Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007905.1 Hibiscus syriacus cultivar Beakdansim tig00110299_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: 2946335
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 14
Found at i:2394605 original size:52 final size:53
Alignment explanation
Indices: 2394458--2394611 Score: 181
Period size: 54 Copynumber: 2.9 Consensus size: 53
2394448 TGTGATGTAT
* * *
2394458 TTTTAATTTAAACATTTCAGTCAC---TTTTTATTTCTGATTTGGCTACAACTA
1 TTTTATTTTATACATTT-AGTCACTATTTTTTATTTCTGATTTGGCTACTACTA
**
2394509 TTTTATTTTATACATTTTAGTCACTATTTTTTATTTCTGATTTGGCTACTGTTA
1 TTTTATTTTATACA-TTTAGTCACTATTTTTTATTTCTGATTTGGCTACTACTA
* * * *
2394563 TTTTATTTTATTCA-TTAGTCATTATTTTTTATTTATGGTTTGGCTACTA
1 TTTTATTTTATACATTTAGTCACTATTTTTTATTTCTGATTTGGCTACTA
2394612 TTTTTTTGTC
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
51 18 0.20
52 34 0.38
54 37 0.42
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.56
Consensus pattern (53 bp):
TTTTATTTTATACATTTAGTCACTATTTTTTATTTCTGATTTGGCTACTACTA
Found at i:2394613 original size:25 final size:25
Alignment explanation
Indices: 2394482--2394617 Score: 78
Period size: 25 Copynumber: 5.2 Consensus size: 25
2394472 TTTCAGTCAC
* *
2394482 TTTTTATTTCTGATTTGGCTACAACT
1 TTTTTATTTATGATTTGGCTACTA-T
* * *
2394508 ATTTTATTTTATACATTTTAG-TCACTAT
1 TTTTTA-TTTAT-GA-TTTGGCT-ACTAT
* *
2394536 TTTTTATTTCTGATTTGGCTACTGT
1 TTTTTATTTATGATTTGGCTACTAT
* * * *
2394561 TATTTTATTTTATTCATTAGTC-ATTAT
1 T-TTTTA-TTTA-TGATTTGGCTACTAT
*
2394588 TTTTTATTTATGGTTTGGCTACTAT
1 TTTTTATTTATGATTTGGCTACTAT
2394613 TTTTT
1 TTTTT
2394618 TGTCTTATTA
Statistics
Matches: 80, Mismatches: 21, Indels: 19
0.67 0.17 0.16
Matches are distributed among these distances:
24 5 0.06
25 22 0.28
26 17 0.21
27 15 0.19
28 14 0.17
29 7 0.09
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (25 bp):
TTTTTATTTATGATTTGGCTACTAT
Found at i:2394626 original size:52 final size:53
Alignment explanation
Indices: 2394482--2394631 Score: 169
Period size: 52 Copynumber: 2.8 Consensus size: 53
2394472 TTTCAGTCAC
* * * *
2394482 TTTTTATTTCTGATTTGGCTACAACTATTTTATTTTA-TACATTTTAGTCACTAT
1 TTTTTATTTATGATTTGGCTACTATTATTTTATCTTATTACA--TTAGTCACTAT
* * * *
2394536 TTTTTATTTCTGATTTGGCTACTGTTATTTTATTTTATT-CATTAGTCATTAT
1 TTTTTATTTATGATTTGGCTACTATTATTTTATCTTATTACATTAGTCACTAT
* * *
2394588 TTTTTATTTATGGTTTGGCTACTATTTTTTTGTCTTATTACATT
1 TTTTTATTTATGATTTGGCTACTATTATTTTATCTTATTACATT
2394632 TGGTCTCTTA
Statistics
Matches: 84, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
52 43 0.51
53 4 0.05
54 36 0.43
55 1 0.01
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (53 bp):
TTTTTATTTATGATTTGGCTACTATTATTTTATCTTATTACATTAGTCACTAT
Found at i:2399316 original size:74 final size:75
Alignment explanation
Indices: 2399233--2399376 Score: 211
Period size: 76 Copynumber: 1.9 Consensus size: 75
2399223 TAGGGAAAGT
* * *
2399233 GGAAAAAATATTATAATAATTCTATATA-TTT-AAAAAACTAAACCACTATAGTTTAAATTAAGA
1 GGAAAAAATAATATAATAACTCTATATATTTTAAAAAAACTAAACCACTATAGCTTAAATTAAGA
2399296 AAACATGTTA
66 AAACATGTTA
* *
2399306 GGAAACAAATAATATAATAACTCTATATATTTTAAAAAAACTATATCACTATAGCTTAAATTAAG
1 GGAAA-AAATAATATAATAACTCTATATATTTTAAAAAAACTAAACCACTATAGCTTAAATTAAG
*
2399371 GAAACA
65 AAAACA
2399377 AATGGGAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
73 5 0.08
74 21 0.34
75 3 0.05
76 33 0.53
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (75 bp):
GGAAAAAATAATATAATAACTCTATATATTTTAAAAAAACTAAACCACTATAGCTTAAATTAAGA
AAACATGTTA
Found at i:2399392 original size:76 final size:74
Alignment explanation
Indices: 2399233--2399398 Score: 201
Period size: 76 Copynumber: 2.2 Consensus size: 74
2399223 TAGGGAAAGT
* *
2399233 GGAAA-AAATATTATAATAATTCTATATATTTAAAAAACTAAACCACTATAGTTTAAATTAAGAA
1 GGAAACAAATATTATAATAACTCTATATATTTAAAAAACTAAACCACTATAGCTTAAATTAAGAA
**
2399297 AACATGTTA
66 AACATAATA
* * *
2399306 GGAAACAAATAATATAATAACTCTATATATTTTAAAAAAACTATATCACTATAGCTTAAATTAAG
1 GGAAACAAATATTATAATAACTCTATATA-TTT-AAAAAACTAAACCACTATAGCTTAAATTAAG
* *
2399371 GAAACA-AATG
64 AAAACATAATA
*
2399381 GGAAAATAAATATTATAA
1 GG-AAACAAATATTATAA
2399399 CGATTTCATA
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
73 5 0.06
74 21 0.27
75 6 0.08
76 46 0.59
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (74 bp):
GGAAACAAATATTATAATAACTCTATATATTTAAAAAACTAAACCACTATAGCTTAAATTAAGAA
AACATAATA
Found at i:2400669 original size:26 final size:26
Alignment explanation
Indices: 2400633--2400727 Score: 136
Period size: 26 Copynumber: 3.7 Consensus size: 26
2400623 GAGTGGTTGG
* *
2400633 AAGCAGTGGTGGCTGTTGAGTGGTCT
1 AAGCGGTGGTGGCTGTTGAGTGGTCC
*
2400659 AAGCGGTGGTGGCTGTTTAGTGGTCC
1 AAGCGGTGGTGGCTGTTGAGTGGTCC
*
2400685 AAGCGGCGGTGGCTGTTGAGTGGTCC
1 AAGCGGTGGTGGCTGTTGAGTGGTCC
* *
2400711 AAGTGGTGGCGGCTGTT
1 AAGCGGTGGTGGCTGTT
2400728 CTGGAAACCC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 61 1.00
ACGTcount: A:0.13, C:0.15, G:0.44, T:0.28
Consensus pattern (26 bp):
AAGCGGTGGTGGCTGTTGAGTGGTCC
Found at i:2401285 original size:93 final size:93
Alignment explanation
Indices: 2401136--2401458 Score: 573
Period size: 93 Copynumber: 3.5 Consensus size: 93
2401126 TAATAGGGAT
* * *
2401136 TTGTTCCGCTT-CTTCTGAAGGAAATATCAGATC-TG--AAAGAAGAGGTGACTCATTCCGCTAT
1 TTGTTCCACTTAC-TCTGAAGGGAATATCAAATCTTGAAAAAGAAGAGGTGACTCATTCCGCTAT
2401197 TCTTCAGGGAAAATTGAATTGAGGCAGAC
65 TCTTCAGGGAAAATTGAATTGAGGCAGAC
2401226 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAAAAGAAGAGGTGACTCATTCCGCTATT
1 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAAAAGAAGAGGTGACTCATTCCGCTATT
2401291 CTTCAGGGAAAATTGAATTGAGGCAGAC
66 CTTCAGGGAAAATTGAATTGAGGCAGAC
2401319 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAAAAGAAGAGGTGACTCATTCCGCTATT
1 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAAAAGAAGAGGTGACTCATTCCGCTATT
*
2401384 CTTCTGGGAAAATTGAATTGAGGCAGAC
66 CTTCAGGGAAAATTGAATTGAGGCAGAC
2401412 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAAAAGAAGAG
1 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAAAAGAAGAG
2401459 ACCTGTTCCG
Statistics
Matches: 225, Mismatches: 4, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
90 28 0.12
91 3 0.01
93 194 0.86
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (93 bp):
TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAAAAGAAGAGGTGACTCATTCCGCTATT
CTTCAGGGAAAATTGAATTGAGGCAGAC
Found at i:2401597 original size:48 final size:48
Alignment explanation
Indices: 2401526--2401649 Score: 203
Period size: 48 Copynumber: 2.6 Consensus size: 48
2401516 TGGGGCAAAT
*
2401526 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGAG
1 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAAAGAGAG
*
2401574 TTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGGGAAAAAGAGAG
1 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAAAGAGAG
* *
2401622 ATGTTCCACTTACTTATGAAGGGAATAT
1 TTGTTCCACTTAC-TCTGAAGGGAATAT
2401650 TAGATATTGG
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
48 57 0.81
49 13 0.19
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (48 bp):
TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAAAGAGAG
Found at i:2416288 original size:26 final size:26
Alignment explanation
Indices: 2416259--2416364 Score: 117
Period size: 26 Copynumber: 4.2 Consensus size: 26
2416249 CAGTGGTGGC
*
2416259 TGTTGAGTGGTCCAAGTGGTGGCGGT
1 TGTTGAGTGGTCCAAGCGGTGGCGGT
* *
2416285 TGTT--CTGGTCCAAGCGGTGGTGGT
1 TGTTGAGTGGTCCAAGCGGTGGCGGT
* ** *
2416309 TGTTGAGTAGTCCAAGCGGCAGTGGT
1 TGTTGAGTGGTCCAAGCGGTGGCGGT
* *
2416335 TGTTGAGTGGTCCAAGTGGTGGCGGC
1 TGTTGAGTGGTCCAAGCGGTGGCGGT
2416361 TGTT
1 TGTT
2416365 CTGGAAACCC
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
24 21 0.32
26 44 0.68
ACGTcount: A:0.12, C:0.14, G:0.42, T:0.31
Consensus pattern (26 bp):
TGTTGAGTGGTCCAAGCGGTGGCGGT
Found at i:2416336 original size:50 final size:51
Alignment explanation
Indices: 2416251--2416364 Score: 131
Period size: 50 Copynumber: 2.2 Consensus size: 51
2416241 GTTGGCAACA
* * **
2416251 GTGGTGGCTGTTGAGTGGTCCAAGTGGTGGCGGTTGTT-CTGGTCCAAGCG
1 GTGGTGGCTGTTGAGTAGTCCAAGCGGCAGCGGTTGTTACTGGTCCAAGCG
* * * *
2416301 GTGGTGGTTGTTGAGTAGTCCAAGCGGCAGTGGTTGTTGAGTGGTCCAAGTG
1 GTGGTGGCTGTTGAGTAGTCCAAGCGGCAGCGGTTGTT-ACTGGTCCAAGCG
*
2416353 GTGGCGGCTGTT
1 GTGGTGGCTGTT
2416365 CTGGAAACCC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 32 0.62
52 20 0.38
ACGTcount: A:0.11, C:0.14, G:0.44, T:0.31
Consensus pattern (51 bp):
GTGGTGGCTGTTGAGTAGTCCAAGCGGCAGCGGTTGTTACTGGTCCAAGCG
Found at i:2416581 original size:18 final size:18
Alignment explanation
Indices: 2416554--2416595 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2416544 TAAATCTGTA
2416554 AAATAA-AAT-ATAATTAT
1 AAATAATAATAATAA-TAT
2416571 AAATAATAATAATAATAT
1 AAATAATAATAATAATAT
2416589 AAATAAT
1 AAATAAT
2416596 GACGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAATAATAATAATAT
Found at i:2417709 original size:18 final size:18
Alignment explanation
Indices: 2417688--2417781 Score: 79
Period size: 18 Copynumber: 5.3 Consensus size: 18
2417678 TGTTTAGACT
*
2417688 TTTGATTGAATTTATCCA
1 TTTGATTAAATTTATCCA
* *
2417706 TTTGATTAAATTTA-ACT
1 TTTGATTAAATTTATCCA
* *
2417723 TTTGGATTGAATTTATCAA
1 TTT-GATTAAATTTATCCA
*
2417742 TTTGATTAAATTTA--AA
1 TTTGATTAAATTTATCCA
2417758 TTCGTGATT-AATTTATCCA
1 TT--TGATTAAATTTATCCA
2417777 TTTGA
1 TTTGA
2417782 ATTTCTTATT
Statistics
Matches: 61, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
16 4 0.07
17 13 0.21
18 38 0.62
19 6 0.10
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (18 bp):
TTTGATTAAATTTATCCA
Found at i:2417733 original size:36 final size:36
Alignment explanation
Indices: 2417680--2417781 Score: 138
Period size: 36 Copynumber: 2.9 Consensus size: 36
2417670 CCGTATTTTG
2417680 TTTAGACTTTT-GATTGAATTTATCCATTTGATTAAA
1 TTTA-ACTTTTGGATTGAATTTATCCATTTGATTAAA
*
2417716 TTTAACTTTTGGATTGAATTTATCAATTTGATTAAA
1 TTTAACTTTTGGATTGAATTTATCCATTTGATTAAA
* *
2417752 TTTAA-ATTCGTGATT-AATTTATCCATTTGA
1 TTTAACTTTTG-GATTGAATTTATCCATTTGA
2417782 ATTTCTTATT
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
35 23 0.38
36 37 0.62
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.50
Consensus pattern (36 bp):
TTTAACTTTTGGATTGAATTTATCCATTTGATTAAA
Found at i:2418601 original size:41 final size:41
Alignment explanation
Indices: 2418552--2418629 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
2418542 ATATTTTTTG
* *
2418552 AAAACATATAATATAGATTTTTTAGAAAA-CGTTTTTTTTAA
1 AAAACATATAATATAGAATTTTTA-AAAATCGGTTTTTTTAA
* *
2418593 AAAACATATTATATATAATTTTTAAAAATCGGTTTTT
1 AAAACATATAATATAGAATTTTTAAAAATCGGTTTTT
2418630 GAAAATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 4 0.12
41 28 0.88
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (41 bp):
AAAACATATAATATAGAATTTTTAAAAATCGGTTTTTTTAA
Found at i:2418764 original size:17 final size:17
Alignment explanation
Indices: 2418739--2418782 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
2418729 CATATATAAT
*
2418739 ATATAATTTTTGAAAAC
1 ATATTATTTTTGAAAAC
*
2418756 ATATTATTTTTGAAAAT
1 ATATTATTTTTGAAAAC
*
2418773 ATAATATTTT
1 ATATTATTTT
2418783 ATAGTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (17 bp):
ATATTATTTTTGAAAAC
Found at i:2418817 original size:32 final size:30
Alignment explanation
Indices: 2418780--2418844 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 30
2418770 AATATAATAT
*
2418780 TTTATAGTTTTTA-TTATATATTATTATTTATA
1 TTTATA-TTTTCATTTATATATT-TTATTT-TA
*
2418812 TTTATATTTTCATTTATTTATTTTATTTTA
1 TTTATATTTTCATTTATATATTTTATTTTA
2418842 TTT
1 TTT
2418845 TTTAAACATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 5 0.17
31 11 0.37
32 14 0.47
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (30 bp):
TTTATATTTTCATTTATATATTTTATTTTA
Found at i:2418819 original size:18 final size:19
Alignment explanation
Indices: 2418791--2418832 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
2418781 TTATAGTTTT
2418791 TATTATATATTATT-ATTTA
1 TATTATATATT-TTCATTTA
2418810 TATT-TATATTTTCATTTA
1 TATTATATATTTTCATTTA
2418828 T-TTAT
1 TATTAT
2418833 TTTATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.19
18 13 0.62
19 4 0.19
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTATATATTTTCATTTA
Found at i:2418847 original size:12 final size:13
Alignment explanation
Indices: 2418777--2418837 Score: 54
Period size: 14 Copynumber: 4.6 Consensus size: 13
2418767 GAAAATATAA
2418777 TATTTTATAGTTTT
1 TATTTTATA-TTTT
* *
2418791 TATTATATATTAT
1 TATTTTATATTTT
*
2418804 TA-TTTATATTTA
1 TATTTTATATTTT
2418816 TATTTTCAT-TTATT
1 TATTTT-ATATT-TT
2418830 TATTTTAT
1 TATTTTAT
2418838 TTTATTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
12 9 0.24
13 12 0.32
14 17 0.45
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (13 bp):
TATTTTATATTTT
Found at i:2423325 original size:37 final size:38
Alignment explanation
Indices: 2423282--2423471 Score: 176
Period size: 37 Copynumber: 5.1 Consensus size: 38
2423272 CTATATAATG
2423282 TAGTTTTTGAAAATA-TTTTTTGAAAACATATAATATA
1 TAGTTTTTGAAAATACTTTTTTGAAAACATATAATATA
* *
2423319 TAGTTTTT-AGAAATCATTTTTATTGAAAGCATATAATATA
1 TAGTTTTTGA-AAAT-ACTTTT-TTGAAAACATATAATATA
* * * * *
2423359 TAATTTTTCAAAATCAGTTTTTTCAAAATATAT-A-ATA
1 TAGTTTTTGAAAAT-ACTTTTTTGAAAACATATAATATA
* * *
2423396 T-GGTTTTGAAAATACGTTTTTGAAAACATATATTATA
1 TAGTTTTTGAAAATACTTTTTTGAAAACATATAATATA
* * * *
2423433 TAG-TTTTGAAAACACATTTTTAAAAACGTATAATATA
1 TAGTTTTTGAAAATACTTTTTTGAAAACATATAATATA
2423470 TA
1 TA
2423472 TAGTTTTAAA
Statistics
Matches: 126, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
35 14 0.11
36 10 0.08
37 51 0.40
38 3 0.02
39 13 0.10
40 34 0.27
41 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (38 bp):
TAGTTTTTGAAAATACTTTTTTGAAAACATATAATATA
Found at i:2423608 original size:17 final size:17
Alignment explanation
Indices: 2423562--2423608 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
2423552 AAACATATAT
2423562 AATATATATAATTTTTGAA
1 AATATA-AT-ATTTTTGAA
* *
2423581 AACATATTATTTTTGAA
1 AATATAATATTTTTGAA
2423598 AATATAATATT
1 AATATAATATT
2423609 ATATAGTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 18 0.75
18 1 0.04
19 5 0.21
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (17 bp):
AATATAATATTTTTGAA
Found at i:2423640 original size:19 final size:19
Alignment explanation
Indices: 2423618--2423662 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
2423608 TATATAGTTT
2423618 TTATTATATATTATTTGTA
1 TTATTATATATTATTTGTA
* * *
2423637 TTATCATTTATTATTTTTA
1 TTATTATATATTATTTGTA
*
2423656 TTTTTAT
1 TTATTAT
2423663 TTTTATTATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
TTATTATATATTATTTGTA
Found at i:2423656 original size:6 final size:6
Alignment explanation
Indices: 2423628--2423690 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
2423618 TTATTATATA
* * * *
2423628 TTATTT GTATTA TCATTT ATTATTT TTATTT TTATTT TTATTAT TT-TAT
1 TTATTT TTATTT TTATTT -TTATTT TTATTT TTATTT TTATT-T TTATTT
*
2423677 TTAATT TTATTT TT
1 TTATTT TTATTT TT
2423691 TAAACAGGTC
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
5 3 0.07
6 33 0.75
7 8 0.18
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (6 bp):
TTATTT
Found at i:2423663 original size:15 final size:15
Alignment explanation
Indices: 2423643--2423690 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
2423633 TGTATTATCA
2423643 TTTATTATTTTTATT
1 TTTATTATTTTTATT
2423658 TTTATT-TTTATTA-T
1 TTTATTATTT-TTATT
*
2423672 TTTATTTAATTTTATT
1 TTTA-TTATTTTTATT
2423688 TTT
1 TTT
2423691 TAAACAGGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 8 0.29
15 14 0.50
16 6 0.21
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATTATTTTTATT
Found at i:2423664 original size:19 final size:18
Alignment explanation
Indices: 2423628--2423690 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
2423618 TTATTATATA
* * *
2423628 TTATTTGTATTATCATTT
1 TTATTTTTATTTTTATTT
2423646 ATTATTTTTATTTTTATTT
1 -TTATTTTTATTTTTATTT
* *
2423665 TTATTATTT-TATTTAATT
1 TTATT-TTTATTTTTATTT
2423683 TTATTTTT
1 TTATTTTT
2423691 TAAACAGGTC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
17 3 0.08
18 17 0.45
19 18 0.47
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (18 bp):
TTATTTTTATTTTTATTT
Found at i:2423670 original size:31 final size:30
Alignment explanation
Indices: 2423628--2423690 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
2423618 TTATTATATA
*
2423628 TTATTTGTATTATCATTTA-TTATTTTTATTT
1 TTATTTGTATTAT--TTTATTTAATTTTATTT
*
2423659 TTATTTTTATTATTTTATTTAATTTTATTT
1 TTATTTGTATTATTTTATTTAATTTTATTT
2423689 TT
1 TT
2423691 TAAACAGGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 4 0.14
30 13 0.45
31 12 0.41
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (30 bp):
TTATTTGTATTATTTTATTTAATTTTATTT
Found at i:2423679 original size:24 final size:24
Alignment explanation
Indices: 2423644--2423690 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2423634 GTATTATCAT
*
2423644 TTATTATTTTTATTTTTATTTTTA
1 TTATTATTTTTAATTTTATTTTTA
2423668 TTATT-TTATTTAATTTTATTTTT
1 TTATTATT-TTTAATTTTATTTTT
2423691 TAAACAGGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (24 bp):
TTATTATTTTTAATTTTATTTTTA
Found at i:2424848 original size:5 final size:5
Alignment explanation
Indices: 2424840--2424878 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
2424830 TTTTAATTCA
*
2424840 TTTAT TTTAT TTT-T ACTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT -TTTAT TTTAT TTTAT TTTAT TTTA
2424879 GTATTTAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 1 0.03
5 28 0.93
6 1 0.03
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:2427921 original size:18 final size:19
Alignment explanation
Indices: 2427864--2427928 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
2427854 AACTCTGGTA
*
2427864 AAAGTCAACGGGTCAGATC
1 AAAGTCAACGGGTCAGGTC
* *
2427883 AAAGTCAATGGGT-TGGTTC
1 AAAGTCAACGGGTCAGG-TC
2427902 -AAGTCAACGGGTCAGGTC
1 AAAGTCAACGGGTCAGGTC
2427920 AAAGTCAAC
1 AAAGTCAAC
2427929 ATGTCAGACT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 14 0.37
19 24 0.63
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (19 bp):
AAAGTCAACGGGTCAGGTC
Found at i:2432568 original size:43 final size:45
Alignment explanation
Indices: 2432464--2432569 Score: 119
Period size: 50 Copynumber: 2.3 Consensus size: 45
2432454 AGGATTATAT
*
2432464 TTATTATTTTATTAGGAATTAAGTTTGAGTTAAAACATTATTTTTAGTTA
1 TTATTATTTTATTAGGAATTAA---TGAGTTAAAAC--TATGTTTAGTTA
*
2432514 TTATTATTTTATTAGGAATT-A-GAGTTAAAAC-ATGTTTAGTTTG
1 TTATTATTTTATTAGGAATTAATGAGTTAAAACTATGTTTAG-TTA
2432557 TTATTATTTTATT
1 TTATTATTTTATT
2432570 CATTAGTTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
42 7 0.13
43 15 0.28
45 10 0.19
49 1 0.02
50 20 0.38
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.54
Consensus pattern (45 bp):
TTATTATTTTATTAGGAATTAATGAGTTAAAACTATGTTTAGTTA
Found at i:2440171 original size:11 final size:11
Alignment explanation
Indices: 2440147--2440221 Score: 63
Period size: 10 Copynumber: 7.2 Consensus size: 11
2440137 TATATAGCAA
2440147 AAAAAAAGGTAAG
1 AAAAAAA-G-AAG
2440160 AAAAAAAGAAG
1 AAAAAAAGAAG
2440171 -AAAAAAGAAG
1 AAAAAAAGAAG
*
2440181 -AAAACAGAA-
1 AAAAAAAGAAG
2440190 AAAAAAAG--G
1 AAAAAAAGAAG
*
2440199 AAAAAGAG-AG
1 AAAAAAAGAAG
*
2440209 AAAAAAAAAAG
1 AAAAAAAGAAG
2440220 AA
1 AA
2440222 TGCAAATAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
9 7 0.13
10 31 0.58
11 7 0.13
12 1 0.02
13 7 0.13
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.01
Consensus pattern (11 bp):
AAAAAAAGAAG
Found at i:2440181 original size:21 final size:21
Alignment explanation
Indices: 2440148--2440214 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 21
2440138 ATATAGCAAA
2440148 AAAAAAGGTAAGAAAAAAAGAAG
1 AAAAAA-G-AAGAAAAAAAGAAG
*
2440171 AAAAAAGAAG-AAAACAGAA-
1 AAAAAAGAAGAAAAAAAGAAG
* *
2440190 AAAAAA-AGGAAAAAGAG-AG
1 AAAAAAGAAGAAAAAAAGAAG
2440209 AAAAAA
1 AAAAAA
2440215 AAAAGAATGC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 3 0.08
19 18 0.46
20 8 0.21
21 3 0.08
22 1 0.03
23 6 0.15
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (21 bp):
AAAAAAGAAGAAAAAAAGAAG
Found at i:2440189 original size:28 final size:28
Alignment explanation
Indices: 2440158--2440212 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
2440148 AAAAAAGGTA
2440158 AGAAAAAAAGAAGAAAAAAGA-AGAAAAC
1 AGAAAAAAA-AAGAAAAAAGAGAGAAAAC
*
2440186 AGAAAAAAAAAGGAAAAAGAGAGAAAA
1 AGAAAAAAAAAGAAAAAAGAGAGAAAA
2440213 AAAAAAGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (28 bp):
AGAAAAAAAAAGAAAAAAGAGAGAAAAC
Found at i:2440215 original size:20 final size:19
Alignment explanation
Indices: 2440162--2440216 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
2440152 AAGGTAAGAA
2440162 AAAAAGA-AGAAAAAAGAAG
1 AAAAAGAGAGAAAAAA-AAG
*
2440181 AAAACAGA-A-AAAAAAAGG
1 AAAA-AGAGAGAAAAAAAAG
2440199 AAAAAGAGAGAAAAAAAA
1 AAAAAGAGAGAAAAAAAA
2440217 AAGAATGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 3 0.10
18 7 0.23
19 17 0.55
20 4 0.13
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAAGAGAGAAAAAAAAG
Found at i:2440215 original size:21 final size:21
Alignment explanation
Indices: 2440145--2440217 Score: 78
Period size: 21 Copynumber: 3.4 Consensus size: 21
2440135 AATATATAGC
2440145 AAAAAAAAAGGTAAGAAAAAAAG
1 AAAAAAAAAGG-AAG-AAAAAAG
* *
2440168 AAGAAAAAA-GAAGAAAACAG
1 AAAAAAAAAGGAAGAAAAAAG
*
2440188 AAAAAAAAAGGAA-AAAGAGAG
1 AAAAAAAAAGGAAGAAA-AAAG
2440209 AAAAAAAAA
1 AAAAAAAAA
2440218 AGAATGCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
20 17 0.39
21 18 0.41
22 1 0.02
23 8 0.18
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.01
Consensus pattern (21 bp):
AAAAAAAAAGGAAGAAAAAAG
Found at i:2442842 original size:31 final size:31
Alignment explanation
Indices: 2442807--2442866 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2442797 CGACCCGTTT
*
2442807 ACCCGACCCATTTACCCGACCAGTTGACCCG
1 ACCCGACCCATTGACCCGACCAGTTGACCCG
* *
2442838 ACCCGACCCGTTGACCCGACCCGTTGACC
1 ACCCGACCCATTGACCCGACCAGTTGACC
2442867 GTTGACCCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.20, C:0.47, G:0.18, T:0.15
Consensus pattern (31 bp):
ACCCGACCCATTGACCCGACCAGTTGACCCG
Found at i:2442853 original size:8 final size:8
Alignment explanation
Indices: 2442842--2442901 Score: 56
Period size: 8 Copynumber: 7.5 Consensus size: 8
2442832 GACCCGACCC
2442842 GACCCGTT
1 GACCCGTT
2442850 GACCC---
1 GACCCGTT
2442855 GACCCGTT
1 GACCCGTT
2442863 GA-CCGTT
1 GACCCGTT
2442870 GACCCGTT
1 GACCCGTT
2442878 GACCCACGTT
1 GA-CC-CGTT
2442888 GACCACTGTT
1 GACC-C-GTT
2442898 GACC
1 GACC
2442902 AAAACTTTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
5 5 0.11
7 7 0.16
8 14 0.31
9 6 0.13
10 13 0.29
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:2442875 original size:15 final size:13
Alignment explanation
Indices: 2442793--2442882 Score: 72
Period size: 13 Copynumber: 6.4 Consensus size: 13
2442783 AACCCGACCC
2442793 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
2442806 TACCCGACCCATT
1 GACCCGACCCGTT
* *
2442819 TACCCGACCAGTT
1 GACCCGACCCGTT
2442832 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
2442850 GACCCGACCCGTT
1 GACCCGACCCGTT
*
2442863 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
2442878 GACCC
1 GACCC
2442883 ACGTTGACCA
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
13 39 0.63
15 12 0.19
18 11 0.18
ACGTcount: A:0.18, C:0.44, G:0.20, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2442889 original size:10 final size:9
Alignment explanation
Indices: 2442855--2442902 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 9
2442845 CCGTTGACCC
2442855 GACC-CGTT
1 GACCACGTT
2442863 GA-C-CGTT
1 GACCACGTT
2442870 GACC-CGTT
1 GACCACGTT
2442878 GACCCACGTT
1 GA-CCACGTT
2442888 GACCACTGTT
1 GACCAC-GTT
2442898 GACCA
1 GACCA
2442903 AAACTTTGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.19
8 9 0.25
9 6 0.17
10 14 0.39
ACGTcount: A:0.19, C:0.35, G:0.23, T:0.23
Consensus pattern (9 bp):
GACCACGTT
Found at i:2444204 original size:18 final size:18
Alignment explanation
Indices: 2444178--2444213 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2444168 TCGAAAGGAC
*
2444178 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
2444196 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
2444214 CGGATGAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:2445386 original size:23 final size:24
Alignment explanation
Indices: 2445359--2445451 Score: 109
Period size: 23 Copynumber: 4.0 Consensus size: 24
2445349 CCGACTTTGA
* *
2445359 ATTCTGTTATGAT-CCTGACTTGG
1 ATTCTGATATGATACTTGACTTGG
* *
2445382 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACTTGG
* * *
2445405 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACTTGG
2445429 ATTCTGATATGATACTTGACTTG
1 ATTCTGATATGATACTTGACTTG
2445452 AATTATGTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
23 32 0.54
24 27 0.46
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACTTGG
Found at i:2445429 original size:24 final size:24
Alignment explanation
Indices: 2445374--2445448 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
2445364 GTTATGATCC
*
2445374 TGACTTGGATTCTGATCTGATA-T
1 TGACATGGATTCTGATCTGATACT
*
2445397 TGACATGGATTCTGATCTGATACA
1 TGACATGGATTCTGATCTGATACT
* *
2445421 TGACCTGGATTCTGATATGATACT
1 TGACATGGATTCTGATCTGATACT
2445445 TGAC
1 TGAC
2445449 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.37
Consensus pattern (24 bp):
TGACATGGATTCTGATCTGATACT
Found at i:2447681 original size:31 final size:31
Alignment explanation
Indices: 2447646--2447705 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2447636 CGACCCGTTT
*
2447646 ACCCGACCCATTTACCCGACCAGTTGACCCG
1 ACCCGACCCATTGACCCGACCAGTTGACCCG
* *
2447677 ACCCGACCCGTTGACCCGACCCGTTGACC
1 ACCCGACCCATTGACCCGACCAGTTGACC
2447706 GTTGACCCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.20, C:0.47, G:0.18, T:0.15
Consensus pattern (31 bp):
ACCCGACCCATTGACCCGACCAGTTGACCCG
Found at i:2447692 original size:8 final size:8
Alignment explanation
Indices: 2447681--2447740 Score: 56
Period size: 8 Copynumber: 7.5 Consensus size: 8
2447671 GACCCGACCC
2447681 GACCCGTT
1 GACCCGTT
2447689 GACCC---
1 GACCCGTT
2447694 GACCCGTT
1 GACCCGTT
2447702 GA-CCGTT
1 GACCCGTT
2447709 GACCCGTT
1 GACCCGTT
2447717 GACCCACGTT
1 GA-CC-CGTT
2447727 GACCACTGTT
1 GACC-C-GTT
2447737 GACC
1 GACC
2447741 AAAACTTTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
5 5 0.11
7 7 0.16
8 14 0.31
9 6 0.13
10 13 0.29
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:2447714 original size:15 final size:13
Alignment explanation
Indices: 2447632--2447721 Score: 72
Period size: 13 Copynumber: 6.4 Consensus size: 13
2447622 AACCCGACCC
2447632 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
2447645 TACCCGACCCATT
1 GACCCGACCCGTT
* *
2447658 TACCCGACCAGTT
1 GACCCGACCCGTT
2447671 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
2447689 GACCCGACCCGTT
1 GACCCGACCCGTT
*
2447702 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
2447717 GACCC
1 GACCC
2447722 ACGTTGACCA
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
13 39 0.63
15 12 0.19
18 11 0.18
ACGTcount: A:0.18, C:0.44, G:0.20, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2447728 original size:10 final size:9
Alignment explanation
Indices: 2447694--2447741 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 9
2447684 CCGTTGACCC
2447694 GACC-CGTT
1 GACCACGTT
2447702 GA-C-CGTT
1 GACCACGTT
2447709 GACC-CGTT
1 GACCACGTT
2447717 GACCCACGTT
1 GA-CCACGTT
2447727 GACCACTGTT
1 GACCAC-GTT
2447737 GACCA
1 GACCA
2447742 AAACTTTGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.19
8 9 0.25
9 6 0.17
10 14 0.39
ACGTcount: A:0.19, C:0.35, G:0.23, T:0.23
Consensus pattern (9 bp):
GACCACGTT
Found at i:2449042 original size:18 final size:18
Alignment explanation
Indices: 2449016--2449051 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2449006 TCGAAAGGAC
*
2449016 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
2449034 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
2449052 CGGATGAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:2450224 original size:23 final size:24
Alignment explanation
Indices: 2450197--2450289 Score: 109
Period size: 23 Copynumber: 4.0 Consensus size: 24
2450187 CCGACTTTGA
* *
2450197 ATTCTGTTATGAT-CCTGACTTGG
1 ATTCTGATATGATACTTGACTTGG
* *
2450220 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACTTGG
* * *
2450243 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACTTGACTTGG
2450267 ATTCTGATATGATACTTGACTTG
1 ATTCTGATATGATACTTGACTTG
2450290 AATTATGTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
23 32 0.54
24 27 0.46
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACTTGG
Found at i:2450267 original size:24 final size:24
Alignment explanation
Indices: 2450212--2450286 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
2450202 GTTATGATCC
*
2450212 TGACTTGGATTCTGATCTGATA-T
1 TGACATGGATTCTGATCTGATACT
*
2450235 TGACATGGATTCTGATCTGATACA
1 TGACATGGATTCTGATCTGATACT
* *
2450259 TGACCTGGATTCTGATATGATACT
1 TGACATGGATTCTGATCTGATACT
2450283 TGAC
1 TGAC
2450287 TTGAATTATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 21 0.46
24 25 0.54
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.37
Consensus pattern (24 bp):
TGACATGGATTCTGATCTGATACT
Found at i:2451250 original size:18 final size:18
Alignment explanation
Indices: 2451227--2451261 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2451217 ACTTAGAATT
*
2451227 TGTCCCGAATGACCACTA
1 TGTCCCGAAAGACCACTA
2451245 TGTCCCGAAAGACCACT
1 TGTCCCGAAAGACCACT
2451262 CCTTAAGAAC
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:0.34, G:0.17, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:2451568 original size:18 final size:18
Alignment explanation
Indices: 2451545--2451579 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2451535 ACTTAGAATT
2451545 TGTCCCGAAGAACCACTA
1 TGTCCCGAAGAACCACTA
*
2451563 TGTCCCGAAGGACCACT
1 TGTCCCGAAGAACCACT
2451580 CTTTAAGAAC
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:0.34, G:0.20, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGAACCACTA
Found at i:2452047 original size:19 final size:18
Alignment explanation
Indices: 2452019--2452064 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
2452009 CACAATCATG
*
2452019 TAACATATATAATCATAT
1 TAACACATATAATCATAT
*
2452037 ATAACACATATACTCATAT
1 -TAACACATATAATCATAT
2452056 TAAACACAT
1 T-AACACAT
2452065 GCTCATGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (18 bp):
TAACACATATAATCATAT
Found at i:2460016 original size:18 final size:18
Alignment explanation
Indices: 2459976--2460018 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
2459966 ATATTATTTC
* **
2459976 ATTATCCTTATTATTATT
1 ATTATCATTATTAACATT
*
2459994 TTTATCATTATTAACATT
1 ATTATCATTATTAACATT
2460012 ATTATCA
1 ATTATCA
2460019 ATCATATCTC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATCATTATTAACATT
Found at i:2460521 original size:23 final size:22
Alignment explanation
Indices: 2460490--2460533 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
2460480 ATGTTCACAT
2460490 ATTCATATCACATAGGCTCATAG
1 ATTCATATCACATA-GCTCATAG
*
2460513 ATTCTTATCACATAGCTCATA
1 ATTCATATCACATAGCTCATA
2460534 TAACAGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (22 bp):
ATTCATATCACATAGCTCATAG
Found at i:2464758 original size:8 final size:8
Alignment explanation
Indices: 2464745--2464775 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
2464735 CTTTTATCAT
2464745 TTCACATA
1 TTCACATA
2464753 TTCACATA
1 TTCACATA
2464761 TTCACATA
1 TTCACATA
2464769 TTCACAT
1 TTCACAT
2464776 CACATAGGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.35, C:0.26, G:0.00, T:0.39
Consensus pattern (8 bp):
TTCACATA
Found at i:2471505 original size:20 final size:20
Alignment explanation
Indices: 2471467--2471505 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2471457 TTTGTATGCT
* *
2471467 AGTATTGATACTGACCCTTC
1 AGTATCGATACTGAACCTTC
*
2471487 AGTATCGATATTGAACCTT
1 AGTATCGATACTGAACCTT
2471506 GGTTATCGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (20 bp):
AGTATCGATACTGAACCTTC
Found at i:2471773 original size:20 final size:20
Alignment explanation
Indices: 2471748--2471799 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2471738 TTTAGACCCC
*
2471748 AGTATCGATACCACCCCATG-
1 AGTATCGATACCAACCC-TGA
*
2471768 AGTATCGAGACCAACCCTGA
1 AGTATCGATACCAACCCTGA
2471788 AGTATCGATACC
1 AGTATCGATACC
2471800 CCTTGAATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (20 bp):
AGTATCGATACCAACCCTGA
Found at i:2475451 original size:14 final size:16
Alignment explanation
Indices: 2475420--2475452 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
2475410 CTTTATGGTT
2475420 TTGACATGTTTGTATA
1 TTGACATGTTTGTATA
2475436 TTGA-ATGTTT-TATA
1 TTGACATGTTTGTATA
2475450 TTG
1 TTG
2475453 TTGTAAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 6 0.35
16 4 0.24
ACGTcount: A:0.24, C:0.03, G:0.18, T:0.55
Consensus pattern (16 bp):
TTGACATGTTTGTATA
Found at i:2476129 original size:30 final size:30
Alignment explanation
Indices: 2476094--2476428 Score: 347
Period size: 30 Copynumber: 11.2 Consensus size: 30
2476084 GTGGTTGTTA
* *
2476094 TGAAAGTGATGGTGTAGAAGTGGATAATGC
1 TGAAAGTGGTGGTGTAGAAATGGATAATGC
2476124 TGAAAGTGGTGGTGTAGAAATGGATAATGC
1 TGAAAGTGGTGGTGTAGAAATGGATAATGC
* * *
2476154 TGAAAGTGGTGGTGCATAAATGGATACTGC
1 TGAAAGTGGTGGTGTAGAAATGGATAATGC
* * *
2476184 TGAAA-TGGGTAGTGTAGAAAGGGACAATGC
1 TGAAAGT-GGTGGTGTAGAAATGGATAATGC
* * * *
2476214 TGAAA-TGGGTAGTGTTGAAAGGGACAATGC
1 TGAAAGT-GGTGGTGTAGAAATGGATAATGC
* *
2476244 TGAAAGTGGTGGTGTATAAATGGATACTGC
1 TGAAAGTGGTGGTGTAGAAATGGATAATGC
* * *
2476274 TGAAA-TGGGTAGTGTAGAAAGGGACAATGC
1 TGAAAGT-GGTGGTGTAGAAATGGATAATGC
*
2476304 TGAAAGTGGTGGTGTAGAAATGGATACTGC
1 TGAAAGTGGTGGTGTAGAAATGGATAATGC
* *
2476334 TGAAA-TGGGTAGTGTAGAAATGGACAATGC
1 TGAAAGT-GGTGGTGTAGAAATGGATAATGC
* * * * *
2476364 TGAAA-TGGGTAGTGTTGAAAGGGACAATGT
1 TGAAAGT-GGTGGTGTAGAAATGGATAATGC
* *
2476394 TGAAAGTGTTGGTGTAGAAATAGATAATGC
1 TGAAAGTGGTGGTGTAGAAATGGATAATGC
2476424 TGAAA
1 TGAAA
2476429 TGAGTAATGT
Statistics
Matches: 259, Mismatches: 40, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
29 3 0.01
30 253 0.98
31 3 0.01
ACGTcount: A:0.34, C:0.06, G:0.35, T:0.25
Consensus pattern (30 bp):
TGAAAGTGGTGGTGTAGAAATGGATAATGC
Found at i:2476249 original size:90 final size:90
Alignment explanation
Indices: 2476105--2476428 Score: 465
Period size: 90 Copynumber: 3.6 Consensus size: 90
2476095 GAAAGTGATG
* *
2476105 GTGTAG-AAGTGGATAATGCTGAAAGTGGTGGTGTAGAAATGGATAATGCTGAAAGTGGTGGTGC
1 GTGTAGAAAG-GGACAATGCTGAAAGTGGTGGTGTAGAAATGGATAATGCTGAAAGTGGTGGTGT
2476169 ATAAATGGATACTGCTGAAATGGGTA
65 ATAAATGGATACTGCTGAAATGGGTA
* * * *
2476195 GTGTAGAAAGGGACAATGCTGAAA-TGGGTAGTGTTGAAAGGGACAATGCTGAAAGTGGTGGTGT
1 GTGTAGAAAGGGACAATGCTGAAAGT-GGTGGTGTAGAAATGGATAATGCTGAAAGTGGTGGTGT
2476259 ATAAATGGATACTGCTGAAATGGGTA
65 ATAAATGGATACTGCTGAAATGGGTA
* *
2476285 GTGTAGAAAGGGACAATGCTGAAAGTGGTGGTGTAGAAATGGATACTGCTGAAA-TGGGTAGTGT
1 GTGTAGAAAGGGACAATGCTGAAAGTGGTGGTGTAGAAATGGATAATGCTGAAAGT-GGTGGTGT
* * *
2476349 AGAAATGGACAATGCTGAAATGGGTA
65 ATAAATGGATACTGCTGAAATGGGTA
* * * *
2476375 GTGTTGAAAGGGACAATGTTGAAAGTGTTGGTGTAGAAATAGATAATGCTGAAA
1 GTGTAGAAAGGGACAATGCTGAAAGTGGTGGTGTAGAAATGGATAATGCTGAAA
2476429 TGAGTAATGT
Statistics
Matches: 210, Mismatches: 20, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
89 2 0.01
90 204 0.97
91 4 0.02
ACGTcount: A:0.34, C:0.06, G:0.35, T:0.25
Consensus pattern (90 bp):
GTGTAGAAAGGGACAATGCTGAAAGTGGTGGTGTAGAAATGGATAATGCTGAAAGTGGTGGTGTA
TAAATGGATACTGCTGAAATGGGTA
Found at i:2478286 original size:20 final size:20
Alignment explanation
Indices: 2478261--2478298 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2478251 TAAGATATGT
*
2478261 TGTTGAAATATGTTGAGATA
1 TGTTGAAATATATTGAGATA
*
2478281 TGTTGAAGTATATTGAGA
1 TGTTGAAATATATTGAGA
2478299 CCATTTGAGA
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:0.34, C:0.00, G:0.26, T:0.39
Consensus pattern (20 bp):
TGTTGAAATATATTGAGATA
Found at i:2479522 original size:22 final size:21
Alignment explanation
Indices: 2479492--2479537 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2479482 TTATTCTTGC
*
2479492 AATTCAATGCAAAATGAAGAAA
1 AATTAAATGCAAAATGAA-AAA
* *
2479514 AATTAAATGCACAATGCAAAA
1 AATTAAATGCAAAATGAAAAA
2479535 AAT
1 AAT
2479538 CAAAGTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.20
Consensus pattern (21 bp):
AATTAAATGCAAAATGAAAAA
Found at i:2479635 original size:15 final size:15
Alignment explanation
Indices: 2479615--2479645 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2479605 AAACACATAC
2479615 AAACTTCCATTACAA
1 AAACTTCCATTACAA
2479630 AAACTTCCATTACAA
1 AAACTTCCATTACAA
2479645 A
1 A
2479646 GCTTTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (15 bp):
AAACTTCCATTACAA
Found at i:2486096 original size:22 final size:23
Alignment explanation
Indices: 2486071--2486118 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
2486061 TATGTGATAG
2486071 ATAAAATCTCAGGGTGGGCAC-C
1 ATAAAATCTCAGGGTGGGCACAC
*
2486093 ATAAAATTTCAGGGTGGGCACAC
1 ATAAAATCTCAGGGTGGGCACAC
2486116 ATA
1 ATA
2486119 CATTAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (23 bp):
ATAAAATCTCAGGGTGGGCACAC
Found at i:2487100 original size:19 final size:20
Alignment explanation
Indices: 2487078--2487123 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
2487068 TTTGTTTATC
2487078 TATATATTAAATAT-ATTTT
1 TATATATTAAATATAATTTT
* *
2487097 TATATCTTAATTATAATTTT
1 TATATATTAAATATAATTTT
2487117 T-TATATT
1 TATATATT
2487124 TATTTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TATATATTAAATATAATTTT
Found at i:2487293 original size:32 final size:32
Alignment explanation
Indices: 2487249--2487342 Score: 163
Period size: 32 Copynumber: 3.0 Consensus size: 32
2487239 CATTATTATA
* *
2487249 TTATTTTGTTACTCCACAAAAGAGCAGGAAGC
1 TTATTTTATTACTCCACAAAAGAGCAGAAAGC
2487281 TTATTTTATTACTCCACAAAAGAGCAGAAAGC
1 TTATTTTATTACTCCACAAAAGAGCAGAAAGC
2487313 TTATTTTATTACTCCACAAAAGAGCA-AAAG
1 TTATTTTATTACTCCACAAAAGAGCAGAAAG
2487343 GCAGGAAGAT
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
31 4 0.07
32 56 0.93
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (32 bp):
TTATTTTATTACTCCACAAAAGAGCAGAAAGC
Found at i:2488203 original size:3 final size:3
Alignment explanation
Indices: 2488195--2488221 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2488185 GAATAGGGTT
2488195 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG
2488222 ATTCACCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:2492972 original size:2 final size:2
Alignment explanation
Indices: 2492965--2493000 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2492955 ATTGTTATGA
2492965 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
2493001 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2493005 original size:2 final size:2
Alignment explanation
Indices: 2493000--2493047 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2492990 TATATATATA
2493000 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2493042 TG TG TG
1 TG TG TG
2493048 AAATATTACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2493296 original size:15 final size:15
Alignment explanation
Indices: 2493251--2493346 Score: 59
Period size: 15 Copynumber: 6.3 Consensus size: 15
2493241 TGAGTTTATG
* *
2493251 TGTTATAAGTGAATA
1 TGTTATATGTGAAAA
* *
2493266 TGTCATACGTGAAAAA
1 TGTTATATGTG-AAAA
2493282 TGTTATATGTGAAAAA
1 TGTTATATGTG-AAAA
* * * *
2493298 TGATCTACGTGAATA
1 TGTTATATGTGAAAA
* *
2493313 TGATATATGT-AAATG
1 TGTTATATGTGAAA-A
*
2493328 TGTTCTATGTGAAAA
1 TGTTATATGTGAAAA
2493343 TGTT
1 TGTT
2493347 TAAGTGAACA
Statistics
Matches: 62, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
14 2 0.03
15 32 0.52
16 28 0.45
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (15 bp):
TGTTATATGTGAAAA
Found at i:2493522 original size:23 final size:23
Alignment explanation
Indices: 2493496--2493610 Score: 87
Period size: 24 Copynumber: 5.0 Consensus size: 23
2493486 TTCTATATAA
*
2493496 TCCTTCGGGACAAACCTATGTGG
1 TCCTTCGGGACAAATCTATGTGG
* *
2493519 TCCTTTGTGACAAATCTATGTGG
1 TCCTTCGGGACAAATCTATGTGG
* *
2493542 TCCTTCAGGAAAAATTCTATGTGG
1 TCCTTCGGGACAAA-TCTATGTGG
*
2493566 -CACTTCAGTG-CAAATTCTATGTGG
1 TC-CTTC-GGGACAAA-TCTATGTGG
2493590 -CACTTCGGTG-CAAAT-TATGTG
1 TC-CTTCGG-GACAAATCTATGTG
2493611 AGCAATGGTG
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
22 6 0.08
23 33 0.43
24 37 0.48
25 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (23 bp):
TCCTTCGGGACAAATCTATGTGG
Found at i:2493565 original size:24 final size:25
Alignment explanation
Indices: 2493511--2493605 Score: 96
Period size: 24 Copynumber: 4.0 Consensus size: 25
2493501 CGGGACAAAC
*
2493511 CTATGTGGTCCTT-TGTGACAAA-T
1 CTATGTGGTCCTTCAGTGACAAATT
*
2493534 CTATGTGGTCCTTCAG-GAAAAATT
1 CTATGTGGTCCTTCAGTGACAAATT
2493558 CTATGTGG-CACTTCAGTG-CAAATT
1 CTATGTGGTC-CTTCAGTGACAAATT
*
2493582 CTATGTGG-CACTTCGGTG-CAAATT
1 CTATGTGGTC-CTTCAGTGACAAATT
2493606 ATGTGAGCAA
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
23 19 0.30
24 44 0.69
25 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (25 bp):
CTATGTGGTCCTTCAGTGACAAATT
Found at i:2495531 original size:12 final size:12
Alignment explanation
Indices: 2495510--2495550 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
2495500 TTGTTGTGCT
*
2495510 TGCTCTTCGGGC
1 TGCTCCTCGGGC
2495522 TGCTCCTCGGGC
1 TGCTCCTCGGGC
2495534 TGCTCCTCGGGC
1 TGCTCCTCGGGC
2495546 TGCTC
1 TGCTC
2495551 AGGTTCATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.00, C:0.39, G:0.32, T:0.29
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:2497139 original size:21 final size:21
Alignment explanation
Indices: 2497113--2497152 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2497103 CAGAACCCCA
*
2497113 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
2497134 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
2497153 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:2497181 original size:20 final size:21
Alignment explanation
Indices: 2497135--2497195 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
2497125 TTCCCCTGTG
2497135 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
2497158 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
2497178 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
2497196 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:2508940 original size:15 final size:15
Alignment explanation
Indices: 2508861--2508948 Score: 63
Period size: 15 Copynumber: 5.8 Consensus size: 15
2508851 GAGTATATGC
* *
2508861 GTTATAAGTAAAAAGT
1 GTTATATGTGAAAA-T
2508877 GTTATATGTGAAAAAT
1 GTTATATGTG-AAAAT
* * * *
2508893 GATCTACGTGAATAT
1 GTTATATGTGAAAAT
* *
2508908 GATATATGT-AAATGT
1 GTTATATGTGAAA-AT
2508923 GTTATATGTGAAAAT
1 GTTATATGTGAAAAT
2508938 GTT-TATGTGAA
1 GTTATATGTGAA
2508949 CACGTATTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
14 10 0.18
15 24 0.42
16 19 0.33
17 4 0.07
ACGTcount: A:0.40, C:0.02, G:0.20, T:0.38
Consensus pattern (15 bp):
GTTATATGTGAAAAT
Found at i:2511616 original size:16 final size:16
Alignment explanation
Indices: 2511595--2511625 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2511585 TTATCATATT
2511595 TGTAAATTGAAAATAA
1 TGTAAATTGAAAATAA
2511611 TGTAAATTGAAAATA
1 TGTAAATTGAAAATA
2511626 TGTGGAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (16 bp):
TGTAAATTGAAAATAA
Found at i:2513355 original size:23 final size:22
Alignment explanation
Indices: 2513324--2513377 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
2513314 ATCCACTAAG
* *
2513324 TGACATATGAAATTTGTCCCGAA
1 TGACCTATG-AATATGTCCCGAA
*
2513347 TGACCTATGTATATGTCCCGAA
1 TGACCTATGAATATGTCCCGAA
*
2513369 GGACCTATG
1 TGACCTATG
2513378 TAACCTGCGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (22 bp):
TGACCTATGAATATGTCCCGAA
Found at i:2513366 original size:22 final size:22
Alignment explanation
Indices: 2513338--2513379 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2513328 ATATGAAATT
*
2513338 TGTCCCGAATGACCTATGTATA
1 TGTCCCGAAGGACCTATGTATA
2513360 TGTCCCGAAGGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
2513380 ACCTGCGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATGTATA
Found at i:2513655 original size:23 final size:23
Alignment explanation
Indices: 2513629--2513683 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
2513619 TCTTATATCA
2513629 TCACATATATCATTTATGCTTAT
1 TCACATATATCATTTATGCTTAT
2513652 TCACATATATCATTTATGCTTAT
1 TCACATATATCATTTATGCTTAT
2513675 TCACATATA
1 TCACATATA
2513684 CACTAATCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.33, C:0.18, G:0.04, T:0.45
Consensus pattern (23 bp):
TCACATATATCATTTATGCTTAT
Found at i:2515970 original size:45 final size:45
Alignment explanation
Indices: 2515915--2516220 Score: 452
Period size: 45 Copynumber: 6.8 Consensus size: 45
2515905 ATGAATGAAT
* * *
2515915 AAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGCC
1 AAAATAATAATGCATATGGGTGCATTATCGGCATGAAAAGATACC
* *
2515960 AAAATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATCATTCC
1 AAAATAATAATGCATATGGGTGCATTATCGGCATGAAAAGAT-A--CC
* * *
2516008 -AAATAATAATGCATATGGGTGCATAATCGGCATGAAAATATATC
1 AAAATAATAATGCATATGGGTGCATTATCGGCATGAAAAGATACC
2516052 AAAATAATAATGCATATGGGTGCATTATCGGCATGAAAAGATACC
1 AAAATAATAATGCATATGGGTGCATTATCGGCATGAAAAGATACC
*
2516097 AAAATAATAATGCATATGGGTACATTATCGGCATGAAAAGATACC
1 AAAATAATAATGCATATGGGTGCATTATCGGCATGAAAAGATACC
* * *
2516142 AAAATAATAATGCATATGGGTACATTATCGGCATGAAAGGATGCC
1 AAAATAATAATGCATATGGGTGCATTATCGGCATGAAAAGATACC
* *
2516187 AAAATAATAATGCATATGGGTGTATTATTGGCAT
1 AAAATAATAATGCATATGGGTGCATTATCGGCAT
2516221 CCATTATCAG
Statistics
Matches: 240, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
44 1 0.00
45 199 0.83
46 1 0.00
47 37 0.15
48 2 0.01
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (45 bp):
AAAATAATAATGCATATGGGTGCATTATCGGCATGAAAAGATACC
Found at i:2516262 original size:57 final size:58
Alignment explanation
Indices: 2516164--2516277 Score: 185
Period size: 57 Copynumber: 2.0 Consensus size: 58
2516154 CATATGGGTA
* *
2516164 CATTATCGGCATGAAAGGATGCCAAAATAATAATGCATATGGGTGTATTATTGGCATC
1 CATTATCAGCATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTATTGGCATC
* *
2516222 CATTATCAGTATGAAAGGATGTC-AAATAATAATGCATATGGGTGCATTATTGGCAT
1 CATTATCAGCATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTATTGGCAT
2516278 GAAAGGATGC
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
57 32 0.62
58 20 0.38
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (58 bp):
CATTATCAGCATGAAAGGATGCCAAAATAATAATGCATATGGGTGCATTATTGGCATC
Found at i:2516331 original size:45 final size:46
Alignment explanation
Indices: 2516232--2516350 Score: 122
Period size: 45 Copynumber: 2.7 Consensus size: 46
2516222 CATTATCAGT
* * **
2516232 ATGAAAGGATGTCA-AA-TAATAATGCATATGGGTGCATTATTGGC
1 ATGAAAGGATGCCATAATTAATAATGCATATGAGTGCATTATTAAC
*
2516276 ATGAAAGGATGCCATAATTGA-AATGCATATGAGTGCATT-TTCAAC
1 ATGAAAGGATGCCATAATTAATAATGCATATGAGTGCATTATT-AAC
**
2516321 AT-AAACGGATGTTATAATTAATAATGCATA
1 ATGAAA-GGATGCCATAATTAATAATGCATA
2516351 ATAGTGTGTT
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
44 18 0.29
45 34 0.55
46 10 0.16
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.30
Consensus pattern (46 bp):
ATGAAAGGATGCCATAATTAATAATGCATATGAGTGCATTATTAAC
Found at i:2518726 original size:18 final size:20
Alignment explanation
Indices: 2518695--2518731 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2518685 GTGATCAGTG
2518695 AAATAGTGAAATC-ACCATA
1 AAATAGTGAAATCAACCATA
*
2518714 AAAT-GTGATATCAACCAT
1 AAATAGTGAAATCAACCAT
2518732 GACTGCAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (20 bp):
AAATAGTGAAATCAACCATA
Found at i:2522556 original size:22 final size:22
Alignment explanation
Indices: 2522529--2522586 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
2522519 GATACTGAAG
*
2522529 GGGTATCGATACTAACAAATGA
1 GGGTATCGATACTAACAAAGGA
2522551 GGGTATCGATACTAACAAAGGA
1 GGGTATCGATACTAACAAAGGA
**
2522573 AAGTATCGATACTA
1 GGGTATCGATACTA
2522587 TGGATCCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.22
Consensus pattern (22 bp):
GGGTATCGATACTAACAAAGGA
Found at i:2523231 original size:44 final size:46
Alignment explanation
Indices: 2523026--2523294 Score: 213
Period size: 45 Copynumber: 5.7 Consensus size: 46
2523016 TTTATTGTAT
* *
2523026 GCATGAAAGGATTCCA-AAATAATAATGCATATGGGTGCATTATTG
1 GCATGAAAGGATGCCATAATTAATAATGCATATGGGTGCATTATTG
* * * * *
2523071 GCATGCAATGATGTCA-AAATAATAATGCATATGGGTGCATTATCG
1 GCATGAAAGGATGCCATAATTAATAATGCATATGGGTGCATTATTG
* * * * * *
2523116 TCATGAAATGATGCTA-AAATAATAATGCATATGGGTGTATTATCG
1 GCATGAAAGGATGCCATAATTAATAATGCATATGGGTGCATTATTG
* ** *
2523161 GCATGTATTATTGGCATGAAATGATGCCAAATAATAATGCATATGGGTGCATTATTG
1 GCATG-A--A-AGG-ATG---CCAT---AATTAATAATGCATATGGGTGCATTATTG
* * *
2523218 GCATGAAAGGATGCCATAATTGA-AATGCATATGGGTGCATTTTTA
1 GCATGAAAGGATGCCATAATTAATAATGCATATGGGTGCATTATTG
* *
2523263 GCATAAAAGGATGCTATAATTAATAATGCATA
1 GCATGAAAGGATGCCATAATTAATAATGCATA
2523295 ATAGTGCGTT
Statistics
Matches: 184, Mismatches: 27, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
45 124 0.67
46 13 0.07
48 1 0.01
49 3 0.02
50 3 0.02
52 3 0.02
53 3 0.02
54 1 0.01
56 1 0.01
57 32 0.17
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.31
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAATTAATAATGCATATGGGTGCATTATTG
Found at i:2523245 original size:102 final size:103
Alignment explanation
Indices: 2523064--2523254 Score: 287
Period size: 102 Copynumber: 1.9 Consensus size: 103
2523054 ATATGGGTGC
* * *
2523064 ATTATTGGCATGCAATGATGTCAAAATAATAATGCATATGGGTGCATTATCGTCATGAAATGATG
1 ATTATTGGCATGAAATGATGTCAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATG
*
2523129 CTAAAATAATAATGCATATGGGTGTATTATCGGCATGT
66 CCAAAATAATAATGCATATGGGTGTATTATCGGCATGT
* *
2523167 ATTATTGGCATGAAATGATG-CCAAATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATG
1 ATTATTGGCATGAAATGATGTCAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATG
* *
2523231 CCATAATTGA-AATGCATATGGGTG
66 CCA-AAATAATAATGCATATGGGTG
2523255 CATTTTTAGC
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
102 56 0.71
103 23 0.29
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.31
Consensus pattern (103 bp):
ATTATTGGCATGAAATGATGTCAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATG
CCAAAATAATAATGCATATGGGTGTATTATCGGCATGT
Found at i:2526107 original size:23 final size:22
Alignment explanation
Indices: 2526077--2526151 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 22
2526067 TCCAGGGTTC
2526077 TATGTGGTCCTTCGGGAAAAAT
1 TATGTGGTCCTTCGGGAAAAAT
* *
2526099 ATATGTGGTCCTTCAGGACAAATT
1 -TATGTGGTCCTTCGGGA-AAAAT
*
2526123 CTATGTGGTACTTCGGTG-AAAAT
1 -TATGTGGTCCTTCGG-GAAAAAT
2526146 TATGTG
1 TATGTG
2526152 AGCAATGGTG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
22 6 0.14
23 20 0.45
24 17 0.39
25 1 0.02
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (22 bp):
TATGTGGTCCTTCGGGAAAAAT
Found at i:2526136 original size:24 final size:23
Alignment explanation
Indices: 2526074--2526146 Score: 83
Period size: 24 Copynumber: 3.1 Consensus size: 23
2526064 GAGTCCAGGG
*
2526074 TTCTATGTGGTCCTTCGGGAAAA
1 TTCTATGTGGTCCTTCAGGAAAA
* *
2526097 ATATATGTGGTCCTTCAGGACAAA
1 TTCTATGTGGTCCTTCAGGA-AAA
* *
2526121 TTCTATGTGGTACTTCGGTGAAAA
1 TTCTATGTGGTCCTTCAG-GAAAA
2526145 TT
1 TT
2526147 ATGTGAGCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
23 17 0.41
24 22 0.54
25 2 0.05
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCAGGAAAA
Found at i:2528913 original size:20 final size:20
Alignment explanation
Indices: 2528880--2528945 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
2528870 TACTGTTCAT
* *
2528880 TACTGTTCACACAGTATCAA
1 TACTATTCATACAGTATCAA
* **
2528900 TACTATTTATACAGTATCGG
1 TACTATTCATACAGTATCAA
*
2528920 TATTATTCATACAGTA-CAA
1 TACTATTCATACAGTATCAA
2528939 TACTATT
1 TACTATT
2528946 ATAAAAACAT
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
19 7 0.19
20 29 0.81
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (20 bp):
TACTATTCATACAGTATCAA
Found at i:2532056 original size:22 final size:22
Alignment explanation
Indices: 2532003--2532056 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
2531993 TACATAAATG
* *
2532003 GTATCGGCACTACTATATAAGG
1 GTATCGGTACTACTATATAAGA
*
2532025 GTATCAGTACTACTATATAAGA
1 GTATCGGTACTACTATATAAGA
2532047 GTATCGGTAC
1 GTATCGGTAC
2532057 CCTACAGGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (22 bp):
GTATCGGTACTACTATATAAGA
Found at i:2532123 original size:21 final size:21
Alignment explanation
Indices: 2532097--2532151 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
2532087 CGATGCTTGG
2532097 GAGGTATCGATACCTGATAAA
1 GAGGTATCGATACCTGATAAA
2532118 GAGGTATCGATACCTGATAAA
1 GAGGTATCGATACCTGATAAA
2532139 GAGGTATCGATAC
1 GAGGTATCGATAC
2532152 TACCCTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (21 bp):
GAGGTATCGATACCTGATAAA
Found at i:2538580 original size:27 final size:27
Alignment explanation
Indices: 2538550--2538614 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
2538540 TTCACTCCCT
2538550 TTCTCTGCACC-CTCTTTCTCCTCAACC
1 TTCTCTGC-CCTCTCTTTCTCCTCAACC
2538577 TTCTCTGCCCTCTCTTTCTCCTCAACC
1 TTCTCTGCCCTCTCTTTCTCCTCAACC
2538604 TTCTCTGCCCT
1 TTCTCTGCCCT
2538615 TTCAAGAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 2 0.05
27 35 0.95
ACGTcount: A:0.08, C:0.48, G:0.05, T:0.40
Consensus pattern (27 bp):
TTCTCTGCCCTCTCTTTCTCCTCAACC
Found at i:2540513 original size:9 final size:9
Alignment explanation
Indices: 2540495--2540534 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
2540485 GCAACGGTCA
*
2540495 GGTCAGACC
1 GGTCAAACC
2540504 GGTCAAACC
1 GGTCAAACC
*
2540513 GGTTCAGACC
1 GG-TCAAACC
2540523 GGTCAAACC
1 GGTCAAACC
2540532 GGT
1 GGT
2540535 TTCCAGCAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:2540521 original size:19 final size:19
Alignment explanation
Indices: 2540497--2540535 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2540487 AACGGTCAGG
2540497 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
2540516 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
2540535 T
1 T
2540536 TCCAGCAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:2547740 original size:5 final size:5
Alignment explanation
Indices: 2547730--2547796 Score: 66
Period size: 5 Copynumber: 12.8 Consensus size: 5
2547720 CACGGTCAAC
*
2547730 GGTCG GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTTAAC- GGTCG
1 GGTCG GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GG-T--CG GGTCG
2547779 GGTCG GGTC- GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC
2547797 AGACCGGTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
4 5 0.09
5 39 0.74
6 2 0.04
7 6 0.11
8 1 0.02
ACGTcount: A:0.06, C:0.21, G:0.52, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:2547760 original size:17 final size:17
Alignment explanation
Indices: 2547740--2547787 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
2547730 GGTCGGGTCG
2547740 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
*
2547757 GGTCGGGTCGGGTTAAC
1 GGTCGGGTCGGGTCAAC
2547774 GGTCGGGTCGGGTC
1 GGTCGGGTCGGGTC
2547788 GGTCGGGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.08, C:0.21, G:0.50, T:0.21
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:2547760 original size:22 final size:22
Alignment explanation
Indices: 2547723--2547789 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
2547713 AATGGTCCAC
2547723 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
* *
2547745 GGTC--GGGTCAACGGTCGGGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
*
2547767 GGTTAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
2547789 G
1 G
2547790 TCGGGTCAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
20 4 0.11
22 28 0.78
24 4 0.11
ACGTcount: A:0.09, C:0.21, G:0.51, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:2547805 original size:9 final size:9
Alignment explanation
Indices: 2547793--2547861 Score: 75
Period size: 9 Copynumber: 7.3 Consensus size: 9
2547783 GGGTCGGTCG
*
2547793 GGTCAGACC
1 GGTCAAACC
2547802 GGTCAAACC
1 GGTCAAACC
*
2547811 GGTTCAGACC
1 GG-TCAAACC
*
2547821 GATCAAACC
1 GGTCAAACC
*
2547830 GGTTCGAACC
1 GG-TCAAACC
2547840 GGTCGAAACC
1 GGTC-AAACC
2547850 GGTCAAACC
1 GGTCAAACC
2547859 GGT
1 GGT
2547862 TTCCAGCAGC
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
9 27 0.54
10 23 0.46
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:2547819 original size:19 final size:19
Alignment explanation
Indices: 2547795--2547861 Score: 84
Period size: 19 Copynumber: 3.5 Consensus size: 19
2547785 GTCGGTCGGG
2547795 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
2547814 TCAGACCGATCAAACCGGT
1 TCAGACCGGTCAAACCGGT
2547833 TC-GAACCGGTCGAAACCGG-
1 TCAG-ACCGGTC-AAACCGGT
*
2547852 TCAAACCGGT
1 TCAGACCGGT
2547862 TTCCAGCAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 1 0.02
19 34 0.81
20 7 0.17
ACGTcount: A:0.28, C:0.31, G:0.25, T:0.15
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:2548804 original size:2 final size:2
Alignment explanation
Indices: 2548797--2548823 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2548787 GCATTTATGC
2548797 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2548824 AACGCAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2565715 original size:36 final size:36
Alignment explanation
Indices: 2565674--2565751 Score: 156
Period size: 36 Copynumber: 2.2 Consensus size: 36
2565664 ATATTTATTT
2565674 ATGTGATTATGTGATGAAATGGTTGACTATATGAAC
1 ATGTGATTATGTGATGAAATGGTTGACTATATGAAC
2565710 ATGTGATTATGTGATGAAATGGTTGACTATATGAAC
1 ATGTGATTATGTGATGAAATGGTTGACTATATGAAC
2565746 ATGTGA
1 ATGTGA
2565752 ATATATGTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (36 bp):
ATGTGATTATGTGATGAAATGGTTGACTATATGAAC
Found at i:2566312 original size:2 final size:2
Alignment explanation
Indices: 2566305--2566329 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2566295 ATTGCATACT
2566305 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 T
2566330 TATCATTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2570599 original size:21 final size:22
Alignment explanation
Indices: 2570573--2570620 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2570563 CAAACTATTT
*
2570573 CAAAATA-TCATCGTGACATTA
1 CAAAATAGTCACCGTGACATTA
* *
2570594 CAAAATAGTCACCTTGATATTA
1 CAAAATAGTCACCGTGACATTA
2570616 CAAAA
1 CAAAA
2570621 ATAATCATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (22 bp):
CAAAATAGTCACCGTGACATTA
Found at i:2573758 original size:24 final size:24
Alignment explanation
Indices: 2573730--2573776 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2573720 CGACCAGAAA
2573730 TAATAGTAGATAGACTTAATAAAT
1 TAATAGTAGATAGACTTAATAAAT
2573754 TAATAGTAGATAGACTTAATAAA
1 TAATAGTAGATAGACTTAATAAA
2573777 GTAACACTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.51, C:0.04, G:0.13, T:0.32
Consensus pattern (24 bp):
TAATAGTAGATAGACTTAATAAAT
Found at i:2577554 original size:22 final size:22
Alignment explanation
Indices: 2577529--2577571 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2577519 TTAATAGCAG
* *
2577529 GAGTTATATGATTTAATTTCAA
1 GAGTTACATGATATAATTTCAA
2577551 GAGTTACATGATATAATTTCA
1 GAGTTACATGATATAATTTCA
2577572 GGCATTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (22 bp):
GAGTTACATGATATAATTTCAA
Found at i:2583141 original size:15 final size:15
Alignment explanation
Indices: 2583123--2583162 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
2583113 CTCGGCACAA
2583123 CACAGCTCGGTTCGG
1 CACAGCTCGGTTCGG
2583138 CACAGCTCGGTTCGG
1 CACAGCTCGGTTCGG
*
2583153 CACAACTCGG
1 CACAGCTCGG
2583163 CTTGTGGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.17, C:0.35, G:0.30, T:0.17
Consensus pattern (15 bp):
CACAGCTCGGTTCGG
Found at i:2583483 original size:22 final size:22
Alignment explanation
Indices: 2583458--2583509 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
2583448 GGAGTTACAA
*
2583458 GAGTTATATGATTTAATTTCAG
1 GAGTTATATGATATAATTTCAG
*
2583480 GAGTTACATGATATAATTTCAG
1 GAGTTATATGATATAATTTCAG
2583502 GAGTTATA
1 GAGTTATA
2583510 ACAGCTGCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (22 bp):
GAGTTATATGATATAATTTCAG
Found at i:2588895 original size:20 final size:20
Alignment explanation
Indices: 2588857--2588895 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2588847 ATTACACGTA
*
2588857 TTTTTATATATCTATTATTT
1 TTTTTATATATCGATTATTT
2588877 TTTTTAT-TATCGATCTATT
1 TTTTTATATATCGAT-TATT
2588896 AATTTTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.23, C:0.08, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTTTATATATCGATTATTT
Found at i:2589125 original size:21 final size:23
Alignment explanation
Indices: 2589091--2589136 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
2589081 AGGTGGAATT
*
2589091 ATTATAATATTTTAAAATTAATA
1 ATTATAATATTTTAAAATAAATA
*
2589114 ATTA-AAT-TTTTATAATAAATA
1 ATTATAATATTTTAAAATAAATA
2589135 AT
1 AT
2589137 ATTAATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 3 0.14
23 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTATAATATTTTAAAATAAATA
Found at i:2589148 original size:22 final size:21
Alignment explanation
Indices: 2589110--2589157 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
2589100 TTTTAAAATT
*
2589110 AATAATTAAATTTTTATAAT-A
1 AATAATTAAATTATTAT-ATCA
*
2589131 AATAATATTAATTATTATATCA
1 AATAAT-TAAATTATTATATCA
2589153 AATAA
1 AATAA
2589158 ATATCATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AATAATTAAATTATTATATCA
Found at i:2592528 original size:138 final size:138
Alignment explanation
Indices: 2592280--2593065 Score: 1288
Period size: 138 Copynumber: 5.7 Consensus size: 138
2592270 TACTATTCAT
* * * *
2592280 GTGAAGGCGCATTCCCAGGGGCGCGCCTTCGATTATTTTGTTAGAGAATATGTTATCATTTCCCT
1 GTGAAAGCGCGTTCCCAGGGGCGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCT
2592345 ATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTTAGGGGACTTG
66 ATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTTAGGGGACTTG
2592410 GCAAAGTG
131 GCAAAGTG
* * *
2592418 GTGAAAGCGTGTTCCCAGGGGGGCCCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 GTGAAAGCGCGTTCCCAGGGGCGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCT
2592483 ATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTTAGGGGACTTG
66 ATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTTAGGGGACTTG
2592548 GCAAAGTG
131 GCAAAGTG
*
2592556 GTGAAAGCGCGTTCTCAGGGGCGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 GTGAAAGCGCGTTCCCAGGGGCGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCT
* * *
2592621 ATTATGTCACTCGTGTCCCCTGAGGAACTATTCATGTCAGTACCTATTATTTCTTAGGGGACTTG
66 ATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTTAGGGGACTTG
*
2592686 GAAAAGTG
131 GCAAAGTG
* *
2592694 GTGAAAGCGCGTTCCCGGGGGTGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 GTGAAAGCGCGTTCCCAGGGGCGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCT
* * * * * *
2592759 ATTATGTCACTCATATCCTCCAGGGAACTATTTATGTTAGTACCTATTATTTC-T-GCGGGAATT
66 ATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTTAG-GGGACTT
2592822 GGCAAAGTG
130 GGCAAAGTG
*
2592831 GTGAAAGCGCGTTCCCAGGGGCGCGCCTTCAATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 GTGAAAGCGCGTTCCCAGGGGCGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCT
* *
2592896 ATTATGTCACTCATTTCCCCTCGGGGAACTATTTATGTCAGTACCTATTATTTCTTAGGGGACTT
66 ATTATGTCACTCATGTCCCC-CGGGGAACTATTCATGTCAGTACCTATTATTTCTTAGGGGACTT
2592961 GGCAAAGTG
130 GGCAAAGTG
* * * *
2592970 GTGAAAGCGTGTTCCCGGGGGCGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGTCTT
1 GTGAAAGCGCGTTCCCAGGGGCGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCT
*
2593035 ATTATGTCAGTCATGTCCCCCGGGGAACTAT
66 ATTATGTCACTCATGTCCCCCGGGGAACTAT
2593066 AGATGGATGG
Statistics
Matches: 601, Mismatches: 43, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
136 1 0.00
137 95 0.16
138 410 0.68
139 94 0.16
140 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (138 bp):
GTGAAAGCGCGTTCCCAGGGGCGCGCCTTCGATTATTTTGTCAGAGAATATGTTATCATTGCCCT
ATTATGTCACTCATGTCCCCCGGGGAACTATTCATGTCAGTACCTATTATTTCTTAGGGGACTTG
GCAAAGTG
Found at i:2593226 original size:23 final size:23
Alignment explanation
Indices: 2593200--2593302 Score: 69
Period size: 23 Copynumber: 4.7 Consensus size: 23
2593190 ATGTGAAGTT
2593200 TGAATAAATTGGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
**
2593223 TGAATAAATTAAAT-AAATGTTAA
1 TGAATAAATTGGATAAAATGTT-A
*
2593246 TTG-ATCAATTGG-T----TGTT-
1 -TGAATAAATTGGATAAAATGTTA
* *
2593263 TGAATATATTAGATAAAATGTTA
1 TGAATAAATTGGATAAAATGTTA
* *
2593286 TGGATAAATTGAATAAA
1 TGAATAAATTGGATAAA
2593303 TGTGAAGTGA
Statistics
Matches: 59, Mismatches: 12, Indels: 18
0.66 0.13 0.20
Matches are distributed among these distances:
16 2 0.03
17 6 0.10
18 1 0.02
19 4 0.07
22 12 0.20
23 32 0.54
24 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.16, T:0.38
Consensus pattern (23 bp):
TGAATAAATTGGATAAAATGTTA
Found at i:2593296 original size:40 final size:41
Alignment explanation
Indices: 2593218--2593296 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 41
2593208 TTGGATAAAA
* *
2593218 TGTTATGAATAAATTAAATAAATGTTAATTGATCAATTGGT
1 TGTTATGAATAAATTAAATAAATGTTAATGGATAAATTGGT
* *
2593259 TGTT-TGAATATATTAGATAAAATGTT-ATGGATAAATTG
1 TGTTATGAATAAATTAAAT-AAATGTTAATGGATAAATTG
2593297 AATAAATGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 22 0.67
41 11 0.33
ACGTcount: A:0.41, C:0.01, G:0.16, T:0.42
Consensus pattern (41 bp):
TGTTATGAATAAATTAAATAAATGTTAATGGATAAATTGGT
Found at i:2593321 original size:63 final size:63
Alignment explanation
Indices: 2593197--2593321 Score: 180
Period size: 63 Copynumber: 2.0 Consensus size: 63
2593187 GTTATGTGAA
* * *
2593197 GTTTGAATAAATTGGATAAAATGTTATGAATAAATTAAATAAATGTTAATTGATCAATTGGTT
1 GTTTGAATAAATTAGATAAAATGTTATGAATAAATTAAATAAATGTGAAGTGATCAATTGGTT
* * *
2593260 GTTTGAATATATTAGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGAT-AAGTTGGT
1 GTTTGAATAAATTAGATAAAATGTTATGAATAAATTAAATAAATGTGAAGTGATCAA-TTGGT
2593322 CGTGACATTA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
62 2 0.04
63 53 0.96
ACGTcount: A:0.42, C:0.01, G:0.19, T:0.38
Consensus pattern (63 bp):
GTTTGAATAAATTAGATAAAATGTTATGAATAAATTAAATAAATGTGAAGTGATCAATTGGTT
Found at i:2593552 original size:34 final size:34
Alignment explanation
Indices: 2593514--2593586 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
2593504 TTAAGTTGAA
2593514 TTTAATGTTAAATTTCGAATACCATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACCATAATTTGTAT
* *
2593548 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACCATAATTTGTAT
*
2593582 ATTAA
1 TTTAA
2593587 AAACATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (34 bp):
TTTAATGTTAAATTTCGAATACCATAATTTGTAT
Found at i:2594162 original size:21 final size:21
Alignment explanation
Indices: 2594106--2594164 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
2594096 ACCCTGCAGA
* *
2594106 CTAGGCATGTAA-CCTGGCGGG
1 CTAGGAATGTAACCCT-GAGGG
*
2594127 CTAGGAATATAACCCTGAGGG
1 CTAGGAATGTAACCCTGAGGG
2594148 CTAGGAATGTAACCCTG
1 CTAGGAATGTAACCCTG
2594165 CAGAGATGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 30 0.91
22 3 0.09
ACGTcount: A:0.27, C:0.22, G:0.31, T:0.20
Consensus pattern (21 bp):
CTAGGAATGTAACCCTGAGGG
Found at i:2595807 original size:28 final size:30
Alignment explanation
Indices: 2595743--2595809 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
2595733 TCATTTTCAT
2595743 AAATAATATGCATTATAAAAATTTATAATTA
1 AAATAATATGCATTAT-AAAATTTATAATTA
* *
2595774 ATATAA-ATTCATTAT-AAATTTA-AATTAA
1 AAATAATATGCATTATAAAATTTATAATT-A
2595802 AAATAATA
1 AAATAATA
2595810 ATAAATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 4 0.13
28 13 0.42
29 1 0.03
30 8 0.26
31 5 0.16
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (30 bp):
AAATAATATGCATTATAAAATTTATAATTA
Found at i:2595820 original size:24 final size:24
Alignment explanation
Indices: 2595787--2595843 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
2595777 TAAATTCATT
2595787 ATAAAT-TTAA-ATTAAAAATAATA
1 ATAAATATTAACATTAAAAATAA-A
**
2595810 ATAAATATTAACATTAATTATAAA
1 ATAAATATTAACATTAAAAATAAA
*
2595834 AAAAATATTA
1 ATAAATATTA
2595844 CCATATCACT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.21
24 14 0.48
25 9 0.31
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAAATATTAACATTAAAAATAAA
Found at i:2596011 original size:18 final size:18
Alignment explanation
Indices: 2595984--2596018 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2595974 AATATTATAT
* *
2595984 AAATATTATTTTTATAAA
1 AAATAATATTTATATAAA
2596002 AAATAATATTTATATAA
1 AAATAATATTTATATAA
2596019 TTATATTACT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATAATATTTATATAAA
Found at i:2596032 original size:32 final size:33
Alignment explanation
Indices: 2595964--2596040 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 33
2595954 TTAATAAATT
**
2595964 TAAATAAATAAATATTATATAAATATTATTTTTA
1 TAAA-AAATAAATATTATATAAATATTATTACTA
*
2595998 TAAAAAAT-AATATTTATATAATTA-TATTACTA
1 TAAAAAATAAATA-TTATATAAATATTATTACTA
*
2596030 TAAAATATAAA
1 TAAAAAATAAA
2596041 AACTATTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 17 0.46
33 16 0.43
34 4 0.11
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (33 bp):
TAAAAAATAAATATTATATAAATATTATTACTA
Done.