Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008182.1 Hibiscus syriacus cultivar Beakdansim tig00110782_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: 1042344
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:526167 original size:33 final size:33
Alignment explanation
Indices: 526085--526212 Score: 159
Period size: 33 Copynumber: 3.8 Consensus size: 33
526075 TAGTTTACTT
* * *
526085 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAA
1 TCGCAACGCGAAA-TGAAAATCGCAA--CGAAA--GAA
*
526123 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
*
526156 TCGCAATGCGAAATGAAAATCGCAACGAAAGAA
1 TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
526189 TCGCAACGCGAAATG-AAATCGCAA
1 TCGCAACGCGAAATGAAAATCGCAA
526213 TGCGATTTTG
Statistics
Matches: 83, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
32 9 0.11
33 47 0.57
35 4 0.05
37 11 0.13
38 12 0.14
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (33 bp):
TCGCAACGCGAAATGAAAATCGCAACGAAAGAA
Found at i:526235 original size:19 final size:19
Alignment explanation
Indices: 526213--526289 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 19
526203 GAAATCGCAA
526213 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
526232 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
526246 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
526265 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
526285 TGCGA
1 TGCGA
526290 AAGTAAACTA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
14 11 0.23
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 20 0.42
20 13 0.27
ACGTcount: A:0.09, C:0.16, G:0.30, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:526617 original size:93 final size:93
Alignment explanation
Indices: 526337--526644 Score: 595
Period size: 93 Copynumber: 3.3 Consensus size: 93
526327 ATGGATTGCA
526337 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
526401 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
526429 TTACTTTCAACC-AAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
526492 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
526520 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
526585 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
526613 TTACTTTCAACCAAAAGACAAAACAAAGACAA
1 TTACTTTCAACCAAAAGACAAAACAAAGACAA
526645 TGTAACACCC
Statistics
Matches: 213, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
91 74 0.35
92 38 0.18
93 101 0.47
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.21
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:527349 original size:22 final size:22
Alignment explanation
Indices: 527308--527374 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
527298 CTCGTATAAA
527308 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
527331 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
527353 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
527375 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:529116 original size:21 final size:21
Alignment explanation
Indices: 529092--529136 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
529082 TCTTGTTCGT
* *
529092 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
529113 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
529134 TTG
1 TTG
529137 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:530448 original size:18 final size:16
Alignment explanation
Indices: 530405--530451 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
530395 TTCATTGCAT
530405 CCTCATTACTTTAATAA
1 CCTCATT-CTTTAATAA
530422 CC-CATTTCTTATACATAA
1 CCTCA-TTCTT-TA-ATAA
530440 CCTCATTCTTTA
1 CCTCATTCTTTA
530452 TCATTCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 5 0.19
17 8 0.31
18 11 0.42
19 2 0.08
ACGTcount: A:0.30, C:0.28, G:0.00, T:0.43
Consensus pattern (16 bp):
CCTCATTCTTTAATAA
Found at i:530987 original size:8 final size:8
Alignment explanation
Indices: 530974--530999 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
530964 TTCTGACCAT
530974 ATCTTATA
1 ATCTTATA
530982 ATCTTATA
1 ATCTTATA
530990 ATCTTATA
1 ATCTTATA
530998 AT
1 AT
531000 TCCAGTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (8 bp):
ATCTTATA
Found at i:532344 original size:22 final size:22
Alignment explanation
Indices: 532303--532369 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
532293 CTCGTATAAA
532303 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
532326 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
532348 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
532370 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:534105 original size:21 final size:21
Alignment explanation
Indices: 534081--534125 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
534071 TCTTGTTCGT
* *
534081 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
534102 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
534123 TTG
1 TTG
534126 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:534938 original size:93 final size:93
Alignment explanation
Indices: 534821--535356 Score: 1056
Period size: 93 Copynumber: 5.8 Consensus size: 93
534811 CGGATGTTAC
534821 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
1 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
534886 ATTTACTTTCAACCAAAAGACAAAACAA
66 ATTTACTTTCAACCAAAAGACAAAACAA
534914 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
1 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
534979 ATTTACTTTCAACCAAAAGACAAAACAA
66 ATTTACTTTCAACCAAAAGACAAAACAA
535007 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
1 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
535072 ATTTACTTTCAACCAAAAGAC-AAACAA
66 ATTTACTTTCAACCAAAAGACAAAACAA
535099 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
1 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
535164 ATTTACTTTCAACCAAAAGACAAAACAA
66 ATTTACTTTCAACCAAAAGACAAAACAA
535192 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
1 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
535257 ATTTACTTTCAACCAAAAGACAAAACAA
66 ATTTACTTTCAACCAAAAGACAAAACAA
*
535285 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAA
1 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
535350 ATTTACT
66 ATTTACT
535357 AAGCAATCTA
Statistics
Matches: 441, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
92 92 0.21
93 349 0.79
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
ATTTACTTTCAACCAAAAGACAAAACAA
Found at i:535181 original size:185 final size:186
Alignment explanation
Indices: 534821--535356 Score: 1056
Period size: 185 Copynumber: 2.9 Consensus size: 186
534811 CGGATGTTAC
534821 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
1 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
534886 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
66 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
534951 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAA
131 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAA
535007 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
1 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
535072 ATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
66 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
535136 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAA
131 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAA
535192 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
1 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
535257 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
66 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
*
535322 TTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
131 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
535357 AAGCAATCTA
Statistics
Matches: 348, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
185 185 0.53
186 163 0.47
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAA
Found at i:535318 original size:278 final size:278
Alignment explanation
Indices: 534821--535356 Score: 1063
Period size: 278 Copynumber: 1.9 Consensus size: 278
534811 CGGATGTTAC
534821 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
1 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
534886 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
66 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
534951 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
131 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
535016 CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTT
196 CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTT
535081 CAACCAAAAGACAAACAA
261 CAACCAAAAGACAAACAA
535099 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
1 AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
535164 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
66 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
535229 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
131 TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
*
535294 CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
196 CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
535357 AAGCAATCTA
Statistics
Matches: 257, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
278 257 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (278 bp):
AGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAA
ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
TTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
CTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTT
CAACCAAAAGACAAACAA
Found at i:537082 original size:14 final size:14
Alignment explanation
Indices: 537063--537152 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
537053 TTGAAATGAA
537063 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
537077 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
537096 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
537110 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
537129 AATCGCAACGAGAG
1 AATCGCAACGAGAG
537143 AATCGCAACG
1 AATCGCAACG
537153 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:537100 original size:33 final size:33
Alignment explanation
Indices: 537055--537169 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
537045 TCTTTTGGTT
537055 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
537088 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
537121 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
537154 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
537170 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:537101 original size:19 final size:19
Alignment explanation
Indices: 537077--537174 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
537067 GCAACGAGAG
*
537077 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
537096 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
537110 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
537129 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
537143 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
537162 AATCGCAATGCGA
1 AATCGCAACGCGA
537175 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 32 0.50
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:537205 original size:14 final size:14
Alignment explanation
Indices: 537186--537239 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
537176 TTTGGTTTCG
537186 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
537200 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
537219 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
537233 CGTTGCG
1 CGTTGCG
537240 CTTTTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.07, C:0.26, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:537218 original size:33 final size:33
Alignment explanation
Indices: 537170--537250 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
537160 AAAATCGCAA
**
537170 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
537203 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
537236 TGCGCTTTTCATTTC
1 TGCGATTTTCATTTC
537251 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.07, C:0.23, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:537286 original size:41 final size:41
Alignment explanation
Indices: 537226--537303 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
537216 TCGCGTTGCG
* *
537226 ATTCTCTCGTTGCGCTTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
537267 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
537304 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:537302 original size:21 final size:21
Alignment explanation
Indices: 537227--537302 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
537217 CGCGTTGCGA
*
537227 TTCTCTCGTTGCGCTTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
537248 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
537268 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
537289 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
537303 CTCTTCTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 17 0.37
21 29 0.63
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:537429 original size:33 final size:33
Alignment explanation
Indices: 537382--537452 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
537372 AATACTAACT
* *
537382 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
537415 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
537448 TGAAA
1 TGAAA
537453 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:537686 original size:22 final size:22
Alignment explanation
Indices: 537634--537688 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
537624 TGGTTGTGAG
**
537634 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
** *
537656 GGAAATCTTCGGAGATGGGGGC
1 GGATTTCTTCGGAGATGGGGAC
537678 GGATTTCTTCG
1 GGATTTCTTCG
537689 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.18, C:0.16, G:0.42, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:537859 original size:20 final size:20
Alignment explanation
Indices: 537834--538027 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
537824 CTTTAAATAT
537834 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
537854 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
537876 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
537895 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
537915 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
*
537935 CGCGTTGCGATTTACTGATA
1 CGCGTTGCGATTTACGGATA
*
537955 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
537975 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
537995 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
538015 CGCGTTGCGATTT
1 CGCGTTGCGATTT
538028 TGGAAAATCG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:537999 original size:60 final size:60
Alignment explanation
Indices: 537836--538007 Score: 236
Period size: 60 Copynumber: 2.9 Consensus size: 60
537826 TTAAATATCG
** *
537836 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACA
* * *** * *
537897 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACTGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
*
537957 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
538008 TCATATTCGC
Statistics
Matches: 94, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 68 0.72
61 26 0.28
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
Found at i:538021 original size:60 final size:59
Alignment explanation
Indices: 537834--538027 Score: 235
Period size: 60 Copynumber: 3.2 Consensus size: 59
537824 CTTTAAATAT
** *
537834 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTAC-TATA
* * *** *
537895 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACTGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACT-ATA
* * * *
537955 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTAC-TATA
538015 CGCGTTGCGATTT
1 CGCGTTGCGATTT
538028 TGGAAAATCG
Statistics
Matches: 111, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
60 82 0.74
61 29 0.26
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (59 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACTATA
Found at i:538044 original size:21 final size:21
Alignment explanation
Indices: 538014--538096 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
538004 ATTTTCATAT
*
538014 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
538035 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
538056 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
538077 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
538097 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:538087 original size:42 final size:43
Alignment explanation
Indices: 537994--538092 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
537984 ATTTATGTGT
* *
537994 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
538035 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
538077 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
538093 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:542112 original size:20 final size:20
Alignment explanation
Indices: 542064--542112 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
542054 ATGTGAAAGT
542064 TGTCCCGAAGGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
* * *
542084 TATCCCGAAGGATCTCTGTA
1 TGTCCCGAAGGACCTATGTA
*
542104 TGTCTCGAA
1 TGTCCCGAA
542113 TTACCTATGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (20 bp):
TGTCCCGAAGGACCTATGTA
Found at i:542879 original size:43 final size:43
Alignment explanation
Indices: 542818--542918 Score: 193
Period size: 43 Copynumber: 2.3 Consensus size: 43
542808 AATGAAGGTA
*
542818 TGCATCGATGCACTACACCATGTATTATGCATCCCTTGACGGG
1 TGCATCGATGCACTACACCATGTATCATGCATCCCTTGACGGG
542861 TGCATCGATGCACTACACCATGTATCATGCATCCCTTGACGGG
1 TGCATCGATGCACTACACCATGTATCATGCATCCCTTGACGGG
542904 TGCATCGATGCACTA
1 TGCATCGATGCACTA
542919 TCTATGCATC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.27
Consensus pattern (43 bp):
TGCATCGATGCACTACACCATGTATCATGCATCCCTTGACGGG
Found at i:543010 original size:64 final size:64
Alignment explanation
Indices: 542942--543061 Score: 152
Period size: 64 Copynumber: 1.9 Consensus size: 64
542932 ACATAAATCC
* * *
542942 CATTCGATGTTTGCATTTT-AAGGGGATGCATCGATGCACTACTTGTGCATCGATACTCTGATGG
1 CATTCGATGTTTGCATTTTAAAGGAG-TGCATCGATACACTACATGTGCATCGATACTCTGATGG
** * * *
543006 CATTCGATGTTTTTATTTTAAATGAGTGCATCGATACACTTCATGTGTATCGATAC
1 CATTCGATGTTTGCATTTTAAAGGAGTGCATCGATACACTACATGTGCATCGATAC
543062 ACCTTGAACA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
64 43 0.91
65 4 0.09
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (64 bp):
CATTCGATGTTTGCATTTTAAAGGAGTGCATCGATACACTACATGTGCATCGATACTCTGATGG
Found at i:543884 original size:16 final size:16
Alignment explanation
Indices: 543863--543893 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
543853 ACACAAATGG
543863 TATGATAAATAACATA
1 TATGATAAATAACATA
*
543879 TATGATATATAACAT
1 TATGATAAATAACAT
543894 GGTAAGTATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (16 bp):
TATGATAAATAACATA
Found at i:546253 original size:18 final size:20
Alignment explanation
Indices: 546216--546254 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
546206 TTTAGTAAAG
*
546216 TATACAAATGATTTTTTTAT
1 TATACAAATGATTATTTTAT
546236 TATA-AAAT-ATTATTTTAT
1 TATACAAATGATTATTTTAT
546254 T
1 T
546255 GAGTTATCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 4 0.22
20 4 0.22
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (20 bp):
TATACAAATGATTATTTTAT
Found at i:547452 original size:21 final size:21
Alignment explanation
Indices: 547401--547453 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
547391 ATTCTGACTA
*
547401 TCGCATTGCGATTTTCTAAAT
1 TCGCATTGTGATTTTCTAAAT
*
547422 TCGCGTTGTGATTTTCCT-AAT
1 TCGCATTGTGATTTT-CTAAAT
*
547443 TCGCAATGTGA
1 TCGCATTGTGA
547454 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (21 bp):
TCGCATTGTGATTTTCTAAAT
Found at i:547468 original size:20 final size:20
Alignment explanation
Indices: 547443--547535 Score: 150
Period size: 20 Copynumber: 4.7 Consensus size: 20
547433 TTTTCCTAAT
*
547443 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
547463 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
547483 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
547503 TCGCAATGCAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
547523 TCGCAACGCGAAT
1 TCGCAATGCGAAT
547536 CTGACTATCG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:547545 original size:20 final size:20
Alignment explanation
Indices: 547522--547588 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
547512 AAATACGTAA
* *
547522 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
547542 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
547562 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
547582 ATCGCAA
1 ATCGCAA
547589 TACTGAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:548460 original size:24 final size:24
Alignment explanation
Indices: 548428--548481 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
548418 GTATTCGAAA
548428 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
548452 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
548476 TTTGAT
1 TTTGAT
548482 GATGTTTCAG
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:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:548639 original size:38 final size:38
Alignment explanation
Indices: 548588--548663 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
548578 ATTGTTGATG
548588 ATAATGAGGAGGAAGTTACGACTGTGAATGAACATGTT
1 ATAATGAGGAGGAAGTTACGACTGTGAATGAACATGTT
548626 ATAATGAGGAGGAAGTTACGACTGTGAATGAACATGTT
1 ATAATGAGGAGGAAGTTACGACTGTGAATGAACATGTT
548664 GAACATCCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.08, G:0.29, T:0.26
Consensus pattern (38 bp):
ATAATGAGGAGGAAGTTACGACTGTGAATGAACATGTT
Found at i:550934 original size:20 final size:20
Alignment explanation
Indices: 550909--550963 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
550899 AGACATTCAT
550909 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
550929 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
*
550949 ATGACTATCGCAACG
1 TTGACTATCGCAACG
550964 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.20
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:550985 original size:33 final size:33
Alignment explanation
Indices: 550935--551031 Score: 131
Period size: 33 Copynumber: 2.8 Consensus size: 33
550925 GGAATTGACT
* **
550935 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
550969 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
551002 ATCGCAATGCGAAAATGAAAAATCGCAACG
1 ATCGCAATGCG-AAATG-AAAATCGCAACG
551032 CGGATTTTCG
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
33 31 0.54
34 14 0.25
35 12 0.21
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:551226 original size:14 final size:14
Alignment explanation
Indices: 551207--551243 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
551197 CATCAATTAA
551207 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
551221 ACAAATCATCTTTT
1 ACAAATCAACATTT
551235 ACAAATCAA
1 ACAAATCAA
551244 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:553262 original size:40 final size:40
Alignment explanation
Indices: 553155--553283 Score: 177
Period size: 40 Copynumber: 3.2 Consensus size: 40
553145 GAAACTTAAA
* *
553155 ATCGCAACGCGAAAATGACTATCGTAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGACT
553195 ATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGACT
* ** * ***
553235 ATCGCAATGCGAATTTGACTATCGCAATGTGATTTTGACT
1 ATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGACT
553275 ATCGCAACG
1 ATCGCAACG
553284 AGAGAATCAC
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (40 bp):
ATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGACT
Found at i:553263 original size:20 final size:20
Alignment explanation
Indices: 553155--553261 Score: 169
Period size: 20 Copynumber: 5.3 Consensus size: 20
553145 GAAACTTAAA
553155 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
553175 ATCGTAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
553195 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
553215 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
553235 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
553255 ATCGCAA
1 ATCGCAA
553262 TGTGATTTTG
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:553271 original size:20 final size:20
Alignment explanation
Indices: 553155--553281 Score: 128
Period size: 20 Copynumber: 6.3 Consensus size: 20
553145 GAAACTTAAA
* **
553155 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAATTTGACT
* * **
553175 ATCGTAACGCGAAAATGACT
1 ATCGCAATGCGAATTTGACT
* **
553195 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAATTTGACT
**
553215 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAATTTGACT
553235 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAATTTGACT
* *
553255 ATCGCAATGTGATTTTGACT
1 ATCGCAATGCGAATTTGACT
553275 ATCGCAA
1 ATCGCAA
553282 CGAGAGAATC
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 100 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATTTGACT
Found at i:553371 original size:20 final size:20
Alignment explanation
Indices: 553326--553464 Score: 92
Period size: 20 Copynumber: 7.6 Consensus size: 20
553316 GCGATTCTTT
*
553326 CGTTGCGATAGTCAAATTT-G
1 CGTTGCGATAGTC-ATTTTCG
*
553346 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
553366 CGTTGCGAT--T--TTGTT--
1 CGTTGCGATAGTCATT-TTCG
**
553381 -GTTGCGATTTTCA-TTTCG
1 CGTTGCGATAGTCATTTTCG
* *
553399 CATTGCGAT--TC--TCTCG
1 CGTTGCGATAGTCATTTTCG
553415 --TTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
553433 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
553453 CATTGCGATAGT
1 CGTTGCGATAGT
553465 AAACTATTCT
Statistics
Matches: 97, Mismatches: 7, Indels: 30
0.72 0.05 0.22
Matches are distributed among these distances:
14 15 0.15
16 11 0.11
17 5 0.05
18 5 0.05
19 11 0.11
20 50 0.52
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:553403 original size:87 final size:87
Alignment explanation
Indices: 553296--553461 Score: 271
Period size: 87 Copynumber: 1.9 Consensus size: 87
553286 AGAATCACAA
*
553296 TGCGATTTTCATTTCACATTGCGATTCTTTCGTTGCGATAGTCAAATTT-GCATTGCGATAGTCA
1 TGCGATTTTCATTTCACATTGCGATTCTCTCGTTGCGATAGTC-AATTTCGCATTGCGATAGTCA
*
553360 TTTTCGCGTTGCGATTTTGTTGT
65 TTTTCGCATTGCGATTTTGTTGT
* * *
553383 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCAT
1 TGCGATTTTCATTTCACATTGCGATTCTCTCGTTGCGATAGTCAATTTCGCATTGCGATAGTCAT
553448 TTTCGCATTGCGAT
66 TTTCGCATTGCGAT
553462 AGTAAACTAT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
86 4 0.05
87 69 0.95
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.43
Consensus pattern (87 bp):
TGCGATTTTCATTTCACATTGCGATTCTCTCGTTGCGATAGTCAATTTCGCATTGCGATAGTCAT
TTTCGCATTGCGATTTTGTTGT
Found at i:553405 original size:33 final size:34
Alignment explanation
Indices: 553348--553441 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
553338 CAAATTTGCA
* * *
553348 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
** *
553382 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
553415 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCGTTGCGAT
553442 AGTCATTTTC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 27 0.54
34 23 0.46
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
Found at i:555383 original size:19 final size:20
Alignment explanation
Indices: 555345--555394 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
555335 CTGAAACTTT
*
555345 AAATCGCAACACGAAAATGA
1 AAATCGCAACGCGAAAATGA
555365 AAATCGCAACGCG-AAATGA
1 AAATCGCAACGCGAAAATGA
555384 AAATCGCAACG
1 AAATCGCAACG
555395 ACAGAATCGC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.50, C:0.22, G:0.18, T:0.10
Consensus pattern (20 bp):
AAATCGCAACGCGAAAATGA
Found at i:555777 original size:22 final size:22
Alignment explanation
Indices: 555752--555793 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
555742 AGATGGAGAC
*
555752 TGATATCGTCGGAGATGGGGGT
1 TGATATCATCGGAGATGGGGGT
*
555774 TGATTTCATCGGAGATGGGG
1 TGATATCATCGGAGATGGGG
555794 ACGGATGTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.10, G:0.43, T:0.29
Consensus pattern (22 bp):
TGATATCATCGGAGATGGGGGT
Found at i:556016 original size:20 final size:20
Alignment explanation
Indices: 555993--556185 Score: 332
Period size: 20 Copynumber: 9.7 Consensus size: 20
555983 CGATAGTCAG
*
555993 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
556013 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
556033 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
556053 ATTCGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
556073 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
556093 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
556113 ATTCGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
556133 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
556153 ATTCGCATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
556173 ATTCGCATTGCGA
1 ATTCGCATTGCGA
556186 ATTAGGAAAA
Statistics
Matches: 162, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 162 1.00
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:556205 original size:21 final size:21
Alignment explanation
Indices: 556175--556227 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
556165 ATTTACGTAT
*
556175 TCGCATTGCGAATTAGGAAAA
1 TCGCAATGCGAATTAGGAAAA
*
556196 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAGGAAAA
556217 TCGCAATGCGA
1 TCGCAATGCGA
556228 TAGTCAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAGGAAAA
Found at i:562579 original size:3 final size:3
Alignment explanation
Indices: 562571--562668 Score: 71
Period size: 3 Copynumber: 32.0 Consensus size: 3
562561 TTGATCCTTG
* *
562571 TTA TTA TTA TT- TT- TTA TTA TTT TTA CCTTA TTTA TAA GTTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA --TTA -TTA TTA -TTA TTA T-TA
562619 TATA TT- TTCA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA
1 T-TA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
562663 CTA TTA
1 TTA TTA
562669 ACGTGTATAT
Statistics
Matches: 79, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
2 9 0.11
3 55 0.70
4 12 0.15
5 3 0.04
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:562681 original size:2 final size:2
Alignment explanation
Indices: 562674--562700 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
562664 TATTAACGTG
562674 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 T
562701 TATTACTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:566309 original size:14 final size:14
Alignment explanation
Indices: 566290--566375 Score: 73
Period size: 14 Copynumber: 5.4 Consensus size: 14
566280 CGATTCAGGA
566290 GCGATTCTCTCGTT
1 GCGATTCTCTCGTT
*
566304 GCGATTTTCATTTCGCGTT
1 GCGA--TTC---TCTCGTT
566323 GCGATTCTCTCGTT
1 GCGATTCTCTCGTT
566337 GCGATTGTCATCTCGCGTT
1 GCGA-T-TC-TCT--CGTT
566356 GCGATTCTCTCGTT
1 GCGATTCTCTCGTT
566370 GCGATT
1 GCGATT
566376 TTCATTTCAA
Statistics
Matches: 60, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
14 24 0.40
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 18 0.30
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
GCGATTCTCTCGTT
Found at i:566327 original size:33 final size:33
Alignment explanation
Indices: 566290--566383 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
566280 CGATTCAGGA
566290 GCGATTCTCTCGTTGCGATTTTCATTTCGCGTT
1 GCGATTCTCTCGTTGCGATTTTCATTTCGCGTT
* *
566323 GCGATTCTCTCGTTGCGATTGTCATCTCGCGTT
1 GCGATTCTCTCGTTGCGATTTTCATTTCGCGTT
566356 GCGATTCTCTCGTTGCGATTTTCATTTC
1 GCGATTCTCTCGTTGCGATTTTCATTTC
566384 AACCAAAAGA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.10, C:0.26, G:0.21, T:0.44
Consensus pattern (33 bp):
GCGATTCTCTCGTTGCGATTTTCATTTCGCGTT
Found at i:568240 original size:93 final size:93
Alignment explanation
Indices: 568081--568459 Score: 726
Period size: 93 Copynumber: 4.1 Consensus size: 93
568071 TAGATTGCTT
*
568081 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
568146 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
568174 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
568239 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
568267 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
568332 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
568360 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
568425 TTTGTCTTTG-TTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
568451 AGTAAATTT
1 AGTAAATTT
568460 ATCCATTCAA
Statistics
Matches: 283, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
91 19 0.07
92 6 0.02
93 258 0.91
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:568543 original size:19 final size:19
Alignment explanation
Indices: 568503--568630 Score: 98
Period size: 19 Copynumber: 7.3 Consensus size: 19
568493 TAGTTTACTT
*
568503 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAAC-CAAAA
568523 TCGCAACACGAAACCAAAA
1 TCGCAACACGAAACCAAAA
* **
568542 TCGCAACGCGAAATGAAAA
1 TCGCAACACGAAACCAAAA
*
568561 TCGC-A-ACG--A-CAGAA
1 TCGCAACACGAAACCAAAA
*
568575 TCGCAACGCGAAACC-AAA
1 TCGCAACACGAAACCAAAA
*
568593 TCGC-A-ACG--A-CAAGA
1 TCGCAACACGAAACCAAAA
*
568607 TCGCAACGCGAAACCAAAA
1 TCGCAACACGAAACCAAAA
568626 TCGCA
1 TCGCA
568631 TTGCGATTTT
Statistics
Matches: 84, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
13 1 0.01
14 14 0.17
15 3 0.04
16 6 0.07
17 3 0.04
18 9 0.11
19 34 0.40
20 14 0.17
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACACGAAACCAAAA
Found at i:568599 original size:32 final size:31
Alignment explanation
Indices: 568539--568630 Score: 130
Period size: 32 Copynumber: 2.8 Consensus size: 31
568529 CACGAAACCA
**
568539 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAA-CCAAATCGCAACGAC
568571 AGAATCGCAACGCGAAACCAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAATCGCAACGAC
568603 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACC-AAATCGCA
568631 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
31 1 0.02
32 31 0.56
33 23 0.42
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (31 bp):
AAATCGCAACGCGAAACCAAATCGCAACGAC
Found at i:568648 original size:19 final size:19
Alignment explanation
Indices: 568626--568760 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
568616 GAAACCAAAA
*
568626 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
568645 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
568661 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
568678 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
568694 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
568711 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
568730 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
568750 TCGTGTTGCGA
1 TCGCGTTGCGA
568761 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:568667 original size:14 final size:14
Alignment explanation
Indices: 568648--568704 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
568638 TTTCATTTCG
568648 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
568662 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
568679 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
568695 CGTTGCGATT
1 CGTTGCGATT
568705 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:568673 original size:33 final size:33
Alignment explanation
Indices: 568631--568723 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
568621 CAAAATCGCA
*
568631 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
568664 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
568697 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
568724 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:570700 original size:14 final size:14
Alignment explanation
Indices: 570681--570716 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
570671 ATTGTTTAAT
570681 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
570695 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
570709 TGATTTGT
1 TGATTTGT
570717 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:570849 original size:19 final size:19
Alignment explanation
Indices: 570823--570922 Score: 129
Period size: 19 Copynumber: 5.5 Consensus size: 19
570813 AAAATTGACT
570823 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
570842 AGCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
570861 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
570875 ATCGCAATGCGAAATGAAT
1 ATCGCAATGCGAAATGAAA
570894 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
570914 ATCGCAATG
1 ATCGCAATG
570923 GGAGAATCGC
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 36 0.52
20 17 0.25
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:570952 original size:53 final size:53
Alignment explanation
Indices: 570823--570939 Score: 191
Period size: 53 Copynumber: 2.2 Consensus size: 53
570813 AAAATTGACT
* *
570823 ATCGCAATGCGAAATGAAAAGCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAATATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
570875 ATCGCAATGCGAAATGAATATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAATATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
570928 ATCGCAATGCGA
1 ATCGCAATGCGA
570940 TTTTAATTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 27 0.45
53 33 0.55
ACGTcount: A:0.43, C:0.17, G:0.26, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAATATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:570957 original size:19 final size:19
Alignment explanation
Indices: 570929--571077 Score: 130
Period size: 19 Copynumber: 8.6 Consensus size: 19
570919 AATGGGAGAA
* *
570929 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
570948 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
570964 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
570981 TCGCATTGTGA--TTC-TC
1 TCGCATTGCGATTTTCATT
570997 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
571014 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
571033 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
571049 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
571066 TCCGCATTGCGA
1 T-CGCATTGCGA
571078 AATGTAATGG
Statistics
Matches: 104, Mismatches: 10, Indels: 31
0.72 0.07 0.21
Matches are distributed among these distances:
14 17 0.16
16 21 0.20
17 18 0.17
18 2 0.02
19 40 0.38
20 6 0.06
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:570972 original size:33 final size:33
Alignment explanation
Indices: 570935--571026 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
570925 AGAATCGCAA
*
570935 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
570968 TGCGATTTTCATTTCGCATTGTGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
571001 TGCGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
571027 TTCATTTCGC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:571023 original size:52 final size:53
Alignment explanation
Indices: 570967--571077 Score: 206
Period size: 52 Copynumber: 2.1 Consensus size: 53
570957 GATTCTCTCG
*
570967 TTGCGATTTTCATTTCGCATTGTGATTCTCTCGTTGCGATTTTCATTT-CGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
571019 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
571072 TTGCGA
1 TTGCGA
571078 AATGTAATGG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 47 0.82
53 10 0.18
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (53 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
Found at i:571093 original size:85 final size:85
Alignment explanation
Indices: 570929--571094 Score: 226
Period size: 85 Copynumber: 2.0 Consensus size: 85
570919 AATGGGAGAA
* *
570929 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGTGATT
1 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATA
* ** *
570994 CTCTCGTTGCGATTTTCATT
66 ATCTAATGGCGATTTTCATT
* *
571014 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGA-
1 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGAT
* *
571078 AATGTAATGGTGATTTT
65 AATCTAATGGCGATTTT
571095 GTTGATTTCA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
85 61 0.87
86 9 0.13
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.45
Consensus pattern (85 bp):
TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATA
ATCTAATGGCGATTTTCATT
Found at i:571159 original size:19 final size:19
Alignment explanation
Indices: 571135--571232 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
571125 AAAATTGACT
571135 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
571154 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
571173 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
571187 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
571206 ATTGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
571226 ATCGCAA
1 ATCGCAA
571233 CGAGAGAATC
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 38 0.55
20 15 0.22
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:571213 original size:52 final size:53
Alignment explanation
Indices: 571135--571251 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
571125 AAAATTGACT
571135 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
571187 ATCGCAATGCGAAATGAAAATTGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
571240 ATCGCAATGCGA
1 ATCGCAATGCGA
571252 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 28 0.44
53 35 0.56
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:574520 original size:20 final size:20
Alignment explanation
Indices: 574492--574741 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
574482 AAATTTCAGT
* *
574492 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
574512 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
574532 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
574552 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
574572 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
* *
574592 GTTGCGATTTATGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
574612 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
574632 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
574652 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* *
574672 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
574692 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
574712 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
574732 GTTGCGATTT
1 GTTGCGATTT
574742 TGGAAAATCG
Statistics
Matches: 200, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 199 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:574758 original size:21 final size:21
Alignment explanation
Indices: 574728--574810 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
574718 ATTTTCATAT
*
574728 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
574749 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
574770 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
574791 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
574811 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:574801 original size:42 final size:43
Alignment explanation
Indices: 574708--574806 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
574698 ATTTATGTGT
* *
574708 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
574749 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
574791 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
574807 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:584060 original size:30 final size:30
Alignment explanation
Indices: 584026--584083 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
584016 ATGACTTAAG
584026 ACACGTAAGATTTATCATATATCATTTGAT
1 ACACGTAAGATTTATCATATATCATTTGAT
*
584056 ACACGTAAGATTTATCGTATATCATTTG
1 ACACGTAAGATTTATCATATATCATTTG
584084 TAAGATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (30 bp):
ACACGTAAGATTTATCATATATCATTTGAT
Found at i:584302 original size:16 final size:16
Alignment explanation
Indices: 584281--584336 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
584271 TGAAGGGTCT
584281 TTAGCCCTTTGGAGAA
1 TTAGCCCTTTGGAGAA
* **
584297 TTAG-CCTTGTGAAGGGTC
1 TTAGCCCTT-TG--GAGAA
584315 TTAGCCCTTTGGAGAA
1 TTAGCCCTTTGGAGAA
584331 TTAGCC
1 TTAGCC
584337 TTGTGAAGGG
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
15 4 0.13
16 14 0.47
18 8 0.27
19 4 0.13
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (16 bp):
TTAGCCCTTTGGAGAA
Found at i:584324 original size:34 final size:34
Alignment explanation
Indices: 584249--584353 Score: 201
Period size: 34 Copynumber: 3.1 Consensus size: 34
584239 TCTTCCCTTT
584249 GCCCTTTGGAGAATTAGCCTTGTGAAGGGTCTTTA
1 GCCCTTTGGAGAATTAGCCTTGTGAAGGGTC-TTA
584284 GCCCTTTGGAGAATTAGCCTTGTGAAGGGTCTTA
1 GCCCTTTGGAGAATTAGCCTTGTGAAGGGTCTTA
584318 GCCCTTTGGAGAATTAGCCTTGTGAAGGGTCTTA
1 GCCCTTTGGAGAATTAGCCTTGTGAAGGGTCTTA
584352 GC
1 GC
584354 ATCATGTCTC
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
34 39 0.56
35 31 0.44
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (34 bp):
GCCCTTTGGAGAATTAGCCTTGTGAAGGGTCTTA
Found at i:587227 original size:14 final size:14
Alignment explanation
Indices: 587210--587242 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
587200 ATTTCTATGT
*
587210 AGGGAATTATTTGC
1 AGGGAATTATTTAC
587224 AGGGAATTATTTAC
1 AGGGAATTATTTAC
587238 AGGGA
1 AGGGA
587243 TTACTTCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:588840 original size:3 final size:3
Alignment explanation
Indices: 588816--588864 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
588806 TATACAAAAA
588816 TAT T-T TAT T-T TAT TA- TATT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
588859 T-T TAT T
1 TAT TAT T
588865 TTTGTAGGCC
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 8 0.20
3 31 0.76
4 2 0.05
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:588955 original size:33 final size:33
Alignment explanation
Indices: 588918--588999 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
588908 GAAAATAAAT
* *
588918 CAACGGATTTGAGTCCTATTGAAATACTAAAAC
1 CAACGCATTTGAGTCCTATTGAAACACTAAAAC
* * * *
588951 CAACGTATTTAAGTCATATTGAAACATTAAAAC
1 CAACGCATTTGAGTCCTATTGAAACACTAAAAC
588984 CGAA-GCATTTGAGTCC
1 C-AACGCATTTGAGTCC
589000 AAGTAGGACT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
33 38 0.95
34 2 0.05
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (33 bp):
CAACGCATTTGAGTCCTATTGAAACACTAAAAC
Found at i:589544 original size:13 final size:13
Alignment explanation
Indices: 589526--589555 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
589516 TATCGAATAC
589526 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
589539 TTTTAATTTTTAA
1 TTTTAAATTTTAA
589552 TTTT
1 TTTT
589556 TGCAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:593433 original size:111 final size:110
Alignment explanation
Indices: 593149--593549 Score: 588
Period size: 110 Copynumber: 3.6 Consensus size: 110
593139 GTGAATGGGA
*
593149 GACTGTCAACAAACAACTTTTCAGTTTCATTCAGAATCAATTTCAACTTCACAACGAAGGATATT
1 GACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATT
* *
593214 GGACTCGAGATAACACAATA-TCAACTTCACAGTGAAGGGGCGACT
66 GGACTCGAGACAACACAA-ACTCAACTTCACAGCGAAGGGGCGACT
* *
593259 GACTGTCAACAAACAACTTTTCAGTTTCCTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATT
1 GACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATT
* * * *
593324 GGACTCGAGACCACACAAGCTCAAATTCACAGCGAAGGGACGACT
66 GGACTCGAGACAACACAAACTCAACTTCACAGCGAAGGGGCGACT
* * *
593369 GACTGTCAAACAAAAAACTTTTCAGTTTCATTCAGTGTCAATTTCAACTTCACAGCGAAGGATAT
1 GACTGTC-AACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATAT
* * *
593434 TAGACTCGAGACAACATAAACTCAACTTCACAGCGAAGGGGTGACT
65 TGGACTCGAGACAACACAAACTCAACTTCACAGCGAAGGGGCGACT
* ** * * *
593480 GACTGTCAACAAACAACATCCCAATTTTATTCAGAGTCAATTTCAGCTTCACAACGAAGGATATT
1 GACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATT
593545 GGACT
66 GGACT
593550 TGAAACAATA
Statistics
Matches: 260, Mismatches: 29, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
110 160 0.62
111 100 0.38
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (110 bp):
GACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATT
GGACTCGAGACAACACAAACTCAACTTCACAGCGAAGGGGCGACT
Found at i:593546 original size:221 final size:220
Alignment explanation
Indices: 593149--593549 Score: 624
Period size: 221 Copynumber: 1.8 Consensus size: 220
593139 GTGAATGGGA
*
593149 GACTGTCAACAAACAACTTTTCAGTTTCATTCAGAATCAATTTCAACTTCACAACGAAGGATATT
1 GACTGTCAACAAAAAACTTTTCAGTTTCATTCAGAATCAATTTCAACTTCACAACGAAGGATATT
* * * * *
593214 GGACTCGAGATAACACAATATCAACTTCACAGTGAAGGGGCGACTGACTGTCAACAAACAACTTT
66 AGACTCGAGACAACACAATATCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACATC
* * * *
593279 TCAGTTTCCTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACCACACAAGC
131 CCAATTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACCACACAAGC
593344 TCAAATTCACAGCGAAGGGACGACT
196 TCAAATTCACAGCGAAGGGACGACT
** *
593369 GACTGTCAAACAAAAAACTTTTCAGTTTCATTCAGTGTCAATTTCAACTTCACAGCGAAGGATAT
1 GACTGTC-AACAAAAAACTTTTCAGTTTCATTCAGAATCAATTTCAACTTCACAACGAAGGATAT
* *
593434 TAGACTCGAGACAACATAA-ACTCAACTTCACAGCGAAGGGGTGACTGACTGTCAACAAACAACA
65 TAGACTCGAGACAACACAATA-TCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACA
* *
593498 TCCCAATTTTATTCAGAGTCAATTTCAGCTTCACAACGAAGGATATTGGACT
129 TCCCAATTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACT
593550 TGAAACAATA
Statistics
Matches: 162, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
220 8 0.05
221 154 0.95
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (220 bp):
GACTGTCAACAAAAAACTTTTCAGTTTCATTCAGAATCAATTTCAACTTCACAACGAAGGATATT
AGACTCGAGACAACACAATATCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACATC
CCAATTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACCACACAAGC
TCAAATTCACAGCGAAGGGACGACT
Found at i:593929 original size:43 final size:43
Alignment explanation
Indices: 593868--593949 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
593858 ATGAAGGGGC
* *
593868 CATCCACGATTTCAACTCCACAATGGATGATATCGTACCCACA
1 CATCCACGATTTCAACTCCACAATGGAGGACATCGTACCCACA
* * *
593911 CATCCATGATTTTAACTCCACGATGGAGGACATCGTACC
1 CATCCACGATTTCAACTCCACAATGGAGGACATCGTACC
593950 ATTTGAGGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.24
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACAATGGAGGACATCGTACCCACA
Found at i:593930 original size:241 final size:241
Alignment explanation
Indices: 593509--594608 Score: 1639
Period size: 241 Copynumber: 4.6 Consensus size: 241
593499 CCCAATTTTA
* * ** * * *
593509 TTCAGAGTCAATTTCAGCTTCACAACGAAGGATATTGGACTTGAAACAATAC-A--TACTTGGAT
1 TTCAGAGCCAATTTCAACTTCACGGCGGATGATATTGGACTCGAAACAATACAACTTACTTGGAT
* ** * * * *
593571 TTCAACATCACGATGAAAAATATTCAAGTCAAGGCTCAACTTCATGACGAATGGGCCATTCACAA
66 TTCAACTTCACGATGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGA
593636 TTTCAACTCCACAACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACGACGGAGGAT
131 TTTCAACTCCACAACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACGACGGAGGAT
*
593701 ATCGTGCCATTTAAGGCTCAACTTCACGACGAAGGGGCTTCCCAGT
196 ATCGTGCCATTTGAGGCTCAACTTCACGACGAAGGGGCTTCCCAGT
* *
593747 TTCAGAGCTAATTTCAACTTCACGGCGGATGATATTGGACTCGAAATAATACAACTTACTTGGAT
1 TTCAGAGCCAATTTCAACTTCACGGCGGATGATATTGGACTCGAAACAATACAACTTACTTGGAT
* * *
593812 TTCAACTTCACGACGAAGGATATTAAAGTCAAGGCTCAACTTCACGATGAAGGGGCCATCCACGA
66 TTCAACTTCACGATGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGA
* * * * * *
593877 TTTCAACTCCACAATGGATGATATCGTACCCACACATCCATGATTTTAACTCCACGATGGAGGAC
131 TTTCAACTCCACAACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACGACGGAGGAT
* *
593942 ATCGTACCATTTGAGGCTCAACTTCACGACGAATGGGCTTCCCAGT
196 ATCGTGCCATTTGAGGCTCAACTTCACGACGAAGGGGCTTCCCAGT
* * *
593988 TTCAGGGCCAATTTCAACTTCACGGCGGATGATATTGGACTTGAAATAATACAACTTACTTGGAT
1 TTCAGAGCCAATTTCAACTTCACGGCGGATGATATTGGACTCGAAACAATACAACTTACTTGGAT
* * * *
594053 TTCAACTTCACGACGAAGGATATTAAAGTCAAGGCTCAACTTCACGACAAAGGGGTCATCCACGA
66 TTCAACTTCACGATGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGA
* * *
594118 TTTTAACTCCACAATGGATGATATCGTACCCACACATCCACGATTTCAACTCCACGACGGAGGAT
131 TTTCAACTCCACAACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACGACGGAGGAT
*
594183 ATCGTGCCATTTGAGGCTCAACTTCACGACGAAGTGGCTTCCCAGT
196 ATCGTGCCATTTGAGGCTCAACTTCACGACGAAGGGGCTTCCCAGT
** * *
594229 TTCAGAGCCAATTTCAACTTCACGGTAGAGGATATTGGATTCGAAACAATACAACTTACTTGGAT
1 TTCAGAGCCAATTTCAACTTCACGGCGGATGATATTGGACTCGAAACAATACAACTTACTTGGAT
* *
594294 TTCAACTTCACGATGAAGGATATTCAAGTCAAGGATCAACTTCACGACGAAGGGGCCATCCACTA
66 TTCAACTTCACGATGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGA
* *
594359 TTTCAACTCCACGACGGAGGATATCGTACCCACATATCCACGATTTCAACTCCACGACGGAGGAT
131 TTTCAACTCCACAACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACGACGGAGGAT
*
594424 ATCGTGCCATTTGAGGCTCAACTTCACGACGAAGGGGCTTCCTAGT
196 ATCGTGCCATTTGAGGCTCAACTTCACGACGAAGGGGCTTCCCAGT
* * * * * *
594470 TTCAAAGCCAATTTTAACTTCGCGGCGGAAGATATTGGACTCGAAAAAAATAAAACTTACTTGGA
1 TTCAGAGCCAATTTCAACTTCACGGCGGATGATATTGGACTCG-AAACAATACAACTTACTTGGA
* * * *
594535 TTTCAACTTCATGATGAAGGATATCCAATTCAAGGCTCAACTTCACGACGGAGGGGCCATCCACG
65 TTTCAACTTCACGATGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACG
*
594600 GTTTCAACT
130 ATTTCAACT
594609 TCACGACGAA
Statistics
Matches: 780, Mismatches: 78, Indels: 4
0.90 0.09 0.00
Matches are distributed among these distances:
238 43 0.06
239 1 0.00
241 650 0.83
242 86 0.11
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (241 bp):
TTCAGAGCCAATTTCAACTTCACGGCGGATGATATTGGACTCGAAACAATACAACTTACTTGGAT
TTCAACTTCACGATGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCCATCCACGA
TTTCAACTCCACAACGGAGGATATCGTACCCACACATCCACGATTTCAACTCCACGACGGAGGAT
ATCGTGCCATTTGAGGCTCAACTTCACGACGAAGGGGCTTCCCAGT
Found at i:595181 original size:33 final size:33
Alignment explanation
Indices: 595139--595204 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
595129 GAAAATAAAT
595139 CAACGTATTTGAGTCATATTGAAACACTAAAAC
1 CAACGTATTTGAGTCATATTGAAACACTAAAAC
*
595172 CAACGTATTTGAGTTATATTGAAACACTAAAAC
1 CAACGTATTTGAGTCATATTGAAACACTAAAAC
595205 TGAAGCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (33 bp):
CAACGTATTTGAGTCATATTGAAACACTAAAAC
Found at i:595215 original size:33 final size:33
Alignment explanation
Indices: 595139--595219 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
595129 GAAAATAAAT
*
595139 CAACGTATTTGAGTCATATTGAAACACTAAAAC
1 CAACGCATTTGAGTCATATTGAAACACTAAAAC
* *
595172 CAACGTATTTGAGTTATATTGAAACACTAAAAC
1 CAACGCATTTGAGTCATATTGAAACACTAAAAC
*
595205 TGAA-GCATTTGAGTC
1 -CAACGCATTTGAGTC
595220 CAAGTAGGAC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 41 0.95
34 2 0.05
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.30
Consensus pattern (33 bp):
CAACGCATTTGAGTCATATTGAAACACTAAAAC
Found at i:595764 original size:13 final size:13
Alignment explanation
Indices: 595746--595775 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
595736 TATCAAATAC
595746 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
595759 TTTTAATTTTTAA
1 TTTTAAATTTTAA
595772 TTTT
1 TTTT
595776 TGTAATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:596514 original size:22 final size:21
Alignment explanation
Indices: 596467--596514 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
596457 TAATGAAGTC
* *
596467 ATAAATTGTTAAATCAAAAGT
1 ATAAATTGTTAAATAAAAAAT
* *
596488 GTAAATTTTTAATATAAAAAAT
1 ATAAATTGTTAA-ATAAAAAAT
596510 ATAAA
1 ATAAA
596515 ATTTAATTTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (21 bp):
ATAAATTGTTAAATAAAAAAT
Found at i:597038 original size:2 final size:2
Alignment explanation
Indices: 597031--597055 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
597021 ATTAATGATC
597031 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 A
597056 GAATATGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:603250 original size:36 final size:35
Alignment explanation
Indices: 603168--603460 Score: 227
Period size: 36 Copynumber: 8.3 Consensus size: 35
603158 TTTTAAAAAG
*
603168 AAAACA-TTTTGAAAA-TATGGGTAATATATAGTTTTTT
1 AAAACATTTTTGAAAACTAT--ATAA-ATATAG-TTTTT
*
603205 AAAATATTTTTGAAAACTATATAACATATAGTTTTT
1 AAAACATTTTTGAAAACTATATAA-ATATAGTTTTT
*
603241 AAAACATTTTAGAAAA-TAAATATAACATATAG-TTTT
1 AAAACATTTTTGAAAACT--ATATAA-ATATAGTTTTT
* *
603277 AAAATCA-TTTTAAAAACTTATATAATATATAGTTTTA
1 AAAA-CATTTTTGAAAAC-TATATAA-ATATAGTTTTT
* *
603314 AAAACATTTTTGAATAAATTATATAATATATAGTTTTA
1 AAAACATTTTTG-A-AAACTATATAA-ATATAGTTTTT
* *
603352 AAAACATTTTTGAATAAAT-TATATAATATAGTTTTA
1 AAAACATTTTTGAA-AACTATATA-AATATAGTTTTT
* *
603388 AAAACGTTTTTTAAAAC--T-T--ATATA-TTTTT
1 AAAACATTTTTGAAAACTATATAAATATAGTTTTT
*
603417 AAAACA-TTTTGAAAACTATAT-AATATAGTTTTG
1 AAAACATTTTTGAAAACTATATAAATATAGTTTTT
*
603450 AAAACTTTTTT
1 AAAACATTTTT
603461 AAATATAATA
Statistics
Matches: 217, Mismatches: 20, Indels: 41
0.78 0.07 0.15
Matches are distributed among these distances:
28 9 0.04
29 9 0.04
30 6 0.03
31 1 0.00
32 5 0.02
33 10 0.05
34 5 0.02
35 3 0.01
36 76 0.35
37 45 0.21
38 42 0.19
39 6 0.03
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (35 bp):
AAAACATTTTTGAAAACTATATAAATATAGTTTTT
Found at i:603276 original size:74 final size:73
Alignment explanation
Indices: 603193--603459 Score: 224
Period size: 74 Copynumber: 3.8 Consensus size: 73
603183 TATGGGTAAT
*
603193 ATATAGTTTTTTAAAATATTTTTGAAAACTATATAACATATAGTTTTTAAAACATTTTAG-A-AA
1 ATATAG-TTTTTAAAATATTTTTGAAAACTATATAA-ATATAGTTTTAAAAACATTTTAGAATAA
603256 ATAAATATAAC
64 AT-AATATAAC
* *
603267 ATATAG-TTTTAAAATCA-TTTTAAAAACTTATATAATATATAGTTTTAAAAACATTTTTGAATA
1 ATATAGTTTTTAAAAT-ATTTTTGAAAAC-TATATAA-ATATAGTTTTAAAAACATTTTAGAATA
* *
603330 AATTATATAAT
63 AATAATATAAC
* * * * *
603341 ATATAGTTTTAAAAACATTTTTGAATAAAT-TATATAATATAGTTTTAAAAACGTTTT---TTAA
1 ATATAGTTTTTAAAATATTTTTGAA-AACTATATA-AATATAGTTTTAAAAACATTTTAGAATAA
*
603402 A-ACT-T---
64 ATAATATAAC
* * *
603407 ATATA-TTTTTAAAACA-TTTTGAAAACTATAT-AATATAGTTTTGAAAACTTTTT
1 ATATAGTTTTTAAAATATTTTTGAAAACTATATAAATATAGTTTTAAAAACATTTT
603460 TAAATATAAT
Statistics
Matches: 166, Mismatches: 18, Indels: 30
0.78 0.08 0.14
Matches are distributed among these distances:
62 20 0.12
63 3 0.02
64 10 0.06
65 10 0.06
66 5 0.03
69 1 0.01
70 1 0.01
71 4 0.02
72 18 0.11
73 29 0.17
74 44 0.27
75 19 0.11
76 2 0.01
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (73 bp):
ATATAGTTTTTAAAATATTTTTGAAAACTATATAAATATAGTTTTAAAAACATTTTAGAATAAAT
AATATAAC
Found at i:603345 original size:38 final size:37
Alignment explanation
Indices: 603129--603411 Score: 251
Period size: 36 Copynumber: 7.5 Consensus size: 37
603119 TTGCAAACGG
603129 TTTTTGAAAATATATATATAATATATAGTTTTTAAAAAGAAAACA
1 TTTTTGAAAA-AT-TATATAATATATAG-TTTT----A-AAAACA
* * *
603174 -TTTTG-AAAA-TATGGGTAATATATAGTTTTTTAAAATA
1 TTTTTGAAAAATTAT--ATAATATATAG-TTTTAAAAACA
* * *
603211 TTTTTG-AAAACTATATAACATATAGTTTTTAAAACA
1 TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA
* * * *
603247 TTTTAG-AAAATAAATATAACATATAGTTTTAAAATCA
1 TTTTTGAAAAAT-TATATAATATATAGTTTTAAAAACA
603284 -TTTT-AAAAACTTATATAATATATAGTTTTAAAAACA
1 TTTTTGAAAAA-TTATATAATATATAGTTTTAAAAACA
603320 TTTTTGAATAAATTATATAATATATAGTTTTAAAAACA
1 TTTTTGAA-AAATTATATAATATATAGTTTTAAAAACA
*
603358 TTTTTGAATAAATTATAT-A-ATATAGTTTTAAAAACG
1 TTTTTGAA-AAATTATATAATATATAGTTTTAAAAACA
* *
603394 TTTTTTAAAACTTATATA
1 TTTTTGAAAAATTATATA
603412 TTTTTAAAAC
Statistics
Matches: 209, Mismatches: 18, Indels: 31
0.81 0.07 0.12
Matches are distributed among these distances:
35 8 0.04
36 71 0.34
37 42 0.20
38 55 0.26
39 6 0.03
40 3 0.01
42 16 0.08
43 3 0.01
44 5 0.02
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (37 bp):
TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA
Found at i:603446 original size:62 final size:65
Alignment explanation
Indices: 603340--603491 Score: 192
Period size: 62 Copynumber: 2.4 Consensus size: 65
603330 AATTATATAA
*
603340 TATATAGTTTTAAAAACATTTTTGAATAAATTATATAATATAGTTTTAAAAACGTTTTTTAAAAC
1 TATATAGTTTTAAAAACATTTTTGAATAAACTATATAATATAGTTTTAAAAAC-TTTTTTAAAAC
603405 T
65 T
* *
603406 TATATA-TTTTTAAAACA-TTTTG-A-AAACTATATAATATAGTTTTGAAAACTTTTTTAAATA-
1 TATATAGTTTTAAAAACATTTTTGAATAAACTATATAATATAGTTTTAAAAACTTTTTTAAA-AC
603466 T
65 T
*
603467 AATATAG-TTTAAAAA-ATATTTTGAA
1 TATATAGTTTTAAAAACAT-TTTTGAA
603492 ATATATGTAT
Statistics
Matches: 76, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
60 1 0.01
61 22 0.29
62 30 0.39
63 2 0.03
64 5 0.07
65 10 0.13
66 6 0.08
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (65 bp):
TATATAGTTTTAAAAACATTTTTGAATAAACTATATAATATAGTTTTAAAAACTTTTTTAAAACT
Found at i:603466 original size:29 final size:30
Alignment explanation
Indices: 603341--603496 Score: 115
Period size: 29 Copynumber: 5.0 Consensus size: 30
603331 ATTATATAAT
603341 ATATAGTTTTAAAAACATTTTTGAATAAATTATATA
1 ATATAGTTTTAAAAACATTTTT---T-AA--ATATA
* *
603377 ATATAGTTTTAAAAACGTTTTTTAAA-ACTT
1 ATATAGTTTTAAAAACATTTTTTAAATA-TA
* **
603407 ATATA-TTTTTAAAACATTTTGAAAACTATATA
1 ATATAGTTTTAAAAACATTTT-TTAA--ATATA
*
603439 ATATAGTTTTGAAAAC-TTTTTTAAATATA
1 ATATAGTTTTAAAAACATTTTTTAAATATA
*
603468 ATATAG-TTTAAAAA-ATATTTTGAAATATA
1 ATATAGTTTTAAAAACAT-TTTTTAAATATA
603497 TGTATTATAT
Statistics
Matches: 100, Mismatches: 12, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
28 8 0.08
29 36 0.36
30 9 0.09
31 2 0.02
32 13 0.13
33 11 0.11
36 21 0.21
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.45
Consensus pattern (30 bp):
ATATAGTTTTAAAAACATTTTTTAAATATA
Found at i:603568 original size:15 final size:14
Alignment explanation
Indices: 603533--603561 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
603523 GTATTATTAT
603533 TTATTTTCTTTTTA
1 TTATTTTCTTTTTA
603547 TTATTTTCTTTTTA
1 TTATTTTCTTTTTA
603561 T
1 T
603562 GTTTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (14 bp):
TTATTTTCTTTTTA
Found at i:604790 original size:2 final size:2
Alignment explanation
Indices: 604785--604819 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
604775 TATGTTTTTC
*
604785 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
604820 TATTATTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:606616 original size:19 final size:19
Alignment explanation
Indices: 606592--606637 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
606582 ATTTAGACAT
606592 TTTGCATTTCGTTATTTTC
1 TTTGCATTTCGTTATTTTC
*
606611 TTTGCATTTTGTTATTTTC
1 TTTGCATTTCGTTATTTTC
*
606630 TTTACATT
1 TTTGCATT
606638 CACATTAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.09, T:0.65
Consensus pattern (19 bp):
TTTGCATTTCGTTATTTTC
Found at i:610169 original size:81 final size:81
Alignment explanation
Indices: 609993--610802 Score: 783
Period size: 81 Copynumber: 9.8 Consensus size: 81
609983 TTAACAAACT
* * * * * * *
609993 ATTTGCAGCTTAGCTCAAGGCCAGAAGGGCTACCTGCCACCAAGA-CCTTCGAGTTCGACTACGC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA--AAGACCCTT-GAGTTCGATTACAC
* *
610057 TCAGC-TCCAAGGCACATC
63 TCAGCTTCGAGGGCACATC
* *
610075 ATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTCGATTACACTCA
610140 GCTTCGAGGGCACATC
66 GCTTCGAGGGCACATC
**
610156 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTCGATTACACTCA
610221 GCTTCGAGGGCACATC
66 GCTTCGAGGGCACATC
* * * * * * *
610237 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGA-CCTTCGAGTTCGACTAC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCTT-GAGTTCGATTAC
** * *
610301 GTTCAGC-TCCAAGGCACATC
61 ACTCAGCTTCGAGGGCACATC
**
610321 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTCGATTACACTCA
610386 GCTTCGAGGGCACATC
66 GCTTCGAGGGCACATC
* * * *
610402 ATTTGCAGCATAACTTAAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTAC
1 ATTTGCAGCATAGCTT-AAGTCGAGAAGGGCTATCTG----CCAAAGACCCTTGAGTTCGATTAC
* * *
610467 GCTCAGC-TCCAAGGCACATC
61 ACTCAGCTTCGAGGGCACATC
* * *
610487 ATTTGCAGAATAGCTTAAGTCAAGAAGAGCTATCTGCCAAAGACCC--GAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTCGATTACACTCA
* * *
610550 GCTTCAAGGGCATAAC
66 GCTTCGAGGGCACATC
* * * * * * * * * *
610566 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAAGACCTTTGAGTTCGACTACG
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC---T-GCCAAAGACCCTTGAGTTCGATTACA
* **
610631 CTCAGC-TCAACAGCACATC
62 CTCAGCTTCGAGGGCACATC
* **
610650 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTCGATTACACTCA
*
610715 GCTTTGAGGGCACATC
66 GCTTCGAGGGCACATC
* * * * * * *
610731 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGA-CCTTCGAGTTCGACTAC
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCTT-GAGTTCGATTAC
*
610795 GCTCAGCT
61 ACTCAGCT
610803 CTAAGACACA
Statistics
Matches: 595, Mismatches: 106, Indels: 51
0.79 0.14 0.07
Matches are distributed among these distances:
78 17 0.03
79 35 0.06
80 76 0.13
81 187 0.31
82 55 0.09
83 13 0.02
84 100 0.17
85 86 0.14
86 26 0.04
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (81 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTCGATTACACTCA
GCTTCGAGGGCACATC
Found at i:610331 original size:165 final size:165
Alignment explanation
Indices: 609993--610937 Score: 1120
Period size: 165 Copynumber: 5.7 Consensus size: 165
609983 TTAACAAACT
* * * * * ** * *
609993 ATTTGCAGCTTAGCTCAAGGCCAGAAGGGCTACCTGCCACCAAGACCTTCGAGTTCGACTACGCT
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA--AAGACCCCCGAGTTCGATTACACT
* * * * * * * * *
610058 CAGC-TCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGA
64 CAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGA
* * * * *
610118 CCCTT-AAGTTCGATTACACTCAGCTTCGAGGGCACATC
129 -CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATC
610156 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
610221 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
*
610286 TTCGAGTTCGACTACGTTCAGCTCCAAGGCACATC
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
610321 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * * * **
610386 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAAGTCGAGAAGGGTTATCTGCCAACC-AAAGA
66 GCTTCGAGGGCACATCATTTACAGCATAAC-TCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGA
*
610450 CCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
129 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * *
610487 ATTTGCAGAATAGCTTAAGTCAAGAAGAGCTATCTGCCAAAGA--CCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * * * *
610550 GCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
* *
610615 TTTGAGTTCGACTACGCTCAGCT-CAACAGCACATC
131 TTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATC
*
610650 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
*
610715 GCTTTGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
* *
610780 TTCGAGTTCGACTACGCTCAGCTCTAAGACACATC
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
** ** * * * * * * * *
610815 ATTCACAATATAACTCAAGGCTAGAAGGGTTATCTGTCAACCGAAGACCTCCGAGTTCGATTATA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCCCGAGTTCGATTACA
* * * * * * *
610880 TTCAACTTAGA-GGCAAATCAAGTTTACAGAATAGCTCAAGGCAAGAAGGGTTATCTGT
62 CTCAGCTTCGAGGGCACATC-A-TTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGT
610938 CAATAAAATT
Statistics
Matches: 686, Mismatches: 77, Indels: 31
0.86 0.10 0.04
Matches are distributed among these distances:
161 24 0.03
162 43 0.06
163 130 0.19
164 48 0.07
165 246 0.36
166 121 0.18
167 3 0.00
168 7 0.01
169 31 0.05
170 33 0.05
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (165 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:610590 original size:329 final size:326
Alignment explanation
Indices: 609993--610817 Score: 1154
Period size: 329 Copynumber: 2.5 Consensus size: 326
609983 TTAACAAACT
* * * * * ** * *
609993 ATTTGCAGCTTAGCTCAAGGCCAGAAGGGCTACCTGCCACCAAGACCTTCGAGTTCGACTACGCT
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA--AAGACCCCCGAGTTCGATTACACT
* * * * * *
610058 CAGC-TCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAGACCC
64 CAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCT
* * * * * * * *
610121 TTAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
129 TTGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGAGC
* *
610186 TATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAAC
193 TATCTGCCAAAGA-CCCCGAGTTCGATTACACTCAGCTTCAAGGGCACAACATTTACAGCATAAC
* *
610251 TCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAA-GG
257 TCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAACAG
610315 CACATC
321 CACATC
610321 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
610386 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAAGTCGAGAAGGGTTATCTGCCAACCAAAGAC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTT-AAGTCGAGAAGGGTTATCTG---ACCAAAGAC
610451 CTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGAG
127 CTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGAG
*
610516 CTATCTGCCAAAGA-CCCGAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAAC
192 CTATCTGCCAAAGACCCCGAGTTCGATTACACTCAGCTTCAAGGGCACAACATTTACAGCATAAC
* * *
610580 TCAAGGCTAGAAGGGTTATCTGTTAGCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACAGC
257 TCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAACAGC
610645 ACATC
322 ACATC
*
610650 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * * * *
610715 GCTTTGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC--TGACC-AAAGACC
* * *
610780 TTCGAGTTCGACTACGCTCAGCTCTAAGACACATCATT
128 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
610818 CACAATATAA
Statistics
Matches: 447, Mismatches: 40, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
326 24 0.05
327 28 0.06
328 114 0.26
329 201 0.45
330 2 0.00
331 51 0.11
332 27 0.06
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (326 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGACCAAAGACCTTT
GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGAGCTAT
CTGCCAAAGACCCCGAGTTCGATTACACTCAGCTTCAAGGGCACAACATTTACAGCATAACTCAA
GGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAACAGCACAT
C
Found at i:611742 original size:38 final size:37
Alignment explanation
Indices: 611535--611906 Score: 293
Period size: 38 Copynumber: 10.2 Consensus size: 37
611525 TTGCAAACGG
611535 TTTTTGAAAATATATATATAATATATAGTTTTTAAAAAGAAAACA
1 TTTTTGAAAA-AT-TATATAATATATAG-TTTT----A-AAAACA
* ** *
611580 -TTTTG-AAAA-TATGGGTAATATATAGTTTTTTTAAATA
1 TTTTTGAAAAATTAT--ATAATATATAG-TTTTAAAAACA
* * *
611617 TTTTTG-AAAACTATATAACATATAGTTTTTAAAACA
1 TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA
* * *
611653 TTTTAG-AAAATATATATAACATATAGTTTTAAAATCA
1 TTTTTGAAAAAT-TATATAATATATAGTTTTAAAAACA
611690 -TTTT-AAAAACTTATATAATATATAGTTTTAAAAACA
1 TTTTTGAAAAA-TTATATAATATATAGTTTTAAAAACA
611726 TTTTTGAATAAATTATATAATATATAGTTTTAAAAACA
1 TTTTTGAA-AAATTATATAATATATAGTTTTAAAAACA
*
611764 TTTTTGAATAAATTATATAATATATAGTTTTAAAAACG
1 TTTTTGAA-AAATTATATAATATATAGTTTTAAAAACA
* *
611802 TTTTTTAAAACTTATAT-A-ATAT--TTTT-AAAACA
1 TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA
* *
611834 -TTTTG-AAAACTATAT-A-ATATAGTTTTGAAAAC-
1 TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA
* * *
611866 TTTTT---TAA--ATATAATATATAGTTTAAAAAATA
1 TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA
611898 TTTTTGAAA
1 TTTTTGAAA
611907 TATATGTATT
Statistics
Matches: 280, Mismatches: 27, Indels: 50
0.78 0.08 0.14
Matches are distributed among these distances:
29 4 0.01
30 14 0.05
31 19 0.07
32 14 0.05
33 13 0.05
35 4 0.01
36 49 0.17
37 49 0.17
38 81 0.29
39 6 0.02
40 3 0.01
42 16 0.06
43 3 0.01
44 5 0.02
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (37 bp):
TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA
Found at i:611832 original size:32 final size:30
Alignment explanation
Indices: 611783--611874 Score: 96
Period size: 32 Copynumber: 2.9 Consensus size: 30
611773 AAATTATATA
*
611783 ATAT-ATAGTTTTAAAAACGTTTTTTAAAACTT
1 ATATAATA-TTTTTAAAAC-TTTTTTAAAAC-T
* *
611815 ATATAATATTTTTAAAACATTTTGAAAACT
1 ATATAATATTTTTAAAACTTTTTTAAAACT
611845 ATATAATATAGTTTTGAAAACTTTTTTAAA
1 ATATAATAT--TTTT-AAAACTTTTTTAAA
611875 TATAATATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
30 10 0.20
31 9 0.18
32 17 0.33
33 15 0.29
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (30 bp):
ATATAATATTTTTAAAACTTTTTTAAAACT
Found at i:611985 original size:15 final size:14
Alignment explanation
Indices: 611950--611978 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
611940 TTATTATTAT
611950 TTATTTTCTTTTTA
1 TTATTTTCTTTTTA
611964 TTATTTTCTTTTTA
1 TTATTTTCTTTTTA
611978 T
1 T
611979 GTTTTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (14 bp):
TTATTTTCTTTTTA
Found at i:615950 original size:26 final size:26
Alignment explanation
Indices: 615904--615955 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
615894 TATTTTTTTT
615904 AATAAAAAATTCAATATTTATTTAAAA
1 AATAAAAAATTCAATATTTA-TTAAAA
*
615931 AATAAAACATT-AA-ATGTTATTAAAA
1 AATAAAAAATTCAATAT-TTATTAAAA
615956 TTATAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 8 0.35
26 5 0.22
27 10 0.43
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (26 bp):
AATAAAAAATTCAATATTTATTAAAA
Found at i:615992 original size:18 final size:19
Alignment explanation
Indices: 615952--615992 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
615942 AAATGTTATT
* *
615952 AAAATTATAATAAATATTA
1 AAAATTATAAGAAATATGA
615971 AAAATT-TAAGAAATATGA
1 AAAATTATAAGAAATATGA
615989 AAAA
1 AAAA
615993 CGTTTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
AAAATTATAAGAAATATGA
Found at i:616081 original size:21 final size:21
Alignment explanation
Indices: 616048--616092 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
616038 TAAAATTTTG
*
616048 AAATTTATTAAAA-AATAAAA
1 AAATTTATGAAAATAATAAAA
*
616068 AAATATTATGAAAATAGTAAAA
1 AAAT-TTATGAAAATAATAAAA
616090 AAA
1 AAA
616093 GATTTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 8 0.38
22 9 0.43
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (21 bp):
AAATTTATGAAAATAATAAAA
Found at i:616896 original size:29 final size:29
Alignment explanation
Indices: 616859--616962 Score: 172
Period size: 29 Copynumber: 3.6 Consensus size: 29
616849 TTTTTCTTTG
* *
616859 ATTGTAATTTATAAATAGTTTTGGTATTT
1 ATTGTAATTTATAAAAAGTTATGGTATTT
*
616888 ATTATAATTTATAAAAAGTTATGGTATTT
1 ATTGTAATTTATAAAAAGTTATGGTATTT
*
616917 ATTGTAGTTTATAAAAAGTTATGGTATTT
1 ATTGTAATTTATAAAAAGTTATGGTATTT
616946 ATTGTAATTTATAAAAA
1 ATTGTAATTTATAAAAA
616963 AAGCTGGCAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 69 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.49
Consensus pattern (29 bp):
ATTGTAATTTATAAAAAGTTATGGTATTT
Found at i:616974 original size:29 final size:29
Alignment explanation
Indices: 616880--616994 Score: 122
Period size: 29 Copynumber: 3.9 Consensus size: 29
616870 TAAATAGTTT
**
616880 TGGTATTTATTATAATTTATAAAAAGTTA
1 TGGTATTTATTATAATTTATAAAAAAATA
* * **
616909 TGGTATTTATTGTAGTTTATAAAAAGTTA
1 TGGTATTTATTATAATTTATAAAAAAATA
* **
616938 TGGTATTTATTGTAATTTATAAAAAAAGC
1 TGGTATTTATTATAATTTATAAAAAAATA
* *
616967 TGGCATTTATTATAATTATTTAAAAAAA
1 TGGTATTTATTATAATT-TATAAAAAAA
616995 ATTAGGCTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
29 66 0.88
30 9 0.12
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (29 bp):
TGGTATTTATTATAATTTATAAAAAAATA
Found at i:616975 original size:58 final size:58
Alignment explanation
Indices: 616859--616992 Score: 160
Period size: 58 Copynumber: 2.3 Consensus size: 58
616849 TTTTTCTTTG
* * *** *
616859 ATTGTAATTTATAAATAGTTTTGGTATTTATTATAATTTATAAAAAGTTATGGTATTT
1 ATTGTAATTTATAAAAAGTTATGGTATTTATTATAATTTATAAAAAAAGATGGCATTT
* * *
616917 ATTGTAGTTTATAAAAAGTTATGGTATTTATTGTAATTTATAAAAAAAGCTGGCATTT
1 ATTGTAATTTATAAAAAGTTATGGTATTTATTATAATTTATAAAAAAAGATGGCATTT
* *
616975 ATTATAATTATTTAAAAA
1 ATTGTAATT-TATAAAAA
616993 AAATTAGGCT
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
58 56 0.89
59 7 0.11
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (58 bp):
ATTGTAATTTATAAAAAGTTATGGTATTTATTATAATTTATAAAAAAAGATGGCATTT
Found at i:621233 original size:32 final size:32
Alignment explanation
Indices: 621196--621282 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 32
621186 TATGACATTT
* *
621196 TCACATGTACT-AAATTATTAACGTGATATATG
1 TCACAT-TACTAAAAATAATAACGTGATATATG
* *
621228 TCACATTACTAAAAATAATGATGTGATATATG
1 TCACATTACTAAAAATAATAACGTGATATATG
* *
621260 TCACATCATCT-AAAGTAATAACG
1 TCACATTA-CTAAAAATAATAACG
621283 CAAGAATTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 4 0.09
32 39 0.87
33 2 0.04
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (32 bp):
TCACATTACTAAAAATAATAACGTGATATATG
Found at i:621555 original size:17 final size:17
Alignment explanation
Indices: 621504--621555 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
621494 ACATGACATC
*
621504 TATTAATAACTCAAATT
1 TATTAATAACTAAAATT
* *
621521 TATT--TTATTAATAATT
1 TATTAATAACTAA-AATT
621537 TATTAATAACTAAAATT
1 TATTAATAACTAAAATT
621554 TA
1 TA
621556 CTTTATTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
15 4 0.15
16 8 0.30
17 10 0.37
18 5 0.19
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTAATAACTAAAATT
Found at i:621584 original size:30 final size:33
Alignment explanation
Indices: 621504--621576 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
621494 ACATGACATC
* *
621504 TATTAATAACTCAAATTTATTTTATTAATAATT
1 TATTAATAACTAAAATTTACTTTATTAATAATT
*
621537 TATTAATAACTAAAATTTACTTTATTAATATTT
1 TATTAATAACTAAAATTTACTTTATTAATAATT
*
621570 TAATAAT
1 TATTAAT
621577 TTAAATTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (33 bp):
TATTAATAACTAAAATTTACTTTATTAATAATT
Found at i:624866 original size:2 final size:2
Alignment explanation
Indices: 624859--624886 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
624849 ACATTTTGAG
624859 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
624887 TAAGTTGATG
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:634498 original size:16 final size:15
Alignment explanation
Indices: 634472--634502 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
634462 ATTATAGAAT
634472 TAAATTAATTATATA
1 TAAATTAATTATATA
634487 TAAATCTAATTATATA
1 TAAAT-TAATTATATA
634503 GTAATTCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAATTAATTATATA
Found at i:635083 original size:31 final size:30
Alignment explanation
Indices: 635048--635106 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
635038 ACTGAATTTC
*
635048 TCAATTAAGTTTCTATTTTTTTAATTAATCT
1 TCAATTAAGTTTCTATTTTTCT-ATTAATCT
*
635079 TCAATTAAGTTTTTATTTTTCTATTAAT
1 TCAATTAAGTTTCTATTTTTCTATTAAT
635107 TTAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.59
Consensus pattern (30 bp):
TCAATTAAGTTTCTATTTTTCTATTAATCT
Found at i:635527 original size:16 final size:17
Alignment explanation
Indices: 635489--635534 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
635479 TGTTTATGAG
635489 GGAATTAGAATCTTTGAA
1 GGAATTAGAATC-TTGAA
*
635507 GGAATTAGAATC-TGTA
1 GGAATTAGAATCTTGAA
*
635523 GGAATTGGAATC
1 GGAATTAGAATC
635535 CAATTCCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 14 0.54
18 12 0.46
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (17 bp):
GGAATTAGAATCTTGAA
Found at i:636152 original size:37 final size:38
Alignment explanation
Indices: 636073--636159 Score: 140
Period size: 39 Copynumber: 2.3 Consensus size: 38
636063 CCTAAACTGA
*
636073 ACCCGACCCGACCCGAATATCACACTTAAAAAAAAATCG
1 ACCCGACCCGACCCGAATATCACACTT-AAAAAAAACCG
*
636112 ACCCGACTCGACCCGAATATCACACTT-AAAAAAACCG
1 ACCCGACCCGACCCGAATATCACACTTAAAAAAAACCG
636149 ACCCGACCCGA
1 ACCCGACCCGA
636160 AAAAAATAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 19 0.42
39 26 0.58
ACGTcount: A:0.40, C:0.37, G:0.11, T:0.11
Consensus pattern (38 bp):
ACCCGACCCGACCCGAATATCACACTTAAAAAAAACCG
Found at i:646180 original size:31 final size:32
Alignment explanation
Indices: 646145--646214 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
646135 TTTTGAACAA
* * * *
646145 TTACAAAATAATCGTTA-AATTTCTCAAACTG
1 TTACAAAACAATCATTATAATTTATCAAAATG
*
646176 TTACAAAACAATCATTATATTTTATCAAAATG
1 TTACAAAACAATCATTATAATTTATCAAAATG
646208 TTACAAA
1 TTACAAA
646215 TTATTATAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 15 0.45
32 18 0.55
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.36
Consensus pattern (32 bp):
TTACAAAACAATCATTATAATTTATCAAAATG
Found at i:650107 original size:23 final size:23
Alignment explanation
Indices: 650076--650201 Score: 137
Period size: 23 Copynumber: 5.4 Consensus size: 23
650066 CGAACGGATG
650076 TAAACGAACACAATAAACGAACA
1 TAAACGAACACAATAAACGAACA
* * ** *
650099 CAAAAGAACGGATGTAAACGAACA
1 TAAACGAACACA-ATAAACGAACA
*
650123 TAAACGAACACAATAAACGAACG
1 TAAACGAACACAATAAACGAACA
* *
650146 TAAATGAACACAA-ACCAACAAACA
1 TAAACGAACACAATA--AACGAACA
*
650170 TAAACGAACACAATAAATGAACA
1 TAAACGAACACAATAAACGAACA
650193 TAAACGAAC
1 TAAACGAAC
650202 GTAAACTAAC
Statistics
Matches: 82, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
22 1 0.01
23 44 0.54
24 36 0.44
25 1 0.01
ACGTcount: A:0.59, C:0.21, G:0.11, T:0.10
Consensus pattern (23 bp):
TAAACGAACACAATAAACGAACA
Found at i:650117 original size:37 final size:37
Alignment explanation
Indices: 650067--650158 Score: 120
Period size: 34 Copynumber: 2.6 Consensus size: 37
650057 AATGATAAAC
650067 GAACGGATGTAAACGAACACAATAAACGAACACAAAA
1 GAACGGATGTAAACGAACACAATAAACGAACACAAAA
*
650104 GAACGGATGTAAACG-A-AC-ATAAACGAACACAATA
1 GAACGGATGTAAACGAACACAATAAACGAACACAAAA
* * *
650138 -AACGAACGTAAATGAACACAA
1 GAACGGATGTAAACGAACACAA
650159 ACCAACAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
33 11 0.23
34 16 0.33
35 4 0.08
36 2 0.04
37 15 0.31
ACGTcount: A:0.55, C:0.18, G:0.16, T:0.10
Consensus pattern (37 bp):
GAACGGATGTAAACGAACACAATAAACGAACACAAAA
Found at i:650126 original size:10 final size:10
Alignment explanation
Indices: 650113--650216 Score: 55
Period size: 10 Copynumber: 9.4 Consensus size: 10
650103 AGAACGGATG
650113 TAAACGAACA
1 TAAACGAACA
650123 TAAACGAACACAA
1 TAAACG-A-AC-A
*
650136 TAAACGAACG
1 TAAACGAACA
*
650146 TAAATGAACACA
1 TAAACG-A-ACA
* *
650158 AACCAACAAACA
1 TA--AACGAACA
650170 TAAACGAACACAA
1 TAAACG-A-AC-A
*
650183 TAAATGAACA
1 TAAACGAACA
*
650193 TAAACGAACG
1 TAAACGAACA
*
650203 TAAACTAACA
1 TAAACGAACA
650213 TAAA
1 TAAA
650217 TGAAAATATA
Statistics
Matches: 71, Mismatches: 13, Indels: 20
0.68 0.12 0.19
Matches are distributed among these distances:
10 35 0.49
11 7 0.10
12 13 0.18
13 14 0.20
14 2 0.03
ACGTcount: A:0.60, C:0.20, G:0.09, T:0.12
Consensus pattern (10 bp):
TAAACGAACA
Found at i:650427 original size:14 final size:14
Alignment explanation
Indices: 650410--650458 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
650400 ACACATAAAA
*
650410 GAACATAAACGAAT
1 GAACATAAACGAAC
650424 GAACATAAACGAAC
1 GAACATAAACGAAC
* *
650438 GAATATAAATGAAC
1 GAACATAAACGAAC
650452 GAACATA
1 GAACATA
650459 TTACCAAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (14 bp):
GAACATAAACGAAC
Done.