Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008670.1 Hibiscus syriacus cultivar Beakdansim tig00111678_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: 969061
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 1 of 5
Found at i:11277 original size:105 final size:105
Alignment explanation
Indices: 11095--11740 Score: 1029
Period size: 105 Copynumber: 6.2 Consensus size: 105
11085 TTTTACCCAT
11095 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
11160 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
*
11200 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
11265 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
11305 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
11370 AAGGGACCGCTGGTTGTCAACAAACGTTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
11410 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTT-AACTTCACG-CG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
11473 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
* *
11513 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * *
11578 AAGGGACCGCTGGTTGTCACCAAACATTTCTCCAACTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
* * * * * * *
11618 AGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAGCACAAGCTCGACTTC-C-AGC
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA-C
* * * *
11681 TAAGGGA-CGAC-CG-TGTCAGCAAACAATTTCTC-AATTCAT
65 GAAGGGACCG-CTGGTTGTCAACAAAC-ATTTCTCAAATTCAG
*
11720 AGCCAATTCCAACTTCACAAC
1 AGCCAATTTCAACTTCACAAC
11741 AGATCAATCC
Statistics
Matches: 511, Mismatches: 25, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
102 34 0.07
103 103 0.20
104 26 0.05
105 348 0.68
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
Found at i:11620 original size:208 final size:208
Alignment explanation
Indices: 11095--11740 Score: 1023
Period size: 208 Copynumber: 3.1 Consensus size: 208
11085 TTTTACCCAT
11095 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
11160 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
*
11225 GATATTGGACTCCAAACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC
131 GATATTGGACTCCAGACAACGCAAGTT-AACTTCACG-CGAAGGGACCGCTGGTTGTCAACAAAC
*
11290 ATTTCTCAGATTCAG
194 ATTTCTCAAATTCAG
11305 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
11370 AAGGGACCGCTGGTTGTCAACAAACGTTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
11435 GATATTGGACTCCAGACAACGCAAGTTAACTTCACGCGAAGGGACCGCTGGTTGTCAACAAACAT
131 GATATTGGACTCCAGACAACGCAAGTTAACTTCACGCGAAGGGACCGCTGGTTGTCAACAAACAT
11500 TTCTCAAATTCAG
196 TTCTCAAATTCAG
* *
11513 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * * *
11578 AAGGGACCGCTGGTTGTCACCAAACATTTCTCCAACTCAGAGCCAATTTCAACTTCACAGCGAAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
* * * * ** * * *
11643 GATATTGAACTCAAGACAGCACAAGCTCGACTTC-CAGCTAAGGGA-CGAC-CG-TGTCAGCAAA
131 GATATTGGACTCCAGACAACGCAAG-TTAACTTCAC-GCGAAGGGACCG-CTGGTTGTCAACAAA
*
11704 CAATTTCTC-AATTCAT
193 C-ATTTCTCAAATTCAG
*
11720 AGCCAATTCCAACTTCACAAC
1 AGCCAATTTCAACTTCACAAC
11741 AGATCAATCC
Statistics
Matches: 411, Mismatches: 21, Indels: 11
0.93 0.05 0.02
Matches are distributed among these distances:
207 36 0.09
208 196 0.48
209 24 0.06
210 155 0.38
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (208 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
GATATTGGACTCCAGACAACGCAAGTTAACTTCACGCGAAGGGACCGCTGGTTGTCAACAAACAT
TTCTCAAATTCAG
Found at i:12140 original size:17 final size:17
Alignment explanation
Indices: 12114--12147 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12104 CGTCCTTATG
*
12114 TTATAATATATATATAT
1 TTATAATATAAATATAT
*
12131 TTATATTATAAATATAT
1 TTATAATATAAATATAT
12148 ATATTTATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATAATATAAATATAT
Found at i:12147 original size:21 final size:22
Alignment explanation
Indices: 12109--12155 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
12099 AATTTCGTCC
*
12109 TTATGTTATAATATATATATAT
1 TTATATTATAATATATATATAT
12131 TTATATTATAA-ATATATATAT
1 TTATATTATAATATATATATAT
12152 TTAT
1 TTAT
12156 TTACATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTATATTATAATATATATATAT
Found at i:13468 original size:34 final size:36
Alignment explanation
Indices: 13385--13476 Score: 91
Period size: 37 Copynumber: 2.5 Consensus size: 36
13375 ATCTTTTATG
* *
13385 TTATGTATATTATATTATATTTTTGTTATTTTCTCATTAC
1 TTATGTATA-TAT-TT-TATTTTTATTATTATCT-ATTAC
* *
13425 ATATATATATATTTTATTTTTATTATTATCT-TT-C
1 TTATGTATATATTTTATTTTTATTATTATCTATTAC
13459 TTATGTATAT-TTTTATTT
1 TTATGTATATATTTTATTT
13477 ATATACTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
33 8 0.17
34 9 0.20
35 2 0.04
37 15 0.33
38 2 0.04
39 3 0.07
40 7 0.15
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.65
Consensus pattern (36 bp):
TTATGTATATATTTTATTTTTATTATTATCTATTAC
Found at i:15883 original size:226 final size:227
Alignment explanation
Indices: 15462--15907 Score: 763
Period size: 226 Copynumber: 2.0 Consensus size: 227
15452 GTAAATTATC
* * *
15462 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
15527 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAATT
*
15592 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
15657 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
15690 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTA-T-TTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
15753 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAA-AAT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAAT
* *
15817 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
15882 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
15908 GCAGTTTTAA
Statistics
Matches: 207, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
225 4 0.02
226 85 0.41
227 68 0.33
228 37 0.18
229 13 0.06
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATAATT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:15995 original size:20 final size:20
Alignment explanation
Indices: 15972--16021 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
15962 CGATATACCA
15972 GGTAAAATTATGATAAAACC
1 GGTAAAATTATGATAAAACC
*
15992 GGTAACAA-AATGATAAAACC
1 GGTAA-AATTATGATAAAACC
16012 GGTAAAATTA
1 GGTAAAATTA
16022 AAAGTGTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (20 bp):
GGTAAAATTATGATAAAACC
Found at i:16159 original size:20 final size:19
Alignment explanation
Indices: 16136--16182 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
16126 CGATATAACA
*
16136 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
16156 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
16176 GGTAAAA
1 GGTAAAA
16183 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:18540 original size:32 final size:32
Alignment explanation
Indices: 18486--18546 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
18476 AAATAGATGG
*
18486 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
***
18518 AGTGGTGAAAGAAGTTTCGGTGTTAAGGG
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGG
18547 GTGATATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.30, C:0.02, G:0.44, T:0.25
Consensus pattern (32 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
Found at i:20398 original size:19 final size:19
Alignment explanation
Indices: 20335--20390 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
20325 AATGTCGAGT
*
20335 TAATTTTGTATAAGATTTA
1 TAATTTTGTATACGATTTA
20354 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
20373 TAATTTTGTATACGATTT
1 TAATTTTGTATACGATTT
20391 TATTTTTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.54
Consensus pattern (19 bp):
TAATTTTGTATACGATTTA
Found at i:21299 original size:198 final size:199
Alignment explanation
Indices: 20479--21495 Score: 1789
Period size: 200 Copynumber: 5.1 Consensus size: 199
20469 TTAAGGGTCA
*
20479 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
20544 AT-AAGTGTCGATCCATATATAAAAAAGTGTCGATCCC-AAATCATCGAA-CCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
20606 TAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
20670 AATG
196 AATG
* *** * *
20674 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
20739 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
20804 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
20869 AATG
196 AATG
* *** *
20873 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
*
20938 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
21003 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
21068 TAATG
195 TAATG
* *
21073 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACGAGGTGAATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
21138 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
21202 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
21267 AATG
196 AATG
*
21271 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTTTTACAAGGTGAATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
21335 ATAAAGTGTCGATCCATATAT--AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
21398 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
21463 AATG
196 AATG
*
21467 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
21496 CTAATTTAAA
Statistics
Matches: 797, Mismatches: 20, Indels: 9
0.96 0.02 0.01
Matches are distributed among these distances:
195 60 0.08
196 173 0.22
197 66 0.08
198 164 0.21
199 136 0.17
200 198 0.25
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
AATG
Found at i:22994 original size:18 final size:18
Alignment explanation
Indices: 22958--23016 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
22948 ATCGGTCGCA
* * *
22958 GAAGATGAAGCTGACGAT
1 GAAGATGACGATGATGAT
22976 GAAGATGACGATGATGAT
1 GAAGATGACGATGATGAT
22994 ---GATGACGATGATGAT
1 GAAGATGACGATGATGAT
23009 GAAGATGA
1 GAAGATGA
23017 TGATCCAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 15 0.43
18 20 0.57
ACGTcount: A:0.39, C:0.07, G:0.34, T:0.20
Consensus pattern (18 bp):
GAAGATGACGATGATGAT
Found at i:22997 original size:15 final size:15
Alignment explanation
Indices: 22973--23020 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
22963 TGAAGCTGAC
*
22973 GATGAAGATGACGAT
1 GATGATGATGACGAT
22988 GATGATGATGACGAT
1 GATGATGATGACGAT
* *
23003 GATGATGAAGATGAT
1 GATGATGATGACGAT
23018 GAT
1 GAT
23021 CCAAACAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.38, C:0.04, G:0.33, T:0.25
Consensus pattern (15 bp):
GATGATGATGACGAT
Found at i:23017 original size:12 final size:12
Alignment explanation
Indices: 22961--23020 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
22951 GGTCGCAGAA
* *
22961 GATGAAGCTGAC
1 GATGAAGATGAT
*
22973 GATGAAGATGAC
1 GATGAAGATGAT
22985 GAT---GATGAT
1 GATGAAGATGAT
*
22994 GATGACGATGAT
1 GATGAAGATGAT
23006 GATGAAGATGAT
1 GATGAAGATGAT
23018 GAT
1 GAT
23021 CCAAACAAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
9 8 0.19
12 34 0.81
ACGTcount: A:0.37, C:0.07, G:0.33, T:0.23
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:24933 original size:184 final size:184
Alignment explanation
Indices: 24387--25054 Score: 1263
Period size: 184 Copynumber: 3.7 Consensus size: 184
24377 CTTTCAACAT
**
24387 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
24452 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
24517 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
24571 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTAT-AA-ATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
24634 GGTCTACAACCTATATCGACACTTTTTAATA-T-TGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
24697 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
24751 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
24816 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
24881 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
24935 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
25000 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
25055 CCATTTAAAA
Statistics
Matches: 475, Mismatches: 5, Indels: 8
0.97 0.01 0.02
Matches are distributed among these distances:
180 123 0.26
181 3 0.01
182 106 0.22
183 3 0.01
184 240 0.51
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:27631 original size:23 final size:23
Alignment explanation
Indices: 27600--27662 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
27590 ATAGGTAAAC
*
27600 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
27623 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
27646 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
27663 ATGGTATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:28055 original size:23 final size:23
Alignment explanation
Indices: 28024--28086 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
28014 ATAGGTAAAC
*
28024 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
28047 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
28070 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
28087 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:28094 original size:23 final size:23
Alignment explanation
Indices: 28024--28096 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
28014 ATAGGTAAAC
* * **
28024 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
28047 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
28070 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
28093 ATAT
1 ATAT
28097 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:30150 original size:21 final size:21
Alignment explanation
Indices: 30120--30247 Score: 84
Period size: 21 Copynumber: 6.0 Consensus size: 21
30110 GATTTACATA
*
30120 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
**
30141 TTCGCGTTGCGATAGTTGAAG
1 TTCGCGTTGCGATAGTCCAAG
** * *
30162 TTCGCGTTGCGTTGCGATTTTTCAAA
1 TT--C---GCGTTGCGATAGTCCAAG
30188 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
30207 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
30230 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
30248 AATCGCAACG
Statistics
Matches: 84, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
19 22 0.26
21 36 0.43
23 10 0.12
26 16 0.19
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:30243 original size:42 final size:40
Alignment explanation
Indices: 30170--30247 Score: 138
Period size: 42 Copynumber: 1.9 Consensus size: 40
30160 AGTTCGCGTT
30170 GCGTTGCGATTTTTCAAATTCGTTGCGATAGTCCAAGTTC
1 GCGTTGCGATTTTTCAAATTCGTTGCGATAGTCCAAGTTC
30210 GCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 GCGTTGCGATTT-TT-CAAATTCGTTGCGATAGTCCAA
30248 AATCGCAACG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 12 0.33
41 2 0.06
42 22 0.61
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (40 bp):
GCGTTGCGATTTTTCAAATTCGTTGCGATAGTCCAAGTTC
Found at i:30348 original size:6 final size:6
Alignment explanation
Indices: 30337--30367 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
30327 GAAACGTATT
30337 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
30368 GACGAGACGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:31142 original size:21 final size:19
Alignment explanation
Indices: 31109--31350 Score: 162
Period size: 21 Copynumber: 11.7 Consensus size: 19
31099 CGTTGCGATT
* *
31109 TTGGACTATCGCAACGAAT
1 TTGGAATATCGCAACGAAC
31128 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* *
31151 TTCGACTATCGCAACGAAC
1 TTGGAATATCGCAACGAAC
31170 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
*
31193 TTGGACTATCGCAACGCGAAC
1 TTGGAATATCGCAA--CGAAC
*
31214 TTGGACTATCGCAACACGAAC
1 TTGGAATATCGC-A-ACGAAC
* * *
31235 TTGGACTATCGCAACAAAT
1 TTGGAATATCGCAACGAAC
31254 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
*
31277 TT-GAACTATCGCAACGAAT
1 TTGGAA-TATCGCAACGAAC
31296 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA--CGAAC
* * *
31319 TTGGACTATCGCAATGAAT
1 TTGGAATATCGCAACGAAC
*
31338 TTGGAAAATCGCA
1 TTGGAATATCGCA
31351 TTGCGATAGT
Statistics
Matches: 184, Mismatches: 19, Indels: 40
0.76 0.08 0.16
Matches are distributed among these distances:
19 47 0.26
20 4 0.02
21 92 0.50
22 4 0.02
23 37 0.20
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (19 bp):
TTGGAATATCGCAACGAAC
Found at i:31174 original size:42 final size:42
Alignment explanation
Indices: 31109--31350 Score: 366
Period size: 42 Copynumber: 5.8 Consensus size: 42
31099 CGTTGCGATT
31109 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
31151 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * *
31193 TTGGACTATCGCAACGCGAACTTGGACT--ATCGCAACACGAAC
1 TTGGACTATCGCAA--CGAATTTGGAATAAATCGCAACGCGAAC
*
31235 TTGGACTATCGCAACAAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
31277 TTGAACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
31319 TTGGACTATCGCAATGAATTTGG-A-AAATCGCA
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCA
31351 TTGCGATAGT
Statistics
Matches: 183, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
40 17 0.09
41 1 0.01
42 154 0.84
44 11 0.06
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:31375 original size:21 final size:21
Alignment explanation
Indices: 31346--31397 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
31336 ATTTGGAAAA
*
31346 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
* *
31367 TCGCGTTGCTATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
31388 TCGCGTTGCG
1 TCGCGTTGCG
31398 TATCTGGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.15, C:0.21, G:0.31, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:33961 original size:2 final size:2
Alignment explanation
Indices: 33950--33993 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
33940 TCTTCAACAA
33950 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
33991 TC T
1 TC T
33994 AATTCAAAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:36730 original size:21 final size:21
Alignment explanation
Indices: 36691--36730 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
36681 CGTGGCACCG
* * *
36691 TTAACCCTTTTTCTTCTCCAC
1 TTAACCCTTCTCCTCCTCCAC
36712 TTAACCCTTCTCCTCCTCC
1 TTAACCCTTCTCCTCCTCC
36731 TCCTCCTCAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.12, C:0.45, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAACCCTTCTCCTCCTCCAC
Found at i:37549 original size:4 final size:4
Alignment explanation
Indices: 37517--37639 Score: 62
Period size: 4 Copynumber: 30.8 Consensus size: 4
37507 ATATTAGAGA
* * * * *
37517 AAAT AAGT AAAT AAA- AAAT AACT -ACT AAAT AAAT CAAAAG AAAA AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT --AAAT AAAT AAAT
* *
37565 AAA- ATAAG AAAT AAAT AAAT AAAT CAAAG AAA- AAAT AAAAT AAAAT
1 AAAT A-AAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT -AAAT -AAAT
*
37611 AAA- AAAC AAAT -AAT AAA- AAAT AAACT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAA
37640 AAAAGGGAAA
Statistics
Matches: 96, Mismatches: 10, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
3 19 0.20
4 57 0.59
5 17 0.18
6 3 0.03
ACGTcount: A:0.75, C:0.05, G:0.03, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:37559 original size:41 final size:36
Alignment explanation
Indices: 37525--37642 Score: 120
Period size: 31 Copynumber: 3.3 Consensus size: 36
37515 GAAAATAAGT
37525 AAATAAAAAATAACTACTAAATAAATCAAAAGAAAAAAATA
1 AAATAAAAAATAA--A-TAAATAAATC-AAAG-AAAAAATA
*
37566 AAATAAGAAATAAATAAATAAATCAAAGAAAAAATA
1 AAATAAAAAATAAATAAATAAATCAAAGAAAAAATA
* *
37602 AAAT--AAAATAAA-AAACAAAT--AATAAAAAATA
1 AAATAAAAAATAAATAAATAAATCAAAGAAAAAATA
*
37633 AACTAAAAAA
1 AAATAAAAAA
37643 AGGGAAAAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
31 13 0.19
33 11 0.16
34 7 0.10
36 12 0.17
37 4 0.06
38 10 0.14
39 1 0.01
41 12 0.17
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (36 bp):
AAATAAAAAATAAATAAATAAATCAAAGAAAAAATA
Found at i:37639 original size:12 final size:11
Alignment explanation
Indices: 37524--37642 Score: 79
Period size: 10 Copynumber: 11.0 Consensus size: 11
37514 AGAAAATAAG
37524 TAAATAAAAAA
1 TAAATAAAAAA
* **
37535 TAACTACTAAA
1 TAAATAAAAAA
*
37546 TAAAT-CAAAA
1 TAAATAAAAAA
* *
37556 GAAA-AAAATA
1 TAAATAAAAAA
*
37566 -AAATAAGAAA
1 TAAATAAAAAA
37576 TAAATAAATAAA
1 TAAATAAA-AAA
*
37588 TCAAAGAAAAAA
1 T-AAATAAAAAA
*
37600 TAAA-ATAAAA
1 TAAATAAAAAA
37610 TAAA-AAACAAA
1 TAAATAAA-AAA
37621 T-AATAAAAAA
1 TAAATAAAAAA
37631 TAAACTAAAAAA
1 TAAA-TAAAAAA
37643 AGGGAAAAAT
Statistics
Matches: 85, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
9 3 0.04
10 31 0.36
11 30 0.35
12 15 0.18
13 6 0.07
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.17
Consensus pattern (11 bp):
TAAATAAAAAA
Found at i:37848 original size:2 final size:2
Alignment explanation
Indices: 37843--37874 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
37833 AAATAAACTA
37843 AT AT AT 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
37875 GAATGTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37957 original size:11 final size:10
Alignment explanation
Indices: 37929--37956 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
37919 ACAGAATAAT
37929 AAAAAAAAGA
1 AAAAAAAAGA
37939 AAAAAAAAGA
1 AAAAAAAAGA
37949 AAAAAAAA
1 AAAAAAAA
37957 ACAATAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:39173 original size:3 final size:3
Alignment explanation
Indices: 39165--39216 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
39155 AATAAACATA
*
39165 AAT AAT AAT AAT AAT AAT AA- AAT AA- AAT AAA AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39210 AAT AAT A
1 AAT AAT A
39217 CTATTGCATA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 6 0.14
3 38 0.86
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:39187 original size:30 final size:30
Alignment explanation
Indices: 39153--39214 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
39143 TGGACCTTGC
*
39153 AAAATAAACATAAATA-ATAATAATAATAAT
1 AAAATAAA-ATAAAAATATAATAATAATAAT
39183 AAAATAAAATAAAAATATAATAATAATAAT
1 AAAATAAAATAAAAATATAATAATAATAAT
39213 AA
1 AA
39215 TACTATTGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 6 0.20
30 24 0.80
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.26
Consensus pattern (30 bp):
AAAATAAAATAAAAATATAATAATAATAAT
Found at i:39307 original size:39 final size:35
Alignment explanation
Indices: 39229--39406 Score: 148
Period size: 39 Copynumber: 4.9 Consensus size: 35
39219 ATTGCATATA
* *
39229 TAAAAATATTTTCAAAAAC-ATATAATATA-A-TTT
1 TAAAAATGTTTT-TAAAACTATATAATATATATTTT
** *
39262 CCAAAATGTTTTTTAAAAGCTATATATTATACGTATTTT
1 TAAAAATG-TTTTTAAAA-CTATATAATATA--TATTTT
39301 TAAAAATG-TTTTAAAACTATATAATATATATTTT
1 TAAAAATGTTTTTAAAACTATATAATATATATTTT
* * *
39335 CAAAAATATTTTTTAAAAAAACTATATATTATATATATTT
1 TAAAAAT-GTTTTT---AAAACTATATAATATATAT-TTT
*
39375 TCAAAATGTTTTTAAAATCTATATAATATATA
1 TAAAAATGTTTTTAAAA-CTATATAATATATA
39407 AATGTTTTCA
Statistics
Matches: 116, Mismatches: 15, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
33 9 0.08
34 17 0.15
35 9 0.08
36 19 0.16
37 21 0.18
38 1 0.01
39 32 0.28
40 8 0.07
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (35 bp):
TAAAAATGTTTTTAAAACTATATAATATATATTTT
Found at i:39349 original size:73 final size:72
Alignment explanation
Indices: 39229--39406 Score: 211
Period size: 75 Copynumber: 2.4 Consensus size: 72
39219 ATTGCATATA
* * * *
39229 TAAAAATATTTTCAAAAAC-ATATAATATA-ATTTCCAAAATGTTTTTT-AAAAGCTATATATTA
1 TAAAAATGTTTT--AAAACTATATAATATATATTTCAAAAATATTTTTTAAAAAACTATATATTA
39291 TACGTAT-TTT
64 TA--TATATTT
39301 TAAAAATGTTTTAAAACTATATAATATATATTTTCAAAAATATTTTTTAAAAAAACTATATATTA
1 TAAAAATGTTTTAAAACTATATAATATATA-TTTCAAAAATATTTTTT-AAAAAACTATATATTA
39366 TATATATTT
64 TATATATTT
*
39375 TCAAAATGTTTTTAAAATCTATATAATATATA
1 TAAAAATG-TTTTAAAA-CTATATAATATATA
39407 AATGTTTTCA
Statistics
Matches: 93, Mismatches: 5, Indels: 12
0.85 0.05 0.11
Matches are distributed among these distances:
70 5 0.05
71 10 0.11
72 12 0.13
73 18 0.19
74 10 0.11
75 24 0.26
76 14 0.15
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (72 bp):
TAAAAATGTTTTAAAACTATATAATATATATTTCAAAAATATTTTTTAAAAAACTATATATTATA
TATATTT
Found at i:39397 original size:28 final size:27
Alignment explanation
Indices: 39378--39469 Score: 129
Period size: 25 Copynumber: 3.5 Consensus size: 27
39368 TATATTTTCA
* *
39378 AAATGTTTTTAAAATCTATATAATATAT
1 AAATGTTTTCAAAA-CTATATATTATAT
39406 AAATGTTTTCAAAACTATATATTATAT
1 AAATGTTTTCAAAACTATATATTATAT
39433 AAA--TTTTCAAAACTATATATTATAT
1 AAATGTTTTCAAAACTATATATTATAT
39458 -AA-GTTTTCAAAA
1 AAATGTTTTCAAAA
39470 TGATTTTAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
24 2 0.03
25 31 0.51
27 15 0.25
28 13 0.21
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (27 bp):
AAATGTTTTCAAAACTATATATTATAT
Found at i:39397 original size:37 final size:36
Alignment explanation
Indices: 39248--39537 Score: 164
Period size: 39 Copynumber: 8.4 Consensus size: 36
39238 TTTCAAAAAC
* *
39248 ATATAATATA-ATTTCCAAAATGTTTTTTAAAAGCTAT
1 ATATTATATATATTTTCAAAATG-TTTTTAAAA-CTAT
*
39285 ATATTATACGTAT-TTTTAAAAATG-TTTTAAAACTAT
1 ATATTATA--TATATTTTCAAAATGTTTTTAAAACTAT
*
39321 ATA--ATATATATTTTCAAAAATATTTTTTAAAAAAACTAT
1 ATATTATATATATTTTC-AAAAT-GTTTTT---AAAACTAT
*
39360 ATATTATATATATTTTCAAAATGTTTTTAAAA-TCT
1 ATATTATATATATTTTCAAAATGTTTTTAAAACTAT
*
39395 ATA-TA-ATATA---T--AAATGTTTTCAAAACTAT
1 ATATTATATATATTTTCAAAATGTTTTTAAAACTAT
*
39424 ATATTAT----A---T--AAA--TTTTCAAAACTAT
1 ATATTATATATATTTTCAAAATGTTTTTAAAACTAT
*
39449 ATATTATATA-AGTTTTCAAAATGATTTTAAAAACTAT
1 ATATTATATATA-TTTTCAAAATG-TTTTTAAAACTAT
**
39486 ATATTATATATGTATTTTCAAAAATCG-TTTGCAAACTAT
1 ATATTATATA--TATTTTC-AAAAT-GTTTTTAAAACTAT
*
39525 ATAATATATATAT
1 ATATTATATATAT
39538 GTATAAAATA
Statistics
Matches: 208, Mismatches: 13, Indels: 64
0.73 0.05 0.22
Matches are distributed among these distances:
25 20 0.10
27 5 0.02
28 14 0.07
29 5 0.02
30 3 0.01
32 4 0.02
33 9 0.04
34 13 0.06
35 5 0.02
36 15 0.07
37 40 0.19
39 51 0.25
40 11 0.05
41 13 0.06
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (36 bp):
ATATTATATATATTTTCAAAATGTTTTTAAAACTAT
Found at i:39457 original size:128 final size:126
Alignment explanation
Indices: 39309--39539 Score: 303
Period size: 128 Copynumber: 1.8 Consensus size: 126
39299 TTTAAAAATG
39309 TTTTAAAACTATATAATATAT-A-TTTTCAAAAAT-ATTTTTTAAAAAAACTATATATTATATA-
1 TTTTAAAACTATATAATATATAAGTTTTC-AAAATGA--TTTT--AAAAACTATATATTATATAG
*
39370 TATTTTC-AAAAT-GTTTTTAAAATCTATATAATATATAAATGTTTTCAAAACTATATATTATAT
61 TATTTTCAAAAATCG-TTTGAAAA-CTATATAATATATAAATGTTTTCAAAACTATATATTATAT
39433 AAA
124 AAA
*
39436 TTTTCAAAACTATATATTATATAAGTTTTCAAAATGATTTTAAAAACTATATATTATATATGTAT
1 TTTT-AAAACTATATAATATATAAGTTTTCAAAATGATTTTAAAAACTATATATTATATA-GTAT
* *
39501 TTTCAAAAATCGTTTGCAAACTATATAATATATATATGT
64 TTTCAAAAATCGTTTGAAAACTATATAATATATAAATGT
39540 ATAAAATAAA
Statistics
Matches: 92, Mismatches: 4, Indels: 15
0.83 0.04 0.14
Matches are distributed among these distances:
126 19 0.21
127 4 0.04
128 45 0.49
129 17 0.18
130 7 0.08
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (126 bp):
TTTTAAAACTATATAATATATAAGTTTTCAAAATGATTTTAAAAACTATATATTATATAGTATTT
TCAAAAATCGTTTGAAAACTATATAATATATAAATGTTTTCAAAACTATATATTATATAAA
Found at i:39522 original size:39 final size:38
Alignment explanation
Indices: 39441--39541 Score: 109
Period size: 37 Copynumber: 2.6 Consensus size: 38
39431 ATAAATTTTC
*
39441 AAAACTATATATTATATAAG--TTTTCAAAATGATTTTA
1 AAAACTATATATTATATATGTATTTTCAAAATGA-TTTA
*
39478 AAAACTATATATTATATATGTATTTTCAAAAATCG-TTTG
1 AAAACTATATATTATATATGTATTTTC-AAAAT-GATTTA
*
39517 CAAACTATATAATATATATATGTAT
1 AAAACTATAT-AT-TATATATGTAT
39542 AAAATAAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
37 19 0.35
39 17 0.31
40 7 0.13
41 12 0.22
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.43
Consensus pattern (38 bp):
AAAACTATATATTATATATGTATTTTCAAAATGATTTA
Found at i:40213 original size:33 final size:34
Alignment explanation
Indices: 40137--40225 Score: 135
Period size: 36 Copynumber: 2.6 Consensus size: 34
40127 AACTCGAAGG
*
40137 TTTTGTGTTTCAAGAGAAACATTTTCAAAGGTTTTT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGG--TTT
*
40173 TTTTGTGTTTCAAGAAAAACAATTTCAAAGG-TT
1 TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTT
40206 TTTTGTGTTTCAAGAGAAAC
1 TTTTGTGTTTCAAGAGAAAC
40226 TGTCACAAGG
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
33 21 0.42
36 29 0.58
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (34 bp):
TTTTGTGTTTCAAGAGAAACAATTTCAAAGGTTT
Found at i:40365 original size:36 final size:36
Alignment explanation
Indices: 40278--40888 Score: 702
Period size: 36 Copynumber: 17.1 Consensus size: 36
40268 CAAATATTGG
*
40278 TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
*
40315 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
40351 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
40388 AGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
40424 AGTTTTAACGA-AAACAGAT-TC-A-A-AG----ATTT
1 TGTTTCAA-GAGAAACTG-TCTCAAGAGAGACAAAATT
*
40453 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
40489 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
40525 TGTTTCAAGAGAAACTGTCTCTAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
40561 TATTTCAA-AGGAAACTGTCTCAAGAGAGACAAATTT
1 TGTTTCAAGA-GAAACTGTCTCAAGAGAGACAAAATT
*
40597 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
40634 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
*
40671 TGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAA--ATT
* *
40710 TGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*** *
40746 TGTTTCAAG-GAAA--G---C-AGATTTA-AAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-AATT
* *
40775 TATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
40811 TGTTTCAA-AGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGA-GAAACTGTCTCAAGAGAGACAAAATT
* * * *
40847 TGTTTCAGGGGAAACTGTCTCGAGGGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
40884 TGTTT
1 TGTTT
40889 TGAGTAAATT
Statistics
Matches: 498, Mismatches: 46, Indels: 60
0.82 0.08 0.10
Matches are distributed among these distances:
28 3 0.01
29 30 0.06
30 6 0.01
31 1 0.00
32 3 0.01
33 3 0.01
35 7 0.01
36 263 0.53
37 144 0.29
38 5 0.01
39 32 0.06
40 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:40534 original size:21 final size:21
Alignment explanation
Indices: 40472--40536 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
40462 GGAAACTGTC
40472 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* *
40493 TCAAG-G-G---AAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
40508 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
40529 TCAAGAGA
1 TCAAGAGA
40537 AACTGTCTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 1 0.03
19 1 0.03
20 4 0.12
21 16 0.47
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.25
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:40642 original size:22 final size:21
Alignment explanation
Indices: 40616--40679 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
40606 AGAAACTGTC
40616 TCAAGCGAGACAAAACTTTGTT
1 TCAAG-GAGACAAAACTTTGTT
*
40638 TCAA-GAG---AAAC--TGTC
1 TCAAGGAGACAAAACTTTGTT
40653 TCAAGAGAGACAAAACTTTGTT
1 TCAAG-GAGACAAAACTTTGTT
40675 TCAAG
1 TCAAG
40680 AGAAACTGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
15 7 0.21
17 7 0.21
20 7 0.21
22 12 0.36
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (21 bp):
TCAAGGAGACAAAACTTTGTT
Found at i:40645 original size:20 final size:20
Alignment explanation
Indices: 40622--40682 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
40612 TGTCTCAAGC
40622 GAGACAAAACTTTGTTTCAA
1 GAGACAAAACTTTGTTTCAA
*
40642 GAG---AAAC--TGTCTCAAGA
1 GAGACAAAACTTTGTTTC-A-A
40659 GAGACAAAACTTTGTTTCAA
1 GAGACAAAACTTTGTTTCAA
40679 GAGA
1 GAGA
40683 AACTGTCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
15 5 0.16
16 1 0.03
17 8 0.25
20 12 0.38
21 1 0.03
22 5 0.16
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.25
Consensus pattern (20 bp):
GAGACAAAACTTTGTTTCAA
Found at i:40811 original size:322 final size:319
Alignment explanation
Indices: 40278--40880 Score: 983
Period size: 322 Copynumber: 1.9 Consensus size: 319
40268 CAAATATTGG
*
40278 TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
40343 ACAAAATTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCT
66 ACAAAATTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCT
* *
40408 CAAGGGAGACAAAATTAGTTTTAACGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCT
131 CAAGGGAGACAAAATTAGTTTCAACGAAAACAGATTCAAAGATTTTATTTCAAGGGAAACTGTCT
*
40473 CAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAA
196 CAAGAGAGACAAAATTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAA
*
40538 ACTGTCTCTAGAGAGACAAAATTTATTTCAAAGGAAACTGTCTCAAGAGAGACAAATTT
261 ACTGTCTCGAGAGAGACAAAATTTATTTCAAAGGAAACTGTCTCAAGAGAGACAAATTT
* *
40597 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
* * * * *
40662 ACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTA-TTTGTTTCAAGAGAAACT
66 ACAAAA-TTTGTTTCAAAAGAAACTGTCTCAAGAGAGAC-AAA--ACTTAGTTCCAAAAGAAACT
* * * * *
40726 GTCTCAAGGGAGACGAAATTTGTTTCAAGGAAAGCAGATTTAAAGATTTTATTTCAAGGGAAACT
127 GTCTCAAGGGAGACAAAATTAGTTTCAACGAAAACAGATTCAAAGATTTTATTTCAAGGGAAACT
*
40791 GTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAGG
192 GTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG
* *
40856 GGAAACTGTCTCGAGGGAGACAAAA
257 AGAAACTGTCTCGAGAGAGACAAAA
40881 CTTTGTTTTG
Statistics
Matches: 260, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
319 68 0.26
320 30 0.12
321 3 0.01
322 158 0.61
323 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.26
Consensus pattern (319 bp):
TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAG
ACAAAATTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCT
CAAGGGAGACAAAATTAGTTTCAACGAAAACAGATTCAAAGATTTTATTTCAAGGGAAACTGTCT
CAAGAGAGACAAAATTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAA
ACTGTCTCGAGAGAGACAAAATTTATTTCAAAGGAAACTGTCTCAAGAGAGACAAATTT
Found at i:41706 original size:21 final size:22
Alignment explanation
Indices: 41670--41710 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
41660 TCAGTCTTCT
41670 TGATTCTGGAATCTTGAATTTC
1 TGATTCTGGAATCTTGAATTTC
*
41692 TGATTCTTG-ATCTTGAATT
1 TGATTCTGGAATCTTGAATT
41711 CTTCAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.22, C:0.12, G:0.17, T:0.49
Consensus pattern (22 bp):
TGATTCTGGAATCTTGAATTTC
Found at i:42027 original size:21 final size:22
Alignment explanation
Indices: 41991--42031 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
41981 TCAGTCTTCT
41991 TGATTCTAGAATCTTGAATTTC
1 TGATTCTAGAATCTTGAATTTC
*
42013 TGATTCTTG-ATCTTGAATT
1 TGATTCTAGAATCTTGAATT
42032 CTTCGATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.49
Consensus pattern (22 bp):
TGATTCTAGAATCTTGAATTTC
Found at i:42070 original size:321 final size:320
Alignment explanation
Indices: 41314--42200 Score: 1497
Period size: 321 Copynumber: 2.8 Consensus size: 320
41304 TAGGATTTGT
41314 AGAGAA-ATCTCAATCTCTGATTGTCAGTCTTCTTGATTCTGAAATCTTGAATTTCTGATTCTTG
1 AGAGAACATCTCAATCTCTGATTGTCAGTCTTCTTGATTCTG-AATCTTGAATTTCTGATTCTTG
41378 ATCTTGAATTCTTCAATATGCTTAAATCTGATGTACAAAACGTTGATCTATGAAGGGAATAATTA
65 ATCTTGAATTCTTCAATATGCTTAAATCTGATGTACAAAACGTTGATCTATGAAGGGAATAATTA
* *
41443 CGTGAGTAGTCTTCAATCTATCCCTGACTCAGTTTGTCTTCATTTCCATCAGGGTGTACTCTTGC
130 CGTGAGCAGTCTTCAATCTATCCCTGACTCAGTTTGTCTTCATTTCCACCAGGGTGTACTCTTGC
**
41508 AAACCTCAACCTAAGATAATTTATTTTCCTTCCCCTATCAAATTTTGCCCCCCAAAAATGGCTTC
195 AAACCTCAACCTAAGATAATTT-TTTTCCTTCCCCTATCAAATTTTG-CCCAAAAAAATGGCTTC
* * * * *
41573 CTTTGCTTTAGCTTCGATCTTGAGTTTCGGAGAGATATTTGTTGAATTTCAAGATATGTTTCC
258 CTTTGCCTCAGCTTCGATCTTGAGCTTCAGAGAGATATTTGTTGAATTTCAAGATATGCTTCC
*
41636 AGAGAACATCTCAATTTCTGATTGTCAGTCTTCTTGATTCTGGAATCTTGAATTTCTGATTCTTG
1 AGAGAACATCTCAATCTCTGATTGTCAGTCTTCTTGATTCT-GAATCTTGAATTTCTGATTCTTG
* * *
41701 ATCTTGAATTCTTCAATATGCTTAAATATGATGTACAAAACATTGATCTATGAAGGGAATAATTG
65 ATCTTGAATTCTTCAATATGCTTAAATCTGATGTACAAAACGTTGATCTATGAAGGGAATAATTA
*
41766 CGTGAACAGTCTTCAATCTATCCCTGACTCAGTTTGTCTTCATTTCCACCAGGGTGTACTCTTGC
130 CGTGAGCAGTCTTCAATCTATCCCTGACTCAGTTTGTCTTCATTTCCACCAGGGTGTACTCTTGC
41831 AAACCTCAACCTAAGATAATTTTTTTCCTTCCCCTATCAAATTTTGCCCAAAAAAATGGCTTCCT
195 AAACCTCAACCTAAGATAATTTTTTTCCTTCCCCTATCAAATTTTGCCCAAAAAAATGGCTTCCT
41896 TTGCCTCAGCTTCGATCTTGAGCTTCAGAGAGATATTTGTTGAATTTCAAGATATGCTTCC
260 TTGCCTCAGCTTCGATCTTGAGCTTCAGAGAGATATTTGTTGAATTTCAAGATATGCTTCC
*
41957 AGAGAACATCACAATCTCTGATTGTCAGTCTTCTTGATTCTAGAATCTTGAATTTCTGATTCTTG
1 AGAGAACATCTCAATCTCTGATTGTCAGTCTTCTTGATTCT-GAATCTTGAATTTCTGATTCTTG
* * * *
42022 ATCTTGAATTCTTCGATATGCTTAAATCCGATGTGCAGAACGTTGATCTATGAAGGGAATAATTA
65 ATCTTGAATTCTTCAATATGCTTAAATCTGATGTACAAAACGTTGATCTATGAAGGGAATAATTA
** * *
42087 CGTGAGCAGTCTTCAATCTATCATTGACTCAGTTTGTCTTCATTTCCACCAAGGTGTACTCTTAC
130 CGTGAGCAGTCTTCAATCTATCCCTGACTCAGTTTGTCTTCATTTCCACCAGGGTGTACTCTTGC
* *
42152 AAACCTCAACCTAAGACAATTGTTTTCCTTCCCCTATCAAATTTTGCCC
195 AAACCTCAACCTAAGATAATTTTTTTCCTTCCCCTATCAAATTTTGCCC
42201 CAAATTTTGA
Statistics
Matches: 532, Mismatches: 31, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
321 300 0.56
322 30 0.06
323 201 0.38
324 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (320 bp):
AGAGAACATCTCAATCTCTGATTGTCAGTCTTCTTGATTCTGAATCTTGAATTTCTGATTCTTGA
TCTTGAATTCTTCAATATGCTTAAATCTGATGTACAAAACGTTGATCTATGAAGGGAATAATTAC
GTGAGCAGTCTTCAATCTATCCCTGACTCAGTTTGTCTTCATTTCCACCAGGGTGTACTCTTGCA
AACCTCAACCTAAGATAATTTTTTTCCTTCCCCTATCAAATTTTGCCCAAAAAAATGGCTTCCTT
TGCCTCAGCTTCGATCTTGAGCTTCAGAGAGATATTTGTTGAATTTCAAGATATGCTTCC
Found at i:42955 original size:4 final size:4
Alignment explanation
Indices: 42939--46395 Score: 6166
Period size: 4 Copynumber: 878.0 Consensus size: 4
42929 TATCCTTATT
42939 CATA CACTA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CA-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
42988 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43036 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C--A CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43082 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
43130 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAGA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
43178 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CCTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43226 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43274 CATA CATA CATA CAT- CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43321 CATA CATA CATA CATA CATA CATA CATA CATA CATA C--A CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43367 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT- CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
43414 CATA CATA CATA CATA CATA CATA CATA CATA CATA CACTA CATA CAGA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CA-TA CATA CATA
43463 C-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43510 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43558 CATA CATA CATA CATA CATA CATA CATA CATA C-TA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43605 CATA CATA CATA CATA CATA C-TA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43652 CATA CATA CATA C--A CATA CATA CAT- CATA CATA CATA CATA C-TA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43696 CATA CATA CATA CATA C--A CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43742 CATA CATA CATA CATA CATA CATA CATA CATA CA-A C-TA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43788 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43836 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43884 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C--A
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43930 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA-A
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
43977 CATA C-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
44024 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
44072 CCATA CATA CATA CATA CATA CATA CATA CATA CATA CA-A CATA CATA
1 -CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
**
44120 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CCGA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
44168 CATA CATA CATA CATA CATA CATA CATA CAT- -ATA CATA CATA CCATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA -CATA
44215 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
44263 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
44311 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
44359 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
44407 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAGA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
44455 CATA CATA C-TA CATA CCTA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
44502 CATA CATA CATA CATA CATA CATA CATA CATA CCTA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
44550 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
44598 CATA CATA CAT- -ATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
44644 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
44692 CATA CATA CATA CATA C-TA CATA CATA CATA CATTA -ATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CA-TA CATA CATA CATA
44739 CATA CATA CCATA CATA CATA CAT- CATA CATA C-TA CATA CACTA CATA
1 CATA CATA -CATA CATA CATA CATA CATA CATA CATA CATA CA-TA CATA
*
44787 CATA CACA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
44835 CA-A CATA CATA CATA CAT- CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
44881 CATA CATA CATA CATA CATA CATA CATA CATAA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CAT-A CATA CATA CATA CATA
*
44930 C--A CATA CATA CATA CATA CATA CATA CCTA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
44976 CATA CATA TATA CAT- CATA C--A CATA CATA CATA CATA CA-A CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
45020 CATA CATA CATA CATA CATA CATA CATA CCATA CATA CAT- CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA -CATA CATA CATA CATA CATA
45068 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
45116 CAT- CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CCTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
45163 CATA CACA CATA CATA CATA CATA C-TA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
45210 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
45258 CATA CATA CATA CATA CATA CATA CATA CAT- CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
45305 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
45353 CATA CATA CATA CATA CATA CCTA CAT- -ATA CATA CATA CATA CATTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA-TA
*
45400 CATA CATA CCTA CATA CATA CATA CATA C-TA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
45447 C-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
45494 CCTA CATA CATA CATA CATA CATA CAT- CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
45541 CATA CATA CATA CATA CATA CAGA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
45589 CATA CATA CATA CATA CATA CATA CA-A CCTA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
45636 CATA CATA CATA CATA CATA CATA CATA CAATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA C-ATA CATA CATA CATA CATA
45685 CATA C--A CATA CATA CATA CCATA CATA CATA CAT- -ATA CATA CATA
1 CATA CATA CATA CATA CATA -CATA CATA CATA CATA CATA CATA CATA
45730 C--A CATA C-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
45775 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
45823 CATA CATA CATA CATA CATA CATA CATA CATA C--A CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
45869 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
45917 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA-A CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
45964 CATA CATA CATA CATA CATA CATA C-TA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
46011 CATA CATA CATA CAT- CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
46058 CATA -ATA CATA CATA CATA CATA CATA CATA CATA CAT- -ATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
46103 C-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
46150 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
46198 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
46246 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
46294 CATA C-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
46341 CA-A CATA CATA CATA CATA CATA CATA CATA CATA CTTA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
46388 CATA CATA
1 CATA CATA
46396 ATATACATGT
Statistics
Matches: 3336, Mismatches: 38, Indels: 158
0.94 0.01 0.04
Matches are distributed among these distances:
2 30 0.01
3 106 0.03
4 3154 0.95
5 46 0.01
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:46807 original size:18 final size:20
Alignment explanation
Indices: 46759--46815 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
46749 CACTGAATAT
46759 TTGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* * *
46779 TTATTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
46798 -TGTCCCGAAGGACCACTG
1 TTGTCCCGAAGGACCACTG
46816 TTTCCCTCGA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 14 0.47
19 1 0.03
20 15 0.50
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:46821 original size:18 final size:18
Alignment explanation
Indices: 46762--46821 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
46752 TGAATATTTG
46762 TCCCGAAGGACCACTGATT
1 TCCCGAAGGACCACTG-TT
* * * *
46781 ATTCCGAAGAACCACTATG
1 -TCCCGAAGGACCACTGTT
46800 TCCCGAAGGACCACTGTT
1 TCCCGAAGGACCACTGTT
46818 TCCC
1 TCCC
46822 TCGACTCTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
18 18 0.56
19 1 0.03
20 13 0.41
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (18 bp):
TCCCGAAGGACCACTGTT
Found at i:49459 original size:95 final size:94
Alignment explanation
Indices: 49260--49513 Score: 372
Period size: 94 Copynumber: 2.7 Consensus size: 94
49250 GGCTAGCTGG
* * **
49260 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTAGAGGGGCATCTCAA--TATCGTTGTAT-TA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACATCTCAAGCT-TTATTGTATATA
*
49322 TAGTCACCTTTATCAGGCTAGCTGAATATT
65 TAATCACCTTTATCAGGCTAGCTGAATATT
* * *
49352 ATCCATAAAGCCGGGGTGTTTAACCAATTTCTCTAGAGGGACAACTCAAGCTTTATTGTATACTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACATCTCAAGCTTTATTGTATA-TA
*
49417 TAATCACCTTTATCAGGCTAGCTGAATCTT
65 TAATCACCTTTATCAGGCTAGCTGAATATT
*
49447 ATCCATAAAGCC-GGGCGTTTAACCAATTGCTTTAGAGGGACATCTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACATCTCAAGCTTTATTGTATATAT
49511 AAT
66 AAT
49514 TATAATATGG
Statistics
Matches: 145, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
92 44 0.30
93 13 0.09
94 46 0.32
95 42 0.29
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (94 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACATCTCAAGCTTTATTGTATATAT
AATCACCTTTATCAGGCTAGCTGAATATT
Found at i:53614 original size:2 final size:2
Alignment explanation
Indices: 53607--53634 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
53597 TAAGTAGTAA
53607 AT 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
53635 GAAAAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53680 original size:15 final size:14
Alignment explanation
Indices: 53660--53737 Score: 54
Period size: 14 Copynumber: 5.5 Consensus size: 14
53650 AGAAAAATGT
*
53660 AATAAATATATACAA
1 AATAAAAATA-ACAA
*
53675 AATAAAAATAATAA
1 AATAAAAATAACAA
53689 AAT-AAAA-AACTAA
1 AATAAAAATAAC-AA
*
53702 AATCAAAAATCA-AA
1 AAT-AAAAATAACAA
*
53716 AATCAAAAATAATAA
1 AAT-AAAAATAACAA
*
53731 ACTAAAA
1 AATAAAA
53738 TAGATACATA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
12 2 0.04
13 9 0.17
14 23 0.44
15 17 0.33
16 1 0.02
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (14 bp):
AATAAAAATAACAA
Found at i:53692 original size:14 final size:14
Alignment explanation
Indices: 53673--53737 Score: 71
Period size: 14 Copynumber: 4.6 Consensus size: 14
53663 AAATATATAC
53673 AAAATAAAAATAAT
1 AAAATAAAAATAAT
*
53687 AAAATAAAAA-ACT
1 AAAATAAAAATAAT
*
53700 AAAATCAAAAATCA-
1 AAAAT-AAAAATAAT
53714 AAAATCAAAAATAAT
1 AAAAT-AAAAATAAT
*
53729 AAACTAAAA
1 AAAATAAAA
53738 TAGATACATA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
13 7 0.16
14 32 0.74
15 4 0.09
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAATAAAAATAAT
Found at i:53697 original size:21 final size:21
Alignment explanation
Indices: 53659--53737 Score: 72
Period size: 21 Copynumber: 3.6 Consensus size: 21
53649 AAGAAAAATG
53659 TAATAAATATATACAAAATAAAAA
1 TAATAAA-ATA-A-AAAATAAAAA
53683 TAATAAAATAAAAAACT-AAAA
1 TAATAAAATAAAAAA-TAAAAA
* *
53704 TCA-AAAATCAAAAATCAAAAA
1 TAATAAAATAAAAAAT-AAAAA
*
53725 TAATAAACTAAAA
1 TAATAAAATAAAA
53738 TAGATACATA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
19 1 0.02
20 10 0.22
21 16 0.35
22 9 0.20
23 3 0.07
24 7 0.15
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (21 bp):
TAATAAAATAAAAAATAAAAA
Found at i:53711 original size:34 final size:34
Alignment explanation
Indices: 53673--53738 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
53663 AAATATATAC
53673 AAAAT-AAAAATAATAAAATAAAAAACTAAAATCA
1 AAAATCAAAAATAA-AAAATAAAAAACTAAAATCA
* *
53707 AAAATCAAAAATCAAAAATAATAAACTAAAAT
1 AAAATCAAAAATAAAAAATAAAAAACTAAAAT
53739 AGATACATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 22 0.76
35 7 0.24
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (34 bp):
AAAATCAAAAATAAAAAATAAAAAACTAAAATCA
Found at i:53840 original size:40 final size:40
Alignment explanation
Indices: 53784--53859 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
53774 AATGTAAATC
* * *
53784 AAAGAAAAATATTAAAAAAATAATAACAGAATAATAAAGA
1 AAAGAAAAAAAATAAAAAAACAATAACAGAATAATAAAGA
* *
53824 AAAGAAAAAAAATAAAAAAACAATAATATAATAATA
1 AAAGAAAAAAAATAAAAAAACAATAACAGAATAATA
53860 TTAAGATATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (40 bp):
AAAGAAAAAAAATAAAAAAACAATAACAGAATAATAAAGA
Found at i:55067 original size:11 final size:11
Alignment explanation
Indices: 55034--55088 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
55024 TGCAAAAAAC
55034 AAAT-AATAAT
1 AAATAAATAAT
55044 -AATAAAATAAAT
1 AAAT-AAAT-AAT
55056 AAATAAATAAT
1 AAATAAATAAT
55067 AAATAAA-AAT
1 AAATAAATAAT
55077 AAA-ATAATAAT
1 AAATA-AATAAT
55088 A
1 A
55089 CTATATTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
9 4 0.10
10 8 0.21
11 17 0.44
12 7 0.18
13 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:55067 original size:15 final size:15
Alignment explanation
Indices: 55034--55073 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
55024 TGCAAAAAAC
55034 AAATAAT-AAT-AAT
1 AAATAATAAATAAAT
55047 -AA-AATAAATAAAT
1 AAATAATAAATAAAT
55060 AAATAATAAATAAA
1 AAATAATAAATAAA
55074 AATAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 3 0.13
12 5 0.22
13 3 0.13
14 2 0.09
15 10 0.43
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AAATAATAAATAAAT
Found at i:55081 original size:26 final size:23
Alignment explanation
Indices: 55029--55088 Score: 70
Period size: 25 Copynumber: 2.6 Consensus size: 23
55019 GGACCTGCAA
*
55029 AAAACAAATAATAATAATAAAAT
1 AAAATAAATAATAATAATAAAAT
55052 -AAATAAATAAATAATAAATAAAAAT
1 AAAATAAAT-AATAAT-AAT-AAAAT
55077 AAAAT-AATAATA
1 AAAATAAATAATA
55089 CTATATTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
22 7 0.22
23 6 0.19
24 7 0.22
25 8 0.25
26 4 0.12
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (23 bp):
AAAATAAATAATAATAATAAAAT
Found at i:55224 original size:35 final size:33
Alignment explanation
Indices: 55111--55579 Score: 311
Period size: 35 Copynumber: 13.7 Consensus size: 33
55101 TATATATATA
* * * *
55111 TTTTCAAAAACATATATATATAATTTCCAAATG
1 TTTTAAAAAATATATATATATATTTTCAAAATG
* * *
55144 TTTTTAAAAACTATATATTATTCGTATTTTCAAAACG
1 -TTTTAAAAAATATATA-TA-T-ATATTTTCAAAATG
* *
55181 TTTT--AAAA-CTATATATATATTTTCAAAAAAG
1 TTTTAAAAAATATATATATATATTTTC-AAAATG
55212 TTTTAAAAAAAACTATATATTATATATATTTCAAAATG
1 TTTT--AAAAAA-TATATA-TATATAT-TTTCAAAATG
* *
55250 TTTT-TAAAA-A-CTATATATA---T--AAATG
1 TTTTAAAAAATATATATATATATTTTCAAAATG
* *
55275 TTTTCAAAACTATATATTATATAAATTTTCAAAAATG
1 TTTT-AAAA-AATATA-TATATATATTTTC-AAAATG
* *
55312 TTTTCAAAACTATATATTATATAAATTTTCAAAAATG
1 TTTT-AAAA-AATATA-TATATATATTTTC-AAAATG
* *
55349 TTTTCAAAACTATATATTATATAAGTTTTCAAAATG
1 TTTTAAAAAATATATA-TATAT-A-TTTTCAAAATG
* *
55385 ATTTTAAAAACTATATATTATATATATTCTAAAATG
1 -TTTTAAAAAATATATA-TATATATTTTC-AAAATG
55421 TTTTAAAAAA-ACTA-ATATAT-TTTTCAAAATG
1 TTTTAAAAAATA-TATATATATATTTTCAAAATG
*
55452 TTTTAAAAACTATATAATATATAGTTTTCAAAATG
1 TTTTAAAAAATATAT-ATATATA-TTTTCAAAATG
* *
55487 TTTTAAAAACTATATATATATATTTTTAAAATG
1 TTTTAAAAAATATATATATATATTTTCAAAATG
* *
55520 ATTTTAAAAACTATATTATATGTATTTTCAAAAATCG
1 -TTTTAAAAAATATA-TATATATATTTTC-AAAAT-G
* *
55557 -TTTACAAACTATAATATATATAT
1 TTTTAAAAAATAT-ATATATATAT
55580 ATATATATAT
Statistics
Matches: 362, Mismatches: 33, Indels: 79
0.76 0.07 0.17
Matches are distributed among these distances:
25 9 0.02
27 3 0.01
28 1 0.00
29 1 0.00
30 7 0.02
31 40 0.11
32 9 0.02
33 26 0.07
34 42 0.12
35 89 0.25
36 28 0.08
37 87 0.24
38 16 0.04
39 4 0.01
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (33 bp):
TTTTAAAAAATATATATATATATTTTCAAAATG
Found at i:55231 original size:37 final size:33
Alignment explanation
Indices: 55111--55579 Score: 396
Period size: 37 Copynumber: 13.7 Consensus size: 33
55101 TATATATATA
* *
55111 TTTTCAAAAAC-ATATATATATAATTTCCAAATG
1 TTTT-AAAAACTATATATATATATTTTCAAAATG
* *
55144 TTTTTAAAAACTATATATTATTCGTATTTTCAAAACG
1 -TTTTAAAAACTATATA-TA-T-ATATTTTCAAAATG
*
55181 TTTT-AAAAC--TATATATATATTTTCAAAAAAG
1 TTTTAAAAACTATATATATATATTTTC-AAAATG
55212 TTTTAAAAAAAACTATATATTATATATATTTCAAAATG
1 TTTT---AAAAACTATATA-TATATAT-TTTCAAAATG
55250 TTTTTAAAAAC----TATATATA---T--AAATG
1 -TTTTAAAAACTATATATATATATTTTCAAAATG
*
55275 TTTTCAAAACTATATATTATATAAATTTTCAAAAATG
1 TTTTAAAAACTATATA-TATAT--ATTTTC-AAAATG
*
55312 TTTTCAAAACTATATATTATATAAATTTTCAAAAATG
1 TTTTAAAAACTATATA-TATAT--ATTTTC-AAAATG
*
55349 TTTTCAAAACTATATATTATATAAGTTTTCAAAATG
1 TTTTAAAAACTATATA-TATAT-A-TTTTCAAAATG
*
55385 ATTTTAAAAACTATATATTATATATATTCTAAAATG
1 -TTTTAAAAACTATATA-TATATATTTTC-AAAATG
*
55421 TTTTAAAAA-AACTA-ATATAT-TTTTCAAAATG
1 TTTTAAAAACTA-TATATATATATTTTCAAAATG
55452 TTTTAAAAACTATATAATATATAGTTTTCAAAATG
1 TTTTAAAAACTATAT-ATATATA-TTTTCAAAATG
*
55487 TTTTAAAAACTATATATATATATTTTTAAAATG
1 TTTTAAAAACTATATATATATATTTTCAAAATG
*
55520 ATTTTAAAAACTATATTATATGTATTTTCAAAAATCG
1 -TTTTAAAAACTATA-TATATATATTTTC-AAAAT-G
*
55557 -TTTACAAACTATAATATATATAT
1 TTTTAAAAACTAT-ATATATATAT
55580 ATATATATAT
Statistics
Matches: 376, Mismatches: 18, Indels: 81
0.79 0.04 0.17
Matches are distributed among these distances:
24 9 0.02
25 5 0.01
27 1 0.00
28 2 0.01
29 5 0.01
30 7 0.02
31 34 0.09
32 9 0.02
33 31 0.08
34 33 0.09
35 83 0.22
36 32 0.09
37 105 0.28
38 12 0.03
39 8 0.02
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (33 bp):
TTTTAAAAACTATATATATATATTTTCAAAATG
Found at i:55264 original size:25 final size:24
Alignment explanation
Indices: 55245--55291 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
55235 ATATATTTCA
55245 AAATGTTTTTAAAAACTATATATAT
1 AAATG-TTTTAAAAACTATATATAT
*
55270 AAATGTTTTCAAAACTATATAT
1 AAATGTTTTAAAAACTATATAT
55292 TATATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (24 bp):
AAATGTTTTAAAAACTATATATAT
Found at i:55283 original size:24 final size:25
Alignment explanation
Indices: 55245--55308 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
55235 ATATATTTCA
*
55245 AAATGTTTTTAAAAACTATATA-TAT
1 AAATG-TTTTCAAAACTATATATTAT
55270 AAATGTTTTCAAAACTATATATTAT
1 AAATGTTTTCAAAACTATATATTAT
*
55295 ATAA-ATTTTCAAAA
1 A-AATGTTTTCAAAA
55309 ATGTTTTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 15 0.43
25 18 0.51
26 2 0.06
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (25 bp):
AAATGTTTTCAAAACTATATATTAT
Found at i:55341 original size:62 final size:60
Alignment explanation
Indices: 55220--55345 Score: 175
Period size: 60 Copynumber: 2.1 Consensus size: 60
55210 AGTTTTAAAA
* *
55220 AAAACTATATATTATATATATTTCAAAATGTTTTTAAAAACTATATATATAAATGTTTTC
1 AAAACTATATATTATATAAATTTCAAAATGTTTTTAAAAACTATATATATAAATATTTTC
*
55280 AAAACTATATATTATATAAATTTTCAAAAATG-TTTTCAAAACTATATATTATATAA-ATTTTC
1 AAAACTATATATTATATAAA-TTTC-AAAATGTTTTTAAAAACTATATA-TATA-AATATTTTC
55342 AAAA
1 AAAA
55346 ATGTTTTCAA
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
60 19 0.32
61 19 0.32
62 19 0.32
63 2 0.03
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (60 bp):
AAAACTATATATTATATAAATTTCAAAATGTTTTTAAAAACTATATATATAAATATTTTC
Found at i:55379 original size:99 final size:98
Alignment explanation
Indices: 55192--55382 Score: 262
Period size: 100 Copynumber: 1.9 Consensus size: 98
55182 TTTAAAACTA
* *
55192 TATATATATTTTCAAAAAAGTTTTAAAAAAAACTATATATTATATATATTTCAAAATGTTTTTAA
1 TATATAAATTTTCAAAAAAGTTTT--AAAAAACTATATATTATATAAATTTCAAAATGTTTTTAA
55257 AAACTATATATATAAATGTTTTCAAAACTATATAT
64 AAACTATATATATAAATGTTTTCAAAACTATATAT
* * *
55292 TATATAAATTTTCAAAAATGTTTT-CAAAACTATATATTATATAAATTTTCAAAAATG-TTTTCA
1 TATATAAATTTTCAAAAAAGTTTTAAAAAACTATATATTATATAAA-TTTC-AAAATGTTTTTAA
55355 AAACTATATATTATATAA-GTTTTCAAAA
64 AAACTATATA-TATA-AATGTTTTCAAAA
55383 TGATTTTAAA
Statistics
Matches: 82, Mismatches: 5, Indels: 9
0.85 0.05 0.09
Matches are distributed among these distances:
97 19 0.23
98 19 0.23
99 20 0.24
100 24 0.29
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (98 bp):
TATATAAATTTTCAAAAAAGTTTTAAAAAACTATATATTATATAAATTTCAAAATGTTTTTAAAA
ACTATATATATAAATGTTTTCAAAACTATATAT
Found at i:66356 original size:41 final size:41
Alignment explanation
Indices: 66311--66396 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 41
66301 TGTTTCCTTG
* * *
66311 TTTGGTTTGCACATGTAGGGTTTTGATTAGTTAGAATTTTA
1 TTTGGTTTGCACATGTAGGGTTTAGATTAGCTAGAATTTAA
* *
66352 TTTGGTTTGCACATGTTGGGTTTAGTTTAGCTAGAATTTAA
1 TTTGGTTTGCACATGTAGGGTTTAGATTAGCTAGAATTTAA
66393 TTTG
1 TTTG
66397 TAAGTGAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.21, C:0.06, G:0.24, T:0.49
Consensus pattern (41 bp):
TTTGGTTTGCACATGTAGGGTTTAGATTAGCTAGAATTTAA
Found at i:84575 original size:23 final size:23
Alignment explanation
Indices: 84549--84632 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
84539 CTCGTATAAA
84549 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
84572 TGCACCGAAATGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
**
84595 TGCACCGAAGTGCCGTGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
84618 TGCATCGAAGTGCCA
1 TGCACCGAAGTGCCA
84633 TATAAAATGT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:85083 original size:19 final size:20
Alignment explanation
Indices: 85059--85097 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
85049 TCTCTTTCAT
85059 ATATCTCATG-TCATGTAAC
1 ATATCTCATGATCATGTAAC
*
85078 ATATCTTATGATCATGTAAC
1 ATATCTCATGATCATGTAAC
85098 CATGTTACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (20 bp):
ATATCTCATGATCATGTAAC
Found at i:86310 original size:21 final size:21
Alignment explanation
Indices: 86284--86339 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
86274 TCTTTAAAGA
86284 GTGCATCGGTACACATTGAAT
1 GTGCATCGGTACACATTGAAT
86305 GTGCATCGGTACACATTGAAT
1 GTGCATCGGTACACATTGAAT
*
86326 GTGCATCGATACAC
1 GTGCATCGGTACAC
86340 TTTGCCCAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (21 bp):
GTGCATCGGTACACATTGAAT
Found at i:88211 original size:59 final size:59
Alignment explanation
Indices: 88119--88239 Score: 197
Period size: 59 Copynumber: 2.1 Consensus size: 59
88109 AATAGATGGA
*
88119 TAAGTGTCTATTCGAACCCTCATAGTCGCAATGAAAGGGAAAACTCGATAATATGGCTC
1 TAAGTGTCTATTCGAACCCTCATAGTCGCAATGAAAAGGAAAACTCGATAATATGGCTC
* * * *
88178 TAAGTGTCTATTTGAACCCTCCTAGTCGCAATGAAAAGGCAAACTTGATAATATGGCTC
1 TAAGTGTCTATTCGAACCCTCATAGTCGCAATGAAAAGGAAAACTCGATAATATGGCTC
88237 TAA
1 TAA
88240 CCAACCCTCA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (59 bp):
TAAGTGTCTATTCGAACCCTCATAGTCGCAATGAAAAGGAAAACTCGATAATATGGCTC
Found at i:90035 original size:23 final size:23
Alignment explanation
Indices: 90009--90053 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
89999 CACCACAACT
* *
90009 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
*
90032 CGTAGAATTACACCGAAGTGCC
1 CGTAGAAATACACCGAAGTGCC
90054 GCTTAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:90063 original size:23 final size:23
Alignment explanation
Indices: 90019--90063 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
90009 CGTATAAATG
*
90019 CACCGAAGTGCCACGTAGAATTA
1 CACCGAAGTGCCACGTAAAATTA
* *
90042 CACCGAAGTGCCGCTTAAAATT
1 CACCGAAGTGCCACGTAAAATT
90064 GTAATGTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAAAATTA
Found at i:90808 original size:22 final size:22
Alignment explanation
Indices: 90747--90798 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
90737 GCACTGTAGC
90747 ACTGTTCATGGTAATGTTTATT
1 ACTGTTCATGGTAATGTTTATT
*
90769 ACTATTCATGGTAATGTTTATT
1 ACTGTTCATGGTAATGTTTATT
90791 ACTGTTCA
1 ACTGTTCA
90799 CAGTAGTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.48
Consensus pattern (22 bp):
ACTGTTCATGGTAATGTTTATT
Found at i:98102 original size:14 final size:15
Alignment explanation
Indices: 98070--98102 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
98060 GTAGCAGATC
*
98070 GAAATCCAGAAGGGG
1 GAAATCCAGAAGCGG
98085 GAAATCCAGAA-CGG
1 GAAATCCAGAAGCGG
98099 GAAA
1 GAAA
98103 GGAATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.45, C:0.15, G:0.33, T:0.06
Consensus pattern (15 bp):
GAAATCCAGAAGCGG
Found at i:103430 original size:20 final size:20
Alignment explanation
Indices: 103405--103446 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
103395 TTAAAGACAC
103405 AACACGACTAAATTGAATAG
1 AACACGACTAAATTGAATAG
103425 AACACGACTAAATTGAATAG
1 AACACGACTAAATTGAATAG
103445 AA
1 AA
103447 TTAAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.19
Consensus pattern (20 bp):
AACACGACTAAATTGAATAG
Found at i:113046 original size:18 final size:18
Alignment explanation
Indices: 113016--113075 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
113006 TATATATAAA
113016 TTATATATATAAACTATAT
1 TTATAT-TATAAACTATAT
113035 TTATATTATAAACTATA-
1 TTATATTATAAACTATAT
* *
113052 TAATTATTATAAGCTATAT
1 TTA-TATTATAAACTATAT
*
113071 ATATA
1 TTATA
113076 AATTATGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 2 0.06
18 26 0.74
19 7 0.20
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (18 bp):
TTATATTATAAACTATAT
Found at i:113080 original size:20 final size:18
Alignment explanation
Indices: 113023--113081 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
113013 AAATTATATA
*
113023 TATAAACTATAT-TTATAT
1 TATAAACTATATAATA-AT
*
113041 TATAAACTATATAATTAT
1 TATAAACTATATAATAAT
*
113059 TATAAGCTATATATATAAAT
1 TATAAACTATATA-AT-AAT
113079 TAT
1 TAT
113082 GTTTATATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 26 0.76
19 3 0.09
20 5 0.15
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (18 bp):
TATAAACTATATAATAAT
Found at i:113177 original size:2 final size:2
Alignment explanation
Indices: 113170--113213 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
113160 TTAATAATAC
113170 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT
113212 AT
1 AT
113214 TATTCAAAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:113336 original size:17 final size:19
Alignment explanation
Indices: 113314--113369 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 19
113304 TTTAGAAATT
113314 TTGAGAATATA-AGG-AAA
1 TTGAGAATATAGAGGAAAA
*
113331 TTGAGAATTTAGAGGAAAA
1 TTGAGAATATAGAGGAAAA
* *
113350 TTGAGAATTTAGAGGGAAA
1 TTGAGAATATAGAGGAAAA
113369 T
1 T
113370 CGGGAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.29
18 3 0.09
19 22 0.63
ACGTcount: A:0.46, C:0.00, G:0.27, T:0.27
Consensus pattern (19 bp):
TTGAGAATATAGAGGAAAA
Found at i:113378 original size:20 final size:19
Alignment explanation
Indices: 113326--113387 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
113316 GAGAATATAA
*
113326 GGAAATTGAGAATTTAGAG
1 GGAAATCGAGAATTTAGAG
* *
113345 GAAAATTGAGAATTTAGAG
1 GGAAATCGAGAATTTAGAG
*
113364 GGAAATCGGGAAATTTAGAG
1 GGAAATCGAG-AATTTAGAG
113384 GGAA
1 GGAA
113388 TATAAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
19 25 0.66
20 13 0.34
ACGTcount: A:0.44, C:0.02, G:0.32, T:0.23
Consensus pattern (19 bp):
GGAAATCGAGAATTTAGAG
Found at i:114591 original size:2 final size:2
Alignment explanation
Indices: 114584--114616 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
114574 ATTTCTCAGC
114584 AT AT AT 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 AT AT AT A
114617 GGCCGACCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:114968 original size:13 final size:13
Alignment explanation
Indices: 114936--114962 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
114926 TCATTTACAT
114936 TTAAATAATTTTA
1 TTAAATAATTTTA
114949 TTAAATAATTTTA
1 TTAAATAATTTTA
114962 T
1 T
114963 ATAATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:115663 original size:2 final size:2
Alignment explanation
Indices: 115609--115654 Score: 58
Period size: 2 Copynumber: 23.0 Consensus size: 2
115599 ATAAACCATG
**
115609 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA -A CC TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
115651 TA TA
1 TA TA
115655 AACTATATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:115783 original size:14 final size:14
Alignment explanation
Indices: 115763--115802 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
115753 AACCCTAATT
115763 ATAAACTCTAAACC
1 ATAAACTCTAAACC
* *
115777 CTAAACTTTAAACC
1 ATAAACTCTAAACC
*
115791 ATAAACACTAAA
1 ATAAACTCTAAA
115803 TCTTAAACCC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.23
Consensus pattern (14 bp):
ATAAACTCTAAACC
Found at i:115795 original size:21 final size:19
Alignment explanation
Indices: 115744--115811 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 19
115734 ATAGAATCTC
115744 TAAATCCTAAACCCT-AATT
1 TAAA-CCTAAACCCTAAATT
115763 ATAAACTCTAAACCCTAAACTT
1 -TAAAC-CTAAACCCTAAA-TT
*
115785 TAAACCATAAACACTAAATCT
1 TAAACC-TAAACCCTAAAT-T
115806 TAAACC
1 TAAACC
115812 CTAATATAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
19 1 0.02
20 15 0.36
21 24 0.57
22 2 0.05
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAACCTAAACCCTAAATT
Found at i:116006 original size:23 final size:23
Alignment explanation
Indices: 115979--116027 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
115969 TTATTTTTTC
115979 TTTATATAAATTAAACTATATAA
1 TTTATATAAATTAAACTATATAA
*
116002 TTTATATAAATTAAACTATATTA
1 TTTATATAAATTAAACTATATAA
116025 TTT
1 TTT
116028 TTCCTTTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTATATAAATTAAACTATATAA
Found at i:117627 original size:32 final size:32
Alignment explanation
Indices: 117548--117709 Score: 231
Period size: 32 Copynumber: 5.1 Consensus size: 32
117538 GCTCGTATAA
*
117548 TAAT-CTGTCCATATGTCCC-GAAGAACATAGG
1 TAATACTGTCCATATGTCCCAAAAG-ACATAGG
* * *
117579 TAA-ATTATCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCAAAAGACATAGG
117610 TAATACTGTCCATATGTCCCAAAAGACATAGG
1 TAATACTGTCCATATGTCCCAAAAGACATAGG
*
117642 TAATACTGTCCATATGTCCCAAAAGACATAAG
1 TAATACTGTCCATATGTCCCAAAAGACATAGG
* *
117674 TAATATTGTCCATATGTCCCAAAAGGCATAGG
1 TAATACTGTCCATATGTCCCAAAAGACATAGG
117706 TAAT
1 TAAT
117710 CCCTCGACTC
Statistics
Matches: 118, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
31 26 0.22
32 92 0.78
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (32 bp):
TAATACTGTCCATATGTCCCAAAAGACATAGG
Found at i:121509 original size:22 final size:22
Alignment explanation
Indices: 121462--121509 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
121452 AAGGTTACCA
*
121462 TTTTATTTCATTCTTCTGA-TT
1 TTTTATTTCATTCTTCTGAGTG
* *
121483 TTTTTTTTCATTTCTTTTGAGTG
1 TTTTATTTCA-TTCTTCTGAGTG
121506 TTTT
1 TTTT
121510 GAAAAATGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 9 0.41
22 8 0.36
23 5 0.23
ACGTcount: A:0.10, C:0.10, G:0.08, T:0.71
Consensus pattern (22 bp):
TTTTATTTCATTCTTCTGAGTG
Found at i:126950 original size:33 final size:33
Alignment explanation
Indices: 126912--126977 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
126902 ATCGTTATTC
126912 ATTTAGGTGTCTGGCCAGTAATAGTGTTAATTT
1 ATTTAGGTGTCTGGCCAGTAATAGTGTTAATTT
*
126945 ATTTAGGTGTCTGTCCAGTAATAGTGTTAATTT
1 ATTTAGGTGTCTGGCCAGTAATAGTGTTAATTT
126978 TTTCGTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.44
Consensus pattern (33 bp):
ATTTAGGTGTCTGGCCAGTAATAGTGTTAATTT
Found at i:137631 original size:26 final size:24
Alignment explanation
Indices: 137602--137663 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 24
137592 GTCAAATTTT
*
137602 TTTTATTAAAAATAAATA-ATTTACGA
1 TTTTAATAAAAA-AAATATATTT--GA
137628 TTTTAAT-AAAAAAATATATTTGA
1 TTTTAATAAAAAAAATATATTTGA
137651 TTTTAATAAAAAA
1 TTTTAATAAAAAA
137664 CAATTCTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 9 0.27
24 10 0.30
25 8 0.24
26 6 0.18
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (24 bp):
TTTTAATAAAAAAAATATATTTGA
Found at i:137828 original size:27 final size:29
Alignment explanation
Indices: 137793--137866 Score: 98
Period size: 27 Copynumber: 2.6 Consensus size: 29
137783 TTAAATAATA
137793 ATTAATAAAAATTAAAAAATATTT-TTT-
1 ATTAATAAAAATTAAAAAATATTTATTTC
* * * *
137820 ATTAGTAAAAGTTAAGAATTATTTATTTC
1 ATTAATAAAAATTAAAAAATATTTATTTC
137849 ATTAATAAAAATTAAAAA
1 ATTAATAAAAATTAAAAA
137867 CAATAATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 20 0.53
28 3 0.08
29 15 0.39
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (29 bp):
ATTAATAAAAATTAAAAAATATTTATTTC
Found at i:139688 original size:20 final size:20
Alignment explanation
Indices: 139656--139703 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
139646 AACAGTACTA
*
139656 TCGCAACGCGATTTTCAAAT
1 TCGCAACGAGATTTTCAAAT
* *
139676 TCGTAACGAGATTTTTAAAT
1 TCGCAACGAGATTTTCAAAT
139696 TCGCAACG
1 TCGCAACG
139704 CTAATTATCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (20 bp):
TCGCAACGAGATTTTCAAAT
Found at i:139709 original size:77 final size:77
Alignment explanation
Indices: 139603--139753 Score: 239
Period size: 77 Copynumber: 2.0 Consensus size: 77
139593 TGTAAATTAA
* * *
139603 AACGTGATTTTCAAATTCCCAACGTTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGAT
1 AACGAGATTTTCAAATTCCCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCAAT
139668 TTTCAAATTCGT
66 TTTCAAATTCGT
* * *
139680 AACGAGATTTTTAAATTCGCAACGCTAATTATCGATATAGGTAAACAGTACTATCGCAACGCAAT
1 AACGAGATTTTCAAATTCCCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCAAT
*
139745 TTTTAAATT
66 TTTCAAATT
139754 TGCAACGCTA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 67 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.32
Consensus pattern (77 bp):
AACGAGATTTTCAAATTCCCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCAAT
TTTCAAATTCGT
Found at i:139759 original size:57 final size:57
Alignment explanation
Indices: 139686--139967 Score: 424
Period size: 57 Copynumber: 4.9 Consensus size: 57
139676 TCGTAACGAG
* * *
139686 ATTTTTAAATTCGCAACGCTAATTATCGATATAGGTAAACAGTACTATCGCAACGCA
1 ATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAATACTATCGCAACGCA
* * *
139743 ATTTTTAAATTTGCAACGCTAATTACCGATATAGGTAAACAATACAATCGCAACG-A
1 ATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAATACTATCGCAACGCA
* *
139799 GATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCG
1 -ATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAATACTATCGCAACGCA
* * *
139857 ATTTTCAAATTCGCAACGTTAATTACCGATATAGGTAAACAATACTATTGCAACGCG
1 ATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAATACTATCGCAACGCA
*
139914 ATTTTCAAATTCGCAACGATAATTACCGATATAGGTAAACACA-ACTATCGCAAC
1 ATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACA-ATACTATCGCAAC
139968 ACGAATTTCG
Statistics
Matches: 208, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
56 1 0.00
57 206 0.99
58 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (57 bp):
ATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAATACTATCGCAACGCA
Found at i:139836 original size:114 final size:114
Alignment explanation
Indices: 139680--140104 Score: 499
Period size: 114 Copynumber: 3.6 Consensus size: 114
139670 TCAAATTCGT
* *
139680 AACGAGATTTTTAAATTCGCAACGCTAATTATCGATATAGGTAAACAGTACTATCGCAACGCAAT
1 AACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCAAT
* *
139745 TTTTAAATTTGCAACGCTAATTACCGATATAGGTAAACAATACAATCGC
66 TTTCAAATTTGCAACGCTAATTACCGATATAGGTAAACAATACTATCGC
*
139794 AACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCGAT
1 AACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCAAT
* * *
139859 TTTCAAATTCGCAACGTTAATTACCGATATAGGTAAACAATACTATTGC
66 TTTCAAATTTGCAACGCTAATTACCGATATAGGTAAACAATACTATCGC
* * ** *
139908 AACGCGATTTTCAAATTCGCAACGATAATTACCGATATAGGTAAACACAACTATCGCAACACGAA
1 AACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGC-AA
* * * * *
139973 TTTCGCAAATGGAATTCGCCAATTTCCCAACTTAATTATCGACATAGGTAAACAGTACTATCGC
65 TTT-TCAAAT----TT-G-CAA-----C-GC-TAATTACCGATATAGGTAAACAATACTATCGC
* * * ** *
140037 AACGCGATTTTCAAATTCGCAACACGAATTACTAATATAGGTAAACAGTACTATCGCAACGCGAT
1 AACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCAAT
140102 TTT
66 TTT
140105 GGAAACTGTG
Statistics
Matches: 264, Mismatches: 32, Indels: 17
0.84 0.10 0.05
Matches are distributed among these distances:
114 163 0.62
115 4 0.02
116 5 0.02
120 1 0.00
121 1 0.00
122 3 0.01
127 1 0.00
128 4 0.02
129 82 0.31
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (114 bp):
AACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCAAT
TTTCAAATTTGCAACGCTAATTACCGATATAGGTAAACAATACTATCGC
Found at i:142129 original size:2 final size:2
Alignment explanation
Indices: 142122--142149 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
142112 AGGATTATGC
142122 AT 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
142150 TGAAGTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:147888 original size:21 final size:21
Alignment explanation
Indices: 147862--147916 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
147852 TAGAGCATGG
* *
147862 GGGTATCGGTGCCCCTTCATA
1 GGGTATCGATACCCCTTCATA
147883 GGGTATCGATACCCCTTCATA
1 GGGTATCGATACCCCTTCATA
*
147904 AGGTATCGATACC
1 GGGTATCGATACC
147917 TGTAGTGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (21 bp):
GGGTATCGATACCCCTTCATA
Found at i:148009 original size:19 final size:20
Alignment explanation
Indices: 147958--148011 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
147948 ATATGCCTTA
*
147958 GGGTATCAGTACCATCTGAG
1 GGGTATCAGTACCATATGAG
147978 GGGTATC-GATACC-TATGAG
1 GGGTATCAG-TACCATATGAG
147997 GGGTATCAGTACCAT
1 GGGTATCAGTACCAT
148012 TCGAGCATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (20 bp):
GGGTATCAGTACCATATGAG
Found at i:150773 original size:44 final size:44
Alignment explanation
Indices: 150724--150824 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 44
150714 GTACCATCAG
* * *
150724 GGGGTATCGATACCCATTC-AAGGATGGTATCGATACCTAT-TGAA
1 GGGGTATCGATACACATTCAAAGG-GGGTATCGATACCAATCT-AA
*
150768 GGGGTATCGATACATATTCAAAGGGGGTATCGATACCAATCTAA
1 GGGGTATCGATACACATTCAAAGGGGGTATCGATACCAATCTAA
150812 GGGGTATCGATAC
1 GGGGTATCGATAC
150825 TCTATGCACA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
44 46 0.90
45 5 0.10
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.26
Consensus pattern (44 bp):
GGGGTATCGATACACATTCAAAGGGGGTATCGATACCAATCTAA
Found at i:150775 original size:21 final size:20
Alignment explanation
Indices: 150724--150829 Score: 104
Period size: 23 Copynumber: 4.8 Consensus size: 20
150714 GTACCATCAG
*
150724 GGGGTATCGATACCCATTCAA
1 GGGGTATCGATACCTATT-AA
150745 GGATGGTATCGATACCTATTGAA
1 GG--GGTATCGATACCTATT-AA
*
150768 GGGGTATCGATACATATTCAAA
1 GGGGTATCGATACCTATT--AA
*
150790 GGGGGTATCGATACCAATCTAA
1 -GGGGTATCGATACCTAT-TAA
150812 GGGGTATCGATACTCTAT
1 GGGGTATCGATAC-CTAT
150830 GCACAAAAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
21 30 0.42
22 7 0.10
23 34 0.47
24 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (20 bp):
GGGGTATCGATACCTATTAA
Found at i:160964 original size:2 final size:2
Alignment explanation
Indices: 160957--160982 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
160947 AAATGAAACA
160957 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
160983 TGGATGGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:168484 original size:129 final size:132
Alignment explanation
Indices: 168197--168659 Score: 440
Period size: 135 Copynumber: 3.4 Consensus size: 132
168187 ATTTGCTGAA
* *
168197 GATGACACTGCTCATACGTGATGAAGAGTTCTTGGTCATCTTTAGGGA-GGAGGATAACACGGTT
1 GATGACACTGCTCATACGTGATGAAGAGTTCTTGGTCATCTTTAGGAATGG-TGATAACA--G-T
* * *
168261 CCACTCTGCTGGGG-ACGACTGGTTATCTGA-GTTGACGCTGCTCCTACATGATGAGGAGATCTG
62 -CACTCTGCTGGGGAACG-CTGGTTATCTGAGGTTGACACGGCTCCTACATGATGAGGAAATCTG
*
168324 GTCAGTGG
125 GTCAGGGG
* ** *
168332 GATGACGCTATTCATACGCGATGAAGAGTTCTTGGTCATCTTTAGGAATGGTGATAACA-T-ACT
1 GATGACACTGCTCATACGTGATGAAGAGTTCTTGGTCATCTTTAGGAATGGTGATAACAGTCACT
* * * * * * *
168395 CTGTTGGGGAATGCTGGTTATCTGAGGTTGATACGGTTCC-ACTCTGCTGGGGAAATCTGGTC-G
66 CTGCTGGGGAACGCTGGTTATCTGAGGTTGACACGGCTCCTAC-ATGATGAGGAAATCTGGTCAG
168458 GGG
130 GGG
* *
168461 GATGACACTGCTCATCCGTGATGAAGAGTTCTTGGCCATCTTTAGGAATGGTGATAACACGGTTC
1 GATGACACTGCTCATACGTGATGAAGAGTTCTTGGTCATCTTTAGGAATGGTGATAACA--G-T-
* * **
168526 CACTCTGCTGGGG-ACGGCTGGTTATCTGAGGTTGACACTGCTCCTACGTGATGAGGAGGTCTGG
62 CACTCTGCTGGGGAAC-GCTGGTTATCTGAGGTTGACACGGCTCCTACATGATGAGGAAATCT-G
*
168590 TCGTCTAAGGGTA
125 --GTC--AGGG-G
* * * * *
168603 GATGACACGGTTCATACGTGATGAAGAATTC-TGGCCATCTTTAGGAAAGGTGATAAC
1 GATGACACTGCTCATACGTGATGAAGAGTTCTTGGTCATCTTTAGGAATGGTGATAAC
168660 TCGGTTCCTA
Statistics
Matches: 270, Mismatches: 39, Indels: 32
0.79 0.11 0.09
Matches are distributed among these distances:
129 81 0.30
130 27 0.10
131 1 0.00
133 1 0.00
134 1 0.00
135 96 0.36
136 5 0.02
138 3 0.01
141 28 0.10
142 27 0.10
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (132 bp):
GATGACACTGCTCATACGTGATGAAGAGTTCTTGGTCATCTTTAGGAATGGTGATAACAGTCACT
CTGCTGGGGAACGCTGGTTATCTGAGGTTGACACGGCTCCTACATGATGAGGAAATCTGGTCAGG
GG
Found at i:168723 original size:141 final size:142
Alignment explanation
Indices: 168196--168731 Score: 381
Period size: 135 Copynumber: 3.9 Consensus size: 142
168186 TATTTGCTGA
* * * * *
168196 AGATGACACTGCTCATACGTGATGAAGAGTTCTTGGTCATCTTTAGG-GAGGAGGATAACACGGT
1 AGATGACACGGCTCATACGTGATGAAGAATTCTTGGCCATCTTTAGGAAAGG-TGATAACACGGT
* * * * * * * *
168260 TCCACTCTGCTGGGGACGACTGGTTATCTGA-GTTGACGCTGCTCCTACATGATGAGGAGATCT-
65 TCCACTATGATGAGGACGGCTGGTTATCTAAGGTTGACACTGCTCCTACGTGACGAGGAGATCTG
168323 G--GTC--AGTGG-
130 GTCGTCTAAG-GGT
* *** * * * *
168332 -GATGACGCTATTCATACGCGATGAAGAGTTCTTGGTCATCTTTAGGAATGGTGATAACA----T
1 AGATGACACGGCTCATACGTGATGAAGAATTCTTGGCCATCTTTAGGAAAGGTGATAACACGGTT
* * * ** * * * * * * *
168392 --ACTCTGTTGGGGAATGCTGGTTATCTGAGGTTGATACGGTTCC-ACTCTG-CTGGGGAAATCT
66 CCACTATGATGAGGACGGCTGGTTATCTAAGGTTGACACTGCTCCTAC-GTGAC-GAGGAGATCT
168453 GGTCG-----GGG-
129 GGTCGTCTAAGGGT
* * * *
168461 -GATGACACTGCTCATCCGTGATGAAGAGTTCTTGGCCATCTTTAGGAATGGTGATAACACGGTT
1 AGATGACACGGCTCATACGTGATGAAGAATTCTTGGCCATCTTTAGGAAAGGTGATAACACGGTT
* * * * * *
168525 CCACTCTGCTGGGGACGGCTGGTTATCTGAGGTTGACACTGCTCCTACGTGATGAGGAGGTCTGG
66 CCACTATGATGAGGACGGCTGGTTATCTAAGGTTGACACTGCTCCTACGTGACGAGGAGATCTGG
168590 TCGTCTAAGGGT
131 TCGTCTAAGGGT
* *
168602 AGATGACACGGTTCATACGTGATGAAGAATTC-TGGCCATCTTTAGGAAAGGTGATAACTCGGTT
1 AGATGACACGGCTCATACGTGATGAAGAATTCTTGGCCATCTTTAGGAAAGGTGATAACACGGTT
* * *
168666 CCTAC-ATGATGAGGACGGCTGGTTATCCTAATGTTGACA-TTCTCCTCCGT-ACCGAGGAGATC
66 CC-ACTATGATGAGGACGGCTGGTTAT-CTAAGGTTGACACTGCTCCTACGTGA-CGAGGAGATC
168728 TGGT
128 TGGT
168732 TAGTTGATGT
Statistics
Matches: 324, Mismatches: 51, Indels: 45
0.77 0.12 0.11
Matches are distributed among these distances:
129 81 0.25
130 21 0.06
131 2 0.01
133 2 0.01
135 100 0.31
136 4 0.01
140 4 0.01
141 71 0.22
142 39 0.12
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (142 bp):
AGATGACACGGCTCATACGTGATGAAGAATTCTTGGCCATCTTTAGGAAAGGTGATAACACGGTT
CCACTATGATGAGGACGGCTGGTTATCTAAGGTTGACACTGCTCCTACGTGACGAGGAGATCTGG
TCGTCTAAGGGT
Found at i:169711 original size:19 final size:19
Alignment explanation
Indices: 169683--169719 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
169673 TCCTTTATTT
169683 ATTTTTTCTTT-TTTTTTC
1 ATTTTTTCTTTCTTTTTTC
169701 ATTTTTCTCTTTCTTTTTT
1 ATTTTT-TCTTTCTTTTTT
169720 TTTCATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (19 bp):
ATTTTTTCTTTCTTTTTTC
Found at i:169713 original size:23 final size:23
Alignment explanation
Indices: 169687--169730 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
169677 TTATTTATTT
169687 TTTCTTTTTTTTTCATTTTTCTC
1 TTTCTTTTTTTTTCATTTTTCTC
169710 TTTCTTTTTTTTTCATTTTTC
1 TTTCTTTTTTTTTCATTTTTC
169731 CATAACCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTCTTTTTTTTTCATTTTTCTC
Found at i:169741 original size:23 final size:23
Alignment explanation
Indices: 169692--169741 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
169682 TATTTTTTCT
** *
169692 TTTTTTTTCATTTTTCTCTTTCT
1 TTTTTTTTCATTTTTCTCTAACC
169715 TTTTTTTTCATTTTTC-CATAACC
1 TTTTTTTTCATTTTTCTC-TAACC
169738 TTTT
1 TTTT
169742 AATTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTTTTTTCATTTTTCTCTAACC
Found at i:176882 original size:30 final size:30
Alignment explanation
Indices: 176848--176910 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
176838 TTAAATTCGA
176848 ATGCATATTATTGGTAAT-AAGTTATAAATG
1 ATGCATATTATTGGTAATGAA-TTATAAATG
* * *
176878 ATGCATTTTATTGGTGATGCATTATAAATG
1 ATGCATATTATTGGTAATGAATTATAAATG
176908 ATG
1 ATG
176911 AATTTACTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (30 bp):
ATGCATATTATTGGTAATGAATTATAAATG
Found at i:179801 original size:4 final size:4
Alignment explanation
Indices: 179792--179818 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
179782 ACATACTCAA
179792 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
179819 AGGTTAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:186667 original size:18 final size:17
Alignment explanation
Indices: 186634--186667 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
186624 GAATAATTAA
186634 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
186651 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
186668 AAACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:187007 original size:2 final size:2
Alignment explanation
Indices: 187000--187030 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
186990 TCAGATCAGA
187000 AT AT 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 AT AT A
187031 CTAGTGTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:196036 original size:2 final size:2
Alignment explanation
Indices: 196029--196057 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
196019 ATTTATCATT
196029 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
196058 TAAATTTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:196653 original size:6 final size:6
Alignment explanation
Indices: 196624--196711 Score: 54
Period size: 6 Copynumber: 14.2 Consensus size: 6
196614 CCAACTCCAG
* * * *
196624 CAGCAG CAGCAG CAGCAA CAGCAA CAGCAA CTAAGCCAG CAGCAA CAGAAA
1 CAGCAA CAGCAA CAGCAA CAGCAA CAGCAA C--AG-CAA CAGCAA CAGCAA
* * *
196675 CAACAA CA--AA TCCAGCAG CAGCAG CAGCAA CAGCAA C
1 CAGCAA CAGCAA --CAGCAA CAGCAA CAGCAA CAGCAA C
196712 TAAGCCAGCA
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
4 2 0.03
6 57 0.85
7 2 0.03
8 3 0.04
9 3 0.04
ACGTcount: A:0.45, C:0.33, G:0.19, T:0.02
Consensus pattern (6 bp):
CAGCAA
Found at i:196663 original size:27 final size:27
Alignment explanation
Indices: 196633--196726 Score: 125
Period size: 27 Copynumber: 3.4 Consensus size: 27
196623 GCAGCAGCAG
196633 CAGCAGCAACAGCAACAGCAACTAAGC
1 CAGCAGCAACAGCAACAGCAACTAAGC
* * * *
196660 CAGCAGCAACAGAAACAACAACAAATC
1 CAGCAGCAACAGCAACAGCAACTAAGC
196687 CAGCAGCAGCAGCAGCAACAGCAACTAAGC
1 CAGCAGCA--A-CAGCAACAGCAACTAAGC
196717 CAGCAGCAAC
1 CAGCAGCAAC
196727 TGCAGACTCA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
27 32 0.57
28 1 0.02
29 1 0.02
30 22 0.39
ACGTcount: A:0.46, C:0.33, G:0.18, T:0.03
Consensus pattern (27 bp):
CAGCAGCAACAGCAACAGCAACTAAGC
Found at i:198487 original size:27 final size:27
Alignment explanation
Indices: 198457--198520 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
198447 TCAAATGCAG
**
198457 CAGCAGCAACAACAAGTACTGCAACAA
1 CAGCAGCAACAACAACAACTGCAACAA
** *
198484 CAGCAGTTACAACAACAACTTCAACAA
1 CAGCAGCAACAACAACAACTGCAACAA
*
198511 CAACAGCAAC
1 CAGCAGCAAC
198521 TATTGCATCA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.48, C:0.31, G:0.11, T:0.09
Consensus pattern (27 bp):
CAGCAGCAACAACAACAACTGCAACAA
Found at i:201062 original size:8 final size:8
Alignment explanation
Indices: 201049--201083 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
201039 CATTCTCTAT
*
201049 CATGCATG
1 CATGCATA
201057 CATGCATA
1 CATGCATA
201065 CATGCATA
1 CATGCATA
*
201073 CATACATA
1 CATGCATA
201081 CAT
1 CAT
201084 ATATTTATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (8 bp):
CATGCATA
Found at i:201957 original size:24 final size:24
Alignment explanation
Indices: 201930--201986 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
201920 TCCTATCCAT
*
201930 GATTTTAGTTGATCCCTCGTTAGG
1 GATTTTAGTTGATCCCTCATTAGG
201954 GATTTTAGTTGATCCCTCATTAGG
1 GATTTTAGTTGATCCCTCATTAGG
201978 GATTTTAGT
1 GATTTTAGT
201987 CATGAATGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.19, C:0.14, G:0.23, T:0.44
Consensus pattern (24 bp):
GATTTTAGTTGATCCCTCATTAGG
Found at i:210296 original size:13 final size:13
Alignment explanation
Indices: 210278--210303 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
210268 ATTTTGTTCA
210278 TAAAAATTATTTG
1 TAAAAATTATTTG
210291 TAAAAATTATTTG
1 TAAAAATTATTTG
210304 CAAACATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TAAAAATTATTTG
Found at i:210312 original size:13 final size:13
Alignment explanation
Indices: 210279--210312 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
210269 TTTTGTTCAT
*
210279 AAAAATTATTTGT
1 AAAAATTATTTGC
210292 AAAAATTATTTGC
1 AAAAATTATTTGC
*
210305 AAACATTA
1 AAAAATTA
210313 ATTATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (13 bp):
AAAAATTATTTGC
Done.