Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000971.1 Hibiscus syriacus cultivar Beakdansim tig00001940_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: 53705
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:3114 original size:19 final size:19
Alignment explanation
Indices: 3076--3114 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3066 ACAAACAAAA
* *
3076 TAAATAAAAAGTTCATAAT
1 TAAATAAAAACTTCACAAT
*
3095 TAAATAAAAACTTTACAAT
1 TAAATAAAAACTTCACAAT
3114 T
1 T
3115 GCTGGTAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.33
Consensus pattern (19 bp):
TAAATAAAAACTTCACAAT
Found at i:5342 original size:29 final size:29
Alignment explanation
Indices: 5267--5342 Score: 66
Period size: 29 Copynumber: 2.5 Consensus size: 29
5257 CTACAAAAAG
5267 TAATAAAAATATTAGTATAATAAAATTTAATA
1 TAATAAAAATATT--T-TAATAAAATTTAATA
* * *
5299 AAATAATACAT-TTTTAA-ATAATTATAATA
1 TAATAA-AAATATTTTAATAAAATT-TAATA
5328 TAATAAAAATATTTT
1 TAATAAAAATATTTT
5343 GCCTTATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
28 8 0.22
29 17 0.47
30 1 0.03
32 7 0.19
33 3 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (29 bp):
TAATAAAAATATTTTAATAAAATTTAATA
Found at i:12174 original size:16 final size:16
Alignment explanation
Indices: 12148--12180 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
12138 TTAATTTTTT
12148 AAAAATATAAAAATAAA
1 AAAAATAT-AAAATAAA
12165 AAAAAT-TAAAATAAA
1 AAAAATATAAAATAAA
12180 A
1 A
12181 TTTTAATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.56
16 1 0.06
17 6 0.38
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAAATATAAAATAAA
Found at i:13762 original size:17 final size:17
Alignment explanation
Indices: 13722--13763 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
13712 AAAAACAACA
13722 TAAAAAT-ATTTAATAT
1 TAAAAATAATTTAATAT
** *
13738 TATTAATAATTTAATTT
1 TAAAAATAATTTAATAT
13755 TAAAAATAA
1 TAAAAATAA
13764 AAAATTTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAAAATAATTTAATAT
Found at i:14849 original size:18 final size:18
Alignment explanation
Indices: 14826--14867 Score: 70
Period size: 16 Copynumber: 2.4 Consensus size: 18
14816 GATTATCAGT
14826 GGGAATAAAGGATTACCA
1 GGGAATAAAGGATTACCA
14844 GGGAAT--AGGATTACCA
1 GGGAATAAAGGATTACCA
14860 GGGAATAA
1 GGGAATAA
14868 GATTACTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 16 0.73
18 6 0.27
ACGTcount: A:0.43, C:0.10, G:0.31, T:0.17
Consensus pattern (18 bp):
GGGAATAAAGGATTACCA
Found at i:14855 original size:16 final size:16
Alignment explanation
Indices: 14834--14873 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
14824 GTGGGAATAA
14834 AGGATTACCAGGGAAT
1 AGGATTACCAGGGAAT
14850 AGGATTACCAGGGAAT
1 AGGATTACCAGGGAAT
*
14866 AAGATTAC
1 AGGATTAC
14874 TGGGAATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.28, T:0.20
Consensus pattern (16 bp):
AGGATTACCAGGGAAT
Found at i:17378 original size:39 final size:39
Alignment explanation
Indices: 17324--17403 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
17314 AAGTATCCCA
17324 CATTATTTATGAGATAAAAAATCATAAGAGAAATGTTAT
1 CATTATTTATGAGATAAAAAATCATAAGAGAAATGTTAT
17363 CATTATTTATGAGATAAAAAATCATAAGAGAAATGTTAT
1 CATTATTTATGAGATAAAAAATCATAAGAGAAATGTTAT
17402 CA
1 CA
17404 AACTTAAAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (39 bp):
CATTATTTATGAGATAAAAAATCATAAGAGAAATGTTAT
Found at i:19421 original size:10 final size:12
Alignment explanation
Indices: 19404--19435 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
19394 GTTTTAATAG
19404 CTGGTCAAAG-T
1 CTGGTCAAAGTT
19415 C-GGTCAAAGTT
1 CTGGTCAAAGTT
19426 CTGGTCAAAG
1 CTGGTCAAAG
19436 GAGGTCAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.42
11 3 0.16
12 8 0.42
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (12 bp):
CTGGTCAAAGTT
Found at i:19556 original size:28 final size:29
Alignment explanation
Indices: 19489--19590 Score: 134
Period size: 29 Copynumber: 3.6 Consensus size: 29
19479 TTTAAAATAA
**
19489 TTACCAGAATAGCACCAAAACCAAATTAT
1 TTACCAGAATAGCACCAAAACTGAATTAT
** *
19518 TTATTAAAATAGCACCAAAA-TGAATTAT
1 TTACCAGAATAGCACCAAAACTGAATTAT
*
19546 TTACCAGAATAGCACTAAAACTGAATTAT
1 TTACCAGAATAGCACCAAAACTGAATTAT
*
19575 TTACTAGAATAGCACC
1 TTACCAGAATAGCACC
19591 GGTCAACGGG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
28 22 0.36
29 39 0.64
ACGTcount: A:0.46, C:0.19, G:0.09, T:0.26
Consensus pattern (29 bp):
TTACCAGAATAGCACCAAAACTGAATTAT
Found at i:19612 original size:13 final size:13
Alignment explanation
Indices: 19594--19618 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19584 TAGCACCGGT
19594 CAACGGGTCGGGC
1 CAACGGGTCGGGC
19607 CAACGGGTCGGG
1 CAACGGGTCGGG
19619 TCGGGTCAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.28, G:0.48, T:0.08
Consensus pattern (13 bp):
CAACGGGTCGGGC
Found at i:19620 original size:18 final size:18
Alignment explanation
Indices: 19597--19639 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
19587 CACCGGTCAA
19597 CGGGTCGGGCCAACGGGT
1 CGGGTCGGGCCAACGGGT
* *
19615 CGGGTCGGGTCAACGGTT
1 CGGGTCGGGCCAACGGGT
19633 CGGGTCG
1 CGGGTCG
19640 TGACCGGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.09, C:0.26, G:0.49, T:0.16
Consensus pattern (18 bp):
CGGGTCGGGCCAACGGGT
Found at i:26836 original size:28 final size:29
Alignment explanation
Indices: 26769--26870 Score: 134
Period size: 29 Copynumber: 3.6 Consensus size: 29
26759 TTTAAAATAA
*
26769 TTACCAGAATAGCACCAAAACCAAATTAT
1 TTACCAGAATAGCACCAAAACTAAATTAT
** * *
26798 TTATTAAAATAGCACCAAAA-TGAATTAT
1 TTACCAGAATAGCACCAAAACTAAATTAT
*
26826 TTACCAGAATAGCACTAAAACTAAATTAT
1 TTACCAGAATAGCACCAAAACTAAATTAT
*
26855 TTACTAGAATAGCACC
1 TTACCAGAATAGCACC
26871 GATCAACGGG
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 22 0.37
29 38 0.63
ACGTcount: A:0.47, C:0.19, G:0.08, T:0.26
Consensus pattern (29 bp):
TTACCAGAATAGCACCAAAACTAAATTAT
Found at i:26900 original size:18 final size:18
Alignment explanation
Indices: 26877--26919 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
26867 CACCGATCAA
26877 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
26895 CGGGTCAGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
26913 CGGGTCG
1 CGGGTCG
26920 TGACCGGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.12, C:0.23, G:0.49, T:0.16
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:26918 original size:13 final size:13
Alignment explanation
Indices: 26873--26901 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
26863 ATAGCACCGA
26873 TCAACGGGTCGGG
1 TCAACGGGTCGGG
26886 TCAACGGGTCGGG
1 TCAACGGGTCGGG
26899 TCA
1 TCA
26902 GGTCAACGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (13 bp):
TCAACGGGTCGGG
Found at i:28322 original size:14 final size:15
Alignment explanation
Indices: 28285--28322 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
28275 ATGGAGTCTC
*
28285 TAATTATTAACCTAAT
1 TAATT-TTAACCAAAT
28301 TAATTTTAACCAAAT
1 TAATTTTAACCAAAT
28316 T-ATTTTA
1 TAATTTTA
28323 TTCGAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 6 0.29
15 10 0.48
16 5 0.24
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (15 bp):
TAATTTTAACCAAAT
Found at i:28361 original size:142 final size:138
Alignment explanation
Indices: 28124--28586 Score: 524
Period size: 139 Copynumber: 3.3 Consensus size: 138
28114 GAACTAAGAG
* * * * * ** *
28124 ATTAAACCTAAAATGTAGGCTCT-A-TATTAATTCAAGTCATTTTTAATGAATTATTGAATT-GA
1 ATTAAA-CTAAAATGGAGGCTCTAATTATTAA-CCTATTCAATTTTAACCAATTATTTAATTCGA
* * * * * *
28186 ATAATAAAAATGGAACCTCGAGCATAAGCGAGGACCAAATCAAAAATTCTCCTAAATTTAAAAGA
64 ATAATTAAAATGGAACCTCGAGCAAAAGTGAGGACCAAATTAAAAATTCACCTAAATTT-AAGGA
*
28251 CT-AGTTATGAA
128 TTAAGTT-TGAA
* *
28262 ATTAAACCTAAAAATGGAGTCTCTAATTATTAACCTAATT-AATTTTAACCAAATTATTTTATTC
1 ATTAAA-CT-AAAATGGAGGCTCTAATTATTAACCT-ATTCAATTTTAACC-AATTATTTAATTC
* *
28326 GAATAATTAAAATGGAACCTCGAGAAAAAGTGAGGACCAAATTAAAAATGT-AACTAAATTTAAG
62 GAATAATTAAAATGGAACCTCGAGCAAAAGTGAGGACCAAATTAAAAAT-TCACCTAAATTTAAG
28390 GATTAAGTTTGAA
126 GATTAAGTTTGAA
* * *
28403 ATTAATTCTAAAATGAAGGCTCTAATTATTAACCTATTCAATTTTAACCAATTATTTAATTCAAA
1 ATTAA-ACTAAAATGGAGGCTCTAATTATTAACCTATTCAATTTTAACCAATTATTTAATTCGAA
* * * *
28468 TAATTAAAATGGAACATCAAGCAAAAGTGAGGATCAAATTAAATATTCACCTAAATTTAAGGATT
65 TAATTAAAATGGAACCTCGAGCAAAAGTGAGGACCAAATTAAAAATTCACCTAAATTTAAGGATT
28533 AAGTTTGAA
130 AAGTTTGAA
* * *
28542 ATTAATACTAAAATGGAGGCTCTAATTACTGACCTAGTCAATTTT
1 ATTAA-ACTAAAATGGAGGCTCTAATTATTAACCTATTCAATTTT
28587 GATCAAGTTT
Statistics
Matches: 279, Mismatches: 35, Indels: 21
0.83 0.10 0.06
Matches are distributed among these distances:
138 10 0.04
139 135 0.48
140 43 0.15
141 34 0.12
142 56 0.20
143 1 0.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (138 bp):
ATTAAACTAAAATGGAGGCTCTAATTATTAACCTATTCAATTTTAACCAATTATTTAATTCGAAT
AATTAAAATGGAACCTCGAGCAAAAGTGAGGACCAAATTAAAAATTCACCTAAATTTAAGGATTA
AGTTTGAA
Found at i:28499 original size:139 final size:140
Alignment explanation
Indices: 28172--28586 Score: 536
Period size: 139 Copynumber: 3.0 Consensus size: 140
28162 ATTTTTAATG
* * * * * *
28172 AATTATTGAATT-GAATAATAAAAATGGAACCTCGAGCATAAGCGAGGACCAAATCAAAAATTCT
1 AATTATTTAATTCGAATAATTAAAATGGAACCTCGAGCAAAAGTGAGGACCAAATTAAAAATTCA
* * *
28236 CCTAAATTTAAAAGACT-AGTTATGAAATTAA-ACCTAAAAATGGAGTCTCTAATTATTAACCTA
66 CCTAAATTT-AAGGATTAAGTT-TGAAATTAATA-CT-AAAATGGAGGCTCTAATTATTAACCT-
28299 ATT-AATTTTAACCA
126 ATTCAATTTTAACCA
* *
28313 AATTATTTTATTCGAATAATTAAAATGGAACCTCGAGAAAAAGTGAGGACCAAATTAAAAATGT-
1 AATTATTTAATTCGAATAATTAAAATGGAACCTCGAGCAAAAGTGAGGACCAAATTAAAAAT-TC
* * *
28377 AACTAAATTTAAGGATTAAGTTTGAAATTAATTCTAAAATGAAGGCTCTAATTATTAACCTATTC
65 ACCTAAATTTAAGGATTAAGTTTGAAATTAATACTAAAATGGAGGCTCTAATTATTAACCTATTC
28442 AATTTTAACC-
130 AATTTTAACCA
* * * * *
28452 AATTATTTAATTCAAATAATTAAAATGGAACATCAAGCAAAAGTGAGGATCAAATTAAATATTCA
1 AATTATTTAATTCGAATAATTAAAATGGAACCTCGAGCAAAAGTGAGGACCAAATTAAAAATTCA
* * *
28517 CCTAAATTTAAGGATTAAGTTTGAAATTAATACTAAAATGGAGGCTCTAATTACTGACCTAGTCA
66 CCTAAATTTAAGGATTAAGTTTGAAATTAATACTAAAATGGAGGCTCTAATTATTAACCTATTCA
28582 ATTTT
131 ATTTT
28587 GATCAAGTTT
Statistics
Matches: 241, Mismatches: 27, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
138 1 0.00
139 123 0.51
140 34 0.14
141 26 0.11
142 56 0.23
143 1 0.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (140 bp):
AATTATTTAATTCGAATAATTAAAATGGAACCTCGAGCAAAAGTGAGGACCAAATTAAAAATTCA
CCTAAATTTAAGGATTAAGTTTGAAATTAATACTAAAATGGAGGCTCTAATTATTAACCTATTCA
ATTTTAACCA
Found at i:28829 original size:26 final size:27
Alignment explanation
Indices: 28782--28838 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
28772 AAAAATGACT
* *
28782 AAATTGAAACAATGAAAAAAAGAATTA
1 AAATTAAAACAATGAAAAAAAGAACTA
* * *
28809 AAATTAAAAC-ATTAAATAAAGGACTA
1 AAATTAAAACAATGAAAAAAAGAACTA
28835 AAAT
1 AAAT
28839 GAAAGAAATC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.65, C:0.05, G:0.09, T:0.21
Consensus pattern (27 bp):
AAATTAAAACAATGAAAAAAAGAACTA
Found at i:29052 original size:113 final size:113
Alignment explanation
Indices: 28844--29052 Score: 328
Period size: 113 Copynumber: 1.8 Consensus size: 113
28834 AAAATGAAAG
* * *
28844 AAATCAGAATATAAAGATTAAATTAAAACAATTCAGAAAATTAAAAGCTAAAGTTTAAAGGACTG
1 AAATCAGAATATAAAGATTAAATTAAAACAATGCAGAAAATTAAAAGCTAAAATTTAAAGGACTA
** * *
28909 AAATATAAATGCTGAAATTTAAAGATCAAAACTGTAAATAACAAAAAT
66 AAATATAAACACTGAAATTAAAAGAACAAAACTGTAAATAACAAAAAT
*
28957 AAATCAGAATATAAAGATTAAATTAAAACAATGCAGAAAATTAAATGCTAAAATTTAAAGGACTA
1 AAATCAGAATATAAAGATTAAATTAAAACAATGCAGAAAATTAAAAGCTAAAATTTAAAGGACTA
* *
29022 AAATATAGACACTGAAATTAAAATAACAAAA
66 AAATATAAACACTGAAATTAAAAGAACAAAA
29053 ATTTAAAGGG
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
113 86 1.00
ACGTcount: A:0.58, C:0.08, G:0.10, T:0.24
Consensus pattern (113 bp):
AAATCAGAATATAAAGATTAAATTAAAACAATGCAGAAAATTAAAAGCTAAAATTTAAAGGACTA
AAATATAAACACTGAAATTAAAAGAACAAAACTGTAAATAACAAAAAT
Found at i:29223 original size:22 final size:21
Alignment explanation
Indices: 29198--29238 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
29188 ATATTTTCTT
*
29198 TTAGAAATTAGTAAGTTAGTGG
1 TTAGAAATTAG-AAATTAGTGG
*
29220 TTAGAAGTTAGAAATTAGT
1 TTAGAAATTAGAAATTAGT
29239 AAAATGTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (21 bp):
TTAGAAATTAGAAATTAGTGG
Found at i:29369 original size:28 final size:28
Alignment explanation
Indices: 29334--29400 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
29324 AACTAGAGCA
*
29334 ATAATAAATTAAAA-ACAATGACTAAAGT
1 ATAATAAAATAAAACACAATG-CTAAAGT
*
29362 ATAATAAAATAAAACACAATGCTAAATT
1 ATAATAAAATAAAACACAATGCTAAAGT
29390 A-AAGTAAAATA
1 ATAA-TAAAATA
29401 GCATGAATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 27 0.77
29 6 0.17
ACGTcount: A:0.63, C:0.07, G:0.06, T:0.24
Consensus pattern (28 bp):
ATAATAAAATAAAACACAATGCTAAAGT
Found at i:30280 original size:3 final size:3
Alignment explanation
Indices: 30272--30311 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
30262 TTTTTTAAAA
30272 TAT TAT TATT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
30312 AATTTTTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:31294 original size:20 final size:21
Alignment explanation
Indices: 31271--31310 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
31261 ATATCTTTGT
31271 ATTTAATAGTA-ATTTTCAAC
1 ATTTAATAGTATATTTTCAAC
* *
31291 ATTTACTCGTATATTTTCAA
1 ATTTAATAGTATATTTTCAA
31311 GTTTCTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.47
Consensus pattern (21 bp):
ATTTAATAGTATATTTTCAAC
Found at i:35743 original size:20 final size:21
Alignment explanation
Indices: 35720--35765 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
35710 AAAAACACAC
35720 AAAAAGAAAGA-AAAAAAAAA
1 AAAAAGAAAGATAAAAAAAAA
*
35740 AAAAAGAAAGATAAAAAATAA
1 AAAAAGAAAGATAAAAAAAAA
35761 AAAAA
1 AAAAA
35766 CGCTGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.87, C:0.00, G:0.09, T:0.04
Consensus pattern (21 bp):
AAAAAGAAAGATAAAAAAAAA
Found at i:35745 original size:16 final size:18
Alignment explanation
Indices: 35720--35763 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 18
35710 AAAAACACAC
*
35720 AAAAAGAAAGAAA-A-AA
1 AAAAAAAAAGAAAGATAA
35736 AAAAAAAAAGAAAGATAA
1 AAAAAAAAAGAAAGATAA
35754 AAAATAAAAA
1 AAAA-AAAAA
35764 AACGCTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 12 0.50
17 1 0.04
18 6 0.25
19 5 0.21
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.05
Consensus pattern (18 bp):
AAAAAAAAAGAAAGATAA
Found at i:35792 original size:51 final size:52
Alignment explanation
Indices: 35736--35846 Score: 127
Period size: 51 Copynumber: 2.1 Consensus size: 52
35726 AAAGAAAAAA
* * ** *
35736 AAAAAAAAAGAAAGATAAAAAATAAAAAAAC-GCTGAAAAAAGAGAAA-AAGGG
1 AAAAAAATAG-AAGATAAA-AAGAAAAAAACAGAAGAAAAAAGAGAAAGAAGAG
* *
35788 AAAAAAATAGAAGATATAAAGAAAAAAACAGAAGAAAAAAGTGAAAGAAGAG
1 AAAAAAATAGAAGATAAAAAGAAAAAAACAGAAGAAAAAAGAGAAAGAAGAG
35840 AAAAAAA
1 AAAAAAA
35847 GAGAGAGAGA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
50 10 0.20
51 20 0.40
52 20 0.40
ACGTcount: A:0.74, C:0.03, G:0.17, T:0.06
Consensus pattern (52 bp):
AAAAAAATAGAAGATAAAAAGAAAAAAACAGAAGAAAAAAGAGAAAGAAGAG
Found at i:35838 original size:16 final size:14
Alignment explanation
Indices: 35806--35874 Score: 50
Period size: 16 Copynumber: 4.5 Consensus size: 14
35796 AGAAGATATA
*
35806 AAGAAAAAA-ACAG
1 AAGAAAAAAGAAAG
35819 AAGAAAAAAGTGAAAG
1 AAGAAAAAA--GAAAG
*
35835 AAGAGAAAAAAAGAGAG
1 -A-AG-AAAAAAGAAAG
35852 AGAGAAAGAAAGAAAG
1 A-AGAAA-AAAGAAAG
35868 AAGAAAA
1 AAGAAAA
35875 TAGACAGATC
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
13 9 0.20
14 1 0.02
15 8 0.17
16 15 0.33
17 5 0.11
18 2 0.04
19 6 0.13
ACGTcount: A:0.72, C:0.01, G:0.25, T:0.01
Consensus pattern (14 bp):
AAGAAAAAAGAAAG
Found at i:35846 original size:33 final size:33
Alignment explanation
Indices: 35809--35871 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
35799 AGATATAAAG
35809 AAAAAAACAGA-AGAAA-AAAGTGAAAGAAGAGAA
1 AAAAAAACAGAGAGAAAGAAA--GAAAGAAGAGAA
* *
35842 AAAAAGAGAGAGAGAAAGAAAGAAAGAAGA
1 AAAAAAACAGAGAGAAAGAAAGAAAGAAGA
35872 AAATAGACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
33 18 0.69
34 5 0.19
35 3 0.12
ACGTcount: A:0.71, C:0.02, G:0.25, T:0.02
Consensus pattern (33 bp):
AAAAAAACAGAGAGAAAGAAAGAAAGAAGAGAA
Found at i:35860 original size:51 final size:49
Alignment explanation
Indices: 35770--35874 Score: 122
Period size: 51 Copynumber: 2.1 Consensus size: 49
35760 AAAAAACGCT
* * * *
35770 GAAAAAAGAGAAAAAGGGAAAAAAATAGAAGATATAAAGAAAAAAACAGAA
1 GAAAAAAGAGAAAAAGAGAAAAAAAGAGAAGAGAGAAAG-AAAAAA-AGAA
* *
35821 GAAAAAAGTGAAAGAAGAGAAAAAAAGAG-AGAGAGAAAGAAAGAAAGAA
1 GAAAAAAGAGAAA-AAGAGAAAAAAAGAGAAGAGAGAAAGAAAAAAAGAA
35870 GAAAA
1 GAAAA
35875 TAGACAGATC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
49 9 0.19
50 5 0.11
51 20 0.43
52 13 0.28
ACGTcount: A:0.71, C:0.01, G:0.24, T:0.04
Consensus pattern (49 bp):
GAAAAAAGAGAAAAAGAGAAAAAAAGAGAAGAGAGAAAGAAAAAAAGAA
Found at i:38601 original size:36 final size:36
Alignment explanation
Indices: 38552--38688 Score: 145
Period size: 36 Copynumber: 3.8 Consensus size: 36
38542 TTTAAACTTC
*
38552 GTCTCGCTTGAGACAGTTTCTCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTT
* * *
38588 GTCTCTCTCGAGACAGTTTCCCTTGAAACAAGTTTT
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTT
* * *
38624 GTTTCCCTTGAGACA-TTTTTCTT-AAA-AACATTTTT
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACAA-A-TTTT
* * *
38659 GTCTCTCTTTAGATAGTTTCTCTTGGAACA
1 GTCTCTCTTGAGACAGTTTCTCTTGAAACA
38689 CAAAATCTTT
Statistics
Matches: 80, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
33 2 0.03
34 3 0.04
35 21 0.26
36 51 0.64
37 2 0.03
38 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (36 bp):
GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTT
Found at i:38739 original size:138 final size:140
Alignment explanation
Indices: 38567--38822 Score: 342
Period size: 138 Copynumber: 1.8 Consensus size: 140
38557 GCTTGAGACA
* * *
38567 GTTTCTCTTGAAACAAATTTTGTCTCTCTCGAGACAGTTTCCCTT-GAAAC-AAGTTTTGTTTCC
1 GTTTCTCTTGAAACAAATTTTGTCTCCCTCGAGACAATTT-CCTTGGAAACAAAGTTTTGTCT-C
** * * *
38630 CTT-GAGACA-TTTTTCTTAAAAACAT-TTTTGTCTCTCTTTAGATAGTTTCTCTTGGAACACAA
64 CTTAGAGACAGTTTCCCTT-AAAACATGTTTTATCTCACTTGAGATAGTTTCTCTTGGAACACAA
38692 AATCTTTGAATAT
128 AATCTTTGAATAT
* * *
38705 GTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTTTGGAAACAAAGTTTTGTCTCTT
1 GTTTCTCTTGAAACAAATTTTGTCTCCCTCGAGACAATTTCCTTGGAAACAAAGTTTTGTCTCCT
*
38770 TAGAGACAGTTTCCCTTGAAACATGTTTTATCTCACTTGAGATAGTTTCTCTT
66 TAGAGACAGTTTCCCTTAAAACATGTTTTATCTCACTTGAGATAGTTTCTCTT
38823 CAAACAAATT
Statistics
Matches: 101, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
137 3 0.03
138 45 0.45
139 22 0.22
140 31 0.31
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (140 bp):
GTTTCTCTTGAAACAAATTTTGTCTCCCTCGAGACAATTTCCTTGGAAACAAAGTTTTGTCTCCT
TAGAGACAGTTTCCCTTAAAACATGTTTTATCTCACTTGAGATAGTTTCTCTTGGAACACAAAAT
CTTTGAATAT
Found at i:39580 original size:139 final size:138
Alignment explanation
Indices: 39100--39960 Score: 851
Period size: 139 Copynumber: 6.3 Consensus size: 138
39090 AATAAATCAG
* * * * *
39100 TCAATATTTCCAGTAGAGAGTTCATAATGAGAAAAACTCATCCGAT-GAGGGAGAAGAAGTTCAT
1 TCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCAT
* * * * *
39164 AATGAGAAGAACTTGTTTAACCTTAGCTCGATTCATCACATATGGAGTTGAATTATCAACACCTC
66 AATGAGAAGAGCTTGTTCAACCTTTGCTCGATTCATCACATAT--AGTTGAATCAGCAACACCTC
*
39229 ACTTGAGGGA
129 ACTCGAGGGA
* *
39239 TCAACATTTCTAA-TGGAAAGTTCATAATGAGAATAACTCATCCGATAAAGGGAGAAGAAGTTCA
1 TCAACATTTC-AAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCA
* ** * * * ** **
39303 TAATGAGAAGAGCTTGTTCGACCTATCACTTGAAATCAT-A-ATAT-TTTGAATCAGTGATGCCT
65 TAATGAGAAGAGCTTGTTCAACCT-TTGCTCG-ATTCATCACATATAGTTGAATCAGCAACACCT
* *
39365 CGCTTGAGGGA
128 CACTCGAGGGA
* * * *
39376 TCAACA-TTAAAATGGAGAGTTCATAATGAAAAGAACTCATCCGACAAAGGGAGAAGAAGTTCAT
1 TCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCAT
* * *
39440 AATGAGAAGAGCTTGTTCAACCTTTGCTCAATTAATCAGATATGGAGTTGAATCAGCAACACCTC
66 AATGAGAAGAGCTTGTTCAACCTTTGCTCGATTCATCACATAT--AGTTGAATCAGCAACACCTC
39505 ACTCGAGGGA
129 ACTCGAGGGA
* *
39515 TCAACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGA-AGAGGGAGAAGAAGTTCAT
1 TCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCAT
* * * * * * *
39579 AATGAGAAGAACATGTTCAACCTTAGCTCGATTCATCACATTTGGAGTTGAATCAACCACACCTT
66 AATGAGAAGAGCTTGTTCAACCTTTGCTCGATTCATCACATAT--AGTTGAATCAGCAACACCTC
39644 ACTCGAGGGA
129 ACTCGAGGGA
* * * *
39654 TCAATATTTCCAGTGGAGAGTTCATAATGAGAAAAACTCATCCGATAAAGGGAGAAGTAGTTCAT
1 TCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCAT
** * * ** *
39719 AATGAGAAGAGCTTAATCAACCTATTGCTCGATTCATGACAT-T--TTGAATCAGCGATGCCTCG
66 AATGAGAAGAGCTTGTTCAACCT-TTGCTCGATTCATCACATATAGTTGAATCAGCAACACCTCA
* *
39781 CTTGAGGGG
130 CTCGAGGGA
* * * * **
39790 TTAACACTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCCGA-CGA-GG-G-AGAAGTTCAT
1 TCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCAT
* * ** * *
39851 AATGAGAAGAGGTTGTTCGACCTATCACTCGATTCAT-A-ATACT--TCGAATCATCAACACCTC
66 AATGAGAAGAGCTTGTTCAACCT-TTGCTCGATTCATCACATA-TAGTTGAATCAGCAACACCTC
*
39912 ACTCAAGGGA
129 ACTCGAGGGA
*
39922 TCAACATGTCCAAG-GGAGAAGTTCATAATGAGAAGAACT
1 TCAACAT-TTCAAGTGGAG-AGTTCATAATGAGAAGAACT
39961 TGTTCAACCT
Statistics
Matches: 601, Mismatches: 104, Indels: 40
0.81 0.14 0.05
Matches are distributed among these distances:
130 2 0.00
131 1 0.00
132 68 0.11
133 25 0.04
134 6 0.01
135 7 0.01
136 134 0.22
137 27 0.04
139 192 0.32
140 113 0.19
141 21 0.03
142 5 0.01
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (138 bp):
TCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTCAT
AATGAGAAGAGCTTGTTCAACCTTTGCTCGATTCATCACATATAGTTGAATCAGCAACACCTCAC
TCGAGGGA
Found at i:40025 original size:41 final size:42
Alignment explanation
Indices: 39980--40083 Score: 131
Period size: 41 Copynumber: 2.5 Consensus size: 42
39970 TTAGTGTGTT
*
39980 TCCATCACATAAGGAGTTGGAACAACACCAAC-TTTTGCTCA-
1 TCCATCACATAAGGAGTTGGAACAACACCAACATTTCGCT-AG
* *** *
40021 TCCATCACATAAGGAGTTGGATCAATGTCATCATTTCGCTAG
1 TCCATCACATAAGGAGTTGGAACAACACCAACATTTCGCTAG
40063 TCCATCACATAAGGAGTTGGA
1 TCCATCACATAAGGAGTTGGA
40084 TCAGCATCAC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
41 28 0.51
42 27 0.49
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (42 bp):
TCCATCACATAAGGAGTTGGAACAACACCAACATTTCGCTAG
Found at i:40080 original size:42 final size:41
Alignment explanation
Indices: 39980--40086 Score: 135
Period size: 42 Copynumber: 2.6 Consensus size: 41
39970 TTAGTGTGTT
* *
39980 TCCATCACATAAGGAGTTGGAACAACACCAACTTTTGCTCA
1 TCCATCACATAAGGAGTTGGATCAACACCAACTTTCGCTCA
*** *
40021 TCCATCACATAAGGAGTTGGATCAATGTCATCATTTCGCT-A
1 TCCATCACATAAGGAGTTGGATCAACACCAAC-TTTCGCTCA
40062 GTCCATCACATAAGGAGTTGGATCA
1 -TCCATCACATAAGGAGTTGGATCA
40087 GCATCACCTT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
41 28 0.48
42 30 0.52
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (41 bp):
TCCATCACATAAGGAGTTGGATCAACACCAACTTTCGCTCA
Found at i:40100 original size:16 final size:16
Alignment explanation
Indices: 40079--40109 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40069 ACATAAGGAG
*
40079 TTGGATCAGCATCACC
1 TTGGATCAACATCACC
40095 TTGGATCAACATCAC
1 TTGGATCAACATCAC
40110 TATATCTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (16 bp):
TTGGATCAACATCACC
Found at i:43631 original size:214 final size:214
Alignment explanation
Indices: 43248--44433 Score: 1641
Period size: 214 Copynumber: 5.5 Consensus size: 214
43238 ATCTTGGTGA
* * * * * * *
43248 AAAACATCCTGCTCGAAGGTCTTATGGATGATCCGAAGGATTTATTC-TCTTGCTCGAGAGACTC
1 AAAACATCCTACCCGAAGGTCTTATGGATGACCCGAAGGACTTA-TCATCTTGCTCTAAAGACTT
* * * * **
43312 ACAAATGACTCGAAGGATTTAAGCATCGTGCTTGAAAGACTTACTGATGGCTTGAAGGACTTATA
65 ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATA
* * * * * *
43377 AATTGTGAAATTTTGAAAATTGCATTCTTAGTTTTCAAAAATTTCATCTTTTTAAAATATCATTT
130 AATTGTGAAATTTTGAAAATCGAATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTT
43442 TTCATTTTCAAATTCATGTG
195 TTCATTTTCAAATTCATGTG
* * * * * * * *
43462 AAAAAATCCTACCGGAAGGTCTTATAGATGATCCGAAGGATTTATTC-TCTTGCTCGAGAGACTC
1 AAAACATCCTACCCGAAGGTCTTATGGATGACCCGAAGGACTTA-TCATCTTGCTCTAAAGACTT
* *
43526 ACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAAGGACTTATA
65 ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATA
* * *
43591 AATTGTGAAAATTTGAAAATCGAATTCTTAGTTTTCAAAAATTTCATCTTCTTAAAACATCATTT
130 AATTGTGAAATTTTGAAAATCGAATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTT
43656 TTCATTTTCAAATTCATGTG
195 TTCATTTTCAAATTCATGTG
* *
43676 AAAACATCCTACCCGAAGGTCTTATGGATGACCCGAAGGACTTGTCATCTTGCT-TAAAAGGCTT
1 AAAACATCCTACCCGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTCT-AAAGACTT
* * * * *
43740 ATATATGACCCGAAGGATTTAAACATCCTGCTCGAAAGACTTACTGATGGCCCAAAGGACTTATA
65 ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATA
* *
43805 AATTGTGAAATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTT
130 AATTGTGAAATTTTGAAAATCGAATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCA--T
43870 TTTTCATTTTCAAATTCATGTG
193 TTTTCATTTTCAAATTCATGTG
* * *
43892 AAAGCATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTCTAAAGACTTA
* *
43957 TAGATAACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
* * * * *
44022 ATTATGAAATTTTGAAAATTC-TATTTTTCGTTTTAAAAAATTCCATCTTCTTAAAACATCAATT
131 ATTGTGAAATTTTGAAAA-TCGAATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTT
44086 TTCATTTTCAAATTCATGTG
195 TTCATTTTCAAATTCATGTG
* * * * *
44106 AAAACATCCTACCCGAAGGTTTTACGGATGGCTCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTCTAAAGACTTA
*
44171 TAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
* * * *
44236 ATTATGAAATTTTGAAAAT-TACATTTTTCGTTTTAAAAAATTCCATCTTCTTAAAACATCATTT
131 ATTGTGAAATTTTGAAAATCGA-ATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTT
44300 TCTCATTCTTCAAATTCATGTG
195 T-TCATT-TTCAAATTCATGTG
* *
44322 AAAACATCCTACCCGAAGGTCTTATGGATGGCTC-AAGGACTTATCATCTTGCT-TAAAGACTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTCTAAAGACTTA
* *
44385 CAGAT-AGCTCGAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGG
66 CAGATGA-CCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
44434 AACTTACCGA
Statistics
Matches: 899, Mismatches: 62, Indels: 22
0.91 0.06 0.02
Matches are distributed among these distances:
213 4 0.00
214 626 0.70
215 24 0.03
216 243 0.27
217 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (214 bp):
AAAACATCCTACCCGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTCTAAAGACTTA
CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
ATTGTGAAATTTTGAAAATCGAATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT
TCATTTTCAAATTCATGTG
Found at i:44010 original size:42 final size:41
Alignment explanation
Indices: 43912--44018 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
43902 ACCCGAAGGT
* * * * *
43912 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGG
1 CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
** *
43953 CTTATAGATAACCCGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGA
43995 CTTACT-GATGGCCCGAAGGACTTA
1 CTTA-TAGATGGCCCGAAGGACTTA
44019 TAAATTATGA
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
41 20 0.38
42 32 0.60
43 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
Found at i:44063 original size:430 final size:428
Alignment explanation
Indices: 43248--44433 Score: 1718
Period size: 430 Copynumber: 2.8 Consensus size: 428
43238 ATCTTGGTGA
* * * * * * * *
43248 AAAACATCCTGCTCGAAGGTCTTATGGATGATCCGAAGGATTTATTC-TCTTGCTCGAGAGACTC
1 AAAACATCCTACCCGAAGGTCTTATGGATGACCCGAAGGACTTA-TCATCTTGCT-TAAAGGCTT
* * * * **
43312 ACAAATGACTCGAAGGATTTAAGCATCGTGCTTGAAAGACTTACTGATGGCTTGAAGGACTTATA
64 ATAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATA
* * * *
43377 AATTGTGAAATTTTGAAAATTGCATTCTTAGTTTTCAAAAATTTCATCTTTTTAAAATATCA-TT
129 AATTGTGAAATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTT
* * * ** *
43441 TTTCATTTTCAAATTCATGTGAAAAAATCCTACCGGAAGGTCTTATAGATGATCCGAAGGATTTA
194 TTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTA
* * * * *
43506 TTC-TCTTGCTCGAGAGACTCACAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
259 -TCATCTTGCTCTAAAGACTTACAGATAACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
* * * *
43570 TGATGGCTCGAAGGACTTATAAATTGTGAAAATTTGAAAATCGAATTCTTAGTTTTCAAAAATTT
323 TGATGGCCCGAAGGACTTATAAATTATGAAAATTTGAAAATCGAATTCTTAGTTTTAAAAAATTC
*
43635 CATCTTCTTAAAACATCATTTTTCATTTTCAAATTCATGTG
388 CATCTTCTTAAAACATCAATTTTCATTTTCAAATTCATGTG
*
43676 AAAACATCCTACCCGAAGGTCTTATGGATGACCCGAAGGACTTGTCATCTTGCTTAAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTT-AAAGGCTTA
* * * *
43741 TATATGACCCGAAGGATTTAAACATCCTGCTCGAAAGACTTACTGATGGCCCAAAGGACTTATAA
65 TAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
43806 ATTGTGAAATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT
130 ATTGTGAAATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCA-TTT
*
43871 TTTCATTTTCAAATTCATGTGAAAGCATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTA
194 TTTCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTA
* *
43936 TCATCTTGCTCTAAAGGCTTATAGATAACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
259 TCATCTTGCTCTAAAGACTTACAGATAACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
* * * *
44001 GATGGCCCGAAGGACTTATAAATTATGAAATTTTGAAAATTC-TATTTTTCGTTTTAAAAAATTC
324 GATGGCCCGAAGGACTTATAAATTATGAAAATTTGAAAA-TCGAATTCTTAGTTTTAAAAAATTC
44065 CATCTTCTTAAAACATCAATTTTCATTTTCAAATTCATGTG
388 CATCTTCTTAAAACATCAATTTTCATTTTCAAATTCATGTG
* * * *
44106 AAAACATCCTACCCGAAGGTTTTACGGATGGCTCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCT-TAAAGGCTTA
*
44171 TAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
65 TAAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
* * * *
44236 ATTATGAAATTTTGAAAATTACATTTTTCGTTTTAAAAAATTCCATCTTCTTAAAACATCATTTT
130 ATTGTGAAATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTT
* *
44301 CTCATTCTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCTC-AAGGACTTA
195 TTCATT-TTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTA
* * *
44365 TCATCTTGCT-TAAAGACTTACAGATAGCTCGAAGGATTTAAGCATCATGCTCGAAAGACTTATT
259 TCATCTTGCTCTAAAGACTTACAGATAACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
44429 GATGG
324 GATGG
44434 AACTTACCGA
Statistics
Matches: 684, Mismatches: 66, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
427 2 0.00
428 219 0.32
429 30 0.04
430 430 0.63
431 3 0.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (428 bp):
AAAACATCCTACCCGAAGGTCTTATGGATGACCCGAAGGACTTATCATCTTGCTTAAAGGCTTAT
AAATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
TTGTGAAATTTTGAAAATTGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTT
TCATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATC
ATCTTGCTCTAAAGACTTACAGATAACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGA
TGGCCCGAAGGACTTATAAATTATGAAAATTTGAAAATCGAATTCTTAGTTTTAAAAAATTCCAT
CTTCTTAAAACATCAATTTTCATTTTCAAATTCATGTG
Found at i:44224 original size:42 final size:41
Alignment explanation
Indices: 44127--44232 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 41
44117 CCCGAAGGTT
* * * * * *
44127 TTACGGATGGCTCGAAGGACTTATCATCTTGCTCTAAAGGC
1 TTACTGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGAC
* *
44168 TTA-TAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGAC
1 TTACT-GATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGAC
44210 TTACTGATGGCCCGAAGGACTTA
1 TTACTGATGGCCCGAAGGACTTA
44233 TAAATTATGA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
41 18 0.35
42 33 0.63
43 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (41 bp):
TTACTGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGAC
Found at i:45436 original size:125 final size:125
Alignment explanation
Indices: 45210--45531 Score: 421
Period size: 125 Copynumber: 2.6 Consensus size: 125
45200 AGTTGTGAGA
* * ** * *
45210 CTCATTC-TCAATGACTTCTTGGTCTGAATCTTGTTTTCTCATCATGACGTGGGTTCAGTCGTGC
1 CTCATTCTTC-ATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGC
* * *
45274 CCCAACCTTATCTTATACTGGTGCAAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGG
65 CCCAACATTATCTTATACTAGTACAAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGG
* *
45335 GTCATTCTTCATTCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCC
1 CTCATTCTTCATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCC
* ** * *
45400 CCCACATTATCTTATACTAGTACGGGCCTTCCAAATGCCTCATCACCTCAAATTGTAAGG
66 CCAACATTATCTTATACTAGTACAAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGG
* ** * * * *
45460 CTCATTCTTCATGCCTCATTGGTCTGAAAGTTTTCATCTAAACATAATGTGGGTTCAATCGTGCC
1 CTCATTCTTCATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCC
45525 CCAACAT
66 CCAACAT
45532 ATCCTAACTT
Statistics
Matches: 170, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
125 168 0.99
126 2 0.01
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (125 bp):
CTCATTCTTCATGCCTCCTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCC
CCAACATTATCTTATACTAGTACAAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGG
Found at i:50566 original size:6 final size:6
Alignment explanation
Indices: 50555--50590 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
50545 CAAAAATAAG
*
50555 AATGCA AATGCA GATGCA AATGCA AATGCA AATGCA
1 AATGCA AATGCA AATGCA AATGCA AATGCA AATGCA
50591 TGAGGTGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (6 bp):
AATGCA
Done.