Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008211.1 Hibiscus syriacus cultivar Beakdansim tig00110833_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: 2208279
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:443268 original size:76 final size:76
Alignment explanation
Indices: 443168--443694 Score: 970
Period size: 76 Copynumber: 7.0 Consensus size: 76
443158 ACTATTTCCC
* *
443168 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTCTTA
1 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
443233 AAGCCTTCGGG
66 AAGCCTTCGGG
*
443244 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
1 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
443309 AAGCCTTCGGG
66 AAGCCTTCGGG
443320 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
1 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
443385 AAGCCTTCGGG
66 AAGCCTTCGGG
* *
443396 TC--CTATAAGT-CTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTCTTA
1 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
443458 AAGCCTTCGGG
66 AAGCCTTCGGG
*
443469 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
1 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
443534 AAGCCTTCGGG
66 AAGCCTTCGGG
443545 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
1 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
443610 AAGCCTTCGGG
66 AAGCCTTCGGG
443621 TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTT
1 TCATCTATAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGGGAGCTTTTTGATGTTTTT
443686 AAAGCCTTC
65 AAAGCCTTC
443695 AGTGCATGAT
Statistics
Matches: 437, Mismatches: 10, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
73 63 0.14
74 8 0.02
75 7 0.02
76 319 0.73
77 40 0.09
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (76 bp):
TCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTA
AAGCCTTCGGG
Found at i:443572 original size:225 final size:227
Alignment explanation
Indices: 443172--443694 Score: 996
Period size: 225 Copynumber: 2.3 Consensus size: 227
443162 TTTCCCTCAT
443172 CTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTCTTAAAGC
1 CTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTCTTAAAGC
443237 CTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAT
66 CTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAT
443302 GTTTTTAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
131 GTTTTTAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
443367 AGCTTTTTGATGTTTTTAAAGCCTTCGGGTC-
196 AGCTTTTTGATGTTTTTAAAGCCTTCGGGTCA
443398 CTATAAGT-CTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTCTTAAAGC
1 CTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTCTTAAAGC
443462 CTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAT
66 CTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAT
443527 GTTTTTAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
131 GTTTTTAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
443592 AGCTTTTTGATGTTTTTAAAGCCTTCGGGTCA
196 AGCTTTTTGATGTTTTTAAAGCCTTCGGGTCA
* *
443624 TCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAA
1 -CTATAAGTCCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCGAGAGCTTTTTGATGTTCTTAAA
443689 GCCTTC
64 GCCTTC
443695 AGTGCATGAT
Statistics
Matches: 291, Mismatches: 2, Indels: 5
0.98 0.01 0.02
Matches are distributed among these distances:
225 217 0.75
226 8 0.03
227 8 0.03
228 20 0.07
229 38 0.13
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (227 bp):
CTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTCTTAAAGC
CTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGAT
GTTTTTAAAGCCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGG
AGCTTTTTGATGTTTTTAAAGCCTTCGGGTCA
Found at i:443737 original size:56 final size:57
Alignment explanation
Indices: 443633--443750 Score: 211
Period size: 56 Copynumber: 2.1 Consensus size: 57
443623 ATCTATAAGT
* *
443633 CCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAG
1 CCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAG
443690 CCTTCAGTGCATGATGTTTCC-AAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAG
1 CCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAG
443746 CCTTC
1 CCTTC
443751 TGGTCATCTG
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 38 0.64
57 21 0.36
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36
Consensus pattern (57 bp):
CCTTCAGTGCATGATGTTTCCAAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAG
Found at i:443822 original size:76 final size:75
Alignment explanation
Indices: 443690--444007 Score: 534
Period size: 76 Copynumber: 4.3 Consensus size: 75
443680 GTTTTTAAAG
*
443690 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCTGGT
1 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
443755 CATCTGTAAGT
66 CATCTGT-AGT
* * *
443766 CCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAGCCTTCGGGT
1 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
443831 CATCTGTAGT
66 CATCTGTAGT
*
443841 CCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATG-TTTCAAAGCCTTCGGGT
1 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
443904 CATCTGTAGT
66 CATCTGTAGT
*
443914 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGT
1 CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
443979 CATCTGTAAG-
66 CATCTGT-AGT
*
443989 CCCTCAGTGCATGATGTTT
1 CCTTCAGTGCATGATGTTT
444008 TCAACATTTC
Statistics
Matches: 230, Mismatches: 9, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
73 47 0.20
74 49 0.21
75 64 0.28
76 70 0.30
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (75 bp):
CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
CATCTGTAGT
Found at i:443961 original size:148 final size:151
Alignment explanation
Indices: 443687--444007 Score: 542
Period size: 148 Copynumber: 2.1 Consensus size: 151
443677 GATGTTTTTA
*
443687 AAGCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCT
1 AAGCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCG
*
443752 GGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
66 GGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTT
* *
443817 TAAAGCCTTCGGGTCATCTGT
131 CAAAGCCTTAGGGTCATCTGT
*
443838 -AGTCCTTCAGTGCATGATGTTTCC-AAAAGCCTTCGGGAGCTTTTTGATG-TTTCAAAGCCTTC
1 AAG-CCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTC
*
443900 GGGTCATCTGT-AGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTT
65 GGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTT
443964 TCAAAGCCTTAGGGTCATCTGT
130 TCAAAGCCTTAGGGTCATCTGT
*
443986 AAGCCCTCAGTGCATGATGTTT
1 AAGCCTTCAGTGCATGATGTTT
444008 TCAACATTTC
Statistics
Matches: 161, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
148 89 0.55
149 25 0.16
150 26 0.16
151 21 0.13
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (151 bp):
AAGCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCG
GGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTT
CAAAGCCTTAGGGTCATCTGT
Found at i:444528 original size:121 final size:122
Alignment explanation
Indices: 444314--444552 Score: 462
Period size: 121 Copynumber: 2.0 Consensus size: 122
444304 TCAAACCCTA
*
444314 GCTCCCAGCCGCCGCTTCCAGAAGGCTCAAGCTGCCTCTCCAGCTTCCCGACGCTGCTGCCGACG
1 GCTCCCAGCCGCCGCTTCCAGAAGGCTCAAGCTGCCTCTCCAGCTTCCAGACGCTGCTGCCGACG
444379 CCTCCACTGCCAGATGGTCCAACCAGTCGCTGCCGACGCTGC-TTTGCCACGCCACC
66 CCTCCACTGCCAGATGGTCCAACCAGTCGCTGCCGACGCTGCTTTTGCCACGCCACC
444435 GCTCCCAGCCGCCGCTTCCAGAAGGCTCAAGCTGCCTCTCCAGCTTCCAGACGCTGCTGCCGACG
1 GCTCCCAGCCGCCGCTTCCAGAAGGCTCAAGCTGCCTCTCCAGCTTCCAGACGCTGCTGCCGACG
444500 CCTCCACTGCCAGATGGTCCAACCAGTCGCTGCCGACGCTGCTTTTGCCACGC
66 CCTCCACTGCCAGATGGTCCAACCAGTCGCTGCCGACGCTGCTTTTGCCACGC
444553 ACCTCGCCGC
Statistics
Matches: 116, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
121 106 0.91
122 10 0.09
ACGTcount: A:0.15, C:0.44, G:0.23, T:0.18
Consensus pattern (122 bp):
GCTCCCAGCCGCCGCTTCCAGAAGGCTCAAGCTGCCTCTCCAGCTTCCAGACGCTGCTGCCGACG
CCTCCACTGCCAGATGGTCCAACCAGTCGCTGCCGACGCTGCTTTTGCCACGCCACC
Found at i:445742 original size:14 final size:14
Alignment explanation
Indices: 445723--445753 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
445713 AAATTATTTT
445723 ATAATTTTGAAATA
1 ATAATTTTGAAATA
445737 ATAATTTTGAAATA
1 ATAATTTTGAAATA
445751 ATA
1 ATA
445754 GGATTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (14 bp):
ATAATTTTGAAATA
Found at i:447599 original size:18 final size:18
Alignment explanation
Indices: 447544--447583 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
447534 ATCAAAAATA
*
447544 TTATTATTTTTAT-CGATT
1 TTATTATTATTATACG-TT
447562 TTATTATTATTATACGTT
1 TTATTATTATTATACGTT
447580 TTAT
1 TTAT
447584 CGATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (18 bp):
TTATTATTATTATACGTT
Found at i:449665 original size:20 final size:20
Alignment explanation
Indices: 449642--449693 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
449632 CCCTAAGTGG
*
449642 AGTATCGATACTC-AAGGGTC
1 AGTATCGATAC-CGAAGGGAC
* *
449662 AGTACCGATACCGAGGGGAC
1 AGTATCGATACCGAAGGGAC
449682 AGTATCGATACC
1 AGTATCGATACC
449694 AACGTATAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (20 bp):
AGTATCGATACCGAAGGGAC
Found at i:451538 original size:4 final size:4
Alignment explanation
Indices: 451529--451557 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
451519 TTTAAACTCG
451529 CCCT CCCT CCCT CCCT CCCT CCCT CCCT C
1 CCCT CCCT CCCT CCCT CCCT CCCT CCCT C
451558 TTTCTTTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.76, G:0.00, T:0.24
Consensus pattern (4 bp):
CCCT
Found at i:457959 original size:26 final size:27
Alignment explanation
Indices: 457904--457959 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
457894 TAATTTTTAA
* *
457904 AAAAATTGAAAATGATTTTTTTAAAAC
1 AAAAATAGAAAATGATTTTTCTAAAAC
457931 AAAAATAGAAAAT-A-TTTTCTAAAATC
1 AAAAATAGAAAATGATTTTTCTAAAA-C
457957 AAA
1 AAA
457960 CGAATCCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 9 0.35
26 5 0.19
27 12 0.46
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.32
Consensus pattern (27 bp):
AAAAATAGAAAATGATTTTTCTAAAAC
Found at i:459540 original size:37 final size:37
Alignment explanation
Indices: 459490--459562 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
459480 TCGAAACAGT
459490 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAG
1 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAG
459527 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAA
1 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAA
459563 ACTTATTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (37 bp):
TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAG
Found at i:459655 original size:55 final size:55
Alignment explanation
Indices: 459579--459998 Score: 501
Period size: 55 Copynumber: 7.6 Consensus size: 55
459569 TTTATGAAGA
* * * ** *
459579 TCGAGTCCTACACTCTATGAAGGAATAGAGAGCGGATACGTTTGT-TGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTT-TATGAAGATTGT
*
459634 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGT
* * *
459689 TCGAGTTCTATACTCTCTGATGGAATAGGGAGCAGACCCATTTTATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGT
* * *
459744 TCGAGTTCTATACTCTCTGAAGAAATAGAGAGCGTACCCATTTGT-TGAAAATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTT-TATGAAGATTGT
*
459799 TCGAGTTCTATACTCTCTTAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGT
* * * * *
459854 TCGAGTTCTATTCTCCCTGAACGAATAGGGAGCGGACCC-GTTTATTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTA-TGAAGATTGT
* * * * * *
459909 TCGAG-TCTTATACTCCCTGAACGAATAGGGAGCAGACACATTTTATAAAGATTGT
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGT
* *
459964 TCGAG-TCTTATACT-TCCTGAAGGAGTAGGGAGCGG
1 TCGAGTTC-TATACTCT-CTGAAGGAATAGAGAGCGG
459999 GCTCGTTATT
Statistics
Matches: 324, Mismatches: 34, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
54 8 0.02
55 311 0.96
56 5 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (55 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGT
Found at i:466568 original size:26 final size:25
Alignment explanation
Indices: 466534--466583 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
466524 CTAATATGTT
466534 TCAATTAAAAATTAATGA-CAATATA
1 TCAATT-AAAATTAATGATCAATATA
466559 TCAAGTTAAAATTAATGATCAATAT
1 TCAA-TTAAAATTAATGATCAATAT
466584 TGAAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.34
Consensus pattern (25 bp):
TCAATTAAAATTAATGATCAATATA
Found at i:466591 original size:19 final size:19
Alignment explanation
Indices: 466567--466603 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
466557 TATCAAGTTA
466567 AAATTAATGATCAATATTG
1 AAATTAATGATCAATATTG
466586 AAATTAATGATCAATATT
1 AAATTAATGATCAATATT
466604 AACATTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (19 bp):
AAATTAATGATCAATATTG
Found at i:466592 original size:25 final size:25
Alignment explanation
Indices: 466536--466592 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
466526 AATATGTTTC
466536 AATTAAAAATTAATGACAATATATCA
1 AATT-AAAATTAATGACAATATATCA
* *
466562 AGTTAAAATTAATGATCAATAT-TGA
1 AATTAAAATTAATGA-CAATATATCA
466587 AATTAA
1 AATTAA
466593 TGATCAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 18 0.67
26 9 0.33
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.33
Consensus pattern (25 bp):
AATTAAAATTAATGACAATATATCA
Found at i:467508 original size:434 final size:434
Alignment explanation
Indices: 466700--467558 Score: 1655
Period size: 434 Copynumber: 2.0 Consensus size: 434
466690 ATAACAAATC
*
466700 ATATGAAATTAAAGCTAATAAAAATAATGAATAAAATAAAATATTAATAATATATTTAAAATTCA
1 ATATGAAATTAAAGCTAATAAAAATAATGAATAAAATAAAATATTAATAATATAGTTAAAATTCA
466765 AAGAGTAAATTCAAAATTAATTATTAAAATAAAAATAAAGTACAAATTATAGAAGATTTAAAACC
66 AAGAGTAAATTCAAAATTAATTATTAAAATAAAAATAAAGTACAAATTATAGAAGATTTAAAACC
466830 TAGAAGTGTAAAATCTAAACAGGGGAAAGAGAGGGGGTTTACCTGAAATTTGACCATTTAAATTA
131 TAGAAGTGTAAAATCTAAACAGGGGAAAGAGAGGGGGTTTACCTGAAATTTGACCATTTAAATTA
*
466895 AAACAAAAATATGGAGGGTGGTAGTGTAATTTAACCATGTCTATTATAACATGAACGTAAGTTTA
196 AAACAAAAATATGGAGGGTGGTAGTGTAATTTAACCATGTCTATTATAAAATGAACGTAAGTTTA
*
466960 TCTAAAATATAAATAGGAGAAAGTATGGGAGGTTCTCATGAAATTTAACCATTAAAAATAAAACA
261 TCTAAAATATAAATAGGAGAAAGTATGGGAGGTTCTCATGAAATTTAAACATTAAAAATAAAACA
* *
467025 CAAATAGGGGTTAGAATGTAATTTAACCATTCAAAATTTAAACTACCTTTCACCTACGTTTAATT
326 CAAATAGGGGTTAGAATGTAATTTAACCATTCAAAATTAAAACTACCTTTCACCTACGTTGAATT
*
467090 CAATGGAAACAGGAAGCGTTGGCAGAAGCAATTCATATGGAATT
391 CAATGGAAACAGGAAGCGTTGACAGAAGCAATTCATATGGAATT
467134 ATATGAAATTAAAGCTAATAAAAATAATGAATAAAATAAAATATTAATAATATAGTTAAAATTCA
1 ATATGAAATTAAAGCTAATAAAAATAATGAATAAAATAAAATATTAATAATATAGTTAAAATTCA
467199 AAGAGTAAATTCAAAATTAATTATTAAAATAAAAATAAAGTACAAATTATAGAAGATTTAAAACC
66 AAGAGTAAATTCAAAATTAATTATTAAAATAAAAATAAAGTACAAATTATAGAAGATTTAAAACC
467264 TAGAAGTGTAAAATCTAAACAGGGGAAAGAGAGGGGGTTTACCTGAAATTTGACCATTTAAATTA
131 TAGAAGTGTAAAATCTAAACAGGGGAAAGAGAGGGGGTTTACCTGAAATTTGACCATTTAAATTA
467329 AAACAAAAATATGGAGGGTGGTAGTGTAATTTAACCATGTCTATTATAAAATGAACGTAAGTTTA
196 AAACAAAAATATGGAGGGTGGTAGTGTAATTTAACCATGTCTATTATAAAATGAACGTAAGTTTA
467394 TCTAAAATATAAATAGGAGAAAGTATGGGAGGTTCTCATGAAATTTAAACATTAAAAATAAAACA
261 TCTAAAATATAAATAGGAGAAAGTATGGGAGGTTCTCATGAAATTTAAACATTAAAAATAAAACA
*
467459 CAAATAGGGGTTAGAATGTAATTTAACCATTCAAAATTAAAACTACCTTTCACGTACGTTGAATT
326 CAAATAGGGGTTAGAATGTAATTTAACCATTCAAAATTAAAACTACCTTTCACCTACGTTGAATT
467524 CAATGGAAACAGGAAGCGTTGACAGAAGCAATTCA
391 CAATGGAAACAGGAAGCGTTGACAGAAGCAATTCA
467559 ATGTAAAATA
Statistics
Matches: 418, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
434 418 1.00
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.28
Consensus pattern (434 bp):
ATATGAAATTAAAGCTAATAAAAATAATGAATAAAATAAAATATTAATAATATAGTTAAAATTCA
AAGAGTAAATTCAAAATTAATTATTAAAATAAAAATAAAGTACAAATTATAGAAGATTTAAAACC
TAGAAGTGTAAAATCTAAACAGGGGAAAGAGAGGGGGTTTACCTGAAATTTGACCATTTAAATTA
AAACAAAAATATGGAGGGTGGTAGTGTAATTTAACCATGTCTATTATAAAATGAACGTAAGTTTA
TCTAAAATATAAATAGGAGAAAGTATGGGAGGTTCTCATGAAATTTAAACATTAAAAATAAAACA
CAAATAGGGGTTAGAATGTAATTTAACCATTCAAAATTAAAACTACCTTTCACCTACGTTGAATT
CAATGGAAACAGGAAGCGTTGACAGAAGCAATTCATATGGAATT
Found at i:471898 original size:18 final size:17
Alignment explanation
Indices: 471869--472009 Score: 100
Period size: 18 Copynumber: 8.4 Consensus size: 17
471859 ATAATATAAA
471869 ATTATA-TATAAACTAT
1 ATTATATTATAAACTAT
471885 ATTTATATTATAAACTAT
1 A-TTATATTATAAACTAT
*
471903 ATAATTATTATAAAC--T
1 ATTA-TATTATAAACTAT
*
471919 A-TATA-TATAAATTAT
1 ATTATATTATAAACTAT
* *
471934 ATT-TA-TGTCAACTGTAT
1 ATTATATTATAAAC--TAT
* *
471951 ATAAAATTATAAACTAT
1 ATTATATTATAAACTAT
471968 ATTTATATTATAAACTAT
1 A-TTATATTATAAACTAT
* *
471986 ATAATTATTATAAGCTAT
1 ATTA-TATTATAAACTAT
472004 A-TATAT
1 ATTATAT
472010 AAATTATGTT
Statistics
Matches: 98, Mismatches: 15, Indels: 24
0.72 0.11 0.18
Matches are distributed among these distances:
13 6 0.06
14 2 0.02
15 9 0.09
16 7 0.07
17 19 0.19
18 50 0.51
19 5 0.05
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (17 bp):
ATTATATTATAAACTAT
Found at i:471934 original size:11 final size:11
Alignment explanation
Indices: 471851--471935 Score: 57
Period size: 11 Copynumber: 7.4 Consensus size: 11
471841 AAAAAATATA
* *
471851 ATATATATATA
1 ATATATAAATT
471862 ATATA-AAATT
1 ATATATAAATT
*
471872 ATATATAAACT
1 ATATATAAATT
* *
471883 ATATTTATATT
1 ATATATAAATT
471894 ATAAACTATATAATT
1 AT--A-TATA-AATT
471909 AT-TATAAACTAT
1 ATATATAAA-T-T
471921 ATATATAAATT
1 ATATATAAATT
471932 ATAT
1 ATAT
471936 TTATGTCAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
10 10 0.17
11 29 0.50
12 4 0.07
13 7 0.12
14 3 0.05
15 5 0.09
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (11 bp):
ATATATAAATT
Found at i:471980 original size:83 final size:83
Alignment explanation
Indices: 471875--472029 Score: 283
Period size: 83 Copynumber: 1.9 Consensus size: 83
471865 TAAAATTATA
471875 TATAAACTATATTTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
1 TATAAACTATATTTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
471940 GTCAACTGTATATAAAAT
66 GTCAACTGTATATAAAAT
* *
471958 TATAAACTATATTTATATTATAAACTATATAATTATTATAAGCTATATATATAAATTATGTTTAT
1 TATAAACTATATTTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
*
472023 GTGAACT
66 GTCAACT
472030 ATACATATAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 69 1.00
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (83 bp):
TATAAACTATATTTATATTATAAACTATATAATTATTATAAACTATATATATAAATTATATTTAT
GTCAACTGTATATAAAAT
Found at i:472070 original size:83 final size:82
Alignment explanation
Indices: 471871--472152 Score: 257
Period size: 83 Copynumber: 3.5 Consensus size: 82
471861 AATATAAAAT
471871 TATATATAAACTATAT-T-TAT--A-T-TATAAACTATATAATTATTATAAACTATATATATAAA
1 TATATATAAACTATATATGTATAAACTATATAAACTATATAATTATTATAAACTATATATATAAA
* *
471930 TTATATTTATGTCAACTG
66 TTATGTTTATGT-AACTA
* * * ** *
471948 TATATA-AAATTATAAACTATATTTA-TATTATAAACTATATAATTATTATAAGCTATATATATA
1 TATATATAAACTATATA-TGTATAAACTA-TATAAACTATATAATTATTATAAACTATATATATA
472011 AATTATGTTTATGTGAACTA
64 AATTATGTTTATGT-AACTA
* * * * *
472031 TACATATAAACTATATATGTATAAACTATAAAAAGTATAT-AGT-TTATAAAATATTATTTATAT
1 TATATATAAACTATATATGTATAAACTATATAAACTATATAATTATTATAAACTA-TA--TATAT
* * *
472094 TAA-TATAGTATATAT-A-TA
63 AAATTAT-GTTTATGTAACTA
472112 TATATATAAACTATATATGTATAAACTATATAAACTATATA
1 TATATATAAACTATATATGTATAAACTATATAAACTATATA
472153 GTTTATATGT
Statistics
Matches: 168, Mismatches: 23, Indels: 23
0.79 0.11 0.11
Matches are distributed among these distances:
76 7 0.04
77 6 0.04
78 1 0.01
79 3 0.02
81 49 0.29
82 5 0.03
83 74 0.44
84 23 0.14
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (82 bp):
TATATATAAACTATATATGTATAAACTATATAAACTATATAATTATTATAAACTATATATATAAA
TTATGTTTATGTAACTA
Found at i:472109 original size:2 final size:2
Alignment explanation
Indices: 472096--472234 Score: 51
Period size: 2 Copynumber: 70.0 Consensus size: 2
472086 ATTTATATTA
* * *
472096 AT AT AGT AT AT AT AT AT AT AT AT AA ACT AT AT AT GT AT AA ACT
1 AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT A-T
* * * *
472139 AT AT AA ACT AT AT AGT TT AT AT GT -T AT A- AT TT AT AT -T A- AT
1 AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
472179 AT AGT AT AT AT AT GT AT GT AT A- AC AA AT AT A- AGT A- AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
472220 AG A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
472235 TAAAGAAACA
Statistics
Matches: 102, Mismatches: 20, Indels: 30
0.67 0.13 0.20
Matches are distributed among these distances:
1 8 0.08
2 85 0.83
3 9 0.09
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.43
Consensus pattern (2 bp):
AT
Found at i:472119 original size:81 final size:81
Alignment explanation
Indices: 472029--472201 Score: 265
Period size: 81 Copynumber: 2.1 Consensus size: 81
472019 TTATGTGAAC
* * *
472029 TATACATATAAACTATATATGTATAAACTATAAAAAGTATATAGTTTATAAAATATTATTTATAT
1 TATATATATAAACTATATATGTATAAACTATAAAAACTATATAGTTTATAAAATATAATTTATAT
472094 TAATATAGTATATATA
66 TAATATAGTATATATA
* ***
472110 TATATATATAAACTATATATGTATAAACTATATAAACTATATAGTTTATATGTTATAATTTATAT
1 TATATATATAAACTATATATGTATAAACTATAAAAACTATATAGTTTATAAAATATAATTTATAT
472175 TAATATAGTATATATA
66 TAATATAGTATATATA
* *
472191 TGTATGTATAA
1 TATATATATAA
472202 CAAATATAAG
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 83 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (81 bp):
TATATATATAAACTATATATGTATAAACTATAAAAACTATATAGTTTATAAAATATAATTTATAT
TAATATAGTATATATA
Found at i:472126 original size:15 final size:15
Alignment explanation
Indices: 472108--472143 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
472098 ATAGTATATA
472108 TATATATATATAAAC
1 TATATATATATAAAC
*
472123 TATATATGTATAAAC
1 TATATATATATAAAC
472138 TATATA
1 TATATA
472144 AACTATATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:472233 original size:81 final size:81
Alignment explanation
Indices: 472029--472231 Score: 225
Period size: 81 Copynumber: 2.5 Consensus size: 81
472019 TTATGTGAAC
* * * *
472029 TATACATATAAACTATATATGTATAAACTATA-AAAAGTATATAGTTTATAAAATATTATTTATA
1 TATATATATAAACAATATAAGTATAAACTATAGAAAA-TATATAGTTTATAAAATATAATTTATA
472093 TTAATATAGTATATATA
65 TTAATATAGTATATATA
* * * * ***
472110 TATATATATAAACTATATATGTATAAACTATATAAACTATATAGTTTATATGTTATAATTTATAT
1 TATATATATAAACAATATAAGTATAAACTATAGAAAATATATAGTTTATAAAATATAATTTATAT
472175 TAATATAGTATATATA
66 TAATATAGTATATATA
* * * *
472191 TGTATGTAT-AACAAATATAAGTA-ATA-TATAGAATATATATA
1 TATATATATAAAC-AATATAAGTATAAACTATAGAAAATATATA
472232 TATTAAAGAA
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
79 12 0.11
80 5 0.05
81 86 0.81
82 3 0.03
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (81 bp):
TATATATATAAACAATATAAGTATAAACTATAGAAAATATATAGTTTATAAAATATAATTTATAT
TAATATAGTATATATA
Found at i:472609 original size:7 final size:7
Alignment explanation
Indices: 472599--472698 Score: 78
Period size: 7 Copynumber: 14.6 Consensus size: 7
472589 TAGTTTATAA
472599 AAACCCT
1 AAACCCT
**
472606 AAACTTT
1 AAACCCT
*
472613 AAATCCT
1 AAACCCT
*
472620 AAATCCT
1 AAACCCT
*
472627 AAATCCT
1 AAACCCT
**
472634 AAACTTT
1 AAACCCT
* *
472641 AAAACTT
1 AAACCCT
472648 AAACCCT
1 AAACCCT
472655 AAACCCT
1 AAACCCT
472662 AAA-CCT
1 AAACCCT
*
472668 AAAACCT
1 AAACCCT
472675 -AACCCT
1 AAACCCT
*
472681 AAACTCT
1 AAACCCT
*
472688 AAACACT
1 AAACCCT
472695 AAAC
1 AAAC
472699 ATACACAATA
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
6 11 0.14
7 65 0.86
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (7 bp):
AAACCCT
Found at i:472635 original size:28 final size:28
Alignment explanation
Indices: 472599--472691 Score: 118
Period size: 28 Copynumber: 3.4 Consensus size: 28
472589 TAGTTTATAA
* *
472599 AAACCCTAAACTTTAAATCCTAAATCCT
1 AAACCCTAAACTTTAAAACCTAAACCCT
* *
472627 AAATCCTAAACTTTAAAACTTAAACCCT
1 AAACCCTAAACTTTAAAACCTAAACCCT
*
472655 AAACCCTAAAC-CTAAAACCT-AACCCT
1 AAACCCTAAACTTTAAAACCTAAACCCT
*
472681 AAACTCTAAAC
1 AAACCCTAAAC
472692 ACTAAACATA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
26 16 0.28
27 7 0.12
28 34 0.60
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (28 bp):
AAACCCTAAACTTTAAAACCTAAACCCT
Found at i:472756 original size:24 final size:23
Alignment explanation
Indices: 472713--472757 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
472703 ACAATAGTTA
*
472713 ATATATATAATGTAACCTATAAT
1 ATATATATAATGTAAACTATAAT
*
472736 ATATGTATACATGTAAACTATA
1 ATATATATA-ATGTAAACTATA
472758 TATGTAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.38
Consensus pattern (23 bp):
ATATATATAATGTAAACTATAAT
Found at i:472779 original size:37 final size:37
Alignment explanation
Indices: 472716--472786 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
472706 ATAGTTAATA
*
472716 TATATAATGTAACCTATAATATATGTATACATGTAAAC
1 TATATAATGTAACCTATAATACATGTAT-CATGTAAAC
* *
472754 TATAT-ATGTAACTTATAGTACATGTATCATGTA
1 TATATAATGTAACCTATAATACATGTATCATGTA
472787 TGTATAAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 6 0.20
37 19 0.63
38 5 0.17
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (37 bp):
TATATAATGTAACCTATAATACATGTATCATGTAAAC
Found at i:472822 original size:24 final size:26
Alignment explanation
Indices: 472754--472838 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 26
472744 ACATGTAAAC
* *
472754 TATATATGT-AACTTATAGTACATGTA
1 TATATATATAAAC-TATAGTATATGTA
*
472780 TCATGTATGTATAAACTAT-GTATA-GTA
1 T-A--TATATATAAACTATAGTATATGTA
*
472807 TATATATATAACCTATAGTATATGTA
1 TATATATATAAACTATAGTATATGTA
472833 TATATA
1 TATATA
472839 CAATCTATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
24 12 0.25
25 5 0.10
26 11 0.23
27 5 0.10
28 4 0.08
29 8 0.17
30 3 0.06
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (26 bp):
TATATATATAAACTATAGTATATGTA
Found at i:472846 original size:24 final size:21
Alignment explanation
Indices: 472775--472873 Score: 87
Period size: 22 Copynumber: 4.5 Consensus size: 21
472765 CTTATAGTAC
*
472775 ATGTATCATGTATGTATAAACT
1 ATGTAT-ATGTATATATAAACT
*
472797 ATGTATAGTATATATATATAACCT
1 ATGTATA-TGTATATATA-AA-CT
472821 ATAGTATATGTATATATACAATCT
1 AT-GTATATGTATATATA-AA-CT
*
472845 ATTTATATGT-TATATAAACT
1 ATGTATATGTATATATAAACT
472865 A--TATATGTA
1 ATGTATATGTA
472874 ACCTATAGTT
Statistics
Matches: 66, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
18 7 0.11
20 3 0.05
21 3 0.05
22 20 0.30
23 9 0.14
24 19 0.29
25 5 0.08
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.43
Consensus pattern (21 bp):
ATGTATATGTATATATAAACT
Found at i:472866 original size:20 final size:22
Alignment explanation
Indices: 472777--472867 Score: 80
Period size: 24 Copynumber: 4.0 Consensus size: 22
472767 TATAGTACAT
*
472777 GTATCATGTATGTATAAACTAT-
1 GTAT-ATGTATATATAAACTATA
*
472799 GTATAGTATATATATATAACCTATA
1 GTATA-TGTATATATA-AA-CTATA
472824 GTATATGTATATATACAATCTAT-
1 GTATATGTATATATA-AA-CTATA
*
472847 TTATATGT-TATATAAACTATA
1 GTATATGTATATATAAACTATA
472868 TATGTAACCT
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
20 4 0.07
21 3 0.05
22 18 0.31
23 9 0.16
24 19 0.33
25 5 0.09
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.43
Consensus pattern (22 bp):
GTATATGTATATATAAACTATA
Found at i:472965 original size:21 final size:21
Alignment explanation
Indices: 472913--472965 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
472903 TTGTGTACTA
* *
472913 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAAAC
* *
472934 TATGGTATATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
472955 TATAGTTTATA
1 TATAGTTTATA
472966 TTAATGTACT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.47
Consensus pattern (21 bp):
TATAGTTTATAATTTATAAAC
Found at i:473018 original size:31 final size:31
Alignment explanation
Indices: 472977--473257 Score: 99
Period size: 31 Copynumber: 8.8 Consensus size: 31
472967 TAATGTACTA
* *
472977 TATAGTTTATATTAATGTTAATTATCTTAAC
1 TATAATTTATATTAATGTTAATTATATTAAC
*
473008 TATAATTTATATTAATATAGTATATAGTT-TATAAAC
1 TATAATTTATATT-A-AT-GT-TA-A-TTATATTAAC
*
473044 TAT-A-TTATATTAATATTAATTATATTAAC
1 TATAATTTATATTAATGTTAATTATATTAAC
* * *
473073 TATAGTTTATAAACTATACTATATAATT-TA-TAAC
1 TATAATTTAT--A-T-TAATGT-TAATTATATTAAC
* *
473107 ATATAGTTTATATTAATATTAATGT-TA-TATAC
1 -TATAATTTATATTAATGTTAAT-TATATTA-AC
* * *
473139 TACATTTTATATTAATATTAATTATAAATTATAAAC
1 TATAATTTATATTAATGTTAATTAT--A-T-T-AAC
*
473175 TAT-A-TTATATTAAT-ATAATTTAATATTAA-
1 TATAATTTATATTAATGTTAA-TT-ATATTAAC
* *
473204 TATTAA-TTATATTAATATTAATTATAAT-A-
1 TA-TAATTTATATTAATGTTAATTATATTAAC
*
473233 TATAA-TTAT-TATAATATTAATTATA
1 TATAATTTATAT-TAATGTTAATTATA
473258 AATAGTTAAT
Statistics
Matches: 205, Mismatches: 15, Indels: 63
0.72 0.05 0.22
Matches are distributed among these distances:
27 1 0.00
28 23 0.11
29 15 0.07
30 14 0.07
31 62 0.30
32 10 0.05
33 10 0.05
34 26 0.13
35 22 0.11
36 19 0.09
37 3 0.01
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (31 bp):
TATAATTTATATTAATGTTAATTATATTAAC
Found at i:473063 original size:65 final size:65
Alignment explanation
Indices: 472983--473237 Score: 251
Period size: 65 Copynumber: 3.9 Consensus size: 65
472973 ACTATATAGT
* * * *
472983 TTATATTAATGTTAATTATCTTAACTATAATTTATATTAATATAGTATATAGTTTATAAACTATA
1 TTATATTAATATTAATTATATTAACTATAATTTATATTAATATAATATATAATTTATAAACTATA
* *
473048 TTATATTAATATTAATTATATTAACTATAGTTTATA--AACTATACTATATAATTTAT-AACATA
1 TTATATTAATATTAATTATATTAACTATAATTTATATTAA-TATAATATATAATTTATAAAC-TA
473110 TA
64 TA
* * *
473112 GTTTATATTAATATTAATGT-TA-TATACTACATTTTATATTAATATTAAT-TATAAATTATAAA
1 --TTATATTAATATTAAT-TATATTA-ACTATAATTTATATTAATA-TAATATATAATTTATAAA
473174 CTATA
61 CTATA
*
473179 TTATATTAATA-TAATTTAATATTAA-TATTAA-TTATATTAATATTAAT-TATAATATATAA
1 TTATATTAATATTAA-TT-ATATTAACTA-TAATTTATATTAATA-TAATATATAATTTATAA
473238 TTATTATAAT
Statistics
Matches: 162, Mismatches: 13, Indels: 30
0.79 0.06 0.15
Matches are distributed among these distances:
63 5 0.03
64 23 0.14
65 75 0.46
66 33 0.20
67 18 0.11
68 8 0.05
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (65 bp):
TTATATTAATATTAATTATATTAACTATAATTTATATTAATATAATATATAATTTATAAACTATA
Found at i:473097 original size:14 final size:14
Alignment explanation
Indices: 473037--473098 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
473027 GTATATAGTT
473037 TATAAACTATATTA
1 TATAAACTATATTA
*
473051 TATTAA-TATTAATTA
1 TATAAACTA-T-ATTA
*
473066 TATTAACTATAGTT-
1 TATAAACTATA-TTA
*
473080 TATAAACTATACTA
1 TATAAACTATATTA
473094 TATAA
1 TATAA
473099 TTTATAACAT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 3 0.08
14 22 0.55
15 13 0.32
16 2 0.05
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (14 bp):
TATAAACTATATTA
Found at i:473114 original size:131 final size:133
Alignment explanation
Indices: 472941--473211 Score: 324
Period size: 131 Copynumber: 2.1 Consensus size: 133
472931 ACCTATGGTA
* * * * *
472941 TATAATTTATAAACTATAGTTTATATTAATGTACTATATAGTTTATATTAATGTTAA--TTATCT
1 TATAATTTATAAACTATACTATATATTAATGAACTATATAGTTTATATTAATATTAATGTTAT-A
* * **
473004 TAACTATAATTTATATTAATA-TAGTATATAGTTTATAAACTATATTATATTAATATTAA-TT-A
65 T-ACTACAATTTATATTAATATTAAT-TATAAATTATAAACTATATTATATTAATA-TAATTTAA
473066 TATTAAC
127 TATTAAC
* *
473073 TATAGTTTATAAACTATACTATATAATTTAT-AAC-ATATAGTTTATATTAATATTAATGTTATA
1 TATAATTTATAAACTATACTATAT-ATTAATGAACTATATAGTTTATATTAATATTAATGTTATA
*
473136 TACTACATTTTATATTAATATTAATTATAAATTATAAACTATATTATATTAATATAATTTAATAT
65 TACTACAATTTATATTAATATTAATTATAAATTATAAACTATATTATATTAATATAATTTAATAT
473201 TAA-
130 TAAC
473204 TATTAATT
1 TA-TAATT
473212 ATATTAATAT
Statistics
Matches: 119, Mismatches: 13, Indels: 14
0.82 0.09 0.10
Matches are distributed among these distances:
130 3 0.03
131 69 0.58
132 38 0.32
133 9 0.08
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.49
Consensus pattern (133 bp):
TATAATTTATAAACTATACTATATATTAATGAACTATATAGTTTATATTAATATTAATGTTATAT
ACTACAATTTATATTAATATTAATTATAAATTATAAACTATATTATATTAATATAATTTAATATT
AAC
Found at i:473127 original size:6 final size:6
Alignment explanation
Indices: 473116--473271 Score: 76
Period size: 6 Copynumber: 25.2 Consensus size: 6
473106 CATATAGTTT
* * * *
473116 ATATTA ATATTA ATGTTA TATACTA CAT-TTT ATATTA ATATTA ATTATAA
1 ATATTA ATATTA ATATTA -ATATTA -ATATTA ATATTA ATATTA A-TATTA
* *
473166 ATTATAA ACTATATT ATATTA ATA-TA AT-TTA ATATTA ATATT- A-ATT-
1 A-TATTA A-TAT-TA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
*
473212 ATATTA ATATTA AT-TATA ATATATA ATTATTATA ATATTA ATTATAA
1 ATATTA ATATTA ATAT-TA ATAT-TA A-TA-T-TA ATATTA A-TATTA
473259 ATAGTTA AT-TTA A
1 ATA-TTA ATATTA A
473272 AAAATTATAT
Statistics
Matches: 122, Mismatches: 14, Indels: 29
0.74 0.08 0.18
Matches are distributed among these distances:
4 4 0.03
5 19 0.16
6 50 0.41
7 39 0.32
8 5 0.04
9 5 0.04
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (6 bp):
ATATTA
Found at i:473165 original size:153 final size:146
Alignment explanation
Indices: 472920--473218 Score: 322
Period size: 153 Copynumber: 2.0 Consensus size: 146
472910 CTATATAGTT
* **
472920 TATACTTTATAACCTATGGTATATAATTTATAAACTATAGTTTATATTAATGTACTATATAGTTT
1 TATACTTTATAAACTATACTATATAATTTATAAACTATAGTTTATATTAA-GTACTATATAGTTT
* * * *
472985 ATATTAATGTTAATTATCTTAACTATAATTTATATTAA-TATAGTATATAGTTTATA-AACTATA
65 ATACTAATGTTAATTATATTAACTATAAATTATA--AACTATA-T-TATA-TTAATATAA-T-T-
*
473048 TTATATTAATATTAATTATATTAAC
122 TAATATTAATATTAATTATATTAAC
* *
473073 TATAGTTTATAAACTATACTATATAATTTAT-AACATATAGTTTATATTAA-TATTA-AT-GTTA
1 TATACTTTATAAACTATACTATATAATTTATAAAC-TATAGTTTATATTAAGTACTATATAGTT-
* *
473134 TATACTACATTTTATATTAATATTAATTATAAATTATAAACTATATTATATTAATATAATTTAAT
64 TATACTA-ATGTTA-ATT-ATATTAACTATAAATTATAAACTATATTATATTAATATAATTTAAT
473199 ATTAATATTAATTATATTAA
126 ATTAATATTAATTATATTAA
473219 TATTAATTAT
Statistics
Matches: 127, Mismatches: 12, Indels: 20
0.80 0.08 0.13
Matches are distributed among these distances:
147 23 0.18
148 1 0.01
149 9 0.07
150 14 0.11
151 12 0.09
152 10 0.08
153 58 0.46
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (146 bp):
TATACTTTATAAACTATACTATATAATTTATAAACTATAGTTTATATTAAGTACTATATAGTTTA
TACTAATGTTAATTATATTAACTATAAATTATAAACTATATTATATTAATATAATTTAATATTAA
TATTAATTATATTAAC
Found at i:473202 original size:21 final size:20
Alignment explanation
Indices: 473145--473257 Score: 70
Period size: 21 Copynumber: 5.2 Consensus size: 20
473135 ATACTACATT
*
473145 TTATATTAATATTAATTATAAA
1 TTATATTAATATT-A-TATTAA
*
473167 TTATA-AACTATATTATATTAA
1 TTATATTA--ATATTATATTAA
473188 -TATAATTTAATATTAATATTAA
1 TTAT-A-TTAATATT-ATATTAA
473210 TTATATTAATATTA-ATTATAA
1 TTATATTAATATTATA-T-TAA
* *
473231 TATATAATTATTATAATATTAA
1 T-TAT-ATTAATATTATATTAA
473253 TTATA
1 TTATA
473258 AATAGTTAAT
Statistics
Matches: 74, Mismatches: 5, Indels: 26
0.70 0.05 0.25
Matches are distributed among these distances:
19 1 0.01
20 6 0.08
21 27 0.36
22 21 0.28
23 18 0.24
24 1 0.01
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATATTAATATTATATTAA
Found at i:473213 original size:43 final size:42
Alignment explanation
Indices: 473149--473259 Score: 120
Period size: 43 Copynumber: 2.6 Consensus size: 42
473139 TACATTTTAT
*
473149 ATTAATATTAATTATAAATTATAAACTATATTATATTAATATA
1 ATTAATATTAA-TATTAATTATAAACTATATTATATTAATATA
*
473192 ATTTAATATTAATATTAATTATATTAA-TATTAATTATAAT-ATATA
1 A-TTAATATTAATATTAATTATA--AACTA-T-ATTATATTAATATA
*
473237 ATTATTA-TAATATTAATTATAAA
1 ATTAATATTAATATTAATTATAAA
473260 TAGTTAATTT
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
41 2 0.03
43 25 0.42
44 17 0.28
45 9 0.15
46 7 0.12
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (42 bp):
ATTAATATTAATATTAATTATAAACTATATTATATTAATATA
Found at i:473245 original size:16 final size:15
Alignment explanation
Indices: 473176--473268 Score: 78
Period size: 15 Copynumber: 6.6 Consensus size: 15
473166 ATTATAAACT
*
473176 ATATTATATTAATATA
1 ATATTA-ATTATTATA
473192 AT-TTAA-TA-T-TA
1 ATATTAATTATTATA
473203 ATATTAATTA-TATTA
1 ATATTAATTATTA-TA
*
473218 ATATTAATTATAAT-
1 ATATTAATTATTATA
473232 ATA-TAATTATTATA
1 ATATTAATTATTATA
473246 ATATTAATTA-TA-A
1 ATATTAATTATTATA
473259 ATAGTTAATT
1 ATA-TTAATT
473269 TAAAAAATTA
Statistics
Matches: 67, Mismatches: 2, Indels: 18
0.77 0.02 0.21
Matches are distributed among these distances:
11 4 0.06
12 5 0.07
13 18 0.27
14 15 0.22
15 22 0.33
16 3 0.04
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
ATATTAATTATTATA
Found at i:473272 original size:13 final size:13
Alignment explanation
Indices: 473152--473272 Score: 92
Period size: 14 Copynumber: 9.2 Consensus size: 13
473142 ATTTTATATT
473152 AATATTAATTATA
1 AATATTAATTATA
* *
473165 AATTATAAACTATA
1 AA-TATTAATTATA
*
473179 TTATATTAA-TAT-
1 -AATATTAATTATA
*
473191 AAT-TTAA-TATT
1 AATATTAATTATA
473202 AATATTAATTATA
1 AATATTAATTATA
473215 TTAATATTAATTAT-
1 --AATATTAATTATA
473229 AATATATAATTATTA
1 AATAT-TAATTA-TA
473244 TAATATTAATTATA
1 -AATATTAATTATA
473258 AATAGTTAATT-TA
1 AATA-TTAATTATA
473271 AA
1 AA
473273 AAATTATATA
Statistics
Matches: 90, Mismatches: 6, Indels: 24
0.75 0.05 0.20
Matches are distributed among these distances:
10 7 0.08
11 5 0.06
12 9 0.10
13 22 0.24
14 23 0.26
15 19 0.21
16 5 0.06
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (13 bp):
AATATTAATTATA
Found at i:473671 original size:10 final size:10
Alignment explanation
Indices: 473656--473682 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
473646 CACTCGAAAT
473656 TTCATCCTTG
1 TTCATCCTTG
473666 TTCATCCTTG
1 TTCATCCTTG
473676 TTCATCC
1 TTCATCC
473683 GAAAACCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.33, G:0.07, T:0.48
Consensus pattern (10 bp):
TTCATCCTTG
Found at i:473985 original size:7 final size:6
Alignment explanation
Indices: 473968--474050 Score: 57
Period size: 6 Copynumber: 14.0 Consensus size: 6
473958 AACCCTAACT
* * *
473968 TAAACC TAAACTC TAAACC T-AACC TGAACC TGAACC CAAACC TAAACC
1 TAAACC TAAAC-C TAAACC TAAACC TAAACC TAAACC TAAACC TAAACC
* * *
474016 CAACCCC T-AA-C TAAATCC T-AACC TTAACC TAAACC
1 TAA-ACC TAAACC TAAA-CC TAAACC TAAACC TAAACC
474051 CAAAACCCAA
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
4 2 0.03
5 10 0.16
6 40 0.65
7 10 0.16
ACGTcount: A:0.42, C:0.37, G:0.02, T:0.18
Consensus pattern (6 bp):
TAAACC
Found at i:474009 original size:12 final size:12
Alignment explanation
Indices: 473969--474131 Score: 56
Period size: 12 Copynumber: 13.8 Consensus size: 12
473959 ACCCTAACTT
*
473969 AAACCTAAACTCT
1 AAACCTAAAC-CC
*
473982 AAACCT-AACCT
1 AAACCTAAACCC
* *
473993 GAACCTGAACCC
1 AAACCTAAACCC
474005 AAACCTAAACCC
1 AAACCTAAACCC
* *
474017 AACCCCT-AA-CT
1 AA-ACCTAAACCC
*
474028 AAATCCT-AACCT
1 AAA-CCTAAACCC
*
474040 TAACCTAAACCC
1 AAACCTAAACCC
* *
474052 AAAACCCAAACTC
1 -AAACCTAAACCC
*
474065 AAA-CTCAACCCC
1 AAACCT-AAACCC
* *
474077 TAA-CTGAACCC
1 AAACCTAAACCC
474088 AAATCC-AAACCC
1 AAA-CCTAAACCC
* *
474100 TAACCCT-AACTC
1 -AAACCTAAACCC
*
474112 AAACCCAAACCC
1 AAACCTAAACCC
474124 -AACCTAAA
1 AAACCTAAA
474132 TTCAAACCTG
Statistics
Matches: 112, Mismatches: 26, Indels: 26
0.68 0.16 0.16
Matches are distributed among these distances:
11 36 0.32
12 55 0.49
13 21 0.19
ACGTcount: A:0.44, C:0.40, G:0.02, T:0.14
Consensus pattern (12 bp):
AAACCTAAACCC
Found at i:474062 original size:6 final size:6
Alignment explanation
Indices: 474041--474125 Score: 55
Period size: 6 Copynumber: 14.2 Consensus size: 6
474031 TCCTAACCTT
* * * * * **
474041 AACCTA AACCCAA AACCCA AACTCA AACTCA ACCCCT AA-CTG AACCCA
1 AACCCA AACCC-A AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* * * *
474089 AATCCA AACCCT AACCCT AACTCA AACCCA AACCCA A
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA A
474126 CCTAAATTCA
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
5 3 0.05
6 52 0.85
7 6 0.10
ACGTcount: A:0.46, C:0.42, G:0.01, T:0.11
Consensus pattern (6 bp):
AACCCA
Found at i:474088 original size:29 final size:31
Alignment explanation
Indices: 474053--474125 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 31
474043 CCTAAACCCA
*
474053 AAACCCAAACT-CAAACTC-AACCCCTAACT-
1 AAACCCAAACTCCAAACCCTAA-CCCTAACTC
*
474082 GAACCCAAA-TCCAAACCCTAACCCTAACTC
1 AAACCCAAACTCCAAACCCTAACCCTAACTC
474112 AAACCCAAAC-CCAA
1 AAACCCAAACTCCAA
474126 CCTAAATTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 1 0.03
29 22 0.59
30 14 0.38
ACGTcount: A:0.45, C:0.42, G:0.01, T:0.11
Consensus pattern (31 bp):
AAACCCAAACTCCAAACCCTAACCCTAACTC
Found at i:474139 original size:23 final size:24
Alignment explanation
Indices: 474054--474127 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 24
474044 CTAAACCCAA
* * *
474054 AACCCAAACTCAAACTCAACCCCT
1 AACCCTAACTCAAACCCAAACCCT
* *
474078 AA--CTGAACCCAAATCCAAACCCT
1 AACCCT-AACTCAAACCCAAACCCT
474101 AACCCTAACTCAAACCCAAACCC-
1 AACCCTAACTCAAACCCAAACCCT
474124 AACC
1 AACC
474128 TAAATTCAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
22 1 0.03
23 20 0.50
24 17 0.43
25 2 0.05
ACGTcount: A:0.43, C:0.45, G:0.01, T:0.11
Consensus pattern (24 bp):
AACCCTAACTCAAACCCAAACCCT
Found at i:474571 original size:102 final size:102
Alignment explanation
Indices: 474395--474630 Score: 400
Period size: 102 Copynumber: 2.3 Consensus size: 102
474385 CTGAAAGAGG
* * *
474395 TAAATAAATTGTTTGATTTGTAGTTACTATTGATTTGTTTGTGTTGTTGGTTGTTCATTCGGATT
1 TAAATAAATTGTTTAATTTGTAGCTACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTCGGATT
*
474460 GCTTTTATAAGGTTGTTAGCTACCTTTATTTACAGTT
66 GCTTTTATAAGGGTGTTAGCTACCTTTATTTACAGTT
474497 TAAATAAATTGTTTAATTTGTAGCTACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTCGGATT
1 TAAATAAATTGTTTAATTTGTAGCTACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTCGGATT
*
474562 GCTTTTATAAGGGTGTTAGCTGCCTTTATTTACAGTT
66 GCTTTTATAAGGGTGTTAGCTACCTTTATTTACAGTT
* * *
474599 TAAATAAACTGTTTAATTTTTTGCTACTGTTG
1 TAAATAAATTGTTTAATTTGTAGCTACTGTTG
474631 GTTGTTCATT
Statistics
Matches: 126, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 126 1.00
ACGTcount: A:0.21, C:0.08, G:0.19, T:0.51
Consensus pattern (102 bp):
TAAATAAATTGTTTAATTTGTAGCTACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTCGGATT
GCTTTTATAAGGGTGTTAGCTACCTTTATTTACAGTT
Found at i:477494 original size:12 final size:12
Alignment explanation
Indices: 477472--477504 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
477462 ACTCAAATGT
477472 TATTCAAATTTTA
1 TATT-AAATTTTA
477485 TATTAAATTTTA
1 TATTAAATTTTA
477497 T-TTAAATT
1 TATTAAATT
477505 ATCATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 7 0.35
12 9 0.45
13 4 0.20
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTAAATTTTA
Found at i:477501 original size:11 final size:11
Alignment explanation
Indices: 477466--477504 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
477456 GAATTGACTC
* *
477466 AAATGTTATTC
1 AAATTTTATTT
477477 AAATTTTATATT
1 AAATTTTAT-TT
477489 AAATTTTATTT
1 AAATTTTATTT
477500 AAATT
1 AAATT
477505 ATCATTATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (11 bp):
AAATTTTATTT
Found at i:477770 original size:17 final size:18
Alignment explanation
Indices: 477729--477770 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
477719 ATATTACATA
477729 ATAAA-TATTTTTATTAT
1 ATAAATTATTTTTATTAT
477746 -TAATATTATTTTT-TTAT
1 ATAA-ATTATTTTTATTAT
477763 ATAAATTA
1 ATAAATTA
477771 AACTATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 3 0.14
17 9 0.41
18 10 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATAAATTATTTTTATTAT
Found at i:477779 original size:14 final size:14
Alignment explanation
Indices: 477760--477806 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
477750 ATTATTTTTT
477760 TATATAAATTAAAC
1 TATATAAATTAAAC
477774 TATAT-AATT----
1 TATATAAATTAAAC
477783 TATATAAATTAAAC
1 TATATAAATTAAAC
*
477797 TATATTAATT
1 TATATAAATT
477807 TTCCTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:477784 original size:23 final size:24
Alignment explanation
Indices: 477758--477807 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
477748 ATATTATTTT
477758 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
477781 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
477805 TTT
1 TTT
477808 TCCTTTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:477873 original size:22 final size:23
Alignment explanation
Indices: 477817--477885 Score: 79
Period size: 22 Copynumber: 3.0 Consensus size: 23
477807 TTCCTTTTCA
*
477817 TTATT-AATAATGTTTATCTAATT
1 TTATTAAATAAT-TTTATATAATT
*
477840 TACATTTAAATAATTTTAT-TAATT
1 T-TA-TTAAATAATTTTATATAATT
477864 TTATTAAATAATTTTATATAAT
1 TTATTAAATAATTTTATATAAT
477886 AGGTTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 14 0.35
23 6 0.15
24 7 0.17
25 7 0.17
26 6 0.15
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (23 bp):
TTATTAAATAATTTTATATAATT
Found at i:478081 original size:16 final size:16
Alignment explanation
Indices: 478060--478098 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
478050 TGGATCATTT
478060 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
*
478076 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
478092 ACAGGTC
1 ACAGGTC
478099 GGGTAATACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.18
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:478198 original size:31 final size:32
Alignment explanation
Indices: 478123--478198 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
478113 ATTTACCAGG
*
478123 TCAATCTCGGGTTCTGGTTCATATTAGTCGGAT
1 TCAAT-TCGGGTTCGGGTTCATATTAGTCGGAT
* * *
478156 GCAGTTCGGGTTCGGGTATCATATT-TTCGG-T
1 TCAATTCGGGTTCGGGT-TCATATTAGTCGGAT
478187 TCAATTCGGGTT
1 TCAATTCGGGTT
478199 TAGGTCGTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
31 11 0.31
32 15 0.42
33 10 0.28
ACGTcount: A:0.16, C:0.17, G:0.28, T:0.39
Consensus pattern (32 bp):
TCAATTCGGGTTCGGGTTCATATTAGTCGGAT
Found at i:487292 original size:21 final size:22
Alignment explanation
Indices: 487245--487303 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 22
487235 TTCCCGTGGA
487245 GGGGAATCGGTTCCCCTTCAAAG
1 GGGGAATCGGTTCCCCTTC-AAG
487268 GGGGAATCGGTTCCCCTTC-AG
1 GGGGAATCGGTTCCCCTTCAAG
* *
487289 GGGGTATCGATTCCC
1 GGGGAATCGGTTCCC
487304 TCTGTCCTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 15 0.44
23 19 0.56
ACGTcount: A:0.17, C:0.27, G:0.32, T:0.24
Consensus pattern (22 bp):
GGGGAATCGGTTCCCCTTCAAG
Found at i:496795 original size:15 final size:15
Alignment explanation
Indices: 496775--496809 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
496765 CTTTTAATAG
496775 TTGATATATGATTTA
1 TTGATATATGATTTA
496790 TTGATATATGATTTA
1 TTGATATATGATTTA
496805 TTGAT
1 TTGAT
496810 CGGTTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.54
Consensus pattern (15 bp):
TTGATATATGATTTA
Found at i:503893 original size:2 final size:2
Alignment explanation
Indices: 503886--503915 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
503876 ATAATTGACG
503886 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
503916 GAGATGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:507359 original size:15 final size:15
Alignment explanation
Indices: 507336--507384 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
507326 CTCGGTAAGC
*
507336 TTCTCTTCTTTCTTT
1 TTCTTTTCTTTCTTT
507351 TTCTTTTCTTTCTTT
1 TTCTTTTCTTTCTTT
* *
507366 TT-TTCT-TTTCTGT
1 TTCTTTTCTTTCTTT
507379 TTCTTT
1 TTCTTT
507385 GCTGCGTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 8 0.28
14 5 0.17
15 16 0.55
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (15 bp):
TTCTTTTCTTTCTTT
Found at i:507868 original size:3 final size:3
Alignment explanation
Indices: 507852--507930 Score: 106
Period size: 3 Copynumber: 26.3 Consensus size: 3
507842 TGTAATATTA
* * *
507852 AAT AAT -AT ATAT AAT AAT AAT AAT AAT AAT AAT TAT TAT TAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
507897 TAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
507931 TAAATAACAT
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.03
3 65 0.93
4 3 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:508199 original size:17 final size:17
Alignment explanation
Indices: 508177--508232 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
508167 TTGAATAAGC
508177 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
*
508194 TCTTCTTC-TCCTGATG-AGT
1 TCTTC-TCAT--T-ATGAACT
508213 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
508230 TCT
1 TCT
508233 CTGGAAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
16 3 0.10
17 12 0.39
18 4 0.13
19 9 0.29
20 3 0.10
ACGTcount: A:0.18, C:0.25, G:0.09, T:0.48
Consensus pattern (17 bp):
TCTTCTCATTATGAACT
Found at i:508378 original size:113 final size:113
Alignment explanation
Indices: 508160--509168 Score: 1586
Period size: 113 Copynumber: 9.0 Consensus size: 113
508150 TAGAGTCATT
* ** *
508160 CAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTT-C-TC--CTGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
508221 TTATGAACTTC--TCTGGAAAA-ACTGACCCATCAAGTGATGGATTTGAG
66 TTATGAAC-TCGAACTGGAAAAGA-TAATCCATCAAGTGATGGATTTGAG
* *
508268 CAAAAAGCTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* **** * * *
508333 TTATGAAATTTCTCTAGAAAAGTTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
* * * * *
508381 CAAAAAGCTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTTAAATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** *
508446 TTATGAACTTC-TTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGAG
66 TTATGAAC-TCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
508494 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
508559 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
508607 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
508672 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
66 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
508720 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
508785 TTATGAACTCGAAATGGAAAAGATAATCCATCAAGTGATAGATTTGAG
66 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
*
508833 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
508898 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
66 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
* *
508946 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAAATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
509011 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAG
66 TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
*
509059 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
** * *
509124 TTATGAACTTC-CTCTGGAAAAGCTGATCCATCAAGTGATGGATTT
66 TTATGAAC-TCGAACTGGAAAAGATAATCCATCAAGTGATGGATTT
509169 AAATCTTTGC
Statistics
Matches: 848, Mismatches: 43, Indels: 15
0.94 0.05 0.02
Matches are distributed among these distances:
108 36 0.04
109 1 0.00
110 2 0.00
111 1 0.00
112 25 0.03
113 780 0.92
114 3 0.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAG
Found at i:508420 original size:20 final size:20
Alignment explanation
Indices: 508397--508460 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
508387 GCTGAACAAA
508397 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAACTTC
* **
508417 TTCTTCATTC-TT-T-AAATGAG
1 TTCTTC--TCATTATGAACT-TC
508437 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAACTTC
508457 TTCT
1 TTCT
508461 GGAAAAGCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
18 2 0.06
19 5 0.16
20 18 0.56
21 5 0.16
22 2 0.06
ACGTcount: A:0.20, C:0.22, G:0.06, T:0.52
Consensus pattern (20 bp):
TTCTTCTCATTATGAACTTC
Found at i:510072 original size:83 final size:83
Alignment explanation
Indices: 509898--510371 Score: 779
Period size: 83 Copynumber: 5.7 Consensus size: 83
509888 AAACCAAATT
* * * * *
509898 AGATTAGATAATTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTT-ATTTCTTTCAAATT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-CACATTCA--TCTTTCAAATT
*
509962 CAATGATTGGTTTTACCAAACC
62 CAATGATTAGTTTTACCAAACC
* *
509984 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAATTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAAT
510049 GATTAGTTTTACCAAACC
66 GATTAGTTTTACCAAACC
* * *
510067 AGATCAGATAACTCAAAGGACACTTCCAGAAGATGCTATGAGCACATTCCTCTTCCAAATTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAAT
510132 GATTAGTTTTACCAAACC
66 GATTAGTTTTACCAAACC
*
510150 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCATT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAAT
510215 GATTAGTTTTACCAAACC
66 GATTAGTTTTACCAAACC
*
510233 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCATT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAAT
510298 GATTAGTTTTACCAAACC
66 GATTAGTTTTACCAAACC
*
510316 AGATCAGATAACTCAAAGGACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
510372 CAGCTAATGT
Statistics
Matches: 373, Mismatches: 14, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
83 330 0.88
84 4 0.01
85 3 0.01
86 36 0.10
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (83 bp):
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAAT
GATTAGTTTTACCAAACC
Found at i:511520 original size:5 final size:5
Alignment explanation
Indices: 511510--511564 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
511500 TGACCCCTCT
* *
511510 TTTTC TTTTC TTTTT TCTTTC TTTT- TTTTT TCTTTC TTTTC -TTT- TTTTC
1 TTTTC TTTTC TTTTC T-TTTC TTTTC TTTTC T-TTTC TTTTC TTTTC TTTTC
511559 TTTTC T
1 TTTTC T
511565 CTTTTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
4 10 0.24
5 24 0.57
6 8 0.19
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTC
Found at i:511523 original size:11 final size:10
Alignment explanation
Indices: 511507--511585 Score: 68
Period size: 11 Copynumber: 7.1 Consensus size: 10
511497 CCTTGACCCC
511507 TCTTTTTCTTT
1 TCTTTTT-TTT
511518 TCTTTTTTCTT
1 TCTTTTTT-TT
511529 TCTTTTTTTTT
1 TC-TTTTTTTT
511540 TCTTTCTTTTCT
1 TCTTT-TTTT-T
*
511552 TTTTTTCTTTT
1 TCTTTT-TTTT
511563 CTCTTTTTTTT
1 -TCTTTTTTTT
*
511574 TATTATTTTTT
1 TCTT-TTTTTT
511585 T
1 T
511586 TCATTAAGCA
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
10 7 0.12
11 32 0.55
12 19 0.33
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.84
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:511532 original size:4 final size:4
Alignment explanation
Indices: 511511--511561 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
511501 GACCCCTCTT
* *
511511 TTTC TTTTC TTT- TTTC TTTC TTT- TTTT TTTC TTTC TTTTC TTTT TTTC
1 TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC
511559 TTT
1 TTT
511562 TCTCTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
3 6 0.15
4 26 0.65
5 8 0.20
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (4 bp):
TTTC
Found at i:511533 original size:22 final size:22
Alignment explanation
Indices: 511507--511571 Score: 80
Period size: 22 Copynumber: 2.9 Consensus size: 22
511497 CCTTGACCCC
511507 TCTTTTTCTTTTC-TTTTTTCTT
1 TCTTTTTCTTTTCTTTTTTTC-T
*
511529 TCTTTTTTTTTTCTTTCTTTTCT
1 TCTTTTTCTTTTCTTT-TTTTCT
511552 T-TTTTTCTTTTCTCTTTTTT
1 TCTTTTTCTTTTCT-TTTTTT
511572 TTTATTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 27 0.71
23 6 0.16
24 5 0.13
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (22 bp):
TCTTTTTCTTTTCTTTTTTTCT
Found at i:511540 original size:15 final size:15
Alignment explanation
Indices: 511511--511574 Score: 83
Period size: 17 Copynumber: 3.9 Consensus size: 15
511501 GACCCCTCTT
511511 TTTCTTTTCTTTTTTC
1 TTTCTTTT-TTTTTTC
511527 TTTCTTTTTTTTTTC
1 TTTCTTTTTTTTTTC
511542 TTTCTTTTCTTTTTTTC
1 TTTC-TTT-TTTTTTTC
511559 TTTTCTCTTTTTTTTT
1 -TTTCT-TTTTTTTTT
511575 ATTATTTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
15 11 0.25
16 11 0.25
17 16 0.36
18 6 0.14
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTCTTTTTTTTTTC
Found at i:511546 original size:31 final size:34
Alignment explanation
Indices: 511511--511574 Score: 107
Period size: 31 Copynumber: 2.0 Consensus size: 34
511501 GACCCCTCTT
511511 TTTCTTTTC-TTTTTTC-TTTCT-TTTTTTTTTC
1 TTTCTTTTCTTTTTTTCTTTTCTCTTTTTTTTTC
511542 TTTCTTTTCTTTTTTTCTTTTCTCTTTTTTTTT
1 TTTCTTTTCTTTTTTTCTTTTCTCTTTTTTTTT
511575 ATTATTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 9 0.30
32 7 0.23
33 5 0.17
34 9 0.30
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (34 bp):
TTTCTTTTCTTTTTTTCTTTTCTCTTTTTTTTTC
Found at i:511582 original size:20 final size:17
Alignment explanation
Indices: 511507--511574 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 17
511497 CCTTGACCCC
*
511507 TCTTTTTCTTTTCTTTTT
1 TCTTTTT-TTTTTTTTTT
511525 TCTTTCTTTTTTTTTTCTT
1 TCTTT-TTTTTTTTTT-TT
511544 TCTTTTCTTTTTTTCTTTT
1 TCTTTT-TTTTTTT-TTTT
511563 CTCTTTTTTTTT
1 -TCTTTTTTTTT
511575 ATTATTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
18 13 0.30
19 23 0.52
20 8 0.18
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TCTTTTTTTTTTTTTTT
Found at i:528997 original size:15 final size:15
Alignment explanation
Indices: 528974--529005 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
528964 TGAAATGAAT
528974 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
528989 AATGTATGTATGCAA
1 AATGAATGTATGCAA
529004 AA
1 AA
529006 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:534378 original size:3 final size:3
Alignment explanation
Indices: 534358--534420 Score: 108
Period size: 3 Copynumber: 21.0 Consensus size: 3
534348 AATTATTTTT
* *
534358 TAA TTA TAA TAA TTA 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
534406 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
534421 AATGAGAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:546233 original size:18 final size:18
Alignment explanation
Indices: 546210--546255 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
546200 AGTTGGAGGA
546210 TGAAGATGAAAGGAAACT
1 TGAAGATGAAAGGAAACT
546228 TGAAGATGAAAGGAAACT
1 TGAAGATGAAAGGAAACT
*
546246 TGTAGATGAA
1 TGAAGATGAA
546256 GATGGTAGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.48, C:0.04, G:0.28, T:0.20
Consensus pattern (18 bp):
TGAAGATGAAAGGAAACT
Found at i:553955 original size:39 final size:38
Alignment explanation
Indices: 553904--553985 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 38
553894 CTCGTGATTT
* * * *
553904 TATCAAACCATGACAAACAATGTTATACATAATAGTCA
1 TATCAAACCATGACAAACAATATCATAAATAACAGTCA
* *
553942 TATCAAAGTCATGATAAACAATATCATAAATAACAGTCA
1 TATCAAA-CCATGACAAACAATATCATAAATAACAGTCA
553981 TATCA
1 TATCA
553986 TATTCTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
38 7 0.19
39 30 0.81
ACGTcount: A:0.49, C:0.17, G:0.07, T:0.27
Consensus pattern (38 bp):
TATCAAACCATGACAAACAATATCATAAATAACAGTCA
Found at i:555856 original size:20 final size:20
Alignment explanation
Indices: 555831--555869 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
555821 CTAAAATAGT
*
555831 CAAATTTCACATTCTAACAC
1 CAAATTTCACACTCTAACAC
*
555851 CAAATTTCTCACTCTAACA
1 CAAATTTCACACTCTAACA
555870 TTAATTTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (20 bp):
CAAATTTCACACTCTAACAC
Found at i:558021 original size:3 final size:3
Alignment explanation
Indices: 558013--558043 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
558003 ACCTTTAAGC
558013 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
558044 ATCAGATTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:559074 original size:60 final size:59
Alignment explanation
Indices: 558952--559079 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 59
558942 AACATAATGA
* * ** *
558952 ATAGTCGGGTGATCATTTTGTAACTTTTGATAGTCGAGGGATTAAAAAAGGCAACACTCT
1 ATAGTCGGATGATCATTTTGTAACTTTTAATAGTCGAAAGATTAAAAAA-GCAACACCCT
* * *
559012 ATAGTCGGATGATCCTTTTGTGACTTTTAATAGTCGAAAGACTTAATAAAA-CAATACCCT
1 ATAGTCGGATGATCATTTTGTAACTTTTAATAGTCGAAAGA-TTAA-AAAAGCAACACCCT
559072 ATAGTCGG
1 ATAGTCGG
559080 GAGACCATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
60 50 0.86
61 4 0.07
62 4 0.07
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (59 bp):
ATAGTCGGATGATCATTTTGTAACTTTTAATAGTCGAAAGATTAAAAAAGCAACACCCT
Found at i:559098 original size:60 final size:59
Alignment explanation
Indices: 558952--559098 Score: 140
Period size: 60 Copynumber: 2.5 Consensus size: 59
558942 AACATAATGA
* * * ** *
558952 ATAGTCGGGTGATCATTT-TGTAACTTTTGATAGTCGAGGGATTAAAAAAGGCAACACTCT
1 ATAGTCGGGAGACCATTTGTGT-ACTTTTAATAGTCGAAAGATTAAAAAA-GCAACACCCT
* *
559012 ATAGTC-GGATGATCCTTTTGTG-ACTTTTAATAGTCGAAAGACTTAATAAAA-CAATACCCT
1 ATAGTCGGGA-GA-CCATTTGTGTACTTTTAATAGTCGAAAGA-TTAA-AAAAGCAACACCCT
559072 ATAGTCGGGAGACCATTTGTGTACTTT
1 ATAGTCGGGAGACCATTTGTGTACTTT
559099 ACCCTTTTCT
Statistics
Matches: 71, Mismatches: 9, Indels: 14
0.76 0.10 0.15
Matches are distributed among these distances:
59 10 0.14
60 44 0.62
61 11 0.15
62 6 0.08
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (59 bp):
ATAGTCGGGAGACCATTTGTGTACTTTTAATAGTCGAAAGATTAAAAAAGCAACACCCT
Found at i:559547 original size:36 final size:36
Alignment explanation
Indices: 559506--559584 Score: 133
Period size: 36 Copynumber: 2.2 Consensus size: 36
559496 ACTAAATTAA
559506 ACGGGGAC-GGAGAAAAACCGTTTATGCTAAACGGAG
1 ACGGGGACGGGA-AAAAACCGTTTATGCTAAACGGAG
*
559542 ACGGGGACGGGAAAAAACCGTTTATGCTAAACGGGG
1 ACGGGGACGGGAAAAAACCGTTTATGCTAAACGGAG
559578 ACGGGGA
1 ACGGGGA
559585 TGAGTTTGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
36 38 0.93
37 3 0.07
ACGTcount: A:0.34, C:0.16, G:0.37, T:0.13
Consensus pattern (36 bp):
ACGGGGACGGGAAAAAACCGTTTATGCTAAACGGAG
Found at i:559705 original size:15 final size:15
Alignment explanation
Indices: 559644--559724 Score: 52
Period size: 13 Copynumber: 5.9 Consensus size: 15
559634 ATAATTATTA
559644 TTATATATATATAAT
1 TTATATATATATAAT
* *
559659 ATTA-ATAAATTTAAT
1 -TTATATATATATAAT
*
559674 TTA-A-AT-TAAAAT
1 TTATATATATATAAT
*
559686 ATATATATA-AT-AT
1 TTATATATATATAAT
559699 TTATATAT-T-TAAT
1 TTATATATATATAAT
*
559712 TTAAATATATATA
1 TTATATATATATA
559725 TATCCGGCCC
Statistics
Matches: 49, Mismatches: 9, Indels: 15
0.67 0.12 0.21
Matches are distributed among these distances:
12 7 0.14
13 20 0.41
14 8 0.16
15 11 0.22
16 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TTATATATATATAAT
Found at i:559726 original size:38 final size:38
Alignment explanation
Indices: 559640--559727 Score: 126
Period size: 38 Copynumber: 2.4 Consensus size: 38
559630 AAAAATAATT
*
559640 ATTATTATATATATATAATATTAATAAATTTAATTTAA
1 ATTAATATATATATATAATATTAATAAATTTAATTTAA
* * *
559678 ATTAAAATATATATATAATATTTATATATTTAATTTAA
1 ATTAATATATATATATAATATTAATAAATTTAATTTAA
559716 A-T-ATATATATAT
1 ATTAATATATATAT
559728 CCGGCCCGAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
36 9 0.20
37 1 0.02
38 35 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (38 bp):
ATTAATATATATATATAATATTAATAAATTTAATTTAA
Found at i:559745 original size:12 final size:12
Alignment explanation
Indices: 559728--559753 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
559718 ATATATATAT
559728 CCGGCCCGATAC
1 CCGGCCCGATAC
559740 CCGGCCCGATAC
1 CCGGCCCGATAC
559752 CC
1 CC
559754 ATTTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.54, G:0.23, T:0.08
Consensus pattern (12 bp):
CCGGCCCGATAC
Found at i:563116 original size:11 final size:12
Alignment explanation
Indices: 563090--563115 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
563080 AATTTAAATT
563090 AAATATTATAAA
1 AAATATTATAAA
563102 AAATATTATAAA
1 AAATATTATAAA
563114 AA
1 AA
563116 TTCTCCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATATTATAAA
Found at i:567152 original size:17 final size:17
Alignment explanation
Indices: 567130--567213 Score: 102
Period size: 17 Copynumber: 5.0 Consensus size: 17
567120 TATTGCTCGG
567130 ATGGTATCTATACCCCC
1 ATGGTATCTATACCCCC
567147 ATGGTATCTATACCCCC
1 ATGGTATCTATACCCCC
*
567164 ATGGTATCGATA---CC
1 ATGGTATCTATACCCCC
*
567178 ATGGTATCGATACCCCCC
1 ATGGTATCTATA-CCCCC
*
567196 AGGGGTATCTATACCCCC
1 A-TGGTATCTATACCCCC
567214 TGGCTGCAAC
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
14 14 0.24
17 28 0.47
18 8 0.14
19 9 0.15
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (17 bp):
ATGGTATCTATACCCCC
Found at i:567181 original size:14 final size:14
Alignment explanation
Indices: 567162--567191 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
567152 ATCTATACCC
567162 CCATGGTATCGATA
1 CCATGGTATCGATA
567176 CCATGGTATCGATA
1 CCATGGTATCGATA
567190 CC
1 CC
567192 CCCCAGGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (14 bp):
CCATGGTATCGATA
Found at i:567270 original size:21 final size:21
Alignment explanation
Indices: 567244--567285 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
567234 ATTTGAATTT
* *
567244 TATGAATGAGTACCGATACCC
1 TATGAAGGAGTACCGAAACCC
*
567265 TATGAAGGGGTACCGAAACCC
1 TATGAAGGAGTACCGAAACCC
567286 CCTATCGTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (21 bp):
TATGAAGGAGTACCGAAACCC
Found at i:567607 original size:34 final size:32
Alignment explanation
Indices: 567568--567637 Score: 77
Period size: 34 Copynumber: 2.1 Consensus size: 32
567558 TTTTGTAAAG
* * *
567568 GGGAAATGATCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAAGATCTAGCTTAGCCCG-G-AAAAACTA
* *
567602 GGGAAAAGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAAGATCTAGCTTAGCCCGGAAAAACTA
567634 GGGA
1 GGGA
567638 GTTGTAAGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 11 0.35
33 1 0.03
34 19 0.61
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (32 bp):
GGGAAAAGATCTAGCTTAGCCCGGAAAAACTA
Found at i:569688 original size:30 final size:29
Alignment explanation
Indices: 569654--569710 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
569644 ATGGAGAGCT
*
569654 TAACATTTTCATATATTTTTCAACAATTGG
1 TAACAATTTCATATATTTTT-AACAATTGG
** *
569684 TAACAATTTGTTATCTTTTTAACAATT
1 TAACAATTTCATATATTTTTAACAATT
569711 AGTATCCTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 7 0.30
30 16 0.70
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.49
Consensus pattern (29 bp):
TAACAATTTCATATATTTTTAACAATTGG
Found at i:569728 original size:20 final size:20
Alignment explanation
Indices: 569683--569740 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
569673 TCAACAATTG
*
569683 GTAACAATTTGTTATCTTTT
1 GTAACAATTAGTTATCTTTT
569703 -TAACAATTAG-TATCCTTTT
1 GTAACAATTAGTTAT-CTTTT
*
569722 GTAACAATT-GATATCTTTT
1 GTAACAATTAGTTATCTTTT
569741 TCATTAAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 3 0.09
19 20 0.59
20 11 0.32
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.50
Consensus pattern (20 bp):
GTAACAATTAGTTATCTTTT
Found at i:569922 original size:29 final size:30
Alignment explanation
Indices: 569852--569911 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
569842 CAATTTAAGG
569852 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
569883 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
569912 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:570097 original size:17 final size:17
Alignment explanation
Indices: 570049--570098 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
570039 TTGATCAGAT
*
570049 GGTATCTATACCCCCAT
1 GGTATCTATACCCCCAG
* *
570066 TGTATCGATACCCCCAGG
1 GGTATCTATACCCCCA-G
570084 GGTATCTATACCCCC
1 GGTATCTATACCCCC
570099 TAGCTGCAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.22, C:0.36, G:0.16, T:0.26
Consensus pattern (17 bp):
GGTATCTATACCCCCAG
Found at i:571073 original size:25 final size:25
Alignment explanation
Indices: 571044--571093 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
571034 GATTAGGGGT
571044 ACTGAAGCATAAACATGTAGGGATA
1 ACTGAAGCATAAACATGTAGGGATA
*
571069 ACTGAAGCATAAACATGTAGTGATA
1 ACTGAAGCATAAACATGTAGGGATA
571094 TGGTGCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (25 bp):
ACTGAAGCATAAACATGTAGGGATA
Found at i:573329 original size:24 final size:24
Alignment explanation
Indices: 573297--573384 Score: 115
Period size: 24 Copynumber: 3.7 Consensus size: 24
573287 TAGTAAGGTA
*
573297 TCGATGCATATTCTACGTGGCACT
1 TCGATGCATATTCTACGTGACACT
*
573321 TCGATGCATATTCAACGTGACACT
1 TCGATGCATATTCTACGTGACACT
*
573345 TC-AGTACATATTCTACGTGACACT
1 TCGA-TGCATATTCTACGTGACACT
* *
573369 TCGGTGCAAATTCTAC
1 TCGATGCATATTCTAC
573385 ACGGTAGTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 1 0.02
24 54 0.98
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (24 bp):
TCGATGCATATTCTACGTGACACT
Found at i:576675 original size:39 final size:39
Alignment explanation
Indices: 576621--576699 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
576611 TTTGATAAAA
*
576621 AAAAAAATATAATACATATATATTTCTTTCATATGGGAT
1 AAAAAAATACAATACATATATATTTCTTTCATATGGGAT
* *
576660 AAAAAAATACAATACATTTATATTTCTTTCATATGTGAT
1 AAAAAAATACAATACATATATATTTCTTTCATATGGGAT
576699 A
1 A
576700 TACATATATC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (39 bp):
AAAAAAATACAATACATATATATTTCTTTCATATGGGAT
Found at i:582016 original size:25 final size:24
Alignment explanation
Indices: 581971--582020 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 24
581961 TTTTTGTCTC
581971 CCTAAAATTTTATAATATTGTTCAT
1 CCTAAAATTTTATAATATTG-TCAT
581996 CCTAAAATTTTATAAGT-TTGTCAT
1 CCTAAAATTTTATAA-TATTGTCAT
582020 C
1 C
582021 TAACATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 5 0.21
25 18 0.75
26 1 0.04
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (24 bp):
CCTAAAATTTTATAATATTGTCAT
Found at i:582284 original size:41 final size:41
Alignment explanation
Indices: 582239--582370 Score: 119
Period size: 41 Copynumber: 3.2 Consensus size: 41
582229 CTGGTTCTCC
582239 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
1 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
* * *** **
582280 CCATGCAGT--G-G-AATAGAGAGGTCGTTCTCCCCATGCGAGGTCC
1 CCATGCA-TACGAGCCATA-CGA-GT-G--CGAGCCATGCGAGGTGG
582323 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
1 CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
582364 CCATGCA
1 CCATGCA
582371 GAGGAATAGA
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.04
39 3 0.04
40 3 0.04
41 27 0.40
42 2 0.03
43 20 0.30
44 3 0.04
45 3 0.04
46 3 0.04
ACGTcount: A:0.23, C:0.28, G:0.32, T:0.17
Consensus pattern (41 bp):
CCATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGG
Found at i:582385 original size:55 final size:55
Alignment explanation
Indices: 582325--582490 Score: 323
Period size: 55 Copynumber: 3.0 Consensus size: 55
582315 CGAGGTCCCC
582325 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
582380 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
*
582435 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGTGGAATAG
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
582490 A
1 A
582491 GAGGTCGTTC
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 110 1.00
ACGTcount: A:0.29, C:0.22, G:0.34, T:0.15
Consensus pattern (55 bp):
ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCCATGCAGAGGAATAG
Found at i:582562 original size:41 final size:41
Alignment explanation
Indices: 582435--582564 Score: 115
Period size: 41 Copynumber: 3.1 Consensus size: 41
582425 AGAGGAATAG
582435 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
* * *** **
582476 ATGCAGT--G-G-AATAGAGAGGTCGTTCTCCCCATGCGAGGTCCCC
1 ATGCA-TACGAGCCATA-CGA-GT-G--CGAGCCATGCGAGGTGGCC
582519 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
1 ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
582560 ATGCA
1 ATGCA
582565 GAGGAATAGG
Statistics
Matches: 65, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.05
39 3 0.05
40 3 0.05
41 25 0.38
42 2 0.03
43 20 0.31
44 3 0.05
45 3 0.05
46 3 0.05
ACGTcount: A:0.24, C:0.27, G:0.32, T:0.17
Consensus pattern (41 bp):
ATGCATACGAGCCATACGAGTGCGAGCCATGCGAGGTGGCC
Found at i:582612 original size:29 final size:29
Alignment explanation
Indices: 582578--582687 Score: 220
Period size: 29 Copynumber: 3.8 Consensus size: 29
582568 GAATAGGGTG
582578 TAGGTCGCCATGTAGTCCCGGCGACCTTA
1 TAGGTCGCCATGTAGTCCCGGCGACCTTA
582607 TAGGTCGCCATGTAGTCCCGGCGACCTTA
1 TAGGTCGCCATGTAGTCCCGGCGACCTTA
582636 TAGGTCGCCATGTAGTCCCGGCGACCTTA
1 TAGGTCGCCATGTAGTCCCGGCGACCTTA
582665 TAGGTCGCCATGTAGTCCCGGCG
1 TAGGTCGCCATGTAGTCCCGGCG
582688 CCATTCCATC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.16, C:0.31, G:0.29, T:0.24
Consensus pattern (29 bp):
TAGGTCGCCATGTAGTCCCGGCGACCTTA
Found at i:582730 original size:23 final size:23
Alignment explanation
Indices: 582703--582754 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
582693 CCATCCATTC
582703 CCATTCACATGCAGCCCCATCAT
1 CCATTCACATGCAGCCCCATCAT
582726 CCATTCACATGCAGCCCCATCAT
1 CCATTCACATGCAGCCCCATCAT
582749 CCATTC
1 CCATTC
582755 CTTCACGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.44, G:0.08, T:0.23
Consensus pattern (23 bp):
CCATTCACATGCAGCCCCATCAT
Found at i:582904 original size:25 final size:25
Alignment explanation
Indices: 582876--582927 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
582866 TGTACAATTA
*
582876 TTGGTGAAATAATTAAGGCAGTCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
*
582901 TTGGTGAAATAATTGAGGCAGCCGG
1 TTGGTGAAATAATTAAGGCAGCCGG
582926 TT
1 TT
582928 ATAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.10, G:0.33, T:0.29
Consensus pattern (25 bp):
TTGGTGAAATAATTAAGGCAGCCGG
Found at i:582998 original size:4 final size:4
Alignment explanation
Indices: 582989--583046 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
582979 ATTGCAGCCG
** **
582989 AGAA AGAA AGAA AGGG AGAA AGGAA AGAA AGAA AGAA AGGG AGAA AGGAA
1 AGAA AGAA AGAA AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA A-GAA
*
583039 AGTA AGAA
1 AGAA AGAA
583047 GAATTCGAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
4 34 0.81
5 8 0.19
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:583016 original size:17 final size:16
Alignment explanation
Indices: 582988--583019 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
582978 GATTGCAGCC
582988 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
583004 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
583020 AAAGAAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:583017 original size:25 final size:25
Alignment explanation
Indices: 582989--583046 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
582979 ATTGCAGCCG
582989 AGAAAGAAAGAAAGGGAGAAAGGAA
1 AGAAAGAAAGAAAGGGAGAAAGGAA
583014 AGAAAGAAAGAAAGGGAGAAAGGAA
1 AGAAAGAAAGAAAGGGAGAAAGGAA
*
583039 AGTAAGAA
1 AGAAAGAA
583047 GAATTCGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (25 bp):
AGAAAGAAAGAAAGGGAGAAAGGAA
Found at i:583313 original size:45 final size:47
Alignment explanation
Indices: 583251--583341 Score: 134
Period size: 45 Copynumber: 2.0 Consensus size: 47
583241 TTATATAGTT
583251 AAAAAATAATTAATTAGTTTGTATT-GTT-AATAGTT-AGTTATATA
1 AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATA
* *
583295 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATAT
583342 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 6 0.15
45 17 0.41
46 3 0.07
47 7 0.17
48 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (47 bp):
AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATA
Found at i:585728 original size:17 final size:17
Alignment explanation
Indices: 585706--585738 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
585696 CAATGATTTT
*
585706 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
585723 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
585739 GATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:585961 original size:11 final size:10
Alignment explanation
Indices: 585941--586118 Score: 68
Period size: 11 Copynumber: 18.3 Consensus size: 10
585931 AATAATGATT
585941 ATTATCAAATC
1 ATTAT-AAATC
585952 ATTACTAAATC
1 ATTA-TAAATC
*
585963 A-T-CAAATC
1 ATTATAAATC
585971 A-T-TAAAT-
1 ATTATAAATC
585978 ATT-TAAATC
1 ATTATAAATC
585987 ATTATCAAATC
1 ATTAT-AAATC
*
585998 ATTACTATAATGATT
1 A-T--TATAA--ATC
586013 ATTATCAAATC
1 ATTAT-AAATC
586024 ATTACTAAATC
1 ATTA-TAAATC
*
586035 A-T-CAAATC
1 ATTATAAATC
586043 A-T-TAAAT-
1 ATTATAAATC
586050 ATT-TAAATC
1 ATTATAAATC
586059 ATTATCAAATC
1 ATTAT-AAATC
586070 ATTACTAAATC
1 ATTA-TAAATC
*
586081 A-T-CAAATC
1 ATTATAAATC
586089 A-T-TAAAT-
1 ATTATAAATC
*
586096 ATT-TAATTC
1 ATTATAAATC
586105 ATTATTAAATC
1 ATTA-TAAATC
586116 ATT
1 ATT
586119 TTTATAATGA
Statistics
Matches: 136, Mismatches: 10, Indels: 42
0.72 0.05 0.22
Matches are distributed among these distances:
7 3 0.02
8 50 0.37
9 9 0.07
10 5 0.04
11 51 0.38
12 7 0.05
13 4 0.03
14 4 0.03
15 3 0.02
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.39
Consensus pattern (10 bp):
ATTATAAATC
Found at i:586023 original size:26 final size:26
Alignment explanation
Indices: 585987--586298 Score: 220
Period size: 26 Copynumber: 12.7 Consensus size: 26
585977 TATTTAAATC
585987 ATTATCAAATCATTACTATAATGATT
1 ATTATCAAATCATTACTATAATGATT
* *
586013 ATTATCAAATCATTACTA-AATCATC
1 ATTATCAAATCATTACTATAATGATT
* * * * * *
586038 A-AATC-ATTAAATA-TTTAA--ATC
1 ATTATCAAATCATTACTATAATGATT
586059 ATTATCAAATCATTAC--T-A--A--
1 ATTATCAAATCATTACTATAATGATT
* * * *
586078 ATCATCAAATCATTA-AATATTTAATT
1 ATTATCAAATCATTACTATA-ATGATT
* **
586104 CATTATTAAATCATTTTTATAATGATT
1 -ATTATCAAATCATTACTATAATGATT
*
586131 ATTAAT-AAATCATTATTATAATGATT
1 ATT-ATCAAATCATTACTATAATGATT
586157 ATTATCAAATCATTACTATAATGATT
1 ATTATCAAATCATTACTATAATGATT
* *
586183 ATTATCAAATCATTACTA-AATCATCAA
1 ATTATCAAATCATTACTATAATGAT--T
* * *
586210 ATCATTAAAT-ATT--TA-AATCATT
1 ATTATCAAATCATTACTATAATGATT
*
586232 A-T-T-AAATCATTATTATAATGATT
1 ATTATCAAATCATTACTATAATGATT
586255 ATTATCAAATCATTACTATAATGATT
1 ATTATCAAATCATTACTATAATGATT
586281 ATTATCAAATCATTACTA
1 ATTATCAAATCATTACTA
586299 AATCATCAAA
Statistics
Matches: 232, Mismatches: 29, Indels: 50
0.75 0.09 0.16
Matches are distributed among these distances:
19 18 0.08
20 5 0.02
21 6 0.03
22 8 0.03
23 19 0.08
24 13 0.06
25 14 0.06
26 120 0.52
27 26 0.11
28 3 0.01
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.42
Consensus pattern (26 bp):
ATTATCAAATCATTACTATAATGATT
Found at i:586030 original size:72 final size:72
Alignment explanation
Indices: 585932--586076 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
585922 AGTATTCTAA
585932 ATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATCAAAT
1 ATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATCAAAT
585997 CATTACT
66 CATTACT
586004 ATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATCAAAT
1 ATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATCAAAT
586069 CATTACT
66 CATTACT
586076 A
1 A
586077 AATCATCAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.39
Consensus pattern (72 bp):
ATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATCAAAT
CATTACT
Found at i:586048 original size:16 final size:15
Alignment explanation
Indices: 585943--586097 Score: 55
Period size: 16 Copynumber: 10.2 Consensus size: 15
585933 TAATGATTAT
585943 TATCAAATCATTACTAAA
1 TATCAAATCA-T--TAAA
585961 TCATCAAATCATTAAA
1 T-ATCAAATCATTAAA
*
585977 TATTTAAATCA-T---
1 TA-TCAAATCATTAAA
*
585989 TATCAAATCATT-AC
1 TATCAAATCATTAAA
* *
586003 TAT--AATGATT-AT
1 TATCAAATCATTAAA
586015 TATCAAATCATTACTAAA
1 TATCAAATCA-T--TAAA
586033 TCATCAAATCATTAAA
1 T-ATCAAATCATTAAA
*
586049 TATTTAAATCA-T---
1 TA-TCAAATCATTAAA
586061 TATCAAATCATTACTAAA
1 TATCAAATCA-T--TAAA
586079 TCATCAAATCATTAAA
1 T-ATCAAATCATTAAA
586095 TAT
1 TAT
586098 TTAATTCATT
Statistics
Matches: 108, Mismatches: 8, Indels: 45
0.67 0.05 0.28
Matches are distributed among these distances:
11 14 0.13
12 15 0.14
14 7 0.06
15 8 0.07
16 29 0.27
17 1 0.01
18 7 0.06
19 27 0.25
ACGTcount: A:0.47, C:0.15, G:0.01, T:0.37
Consensus pattern (15 bp):
TATCAAATCATTAAA
Found at i:586070 original size:46 final size:46
Alignment explanation
Indices: 586013--586118 Score: 194
Period size: 46 Copynumber: 2.3 Consensus size: 46
586003 TATAATGATT
586013 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
1 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
*
586059 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAATTC
1 ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
*
586105 ATTATTAAATCATT
1 ATTATCAAATCATT
586119 TTTATAATGA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (46 bp):
ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
Found at i:586092 original size:19 final size:18
Alignment explanation
Indices: 585944--586071 Score: 72
Period size: 19 Copynumber: 7.1 Consensus size: 18
585934 AATGATTATT
585944 ATCAAATCATTACTAAATC
1 ATCAAATCATTA-TAAATC
585963 ATCAAATCA-T-TAAAT-
1 ATCAAATCATTATAAATC
*
585978 ATTTAAATCATTATCAAATC
1 A-TCAAATCATTAT-AAATC
* * * * * *
585998 ATTACTATAATGAT-TATT
1 ATCA-AATCATTATAAATC
586016 ATCAAATCATTACTAAATC
1 ATCAAATCATTA-TAAATC
586035 ATCAAATCA-T-TAAAT-
1 ATCAAATCATTATAAATC
*
586050 ATTTAAATCATTATCAAATC
1 A-TCAAATCATTAT-AAATC
586070 AT
1 AT
586072 TACTAAATCA
Statistics
Matches: 83, Mismatches: 13, Indels: 26
0.68 0.11 0.21
Matches are distributed among these distances:
15 2 0.02
16 24 0.29
17 7 0.08
18 10 0.12
19 32 0.39
20 8 0.10
ACGTcount: A:0.47, C:0.15, G:0.01, T:0.38
Consensus pattern (18 bp):
ATCAAATCATTATAAATC
Found at i:586173 original size:98 final size:96
Alignment explanation
Indices: 586059--586353 Score: 319
Period size: 98 Copynumber: 3.0 Consensus size: 96
586049 TATTTAAATC
* ** * *
586059 ATTATCAAATCATTACTA-AATCATCAAATCATTAAAT-ATTTAATTCATTATTAAATCATT-T-
1 ATTATCAAATCATTACTATAATCAT--AATCATCAAATCA-TTAATAAATCATCAAATCATTATA
*
586120 TTATAATGATTATTAATAAATCATTATTATAATGATT
63 TT-TAA--ATCATTAATAAATCATTATTATAATGATT
* * * *
586157 ATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATAT
1 ATTATCAAATCATTACTATAATCATAATCATCAAATCATTAATAAATCATCAAATCATT--ATAT
*
586222 TTAAATCATTATTAAATCATTATTATAATGATT
64 TTAAATCATTAATAAATCATTATTATAATGATT
* * * *
586255 ATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATAT
1 ATTATCAAATCATTACTATAATCATAATCATCAAATCATTAATAAATCATCAAATCATT--ATAT
* *
586320 TTAAATCATTATTAAATCATTTTTATAATGATT
64 TTAAATCATTAATAAATCATTATTATAATGATT
586353 A
1 A
586354 ATAAATACAT
Statistics
Matches: 179, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
97 24 0.13
98 144 0.80
99 5 0.03
100 4 0.02
101 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (96 bp):
ATTATCAAATCATTACTATAATCATAATCATCAAATCATTAATAAATCATCAAATCATTATATTT
AAATCATTAATAAATCATTATTATAATGATT
Found at i:586220 original size:124 final size:124
Alignment explanation
Indices: 585932--586298 Score: 559
Period size: 124 Copynumber: 3.0 Consensus size: 124
585922 AGTATTCTAA
*
585932 ATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATCAAAT
1 ATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAAT
* * * * * * *
585997 CATTACTATAATGATTATTATCAAATCATTACTA-AATCATCA-AATC-ATTAAATA-T
66 CATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACT
* * *
586052 TTAA--ATCATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAATTCATTATTAAAT
1 ATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAAT
* *
586115 CATTTTTATAATGATTATTAAT-AAATCATTATTATAATGATTATTATCAAATCATTACT
66 CATTATTATAATGATTATT-ATCAAATCATTACTATAATGATTATTATCAAATCATTACT
586174 ATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAAT
1 ATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAAT
586239 CATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACT
66 CATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACT
586298 A
1 A
586299 AATCATCAAA
Statistics
Matches: 221, Mismatches: 18, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
118 84 0.38
119 8 0.04
120 6 0.03
121 5 0.02
122 4 0.02
123 2 0.01
124 112 0.51
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (124 bp):
ATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCATTATTAAAT
CATTATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACT
Found at i:589238 original size:26 final size:24
Alignment explanation
Indices: 589180--589238 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
589170 CTAATAAACC
*
589180 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
589204 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
589232 TAATAAT
1 TAATAAT
589239 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:590087 original size:28 final size:30
Alignment explanation
Indices: 590047--590109 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
590037 ATTTTTTATA
*
590047 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
590077 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
590105 TAATA
1 TAATA
590110 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Done.