Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008426.1 Hibiscus syriacus cultivar Beakdansim tig00111210_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: 4445546
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 18
Found at i:201883 original size:39 final size:39
Alignment explanation
Indices: 201827--201903 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
201817 AGGAATCTCT
*
201827 CAGCTATGGATGCATGATGAGGGATAGGGTTAAAGTTTC
1 CAGCTATGGATGAATGATGAGGGATAGGGTTAAAGTTTC
201866 CAGCTATGGATGAATGATGAGGGATAGGGTTAAAGTTT
1 CAGCTATGGATGAATGATGAGGGATAGGGTTAAAGTTT
201904 GGGCGTGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.30, C:0.08, G:0.34, T:0.29
Consensus pattern (39 bp):
CAGCTATGGATGAATGATGAGGGATAGGGTTAAAGTTTC
Found at i:202015 original size:36 final size:36
Alignment explanation
Indices: 201975--202093 Score: 139
Period size: 36 Copynumber: 3.0 Consensus size: 36
201965 TCCCCAATCT
201975 CCCCATGCATGAACCGATCCTTGGTCGCCTCGAGTG
1 CCCCATGCATGAACCGATCCTTGGTCGCCTCGAGTG
202011 CCCCATGCATGAACCGATCCTTGGTCATTCTTGGTCGCCTCGAGTG
1 CCCCATGCATGAACCGA-------TC---CTTGGTCGCCTCGAGTG
*
202057 CCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
1 CCCCATGCATGAACCGATCCTTGGTCGCCTCGAGTG
202093 C
1 C
202094 ATGGCGACCT
Statistics
Matches: 72, Mismatches: 1, Indels: 20
0.77 0.01 0.22
Matches are distributed among these distances:
36 34 0.47
39 2 0.03
43 2 0.03
46 34 0.47
ACGTcount: A:0.16, C:0.36, G:0.24, T:0.24
Consensus pattern (36 bp):
CCCCATGCATGAACCGATCCTTGGTCGCCTCGAGTG
Found at i:202047 original size:46 final size:46
Alignment explanation
Indices: 201994--202082 Score: 178
Period size: 46 Copynumber: 1.9 Consensus size: 46
201984 TGAACCGATC
201994 CTTGGTCGCCTCGAGTGCCCCATGCATGAACCGATCCTTGGTCATT
1 CTTGGTCGCCTCGAGTGCCCCATGCATGAACCGATCCTTGGTCATT
202040 CTTGGTCGCCTCGAGTGCCCCATGCATGAACCGATCCTTGGTC
1 CTTGGTCGCCTCGAGTGCCCCATGCATGAACCGATCCTTGGTC
202083 GCCCCGAGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.15, C:0.34, G:0.25, T:0.27
Consensus pattern (46 bp):
CTTGGTCGCCTCGAGTGCCCCATGCATGAACCGATCCTTGGTCATT
Found at i:202106 original size:29 final size:29
Alignment explanation
Indices: 202074--202140 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
202064 CATGAACCGA
202074 TCCTTGGTCGCCCCGAGTGCATGGCGACC
1 TCCTTGGTCGCCCCGAGTGCATGGCGACC
**** *
202103 TCCTTGGTCGTTGGGCGTGCATGGCGACC
1 TCCTTGGTCGCCCCGAGTGCATGGCGACC
*
202132 TCTTTGGTC
1 TCCTTGGTC
202141 ACTGTACAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.07, C:0.31, G:0.33, T:0.28
Consensus pattern (29 bp):
TCCTTGGTCGCCCCGAGTGCATGGCGACC
Found at i:205721 original size:17 final size:18
Alignment explanation
Indices: 205692--205730 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
205682 TATTTTAAAG
205692 AAAGTATTTTGAGAGTA-
1 AAAGTATTTTGAGAGTAT
205709 AAAG-ATTTATGAGAGTAT
1 AAAGTATTT-TGAGAGTAT
205727 AAAG
1 AAAG
205731 GAGTCAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 4 0.20
17 12 0.60
18 4 0.20
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (18 bp):
AAAGTATTTTGAGAGTAT
Found at i:206861 original size:25 final size:25
Alignment explanation
Indices: 206823--206871 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
206813 ATCGAAAATA
206823 TGATCCAACATGACATGACATGATG
1 TGATCCAACATGACATGACATGATG
* *
206848 TGATCCAACCTGACATGATATGAT
1 TGATCCAACATGACATGACATGAT
206872 CCCTATACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (25 bp):
TGATCCAACATGACATGACATGATG
Found at i:212531 original size:59 final size:60
Alignment explanation
Indices: 212436--212553 Score: 143
Period size: 59 Copynumber: 2.0 Consensus size: 60
212426 CATACTTAAA
* *
212436 CTATGAATATCATTCTAAATTTGACCTCAAACTTTTAAATATTCC-ATTTTCA-CCCCAAG
1 CTATGAATATCATTCTAAATTGGACCTCAAAATTTTAAATATTCCAATTTT-ATCCCCAAG
* * * *
212495 CTATGAATCTCATTCTAAATTGGTCC-CTAAAATTTTAGATCTTCCAATTTTATCCCCAA
1 CTATGAATATCATTCTAAATTGGACCTC-AAAATTTTAAATATTCCAATTTTATCCCCAA
212554 ATTCATCCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
58 1 0.02
59 38 0.76
60 11 0.22
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (60 bp):
CTATGAATATCATTCTAAATTGGACCTCAAAATTTTAAATATTCCAATTTTATCCCCAAG
Found at i:213197 original size:2 final size:2
Alignment explanation
Indices: 213190--213215 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
213180 TTAATACTAT
213190 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
213216 ATTTATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:217743 original size:77 final size:77
Alignment explanation
Indices: 217616--217761 Score: 220
Period size: 77 Copynumber: 1.9 Consensus size: 77
217606 TTTATTACTA
* *
217616 TTGTCACGCCCTCAGAACCTTCAAGCCCAAACTGTCAAAATATCAGAGTTAAGGTCTGACGGGAC
1 TTGTCACGCCCTCAGAACCTTCAAACCCAAACCGTCAAAATATCAGAGTTAAGGTCTGACGGGAC
217681 GTGCGGCTAATC
66 GTGCGGCTAATC
* * * * * *
217693 TTGTCATGCCCTCATAACTTTCAAACCTAAACCGTCGAAATATCAGAGTTAAGGTCTGATGGGAC
1 TTGTCACGCCCTCAGAACCTTCAAACCCAAACCGTCAAAATATCAGAGTTAAGGTCTGACGGGAC
217758 GTGC
66 GTGC
217762 ACCCTTAGAC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
77 61 1.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (77 bp):
TTGTCACGCCCTCAGAACCTTCAAACCCAAACCGTCAAAATATCAGAGTTAAGGTCTGACGGGAC
GTGCGGCTAATC
Found at i:221240 original size:65 final size:68
Alignment explanation
Indices: 221157--221311 Score: 169
Period size: 65 Copynumber: 2.3 Consensus size: 68
221147 ATATCCTTTA
* * *
221157 TTGAATATTCTAAATTAAAA-GATATTTA-TCTCT-TTAA-TTTGAATATTAGTAGGATAATTAT
1 TTGAATATTCTAAATTAAAAGGAT-TTTATTATCTATTAACTTTGAATATTA-AAAGATAATTAT
221218 -TCTT
64 ATCTT
* *
221222 TTGAATATTTTAAGTTAAAAGGATTTTATTATCTAGTTAACTTTGAATATTAAAAGATAATTATA
1 TTGAATATTCTAAATTAAAAGGATTTTATTATCTA-TTAACTTTGAATATTAAAAGATAATTATA
221287 TCTTT
65 TC-TT
*
221292 TTAAATACTTC-AAATTAAAA
1 TTGAATA-TTCTAAATTAAAA
221312 TAATATCTAT
Statistics
Matches: 74, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
65 22 0.30
66 7 0.09
68 14 0.19
69 13 0.18
70 16 0.22
71 2 0.03
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (68 bp):
TTGAATATTCTAAATTAAAAGGATTTTATTATCTATTAACTTTGAATATTAAAAGATAATTATAT
CTT
Found at i:231541 original size:44 final size:44
Alignment explanation
Indices: 231475--231669 Score: 338
Period size: 44 Copynumber: 4.4 Consensus size: 44
231465 GTGCAATATT
*
231475 TTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATAC
1 TTACCATTT-AT-CCATAAGCTCGTAGGCTTATTTTACCAATATAC
231521 TTACCATTTATCCATAAGCTCGTAGGCTTATTTTACCAATATAC
1 TTACCATTTATCCATAAGCTCGTAGGCTTATTTTACCAATATAC
231565 TTACCATTTATCCATAAGCTCGTAGGCTTATTTTACCAATATAC
1 TTACCATTTATCCATAAGCTCGTAGGCTTATTTTACCAATATAC
*
231609 TTACCATTTATCCATAAGTTCGTAGGCTTATTTTACCAATATAC
1 TTACCATTTATCCATAAGCTCGTAGGCTTATTTTACCAATATAC
231653 TTACCA-TTATTCCATAA
1 TTACCATTTA-TCCATAA
231670 CCATATACCA
Statistics
Matches: 146, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
43 3 0.02
44 132 0.90
45 2 0.01
46 9 0.06
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (44 bp):
TTACCATTTATCCATAAGCTCGTAGGCTTATTTTACCAATATAC
Found at i:231553 original size:24 final size:24
Alignment explanation
Indices: 231526--231597 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
231516 TATACTTACC
231526 ATTTATCCATAAGCTCGTAGGCTT
1 ATTTATCCATAAGCTCGTAGGCTT
*
231550 ATTT-TACCAATATA-CT--TA--C-C
1 ATTTAT-CC-ATA-AGCTCGTAGGCTT
231570 ATTTATCCATAAGCTCGTAGGCTT
1 ATTTATCCATAAGCTCGTAGGCTT
231594 ATTT
1 ATTT
231598 TACCAATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 20
0.62 0.03 0.34
Matches are distributed among these distances:
18 1 0.03
19 5 0.14
20 6 0.17
21 4 0.11
23 4 0.11
24 10 0.28
25 5 0.14
26 1 0.03
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (24 bp):
ATTTATCCATAAGCTCGTAGGCTT
Found at i:232964 original size:14 final size:14
Alignment explanation
Indices: 232945--232978 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
232935 TGATCAACAT
232945 AATCTGTTTTGTAG
1 AATCTGTTTTGTAG
232959 AATCTGTTTTGTAG
1 AATCTGTTTTGTAG
232973 AATCTG
1 AATCTG
232979 CTGTCCGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.47
Consensus pattern (14 bp):
AATCTGTTTTGTAG
Found at i:234275 original size:3 final size:3
Alignment explanation
Indices: 234267--234301 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
234257 TATTTCCCCA
234267 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
234302 ATATAAAAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:236625 original size:29 final size:31
Alignment explanation
Indices: 236581--236638 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
236571 TTATTTCTGC
236581 TTTTATTAATTCTATTTT-GACACTGATTCT
1 TTTTATTAATTCTATTTTAGACACTGATTCT
* *
236611 TTTTATT-ATTTTATTTTAGTCACTGATT
1 TTTTATTAATTCTATTTTAGACACTGATT
236639 AACTTCTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.22, C:0.10, G:0.07, T:0.60
Consensus pattern (31 bp):
TTTTATTAATTCTATTTTAGACACTGATTCT
Found at i:240480 original size:16 final size:15
Alignment explanation
Indices: 240457--240515 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 15
240447 TTGACAACAC
240457 AGAGAAAAAAAAAGA
1 AGAGAAAAAAAAAGA
* *
240472 TACAGAAAAAAGAAGA
1 -AGAGAAAAAAAAAGA
*
240488 AGAAAAATAAAAAAG-
1 AGAGAAA-AAAAAAGA
240503 AGAGAAAAAAAAA
1 AGAGAAAAAAAAA
240516 AGAAAGTAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 6 0.17
15 11 0.31
16 19 0.53
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (15 bp):
AGAGAAAAAAAAAGA
Found at i:240499 original size:18 final size:18
Alignment explanation
Indices: 240477--240519 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
240467 AAAGATACAG
240477 AAAAAAGAAGA-AGAAAA
1 AAAAAAGAAGAGAGAAAA
*
240494 ATAAAA-AAGAGAGAAAA
1 AAAAAAGAAGAGAGAAAA
240511 AAAAAAGAA
1 AAAAAAGAA
240520 AGTAAGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 4 0.18
17 16 0.73
18 2 0.09
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (18 bp):
AAAAAAGAAGAGAGAAAA
Found at i:240579 original size:22 final size:22
Alignment explanation
Indices: 240457--240579 Score: 99
Period size: 22 Copynumber: 5.5 Consensus size: 22
240447 TTGACAACAC
*
240457 AGAGA-AAAAAAAAGATACAGAA
1 AGAGAGAAAAAAAA-ATAAAGAA
*
240479 A-AAAGAAGAAGAAAAATAAA-AA
1 AGAGAGAA-AA-AAAAATAAAGAA
* *
240501 AGAGAGAAAAAAAAAAGAAAGTA
1 AGAGAG-AAAAAAAAATAAAGAA
* * *
240524 AGAGAGAGAAAAAAAGAAAGCA
1 AGAGAGAAAAAAAAATAAAGAA
240546 AGAGAGAGAAAAAAAATAAAGAA
1 AGAGAGA-AAAAAAAATAAAGAA
* *
240569 AAAAAGAAAAA
1 AGAGAGAAAAA
240580 TACTTAAGAC
Statistics
Matches: 82, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
21 2 0.02
22 39 0.48
23 35 0.43
24 6 0.07
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.03
Consensus pattern (22 bp):
AGAGAGAAAAAAAAATAAAGAA
Found at i:245032 original size:16 final size:16
Alignment explanation
Indices: 244999--245049 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
244989 TTTATCTTTA
244999 TTTTTAT-TTTATGT-T
1 TTTTTATGTTTAT-TAT
245014 TTTTTACTGTTT-TTAT
1 TTTTTA-TGTTTATTAT
*
245030 TTTTTATTTTTATTAT
1 TTTTTATGTTTATTAT
245046 TTTT
1 TTTT
245050 ATTATTTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 11 0.35
16 17 0.55
17 3 0.10
ACGTcount: A:0.14, C:0.02, G:0.04, T:0.80
Consensus pattern (16 bp):
TTTTTATGTTTATTAT
Found at i:245045 original size:9 final size:9
Alignment explanation
Indices: 245029--245062 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
245019 ACTGTTTTTA
245029 TTTT-TTAT
1 TTTTATTAT
245037 TTTTATTAT
1 TTTTATTAT
245046 TTTTATTAT
1 TTTTATTAT
*
245055 TTCTATTA
1 TTTTATTA
245063 ATTGTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 4 0.17
9 20 0.83
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTATTAT
Found at i:245070 original size:22 final size:22
Alignment explanation
Indices: 245021--245070 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
245011 GTTTTTTTAC
* * *
245021 TGTTTTTATTTTTTATTTTTAT
1 TGTTTTTATTATTTATATTAAT
* *
245043 TATTTTTATTATTTCTATTAAT
1 TGTTTTTATTATTTATATTAAT
245065 TGTTTT
1 TGTTTT
245071 AATATTTTAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (22 bp):
TGTTTTTATTATTTATATTAAT
Found at i:248506 original size:203 final size:202
Alignment explanation
Indices: 247952--248508 Score: 738
Period size: 203 Copynumber: 2.7 Consensus size: 202
247942 TTTGATCATT
* *
247952 CATCGCATATAGAGTTGGATTCGCATCATCACTTTGTTCGATTCTATCACAAAAGGGGGTGGATC
1 CATCGCATATAGAGTTGGA-TCGCATCATCACTTTGTTCGATTCCATCACAAAAGGAGGTGGATC
* * ** *
248017 AACATTTCCAGTGGAGAGTTTATAATGAGAAGAACTCATAAGATGAGGGAGAAGAAGTTCATAAT
65 AACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAATTTCATAAT
* * * * *
248082 GAGAAGAACTTGTTCAAACTTAGCTCGTTTCCATCATATAAGGAGTTGGAACAACACCAATACTT
130 GAGAAGAACTTGTTCAACCTTAGATAGTTTCCATCATATAAGGAGTTAGAACAACACCAATAATT
*
248147 GGCTCATC
195 GGCCCATC
* * * * *
248155 CATCGCATATGGATTTGGATCGGCATCATCACTTTGTTTGATTCCATCACAGAAGGAGGTGGATT
1 CATCGCATATAGAGTTGGATC-GCATCATCACTTTGTTCGATTCCATCACAAAAGGAGGTGGATC
* * * *
248220 AACATTTTTAGTTGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGGGAAGAAGTTT-ATAA
65 AACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAA-TTTCATAA
* *
248284 TGAGAATAACTTGTTCAACCTTAGATAGTTTCCATTATATAAGGAGTTAGAACAACACCAATAAT
129 TGAGAAGAACTTGTTCAACCTTAGATAGTTTCCATCATATAAGGAGTTAGAACAACACCAATAAT
248349 TGGCCCATC
194 TGGCCCATC
* * * * *
248358 CATCGCATATAAAGTTGGATCAGCATTATCACTTTGTTCAATTCCATTACAAAAGGAGTTGGATC
1 CATCGCATATAGAGTTGGATC-GCATCATCACTTTGTTCGATTCCATCACAAAAGGAGGTGGATC
* * * ** * *
248423 AACATTTCTAGTGGAGAGTTCCTAATAAGAAGAAATCATCCGACAAGAGATAAGAATTTCATAAT
65 AACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAATTTCATAAT
*
248488 GAGAAGAACTTATTCAACCTT
130 GAGAAGAACTTGTTCAACCTT
248509 GGTTTGATTC
Statistics
Matches: 303, Mismatches: 48, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
202 5 0.02
203 296 0.98
204 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (202 bp):
CATCGCATATAGAGTTGGATCGCATCATCACTTTGTTCGATTCCATCACAAAAGGAGGTGGATCA
ACATTTCTAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAATTTCATAATG
AGAAGAACTTGTTCAACCTTAGATAGTTTCCATCATATAAGGAGTTAGAACAACACCAATAATTG
GCCCATC
Found at i:248689 original size:42 final size:41
Alignment explanation
Indices: 248642--248822 Score: 213
Period size: 42 Copynumber: 4.3 Consensus size: 41
248632 ATTCATCGTG
* *
248642 TAAGGAGTTGTATCAATATCACCATTTCTCTCATCCATCACA
1 TAAGGAGTTG-ATCAACATCACCATTTCGCTCATCCATCACA
* * **
248684 TAAGGAGTTAGATCAACATCACTATTTTGCTTGTCCATCACA
1 TAAGGAGTT-GATCAACATCACCATTTCGCTCATCCATCACA
* *
248726 TAAGGAGTTAGATCAACATCATCATTTCGCTCGTCCATCACA
1 TAAGGAGTT-GATCAACATCACCATTTCGCTCATCCATCACA
* *
248768 TAAGGAGTTGGATCAATATCA-CA-TTGGCTCATCCATCACA
1 TAAGGAGTT-GATCAACATCACCATTTCGCTCATCCATCACA
248808 TAAGGAGTTGGATCA
1 TAAGGAGTT-GATCA
248823 TCGTCACCTT
Statistics
Matches: 124, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
40 30 0.24
41 2 0.02
42 91 0.73
43 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.30
Consensus pattern (41 bp):
TAAGGAGTTGATCAACATCACCATTTCGCTCATCCATCACA
Found at i:248703 original size:23 final size:23
Alignment explanation
Indices: 248677--248746 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
248667 TTCTCTCATC
248677 CATCACATAAGGAGTTAGATCAA
1 CATCACATAAGGAGTTAGATCAA
*** *
248700 CATCACTATTTTG-CTT-G-TC--
1 CATCAC-ATAAGGAGTTAGATCAA
248719 CATCACATAAGGAGTTAGATCAA
1 CATCACATAAGGAGTTAGATCAA
248742 CATCA
1 CATCA
248747 TCATTTCGCT
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
18 3 0.09
19 8 0.24
20 1 0.03
21 4 0.12
22 1 0.03
23 13 0.39
24 3 0.09
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (23 bp):
CATCACATAAGGAGTTAGATCAA
Found at i:248783 original size:84 final size:81
Alignment explanation
Indices: 248642--248822 Score: 236
Period size: 84 Copynumber: 2.2 Consensus size: 81
248632 ATTCATCGTG
* *
248642 TAAGGAGTTGTATCAATATCACCATTTCTCTCATCCATCACATAAGGAGTTAGATCAACATCACT
1 TAAGGAGTTG-ATCAACATCACCATTTCGCTCATCCATCACATAAGGAGTTAGATCAACATCAC-
* **
248707 ATTTTGCTTGTCCATCACA
64 A-TTGGCTCATCCATCACA
* * * *
248726 TAAGGAGTTAGATCAACATCATCATTTCGCTCGTCCATCACATAAGGAGTTGGATCAATATCACA
1 TAAGGAGTT-GATCAACATCACCATTTCGCTCATCCATCACATAAGGAGTTAGATCAACATCACA
248791 TTGGCTCATCCATCACA
65 TTGGCTCATCCATCACA
248808 TAAGGAGTTGGATCA
1 TAAGGAGTT-GATCA
248823 TCGTCACCTT
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
82 28 0.33
83 1 0.01
84 56 0.65
85 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.30
Consensus pattern (81 bp):
TAAGGAGTTGATCAACATCACCATTTCGCTCATCCATCACATAAGGAGTTAGATCAACATCACAT
TGGCTCATCCATCACA
Found at i:248844 original size:40 final size:40
Alignment explanation
Indices: 248642--248857 Score: 166
Period size: 42 Copynumber: 5.3 Consensus size: 40
248632 ATTCATCGTG
* ** *
248642 TAAGGAGTTGTATCAATATCACCATTTCTCTCATCCATCACA
1 TAAGGAGTTGGATCAATATCA-CA-TTGGCTCAACCATCACA
* * * ***
248684 TAAGGAGTTAGATCAACATCACTATTTTGCTTGTCCATCACA
1 TAAGGAGTTGGATCAATATCAC-A-TTGGCTCAACCATCACA
* * * **
248726 TAAGGAGTTAGATCAACATCATCATTTCGCTCGTCCATCACA
1 TAAGGAGTTGGATCAATATCA-CA-TTGGCTCAACCATCACA
*
248768 TAAGGAGTTGGATCAATATCACATTGGCTCATCCATCACA
1 TAAGGAGTTGGATCAATATCACATTGGCTCAACCATCACA
* * * *
248808 TAAGGAGTTGGATC-ATCGTCACCTTGGGTCAACCATCGCA
1 TAAGGAGTTGGATCAAT-ATCACATTGGCTCAACCATCACA
*
248848 -AATGAGTTGG
1 TAAGGAGTTGG
248858 GCCAACGTTT
Statistics
Matches: 152, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
39 11 0.07
40 47 0.31
41 3 0.02
42 90 0.59
43 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (40 bp):
TAAGGAGTTGGATCAATATCACATTGGCTCAACCATCACA
Found at i:250990 original size:18 final size:18
Alignment explanation
Indices: 250904--250982 Score: 104
Period size: 18 Copynumber: 4.4 Consensus size: 18
250894 GGATTATCAA
* * *
250904 TGGTCCTTTGGTACATAG
1 TGGTCCTTCGGGACACAG
*
250922 TGGTCCTTCGGGACATAG
1 TGGTCCTTCGGGACACAG
* *
250940 TGGTCATTCGGGACACAA
1 TGGTCCTTCGGGACACAG
250958 TGGTCCTTCGGGACACAG
1 TGGTCCTTCGGGACACAG
250976 TGGTCCT
1 TGGTCCT
250983 ACGAGACAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.18, C:0.23, G:0.30, T:0.29
Consensus pattern (18 bp):
TGGTCCTTCGGGACACAG
Found at i:252251 original size:2 final size:2
Alignment explanation
Indices: 252244--252280 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
252234 AGCGTATAAG
252244 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
252281 GTCAAAGCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:255135 original size:18 final size:18
Alignment explanation
Indices: 255111--255192 Score: 119
Period size: 18 Copynumber: 4.6 Consensus size: 18
255101 AAGGGATTAT
*
255111 CAGTGGTCCTTTGGGACA
1 CAGTGGTCCTTCGGGACA
*
255129 TAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
*
255147 TAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
*
255165 CGGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
*
255183 CGGTGGTCCT
1 CAGTGGTCCT
255193 ACGAGACAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.35, T:0.27
Consensus pattern (18 bp):
CAGTGGTCCTTCGGGACA
Found at i:256332 original size:36 final size:36
Alignment explanation
Indices: 256265--256334 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
256255 GAAGAAAGGG
* *
256265 AGGGGAATAAGTTTTTCCTTTGGTTGATTGGGTATT
1 AGGGGAATAAGTTTTACCTTTGGTAGATTGGGTATT
*
256301 AGGGGAGTAAGTTTTACCTTTGGTCAG-TTGGGTA
1 AGGGGAATAAGTTTTACCTTTGGT-AGATTGGGTA
256335 CCCCGTTGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 29 0.97
37 1 0.03
ACGTcount: A:0.20, C:0.07, G:0.33, T:0.40
Consensus pattern (36 bp):
AGGGGAATAAGTTTTACCTTTGGTAGATTGGGTATT
Found at i:258775 original size:13 final size:15
Alignment explanation
Indices: 258736--258777 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
258726 TTTTAGGTAT
258736 AGTCCTTAAATTTAG
1 AGTCCTTAAATTTAG
*
258751 ACTCCTTTAAATTT-G
1 AGTCC-TTAAATTTAG
258766 -GTCCTTAAATTT
1 AGTCCTTAAATTT
258778 TAATTTAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 8 0.33
14 3 0.12
15 5 0.21
16 8 0.33
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (15 bp):
AGTCCTTAAATTTAG
Found at i:260460 original size:2 final size:2
Alignment explanation
Indices: 260415--260445 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
260405 GTATTAAGTA
260415 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
260446 CACACACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:260712 original size:28 final size:28
Alignment explanation
Indices: 260650--260705 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
260640 GGAATTTCAA
260650 AATAATGGATTCTTGATATCAGGTATTT
1 AATAATGGATTCTTGATATCAGGTATTT
260678 AATAATGGATTCTTGATATCAGGTATTT
1 AATAATGGATTCTTGATATCAGGTATTT
260706 GAAAATGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (28 bp):
AATAATGGATTCTTGATATCAGGTATTT
Found at i:261052 original size:15 final size:15
Alignment explanation
Indices: 261022--261054 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
261012 TAATATGACT
261022 AAAATATAAATATTA
1 AAAATATAAATATTA
261037 AAAAT-TAAATACTTA
1 AAAATATAAATA-TTA
261052 AAA
1 AAA
261055 CAGAATAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATATAAATATTA
Found at i:261399 original size:2 final size:2
Alignment explanation
Indices: 261392--261429 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
261382 TTTGTAACAC
261392 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
261430 TTTCAAGGCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:265098 original size:11 final size:11
Alignment explanation
Indices: 265082--265116 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
265072 ATGGGTTCTC
265082 ATTTATTATTA
1 ATTTATTATTA
265093 ATTTATTATTA
1 ATTTATTATTA
265104 ATACTTATTATTA
1 AT--TTATTATTA
265117 TTATATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.59
13 9 0.41
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTTATTATTA
Found at i:265557 original size:11 final size:11
Alignment explanation
Indices: 265537--265569 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
265527 CCACTATTAT
*
265537 CATCAGAAATC
1 CATCATAAATC
265548 CATCATAAATC
1 CATCATAAATC
265559 CATCATAAATC
1 CATCATAAATC
265570 AACATGCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.45, C:0.27, G:0.03, T:0.24
Consensus pattern (11 bp):
CATCATAAATC
Found at i:272438 original size:66 final size:66
Alignment explanation
Indices: 272324--272720 Score: 647
Period size: 66 Copynumber: 6.0 Consensus size: 66
272314 AAACAAATTG
* *
272324 ATAAACCTTTGAGATTGTTTCTCGTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTC-TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
272389 AC
65 AC
*
272391 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGAAAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
272456 C
66 C
* * *
272457 ATAAACCTTTGAGTTTGTTTCTCTTGAAAGAAA-TTT-TCCCTCTTGAGACAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
*
272520 T
66 C
272521 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
272586 C
66 C
*
272587 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACATTTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
272652 AC
65 AC
* * *
272654 ATAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCT-TGCTTGAGACAATTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCT-CTTGAGACAGTTTCTCTTGAA
272718 AC
65 AC
272720 A
1 A
272721 AATTATCTCT
Statistics
Matches: 311, Mismatches: 15, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
64 56 0.18
65 7 0.02
66 162 0.52
67 86 0.28
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (66 bp):
ATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
C
Found at i:272447 original size:36 final size:36
Alignment explanation
Indices: 272332--272724 Score: 232
Period size: 30 Copynumber: 11.8 Consensus size: 36
272322 TGATAAACCT
* *
272332 TTGAGATTGTTTCTCGTTGAAACAAATTTTGTCTCGC
1 TTGAGATAGTTTCTC-TTGAAACAAATTTTGTCTCTC
*
272369 TTGAGATAGTTTCTCTTGAAACATAA-----AC-CT-
1 TTGAGATAGTTTCTCTTGAAACA-AATTTTGTCTCTC
*
272399 TTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTC
1 TTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCTC
* *
272435 TTGAGAAAGTTTCTCTTGAAACATAA-----AC-CT-
1 TTGAGATAGTTTCTCTTGAAACA-AATTTTGTCTCTC
* * * *
272465 TTGAGTTTGTTTCTCTTGAAAGAAA-TTT-TCCCTC
1 TTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCTC
* * *
272499 TTGAGACAGTTTCTCTTGAAATATAA-----AC-CT-
1 TTGAGATAGTTTCTCTTGAAACA-AATTTTGTCTCTC
*
272529 TTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTC
1 TTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCTC
* *
272565 TTGAGACAGTTTCTCTTGAAACATAA-----AC-CT-
1 TTGAGATAGTTTCTCTTGAAACA-AATTTTGTCTCTC
*
272595 TTGAGATTGTTTCTCTTGAAACAAAATTTTGTCTCTC
1 TTGAGATAGTTTCTCTTGAAAC-AAATTTTGTCTCTC
* * *
272632 TTGAGACATTTTCTCTTGAAACATAA------ATCT-
1 TTGAGATAGTTTCTCTTGAAACA-AATTTTGTCTCTC
* *
272662 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCT-TGC
1 TTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCT-C
* *
272698 TTGAGACAATTTCTCTTGAAACAAATT
1 TTGAGATAGTTTCTCTTGAAACAAATT
272725 ATCTCTAAAG
Statistics
Matches: 275, Mismatches: 41, Indels: 81
0.69 0.10 0.20
Matches are distributed among these distances:
29 8 0.03
30 102 0.37
31 11 0.04
32 5 0.02
33 2 0.01
34 22 0.08
35 8 0.03
36 76 0.28
37 41 0.15
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (36 bp):
TTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCTC
Found at i:272525 original size:130 final size:132
Alignment explanation
Indices: 272324--272720 Score: 631
Period size: 130 Copynumber: 3.0 Consensus size: 132
272314 AAACAAATTG
* * *
272324 ATAAACCTTTGAGATTGTTTCTCGTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTC-TTGAAAAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
272389 ACATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGAAAGTTTCTCTTGA
65 ACATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGAAAGTTTCTCTTGA
272454 AAC
130 AAC
* * *
272457 ATAAACCTTTGAGTTTGTTTCTCTTGAAAGAAA-TTT-TCCCTCTTGAGACAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAAAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
* *
272520 TATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
66 CATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGAAAGTTTCTCTTGAA
272585 AC
131 AC
*
272587 ATAAACCTTTGAGATTGTTTCTCTTGAAACAAAATTTTGTCTCTCTTGAGACATTTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTTGAAA-AAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAA
* *
272652 ACATAAATCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCT-TGCTTGAGACAA-TTTCTCTT
65 ACATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCT-CTTGAGA-AAGTTTCTCTT
272715 GAAAC
128 GAAAC
272720 A
1 A
272721 AATTATCTCT
Statistics
Matches: 244, Mismatches: 15, Indels: 10
0.91 0.06 0.04
Matches are distributed among these distances:
130 117 0.48
131 6 0.02
132 13 0.05
133 107 0.44
134 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (132 bp):
ATAAACCTTTGAGATTGTTTCTCTTGAAAAAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
CATAAACCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGAAAGTTTCTCTTGAA
AC
Found at i:277773 original size:14 final size:15
Alignment explanation
Indices: 277743--277772 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
277733 CACATTTATA
277743 TATTTTAAAATTTTT
1 TATTTTAAAATTTTT
277758 TATTTTAAAATTTTT
1 TATTTTAAAATTTTT
277773 AAAATAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTAAAATTTTT
Found at i:278724 original size:26 final size:25
Alignment explanation
Indices: 278678--278729 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 25
278668 CTCTAAATTT
*
278678 TTTTATAAGTTTATTGTTATTAAAA
1 TTTTATAAGTTTATTGCTATTAAAA
278703 TTTTATAAGTTTTATCT-CTATTAAAA
1 TTTTATAAG-TTTAT-TGCTATTAAAA
278729 T
1 T
278730 CTTACGCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 9 0.38
26 14 0.58
27 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (25 bp):
TTTTATAAGTTTATTGCTATTAAAA
Found at i:279681 original size:134 final size:136
Alignment explanation
Indices: 279513--279774 Score: 449
Period size: 134 Copynumber: 1.9 Consensus size: 136
279503 AATATTAGAG
279513 ATCTAAATTGATTTAAAAAATTTAAATAACTAAATATAAAAATGTGTAATTTATATA-TTTTCTG
1 ATCTAAATTGATTTAAAAAATTTAAATAACTAAATATAAAAATGTGTAATTTATATATTTTTCTG
*
279577 TATTAAATTAAAAATATATAAATTTGCTACAAGAAATTCTATTGATAATAGATCGAATATATATA
66 TATTAAATTAAAAATATATAAATTTGCTACAA-AAACTCTATTGATAATAGATCGAATATATATA
279642 TATATAT
130 TATATAT
*
279649 ATCTAAATTGA-TTAAAAAA-TTAAATAATTAAATATAAAAATGTGTAATTTATATATTTTTCTG
1 ATCTAAATTGATTTAAAAAATTTAAATAACTAAATATAAAAATGTGTAATTTATATATTTTTCTG
* * *
279712 TATTAAATTAAAATTATATAAATTTGCTCCAAAAACTCTATTGATAGTAGATCGAATATATAT
66 TATTAAATTAAAAATATATAAATTTGCTACAAAAACTCTATTGATAATAGATCGAATATATAT
279775 GTCCATATTT
Statistics
Matches: 120, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
134 64 0.53
135 45 0.38
136 11 0.09
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.40
Consensus pattern (136 bp):
ATCTAAATTGATTTAAAAAATTTAAATAACTAAATATAAAAATGTGTAATTTATATATTTTTCTG
TATTAAATTAAAAATATATAAATTTGCTACAAAAACTCTATTGATAATAGATCGAATATATATAT
ATATAT
Found at i:282259 original size:22 final size:22
Alignment explanation
Indices: 282227--282269 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
282217 TAGCCCTCAC
*
282227 TCTATTCTACAACATCTCTATT
1 TCTATTATACAACATCTCTATT
* *
282249 TCTATTATACAATATTTCTAT
1 TCTATTATACAACATCTCTAT
282270 CTTTACTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.49
Consensus pattern (22 bp):
TCTATTATACAACATCTCTATT
Found at i:282363 original size:16 final size:14
Alignment explanation
Indices: 282341--282377 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 14
282331 TTTTATTTTA
282341 TTTATAATATTTAAT
1 TTTATAATA-TTAAT
282356 TATTATAATATTAAT
1 T-TTATAATATTAAT
282371 TTTATAA
1 TTTATAA
282378 ATATAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 7 0.33
16 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATAATATTAAT
Found at i:282614 original size:15 final size:15
Alignment explanation
Indices: 282594--282622 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
282584 GTATCAAGTT
282594 GAGTAAAATTTGACC
1 GAGTAAAATTTGACC
282609 GAGTAAAATTTGAC
1 GAGTAAAATTTGAC
282623 TTTTGACTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (15 bp):
GAGTAAAATTTGACC
Found at i:283426 original size:14 final size:14
Alignment explanation
Indices: 283393--283431 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
283383 AAACAAATAA
*
283393 GAATAAAAGAACAT
1 GAATAAATGAACAT
283407 GAATAAATGAACAT
1 GAATAAATGAACAT
283421 -ATATAAATGAA
1 GA-ATAAATGAA
283432 TTATTGAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 1 0.04
14 22 0.96
ACGTcount: A:0.62, C:0.05, G:0.13, T:0.21
Consensus pattern (14 bp):
GAATAAATGAACAT
Found at i:288459 original size:21 final size:21
Alignment explanation
Indices: 288435--288476 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
288425 CAGGTTTCTT
*
288435 GGCATTTGTTCGGTCTTTGAA
1 GGCATTTGTTCAGTCTTTGAA
288456 GGCATTTGTTCAGTCTTTGAA
1 GGCATTTGTTCAGTCTTTGAA
288477 AGTGAACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.43
Consensus pattern (21 bp):
GGCATTTGTTCAGTCTTTGAA
Found at i:289059 original size:73 final size:75
Alignment explanation
Indices: 288974--289122 Score: 257
Period size: 73 Copynumber: 2.0 Consensus size: 75
288964 CAAATAATTT
*
288974 AGTTTTTTGACTCGACTCAATTGAACGCTCACCTTCAA-T-TATATATATATATATATATAGATA
1 AGTTTTTTGACTCGACTCAATTGAACGCTCACCTCCAATTATATATATATATATATATATAGATA
289037 CACACATGAC
66 CACACATGAC
* *
289047 AGTTTTTTGACTCGACTTAATTGAATGCTCACCTCCAATTATATATATATATATATATATAGATA
1 AGTTTTTTGACTCGACTCAATTGAACGCTCACCTCCAATTATATATATATATATATATATAGATA
289112 CACACATGAC
66 CACACATGAC
289122 A
1 A
289123 CTCTATTGCA
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
73 35 0.49
74 1 0.01
75 35 0.49
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (75 bp):
AGTTTTTTGACTCGACTCAATTGAACGCTCACCTCCAATTATATATATATATATATATATAGATA
CACACATGAC
Found at i:290060 original size:20 final size:20
Alignment explanation
Indices: 290019--290060 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
290009 GATAAAAAAA
* *
290019 AAACAACGACAAAAAGCTGT
1 AAACAACGACAAAAACCCGT
290039 AAACAACGACAAAAACCCGT
1 AAACAACGACAAAAACCCGT
290059 AA
1 AA
290061 GCTACCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.57, C:0.24, G:0.12, T:0.07
Consensus pattern (20 bp):
AAACAACGACAAAAACCCGT
Found at i:292346 original size:32 final size:31
Alignment explanation
Indices: 292273--292376 Score: 93
Period size: 32 Copynumber: 3.3 Consensus size: 31
292263 TATCATACGA
* * *
292273 TTGATTTTTGGGTCGGATTAATATCAGATCAG
1 TTGATTTTT-GATCGGGTCAATATCAGATCAG
*
292305 TT-ACATTTTGATTCGGGTCAATATCAGATCAG
1 TTGA-TTTTTGA-TCGGGTCAATATCAGATCAG
** * *
292337 TTGATTTTTGGATCAAGTCAATACCAGATTAG
1 TTGATTTTT-GATCGGGTCAATATCAGATCAG
292369 TTGATTTT
1 TTGATTTT
292377 CAGTTTGTGT
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
31 2 0.03
32 54 0.92
33 3 0.05
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (31 bp):
TTGATTTTTGATCGGGTCAATATCAGATCAG
Found at i:293598 original size:20 final size:21
Alignment explanation
Indices: 293556--293598 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
293546 CAAAATATCA
*
293556 TTCATGTTAAACATCGTATATG
1 TTCATGATAAACATCG-ATATG
293578 TTCATGATAAACATC-ATATG
1 TTCATGATAAACATCGATATG
293598 T
1 T
293599 AACGATAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (21 bp):
TTCATGATAAACATCGATATG
Found at i:295089 original size:23 final size:23
Alignment explanation
Indices: 295056--295107 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
295046 TTATGATTAT
295056 ATTCAAACATGAAATCAACATCG
1 ATTCAAACATGAAATCAACATCG
* * *
295079 ATTCAAGCATGAAATCATCATCT
1 ATTCAAACATGAAATCAACATCG
295102 ATTCAA
1 ATTCAA
295108 CCTTATACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (23 bp):
ATTCAAACATGAAATCAACATCG
Found at i:299005 original size:23 final size:23
Alignment explanation
Indices: 298979--299047 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
298969 CACCACAACT
*
298979 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
299002 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
299025 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
299048 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:299234 original size:103 final size:103
Alignment explanation
Indices: 299063--299278 Score: 387
Period size: 103 Copynumber: 2.1 Consensus size: 103
299053 TAATGTCCAT
* *
299063 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
299128 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
299166 AAGGACCACATATCATTCCTTAAGAATTATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
299231 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
299269 AAAGACCACA
1 AAGGACCACA
299279 CAGACCCTCG
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:304214 original size:23 final size:23
Alignment explanation
Indices: 304188--304256 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
304178 CACCACAGCT
*
304188 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
304211 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
304234 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
304257 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:304443 original size:103 final size:103
Alignment explanation
Indices: 304272--304489 Score: 418
Period size: 103 Copynumber: 2.1 Consensus size: 103
304262 TAATGTCCAT
* *
304272 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
304337 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
304375 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
304440 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
304478 AAGGACCACATA
1 AAGGACCACATA
304490 GACCCTCGAC
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:308122 original size:20 final size:20
Alignment explanation
Indices: 308086--308128 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
308076 TTTTCTCTTG
* *
308086 AAAGCAAAATTGGATTTTGA
1 AAAGCAAAATTGAATTTAGA
308106 AAAGCAAAA-TGAAATTTAGA
1 AAAGCAAAATTG-AATTTAGA
308126 AAA
1 AAA
308129 ATGATTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.56, C:0.05, G:0.16, T:0.23
Consensus pattern (20 bp):
AAAGCAAAATTGAATTTAGA
Found at i:311008 original size:2 final size:2
Alignment explanation
Indices: 311003--311027 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
310993 ATATATATAT
311003 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
311028 TATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:312490 original size:20 final size:20
Alignment explanation
Indices: 312462--312504 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
312452 TTTTCTCTTG
*
312462 AAAGAAAAATTG-GATTTTGA
1 AAAGAAAAA-TGAAATTTTGA
*
312482 AAAGCAAAATGAAATTTTGA
1 AAAGAAAAATGAAATTTTGA
312502 AAA
1 AAA
312505 ATGATTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.56, C:0.02, G:0.16, T:0.26
Consensus pattern (20 bp):
AAAGAAAAATGAAATTTTGA
Found at i:316039 original size:26 final size:26
Alignment explanation
Indices: 316003--316056 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
315993 ACCGAAGTGC
*
316003 TAATATACATAACGTCGTGCCCACCA
1 TAATACACATAACGTCGTGCCCACCA
* *
316029 TAATACACATAAGGTCGTGCCCATCA
1 TAATACACATAACGTCGTGCCCACCA
316055 TA
1 TA
316057 TGCGCTTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (26 bp):
TAATACACATAACGTCGTGCCCACCA
Found at i:318924 original size:12 final size:13
Alignment explanation
Indices: 318897--318921 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
318887 AAAAATTTAT
318897 TTTCAATCAAAAA
1 TTTCAATCAAAAA
318910 TTTCAATCAAAA
1 TTTCAATCAAAA
318922 TTTAAAATTT
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:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (13 bp):
TTTCAATCAAAAA
Found at i:318960 original size:19 final size:18
Alignment explanation
Indices: 318906--318967 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
318896 TTTTCAATCA
*
318906 AAAATTTCAATCAAAATTT
1 AAAATTT-AATTAAAATTT
318925 AAAATTTAATTATAAATTT
1 AAAATTTAATTA-AAATTT
* *
318944 AATATTTTTATTAAAATTTT
1 AA-AATTTAATTAAAA-TTT
318964 AAAA
1 AAAA
318968 AAATACATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 4 0.11
19 19 0.53
20 13 0.36
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAATTTAATTAAAATTT
Found at i:319144 original size:33 final size:33
Alignment explanation
Indices: 319083--319159 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 33
319073 TCGAATTAGA
319083 TCGGGTTAAA-TTCAGTTCAGATTGCTTTCAGT
1 TCGGGTTAAATTTCAGTTCAGATTGCTTTCAGT
* * **
319115 TTGGGTTAAATTTCGGTTTGGATTGCTTTCAGT
1 TCGGGTTAAATTTCAGTTCAGATTGCTTTCAGT
*
319148 TCGGGTCAAATT
1 TCGGGTTAAATT
319160 GGATATGGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
32 9 0.24
33 29 0.76
ACGTcount: A:0.19, C:0.13, G:0.25, T:0.43
Consensus pattern (33 bp):
TCGGGTTAAATTTCAGTTCAGATTGCTTTCAGT
Found at i:321196 original size:7 final size:7
Alignment explanation
Indices: 321184--321208 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
321174 GTTTTACTTG
321184 AATTTTA
1 AATTTTA
321191 AATTTTA
1 AATTTTA
321198 AATTTTA
1 AATTTTA
321205 AATT
1 AATT
321209 AAATTCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:324357 original size:21 final size:21
Alignment explanation
Indices: 324333--324383 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
324323 AATTCAAGAA
324333 ATTTTCTTC-TCTTGAAAAAAT
1 ATTTTCTTCTTCTT-AAAAAAT
* *
324354 ATTTAC-TCTTCTTATAAAAT
1 ATTTTCTTCTTCTTAAAAAAT
324374 ATTCTTCTTC
1 ATT-TTCTTC
324384 CCCCTTAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
20 11 0.46
21 11 0.46
22 2 0.08
ACGTcount: A:0.29, C:0.18, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTTTCTTCTTCTTAAAAAAT
Found at i:341082 original size:10 final size:10
Alignment explanation
Indices: 341067--341093 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
341057 GTTTATTAAT
341067 ATTTGATTGA
1 ATTTGATTGA
341077 ATTTGATTGA
1 ATTTGATTGA
341087 ATTTGAT
1 ATTTGAT
341094 GTTATGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.52
Consensus pattern (10 bp):
ATTTGATTGA
Found at i:344436 original size:6 final size:6
Alignment explanation
Indices: 344425--344460 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
344415 GAATGTAGAA
344425 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG
344461 ATGGATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
TGATGG
Found at i:347077 original size:87 final size:87
Alignment explanation
Indices: 346930--347089 Score: 209
Period size: 87 Copynumber: 1.8 Consensus size: 87
346920 ACACTTGAGA
* * * * *
346930 GGTTGAGTTTTTATACTCTTAATGAATCCATAGCCTAGGATTTAGGTAGTCCTAGTGAGACAGAC
1 GGTTGAGTTTTTACACTCTTAATGAATCCATAGCCCAAGATTTAGGTAGCCCTAGTGAGAC-GAA
346995 TTGATGAATACATTGATTTATAT
65 TTGATGAATACATTGATTTATAT
* *
347018 GGTTGAG-TTTTACACTCTTAATGAA-CTCATAGCCCAAG-TTTGTGGTGGCCCTAGTGAGACGA
1 GGTTGAGTTTTTACACTCTTAATGAATC-CATAGCCCAAGATTT-AGGTAGCCCTAGTGAGACGA
347080 ATTGATGAAT
64 ATTGATGAAT
347090 TCACCAAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
86 15 0.24
87 41 0.65
88 7 0.11
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (87 bp):
GGTTGAGTTTTTACACTCTTAATGAATCCATAGCCCAAGATTTAGGTAGCCCTAGTGAGACGAAT
TGATGAATACATTGATTTATAT
Found at i:350808 original size:152 final size:152
Alignment explanation
Indices: 350533--350842 Score: 538
Period size: 152 Copynumber: 2.0 Consensus size: 152
350523 AATTATTAAT
350533 ATAAGAGAACTAATCAAGGATCTTAATAAGTAAAAGATCACCAGATAATCAAATAAATATTAACT
1 ATAAGAGAACTAATCAAGGATCTTAATAAGTAAAAGATCACCAGATAATCAAATAAATATTAACT
350598 AAAGAAACAACATCAAATCTAATATAAAAAAGAGAATAACACACTGCAAGTGCAG-AAAAACATC
66 AAAGAAACAACATCAAATCTAATATAAAAAAGAGAATAACACACTGCAAGTGCAGAAAAAACATC
350662 GATAATTTTCATTTAAGAGATG
131 GATAATTTTCATTTAAGAGATG
*
350684 ATAAGAGAACTAATTCAAGGATCTTAATAAGTAAATGATCACCAAGATAATC-AAT-AATATTAA
1 ATAAGAGAACTAA-TCAAGGATCTTAATAAGTAAAAGATCACC-AGATAATCAAATAAATATTAA
350747 CTAAAGAAACAACATCAAATCTAATATTAAAAAATGAGAAT-ACACACTGCAAGTGCAGAAAAAA
64 CTAAAGAAACAACATCAAATCTAATA-TAAAAAA-GAGAATAACACACTGCAAGTGCAGAAAAAA
350811 CATCGATAATTTTCATTTAAGAGATG
127 CATCGATAATTTTCATTTAAGAGATG
*
350837 AGAAGA
1 ATAAGA
350843 CTTGTTAAAA
Statistics
Matches: 152, Mismatches: 2, Indels: 8
0.94 0.01 0.05
Matches are distributed among these distances:
151 47 0.31
152 55 0.36
153 50 0.33
ACGTcount: A:0.52, C:0.13, G:0.12, T:0.23
Consensus pattern (152 bp):
ATAAGAGAACTAATCAAGGATCTTAATAAGTAAAAGATCACCAGATAATCAAATAAATATTAACT
AAAGAAACAACATCAAATCTAATATAAAAAAGAGAATAACACACTGCAAGTGCAGAAAAAACATC
GATAATTTTCATTTAAGAGATG
Found at i:353788 original size:48 final size:48
Alignment explanation
Indices: 353731--353824 Score: 170
Period size: 48 Copynumber: 2.0 Consensus size: 48
353721 TTCATGTAAA
*
353731 AAAAAAAAGTTAGAAATTGTCTAGCTAACACTTGAGATTGGTATGATT
1 AAAAAAAAGTTAGAAATTGTCTAACTAACACTTGAGATTGGTATGATT
*
353779 AAAACAAAGTTAGAAATTGTCTAACTAACACTTGAGATTGGTATGA
1 AAAAAAAAGTTAGAAATTGTCTAACTAACACTTGAGATTGGTATGA
353825 CGTCTAGACC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.43, C:0.10, G:0.18, T:0.30
Consensus pattern (48 bp):
AAAAAAAAGTTAGAAATTGTCTAACTAACACTTGAGATTGGTATGATT
Found at i:354071 original size:27 final size:27
Alignment explanation
Indices: 354033--354101 Score: 122
Period size: 26 Copynumber: 2.6 Consensus size: 27
354023 AGGATCTACT
*
354033 TACACGATGTAAAATTCTTTAGTTTTA
1 TACACAATGTAAAATTCTTTAGTTTTA
354060 TACACAATGT-AAATTCTTTAGTTTTA
1 TACACAATGTAAAATTCTTTAGTTTTA
354086 TACACAATGTAAAATT
1 TACACAATGTAAAATT
354102 GTTGATGAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 26 0.65
27 14 0.35
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.42
Consensus pattern (27 bp):
TACACAATGTAAAATTCTTTAGTTTTA
Found at i:356891 original size:13 final size:13
Alignment explanation
Indices: 356869--356906 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
356859 AATTAACACC
356869 TTTTGCATTTGCA
1 TTTTGCATTTGCA
*
356882 TTTTGTATTTGCA
1 TTTTGCATTTGCA
356895 -TTTGCA-TTGCA
1 TTTTGCATTTGCA
356906 T
1 T
356907 GTATTTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 5 0.23
12 5 0.23
13 12 0.55
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.55
Consensus pattern (13 bp):
TTTTGCATTTGCA
Found at i:357079 original size:13 final size:13
Alignment explanation
Indices: 357057--357086 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
357047 TGAGAAATCA
*
357057 CAAGATCAGTTTG
1 CAAGAGCAGTTTG
357070 CAAGAGCAGTTTG
1 CAAGAGCAGTTTG
357083 CAAG
1 CAAG
357087 GCGCATCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (13 bp):
CAAGAGCAGTTTG
Found at i:362595 original size:51 final size:51
Alignment explanation
Indices: 362536--364525 Score: 2021
Period size: 51 Copynumber: 38.2 Consensus size: 51
362526 AGCTAAGAAA
362536 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* * *
362587 ATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACTCGTGTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* * * * *
362638 TTATTGGAGTT-C-TATTTCCT-GAAGAAAGAGGGAGCGAA-CCGTTTGAAG
1 ATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAG
* * *
362686 AAGTGTCCGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCG-ACCCGTTTGAAGAAG
1 -A-TGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT---GAAG
* *
362741 ATGTTCGAGTTCCA-ACTCCCTAGAG-AAGAGGGAGC-AAACCGTTTGAAT
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* *
362789 ATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTGTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* * * ** * *
362840 TTATTGGAGTTATATACTTCCT-GAAGAAAAAGGGAGCGAACCCGTTTGAAG
1 ATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAG
* * *
362891 ATGTCCGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTTGAAGAAG
1 ATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT---GAAG
*
362945 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTAAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* *
362996 ATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTGTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* * * * * *
363047 TTATTGGAGTTCTATACTTCCT-GAAGAAAGAGGGAGAGAACCCGTTTGAAGAAG
1 ATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT---GAAG
* * * *
363101 ATGTCCGAGTTCTATACTTCCT-GAAGAAAGAGGGAGTGAACCCGTTTGAAGAAG
1 ATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT---GAAG
*
363155 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
** * *
363206 ATGTTCGAGTTCCATACTCTTTAGAGAAAAAGGGAGCGAACCCGTGTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* * * * *
363257 TTATTGGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTTGAAGAAG
1 ATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT---GAAG
* * *
363311 ATGTTCGAGTTCTATACTTCCT-GAAGAAAGAGGGAGTGAACCCGTTTGAAGAAG
1 ATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT---GAAG
* *
363365 ATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCCGTTTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
*
363416 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCCGTTTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* * * *
363467 ATGTTCGAGTTCCATACTCCTTAGAGAAAAAGGGAGCGAACCCATGTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* * * * * **
363518 TTATTGGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCAATTGAAG
1 ATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAG
* * * *
363569 AAGATGTCTGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCATTTGAAGAAG
1 ATG-T-TC-GAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT---GAAG
*
363626 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTTTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* *
363677 ATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTGTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* * * * * *
363728 TTATTGGAGTTCTATACTTCCT-GAAGAAATAGGGAGCGAACCCGTTTGAAGAAG
1 ATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT---GAAG
* * * *
363782 ATGTCCGAGTTCTATACTTCCT-GAAGAAAGAGAGAGCGAACCCGTTTGAAGAAG
1 ATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT---GAAG
*
363836 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTAAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* * *
363887 ATGTTCGAGTACCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTGTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* * * * * *
363938 TTATTGGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACTCGTTTGAAG
1 ATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAG
* * * * *
363989 AAGATGTCTAAGTTCTATACTTCCT-GAAGAAAGAGGGAGTGAACCCGTTTGAAGAAG
1 ATG-T-TC-GAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT---GAAG
364046 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* * *
364097 ATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGTGAACCCGTGTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* * * * *
364148 TTATTGGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTTGAAGAAG
1 ATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT---GAAG
* * ** *
364202 ATGTCCAAGTTTTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTTGAAGAAG
1 ATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT---GAAG
*
364256 ATGTACGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
*
364307 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCCGTTTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* * * **
364358 ATGTTCGAGTTCCATACTCCTTAGAGAAAAAGGGAGTGAACCCGCGTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* * * * * * * **
364409 TTATTGGAGTTCTATACTTCCT-GAAGAAAGAGAGAGCGAACACGTAAGAAGAAG
1 ATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGT---TTGAAG
* * * * * **
364463 ATTTTTGAGTTCTATACTTCCTATAGAAAGAGGGAGCGAATTCGTTTGAAG
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
* *
364514 ATTTTTGAGTTC
1 ATGTTCGAGTTC
364526 TTTATTCTCT
Statistics
Matches: 1669, Mismatches: 210, Indels: 120
0.83 0.11 0.06
Matches are distributed among these distances:
48 26 0.02
49 32 0.02
50 25 0.01
51 896 0.54
52 39 0.02
53 14 0.01
54 608 0.36
55 15 0.01
56 2 0.00
57 12 0.01
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.24
Consensus pattern (51 bp):
ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAG
Found at i:363191 original size:210 final size:209
Alignment explanation
Indices: 362530--364525 Score: 2383
Period size: 210 Copynumber: 9.6 Consensus size: 209
362520 TAGTGAAGCT
* *
362530 AAGAAAATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGA
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTAAAGATGTTCGA
* * * * * * *
362595 GTTCCATACTCCCTAGAGAAAAAGGGAGCGAACTCGTGTGAAGTTATTGGAGTT-C-TATTTCCT
66 GTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTTCCT
*
362658 -GAAGAAAGAGGGAGCGAA-CCGTTTGAAGAAG-TGTCCGAGTTCTATACTTCCTGAAGAAAGAG
131 AG-AGAAAAAGGGAGCGAACCCGTTTGAAGAAGATGT-CGAGTTCTATACTTCCTGAAGAAAGAG
362720 GGAGCG-ACCCGTTTG
194 GGAGCGAACCCGTTTG
* * *
362735 AAGAAGATGTTCGAGTTCCA-ACTCCCTAGAG-AAGAGGGAGC-AAACCGTTTGAATATGTTCGA
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTAAAGATGTTCGA
* * * * * **
362797 GTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTATATACTTCCT
66 GTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTTCCT
362862 -GAAGAAAAAGGGAGCGAACCCGTTT---GAAGATGTCCGAGTTCTATACTTCCTGAAGAAAGAG
131 AG-AGAAAAAGGGAGCGAACCCGTTTGAAGAAGATGT-CGAGTTCTATACTTCCTGAAGAAAGAG
362923 GGAGCGAACCCGTTTG
194 GGAGCGAACCCGTTTG
362939 AAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTAAAGATGTTCGA
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTAAAGATGTTCGA
* * * * * *
363004 GTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTATACTTCCT
66 GTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTTCCT
* *
363069 -GAAGAAAGAGGGAGAGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTTCCTGAAGAAAGAG
131 AG-AGAAAAAGGGAGCGAACCCGTTTGAAGAAGATGT-CGAGTTCTATACTTCCTGAAGAAAGAG
*
363133 GGAGTGAACCCGTTTG
194 GGAGCGAACCCGTTTG
* *
363149 AAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTTGAAGATGTTCGA
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTAAAGATGTTCGA
** * * * * * *
363214 GTTCCATACTCTTTAGAGAAAAAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTATACTTCCT
66 GTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTTCCT
*
363279 -GAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCTATACTTCCTGAAGAAAGAG
131 AG-AGAAAAAGGGAGCGAACCCGTTTGAAGAAGATG-TCGAGTTCTATACTTCCTGAAGAAAGAG
*
363343 GGAGTGAACCCGTTTG
194 GGAGCGAACCCGTTTG
* * *
363359 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCCGTTTGAAGATGTTCGA
1 AAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTAAAGATGTTCGA
*
363424 GTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCCGTTTGAAGATGTTCGAGTTCCATAC-TCCT
66 GTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTTCC-
* * ** *
363488 TAGAGAAAAAGGGAGCGAACCCATGTGAAG-TTAT-TGGAGTTCTATACTTCCTGAAGAAAGAGG
130 TAGAGAAAAAGGGAGCGAACCCGTTTGAAGAAGATGTCGAGTTCTATACTTCCTGAAGAAAGAGG
**
363551 GAGCGAACCCAATTG
195 GAGCGAACCCGTTTG
* * *
363566 AAGAAGATG-TCTGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCATTTGAAGAAGATG
1 AAGAAGATGTTC-GAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT--A-AAGATG
*
363629 TTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTTTGAAGATGTTCGAGTTCCATAC
61 TTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATAC
* * ** *
363694 TCCCTAGAGAAAAAGGGAGCGAACCCGTGTGAAG-TTAT-TGGAGTTCTATACTTCCTGAAGAAA
126 TTCCTAGAGAAAAAGGGAGCGAACCCGTTTGAAGAAGATGTCGAGTTCTATACTTCCTGAAGAAA
*
363757 TAGGGAGCGAACCCGTTTG
191 GAGGGAGCGAACCCGTTTG
* * * *
363776 AAGAAGATGTCCGAGTTCTATACTTCCT-GAAGAAAGAGAGAGCGAACCCGTTTGAAGAAGATGT
1 AAGAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT--A-AAGATGT
* *
363840 TCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTAAAGATGTTCGAGTACCATACT
62 TCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACT
* * ** *
363905 CCCTAGAGAAAAAGGGAGCGAACCCGTGTGAAG-TTAT-TGGAGTTCTATACTTCCTGAAGAAAG
127 TCCTAGAGAAAAAGGGAGCGAACCCGTTTGAAGAAGATGTCGAGTTCTATACTTCCTGAAGAAAG
*
363968 AGGGAGCGAACTCGTTTG
192 AGGGAGCGAACCCGTTTG
* * * *
363986 AAGAAGATG-TCTAAGTTCTATACTTCCT-GAAGAAAGAGGGAGTGAACCCGTTTGAAGAAGATG
1 AAGAAGATGTTC-GAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT--A-AAGATG
364049 TTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATAC
61 TTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATAC
* * * ** *
364114 TCCCTAGAGAAAAAGGGAGTGAACCCGTGTGAAG-TTAT-TGGAGTTCTATACTTCCTGAAGAAA
126 TTCCTAGAGAAAAAGGGAGCGAACCCGTTTGAAGAAGATGTCGAGTTCTATACTTCCTGAAGAAA
364177 GAGGGAGCGAACCCGTTTG
191 GAGGGAGCGAACCCGTTTG
* * ** *
364196 AAGAAGATGTCCAAGTTTTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGT
1 AAGAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTT--A-AAGATGT
*
364260 ACGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACT
62 TCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACT
* * * * * *
364325 CCCTAGAGAAAGAGGGAGCAAACCCGTTTGAAGATG-T-TCGAGTTCCATAC-TCCTTAGAGAAA
127 TCCTAGAGAAAAAGGGAGCGAACCCGTTTGAAGAAGATGTCGAGTTCTATACTTCCTGA-AGAAA
* * *
364387 AAGGGAGTGAACCCG--CG
191 GAGGGAGCGAACCCGTTTG
* * * * * * * * ** *
364404 -TGAAGTTATTGGAGTTCTATACTTCCT-GAAGAAAGAGAGAGCGAACACGTAAGAAGAAGATTT
1 AAGAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGT--TTA-AAGATGT
* * * * ** * *
364467 TTGAGTTCTATACTTCCTATAGAAAGAGGGAGCGAATTCGTTTGAAGATTTTTGAGTTC
62 TCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTC
364526 TTTATTCTCT
Statistics
Matches: 1659, Mismatches: 105, Indels: 52
0.91 0.06 0.03
Matches are distributed among these distances:
202 76 0.05
203 47 0.03
204 64 0.04
205 36 0.02
206 12 0.01
207 288 0.17
208 1 0.00
209 11 0.01
210 1117 0.67
211 7 0.00
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (209 bp):
AAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTAAAGATGTTCGA
GTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTTCCT
AGAGAAAAAGGGAGCGAACCCGTTTGAAGAAGATGTCGAGTTCTATACTTCCTGAAGAAAGAGGG
AGCGAACCCGTTTG
Found at i:363211 original size:261 final size:258
Alignment explanation
Indices: 362536--364525 Score: 1958
Period size: 261 Copynumber: 7.7 Consensus size: 258
362526 AGCTAAGAAA
* *
362536 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATG-T-TCGAGTTC
1 ATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCGAGTTC
* * * * * * * *
362599 CATACTCCCT-AGAGAAAAAGGGAGCGAACTCGTGT-GAAGTTATTGGAGTTCTAT--TTCCT-G
66 TATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTTGGAAGATGTTCGAGTTCTATACTTCCTAG
* * *
362659 AAGAAAGAGGGAGCGAA-CCGTTTGAAGAAGTGTCCGAGTTCTATACTTCCT-GAAGAAAGAGGG
130 -AGAAAGAGGGAGCGAACCCGTTTGAAG-A-TGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGG
*
362722 AGCG-ACCCGTTTGAAGAAGATGTTCGAGTTCCA-ACTCCCTAGAG-AAGAGGGAGC-AAACCGT
191 AGCGAACCCGTTT--A-AAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
* *
362783 TTGAAT
253 GTGAAG
* * * ** * *
362789 ATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTGTGAAG-TTAT-TGGAGTTA
1 ATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCGAGTTC
* *
362852 TATACTTCCTGAAGAAAAAGGGAGCGAACCCGTTT-GAAGATGTCCGAGTTCTATACTTCCT-GA
66 TATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGGAAGATGTTCGAGTTCTATACTTCCTAG-
362915 AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGA
130 AGAAAGAGGGAGCGAACCCGTTT---GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGA
*
362980 GCGAACCCGTTTAAAGATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTGTGA
192 GCGAACCCGTTTAAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGA
363045 AG
257 AG
* * * * *
363047 TTATTGGAGTTCTATACTTCCT-GAAGAAAGAGGGAGAGAACCCGTTTGAAGAAGATGTCCGAGT
1 ATGTTCGAGTTCCATACTTCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGT-CGAGT
* * *
363111 TCTATACTTCCTGAAGAAAGAGGGAGTGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCC
64 TCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTG--GAAGATGTTCGAGTTCTATACTTCC
* ** *
363176 TAGAGAAAGAGGGAGCGAACTCGTTTGAAGATGTTCGAGTTCCATACTCTTTAGAGAAAAAGGGA
127 TAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGA
* * * * * * *
363241 GCGAACCCGTGTGAAGTTATTGGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTTG
192 GCGAACCCGTTTAAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCG--TG
*
363305 AAGAAG
254 -TGAAG
* *
363311 ATGTTCGAGTTCTATACTTCCT-GAAGAAAGAGGGAGTGAACCCGTTTGAAGAAGATGTCCGAGT
1 ATGTTCGAGTTCCATACTTCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGT-CGAGT
* * * * *
363375 TCCATACTCCCT-AGAGAAAGAGGGAGCAAACCCGTTT-GAAGATGTTCGAGTTCCATACTCCCT
64 TCTATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTTGGAAGATGTTCGAGTTCTATACTTCCT
* * *
363438 AGAGAAAGAGGGAGCAAACCCGTTTGAAGATGTTCGAGTTCCATACTCCTTAGAGAAAAAGGGAG
128 AGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAG
* * * * * * * * *
363503 CGAACCCATGTGAAGTTATTGGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCAAT-TG
193 CGAACCCGTTTAAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCC-GTGTG
363566 AAG
256 AAG
* * *
363569 AAGATGTCTGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCATTTGAAGAAGATGTTCG
1 ATG-T-TC-GAGTTCCATACTTCCTAG-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATG-TCG
* * * * *
363633 AGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCTGTTT-GAAGATGTTCGAGTTCCATACTC
61 AGTTCTATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTTGGAAGATGTTCGAGTTCTATACTT
* * * * * * * *
363696 CCTAGAGAAAAAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTATACTTCCT-GAAGAAATAG
125 CCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAG
* * * *
363760 GGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTTCCT-GAAGAAAGAGAGAGCGAACC
189 GGAGCGAACCCGTTT--A-AAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACC
*
363824 CGTTTGAAGAAG
250 CG--TG-TGAAG
* *
363836 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT--A-AAGATGTTCGAGTA
1 ATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATG-TCGAGTT
* * * * * * *
363898 CCATACTCCCT-AGAGAAAAAGGGAGCGAACCCGTGT-GAAGTTATTGGAGTTCTATACTTCCT-
65 CTATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTTGGAAGATGTTCGAGTTCTATACTTCCTA
* * * * *
363960 GAAGAAAGAGGGAGCGAACTCGTTTGAAGAAGATGTCTAAGTTCTATACTTCCT-GAAGAAAGAG
129 G-AGAAAGAGGGAGCGAACCCGTTTGAAGATG-T-TC-GAGTTCCATACTCCCTAG-AGAAAGAG
*
364024 GGAGTGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCC
189 GGAGCGAACCCGTTT--A-AAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCC
*
364089 GTTTGAAG
251 GTGTGAAG
* * * * ** *
364097 ATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGTGAACCCGTGTGAAG-TTAT-TGGAGTTC
1 ATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCGAGTTC
* * *
364160 TATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCAAGTTTTATACTTCCT-
66 TATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTG--GAAGATGTTCGAGTTCTATACTTCCTA
*
364224 GAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTACGAGTTCCATACTCCCTAGAGAAAGAGG
129 G-AGAAAGAGGGAGCGAACCCGTTT---GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGG
* * *
364289 GAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCAAACCCGTTT
190 GAGCGAACCCGTTTAAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGT
364354 GAAG
255 GAAG
* * ** ** *
364358 ATGTTCGAGTTCCATAC-TCCTTAGAGAAAAAGGGAGTGAACCCGCGTGAAG-TTAT-TGGAGTT
1 ATGTTCGAGTTCCATACTTCC-TAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCGAGTT
* * ** * *
364420 CTATACTTCCTGAAGAAAGAGAGAGCGAACACGTAAGAAGAAGATTTTTGAGTTCTATACTTCCT
65 CTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTG--GAAGATGTTCGAGTTCTATACTTCCT
* ** * *
364485 ATAGAAAGAGGGAGCGAATTCGTTTGAAGATTTTTGAGTTC
128 AGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTC
364526 TTTATTCTCT
Statistics
Matches: 1518, Mismatches: 161, Indels: 111
0.85 0.09 0.06
Matches are distributed among these distances:
252 1 0.00
253 100 0.07
254 1 0.00
255 40 0.03
256 18 0.01
257 42 0.03
258 80 0.05
259 7 0.00
260 9 0.01
261 807 0.53
262 5 0.00
263 7 0.00
264 379 0.25
265 8 0.01
266 2 0.00
267 12 0.01
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.24
Consensus pattern (258 bp):
ATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCGAGTTC
TATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGGAAGATGTTCGAGTTCTATACTTCCTAGA
GAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGA
ACCCGTTTAAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAG
Found at i:363423 original size:471 final size:468
Alignment explanation
Indices: 362536--364514 Score: 2486
Period size: 471 Copynumber: 4.2 Consensus size: 468
362526 AGCTAAGAAA
* * * * *
362536 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCA
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTA
* * * * ** *
362601 TACTCCCT-AGAGAAAAAGGGAGCGAACTCGTGTGAAG-TTAT-T-GGAGTTCTAT--TTCCTGA
66 TACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTTCCTGA
* * *
362660 AGAAAGAGGGAGCGAA-CCGTTTGAAGAAG-TGTCCGAGTTCTATACTTCCT-GAAGAAAGAGGG
130 AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGG
* *
362722 AGCG-ACCCGTTTGAAGAAGATGTTCGAGTTCCA-ACTCCCTAGAG-AAGAGGGAGC-AAACCGT
194 AGCGAACCCGTTT---GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGT
* * * * * * * *
362783 TTGAA-TATGTTCGAGTTCCATACTCCCT-AGAGAAAAAGGGAGCGAACCCG--TG-TGAAGTTA
256 GTGAAGT-TATTCGAGTTCTATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATG
* * * *
362843 TTGGAGTTATATACTTCCTGAAGAAAAAGGGAGCGAACCCGTTTGAAGATGTCCGAGTTCTATAC
319 TTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCCGAGTTCCATAC
* *
362908 TTCCT-GAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGA
384 TCCCTAG-AGAAAGAGGGAGCAAACCCGTTT---GAAGATGTTCGAGTTCCATACTCCCTAGAGA
* * *
362972 AAGAGGGAGCGAACCCGTTTAAAG
445 AAAAGGGAGCGAACCCGTGTGAAG
*
362996 ATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTA
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTA
*
363061 TACTTCCTGAAGAAAGAGGGAGAGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTTCCTGAA
66 TACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTTCCTGAA
*
363126 GAAAGAGGGAGTGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAG
131 GAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAG
* **
363191 CGAACTCGTTTGAAGATGTTCGAGTTCCATACTCTTTAGAGAAAAAGGGAGCGAACCCGTGTGAA
196 CGAACCCGTTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTGTGAA
*
363256 GTTATTGGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGT
261 GTTATTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGT
*
363321 TCTATACTTCCTGAAGAAAGAGGGAGTGAACCCGTTTGAAGAAGATGTCCGAGTTCCATACTCCC
326 TCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTT---GAAGATGTCCGAGTTCCATACTCCC
*
363386 TAGAGAAAGAGGGAGCAAACCCGTTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGA
388 TAGAGAAAGAGGGAGCAAACCCGTTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGA
* *
363451 GCAAACCCGTTTGAAG
453 GCGAACCCGTGTGAAG
* * *
363467 ATGTTCGAGTTCCATACTCCTTAGAGAAAAAGGGAGCGAACCCATGTGAAGTTATTGGAGTTCTA
1 ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTA
** *
363532 TACTTCCTGAAGAAAGAGGGAGCGAACCCAATTGAAGAAGATGTCTGAGTTCTATACTTCCTGAA
66 TACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTTCCTGAA
*
363597 GAAAGAGGGAGCGAACCCATTTGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAG
131 GAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAG
*
363662 CGAACCTGTTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTGTGAA
196 CGAACCCGTTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTGTGAA
* * *
363727 GTTATTGGAGTTCTATACTTCCTGAAGAAATAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGT
261 GTTATTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGT
* *
363792 TCTATACTTCCTGAAGAAAGAGAGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCC
326 TCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTT---GAAGATGTCCGAGTTCCATACTCCC
* * *
363857 TAGAGAAAGAGGGAGCGAACCCGTTTAAAGATGTTCGAGTACCATACTCCCTAGAGAAAAAGGGA
388 TAGAGAAAGAGGGAGCAAACCCGTTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGA
363922 GCGAACCCGTGTGAAG
453 GCGAACCCGTGTGAAG
* * * * * * * ** **
363938 TTATTGGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACTCGTTTGAAGAAGATGTCTAAGT
1 ATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTGTGAAG-TTAT-T-GGAGT
* * * *
364002 TCTATACTTCCTGAAGAAAGAGGGAGTGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCC
62 TCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTTCC
*
364067 T-AGAGAAAGAGGGAGCGAACCCGTTT---GAAGATGTTCGAGTTCCATACTCCCTAGAGAAAAA
127 TGA-AGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGA
* * * * * * * *
364128 GGGAGTGAACCCGTGTGAAGTTATTGGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCG
191 GGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTCCCTAG-AGAAAAAGGGAGCGAACCCG
* ** * *
364192 TTTGAAGAAGATGTCCAAGTTTTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA
255 TGTGAAG-TTAT-T-CGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGA
* * * *
364257 TGTACGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCA
317 TGTTCGAGTTCTATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTTGAAGATGTCCGAGTTCCA
*
364321 TACTCCCTAGAGAAAGAGGGAGCAAACCCGTTTGAAGATGTTCGAGTTCCATACTCCTTAGAGAA
381 TACTCCCTAGAGAAAGAGGGAGCAAACCCGTTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAA
* *
364386 AAAGGGAGTGAACCCGCGTGAAG
446 AAAGGGAGCGAACCCGTGTGAAG
* * * * * * * * *
364409 TTATTGGAGTTCTATACTTCCT-GAAGAAAGAGAGAGCGAACACGTAAGAAGAAGATT-TTTGAG
1 ATGTTCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGT--G-TGAAG-TTATTGGAG
**
364472 TTCTATACTTCCT-ATAGAAAGAGGGAGCGAATTCGTTTGAAGA
61 TTCTATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTTGAAGA
364515 TTTTTGAGTT
Statistics
Matches: 1360, Mismatches: 123, Indels: 61
0.88 0.08 0.04
Matches are distributed among these distances:
460 89 0.07
461 3 0.00
462 1 0.00
463 9 0.01
465 40 0.03
466 22 0.02
467 41 0.03
468 54 0.04
469 2 0.00
470 5 0.00
471 862 0.63
472 5 0.00
473 5 0.00
474 221 0.16
475 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (468 bp):
ATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTGTGAAGTTATTGGAGTTCTA
TACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTTCCTGAA
GAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAG
CGAACCCGTTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTGTGAA
GTTATTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTTCGAGT
TCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTCCGAGTTCCATACTCCCTAG
AGAAAGAGGGAGCAAACCCGTTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCG
AACCCGTGTGAAG
Found at i:364665 original size:109 final size:112
Alignment explanation
Indices: 364531--364770 Score: 353
Period size: 109 Copynumber: 2.2 Consensus size: 112
364521 AGTTCTTTAT
* * * * *
364531 TCTCTGAAG-AATAGGGAACGGACACGATTGTTGAAGATTGTTTGAGTCTTATACTCTCTGAAAG
1 TCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATTGTTCGAGTCTTATACTCTCTAAAAG
*
364595 AATA-G-GG-GCAGACACGATTATTGAAGATTGTTCGAGTCTCATAC
66 AATAGGAGGAGCAAACACGATTATTGAAGATTGTTCGAGTCTCATAC
*
364639 TCTCTGAAGAAATAGGGAGCAGACACGATTATTGGAGATTGTTCGAGTCTTATACTCTCTAAAAG
1 TCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATTGTTCGAGTCTTATACTCTCTAAAAG
* *
364704 AATAGGGAGGAGCAAACACGATTATTGAAGTTTGTTCGAGTCTTATAC
66 AATA-GGAGGAGCAAACACGATTATTGAAGATTGTTCGAGTCTCATAC
*
364752 TCCCTGAAGAAATAGGGAG
1 TCTCTGAAGAAATAGGGAG
364771 TGAACATGTT
Statistics
Matches: 117, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
108 9 0.08
109 53 0.45
111 1 0.01
112 2 0.02
113 52 0.44
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (112 bp):
TCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATTGTTCGAGTCTTATACTCTCTAAAAG
AATAGGAGGAGCAAACACGATTATTGAAGATTGTTCGAGTCTCATAC
Found at i:364682 original size:55 final size:55
Alignment explanation
Indices: 364508--364770 Score: 322
Period size: 54 Copynumber: 4.8 Consensus size: 55
364498 GCGAATTCGT
* * * * *
364508 TTGAAGATT-TTTGAGTTCTT-TATTCTCTGAAG-AATAGGGAACGGACACGATTG
1 TTGAAGATTGTTCGAG-TCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTA
*
364561 TTGAAGATTGTTTGAGTCTTATACTCTCTGAA-AGAATAGGG-GCAGACACGATTA
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGA-AATAGGGAGCAGACACGATTA
*
364615 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTA
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTA
* * *
364670 TTGGAGATTGTTCGAGTCTTATACTCTCT-AAAAGAATAGGGAGGAGCAAACACGATTA
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGA-AATA--G-GGAGCAGACACGATTA
* *
364728 TTGAAGTTTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGAG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAG
364771 TGAACATGTT
Statistics
Matches: 185, Mismatches: 14, Indels: 20
0.84 0.06 0.09
Matches are distributed among these distances:
53 13 0.07
54 66 0.36
55 56 0.30
56 1 0.01
57 1 0.01
58 45 0.24
59 3 0.02
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (55 bp):
TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTA
Found at i:364743 original size:58 final size:55
Alignment explanation
Indices: 364508--364770 Score: 304
Period size: 55 Copynumber: 4.8 Consensus size: 55
364498 GCGAATTCGT
* * * * * *
364508 TTGAAGATT-TTTGAGTTCTT-TATTCTCTGAAG-AATAGGGAACGGACACGATTG
1 TTGAAGATTGTTCGAG-TCTTATACTCTCTAAAGAAATAGGGAGCAGACACGATTA
*
364561 TTGAAGATTGTTTGAGTCTTATACTCTCTGAAAG-AATAGGG-GCAGACACGATTA
1 TTGAAGATTGTTCGAGTCTTATACTCTCT-AAAGAAATAGGGAGCAGACACGATTA
* *
364615 TTGAAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTA
1 TTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAGGGAGCAGACACGATTA
* *
364670 TTGGAGATTGTTCGAGTCTTATACTCTCTAAA-AGAATAGGGAGGAGCAAACACGATTA
1 TTGAAGATTGTTCGAGTCTTATACTCTCTAAAGA-AATA--G-GGAGCAGACACGATTA
* * *
364728 TTGAAGTTTGTTCGAGTCTTATACTCCCTGAAGAAATAGGGAG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAGGGAG
364771 TGAACATGTT
Statistics
Matches: 184, Mismatches: 16, Indels: 18
0.84 0.07 0.08
Matches are distributed among these distances:
53 16 0.09
54 58 0.32
55 60 0.33
56 1 0.01
57 1 0.01
58 47 0.26
59 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (55 bp):
TTGAAGATTGTTCGAGTCTTATACTCTCTAAAGAAATAGGGAGCAGACACGATTA
Found at i:368705 original size:20 final size:18
Alignment explanation
Indices: 368656--368707 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
368646 TCCGATCGAA
368656 TTGGAATT-TTATAAAAG
1 TTGGAATTGTTATAAAAG
*
368673 TTGGAAGGATGTTATAAAATGG
1 TTGGAA--TTGTTATAAAA--G
368695 TTGGAATTGTTAT
1 TTGGAATTGTTAT
368708 TTTAATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
17 6 0.21
19 1 0.04
20 14 0.50
22 7 0.25
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (18 bp):
TTGGAATTGTTATAAAAG
Found at i:370487 original size:40 final size:40
Alignment explanation
Indices: 370443--370564 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
370433 AGGTTTATAA
*
370443 TAATACACTTCGGTGTATATGGTGGGCACGACTTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
370483 TAATACACTTCGGTGTATATGGTGGCCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
370523 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
370563 TA
1 TA
370565 GCACTATGGT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:370767 original size:47 final size:44
Alignment explanation
Indices: 370669--370786 Score: 146
Period size: 47 Copynumber: 2.6 Consensus size: 44
370659 GTAAGCATAC
* *
370669 AAATAAGCTTACGAGCTTTTGGAATAATGGCAAGTATATGGGTA
1 AAATAAGCTTACGAGCTTATGGAATAATGACAAGTATATGGGTA
* * * *
370713 AAATAAGCTTACGAGCTTATGGATTTTAAATGATAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGA--AT-AATGACAAGTATATGGGTA
*
370760 AAATAAGCTTACGAGCTTATGGGATAA
1 AAATAAGCTTACGAGCTTATGGAATAA
370787 ATGGTAAGAG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
44 24 0.38
45 1 0.02
46 1 0.02
47 37 0.59
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.32
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGACAAGTATATGGGTA
Found at i:375050 original size:19 final size:18
Alignment explanation
Indices: 375031--375077 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
375021 TGAAAGCTCA
375031 AAATCATTTTTCAAAATC
1 AAATCATTTTTCAAAATC
*
375049 AAA-CTTTGCTTTCAAAATC
1 AAATCATT--TTTCAAAATC
375068 AAATCATTTT
1 AAATCATTTT
375078 CAACTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 3 0.12
18 5 0.21
19 13 0.54
20 3 0.12
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (18 bp):
AAATCATTTTTCAAAATC
Found at i:378285 original size:2 final size:2
Alignment explanation
Indices: 378278--378315 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
378268 CTTAGACACA
378278 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
378316 TAAATGTCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:380271 original size:13 final size:14
Alignment explanation
Indices: 380253--380282 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
380243 AAAGTCAATT
380253 GTCAACGGTC-ACG
1 GTCAACGGTCAACG
380266 GTCAACGGTCAACG
1 GTCAACGGTCAACG
380280 GTC
1 GTC
380283 GGGTCGGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:380294 original size:17 final size:17
Alignment explanation
Indices: 380272--380329 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
380262 CACGGTCAAC
380272 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
380289 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
380306 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
380323 GGTCAAC
1 GGTCAAC
380330 CTGGTTCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:380299 original size:7 final size:7
Alignment explanation
Indices: 380253--380282 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
380243 AAAGTCAATT
380253 GTCAACG
1 GTCAACG
380260 GTC-ACG
1 GTCAACG
380266 GTCAACG
1 GTCAACG
380273 GTCAACG
1 GTCAACG
380280 GTC
1 GTC
380283 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:380347 original size:19 final size:19
Alignment explanation
Indices: 380323--380390 Score: 93
Period size: 19 Copynumber: 3.5 Consensus size: 19
380313 AGTCGGGTCG
380323 GGTC-AACCTGGTTCAGACT
1 GGTCAAACC-GGTTCAGACT
*
380342 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACT
*
380361 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACT
380381 GGTCAAACCG
1 GGTCAAACCG
380391 ATTTTCCAGC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 27 0.61
20 17 0.39
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACT
Found at i:380361 original size:10 final size:10
Alignment explanation
Indices: 380344--380390 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 10
380334 TTCAGACTGG
380344 TCAAACCGGT
1 TCAAACCGGT
*
380354 TCAGACCGG-
1 TCAAACCGGT
380363 TCAAACCGGT
1 TCAAACCGGT
*
380373 TCAAAACTGG-
1 TC-AAACCGGT
380383 TCAAACCG
1 TCAAACCG
380391 ATTTTCCAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
9 13 0.42
10 12 0.39
11 6 0.19
ACGTcount: A:0.32, C:0.30, G:0.21, T:0.17
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:394440 original size:12 final size:13
Alignment explanation
Indices: 394420--394446 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
394410 TACTATTTTT
394420 TATTTTTTTAAAA
1 TATTTTTTTAAAA
394433 TATTTTTTTAAAA
1 TATTTTTTTAAAA
394446 T
1 T
394447 TATCAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTTTTTTAAAA
Found at i:394624 original size:2 final size:2
Alignment explanation
Indices: 394617--394647 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
394607 AGTAAAACCT
394617 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
394648 GAAATTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:396007 original size:25 final size:25
Alignment explanation
Indices: 395973--396038 Score: 132
Period size: 25 Copynumber: 2.6 Consensus size: 25
395963 AGACAATTGA
395973 ATTCTTTTTATAATGATCTTTCTCG
1 ATTCTTTTTATAATGATCTTTCTCG
395998 ATTCTTTTTATAATGATCTTTCTCG
1 ATTCTTTTTATAATGATCTTTCTCG
396023 ATTCTTTTTATAATGA
1 ATTCTTTTTATAATGA
396039 ATTCTTTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.23, C:0.14, G:0.08, T:0.56
Consensus pattern (25 bp):
ATTCTTTTTATAATGATCTTTCTCG
Found at i:396044 original size:16 final size:16
Alignment explanation
Indices: 396023--396054 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
396013 ATCTTTCTCG
396023 ATTCTTTTTATAATGA
1 ATTCTTTTTATAATGA
396039 ATTCTTTTTATAATGA
1 ATTCTTTTTATAATGA
396055 TCATTCTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (16 bp):
ATTCTTTTTATAATGA
Found at i:401809 original size:51 final size:50
Alignment explanation
Indices: 401709--401836 Score: 134
Period size: 51 Copynumber: 2.5 Consensus size: 50
401699 GTAGCAGTAA
* * ** *
401709 AGCGCGCCCCCTGCCTCGCGCTATATGCTGATTTGGCGCCACGTGGGGTAT
1 AGCGCG-CCCCTGCCCCGCGCTATACGCTGACATGGCGACACGTGGGGTAT
401760 AGCGCGCCCTCTGCCCCGCGCTATACGCTGACATGG-GTTACACGT-GGGTAT
1 AGCGCGCCC-CTGCCCCGCGCTATACGCTGACATGGCG--ACACGTGGGGTAT
**
401811 AGCGCGACCCCTGATCCGCGCTATAC
1 AGCGCG-CCCCTGCCCCGCGCTATAC
401837 ACCACGTAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
50 4 0.06
51 54 0.82
52 8 0.12
ACGTcount: A:0.15, C:0.35, G:0.29, T:0.21
Consensus pattern (50 bp):
AGCGCGCCCCTGCCCCGCGCTATACGCTGACATGGCGACACGTGGGGTAT
Found at i:402109 original size:17 final size:18
Alignment explanation
Indices: 402072--402112 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
402062 ATATTATGTA
*
402072 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
402090 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
402107 TTTACT
1 TTTACT
402113 AATATAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:403820 original size:18 final size:18
Alignment explanation
Indices: 403793--403832 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
403783 ACAGCAGCCA
* *
403793 CCGCAGCCATTTATGATG
1 CCGCAACCATATATGATG
403811 CCGCAACCATATATGATG
1 CCGCAACCATATATGATG
403829 CCGC
1 CCGC
403833 CATCGCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.23
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:404069 original size:9 final size:9
Alignment explanation
Indices: 404055--404079 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
404045 GCGATGTCTG
404055 AGTTTTCCC
1 AGTTTTCCC
404064 AGTTTTCCC
1 AGTTTTCCC
404073 AGTTTTC
1 AGTTTTC
404080 GTAGGTCGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.28, G:0.12, T:0.48
Consensus pattern (9 bp):
AGTTTTCCC
Found at i:404390 original size:26 final size:24
Alignment explanation
Indices: 404319--404390 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 24
404309 TTATATTTGT
404319 ATTTACTTTATTTTGTTTAATTATA
1 ATTTACTTTATTTTGTTTAATT-TA
*
404344 ATTT--TTTATTTT-TTCTCATTTA
1 ATTTACTTTATTTTGTT-TAATTTA
*
404366 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTTAATTT
404391 GTTGGACTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
22 6 0.16
23 12 0.32
24 2 0.05
25 4 0.11
26 12 0.32
27 2 0.05
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.65
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTTAATTTA
Found at i:410428 original size:15 final size:15
Alignment explanation
Indices: 410410--410458 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 15
410400 TATTTTTTAA
410410 AAAAAATTCTAATTT
1 AAAAAATTCTAATTT
**
410425 AAAAAATAATAATTTT
1 AAAAAATTCTAA-TTT
*
410441 TAAAAATTCTAA-TT
1 AAAAAATTCTAATTT
410455 AAAA
1 AAAA
410459 TAGGAATCAC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
14 5 0.19
15 10 0.37
16 12 0.44
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAAAATTCTAATTT
Found at i:410428 original size:16 final size:16
Alignment explanation
Indices: 410409--410458 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
410399 ATATTTTTTA
410409 AAAAAAATTCTAATTT
1 AAAAAAATTCTAATTT
**
410425 -AAAAAATAATAATTT
1 AAAAAAATTCTAATTT
**
410440 TTAAAAATTCTAA-TT
1 AAAAAAATTCTAATTT
410455 AAAA
1 AAAA
410459 TAGGAATCAC
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAAAAATTCTAATTT
Found at i:410852 original size:20 final size:20
Alignment explanation
Indices: 410822--411196 Score: 173
Period size: 20 Copynumber: 18.6 Consensus size: 20
410812 ATAACCAACA
*
410822 AATTT-GCAACACGAACTTC
1 AATTTCGCAACACGAATTTC
*
410841 AATTTCGCAACAC-AGTTTCC
1 AATTTCGCAACACGAATTT-C
*
410861 AAATTCGCAACACGGAATTTC
1 AATTTCGCAACAC-GAATTTC
*
410882 GAA-TTCGCAACTCG-ATTTC
1 -AATTTCGCAACACGAATTTC
*
410901 TGAA-TTCGCAACGCGAATTTGAC
1 --AATTTCGCAACACGAATTT--C
**
410924 AATTTCGCAATGCGAATTTC
1 AATTTCGCAACACGAATTTC
* * *
410944 -TTTTACGCAACGCGATTTTC
1 AATTT-CGCAACACGAATTTC
* * * *
410964 AAATTCGCAACATGAACTCC
1 AATTTCGCAACACGAATTTC
* *
410984 AATTT-GACAACGC-ATTTTCC
1 AATTTCG-CAACACGAATTT-C
*
411004 AAATTCGCAACACGAAATTTC
1 AATTTCGCAACACG-AATTTC
* *
411025 AAATTCGCAACTCG-ATTTC
1 AATTTCGCAACACGAATTTC
* * *
411044 TGGA-TTCGCAACGCGAATCTC
1 --AATTTCGCAACACGAATTTC
**
411065 TTTTTCGCAACACGAATTTC
1 AATTTCGCAACACGAATTTC
**
411085 TTTTTCGCAACAC-AAGTTTC
1 AATTTCGCAACACGAA-TTTC
** * *
411105 CTTTTCGCAACAAGATTTTC
1 AATTTCGCAACACGAATTTC
*
411125 TAA-TTCGCAACACGAATTTT
1 -AATTTCGCAACACGAATTTC
** * * *
411145 GTTTTCGCAACTCCATTTTC
1 AATTTCGCAACACGAATTTC
* *
411165 GAA-TTCGCAACACGACTTTT
1 -AATTTCGCAACACGAATTTC
411185 AATTTCGCAACA
1 AATTTCGCAACA
411197 ACTTTTATTT
Statistics
Matches: 275, Mismatches: 54, Indels: 53
0.72 0.14 0.14
Matches are distributed among these distances:
19 28 0.10
20 182 0.66
21 39 0.14
22 25 0.09
23 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (20 bp):
AATTTCGCAACACGAATTTC
Found at i:411144 original size:143 final size:142
Alignment explanation
Indices: 410820--411144 Score: 359
Period size: 143 Copynumber: 2.3 Consensus size: 142
410810 AAATAACCAA
* * * * * *
410820 CAAATTTGCAACACGAACTTCAATTTCGCAACAC-AGTTTCCAAATTCGCAACACGGAATTTCGA
1 CAAATTCGCAACAAGAACTCCAA-TTCGCAACACGATTTTCCAAATTCGCAACACGAAATTTCAA
* **
410884 ATTCGCAACTCGATTTCTGAATTCGCAACGCGAATTTGACAATTTCGCAATGCGAATTTCTTTTA
65 ATTCGCAACTCGATTTCTGAATTCGCAACGCGAATCT-ACAATTTCGCAACACGAATTTCTTTTA
* * *
410949 CGCAACGCGATTTT
129 CGCAACACAAGTTT
* * *
410963 CAAATTCGCAACATGAACTCCAATTTGACAACGC-ATTTTCCAAATTCGCAACACGAAATTTCAA
1 CAAATTCGCAACAAGAACTCCAATTCG-CAACACGATTTTCCAAATTCGCAACACGAAATTTCAA
* ** *
411027 ATTCGCAACTCGATTTCTGGATTCGCAACGCGAATCT-CTTTTTCGCAACACGAATTTCTTTTTC
65 ATTCGCAACTCGATTTCTGAATTCGCAACGCGAATCTACAATTTCGCAACACGAATTTCTTTTAC
411091 GCAACACAAGTTT
130 GCAACACAAGTTT
*** ** *
411104 CCTTTTCGCAACAAGATTTTCTAATTCGCAACACGAATTTT
1 CAAATTCGCAACAAGA-ACTCCAATTCGCAACACG-ATTTT
411145 GTTTTCGCAA
Statistics
Matches: 151, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
141 49 0.32
142 10 0.07
143 92 0.61
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (142 bp):
CAAATTCGCAACAAGAACTCCAATTCGCAACACGATTTTCCAAATTCGCAACACGAAATTTCAAA
TTCGCAACTCGATTTCTGAATTCGCAACGCGAATCTACAATTTCGCAACACGAATTTCTTTTACG
CAACACAAGTTT
Found at i:411202 original size:18 final size:19
Alignment explanation
Indices: 411168--411216 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
411158 CATTTTCGAA
411168 TTCGCAACACGACTTTTAAT
1 TTCGCAACAC-ACTTTTAAT
*
411188 TTCGCAACA-ACTTTTATT
1 TTCGCAACACACTTTTAAT
*
411206 TTTGCAACACA
1 TTCGCAACACA
411217 AATGTTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 16 0.62
19 1 0.04
20 9 0.35
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (19 bp):
TTCGCAACACACTTTTAAT
Found at i:411961 original size:12 final size:12
Alignment explanation
Indices: 411940--411973 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
411930 ACCACATTTC
*
411940 CAATACCAAACA
1 CAATATCAAACA
411952 CAATATCAAACA
1 CAATATCAAACA
*
411964 CAATCTCAAA
1 CAATATCAAA
411974 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:414450 original size:18 final size:18
Alignment explanation
Indices: 414417--414452 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
414407 AAACAAAAGG
**
414417 AAATCAAAATTGCAATCA
1 AAATCAAAATCCCAATCA
414435 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
414453 CAACTGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:414720 original size:20 final size:20
Alignment explanation
Indices: 414697--414744 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
414687 TCCGATTCGT
* *
414697 AACGCGAAAGTCAAATTCAC
1 AACGCGAAAATAAAATTCAC
* *
414717 AACGCAAAAATAAAATTCGC
1 AACGCGAAAATAAAATTCAC
414737 AACGCGAA
1 AACGCGAA
414745 TTTGATTTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.23, G:0.15, T:0.12
Consensus pattern (20 bp):
AACGCGAAAATAAAATTCAC
Found at i:416299 original size:21 final size:21
Alignment explanation
Indices: 416273--416313 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
416263 AGTATGCCAT
*
416273 GTGGATCCTGAACGGTGGGAA
1 GTGGATCCTGAACGATGGGAA
416294 GTGGATCCTGAACGATGGGA
1 GTGGATCCTGAACGATGGGA
416314 GGGGCCTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.41, T:0.20
Consensus pattern (21 bp):
GTGGATCCTGAACGATGGGAA
Found at i:416358 original size:21 final size:21
Alignment explanation
Indices: 416334--416380 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
416324 GAACGATGAC
*
416334 AGGTGAATCTTAAACAATGGG
1 AGGTGAATCCTAAACAATGGG
* * *
416355 AGGTGGATCCTGAACAATGGT
1 AGGTGAATCCTAAACAATGGG
416376 AGGTG
1 AGGTG
416381 TATCGAGCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.11, G:0.34, T:0.23
Consensus pattern (21 bp):
AGGTGAATCCTAAACAATGGG
Found at i:416774 original size:42 final size:43
Alignment explanation
Indices: 416681--416777 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 43
416671 CATAGAGCAG
416681 ATACCTCATCACGTAAAGAAAATACCTCACCACGTAAAGCACC
1 ATACCTCATCACGTAAAGAAAATACCTCACCACGTAAAGCACC
** ** *
416724 AT-TGTCATCACGTAAA-ACATCTACCTCACTACGTAAAG-ACC
1 ATACCTCATCACGTAAAGA-AAATACCTCACCACGTAAAGCACC
*
416765 CTACCTCATCACG
1 ATACCTCATCACG
416778 CCATGCACCA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
41 5 0.11
42 37 0.84
43 2 0.05
ACGTcount: A:0.37, C:0.33, G:0.09, T:0.21
Consensus pattern (43 bp):
ATACCTCATCACGTAAAGAAAATACCTCACCACGTAAAGCACC
Found at i:416818 original size:21 final size:21
Alignment explanation
Indices: 416682--416823 Score: 87
Period size: 21 Copynumber: 6.8 Consensus size: 21
416672 ATAGAGCAGA
* **
416682 TACCTCATCACGTAAAGAAAA
1 TACCTCATCACGTAAAGCACC
*
416703 TACCTCACCACGTAAAGCACC
1 TACCTCATCACGTAAAGCACC
** * *
416724 -ATTGTCATCACGTAAAACATC
1 TA-CCTCATCACGTAAAGCACC
416745 TACCTCA-CTACGTAAAG-ACCC
1 TACCTCATC-ACGTAAAGCA-CC
** *
416766 TACCTCATCACGCCATGCACC
1 TACCTCATCACGTAAAGCACC
*
416787 ATTA--TCGTCACGTAAAGCACC
1 --TACCTCATCACGTAAAGCACC
*
416808 GACCTCATCACGTAAA
1 TACCTCATCACGTAAA
416824 AAACTGACCT
Statistics
Matches: 89, Mismatches: 22, Indels: 20
0.68 0.17 0.15
Matches are distributed among these distances:
19 1 0.01
20 3 0.03
21 80 0.90
22 3 0.03
23 2 0.02
ACGTcount: A:0.35, C:0.34, G:0.11, T:0.20
Consensus pattern (21 bp):
TACCTCATCACGTAAAGCACC
Found at i:416832 original size:21 final size:21
Alignment explanation
Indices: 416794--416843 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
416784 ACCATTATCG
**
416794 TCACGTAAAGCACCGACCTCA
1 TCACGTAAAAAACCGACCTCA
* *
416815 TCACGTAAAAAACTGACCTCG
1 TCACGTAAAAAACCGACCTCA
*
416836 TTACGTAA
1 TCACGTAA
416844 CTCCCCTAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.36, C:0.30, G:0.14, T:0.20
Consensus pattern (21 bp):
TCACGTAAAAAACCGACCTCA
Found at i:416834 original size:63 final size:63
Alignment explanation
Indices: 416683--416834 Score: 164
Period size: 63 Copynumber: 2.4 Consensus size: 63
416673 TAGAGCAGAT
* * * * *
416683 ACCTCATCACGTAAAGAAAATACCTCACCACGTAAAGCACCATTGTCATCACGTAAAACATCT
1 ACCTCATCACGTAAAGAAACTACCTCACCACGCAAAGCACCATTATCATCACGTAAAACACCG
** * * * * *
416746 ACCTCA-CTACGTAAAGACCCTACCTCATCACGCCATGCACCATTATCGTCACGTAAAGCACCG
1 ACCTCATC-ACGTAAAGAAACTACCTCACCACGCAAAGCACCATTATCATCACGTAAAACACCG
416809 ACCTCATCACGTAAA-AAACTGACCTC
1 ACCTCATCACGTAAAGAAACT-ACCTC
416835 GTTACGTAAC
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
62 4 0.06
63 67 0.93
64 1 0.01
ACGTcount: A:0.36, C:0.34, G:0.11, T:0.20
Consensus pattern (63 bp):
ACCTCATCACGTAAAGAAACTACCTCACCACGCAAAGCACCATTATCATCACGTAAAACACCG
Found at i:417025 original size:42 final size:42
Alignment explanation
Indices: 416958--417061 Score: 113
Period size: 42 Copynumber: 2.5 Consensus size: 42
416948 ATGATGGAAT
* *
416958 AGGTGATGGCTCTCGCTATCGAGGTG-TAGAAT-CGACTCGATC
1 AGGTGATGGCTCTCGATGTCGAGGTGCT-GAATCCG-CTCGATC
* * **
417000 AGGTGATGGCTCTCGGTGTCTAGGTGCTGGCTCCGCTCGATC
1 AGGTGATGGCTCTCGATGTCGAGGTGCTGAATCCGCTCGATC
*
417042 AGGTGATGGATCTCGATGTC
1 AGGTGATGGCTCTCGATGTC
417062 AAAGTAGAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 50 0.94
43 3 0.06
ACGTcount: A:0.16, C:0.22, G:0.34, T:0.28
Consensus pattern (42 bp):
AGGTGATGGCTCTCGATGTCGAGGTGCTGAATCCGCTCGATC
Found at i:417045 original size:21 final size:22
Alignment explanation
Indices: 416993--417056 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
416983 GTAGAATCGA
416993 CTCGATCAGGTGATGGCTCTCG
1 CTCGATCAGGTGATGGCTCTCG
* *
417015 GT-G-TCTAGGTGCTGGCTC-CG
1 CTCGATC-AGGTGATGGCTCTCG
*
417035 CTCGATCAGGTGATGGATCTCG
1 CTCGATCAGGTGATGGCTCTCG
417057 ATGTCAAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 5 0.15
21 23 0.70
22 5 0.15
ACGTcount: A:0.12, C:0.25, G:0.34, T:0.28
Consensus pattern (22 bp):
CTCGATCAGGTGATGGCTCTCG
Found at i:418645 original size:20 final size:20
Alignment explanation
Indices: 418563--418636 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
418553 GTTTATTCTT
* * *
418563 GAAAATTAAATTCGCAACAC
1 GAAAATAAAATTTGCAACGC
* * * * *
418583 AAAAATGAAATTCGTAACGT
1 GAAAATAAAATTTGCAACGC
418603 GAAAATAAAATTTGCAACGC
1 GAAAATAAAATTTGCAACGC
418623 GAAAACTAAAATTT
1 GAAAA-TAAAATTT
418637 CATTGCGAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
20 35 0.81
21 8 0.19
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (20 bp):
GAAAATAAAATTTGCAACGC
Found at i:418662 original size:20 final size:19
Alignment explanation
Indices: 418639--418701 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 19
418629 TAAAATTTCA
*
418639 TTGCGAATTTTATTTTCGCG
1 TTGCGAA-TTTATTTTCGTG
418659 TTGCG-A--T--TTTCGTG
1 TTGCGAATTTATTTTCGTG
418673 TTGCGAATTTCATTTTCGTG
1 TTGCGAATTT-ATTTTCGTG
418693 TTGCGAATT
1 TTGCGAATT
418702 AAGTTTCAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
14 11 0.31
15 1 0.03
16 1 0.03
17 1 0.03
19 1 0.03
20 21 0.58
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.49
Consensus pattern (19 bp):
TTGCGAATTTATTTTCGTG
Found at i:418669 original size:14 final size:14
Alignment explanation
Indices: 418650--418683 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
418640 TGCGAATTTT
418650 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
*
418664 ATTTTCGTGTTGCG
1 ATTTTCGCGTTGCG
*
418678 AATTTC
1 ATTTTC
418684 ATTTTCGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:419069 original size:22 final size:22
Alignment explanation
Indices: 419039--419089 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
419029 ATAGAGGGAG
* *
419039 GTCGTCGGATATGGGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
419061 GTCGCCGGAGATGGGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
419083 GTCGCCG
1 GTCGCCG
419090 TAGAGAGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.16, C:0.20, G:0.47, T:0.18
Consensus pattern (22 bp):
GTCGCCGGAGATGGGGACGGAT
Done.