Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 78 of 78
Found at i:16979106 original size:30 final size:33
Alignment explanation
Indices: 16979067--16979134 Score: 79
Period size: 36 Copynumber: 2.1 Consensus size: 33
16979057 AGCAAACTAA
16979067 AAATATTTTT-ACT-C-TAATTCCTAATAAAAT
1 AAATATTTTTAACTACTTAATTCCTAATAAAAT
*
16979097 AAATGTTTTTAACTCAACCTTAATTCCTAATAAAAT
1 AAATATTTTTAACT--A-CTTAATTCCTAATAAAAT
16979133 AA
1 AA
16979135 TAAATCTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
30 9 0.29
31 3 0.10
35 1 0.03
36 18 0.58
ACGTcount: A:0.44, C:0.15, G:0.01, T:0.40
Consensus pattern (33 bp):
AAATATTTTTAACTACTTAATTCCTAATAAAAT
Found at i:16981262 original size:12 final size:13
Alignment explanation
Indices: 16981242--16981276 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
16981232 TAAGAAAAAG
16981242 AAAGAGAAAAGGA
1 AAAGAGAAAAGGA
16981255 AAAG-GAAAAGGA
1 AAAGAGAAAAGGA
*
16981267 AAAAAGAAAA
1 AAAGAGAAAA
16981277 AACAAAGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AAAGAGAAAAGGA
Found at i:16982925 original size:15 final size:15
Alignment explanation
Indices: 16982907--16982980 Score: 68
Period size: 14 Copynumber: 5.2 Consensus size: 15
16982897 CATATGAGTA
*
16982907 TATAATAGTGCATGT
1 TATAATAGTGCATAT
16982922 TATAAT--TGCATAT
1 TATAATAGTGCATAT
*
16982935 TAT-ATAGTCCATAT
1 TATAATAGTGCATAT
*
16982949 TA-AATAGTTTCATAT
1 TATAATAG-TGCATAT
*
16982964 TAT-ATAGTACATAT
1 TATAATAGTGCATAT
16982978 TAT
1 TAT
16982981 GATTTCGTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
12 2 0.04
13 9 0.18
14 21 0.42
15 18 0.36
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (15 bp):
TATAATAGTGCATAT
Found at i:16982964 original size:29 final size:29
Alignment explanation
Indices: 16982930--16983044 Score: 101
Period size: 29 Copynumber: 3.9 Consensus size: 29
16982920 GTTATAATTG
16982930 CATATTATATAGTCCATATTAAATAGTTT
1 CATATTATATAGTCCATATTAAATAGTTT
*
16982959 CATATTATATAGTACATATT--AT-GATTT
1 CATATTATATAGTCCATATTAAATAG-TTT
* * * *
16982986 CGTATTATATTACTAGTCCATATTATATTGTTAG
1 CATA-T-TA-TA-TAGTCCATATTAAATAGTT-T
*
16983020 CATATTATATATTCCATATTAAATA
1 CATATTATATAGTCCATATTAAATA
16983045 ATAGTAGATT
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
26 1 0.01
27 8 0.12
28 1 0.01
29 21 0.30
30 15 0.22
31 12 0.17
32 2 0.03
33 5 0.07
34 4 0.06
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (29 bp):
CATATTATATAGTCCATATTAAATAGTTT
Found at i:16982986 original size:27 final size:26
Alignment explanation
Indices: 16982911--16982995 Score: 80
Period size: 27 Copynumber: 3.1 Consensus size: 26
16982901 TGAGTATATA
* * *
16982911 ATAGTGCATGTTATAATTGCATATTAT
1 ATAGTACATATTAT-ATTTCATATTAT
*
16982938 ATAGTCCATATTAAATAGTTTCATATTAT
1 ATAGTACATATT--ATA-TTTCATATTAT
*
16982967 ATAGTACATATTATGATTTCGTATTAT
1 ATAGTACATATTAT-ATTTCATATTAT
16982994 AT
1 AT
16982996 TACTAGTCCA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
27 24 0.49
28 2 0.04
29 23 0.47
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (26 bp):
ATAGTACATATTATATTTCATATTAT
Found at i:16983039 original size:14 final size:14
Alignment explanation
Indices: 16982921--16983040 Score: 66
Period size: 14 Copynumber: 8.2 Consensus size: 14
16982911 ATAGTGCATG
*
16982921 TTATA-ATTGCATA
1 TTATATATTCCATA
*
16982934 TTATATAGTCCATA
1 TTATATATTCCATA
* *
16982948 TTAAATAGTTTCATA
1 TTATATA-TTCCATA
* *
16982963 TTATATAGTACATA
1 TTATATATTCCATA
*
16982977 TTATGAT-TT-CGTA
1 TTAT-ATATTCCATA
16982990 TTATATTACTAGTCCATA
1 TTATA-TA-T--TCCATA
* *
16983008 TTATATTGTTAGCATA
1 TTATA-TATT-CCATA
16983024 TTATATATTCCATA
1 TTATATATTCCATA
16983038 TTA
1 TTA
16983041 AATAATAGTA
Statistics
Matches: 82, Mismatches: 15, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
12 1 0.01
13 13 0.16
14 29 0.35
15 18 0.22
16 9 0.11
17 2 0.02
18 10 0.12
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (14 bp):
TTATATATTCCATA
Found at i:16984488 original size:11 final size:11
Alignment explanation
Indices: 16984472--16984532 Score: 70
Period size: 11 Copynumber: 5.5 Consensus size: 11
16984462 ATATCTTTTT
16984472 AAAAAAAAACC
1 AAAAAAAAACC
*
16984483 AAAAAAAAGCC
1 AAAAAAAAACC
*
16984494 AAAAAAACAA-T
1 AAAAAAA-AACC
**
16984505 AAAAAAACCCC
1 AAAAAAAAACC
16984516 AAAAAAAAACC
1 AAAAAAAAACC
16984527 AAAAAA
1 AAAAAA
16984533 GCCAAAATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 39 0.98
12 1 0.03
ACGTcount: A:0.79, C:0.18, G:0.02, T:0.02
Consensus pattern (11 bp):
AAAAAAAAACC
Found at i:16984499 original size:21 final size:21
Alignment explanation
Indices: 16984473--16984539 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
16984463 TATCTTTTTA
16984473 AAAAAAAACCAAAAAAAAGCC
1 AAAAAAAACCAAAAAAAAGCC
* *
16984494 -AAAAAAACAATAAAAAAACCCC
1 AAAAAAAACCA-AAAAAAA-GCC
16984516 AAAAAAAAACC--AAAAAAGCC
1 -AAAAAAAACCAAAAAAAAGCC
16984536 AAAA
1 AAAA
16984540 TTTCAAACAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
19 4 0.11
20 11 0.29
21 13 0.34
22 2 0.05
24 8 0.21
ACGTcount: A:0.76, C:0.19, G:0.03, T:0.01
Consensus pattern (21 bp):
AAAAAAAACCAAAAAAAAGCC
Found at i:16991806 original size:15 final size:16
Alignment explanation
Indices: 16991779--16991815 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
16991769 CTTTATTATC
16991779 TTATTTCATCTTTCGT
1 TTATTTCATCTTTCGT
*
16991795 TTATTT-ATCTTTTGT
1 TTATTTCATCTTTCGT
16991810 TTATTT
1 TTATTT
16991816 TATTCTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTTCGT
Found at i:16992203 original size:31 final size:30
Alignment explanation
Indices: 16992165--16992233 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 30
16992155 CTATTTTTTT
*
16992165 CAAAAAAAA-CAAAAAAAAAACAAAAAAAAGG
1 CAAAAAAAAGC-AAAAAAAAAC-AAAAAAAGC
16992196 CAAAAAAAAGGCAAAAAAAAACAAAAAAAGC
1 CAAAAAAAA-GCAAAAAAAAACAAAAAAAGC
16992227 CAAAAAA
1 CAAAAAA
16992234 GCTAAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
31 24 0.69
32 10 0.29
33 1 0.03
ACGTcount: A:0.81, C:0.12, G:0.07, T:0.00
Consensus pattern (30 bp):
CAAAAAAAAGCAAAAAAAAACAAAAAAAGC
Found at i:16992230 original size:10 final size:10
Alignment explanation
Indices: 16992177--16992233 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
16992167 AAAAAAACAA
* *
16992177 AAAAAAAACA
1 AAAAAAAGCC
*
16992187 AAAAAAAGGCA
1 AAAAAAA-GCC
*
16992198 AAAAAAAGGC
1 AAAAAAAGCC
**
16992208 AAAAAAAAAC
1 AAAAAAAGCC
16992218 AAAAAAAGCC
1 AAAAAAAGCC
16992228 AAAAAA
1 AAAAAA
16992234 GCTAAAATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
10 30 0.77
11 9 0.23
ACGTcount: A:0.81, C:0.11, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAAAGCC
Found at i:16992232 original size:11 final size:11
Alignment explanation
Indices: 16992166--16992233 Score: 79
Period size: 11 Copynumber: 6.5 Consensus size: 11
16992156 TATTTTTTTC
16992166 AAAAAAA-ACA
1 AAAAAAAGACA
*
16992176 AAAAAAAAACA
1 AAAAAAAGACA
*
16992187 AAAAAAAGGCA
1 AAAAAAAGACA
*
16992198 AAAAAAAGGCA
1 AAAAAAAGACA
16992209 AAAAAAA-AC-
1 AAAAAAAGACA
*
16992218 AAAAAAAGCCA
1 AAAAAAAGACA
16992229 AAAAA
1 AAAAA
16992234 GCTAAAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
9 7 0.14
10 9 0.18
11 35 0.69
ACGTcount: A:0.82, C:0.10, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAGACA
Found at i:16996521 original size:15 final size:16
Alignment explanation
Indices: 16996494--16996530 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
16996484 CTTTATTATC
16996494 TTATTTCATCTTTCGT
1 TTATTTCATCTTTCGT
*
16996510 TTATTT-ATCTTTTGT
1 TTATTTCATCTTTCGT
16996525 TTATTT
1 TTATTT
16996531 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTTCGT
Found at i:16999945 original size:12 final size:12
Alignment explanation
Indices: 16999930--16999954 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16999920 ATAAATGAGT
16999930 AAATAAGGAATA
1 AAATAAGGAATA
16999942 AAATAAGGAATA
1 AAATAAGGAATA
16999954 A
1 A
16999955 CTCCCTTAGA
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:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
AAATAAGGAATA
Found at i:17002302 original size:246 final size:246
Alignment explanation
Indices: 17001868--17002358 Score: 946
Period size: 246 Copynumber: 2.0 Consensus size: 246
17001858 ATTGGAAATA
17001868 GACAAATATTGTGTGTTCATCCTAAAATCCTTAATTATGTTAAAATGTTTTATTTTAGGGAATAA
1 GACAAATATTGTGTGTTCATCCTAAAATCCTTAATTATGTTAAAATGTTTTATTTTAGGGAATAA
17001933 AAAGATCATTAATTAAATAAAAATTCAAATTTTTAAACTTTCAGTAAATGGACCAATTCATAATT
66 AAAGATCATTAATTAAATAAAAATTCAAATTTTTAAACTTTCAGTAAATGGACCAATTCATAATT
*
17001998 GAAGGTACCAATTTTGGGCATTGTGTGGGTCCTTCTCCAAGCGTATCAAGTCCCAAACCCATAAT
131 GAAGATACCAATTTTGGGCATTGTGTGGGTCCTTCTCCAAGCGTATCAAGTCCCAAACCCATAAT
17002063 CTCTAAAAATGTAGATTGAATCACGACTTTTTGAATTTTTTCATTTAAAAG
196 CTCTAAAAATGTAGATTGAATCACGACTTTTTGAATTTTTTCATTTAAAAG
* *
17002114 GACAAATATTGTGTTTTCCTCCTAAAATCCTTAATTATGTTAAAATGTTTTATTTTAGGGAATAA
1 GACAAATATTGTGTGTTCATCCTAAAATCCTTAATTATGTTAAAATGTTTTATTTTAGGGAATAA
17002179 AAAGATCATTAATTAAATAAAAATTCAAATTTTTAAACTTTCAGTAAATGGACCAATTCATAATT
66 AAAGATCATTAATTAAATAAAAATTCAAATTTTTAAACTTTCAGTAAATGGACCAATTCATAATT
*
17002244 GAAGATACCAATTTTGGGCATTGTGTGGGTCCTTCTCCAAGTGTATCAAGTCCCAAACCCATAAT
131 GAAGATACCAATTTTGGGCATTGTGTGGGTCCTTCTCCAAGCGTATCAAGTCCCAAACCCATAAT
17002309 CTCTAAAAATGTAGATTGAATCACGACTTTTTGAATTTTTTCATTTAAAA
196 CTCTAAAAATGTAGATTGAATCACGACTTTTTGAATTTTTTCATTTAAAA
17002359 TGACGTATCA
Statistics
Matches: 241, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
246 241 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (246 bp):
GACAAATATTGTGTGTTCATCCTAAAATCCTTAATTATGTTAAAATGTTTTATTTTAGGGAATAA
AAAGATCATTAATTAAATAAAAATTCAAATTTTTAAACTTTCAGTAAATGGACCAATTCATAATT
GAAGATACCAATTTTGGGCATTGTGTGGGTCCTTCTCCAAGCGTATCAAGTCCCAAACCCATAAT
CTCTAAAAATGTAGATTGAATCACGACTTTTTGAATTTTTTCATTTAAAAG
Found at i:17004312 original size:2 final size:2
Alignment explanation
Indices: 17004305--17004372 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
17004295 ATATGAAGAA
17004305 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17004347 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
17004373 TATGGTTAGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17005722 original size:19 final size:19
Alignment explanation
Indices: 17005683--17005722 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
17005673 TTAATTTCAA
17005683 TTGTTTTTAGTTATGCTCT
1 TTGTTTTTAGTTATGCTCT
*
17005702 TTGTTGTTTATTTATGC-CT
1 TTGTT-TTTAGTTATGCTCT
17005721 TT
1 TT
17005723 CAGCTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.10, C:0.10, G:0.15, T:0.65
Consensus pattern (19 bp):
TTGTTTTTAGTTATGCTCT
Found at i:17008051 original size:3 final size:3
Alignment explanation
Indices: 17008043--17008110 Score: 100
Period size: 3 Copynumber: 22.7 Consensus size: 3
17008033 CTAAAATAGG
* * * *
17008043 TAA TAA TAA TAA TAA TAA TAG TAT TAA TAA TAA TAA TAA TGA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17008091 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
17008111 TATTTGTTCA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17012465 original size:170 final size:170
Alignment explanation
Indices: 17012181--17012489 Score: 582
Period size: 170 Copynumber: 1.8 Consensus size: 170
17012171 AAAGGCCTAA
17012181 CTACTAGTGTTTAGTTGCTATAGGTGTGTCCCCTTGACCCGTATAATACCTTTAATAAATTTTAT
1 CTACTAGTGTTTAGTTGCTATAGGTGTGTCCCCTTGACCCGTATAATACCTTTAATAAATTTTAT
*
17012246 GTTAATGTATTGTATAATACTAATTGTAAGCATGTTAGTATTTTGATTATGAATATCTGTTATAT
66 GTTAATGTATTGTATAATACTAATTGTAAGCATGTTAGTATTCTGATTATGAATATCTGTTATAT
17012311 GTCTGATTTCTGATTAGATTGTAGGAAGCGTAACGCTTAG
131 GTCTGATTTCTGATTAGATTGTAGGAAGCGTAACGCTTAG
17012351 CTACTAGTGTTTAGTTGCTATAGGTGTGTCCCCTTGACCCGTATAATACCTTTAATAAATTTTAT
1 CTACTAGTGTTTAGTTGCTATAGGTGTGTCCCCTTGACCCGTATAATACCTTTAATAAATTTTAT
* * *
17012416 GTTAATGTATTGTATAATACTATTTGTAAGCATGTTTGTATTCTGATTATGAATATTTGTTATAT
66 GTTAATGTATTGTATAATACTAATTGTAAGCATGTTAGTATTCTGATTATGAATATCTGTTATAT
17012481 GTCTGATTT
131 GTCTGATTT
17012490 TTTATTATGG
Statistics
Matches: 135, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
170 135 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (170 bp):
CTACTAGTGTTTAGTTGCTATAGGTGTGTCCCCTTGACCCGTATAATACCTTTAATAAATTTTAT
GTTAATGTATTGTATAATACTAATTGTAAGCATGTTAGTATTCTGATTATGAATATCTGTTATAT
GTCTGATTTCTGATTAGATTGTAGGAAGCGTAACGCTTAG
Found at i:17012606 original size:29 final size:29
Alignment explanation
Indices: 17012535--17012599 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
17012525 TATACATACA
* * *
17012535 TGTTTCTTCATGGGATTATATCCCCATCC
1 TGTTTCTACATGGGATTAAATCCACATCC
*
17012564 TGTTTCTACATGGGGTTAAATCCACATCC
1 TGTTTCTACATGGGATTAAATCCACATCC
17012593 TGTTTCT
1 TGTTTCT
17012600 GTTTGGGATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.42
Consensus pattern (29 bp):
TGTTTCTACATGGGATTAAATCCACATCC
Found at i:17013397 original size:23 final size:23
Alignment explanation
Indices: 17013371--17013425 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
17013361 GTTATCCATA
*
17013371 AATTTTGTACTATACTGTAAAAT
1 AATTTTGCACTATACTGTAAAAT
*
17013394 AATTTTGCACTATATTGTAAAAT
1 AATTTTGCACTATACTGTAAAAT
17013417 AATTTTGCA
1 AATTTTGCA
17013426 TGTATTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (23 bp):
AATTTTGCACTATACTGTAAAAT
Found at i:17019336 original size:14 final size:14
Alignment explanation
Indices: 17019319--17019352 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
17019309 AAATTAAATG
*
17019319 AATAAAATCATTTA
1 AATAAAATCACTTA
17019333 AATAAAATCACTTA
1 AATAAAATCACTTA
17019347 AATAAA
1 AATAAA
17019353 TATGCACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (14 bp):
AATAAAATCACTTA
Found at i:17024847 original size:17 final size:18
Alignment explanation
Indices: 17024833--17024866 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17024823 TTTTTATTAT
17024833 ATAT-TTTAATTTATTTA
1 ATATCTTTAATTTATTTA
*
17024850 ATATCTTTAATTAATTT
1 ATATCTTTAATTTATTT
17024867 GTTAATTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
ATATCTTTAATTTATTTA
Found at i:17025120 original size:16 final size:17
Alignment explanation
Indices: 17025091--17025123 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
17025081 TCCTTTGGGT
*
17025091 TTTATATTTTCTTTTAA
1 TTTATATTTCCTTTTAA
17025108 TTTA-ATTTCCTTTTAA
1 TTTATATTTCCTTTTAA
17025124 AAATGATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATATTTCCTTTTAA
Found at i:17027226 original size:35 final size:37
Alignment explanation
Indices: 17027157--17027236 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
17027147 ATACTATTTC
*
17027157 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
17027194 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
17027229 CATCACCA
1 CATCACCA
17027237 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:17031128 original size:35 final size:37
Alignment explanation
Indices: 17031059--17031138 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
17031049 ATACTATTTC
*
17031059 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
17031096 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
17031131 CATCACCA
1 CATCACCA
17031139 AATTATCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:17031539 original size:26 final size:23
Alignment explanation
Indices: 17031510--17031557 Score: 60
Period size: 26 Copynumber: 2.0 Consensus size: 23
17031500 GTGCCACAAC
17031510 AACAAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAAG-AA-AAGAAA-AAGAA
*
17031536 AACAAAAGAGAAAAGAAAAAGA
1 AACAAAAAAGAAAAGAAAAAGA
17031558 CTCCTACATC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 2 0.10
26 9 0.43
ACGTcount: A:0.75, C:0.08, G:0.17, T:0.00
Consensus pattern (23 bp):
AACAAAAAAGAAAAGAAAAAGAA
Found at i:17031613 original size:14 final size:15
Alignment explanation
Indices: 17031579--17031625 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
17031569 AATTTGGAGT
17031579 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
17031594 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
17031608 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
17031625 G
1 G
17031626 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:17035370 original size:35 final size:37
Alignment explanation
Indices: 17035301--17035380 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
17035291 ATATTATTTC
*
17035301 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
* *
17035338 CATCACCATACTCCATC-ACCA-TATCATGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
17035373 CATCACCA
1 CATCACCA
17035381 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.31, C:0.38, G:0.03, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:17043641 original size:88 final size:87
Alignment explanation
Indices: 17043537--17043734 Score: 252
Period size: 87 Copynumber: 2.3 Consensus size: 87
17043527 ATTCACTCAT
* * * ** **
17043537 ATACAGCATAATTTGGGAAAATATATTGTATTAAATGGCGTATTGGGAAAAGAAGATGACATTAA
1 ATACTGCATAATTTGGGAAAATATAATATATTAAACAGCAAATTGGGAAAA-AAGATGACATTAA
17043602 TGCTATTAACTATTGTTATACCA
65 TGCTATTAACTATTGTTATACCA
* * * *
17043625 GTACTGCATAATTTGGGAAAAGATAATATATTAAACATCAAATTGGGGAAAAAGATGACATTAAT
1 ATACTGCATAATTTGGGAAAATATAATATATTAAACAGCAAATTGGGAAAAAAGATGACATTAAT
*
17043690 GCTATTAACTATTGTTGTACCA
66 GCTATTAACTATTGTTATACCA
* * *
17043712 ATATTTCATAATTTGCGAAAATA
1 ATACTGCATAATTTGGGAAAATA
17043735 GGATGCGTCA
Statistics
Matches: 93, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
87 53 0.57
88 40 0.43
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.33
Consensus pattern (87 bp):
ATACTGCATAATTTGGGAAAATATAATATATTAAACAGCAAATTGGGAAAAAAGATGACATTAAT
GCTATTAACTATTGTTATACCA
Found at i:17045646 original size:2 final size:2
Alignment explanation
Indices: 17045639--17045672 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
17045629 CGTCAACAAA
17045639 AT AT AT AT AT AT AT -T 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 AT AT A
17045673 CACACTATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17045681 original size:19 final size:19
Alignment explanation
Indices: 17045639--17045681 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17045629 CGTCAACAAA
* *
17045639 ATATATATATATATTATAT
1 ATATATATATATATTACAC
17045658 ATATATATATATA-TACAC
1 ATATATATATATATTACAC
17045676 ACTATA
1 A-TATA
17045682 AGCAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATATATATATATTACAC
Found at i:17047412 original size:5 final size:5
Alignment explanation
Indices: 17047402--17047540 Score: 278
Period size: 5 Copynumber: 27.8 Consensus size: 5
17047392 GGTGTATAAG
17047402 ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA
1 ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA
17047452 ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA
1 ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA
17047502 ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTG
1 ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA ATTG
17047541 GTTACCCCAG
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 134 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
ATTGA
Found at i:17048840 original size:25 final size:25
Alignment explanation
Indices: 17048806--17048857 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
17048796 AATAAATCGA
17048806 TTCGGGTAATCGGGTACGGATCAAC
1 TTCGGGTAATCGGGTACGGATCAAC
*
17048831 TTCGGGTAATTGGGTACGGATCAAC
1 TTCGGGTAATCGGGTACGGATCAAC
17048856 TT
1 TT
17048858 TGCCAAGTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (25 bp):
TTCGGGTAATCGGGTACGGATCAAC
Found at i:17049391 original size:26 final size:26
Alignment explanation
Indices: 17049360--17049413 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
17049350 AAATAATCAC
*
17049360 GATGTTTTTATTAAAATAAAGATGTA
1 GATGTTTTTACTAAAATAAAGATGTA
17049386 GATGTTTTTACTAAAATAAAGATGTA
1 GATGTTTTTACTAAAATAAAGATGTA
17049412 GA
1 GA
17049414 AAAATAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.02, G:0.17, T:0.39
Consensus pattern (26 bp):
GATGTTTTTACTAAAATAAAGATGTA
Found at i:17050117 original size:6 final size:6
Alignment explanation
Indices: 17050108--17050197 Score: 171
Period size: 6 Copynumber: 15.0 Consensus size: 6
17050098 TTAAATATAT
*
17050108 ATACAT ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
17050156 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC
17050198 GTAAATATAA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 83 1.00
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (6 bp):
ATACAC
Found at i:17050290 original size:2 final size:2
Alignment explanation
Indices: 17050283--17050358 Score: 120
Period size: 2 Copynumber: 38.5 Consensus size: 2
17050273 AAGAAAGCTT
*
17050283 TA TA TA TA -A T- TA TA TT TGA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
17050324 TA 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 TA T
17050359 GTGTGTGTGT
Statistics
Matches: 69, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
1 2 0.03
2 66 0.96
3 1 0.01
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17050769 original size:17 final size:18
Alignment explanation
Indices: 17050742--17050781 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
17050732 TAAATACTCA
17050742 AAATATAAATATAGTCTT
1 AAATATAAATATAGTCTT
17050760 AAAT-TAAATATAGTCTT
1 AAATATAAATATAGTCTT
17050777 AAATA
1 AAATA
17050782 GGTAAACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (18 bp):
AAATATAAATATAGTCTT
Found at i:17051031 original size:30 final size:30
Alignment explanation
Indices: 17050949--17051054 Score: 94
Period size: 30 Copynumber: 3.6 Consensus size: 30
17050939 AAATTGCAGA
* * * *
17050949 AAATAAAGGTACCGGAACATAAAT-AAAGG
1 AAATAAAGGTGCTGAAATATAAATAAAAGG
* * *
17050978 AAACTAAA-GTGTTGAAATGTAAATAAAATG
1 AAA-TAAAGGTGCTGAAATATAAATAAAAGG
17051008 AAATAAAGGTGCTGAAATATAAAT-AAAGG
1 AAATAAAGGTGCTGAAATATAAATAAAAGG
*
17051037 AAAATAAA-GTGCTTAAAT
1 -AAATAAAGGTGCTGAAAT
17051055 TAAGAGAACA
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
29 30 0.48
30 32 0.52
ACGTcount: A:0.55, C:0.06, G:0.18, T:0.22
Consensus pattern (30 bp):
AAATAAAGGTGCTGAAATATAAATAAAAGG
Found at i:17051049 original size:29 final size:29
Alignment explanation
Indices: 17050967--17051054 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 29
17050957 GTACCGGAAC
* *
17050967 ATAAATAAAGGAAACTAAAGTGTTGAAAT
1 ATAAATAAAGGAAAATAAAGTGCTGAAAT
* *
17050996 GTAAATAAAATG-AAATAAAGGTGCTGAAAT
1 ATAAAT-AAAGGAAAATAAA-GTGCTGAAAT
*
17051026 ATAAATAAAGGAAAATAAAGTGCTTAAAT
1 ATAAATAAAGGAAAATAAAGTGCTGAAAT
17051055 TAAGAGAACA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
29 24 0.49
30 25 0.51
ACGTcount: A:0.56, C:0.03, G:0.17, T:0.24
Consensus pattern (29 bp):
ATAAATAAAGGAAAATAAAGTGCTGAAAT
Found at i:17051379 original size:10 final size:11
Alignment explanation
Indices: 17051359--17051383 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17051349 GAGCCCCTTC
17051359 AAAGAAAAAAA
1 AAAGAAAAAAA
17051370 AAAGAAAAAAA
1 AAAGAAAAAAA
17051381 AAA
1 AAA
17051384 ACGTAAGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:17051609 original size:38 final size:38
Alignment explanation
Indices: 17051517--17051689 Score: 135
Period size: 38 Copynumber: 4.6 Consensus size: 38
17051507 TTTTAAAAGT
* *
17051517 ATATAATATATAGTTTTTAAAAAATTA-GTTTTTG-AAA-
1 ATATATTATATAG-TTTTGAAAAA-TACGTTTTTGAAAAC
*
17051554 ATATATAATAT-GATTTTGAAAAATACGTTTTTGAAAAC
1 ATATATTATATAG-TTTTGAAAAATACGTTTTTGAAAAC
* ** *
17051592 ATATATTATATAGTTTTGAAAAAAATATTTTTGAAAAT
1 ATATATTATATAGTTTTGAAAAATACGTTTTTGAAAAC
* *
17051630 GTATAATATACATAGTTTT--AAAA-ACGATTTTTGAAAAC
1 ATAT-AT-TATATAGTTTTGAAAAATACG-TTTTTGAAAAC
* * *
17051668 TTATATAATATAATTTTGAAAA
1 ATATATTATATAGTTTTGAAAA
17051690 CGTATATATA
Statistics
Matches: 109, Mismatches: 18, Indels: 17
0.76 0.12 0.12
Matches are distributed among these distances:
35 2 0.02
36 25 0.23
37 15 0.14
38 54 0.50
39 3 0.03
40 10 0.09
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (38 bp):
ATATATTATATAGTTTTGAAAAATACGTTTTTGAAAAC
Found at i:17051679 original size:76 final size:75
Alignment explanation
Indices: 17051524--17051689 Score: 203
Period size: 76 Copynumber: 2.2 Consensus size: 75
17051514 AGTATATAAT
* * *
17051524 ATATAGTTTTTAAAAAATTAGTTTTTGAAAATATATAATATGATTTTGAAAAATACGTTTTTGAA
1 ATATAGTTTTGAAAAAAATAGTTTTTGAAAATATATAATATCATTTTGAAAAATACGTTTTTGAA
*
17051589 AACATATATT
66 AACATATATA
* *
17051599 ATATAGTTTTGAAAAAAATA-TTTTTGAAAATGTATAATATACATAGTTT-TAAAA-ACGATTTT
1 ATATAGTTTTGAAAAAAATAGTTTTTGAAAATATATAATAT-CAT--TTTGAAAAATACG-TTTT
*
17051661 TGAAAACTTATATA
62 TGAAAACATATATA
*
17051675 ATATAATTTTGAAAA
1 ATATAGTTTTGAAAA
17051690 CGTATATATA
Statistics
Matches: 79, Mismatches: 8, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
74 19 0.24
75 23 0.29
76 34 0.43
77 3 0.04
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (75 bp):
ATATAGTTTTGAAAAAAATAGTTTTTGAAAATATATAATATCATTTTGAAAAATACGTTTTTGAA
AACATATATA
Found at i:17051707 original size:23 final size:24
Alignment explanation
Indices: 17051656--17051714 Score: 86
Period size: 23 Copynumber: 2.5 Consensus size: 24
17051646 TTTAAAAACG
*
17051656 ATTTTTGAAAACTTATATAATATA
1 ATTTTTGAAAACGTATATAATATA
17051680 A-TTTTGAAAACGTATAT-ATATA
1 ATTTTTGAAAACGTATATAATATA
*
17051702 ATTTTTTAAAACG
1 ATTTTTGAAAACG
17051715 ATTTTTTGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 6 0.19
23 25 0.78
24 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (24 bp):
ATTTTTGAAAACGTATATAATATA
Found at i:17051721 original size:60 final size:60
Alignment explanation
Indices: 17051620--17051739 Score: 163
Period size: 60 Copynumber: 2.0 Consensus size: 60
17051610 AAAAAAATAT
* *
17051620 TTTTGAAAATGTATAATATACATAGTTTTAAAAACGATTTTTGAAAACTTATATAATATAA
1 TTTTGAAAACGTATAATATACATA-TTTTAAAAACGATTTTTGAAAACATATATAATATAA
* *
17051681 TTTTGAAAACGTATATATATA-AT-TTTTTAAAACGATTTTTTGGAAACATATATAATATA
1 TTTTGAAAACGTATA-ATATACATATTTTAAAAACGA-TTTTTGAAAACATATATAATATA
17051740 TAATTTTTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
59 11 0.21
60 21 0.40
61 16 0.30
62 5 0.09
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.42
Consensus pattern (60 bp):
TTTTGAAAACGTATAATATACATATTTTAAAAACGATTTTTGAAAACATATATAATATAA
Found at i:17051745 original size:40 final size:42
Alignment explanation
Indices: 17051695--17051788 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
17051685 GAAAACGTAT
17051695 ATATATAATTTTTTAAAAC-GATT-TTTTGGAAACATAT-ATA
1 ATATATAATTTTTTAAAACAGATTATTTTGGAAA-ATATAATA
* *
17051735 ATATATAATTTTTTAAAACATATTATTTTTGAAAATATAATA
1 ATATATAATTTTTTAAAACAGATTATTTTGGAAAATATAATA
* *
17051777 TTATATAGTTTT
1 ATATATAATTTT
17051789 ATTATATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
40 19 0.40
41 7 0.15
42 21 0.45
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (42 bp):
ATATATAATTTTTTAAAACAGATTATTTTGGAAAATATAATA
Found at i:17051773 original size:39 final size:37
Alignment explanation
Indices: 17051681--17051777 Score: 106
Period size: 40 Copynumber: 2.5 Consensus size: 37
17051671 TATAATATAA
17051681 TTTTGAAAACGTAT-ATATATAATTTTTTAAAACGATTT
1 TTTTGAAAA--TATAATATATAATTTTTTAAAACGATTT
* *
17051719 TTTGGAAACATATATAATATATAATTTTTTAAAACATATTAT
1 TTTTG-AA-A-ATATAATATATAATTTTTTAAAAC-GATT-T
17051761 TTTTGAAAATATAATAT
1 TTTTGAAAATATAATAT
17051778 TATATAGTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
38 4 0.08
39 14 0.28
40 21 0.42
41 6 0.12
42 5 0.10
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (37 bp):
TTTTGAAAATATAATATATAATTTTTTAAAACGATTT
Found at i:17051778 original size:17 final size:16
Alignment explanation
Indices: 17051737--17051778 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
17051727 CATATATAAT
17051737 ATATAAT-TTTTTAAA
1 ATATAATATTTTTAAA
* *
17051752 ACATATTATTTTTGAAA
1 ATATAATATTTTT-AAA
17051769 ATATAATATT
1 ATATAATATT
17051779 ATATAGTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 5 0.24
16 5 0.24
17 11 0.52
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (16 bp):
ATATAATATTTTTAAA
Found at i:17051809 original size:16 final size:17
Alignment explanation
Indices: 17051786--17051856 Score: 76
Period size: 17 Copynumber: 4.2 Consensus size: 17
17051776 ATTATATAGT
17051786 TTTATTATATATTAT-TTA
1 TTTATT-TAT-TTATATTA
* *
17051804 TATTATTAATTTATATTT
1 T-TTATTTATTTATATTA
17051822 TTTATTTATTTATATT-
1 TTTATTTATTTATATTA
17051838 TTTATTTATTTAT-TTA
1 TTTATTTATTTATATTA
17051854 TTT
1 TTT
17051857 TCATTTTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
15 2 0.04
16 16 0.34
17 18 0.38
18 6 0.13
19 5 0.11
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATTTATTTATATTA
Found at i:17051815 original size:13 final size:12
Alignment explanation
Indices: 17051790--17051854 Score: 55
Period size: 13 Copynumber: 5.3 Consensus size: 12
17051780 TATAGTTTTA
17051790 TTATA-TATTAT
1 TTATATTATTAT
17051801 TTATATTATTAAT
1 TTATATTATT-AT
*
17051814 TTATATTTTTTAT
1 TTATA-TTATTAT
17051827 TTAT-TTA-TAT
1 TTATATTATTAT
*
17051837 TTTTATTTATTTAT
1 TTATA-TTA-TTAT
17051851 TTAT
1 TTAT
17051855 TTTCATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
10 6 0.14
11 7 0.16
12 7 0.16
13 13 0.30
14 10 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATATTATTAT
Found at i:17051826 original size:17 final size:16
Alignment explanation
Indices: 17051775--17051850 Score: 73
Period size: 17 Copynumber: 4.4 Consensus size: 16
17051765 GAAAATATAA
*
17051775 TATTATATAGTTTTATT
1 TATT-TATATTTTTATT
17051792 ATATATTAT-TTATATTATT
1 -TAT-TTATATT-T-TTATT
*
17051811 AATTTATATTTTTTATT
1 TATTTATA-TTTTTATT
17051828 TATTTATATTTTTATT
1 TATTTATATTTTTATT
17051844 TATTTAT
1 TATTTAT
17051851 TTATTTTCAT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
16 15 0.30
17 17 0.34
18 10 0.20
19 8 0.16
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (16 bp):
TATTTATATTTTTATT
Found at i:17051831 original size:4 final size:4
Alignment explanation
Indices: 17051786--17051856 Score: 72
Period size: 4 Copynumber: 16.8 Consensus size: 4
17051776 ATTATATAGT
* *
17051786 TTTA TTATA TATTA TTTA TATTA TTAA TTTA TATTT TTTA TTTA TTTA
1 TTTA TT-TA T-TTA TTTA T-TTA TTTA TTTA T-TTA TTTA TTTA TTTA
17051834 TATT- TTTA TTTA TTTA TTTA TTT
1 T-TTA TTTA TTTA TTTA TTTA TTT
17051857 TCATTTTTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
3 2 0.04
4 39 0.68
5 15 0.26
6 1 0.02
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:17051856 original size:24 final size:25
Alignment explanation
Indices: 17051785--17051865 Score: 87
Period size: 24 Copynumber: 3.2 Consensus size: 25
17051775 TATTATATAG
17051785 TTTTATTATATATTATTTATATTATTAAT
1 TTTTATT-TAT-TTATTTAT-TTA-TAAT
*
17051814 TTATATTT-TTTATTTATTTAT-AT
1 TTTTATTTATTTATTTATTTATAAT
*
17051837 TTTTATTTATTTATTTATTT-TCAT
1 TTTTATTTATTTATTTATTTATAAT
17051861 TTTTA
1 TTTTA
17051866 ACAGGTCCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
23 10 0.21
24 19 0.40
25 3 0.06
26 8 0.17
27 1 0.02
28 1 0.02
29 6 0.12
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTTATTTATTTATTTATTTATAAT
Found at i:17055306 original size:63 final size:63
Alignment explanation
Indices: 17055204--17055435 Score: 272
Period size: 63 Copynumber: 3.7 Consensus size: 63
17055194 TTTGAGAATG
* ** * * *
17055204 ATTCACCTCCACTGAAGCAACATT-CACACACTCTACATCATC-ATCAAAGATTGCTTTGGGATC
1 ATTCACCTCCACCGAAGTGAC-TTCCACACATTCTTCATCATCAAT-AAAGATTACTTTGGGATC
* * * **
17055267 ATTCACCACCACTGAAGTGACTTGCACACATTCTTCATCATCAATAAAGATTACTTCAGGATC
1 ATTCACCTCCACCGAAGTGACTTCCACACATTCTTCATCATCAATAAAGATTACTTTGGGATC
* * * *
17055330 ATTAATCTCCACCGAAGTGGA-TTCCATACATTCTTCATCATCAATAAAGATTACTTTGGGATT
1 ATTCACCTCCACCGAAGT-GACTTCCACACATTCTTCATCATCAATAAAGATTACTTTGGGATC
*
17055393 ATTCACCTCCACCGAAGTGGCTTCCACACATTCTTCATCATCA
1 ATTCACCTCCACCGAAGTGACTTCCACACATTCTTCATCATCA
17055436 TTAGAGGTTT
Statistics
Matches: 144, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
62 3 0.02
63 137 0.95
64 4 0.03
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (63 bp):
ATTCACCTCCACCGAAGTGACTTCCACACATTCTTCATCATCAATAAAGATTACTTTGGGATC
Found at i:17055450 original size:63 final size:63
Alignment explanation
Indices: 17055228--17055435 Score: 274
Period size: 63 Copynumber: 3.3 Consensus size: 63
17055218 AAGCAACATT
* * * * * * *
17055228 CACACACTCTACATCATC-ATCAAAGATTGCTTTGGGATCATTCACCACCACTGAAGTGACTTG
1 CACACATTCTTCATCATCAAT-AAAGATTACTTTGGGATCATTCACCTCCACCGAAGTGGCTTC
** * * *
17055291 CACACATTCTTCATCATCAATAAAGATTACTTCAGGATCATTAATCTCCACCGAAGTGGATTC
1 CACACATTCTTCATCATCAATAAAGATTACTTTGGGATCATTCACCTCCACCGAAGTGGCTTC
* *
17055354 CATACATTCTTCATCATCAATAAAGATTACTTTGGGATTATTCACCTCCACCGAAGTGGCTTC
1 CACACATTCTTCATCATCAATAAAGATTACTTTGGGATCATTCACCTCCACCGAAGTGGCTTC
17055417 CACACATTCTTCATCATCA
1 CACACATTCTTCATCATCA
17055436 TTAGAGGTTT
Statistics
Matches: 124, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
63 122 0.98
64 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.30
Consensus pattern (63 bp):
CACACATTCTTCATCATCAATAAAGATTACTTTGGGATCATTCACCTCCACCGAAGTGGCTTC
Found at i:17062943 original size:27 final size:27
Alignment explanation
Indices: 17062881--17062943 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
17062871 TTTTACCCTA
* *
17062881 AAAATAAAAGTAAAATAAAATAACATT
1 AAAATAATAGTAAAATAAAATAACACT
* * *
17062908 AAAAAAATAGTAAGAT-AAATAATACT
1 AAAATAATAGTAAAATAAAATAACACT
17062934 AATAATAATA
1 AA-AATAATA
17062944 ATAATAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
26 10 0.34
27 19 0.66
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (27 bp):
AAAATAATAGTAAAATAAAATAACACT
Found at i:17063099 original size:104 final size:102
Alignment explanation
Indices: 17062999--17063199 Score: 241
Period size: 104 Copynumber: 2.0 Consensus size: 102
17062989 AAAAAAATAT
* *
17062999 TTTTTAAAAACTATATA-T-TATACGTATTTCAAAAACGGATTAAAAA-TATATAATATATATA-
1 TTTTAAAAAACTATATACTATATAAGT-TTTC-AAAACGGATTAAAAACTATATAATATATA-AG
**
17063060 TTTTCAAAAT-TATTTTTAAACTATATATTATATTTAAAAATG
63 TTTTCAAAATGT-TTTAAAAACTATATA--ATATTTAAAAATG
* ** *
17063102 TTTTAAAAAACTATATACTATATAAGTTTTCAAAATGTTTTAAAAACTATATATTATATAAGTTT
1 TTTTAAAAAACTATATACTATATAAGTTTTCAAAACGGATTAAAAACTATATAATATATAAGTTT
17063167 TCAAAATGTTTTAAAAACTATATAATATTTAAA
66 TCAAAATGTTTTAAAAACTATATAATATTTAAA
17063200 TGTTTTCAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
102 9 0.11
103 29 0.34
104 40 0.47
105 7 0.08
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (102 bp):
TTTTAAAAAACTATATACTATATAAGTTTTCAAAACGGATTAAAAACTATATAATATATAAGTTT
TCAAAATGTTTTAAAAACTATATAATATTTAAAAATG
Found at i:17063133 original size:68 final size:71
Alignment explanation
Indices: 17063000--17063209 Score: 204
Period size: 68 Copynumber: 3.0 Consensus size: 71
17062990 AAAAAATATT
* **
17063000 TTTTAAAAACTATATATTATACGT-A-TTTCAAAAACGGATTAAAAA-TATATAATATATATA-T
1 TTTTAAAAACTATATATTATA--TAAGTTT-AAAAATGTTTTAAAAACTATATAATATATA-AGT
17063061 TTTCAAAAT-
62 TTTCAAAATG
** *
17063070 TATTTTTAAACTATATA-T-TAT-A-TTTAAAAATGTTTTAAAAAACTATATACTATATAAGTTT
1 T-TTTAAAAACTATATATTATATAAGTTTAAAAATGTTTT-AAAAACTATATAATATATAAGTTT
17063131 TCAAAATG
64 TCAAAATG
* *
17063139 TTTTAAAAACTATATATTATATAAGTTTTCAAAATGTTTTAAAAACTATATAATATTTAAATGTT
1 TTTTAAAAACTATATATTATATAAG-TTTAAAAATGTTTTAAAAACTATATAATATAT-AA-GTT
17063204 TTCAAA
63 TTCAAA
17063210 CTATACATTA
Statistics
Matches: 117, Mismatches: 11, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
66 8 0.07
67 11 0.09
68 35 0.30
69 4 0.03
70 5 0.04
71 14 0.12
72 16 0.14
73 15 0.13
74 9 0.08
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (71 bp):
TTTTAAAAACTATATATTATATAAGTTTAAAAATGTTTTAAAAACTATATAATATATAAGTTTTC
AAAATG
Found at i:17063137 original size:37 final size:36
Alignment explanation
Indices: 17063000--17063209 Score: 197
Period size: 36 Copynumber: 5.9 Consensus size: 36
17062990 AAAAAATATT
* *
17063000 TTTTAAAAACTATAT-AT-TATACGTATTTCAAAAACG
1 TTTTAAAAACTATATAATATATAAGT-TTTC-AAAATG
**
17063036 GATTAAAAA-TATATAATATATATA-TTTTCAAAAT-
1 TTTTAAAAACTATATAATATATA-AGTTTTCAAAATG
** *
17063070 TATTTTTAAACTATAT-AT-TAT-A--TTTAAAAATG
1 T-TTTAAAAACTATATAATATATAAGTTTTCAAAATG
*
17063102 TTTTAAAAAACTATATACTATATAAGTTTTCAAAATG
1 TTTT-AAAAACTATATAATATATAAGTTTTCAAAATG
*
17063139 TTTTAAAAACTATATATTATATAAGTTTTCAAAATG
1 TTTTAAAAACTATATAATATATAAGTTTTCAAAATG
*
17063175 TTTTAAAAACTATATAATATTTAAATGTTTTCAAA
1 TTTTAAAAACTATATAATATAT-AA-GTTTTCAAA
17063210 CTATACATTA
Statistics
Matches: 144, Mismatches: 16, Indels: 26
0.77 0.09 0.14
Matches are distributed among these distances:
31 11 0.08
32 11 0.08
33 1 0.01
34 6 0.04
35 17 0.12
36 69 0.48
37 20 0.14
38 9 0.06
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (36 bp):
TTTTAAAAACTATATAATATATAAGTTTTCAAAATG
Found at i:17063220 original size:62 final size:62
Alignment explanation
Indices: 17063134--17063255 Score: 167
Period size: 61 Copynumber: 2.0 Consensus size: 62
17063124 TAAGTTTTCA
* * * *
17063134 AAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATGTTTT-AAAAACTATATAATATTT
1 AAATGTTTTAAAAACTATACATTATAT-A-TTTTAAAAATATTTTCAAAAACCATATAATATTT
*
17063197 AAATGTTTT-CAAACTATACATTATATATTTTAAAAATATTTTCAAAAACCATATAATAT
1 AAATGTTTTAAAAACTATACATTATATATTTTAAAAATATTTTCAAAAACCATATAATAT
17063256 ATATTTTCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
60 13 0.25
61 16 0.30
62 15 0.28
63 9 0.17
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (62 bp):
AAATGTTTTAAAAACTATACATTATATATTTTAAAAATATTTTCAAAAACCATATAATATTT
Found at i:17063324 original size:36 final size:36
Alignment explanation
Indices: 17063206--17063325 Score: 138
Period size: 38 Copynumber: 3.3 Consensus size: 36
17063196 TAAATGTTTT
*
17063206 CAAACTATACATTATATATTTT-AAAAATATTTTCA
1 CAAACTATATATTATATATTTTCAAAAATATTTTCA
* * *
17063241 AAAACCATATAATATATATTTTCAAAAATCATTTTCTGA
1 CAAACTATATATTATATATTTTCAAAAAT-ATTTTC--A
*
17063280 -AAATTATATATTATAT-TTTGTCAAAAATATTTTCA
1 CAAACTATATATTATATATTT-TCAAAAATATTTTCA
17063315 CAAACTATATA
1 CAAACTATATA
17063326 AAAGAGAAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
35 19 0.27
36 15 0.21
37 15 0.21
38 21 0.30
39 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.42
Consensus pattern (36 bp):
CAAACTATATATTATATATTTTCAAAAATATTTTCA
Found at i:17064040 original size:84 final size:83
Alignment explanation
Indices: 17063952--17065139 Score: 1147
Period size: 84 Copynumber: 14.4 Consensus size: 83
17063942 CCGAGTGTAA
* * * *
17063952 TCGAACTCGAAGGTCTTCTGTTGGAAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGT
1 TCGAACTCGAAGGTCTT-TGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
17064017 GCTTTGGAGCTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * * * * *
17064036 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTACGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * * *
17064101 GCCCTCGAAGCTGAGTGTAA
65 G-CCTTGGAGCTGAGCGTAG
* ** ** *
17064121 TCGAACTCGAGGGTC--T-TTGGCAGATTGCCCTTCTCGACTTAAACTATGCTGCAAATGATGCG
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
17064183 CCTTGGAGCTGAGCGTAG
66 CCTTGGAGCTGAGCGTAG
* * * * * * *
17064201 TCGAACTCGAAGGTATTTGGTTGGCATATAACCCTTCTCGATTTAAGTTATACTGTAAATAATAT
1 TCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
17064266 GCCTTGGAGCTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * * * *
17064285 TCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
* *
17064350 CCTTTGAAGCTGAGCATAG
66 CC-TTGGAGCTGAGCGTAG
* * * * * * **
17064369 TTGGACTCGAGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGCA
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
*
17064431 CATTGGAGCTGAGCGTAG
66 CCTTGGAGCTGAGCGTAG
* * * * * *
17064449 TCAAACTTGAAGGTATTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTACAAATGATAT
1 TCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
17064514 GCCTTGGAGCTGAACGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * * * * *
17064533 TCGAACTCAAAGG-CTTTGATGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
* *
17064597 CCCTCGAAGCTGAGCGTAG
66 -CCTTGGAGCTGAGCGTAG
* * * * **
17064616 TCGAACTCGAGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGCA
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
*
17064678 CCTTGGAGCTGAGCGTAA
66 CCTTGGAGCTGAGCGTAG
* ** * * * *
17064696 TTGAACTCGAAGGTCTTTGGTTAACAGATAACCCTTCTTGATTTAAGTTATGTTGCAAATGATAT
1 TCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
17064761 GCCTTGGAGTTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * * * * * **
17064780 TCAAACTCGAAGGTCTTTGATGACAAATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
* * *
17064845 CCCTCGAAGTTGAGCGTAG
66 -CCTTGGAGCTGAGCGTAG
* * * *
17064864 TCAAACTTGAGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGCTT-TGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAG-TTATGCTGCAAATGATGT
*
17064925 TCCTTGGAGCTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * *
17064944 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
17065009 GCCTTGGAGCTGAGCGTAG
65 GCCTTGGAGCTGAGCGTAG
* * * * * * * *
17065028 T----CT-GAAGGTC-TTGGTGGCAGATAGCCCTTCTGGCCCTGAGCTATGCTACAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
*
17065087 CCTTAGAGCTGAGCGTAG
66 CCTTGGAGCTGAGCGTAG
* * * *
17065105 TCGAACTCGAAGGTCTTGGCTGACAGACAACCCTT
1 TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTT
17065140 GAGTTATGCT
Statistics
Matches: 882, Mismatches: 192, Indels: 61
0.78 0.17 0.05
Matches are distributed among these distances:
77 54 0.06
78 2 0.00
79 7 0.01
80 107 0.12
81 140 0.16
82 55 0.06
83 120 0.14
84 368 0.42
85 29 0.03
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (83 bp):
TCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAG
Found at i:17064391 original size:248 final size:248
Alignment explanation
Indices: 17063952--17065121 Score: 1710
Period size: 248 Copynumber: 4.7 Consensus size: 248
17063942 CCGAGTGTAA
* * * * * *
17063952 TCGAACTCGAAGGTCTTCT-GTTGGAAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATG
1 TCGAACTCGAAGGTCTT-TGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATA
*
17064016 TGCTTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTG
65 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGCCTTG
* * *
17064081 AGTTACGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGAT
129 AGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGAT
* * * *
17064146 TGCCCTTCTCGACTTAAACTATGCTGCAAATGATGCGCCTTGGAGCTGAGCGTAG
194 AGCCCTTCTCGACTTAAGCTATGCTACAAATGATGCACCTTGGAGCTGAGCGTAG
* * * * *
17064201 TCGAACTCGAAGGTATTTGGTTGGCATATAACCCTTCTCGATTTAAGTTATACTGTAAATAATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATAT
17064266 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
* * * * *
17064331 TTATGCTGTAAATGATGTGCCTTTGAAGCTGAGCATAGTTGGACTCGAGGGTCTTTGGCAGATAG
131 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGATAG
*
17064396 CCCTTCTCGACTTAAGCTATGCTACAAATGATGCACATTGGAGCTGAGCGTAG
196 CCCTTCTCGACTTAAGCTATGCTACAAATGATGCACCTTGGAGCTGAGCGTAG
* * * *
17064449 TCAAACTTGAAGGTATTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTACAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATAT
* * *
17064514 GCCTTGGAGCTGAACGTAGTCGAACTCAAAGG-CTTTGATGACAGATAACCCTTCTAGCCTTGAG
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
17064578 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGATAG
131 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGATAG
*
17064643 CCCTTCTCGACTTAAGCTATGCTACAAATGATGCACCTTGGAGCTGAGCGTAA
196 CCCTTCTCGACTTAAGCTATGCTACAAATGATGCACCTTGGAGCTGAGCGTAG
* ** * *
17064696 TTGAACTCGAAGGTCTTTGGTTAACAGATAACCCTTCTTGATTTAAGTTATGTTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATAT
* * * *
17064761 GCCTTGGAGTTGAGCGTAGTCAAACTCGAAGGTCTTTGATGACAAATAACCCTTCTAGCCTTGAG
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
* * * *
17064826 TTATGCTATAAATGATGTGCCCTCGAAGTTGAGCGTAGTCAAACTTGAGGGTCTTTGGCAGATAG
131 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGATAG
* * **
17064891 CCCTTCTCGACTTAAGCTTTGCTGCAAATGATGTTCCTTGGAGCTGAGCGTAG
196 CCCTTCTCGACTTAAGCTATGCTACAAATGATGCACCTTGGAGCTGAGCGTAG
*
17064944 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATAT
* * * *
17065009 GCCTTGGAGCTGAGCGTAGT----CT-GAAGGTC-TTGGTGGCAGATAGCCCTTCTGGCCCTGAG
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
* ** * * *
17065068 CTATGCTACAAATGATGTGCCTTAG-AGCTGAGCGTAGTCGAACTCGAAGGTCTT
131 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTT
17065122 GGCTGACAGA
Statistics
Matches: 833, Mismatches: 86, Indels: 12
0.89 0.09 0.01
Matches are distributed among these distances:
241 25 0.03
242 45 0.05
243 7 0.01
244 2 0.00
247 226 0.27
248 443 0.53
249 85 0.10
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (248 bp):
TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATAT
GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAG
TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGATAG
CCCTTCTCGACTTAAGCTATGCTACAAATGATGCACCTTGGAGCTGAGCGTAG
Found at i:17064987 original size:495 final size:495
Alignment explanation
Indices: 17063952--17065121 Score: 1708
Period size: 495 Copynumber: 2.4 Consensus size: 495
17063942 CCGAGTGTAA
* * * * *
17063952 TCGAACTCGAAGGTCTTCT-GTTGGAAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATG
1 TCGAACTCGAAGGTCTT-TGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTACAAATGATA
*
17064016 TGCTTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTG
65 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG-C-TTTGGTGACAGATAACCCTTCTAGCCTTG
* * *
17064081 AGTTACGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGAT
128 AGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGAT
* * * *
17064146 TGCCCTTCTCGACTTAAACTATGCTGCAAATGATGCGCCTTGGAGCTGAGCGTAGTCGAACTCGA
193 AGCCCTTCTCGACTTAAACTATGCTACAAATGATGCACCTTGGAGCTGAGCGTAATCGAACTCGA
** * *
17064211 AGGTATTTGGTTGGCATATAACCCTTCTCGATTTAAGTTATACTGTAAATAATATGCCTTGGAGC
258 AGGTATTTGGTTAACAGATAACCCTTCTCGATTTAAGTTATACTGCAAATAATATGCCTTGGAGC
* * * *
17064276 TGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTA
323 TGAGCGTAGTCAAACTCGAAGGTCTTTGATGACAAATAACCCTTCTAGCCTTGAGTTATGCTATA
* * ***
17064341 AATGATGTGCCTTTGAAGCTGAGCATAGTTGGACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGA
388 AATGATGTGCCCTCGAAGCTGAGCATAGTCAAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGA
17064406 CTTAAGCTATGCTACAAATGATGCACATTGGAGCTGAGCGTAG
453 CTTAAGCTATGCTACAAATGATGCACATTGGAGCTGAGCGTAG
* * *
17064449 TCAAACTTGAAGGTATTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTACAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTACAAATGATAT
* * *
17064514 GCCTTGGAGCTGAACGTAGTCGAACTCAAAGGCTTTGATGACAGATAACCCTTCTAGCCTTGAGT
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGCTTTGGTGACAGATAACCCTTCTAGCCTTGAGT
17064579 TATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGATAGC
131 TATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGATAGC
* *
17064644 CCTTCTCGACTTAAGCTATGCTACAAATGATGCACCTTGGAGCTGAGCGTAATTGAACTCGAAGG
196 CCTTCTCGACTTAAACTATGCTACAAATGATGCACCTTGGAGCTGAGCGTAATCGAACTCGAAGG
* * ** * *
17064709 TCTTTGGTTAACAGATAACCCTTCTTGATTTAAGTTATGTTGCAAATGATATGCCTTGGAGTTGA
261 TATTTGGTTAACAGATAACCCTTCTCGATTTAAGTTATACTGCAAATAATATGCCTTGGAGCTGA
17064774 GCGTAGTCAAACTCGAAGGTCTTTGATGACAAATAACCCTTCTAGCCTTGAGTTATGCTATAAAT
326 GCGTAGTCAAACTCGAAGGTCTTTGATGACAAATAACCCTTCTAGCCTTGAGTTATGCTATAAAT
* * *
17064839 GATGTGCCCTCGAAGTTGAGCGTAGTCAAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTT
391 GATGTGCCCTCGAAGCTGAGCATAGTCAAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTT
* * ** *
17064904 AAGCTTTGCTGCAAATGATGTTCCTTGGAGCTGAGCGTAG
456 AAGCTATGCTACAAATGATGCACATTGGAGCTGAGCGTAG
**
17064944 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTACAAATGATAT
* * * *
17065009 GCCTTGGAGCTGAGCGTAGT----CT-GAAGG-TCTTGGTGGCAGATAGCCCTTCTGGCCCTGAG
66 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGCT-TTGGTGACAGATAACCCTTCTAGCCTTGAG
* ** * * *
17065068 CTATGCTACAAATGATGTGCCTTAG-AGCTGAGCGTAGTCGAACTCGAAGGTCTT
130 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTT
17065122 GGCTGACAGA
Statistics
Matches: 605, Mismatches: 66, Indels: 12
0.89 0.10 0.02
Matches are distributed among these distances:
489 29 0.05
490 49 0.08
491 2 0.00
495 439 0.73
496 2 0.00
497 84 0.14
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (495 bp):
TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTACAAATGATAT
GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGCTTTGGTGACAGATAACCCTTCTAGCCTTGAGT
TATGCTGTAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAGGGTCTTTGGCAGATAGC
CCTTCTCGACTTAAACTATGCTACAAATGATGCACCTTGGAGCTGAGCGTAATCGAACTCGAAGG
TATTTGGTTAACAGATAACCCTTCTCGATTTAAGTTATACTGCAAATAATATGCCTTGGAGCTGA
GCGTAGTCAAACTCGAAGGTCTTTGATGACAAATAACCCTTCTAGCCTTGAGTTATGCTATAAAT
GATGTGCCCTCGAAGCTGAGCATAGTCAAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTT
AAGCTATGCTACAAATGATGCACATTGGAGCTGAGCGTAG
Found at i:17066330 original size:83 final size:87
Alignment explanation
Indices: 17066199--17066425 Score: 266
Period size: 95 Copynumber: 2.6 Consensus size: 87
17066189 GGCTAGCTGA
* *
17066199 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAA-TAT-GTA-AAT-ACC
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATAGTATAATCACC
*
17066260 TTTATCAGGTTAGCTGAATCTT
66 TTTATCAGGTTAGCTGAATATT
* *
17066282 ATCCACAAAGCCTGGGCGTTTAACCAATTGC-CTTAGAGGGACAACTCAAGCTTTATTGTATAGT
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTC-TAGAGGGACAACTC-A-----A-T-TATAGT
17066346 ATAATCACCTTTATCAGGTTAGCTGAATATT
57 ATAATCACCTTTATCAGGTTAGCTGAATATT
* * *
17066377 ATCCATAAAGCCAGAGCTTTTAACCAATTGCTCTAGAGGGATAACTCAA
1 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA
17066426 GCTTTATTAT
Statistics
Matches: 121, Mismatches: 9, Indels: 22
0.80 0.06 0.14
Matches are distributed among these distances:
82 1 0.01
83 42 0.35
84 1 0.01
89 2 0.02
92 3 0.02
93 3 0.02
94 4 0.03
95 64 0.53
96 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (87 bp):
ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATAGTATAATCACC
TTTATCAGGTTAGCTGAATATT
Found at i:17066423 original size:95 final size:94
Alignment explanation
Indices: 17066257--17066444 Score: 288
Period size: 95 Copynumber: 2.0 Consensus size: 94
17066247 ATATGTAAAT
* * *
17066257 ACCTTTATCAGGTTAGCTGAATCTTATCCACAAAGCCTGGGCGTTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGTTAGCTGAATATTATCCACAAAGCCAGAGCGTTTAACCAATTGCCTTAGAGGG
*
17066322 ACAACTCAAGCTTTATTGTATAGTATAATC
66 ACAACTCAAGCTTTATTATATA-TATAATC
* *
17066352 ACCTTTATCAGGTTAGCTGAATATTATCCATAAAGCCAGAGCTTTTAACCAATTG-CTCTAGAGG
1 ACCTTTATCAGGTTAGCTGAATATTATCCACAAAGCCAGAGCGTTTAACCAATTGCCT-TAGAGG
*
17066416 GATAACTCAAGCTTTATTATATATATAAT
65 GACAACTCAAGCTTTATTATATATATAAT
17066445 ATTATAATGT
Statistics
Matches: 85, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
94 8 0.09
95 77 0.91
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (94 bp):
ACCTTTATCAGGTTAGCTGAATATTATCCACAAAGCCAGAGCGTTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTATATATATAATC
Found at i:17070167 original size:2 final size:2
Alignment explanation
Indices: 17070160--17070231 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
17070150 AGTAGTAATA
17070160 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17070202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17070232 GAAAAAACAC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17070390 original size:26 final size:26
Alignment explanation
Indices: 17070356--17070424 Score: 86
Period size: 26 Copynumber: 2.7 Consensus size: 26
17070346 ATATAAATGT
17070356 AAATAAAGAAAATAATAATAACAAAA
1 AAATAAAGAAAATAATAATAACAAAA
* * *
17070382 TAATAAAGAAAATAAAAATAAGAAAA
1 AAATAAAGAAAATAATAATAACAAAA
* *
17070408 AAACAAA-ATAATAATAA
1 AAATAAAGAAAATAATAA
17070425 AATGTGCATG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
25 8 0.22
26 28 0.78
ACGTcount: A:0.77, C:0.03, G:0.04, T:0.16
Consensus pattern (26 bp):
AAATAAAGAAAATAATAATAACAAAA
Found at i:17070401 original size:18 final size:16
Alignment explanation
Indices: 17070378--17070426 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 16
17070368 TAATAATAAC
17070378 AAAATAATAAAGAAAATA
1 AAAATAATAAA-AAAA-A
* *
17070396 AAAATAAGAAAAAAAC
1 AAAATAATAAAAAAAA
17070412 AAAATAATAATAAAA
1 AAAATAATAA-AAAA
17070427 TGTGCATGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 9 0.33
17 8 0.30
18 10 0.37
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (16 bp):
AAAATAATAAAAAAAA
Found at i:17070404 original size:14 final size:14
Alignment explanation
Indices: 17070356--17070407 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
17070346 ATATAAATGT
17070356 AAATAAAGAAAATAA
1 AAAT-AAGAAAATAA
* *
17070371 TAATAACAAAAT-A
1 AAATAAGAAAATAA
*
17070384 ATA-AAGAAAATAA
1 AAATAAGAAAATAA
17070397 AAATAAGAAAA
1 AAATAAGAAAA
17070408 AAACAAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
12 7 0.24
13 5 0.17
14 14 0.48
15 3 0.10
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (14 bp):
AAATAAGAAAATAA
Found at i:17070697 original size:26 final size:26
Alignment explanation
Indices: 17070658--17070709 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
17070648 TGGAGGGGAA
* * **
17070658 CAAAACTACGCCGTTTTGATTGACGC
1 CAAAACGACACCGTTTCAATTGACGC
17070684 CAAAACGACACCGTTTCAATTGACGC
1 CAAAACGACACCGTTTCAATTGACGC
17070710 ATAAAAGCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (26 bp):
CAAAACGACACCGTTTCAATTGACGC
Found at i:17071643 original size:42 final size:44
Alignment explanation
Indices: 17071596--17071682 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
17071586 ATAAATAAAT
17071596 AAATAA-CTTTTT-AAAAAACTATATAATATA-TAGTTTCAAAAA
1 AAATAATCTTTTTAAAAAAACTATATAATATACTA-TTTCAAAAA
* *
17071638 AAATAATTTTTTTAAAAAAACTATATATTATACGTATTTCAAAAA
1 AAATAATCTTTTTAAAAAAACTATATAATATAC-TATTTCAAAAA
17071683 CGGTTTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
42 6 0.15
43 5 0.13
44 17 0.44
45 9 0.23
46 2 0.05
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (44 bp):
AAATAATCTTTTTAAAAAAACTATATAATATACTATTTCAAAAA
Found at i:17071785 original size:69 final size:69
Alignment explanation
Indices: 17071653--17071812 Score: 173
Period size: 69 Copynumber: 2.3 Consensus size: 69
17071643 ATTTTTTTAA
17071653 AAAAACTATATATTATACGTATTTCAAAAACGGTTTAAAAATATATAATATATAATATATTCAAA
1 AAAAACTATATA--ATA--TATTTCAAAAACGGTTTAAAAATATATAATATATAATATATTCAAA
17071718 AATATTTT
62 AATATTTT
** * * * *
17071726 TTAAACTATATATTATATTT-AAAAATGTTTTAAAAAACTATATACTATATAAGT-T-TTCAAAA
1 AAAAACTATATAATATATTTCAAAAACGGTTT-AAAAA-TATATAATATATAA-TATATTCAAAA
*
17071788 ATGTTTT
63 ATATTTT
17071795 AAAAACTATATAATATAT
1 AAAAACTATATAATATAT
17071813 AAATGTTTTC
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
68 9 0.12
69 38 0.51
70 14 0.19
71 3 0.04
73 10 0.14
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (69 bp):
AAAAACTATATAATATATTTCAAAAACGGTTTAAAAATATATAATATATAATATATTCAAAAATA
TTTT
Found at i:17071812 original size:37 final size:37
Alignment explanation
Indices: 17071653--17071825 Score: 159
Period size: 37 Copynumber: 4.8 Consensus size: 37
17071643 ATTTTTTTAA
* * *
17071653 AAAAACTATAT-AT-TATACGTATTTCAAAAACGGTTT
1 AAAAACTATATAATATATAAGT-TTTCAAAAATGTTTT
*
17071689 AAAAA-TATATAATATATAA-TATATTCAAAAATATTTT
1 AAAAACTATATAATATATAAGT-T-TTCAAAAATGTTTT
**
17071726 TTAAACTATAT-AT-TAT-A--TTT-AAAAATGTTTT
1 AAAAACTATATAATATATAAGTTTTCAAAAATGTTTT
*
17071757 AAAAAACTATATACTATATAAGTTTTCAAAAATGTTTT
1 -AAAAACTATATAATATATAAGTTTTCAAAAATGTTTT
17071795 AAAAACTATATAATATATAAATGTTTTCAAA
1 AAAAACTATATAATATAT-AA-GTTTTCAAA
17071826 CTATACATTA
Statistics
Matches: 113, Mismatches: 11, Indels: 23
0.77 0.07 0.16
Matches are distributed among these distances:
31 10 0.09
32 11 0.10
33 2 0.02
34 3 0.03
35 7 0.06
36 13 0.12
37 40 0.35
38 18 0.16
39 9 0.08
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (37 bp):
AAAAACTATATAATATATAAGTTTTCAAAAATGTTTT
Found at i:17071837 original size:26 final size:27
Alignment explanation
Indices: 17071786--17071839 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
17071776 AAGTTTTCAA
*
17071786 AAATGTTTTAAAAACTATATAATATAT
1 AAATGTTTTAAAAACTATACAATATAT
* *
17071813 AAATGTTTT-CAAACTATACATTATAT
1 AAATGTTTTAAAAACTATACAATATAT
17071839 A
1 A
17071840 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (27 bp):
AAATGTTTTAAAAACTATACAATATAT
Found at i:17071855 original size:33 final size:35
Alignment explanation
Indices: 17071813--17071885 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
17071803 TATAATATAT
* * *
17071813 AAATGTTTTC-AAACTATACATTATATATTTT-AA
1 AAATATTTTCAAAACCATACAATATATATTTTCAA
*
17071846 AAATATTTTCAAAAACCATATAATATATATTTTCAA
1 AAATATTTTC-AAAACCATACAATATATATTTTCAA
17071882 AAAT
1 AAAT
17071886 CGTTTTCTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 9 0.27
35 18 0.55
36 6 0.18
ACGTcount: A:0.48, C:0.10, G:0.01, T:0.41
Consensus pattern (35 bp):
AAATATTTTCAAAACCATACAATATATATTTTCAA
Found at i:17071940 original size:36 final size:36
Alignment explanation
Indices: 17071822--17071941 Score: 120
Period size: 38 Copynumber: 3.3 Consensus size: 36
17071812 TAAATGTTTT
* *
17071822 CAAACTATACATTATATATTTT-AAAAATATTTTCA
1 CAAACTATATATTATATATTTTCAAAAACATTTTCA
* * * *
17071857 AAAACCATATAATATATATTTTCAAAAATCGTTTTCTGA
1 CAAACTATATATTATATATTTTCAAAAA-CATTTTC--A
*
17071896 -AAATTATATATTATAT-TTTGTCAAAAACATTTTCA
1 CAAACTATATATTATATATTT-TCAAAAACATTTTCA
17071931 CAAACTATATA
1 CAAACTATATA
17071942 AAAGCAAAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
35 19 0.28
36 14 0.21
37 14 0.21
38 20 0.29
39 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.41
Consensus pattern (36 bp):
CAAACTATATATTATATATTTTCAAAAACATTTTCA
Found at i:17073432 original size:103 final size:102
Alignment explanation
Indices: 17073251--17073443 Score: 298
Period size: 103 Copynumber: 1.9 Consensus size: 102
17073241 CACAAACAAG
* *
17073251 ATATTTAGTTAAAAATAATATATGTATTTGATACATATAATATTTTACCTAAAATAAATATATTA
1 ATATTTAGTTAAAAATAATATATGTATTTGAAACATATAATATTTTAACTAAAATAAATATATTA
* *
17073316 TAATTATTGTAATTATAAATCATATATATATATATATA
66 TAATCATTATAATTATAAAT-ATATATATATATATATA
* *
17073354 ATATTTAGTTAAAATTAATATATGTATTTGAAACATATAATATTTTAACTAAAATGAAT-TAATT
1 ATATTTAGTTAAAAATAATATATGTATTTGAAACATATAATATTTTAACTAAAATAAATAT-ATT
*
17073418 ATAATCATTATAATTATATATATATA
65 ATAATCATTATAATTATAAATATATA
17073444 GGAGATAATT
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
102 6 0.07
103 76 0.93
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (102 bp):
ATATTTAGTTAAAAATAATATATGTATTTGAAACATATAATATTTTAACTAAAATAAATATATTA
TAATCATTATAATTATAAATATATATATATATATATA
Found at i:17079411 original size:13 final size:14
Alignment explanation
Indices: 17079378--17079408 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
17079368 GCAAGCACTC
17079378 AAAAGAAGAAAACA
1 AAAAGAAGAAAACA
*
17079392 AAAAGAAGAAAAGA
1 AAAAGAAGAAAACA
17079406 AAA
1 AAA
17079409 GAAAATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAAACA
Found at i:17081665 original size:20 final size:21
Alignment explanation
Indices: 17081624--17081685 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
17081614 ATTAAACTTC
* * *
17081624 CAAAAGTGATGGATCCTATTT
1 CAAAAGGGATTGATCCTTTTT
* *
17081645 C-TAAGGGATTTATCCTTTTT
1 CAAAAGGGATTGATCCTTTTT
*
17081665 CAAAAGGGATTGATCTTTTTT
1 CAAAAGGGATTGATCCTTTTT
17081686 GTGGAAAATA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (21 bp):
CAAAAGGGATTGATCCTTTTT
Found at i:17083719 original size:41 final size:41
Alignment explanation
Indices: 17083674--17083755 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
17083664 CAAAACTAAA
17083674 GTAAGTATATCTTTTAGGTTTCTATAAGCAGGATATTTATT
1 GTAAGTATATCTTTTAGGTTTCTATAAGCAGGATATTTATT
17083715 GTAAGTATATCTTTTAGGTTTCTATAAGCAGGATATTTATT
1 GTAAGTATATCTTTTAGGTTTCTATAAGCAGGATATTTATT
17083756 TATTTTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.46
Consensus pattern (41 bp):
GTAAGTATATCTTTTAGGTTTCTATAAGCAGGATATTTATT
Found at i:17083889 original size:2 final size:2
Alignment explanation
Indices: 17083882--17083925 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
17083872 TGAATCTTTC
17083882 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17083924 AT
1 AT
17083926 TCATATGACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17085244 original size:3 final size:3
Alignment explanation
Indices: 17085236--17085301 Score: 73
Period size: 3 Copynumber: 22.0 Consensus size: 3
17085226 ATACTTGTAT
*
17085236 TAA TAA TAA TAA TTAA TAA -ACA TAA TAA TGA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA -TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* *
17085282 TAT TAA TAA TAT TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
17085302 AACGGGACAA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 3 0.06
3 46 0.87
4 4 0.08
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17092412 original size:9 final size:9
Alignment explanation
Indices: 17092398--17092430 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
17092388 TACATATATT
17092398 AACAACAAA
1 AACAACAAA
17092407 AACAACAAA
1 AACAACAAA
*
17092416 AACAACAAC
1 AACAACAAA
17092425 AACAAC
1 AACAAC
17092431 CCTATTCCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.73, C:0.27, G:0.00, T:0.00
Consensus pattern (9 bp):
AACAACAAA
Found at i:17097989 original size:74 final size:74
Alignment explanation
Indices: 17097868--17098012 Score: 272
Period size: 74 Copynumber: 2.0 Consensus size: 74
17097858 TTTTAGTATA
*
17097868 ATTTGCATTAAATGCATTATGATAACGAGTTGGTGAATTTTGGGACTAATGTGACTACTTTTTTT
1 ATTTGCATTAAATGCATTATGATAACGAGTTGATGAATTTTGGGACTAATGTGACTACTTTTTTT
17097933 GTGATAGTG
66 GTGATAGTG
*
17097942 ATTTGCATTAAATGCATTATGATAACGAGTTGATGAATTTTGGGACTAATGTGACTCCTTTTTTT
1 ATTTGCATTAAATGCATTATGATAACGAGTTGATGAATTTTGGGACTAATGTGACTACTTTTTTT
17098007 GTGATA
66 GTGATA
17098013 ATGCTTATAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (74 bp):
ATTTGCATTAAATGCATTATGATAACGAGTTGATGAATTTTGGGACTAATGTGACTACTTTTTTT
GTGATAGTG
Found at i:17101625 original size:139 final size:137
Alignment explanation
Indices: 17101470--17101763 Score: 319
Period size: 139 Copynumber: 2.1 Consensus size: 137
17101460 ATTAGTCTTT
* * ** *
17101470 ATTTTA-GGGAAATTTTAACTTGGTTATCGCTTTTGTTTGAGGTTTCATTT-TAATTATTCA-A-
1 ATTTTAGGGGAATTTTTAACTTGGTCATCGCTTTTACTCGAGG-TTCATTTCTAATTATT-AGAT
* * *
17101531 TCAAAAAATTGGTTAAAATTAACTAGATTAATAATTAGAGTC-TTCATTTTAAGCTTAATTTCAA
64 TC-AAAAATTGATTAAAATTAACTAGATTAATAA-TAGAG-CATCCATTTTAAGATTAATTTCAA
* *
17101595 ACTTATTCTTTTA
126 ACTTAATC-CTTA
* * * *
17101608 ATTTTAGGGGAATTTTTAATTTGGTCATCGTTTTTACTCGTGGTTCTTTTCTAATTATTAGATTC
1 ATTTTAGGGGAATTTTTAACTTGGTCATCGCTTTTACTCGAGGTTCATTTCTAATTATTAGATTC
* * * * *
17101673 AATAATTGATTAAAATTGACTAGGTTAATAATAGAGCATCCATTTTAGGATTAATTTCATACTTA
66 AAAAATTGATTAAAATTAACTAGATTAATAATAGAGCATCCATTTTAAGATTAATTTCAAACTTA
17101738 ATCCTTA
131 ATCCTTA
*
17101745 AATTTAGGGGAATTTTTAA
1 ATTTTAGGGGAATTTTTAA
17101764 TACATGCTAG
Statistics
Matches: 131, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
137 22 0.17
138 43 0.33
139 64 0.49
140 2 0.02
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.46
Consensus pattern (137 bp):
ATTTTAGGGGAATTTTTAACTTGGTCATCGCTTTTACTCGAGGTTCATTTCTAATTATTAGATTC
AAAAATTGATTAAAATTAACTAGATTAATAATAGAGCATCCATTTTAAGATTAATTTCAAACTTA
ATCCTTA
Found at i:17102252 original size:49 final size:49
Alignment explanation
Indices: 17102183--17102463 Score: 357
Period size: 49 Copynumber: 5.7 Consensus size: 49
17102173 AATGGTCATT
* * *
17102183 CACCTTTTATACCGATAATGCACCGTTATGCATTTAACTATCATTAATGG
1 CACCTTTTATGCCGA-AATGCACCGTTATGCATTTAACTTTCATTAGTGG
* * * *
17102233 AACCTTTTATGTCGAAATGCACCGTTATGCATGTAACTTTCATTAGTGA
1 CACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGG
* *
17102282 CACCTTTTATGCCGAAATGCACCGGTATGCATTTAATTTTCATTAGTGG
1 CACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGG
* * * *
17102331 CACATTTTATGCCAAAATGTACCGTTATG-ATTTTAATTTTCATTAGTGG
1 CACCTTTTATGCCGAAATGCACCGTTATGCA-TTTAACTTTCATTAGTGG
* * * * * *
17102380 CACCTTGTATACCGAAATACACTGTTATGCATTTAACTGTCATTAATGG
1 CACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGG
*
17102429 CATCTTTTATGCCGAAATGCACCGTTATGCATTTA
1 CACCTTTTATGCCGAAATGCACCGTTATGCATTTA
17102464 TTTTGGCAAC
Statistics
Matches: 197, Mismatches: 32, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
48 1 0.01
49 183 0.93
50 13 0.07
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (49 bp):
CACCTTTTATGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGG
Found at i:17102726 original size:49 final size:49
Alignment explanation
Indices: 17102666--17102759 Score: 125
Period size: 49 Copynumber: 1.9 Consensus size: 49
17102656 GCAATAATTT
* * *
17102666 TCATTAGTGGCACCTTTTATACCTAAATACACTGTTATGCATTTAACTG
1 TCATTAATGGCACCTTTTATACCGAAATACACCGTTATGCATTTAACTG
* * * *
17102715 TCATTAATGGCATCTTTTATGCCGAAATGCCCCGTTATGCATTTA
1 TCATTAATGGCACCTTTTATACCGAAATACACCGTTATGCATTTA
17102760 TTTTTGCAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 38 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (49 bp):
TCATTAATGGCACCTTTTATACCGAAATACACCGTTATGCATTTAACTG
Found at i:17102898 original size:296 final size:296
Alignment explanation
Indices: 17102364--17102958 Score: 1109
Period size: 296 Copynumber: 2.0 Consensus size: 296
17102354 GTTATGATTT
17102364 TAATTTTCATTAGTGGCACCTTGTATACCGAAATACACTGTTATGCATTTAACTGTCATTAATGG
1 TAATTTTCATTAGTGGCACCTTGTATACCGAAATACACTGTTATGCATTTAACTGTCATTAATGG
17102429 CATCTTTTATGCCGAAATGCACCGTTATGCATTTATTTTGGCAACATCGATAACCATTGTACAAC
66 CATCTTTTATGCCGAAATGCACCGTTATGCATTTATTTTGGCAACATCGATAACCATTGTACAAC
*
17102494 ATTAACATTCATCCATTCATTTTAGAGCAGTTCATACTCTAAAACTTATTCATAATATCATTTAT
131 ATTAACATTCATCCATTCATATTAGAGCAGTTCATACTCTAAAACTTATTCATAATATCATTTAT
*
17102559 ATATACGTTACGAAATTATACCAAAATGTTGTAAAACATACATTTAACAAAACATTCGAGGTTGA
196 ATATACGTTACAAAATTATACCAAAATGTTGTAAAACATACATTTAACAAAACATTCGAGGTTGA
*
17102624 CTCATCGTGAGTCTTCCTCTTTTTATACAAGTGCAA
261 CTCATCGTGAGTCCTCCTCTTTTTATACAAGTGCAA
* *
17102660 TAATTTTCATTAGTGGCACCTTTTATACCTAAATACACTGTTATGCATTTAACTGTCATTAATGG
1 TAATTTTCATTAGTGGCACCTTGTATACCGAAATACACTGTTATGCATTTAACTGTCATTAATGG
* * *
17102725 CATCTTTTATGCCGAAATGCCCCGTTATGCATTTATTTTTGCAATATCGATAACCATTGTACAAC
66 CATCTTTTATGCCGAAATGCACCGTTATGCATTTATTTTGGCAACATCGATAACCATTGTACAAC
17102790 ATTAACATTCATCCATTCATATTAGAGCAGTTCATACTCTAAAACTTATTCATAATATCATTTAT
131 ATTAACATTCATCCATTCATATTAGAGCAGTTCATACTCTAAAACTTATTCATAATATCATTTAT
*
17102855 ATATACGTTACAAAATTATACCAAAATGTTGTAAAATATACATTTAACAAAACATTCGAGGTTGA
196 ATATACGTTACAAAATTATACCAAAATGTTGTAAAACATACATTTAACAAAACATTCGAGGTTGA
17102920 CTCATCGTGAGTCCTCCTCTTTTTATACAAGTGCAA
261 CTCATCGTGAGTCCTCCTCTTTTTATACAAGTGCAA
17102956 TAA
1 TAA
17102959 ATGCACTCAC
Statistics
Matches: 290, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
296 290 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (296 bp):
TAATTTTCATTAGTGGCACCTTGTATACCGAAATACACTGTTATGCATTTAACTGTCATTAATGG
CATCTTTTATGCCGAAATGCACCGTTATGCATTTATTTTGGCAACATCGATAACCATTGTACAAC
ATTAACATTCATCCATTCATATTAGAGCAGTTCATACTCTAAAACTTATTCATAATATCATTTAT
ATATACGTTACAAAATTATACCAAAATGTTGTAAAACATACATTTAACAAAACATTCGAGGTTGA
CTCATCGTGAGTCCTCCTCTTTTTATACAAGTGCAA
Found at i:17105377 original size:21 final size:21
Alignment explanation
Indices: 17105353--17105400 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
17105343 AGAGTTTTAA
*
17105353 TGCATAGTCAAGGCACCTTAT
1 TGCATAGTCAAGGCACCTTAC
* *
17105374 TGCATAGTTAAGGTACCTTAC
1 TGCATAGTCAAGGCACCTTAC
17105395 TGCATA
1 TGCATA
17105401 ACCATAGCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (21 bp):
TGCATAGTCAAGGCACCTTAC
Found at i:17112966 original size:20 final size:20
Alignment explanation
Indices: 17112937--17112989 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
17112927 TAGTAAGGAG
*
17112937 TGACATCAATCACACTCTAA
1 TGACACCAATCACACTCTAA
17112957 TGACACCAATCACACTCTAA
1 TGACACCAATCACACTCTAA
*
17112977 TAACACCATATCA
1 TGACACCA-ATCA
17112990 GTAACCTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.42, C:0.32, G:0.04, T:0.23
Consensus pattern (20 bp):
TGACACCAATCACACTCTAA
Found at i:17113823 original size:31 final size:31
Alignment explanation
Indices: 17113762--17113823 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
17113752 TGCATTTAAC
17113762 TATCATTAATGGCACCTTTTATGCCGAAATG
1 TATCATTAATGGCACCTTTTATGCCGAAATG
*
17113793 TATCATTAGTGGCACCTTTTATGCCGAAATG
1 TATCATTAATGGCACCTTTTATGCCGAAATG
17113824 CACCGTTATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.35
Consensus pattern (31 bp):
TATCATTAATGGCACCTTTTATGCCGAAATG
Found at i:17113848 original size:49 final size:49
Alignment explanation
Indices: 17113795--17113981 Score: 248
Period size: 49 Copynumber: 3.8 Consensus size: 49
17113785 CCGAAATGTA
17113795 TCATTAGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAAATT
1 TCATTAGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAAATT
* *
17113844 TCATTAGTGGCACCTTTTATTCCGAAATGCACCGTTATGCATTTAATTT
1 TCATTAGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAAATT
* ** * * * *
17113893 TCATTACTATCACCTTTTATGCCTAAATGCACAGTTATGCATTTAACTG
1 TCATTAGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAAATT
* * * * *
17113942 TCATTAATGGCACTTTTTATGCCAAAATACATCGTTATGC
1 TCATTAGTGGCACCTTTTATGCCGAAATGCACCGTTATGC
17113982 CAAAATACAC
Statistics
Matches: 120, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 120 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (49 bp):
TCATTAGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAAATT
Found at i:17113883 original size:98 final size:97
Alignment explanation
Indices: 17113780--17113987 Score: 238
Period size: 98 Copynumber: 2.1 Consensus size: 97
17113770 ATGGCACCTT
* * * * *
17113780 TTATGCCGAAATGTATCATTAGTGGCACCTTTTATGCCGAAATGCACCGTTATGCATTTAAATTT
1 TTATGCCAAAAT-TATCATTACTAGCACCTTTTATGCCGAAATGCACAGTTATGCATTTAAATGT
* * * *
17113845 CATTAGTGGCACCTTTTATTCCGAAATGCACCG
65 CATTAATGGCACCTTTTATGCCAAAATACACCG
* * * * *
17113878 TTATG-CATTTAATTTTCATTACTATCACCTTTTATGCCTAAATGCACAGTTATGCATTTAACTG
1 TTATGCCA--AAATTATCATTACTAGCACCTTTTATGCCGAAATGCACAGTTATGCATTTAAATG
* *
17113942 TCATTAATGGCACTTTTTATGCCAAAATACATCG
64 TCATTAATGGCACCTTTTATGCCAAAATACACCG
17113976 TTATGCCAAAAT
1 TTATGCCAAAAT
17113988 ACACCGTTAT
Statistics
Matches: 90, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
97 4 0.04
98 81 0.90
99 5 0.06
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (97 bp):
TTATGCCAAAATTATCATTACTAGCACCTTTTATGCCGAAATGCACAGTTATGCATTTAAATGTC
ATTAATGGCACCTTTTATGCCAAAATACACCG
Found at i:17113981 original size:18 final size:18
Alignment explanation
Indices: 17113958--17113997 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
17113948 ATGGCACTTT
*
17113958 TTATGCCAAAATACATCG
1 TTATGCCAAAATACACCG
17113976 TTATGCCAAAATACACCG
1 TTATGCCAAAATACACCG
17113994 TTAT
1 TTAT
17113998 ACATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.30
Consensus pattern (18 bp):
TTATGCCAAAATACACCG
Found at i:17119753 original size:6 final size:6
Alignment explanation
Indices: 17119744--17119786 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
17119734 TAGGAAAAAG
* * *
17119744 AAATAA AAATAA AAATAA AAATAA AGATGA CAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A
17119787 TTCATTATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:17122015 original size:59 final size:59
Alignment explanation
Indices: 17121916--17122040 Score: 169
Period size: 59 Copynumber: 2.1 Consensus size: 59
17121906 TAGCAGGCTG
** * * *
17121916 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACTACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
* ** *
17121975 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
17122034 CATATTC
1 CATATTC
17122041 AGGATAGCAC
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
Found at i:17129164 original size:59 final size:59
Alignment explanation
Indices: 17129067--17129196 Score: 197
Period size: 59 Copynumber: 2.2 Consensus size: 59
17129057 CAGCAGGCTG
* ** *
17129067 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGATTACACTAAAGGATACCTAGTACATATGGTGGACACGACCTTATGTGT
** *
17129126 CATATTCGGGATTGTACTTAAGGATACCTAGTACATATGGTGGACACGACCTTATGTGT
1 CATATTCGGGATTACACTAAAGGATACCTAGTACATATGGTGGACACGACCTTATGTGT
17129185 CATATTCGGGAT
1 CATATTCGGGAT
17129197 AGCACTACGG
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 64 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (59 bp):
CATATTCGGGATTACACTAAAGGATACCTAGTACATATGGTGGACACGACCTTATGTGT
Found at i:17129397 original size:47 final size:46
Alignment explanation
Indices: 17129304--17129429 Score: 161
Period size: 47 Copynumber: 2.8 Consensus size: 46
17129294 GTAAGTATAC
*
17129304 AAATAAGCTTACGAGCTTTAT--AATT-AATGGCAAGTATATGGGTA
1 AAATAAGCTTACGAGC-TTATGGAATTAAATGGTAAGTATATGGGTA
* *
17129348 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA-TTAAATGGTAAGTATATGGGTA
* *
17129395 AAATAAGCTTATGAGCTTATGGGA-TAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAG
17129430 GGATTTTATA
Statistics
Matches: 73, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
43 4 0.05
44 16 0.22
45 13 0.18
46 2 0.03
47 38 0.52
ACGTcount: A:0.38, C:0.07, G:0.22, T:0.33
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGAATTAAATGGTAAGTATATGGGTA
Found at i:17139768 original size:8 final size:8
Alignment explanation
Indices: 17139755--17139784 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
17139745 CTACTTTTTA
17139755 AAAAAAAC
1 AAAAAAAC
17139763 AAAAAAA-
1 AAAAAAAC
17139770 AAAAAAAC
1 AAAAAAAC
17139778 AAAAAAA
1 AAAAAAA
17139785 GCCAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:17139791 original size:15 final size:15
Alignment explanation
Indices: 17139754--17139784 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
17139744 GCTACTTTTT
17139754 AAAAAAAACAAAAAA
1 AAAAAAAACAAAAAA
17139769 AAAAAAAACAAAAAA
1 AAAAAAAACAAAAAA
17139784 A
1 A
17139785 GCCAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAACAAAAAA
Found at i:17144049 original size:11 final size:11
Alignment explanation
Indices: 17144035--17144079 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
17144025 TTGCAATTCA
17144035 TTTATCTT-TT
1 TTTATCTTATT
*
17144045 CTTTATCTTGTT
1 -TTTATCTTATT
*
17144057 TTAATCTTATT
1 TTTATCTTATT
17144068 TTTATCTTATT
1 TTTATCTTATT
17144079 T
1 T
17144080 CCAGCACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 28 0.93
12 2 0.07
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (11 bp):
TTTATCTTATT
Found at i:17148152 original size:14 final size:15
Alignment explanation
Indices: 17148128--17148177 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 15
17148118 CTAAAAAAAG
17148128 AATAAAAAATA-AAA
1 AATAAAAAATACAAA
* *
17148142 AGTAAACAATACAAA
1 AATAAAAAATACAAA
* *
17148157 AATAAAGAA-CCAAA
1 AATAAAAAATACAAA
17148171 AATAAAA
1 AATAAAA
17148178 TGCTTTGGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.76, C:0.08, G:0.04, T:0.12
Consensus pattern (15 bp):
AATAAAAAATACAAA
Found at i:17148174 original size:22 final size:21
Alignment explanation
Indices: 17148128--17148177 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
17148118 CTAAAAAAAG
**
17148128 AATAAAAAATAAAAAGTAAAC
1 AATAAAAAATAAAAACCAAAC
17148149 AATACAAAAATAAAGAACCAAA-
1 AATA-AAAAATAAA-AACCAAAC
17148171 AATAAAA
1 AATAAAA
17148178 TGCTTTGGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 7 0.28
22 13 0.52
23 5 0.20
ACGTcount: A:0.76, C:0.08, G:0.04, T:0.12
Consensus pattern (21 bp):
AATAAAAAATAAAAACCAAAC
Found at i:17151589 original size:15 final size:14
Alignment explanation
Indices: 17151568--17151623 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
17151558 ATTGGTTTTA
*
17151568 TGGAAATTGAATTC
1 TGGAAAATGAATTC
17151582 TGGAAAATGAATTAC
1 TGGAAAATGAATT-C
**
17151597 TGGAATTTGAATTC
1 TGGAAAATGAATTC
*
17151611 TAGAAAATGAATT
1 TGGAAAATGAATT
17151624 ACATTTCTGG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 23 0.66
15 12 0.34
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (14 bp):
TGGAAAATGAATTC
Found at i:17151610 original size:29 final size:29
Alignment explanation
Indices: 17151568--17151625 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
17151558 ATTGGTTTTA
*
17151568 TGGAAATTGAATTCTGGAAAATGAATTAC
1 TGGAAATTGAATTCTAGAAAATGAATTAC
*
17151597 TGGAATTTGAATTCTAGAAAATGAATTAC
1 TGGAAATTGAATTCTAGAAAATGAATTAC
17151626 ATTTCTGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (29 bp):
TGGAAATTGAATTCTAGAAAATGAATTAC
Found at i:17151919 original size:30 final size:29
Alignment explanation
Indices: 17151846--17151919 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 29
17151836 TATCATAAAA
17151846 TTTAAT-ATTAA-AAATATAATTTTATAT
1 TTTAATAATTAATAAATATAATTTTATAT
*
17151873 TATTAGAAATATTAATAAATAT-ATTTTAAATAT
1 T-TTA-ATA-ATTAATAAATATAATTTT--ATAT
17151906 TTTAATAATTAATA
1 TTTAATAATTAATA
17151920 TTTTGATTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
27 1 0.03
28 3 0.08
29 1 0.03
30 7 0.18
31 12 0.32
32 9 0.24
33 5 0.13
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
TTTAATAATTAATAAATATAATTTTATAT
Found at i:17151963 original size:24 final size:25
Alignment explanation
Indices: 17151916--17151964 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
17151906 TTTAATAATT
*
17151916 AATATTTTGATTAAAATGATATTAA
1 AATATTTTGATTAAAATGAAATTAA
* *
17151941 AATATTTT-ATTAATATTAAATTAA
1 AATATTTTGATTAAAATGAAATTAA
17151965 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (25 bp):
AATATTTTGATTAAAATGAAATTAA
Found at i:17152167 original size:43 final size:43
Alignment explanation
Indices: 17152119--17152210 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 43
17152109 TTCTCCAACC
*
17152119 AAACACTGGAAAACATTTTCCGTA-AAAA-AAATTACGTGAAAAA
1 AAACACGGGAAAACATTTT-C-TAGAAAATAAATTACGTGAAAAA
* * *
17152162 AAACACGGGAAAATATTTTCTAGAAAATGAATTACGTG-AAAT
1 AAACACGGGAAAACATTTTCTAGAAAATAAATTACGTGAAAAA
17152204 AAACACG
1 AAACACG
17152211 ATATTTCGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
41 2 0.05
42 15 0.35
43 26 0.60
ACGTcount: A:0.51, C:0.13, G:0.14, T:0.22
Consensus pattern (43 bp):
AAACACGGGAAAACATTTTCTAGAAAATAAATTACGTGAAAAA
Found at i:17153574 original size:36 final size:34
Alignment explanation
Indices: 17153515--17153593 Score: 95
Period size: 36 Copynumber: 2.3 Consensus size: 34
17153505 AGCTCGTCCT
* * *
17153515 CATCCCCGTCCCTATTTAGCATAAACGGTTTTTTCC
1 CATCCCCGTCCCCATTTAACATAAAC--ATTTTTCC
* *
17153551 CGTCCCCGTCCCCGTTTAACATAAACATTTTTCC
1 CATCCCCGTCCCCATTTAACATAAACATTTTTCC
17153585 CATCCCCGT
1 CATCCCCGT
17153594 TTAATTTGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
34 15 0.41
36 22 0.59
ACGTcount: A:0.19, C:0.38, G:0.10, T:0.33
Consensus pattern (34 bp):
CATCCCCGTCCCCATTTAACATAAACATTTTTCC
Found at i:17155305 original size:138 final size:138
Alignment explanation
Indices: 17154804--17155345 Score: 560
Period size: 138 Copynumber: 3.9 Consensus size: 138
17154794 CTATTTATAA
* * * *
17154804 TTAGT-CTTTAATTTA-GGGATTTTTTAACTTGGTTCTCGCTTTTGCTAGAGGTTCCATTTTAAT
1 TTAGTCCTTTAATTTAGGGGAATTTTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAAT
* * * * * * * *
17154867 TA-CTCAATAAAAAAATTGGTTAAAATTAACTAGATTAATAATTAGAGTCTCCATTTTAGGCTTA
66 TATTTGAAT-CAATAATTGATTAAAATTAACTAGGTTAATAATTAGAGCCTCCATTTTAGGTTTA
*
17154931 ATTTCAAAA
130 ATTTCAAAC
* * *
17154940 TTAGTCTTTTAATTTAGGGGAATTTTTAATTTGG-CCATCGCTTCTGCTCGAGGTTCTATTTTTT
1 TTAGTCCTTTAATTTAGGGGAATTTTTAATTTGGTCC-TCGCTTTTGCTCGAGGTTCCA---TTT
* * * * *** *
17155004 TAATTATTAGATTCAATAATAGATTAAAA-TAACTACGTTAATAA-TAGATAATCCATTTTAGGA
62 TAATTATTTGAATCAATAATTGATTAAAATTAACTAGGTTAATAATTAGAGCCTCCATTTTAGGT
*
17155067 TTAATTTCATAC
127 TTAATTTCAAAC
* * * * *
17155079 TTAATCCTTAAATTAAGGGGAATTTTTAATTTGGTCCTCGTTTTTGCTCGAGGTTCTATTTTAAT
1 TTAGTCCTTTAATTTAGGGGAATTTTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAAT
* * *
17155144 TATTCGAATCAATAACT-AGTTAAAATTGACTAGGTTAATAATTAGAGCCTCCATTTTAGGTTTA
66 TATTTGAATCAATAATTGA-TTAAAATTAACTAGGTTAATAATTAGAGCCTCCATTTTAGGTTTA
*
17155208 ATTTTAAAC
130 ATTTCAAAC
* * *
17155217 TTAGTCCTTTAATTTAGGGGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGATCCATTATAAT
1 TTAGTCCTTTAATTTAGGGGAATTTTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAAT
* * * ** * * *
17155282 TATTTGACTCAATAATTTATTAAAAATGGCTTGGATTAAT-ATTAGAGCCTACATTTTAAGTTTA
66 TATTTGAATCAATAATTGATTAAAATTAACTAGG-TTAATAATTAGAGCCTCCATTTTAGGTTTA
17155346 TACCCTGTGT
Statistics
Matches: 336, Mismatches: 57, Indels: 24
0.81 0.14 0.06
Matches are distributed among these distances:
135 1 0.00
136 31 0.09
137 23 0.07
138 163 0.49
139 80 0.24
140 15 0.04
141 21 0.06
142 2 0.01
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (138 bp):
TTAGTCCTTTAATTTAGGGGAATTTTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCATTTTAAT
TATTTGAATCAATAATTGATTAAAATTAACTAGGTTAATAATTAGAGCCTCCATTTTAGGTTTAA
TTTCAAAC
Done.