Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002418.1 Hibiscus syriacus cultivar Beakdansim tig00004945_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: 225670
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:6972 original size:18 final size:19
Alignment explanation
Indices: 6930--6974 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
6920 TTTGGTTCAC
*
6930 GGAATATAAGATTATCAGTG
1 GGAATATAAGATTACCAG-G
*
6950 GGAATGTAAGATTACCA-G
1 GGAATATAAGATTACCAGG
6968 GGAATAT
1 GGAATAT
6975 GATTACTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.27
Consensus pattern (19 bp):
GGAATATAAGATTACCAGG
Found at i:7188 original size:36 final size:35
Alignment explanation
Indices: 7115--7189 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 35
7105 TAACAAGTTG
* *
7115 AAAATTTATATATTTCTTTAAAAATTTAAATTCAT
1 AAAATTTATATATTTCTTTAAAAATTAAAAATCAT
*
7150 AAAATTTATATAATTTTTTTACAAAATTAAAAAT-AT
1 AAAATTTATAT-ATTTCTTTA-AAAATTAAAAATCAT
7186 AAAA
1 AAAA
7190 GGTTTAATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 11 0.31
36 14 0.40
37 10 0.29
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (35 bp):
AAAATTTATATATTTCTTTAAAAATTAAAAATCAT
Found at i:8459 original size:66 final size:66
Alignment explanation
Indices: 8321--8524 Score: 338
Period size: 66 Copynumber: 3.1 Consensus size: 66
8311 ACCTTTGCCG
* * * * *
8321 CCGACGCTCACATGAGTGCCACCTCCTCGCTTTCCTTTCCC-GTGTTCACTCCAATTCCGCCCTT
1 CCGACGTTCACATGGGTGCCACCCCCTGGCTTTCCTTTCCCGGTGTTCACTCCAACTCCGCCCTT
8385 T
66 T
*
8386 CCAACGTTCACATGGGTGCCACCCCCTGGCTTTCCTTTCCCGGTGTTCACTCCAACTCCGCCCTT
1 CCGACGTTCACATGGGTGCCACCCCCTGGCTTTCCTTTCCCGGTGTTCACTCCAACTCCGCCCTT
8451 T
66 T
*
8452 CCGACGTTTACATGGGTGCCACCCCCTGGCTTTCCTTTCCCGGTGTTCACTCCAACTCCGCCCTT
1 CCGACGTTCACATGGGTGCCACCCCCTGGCTTTCCTTTCCCGGTGTTCACTCCAACTCCGCCCTT
8517 T
66 T
8518 CCGACGT
1 CCGACGT
8525 CCACGGAAGT
Statistics
Matches: 130, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
65 36 0.28
66 94 0.72
ACGTcount: A:0.12, C:0.42, G:0.17, T:0.29
Consensus pattern (66 bp):
CCGACGTTCACATGGGTGCCACCCCCTGGCTTTCCTTTCCCGGTGTTCACTCCAACTCCGCCCTT
T
Found at i:16100 original size:21 final size:21
Alignment explanation
Indices: 16086--16132 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
16076 ACTTGACTTC
16086 CATAACAACAAACTTGAAATT
1 CATAACAACAAACTTGAAATT
* *
16107 CATAACAACAAACTTAAAATC
1 CATAACAACAAACTTGAAATT
16128 CATAA
1 CATAA
16133 TAATAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.55, C:0.21, G:0.02, T:0.21
Consensus pattern (21 bp):
CATAACAACAAACTTGAAATT
Found at i:20936 original size:6 final size:7
Alignment explanation
Indices: 20917--20941 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20907 GTAAATCTTC
20917 AATTTTT
1 AATTTTT
20924 AATTTTT
1 AATTTTT
20931 AATTTTT
1 AATTTTT
20938 AATT
1 AATT
20942 AATGAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:26067 original size:18 final size:18
Alignment explanation
Indices: 26040--26077 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
26030 TATTTAAATT
*
26040 TAATTAGAATAATTCATA
1 TAATTAGAATAACTCATA
*
26058 TAATTTGAATAACTCATA
1 TAATTAGAATAACTCATA
26076 TA
1 TA
26078 CTCTATACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (18 bp):
TAATTAGAATAACTCATA
Found at i:26471 original size:59 final size:58
Alignment explanation
Indices: 26407--26567 Score: 153
Period size: 61 Copynumber: 2.7 Consensus size: 58
26397 TAGAATGTGT
* *
26407 AAAAGTTTAGAGACTAATTTAGAATGACGGTCATAATTTGATATAAAATTGAAATA-TTC
1 AAAAGTTTA-AGACTAATTTAGAATGA-GGTCATAATTTGAGATAAAATTGAAATATTTA
* * * * * * *
26466 AAAAGTTTAATAACTAAATTAGAATGAAAGTCGTAGTTTGGGGATGAAATTGAAATATTTA
1 AAAAGTTTAA-GACTAATTTAGAATG-AGGTCATAATTT-GAGATAAAATTGAAATATTTA
* *
26527 AAAAATTTAAGTACTAATTTAAAATGAGAGTCATAATTTGA
1 AAAAGTTTAAG-ACTAATTTAGAATGAG-GTCATAATTTGA
26568 AGATTATGAT
Statistics
Matches: 79, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
58 1 0.01
59 30 0.38
60 17 0.22
61 31 0.39
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (58 bp):
AAAAGTTTAAGACTAATTTAGAATGAGGTCATAATTTGAGATAAAATTGAAATATTTA
Found at i:31861 original size:32 final size:33
Alignment explanation
Indices: 31825--31910 Score: 88
Period size: 32 Copynumber: 2.6 Consensus size: 33
31815 TGTTCGCTAA
31825 AAATTAATTTTTTATTTAATCACT-TAACATTC
1 AAATTAATTTTTTATTTAATCACTCTAACATTC
** * *
31857 AAATTAA--TCCTAGTTTAATTACTCTAACTTTC
1 AAATTAATTTTTTA-TTTAATCACTCTAACATTC
31889 AAATTTAATTTTTTATTGTAAT
1 AAA-TTAATTTTTTATT-TAAT
31911 TATTTACTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
30 3 0.07
31 9 0.21
32 17 0.40
33 4 0.10
34 2 0.05
35 7 0.17
ACGTcount: A:0.36, C:0.12, G:0.02, T:0.50
Consensus pattern (33 bp):
AAATTAATTTTTTATTTAATCACTCTAACATTC
Found at i:32223 original size:31 final size:28
Alignment explanation
Indices: 32169--32228 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 28
32159 GTATGATTTT
32169 GAAATAAATGAAAATTTAAGTACTTAAAC
1 GAAATAAATGAAAATTTAAGTAC-TAAAC
* *
32198 GAAATAAAACTGATAATTTAGGTACTAAAC
1 GAAAT-AAA-TGAAAATTTAAGTACTAAAC
32228 G
1 G
32229 TATAGTTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 5 0.19
30 9 0.33
31 13 0.48
ACGTcount: A:0.52, C:0.08, G:0.13, T:0.27
Consensus pattern (28 bp):
GAAATAAATGAAAATTTAAGTACTAAAC
Found at i:39685 original size:21 final size:21
Alignment explanation
Indices: 39661--39700 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
39651 TTTATTTTAT
39661 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
39682 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
39701 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:39748 original size:33 final size:33
Alignment explanation
Indices: 39695--39793 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
39685 TTTGTTTCAA
39695 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
39727 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
39760 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
39793 T
1 T
39794 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:39822 original size:13 final size:13
Alignment explanation
Indices: 39779--39833 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
39769 TTGGAAGTAT
39779 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
39792 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
39806 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
39819 TTAAGTATTTGAA
1 TTAAGTATTTCAA
39832 TT
1 TT
39834 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:40283 original size:17 final size:17
Alignment explanation
Indices: 40240--40283 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
40230 TTAAAATCGG
*
40240 TTTTTTT-ATAACCGGT
1 TTTTTTTAAAAACCGGT
**
40256 TTTTTAAAAAAACCGGT
1 TTTTTTTAAAAACCGGT
40273 TTTTTTTAAAA
1 TTTTTTTAAAA
40284 CCGAAACCGG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (17 bp):
TTTTTTTAAAAACCGGT
Found at i:40409 original size:21 final size:21
Alignment explanation
Indices: 40385--40434 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
40375 GAAAAAACCG
40385 GATCGGATAAAAACCGATCCA
1 GATCGGATAAAAACCGATCCA
*
40406 GATCGGATAAAAACCGATCCG
1 GATCGGATAAAAACCGATCCA
40427 GATCGGAT
1 GATCGGAT
40435 TGAAATCCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (21 bp):
GATCGGATAAAAACCGATCCA
Found at i:58169 original size:25 final size:27
Alignment explanation
Indices: 58140--58198 Score: 95
Period size: 25 Copynumber: 2.2 Consensus size: 27
58130 CACTTTAAAG
58140 AATATTATCTATTATTTTTC-AAA-AT
1 AATATTATCTATTATTTTTCTAAATAT
58165 AATATTATCTATTATTTTTCTAAATTAT
1 AATATTATCTATTATTTTTCTAAA-TAT
58193 AATATT
1 AATATT
58199 TTAAATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 20 0.65
26 3 0.10
28 8 0.26
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (27 bp):
AATATTATCTATTATTTTTCTAAATAT
Found at i:58646 original size:84 final size:85
Alignment explanation
Indices: 58532--58708 Score: 302
Period size: 84 Copynumber: 2.1 Consensus size: 85
58522 ATATATATTA
* * *
58532 AAATAATACATAAAATAAAAGTATATTATATTAAATGTATCTGTTAACTGTTGACGAAATATATA
1 AAATATTACATAAAATAAAAGTATATTATATTAAAAGTATCTGTTAACTATTGACGAAATATATA
58597 TTTATTTTAATTATAAAAAT
66 TTTATTTTAATTATAAAAAT
* *
58617 AAATATTA-ATAAAATAAAAGTATATTATATTAAAAGTATCTGTTAGCTATTGACGAAATATATT
1 AAATATTACATAAAATAAAAGTATATTATATTAAAAGTATCTGTTAACTATTGACGAAATATATA
58681 TTTATTTTAATTATAAAAAT
66 TTTATTTTAATTATAAAAAT
58701 AAATATTA
1 AAATATTA
58709 TTTTCGTAAA
Statistics
Matches: 87, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
84 80 0.92
85 7 0.08
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.41
Consensus pattern (85 bp):
AAATATTACATAAAATAAAAGTATATTATATTAAAAGTATCTGTTAACTATTGACGAAATATATA
TTTATTTTAATTATAAAAAT
Found at i:61994 original size:123 final size:123
Alignment explanation
Indices: 61834--62062 Score: 325
Period size: 123 Copynumber: 1.9 Consensus size: 123
61824 GTGACCACTG
* * **
61834 AAGTCTTGATATAACTGGCATTTGTGTCAGAATTTGGTTGTAAATGCTCAAATCTGTCAGTATGT
1 AAGTCTTGATATAACTGACATTTGTGTAAGAATTTGGTTGTAAATGCTCAAATCCATCAGTATGT
* * *
61899 GAGCCAGTTTTTCAGTGTAAGCTTCATGTTTTTCCATCTCTATTTAAAGTGGCTACTC
66 GAGCCAGTTTTTCAATGTAAACTTCATGTTTTTCCAGCTCTATTTAAAGTGGCTACTC
* * *
61957 AAGTCTTGATATAGCTGACATTTTTGTAATG-ATTTGGTTGTAAATGCTCGAATCCATCAGTATG
1 AAGTCTTGATATAACTGACATTTGTGTAA-GAATTTGGTTGTAAATGCTCAAATCCATCAGTATG
* * *
62021 TGAGCTAGTTTTTGAATTTAAACTTCATGTTTTTCCAGCTCT
65 TGAGCCAGTTTTTCAATGTAAACTTCATGTTTTTCCAGCTCT
62063 TACCATTAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
123 91 0.99
124 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (123 bp):
AAGTCTTGATATAACTGACATTTGTGTAAGAATTTGGTTGTAAATGCTCAAATCCATCAGTATGT
GAGCCAGTTTTTCAATGTAAACTTCATGTTTTTCCAGCTCTATTTAAAGTGGCTACTC
Found at i:63617 original size:114 final size:113
Alignment explanation
Indices: 63240--63794 Score: 701
Period size: 114 Copynumber: 4.9 Consensus size: 113
63230 AACAACAAAG
* * * **
63240 TTTTCATGCGAATGGAACTGTACCAAACACGGGATTGCCTCGATATGAGCAGTCATATGCTCAAG
1 TTTTCATGCAAATGGAACTGTATCAAACATGGGATCACCTCGATATGAGCAGTCATATGCTCAAG
* * * *
63305 GTACAGGTCCTGCCTGGAATGGACAGAC-GGTTCAGCA--ACAGCAGAA
66 GCACAAGTCCTGCCTGGAATGGCCAG-CTGGTTCAGCAGCACCGCAGAA
* * * *
63351 TTTTTC-TGCGAATGGAACCGTACCAAACATGGGATCACCTGGATATGAGCAGTCATATGCTCAA
1 -TTTTCATGCAAATGGAACTGTATCAAACATGGGATCACCTCGATATGAGCAGTCATATGCTCAA
* * * *
63415 GGCACAGGTCCTTCCTGGAATGGACAGATGGTTCAGCAGCA--GCAGAA
65 GGCACAAGTCCTGCCTGGAATGGCCAGCTGGTTCAGCAGCACCGCAGAA
* * * * * *
63462 TTTTCATGCAAATGGAACTGTATTAAACATGGGATCGCCTCGCTATGAGCAGACATGTTCTCAAG
1 TTTTCATGCAAATGGAACTGTATCAAACATGGGATCACCTCGATATGAGCAGTCATATGCTCAAG
*
63527 GCACAAGTCCTGCCTGGAGTGGCCAGCTGGTTCAGCAGCACCCGCAGAA
66 GCACAAGTCCTGCCTGGAATGGCCAGCTGGTTCAGCAGCA-CCGCAGAA
* * * * * *
63576 TATTCATGTC-AATGGAACTGTATCAAACATGGGATCACCTCGCTATGGGCAGACATGTGATCAA
1 TTTTCATG-CAAATGGAACTGTATCAAACATGGGATCACCTCGATATGAGCAGTCATATGCTCAA
* *
63640 GGCACAAGTCCTGCCTGGAGTGGCCAGCTGGTTCAGCAGCAGCCGCATAA
65 GGCACAAGTCCTGCCTGGAATGGCCAGCTGGTTCAGCAGCA-CCGCAGAA
* *
63690 TTTTCATGCAAATGGAACTGTATCAAACATAGGATCACCTCGATATGAGCAGTCCTATGCTCAAG
1 TTTTCATGCAAATGGAACTGTATCAAACATGGGATCACCTCGATATGAGCAGTCATATGCTCAAG
*
63755 GCACAACTCCTGCCTGGAATGGCCAGCTGGTTCAGCAGCA
66 GCACAAGTCCTGCCTGGAATGGCCAGCTGGTTCAGCAGCA
63795 GAAGCCCCTC
Statistics
Matches: 393, Mismatches: 41, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
110 5 0.01
111 177 0.45
112 5 0.01
113 2 0.01
114 203 0.52
115 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (113 bp):
TTTTCATGCAAATGGAACTGTATCAAACATGGGATCACCTCGATATGAGCAGTCATATGCTCAAG
GCACAAGTCCTGCCTGGAATGGCCAGCTGGTTCAGCAGCACCGCAGAA
Found at i:67675 original size:13 final size:13
Alignment explanation
Indices: 67632--67680 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
67622 CAATACCTTC
67632 CTTTTGAGCATAT
1 CTTTTGAGCATAT
* * *
67645 CCTATGACCATGTAT
1 CTTTTGAGCA--TAT
67660 CTTTTGAGCATAT
1 CTTTTGAGCATAT
67673 CTTTTGAG
1 CTTTTGAG
67681 TAGTCTCTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
13 18 0.64
15 10 0.36
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.43
Consensus pattern (13 bp):
CTTTTGAGCATAT
Found at i:73959 original size:16 final size:16
Alignment explanation
Indices: 73935--73970 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
73925 AAAATTTGAT
*
73935 AATTTTATTCTTTTAA
1 AATTGTATTCTTTTAA
73951 AATTGTATTCTTTTAA
1 AATTGTATTCTTTTAA
73967 AATT
1 AATT
73971 TTATAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (16 bp):
AATTGTATTCTTTTAA
Found at i:73969 original size:40 final size:42
Alignment explanation
Indices: 73894--73981 Score: 108
Period size: 40 Copynumber: 2.1 Consensus size: 42
73884 ATTTAAATTT
* * *
73894 ATTTTATATCTTTTACTAATTTTTTTCTCTTAAAATTTGATA
1 ATTTTATATCTTTTACAAATTGTATTCTCTTAAAATTTGATA
* *
73936 ATTTTAT-TCTTTTA-AAATTGTATTCTTTTAAAATTTTATA
1 ATTTTATATCTTTTACAAATTGTATTCTCTTAAAATTTGATA
*
73976 AATTTA
1 ATTTTA
73982 ATCCTTATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
40 26 0.65
41 7 0.17
42 7 0.17
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (42 bp):
ATTTTATATCTTTTACAAATTGTATTCTCTTAAAATTTGATA
Found at i:78758 original size:3 final size:3
Alignment explanation
Indices: 78750--78776 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
78740 ATTCGGTGCT
78750 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
78777 ATTAATGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:80458 original size:39 final size:37
Alignment explanation
Indices: 80415--80489 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
80405 CATAACTATT
*
80415 TAAAAAA-ATTAAATTAAATTATTTTATAAAATATATATC
1 TAAAAAATATTAAATT--ATGATTTT-TAAAATATATATC
**
80454 TAAAAAATATTTGATTATGATTTTTAAAATATATAT
1 TAAAAAATATTAAATTATGATTTTTAAAATATATAT
80490 TCTTATTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 12 0.38
38 7 0.22
39 7 0.22
40 6 0.19
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (37 bp):
TAAAAAATATTAAATTATGATTTTTAAAATATATATC
Found at i:81309 original size:28 final size:30
Alignment explanation
Indices: 81263--81320 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
81253 TCAAATAATA
*
81263 ATATTTTTTTTTGAGTAAATCACA-ATTAT
1 ATATTATTTTTTGAGTAAATCACACATTAT
81292 ATATTATTTTTT-AGTAAATCACACATTAT
1 ATATTATTTTTTGAGTAAATCACACATTAT
81321 CTTTTGGGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (30 bp):
ATATTATTTTTTGAGTAAATCACACATTAT
Found at i:82010 original size:25 final size:25
Alignment explanation
Indices: 81959--82010 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
81949 TTAGAAGTAT
*
81959 ATTTTTAAAACTTTAAGAAAAATAA
1 ATTTTTAAAACTTTAAGAAAAAAAA
**
81984 ATTTTTAAATTTTTAA-AAATAAAAA
1 ATTTTTAAAACTTTAAGAAA-AAAAA
82009 AT
1 AT
82011 AAATTATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
ATTTTTAAAACTTTAAGAAAAAAAA
Found at i:83849 original size:4 final size:4
Alignment explanation
Indices: 83840--83865 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
83830 TCGATAAGAT
83840 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
83866 ATTGTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:86577 original size:21 final size:21
Alignment explanation
Indices: 86551--86591 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
86541 AAATAATCAC
86551 ATCATA-AATTAGATTAAAAAT
1 ATCATATAATTA-ATTAAAAAT
86572 ATCATATTAATTAATTAAAA
1 ATCATA-TAATTAATTAAAA
86592 TTTAATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 7 0.39
23 5 0.28
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (21 bp):
ATCATATAATTAATTAAAAAT
Found at i:88753 original size:26 final size:26
Alignment explanation
Indices: 88717--88785 Score: 129
Period size: 26 Copynumber: 2.7 Consensus size: 26
88707 ATTTTCATCA
88717 CTTCTAAGATTTTATAAGTTAATTAT
1 CTTCTAAGATTTTATAAGTTAATTAT
88743 CTTCTAAGATTTTATAAGTTAATTAT
1 CTTCTAAGATTTTATAAGTTAATTAT
*
88769 CTTCTAAAATTTTATAA
1 CTTCTAAGATTTTATAA
88786 TTTCATCTCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (26 bp):
CTTCTAAGATTTTATAAGTTAATTAT
Found at i:89242 original size:186 final size:187
Alignment explanation
Indices: 89005--89355 Score: 584
Period size: 186 Copynumber: 1.9 Consensus size: 187
88995 ATTAAATTTT
* *
89005 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAA-TCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACT-CAATTAATA
*
89069 ATTTAATATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATAT-AAATT
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATGAAA--
89133 TTTTTATTTTATAA-T-TATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAAA
128 TTTTTATTTTATAATTATATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAAA
*
89191 AAATATTAAATATATTATATATAACATTTGGGCTAAGCCCAAACAATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACTCAATTAATAA
* * *
89256 TTTAAGATCCAATAACTTTTAAATCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATGAAATTT
89321 TTATTTTATAATTATATATATTATTTAAATTAATT
131 TTATTTTATAATTATATATATTATTTAAATTAATT
89356 ATACACTTTT
Statistics
Matches: 154, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
185 14 0.09
186 115 0.75
187 25 0.16
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (187 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACAATTTAAAACTCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATGAAATTT
TTATTTTATAATTATATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAAA
Found at i:99172 original size:16 final size:17
Alignment explanation
Indices: 99151--99182 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
99141 TCAGTTCTTT
99151 TATTTA-TTTATTTAAA
1 TATTTATTTTATTTAAA
99167 TATTTATTTTATTTAA
1 TATTTATTTTATTTAA
99183 TTATAAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTATTTTATTTAAA
Found at i:105339 original size:43 final size:43
Alignment explanation
Indices: 105291--105412 Score: 208
Period size: 43 Copynumber: 2.8 Consensus size: 43
105281 TTTTTGTGTA
*
105291 ATTTTAACTTTTAAAATATAATTTATATATAGAGATTAATCTT
1 ATTTTAACTTTTAAAATATAATTTATATATACAGATTAATCTT
* *
105334 ATTTTAACTTTTAAAATATAATTTATGTATTCAGATTAATCTT
1 ATTTTAACTTTTAAAATATAATTTATATATACAGATTAATCTT
*
105377 ATTTTAACTTTTAAAATATAATTTATATATTCAGAT
1 ATTTTAACTTTTAAAATATAATTTATATATACAGAT
105413 CTTTGAGCAT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (43 bp):
ATTTTAACTTTTAAAATATAATTTATATATACAGATTAATCTT
Found at i:106864 original size:32 final size:32
Alignment explanation
Indices: 106812--106874 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
106802 TCGAATTACA
* * *
106812 TAGTTCAATATCCAACCATAATTAAAAAATGT
1 TAGTCCAACATCCAAACATAATTAAAAAATGT
106844 TAGTCCAACATCCAAACATAATTAAAAAATG
1 TAGTCCAACATCCAAACATAATTAAAAAATG
106875 GCATGTTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.27
Consensus pattern (32 bp):
TAGTCCAACATCCAAACATAATTAAAAAATGT
Found at i:107139 original size:31 final size:30
Alignment explanation
Indices: 107094--107212 Score: 94
Period size: 31 Copynumber: 3.6 Consensus size: 30
107084 TTTACCCTAA
*
107094 ATAATAATATAGTGAGCAAAACATAAATTAG
1 ATAATAATA-AGTGACCAAAACATAAATTAG
* ** *
107125 ATAATATATAAGTGACCAAATAGGTAGTTTATCCTAA
1 ATAATA-ATAAGTGACCAAA-A--CA-TAAAT--TAG
*
107162 ATAATAATCGAGTGACCAAAACATAAATTAG
1 ATAATAAT-AAGTGACCAAAACATAAATTAG
107193 ATAATATATAAGTGACCAAA
1 ATAATA-ATAAGTGACCAAA
107213 TAGGTAGTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
31 33 0.49
32 6 0.09
33 3 0.04
34 2 0.03
35 3 0.04
36 3 0.04
37 18 0.26
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (30 bp):
ATAATAATAAGTGACCAAAACATAAATTAG
Found at i:107161 original size:68 final size:68
Alignment explanation
Indices: 106956--107230 Score: 444
Period size: 68 Copynumber: 4.0 Consensus size: 68
106946 ATTTTGAAAA
* * *
106956 AAATAATAATCAAGAGACC-AAACATAAATTAGATAATATACAAGTGACCAAATAGGTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
107020 CCT
66 CCT
* * *
107023 AAATAATAATCGAGTGACCAAAATATAAAATTAGATAATATATAAGTGACTAAATGGGTAGTTTA
1 AAATAATAATCGAGTGACCAAAACAT-AAATTAGATAATATATAAGTGACCAAATAGGTAGTTTA
107088 CCCT
65 CCCT
** * *
107092 AAATAATAATATAGTGAGCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAT
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
107157 CCT
66 CCT
107160 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
107225 CCT
66 CCT
107228 AAA
1 AAA
107231 AAAAATCCCT
Statistics
Matches: 189, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
67 17 0.09
68 111 0.59
69 61 0.32
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (68 bp):
AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
CCT
Found at i:125754 original size:19 final size:17
Alignment explanation
Indices: 125714--125747 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
125704 TGATAAAACG
125714 ACGATAAATTCTAAGCA
1 ACGATAAATTCTAAGCA
125731 ACGATAAATTCTAAGCA
1 ACGATAAATTCTAAGCA
125748 CAACGATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.24
Consensus pattern (17 bp):
ACGATAAATTCTAAGCA
Found at i:126999 original size:30 final size:30
Alignment explanation
Indices: 126945--127026 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
126935 CTTAAATTTT
* * * *
126945 TTAATTATCTTTTGTTTTTGTTTTAACT-TA
1 TTAAATATATTTTATTTTTATTTTAA-TGTA
126975 TTAAATATATTTTATTTTTATTTTAATGTA
1 TTAAATATATTTTATTTTTATTTTAATGTA
** *
127005 AAAATATATATTTTATCTTTAT
1 TTAA-ATATATTTTATTTTTAT
127027 CATCACTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 1 0.02
30 26 0.60
31 16 0.37
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (30 bp):
TTAAATATATTTTATTTTTATTTTAATGTA
Found at i:127176 original size:27 final size:30
Alignment explanation
Indices: 127127--127197 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 30
127117 ATATCTTCAC
*
127127 TTAAAAATATATTTCATTCTTAT-TTCAAA-
1 TTAAAAATATATTTCATTATTATCTT-AAAT
127156 TTAAAAATAT-TTT-ATTATTATCTTAAATT
1 TTAAAAATATATTTCATTATTATCTTAAA-T
127185 TTAAAAATATATT
1 TTAAAAATATATT
127198 AAAATAACTG
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
27 10 0.27
28 5 0.14
29 20 0.54
30 2 0.05
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.51
Consensus pattern (30 bp):
TTAAAAATATATTTCATTATTATCTTAAAT
Found at i:129326 original size:4 final size:4
Alignment explanation
Indices: 129317--129387 Score: 54
Period size: 4 Copynumber: 16.8 Consensus size: 4
129307 AAATGTGGTG
*
129317 CATA CATA CATA CATA TATCA GCTTATA CAATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CAT-A -C--ATA C-ATA CATA CATA CATA CATA
* **
129366 CAT- CATA TATA GTTA CATA CAT
1 CATA CATA CATA CATA CATA CAT
129388 GTATTAGCTT
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
3 3 0.06
4 42 0.78
5 5 0.09
6 1 0.02
7 1 0.02
8 2 0.04
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.31
Consensus pattern (4 bp):
CATA
Found at i:136236 original size:17 final size:17
Alignment explanation
Indices: 136200--136236 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
136190 TATTTATATT
*
136200 TTTATTATTATAATTTA
1 TTTATTATTATAATTAA
*
136217 TTTATTATTATTATTAA
1 TTTATTATTATAATTAA
136234 TTT
1 TTT
136237 CTTTGTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATTATTATAATTAA
Found at i:136248 original size:20 final size:20
Alignment explanation
Indices: 136187--136236 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
136177 TGACCGGGTT
*
136187 TTAT-ATTTATATTTTTATTA
1 TTATAATTTAT-TTATTATTA
136207 TTATAATTTATTTATTATTA
1 TTATAATTTATTTATTATTA
136227 TTATTAATTT
1 TTA-TAATTT
136237 CTTTGTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATAATTTATTTATTATTA
Found at i:145855 original size:98 final size:98
Alignment explanation
Indices: 145686--145865 Score: 333
Period size: 98 Copynumber: 1.8 Consensus size: 98
145676 AACTTGGTGA
*
145686 AAGCATCGTATACATGCTGAAGCTGGCTCTTTCCATTTTGATTTTATAAAGATGAACCTGAAATG
1 AAGCATCGTATACATGCTGAAGCTGGCTCATTCCATTTTGATTTTATAAAGATGAACCTGAAATG
*
145751 TTGGCGTCAAGGCCCAATATCGGCCGAAGGTTC
66 TTGGCGTCAACGCCCAATATCGGCCGAAGGTTC
*
145784 AAGCATCGTATACATGCTGAAGCTGGCTCATTCCATTTTGATTTTCTAAAGATGAACCTGAAATG
1 AAGCATCGTATACATGCTGAAGCTGGCTCATTCCATTTTGATTTTATAAAGATGAACCTGAAATG
145849 TTGGCGTCAACGCCCAA
66 TTGGCGTCAACGCCCAA
145866 AACCACGACC
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 79 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (98 bp):
AAGCATCGTATACATGCTGAAGCTGGCTCATTCCATTTTGATTTTATAAAGATGAACCTGAAATG
TTGGCGTCAACGCCCAATATCGGCCGAAGGTTC
Found at i:148724 original size:110 final size:108
Alignment explanation
Indices: 148531--148978 Score: 593
Period size: 110 Copynumber: 4.1 Consensus size: 108
148521 TTTCAATAAA
* ** * * **
148531 GTATCGATACATGTACAAAAAGTATCGATACTTTTAACATATCCAGTAATTCTTTACCGGTTTTG
1 GTATCGATACATTTTTATAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTG
148596 TCATAATGAAACTGGTTTTTATATTTTTACCTGTTATATTATTAT
66 TCATAATGAAACTGG-TTTTAT-TTTTTACCTGTTATATTATTAT
* *
148641 GTATCGAAACATTTTTATAAAGTATCGATACTTTTAACATATCCGGTAGCTATTTACCGGTTTTG
1 GTATCGATACATTTTTATAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTG
*
148706 TCATAATGAAACTGGTTTTATAATTTTTACCTGTTATATTGTTAT
66 TCATAATGAAACTGGTTTTAT--TTTTTACCTGTTATATTATTAT
** * *** *
148751 GTATCGATACATTTTTATAAAGTATTAATACTTTTAACATATTCGGTAGCTCTTTACTATTTTTT
1 GTATCGATACATTTTTATAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTG
*
148816 TCATAATGAAACTGG-----TTTTTTACCTATTATATTATTAT
66 TCATAATGAAACTGGTTTTATTTTTTACCTGTTATATTATTAT
* *
148854 GTATCGATACATTTTTATAAAGTATCGATACTTTTAACATATCTGGTAGCTCTTTACCGGTTTTA
1 GTATCGATACATTTTTATAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTG
*
148919 TCATAATGAAACTGGTTTTGTCATTTTTTACCTGTTATATTGTTAT
66 TCATAATGAAACTGG-TTT-T-ATTTTTTACCTGTTATATTATTAT
*
148965 CTATCGATAC-TTTT
1 GTATCGATACATTTT
148979 AACATATACG
Statistics
Matches: 297, Mismatches: 32, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
103 92 0.31
105 1 0.00
109 6 0.02
110 168 0.57
111 30 0.10
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (108 bp):
GTATCGATACATTTTTATAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTG
TCATAATGAAACTGGTTTTATTTTTTACCTGTTATATTATTAT
Found at i:148885 original size:103 final size:105
Alignment explanation
Indices: 148531--149298 Score: 588
Period size: 110 Copynumber: 7.2 Consensus size: 105
148521 TTTCAATAAA
* ** * * **
148531 GTATCGATACATGTACAAAAAGTATCGATACTTTTAACATATCCAGTAATTCTTTACCGGTTTTG
1 GTATCGATACATTTTTATAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTG
148596 TCATAATGAAACTGGTTTTTATATTTTTACCTGTTATATTATTAT
66 TCATAATGAAACTGG----T-TATTTTTACCTGTTATATTATTAT
* *
148641 GTATCGAAACATTTTTATAAAGTATCGATACTTTTAACATATCCGGTAGCTATTTACCGGTTTTG
1 GTATCGATACATTTTTATAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTG
*
148706 TCATAATGAAACTGGTTTTATAATTTTTACCTGTTATATTGTTAT
66 TCATAATGAAACTGG---T-T-ATTTTTACCTGTTATATTATTAT
** * *** *
148751 GTATCGATACATTTTTATAAAGTATTAATACTTTTAACATATTCGGTAGCTCTTTACTATTTTTT
1 GTATCGATACATTTTTATAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTG
*
148816 TCATAATGAAACTGG-T-TTTTTACCTATTATATTATTAT
66 TCATAATGAAACTGGTTATTTTTACCTGTTATATTATTAT
* *
148854 GTATCGATACATTTTTATAAAGTATCGATACTTTTAACATATCTGGTAGCTCTTTACCGGTTTTA
1 GTATCGATACATTTTTATAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTG
*
148919 TCATAATGAAACTGGTTTTGTCATTTTTTACCTGTTATATTGTTAT
66 TCATAATGAAACTGG---T-T-A-TTTTTACCTGTTATATTATTAT
* * * * *
148965 CTATCGATAC--TTTTA-ACA-TATACGATAGCTCTT----TA-CCGGT---T-TTT-TC---AT
1 GTATCGATACATTTTTATAAAGTAT-CGATA-CTTTTAACATATCCGGTAGCTCTTTACCGGTTT
** * * * **** ** * *
149013 AATAAAATTGGTTTTGTCAT-TTTTTACATGTTATATTGTTAT
64 TGTCATAATGAAACTG-GTTATTTTTACCTGTTATATTATTAT
* * * *
149055 CTATCGATACTTTTTTATAAAGTATCGATACTTGTAACATATCCGATAGCTCTTTACCGGTTTTG
1 GTATCGATACATTTTTATAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTG
* * *
149120 TTATAATGAAA-TAGGTTTTGTCATTTTTTACATGTTATATTGTTAT
66 TCATAATGAAACT-GG---T-T-A-TTTTTACCTGTTATATTATTAT
* * * * *
149166 GTATAGATACATTTTTATAAAAATATTGATACTTTTAACATATCCGATAGCTCTTTACCGATTTT
1 GTATCGATACATTTTTAT-AAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTT
* * * * *
149231 GTCATAATAAAATTGATTTTATCATTTTTTACCTGTTATATTGTTAC
65 GTCATAATGAAACTG---GT-T-A-TTTTTACCTGTTATATTATTAT
149278 GTATCGATACATTTTTATAAA
1 GTATCGATACATTTTTATAAA
149299 TTATTAATAC
Statistics
Matches: 538, Mismatches: 78, Indels: 83
0.77 0.11 0.12
Matches are distributed among these distances:
90 31 0.06
92 8 0.01
93 8 0.01
94 3 0.01
96 11 0.02
97 4 0.01
99 1 0.00
100 4 0.01
101 4 0.01
102 1 0.00
103 92 0.17
104 5 0.01
105 10 0.02
107 3 0.01
108 9 0.02
109 15 0.03
110 164 0.30
111 69 0.13
112 95 0.18
113 1 0.00
ACGTcount: A:0.29, C:0.13, G:0.12, T:0.46
Consensus pattern (105 bp):
GTATCGATACATTTTTATAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTG
TCATAATGAAACTGGTTATTTTTACCTGTTATATTATTAT
Found at i:149029 original size:90 final size:90
Alignment explanation
Indices: 148876--149068 Score: 325
Period size: 90 Copynumber: 2.1 Consensus size: 90
148866 TTTTATAAAG
* *
148876 TATCGATACTTTTAACATATCTGGTAGCTCTTTACCGGTTTTATCATAATGAAACTGGTTTTGTC
1 TATCGATACTTTTAACATATCTGATAGCTCTTTACCGGTTTTATCATAATAAAACTGGTTTTGTC
*
148941 ATTTTTTACCTGTTATATTGTTATC
66 ATTTTTTACATGTTATATTGTTATC
* *
148966 TATCGATACTTTTAACATATAC-GATAGCTCTTTACCGGTTTTTTCATAATAAAATTGGTTTTGT
1 TATCGATACTTTTAACATAT-CTGATAGCTCTTTACCGGTTTTATCATAATAAAACTGGTTTTGT
149030 CATTTTTTACATGTTATATTGTTATC
65 CATTTTTTACATGTTATATTGTTATC
149056 TATCGATACTTTT
1 TATCGATACTTTT
149069 TTATAAAGTA
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
90 96 0.99
91 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.49
Consensus pattern (90 bp):
TATCGATACTTTTAACATATCTGATAGCTCTTTACCGGTTTTATCATAATAAAACTGGTTTTGTC
ATTTTTTACATGTTATATTGTTATC
Found at i:149231 original size:112 final size:111
Alignment explanation
Indices: 148970--149311 Score: 506
Period size: 111 Copynumber: 3.1 Consensus size: 111
148960 GTTATCTATC
*
148970 GATACTTTTAACATATACGATAGCTCTTTACCGGTTTT-TTCATAATAAAATTGGTTTTGTCATT
1 GATACTTTTAACATATCCGATAGCTCTTTACCGGTTTTGTT-ATAATAAAATTGGTTTTGTCATT
* * * *
149034 TTTTACATGTTATATTGTTATCTATCGATACTTTTTTATAAAGTATC
65 TTTTACATGTTATATTGTTATGTATCGATACATTTTTATAAAATATT
* * *
149081 GATACTTGTAACATATCCGATAGCTCTTTACCGGTTTTGTTATAATGAAATAGGTTTTGTCATTT
1 GATACTTTTAACATATCCGATAGCTCTTTACCGGTTTTGTTATAATAAAATTGGTTTTGTCATTT
*
149146 TTTACATGTTATATTGTTATGTATAGATACATTTTTATAAAAATATT
66 TTTACATGTTATATTGTTATGTATCGATACATTTTTAT-AAAATATT
* * * *
149193 GATACTTTTAACATATCCGATAGCTCTTTACCGATTTTGTCATAATAAAATTGATTTTATCATTT
1 GATACTTTTAACATATCCGATAGCTCTTTACCGGTTTTGTTATAATAAAATTGGTTTTGTCATTT
* * *
149258 TTTACCTGTTATATTGTTACGTATCGATACATTTTTATAAATTATT
66 TTTACATGTTATATTGTTATGTATCGATACATTTTTATAAAATATT
*
149304 AATACTTT
1 GATACTTT
149312 ATAGGTGCTA
Statistics
Matches: 208, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
111 107 0.51
112 101 0.49
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.48
Consensus pattern (111 bp):
GATACTTTTAACATATCCGATAGCTCTTTACCGGTTTTGTTATAATAAAATTGGTTTTGTCATTT
TTTACATGTTATATTGTTATGTATCGATACATTTTTATAAAATATT
Found at i:149586 original size:73 final size:73
Alignment explanation
Indices: 149482--149629 Score: 208
Period size: 73 Copynumber: 2.0 Consensus size: 73
149472 GTAACGCCTG
* * *
149482 TTTTTTACCGTTTACATTATTAGCAATCTTAAAAAAATCGATAGGT-TGTTTAATGTAATAGGTA
1 TTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAACCGATAGATAT-TTTAATGTAATAGGTA
* *
149546 GCGTCTATT
65 ACCTCTATT
* * *
149555 TTTTTTACCGTTTACATTGTTAGTAACCTTAAAAAAACCGATAGATATTTTAATGTAGTAGGTAA
1 TTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAACCGATAGATATTTTAATGTAATAGGTAA
149620 CCTCTATT
66 CCTCTATT
149628 TT
1 TT
149630 ATATTTTTGA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
73 65 0.98
74 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.43
Consensus pattern (73 bp):
TTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAACCGATAGATATTTTAATGTAATAGGTAA
CCTCTATT
Found at i:153779 original size:57 final size:53
Alignment explanation
Indices: 153718--153862 Score: 141
Period size: 57 Copynumber: 2.6 Consensus size: 53
153708 TTTAGTTTTA
*
153718 CAATATTAAAATTT-AAAT-AATCTATATAACTACAATAATAAATTATTTAAAATAAAT
1 CAATA-TAAAATTTAAAATAAATCAATAT-A-TAC--TAATAAATTA-TTAAAATAAAT
* *
153775 CAATATATATTTTAAAATAAATCAATATATACTAATAAATTATTAAAATAAAT
1 CAATATAAAATTTAAAATAAATCAATATATACTAATAAATTATTAAAATAAAT
* *
153828 CAATCTATACAATTATAATAATAAATCAATCTATA
1 CAA--TATAAAATT-TAA-AATAAATCAATATATA
153863 TTTTAAAATA
Statistics
Matches: 76, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
53 14 0.18
54 10 0.13
55 7 0.09
56 12 0.16
57 25 0.33
58 8 0.11
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (53 bp):
CAATATAAAATTTAAAATAAATCAATATATACTAATAAATTATTAAAATAAAT
Found at i:153788 original size:22 final size:22
Alignment explanation
Indices: 153763--153805 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
153753 TAATAAATTA
153763 TTTAAAATAAATCAATATATAT
1 TTTAAAATAAATCAATATATAT
153785 TTTAAAATAAATCAATATATA
1 TTTAAAATAAATCAATATATA
153806 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATATATAT
Found at i:153796 original size:26 final size:26
Alignment explanation
Indices: 153767--153875 Score: 75
Period size: 31 Copynumber: 4.2 Consensus size: 26
153757 AAATTATTTA
153767 AAATAAATCAATATATATTTTAAAAT
1 AAATAAATCAATATATATTTTAAAAT
*
153793 AAATCAATAT-ATACTAATAAATTATTAAAAT
1 AAAT-AA-ATCA-A-T-ATATATT-TTAAAAT
* * * *
153824 AAATCAATC--TATACA-ATTATAAT
1 AAATAAATCAATATATATTTTAAAAT
*
153847 -AATAAATCAATCTATATTTTAAAAT
1 AAATAAATCAATATATATTTTAAAAT
153872 AAAT
1 AAAT
153876 CAATTCATAC
Statistics
Matches: 62, Mismatches: 10, Indels: 22
0.66 0.11 0.23
Matches are distributed among these distances:
22 7 0.11
23 6 0.10
24 4 0.06
25 10 0.16
26 8 0.13
27 3 0.05
28 3 0.05
29 3 0.05
30 7 0.11
31 11 0.18
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (26 bp):
AAATAAATCAATATATATTTTAAAAT
Found at i:153814 original size:22 final size:22
Alignment explanation
Indices: 153765--153813 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
153755 ATAAATTATT
**
153765 TAAAATAAATCAATATATATTT
1 TAAAATAAATCAATATATATAA
153787 TAAAATAAATCAATATATACTAA
1 TAAAATAAATCAATATATA-TAA
153810 TAAA
1 TAAA
153814 TTATTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAATAAATCAATATATATAA
Found at i:153872 original size:22 final size:23
Alignment explanation
Indices: 153812--153879 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 23
153802 TATACTAATA
153812 AATTATTAAAATAAATCAATCTAT
1 AATT-TTAAAATAAATCAATCTAT
*
153836 ACAATTATAATAATAAATCAATCTAT
1 --AATTTTAA-AATAAATCAATCTAT
153862 -ATTTTAAAATAAATCAAT
1 AATTTTAAAATAAATCAAT
153880 TCATACTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 11 0.28
23 6 0.15
25 3 0.08
26 19 0.49
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (23 bp):
AATTTTAAAATAAATCAATCTAT
Found at i:153941 original size:103 final size:101
Alignment explanation
Indices: 153815--154041 Score: 339
Period size: 103 Copynumber: 2.2 Consensus size: 101
153805 ACTAATAAAT
* * *
153815 TATTAAAATAAATCAATCTATACAATTATAATAATAAATCAATCTATATTTTAAAATAAATCAAT
1 TATTAAAATAAATCAATC-ATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAAT
*
153880 -TCATACTAATAAATTATTTAAAATAAATTAATCGATA
65 CT-ATACTAATAAATTATTTAAAATAAATCAATCGATA
*
153917 TTTTTAAAATAAATCAATACATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAA
1 -TATTAAAATAAATCAAT-CATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAA
**
153982 TCTATACTAATAAATTATTTAAAATAAATCAATTTATA
64 TCTATACTAATAAATTATTTAAAATAAATCAATCGATA
154020 TATTAAAATAAATCAATTCATA
1 TATTAAAATAAATCAA-TCATA
154042 TTAATAAATT
Statistics
Matches: 113, Mismatches: 8, Indels: 7
0.88 0.06 0.05
Matches are distributed among these distances:
102 19 0.17
103 92 0.81
104 2 0.02
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (101 bp):
TATTAAAATAAATCAATCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
TATACTAATAAATTATTTAAAATAAATCAATCGATA
Found at i:153978 original size:22 final size:22
Alignment explanation
Indices: 153896--153983 Score: 77
Period size: 23 Copynumber: 3.8 Consensus size: 22
153886 TAATAAATTA
* *
153896 TTTAAAATAAATTAATCGATATT
1 TTTAAAATAAATCAATCCATA-T
* *
153919 TTTAAAATAAATCAATACATACAAC
1 TTTAAAATAAATCAATCCAT---AT
**
153944 TACAATAATAAATCAATCCATAT
1 TTTAA-AATAAATCAATCCATAT
153967 TTTAAAATAAATCAATC
1 TTTAAAATAAATCAATC
153984 TATACTAATA
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
22 12 0.24
23 21 0.41
25 3 0.06
26 15 0.29
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.34
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:154006 original size:32 final size:32
Alignment explanation
Indices: 153967--154106 Score: 167
Period size: 32 Copynumber: 4.7 Consensus size: 32
153957 CAATCCATAT
153967 TTTAAAATAAATCAA-TCTATACTAATAAATTA
1 TTTAAAATAAATCAATTC-ATACTAATAAATTA
153999 TTTAAAATAAATCAA-T--T--T-AT--A-TA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
*
154022 -TTAAAATAAATCAATTCATATTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
154053 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
*
154085 TTTTAAAATAAATCAATCCATA
1 -TTTAAAATAAATCAATTCATA
154107 TTTTATAATA
Statistics
Matches: 95, Mismatches: 2, Indels: 21
0.81 0.02 0.18
Matches are distributed among these distances:
22 14 0.15
23 3 0.03
24 1 0.01
25 1 0.01
26 2 0.02
27 2 0.02
28 2 0.02
29 1 0.01
30 1 0.01
31 2 0.02
32 46 0.48
33 20 0.21
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.39
Consensus pattern (32 bp):
TTTAAAATAAATCAATTCATACTAATAAATTA
Found at i:154025 original size:22 final size:22
Alignment explanation
Indices: 154000--154042 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
153990 AATAAATTAT
*
154000 TTAAAATAAATCAATTTATATA
1 TTAAAATAAATCAATTCATATA
154022 TTAAAATAAATCAATTCATAT
1 TTAAAATAAATCAATTCATAT
154043 TAATAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAATAAATCAATTCATATA
Found at i:154050 original size:22 final size:22
Alignment explanation
Indices: 154001--154049 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
153991 ATAAATTATT
* *
154001 TAAAATAAATCAATTTATATAT
1 TAAAATAAATCAATTCATATAA
154023 TAAAATAAATCAATTCATATTAA
1 TAAAATAAATCAATTCATA-TAA
154046 TAAA
1 TAAA
154050 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAATAAATCAATTCATATAA
Found at i:154069 original size:54 final size:54
Alignment explanation
Indices: 153847--154068 Score: 289
Period size: 54 Copynumber: 4.2 Consensus size: 54
153837 CAATTATAAT
153847 AATAAATCAATCTATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
* * * *
153901 AATAAATTAATCGATATTTTTAAAATAAATCAATACATAC-AACTACA--A--T--
1 AATAAATCAATCTATA-TTTTAAAATAAATCAATTCATACTAA-TAAATTATTTAA
*
153950 AATAAATCAATCCATATTTTAAAATAAATCAA-TCTATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATTC-ATACTAATAAATTATTTAA
* * *
154004 AATAAATCAATTTATATATTAAAATAAATCAATTCATATTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
154058 AATAAATCAAT
1 AATAAATCAAT
154069 TCATACTAAT
Statistics
Matches: 145, Mismatches: 12, Indels: 22
0.81 0.07 0.12
Matches are distributed among these distances:
47 1 0.01
48 23 0.16
49 16 0.11
50 1 0.01
51 1 0.01
52 1 0.01
53 1 0.01
54 74 0.51
55 27 0.19
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (54 bp):
AATAAATCAATCTATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
Found at i:154079 original size:18 final size:17
Alignment explanation
Indices: 154026--154082 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
154016 TATATATTAA
154026 AATAAATCAATTCATATT
1 AATAAATCAATTCATA-T
* *
154044 AATAAAT-TATT--TAA
1 AATAAATCAATTCATAT
154058 AATAAATCAATTCATACT
1 AATAAATCAATTCATA-T
154076 AATAAAT
1 AATAAAT
154083 TATTTTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 7 0.23
15 5 0.16
17 5 0.16
18 14 0.45
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (17 bp):
AATAAATCAATTCATAT
Found at i:154096 original size:15 final size:15
Alignment explanation
Indices: 154044--154180 Score: 105
Period size: 15 Copynumber: 8.5 Consensus size: 15
154034 AATTCATATT
154044 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
* * *
154058 AATAAATCAATTCATACT
1 AATAAAT-TATT-TTA-A
154076 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
154091 AATAAATCAATCCATATTTTAT
1 AATAAAT---T--A--TTTTAA
*
154113 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
154128 AATAAATTATGTTAT
1 AATAAATTATTTTAA
154143 AATAAATTAATTTTAA
1 AATAAATT-ATTTTAA
154159 AATAAATTATTTTAA
1 AATAAATTATTTTAA
154174 AATAAAT
1 AATAAAT
154181 AACCTTATTA
Statistics
Matches: 97, Mismatches: 14, Indels: 23
0.72 0.10 0.17
Matches are distributed among these distances:
14 7 0.07
15 47 0.48
16 16 0.16
17 6 0.06
18 8 0.08
19 1 0.01
20 1 0.01
22 11 0.11
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:154101 original size:65 final size:66
Alignment explanation
Indices: 154022--154165 Score: 172
Period size: 65 Copynumber: 2.2 Consensus size: 66
154012 AATTTATATA
*
154022 TTAAAATAAATCAATTCATA-T-TAATAAATTA-TTTAAAATAAATCAAT-TCATACTAATAAAT
1 TTAAAATAAATCAATCCATATTATAATAAATTATTTTAAAATAAAT-AATGT--TA-TAATAAAT
154083 T-ATT
62 TAATT
* *
154087 TTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAATTATGTTATAATAAATTA
1 TTAAAATAAATCAATCCATA--TTATAATAAATTATTTTAAAATAAATAATGTTATAATAAATTA
154152 ATT
64 ATT
154155 TTAAAATAAAT
1 TTAAAATAAAT
154166 TATTTTAAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
65 19 0.28
67 9 0.13
68 17 0.25
69 11 0.16
70 13 0.19
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (66 bp):
TTAAAATAAATCAATCCATATTATAATAAATTATTTTAAAATAAATAATGTTATAATAAATTAAT
T
Found at i:154125 original size:37 final size:33
Alignment explanation
Indices: 154022--154165 Score: 163
Period size: 32 Copynumber: 4.3 Consensus size: 33
154012 AATTTATATA
154022 TTAAAATAAATCAATTCATATTAATAAATTA-T
1 TTAAAATAAATCAATTCATATTAATAAATTATT
*
154054 TTAAAATAAATCAATTCATACTAATAAATTATT
1 TTAAAATAAATCAATTCATATTAATAAATTATT
* *
154087 TTAAAATAAATCAATCCATATTTTATAATAATTTATT
1 TTAAAATAAATCAATTCATA---T-TAATAAATTATT
*
154124 TTAAAATAAAT-TATGT--TA-TAATAAATTAATT
1 TTAAAATAAATCAAT-TCATATTAATAAATT-ATT
154155 TTAAAATAAAT
1 TTAAAATAAAT
154166 TATTTTAAAA
Statistics
Matches: 98, Mismatches: 7, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
30 8 0.08
31 14 0.14
32 30 0.31
33 20 0.20
35 2 0.02
36 2 0.02
37 22 0.22
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (33 bp):
TTAAAATAAATCAATTCATATTAATAAATTATT
Found at i:154159 original size:31 final size:31
Alignment explanation
Indices: 154109--154180 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
154099 AATCCATATT
*
154109 TTATAAT-AATTTATTTTAAAATAAATTATG
1 TTATAATAAATTAATTTTAAAATAAATTATG
*
154139 TTATAATAAATTAATTTTAAAATAAATTATT
1 TTATAATAAATTAATTTTAAAATAAATTATG
*
154170 TTAAAATAAAT
1 TTATAATAAAT
154181 AACCTTATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 7 0.18
31 31 0.82
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (31 bp):
TTATAATAAATTAATTTTAAAATAAATTATG
Found at i:154310 original size:21 final size:21
Alignment explanation
Indices: 154286--154334 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
154276 GTTTGCACCA
*
154286 AGAAGAGCTCGCGTAGACATT
1 AGAAGAGCTCGCGCAGACATT
*
154307 AGAAGAACTCGCGCAGACATT
1 AGAAGAGCTCGCGCAGACATT
154328 AGAAGAG
1 AGAAGAG
154335 TTTATATCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.39, C:0.18, G:0.29, T:0.14
Consensus pattern (21 bp):
AGAAGAGCTCGCGCAGACATT
Found at i:167421 original size:2 final size:2
Alignment explanation
Indices: 167414--167438 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
167404 AAAATGACCT
167414 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
167439 TATCTTGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:168555 original size:51 final size:52
Alignment explanation
Indices: 168430--168560 Score: 230
Period size: 52 Copynumber: 2.6 Consensus size: 52
168420 TCTACTTAAA
168430 AATTATTTTTGAAGTAGTGCAGGCTGTTGGAAATAGTGAATGTCATATCCAT
1 AATTATTTTTGAAGTAGTGCAGGCTGTTGGAAATAGTGAATGTCATATCCAT
*
168482 AATTATTTTTGAAGTAGTGCAGGCTGTTGGGAATAGTGAATGTCATAT-CAT
1 AATTATTTTTGAAGTAGTGCAGGCTGTTGGAAATAGTGAATGTCATATCCAT
*
168533 AATTATTGTTGAAGTAGTGCAGGC-GTTG
1 AATTATTTTTGAAGTAGTGCAGGCTGTTG
168561 AAGCCCTTTA
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
50 4 0.05
51 26 0.34
52 47 0.61
ACGTcount: A:0.29, C:0.08, G:0.26, T:0.37
Consensus pattern (52 bp):
AATTATTTTTGAAGTAGTGCAGGCTGTTGGAAATAGTGAATGTCATATCCAT
Found at i:176912 original size:32 final size:31
Alignment explanation
Indices: 176831--176912 Score: 74
Period size: 37 Copynumber: 2.4 Consensus size: 31
176821 ATAATATTAC
176831 AAATTATAAAATATGTATATATTTTCTTTAAA
1 AAATTA-AAAATATGTATATATTTTCTTTAAA
* * *
176863 AAATTAAATTCATAATATTTATATAATTTTTTTTATA
1 AAATT-AA---A-AATATGTATAT-ATTTTCTTTAAA
176900 AAATTAAAAATAT
1 AAATTAAAAATAT
176913 AAAAAAGGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
32 11 0.27
33 2 0.05
35 1 0.02
36 12 0.29
37 15 0.37
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (31 bp):
AAATTAAAAATATGTATATATTTTCTTTAAA
Found at i:177398 original size:19 final size:20
Alignment explanation
Indices: 177376--177416 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
177366 TTGTGCTCCA
177376 TTTTTTATTTTACTT-TTGG
1 TTTTTTATTTTACTTGTTGG
* *
177395 TTTTTTCTTTTCCTTGTTGG
1 TTTTTTATTTTACTTGTTGG
177415 TT
1 TT
177417 CCAACTTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.05, C:0.10, G:0.12, T:0.73
Consensus pattern (20 bp):
TTTTTTATTTTACTTGTTGG
Found at i:178896 original size:57 final size:58
Alignment explanation
Indices: 178816--178932 Score: 173
Period size: 57 Copynumber: 2.0 Consensus size: 58
178806 GTTTGAAGAT
* * * *
178816 TGATATAAAATGTTTTAAGGTTTAAGGGTCATTTTAGAAT-GGTCATAGTTTGGGGAC
1 TGATATAAAATGTTTTAAAGTTTAAGGATCAATTTAGAATAGGTCATAGATTGGGGAC
*
178873 TGATATAAAATGTTTTAAAGTTTAAGTATCAATTTAGAATAGGGTCATAGATTGGGGAC
1 TGATATAAAATGTTTTAAAGTTTAAGGATCAATTTAGAATA-GGTCATAGATTGGGGAC
178932 T
1 T
178933 TTTATAGAAC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
57 36 0.68
59 17 0.32
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (58 bp):
TGATATAAAATGTTTTAAAGTTTAAGGATCAATTTAGAATAGGTCATAGATTGGGGAC
Found at i:180212 original size:49 final size:49
Alignment explanation
Indices: 180140--180278 Score: 192
Period size: 49 Copynumber: 2.9 Consensus size: 49
180130 ACATACCCAC
* *
180140 TTAGCATCTGATCATCTACATTGTTTCCCTGACCATTGCGGAATCCATT
1 TTAGCATCTGATGATCTACATTGTTTCCCTGACCATTGCAGAATCCATT
* *
180189 TTAGCATCTGATGATCTACATTGTTTTCC-GTACCATTGCAGATTCCATT
1 TTAGCATCTGATGATCTACATTGTTTCCCTG-ACCATTGCAGAATCCATT
* * *
180238 TTAGCATCTGCTGTTCTACATTATTTCCCTG-CCATTGCAGA
1 TTAGCATCTGATGATCTACATTGTTTCCCTGACCATTGCAGA
180279 TTCTATTTGC
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
48 11 0.14
49 68 0.85
50 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (49 bp):
TTAGCATCTGATGATCTACATTGTTTCCCTGACCATTGCAGAATCCATT
Found at i:183703 original size:22 final size:22
Alignment explanation
Indices: 183661--183704 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
183651 TCGTTGAATT
* *
183661 CCAAGAGAAGCAATGTTTTCAG
1 CCAAGAAAAGCAAGGTTTTCAG
183683 CCAAGAAAAG-AAGGTTGTTCAG
1 CCAAGAAAAGCAAGGTT-TTCAG
183705 ATGGCAGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (22 bp):
CCAAGAAAAGCAAGGTTTTCAG
Found at i:184312 original size:2 final size:2
Alignment explanation
Indices: 184305--184331 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
184295 TTGTAGTTTG
184305 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
184332 AACATTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:184808 original size:3 final size:3
Alignment explanation
Indices: 184800--184833 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
184790 TGCACGGATG
*
184800 TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
184834 CGATGGTGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:193440 original size:6 final size:6
Alignment explanation
Indices: 193431--193458 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
193421 TCCGACCACG
193431 ACCATT ACCATT ACCATT ACCATT ACCA
1 ACCATT ACCATT ACCATT ACCATT ACCA
193459 CGACCACGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (6 bp):
ACCATT
Found at i:193464 original size:18 final size:18
Alignment explanation
Indices: 193423--193469 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
193413 TTTCCAGATC
193423 CGACCACGACCATTACCA
1 CGACCACGACCATTACCA
** **
193441 TTACCATTACCATTACCA
1 CGACCACGACCATTACCA
193459 CGACCACGACC
1 CGACCACGACC
193470 CCGACCCGAG
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.32, C:0.43, G:0.09, T:0.17
Consensus pattern (18 bp):
CGACCACGACCATTACCA
Found at i:193998 original size:6 final size:6
Alignment explanation
Indices: 193988--194040 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
193978 TCTCGTCTCG
* ** **
193988 GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT GGTAAT GGTAAT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
194036 GGTCG
1 GGTCG
194041 GATCTGGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.08, C:0.13, G:0.49, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:203775 original size:228 final size:230
Alignment explanation
Indices: 203309--203721 Score: 645
Period size: 230 Copynumber: 1.8 Consensus size: 230
203299 ATTCATATAT
* * * *
203309 TCGGGTCGGGTCGGGTTGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCGAATATATAT
1 TCGGGTCGCGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAATATAT
* *
203374 ATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCTTTTATATATAATTTTTTTCAA
66 ATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCCTTCTATATATAA-TTTTTTCAA
**
203439 TTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTTATTATTTCGGGTTGGGTGAAACTTTAT
130 TTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTTATTATTTCGGGTCAGGTGAAACTTTAT
*** *
203504 TTTGATCGGGTCGGGTCGTTTTTTTTAGTGTGATAT
195 TTTGATCGGGTCGGGTCGTAAATTTTAGTGTGATAG
*
203540 TCGGGTCGCGTC-GGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAATATAT
1 TCGGGTCGCGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAATATAT
203604 ATAATTTTACCTTATATATTTAGAAATAATTACAATAATA-CCTCTCTATATATAA-TTTTTCAA
66 ATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCCT-TCTATATATAATTTTTTCAA
*
203667 TTAAGTCACTGTTTTTATTGAATAAAAATGTTTTTTTT-TTATTTCGGGGTCAGGT
130 TTAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTTATTATTTC-GGGTCAGGT
203722 CGGGTTTCTA
Statistics
Matches: 170, Mismatches: 10, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
227 7 0.04
228 52 0.31
229 3 0.02
230 97 0.57
231 11 0.06
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (230 bp):
TCGGGTCGCGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGACCCAAAAATATAT
ATAATTTTACCTTATATATTTAGAAATAATTACAATAATACCCTTCTATATATAATTTTTTCAAT
TAAGTCACTGTTTTTATTGAATAAAAATATTTTTTTTATTATTTCGGGTCAGGTGAAACTTTATT
TTGATCGGGTCGGGTCGTAAATTTTAGTGTGATAG
Found at i:205290 original size:161 final size:160
Alignment explanation
Indices: 205018--205324 Score: 546
Period size: 161 Copynumber: 1.9 Consensus size: 160
205008 GTCAATTCTT
205018 TGTTTTTCTTTGCTGTTATGTCAGAAAAGTATTCCCTTCATCCAAACCCACCACCACGGCTGCTC
1 TGTTTTTCTTTGCTGTTATGTCAGAAAAGTATTCCCTTCATCCAAACCCACCACCACGGCTGCTC
**
205083 CACCGGCCGCCAATGGAGCTCCAGCCAGTACGAACGGTACAACCAACGGTGGCGCAACAAAATCC
66 CACCGGCCGCCAATGGAGAGCCAGCCAGTACGAACGGTACAACCAACGGTGGCGCAACAAAATCC
205148 CACC-TTACAATCCGAGTCAATTCTTTGTG
131 CACCTTTACAATCCGAGTCAATTCTTTGTG
205177 TGTTTTTCTTTGCTGTTAATGTCAGAAAAAGTATTCCCTTCATCC-AACCCACCACCACGGCTGC
1 TGTTTTTCTTTGCTGTT-ATGTCAG-AAAAGTATTCCCTTCATCCAAACCCACCACCACGGCTGC
*
205241 TCCACCGGCCGCCAATGGTGGAGCCAGCCAGTACGAACGGTACAACCAACGGTGGCGCAACAAAA
64 TCCACCGGCCGCCAATGG-AGAGCCAGCCAGTACGAACGGTACAACCAACGGTGGCGCAACAAAA
205306 TCCCACCTTTACAATCCGA
128 TCCCACCTTTACAATCCGA
205325 CTTCTCGCCC
Statistics
Matches: 141, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
159 17 0.12
160 44 0.31
161 69 0.49
162 11 0.08
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (160 bp):
TGTTTTTCTTTGCTGTTATGTCAGAAAAGTATTCCCTTCATCCAAACCCACCACCACGGCTGCTC
CACCGGCCGCCAATGGAGAGCCAGCCAGTACGAACGGTACAACCAACGGTGGCGCAACAAAATCC
CACCTTTACAATCCGAGTCAATTCTTTGTG
Found at i:218958 original size:2 final size:2
Alignment explanation
Indices: 218946--218976 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
218936 AATAATATTG
218946 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
218977 TAATGCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.