Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 81 of 295
Found at i:23706389 original size:33 final size:33
Alignment explanation
Indices: 23706351--23706419 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
23706341 AGATGAAAAG
23706351 TTAGAACTTAATTATAAATCATTTGAACTTTAA
1 TTAGAACTTAATTATAAATCATTTGAACTTTAA
23706384 TTAGAACTTAATTATAAATCATTTGAACTTTAA
1 TTAGAACTTAATTATAAATCATTTGAACTTTAA
23706417 TTA
1 TTA
23706420 CATATGTCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (33 bp):
TTAGAACTTAATTATAAATCATTTGAACTTTAA
Found at i:23713359 original size:28 final size:28
Alignment explanation
Indices: 23713327--23713381 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
23713317 GCAGAGTTTC
23713327 CCTCTTCATTGTTTTACAATATTTTATG
1 CCTCTTCATTGTTTTACAATATTTTATG
23713355 CCTCTTCATTGTTTTACAATATTTTAT
1 CCTCTTCATTGTTTTACAATATTTTAT
23713382 ATATTTGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.05, T:0.55
Consensus pattern (28 bp):
CCTCTTCATTGTTTTACAATATTTTATG
Found at i:23715921 original size:29 final size:29
Alignment explanation
Indices: 23715884--23715939 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
23715874 AAGCTTCTTC
23715884 AAAGAATGAAATATTCACAAAAAGGTGTA
1 AAAGAATGAAATATTCACAAAAAGGTGTA
* *
23715913 AAAGCATGAAATATTCATAAAAAGGTG
1 AAAGAATGAAATATTCACAAAAAGGTG
23715940 CAGTAGTGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.54, C:0.07, G:0.18, T:0.21
Consensus pattern (29 bp):
AAAGAATGAAATATTCACAAAAAGGTGTA
Found at i:23732767 original size:41 final size:42
Alignment explanation
Indices: 23732666--23732780 Score: 135
Period size: 44 Copynumber: 2.7 Consensus size: 42
23732656 TATTGCAAAT
*
23732666 CTTATCGCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAAC
1 CTTATCCCTCTGAAGTTGCAGTAGAGCAGATTAAA-C-ATAAAC
* * **
23732710 CTTATCCCTCTGAAGTTGCAGTAGAGCAGGTTAAA-ATTAGT
1 CTTATCCCTCTGAAGTTGCAGTAGAGCAGATTAAACATAAAC
*
23732751 CTTATCTCCT-TGAAGTTGCAGTGGAGCAGA
1 CTTATC-CCTCTGAAGTTGCAGTAGAGCAGA
23732781 CTGAAGATAG
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
41 27 0.43
42 3 0.05
44 33 0.52
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (42 bp):
CTTATCCCTCTGAAGTTGCAGTAGAGCAGATTAAACATAAAC
Found at i:23733114 original size:44 final size:44
Alignment explanation
Indices: 23732947--23733149 Score: 156
Period size: 44 Copynumber: 4.6 Consensus size: 44
23732937 CATGGCGAAT
* * * * *
23732947 CTTATCTCCCTGAAGTTGCAGAGGAGCAGATTGAAATC-ACTAAT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATT-AAAGCTACAAAC
* * * ** * * *
23732991 CTTTTCTCCTTGAAGTTGCAGTGGAGTGGATTGAAGATAGCAAAT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTA-CAAAC
* * * * * * *
23733036 TTTACCTCTCTGAAGTTGCATTAGAGCAGATTAAAGCTATAAAC
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAAC
* * **
23733080 CTTATCTCCCTAAAGTTGCAGTGGAGCAGGTTAAAGTTACAAGT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAAC
*
23733124 CTTATCTCCCTGAAGTTGCAGTGGAG
1 CTTATCTCCCTAAAGTTGCAGTGGAG
23733150 TGGATCGACT
Statistics
Matches: 123, Mismatches: 34, Indels: 4
0.76 0.21 0.02
Matches are distributed among these distances:
43 2 0.02
44 89 0.72
45 32 0.26
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (44 bp):
CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAAC
Found at i:23733676 original size:35 final size:35
Alignment explanation
Indices: 23733620--23733687 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
23733610 TTTATTTAAT
*
23733620 ATTTCTTTATTCTTTTATTTATTTGCTTATTTTCA
1 ATTTCTTTATTCTTTTATTTATTTACTTATTTTCA
* *
23733655 ATTT-TTTATTTTATTTGTTTATTTACTTATTTT
1 ATTTCTTTATTCT-TTTATTTATTTACTTATTTT
23733688 TTAACTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 7 0.24
35 22 0.76
ACGTcount: A:0.18, C:0.07, G:0.03, T:0.72
Consensus pattern (35 bp):
ATTTCTTTATTCTTTTATTTATTTACTTATTTTCA
Found at i:23733711 original size:27 final size:26
Alignment explanation
Indices: 23733625--23733743 Score: 89
Period size: 27 Copynumber: 4.4 Consensus size: 26
23733615 TTAATATTTC
* *
23733625 TTTATTCTTTTATTTATTTG-CTTATT
1 TTTATT-TTTTAATTATTTGTTTTATT
* *
23733651 TTCAATTTTTTATTTTATTTG-TTTATT
1 TT-TATTTTTTA-ATTATTTGTTTTATT
*
23733678 TACTTATTTTTTAACTTGTTTGTTTTATT
1 T--TTATTTTTTAA-TTATTTGTTTTATT
* * *
23733707 TTTATTTCTTTTATTATTTATCTTATT
1 TTTATTT-TTTAATTATTTGTTTTATT
23733734 TTTATTTTTT
1 TTTATTTTTT
23733744 GCTCTTATTA
Statistics
Matches: 77, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
26 10 0.13
27 41 0.53
28 18 0.23
29 8 0.10
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.74
Consensus pattern (26 bp):
TTTATTTTTTAATTATTTGTTTTATT
Found at i:23734552 original size:3 final size:3
Alignment explanation
Indices: 23734546--23734589 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
23734536 GGTTTCGACA
23734546 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
23734590 CAACTTGTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:23736437 original size:17 final size:15
Alignment explanation
Indices: 23736416--23736455 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
23736406 TAATTGAGAT
23736416 ATTAAATTATATAAAA
1 ATTAAA-TATATAAAA
23736432 ATTTAAA-ATATAAAA
1 A-TTAAATATATAAAA
23736447 ATTAAATAT
1 ATTAAATAT
23736456 TGAATTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.23
15 11 0.50
16 1 0.05
17 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATTAAATATATAAAA
Found at i:23737492 original size:20 final size:20
Alignment explanation
Indices: 23737467--23737505 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
23737457 TAAATGTATA
23737467 TTAAAAAAT-TACTAAAAATC
1 TTAAAAAATATA-TAAAAATC
*
23737487 TTAAAAGATATATAAAAAT
1 TTAAAAAATATATAAAAAT
23737506 ACTAATCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (20 bp):
TTAAAAAATATATAAAAATC
Found at i:23738009 original size:17 final size:17
Alignment explanation
Indices: 23737987--23738024 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
23737977 TCTCCATTGG
23737987 ATGTTCATTGATAGATA
1 ATGTTCATTGATAGATA
*
23738004 ATGTTCATTGGTAGATA
1 ATGTTCATTGATAGATA
23738021 ATGT
1 ATGT
23738025 GGCTCGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (17 bp):
ATGTTCATTGATAGATA
Found at i:23739839 original size:11 final size:11
Alignment explanation
Indices: 23739825--23739869 Score: 63
Period size: 11 Copynumber: 3.9 Consensus size: 11
23739815 AAATAACTAT
23739825 TATTTTATTAA
1 TATTTTATTAA
*
23739836 TATTTTAATAAGA
1 TATTTT-ATTA-A
23739849 TATTTTATTAA
1 TATTTTATTAA
23739860 TATTTTATTA
1 TATTTTATTA
23739870 GTATATAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 17 0.57
12 6 0.20
13 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:23741764 original size:46 final size:46
Alignment explanation
Indices: 23741712--23742084 Score: 478
Period size: 46 Copynumber: 8.1 Consensus size: 46
23741702 GCTCCCTGAA
** *
23741712 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * *
23741758 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
23741804 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAG
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
23741850 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
23741896 ATGAAAAGAATAAGACCATGGTTGAGAGATACCATGGAAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * * * * *
23741942 GGGAAATGAATAAGACCATGGTTAAAAGATACTATGGCAGCGTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
23741988 GTGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
23742034 ATGAAAAGAATAAAACCATGGTTGAAAAATACCATGACAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
23742080 A-GAAA
1 ATGAAA
23742085 ATGAGTATTT
Statistics
Matches: 295, Mismatches: 32, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
45 4 0.01
46 291 0.99
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:23741783 original size:21 final size:21
Alignment explanation
Indices: 23741759--23741830 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
23741749 CAACATGATA
23741759 TGAAATGTGTAAGACCATGGT
1 TGAAATGTGTAAGACCATGGT
* *
23741780 TGAAA-G-ATACCATGACAACATGAT
1 TGAAATGTGTA--A-GAC--CATGGT
23741804 ATGAAATGTGTAAGACCATGGT
1 -TGAAATGTGTAAGACCATGGT
23741826 TGAAA
1 TGAAA
23741831 GATACCATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 11 0.28
22 8 0.21
24 8 0.21
25 6 0.15
26 1 0.03
27 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (21 bp):
TGAAATGTGTAAGACCATGGT
Found at i:23741960 original size:138 final size:139
Alignment explanation
Indices: 23741712--23742088 Score: 544
Period size: 138 Copynumber: 2.7 Consensus size: 139
23741702 GCTCCCTGAA
* * * **
23741712 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCAT
* * ** *
23741777 GGTTGAAAGATACCATGACAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGC
66 GGTTGAAAGATACCATGACAACATGACAGGAAATGAATAAGACCATGGTTAAAAGATACCATGGC
23741842 AACATGA-G
131 AACATGATG
23741850 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCAT
* * *
23741915 GGTTGAGAGATACCATGGA-AACATGACGGGAAATGAATAAGACCATGGTTAAAAGATACTATGG
66 GGTTGAAAGATACCAT-GACAACATGACAGGAAATGAATAAGACCATGGTTAAAAGATACCATGG
* *
23741979 CAGCGTGATG
130 CAACATGATG
** *
23741989 -TGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAAACCAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCAT
* *
23742053 GGTTGAAAAATACCATGACAACATGACAGAAAATGA
66 GGTTGAAAGATACCATGACAACATGACAGGAAATGA
23742089 GTATTTATAA
Statistics
Matches: 214, Mismatches: 22, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
137 2 0.01
138 209 0.98
139 3 0.01
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (139 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAGACCAT
GGTTGAAAGATACCATGACAACATGACAGGAAATGAATAAGACCATGGTTAAAAGATACCATGGC
AACATGATG
Found at i:23744682 original size:20 final size:20
Alignment explanation
Indices: 23744657--23744695 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
23744647 TAAATGTATA
23744657 TTAAAAAAT-TACTAAAAATC
1 TTAAAAAATATA-TAAAAATC
*
23744677 TTAAAAGATATATAAAAAT
1 TTAAAAAATATATAAAAAT
23744696 ACTAATCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (20 bp):
TTAAAAAATATATAAAAATC
Found at i:23746630 original size:48 final size:46
Alignment explanation
Indices: 23746567--23746700 Score: 153
Period size: 48 Copynumber: 2.8 Consensus size: 46
23746557 GTGATAATTT
*
23746567 TAAATTTTCAATACTATTCGATATTTTTTTAATTTATGCAAATT-TAAA
1 TAAA-TTTCAATACTATT-GATATTTTTTTCATTTATGC-AATTATAAA
* *
23746615 TAAATTTGCAATACTATTTGATATTTTATTCATTTATGCAATTATAAT
1 TAAATTT-CAATACTA-TTGATATTTTTTTCATTTATGCAATTATAAA
* *
23746663 TACAATTTCAATACTGCTTGATTTTTTTTTCATTTATG
1 TA-AATTTCAATACT-ATTGATATTTTTTTCATTTATG
23746701 ATGTTTGCAT
Statistics
Matches: 75, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
47 7 0.09
48 61 0.81
49 7 0.09
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (46 bp):
TAAATTTCAATACTATTGATATTTTTTTCATTTATGCAATTATAAA
Found at i:23748300 original size:18 final size:18
Alignment explanation
Indices: 23748277--23748314 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
23748267 TGACAGGTGC
*
23748277 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
23748295 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
23748313 GT
1 GT
23748315 TTTTTTTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:23752123 original size:251 final size:252
Alignment explanation
Indices: 23751677--23752222 Score: 925
Period size: 251 Copynumber: 2.2 Consensus size: 252
23751667 GCCCAAGTTA
* * *
23751677 TTTCAGAAACCACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGAAAA
**
23751742 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTATGCAGACACGTCTTCTCAAAATTATTTTTTC
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTACACAGACACGTCTTCTCAAAATTATTTTTTC
23751807 AGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAATGCA
131 AGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAATGCA
23751872 TCCTGCTTGAAGCGTTTTT-ACCACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
196 TCCTGCTTGAAGCGTTTTTGA-CACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
*
23751929 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGACAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGAAAA
* *
23751994 TGCATCCTGCTTGAAGC-TTTTTTACACTATTTGCACAGACACGTCTTCTCAAAATTATTTTTTC
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTACACAGACACGTCTTCTCAAAATTATTTTTTC
* * * * * *
23752058 AGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAATGCA
131 AGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAATGCA
*
23752123 TCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAATTTATTT
196 TCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
*
23752180 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTAGAAGCTT
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTT
23752223 TTTTAGATTA
Statistics
Matches: 277, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
251 198 0.71
252 79 0.29
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (252 bp):
TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGAAAA
TGCATCCTGCTTGAAGCGTTTTTGACACTATTTACACAGACACGTCTTCTCAAAATTATTTTTTC
AGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAATGCA
TCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
Found at i:23752222 original size:126 final size:126
Alignment explanation
Indices: 23751677--23752214 Score: 918
Period size: 126 Copynumber: 4.3 Consensus size: 126
23751667 GCCCAAGTTA
* *
23751677 TTTCAGAAACCACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
**
23751742 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTATGCAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* * * *
23751803 TTTCAGAGACCACTGTAGCAAAAGAGCATCCACGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
23751868 TGCATCCTGCTTGAAGCGTTTTT-ACCACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGA-CACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* *
23751929 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGACAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
* *
23751994 TGCATCCTGCTTGAAGC-TTTTTTACACTATTTGCACAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* *
23752054 TTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
*
23752119 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAATTTATTT
66 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
23752180 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGT
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGT
23752215 AGAAGCTTTT
Statistics
Matches: 390, Mismatches: 19, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
125 121 0.31
126 269 0.69
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.33
Consensus pattern (126 bp):
TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
TGCATCCTGCTTGAAGCGTTTTTGACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
Found at i:23752316 original size:14 final size:15
Alignment explanation
Indices: 23752297--23752325 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
23752287 TTTCTTAAAT
23752297 ACCCTAAAA-CCTAA
1 ACCCTAAAATCCTAA
23752311 ACCCTAAAATCCTAA
1 ACCCTAAAATCCTAA
23752326 TCTAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.34, G:0.00, T:0.17
Consensus pattern (15 bp):
ACCCTAAAATCCTAA
Found at i:23762447 original size:17 final size:16
Alignment explanation
Indices: 23762425--23762456 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
23762415 TTTGATATTA
23762425 TATTATTTAATTAATAC
1 TATTATTT-ATTAATAC
23762442 TATTATTTATTAATA
1 TATTATTTATTAATA
23762457 TTTAATAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTATTTATTAATAC
Found at i:23764364 original size:46 final size:46
Alignment explanation
Indices: 23764312--23764683 Score: 478
Period size: 46 Copynumber: 8.1 Consensus size: 46
23764302 GCTCCCTGAA
** *
23764312 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * *
23764358 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
23764404 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAG
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** *
23764450 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
23764496 ATGAAA-GAATAAGACCATGGTTGAGAGATACCATGGAAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * * * * *
23764541 GGGAAATGAATAAGACCATGGTTAAAAGATACTATGGCAGCGTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
23764587 GTGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
23764633 ATGAAAAGAATAAAACCATGGTTGAAAAATACCATGACAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
23764679 A-GAAA
1 ATGAAA
23764684 ATGAGTATTT
Statistics
Matches: 295, Mismatches: 30, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
45 42 0.14
46 253 0.86
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:23764383 original size:21 final size:21
Alignment explanation
Indices: 23764359--23764430 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
23764349 CAACATGATA
23764359 TGAAATGTGTAAGACCATGGT
1 TGAAATGTGTAAGACCATGGT
* *
23764380 TGAAA-G-ATACCATGACAACATGAT
1 TGAAATGTGTA--A-GAC--CATGGT
23764404 ATGAAATGTGTAAGACCATGGT
1 -TGAAATGTGTAAGACCATGGT
23764426 TGAAA
1 TGAAA
23764431 GATACCATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 11 0.28
22 8 0.21
24 8 0.21
25 6 0.15
26 1 0.03
27 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (21 bp):
TGAAATGTGTAAGACCATGGT
Found at i:23764653 original size:183 final size:182
Alignment explanation
Indices: 23764322--23764683 Score: 499
Period size: 183 Copynumber: 2.0 Consensus size: 182
23764312 ATGAAATGTG
* * * ** *
23764322 TAAGACCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGAAACATGACAGGAAATGAATAAGACCATGGTTAAAAGA
** *
23764387 TACCATGACAACATGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAGAT
66 TACCATGACAACATGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAT
* ** * * * *
23764452 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAGAA
131 GAAAAGAATAAAACCATGGTTGAAAAATACCATGACAACATGACA-GAAAGAA
* *
23764505 TAAGACCATGGTTGAGAGATACCATGGAAACATGACGGGAAATGAATAAGACCATGGTTAAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGAAACATGACAGGAAATGAATAAGACCATGGTTAAAAGA
* * * * * *
23764570 TACTATGGCAGCGTGATGTGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGACAT
66 TACCATGACAACATGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAT
23764635 GAAAAGAATAAAACCATGGTTGAAAAATACCATGACAACATGACAGAAA
131 GAAAAGAATAAAACCATGGTTGAAAAATACCATGACAACATGACAGAAA
23764684 ATGAGTATTT
Statistics
Matches: 155, Mismatches: 24, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
182 4 0.03
183 151 0.97
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (182 bp):
TAAGACCATGGTTGAAAGATACCATGGAAACATGACAGGAAATGAATAAGACCATGGTTAAAAGA
TACCATGACAACATGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAT
GAAAAGAATAAAACCATGGTTGAAAAATACCATGACAACATGACAGAAAGAA
Found at i:23767282 original size:20 final size:20
Alignment explanation
Indices: 23767257--23767295 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
23767247 TAAATGTATA
23767257 TTAAAAAAT-TACTAAAAATC
1 TTAAAAAATATA-TAAAAATC
*
23767277 TTAAAAGATATATAAAAAT
1 TTAAAAAATATATAAAAAT
23767296 ACTAATCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (20 bp):
TTAAAAAATATATAAAAATC
Found at i:23769232 original size:48 final size:46
Alignment explanation
Indices: 23769169--23769302 Score: 153
Period size: 48 Copynumber: 2.8 Consensus size: 46
23769159 GTGATAATTT
*
23769169 TAAATTTTCAATACTATTCGATATTTTTTTAATTTATGCAAATT-TAAA
1 TAAA-TTTCAATACTATT-GATATTTTTTTCATTTATGC-AATTATAAA
* *
23769217 TAAATTTGCAATACTATTTGATATTTTATTCATTTATGCAATTATAAT
1 TAAATTT-CAATACTA-TTGATATTTTTTTCATTTATGCAATTATAAA
* *
23769265 TACAATTTCAATACTGCTTGATTTTTTTTTCATTTATG
1 TA-AATTTCAATACT-ATTGATATTTTTTTCATTTATG
23769303 ATGTTTGCAT
Statistics
Matches: 75, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
47 7 0.09
48 61 0.81
49 7 0.09
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (46 bp):
TAAATTTCAATACTATTGATATTTTTTTCATTTATGCAATTATAAA
Found at i:23770907 original size:18 final size:18
Alignment explanation
Indices: 23770884--23770921 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
23770874 TGACAGGTGC
*
23770884 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
23770902 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
23770920 GT
1 GT
23770922 TTTTTTTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:23774833 original size:16 final size:16
Alignment explanation
Indices: 23774814--23774844 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
23774804 CTTCTTCACT
23774814 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
23774830 TACTTACTTACTTAA
1 TACTCACTTACTTAA
23774845 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:23774850 original size:20 final size:20
Alignment explanation
Indices: 23774811--23774850 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
23774801 AAACTTCTTC
* *
23774811 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
23774831 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
23774851 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:23775230 original size:55 final size:53
Alignment explanation
Indices: 23775092--23775295 Score: 198
Period size: 55 Copynumber: 3.8 Consensus size: 53
23775082 TTTGAAAATT
* *
23775092 ACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAACTC
1 ACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTC
* * *
23775145 ACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTT
1 ACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AACTC
* *** * *
23775200 ATCAATGCCATGTCTTGACATGGTCTTACATGATTTTCTTGCCTTA-GAAACCTT
1 ACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA-CTC
* * *
23775254 ACCAATTGTCATGCCTT-AGCATGGTCTTACATGGTATCCTTG
1 ACCAA-TGCCATGTCTTGA-CATGGTCTTACATGGGATCCTTG
23775296 AACCCTAATG
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
52 2 0.02
53 43 0.34
54 9 0.07
55 70 0.56
56 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.36
Consensus pattern (53 bp):
ACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAACTC
Found at i:23777425 original size:126 final size:126
Alignment explanation
Indices: 23777200--23777833 Score: 1027
Period size: 126 Copynumber: 5.0 Consensus size: 126
23777190 TTATAGCCTC
* * *
23777200 ATTTTTCTACGATCTACTGTAGCAAAAAAGCGTCCACGTGGGAGCTTTTTCCAGAAATGTTGCTG
1 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGAAATTTTGCTG
23777265 ACAGTGCATCCTGCTTGAAGCATTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAATT
66 ACAGTGCATCCTGCTTGAAGCATTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAATT
* *
23777326 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCATGTGGGAGCTTTTTCCCGAAATTTTGCTG
1 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGAAATTTTGCTG
23777391 ACAGTGCATCCTGCTTGAAGCATTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAATT
66 ACAGTGCATCCTGCTTGAAGCATTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAATT
* *
23777452 ATTTTTCTACAAACTACTGTAGCAAAAGAGCGTCCATGTGGGAGCTTTTTCCAGAAATTTTGCTG
1 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGAAATTTTGCTG
* *
23777517 ACAGTGCATCCTGCTTGAAGCGTTTTCGACACTATTTGTTTAGAAACGTCTACTC-GAAATT
66 ACAGTGCATCCTGCTTGAAGCATTTTCGACACTATTTGTTCAGAAACGTCTACTCAG-AATT
* * * * *
23777578 ATTTTTCTACGAACTACTGTAGTAAAAGAGCGTTCAAGTGAGAGCATTTTCCAGAAATTTTGCTG
1 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGAAATTTTGCTG
* * * *
23777643 ACAGTGCATCCTGCTTGAAGCGTTTTCGACATTATTTGTTCATAAATGTCTACTCAGAATT
66 ACAGTGCATCCTGCTTGAAGCATTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAATT
* * *
23777704 ATTTTTCTACGAACTACTGTAGCAAAAGAGCATCCACGTGGGAGCTTTTTCTAGAAATTTTACTG
1 ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGAAATTTTGCTG
* * *
23777769 ACAGTGCATCCTGCTTGAAGCGTTTTTCGACACTATTTGTCCAGAAACGTCTGCTCAGAATT
66 ACAGTGCATCCTGCTTGAAGC-ATTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAATT
23777831 ATT
1 ATT
23777834 CTTACAGAAA
Statistics
Matches: 472, Mismatches: 33, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
125 1 0.00
126 433 0.92
127 38 0.08
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (126 bp):
ATTTTTCTACGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTCCAGAAATTTTGCTG
ACAGTGCATCCTGCTTGAAGCATTTTCGACACTATTTGTTCAGAAACGTCTACTCAGAATT
Found at i:23778404 original size:20 final size:20
Alignment explanation
Indices: 23778379--23778450 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
23778369 CCATTATGTC
23778379 TCAATTAACCCTAAAATTAA
1 TCAATTAACCCTAAAATTAA
* * *
23778399 TCAATTAATCCTAAACCCTAAA
1 TCAATTAACCCTAAA--ATTAA
*
23778421 TCAA-T--CCCT-AATTTAA
1 TCAATTAACCCTAAAATTAA
23778437 TCAATTAACCCTAA
1 TCAATTAACCCTAA
23778451 TACCCTAAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
16 7 0.17
17 1 0.03
18 2 0.05
19 7 0.17
20 15 0.38
21 1 0.03
22 7 0.17
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (20 bp):
TCAATTAACCCTAAAATTAA
Found at i:23778471 original size:34 final size:36
Alignment explanation
Indices: 23778395--23778471 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 36
23778385 AACCCTAAAA
*
23778395 TTAATCAATTAATCCTAAACCCTAAATCAATCCCTAAT
1 TTAATCAATTAACCCTAAACCCTAAATC-AT-CCTAAT
23778433 TTAATCAATTAACCCTAATACCCTAAA-C-T-CTAAT
1 TTAATCAATTAACCCTAA-ACCCTAAATCATCCTAAT
23778467 TTAAT
1 TTAAT
23778472 ATTTAGTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
34 10 0.27
36 1 0.03
38 18 0.49
39 8 0.22
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.34
Consensus pattern (36 bp):
TTAATCAATTAACCCTAAACCCTAAATCATCCTAAT
Found at i:23778561 original size:16 final size:16
Alignment explanation
Indices: 23778537--23778576 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
23778527 TTAAAACCTT
* *
23778537 AAAACCCTAAGACCCA
1 AAAAACCTAAAACCCA
23778553 AAAAACCTAAAACCCA
1 AAAAACCTAAAACCCA
23778569 AAAAACCT
1 AAAAACCT
23778577 TAACCATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.57, C:0.33, G:0.03, T:0.07
Consensus pattern (16 bp):
AAAAACCTAAAACCCA
Found at i:23778587 original size:22 final size:22
Alignment explanation
Indices: 23778562--23778608 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
23778552 AAAAAACCTA
*
23778562 AAACCCAAAAAACCTTAACCAT
1 AAACCCAAAAAACCCTAACCAT
* *
23778584 AAACCCTAAAAACCCTAACCCT
1 AAACCCAAAAAACCCTAACCAT
23778606 AAA
1 AAA
23778609 TCAATTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.53, C:0.34, G:0.00, T:0.13
Consensus pattern (22 bp):
AAACCCAAAAAACCCTAACCAT
Found at i:23778935 original size:16 final size:16
Alignment explanation
Indices: 23778914--23778965 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
23778904 TTTGGTTCGC
23778914 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
23778930 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
23778946 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
23778962 TGTA
1 TGTA
23778966 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:23779012 original size:45 final size:44
Alignment explanation
Indices: 23778946--23779040 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
23778936 GGATTAGAGG
* *
23778946 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
23778991 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
23779035 TGTAAT
1 TGTAAT
23779041 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:23779210 original size:25 final size:25
Alignment explanation
Indices: 23779178--23779232 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
23779168 TAATTTAATC
*
23779178 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
23779202 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
23779227 ATATAT
1 ATATAT
23779233 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:23779414 original size:47 final size:46
Alignment explanation
Indices: 23779363--23779523 Score: 140
Period size: 47 Copynumber: 3.6 Consensus size: 46
23779353 GATTTAATAA
23779363 AATTTAAAATAATTATAACTAATAAATTATCTTATATGAATTTGTAT
1 AATTTAAAATAATTATAA-TAATAAATTATCTTATATGAATTTGTAT
* * * * *
23779410 AATTTAAAATAATTATTATTACATATAAT-TTA-AT-AA---GATAT
1 AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTG-TAT
* * * *
23779451 AATTTCATAA-AATTATTGATAATAAATTTTCTTATATGAATTTATAT
1 AATTT-AAAATAATTA-TAATAATAAATTATCTTATATGAATTTGTAT
23779498 AATTTAAAATAATT-TATATAATAAAT
1 AATTTAAAATAATTATA-ATAATAAAT
23779524 CTATTGTATA
Statistics
Matches: 88, Mismatches: 15, Indels: 23
0.70 0.12 0.18
Matches are distributed among these distances:
40 1 0.01
41 13 0.15
42 11 0.12
43 5 0.06
44 4 0.05
45 6 0.07
46 19 0.22
47 29 0.33
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (46 bp):
AATTTAAAATAATTATAATAATAAATTATCTTATATGAATTTGTAT
Found at i:23786231 original size:21 final size:21
Alignment explanation
Indices: 23786207--23786247 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
23786197 TCAAAACGAT
*
23786207 ATAGTTTAGCCTTTTAACTTA
1 ATAGTTTAGACTTTTAACTTA
*
23786228 ATAGTTTTGACTTTTAACTT
1 ATAGTTTAGACTTTTAACTT
23786248 TAGAAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (21 bp):
ATAGTTTAGACTTTTAACTTA
Found at i:23786451 original size:21 final size:21
Alignment explanation
Indices: 23786425--23786464 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
23786415 TACCATGTAG
23786425 TTGGTCGGAGGTTGAATTGAA
1 TTGGTCGGAGGTTGAATTGAA
23786446 TTGGTCGGAGGTTGAATTG
1 TTGGTCGGAGGTTGAATTG
23786465 TATTATTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.05, G:0.40, T:0.35
Consensus pattern (21 bp):
TTGGTCGGAGGTTGAATTGAA
Found at i:23797021 original size:61 final size:60
Alignment explanation
Indices: 23796889--23797026 Score: 174
Period size: 61 Copynumber: 2.3 Consensus size: 60
23796879 CAACGTGGGA
* * *
23796889 AATC-AACACGGCCTGGACTTCTTTACACGGGTAGACCACATGCCCTTCTAGTTTTAGCAG
1 AATCTAACACGGCCTGGACTTCCTTACACGGGTAGACCACATGCCCTTCTAG-TTCAACAG
* * *
23796949 ACTCTAGCACGGCCTGGACTTCCTTACATGGGTAGACCACATGCCCGTGTCTA-TTCAACAG
1 AATCTAACACGGCCTGGACTTCCTTACACGGGTAGACCACATGCCC-T-TCTAGTTCAACAG
23797010 AATCTAACACGG-CTGGA
1 AATCTAACACGGCCTGGA
23797027 AGCACTTACA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
60 8 0.12
61 54 0.81
62 1 0.01
63 4 0.06
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (60 bp):
AATCTAACACGGCCTGGACTTCCTTACACGGGTAGACCACATGCCCTTCTAGTTCAACAG
Found at i:23799679 original size:30 final size:28
Alignment explanation
Indices: 23799643--23799700 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
23799633 ACTATTGAAG
*
23799643 TATTTTTAGTTTCACACTTTGATACTTAAA
1 TATTTTTAGTCTCA-A-TTTGATACTTAAA
* *
23799673 TATTTTTTGTCTCAATTTGGTACTTAAA
1 TATTTTTAGTCTCAATTTGATACTTAAA
23799701 ATATCAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 12 0.48
29 1 0.04
30 12 0.48
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.52
Consensus pattern (28 bp):
TATTTTTAGTCTCAATTTGATACTTAAA
Found at i:23799921 original size:29 final size:29
Alignment explanation
Indices: 23799868--23799930 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
23799858 TATACATTAA
* *
23799868 AAAAATATGAAAAATAGAAATAAATATAT
1 AAAAATATCAAAAATAGAAATAAATATAG
*
23799897 AAAAAT-TCAAAAATA-AACATAAAATCTAG
1 AAAAATATCAAAAATAGAA-AT-AAATATAG
23799926 AAAAA
1 AAAAA
23799931 AAATATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 2 0.07
28 10 0.34
29 17 0.59
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.21
Consensus pattern (29 bp):
AAAAATATCAAAAATAGAAATAAATATAG
Found at i:23799929 original size:20 final size:20
Alignment explanation
Indices: 23799905--23799951 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
23799895 ATAAAAATTC
23799905 AAAAATAAACATA-AAATCT
1 AAAAATAAACATATAAATCT
* * *
23799924 AGAAAAAAAATATATAAATTT
1 A-AAAATAAACATATAAATCT
23799945 AAAAATA
1 AAAAATA
23799952 TTTTTTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 1 0.05
20 15 0.68
21 6 0.27
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAAATAAACATATAAATCT
Found at i:23801523 original size:26 final size:26
Alignment explanation
Indices: 23801494--23801545 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
23801484 GAATATATTT
23801494 GATGGAAGATAATTTCAACCAAAAAA
1 GATGGAAGATAATTTCAACCAAAAAA
23801520 GATGGAAGATAATTTCAACCAAAAAA
1 GATGGAAGATAATTTCAACCAAAAAA
23801546 TATCGGCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.12, G:0.15, T:0.19
Consensus pattern (26 bp):
GATGGAAGATAATTTCAACCAAAAAA
Found at i:23806389 original size:23 final size:22
Alignment explanation
Indices: 23806362--23806411 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
23806352 TGCCTAAAAT
23806362 GACACACGAGGTGCCTG-ATAC
1 GACACACGAGGTGCCTGAATAC
23806383 GACACACGAGGTGCCTGAAATAC
1 GACACACGAGGTGCCTG-AATAC
23806406 GACACA
1 GACACA
23806412 TAAAGTGCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 17 0.63
23 10 0.37
ACGTcount: A:0.34, C:0.28, G:0.26, T:0.12
Consensus pattern (22 bp):
GACACACGAGGTGCCTGAATAC
Found at i:23806419 original size:23 final size:23
Alignment explanation
Indices: 23806338--23806423 Score: 81
Period size: 21 Copynumber: 3.9 Consensus size: 23
23806328 CTGATCAGAG
*
23806338 TACGACACATAAAGTGCCT-AAA
1 TACGACACACAAAGTGCCTGAAA
* * *
23806360 -ATGACACACGAGGTGCCTG--A
1 TACGACACACAAAGTGCCTGAAA
* *
23806380 TACGACACACGAGGTGCCTGAAA
1 TACGACACACAAAGTGCCTGAAA
*
23806403 TACGACACATAAAGTGCCTGA
1 TACGACACACAAAGTGCCTGA
23806424 TCAGTAAAGC
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
20 1 0.02
21 32 0.62
23 19 0.37
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
TACGACACACAAAGTGCCTGAAA
Found at i:23806821 original size:15 final size:15
Alignment explanation
Indices: 23806796--23806853 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
23806786 ATATATATAT
23806796 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
23806812 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
23806827 AATAATTTCAATCAA
1 TATAAATTCAATCAA
23806842 TATAAATTCAAT
1 TATAAATTCAAT
23806854 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:23808107 original size:5 final size:5
Alignment explanation
Indices: 23808099--23808125 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
23808089 TCTTTAGTTT
23808099 ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA AT
23808126 TAAAACATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:23808161 original size:8 final size:8
Alignment explanation
Indices: 23808148--23808176 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
23808138 TATCTTTATT
23808148 ATATAATA
1 ATATAATA
23808156 ATATAATA
1 ATATAATA
23808164 ATATAATA
1 ATATAATA
23808172 ATATA
1 ATATA
23808177 CTAAGCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:23810644 original size:18 final size:18
Alignment explanation
Indices: 23810604--23810645 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
23810594 AACAAATTAA
23810604 TAAAATTAAAAAAAGATG
1 TAAAATTAAAAAAAGATG
* *
23810622 AAAAATTAAATAAAA-ATT
1 TAAAATTAAA-AAAAGATG
23810640 TAAAAT
1 TAAAAT
23810646 AGTTATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (18 bp):
TAAAATTAAAAAAAGATG
Found at i:23815119 original size:21 final size:21
Alignment explanation
Indices: 23815095--23815135 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
23815085 TCAAAACGAC
*
23815095 ATAGTTTAGCCTTTTAACTTA
1 ATAGTTTAGACTTTTAACTTA
*
23815116 ATAGTTTTGACTTTTAACTT
1 ATAGTTTAGACTTTTAACTT
23815136 TAGAAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (21 bp):
ATAGTTTAGACTTTTAACTTA
Found at i:23820613 original size:30 final size:30
Alignment explanation
Indices: 23820579--23820639 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
23820569 TCCTTAACTC
23820579 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
23820609 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
23820639 A
1 A
23820640 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:23822935 original size:20 final size:23
Alignment explanation
Indices: 23822905--23822953 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
23822895 TGCTTTTGTC
*
23822905 TTCTATCTTGTT-TT-TGTTTTT
1 TTCTATCTTGTTGTTATGTTATT
23822926 TTCT-TCTTGTTGTTATGTTATT
1 TTCTATCTTGTTGTTATGTTATT
23822948 TTCTAT
1 TTCTAT
23822954 TTCAATTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 10 0.42
23 1 0.04
ACGTcount: A:0.08, C:0.10, G:0.10, T:0.71
Consensus pattern (23 bp):
TTCTATCTTGTTGTTATGTTATT
Found at i:23823877 original size:3 final size:3
Alignment explanation
Indices: 23823858--23823922 Score: 51
Period size: 3 Copynumber: 22.0 Consensus size: 3
23823848 TCATTTTTCC
* * * * * *
23823858 TCT TCT CCT TAT TCT TCT TCT T-T TCT TCA TCT TCA TCT TCA TCT TCA
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
23823905 TCT TCT TTT TCT TTT TCT
1 TCT TCT TCT TCT TCT TCT
23823923 CTAACCCTAA
Statistics
Matches: 45, Mismatches: 16, Indels: 2
0.71 0.25 0.03
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.08, C:0.29, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:23823890 original size:6 final size:6
Alignment explanation
Indices: 23823881--23823909 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
23823871 CTTCTTCTTT
23823881 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
23823910 TTTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCA
Found at i:23825073 original size:32 final size:31
Alignment explanation
Indices: 23825037--23825143 Score: 124
Period size: 32 Copynumber: 3.4 Consensus size: 31
23825027 CGTGGTTCTA
* * *
23825037 TGAAATAATAACAAATATCAGCTTTCATTTTG
1 TGAAATGATAACAAAT-TCAACTTTAATTTTG
* *
23825069 TGAAATGGTAACAAATTACAACTTTAATTTTT
1 TGAAATGATAACAAATT-CAACTTTAATTTTG
*
23825101 TGAAATGATAATAAATGTCAACTTTAATTTTG
1 TGAAATGATAACAAAT-TCAACTTTAATTTTG
*
23825133 TTAAATGATAA
1 TGAAATGATAA
23825144 TAATATTCTT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
31 1 0.02
32 62 0.97
33 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.39
Consensus pattern (31 bp):
TGAAATGATAACAAATTCAACTTTAATTTTG
Found at i:23834272 original size:14 final size:13
Alignment explanation
Indices: 23834252--23834283 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
23834242 AATATTTAAC
23834252 TTGTTCTTAATTA
1 TTGTTCTTAATTA
23834265 TGTGTTCTTAATTA
1 T-TGTTCTTAATTA
23834279 TTGTT
1 TTGTT
23834284 TTGATATCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (13 bp):
TTGTTCTTAATTA
Found at i:23838167 original size:13 final size:13
Alignment explanation
Indices: 23838134--23838218 Score: 57
Period size: 12 Copynumber: 6.3 Consensus size: 13
23838124 TTTAGAAATA
*
23838134 TTTATTTTATTATT
1 TTTATTTT-TAATT
23838148 TTATATTTTTAATT
1 TT-TATTTTTAATT
** *
23838162 TTTATTCAAACTATTT
1 TTTATT---TTTAATT
23838178 TTTATTTTT-ATT
1 TTTATTTTTAATT
23838190 TTTATTTTT-ATT
1 TTTATTTTTAATT
* *
23838202 TTTATTCTTATTT
1 TTTATTTTTAATT
23838215 TTTA
1 TTTA
23838219 GCAGATTTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
12 22 0.39
13 11 0.19
14 8 0.14
15 6 0.11
16 10 0.18
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTATTTTTAATT
Found at i:23838187 original size:6 final size:6
Alignment explanation
Indices: 23838176--23838216 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
23838166 TTCAAACTAT
*
23838176 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTCTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
23838217 TAGCAGATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.02, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:23840814 original size:19 final size:19
Alignment explanation
Indices: 23840786--23840824 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
23840776 AGAGCGAAAG
23840786 AAACGAG-AAACGGGCCAA
1 AAACGAGAAAACGGGCCAA
*
23840804 AAACAGAGAAAATGGGCCAA
1 AAAC-GAGAAAACGGGCCAA
23840824 A
1 A
23840825 GTACTAACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 3 0.17
20 11 0.61
ACGTcount: A:0.54, C:0.18, G:0.26, T:0.03
Consensus pattern (19 bp):
AAACGAGAAAACGGGCCAA
Found at i:23840949 original size:52 final size:51
Alignment explanation
Indices: 23840855--23840953 Score: 128
Period size: 52 Copynumber: 1.9 Consensus size: 51
23840845 GGACTTCCTC
23840855 ACACGGGCAGACCACACGGCCGTGCTAACTTGGCAGAATCGAAGCACGATTT
1 ACACGGGCAGACCACACGGCCGTGCTAACTTGGCAGAATCGAA-CACGATTT
* * * **
23840907 ACACGGGTAGACCACACGGTCGTG-TCAATTTGGCAGGCTCGAACACG
1 ACACGGGCAGACCACACGGCCGTGCT-AACTTGGCAGAATCGAACACG
23840954 GCCTGGAGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
51 5 0.12
52 36 0.88
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.16
Consensus pattern (51 bp):
ACACGGGCAGACCACACGGCCGTGCTAACTTGGCAGAATCGAACACGATTT
Found at i:23841374 original size:14 final size:13
Alignment explanation
Indices: 23841354--23841385 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
23841344 TATTTTTAAC
23841354 TTGTTCTTAATTA
1 TTGTTCTTAATTA
23841367 TGTGTTCTTAATTA
1 T-TGTTCTTAATTA
23841381 TTGTT
1 TTGTT
23841386 TTGATATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (13 bp):
TTGTTCTTAATTA
Found at i:23845344 original size:16 final size:16
Alignment explanation
Indices: 23845323--23845356 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
23845313 GAAGATGTAA
23845323 CATGAAAGTTTTGTTT
1 CATGAAAGTTTTGTTT
23845339 CATGAAAGTTTTGTTT
1 CATGAAAGTTTTGTTT
23845355 CA
1 CA
23845357 AAACCCTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.47
Consensus pattern (16 bp):
CATGAAAGTTTTGTTT
Found at i:23866098 original size:34 final size:34
Alignment explanation
Indices: 23866055--23866119 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
23866045 CATCATTTAC
23866055 TGCCAAGCAATAACTCCA-TTGACAATAATAGAAA
1 TGCCAAGCAATAACTCCACTT-ACAATAATAGAAA
23866089 TGCCAAGCAATAACTCCACTTACAATAATAG
1 TGCCAAGCAATAACTCCACTTACAATAATAG
23866120 GCATCCTACC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 28 0.93
35 2 0.07
ACGTcount: A:0.45, C:0.23, G:0.11, T:0.22
Consensus pattern (34 bp):
TGCCAAGCAATAACTCCACTTACAATAATAGAAA
Found at i:23870863 original size:21 final size:21
Alignment explanation
Indices: 23870839--23870879 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
23870829 ATGTTGAATA
*
23870839 ATATTTTTTAATAAA-TAATTT
1 ATATTTTGTAA-AAATTAATTT
23870860 ATATTTTGTAAAAATTAATT
1 ATATTTTGTAAAAATTAATT
23870880 AATTATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
ATATTTTGTAAAAATTAATTT
Found at i:23873272 original size:131 final size:130
Alignment explanation
Indices: 23873124--23873595 Score: 315
Period size: 130 Copynumber: 3.6 Consensus size: 130
23873114 AATAAAGACC
* * * * *
23873124 TAAAGGAATACTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAAGGCATGATTC
1 TAAAGGGATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAACACGATAAGGCACGATCC
* * * *
23873189 C-CGAATTGTCAAACACC-GAGTATTGCCCTCGTTTTAAAGGATTTTTAGAAGAGC-CGAGTGAA
66 CACGAATTGCCAAACACCAGA-TATCGCCCTCGTTTT-AAGGA-TTTTAAAAGA-CACGAGCGAA
23873251 ATTT
127 ATTT
* * * * ** * * *
23873255 TGAAGGGATATTTGATTGTTTTAAACAATCGAGAAATTGCTACCCAACACGTTAGGGCACGATCC
1 TAAAGGGATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAACACGATAAGGCACGATCC
* * *
23873320 CACGAATTGCCAAATACCAGATATCGCCTTCGTTTTAGGGATTTTAAAAGACACGAGCGAAATTT
66 CACGAATTGCCAAACACCAGATATCGCCCTCGTTTTAAGGATTTTAAAAGACACGAGCGAAATTT
* * * * ** * * * *
23873385 TAAAGTGATATTCGATTATTTTGAGCAAA-TACGAAATTGCAACCCAACATGTTAGGGCACGATT
1 TAAAGGGATATTCGATTGTTTTGAACAAACGA-GAAATCACAACCCAACACGATAAGGCACGATC
* * * * * * ** * *** ** *
23873449 TCGCGAATTGCAAAACATCAAATCTCATCTTCG-TTTAAGGGATTTTAAAAGATGTGAATGGAAT
65 CCACGAATTGCCAAACACCAGATATCGCCCTCGTTTTAA-GGATTTTAAAAGACACGAGCGAAAT
23873513 TT
129 TT
** * * * * * ** * * *
23873515 CGAAGGGAAATTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGGCACGATTC
1 TAAAGGGATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAACACGATAAGGCACGATCC
* *
23873580 CGCGAATTGCCGAACA
66 CACGAATTGCCAAACA
23873596 TCAAATTTCA
Statistics
Matches: 277, Mismatches: 58, Indels: 13
0.80 0.17 0.04
Matches are distributed among these distances:
129 6 0.02
130 186 0.67
131 56 0.20
132 27 0.10
133 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (130 bp):
TAAAGGGATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAACACGATAAGGCACGATCC
CACGAATTGCCAAACACCAGATATCGCCCTCGTTTTAAGGATTTTAAAAGACACGAGCGAAATTT
Found at i:23873421 original size:130 final size:130
Alignment explanation
Indices: 23873287--23873614 Score: 404
Period size: 130 Copynumber: 2.5 Consensus size: 130
23873277 AAACAATCGA
* * * * * *
23873287 GAAATTGCTACCCAACACGTTAGGGCACGATCCCACGAATTGCCAAATACCAGATATCGCCTTCG
1 GAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACACCAAATATCACCTTCG
* * * * *
23873352 TTTTAGGGATTTTAAAAGACACGAGCGAAATTTTAAAGTGATATTCGATTATTTTGAGCAAATAC
66 TTTAAGGGATTTTAAAAGACACGAACGAAATTTCAAAGGGAAATTCGATTATTTTGAGCAAATAC
* * * * * *
23873417 GAAATTGCAACCCAACATGTTAGGGCACGATTTCGCGAATTGCAAAACATCAAATCTCATCTTCG
1 GAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACACCAAATATCACCTTCG
*** * * * *
23873482 TTTAAGGGATTTTAAAAGATGTGAATGGAATTTCGAAGGGAAATTCGATTATTTTGAGCAAATGC
66 TTTAAGGGATTTTAAAAGACACGAACGAAATTTCAAAGGGAAATTCGATTATTTTGAGCAAATAC
* * * *
23873547 GAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCGAACATCAAATTTCATCTTCG
1 GAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACACCAAATATCACCTTCG
23873612 TTT
66 TTT
23873615 TGAAGAATTT
Statistics
Matches: 169, Mismatches: 29, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
130 169 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (130 bp):
GAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACACCAAATATCACCTTCG
TTTAAGGGATTTTAAAAGACACGAACGAAATTTCAAAGGGAAATTCGATTATTTTGAGCAAATAC
Found at i:23880182 original size:131 final size:130
Alignment explanation
Indices: 23880034--23880410 Score: 314
Period size: 130 Copynumber: 2.9 Consensus size: 130
23880024 AATAAAGACC
* * * * *
23880034 TAAAGGAATACTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAAGGCATGATTC
1 TAAAGGGATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAACACGATAAGGCACGATCC
* * * **
23880099 C-CGAATTGTCAAACACC-GAGTATTGCCCTCGTTTTAAAGGATTTTTAGAAGAGC-CGAGTGAA
66 CACGAATTGCCAAACACCAGA-TATCGCCCTCGTTTT-AAGGA-TTTTAAAAGA-CACGAGCAAA
23880161 ATTT
127 ATTT
* * * * ** * * *
23880165 TGAAGGGATATTTGATTGTTTTAAACAATCGAGAAATTGCTACCCAACACGTTAGGGCACGATCC
1 TAAAGGGATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAACACGATAAGGCACGATCC
* * *
23880230 CACGAATTGCCAAATACCAGATATCGCCTTCGTTTTAGGGATTTTAAAAGACACGAGCAAAATTT
66 CACGAATTGCCAAACACCAGATATCGCCCTCGTTTTAAGGATTTTAAAAGACACGAGCAAAATTT
* * * * ** * * *
23880295 TAAAGTGATATTCGATTATTTTGAGCAAA-TACGAAATTGCAACCCAACACGTTAGGGCACGATT
1 TAAAGGGATATTCGATTGTTTTGAACAAACGA-GAAATCACAACCCAACACGATAAGGCACGATC
* * * * * ** *
23880359 TCGCGAATTGCCAAACATCAAATCTCATCTTCG-TTTAAGGGATTTTAAAAGA
65 CCACGAATTGCCAAACACCAGATATCGCCCTCGTTTTAA-GGATTTTAAAAGA
23880411 TGTGAATGGA
Statistics
Matches: 200, Mismatches: 41, Indels: 11
0.79 0.16 0.04
Matches are distributed among these distances:
129 6 0.03
130 109 0.55
131 56 0.28
132 27 0.14
133 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (130 bp):
TAAAGGGATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAACACGATAAGGCACGATCC
CACGAATTGCCAAACACCAGATATCGCCCTCGTTTTAAGGATTTTAAAAGACACGAGCAAAATTT
Found at i:23880520 original size:130 final size:130
Alignment explanation
Indices: 23880197--23880524 Score: 422
Period size: 130 Copynumber: 2.5 Consensus size: 130
23880187 AAACAATCGA
* * * * * * *
23880197 GAAATTGCTACCCAACACGTTAGGGCACGATCCCACGAATTGCCAAATACCAGATATCGCCTTCG
1 GAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACATCAAATATCGTCTTCG
* * * * *
23880262 TTTTAGGGATTTTAAAAGACACGAGCAAAATTTTAAAGTGATATTCGATTATTTTGAGCAAATAC
66 TTTAAGGGATTTTAAAAGACACGAACAAAATTTCAAAGGGAAATTCGATTATTTTGAGCAAATAC
* * *
23880327 GAAATTGCAACCCAACACGTTAGGGCACGATTTCGCGAATTGCCAAACATCAAATCTCATCTTCG
1 GAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACATCAAATATCGTCTTCG
*** *** * *
23880392 TTTAAGGGATTTTAAAAGATGTGAATGGAATTTCGAAGGGAAATTCGATTATTTTGAGCAAATGC
66 TTTAAGGGATTTTAAAAGACACGAACAAAATTTCAAAGGGAAATTCGATTATTTTGAGCAAATAC
* * *
23880457 GAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTACCGAACATCAAATTTCGTCTTCG
1 GAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACATCAAATATCGTCTTCG
23880522 TTT
66 TTT
23880525 TGAAGAATTT
Statistics
Matches: 170, Mismatches: 28, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
130 170 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (130 bp):
GAAATTGCAACCCAACACGTTAGGGCACGATTCCGCGAATTGCCAAACATCAAATATCGTCTTCG
TTTAAGGGATTTTAAAAGACACGAACAAAATTTCAAAGGGAAATTCGATTATTTTGAGCAAATAC
Found at i:23885438 original size:52 final size:52
Alignment explanation
Indices: 23885368--23885539 Score: 193
Period size: 52 Copynumber: 3.2 Consensus size: 52
23885358 GACGGAAAAG
* **
23885368 ATGTGATATGTGCGCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTA
1 ATGTGATACGTGTTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTA
* * *
23885420 ATGTGATACGTGTTCCCGTATAAAACCATAGTTGGGCTATGGCGTCGGTGTA
1 ATGTGATACGTGTTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTA
* * * * *
23885472 ATGTGATAATGTGATT-CCGTATAAGACAATATCTGGGATATGGCATCGGTATTA
1 ATGTGAT-ACGTG-TTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGT-GTA
*
23885526 CATGTGATCCGTGT
1 -ATGTGATACGTGT
23885540 AAGACCATGG
Statistics
Matches: 100, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
52 53 0.53
53 33 0.33
54 7 0.07
55 7 0.07
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (52 bp):
ATGTGATACGTGTTCCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTA
Found at i:23886411 original size:13 final size:13
Alignment explanation
Indices: 23886395--23886419 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23886385 TAGCCACATG
23886395 GCCGTGTGCCCAA
1 GCCGTGTGCCCAA
23886408 GCCGTGTGCCCA
1 GCCGTGTGCCCA
23886420 TCTGATACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.40, G:0.32, T:0.16
Consensus pattern (13 bp):
GCCGTGTGCCCAA
Found at i:23895601 original size:17 final size:18
Alignment explanation
Indices: 23895568--23895601 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23895558 GAATTATATA
*
23895568 ATAGAAAGATGCAACGAG
1 ATAGAAAGATACAACGAG
23895586 ATAGAAAGA-ACAACGA
1 ATAGAAAGATACAACGA
23895602 ATCTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.56, C:0.12, G:0.24, T:0.09
Consensus pattern (18 bp):
ATAGAAAGATACAACGAG
Found at i:23900959 original size:53 final size:52
Alignment explanation
Indices: 23900820--23900959 Score: 154
Period size: 52 Copynumber: 2.7 Consensus size: 52
23900810 GATATGTGCA
* *
23900820 CCCGTATAAGACCATAGCTGGGCTATGGCATTGATGCAATGTGATACGCGTT
1 CCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATACGCGTT
* * * ** * *
23900872 CCCGTATAAAACCATAGCTGGGCTATGACGTCGGTGTGATGTGATAATGTGTT
1 CCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGAT-ACGCGTT
* * * *
23900925 TCCGTATAAGACAATATCTGGGATATGGCATCGGT
1 CCCGTATAAGACCATAGCTGGGCTATGGCATCGGT
23900960 ATTACATGTG
Statistics
Matches: 71, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
52 38 0.54
53 33 0.46
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.29
Consensus pattern (52 bp):
CCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATACGCGTT
Found at i:23901979 original size:29 final size:29
Alignment explanation
Indices: 23901937--23902013 Score: 127
Period size: 29 Copynumber: 2.7 Consensus size: 29
23901927 TTCCATACGA
*
23901937 GCTGGCTACACGGCCATGTAATCCCACGG
1 GCTGGCCACACGGCCATGTAATCCCACGG
* *
23901966 GCTGGTCACACGGCCATGTGATCCCACGG
1 GCTGGCCACACGGCCATGTAATCCCACGG
23901995 GCTGGCCACACGGCCATGT
1 GCTGGCCACACGGCCATGT
23902014 CCCAGGCCAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.18, C:0.35, G:0.30, T:0.17
Consensus pattern (29 bp):
GCTGGCCACACGGCCATGTAATCCCACGG
Found at i:23903270 original size:3 final size:3
Alignment explanation
Indices: 23903262--23903342 Score: 153
Period size: 3 Copynumber: 26.7 Consensus size: 3
23903252 ACTTGCGCCT
23903262 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
23903310 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
23903343 TATTTATCAC
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 74 0.96
4 3 0.04
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:23903652 original size:3 final size:3
Alignment explanation
Indices: 23903639--23903669 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
23903629 TTCATATCTA
23903639 TAT TCAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
23903670 AATTTGTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:23912284 original size:48 final size:47
Alignment explanation
Indices: 23912213--23912422 Score: 206
Period size: 47 Copynumber: 4.6 Consensus size: 47
23912203 AAAAAATGTT
* * *
23912213 GTGCTAAGTGGATATACCACGATTACACATATTGATACATGTAACGTG
1 GTGCTAAGTGGATATGCCACGATTACACATATTGATTCAT-TAACATG
* * *
23912261 GTGCTAAGTGGATATGTCACGATTACATATATTGATTCATTAACGTG
1 GTGCTAAGTGGATATGCCACGATTACACATATTGATTCATTAACATG
* * *
23912308 GTGCTAAGTGGATATACCATG-GT-----TA---A-TCATGTAACATG
1 GTGCTAAGTGGATATGCCACGATTACACATATTGATTCAT-TAACATG
* *
23912346 GTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACATG
1 GTGCTAAGTGGATATGCCACGATTACACATATTGATTCATTAACATG
* * *
23912393 GTGCTAAGTGGATATACCACGGTTAAACAT
1 GTGCTAAGTGGATATGCCACGATTACACAT
23912423 GTAACGTGGT
Statistics
Matches: 136, Mismatches: 15, Indels: 23
0.78 0.09 0.13
Matches are distributed among these distances:
37 4 0.03
38 26 0.19
39 1 0.01
41 2 0.01
44 2 0.01
46 1 0.01
47 60 0.44
48 40 0.29
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (47 bp):
GTGCTAAGTGGATATGCCACGATTACACATATTGATTCATTAACATG
Found at i:23912357 original size:38 final size:38
Alignment explanation
Indices: 23912297--23912455 Score: 158
Period size: 38 Copynumber: 4.0 Consensus size: 38
23912287 ATATATTGAT
* *
23912297 TCAT-TAACGTGGTGCTAAGTGGATATACCATGGTTAA
1 TCATGTAACATGGTGCTAAGTGGATATACCACGGTTAA
*
23912334 TCATGTAACATGGTGCTAAGTGGATATGCCACGGTTACA
1 TCATGTAACATGGTGCTAAGTGGATATACCACGGTTA-A
*
23912373 TATATTGATTCATTAACATGGTGCTAAGTGGATATACCACGGTTAA
1 T-CA-TG------TAACATGGTGCTAAGTGGATATACCACGGTTAA
* * * *
23912419 ACATGTAACGTGGTGCTAAGTGGATATGCCACAGTTA
1 TCATGTAACATGGTGCTAAGTGGATATACCACGGTTA
23912456 TACATGTTAA
Statistics
Matches: 102, Mismatches: 10, Indels: 19
0.78 0.08 0.15
Matches are distributed among these distances:
37 4 0.04
38 58 0.57
39 2 0.02
40 1 0.01
41 2 0.02
44 2 0.02
45 1 0.01
46 1 0.01
47 31 0.30
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (38 bp):
TCATGTAACATGGTGCTAAGTGGATATACCACGGTTAA
Found at i:23912395 original size:85 final size:85
Alignment explanation
Indices: 23912249--23912455 Score: 351
Period size: 85 Copynumber: 2.4 Consensus size: 85
23912239 ACATATTGAT
* * *
23912249 ACATGTAACGTGGTGCTAAGTGGATATGTCACGATTACATATATTGATTCATTAACGTGGTGCTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACATGGTGCTA
*
23912314 AGTGGATATACCATGGTTAA
66 AGTGGATATACCACGGTTAA
* *
23912334 TCATGTAACATGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACATGGTGCTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACATGGTGCTA
23912399 AGTGGATATACCACGGTTAA
66 AGTGGATATACCACGGTTAA
*
23912419 ACATGTAACGTGGTGCTAAGTGGATATGCCACAGTTA
1 ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTA
23912456 TACATGTTAA
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 113 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (85 bp):
ACATGTAACGTGGTGCTAAGTGGATATGCCACGGTTACATATATTGATTCATTAACATGGTGCTA
AGTGGATATACCACGGTTAA
Found at i:23916329 original size:27 final size:27
Alignment explanation
Indices: 23916261--23916341 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
23916251 CTATTTTGCA
* *
23916261 AAATTTAAATTCCTAATTATCTTATCT
1 AAATTTAAACTCCTAATTATCTAATCT
*
23916288 AAATTAAAACT-CTAATTATCCTAAT-T
1 AAATTTAAACTCCTAATTAT-CTAATCT
** *
23916314 TGATTTAAACTCCTAATTATTTAATCT
1 AAATTTAAACTCCTAATTATCTAATCT
23916341 A
1 A
23916342 CATAAAATCT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
26 21 0.49
27 22 0.51
ACGTcount: A:0.40, C:0.15, G:0.01, T:0.44
Consensus pattern (27 bp):
AAATTTAAACTCCTAATTATCTAATCT
Found at i:23916338 original size:26 final size:28
Alignment explanation
Indices: 23916261--23916341 Score: 89
Period size: 26 Copynumber: 3.0 Consensus size: 28
23916251 CTATTTTGCA
*
23916261 AAATTTAAATTCCTAATTATCTT-ATCT
1 AAATTTAAACTCCTAATTATCTTAATCT
* *
23916288 AAATTAAAACT-CTAATTATCCTAAT-T
1 AAATTTAAACTCCTAATTATCTTAATCT
**
23916314 TGATTTAAACTCCTAATTAT-TTAATCT
1 AAATTTAAACTCCTAATTATCTTAATCT
23916341 A
1 A
23916342 CATAAAATCT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
26 23 0.53
27 20 0.47
ACGTcount: A:0.40, C:0.15, G:0.01, T:0.44
Consensus pattern (28 bp):
AAATTTAAACTCCTAATTATCTTAATCT
Found at i:23919468 original size:17 final size:17
Alignment explanation
Indices: 23919446--23919480 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
23919436 GGTTCAATCG
*
23919446 ATTTCCAATGCAATTCA
1 ATTTCCAATCCAATTCA
23919463 ATTTCCAATCCAATTCA
1 ATTTCCAATCCAATTCA
23919480 A
1 A
23919481 ATATGATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (17 bp):
ATTTCCAATCCAATTCA
Found at i:23924043 original size:6 final size:6
Alignment explanation
Indices: 23924032--23924075 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
23924022 GTTTGACAGG
* * *
23924032 GAGTAT GAGTAT GAGTAT GAGTAT GAGCAT GAGCAT GAGCAT GA
1 GAGTAT GAGTAT GAGTAT GAGTAT GAGTAT GAGTAT GAGTAT GA
23924076 AAGGAAGGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.34, C:0.07, G:0.34, T:0.25
Consensus pattern (6 bp):
GAGTAT
Found at i:23929946 original size:20 final size:20
Alignment explanation
Indices: 23929918--23929998 Score: 58
Period size: 20 Copynumber: 4.0 Consensus size: 20
23929908 AAATTTTATA
*
23929918 TTATTTAATTTTCTAATAAT
1 TTATATAATTTTCTAATAAT
* *
23929938 TTATATAATTTTTTTATAATT
1 TTATATAATTTTCTAATAA-T
* * * *
23929959 TTCTAAAATTTTTATAATGAT
1 TTATATAA-TTTTCTAATAAT
*
23929980 TTA-ATAA-TTTCCAATAAT
1 TTATATAATTTTCTAATAAT
23929998 T
1 T
23929999 GCAAAAACTT
Statistics
Matches: 46, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
18 9 0.20
20 19 0.41
21 10 0.22
22 8 0.17
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.57
Consensus pattern (20 bp):
TTATATAATTTTCTAATAAT
Found at i:23929987 original size:30 final size:31
Alignment explanation
Indices: 23929923--23929998 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
23929913 TTATATTATT
** *
23929923 TAATTTTCTAATAATTTATATAATTTTTTTA
1 TAATTTTCTAATAATTTATATAATGATTTAA
*
23929954 TAATTTTCTAA-AATTTTTATAATGATTTAA
1 TAATTTTCTAATAATTTATATAATGATTTAA
*
23929984 TAA-TTTCCAATAATT
1 TAATTTTCTAATAATT
23929999 GCAAAAACTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 6 0.15
30 22 0.56
31 11 0.28
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.55
Consensus pattern (31 bp):
TAATTTTCTAATAATTTATATAATGATTTAA
Found at i:23930291 original size:10 final size:10
Alignment explanation
Indices: 23930276--23930337 Score: 56
Period size: 11 Copynumber: 6.2 Consensus size: 10
23930266 GCCTTTTTAT
23930276 ATTTTTAATA
1 ATTTTTAATA
23930286 ATTTTTTAATA
1 A-TTTTTAATA
*
23930297 ACTTTTAA-A
1 ATTTTTAATA
**
23930306 AACTTTAATA
1 ATTTTTAATA
*
23930316 A-GTTTAATA
1 ATTTTTAATA
23930325 ATTCTTTAATA
1 ATT-TTTAATA
23930336 AT
1 AT
23930338 GTTGTATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
9 15 0.35
10 9 0.21
11 19 0.44
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:23933621 original size:48 final size:48
Alignment explanation
Indices: 23933491--23933678 Score: 137
Period size: 48 Copynumber: 3.9 Consensus size: 48
23933481 ACTTAGGAGT
* * * **
23933491 CTCGCACACTAAGTGCTC-ATATCATGGCCCGAAGCCAACTCAAT-GTG
1 CTCGCACCCGAAGTGC-CAATATCATGGCCCGAAGCCAAATCAATAAAG
* * * * * * *
23933538 TTTCGTACCCAAAGTGCTAATTTAATAGCCCGAAGCCAAATCAATAAAG
1 -CTCGCACCCGAAGTGCCAATATCATGGCCCGAAGCCAAATCAATAAAG
* ** * * ***
23933587 CTTGCACTTGAAGTGCCGATATCATGGCCTGAAGCCAAATTGGTAAAG
1 CTCGCACCCGAAGTGCCAATATCATGGCCCGAAGCCAAATCAATAAAG
* * *
23933635 CTCGCACCCGAAGTGCTAATATCATGGCCCAAATCCAAATCAAT
1 CTCGCACCCGAAGTGCCAATATCATGGCCCGAAGCCAAATCAAT
23933679 GAATTTCCTA
Statistics
Matches: 101, Mismatches: 37, Indels: 4
0.71 0.26 0.03
Matches are distributed among these distances:
48 100 0.99
49 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (48 bp):
CTCGCACCCGAAGTGCCAATATCATGGCCCGAAGCCAAATCAATAAAG
Found at i:23937179 original size:22 final size:21
Alignment explanation
Indices: 23937126--23937180 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
23937116 AATTTTGAAG
23937126 CACGAAA-TTTTTTTTAAAAA
1 CACGAAATTTTTTTTTAAAAA
*
23937146 -ATGAAAGTTTTTTTTTTAAAAA
1 CACGAAA--TTTTTTTTTAAAAA
23937168 CACGAGAATTTTT
1 CACGA-AATTTTT
23937181 AAACACGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
19 5 0.18
22 18 0.64
23 3 0.11
24 2 0.07
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (21 bp):
CACGAAATTTTTTTTTAAAAA
Found at i:23937218 original size:17 final size:17
Alignment explanation
Indices: 23937158--23937680 Score: 217
Period size: 17 Copynumber: 29.8 Consensus size: 17
23937148 GAAAGTTTTT
*
23937158 TTTTTAAAAACACGAGAA
1 TTTTT-AAAACACGAAAA
*
23937176 TTTTT-AAACACGGAAA
1 TTTTTAAAACACGAAAA
*
23937192 -TTTCAGAAACACGAAAA
1 TTTTTA-AAACACGAAAA
* *
23937209 TTTTTAAAACACGACAT
1 TTTTTAAAACACGAAAA
* *
23937226 TTTTTGAAACACGAGAA
1 TTTTTAAAACACGAAAA
* * *
23937243 TTTTTAAAACAAGACAT
1 TTTTTAAAACACGAAAA
* **
23937260 TTTTTGAAACAC-AATT
1 TTTTTAAAACACGAAAA
**
23937276 TTTTTCTTAA-A--AAAA
1 TTTTT-AAAACACGAAAA
* *
23937291 --TTTAAAATACGAGAA
1 TTTTTAAAACACGAAAA
23937306 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
23937323 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAAAA
* *
23937340 TTTTTGAAACACGGAAAT
1 TTTTTAAAACAC-GAAAA
***
23937358 TTTTTAGAAA-ACGATTTTT
1 TTTTTA-AAACACGA--AAA
* * *
23937377 TTTTTAAATCACCG-GAG
1 TTTTTAAAACA-CGAAAA
23937394 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
* *
23937412 TCTTTGAAACACCG-AAA
1 TTTTTAAAACA-CGAAAA
*
23937429 TTTTTGAAACACACGAAGA
1 TTTTT-AAA-ACACGAAAA
* *
23937448 TTTTTGAAACACAAAAA
1 TTTTTAAAACACGAAAA
* *
23937465 TTTTTTGAAAATACGAAGATT
1 -TTTTT-AAAACACGAA-A-A
** *
23937486 TTTTTTTAACACGGAAA
1 TTTTTAAAACACGAAAA
* ***
23937503 TTTTTGAAACACGGTCATTT
1 TTTTTAAAACAC-G--AAAA
23937523 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAAAA
* **
23937541 TTTTTGAAAGACATG-ATT
1 TTTTT-AAA-ACACGAAAA
*
23937559 TTTTTGAAAATAC-AGAAA
1 TTTTT-AAAACACGA-AAA
*
23937577 TTTATAAAACACGAAAA
1 TTTTTAAAACACGAAAA
*
23937594 TTTTTTCTAAAAACAAGAAAA
1 --TTTT-T-AAAACACGAAAA
* * *
23937615 TTTTTGAAACACTAGAA
1 TTTTTAAAACACGAAAA
* *
23937632 TTTTGAAAACACGAAGA
1 TTTTTAAAACACGAAAA
* * *
23937649 TTTTTGAAACATGAGAA
1 TTTTTAAAACACGAAAA
23937666 TTTTTAAAAGCACGA
1 TTTTTAAAA-CACGA
23937681 GGATTATTGA
Statistics
Matches: 374, Mismatches: 93, Indels: 76
0.69 0.17 0.14
Matches are distributed among these distances:
12 2 0.01
13 4 0.01
15 8 0.02
16 17 0.05
17 188 0.50
18 78 0.21
19 45 0.12
20 15 0.04
21 17 0.05
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (17 bp):
TTTTTAAAACACGAAAA
Found at i:23937469 original size:89 final size:88
Alignment explanation
Indices: 23937306--23937470 Score: 194
Period size: 89 Copynumber: 1.9 Consensus size: 88
23937296 AATACGAGAA
* *
23937306 TTTTTAAAACACGAAAATTTTTAAAACACGAAAATTTTTGAAACACGGAAATTTTTTAGAAAACG
1 TTTTTAAAACACGAAAATCTTTAAAACACGAAAATTTTTGAAACACCGAAATTTTTTAGAAAACG
****
23937371 ATTTTTTTTTTAAATCACCGGAG
66 AAAAATTTTTTAAATCACCGGAG
*
23937394 TTTTTGAAAACACGAAAATCTTTGAAACACCG-AAATTTTTGAAACACACGAAGA-TTTTT-GAA
1 TTTTT-AAAACACGAAAATCTTTAAAACA-CGAAAATTTTTGAAACAC-CGAA-ATTTTTTAGAA
23937456 ACAC-AAAAATTTTTT
62 A-ACGAAAAATTTTTT
23937471 GAAAATACGA
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
88 5 0.08
89 47 0.72
90 12 0.18
91 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.35
Consensus pattern (88 bp):
TTTTTAAAACACGAAAATCTTTAAAACACGAAAATTTTTGAAACACCGAAATTTTTTAGAAAACG
AAAAATTTTTTAAATCACCGGAG
Found at i:23937562 original size:38 final size:38
Alignment explanation
Indices: 23937414--23937626 Score: 122
Period size: 38 Copynumber: 5.7 Consensus size: 38
23937404 CACGAAAATC
* ***
23937414 TTTGAAACACCG-AAATTTTTGAAACAC-ACGA-AGATT
1 TTTGAAACA-CGAAAATTTTTGAAACACGATGATTTTTT
* * *
23937450 TTTGAAACACAAAAATTTTTTGAAAATACGAAGATTTTTT
1 TTTGAAACACGAAAA-TTTTTG-AAACACGATGATTTTTT
* * *
23937490 TTT--AACACGGAAATTTTTGAAACACGGTCA-TTTTT
1 TTTGAAACACGAAAATTTTTGAAACACGATGATTTTTT
*
23937525 TTTGAAAACACGAAAATTTTTGAAAGAC-ATGA--TTTT
1 TTTG-AAACACGAAAATTTTTGAAACACGATGATTTTTT
* * * **
23937561 TTTGAAAATAC-AGAAATTTATAAAACACGAAAATTTTTT
1 TTTG-AAACACGA-AAATTTTTGAAACACGATGATTTTTT
* ** *
23937600 CTAAAAACAAGAAAATTTTTGAAACAC
1 TTTGAAACACGAAAATTTTTGAAACAC
23937627 TAGAATTTTG
Statistics
Matches: 135, Mismatches: 29, Indels: 24
0.72 0.15 0.13
Matches are distributed among these distances:
35 10 0.07
36 45 0.33
37 16 0.12
38 50 0.37
39 9 0.07
40 5 0.04
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (38 bp):
TTTGAAACACGAAAATTTTTGAAACACGATGATTTTTT
Found at i:23937562 original size:74 final size:74
Alignment explanation
Indices: 23937306--23937670 Score: 170
Period size: 72 Copynumber: 5.0 Consensus size: 74
23937296 AATACGAGAA
* * * * *
23937306 TTTTT-AAAACACGAAAATTTTTAAAACACGAA-AATTTTTG-AAACACGGAAATTTTTTAGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAAGACGAAGATTTTTTGAAAACACAGAAA-TTTATA-AAA
*
23937368 -ACG--ATTTT
64 CACGAAAATTT
* * * * * * * * *
23937376 TTTTTTAAATCACCG-GAGTTTTTGAAAACACGAA-AATCTTTG-AAACACCGAAATTTTTGAAA
1 TTTTTGAAAACA-CGAAAATTTTTG-AAAGACGAAGATTTTTTGAAAACACAGAAATTTAT-AAA
*
23937438 CACACGAAGA---
63 -ACACGAAAATTT
* * *** * * *
23937448 TTTTTG-AAACACAAAAATTTTTTGAAAATACGAAGATTTTTTTTTAACACGGAAATTTTTGAAA
1 TTTTTGAAAACACGAAAA-TTTTTG-AAAGACGAAGATTTTTTGAAAACACAGAAATTTATAAAA
***
23937512 CACGGTCATTT
64 CACGAAAATTT
* *
23937523 TTTTTGAAAACACGAAAATTTTTGAAAGAC-ATGATTTTTTTGAAAATACAGAAATTTATAAAAC
1 TTTTTGAAAACACGAAAATTTTTGAAAGACGAAGA-TTTTTTGAAAACACAGAAATTTATAAAAC
23937587 ACGAAAATTT
65 ACGAAAATTT
* * * * * * * *
23937597 TTTCTAAAAACAAGAAAATTTTTGAAACAC-TAGA-ATTTTGAAAACAC-GAAGATTTTTGAAAC
1 TTTTTGAAAACACGAAAATTTTTGAAAGACGAAGATTTTTTGAAAACACAGAA-ATTTATAAAAC
* *
23937659 ATGAGAATTT
65 ACGAAAATTT
23937669 TT
1 TT
23937671 AAAAGCACGA
Statistics
Matches: 229, Mismatches: 48, Indels: 34
0.74 0.15 0.11
Matches are distributed among these distances:
70 6 0.03
71 26 0.11
72 86 0.38
73 13 0.06
74 76 0.33
75 12 0.05
76 10 0.04
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (74 bp):
TTTTTGAAAACACGAAAATTTTTGAAAGACGAAGATTTTTTGAAAACACAGAAATTTATAAAACA
CGAAAATTT
Found at i:23937634 original size:38 final size:36
Alignment explanation
Indices: 23937426--23937670 Score: 112
Period size: 37 Copynumber: 6.7 Consensus size: 36
23937416 TGAAACACCG
* * *
23937426 AAATTTTTGAAACACACGAAGATTTTTGAAACACAA-A
1 AAATTTTTGAAACACA-GAA-TTTTTTTAAAAACAAGA
* * ** * *
23937463 AATTTTTTGAAA-ATACGAAGATTTTTTT-TTAACACGG
1 AAATTTTTGAAACACA-G-A-ATTTTTTTAAAAACAAGA
* * * *
23937500 AAATTTTTGAAACACGGTCATTTTTTTTGAAAACACGA
1 AAATTTTTGAAACACAG--AATTTTTTTAAAAACAAGA
*
23937538 AAATTTTTGAAAGACATG-ATTTTTTTGAAAATAC-AG-
1 AAATTTTTGAAACACA-GAATTTTTTT-AAAA-ACAAGA
* * *
23937574 AAATTTATAAAACACGAAAATTTTTTCTAAAAACAAGA
1 AAATTTTTGAAACAC-AGAATTTTTT-TAAAAACAAGA
* *
23937612 AAATTTTTGAAACACTAGAA---TTTTGAAAACACGA
1 AAATTTTTGAAACAC-AGAATTTTTTTAAAAACAAGA
* *
23937646 AGATTTTTGAAACATGAGAATTTTT
1 AAATTTTTGAAACA-CAGAATTTTT
23937671 AAAAGCACGA
Statistics
Matches: 156, Mismatches: 34, Indels: 36
0.69 0.15 0.16
Matches are distributed among these distances:
34 26 0.17
35 3 0.02
36 28 0.18
37 56 0.36
38 42 0.27
39 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (36 bp):
AAATTTTTGAAACACAGAATTTTTTTAAAAACAAGA
Found at i:23937637 original size:16 final size:16
Alignment explanation
Indices: 23937616--23937669 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
23937606 ACAAGAAAAT
23937616 TTTTGAAACACTAGAA
1 TTTTGAAACACTAGAA
* *
23937632 TTTTGAAAACACGAAGAT
1 TTTTG-AAACAC-TAGAA
23937650 TTTTGAAACA-TGAGAA
1 TTTTGAAACACT-AGAA
23937666 TTTT
1 TTTT
23937670 TAAAAGCACG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 12 0.39
17 11 0.35
18 8 0.26
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (16 bp):
TTTTGAAACACTAGAA
Found at i:23937866 original size:17 final size:16
Alignment explanation
Indices: 23937832--23937882 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
23937822 AAAATTATTT
23937832 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
* *
23937848 AAAATCAAATTAAATTA
1 AAAAT-AAAATAAAATA
23937865 AAAATATAAATATAAATA
1 AAAATA-AAATA-AAATA
23937883 TGCATAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.21
17 18 0.64
18 4 0.14
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:23938361 original size:3 final size:3
Alignment explanation
Indices: 23938334--23938395 Score: 58
Period size: 3 Copynumber: 21.0 Consensus size: 3
23938324 TTTATTTTTT
* * *
23938334 TTC TTT TTC TTT TTC TT- TT- TTC TTC TTC CTC TT- TTC TTC TTCC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C
23938377 TTC TTCC TTC TTC TTC TTC
1 TTC TT-C TTC TTC TTC TTC
23938396 AAAGTCTAGC
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
2 6 0.12
3 37 0.76
4 6 0.12
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:23938368 original size:14 final size:14
Alignment explanation
Indices: 23938338--23938392 Score: 58
Period size: 14 Copynumber: 3.8 Consensus size: 14
23938328 TTTTTTTTCT
* *
23938338 TTTTCTT-TTTCTT
1 TTTTCTTCTTCCTC
23938351 TTTTCTTCTTCCTC
1 TTTTCTTCTTCCTC
23938365 TTTTCTTCTTCCTTC
1 TTTTCTTCTTCC-TC
23938380 TTCCTTCTTCTTC
1 TT--TTCTTCTTC
23938393 TTCAAAGTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
13 7 0.19
14 16 0.44
15 4 0.11
17 9 0.25
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCTTCTTCCTC
Found at i:23938381 original size:7 final size:7
Alignment explanation
Indices: 23938355--23938395 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
23938345 TTTCTTTTTT
23938355 CTTCTTC
1 CTTCTTC
*
23938362 C-TCTTTT
1 CTTC-TTC
23938369 CTTCTTC
1 CTTCTTC
23938376 CTTCTTC
1 CTTCTTC
23938383 CTTCTT-
1 CTTCTTC
23938389 CTTCTTC
1 CTTCTTC
23938396 AAAGTCTAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 8 0.28
7 19 0.66
8 2 0.07
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (7 bp):
CTTCTTC
Found at i:23938486 original size:10 final size:10
Alignment explanation
Indices: 23938455--23938500 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
23938445 CGGTACTTTT
23938455 TCTTTTCTTC
1 TCTTTTCTTC
* *
23938465 TCCTCT-TTC
1 TCTTTTCTTC
23938474 TCTTTTCTTC
1 TCTTTTCTTC
23938484 TCTTTTCTTC
1 TCTTTTCTTC
*
23938494 TTTTTTC
1 TCTTTTC
23938501 CTTCGAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
9 7 0.23
10 23 0.77
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
TCTTTTCTTC
Found at i:23938498 original size:19 final size:19
Alignment explanation
Indices: 23938450--23938497 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
23938440 GACGCCGGTA
*
23938450 CTTTTTCTTTTCTTCTCCT
1 CTTTCTCTTTTCTTCTCCT
23938469 CTTTCTCTTTTCTTCT-CT
1 CTTTCTCTTTTCTTCTCCT
23938487 -TTTCTTCTTTT
1 CTTTC-TCTTTT
23938498 TTCCTTCGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 8 0.30
19 15 0.56
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (19 bp):
CTTTCTCTTTTCTTCTCCT
Found at i:23938782 original size:29 final size:29
Alignment explanation
Indices: 23938749--23938865 Score: 94
Period size: 30 Copynumber: 3.9 Consensus size: 29
23938739 TGTAATTTTT
*
23938749 AGAAAATTTAGGATTAAAATGAAATTTAA
1 AGAAAATTTAGGGTTAAAATGAAATTTAA
* * *
23938778 TGAAAGTTTAGGGGTCT-AATTGAAATTTAA
1 AGAAAATTTA-GGGT-TAAAATGAAATTTAA
* *
23938808 AGAAAGTTTAAGGGTCAAAATGAAATTT-A
1 AGAAAATTT-AGGGTTAAAATGAAATTTAA
* * *
23938837 GGAAAAGTTTAGGGGTCAAAATGCAATTT
1 AGAAAA-TTTA-GGGTTAAAATGAAATTT
23938866 TTATTTTTAA
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 14 0.19
30 56 0.78
31 2 0.03
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.31
Consensus pattern (29 bp):
AGAAAATTTAGGGTTAAAATGAAATTTAA
Found at i:23938804 original size:30 final size:30
Alignment explanation
Indices: 23938764--23938865 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
23938754 ATTTAGGATT
*
23938764 AAAATGAAATTTAATGAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
* * *
23938794 TAATTGAAATTTAAAGAAAGTTTAAGGGTC
1 AAAATGAAATTTAAAGAAAGTTTAGGGGTC
*
23938824 AAAATGAAATTT-AGGAAAAGTTTAGGGGTC
1 AAAATGAAATTTAAAG-AAAGTTTAGGGGTC
*
23938854 AAAATGCAATTT
1 AAAATGAAATTT
23938866 TTATTTTTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 2 0.03
30 60 0.97
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.30
Consensus pattern (30 bp):
AAAATGAAATTTAAAGAAAGTTTAGGGGTC
Found at i:23939322 original size:54 final size:55
Alignment explanation
Indices: 23939136--23939353 Score: 315
Period size: 54 Copynumber: 4.1 Consensus size: 55
23939126 CACGTGAGCC
* *
23939136 AAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTG-AAAACAGAATTTGCAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AA
*
23939191 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAG--A---AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAA
* *
23939242 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
*
23939296 AAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
23939351 AAG
1 AAG
23939354 TAGAAATTGA
Statistics
Matches: 149, Mismatches: 7, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
50 14 0.09
51 34 0.23
52 1 0.01
54 51 0.34
55 37 0.25
56 6 0.04
57 6 0.04
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
Found at i:23939351 original size:14 final size:14
Alignment explanation
Indices: 23939332--23939366 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
23939322 GAGTTGATTT
23939332 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
**
23939346 TTGAAAAGTAGAAA
1 TTGAAAAACAGAAA
23939360 TTGAAAA
1 TTGAAAA
23939367 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:23939599 original size:85 final size:87
Alignment explanation
Indices: 23939455--23939702 Score: 299
Period size: 85 Copynumber: 2.8 Consensus size: 87
23939445 AGCAGAAATT
* * *
23939455 AAAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
23939520 TTGATTTGAAAAG-TAGAATT-AG
65 TTGATTTGAAAAGATAG-ATTGAA
* ** * *
23939542 TAAAGTAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
23939605 TTGATTTTTGAAAAGCATAGATTGAA
65 TTGA--TTTGAAAAG-ATAGATTGAA
*
23939631 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
23939695 GTTGATTT
64 GTTGATTT
23939703 TTGAAAAACA
Statistics
Matches: 136, Mismatches: 15, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
84 3 0.02
85 33 0.24
87 31 0.23
88 3 0.02
89 30 0.22
91 33 0.24
93 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (87 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTGAAAAGATAGATTGAA
Found at i:23939648 original size:15 final size:16
Alignment explanation
Indices: 23939615--23939648 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
23939605 TTGATTTTTG
* *
23939615 AAAAGCATAGATTGAA
1 AAAAACATAAATTGAA
23939631 AAAAACATAAATTGAA
1 AAAAACATAAATTGAA
23939647 AA
1 AA
23939649 TACCTCAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (16 bp):
AAAAACATAAATTGAA
Found at i:23939690 original size:91 final size:88
Alignment explanation
Indices: 23939455--23939709 Score: 315
Period size: 91 Copynumber: 2.9 Consensus size: 88
23939445 AGCAGAAATT
* * *
23939455 AAAAACAGAATTTGAAAAGACCTCAGCGTGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
*
23939520 TTGA--TTTGAAAAGTAGAATTAG
65 TTGATTTTTGAAAAGTAGAATTAA
* ** * *
23939542 TAAAGTAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAAG
1 AAAAACAGAAATTGAAAATACCTCAGCTGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGAG
23939605 TTGATTTTTGAAAAGCATAG-ATTGAA
65 TTGATTTTTGAAAAG--TAGAATT-AA
*
23939631 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC-TGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
23939695 GTTGATTTTTGAAAA
64 GTTGATTTTTGAAAA
23939710 ACAAAAATTA
Statistics
Matches: 143, Mismatches: 15, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
84 3 0.02
85 33 0.23
87 31 0.22
88 3 0.02
89 27 0.19
91 43 0.30
93 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (88 bp):
AAAAACAGAAATTGAAAATACCTCAGCTGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTTTGAAAAGTAGAATTAA
Found at i:23939853 original size:123 final size:123
Alignment explanation
Indices: 23939632--23939950 Score: 523
Period size: 123 Copynumber: 2.6 Consensus size: 123
23939622 TAGATTGAAA
* * * ** * *
23939632 AAAACATAAATTGAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTTGCAATATGAGT
1 AAAACATAAACTAAAAATACCTCGGC--GTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGT
23939697 TGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
64 TGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
*
23939757 AAAACATAAACTAAAAATACCTCGGCGTGCCCC-ACGGCTCAACTCATTTCTCGCAATATGAGTT
1 AAAACATAAACTAAAAATACCTCGGCGTGCCCCGA-GGCTCAACTCACTTCTCGCAATATGAGTT
23939821 GATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
65 GATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
*
23939880 AAAACATAAACTAAAAATACCTTGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
1 AAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
23939945 ATTTTT
66 ATTTTT
23939951 TTTAAAAAAT
Statistics
Matches: 182, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
122 1 0.01
123 157 0.86
124 1 0.01
125 23 0.13
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (123 bp):
AAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTG
ATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCACCTCTCGCAATATGAGTCAATTT
Found at i:23940063 original size:193 final size:192
Alignment explanation
Indices: 23939792--23940598 Score: 1533
Period size: 193 Copynumber: 4.2 Consensus size: 192
23939782 CGTGCCCCAC
23939792 GGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTGAAAAACAAAAATTAAAAGGCTTAACTCA
1 GGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTGAAAAACAAAAATTAAAAGGCTTAACTCA
*
23939857 CCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTTGGCGTGCCCCGAGGCTCAA
65 CCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAA
23939922 CTCACTTCTCGCAATATGAGTTGATTTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTGA
130 CTCACTTCTCGCAATATGAGTTGA-TTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTGA
23939986 GGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCAC
1 GGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCAC
23940051 CTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAAC
66 CTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAAC
23940116 TCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAAATTTAAAAATACCTCAACGTGTCTTGA
131 TCACTTCTCGCAATATGAGTTGATTTTTTT-AAAAAATTTAAAAATACCTCAACGTGTCTTGA
*
23940179 GGCTCAACTCATTTCTCACAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCAC
1 GGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCAC
23940244 CTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAAC
66 CTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAAC
23940309 TCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTGA
131 TCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTGA
* *
23940371 GTCTCAACTCATTTCTCTCAATATGAGTTGATTTTGAAAAACAAAAAATTAAAAGGCTTAACTCA
1 GGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAAC-AAAAATTAAAAGGCTTAACTCA
23940436 CCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAA
65 CCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAA
*
23940501 CTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCACAACGTGTCTTGA
130 CTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTGA
23940564 GGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 GGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
23940599 CCTTGGAAAG
Statistics
Matches: 604, Mismatches: 7, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
192 79 0.13
193 494 0.82
194 31 0.05
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (192 bp):
GGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACTCAC
CTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTCAAC
TCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCTTGA
Found at i:23948785 original size:16 final size:17
Alignment explanation
Indices: 23948760--23949280 Score: 185
Period size: 17 Copynumber: 29.9 Consensus size: 17
23948750 TGAAAGTTTT
23948760 TTTTTAAAACACGAGAA
1 TTTTTAAAACACGAGAA
23948777 TTTTT-AAACACG-GAA
1 TTTTTAAAACACGAGAA
* * *
23948792 ATTTCAGAAACACGAAAA
1 TTTTTA-AAACACGAGAA
* *
23948810 TTTTTAAAACACGACAT
1 TTTTTAAAACACGAGAA
*
23948827 TTTTTGAAACACGAGAA
1 TTTTTAAAACACGAGAA
* * *
23948844 TTTTTAAAACAAGACAT
1 TTTTTAAAACACGAGAA
* * ***
23948861 TTTTTGAAACACAATTTT
1 TTTTTAAAACACGA-GAA
23948879 TTTCTTAAAA-A--A-AA
1 TTT-TTAAAACACGAGAA
* *
23948893 --TTTAAAATACAAGAA
1 TTTTTAAAACACGAGAA
*
23948908 TTTTTAAAACACGAAAA
1 TTTTTAAAACACGAGAA
* *
23948925 TTTTTAAAACATGAAAA
1 TTTTTAAAACACGAGAA
*
23948942 TTTTTGAAACACG-GAAA
1 TTTTTAAAACACGAG-AA
***
23948959 TTTTTTAGAAA-ACGATTTT
1 -TTTTTA-AAACACGA-GAA
* *
23948978 TTTTTAAATCACCG-GAG
1 TTTTTAAAACA-CGAGAA
*
23948995 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAGAA
* *
23949013 TCTTTGAAACACCGA-AA
1 TTTTTAAAACA-CGAGAA
23949030 TTTTTGAAAACACGA-AGA
1 TTTTT-AAAACACGAGA-A
* *
23949048 TTTTTGAAACACGAAAA
1 TTTTTAAAACACGAGAA
* *
23949065 TTTTTTGAAAATACGAAGAT
1 -TTTTT-AAAACACG-AGAA
**
23949085 TTTTTTTAACACG-GAAA
1 TTTTTAAAACACGAG-AA
* *
23949102 TTTTTGAAACACG-GTCATTT
1 TTTTTAAAACACGAG--A--A
*
23949122 TTTTTGAAAACACGAAAA
1 TTTTT-AAAACACGAGAA
* * * *
23949140 TTTTTGAAAGACGTGATT
1 TTTTTAAAACACGAGA-A
*
23949158 TTTTTGAAAATACG-GAAA
1 TTTTT-AAAACACGAG-AA
* *
23949176 TTTATAAAACACGAAAA
1 TTTTTAAAACACGAGAA
* *
23949193 TTTTTTCTGAAAACAAGAAAA
1 --TTTT-T-AAAACACGAGAA
* *
23949214 TTTTTGAAACACTAGAA
1 TTTTTAAAACACGAGAA
*
23949231 TTTTGAAAACACGA-AGA
1 TTTTTAAAACACGAGA-A
* * *
23949248 GTTTTGAAACATGAGAA
1 TTTTTAAAACACGAGAA
23949265 TTTTTAAAAGCACGAG
1 TTTTTAAAA-CACGAG
23949281 GATTATTGAA
Statistics
Matches: 373, Mismatches: 87, Indels: 87
0.68 0.16 0.16
Matches are distributed among these distances:
11 6 0.02
12 2 0.01
14 1 0.00
15 8 0.02
16 10 0.03
17 200 0.54
18 84 0.23
19 35 0.09
20 9 0.02
21 18 0.05
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.33
Consensus pattern (17 bp):
TTTTTAAAACACGAGAA
Found at i:23948981 original size:35 final size:35
Alignment explanation
Indices: 23948942--23949178 Score: 132
Period size: 35 Copynumber: 6.6 Consensus size: 35
23948932 AACATGAAAA
23948942 TTTTTGAAACACGGAAATTTTTTAGAAA-ACGATTT
1 TTTTTGAAACACGGAAATTTTTT-GAAACACGATTT
* * ***
23948977 TTTTTTAAATCACCGG--AGTTTTTGAAAACACGAAAA
1 TTTTTGAAA-CA-CGGAAATTTTTTG-AAACACGATTT
* * ***
23949013 TCTTTGAAACACCGAAA-TTTTTGAAAACACGAAGA
1 TTTTTGAAACACGGAAATTTTTTG-AAACACGATTT
* *
23949048 TTTTTGAAACACGAAAATTTTTTGAAAATACGAAGATTT
1 TTTTTGAAACACGGAAATTTTTTG--AA-AC-ACGATTT
23949087 TTTTT--AACACGGAAA-TTTTTGAAACACGGTCATTT
1 TTTTTGAAACACGGAAATTTTTTGAAACAC-G--ATTT
* *
23949122 TTTTTGAAAACAC-GAAAATTTTTGAAAGACG-TGATT
1 TTTTTG-AAACACGGAAATTTTTTGAAACACGAT--TT
*
23949158 TTTTTGAAAATACGGAAATTT
1 TTTTTG-AAACACGGAAATTT
23949179 ATAAAACACG
Statistics
Matches: 161, Mismatches: 21, Indels: 38
0.73 0.10 0.17
Matches are distributed among these distances:
32 1 0.01
33 3 0.02
34 6 0.04
35 59 0.37
36 40 0.25
37 26 0.16
38 18 0.11
39 8 0.05
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (35 bp):
TTTTTGAAACACGGAAATTTTTTGAAACACGATTT
Found at i:23949122 original size:54 final size:55
Alignment explanation
Indices: 23948908--23949144 Score: 167
Period size: 54 Copynumber: 4.4 Consensus size: 55
23948898 AATACAAGAA
** * * *
23948908 TTTTT-AAAACACGAAAA-TTTTTAAAACATGAAAATTTTTGAAACACGGAAATT
1 TTTTTGAAAACACGAAAATTTTTTTTAACACGAAGATTTTTGAAACACGAAAATT
* * *
23948961 TTTTAG-AAA-ACG--ATTTTTTTTTAAATCACCGGAG-TTTTTGAAAACACGAAAA--
1 TTTTTGAAAACACGAAAATTTTTTTT-AA-CA-CGAAGATTTTTG-AAACACGAAAATT
* ***
23949013 TCTTTG-AAACACCG-AAATTTTTGAAAACACGAAGATTTTTGAAACACGAAAA-T
1 TTTTTGAAAACA-CGAAAATTTTTTTTAACACGAAGATTTTTGAAACACGAAAATT
* * ** *
23949066 TTTTTGAAAATACGAAGATTTTTTTTAACACGGAA-ATTTTTGAAACACGGTCATTT
1 TTTTTGAAAACACGAAAATTTTTTTTAACAC-GAAGATTTTTGAAACAC-GAAAATT
23949122 TTTTTGAAAACACGAAAATTTTT
1 TTTTTGAAAACACGAAAATTTTT
23949145 GAAAGACGTG
Statistics
Matches: 142, Mismatches: 26, Indels: 29
0.72 0.13 0.15
Matches are distributed among these distances:
50 1 0.01
51 5 0.04
52 27 0.19
53 31 0.22
54 45 0.32
55 11 0.08
56 22 0.15
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (55 bp):
TTTTTGAAAACACGAAAATTTTTTTTAACACGAAGATTTTTGAAACACGAAAATT
Found at i:23949126 original size:38 final size:37
Alignment explanation
Indices: 23949048--23949258 Score: 150
Period size: 38 Copynumber: 5.8 Consensus size: 37
23949038 AACACGAAGA
* **
23949048 TTTTTG-AAACACGAAAATTTTTTGAAAATACGAAGATTT
1 TTTTTGAAAACACGAAAA-TTTTTG-AAACACG-TCATTT
*
23949087 TTTTT---AACACGGAAATTTTTGAAACACGGTCATTT
1 TTTTTGAAAACACGAAAATTTTTGAAACAC-GTCATTT
* *
23949122 TTTTTGAAAACACGAAAATTTTTGAAAGACGTGA-TT
1 TTTTTGAAAACACGAAAATTTTTGAAACACGTCATTT
* * * * **
23949158 TTTTTGAAAATACGGAAATTTATAAAACACGAAAATTT
1 TTTTTGAAAACACGAAAATTTTTGAAACACG-TCATTT
* * **
23949196 TTTCTGAAAACAAGAAAATTTTTGAAACAC-T-A-GA
1 TTTTTGAAAACACGAAAATTTTTGAAACACGTCATTT
* * *
23949230 ATTTTGAAAACACGAAGAGTTTTGAAACA
1 TTTTTGAAAACACGAAAATTTTTGAAACA
23949259 TGAGAATTTT
Statistics
Matches: 138, Mismatches: 28, Indels: 17
0.75 0.15 0.09
Matches are distributed among these distances:
34 24 0.17
35 15 0.11
36 35 0.25
37 13 0.09
38 46 0.33
39 5 0.04
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (37 bp):
TTTTTGAAAACACGAAAATTTTTGAAACACGTCATTT
Found at i:23949173 original size:74 final size:73
Alignment explanation
Indices: 23948908--23949222 Score: 206
Period size: 74 Copynumber: 4.4 Consensus size: 73
23948898 AATACAAGAA
* * * * * *
23948908 TTTTT-AAAACACGAAAATTTTTAAAACATGAA-AATTTTTGAAACACGGAAATTTTTTAGAAA-
1 TTTTTGAAAACACGAAAATTTTTGAAAGACGAAGATTTTTTTAAACACGGAAA-TTTATA-AAAC
23948970 ACG---ATTT
64 ACGAAAATTT
* * * * * * * * * *
23948977 TTTTTTAAATCACCG-GAGTTTTTGAAAACACGAA-AATCTTTGAAACACCGAAATTTTTGAAAA
1 TTTTTGAAAACA-CGAAAATTTTTG-AAAGACGAAGATTTTTTTAAACACGGAAATTTAT-AAAA
*
23949040 CACGAAGA---
63 CACGAAAATTT
* * * *
23949048 TTTTTG-AAACACGAAAATTTTTTGAAAATACGAAGATTTTTTTTAACACGGAAATTTTTGAAAC
1 TTTTTGAAAACACGAAAA-TTTTTG-AAAGACGAAGATTTTTTTAAACACGGAAATTTATAAAAC
***
23949112 ACGGTCATTT
64 ACGAAAATTT
* *
23949122 TTTTTGAAAACACGAAAATTTTTGAAAGACG-TGATTTTTTTGAAAATACGGAAATTTATAAAAC
1 TTTTTGAAAACACGAAAATTTTTGAAAGACGAAGATTTTTTT--AAACACGGAAATTTATAAAAC
23949186 ACGAAAATTT
64 ACGAAAATTT
* *
23949196 TTTCTGAAAACAAGAAAATTTTTGAAA
1 TTTTTGAAAACACGAAAATTTTTGAAA
23949223 CACTAGAATT
Statistics
Matches: 197, Mismatches: 32, Indels: 29
0.76 0.12 0.11
Matches are distributed among these distances:
69 7 0.04
70 24 0.12
71 59 0.30
72 28 0.14
73 6 0.03
74 62 0.31
75 11 0.06
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (73 bp):
TTTTTGAAAACACGAAAATTTTTGAAAGACGAAGATTTTTTTAAACACGGAAATTTATAAAACAC
GAAAATTT
Found at i:23949466 original size:17 final size:16
Alignment explanation
Indices: 23949432--23949482 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
23949422 AAAATTATTT
23949432 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
* *
23949448 AAAATCAAATTAAATTA
1 AAAAT-AAAATAAAATA
23949465 AAAATATAAATATAAATA
1 AAAATA-AAATA-AAATA
23949483 TGCATAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.21
17 18 0.64
18 4 0.14
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:23949629 original size:12 final size:12
Alignment explanation
Indices: 23949609--23949671 Score: 60
Period size: 11 Copynumber: 5.3 Consensus size: 12
23949599 GAATTGGACC
23949609 TTTTT-TTTCTT
1 TTTTTCTTTCTT
23949620 TTTTTCTTTC-T
1 TTTTTCTTTCTT
* *
23949631 TTTTTCCTTCTA
1 TTTTTCTTTCTT
*
23949643 TTTTTCTTATTTT
1 TTTTTCTT-TCTT
23949656 TCTTTTCTTT-TT
1 T-TTTTCTTTCTT
23949668 TTTT
1 TTTT
23949672 CTCTGTTGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
11 18 0.42
12 14 0.33
13 4 0.09
14 7 0.16
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:23949850 original size:15 final size:15
Alignment explanation
Indices: 23949824--23949860 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
23949814 TTTTTTGGGC
23949824 TTGTTTCTT-TTTTT-
1 TTGTTT-TTGTTTTTG
23949838 TTGTTTTTGTTTTTG
1 TTGTTTTTGTTTTTG
23949853 TTGTTTTT
1 TTGTTTTT
23949861 TCTTGGGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 11 0.52
15 8 0.38
ACGTcount: A:0.00, C:0.03, G:0.14, T:0.84
Consensus pattern (15 bp):
TTGTTTTTGTTTTTG
Done.