Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008665.1 Hibiscus syriacus cultivar Beakdansim tig00111668_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: 71518
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4539 original size:29 final size:29
Alignment explanation
Indices: 4469--4547 Score: 103
Period size: 25 Copynumber: 2.8 Consensus size: 29
4459 CTCACCTAAC
*
4469 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGTAATGACATCATTAAT
*
4499 TAAATGA--T--GTAATGACATCTTTAAT
1 TAAATGATGTAAGTAATGACATCATTAAT
4524 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGTAATGACATCA
4548 ATTTAGTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
25 22 0.52
27 2 0.05
29 14 0.33
30 4 0.10
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (29 bp):
TAAATGATGTAAGTAATGACATCATTAAT
Found at i:11116 original size:12 final size:12
Alignment explanation
Indices: 11099--11123 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11089 GATTTTAAAA
11099 AATCAATCAACC
1 AATCAATCAACC
11111 AATCAATCAACC
1 AATCAATCAACC
11123 A
1 A
11124 GTACATGGGT
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:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (12 bp):
AATCAATCAACC
Found at i:23370 original size:2 final size:2
Alignment explanation
Indices: 23363--23390 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23353 TATTTATGTA
23363 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
23391 TGTTTTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24293 original size:13 final size:13
Alignment explanation
Indices: 24275--24322 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
24265 AAATTAGTCC
24275 TGAATAATTTTTT
1 TGAATAATTTTTT
* **
24288 TGAATAAATTAGTCC
1 TGAAT-AATT-TTTT
24303 TGAATAATTTTTT
1 TGAATAATTTTTT
24316 TGAATAA
1 TGAATAA
24323 ATTAGTCCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 13 0.48
14 8 0.30
15 6 0.22
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (13 bp):
TGAATAATTTTTT
Found at i:24295 original size:28 final size:28
Alignment explanation
Indices: 24259--24331 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
24249 TAACAGGAAC
*
24259 TTGATTAAATTAGTCCTGAATAATTTTT
1 TTGAATAAATTAGTCCTGAATAATTTTT
24287 TTGAATAAATTAGTCCTGAATAATTTTT
1 TTGAATAAATTAGTCCTGAATAATTTTT
24315 TTGAATAAATTAGTCCT
1 TTGAATAAATTAGTCCT
24332 TAATTATTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (28 bp):
TTGAATAAATTAGTCCTGAATAATTTTT
Found at i:27715 original size:222 final size:225
Alignment explanation
Indices: 27310--27751 Score: 741
Period size: 222 Copynumber: 2.0 Consensus size: 225
27300 GTAAATTATC
* *
27310 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTA-CTTTAGT
* *
27375 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
65 TAATATTATTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
*
27440 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
130 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
27505 AAACATAAATTACATAACTTTCAAAAAGTATA
195 AAACATAAATTACATAACTTT-AAAAAGTATA
*
27537 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTA-TA-TTTGGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTACTTTAGT
*
27600 TAATATTATTAAATTTAAATTCTAAATAATATTTTATAAAATATC-AAACAATCAAA-AA-ATTT
65 TAATATTATTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
* *
27662 TGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATTG
130 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
27727 AAACATAAATTACATAACTTTAAAA
195 AAACATAAATTACATAACTTTAAAA
27752 GCAGTTTTAA
Statistics
Matches: 205, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
221 4 0.02
222 86 0.42
223 2 0.01
224 11 0.05
225 48 0.23
227 38 0.19
228 16 0.08
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (225 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTACTTTAGTT
AATATTATTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTTT
GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGA
AACATAAATTACATAACTTTAAAAAGTATA
Found at i:27837 original size:20 final size:19
Alignment explanation
Indices: 27814--27860 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
27804 CGATATACCA
27814 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
27834 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
27854 GGTAAAA
1 GGTAAAA
27861 TTAAAAGTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:28003 original size:20 final size:19
Alignment explanation
Indices: 27980--28026 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
27970 CGATATAACA
*
27980 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
28000 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
28020 GGTAAAA
1 GGTAAAA
28027 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:30366 original size:33 final size:33
Alignment explanation
Indices: 30324--30389 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
30314 AAATAGATGG
*
30324 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
30357 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
30390 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:32224 original size:19 final size:19
Alignment explanation
Indices: 32180--32223 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
32170 AATGTCGAGT
32180 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
32199 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
32218 T-ATTTT
1 TAATTTT
32224 TTTATGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:32749 original size:199 final size:199
Alignment explanation
Indices: 32306--35117 Score: 5229
Period size: 199 Copynumber: 14.1 Consensus size: 199
32296 TTAAGGGTCA
* * * *
32306 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT-TAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
*
32370 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
32435 TAATATGTAATTTTT-AATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
32499 AATG
196 AATG
* * *
32503 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
*
32568 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
32633 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
32698 AATG
196 AATG
32702 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
32767 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
32832 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
32897 AATG
196 AATG
32901 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
32966 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
33031 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
33096 AATG
196 AATG
* *
33100 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
*
33165 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* *
33230 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
33295 AATG
196 AATG
* * *
33299 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
*
33364 AATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
33428 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
33493 AATG
196 AATG
33497 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
33562 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
33627 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
33692 AATG
196 AATG
33696 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
33760 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
33825 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
33890 AATG
196 AATG
*
33894 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
33959 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* * *
34024 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
34089 TAATG
195 TAATG
34094 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
34159 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
34224 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
34289 AATG
196 AATG
34293 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
34358 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
34423 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
34488 AATG
196 AATG
* *
34492 TGTCGACACTAATATAGTCTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
34557 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
* * *
34622 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATAAGAGAATAAGTCTAAA
130 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
34687 TAATG
195 TAATG
34692 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
34757 CATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
34821 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
34886 AATG
196 AATG
*
34890 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
*
34955 CATAAAGTGTCGATCCATATATAAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
35020 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
131 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
35085 AATG
196 AATG
*
35089 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
35118 CTAATTTAAA
Statistics
Matches: 2562, Mismatches: 46, Indels: 12
0.98 0.02 0.00
Matches are distributed among these distances:
197 47 0.02
198 680 0.27
199 1446 0.56
200 389 0.15
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (199 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATAAAAAACAAGGTGCACC
CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAAT
AATG
Found at i:36602 original size:18 final size:18
Alignment explanation
Indices: 36579--36646 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
36569 ATCGGTCGCA
36579 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
36597 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
36618 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
36639 GAAGATGA
1 GAAGATGA
36647 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:36603 original size:6 final size:6
Alignment explanation
Indices: 36579--36676 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
36569 ATCGGTCGCA
* * * * * *
36579 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
36627 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
36675 GA
1 GA
36677 TGATCCAAAC
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:36614 original size:3 final size:3
Alignment explanation
Indices: 36594--36680 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
36584 TGAAGCTGAC
* * * * * ** *
36594 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
36642 GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
36681 CCAAACAAGT
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:36629 original size:42 final size:42
Alignment explanation
Indices: 36582--36672 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
36572 GGTCGCAGAA
*
36582 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* * *
36624 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
36666 GATGAAG
1 GATGAAG
36673 ATGATGATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
Found at i:36680 original size:18 final size:18
Alignment explanation
Indices: 36579--36676 Score: 88
Period size: 18 Copynumber: 5.4 Consensus size: 18
36569 ATCGGTCGCA
* *
36579 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
36597 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
36615 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
** *
36633 GGCGATGAAGATGATGAC
1 GAAGATGAAGATGATGAT
* *
36651 GATGATGATGATGATGAT
1 GAAGATGAAGATGATGAT
36669 GAAGATGA
1 GAAGATGA
36677 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:38358 original size:183 final size:184
Alignment explanation
Indices: 38046--38715 Score: 1272
Period size: 183 Copynumber: 3.7 Consensus size: 184
38036 CTTTCAACAT
**
38046 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
38111 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
38176 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
38230 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
38295 -GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
38359 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
38413 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
38478 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
38542 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
38596 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
38661 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
38716 CCATTTAAAA
Statistics
Matches: 478, Mismatches: 7, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
183 354 0.74
184 124 0.26
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:41297 original size:23 final size:23
Alignment explanation
Indices: 41266--41328 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
41256 ATAGGTAAAC
*
41266 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
41289 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
41312 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
41329 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:41336 original size:23 final size:23
Alignment explanation
Indices: 41266--41338 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
41256 ATAGGTAAAC
* * **
41266 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
41289 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
41312 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
41335 ATAT
1 ATAT
41339 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:41725 original size:23 final size:23
Alignment explanation
Indices: 41694--41756 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
41684 ATAGGTAAAC
*
41694 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
41717 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
41740 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
41757 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:41764 original size:23 final size:23
Alignment explanation
Indices: 41694--41766 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
41684 ATAGGTAAAC
* * **
41694 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
41717 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
41740 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
41763 ATAT
1 ATAT
41767 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:42153 original size:23 final size:23
Alignment explanation
Indices: 42122--42184 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
42112 ATAGGTAAAC
*
42122 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
42145 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
42168 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
42185 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:42192 original size:23 final size:23
Alignment explanation
Indices: 42122--42194 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
42112 ATAGGTAAAC
* * **
42122 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
42145 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
42168 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
42191 ATAT
1 ATAT
42195 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:42222 original size:20 final size:20
Alignment explanation
Indices: 42197--42235 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42187 GGTTATATTG
* *
42197 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
42217 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
42236 TCACTGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:42582 original size:23 final size:23
Alignment explanation
Indices: 42551--42613 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
42541 ATAGGTAAAC
*
42551 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
42574 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
42597 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
42614 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:42621 original size:23 final size:23
Alignment explanation
Indices: 42551--42623 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
42541 ATAGGTAAAC
* * **
42551 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
42574 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
42597 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
42620 ATAT
1 ATAT
42624 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:42651 original size:20 final size:20
Alignment explanation
Indices: 42626--42664 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42616 GGTTATATTG
* *
42626 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
42646 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
42665 TCACTGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:43009 original size:23 final size:23
Alignment explanation
Indices: 42978--43040 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
42968 ATAGGTAAAC
*
42978 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
43001 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
43024 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
43041 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:43048 original size:23 final size:23
Alignment explanation
Indices: 42978--43050 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
42968 ATAGGTAAAC
* * **
42978 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
43001 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
43024 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
43047 ATAT
1 ATAT
43051 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:43338 original size:427 final size:431
Alignment explanation
Indices: 41168--43890 Score: 5217
Period size: 428 Copynumber: 6.4 Consensus size: 431
41158 AATTCGCAAT
41168 ACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTATAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTATAAAAAAAGTATCGATCCTTTTTATA
41232 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
41297 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
41362 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
41427 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA-TTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
41491 ATTAAATTAAAAATTCT-AATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
41555 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
41596 ACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTATAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTATAAAAAAAGTATCGATCCTTTTTATA
41660 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
41725 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
41790 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
41855 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGG--TATA-TATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
41917 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
41982 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
42023 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTATAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTATAAAAAAAGTATCGATCCTTTTTATA
42088 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
42153 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
*
42218 -AAAGTGTCCATACTTTTTTCACTGTGG-AAATATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
42281 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
42346 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
42411 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
42452 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTATAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTATAAAAAAAGTATCGATCCTTTTTATA
42517 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
42582 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
42647 -AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
42711 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
42776 ATTAAATT-AAAATTCTAAATAATATTTTATAAAATAT-AAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
42839 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
* *
42880 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCATTTTTAT-
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTATAAAAAAAGTATCGATCCTTTTTATA
42944 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
43009 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
43074 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
43139 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
43204 ATTAAATT-AAAATTCTAAATAATA-TTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
43267 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
*
43308 ACACTGTTAAAAAAATTGAAACAT-AATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTATAAAAAAAGTATCGATCCTTTTTATA
43372 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
*
43437 TAATAGGTGTCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
43502 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATC-TTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
43566 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
43631 ATTAAATTAAAAATTCTAAATAATATTTTAT-AAATATAAAAACAATC-AATAATTTTTTGTGCA
326 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
43694 AATG-AA--ATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
*
43732 ACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTATAAAAAAAGTATCGATCCTTTTTATA
43796 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCC-T-TATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
43859 TAATAGGTATCGTTTATATAATGTAATAGGTA
131 TAATAGGTATCGTTTATATAATGTAATAGGTA
43891 TCTATCTCGC
Statistics
Matches: 2275, Mismatches: 7, Indels: 32
0.98 0.00 0.01
Matches are distributed among these distances:
422 38 0.02
423 16 0.01
424 135 0.06
426 112 0.05
427 414 0.18
428 1072 0.47
429 380 0.17
430 108 0.05
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (431 bp):
ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTATAAAAAAAGTATCGATCCTTTTTATA
AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:43437 original size:23 final size:24
Alignment explanation
Indices: 43406--43468 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
43396 ATAGGTAAAC
*
43406 ATATGATGTAATAGGTAG-CCCTT
1 ATATAATGTAATAGGTAGTCCCTT
**
43429 ATATAATGTAATAGGT-GTCGTTT
1 ATATAATGTAATAGGTAGTCCCTT
43452 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
43469 ATGGTTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.03
23 34 0.97
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (24 bp):
ATATAATGTAATAGGTAGTCCCTT
Found at i:43476 original size:23 final size:23
Alignment explanation
Indices: 43406--43478 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
43396 ATAGGTAAAC
* * **
43406 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
* *
43429 ATATAATGTAATAGGTGTCGTTT
1 ATATAATGTAATAGGTATCGGTT
43452 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
43475 ATAT
1 ATAT
43479 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 41 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:43861 original size:21 final size:23
Alignment explanation
Indices: 43830--43890 Score: 72
Period size: 21 Copynumber: 2.7 Consensus size: 23
43820 ATAGGTAAAC
*
43830 ATATGATGTAATAGGTAGC-CCT
1 ATATAATGTAATAGGTAGCGCCT
* **
43852 -TATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCCT
43874 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
43891 TCTATCTCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 16 0.48
22 1 0.03
23 16 0.48
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCCT
Found at i:44117 original size:18 final size:18
Alignment explanation
Indices: 44096--44132 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
44086 GTAATTGGAG
44096 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
44114 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
44132 T
1 T
44133 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:44140 original size:24 final size:24
Alignment explanation
Indices: 44088--44134 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
44078 TTTCATATGT
* *
44088 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
44112 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
44135 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:52914 original size:27 final size:25
Alignment explanation
Indices: 52884--52965 Score: 92
Period size: 27 Copynumber: 3.1 Consensus size: 25
52874 GTGGCAGACG
52884 AAATTTAGGTATTCTAGGGTTTTGTAA
1 AAATTTAGG-ATTCTAGGGTTTT-TAA
* *
52911 AAATTTAGGGATTCTAGGTATTTTTGA
1 AAATTTA-GGATTCTAGG-GTTTTTAA
* *
52938 AAATTAAGGATTCTAGGGTTCTTAA
1 AAATTTAGGATTCTAGGGTTTTTAA
52963 AAA
1 AAA
52966 AATAAAGAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
25 8 0.17
26 10 0.21
27 23 0.49
28 6 0.13
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (25 bp):
AAATTTAGGATTCTAGGGTTTTTAA
Found at i:52966 original size:26 final size:26
Alignment explanation
Indices: 52884--52966 Score: 78
Period size: 26 Copynumber: 3.1 Consensus size: 26
52874 GTGGCAGACG
*
52884 AAATTTAGGTATTCTAGGGTTTTGTAAA
1 AAATTAAGG-ATTCTAGGGTTTT-TAAA
* * **
52912 AATTTAGGGATTCTA-GGTATTTTTGA
1 AAATTAAGGATTCTAGGGT-TTTTAAA
*
52938 AAATTAAGGATTCTAGGGTTCTTAAA
1 AAATTAAGGATTCTAGGGTTTTTAAA
52964 AAA
1 AAA
52967 ATAAAGAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
26 25 0.58
27 12 0.28
28 6 0.14
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (26 bp):
AAATTAAGGATTCTAGGGTTTTTAAA
Found at i:55102 original size:31 final size:31
Alignment explanation
Indices: 55061--55122 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
55051 TTACGATTCA
*
55061 AACTCGAAATTTGAGTTGACTCGAATAACTC
1 AACTCAAAATTTGAGTTGACTCGAATAACTC
55092 AACTCAAAATTTGAGTTGACTCGAATAACTC
1 AACTCAAAATTTGAGTTGACTCGAATAACTC
55123 GAAATTTGAA
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:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (31 bp):
AACTCAAAATTTGAGTTGACTCGAATAACTC
Found at i:55121 original size:26 final size:29
Alignment explanation
Indices: 55061--55131 Score: 94
Period size: 31 Copynumber: 2.5 Consensus size: 29
55051 TTACGATTCA
55061 AACTCGAAATTTGAGTTGACTCGAATAACTC
1 AACTCGAAATTTGAGTTGACTCG-A-AACTC
*
55092 AACTCAAAATTTGAGTTGACTCG-AA-T-
1 AACTCGAAATTTGAGTTGACTCGAAACTC
55118 AACTCGAAATTTGA
1 AACTCGAAATTTGA
55132 AGGAAAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
26 13 0.34
27 1 0.03
28 2 0.05
31 22 0.58
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (29 bp):
AACTCGAAATTTGAGTTGACTCGAAACTC
Found at i:58660 original size:15 final size:16
Alignment explanation
Indices: 58624--58657 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
58614 AATTTTCTTC
58624 TTTTA-TTTATTGAAT
1 TTTTATTTTATTGAAT
*
58639 TTTTATTTTATTGTAT
1 TTTTATTTTATTGAAT
58655 TTT
1 TTT
58658 ATTCTATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTATTTTATTGAAT
Found at i:59088 original size:54 final size:54
Alignment explanation
Indices: 59024--59129 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 54
59014 AAACCATATT
* *
59024 TTGATTAAAACATTGACGTGTCAAGCCTTGGTTGATTTTATTCGGACATGTCTA
1 TTGATTAAAACATTGACGTGTCAAACATTGGTTGATTTTATTCGGACATGTCTA
* * * *
59078 TTGATTAAAACATTGAGGTGTCAAACATTTGTTGATTTTATTTGTACATGTC
1 TTGATTAAAACATTGACGTGTCAAACATTGGTTGATTTTATTCGGACATGTC
59130 ATTTCTTTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (54 bp):
TTGATTAAAACATTGACGTGTCAAACATTGGTTGATTTTATTCGGACATGTCTA
Found at i:65852 original size:29 final size:29
Alignment explanation
Indices: 65810--65866 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
65800 CTGACCCAGA
65810 GACAAGTACCATAGAGCAACATGTTAAGG
1 GACAAGTACCATAGAGCAACATGTTAAGG
65839 GACAAGTACCATAGAGCAACATGTTAAG
1 GACAAGTACCATAGAGCAACATGTTAAG
65867 CAATATGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.18
Consensus pattern (29 bp):
GACAAGTACCATAGAGCAACATGTTAAGG
Found at i:67011 original size:6 final size:6
Alignment explanation
Indices: 67000--67024 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
66990 AATTCAAGCT
67000 TGAACC TGAACC TGAACC TGAACC T
1 TGAACC TGAACC TGAACC TGAACC T
67025 TAAGTACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (6 bp):
TGAACC
Found at i:68315 original size:13 final size:14
Alignment explanation
Indices: 68288--68316 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
68278 TAGGTTAAAG
68288 TTTTATCTGGGTTC
1 TTTTATCTGGGTTC
68302 TTTTATCT-GGTTC
1 TTTTATCTGGGTTC
68315 TT
1 TT
68317 GGGTCATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.07, C:0.14, G:0.17, T:0.62
Consensus pattern (14 bp):
TTTTATCTGGGTTC
Found at i:68997 original size:30 final size:31
Alignment explanation
Indices: 68953--69038 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
68943 GAAATGATCA
*
68953 CTAACGTCATCGGTCCGTCCGATTT-AAGT-T
1 CTAACGTTATCGGTCCGTCCGATTTCAA-TCT
* *
68983 CTAA-GATTATCGGTCCATCCAATTTCAATCT
1 CTAACG-TTATCGGTCCGTCCGATTTCAATCT
* *
69014 CTAACGTTATCGGTTCGTTCGATTT
1 CTAACGTTATCGGTCCGTCCGATTT
69039 TAGTCCCTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
29 1 0.02
30 21 0.47
31 22 0.49
32 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.37
Consensus pattern (31 bp):
CTAACGTTATCGGTCCGTCCGATTTCAATCT
Found at i:69024 original size:31 final size:30
Alignment explanation
Indices: 68953--69027 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
68943 GAAATGATCA
* * *
68953 CTAACGTCATCGGTCCGTCCGATTTAAGTT
1 CTAACGTTATCGGTCCATCCAATTTAAGTT
68983 CTAA-GATTATCGGTCCATCCAATTTCAA-TCT
1 CTAACG-TTATCGGTCCATCCAATTT-AAGT-T
69014 CTAACGTTATCGGT
1 CTAACGTTATCGGT
69028 TCGTTCGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
29 1 0.03
30 21 0.55
31 15 0.39
32 1 0.03
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (30 bp):
CTAACGTTATCGGTCCATCCAATTTAAGTT
Found at i:70246 original size:30 final size:31
Alignment explanation
Indices: 70212--70271 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 31
70202 TAGTGTATTT
70212 AAGCCTATTTACAAAAAAGAA-TTGTGTTTA
1 AAGCCTATTTACAAAAAAGAATTTGTGTTTA
70242 AAGCCTATTTACAAAAAAGAATTTGTGTTT
1 AAGCCTATTTACAAAAAAGAATTTGTGTTT
70272 TAAGTAAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (31 bp):
AAGCCTATTTACAAAAAAGAATTTGTGTTTA
Found at i:70362 original size:22 final size:23
Alignment explanation
Indices: 70319--70363 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
70309 TAGATATTAT
**
70319 ATTATTTATATTATAATTTTGAA
1 ATTATTTATATTATAACATTGAA
70342 ATTATTTA-ATTATAACATTGAA
1 ATTATTTATATTATAACATTGAA
70364 TTTTAATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (23 bp):
ATTATTTATATTATAACATTGAA
Done.