAGGGAGAAGAAGTTCATAATGAGAAGAGCTT
1 GGAGAGCTCATAATGAGAATAACTCATACGATAAAGGGAGAAGAAATTCATAATGAGAAGAACTT
* ** *** * ** *
427793 ATTCGACCTATCACTCGATTCATGGTATTTTGAATCAGTGACACCTCGCTTTAGGGATCAACATT
66 ATTCAACCTA-CACTCGATTCATCATATTTTGAATCAACAACACCTCACTCGAGGAATCAACATT
*
427858 TCAAATGGAGAGTTCATAATGAGAATAACTCATTCAACAAAGGGAGAAGAAGTTCATAATGAGAA
130 TCAAATGGAGAGTTCATAATGAGAAGAACTCATTCAACAAAGGGAGAAGAAGTTCATAATGAGAA
*
427923 AAACTTGTTCAACCTTAGCTCGATTAATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGG
195 AAACTTGTTCAACCTTAGCTCGATTAATCACATAAGGAGTTGAATCAGCAACACCTCACTCGAGG
427988 GATCAACATTTCCAGT
260 GATCAACATTTCCAGT
*
428004 GGAGAGCTCATAATGAGAATAACTCAT-CTGATGAA-GGAGAAGAAATTCATAATGAGAAGAACT
1 GGAGAGCTCATAATGAGAATAACTCATAC-GATAAAGGGAGAAGAAATTCATAATGAGAAGAACT
*
428067 TGTTCAACCT-CAACTCGATTCATCACATATTGAGTTGAATCAACAACACCTCACTCGAGGAATC
65 TATTCAACCTAC-ACTCGATTCAT--CATATT---TTGAATCAACAACACCTCACTCGAGGAATC
* * * **
428131 AATATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCA-TCTAA-TGAGGGAGAAGAAGTTCATA
124 AACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATTC-AACAAAGGGAGAAGAAGTTCATA
* * *
428194 ATGAGAAGAACTTGTTCAACCTTAGCTCGTTTCCATCACATAAGGAGTTG
188 ATGAGAAAAACTTGTTCAACCTTAGCTCGATT-AATCACATAAGGAGTTG
428244 GAACAACACC
Statistics
Matches: 205, Mismatches: 26, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
273 1 0.00
274 11 0.05
275 35 0.17
276 34 0.17
278 50 0.24
279 74 0.36
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (275 bp):
GGAGAGCTCATAATGAGAATAACTCATACGATAAAGGGAGAAGAAATTCATAATGAGAAGAACTT
ATTCAACCTACACTCGATTCATCATATTTTGAATCAACAACACCTCACTCGAGGAATCAACATTT
CAAATGGAGAGTTCATAATGAGAAGAACTCATTCAACAAAGGGAGAAGAAGTTCATAATGAGAAA
AACTTGTTCAACCTTAGCTCGATTAATCACATAAGGAGTTGAATCAGCAACACCTCACTCGAGGG
ATCAACATTTCCAGT
Found at i:431452 original size:28 final size:28
Alignment explanation
Indices: 431410--431466 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
431400 CTTTAGTCCC
431410 TTGTTTGTTTCTTTCAAGAGATGTTTCA
1 TTGTTTGTTTCTTTCAAGAGATGTTTCA
*
431438 TTGTTTGTTTGTTTCAAGAGATGTTTCA
1 TTGTTTGTTTCTTTCAAGAGATGTTTCA
431466 T
1 T
431467 AGTGGTGCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.18, C:0.09, G:0.19, T:0.54
Consensus pattern (28 bp):
TTGTTTGTTTCTTTCAAGAGATGTTTCA
Found at i:431601 original size:3 final size:3
Alignment explanation
Indices: 431595--431631 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
431585 ACAAAAAAAT
431595 TTA TTA -TA TTA TTA TT- TTA TTA TTA TTA TTAA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TT
431632 TTTTATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.13
3 24 0.77
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:431615 original size:11 final size:11
Alignment explanation
Indices: 431595--431645 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
431585 ACAAAAAAAT
*
431595 TTATTATATTA
1 TTATTTTATTA
431606 TTATTTTATTA
1 TTATTTTATTA
431617 TTA--TTATTAA
1 TTATTTTATT-A
431627 TTATTTT-TTA
1 TTATTTTATTA
431637 TT-TTTTATT
1 TTATTTTATT
431646 TTTTTGTAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
9 9 0.26
10 9 0.26
11 15 0.43
12 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:431620 original size:14 final size:14
Alignment explanation
Indices: 431601--431645 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
431591 AAATTTATTA
431601 TATTATTATTTTAT
1 TATTATTATTTTAT
431615 TATTATTATTAATTAT
1 TATTATTATT--TTAT
431631 T-TT-TTATTTT-T
1 TATTATTATTTTAT
431642 TATT
1 TATT
431646 TTTTTGTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 2 0.07
12 4 0.14
14 15 0.54
15 2 0.07
16 5 0.18
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTATTATTTTAT
Found at i:436687 original size:106 final size:106
Alignment explanation
Indices: 436530--436850 Score: 464
Period size: 106 Copynumber: 3.0 Consensus size: 106
436520 ATATCGTGCC
* *
436530 ACTCGAGACAATACAAGTTCAACTTCACAACAAAGGGACGGCTGGTTGTCAACAAATAATTTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTTCC
*
436595 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
436636 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTTCC
* *
436701 AATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* ** ** * *
436742 ACTCGAGACAGCACAAACTCAACTTCACAGTGAAGGGGCGGCTGGCTGTCAACAAATAA-TTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTTCC
* * * *
436806 TAGTTCCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGG
66 -AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
436848 ACT
1 ACT
436851 TGAAACAATA
Statistics
Matches: 192, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
105 4 0.02
106 188 0.98
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (106 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTTCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:437151 original size:37 final size:35
Alignment explanation
Indices: 437052--437210 Score: 201
Period size: 37 Copynumber: 4.4 Consensus size: 35
437042 TTGAATATCT
* * *
437052 TTTCCTTGAAACAAATTTCGTCTCCCCTTGAGACAA
1 TTTCCTTGAAACAAATTTTGTCT-CTCTTGAGACAG
* * * *
437088 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTTAGACAG
1 TTTC-CTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
437125 TTTCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
437160 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTT-CCTTGAAACAAA-TTTTGTCTCTCTTGAGACAG
437197 TTTCTCTTGAAACA
1 TTTC-CTTGAAACA
437211 CCAATCTTTG
Statistics
Matches: 107, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
35 24 0.22
36 23 0.21
37 51 0.48
38 9 0.08
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (35 bp):
TTTCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:437187 original size:72 final size:73
Alignment explanation
Indices: 437052--437210 Score: 230
Period size: 72 Copynumber: 2.2 Consensus size: 73
437042 TTGAATATCT
** * *
437052 TTTCCTTGAAACAAATTTCGTCTCCCCTTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCTTGAAACAAATTTCGTCTCCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCT
*
437117 TTAGACAG
66 TGAGACAG
* * *
437125 TTTCCTTGAAACAAATTTTGTCT-CTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCT
1 TTTCCTTGAAACAAATTTCGTCTCCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCT
437189 TGAGACAG
66 TGAGACAG
437197 TTTCTCTTGAAACA
1 TTTC-CTTGAAACA
437211 CCAATCTTTG
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
72 46 0.60
73 31 0.40
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (73 bp):
TTTCCTTGAAACAAATTTCGTCTCCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCT
TGAGACAG
Found at i:437278 original size:29 final size:29
Alignment explanation
Indices: 437196--437295 Score: 141
Period size: 29 Copynumber: 3.4 Consensus size: 29
437186 TCTTGAGACA
** *
437196 GTTTCTCTTGAAACACCAATCTTTGAATAT-
1 GTTTCTCTTGAAA-AAAAACCTTTGAA-ATC
437226 GTTTCTCTTG-AAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAAAAAAACCTTTGAAATC
437254 GTTTCTCTTGAAAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAAAAAAACCTTTGAAATC
437283 GTTTCTCTTGAAA
1 GTTTCTCTTGAAA
437296 CACCAAAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
27 2 0.03
28 20 0.31
29 33 0.51
30 10 0.15
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (29 bp):
GTTTCTCTTGAAAAAAAACCTTTGAAATC
Found at i:437311 original size:36 final size:36
Alignment explanation
Indices: 437264--437334 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
437254 GTTTCTCTTG
437264 AAAAAAAACCTTTGAAATCGTTTCTCTTGAAACACC
1 AAAAAAAACCTTTGAAATCGTTTCTCTTGAAACACC
* *
437300 AAAAAAAACCTTTGAAGTTGTTTCTCTTGAAACAC
1 AAAAAAAACCTTTGAAATCGTTTCTCTTGAAACAC
437335 AAAGACCTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.30
Consensus pattern (36 bp):
AAAAAAAACCTTTGAAATCGTTTCTCTTGAAACACC
Found at i:437475 original size:84 final size:84
Alignment explanation
Indices: 437334--437493 Score: 284
Period size: 84 Copynumber: 1.9 Consensus size: 84
437324 TCTTGAAACA
* *
437334 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCA
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTACAACATAGCTCAAGGCA
437399 AGAAGGGCTATTTTCCAAC
66 AGAAGGGCTATTTTCCAAC
* *
437418 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTACAGCATAGCTCAAGGCG
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTACAACATAGCTCAAGGCA
437483 AGAAGGGCTAT
66 AGAAGGGCTAT
437494 CTGTCAACAA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 72 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.21
Consensus pattern (84 bp):
CAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAAGGCACATCATTTACAACATAGCTCAAGGCA
AGAAGGGCTATTTTCCAAC
Found at i:437756 original size:3 final size:3
Alignment explanation
Indices: 437750--437800 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
437740 ATAAATTTTT
437750 TTA TTA -TA TTA -TA TTA -TA TTA -TA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
437792 TTAA TTA TT
1 TT-A TTA TT
437801 TTTTGTTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
2 8 0.19
3 28 0.67
4 6 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:437761 original size:5 final size:5
Alignment explanation
Indices: 437751--437792 Score: 59
Period size: 5 Copynumber: 8.2 Consensus size: 5
437741 TAAATTTTTT
437751 TATTA TATTA TATTA TATTA TATTA T-TTA TTATTA TTATTA T
1 TATTA TATTA TATTA TATTA TATTA TATTA -TATTA -TATTA T
437793 TAATTATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
4 3 0.09
5 23 0.66
6 9 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TATTA
Found at i:437783 original size:7 final size:7
Alignment explanation
Indices: 437750--437821 Score: 51
Period size: 7 Copynumber: 10.3 Consensus size: 7
437740 ATAAATTTTT
437750 TTATTATA
1 TTATT-TA
437758 TTATATTA
1 TTAT-TTA
437766 -TATTATA
1 TTATT-TA
437773 TTATTTA
1 TTATTTA
437780 TTA-TTA
1 TTATTTA
437786 TTA-TTA
1 TTATTTA
*
437792 TTAATTA
1 TTATTTA
* *
437799 TTTTTTG
1 TTATTTA
*
437806 TTTTTTA
1 TTATTTA
*
437813 TTTTTTA
1 TTATTTA
437820 TT
1 TT
437822 TTTTTTGTAG
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
6 13 0.23
7 32 0.57
8 10 0.18
9 1 0.02
ACGTcount: A:0.28, C:0.00, G:0.01, T:0.71
Consensus pattern (7 bp):
TTATTTA
Found at i:437798 original size:10 final size:10
Alignment explanation
Indices: 437750--437800 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
437740 ATAAATTTTT
437750 TTATTATATTA
1 TTATTA-ATTA
437761 -TATTATATTA
1 TTATTA-ATTA
*
437771 -TATTATTTA
1 TTATTAATTA
437780 TTATT-ATTA
1 TTATTAATTA
437789 TTATTAATTA
1 TTATTAATTA
437799 TT
1 TT
437801 TTTTGTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
9 11 0.31
10 25 0.69
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTATTAATTA
Found at i:437826 original size:8 final size:7
Alignment explanation
Indices: 437773--437825 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
437763 TTATATTATA
*
437773 TTATTTA
1 TTATTTT
437780 TTATTATT
1 TTATT-TT
**
437788 ATTATTAA
1 -TTATTTT
437796 TTATTTT
1 TTATTTT
*
437803 TTGTTTT
1 TTATTTT
437810 TTATTTT
1 TTATTTT
437817 TTATTTT
1 TTATTTT
437824 TT
1 TT
437826 TTGTAGGCCC
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
7 31 0.84
8 1 0.03
9 5 0.14
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (7 bp):
TTATTTT
Found at i:439073 original size:13 final size:13
Alignment explanation
Indices: 439055--439084 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
439045 CGAATAGAAT
439055 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
439068 TTTTAATTTTTAA
1 TTTTAAATTTTAA
439081 TTTT
1 TTTT
439085 CGCAACTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:439966 original size:22 final size:22
Alignment explanation
Indices: 439922--439978 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
439912 GTTAGATTAT
439922 AAAATA-GAATAAATAAATAAA
1 AAAATATGAATAAATAAATAAA
*
439943 AAAATATGAAATAAA-ACATAAA
1 AAAATATG-AATAAATAAATAAA
439965 AAAATAT-AA-AAATA
1 AAAATATGAATAAATA
439979 TAAAAACAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
19 3 0.09
20 3 0.09
21 6 0.19
22 14 0.44
23 6 0.19
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (22 bp):
AAAATATGAATAAATAAATAAA
Found at i:439973 original size:10 final size:10
Alignment explanation
Indices: 439938--439984 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
439928 GAATAAATAA
439938 ATAAAAAAAT
1 ATAAAAAAAT
*
439948 ATGAAATAAAAC
1 AT-AAA-AAAAT
439960 ATAAAAAAAT
1 ATAAAAAAAT
439970 AT--AAAAAT
1 ATAAAAAAAT
439978 ATAAAAA
1 ATAAAAA
439985 CAAGTTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
8 8 0.26
10 11 0.35
11 6 0.19
12 6 0.19
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (10 bp):
ATAAAAAAAT
Found at i:441436 original size:25 final size:25
Alignment explanation
Indices: 441395--441443 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
441385 AATATATTGA
441395 AAAGCTATATATGTATAAACTATAT
1 AAAGCTATATATGTATAAACTATAT
*
441420 AAAG-TATATAGTTTATAAACTATA
1 AAAGCTATATA-TGTATAAACTATA
441444 ATTTATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (25 bp):
AAAGCTATATATGTATAAACTATAT
Found at i:442479 original size:55 final size:55
Alignment explanation
Indices: 442413--442519 Score: 142
Period size: 55 Copynumber: 1.9 Consensus size: 55
442403 CTTCGTTAAT
* ** *
442413 TTAAAAGAGAAGTAAATTTATCGCCTATAAAGTATCGATACTTTCAAAAAATATA
1 TTAAAAGAGAAGTAAATTTAGCGCCTATAAAGTATAAATACTTTAAAAAAATATA
** * *
442468 TTAAAAGAGAAGTAGTTTTAGCGTCTATAAAGTGTAAATACTTTAAAAAAAT
1 TTAAAAGAGAAGTAAATTTAGCGCCTATAAAGTATAAATACTTTAAAAAAAT
442520 GTATCGATCA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (55 bp):
TTAAAAGAGAAGTAAATTTAGCGCCTATAAAGTATAAATACTTTAAAAAAATATA
Found at i:442568 original size:20 final size:19
Alignment explanation
Indices: 442545--442591 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
442535 CGATATAACA
*
442545 GGTAAAAATATGATAAAATC
1 GGTAAAAA-ATGATAAAACC
*
442565 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
442585 GGTAAAA
1 GGTAAAA
442592 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:443632 original size:182 final size:182
Alignment explanation
Indices: 442964--445252 Score: 3908
Period size: 182 Copynumber: 12.6 Consensus size: 182
442954 TTTTACCTTT
* * * *
442964 TTTAAAAGAGAATAAGTTATATCGTCAATAAAGTGTAGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
443029 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
443094 CGGTTATGTTGAAAGTGTCAATAATTTATTATATGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* * *
443146 TTTAAAAGAGAAG-AGTTATAGCGCAAATAAAGTGTCGATATTTTATAAAAATGTATCGTTCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
443210 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
443275 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG--ACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
443325 -TTAATAAGAGAAGAAGTTATAGCGCCAATAACA-TGTCGATACTTTATAAAAATGTATCGATCC
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAA-AGTGTCGATACTTTATAAAAATGTATCGATCC
443388 ATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCT
64 ATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCT
* **
443453 ACCGGTTATGTTGAAAGTGTCAATAATTTATTATAAGTATCGACACTTTTAAAA
129 ACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* *
443507 TTTAAAAGAGAAGAAGTTATAGCGCGAATAAAGTGTCGATATTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
443572 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
443637 CGGATATGTTGAAATTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* *
443689 TTTAAAAGAGAAGAAGTTATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
443754 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* * *
443819 CGGTTATGTTGAAATTGTCAATAATTTATTATACGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* * *
443871 TTTAAAAGAGAAG-AGTTATAGCGTCAATAAAGTGTCGATATTTTATAAACATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
443935 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
444000 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG--ACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
444050 -TTAATAAGAGAAGAAGTTATAGCGCCAATAACA-TGTCGATACTTTATAAAAATGTATCAATCC
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAA-AGTGTCGATACTTTATAAAAATGTATCGATCC
444113 ATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCT
64 ATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCT
* *
444178 ACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACGCTTTTGAAA
129 ACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* *
444232 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATATTTTATAAAAATCTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * * *
444297 AACAATATAACAGGTAAAAATATGACAAAACC-GCCTCGAAATGATAAAATAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
444361 CGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
444413 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
444478 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGATAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
444543 CGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
444595 TTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
444659 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGATAAAGCGCTAT
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
444724 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG--ACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
444774 -TTAATAAGAGAAGAAGTTATAGCGCCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
*
444838 TAACAATATAACATGTAAAAATATGACAAAATCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
65 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
* *
444903 CCGGTTATGTTAAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTAGAA
130 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
444956 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATATTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * *
445021 AACAATATAACATATAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAAGTAAAGCGTTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
445086 CGGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTTGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
445138 -TTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* * **
445202 TAATAATATAACATGTAAAAATATGATAAAACCGGTCTATAAATGACAAAA
65 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAA
445253 GGTGAACGCA
Statistics
Matches: 2000, Mismatches: 86, Indels: 42
0.94 0.04 0.02
Matches are distributed among these distances:
178 12 0.01
179 54 0.03
180 451 0.23
181 628 0.31
182 843 0.42
183 12 0.01
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (182 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
Found at i:444061 original size:543 final size:545
Alignment explanation
Indices: 442964--445252 Score: 3888
Period size: 543 Copynumber: 4.2 Consensus size: 545
442954 TTTTACCTTT
* * * *
442964 TTTAAAAGAGAATAAGTTATATCGTCAATAAAGTGTAGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
443029 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
443094 CGGTTATGTTGAAAGTGTCAATAATTTATTATATGTATCGACACTTTTGGAATTTAAAAGAGAAG
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAG
* * * *
443159 -AGTTATAGCGCAAATAAAGTGTCGATATTTTATAAAAATGTATCGTTCCATAACAATATAACAT
196 AAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAG
443223 GTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAA
261 GTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAA
443288 AGTGTCGATAATTTATTATAAGTATCG--ACTTTTGGAA-TTAATAAGAGAAGAAGTTATAGCGC
326 AGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAA-AAGAGAAGAAGTTATAGCGC
443350 CAATAACA-TGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATG
390 CAATAA-AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATG
*
443414 ACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCAATAA
454 ACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAA
**
443479 TTTATTATAAGTATCGACACTTTTAAAA
519 TTTATTATAAGTATCGA-ACTTTTGGAA
* *
443507 TTTAAAAGAGAAGAAGTTATAGCGCGAATAAAGTGTCGATATTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
443572 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
443637 CGGATATGTTGAAATTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAG
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAG
* *
443702 AAGTTATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAG
196 AAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAG
443767 GTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAA
261 GTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAA
* * * *
443832 ATTGTCAATAATTTATTATACGTATCGACACTTTTGGAATTTAAAAGAGAAG-AGTTATAGCGTC
326 AGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCC
* *
443896 AATAAAGTGTCGATATTTTATAAACATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
391 AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
443961 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
456 AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
444026 TATTATAAGTATCG-ACTTTTGGAA
521 TATTATAAGTATCGAACTTTTGGAA
*
444050 -TTAATAAGAGAAGAAGTTATAGCGCCAATAACA-TGTCGATACTTTATAAAAATGTATCAATCC
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAA-AGTGTCGATACTTTATAAAAATGTATCGATCC
444113 ATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCT
64 ATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCT
* *
444178 ACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACGCTTTTGAAATTTAAAAGAGA
129 ACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGA
* *
444243 AGAAGTTATAGCGCCAATAAAGTGTCGATATTTTATAAAAATCTATCGATCCATAACAATATAAC
194 AGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAAC
* * * *
444308 AGGTAAAAATATGACAAAACC-GCCTCGAAATGATAAAATAGGTAAAGCGCTACCGGATATGTTG
259 AGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTG
444372 AAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCG
324 AAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCG
*
444437 CCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATG
389 CCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATG
*
444502 ACAAAACCGGTCTCGAAATGATAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAA
454 ACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAA
*
444567 TTTATTATACGTATCGACACTTTTGGAA
519 TTTATTATAAGTATCGA-ACTTTTGGAA
444595 TTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
444659 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGATAAAGCGCTAT
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
444724 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG--ACTTTTGGAA-TTAATAAGAGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAA-AAGAGAA
*
444786 GAAGTTATAGCGCCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACA
195 GAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACA
* * *
444851 TGTAAAAATATGACAAAATCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTAA
260 GGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGA
*
444916 AAGTGTCGATAATTTATTATAAGTATCGACACTTTTAGAATTTAAAAGAGAAGAAGTTATAGCGC
325 AAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGC
* *
444981 CAATAAAGTGTCGATATTTTATAAAAATGTATCGATCCATAACAATATAACATATAAAAATATGA
390 CAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGA
* * *
445046 CAAAACCGGTCTCGAAATGACAAAACAAGTAAAGCGTTACCGGATATGTTGAAAGTGTCGATAAT
455 CAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAAT
*
445111 TTATTATAAGTATCGACACTTTTTGAA
520 TTATTATAAGTATCGA-ACTTTTGGAA
445138 -TTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* * **
445202 TAATAATATAACATGTAAAAATATGATAAAACCGGTCTATAAATGACAAAA
65 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAA
445253 GGTGAACGCA
Statistics
Matches: 1651, Mismatches: 79, Indels: 31
0.94 0.04 0.02
Matches are distributed among these distances:
541 4 0.00
542 193 0.12
543 863 0.52
544 397 0.24
545 168 0.10
546 22 0.01
547 4 0.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (545 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAG
AAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAG
GTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAA
AGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCC
AATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGAC
AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGATAATT
TATTATAAGTATCGAACTTTTGGAA
Found at i:445496 original size:87 final size:87
Alignment explanation
Indices: 445388--445550 Score: 283
Period size: 87 Copynumber: 1.9 Consensus size: 87
445378 AAATAAGTCA
* *
445388 ATATAAGCGCTACTTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGAGCTACTTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
445453 CCGGTTAAATACCTATTTTATT
66 CCGGTTAAATACCTATTTTATT
*
445475 ATATAAGAGCTA-TCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTAATAATATT
1 ATATAAGAGCTACT-TATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATT
445539 TCCGGTTAAATA
65 TCCGGTTAAATA
445551 ATATAACATA
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
86 1 0.01
87 71 0.99
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAGAGCTACTTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATATTT
CCGGTTAAATACCTATTTTATT
Found at i:446706 original size:12 final size:11
Alignment explanation
Indices: 446678--446717 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
446668 TGTATTCAAC
446678 TCAAATGTTAT
1 TCAAATGTTAT
*
446689 TCAAATTTTAT
1 TCAAATGTTAT
446700 ATCAAATGTTAT
1 -TCAAATGTTAT
*
446712 TTAAAT
1 TCAAAT
446718 TATCATTATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (11 bp):
TCAAATGTTAT
Found at i:447000 original size:23 final size:24
Alignment explanation
Indices: 446969--447022 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
446959 TTATTTTTTC
*
446969 TTTAAATAAATTAAACTATA-TAA
1 TTTACATAAATTAAACTATATTAA
446992 TTTACATAAATTAAACTATATTAA
1 TTTACATAAATTAAACTATATTAA
447016 TTTACAT
1 TTTACAT
447023 TTAATCATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 19 0.66
24 10 0.34
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTACATAAATTAAACTATATTAA
Found at i:447447 original size:11 final size:11
Alignment explanation
Indices: 447431--447462 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
447421 TGTTCTCAGG
*
447431 TCGGGTGCAGT
1 TCGGGTGCAAT
447442 TCGGGTGCAAT
1 TCGGGTGCAAT
447453 TCGGGTGCAA
1 TCGGGTGCAA
447463 ATTCACAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.19, G:0.41, T:0.25
Consensus pattern (11 bp):
TCGGGTGCAAT
Found at i:452134 original size:15 final size:15
Alignment explanation
Indices: 452114--452144 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
452104 CAACTGATAG
452114 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
452129 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
452144 A
1 A
452145 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:455500 original size:21 final size:21
Alignment explanation
Indices: 455448--455491 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
455438 CAGGAATTAC
* *
455448 AGTGGCTGTAGGATTTTCAGT
1 AGTGGTTGTAGCATTTTCAGT
455469 AGTGGTTGTAGCATTTTCAGT
1 AGTGGTTGTAGCATTTTCAGT
455490 AG
1 AG
455492 GTTTTGTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.09, G:0.32, T:0.39
Consensus pattern (21 bp):
AGTGGTTGTAGCATTTTCAGT
Found at i:466149 original size:122 final size:122
Alignment explanation
Indices: 465906--466154 Score: 367
Period size: 122 Copynumber: 2.0 Consensus size: 122
465896 TCTAATTATT
* *
465906 TCCAA-AAAAAAAGAGTTATATATTCAAAGCATGTCCTTGATCGGATATTTGGCAGTTCGATGTT
1 TCCAATAAAAAAAGAGTCATATATTCAAAGCATGACCTTGATCGGATATTTGGCAGTTCGATGTT
* * * ** * *
465970 TGCTCCACTGTGATTGTCAAGCCAAAGATATTGTTATGAGTTTAACCCTTTAGTTAG
66 TGCTCCACTATGATTGTCAAGCCAAAGAAATTGTGATGACCTGAACCCTTTAATTAG
*
466027 TCCAATAAAAAAAGAGTCATATATTCAAAGCATGACCTTGATCCGG-TATTTGGCAGTTCGGTGT
1 TCCAATAAAAAAAGAGTCATATATTCAAAGCATGACCTTGAT-CGGATATTTGGCAGTTCGATGT
* *
466091 TTGCTCCACTATGATTGTCAAGTCAAAGAAATTGTGATGACCTGAACCGTTTAATTAG
65 TTGCTCCACTATGATTGTCAAGCCAAAGAAATTGTGATGACCTGAACCCTTTAATTAG
466149 TCCAAT
1 TCCAAT
466155 TAAGGCTAAT
Statistics
Matches: 114, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
121 5 0.04
122 106 0.93
123 3 0.03
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (122 bp):
TCCAATAAAAAAAGAGTCATATATTCAAAGCATGACCTTGATCGGATATTTGGCAGTTCGATGTT
TGCTCCACTATGATTGTCAAGCCAAAGAAATTGTGATGACCTGAACCCTTTAATTAG
Found at i:469276 original size:75 final size:75
Alignment explanation
Indices: 469174--469317 Score: 200
Period size: 75 Copynumber: 1.9 Consensus size: 75
469164 ATCAACAAGA
* * * * *
469174 AGCAAATGATGGGGTATGCTGAGAGCCCATTTCAATTAGAAGTT-GGAATATTAATGCGTTTTGA
1 AGCAAATGATGGGGCATGCTGAAAGCCCATTTCAATCAGAA-TTAGGAATATTAACGCATTTTGA
469238 ACGTTTGTAAC
65 ACGTTTGTAAC
* * *
469249 AGCAAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGGAATGTTGACGCATTTTGAA
1 AGCAAATGATGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGGAATATTAACGCATTTTGAA
469314 CGTT
66 CGTT
469318 GGGGCATGCT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
74 2 0.03
75 58 0.97
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (75 bp):
AGCAAATGATGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGGAATATTAACGCATTTTGAA
CGTTTGTAAC
Found at i:470729 original size:21 final size:22
Alignment explanation
Indices: 470687--470729 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
470677 ATCTACATTC
* *
470687 TTCAAAGATGATAGATTTTATT
1 TTCAAAGATGAAAGACTTTATT
470709 TTCAAAGATGAAAG-CTTTATT
1 TTCAAAGATGAAAGACTTTATT
470730 GGATTTCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGAAAGACTTTATT
Found at i:470955 original size:10 final size:10
Alignment explanation
Indices: 470940--470965 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
470930 TAGGATCATG
470940 TAGTTGCATA
1 TAGTTGCATA
470950 TAGTTGCATA
1 TAGTTGCATA
470960 TAGTTG
1 TAGTTG
470966 TATTTGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (10 bp):
TAGTTGCATA
Found at i:472242 original size:16 final size:16
Alignment explanation
Indices: 472208--472241 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
472198 CACGTGAGGA
472208 TTATTTTCTTTTTATT
1 TTATTTTCTTTTTATT
472224 TTATTTATCTTTTTATT
1 TTATTT-TCTTTTTATT
472241 T
1 T
472242 ACTGTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTTCTTTTTATT
Found at i:478620 original size:19 final size:21
Alignment explanation
Indices: 478583--478625 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
478573 TAACTTTTTC
478583 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
478603 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
478623 TTT
1 TTT
478626 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:478633 original size:20 final size:20
Alignment explanation
Indices: 478583--478633 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
478573 TAACTTTTTC
478583 TTTTA-TCTTTCATTATTAA
1 TTTTACTCTTTCATTATTAA
*
478602 TTTTTCTCTTTCATT-TTAA
1 TTTTACTCTTTCATTATTAA
*
478621 CTTTTACTTTTTC
1 -TTTTACTCTTTC
478634 TCTTTCTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTACTCTTTCATTATTAA
Found at i:482487 original size:16 final size:16
Alignment explanation
Indices: 482453--482486 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
482443 CACGTGAGGA
482453 TTATTTTCTTTTTATT
1 TTATTTTCTTTTTATT
482469 TTATTTATCTTTTTATT
1 TTATTT-TCTTTTTATT
482486 T
1 T
482487 ACTGTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTTCTTTTTATT
Found at i:483394 original size:45 final size:45
Alignment explanation
Indices: 483330--483985 Score: 1118
Period size: 45 Copynumber: 14.6 Consensus size: 45
483320 CTATTTCCCA
* *
483330 CATCTGTAAGCCCTTCAGTGCATGATGTTCTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
483375 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
483420 CATCTGTAAGCCCTTCAGTGCATGATGTGTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
483465 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
483510 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
483555 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
483600 CATCTGTAAGCCCTTCAGTGCATGATGTTCTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
483645 CATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
483690 CATCTGTAAGCCCTTTAGTGCATGATGTTTTCAAAACTTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
483735 CATCTGTAAGCCCTTCAGTGGATGATGTTCTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
483780 CATCTGTAAGCCCTTCAGTGAAGGATGTTTTCAAAACC-TCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
483824 CATCTGTAATCCCTTCAGTGCATGATGTTTTCAAAACCTTCTGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
483869 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
483914 CATCTGTAATCCCTTCAGTGCATAATGTTATCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
483959 CATCTGTAAGACCTAT-AGTGCAAGATG
1 CATCTGTAAGCCCT-TCAGTGCATGATG
483986 ATAAGACCTC
Statistics
Matches: 579, Mismatches: 30, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
44 41 0.07
45 537 0.93
46 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:483863 original size:25 final size:25
Alignment explanation
Indices: 483835--483909 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
483825 ATCTGTAATC
483835 CCTTCAGTGCATGATGTTTTCAAAA
1 CCTTCAGTGCATGATGTTTTCAAAA
* * **
483860 CCTTCTG-GTCAT-CTG---T-AAGC
1 CCTTCAGTG-CATGATGTTTTCAAAA
483880 CCTTCAGTGCATGATGTTTTCAAAA
1 CCTTCAGTGCATGATGTTTTCAAAA
483905 CCTTC
1 CCTTC
483910 GGGTCATCTG
Statistics
Matches: 35, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
20 11 0.31
21 4 0.11
24 4 0.11
25 16 0.46
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (25 bp):
CCTTCAGTGCATGATGTTTTCAAAA
Found at i:484167 original size:3 final size:3
Alignment explanation
Indices: 484159--484187 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
484149 TCAGTTTACA
484159 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
484188 AATAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:486031 original size:2 final size:2
Alignment explanation
Indices: 486024--486066 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
486014 AAAACCCTAA
486024 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
486065 AT
1 AT
486067 TTTTCCTTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:494898 original size:14 final size:13
Alignment explanation
Indices: 494879--494956 Score: 70
Period size: 13 Copynumber: 5.8 Consensus size: 13
494869 CGAAGGAGAG
494879 AGAAAAAGATAAAA
1 AGAAAAAGA-AAAA
494893 AGAAAAAGAAAAA
1 AGAAAAAGAAAAA
494906 AGGAAAAA-AAGAAA
1 A-GAAAAAGAA-AAA
494920 ATG-AAAAGAAAAA
1 A-GAAAAAGAAAAA
* * *
494933 TGAGAAAGAAGAA
1 AGAAAAAGAAAAA
494946 AGAAAATAGAA
1 AGAAAA-AGAA
494957 CAAGTATTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
12 1 0.02
13 26 0.49
14 26 0.49
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (13 bp):
AGAAAAAGAAAAA
Found at i:494904 original size:20 final size:19
Alignment explanation
Indices: 494879--494956 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 19
494869 CGAAGGAGAG
494879 AGAAAAAGATAAAAAGAAAA
1 AGAAAAAGA-AAAAAGAAAA
494899 AGAAAAAAGGAAAAAAAGAAAA
1 AG-AAAAA-G-AAAAAAGAAAA
* * *
494921 TG-AAAAGAAAAATGAGAA
1 AGAAAAAGAAAAAAGAAAA
*
494939 AGAAGAAAGAAAATAGAA
1 AGAA-AAAGAAAAAAGAA
494957 CAAGTATTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
18 10 0.22
19 2 0.04
20 16 0.35
21 5 0.11
22 12 0.26
23 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (19 bp):
AGAAAAAGAAAAAAGAAAA
Found at i:494956 original size:7 final size:6
Alignment explanation
Indices: 494879--494956 Score: 54
Period size: 6 Copynumber: 12.7 Consensus size: 6
494869 CGAAGGAGAG
** *
494879 AGAAAA AGATAAAA AGAAAA AGAAAA A-AGGA A-AAAA AGAAAA TG-AAA
1 AGAAAA AG--AAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
*
494926 AGAAAA ATGAGAA AGAAGAA AGAAAA TAGAA
1 AGAAAA A-GAAAA AGAA-AA AGAAAA -AGAA
494957 CAAGTATTTC
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
5 10 0.18
6 26 0.46
7 15 0.26
8 6 0.11
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (6 bp):
AGAAAA
Found at i:496982 original size:4 final size:4
Alignment explanation
Indices: 496968--497003 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
496958 TGAATCATTT
*
496968 CATA TATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA
497004 TATAATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (4 bp):
CATA
Found at i:497645 original size:29 final size:29
Alignment explanation
Indices: 497599--497654 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
497589 ATTCTTTGGG
*
497599 CCATCTATAAGCCTTTCGAGCAAGATGAT
1 CCATCCATAAGCCTTTCGAGCAAGATGAT
*
497628 CCATCCATAAGACC-TTCGGGCAAGATG
1 CCATCCATAAG-CCTTTCGAGCAAGATG
497655 CTTTCACAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (29 bp):
CCATCCATAAGCCTTTCGAGCAAGATGAT
Found at i:498430 original size:138 final size:138
Alignment explanation
Indices: 497974--498477 Score: 559
Period size: 138 Copynumber: 3.7 Consensus size: 138
497964 GCAAATCGAA
* * *
497974 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAACATTTTC-GAATCTGATTTACCTTG
1 CTCGATTCAATCTTCCTTGAAGAACAGTGGAATGAATCAACATTTCCAG-ATCTGATTTACCCTG
* * * **
498038 AAGAAGCAGCGGAGCATATCCCCTTTC-TTTTTCCAGATTTGATCATT-CCTGAAAAAGCAGTGG
65 AAGAAGCAGCGGAACAGATCCCTTTTCTTTTTTCCAGATTTGATC-TTCCCTGAGGAA-CAGTGG
*
498101 AACAAGTATGA-
128 AACAAGTCT-AC
* * * * * *
498112 TTCGATTTAATCTTCCTTGAAGAATAGTGGAATGAATCAAAATTTCGAGATCTGATTTTCCCTGA
1 CTCGATTCAATCTTCCTTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTACCCTGA
* * * * * * *
498177 AAAAGTAGCAGAAGAAATCCCTTTTCTTTTTCTCCAGATATGATCTTCCCTAAGGAACAGT-GAA
66 AGAAGCAGCGGAACAGATCCCTTTTCTTTTT-TCCAGATTTGATCTTCCCTGAGGAACAGTGGAA
*
498241 CAAGTCTGC
130 CAAGTCTAC
* * * * *
498250 CTCGATTCAATCTTTCTTGAAGAATAATGGAATGAATCAACGTTTCCAGATCTGATTTTCCCTGA
1 CTCGATTCAATCTTCCTTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTACCCTGA
* * ** *
498315 AGAAGTAGTGGAACAGATCCCTTTTCTTTTTTCTGGATTTGATCTTCCCCGAGGAACAGTGGAAC
66 AGAAGCAGCGGAACAGATCCCTTTTCTTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAAC
498380 AAGTCTAC
131 AAGTCTAC
* * * * * *
498388 CTCGATTCAATCTTCCTTGAAGAACAGTGGAATGAATTAACGTTTCTAGATCTAATTTACCATGG
1 CTCGATTCAATCTTCCTTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTACCCTGA
* *
498453 AGAAGCAGTGGAGCAGATCCCTTTT
66 AGAAGCAGCGGAACAGATCCCTTTT
498478 TAGATTTGAT
Statistics
Matches: 309, Mismatches: 51, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
137 24 0.08
138 256 0.83
139 11 0.04
140 18 0.06
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (138 bp):
CTCGATTCAATCTTCCTTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATTTACCCTGA
AGAAGCAGCGGAACAGATCCCTTTTCTTTTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAAC
AAGTCTAC
Found at i:498676 original size:3 final size:3
Alignment explanation
Indices: 498668--498702 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
498658 CCGAAGATCG
* *
498668 TTA TTA TTA TTA ATA TTA TTA TTA CTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
498703 TTTTTCTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:498686 original size:12 final size:12
Alignment explanation
Indices: 498669--498702 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
498659 CGAAGATCGT
498669 TATTATTATTAA
1 TATTATTATTAA
*
498681 TATTATTATTAC
1 TATTATTATTAA
498693 TATTATTATT
1 TATTATTATT
498703 TTTTTCTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:498889 original size:26 final size:26
Alignment explanation
Indices: 498860--498947 Score: 113
Period size: 26 Copynumber: 3.4 Consensus size: 26
498850 TAACACCATT
*
498860 ATCTACACCAGTCCTCTGTCACCGTC
1 ATCTACACCAGTCCCCTGTCACCGTC
* *
498886 ATCTGCACCAGTCCCCTGCCACCGTC
1 ATCTACACCAGTCCCCTGTCACCGTC
* * *
498912 ATCAACACCAGTCCCCTATCACCATC
1 ATCTACACCAGTCCCCTGTCACCGTC
*
498938 ATCTCCACCA
1 ATCTACACCA
498948 ACTCTGAAGC
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.23, C:0.47, G:0.09, T:0.22
Consensus pattern (26 bp):
ATCTACACCAGTCCCCTGTCACCGTC
Found at i:499613 original size:13 final size:13
Alignment explanation
Indices: 499595--499624 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
499585 GATTTATAGG
499595 CGTCCTAAAACGA
1 CGTCCTAAAACGA
*
499608 CGTCCTGAAACGA
1 CGTCCTAAAACGA
499621 CGTC
1 CGTC
499625 GTTTTGGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (13 bp):
CGTCCTAAAACGA
Found at i:504589 original size:19 final size:20
Alignment explanation
Indices: 504562--504599 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
504552 AAATAAATTT
504562 AAAACTATACC-CAAACCCA
1 AAAACTATACCACAAACCCA
*
504581 AAAAGTATACCACAAACCC
1 AAAACTATACCACAAACCC
504600 CAAATCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.53, C:0.34, G:0.03, T:0.11
Consensus pattern (20 bp):
AAAACTATACCACAAACCCA
Found at i:513102 original size:20 final size:21
Alignment explanation
Indices: 513077--513121 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
513067 GATTGAATTT
*
513077 ATTCAAAG-CTTTAAAAAATA
1 ATTCAAAGCCATTAAAAAATA
513097 ATTCAAAGTCCATTAAAAAATA
1 ATTCAAAG-CCATTAAAAAATA
513119 ATT
1 ATT
513122 AAAAAAGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
22 14 0.64
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.31
Consensus pattern (21 bp):
ATTCAAAGCCATTAAAAAATA
Found at i:513998 original size:15 final size:15
Alignment explanation
Indices: 513978--514007 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
513968 CAAAGGTAAA
513978 AGAAGTATCGATACT
1 AGAAGTATCGATACT
513993 AGAAGTATCGATACT
1 AGAAGTATCGATACT
514008 CCTATGGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (15 bp):
AGAAGTATCGATACT
Found at i:514021 original size:20 final size:21
Alignment explanation
Indices: 513996--514034 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
513986 CGATACTAGA
513996 AGTATCGATACT-CCTATGGT
1 AGTATCGATACTACCTATGGT
514016 AGTATCGATACTACCTATG
1 AGTATCGATACTACCTATG
514035 ATTTTCAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (21 bp):
AGTATCGATACTACCTATGGT
Found at i:514661 original size:32 final size:31
Alignment explanation
Indices: 514625--514700 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
514615 TTGGGTATAG
* *
514625 GAGCCAACCTAAGAGAGCAACTTGGGGCCTAT
1 GAGCCAACCCAAGAAAGCAA-TTGGGGCCTAT
* ** *
514657 GAGCCTACCCAAGAAAGTTATTGGGGCTTAT
1 GAGCCAACCCAAGAAAGCAATTGGGGCCTAT
*
514688 GAGCCTACCCAAG
1 GAGCCAACCCAAG
514701 GGTTACCTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 23 0.61
32 15 0.39
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.18
Consensus pattern (31 bp):
GAGCCAACCCAAGAAAGCAATTGGGGCCTAT
Found at i:515491 original size:16 final size:16
Alignment explanation
Indices: 515472--515537 Score: 60
Period size: 16 Copynumber: 3.8 Consensus size: 16
515462 GCTGGTCAAG
515472 GTCAAAGTCAACTCTT
1 GTCAAAGTCAACTCTT
*
515488 GTCAAAGTCAACGTTGGTCATG
1 GTCAAAGTCAAC-----TC-TT
*
515510 GTCAAGGTCAACTCTT
1 GTCAAAGTCAACTCTT
515526 GTCAAAGTCAAC
1 GTCAAAGTCAAC
515538 AAGTTGACTG
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
16 24 0.60
17 2 0.05
21 2 0.05
22 12 0.30
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (16 bp):
GTCAAAGTCAACTCTT
Found at i:515491 original size:22 final size:22
Alignment explanation
Indices: 515442--515498 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
515432 AATGAATTTT
* *
515442 TGGTCATAGTCAAAGTCAGCGC
1 TGGTCAAAGTCAAAGTCAACGC
* *
515464 TGGTCAAGGTCAAAGTCAACTC
1 TGGTCAAAGTCAAAGTCAACGC
*
515486 TTGTCAAAGTCAA
1 TGGTCAAAGTCAA
515499 CGTTGGTCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (22 bp):
TGGTCAAAGTCAAAGTCAACGC
Found at i:515506 original size:38 final size:38
Alignment explanation
Indices: 515450--515537 Score: 140
Period size: 38 Copynumber: 2.3 Consensus size: 38
515440 TTTGGTCATA
*
515450 GTCAAAGTCAGCGCTGGTCAAGGTCAAAGTCAACTCTT
1 GTCAAAGTCAACGCTGGTCAAGGTCAAAGTCAACTCTT
* * *
515488 GTCAAAGTCAACGTTGGTCATGGTCAAGGTCAACTCTT
1 GTCAAAGTCAACGCTGGTCAAGGTCAAAGTCAACTCTT
515526 GTCAAAGTCAAC
1 GTCAAAGTCAAC
515538 AAGTTGACTG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (38 bp):
GTCAAAGTCAACGCTGGTCAAGGTCAAAGTCAACTCTT
Found at i:515513 original size:22 final size:22
Alignment explanation
Indices: 515441--515521 Score: 66
Period size: 22 Copynumber: 4.0 Consensus size: 22
515431 AAATGAATTT
* *
515441 TTGGTCATAGTCAAAGTCAGCG
1 TTGGTCATGGTCAAAGTCAACG
* *
515463 CTGGTCAAGGTCAAAGTCAAC-
1 TTGGTCATGGTCAAAGTCAACG
*
515484 ----TC-TTGTCAAAGTCAACG
1 TTGGTCATGGTCAAAGTCAACG
*
515501 TTGGTCATGGTCAAGGTCAAC
1 TTGGTCATGGTCAAAGTCAAC
515522 TCTTGTCAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 12
0.69 0.12 0.18
Matches are distributed among these distances:
16 12 0.27
17 2 0.04
21 2 0.04
22 29 0.64
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (22 bp):
TTGGTCATGGTCAAAGTCAACG
Found at i:516913 original size:18 final size:18
Alignment explanation
Indices: 516890--516931 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
516880 TTGAACCGGT
516890 TTGACCGGTCATGACCCG
1 TTGACCGGTCATGACCCG
516908 TTGACCGGTCATGACCCG
1 TTGACCGGTCATGACCCG
516926 TTGACC
1 TTGACC
516932 CAACCCGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.17, C:0.33, G:0.26, T:0.24
Consensus pattern (18 bp):
TTGACCGGTCATGACCCG
Found at i:516950 original size:13 final size:13
Alignment explanation
Indices: 516934--516982 Score: 89
Period size: 13 Copynumber: 3.8 Consensus size: 13
516924 CGTTGACCCA
516934 ACCCGACCCGTTG
1 ACCCGACCCGTTG
516947 ACCCGACCCGTTG
1 ACCCGACCCGTTG
*
516960 ACCCGACCCGTTA
1 ACCCGACCCGTTG
516973 ACCCGACCCG
1 ACCCGACCCG
516983 ACCGTTGACC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.18, C:0.49, G:0.20, T:0.12
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:516969 original size:18 final size:18
Alignment explanation
Indices: 516920--516956 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
516910 GACCGGTCAT
516920 GACCCGTTGACCCAACCC
1 GACCCGTTGACCCAACCC
*
516938 GACCCGTTGACCCGACCC
1 GACCCGTTGACCCAACCC
516956 G
1 G
516957 TTGACCCGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.49, G:0.22, T:0.11
Consensus pattern (18 bp):
GACCCGTTGACCCAACCC
Found at i:517042 original size:29 final size:29
Alignment explanation
Indices: 517000--517081 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
516990 ACCGTTGATC
*
517000 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGGTTTA
*
517029 GGTGCTATTCTGGGAATTAATTCAGTTTA
1 GGTGCTATTCTGGGAATTAATTCGGTTTA
517058 GGTGCTATTCTGGGAATTAATTCG
1 GGTGCTATTCTGGGAATTAATTCG
517082 AAAAGGGTGC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.21, C:0.11, G:0.27, T:0.41
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGGTTTA
Found at i:517090 original size:29 final size:29
Alignment explanation
Indices: 517000--517124 Score: 108
Period size: 29 Copynumber: 4.3 Consensus size: 29
516990 ACCGTTGATC
*****
517000 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAAAG
***
517029 GGTGCTATTCTGGGAATTAATTCAGTTTA-
1 GGTGCTATTCTGGGAATTAATTC-GAAAAG
517058 GGTGCTATTCTGGGAATTAATTCGAAAAG
1 GGTGCTATTCTGGGAATTAATTCGAAAAG
* * * **
517087 GGTGCTATTGTGGTAATTATTTTAAAAAG
1 GGTGCTATTCTGGGAATTAATTCGAAAAG
*
517116 TGTGCTATT
1 GGTGCTATT
517125 TGTGTAAAAT
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
28 2 0.02
29 78 0.94
30 3 0.04
ACGTcount: A:0.25, C:0.09, G:0.26, T:0.41
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAAAG
Found at i:524274 original size:29 final size:29
Alignment explanation
Indices: 524228--524307 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
524218 ACCGTTGACC
*
524228 GGTGCTATTCTGGAAATTAATTTGGTTTT
1 GGTGCTATTCTGGAAATTAATTTGGTTTA
*
524257 GGTGCTATTCTGGGAATTAATTTGGTTTA
1 GGTGCTATTCTGGAAATTAATTTGGTTTA
*
524286 GGTGCTATTCTGGTAATTAATT
1 GGTGCTATTCTGGAAATTAATT
524308 CAAAAAGGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.21, C:0.07, G:0.25, T:0.46
Consensus pattern (29 bp):
GGTGCTATTCTGGAAATTAATTTGGTTTA
Found at i:524318 original size:29 final size:29
Alignment explanation
Indices: 524286--524352 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
524276 ATTTGGTTTA
524286 GGTGCTATTCTGGTAATTAATTCAAAAAG
1 GGTGCTATTCTGGTAATTAATTCAAAAAG
* * * *
524315 GGTGATATTGTGGTAATTATTTTAAAAAG
1 GGTGCTATTCTGGTAATTAATTCAAAAAG
524344 GGTGCTATT
1 GGTGCTATT
524353 TGTGTAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.39
Consensus pattern (29 bp):
GGTGCTATTCTGGTAATTAATTCAAAAAG
Found at i:526950 original size:23 final size:24
Alignment explanation
Indices: 526918--526965 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
526908 AGGGTCTATA
* *
526918 TGGTCCTTCGTGAC-ATTTCATAG
1 TGGTCATTCGGGACAATTTCATAG
526941 TGGTCATTCGGGACAAATTTCATAG
1 TGGTCATTCGGGAC-AATTTCATAG
526966 CCCTTAGTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
25 9 0.43
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (24 bp):
TGGTCATTCGGGACAATTTCATAG
Found at i:530335 original size:63 final size:62
Alignment explanation
Indices: 530264--530399 Score: 166
Period size: 63 Copynumber: 2.2 Consensus size: 62
530254 TTCAATGTGT
* *
530264 ATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTAGTGCATCGATGCATAAGG-AGTGC
1 ATCGATGCACTCCTTAAA-AAGAAACATCGAAGGCAATTAGTGCATCGATGCAT-AGGTAGTGC
* ** * * *
530327 ATCGATGCACCTCCTTAAAATGAAACATCGAAGGTGATTTGTGTATCGATGCATGGGTAGTGC
1 ATCGATGCA-CTCCTTAAAAAGAAACATCGAAGGCAATTAGTGCATCGATGCATAGGTAGTGC
530390 ATCGATGCAC
1 ATCGATGCAC
530400 ATGTTAAAGA
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
62 3 0.05
63 52 0.83
64 8 0.13
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (62 bp):
ATCGATGCACTCCTTAAAAAGAAACATCGAAGGCAATTAGTGCATCGATGCATAGGTAGTGC
Found at i:530414 original size:24 final size:20
Alignment explanation
Indices: 530387--530444 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
530377 GCATGGGTAG
530387 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
530411 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
530431 TGTATCGATGCACT
1 TGCATCGATGCACT
530445 TCAATGGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:530881 original size:32 final size:33
Alignment explanation
Indices: 530835--530897 Score: 78
Period size: 32 Copynumber: 1.9 Consensus size: 33
530825 GTCCATGGTC
530835 TATGTACACATGATA-ATATGA-TATAAGTTAAAT
1 TATGTACACATGATACATA--ACTATAAGTTAAAT
*
530868 TATGTA-ATATGATACATAACTATAAGTTAA
1 TATGTACACATGATACATAACTATAAGTTAA
530898 GTGAATGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 1 0.04
32 17 0.63
33 9 0.33
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (33 bp):
TATGTACACATGATACATAACTATAAGTTAAAT
Found at i:532116 original size:19 final size:19
Alignment explanation
Indices: 532087--532162 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 19
532077 GACTCAGTTT
*
532087 GATCTGATTTGGTTTGACTG
1 GATC-GATTTGGTCTGACTG
*
532107 GATCGATTTGGTCTGACTC
1 GATCGATTTGGTCTGACTG
*
532126 GATC-AGTTCGGTCTGACTG
1 GATCGA-TTTGGTCTGACTG
*
532145 GATC-AGTTCGGTCTGACT
1 GATCGA-TTTGGTCTGACT
532163 AGACTAATTC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
18 1 0.02
19 46 0.90
20 4 0.08
ACGTcount: A:0.16, C:0.18, G:0.29, T:0.37
Consensus pattern (19 bp):
GATCGATTTGGTCTGACTG
Found at i:539760 original size:18 final size:18
Alignment explanation
Indices: 539737--539777 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
539727 CAACGGTCAA
539737 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
539755 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
539773 CGGGT
1 CGGGT
539778 AAACGGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:539777 original size:13 final size:13
Alignment explanation
Indices: 539731--539760 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
539721 CACGGTCAAC
539731 GGTCAACGGGTCG
1 GGTCAACGGGTCG
539744 GGTCAACGGGTCG
1 GGTCAACGGGTCG
539757 GGTC
1 GGTC
539761 GGGTCAACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:539821 original size:10 final size:10
Alignment explanation
Indices: 539801--539855 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
539791 GTCGGTCGTG
539801 ACCGGTC-AA
1 ACCGGTCAAA
539810 ACCGGTCAAA
1 ACCGGTCAAA
539820 ACCGGTTCAAA
1 ACCGG-TCAAA
*
539831 ACCGGT-TAA
1 ACCGGTCAAA
539840 ACCGGTCAAA
1 ACCGGTCAAA
539850 ACCGGT
1 ACCGGT
539856 TTCCAACGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:539856 original size:19 final size:19
Alignment explanation
Indices: 539801--539856 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
539791 GTCGGTCGTG
*
539801 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
539820 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
539840 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
539857 TCCAACGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:546914 original size:13 final size:13
Alignment explanation
Indices: 546896--546948 Score: 70
Period size: 13 Copynumber: 3.8 Consensus size: 13
546886 CACGGTCAAC
546896 GGTCAACGGGTCG
1 GGTCAACGGGTCG
546909 GGTCAACGGGGGTCGG
1 GGTCAAC--GGGTC-G
546925 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
546938 GGTAAACGGGT
1 GGTCAACGGGT
546949 AAACGGGTCG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
13 18 0.50
14 5 0.14
15 5 0.14
16 8 0.22
ACGTcount: A:0.17, C:0.19, G:0.49, T:0.15
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:546929 original size:16 final size:15
Alignment explanation
Indices: 546903--546947 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 15
546893 AACGGTCAAC
546903 GGGTCGGGTCAACGG
1 GGGTCGGGTCAACGG
546918 GGGTCGGGGTCAAC--
1 GGGTC-GGGTCAACGG
*
546932 GGGTCGGGTAAACGG
1 GGGTCGGGTCAACGG
546947 G
1 G
546948 TAAACGGGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 7 0.27
14 5 0.19
15 6 0.23
16 8 0.31
ACGTcount: A:0.16, C:0.18, G:0.53, T:0.13
Consensus pattern (15 bp):
GGGTCGGGTCAACGG
Found at i:546957 original size:29 final size:29
Alignment explanation
Indices: 546896--546955 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
546886 CACGGTCAAC
* ***
546896 GGTCAACGGGTCGGGTCAACGGGGGTCGG
1 GGTCAACGGGTCGGGTAAACGGGAAACGG
546925 GGTCAACGGGTCGGGTAAACGGGTAAACGG
1 GGTCAACGGGTCGGGTAAACGGG-AAACGG
546955 G
1 G
546956 TCGTGACCGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.20, C:0.18, G:0.48, T:0.13
Consensus pattern (29 bp):
GGTCAACGGGTCGGGTAAACGGGAAACGG
Found at i:546981 original size:10 final size:10
Alignment explanation
Indices: 546961--547015 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
546951 ACGGGTCGTG
546961 ACCGGTC-AA
1 ACCGGTCAAA
546970 ACCGGTCAAA
1 ACCGGTCAAA
546980 ACCGGTTCAAA
1 ACCGG-TCAAA
*
546991 ACCGGT-TAA
1 ACCGGTCAAA
547000 ACCGGTCAAA
1 ACCGGTCAAA
547010 ACCGGT
1 ACCGGT
547016 TTCCAACGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:547016 original size:19 final size:19
Alignment explanation
Indices: 546961--547016 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
546951 ACGGGTCGTG
*
546961 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
546980 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
547000 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
547017 TCCAACGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:554269 original size:21 final size:21
Alignment explanation
Indices: 554244--554299 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
554234 TTCAAGGGAA
* *
554244 GGATCAATCTTTTTCATCGAT
1 GGATCGATCTTTTTCATCGAG
*
554265 GGATCGATCTTTTTCCTCGAG
1 GGATCGATCTTTTTCATCGAG
*
554286 GGATCGATCCTTTT
1 GGATCGATCTTTTT
554300 ATGAAGGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (21 bp):
GGATCGATCTTTTTCATCGAG
Found at i:557329 original size:14 final size:14
Alignment explanation
Indices: 557310--557342 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
557300 TATCGATTTA
557310 GAATTTTTATTATT
1 GAATTTTTATTATT
*
557324 GAATTTTTTTTATT
1 GAATTTTTATTATT
557338 -AATTT
1 GAATTT
557343 AGGGTGAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (14 bp):
GAATTTTTATTATT
Found at i:558769 original size:19 final size:19
Alignment explanation
Indices: 558745--558804 Score: 52
Period size: 19 Copynumber: 3.3 Consensus size: 19
558735 TCGAAACCAA
558745 TTTTTTCAGTTCGGTTCAG
1 TTTTTTCAGTTCGGTTCAG
* * *
558764 TTTTTTTA--ACGGTTCGG
1 TTTTTTCAGTTCGGTTCAG
* * *
558781 ATTTTTCGGTTCGGTTTAG
1 TTTTTTCAGTTCGGTTCAG
558800 TTTTT
1 TTTTT
558805 CGGTTTTTCA
Statistics
Matches: 29, Mismatches: 10, Indels: 4
0.67 0.23 0.09
Matches are distributed among these distances:
17 12 0.41
19 17 0.59
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.57
Consensus pattern (19 bp):
TTTTTTCAGTTCGGTTCAG
Found at i:559805 original size:19 final size:19
Alignment explanation
Indices: 559770--559807 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
559760 CTAAAATTAT
*
559770 TTTTATTATATTATATTTA
1 TTTTATTATATGATATTTA
559789 TTTTA-TATATGATTATTTA
1 TTTTATTATATGA-TATTTA
559808 AAAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTTATTATATGATATTTA
Found at i:563139 original size:16 final size:16
Alignment explanation
Indices: 563118--563169 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
563108 ACAATCAAAC
*
563118 AATTAAGTAATAAAAA
1 AATTAAGAAATAAAAA
*
563134 AATTAAGAAACAAAATA
1 AATTAAGAAATAAAA-A
563151 AA-TAA-AAAT-AAAA
1 AATTAAGAAATAAAAA
563164 AATTAA
1 AATTAA
563170 ATAAAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 3 0.10
14 6 0.19
15 3 0.10
16 16 0.52
17 3 0.10
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (16 bp):
AATTAAGAAATAAAAA
Found at i:563676 original size:21 final size:21
Alignment explanation
Indices: 563650--563701 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
563640 GATGCAGTGA
* *
563650 CATATGAAATGGTTGTGGTGC
1 CATATGAAATGGTTGCGATGC
* *
563671 CATATGATATGGTTGCGATTC
1 CATATGAAATGGTTGCGATGC
563692 CATATGAAAT
1 CATATGAAAT
563702 AATATTTATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.35
Consensus pattern (21 bp):
CATATGAAATGGTTGCGATGC
Done.