Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6915314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 30
Found at i:5228789 original size:31 final size:30
Alignment explanation
Indices: 5228721--5228797 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
5228711 CTTTTAAAAC
** **
5228721 TTGCAATACAGTCCCCCAACATTAGTCTGT
1 TTGCAATATGGTCCCCCAACATTAGTCCAT
5228751 TTGCAATATGGTCCCCCAACATTTAGTCCAT
1 TTGCAATATGGTCCCCCAACA-TTAGTCCAT
*
5228782 TTTCAATATGGTCCCC
1 TTGCAATATGGTCCCC
5228798 GACGTAACTG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 19 0.46
31 22 0.54
ACGTcount: A:0.25, C:0.30, G:0.13, T:0.32
Consensus pattern (30 bp):
TTGCAATATGGTCCCCCAACATTAGTCCAT
Found at i:5230004 original size:13 final size:12
Alignment explanation
Indices: 5229981--5230015 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
5229971 AATGTTTAGT
*
5229981 TTATGATTTTTA
1 TTATAATTTTTA
5229993 TTATAAATTTTTA
1 TTAT-AATTTTTA
5230006 TTATAATTTT
1 TTATAATTTT
5230016 AAATATTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (12 bp):
TTATAATTTTTA
Found at i:5244642 original size:15 final size:16
Alignment explanation
Indices: 5244622--5244654 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5244612 TATGCAGGAT
5244622 ATTTGAA-TAAATGCA
1 ATTTGAAGTAAATGCA
5244637 ATTTGAATGTAAATGCA
1 ATTTGAA-GTAAATGCA
5244654 A
1 A
5244655 ATTCACAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.33
Consensus pattern (16 bp):
ATTTGAAGTAAATGCA
Found at i:5247582 original size:2 final size:2
Alignment explanation
Indices: 5247575--5247627 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
5247565 TGTACCCGGT
5247575 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5247617 TA TA TA -A TA TA
1 TA TA TA TA TA TA
5247628 ATGAATTATT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5248463 original size:19 final size:19
Alignment explanation
Indices: 5248439--5248475 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5248429 TATTTTTTTA
*
5248439 GTGATATTAAGAATGATTG
1 GTGATATTAAAAATGATTG
5248458 GTGATATTAAAAATGATT
1 GTGATATTAAAAATGATT
5248476 AATAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (19 bp):
GTGATATTAAAAATGATTG
Found at i:5249044 original size:73 final size:73
Alignment explanation
Indices: 5248899--5249045 Score: 177
Period size: 73 Copynumber: 2.0 Consensus size: 73
5248889 TGTTAAGTTT
* ** ** * ** *
5248899 AATAATTTAAAAATATTTTTAAACGTGTTTTTTTATTTCAAACACTTGAAAATATGATAATTTAG
1 AATAATTTAAAAATATTTTTAAACATCATTTTTTATTAAAAAAACTTGAAAATATGATAATCCAA
*
5248964 TGGGCCCC
66 TGAGCCCC
* * *
5248972 AATAATTTAAAAATATTTTTAAACATCATTTTTTATTAAAAAAATTTGAAAATATGGTGATCCAA
1 AATAATTTAAAAATATTTTTAAACATCATTTTTTATTAAAAAAACTTGAAAATATGATAATCCAA
5249037 TGAGCCCC
66 TGAGCCCC
5249045 A
1 A
5249046 TTATAATGAT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
73 61 1.00
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.39
Consensus pattern (73 bp):
AATAATTTAAAAATATTTTTAAACATCATTTTTTATTAAAAAAACTTGAAAATATGATAATCCAA
TGAGCCCC
Found at i:5251188 original size:17 final size:17
Alignment explanation
Indices: 5251168--5251200 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5251158 TATTATTAAT
5251168 TTATTATTTAT-TTAAAA
1 TTATT-TTTATATTAAAA
5251185 TTATTTTTATATTAAA
1 TTATTTTTATATTAAA
5251201 TAATAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATTTTTATATTAAAA
Found at i:5251201 original size:16 final size:17
Alignment explanation
Indices: 5251161--5251201 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
5251151 CATTTATTAT
*
5251161 TATTAATTTATTATTTA
1 TATTAAATTATTATTTA
5251178 T-TTAAAATTATT-TTTA
1 TATT-AAATTATTATTTA
5251194 TATTAAAT
1 TATTAAAT
5251202 AATAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTAAATTATTATTTA
Found at i:5253584 original size:21 final size:21
Alignment explanation
Indices: 5253560--5253609 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
5253550 ATTCTAAATT
*
5253560 CGTTGCGATAGTTC-AAGTTTG
1 CGTTGCGATAG-TCAAAGTTCG
5253581 CGTTGCGATAGTCAAAGTTCG
1 CGTTGCGATAGTCAAAGTTCG
5253602 CGTTGCGA
1 CGTTGCGA
5253610 ATTTGGAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (21 bp):
CGTTGCGATAGTCAAAGTTCG
Found at i:5257638 original size:30 final size:30
Alignment explanation
Indices: 5257603--5257706 Score: 174
Period size: 30 Copynumber: 3.5 Consensus size: 30
5257593 AAAAAAGATC
* *
5257603 AAATTGCATGATTATAAT-GTAAAATTGATG
1 AAATTGCATGACTATTATAG-AAAATTGATG
5257633 AAATTGCATGACTATTATAGAAAATTGATG
1 AAATTGCATGACTATTATAGAAAATTGATG
5257663 AAATTGCATGACTATTATAGAAAATTGATG
1 AAATTGCATGACTATTATAGAAAATTGATG
5257693 AAATTGCATGACTA
1 AAATTGCATGACTA
5257707 CTGTAGGTAG
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
30 70 0.99
31 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (30 bp):
AAATTGCATGACTATTATAGAAAATTGATG
Found at i:5257865 original size:22 final size:20
Alignment explanation
Indices: 5257830--5257869 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
5257820 GCATTTATCA
5257830 TAACAACCCTAACAACCAAG
1 TAACAACCCTAACAACCAAG
5257850 TAACAACTTCCTAACAACCA
1 TAACAAC--CCTAACAACCA
5257870 GCCAACATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.47, C:0.35, G:0.03, T:0.15
Consensus pattern (20 bp):
TAACAACCCTAACAACCAAG
Found at i:5261314 original size:14 final size:14
Alignment explanation
Indices: 5261295--5261322 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5261285 TCGTAAAGTT
5261295 ACTTGTAGAGGAGG
1 ACTTGTAGAGGAGG
5261309 ACTTGTAGAGGAGG
1 ACTTGTAGAGGAGG
5261323 TAGCCTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.43, T:0.21
Consensus pattern (14 bp):
ACTTGTAGAGGAGG
Found at i:5267576 original size:21 final size:19
Alignment explanation
Indices: 5267538--5267583 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
5267528 AATTAATCCT
5267538 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
5267558 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
5267579 A-TAAT
1 ACTAAT
5267584 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:5282009 original size:13 final size:13
Alignment explanation
Indices: 5281991--5282015 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5281981 AACTTTTTGG
5281991 TCAAAGTCAACGT
1 TCAAAGTCAACGT
5282004 TCAAAGTCAACG
1 TCAAAGTCAACG
5282016 AGTTGACTTA
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:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (13 bp):
TCAAAGTCAACGT
Found at i:5282287 original size:51 final size:52
Alignment explanation
Indices: 5282202--5282301 Score: 184
Period size: 51 Copynumber: 1.9 Consensus size: 52
5282192 GCAGCTACAC
*
5282202 ACCATTTCAGACAAAAAATCAAACCAAAAGCATCAACCAAACATAGCCACAT
1 ACCATTTCAGACAAAAAATCAAACCAAAAACATCAACCAAACATAGCCACAT
5282254 ACCATTTCAGAC-AAAAATCAAACCAAAAACATCAACCAAACATAGCCA
1 ACCATTTCAGACAAAAAATCAAACCAAAAACATCAACCAAACATAGCCA
5282302 AATTAACCGA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 35 0.74
52 12 0.26
ACGTcount: A:0.53, C:0.29, G:0.05, T:0.13
Consensus pattern (52 bp):
ACCATTTCAGACAAAAAATCAAACCAAAAACATCAACCAAACATAGCCACAT
Found at i:5283299 original size:21 final size:21
Alignment explanation
Indices: 5283261--5283300 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5283251 TTATAAAATT
*
5283261 TAAAATAAATTAGGATTAATG
1 TAAAATAAATTAGAATTAATG
5283282 TAAAATTAAATT-GAATTAA
1 TAAAA-TAAATTAGAATTAA
5283301 ATTGAATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (21 bp):
TAAAATAAATTAGAATTAATG
Found at i:5288361 original size:17 final size:17
Alignment explanation
Indices: 5288339--5288371 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5288329 TCAGTTTTTC
5288339 TAAATGTCATGGAAAGT
1 TAAATGTCATGGAAAGT
5288356 TAAATGTCATGGAAAG
1 TAAATGTCATGGAAAG
5288372 CTCGAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.27
Consensus pattern (17 bp):
TAAATGTCATGGAAAGT
Found at i:5290539 original size:29 final size:28
Alignment explanation
Indices: 5290495--5290611 Score: 135
Period size: 29 Copynumber: 4.1 Consensus size: 28
5290485 CCCGACCCGG
*
5290495 TGATATTTAGGGAATTATTTTGGAAAAAA
1 TGATATTTTGGGAATTATTTT-GAAAAAA
* * *
5290524 TGATATTTTGGTAATTATTTAGAAAAAGG
1 TGATATTTTGGGAATTATTTTGAAAAA-A
**
5290553 TGATATTTTGGGAATTATTTTGAAAATGG
1 TGATATTTTGGGAATTATTTTGAAAA-AA
* *
5290582 TGATATTTTGGTAATTATTTTAAAAAAA
1 TGATATTTTGGGAATTATTTTGAAAAAA
5290610 TG
1 TG
5290612 GTACTTTTTT
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
28 8 0.11
29 67 0.89
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.43
Consensus pattern (28 bp):
TGATATTTTGGGAATTATTTTGAAAAAA
Found at i:5291692 original size:58 final size:58
Alignment explanation
Indices: 5291602--5291717 Score: 205
Period size: 58 Copynumber: 2.0 Consensus size: 58
5291592 TTTGTTGTGT
*
5291602 GCTTAGGATAAGCCCTACGGACTTACGGACTTAAGGATACAGGGCCGAAAAACTATCC
1 GCTTAGGATAAGCCCTACGGACTTACGGACTTAAGGATACAAGGCCGAAAAACTATCC
* *
5291660 GCTTAGGGTAAGCCCTACGGACTTACGGACTTAAGGATACAAGGTCGAAAAACTATCC
1 GCTTAGGATAAGCCCTACGGACTTACGGACTTAAGGATACAAGGCCGAAAAACTATCC
5291718 TTAGGTTGGC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (58 bp):
GCTTAGGATAAGCCCTACGGACTTACGGACTTAAGGATACAAGGCCGAAAAACTATCC
Found at i:5298891 original size:17 final size:17
Alignment explanation
Indices: 5298851--5298926 Score: 57
Period size: 17 Copynumber: 4.5 Consensus size: 17
5298841 AAGTATGTTG
* *
5298851 TTCATTAAAGCATGCAT
1 TTCATTTAAGCATGTAT
5298868 TGT-ATTTAAGCATGTAT
1 T-TCATTTAAGCATGTAT
* * * *
5298885 TTCATTTAGGGAAGTAG
1 TTCATTTAAGCATGTAT
* *
5298902 TTCATTTATGCATATAT
1 TTCATTTAAGCATGTAT
5298919 TT-ATTTAA
1 TTCATTTAA
5298927 TAAACTACTT
Statistics
Matches: 45, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
16 6 0.13
17 38 0.84
18 1 0.02
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (17 bp):
TTCATTTAAGCATGTAT
Found at i:5298971 original size:17 final size:17
Alignment explanation
Indices: 5298948--5299001 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
5298938 ATTCATGCAT
5298948 TTAGTTCATTAATTAAA
1 TTAGTTCATTAATTAAA
* * *
5298965 TTGGTTCATTCATCAAA
1 TTAGTTCATTAATTAAA
* *
5298982 CTAGTTCATTTATTAAA
1 TTAGTTCATTAATTAAA
5298999 TTA
1 TTA
5299002 AATCTTAATT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.46
Consensus pattern (17 bp):
TTAGTTCATTAATTAAA
Found at i:5301557 original size:4 final size:4
Alignment explanation
Indices: 5301532--5301575 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
5301522 TCATCACTTT
*
5301532 TTTA TTTTA TTTA -TAA TATTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA -TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTT
5301576 TCATTGGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
3 2 0.06
4 26 0.74
5 7 0.20
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:5304511 original size:64 final size:64
Alignment explanation
Indices: 5304410--5304539 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 64
5304400 GCAAAACGGT
*
5304410 ACATATATCTGGAAGAACCGTACACCATTGTAGCTCGAAGCAACCTCCTCAATGGTACAACTCG
1 ACATATATCTGGAAGAACCGAACACCATTGTAGCTCGAAGCAACCTCCTCAATGGTACAACTCG
5304474 ACATATATCTGGAAGAACCGAACACCATTGTAGCTCGAAGCAACCTCCTCAATGGTACAACTCG
1 ACATATATCTGGAAGAACCGAACACCATTGTAGCTCGAAGCAACCTCCTCAATGGTACAACTCG
5304538 AC
1 AC
5304540 CTGTAGGATA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (64 bp):
ACATATATCTGGAAGAACCGAACACCATTGTAGCTCGAAGCAACCTCCTCAATGGTACAACTCG
Found at i:5304926 original size:21 final size:21
Alignment explanation
Indices: 5304899--5304957 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
5304889 TTCCGAGTTA
5304899 CCCGCGACAGCCGCAATAGCG
1 CCCGCGACAGCCGCAATAGCG
*
5304920 TCCGCGACAGCCGCAATAGCG
1 CCCGCGACAGCCGCAATAGCG
*
5304941 CCCGCGACGGCCGCAAT
1 CCCGCGACAGCCGCAAT
5304958 CACGGTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.22, C:0.42, G:0.29, T:0.07
Consensus pattern (21 bp):
CCCGCGACAGCCGCAATAGCG
Found at i:5309762 original size:129 final size:129
Alignment explanation
Indices: 5309526--5309782 Score: 329
Period size: 129 Copynumber: 2.0 Consensus size: 129
5309516 CTGTTGACTG
* * *
5309526 TTGACTTTGACCAAAAAGTCAAATTTTTTGAAAAGTATTATTTTATGCTTTTCGACGTCCTGAGT
1 TTGACTTTGACCAAAAAGTCAAAATTTTTGAAAAGTAATATGTTATGCTTTTCGACGTCCTGAGT
* * * * * *
5309591 CTGAATCCAAAGTTAGTTTTTCCTAATTCGAACCAGAGAGCCTCGAAATTGTTAGTCAAACCCT
66 CTGAATCCAAAGTCAGTTTTGCCAAATTCGAACCAGAAAGCCTCCAAATTGTCAGTCAAACCCT
* * *
5309655 TTGACTTTGACCAAAAAGTCAAAATTTTTGAAAAG-ACATATGTTATGTTTTTTGACGTCCTGAT
1 TTGACTTTGACCAAAAAGTCAAAATTTTTGAAAAGTA-ATATGTTATGCTTTTCGACGTCCTGAG
* *** *
5309719 TCTGATTCTGCAGTCCGTTTTGCCAAATTCGAAGCC-GAAAGCCTCCAAATTGTCAGTCAAACCC
65 TCTGAATCCAAAGTCAGTTTTGCCAAATTCGAA-CCAGAAAGCCTCCAAATTGTCAGTCAAACCC
5309783 AAAAAAATGC
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
128 1 0.01
129 106 0.97
130 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (129 bp):
TTGACTTTGACCAAAAAGTCAAAATTTTTGAAAAGTAATATGTTATGCTTTTCGACGTCCTGAGT
CTGAATCCAAAGTCAGTTTTGCCAAATTCGAACCAGAAAGCCTCCAAATTGTCAGTCAAACCCT
Found at i:5310493 original size:191 final size:193
Alignment explanation
Indices: 5310179--5310584 Score: 511
Period size: 191 Copynumber: 2.1 Consensus size: 193
5310169 TAAATGACGT
* * * *
5310179 TTATACATAACGTCACTTTATAATTGATACTCAATGACAACTAGTTACGTCATTAAATTATATAA
1 TTATGCATAACGTCACTTTATAATTGATACTCAATGACAACTAATTACATCACTAAATTATATAA
*
5310244 AATTTTGTTATTAATAATTCACATCGTCACGAATAATACATTAAAATCAATCTATATGTGA-AGA
66 AATTTTGTTATTAATAATTCACATCGTCACGAATAATACAATAAAATCAATCTATATGTGACA-A
*
5310308 AAGAGATATTGTCACA-TTTTCAGTGACGTAATATAACATTACCTAATAGTATTATGAATGA-CA
130 AAGAGATATTGTCA-AGTTTTCAGTGACATAATATAACATTACCTAATAGTATTATGAATGATCA
* * **
5310371 CTTATGCATAACGTCATTTTATAACTT-ATATTGC-ATGACAGTTAATTACATCACTAAATTATA
1 -TTATGCATAACGTCACTTTATAA-TTGATACT-CAATGACAACTAATTACATCACTAAATTATA
* * * * *
5310434 TAATA-TTT-TTATTAATAATTTATATCGTCACGAATACTACAATAAAATCAATCTATATGTTAC
63 TAAAATTTTGTTATTAATAATTCACATCGTCACGAATAATACAATAAAATCAATCTATATGTGAC
* ** * * *
5310497 AAAAGAGATATTGTCAAGTTTTTAGTGACATAATATAATGTTATCTAATAGTATTTTGAATGATG
128 AAAAGAGATATTGTCAAGTTTTCAGTGACATAATATAACATTACCTAATAGTATTATGAATGATC
5310562 A
193 A
* *
5310563 TTATGCATAACTTCACCTTATA
1 TTATGCATAACGTCACTTTATA
5310585 CAATTTTCTC
Statistics
Matches: 184, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
190 1 0.01
191 122 0.66
192 5 0.03
193 53 0.29
194 3 0.02
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (193 bp):
TTATGCATAACGTCACTTTATAATTGATACTCAATGACAACTAATTACATCACTAAATTATATAA
AATTTTGTTATTAATAATTCACATCGTCACGAATAATACAATAAAATCAATCTATATGTGACAAA
AGAGATATTGTCAAGTTTTCAGTGACATAATATAACATTACCTAATAGTATTATGAATGATCA
Found at i:5319685 original size:18 final size:18
Alignment explanation
Indices: 5319643--5319690 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
5319633 CAGTTTTGAA
* *
5319643 CCGACCCGTTGACCCGAC
1 CCGACCTGTTGAACCGAC
*
5319661 CCGACCTGTTGAACCGAT
1 CCGACCTGTTGAACCGAC
*
5319679 CCGACCTATTGA
1 CCGACCTGTTGA
5319691 CCCTTGATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.21, C:0.40, G:0.21, T:0.19
Consensus pattern (18 bp):
CCGACCTGTTGAACCGAC
Found at i:5321577 original size:2 final size:2
Alignment explanation
Indices: 5321570--5321612 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
5321560 TATTTAATTC
* *
5321570 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5321612 A
1 A
5321613 ATTATAACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5321618 original size:14 final size:15
Alignment explanation
Indices: 5321570--5321618 Score: 68
Period size: 14 Copynumber: 3.5 Consensus size: 15
5321560 TATTTAATTC
*
5321570 ATATATATATATAT-
1 ATATATATATGTATA
5321584 ATATATATATGTAT-
1 ATATATATATGTATA
5321598 ATATATATATGTATA
1 ATATATATATGTATA
5321613 AT-TATA
1 ATATATA
5321619 ACTCACTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
14 31 0.94
15 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (15 bp):
ATATATATATGTATA
Found at i:5323725 original size:17 final size:15
Alignment explanation
Indices: 5323694--5323727 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
5323684 GACCAACATC
5323694 AATCTTTTGTTTTGA
1 AATCTTTTGTTTTGA
5323709 AATCGTTTTGATTTTGA
1 AATC-TTTTG-TTTTGA
5323726 AA
1 AA
5323728 ACAAACTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 5 0.29
17 8 0.47
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.53
Consensus pattern (15 bp):
AATCTTTTGTTTTGA
Found at i:5326252 original size:24 final size:24
Alignment explanation
Indices: 5326225--5326274 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5326215 TTGTGGTTGA
*
5326225 TTTAATGAT-TGTTTGAACTTTATT
1 TTTAATGATATATTT-AACTTTATT
*
5326249 TTTAATGATATATTTAAGTTTATT
1 TTTAATGATATATTTAACTTTATT
5326273 TT
1 TT
5326275 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.28, C:0.02, G:0.10, T:0.60
Consensus pattern (24 bp):
TTTAATGATATATTTAACTTTATT
Found at i:5326736 original size:16 final size:16
Alignment explanation
Indices: 5326712--5326744 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5326702 CACGTGAGGA
5326712 TTATATTCTTTTTATT
1 TTATATTCTTTTTATT
*
5326728 TTATTTTCTTTTTATT
1 TTATATTCTTTTTATT
5326744 T
1 T
5326745 ATTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATATTCTTTTTATT
Found at i:5333131 original size:21 final size:21
Alignment explanation
Indices: 5333088--5333131 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5333078 TAACGTTTTC
* *
5333088 TTTTCTCTTTCTTTATTATTT
1 TTTTCTCTTTCTTTATAACTT
5333109 TTTTCTCTTTCATTT-TAACTT
1 TTTTCTCTTTC-TTTATAACTT
5333130 TT
1 TT
5333132 ACTTTTTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTCTCTTTCTTTATAACTT
Found at i:5339729 original size:20 final size:20
Alignment explanation
Indices: 5339706--5339745 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5339696 ATGCCGATTT
*
5339706 TACCGGTTCTCAGCCGGTTC
1 TACCGGTTCTCAACCGGTTC
*
5339726 TACCGGTTTTCAACCGGTTC
1 TACCGGTTCTCAACCGGTTC
5339746 ATTGCAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.33, G:0.23, T:0.33
Consensus pattern (20 bp):
TACCGGTTCTCAACCGGTTC
Found at i:5343183 original size:21 final size:21
Alignment explanation
Indices: 5343159--5343212 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
5343149 TCTTTATAAA
* *
5343159 CATCAAACTCTACGATCTCAC
1 CATCAAAATCCACGATCTCAC
5343180 CATCAAAATCCACGATCTCAC
1 CATCAAAATCCACGATCTCAC
5343201 CATCAAAATCCA
1 CATCAAAATCCA
5343213 TTGTTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.39, C:0.37, G:0.04, T:0.20
Consensus pattern (21 bp):
CATCAAAATCCACGATCTCAC
Found at i:5351984 original size:17 final size:17
Alignment explanation
Indices: 5351921--5351977 Score: 105
Period size: 17 Copynumber: 3.3 Consensus size: 17
5351911 ACTTGAAGAG
5351921 GAAGAGGAGAAGGAAAAT
1 GAAGA-GAGAAGGAAAAT
5351939 GAAGAGAGAAGGAAAAT
1 GAAGAGAGAAGGAAAAT
5351956 GAAGAGAGAAGGAAAAT
1 GAAGAGAGAAGGAAAAT
5351973 GAAGA
1 GAAGA
5351978 ATGAAGGGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
17 34 0.87
18 5 0.13
ACGTcount: A:0.58, C:0.00, G:0.37, T:0.05
Consensus pattern (17 bp):
GAAGAGAGAAGGAAAAT
Found at i:5351984 original size:34 final size:37
Alignment explanation
Indices: 5351921--5351993 Score: 109
Period size: 34 Copynumber: 2.1 Consensus size: 37
5351911 ACTTGAAGAG
5351921 GAAGAGGAGAAGGAAAATGAAGAGAGAA-GGAA-AAT
1 GAAGAGGAGAAGGAAAATGAAGAGAGAAGGGAAGAAT
5351956 GAAGA-GAGAAGGAAAATGAAGA-ATGAAGGGAAGAAT
1 GAAGAGGAGAAGGAAAATGAAGAGA-GAAGGGAAGAAT
5351992 GA
1 GA
5351994 GATGAAAGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
33 1 0.03
34 20 0.57
35 9 0.26
36 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.37, T:0.07
Consensus pattern (37 bp):
GAAGAGGAGAAGGAAAATGAAGAGAGAAGGGAAGAAT
Found at i:5357651 original size:25 final size:26
Alignment explanation
Indices: 5357617--5357688 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 26
5357607 ACATTTTCTG
*
5357617 TTTGTAATATTGT-T-ATGTTATAATT
1 TTTGTAATATT-TATAATATTATAATT
*
5357642 TTTGTTATATTTATAATATTATAA-T
1 TTTGTAATATTTATAATATTATAATT
5357667 TTTG--ATATTTATAA-ATTATAAT
1 TTTGTAATATTTATAATATTATAAT
5357689 ATTATAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
22 7 0.17
23 10 0.24
24 1 0.02
25 16 0.38
26 8 0.19
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (26 bp):
TTTGTAATATTTATAATATTATAATT
Found at i:5357665 original size:8 final size:8
Alignment explanation
Indices: 5357652--5357721 Score: 58
Period size: 8 Copynumber: 9.1 Consensus size: 8
5357642 TTTGTTATAT
5357652 TTATAATA
1 TTATAATA
5357660 TTATAAT-
1 TTATAATA
*
5357667 TT-TGATA
1 TTATAATA
5357674 TTTATAA-A
1 -TTATAATA
5357682 TTATAATA
1 TTATAATA
*
5357690 TTATAAAA
1 TTATAATA
*
5357698 TTTTAATA
1 TTATAATA
*
5357706 TT-TAAAA
1 TTATAATA
*
5357713 TAATAATA
1 TTATAATA
5357721 T
1 T
5357722 CATTTGGACT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
6 3 0.06
7 13 0.27
8 31 0.63
9 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (8 bp):
TTATAATA
Found at i:5357674 original size:23 final size:23
Alignment explanation
Indices: 5357634--5357688 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
5357624 TATTGTTATG
5357634 TTATAATTTTTGTTATATTTATAATA
1 TTATAA-TTTTG-TATATTTATAA-A
5357660 TTATAATTTTG-ATATTTATAAA
1 TTATAATTTTGTATATTTATAAA
5357682 TTATAAT
1 TTATAAT
5357689 ATTATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.28
23 10 0.34
25 5 0.17
26 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (23 bp):
TTATAATTTTGTATATTTATAAA
Found at i:5357686 original size:30 final size:30
Alignment explanation
Indices: 5357652--5357721 Score: 97
Period size: 32 Copynumber: 2.3 Consensus size: 30
5357642 TTTGTTATAT
*
5357652 TTATAATATTAT-AATTTTGATATTTATAAA
1 TTATAATATTATAAATTTTAATATTTA-AAA
5357682 TTATAATATTATAAAATTTTAATATTTAAAA
1 TTATAATATTAT-AAATTTTAATATTTAAAA
*
5357713 TAATAATAT
1 TTATAATAT
5357722 CATTTGGACT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 12 0.33
31 11 0.31
32 13 0.36
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (30 bp):
TTATAATATTATAAATTTTAATATTTAAAA
Found at i:5357719 original size:15 final size:15
Alignment explanation
Indices: 5357652--5357721 Score: 70
Period size: 16 Copynumber: 4.6 Consensus size: 15
5357642 TTTGTTATAT
*
5357652 TTATAATA-TTATAA
1 TTATAATATTTAAAA
* *
5357666 TTTTGATATTTATAAA
1 TTATAATATTTA-AAA
5357682 TTATAATATTATAAAA
1 TTATAATATT-TAAAA
*
5357698 TTTTAATATTTAAAA
1 TTATAATATTTAAAA
*
5357713 TAATAATAT
1 TTATAATAT
5357722 CATTTGGACT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
14 6 0.13
15 15 0.33
16 22 0.49
17 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (15 bp):
TTATAATATTTAAAA
Found at i:5360725 original size:34 final size:34
Alignment explanation
Indices: 5360687--5360767 Score: 116
Period size: 30 Copynumber: 2.4 Consensus size: 34
5360677 TCGTGAACGC
5360687 TAAACAAATGAACATGAATCCCTTCAAAGATAAA
1 TAAACAAATGAACATGAATCCCTTCAAAGATAAA
5360721 TAAAC--A--AACATGAATCCCTTCAAAGATAAA
1 TAAACAAATGAACATGAATCCCTTCAAAGATAAA
5360751 TAAACAAACATGAACAT
1 TAAAC-AA-ATGAACAT
5360768 AATATTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
30 29 0.71
32 1 0.02
34 6 0.15
36 5 0.12
ACGTcount: A:0.54, C:0.19, G:0.07, T:0.20
Consensus pattern (34 bp):
TAAACAAATGAACATGAATCCCTTCAAAGATAAA
Found at i:5360731 original size:30 final size:30
Alignment explanation
Indices: 5360697--5360764 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
5360687 TAAACAAATG
5360697 AACATGAATCCCTTCAAAGATAAATAAACA
1 AACATGAATCCCTTCAAAGATAAATAAACA
5360727 AACATGAATCCCTTCAAAGATAAATAAACA
1 AACATGAATCCCTTCAAAGATAAATAAACA
5360757 AACATGAA
1 AACATGAA
5360765 CATAATATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.54, C:0.19, G:0.07, T:0.19
Consensus pattern (30 bp):
AACATGAATCCCTTCAAAGATAAATAAACA
Found at i:5361855 original size:16 final size:17
Alignment explanation
Indices: 5361829--5361860 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5361819 AATAAATGTT
5361829 AAAAATAATTTATTTAA
1 AAAAATAATTTATTTAA
5361846 AAAAAT-ATTTATTTA
1 AAAAATAATTTATTTA
5361861 TTATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAAATAATTTATTTAA
Found at i:5363226 original size:3 final size:3
Alignment explanation
Indices: 5363218--5363309 Score: 123
Period size: 3 Copynumber: 31.0 Consensus size: 3
5363208 ATATATTTAT
* *
5363218 TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
5363266 T-A TAA TTA TAA TAA TAA TTA TAA TTA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5363310 ATAAATAAAT
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
2 2 0.03
3 74 0.97
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:5363817 original size:73 final size:74
Alignment explanation
Indices: 5363684--5363846 Score: 224
Period size: 73 Copynumber: 2.2 Consensus size: 74
5363674 TTCAGATGAG
** * * *
5363684 TTCTTCTCATTATGAA--CTTCTCTGGAAAAGCTGCTCCATCAAGTGATGGATTTGAGCAAAAGG
1 TTCTTCTCATTATGAACTCTTCTCTGGAAAAGCTAATCCATCAAGTGATGAATTTAAACAAAAGG
5363747 TTGAACAAA
66 TTGAACAAA
* * * *
5363756 TTCTTCTCATTATGAACTCTTC-CTGGCAATGTTAATCCATCAATTGATGAATTTAAACAAAAGG
1 TTCTTCTCATTATGAACTCTTCTCTGGAAAAGCTAATCCATCAAGTGATGAATTTAAACAAAAGG
5363820 TTGAACAAA
66 TTGAACAAA
5363829 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
5363847 TTTTCTTCCT
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
72 16 0.20
73 60 0.75
74 4 0.05
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (74 bp):
TTCTTCTCATTATGAACTCTTCTCTGGAAAAGCTAATCCATCAAGTGATGAATTTAAACAAAAGG
TTGAACAAA
Found at i:5363884 original size:113 final size:114
Alignment explanation
Indices: 5363756--5364463 Score: 880
Period size: 113 Copynumber: 6.2 Consensus size: 114
5363746 GTTGAACAAA
* * * * ** *
5363756 TTCTTCTCATTATGAACTCTTC-CTGGCAATGTTAATCCATCAATTGATGAATTTAAACAAAAGG
1 TTCTTCTCATTATGAACTCTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCGAGCAAAAGG
*
5363820 TTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAA
66 TTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAG
5363869 TTCTTCTCATTATGAAC-CTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTC-AGGCAAAAG
1 TTCTTCTCATTATGAACTCTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCGA-GCAAAAG
5363932 GTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAG
65 GTTGAACAAATTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAG
* * * *
5363982 TTCTTCTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGG
1 TTCTTCTCATTATGAACTCTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCGAGCAAAAGG
**
5364046 TTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAG
66 TTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAG
* * * * *
5364095 TTCTTCTCATTATGAACT-TTCTCTGGCAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGG
1 TTCTTCTCATTATGAACTCTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCGAGCAAAAGG
5364159 TTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAG
66 TTGAACAAATTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAG
* **
5364208 TTCTTCTCATTATGAACT-TTTTCTGGAAAAGTTGATGCCGATCTATCTCATTCTGTGAT-AGCG
1 TTCTTCTCATTATGAACTCTTCTCTGGAAAAGTTGAT-CC-ATC-A----A----GTGATGA-AT
* * * *
5364271 TCGGGCAAGAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
54 TCGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAG
* * * * *
5364332 TTCTTCTCATTATGAACAC-T-TCTGGCAAATGTTTATCCATCAAGAGATGAATTCGAGCAAAAA
1 TTCTTCTCATTATGAACTCTTCTCTGG-AAAAGTTGATCCATCAAGTGATGAATTCGAGCAAAAG
* * * *
5364395 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTAATATGAG
65 GTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAG
5364445 TTCTTCTCATTATGAACTC
1 TTCTTCTCATTATGAACTC
5364464 GATCTAGCAA
Statistics
Matches: 528, Mismatches: 44, Indels: 46
0.85 0.07 0.07
Matches are distributed among these distances:
112 11 0.02
113 407 0.77
114 7 0.01
115 3 0.01
116 1 0.00
117 1 0.00
120 1 0.00
121 1 0.00
122 3 0.01
123 7 0.01
124 84 0.16
125 2 0.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (114 bp):
TTCTTCTCATTATGAACTCTTCTCTGGAAAAGTTGATCCATCAAGTGATGAATTCGAGCAAAAGG
TTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAG
Found at i:5365579 original size:82 final size:83
Alignment explanation
Indices: 5365280--5365614 Score: 530
Period size: 83 Copynumber: 4.0 Consensus size: 83
5365270 CTTATTTTTA
* * * * * *
5365280 CTATGAGCAAATTCATCTTTCAATTTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTTCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAAA
5365345 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * * *
5365363 CTATGAGCACATTCCTCTTTCAAATTCAATGATTGGTTTTACCAAACCAGATTAGATAACTCAAA
1 CTATGAGCACATTCATCTTTCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAAA
5365428 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
5365446 CTATTGGGCACATTCATC-TTCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAA
1 CTA-TGAGCACATTCATCTTTCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAA
5365510 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
*
5365529 CTATGAGCACATTCATC-TTCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTTCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAAA
5365593 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
5365611 CTAT
1 CTAT
5365615 TGAATCTTCT
Statistics
Matches: 238, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
82 82 0.34
83 144 0.61
84 12 0.05
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (83 bp):
CTATGAGCACATTCATCTTTCAAATTCAATGATTGATTCTACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:5365992 original size:82 final size:82
Alignment explanation
Indices: 5365854--5366043 Score: 353
Period size: 82 Copynumber: 2.3 Consensus size: 82
5365844 TCTTCCTGGG
* *
5365854 AAAGAACACTTCCAGAAGATGCTATTGGGCATATTCATCTTCAAATTCAATGATTGATTCTGCCA
1 AAAGAACACTTCCAGAAGATGCTA-TGAGCACATTCATCTTCAAATTCAATGATTGATTCTGCCA
5365919 AACCAGATCAGATAACTC
65 AACCAGATCAGATAACTC
5365937 AAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTGCCAA
1 AAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTGCCAA
5366002 ACCAGATCAGATAACTC
66 ACCAGATCAGATAACTC
5366019 AAAGAACACTTCCAGAAGATGCTAT
1 AAAGAACACTTCCAGAAGATGCTAT
5366044 TGAATCTTCT
Statistics
Matches: 105, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
82 81 0.77
83 24 0.23
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (82 bp):
AAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCAAATTCAATGATTGATTCTGCCAA
ACCAGATCAGATAACTC
Found at i:5366224 original size:429 final size:429
Alignment explanation
Indices: 5365425--5366283 Score: 1691
Period size: 429 Copynumber: 2.0 Consensus size: 429
5365415 TAGATAACTC
5365425 AAAGAACACTTCCAGAAGATGCTATTGGGCACATTCATCTTCAAATTCAATGATTGATTCTGCCA
1 AAAGAACACTTCCAGAAGATGCTATTGGGCACATTCATCTTCAAATTCAATGATTGATTCTGCCA
5365490 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCAAATTC
66 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCAAATTC
5365555 AATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAAT
131 AATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAAT
*
5365620 CTTCTTATTTCTACTATGAGCACATGGCACTTGCTCCAGTTAATGTTTAGACTGGAATATCACAG
196 CTTCTTATTTCTACTATGAGCACATGGCACTTACTCCAGTTAATGTTTAGACTGGAATATCACAG
5365685 TACTTATTCGATGTAGAGCCAGAATTTGTAGATTCGAAGCATTTTCATGCTATTACACTGAAAAG
261 TACTTATTCGATGTAGAGCCAGAATTTGTAGATTCGAAGCATTTTCATGCTATTACACTGAAAAG
5365750 GGCTATATTCATAATTCTGCCAATTGAGAACAGATTTTCTCTTATTCTGCTTCCTCCATTTGCTG
326 GGCTATATTCATAATTCTGCCAATTGAGAACAGATTTTCTCTTATTCTGCTTCCTCCATTTGCTG
5365815 ATGCTTTTCCATTAACAAAGAAATGATGGTCTTCCTGGG
391 ATGCTTTTCCATTAACAAAGAAATGATGGTCTTCCTGGG
*
5365854 AAAGAACACTTCCAGAAGATGCTATTGGGCATATTCATCTTCAAATTCAATGATTGATTCTGCCA
1 AAAGAACACTTCCAGAAGATGCTATTGGGCACATTCATCTTCAAATTCAATGATTGATTCTGCCA
5365919 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCAAATTC
66 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCAAATTC
5365984 AATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAAT
131 AATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAAT
5366049 CTTCTTATTTCTACTATGAGCACATGGCACTTACTCCAGTTAATGTTTAGACTGGAATATCACAG
196 CTTCTTATTTCTACTATGAGCACATGGCACTTACTCCAGTTAATGTTTAGACTGGAATATCACAG
5366114 TACTTATTCGATGTAGAGCCAGAATTTGTAGATTCGAAGCATTTTCATGCTATTACACTGAAAAG
261 TACTTATTCGATGTAGAGCCAGAATTTGTAGATTCGAAGCATTTTCATGCTATTACACTGAAAAG
*
5366179 GGCTATATTCATAATTCTGCCAATTGAGAACATATTTTCTCTTATTCTGCTTCCTCCATTTGCTG
326 GGCTATATTCATAATTCTGCCAATTGAGAACAGATTTTCTCTTATTCTGCTTCCTCCATTTGCTG
5366244 ATGCTTTTCCATTAACAAAGAAATGATGGTCTTCCTGGG
391 ATGCTTTTCCATTAACAAAGAAATGATGGTCTTCCTGGG
5366283 A
1 A
5366284 TCCAAGAACA
Statistics
Matches: 427, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
429 427 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (429 bp):
AAAGAACACTTCCAGAAGATGCTATTGGGCACATTCATCTTCAAATTCAATGATTGATTCTGCCA
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCAAATTC
AATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAAT
CTTCTTATTTCTACTATGAGCACATGGCACTTACTCCAGTTAATGTTTAGACTGGAATATCACAG
TACTTATTCGATGTAGAGCCAGAATTTGTAGATTCGAAGCATTTTCATGCTATTACACTGAAAAG
GGCTATATTCATAATTCTGCCAATTGAGAACAGATTTTCTCTTATTCTGCTTCCTCCATTTGCTG
ATGCTTTTCCATTAACAAAGAAATGATGGTCTTCCTGGG
Found at i:5367239 original size:7 final size:7
Alignment explanation
Indices: 5367227--5367270 Score: 61
Period size: 7 Copynumber: 6.0 Consensus size: 7
5367217 CTTGACCCTC
5367227 CTTTTTT
1 CTTTTTT
5367234 CTTTTTT
1 CTTTTTT
5367241 CTTTTTCT
1 CTTTTT-T
5367249 CTTTTTT
1 CTTTTTT
*
5367256 TTTTCTTT
1 CTTT-TTT
5367264 CTTTTTT
1 CTTTTTT
5367271 TTTCAAGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 20 0.61
8 13 0.39
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
CTTTTTT
Found at i:5367247 original size:13 final size:12
Alignment explanation
Indices: 5367228--5367272 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 12
5367218 TTGACCCTCC
5367228 TTTTTTCTTTTT
1 TTTTTTCTTTTT
5367240 TCTTTTTCTCTTTT
1 T-TTTTTCT-TTTT
5367254 TTTTTTCTTTCTT
1 TTTTTTCTTT-TT
5367267 TTTTTT
1 TTTTTT
5367273 TCAAGCATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.10
13 22 0.73
14 5 0.17
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:5367257 original size:17 final size:17
Alignment explanation
Indices: 5367235--5367274 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
5367225 TCCTTTTTTC
5367235 TTTTTTCTT-TTTCTCTT
1 TTTTTTCTTCTTTCT-TT
5367252 TTTTTT-TTCTTTCTTT
1 TTTTTTCTTCTTTCTTT
5367268 TTTTTTC
1 TTTTTTC
5367275 AAGCATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTCTTCTTTCTTT
Found at i:5367264 original size:23 final size:22
Alignment explanation
Indices: 5367227--5367269 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
5367217 CTTGACCCTC
5367227 CTTTTTTCTTTTTTCTTTTTCT
1 CTTTTTTCTTTTTTCTTTTTCT
*
5367249 CTTTTTTTTTTCTTTCTTTTT
1 CTTTTTTCTTT-TTTCTTTTT
5367270 TTTTCAAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (22 bp):
CTTTTTTCTTTTTTCTTTTTCT
Found at i:5367271 original size:15 final size:14
Alignment explanation
Indices: 5367228--5367273 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 14
5367218 TTGACCCTCC
5367228 TTTTTTCTTTTTTCT
1 TTTTTTCTTTTTT-T
*
5367243 TTTTCTCTTTTTTT
1 TTTTTTCTTTTTTT
5367257 TTTCTTTCTTTTTTT
1 TTT-TTTCTTTTTTT
5367272 TT
1 TT
5367274 CAAGCATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTTCTTTTTTT
Found at i:5377963 original size:24 final size:23
Alignment explanation
Indices: 5377936--5378006 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 23
5377926 ATAAAATATT
5377936 AATAATATATATAAATACTATAAA
1 AATAATATATATAAATA-TATAAA
* *
5377960 AATAATATGTATATATATA-AAA
1 AATAATATATATAAATATATAAA
* * *
5377982 AATTATAAAT-TAAATATATGAA
1 AATAATATATATAAATATATAAA
5378004 AAT
1 AAT
5378007 TTTAATTTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 7 0.18
22 15 0.38
23 2 0.05
24 15 0.38
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (23 bp):
AATAATATATATAAATATATAAA
Found at i:5378545 original size:22 final size:22
Alignment explanation
Indices: 5378519--5378578 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
5378509 TTGATATTAA
* *
5378519 TAAATATTAATTTGAATAAAAT
1 TAAATATTAATTTAAAAAAAAT
*
5378541 TAAATAGTAA-TTAAAAAAAAT
1 TAAATATTAATTTAAAAAAAAT
* *
5378562 TATAT-TTAATTTTAAAA
1 TAAATATTAATTTAAAAA
5378579 TATCGGAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 3 0.10
21 19 0.61
22 9 0.29
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (22 bp):
TAAATATTAATTTAAAAAAAAT
Found at i:5380036 original size:3 final size:3
Alignment explanation
Indices: 5380028--5380164 Score: 204
Period size: 3 Copynumber: 46.0 Consensus size: 3
5380018 TATATATATT
* *
5380028 TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
5380076 TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
5380123 TAA TTA TAA TAA TAA TAA TTA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5380165 ATAAATTAAT
Statistics
Matches: 121, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
2 2 0.02
3 119 0.98
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:5381182 original size:73 final size:73
Alignment explanation
Indices: 5381105--5381252 Score: 217
Period size: 73 Copynumber: 2.0 Consensus size: 73
5381095 TCACATTTAC
* * * *
5381105 ATTCATTTATTTACAAATGAGAT-AATTTCACGAATTTATTGAATGATATCAAGAATTAAATAGA
1 ATTCATTTATTTACAAATAAGATAAAATT-ACGAATTTATTGAATGATATCAAAAATTAAAGAGA
5381169 ATTTATTAA
65 ATTTATTAA
* * *
5381178 ATTCATTTATTTACAAATAAGATAAAATTATGAATTTATTGAGTGATATCAAAAATTAAAGAGAG
1 ATTCATTTATTTACAAATAAGATAAAATTACGAATTTATTGAATGATATCAAAAATTAAAGAGAA
5381243 TTTATTAA
66 TTTATTAA
5381251 AT
1 AT
5381253 GTATGATATG
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
73 63 0.94
74 4 0.06
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.39
Consensus pattern (73 bp):
ATTCATTTATTTACAAATAAGATAAAATTACGAATTTATTGAATGATATCAAAAATTAAAGAGAA
TTTATTAA
Found at i:5384137 original size:44 final size:43
Alignment explanation
Indices: 5384088--5384187 Score: 139
Period size: 44 Copynumber: 2.3 Consensus size: 43
5384078 TTTAGCGATG
5384088 TTTTTGTATAAACA-TCGAAACAGGTTATGATATTTAACGGCAT
1 TTTTTGTATAAACACT-GAAACAGGTTATGATATTTAACGGCAT
* * * *
5384131 CTTTTTGCATAAACACTGTAACATGTTATGATATTTAGCGGCAT
1 -TTTTTGTATAAACACTGAAACAGGTTATGATATTTAACGGCAT
5384175 TTTTTGTATAAAC
1 TTTTTGTATAAAC
5384188 GGCGCAACAA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
43 12 0.24
44 37 0.74
45 1 0.02
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (43 bp):
TTTTTGTATAAACACTGAAACAGGTTATGATATTTAACGGCAT
Found at i:5384202 original size:43 final size:43
Alignment explanation
Indices: 5384088--5384212 Score: 135
Period size: 44 Copynumber: 2.9 Consensus size: 43
5384078 TTTAGCGATG
*
5384088 TTTTTGTATAAACATCGAAACAGGTTATGATATTTAACGGCATC
1 TTTTTGTATAAACA-CGAAACAAGTTATGATATTTAACGGCATC
* * * *
5384132 TTTTTGCATAAACACTGTAACATGTTATGATATTTAGCGGCAT-
1 TTTTTGTATAAACAC-GAAACAAGTTATGATATTTAACGGCATC
* * * *
5384175 TTTTTGTATAAACGGCGCAACAAGTTATTACATTTAAC
1 TTTTTGTATAAAC-ACGAAACAAGTTATGATATTTAAC
5384213 AGTGTTTTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
43 30 0.44
44 38 0.56
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (43 bp):
TTTTTGTATAAACACGAAACAAGTTATGATATTTAACGGCATC
Found at i:5390130 original size:21 final size:21
Alignment explanation
Indices: 5390104--5390148 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
5390094 TGAAGGAATG
*
5390104 CATTTGTTTTGTATAATAATA
1 CATTTGCTTTGTATAATAATA
5390125 CATTTGCTTTGTATAATAATA
1 CATTTGCTTTGTATAATAATA
5390146 CAT
1 CAT
5390149 CCCAACTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (21 bp):
CATTTGCTTTGTATAATAATA
Found at i:5391858 original size:180 final size:180
Alignment explanation
Indices: 5391556--5391921 Score: 732
Period size: 180 Copynumber: 2.0 Consensus size: 180
5391546 TTAAAAATAA
5391556 TAATTATTTCTTTGATCATTAAGATAATTTAGTTGGTGTTTAGTTAGATCAAAATTAATGAAACG
1 TAATTATTTCTTTGATCATTAAGATAATTTAGTTGGTGTTTAGTTAGATCAAAATTAATGAAACG
5391621 TGACGATCTCATACATAAATCTTCCATAAACTCATAATACATAGTATAGATGTAACTGATCTCTT
66 TGACGATCTCATACATAAATCTTCCATAAACTCATAATACATAGTATAGATGTAACTGATCTCTT
5391686 TAAATAATTATGTTATTAAAAGTGAAATAAACCTGATTGAACACATAAGG
131 TAAATAATTATGTTATTAAAAGTGAAATAAACCTGATTGAACACATAAGG
5391736 TAATTATTTCTTTGATCATTAAGATAATTTAGTTGGTGTTTAGTTAGATCAAAATTAATGAAACG
1 TAATTATTTCTTTGATCATTAAGATAATTTAGTTGGTGTTTAGTTAGATCAAAATTAATGAAACG
5391801 TGACGATCTCATACATAAATCTTCCATAAACTCATAATACATAGTATAGATGTAACTGATCTCTT
66 TGACGATCTCATACATAAATCTTCCATAAACTCATAATACATAGTATAGATGTAACTGATCTCTT
5391866 TAAATAATTATGTTATTAAAAGTGAAATAAACCTGATTGAACACATAAGG
131 TAAATAATTATGTTATTAAAAGTGAAATAAACCTGATTGAACACATAAGG
5391916 TAATTA
1 TAATTA
5391922 AAAAAATTTA
Statistics
Matches: 186, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
180 186 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (180 bp):
TAATTATTTCTTTGATCATTAAGATAATTTAGTTGGTGTTTAGTTAGATCAAAATTAATGAAACG
TGACGATCTCATACATAAATCTTCCATAAACTCATAATACATAGTATAGATGTAACTGATCTCTT
TAAATAATTATGTTATTAAAAGTGAAATAAACCTGATTGAACACATAAGG
Found at i:5392655 original size:24 final size:24
Alignment explanation
Indices: 5392623--5392674 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
5392613 GATTCAATCC
5392623 TAATAATAAAAATTACTTTAATTT
1 TAATAATAAAAATTACTTTAATTT
*
5392647 TAATAATAAATATTACTTTAATTT
1 TAATAATAAAAATTACTTTAATTT
5392671 TAAT
1 TAAT
5392675 TGAAATTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TAATAATAAAAATTACTTTAATTT
Found at i:5393988 original size:10 final size:10
Alignment explanation
Indices: 5393973--5394004 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
5393963 GAAGTTTGGG
5393973 GACCAAAACA
1 GACCAAAACA
5393983 GACCAAAACA
1 GACCAAAACA
5393993 GACCAAAACA
1 GACCAAAACA
5394003 GA
1 GA
5394005 TAGTTTAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.59, C:0.28, G:0.12, T:0.00
Consensus pattern (10 bp):
GACCAAAACA
Found at i:5396912 original size:13 final size:13
Alignment explanation
Indices: 5396896--5396925 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5396886 CTATATAGTG
5396896 TATATATAAACTA
1 TATATATAAACTA
*
5396909 TATATATAAATTA
1 TATATATAAACTA
5396922 TATA
1 TATA
5396926 GTTTATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:5396966 original size:2 final size:2
Alignment explanation
Indices: 5396820--5396957 Score: 90
Period size: 2 Copynumber: 69.0 Consensus size: 2
5396810 TTGAAACAAT
*
5396820 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
5396861 TA AA CA TA TA GTT TA T- TA -A TA TA AA CTA TA TA GTG TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * * *
5396902 TA AA CTA TA TA TA TA AA T- TA TA TA GTT TA TA TT TA TA -A TA T-
1 TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
5396943 TA TA TA CTA TA TA TA
1 TA TA TA -TA TA TA TA
5396958 AACTATATAG
Statistics
Matches: 105, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
1 6 0.06
2 92 0.88
3 7 0.07
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5397006 original size:9 final size:10
Alignment explanation
Indices: 5396975--5397061 Score: 54
Period size: 11 Copynumber: 8.3 Consensus size: 10
5396965 TAGTTTTTGA
5396975 ATATA-AATT
1 ATATATAATT
5396984 ATATAGTTAA-T
1 ATATA--TAATT
5396995 ATATA-AATT
1 ATATATAATT
5397004 ATATATGAATT
1 ATATAT-AATT
* *
5397015 ATATTTAAAT
1 ATATATAATT
*
5397025 ATATACAAGTT
1 ATATATAA-TT
5397036 ATATTTATATATT
1 ATA--TATA-ATT
*
5397049 ATGTATAATT
1 ATATATAATT
5397059 ATA
1 ATA
5397062 AATACTATGT
Statistics
Matches: 60, Mismatches: 8, Indels: 19
0.69 0.09 0.22
Matches are distributed among these distances:
8 2 0.03
9 11 0.18
10 14 0.23
11 23 0.38
12 2 0.03
13 7 0.12
14 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (10 bp):
ATATATAATT
Found at i:5397018 original size:20 final size:20
Alignment explanation
Indices: 5396910--5397017 Score: 71
Period size: 22 Copynumber: 5.3 Consensus size: 20
5396900 TATAAACTAT
*
5396910 ATATATAAATTATATAGTTTA
1 ATATATAAATTATATAG-TGA
* *
5396931 TATTTATAATATTATATACT--
1 -ATATATAA-ATTATATAGTGA
* **
5396951 ATATATAAACTATATAGTTT
1 ATATATAAATTATATAGTGA
* *
5396971 TTGAATATAAATTATATAGTTA
1 AT--ATATAAATTATATAGTGA
5396993 ATATATAAATTATATA-TGA
1 ATATATAAATTATATAGTGA
5397012 AT-TATA
1 ATATATA
5397018 TTTAAATATA
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
18 12 0.17
19 11 0.15
20 15 0.21
22 25 0.35
23 8 0.11
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (20 bp):
ATATATAAATTATATAGTGA
Found at i:5397158 original size:48 final size:48
Alignment explanation
Indices: 5397058--5397159 Score: 134
Period size: 48 Copynumber: 2.1 Consensus size: 48
5397048 TATGTATAAT
* * * *
5397058 TATAAATACTATGTATAAATTATATTTTTATTAATGTAAACTATTAAT
1 TATATATACTATGTATAAATTATATATTTATTAATGTAAACTATAAAG
* *
5397106 TATATATACTATGTATAAATTATATATTTATATAGTTTAAA-TATAAAG
1 TATATATACTATGTATAAATTATATATTTAT-TAATGTAAACTATAAAG
5397154 TATATA
1 TATATA
5397160 ATATAAATTA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 40 0.85
49 7 0.15
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (48 bp):
TATATATACTATGTATAAATTATATATTTATTAATGTAAACTATAAAG
Found at i:5397418 original size:65 final size:67
Alignment explanation
Indices: 5397335--5397470 Score: 188
Period size: 67 Copynumber: 2.1 Consensus size: 67
5397325 ACATGTAAAC
* * * *
5397335 TATATATGTAACTTATAGTACATGTATGTATA-AAT-TATGTATA-GTATATATAAACTATATAT
1 TATATATATAACCTATAGTACATGTATATATACAATCCATGTATATGT-TATATAAACTATATAT
5397397 ATA
65 ATA
* *
5397400 TATATATATAACCTATAGTATATGTATATATACAATCCATTTATATGTTATATAAACTATATATA
1 TATATATATAACCTATAGTACATGTATATATACAATCCATGTATATGTTATATAAACTATATATA
5397465 TA
66 TA
5397467 TATA
1 TATA
5397471 ACCTATAGTT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
65 28 0.45
66 3 0.05
67 29 0.47
68 2 0.03
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (67 bp):
TATATATATAACCTATAGTACATGTATATATACAATCCATGTATATGTTATATAAACTATATATA
TA
Found at i:5397673 original size:21 final size:21
Alignment explanation
Indices: 5397647--5397700 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
5397637 GCGTTGCATT
5397647 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
5397668 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
5397689 TCGCGTTGCGAT
1 TCGCGTTGCGAT
5397701 TTTCCATTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:5397717 original size:20 final size:20
Alignment explanation
Indices: 5397689--5397842 Score: 152
Period size: 20 Copynumber: 7.6 Consensus size: 20
5397679 TAGTTGAAAA
*
5397689 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
*
5397709 TCGCATTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* *
5397729 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
*
5397751 T-GTCGTTGCGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
* ** **
5397772 T--CGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAGT
5397791 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
5397811 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
5397831 TCGCGTTGCGAT
1 TCGCGTTGCGAT
5397843 AGTTGAAAAT
Statistics
Matches: 110, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
19 12 0.11
20 69 0.63
21 13 0.12
22 16 0.15
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:5397732 original size:82 final size:82
Alignment explanation
Indices: 5397646--5397866 Score: 216
Period size: 82 Copynumber: 2.7 Consensus size: 82
5397636 CGCGTTGCAT
* * **
5397646 TTCGCGTTGCGATAATTGAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCATTT
1 TTCGCGTTGCGATAATT-AAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTCAAAAT
5397710 CGCATTGCGATTTTCCAG
65 CGCATTGCGATTTTCCAG
* * * * * ** * *
5397728 TTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGAT-TTTCCAAAT-TCGTTGCGATAGTTGAAAA
1 TTCGCGTTGCGATAAT-TAAAATCG-CGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTCAAAA
*
5397791 TCGCGTTGCGATTTTCCAG
64 TCGCATTGCGATTTTCCAG
* * **
5397810 TTCGCGTTGCGAT-TTTCCAGTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGT
1 TTCGCGTTGCGATAATT-AAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGT
5397867 CTACAGTTGT
Statistics
Matches: 109, Mismatches: 24, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
80 10 0.09
81 18 0.17
82 71 0.65
83 10 0.09
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (82 bp):
TTCGCGTTGCGATAATTAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTCAAAATC
GCATTGCGATTTTCCAG
Found at i:5397799 original size:21 final size:21
Alignment explanation
Indices: 5397647--5397866 Score: 121
Period size: 20 Copynumber: 10.7 Consensus size: 21
5397637 GCGTTGCATT
* *
5397647 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAGTTCAAAA
*
5397668 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTCAAAA
* * **
5397689 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTCAAAA
* * * **
5397709 TCGCATTGCGAT-TTTCCAGT
1 TCGCGTTGCGATAGTTCAAAA
* *
5397729 TCGCGTTGCGATAG-TCTACAG
1 TCGCGTTGCGATAGTTC-AAAA
* * *
5397750 TTGTCGTTGCGAT-TTTCCAAA
1 TCG-CGTTGCGATAGTTCAAAA
* *
5397771 T-TCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTCAAAA
* * **
5397791 TCGCGTTGCGAT-TTTCCAGT
1 TCGCGTTGCGATAGTTCAAAA
* * **
5397811 TCGCGTTGCGAT-TTTCCAGT
1 TCGCGTTGCGATAGTTCAAAA
*
5397831 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTCAAAA
5397852 TCGCGTTGCGATAGT
1 TCGCGTTGCGATAGT
5397867 CTACAGTTGT
Statistics
Matches: 158, Mismatches: 34, Indels: 14
0.77 0.17 0.07
Matches are distributed among these distances:
19 9 0.06
20 75 0.47
21 63 0.40
22 11 0.07
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTCAAAA
Found at i:5397859 original size:123 final size:123
Alignment explanation
Indices: 5397650--5397880 Score: 329
Period size: 123 Copynumber: 1.9 Consensus size: 123
5397640 TTGCATTTCG
* *
5397650 CGTTGCGATAATTGAAAATCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCAT
1 CGTTGCGATAATTGAAAATCGCGTTGCGATAGTTCAAAATCGCGTTGCGATTTTCCAGTTCGCAT
* * **
5397715 TGCGATTTTCCAGTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
66 TGCGATGTTCAAAATCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
* * * ** *
5397773 CGTTGCGATAGTTGAAAATCGCGTTGCGAT-TTTCCAGTTCGCGTTGCGATTTTCCAGTTCGCGT
1 CGTTGCGATAATTGAAAATCGCGTTGCGATAGTTCAAAATCGCGTTGCGATTTTCCAGTTCGCAT
*
5397837 TGCGATAGTTGAAAATCGCGTTGCGATAGTCTACAGTTGTCGTT
66 TGCGAT-GTTCAAAATCGCGTTGCGATAGTCTACAGTTGTCGTT
5397881 CGTTGCGATA
Statistics
Matches: 94, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
122 33 0.35
123 61 0.65
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (123 bp):
CGTTGCGATAATTGAAAATCGCGTTGCGATAGTTCAAAATCGCGTTGCGATTTTCCAGTTCGCAT
TGCGATGTTCAAAATCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
Found at i:5397885 original size:26 final size:26
Alignment explanation
Indices: 5397855--5397906 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
5397845 TTGAAAATCG
*
5397855 CGTTGCGATAGTCTACAGTTGTCGTT
1 CGTTGCGATAGTCTACAGTTATCGTT
5397881 CGTTGCGATAGTCTACAGTTATCGTT
1 CGTTGCGATAGTCTACAGTTATCGTT
5397907 GCGATTTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.38
Consensus pattern (26 bp):
CGTTGCGATAGTCTACAGTTATCGTT
Found at i:5398022 original size:6 final size:6
Alignment explanation
Indices: 5398011--5398059 Score: 98
Period size: 6 Copynumber: 8.2 Consensus size: 6
5398001 GACACGTATT
5398011 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
5398059 A
1 A
5398060 ACCGAGACGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:5398584 original size:6 final size:6
Alignment explanation
Indices: 5398554--5398636 Score: 129
Period size: 6 Copynumber: 14.5 Consensus size: 6
5398544 GTCCGTCCCA
*
5398554 GGTCG- GGTCG- GGTCG- GGTCG- GGTCGG GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
5398598 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
5398637 AATACGTGTC
Statistics
Matches: 76, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
5 20 0.26
6 56 0.74
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:5398785 original size:20 final size:20
Alignment explanation
Indices: 5398760--5398870 Score: 105
Period size: 20 Copynumber: 5.5 Consensus size: 20
5398750 GTAGACTATA
5398760 GCAACGCGAAATGGAAAATC
1 GCAACGCGAAATGGAAAATC
** ** *
5398780 GCAACGCGATTTTCAACTATC
1 GCAACGCGAAATGGAA-AATC
** ** *
5398801 GCAACGCGATTTTCAACTATC
1 GCAACGCGAAATGGAA-AATC
5398822 GCAACGCGAAATGGAAAATC
1 GCAACGCGAAATGGAAAATC
5398842 GCAACGCGAAATGGAAAATC
1 GCAACGCGAAATGGAAAATC
*
5398862 GTAACGCGA
1 GCAACGCGA
5398871 TTTCCAACTA
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 43 0.54
21 36 0.46
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (20 bp):
GCAACGCGAAATGGAAAATC
Found at i:5398799 original size:41 final size:41
Alignment explanation
Indices: 5398730--5398895 Score: 158
Period size: 41 Copynumber: 4.0 Consensus size: 41
5398720 GCAATGAATT
* *
5398730 TGGAAAATCGCAACGAC-ATTGT-AGACTATAGCAACGCGAAA
1 TGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAA
**
5398771 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGATT
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
** * ** ** *
5398812 TTCAACTATCGCAACGCGAAATGGAA-AATCGCAACGCGAAA
1 TGGAA-AATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
* *
5398853 TGGAAAATCGTAACGCGATTTCCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
5398894 TG
1 TG
5398896 CAACGCGAAT
Statistics
Matches: 98, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
40 15 0.15
41 67 0.68
42 16 0.16
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.19
Consensus pattern (41 bp):
TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
Found at i:5398899 original size:21 final size:21
Alignment explanation
Indices: 5398754--5398899 Score: 118
Period size: 21 Copynumber: 7.1 Consensus size: 21
5398744 GACATTGTAG
* *
5398754 ACTATAGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
5398775 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
** *
5398795 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
5398816 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* *
5398837 A-AATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
5398857 A-AATCGTAACGCGATTTCCA
1 ACTATCGCAACGCGAAATGCA
5398877 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
5398898 AC
1 AC
5398900 GCGAATTTGC
Statistics
Matches: 101, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
20 48 0.48
21 53 0.52
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:5399124 original size:14 final size:14
Alignment explanation
Indices: 5399107--5399167 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
5399097 TAATATAGTA
5399107 TATAGTTTATAAAC
1 TATAGTTTATAAAC
* * *
5399121 TATACTATATTAA-
1 TATAGTTTATAAAC
* *
5399134 TATTAATTATATTAAC
1 TA-TAGTT-TATAAAC
5399150 TATAGTTTATAAAC
1 TATAGTTTATAAAC
5399164 TATA
1 TATA
5399168 CTATATAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
13 2 0.05
14 23 0.62
15 10 0.27
16 2 0.05
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (14 bp):
TATAGTTTATAAAC
Found at i:5399151 original size:29 final size:30
Alignment explanation
Indices: 5399061--5399306 Score: 97
Period size: 31 Copynumber: 7.6 Consensus size: 30
5399051 CTATATAGTT
* * *
5399061 TATATTAATGTTAATTATCTTAACTATAATT
1 TATATTAATATTAATTATATTAACTAT-ATC
* *
5399092 TATATTAATATAGTATATAGTTTATAAACTATA-C
1 TATATTAATAT--TA-AT--TATATTAACTATATC
*
5399126 TATATTAATATTAATTATATTAACTATAGTT
1 TATATTAATATTAATTATATTAACTATA-TC
* *
5399157 TATAAACTATACTATATAATT-TA-TAACATATAGTT
1 TAT--A-T-TAATAT-TAATTATATTAAC-TATA-TC
* * *
5399192 TATATTAATATTAATTTTA-TAGATTATATTT
1 TATATTAATATTAATTATATTA-ACTATA-TC
* * * *
5399223 TATATTAATATTCATTACAAATTATAATATAAAGTT
1 TATATTAATATTAATT--ATATTA-ACTAT--A-TC
*
5399259 TATATTAATATTAATTTTA-TAGACTATATC
1 TATATTAATATTAATTATATTA-ACTATATC
5399289 TTATATTAATATTAATTA
1 -TATATTAATATTAATTA
5399307 CAAATTATAA
Statistics
Matches: 169, Mismatches: 25, Indels: 42
0.72 0.11 0.18
Matches are distributed among these distances:
29 11 0.07
30 6 0.04
31 62 0.37
32 4 0.02
33 11 0.07
34 25 0.15
35 18 0.11
36 32 0.19
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (30 bp):
TATATTAATATTAATTATATTAACTATATC
Found at i:5399157 original size:43 final size:40
Alignment explanation
Indices: 5399083--5399195 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 40
5399073 AATTATCTTA
*
5399083 ACTATAATTTATATTAATATAGTATATAGTTTATAAACTAT
1 ACTAT-ATTAATATTAATATAGTATATAGTTTATAAACTAT
*
5399124 ACTATATTAATATTAATTATATTAACTATAGTTTATAAACTAT
1 ACTATATTAATATTAA-TATAGT-A-TATAGTTTATAAACTAT
*
5399167 ACTATA-TAAT-TT-ATA-A-CATATAGTTTATA
1 ACTATATTAATATTAATATAGTATATAGTTTATA
5399196 TTAATATTAA
Statistics
Matches: 66, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
35 11 0.17
36 1 0.02
38 1 0.02
39 2 0.03
40 11 0.17
41 12 0.18
42 5 0.08
43 23 0.35
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (40 bp):
ACTATATTAATATTAATATAGTATATAGTTTATAAACTAT
Found at i:5399174 original size:14 final size:14
Alignment explanation
Indices: 5399114--5399175 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
5399104 GTATATAGTT
5399114 TATAAACTATACTA
1 TATAAACTATACTA
* *
5399128 TATTAA-TATTAATTA
1 TATAAACTA-T-ACTA
* * *
5399143 TATTAACTATAGTT
1 TATAAACTATACTA
5399157 TATAAACTATACTA
1 TATAAACTATACTA
5399171 TATAA
1 TATAA
5399176 TTTATAACAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 2 0.05
14 24 0.63
15 10 0.26
16 2 0.05
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.44
Consensus pattern (14 bp):
TATAAACTATACTA
Found at i:5399212 original size:24 final size:25
Alignment explanation
Indices: 5399185--5399231 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
5399175 ATTTATAACA
*
5399185 TATAGTTTATA-TTAATATTAATTT
1 TATAGATTATATTTAATATTAATTT
*
5399209 TATAGATTATATTTTATATTAAT
1 TATAGATTATATTTAATATTAAT
5399232 ATTCATTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
TATAGATTATATTTAATATTAATTT
Found at i:5399248 original size:36 final size:36
Alignment explanation
Indices: 5399177--5399334 Score: 130
Period size: 31 Copynumber: 4.7 Consensus size: 36
5399167 ACTATATAAT
*
5399177 TTATA-ACATATAGTTTATATTAATATTAATT-----
1 TTATAGAC-TATATTTTATATTAATATTAATTACAAA
* *
5399208 TTATAGATTATATTTTATATTAATATTCATTACAAA
1 TTATAGACTATATTTTATATTAATATTAATTACAAA
*
5399244 TTATA-A-TATAAAGTTTATATTAATATTAATT-----
1 TTATAGACTAT--ATTTTATATTAATATTAATTACAAA
*
5399275 TTATAGACTATATCTTATATTAATATTAATTACAAA
1 TTATAGACTATATTTTATATTAATATTAATTACAAA
*
5399311 TTATAAACTATA--TTATATTAATAT
1 TTATAGACTATATTTTATATTAATAT
5399335 AAGTAAAGGA
Statistics
Matches: 104, Mismatches: 8, Indels: 27
0.75 0.06 0.19
Matches are distributed among these distances:
31 49 0.47
32 2 0.02
33 3 0.03
34 15 0.14
35 1 0.01
36 34 0.33
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (36 bp):
TTATAGACTATATTTTATATTAATATTAATTACAAA
Found at i:5399270 original size:67 final size:67
Alignment explanation
Indices: 5399177--5399316 Score: 235
Period size: 67 Copynumber: 2.1 Consensus size: 67
5399167 ACTATATAAT
* * * *
5399177 TTATAACATATAGTTTATATTAATATTAATTTTATAGATTATATTTTATATTAATATTCATTACA
1 TTATAACATAAAGTTTATATTAATATTAATTTTATAGACTATATCTTATATTAATATTAATTACA
5399242 AA
66 AA
*
5399244 TTATAATATAAAGTTTATATTAATATTAATTTTATAGACTATATCTTATATTAATATTAATTACA
1 TTATAACATAAAGTTTATATTAATATTAATTTTATAGACTATATCTTATATTAATATTAATTACA
5399309 AA
66 AA
5399311 TTATAA
1 TTATAA
5399317 ACTATATTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (67 bp):
TTATAACATAAAGTTTATATTAATATTAATTTTATAGACTATATCTTATATTAATATTAATTACA
AA
Found at i:5399780 original size:10 final size:10
Alignment explanation
Indices: 5399765--5399804 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
5399755 TTTATCACAC
5399765 CAAATTCTCT
1 CAAATTCTCT
5399775 CAAATTCTCT
1 CAAATTCTCT
5399785 -AAATTTCTCT
1 CAAA-TTCTCT
*
5399795 CAAATACTCT
1 CAAATTCTCT
5399805 ATCTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:5400125 original size:111 final size:111
Alignment explanation
Indices: 5399931--5400263 Score: 594
Period size: 111 Copynumber: 3.0 Consensus size: 111
5399921 TGGAAATCAT
* *
5399931 ATATCTCTATACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
5399996 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
5400042 ATATCTCGACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTTTTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
5400107 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
5400153 ATATCTCGACACTTTGCTGATACGGTAACATTTTAAAGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
5400218 TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAATAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
5400264 TTTTTGTAAT
Statistics
Matches: 212, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 212 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:5401483 original size:51 final size:51
Alignment explanation
Indices: 5401374--5401493 Score: 116
Period size: 51 Copynumber: 2.4 Consensus size: 51
5401364 TAGCGCGGAG
* * * * ***
5401374 CAGGGGGCGCGCTATACTCCACGTGTAACCCAGTCAGCGTATAGCGTGGTA
1 CAGGGGGCGCGCTATACTCCACGTGTAACCCAATCAACATATAACGCAATA
* * *
5401425 CAAGGGGCGCGCTATACTCCACGTG-ACCCCAAATCAACATATAACGCAATT
1 CAGGGGGCGCGCTATACTCCACGTGTAACCC-AATCAACATATAACGCAATA
* *
5401476 CAGGGGGCGTGCTTTACT
1 CAGGGGGCGCGCTATACT
5401494 GCTACGGGTG
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
50 4 0.07
51 51 0.93
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.20
Consensus pattern (51 bp):
CAGGGGGCGCGCTATACTCCACGTGTAACCCAATCAACATATAACGCAATA
Found at i:5401863 original size:23 final size:23
Alignment explanation
Indices: 5401837--5401885 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
5401827 CAATAATTTT
5401837 TTTATATAAATTAAACTATATAA
1 TTTATATAAATTAAACTATATAA
*
5401860 TTTATATAAATTAAACTATATTA
1 TTTATATAAATTAAACTATATAA
5401883 TTT
1 TTT
5401886 TTTACATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTATATAAATTAAACTATATAA
Found at i:5401948 original size:22 final size:25
Alignment explanation
Indices: 5401903--5401960 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 25
5401893 TATTAATCAT
5401903 TTTTATATAATTTATATTTAAATAA
1 TTTTATATAATTTATATTTAAATAA
5401928 TTTTATA-AATTT-TA-TTAAATAA
1 TTTTATATAATTTATATTTAAATAA
5401950 TTTTATATAAT
1 TTTTATATAAT
5401961 AGGTCTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 15 0.47
23 5 0.16
24 5 0.16
25 7 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTTATATAATTTATATTTAAATAA
Found at i:5413979 original size:31 final size:31
Alignment explanation
Indices: 5413944--5414033 Score: 94
Period size: 31 Copynumber: 2.9 Consensus size: 31
5413934 CTAAGATGAC
* * *
5413944 TCTTGGGTAGGCT-TTGCGGCCCTAAGATTTT
1 TCTTGGGTAGGCTCTT-CGGCCCCAAGAATTG
* *
5413975 TCTTGGGTAAGCCTCTTTGGCCCCAAGAATTG
1 TCTTGGGT-AGGCTCTTCGGCCCCAAGAATTG
5414007 TCTTGGGTAGGCTC-TCAGGCCCCAAGA
1 TCTTGGGTAGGCTCTTC-GGCCCCAAGA
5414034 TACTCCCTTA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
30 1 0.02
31 23 0.47
32 23 0.47
33 2 0.04
ACGTcount: A:0.17, C:0.24, G:0.28, T:0.31
Consensus pattern (31 bp):
TCTTGGGTAGGCTCTTCGGCCCCAAGAATTG
Found at i:5418336 original size:3 final size:3
Alignment explanation
Indices: 5418328--5418367 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
5418318 TTAATAACAC
*
5418328 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5418368 TTTTTTAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 33 0.97
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:5418671 original size:105 final size:105
Alignment explanation
Indices: 5418537--5418788 Score: 335
Period size: 105 Copynumber: 2.4 Consensus size: 105
5418527 TCTCGTGGAT
* * * *
5418537 GAGTTCTTCTCATTATGAACTCTTTTGGAAATGTTGATCCAAATCCTTTTGCGGTGGACTTAGAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCAAATCCATCTGCGGT-GAATTAGAA
* *
5418602 A-GAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGAC
65 AGGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGAC
* * ** * *
5418642 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCATCTGTGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCAAATCCATCTGCGGTGAATTAGAAA
* *
5418707 GGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTATGAT
66 GGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGAC
*
5418747 GAGTTCTTCTCATTATGAACTCTTCATTGGAAATGTCGATCC
1 GAGTTCTTCTCATTATGAACTCTTC--TGGAAATGTTGATCC
5418789 CTCAAGCGAG
Statistics
Matches: 127, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
104 8 0.06
105 107 0.84
107 12 0.09
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATCCAAATCCATCTGCGGTGAATTAGAAA
GGAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGAC
Found at i:5418770 original size:16 final size:16
Alignment explanation
Indices: 5418716--5418771 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
5418706 AGGAACAAGT
5418716 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
* *
5418732 T-TTCTCCTTTATGATGAGT
1 TCTTCT-CATTATGA--A-C
5418751 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
5418767 TCTTC
1 TCTTC
5418772 ATTGGAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
15 4 0.13
16 13 0.42
17 1 0.03
18 1 0.03
19 8 0.26
20 4 0.13
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.48
Consensus pattern (16 bp):
TCTTCTCATTATGAAC
Found at i:5419097 original size:225 final size:223
Alignment explanation
Indices: 5418708--5419141 Score: 640
Period size: 225 Copynumber: 1.9 Consensus size: 223
5418698 AATTTGAAAG
*
5418708 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTATGATGAGTTCTTCTCATTATGAACTCTTCA
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTTCA
* * * * * * *
5418773 TTGGAAATGTCGATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCAAGTGATAGGT
66 CTGAAAATGTCAATCCCTCAAGCAAGGCGTCACTGATTCAAAATGTCATAAATCAAGTGATAGGT
* * *
5418838 TAAAAAAGCTCTTCTCATTATGAACTTATTCTCCCTCTATTGGATGAGTTCTTCTCATTATGAAC
131 CAAAAAAGCTCTTCTCATTATGAACTTATTCTCCCTCTATCGAATGAGTTCTTCTCATTATGAAC
5418903 TCTCCATTGAAAATGTTGATGCGAAGTT
196 TCTCCATTGAAAATGTTGATGCGAAGTT
5418931 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTT-GGATGAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAAC-T-TTC-TCCT--TTAGGATGAGTTCTTCTCATTATGAACT
* *
5418995 C-TC-CTGAAAATGTCAATCCCTCAAGCAAGGTGTCACTGATTCAAAATGTCATAAATCTAGTGA
61 CTTCACTGAAAATGTCAATCCCTCAAGCAAGGCGTCACTGATTCAAAATGTCATAAATCAAGTGA
* * * *
5419058 TAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGAATGAGTTCTTCTCATTA
126 TAGGTCAAAAAAGCTCTTCTCATTATGAACTTATTCTCCCTCTATCGAATGAGTTCTTCTCATTA
*
5419123 TGAACTCTCCATTGGAAAT
191 TGAACTCTCCATTGAAAAT
5419142 TTTGGTTCAC
Statistics
Matches: 188, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
223 24 0.13
224 1 0.01
225 130 0.69
226 6 0.03
227 25 0.13
228 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (223 bp):
GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTTCA
CTGAAAATGTCAATCCCTCAAGCAAGGCGTCACTGATTCAAAATGTCATAAATCAAGTGATAGGT
CAAAAAAGCTCTTCTCATTATGAACTTATTCTCCCTCTATCGAATGAGTTCTTCTCATTATGAAC
TCTCCATTGAAAATGTTGATGCGAAGTT
Found at i:5420038 original size:25 final size:24
Alignment explanation
Indices: 5420017--5420110 Score: 86
Period size: 24 Copynumber: 3.8 Consensus size: 24
5420007 CCTTTTTCTC
5420017 TTTTT-ATTTTTTCATTTCTTTTTTCA
1 TTTTTCATTTTTT--TTTC-TTTTTCA
5420043 TTTTTCATTTTTTTTTCTTTTTCA
1 TTTTTCATTTTTTTTTCTTTTTCA
**
5420067 TTTTTTTCA-TTTTTCATCTTTTT-A
1 --TTTTTCATTTTTTTTTCTTTTTCA
*
5420091 TTTGTTCCTTTTTTTTTCTT
1 TTT-TTCATTTTTTTTTCTT
5420111 CAAGCATAGT
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
22 3 0.05
23 3 0.05
24 17 0.29
25 16 0.28
26 12 0.21
27 7 0.12
ACGTcount: A:0.09, C:0.13, G:0.01, T:0.78
Consensus pattern (24 bp):
TTTTTCATTTTTTTTTCTTTTTCA
Found at i:5420038 original size:26 final size:25
Alignment explanation
Indices: 5420010--5420110 Score: 84
Period size: 25 Copynumber: 4.0 Consensus size: 25
5420000 AAACCCTCCT
5420010 TTTTCTCTTTTT-ATTTTTTCATTTCT
1 TTTTCTCTTTTTCATTTTTT--TTTCT
5420036 TTTT-TCATTTTTCATTTTTTTTTCT
1 TTTTCTC-TTTTTCATTTTTTTTTCT
* **
5420061 TTTTCATTTTTTTCA-TTTTTCATCT
1 TTTTC-TCTTTTTCATTTTTTTTTCT
* * *
5420086 TTTTAT-TTGTTCCTTTTTTTTTCT
1 TTTTCTCTTTTTCATTTTTTTTTCT
5420110 T
1 T
5420111 CAAGCATAGT
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
23 5 0.08
24 10 0.16
25 23 0.37
26 16 0.26
27 8 0.13
ACGTcount: A:0.08, C:0.14, G:0.01, T:0.77
Consensus pattern (25 bp):
TTTTCTCTTTTTCATTTTTTTTTCT
Found at i:5420040 original size:20 final size:19
Alignment explanation
Indices: 5420011--5420083 Score: 86
Period size: 19 Copynumber: 4.1 Consensus size: 19
5420001 AACCCTCCTT
5420011 TTTCTCTTTTT-ATTTTTTCA
1 TTTCT-TTTTTCA-TTTTTCA
5420031 TTTCTTTTTTCATTTTTCA
1 TTTCTTTTTTCATTTTTCA
5420050 TTT-TTTTTTC-TTTTTCA
1 TTTCTTTTTTCATTTTTCA
5420067 --T-TTTTTTCATTTTTCA
1 TTTCTTTTTTCATTTTTCA
5420083 T
1 T
5420084 CTTTTTATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 9
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.16
16 7 0.14
17 7 0.14
18 7 0.14
19 15 0.30
20 6 0.12
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTCTTTTTTCATTTTTCA
Found at i:5420054 original size:33 final size:33
Alignment explanation
Indices: 5420009--5420108 Score: 100
Period size: 33 Copynumber: 3.0 Consensus size: 33
5419999 CAAACCCTCC
*
5420009 TTTTTCTCTTTTTATTTTTTCATTTCTTTTTTCA
1 TTTTTCACTTTTTATTTTTTC-TTTCTTTTTTCA
5420043 TTTTTCA-TTTTT-TTTTCTT-TTTCATTTTTTTCA
1 TTTTTCACTTTTTATTTT-TTCTTTC--TTTTTTCA
*
5420076 TTTTTCATCTTTTTATTTGTTCCTTT-TTTTTTC
1 TTTTTCA-CTTTTTATTT-TTTCTTTCTTTTTTC
5420109 TTCAAGCATA
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
31 4 0.07
32 4 0.07
33 22 0.39
34 13 0.23
35 5 0.09
36 4 0.07
37 4 0.07
ACGTcount: A:0.08, C:0.14, G:0.01, T:0.77
Consensus pattern (33 bp):
TTTTTCACTTTTTATTTTTTCTTTCTTTTTTCA
Found at i:5420056 original size:16 final size:16
Alignment explanation
Indices: 5420035--5420105 Score: 83
Period size: 16 Copynumber: 4.4 Consensus size: 16
5420025 TTTTCATTTC
5420035 TTTTTTCATTTTTCATTT
1 TTTTTTCATTTTTCA--T
5420053 TTTTTTC-TTTTTCAT
1 TTTTTTCATTTTTCAT
5420068 TTTTTTCATTTTTCAT
1 TTTTTTCATTTTTCAT
* *
5420084 CTTTTT-ATTTGTTCCT
1 TTTTTTCATTT-TTCAT
5420100 TTTTTT
1 TTTTTT
5420106 TTCTTCAAGC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
15 12 0.25
16 22 0.46
17 7 0.15
18 7 0.15
ACGTcount: A:0.08, C:0.13, G:0.01, T:0.77
Consensus pattern (16 bp):
TTTTTTCATTTTTCAT
Found at i:5433401 original size:3 final size:3
Alignment explanation
Indices: 5433386--5433446 Score: 97
Period size: 3 Copynumber: 20.7 Consensus size: 3
5433376 TAAACACACT
*
5433386 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
5433434 TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TA
5433447 TTTTTTAACT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 1 0.02
3 52 0.98
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5448056 original size:17 final size:16
Alignment explanation
Indices: 5448019--5448071 Score: 65
Period size: 17 Copynumber: 3.3 Consensus size: 16
5448009 TATTTCGCCT
*
5448019 AAAAAATGAAAAAGACT
1 AAAAAATGAAAAAGA-A
5448036 AAAAAATGAAAAATGAA
1 AAAAAATGAAAAA-GAA
5448053 AAAAAA-G-AAAAGAA
1 AAAAAATGAAAAAGAA
5448067 AAAAA
1 AAAAA
5448072 TAAAAGGATG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
14 8 0.24
15 4 0.12
16 1 0.03
17 19 0.56
18 2 0.06
ACGTcount: A:0.79, C:0.02, G:0.11, T:0.08
Consensus pattern (16 bp):
AAAAAATGAAAAAGAA
Found at i:5449378 original size:48 final size:48
Alignment explanation
Indices: 5449315--5449446 Score: 205
Period size: 46 Copynumber: 2.8 Consensus size: 48
5449305 TCAACTTCTC
* * **
5449315 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTTTA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
*
5449363 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAG--TCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
5449409 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
1 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
5449447 GCTGATTCAA
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
46 43 0.57
48 33 0.43
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (48 bp):
AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
Found at i:5449380 original size:112 final size:112
Alignment explanation
Indices: 5449182--5449404 Score: 358
Period size: 112 Copynumber: 2.0 Consensus size: 112
5449172 TTTGATCCCA
* *
5449182 ATTCAATGGATCAACTCCCCCAGAGCTGATATTCCCTTCAGAGTAATTGGAACATGTCTCTCTTC
1 ATTCAATGGATCAACTCCCCCAGAGCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTC
*
5449247 TCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTGCTTCG
66 TCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCT-CTTCG
* * *
5449295 ATTCAATGGATCAACT-TCTCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTC
1 ATTCAATGGATCAACTCCCCCAGAGCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTC
**
5449359 TTTAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTC
66 TCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTC
5449405 TCCAAGATTT
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
111 4 0.04
112 82 0.80
113 16 0.16
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32
Consensus pattern (112 bp):
ATTCAATGGATCAACTCCCCCAGAGCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTC
TCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACAAGTCTCTTCG
Found at i:5449603 original size:113 final size:113
Alignment explanation
Indices: 5449363--5449770 Score: 657
Period size: 113 Copynumber: 3.7 Consensus size: 113
5449353 CTCTTCTTTA
* * *
5449363 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAG--TCTCTTCTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
* * *
5449426 CAGAGTAAGTGGAACAAGTCT--GCTGATTCAATGGATAAACTTCCCC
66 CAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCCC
*
5449472 AGATCTGATATTCCCTTCAGAGTAAGCAGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
*
5449537 TAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCCC
66 CAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCCC
*
5449585 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTTTCTCTTTTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
* *
5449650 CAGAGTAAGTGGAACAAGTCTACCCTGATTCAATGGATCAAC-CCCCTC
66 CAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCC-C
*
5449698 AGATCTGATATTCCCTTCAGAGTAAGCGAAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
5449763 CAGA-AAAG
66 CAGAGAAAG
5449771 AAGCGGAACA
Statistics
Matches: 278, Mismatches: 16, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
109 32 0.12
111 46 0.17
112 6 0.02
113 194 0.70
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (113 bp):
AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
CAGAGAAAGTGGAACAAGTCTACCCTGATTCAATGGATCAACTTCCCC
Found at i:5452166 original size:16 final size:16
Alignment explanation
Indices: 5452147--5452177 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5452137 ATATTATAAA
*
5452147 TATTATTATTTATTAT
1 TATTATTATTAATTAT
5452163 TATTATTATTAATTA
1 TATTATTATTAATTA
5452178 ACTAATTTAT
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:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTATTATTAATTAT
Found at i:5453314 original size:16 final size:16
Alignment explanation
Indices: 5453293--5453323 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5453283 GATTATGGCT
*
5453293 ATTTTGATCTTTGTTC
1 ATTTTGATCATTGTTC
5453309 ATTTTGATCATTGTT
1 ATTTTGATCATTGTT
5453324 TGAGTATCAT
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:0.16, C:0.10, G:0.13, T:0.61
Consensus pattern (16 bp):
ATTTTGATCATTGTTC
Found at i:5453898 original size:18 final size:20
Alignment explanation
Indices: 5453875--5453917 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
5453865 TTGCATCAAT
*
5453875 AAATAATTT-TAAAT-TATA
1 AAATAATTTAAAAATATATA
5453893 AAATAATTTAAAAATATATA
1 AAATAATTTAAAAATATATA
5453913 AAATA
1 AAATA
5453918 TACATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 4 0.18
20 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATAATTTAAAAATATATA
Found at i:5456216 original size:15 final size:15
Alignment explanation
Indices: 5456193--5456239 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
5456183 GCAATAATCC
*
5456193 AATATTAATATATAA
1 AATAATAATATATAA
5456208 AATAATAATA-ATAA
1 AATAATAATATATAA
*
5456222 AAT-ATATTATTATAA
1 AATAATAATA-TATAA
5456237 AAT
1 AAT
5456240 CAAGGGAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 5 0.18
14 7 0.25
15 16 0.57
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAATAATATATAA
Found at i:5457517 original size:18 final size:20
Alignment explanation
Indices: 5457473--5457518 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
5457463 ATAGTGCTGC
5457473 ATGTTTTTAAATATTTAATA
1 ATGTTTTTAAATATTTAATA
* *
5457493 AT-ATTTT-GATATTTAAT-
1 ATGTTTTTAAATATTTAATA
5457510 ATGTTTTTA
1 ATGTTTTTA
5457519 TTAATATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 5
0.72 0.10 0.17
Matches are distributed among these distances:
17 2 0.10
18 13 0.62
19 4 0.19
20 2 0.10
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.59
Consensus pattern (20 bp):
ATGTTTTTAAATATTTAATA
Found at i:5463497 original size:79 final size:79
Alignment explanation
Indices: 5463400--5463557 Score: 316
Period size: 79 Copynumber: 2.0 Consensus size: 79
5463390 ATTATATGGG
5463400 TCCTTTTATTTCGTCATTTGGAAATACTTATATTATTTTAGCTATAAATTATGATTCTAAATGGG
1 TCCTTTTATTTCGTCATTTGGAAATACTTATATTATTTTAGCTATAAATTATGATTCTAAATGGG
5463465 TGGAAGCTAAGGCT
66 TGGAAGCTAAGGCT
5463479 TCCTTTTATTTCGTCATTTGGAAATACTTATATTATTTTAGCTATAAATTATGATTCTAAATGGG
1 TCCTTTTATTTCGTCATTTGGAAATACTTATATTATTTTAGCTATAAATTATGATTCTAAATGGG
5463544 TGGAAGCTAAGGCT
66 TGGAAGCTAAGGCT
5463558 ACCCGAAATA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.43
Consensus pattern (79 bp):
TCCTTTTATTTCGTCATTTGGAAATACTTATATTATTTTAGCTATAAATTATGATTCTAAATGGG
TGGAAGCTAAGGCT
Found at i:5464488 original size:18 final size:19
Alignment explanation
Indices: 5464442--5464486 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
5464432 AAGTTATCTC
* *
5464442 TTTTCTTTTCTTTTCAAGT
1 TTTTATTTTATTTTCAAGT
5464461 TTTTATTTTATTTT-AAG-
1 TTTTATTTTATTTTCAAGT
5464478 TTTTATTTT
1 TTTTATTTT
5464487 TAAACATGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 3 0.12
19 12 0.50
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.73
Consensus pattern (19 bp):
TTTTATTTTATTTTCAAGT
Found at i:5466585 original size:113 final size:113
Alignment explanation
Indices: 5466416--5466819 Score: 665
Period size: 113 Copynumber: 3.6 Consensus size: 113
5466406 CCGCTTCTTT
*
5466416 TCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACCTGTTTCGCTTACTCTGAAGGGAATATCAG
1 TCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACCTGTTCCGCTTACTCTGAAGGGAATATCAG
*
5466481 ATCTGAGGG-GGTTGATCCATTGAATCAGGGTAGACTTGTTCCACTTAC
66 ATCTG-GGGAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCACTTAC
*
5466529 TCTGAAGGGAATATCAAATCTTGGAAAAGAGAAACCTGTTCCGCTTACTCTGAAGGGAATATCAG
1 TCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACCTGTTCCGCTTACTCTGAAGGGAATATCAG
*
5466594 ATCTGGGGAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCACTTTC
66 ATCTGGGGAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCACTTAC
* *
5466642 TCTAAAGGGAATATCAAATCTTGGAAAAGAGAGACCTGTTCTGCTTACTCTGAAGGGAATATCAG
1 TCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACCTGTTCCGCTTACTCTGAAGGGAATATCAG
* *
5466707 ATCTGGGGAAGTTTATCCATTGAATCA--GCAGACTTGTTCCACTTAC
66 ATCTGGGGAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCACTTAC
* * *
5466753 TCTGAAGGGAATATCAAATCTTGG-AGA-AGAGACTTGTTCCGCTTACTCTGAAGGGAATATCAA
1 TCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACCTGTTCCGCTTACTCTGAAGGGAATATCAG
5466816 ATCT
66 ATCT
5466820 TAAAGAAGAG
Statistics
Matches: 275, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
109 37 0.13
110 2 0.01
111 40 0.15
112 3 0.01
113 193 0.70
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (113 bp):
TCTGAAGGGAATATCAAATCTTGGAAAAGAGAGACCTGTTCCGCTTACTCTGAAGGGAATATCAG
ATCTGGGGAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCACTTAC
Found at i:5466789 original size:46 final size:46
Alignment explanation
Indices: 5466736--5466865 Score: 215
Period size: 46 Copynumber: 2.8 Consensus size: 46
5466726 TTGAATCAGC
**
5466736 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAG
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTAAAGAAG
*
5466782 AGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTAAAGAAG
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTAAAGAAG
* *
5466828 AGACCTGTTCCACTTACTCTGAAGGGAATATCAGATCT
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCT
5466866 GAGAAGTTGA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (46 bp):
AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTAAAGAAG
Found at i:5466909 original size:110 final size:111
Alignment explanation
Indices: 5466778--5466998 Score: 340
Period size: 110 Copynumber: 2.0 Consensus size: 111
5466768 AAATCTTGGA
* * *
5466778 GAAGAGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTT-A-AAGAAGAGACCTGTTCCAC
1 GAAGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAGAAG-AGAGACATGTTCCAA
5466841 TTACTCTGAAGGGAATATCAGATCT-GAGAAGTTGATCCATTGAATC
65 TTACTCTGAAGGGAATATCAGATCTGGAGAAGTTGATCCATTGAATC
5466887 GAAGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGAGACATGTTCCA
1 GAAG-AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTT-GAGAAGAGAGACATGTTCCA
* * *
5466952 ATTACTCTGAAGGGAATATCAGCTCTGGGGGAGTTGATCCATTGAAT
64 ATTACTCTGAAGGGAATATCAGATCTGGAGAAGTTGATCCATTGAAT
5466999 TGGGATCAAA
Statistics
Matches: 101, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
109 4 0.04
110 38 0.38
112 38 0.38
113 21 0.21
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (111 bp):
GAAGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAGAAGAGAGACATGTTCCAAT
TACTCTGAAGGGAATATCAGATCTGGAGAAGTTGATCCATTGAATC
Done.