Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008654.1 Hibiscus syriacus cultivar Beakdansim tig00111648_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: 3533819
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 18
Found at i:633320 original size:26 final size:26
Alignment explanation
Indices: 633264--633321 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
633254 AAAGCTAGTT
633264 TTAAAAAAAGAAAAAATAAAAAAGGA
1 TTAAAAAAAGAAAAAATAAAAAAGGA
* * *
633290 ATAAAACAAGAAGAAAATAAAAGA-GA
1 TTAAAAAAAGAA-AAAATAAAAAAGGA
633316 TTAAAA
1 TTAAAA
633322 TAATATAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.74, C:0.02, G:0.12, T:0.12
Consensus pattern (26 bp):
TTAAAAAAAGAAAAAATAAAAAAGGA
Found at i:633862 original size:3 final size:3
Alignment explanation
Indices: 633856--633894 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
633846 ACTAAGTAAC
633856 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
633895 TAAAAAAAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:633882 original size:17 final size:17
Alignment explanation
Indices: 633860--633897 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
633850 AGTAACAATA
633860 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
633877 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
633894 ATAA
1 ATAA
633898 AAAAAGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:633882 original size:20 final size:20
Alignment explanation
Indices: 633857--633894 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
633847 CTAAGTAACA
633857 ATAATAATAATAATAATAAT
1 ATAATAATAATAATAATAAT
633877 ATAATAATAATAATAATA
1 ATAATAATAATAATAATA
633895 TAAAAAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
ATAATAATAATAATAATAAT
Found at i:633914 original size:26 final size:25
Alignment explanation
Indices: 633840--633924 Score: 64
Period size: 26 Copynumber: 3.1 Consensus size: 25
633830 CTGAAAAAAA
*
633840 AAAAAAACTAAGTAACAATAATAATAAT
1 AAAAAAA-TAA-TAAAAATAATAAT-AT
*
633868 AATAATAATATAATAATAATAATAATAT
1 AA-AA-AA-ATAATAAAAATAATAATAT
*
633896 AAAAAAAGTATTAAAAAT-ATATATAT
1 AAAAAAA-TAATAAAAATAATA-ATAT
633922 AAA
1 AAA
633925 TTTTTTCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
25 4 0.08
26 17 0.35
27 2 0.04
28 6 0.12
29 14 0.29
30 5 0.10
31 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (25 bp):
AAAAAAATAATAAAAATAATAATAT
Found at i:633977 original size:38 final size:37
Alignment explanation
Indices: 633927--634113 Score: 297
Period size: 38 Copynumber: 4.9 Consensus size: 37
633917 TATATAAATT
633927 TTTTCAAAATGTTTTCAAAAACTATATATTATATAAG
1 TTTTCAAAATGTTTTCAAAAACTATATATTATATAAG
633964 TTTTCAAAGATGTTTTCAAAAAACTATATATTATATAAG
1 TTTTCAAA-ATGTTTTC-AAAAACTATATATTATATAAG
634003 TTTTCAAAAATGTTTTCAAAAACTATATATTATATAAG
1 TTTTC-AAAATGTTTTCAAAAACTATATATTATATAAG
634041 TTTTCAAAAGTGTTTT-AAAAACTATATATTATATACA-
1 TTTTCAAAA-TGTTTTCAAAAACTATATATTATATA-AG
*
634078 TTTTCAAAATGCTTTTTAAAAACTATATATTATATA
1 TTTTCAAAATG-TTTTCAAAAACTATATATTATATA
634114 CATATTTTCA
Statistics
Matches: 143, Mismatches: 0, Indels: 13
0.92 0.00 0.08
Matches are distributed among these distances:
36 2 0.01
37 44 0.31
38 60 0.42
39 34 0.24
40 3 0.02
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (37 bp):
TTTTCAAAATGTTTTCAAAAACTATATATTATATAAG
Found at i:634116 original size:38 final size:37
Alignment explanation
Indices: 633906--634113 Score: 282
Period size: 38 Copynumber: 5.6 Consensus size: 37
633896 AAAAAAAGTA
*
633906 TTAAAAA-TATATA-TATA-AATTTTTTCAAAATGTTT
1 TTAAAAACTATATATTATATAA-GTTTTCAAAATGTTT
*
633941 TCAAAAACTATATATTATATAAGTTTTCAAAGATGTTT
1 TTAAAAACTATATATTATATAAGTTTTCAAA-ATGTTT
*
633979 TCAAAAAACTATATATTATATAAGTTTTCAAAAATGTTT
1 T-TAAAAACTATATATTATATAAGTTTTC-AAAATGTTT
*
634018 TCAAAAACTATATATTATATAAGTTTTCAAAA-GTGTT
1 TTAAAAACTATATATTATATAAGTTTTCAAAATGT-TT
634055 TTAAAAACTATATATTATATACA-TTTTCAAAATGCTTT
1 TTAAAAACTATATATTATATA-AGTTTTCAAAATG-TTT
634093 TTAAAAACTATATATTATATA
1 TTAAAAACTATATATTATATA
634114 CATATTTTCA
Statistics
Matches: 158, Mismatches: 5, Indels: 17
0.88 0.03 0.09
Matches are distributed among these distances:
35 6 0.04
36 8 0.05
37 47 0.30
38 60 0.38
39 34 0.22
40 3 0.02
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (37 bp):
TTAAAAACTATATATTATATAAGTTTTCAAAATGTTT
Found at i:634124 original size:77 final size:74
Alignment explanation
Indices: 633906--634113 Score: 300
Period size: 75 Copynumber: 2.8 Consensus size: 74
633896 AAAAAAAGTA
633906 TTAAAAA-TATATA-TATA-AATTTTTTCAAAATGTTTTCAAAAACTATATATTATATAAGTTTT
1 TTAAAAACTATATATTATATAA--TTTTCAAAATGTTTTCAAAAACTATATATTATATAAGTTTT
633968 C-AAAGATGTT
64 CAAAAGATGTT
633978 TTCAAAAAACTATATATTATATAAGTTTTCAAAAATGTTTTCAAAAACTATATATTATATAAGTT
1 TT--AAAAACTATATATTATATAA-TTTTC-AAAATGTTTTCAAAAACTATATATTATATAAGTT
634043 TTCAAAAG-TGTT
62 TTCAAAAGATGTT
*
634055 TTAAAAACTATATATTATATACATTTTCAAAATGCTTTTTAAAAACTATATATTATATA
1 TTAAAAACTATATATTATATA-ATTTTCAAAATG-TTTTCAAAAACTATATATTATATA
634114 CATATTTTCA
Statistics
Matches: 125, Mismatches: 2, Indels: 15
0.88 0.01 0.11
Matches are distributed among these distances:
72 2 0.02
74 11 0.09
75 53 0.42
76 10 0.08
77 45 0.36
78 4 0.03
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (74 bp):
TTAAAAACTATATATTATATAATTTTCAAAATGTTTTCAAAAACTATATATTATATAAGTTTTCA
AAAGATGTT
Found at i:634143 original size:77 final size:73
Alignment explanation
Indices: 633927--634154 Score: 269
Period size: 77 Copynumber: 3.0 Consensus size: 73
633917 TATATAAATT
* *
633927 TTTTCAAAATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAGATGTTTTCAAAAAACTATA
1 TTTTCAAAATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAAATG-TTT--ACAAACTATA
633992 TATTATATAAG
63 TATTATATAAG
* *
634003 TTTTCAAAAATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAAGTGTTTTAAAAACTATAT
1 TTTTC-AAAATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAAATG-TTTACAAACTATAT
634068 ATTATATACA-
64 ATTATATA-AG
* * * *
634078 TTTTCAAAATGCTTTTTAAAAACTATATATTATATACATATTTTCAAAAACCGTTTGCAAACTAT
1 TTTTCAAAATG-TTTTCAAAAACTATATATTATATA-A-GTTTTCAAAAA-TGTTTACAAACTAT
634143 AATATATATATA
62 -ATAT-TATATA
634155 TATATATATA
Statistics
Matches: 136, Mismatches: 8, Indels: 13
0.87 0.05 0.08
Matches are distributed among these distances:
74 6 0.04
75 47 0.35
76 7 0.05
77 65 0.48
78 5 0.04
79 6 0.04
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.42
Consensus pattern (73 bp):
TTTTCAAAATGTTTTCAAAAACTATATATTATATAAGTTTTCAAAAATGTTTACAAACTATATAT
TATATAAG
Found at i:634174 original size:5 final size:5
Alignment explanation
Indices: 634164--634189 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
634154 ATATATATAT
634164 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
634190 AATGGACGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:635066 original size:21 final size:21
Alignment explanation
Indices: 635005--635070 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
634995 AGAAACTATC
635005 TCAAGAGAGACAAAACTTTGTT
1 TCAAGAGAGACAAAA-TTTGTT
*
635027 TCAAG-G-G---AAA-TTGTC
1 TCAAGAGAGACAAAATTTGTT
635042 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
635063 TCAAGAGA
1 TCAAGAGA
635071 AACTATCTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
15 9 0.25
16 1 0.03
17 4 0.11
20 4 0.11
21 13 0.36
22 5 0.14
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:635080 original size:36 final size:37
Alignment explanation
Indices: 634986--635113 Score: 195
Period size: 37 Copynumber: 3.5 Consensus size: 37
634976 CAAAGATTGG
634986 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
* * *
635023 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
635059 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
* * *
635096 AGTTCCAAAAGAAACTAT
1 TGTTTCAAGAGAAACTAT
635114 GAGCTATGCT
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
36 33 0.41
37 48 0.59
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
Found at i:635429 original size:374 final size:374
Alignment explanation
Indices: 634740--635487 Score: 1408
Period size: 374 Copynumber: 2.0 Consensus size: 374
634730 TTCTTGCCTC
634740 GAGCTATGCTGTAAATGATGTGCCTTTGATCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGC
1 GAGCTATGCTGTAAATGATGTGCCTTTGATCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGC
* * *
634805 AGATAGCTCTTCTCGACTTAAGCTATGATGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
66 AGATAACCCTTCTCGACTTAAGCTATGATGCAAATGATGTGCCTTGGAGCTAAGCGTAGTCGAAC
634870 TCGAAGGTCTTGGTGTTCAAGAGAAACATTTTCAAAGGTCTTTTTTTTCTATTTCAAGAGAAACT
131 TCGAAGGTCTTGGTGTTCAAGAGAAACATTTTCAAAGGTCTTTTTTTTCTATTTCAAGAGAAACT
*
634935 GACTCAAGGGAGGAAAAATTTTGTTTCAAGAGAAGCATATTCAAAGATTGGTGTTTCAAGAGAAA
196 AACTCAAGGGAGGAAAAATTTTGTTTCAAGAGAAGCATATTCAAAGATTGGTGTTTCAAGAGAAA
* *
635000 CTATCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTGTTTC
261 CTATCTCAAGAGAGACAAAACTTTGTCTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTC
*
635065 AAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTAT
326 AAGAGAAACTATCTCAAGAGAGACAAAACTTAGTCCCAAAAGAAACTAT
635114 GAGCTATGCTGTAAATGATGTGCCTTTGATCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGC
1 GAGCTATGCTGTAAATGATGTGCCTTTGATCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGC
635179 AGATAACCCTTCTCGACTTAAGCTATGATGCAAATGATGTGCCTTGGAGCTAAGCGTAGTCGAAC
66 AGATAACCCTTCTCGACTTAAGCTATGATGCAAATGATGTGCCTTGGAGCTAAGCGTAGTCGAAC
635244 TCGAAGGTCTTGGTGTTTCAAGAGAAACATTTTCAAAGGT-TTTTTTTTCTATTTCAAGAGAAAC
131 TCGAAGGTCTTGGTG-TTCAAGAGAAACATTTTCAAAGGTCTTTTTTTTCTATTTCAAGAGAAAC
635308 TAACTCAAGGGAGGAAAAATTTTGTTTCAAGAGAAGCATATTCAAAGATTGGTGTTTCAAGAGAA
195 TAACTCAAGGGAGGAAAAATTTTGTTTCAAGAGAAGCATATTCAAAGATTGGTGTTTCAAGAGAA
635373 ACTATCTCAAGAGAGACAAAACTTTGTCTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTT
260 ACTATCTCAAGAGAGACAAAACTTTGTCTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTT
*
635438 CAATAGAAACTATCTCAAGAGAGACAAAACTTAGTCCCAAAAGAAACTAT
325 CAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTCCCAAAAGAAACTAT
635488 CTCAAGGGAG
Statistics
Matches: 365, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
374 341 0.93
375 24 0.07
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (374 bp):
GAGCTATGCTGTAAATGATGTGCCTTTGATCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGC
AGATAACCCTTCTCGACTTAAGCTATGATGCAAATGATGTGCCTTGGAGCTAAGCGTAGTCGAAC
TCGAAGGTCTTGGTGTTCAAGAGAAACATTTTCAAAGGTCTTTTTTTTCTATTTCAAGAGAAACT
AACTCAAGGGAGGAAAAATTTTGTTTCAAGAGAAGCATATTCAAAGATTGGTGTTTCAAGAGAAA
CTATCTCAAGAGAGACAAAACTTTGTCTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTC
AAGAGAAACTATCTCAAGAGAGACAAAACTTAGTCCCAAAAGAAACTAT
Found at i:635447 original size:36 final size:36
Alignment explanation
Indices: 635360--635864 Score: 436
Period size: 36 Copynumber: 14.1 Consensus size: 36
635350 CAAAGATTGG
635360 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TT
* * *
635397 TGTCTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
*
635433 TGTTTCAATAGAAACTATCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TT
* ** * * *
635470 AGTCCCAAAAGAAACTATCTCAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
* *
635506 TATTTCAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TATCTCAAGAGAGACAAAATT
*
635535 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
* *
635571 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
*
635607 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGACAAAATT
1 TGTTTCAAGAGAAACTATCTC-A-AGAG----AGACAAAATT
* *
635649 TGTTTCAAGAGAAACTATCTCAAGAAAGACAAAACT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
* * * * *
635685 TATTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTT-CAAGAGAAACTATCTCAAGAGAGACAAAATT
* *
635722 TGTTT-AATGTA-AAACATAT-TC-----A-A-ATATTT
1 TGTTTCAA-G-AGAAAC-TATCTCAAGAGAGACAAAATT
* * * *
635751 TGTTTCAAGGGAAATTGTCTCAAGAGAGATAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
* * * * *
635787 TGTCTCAAGGGAAACTGTCTCAAGATAGACAAAGTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
635823 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA-TT
635860 TGTTT
1 TGTTT
635865 TGAGTAAATT
Statistics
Matches: 380, Mismatches: 55, Indels: 66
0.76 0.11 0.13
Matches are distributed among these distances:
28 5 0.01
29 31 0.08
30 5 0.01
31 2 0.01
32 2 0.01
33 2 0.01
34 1 0.00
35 5 0.01
36 185 0.49
37 104 0.27
38 4 0.01
40 3 0.01
41 1 0.00
42 30 0.08
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
Found at i:635607 original size:174 final size:177
Alignment explanation
Indices: 635302--635639 Score: 542
Period size: 174 Copynumber: 1.9 Consensus size: 177
635292 CTATTTCAAG
* *
635302 AGAAACTAACTCAAGGGAGGAAAAATTTTGTTTCAAGAGAAGCATATTCAAAGATTGGTGTTTCA
1 AGAAACTAACTCAAGGGAGGAAAAATTTTATTTCAAGAGAAACATATTCAAAGATTGGTGTTTCA
635367 AGAGAAACTATCTCAAGAGAGACAAAACTTTGTCTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
66 AGAGAAACTATCTCAAGAGAGACAAAACTTTGTCTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
*
635432 TTGTTTCAATAGAAACTATCTCAAGAGAGACAAAACTTAGTCCCAAA
131 TTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTCCCAAA
* * *
635479 AGAAACTATCTCAAGGGA-GACGAAA-TTTATTTCAAG-GAAAACATATTCAAAGATT-TTGTTT
1 AGAAACTAACTCAAGGGAGGA-AAAATTTTATTTCAAGAG-AAACATATTCAAAGATTGGTGTTT
* *
635540 CAAGGGAAACTATCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
64 CAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTCTCAAGGGAAACTGTCTCAAGAGAGACAAA
*
635604 ATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
129 ATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAA
635640 GACAAAATTT
Statistics
Matches: 150, Mismatches: 9, Indels: 7
0.90 0.05 0.04
Matches are distributed among these distances:
174 68 0.45
175 34 0.23
176 28 0.19
177 20 0.13
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.24
Consensus pattern (177 bp):
AGAAACTAACTCAAGGGAGGAAAAATTTTATTTCAAGAGAAACATATTCAAAGATTGGTGTTTCA
AGAGAAACTATCTCAAGAGAGACAAAACTTTGTCTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
TTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTCCCAAA
Found at i:635616 original size:21 final size:21
Alignment explanation
Indices: 635554--635618 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
635544 GGAAACTATC
635554 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* *
635575 TCAAG-G-G---AAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
635590 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
635611 TCAAGAGA
1 TCAAGAGA
635619 AACTGTCTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 8 0.24
16 4 0.12
17 1 0.03
19 1 0.03
20 4 0.12
21 16 0.47
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.25
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:635648 original size:42 final size:42
Alignment explanation
Indices: 635561--635681 Score: 173
Period size: 42 Copynumber: 3.0 Consensus size: 42
635551 ATCTCAAGAG
*
635561 AGACAAAATTTGTTTCAAGGGAAACTGTCTC-A-AGAG----
1 AGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
635597 AGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
1 AGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
* *
635639 AGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAAAGACAA
1 AGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
635681 A
1 A
635682 ACTTATTTCC
Statistics
Matches: 76, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
36 30 0.39
37 1 0.01
38 4 0.05
42 41 0.54
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.22
Consensus pattern (42 bp):
AGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
Found at i:635665 original size:216 final size:216
Alignment explanation
Indices: 635360--635855 Score: 754
Period size: 216 Copynumber: 2.3 Consensus size: 216
635350 CAAAGATTGG
* * * *
635360 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTCTCAAGGGAAACTGTCTC-A-AGAG
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAG
* *
635423 ----AGACAAAATTTGTTTCAATAGAAACTATCTCAAGAGAGACAAAACTTAGTCCCAAAAGAAA
65 ACAAAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAAAGACAAAACTTAGTCCCAAAAGAAA
635484 CTATCTCAAGGGAGACGAAATTTATTTCAA-GGAAAACATATTCAAAGATTTTGTTTCAAGGGAA
130 CTATCTCAAGGGAGACGAAATTTATTT-AATGGAAAACATATTCAAAGATTTTGTTTCAAGGGAA
635548 ACTATCTCAAGAGAGACAAAATT
194 ACTATCTCAAGAGAGACAAAATT
635571 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
* *
635636 CAAAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAAAGACAAAACTTATTTCCAAAAGAAAC
66 CAAAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAAAGACAAAACTTAGTCCCAAAAGAAAC
* * * * *
635701 TGTCTCAAGGGAGACGAAATTTGTTTAATGTAAAACATATTCAAATATTTTGTTTCAAGGGAAAT
131 TATCTCAAGGGAGACGAAATTTATTTAATGGAAAACATATTCAAAGATTTTGTTTCAAGGGAAAC
* *
635766 TGTCTCAAGAGAGATAAAATT
196 TATCTCAAGAGAGACAAAATT
* * * *
635787 TGTCTCAAGGGAAACTGTCTCAAGATAGACAAAGTTTGTTTCAAGAGAAACTATCTCAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
635852 CAAA
66 CAAA
635856 ACTTTGTTTT
Statistics
Matches: 259, Mismatches: 19, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
210 21 0.08
211 33 0.13
212 4 0.02
215 2 0.01
216 199 0.77
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.26
Consensus pattern (216 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
CAAAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAAAGACAAAACTTAGTCCCAAAAGAAAC
TATCTCAAGGGAGACGAAATTTATTTAATGGAAAACATATTCAAAGATTTTGTTTCAAGGGAAAC
TATCTCAAGAGAGACAAAATT
Found at i:635773 original size:15 final size:15
Alignment explanation
Indices: 635750--635810 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 15
635740 TTCAAATATT
*
635750 TTGTTTCAAGGGAAA
1 TTGTCTCAAGGGAAA
635765 TTGTCTCAAGAGAGATAAAA
1 TTGTCTCAAG-G-G---AAA
635785 TTTGTCTCAAGGGAAA
1 -TTGTCTCAAGGGAAA
*
635801 CTGTCTCAAG
1 TTGTCTCAAG
635811 ATAGACAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
15 18 0.47
16 4 0.11
17 1 0.03
19 1 0.03
20 4 0.11
21 10 0.26
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (15 bp):
TTGTCTCAAGGGAAA
Found at i:637228 original size:95 final size:95
Alignment explanation
Indices: 637107--637292 Score: 286
Period size: 95 Copynumber: 2.0 Consensus size: 95
637097 TTATATAGGT
* *
637107 ATTATAATCACCTTTATCATGCTAGCTGAATAC-TATCCATAAAG-CTGGGGCGTTTAACCAATT
1 ATTATAATCACCTTTATCAGGCTAGCTGAAT-CTTATCCATAAAGTC-AGGGCGTTTAACCAATT
*
637170 GCTCTAGAGGAACAACTCAAGCTTTATTGTAC
64 ACTCTAGAGGAACAACTCAAGCTTTATTGTAC
*
637202 ATTATAATCACCTTTATCAGGCTAGCTGAATCTTATTCATAAAGTCAGGGCGTTTAACCAATTAC
1 ATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTCAGGGCGTTTAACCAATTAC
* *
637267 TTTAGAGGGACAACTCAAGCTTTATT
66 TCTAGAGGAACAACTCAAGCTTTATT
637293 AAGTTTGTTA
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
94 1 0.01
95 81 0.98
96 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33
Consensus pattern (95 bp):
ATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTCAGGGCGTTTAACCAATTAC
TCTAGAGGAACAACTCAAGCTTTATTGTAC
Found at i:646599 original size:16 final size:16
Alignment explanation
Indices: 646578--646620 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
646568 CTTACAAAAA
*
646578 GATAAAAGTAAGTAAC
1 GATAAAAATAAGTAAC
646594 GATAAAAATAAGTAAC
1 GATAAAAATAAGTAAC
*
646610 AATAAAAATAA
1 GATAAAAATAA
646621 TAATAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.65, C:0.05, G:0.12, T:0.19
Consensus pattern (16 bp):
GATAAAAATAAGTAAC
Found at i:646629 original size:16 final size:16
Alignment explanation
Indices: 646574--646631 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
646564 GGCGCTTACA
*
646574 AAAAGATAAAAGTAAGT
1 AAAA-ATAAAAATAAGT
**
646591 AACGATAAAAATAAGT
1 AAAAATAAAAATAAGT
*
646607 AACAATAAAAATAA-T
1 AAAAATAAAAATAAGT
646622 AATAAATAAA
1 AA-AAATAAA
646632 TAAATATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 3 0.09
16 30 0.86
17 2 0.06
ACGTcount: A:0.69, C:0.03, G:0.09, T:0.19
Consensus pattern (16 bp):
AAAAATAAAAATAAGT
Found at i:646630 original size:26 final size:25
Alignment explanation
Indices: 646595--646643 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
646585 GTAAGTAACG
*
646595 ATAAAAATAAGTAACA-ATAAAAATA
1 ATAAAAATAAATAA-ATATAAAAATA
646620 ATAATAAATAAATAAATATAAAAA
1 ATAA-AAATAAATAAATATAAAAA
646644 GTATTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (25 bp):
ATAAAAATAAATAAATATAAAAATA
Found at i:646732 original size:77 final size:76
Alignment explanation
Indices: 646646--646902 Score: 240
Period size: 77 Copynumber: 3.3 Consensus size: 76
646636 TATAAAAAGT
* * **
646646 ATTTTAAAAACTGTATAATATAATTTTTTTCAAAAATGTTTTAAAATTTATATATTATATATGAA
1 ATTTTAAAAACTATATAATATAA-TATTTTCAAAAATGTTTTAAAAACTATATATTATATATGAA
646711 TTTTCAAAAATG
65 TTTTCAAAAATG
* *
646723 ATTTCAAAAAACTATATATTATATAA-GTTTTCAAAAATGTTTTCAAAAACTATATATTATATA-
1 ATTT-TAAAAACTATATA--ATATAATATTTTCAAAAATGTTTT-AAAAACTATATATTATATAT
* *
646786 -AGTTTTCAAAAGTG
62 GAATTTTCAAAAATG
* * * *
646800 -TTTTAAAAACTATCTATTATATACATTTTC-AAAATGCTTTTTAAAAACTATATATTATGTATG
1 ATTTTAAAAACTATATAATATA-ATATTTTCAAAAATG--TTTTAAAAACTATATATTATATATG
*
646863 TATTTTCAAAAATCG
63 AATTTTCAAAAAT-G
**
646878 --TTTGCAAACTATATAATATATATAT
1 ATTTTAAAAACTATATAATATA-ATAT
646903 ATATATAATA
Statistics
Matches: 149, Mismatches: 20, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
73 4 0.03
74 7 0.05
75 34 0.23
76 7 0.05
77 46 0.31
78 28 0.19
79 17 0.11
80 6 0.04
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.44
Consensus pattern (76 bp):
ATTTTAAAAACTATATAATATAATATTTTCAAAAATGTTTTAAAAACTATATATTATATATGAAT
TTTCAAAAATG
Found at i:646780 original size:38 final size:38
Alignment explanation
Indices: 646672--646899 Score: 243
Period size: 38 Copynumber: 5.9 Consensus size: 38
646662 AATATAATTT
** *
646672 TTTTCAAAAATGTTTT-AAAATTTATATATTATATATGAA
1 TTTTCAAAAATGTTTTCAAAAACTATATATTATATA--AG
*
646711 TTTTCAAAAATGATTTCAAAAAACTATATATTATATAAG
1 TTTTCAAAAATGTTTTC-AAAAACTATATATTATATAAG
646750 TTTTCAAAAATGTTTTCAAAAACTATATATTATATAAG
1 TTTTCAAAAATGTTTTCAAAAACTATATATTATATAAG
* *
646788 TTTTCAAAAGTGTTTT-AAAAACTATCTATTATATACA-
1 TTTTCAAAAATGTTTTCAAAAACTATATATTATATA-AG
* * *
646825 TTTTC-AAAATGCTTTTTAAAAACTATATATTATGTATG
1 TTTTCAAAAATG-TTTTCAAAAACTATATATTATATAAG
* *
646863 TATTTTCAAAAATCGTTTGC--AAACTATATAATATATA
1 --TTTTCAAAAAT-GTTTTCAAAAACTATATATTATATA
646900 TATATATATA
Statistics
Matches: 164, Mismatches: 15, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
36 5 0.03
37 27 0.16
38 54 0.33
39 47 0.29
40 5 0.03
41 25 0.15
42 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (38 bp):
TTTTCAAAAATGTTTTCAAAAACTATATATTATATAAG
Found at i:646829 original size:75 final size:77
Alignment explanation
Indices: 646672--646875 Score: 247
Period size: 75 Copynumber: 2.6 Consensus size: 77
646662 AATATAATTT
**
646672 TTTTCAAAAATGTTTTAAAATTTATATATTATATATGAATTTTCAAAAATGATTTCAAAAAACTA
1 TTTTCAAAAATGTTTTAAAAACTATATATTATATA-GAATTTTCAAAAATGATTTCAAAAAACTA
646737 TATATTATATAAG
65 TATATTATATAAG
* * *
646750 TTTTCAAAAATGTTTTCAAAAACTATATATTATATA-AGTTTTCAAAAGTG-TTT-TAAAAACTA
1 TTTTCAAAAATGTTTT-AAAAACTATATATTATATAGAATTTTCAAAAATGATTTCAAAAAACTA
*
646812 TCTATTATATACA-
65 TATATTATATA-AG
* *
646825 TTTTC-AAAATGCTTTTTAAAAACTATATATTATGTATGTATTTTCAAAAAT
1 TTTTCAAAAATG--TTTTAAAAACTATATATTATATA-GAATTTTCAAAAAT
646876 CGTTTGCAAA
Statistics
Matches: 110, Mismatches: 10, Indels: 13
0.83 0.08 0.10
Matches are distributed among these distances:
74 6 0.05
75 41 0.37
76 8 0.07
77 22 0.20
78 16 0.15
79 17 0.15
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.44
Consensus pattern (77 bp):
TTTTCAAAAATGTTTTAAAAACTATATATTATATAGAATTTTCAAAAATGATTTCAAAAAACTAT
ATATTATATAAG
Found at i:651878 original size:12 final size:12
Alignment explanation
Indices: 651863--651887 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
651853 TTAAATAGAG
651863 GTTTTATCTTGT
1 GTTTTATCTTGT
651875 GTTTTATCTTGT
1 GTTTTATCTTGT
651887 G
1 G
651888 AAAAAGGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.20, T:0.64
Consensus pattern (12 bp):
GTTTTATCTTGT
Found at i:652498 original size:90 final size:89
Alignment explanation
Indices: 652339--652506 Score: 291
Period size: 90 Copynumber: 1.9 Consensus size: 89
652329 TAACACACCC
*
652339 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTAATTATTTCAAATTAATTAAATCTATATT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTAATTATTTCAAATTAATTAAATCTATATG
652404 TAATTAATTGAAATTTAATAATCA
66 TAATTAATTGAAATTTAATAATCA
* * *
652428 TTTTATATCCAAGTTACCTTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTAATTATTTCAAATTAATTAAATCTATAT
652493 GTAATTAATTGAAA
65 GTAATTAATTGAAA
652507 GTAAATATTC
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 31 0.42
90 43 0.58
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.45
Consensus pattern (89 bp):
TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTAATTATTTCAAATTAATTAAATCTATATG
TAATTAATTGAAATTTAATAATCA
Found at i:659192 original size:90 final size:89
Alignment explanation
Indices: 659039--659215 Score: 300
Period size: 90 Copynumber: 2.0 Consensus size: 89
659029 CCTAACACGC
659039 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
* * *
659104 TTTAATTAATTGGAATTTAATAAT
66 TTTAATGAATTGAAATTAAATAAT
* *
659128 CCTTTTATATCCAATTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTAT
659193 ATTTAATGAATTGAAATTAAATA
65 ATTTAATGAATTGAAATTAAATA
659216 TTCGGGATTA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 33 0.40
90 49 0.60
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATGAATTGAAATTAAATAAT
Found at i:664353 original size:24 final size:22
Alignment explanation
Indices: 664312--664402 Score: 69
Period size: 22 Copynumber: 4.0 Consensus size: 22
664302 TTATTTAAGA
*
664312 ATAAAAA-ATTAATTAATTAATT
1 ATAAAAATAATAATTAATT-ATT
664334 ATAAAAATAGATAATTAATTCATT
1 ATAAAAATA-ATAATTAATT-ATT
* *
664358 GTAAAATTAAT-ATTAAATTATT
1 ATAAAAATAATAATT-AATTATT
* * *
664380 TTAAAAATTATATTTATATTATT
1 ATAAAAATAATAATTA-ATTATT
664403 TATTAATAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
22 22 0.39
23 15 0.27
24 19 0.34
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (22 bp):
ATAAAAATAATAATTAATTATT
Found at i:664368 original size:20 final size:21
Alignment explanation
Indices: 664315--664368 Score: 56
Period size: 24 Copynumber: 2.5 Consensus size: 21
664305 TTTAAGAATA
664315 AAAAATTAATTAATTAATTAT
1 AAAAATTAATTAATTAATTAT
* *
664336 AAAAATAGATAATTAATTCATTGT
1 AAAAAT---TAATTAATTAATTAT
664360 -AAAATTAAT
1 AAAAATTAAT
664369 ATTAAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 4 0.14
21 6 0.21
23 5 0.18
24 13 0.46
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.39
Consensus pattern (21 bp):
AAAAATTAATTAATTAATTAT
Found at i:664376 original size:23 final size:22
Alignment explanation
Indices: 664315--664402 Score: 58
Period size: 23 Copynumber: 3.9 Consensus size: 22
664305 TTTAAGAATA
*
664315 AAAAATTA-ATT-AATTAATTAT
1 AAAAATTATATTAAATT-ATTGT
*
664336 AAAAATAGATAATT-AATTCATTGT
1 AAAAAT-TAT-ATTAAATT-ATTGT
*
664360 -AAAATTAATATTAAATTATTTT
1 AAAAATT-ATATTAAATTATTGT
*
664382 AAAAATTATATTTATATTATT
1 AAAAATTATA-TTAAATTATT
664403 TATTAATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
21 6 0.11
22 11 0.20
23 26 0.48
24 11 0.20
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (22 bp):
AAAAATTATATTAAATTATTGT
Found at i:664404 original size:22 final size:23
Alignment explanation
Indices: 664360--664403 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
664350 AATTCATTGT
664360 AAAATTAATATTAAATTATTTTA
1 AAAATTAATATTAAATTATTTTA
*
664383 AAAATT-ATATTTATATTATTT
1 AAAATTAATA-TTAAATTATTT
664404 ATTAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AAAATTAATATTAAATTATTTTA
Found at i:664429 original size:45 final size:46
Alignment explanation
Indices: 664366--664452 Score: 108
Period size: 45 Copynumber: 1.9 Consensus size: 46
664356 TTGTAAAATT
*
664366 AATATTAAATTATTTTAAAAATTATATTTATATT-ATTTATTAATAA
1 AATATTAAATTATTTT-AAAATAATATTTATATTAATTTATTAATAA
* *
664412 AATA-TAAATTCA-TTTAAAATAATTTTTATTTTAATTTATTA
1 AATATTAAATT-ATTTTAAAATAATATTTATATTAATTTATTA
664453 TTTTAATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
44 14 0.39
45 17 0.47
46 5 0.14
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (46 bp):
AATATTAAATTATTTTAAAATAATATTTATATTAATTTATTAATAA
Found at i:664455 original size:13 final size:12
Alignment explanation
Indices: 664431--664491 Score: 59
Period size: 13 Copynumber: 4.8 Consensus size: 12
664421 TCATTTAAAA
664431 TAATTTTTATTT
1 TAATTTTTATTT
664443 TAATTTATTATTT
1 TAATTT-TTATTT
*
664456 TAATTTTAACATTT
1 TAATTTT--TATTT
* *
664470 AAATTTGTTATAT
1 TAATTT-TTATTT
664483 TAATTTTTA
1 TAATTTTTA
664492 AATGATATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
12 10 0.25
13 20 0.50
14 9 0.22
15 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (12 bp):
TAATTTTTATTT
Found at i:666637 original size:15 final size:13
Alignment explanation
Indices: 666607--666654 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
666597 TATATATATA
666607 TATTTTAAAATTT
1 TATTTTAAAATTT
666620 TATTTTAAAATTTTT
1 TATTTTAAAA--TTT
666635 TATTTT--AATTT
1 TATTTTAAAATTT
*
666646 TTTTTTAAA
1 TATTTTAAA
666655 TTACCATGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
11 8 0.27
13 13 0.43
15 9 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTTAAAATTT
Found at i:666649 original size:14 final size:15
Alignment explanation
Indices: 666607--666642 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
666597 TATATATATA
666607 TATTTTAAAA--TTT
1 TATTTTAAAATTTTT
666620 TATTTTAAAATTTTT
1 TATTTTAAAATTTTT
666635 TATTTTAA
1 TATTTTAA
666643 TTTTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.48
15 11 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTTTAAAATTTTT
Found at i:667949 original size:31 final size:31
Alignment explanation
Indices: 667914--668003 Score: 144
Period size: 31 Copynumber: 2.9 Consensus size: 31
667904 TGGAGTGACC
* *
667914 ATTTTGTTATAAATCGATAACGTTAGTGGTT
1 ATTTTATTACAAATCGATAACGTTAGTGGTT
667945 ATTTTATTACAAATCGATAACGTTAGTGGTT
1 ATTTTATTACAAATCGATAACGTTAGTGGTT
* *
667976 ATTTTATTACAAATCGACAACATTAGTG
1 ATTTTATTACAAATCGATAACGTTAGTG
668004 ACCAGATCGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (31 bp):
ATTTTATTACAAATCGATAACGTTAGTGGTT
Found at i:668435 original size:43 final size:43
Alignment explanation
Indices: 668366--668549 Score: 187
Period size: 43 Copynumber: 4.2 Consensus size: 43
668356 ATTTTTTGAA
* * *
668366 ATTGTAAAAAAATAGAGGCCTTAATTATAAAGGTAGAAA-TCGAG
1 ATTG-AAAAAAATAGGGGGCTCAATTATAAAGGTAGAAAGT-GAG
* * *
668410 ATTGAAAAAAATGGGGGGCTCAATTATAAAGGTA-TAATTGAG
1 ATTGAAAAAAATAGGGGGCTCAATTATAAAGGTAGAAAGTGAG
* * * * *
668452 ATCGAAAAAACTTAGGGGCCTCAATTAGAAAGTTAGAAAGTGAG
1 ATTGAAAAAA-ATAGGGGGCTCAATTATAAAGGTAGAAAGTGAG
668496 ATT-AAAAAAACTTAGGGGGCTCAATTGA-AAAGGTAGAAAGTGAG
1 ATTGAAAAAAA--TAGGGGGCTCAATT-ATAAAGGTAGAAAGTGAG
668540 ATTGAAAAAA
1 ATTGAAAAAA
668550 CTTAAAAGTC
Statistics
Matches: 116, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
42 14 0.12
43 52 0.45
44 43 0.37
45 7 0.06
ACGTcount: A:0.46, C:0.07, G:0.24, T:0.23
Consensus pattern (43 bp):
ATTGAAAAAAATAGGGGGCTCAATTATAAAGGTAGAAAGTGAG
Found at i:668478 original size:86 final size:87
Alignment explanation
Indices: 668382--668553 Score: 217
Period size: 86 Copynumber: 2.0 Consensus size: 87
668372 AAAAAATAGA
* * *
668382 GGCCTTAATTATAAAGGTAGAAA-TCGAGATTGAAAAAAA-TGGGGGGCTCAATT-ATAAAGGTA
1 GGCCTCAATTAGAAAGGTAGAAAGT-GAGATT-AAAAAAACTAGGGGGCTCAATTGA-AAAGGTA
* *
668444 -TAATTGAGATCGAAAAAACTTAGG
63 GAAAGTGAGATCGAAAAAACTTAGG
*
668468 GGCCTCAATTAGAAAGTTAGAAAGTGAGATTAAAAAAACTTAGGGGGCTCAATTGAAAAGGTAGA
1 GGCCTCAATTAGAAAGGTAGAAAGTGAGATTAAAAAAAC-TAGGGGGCTCAATTGAAAAGGTAGA
*
668533 AAGTGAGATTGAAAAAACTTA
65 AAGTGAGATCGAAAAAACTTA
668554 AAAGTCTCAA
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
85 7 0.09
86 26 0.35
87 21 0.28
88 20 0.27
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.23
Consensus pattern (87 bp):
GGCCTCAATTAGAAAGGTAGAAAGTGAGATTAAAAAAACTAGGGGGCTCAATTGAAAAGGTAGAA
AGTGAGATCGAAAAAACTTAGG
Found at i:668565 original size:44 final size:44
Alignment explanation
Indices: 668382--668553 Score: 190
Period size: 44 Copynumber: 4.0 Consensus size: 44
668372 AAAAAATAGA
* * * *
668382 GGCCTTAATTATAAAGGTAGAAA-TCGAGATTGAAAAAA-ATGGG
1 GGCCTCAATTAGAAAGGTAGAAAGT-GAGATTGAAAAAACTTAGG
* * * * *
668425 GGGCTCAATTATAAAGGTA-TAATTGAGATCGAAAAAACTTAGG
1 GGCCTCAATTAGAAAGGTAGAAAGTGAGATTGAAAAAACTTAGG
* *
668468 GGCCTCAATTAGAAAGTTAGAAAGTGAGATTAAAAAAACTTAGG
1 GGCCTCAATTAGAAAGGTAGAAAGTGAGATTGAAAAAACTTAGG
*
668512 GGGCTCAATT-GAAAAGGTAGAAAGTGAGATTGAAAAAACTTA
1 GGCCTCAATTAG-AAAGGTAGAAAGTGAGATTGAAAAAACTTA
668554 AAAGTCTCAA
Statistics
Matches: 109, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
42 14 0.13
43 38 0.35
44 57 0.52
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.23
Consensus pattern (44 bp):
GGCCTCAATTAGAAAGGTAGAAAGTGAGATTGAAAAAACTTAGG
Found at i:671550 original size:7 final size:7
Alignment explanation
Indices: 671538--671562 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
671528 TTCAATTGAG
671538 TGGATTC
1 TGGATTC
671545 TGGATTC
1 TGGATTC
671552 TGGATTC
1 TGGATTC
671559 TGGA
1 TGGA
671563 GCAACTGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.12, G:0.32, T:0.40
Consensus pattern (7 bp):
TGGATTC
Found at i:675882 original size:60 final size:58
Alignment explanation
Indices: 675750--675882 Score: 135
Period size: 60 Copynumber: 2.2 Consensus size: 58
675740 TTGTTTTAGT
* * *
675750 TTTATTCCTAAACTATGACTATGATTCTAAATTAGTCCTCAAACTTTTGAATATTTCAA
1 TTTATTCC-AAACTATGACTATCATTCTAAATTAGTCCCCAAACTTTTGAACATTTCAA
* * *
675809 TTTCATCCTCAAACTTTGAC-ATACATTCTAAATTGGTCCCCAAACTTTTTTGAACA-TTCTAA
1 TTT-ATTC-CAAACTATGACTAT-CATTCTAAATTAGTCCCCAAAC--TTTTGAACATTTC-AA
675871 TTTATTCCAAAC
1 TTTATTCCAAAC
675883 CATATGTATA
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
59 5 0.08
60 36 0.59
61 7 0.11
62 13 0.21
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (58 bp):
TTTATTCCAAACTATGACTATCATTCTAAATTAGTCCCCAAACTTTTGAACATTTCAA
Found at i:676131 original size:59 final size:58
Alignment explanation
Indices: 676013--676178 Score: 163
Period size: 60 Copynumber: 2.8 Consensus size: 58
676003 AATGAATTTG
* ** * * *
676013 GGATGAAATTAGAATATTCAAAAGTTTGGGGATCAATTTAAAAAAAAGAGTCATGTTTAA
1 GGATAAAATTAGAATATTCAAAAGTTTAAGGAT-AATTT-AAAATAAGACTCATATTTAA
* * *
676073 TGAT-TAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGACTCATTATTTAA
1 GGATAAAATTAGAATATTCAAAAGTTTAAGGA-TAATTTAAAATAAGACTCA-TATTTAA
* * **
676132 GGATAAAAATAAAATATTCAAAAGTTTAAAAATTAATTTAAAATAAG
1 GGATAAAATTAGAATATTCAAAAGTTTAAGGA-TAATTTAAAATAAG
676179 GATTACAATT
Statistics
Matches: 87, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
58 10 0.11
59 38 0.44
60 39 0.45
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.33
Consensus pattern (58 bp):
GGATAAAATTAGAATATTCAAAAGTTTAAGGATAATTTAAAATAAGACTCATATTTAA
Found at i:676619 original size:3 final size:3
Alignment explanation
Indices: 676611--676638 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
676601 TTTTGTTTTA
676611 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
676639 TACATAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:677239 original size:31 final size:31
Alignment explanation
Indices: 677201--677271 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
677191 TTAGTTTAAA
677201 AAAGGAAATATTTTCTTTTGACAGCTGAAGC
1 AAAGGAAATATTTTCTTTTGACAGCTGAAGC
677232 AAAGGAAATATTTTCTTTTGACAGCTGAAGC
1 AAAGGAAATATTTTCTTTTGACAGCTGAAGC
*
677263 AAAGAAAAT
1 AAAGGAAAT
677272 CAAAAGAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (31 bp):
AAAGGAAATATTTTCTTTTGACAGCTGAAGC
Found at i:680817 original size:42 final size:42
Alignment explanation
Indices: 680771--681008 Score: 193
Period size: 42 Copynumber: 5.7 Consensus size: 42
680761 AATTGACATA
* * *
680771 TAGCGGCGTTTTTACAAAAAACGTCGCAATAGGGTGGTAAAT
1 TAGCGGCGTTTTTACCAAAAACGCCGCAATAGAGTGGTAAAT
* * * *
680813 TAGCGGTGTTTATACCACAAACGCCGCAATAGAGT-ATAAATT
1 TAGCGGCGTTTTTACCAAAAACGCCGCAATAGAGTGGTAAA-T
* *
680855 TTGCGGCG-ATTTAGCC-AAAACGCCGCAATAGAGTGGTAAAT
1 TAGCGGCGTTTTTA-CCAAAAACGCCGCAATAGAGTGGTAAAT
* * * *
680896 TAACGGCGTTTGTACCATAAACGCCGCAATAGA-T-ATAAATT
1 TAGCGGCGTTTTTACCAAAAACGCCGCAATAGAGTGGTAAA-T
* * * * *
680937 TTGCAGCG-ATTGAGCC-AAAACGCCGTAATAGAGTGGTAAAT
1 TAGCGGCGTTTTTA-CCAAAAACGCCGCAATAGAGTGGTAAAT
* * * *
680978 TAGTGGCGTTTATACCACAAACGTCGCAATA
1 TAGCGGCGTTTTTACCAAAAACGCCGCAATA
681009 TATTACACAT
Statistics
Matches: 148, Mismatches: 37, Indels: 22
0.71 0.18 0.11
Matches are distributed among these distances:
40 20 0.14
41 51 0.34
42 77 0.52
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (42 bp):
TAGCGGCGTTTTTACCAAAAACGCCGCAATAGAGTGGTAAAT
Found at i:680876 original size:41 final size:41
Alignment explanation
Indices: 680831--680970 Score: 169
Period size: 41 Copynumber: 3.4 Consensus size: 41
680821 TTTATACCAC
680831 AAACGCCGCAATAGAGTATAAATTTTGCGGCGATTTAGCCA
1 AAACGCCGCAATAGAGTATAAATTTTGCGGCGATTTAGCCA
* ** *
680872 AAACGCCGCAATAGAGTGGTAAA-TTAACGGCGTTTGTA-CCA
1 AAACGCCGCAATAGAGT-ATAAATTTTGCGGCGATT-TAGCCA
* *
680913 TAAACGCCGCAATAGA-TATAAATTTTGCAGCGATTGAGCCA
1 -AAACGCCGCAATAGAGTATAAATTTTGCGGCGATTTAGCCA
*
680954 AAACGCCGTAATAGAGT
1 AAACGCCGCAATAGAGT
680971 GGTAAATTAG
Statistics
Matches: 82, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
40 19 0.23
41 42 0.51
42 21 0.26
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (41 bp):
AAACGCCGCAATAGAGTATAAATTTTGCGGCGATTTAGCCA
Found at i:680968 original size:82 final size:83
Alignment explanation
Indices: 680788--681008 Score: 336
Period size: 82 Copynumber: 2.7 Consensus size: 83
680778 GTTTTTACAA
* * *
680788 AAAACGTCGCAATAGGGTGGTAAATTAGCGGTGTTTATACCACAAACGCCGCAATAGAGTATAAA
1 AAAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCGCAATAGAGTATAAA
* *
680853 TTTTGCGGCGATTTAGCC
66 TTTTGCAGCGATTGAGCC
* * *
680871 AAAACGCCGCAATAGAGTGGTAAATTAACGGCGTTTGTACCATAAACGCCGCAATAGA-TATAAA
1 AAAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCGCAATAGAGTATAAA
680935 TTTTGCAGCGATTGAGCC
66 TTTTGCAGCGATTGAGCC
* * *
680953 AAAACGCCGTAATAGAGTGGTAAATTAGTGGCGTTTATACCACAAACGTCGCAATA
1 AAAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCGCAATA
681009 TATTACACAT
Statistics
Matches: 124, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
82 72 0.58
83 52 0.42
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (83 bp):
AAAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCGCAATAGAGTATAAA
TTTTGCAGCGATTGAGCC
Found at i:681280 original size:41 final size:41
Alignment explanation
Indices: 681037--681278 Score: 353
Period size: 41 Copynumber: 5.9 Consensus size: 41
681027 GTTTATTCCT
* *
681037 CAAACGCCGTAATAGTGATAATCAATAGTGGCGTTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
* *
681078 CAAACGCCACAATAGTGTTAATCAATAGTGGTGTTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
* *
681119 CAAACGCCGCAATAGTGTTAATCAATAATGGCATTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
*
681160 GAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
* * *
681201 CAAATGTCGCAATAGTGTTAATCAATAGTGGCATTTTTTA-A
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGC-GTTTTTAGA
**
681242 CAAACGCCATAATAGTG-TAATCAATAGTGGCGTTTTT
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTT
681279 TTGTATAAAC
Statistics
Matches: 180, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 5 0.03
40 14 0.08
41 155 0.86
42 6 0.03
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (41 bp):
CAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
Found at i:682006 original size:41 final size:41
Alignment explanation
Indices: 681961--682041 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
681951 TTGTTATTAG
* *
681961 GTGGCGTTTT-TTAAAAAACACCGCAATAGAATAGTTCCTTA
1 GTGGCGTTTTCAT-AAAAACACAGCAATAGAATAGTTCCTTA
*
682002 GTGGCGTTTTCATAAAAACACAGCAATAGAGTAGTTCCTT
1 GTGGCGTTTTCATAAAAACACAGCAATAGAATAGTTCCTT
682042 TGCGGCATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 35 0.97
42 1 0.03
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (41 bp):
GTGGCGTTTTCATAAAAACACAGCAATAGAATAGTTCCTTA
Found at i:682301 original size:18 final size:18
Alignment explanation
Indices: 682280--682322 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
682270 TCTCTACCAG
682280 CGCAACCTTCTCCAACAA
1 CGCAACCTTCTCCAACAA
* * *
682298 CGCAAGCTTCTCCACCAG
1 CGCAACCTTCTCCAACAA
682316 CGCAACC
1 CGCAACC
682323 ACCACCAGCG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.47, G:0.12, T:0.14
Consensus pattern (18 bp):
CGCAACCTTCTCCAACAA
Found at i:683290 original size:35 final size:36
Alignment explanation
Indices: 683228--683301 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 36
683218 TAGTGTTTAG
683228 CATTAAAATAGACATTTATTGTATAAATTATTTGTTA
1 CATTAAAATAGACA-TTATTGTATAAATTATTTGTTA
683265 CATTAAAATAGACA-TATTGTATAAATTATTTGTTA
1 CATTAAAATAGACATTATTGTATAAATTATTTGTTA
683300 CA
1 CA
683302 CAATATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 23 0.62
37 14 0.38
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (36 bp):
CATTAAAATAGACATTATTGTATAAATTATTTGTTA
Found at i:684759 original size:21 final size:23
Alignment explanation
Indices: 684733--684775 Score: 63
Period size: 21 Copynumber: 1.9 Consensus size: 23
684723 GAAAATGAAG
684733 GGAAGCAG-AGAG-AGCAGCAAT
1 GGAAGCAGCAGAGTAGCAGCAAT
684754 GGAAGCAGCTAGAGTAGCAGCA
1 GGAAGCAGC-AGAGTAGCAGCA
684776 GAAGCGGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.40, C:0.16, G:0.37, T:0.07
Consensus pattern (23 bp):
GGAAGCAGCAGAGTAGCAGCAAT
Found at i:684830 original size:23 final size:21
Alignment explanation
Indices: 684783--684835 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
684773 GCAGAAGCGG
*
684783 AGAGAGAAGCAGCGGCAGTAC
1 AGAGAGAAGCAGCGGCAGCAC
*
684804 AGAGAGAAGCAGTGGCAGCAC
1 AGAGAGAAGCAGCGGCAGCAC
*
684825 AAAGAGAAGCA
1 AGAGAGAAGCA
684836 TCATATCAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.43, C:0.17, G:0.36, T:0.04
Consensus pattern (21 bp):
AGAGAGAAGCAGCGGCAGCAC
Found at i:685494 original size:43 final size:44
Alignment explanation
Indices: 685259--685514 Score: 191
Period size: 43 Copynumber: 5.9 Consensus size: 44
685249 GTTTGTATCC
** * * *
685259 TAAAAACGCCGCTAAATCGCAACACCTATTGCGAC-GTTTATGA
1 TAAAAACGCCGCTAAATATCAACACCTATTGCGGCATTTTGTGA
** * * ** * *
685302 GGAAAATGCCACTAAACCTCAACACTTATTGCGGCA-TTTGCGA
1 TAAAAACGCCGCTAAATATCAACACCTATTGCGGCATTTTGTGA
* * * * *
685345 TAAAAACGCCGCTAAATCTCAACAACTACTACGGC-GTTTGTGA
1 TAAAAACGCCGCTAAATATCAACACCTATTGCGGCATTTTGTGA
* * * ** * *
685388 GAAAAAACGCCGCTAAACATCAACACCGATTGCACCGTTTT-TAA
1 -TAAAAACGCCGCTAAATATCAACACCTATTGCGGCATTTTGTGA
* *
685432 TACAAACGCCGCTAAATATCAACACCTATTACGGCATTTTGTGA
1 TAAAAACGCCGCTAAATATCAACACCTATTGCGGCATTTTGTGA
* *
685476 -ACAAACGCCGCTATATATCATA-ACCTATTGCGGCATTTT
1 TAAAAACGCCGCTAAATATCA-ACACCTATTGCGGCATTTT
685515 TTGTTCACAA
Statistics
Matches: 165, Mismatches: 42, Indels: 12
0.75 0.19 0.05
Matches are distributed among these distances:
43 131 0.79
44 31 0.19
45 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (44 bp):
TAAAAACGCCGCTAAATATCAACACCTATTGCGGCATTTTGTGA
Found at i:699187 original size:2 final size:2
Alignment explanation
Indices: 699180--699212 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
699170 GGTCTTAAGA
*
699180 AT AT AT AT AT AT AT AT AT AT -T AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
699213 GTGTATGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:699234 original size:25 final size:25
Alignment explanation
Indices: 699206--699254 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
699196 ATATTATATG
699206 TATATATGTGTATGTATGTATGTAA
1 TATATATGTGTATGTATGTATGTAA
699231 TATATATGTGTATGTATGTATGTA
1 TATATATGTGTATGTATGTATGTA
699255 CTTTAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (25 bp):
TATATATGTGTATGTATGTATGTAA
Found at i:712877 original size:21 final size:21
Alignment explanation
Indices: 712853--713039 Score: 112
Period size: 21 Copynumber: 9.1 Consensus size: 21
712843 GCAAATTCGC
*
712853 GTTGCATTTCGCGTTGAGATA
1 GTTGCATTTCGCGTTGCGATA
* ** *
712874 GTTGAAAATCGTGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
712894 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
712915 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* * *
712935 TTTCCATTTCGCGTTGCTATA
1 GTTGCATTTCGCGTTGCGATA
* ** *** *
712956 GTTGAAAATCGCAACGCGATT
1 GTTGCATTTCGCGTTGCGATA
*
712977 G-TCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
712997 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
713017 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
713038 GT
1 GT
713040 CTACAGTTGT
Statistics
Matches: 112, Mismatches: 50, Indels: 8
0.66 0.29 0.05
Matches are distributed among these distances:
20 55 0.49
21 57 0.51
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:712902 original size:41 final size:41
Alignment explanation
Indices: 712857--713039 Score: 303
Period size: 41 Copynumber: 4.5 Consensus size: 41
712847 ATTCGCGTTG
* *
712857 CATTTCGCGTTGAGATAGTTGAAAATCGTGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
712898 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *** *
712939 CATTTCGCGTTGCTATAGTTGAAAATCGCAACGCGATTGTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
712980 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
713021 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
713040 CTACAGTTGT
Statistics
Matches: 130, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 130 1.00
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:712911 original size:20 final size:20
Alignment explanation
Indices: 712886--713036 Score: 95
Period size: 20 Copynumber: 7.4 Consensus size: 20
712876 TGAAAATCGT
712886 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
* ** **
712906 GTTGCGATAGTTGAAAATCGC
1 GTTGCGAT-TTTCCATTTCGC
712927 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
* * ** **
712947 GTTGCTATAGTTGAAAATCGC
1 GTTGCGAT-TTTCCATTTCGC
*** *
712968 AACGCGATTGTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
* ** **
712988 GTTGCGATAGTTGAAAATCGC
1 GTTGCGAT-TTTCCATTTCGC
713009 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGC
713029 GTTGCGAT
1 GTTGCGAT
713037 AGTCTACAGT
Statistics
Matches: 88, Mismatches: 40, Indels: 6
0.66 0.30 0.04
Matches are distributed among these distances:
20 48 0.55
21 40 0.45
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTTCCATTTCGC
Found at i:713056 original size:22 final size:22
Alignment explanation
Indices: 713028--713080 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
713018 TTCCATTTCG
713028 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
713050 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
713072 CGTTGCGAT
1 CGTTGCGAT
713081 TTTCCAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:713695 original size:6 final size:6
Alignment explanation
Indices: 713684--713715 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
713674 TCGTCTCGTC
713684 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TC
713716 ATACGTGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.47, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:713876 original size:41 final size:41
Alignment explanation
Indices: 713831--714006 Score: 325
Period size: 41 Copynumber: 4.3 Consensus size: 41
713821 ACAACTGTAG
*
713831 ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCATTGCGATTTTCA
*
713872 ACTATCGCAACGCGAAATGGAAAATCGCGTTGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCATTGCGATTTTCA
713913 ACTATCGCAACGCGAAATGGAAAATCGCATTGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCATTGCGATTTTCA
*
713954 ACTATCGCAACGCGAAATGGAAAATCGCATTGCGATTTGCA
1 ACTATCGCAACGCGAAATGGAAAATCGCATTGCGATTTTCA
713995 ACTATCGCAACG
1 ACTATCGCAACG
714007 ACAACTGTAG
Statistics
Matches: 133, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 133 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCATTGCGATTTTCA
Found at i:713878 original size:21 final size:21
Alignment explanation
Indices: 713854--713920 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
713844 GAAATGGAAA
713854 ATCGCGTTGCGATTTTCAACT
1 ATCGCGTTGCGATTTTCAACT
*** ** ** *
713875 ATCGCAACGCGAAATGGAA-A
1 ATCGCGTTGCGATTTTCAACT
713895 ATCGCGTTGCGATTTTCAACT
1 ATCGCGTTGCGATTTTCAACT
713916 ATCGC
1 ATCGC
713921 AACGCGAAAT
Statistics
Matches: 29, Mismatches: 16, Indels: 2
0.62 0.34 0.04
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTCAACT
Found at i:714021 original size:104 final size:104
Alignment explanation
Indices: 713913--714110 Score: 351
Period size: 104 Copynumber: 1.9 Consensus size: 104
713903 GCGATTTTCA
**
713913 ACTATCGCAACGCGAAATGGAAAATCGCATTGCGATTTTCAACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAA
**
713978 TCGCATTGCGATTTGCAACTATCGCAACGACAACTGTAG
66 TCGCAACGCGATTTGCAACTATCGCAACGACAACTGTAG
714017 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAA
*
714082 TCGCAACGCGATTTTCAACTATCGCAACG
66 TCGCAACGCGATTTGCAACTATCGCAACG
714111 CGAAATGCAA
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
104 89 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (104 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAA
TCGCAACGCGATTTGCAACTATCGCAACGACAACTGTAG
Found at i:714066 original size:41 final size:41
Alignment explanation
Indices: 714017--714117 Score: 202
Period size: 41 Copynumber: 2.5 Consensus size: 41
714007 ACAACTGTAG
714017 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
714058 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
714099 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
714118 CAACGCGAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:714542 original size:3 final size:3
Alignment explanation
Indices: 714523--714565 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
714513 TTAATAAAGA
* * * *
714523 AAT ATT AAT ATT AAT AAT AAT AAT AAA AAT ATT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
714566 TTTAAAATAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:714547 original size:21 final size:21
Alignment explanation
Indices: 714507--714565 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
714497 TTAGGTTAGG
*
714507 TAATAATTAATAA-AGA-AATAT
1 TAAT-ATTAATAATA-ATAATAA
714528 TAATATTAATAATAATAATAA
1 TAATATTAATAATAATAATAA
*
714549 AAATATTAATAATAATA
1 TAATATTAATAATAATA
714566 TTTAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
TAATATTAATAATAATAATAA
Found at i:714572 original size:21 final size:21
Alignment explanation
Indices: 714529--714576 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
714519 AAGAAATATT
714529 AATATTAATAATAATAATAAA
1 AATATTAATAATAATAATAAA
* *
714550 AATATTAATAATAATATTTAA
1 AATATTAATAATAATAATAAA
714571 AATATT
1 AATATT
714577 TTTTTCGACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATATTAATAATAATAATAAA
Found at i:714745 original size:84 final size:84
Alignment explanation
Indices: 714624--714792 Score: 284
Period size: 84 Copynumber: 2.0 Consensus size: 84
714614 CCCTATTTGC
* *
714624 ACATTCTTGTGTTAACAAGGATAAGACAAAGAAGAAAAAGACAACCAATTTTTGTCCGATAAATG
1 ACATTCTTGTGTTAACAAAGATAAGACAAAGAAGAAAAAGACAAACAATTTTTGTCCGATAAATG
714689 AAACATGTGACATAAACAA
66 AAACATGTGACATAAACAA
* * * *
714708 ACATTCTTGTGTTAATAAAGATATGACAAAGACGAAAAAGACAAACAGTTTTTGTCCGATAAATG
1 ACATTCTTGTGTTAACAAAGATAAGACAAAGAAGAAAAAGACAAACAATTTTTGTCCGATAAATG
714773 AAACATGTGACATAAACAA
66 AAACATGTGACATAAACAA
714792 A
1 A
714793 AATATATCTG
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 79 1.00
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (84 bp):
ACATTCTTGTGTTAACAAAGATAAGACAAAGAAGAAAAAGACAAACAATTTTTGTCCGATAAATG
AAACATGTGACATAAACAA
Found at i:714813 original size:18 final size:19
Alignment explanation
Indices: 714784--714825 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
714774 AACATGTGAC
*
714784 ATAAACAAAAATATATCTG
1 ATAAACAAAAATATATCCG
714803 ATAAA-AAAAATATATCCG
1 ATAAACAAAAATATATCCG
714821 ATAAA
1 ATAAA
714826 TTTTACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.24
Consensus pattern (19 bp):
ATAAACAAAAATATATCCG
Found at i:716196 original size:3 final size:3
Alignment explanation
Indices: 716188--716252 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
716178 TCCATATTTA
*
716188 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
716236 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
716253 AATATATATT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:716279 original size:14 final size:15
Alignment explanation
Indices: 716251--716285 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
716241 TTATTATTAT
716251 TAAATATATATTAAA
1 TAAATATATATTAAA
716266 TAAATATATA-TAAA
1 TAAATATATATTAAA
716280 TAAATA
1 TAAATA
716286 ATTACAGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:716488 original size:15 final size:15
Alignment explanation
Indices: 716468--716506 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
716458 CCAGATGGAA
716468 ACCCTAGGGTCTGAT
1 ACCCTAGGGTCTGAT
716483 ACCCTAGGGTCTGAT
1 ACCCTAGGGTCTGAT
716498 ACCCTAGGG
1 ACCCTAGGG
716507 ACACGCGGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.23
Consensus pattern (15 bp):
ACCCTAGGGTCTGAT
Found at i:729069 original size:6 final size:6
Alignment explanation
Indices: 729058--729105 Score: 62
Period size: 6 Copynumber: 7.7 Consensus size: 6
729048 TGAAGAAAAG
729058 AAAGAA AAAGAA AAA-AA AAAGGAAA AAAGAGA AAAGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAGAA AAA-G-AA AAAGA-A AAAGAA AAAGAA AAAG
729106 GAGGGTCAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.13
6 21 0.55
7 7 0.18
8 5 0.13
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:729090 original size:21 final size:20
Alignment explanation
Indices: 729053--729104 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
729043 ATGCTTGAAG
729053 AAAAGAAAGAAAAAGAAAAAA
1 AAAAGAAA-AAAAAGAAAAAA
* *
729074 AAAAGGAAAAAAGAGAAAAGA
1 AAAA-GAAAAAAAAGAAAAAA
729095 AAAAGAAAAA
1 AAAAGAAAAA
729105 GGAGGGTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 6 0.21
21 18 0.64
22 4 0.14
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAAAAGAAAAAA
Found at i:729090 original size:27 final size:27
Alignment explanation
Indices: 729052--729107 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
729042 TATGCTTGAA
729052 GAAAAGAAAGAAAAAGAAAAA-AAAAAG
1 GAAAAGAAAG-AAAAGAAAAAGAAAAAG
729079 GAAAA-AAGAGAAAAGAAAAAGAAAAAG
1 GAAAAGAA-AGAAAAGAAAAAGAAAAAG
729106 GA
1 GA
729108 GGGTCAAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (27 bp):
GAAAAGAAAGAAAAGAAAAAGAAAAAG
Found at i:730357 original size:83 final size:83
Alignment explanation
Indices: 730216--730624 Score: 727
Period size: 83 Copynumber: 5.0 Consensus size: 83
730206 GATATCCCAG
730216 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
730281 CTGATCTGGTTTGGACAGA
66 CTGATCTGGTTTGG-CAGA
730300 A-CAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
730364 CTGATCTGGTTTGGCAGA
66 CTGATCTGGTTTGGCAGA
730382 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
730447 CTGATCTGG-TTGGCAGA
66 CTGATCTGGTTTGGCAGA
*
730464 ACCAATCATTGAATTTAGAAGATGAATTTGTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
730528 CTGATCTGG-TTGGACAGA
66 CTGATCTGGTTTGG-CAGA
* * *
730546 ACCAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
*
730611 CTGATCTAGTTTGG
66 CTGATCTGGTTTGG
730625 TAGGAACTAC
Statistics
Matches: 317, Mismatches: 4, Indels: 8
0.96 0.01 0.02
Matches are distributed among these distances:
81 44 0.14
82 79 0.25
83 189 0.60
84 5 0.02
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (83 bp):
ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
CTGATCTGGTTTGGCAGA
Found at i:730583 original size:164 final size:166
Alignment explanation
Indices: 730216--730624 Score: 727
Period size: 164 Copynumber: 2.5 Consensus size: 166
730206 GATATCCCAG
730216 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
730281 CTGATCTGGTTTGGACAGAACAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAG
66 CTGATCTGGTTTGGACAGAACAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAG
730346 AAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
131 AAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
730382 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
*
730447 CTGATCTGG-TTGG-CAGAACCAATCATTGAATTTAGAAGATGAATTTGTC-ATAGCATCTTCTG
66 CTGATCTGGTTTGGACAGAA-CAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTA
730509 GAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGA
130 GAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGA
* * *
730546 ACCAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
*
730611 CTGATCTAGTTTGG
66 CTGATCTGGTTTGG
730625 TAGGAACTAC
Statistics
Matches: 235, Mismatches: 5, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
163 4 0.02
164 119 0.51
165 38 0.16
166 74 0.31
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (166 bp):
ACCAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTAT
CTGATCTGGTTTGGACAGAACAATCATTGAATTTAGAAGATGAATTTGTCAATAGCATCTTCTAG
AAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
Found at i:731554 original size:113 final size:112
Alignment explanation
Indices: 731370--732240 Score: 770
Period size: 113 Copynumber: 7.8 Consensus size: 112
731360 TGTATTGACA
731370 TTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* *
731435 AGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATT
66 AGAATTTGTTCAACCTTTTGTCTGAATTCATCATTTGATGGATCATT
731482 TTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTT-CCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * *
731547 AAGAATTTGTTCAACCTTTT-ACTTGAATCCATCATTTGATGGATCAGCT
65 AAGAATTTGTTCAACCTTTTGTC-TGAATTCATCATTTGATGGATCA-TT
*
731596 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
731661 AGAATTTGTTCAACCTTTT-ACTTGAATCCATCATTTGATGGATCAGCT
66 AGAATTTGTTCAACCTTTTGTC-TGAATTCATCATTTGATGGATCA-TT
* * ***
731709 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAATTTGTTCA-AACCTTT
1 TTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAA----T
* * * *** * * * *** * *
731773 TACATGAATCCATT--A-C--TTG-ATGGA-GCATCATCCCCAGCGGA-AAGTT
62 GAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCAT-TTGA-TGGATCA-TT
** * **
731819 CAT-AATGAGAAGAACTCAT-AT--GAA-AA---A---G-A-AA-GAAGAAGAAGTTCATAATGA
1 TTTCCA-GAGAAG-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
* ** * **
731870 GAAGAACTTGTTCAATTTTTTGGTTTGAATTCATCATTTGATGGATCAACA
64 GAAGAATTTGTTCAACCTTTT-GTCTGAATTCATCATTTGATGGATC-ATT
* * *
731921 TTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAAAAGAAGTTCATAAT
1 TTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * * **
731985 AAGAAGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCACA
62 GAGAAGAATTTGTTCAACCTTTT-GTCTGAATTCATCATTTGATGGATCATT
*
732037 TTGCCAG-GAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 TTTCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * * *
732101 GAGAAGAATTTGTTCAACCTTTTATCTGAATTCATCACTGGATGGATTATT
62 GAGAAGAATTTGTTCAACCTTTTGTCTGAATTCATCATTTGATGGATCATT
* * *
732152 TCTTCCAGAGAAAGTTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAAT
1 T-TTCCAGAGAAGGTTCATAATGAGAAGAA---CTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * *
732217 AAGAAGAACTTGTTCAACTTTTTG
62 GAGAAGAATTTGTTCAACCTTTTG
732241 CATAATTCTA
Statistics
Matches: 630, Mismatches: 86, Indels: 82
0.79 0.11 0.10
Matches are distributed among these distances:
95 8 0.01
97 1 0.00
98 11 0.02
99 4 0.01
100 3 0.00
101 12 0.02
102 7 0.01
103 8 0.01
104 4 0.01
105 2 0.00
107 2 0.00
108 3 0.00
109 7 0.01
110 15 0.02
111 10 0.02
112 6 0.01
113 264 0.42
114 6 0.01
115 23 0.04
116 167 0.27
117 67 0.11
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (112 bp):
TTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAATTTGTTCAACCTTTTGTCTGAATTCATCATTTGATGGATCATT
Found at i:731752 original size:226 final size:225
Alignment explanation
Indices: 731370--732239 Score: 962
Period size: 226 Copynumber: 3.9 Consensus size: 225
731360 TGTATTGACA
731370 TTTCCAGAGAAG-GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTTCCAGAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * * *
731434 AAGAATTTGTTCAACCTTTTGTCTGAATTCATCACTTGATGGATTATTTTTGCCAGAGAAGGTTC
66 AAGAATTTGTTCAACCTTTTATCTGAATTCATCACTTGATGGATCACTTTT-CCAGAGAAAGTTC
* * *
731499 ATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCT
130 ATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCT
731564 TTTACTTGAATCCATCATTTGATGGATCAGCT
195 TTTA-TTGAATCCATCATTTGATGGATCAGCT
731596 TTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTTCCAGAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* *
731660 AAGAATTTGTTCAACCTTTTA-CTTGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTT
66 AAGAATTTGTTCAACCTTTTATC-TGAATTCATCACTTGATGGATCA-CTTTTCCAGAGAAAGTT
* ** *
731724 CATAATGAGAAGAACTCATCTAAAGAA-G--GAAGAA-TT--T-GT-TCAA-ACCTT-TT--A-C
129 CATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACC
* * * * *
731776 ----A-TGAATCCATTACTTGATGGAGCATCA
194 TTTTATTGAATCCATCATTTGATGGATCAGCT
** * * *
731803 TCCCCAGCGGAA-AGTTCATAATGAGAAGAACTCATATGAAAAAGAAAGAAGAAGAAGTTCATAA
1 TTTCCAG-AGAAGAGTTCATAATGAGAAGAACTCATCTG---AAGAAGGAAGAAGAAGTTCATAA
* ** * * * * *
731867 TGAGAAGAACTTGTTCAATTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTA
62 TGAGAAGAATTTGTTCAACCTTTT-ATCTGAATTCATCACTTGATGGATC-ACTTTTCCAGAG-A
* * *
731931 GAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAAAAGAAGTTCATAATAAGAAGAACTT
124 AAGTTCATAATGAGAAGAA--C-TCATCTAAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTT
* * *
731996 GTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCA-CA
186 GTTCAACCTTTT--ATTGAATCCATCATTTGATGGATCAGCT
*
732037 TTGCCAG-GAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 TTTCCAGAGAAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAAT
* * *
732101 GAGAAGAATTTGTTCAACCTTTTATCTGAATTCATCACTGGATGGATTATTTCTTCCAGAGAAAG
63 GAGAAGAATTTGTTCAACCTTTTATCTGAATTCATCACTTGATGGATCACTT-TTCCAGAGAAAG
* *
732166 TTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTT
127 TTCATAATGAGAAGAACTCATC-TA--AAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
*
732231 CAACTTTTT
189 CAACCTTTT
732240 GCATAATTCT
Statistics
Matches: 538, Mismatches: 63, Indels: 80
0.79 0.09 0.12
Matches are distributed among these distances:
207 26 0.05
208 28 0.05
209 1 0.00
211 44 0.08
212 47 0.09
213 2 0.00
214 2 0.00
215 11 0.02
216 3 0.01
217 3 0.01
218 7 0.01
219 3 0.01
220 1 0.00
221 1 0.00
222 3 0.01
223 8 0.01
224 4 0.01
225 4 0.01
226 140 0.26
227 5 0.01
228 1 0.00
229 4 0.01
230 2 0.00
231 2 0.00
232 91 0.17
233 62 0.12
234 7 0.01
235 20 0.04
236 6 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (225 bp):
TTTCCAGAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
AAGAATTTGTTCAACCTTTTATCTGAATTCATCACTTGATGGATCACTTTTCCAGAGAAAGTTCA
TAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTT
TTATTGAATCCATCATTTGATGGATCAGCT
Found at i:731852 original size:95 final size:93
Alignment explanation
Indices: 731660--731852 Score: 253
Period size: 94 Copynumber: 2.1 Consensus size: 93
731650 TCATAATGAG
* * * * **
731660 AAGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTC
1 AAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGAGAAAGTTC
* *
731725 ATAATGAGAAGAACTCATCTAAAGAAGG
66 ATAATGAGAAGAACTCATATAAAGAAGA
* * *
731753 AAGAATTTGTTCAAACCTTTTACATGAATCCATTACTTGATGGAGCATCATCCCCAGCGGAAAGT
1 AAGAATTTGTTC-AACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAG-AGAAAGT
731818 TCATAATGAGAAGAACTCATATGAAA-AAGA
64 TCATAATGAGAAGAACTCATAT-AAAGAAGA
731848 AAGAA
1 AAGAA
731853 GAAGAAGTTC
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
93 12 0.14
94 36 0.42
95 35 0.41
96 3 0.03
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (93 bp):
AAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGAGAAAGTTC
ATAATGAGAAGAACTCATATAAAGAAGA
Found at i:731949 original size:212 final size:206
Alignment explanation
Indices: 731546--731955 Score: 561
Period size: 212 Copynumber: 2.0 Consensus size: 206
731536 TTCATAATGA
* * * * **
731546 GAAGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTT
1 GAAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGAGAAAGTT
* * *
731611 CATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC
66 CATAATGAGAAGAACTCATATGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
* * *
731676 TTTTACTTGAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTC
131 TTTTACTTGAATCCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTC
731741 ATCTAAAGAAG
196 ATCTAAAGAAG
* * *
731752 GAAGAATTTGTTCAAACCTTTTACATGAATCCATTACTTGATGGAGCATCATCCCCAGCGGAAAG
1 GAAGAATTTGTTC-AACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAG-AGAAAG
731817 TTCATAATGAGAAGAACTCATATGAAAAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
64 TTCATAATGAGAAGAACTCATATG---AAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
** ** * *
731882 CAATTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGA
126 CAACCTTTT-ACTTGAATCCATCATTTGATGGATCAACATTGCCAGAG-AAAGTTCATAATGAGA
731946 AGAACTCATC
189 AGAACTCATC
731956 ATCTGAAGAA
Statistics
Matches: 176, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
206 13 0.07
207 36 0.20
208 28 0.16
211 44 0.25
212 55 0.31
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (206 bp):
GAAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGAGAAAGTT
CATAATGAGAAGAACTCATATGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
TTTTACTTGAATCCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTC
ATCTAAAGAAG
Found at i:732097 original size:116 final size:115
Alignment explanation
Indices: 731811--732240 Score: 576
Period size: 116 Copynumber: 3.7 Consensus size: 115
731801 CATCCCCAGC
** * *
731811 GGAAAGTTCATAATGAGAAGAACTCAT-ATGAAAAAGAAAGAAGAAGAAGTTCATAATGAGAAGA
1 GGAAAGTTCATAATGAGAAGAACTCATCAT-ATGAAGAAGGAAGAAGAAGTTCATAATAAGAAGA
**
731875 ACTTGTTCAATTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCA
65 ACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATC-ACATTGCCA
* * *
731927 GGTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAAAAGAAGTTCATAATAAGAAGA
1 GG-AAAGTTCATAATGAGAAGAACTCATCATATGAAGAAGGAAGAAGAAGTTCATAATAAGAAGA
731992 ACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCACATTGCCA
65 ACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCACATTGCCA
* * *
732043 GGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
1 GGAA-AGTTCATAATGAGAAGAACTCATCATATGAAGAAGGAAGAAGAAGTTCATAATAAGAAGA
* * * * * * ** *
732108 ATTTGTTCAACCTTTT-ATCTGAATTCATCACTGGATGGATTATTTCTTCCA
65 ACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCACAT-TGCCA
* *
732159 GAGAAAGTTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAAGAAGA
1 G-GAAAGTTCATAATGAGAAGAACTCATCATATGAAGAAGGAAGAAGAAGTTCATAATAAGAAGA
*
732224 ACTTGTTCAACTTTTTG
65 ACTTGTTCAACCTTTTG
732241 CATAATTCTA
Statistics
Matches: 280, Mismatches: 28, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
115 23 0.08
116 160 0.57
117 95 0.34
118 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (115 bp):
GGAAAGTTCATAATGAGAAGAACTCATCATATGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAA
CTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCACATTGCCA
Found at i:732254 original size:116 final size:114
Alignment explanation
Indices: 731752--732254 Score: 497
Period size: 116 Copynumber: 4.3 Consensus size: 114
731742 TCTAAAGAAG
* * * * * * *
731752 GAAGAATTTGTTCAAACC-TTTTACATGAATCCATTACTTGATGGAGCATCATCCCCAGCGGAAA
1 GAAGAACTTGTTC-AACCTTTTTGCTTGAATTCATCACTTGATGGATCATC-T-TCCA--GGAAA
* *
731816 GTTCATAATGAGAAGAA---CTCATATGAAAAAGAAAGAAGAAGAAGTTCATAATGA
61 GTTCATAATGAGAAGAACTCCTCATATGAAGAAG--A-AAGAAGAAGTTCATAATAA
* * * * *
731870 GAAGAACTTGTTCAA-TTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAG
1 GAAGAACTTGTTCAACCTTTTT-GCTTGAATTCATCACTTGATGGATCATC-TT-CCAGG-AAAG
* *
731934 TTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAA-AAGAAGTTCATAATAA
62 TTCATAATGAGAAGAACTCCTCATATGAAGAA-GAAAGAAGAAGTTCATAATAA
* * *
731987 GAAGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCA-CATTGCCAGGAAGAGT
1 GAAGAACTTGTTCAACCTTTTTGCTTGAATTCATCACTTGATGGATCATC-TT-CCAGGAA-AGT
* * * *
732051 TCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
63 TCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAA
* * *
732103 GAAGAATTTGTTCAACCTTTTAT-C-TGAATTCATCACTGGATGGATTATTTCTTCCAGAGAAAG
1 GAAGAACTTGTTCAACCTTTT-TGCTTGAATTCATCACTTGATGGATCA--TCTTCCAG-GAAAG
732166 TTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAA
62 TTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAA
*
732219 GAAGAACTTGTTCAA-CTTTTTGCAT-AATTCTATCAC
1 GAAGAACTTGTTCAACCTTTTTGCTTGAATTC-ATCAC
732255 AGAAGGAGAT
Statistics
Matches: 333, Mismatches: 33, Indels: 40
0.82 0.08 0.10
Matches are distributed among these distances:
114 1 0.00
115 35 0.11
116 155 0.47
117 86 0.26
118 44 0.13
119 1 0.00
120 10 0.03
121 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (114 bp):
GAAGAACTTGTTCAACCTTTTTGCTTGAATTCATCACTTGATGGATCATCTTCCAGGAAAGTTCA
TAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAA
Found at i:732472 original size:3 final size:3
Alignment explanation
Indices: 732464--732510 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
732454 TCCATATTTA
*
732464 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
732511 AATATATATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:732537 original size:14 final size:15
Alignment explanation
Indices: 732509--732543 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
732499 TTATTATTAT
732509 TAAATATATATTAAA
1 TAAATATATATTAAA
732524 TAAATATATA-TAAA
1 TAAATATATATTAAA
732538 TAAATA
1 TAAATA
732544 ATTACAGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:732970 original size:19 final size:19
Alignment explanation
Indices: 732946--732986 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
732936 ACCCCAACCT
732946 GAAAAAAAAAACG-GAGACA
1 GAAAAAAAAAA-GAGAGACA
*
732965 GAAAAAAAAGAGAGAGACA
1 GAAAAAAAAAAGAGAGACA
732984 GAA
1 GAA
732987 CCGAAGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.68, C:0.07, G:0.24, T:0.00
Consensus pattern (19 bp):
GAAAAAAAAAAGAGAGACA
Found at i:732971 original size:16 final size:16
Alignment explanation
Indices: 732946--733019 Score: 64
Period size: 16 Copynumber: 4.8 Consensus size: 16
732936 ACCCCAACCT
*
732946 GAAA-AAAAAAACGGA
1 GAAAGAAAAAAACAGA
*
732961 GACAGAAAAAAA-AGA
1 GAAAGAAAAAAACAGA
* * * *
732976 GAGAG-ACAGAACCGAA
1 GAAAGAAAAAAACAG-A
732992 GAAAGAAAAAAACAGA
1 GAAAGAAAAAAACAGA
733008 GAAAGAAAAAAA
1 GAAAGAAAAAAA
733020 AACCTACTAA
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
14 4 0.09
15 10 0.22
16 25 0.56
17 6 0.13
ACGTcount: A:0.70, C:0.08, G:0.22, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAAAACAGA
Found at i:734629 original size:2 final size:2
Alignment explanation
Indices: 734622--734682 Score: 72
Period size: 2 Copynumber: 31.5 Consensus size: 2
734612 AATTTTACAC
* ** *
734622 TA TA TA TA TA TA TA TA TA T- TG CC TT TA T- 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
734662 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
734683 TTGCCTTTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:737995 original size:18 final size:19
Alignment explanation
Indices: 737958--737995 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
737948 TCTGTTGGGA
*
737958 TTGGGCCTGAACCGGGTTG
1 TTGGGCCTAAACCGGGTTG
737977 TTGGGCCTAAACC-GGTTG
1 TTGGGCCTAAACCGGGTTG
737995 T
1 T
737996 AACTGAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.13, C:0.21, G:0.37, T:0.29
Consensus pattern (19 bp):
TTGGGCCTAAACCGGGTTG
Found at i:741735 original size:132 final size:131
Alignment explanation
Indices: 741403--741750 Score: 520
Period size: 130 Copynumber: 2.7 Consensus size: 131
741393 ATTCTAAGGA
* * *
741403 AGAAAACGATAACATCTAATTATTTCTGATCGAGAATAAATGACCTCTCATGTCTTAAAGCAGTC
1 AGAAAACGATAATATCTAATTATTTCTAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
* * * * *
741468 ATTTATTACTCCAATCGAAATGAAGACATATCAATATTTCGTCTTAAAACTCAATATTGATTCGA
66 ATTTATTACTCCAATCGAAATAAAGAAATATCAATATTCCGTCTTAAAAATCAATATTGATTCAA
741533 G
131 G
* * * * * *
741534 TGAAACCGATAATATATAATGATTTC-AATCAAGAATAAATGACCTCTCATGCCTTAAAGCAGAC
1 AGAAAACGATAATATCTAATTATTTCTAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
*
741598 ATTTATTACTCCAATCGAAATAAAGAAATATCATTATTCCGTCTTAAAAATCAAATATTGATTCA
66 ATTTATTACTCCAATCGAAATAAAGAAATATCAATATTCCGTCTTAAAAATC-AATATTGATTCA
741663 AG
130 AG
*
741665 AGAAAAC-AGTAATATCGAATTATTTCTAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGT
1 AGAAAACGA-TAATATCTAATTATTTCTAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGT
741729 CATTTATTACTCCAATCGAAAT
65 CATTTATTACTCCAATCGAAAT
741751 GAAATGATAT
Statistics
Matches: 192, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
130 82 0.43
131 53 0.28
132 57 0.30
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (131 bp):
AGAAAACGATAATATCTAATTATTTCTAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
ATTTATTACTCCAATCGAAATAAAGAAATATCAATATTCCGTCTTAAAAATCAATATTGATTCAA
G
Found at i:743522 original size:22 final size:22
Alignment explanation
Indices: 743496--743537 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
743486 TGGGTCGATC
*
743496 CTGTTGGGCTTGAGTTTTGGTT
1 CTGTTGGGCTCGAGTTTTGGTT
743518 CTGTTGGGCTCGAGTTTTGG
1 CTGTTGGGCTCGAGTTTTGG
743538 GTCGAATTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.05, C:0.12, G:0.38, T:0.45
Consensus pattern (22 bp):
CTGTTGGGCTCGAGTTTTGGTT
Found at i:744144 original size:133 final size:135
Alignment explanation
Indices: 743834--744192 Score: 490
Period size: 133 Copynumber: 2.7 Consensus size: 135
743824 GTCTAAAAAG
* *
743834 AGATTTGGAAATGTTGATTCATTCTGTTGTTCTTC-AGAGAAGATTGAATCGAGGCAGACTTGTT
1 AGATTTGGAAATGTTGATTTATTCTATTGTTCTTCAAG-GAAGATTGAATCGAGGCAGACTTGTT
* * * * *
743898 TCACTGTTCCTCGGGGAAGATCAAATCTAAAAAAAAAGAGGGATATATTCCGCTGCTTCTTGAGG
65 CCACTGTTCCTCAGGGAAGATCAAATCTAAAAAAAAACAGGGA-ATATTCCACTGCTTCTTGAGA
743963 GAAAATC
129 GAAAATC
** * * * *
743970 AGATCAGGAAATGTTGATTTATTGTATTGTTCTTCAGGGAAGATTGAATCAAGGTAGACTTGTTC
1 AGATTTGGAAATGTTGATTTATTCTATTGTTCTTCAAGGAAGATTGAATCGAGGCAGACTTGTTC
* * * *
744035 CACTGTTCCTTAGGGAAGATCAAATCT-AGAAAAAACTGGG-ATGTTCCACTGCTTCTTGAGAGA
66 CACTGTTCCTCAGGGAAGATCAAATCTAAAAAAAAACAGGGAATATTCCACTGCTTCTTGAGAGA
744098 AAATC
131 AAATC
* * *
744103 AGATTTGGAAATGTTGATTTATTCCACTGTTCTTCAAGGAAGATTGAATCGAGGCAAACTTGTTC
1 AGATTTGGAAATGTTGATTTATTCTATTGTTCTTCAAGGAAGATTGAATCGAGGCAGACTTGTTC
*
744168 CACTGTTCCTCAGGGAATATCAAAT
66 CACTGTTCCTCAGGGAAGATCAAAT
744193 TTGGAAAGAA
Statistics
Matches: 194, Mismatches: 28, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
133 104 0.54
135 10 0.05
136 79 0.41
137 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (135 bp):
AGATTTGGAAATGTTGATTTATTCTATTGTTCTTCAAGGAAGATTGAATCGAGGCAGACTTGTTC
CACTGTTCCTCAGGGAAGATCAAATCTAAAAAAAAACAGGGAATATTCCACTGCTTCTTGAGAGA
AAATC
Found at i:745694 original size:66 final size:66
Alignment explanation
Indices: 745615--745753 Score: 260
Period size: 66 Copynumber: 2.1 Consensus size: 66
745605 CATTTTAGTA
*
745615 ATTTTAAGATTTTGAAATCAAGTTTTGAAATTACTCCCCCTTACTTTAACACTTCTCCCATTTAT
1 ATTTTAAGATTTTGAAATCAAGTTTTGAAATTACTCCCCCTTACTTTAACACCTCTCCCATTTAT
745680 C
66 C
*
745681 ATTTTAAGATTTTGAAATCAAGTTTTGAAATTACTCCCCCTTACTTTAACACCTCTCTCATTTAT
1 ATTTTAAGATTTTGAAATCAAGTTTTGAAATTACTCCCCCTTACTTTAACACCTCTCCCATTTAT
745746 C
66 C
745747 ATTTTAA
1 ATTTTAA
745754 AAGCACACTT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 71 1.00
ACGTcount: A:0.29, C:0.22, G:0.06, T:0.43
Consensus pattern (66 bp):
ATTTTAAGATTTTGAAATCAAGTTTTGAAATTACTCCCCCTTACTTTAACACCTCTCCCATTTAT
C
Found at i:748009 original size:21 final size:21
Alignment explanation
Indices: 747983--748022 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
747973 TAGAACCCCA
*
747983 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
748004 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
748023 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:748057 original size:20 final size:21
Alignment explanation
Indices: 748003--748065 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
747993 GATTCCCCTG
748003 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
748027 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
748047 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
748066 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:754080 original size:11 final size:10
Alignment explanation
Indices: 754059--754090 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
754049 ATTTATTATA
*
754059 TTTTATTTTT
1 TTTTCTTTTT
754069 TTTTCTTTTT
1 TTTTCTTTTT
754079 TTTTCTTTTT
1 TTTTCTTTTT
754089 TT
1 TT
754091 CTTTAGGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.03, C:0.06, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:766742 original size:23 final size:23
Alignment explanation
Indices: 766703--766746 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
766693 TGGGTCGATC
*
766703 CTATTGGGCTTTGGGTTTTGGTT
1 CTATTGGGCTTCGGGTTTTGGTT
766726 CTATTGGGC-TCGAGGTTTTGG
1 CTATTGGGCTTCG-GGTTTTGG
766747 GTGTAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.07, C:0.11, G:0.36, T:0.45
Consensus pattern (23 bp):
CTATTGGGCTTCGGGTTTTGGTT
Found at i:766867 original size:3 final size:3
Alignment explanation
Indices: 766839--766901 Score: 56
Period size: 3 Copynumber: 21.3 Consensus size: 3
766829 CTTTACAATA
* * * * * * *
766839 AAT AAA AAT AAT -AT TAT AAT ACT AAT AAT TAT AAT TAT AAT AGT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
766886 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
766902 GCAGGATGAA
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:766902 original size:21 final size:21
Alignment explanation
Indices: 766845--766902 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
766835 AATAAATAAA
*
766845 AATAAT-ATTATAATACTAAT
1 AATAATAATTATAATAGTAAT
* *
766865 AATTATAATTATAATAGTACT
1 AATAATAATTATAATAGTAAT
*
766886 AATAATAATAATAATAG
1 AATAATAATTATAATAG
766903 CAGGATGAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 5 0.16
21 27 0.84
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
AATAATAATTATAATAGTAAT
Found at i:767059 original size:35 final size:35
Alignment explanation
Indices: 766981--767116 Score: 163
Period size: 35 Copynumber: 3.9 Consensus size: 35
766971 GACTACAAGG
* *
766981 TGCTTCTCCAAAGGACATGATG-TT-ATCATGAGA
1 TGCTTCTCCAAAGGACATGATGCTTCACCAAGAGA
*
767014 TGCTTCTCCAAAGGACATGATGCTTCATCAAGAGA
1 TGCTTCTCCAAAGGACATGATGCTTCACCAAGAGA
* * *
767049 TGCTTTTCCAAAGGACTTGATGCTTAACCAAGAGA
1 TGCTTCTCCAAAGGACATGATGCTTCACCAAGAGA
*
767084 TGTCTT-TCC-AAGAGACATGATGTTTCACCAAGA
1 TG-CTTCTCCAAAG-GACATGATGCTTCACCAAGA
767117 AGTGCCTTCC
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
33 22 0.24
34 5 0.05
35 61 0.67
36 3 0.03
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.29
Consensus pattern (35 bp):
TGCTTCTCCAAAGGACATGATGCTTCACCAAGAGA
Found at i:770574 original size:137 final size:138
Alignment explanation
Indices: 769897--770930 Score: 1282
Period size: 137 Copynumber: 7.5 Consensus size: 138
769887 ATAACGAATA
* * * * *
769897 ATAGGTGTTGACGTGAATATTG-CCCACCGGGGGACATCACACATAATAGGGCAATTATAACATA
1 ATAGGTGTTGATGTGAATAGTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTA
* * * * *
769961 TTCTCTAAC-AAAAAGGAAAGGCGTGTCCCATAAGAAACGCTTTCACCACATTGTTGCGTCCCCT
66 TTTTCTGACAAAAAAGGAAAGGCGCGTCCCACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCT
770025 CAAACATG
131 CAAACATG
* * * * * * *
770033 ATAGGTGTTGATGTGAATAGT--TCCACCAGGGGACATCACACATAATAGGGTAATTACAACATA
1 ATAGGTGTTGATGTGAATAGTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTA
* * **
770096 TTCTCTGAC-AAAAAGGAAAGACGCGTCCCAC---AAGTTCTTTCACCACATTGTTGCGTCCCCT
66 TTTTCTGACAAAAAAGGAAAGGCGCGTCCCACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCT
770157 CAAACATG
131 CAAACATG
* * * * * *
770165 ATAGGTGTTTATATGAATAATGCCCTGTCGGGGGACATGACGCATAATAGGGCAATTATAACCTA
1 ATAGGTGTTGATGTGAATAGTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTA
* * *
770230 TTTTCTAACAAAAAAAGAAAAGGCGCGTCCCACAAGAAGCGTTTTCACCACATTGTTGCGTCCCC
66 TTTTCTGAC-AAAAAAGGAAAGGCGCGTCCCACAAGAAGCGCTTTCACCACATTGTTGCGTCCCC
*
770295 TCAAACATA
130 TCAAACATG
** * * * * * *
770304 ATAGGTGTTGACATCAATTGTG-CCCACCGGGGGACATCACACATAATAGAGCAATTATAACATA
1 ATAGGTGTTGATGTGAATAGTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTA
* * * * * * * *
770368 TTCTCTAAC-AAAAATGAAAGGCGTGTCCCACAAGAAGCGCTTTTACAATATTGTTGCATCCCCT
66 TTTTCTGACAAAAAAGGAAAGGCGCGTCCCACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCT
770432 CAAACATG
131 CAAACATG
* * * * * *
770440 ATAGGTGTTAACGTGAATAGT-CCTCGTCAGGGGACATGACACATAATAGGGTAATTATAACCTA
1 ATAGGTGTTGATGTGAATAGTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTA
* * *
770504 TTTTCTGACAAAAAAGGAAAGGCGCGTCCCATAAGAAGCGTTTTCACCATATTGTTGCGTCCCCT
66 TTTTCTGACAAAAAAGGAAAGGCGCGTCCCACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCT
770569 CAAACATG
131 CAAACATG
* * * * *
770577 ATAGATGTTTATGTGAATAGTGCCCCGCCTGGGGACATGACATATAATAGGGAAATTATAACCTA
1 ATAGGTGTTGATGTGAATAGTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTA
* * *
770642 TTTTCTGACCAAAAAGAAAAAGAAAGGCGCGTCCCACAAGAAGTGCTTTCACCACATTGTTACGT
66 TTTTCTGA-C---AA-AAAAGGAAAGGCGCGTCCCACAAGAAGCGCTTTCACCACATTGTTGCGT
770707 CCCCTCAAACATG
126 CCCCTCAAACATG
* *
770720 ATAGGTGTTGATGCGAATAGTGCCCCGCCGGGGGACATGACACAAAATAGGGCAATTATAACCTA
1 ATAGGTGTTGATGTGAATAGTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTA
*** *
770785 TTTTCTGACAAAAAAGGAAA-GTATGTCCCACAAGAAGCGCTTTCACCACATTGTTGCGTCCTCT
66 TTTTCTGACAAAAAAGGAAAGGCGCGTCCCACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCT
770849 CAAACATG
131 CAAACATG
770857 ATAGGTGTTGATGTGAATAGTGCCCCGCCGGGGGACATGACACATAATAGGGCAAAATTATAACC
1 ATAGGTGTTGATGTGAATAGTGCCCCGCCGGGGGACATGACACATAATAGGGC--AATTATAACC
770922 TATTTTCTG
64 TATTTTCTG
770931 GGAAAAAAAG
Statistics
Matches: 774, Mismatches: 107, Indels: 31
0.85 0.12 0.03
Matches are distributed among these distances:
132 53 0.07
134 39 0.05
135 65 0.08
136 151 0.20
137 171 0.22
138 97 0.13
139 73 0.09
142 3 0.00
143 122 0.16
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (138 bp):
ATAGGTGTTGATGTGAATAGTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTA
TTTTCTGACAAAAAAGGAAAGGCGCGTCCCACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCT
CAAACATG
Found at i:770822 original size:280 final size:279
Alignment explanation
Indices: 769897--770976 Score: 1305
Period size: 280 Copynumber: 3.9 Consensus size: 279
769887 ATAACGAATA
* * * *
769897 ATAGGTGTTGACGTGAATATTG-CCCACCGGGGGACATCACACATAATAGGGCAATTATAACATA
1 ATAGGTGTTGACGTGAATAGTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTA
* * * *
769961 TTCTCTAAC-AAAAAGGAAAGGCGTGTCCCATAAGAAACGCTTTCACCACATTGTTGCGTCCCCT
66 TTTTCTAACAAAAAAGGAAAGGCGCGTCCCACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCT
* * *
770025 CAAACATGATAGGTGTTGATGTGAATAGT-TCCACCAGGGGACATCACACATAATAGGGTAATTA
131 CAAACATGATAGGTGTTGATGTGAATAGTGCCCACCGGGGGACATCACACATAATAGGGAAATTA
* * * * **
770089 CAACATATTCTCTGACAAAAAG-----GAAAGACGCGTCCCAC---AAGTTCTTTCACCACATTG
196 TAACCTATTTTCTGACAAAAAGAAAAAGAAAGGCGCGTCCCACAAGAAGCGCTTTCACCACATTG
770146 TTGCGTCCCCTCAAACATG
261 TTGCGTCCCCTCAAACATG
* ** * * * *
770165 ATAGGTGTTTATATGAATAATGCCCTGTCGGGGGACATGACGCATAATAGGGCAATTATAACCTA
1 ATAGGTGTTGACGTGAATAGTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTA
* *
770230 TTTTCTAACAAAAAAAGAAAAGGCGCGTCCCACAAGAAGCGTTTTCACCACATTGTTGCGTCCCC
66 TTTTCTAAC-AAAAAAGGAAAGGCGCGTCCCACAAGAAGCGCTTTCACCACATTGTTGCGTCCCC
* ** * * * *
770295 TCAAACATAATAGGTGTTGACATCAATTGTGCCCACCGGGGGACATCACACATAATAGAGCAATT
130 TCAAACATGATAGGTGTTGATGTGAATAGTGCCCACCGGGGGACATCACACATAATAGGGAAATT
* * * * * * * *
770360 ATAA-C-ATATTCT--CTAACA-AAAATGAAAGGCGTGTCCCACAAGAAGCGCTTTTACAATATT
195 ATAACCTATTTTCTGACAAAAAGAAAAAGAAAGGCGCGTCCCACAAGAAGCGCTTTCACCACATT
*
770420 GTTGCATCCCCTCAAACATG
260 GTTGCGTCCCCTCAAACATG
* * * * *
770440 ATAGGTGTTAACGTGAATAGT-CCTCGTCAGGGGACATGACACATAATAGGGTAATTATAACCTA
1 ATAGGTGTTGACGTGAATAGTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTA
* * * *
770504 TTTTCTGACAAAAAAGGAAAGGCGCGTCCCATAAGAAGCGTTTTCACCATATTGTTGCGTCCCCT
66 TTTTCTAACAAAAAAGGAAAGGCGCGTCCCACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCT
* * * * * *
770569 CAAACATGATAGATGTTTATGTGAATAGTGCCCCGCCTGGGGACATGACATATAATAGGGAAATT
131 CAAACATGATAGGTGTTGATGTGAATAGTG-CCCACCGGGGGACATCACACATAATAGGGAAATT
*
770634 ATAACCTATTTTCTGACCAAAAAGAAAAAGAAAGGCGCGTCCCACAAGAAGTGCTTTCACCACAT
195 ATAACCTATTTTCTGA-CAAAAAGAAAAAGAAAGGCGCGTCCCACAAGAAGCGCTTTCACCACAT
*
770699 TGTTACGTCCCCTCAAACATG
259 TGTTGCGTCCCCTCAAACATG
* * *
770720 ATAGGTGTTGATGCGAATAGTGCCCCGCCGGGGGACATGACACAAAATAGGGCAATTATAACCTA
1 ATAGGTGTTGACGTGAATAGTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTA
* *** *
770785 TTTTCTGACAAAAAAGGAAA-GTATGTCCCACAAGAAGCGCTTTCACCACATTGTTGCGTCCTCT
66 TTTTCTAACAAAAAAGGAAAGGCGCGTCCCACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCT
* *
770849 CAAACATGATAGGTGTTGATGTGAATAGTGCCCCGCCGGGGGACATGACACATAATAGGGCAAAA
131 CAAACATGATAGGTGTTGATGTGAATAGTG-CCCACCGGGGGACATCACACATAATAGGG--AAA
* * *
770914 TTATAACCTATTTTCTGGGAAAAAAAGAAAAAAGAAAGGTGCATCCCACAAGAAGCGCTTTCA
193 TTATAACCTATTTTCT--GACAAAAAG-AAAAAGAAAGGCGCGTCCCACAAGAAGCGCTTTCA
770977 AGTGAATAGT
Statistics
Matches: 688, Mismatches: 99, Indels: 34
0.84 0.12 0.04
Matches are distributed among these distances:
268 22 0.03
269 44 0.06
270 5 0.01
271 74 0.11
272 47 0.07
273 76 0.11
274 78 0.11
275 50 0.07
276 6 0.01
279 4 0.01
280 165 0.24
281 58 0.08
282 19 0.03
283 6 0.01
284 34 0.05
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (279 bp):
ATAGGTGTTGACGTGAATAGTGCCCCGCCGGGGGACATGACACATAATAGGGCAATTATAACCTA
TTTTCTAACAAAAAAGGAAAGGCGCGTCCCACAAGAAGCGCTTTCACCACATTGTTGCGTCCCCT
CAAACATGATAGGTGTTGATGTGAATAGTGCCCACCGGGGGACATCACACATAATAGGGAAATTA
TAACCTATTTTCTGACAAAAAGAAAAAGAAAGGCGCGTCCCACAAGAAGCGCTTTCACCACATTG
TTGCGTCCCCTCAAACATG
Found at i:774352 original size:13 final size:14
Alignment explanation
Indices: 774334--774368 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
774324 AATAATTTTA
774334 AACCCTAAA-CCTT
1 AACCCTAAACCCTT
774347 AACCCTAAACCCTT
1 AACCCTAAACCCTT
774361 AACCCTAA
1 AACCCTAA
774369 TTAAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (14 bp):
AACCCTAAACCCTT
Found at i:781073 original size:29 final size:26
Alignment explanation
Indices: 781026--781089 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
781016 AATTTAGCTT
781026 TCCC-TTTT-TTCTTCATTTTCCATCTTC
1 TCCCATTTTATTCTTCATTTT-C-T-TTC
*
781053 TCCCATTTTATTCTTCTTTTTCTTTC
1 TCCCATTTTATTCTTCATTTTCTTTC
*
781079 TCTCATTTTAT
1 TCCCATTTTAT
781090 ATCAATCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 13 0.39
27 5 0.15
28 5 0.15
29 10 0.30
ACGTcount: A:0.09, C:0.28, G:0.00, T:0.62
Consensus pattern (26 bp):
TCCCATTTTATTCTTCATTTTCTTTC
Found at i:786424 original size:19 final size:20
Alignment explanation
Indices: 786400--786450 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
786390 AAAATGATTT
786400 GATTTTGAAAA-CAAAAATG-
1 GATTTTGAAAATC-AAAATGA
786419 GATTTTGAAAATCAAAATGA
1 GATTTTGAAAATCAAAATGA
*
786439 AATTTTGAAAAT
1 GATTTTGAAAAT
786451 GGATTTAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.51, C:0.04, G:0.14, T:0.31
Consensus pattern (20 bp):
GATTTTGAAAATCAAAATGA
Found at i:789114 original size:60 final size:61
Alignment explanation
Indices: 789042--789229 Score: 201
Period size: 60 Copynumber: 3.1 Consensus size: 61
789032 TTTGGGTGCC
*
789042 TTTTGA-GATGAAATTAAAAGATTCAAAAGTTTAAGGACCAATTTAAG-GT-AAGAGTCATA
1 TTTTGAGGATGAAATTAAAAGATTCAAAAGTTTAAGGACCAATTTAAGAATGAA-AGTCATA
* *
789101 TTTTGAGGATGAAATTGAAATG-TTCAAAAGTTTAAGGACTAATTT-AGAATGAAAGTCATA
1 TTTTGAGGATGAAATT-AAAAGATTCAAAAGTTTAAGGACCAATTTAAGAATGAAAGTCATA
* * * * * * *
789161 GTTTAAGGATAAAATTAGAATATTCAAAAGTTTGAGGAACAATTTAA-AATGATAA-TCATA
1 TTTTGAGGATGAAATTAAAAGATTCAAAAGTTTAAGGACCAATTTAAGAATGA-AAGTCATA
*
789221 GTTTGAGGA
1 TTTTGAGGA
789230 CATATGATGC
Statistics
Matches: 109, Mismatches: 13, Indels: 13
0.81 0.10 0.10
Matches are distributed among these distances:
59 10 0.09
60 90 0.83
61 9 0.08
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (61 bp):
TTTTGAGGATGAAATTAAAAGATTCAAAAGTTTAAGGACCAATTTAAGAATGAAAGTCATA
Found at i:789151 original size:29 final size:29
Alignment explanation
Indices: 789119--789211 Score: 66
Period size: 29 Copynumber: 3.1 Consensus size: 29
789109 ATGAAATTGA
789119 AATGTTCAAAAGTTTAAGGACTAATTTAG
1 AATGTTCAAAAGTTTAAGGACTAATTTAG
* * *
789148 AATGAAAGTC-ATAGTTTAAGGA-TAAAATTAG
1 AATG---TTCAAAAGTTTAAGGACT-AATTTAG
* * *
789179 AATATTCAAAAGTTTGAGGAAC-AATTTAA
1 AATGTTCAAAAGTTTAAGG-ACTAATTTAG
789208 AATG
1 AATG
789212 ATAATCATAG
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
28 2 0.04
29 21 0.45
30 2 0.04
31 20 0.43
32 2 0.04
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.31
Consensus pattern (29 bp):
AATGTTCAAAAGTTTAAGGACTAATTTAG
Found at i:791511 original size:11 final size:11
Alignment explanation
Indices: 791473--791659 Score: 58
Period size: 11 Copynumber: 15.0 Consensus size: 11
791463 AATTAGTAGT
791473 AATCATTATTA
1 AATCATTATTA
*
791484 AAACATTATTATCA
1 AATCATTA-T-T-A
791498 AATCATTATTA
1 AATCATTATTA
791509 AATC-TTA-TA
1 AATCATTATTA
791518 ATTAT-ATTATTA
1 A--ATCATTATTA
*
791530 GTAATCATTAATA
1 --AATCATTATTA
791543 AATCATTAGTATCA
1 AATCATTA-T-T-A
*
791557 AATCCAAATAATTA
1 AAT-C--ATTATTA
791571 AAT-ATTTATAATA
1 AATCA-TTAT--TA
*
791584 AATAATTATTA
1 AATCATTATTA
*
791595 GTAATCATTACTA
1 --AATCATTATTA
791608 AATCATTAAATATCA
1 AATCATT--AT-T-A
791623 AATCATTAGATTAA
1 AATCATT--ATT-A
*
791637 TAATAATTATTA
1 -AATCATTATTA
791649 AATCATTATTA
1 AATCATTATTA
791660 GTAACATTAA
Statistics
Matches: 136, Mismatches: 13, Indels: 54
0.67 0.06 0.27
Matches are distributed among these distances:
9 3 0.02
10 4 0.03
11 47 0.35
12 7 0.05
13 31 0.23
14 21 0.15
15 19 0.14
16 1 0.01
17 3 0.02
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (11 bp):
AATCATTATTA
Found at i:791598 original size:65 final size:63
Alignment explanation
Indices: 791463--791672 Score: 209
Period size: 65 Copynumber: 3.3 Consensus size: 63
791453 AAAATTATCA
* * * * * * *
791463 AATTAGTAGTAATCATTATTAAAACATTATTATCAAATC-ATTATTAAAT-CTTATAAT-TAT
1 AATTATTAGTAATCATTAATAAATCATTAATATCAAATCAATAATTAAATAATTATAATAAAT
* *
791523 -ATTATTAGTAATCATTAATAAATCATTAGTATCAAATCCAAATAATTAAATATTTATAATAAAT
1 AATTATTAGTAATCATTAATAAATCATTAATATCAAAT-C-AATAATTAAATAATTATAATAAAT
* *
791587 AATTATTAGTAATCATTACTAAATCATTAAATATCAAATCATTAGATTAATAATAATTAT--TAA
1 AATTATTAGTAATCATTAATAAATCATT-AATATCAAATCAATA-ATT-A-AATAATTATAATAA
791650 AT
62 AT
*
791652 CATTATTAGTAA-CATTAATAA
1 AATTATTAGTAATCATTAATAA
791673 TCAACCAATC
Statistics
Matches: 127, Mismatches: 13, Indels: 16
0.81 0.08 0.10
Matches are distributed among these distances:
59 33 0.26
60 1 0.01
62 9 0.07
63 7 0.06
64 13 0.10
65 46 0.36
66 10 0.08
67 8 0.06
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.40
Consensus pattern (63 bp):
AATTATTAGTAATCATTAATAAATCATTAATATCAAATCAATAATTAAATAATTATAATAAAT
Found at i:791840 original size:16 final size:18
Alignment explanation
Indices: 791818--791860 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
791808 TTTAACTATT
*
791818 TATAAATAAT-AATAAGA
1 TATAAATAATAAATAAAA
791835 TA-AAAT-ATAAATAAAA
1 TATAAATAATAAATAAAA
791851 TATAAATAAT
1 TATAAATAAT
791861 TCAATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 2 0.09
16 12 0.55
17 6 0.27
18 2 0.09
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
TATAAATAATAAATAAAA
Found at i:791848 original size:11 final size:11
Alignment explanation
Indices: 791818--791859 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
791808 TTTAACTATT
791818 TATAAATAATAA
1 TATAAATAA-AA
*
791830 TA-AGATAAAA
1 TATAAATAAAA
791840 TATAAATAAAA
1 TATAAATAAAA
791851 TATAAATAA
1 TATAAATAA
791860 TTCAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 4 0.15
11 21 0.78
12 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
TATAAATAAAA
Found at i:795729 original size:27 final size:27
Alignment explanation
Indices: 795706--795771 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
795696 CAGGCTTTGT
795706 TCCAGGCTCTACAACCACGAGCTTTTC
1 TCCAGGCTCTACAACCACGAGCTTTTC
* * *
795733 TGCAGGCACTACAACCATGAGCTTTTC
1 TCCAGGCTCTACAACCACGAGCTTTTC
*
795760 TCCAGGATCTAC
1 TCCAGGCTCTAC
795772 GGCTGGGACC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (27 bp):
TCCAGGCTCTACAACCACGAGCTTTTC
Found at i:799503 original size:9 final size:9
Alignment explanation
Indices: 799484--799513 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
799474 AATTTTTTTC
799484 TTCTCATAAA
1 TTCT-ATAAA
799494 TTCTATAAA
1 TTCTATAAA
799503 TTCTATAAA
1 TTCTATAAA
799512 TT
1 TT
799514 TTAATGGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.80
10 4 0.20
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (9 bp):
TTCTATAAA
Found at i:800653 original size:16 final size:16
Alignment explanation
Indices: 800623--800653 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
800613 TAAAACTCGA
*
800623 CTCGAACTCGAAAAAG
1 CTCGAACTCAAAAAAG
800639 CTCGAACTCAAAAAA
1 CTCGAACTCAAAAAA
800654 CAATTTAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.26, G:0.13, T:0.13
Consensus pattern (16 bp):
CTCGAACTCAAAAAAG
Found at i:802617 original size:21 final size:21
Alignment explanation
Indices: 802591--802640 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
802581 ATGTGTATAA
* *
802591 CTTAAACCCTTAACTCTAAAC
1 CTTAAACCCTAAACTATAAAC
*
802612 CTTAAACTCTAAACTATAAAC
1 CTTAAACCCTAAACTATAAAC
*
802633 CATAAACC
1 CTTAAACC
802641 TTGCACCCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (21 bp):
CTTAAACCCTAAACTATAAAC
Found at i:802631 original size:14 final size:14
Alignment explanation
Indices: 802589--802642 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
802579 TCATGTGTAT
802589 AACT-TAAACCCTT-
1 AACTCTAAA-CCTTA
802602 AACTCTAAACCTTA
1 AACTCTAAACCTTA
802616 AACTCTAAA-CTATA
1 AACTCTAAACCT-TA
802630 AAC-CATAAACCTT
1 AACTC-TAAACCTT
802643 GCACCCTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 11 0.31
14 23 0.64
15 2 0.06
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (14 bp):
AACTCTAAACCTTA
Found at i:802638 original size:28 final size:28
Alignment explanation
Indices: 802607--802746 Score: 115
Period size: 28 Copynumber: 5.0 Consensus size: 28
802597 CCCTTAACTC
*
802607 TAAACCTTAAACTCTAAA-CTATAAACCA
1 TAAACCTTAAACACTAAATC-ATAAACCA
** *
802635 TAAACCTTGCACCCTAAATCATAAACCA
1 TAAACCTTAAACACTAAATCATAAACCA
*
802663 TAAACAC-TAAACACTAAATCATAAACTAA
1 TAAAC-CTTAAACACTAAATCATAAAC-CA
* * * *
802692 AAAACCCTAAATC-CTATATCATATACCA
1 TAAACCTTAAA-CACTAAATCATAAACCA
* * *
802720 TAAACCCTAAATACTAAACCATAAACC
1 TAAACCTTAAACACTAAATCATAAACC
802747 CTATCACATA
Statistics
Matches: 90, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
28 67 0.74
29 22 0.24
30 1 0.01
ACGTcount: A:0.50, C:0.27, G:0.01, T:0.22
Consensus pattern (28 bp):
TAAACCTTAAACACTAAATCATAAACCA
Done.