Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008930.1 Hibiscus syriacus cultivar Beakdansim tig00112236_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: 792381
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:188838 original size:13 final size:13
Alignment explanation
Indices: 188822--188850 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
188812 GTGTATATCG
188822 ATGTACATCATTA
1 ATGTACATCATTA
188835 ATGTACATCATTA
1 ATGTACATCATTA
188848 ATG
1 ATG
188851 GTGCATATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (13 bp):
ATGTACATCATTA
Found at i:191697 original size:2 final size:2
Alignment explanation
Indices: 191690--191741 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
191680 TTACCACCTA
191690 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
191732 AT AT AT AT AT
1 AT AT AT AT AT
191742 GTATTTTATC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:192077 original size:17 final size:18
Alignment explanation
Indices: 192051--192093 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
192041 TCTTAAGATG
*
192051 TTATATTTTGAG-TTAAA
1 TTATAATTTGAGATTAAA
*
192068 TTATAATTTGTGATTAAA
1 TTATAATTTGAGATTAAA
192086 TT-TAATTT
1 TTATAATTT
192094 TATTATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (18 bp):
TTATAATTTGAGATTAAA
Found at i:192084 original size:18 final size:18
Alignment explanation
Indices: 192051--192094 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
192041 TCTTAAGATG
192051 TTAT-ATTTTGAGTTAAA
1 TTATAATTTTGAGTTAAA
192068 TTATAATTTGTGA-TTAAA
1 TTATAATTT-TGAGTTAAA
192086 TT-TAATTTT
1 TTATAATTTT
192095 ATTATAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.04
17 10 0.40
18 11 0.44
19 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (18 bp):
TTATAATTTTGAGTTAAA
Found at i:192585 original size:9 final size:9
Alignment explanation
Indices: 192571--192604 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
192561 TAAAAGGGAA
192571 AAATAAAAT
1 AAATAAAAT
192580 AAATAAAAT
1 AAATAAAAT
192589 AAAT-AAAT
1 AAATAAAAT
192597 AAGATAAA
1 AA-ATAAA
192605 GAAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:192592 original size:13 final size:13
Alignment explanation
Indices: 192570--192614 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
192560 GTAAAAGGGA
192570 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
192584 AAAATAAATAAAT
1 AAAATAAATAAAT
* *
192597 AAGATAAAGAAA-
1 AAAATAAATAAAT
192609 AAAATA
1 AAAATA
192615 GTAAAGTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 5 0.18
13 18 0.64
14 5 0.18
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:193089 original size:14 final size:14
Alignment explanation
Indices: 193058--193117 Score: 54
Period size: 13 Copynumber: 4.3 Consensus size: 14
193048 AAAGAAATAT
*
193058 ATATATATATATACAC
1 ATATA-ATA-ATAAAC
193074 ATATAATAATAAAC
1 ATATAATAATAAAC
*
193088 ATA-AATAATAAAA
1 ATATAATAATAAAC
193101 ATA-AATGAATAAA-
1 ATATAAT-AATAAAC
193114 ATAT
1 ATAT
193118 CCATATAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
13 18 0.45
14 14 0.35
15 3 0.08
16 5 0.12
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (14 bp):
ATATAATAATAAAC
Found at i:193096 original size:13 final size:13
Alignment explanation
Indices: 193072--193113 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
193062 ATATATATAC
193072 ACATATAATAATAA
1 ACATA-AATAATAA
193086 ACATAAATAATAA
1 ACATAAATAATAA
*
193099 AAATAAATGAATAA
1 ACATAAAT-AATAA
193113 A
1 A
193114 ATATCCATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (13 bp):
ACATAAATAATAA
Found at i:194414 original size:105 final size:105
Alignment explanation
Indices: 194115--195187 Score: 1552
Period size: 105 Copynumber: 10.3 Consensus size: 105
194105 CATTGTTCCA
* * **
194115 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAATTG-TTGTTGACAA
* * * * * *
194179 CCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
194221 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
194281 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
194321 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
*
194386 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
194426 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
194486 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
194526 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAA-TTGTTGTTGACAAG
* *
194590 CAGCGGTCCCTCCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
194631 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
*
194691 AGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
194731 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAA-TTGTTGTTGACAAG
* *
194795 CAGCGGCCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
194836 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
194901 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
194941 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAATTG-TTGTTGACAA
*
195006 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
195048 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTG-TTGTTGACAAG
* * * *
195113 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
195154 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
195188 CGCGGATGGC
Statistics
Matches: 889, Mismatches: 56, Indels: 41
0.90 0.06 0.04
Matches are distributed among these distances:
100 258 0.29
101 10 0.01
102 13 0.01
103 10 0.01
104 11 0.01
105 366 0.41
106 100 0.11
107 99 0.11
109 22 0.02
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:194468 original size:205 final size:205
Alignment explanation
Indices: 194115--195187 Score: 1608
Period size: 205 Copynumber: 5.2 Consensus size: 205
194105 CATTGTTCCA
* * ** *
194115 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * ** *
194179 CCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAA
**
194244 GTTGAAATTGAATCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
129 GTTGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
194309 TGCGTTGTCTGG
194 TGCGTTGTCTGG
* * *
194321 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
*
194386 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
194451 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
131 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
194516 CGTTGTCTGG
196 CGTTGTCTGG
* * *
194526 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
* *
194591 AGCGGTCCCTCCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
194656 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCATCGTGAAGTTGAACTTG
131 TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
194721 CGTTGTCTGG
196 CGTTGTCTGG
* *
194731 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
*
194796 AGCGGCCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* *
194861 TGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGA
131 TGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
194926 ACTTGCGTTGTCTGG
191 ACTTGCGTTGTCTGG
* * * *
194941 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAGTTG-TTGTTGACAA
*
195006 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * *
195071 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
129 GTTGAAATTGGCTCTG-AA-TGA-AA--T-TTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGT
* *
195136 TGAACTTGTGTTGTCTCG
188 TGAACTTGCGTTGTCTGG
* * *
195154 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
195188 CGCGGATGGC
Statistics
Matches: 804, Mismatches: 47, Indels: 22
0.92 0.05 0.03
Matches are distributed among these distances:
205 481 0.60
206 46 0.06
207 2 0.00
209 5 0.01
210 96 0.12
211 6 0.01
212 90 0.11
213 53 0.07
214 4 0.00
216 21 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (205 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTCTGAATGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CGTTGTCTGG
Found at i:194667 original size:310 final size:311
Alignment explanation
Indices: 194115--195187 Score: 1540
Period size: 310 Copynumber: 3.4 Consensus size: 311
194105 CATTGTTCCA
* * * *
194115 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAA-C-TGAAAGTGTTTGTTGACAAC
* * *
194180 CATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
63 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
** *
194245 TTGAAATTGAATCT-GAAT-GAAA-TT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
128 TTGAAATTGGCTCTAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
* * *
194306 ACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAG
193 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GGATTGGGAAA
*
194371 TTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
257 TTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
194426 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA-TGAAA-T-TTTGTTGACAAGCAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAACTGAAAGTGTTTGTTGACAACCAG
* *
194488 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
66 CCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTG
*
194553 AAATTGGCTCTAAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTCCGTCGTGAAGTTGAAC
131 AAATTGGCTCT-AGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
* *
194618 TTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAT--GAAATT-
195 TTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTG
* *
194679 TTGTTGACAAGCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGG
260 TTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
194731 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGT-TGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ACT-GAAAGTGT-TTGTTGACAAC
* * * *
194795 CAGCGGCCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
63 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
* *
194860 TTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
128 TTGAAATTGGCTCT-AGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
*
194925 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA
192 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG-GATTGGG-A
* *
194990 AATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
255 AATTG-TTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
195048 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AACTGA-AAG-TGTTTGTTGACAAC
* * * *
195113 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCCACGATATCCTCCGTCGTG
63 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGT-CCA--ATATCCTTCGTTGTG
*
195178 GAGTTGAAAT
125 AAGTTGAAAT
195188 CGCGGATGGC
Statistics
Matches: 693, Mismatches: 45, Indels: 38
0.89 0.06 0.05
Matches are distributed among these distances:
305 171 0.25
306 7 0.01
307 8 0.01
308 11 0.02
309 4 0.01
310 277 0.40
311 35 0.05
312 2 0.00
314 1 0.00
315 5 0.01
316 2 0.00
317 94 0.14
318 50 0.07
319 4 0.01
321 22 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (311 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAACTGAAAGTGTTTGTTGACAACCAG
CCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTG
AAATTGGCTCTAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
TGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGT
TGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:195637 original size:29 final size:28
Alignment explanation
Indices: 195573--195639 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
195563 GCCTGTCTGG
* *
195573 AATCTTGATTCTTGAATCTTCAAATTTTGA
1 AATC-TGA-TCTTGAATCTTCAAATGTTCA
**
195603 TCTCTGATCTTGAATTCTTCAAATGTTCA
1 AATCTGATCTTGAA-TCTTCAAATGTTCA
195632 AATCTGAT
1 AATCTGAT
195640 GTGTACATTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 7 0.23
29 21 0.70
30 2 0.07
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.45
Consensus pattern (28 bp):
AATCTGATCTTGAATCTTCAAATGTTCA
Found at i:196072 original size:65 final size:65
Alignment explanation
Indices: 195968--196148 Score: 290
Period size: 65 Copynumber: 2.8 Consensus size: 65
195958 GACAAAATTT
*
195968 TGTTTCAAGAGAAACTGTCTCAATAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
196033 TGTTTCAAGAGAAACTATCTCAAGAGAGACGGAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * **
196098 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA-TTCATTTCAAGGGAAA
196149 CTATCTCAAG
Statistics
Matches: 106, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
65 92 0.87
66 14 0.13
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:196139 original size:102 final size:102
Alignment explanation
Indices: 196033--196388 Score: 577
Period size: 102 Copynumber: 3.5 Consensus size: 102
196023 TCAATGTTTA
* **
196033 TGTTTCAAGAGAAACTATCTCAAGAGAGACGGAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
196098 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
196135 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* **
196200 TGTTTCAAGAGAAACTGTCTCAATGGAGACGGAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* *
196237 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAATGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
196302 TGTTTCAAGAGGAACTGTCTCAAGGGAGAAAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * * **
196339 TGTTTCAAGGGAAACTGTCTCAATAGAGACAAAGTTTGTTTCAAGGGAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
196389 CTGTCTCAAG
Statistics
Matches: 234, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 234 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:196149 original size:37 final size:37
Alignment explanation
Indices: 196098--196406 Score: 200
Period size: 37 Copynumber: 8.9 Consensus size: 37
196088 TCAATGTTTA
* *
196098 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
196135 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
196171 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* **
196199 ATGTTTCAAGAGAAACTGTCTCAATG-GAGACGGAATTT
1 -TGTTTCAAGGGAAACTGTCTCAA-GAGAGACAAAATTT
* *
196237 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * * *
196273 CATTTCAATGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* *
196301 ATGTTTCAAGAGG-AACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAG-GGAAACTGTCTCAAGAGAGACAAAATTT
* *
196339 TGTTTCAAGGGAAACTGTCTCAATAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
196375 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
196407 TGGTGAGCAC
Statistics
Matches: 205, Mismatches: 36, Indels: 62
0.68 0.12 0.20
Matches are distributed among these distances:
28 3 0.01
29 25 0.12
30 8 0.04
32 2 0.01
33 2 0.01
34 2 0.01
35 4 0.02
36 69 0.34
37 84 0.41
38 6 0.03
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:196231 original size:167 final size:169
Alignment explanation
Indices: 195933--196250 Score: 534
Period size: 167 Copynumber: 1.9 Consensus size: 169
195923 AAAATGATGC
* *
195933 TTCAAGAGAAAACTATCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTGTCTCAATAGAGAC
1 TTCAAGAGAAAACTATCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
*
195998 GAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
66 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
196063 GGAA-TTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
131 GGAATTTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
* *
196101 TTCAAGAG-AAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
1 TTCAAGAGAAAACTATCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
*
196165 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAATG-GAGA
66 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAA-GAGAGA
**
196229 CGGAATTTTGTTTCAAGGGAAA
130 CGGAATTTCATTTCAAGGGAAA
196251 CTATCTCAAG
Statistics
Matches: 140, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
167 117 0.84
168 23 0.16
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (169 bp):
TTCAAGAGAAAACTATCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
GGAATTTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
Found at i:196384 original size:36 final size:36
Alignment explanation
Indices: 196302--196406 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 36
196292 TCAATGTTTA
* * *
196302 TGTTTCAAGAGG-AACTGTCTCAAGGGAGAAAAAATTT
1 TGTTTCAAG-GGAAACTGTCTCAAGAGAG-ACAAAGTT
*
196339 TGTTTCAAGGGAAACTGTCTCAATAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
196375 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
196407 TGGTGAGCAC
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
36 39 0.63
37 23 0.37
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
Found at i:197289 original size:22 final size:22
Alignment explanation
Indices: 197264--197314 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
197254 TTGTGTTTGG
197264 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
197286 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
197308 TCAAAGG
1 TCAAAGG
197315 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:197982 original size:16 final size:16
Alignment explanation
Indices: 197961--198007 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
197951 GTTCTTGTTT
197961 TTTCCTTTTTTGCTTC
1 TTTCCTTTTTTGCTTC
197977 TTTCCTTTTTT-CTT-
1 TTTCCTTTTTTGCTTC
*
197991 TTTGCCCTTTTTG-TTC
1 TTT-CCTTTTTTGCTTC
198007 T
1 T
198008 GATTGAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 3 0.11
15 12 0.44
16 12 0.44
ACGTcount: A:0.00, C:0.23, G:0.06, T:0.70
Consensus pattern (16 bp):
TTTCCTTTTTTGCTTC
Found at i:197986 original size:23 final size:21
Alignment explanation
Indices: 197925--197978 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
197915 TTTGTCCATT
* * *
197925 TTTTTTATTTTTGTTCTTT-C
1 TTTTTTGTTCTTGTTTTTTCC
197945 TTTTTTGTTCTTGTTTTTTCC
1 TTTTTTGTTCTTGTTTTTTCC
197966 TTTTTTGCTTCTT
1 TTTTTTG-TTCTT
197979 TCCTTTTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 16 0.55
21 8 0.28
22 5 0.17
ACGTcount: A:0.02, C:0.13, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTTGTTCTTGTTTTTTCC
Found at i:201030 original size:9 final size:9
Alignment explanation
Indices: 201016--201049 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
201006 TAAAAGGGAA
201016 AAATAAAAT
1 AAATAAAAT
201025 AAATAAAAT
1 AAATAAAAT
201034 AAAT-AAAT
1 AAATAAAAT
201042 AAGATAAA
1 AA-ATAAA
201050 GAAAAAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:201037 original size:13 final size:13
Alignment explanation
Indices: 201015--201049 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
201005 GTAAAAGGGA
201015 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
201029 AAAATAAATAAAT
1 AAAATAAATAAAT
*
201042 AAGATAAA
1 AAAATAAA
201050 GAAAAAATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:201553 original size:18 final size:17
Alignment explanation
Indices: 201532--201574 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
201522 ATATACACAT
201532 ATAATAATAATAACATAA
1 ATAATAATAATAA-ATAA
* *
201550 ATAATAAAAATAAATGA
1 ATAATAATAATAAATAA
201567 ATAA-AATA
1 ATAATAATA
201575 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:201571 original size:14 final size:13
Alignment explanation
Indices: 201534--201572 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
201524 ATACACATAT
201534 AATAATAATAACATA
1 AATAATAA-AA-ATA
201549 AATAATAAAAATA
1 AATAATAAAAATA
201562 AATGAATAAAA
1 AAT-AATAAAA
201573 TATCCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:202140 original size:19 final size:19
Alignment explanation
Indices: 202104--202141 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
202094 TTTAGGGTTA
*
202104 AGTGAGAGAGAATTATTTT
1 AGTGAGAGAGAATCATTTT
202123 AGTGAGATGA-AATCATTTT
1 AGTGAGA-GAGAATCATTTT
202142 TTGAGATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37
Consensus pattern (19 bp):
AGTGAGAGAGAATCATTTT
Found at i:203809 original size:31 final size:31
Alignment explanation
Indices: 203732--203792 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
203722 CAGTTACGTT
**
203732 AGGGACCATATTGCAAACGGACTAAATGTTA
1 AGGGACCATATTGCAAACAAACTAAATGTTA
203763 AGGGACCATATTGCAAACAAACTAAATGTT
1 AGGGACCATATTGCAAACAAACTAAATGTT
203793 GGGGGATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (31 bp):
AGGGACCATATTGCAAACAAACTAAATGTTA
Found at i:205454 original size:31 final size:31
Alignment explanation
Indices: 205377--205438 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
205367 CAGTTACGTC
*
205377 AGGGACCATATTGCAAACGGACTAAATGTTG
1 AGGGACCATATTGCAAACAGACTAAATGTTG
*
205408 AGGGACCATATTGCAAACAGAGTAAATGTTG
1 AGGGACCATATTGCAAACAGACTAAATGTTG
205439 GGAGATTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.23
Consensus pattern (31 bp):
AGGGACCATATTGCAAACAGACTAAATGTTG
Found at i:205550 original size:15 final size:15
Alignment explanation
Indices: 205530--205575 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
205520 CCCTTAATTT
*
205530 TATGTATTTCTATAA
1 TATGTATTTATATAA
*
205545 TATGTATTTATTTAA
1 TATGTATTTATATAA
* *
205560 TATGTTTTTATTTAA
1 TATGTATTTATATAA
205575 T
1 T
205576 TTTCAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (15 bp):
TATGTATTTATATAA
Found at i:207635 original size:24 final size:24
Alignment explanation
Indices: 207606--207684 Score: 67
Period size: 24 Copynumber: 3.5 Consensus size: 24
207596 AATTAAAGGT
*
207606 AATTTTT-TTAATATTTTTAATTC
1 AATTTTTATTTATATTTTTAATTC
* *
207629 AATTTTTATTTTTATTTTTATTTC
1 AATTTTTATTTATATTTTTAATTC
* ** *
207653 AA---ATATTTATATTTTTTCTTA
1 AATTTTTATTTATATTTTTAATTC
207674 AATTTTTATTT
1 AATTTTTATTT
207685 CCGATAATGA
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
21 16 0.37
23 7 0.16
24 20 0.47
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (24 bp):
AATTTTTATTTATATTTTTAATTC
Found at i:207716 original size:2 final size:2
Alignment explanation
Indices: 207711--207738 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
207701 AGACACACAA
207711 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
207739 GGAAATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:213114 original size:22 final size:22
Alignment explanation
Indices: 213072--213114 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
213062 TACACTTAGC
*
213072 TTAAAATCAATATAATTGAATA
1 TTAAAATCAATATAATAGAATA
*
213094 TTAAATTCAAT-TAATGAGAAT
1 TTAAAATCAATATAAT-AGAAT
213115 TTCCATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (22 bp):
TTAAAATCAATATAATAGAATA
Found at i:214935 original size:31 final size:32
Alignment explanation
Indices: 214877--214941 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
214867 AAATTAAAAT
*
214877 CAAAGTTTGGCACTGCCGAGTATGCTTGTTTCAA
1 CAAAGTTTGGCAC--CCGAGTATGCTTGGTTCAA
*
214911 CAAAGTTTGGCA-CCGATTATGCTTGGTTCAA
1 CAAAGTTTGGCACCCGAGTATGCTTGGTTCAA
214942 AGTTTGGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 17 0.59
34 12 0.41
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (32 bp):
CAAAGTTTGGCACCCGAGTATGCTTGGTTCAA
Found at i:220922 original size:18 final size:18
Alignment explanation
Indices: 220882--220919 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
220872 TTTATTTGCT
220882 TTATTTATTTTCTCATTA
1 TTATTTATTTTCTCATTA
220900 TTATTTATTTT-T-ATTA
1 TTATTTATTTTCTCATTA
220916 TTAT
1 TTAT
220920 ATTACTTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 1 0.05
18 11 0.55
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTTATTTTCTCATTA
Found at i:241852 original size:21 final size:23
Alignment explanation
Indices: 241828--241875 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
241818 AGAAAATCGA
241828 TCCCCCCTTG-A-GGGAACCGAT
1 TCCCCCCTTGAAGGGGAACCGAT
*
241849 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCTTGAAGGGGAACCGAT
241872 TCCC
1 TCCC
241876 TCCACAGGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 9 0.38
22 1 0.04
23 14 0.58
ACGTcount: A:0.19, C:0.38, G:0.23, T:0.21
Consensus pattern (23 bp):
TCCCCCCTTGAAGGGGAACCGAT
Found at i:243886 original size:16 final size:17
Alignment explanation
Indices: 243845--243887 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
243835 TTTTAACATT
*
243845 TTGAATATTTTGGAATGT
1 TTGAAT-TTTTGGAATGA
*
243863 TTGAATTTTTGGATTGA
1 TTGAATTTTTGGAATGA
243880 TTG-ATTTT
1 TTGAATTTT
243888 GAATTTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 5 0.22
17 12 0.52
18 6 0.26
ACGTcount: A:0.23, C:0.00, G:0.21, T:0.56
Consensus pattern (17 bp):
TTGAATTTTTGGAATGA
Found at i:247913 original size:22 final size:21
Alignment explanation
Indices: 247871--247910 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
247861 GAGTTTATTT
*
247871 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
247892 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
247911 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:256330 original size:39 final size:39
Alignment explanation
Indices: 256213--256330 Score: 146
Period size: 39 Copynumber: 3.0 Consensus size: 39
256203 TGTACACCAA
* * * * *
256213 GTAAGGGCTTAACCTGTGCACAAAGCAGAGAAGCCTGCA
1 GTAAGGACTTAACATGTGCACAAAGCCGAGGAGCCTGCG
* * * *
256252 GTAAGGACATACCTTGTGCACAAAGCCGAGGAGCATGCG
1 GTAAGGACTTAACATGTGCACAAAGCCGAGGAGCCTGCG
*
256291 GTAAGGACTTAACATGAGCACAAAGCCGAGGAGCCTGCG
1 GTAAGGACTTAACATGTGCACAAAGCCGAGGAGCCTGCG
256330 G
1 G
256331 AAAGCGATAA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 66 1.00
ACGTcount: A:0.32, C:0.23, G:0.31, T:0.14
Consensus pattern (39 bp):
GTAAGGACTTAACATGTGCACAAAGCCGAGGAGCCTGCG
Found at i:258697 original size:19 final size:21
Alignment explanation
Indices: 258654--258701 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
258644 TTCATGGTAT
*
258654 TGTTCATACGGTATTGTTCAC
1 TGTTCATACCGTATTGTTCAC
258675 TGTTCATACCGTATT-TT-AC
1 TGTTCATACCGTATTGTTCAC
258694 TGTTCATA
1 TGTTCATA
258702 AAATGTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 10 0.38
20 2 0.08
21 14 0.54
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.46
Consensus pattern (21 bp):
TGTTCATACCGTATTGTTCAC
Found at i:259053 original size:29 final size:29
Alignment explanation
Indices: 259013--259079 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
259003 AATATACGAT
* *
259013 AAATCAGATGTCGGATAAGCAATATTAAG
1 AAATCAGGTGTCGAATAAGCAATATTAAG
* *
259042 AAATCAGGTGTCGAATAAGCAGTATTCAG
1 AAATCAGGTGTCGAATAAGCAATATTAAG
259071 AAATCAGGT
1 AAATCAGGT
259080 ATCATATCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (29 bp):
AAATCAGGTGTCGAATAAGCAATATTAAG
Found at i:262935 original size:21 final size:21
Alignment explanation
Indices: 262907--262946 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
262897 TTTGCCTTCC
262907 AAACAAAATAG-AATATTTAA
1 AAACAAAATAGAAATATTTAA
*
262927 AAACTAAAATCGAAATATTT
1 AAAC-AAAATAGAAATATTT
262947 TAGTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 6 0.35
22 7 0.41
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (21 bp):
AAACAAAATAGAAATATTTAA
Found at i:268837 original size:154 final size:157
Alignment explanation
Indices: 268628--268939 Score: 571
Period size: 153 Copynumber: 2.0 Consensus size: 157
268618 CTTCAAACTA
268628 TTTTTTATGCTATTCGAAAATATATATTTTACTATTAACATCCGAATGTTATTTTTTTATGATAT
1 TTTTTTATGCTATTCGAAAATATATATTTTACTATTAACATCCGAATGTTATTTTTTTATGATAT
268693 TCAAACTATTATTTTAAAATATTTATATATTTTATAAGAGAAATCGCCTCAGTGA-CAAAAATGT
66 TCAAACTATTATTTTAAAATATTTATATATTTTATAA-AGAAATCGCCTCAGTGACCAAAAATGT
268757 C-T-T-ATATACGATTTTAACCAACTTT
130 CTTATAATATACGATTTTAACCAACTTT
*
268782 TTTTTTTTGCTATTCGAAAATATATA-TTTACTATTAACATCCGAATGTTATTTTTTTATGATAT
1 TTTTTTATGCTATTCGAAAATATATATTTTACTATTAACATCCGAATGTTATTTTTTTATGATAT
268846 TCAAACTATTATTTTAAAATATTTATATATTTTATAAAGAAATCGCCTCAGTGACCAAAAATGTC
66 TCAAACTATTATTTTAAAATATTTATATATTTTATAAAGAAATCGCCTCAGTGACCAAAAATGTC
268911 TTATAATATACGATTTTAACCAACTTT
131 TTATAATATACGATTTTAACCAACTTT
268938 TT
1 TT
268940 CCGGATTTGC
Statistics
Matches: 153, Mismatches: 1, Indels: 6
0.96 0.01 0.04
Matches are distributed among these distances:
152 17 0.11
153 85 0.56
154 26 0.17
155 1 0.01
156 24 0.16
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (157 bp):
TTTTTTATGCTATTCGAAAATATATATTTTACTATTAACATCCGAATGTTATTTTTTTATGATAT
TCAAACTATTATTTTAAAATATTTATATATTTTATAAAGAAATCGCCTCAGTGACCAAAAATGTC
TTATAATATACGATTTTAACCAACTTT
Found at i:269101 original size:21 final size:21
Alignment explanation
Indices: 269077--269129 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
269067 TTTTCCCAAT
*
269077 TCGCAATGCGAATAAGTAAAA
1 TCGCAATGCGAATAAGGAAAA
* **
269098 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGGAAAA
269119 TCGCAATGCGA
1 TCGCAATGCGA
269130 TACTGACTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATAAGGAAAA
Found at i:269143 original size:20 final size:20
Alignment explanation
Indices: 269118--269230 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
269108 AATTGGGAAA
*
269118 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
269138 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
269158 ATCGCAA-GCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
269178 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
*
269198 -TCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
269217 TTCGCAACGCGATA
1 ATCGCAACGCGATA
269231 ATACATAATC
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
18 2 0.03
19 24 0.30
20 45 0.57
21 6 0.08
22 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:269192 original size:60 final size:60
Alignment explanation
Indices: 269115--269244 Score: 181
Period size: 60 Copynumber: 2.2 Consensus size: 60
269105 GCGAATTGGG
* * * *
269115 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAA-GCGATAATAC
1 AAAATCGCAACGAGATACTGACT-TCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* *
269175 AAAATCGCAACGAGATACTGACTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTTCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
269235 ATAATCGCAA
1 AAAATCGCAA
269245 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 22 0.35
60 40 0.65
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (60 bp):
AAAATCGCAACGAGATACTGACTTCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:269203 original size:19 final size:20
Alignment explanation
Indices: 269179--269230 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
269169 TAATACAAAA
*
269179 TCGCAACGAGATACTGAC-T
1 TCGCAACGCGATACTGACTT
*
269198 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTT
269218 TCGCAACGCGATA
1 TCGCAACGCGATA
269231 ATACATAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:269443 original size:22 final size:22
Alignment explanation
Indices: 269415--269458 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
269405 CACTCTCTCA
269415 CCCATCTCC-GACGAAATCCGTC
1 CCCATCTCCAG-CGAAATCCGTC
269437 CCCATCTCCAGCGAAATCCGTC
1 CCCATCTCCAGCGAAATCCGTC
269459 TATCTCCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCAGCGAAATCCGTC
Found at i:269465 original size:20 final size:21
Alignment explanation
Indices: 269415--269466 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
269405 CACTCTCTCA
269415 CCCATCTCC-GACGAAATCCGT
1 CCCATCTCCAG-CGAAATCCGT
269436 CCCCATCTCCAGCGAAATCCGT
1 -CCCATCTCCAGCGAAATCCGT
*
269458 -CTATCTCCA
1 CCCATCTCCA
269467 TCTCTCAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 8 0.29
22 19 0.68
23 1 0.04
ACGTcount: A:0.23, C:0.44, G:0.12, T:0.21
Consensus pattern (21 bp):
CCCATCTCCAGCGAAATCCGT
Found at i:269721 original size:20 final size:20
Alignment explanation
Indices: 269704--269741 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
269694 CAATTTTCTC
269704 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
269724 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
269742 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:269931 original size:25 final size:24
Alignment explanation
Indices: 269877--269931 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
269867 TGTTTATTAT
* *
269877 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
269901 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
269927 TGTTT
1 TGTTT
269932 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:271065 original size:18 final size:18
Alignment explanation
Indices: 271039--271083 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
271029 TCCACTTCGG
*
271039 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
271057 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
271075 GAGCCATCA
1 GAGCCATCA
271084 TCTGAATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:271398 original size:19 final size:19
Alignment explanation
Indices: 271376--271470 Score: 93
Period size: 19 Copynumber: 5.5 Consensus size: 19
271366 GGAAATGGCT
271376 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
271395 ATCGCAA--CGACA--AAA
1 ATCGCAATGCGAAATGAAA
271410 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
271428 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
271442 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
271461 ATCGCAATGC
1 ATCGCAATGC
271471 AATTGTGTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
14 10 0.16
15 10 0.16
16 4 0.07
17 8 0.13
18 10 0.16
19 19 0.31
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:271435 original size:33 final size:33
Alignment explanation
Indices: 271376--271467 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
271366 GGAAATGGCT
271376 ATCGCAATGCGAAATGAAAATCGCAACGACAAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAC-AAA
271410 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
271442 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
271468 TGCAATTGTG
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
32 18 0.32
33 22 0.39
34 16 0.29
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:271445 original size:14 final size:14
Alignment explanation
Indices: 271392--271450 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
271382 ATGCGAAATG
271392 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
271406 AAAAATCGCAATGCGAA
1 -AAAATCGCAA--CGAC
271423 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
271439 AAAATCGCAACG
1 AAAATCGCAACG
271451 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 11 0.29
15 10 0.26
16 5 0.13
17 3 0.08
18 9 0.24
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:271502 original size:14 final size:14
Alignment explanation
Indices: 271483--271541 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
271473 TTGTGTTTCA
271483 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
271497 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
271514 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
271530 CGTTGCGATTTT
1 CGTTGCGATTTT
271542 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:271523 original size:19 final size:19
Alignment explanation
Indices: 271499--271768 Score: 108
Period size: 19 Copynumber: 15.5 Consensus size: 19
271489 GATTTTGTCG
271499 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
271518 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
271532 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
271551 TTGCG---TGCATTCCGCG
1 TTGCGATTTTCATTTCGCA
** *
271567 TTGCGATAGTCATTTTCGCG
1 TTGCGATTTTCA-TTTCGCA
*** **
271587 TTGCGATTTAGGTTTCGTG
1 TTGCGATTTTCATTTCGCA
271606 TTGCG---TTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
271622 TTGCGA--TT--TGTCG--
1 TTGCGATTTTCATTTCGCA
*
271635 TTACGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
271654 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
271668 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
271687 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
*
271701 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*** * *
271720 TTGCGATAGCCATTCCGCG
1 TTGCGATTTTCATTTCGCA
** *
271739 TTGCGATAGTCATTTTCGCG
1 TTGCGATTTTCA-TTTCGCA
271759 TTGCGATTTT
1 TTGCGATTTT
271769 AGTTTCGTGT
Statistics
Matches: 187, Mismatches: 37, Indels: 53
0.68 0.13 0.19
Matches are distributed among these distances:
13 5 0.03
14 18 0.10
15 15 0.08
16 36 0.19
17 18 0.10
18 9 0.05
19 59 0.32
20 27 0.14
ACGTcount: A:0.13, C:0.20, G:0.23, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:271527 original size:33 final size:33
Alignment explanation
Indices: 271485--271726 Score: 296
Period size: 33 Copynumber: 7.2 Consensus size: 33
271475 GTGTTTCACG
271485 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
271518 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
** ** *
271551 TTGCGTGCATTCCG-CGTTGCGATAGTCATTTTCGCG
1 TTGC--G-ATTTTGTCGTTGCGATTTTCA-TTTCGCA
*
271587 TTGCGATTTAGGTTTCGTGTTGCG---TTCATTTCGCA
1 TTGCGATTT---TGTC--GTTGCGATTTTCATTTCGCA
*
271622 TTGCGA-TTTGTCGTTACGATTTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
271654 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
*
271687 TTGCGATTTTGTCGTTGCGATTTTCATTTCGTA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
271720 TTGCGAT
1 TTGCGAT
271727 AGCCATTCCG
Statistics
Matches: 181, Mismatches: 14, Indels: 28
0.81 0.06 0.13
Matches are distributed among these distances:
29 5 0.03
31 3 0.02
32 17 0.09
33 104 0.57
34 3 0.02
35 25 0.14
36 17 0.09
37 1 0.01
39 6 0.03
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
Found at i:271673 original size:14 final size:14
Alignment explanation
Indices: 271654--271710 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
271644 TCATTTCGCA
271654 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
271668 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
271685 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
271701 TTGCGATTTT
1 TTGCGATTTT
271711 CATTTCGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.17
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.51
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:271752 original size:136 final size:135
Alignment explanation
Indices: 271485--271767 Score: 351
Period size: 136 Copynumber: 2.1 Consensus size: 135
271475 GTGTTTCACG
*
271485 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGC
1 TTGCGA-TTTGTCGTTACGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGC
* * * *
271550 ATTGCGTGCATTCCGCGTTGCGATAGTCATTTTCGCGTTGCGATTTAGGTTTCGTGTTGCGTTCA
65 ATTGCG-GCATTCCGCGTTGCGATAGTCATTTTCGCATTGCGA-TTAGATTCCGCGTTGCGTTCA
271615 -TTTCGCA
128 TTTTCGCA
271622 TTGCGATTTGTCGTTACGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTGTCGTTACGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
** ** *
271687 TTGC-G-ATTTTGTCGTTGCGATTTTCA-TTTCGTATTGCGA-TAGCCATTCCGCGTTGCGATAG
66 TTGCGGCATTCCG-CGTTGCGATAGTCATTTTCGCATTGCGATTAG--ATTCCGCGTTGCG-T--
*
271748 TCATTTTCGCG
125 TCATTTTCGCA
271759 TTGCGATTT
1 TTGCGATTT
271768 TAGTTTCGTG
Statistics
Matches: 128, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
131 3 0.02
133 25 0.20
134 14 0.11
136 65 0.51
137 21 0.16
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (135 bp):
TTGCGATTTGTCGTTACGATTTTCATTTCGCATTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
TTGCGGCATTCCGCGTTGCGATAGTCATTTTCGCATTGCGATTAGATTCCGCGTTGCGTTCATTT
TCGCA
Found at i:271760 original size:20 final size:19
Alignment explanation
Indices: 271720--271765 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
271710 TCATTTCGTA
271720 TTGCGATAGCCATTCCGCG
1 TTGCGATAGCCATTCCGCG
* *
271739 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCA-TTCCGCG
271759 TTGCGAT
1 TTGCGAT
271766 TTTAGTTTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (19 bp):
TTGCGATAGCCATTCCGCG
Found at i:273276 original size:90 final size:89
Alignment explanation
Indices: 273097--273279 Score: 280
Period size: 90 Copynumber: 2.0 Consensus size: 89
273087 ATTTCAAACT
*
273097 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTAGCA
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTAGCA
273162 GAATTGGCAGCAACCGAATAAATTTAC
63 GAATTGGCAGCAACCGAATAAATTTAC
273189 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAG-TTAGCA
*
273253 -TATTGGCAGCAACCGAATAAATTTAC
63 GAATTGGCAGCAACCGAATAAATTTAC
273279 T
1 T
273280 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
90 34 0.40
91 6 0.07
92 19 0.22
94 27 0.31
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (89 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTAGCAGAA
TTGGCAGCAACCGAATAAATTTAC
Found at i:275009 original size:19 final size:19
Alignment explanation
Indices: 274945--275076 Score: 121
Period size: 19 Copynumber: 7.1 Consensus size: 19
274935 TCTTTTGGTT
*
274945 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
274964 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
** *
274984 GGAAATGACTATCGCAATGC
1 -GAAATGAAAATCGCAACGC
** *
275004 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
275021 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
275037 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
275056 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
275075 GA
1 GA
275077 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
14 8 0.08
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 50 0.53
20 29 0.31
21 2 0.02
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:275069 original size:52 final size:53
Alignment explanation
Indices: 274970--275069 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 53
274960 ACGAGATAAT
** * **
274970 GAGAATCGCAACGCGGAAATGACTATCGCAATGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGGAAATGAAAATCGCAACGCGAAATGAAAATCGCGACGA
275023 GAGAATCGCAACGC-GAAATGAAAATCGCAACGCGAAATGAAAATCGC
1 GAGAATCGCAACGCGGAAATGAAAATCGCAACGCGAAATGAAAATCGC
275070 AATGCGATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 28 0.67
53 14 0.33
ACGTcount: A:0.40, C:0.22, G:0.25, T:0.13
Consensus pattern (53 bp):
GAGAATCGCAACGCGGAAATGAAAATCGCAACGCGAAATGAAAATCGCGACGA
Found at i:275099 original size:19 final size:19
Alignment explanation
Indices: 275072--275115 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
275062 AAAATCGCAA
**
275072 TGCGATTTTGGTTTCGCG-
1 TGCGATTTTTATTTCGCGT
275090 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
275109 TGCGATT
1 TGCGATT
275116 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:275691 original size:20 final size:20
Alignment explanation
Indices: 275666--275718 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
275656 GCGCTATGTA
275666 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
275686 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
275706 TATCTCGTTGCGA
1 AATCGCGTTGCGA
275719 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:275752 original size:20 final size:20
Alignment explanation
Indices: 275727--275780 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
275717 GATTTTGTAT
275727 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
275747 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
275767 TATCGCATTGCGAT
1 TATCGCATTGCGAT
275781 TTTCCCATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:275765 original size:61 final size:61
Alignment explanation
Indices: 275667--275783 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
275657 CGCTATGTAA
* * * * *
275667 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
275728 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
275784 CCCATTCGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:275792 original size:20 final size:20
Alignment explanation
Indices: 275769--275819 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
275759 ATAGTCAGTA
*
275769 TCGCATTGCGATTTTCCCAT
1 TCGCATTGCGATTTACCCAT
* **
275789 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCCAT
275809 TCGCATTGCGA
1 TCGCATTGCGA
275820 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACCCAT
Found at i:276358 original size:21 final size:21
Alignment explanation
Indices: 276334--276402 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
276324 AGGGGAGTAG
276334 ACTAGATGAGTAGGGGTTCAA
1 ACTAGATGAGTAGGGGTTCAA
** * **
276355 ACTAGGCGAGGAGGGGAGCAA
1 ACTAGATGAGTAGGGGTTCAA
*
276376 GAGTAGATGAGTAGGGGTTCAA
1 -ACTAGATGAGTAGGGGTTCAA
276398 ACTAG
1 ACTAG
276403 GCGAGCAGGG
Statistics
Matches: 35, Mismatches: 12, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
21 20 0.57
22 15 0.43
ACGTcount: A:0.33, C:0.10, G:0.39, T:0.17
Consensus pattern (21 bp):
ACTAGATGAGTAGGGGTTCAA
Found at i:276385 original size:43 final size:43
Alignment explanation
Indices: 276319--276424 Score: 169
Period size: 43 Copynumber: 2.5 Consensus size: 43
276309 TCAGGTAGCA
*
276319 CGAGCAGGGGAG-TAGACTAGATGAGTAGGGGTTCAAACTAGG
1 CGAGCAGGGGAGCAAGACTAGATGAGTAGGGGTTCAAACTAGG
* *
276361 CGAGGAGGGGAGCAAGAGTAGATGAGTAGGGGTTCAAACTAGG
1 CGAGCAGGGGAGCAAGACTAGATGAGTAGGGGTTCAAACTAGG
*
276404 CGAGCAGGGGAGCAGGACTAG
1 CGAGCAGGGGAGCAAGACTAG
276425 GCTATTAACT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 11 0.19
43 46 0.81
ACGTcount: A:0.31, C:0.12, G:0.43, T:0.13
Consensus pattern (43 bp):
CGAGCAGGGGAGCAAGACTAGATGAGTAGGGGTTCAAACTAGG
Found at i:276413 original size:21 final size:21
Alignment explanation
Indices: 276345--276413 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
276335 CTAGATGAGT
*
276345 AGGGGTTCAAACTAGGCGAGG
1 AGGGGTTCAAACTAGGCGAGC
** * ** *
276366 AGGGGAGCAAGAGTAGATGAGT
1 AGGGGTTCAA-ACTAGGCGAGC
276388 AGGGGTTCAAACTAGGCGAGC
1 AGGGGTTCAAACTAGGCGAGC
276409 AGGGG
1 AGGGG
276414 AGCAGGACTA
Statistics
Matches: 35, Mismatches: 12, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
21 20 0.57
22 15 0.43
ACGTcount: A:0.30, C:0.12, G:0.45, T:0.13
Consensus pattern (21 bp):
AGGGGTTCAAACTAGGCGAGC
Found at i:276744 original size:21 final size:20
Alignment explanation
Indices: 276712--276754 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
276702 ATGTACATGT
*
276712 ATTTTTTATTGTA-AATAAAA
1 ATTTTTAATTGTAGAA-AAAA
276732 ATTTTTAATTTGTAGAAAAAA
1 ATTTTTAA-TTGTAGAAAAAA
276753 AT
1 AT
276755 GAGCAACAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 7 0.35
21 11 0.55
22 2 0.10
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
ATTTTTAATTGTAGAAAAAA
Found at i:280469 original size:2 final size:2
Alignment explanation
Indices: 280462--280542 Score: 119
Period size: 2 Copynumber: 41.0 Consensus size: 2
280452 TCATTATAAA
* ** *
280462 AT AT AT AT AT AT AT AT TT GC CT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
280503 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
280543 TTCTTCTAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
1 1 0.01
2 72 0.99
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (2 bp):
AT
Found at i:291058 original size:29 final size:29
Alignment explanation
Indices: 291016--291078 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
291006 GATTTGCCTT
* * *
291016 GACTTGGACCCCCTTAGTCCTTCGACAAA
1 GACTTAGACCCCCTTAATCCTTCAACAAA
291045 GACTTAGACCCCCTTAATCCTTCAACAAA
1 GACTTAGACCCCCTTAATCCTTCAACAAA
291074 GACTT
1 GACTT
291079 GGATGACTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.29, C:0.33, G:0.13, T:0.25
Consensus pattern (29 bp):
GACTTAGACCCCCTTAATCCTTCAACAAA
Found at i:291792 original size:60 final size:57
Alignment explanation
Indices: 291615--291797 Score: 152
Period size: 60 Copynumber: 3.1 Consensus size: 57
291605 GTCCTTAAAT
* * * * * * *
291615 TATGACTCTAATTTTAAATTGTTCTCTAAATTTTTAAACGTTCCAATTTTATTTCTAAGC
1 TATGACTATCATTCTAAATTGTT-TCTAAA-TTTTAAACATTCCAATTTCA-TCCCAAGC
* * * * *
291675 TATGGCTATCATTCTAAATTAGTCATCAAAATTTTGAACATTTCAATTTCATCCCCAAGC
1 TATGACTATCATTCTAAATT-GT-TTCTAAATTTTAAACATTCCAATTTCAT-CCCAAGC
*
291735 TATGAC-ATTCATTCTAAATTGGTTTCTAAACTTATTAAACATTCCAATTTCATCCCAAAC
1 TATGACTA-TCATTCTAAATT-GTTTCTAAA-TT-TTAAACATTCCAATTTCATCCCAAGC
291795 TAT
1 TAT
291798 ACGTATATGC
Statistics
Matches: 98, Mismatches: 19, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
59 7 0.07
60 67 0.68
61 24 0.24
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.42
Consensus pattern (57 bp):
TATGACTATCATTCTAAATTGTTTCTAAATTTTAAACATTCCAATTTCATCCCAAGC
Found at i:292021 original size:29 final size:29
Alignment explanation
Indices: 291937--292025 Score: 76
Period size: 29 Copynumber: 3.0 Consensus size: 29
291927 AATTGAAATA
*
291937 TTCAAAAGTTTAGGGACTAATTTAGAAATATG
1 TTCAAAAGTTTAAGGACTAATTTAG--A-ATG
* * *
291969 ATC-ATAGTTT-AGAGA-TGAAATTAGAATG
1 TTCAAAAGTTTAAG-GACT-AATTTAGAATG
291997 TTCAAAAGTTTAAGGACTAATTTAGAATG
1 TTCAAAAGTTTAAGGACTAATTTAGAATG
292026 AGATTTATAA
Statistics
Matches: 45, Mismatches: 7, Indels: 13
0.69 0.11 0.20
Matches are distributed among these distances:
28 5 0.11
29 19 0.42
30 5 0.11
31 14 0.31
32 2 0.04
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.34
Consensus pattern (29 bp):
TTCAAAAGTTTAAGGACTAATTTAGAATG
Found at i:292046 original size:60 final size:58
Alignment explanation
Indices: 291915--292098 Score: 192
Period size: 60 Copynumber: 3.1 Consensus size: 58
291905 ATTTTGATGA
* * *
291915 AATTGAGGATGAAATT-GAAATATTCAAAAGTTTAGGGACTAATTTAGAAAT-ATGATCAT
1 AATTTAGGATGAAATTAG-AATATTCAAAAGTTTAAGGACTAATTTAG-AATGA-GATTAT
* *
291974 AGTTTAGAGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGATTTAT
1 AATTTAG-GATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGA-TTAT
* * * * * *
292034 AATTTAAGGATGAAACTAAAATATTTAAAAGTTTAAGAACCAATTTAAAATGAAGATTAT
1 AATTT-AGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATG-AGATTAT
292094 AATTT
1 AATTT
292099 GGAGACATAT
Statistics
Matches: 106, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
59 10 0.09
60 90 0.85
61 6 0.06
ACGTcount: A:0.46, C:0.04, G:0.16, T:0.34
Consensus pattern (58 bp):
AATTTAGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGATTAT
Found at i:297639 original size:12 final size:11
Alignment explanation
Indices: 297589--297641 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
297579 AATATGTAAA
* *
297589 AATATAATATT
1 AATAAAATAAT
297600 AATAAAATAAT
1 AATAAAATAAT
297611 AATATAAAT-AT
1 AATA-AAATAAT
297622 AA-AAAATAAT
1 AATAAAATAAT
297632 AATTAAAATA
1 AA-TAAAATA
297642 GCGATAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
9 4 0.11
10 5 0.14
11 17 0.47
12 10 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:297641 original size:21 final size:23
Alignment explanation
Indices: 297589--297638 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
297579 AATATGTAAA
297589 AATAT-AATATTAATAAAATAAT
1 AATATAAATATTAATAAAATAAT
297611 AATATAAATA-TAA-AAAATAAT
1 AATATAAATATTAATAAAATAAT
297632 AAT-TAAA
1 AATATAAA
297639 ATAGCGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.15
21 11 0.41
22 8 0.30
23 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
AATATAAATATTAATAAAATAAT
Found at i:297968 original size:91 final size:92
Alignment explanation
Indices: 297812--298025 Score: 245
Period size: 91 Copynumber: 2.3 Consensus size: 92
297802 GGGGGGGGAC
* * * * ** *
297812 GACACTGCTCATACGTGATGAAGAGGTCTGGTCGTCTAAGGGTGGATGATAACTCGGTTCCTACG
1 GACACGGCTCATACGTGATGAAGAGATCTGGCCATCTAAGGAAGGATGATAACACGGTTCCTACG
* *
297877 TGATGAGGA-TGACTGGTT-GGT-GGAT
66 TGATGAGGACAG-CTGGTTAGCTAGGAT
* * * * *
297902 GACATGGCTCGTACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACACGGTTCCTAC
1 GACACGGCTCATACGTGATGAAGAGATCTGGCCATC-TAAGGAAGGATGATAACACGGTTCCTAC
* *
297967 GTGATGAGGACAGCTGGTTATCTAGGGT
65 GTGATGAGGACAGCTGGTTAGCTAGGAT
297995 GACACGGCTCATACGTGATGAAGAGATCTGG
1 GACACGGCTCATACGTGATGAAGAGATCTGG
298026 TCGGGGAATG
Statistics
Matches: 102, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
90 30 0.29
91 39 0.38
92 2 0.02
93 31 0.30
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (92 bp):
GACACGGCTCATACGTGATGAAGAGATCTGGCCATCTAAGGAAGGATGATAACACGGTTCCTACG
TGATGAGGACAGCTGGTTAGCTAGGAT
Found at i:298048 original size:40 final size:41
Alignment explanation
Indices: 297954--298314 Score: 171
Period size: 46 Copynumber: 8.5 Consensus size: 41
297944 AAGGGTGATA
* * * * * *
297954 ACACGGTTCCTACGTGATGAGGACAGCTGGTTATCTAGGG-TG
1 ACACGGCTCATACGTGATGAAGAGATCTGG--ATCAAGGGATG
*
297996 ACACGGCTCATACGTGATGAAGAGATCTGG-TC-GGGGAATG
1 ACACGGCTCATACGTGATGAAGAGATCTGGATCAAGGG-ATG
* *
298036 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGATCTGG--ATC--AAGG-GATG
* * * * * * *
298082 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCATACGTGATGAAGA-GATCTGG--ATCAAGGGATG
* *
298125 ACACGGCTCCTACGTGATGAAGAGATCT-GATCTAGGGAATG
1 ACACGGCTCATACGTGATGAAGAGATCTGGATCAAGGG-ATG
* *
298166 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGATCTGG--ATC--AAGG-GATG
* * * * * * * *
298212 ACACGGTTCCTATGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCATACGTGATGAAGA-GATCTGG--ATCAAGGGATG
* * *
298255 ACACGGCTCCTACGTGATGAGGAGATCTGG-TC-TGGTGATG
1 ACACGGCTCATACGTGATGAAGAGATCTGGATCAAGG-GATG
* * *
298295 ACACGGTTCCTACATGATGA
1 ACACGGCTCATACGTGATGA
298315 GGACGGCTGG
Statistics
Matches: 251, Mismatches: 47, Indels: 44
0.73 0.14 0.13
Matches are distributed among these distances:
38 3 0.01
39 3 0.01
40 61 0.24
41 28 0.11
42 29 0.12
43 54 0.22
44 7 0.03
46 62 0.25
47 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (41 bp):
ACACGGCTCATACGTGATGAAGAGATCTGGATCAAGGGATG
Found at i:298201 original size:130 final size:129
Alignment explanation
Indices: 297870--298314 Score: 655
Period size: 130 Copynumber: 3.4 Consensus size: 129
297860 ATAACTCGGT
* * * *
297870 TCCTACGTGATGAGGATGA-CTGGT-TGGTGGATGACATGGCTCGTACGTGATGAAGAGTTCTGG
1 TCCTACGTGATGAAGA-GATCTGGTCTGG-GAATGACACGGCTCATACGTGATGAAGAGTTCTGG
* *
297933 CCATCTTTAGGAAGGGTGATAACACGGTTCCTACGTGATGAGGACAGCTGGTTATCTA-GGGTGA
64 CCATC--TA--AA-GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGA
297997 CACGGC
124 CACGGC
* *
298003 TCATACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
1 TCCTACGTGATGAAGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
298068 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
66 ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
*
298132 TCCTACGTGATGAAGAGATCTGATCTAGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGC
1 TCCTACGTGATGAAGAGATCTGGTCT-GGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGC
*
298197 CATCTAAAGGTGATAACACGGTTCCTATGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
65 CATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
* * * *
298262 TCCTACGTGATGAGGAGATCTGGTCTGGTG-ATGACACGGTTCCTACATGATGA
1 TCCTACGTGATGAAGAGATCTGGTCTGG-GAATGACACGGCTCATACGTGATGA
298315 GGACGGCTGG
Statistics
Matches: 290, Mismatches: 17, Indels: 14
0.90 0.05 0.04
Matches are distributed among these distances:
128 43 0.15
129 58 0.20
130 127 0.44
131 2 0.01
132 2 0.01
133 56 0.19
134 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.26
Consensus pattern (129 bp):
TCCTACGTGATGAAGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCC
ATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGC
Found at i:298809 original size:95 final size:93
Alignment explanation
Indices: 298649--298820 Score: 231
Period size: 95 Copynumber: 1.8 Consensus size: 93
298639 TGTTTCCAAA
298649 GAAACAAACTCAAAGATTTTTCTCAAAGAAACTGTCTCGAGAGAAACAAAATTTCGTTTACAAAG
1 GAAACAAACTCAAAGATTTTTCTCAAAGAAACTGTCTCGAGAGAAACAAAATTTCGTTTACAAAG
*
298714 AAAGAGATTCAATGATTTTTTTTTAAAG
66 AAACAGATTCAATGATTTTTTTTTAAAG
* ** * * *
298742 GAAACAAACTCAAAGATTTTTTTCTCAAAAGAAATTGTCTTTA-AGAGATAAAATTTTGTTT-CA
1 GAAACAAACTCAAAGA--TTTTTCTC-AAAGAAACTGTCTCGAGAGAAACAAAATTTCGTTTAC-
298805 AAAGAAACAGATTCAA
62 AAAGAAACAGATTCAA
298821 AGATGGATTA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
93 16 0.24
94 1 0.01
95 38 0.56
96 13 0.19
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (93 bp):
GAAACAAACTCAAAGATTTTTCTCAAAGAAACTGTCTCGAGAGAAACAAAATTTCGTTTACAAAG
AAACAGATTCAATGATTTTTTTTTAAAG
Found at i:299140 original size:29 final size:29
Alignment explanation
Indices: 299099--299535 Score: 165
Period size: 30 Copynumber: 14.1 Consensus size: 29
299089 AGAGACAAAA
299099 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTT-CAAAGAAACAAACTCAAAGAT
** * * *
299129 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTC-AAAGAAACAAAC-TCA-A-AG----AT
299166 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTT-CAAAGAAACAAACTCAAAGAT
** * * *
299196 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTC-AAAGAAACAAAC-TCA-A-AG----AT
299233 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTT-CAAAGAAACAAACTCAAAGAT
* * * *
299263 TTTTGTTTCAAAAGAAACTATCTTAAAAGAGACAAAA
1 TTTTGTTTC-AAAGAAACAAAC-T-CAA-AG----AT
299300 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTT-CAAAGAAACAAACTCAAAGAT
*
299330 TTTTGTTTCAAAAGAAACAATCTCAAAGAT
1 TTTTGTTTC-AAAGAAACAAACTCAAAGAT
** *** **
299360 TTTT-TCACAAAATTGTCTCAAGAGACAAA-A-
1 TTTTGTTTC-AAA--GAAACAA-ACTCAAAGAT
* * *
299390 CTTTGTTTCAAAGTAAATAGACTCAAAGA-
1 TTTTGTTTCAAAG-AAACAAACTCAAAGAT
*
299419 TTTT-TTTCAAACGAAAC-AACTCACAGAT
1 TTTTGTTTCAAA-GAAACAAACTCAAAGAT
* * * *
299447 TTTTATTCCAAAGGAACAAACTCCAAGAT
1 TTTTGTTTCAAAGAAACAAACTCAAAGAT
* * *
299476 TTTT-ATTCAAAAGGAACAAACCCAAAGA-
1 TTTTGTTTC-AAAGAAACAAACTCAAAGAT
*
299504 -TTT-TTTCAAGAGGAACAAACTCAAAGAT
1 TTTTGTTTCAA-AGAAACAAACTCAAAGAT
299532 TTTT
1 TTTT
299536 TCCTCAAAAG
Statistics
Matches: 304, Mismatches: 61, Indels: 85
0.68 0.14 0.19
Matches are distributed among these distances:
26 2 0.01
27 30 0.10
28 26 0.09
29 55 0.18
30 92 0.30
31 12 0.04
32 8 0.03
33 6 0.02
34 6 0.02
35 4 0.01
36 5 0.02
37 55 0.18
38 3 0.01
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.31
Consensus pattern (29 bp):
TTTTGTTTCAAAGAAACAAACTCAAAGAT
Found at i:299150 original size:67 final size:67
Alignment explanation
Indices: 299003--299346 Score: 543
Period size: 67 Copynumber: 5.2 Consensus size: 67
298993 AAAGATTTAC
* * * * * * *
299003 TTCAAAAGAAACTGTCTCAAGAGATACAAAATTCAT-TTT--AAGAGAAACAGATTCAAAGATTT
1 TTCAAAAGAAATTATCTTAAGAGAGACAAAATT-TTGTTTCCAA-AGAAACAAACTCAAAGATTT
299065 TT-T
64 TTGT
**
299068 CCCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
299133 GT
66 GT
299135 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
299200 GT
66 GT
299202 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
299267 GT
66 GT
* *
299269 TTCAAAAGAAACTATCTTAAAAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
299334 GT
66 GT
299336 TTCAAAAGAAA
1 TTCAAAAGAAA
299347 CAATCTCAAA
Statistics
Matches: 262, Mismatches: 13, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
64 1 0.00
65 30 0.11
66 20 0.08
67 211 0.81
ACGTcount: A:0.46, C:0.13, G:0.12, T:0.30
Consensus pattern (67 bp):
TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
GT
Found at i:299180 original size:37 final size:36
Alignment explanation
Indices: 299129--299317 Score: 150
Period size: 37 Copynumber: 5.5 Consensus size: 36
299119 ACTCAAAGAT
*
299129 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACTATCTTAA-AGAGACAAAA
* * * * *
299166 TTTTGTTTCCAAAGAAACAAAC-TCAA-AG----AT
1 TTTTGTTTCAAAAGAAACTATCTTAAAGAGACAAAA
*
299196 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACTATCTTAA-AGAGACAAAA
* * * * *
299233 TTTTGTTTCCAAAGAAACAAAC-TCAA-AG----AT
1 TTTTGTTTCAAAAGAAACTATCTTAAAGAGACAAAA
299263 TTTTGTTTCAAAAGAAACTATCTTAAAAGAGACAAAA
1 TTTTGTTTCAAAAGAAACTATCTT-AAAGAGACAAAA
*
299300 TTTTGTTTCCAAAGAAAC
1 TTTTGTTTCAAAAGAAAC
299318 AAACTCAAAG
Statistics
Matches: 114, Mismatches: 24, Indels: 28
0.69 0.14 0.17
Matches are distributed among these distances:
30 39 0.34
31 3 0.03
32 3 0.03
33 4 0.04
34 4 0.04
35 2 0.02
36 4 0.04
37 55 0.48
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (36 bp):
TTTTGTTTCAAAAGAAACTATCTTAAAGAGACAAAA
Found at i:299365 original size:27 final size:28
Alignment explanation
Indices: 299295--299548 Score: 176
Period size: 29 Copynumber: 8.8 Consensus size: 28
299285 TTAAAAGAGA
*
299295 CAAA-ATTTTGTTTCCAAAGAAACAAACT
1 CAAAGATTTT-TTTCAAAAGAAACAAACT
*
299323 CAAAGATTTTTGTTTCAAAAGAAACAATCT
1 CAAAGA-TTTT-TTTCAAAAGAAACAAACT
* *** **
299353 CAAAGATTTTTTCACAAAATTGTCTCAAGAGA
1 CAAAGATTTTTT-TCAAAA--GAAACAA-ACT
* * *
299385 CAAA-ACTTTGTTTC-AAAGTAAATAGACT
1 CAAAGA-TTTTTTTCAAAAG-AAACAAACT
*
299413 CAAAGATTTTTTTCAAACGAAAC-AACT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
* * *
299440 CACAGATTTTTATTCCAAAGGAACAAACT
1 CAAAGATTTTT-TTCAAAAGAAACAAACT
* * *
299469 CCAAGATTTTTATTCAAAAGGAACAAACC
1 CAAAGATTTTT-TTCAAAAGAAACAAACT
* *
299498 CAAAGA-TTTTTTCAAGAGGAACAAACT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
299525 CAAAGATTTTTTCCTCAAAAGAAA
1 CAAAGATTTTTT--TCAAAAGAAA
299549 TTGTCTTTAA
Statistics
Matches: 176, Mismatches: 35, Indels: 28
0.74 0.15 0.12
Matches are distributed among these distances:
27 34 0.19
28 40 0.23
29 49 0.28
30 38 0.22
31 6 0.03
32 9 0.05
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.29
Consensus pattern (28 bp):
CAAAGATTTTTTTCAAAAGAAACAAACT
Found at i:299398 original size:90 final size:87
Alignment explanation
Indices: 299289--299450 Score: 236
Period size: 90 Copynumber: 1.8 Consensus size: 87
299279 ACTATCTTAA
*
299289 AAGAGACAAAATTTTGTTTCCAAAG-AAACAAACTCAAAGATTTTTGTTTCAAAAGAAACAATCT
1 AAGAGACAAAACTTTGTTT-CAAAGTAAACAAACTCAAAGA-TTTT-TTTCAAAAGAAACAA-CT
299353 CAAAGATTTTTTCACAAAATTGTCTC
62 CAAAGATTTTTTCACAAAATTGTCTC
* * * *
299379 AAGAGACAAAACTTTGTTTCAAAGTAAATAGACTCAAAGATTTTTTTCAAACGAAACAACTCACA
1 AAGAGACAAAACTTTGTTTCAAAGTAAACAAACTCAAAGATTTTTTTCAAAAGAAACAACTCAAA
299444 GATTTTT
66 GATTTTT
299451 ATTCCAAAGG
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
87 12 0.18
88 14 0.21
89 9 0.14
90 31 0.47
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.31
Consensus pattern (87 bp):
AAGAGACAAAACTTTGTTTCAAAGTAAACAAACTCAAAGATTTTTTTCAAAAGAAACAACTCAAA
GATTTTTTCACAAAATTGTCTC
Found at i:299518 original size:56 final size:56
Alignment explanation
Indices: 299410--299548 Score: 167
Period size: 56 Copynumber: 2.4 Consensus size: 56
299400 AAGTAAATAG
* * *
299410 ACTCAAAGATTTTTTTCAAACGAAACAACTCACAGATTTTTATTCCAAAGGAACAA
1 ACTCAAAGATTTTTTTCAAAAGAAACAACCCAAAGATTTTTATTCCAAAGGAACAA
* *
299466 ACTCCAAGATTTTTATTCAAAAGGAACAAACCCAAAGA-TTTT-TT-CAAGAGGAACAA
1 ACTCAAAGATTTTT-TTCAAAAGAAAC-AACCCAAAGATTTTTATTCCAA-AGGAACAA
299522 ACTCAAAGATTTTTTCCTCAAAAGAAA
1 ACTCAAAGATTTTTT--TCAAAAGAAA
299549 TTGTCTTTAA
Statistics
Matches: 71, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
55 4 0.06
56 36 0.51
57 23 0.32
58 8 0.11
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (56 bp):
ACTCAAAGATTTTTTTCAAAAGAAACAACCCAAAGATTTTTATTCCAAAGGAACAA
Found at i:299837 original size:34 final size:32
Alignment explanation
Indices: 299790--299917 Score: 112
Period size: 33 Copynumber: 3.8 Consensus size: 32
299780 AGAAAATGAT
**
299790 GTCTCAAGCGAGACGAAATTTGCTTTAAGATATA
1 GTCTCAAATGAGAC-AAATTTG-TTTAAGATATA
**
299824 GTCTCAAATGAGACAAAGTTTGTTTTTGATATA
1 GTCTCAAATGAGACAAA-TTTGTTTAAGATATA
* *
299857 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAATGAGAC-AAATTTG--TTTA-AGATATA
**
299893 GTCTCAAGCGAGACAAAGTTTGTTT
1 GTCTCAAATGAGACAAA-TTTGTTT
299918 TTGAGAAACG
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
33 30 0.38
34 22 0.28
35 6 0.08
36 20 0.26
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (32 bp):
GTCTCAAATGAGACAAATTTGTTTAAGATATA
Found at i:299913 original size:69 final size:67
Alignment explanation
Indices: 299790--299921 Score: 174
Period size: 69 Copynumber: 1.9 Consensus size: 67
299780 AGAAAATGAT
* * * *
299790 GTCTCAAGCGAGACGAAATTTGCTTTAAGATATAGTCTCAAATGAGACAAAGTTTGTTTTTGATA
1 GTCTCAAACGAGACAAAATTTGCTTTAAGAAATAGTCTCAAACGAGACAAAGTTTGTTTTTGATA
299855 TA
66 TA
* * * *
299857 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGACAAAGTTTGTTTTTGA
1 GTCTCAAACGAGACAAAATTTG-CTTTA-AGAAATAGTCTCAAACGAGACAAAGTTTGTTTTTGA
299922 GAAACGATCT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
67 19 0.35
68 4 0.07
69 32 0.58
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (67 bp):
GTCTCAAACGAGACAAAATTTGCTTTAAGAAATAGTCTCAAACGAGACAAAGTTTGTTTTTGATA
TA
Found at i:299952 original size:35 final size:33
Alignment explanation
Indices: 299823--299940 Score: 137
Period size: 33 Copynumber: 3.4 Consensus size: 33
299813 TTTAAGATAT
* *
299823 AGTCTCAAATGAGACAAAGTTTGTTTTTGATAT
1 AGTCTCAAATGAGACAAAGTTTGTTTTTGAGAA
*
299856 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAA
1 AGTCTCAAATGAGACAAAGTTTGTTTTT-GAGAA
**
299890 ATTGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAA
1 A--GTCTCAAATGAGACAAAGTTTGTTTTTGAGAA
*
299925 ACGATCTCAAGTGAGA
1 A-G-TCTCAAATGAGA
299941 TCAACTTTGT
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
33 27 0.37
34 5 0.07
35 17 0.23
36 24 0.33
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (33 bp):
AGTCTCAAATGAGACAAAGTTTGTTTTTGAGAA
Found at i:300006 original size:101 final size:99
Alignment explanation
Indices: 299893--300120 Score: 250
Period size: 101 Copynumber: 2.3 Consensus size: 99
299883 TAGAGAAATT
* *
299893 GTCTCAAGCGAGACAAAGTTTGTTTTTG-AGAAAC--GATCTCAA-GTGAGATCAACTTTGTTTA
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAAGAAACAACATCT-AAGGTGAGAT----TTTGTTTA
* *
299954 -ATGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
60 TA-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
299994 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTTTGTTTTTAGT
1 GTCTCAAGCGAGACAAAATTTGTTTTG-AAGAAACAAC-ATCTAAGGTGAGATTTTGTTTATAGT
* * *
300059 GAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
64 GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
**
300095 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
300121 AAAATTCTCA
Statistics
Matches: 110, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
100 5 0.05
101 85 0.77
102 7 0.06
104 2 0.02
105 11 0.10
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (99 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAAGAAACAACATCTAAGGTGAGATTTTGTTTATAGTGA
AACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:300283 original size:36 final size:35
Alignment explanation
Indices: 300243--300341 Score: 153
Period size: 36 Copynumber: 2.7 Consensus size: 35
300233 AAAGGGAAAA
**
300243 TGTCTCAAATGAGACAAAGTTTGTTTTGAAATAAAT
1 TGTCTCAAGCGAGACAAA-TTTGTTTTGAAATAAAT
300279 TGTCTCAAGCGAGACAATATTTGTTTTGAAATAAAT
1 TGTCTCAAGCGAGACAA-ATTTGTTTTGAAATAAAT
300315 TGTCTCAAGCGAGACAAAATTTGTTTT
1 TGTCTCAAGCGAGAC-AAATTTGTTTT
300342 TAGAAAAATC
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
36 56 0.95
37 3 0.05
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.36
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAATTTGTTTTGAAATAAAT
Found at i:306626 original size:22 final size:22
Alignment explanation
Indices: 306583--306626 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
306573 AAATTTACAT
*
306583 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
306605 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
306627 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:308591 original size:12 final size:11
Alignment explanation
Indices: 308541--308593 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
308531 AATATGTAAA
* *
308541 AATATAATATT
1 AATAAAATAAT
308552 AATAAAATAAT
1 AATAAAATAAT
308563 AATATAAAT-AT
1 AATA-AAATAAT
308574 AA-AAAATAAT
1 AATAAAATAAT
308584 AATTAAAATA
1 AA-TAAAATA
308594 GCGATAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
9 4 0.11
10 5 0.14
11 17 0.47
12 10 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:308593 original size:21 final size:23
Alignment explanation
Indices: 308541--308590 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
308531 AATATGTAAA
308541 AATAT-AATATTAATAAAATAAT
1 AATATAAATATTAATAAAATAAT
308563 AATATAAATA-TAA-AAAATAAT
1 AATATAAATATTAATAAAATAAT
308584 AAT-TAAA
1 AATATAAA
308591 ATAGCGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.15
21 11 0.41
22 8 0.30
23 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
AATATAAATATTAATAAAATAAT
Found at i:313145 original size:70 final size:70
Alignment explanation
Indices: 313032--313172 Score: 237
Period size: 70 Copynumber: 2.0 Consensus size: 70
313022 TCTTAAGAAA
* *
313032 AGCCGATTATTAGAACTACAGAGTTTTTAACCAACACATTATGGGTAATGATGTTATAATTCACG
1 AGCCGATTATTAGAACTACAGAGTTTTTAACCAACACACTATGGGTAATGATGCTATAATTCACG
313097 GATAG
66 GATAG
* * *
313102 AGCCGGTTATTAGAACTATAGAGTTTTTAACCAACACACTATGGGTAATGATGCTATGATTCACG
1 AGCCGATTATTAGAACTACAGAGTTTTTAACCAACACACTATGGGTAATGATGCTATAATTCACG
313167 GATAG
66 GATAG
313172 A
1 A
313173 CAATAAGTTC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (70 bp):
AGCCGATTATTAGAACTACAGAGTTTTTAACCAACACACTATGGGTAATGATGCTATAATTCACG
GATAG
Found at i:325867 original size:30 final size:30
Alignment explanation
Indices: 325822--325894 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
325812 GGTTCTTCAG
* * *
325822 GACCTATGGACAGTTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
325852 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
325882 GACCTCTGGATAG
1 GACCTCTGGATAG
325895 GTCCTTCGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:332297 original size:22 final size:21
Alignment explanation
Indices: 332272--332342 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 21
332262 TCAATACACG
*
332272 AAAGTGCATTAGCACTGGTACT
1 AAAGTG-ATTAGCACTGATACT
* *
332294 AAAGTGACTTAACACTGATACG
1 AAAGTGA-TTAGCACTGATACT
*
332316 AAAGTGTATTTGCACTGATACT
1 AAAGTG-ATTAGCACTGATACT
332338 AAAGT
1 AAAGT
332343 ATCTTAGCAC
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 1 0.02
22 39 0.95
23 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (21 bp):
AAAGTGATTAGCACTGATACT
Found at i:332352 original size:22 final size:22
Alignment explanation
Indices: 332280--332354 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
332270 CGAAAGTGCA
*
332280 TTAGCACTGGTACTAAAGTGA-C
1 TTAGCACTGATACTAAAGT-ATC
* * * *
332302 TTAACACTGATACGAAAGTGTA
1 TTAGCACTGATACTAAAGTATC
*
332324 TTTGCACTGATACTAAAGTATC
1 TTAGCACTGATACTAAAGTATC
332346 TTAGCACTG
1 TTAGCACTG
332355 CTGTCATATA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (22 bp):
TTAGCACTGATACTAAAGTATC
Found at i:335173 original size:21 final size:22
Alignment explanation
Indices: 335125--335176 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
335115 ACGTATAATT
*
335125 ATAAATTAGTTAAAATTTTAAAG
1 ATAAATTAGTTAAAA-TTAAAAG
* *
335148 GTAAATTATTTAAAA-TAAAAG
1 ATAAATTAGTTAAAATTAAAAG
335169 ATAAATTA
1 ATAAATTA
335177 CATCAGTGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 12 0.48
23 13 0.52
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.37
Consensus pattern (22 bp):
ATAAATTAGTTAAAATTAAAAG
Found at i:336833 original size:3 final size:3
Alignment explanation
Indices: 336825--336918 Score: 188
Period size: 3 Copynumber: 31.3 Consensus size: 3
336815 TTTTACCAAT
336825 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
336873 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG G
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG G
336919 TTGGCAGGCC
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:338608 original size:16 final size:17
Alignment explanation
Indices: 338587--338620 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
338577 TTTTATTATT
*
338587 ATTTAATATAAA-AATA
1 ATTTAAAATAAATAATA
338603 ATTTAAAATAAATAATA
1 ATTTAAAATAAATAATA
338620 A
1 A
338621 AATAATATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTTAAAATAAATAATA
Found at i:339209 original size:16 final size:17
Alignment explanation
Indices: 339176--339209 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
339166 TTTTATGTTT
*
339176 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
339193 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
339209 T
1 T
339210 AATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:340272 original size:13 final size:13
Alignment explanation
Indices: 340251--340284 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
340241 CAAAGATTTT
340251 TAATTTTAAAAAA
1 TAATTTTAAAAAA
* *
340264 TATTTTTAAAATA
1 TAATTTTAAAAAA
340277 TAATTTTA
1 TAATTTTA
340285 TTTTGGGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATTTTAAAAAA
Found at i:340393 original size:31 final size:31
Alignment explanation
Indices: 340358--340425 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
340348 TCAAAAAACA
* **
340358 TAAGATATAATCACTTTTGTTTTTACTTAAT
1 TAAGATATAACCACTTTCATTTTTACTTAAT
* *
340389 TAAGATATGACCACTTTCATTTTTATTTAAT
1 TAAGATATAACCACTTTCATTTTTACTTAAT
340420 TAAGAT
1 TAAGAT
340426 GTGGTCACTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.10, G:0.07, T:0.49
Consensus pattern (31 bp):
TAAGATATAACCACTTTCATTTTTACTTAAT
Found at i:340801 original size:13 final size:14
Alignment explanation
Indices: 340774--340812 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
340764 CGGTACCCAA
*
340774 TTTATTATATATTT
1 TTTATTTTATATTT
340788 TTTATTTT-TA-TT
1 TTTATTTTATATTT
340800 TTTATTTTATATT
1 TTTATTTTATATT
340813 AAATTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 10 0.45
13 4 0.18
14 8 0.36
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATATTT
Found at i:341214 original size:24 final size:23
Alignment explanation
Indices: 341186--341252 Score: 68
Period size: 25 Copynumber: 2.9 Consensus size: 23
341176 ATATAATATA
341186 ATTTTATATATATTAACTTAAAAT
1 ATTTT-TATATATTAACTTAAAAT
341210 A-TTTT-TATATTAACTTATTAAAT
1 ATTTTTATATATTAACTTA--AAAT
*
341233 ATATTTTA-CTATTAACTTAA
1 AT-TTTTATATATTAACTTAA
341253 TTTAAAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
21 12 0.32
22 1 0.03
23 9 0.24
24 1 0.03
25 14 0.38
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTTTTATATATTAACTTAAAAT
Found at i:341218 original size:21 final size:22
Alignment explanation
Indices: 341194--341252 Score: 84
Period size: 21 Copynumber: 2.6 Consensus size: 22
341184 TAATTTTATA
341194 TATATTAACTTAAAATAT-TTT
1 TATATTAACTTAAAATATATTT
341215 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA--AAATATATTT
341239 TACTATTAACTTAA
1 TA-TATTAACTTAA
341253 TTTAAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.35
23 7 0.21
24 5 0.15
25 10 0.29
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATTAACTTAAAATATATTT
Found at i:341236 original size:25 final size:27
Alignment explanation
Indices: 341198--341266 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 27
341188 TTTATATATA
*
341198 TTAACTTAAAATATTTTTA-TATTAAC
1 TTAATTTAAAATATTTTTACTATTAAC
341224 TT-A-TT-AAATATATTTTACTATTAAC
1 TTAATTTAAAATAT-TTTTACTATTAAC
341249 TTAATTTAAAAATATTTT
1 TTAATTT-AAAATATTTT
341267 ATTTATAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
23 6 0.16
24 7 0.19
25 10 0.27
26 3 0.08
27 2 0.05
28 3 0.08
29 6 0.16
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (27 bp):
TTAATTTAAAATATTTTTACTATTAAC
Found at i:341264 original size:27 final size:24
Alignment explanation
Indices: 341194--341268 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 24
341184 TAATTTTATA
*
341194 TATATTAACTTA--AAATAT-TTT
1 TATATTAACTTATTAAAAATATTT
*
341215 TATATTAACTTATTAAATATATTT
1 TATATTAACTTATTAAAAATATTT
341239 TACTATTAACTTAATTTAAAAATATTT
1 TA-TATTAACTT-A-TTAAAAATATTT
341266 TAT
1 TAT
341269 TTATAATTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
21 12 0.26
23 6 0.13
24 5 0.11
25 9 0.19
26 2 0.04
27 13 0.28
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (24 bp):
TATATTAACTTATTAAAAATATTT
Found at i:341284 original size:27 final size:27
Alignment explanation
Indices: 341205--341267 Score: 87
Period size: 25 Copynumber: 2.4 Consensus size: 27
341195 ATATTAACTT
341205 AAAATATTTTTA-TATTAACTT-A-TTA
1 AAAATA-TTTTACTATTAACTTAATTTA
*
341230 AATATATTTTACTATTAACTTAATTTA
1 AAAATATTTTACTATTAACTTAATTTA
341257 AAAATATTTTA
1 AAAATATTTTA
341268 TTTATAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 5 0.15
25 14 0.42
26 1 0.03
27 13 0.39
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (27 bp):
AAAATATTTTACTATTAACTTAATTTA
Found at i:342715 original size:85 final size:81
Alignment explanation
Indices: 342609--342778 Score: 198
Period size: 81 Copynumber: 2.0 Consensus size: 81
342599 GCTAACAAGT
* * * *
342609 AGCTCCATATAAACCATCCAATTGATATAAGGAAAAAATAGAACATATTCCATTATGT-TTACCA
1 AGCTCCACATAAACCATCCAATGGACAT-A--AAAAAA-A-AACATATTCCATTATGTCTGACCA
*
342673 TCCAATAGATAAATCATGACC
61 TCCAATAGACAAATCATGACC
* * * *
342694 AGCTCCACATAATCCATCCAATGGCCATAAAGAAAAAACATATTCCGTTATGTCTGACCATCCAA
1 AGCTCCACATAAACCATCCAATGGACATAAAAAAAAAACATATTCCATTATGTCTGACCATCCAA
*
342759 TAGACAGATCATGACC
66 TAGACAAATCATGACC
342775 AGCT
1 AGCT
342779 TTATATAATT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
80 16 0.22
81 29 0.39
82 5 0.07
84 1 0.01
85 23 0.31
ACGTcount: A:0.41, C:0.24, G:0.11, T:0.25
Consensus pattern (81 bp):
AGCTCCACATAAACCATCCAATGGACATAAAAAAAAAACATATTCCATTATGTCTGACCATCCAA
TAGACAAATCATGACC
Found at i:349035 original size:38 final size:38
Alignment explanation
Indices: 348992--349065 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
348982 ATTCAATTTG
348992 TTTTTATAAACAATTATATGAAATTATTTGATAAATTA
1 TTTTTATAAACAATTATATGAAATTATTTGATAAATTA
349030 TTTTTATAAACAATTATATGAAATTATTTGATAAAT
1 TTTTTATAAACAATTATATGAAATTATTTGATAAAT
349066 GTAACAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (38 bp):
TTTTTATAAACAATTATATGAAATTATTTGATAAATTA
Found at i:349455 original size:2 final size:2
Alignment explanation
Indices: 349448--349482 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
349438 AACAATAATT
349448 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
349483 CATCAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:354442 original size:9 final size:9
Alignment explanation
Indices: 354430--354455 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
354420 ATCATCACCA
354430 TCGTCATCG
1 TCGTCATCG
354439 TCGTCATCG
1 TCGTCATCG
354448 TCGTCATC
1 TCGTCATC
354456 CTGAGCAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.19, T:0.35
Consensus pattern (9 bp):
TCGTCATCG
Found at i:356408 original size:17 final size:18
Alignment explanation
Indices: 356388--356428 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
356378 AAATTATATT
356388 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
356405 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
356423 ATTAAA
1 AGTAAA
356429 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:356628 original size:50 final size:51
Alignment explanation
Indices: 356568--356686 Score: 152
Period size: 50 Copynumber: 2.3 Consensus size: 51
356558 CCCCCCTGTA
* *
356568 CCGCGTTATACCCCACGTGTCAGATAAAC-AG-ATATAGCGTGGATCAGGGG
1 CCGCGCTATACCCCACGTGTCAGATAAACGAGCATATAGCGCGGATCA-GGG
* *
356618 CCGCGCTATACCCCACGTGTCAGATAAACGTGGCGTATAGCGCGGATCAGGG
1 CCGCGCTATACCCCACGTGTCAGATAAACG-AGCATATAGCGCGGATCAGGG
*
356670 CGCGTGCTATACCCCAC
1 C-CGCGCTATACCCCAC
356687 ATGGCGCCAA
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
50 28 0.47
52 5 0.08
53 27 0.45
ACGTcount: A:0.24, C:0.29, G:0.28, T:0.18
Consensus pattern (51 bp):
CCGCGCTATACCCCACGTGTCAGATAAACGAGCATATAGCGCGGATCAGGG
Found at i:358450 original size:22 final size:22
Alignment explanation
Indices: 358408--358466 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
358398 TATTTCTATT
*
358408 TTTATATTTTGAAATTAAAATG
1 TTTATATTTTAAAATTAAAATG
* *
358430 TTTATATTTGTAAAATTAAATTA
1 TTTATATTT-TAAAATTAAAATG
*
358453 TTTTTATTTTAAAA
1 TTTATATTTTAAAA
358467 AATAAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (22 bp):
TTTATATTTTAAAATTAAAATG
Found at i:366871 original size:12 final size:13
Alignment explanation
Indices: 366827--366870 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
366817 CGCCCCGATT
*
366827 ACCCGATTACTCG
1 ACCCGATTACCCG
*
366840 CCCCGATTACCCG
1 ACCCGATTACCCG
366853 -CCCGA-TACCCG
1 ACCCGATTACCCG
366864 ACCCGAT
1 ACCCGAT
366871 AAATATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 6 0.22
12 10 0.37
13 11 0.41
ACGTcount: A:0.20, C:0.48, G:0.16, T:0.16
Consensus pattern (13 bp):
ACCCGATTACCCG
Done.