Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008463.1 Hibiscus syriacus cultivar Beakdansim tig00111276_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: 1833679
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:109439 original size:15 final size:16
Alignment explanation
Indices: 109405--109441 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
109395 GAAACTCCTC
*
109405 TTTTCTTTCTCTCAAT
1 TTTTCTTTCTCTCAAA
109421 TTTTCTTTCTC-CAAA
1 TTTTCTTTCTCTCAAA
109436 TTTTCT
1 TTTTCT
109442 CAATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTCTTTCTCTCAAA
Found at i:113334 original size:24 final size:24
Alignment explanation
Indices: 113244--113334 Score: 123
Period size: 23 Copynumber: 3.9 Consensus size: 24
113234 TATTATATGA
*
113244 CACTACGGTGC-ATTTCTACGCGG
1 CACTTCGGTGCAATTTCTACGCGG
113267 CACTTCGGTGC-ATTTCTACGCGG
1 CACTTCGGTGCAATTTCTACGCGG
* *
113290 CACTTCGGTGCAAATTCTACGTGG
1 CACTTCGGTGCAATTTCTACGCGG
* *
113314 CACTTCGGTACAATTTATACG
1 CACTTCGGTGCAATTTCTACG
113335 AGCTGTGGTG
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
23 33 0.54
24 28 0.46
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (24 bp):
CACTTCGGTGCAATTTCTACGCGG
Found at i:113983 original size:21 final size:21
Alignment explanation
Indices: 113953--113992 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
113943 AGCAGTACTG
*
113953 TAGCATTGCATCGATGCACTA
1 TAGCAATGCATCGATGCACTA
113974 TAGCAATGCATCGATGCAC
1 TAGCAATGCATCGATGCAC
113993 AATTTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
TAGCAATGCATCGATGCACTA
Found at i:118708 original size:90 final size:90
Alignment explanation
Indices: 118552--118729 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 90
118542 CCTAACACAC
* *
118552 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGCTTTCATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTCATTATTTCAAATTAATTAAATATAT
* *
118617 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
* * *
118642 CCTTTTATATCCAAGTTACCCTAATCATATTATGGATTTTATTATTTCAAATTAATTAAATATAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTCATTATTTCAAATTAATTAAATATAT
118707 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
118730 TTCAGGATTA
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTCATTATTTCAAATTAATTAAATATAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:118709 original size:22 final size:23
Alignment explanation
Indices: 118684--118754 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 23
118674 TGGATTTTAT
118684 TATTTCAAATTAATT-AAATATA
1 TATTTCAAATTAATTAAAATATA
*
118706 TATTT--AATTAATTGAAAT-TA
1 TATTTCAAATTAATTAAAATATA
* *
118726 AATATTCAGGATT-ATTAAAATATA
1 TAT-TTCA-AATTAATTAAAATATA
118750 TATTT
1 TATTT
118755 AATTAGCTCC
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
20 12 0.31
21 6 0.15
22 5 0.13
23 9 0.23
24 7 0.18
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (23 bp):
TATTTCAAATTAATTAAAATATA
Found at i:118716 original size:20 final size:21
Alignment explanation
Indices: 118691--118759 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
118681 TATTATTTCA
118691 AATTAATT-AAATATATATTT
1 AATTAATTAAAATATATATTT
* * *
118711 AATTAATTGAAATTAAATATTC
1 AATTAATT-AAAATATATATTT
118733 AGGATT-ATTAAAATATATATTT
1 A--ATTAATTAAAATATATATTT
118755 AATTA
1 AATTA
118760 GCTCCAGATA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
20 11 0.29
22 21 0.55
23 3 0.08
24 3 0.08
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (21 bp):
AATTAATTAAAATATATATTT
Found at i:125116 original size:20 final size:20
Alignment explanation
Indices: 125093--125130 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
125083 ATCATTATAC
*
125093 TCCTTAATATTTACATAAAT
1 TCCTTAATATTTAAATAAAT
125113 TCCTTAATATTTAAATAA
1 TCCTTAATATTTAAATAA
125131 GTCATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.00, T:0.45
Consensus pattern (20 bp):
TCCTTAATATTTAAATAAAT
Found at i:130050 original size:2 final size:2
Alignment explanation
Indices: 130045--130079 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
130035 AAATTAAAAT
130045 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
130080 TAAAAAAGAA
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:130469 original size:19 final size:21
Alignment explanation
Indices: 130432--130475 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
130422 GAAATGAAGG
*
130432 TTTTCAAAGTTTTGAG-TTTA
1 TTTTCAAAGATTTGAGTTTTA
*
130452 TTTTCAAA-ATTTGTGTTTTA
1 TTTTCAAAGATTTGAGTTTTA
130472 TTTT
1 TTTT
130476 TAAATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.23, C:0.05, G:0.11, T:0.61
Consensus pattern (21 bp):
TTTTCAAAGATTTGAGTTTTA
Found at i:133831 original size:18 final size:18
Alignment explanation
Indices: 133805--133843 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
133795 ATATTATTTT
* *
133805 AAAATTTAAATATTAATA
1 AAAAGTTAAACATTAATA
133823 AAAAGTTAAACATTAATA
1 AAAAGTTAAACATTAATA
133841 AAA
1 AAA
133844 CAATACAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAAGTTAAACATTAATA
Found at i:141254 original size:31 final size:31
Alignment explanation
Indices: 141192--141255 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
141182 ATTTGGGTTT
**
141192 GGATTTTTTTTAAAAAAATCGGGATTGAGTC
1 GGATTTTTTTTAAAAAAATCGGGATCAAGTC
141223 GGATTTTTTTTAAAAAAATCGAGG-TCAAGTC
1 GGATTTTTTTTAAAAAAATCG-GGATCAAGTC
141254 GG
1 GG
141256 GTCGGGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (31 bp):
GGATTTTTTTTAAAAAAATCGGGATCAAGTC
Found at i:141875 original size:18 final size:18
Alignment explanation
Indices: 141852--141899 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
141842 AAACAGGTTT
141852 CAGATTCTAATTCCTTCA
1 CAGATTCTAATTCCTTCA
*
141870 CAGATT-TCAATTCTTTCA
1 CAGATTCT-AATTCCTTCA
141888 CAGATTCTAATT
1 CAGATTCTAATT
141900 TCCTCATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 1 0.04
18 25 0.93
19 1 0.04
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (18 bp):
CAGATTCTAATTCCTTCA
Found at i:142455 original size:2 final size:2
Alignment explanation
Indices: 142448--142473 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
142438 GTAAAATCTG
142448 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
142474 ACTTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:155240 original size:16 final size:16
Alignment explanation
Indices: 155204--155244 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
155194 AATTTCATCC
155204 TTATA-TTATATAATA
1 TTATATTTATATAATA
155219 TATATATTTATTATAA-A
1 T-TATATTTA-TATAATA
155236 TTATATTTA
1 TTATATTTA
155245 CATTTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 12 0.52
17 5 0.22
18 5 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATTTATATAATA
Found at i:156266 original size:20 final size:19
Alignment explanation
Indices: 156231--156271 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
156221 TTAATTATCT
156231 TTTATATTACATTATAATA
1 TTTATATTACATTATAATA
* *
156250 TTTATATATATATTATATTA
1 TTTATAT-TACATTATAATA
156270 TT
1 TT
156272 ATTAGTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATATTACATTATAATA
Found at i:156452 original size:18 final size:18
Alignment explanation
Indices: 156429--156488 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
156419 TTTTTATTTT
156429 TATTATTATTATTCTTTA
1 TATTATTATTATTCTTTA
** * *
156447 TATTATCCTTATTATTTC
1 TATTATTATTATTCTTTA
*
156465 TATTATTACTATTCTTTA
1 TATTATTATTATTCTTTA
156483 T-TTATT
1 TATTATT
156489 CATGTAATTA
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTATTATTATTCTTTA
Found at i:156880 original size:24 final size:25
Alignment explanation
Indices: 156837--156884 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
156827 TTACTTTTTA
156837 CTATTATTATTATTTATTTATTATG
1 CTATTATTATTATTTATTTATTATG
156862 CTATTA-TATTATATT-TTTATTAT
1 CTATTATTATTAT-TTATTTATTAT
156885 TACATTCGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (25 bp):
CTATTATTATTATTTATTTATTATG
Found at i:162176 original size:1 final size:1
Alignment explanation
Indices: 162139--162168 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
162129 TCTTAAGTTG
162139 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
162169 GAGAAAAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:162765 original size:1 final size:1
Alignment explanation
Indices: 162759--162785 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
162749 GAGCATCTTC
162759 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
162786 TCATCAAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:163607 original size:105 final size:105
Alignment explanation
Indices: 162978--163587 Score: 1202
Period size: 105 Copynumber: 5.8 Consensus size: 105
162968 GGTTTTACCC
162978 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
163043 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
163083 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
163148 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
163188 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
163253 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
163293 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
163358 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
163398 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
163463 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
66 CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
* *
163503 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAGGTTCAACTTCATGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
163568 CGAAGGGACCGCTGGTTGTC
66 CGAAGGGACCGCTGGTTGTC
163588 GATAAACAAT
Statistics
Matches: 503, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 503 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (105 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATTT
Found at i:163693 original size:20 final size:20
Alignment explanation
Indices: 163668--163709 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
163658 CCAGAACTCT
163668 GAGTTCGACTTCAACTTCAC
1 GAGTTCGACTTCAACTTCAC
* *
163688 GAGTTCGATTTCAATTTCAC
1 GAGTTCGACTTCAACTTCAC
163708 GA
1 GA
163710 CGAAGGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (20 bp):
GAGTTCGACTTCAACTTCAC
Found at i:164486 original size:3 final size:3
Alignment explanation
Indices: 164464--164506 Score: 50
Period size: 3 Copynumber: 13.3 Consensus size: 3
164454 CTTATACGTT
*
164464 TTA TTA TATA TATA TATA TTA TTA TTG TTA TTA TTA TTA TTA T
1 TTA TTA T-TA T-TA T-TA TTA TTA TTA TTA TTA TTA TTA TTA T
164507 ACGTATATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 26 0.70
4 11 0.30
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:164984 original size:23 final size:21
Alignment explanation
Indices: 164957--165010 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
164947 TATTTCTCCC
164957 TTTTACTT-TTTACTATTATTAT
1 TTTTACTTATTTA-TATTA-TAT
*
164979 TATTTATTTATTTATATTATAT
1 T-TTTACTTATTTATATTATAT
165001 TTTTA-TTATT
1 TTTTACTTATT
165011 ACATTCGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 5 0.17
21 4 0.14
22 5 0.17
23 11 0.38
24 4 0.14
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTACTTATTTATATTATAT
Found at i:165010 original size:20 final size:24
Alignment explanation
Indices: 164965--165007 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
164955 CCTTTTACTT
164965 TTTACTATTATTATTATTTATTTA
1 TTTACTATTATTATTATTTATTTA
164989 TTTA-TATTA-TATT-TTTATT
1 TTTACTATTATTATTATTTATT
165008 ATTACATTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 4 0.21
23 5 0.26
24 4 0.21
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTACTATTATTATTATTTATTTA
Found at i:168879 original size:33 final size:33
Alignment explanation
Indices: 168834--168900 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
168824 CGACTTTAAA
168834 TTTAAATGAAAGATTTATAGAAATAAAGTGGGT
1 TTTAAATGAAAGATTTATAGAAATAAAGTGGGT
* *
168867 TTTAAATTAAAGATTTATAGTAATAAAGTGGGT
1 TTTAAATGAAAGATTTATAGAAATAAAGTGGGT
168900 T
1 T
168901 CAAAATTGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.37
Consensus pattern (33 bp):
TTTAAATGAAAGATTTATAGAAATAAAGTGGGT
Found at i:169775 original size:29 final size:29
Alignment explanation
Indices: 169742--169845 Score: 113
Period size: 30 Copynumber: 3.5 Consensus size: 29
169732 TTTAATTATA
169742 TAAAAATATATTTTATTCTTATCTTTACT
1 TAAAAATATATTTTATTCTTATCTTTACT
169771 TAAAAATATATATTTATTCTTAT-TTTACCT
1 TAAAAATATAT-TTTATTCTTATCTTTA-CT
* * * **
169801 TTAAAATGT-TTTTATTCTTACCTTAATTTT
1 TAAAAATATATTTTATTCTTATCTT--TACT
169831 TAAAAATATATTTTA
1 TAAAAATATATTTTA
169846 AAATATCTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
28 10 0.16
29 18 0.29
30 28 0.45
31 6 0.10
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.55
Consensus pattern (29 bp):
TAAAAATATATTTTATTCTTATCTTTACT
Found at i:170012 original size:2 final size:2
Alignment explanation
Indices: 170005--170032 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
169995 AATAAGAATA
170005 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
170033 TAAAATAAGA
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:170032 original size:41 final size:40
Alignment explanation
Indices: 169978--170061 Score: 132
Period size: 41 Copynumber: 2.1 Consensus size: 40
169968 ATGAAAAAAG
* *
169978 TATATATATTATATTAAAATAAGAATAATATATATATATA
1 TATATATATTATATTAAAATAAGAATAAAATATATAAATA
*
170018 TATATATATATATATTAAAATAAGAATAAAATATTTAAATA
1 TATATATAT-TATATTAAAATAAGAATAAAATATATAAATA
170059 TAT
1 TAT
170062 TTTATGCTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 9 0.22
41 31 0.77
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (40 bp):
TATATATATTATATTAAAATAAGAATAAAATATATAAATA
Found at i:170165 original size:28 final size:29
Alignment explanation
Indices: 170085--170204 Score: 99
Period size: 30 Copynumber: 4.1 Consensus size: 29
170075 ATTTTAAAGC
*
170085 ATATATTTTAAAAAGTT-AAGATAA-AATAAA
1 ATATATTTT-CAAA-TTAAAGATAAGAAT-AA
170115 ATATACTTTTCAAATTAAA-ATAAGAATACA
1 ATATA-TTTTCAAATTAAAGATAAGAATA-A
170145 ATATATTTT-AAA-TAAAGATAAGAATAA
1 ATATATTTTCAAATTAAAGATAAGAATAA
* *
170172 GATATATGTTTTTATATTAAA-ATAAGAATAA
1 -ATATA--TTTTCAAATTAAAGATAAGAATAA
170203 AT
1 AT
170205 TGTATTTAAT
Statistics
Matches: 78, Mismatches: 2, Indels: 20
0.78 0.02 0.20
Matches are distributed among these distances:
27 5 0.06
28 17 0.22
29 11 0.14
30 25 0.32
31 16 0.21
32 4 0.05
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.36
Consensus pattern (29 bp):
ATATATTTTCAAATTAAAGATAAGAATAA
Found at i:170197 original size:31 final size:26
Alignment explanation
Indices: 170100--170204 Score: 86
Period size: 31 Copynumber: 3.7 Consensus size: 26
170090 TTTTAAAAAG
*
170100 TTAAGATAA-AATAAAATATACTTTTCAAA
1 TTAAAATAAGAAT-AAATATA-TTTT--AA
170129 TTAAAATAAGAATACAATATATTTTAA
1 TTAAAATAAGAATA-AATATATTTTAA
*
170156 ATAAAGATAAGAATAAGATATATGTTTTTATA
1 TTAAA-ATAAGAATAA-ATATA---TTTTA-A
170188 TTAAAATAAGAATAAAT
1 TTAAAATAAGAATAAAT
170205 TGTATTTAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 15
0.78 0.04 0.18
Matches are distributed among these distances:
27 7 0.11
28 14 0.22
29 13 0.20
30 11 0.17
31 15 0.23
32 5 0.08
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (26 bp):
TTAAAATAAGAATAAATATATTTTAA
Found at i:170649 original size:2 final size:2
Alignment explanation
Indices: 170642--170688 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
170632 AGTTACACAT
170642 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
170684 TA TA T
1 TA TA T
170689 GATCCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:172595 original size:7 final size:6
Alignment explanation
Indices: 172585--172684 Score: 69
Period size: 6 Copynumber: 16.7 Consensus size: 6
172575 AAAGCATAAG
* * * * *
172585 TAAAGTA TAAAGTA TATATA TAAATA TATATA TATATA TATATA TATATA
1 TAAA-TA TAAA-TA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
* * * * * *
172635 TATATA TATATA TATAT- TATATA TAAATA TAAGTA T-AATA TATATA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA TAAATA
172681 TAAA
1 TAAA
172685 GTAATTATGC
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
5 9 0.11
6 64 0.77
7 10 0.12
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (6 bp):
TAAATA
Found at i:172604 original size:2 final size:2
Alignment explanation
Indices: 172597--172682 Score: 124
Period size: 2 Copynumber: 44.0 Consensus size: 2
172587 AAGTATAAAG
*
172597 TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
172639 TA TA TA TA TA TA T- TA TA TA TA AA TA TA -A GTA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
172679 TA TA
1 TA TA
172683 AAGTAATTAT
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
1 3 0.04
2 72 0.95
3 1 0.01
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:173232 original size:27 final size:26
Alignment explanation
Indices: 173194--173249 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
173184 AATAAAAAAA
* * *
173194 TAAAAAATTAATTTCATGATTATAAT
1 TAAAAAATTAATATAAAGATTATAAT
*
173220 TAAAAATTATAATATAAAGATTATAAT
1 TAAAAAAT-TAATATAAAGATTATAAT
173247 TAA
1 TAA
173250 GATAATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (26 bp):
TAAAAAATTAATATAAAGATTATAAT
Found at i:173237 original size:14 final size:13
Alignment explanation
Indices: 173212--173249 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
173202 TAATTTCATG
173212 ATTATAATTAAAA
1 ATTATAATTAAAA
*
173225 ATTATAATATAAAG
1 ATTATAAT-TAAAA
173239 ATTATAATTAA
1 ATTATAATTAA
173250 GATAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (13 bp):
ATTATAATTAAAA
Found at i:179242 original size:2 final size:2
Alignment explanation
Indices: 179235--179265 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
179225 ATGTTTCCTC
179235 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
179266 GATTGAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:183792 original size:30 final size:30
Alignment explanation
Indices: 183753--183809 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
183743 CTATCTTGTG
* *
183753 TTTTCTTGCATTTTAGTCAATATAATTAGA
1 TTTTATTGCATTTTAGTCAACATAATTAGA
183783 TTTTATTGCATTTTAGTCAACATAATT
1 TTTTATTGCATTTTAGTCAACATAATT
183810 TTATGTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (30 bp):
TTTTATTGCATTTTAGTCAACATAATTAGA
Found at i:184024 original size:30 final size:29
Alignment explanation
Indices: 183990--184084 Score: 88
Period size: 28 Copynumber: 3.3 Consensus size: 29
183980 TTATTATTTG
*
183990 GTCCTTTAACTCTCTATTTTTTCTATTTTA
1 GTCCTTTAACT-TCTATTTTTACTATTTTA
* *
184020 GTCCTTTAAGTTTTATTTTTACTA-TTTA
1 GTCCTTTAACTTCTATTTTTACTATTTTA
* * *
184048 ATCCCTTAAGTT-TATGTTTTACTATTTTA
1 GTCCTTTAACTTCTAT-TTTTACTATTTTA
*
184077 CT-CTTTAA
1 GTCCTTTAA
184085 GCTTATAAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
27 3 0.05
28 27 0.48
29 16 0.29
30 10 0.18
ACGTcount: A:0.21, C:0.16, G:0.05, T:0.58
Consensus pattern (29 bp):
GTCCTTTAACTTCTATTTTTACTATTTTA
Found at i:184047 original size:28 final size:28
Alignment explanation
Indices: 183984--184074 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
183974 CTTTAATTAT
* * * *
183984 TATTTGGTCCTTTAACTCTCTATTTTTTC
1 TATTTAGTCCTTTAAGT-TTTATTTTTAC
184013 TATTTTAGTCCTTTAAGTTTTATTTTTAC
1 TA-TTTAGTCCTTTAAGTTTTATTTTTAC
* *
184042 TATTTAATCCCTTAAG-TTTATGTTTTAC
1 TATTTAGTCCTTTAAGTTTTAT-TTTTAC
184070 TATTT
1 TATTT
184075 TACTCTTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 5 0.09
28 23 0.43
29 13 0.24
30 13 0.24
ACGTcount: A:0.20, C:0.14, G:0.07, T:0.59
Consensus pattern (28 bp):
TATTTAGTCCTTTAAGTTTTATTTTTAC
Found at i:184084 original size:28 final size:28
Alignment explanation
Indices: 184004--184090 Score: 97
Period size: 28 Copynumber: 3.1 Consensus size: 28
183994 TTTAACTCTC
* *
184004 TATTTTTTCTATTTTAGTCCTTTAAGTTT
1 TATTTTTACTATTTTAATCCTTTAAG-TT
*
184033 TATTTTTACTA-TTTAATCCCTTAAGTT
1 TATTTTTACTATTTTAATCCTTTAAGTT
* *
184060 TATGTTTTACTATTTTACT-CTTTAAGCT
1 TAT-TTTTACTATTTTAATCCTTTAAGTT
184088 TAT
1 TAT
184091 AAACGTCAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
27 5 0.10
28 30 0.60
29 15 0.30
ACGTcount: A:0.22, C:0.13, G:0.06, T:0.60
Consensus pattern (28 bp):
TATTTTTACTATTTTAATCCTTTAAGTT
Found at i:186865 original size:17 final size:17
Alignment explanation
Indices: 186815--186854 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
186805 TGTGTAATGG
186815 ATCGTTTAAGTGCTTAA
1 ATCGTTTAAGTGCTTAA
*
186832 ATTGTTTAAGTGCTTAA
1 ATCGTTTAAGTGCTTAA
186849 ATCGTT
1 ATCGTT
186855 AATTGCGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (17 bp):
ATCGTTTAAGTGCTTAA
Found at i:187526 original size:26 final size:28
Alignment explanation
Indices: 187497--187551 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
187487 GTTTACCAAT
*
187497 ATTTGATATATAATCCATT-T-ATATAA
1 ATTTAATATATAATCCATTGTAATATAA
*
187523 ATTTAATATATAGTCCATTGTAATATAA
1 ATTTAATATATAATCCATTGTAATATAA
187551 A
1 A
187552 CGCAAACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 17 0.68
27 1 0.04
28 7 0.28
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (28 bp):
ATTTAATATATAATCCATTGTAATATAA
Found at i:188344 original size:183 final size:178
Alignment explanation
Indices: 188024--188396 Score: 651
Period size: 183 Copynumber: 2.1 Consensus size: 178
188014 TGTAAAATTA
*
188024 TTTTATTATAAT-ATAATTATTAAATAGTTTATTATTTATTATATTTTATTGTGCTCTATTTTTA
1 TTTTATT-TAATAATAATTATTAAATAGTTTATTATTTATTATATTTTATTGTGCTATATTTTTA
188088 TGTTTGCAGTTATAAAATGGAATAGGATAACTATGTTTAAGTAGAATCATATCTCGAGTCATTTT
65 TGTTTGCAGTTATAAAATGGAATAGGATAACTATGTTTAAGTAGAATCATATCTCGAGTCATTTT
188153 ACCGATACGATAACAATTTTAAATTGGGTTATGTTAATTATTGTGAATG
130 ACCGATACGATAACAATTTTAAATTGGGTTATGTTAATTATTGTGAATG
188202 TTTTA-TTAATAATAATATATTAAATAGTTTATTATTTTATTATATTTTATTGTGCTATATTTTT
1 TTTTATTTAATAATAAT-TATTAAATAGTTTATTA-TTTATTATATTTTATTGTGCTATA-TTTT
188266 TATGTTTTGCAGTTATAAAATGGAATATGGATAACTATGTTTAAGTAGAAATCATATCTCGAGTC
63 TATG-TTTGCAGTTATAAAATGGAATA-GGATAACTATGTTTAAGTAG-AATCATATCTCGAGTC
*
188331 ATTTTACCGATACGATAACAATTTTAAATTGTGTTATGTTAATTATTGTGAATG
125 ATTTTACCGATACGATAACAATTTTAAATTGGGTTATGTTAATTATTGTGAATG
188385 TTTTATTTAATA
1 TTTTATTTAATA
188397 TTTTTTAGTA
Statistics
Matches: 185, Mismatches: 2, Indels: 10
0.94 0.01 0.05
Matches are distributed among these distances:
176 4 0.02
177 6 0.03
178 22 0.12
179 23 0.12
180 8 0.04
181 22 0.12
182 20 0.11
183 74 0.40
184 6 0.03
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.48
Consensus pattern (178 bp):
TTTTATTTAATAATAATTATTAAATAGTTTATTATTTATTATATTTTATTGTGCTATATTTTTAT
GTTTGCAGTTATAAAATGGAATAGGATAACTATGTTTAAGTAGAATCATATCTCGAGTCATTTTA
CCGATACGATAACAATTTTAAATTGGGTTATGTTAATTATTGTGAATG
Found at i:194312 original size:64 final size:64
Alignment explanation
Indices: 194244--194423 Score: 208
Period size: 65 Copynumber: 2.8 Consensus size: 64
194234 TTAGACCCTT
*
194244 AGTGCATCGGTGCACTAAG-AGTGCATCGATGCATAAAATGCATTCGATGTTTCA-AAATAGC-C
1 AGTGCATCGATGCA-T-AGTAGTGCATCGATGCATAAAATGCATTCGATGTTTCATAAA-A-CTC
194306 -AA
62 TAA
* * *
194308 AGTGCATCGATGCATAGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACTCTG
1 AGTGCATCGATGCATAG-TAGTGCATCGATGCATAAAATGCATTCGATG-TTTCATAAAACTCTA
194373 A
64 A
* *
194374 A-TGCATCGATGCATAGTATGTGCATCGGTGCATAAAATACATTCGATGTT
1 AGTGCATCGATGCATAGTA-GTGCATCGATGCATAAAATGCATTCGATGTT
194424 CAATTTATTC
Statistics
Matches: 101, Mismatches: 8, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
62 2 0.02
63 1 0.01
64 45 0.45
65 48 0.48
66 5 0.05
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (64 bp):
AGTGCATCGATGCATAGTAGTGCATCGATGCATAAAATGCATTCGATGTTTCATAAAACTCTAA
Found at i:197768 original size:19 final size:19
Alignment explanation
Indices: 197744--197795 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
197734 AATAGCCAGA
197744 GTGCATCGATGCATAGCTG
1 GTGCATCGATGCATAGCTG
*
197763 GTGCATCGATGCGTAGCTG
1 GTGCATCGATGCATAGCTG
197782 GTGCATCGATGCAT
1 GTGCATCGATGCAT
197796 GAAATGCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.19, C:0.21, G:0.33, T:0.27
Consensus pattern (19 bp):
GTGCATCGATGCATAGCTG
Found at i:200582 original size:21 final size:22
Alignment explanation
Indices: 200520--200601 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 22
200510 GCATGGCCTT
200520 GTGCATCGATGCACATTCAAGGC
1 GTGCATCGATGCACATTC-AGGC
* * * *
200543 GTGCATTGGTGCACCTTCATG-
1 GTGCATCGATGCACATTCAGGC
*
200564 GTGTATCGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC--AGGC
200587 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
200602 TGTTAAGTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
21 14 0.30
22 2 0.04
23 18 0.39
24 12 0.26
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGC
Found at i:204627 original size:19 final size:19
Alignment explanation
Indices: 204605--204648 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
204595 ATTAATGCTA
*
204605 AATATATA-TATATATAAAT
1 AATATATAGTAAAT-TAAAT
204624 AATATATAGTAAATTAAAT
1 AATATATAGTAAATTAAAT
204643 AATATA
1 AATATA
204649 ATTTAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
AATATATAGTAAATTAAAT
Found at i:204787 original size:10 final size:11
Alignment explanation
Indices: 204756--204801 Score: 53
Period size: 10 Copynumber: 4.5 Consensus size: 11
204746 TATTGGTCAA
204756 ATAAT-TAAAT
1 ATAATATAAAT
*
204766 ATAAAATAAAT
1 ATAATATAAAT
204777 ATAATAT-AAT
1 ATAATATAAAT
*
204787 ATAATA-AAAA
1 ATAATATAAAT
204797 ATAAT
1 ATAAT
204802 TTTGCCTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 20 0.65
11 11 0.35
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:207837 original size:11 final size:11
Alignment explanation
Indices: 207821--207845 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
207811 TATATTTGAT
207821 ATTAATTATTA
1 ATTAATTATTA
207832 ATTAATTATTA
1 ATTAATTATTA
207843 ATT
1 ATT
207846 TATGCATCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTAATTATTA
Found at i:208322 original size:60 final size:59
Alignment explanation
Indices: 208248--208371 Score: 223
Period size: 60 Copynumber: 2.1 Consensus size: 59
208238 TATCTTTTAT
*
208248 TATTTTTTTGTTTAAAGAGAATAAATAAGCATTTTAATTTTGTGGACTTAAATAAAACCC
1 TATTTATTTGTTTAAAGAGAATAAATAAGCATTTTAATTTTGTGGACTTAAAT-AAACCC
208308 TATTTATTTGTTTAAAGAGAATAAATAAGCATTTTAATTTTGTGGACTTAAATAAACCC
1 TATTTATTTGTTTAAAGAGAATAAATAAGCATTTTAATTTTGTGGACTTAAATAAACCC
208367 T-TTTA
1 TATTTA
208372 AATTAAAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
58 4 0.06
59 7 0.11
60 52 0.83
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (59 bp):
TATTTATTTGTTTAAAGAGAATAAATAAGCATTTTAATTTTGTGGACTTAAATAAACCC
Found at i:214216 original size:19 final size:18
Alignment explanation
Indices: 214194--214237 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
214184 CGATATACCA
*
214194 GGTAAAATATGATAAAACC
1 GGTAAAAAATGATAAAA-C
214213 GGTAACAAAATGATAAAAC
1 GGTAA-AAAATGATAAAAC
214232 GGTAAA
1 GGTAAA
214238 TTTAAAAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 11 0.48
20 11 0.48
ACGTcount: A:0.55, C:0.09, G:0.18, T:0.18
Consensus pattern (18 bp):
GGTAAAAAATGATAAAAC
Found at i:214378 original size:20 final size:19
Alignment explanation
Indices: 214355--214401 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
214345 CGATATAACA
214355 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
214375 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
214395 GGTAAAA
1 GGTAAAA
214402 TGATACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:214403 original size:17 final size:18
Alignment explanation
Indices: 214359--214406 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
214349 ATAACAGGTA
214359 AAAATATGATAAAACCGGT
1 AAAA-ATGATAAAACCGGT
214378 AACAAAATGATAAAACCGGT
1 -A-AAAATGATAAAACCGGT
214398 -AAAATGATA
1 AAAAATGATA
214407 CCGGATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.33
20 15 0.56
21 3 0.11
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (18 bp):
AAAAATGATAAAACCGGT
Found at i:216360 original size:21 final size:21
Alignment explanation
Indices: 216313--216377 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
216303 AAGACAATCA
* *
216313 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
216335 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
216355 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
216376 AG
1 AG
216378 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:216450 original size:32 final size:32
Alignment explanation
Indices: 216409--216469 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
216399 AAAATAGATG
*
216409 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
* *
216441 AGTGGTGAAAGAAGTTGGGGTGTTAAGGG
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGG
216470 GTGATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.48, T:0.23
Consensus pattern (32 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
Found at i:218279 original size:18 final size:19
Alignment explanation
Indices: 218236--218283 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
218226 AATGTCGAGT
218236 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
218255 TAATTTTGTATACGA-TTA
1 TAATTTTGTATAAGATTTA
*
218273 TATTTTTGTAT
1 TAATTTTGTAT
218284 GTGAATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:218881 original size:194 final size:199
Alignment explanation
Indices: 218400--219741 Score: 2209
Period size: 195 Copynumber: 6.9 Consensus size: 199
218390 CAATATGGCC
* *
218400 AACAGGGTGCACCC-TAAAGTGTCGATCCATATATAAAAAGTGTCAATCCC-AAA--ATCGAAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
218461 CCAAAAGTATAATGTAATATGTAA-TTTTCAATCTAA-CGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
218524 G-AT-TGTCTAAAT-ATGTGTCGACACTAATATAG-TTGTGTCGATATTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAA
218585 TGGAA
195 TGGAA
218590 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
218655 C-AAAGTATAATGTTAATATGTAATTTTTCAATCTAACCGGTACAA-TATA-CGGTTTTATGAGA
66 CAAAAGTATAATG-TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
218717 G-A-ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAA
218780 TGGAA
195 TGGAA
* *
218785 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAATAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
218850 C-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
218913 AATATGTCTAAATAATGTGTCGACACTAATATAG-TTGTGGCGATA-TTTTTTCCC---A-GAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
218972 GGAA
196 GGAA
*
218976 AACAAGGTGCAACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGAT-CCAAAATCATCGAA
1 AACAGGGTGC-ACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAA
*
219040 CCCAAAAGTAT-ATTTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
219104 -GAATATGTCTAAATAATGTGTCGACA-TAATATAGTTTGTGTCGATATTTTTTT-CCAG-ATG-
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGA
219164 ATGGAA
194 ATGGAA
219170 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGAT-CCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
219234 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAAACCGGTACAATTATACCGGTTTTATGAGA
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCT-AACCGGTACAATTATACCGGTTTTATGAGA
*
219299 GAATATGTCTAAATAA-GTGTCGACACTAATATAGTTTGTGTCGATA--TTTTTCCGAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAA
219361 TGGAA
195 TGGAA
*
219366 AACAAGGTGCACCCATAAAGTGTCGATCCA-ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
219430 CAAAAGTATAA-GTAATATGTAA-TTTTCAATCTAACCGGTACAATTATA-CGGTTTATATGAGA
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT-TATGAGA
*
219492 GCAATATGTCTAAATAATGTGTCGACACT-ATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
130 G-AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGA
219556 ATGGAA
194 ATGGAA
219562 AACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
219625 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
219689 AATATGTC--AATAATGTGTCGACA-TAATATAG-TTGTGTCGATATTTTTTTCCCA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCA
219742 ATGTGTCGAC
Statistics
Matches: 1097, Mismatches: 16, Indels: 76
0.92 0.01 0.06
Matches are distributed among these distances:
190 14 0.01
191 61 0.06
192 200 0.18
193 173 0.16
194 172 0.16
195 276 0.25
196 139 0.13
197 59 0.05
198 3 0.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (199 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
GGAA
Found at i:219774 original size:43 final size:41
Alignment explanation
Indices: 219700--219780 Score: 144
Period size: 43 Copynumber: 1.9 Consensus size: 41
219690 ATATGTCAAT
219700 AATGTGTCGACATAATATAGTTGTGTCGATATTTTTTTCCC
1 AATGTGTCGACATAATATAGTTGTGTCGATATTTTTTTCCC
219741 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT
1 AATGTGTCGACA-TAATATAG-TTGTGTCGATATTTTTTT
219781 TCCAGAATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 12 0.32
42 8 0.21
43 18 0.47
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.46
Consensus pattern (41 bp):
AATGTGTCGACATAATATAGTTGTGTCGATATTTTTTTCCC
Found at i:219778 original size:41 final size:40
Alignment explanation
Indices: 219700--219779 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 40
219690 ATATGTCAAT
219700 AATGTGTCGACATAATATAGTTGTGTCGATATTTTTTTCCC
1 AATGTGTCGACATAATATAGTTGTGTCGATA-TTTTTTCCC
219741 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTT
1 AATGTGTCGACA-TAATATAG-TTGTGTCGATATTTTTT
219780 TTCCAGAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
41 12 0.32
42 14 0.38
43 11 0.30
ACGTcount: A:0.25, C:0.12, G:0.17, T:0.45
Consensus pattern (40 bp):
AATGTGTCGACATAATATAGTTGTGTCGATATTTTTTCCC
Found at i:220166 original size:196 final size:198
Alignment explanation
Indices: 219741--220353 Score: 1102
Period size: 195 Copynumber: 3.1 Consensus size: 198
219731 TTTTTTTCCC
* *
219741 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATGGAAAACAGGGTG
1 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGGAAAACAAGGTG
219806 CACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAATCATCGAACCCAAAAGTATA
66 CACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAATCATCGAACCCAAAAGTATA
219870 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG-A-ATGTCTA
131 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTA
219933 AAT
196 AAT
219936 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGGAAAACAAGGTG
1 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGGAAAACAAGGTG
220001 CACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTAT
66 CACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAATCATCGAACCCAAAAGTAT
220065 AATGT-ATATGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTATGAGAGAATATGTCT
130 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCT
220128 AAAT
195 AAAT
220132 AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCCAGAATGAATGGAAAACAAGGT
1 AATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCCAGAATGAATGGAAAACAAGGT
*
220197 GCACCCATAAAGTGTCGATCC--ATATAAATAGTGTCGATCCCAAATCATCGAACCCAAAAAGTA
65 GCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAATCATCGAACCC-AAAAGTA
220260 TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTA-ACCGG-TTTATGAGAGAATATGTC
129 TAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTC
220323 TAAAT
194 TAAAT
220328 AATGTGTCGACACTAATATAGTTTGT
1 AATGTGTCGACACTAATATAGTTTGT
220354 CGATACTAAT
Statistics
Matches: 406, Mismatches: 3, Indels: 17
0.95 0.01 0.04
Matches are distributed among these distances:
194 40 0.10
195 132 0.33
196 131 0.32
197 94 0.23
198 9 0.02
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (198 bp):
AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATGGAAAACAAGGTG
CACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAATCATCGAACCCAAAAGTATA
ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTA
AAT
Found at i:221827 original size:18 final size:18
Alignment explanation
Indices: 221806--221873 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
221796 AGCGGTCGCA
221806 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
221824 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
221845 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
221866 GAAGATGA
1 GAAGATGA
221874 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:221830 original size:6 final size:6
Alignment explanation
Indices: 221806--221901 Score: 57
Period size: 6 Copynumber: 15.3 Consensus size: 6
221796 AGCGGTCGCA
* * * * * *
221806 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * *
221854 GAAGCT GGCGAT GAAGAT GATGACGAT GATGAT GATGAT GGAAGAT GA
1 GAAGAT GAAGAT GAAGAT GA--A-GAT GAAGAT GAAGAT -GAAGAT GA
221902 TGATCCAAAC
Statistics
Matches: 70, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
6 59 0.84
7 5 0.07
8 1 0.01
9 5 0.07
ACGTcount: A:0.36, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:221841 original size:3 final size:3
Alignment explanation
Indices: 221821--221905 Score: 71
Period size: 3 Copynumber: 28.0 Consensus size: 3
221811 TGAAGCTGAC
* * * * * ** *
221821 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
221869 GAT GAT GAC GAT GAT GAT GAT GAT GGAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT -GAT GAT GAT GAT
221906 CCAAACAAGT
Statistics
Matches: 62, Mismatches: 19, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
3 60 0.97
4 2 0.03
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:221856 original size:42 final size:42
Alignment explanation
Indices: 221809--221891 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
221799 GGTCGCAGAA
*
221809 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* *
221851 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGA
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGA
221892 TGGAAGATGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
Found at i:223631 original size:182 final size:180
Alignment explanation
Indices: 223318--223654 Score: 498
Period size: 181 Copynumber: 1.9 Consensus size: 180
223308 CTTTCAACTA
* *
223318 TTATAATAAAATAGGTAAATTTGCAATATAACGGTATAAAATACCGGTCTTATGCGCGAATAGGT
1 TTATAATAAAATAGATAAATTTGCAATATAACGGTATAAAATACCGGTCTTATGAGCGAATAGGT
* *
223383 ATACAACCTATATCGACACTTTTTAATATTGTGCGGTACTTTATGTCCATATTGGAAGAAAATGT
66 ATACAACCTATATCGACACTTTATAATATTGTGCGGTACTTTATGTCCAGATTGGAAGAAAATGT
*
223448 GTCGAATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCATAAT
131 GTCG-ATACCATTTAAAAAAGTGTCGACATTTTACACATCGGAACCATAAT
** * * *
223499 TTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAG
1 TTATAATAAAATAGATAAATTTGCAATATAA-CGGTATAAA-ATACCGGTCTTATGAGCGAATAG
* ***
223564 GTCTACAACCTATATCGACAC-TTAT-ATATTGTGTCGGTACTTTATGTCCAGATTGGAATTGAA
64 GTATACAACCTATATCGACACTTTATAATATTGTG-CGGTACTTTATGTCCAGATTGGAAGAAAA
223627 TGTGTCGATACCATTTAAAAAAGTGTCG
128 TGTGTCGATACCATTTAAAAAAGTGTCG
223655 GTAATTTGAA
Statistics
Matches: 139, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
181 54 0.39
182 44 0.32
183 41 0.29
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (180 bp):
TTATAATAAAATAGATAAATTTGCAATATAACGGTATAAAATACCGGTCTTATGAGCGAATAGGT
ATACAACCTATATCGACACTTTATAATATTGTGCGGTACTTTATGTCCAGATTGGAAGAAAATGT
GTCGATACCATTTAAAAAAGTGTCGACATTTTACACATCGGAACCATAAT
Found at i:226123 original size:25 final size:25
Alignment explanation
Indices: 226089--226153 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
226079 TTATCATTAA
226089 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
226114 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
226139 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
226154 TCTTTGAGTG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:226467 original size:22 final size:23
Alignment explanation
Indices: 226437--226497 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
226427 ATAGGTAAAC
*
226437 ATATGATGTAATAGGTA-CCCTT
1 ATATAATGTAATAGGTATCCCTT
**
226459 ATATAATGT-ATAGGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
226481 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
226498 GTGGTTATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.21
22 20 0.59
23 7 0.21
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:226505 original size:23 final size:22
Alignment explanation
Indices: 226457--226505 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
226447 ATAGGTACCC
*
226457 TTATATAATGTATAGGTATCGT
1 TTATATAATGTATAGGTATCGG
226479 TTATATAATGTAATAGGTAGT-GG
1 TTATATAATGT-ATAGGTA-TCGG
226502 TTAT
1 TTAT
226506 TGTAAAGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 11 0.46
23 12 0.50
24 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (22 bp):
TTATATAATGTATAGGTATCGG
Found at i:226533 original size:20 final size:20
Alignment explanation
Indices: 226508--226546 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
226498 GTGGTTATTG
* *
226508 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
226528 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
226547 TCACTGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:226885 original size:23 final size:23
Alignment explanation
Indices: 226854--226917 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
226844 ATAGGTAAAC
*
226854 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
226877 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
226900 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
226918 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:226924 original size:23 final size:23
Alignment explanation
Indices: 226854--226926 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
226844 ATAGGTAAAC
* **
226854 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
226877 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
226900 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
226923 ATAT
1 ATAT
226927 TGTAAAGTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:227225 original size:25 final size:25
Alignment explanation
Indices: 227191--227241 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
227181 ACAACAAATC
*
227191 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
227216 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
227241 A
1 A
227242 TTTGGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:227867 original size:39 final size:39
Alignment explanation
Indices: 227824--227910 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
227814 TCCGATGCTC
*
227824 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
227863 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
227902 ATCAAAATC
1 ATCAAAATC
227911 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:228156 original size:29 final size:28
Alignment explanation
Indices: 228097--228163 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
228087 ACGTTACGAT
* *
228097 ATATATTATTATTAAATTAAAAATTCTAA
1 ATATATT-TTATAAAATTAAAAAATCTAA
228126 ATATATTTTATAAAATATAAAATAATC-AA
1 ATATATTTTATAAAAT-TAAAA-AATCTAA
*
228155 ATATTTTTT
1 ATATATTTT
228164 GTGCAAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 8 0.24
29 22 0.67
30 3 0.09
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
ATATATTTTATAAAATTAAAAAATCTAA
Found at i:228287 original size:21 final size:22
Alignment explanation
Indices: 228241--228287 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
228231 TAATTACATA
228241 ACTTTTAAAAAAAGTATCGATC
1 ACTTTTAAAAAAAGTATCGATC
* * *
228263 -CTTTTTATAAAAGTATGGA-C
1 ACTTTTAAAAAAAGTATCGATC
228283 ACTTT
1 ACTTT
228288 CAATATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (22 bp):
ACTTTTAAAAAAAGTATCGATC
Found at i:228336 original size:23 final size:23
Alignment explanation
Indices: 228305--228368 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
228295 ATAGGTAAAC
*
228305 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
228328 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
228351 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
228369 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:228375 original size:23 final size:23
Alignment explanation
Indices: 228305--228377 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
228295 ATAGGTAAAC
* **
228305 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
228328 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
228351 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
228374 ATAT
1 ATAT
228378 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:229722 original size:2 final size:2
Alignment explanation
Indices: 229711--229760 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
229701 TATTAACTAT
229711 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
229752 TA TA TA TA T
1 TA TA TA TA T
229761 GTTTATTGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:230937 original size:16 final size:15
Alignment explanation
Indices: 230895--230947 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 15
230885 TATTGAAAAT
230895 AAAAAATAAAATAAA
1 AAAAAATAAAATAAA
*
230910 ATAAATATATAATATAGAA
1 A-AAA-A-ATAAAATA-AA
230929 AAAAAATAAAAATAAA
1 AAAAAAT-AAAATAAA
230945 AAA
1 AAA
230948 TACTGACTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 1 0.03
16 10 0.32
17 7 0.23
18 10 0.32
19 3 0.10
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (15 bp):
AAAAAATAAAATAAA
Found at i:231054 original size:2 final size:2
Alignment explanation
Indices: 231043--231088 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
231033 GCTTCAATCT
231043 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
231084 TA TA T
1 TA TA T
231089 TTCTATATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:232519 original size:20 final size:20
Alignment explanation
Indices: 232494--232546 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
232484 GACCAACAAA
232494 TTCGCAACGCGAACTCCAAT
1 TTCGCAACGCGAACTCCAAT
* **
232514 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ACTCCAAT
232534 TTCGCAACGCGAA
1 TTCGCAACGCGAA
232547 TATGTAAATC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (20 bp):
TTCGCAACGCGAACTCCAAT
Found at i:232622 original size:20 final size:19
Alignment explanation
Indices: 232593--232641 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
232583 GTAATTTTCT
* *
232593 AAATTCGCAACGCGATAGTC
1 AAATTCGCAACAC-AAAGTC
*
232613 AAATTTGCAACACAAAGTC
1 AAATTCGCAACACAAAGTC
232632 AAATTCGCAA
1 AAATTCGCAA
232642 ATTCGCAACG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.20
Consensus pattern (19 bp):
AAATTCGCAACACAAAGTC
Found at i:233224 original size:19 final size:20
Alignment explanation
Indices: 233200--233238 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
233190 AAATCGTAAC
233200 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
*
233219 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCAGTTTCGCGTT
233239 ACAAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.10, C:0.18, G:0.23, T:0.49
Consensus pattern (20 bp):
GCGATTTTCAGTTTCGCGTT
Found at i:234960 original size:21 final size:21
Alignment explanation
Indices: 234936--234981 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
234926 AGTTAGGAGA
* *
234936 TTTACGTGATGAGGTCGGTGC
1 TTTACGTCATGAGGTCGGTAC
234957 TTTACGTCATGAGGTCGGTAC
1 TTTACGTCATGAGGTCGGTAC
234978 TTTA
1 TTTA
234982 TGTAAAGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.37
Consensus pattern (21 bp):
TTTACGTCATGAGGTCGGTAC
Found at i:235234 original size:19 final size:19
Alignment explanation
Indices: 235210--235246 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
235200 TTTTCGGCAT
* *
235210 TATTTATTTATTTATTTAC
1 TATTTATGTATTAATTTAC
235229 TATTTATGTATTAATTTA
1 TATTTATGTATTAATTTA
235247 TTTTCAGCGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
TATTTATGTATTAATTTAC
Found at i:235447 original size:21 final size:21
Alignment explanation
Indices: 235416--235491 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
235406 GGCGCCTCCT
*
235416 ATCGTTCAAGAGGCCCCTCTC
1 ATCGATCAAGAGGCCCCTCTC
* *
235437 ATC-ATCGAAGAAGCCCCTCCC
1 ATCGATC-AAGAGGCCCCTCTC
* * *
235458 ACCGTTCAAGAGGCCCCTGTC
1 ATCGATCAAGAGGCCCCTCTC
*
235479 ATCGTTCAAGAGG
1 ATCGATCAAGAGG
235492 TCCCGCCCGC
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 2 0.05
21 40 0.91
22 2 0.05
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.20
Consensus pattern (21 bp):
ATCGATCAAGAGGCCCCTCTC
Found at i:235505 original size:42 final size:42
Alignment explanation
Indices: 235418--235511 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
235408 CGCCTCCTAT
*
235418 CGTTCAAGAGGCCCCTCTCATCATCGAAGAAGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTCTCATCATCGAAGAAGCCCCGCCCAC
* * * * *
235460 CGTTCAAGAGGCCCCTGTCATCGTTC-AAGAGGTCCCGCCCGC
1 CGTTCAAGAGGCCCCTCTCATC-ATCGAAGAAGCCCCGCCCAC
235502 CGTTCAAGAG
1 CGTTCAAGAG
235512 CCCGATTCAC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 43 0.96
43 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.22, T:0.18
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTCTCATCATCGAAGAAGCCCCGCCCAC
Found at i:236919 original size:66 final size:60
Alignment explanation
Indices: 236788--236927 Score: 192
Period size: 66 Copynumber: 2.2 Consensus size: 60
236778 TTTTACATTG
236788 AAAGTTGATTTGTTTAATTGATGATGAAATAAGATTTATTTTTTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGATGAAATAAGATTTATTTTTTGATTAATTGATTTGTA
* *
236848 AAAGTTGATTTGTTTAATTTGATG-TGTAAATAAGAATTGTTTTTTTGCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTAA-TTGATGATG-AAATAAG-A-T-TTATTTT--TTGATTAATTGATTTG
236912 TA
59 TA
236914 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
236928 GTTTCTAAAA
Statistics
Matches: 71, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
60 19 0.27
61 13 0.18
62 1 0.01
63 1 0.01
64 6 0.08
66 31 0.44
ACGTcount: A:0.30, C:0.01, G:0.18, T:0.51
Consensus pattern (60 bp):
AAAGTTGATTTGTTTAATTGATGATGAAATAAGATTTATTTTTTGATTAATTGATTTGTA
Found at i:237011 original size:20 final size:20
Alignment explanation
Indices: 236986--237075 Score: 84
Period size: 20 Copynumber: 4.8 Consensus size: 20
236976 GTTGAAGGTA
236986 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
237006 CAAATTTGCAACGCGAAA-T
1 CAAATTCGCAACGCGAAAGT
*** *
237025 --AA---GCGTTGCGATAGT
1 CAAATTCGCAACGCGAAAGT
*
237040 CAAATTCGCAACACGAAAGT
1 CAAATTCGCAACGCGAAAGT
237060 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
237076 TTTTTGGTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
14 7 0.13
15 1 0.02
17 4 0.08
19 1 0.02
20 40 0.75
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:237698 original size:18 final size:18
Alignment explanation
Indices: 237675--237713 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
237665 CAAAATTTAT
237675 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
237693 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
237711 ATT
1 ATT
237714 CCAATTACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:240864 original size:24 final size:24
Alignment explanation
Indices: 240830--240883 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
240820 CCATCACATC
240830 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
240854 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
240878 ATCAAA
1 ATCAAA
240884 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:241831 original size:81 final size:81
Alignment explanation
Indices: 241724--241886 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
241714 GTTGCGAATT
241724 TGTTGGTCATTTTGGCAAATCCAAAAAAAATTAGTTAAATTCGTATATTATAAGACATTTTTTGT
1 TGTTGGTCATTTTGGCAAATCCAAAAAAAATTAGTTAAATTCGTATATTATAAGACATTTTTTGT
241789 CACTGATGTTATTTTC
66 CACTGATGTTATTTTC
241805 TGTTGGTCATTTTGGCAAATCCAAAAAAAATTAGTTAAATTCGTATATTATAAGACATTTTTTGT
1 TGTTGGTCATTTTGGCAAATCCAAAAAAAATTAGTTAAATTCGTATATTATAAGACATTTTTTGT
241870 CACTGATGTTATTTTC
66 CACTGATGTTATTTTC
241886 T
1 T
241887 CATATATATA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (81 bp):
TGTTGGTCATTTTGGCAAATCCAAAAAAAATTAGTTAAATTCGTATATTATAAGACATTTTTTGT
CACTGATGTTATTTTC
Found at i:255214 original size:14 final size:14
Alignment explanation
Indices: 255195--255221 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
255185 TGAACAGTAA
255195 AATACGGTATGAAC
1 AATACGGTATGAAC
255209 AATACGGTATGAA
1 AATACGGTATGAA
255222 TACTATGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (14 bp):
AATACGGTATGAAC
Found at i:255260 original size:14 final size:15
Alignment explanation
Indices: 255241--255270 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
255231 CAGTAATAAT
255241 TTCGAATATC-ATTG
1 TTCGAATATCAATTG
255255 TTCGAATATCAATTG
1 TTCGAATATCAATTG
255270 T
1 T
255271 GTATCGATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (15 bp):
TTCGAATATCAATTG
Found at i:269459 original size:16 final size:17
Alignment explanation
Indices: 269425--269467 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
269415 ATTTTACTAT
*
269425 TTTATAA-TTTATATAA
1 TTTATAATTTTAAATAA
269441 TTTATAATTTTAAAT-A
1 TTTATAATTTTAAATAA
269457 TTT-TAATTTTA
1 TTTATAATTTTA
269468 CACAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 8 0.32
16 11 0.44
17 6 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATAATTTTAAATAA
Found at i:269645 original size:20 final size:20
Alignment explanation
Indices: 269614--269669 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
269604 ACAAATATCG
269614 CAACACAGAAGTCAAATTCA
1 CAACACAGAAGTCAAATTCA
* * *
269634 CAACTCATAAGTCAAATTCG
1 CAACACAGAAGTCAAATTCA
269654 CAACACAGAAGTCAAA
1 CAACACAGAAGTCAAA
269670 GCGCGTTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.48, C:0.25, G:0.11, T:0.16
Consensus pattern (20 bp):
CAACACAGAAGTCAAATTCA
Found at i:269818 original size:23 final size:23
Alignment explanation
Indices: 269792--269843 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
269782 CTACGGCGAC
269792 ATCCGTCCCCCATCTCCGACGAA
1 ATCCGTCCCCCATCTCCGACGAA
**
269815 ATCCGT-CTTCATCTCCGACGAA
1 ATCCGTCCCCCATCTCCGACGAA
269837 ATCCGTC
1 ATCCGTC
269844 TATCTCCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.21, C:0.42, G:0.13, T:0.23
Consensus pattern (23 bp):
ATCCGTCCCCCATCTCCGACGAA
Found at i:269830 original size:22 final size:22
Alignment explanation
Indices: 269802--269844 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
269792 ATCCGTCCCC
269802 CATCTCCGACGAAATCCGTCTT
1 CATCTCCGACGAAATCCGTCTT
269824 CATCTCCGACGAAATCCGTCT
1 CATCTCCGACGAAATCCGTCT
269845 ATCTCCATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.37, G:0.14, T:0.26
Consensus pattern (22 bp):
CATCTCCGACGAAATCCGTCTT
Found at i:270213 original size:14 final size:14
Alignment explanation
Indices: 270194--270224 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
270184 ACACGAAAAT
270194 GAAAATCGCAACAC
1 GAAAATCGCAACAC
*
270208 GAAAATCGCAACGC
1 GAAAATCGCAACAC
270222 GAA
1 GAA
270225 TTTAGTTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.26, G:0.19, T:0.06
Consensus pattern (14 bp):
GAAAATCGCAACAC
Found at i:272403 original size:21 final size:21
Alignment explanation
Indices: 272378--272492 Score: 96
Period size: 21 Copynumber: 5.6 Consensus size: 21
272368 TGCTCCTTTC
*
272378 ATCGTTTAAGAGGCGCCTCCT
1 ATCGTTCAAGAGGCGCCTCCT
*
272399 ATCGTTCAAGAGGC-CCTTCT
1 ATCGTTCAAGAGGCGCCTCCT
272419 CATCGTTCAAGA-G-G-CTCCT
1 -ATCGTTCAAGAGGCGCCTCCT
* * *
272438 ACCGTTCAAGAGGCCCCTCCC
1 ATCGTTCAAGAGGCGCCTCCT
* * * *
272459 ACCATTCAAGAGGCTCCT-GT
1 ATCGTTCAAGAGGCGCCTCCT
272479 CATCGTTCAAGAGG
1 -ATCGTTCAAGAGG
272493 TCTCTCCCAC
Statistics
Matches: 76, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
18 10 0.13
19 5 0.07
20 6 0.08
21 55 0.72
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (21 bp):
ATCGTTCAAGAGGCGCCTCCT
Found at i:272448 original size:39 final size:39
Alignment explanation
Indices: 272372--272476 Score: 122
Period size: 39 Copynumber: 2.6 Consensus size: 39
272362 GCCCAATGCT
* *
272372 CCTT-TCATCGTTTAAGAGGCGCCTCCTATCGTTCAAGAGGC
1 CCTTCTCATCGTTCAAGA-G-G-CTCCTACCGTTCAAGAGGC
272413 CCTTCTCATCGTTCAAGAGGCTCCTACCGTTCAAGAGGC
1 CCTTCTCATCGTTCAAGAGGCTCCTACCGTTCAAGAGGC
* * * *
272452 CCCTCCCACCATTCAAGAGGCTCCT
1 CCTTCTCATCGTTCAAGAGGCTCCT
272477 GTCATCGTTC
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
39 39 0.68
40 1 0.02
41 5 0.09
42 12 0.21
ACGTcount: A:0.20, C:0.35, G:0.19, T:0.26
Consensus pattern (39 bp):
CCTTCTCATCGTTCAAGAGGCTCCTACCGTTCAAGAGGC
Found at i:272457 original size:60 final size:61
Alignment explanation
Indices: 272380--272512 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 61
272370 CTCCTTTCAT
* * * * * *
272380 CGTTTAAGAGGCGCCTCCTATCGTTCAAGAGGC-CCTTCTCATCGTTCAAGAGG-CTCCTAC
1 CGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCTCC-TCTCATCGTTCAAGAGGTCTCCCAC
*
272440 CGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCTCCTGTCATCGTTCAAGAGGTCTCTCCCAC
1 CGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCTCCTCTCATCGTTCAAGAGG--TCTCCCAC
272503 CGTTCAAGAG
1 CGTTCAAGAG
272513 CCCGATTCAC
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
60 44 0.71
61 2 0.03
63 16 0.26
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (61 bp):
CGTTCAAGAGGCCCCTCCCACCATTCAAGAGGCTCCTCTCATCGTTCAAGAGGTCTCCCAC
Found at i:272500 original size:42 final size:39
Alignment explanation
Indices: 272394--272512 Score: 130
Period size: 39 Copynumber: 3.0 Consensus size: 39
272384 TAAGAGGCGC
* * * * *
272394 CTCCTATCGTTCAAGAGGCCCTTCTCATCGTTCAAGAGG
1 CTCCTACCGTTCAAGAGGCCCCTCCCACCATTCAAGAGG
272433 CTCCTACCGTTCAAGAGGCCCCTCCCACCATTCAAGAGG
1 CTCCTACCGTTCAAGAGGCCCCTCCCACCATTCAAGAGG
* * * *
272472 CTCCTGTCATCGTTCAAGAGGTCTCTCCCACCGTTCAAGAG
1 CTCC--T-ACCGTTCAAGAGGCCCCTCCCACCATTCAAGAG
272513 CCCGATTCAC
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
39 38 0.56
41 1 0.01
42 29 0.43
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.24
Consensus pattern (39 bp):
CTCCTACCGTTCAAGAGGCCCCTCCCACCATTCAAGAGG
Found at i:272506 original size:21 final size:20
Alignment explanation
Indices: 272401--272512 Score: 93
Period size: 21 Copynumber: 5.5 Consensus size: 20
272391 CGCCTCCTAT
* * *
272401 CGTTCAAGAGGCCCTTCTCAT
1 CGTTCAAGAGGCTC-TCCCAC
*
272422 CGTTCAAGAGG--CTCCTAC
1 CGTTCAAGAGGCTCTCCCAC
*
272440 CGTTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGG-CTCTCCCAC
* ** *
272461 CATTCAAGAGGCTCCTGTCAT
1 CGTTCAAGAGGCT-CTCCCAC
272482 CGTTCAAGAGGTCTCTCCCAC
1 CGTTCAAGAGG-CTCTCCCAC
272503 CGTTCAAGAG
1 CGTTCAAGAG
272513 CCCGATTCAC
Statistics
Matches: 73, Mismatches: 13, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
18 14 0.19
19 1 0.01
20 1 0.01
21 55 0.75
22 2 0.03
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (20 bp):
CGTTCAAGAGGCTCTCCCAC
Found at i:273982 original size:64 final size:64
Alignment explanation
Indices: 273872--274029 Score: 280
Period size: 64 Copynumber: 2.5 Consensus size: 64
273862 TTAATTGAAT
273872 TTTACATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
1 TTTA-ATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
* * *
273937 TTTAATTGATTTATAAAAGTTGATTTGTTTAATTGATGTGTAAATAAGAATTATTTTTTGCTTG
1 TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
274001 TTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTAATTGATTTGTAAAAGTTGATTTGTT
274030 GTTTATTCAA
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
64 85 0.96
65 4 0.04
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.51
Consensus pattern (64 bp):
TTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTG
Found at i:274228 original size:20 final size:20
Alignment explanation
Indices: 274132--274222 Score: 128
Period size: 20 Copynumber: 4.5 Consensus size: 20
274122 GTTGCGATAT
274132 TCAAATTCGCAACGCGAAAG
1 TCAAATTCGCAACGCGAAAG
* **
274152 TCAAATTTGCAACGTTAAAG
1 TCAAATTCGCAACGCGAAAG
* **
274172 TCAAATTTGCAACGTTAAAG
1 TCAAATTCGCAACGCGAAAG
274192 TCAAATTCGCAACGCGAAAG
1 TCAAATTCGCAACGCGAAAG
274212 TCAAATTCGCA
1 TCAAATTCGCA
274223 TTGCGATTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (20 bp):
TCAAATTCGCAACGCGAAAG
Found at i:274578 original size:6 final size:6
Alignment explanation
Indices: 274569--274603 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
274559 TTGTGATTGG
**
274569 GATTTT GATTTT GATTTT GATTGC GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
274604 CCTTTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:276883 original size:24 final size:24
Alignment explanation
Indices: 276849--276902 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
276839 CTGAAACATC
276849 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
276873 ATCAAAGTCCGTGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
276897 ATCAAA
1 ATCAAA
276903 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:276916 original size:24 final size:24
Alignment explanation
Indices: 276849--276916 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
276839 CTGAAACATC
* * *
276849 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
276873 ATCAAAGTCCGTGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
276897 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
276917 TAGTACTTAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:277860 original size:19 final size:20
Alignment explanation
Indices: 277836--277903 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
277826 AACTAAAACC
277836 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAAATTGAAATTCG
*
277855 TGTTGCG-AATTCGAAAATCG
1 TGTTGCGAAATT-GAAATTCG
* *
277875 AGTTGCGAATTTGAAATTCAG
1 TGTTGCGAAATTGAAATTC-G
*
277896 TATTGCGA
1 TGTTGCGA
277904 TTTTGGCAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 4 0.10
19 7 0.18
20 18 0.46
21 10 0.26
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.34
Consensus pattern (20 bp):
TGTTGCGAAATTGAAATTCG
Found at i:278040 original size:19 final size:19
Alignment explanation
Indices: 277998--278048 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
277988 TGGAAACTGG
* * *
277998 GTTGCGAAATTGGAGTTCGT
1 GTTGCG-AATTTGAGATCGC
278018 GTTGCGAATTTGAGATCGC
1 GTTGCGAATTTGAGATCGC
278037 GTTGCGAATTTG
1 GTTGCGAATTTG
278049 TTGGTCATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 22 0.79
20 6 0.21
ACGTcount: A:0.20, C:0.12, G:0.33, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTTGAGATCGC
Found at i:278643 original size:103 final size:102
Alignment explanation
Indices: 278504--278847 Score: 456
Period size: 103 Copynumber: 3.4 Consensus size: 102
278494 TACTTATATC
* ** * * *
278504 GGTGTAAGTATGTGTTAAGTGTTACATTTTTTTATTTTATTCACTTACATTGATGTAGCATGCGT
1 GGTGTAAGTATGTGTTAAGTGTTACACTTTTTTATTTTATTCACTTACACCGGTGTAGTATGTGT
*
278569 TAAGTGCTACATTTTTTTTTGTTTTATCCACTTACACT
66 TAAGTGCTACA-TTTTTTTTATTTTATCCACTTACACT
* * *
278607 GGTATAAGTATGTGTCAAGTGCTACACTTTTTTATTTTATTCACTTACACCGGTGTAGTATGTGT
1 GGTGTAAGTATGTGTTAAGTGTTACACTTTTTTATTTTATTCACTTACACCGGTGTAGTATGTGT
* * * *
278672 TAAATGCTACACTTTTTTTTATTTTATCTACTTGCACA
66 TAAGTGCTACA-TTTTTTTTATTTTATCCACTTACACT
* **
278710 GGTGTAAGTATGTGTTAAGTGATACACTAGTTTATTTTATTCACTTACACCGGTGTAAGTATGTG
1 GGTGTAAGTATGTGTTAAGTGTTACACTTTTTTATTTTATTCACTTACACCGGTGT-AGTATGTG
* * *
278775 TTAAGTGCTACA-ATTGTTTATTTTATTCACTTACACT
65 TTAAGTGCTACATTTTTTTTATTTTATCCACTTACACT
* *
278812 GGTGTAAGTATGTGTTAAGAGTTACATTTTTTTATT
1 GGTGTAAGTATGTGTTAAGTGTTACACTTTTTTATT
278848 GTGAATTATG
Statistics
Matches: 208, Mismatches: 32, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
102 50 0.24
103 139 0.67
104 19 0.09
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (102 bp):
GGTGTAAGTATGTGTTAAGTGTTACACTTTTTTATTTTATTCACTTACACCGGTGTAGTATGTGT
TAAGTGCTACATTTTTTTTATTTTATCCACTTACACT
Found at i:278652 original size:51 final size:51
Alignment explanation
Indices: 278504--278847 Score: 406
Period size: 51 Copynumber: 6.7 Consensus size: 51
278494 TACTTATATC
* * *
278504 GGTGTAAGTATGTGTTAAGTGTTACATTTTTTTATTTTATTCACTTACATT
1 GGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACT
* * * * * *
278555 GATGT-AGCATGCGTTAAGTGCTACATTTTTTTTTGTTTTATCCACTTACACT
1 GGTGTAAGTATGTGTTAAGTGCTACA--CTTTTTTATTTTATTCACTTACACT
* * *
278607 GGTATAAGTATGTGTCAAGTGCTACACTTTTTTATTTTATTCACTTACACC
1 GGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACT
* * *
278658 GGTGT-AGTATGTGTTAAATGCTACACTTTTTTTTATTTTA-TCTACTTGCACA
1 GGTGTAAGTATGTGTTAAGTGCTACAC--TTTTTTATTTTATTC-ACTTACACT
* ** *
278710 GGTGTAAGTATGTGTTAAGTGATACACTAGTTTATTTTATTCACTTACACC
1 GGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACT
* *
278761 GGTGTAAGTATGTGTTAAGTGCTACAATTGTTTATTTTATTCACTTACACT
1 GGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACT
* * *
278812 GGTGTAAGTATGTGTTAAGAGTTACATTTTTTTATT
1 GGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATT
278848 GTGAATTATG
Statistics
Matches: 250, Mismatches: 35, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
50 36 0.14
51 127 0.51
52 51 0.20
53 36 0.14
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (51 bp):
GGTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTCACTTACACT
Found at i:278842 original size:154 final size:154
Alignment explanation
Indices: 278503--278844 Score: 424
Period size: 154 Copynumber: 2.2 Consensus size: 154
278493 ATACTTATAT
* **
278503 CGGTGTAAGTATGTGTTAAGTGTTACA-TTTTTTTATTTTATTCACTTACATTGATGTAGCATGC
1 CGGTGTAAGTATGTGTTAAGAGTTACATTTTTTTTATTTTATTCACTTACACAGATGTAGCATGC
* * ** * *
278567 GTTAAGTGCTACATTTTTTTTTGTTTTATCCACTTACACTGGTATAAGTATGTGTCAAGTGCTAC
66 GTTAAGTGATACA-TCTAGTTTATTTTATCCACTTACACCGGTATAAGTATGTGTCAAGTGCTAC
* *
278632 ACTTTTTTATTTTATTCACTTACAC
130 AATTGTTTATTTTATTCACTTACAC
* * * *
278657 CGGTGT-AGTATGTGTTAA-ATGCTACACTTTTTTTTATTTTA-TCTACTTGCACAGGTGTAAGT
1 CGGTGTAAGTATGTGTTAAGA-GTTACA-TTTTTTTTATTTTATTC-ACTTACACAGATGT-AGC
* * * *
278719 ATGTGTTAAGTGATACA-CTAGTTTATTTTATTCACTTACACCGGTGTAAGTATGTGTTAAGTGC
62 ATGCGTTAAGTGATACATCTAGTTTATTTTATCCACTTACACCGGTATAAGTATGTGTCAAGTGC
278783 TACAATTGTTTATTTTATTCACTTACAC
127 TACAATTGTTTATTTTATTCACTTACAC
*
278811 TGGTGTAAGTATGTGTTAAGAGTTACATTTTTTT
1 CGGTGTAAGTATGTGTTAAGAGTTACATTTTTTT
278845 ATTGTGAATT
Statistics
Matches: 160, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
153 17 0.11
154 85 0.53
155 40 0.25
156 18 0.11
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (154 bp):
CGGTGTAAGTATGTGTTAAGAGTTACATTTTTTTTATTTTATTCACTTACACAGATGTAGCATGC
GTTAAGTGATACATCTAGTTTATTTTATCCACTTACACCGGTATAAGTATGTGTCAAGTGCTACA
ATTGTTTATTTTATTCACTTACAC
Found at i:279533 original size:31 final size:31
Alignment explanation
Indices: 279498--279569 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
279488 ATAATTATAT
279498 ATTTAGTCTTTAG-TACATATATATTCTATCA
1 ATTTAGTCTTT-GTTACATATATATTCTATCA
* *
279529 ATTTAGTCATTGTTACTTATATATTCTATCA
1 ATTTAGTCTTTGTTACATATATATTCTATCA
* *
279560 GTTTGGTCTT
1 ATTTAGTCTT
279570 AATTTTAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.26, C:0.12, G:0.10, T:0.51
Consensus pattern (31 bp):
ATTTAGTCTTTGTTACATATATATTCTATCA
Found at i:284970 original size:64 final size:63
Alignment explanation
Indices: 284854--284994 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
284844 CACATTGAAT
* *
284854 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAAATGGTGCATCGATGAATAAGG-A
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAAATGGTGCATCGATGAAT-AGGTA
* * * * * * *
284917 GTGCATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCA-CCCTTTAAAGAAG-AAACATCGAAGGCAAATGGTGCATCGATGAATAGGTA
284981 GTGCATCGATGCAC
1 GTGCATCGATGCAC
284995 ATGTTAAAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 18 0.27
64 48 0.73
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAAATGGTGCATCGATGAATAGGTA
Found at i:285999 original size:31 final size:31
Alignment explanation
Indices: 285961--286025 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
285951 AGAGTCGAGG
*
285961 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCGTCGGGACCTATGGACA
285992 GTTTACCTAGGTTCGTCGGGACCTATGGACA
1 GTTTACCTAGGTTCGTCGGGACCTATGGACA
286023 GTT
1 GTT
286026 GCCGAGGTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.18, C:0.22, G:0.28, T:0.32
Consensus pattern (31 bp):
GTTTACCTAGGTTCGTCGGGACCTATGGACA
Found at i:286067 original size:29 final size:30
Alignment explanation
Indices: 286011--286082 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
286001 GGTTCGTCGG
* * * *
286011 GACCTATGGACAGTTGCCGAGGTTCTTTAT
1 GACCTCTGGATAGTTACCGAGGGTCTTTAT
*
286041 GACCTCTGGATAGTTACCG-GGGTCTTTGT
1 GACCTCTGGATAGTTACCGAGGGTCTTTAT
286070 GACCTCTGGATAG
1 GACCTCTGGATAG
286083 GTCCTTCGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 21 0.57
30 16 0.43
ACGTcount: A:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGGTCTTTAT
Found at i:288685 original size:2 final size:2
Alignment explanation
Indices: 288678--288705 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
288668 TATATTTTTA
288678 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
288706 GATAAAGTAA
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:293962 original size:25 final size:25
Alignment explanation
Indices: 293934--293990 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
293924 TCAAATAATG
293934 CATAAAAT-ATATAATTCATCATTTA
1 CATAAAATCATATAATTCAT-ATTTA
* *
293959 CATAAATATCATCTAATTTATATTTA
1 CATAAA-ATCATATAATTCATATTTA
293985 CA-AAAA
1 CATAAAA
293991 CTGATCAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 1 0.04
25 9 0.32
26 9 0.32
27 9 0.32
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (25 bp):
CATAAAATCATATAATTCATATTTA
Done.