Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001621.1 Hibiscus syriacus cultivar Beakdansim tig00003222_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: 84792
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:3078 original size:24 final size:25
Alignment explanation
Indices: 3037--3086 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
3027 GATATCATAG
3037 ATACAAACTTTGCTGGGAGTTTGGA
1 ATACAAACTTTGCTGGGAGTTTGGA
3062 ATACAAAC-TTGCTGGGAGTTTGGA
1 ATACAAACTTTGCTGGGAGTTTGGA
3086 A
1 A
3087 CTCTTAGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (25 bp):
ATACAAACTTTGCTGGGAGTTTGGA
Found at i:4306 original size:2 final size:2
Alignment explanation
Indices: 4299--4328 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4289 AATAGAAATA
4299 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
4329 TACGGGTCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5539 original size:32 final size:32
Alignment explanation
Indices: 5503--5569 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
5493 TAAAAGTTAT
*
5503 AAAATAGTCATTAAACTTCATCAAACTATTAC
1 AAAATAATCATTAAACTTCATCAAACTATTAC
* * **
5535 AAAATAATCATTAAATTTTATTTAACTATTAC
1 AAAATAATCATTAAACTTCATCAAACTATTAC
5567 AAA
1 AAA
5570 GTGATCCTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.49, C:0.13, G:0.01, T:0.36
Consensus pattern (32 bp):
AAAATAATCATTAAACTTCATCAAACTATTAC
Found at i:5841 original size:2 final size:2
Alignment explanation
Indices: 5834--5858 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5824 TAAAACTAAT
5834 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5859 GCATTCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6018 original size:13 final size:13
Alignment explanation
Indices: 6000--6024 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5990 CTTATACATA
6000 TTTTAAATATTCG
1 TTTTAAATATTCG
6013 TTTTAAATATTC
1 TTTTAAATATTC
6025 TCAACCATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
TTTTAAATATTCG
Found at i:10009 original size:15 final size:16
Alignment explanation
Indices: 9989--10019 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
9979 GAAATGAGCT
9989 TGTTTTAAAA-AATAA
1 TGTTTTAAAATAATAA
10004 TGTTTTAAAATAATAA
1 TGTTTTAAAATAATAA
10020 CTCTTTACGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
TGTTTTAAAATAATAA
Found at i:19977 original size:25 final size:25
Alignment explanation
Indices: 19946--19996 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
19936 AAATGGGTGG
*
19946 TTGAGAATTATTTTGGGATTTAGGT
1 TTGAGAATTATTTTAGGATTTAGGT
19971 TTGAGAATTATTTTAGGATTTAGGT
1 TTGAGAATTATTTTAGGATTTAGGT
19996 T
1 T
19997 ATTTGTTACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (25 bp):
TTGAGAATTATTTTAGGATTTAGGT
Found at i:21703 original size:13 final size:13
Alignment explanation
Indices: 21685--21709 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21675 AAGTTTTGCA
21685 GGTAGTGACGTTT
1 GGTAGTGACGTTT
21698 GGTAGTGACGTT
1 GGTAGTGACGTT
21710 ATGCAATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.40, T:0.36
Consensus pattern (13 bp):
GGTAGTGACGTTT
Found at i:22272 original size:37 final size:36
Alignment explanation
Indices: 22196--22272 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
22186 CTTTTATATT
*
22196 TTTAATTTTGTAAAAAAATTTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAA-TTATATAAATATTATCAA
* *
22233 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
22270 TTT
1 TTT
22273 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 18 0.51
38 4 0.11
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:22454 original size:20 final size:20
Alignment explanation
Indices: 22418--22455 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
22408 ATCCTATTCC
**
22418 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
22438 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
22456 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:26957 original size:229 final size:226
Alignment explanation
Indices: 26552--26999 Score: 790
Period size: 229 Copynumber: 2.0 Consensus size: 226
26542 GTAAATTATC
* *
26552 TATCATTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGTT
1 TATCATTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGTT
*
26617 AATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTT
66 AATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTTT
26682 GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
131 GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
26747 AACATAAATTACATAACTTTCAAAAAAGTATA
196 AACATAAATTACATAACTTT-AAAAAAGTATA
*
26779 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCA-TTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
26844 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-ATAAT
64 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT-AT
* *
26908 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
128 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
26973 TGAAACATAAATTACATAACTTTAAAA
193 TGAAACATAAATTACATAACTTTAAAA
27000 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 7, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
227 5 0.02
228 37 0.18
229 169 0.80
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (226 bp):
TATCATTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGTT
AATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTTT
GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
AACATAAATTACATAACTTTAAAAAAGTATA
Found at i:27088 original size:20 final size:19
Alignment explanation
Indices: 27065--27110 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
27055 CGATATACCA
27065 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
27085 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
27105 GGTAAA
1 GGTAAA
27111 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:27255 original size:20 final size:20
Alignment explanation
Indices: 27232--27278 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
27222 CGATATAACA
*
27232 GGTAAAAATATGATAAAACC
1 GGTAAAAAAATGATAAAACC
27252 GGTAAAAAAATGATAAAACC
1 GGTAAAAAAATGATAAAACC
27272 GGTAAAA
1 GGTAAAA
27279 TGATACCGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (20 bp):
GGTAAAAAAATGATAAAACC
Found at i:27280 original size:17 final size:18
Alignment explanation
Indices: 27236--27283 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
27226 ATAACAGGTA
27236 AAAATATGATAAAACCGGT
1 AAAA-ATGATAAAACCGGT
27255 AAAAAAATGATAAAACCGGT
1 --AAAAATGATAAAACCGGT
27275 -AAAATGATA
1 AAAAATGATA
27284 CCGGATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.33
20 14 0.52
21 4 0.15
ACGTcount: A:0.58, C:0.08, G:0.15, T:0.19
Consensus pattern (18 bp):
AAAAATGATAAAACCGGT
Found at i:29559 original size:21 final size:21
Alignment explanation
Indices: 29512--29576 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
29502 AAGACAATCA
* *
29512 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
29534 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
29554 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
29575 AG
1 AG
29577 GAATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:29652 original size:33 final size:33
Alignment explanation
Indices: 29610--29675 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
29600 AAATAGATGG
*
29610 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
29643 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
29676 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:31491 original size:19 final size:19
Alignment explanation
Indices: 31467--31515 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
31457 AATGTCGAGT
31467 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
31486 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
31505 TATTTTTGTAT
1 TAATTTTGTAT
31516 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:31932 original size:198 final size:198
Alignment explanation
Indices: 31593--33319 Score: 3233
Period size: 198 Copynumber: 8.8 Consensus size: 198
31583 TTAAGGGTCA
*
31593 TGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAACCCAAAAGTATAATGTAATAT
1 TGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATAT
31658 GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTG
65 GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTG
31723 TCGACACTAATATAGTTTGTGTCGATAC-TTTTTCCCAGAATGAATGGAAAACAAGGTGCACCCA
130 TCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG-AAACAAGGTGCACCCA
31787 TAAAG
194 TAAAG
31792 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
1 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
*
31857 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGGGAGAATATGTCTAAATAATGTGT
66 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
31922 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGGTGCACCCAT
131 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG-AAACAAGGTGCACCCAT
31987 AAAG
195 AAAG
31991 TGTCGATCCATATATAAAAA--GT-G-T--C---A--AT----CCCAAAAGTATAATGTAATATG
1 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
*
32041 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGGGAGAATATGTCTAAATAATGTGT
66 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
32106 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGGTGCACCCAT
131 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG-AAACAAGGTGCACCCAT
32171 AAAG
195 AAAG
32175 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
1 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
32240 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
66 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
32305 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAACAAGGTGCACCCATA
131 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAACAAGGTGCACCCATA
32370 AAG
196 AAG
32373 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
1 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
32438 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
66 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
*
32503 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATAGAAACAAGGTGCACCCATA
131 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAACAAGGTGCACCCATA
32568 AAG
196 AAG
32571 TGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
1 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
32635 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
66 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
32700 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAACAAGGTGCACCCATA
131 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAACAAGGTGCACCCATA
32765 AAG
196 AAG
32768 TGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
1 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
32832 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
66 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
32897 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAACAAGGTGCACCCATA
131 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAACAAGGTGCACCCATA
32962 AAG
196 AAG
32965 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
1 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
33030 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
66 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
33095 CGACACTAATATAGTTTGTGTCGATAC-TTTTTCCCAGAATGAATGGAAAACAAGGTGCACCCAT
131 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG-AAACAAGGTGCACCCAT
33159 AAAG
195 AAAG
33163 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAATGTAATATG
1 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
33227 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
66 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
33292 CGACACTAATATAGTTTGTGTCGATACT
131 CGACACTAATATAGTTTGTGTCGATACT
33320 AATTTAAATA
Statistics
Matches: 1504, Mismatches: 5, Indels: 39
0.97 0.00 0.03
Matches are distributed among these distances:
184 176 0.12
186 2 0.00
187 1 0.00
188 3 0.00
190 2 0.00
193 2 0.00
195 3 0.00
196 1 0.00
197 524 0.35
198 581 0.39
199 209 0.14
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (198 bp):
TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAACAAGGTGCACCCATA
AAG
Found at i:32716 original size:395 final size:398
Alignment explanation
Indices: 31593--33319 Score: 3241
Period size: 395 Copynumber: 4.4 Consensus size: 398
31583 TTAAGGGTCA
*
31593 TGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAACCCAAAAGTATAATGTAATAT
1 TGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATAT
31658 GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTG
65 GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTG
31723 TCGACACTAATATAGTTTGTGTCGATAC-TTTTTCCCAGAATGAATGGAAAACAAGGTGCACCCA
130 TCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGGTGCACCCA
31787 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
195 TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
*
31852 ATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGGGAGAATATGTCTAAATAA
260 ATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAA
31917 TGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGGTGCA
325 TGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGGTGCA
31982 CCCATAAAG
390 CCCATAAAG
31991 TGTCGATCCATATATAAAAA--GT-G-T--C---A--AT----CCCAAAAGTATAATGTAATATG
1 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
*
32041 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGGGAGAATATGTCTAAATAATGTGT
66 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
32106 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGGTGCACCCAT
131 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGGTGCACCCAT
32171 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
196 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
32236 TATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAAT
261 TATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAAT
32301 GTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG-AAACAAGGTGCAC
326 GTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGGTGCAC
32365 CCATAAAG
391 CCATAAAG
32373 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
1 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
32438 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
66 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
*
32503 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATAG-AAACAAGGTGCACCCAT
131 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGGTGCACCCAT
32567 AAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
196 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
32631 TATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAAT
261 TATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAAT
32696 GTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG-AAACAAGGTGCAC
326 GTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGGTGCAC
32760 CCATAAAG
391 CCATAAAG
32768 TGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
1 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
32832 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
66 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
32897 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG-AAACAAGGTGCACCCAT
131 CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGGTGCACCCAT
32961 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
196 AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
33026 TATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAAT
261 TATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAAT
33091 GTGTCGACACTAATATAGTTTGTGTCGATAC-TTTTTCCCAGAATGAATGGAAAACAAGGTGCAC
326 GTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGGTGCAC
33155 CCATAAAG
391 CCATAAAG
33163 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAATGTAATATG
1 TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
33227 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
66 TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
33292 CGACACTAATATAGTTTGTGTCGATACT
131 CGACACTAATATAGTTTGTGTCGATACT
33320 AATTTAAATA
Statistics
Matches: 1304, Mismatches: 6, Indels: 41
0.97 0.00 0.03
Matches are distributed among these distances:
382 154 0.12
383 217 0.17
384 2 0.00
385 1 0.00
386 3 0.00
388 2 0.00
391 2 0.00
393 3 0.00
394 215 0.16
395 487 0.37
396 66 0.05
397 137 0.11
398 15 0.01
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (398 bp):
TGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAATATG
TAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGT
CGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGGTGCACCCAT
AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTAA
TATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAAT
GTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGGTGCAC
CCATAAAG
Found at i:32724 original size:197 final size:198
Alignment explanation
Indices: 32019--33319 Score: 2538
Period size: 197 Copynumber: 6.6 Consensus size: 198
32009 AAGTGTCAAT
*
32019 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGGG
1 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
32084 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGA
66 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGA
32149 ATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
131 ATGG-AAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
32214 CGAA
195 CGAA
32218 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
1 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
32283 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGA
66 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGA
32348 ATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
131 ATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
32413 GAA
196 GAA
32416 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
1 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
32481 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGA
66 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGA
*
32546 ATAGAAACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATC
131 ATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
32610 GAA
196 GAA
32613 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
1 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
32678 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGA
66 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGA
32743 ATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATC
131 ATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
32807 GAA
196 GAA
32810 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
1 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
32875 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGA
66 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGA
32940 ATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
131 ATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
33005 GAA
196 GAA
33008 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
1 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
33073 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATAC-TTTTTCCCAGAATGA
66 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGA
33137 ATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
131 ATGG-AAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
33202 CGAA
195 CGAA
33206 CCC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
1 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
33270 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
66 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
33320 AATTTAAATA
Statistics
Matches: 1096, Mismatches: 3, Indels: 7
0.99 0.00 0.01
Matches are distributed among these distances:
197 522 0.48
198 441 0.40
199 133 0.12
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (198 bp):
CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGA
ATGGAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
GAA
Found at i:34801 original size:3 final size:3
Alignment explanation
Indices: 34793--34867 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
34783 TGAAGCTGAC
* * * ** * *
34793 GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
34841 GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
34868 CCAAACAAGT
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.35, C:0.05, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:36413 original size:183 final size:183
Alignment explanation
Indices: 36065--36576 Score: 884
Period size: 183 Copynumber: 2.8 Consensus size: 183
36055 CAAAGTTTTC
* * * *
36065 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAATGAAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* *
36130 AAAAAAGTGTCG--ATTGAAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
66 AAAAAAGTGTCGACATT---TACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
*
36193 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
128 TATAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
36249 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* *
36314 AAAAAAGTGTCGACATTTACACATTGAAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
*
36379 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
131 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
36432 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
36497 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
36562 AACCGGTATAAAAAT
131 AACCGGTATAAAAAT
36577 GTGTCGATAC
Statistics
Matches: 313, Mismatches: 13, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
183 237 0.76
184 73 0.23
186 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (183 bp):
ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:36608 original size:22 final size:23
Alignment explanation
Indices: 36572--36614 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
36562 AACCGGTATA
36572 AAAATGTGTCGATACCTTTTTAT
1 AAAATGTGTCGATACCTTTTTAT
* *
36595 AAAA-GTGTCTATACTTTTTT
1 AAAATGTGTCGATACCTTTTT
36615 CACTGTGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (23 bp):
AAAATGTGTCGATACCTTTTTAT
Found at i:39765 original size:23 final size:23
Alignment explanation
Indices: 39734--39797 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
39724 ATAGGTAAAC
*
39734 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
39757 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
39780 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
39798 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:39804 original size:23 final size:23
Alignment explanation
Indices: 39734--39806 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
39724 ATAGGTAAAC
* **
39734 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
39757 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
39780 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
39803 ATAT
1 ATAT
39807 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:40147 original size:22 final size:22
Alignment explanation
Indices: 40102--40147 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
40092 ATTACATAAG
*
40102 TTTTAAAAAAAGTATCGATCCT
1 TTTTAAAAAAAGTATCGAACCT
*
40124 TTTTATAAAAAGTAT-GAACACT
1 TTTTAAAAAAAGTATCGAAC-CT
40146 TT
1 TT
40148 CAATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (22 bp):
TTTTAAAAAAAGTATCGAACCT
Found at i:40196 original size:23 final size:23
Alignment explanation
Indices: 40165--40228 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
40155 ATAGGTAAAC
*
40165 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
40188 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
40211 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
40229 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:40235 original size:23 final size:23
Alignment explanation
Indices: 40165--40237 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
40155 ATAGGTAAAC
* **
40165 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
40188 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
40211 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
40234 ATAT
1 ATAT
40238 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:40447 original size:431 final size:431
Alignment explanation
Indices: 39637--42457 Score: 2531
Period size: 431 Copynumber: 6.4 Consensus size: 431
39627 AATTCGCAGT
39637 ACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTAT-
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
39700 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
39765 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
39830 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
39895 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
*
39960 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCA
40025 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
40066 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
*
40131 AAAAGTATGAACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
40196 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
40261 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
*
40326 AAGATATTAATTTAGTAATTATAGGCGTAC-AATGATTTATTTTTTACGTTACGATATATATTAT
261 AAGATATTAATTTAGTAATTATAGGCGT-CTAATGATTTATTTTTTACGTTACGGTATATATTAT
*
40390 TATTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGC
325 TATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGC
* ** *
40455 AAATGAAATTATTAAATCAAATAATT-CAAATTGAAAA-AT-AA
390 AAATGAAATTATTAAATC-AAT-ATTGTAGGTGGAAAACATGAA
** *** *** * * ** * * *
40496 ACAAC----AAATCAATT-AAACATTGTTGTGGGTACA-TTAATTGAACATTGTTATGGGTACAT
1 AC-ACTGTTAAAAAAATTGAAACATAAAT-TACATA-AGTT--TTAAAAAAAG-TATCGAT-CCT
*** **** * * * * *** *
40555 TATTTGGATTAATTTCGT-TGAGATGGGTT-ATGTATAACA---AAACA-ATCTATCTCGCATGT
59 T-TTT--A-TAA-AAAGTATG-GACACTTTCA-ATATAATAGGTAAACATAT-GATGTAATAGGT
** *** ** ** *
40614 GAGTACTT-TATTCCAACCATGTGACA-AGTGTGA-CAACTCCATCAACTCACAACTCAGCT--T
116 -AGCCCTTATA-T---A--ATGT-A-ATAG-GT-ATCGTTTATAT-AA-T-GTAA-T-AGGTAGT
* * * * * * * ***
40674 TG-AACTCAAT-CAATATTGTCTTTTAGCTTGATGGTTCAT-AAAGCATGT---TAC-TTGAACA
165 GGTTA-T-ATTGTAA-AGTGTC-TAT-CCTT--T--TT-ATAAAAG--TGTCCATACTTTTTTCA
* * * * * * *** * * *
40732 GTAT-GAATCAATTATGCAATTTTCATGTTCAAT-TTAACACTGCA--TTTCA-A-ATTCATTTC
218 CTGTGGAA--AA-CAT-TAA-TTTAAGGTT--ATCTTTTGAGTG-AGTTTTAAGATATTAATTT-
* * * * * * **
40791 A-T-ATGTAATTGGAGTTTGAATTTAAATTTCAATTTGAGTTTGA-ATTTCAATATATATT-TCG
274 AGTAAT-T-ATAGGCGTCT-AA--T-GATTT--ATTT---TTT-ACGTTACGGTATATATTAT--
** ** * * * ** * * ** ** *
40852 GCTCCACTATAAATATTAGCCCAAGCCAATATGCATGTTATCATTGATTATTCCTAA-TTTC-CA
325 TATTAAAT-TAAAAATT---CTAA-ATAATAT---T-TTAT-A--AAATA-TCAAAACAATCAAA
** * * ** ** * * *** ** * *
40915 TTGTTTTTTTTCCAACGTAT-AAACGCGAGGGAAATCCCGACCATTTTATTTTTTGGTCAACTTT
377 TAATTTTTTGTGCAA---ATGAAA--TTA-TTAAAT--C-A--ATATT-GTAGGTGGAAAACATG
40979 AA
430 AA
* * *** ** * * ** * * * *
40981 A-GC-GTCAGAAACGTTTCG-GGCGT--ATGATC-TGGGTGGTATACAAGAAATGTAACAAATAG
1 ACACTGTTA-AAAAAATT-GAAACATAAATTA-CATAAGT--TTTA-AA-AAAAGTATC-GAT--
*** * * * ** * * ** *
41040 CAAC-TAAAATCATAAGT-TGAGTACCAC--CCAAATCATAAGTCTGAAATACTTCCGATGCTCA
56 C--CTTTTTATAAAAAGTATG-G-A-CACTTTC-AAT-ATAA-TAGGTAA-ACATATGATG-TAA
** * * * * *
41101 TCAAAATCCAAAGCTCATT-TGGTGCCAA-GCAAAAGGAAATCAAAATCCAAATCTCATATGATG
111 T--AGGT----AGC-CCTTAT-AT---AATGTAATAGG---T----AT-C--GT-T--TAT-AT-
*
41164 CCAA-GCAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTT
150 --AATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTT
41228 TTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAG-TTTAAGATATTAATTTAGTA
213 TTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTA
41292 ATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAATTCT
278 ATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAATTCT
41357 AAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATC
343 AAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATC
41422 AATATTGTAGGTGGAAAACATGAA
408 AATATTGTAGGTGGAAAACATGAA
41446 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
41511 AAAAGTATGGACACTTTCAATAT-ATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
*
41575 TAATAGGTATCG-TTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
41639 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
41704 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA-TTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
41768 ATTAAATTAAAAATTCTAAAT-A-A-TTTATAAAATAT-AAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCA
41829 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
41870 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCC-TTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
41934 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
*
41999 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
42064 AAAAGTGTCCATAC-TTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
42128 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
*
42193 ATT-AATTTAAAATTCTAAATAATATTTTATAAAATAT-AAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCA
42256 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
42297 ACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
42361 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
42426 TAATAGGTATCGTTTATATAATGTAATAGGTA
131 TAATAGGTATCGTTTATATAATGTAATAGGTA
42458 TCTATCTCGC
Statistics
Matches: 1925, Mismatches: 274, Indels: 388
0.74 0.11 0.15
Matches are distributed among these distances:
423 30 0.02
424 282 0.15
425 107 0.06
426 57 0.03
427 206 0.11
428 149 0.08
429 56 0.03
430 66 0.03
431 346 0.18
432 16 0.01
433 17 0.01
434 7 0.00
435 6 0.00
436 11 0.01
437 2 0.00
438 2 0.00
439 4 0.00
440 3 0.00
441 7 0.00
442 4 0.00
443 2 0.00
444 9 0.00
445 14 0.01
446 5 0.00
447 7 0.00
448 7 0.00
449 7 0.00
450 7 0.00
451 17 0.01
452 14 0.01
453 16 0.01
454 8 0.00
455 11 0.01
456 8 0.00
457 1 0.00
458 9 0.00
459 5 0.00
460 11 0.01
461 18 0.01
462 4 0.00
463 9 0.00
464 7 0.00
465 14 0.01
466 18 0.01
467 8 0.00
468 7 0.00
469 1 0.00
470 1 0.00
471 8 0.00
472 2 0.00
473 14 0.01
474 12 0.01
475 12 0.01
476 14 0.01
477 2 0.00
478 8 0.00
479 1 0.00
480 2 0.00
481 2 0.00
482 7 0.00
483 8 0.00
484 8 0.00
485 10 0.01
486 19 0.01
487 14 0.01
488 17 0.01
489 2 0.00
490 2 0.00
491 8 0.00
492 2 0.00
493 6 0.00
494 6 0.00
495 4 0.00
496 13 0.01
497 21 0.01
498 19 0.01
499 11 0.01
500 5 0.00
501 8 0.00
502 3 0.00
503 4 0.00
504 5 0.00
505 8 0.00
506 9 0.00
507 3 0.00
509 3 0.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (431 bp):
ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCA
AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:40540 original size:25 final size:25
Alignment explanation
Indices: 40506--40556 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
40496 ACAACAAATC
*
40506 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
40531 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
40556 A
1 A
40557 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:40826 original size:18 final size:18
Alignment explanation
Indices: 40805--40841 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
40795 GTAATTGGAG
40805 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
40823 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
40841 T
1 T
40842 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:40849 original size:24 final size:24
Alignment explanation
Indices: 40797--40843 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
40787 TTTCATATGT
* *
40797 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
40821 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
40844 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:41575 original size:23 final size:22
Alignment explanation
Indices: 41544--41605 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
41534 ATAGGTAAAC
*
41544 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTA-CCCTT
* *
41567 ATATAATGTAATAGGTATCGTT
1 ATATAATGTAATAGGTACCCTT
41589 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
41606 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 20 0.56
23 16 0.44
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.37
Consensus pattern (22 bp):
ATATAATGTAATAGGTACCCTT
Found at i:41593 original size:22 final size:22
Alignment explanation
Indices: 41544--41615 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
41534 ATAGGTAAAC
* * *
41544 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTA-TCGTT
41567 ATATAATGTAATAGGTATCGTT
1 ATATAATGTAATAGGTATCGTT
*
41589 ATATAATGTAATAGGTAATGGTT
1 ATATAATGTAATAGGT-ATCGTT
41612 ATAT
1 ATAT
41616 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 19 0.43
23 25 0.57
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (22 bp):
ATATAATGTAATAGGTATCGTT
Found at i:41999 original size:23 final size:23
Alignment explanation
Indices: 41968--42030 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
41958 ATAGGTAAAC
*
41968 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
41991 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
42014 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
42031 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:42038 original size:23 final size:23
Alignment explanation
Indices: 41968--42040 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
41958 ATAGGTAAAC
* * **
41968 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
41991 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
42014 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
42037 ATAT
1 ATAT
42041 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:42424 original size:427 final size:430
Alignment explanation
Indices: 41170--42457 Score: 2472
Period size: 424 Copynumber: 3.0 Consensus size: 430
41160 GATGCCAAGC
*
41170 AATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACT
1 AATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACT
41235 GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAG-TTTAAGATATTAATTTAGTAATTATAG
66 GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
41299 GCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAATTCTAAATAAT
131 GCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAATTCTAAATAAT
41364 ATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATCAATATTG
196 ATTTTATAAAATAT-AAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATCAATATTG
41429 TAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAG
260 TAGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAG
41494 TATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATAT-ATAGGTAAACATATGATGTAATAG
325 TATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAG
41558 GTAGCCCTTATATAATGTAATAGGTATCG-TTATATAATGT
390 GTAGCCCTTATATAATGTAATAGGTATCGTTTATATAATGT
41598 AATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACT
1 AATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACT
41663 GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
66 GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
41728 GCGTCTAATGATTTA-TTTTTACGTTACGGTATATATTATTATTAAATTAAAAATTCTAAAT-A-
131 GCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAATTCTAAATAAT
41790 A-TTTATAAAATATAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATCAATATTGT
196 ATTTTATAAAATATAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATCAATATTGT
41854 AGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGT
261 AGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGT
41919 ATCGATCC-TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGG
326 ATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGG
41983 TAGCCCTTATATAATGTAATAGGTATCGTTTATATAATGT
391 TAGCCCTTATATAATGTAATAGGTATCGTTTATATAATGT
42023 AATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATAC-TTTTTCACT
1 AATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACT
42087 GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
66 GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
*
42152 GCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATT-AATTTAAAATTCTAAATAAT
131 GCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAATTCTAAATAAT
42216 ATTTTATAAAATATAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATCAATATTGT
196 ATTTTATAAAATATAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATCAATATTGT
42281 AGGTGGAAAACATGAAACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGT
261 AGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGT
42345 ATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGG
326 ATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGG
42410 TAGCCCTTATATAATGTAATAGGTATCGTTTATATAATGT
391 TAGCCCTTATATAATGTAATAGGTATCGTTTATATAATGT
42450 AATAGGTA
1 AATAGGTA
42458 TCTATCTCGC
Statistics
Matches: 850, Mismatches: 2, Indels: 17
0.98 0.00 0.02
Matches are distributed among these distances:
423 30 0.04
424 282 0.33
425 107 0.13
426 50 0.06
427 192 0.23
428 147 0.17
429 42 0.05
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (430 bp):
AATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACT
GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
GCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAATTCTAAATAAT
ATTTTATAAAATATAAAACAATCAAATAATTTTTTGTGCAAATGAAATTATTAAATCAATATTGT
AGGTGGAAAACATGAAACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGT
ATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGG
TAGCCCTTATATAATGTAATAGGTATCGTTTATATAATGT
Found at i:42458 original size:23 final size:23
Alignment explanation
Indices: 42395--42459 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
42385 ATAGGTAAAC
* *
42395 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCCCTT
**
42418 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
42441 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
42460 TATCTCGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:42684 original size:18 final size:18
Alignment explanation
Indices: 42663--42699 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42653 GTAATTGGAG
42663 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
42681 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
42699 T
1 T
42700 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:42707 original size:24 final size:24
Alignment explanation
Indices: 42655--42701 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
42645 TTTCATATGT
* *
42655 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
42679 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
42702 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:43000 original size:39 final size:39
Alignment explanation
Indices: 42957--43081 Score: 225
Period size: 39 Copynumber: 3.2 Consensus size: 39
42947 TCCGATGCTC
* *
42957 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
42996 ATC-AAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
43034 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
43073 ATCAAAATC
1 ATCAAAATC
43082 TACAACTTGA
Statistics
Matches: 83, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
38 36 0.43
39 47 0.57
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
Found at i:43004 original size:38 final size:38
Alignment explanation
Indices: 42961--43078 Score: 209
Period size: 38 Copynumber: 3.1 Consensus size: 38
42951 ATGCTCATCA
* *
42961 AAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAAATC
1 AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATC
42999 AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATC
1 AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATC
43037 AAAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATC
1 -AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATC
43076 AAA
1 AAA
43079 ATCTACAACT
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
38 39 0.51
39 38 0.49
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.17
Consensus pattern (38 bp):
AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATC
Found at i:43513 original size:23 final size:23
Alignment explanation
Indices: 43482--43545 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
43472 ATAGGTAAAC
*
43482 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
43505 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
43528 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
43546 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:43552 original size:23 final size:23
Alignment explanation
Indices: 43482--43554 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
43472 ATAGGTAAAC
* **
43482 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
43505 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
43528 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
43551 ATAT
1 ATAT
43555 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:44792 original size:21 final size:21
Alignment explanation
Indices: 44742--44794 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
44732 TGTATAGCGT
* *
44742 TATCTAAAATATTATTTTTTC
1 TATCTAAAATATTAATTTTAC
*
44763 TATCGAAAATATTAATTTTAC
1 TATCTAAAATATTAATTTTAC
44784 TA-CTTAAAATA
1 TATC-TAAAATA
44795 AATATTTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (21 bp):
TATCTAAAATATTAATTTTAC
Found at i:52503 original size:20 final size:21
Alignment explanation
Indices: 52466--52506 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
52456 ATCATTTAAT
52466 TTTACTATCAATTATAAAATA
1 TTTACTATCAATTATAAAATA
52487 TTTACTA-CAA-TATTAAAATA
1 TTTACTATCAATTA-TAAAATA
52507 AGGGGTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 10 0.53
21 7 0.37
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (21 bp):
TTTACTATCAATTATAAAATA
Found at i:54184 original size:13 final size:13
Alignment explanation
Indices: 54166--54191 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54156 ATTCTTTTAT
54166 TTTTGTTAAATTG
1 TTTTGTTAAATTG
54179 TTTTGTTAAATTG
1 TTTTGTTAAATTG
54192 ATGACAAACG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (13 bp):
TTTTGTTAAATTG
Found at i:59142 original size:21 final size:22
Alignment explanation
Indices: 59118--59159 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
59108 ATACAATTTG
*
59118 AAATTTATTTAAT-ATTAAAAA
1 AAATTAATTTAATAATTAAAAA
*
59139 AAATTAATTTTATAATTAAAA
1 AAATTAATTTAATAATTAAAA
59160 TAATAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATTAATTTAATAATTAAAAA
Found at i:59535 original size:41 final size:41
Alignment explanation
Indices: 59478--59559 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
59468 ACGGTGCAAA
*
59478 GTCCTCAGATTGTACAGCTTCAAGGTT-CCGTAAAACAACCG
1 GTCCTCAGATTGTACAGCATCAA-GTTCCCGTAAAACAACCG
59519 GTCCTCAGATTGTACAGCATCAAGTTCCCGTAAAACAACCG
1 GTCCTCAGATTGTACAGCATCAAGTTCCCGTAAAACAACCG
59560 ATTTTCAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 3 0.08
41 36 0.92
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.23
Consensus pattern (41 bp):
GTCCTCAGATTGTACAGCATCAAGTTCCCGTAAAACAACCG
Found at i:61979 original size:66 final size:67
Alignment explanation
Indices: 61815--61992 Score: 261
Period size: 66 Copynumber: 2.6 Consensus size: 67
61805 CCTGGTTTTT
* * *
61815 TTTCCCGGTGTTCACTCCAACTCCGCCCTTTCCGACATTTACGTGAGTGCCGCCGCCCCCTGGCT
1 TTTCCCGGTGTTCACTCCAACTCCGCCCTTTCCGACATTCACGTGAGT--CGCCACCACCTGGCT
61880 TTCC
64 TTCC
61884 TTTCCCGGTGTTCACTCCAACTCCGCCCTTTCCGACATTCACGTGAGT-GCCACCACCTGGCTTT
1 TTTCCCGGTGTTCACTCCAACTCCGCCCTTTCCGACATTCACGTGAGTCGCCACCACCTGGCTTT
61948 CC
66 CC
** *
61950 TTTCCCGGTGTTCACAT-GTACTCCGCCCTTTCCGACGTTCACG
1 TTTCCCGGTGTTCAC-TCCAACTCCGCCCTTTCCGACATTCACG
61993 GCGGTACCCC
Statistics
Matches: 102, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
66 54 0.53
67 1 0.01
69 47 0.46
ACGTcount: A:0.12, C:0.40, G:0.18, T:0.30
Consensus pattern (67 bp):
TTTCCCGGTGTTCACTCCAACTCCGCCCTTTCCGACATTCACGTGAGTCGCCACCACCTGGCTTT
CC
Found at i:67723 original size:60 final size:60
Alignment explanation
Indices: 67608--67749 Score: 149
Period size: 60 Copynumber: 2.4 Consensus size: 60
67598 GATGAAAGCG
* * * * * * *
67608 GAATATTCAATAGTTTAGGGACCAATTTAGAAGAAGGGTCATAGTTTAAGTATGAAATTA
1 GAATATTCAAAAGTTCAAGGACTAAATTAGAAGAAGAGTCATAGTTTAAGCATGAAATTA
* ** * * * *
67668 GAATGTTTTAAAGTTCAAGGACTAAATTAGAATAAGAGTCATGGTTTGAGCATGAAATTG
1 GAATATTCAAAAGTTCAAGGACTAAATTAGAAGAAGAGTCATAGTTTAAGCATGAAATTA
*
67728 GAATATTCAAAAGTTTAAGGAC
1 GAATATTCAAAAGTTCAAGGAC
67750 AATTCAAAAT
Statistics
Matches: 64, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (60 bp):
GAATATTCAAAAGTTCAAGGACTAAATTAGAAGAAGAGTCATAGTTTAAGCATGAAATTA
Found at i:76859 original size:35 final size:36
Alignment explanation
Indices: 76786--76859 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 36
76776 TTTTTATATT
*
76786 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
76822 TTTAATTTT-TAAAGAAATT-TATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTAT-CAA
76857 TTT
1 TTT
76860 GTAATATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 11 0.32
35 14 0.41
36 9 0.26
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:79726 original size:184 final size:185
Alignment explanation
Indices: 79405--79793 Score: 624
Period size: 184 Copynumber: 2.1 Consensus size: 185
79395 TTTTATAATT
* * *
79405 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
* *
79469 TTATAAAATAAAAATTTCAGATAAATTTTCTAATTATTTAATATTGATTTAGGTTTAAAAGTTAT
66 TTATAAAATAAAAATTTCAGATAAATTTTCAAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
* *
79534 TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTAGGCTTAGCCCATATGTTA
131 TAGATCTTAAATTATTAATTGAGTTTTAAATGGTTTAGGCTGAGCCCATATGTTA
79589 TATATAATATATTTAATATTTTTTAATT-AAAAAAACAGTTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAA-AGTTTACAATTAATTTAAATAATATATA
* *
79653 ATTATAAAAT-AAAATTTTATATAAAATTTT-AAATTAATTAATATTGATTTAGGTTTAAAAGTT
65 ATTATAAAATAAAAATTTCAGAT-AAATTTTCAAATTAATTAATATTGATTTAGGTTTAAAAGTT
* * *
79716 ATTAGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGTCTATATGTTA
129 ATTAGATCTTAAATTATTAATTGAGTTTTAAATGGTTTAGGCTGAGCCCATATGTTA
79773 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
79794 AATTTCGGTT
Statistics
Matches: 190, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
184 128 0.67
185 62 0.33
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (185 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
TTATAAAATAAAAATTTCAGATAAATTTTCAAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
TAGATCTTAAATTATTAATTGAGTTTTAAATGGTTTAGGCTGAGCCCATATGTTA
Done.