Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007987.1 Hibiscus syriacus cultivar Beakdansim tig00110432_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: 872063
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:419414 original size:14 final size:14
Alignment explanation
Indices: 419395--419452 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
419385 ATGCGAAATG
*
419395 AAAATCGTAACGAC
1 AAAATCGCAACGAC
*
419409 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
419425 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
419441 AAAATCGCAACG
1 AAAATCGCAACG
419453 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:419439 original size:32 final size:33
Alignment explanation
Indices: 419379--419457 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
419369 GGAAATGGCT
* *
419379 ATCGCAATGCGAAATGAAAATCGTAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
419412 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
419444 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
419458 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:419505 original size:14 final size:14
Alignment explanation
Indices: 419486--419543 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
419476 TTTCATTTCG
419486 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
419500 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
419516 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
419532 CGTTGCGATTTT
1 CGTTGCGATTTT
419544 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:419550 original size:33 final size:33
Alignment explanation
Indices: 419469--419559 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
419459 ACAAATCGCA
*
419469 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
419502 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
419534 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
419560 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:419578 original size:20 final size:19
Alignment explanation
Indices: 419544--419598 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
419534 TTGCGATTTT
*
419544 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
419563 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
419583 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
419599 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:420096 original size:17 final size:18
Alignment explanation
Indices: 420071--420114 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
420061 GTCGATCAGA
*
420071 TGATGGCTCT-GGTGAGG
1 TGATGGCTCTGGGCGAGG
*
420088 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
420106 TGATGGCTC
1 TGATGGCTC
420115 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.14, C:0.16, G:0.43, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:421458 original size:20 final size:20
Alignment explanation
Indices: 421433--421470 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
421423 AATAGTTTCT
421433 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
421453 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
421471 GAGAGAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:421993 original size:20 final size:20
Alignment explanation
Indices: 421968--422020 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
421958 GATTATGTAT
*
421968 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
421988 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
422008 TATCTCGTTGCGA
1 TATCGCGTTGCGA
422021 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:422033 original size:41 final size:41
Alignment explanation
Indices: 421988--422065 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
421978 CGAAAGTCAG
* * *
421988 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* * *
422029 TATCGTATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
422066 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:422058 original size:20 final size:20
Alignment explanation
Indices: 421948--422062 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
421938 CGCTTTGAAA
*
421948 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
421969 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
421989 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
422009 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
*
422030 ATCGTATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
422050 ATCGCATTGCGAT
1 ATCGCATTGCGAT
422063 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 49 0.66
21 23 0.31
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:422083 original size:21 final size:21
Alignment explanation
Indices: 422051--422126 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
422041 ATAGTCAGTA
*
422051 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* * **
422072 TCGCGTTCCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
*
422092 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
422113 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
422127 ACTTATTCGC
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.16, C:0.26, G:0.17, T:0.41
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:422095 original size:20 final size:20
Alignment explanation
Indices: 422070--422143 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
422060 GATTTTCCCA
*
422070 ATTCGCGTTCCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* * **
422090 ATTCGCATTGCGATTTTCCCA
1 ATTCGCGTTGCGA-TTTACTT
422111 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
*
422131 ATTCGCATTGCGA
1 ATTCGCGTTGCGA
422144 ATTGGGAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:422096 original size:41 final size:41
Alignment explanation
Indices: 422051--422143 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
422041 ATAGTCAGTA
422051 TCGCATTGCGATTTTCCCAATTCGCGTTCCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTCCGATTTACTTAT
*
422092 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTCCGATTTACTTAT
422133 TCGCATTGCGA
1 TCGCATTGCGA
422144 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTCCGATTTACTTAT
Found at i:423079 original size:22 final size:23
Alignment explanation
Indices: 423036--423080 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
423026 AACACAGACC
* *
423036 TTAATTTGTTATTTTAATTAAAA
1 TTAATTTGTTATTTAAAATAAAA
423059 TTAATTT-TTATTTAAAATAAAA
1 TTAATTTGTTATTTAAAATAAAA
423081 AATATTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TTAATTTGTTATTTAAAATAAAA
Found at i:423081 original size:23 final size:22
Alignment explanation
Indices: 423036--423089 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
423026 AACACAGACC
* *
423036 TTAATTTGTTATTTTAATTAAAA
1 TTAATTT-TTATTTAAATAAAAA
423059 TTAATTTTTATTTAAAATAAAAA
1 TTAATTTTTATTT-AAATAAAAA
*
423082 AT-ATTTTT
1 TTAATTTTT
423090 GGGTGCCCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTAATTTTTATTTAAATAAAAA
Found at i:426582 original size:13 final size:13
Alignment explanation
Indices: 426559--426591 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
426549 AATGGCACCT
426559 TTTGT-ATTTGCA
1 TTTGTCATTTGCA
426571 TTTGTCATTTGCA
1 TTTGTCATTTGCA
426584 TTTG-CATT
1 TTTGTCATT
426592 ACATGTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (13 bp):
TTTGTCATTTGCA
Found at i:430838 original size:42 final size:41
Alignment explanation
Indices: 430791--430887 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 41
430781 ACAATTTAAG
* * *
430791 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATGAAA
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGAT-AAA
* * *
430833 TCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAG
1 TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
*
430874 TCATTCGGGCCATC
1 TCCTTCGGGCCATC
430888 CATAAGACCT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 14 0.30
42 33 0.70
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.29
Consensus pattern (41 bp):
TCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATGATAAA
Found at i:431068 original size:42 final size:42
Alignment explanation
Indices: 431006--431090 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
430996 ACTTAGTAAG
* * *
431006 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATAATGATTAAA
*
431048 TCCTTCAGGCCATCAGTAAGTCTTTCGAGCATAATGATTAAA
1 TCCTTCAGGCCATCAATAAGTCTTTCGAGCATAATGATTAAA
431090 T
1 T
431091 TCTTTGGGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (42 bp):
TCCTTCAGGCCATCAATAAGTCTTTCGAGCATAATGATTAAA
Found at i:431225 original size:42 final size:42
Alignment explanation
Indices: 431146--431673 Score: 189
Period size: 42 Copynumber: 12.6 Consensus size: 42
431136 CCCATCAGTA
* * *
431146 TCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTTTT
1 TCGAGCATGATGATGAAATCCTTCAGGCAATCAGTAAGTTTT
* * ** **
431188 TCGAGCATGATGATTAAATCCTTCAGGTAATTTGTAAG-CCT
1 TCGAGCATGATGATGAAATCCTTCAGGCAATCAGTAAGTTTT
* * * ** *
431229 TC-ACGGAAGA-GTAGTG-AAGCAAATC---CA-TCAGTAAGTCTT
1 TCGA-GCATGATG-A-TGAAATC-CTTCAGGCAATCAGTAAGTTTT
* * *
431268 TCGAGCATGATGATGAAATTCTTCAGGCCATCAGTAAGTCTT
1 TCGAGCATGATGATGAAATCCTTCAGGCAATCAGTAAGTTTT
* * * *
431310 TCGAGCATGATGCTTAAATCCTTCAGGCCATCAGTAAGTCTT
1 TCGAGCATGATGATGAAATCCTTCAGGCAATCAGTAAGTTTT
* * ** * ** **
431352 TCGAGCATGATGATTAAATTCTTTGGGTAATTTGTAAGCCTTCA
1 TCGAGCATGATGATGAAATCCTTCAGGCAATCAGTAAG--TTTT
* * * * * *
431396 CCGAAG-ATTAGTGAAGCAAACCCATCAGTAAGTGTC-ATCAGTAAGTCTT
1 TCG-AGCATGA-TGATG-AAATCC-T---TCAG-G-CAATCAGTAAGTTTT
* ** *
431445 TCGAGCATGATGATGAAGTCCTTTGGGCCATCAGTAAGTTTT
1 TCGAGCATGATGATGAAATCCTTCAGGCAATCAGTAAGTTTT
* * ** * *
431487 TCGAGCATGATGATTAAATCCTTCAGGTAATTTGTAAGCCTTC
1 TCGAGCATGATGATGAAATCCTTCAGGCAATCAGTAAG-TTTT
* * * *
431530 ACG-GAAGTGTAGTGAAGCAAA----TC---C-ATCAGTAAGTCTT
1 TCGAGCA-TG-A-TGATG-AAATCCTTCAGGCAATCAGTAAGTTTT
* * * *
431567 TCGAGCATGATGATGAAATTCTTCAGGCCATTAGTAAGTCTT
1 TCGAGCATGATGATGAAATCCTTCAGGCAATCAGTAAGTTTT
* * *
431609 TCGAGCATGATGATTAAATCCTTCGGGCCATCAGTAAGTTTT
1 TCGAGCATGATGATGAAATCCTTCAGGCAATCAGTAAGTTTT
*
431651 TC-AGGCAAGATGAT-AAATCCTTC
1 TCGA-GCATGATGATGAAATCCTTC
431674 GGGTCATCCA
Statistics
Matches: 354, Mismatches: 92, Indels: 81
0.67 0.17 0.15
Matches are distributed among these distances:
34 3 0.01
35 4 0.01
36 1 0.00
37 5 0.01
38 21 0.06
39 12 0.03
40 4 0.01
41 24 0.07
42 222 0.63
43 8 0.02
44 7 0.02
45 8 0.02
46 8 0.02
47 5 0.01
48 6 0.02
49 6 0.02
50 2 0.01
51 8 0.02
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (42 bp):
TCGAGCATGATGATGAAATCCTTCAGGCAATCAGTAAGTTTT
Found at i:431238 original size:116 final size:118
Alignment explanation
Indices: 431029--431336 Score: 449
Period size: 116 Copynumber: 2.6 Consensus size: 118
431019 CAATAAGTCT
* * * *
431029 TTCGAGCATGATGCTTAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGCATAATGATTAAATTCT
1 TTCGAGCATGATGATGAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCT
**
431094 TTGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAACCCATCAGT-A
66 TCAGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAACCCATCAGTAA
* * *
431146 -TCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTTTTTCGAGCATGATGATTAAATCCT
1 TTCGAGCATGATGATGAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCT
* *
431210 TCAGGTAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCCATCAGTAA
66 TCAGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAACCCATCAGTAA
* *
431263 GTCTTTCGAGCATGATGATGAAATTCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAA
1 ----TTCGAGCATGATGATGAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
431328 TCCTTCAGG
62 TCCTTCAGG
431337 CCATCAGTAA
Statistics
Matches: 169, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
116 104 0.62
117 1 0.01
122 64 0.38
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (118 bp):
TTCGAGCATGATGATGAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCT
TCAGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAACCCATCAGTAA
Found at i:431357 original size:164 final size:167
Alignment explanation
Indices: 431146--431513 Score: 490
Period size: 164 Copynumber: 2.2 Consensus size: 167
431136 CCCATCAGTA
* * * *
431146 TCGAGCATGATGATGAAGTCCTTCGGGCCATCAGTAAGTTTTTCGAGCATGATGATTAAATCCTT
1 TCGAGCATGATGATTAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
*
431211 CAGGTAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGC-AA-ATC-CATCAGTAAGTCTTTCGAG
66 CAGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAACATCACATCAGTAAGTCTTTCGAG
*
431273 CATGATGATGAAATTCTTCAGGCCATCAGTAAGTCTT
131 CATGATGATGAAATCCTTCAGGCCATCAGTAAGTCTT
* *
431310 TCGAGCATGATGCTTAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATTCTT
1 TCGAGCATGATGATTAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
** *
431375 TGGGTAATTTGTAAGCCTTCACCGAAGATTAGTGAAGCAAACCCATCAGTAAGTGTCATCAGTAA
66 CAGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAA--CATC----A----CATCAGTAA
* ** *
431440 GTCTTTCGAGCATGATGATGAAGTCCTTTGGGCCATCAGTAAGTTTT
121 GTCTTTCGAGCATGATGATGAAATCCTTCAGGCCATCAGTAAGTCTT
431487 TCGAGCATGATGATTAAATCCTTCAGG
1 TCGAGCATGATGATTAAATCCTTCAGG
431514 TAATTTGTAA
Statistics
Matches: 175, Mismatches: 16, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
164 93 0.53
165 2 0.01
168 3 0.02
177 77 0.44
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (167 bp):
TCGAGCATGATGATTAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
CAGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAGCAAACATCACATCAGTAAGTCTTTCGAG
CATGATGATGAAATCCTTCAGGCCATCAGTAAGTCTT
Found at i:431421 original size:122 final size:124
Alignment explanation
Indices: 431295--431632 Score: 430
Period size: 135 Copynumber: 2.7 Consensus size: 124
431285 ATTCTTCAGG
* *
431295 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGCAT
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGCAT
* **
431360 GATGATTAAATTCTTTGGGTAATTTGTAAGCCTTCACCGAAGAT-TAGTGAAGCAAACCCA
66 GATGATTAAATCCTTCAGGTAATTTGTAAGCCTTCACCGAAG-TGTAGTGAAGCAAA-CCA
* ** *
431420 TCAGTAAGTGTCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTTGGGCCATCAGTAAGTT
1 -C---------CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCAGGCCATCAGTAAGTC
*
431485 TTTCGAGCATGATGATTAAATCCTTCAGGTAATTTGTAAGCCTTCACGGAAGTGTAGTGAAGCAA
56 TTTCGAGCATGATGATTAAATCCTTCAGGTAATTTGTAAGCCTTCACCGAAGTGTAGTGAAGCAA
*
431550 A--T
121 ACCA
* *
431552 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATTCTTCAGGCCATTAGTAAGTCTTTCGAGCAT
1 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGCAT
431617 GATGATTAAATCCTTC
66 GATGATTAAATCCTTC
431633 GGGCCATCAG
Statistics
Matches: 185, Mismatches: 17, Indels: 24
0.82 0.08 0.11
Matches are distributed among these distances:
122 74 0.40
126 1 0.01
131 1 0.01
134 1 0.01
135 108 0.58
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.32
Consensus pattern (124 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGCAT
GATGATTAAATCCTTCAGGTAATTTGTAAGCCTTCACCGAAGTGTAGTGAAGCAAACCA
Found at i:432200 original size:53 final size:53
Alignment explanation
Indices: 432115--432261 Score: 195
Period size: 53 Copynumber: 2.8 Consensus size: 53
432105 TAATCACACA
*
432115 AGAAGATTGTTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCAAACCCATAGAC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCAAACCCATAGAC
* * ** ** *
432168 AGAAAATTGTTCGAGTTCTACTCCCTGAAGCAAAAGGGAGTGAACCTGTAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCAAACCCATAGAC
* * *
432221 AGAAGATTGTTCGAGTTCTACTTCTTGAAGCAAGAAGGAGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGC
432262 GAACTCGCTG
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 80 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.22
Consensus pattern (53 bp):
AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCAAACCCATAGAC
Found at i:432279 original size:53 final size:52
Alignment explanation
Indices: 432115--432285 Score: 179
Period size: 53 Copynumber: 3.2 Consensus size: 52
432105 TAATCACACA
* * * *
432115 AGAAGATTGTTCAAGTTCTACTCCCTGAAGCAAGAGGGAGCAAACC-CATAGAC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAAGGAGCGAACCGC-T-GGC
* *
432168 AGAAAATTGTTCGAGTTCTACTCCCTGAAGCAA-AAGGGAGTGAACCTG-TAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAA-GGAGCGAACC-GCT-GGC
* *
432221 AGAAGATTGTTCGAGTTCTACTTCTTGAAGCAAGAAGGAGCGAACTCGCTGGTC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAAGGAGCGAAC-CGCTGG-C
432275 -GAAGATTGTTC
1 AGAAGATTGTTC
432286 AAAGAAGAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
52 1 0.01
53 95 0.94
54 5 0.05
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (52 bp):
AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAAGGAGCGAACCGCTGGC
Found at i:434927 original size:16 final size:16
Alignment explanation
Indices: 434892--434930 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
434882 CACTTCGATT
*
434892 TAAAATTTTGAATATT
1 TAAAATTTTGAATATC
* *
434908 TAAAATTTTGTATCTC
1 TAAAATTTTGAATATC
434924 TAAAATT
1 TAAAATT
434931 ATGATCAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (16 bp):
TAAAATTTTGAATATC
Found at i:435747 original size:2 final size:2
Alignment explanation
Indices: 435740--435769 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
435730 GTGTAATTTA
435740 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
435770 TAAAAGGAAC
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:439173 original size:185 final size:185
Alignment explanation
Indices: 438940--439329 Score: 615
Period size: 185 Copynumber: 2.1 Consensus size: 185
438930 TTTTCTAATT
* * * *
438940 TATATAA-AAATTAAATGTTTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
* *
439004 TTATAAAATAAAAATTTTAGATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
66 TTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
*
439069 TGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTG-GACTTAACCCATATGTTA
131 TGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGAG-CTGAACCCATATGTTA
439124 TATATAATATATTTAATATTTTTTAATT-AAAAAAACAGTTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAA-AGTTTACAATTAATTTAAATAATATATA
* * * *
439188 ATTATAAAATAAAAAATTTATATAATTTTTTTTATTAATTAATATTGATTTAAGTTTAAAATTTA
65 ATTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
* *
439253 TTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGAGCTGAGCTCATATGTTA
130 TTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGAGCTGAACCCATATGTTA
*
439309 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
439330 AAAATTTAAT
Statistics
Matches: 189, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
184 14 0.07
185 174 0.92
186 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (185 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
TTATAAAATAAAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
TGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGAGCTGAACCCATATGTTA
Found at i:443376 original size:42 final size:42
Alignment explanation
Indices: 443323--443567 Score: 190
Period size: 42 Copynumber: 5.9 Consensus size: 42
443313 CGCAATAAAG
* *
443323 TAGTACTTTAGTGGCGTTTGTGCTTAAAATGCCACTAAAGTAC
1 TAGT-CTTTAGTGGCGTTTATGCTTAAAACGCCACTAAAGTAC
* * * *
443366 TAGTCTTTAGTGGCGTTTTTG--TACAAACGTCGCTAAA--AA
1 TAGTCTTTAGTGGCGTTTATGCTTA-AAACGCCACTAAAGTAC
*
443405 TAGTACTTTAGTGGCGTTTTAAGC--ACAAACGCCACTAAAGTAC
1 TAGT-CTTTAGTGGCG-TTTATGCTTA-AAACGCCACTAAAGTAC
* * * *
443448 TA--CTTTATTGTGGCATTTGTGCCTAAAACGCCACTACAGTAC
1 TAGTCTTTA--GTGGCGTTTATGCTTAAAACGCCACTAAAGTAC
* * *
443490 GT-GTCTTTAGCGGCGTTTATCCTTAAAACGCCACTGAAGTA-
1 -TAGTCTTTAGTGGCGTTTATGCTTAAAACGCCACTAAAGTAC
*
443531 TGAGT-TTTAGCGGCGTTTATGCTT-AAACGCCACTAAA
1 T-AGTCTTTAGTGGCGTTTATGCTTAAAACGCCACTAAA
443568 CTAGCGTGAT
Statistics
Matches: 164, Mismatches: 23, Indels: 33
0.75 0.10 0.15
Matches are distributed among these distances:
39 5 0.03
40 31 0.19
41 50 0.30
42 64 0.39
43 9 0.05
44 5 0.03
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (42 bp):
TAGTCTTTAGTGGCGTTTATGCTTAAAACGCCACTAAAGTAC
Found at i:443439 original size:82 final size:80
Alignment explanation
Indices: 443219--443449 Score: 208
Period size: 82 Copynumber: 2.9 Consensus size: 80
443209 TAGAGGCATT
*** * * *
443219 TTTTTTAACAAACGCCATTATAGAGTAGTACTTTAGTGG-GTTTTAAGCATAAACGACGCTAAA-
1 TTTTTT-ACAAACGCCGCAATAAAGTAGTACTTTAGTGGCGTTTTAAGCA-AAACGCCACTAAAG
*
443282 -ACTCATATTTTAGTGCA
64 TACT-ATACTTTAGTGCA
* *
443299 TTTTTTATAAACGCCGCAATAAAGTAGTACTTTAGTGGCGTTTGT--GCTTAAAATGCCACTAAA
1 TTTTTTACAAACGCCGCAATAAAGTAGTACTTTAGTGGCGTTT-TAAGC--AAAACGCCACTAAA
*
443362 GTACTAGT-CTTTAGTGGCG
63 GTACTA-TACTTTAGT-GCA
*
443381 TTTTTGTACAAACGTCGCTAA-AAA-TAGTACTTTAGTGGCGTTTTAAGCACAAACGCCACTAAA
1 TTTTT-TACAAACGCCGC-AATAAAGTAGTACTTTAGTGGCGTTTTAAGCA-AAACGCCACTAAA
443444 GTACTA
63 GTACTA
443450 CTTTATTGTG
Statistics
Matches: 125, Mismatches: 13, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
79 29 0.23
80 20 0.16
81 11 0.09
82 48 0.38
83 15 0.12
84 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (80 bp):
TTTTTTACAAACGCCGCAATAAAGTAGTACTTTAGTGGCGTTTTAAGCAAAACGCCACTAAAGTA
CTATACTTTAGTGCA
Found at i:446966 original size:43 final size:43
Alignment explanation
Indices: 446904--447009 Score: 135
Period size: 43 Copynumber: 2.5 Consensus size: 43
446894 AATTAGTGGA
* **
446904 GTTTGTT-CAAAAACACCGCTACAGATATCGACCTTTTGCGAC
1 GTTTGTTCCAAAAACGCCGCTACAGATATCGACCACTTGCGAC
* * *
446946 GTTTGTTCCAAAAATGCCGCTATAGATATTGACCACTTGCGAC
1 GTTTGTTCCAAAAACGCCGCTACAGATATCGACCACTTGCGAC
*
446989 GTTTATTCC-AAAACGCCGCTA
1 GTTTGTTCCAAAAACGCCGCTA
447010 AATATAAACA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 18 0.33
43 37 0.67
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (43 bp):
GTTTGTTCCAAAAACGCCGCTACAGATATCGACCACTTGCGAC
Found at i:447851 original size:9 final size:9
Alignment explanation
Indices: 447839--447890 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
447829 TAATATTTTG
447839 TATTTAATT
1 TATTTAATT
*
447848 TATTTAA-A
1 TATTTAATT
447856 TATTTAATT
1 TATTTAATT
447865 TATTTAA--
1 TATTTAATT
*
447872 TATTTTATT
1 TATTTAATT
*
447881 TAATTAATT
1 TATTTAATT
447890 T
1 T
447891 TTTTTGCAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:447861 original size:17 final size:17
Alignment explanation
Indices: 447839--447887 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
447829 TAATATTTTG
447839 TATTTAATTTATTTAAA
1 TATTTAATTTATTTAAA
447856 TATTTAATTTATTT-AA
1 TATTTAATTTATTTAAA
* *
447872 TATTTTATTTAATTAA
1 TATTTAATTTATTTAA
447888 TTTTTTTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 14 0.48
17 15 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTAATTTATTTAAA
Found at i:447875 original size:16 final size:16
Alignment explanation
Indices: 447839--447888 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
447829 TAATATTTTG
447839 TATTTAATTTATTTAAA
1 TATTTAATTTATTT-AA
447856 TATTTAATTTATTTAA
1 TATTTAATTTATTTAA
* *
447872 TATTTTATTTAATTAA
1 TATTTAATTTATTTAA
447888 T
1 T
447889 TTTTTTTGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTAATTTATTTAA
Found at i:450150 original size:27 final size:27
Alignment explanation
Indices: 450093--450151 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
450083 ATAGATTTTG
* * *
450093 TTTTTTTATTATATTTGTATTTAGTAT
1 TTTTTTTATTATAGTTGTATTTAGGAC
* * *
450120 TTTTTTTATTGTAGTTGTTTTTTGGAC
1 TTTTTTTATTATAGTTGTATTTAGGAC
450147 TTTTT
1 TTTTT
450152 ATTGTAATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.15, C:0.02, G:0.12, T:0.71
Consensus pattern (27 bp):
TTTTTTTATTATAGTTGTATTTAGGAC
Found at i:450939 original size:18 final size:18
Alignment explanation
Indices: 450903--450940 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
450893 TCTTAAACTA
*
450903 TTTTTATATTTAATTATT
1 TTTTTATATTTAATAATT
450921 TTTTTATAATTTAA-AATT
1 TTTTTAT-ATTTAATAATT
450939 TT
1 TT
450941 ATTAATTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTATATTTAATAATT
Found at i:451059 original size:18 final size:18
Alignment explanation
Indices: 451036--451070 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
451026 TTACAAGATA
451036 TTTTTAAAATTTTATTAC
1 TTTTTAAAATTTTATTAC
* *
451054 TTTTTAGATTTTTATTA
1 TTTTTAAAATTTTATTA
451071 AAAAATTTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTTAAAATTTTATTAC
Found at i:451458 original size:31 final size:31
Alignment explanation
Indices: 451420--451486 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
451410 TATTTAGTCT
*
451420 GTTTGCAATATGGTCCCCGACGTAACTGGCC
1 GTTTGCAATATGGTCCCCGACGTAACCGGCC
451451 GTTTGCAATATGGTCCCCGACGTAACCGGCC
1 GTTTGCAATATGGTCCCCGACGTAACCGGCC
*
451482 TTTTG
1 GTTTG
451487 ATGTCGTTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.18, C:0.28, G:0.25, T:0.28
Consensus pattern (31 bp):
GTTTGCAATATGGTCCCCGACGTAACCGGCC
Found at i:454237 original size:20 final size:20
Alignment explanation
Indices: 454203--454294 Score: 103
Period size: 20 Copynumber: 4.5 Consensus size: 20
454193 ACTCAGTTTT
454203 GAAATTCGCAACGCGAATATG
1 GAAA-TCGCAACGCGAATATG
*
454224 GAAATCGTAACGCGAATATG
1 GAAATCGCAACGCGAATATG
* *
454244 TAATTCGCAACGCGAATATG
1 GAAATCGCAACGCGAATATG
* * * *
454264 TAATTCACAACGCGAATTTG
1 GAAATCGCAACGCGAATATG
*
454284 TAAATCGCAAC
1 GAAATCGCAAC
454295 ACATAAGTCA
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
20 59 0.94
21 4 0.06
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
GAAATCGCAACGCGAATATG
Found at i:454249 original size:40 final size:40
Alignment explanation
Indices: 454205--454294 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 40
454195 TCAGTTTTGA
**
454205 AATTCGCAACGCGAATATGGAAATCGTAACGCGAATATGT
1 AATTCGCAACGCGAATATGGAAATCACAACGCGAATATGT
* * *
454245 AATTCGCAACGCGAATATGTAATTCACAACGCGAATTTGT
1 AATTCGCAACGCGAATATGGAAATCACAACGCGAATATGT
*
454285 AAATCGCAAC
1 AATTCGCAAC
454295 ACATAAGTCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (40 bp):
AATTCGCAACGCGAATATGGAAATCACAACGCGAATATGT
Found at i:454488 original size:22 final size:22
Alignment explanation
Indices: 454463--454505 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
454453 CTCTCTAAAA
*
454463 CGACATCCGTCCCCATCTCCGG
1 CGACATCCGTCCCCATATCCGG
454485 CGACATCCGTCCCCATATCCG
1 CGACATCCGTCCCCATATCCG
454506 ATGACCCCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.16, C:0.49, G:0.16, T:0.19
Consensus pattern (22 bp):
CGACATCCGTCCCCATATCCGG
Found at i:454865 original size:20 final size:20
Alignment explanation
Indices: 454837--454882 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
454827 AATAGTTTTT
* *
454837 GAAACTTAAATTCGCGACAC
1 GAAAATTAAATTCGCAACAC
454857 GAAAATTAAATTCGCAACAC
1 GAAAATTAAATTCGCAACAC
*
454877 AAAAAT
1 GAAAAT
454883 CGCAACGCGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.20, G:0.11, T:0.20
Consensus pattern (20 bp):
GAAAATTAAATTCGCAACAC
Found at i:454924 original size:20 final size:20
Alignment explanation
Indices: 454899--454949 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
454889 GCGAATTTAG
454899 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
454919 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
454939 TTTCGTGTTGC
1 TTTCGCGTTGC
454950 AAATTTAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.08, C:0.20, G:0.22, T:0.51
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:456526 original size:42 final size:42
Alignment explanation
Indices: 456433--456530 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
456423 CCTCTACTTT
* * * *
456433 GAGAGCCATCACCTGATCGAGCCGATTCTACAGCTCGACACC
1 GAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAAC
* * *
456475 CAAAGCCATCACCTGATTGAGCCGATTATACACCTCCACAAC
1 GAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAAC
*
456517 GAGATCCATCACCT
1 GAGAGCCATCACCT
456531 ATTCTATCAT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.30, C:0.36, G:0.16, T:0.18
Consensus pattern (42 bp):
GAGAGCCATCACCTGATCGAGCCGATTATACACCTCCACAAC
Found at i:456688 original size:21 final size:21
Alignment explanation
Indices: 456645--456694 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
456635 GTTAGGGGAG
* *
456645 TTACGTGATGAGGTCATTGCT
1 TTACGTGATGAGGTCAGTACT
*
456666 TTGCGTGATGAGGTCAGTACT
1 TTACGTGATGAGGTCAGTACT
456687 TTACGTGA
1 TTACGTGA
456695 CAACAATAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.14, G:0.30, T:0.36
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:456735 original size:21 final size:20
Alignment explanation
Indices: 456711--456760 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
456701 TAGTGCATGG
456711 CGTGATGAGGTACG-GTCTTTA
1 CGTGATGAGGTA-GAGT-TTTA
*
456732 CGTGGTGAGGTAGATGTTTTA
1 CGTGATGAGGTAGA-GTTTTA
456753 CGTGATGA
1 CGTGATGA
456761 CAATGGTGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.04
21 22 0.88
22 2 0.08
ACGTcount: A:0.20, C:0.10, G:0.36, T:0.34
Consensus pattern (20 bp):
CGTGATGAGGTAGAGTTTTA
Found at i:456757 original size:42 final size:43
Alignment explanation
Indices: 456711--456806 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 43
456701 TAGTGCATGG
* **
456711 CGTGATGAGGTACGGT-CTTTACGTGGTGAGGTAGATGTTTTA
1 CGTGATGAGGTACGGTGCTTTACGTGGTGAGGCAGATACTTTA
** * **
456753 CGTGATGA-CAATGGTGCTTTACGTGGTGAGGCATCTACTTTA
1 CGTGATGAGGTACGGTGCTTTACGTGGTGAGGCAGATACTTTA
456795 CGTGATGAGGTA
1 CGTGATGAGGTA
456807 ACCGCTCTAT
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
41 4 0.10
42 37 0.88
43 1 0.02
ACGTcount: A:0.21, C:0.12, G:0.33, T:0.33
Consensus pattern (43 bp):
CGTGATGAGGTACGGTGCTTTACGTGGTGAGGCAGATACTTTA
Found at i:457133 original size:21 final size:21
Alignment explanation
Indices: 457102--457220 Score: 150
Period size: 21 Copynumber: 5.7 Consensus size: 21
457092 GATTCACCTT
*
457102 TCATCGTTCAAGAGACCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
457123 -CTATTGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* *
457144 TCATTGTTCAAAAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
457165 TCATCATTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
*
457186 TCATCATTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
457207 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
457221 CCTGATTCAC
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
20 1 0.01
21 85 0.98
22 1 0.01
ACGTcount: A:0.24, C:0.36, G:0.16, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:458626 original size:16 final size:16
Alignment explanation
Indices: 458602--458632 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
458592 AAGAATTATT
*
458602 ATTTTTTGTTTAATTG
1 ATTTGTTGTTTAATTG
458618 ATTTGTTGTTTAATT
1 ATTTGTTGTTTAATT
458633 TCAATCTGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.13, T:0.68
Consensus pattern (16 bp):
ATTTGTTGTTTAATTG
Found at i:458775 original size:29 final size:29
Alignment explanation
Indices: 458726--458785 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
458716 TTGCGTTGCA
** * *
458726 AATTTGACTTTCGCAATAATCGCAACGCG
1 AATTTGACTTTCAAAACAATCGCAACACG
458755 AATTTGACTTTCAAAACAATCGCAACACG
1 AATTTGACTTTCAAAACAATCGCAACACG
458784 AA
1 AA
458786 AATCACAACG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (29 bp):
AATTTGACTTTCAAAACAATCGCAACACG
Found at i:459046 original size:18 final size:18
Alignment explanation
Indices: 459023--459058 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
459013 AAGCCGGTTG
*
459023 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
459041 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
459059 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:461355 original size:24 final size:24
Alignment explanation
Indices: 461321--461374 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
461311 CTGAAACATC
461321 ATCAAAATCCGAG-TATTGACCAAG
1 ATCAAAATCCG-GTTATTGACCAAG
*
461345 ATCAAAGTCCGGTTATTGACCAAG
1 ATCAAAATCCGGTTATTGACCAAG
461369 ATCAAA
1 ATCAAA
461375 TTTCAAATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGGTTATTGACCAAG
Found at i:462133 original size:16 final size:16
Alignment explanation
Indices: 462111--462149 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
462101 GAAATCATTG
*
462111 AAAAATTATATAGAAA
1 AAAAATTATATAAAAA
* *
462127 TAAAATTATGTAAAAA
1 AAAAATTATATAAAAA
462143 AAAAATT
1 AAAAATT
462150 GAGACAGGGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
AAAAATTATATAAAAA
Found at i:462196 original size:22 final size:21
Alignment explanation
Indices: 462157--462197 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
462147 ATTGAGACAG
**
462157 GGAAGGATGTCGTTGGATATA
1 GGAAGGATGTCGCCGGATATA
462178 GGAATGGATGTCGCCGGATA
1 GGAA-GGATGTCGCCGGATA
462198 GAGTGATAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.27, C:0.10, G:0.39, T:0.24
Consensus pattern (21 bp):
GGAAGGATGTCGCCGGATATA
Found at i:462322 original size:20 final size:20
Alignment explanation
Indices: 462297--462425 Score: 88
Period size: 20 Copynumber: 6.5 Consensus size: 20
462287 AAATAAAAGA
462297 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
462317 TGTTGCG-AATTCGAAAA-TCG
1 TGTTGCGAAATT--AAAATTCG
* *
462337 AGTTGCGAAAATAAAATTCG
1 TGTTGCGAAATTAAAATTCG
* * *
462357 TGTTGCG-ATTTAGAAAATCT
1 TGTTGCGAAATTA-AAATTCG
** *
462377 TGTTGCGAAAAGGAAACTT-G
1 TGTTGCG-AAATTAAAATTCG
*
462397 TGTTGCGAAA-AAGAAATTCG
1 TGTTGCGAAATTA-AAATTCG
*
462417 CGTTGCGAA
1 TGTTGCGAA
462426 TTCAGAAATC
Statistics
Matches: 84, Mismatches: 16, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
18 1 0.01
19 18 0.21
20 53 0.63
21 10 0.12
22 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:462344 original size:40 final size:40
Alignment explanation
Indices: 462298--462425 Score: 141
Period size: 40 Copynumber: 3.2 Consensus size: 40
462288 AATAAAAGAT
* *
462298 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAAATAAAATTCGTGTTGCGAATTAGAAAATCGA
* **
462338 GTTGCGAAAATAAAATTCGTGTTGCGATTTAGAAAATCTT
1 GTTGCGAAAATAAAATTCGTGTTGCGAATTAGAAAATCGA
* * ** * *
462378 GTTGCGAAAAGGAAACTT-GTGTTGCGAAAAAGAAATTCGC
1 GTTGCGAAAA-TAAAATTCGTGTTGCGAATTAGAAAATCGA
462418 GTTGCGAA
1 GTTGCGAA
462426 TTCAGAAATC
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 69 0.93
41 5 0.07
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (40 bp):
GTTGCGAAAATAAAATTCGTGTTGCGAATTAGAAAATCGA
Found at i:462381 original size:60 final size:60
Alignment explanation
Indices: 462317--462466 Score: 142
Period size: 60 Copynumber: 2.5 Consensus size: 60
462307 TTAAAATTCG
* * *
462317 TGTTGCGAATTCGAAAATCGAGTTGCGAAAATA-AAATTCGTGTTGCG-ATTTAGAAAATCT
1 TGTTGCGAATTCGAAAATCGAGTTGCGAAAA-AGAAATTCGCGTTGCGAATTCAG-AAATCA
*** * * *
462377 TGTTGCGAAAAGGAAACTTGTGTTGCGAAAAAGAAATTCGCGTTGCGAATTCAGAAATCA
1 TGTTGCGAATTCGAAAATCGAGTTGCGAAAAAGAAATTCGCGTTGCGAATTCAGAAATCA
* * * *
462437 AGTTGCGAATTTGAAATTCCATGTTGCGAA
1 TGTTGCGAATTCGAAAATCGA-GTTGCGAA
462467 TTTGGAAATC
Statistics
Matches: 70, Mismatches: 17, Indels: 5
0.76 0.18 0.05
Matches are distributed among these distances:
59 1 0.01
60 56 0.80
61 13 0.19
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (60 bp):
TGTTGCGAATTCGAAAATCGAGTTGCGAAAAAGAAATTCGCGTTGCGAATTCAGAAATCA
Found at i:462484 original size:20 final size:20
Alignment explanation
Indices: 462298--462485 Score: 80
Period size: 20 Copynumber: 9.3 Consensus size: 20
462288 AATAAAAGAT
* * *
462298 GTTGCGAAATTAAAATTCGT
1 GTTGCGAATTTGAAATTCGC
* * *
462318 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGAAATTCGC
** * *
462338 GTTGCGAAAATAAAATTCGT
1 GTTGCGAATTTGAAATTCGC
* **
462358 GTTGCG-ATTTAGAAAATCTT
1 GTTGCGAATTT-GAAATTCGC
*** *
462378 GTTGCGAAAAGGAAACTT-GT
1 GTTGCGAATTTGAAA-TTCGC
***
462398 GTTGCGAAAAAGAAATTCGC
1 GTTGCGAATTTGAAATTCGC
* **
462418 GTTGCGAATTCAGAAA-TCAA
1 GTTGCGAATT-TGAAATTCGC
462438 GTTGCGAATTTGAAATTC-C
1 GTTGCGAATTTGAAATTCGC
462457 ATGTTGCGAATTTGGAAA-TCGC
1 --GTTGCGAATTT-GAAATTCGC
462479 GTTGCGA
1 GTTGCGA
462486 GAAAGAAATT
Statistics
Matches: 129, Mismatches: 29, Indels: 20
0.72 0.16 0.11
Matches are distributed among these distances:
19 8 0.06
20 96 0.74
21 20 0.16
22 5 0.04
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.30
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:462494 original size:41 final size:39
Alignment explanation
Indices: 462398--462505 Score: 94
Period size: 41 Copynumber: 2.7 Consensus size: 39
462388 GGAAACTTGT
462398 GTTGCGAAAAAGAAATTCGC-GTTGCGAATTCAGAAATCAA
1 GTTGCG-AAAAGAAATTC-CAGTTGCGAATTCAGAAATCAA
** ** **
462438 GTTGCGAATTTGAAATTCCATGTTGCGAATTTGGAAATCGC
1 GTTGCGAA-AAGAAATTCCA-GTTGCGAATTCAGAAATCAA
462479 GTTGCGAGAAAGAAATT-CACGTTGCGA
1 GTTGCGA-AAAGAAATTCCA-GTTGCGA
462506 GAAAGAAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
39 3 0.05
40 22 0.40
41 29 0.53
42 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (39 bp):
GTTGCGAAAAGAAATTCCAGTTGCGAATTCAGAAATCAA
Found at i:462501 original size:20 final size:20
Alignment explanation
Indices: 462478--462525 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
462468 TTGGAAATCG
462478 CGTTGCGAGAAAGAAATTCA
1 CGTTGCGAGAAAGAAATTCA
462498 CGTTGCGAGAAAGAAATTCA
1 CGTTGCGAGAAAGAAATTCA
462518 CGTTGCGA
1 CGTTGCGA
462526 TTGCAGAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (20 bp):
CGTTGCGAGAAAGAAATTCA
Found at i:462554 original size:20 final size:20
Alignment explanation
Indices: 462531--462571 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
462521 TGCGATTGCA
*
462531 GAAACTGAGTTGCGAATTTG
1 GAAACTGAGTTGCGAAATTG
*
462551 GAAACTGTGTTGCGAAATTG
1 GAAACTGAGTTGCGAAATTG
462571 G
1 G
462572 GGTTCGCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.10, G:0.32, T:0.29
Consensus pattern (20 bp):
GAAACTGAGTTGCGAAATTG
Found at i:467811 original size:18 final size:18
Alignment explanation
Indices: 467790--467824 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
467780 TATTTGTCTC
*
467790 GAATTACCACTATGTCCT
1 GAATGACCACTATGTCCT
467808 GAATGACCACTATGTCC
1 GAATGACCACTATGTCC
467825 CAAAGGATCA
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:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (18 bp):
GAATGACCACTATGTCCT
Found at i:470314 original size:50 final size:50
Alignment explanation
Indices: 470239--470338 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
470229 ATCCGAAACA
470239 ATAGAAACAGATACTCCATGTAGACGTATAATATCCCTGATATACAACTC
1 ATAGAAACAGATACTCCATGTAGACGTATAATATCCCTGATATACAACTC
*
470289 ATAGAAACAGATACTCCATGTAGACGTATAATATCCCTGATATATAACTC
1 ATAGAAACAGATACTCCATGTAGACGTATAATATCCCTGATATACAACTC
470339 GGCATACTTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (50 bp):
ATAGAAACAGATACTCCATGTAGACGTATAATATCCCTGATATACAACTC
Found at i:474787 original size:18 final size:18
Alignment explanation
Indices: 474766--474802 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
474756 GAATAACCAT
*
474766 TATGTCCCGAAGGAACAC
1 TATGTCCCAAAGGAACAC
*
474784 TATGTCCCAAAGGACCAC
1 TATGTCCCAAAGGAACAC
474802 T
1 T
474803 GATAATCCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (18 bp):
TATGTCCCAAAGGAACAC
Found at i:476397 original size:28 final size:28
Alignment explanation
Indices: 476366--476421 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
476356 GACTAATATT
*
476366 TAATTTTTAAAATCATAATAATTATTTA
1 TAATTTATAAAATCATAATAATTATTTA
* * *
476394 TAATTTATAATATTATAATATTTATTTA
1 TAATTTATAAAATCATAATAATTATTTA
476422 AAACTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (28 bp):
TAATTTATAAAATCATAATAATTATTTA
Found at i:479943 original size:21 final size:21
Alignment explanation
Indices: 479917--479956 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
479907 CCGAAGTACC
*
479917 ACATATATGTTCCAAAGGATT
1 ACATATATGTCCCAAAGGATT
*
479938 ACATATATGTCCCGAAGGA
1 ACATATATGTCCCAAAGGA
479957 CCACGTAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
ACATATATGTCCCAAAGGATT
Found at i:483078 original size:30 final size:30
Alignment explanation
Indices: 483037--483101 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
483027 ATGAGCAAAA
* *
483037 ATGACTTCTTTCATTTTATCCTCGTAGGTG
1 ATGACTTCTTTCATTTTATACTCATAGGTG
*
483067 ATGATTTCTTTCATTTTATACTCATAGGTG
1 ATGACTTCTTTCATTTTATACTCATAGGTG
483097 ATGAC
1 ATGAC
483102 ACATAACATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (30 bp):
ATGACTTCTTTCATTTTATACTCATAGGTG
Found at i:488970 original size:16 final size:16
Alignment explanation
Indices: 488949--488984 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
488939 TATTTGTACA
488949 TAAACTAAAA-TACTAT
1 TAAACTAAAATTA-TAT
488965 TAAACTAAAATTATAT
1 TAAACTAAAATTATAT
488981 TAAA
1 TAAA
488985 TATACAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 17 0.89
17 2 0.11
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAACTAAAATTATAT
Found at i:489400 original size:22 final size:21
Alignment explanation
Indices: 489372--489417 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
489362 TCGGAAATGT
*
489372 TAAAAAATATTAACATTTTAGG
1 TAAAAAA-AATAACATTTTAGG
*
489394 TAAAAAAAATAATATTTTAGG
1 TAAAAAAAATAACATTTTAGG
489415 TAA
1 TAA
489418 TTTTTTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.54, C:0.02, G:0.09, T:0.35
Consensus pattern (21 bp):
TAAAAAAAATAACATTTTAGG
Found at i:490412 original size:21 final size:21
Alignment explanation
Indices: 490386--490425 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
490376 TAATATTTAA
490386 ATATAATAAAATTCGAAATTG
1 ATATAATAAAATTCGAAATTG
* *
490407 ATATAATAAGATTCTAAAT
1 ATATAATAAAATTCGAAAT
490426 CTTAATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (21 bp):
ATATAATAAAATTCGAAATTG
Found at i:490728 original size:2 final size:2
Alignment explanation
Indices: 490721--490746 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
490711 TGTTAAGATA
490721 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
490747 CATAAAGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:493003 original size:90 final size:89
Alignment explanation
Indices: 492829--493006 Score: 241
Period size: 90 Copynumber: 2.0 Consensus size: 89
492819 CTGTAAAAAT
* * * *
492829 TTGGAGATCTTTTCTTTTTGGGAATGGCAGGGAAGATTTGGGATGTTTTAGTCAATAATAAGATA
1 TTGGAGATCTTTTCTTTTGGGGAATGACAGGGAAGATTTGGGATATTTTAGTCAATAATAAGAAA
* * **
492894 TTGTTGTTTAAAGTATCTCTAATC
66 CTGCTGCGTAAAGTATCTCTAATC
492918 TTGGAGATCTTTTTCTTTTGGGGAATGACAGGGACA-ATTTGGGATATTTTAGTCAATAATAAGA
1 TTGGAGATC-TTTTCTTTTGGGGAATGACAGGGA-AGATTTGGGATATTTTAGTCAATAATAAGA
* *
492982 AACTGCTGCGTGAAGTTTCTCTAAT
64 AACTGCTGCGTAAAGTATCTCTAAT
493007 TTGAAGAGTC
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
89 9 0.12
90 67 0.87
91 1 0.01
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.39
Consensus pattern (89 bp):
TTGGAGATCTTTTCTTTTGGGGAATGACAGGGAAGATTTGGGATATTTTAGTCAATAATAAGAAA
CTGCTGCGTAAAGTATCTCTAATC
Found at i:495460 original size:3 final size:3
Alignment explanation
Indices: 495452--495477 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
495442 GAATTGGGTT
495452 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
495478 CTTTCCTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:534466 original size:9 final size:9
Alignment explanation
Indices: 534452--534496 Score: 72
Period size: 9 Copynumber: 5.0 Consensus size: 9
534442 GGCCACCCAT
534452 GCCCATGCC
1 GCCCATGCC
534461 GCCCATGCC
1 GCCCATGCC
534470 GCCCATGCC
1 GCCCATGCC
* *
534479 ACCCATACC
1 GCCCATGCC
534488 GCCCATGCC
1 GCCCATGCC
534497 CTCAAACAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.16, C:0.56, G:0.18, T:0.11
Consensus pattern (9 bp):
GCCCATGCC
Found at i:550532 original size:20 final size:21
Alignment explanation
Indices: 550494--550536 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
550484 TTATTTTTAT
550494 ATGTTTTAATTATAAAATAAA
1 ATGTTTTAATTATAAAATAAA
550515 ATGTTTT-ATTA-AATAATAAA
1 ATGTTTTAATTATAA-AATAAA
550535 AT
1 AT
550537 ATAAATGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.10
20 12 0.57
21 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
ATGTTTTAATTATAAAATAAA
Found at i:557320 original size:7 final size:7
Alignment explanation
Indices: 557310--557341 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
557300 TAATGATTAA
557310 TGCTTAT
1 TGCTTAT
557317 TGCTTAT
1 TGCTTAT
557324 TGCTTAT
1 TGCTTAT
*
557331 TGCTTAA
1 TGCTTAT
557338 TGCT
1 TGCT
557342 GAAGGGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (7 bp):
TGCTTAT
Found at i:557329 original size:14 final size:14
Alignment explanation
Indices: 557306--557341 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
557296 ATAATAATGA
557306 TTAATGCTTATTGC
1 TTAATGCTTATTGC
*
557320 TTATTGCTTATTGC
1 TTAATGCTTATTGC
557334 TTAATGCT
1 TTAATGCT
557342 GAAGGGAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.53
Consensus pattern (14 bp):
TTAATGCTTATTGC
Found at i:559225 original size:2 final size:2
Alignment explanation
Indices: 559218--559259 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
559208 AACTGAAATA
559218 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
559260 CTGAATTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:565479 original size:98 final size:98
Alignment explanation
Indices: 565364--565559 Score: 392
Period size: 98 Copynumber: 2.0 Consensus size: 98
565354 TTGACGGCGT
565364 AAATGTGATTTTATTTTTTTAGTAAGTTCCATTTTCCTAATTTTAGAGATGAAAATCAAATTGAT
1 AAATGTGATTTTATTTTTTTAGTAAGTTCCATTTTCCTAATTTTAGAGATGAAAATCAAATTGAT
565429 CAAGAGAACTTCAAAATATCAGAATTAGTGAAC
66 CAAGAGAACTTCAAAATATCAGAATTAGTGAAC
565462 AAATGTGATTTTATTTTTTTAGTAAGTTCCATTTTCCTAATTTTAGAGATGAAAATCAAATTGAT
1 AAATGTGATTTTATTTTTTTAGTAAGTTCCATTTTCCTAATTTTAGAGATGAAAATCAAATTGAT
565527 CAAGAGAACTTCAAAATATCAGAATTAGTGAAC
66 CAAGAGAACTTCAAAATATCAGAATTAGTGAAC
565560 GCAGGTAATA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (98 bp):
AAATGTGATTTTATTTTTTTAGTAAGTTCCATTTTCCTAATTTTAGAGATGAAAATCAAATTGAT
CAAGAGAACTTCAAAATATCAGAATTAGTGAAC
Found at i:572452 original size:20 final size:20
Alignment explanation
Indices: 572427--572464 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
572417 CATATGTTAA
572427 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
*
572447 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
572465 TCAAAGGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:573306 original size:23 final size:23
Alignment explanation
Indices: 573276--573327 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
573266 TAAGATAAGT
573276 TATATGCTAAAGATTTATGGAGC
1 TATATGCTAAAGATTTATGGAGC
573299 TATATGCTAAAGATTTATGGAGC
1 TATATGCTAAAGATTTATGGAGC
573322 TATATG
1 TATATG
573328 AAAAGGTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.37
Consensus pattern (23 bp):
TATATGCTAAAGATTTATGGAGC
Found at i:574059 original size:23 final size:23
Alignment explanation
Indices: 573991--574051 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
573981 ACATTTTATA
573991 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
** *
574014 CAGCACTTCGGTGAAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
574037 TGGCAGTTCGGTGCA
1 TGGCACTTCGGTGCA
574052 TTTATACGAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:581805 original size:18 final size:18
Alignment explanation
Indices: 581779--581830 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
581769 AAGATTGGGT
*
581779 AGTGATCCAGCATGGGGC
1 AGTGGTCCAGCATGGGGC
*
581797 AGTGGTCCAACATGGGGC
1 AGTGGTCCAGCATGGGGC
581815 AGTGGTCCAGCATGGG
1 AGTGGTCCAGCATGGG
581831 CATCTAGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.21, C:0.21, G:0.40, T:0.17
Consensus pattern (18 bp):
AGTGGTCCAGCATGGGGC
Found at i:581906 original size:9 final size:10
Alignment explanation
Indices: 581878--581916 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
581868 ACCTGACATC
581878 TGCAGCATGG
1 TGCAGCATGG
*
581888 TCCAGCATGG
1 TGCAGCATGG
*
581898 -GCGGCATGG
1 TGCAGCATGG
581907 TGCAGCATGG
1 TGCAGCATGG
581917 CCTGTGCAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.18, C:0.23, G:0.41, T:0.18
Consensus pattern (10 bp):
TGCAGCATGG
Found at i:582208 original size:20 final size:20
Alignment explanation
Indices: 582171--582213 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
582161 ATTCCACCAC
* *
582171 ATGCAACTATATGTTCCTAA
1 ATGCAACTACATGGTCCTAA
*
582191 ATGCATCTACATGGTCCTAA
1 ATGCAACTACATGGTCCTAA
582211 ATG
1 ATG
582214 AGATCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTACATGGTCCTAA
Found at i:589800 original size:41 final size:41
Alignment explanation
Indices: 589755--589852 Score: 135
Period size: 41 Copynumber: 2.4 Consensus size: 41
589745 GCGAATTGGG
*
589755 AAAATCGCAATACGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAATACGATACTGACTATCGCAACGCGATAATAC
* *
589796 AAAATCGCAACGA-GATACTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAA-TACGATACTGACTATCGCAACGCGATAATAC
* *
589837 ATAATCGCAATGCGAT
1 AAAATCGCAATACGAT
589853 TTTCAAAGCG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
41 48 0.98
42 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.21
Consensus pattern (41 bp):
AAAATCGCAATACGATACTGACTATCGCAACGCGATAATAC
Found at i:589804 original size:21 final size:20
Alignment explanation
Indices: 589778--589852 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
589768 GATACTGACT
*
589778 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATAATAC-AA
* * *
589799 ATCGCAACGAGATACTGAC-T
1 ATCGCAACGCGATAAT-ACAA
*
589819 TTCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACA-A
*
589840 ATCGCAATGCGAT
1 ATCGCAACGCGAT
589853 TTTCAAAGCG
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.32
21 24 0.59
22 2 0.05
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGATAATACAA
Found at i:589926 original size:17 final size:17
Alignment explanation
Indices: 589904--589940 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
589894 TAAATTCCAA
589904 ACATAAAACCAAAAATC
1 ACATAAAACCAAAAATC
*
589921 ACATAAAACCTAAAATC
1 ACATAAAACCAAAAATC
589938 ACA
1 ACA
589941 ACTCAGCCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.62, C:0.24, G:0.00, T:0.14
Consensus pattern (17 bp):
ACATAAAACCAAAAATC
Found at i:590002 original size:22 final size:22
Alignment explanation
Indices: 589974--590017 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
589964 ACTCTCTCAC
589974 CCATCTCCGACGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
*
589996 CCATCTCCGGCGAAATCCGTCT
1 CCATCTCCGACGAAATCCGTCT
590018 ATCTCCATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.41, G:0.16, T:0.23
Consensus pattern (22 bp):
CCATCTCCGACGAAATCCGTCT
Found at i:590300 original size:20 final size:20
Alignment explanation
Indices: 590241--590304 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
590231 GCGATTTTAG
*
590241 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
590261 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
590281 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
590301 TTTC
1 TTTC
590305 AGAAACTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:590495 original size:25 final size:24
Alignment explanation
Indices: 590441--590495 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
590431 TGTTTATTAT
* *
590441 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
590465 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
590491 TGTTT
1 TGTTT
590496 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:591646 original size:18 final size:18
Alignment explanation
Indices: 591625--591669 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
591615 TCCACTTCGG
*
591625 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
591643 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
591661 GAGCCATCA
1 GAGCCATCA
591670 TCTGAACGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:592164 original size:20 final size:20
Alignment explanation
Indices: 592139--592184 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
592129 TAGTTTACTT
592139 TCGCAACACGAAAAT-GACTA
1 TCGCAACACGAAAATGGA-TA
* *
592159 TCGCAACGCGGAAATGGATA
1 TCGCAACACGAAAATGGATA
592179 TCGCAA
1 TCGCAA
592185 TGCGAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGGATA
Found at i:592193 original size:19 final size:19
Alignment explanation
Indices: 592158--592259 Score: 99
Period size: 19 Copynumber: 5.6 Consensus size: 19
592148 GAAAATGACT
* *
592158 ATCGCAACGCGGAAATGGAT
1 ATCGCAATGC-GAAATGGAA
*
592178 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGGAA
592197 ATCGCAATGCGAAAT-GAA
1 ATCGCAATGCGAAATGGAA
*
592215 ATCGCAA--CGACA---AA
1 ATCGCAATGCGAAATGGAA
* *
592229 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGGAA
592248 ATCGCAATGCGA
1 ATCGCAATGCGA
592260 TTTGTGTTTC
Statistics
Matches: 70, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
14 9 0.13
16 8 0.11
18 9 0.13
19 35 0.50
20 9 0.13
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGGAA
Found at i:592293 original size:14 final size:14
Alignment explanation
Indices: 592271--592328 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
592261 TTGTGTTTCA
592271 CGTTACGATTTTGT
1 CGTTACGATTTTGT
* *
592285 CGTTGCGATTTCATTT
1 CGTTACGATTT--TGT
*
592301 CGCATTGCGATTTTGT
1 CG--TTACGATTTTGT
592317 CGTTACGATTTT
1 CGTTACGATTTT
592329 AATTTCGCGT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.53
16 8 0.22
18 9 0.25
ACGTcount: A:0.14, C:0.17, G:0.21, T:0.48
Consensus pattern (14 bp):
CGTTACGATTTTGT
Found at i:592315 original size:32 final size:33
Alignment explanation
Indices: 592276--592344 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
592266 TTTCACGTTA
* *
592276 CGATTTTGTCGTTGCGA-TTTCATTTCGCATTG
1 CGATTTTGTCGTTACGATTTTAATTTCGCATTG
*
592308 CGATTTTGTCGTTACGATTTTAATTTCGCGTTG
1 CGATTTTGTCGTTACGATTTTAATTTCGCATTG
592341 CGAT
1 CGAT
592345 AGCAATTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 16 0.48
33 17 0.52
ACGTcount: A:0.14, C:0.17, G:0.22, T:0.46
Consensus pattern (33 bp):
CGATTTTGTCGTTACGATTTTAATTTCGCATTG
Found at i:592344 original size:19 final size:20
Alignment explanation
Indices: 592329--592366 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
592319 TTACGATTTT
592329 AATTTC-GCGTTGCGATAGC
1 AATTTCTGCGTTGCGATAGC
592348 AATTTCTGCGTTGCGATAG
1 AATTTCTGCGTTGCGATAG
592367 TCATTTTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.34
Consensus pattern (20 bp):
AATTTCTGCGTTGCGATAGC
Found at i:592379 original size:20 final size:20
Alignment explanation
Indices: 592336--592380 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
592326 TTTAATTTCG
*
592336 CGTTGCGATAGCAATTTCTG
1 CGTTGCGATAGCAATTTCTA
*
592356 CGTTGCGATAGTC-ATTTTTA
1 CGTTGCGATAG-CAATTTCTA
592376 CGTTG
1 CGTTG
592381 AGATTTTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGCAATTTCTA
Found at i:594271 original size:14 final size:14
Alignment explanation
Indices: 594252--594287 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
594242 ATTGTTTAAT
594252 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
594266 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
594280 TGATTTGT
1 TGATTTGT
594288 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:594420 original size:14 final size:14
Alignment explanation
Indices: 594401--594454 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
594391 AAAACTGACT
*
594401 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
594415 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
594434 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
594448 ATCGCAA
1 ATCGCAA
594455 TGCGATTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:594438 original size:19 final size:17
Alignment explanation
Indices: 594414--594459 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 17
594404 GCAACGAGAG
594414 AATCGCAATGCGAAATGAA
1 AATCGCAATGCG-AA-GAA
594433 AATCGCAA--CG-AGAA
1 AATCGCAATGCGAAGAA
594447 AATCGCAATGCGA
1 AATCGCAATGCGA
594460 TTTTCATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
14 11 0.46
15 1 0.04
16 2 0.08
17 2 0.08
19 8 0.33
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.13
Consensus pattern (17 bp):
AATCGCAATGCGAAGAA
Found at i:594531 original size:22 final size:20
Alignment explanation
Indices: 594485--594554 Score: 115
Period size: 22 Copynumber: 3.5 Consensus size: 20
594475 GCGATTTTGT
594485 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
594504 CGTTGCGATAGCCATTTTCGTG
1 CGTTGCGATAGCCATTTTC--G
594526 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
594546 CGTTGCGAT
1 CGTTGCGAT
594555 TGTCAAATGA
Statistics
Matches: 48, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
19 14 0.29
20 14 0.29
22 20 0.42
ACGTcount: A:0.14, C:0.24, G:0.27, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:594533 original size:41 final size:40
Alignment explanation
Indices: 594478--594554 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 40
594468 TCGCATTGCG
594478 ATTTTGTCGTTGCGATAGCCA-TTTCGCGTTGCGATAGCC
1 ATTTTGTCGTTGCGATAGCCATTTTCGCGTTGCGATAGCC
594517 ATTTTCGTGCGTTGCGATAGCCATTTTCGCGTTGCGAT
1 ATTTT-GT-CGTTGCGATAGCCATTTTCGCGTTGCGAT
594555 TGTCAAATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
39 5 0.14
40 2 0.06
41 14 0.40
42 14 0.40
ACGTcount: A:0.14, C:0.22, G:0.26, T:0.38
Consensus pattern (40 bp):
ATTTTGTCGTTGCGATAGCCATTTTCGCGTTGCGATAGCC
Found at i:594819 original size:20 final size:20
Alignment explanation
Indices: 594769--594819 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
594759 AAATGATTAC
*
594769 CTTTCGCAACACGATTCTGA
1 CTTTCGCAACGCGATTCTGA
* *
594789 CTTTCGCAACGCTATTCTTA
1 CTTTCGCAACGCGATTCTGA
594809 CTTTCGCAACG
1 CTTTCGCAACG
594820 AGATAATACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.31, G:0.14, T:0.33
Consensus pattern (20 bp):
CTTTCGCAACGCGATTCTGA
Found at i:595591 original size:24 final size:24
Alignment explanation
Indices: 595564--595617 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
595554 GTATTCAAAA
*
595564 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
595588 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
595612 TTTGAT
1 TTTGAT
595618 GATGTTTAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:595809 original size:12 final size:12
Alignment explanation
Indices: 595792--595816 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
595782 ATATAATCCT
595792 GAAGAAGAAAAA
1 GAAGAAGAAAAA
595804 GAAGAAGAAAAA
1 GAAGAAGAAAAA
595816 G
1 G
595817 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:598150 original size:33 final size:33
Alignment explanation
Indices: 598108--598234 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
598098 GGAAATTACT
*
598108 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
598141 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
598173 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
598207 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
598235 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:598191 original size:66 final size:66
Alignment explanation
Indices: 598109--598241 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
598099 GAAATTACTA
*
598109 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
598174 T
66 T
* *
598175 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
598240 T
66 T
598241 T
1 T
598242 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:598279 original size:30 final size:32
Alignment explanation
Indices: 598238--598320 Score: 125
Period size: 30 Copynumber: 2.6 Consensus size: 32
598228 CGCAACGCGA
*
598238 ATTTAATTTCGCGTTGCGATT-T-TCGTTGCG
1 ATTTCATTTCGCGTTGCGATTCTCTCGTTGCG
598268 ATTTCATTTCGCGTTGCGATTCTCTCGTTGCG
1 ATTTCATTTCGCGTTGCGATTCTCTCGTTGCG
*
598300 ATTTTCATTTCGCATTGCGAT
1 A-TTTCATTTCGCGTTGCGAT
598321 AGTACTTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
30 20 0.42
31 1 0.02
32 9 0.19
33 18 0.38
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (32 bp):
ATTTCATTTCGCGTTGCGATTCTCTCGTTGCG
Found at i:598448 original size:14 final size:14
Alignment explanation
Indices: 598429--598463 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
598419 TCAATTAAAT
598429 AAATCAACTTTTAC
1 AAATCAACTTTTAC
*
598443 AAATCACCTTTTAC
1 AAATCAACTTTTAC
598457 AAATCAA
1 AAATCAA
598464 TTAAACAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:599888 original size:21 final size:21
Alignment explanation
Indices: 599822--599888 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
599812 GTGAATCGGG
*
599822 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
599842 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
599864 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
599885 CTCT
1 CTCT
599889 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:599907 original size:42 final size:41
Alignment explanation
Indices: 599822--599944 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
599812 GTGAATCGGG
* * * *
599822 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
599864 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
599906 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
599945 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:600330 original size:78 final size:79
Alignment explanation
Indices: 600181--600333 Score: 227
Period size: 78 Copynumber: 1.9 Consensus size: 79
600171 AAGACAAAAC
*
600181 AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAATTTAGCAGAATTGGCAGCAACAGAA
1 AAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAATTTAGCAGAATTGGCAGCAACAGAA
600246 TAAATTTACTTCAACCA
63 TAAATTTACTTCAACCA
* ** *
600263 AAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCAGTTTTGGCAGCAACCGAATAA
1 AAAGACAAATACTAACTTCACAGTGTTAAATAAACAATTTAGCAGAATTGGCAGCAACAGAATAA
600327 ATTTACT
66 ATTTACT
600334 AAGCAATCTA
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
78 39 0.59
82 27 0.41
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (79 bp):
AAAGACAAATACTAACTTCACAGTGTTAAATAAACAATTTAGCAGAATTGGCAGCAACAGAATAA
ATTTACTTCAACCA
Found at i:602037 original size:20 final size:19
Alignment explanation
Indices: 602006--602146 Score: 95
Period size: 19 Copynumber: 7.8 Consensus size: 19
601996 TCTTTTGGTT
602006 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
602025 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
602046 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
602065 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
602079 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
602098 G--A-G--AATCGCAACGT
1 GAAATGAAAATCGCAACGA
* *
602112 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
602131 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
602147 TGCAATTTTG
Statistics
Matches: 94, Mismatches: 16, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
14 19 0.20
16 4 0.04
17 3 0.03
19 37 0.39
20 29 0.31
21 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:602125 original size:33 final size:33
Alignment explanation
Indices: 602031--602116 Score: 145
Period size: 33 Copynumber: 2.6 Consensus size: 33
602021 ACGAGATAAT
602031 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
602065 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
*
602098 GAGAATCGCAACGTGAAAT
1 GAGAATCGCAACGCGAAAT
602117 AAAAATCGCA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 36 0.72
34 14 0.28
ACGTcount: A:0.38, C:0.22, G:0.27, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:602174 original size:19 final size:19
Alignment explanation
Indices: 602152--602188 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
602142 CGCAATGCAA
602152 TTTTGGTTTCGCGTTGCGT
1 TTTTGGTTTCGCGTTGCGT
**
602171 TTTTTTTTTCGCGTTGCG
1 TTTTGGTTTCGCGTTGCG
602189 ATAGTTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.27, T:0.57
Consensus pattern (19 bp):
TTTTGGTTTCGCGTTGCGT
Found at i:602199 original size:19 final size:19
Alignment explanation
Indices: 602158--602210 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
602148 GCAATTTTGG
* ** *
602158 TTTCGCGTTGCGTTTTTTT
1 TTTCGCGTTGCGATAGTTA
602177 TTTCGCGTTGCGATAGTTA
1 TTTCGCGTTGCGATAGTTA
602196 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
602211 TTTCATTCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.08, C:0.19, G:0.25, T:0.49
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTTA
Found at i:602753 original size:20 final size:20
Alignment explanation
Indices: 602728--602780 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
602718 ACGCTATGTA
602728 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
602748 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
602768 TATCTCGTTGCGA
1 AATCGCGTTGCGA
602781 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:602814 original size:20 final size:20
Alignment explanation
Indices: 602789--602842 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
602779 GATTTTGTAT
602789 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
602809 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
602829 TATCGCATTGCGAT
1 TATCGCATTGCGAT
602843 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:602827 original size:61 final size:61
Alignment explanation
Indices: 602729--602845 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
602719 CGCTATGTAA
* * * * *
602729 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
602790 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
602846 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:602861 original size:61 final size:61
Alignment explanation
Indices: 602729--602863 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
602719 CGCTATGTAA
* * * * * ** *
602729 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
602790 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
602852 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
602864 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Done.