Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007849.1 Hibiscus syriacus cultivar Beakdansim tig00110206_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: 3141433
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 12
Found at i:367015 original size:54 final size:54
Alignment explanation
Indices: 366956--368013 Score: 1717
Period size: 54 Copynumber: 19.6 Consensus size: 54
366946 GTAGTGAAGC
*
366956 GAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
*
367010 GAAGAAGATATCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* ** * * * *
367064 GAAGAATATGTTTGAGTTCCATACTCACTAAAGAAAGAAGGAGCGAACCTGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
*
367118 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* *
367172 GAAAAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGTGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* *
367226 GAAGAAGATGTTCGAGTTTCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* *
367280 GAAGAAGATGTCCAAGTTCCATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * *
367334 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGAGAGCGAATCCATTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* *
367388 GAAAAAGATGTCCGATTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
*
367442 GAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--T
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
367494 -AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* *
367547 GAAGAAAATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * * *
367601 GAATAAAATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * * *
367655 GAAGAAGATTTCCAAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACCTGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* *
367709 GAAGAAGATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
** * *
367763 GAAGAAGATGTCTAAGTTCCATACTCCCTAGAGAAAGAGGGAGTGAACTCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
*
367817 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAATCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
*
367871 GAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
*
367925 GAAGAAAATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
*
367979 GAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAA
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAA
368014 TAGGGAACAT
Statistics
Matches: 923, Mismatches: 78, Indels: 6
0.92 0.08 0.01
Matches are distributed among these distances:
51 49 0.05
52 1 0.00
53 1 0.00
54 872 0.94
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (54 bp):
GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
Found at i:368084 original size:55 final size:55
Alignment explanation
Indices: 367982--368313 Score: 383
Period size: 55 Copynumber: 6.1 Consensus size: 55
367972 CCCGTTTGAA
* * * *
367982 GAAGA-TGTTCGAGT-TCCATACTCCCT-AGAGAATAGGGAACATACACGATTGTT
1 GAAGATTGTTCGAGTCT-CATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTT
* *
368035 GGAGTTTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTT
* * *
368090 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGATTGTT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTT
* * *
368145 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGTAGACACG-TT-TT
1 GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTT
* * * * *
368198 GAAGATTGTTCAAGTC-CTATACTCTCTGAAGGAATAGGGAGCAAACACGTTTATT
1 GAAGATTGTTCGAGTCTC-ATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTT
* * * * *
368253 AAAGGTTGTTCAAGTCAT-ATACTCTCTG-AAGAATAGGGAGCGGACACGTTTGTT
1 GAAGATTGTTCGAGTC-TCATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTT
368307 GAAGATT
1 GAAGATT
368314 AAGAGAAGGA
Statistics
Matches: 246, Mismatches: 25, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
53 49 0.20
54 49 0.20
55 148 0.60
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTT
Found at i:368094 original size:108 final size:107
Alignment explanation
Indices: 367982--368313 Score: 395
Period size: 108 Copynumber: 3.1 Consensus size: 107
367972 CCCGTTTGAA
* * * * *
367982 GAAGA-TGTTCGAGTTCCATACTCCCT--AGAGAATAGGGAACATACACGATTGTTGGAGTTTGT
1 GAAGATTGTTCGAG-TCCATACTCTCTGAAG-GAATAGGGAGCAAACACGATTGTTGAAGATTGT
368044 TCGAGTCTCATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTT
64 TCGAGTCT-ATACTCTCTGAAAGAATAGGGAGCAGACACG-TTGTT
* **
368090 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACACGATTGTTGAAGATTGTT
1 GAAGATTGTTCGAGTC-CATACTCTCTGAAGGAATAGGGAGCAAACACGATTGTTGAAGATTGTT
* *
368155 CGAGTCTTATACTCTCTGAAGGAATAGGGAGTAGACACGTT-TT
65 CGAGTC-TATACTCTCTGAAAGAATAGGGAGCAGACACGTTGTT
* * * * *
368198 GAAGATTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCAAACACGTTTATTAAAGGTTGTT
1 GAAGATTGTTCGAGTCC-ATACTCTCTGAAGGAATAGGGAGCAAACACGATTGTTGAAGATTGTT
* *
368263 CAAGTCATATACTCTCTG-AAGAATAGGGAGCGGACACGTTTGTT
65 CGAGTC-TATACTCTCTGAAAGAATAGGGAGCAGACACG-TTGTT
368307 GAAGATT
1 GAAGATT
368314 AAGAGAAGGA
Statistics
Matches: 194, Mismatches: 22, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
107 17 0.09
108 83 0.43
109 27 0.14
110 64 0.33
111 3 0.02
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (107 bp):
GAAGATTGTTCGAGTCCATACTCTCTGAAGGAATAGGGAGCAAACACGATTGTTGAAGATTGTTC
GAGTCTATACTCTCTGAAAGAATAGGGAGCAGACACGTTGTT
Found at i:385974 original size:2 final size:2
Alignment explanation
Indices: 385967--385994 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
385957 AATATAAGAT
385967 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
385995 CTTACTAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:389614 original size:24 final size:23
Alignment explanation
Indices: 389563--389623 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
389553 TTTAAGGTAT
*
389563 ATTTTATTATATTTAATATTTTA
1 ATTTTATTATATTTAATATTTAA
*
389586 TTTTTAATT-TATTTAAGTATTTAA
1 ATTTT-ATTATATTTAA-TATTTAA
389610 ATTTT-TTAATATTT
1 ATTTTATT-ATATTT
389624 TATTTCTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 2 0.06
23 11 0.35
24 18 0.58
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
ATTTTATTATATTTAATATTTAA
Found at i:389624 original size:8 final size:8
Alignment explanation
Indices: 389561--389625 Score: 53
Period size: 8 Copynumber: 8.0 Consensus size: 8
389551 TGTTTAAGGT
389561 ATATTTTA
1 ATATTTTA
*
389569 TTATATTTA
1 ATAT-TTTA
389578 ATATTTT-
1 ATATTTTA
389585 AT-TTTTA
1 ATATTTTA
*
389592 ATTTATTTA
1 ATAT-TTTA
*
389601 AGTATTTAA
1 A-TATTTTA
*
389610 ATTTTTTA
1 ATATTTTA
389618 ATATTTTA
1 ATATTTTA
389626 TTTCTTTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
6 4 0.09
7 4 0.09
8 19 0.42
9 16 0.36
10 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (8 bp):
ATATTTTA
Found at i:389625 original size:17 final size:19
Alignment explanation
Indices: 389584--389625 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
389574 TTTAATATTT
*
389584 TATTTTTAATTTATTTAAG
1 TATTTTAAATTTATTTAAG
389603 TA-TTTAAATTT-TTTAA-
1 TATTTTAAATTTATTTAAG
389619 TATTTTA
1 TATTTTA
389626 TTTCTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.10
17 9 0.43
18 8 0.38
19 2 0.10
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TATTTTAAATTTATTTAAG
Found at i:389637 original size:9 final size:8
Alignment explanation
Indices: 389574--389640 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
389564 TTTTATTATA
*
389574 TTTAATAT
1 TTTAATTT
389582 TTT-A-TT
1 TTTAATTT
389588 TTTAATTT
1 TTTAATTT
*
389596 ATTTAAGTAT
1 -TTTAA-TTT
*
389606 TTAAATTT
1 TTTAATTT
*
389614 TTTAATAT
1 TTTAATTT
389622 TTT-ATTT
1 TTTAATTT
389629 CTTTAATTT
1 -TTTAATTT
389638 TTT
1 TTT
389641 TTGCAGATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
6 4 0.09
7 5 0.11
8 22 0.48
9 13 0.28
10 2 0.04
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (8 bp):
TTTAATTT
Found at i:391953 original size:24 final size:23
Alignment explanation
Indices: 391904--391953 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
391894 TAATACTTAC
**
391904 TTTATTTTATTAATTTTGTTGGA
1 TTTATTTTATTAATTTTGTTAAA
*
391927 TTTATTTTAATTTATTTTGTTAAA
1 TTTATTTT-ATTAATTTTGTTAAA
391951 TTT
1 TTT
391954 GTTGGACTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (23 bp):
TTTATTTTATTAATTTTGTTAAA
Found at i:391971 original size:34 final size:33
Alignment explanation
Indices: 391904--391991 Score: 115
Period size: 33 Copynumber: 2.6 Consensus size: 33
391894 TAATACTTAC
*
391904 TTTATTTTATTAATTTTGTTGGATTTATTTTAA
1 TTTATTTTGTTAATTTTGTTGGATTTATTTTAA
*
391937 TTTATTTTGTTAAATTTGTTGGACTTT-TTGTTAA
1 TTTATTTTGTTAATTTTGTTGGA-TTTATT-TTAA
*
391971 TATATTTTGGTTAATTTTGTT
1 TTTATTTT-GTTAATTTTGTT
391992 TATTACCATT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
33 23 0.48
34 14 0.29
35 11 0.23
ACGTcount: A:0.22, C:0.01, G:0.12, T:0.65
Consensus pattern (33 bp):
TTTATTTTGTTAATTTTGTTGGATTTATTTTAA
Found at i:392021 original size:35 final size:31
Alignment explanation
Indices: 391986--392066 Score: 81
Period size: 38 Copynumber: 2.3 Consensus size: 31
391976 TTTGGTTAAT
391986 TTTGTTTATTACCATTTAATATCAGTTATTGTAA
1 TTTGTTTATTACCATTTAATA-C--TTATTGTAA
392020 TTTGTTTACCATTTACCATTTAATACTTATTGTAA
1 TTTGTTT---A-TTACCATTTAATACTTATTGTAA
392055 GTTTGTTGTATT
1 -TTTGTT-TATT
392067 TAAAATTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
33 2 0.05
34 8 0.20
35 9 0.22
36 6 0.15
37 3 0.07
38 13 0.32
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (31 bp):
TTTGTTTATTACCATTTAATACTTATTGTAA
Found at i:397319 original size:16 final size:16
Alignment explanation
Indices: 397294--397327 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
397284 TGCCTTTTCT
*
397294 GATGCGAATTATGGAG
1 GATGCAAATTATGGAG
*
397310 GATGCAAATTATGTAG
1 GATGCAAATTATGGAG
397326 GA
1 GA
397328 AAAGCACCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.32, T:0.26
Consensus pattern (16 bp):
GATGCAAATTATGGAG
Found at i:397999 original size:22 final size:23
Alignment explanation
Indices: 397973--398024 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
397963 ATAGGGCAGA
*
397973 GGGAATCAATACCCCC-TTGAAG
1 GGGAACCAATACCCCCTTTGAAG
* * *
397995 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCAATACCCCCTTTGAAG
398018 GGGAACC
1 GGGAACC
398025 GATTCACTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (23 bp):
GGGAACCAATACCCCCTTTGAAG
Found at i:398015 original size:23 final size:22
Alignment explanation
Indices: 397984--398054 Score: 74
Period size: 23 Copynumber: 3.2 Consensus size: 22
397974 GGAATCAATA
397984 CCCCCTTGAAGGGGAACCGATT
1 CCCCCTTGAAGGGGAACCGATT
*
398006 CCCCCTTTGAATGGGAACCGATT
1 CCCCC-TTGAAGGGGAACCGATT
* * *
398029 CACTCCTTG-A-GGGAATCGATA
1 C-CCCCTTGAAGGGGAACCGATT
398050 CCCCC
1 CCCCC
398055 AATGGGTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
20 3 0.07
21 10 0.24
22 6 0.14
23 20 0.48
24 3 0.07
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.21
Consensus pattern (22 bp):
CCCCCTTGAAGGGGAACCGATT
Found at i:399986 original size:90 final size:90
Alignment explanation
Indices: 399870--400048 Score: 270
Period size: 90 Copynumber: 2.0 Consensus size: 90
399860 TAATCCTGAA
* * *
399870 TATTTAATTTCAATTAATCAAATATAGATTTAATTAATTTGAAATAAT-AAAATCTCTGATATAA
1 TATTAAATTCCAATTAATCAAATATAGATTTAATTAATTTGAAATAATAAAAATC-CTAATATAA
*
399934 TTAGGGTAACTTGGATATAAAAGGAT
65 CTAGGGTAACTTGGATATAAAAGGAT
* *
399960 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAATCCTAATATGA
1 TATTAAATTCCAATTAATCAAATATAGATTTAATTAATTTGAAATAAT-AAAAATCCTAATATAA
*
400025 CTAGGGTAACTTGGCTATAAAAGG
65 CTAGGGTAACTTGGATATAAAAGG
400049 GTGTGTTAGG
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
90 45 0.56
91 29 0.36
92 6 0.08
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATCAAATATAGATTTAATTAATTTGAAATAATAAAAATCCTAATATAAC
TAGGGTAACTTGGATATAAAAGGAT
Found at i:403098 original size:13 final size:13
Alignment explanation
Indices: 403080--403105 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
403070 TGATCCCAGC
403080 TCCGCGATCTGAA
1 TCCGCGATCTGAA
403093 TCCGCGATCTGAA
1 TCCGCGATCTGAA
403106 ATGACATAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (13 bp):
TCCGCGATCTGAA
Found at i:407928 original size:87 final size:87
Alignment explanation
Indices: 407782--407956 Score: 260
Period size: 87 Copynumber: 2.0 Consensus size: 87
407772 CTCTATCTGG
* ** * *
407782 AGATTCCTGTTTCTTTTGTATTTCTTAACAGTATTTTATGGTTACTGAATTTTCATTCTTATACA
1 AGATTCCCGTTTCTTTCATATTTCTCAACAGTATTTTATGGTTACTGAATTTTCATTCTTACACA
*
407847 GTGCTTTATCATTTACATTCCT
66 GTGCTTTATCATTCACATTCCT
* * *
407869 AGATTCCCGTTTCTTTCATATTTCTCAACAGTATTTTATGGTTACTGCATTTTCATTCTTGCACG
1 AGATTCCCGTTTCTTTCATATTTCTCAACAGTATTTTATGGTTACTGAATTTTCATTCTTACACA
*
407934 GTGCTTTCTCATTCACATTCCT
66 GTGCTTTATCATTCACATTCCT
407956 A
1 A
407957 TAACATTATA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.21, C:0.20, G:0.11, T:0.49
Consensus pattern (87 bp):
AGATTCCCGTTTCTTTCATATTTCTCAACAGTATTTTATGGTTACTGAATTTTCATTCTTACACA
GTGCTTTATCATTCACATTCCT
Found at i:410147 original size:2 final size:2
Alignment explanation
Indices: 410140--410212 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
410130 AATGAAGAAC
410140 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
410182 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
410213 TACTGGATAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:412143 original size:22 final size:23
Alignment explanation
Indices: 412093--412144 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
412083 AAGACTTGTA
* *
412093 ATAAAAAATTGATATTATTCATT
1 ATAAAAACTTAATATTATTCATT
412116 AT-AAAACTTAATATTATT-ATT
1 ATAAAAACTTAATATTATTCATT
*
412137 TTAAAAAC
1 ATAAAAAC
412145 ATTATAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 4 0.16
22 19 0.76
23 2 0.08
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (23 bp):
ATAAAAACTTAATATTATTCATT
Found at i:414419 original size:184 final size:187
Alignment explanation
Indices: 414131--414503 Score: 623
Period size: 184 Copynumber: 2.0 Consensus size: 187
414121 AAATTAAATG
* *
414131 TTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAT
1 TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAT
414196 ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
66 ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
* *
414261 GAGTTTTAAATTGTTTGGGCTTAGCCCA-A-ATGT-TATAT-ATAATATATTTAATAT
131 GAGTTTTAAATGGTTTGGGCTGAGCCCATATAT-TATATATAATAATATATTTAATAT
414315 TTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAATTT-
1 TTTTTAATTAAAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAAT-AAAAATTTC
*
414379 ATAT-AATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
64 ATATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAA
*
414443 TTGGGTTTTAAATGGTTTGGGCTGAGCCCATATATTATATATAATAATATATTTAATAT
129 TTGAGTTTTAAATGGTTTGGGCTGAGCCCATATATTATATATAATAATATATTTAATAT
414502 TT
1 TT
414504 AAAATTTAAT
Statistics
Matches: 177, Mismatches: 6, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
184 101 0.57
185 43 0.24
186 15 0.08
187 18 0.10
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (187 bp):
TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTCAT
ATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTATTGGATCTTAAATTATTAATT
GAGTTTTAAATGGTTTGGGCTGAGCCCATATATTATATATAATAATATATTTAATAT
Found at i:421966 original size:17 final size:17
Alignment explanation
Indices: 421925--421969 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
421915 CCCTAATTGA
421925 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** **
421942 TTGTATATTTTTTAAAT
1 TTAAATATTTAATAAAT
421959 TTAAATATTTA
1 TTAAATATTTA
421970 TTTTTACATG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:422001 original size:16 final size:16
Alignment explanation
Indices: 421980--422013 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
421970 TTTTTACATG
421980 AACTAAAA-TATTATTA
1 AACTAAAATTA-TATTA
421996 AACTAAAATTATATTA
1 AACTAAAATTATATTA
422012 AA
1 AA
422014 TATATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
AACTAAAATTATATTA
Found at i:428662 original size:36 final size:37
Alignment explanation
Indices: 428617--428712 Score: 122
Period size: 36 Copynumber: 2.6 Consensus size: 37
428607 GGATCATATC
* *
428617 TTTAAGAGTTTAAATCATAGTAGAACTCTATCCTA-T
1 TTTAGGAGTTTAAATCCTAGTAGAACTCTATCCTATT
* ** * *
428653 TTTAGGAGTTTGAATCCTAACAAAATTCTATCCTATT
1 TTTAGGAGTTTAAATCCTAGTAGAACTCTATCCTATT
428690 TTTAGGAGTTTAAATCCTAGTAG
1 TTTAGGAGTTTAAATCCTAGTAG
428713 GACGAAAAGG
Statistics
Matches: 48, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
36 28 0.58
37 20 0.42
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTAGGAGTTTAAATCCTAGTAGAACTCTATCCTATT
Found at i:429640 original size:106 final size:106
Alignment explanation
Indices: 429455--430090 Score: 934
Period size: 106 Copynumber: 6.0 Consensus size: 106
429445 AGGATTGTTC
* *
429455 CGAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
* ** * *
429519 AATCAGCGGTCCCTTCGTTTTGAAGTTGAACTTGCATCGTCT
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
429561 CGAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
429626 ACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
429667 GGAGTCCAATATCCTTCGTTGTGATGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
429732 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
429773 GGAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
429838 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
429879 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAGTTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
** * * * * *
429944 GTCAGCCGCCCCTTCG-CTGTGAAGTTGAGCTTGTGCTGTCT
66 ACCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCT
* ** *
429985 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTAACTCTGAAATTGGGAAATTGTTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * *
430050 ACCAACGGTCCCTTCGTCGTAAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
430091 GGAGAGAAAC
Statistics
Matches: 479, Mismatches: 48, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
105 1 0.00
106 476 0.99
107 2 0.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:430146 original size:36 final size:37
Alignment explanation
Indices: 430097--430200 Score: 138
Period size: 36 Copynumber: 2.8 Consensus size: 37
430087 GTCTGGAGAG
*
430097 AAACTGTCTCAAGGGAGATAAAATTTGTTTC-AAGGA
1 AAACTGTCTCAAGGGAGATAAAATTTGTTTCAAAGAA
* **
430133 AGACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAA
1 AAACTGTCTCAAGGGAGATAAAATTTGTTTCAAAGAA
* *
430170 AAACTATCTCAAGCGAGATAAAATCTTGTTT
1 AAACTGTCTCAAGGGAGATAAAAT-TTGTTT
430201 TAAATGAGAC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 28 0.49
37 23 0.40
38 6 0.11
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (37 bp):
AAACTGTCTCAAGGGAGATAAAATTTGTTTCAAAGAA
Found at i:431009 original size:22 final size:22
Alignment explanation
Indices: 430983--431059 Score: 102
Period size: 22 Copynumber: 3.5 Consensus size: 22
430973 TTGTGTTTGG
*
430983 TCAAAGGTTTAGCATTTGATTC
1 TCAAAGGTTTGGCATTTGATTC
* *
431005 TCAAATGTTTGGTATTTGATGT-
1 TCAAAGGTTTGGCATTTGAT-TC
*
431027 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATTC
431049 TCAAAGGTTTG
1 TCAAAGGTTTG
431060 ATGGGGTAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
22 46 0.98
23 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATTC
Found at i:431697 original size:20 final size:18
Alignment explanation
Indices: 431672--431712 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
431662 TTTCCTTTTT
*
431672 TCTTTTTGATTTTGTTCTC
1 TCTTTTTTATTTTGTT-TC
*
431691 TCTTTTTTCTTTTGTTTC
1 TCTTTTTTATTTTGTTTC
431709 TCTT
1 TCTT
431713 GTTTCTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.02, C:0.17, G:0.07, T:0.73
Consensus pattern (18 bp):
TCTTTTTTATTTTGTTTC
Found at i:431710 original size:18 final size:18
Alignment explanation
Indices: 431681--431724 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
431671 TTCTTTTTGA
*
431681 TTTTGTTCTCTCTTTTTTC
1 TTTTGTT-TCTCTTGTTTC
431700 TTTTGTTTCTCTTGTTTC
1 TTTTGTTTCTCTTGTTTC
431718 -TTTGTTT
1 TTTTGTTT
431725 TTGATTGGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 7 0.29
18 10 0.42
19 7 0.29
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.75
Consensus pattern (18 bp):
TTTTGTTTCTCTTGTTTC
Found at i:431714 original size:9 final size:9
Alignment explanation
Indices: 431683--431724 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
431673 CTTTTTGATT
431683 TTGTTCTCTC
1 TTGTT-TCTC
* *
431693 TTTTTTCTT
1 TTGTTTCTC
431702 TTGTTTCTC
1 TTGTTTCTC
431711 TTGTTTCT-
1 TTGTTTCTC
431719 TTGTTT
1 TTGTTT
431725 TTGATTGGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 6 0.21
9 18 0.64
10 4 0.14
ACGTcount: A:0.00, C:0.17, G:0.10, T:0.74
Consensus pattern (9 bp):
TTGTTTCTC
Found at i:434924 original size:22 final size:21
Alignment explanation
Indices: 434899--434959 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
434889 AAAAATAAAA
* *
434899 AAAAATAAATAAATAAATGAGT
1 AAAAATATATAAATAAA-AAGT
434921 -AAAATATATAAA-AAAAAGT
1 AAAAATATATAAATAAAAAGT
434940 AAAAGTATATATAAATAAAA
1 AAAA--ATATATAAATAAAA
434960 TAAAAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
19 3 0.09
20 6 0.18
21 11 0.33
22 9 0.27
23 4 0.12
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (21 bp):
AAAAATATATAAATAAAAAGT
Found at i:434926 original size:21 final size:20
Alignment explanation
Indices: 434840--434959 Score: 72
Period size: 18 Copynumber: 5.8 Consensus size: 20
434830 AATGATAATC
434840 AAATAAATAAATAAAAAGTA
1 AAATAAATAAATAAAAAGTA
* *
434860 AAA-GAAT--ATAAAAACATA
1 AAATAAATAAATAAAAA-GTA
434878 AAATATAGGATAAAAATAAAAA--A
1 AAATA-A--AT--AAATAAAAAGTA
*
434901 AAATAAATAAATAAATGAGTA
1 AAATAAATAAATAAA-AAGTA
*
434922 AAATATATAAA-AAAAAGTA
1 AAATAAATAAATAAAAAGTA
434941 AAAGTATATATAAATAAAA
1 AAA-TA-A-ATAAATAAAA
434960 TAAAAAAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 29
0.68 0.06 0.26
Matches are distributed among these distances:
17 7 0.09
18 12 0.16
19 11 0.14
20 11 0.14
21 11 0.14
22 8 0.10
23 10 0.13
26 7 0.09
ACGTcount: A:0.72, C:0.01, G:0.07, T:0.21
Consensus pattern (20 bp):
AAATAAATAAATAAAAAGTA
Found at i:434950 original size:20 final size:21
Alignment explanation
Indices: 434846--434964 Score: 76
Period size: 22 Copynumber: 5.8 Consensus size: 21
434836 AATCAAATAA
*
434846 ATAAATAAAAAGTAAAAGA-AT
1 ATAAAT-AAAAGTAAAATATAT
*
434867 ATAAA-AACA-TAAAATATAGGAT
1 ATAAATAAAAGTAAAATAT---AT
* *
434889 AAAAATAAAA--AAAA-ATAA
1 ATAAATAAAAGTAAAATATAT
434907 ATAAATAAATGAGTAAAATATAT
1 ATAAATAAA--AGTAAAATATAT
434930 A-AAA-AAAAGTAAAAGTATAT
1 ATAAATAAAAGTAAAA-TATAT
434950 ATAAATAAAA-TAAAA
1 ATAAATAAAAGTAAAA
434965 AAAAAAAAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 26
0.70 0.06 0.23
Matches are distributed among these distances:
18 15 0.19
19 10 0.13
20 7 0.09
21 18 0.23
22 21 0.27
23 7 0.09
ACGTcount: A:0.71, C:0.01, G:0.07, T:0.21
Consensus pattern (21 bp):
ATAAATAAAAGTAAAATATAT
Found at i:434956 original size:61 final size:60
Alignment explanation
Indices: 434840--434976 Score: 142
Period size: 61 Copynumber: 2.3 Consensus size: 60
434830 AATGATAATC
*
434840 AAATAAATAAATAAAAAGTAAAAGAATATAAAAACATAAAATATAGGATAAAAATAAAA-AA
1 AAATAAATAAATAAAAAGTAAAAGAATATAAAAAAATAAAATAT--GATAAAAATAAAATAA
* * *
434901 AAATAAATAAATAAATGAGTAAAA-TATATAAAAAAAAGTAAAAGTAT-ATATAAATAAAATAA
1 AAATAAATAAATAAA-AAGTAAAAGAATAT-AAAAAAA-TAAAA-TATGATAAAAATAAAATAA
434963 AAA-AAA-AAA-AAAAA
1 AAATAAATAAATAAAAA
434977 TAATATATTT
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
58 1 0.02
59 3 0.05
60 3 0.05
61 33 0.50
62 18 0.27
63 5 0.08
64 3 0.05
ACGTcount: A:0.74, C:0.01, G:0.06, T:0.19
Consensus pattern (60 bp):
AAATAAATAAATAAAAAGTAAAAGAATATAAAAAAATAAAATATGATAAAAATAAAATAA
Found at i:434983 original size:31 final size:31
Alignment explanation
Indices: 434890--434983 Score: 91
Period size: 33 Copynumber: 2.9 Consensus size: 31
434880 ATATAGGATA
* * *
434890 AAAATAAAAAAAAATAAATAAATAA-ATGAGT
1 AAAATAAAAAAAAA-AAAAAAATAATATAAAT
* *
434921 AAAATATATAAAAAAAAGTAAAAGTATATATAAAT
1 AAAATA-A-AAAAAAAA-AAAAAATA-ATATAAAT
434956 AAAATAAAAAAAAAAAAAAAATAATATA
1 AAAATAAAAAAAAAAAAAAAATAATATA
434984 TTTATACATG
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
31 11 0.22
32 8 0.16
33 20 0.39
34 2 0.04
35 10 0.20
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (31 bp):
AAAATAAAAAAAAAAAAAAAATAATATAAAT
Found at i:435465 original size:35 final size:35
Alignment explanation
Indices: 435426--435511 Score: 111
Period size: 34 Copynumber: 2.5 Consensus size: 35
435416 TCCTATCTTA
* *
435426 AGAGTTTAAATCATAGTAGAACTCTATCATATTTT
1 AGAGTTTGAATCATAGTAAAACTCTATCATATTTT
* * *
435461 AGAGTTTGAATCCTA-AAAAATTCTATCATATTTT
1 AGAGTTTGAATCATAGTAAAACTCTATCATATTTT
*
435495 AGAGTTTGAATCTTAGT
1 AGAGTTTGAATCATAGT
435512 TCTTGAAATC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 30 0.70
35 13 0.30
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (35 bp):
AGAGTTTGAATCATAGTAAAACTCTATCATATTTT
Found at i:436127 original size:43 final size:43
Alignment explanation
Indices: 436064--436151 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 43
436054 GGTACAACAC
* *
436064 TTGAACCGGTTCTAACGCGTGTTCGAGCTATTTTAACAAATCT
1 TTGAACCGGTTCTAACGCGTGTTCAACCTATTTTAACAAATCT
* *
436107 TTGAACCGGTTCTAATGCGTGTTCAACCTATTTTAATAAATCT
1 TTGAACCGGTTCTAACGCGTGTTCAACCTATTTTAACAAATCT
436150 TT
1 TT
436152 TATAAGTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (43 bp):
TTGAACCGGTTCTAACGCGTGTTCAACCTATTTTAACAAATCT
Found at i:436354 original size:16 final size:17
Alignment explanation
Indices: 436333--436368 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
436323 AAATATACCA
436333 AAATTTT-AATCAAAAT
1 AAATTTTAAATCAAAAT
436349 AAATTTTAAAATCAAAAT
1 AAATTTT-AAATCAAAAT
436367 AA
1 AA
436369 TTCGTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
18 11 0.61
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATTTTAAATCAAAAT
Found at i:440309 original size:23 final size:23
Alignment explanation
Indices: 440279--440335 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
440269 GACCCTAAAT
440279 AATAAAAAATATTATTTTTATTC
1 AATAAAAAATATTATTTTTATTC
440302 AATAAAAAATATTATTTTTATTC
1 AATAAAAAATATTATTTTTATTC
440325 AATAAAAAATA
1 AATAAAAAATA
440336 ATGATTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
AATAAAAAATATTATTTTTATTC
Found at i:441456 original size:2 final size:2
Alignment explanation
Indices: 441440--441475 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
441430 AGTCTTTCAC
*
441440 TA TA CA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
441476 TCGACTCTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:449336 original size:29 final size:30
Alignment explanation
Indices: 449277--449336 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
449267 TTATATATTA
449277 AAAATAATATTTTAAAATATTTATTTTGTT
1 AAAATAATATTTTAAAATATTTATTTTGTT
*
449307 AAAATAGATA-TTTAATAT-TTTATTTTGTT
1 AAAATA-ATATTTTAAAATATTTATTTTGTT
449336 A
1 A
449337 TTATTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 12 0.43
30 13 0.46
31 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (30 bp):
AAAATAATATTTTAAAATATTTATTTTGTT
Found at i:457912 original size:50 final size:50
Alignment explanation
Indices: 457858--457970 Score: 138
Period size: 50 Copynumber: 2.3 Consensus size: 50
457848 TAGCGCAGAT
*
457858 CAGGGGGTGCGCTATACCCACGTGGCGCCAAATCACCGTAT-GTCGCGGGG
1 CAGGGGGTGCGCTATACCCACGTGACGCCAAATCACCGTATAG-CGCGGGG
* * * * **
457908 CAGGGGGCGTGCTATACCCACGTGACGTCAAATCAGCGTATAGCGCGGTT
1 CAGGGGGTGCGCTATACCCACGTGACGCCAAATCACCGTATAGCGCGGGG
*
457958 CAGGAGGTGCGCT
1 CAGGGGGTGCGCT
457971 TTACTGCTAC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 51 0.98
51 1 0.02
ACGTcount: A:0.19, C:0.27, G:0.35, T:0.18
Consensus pattern (50 bp):
CAGGGGGTGCGCTATACCCACGTGACGCCAAATCACCGTATAGCGCGGGG
Found at i:461214 original size:69 final size:69
Alignment explanation
Indices: 461128--461268 Score: 264
Period size: 69 Copynumber: 2.0 Consensus size: 69
461118 TCCAAATTCA
461128 CGTTGCGAAATTGGAGTTCGTATTACGAATTTGTTGGTTAATTTTATAAATAAAAAAATTAATTA
1 CGTTGCGAAATTGGAGTTCGTATTACGAATTTGTTGGTTAATTTTATAAATAAAAAAATTAATTA
461193 AAAT
66 AAAT
* *
461197 CGTTGCGAAATTGGAGTTCGTGTTACGAATTTGTTGGTTATTTTTATAAATAAAAAAATTAATTA
1 CGTTGCGAAATTGGAGTTCGTATTACGAATTTGTTGGTTAATTTTATAAATAAAAAAATTAATTA
461262 AAAT
66 AAAT
461266 CGT
1 CGT
461269 ATATTATAAG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (69 bp):
CGTTGCGAAATTGGAGTTCGTATTACGAATTTGTTGGTTAATTTTATAAATAAAAAAATTAATTA
AAAT
Found at i:464212 original size:30 final size:30
Alignment explanation
Indices: 464176--464238 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
464166 TTCATTAGAA
464176 AAATGATTTAATACTTAAATCAACAAAAGC
1 AAATGATTTAATACTTAAATCAACAAAAGC
464206 AAATGATTTAATACTTAAATCAACAAAAGC
1 AAATGATTTAATACTTAAATCAACAAAAGC
464236 AAA
1 AAA
464239 AACCCTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.56, C:0.13, G:0.06, T:0.25
Consensus pattern (30 bp):
AAATGATTTAATACTTAAATCAACAAAAGC
Found at i:469527 original size:26 final size:28
Alignment explanation
Indices: 469481--469532 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
469471 TTAAATTAAA
*
469481 AAATATATAATAATAATAATAATATAGT
1 AAATATATAATAATAAAAATAATATAGT
469509 AAATA-ATAA-AATAAAAATAATATA
1 AAATATATAATAATAAAAATAATATA
469533 TATATATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 14 0.61
27 4 0.17
28 5 0.22
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (28 bp):
AAATATATAATAATAAAAATAATATAGT
Found at i:470708 original size:5 final size:5
Alignment explanation
Indices: 470692--470826 Score: 72
Period size: 5 Copynumber: 26.6 Consensus size: 5
470682 ATAAAATCGA
*
470692 ATAAT AATAAT ATAAT ATTATAT ATAAT A-AAT AT-AT ATTA- AT-AT
1 ATAAT -ATAAT ATAAT A-TA-AT ATAAT ATAAT ATAAT ATAAT ATAAT
* *
470736 ATAAT ATAAT A-AAT AT-AT TTACT ATAATAT ATAAT ATAAT ACT-AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT A-TAAT
*
470781 AATAAT AATAAT ATATTAT ATAAT -TCAAT AT-AT ATACT ATAAT ATA
1 -ATAAT -ATAAT ATA--AT ATAAT AT-AAT ATAAT ATAAT ATAAT ATA
470827 TATCCCGGAC
Statistics
Matches: 105, Mismatches: 6, Indels: 37
0.71 0.04 0.25
Matches are distributed among these distances:
3 1 0.01
4 24 0.23
5 47 0.45
6 22 0.21
7 11 0.10
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:470717 original size:2 final size:2
Alignment explanation
Indices: 470701--470829 Score: 62
Period size: 2 Copynumber: 72.0 Consensus size: 2
470691 AATAATAATA
*
470701 AT AT A- AT AT -T AT AT AT A- AT AA AT AT AT AT -T A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
470738 A- AT AT A- AT AA AT AT AT TT ACT AT A- AT AT AT A- AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
470776 ACT AT A- AT A- AT A- AT A- AT AT AT -T AT AT A- AT -T CA- AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
470812 AT AT ACT AT A- AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT
470830 CCCGGACGAA
Statistics
Matches: 98, Mismatches: 6, Indels: 46
0.65 0.04 0.31
Matches are distributed among these distances:
1 19 0.19
2 73 0.74
3 6 0.06
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:470718 original size:23 final size:23
Alignment explanation
Indices: 470692--470795 Score: 112
Period size: 22 Copynumber: 4.6 Consensus size: 23
470682 ATAAAATCGA
470692 ATAATAATAATATAATATTATAT
1 ATAATAATAATATAATATTATAT
470715 ATAAT-A-AATAT-ATATTAATAT
1 ATAATAATAATATAATATT-ATAT
*
470736 ATAAT-ATAATA-AATATATTTACT
1 ATAATAATAATATAATAT-TATA-T
*
470759 ATAATATATAATATAATACTATA-
1 ATAATA-ATAATATAATATTATAT
470782 ATAATAATAATATA
1 ATAATAATAATATA
470796 TTATATAATT
Statistics
Matches: 70, Mismatches: 3, Indels: 17
0.78 0.03 0.19
Matches are distributed among these distances:
20 5 0.07
21 15 0.21
22 19 0.27
23 18 0.26
25 9 0.13
26 4 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
ATAATAATAATATAATATTATAT
Found at i:470733 original size:26 final size:26
Alignment explanation
Indices: 470692--470829 Score: 105
Period size: 26 Copynumber: 5.4 Consensus size: 26
470682 ATAAAATCGA
470692 ATAAT-AATA-ATA-TAATATTATAT
1 ATAATAAATATATATTAATATTATAT
470715 ATAATAAATATATATTAATA-TATAAT
1 ATAATAAATATATATTAATATTAT-AT
* *
470741 ATAATAAATATAT-TTACTATAATAT
1 ATAATAAATATATATTAATATTATAT
* *
470766 ATAATATAATACTATAATAATAATA-AT
1 ATAATA-AATA-TATATTAATATTATAT
*
470793 AT-AT-TATATA-ATTCAATATATATACT
1 ATAATAAATATATATT-AATAT-TATA-T
*
470819 ATAATATATAT
1 ATAATAAATAT
470830 CCCGGACGAA
Statistics
Matches: 92, Mismatches: 9, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
22 2 0.02
23 11 0.12
24 9 0.10
25 20 0.22
26 31 0.34
27 9 0.10
28 10 0.11
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (26 bp):
ATAATAAATATATATTAATATTATAT
Found at i:470815 original size:21 final size:20
Alignment explanation
Indices: 470695--470821 Score: 75
Period size: 21 Copynumber: 6.0 Consensus size: 20
470685 AAATCGAATA
470695 ATAA-TAATATA-ATATTATAT
1 ATAATTAATATATATA-T-TAT
* *
470715 ATAATAAATATATATTAATAT
1 ATAATTAATATATA-TATTAT
*
470736 ATAATATAATAAATATATTTACT
1 ATAAT-TAATATATATA-TTA-T
*
470759 ATAA-T-ATATAATATAATACT
1 ATAATTAATAT-ATATATTA-T
470779 ATAA-TAATAATAATATATTAT
1 ATAATTAAT-AT-ATATATTAT
*
470800 ATAATTCAATATATATACTAT
1 ATAATT-AATATATATATTAT
470821 A
1 A
470822 ATATATATCC
Statistics
Matches: 87, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
20 16 0.18
21 38 0.44
22 23 0.26
23 10 0.11
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAATTAATATATATATTAT
Found at i:472348 original size:20 final size:20
Alignment explanation
Indices: 472282--472349 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
472272 GTTTCCAATT
*
472282 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATTTGTAAA
* ** * **
472302 TCACATTGCGATTTTCCAAA
1 TCGCAACGCGAATTTGTAAA
472322 TTCGCAACGCGAATTTGTAAA
1 -TCGCAACGCGAATTTGTAAA
472343 TCGCAAC
1 TCGCAAC
472350 ACATAAGCCA
Statistics
Matches: 34, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 20 0.59
21 14 0.41
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:472366 original size:20 final size:21
Alignment explanation
Indices: 472318--472503 Score: 140
Period size: 20 Copynumber: 9.2 Consensus size: 21
472308 TGCGATTTTC
* **
472318 CAAATTCGCAACGCGAATTTGT
1 CAAATTCGCAACACG-ATAAGT
*
472340 -AAA-TCGCAACAC-ATAAGC
1 CAAATTCGCAACACGATAAGT
*
472358 CAAATTCGCAACGCGA-AAGT
1 CAAATTCGCAACACGATAAGT
*
472378 CAAATTCGCAACGCGAT-AGT
1 CAAATTCGCAACACGATAAGT
* *
472398 CAAATTCGCAACACAAAAAGT
1 CAAATTCGCAACACGATAAGT
* ** * **
472419 CAAATTCGTAATGCTAATTTGT
1 CAAATTCGCAACAC-GATAAGT
*
472441 -AAA-TCGCAACAC-AGAAGT
1 CAAATTCGCAACACGATAAGT
*
472459 CAAATTCGCAACGCGAT-AGT
1 CAAATTCGCAACACGATAAGT
472479 CAAATTCGCAACACGA-AAGT
1 CAAATTCGCAACACGATAAGT
472499 CAAAT
1 CAAAT
472504 GTTTTTACGC
Statistics
Matches: 130, Mismatches: 24, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
18 6 0.05
19 6 0.05
20 92 0.71
21 22 0.17
22 4 0.03
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (21 bp):
CAAATTCGCAACACGATAAGT
Found at i:472423 original size:101 final size:101
Alignment explanation
Indices: 472318--472503 Score: 300
Period size: 101 Copynumber: 1.8 Consensus size: 101
472308 TGCGATTTTC
*
472318 CAAATTCGCAACGCGAATTTGTAAATCGCAACACATAAGCCAAATTCGCAACGCGAAAGTCAAAT
1 CAAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGCCAAATTCGCAACGCGAAAGTCAAAT
* *
472383 TCGCAACGCGATAGTCAAATTCGCAACACAAAAAGT
66 TCGCAACACGAAAGTCAAATTCGCAACACAAAAAGT
* * * * *
472419 CAAATTCGTAATGCTAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
1 CAAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGCCAAATTCGCAACGCGAAAGTCAAAT
472484 TCGCAACACGAAAGTCAAAT
66 TCGCAACACGAAAGTCAAAT
472504 GTTTTTACGC
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 77 1.00
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (101 bp):
CAAATTCGCAACGCGAATTTGTAAATCGCAACACAGAAGCCAAATTCGCAACGCGAAAGTCAAAT
TCGCAACACGAAAGTCAAATTCGCAACACAAAAAGT
Found at i:473001 original size:20 final size:19
Alignment explanation
Indices: 472966--473019 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
472956 AAATCGTAAC
*
472966 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCATT
*
472985 GCGATTTTCATTTTCGCATT
1 GCGATTTT-AGTTTCGCATT
*
473005 GCGAATTTAAGTTTC
1 GCG-ATTTTAGTTTC
473020 AGAAACTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 8 0.28
20 17 0.59
21 4 0.14
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCATT
Found at i:475161 original size:21 final size:20
Alignment explanation
Indices: 475142--475239 Score: 81
Period size: 21 Copynumber: 4.7 Consensus size: 20
475132 GATGCACCTA
* *
475142 TCATCATTCAAGAGGCACCT
1 TCATCGTTCAAGAGGCCCCT
*
475162 CCTATCGTTCAAGAGGCCCCT
1 TC-ATCGTTCAAGAGGCCCCT
* *
475183 CTCATC-ATCAAAGAAGCCCCT
1 -TCATCGTTC-AAGAGGCCCCT
*
475204 TCCACCGTTCAAGAGGCCCCCT
1 T-CATCGTTCAAGAGG-CCCCT
475226 ATCATCGTTCAAGA
1 -TCATCGTTCAAGA
475240 TGTCCCGTCT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
20 4 0.07
21 37 0.61
22 19 0.31
23 1 0.02
ACGTcount: A:0.27, C:0.36, G:0.15, T:0.22
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCCT
Found at i:475189 original size:42 final size:43
Alignment explanation
Indices: 475138--475239 Score: 120
Period size: 42 Copynumber: 2.4 Consensus size: 43
475128 GCCCGATGCA
* *
475138 CCTATCATCATTCAAGAGGCACC-TCCTATCGTTCAAGAGG-CC
1 CCTATCATCATTCAAGAAGCACCTTCC-ACCGTTCAAGAGGCCC
* *
475180 CCTCTCATCA-TCAAAGAAGCCCCTTCCACCGTTCAAGAGGCCC
1 CCTATCATCATTC-AAGAAGCACCTTCCACCGTTCAAGAGGCCC
*
475223 CCTATCATCGTTCAAGA
1 CCTATCATCATTCAAGA
475240 TGTCCCGTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
41 2 0.04
42 29 0.58
43 17 0.34
44 2 0.04
ACGTcount: A:0.26, C:0.36, G:0.15, T:0.23
Consensus pattern (43 bp):
CCTATCATCATTCAAGAAGCACCTTCCACCGTTCAAGAGGCCC
Found at i:476679 original size:14 final size:14
Alignment explanation
Indices: 476660--476696 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
476650 TTTTGATTAA
476660 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
476674 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
476688 TTTATTTGT
1 TTGATTTGT
476697 TTAATTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:476758 original size:80 final size:74
Alignment explanation
Indices: 476610--476762 Score: 207
Period size: 80 Copynumber: 2.0 Consensus size: 74
476600 TTTTACATTG
476610 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTGATTAATTGATTTGTAAAAGT
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTGATTAATTGATTTGTAAAAGT
476675 TGATTTGTA
66 TGATTTGTA
* * * * *
476684 AAAGTTTATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAG-A-T-TTATTTT--TTGATTAATTGATTTGT
476749 AAAAGTTGATTTGT
60 AAAAGTTGATTTGT
476763 TGCTTCTAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
74 16 0.24
75 14 0.21
76 1 0.01
77 1 0.01
78 6 0.09
80 30 0.44
ACGTcount: A:0.31, C:0.01, G:0.18, T:0.50
Consensus pattern (74 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTGATTAATTGATTTGTAAAAGT
TGATTTGTA
Found at i:476923 original size:20 final size:20
Alignment explanation
Indices: 476900--476942 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
476890 GATTTTCGGT
*
476900 TTGCAAATTTGACTTTCGCG
1 TTGCAAATTTAACTTTCGCG
*
476920 TTGCGAATTTAACTTTCGCG
1 TTGCAAATTTAACTTTCGCG
476940 TTG
1 TTG
476943 ATCGCGACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (20 bp):
TTGCAAATTTAACTTTCGCG
Found at i:477172 original size:39 final size:39
Alignment explanation
Indices: 477118--477204 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
477108 TCAAGTTGTA
*
477118 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
477157 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
477196 GATTTTGAT
1 GATTTTGAT
477205 GAGCATCAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:477522 original size:12 final size:12
Alignment explanation
Indices: 477505--477540 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
477495 TAGTGGAGCC
*
477505 GAAATTTATATT
1 GAAATTTAAATT
*
477517 GAAATTCAAATT
1 GAAATTTAAATT
477529 GAAATTTAAATT
1 GAAATTTAAATT
477541 CAAACTCCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (12 bp):
GAAATTTAAATT
Found at i:478027 original size:20 final size:20
Alignment explanation
Indices: 478004--478048 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
477994 AATAAGTGTT
*
478004 GCGATAGTCAAATTCGCAAC
1 GCGATAGCCAAATTCGCAAC
*
478024 GCGAAAGCCAAATTCGCAAC
1 GCGATAGCCAAATTCGCAAC
478044 GCGAT
1 GCGAT
478049 TTTCGATTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.27, G:0.22, T:0.16
Consensus pattern (20 bp):
GCGATAGCCAAATTCGCAAC
Found at i:480673 original size:24 final size:24
Alignment explanation
Indices: 480639--480692 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
480629 CCATCACATC
*
480639 ATCAAAATCCGTGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
* *
480663 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
480687 ATCAAA
1 ATCAAA
480693 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:481511 original size:23 final size:23
Alignment explanation
Indices: 481485--481553 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
481475 CACCACCGCT
*
481485 CGTATAATTACACCGAAGTGCCA
1 CGTAGAATTACACCGAAGTGCCA
* * * *
481508 CGTAGAATTGCATCGGAGTGCCG
1 CGTAGAATTACACCGAAGTGCCA
*
481531 CGTAGAATTACACCGTAGTGCCA
1 CGTAGAATTACACCGAAGTGCCA
481554 TATAATAATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
CGTAGAATTACACCGAAGTGCCA
Found at i:484031 original size:12 final size:12
Alignment explanation
Indices: 484010--484043 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
484000 GGTTGTGGGT
*
484010 TTTGAGATTGTG
1 TTTGATATTGTG
484022 TTTGATATTGTG
1 TTTGATATTGTG
*
484034 TTTGGTATTG
1 TTTGATATTG
484044 GAAATGCGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:484840 original size:20 final size:19
Alignment explanation
Indices: 484773--484882 Score: 98
Period size: 19 Copynumber: 5.6 Consensus size: 19
484763 AAACATTTGT
* * *
484773 GTTGCGAAATTAAATTCGC
1 GTTGCGAATTTGACTTCGC
* *
484792 GTTGCGAATTTGACTTTGT
1 GTTGCGAATTTGACTTCGC
484811 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACT-TCGC
* *
484831 GTTACGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTC-GC
484851 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGAC---TTCGC
484871 GTTGCGAATTTG
1 GTTGCGAATTTG
484883 GAAACTGGAT
Statistics
Matches: 73, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
18 2 0.03
19 35 0.48
20 29 0.40
21 7 0.10
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.39
Consensus pattern (19 bp):
GTTGCGAATTTGACTTCGC
Found at i:484871 original size:40 final size:39
Alignment explanation
Indices: 484768--484882 Score: 155
Period size: 39 Copynumber: 2.9 Consensus size: 39
484758 ACCCAAAACA
*
484768 TTTGTGTTGCGAAATTA-AATTCGCGTTGCGAATTTGAC
1 TTTGTGTTGCGAATTTACAATTCGCGTTGCGAATTTGAC
* *
484806 TTTGTGTTGCGAATTTGACTA-TCGCGTTACGAATTTGAC
1 TTTGTGTTGCGAATTT-ACAATTCGCGTTGCGAATTTGAC
484845 TTCTGTGTTGCG-ATTTACAGATTCGCGTTGCGAATTTG
1 TT-TGTGTTGCGAATTTACA-ATTCGCGTTGCGAATTTG
484883 GAAACTGGAT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
38 17 0.25
39 25 0.37
40 25 0.37
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (39 bp):
TTTGTGTTGCGAATTTACAATTCGCGTTGCGAATTTGAC
Found at i:488281 original size:2 final size:2
Alignment explanation
Indices: 488274--488322 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
488264 AGGATTAAAT
488274 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
488316 TA TA TA T
1 TA TA TA T
488323 TATCAATTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:488832 original size:3 final size:3
Alignment explanation
Indices: 488824--488852 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
488814 ATGATTAAAT
488824 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
488853 TAGTATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:489515 original size:60 final size:60
Alignment explanation
Indices: 489435--489556 Score: 172
Period size: 60 Copynumber: 2.0 Consensus size: 60
489425 TTTGGATGAA
* * * ** * *
489435 TTTATGGATGAAATTGGAATATTCACAAGTTTGGGGACTAATTTAGAAAGAGGGTCATAG
1 TTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGAATAATTTAGAAAGAGAGTCATAG
*
489495 TTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGAATAATTTAGAATGAGAGTCATAG
1 TTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGAATAATTTAGAAAGAGAGTCATAG
489555 TT
1 TT
489557 CGAATATATA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.33
Consensus pattern (60 bp):
TTTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGAATAATTTAGAAAGAGAGTCATAG
Found at i:502161 original size:31 final size:31
Alignment explanation
Indices: 502118--502178 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
502108 CATATATGAT
*
502118 TAAATTTCAACTCGAATAACTTCAATAAGAC
1 TAAAGTTCAACTCGAATAACTTCAATAAGAC
502149 TAAAGTTCAACTCGAATAACTTCAATAAGA
1 TAAAGTTCAACTCGAATAACTTCAATAAGA
502179 TTTAAAATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (31 bp):
TAAAGTTCAACTCGAATAACTTCAATAAGAC
Found at i:505984 original size:30 final size:30
Alignment explanation
Indices: 505949--506009 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
505939 CCGCTTATCA
505949 ACACACTTAATAGATATAATCACCCCATAG
1 ACACACTTAATAGATATAATCACCCCATAG
505979 ACACACTTAATAGATATAATCACCCCATAG
1 ACACACTTAATAGATATAATCACCCCATAG
506009 A
1 A
506010 GATCTGAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.23
Consensus pattern (30 bp):
ACACACTTAATAGATATAATCACCCCATAG
Found at i:508941 original size:2 final size:2
Alignment explanation
Indices: 508934--508958 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
508924 AAAGTTAAAT
508934 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
508959 TTAAATTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:511332 original size:104 final size:104
Alignment explanation
Indices: 511155--511353 Score: 301
Period size: 104 Copynumber: 1.9 Consensus size: 104
511145 GCATAGCATC
* *
511155 AAATGGAATATAGTAATGATTGATTAAAATCCACTTAGTCACCCTTAACTGGTTGGGTAATCCGC
1 AAATGGAATATAGTAATAATTGATTAAAATCCACTTAGTCACCCTTAACTGGTTGGGGAATCCGC
* *
511220 ACATCTTGTGTTAAACTAAAAGTAGATAAAATTAGCACA
66 ACACCTTGTGTTAAAATAAAAGTAGATAAAATTAGCACA
* * * * *
511259 AAATGGACTATAGTAATAATTGATTAAAATCCACTTAGTTAGCCTTAATTGGTTGGGCGATTCC-
1 AAATGGAATATAGTAATAATTGATTAAAATCCACTTAGTCACCCTTAACTGGTTGGG-GAATCCG
511323 CACACCTTGTGTTAAAATAAAAGTAGATAAA
65 CACACCTTGTGTTAAAATAAAAGTAGATAAA
511354 GTGAGTGGAA
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
104 81 0.95
105 4 0.05
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (104 bp):
AAATGGAATATAGTAATAATTGATTAAAATCCACTTAGTCACCCTTAACTGGTTGGGGAATCCGC
ACACCTTGTGTTAAAATAAAAGTAGATAAAATTAGCACA
Found at i:516569 original size:13 final size:14
Alignment explanation
Indices: 516543--516574 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
516533 TATTATATAT
516543 ACTTTATGAATTTA
1 ACTTTATGAATTTA
516557 ACTTTAT-AATTTA
1 ACTTTATGAATTTA
516570 A-TTTA
1 ACTTTA
516575 GTCAAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.22
13 7 0.39
14 7 0.39
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (14 bp):
ACTTTATGAATTTA
Found at i:522223 original size:14 final size:15
Alignment explanation
Indices: 522188--522220 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
522178 TCGAAATACA
522188 GAAATCAGATATCAG
1 GAAATCAGATATCAG
522203 GAAATCA-ATATTCAG
1 GAAATCAGATA-TCAG
522218 GAA
1 GAA
522221 TCATGTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (15 bp):
GAAATCAGATATCAG
Found at i:523012 original size:29 final size:29
Alignment explanation
Indices: 522980--523143 Score: 183
Period size: 29 Copynumber: 5.7 Consensus size: 29
522970 TTTTTAAAAT
*
522980 AATTACCAAAATAGCACCTTTTCGAATTA
1 AATTCCCAAAATAGCACCTTTTCGAATTA
* ** *
523009 AATT-CCAAAAAAGCAATTTTTCAAATTA
1 AATTCCCAAAATAGCACCTTTTCGAATTA
* *
523037 AATCCCCAAAATAGCACTTTTTTCCGAA-TA
1 AATTCCCAAAATAGCAC-CTTTT-CGAATTA
523067 AATTCCCAAAATAGCACTCTTTTCGAATT-
1 AATTCCCAAAATAGCAC-CTTTTCGAATTA
*
523096 AATTCCCAAAATAACACCTATTTCGAATT-
1 AATTCCCAAAATAGCACCT-TTTCGAATTA
*
523125 AATTCCCAAAATATCACCT
1 AATTCCCAAAATAGCACCT
523144 GGTCAACGGG
Statistics
Matches: 118, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
28 25 0.21
29 61 0.52
30 29 0.25
31 3 0.03
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.31
Consensus pattern (29 bp):
AATTCCCAAAATAGCACCTTTTCGAATTA
Found at i:523104 original size:59 final size:56
Alignment explanation
Indices: 522959--523137 Score: 182
Period size: 59 Copynumber: 3.1 Consensus size: 56
522949 TATTTTACAG
* * *
522959 AAATAGCACCATTTTT-AAAATAATTACCAAAATAGCACCTTTTCGAATTAAATT-CCA
1 AAATAGCA--ATTTTTCAAATTAATTCCCAAAATAGCACTTTTTCGAA-TAAATTCCCA
* *
523016 AAAAAGCAATTTTTCAAATTAAATCCCCAAAATAGCACTTTTTTCCGAATAAATTCCCA
1 AAATAGCAATTTTTCAAATT-AATTCCCAAAATAGCAC-TTTTT-CGAATAAATTCCCA
* * * * *
523075 AAATAGCACTCTTTTCGAATTAATTCCCAAAATAACACCTATTTCGAATTAATTCCCA
1 AAATAGCAAT-TTTTCAAATTAATTCCCAAAATAGCA-CTTTTTCGAATAAATTCCCA
523133 AAATA
1 AAATA
523138 TCACCTGGTC
Statistics
Matches: 103, Mismatches: 12, Indels: 13
0.80 0.09 0.10
Matches are distributed among these distances:
55 6 0.06
56 4 0.04
57 22 0.21
58 28 0.27
59 33 0.32
60 10 0.10
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.31
Consensus pattern (56 bp):
AAATAGCAATTTTTCAAATTAATTCCCAAAATAGCACTTTTTCGAATAAATTCCCA
Found at i:529390 original size:14 final size:15
Alignment explanation
Indices: 529355--529387 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
529345 TCGAAATACA
529355 GAAATCAGATATCAG
1 GAAATCAGATATCAG
529370 GAAATCA-ATATTCAG
1 GAAATCAGATA-TCAG
529385 GAA
1 GAA
529388 TCACGTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (15 bp):
GAAATCAGATATCAG
Found at i:530177 original size:29 final size:29
Alignment explanation
Indices: 530124--530272 Score: 159
Period size: 29 Copynumber: 5.1 Consensus size: 29
530114 CATTTTACAG
* *
530124 AAATAGCACCATTTTT-AAAAT-AATTACCA
1 AAATAGCACC-TTTTTCGAATTAAATT-CCA
530153 AAATAGCACCTTTTT-GAATTAAATTCTCA
1 AAATAGCACCTTTTTCGAATTAAATTC-CA
*
530182 AAAAAGCA-CTTTTTCGAATTAAATCTCCA
1 AAATAGCACCTTTTTCGAATTAAAT-TCCA
530211 AAATAGCACCTTTTTCCGAA-TAAATTCCCA
1 AAATAGCACCTTTTT-CGAATTAAATT-CCA
530241 AAATAGCA-CTTTTTCGAATT-AATTCCCA
1 AAATAGCACCTTTTTCGAATTAAATT-CCA
530269 AAAT
1 AAAT
530273 GTTACGGGTC
Statistics
Matches: 108, Mismatches: 4, Indels: 17
0.84 0.03 0.13
Matches are distributed among these distances:
28 31 0.29
29 49 0.45
30 24 0.22
31 4 0.04
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (29 bp):
AAATAGCACCTTTTTCGAATTAAATTCCA
Found at i:530250 original size:59 final size:57
Alignment explanation
Indices: 530150--530272 Score: 185
Period size: 59 Copynumber: 2.1 Consensus size: 57
530140 AAAATAATTA
*
530150 CCAAAATAGCACCTTTTTGAATTAAATTCTCAAAAAAGCACTTTTTCGAATTAAATC
1 CCAAAATAGCACCTTTTTGAATTAAATTCCCAAAAAAGCACTTTTTCGAATTAAATC
* *
530207 TCCAAAATAGCACCTTTTTCCGAA-TAAATTCCCAAAATAGCACTTTTTCGAATTAATTC
1 -CCAAAATAGCACCTTTTT--GAATTAAATTCCCAAAAAAGCACTTTTTCGAATTAAATC
530266 CCAAAAT
1 CCAAAAT
530273 GTTACGGGTC
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
58 25 0.42
59 32 0.53
60 3 0.05
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.33
Consensus pattern (57 bp):
CCAAAATAGCACCTTTTTGAATTAAATTCCCAAAAAAGCACTTTTTCGAATTAAATC
Found at i:530294 original size:13 final size:13
Alignment explanation
Indices: 530276--530300 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
530266 CCAAAATGTT
530276 ACGGGTCGGGTCA
1 ACGGGTCGGGTCA
530289 ACGGGTCGGGTC
1 ACGGGTCGGGTC
530301 GGGTCAAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.16
Consensus pattern (13 bp):
ACGGGTCGGGTCA
Found at i:532014 original size:58 final size:57
Alignment explanation
Indices: 531877--532014 Score: 152
Period size: 57 Copynumber: 2.4 Consensus size: 57
531867 TAAGTAATAG
* * ** ** *
531877 ATTATTAAAAGTTATAAAATGATTTTTTAGTTATAGTGTGTTGTTTTTTAAGTCCCC
1 ATTATTAAAAGTTACAAAATGATTCTCAAACTATAGTGTGTTGTTTGTTAAGTCCCC
* * **
531934 A-CAATAAAAGGTTACAAAATGATTCTCAAACTATAGTGTGTTGCTTTGTTGCGTCCCC
1 ATTATTAAAA-GTTACAAAATGATTCTCAAACTATAGTGTGTTG-TTTGTTAAGTCCCC
531992 ATTATTAAAAGTTACAAAATGAT
1 ATTATTAAAAGTTACAAAATGAT
532015 CACTCAACTA
Statistics
Matches: 65, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
56 6 0.09
57 28 0.43
58 25 0.38
59 6 0.09
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (57 bp):
ATTATTAAAAGTTACAAAATGATTCTCAAACTATAGTGTGTTGTTTGTTAAGTCCCC
Found at i:532024 original size:58 final size:57
Alignment explanation
Indices: 531908--532025 Score: 141
Period size: 58 Copynumber: 2.1 Consensus size: 57
531898 ATTTTTTAGT
* *
531908 TATAGTGTGTTGTTTTTTAAGTCCCCACAATAAAAGGTTACAAAATGATTCTCAAAC
1 TATAGTGTGTTGTTTGTTAAGTCCCCACAATAAAAGGTTACAAAATGATACTCAAAC
** * *
531965 TATAGTGTGTTGCTTTGTTGCGTCCCCATTATTAAAA-GTTACAAAATGATCACTC-AAC
1 TATAGTGTGTTG-TTTGTTAAGTCCCCA-CAATAAAAGGTTACAAAATGAT-ACTCAAAC
532023 TAT
1 TAT
532026 TTATATGTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
57 12 0.23
58 31 0.60
59 9 0.17
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (57 bp):
TATAGTGTGTTGTTTGTTAAGTCCCCACAATAAAAGGTTACAAAATGATACTCAAAC
Found at i:533572 original size:17 final size:17
Alignment explanation
Indices: 533550--533585 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
533540 AAAAACGACA
* *
533550 TGGTTAATTATATTCTT
1 TGGTTAACTATATACTT
533567 TGGTTAACTATATACTT
1 TGGTTAACTATATACTT
533584 TG
1 TG
533586 CGGTGTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.53
Consensus pattern (17 bp):
TGGTTAACTATATACTT
Found at i:533998 original size:20 final size:20
Alignment explanation
Indices: 533973--534013 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
533963 TCATTTCATT
533973 TAAAGGTCTTAACCTTTCAA
1 TAAAGGTCTTAACCTTTCAA
533993 TAAAGGTCTTAACCTTTCAA
1 TAAAGGTCTTAACCTTTCAA
534013 T
1 T
534014 CCTCTCCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TAAAGGTCTTAACCTTTCAA
Found at i:535309 original size:18 final size:18
Alignment explanation
Indices: 535286--535337 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
535276 TGGAAGTTAA
535286 AAAGGACTTCAAGAAAAG
1 AAAGGACTTCAAGAAAAG
*
535304 AAAGG-----AAGTAAA-
1 AAAGGACTTCAAGAAAAG
535316 AAAGGACTTCAAGAAAAG
1 AAAGGACTTCAAGAAAAG
535334 AAAG
1 AAAG
535338 CAAGCTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 12
0.65 0.05 0.30
Matches are distributed among these distances:
12 5 0.19
13 6 0.23
17 6 0.23
18 9 0.35
ACGTcount: A:0.60, C:0.08, G:0.23, T:0.10
Consensus pattern (18 bp):
AAAGGACTTCAAGAAAAG
Found at i:535311 original size:30 final size:30
Alignment explanation
Indices: 535277--535337 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
535267 CAAATGTGGT
*
535277 GGAAGTTAAAAAGGACTTCAAGAAAAGAAA
1 GGAAGTAAAAAAGGACTTCAAGAAAAGAAA
535307 GGAAGTAAAAAAGGACTTCAAGAAAAGAAA
1 GGAAGTAAAAAAGGACTTCAAGAAAAGAAA
535337 G
1 G
535338 CAAGCTCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.07, G:0.25, T:0.11
Consensus pattern (30 bp):
GGAAGTAAAAAAGGACTTCAAGAAAAGAAA
Found at i:539315 original size:20 final size:20
Alignment explanation
Indices: 539290--539330 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
539280 TCATTTCATT
539290 TAAAGGTCTTAACCTTTCAA
1 TAAAGGTCTTAACCTTTCAA
539310 TAAAGGTCTTAACCTTTCAA
1 TAAAGGTCTTAACCTTTCAA
539330 T
1 T
539331 CATCTCCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TAAAGGTCTTAACCTTTCAA
Found at i:541178 original size:18 final size:19
Alignment explanation
Indices: 541149--541184 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
541139 ATATATTAAA
*
541149 TTAAAAATTATAATAATAT
1 TTAAAAATTATAAAAATAT
541168 TTAAAAA-TATAAAAATA
1 TTAAAAATTATAAAAATA
541185 AAAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TTAAAAATTATAAAAATAT
Found at i:541242 original size:14 final size:16
Alignment explanation
Indices: 541217--541249 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
541207 TTCTAGAAAA
541217 AAATTAAAGTTTTT-T
1 AAATTAAAGTTTTTCT
541232 AAATT-AAGTTTTTCT
1 AAATTAAAGTTTTTCT
541247 AAA
1 AAA
541250 ATTATATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (16 bp):
AAATTAAAGTTTTTCT
Found at i:541253 original size:16 final size:15
Alignment explanation
Indices: 541216--541253 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
541206 TTTCTAGAAA
541216 AAAATTAAAGTTTTTT
1 AAAATT-AAGTTTTTT
541232 -AAATTAAGTTTTTCT
1 AAAATTAAGTTTTT-T
541247 AAAATTA
1 AAAATTA
541254 TATAGTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.40
15 6 0.30
16 6 0.30
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (15 bp):
AAAATTAAGTTTTTT
Found at i:543290 original size:14 final size:15
Alignment explanation
Indices: 543271--543300 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
543261 AAAAATTGAT
543271 TATATTATTTA-AAA
1 TATATTATTTATAAA
543285 TATATTATTTATAAA
1 TATATTATTTATAAA
543300 T
1 T
543301 GAATAGAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATTATTTATAAA
Found at i:558239 original size:27 final size:27
Alignment explanation
Indices: 558207--558294 Score: 158
Period size: 27 Copynumber: 3.3 Consensus size: 27
558197 AATTACAGAG
558207 ATGATTTGTTACCATTCCTATAGAGAT
1 ATGATTTGTTACCATTCCTATAGAGAT
*
558234 ATGATTTGTTATCATTCCTATAGAGAT
1 ATGATTTGTTACCATTCCTATAGAGAT
*
558261 ATGATTTGTTACTATTCCTATAGAGAT
1 ATGATTTGTTACCATTCCTATAGAGAT
558288 ATGATTT
1 ATGATTT
558295 TGTAAATAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (27 bp):
ATGATTTGTTACCATTCCTATAGAGAT
Found at i:562035 original size:27 final size:27
Alignment explanation
Indices: 561993--562060 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
561983 GTGTAGGAAT
*
561993 TATAGAG--ATGATTTGTTACCGTTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
562018 TATAGAGATATGATTTGTTACTATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
562045 TATAGATATATGATTT
1 TATAGAGATATGATTT
562061 TGTAAATAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 7 0.18
27 31 0.82
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.44
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:577834 original size:14 final size:14
Alignment explanation
Indices: 577806--577842 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
577796 GTATTCAGAA
577806 TTATAA-TAAAAGT
1 TTATAACTAAAAGT
*
577819 TTATAACTATAAGT
1 TTATAACTAAAAGT
577833 TTA-AACTAAA
1 TTATAACTAAA
577843 CATATAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (14 bp):
TTATAACTAAAAGT
Found at i:588718 original size:35 final size:35
Alignment explanation
Indices: 588586--588697 Score: 179
Period size: 35 Copynumber: 3.2 Consensus size: 35
588576 GTTGGTAGAA
* * *
588586 TAAGTTGAGAGGGGCATGGGACTCGAACCCAACGG
1 TAAGTAGAGAGGGGTATGGGACCCGAACCCAACGG
* *
588621 TAAGTAGAGAGGGGTATAGGACCCGAATCCAACGG
1 TAAGTAGAGAGGGGTATGGGACCCGAACCCAACGG
588656 TAAGTAGAGAGGGGTATGGGACCCGAACCCAACGG
1 TAAGTAGAGAGGGGTATGGGACCCGAACCCAACGG
588691 TAAGTAG
1 TAAGTAG
588698 GGATGAATAT
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 70 1.00
ACGTcount: A:0.32, C:0.18, G:0.36, T:0.14
Consensus pattern (35 bp):
TAAGTAGAGAGGGGTATGGGACCCGAACCCAACGG
Found at i:595806 original size:15 final size:15
Alignment explanation
Indices: 595782--595824 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
595772 ACATCATTAA
*
595782 ATTAATTTATAAAGT
1 ATTAAATTATAAAGT
595797 ATTAAATTATAAAGT
1 ATTAAATTATAAAGT
595812 ATTAAATATATAA
1 ATTAAAT-TATAA
595825 TTATAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 21 0.81
16 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (15 bp):
ATTAAATTATAAAGT
Found at i:599993 original size:17 final size:16
Alignment explanation
Indices: 599963--599999 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
599953 TTTTAATAAA
599963 AAATATTAAATTTAAT
1 AAATATTAAATTTAAT
*
599979 AAATGATTAATTTTAAT
1 AAAT-ATTAAATTTAAT
599996 AAAT
1 AAAT
600000 TCGTATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
AAATATTAAATTTAAT
Found at i:600203 original size:24 final size:25
Alignment explanation
Indices: 600167--600213 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
600157 TTATGTAATT
* **
600167 AAAAAATTAAATATTTAATTACAAC
1 AAAAAACTAAATATCAAATTACAAC
600192 AAAAAACT-AATATCAAATTACA
1 AAAAAACTAAATATCAAATTACA
600214 CCATTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.28
Consensus pattern (25 bp):
AAAAAACTAAATATCAAATTACAAC
Found at i:600319 original size:22 final size:20
Alignment explanation
Indices: 600293--600339 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 20
600283 AAATTATATA
600293 TTAGGAGAAGAGTTATAAAATT
1 TTAGGA-AA-AGTTATAAAATT
*
600315 TTAGGAAAATTTATAAAATT
1 TTAGGAAAAGTTATAAAATT
600335 TTAGG
1 TTAGG
600340 GAACAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 16 0.67
21 2 0.08
22 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.36
Consensus pattern (20 bp):
TTAGGAAAAGTTATAAAATT
Found at i:601475 original size:21 final size:21
Alignment explanation
Indices: 601451--601562 Score: 54
Period size: 21 Copynumber: 5.3 Consensus size: 21
601441 TTTAATATAT
601451 ATATTATATATATTAATTTTA
1 ATATTATATATATTAATTTTA
* * * *
601472 ATATTAATTTTAAAATAA-TTAA
1 ATATT-A-TATATATTAATTTTA
* * *
601494 ATATTA-ATTTTTTTAATATT-
1 ATATTATA-TATATTAATTTTA
*
601514 ATATTATAGATATTTAATTTT-
1 ATATTATATATA-TTAATTTTA
* *
601535 ATATCATATAAATT-ATTTTA
1 ATATTATATATATTAATTTTA
601555 TATATTAT
1 -ATATTAT
601563 TAAAATTTTA
Statistics
Matches: 64, Mismatches: 19, Indels: 16
0.65 0.19 0.16
Matches are distributed among these distances:
19 5 0.08
20 13 0.20
21 30 0.47
22 9 0.14
23 7 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (21 bp):
ATATTATATATATTAATTTTA
Found at i:601483 original size:59 final size:63
Alignment explanation
Indices: 601385--601544 Score: 178
Period size: 59 Copynumber: 2.6 Consensus size: 63
601375 TTATATTTAA
* *
601385 TTTT-ATATTATATT-T-GAT-TTTAATTTTAATATATTTTTTAAAA-AGTT-ATATT-A-TT
1 TTTTAATATTATATTATAGATATTTAATTTTAATATATATTTTAAAATAATTAATATTAATTT
*
601440 TTTTAATATATATATTATATATA-TTAATTTTAATAT-TAATTTTAAAATAATTAAATATTAATT
1 TTTTAATAT-TATATTATAGATATTTAATTTTAATATAT-ATTTTAAAATAATT-AATATTAATT
601503 T
63 T
601504 TTTTAATATTATATTATAGATATTTAATTTTATATCATATA
1 TTTTAATATTATATTATAGATATTTAATTTTA-AT-ATATA
601545 AATTATTTTA
Statistics
Matches: 86, Mismatches: 4, Indels: 19
0.79 0.04 0.17
Matches are distributed among these distances:
55 4 0.05
56 4 0.05
57 6 0.07
58 2 0.02
59 23 0.27
60 3 0.03
62 5 0.06
63 13 0.15
64 20 0.23
65 2 0.02
66 3 0.03
67 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (63 bp):
TTTTAATATTATATTATAGATATTTAATTTTAATATATATTTTAAAATAATTAATATTAATTT
Found at i:601562 original size:26 final size:24
Alignment explanation
Indices: 601494--601562 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 24
601484 AAATAATTAA
* *
601494 ATATTAATTTTTTTAATATTATAT
1 ATATAAATTATTTTAATATTATAT
* *
601518 -TATAGA-TA-TTTAATTTTATAT
1 ATATAAATTATTTTAATATTATAT
601539 CATATAAATTATTTTATATATTAT
1 -ATATAAATTATTTTA-ATATTAT
601563 TAAAATTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
21 12 0.35
22 1 0.03
23 9 0.26
24 2 0.06
25 4 0.12
26 6 0.18
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (24 bp):
ATATAAATTATTTTAATATTATAT
Found at i:601590 original size:20 final size:19
Alignment explanation
Indices: 601530--601591 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
601520 TAGATATTTA
*
601530 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
601549 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
601567 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
601587 ATTTT
1 ATTTT
601592 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:602805 original size:2 final size:2
Alignment explanation
Indices: 602800--602833 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
602790 TACGAAAATA
602800 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
602834 CAAATTTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:602947 original size:174 final size:179
Alignment explanation
Indices: 602655--603011 Score: 629
Period size: 174 Copynumber: 2.0 Consensus size: 179
602645 ATATCTTTAC
602655 TATCAAATTTTCAAATACCCTAAAAATATTAAAGATTCAAAATTTTTATTTTCTGTTGATTTTCT
1 TATCAAATTTTCAAATACCCTAAAAATATTAAAGATTCAAAATTTTTATTTTCTGTTGATTTTCT
602720 TAACCATCTAAACAAAAGAATATGAACCGAATATAAAATAAAATAATCATGATTCCACAAT-AAA
66 TAACCATCTAAACAAAAGAATATGAACCGAATATAAAATAAAATAATCATGATTCCACAATAAAA
602784 -A-ATATAT-ACGAAAATAATATATATATATATATATATATATATATATA
131 CATATATATGACGAAAATAATATATATATATAT-TATATATATATATATA
602831 TATCAAATTTTCAAATACCCT-AAAATATTAAAGATTCAAAA-TTTTATTTTCTGTTGATTTTCT
1 TATCAAATTTTCAAATACCCTAAAAATATTAAAGATTCAAAATTTTTATTTTCTGTTGATTTTCT
602894 TAACCATCTAAACAAAAGAATA-GAACCGAATATAAAATAAAATAATTCATGATTCCACAATAAA
66 TAACCATCTAAACAAAAGAATATGAACCGAATATAAAATAAAATAA-TCATGATTCCACAAT-AA
602958 AATCATATATATGACGAAAATAATATATATATATATTATATATATATATATA
129 AA-CATATATATGACGAAAATAATATATATATATATTATATATATATATATA
603010 TA
1 TA
603012 CAACGAAGAG
Statistics
Matches: 174, Mismatches: 0, Indels: 11
0.94 0.00 0.06
Matches are distributed among these distances:
173 23 0.13
174 59 0.34
175 20 0.11
176 24 0.14
178 1 0.01
179 24 0.14
180 23 0.13
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (179 bp):
TATCAAATTTTCAAATACCCTAAAAATATTAAAGATTCAAAATTTTTATTTTCTGTTGATTTTCT
TAACCATCTAAACAAAAGAATATGAACCGAATATAAAATAAAATAATCATGATTCCACAATAAAA
CATATATATGACGAAAATAATATATATATATATTATATATATATATATA
Found at i:602985 original size:2 final size:2
Alignment explanation
Indices: 602980--603011 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
602970 GACGAAAATA
602980 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
603012 CAACGAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:603000 original size:15 final size:15
Alignment explanation
Indices: 602980--603008 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
602970 GACGAAAATA
602980 ATATATATATATATT
1 ATATATATATATATT
602995 ATATATATATATAT
1 ATATATATATATAT
603009 ATACAACGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:614071 original size:23 final size:23
Alignment explanation
Indices: 614045--614092 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
614035 ATAAAGTACA
*
614045 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
614068 ATAATTTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
614091 AT
1 AT
614093 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:614507 original size:23 final size:23
Alignment explanation
Indices: 614481--614543 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
614471 CAATAACCAT
614481 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
614504 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
614527 TACCTATTACATCATAT
1 TACCTATTACATTATAT
614544 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:614887 original size:428 final size:426
Alignment explanation
Indices: 614204--615068 Score: 1646
Period size: 428 Copynumber: 2.0 Consensus size: 426
614194 GGATCGATAC
614204 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
614269 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
66 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
614334 GTAACGAAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
131 GTAACGAAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
*
614399 AAGATAACCTTAAATTAATGTTTTTCACAGTGAAAAAAGTATGGACACTTTTATAAAAGGATAGA
196 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAGGATAGA
614464 CACTTTAC-A-ATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGC
261 CACTTTACAATATAACCATTACCTATTACA-T-TATAAACGATACCTATTACATTATATAAGGGC
614527 TACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCG
324 TACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCG
614592 ATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
389 ATAC-TTTTTTAAAACTTATGTAATTTATGTTTCAA-TTT
614632 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
614697 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
66 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
*
614762 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC-A
131 GTAACGAAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
614826 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
196 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTAT-AAAAGGATAG
614891 ACACTTTACAATATAACCATTACCTATTACATTATAAACGATACCTATTACATTATATAAGGGCT
260 ACACTTTACAATATAACCATTACCTATTACATTATAAACGATACCTATTACATTATATAAGGGCT
614956 ACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGA
325 ACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGA
615021 TACTTTTTTAAAACTTATGTAATTTATGTTTCAATTT
390 TACTTTTTTAAAACTTATGTAATTTATGTTTCAATTT
615058 TTTAACAGTGT
1 TTTAACAGTGT
615069 ACTGCGAATT
Statistics
Matches: 432, Mismatches: 2, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
426 14 0.03
427 85 0.20
428 312 0.72
429 2 0.00
430 19 0.04
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (426 bp):
TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATATACC
GTAACGAAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAGGATAGA
CACTTTACAATATAACCATTACCTATTACATTATAAACGATACCTATTACATTATATAAGGGCTA
CCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGAT
ACTTTTTTAAAACTTATGTAATTTATGTTTCAATTT
Found at i:614926 original size:21 final size:20
Alignment explanation
Indices: 614896--614947 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
614886 GATAGACACT
*
614896 TTACAATATAACCATTACCTA
1 TTACATTATAACCA-TACCTA
*
614917 TTACATTATAAACGATACCTA
1 TTACATTAT-AACCATACCTA
614938 TTACATTATA
1 TTACATTATA
614948 TAAGGGCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.82
22 4 0.14
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:614958 original size:23 final size:22
Alignment explanation
Indices: 614901--614971 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 22
614891 ACACTTTACA
*
614901 ATATAACCATTACCTATTACATT
1 ATATAACGA-TACCTATTACATT
614924 ATA-AACGATACCTATTACATT
1 ATATAACGATACCTATTACATT
* * *
614945 ATATAAGGGCTACCTATTACATC
1 ATATAA-CGATACCTATTACATT
614968 ATAT
1 ATAT
614972 GTTTACCTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.38
22 6 0.14
23 20 0.48
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.35
Consensus pattern (22 bp):
ATATAACGATACCTATTACATT
Found at i:618053 original size:191 final size:184
Alignment explanation
Indices: 617525--618203 Score: 1223
Period size: 184 Copynumber: 3.7 Consensus size: 184
617515 TTTTAAATGG
*
617525 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
617590 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
* *
617655 GATGTGTAAAATGTCGACACTTTTTTAAATTATATCGACACAATTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
617709 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
617774 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
617839 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
617893 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGGTTGTAGACCTAT
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCG--ATA-----TAGGTTGTAGACCTAT
*
617958 TCGCGCATAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCGATTACATTATAATTAT
59 TCGCGCATAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTAT
*
618023 GGGTTCCGATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
124 GGGTTCCGATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
618084 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
**
618149 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
618204 ATGTTGAAAG
Statistics
Matches: 479, Mismatches: 9, Indels: 14
0.95 0.02 0.03
Matches are distributed among these distances:
184 294 0.61
186 3 0.01
189 3 0.01
191 179 0.37
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
Found at i:620337 original size:32 final size:32
Alignment explanation
Indices: 620301--620366 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
620291 CATCTTAATA
*
620301 TCACCCCTTAACACCGAAACTTCTTTCACCAC
1 TCACCCCTCAACACCGAAACTTCTTTCACCAC
***
620333 TCACCCCTCAACACCTCTACTTCTTTCACCAC
1 TCACCCCTCAACACCGAAACTTCTTTCACCAC
620365 TC
1 TC
620367 CATCTATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.24, C:0.47, G:0.02, T:0.27
Consensus pattern (32 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCAC
Found at i:622515 original size:24 final size:24
Alignment explanation
Indices: 622478--622530 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
622468 CCGTTCTATC
622478 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
622502 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
622526 TATTT
1 TATTT
622531 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:622720 original size:20 final size:19
Alignment explanation
Indices: 622674--622720 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
622664 TCCGGTATCA
*
622674 TTTTACCGTTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
622693 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
622714 TTTTACC
1 TTTTACC
622721 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:622884 original size:20 final size:20
Alignment explanation
Indices: 622836--622885 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
622826 TCGACACTTT
*
622836 TAATTTTACCGGTTTTATCA
1 TAATTTTACCGGTTTGATCA
*
622856 T-TTTGTTACCGGTTTGATCA
1 TAATT-TTACCGGTTTGATCA
622876 TAATTTTACC
1 TAATTTTACC
622886 TGGTATATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 2 0.08
20 21 0.84
21 2 0.08
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.50
Consensus pattern (20 bp):
TAATTTTACCGGTTTGATCA
Found at i:623349 original size:226 final size:224
Alignment explanation
Indices: 622951--623396 Score: 784
Period size: 226 Copynumber: 2.0 Consensus size: 224
622941 TTAAAACTGC
*
622951 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTTATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
623016 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* *
623081 TTAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAA
131 TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTC-ACAGTGAAATAA
*
623146 GTATGGACACTTTTATAAAAATGATATACT
195 GTATGGACACTTTTATAAAAAGGATATACT
*
623176 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
623241 ATTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
65 ATTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
* *
623306 TTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTCACAGTGAAATAA
130 TTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAA
623371 GTATGGACACTTTTATAAAAAGGATA
195 GTATGGACACTTTTATAAAAAGGATA
623397 GATAATTTAC
Statistics
Matches: 210, Mismatches: 10, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
225 41 0.20
226 169 0.80
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (224 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
TATGGACACTTTTATAAAAAGGATATACT
Found at i:629706 original size:16 final size:16
Alignment explanation
Indices: 629685--629729 Score: 90
Period size: 16 Copynumber: 2.8 Consensus size: 16
629675 TCAGAGCCTC
629685 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
629701 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
629717 TGAATCATTCAGC
1 TGAATCATTCAGC
629730 GCTTAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Done.