Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000426.1 Hibiscus syriacus cultivar Beakdansim tig00000778_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: 3165331
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 15
Found at i:476243 original size:40 final size:39
Alignment explanation
Indices: 476196--476389 Score: 217
Period size: 40 Copynumber: 4.8 Consensus size: 39
476186 GATTTTCCAG
* ** *
476196 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
476236 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* * *
476276 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
476316 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
476357 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
476390 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 98 0.74
41 33 0.25
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:476279 original size:60 final size:60
Alignment explanation
Indices: 476196--476388 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
476186 GATTTTCCAG
* ** *
476196 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
* * * *
476256 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTA
* ** *
476316 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT-AAATCGCAACGCGTATCCGTA
476377 AATCGCAACGCG
1 AATCGCAACGCG
476389 ATATTTAAAG
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
59 1 0.01
60 79 0.70
61 33 0.29
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
Found at i:476803 original size:32 final size:32
Alignment explanation
Indices: 476765--476833 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
476755 ATTTCACTTA
476765 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
* *
476797 GATTTCATTTCGCGTTGCTATTCTCTCGTTGC
1 GATTTCATTTCGCGTTACGATTCTCTCGTTGC
476829 GATTT
1 GATTT
476834 TCAAGTTAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (32 bp):
GATTTCATTTCGCGTTACGATTCTCTCGTTGC
Found at i:476814 original size:18 final size:18
Alignment explanation
Indices: 476765--476814 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
476755 ATTTCACTTA
*
476765 GATTTCATTTCGCGTTAC
1 GATTTCATTTCGCGTTGC
*
476783 GA-TTC---TCTCGTTGC
1 GATTTCATTTCGCGTTGC
476797 GATTTCATTTCGCGTTGC
1 GATTTCATTTCGCGTTGC
476815 TATTCTCTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 9 0.36
15 3 0.12
17 3 0.12
18 10 0.40
ACGTcount: A:0.12, C:0.24, G:0.20, T:0.44
Consensus pattern (18 bp):
GATTTCATTTCGCGTTGC
Found at i:476960 original size:20 final size:20
Alignment explanation
Indices: 476916--477025 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
476906 TGCAGAAGAG
*
476916 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
476937 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
476957 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
476978 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
476992 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
477011 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
477026 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:476973 original size:41 final size:38
Alignment explanation
Indices: 476909--477025 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
476899 TTCAATTTGC
* *
476909 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
476947 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
476988 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
477021 AGAAT
1 AGAAT
477026 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:476995 original size:14 final size:14
Alignment explanation
Indices: 476976--477032 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
476966 GAGAAATGAA
476976 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
476990 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
477009 AATCGCAACGAGAG
1 AATCGCAACGAGAG
477023 AATCGCAACG
1 AATCGCAACG
477033 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:477008 original size:33 final size:33
Alignment explanation
Indices: 476968--477048 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
476958 CGCAACGAGA
476968 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
477001 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
477034 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
477049 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:477066 original size:19 final size:19
Alignment explanation
Indices: 477044--477171 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
477034 GAAACCAAAA
*
477044 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
477063 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
477077 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
477096 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
477110 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
477130 ATCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
477150 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
477170 TC
1 TC
477172 AACCAAAAGA
Statistics
Matches: 86, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.26
20 18 0.21
21 14 0.16
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:477085 original size:14 final size:14
Alignment explanation
Indices: 477066--477122 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
477056 TTTCATTTCG
477066 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
477080 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
477099 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
477113 CGTTGCGATT
1 CGTTGCGATT
477123 TTCATTTATC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:477091 original size:33 final size:33
Alignment explanation
Indices: 477049--477171 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
477039 CAAAATCGCA
477049 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
477082 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
477115 TTGCGATTTTCATTTATCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
477156 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
477172 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:477136 original size:21 final size:21
Alignment explanation
Indices: 477110--477170 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 21
477100 GTTGCGATTC
477110 TCTCGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTA
*** *
477131 TCTCGTTGCGACAGTCA-TTC
1 TCTCGTTGCGATTTTCATTTA
477151 TCTCGTTGCGATTTTCATTT
1 TCTCGTTGCGATTTTCATTT
477171 CAACCAAAAG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTA
Found at i:477156 original size:20 final size:20
Alignment explanation
Indices: 477106--477161 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
477096 TCGCGTTGCG
***
477106 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACAGTC
*
477126 ATTTATCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGACAGTC
477147 ATTCTCTCGTTGCGA
1 ATTCTCTCGTTGCGA
477162 TTTTCATTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACAGTC
Found at i:479029 original size:93 final size:93
Alignment explanation
Indices: 478870--479245 Score: 727
Period size: 93 Copynumber: 4.1 Consensus size: 93
478860 TAGATTGCTT
*
478870 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
478935 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
478963 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
479028 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
479056 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
479121 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
479149 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATTGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
479214 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
479241 AGTAA
1 AGTAA
479246 TGCAATCCAT
Statistics
Matches: 281, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 275 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:479349 original size:19 final size:18
Alignment explanation
Indices: 479290--479417 Score: 119
Period size: 19 Copynumber: 7.3 Consensus size: 18
479280 TAGTTTACTT
*
479290 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC--AAAA
*
479310 TCGCAACGCGAAACCAAA
1 TCGCAACGCGAAACAAAA
*
479328 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAA-CAAAA
*
479347 TCGCAA--C-AAA-AGAA
1 TCGCAACGCGAAACAAAA
479361 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-CAAAA
479380 TCGCAA--CG--ACAAAA
1 TCGCAACGCGAAACAAAA
479394 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAA-CAAAA
479413 TCGCA
1 TCGCA
479418 TTGCGATTTT
Statistics
Matches: 91, Mismatches: 6, Indels: 23
0.76 0.05 0.19
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 6 0.07
18 17 0.19
19 28 0.31
20 13 0.14
ACGTcount: A:0.48, C:0.28, G:0.16, T:0.09
Consensus pattern (18 bp):
TCGCAACGCGAAACAAAA
Found at i:479368 original size:33 final size:33
Alignment explanation
Indices: 479290--479417 Score: 150
Period size: 33 Copynumber: 3.7 Consensus size: 33
479280 TAGTTTACTT
* *
479290 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAA
1 TCGCAACGCGAAAC-CAAAATCGCAA--CGAAA--AAA
**
479328 TCGCAACGCGAAATGAAAATCGCAAC-AAAAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGAAAA-AA
*
479361 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGAAAAAA
479394 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
479418 TTGCGATTTT
Statistics
Matches: 82, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
32 1 0.01
33 52 0.63
34 6 0.07
35 1 0.01
37 10 0.12
38 12 0.15
ACGTcount: A:0.48, C:0.28, G:0.16, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGAAAAAA
Found at i:479394 original size:14 final size:14
Alignment explanation
Indices: 479375--479401 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
479365 AACGCGAAAC
479375 CAAAATCGCAACGA
1 CAAAATCGCAACGA
479389 CAAAATCGCAACG
1 CAAAATCGCAACG
479402 CGAAACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAAATCGCAACGA
Found at i:479435 original size:19 final size:19
Alignment explanation
Indices: 479413--479585 Score: 141
Period size: 19 Copynumber: 9.6 Consensus size: 19
479403 GAAACCAAAA
*
479413 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
479432 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
479448 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
479465 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
* *
479481 T--CGTTGCAATTTTAATT
1 TCGCGTTGCGATTTTCATT
* **
479498 TCGCGCTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
479517 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
479536 TCTCGTTGCGATTATCATT
1 TCGCGTTGCGATTTTCATT
*
479555 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
479575 TCGTGTTGCGA
1 TCGCGTTGCGA
479586 AAGTAAACTA
Statistics
Matches: 123, Mismatches: 20, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
14 14 0.11
16 10 0.08
17 11 0.09
19 76 0.62
20 12 0.10
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:479454 original size:14 final size:14
Alignment explanation
Indices: 479435--479487 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 14
479425 TTTCATTTCG
479435 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
479449 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
479466 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
479482 CGTTGC
1 CGTTGC
479488 AATTTTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
14 12 0.36
16 7 0.21
17 8 0.24
19 6 0.18
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:479460 original size:33 final size:33
Alignment explanation
Indices: 479418--479510 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
479408 CAAAATCGCA
*
479418 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
479451 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
* * *
479484 TTGCAATTTTAATTTCGCGCTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
479511 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:481528 original size:14 final size:14
Alignment explanation
Indices: 481509--481546 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
481499 ATTGTTTAAT
481509 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
481523 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
481537 TGATTTGTAA
1 TGATTTGTAA
481547 TTGATGCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:481664 original size:19 final size:19
Alignment explanation
Indices: 481648--481742 Score: 128
Period size: 19 Copynumber: 5.2 Consensus size: 19
481638 AAAAATGACT
481648 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
481667 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
481686 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
481700 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
481719 ATCGCAATTCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
481739 ATCG
1 ATCG
481743 AAACGAGAGA
Statistics
Matches: 67, Mismatches: 3, Indels: 11
0.83 0.04 0.14
Matches are distributed among these distances:
14 10 0.15
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 38 0.57
20 13 0.19
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:481777 original size:53 final size:52
Alignment explanation
Indices: 481648--481764 Score: 207
Period size: 53 Copynumber: 2.2 Consensus size: 52
481638 AAAAATGACT
*
481648 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGAAACGAGAGA
*
481700 ATCGCAATGCGAAATGAAAATCGCAATTCGGAAATGAAAATCGAAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGAAACGAGAGA
481753 ATCGCAATGCGA
1 ATCGCAATGCGA
481765 TTTTAATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 28 0.45
53 34 0.55
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGAAACGAGAGA
Found at i:481807 original size:33 final size:33
Alignment explanation
Indices: 481760--481923 Score: 163
Period size: 33 Copynumber: 4.8 Consensus size: 33
481750 AGAATCGCAA
*
481760 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
481793 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
481831 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
481864 TGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
481898 TGCGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
481924 TTCATTTCCG
Statistics
Matches: 106, Mismatches: 13, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
31 4 0.04
32 6 0.06
33 47 0.44
34 18 0.17
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.08
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:481921 original size:86 final size:84
Alignment explanation
Indices: 481811--481990 Score: 242
Period size: 86 Copynumber: 2.1 Consensus size: 84
481801 TCATTTCGCA
481811 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-TTGCGATTTTCATTTCGCATTGCGATTT
1 TTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTCA--T-G--TTGCGATTT
481872 TCATTTCCGCATTGCGATTCTCTCG
61 TCATTT-CGCATTGCGATTCTCTCG
* *
481897 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCCG-ATTGCGATTTTCATGTTGCGATTTTCA
481962 TTTCGCATTGCGATTCTCTCG
64 TTTCGCATTGCGATTCTCTCG
481983 TTGCGATT
1 TTGCGATT
481991 GTAATTTCCG
Statistics
Matches: 86, Mismatches: 2, Indels: 12
0.86 0.02 0.12
Matches are distributed among these distances:
86 51 0.59
87 14 0.16
88 3 0.03
89 3 0.03
90 3 0.03
92 12 0.14
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (84 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTCATGTTGCGATTTTCATT
TCGCATTGCGATTCTCTCG
Found at i:481974 original size:33 final size:34
Alignment explanation
Indices: 481792--481990 Score: 185
Period size: 33 Copynumber: 5.7 Consensus size: 34
481782 GATTCTCTCG
481792 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCA--TCG--TTGCGATTTTCATTTCGCA
*
481830 TTGCGATTCTC-TCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
* * * *
481863 TTGCGATTTTCAT--TTCCGCA-TTGCGATTCTCTCG
1 TTGCGATTTTCATCGTTGCG-ATTTTC-ATT-TCGCA
481897 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCA--TCG--TTGCGATTTTCATTT-CGCA
*
481936 TTGCGATTTTCAT-GTTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
*
481969 TTGCGATTCTC-TCGTTGCGATT
1 TTGCGATTTTCATCGTTGCGATT
481991 GTAATTTCCG
Statistics
Matches: 135, Mismatches: 13, Indels: 31
0.75 0.07 0.17
Matches are distributed among these distances:
32 8 0.06
33 55 0.41
34 30 0.22
35 3 0.02
36 2 0.01
37 1 0.01
38 11 0.08
39 18 0.13
40 7 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (34 bp):
TTGCGATTTTCATCGTTGCGATTTTCATTTCGCA
Found at i:481976 original size:19 final size:19
Alignment explanation
Indices: 481754--481976 Score: 234
Period size: 19 Copynumber: 12.7 Consensus size: 19
481744 AACGAGAGAA
* *
481754 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
481773 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
481789 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
481806 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
481825 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
481841 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
481858 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
481877 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
481894 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
481911 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
481930 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
481948 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
481964 TCGCATTGCGATT
1 TCGCATTGCGATT
481977 CTCTCGTTGC
Statistics
Matches: 172, Mismatches: 10, Indels: 44
0.76 0.04 0.19
Matches are distributed among these distances:
14 29 0.17
16 21 0.12
17 20 0.12
18 4 0.02
19 72 0.42
20 26 0.15
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:482005 original size:53 final size:53
Alignment explanation
Indices: 481754--481976 Score: 380
Period size: 53 Copynumber: 4.2 Consensus size: 53
481744 AACGAGAGAA
* *
481754 TCGCAATGCGATTTTAATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
481806 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
481858 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
* *
481911 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTGCGATTTTCATT
481964 TCGCATTGCGATT
1 TCGCATTGCGATT
481977 CTCTCGTTGC
Statistics
Matches: 165, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
52 70 0.42
53 94 0.57
54 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:484486 original size:24 final size:24
Alignment explanation
Indices: 484452--484498 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
484442 CTGAAACATC
484452 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
484476 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
484499 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:485214 original size:20 final size:20
Alignment explanation
Indices: 485186--485414 Score: 244
Period size: 20 Copynumber: 11.4 Consensus size: 20
485176 AAATTTCAGT
* * *
485186 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
485206 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
485226 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
485246 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
485266 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
485286 GTTGCGATATACGGATACTC
1 GTTGCGATTTACGGATTCGC
* *
485306 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
485326 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
485346 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
485366 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
485386 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
485406 GTTGCGATT
1 GTTGCGATT
485415 CTGGAAAATC
Statistics
Matches: 183, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 182 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:485475 original size:42 final size:41
Alignment explanation
Indices: 485382--485479 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 41
485372 ATTTATGTGT
* *
485382 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTCTGGAAAA
1 TCGCGTTGCGATTTTCATATTCGCATTGCGATTCTGCAAAA
** * *
485423 TCGCAATGCGAATTTTTACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCG-ATTTTCA-TATTCGCATTGCGATTCTGCAA-AA
485465 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
485480 GGAAACTGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
41 16 0.35
42 28 0.61
43 2 0.04
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCATATTCGCATTGCGATTCTGCAAAA
Found at i:485960 original size:17 final size:17
Alignment explanation
Indices: 485935--485986 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 17
485925 TAAACTTAGA
*
485935 AAATAAAAAATAATTTT
1 AAATTAAAAATAATTTT
*
485952 AAATTAAAATAGAAGTTTT
1 AAATTAAAA-ATAA-TTTT
*
485971 ATATTAATAAATAATT
1 AAATTAA-AAATAATT
485987 AGAATTGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 8 0.29
18 5 0.18
19 13 0.46
20 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (17 bp):
AAATTAAAAATAATTTT
Found at i:486923 original size:15 final size:15
Alignment explanation
Indices: 486903--486939 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
486893 TGTCACGTTC
486903 ATATTTTTGTTAAA-A
1 ATATTTTT-TTAAATA
486918 ATA-TTTTTTAAATA
1 ATATTTTTTTAAATA
486932 ATATTTTT
1 ATATTTTT
486940 ATTTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.25
14 8 0.40
15 7 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
ATATTTTTTTAAATA
Found at i:487878 original size:59 final size:59
Alignment explanation
Indices: 487780--487942 Score: 177
Period size: 59 Copynumber: 2.7 Consensus size: 59
487770 AATGGATTTA
* * * * ***
487780 GGGATGAAATTGGAAGA--TAAAAATGTTTAGGGACCAATTTAGAATGAGTTTCATAGTTT
1 GGGATGAAATTGGAATATTTAAAAA--TTTAAGGACTAATTTAAAATGAGAAACATAGTTT
487839 GGGATGAAATTGGAATATTTAAAAATTTAAGGACTAATTTAAAATGAGAAACATAGTTT
1 GGGATGAAATTGGAATATTTAAAAATTTAAGGACTAATTTAAAATGAGAAACATAGTTT
* * * **
487898 GAGGATGAATTTGAAATTTTTAAAAATTTAAAAACTAATTTAAAA
1 G-GGATGAAATTGGAATATTTAAAAATTTAAGGACTAATTTAAAA
487943 AGAAAATCAT
Statistics
Matches: 89, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
59 45 0.51
60 38 0.43
61 6 0.07
ACGTcount: A:0.44, C:0.04, G:0.19, T:0.33
Consensus pattern (59 bp):
GGGATGAAATTGGAATATTTAAAAATTTAAGGACTAATTTAAAATGAGAAACATAGTTT
Found at i:487935 original size:60 final size:59
Alignment explanation
Indices: 487831--487942 Score: 170
Period size: 60 Copynumber: 1.9 Consensus size: 59
487821 GAATGAGTTT
* **
487831 CATAGTTTGGGATGAAATTGGAATATTTAAAAATTTAAGGACTAATTTAAAATGAGAAA
1 CATAGTTTGGGATGAAATTGAAATATTTAAAAATTTAAAAACTAATTTAAAATGAGAAA
* *
487890 CATAGTTTGAGGATGAATTTGAAATTTTTAAAAATTTAAAAACTAATTTAAAA
1 CATAGTTTG-GGATGAAATTGAAATATTTAAAAATTTAAAAACTAATTTAAAA
487943 AGAAAATCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 9 0.19
60 38 0.81
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (59 bp):
CATAGTTTGGGATGAAATTGAAATATTTAAAAATTTAAAAACTAATTTAAAATGAGAAA
Found at i:487963 original size:60 final size:60
Alignment explanation
Indices: 487840--487963 Score: 160
Period size: 60 Copynumber: 2.1 Consensus size: 60
487830 TCATAGTTTG
* ** * * *
487840 GGATGAAATTGGAATATTTAAAAATTTAAGGACTAATTTAAAATGAGAAACATAGTTTGA
1 GGATGAAATTGAAATATTTAAAAATTTAAAAACTAATTTAAAAAGAGAAACATAATTTAA
* *
487900 GGATGAATTTGAAATTTTTAAAAATTTAAAAACTAATTTAAAAAGA-AAATCATAATTTAA
1 GGATGAAATTGAAATATTTAAAAATTTAAAAACTAATTTAAAAAGAGAAA-CATAATTTAA
487960 GGAT
1 GGAT
487964 ATATGATACA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 3 0.05
60 52 0.95
ACGTcount: A:0.49, C:0.03, G:0.15, T:0.33
Consensus pattern (60 bp):
GGATGAAATTGAAATATTTAAAAATTTAAAAACTAATTTAAAAAGAGAAACATAATTTAA
Found at i:488771 original size:12 final size:12
Alignment explanation
Indices: 488754--488779 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
488744 TAAATTAGAA
488754 AATTCCAATCAT
1 AATTCCAATCAT
488766 AATTCCAATCAT
1 AATTCCAATCAT
488778 AA
1 AA
488780 ACATGGACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (12 bp):
AATTCCAATCAT
Found at i:489747 original size:31 final size:33
Alignment explanation
Indices: 489702--489766 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 33
489692 ATTAGGGTTT
489702 AAGGTACTCCTTTGGGGAGGCTCTAAGG-CCCC
1 AAGGTACTCCTTTGGGGAGGCTCTAAGGACCCC
* * * *
489734 AAGGTA-TTCTTTGGGTAGGGTTTAAGGACCCC
1 AAGGTACTCCTTTGGGGAGGCTCTAAGGACCCC
489766 A
1 A
489767 GGTGTTCCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.26
Consensus pattern (33 bp):
AAGGTACTCCTTTGGGGAGGCTCTAAGGACCCC
Found at i:494811 original size:6 final size:6
Alignment explanation
Indices: 494800--494824 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
494790 GAAGACACGT
494800 ATTACC ATTACC ATTACC ATTACC A
1 ATTACC ATTACC ATTACC ATTACC A
494825 CGACCCCGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (6 bp):
ATTACC
Found at i:496201 original size:16 final size:17
Alignment explanation
Indices: 496170--496202 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
496160 TGGGTGAATT
496170 ACTTTCTTCATCACTCA
1 ACTTTCTTCATCACTCA
496187 ACTTTCTTC-TCACTCA
1 ACTTTCTTCATCACTCA
496203 TGTTTTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.21, C:0.36, G:0.00, T:0.42
Consensus pattern (17 bp):
ACTTTCTTCATCACTCA
Found at i:497546 original size:30 final size:31
Alignment explanation
Indices: 497510--497574 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 31
497500 TTTCATAAAA
*
497510 AAAAGTAAAAT-AAAATATGATAAA-AAGAGG
1 AAAAGT-AAATGAAAATATGATAAAGAAGAGC
*
497540 AAAAGTAAATGAAAATATGGTAAAGAAGAGC
1 AAAAGTAAATGAAAATATGATAAAGAAGAGC
497571 AAAA
1 AAAA
497575 TAGTGCCTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 4 0.13
30 18 0.58
31 9 0.29
ACGTcount: A:0.65, C:0.02, G:0.18, T:0.15
Consensus pattern (31 bp):
AAAAGTAAATGAAAATATGATAAAGAAGAGC
Found at i:499363 original size:15 final size:15
Alignment explanation
Indices: 499343--499373 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
499333 CCGCCTGGGC
499343 GAGCTGCCTCTCCGA
1 GAGCTGCCTCTCCGA
*
499358 GAGCTGCTTCTCCGA
1 GAGCTGCCTCTCCGA
499373 G
1 G
499374 GATTGTTCGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.35, G:0.29, T:0.23
Consensus pattern (15 bp):
GAGCTGCCTCTCCGA
Found at i:517046 original size:24 final size:23
Alignment explanation
Indices: 517019--517063 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
517009 AATTGGTTTT
517019 TTCGGTTCAGTTCGGGTTTTTCAG
1 TTCGGTTCAGTT-GGGTTTTTCAG
*
517043 TTCGGTTCAGTTTGGTTTTTC
1 TTCGGTTCAGTTGGGTTTTTC
517064 GGTTTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.07, C:0.16, G:0.27, T:0.51
Consensus pattern (23 bp):
TTCGGTTCAGTTGGGTTTTTCAG
Found at i:522877 original size:33 final size:31
Alignment explanation
Indices: 522822--522889 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 31
522812 ATTTTATATA
522822 ATATATAGTTTTAAAAATATTTTGGAAAACT
1 ATATATAGTTTTAAAAATATTTTGGAAAACT
* *
522853 CATATAATA-TTTTTAAAATCATTTTTGAAAACT
1 -ATAT-ATAGTTTTAAAAAT-ATTTTGGAAAACT
522886 ATAT
1 ATAT
522890 GGTATATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (31 bp):
ATATATAGTTTTAAAAATATTTTGGAAAACT
Found at i:523015 original size:18 final size:18
Alignment explanation
Indices: 522994--523032 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
522984 ATTATTTCTT
*
522994 TTCATTTTA-TTCACTTTA
1 TTCATTTAATTTCA-TTTA
523012 TTCATTTAATTTCATTTA
1 TTCATTTAATTTCATTTA
523030 TTC
1 TTC
523033 TGTTTATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCATTTAATTTCATTTA
Found at i:528331 original size:106 final size:106
Alignment explanation
Indices: 528141--529042 Score: 1599
Period size: 106 Copynumber: 8.5 Consensus size: 106
528131 AGAGTAAATT
* *
528141 ACAAATTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
528206 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
* * *
528247 ACAACTTCTCAATTTCAGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
*
528312 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
* *
528353 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
1 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
528418 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
528459 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGC
1 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
528524 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
528565 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
1 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
528630 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
* *
528671 AAAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGC
1 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
528736 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
* *
528777 ATAATTTCTCAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
1 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
528842 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
*
528883 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGC
1 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
528948 AAGTTCAACTTCACGACGAAGGGA-CGACTGGTTGTCAACAA
66 AAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAA
* * * * * * *
528989 ACAATTTCCCAGTTCCAAAGCCAATTTCAACTTCACGACGGAGGATGTTGGACT
1 ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
529043 TGAAACAATA
Statistics
Matches: 771, Mismatches: 24, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
105 2 0.00
106 769 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAA
Found at i:529933 original size:111 final size:110
Alignment explanation
Indices: 529818--530023 Score: 260
Period size: 111 Copynumber: 1.9 Consensus size: 110
529808 TAGTTTTTTT
* *
529818 TAAAAACGTTTCT-AAAAACTTATATACAATATATAAGTTTTAAAAACATTTT-GAAAA-TTATA
1 TAAAAACATTTCTGAAAAA-TTATATACAATATAT-AGTTTTAAAAACATTTTGGAAAACTCATA
*
529880 TAACATATATTTTTGAAATCA-TTTTGAAAA-TATAATGTATAGTTTAAAA
64 T---A-ATATTTTTAAAATCATTTTTGAAAACTATAATGTATAGTTTAAAA
* * * *
529929 TAAAAACATTTTTGAAAAATTTTATATAATATATAGTTTTAAAAATATTTTGGAAAACTCATATA
1 TAAAAACATTTCTGAAAAATTATATACAATATATAGTTTTAAAAACATTTTGGAAAACTCATATA
529994 ATATTTTTAAAATCATTTTTGAAAACTATA
66 ATATTTTTAAAATCATTTTTGAAAACTATA
530024 TGGTATATAG
Statistics
Matches: 83, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
108 14 0.17
109 10 0.12
110 20 0.24
111 29 0.35
112 10 0.12
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (110 bp):
TAAAAACATTTCTGAAAAATTATATACAATATATAGTTTTAAAAACATTTTGGAAAACTCATATA
ATATTTTTAAAATCATTTTTGAAAACTATAATGTATAGTTTAAAA
Found at i:530006 original size:32 final size:32
Alignment explanation
Indices: 529957--530024 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
529947 ATTTTATATA
529957 ATATATAGTTTTAAAAAT-ATTTTGGAAAACT
1 ATATATAGTTTTAAAAATCATTTTGGAAAACT
* *
529988 CATATAATA-TTTTTAAAATCATTTTTGAAAACT
1 -ATAT-ATAGTTTTAAAAATCATTTTGGAAAACT
530021 ATAT
1 ATAT
530025 GGTATATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (32 bp):
ATATATAGTTTTAAAAATCATTTTGGAAAACT
Found at i:530150 original size:18 final size:18
Alignment explanation
Indices: 530129--530167 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
530119 ATTATTTCTT
*
530129 TTCATTTTA-TTCACTTTA
1 TTCATTTAATTTCA-TTTA
530147 TTCATTTAATTTCATTTA
1 TTCATTTAATTTCATTTA
530165 TTC
1 TTC
530168 TGTTTATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCATTTAATTTCATTTA
Found at i:536116 original size:11 final size:11
Alignment explanation
Indices: 536100--536126 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
536090 CCATATATCT
536100 CAAGATATGGA
1 CAAGATATGGA
536111 CAAGATATGGA
1 CAAGATATGGA
536122 CAAGA
1 CAAGA
536127 CATATTAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.11, G:0.26, T:0.15
Consensus pattern (11 bp):
CAAGATATGGA
Found at i:536996 original size:184 final size:183
Alignment explanation
Indices: 536760--537149 Score: 602
Period size: 184 Copynumber: 2.1 Consensus size: 183
536750 ATAAAATTTT
* *
536760 AAATTTTAAATATATTATATATAACATATGGCTCAACCCAAACCATTTAAAACTCAATTAATAAT
1 AAATATTAAATATA-T-TATATAACATATGGCTCAACCCAAACCATTTAAAACCCAATTAATAAT
* *
536825 TTAAGATCCAATAACCTTTAAACCTAAATTAATATTAATTAATTAAAAAATTTATATAAAATTTT
64 TTAAGATCCAATAACCTTTAAACATAAATCAATATTAATTAATTAAAAAATTTATATAAAATTTT
* *
536890 TATTTTATAATTATATATTATTTAAATTAATTGTAAATTATTTTTCTGAATTAAA
129 TATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTCTGAATTAAA
* * *
536945 AAATATTAAATATATTATATAACATATGGACTTAGCCCAAACTATTTAAAACCCAATTAATAATT
1 AAATATTAAATATATTATATAACATATGG-CTCAACCCAAACCATTTAAAACCCAATTAATAATT
* * *
537010 TAATATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAGTTTATATAAAATTTTT
65 TAAGATCCAATAACCTTTAAACATAAATCAATATTAATTAATTAAAAAATTTATATAAAATTTTT
* *
537075 ATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTTTGAATTATA
130 ATTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTCTGAATTAAA
* *
537129 AAATATTTAAT-TTTTATATAA
1 AAATATTAAATATATTATATAA
537150 ATTAAAAAAA
Statistics
Matches: 188, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
183 23 0.12
184 152 0.81
185 13 0.07
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATAACATATGGCTCAACCCAAACCATTTAAAACCCAATTAATAATTT
AAGATCCAATAACCTTTAAACATAAATCAATATTAATTAATTAAAAAATTTATATAAAATTTTTA
TTTTATAATTATATATTATTTAAATTAATTATAAACTATTTTTCTGAATTAAA
Found at i:537115 original size:20 final size:20
Alignment explanation
Indices: 537081--537138 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
537071 TTTTATTTTA
* *
537081 TAATTATATATTATTTAAAT
1 TAATTATAAAATATTTAAAT
* **
537101 TAATTATAAACTATTT-TTT
1 TAATTATAAAATATTTAAAT
537120 TGAATTATAAAATATTTAA
1 T-AATTATAAAATATTTAA
537139 TTTTTATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATTATAAAATATTTAAAT
Found at i:543820 original size:13 final size:13
Alignment explanation
Indices: 543816--543878 Score: 72
Period size: 13 Copynumber: 4.5 Consensus size: 13
543806 CCGTTTACCC
543816 GACCCGACCCGTT
1 GACCCGACCCGTT
*
543829 TACCCGACCCGTT
1 GACCCGACCCGTT
543842 GACCCGACTCGACTCGTT
1 GACCCGA--C--C-CGTT
543860 GACCCGACCCGTT
1 GACCCGACCCGTT
543873 GACCCG
1 GACCCG
543879 TTGACCGTTG
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
13 28 0.65
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 11 0.26
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:543839 original size:18 final size:18
Alignment explanation
Indices: 543794--543839 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
543784 ACCGGTCACA
*
543794 ACCCGACCCAACCCGTTT
1 ACCCGACCCGACCCGTTT
543812 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
543830 ACCCGACCCG
1 ACCCGACCCG
543840 TTGACCCGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.20, C:0.52, G:0.15, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:543839 original size:31 final size:31
Alignment explanation
Indices: 543798--543878 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
543788 GTCACAACCC
* *
543798 GACCCAACCCGTTTACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
* * *
543829 TACCCGACCCGTTGACCCGACTCGACTCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
543860 GACCCGACCCGTTGACCCG
1 GACCCGACCCGTTGACCCG
543879 TTGACCGTTG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.17, C:0.46, G:0.20, T:0.17
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:543845 original size:8 final size:8
Alignment explanation
Indices: 543834--543905 Score: 73
Period size: 8 Copynumber: 9.4 Consensus size: 8
543824 CCGTTTACCC
543834 GACCCGTT
1 GACCCGTT
*
543842 GACCCGACTC
1 GACCCG--TT
*
543852 GACTCGTT
1 GACCCGTT
543860 GACCC---
1 GACCCGTT
543865 GACCCGTT
1 GACCCGTT
543873 GACCCGTT
1 GACCCGTT
543881 GA-CCGTT
1 GACCCGTT
543888 GACCCGTT
1 GACCCGTT
543896 GA-CCGTT
1 GACCCGTT
543903 GAC
1 GAC
543906 TACTGTTGAC
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
5 5 0.09
7 14 0.26
8 28 0.53
10 6 0.11
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:543854 original size:18 final size:18
Alignment explanation
Indices: 543833--543867 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
543823 CCCGTTTACC
543833 CGACCCGTTGACCCGACT
1 CGACCCGTTGACCCGACT
*
543851 CGACTCGTTGACCCGAC
1 CGACCCGTTGACCCGAC
543868 CCGTTGACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (18 bp):
CGACCCGTTGACCCGACT
Found at i:543888 original size:7 final size:7
Alignment explanation
Indices: 543868--543905 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
543858 TTGACCCGAC
543868 CCGTTGA
1 CCGTTGA
543875 CCCGTTGA
1 -CCGTTGA
543883 CCGTTGA
1 CCGTTGA
543890 CCCGTTGA
1 -CCGTTGA
543898 CCGTTGA
1 CCGTTGA
543905 C
1 C
543906 TACTGTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 15 0.52
8 14 0.48
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:543888 original size:15 final size:15
Alignment explanation
Indices: 543868--543905 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
543858 TTGACCCGAC
543868 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
543883 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
543898 CCGTTGAC
1 CCGTTGAC
543906 TACTGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:552179 original size:22 final size:22
Alignment explanation
Indices: 552151--552214 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
552141 TGTTAGACTT
*
552151 GCTAAACCCGGGTTCGACACTG-
1 GCTAAACCCGGGTTCAACAC-GA
* *
552173 GCTAAACTCGGGTTTAACACGA
1 GCTAAACCCGGGTTCAACACGA
*
552195 GCTAGACCCGGGTTCAACAC
1 GCTAAACCCGGGTTCAACAC
552215 AGTTGTCTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.19
Consensus pattern (22 bp):
GCTAAACCCGGGTTCAACACGA
Found at i:560819 original size:2 final size:2
Alignment explanation
Indices: 560812--560860 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
560802 CTTTACCGTT
560812 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
560854 TA TA TA T
1 TA TA TA T
560861 GCCGAATCTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:562493 original size:2 final size:2
Alignment explanation
Indices: 562488--562536 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
562478 ACATACATGC
562488 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
562530 AT AT AT A
1 AT AT AT A
562537 CACAATCACT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:562884 original size:23 final size:22
Alignment explanation
Indices: 562857--562926 Score: 79
Period size: 22 Copynumber: 3.1 Consensus size: 22
562847 AAGTCCCACT
* *
562857 GAATGGCATATGAACTTTGTCCC
1 GAATGGCCTATGTA-TTTGTCCC
* *
562880 GAATGACCTATGTATTTGTCCT
1 GAATGGCCTATGTATTTGTCCC
562902 GAA-GGACCTATGTATTTGTCCC
1 GAATGG-CCTATGTATTTGTCCC
562924 GAA
1 GAA
562927 GGACCGCGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
21 1 0.03
22 28 0.70
23 11 0.28
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (22 bp):
GAATGGCCTATGTATTTGTCCC
Found at i:562900 original size:22 final size:22
Alignment explanation
Indices: 562872--562931 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
562862 GCATATGAAC
*
562872 TTTGTCCCGAATGACCTATGTA
1 TTTGTCCCGAAGGACCTATGTA
*
562894 TTTGTCCTGAAGGACCTATGTA
1 TTTGTCCCGAAGGACCTATGTA
562916 TTTGTCCCGAAGGACC
1 TTTGTCCCGAAGGACC
562932 GCGTAGACTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.33
Consensus pattern (22 bp):
TTTGTCCCGAAGGACCTATGTA
Found at i:565542 original size:2 final size:2
Alignment explanation
Indices: 565535--565586 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
565525 CATACATTGT
565535 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
565577 TA TA TA TA TA
1 TA TA TA TA TA
565587 ACATTGTACG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:567066 original size:28 final size:26
Alignment explanation
Indices: 567034--567085 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
567024 ATAATACATC
* *
567034 CAATCATATTATAAAACAATACAATACA
1 CAATCAAATT-TAAAA-AATAAAATACA
567062 CAATCAAATTTAAAAAATAAAATA
1 CAATCAAATTTAAAAAATAAAATA
567086 AATAAATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
27 5 0.23
28 9 0.41
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.25
Consensus pattern (26 bp):
CAATCAAATTTAAAAAATAAAATACA
Found at i:567926 original size:22 final size:22
Alignment explanation
Indices: 567881--567926 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
567871 ATTTTCGATT
* *
567881 TCTAAAATTTTATAACTTCTTC
1 TCTAAAATTGTATAACTTCGTC
**
567903 TCTAAAATTGTATATGTTCGTC
1 TCTAAAATTGTATAACTTCGTC
567925 TC
1 TC
567927 CCTCCTTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (22 bp):
TCTAAAATTGTATAACTTCGTC
Found at i:571252 original size:54 final size:54
Alignment explanation
Indices: 571186--571304 Score: 148
Period size: 54 Copynumber: 2.2 Consensus size: 54
571176 GAGTACAAAT
* * * * * * *
571186 CACCATCACCACCTTCTCCTTCTCCACCGCCGCCTTATGTGTATAAATCTCCAC
1 CACCACCACCACCATCGCCTTCTCCACCACCGCCTTATGAGTACAAATCCCCAC
* * *
571240 CACCACCACCACCATCGCCTTCTCCACCACCTCCTTATGAGTACAAGTCCCCTC
1 CACCACCACCACCATCGCCTTCTCCACCACCGCCTTATGAGTACAAATCCCCAC
571294 CACCACCACCA
1 CACCACCACCA
571305 AAACACGAAG
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.23, C:0.49, G:0.07, T:0.22
Consensus pattern (54 bp):
CACCACCACCACCATCGCCTTCTCCACCACCGCCTTATGAGTACAAATCCCCAC
Found at i:571637 original size:51 final size:51
Alignment explanation
Indices: 571458--572330 Score: 328
Period size: 51 Copynumber: 17.6 Consensus size: 51
571448 TTCTCCTCCA
* * * * * *
571458 CCTCCATACGT-CTACAAATCTCCACCACCTCCACCGAAACACAAGGAGCAA
1 CCTCCATAC-TACTACAAGTCTCCACCACCACCACCTAAACACGAGGACCAG
* * * * **
571509 CCCCCATACTACTACAAGTCTCCACCACCA-C-CTTCACCATC--CCACCA-
1 CCTCCATACTACTACAAGTCTCCACCACCACCACCTAAACA-CGAGGACCAG
* * * *
571556 CCTCCATACGT-CTATAAATCTCCGCCACCACCACCTAAACACGAGGAGCAG
1 CCTCCATAC-TACTACAAGTCTCCACCACCACCACCTAAACACGAGGACCAG
* * * * * * ***
571607 CCCCCCTACTACTACAAGTCTCCTCCACCA-C-CTTCACCATCCCCG-CCA-
1 CCTCCATACTACTACAAGTCTCCACCACCACCACCTAAACA-CGAGGACCAG
* *
571655 CCTCCATACGT-CTATAAGTCTCCACCACCACCACCTAAACACGAGGAGCAG
1 CCTCCATAC-TACTACAAGTCTCCACCACCACCACCTAAACACGAGGACCAG
* * * ***
571706 CCTCCGTACTACTACAAG--TCC-CCACCACCACCTTCACCATCCCCG-CCA-
1 CCTCCATACTACTACAAGTCTCCACCACCACCACC-TAAACA-CGAGGACCAG
* * * * *
571754 CCTCCATACGT-CTATAAATCTCCACCACCACCACCGAAACATGTA-GAGCAG
1 CCTCCATAC-TACTACAAGTCTCCACCACCACCACCTAAACACG-AGGACCAG
* * * * ***
571805 CCTCCATACTACTACAAGTCTCCTCCACCA-C-CTTCACCATC-CCCACCA-
1 CCTCCATACTACTACAAGTCTCCACCACCACCACCTAAACA-CGAGGACCAG
*
571853 CCTCCATACGT-CTACAAGTCTCCACCACCACCACCTAAACACGAGGAACAG
1 CCTCCATAC-TACTACAAGTCTCCACCACCACCACCTAAACACGAGGACCAG
* * * * * ***
571904 CCCCCGTATTACTACAAG--TCC-CCACCACCACCTTCACCATC-CCCACCA-
1 CCTCCATACTACTACAAGTCTCCACCACCACCACC-TAAACA-CGAGGACCAG
* * * * * *
571952 CCTCCATA-TATCTATAAATCTCCACCACCACCACCGAAACATGAAGAGCAG
1 CCTCCATACTA-CTACAAGTCTCCACCACCACCACCTAAACACGAGGACCAG
* * * * * ***
572003 CCTCCATATTACTAC-AGTCTCCTCCACCA-C-CTTCACCATC-CCCACCA-
1 CCTCCATACTACTACAAGTCTCCACCACCACCACCTAAACA-CGAGGACCAG
* * * * * * *
572050 CCTCCATACGT-CTACAAGTCCCCTCCTCCTCCACCGAAACATGAGGAGCAG
1 CCTCCATAC-TACTACAAGTCTCCACCACCACCACCTAAACACGAGGACCAG
* * * * * *** *
572101 CCCCCATACTACTACAAATCTCCACCACCA-C-CTTCACCATC-CCCATCA-
1 CCTCCATACTACTACAAGTCTCCACCACCACCACCTAAACA-CGAGGACCAG
* * *
572149 CCTCCATA-TGTCTACAAGTCTCCACCACCACCACCGAAACACGAGGAGCAG
1 CCTCCATACT-ACTACAAGTCTCCACCACCACCACCTAAACACGAGGACCAG
* * * * * * **
572200 CCCCCATACTATTACAAGTCTCCACCACC-GC-CTTCACCATCG-CCACCA-
1 CCTCCATACTACTACAAGTCTCCACCACCACCACCTAAACA-CGAGGACCAG
* * * * *
572248 CCTCCATATGTA-TACAAGTCTCCACCACCGCCACC-AAAGCACGAAGAGCAA
1 CCTCCATA-CTACTACAAGTCTCCACCACCACCACCTAAA-CACGAGGACCAG
572299 CCTCCATACTACTACAAGTCTCCACCACCACC
1 CCTCCATACTACTACAAGTCTCCACCACCACC
572331 GGTGAAATCT
Statistics
Matches: 582, Mismatches: 174, Indels: 132
0.66 0.20 0.15
Matches are distributed among these distances:
47 39 0.07
48 171 0.29
49 75 0.13
50 88 0.15
51 206 0.35
52 3 0.01
ACGTcount: A:0.29, C:0.45, G:0.08, T:0.17
Consensus pattern (51 bp):
CCTCCATACTACTACAAGTCTCCACCACCACCACCTAAACACGAGGACCAG
Found at i:571674 original size:48 final size:48
Alignment explanation
Indices: 571512--572276 Score: 274
Period size: 48 Copynumber: 15.5 Consensus size: 48
571502 GGAGCAACCC
*
571512 CCATAC-TACTACAAGTCTCCACCACCACCTTCACCAT-CCCACCACCT
1 CCATACGT-CTACAAGTCTCCACCACCACCTTCACCATCCCCGCCACCT
* * * * *** *
571559 CCATACGTCTATAAATCTCCGCCACCACCACCTAAACACGAGGAGCAGCC-CC-
1 CCATACGTCTACAAGTCT---CCACCACCACCT--TCACCA-TCCCCGCCACCT
*
571611 CC-TAC-TACTACAAGTCTCCTCCACCACCTTCACCATCCCCGCCACCT
1 CCATACGT-CTACAAGTCTCCACCACCACCTTCACCATCCCCGCCACCT
* * * * *** *
571658 CCATACGTCTATAAGTCTCCACCACCACCACCTAAACA-CGAGGAGCAGCCT
1 CCATACGTCTACAAGTCTCCACCACCA-C-CTTCACCATCCCCG-CCA-CCT
* *
571709 CCGTAC-TACTACAAGTCCCCACCACCACCTTCACCATCCCCGCCACCT
1 CCATACGT-CTACAAGTCTCCACCACCACCTTCACCATCCCCGCCACCT
* * ** * *** *
571757 CCATACGTCTATAAATCTCCACCACCACCACCGAAACAT-GTAGAGCAGCCT
1 CCATACGTCTACAAGTCTCCACCACCACCTTC--ACCATCCCCG-CCA-CCT
* *
571808 CCATAC-TACTACAAGTCTCCTCCACCACCTTCACCATCCCCACCACCT
1 CCATACGT-CTACAAGTCTCCACCACCACCTTCACCATCCCCGCCACCT
* * * *** * *
571856 CCATACGTCTACAAGTCTCCACCACCACCACCTAAACA-CGAGGAACAGCCC
1 CCATACGTCTACAAGTCTCCACCACCA-C-CTTCACCATCCCCG-CCA-CCT
* * * *
571907 CCGTA-TTACTACAAGTCCCCACCACCACCTTCACCATCCCCACCACCT
1 CCATACGT-CTACAAGTCTCCACCACCACCTTCACCATCCCCGCCACCT
** * * ** * *** *
571955 CCATATATCTATAAATCTCCACCACCACCACCGAAACAT-GAAGAGCAGCCT
1 CCATACGTCTACAAGTCTCCACCACCACCTTC--ACCATCCCCG-CCA-CCT
* * *
572006 CCATA-TTACTAC-AGTCTCCTCCACCACCTTCACCATCCCCACCACCT
1 CCATACGT-CTACAAGTCTCCACCACCACCTTCACCATCCCCGCCACCT
* * ** * *** * *
572053 CCATACGTCTACAAGTCCCCTCCTCCTCCACC-GAAACAT-GAGGAGCAGCCC
1 CCATACGTCTACAAGT---CTCCACCACCACCTTCACCATCCCCG-CCA-CCT
* **
572104 CCATAC-TACTACAAATCTCCACCACCACCTTCACCATCCCCATCACCT
1 CCATACGT-CTACAAGTCTCCACCACCACCTTCACCATCCCCGCCACCT
* ** * *** * *
572152 CCATATGTCTACAAGTCTCCACCACCACCACCGAAACA-CGAGGAGCAGCCC
1 CCATACGTCTACAAGTCTCCACCACCACCTTC--ACCATCCCCG-CCA-CCT
* * * *
572203 CCATAC-TATTACAAGTCTCCACCACCGCCTTCACCATCGCCACCACCT
1 CCATACGT-CTACAAGTCTCCACCACCACCTTCACCATCCCCGCCACCT
* *
572251 CCATATGTATACAAGTCTCCACCACC
1 CCATACGTCTACAAGTCTCCACCACC
572277 GCCACCAAAG
Statistics
Matches: 508, Mismatches: 152, Indels: 115
0.66 0.20 0.15
Matches are distributed among these distances:
45 4 0.01
46 6 0.01
47 28 0.06
48 184 0.36
49 44 0.09
50 78 0.15
51 153 0.30
52 6 0.01
53 2 0.00
54 3 0.01
ACGTcount: A:0.28, C:0.46, G:0.08, T:0.18
Consensus pattern (48 bp):
CCATACGTCTACAAGTCTCCACCACCACCTTCACCATCCCCGCCACCT
Found at i:571686 original size:99 final size:99
Alignment explanation
Indices: 571242--572330 Score: 1270
Period size: 99 Copynumber: 11.1 Consensus size: 99
571232 ATCTCCACCA
* * * * * * ** * * *
571242 CCACCACCACCATCGCCTTCTCCACCACCTCCTTATGAGTACAAGTCCCCTCCACCACCACCAAA
1 CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCGAA
* * * * * *
571307 ACACGAAGAGAAG---CCATATTATTATAAGTCC
66 ACACGAGGAGCAGCCCCCATACTACTACAAGTCT
* * * ** *
571338 CCACCACCACCATCACCTTCTCCC-CCACCTCCTTACGAGTACAAGTCTCCTCCACCACCA---A
1 CCACCACCACCTTCACCATC-CCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCGA
* ** * * * *
571399 AGCACGAGGAG-A--AACCGTACTATTATAAATCT
65 AACACGAGGAGCAGCCCCCATACTACTACAAGTCT
* * * * * *
571431 CCACCACCACCATCACCTTCTCCTCCACCTCCATACGTCTACAAATCTCCACCACCTCCACCGAA
1 CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCGAA
* *
571496 ACACAAGGAGCAACCCCCATACTACTACAAGTCT
66 ACACGAGGAGCAGCCCCCATACTACTACAAGTCT
* * * *
571530 CCACCACCACCTTCACCAT-CCCACCACCTCCATACGTCTATAAATCTCCGCCACCACCACCTAA
1 CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCGAA
*
571594 ACACGAGGAGCAGCCCCCCTACTACTACAAGTCT
66 ACACGAGGAGCAGCCCCCATACTACTACAAGTCT
* * * *
571628 CCTCCACCACCTTCACCATCCCCGCCACCTCCATACGTCTATAAGTCTCCACCACCACCACCTAA
1 CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCGAA
* * *
571693 ACACGAGGAGCAGCCTCCGTACTACTACAAGTCC
66 ACACGAGGAGCAGCCCCCATACTACTACAAGTCT
* * *
571727 CCACCACCACCTTCACCATCCCCGCCACCTCCATACGTCTATAAATCTCCACCACCACCACCGAA
1 CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCGAA
* *
571792 ACATGTA-GAGCAGCCTCCATACTACTACAAGTCT
66 ACACG-AGGAGCAGCCCCCATACTACTACAAGTCT
* *
571826 CCTCCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCTAA
1 CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCGAA
* * * *
571891 ACACGAGGAACAGCCCCCGTATTACTACAAGTCC
66 ACACGAGGAGCAGCCCCCATACTACTACAAGTCT
** * *
571925 CCACCACCACCTTCACCATCCCCACCACCTCCATATATCTATAAATCTCCACCACCACCACCGAA
1 CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCGAA
* * * *
571990 ACATGAAGAGCAGCCTCCATATTACTAC-AGTCT
66 ACACGAGGAGCAGCCCCCATACTACTACAAGTCT
* * * * *
572023 CCTCCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCCCCTCCTCCTCCACCGAA
1 CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCGAA
* *
572088 ACATGAGGAGCAGCCCCCATACTACTACAAATCT
66 ACACGAGGAGCAGCCCCCATACTACTACAAGTCT
* *
572122 CCACCACCACCTTCACCATCCCCATCACCTCCATATGTCTACAAGTCTCCACCACCACCACCGAA
1 CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCGAA
*
572187 ACACGAGGAGCAGCCCCCATACTATTACAAGTCT
66 ACACGAGGAGCAGCCCCCATACTACTACAAGTCT
* * * * *
572221 CCACCACCGCCTTCACCATCGCCACCACCTCCATATGTATACAAGTCTCCACCACCGCCACC-AA
1 CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCGAA
* * *
572285 AGCACGAAGAGCAACCTCCATACTACTACAAGTCT
66 A-CACGAGGAGCAGCCCCCATACTACTACAAGTCT
572320 CCACCACCACC
1 CCACCACCACC
572331 GGTGAAATCT
Statistics
Matches: 873, Mismatches: 105, Indels: 27
0.87 0.10 0.03
Matches are distributed among these distances:
92 3 0.00
93 74 0.08
96 63 0.07
97 3 0.00
98 177 0.20
99 552 0.63
100 1 0.00
ACGTcount: A:0.29, C:0.45, G:0.08, T:0.17
Consensus pattern (99 bp):
CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCGAA
ACACGAGGAGCAGCCCCCATACTACTACAAGTCT
Found at i:571775 original size:296 final size:296
Alignment explanation
Indices: 571242--572330 Score: 1322
Period size: 296 Copynumber: 3.7 Consensus size: 296
571232 ATCTCCACCA
* * * * * * ** * * *
571242 CCACCACCACCATCGCCTTCTCCACCACCTCCTTATGAGTACAAGTCCCCTCCACCACCACCAAA
1 CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCTAA
* * * * * * * *
571307 ACACGAAGAGAAG---CCATATTATTATAAGTCCCCACCACCACCATCACCTTCTCCC-CCACCT
66 ACACGAGGAGCAGCCCCCATACTACTACAAGTCTCCACCACCACCTTCACCATC-CCCACCACCT
* * ** * * * * * * * *
571368 CCTTACGAGTACAAGTCTCCTCCACCACCA--AAGCACGAGGAGAAACCGTAC-TATTA-TA-AA
130 CCATATGTCTATAAGTCTCCACCACCACCACCAAACACGAAGAGCAGCC-TCCATACTACTACAA
* * * *
571428 -TCTCCACCACCACCATCACCTTCTCCTCCACCTCCATACGTCTACAAATCTCCACCACCTCCAC
194 GTCTCCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAATCTCCACCACCTCCAC
*
571492 CGAAACACAAGGAGCAACCCCCATACTACTACAAGTCT
259 CGAAACACAAGGAGCAGCCCCCATACTACTACAAGTCT
* * *
571530 CCACCACCACCTTCACCAT-CCCACCACCTCCATACGTCTATAAATCTCCGCCACCACCACCTAA
1 CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCTAA
* * *
571594 ACACGAGGAGCAGCCCCCCTACTACTACAAGTCTCCTCCACCACCTTCACCATCCCCGCCACCTC
66 ACACGAGGAGCAGCCCCCATACTACTACAAGTCTCCACCACCACCTTCACCATCCCCACCACCTC
* * *
571659 CATACGTCTATAAGTCTCCACCACCACCACCTAAACACGAGGAGCAGCCTCCGTACTACTACAAG
131 CATATGTCTATAAGTCTCCACCACCACCACC-AAACACGAAGAGCAGCCTCCATACTACTACAAG
* * * *
571724 TCCCCACCACCACCTTCACCATCCCCGCCACCTCCATACGTCTATAAATCTCCACCACCACCACC
195 TCTCCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAATCTCCACCACCTCCACC
** *
571789 GAAACATGTA-GAGCAGCCTCCATACTACTACAAGTCT
260 GAAACA-CAAGGAGCAGCCCCCATACTACTACAAGTCT
*
571826 CCTCCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCTAA
1 CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCTAA
* * * *
571891 ACACGAGGAACAGCCCCCGTATTACTACAAGTCCCCACCACCACCTTCACCATCCCCACCACCTC
66 ACACGAGGAGCAGCCCCCATACTACTACAAGTCTCCACCACCACCTTCACCATCCCCACCACCTC
* * * *
571956 CATATATCTATAAATCTCCACCACCACCACCGAAACATGAAGAGCAGCCTCCATATTACTAC-AG
131 CATATGTCTATAAGTCTCCACCACCACCACC-AAACACGAAGAGCAGCCTCCATACTACTACAAG
* * * * *
572020 TCTCCTCCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCCCCTCCTCCTCCACC
195 TCTCCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAATCTCCACCACCTCCACC
** *
572085 GAAACATGAGGAGCAGCCCCCATACTACTACAAATCT
260 GAAACACAAGGAGCAGCCCCCATACTACTACAAGTCT
* * *
572122 CCACCACCACCTTCACCATCCCCATCACCTCCATATGTCTACAAGTCTCCACCACCACCACCGAA
1 CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCTAA
* * *
572187 ACACGAGGAGCAGCCCCCATACTATTACAAGTCTCCACCACCGCCTTCACCATCGCCACCACCTC
66 ACACGAGGAGCAGCCCCCATACTACTACAAGTCTCCACCACCACCTTCACCATCCCCACCACCTC
* * * *
572252 CATATGTATACAAGTCTCCACCACCGCCACCAAAGCACGAAGAGCAACCTCCATACTACTACAAG
131 CATATGTCTATAAGTCTCCACCACCACCACCAAA-CACGAAGAGCAGCCTCCATACTACTACAAG
572317 TCTCCACCACCACC
195 TCTCCACCACCACC
572331 GGTGAAATCT
Statistics
Matches: 690, Mismatches: 95, Indels: 23
0.85 0.12 0.03
Matches are distributed among these distances:
287 46 0.07
288 16 0.02
289 3 0.00
290 61 0.09
292 2 0.00
293 18 0.03
294 2 0.00
295 6 0.01
296 365 0.53
297 171 0.25
ACGTcount: A:0.29, C:0.45, G:0.08, T:0.17
Consensus pattern (296 bp):
CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCTAA
ACACGAGGAGCAGCCCCCATACTACTACAAGTCTCCACCACCACCTTCACCATCCCCACCACCTC
CATATGTCTATAAGTCTCCACCACCACCACCAAACACGAAGAGCAGCCTCCATACTACTACAAGT
CTCCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAATCTCCACCACCTCCACCG
AAACACAAGGAGCAGCCCCCATACTACTACAAGTCT
Found at i:571920 original size:395 final size:394
Alignment explanation
Indices: 571245--572330 Score: 1323
Period size: 395 Copynumber: 2.8 Consensus size: 394
571235 TCCACCACCA
* * * * * * ** * *
571245 CCACCACCATCGCCTTCTCCACCACCTCCTTATGAGTACAAGTCCCCTCCACCACCACCAAAACA
1 CCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCCCCACCACCACCACCGAAACA
* * * * * * * * *
571310 CGAAGAGAAG---CCATATTATTATAAGTCCCCACCACCACCATCACCTTCTCCC-CCACCTCCT
66 CGAGGAGCAGCCCCCATACTACTACAAATCCCCACCACCACCTTCACCATC-CCCACCACCTCCA
** * * * ** * * * *
571371 TACGAGTACAAGTCTCCTCCACCACCA---AAGCACGAGGAG-A--AACCGTACTATTATAAATC
130 TACGTCTACAAATCTCCACCACCACCACCGAAACACGAGGAGCAGCCCCCATACTACTACAAGTC
* * * * * *
571430 TCCACCACCACCATCACCTTCTCCTCCACCTCCATACGTCTACAAATCTCCACCACCTCCACCGA
195 TCCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACC-A
*
571495 AACACAAGGAGCAACCCCCATACTACTACAAGTCTCCACCACCACCTTCACCAT-CCCACCACCT
259 AACACGAGGAGCAACCCCCATACTACTACAAGTCTCCACCACCACCTTCACCATCCCCACCACCT
* * * * *
571559 CCATACGTCTATAAATCTCCGCCACCACCACCTAAACACGAGGAGCAGCCCCCCTACTACTACAA
324 CCATACATCTATAAATCTCCACCACCACCACCGAAACACGAAGAGCAGCCCCCATACTACTAC-A
571624 GTCTCCT
388 GTCTCCT
* * * *
571631 CCACCACCTTCACCATCCCCGCCACCTCCATACGTCTATAAGTCTCCACCACCACCACCTAAACA
1 CCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCCCCACCACCACCACCGAAACA
* * * *
571696 CGAGGAGCAGCCTCCGTACTACTACAAGTCCCCACCACCACCTTCACCATCCCCGCCACCTCCAT
66 CGAGGAGCAGCCCCCATACTACTACAAATCCCCACCACCACCTTCACCATCCCCACCACCTCCAT
* * *
571761 ACGTCTATAAATCTCCACCACCACCACCGAAACATGTA-GAGCAGCCTCCATACTACTACAAGTC
131 ACGTCTACAAATCTCCACCACCACCACCGAAACACG-AGGAGCAGCCCCCATACTACTACAAGTC
*
571825 TCCTCCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCTA
195 TCCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACC-A
* * * * *
571890 AACACGAGGAACAGCCCCCGTATTACTACAAGTCCCCACCACCACCTTCACCATCCCCACCACCT
259 AACACGAGGAGCAACCCCCATACTACTACAAGTCTCCACCACCACCTTCACCATCCCCACCACCT
* * * *
571955 CCATATATCTATAAATCTCCACCACCACCACCGAAACATGAAGAGCAGCCTCCATATTACTACAG
324 CCATACATCTATAAATCTCCACCACCACCACCGAAACACGAAGAGCAGCCCCCATACTACTACAG
572020 TCTCCT
389 TCTCCT
* * *
572026 CCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCCCCTCCTCCTCCACCGAAACA
1 CCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCCCCACCACCACCACCGAAACA
* * *
572091 TGAGGAGCAGCCCCCATACTACTACAAATCTCCACCACCACCTTCACCATCCCCATCACCTCCAT
66 CGAGGAGCAGCCCCCATACTACTACAAATCCCCACCACCACCTTCACCATCCCCACCACCTCCAT
* * *
572156 ATGTCTACAAGTCTCCACCACCACCACCGAAACACGAGGAGCAGCCCCCATACTATTACAAGTCT
131 ACGTCTACAAATCTCCACCACCACCACCGAAACACGAGGAGCAGCCCCCATACTACTACAAGTCT
* * * * *
572221 CCACCACCGCCTTCACCATCGCCACCACCTCCATATGTATACAAGTCTCCACCACCGCCACCAAA
196 CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCAAA
* *
572286 GCACGAAGAGCAACCTCCATACTACTACAAGTCTCCACCACCACC
261 -CACGAGGAGCAACCCCCATACTACTACAAGTCTCCACCACCACC
572331 GGTGAAATCT
Statistics
Matches: 595, Mismatches: 91, Indels: 19
0.84 0.13 0.03
Matches are distributed among these distances:
386 60 0.10
388 3 0.01
389 62 0.10
392 8 0.01
393 2 0.00
394 4 0.01
395 392 0.66
396 64 0.11
ACGTcount: A:0.29, C:0.45, G:0.08, T:0.17
Consensus pattern (394 bp):
CCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCCCCACCACCACCACCGAAACA
CGAGGAGCAGCCCCCATACTACTACAAATCCCCACCACCACCTTCACCATCCCCACCACCTCCAT
ACGTCTACAAATCTCCACCACCACCACCGAAACACGAGGAGCAGCCCCCATACTACTACAAGTCT
CCACCACCACCTTCACCATCCCCACCACCTCCATACGTCTACAAGTCTCCACCACCACCACCAAA
CACGAGGAGCAACCCCCATACTACTACAAGTCTCCACCACCACCTTCACCATCCCCACCACCTCC
ATACATCTATAAATCTCCACCACCACCACCGAAACACGAAGAGCAGCCCCCATACTACTACAGTC
TCCT
Found at i:573503 original size:36 final size:36
Alignment explanation
Indices: 573463--573551 Score: 99
Period size: 36 Copynumber: 2.5 Consensus size: 36
573453 TCTTTACGTC
* * *
573463 TACAAGTCACCACCTCCACC-GGCTCCTACTTATGTA
1 TACAAGTCACCACCTCCACCAAG-TCCCACCTATGTA
** * *
573499 TACAAGTCTTCACCACCACCAAGTCCCACCTATGTT
1 TACAAGTCACCACCTCCACCAAGTCCCACCTATGTA
573535 TACAAGTCACCACCTCC
1 TACAAGTCACCACCTCC
573552 TCCGCCGTAT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
36 41 0.98
37 1 0.02
ACGTcount: A:0.27, C:0.40, G:0.09, T:0.24
Consensus pattern (36 bp):
TACAAGTCACCACCTCCACCAAGTCCCACCTATGTA
Found at i:573662 original size:36 final size:36
Alignment explanation
Indices: 573613--573704 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 36
573603 CCCGTACTAC
* **
573613 TACAAGTCTCCACCACCACCGA-GTCCCATTTACGTT
1 TACAAGTCACCACCACCACCGACG-CCCACCTACGTT
*
573649 TACAAGTCACCACCACCACCGACGCCCACCTATGTT
1 TACAAGTCACCACCACCACCGACGCCCACCTACGTT
*
573685 TACAAGTCACCACCTCCACC
1 TACAAGTCACCACCACCACC
573705 ACCATACTAC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
36 49 0.98
37 1 0.02
ACGTcount: A:0.27, C:0.43, G:0.10, T:0.20
Consensus pattern (36 bp):
TACAAGTCACCACCACCACCGACGCCCACCTACGTT
Found at i:573664 original size:150 final size:150
Alignment explanation
Indices: 573499--574196 Score: 941
Period size: 150 Copynumber: 4.6 Consensus size: 150
573489 TACTTATGTA
** * * *
573499 TACAAGTCTTCACCACCACCAAGTCCCACCTATGTTTACAAGTCACCACCTCCTCCGCCGTATTA
1 TACAAGTCACCACCACCACCAAGACCCACCTATGTTTACAAGTCACCACCTCCTCCACCGTACTA
* * * * *
573564 CTACAAGTCTCCACCACCACCGAAGCATGTTGTGAACCCCCCGTACTACTACAAGTCTCCACCAC
66 CTACAAATCTCCACCACCACCGAAGCATGTAGAGAATCCCCCGTACTACTACAAGTCCCCACCAC
* **
573629 CACCGAGTCCCATTTACGTT
131 CACCAAGTCCCACATACGTT
* * *
573649 TACAAGTCACCACCACCACCGACG-CCCACCTATGTTTACAAGTCACCACCTCCACCACCATACT
1 TACAAGTCACCACCACCACC-AAGACCCACCTATGTTTACAAGTCACCACCTCCTCCACCGTACT
* *
573713 ACTACAAATCTCCACCACCACCGAAGCATGTAGAGATTCCCCCGTACTACTACAAATCCCCACCA
65 ACTACAAATCTCCACCACCACCGAAGCATGTAGAGAATCCCCCGTACTACTACAAGTCCCCACCA
* *
573778 CCACCAAGCCCCACATACATT
130 CCACCAAGTCCCACATACGTT
* * * *
573799 TACAAGTCACCACCACCACCAACACCTACCTATGTTTACAAGTCACCACCTCCACCACCATACTA
1 TACAAGTCACCACCACCACCAAGACCCACCTATGTTTACAAGTCACCACCTCCTCCACCGTACTA
573864 CTACAAATCTCCACCACCACCGAAGCATGTAGAGAATCCCCCGTACTACTACAAGTCCCCACCAC
66 CTACAAATCTCCACCACCACCGAAGCATGTAGAGAATCCCCCGTACTACTACAAGTCCCCACCAC
*
573929 CACCAAGCCCCACATACGTT
131 CACCAAGTCCCACATACGTT
* *
573949 TACAAGTCACCACCACCACCAACACCCACCTATGTTTACAAGTCACCACCTCCTCCCCCGTACTA
1 TACAAGTCACCACCACCACCAAGACCCACCTATGTTTACAAGTCACCACCTCCTCCACCGTACTA
* *
574014 CTACAAGTCTCCACCACCACCGAAGCATGTAGAGAATCCCCCATACTACTACAAGTCCCCACCAC
66 CTACAAATCTCCACCACCACCGAAGCATGTAGAGAATCCCCCGTACTACTACAAGTCCCCACCAC
*
574079 CACCAAAACACGTCGAAAAACCACCATAC-TAC
131 CACC---A-A-GTC------CCA-CATACGT-T
* * * * *
574111 TACAACTCTCCACCACCACCAAGCCCCACCTATGTTTACAAGTCACCACCACCTCCTCCGTACTA
1 TACAAGTCACCACCACCACCAAGACCCACCTATGTTTACAAGTCACCACCTCCTCCACCGTACTA
574176 CTACAAATCTCCACCACCACC
66 CTACAAATCTCCACCACCACC
574197 AGTCCACTCT
Statistics
Matches: 493, Mismatches: 40, Indels: 18
0.89 0.07 0.03
Matches are distributed among these distances:
149 1 0.00
150 398 0.81
151 2 0.00
153 1 0.00
154 1 0.00
155 2 0.00
161 4 0.01
162 84 0.17
ACGTcount: A:0.31, C:0.43, G:0.08, T:0.18
Consensus pattern (150 bp):
TACAAGTCACCACCACCACCAAGACCCACCTATGTTTACAAGTCACCACCTCCTCCACCGTACTA
CTACAAATCTCCACCACCACCGAAGCATGTAGAGAATCCCCCGTACTACTACAAGTCCCCACCAC
CACCAAGTCCCACATACGTT
Found at i:573812 original size:36 final size:36
Alignment explanation
Indices: 573763--573855 Score: 107
Period size: 36 Copynumber: 2.6 Consensus size: 36
573753 CCCGTACTAC
* *
573763 TACAAATCCCCACCACCACCAAGC-CCCACATACATT
1 TACAAGTCACCACCACCACCAA-CACCCACATACATT
* * **
573799 TACAAGTCACCACCACCACCAACACCTACCTATGTT
1 TACAAGTCACCACCACCACCAACACCCACATACATT
*
573835 TACAAGTCACCACCTCCACCA
1 TACAAGTCACCACCACCACCA
573856 CCATACTACT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
35 1 0.02
36 48 0.98
ACGTcount: A:0.34, C:0.45, G:0.04, T:0.16
Consensus pattern (36 bp):
TACAAGTCACCACCACCACCAACACCCACATACATT
Found at i:573962 original size:36 final size:36
Alignment explanation
Indices: 573913--573998 Score: 129
Period size: 36 Copynumber: 2.4 Consensus size: 36
573903 CCCGTACTAC
*
573913 TACAAGTCCCCACCACCACCAAGC-CCCACATACGTT
1 TACAAGTCACCACCACCACCAA-CACCCACATACGTT
* *
573949 TACAAGTCACCACCACCACCAACACCCACCTATGTT
1 TACAAGTCACCACCACCACCAACACCCACATACGTT
573985 TACAAGTCACCACC
1 TACAAGTCACCACC
573999 TCCTCCCCCG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
35 1 0.02
36 45 0.98
ACGTcount: A:0.33, C:0.45, G:0.07, T:0.15
Consensus pattern (36 bp):
TACAAGTCACCACCACCACCAACACCCACATACGTT
Found at i:574054 original size:48 final size:47
Alignment explanation
Indices: 574002--574134 Score: 167
Period size: 48 Copynumber: 2.8 Consensus size: 47
573992 CACCACCTCC
* * *
574002 TCCCCCGTACTACTACAAGTCTCCACCACCACCGAAGCATGTAGAGAA
1 TCCCCCATACTACTACAAGTCTCCACCACCACC-AAGCACGTAGAAAA
* * *
574050 TCCCCCATACTACTACAAGTCCCCACCACCACCAAAACACGTCGAAAA
1 TCCCCCATACTACTACAAGTCTCCACCACCACC-AAGCACGTAGAAAA
* * *
574098 ACCACCATACTACTACAACTCTCCACCACCACCAAGC
1 TCCCCCATACTACTACAAGTCTCCACCACCACCAAGC
574135 CCCACCTATG
Statistics
Matches: 73, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
47 3 0.04
48 70 0.96
ACGTcount: A:0.35, C:0.43, G:0.08, T:0.14
Consensus pattern (47 bp):
TCCCCCATACTACTACAAGTCTCCACCACCACCAAGCACGTAGAAAA
Found at i:574211 original size:48 final size:48
Alignment explanation
Indices: 574159--574835 Score: 313
Period size: 48 Copynumber: 13.9 Consensus size: 48
574149 CAAGTCACCA
* * *
574159 CCACCTCCTCCGTACTACTACAAATCTCCACCACCACCAGTCCACTCT
1 CCACCTCCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCT
* * * *** ***
574207 CCACCACCACCATACTATTACAAGTCCCCACCTCCACCACCAAAACACGAA
1 CCACCTCCACCATACTACTACAAATCCCCA---CCACCACCAGTCCACTCT
** ** * * * *
574258 GAACAACCTCCATACTACTACAAATCTCCTCCCCCACCA-TCGC-CATCT
1 CCACCTCCACCATACTACTACAAATCCCCACCACCACCAGTC-CAC-TCT
* * * *
574306 CCTCCTCCACCATATTACTACAAATCCCCGCCACCACCAGTACACTCT
1 CCACCTCCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCT
* * * * ** * *
574354 CCACCTTCACCATACTACTACAAGTCCCCACCGCCATCACCACCAAAACACGA
1 CCACCTCCACCATACTACTACAAATCCCCACCACCACCA-GTCC---ACTC-T
** ** * * *
574407 AGAGCAACCACCGTACTACTACAAATCACCTCCACCACCA-T-CACTGTCT
1 CCA-CCTCCACCATACTACTACAAATCCCCACCACCACCAGTCCAC--TCT
* * * * *
574456 CCTCCTCCACCATACTATTACAAATCACCTCCACCACCAGTCCATTCT
1 CCACCTCCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCT
* * *
574504 CCACCTCCACCATACTACTACAAGTCCCCACCACCACC-G-CCAAAACACAA
1 CCACCTCCACCATACTACTACAAATCCCCACCACCACCAGTCC---ACTC-T
** ** * * *
574554 AGAGCAACCCCCATACTACTACAAATCTCCTCCACCACCATTGT-CA-TCT
1 CCA-CCTCCACCATACTACTACAAATCCCCACCACCACCA--GTCCACTCT
* * * * * *
574603 CCTCCTCCACCATATTATTACAAGTCTCCACCACCACCAGCCCACTCT
1 CCACCTCCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCT
* * ** *
574651 CCACCTCCACCTTACTACTACAAATCACCC-CCACCTCCA-TCGCGGTTT
1 CCACCTCCACCATACTACTACAAATC-CCCACCACCACCAGTC-CACTCT
* * * *
574699 CCTCCAT-CACCATATTACTACAAATCCCCACCACCTCCA-TCTC-CTTCA
1 CCACC-TCCACCATACTACTACAAATCCCCACCACCACCAGTC-CAC-TCT
* * ** *
574747 CCACCCCCACCATACTACTACAAATCACCC-CCACCACCGGTTTATTCT
1 CCACCTCCACCATACTACTACAAATC-CCCACCACCACCAGTCCACTCT
* * *
574795 CCACCACCACCATACTACTACAAGTCTCCC-CCACCTCCAGT
1 CCACCTCCACCATACTACTACAAATC-CCCACCACCACCAGT
574836 AGAAGTTCCA
Statistics
Matches: 460, Mismatches: 132, Indels: 74
0.69 0.20 0.11
Matches are distributed among these distances:
46 3 0.01
47 8 0.02
48 333 0.72
49 13 0.03
50 5 0.01
51 65 0.14
52 3 0.01
53 1 0.00
54 29 0.06
ACGTcount: A:0.29, C:0.47, G:0.04, T:0.19
Consensus pattern (48 bp):
CCACCTCCACCATACTACTACAAATCCCCACCACCACCAGTCCACTCT
Found at i:574222 original size:162 final size:162
Alignment explanation
Indices: 573949--574296 Score: 434
Period size: 162 Copynumber: 2.1 Consensus size: 162
573939 CACATACGTT
* * *
573949 TACAAGTCACCACCACCACCAACACCCACCTATGTTTACAAGTCACCACCTCCTCCCCCGTACTA
1 TACAAATCTCCACCACCACCAACACCCACCTATGTTTACAAGTCACCACCACCTCCCCCGTACTA
* * * * *
574014 CTACAAGTCTCCACCACCACCGAAGCATGTAGAGAATCCCCCATACTACTACAAGTCCCCA-CCA
66 CTACAAATCTCCACCACCACC-AAGCATCTACACAATCCACCATACTACTACAAGTCCCCACCCA
**
574078 CCACCAAAACACGTCGAAAAACCACCATACTAC
130 CCACCAAAACACGAAGAAAAACCACCATACTAC
* *
574111 TACAACTCTCCACCACCACCAAGC-CCCACCTATGTTTACAAGTCACCACCACCTCCTCCGTACT
1 TACAAATCTCCACCACCACCAA-CACCCACCTATGTTTACAAGTCACCACCACCTCCCCCGTACT
* * *
574175 ACTACAAATCTCCACCACCACC-AGTCCACTCTCCACCA-CCACCATACTATTACAAGTCCCCAC
65 ACTACAAATCTCCACCACCACCAAG--CA-TCTACACAATCCACCATACTACTACAAGTCCCCA-
* *
574238 CTCCACCACCAAAACACGAAGAACAACCTCCATACTAC
126 C-CCACCACCAAAACACGAAGAAAAACCACCATACTAC
* *
574276 TACAAATCTCCTCCCCCACCA
1 TACAAATCTCCACCACCACCA
574297 TCGCCATCTC
Statistics
Matches: 160, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
160 2 0.01
162 103 0.64
163 5 0.03
165 50 0.31
ACGTcount: A:0.33, C:0.45, G:0.06, T:0.16
Consensus pattern (162 bp):
TACAAATCTCCACCACCACCAACACCCACCTATGTTTACAAGTCACCACCACCTCCCCCGTACTA
CTACAAATCTCCACCACCACCAAGCATCTACACAATCCACCATACTACTACAAGTCCCCACCCAC
CACCAAAACACGAAGAAAAACCACCATACTAC
Found at i:574277 original size:99 final size:99
Alignment explanation
Indices: 574165--574344 Score: 238
Period size: 99 Copynumber: 1.8 Consensus size: 99
574155 ACCACCACCT
* *
574165 CCTCCGTACTACTACAAATCTCCACCACCACCA--GTCCACTCTCCACCACCACCATACTATTAC
1 CCTCCATACTACTACAAATCTCCACCACCACCATCG-CCA-TCTCCACCACCACCATACTACTAC
* *
574228 AAGTCCCCACCTCCACCACCAAAACACGAAGAACAA
64 AAATCCCCACCACCACCACCAAAACACGAAGAACAA
* * * * *
574264 CCTCCATACTACTACAAATCTCCTCCCCCACCATCGCCATCTCCTCCTCCACCATATTACTACAA
1 CCTCCATACTACTACAAATCTCCACCACCACCATCGCCATCTCCACCACCACCATACTACTACAA
*
574329 ATCCCCGCCACCACCA
66 ATCCCCACCACCACCA
574345 GTACACTCTC
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
99 65 0.94
100 3 0.04
101 1 0.01
ACGTcount: A:0.31, C:0.48, G:0.04, T:0.18
Consensus pattern (99 bp):
CCTCCATACTACTACAAATCTCCACCACCACCATCGCCATCTCCACCACCACCATACTACTACAA
ATCCCCACCACCACCACCAAAACACGAAGAACAA
Found at i:574340 original size:147 final size:147
Alignment explanation
Indices: 574174--574673 Score: 703
Period size: 147 Copynumber: 3.4 Consensus size: 147
574164 TCCTCCGTAC
* *
574174 TACTACAAATCTCCACCACCACCAGTCCACTCTCCACCACCACCATACTATTACAAGTCCCCACC
1 TACTACAAATCTCCACCACCACCAGTCCACTCTCCACCTCCACCATACTACTACAAGTCCCCACC
* * * *
574239 TCCACCACCAAAACACGAAGAACAACCTCCATACTACTACAAATCTCCTCCCCCACCATCGCCAT
66 ACCACCACCAAAACACGAAGAGCAACCACCATACTACTACAAATCTCCTCCACCACCATCGCCAT
574304 CTCCTCCTCCACCATAT
131 CTCCTCCTCCACCATAT
* * * *
574321 TACTACAAATCCCCGCCACCACCAGTACACTCTCCACCTTCACCATACTACTACAAGTCCCCACC
1 TACTACAAATCTCCACCACCACCAGTCCACTCTCCACCTCCACCATACTACTACAAGTCCCCA--
* * * *
574386 GCCATCACCACCAAAACACGAAGAGCAACCACCGTACTACTACAAATCACCTCCACCACCATCAC
64 -CCACCACCACCAAAACACGAAGAGCAACCACCATACTACTACAAATCTCCTCCACCACCATCGC
** *
574451 TGTCTCCTCCTCCACCATAC
128 CATCTCCTCCTCCACCATAT
* * * *
574471 TATTACAAATCACCTCCACCACCAGTCCATTCTCCACCTCCACCATACTACTACAAGTCCCCACC
1 TACTACAAATCTCCACCACCACCAGTCCACTCTCCACCTCCACCATACTACTACAAGTCCCCACC
* * * * *
574536 ACCACCGCCAAAACACAAAGAGCAACCCCCATACTACTACAAATCTCCTCCACCACCATTGTCAT
66 ACCACCACCAAAACACGAAGAGCAACCACCATACTACTACAAATCTCCTCCACCACCATCGCCAT
574601 CTCCTCCTCCACCATAT
131 CTCCTCCTCCACCATAT
* * * *
574618 TATTACAAGTCTCCACCACCACCAGCCCACTCTCCACCTCCACCTTACTACTACAA
1 TACTACAAATCTCCACCACCACCAGTCCACTCTCCACCTCCACCATACTACTACAA
574674 ATCACCCCCA
Statistics
Matches: 309, Mismatches: 41, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
147 179 0.58
150 130 0.42
ACGTcount: A:0.31, C:0.46, G:0.04, T:0.19
Consensus pattern (147 bp):
TACTACAAATCTCCACCACCACCAGTCCACTCTCCACCTCCACCATACTACTACAAGTCCCCACC
ACCACCACCAAAACACGAAGAGCAACCACCATACTACTACAAATCTCCTCCACCACCATCGCCAT
CTCCTCCTCCACCATAT
Found at i:574538 original size:96 final size:95
Alignment explanation
Indices: 574157--574829 Score: 353
Period size: 96 Copynumber: 6.9 Consensus size: 95
574147 TACAAGTCAC
* * * * * *
574157 CACCACCTCCTCCGTACTACTACAAATCTCCACCACCACCAGTCCACTCTCCACCACCACCATAC
1 CACCACCTCCACCATACTACTACAAATCACCCCCACCACCAGTCCATTCTCCACCTCCACCATAC
* * * * *
574222 TATTACAAGTCCCCACCTCCACCACCAAAA
66 TACTACAAGTCCCCACCACCACCATCACAT
* ** * * *
574252 CACGAAGAACAACCTCCATACTACTACAAATCTCCTCCC-CCACCA-TCGCCA-TCTCCTCCTCC
1 CAC----CACCTCCACCATACTACTACAAATCACC-CCCACCACCAGT--CCATTCTCCACCTCC
* * *
574314 ACCATATTACTACAAATCCCCGCCACCACCAGT-ACACT
59 ACCATACTACTACAAGTCCCCACCACCACCA-TCACA-T
* * * *** *** **
574352 CTCCACCTTCACCATACTACTACAAGTCCCCACCGCCATCACCACCAAAACA--CGAAGAGCAAC
1 CACCACCTCCACCATACTACTACAAAT---CACC-CC--CACCACCAGTCCATTC-TCCA-CCTC
* * * * *
574415 CACCGTACTACTACAAATCACCTCCACCACCATCACTGT
58 CACCATACTACTACAAGTCCCCACCACCACCATCAC-AT
* * * *
574454 CTCCTCCTCCACCATACTATTACAAATCACCTCCACCACCAGTCCATTCTCCACCTCCACCATAC
1 CACCACCTCCACCATACTACTACAAATCACCCCCACCACCAGTCCATTCTCCACCTCCACCATAC
** * *
574519 TACTACAAGTCCCCACCACCACCGCCAAAA
66 TACTACAAGTCCCCACCACCACCATCACAT
* ** * * * *
574549 CACAAAGAGCAACCCCCATACTACTACAAATCTCCTCCACCACCATTGT-CA-TCTCCTCCTCCA
1 CAC---CA-CCTCCACCATACTACTACAAATCACCCCCACCACCA--GTCCATTCTCCACCTCCA
* * * * *
574612 CCATATTATTACAAGTCTCCACCACCACCAGCCCACT
60 CCATACTACTACAAGTCCCCACCACCACCATCACA-T
* * * * *
574649 CTCCACCTCCACCTTACTACTACAAATCACCCCCACCTCCA-TCGCGGTT-TCCTCCAT-CACCA
1 CACCACCTCCACCATACTACTACAAATCACCCCCACCACCAGTC-C-ATTCTCCACC-TCCACCA
* * * * *
574711 TATTACTACAAATCCCCACCACCTCCATCTCCTT
63 TACTACTACAAGTCCCCACCACCACCATC-ACAT
* * ** *
574745 CACCACCCCCACCATACTACTACAAATCACCCCCACCACCGGTTTATTCTCCACCACCACCATAC
1 CACCACCTCCACCATACTACTACAAATCACCCCCACCACCAGTCCATTCTCCACCTCCACCATAC
574810 TACTACAAGTCTCCC-CCACC
66 TACTACAAGTC-CCCACCACC
574830 TCCAGTAGAA
Statistics
Matches: 435, Mismatches: 104, Indels: 77
0.71 0.17 0.12
Matches are distributed among these distances:
93 1 0.00
95 8 0.02
96 187 0.43
97 10 0.02
98 3 0.01
99 146 0.34
100 12 0.03
101 6 0.01
102 62 0.14
ACGTcount: A:0.29, C:0.47, G:0.04, T:0.19
Consensus pattern (95 bp):
CACCACCTCCACCATACTACTACAAATCACCCCCACCACCAGTCCATTCTCCACCTCCACCATAC
TACTACAAGTCCCCACCACCACCATCACAT
Found at i:574895 original size:18 final size:18
Alignment explanation
Indices: 574872--574918 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
574862 ACAAGTCCCC
574872 ACCACCACCATCTCCTTT
1 ACCACCACCATCTCCTTT
574890 ACCACCACCATCTCCTTT
1 ACCACCACCATCTCCTTT
574908 ACCACCACCAT
1 ACCACCACCAT
574919 ACTACTACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.26, C:0.51, G:0.00, T:0.23
Consensus pattern (18 bp):
ACCACCACCATCTCCTTT
Found at i:575016 original size:48 final size:48
Alignment explanation
Indices: 574964--575088 Score: 135
Period size: 48 Copynumber: 2.6 Consensus size: 48
574954 CCAGCACCTG
* * * *
574964 CATACCACTACAATTCCCCTCCTCCACCATCACCATCTCCTCCTCTCC
1 CATACCACTACAAATCCCCTCCTCCACCATCACCATCACCCCCTCCCC
* * *
575012 CATACCACTACAAATCTCCC-CCACCACCATCTCCCTCACCCCCTCCCC
1 CATACCACTACAAATC-CCCTCCTCCACCATCACCATCACCCCCTCCCC
* * * *
575060 CATACTACTACCACTCACCTCCTCCACCA
1 CATACCACTACAAATCCCCTCCTCCACCA
575089 GTGAAATCAC
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
47 2 0.03
48 58 0.92
49 3 0.05
ACGTcount: A:0.23, C:0.56, G:0.00, T:0.21
Consensus pattern (48 bp):
CATACCACTACAAATCCCCTCCTCCACCATCACCATCACCCCCTCCCC
Found at i:588876 original size:41 final size:39
Alignment explanation
Indices: 588794--588877 Score: 105
Period size: 41 Copynumber: 2.1 Consensus size: 39
588784 CTACGGCCTG
* *
588794 GCCTATTTAATAAAAAGGCCAGACCAGGCCTTTTTAAAA
1 GCCTATTTAATAAAAAGGCCAGACCAGGCCTATTAAAAA
* * *
588833 GCCTATTTAATTAAACAGGCCAGGCTTAGGCCTATTAAAAA
1 GCCTATTTAA-TAAAAAGGCCAGAC-CAGGCCTATTAAAAA
588874 GCCT
1 GCCT
588878 TATAAGCTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
39 10 0.26
40 12 0.32
41 16 0.42
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (39 bp):
GCCTATTTAATAAAAAGGCCAGACCAGGCCTATTAAAAA
Found at i:589043 original size:17 final size:17
Alignment explanation
Indices: 589021--589053 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
589011 TTTTAAACAT
589021 GCTTTTAAACAGGCCAA
1 GCTTTTAAACAGGCCAA
*
589038 GCTTTTAAATAGGCCA
1 GCTTTTAAACAGGCCA
589054 GGCCAGTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (17 bp):
GCTTTTAAACAGGCCAA
Found at i:589537 original size:25 final size:25
Alignment explanation
Indices: 589518--589569 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
589508 GATTATTGTT
589518 TTCTATTTAGTATCGTATTATGGAC
1 TTCTATTTAGTATCGTATTATGGAC
589543 TTCTATTTAGTATCGTATTATGGAC
1 TTCTATTTAGTATCGTATTATGGAC
589568 TT
1 TT
589570 GAAATTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (25 bp):
TTCTATTTAGTATCGTATTATGGAC
Found at i:589854 original size:2 final size:2
Alignment explanation
Indices: 589847--589883 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
589837 CTTTTAAACT
589847 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
589884 TGAGGCCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:594656 original size:23 final size:23
Alignment explanation
Indices: 594626--594671 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
594616 GTTTAACAGA
*
594626 AAATATAT-TTTGTTTTCGTGAT
1 AAATATATCTTTGTTGTCGTGAT
594648 AAATAATATCTTTGTTGTCGTGAT
1 AAAT-ATATCTTTGTTGTCGTGAT
594672 CGGAAATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 4 0.19
24 13 0.62
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (23 bp):
AAATATATCTTTGTTGTCGTGAT
Found at i:601147 original size:33 final size:33
Alignment explanation
Indices: 601120--601387 Score: 466
Period size: 33 Copynumber: 8.1 Consensus size: 33
601110 TGCTAATCCC
* * *
601120 TATGGCCAACCCT-CACAGCCAAATGCTAATCCA
1 TATGGTCAA-CCTGCACAGCCAAATGCCAGTCCA
601153 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
1 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
*
601186 TATGGTCAACCTGCTCAGCCAAATGCCAGTCCA
1 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
601219 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
1 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
601252 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
1 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
601285 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
1 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
*
601318 TATGGTCTACCTGCACAGCCAAATGCCAGTCCA
1 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
*
601351 TATGGTCAACCTGCACAGCCAAATGTCAGTCCA
1 TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
601384 TATG
1 TATG
601388 CCCAAACCAT
Statistics
Matches: 226, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
32 3 0.01
33 223 0.99
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.20
Consensus pattern (33 bp):
TATGGTCAACCTGCACAGCCAAATGCCAGTCCA
Found at i:602119 original size:15 final size:15
Alignment explanation
Indices: 602095--602153 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
602085 GGGCATGGGA
602095 ATGGGGATGAACAAC
1 ATGGGGATGAACAAC
*
602110 ATGGGAATGAATCCAGGA-
1 ATGGGGATGAA--CA--AC
602128 ATGGGGATGAACAAC
1 ATGGGGATGAACAAC
*
602143 ATGGGCATGAA
1 ATGGGGATGAA
602154 TCCGGGAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 1 0.03
15 20 0.56
16 2 0.06
17 2 0.06
18 10 0.28
19 1 0.03
ACGTcount: A:0.39, C:0.12, G:0.34, T:0.15
Consensus pattern (15 bp):
ATGGGGATGAACAAC
Found at i:602129 original size:33 final size:33
Alignment explanation
Indices: 602092--602166 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
602082 TATGGGCATG
602092 GGAATGGGGATGAACAACATGGGAATGAATCCA
1 GGAATGGGGATGAACAACATGGGAATGAATCCA
* *
602125 GGAATGGGGATGAACAACATGGGCATGAATCCG
1 GGAATGGGGATGAACAACATGGGAATGAATCCA
602158 GGAATGGGG
1 GGAATGGGG
602167 CAGAGACCCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.35, C:0.12, G:0.39, T:0.15
Consensus pattern (33 bp):
GGAATGGGGATGAACAACATGGGAATGAATCCA
Found at i:602137 original size:18 final size:18
Alignment explanation
Indices: 602110--602166 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
602100 GATGAACAAC
*
602110 ATGGGAATGAATCCAGGA
1 ATGGGGATGAATCCAGGA
602128 ATGGGGATGAA--CA--A
1 ATGGGGATGAATCCAGGA
* *
602142 CATGGGCATGAATCCGGGA
1 -ATGGGGATGAATCCAGGA
602161 ATGGGG
1 ATGGGG
602167 CAGAGACCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
14 1 0.03
15 10 0.33
16 2 0.07
17 1 0.03
18 15 0.50
19 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.39, T:0.16
Consensus pattern (18 bp):
ATGGGGATGAATCCAGGA
Found at i:602840 original size:19 final size:19
Alignment explanation
Indices: 602816--602856 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
602806 CTAAATTATT
602816 TTTTGGTCATATGTAATCA
1 TTTTGGTCATATGTAATCA
602835 TTTTGGTCATATGTAATCA
1 TTTTGGTCATATGTAATCA
602854 TTT
1 TTT
602857 AAACTATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.51
Consensus pattern (19 bp):
TTTTGGTCATATGTAATCA
Found at i:605964 original size:32 final size:32
Alignment explanation
Indices: 605923--605986 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
605913 TCACACTTCT
605923 CTTCTACTAAACATCACAACATATATTCAACA
1 CTTCTACTAAACATCACAACATATATTCAACA
605955 CTTCTACTAAACATCACAACATATATTCAACA
1 CTTCTACTAAACATCACAACATATATTCAACA
605987 ACAAATACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.28, G:0.00, T:0.28
Consensus pattern (32 bp):
CTTCTACTAAACATCACAACATATATTCAACA
Found at i:625069 original size:14 final size:15
Alignment explanation
Indices: 625042--625073 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
625032 TTAGTTGAAA
625042 ATTTAAAGATAAAAT
1 ATTTAAAGATAAAAT
625057 ATTTAAA-ATAAAAT
1 ATTTAAAGATAAAAT
625071 ATT
1 ATT
625074 AATTACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
ATTTAAAGATAAAAT
Found at i:625075 original size:13 final size:14
Alignment explanation
Indices: 625039--625075 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
625029 AAATTAGTTG
625039 AAAAT-TTAAAGAT
1 AAAATATTAAAGAT
625052 AAAATATTTAAA-AT
1 AAAATA-TTAAAGAT
625066 AAAATATTAA
1 AAAATATTAA
625076 TTACATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.41
14 8 0.36
15 5 0.23
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
AAAATATTAAAGAT
Found at i:639906 original size:2 final size:2
Alignment explanation
Indices: 639899--639928 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
639889 AATTAAATTG
639899 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
639929 TAAATTTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:640382 original size:13 final size:13
Alignment explanation
Indices: 640343--640383 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
640333 ATATGTACAC
640343 AAATGTAATGAAA
1 AAATGTAATGAAA
* **
640356 AATTGTAACAAAA
1 AAATGTAATGAAA
640369 AAATGTAATGAAA
1 AAATGTAATGAAA
640382 AA
1 AA
640384 TAAAGAAATA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.22
Consensus pattern (13 bp):
AAATGTAATGAAA
Found at i:643892 original size:22 final size:21
Alignment explanation
Indices: 643867--643907 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
643857 TGAAATTGAG
643867 TGAAAAGATTTGCTGGAAATTC
1 TGAAAAG-TTTGCTGGAAATTC
* *
643889 TGAACAGTTTGCTGTAAAT
1 TGAAAAGTTTGCTGGAAAT
643908 GGTAAACCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (21 bp):
TGAAAAGTTTGCTGGAAATTC
Found at i:644801 original size:17 final size:17
Alignment explanation
Indices: 644779--644826 Score: 96
Period size: 17 Copynumber: 2.8 Consensus size: 17
644769 TATCTGCTTT
644779 ATGAATGTGCTGCTGAC
1 ATGAATGTGCTGCTGAC
644796 ATGAATGTGCTGCTGAC
1 ATGAATGTGCTGCTGAC
644813 ATGAATGTGCTGCT
1 ATGAATGTGCTGCT
644827 TCATGTCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (17 bp):
ATGAATGTGCTGCTGAC
Found at i:652651 original size:15 final size:16
Alignment explanation
Indices: 652631--652660 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
652621 TACAAATCTA
652631 TTAAAAGTAA-AACTT
1 TTAAAAGTAATAACTT
652646 TTAAAAGTAATAACT
1 TTAAAAGTAATAACT
652661 GGCGTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (16 bp):
TTAAAAGTAATAACTT
Found at i:664751 original size:19 final size:19
Alignment explanation
Indices: 664727--664764 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
664717 ACCGAAGGAA
664727 CTTATGCTTCCTACATATG
1 CTTATGCTTCCTACATATG
664746 CTTATGCTTCCTACATATG
1 CTTATGCTTCCTACATATG
664765 TTCTACATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (19 bp):
CTTATGCTTCCTACATATG
Found at i:671724 original size:18 final size:18
Alignment explanation
Indices: 671697--671749 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
671687 TCATCATCGC
* *
671697 CTTCATCCTCTTCTTCAT
1 CTTCACCCTCATCTTCAT
* *
671715 CTTCACCCTCAGCTTCTT
1 CTTCACCCTCATCTTCAT
*
671733 CATCACCCTCATCTTCA
1 CTTCACCCTCATCTTCA
671750 GCATCATTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.43, G:0.02, T:0.40
Consensus pattern (18 bp):
CTTCACCCTCATCTTCAT
Found at i:671754 original size:18 final size:18
Alignment explanation
Indices: 671703--671755 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
671693 TCGCCTTCAT
* *
671703 CCTCTTCTTCATCTTCAC
1 CCTCATCTTCATCATCAC
* *
671721 CCTCAGCTTCTTCATCAC
1 CCTCATCTTCATCATCAC
*
671739 CCTCATCTTCAGCATCA
1 CCTCATCTTCATCATCA
671756 TTTTGGTCAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.43, G:0.04, T:0.36
Consensus pattern (18 bp):
CCTCATCTTCATCATCAC
Found at i:678169 original size:27 final size:27
Alignment explanation
Indices: 678137--678199 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 27
678127 ATATTTGGTT
*
678137 CGTATTCGTTTATTTAATATTTACGAA
1 CGTATTCGTTTATTTAATATTCACGAA
*
678164 CGTA----TTTATTTAATATTCATGAA
1 CGTATTCGTTTATTTAATATTCACGAA
*
678187 CATATTCGTTTAT
1 CGTATTCGTTTAT
678200 CGTCCACGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
23 20 0.69
27 9 0.31
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (27 bp):
CGTATTCGTTTATTTAATATTCACGAA
Found at i:679854 original size:15 final size:16
Alignment explanation
Indices: 679834--679868 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
679824 TAATATTTTT
679834 TAATA-TTTTTTAAAA
1 TAATATTTTTTTAAAA
679849 TAATATTTTTTTAAAA
1 TAATATTTTTTTAAAA
679865 -AATA
1 TAATA
679869 CTAATATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATATTTTTTTAAAA
Found at i:687519 original size:23 final size:24
Alignment explanation
Indices: 687477--687525 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
687467 ATCCGATTCG
* *
687477 AATTAATATATTTATATTTTTTAA
1 AATTAATATATTAATATTTTTAAA
*
687501 AATTAA-ATATTAATTTTTTTAAA
1 AATTAATATATTAATATTTTTAAA
687524 AA
1 AA
687526 AATTTGATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
AATTAATATATTAATATTTTTAAA
Found at i:687521 original size:22 final size:24
Alignment explanation
Indices: 687477--687524 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
687467 ATCCGATTCG
*
687477 AATTAATATATTTATATTTTTTAA
1 AATTAATATATTAATATTTTTTAA
687501 AATTAA-ATATTAAT-TTTTTTAA
1 AATTAATATATTAATATTTTTTAA
687523 AA
1 AA
687525 AAATTTGATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.43
23 7 0.30
24 6 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATTAATATATTAATATTTTTTAA
Found at i:690540 original size:23 final size:24
Alignment explanation
Indices: 690511--690568 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 24
690501 GTTTGAGAAT
690511 ATTTGAGTTC-AACTTC-TTTTTG
1 ATTTGAGTTCAAACTTCATTTTTG
690533 ATATTGAG-TCAAACTTCAATTTTTG
1 AT-TTGAGTTCAAACTTC-ATTTTTG
690558 ATTTCGAGTTC
1 ATTT-GAGTTC
690569 GATTCGAGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
22 4 0.13
23 11 0.37
24 2 0.07
25 11 0.37
26 2 0.07
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (24 bp):
ATTTGAGTTCAAACTTCATTTTTG
Found at i:691990 original size:13 final size:13
Alignment explanation
Indices: 691972--691997 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
691962 ATACTTGTGA
691972 TTTCAATCTGGAC
1 TTTCAATCTGGAC
691985 TTTCAATCTGGAC
1 TTTCAATCTGGAC
691998 ATCAACTGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
TTTCAATCTGGAC
Found at i:694270 original size:11 final size:11
Alignment explanation
Indices: 694226--694264 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
694216 CCAACAAATC
*
694226 ATAACAAACAA
1 ATAACAAACTA
694237 TATAAC-AACTA
1 -ATAACAAACTA
694248 ATAACAAACTA
1 ATAACAAACTA
694259 ATAACA
1 ATAACA
694265 CTCTAACATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 5 0.20
11 15 0.60
12 5 0.20
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (11 bp):
ATAACAAACTA
Found at i:695972 original size:16 final size:16
Alignment explanation
Indices: 695951--695983 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
695941 AACAAACTAA
*
695951 TAACAAGTAATAACAC
1 TAACAACTAATAACAC
695967 TAACAACTAATAACAC
1 TAACAACTAATAACAC
695983 T
1 T
695984 CTAACAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.21, G:0.03, T:0.21
Consensus pattern (16 bp):
TAACAACTAATAACAC
Found at i:703766 original size:21 final size:20
Alignment explanation
Indices: 703724--703766 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
703714 GATTCTATAG
*
703724 AAATAAATAATATTAAGGAA
1 AAATAAATAATATGAAGGAA
*
703744 AAATAAATAAGTATGAGGGAA
1 AAATAAATAA-TATGAAGGAA
703765 AA
1 AA
703767 TAGGATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.16, T:0.21
Consensus pattern (20 bp):
AAATAAATAATATGAAGGAA
Found at i:704813 original size:5 final size:5
Alignment explanation
Indices: 704772--704880 Score: 71
Period size: 5 Copynumber: 21.0 Consensus size: 5
704762 AAAATAATAT
* * *
704772 TATAA TGTAA TATAA -ATAA -AAAA TAATAC TAATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA T-ATAA T-ATAA TATAA TATAA TATAA
* * **
704822 TATATA AATAC TATAA TACCA TATACTA TATAA TATATA TATAA TATAAA
1 TATA-A TATAA TATAA TATAA TATA--A TATAA TATA-A TATAA TAT-AA
704872 TATAA -ATAA
1 TATAA TATAA
704881 AGTCCCGGAC
Statistics
Matches: 83, Mismatches: 14, Indels: 15
0.74 0.12 0.13
Matches are distributed among these distances:
4 11 0.13
5 45 0.54
6 22 0.27
7 5 0.06
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.36
Consensus pattern (5 bp):
TATAA
Found at i:704829 original size:38 final size:40
Alignment explanation
Indices: 704764--704869 Score: 103
Period size: 40 Copynumber: 2.6 Consensus size: 40
704754 TCAAACCAAA
* *
704764 AATAATAT--TATAATGTAATATAAATAAA-A-AATAATACT
1 AATAATATAATATAATATAATAT--ATAAATACAATAATACC
*
704802 AATAATATAATATAATATAATATATAAATACTATAATACC
1 AATAATATAATATAATATAATATATAAATACAATAATACC
704842 ATATACTATATAATATATATATAATATA
1 A-ATA--ATATAATATA-ATATAATATA
704870 AATATAAATA
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
38 13 0.23
39 1 0.02
40 20 0.35
41 3 0.05
43 10 0.18
44 10 0.18
ACGTcount: A:0.58, C:0.05, G:0.01, T:0.37
Consensus pattern (40 bp):
AATAATATAATATAATATAATATATAAATACAATAATACC
Found at i:704831 original size:26 final size:26
Alignment explanation
Indices: 704802--704880 Score: 94
Period size: 26 Copynumber: 3.2 Consensus size: 26
704792 AAATAATACT
704802 AATAATATAATATAATATAATATATA
1 AATAATATAATATAATATAATATATA
* ** *
704828 AATACTATAATACCATATACTATAT-
1 AATAATATAATATAATATAATATATA
704853 AAT-ATAT-ATATAATATAA-ATATA
1 AATAATATAATATAATATAATATATA
704876 AATAA
1 AATAA
704881 AGTCCCGGAC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
22 4 0.09
23 11 0.26
24 4 0.09
25 3 0.07
26 21 0.49
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (26 bp):
AATAATATAATATAATATAATATATA
Found at i:704831 original size:35 final size:34
Alignment explanation
Indices: 704765--704876 Score: 102
Period size: 35 Copynumber: 3.1 Consensus size: 34
704755 CAAACCAAAA
* * *
704765 ATAATATTATAATGTAATATAA-ATAAAAAATAAT
1 ATAATAATATAATATAATATAATAT-ATAAATAAT
*
704799 ACTAATAATATAATATAATATAATATATAAATACT
1 A-TAATAATATAATATAATATAATATATAAATAAT
704834 ATAATACCATATACTATATAATAT-ATATATAATATAAAT
1 ATAATA--ATATA--ATATAATATAATATATAA-AT-AAT
704873 ATAA
1 ATAA
704877 ATAAAGTCCC
Statistics
Matches: 65, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
34 6 0.09
35 27 0.42
36 7 0.11
37 8 0.12
38 11 0.17
39 6 0.09
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (34 bp):
ATAATAATATAATATAATATAATATATAAATAAT
Done.