Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008533.1 Hibiscus syriacus cultivar Beakdansim tig00111411_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: 90926
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:10125 original size:14 final size:14
Alignment explanation
Indices: 10097--10137 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
10087 ATGCTTGAAG
10097 AAAAAAATGAA-AA
1 AAAAAAATGAAGAA
10110 AATAAAAA-GAAGAA
1 AA-AAAAATGAAGAA
10124 AAAAAAATGAAGAA
1 AAAAAAATGAAGAA
10138 GGAGGGTTCG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (14 bp):
AAAAAAATGAAGAA
Found at i:11500 original size:271 final size:270
Alignment explanation
Indices: 11098--11588 Score: 797
Period size: 271 Copynumber: 1.8 Consensus size: 270
11088 AAAAAGAGGT
* *
11098 GGATCAGCATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTT
* *
11163 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
66 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCAAGACATTTCGAATCAGGGACACCTCG
** * * *
11228 CTTGAGGAATTGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAA
131 CTTGAGGAATCAACATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCC--AAAAGAGAGAA
*
11293 GAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGAC
194 GAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGAC
11358 ACCTCGCTTGAG
259 ACCTCGCTTGAG
11370 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAC-GAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTT
* *
11434 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAG-CATTTCGAGTCAGGGACGCCTC
66 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCA-AGACATTTCGAATCAGGGACACCTC
* * *
11498 GCTTGAGGGATCAACATTTTCAGTGAAGAGTTCATAATGAGAAAAACTCATCCAAAAGAGAGAAG
130 GCTTGAGGAATCAACATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCCAAAAGAGAGAAG
*
11563 AAGTTCATAATGCGAAGAACTTGTTC
195 AAGTTCATAATGAGAAGAACTTGTTC
11589 AATCTAACAA
Statistics
Matches: 202, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
269 35 0.17
271 119 0.59
272 48 0.24
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (270 bp):
GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGGAGAAGAAGTT
CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCAAGACATTTCGAATCAGGGACACCTCG
CTTGAGGAATCAACATTTCCAATGAAGAGTTCATAATGAGAAAAACTCATCCAAAAGAGAGAAGA
AGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACAC
CTCGCTTGAG
Found at i:11506 original size:135 final size:135
Alignment explanation
Indices: 11098--11588 Score: 779
Period size: 136 Copynumber: 3.6 Consensus size: 135
11088 AAAAAGAGGT
* *
11098 GGATCAGCATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACA-AGGGAGAAGAAGTT
11163 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
65 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
11228 CTTGAG
130 CTTGAG
* ** * *
11234 GAATTGACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAAGGGAGAAGAAGTT
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCC-AACAAGGGAGAAGAAGTT
11299 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
65 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCG
11364 CTTGAG
130 CTTGAG
*
11370 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTC
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTC
* * * *
11435 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCA-CAGCATTTCGAGTCAGGGACGCCTCG
66 ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGA-CATTTCGAATCAGTGACACCTCG
11499 CTTGAG
130 CTTGAG
* * * *
11505 GGATCAACATTTTCAGTGAAGAGTTCATAATGAGAAAAACTCATCCAA-AAGAGAGAAGAAGTTC
1 GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTC
* *
11569 ATAATGCGAAGAACTTGTTC
66 ATAATGAGAAGAGCTTGTTC
11589 AATCTAACAA
Statistics
Matches: 329, Mismatches: 24, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
134 33 0.10
135 126 0.38
136 168 0.51
137 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (135 bp):
GGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTC
ATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCATGACATTTCGAATCAGTGACACCTCGC
TTGAG
Found at i:14952 original size:59 final size:58
Alignment explanation
Indices: 14876--14992 Score: 182
Period size: 59 Copynumber: 2.0 Consensus size: 58
14866 TATAATTAAC
*
14876 TTATTGGGTCTGTTTTGGTCCAAACATAAAACATTAAAAGTAAAA-AATTAATTAATTTA
1 TTATTGGGTCTGTTTTGGTCCAAACACAAAACATTAAAAGTAAAATAA-TAATT-ATTTA
* *
14935 TTATTGGGTTTGTTTTGGTCCAAACCCAAAACATTAAAAGTAAAATAATAATTATTTA
1 TTATTGGGTCTGTTTTGGTCCAAACACAAAACATTAAAAGTAAAATAATAATTATTTA
14993 AAACATAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
58 5 0.09
59 47 0.87
60 2 0.04
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (58 bp):
TTATTGGGTCTGTTTTGGTCCAAACACAAAACATTAAAAGTAAAATAATAATTATTTA
Found at i:16916 original size:20 final size:20
Alignment explanation
Indices: 16891--16943 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
16881 ATCCCATAGA
16891 TGGTCCATGGTCCCCCTGTG
1 TGGTCCATGGTCCCCCTGTG
16911 TGGTCCATGGTCCCCCTGTG
1 TGGTCCATGGTCCCCCTGTG
*
16931 TGGCCCATGGTCC
1 TGGTCCATGGTCC
16944 TAGACTCATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.06, C:0.36, G:0.30, T:0.28
Consensus pattern (20 bp):
TGGTCCATGGTCCCCCTGTG
Found at i:18498 original size:60 final size:58
Alignment explanation
Indices: 18433--18585 Score: 171
Period size: 60 Copynumber: 2.6 Consensus size: 58
18423 GATGATTTTG
* *
18433 GGGATGAAATTGAAATATTAAAAAGTTTATGGACCACTTTAGAAAGAGAGCCATAGTTT
1 GGGATGAAATT-AAATATTCAAAAGTTTAAGGACCACTTTAGAAAGAGAGCCATAGTTT
* * * * * * *
18492 ATGGATGTAATTAGAATGTTCAAAAGTTTAAGGACTAGTTTAGAATGAGAGTCATAGTTT
1 -GGGATGAAATTA-AATATTCAAAAGTTTAAGGACCACTTTAGAAAGAGAGCCATAGTTT
*
18552 GGGTATGAAATTAAAATAGTCAAAAGTTTAAGGA
1 GGG-ATGAAATT-AAATATTCAAAAGTTTAAGGA
18586 TCAATTTAAA
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
59 3 0.04
60 73 0.95
61 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.23, T:0.31
Consensus pattern (58 bp):
GGGATGAAATTAAATATTCAAAAGTTTAAGGACCACTTTAGAAAGAGAGCCATAGTTT
Found at i:21029 original size:23 final size:24
Alignment explanation
Indices: 20999--21045 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
20989 TTTTATTGAA
20999 AAACCGAAAAAC-CGAACCGAACC
1 AAACCGAAAAACTCGAACCGAACC
21022 AAACCGAAAAACTCGAACCGAACC
1 AAACCGAAAAACTCGAACCGAACC
21046 GAAAAAATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.51, C:0.34, G:0.13, T:0.02
Consensus pattern (24 bp):
AAACCGAAAAACTCGAACCGAACC
Found at i:28694 original size:39 final size:38
Alignment explanation
Indices: 28650--28725 Score: 107
Period size: 39 Copynumber: 2.0 Consensus size: 38
28640 ATTCCTAAAG
* * *
28650 TTTAGTTTTTGTTTCTTTTTATTACCCATCGTTAAAAAC
1 TTTAGTTTTTGTTTCATTTCAGTA-CCATCGTTAAAAAC
*
28689 TTTAGTTTTTGTTTCATTTCAGTACCATCGTTCAAAA
1 TTTAGTTTTTGTTTCATTTCAGTACCATCGTTAAAAA
28726 GTTTTTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 12 0.36
39 21 0.64
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (38 bp):
TTTAGTTTTTGTTTCATTTCAGTACCATCGTTAAAAAC
Found at i:29910 original size:13 final size:13
Alignment explanation
Indices: 29892--29918 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29882 TTGATAGTTG
29892 GAAAATATTTTTC
1 GAAAATATTTTTC
29905 GAAAATATTTTTC
1 GAAAATATTTTTC
29918 G
1 G
29919 GTGTTTGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (13 bp):
GAAAATATTTTTC
Found at i:30324 original size:16 final size:15
Alignment explanation
Indices: 30289--30341 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
30279 TATGTAATAA
30289 ATTATTAATATAAGT
1 ATTATTAATATAAGT
*
30304 ATTATTATATATTAGT
1 ATTATTA-ATATAAGT
* *
30320 TTTATAAATATAA-T
1 ATTATTAATATAAGT
30334 ATTATTAA
1 ATTATTAA
30342 ATTATTAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 7 0.23
15 12 0.39
16 12 0.39
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (15 bp):
ATTATTAATATAAGT
Found at i:30342 original size:15 final size:15
Alignment explanation
Indices: 30285--30343 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
30275 GTAATATGTA
30285 ATAA-ATTATT-AAT
1 ATAATATTATTAAAT
*
30298 ATAAGTATTATTATAT
1 ATAA-TATTATTAAAT
* *
30314 ATTAGTTTTA-TAAAT
1 A-TAATATTATTAAAT
30329 ATAATATTATTAAAT
1 ATAATATTATTAAAT
30344 TATTAATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
13 4 0.11
14 6 0.17
15 16 0.46
16 7 0.20
17 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (15 bp):
ATAATATTATTAAAT
Found at i:30348 original size:31 final size:31
Alignment explanation
Indices: 30290--30348 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
30280 ATGTAATAAA
* *
30290 TTATTAATATAAGTATTATTATATATTAGTT
1 TTATAAATATAAGTATTATTAAATATTAGTT
30321 TTATAAATATAA-TATTATTAAATTATTA
1 TTATAAATATAAGTATTATTAAA-TATTA
30349 ATAATGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
TTATAAATATAAGTATTATTAAATATTAGTT
Found at i:30395 original size:19 final size:19
Alignment explanation
Indices: 30373--30411 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
30363 TAATTTATGC
30373 ATTTAATATTA-ATATAATA
1 ATTTAATATTATAT-TAATA
*
30392 ATTTAGTATTATATTAATA
1 ATTTAATATTATATTAATA
30411 A
1 A
30412 AATATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
ATTTAATATTATATTAATA
Found at i:30420 original size:27 final size:27
Alignment explanation
Indices: 30346--30420 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
30336 TATTAAATTA
30346 TTAATAATGAGAAATATTAATTTATGCAT
1 TTAATAAT-A-AAATATTAATTTATGCAT
* * * *
30375 TTAATATTAATATAATAATTTA-GTAT
1 TTAATAATAAAATATTAATTTATGCAT
*
30401 TATATTAATAAAATATTAAT
1 T-TAATAATAAAATATTAAT
30421 AATTAAAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 4 0.11
27 25 0.68
28 1 0.03
29 7 0.19
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.45
Consensus pattern (27 bp):
TTAATAATAAAATATTAATTTATGCAT
Found at i:30733 original size:30 final size:31
Alignment explanation
Indices: 30674--30755 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
30664 TTTTCCAGAA
*
30674 AATGTAATTCATTTTACGTAAAACAG-TTTT
1 AATGTAATTTATTTTACGTAAAACAGTTTTT
* **
30704 AATGTAATTTATTTTATGTAAAATTGTTTTT
1 AATGTAATTTATTTTACGTAAAACAGTTTTT
* *
30735 AAT-TAATCTATTTTACATAAA
1 AATGTAATTTATTTTACGTAAA
30756 CTATTTTCCA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 37 0.84
31 7 0.16
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.49
Consensus pattern (31 bp):
AATGTAATTTATTTTACGTAAAACAGTTTTT
Found at i:30902 original size:2 final size:2
Alignment explanation
Indices: 30895--30934 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
30885 TTGTCTCCAT
30895 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30935 GAGTGTAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30960 original size:17 final size:17
Alignment explanation
Indices: 30938--30978 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
30928 ATAATATGAG
30938 TGTAAAGAAAAAAAGAA
1 TGTAAAGAAAAAAAGAA
*
30955 TGTAAAGAAAAACAGAA
1 TGTAAAGAAAAAAAGAA
*
30972 TGGAAAG
1 TGTAAAG
30979 GATTGAAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.63, C:0.02, G:0.22, T:0.12
Consensus pattern (17 bp):
TGTAAAGAAAAAAAGAA
Found at i:31178 original size:31 final size:28
Alignment explanation
Indices: 31126--31283 Score: 158
Period size: 28 Copynumber: 5.5 Consensus size: 28
31116 TCTCATTGAA
*
31126 GTACCTAAAGTATTTTTTTTATCAAAATAT
1 GTACCTAAAGTA--TTTTTTATCAAAATAG
*
31156 GTACCTGAAGTTATATTTTTTATCAAAATAG
1 GTACCTAAAG---TATTTTTTATCAAAATAG
* *
31187 GTACTTAAAGTATTTTTGATCAAAATAG
1 GTACCTAAAGTATTTTTTATCAAAATAG
*
31215 GTACTTAAAGTATTTTTTATCAAAATAG
1 GTACCTAAAGTATTTTTTATCAAAATAG
* * *
31243 GT--TTGAAGTATTTTTGAGTCAAAATAG
1 GTACCTAAAGTATTTTTTA-TCAAAATAG
* *
31270 GTACATGAAGTATT
1 GTACCTAAAGTATT
31284 CAACTCTTTC
Statistics
Matches: 113, Mismatches: 9, Indels: 13
0.84 0.07 0.10
Matches are distributed among these distances:
26 13 0.12
27 11 0.10
28 46 0.41
29 9 0.08
30 9 0.08
31 23 0.20
33 2 0.02
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.42
Consensus pattern (28 bp):
GTACCTAAAGTATTTTTTATCAAAATAG
Found at i:31209 original size:28 final size:28
Alignment explanation
Indices: 31169--31283 Score: 162
Period size: 28 Copynumber: 4.1 Consensus size: 28
31159 CCTGAAGTTA
*
31169 TATTTTTTATCAAAATAGGTACTTAAAG
1 TATTTTTGATCAAAATAGGTACTTAAAG
31197 TATTTTTGATCAAAATAGGTACTTAAAG
1 TATTTTTGATCAAAATAGGTACTTAAAG
* *
31225 TATTTTTTATCAAAATAGGT--TTGAAG
1 TATTTTTGATCAAAATAGGTACTTAAAG
* *
31251 TATTTTTGAGTCAAAATAGGTACATGAAG
1 TATTTTTGA-TCAAAATAGGTACTTAAAG
31280 TATT
1 TATT
31284 CAACTCTTTC
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
26 13 0.16
27 11 0.14
28 46 0.58
29 9 0.11
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (28 bp):
TATTTTTGATCAAAATAGGTACTTAAAG
Found at i:31272 original size:55 final size:55
Alignment explanation
Indices: 31169--31283 Score: 178
Period size: 55 Copynumber: 2.1 Consensus size: 55
31159 CCTGAAGTTA
*
31169 TATTTTTTATCAAAATAGGTACTTAAAGTATTTTTGATCAAAATAGGTACTTAAAG
1 TATTTTTTATCAAAATAGGTA-TTAAAGTATTTTTGATCAAAATAGGTACATAAAG
* *
31225 TATTTTTTATCAAAATAGGT-TTGAAGTATTTTTGAGTCAAAATAGGTACATGAAG
1 TATTTTTTATCAAAATAGGTATTAAAGTATTTTTGA-TCAAAATAGGTACATAAAG
31280 TATT
1 TATT
31284 CAACTCTTTC
Statistics
Matches: 55, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
54 14 0.25
55 21 0.38
56 20 0.36
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (55 bp):
TATTTTTTATCAAAATAGGTATTAAAGTATTTTTGATCAAAATAGGTACATAAAG
Found at i:33198 original size:13 final size:14
Alignment explanation
Indices: 33180--33208 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
33170 AAGGGTCTGC
33180 ATTTTCTTTTT-CG
1 ATTTTCTTTTTACG
33193 ATTTTCTTTTTACG
1 ATTTTCTTTTTACG
33207 AT
1 AT
33209 CTTGGTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.66
Consensus pattern (14 bp):
ATTTTCTTTTTACG
Found at i:34749 original size:42 final size:42
Alignment explanation
Indices: 34701--34957 Score: 122
Period size: 42 Copynumber: 6.2 Consensus size: 42
34691 GCGTTTTAAT
* *
34701 CCACTAAGATACAAATCTATTGCGGCGTTTTAATAACAAACT
1 CCACTAAGATACAAATCTATTGCGGCATTTTAATAACAAACG
* * * ** **
34743 TCACTAAGTTTCACTTCTATTGCGGCATTTTTCTAACAAACG
1 CCACTAAGATACAAATCTATTGCGGCATTTTAATAACAAACG
* **** * * ** * *
34785 CCACTAAGGTATGGCTCTATAGTGGTGTTTTAGTGACAAACG
1 CCACTAAGATACAAATCTATTGCGGCATTTTAATAACAAACG
* * *** * *
34827 CCACTAAGGTTCGCCTCTATTGCGGCGTTTTAGTAACAAACG
1 CCACTAAGATACAAATCTATTGCGGCATTTTAATAACAAACG
* * * * * * *
34869 CCGCTAAGGTGC--CTCTATTGAGGCGTTTTTATAACAAACG
1 CCACTAAGATACAAATCTATTGCGGCATTTTAATAACAAACG
* ** ** **
34909 CCACTAAGGTACGGATCTATAACGGCATTTTAACGACAAACG
1 CCACTAAGATACAAATCTATTGCGGCATTTTAATAACAAACG
*
34951 CCGCTAA
1 CCACTAA
34958 TTTTGACATT
Statistics
Matches: 167, Mismatches: 46, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
40 35 0.21
42 132 0.79
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (42 bp):
CCACTAAGATACAAATCTATTGCGGCATTTTAATAACAAACG
Found at i:34894 original size:40 final size:40
Alignment explanation
Indices: 34716--34918 Score: 201
Period size: 42 Copynumber: 4.9 Consensus size: 40
34706 AAGATACAAA
* ** * *
34716 TCTATTGCGGCGTTTTAATAACAAACTTCACTAAGTTTCAC
1 TCTATTGCGGCGTTTTAGTAACAAACGCCACTAAGGTGC-C
* ** *
34757 TTCTATTGCGGCATTTTTCTAACAAACGCCACTAAGGTATGGC
1 -TCTATTGCGGCGTTTTAGTAACAAACGCCACTAAGG--TGCC
* * * *
34800 TCTATAGTGGTGTTTTAGTGACAAACGCCACTAAGGTTCGCC
1 TCTATTGCGGCGTTTTAGTAACAAACGCCACTAAGG-T-GCC
*
34842 TCTATTGCGGCGTTTTAGTAACAAACGCCGCTAAGGTGCC
1 TCTATTGCGGCGTTTTAGTAACAAACGCCACTAAGGTGCC
*
34882 TCTATTGAGGCGTTTTTA-TAACAAACGCCACTAAGGT
1 TCTATTGCGGCG-TTTTAGTAACAAACGCCACTAAGGT
34919 ACGGATCTAT
Statistics
Matches: 133, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
40 32 0.24
41 7 0.05
42 92 0.69
43 1 0.01
44 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (40 bp):
TCTATTGCGGCGTTTTAGTAACAAACGCCACTAAGGTGCC
Found at i:34940 original size:124 final size:126
Alignment explanation
Indices: 34716--34957 Score: 308
Period size: 124 Copynumber: 1.9 Consensus size: 126
34706 AAGATACAAA
** * * * *
34716 TCTATTGCGGCGTTTTAATAACAAACTTCACTAAGTTTCACTTCTATTGCGGCATTTTTCTAACA
1 TCTATTGCGGCGTTTTAATAACAAACGCCACTAAGGTGCACTTCTATTGAGGCATTTTTATAACA
* * ** ** **
34781 AACGCCACTAAGGTATGGCTCTATAGTGGTGTTTTAGTGACAAACGCCACTAAGGTTCGCC
66 AACGCCACTAAGGTACGGATCTATAACGGCATTTTAACGACAAACGCCACTAAGGTTCGCC
* * *
34842 TCTATTGCGGCGTTTTAGTAACAAACGCCGCTAAGGTGC-C-TCTATTGAGGCGTTTTTATAACA
1 TCTATTGCGGCGTTTTAATAACAAACGCCACTAAGGTGCACTTCTATTGAGGCATTTTTATAACA
*
34905 AACGCCACTAAGGTACGGATCTATAACGGCATTTTAACGACAAACGCCGCTAA
66 AACGCCACTAAGGTACGGATCTATAACGGCATTTTAACGACAAACGCCACTAA
34958 TTTTGACATT
Statistics
Matches: 98, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
124 64 0.65
125 1 0.01
126 33 0.34
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (126 bp):
TCTATTGCGGCGTTTTAATAACAAACGCCACTAAGGTGCACTTCTATTGAGGCATTTTTATAACA
AACGCCACTAAGGTACGGATCTATAACGGCATTTTAACGACAAACGCCACTAAGGTTCGCC
Found at i:35280 original size:2 final size:2
Alignment explanation
Indices: 35273--35305 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35263 TGTTGTCGGC
35273 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35306 GGAGCAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37767 original size:45 final size:45
Alignment explanation
Indices: 37703--37796 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
37693 GTACCTTAGA
37703 ATGGCTACCTTCCTATACCCTACACCTCACTCTCATTGCATTTTC
1 ATGGCTACCTTCCTATACCCTACACCTCACTCTCATTGCATTTTC
37748 ATGGCTACCTTCCTATACCCTACACCTCACTCTCATTGCATTTTC
1 ATGGCTACCTTCCTATACCCTACACCTCACTCTCATTGCATTTTC
37793 ATGG
1 ATGG
37797 TATTTGAGTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.20, C:0.36, G:0.09, T:0.35
Consensus pattern (45 bp):
ATGGCTACCTTCCTATACCCTACACCTCACTCTCATTGCATTTTC
Found at i:38951 original size:59 final size:60
Alignment explanation
Indices: 38860--38998 Score: 156
Period size: 59 Copynumber: 2.3 Consensus size: 60
38850 TGGTCATTAT
* * * * *
38860 ATTTTTAAACATTCTAATTTTATTATTTAACTAAGAGTCTCATTTTAAATCGATCCTCAA
1 ATTTTTAAATATTCTAATTTCATTATTAAACTAAGAGTCTCATTCTAAATCAATCCTCAA
* * * * *
38920 A-TTTTAAATATTCAAATTTCATCTA-TAAACTATGATTCTCGTTCTAAATTAATCCTCAA
1 ATTTTTAAATATTCTAATTTCAT-TATTAAACTAAGAGTCTCATTCTAAATCAATCCTCAA
*
38979 ATTTTTGAATATTCTAATTT
1 ATTTTTAAATATTCTAATTT
38999 TATTTCTAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
59 46 0.71
60 19 0.29
ACGTcount: A:0.35, C:0.14, G:0.04, T:0.46
Consensus pattern (60 bp):
ATTTTTAAATATTCTAATTTCATTATTAAACTAAGAGTCTCATTCTAAATCAATCCTCAA
Found at i:40605 original size:31 final size:31
Alignment explanation
Indices: 40538--40598 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
40528 GAATAAATCG
** *
40538 ATCACTAATGATATCGATTTGTAACAAAATA
1 ATCACTAACAATATCAATTTGTAACAAAATA
*
40569 ATCACTAACAATATCAATTTGTAATAAAAT
1 ATCACTAACAATATCAATTTGTAACAAAAT
40599 TGTCACTCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (31 bp):
ATCACTAACAATATCAATTTGTAACAAAATA
Found at i:44950 original size:31 final size:31
Alignment explanation
Indices: 44912--44972 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
44902 GTAAATTGAT
*
44912 CATTTTGTTACAAACCGATAACGTTAGTGAC
1 CATTTTGTTACAAACCGATAACATTAGTGAC
* * *
44943 CATTTTGTTATAAATCGATAATATTAGTGA
1 CATTTTGTTACAAACCGATAACATTAGTGA
44973 TAAGTTTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (31 bp):
CATTTTGTTACAAACCGATAACATTAGTGAC
Found at i:45233 original size:2 final size:2
Alignment explanation
Indices: 45228--45258 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
45218 AAATTTAATC
45228 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45259 TGACAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45328 original size:2 final size:2
Alignment explanation
Indices: 45321--45351 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
45311 ACATAAAATC
45321 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45352 CACGTACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46471 original size:3 final size:3
Alignment explanation
Indices: 46463--46491 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
46453 TATACTAATT
46463 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
46492 TATAGTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:47675 original size:29 final size:29
Alignment explanation
Indices: 47630--47687 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
47620 AACAACCGAT
*
47630 CAAACATCGATTGCGACTCCTCGTCCAAA
1 CAAACATCGATTACGACTCCTCGTCCAAA
47659 CAAACATCGATTACGACTCCTCGTCCAAA
1 CAAACATCGATTACGACTCCTCGTCCAAA
47688 ACAGAAGAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.34, G:0.12, T:0.21
Consensus pattern (29 bp):
CAAACATCGATTACGACTCCTCGTCCAAA
Found at i:52211 original size:18 final size:19
Alignment explanation
Indices: 52178--52213 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
52168 AAATTAATTT
*
52178 TACTTAGGAATCTATATTA
1 TACTTAGGAATATATATTA
52197 TACTT-GGAATATATATT
1 TACTTAGGAATATATATT
52214 TGATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (19 bp):
TACTTAGGAATATATATTA
Found at i:59201 original size:2 final size:2
Alignment explanation
Indices: 59194--59236 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
59184 GAGATTGCAT
59194 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59236 T
1 T
59237 CGCTTTGTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:64185 original size:22 final size:22
Alignment explanation
Indices: 64160--64201 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
64150 CGAACGCATA
64160 ATTTTAATAAAAA-ATATATATT
1 ATTTT-ATAAAAATATATATATT
*
64182 ATTTTTTAAAAATATATATA
1 ATTTTATAAAAATATATATA
64202 ATAACTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTTATAAAAATATATATATT
Found at i:65025 original size:42 final size:41
Alignment explanation
Indices: 64967--65105 Score: 174
Period size: 42 Copynumber: 3.3 Consensus size: 41
64957 TATATAACAA
*
64967 AAAACGCCGCAATAGAGTGGTAAATTAGCGACGTTAATACC
1 AAAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTAATACC
* * * *
65008 ACAAACGCCGCAATAGAGT-ATAAATTTTGCGGCGATTGA-GCC
1 A-AAACGCCGCAATAGAGTGGTAAA-TTAGCGGCG-TTAATACC
*
65050 AAAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACC
1 AAAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTAATACC
65091 ATAAACGCCGCAATA
1 A-AAACGCCGCAATA
65106 TATTACACAT
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
40 3 0.04
41 33 0.40
42 44 0.53
43 3 0.04
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (41 bp):
AAAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTAATACC
Found at i:65182 original size:83 final size:83
Alignment explanation
Indices: 65135--65295 Score: 259
Period size: 83 Copynumber: 1.9 Consensus size: 83
65125 TTTATTCCTC
*
65135 AAACGCCACAATAGTGATAATCAATAGTGGCGTTTTTAGACAAACGCCGCAATAGTATTAATCAA
1 AAACGCCACAAAAGTGATAATCAATAGTGGCGTTTTTAGACAAACGCCGCAATAGTATTAATCAA
*
65200 TAATGGCGTTTTTAGAAA
66 TAATGGCGTTTTTACAAA
* * *
65218 AAACGCCGCAAAAGTGTTAATCAATAGTGGCGTTTTTAGACAAACGCCGCAATAGTGTTAATCAA
1 AAACGCCACAAAAGTGATAATCAATAGTGGCGTTTTTAGACAAACGCCGCAATAGTATTAATCAA
* *
65283 TAGTGGCATTTTT
66 TAATGGCGTTTTT
65296 TTTGTATAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 72 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (83 bp):
AAACGCCACAAAAGTGATAATCAATAGTGGCGTTTTTAGACAAACGCCGCAATAGTATTAATCAA
TAATGGCGTTTTTACAAA
Found at i:65296 original size:42 final size:41
Alignment explanation
Indices: 65134--65295 Score: 252
Period size: 41 Copynumber: 3.9 Consensus size: 41
65124 GTTTATTCCT
* *
65134 CAAACGCCACAATAGTGATAATCAATAGTGGCGTTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
* *
65175 CAAACGCCGCAATAGTATTAATCAATAATGGCGTTTTTAGAA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAG-A
* *
65217 AAAACGCCGCAAAAGTGTTAATCAATAGTGGCGTTTTTAGA
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
*
65258 CAAACGCCGCAATAGTGTTAATCAATAGTGGCATTTTT
1 CAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTT
65296 TTTGTATAAA
Statistics
Matches: 109, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 72 0.66
42 37 0.34
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (41 bp):
CAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
Found at i:66047 original size:41 final size:41
Alignment explanation
Indices: 65975--66132 Score: 138
Period size: 42 Copynumber: 3.8 Consensus size: 41
65965 AAGTTATACT
* *
65975 TTAGTGGCGTTTTTTGATACAAACGCCGCAATAGAGTTGTT-A
1 TTAGTGGCGTTTTTT-A-AAAAACGCCGCAATAGAGTAGTTCA
* * *
66017 TTAGGTGGCGTTTTTTAATAAACGCCGCAATAGAATAGTTCC
1 TTA-GTGGCGTTTTTTAAAAAACGCCGCAATAGAGTAGTTCA
* * * *
66059 TTAGTGGCATTTTCGTAAAAAACGCAGCAATAGAGTAGTTCC
1 TTAGTGGCGTTTT-TTAAAAAACGCCGCAATAGAGTAGTTCA
* * * * *
66101 TTTGCGGCGTTTTTATTAGAAACGCCGTAATA
1 TTAGTGGCGTTTTT-TAAAAAACGCCGCAATA
66133 TTCTGATATA
Statistics
Matches: 95, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
41 29 0.31
42 54 0.57
43 12 0.13
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (41 bp):
TTAGTGGCGTTTTTTAAAAAACGCCGCAATAGAGTAGTTCA
Found at i:66338 original size:18 final size:18
Alignment explanation
Indices: 66309--66363 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
66299 GTTCCTAACA
*
66309 TTCTCTACCAGCGCAACC
1 TTCTCCACCAGCGCAACC
* *
66327 TTCTCCAGCAGCGCAAGC
1 TTCTCCACCAGCGCAACC
66345 TTCTCCACCAGCGCAACC
1 TTCTCCACCAGCGCAACC
66363 T
1 T
66364 CACGTTGCCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.22, C:0.44, G:0.15, T:0.20
Consensus pattern (18 bp):
TTCTCCACCAGCGCAACC
Found at i:69005 original size:3 final size:3
Alignment explanation
Indices: 68997--69066 Score: 122
Period size: 3 Copynumber: 23.3 Consensus size: 3
68987 TACCCATATC
*
68997 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
69045 ATT ATC ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
69067 AATATATTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:69074 original size:18 final size:18
Alignment explanation
Indices: 68997--69075 Score: 115
Period size: 18 Copynumber: 4.4 Consensus size: 18
68987 TACCCATATC
*
68997 ATTATTATTATTATTATT
1 ATTATTATTATTATTATA
*
69015 ATTATTATTATTATTATC
1 ATTATTATTATTATTATA
*
69033 ATTATTATTATTATTATC
1 ATTATTATTATTATTATA
69051 ATTATTATTATTATTA-A
1 ATTATTATTATTATTATA
69068 ATATATTA
1 AT-TATTA
69076 AATACATATA
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
17 2 0.03
18 56 0.97
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTATTATTATTATTATA
Found at i:69621 original size:16 final size:17
Alignment explanation
Indices: 69600--69631 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
69590 ACAGAACCGG
69600 AGAGAAA-AAAAAAAAC
1 AGAGAAAGAAAAAAAAC
69616 AGAGAAAGAAAAAAAA
1 AGAGAAAGAAAAAAAA
69632 AACAACAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (17 bp):
AGAGAAAGAAAAAAAAC
Found at i:70562 original size:20 final size:21
Alignment explanation
Indices: 70525--70565 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
70515 GATATTTTTA
**
70525 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
70546 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
70566 ACATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:70809 original size:2 final size:2
Alignment explanation
Indices: 70804--70831 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
70794 GATTAAAAAA
70804 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70832 TTTGTATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71312 original size:18 final size:18
Alignment explanation
Indices: 71267--71313 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
71257 TTTCAAATTA
71267 TTTA-TTTATTTATTATT
1 TTTATTTTATTTATTATT
**
71284 TTTATAATATTTA-TATGT
1 TTTATTTTATTTATTAT-T
71302 TTTATTTTATTT
1 TTTATTTTATTT
71314 GCAAGATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTATTTTATTTATTATT
Found at i:81928 original size:12 final size:12
Alignment explanation
Indices: 81911--81973 Score: 78
Period size: 12 Copynumber: 5.4 Consensus size: 12
81901 ATGCTTGAAG
81911 AGAAAAGAAAAA
1 AGAAAAGAAAAA
*
81923 AGAAAAAAAAAA
1 AGAAAAGAAAAA
81935 AG-AAA-AAAAA
1 AGAAAAGAAAAA
*
81945 AGAGAAGAAAAA
1 AGAAAAGAAAAA
81957 A-AAAAGAGAAAA
1 AGAAAAGA-AAAA
81969 AGAAA
1 AGAAA
81974 GGGGGTCAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
10 7 0.16
11 10 0.23
12 24 0.55
13 3 0.07
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AGAAAAGAAAAA
Found at i:81932 original size:16 final size:16
Alignment explanation
Indices: 81916--81969 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
81906 TGAAGAGAAA
81916 AGAAAAAAGAAAAAAA-
1 AGAAAAAA-AAAAAAAG
*
81932 A-AAAGAAAAAAAAAG
1 AGAAAAAAAAAAAAAG
*
81947 AGAAGAAAAAAAAAAG
1 AGAAAAAAAAAAAAAG
81963 AGAAAAA
1 AGAAAAA
81970 GAAAGGGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 7 0.22
15 6 0.19
16 19 0.59
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAAAAAAAG
Found at i:81940 original size:24 final size:24
Alignment explanation
Indices: 81911--81973 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 24
81901 ATGCTTGAAG
81911 AGAAAAGAAAAAAGAAAAAAAAAA
1 AGAAAAGAAAAAAGAAAAAAAAAA
* *
81935 AG-AAA-AAAAAAGAGAAGAAAAA
1 AGAAAAGAAAAAAGAAAAAAAAAA
81957 A-AAAAGAGAAAAAGAAA
1 AGAAAAGA-AAAAAGAAA
81974 GGGGGTCAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 19 0.58
23 4 0.12
24 10 0.30
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (24 bp):
AGAAAAGAAAAAAGAAAAAAAAAA
Found at i:81952 original size:27 final size:28
Alignment explanation
Indices: 81922--81974 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
81912 GAAAAGAAAA
81922 AAGAAAAAAAAAA-AGAAAAAAAAAGAG
1 AAGAAAAAAAAAAGAGAAAAAAAAAGAG
*
81949 AAGAAAAAAAAAAGAGAAAAAGAAAG
1 AAGAAAAAAAAAAGAGAAAAAAAAAG
81975 GGGGTCAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (28 bp):
AAGAAAAAAAAAAGAGAAAAAAAAAGAG
Found at i:82310 original size:16 final size:16
Alignment explanation
Indices: 82289--82328 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
82279 ATACAATTCT
*
82289 ATTTATTTCAAG-TTCA
1 ATTTATTT-AAGAGTCA
82305 ATTTATTTAAGAGTCA
1 ATTTATTTAAGAGTCA
82321 ATTTATTT
1 ATTTATTT
82329 TTGGAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (16 bp):
ATTTATTTAAGAGTCA
Found at i:83539 original size:84 final size:84
Alignment explanation
Indices: 83097--83529 Score: 800
Period size: 84 Copynumber: 5.2 Consensus size: 84
83087 ATATCTTAGT
83097 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
83161 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
83180 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
83244 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
83263 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
83328 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
83347 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
83412 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
83431 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* *
83496 CTAATCTG-GTTGGACAGAA
66 CTGATCTGATTTGG-CAGAA
*
83515 CCAATCGTTGGAATT
1 CCAATCATT-GAATT
83530 AAAAGATGAA
Statistics
Matches: 344, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
83 117 0.34
84 222 0.65
85 5 0.01
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (84 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGATTTGGCAGAA
Found at i:84340 original size:113 final size:113
Alignment explanation
Indices: 84144--85262 Score: 1579
Period size: 113 Copynumber: 10.0 Consensus size: 113
84134 GCAAAGATTC
* **
84144 AAATCTATCAATTGATGGATTATTTTTTGAAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
84209 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTG
84257 AAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
84322 AAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTG
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TG
* * *** * *
84371 AATTC-ATCA-TCTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGA
1 AAATCTATCACT-TGATGGATTATTTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGA
*
84433 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTG
84483 AAATCTATCACTTGATGGATTA-TTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
84547 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTG
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-CTG
* * *** *
84596 AATTC-ATCA-TTGGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCTATCACTT-GATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* *
84659 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT-TTG
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTG
* * *
84706 AATTC-ATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
84770 AAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTAAT-CTG
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT--TGCTG
* * *
84819 AATTC-ATCACTGGATGGAATA-TTTTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
84881 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTG
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-CTG
* * *
84930 AATTC-ATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
84994 AAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTAAT-CTG
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT--TGCTG
* * *
85043 AATTC-ATCACTGGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAATAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
85107 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-GCTG
* * * ***
85156 AATTC-ATCAATTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
85220 AAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
85263 GTTTGATGCT
Statistics
Matches: 918, Mismatches: 67, Indels: 42
0.89 0.07 0.04
Matches are distributed among these distances:
109 1 0.00
110 95 0.10
111 102 0.11
112 120 0.13
113 593 0.65
114 6 0.01
115 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (113 bp):
AAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTG
Found at i:85590 original size:3 final size:3
Alignment explanation
Indices: 85582--85696 Score: 212
Period size: 3 Copynumber: 38.3 Consensus size: 3
85572 TACCCATATC
85582 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
85630 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
85678 ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
85697 AATATATTAA
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 110 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:85741 original size:23 final size:21
Alignment explanation
Indices: 85695--85741 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
85685 TTATTATTAT
* *
85695 TAAATATATTAAATACATATA
1 TAAATATATTAAATAAATAAA
85716 TAAATATTATTAAAATAAATAAA
1 TAAATA-TATT-AAATAAATAAA
85739 TAA
1 TAA
85742 TAAAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 4 0.18
23 12 0.55
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATATATTAAATAAATAAA
Found at i:86251 original size:15 final size:16
Alignment explanation
Indices: 86231--86260 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
86221 ACAGAACCGG
86231 AGAGAAA-AAAAAAAC
1 AGAGAAAGAAAAAAAC
86246 AGAGAAAGAAAAAAA
1 AGAGAAAGAAAAAAA
86261 AAAACAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (16 bp):
AGAGAAAGAAAAAAAC
Found at i:86255 original size:29 final size:28
Alignment explanation
Indices: 86201--86255 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
86191 AAAAAAAAGA
* * *
86201 GGAGAGACAAAAAAACCGAGACAGAACC
1 GGAGAGAAAAAAAAACAGAGAAAGAACC
86229 GGAGAGAAAAAAAAAACAGAGAAAGAA
1 GGAGAG-AAAAAAAAACAGAGAAAGAA
86256 AAAAAAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.62, C:0.13, G:0.25, T:0.00
Consensus pattern (28 bp):
GGAGAGAAAAAAAAACAGAGAAAGAACC
Done.