Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007850.1 Hibiscus syriacus cultivar Beakdansim tig00110209_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: 1775394
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 9
Found at i:541048 original size:20 final size:20
Alignment explanation
Indices: 541023--541062 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
541013 ATCGCGTTGC
541023 CATTTTCATGTTGCGAATTT
1 CATTTTCATGTTGCGAATTT
* *
541043 CATTTTCGTGTTGTGAATTT
1 CATTTTCATGTTGCGAATTT
541063 AAGTTTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.53
Consensus pattern (20 bp):
CATTTTCATGTTGCGAATTT
Found at i:541069 original size:20 final size:20
Alignment explanation
Indices: 541026--541070 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
541016 GCGTTGCCAT
* *
541026 TTTCATGTTGCGAATTTCAT
1 TTTCATGTTGCGAATTTAAG
* *
541046 TTTCGTGTTGTGAATTTAAG
1 TTTCATGTTGCGAATTTAAG
541066 TTTCA
1 TTTCA
541071 AAAATCTTCT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.11, G:0.18, T:0.51
Consensus pattern (20 bp):
TTTCATGTTGCGAATTTAAG
Found at i:541427 original size:22 final size:22
Alignment explanation
Indices: 541397--541450 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
541387 GATGGAGATA
*
541397 GACGGATTTTGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
541419 GACGAATTTCGCTGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
541441 GACGGATTTC
1 GACGGATTTC
541451 ACCGTAGAGA
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:0.20, C:0.15, G:0.41, T:0.24
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:541590 original size:19 final size:19
Alignment explanation
Indices: 541566--541607 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
541556 GTTTCGAATT
**
541566 CGAAAATAAATTCGCTTTG
1 CGAAAATAAACGCGCTTTG
541585 CGAAAATAAACGCGCTTTG
1 CGAAAATAAACGCGCTTTG
541604 CGAA
1 CGAA
541608 TTTGACTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (19 bp):
CGAAAATAAACGCGCTTTG
Found at i:541657 original size:20 final size:20
Alignment explanation
Indices: 541629--541666 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
541619 TGTTGAGAAC
541629 TACAAATTCGCATTGCGATT
1 TACAAATTCGCATTGCGATT
* *
541649 TACATATTCGCGTTGCGA
1 TACAAATTCGCATTGCGA
541667 ATTTGGAAAC
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:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (20 bp):
TACAAATTCGCATTGCGATT
Found at i:554143 original size:2 final size:2
Alignment explanation
Indices: 554136--554184 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
554126 TTAAGAAATC
554136 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
554178 TA GA TA T
1 TA TA TA T
554185 TTATTTATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:555966 original size:3 final size:3
Alignment explanation
Indices: 555958--556023 Score: 62
Period size: 3 Copynumber: 22.0 Consensus size: 3
555948 CTGTAATATG
* * * *
555958 TAA TAA TAA TATT TAT TAT TAA TAA TAA AAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
556003 TAA TTA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
556024 AACGGGCAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.92
4 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:556505 original size:121 final size:112
Alignment explanation
Indices: 556376--556819 Score: 409
Period size: 113 Copynumber: 3.9 Consensus size: 112
556366 AAAGGCAAGA
* *
556376 TTGAACAAGTTCTTCTCATTATGAACTTCTT-TTCATTCTTCAGATGAGTTCTTCTAATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAATTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATTATGAA
* *
556440 CACTTC-TGGAAATATTGATGCTGATCTATCTCCTTCTGTGATAGAA-TCAAAC-AAAGG-
65 C-CTTCTTGGAAA-A--G-T--TGATCCA--T-C--CAGTGAT-GAATTCAAACAAAAGGT
* * *
556497 TTGAACAAGTTCTTCTCATTATGATTTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC
* *
556562 TTTCTTTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAAAAGGT
66 CTTC-TTGGAAAAGTTGATCCATCCAGTGATGAATTCAAACAAAAGGT
* *
556610 TTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGGTGAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAATTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * * * *
556675 CTCTACCTGGCAATGATGATCCATCAAGTGATGAATTCGAGA-AAAAGG-
65 C-CTTCTTGGAAAAGTTGATCCATCCAGTGATGAATTC-AAACAAAAGGT
* * * *
556723 TTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATAAA
1 TTGAACAAGTTCTTCTCATTATGAATTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAA
** * **
556788 CTCTTC-CAGAAATGTTGATCCATTGAGTGATG
65 C-CTTCTTGGAAAAGTTGATCCATCCAGTGATG
556820 GATTTGAATC
Statistics
Matches: 279, Mismatches: 35, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
110 3 0.01
111 11 0.04
112 25 0.09
113 97 0.35
114 62 0.22
115 4 0.01
116 6 0.02
118 1 0.00
119 1 0.00
120 3 0.01
121 57 0.20
122 9 0.03
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (112 bp):
TTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC
CTTCTTGGAAAAGTTGATCCATCCAGTGATGAATTCAAACAAAAGGT
Found at i:556698 original size:114 final size:113
Alignment explanation
Indices: 556477--556819 Score: 455
Period size: 113 Copynumber: 3.1 Consensus size: 113
556467 ATCTCCTTCT
*
556477 GTGATAGAA-TCAAAC-AAAGGTTGAACAAGTTCTTCTCATTATGATTTTCTTCTTCC-TCTTCA
1 GTGAT-GAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
* * *
556539 GATAAGTTCTTCTCATTATGAACT-TTCTTTGGAAAAGTTGATCCATCGA
65 GATGAGTTCTTCTCATTATGAACTCTTC-CTGGAAATGTTGATCCATCGA
*
556588 GTGATGAATTCAAACAAAAGGTTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
1 GTGATGAATTCAAACAAAAGG-TTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
* * * * *
556653 GGTGAGTTCTTCTCATTATGAACTCTACCTGGCAATGATGATCCATCAA
65 GATGAGTTCTTCTCATTATGAACTCTTCCTGGAAATGTTGATCCATCGA
* * *
556702 GTGATGAATTCGAGA-AAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
1 GTGATGAATTC-AAACAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
* * * *
556766 AATGAGTTCTTCTCATTATAAACTCTTCC-AGAAATGTTGATCCATTGA
65 GATGAGTTCTTCTCATTATGAACTCTTCCTGGAAATGTTGATCCATCGA
556814 GTGATG
1 GTGATG
556820 GATTTGAATC
Statistics
Matches: 203, Mismatches: 23, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
110 3 0.01
111 11 0.05
112 25 0.12
113 99 0.49
114 61 0.30
115 4 0.02
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
GTGATGAATTCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACTCTTCCTGGAAATGTTGATCCATCGA
Found at i:559732 original size:175 final size:175
Alignment explanation
Indices: 559441--559789 Score: 698
Period size: 175 Copynumber: 2.0 Consensus size: 175
559431 TTGCACGTGT
559441 TCCACATATCCCACTATGTACTTCTTCAATGATGCTTCTGACTTCACTATTATTGACACATCTCA
1 TCCACATATCCCACTATGTACTTCTTCAATGATGCTTCTGACTTCACTATTATTGACACATCTCA
559506 ATAGCATTTGATCATTGCTTCTTCTATACAAAGTCTCGCCATCAAGAAAGTATCCAGCAGCCATT
66 ATAGCATTTGATCATTGCTTCTTCTATACAAAGTCTCGCCATCAAGAAAGTATCCAGCAGCCATT
559571 CTTCTCAATGTTCTTTTATTAATCTCAGATGCATTTTGTGGATAG
131 CTTCTCAATGTTCTTTTATTAATCTCAGATGCATTTTGTGGATAG
559616 TCCACATATCCCACTATGTACTTCTTCAATGATGCTTCTGACTTCACTATTATTGACACATCTCA
1 TCCACATATCCCACTATGTACTTCTTCAATGATGCTTCTGACTTCACTATTATTGACACATCTCA
559681 ATAGCATTTGATCATTGCTTCTTCTATACAAAGTCTCGCCATCAAGAAAGTATCCAGCAGCCATT
66 ATAGCATTTGATCATTGCTTCTTCTATACAAAGTCTCGCCATCAAGAAAGTATCCAGCAGCCATT
559746 CTTCTCAATGTTCTTTTATTAATCTCAGATGCATTTTGTGGATA
131 CTTCTCAATGTTCTTTTATTAATCTCAGATGCATTTTGTGGATA
559790 TATAACAGCT
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
175 174 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (175 bp):
TCCACATATCCCACTATGTACTTCTTCAATGATGCTTCTGACTTCACTATTATTGACACATCTCA
ATAGCATTTGATCATTGCTTCTTCTATACAAAGTCTCGCCATCAAGAAAGTATCCAGCAGCCATT
CTTCTCAATGTTCTTTTATTAATCTCAGATGCATTTTGTGGATAG
Found at i:566592 original size:15 final size:15
Alignment explanation
Indices: 566572--566603 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
566562 TGCAATGAAT
566572 AATGAATGTATGCAA
1 AATGAATGTATGCAA
566587 AATGAATGTATGCAA
1 AATGAATGTATGCAA
566602 AA
1 AA
566604 GGTATTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:566885 original size:12 final size:12
Alignment explanation
Indices: 566864--566897 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
566854 CTATACTGCC
566864 TCTTTCTTCATT
1 TCTTTCTTCATT
*
566876 TCTTTTTTCATT
1 TCTTTCTTCATT
566888 TCTTTCTTCA
1 TCTTTCTTCA
566898 AAGAAGTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.68
Consensus pattern (12 bp):
TCTTTCTTCATT
Found at i:573382 original size:23 final size:23
Alignment explanation
Indices: 573354--573436 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
573344 TTAGTACAGA
573354 GGGAATCGATACCCCCCTTGAAG
1 GGGAATCGATACCCCCCTTGAAG
* * * *
573377 GGGAATCAATTCCCCCTTTGATG
1 GGGAATCGATACCCCCCTTGAAG
* * *
573400 GGGAACCGAT-TCCCCC-TGTAG
1 GGGAATCGATACCCCCCTTGAAG
573421 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
573437 TGGGGTTCTG
Statistics
Matches: 47, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
21 12 0.26
22 8 0.17
23 27 0.57
ACGTcount: A:0.23, C:0.31, G:0.25, T:0.20
Consensus pattern (23 bp):
GGGAATCGATACCCCCCTTGAAG
Found at i:575045 original size:18 final size:18
Alignment explanation
Indices: 575008--575048 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
574998 AGAATAACAC
* *
575008 GAGGAACAAGAACGAGCA
1 GAGGAACAAGAACAACCA
*
575026 GAGGAACAAGCACAACCA
1 GAGGAACAAGAACAACCA
575044 GAGGA
1 GAGGA
575049 TCAAATGCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.49, C:0.20, G:0.32, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGAACAACCA
Found at i:579277 original size:28 final size:28
Alignment explanation
Indices: 579246--579302 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
579236 TAAAGTAAAG
*
579246 ATATTAATAAAAAAAATAA-TATGTATAA
1 ATATT-ATAAAAAAAATAAGTATATATAA
* *
579274 ATATTATGAAAATAATAAGTATATATAA
1 ATATTATAAAAAAAATAAGTATATATAA
579302 A
1 A
579303 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (28 bp):
ATATTATAAAAAAAATAAGTATATATAA
Found at i:579817 original size:2 final size:2
Alignment explanation
Indices: 579810--579838 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
579800 AAATCTATTA
579810 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
579839 AATAAGATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:581460 original size:3 final size:3
Alignment explanation
Indices: 581446--581548 Score: 120
Period size: 3 Copynumber: 34.0 Consensus size: 3
581436 TTTGGGCATG
* * * * *
581446 TAA TATA TAA TAA TAA TATT TAT TAT TAA TAA TAA TATT TAT TAA TAA
1 TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA TAA TA-A TAA TAA TAA
581494 TAA TAA TAA TAA TAA TAA T-A TAA TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
581540 TAA TAA TAA
1 TAA TAA TAA
581549 AACGGGCAAA
Statistics
Matches: 91, Mismatches: 4, Indels: 10
0.87 0.04 0.10
Matches are distributed among these distances:
2 4 0.04
3 80 0.88
4 7 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:581477 original size:19 final size:19
Alignment explanation
Indices: 581452--581538 Score: 106
Period size: 19 Copynumber: 4.6 Consensus size: 19
581442 CATGTAATAT
581452 ATAATAATAATATTTATTA
1 ATAATAATAATATTTATTA
*
581471 TTAATAATAATATTTATTA
1 ATAATAATAATATTTATTA
* *
581490 ATAATAATAATA-ATAATA
1 ATAATAATAATATTTATTA
* *
581508 ATAAT-ATAATAATATAATA
1 ATAATAATAAT-ATTTATTA
581527 ATAATAATAATA
1 ATAATAATAATA
581539 ATAATAATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
17 5 0.08
18 10 0.16
19 41 0.67
20 5 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAATAATAATATTTATTA
Found at i:581526 original size:34 final size:33
Alignment explanation
Indices: 581446--581547 Score: 127
Period size: 34 Copynumber: 3.0 Consensus size: 33
581436 TTTGGGCATG
*
581446 TAATATATAATAATAATATTTATTATTAATAATAATA
1 TAATATATAATAATAATA---A-TAATAATAATAATA
*
581483 T-TTAT-TAATAATAATAATAATAATAATAATA
1 TAATATATAATAATAATAATAATAATAATAATA
581514 TAATAATATAATAATAATAATAATAATAATAATA
1 TAAT-ATATAATAATAATAATAATAATAATAATA
581548 AAACGGGCAA
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
31 14 0.24
32 2 0.03
33 2 0.03
34 26 0.44
35 11 0.19
36 3 0.05
37 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
TAATATATAATAATAATAATAATAATAATAATA
Found at i:582818 original size:3 final size:3
Alignment explanation
Indices: 582810--582948 Score: 62
Period size: 3 Copynumber: 47.0 Consensus size: 3
582800 TCTTCACATT
* * * * *
582810 TTA TTA TTA TTA TTA TT- TTA TTTC TTA TTT TTT TTA TT- TAA ATA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
582854 GTA -TA TTTA TTA -TA TT- TAA TTA TATA TTT TTA TTA TATA TTT TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA
*
582899 TTA TTTA TTA TTT TTA TTA TT- TTA TT- TTCA TT- TT- TTA TTCA TTA
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TT-A TTA
582943 TTA TTA
1 TTA TTA
582949 CTTCTTTCGG
Statistics
Matches: 105, Mismatches: 16, Indels: 30
0.70 0.11 0.20
Matches are distributed among these distances:
2 16 0.15
3 71 0.68
4 18 0.17
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:582869 original size:22 final size:20
Alignment explanation
Indices: 582838--582886 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
582828 TATTTCTTAT
*
582838 TTTTTTTATTTAAATAGTATA
1 TTTTTATATTTAAATA-TATA
*
582859 TTTATTATATTTAATTATATA
1 TTT-TTATATTTAAATATATA
582880 TTTTTAT
1 TTTTTAT
582887 TATATATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.16
21 10 0.40
22 11 0.44
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTATATTTAAATATATA
Found at i:582899 original size:23 final size:22
Alignment explanation
Indices: 582810--582910 Score: 84
Period size: 23 Copynumber: 4.6 Consensus size: 22
582800 TCTTCACATT
* *
582810 TTATTATTATTATTAT-TTTAT
1 TTATTATTTTTATTATATTTAA
*
582831 TTCTTATTTTT-TT-TATTTAA
1 TTATTATTTTTATTATATTTAA
* * *
582851 ATAGTATATTTATTATATTTAA
1 TTATTATTTTTATTATATTTAA
*
582873 TTATATATTTTTATTATATATT-T
1 TTAT-TATTTTTATTATAT-TTAA
582896 TTATTATTTATTATT
1 TTATTATTT-TTATT
582911 TTTATTATTT
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
19 1 0.02
20 13 0.21
21 11 0.17
22 14 0.22
23 22 0.35
24 2 0.03
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (22 bp):
TTATTATTTTTATTATATTTAA
Found at i:582973 original size:2 final size:2
Alignment explanation
Indices: 582966--583000 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
582956 CGGTATTTTA
582966 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
583001 CACTACTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:583154 original size:4 final size:4
Alignment explanation
Indices: 583145--583179 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
583135 TTATTTTCAT
583145 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
583180 TTATTTCGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:583316 original size:9 final size:8
Alignment explanation
Indices: 583252--583325 Score: 51
Period size: 8 Copynumber: 8.8 Consensus size: 8
583242 ATTTTTACTA
583252 TTTTATTT
1 TTTTATTT
583260 TTTTA-TT
1 TTTTATTT
* * *
583267 TTATGTCT
1 TTTTATTT
*
583275 TTTCATTT
1 TTTTATTT
*
583283 TTGTTTTTGT
1 TT-TTATT-T
583293 TTTTATTCCT
1 TTTTATT--T
583303 TTTTATTT
1 TTTTATTT
583311 TCTTTATTT
1 T-TTTATTT
583320 TTTTAT
1 TTTTAT
583326 CTTCATATGG
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
7 5 0.10
8 19 0.38
9 15 0.30
10 11 0.22
ACGTcount: A:0.11, C:0.07, G:0.04, T:0.78
Consensus pattern (8 bp):
TTTTATTT
Found at i:583323 original size:28 final size:26
Alignment explanation
Indices: 583250--583325 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 26
583240 ATATTTTTAC
583250 TATTTTATTTTTTTATTTTATGTCTTTT
1 TATTTT-TTTTTTT-TTTTATGTCTTTT
*
583278 CATTTTTGTTTTTGTTTTTAT-TCCTTTT
1 TATTTTT-TTTTT-TTTTTATGT-CTTTT
*
583306 TATTTTCTTTATTTTTTTAT
1 TATTTT-TTTTTTTTTTTAT
583326 CTTCATATGG
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
27 9 0.22
28 30 0.73
29 2 0.05
ACGTcount: A:0.12, C:0.07, G:0.04, T:0.78
Consensus pattern (26 bp):
TATTTTTTTTTTTTTTTATGTCTTTT
Found at i:584312 original size:18 final size:18
Alignment explanation
Indices: 584276--584313 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
584266 AACCATGCAG
*
584276 TTTACCTTTTTTTTCTCA
1 TTTACCTTTTATTTCTCA
584294 TTTACCTCTTTATTT-TCA
1 TTTACCT-TTTATTTCTCA
584312 TT
1 TT
584314 ATGCATCGCT
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:0.13, C:0.21, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTACCTTTTATTTCTCA
Found at i:584420 original size:161 final size:160
Alignment explanation
Indices: 584155--584475 Score: 633
Period size: 161 Copynumber: 2.0 Consensus size: 160
584145 GCCCAAGGGG
584155 GCATCGCTAAGGAGAACTCGAGTACCATTTTTTAAAACCTAAACCGGGAGACTATGGAGAAATAG
1 GCATCGCTAAGGAGAACTCGAGTACCATTTTTTAAAACCTAAACCGGGAGACTATGGAGAAATAG
584220 AGCCTACCCTGTTACTCCATTTTAAACCCTATGACATTTTTACCCTAACCATGCAGTTTACCTTT
66 AGCCTACCCTGTTACTCCATTTTAAACCCTATGACATTTTTACCCTAACCATGCAGTTTACC-TT
584285 TTTTTCTCATTTACCTCTTTATTTTCATTAT
130 TTTTTCTCATTTACCTCTTTATTTTCATTAT
584316 GCATCGCTAAGGAGAACTCGAGTACCATTTTTTAAAACCTAAACCGGGAGACTATGGAGAAATAG
1 GCATCGCTAAGGAGAACTCGAGTACCATTTTTTAAAACCTAAACCGGGAGACTATGGAGAAATAG
584381 AGCCTACCCTGTTACTCCATTTTAAACCCTATGACATTTTTACCCTAACCATGCAGTTTACCTTT
66 AGCCTACCCTGTTACTCCATTTTAAACCCTATGACATTTTTACCCTAACCATGCAGTTTACCTTT
584446 TTTTCTCATTTACCTCTTTATTTTCATTAT
131 TTTTCTCATTTACCTCTTTATTTTCATTAT
584476 TATTATTCTT
Statistics
Matches: 160, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
160 33 0.21
161 127 0.79
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (160 bp):
GCATCGCTAAGGAGAACTCGAGTACCATTTTTTAAAACCTAAACCGGGAGACTATGGAGAAATAG
AGCCTACCCTGTTACTCCATTTTAAACCCTATGACATTTTTACCCTAACCATGCAGTTTACCTTT
TTTTCTCATTTACCTCTTTATTTTCATTAT
Found at i:584459 original size:17 final size:18
Alignment explanation
Indices: 584437--584473 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
584427 AACCATGCAG
584437 TTTACCT-TTT-TTTCTCA
1 TTTACCTCTTTATTT-TCA
584454 TTTACCTCTTTATTTTCA
1 TTTACCTCTTTATTTTCA
584472 TT
1 TT
584474 ATTATTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
18 8 0.44
19 3 0.17
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTACCTCTTTATTTTCA
Found at i:590004 original size:23 final size:23
Alignment explanation
Indices: 589937--589996 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
589927 CATTTTATAT
*
589937 GGCACTTCGGTGAAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
589960 GGCACTTCGGTGCAATCCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
589983 GGCACTTCAGTGCA
1 GGCACTTCGGTGCA
589997 TTTATACGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.30, G:0.27, T:0.23
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:596302 original size:10 final size:10
Alignment explanation
Indices: 596287--596327 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
596277 GCCCTAAATT
596287 GAAAAAAAAA
1 GAAAAAAAAA
596297 GAAAAAAAAA
1 GAAAAAAAAA
*
596307 GAAAAAATAA
1 GAAAAAAAAA
*
596317 CAAAAGAAAAA
1 GAAAA-AAAAA
596328 AGAGAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 23 0.85
11 4 0.15
ACGTcount: A:0.85, C:0.02, G:0.10, T:0.02
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:596311 original size:15 final size:15
Alignment explanation
Indices: 596288--596328 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
596278 CCCTAAATTG
*
596288 AAAAAA-AAAGAA-A
1 AAAAAAGAAAAAATA
596301 AAAAAAGAAAAAATA
1 AAAAAAGAAAAAATA
*
596316 ACAAAAGAAAAAA
1 AAAAAAGAAAAAA
596329 GAGAAATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 6 0.25
14 5 0.21
15 13 0.54
ACGTcount: A:0.88, C:0.02, G:0.07, T:0.02
Consensus pattern (15 bp):
AAAAAAGAAAAAATA
Found at i:597260 original size:41 final size:41
Alignment explanation
Indices: 597215--597293 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
597205 CGAAGGGGTA
* * *
597215 ATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCAC
1 ATCCACGACTTCAACTCCACGACGAAGGATATCATGCCCAC
* *
597256 ATCCATGACTTCAACTTCACGACGAAGGATATCATGCC
1 ATCCACGACTTCAACTCCACGACGAAGGATATCATGCC
597294 AACTCTACAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.22
Consensus pattern (41 bp):
ATCCACGACTTCAACTCCACGACGAAGGATATCATGCCCAC
Found at i:598161 original size:2 final size:2
Alignment explanation
Indices: 598150--598189 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
598140 TACACTACTT
598150 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
598190 TCACATTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:599357 original size:16 final size:16
Alignment explanation
Indices: 599336--599390 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 16
599326 TTTAATTATA
599336 TATTTTTATTTTTCAT
1 TATTTTTATTTTTCAT
599352 TATTTTTTATTTTT-AT
1 TA-TTTTTATTTTTCAT
*
599368 TA-TTTT-GTTTTCAT
1 TATTTTTATTTTTCAT
599382 T-TTTTTATT
1 TATTTTTATT
599391 CATTATTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
13 4 0.12
14 11 0.33
15 1 0.03
16 6 0.18
17 11 0.33
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (16 bp):
TATTTTTATTTTTCAT
Found at i:599358 original size:17 final size:16
Alignment explanation
Indices: 599338--599373 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
599328 TAATTATATA
599338 TTTTTATTTTTCATTAT
1 TTTTTATTTTT-ATTAT
599355 TTTTTATTTTTATTAT
1 TTTTTATTTTTATTAT
599371 TTT
1 TTT
599374 GTTTTCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTATTTTTATTAT
Found at i:599738 original size:9 final size:8
Alignment explanation
Indices: 599679--599747 Score: 57
Period size: 9 Copynumber: 7.8 Consensus size: 8
599669 TACTATTTTA
*
599679 TTTTATTA
1 TTTTATTT
599687 TTTTATGTT
1 TTTTAT-TT
599696 TTTTCATTT
1 TTTT-ATTT
*
599705 TTATTTTTGT
1 TT-TTATT-T
599715 TTTTATTCCT
1 TTTTATT--T
599725 TTTTATTT
1 TTTTATTT
599733 TCTTTATTT
1 T-TTTATTT
599742 TTTTAT
1 TTTTAT
599748 CTTCATGTGG
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
8 13 0.25
9 23 0.45
10 15 0.29
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.78
Consensus pattern (8 bp):
TTTTATTT
Found at i:606378 original size:23 final size:20
Alignment explanation
Indices: 606306--606357 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
606296 CCAGGGGGGT
*
606306 ATCGATTCCCCTAGGGGAGA
1 ATCGGTTCCCCTAGGGGAGA
606326 ATCGGTTCCCCTAGGGGAGA
1 ATCGGTTCCCCTAGGGGAGA
606346 ATCGGTTCCCCT
1 ATCGGTTCCCCT
606358 TCAAAGGGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.29, G:0.29, T:0.23
Consensus pattern (20 bp):
ATCGGTTCCCCTAGGGGAGA
Found at i:606392 original size:20 final size:20
Alignment explanation
Indices: 606363--606400 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
606353 CCCCTTCAAA
*
606363 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
606383 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
606401 TACACCAAAA
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:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:606398 original size:43 final size:39
Alignment explanation
Indices: 606300--606398 Score: 103
Period size: 43 Copynumber: 2.4 Consensus size: 39
606290 AGAACCCCAG
606300 GGGGGTATCGATTCCCCTAGGGGAGAATCGGTTCCCCTA
1 GGGGGTATCGATTCCCCTAGGGGAGAATCGGTTCCCCTA
* *
606339 GGGGAGAATCGGTTCCCCTTCAAAGGGG-GAATCGGTT-CCCTCA
1 GGGG-GTATCGATTCCCC-T---AGGGGAGAATCGGTTCCCCT-A
606382 TGGGGGTATCGATTCCC
1 -GGGGGTATCGATTCCC
606399 TCTACACCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
39 4 0.08
40 11 0.22
41 1 0.02
42 4 0.08
43 20 0.41
44 9 0.18
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.23
Consensus pattern (39 bp):
GGGGGTATCGATTCCCCTAGGGGAGAATCGGTTCCCCTA
Found at i:610254 original size:22 final size:21
Alignment explanation
Indices: 610212--610251 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
610202 GAGTTTATTT
*
610212 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
610233 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
610252 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:612616 original size:16 final size:17
Alignment explanation
Indices: 612595--612630 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
612585 TTAACGTTAT
612595 TTTAAAATTAAATT-AA
1 TTTAAAATTAAATTGAA
*
612611 TTTAAATTTAAATTGAA
1 TTTAAAATTAAATTGAA
612628 TTT
1 TTT
612631 TTCTTATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTAAAATTAAATTGAA
Found at i:614450 original size:19 final size:20
Alignment explanation
Indices: 614406--614450 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
614396 ATTTGTTTTT
*
614406 AATAAATTTTTATATATGAA
1 AATAAATTTTTATATATCAA
* *
614426 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATATATCAA
614445 AATAAA
1 AATAAA
614451 ATATTAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATATATCAA
Found at i:616390 original size:23 final size:23
Alignment explanation
Indices: 616346--616390 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
616336 AAAGACAGAA
* *
616346 AAAAATATGTCATAACATTAAAG
1 AAAAATATGTCATAAAAATAAAG
616369 AAAAATATGTCATAAAAATAAA
1 AAAAATATGTCATAAAAATAAA
616391 ATTATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (23 bp):
AAAAATATGTCATAAAAATAAAG
Found at i:620900 original size:45 final size:45
Alignment explanation
Indices: 620798--620906 Score: 123
Period size: 44 Copynumber: 2.4 Consensus size: 45
620788 CTAATTTCTG
* *
620798 GTAGAAAAATATTGTTTTAGGTAGCATCCAATATTATCATTTCAT
1 GTAGAAAAATAATGTTTTAGGTAGCATCCAATATTAACATTTCAT
* * * *
620843 GTAAAAAAATAATG-TTTAGGTAGCGTTCAATATTAACATTT-TT
1 GTAGAAAAATAATGTTTTAGGTAGCATCCAATATTAACATTTCAT
*
620886 GATAGAACAAATAATATTTTA
1 G-TAGAA-AAATAATGTTTTA
620907 ACTAACGTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
43 2 0.04
44 28 0.53
45 19 0.36
46 4 0.08
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (45 bp):
GTAGAAAAATAATGTTTTAGGTAGCATCCAATATTAACATTTCAT
Found at i:624000 original size:18 final size:17
Alignment explanation
Indices: 623967--624000 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
623957 GAATAATTAA
623967 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
623984 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
624001 ATACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:627659 original size:51 final size:51
Alignment explanation
Indices: 627578--627861 Score: 410
Period size: 51 Copynumber: 5.6 Consensus size: 51
627568 AAAAAAGTAG
* *
627578 CACTTAACACATACTTAAACCGGTGTAAGTGAATAAAATAAACAAGTGTAT
1 CACTTAACACATACTTACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAT
* *
627629 CACTTAACACATACTTACACCGGTGCAAGTGAATAAAATAAACAAGTGTAT
1 CACTTAACACATACTTACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAT
* * * *
627680 CACTTAACACATACTTATACCGGTGCAAGTGAATAAAAACAAAAAAGTATAT
1 CACTTAACACATACTTACACCGGTGTAAGTGAAT-AAAATAAAAAAGTGTAT
* *
627732 CACTTAACACATAC-TACACCGGTGTAAGTGAATAAAATAAAAAAGTATAA
1 CACTTAACACATACTTACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAT
* * *
627782 CACTTAACACATACTTACAACGGTGTAAGTAAATAAAAT-AAAAAGTGTAA
1 CACTTAACACATACTTACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAT
* *
627832 CACTTAACATATACTTACACCGATGTAAGT
1 CACTTAACACATACTTACACCGGTGTAAGT
627862 ATGTATATCT
Statistics
Matches: 215, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
50 66 0.31
51 121 0.56
52 28 0.13
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.24
Consensus pattern (51 bp):
CACTTAACACATACTTACACCGGTGTAAGTGAATAAAATAAAAAAGTGTAT
Found at i:627955 original size:2 final size:2
Alignment explanation
Indices: 627948--627973 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
627938 AAAGAATTTA
627948 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
627974 TAAGTTATTT
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:634993 original size:21 final size:21
Alignment explanation
Indices: 634967--635018 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 21
634957 ATGAGATATT
*
634967 TAAATAATAAAAGCGA-TTAAA
1 TAAA-AATAAAAGCAATTTAAA
634988 T--AAATAAAAGCAATTTAAA
1 TAAAAATAAAAGCAATTTAAA
635007 TAAAAATAAAAG
1 TAAAAATAAAAG
635019 AATAGAGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 10 0.37
19 7 0.26
21 10 0.37
ACGTcount: A:0.65, C:0.04, G:0.08, T:0.23
Consensus pattern (21 bp):
TAAAAATAAAAGCAATTTAAA
Found at i:634995 original size:18 final size:19
Alignment explanation
Indices: 634964--635010 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
634954 GTAATGAGAT
*
634964 ATTTAAAT-AATAAAAGCG
1 ATTTAAATAAATAAAAGCA
634982 A-TTAAATAAATAAAAGCA
1 ATTTAAATAAATAAAAGCA
635000 ATTTAAATAAA
1 ATTTAAATAAA
635011 AATAAAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.23
18 11 0.42
19 9 0.35
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (19 bp):
ATTTAAATAAATAAAAGCA
Found at i:644918 original size:18 final size:19
Alignment explanation
Indices: 644887--644933 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
644877 GTAATGAGAT
*
644887 ATTTAAAT-AATAAAAGCG
1 ATTTAAATAAATAAAAGCA
644905 A-TTAAATAAATAAAAGCA
1 ATTTAAATAAATAAAAGCA
644923 ATTTAAATAAA
1 ATTTAAATAAA
644934 AATAAGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.23
18 11 0.42
19 9 0.35
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (19 bp):
ATTTAAATAAATAAAAGCA
Found at i:644936 original size:21 final size:20
Alignment explanation
Indices: 644890--644938 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
644880 ATGAGATATT
*
644890 TAAATAATAAAAGCGATTAAA
1 TAAA-AATAAAAGCAATTAAA
644911 T--AAATAAAAGCAATTTAAA
1 TAAAAATAAAAGCAA-TTAAA
644930 TAAAAATAA
1 TAAAAATAA
644939 GAGAATAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 10 0.42
19 7 0.29
21 7 0.29
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.24
Consensus pattern (20 bp):
TAAAAATAAAAGCAATTAAA
Found at i:652691 original size:18 final size:18
Alignment explanation
Indices: 652668--652720 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
652658 GGATATATGG
652668 ATAGTGGTCCTTCGGGAC
1 ATAGTGGTCCTTCGGGAC
* * *
652686 ATAGTGATCCTTTGGAAC
1 ATAGTGGTCCTTCGGGAC
*
652704 ATAGTAGTCCTTCGGGA
1 ATAGTGGTCCTTCGGGA
652721 AAGTTAAGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (18 bp):
ATAGTGGTCCTTCGGGAC
Found at i:658862 original size:21 final size:21
Alignment explanation
Indices: 658838--658891 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 21
658828 CTCCTTGCTA
658838 TGTATCGATACA-CTATGAATG
1 TGTATCGATACATCT-TGAATG
*
658859 TGTACCGATACATTCCTTGAATG
1 TGTATCGATACA-T-CTTGAATG
658882 TGTATCGATA
1 TGTATCGATA
658892 TACTCACAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 11 0.39
23 15 0.54
24 2 0.07
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (21 bp):
TGTATCGATACATCTTGAATG
Found at i:663107 original size:21 final size:22
Alignment explanation
Indices: 663078--663128 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
663068 AATTAGCTGA
*
663078 TTATCGATACCCTTACC-TAGT
1 TTATCGATACCCTCACCATAGT
*
663099 TTATTGATACCCTCACCATAG-
1 TTATCGATACCCTCACCATAGT
663120 -TATCGATAC
1 TTATCGATAC
663129 TTCTTTGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 8 0.31
21 15 0.58
22 3 0.12
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.35
Consensus pattern (22 bp):
TTATCGATACCCTCACCATAGT
Found at i:666265 original size:18 final size:18
Alignment explanation
Indices: 666212--666257 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
666202 GAGGGATTAT
666212 CAGTGGTCCTTCGAGACA
1 CAGTGGTCCTTCGAGACA
666230 CAGTGGTCCTTCGAGACA
1 CAGTGGTCCTTCGAGACA
666248 CAGTGGTCCT
1 CAGTGGTCCT
666258 ACGGGACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.24
Consensus pattern (18 bp):
CAGTGGTCCTTCGAGACA
Found at i:671041 original size:19 final size:21
Alignment explanation
Indices: 670996--671047 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
670986 TGTTGAGAGT
*
670996 GGTATTGATACCTTAAGGGATA
1 GGTATCGATACCTTAAGGGA-A
671018 GGTATCGATACCTTAA-GG-A
1 GGTATCGATACCTTAAGGGAA
671037 GGTATCGATAC
1 GGTATCGATAC
671048 TCTTGCATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 12 0.41
21 2 0.07
22 15 0.52
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (21 bp):
GGTATCGATACCTTAAGGGAA
Found at i:671118 original size:22 final size:20
Alignment explanation
Indices: 671091--671143 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
671081 ACCCTGAGGA
671091 GGTATCGATACCCTTGAAGGGT
1 GGTATCGATACCCTT--AGGGT
671113 GGTATC-AGTACCCTTAGGGT
1 GGTATCGA-TACCCTTAGGGT
*
671133 GGTACCGATAC
1 GGTATCGATAC
671144 TTCCAAGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 13 0.46
21 2 0.07
22 13 0.46
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (20 bp):
GGTATCGATACCCTTAGGGT
Found at i:671859 original size:21 final size:21
Alignment explanation
Indices: 671829--671885 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
671819 GTCGAGGGTC
* *
671829 TATGTAGTCCTTCGGGATAAT
1 TATGTGGTCCTTCGGGACAAT
*
671850 TATGTGGTCCTCCGGGACAAT
1 TATGTGGTCCTTCGGGACAAT
671871 TATGTGG-CACTTCGG
1 TATGTGGTC-CTTCGG
671886 TGCAACCCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.33
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACAAT
Found at i:673653 original size:283 final size:281
Alignment explanation
Indices: 673142--673679 Score: 868
Period size: 283 Copynumber: 1.9 Consensus size: 281
673132 TCAATTTATC
* *
673142 GCGTTTACCTATATATGTAATTATAAACCAATGCTTTGATGTAAGTTACAGAATTTAAGTTACAT
1 GCGTTTACCTATATAGGTAATTAGAAACCAATGCTTTGATGTAAGTTACAGAATTTAAGTTACAT
* * *
673207 ATTGTAACAAAATAACAAAAAAAGAAAAATAAATTTCAAAATAATATTTTTAATATTTTTTTAAT
66 ATTGTAACAAAATAAAAAAAAAAGAAAAATAAATTTCAAAAAAATAATTTTAATATTTTTTTAAT
*
673272 AATATCATGATTATATTTTTAAATTGAATTATTAACAAAACCGGTAAAAATGATCAAAAATATCA
131 AATATCATGATTATATTTTTAAATTGAATTATTAACAAAACCGGTAAAAATGATCAAAAACATCA
* *
673337 TTATTTTGACCGGTTATAATTACCTAGATAGGTAAACTCGGTAAAATTGAGTTGCGAAATCTGAA
196 TTATTTAGACCGGTTATAATTACCTAGATAGGTAAACACGGTAAAATTGAGTTGCGAAATCTGAA
673402 TTCCAGTTGCGAATTTTTACG
261 TTCCAGTTGCGAATTTTTACG
* * * *
673423 GCGTTTACCTATATAGGTAATTCGAAACCGATGCTTTGATGTAAGTTGCATAATTTAAGTTACAT
1 GCGTTTACCTATATAGGTAATTAGAAACCAATGCTTTGATGTAAGTTACAGAATTTAAGTTACAT
673488 ATTGTAACAAAATGACAAAAAAAAAAAGAAAAA-AAATTTCAAAAAAATAATTTTAATA-TTTTT
66 ATTGTAACAAAAT----AAAAAAAAAAGAAAAATAAATTTCAAAAAAATAATTTTAATATTTTTT
*
673551 TAATAATATCATG-TATATATTTTT-AATTGAATTATTAACAAAACCGGTAAAAAATGATCGAAA
127 TAATAATATCATGAT-TATATTTTTAAATTGAATTATTAACAAAACCGGT-AAAAATGATCAAAA
*
673614 ACATCATTATTTAGACCGGTTATAATTACCTATATAGGTAAACACGGTAAAATTGAGTTGCGAAA
190 ACATCATTATTTAGACCGGTTATAATTACCTAGATAGGTAAACACGGTAAAATTGAGTTGCGAAA
673679 T
255 T
673680 TGACGAATTC
Statistics
Matches: 237, Mismatches: 14, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
281 72 0.30
282 25 0.11
283 102 0.43
284 23 0.10
285 15 0.06
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (281 bp):
GCGTTTACCTATATAGGTAATTAGAAACCAATGCTTTGATGTAAGTTACAGAATTTAAGTTACAT
ATTGTAACAAAATAAAAAAAAAAGAAAAATAAATTTCAAAAAAATAATTTTAATATTTTTTTAAT
AATATCATGATTATATTTTTAAATTGAATTATTAACAAAACCGGTAAAAATGATCAAAAACATCA
TTATTTAGACCGGTTATAATTACCTAGATAGGTAAACACGGTAAAATTGAGTTGCGAAATCTGAA
TTCCAGTTGCGAATTTTTACG
Found at i:673708 original size:20 final size:22
Alignment explanation
Indices: 673669--673761 Score: 77
Period size: 20 Copynumber: 4.4 Consensus size: 22
673659 GGTAAAATTG
673669 AGTTGCGAAATTGACGAATTCA
1 AGTTGCGAAATTGACGAATTCA
* *
673691 AGTTGCGAAA-T-CCGAATTCG
1 AGTTGCGAAATTGACGAATTCA
* * *
673711 AGTTGCGAATTTGA-AAATT-G
1 AGTTGCGAAATTGACGAATTCA
* * *
673731 AGTTGCGAATTTGACAAATTCG
1 AGTTGCGAAATTGACGAATTCA
*
673753 TGTTGCGAA
1 AGTTGCGAA
673762 TTCGAAAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
20 31 0.51
21 11 0.18
22 19 0.31
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (22 bp):
AGTTGCGAAATTGACGAATTCA
Found at i:673751 original size:42 final size:41
Alignment explanation
Indices: 673705--673822 Score: 141
Period size: 42 Copynumber: 2.9 Consensus size: 41
673695 GCGAAATCCG
* *
673705 AATTCGAGTTGCGAATTTGAAAATTGAGTTGCGAATTTGAC
1 AATTCGTGTTGCGAATTCGAAAATTGAGTTGCGAATTTGAC
* * *
673746 AAATTCGTGTTGCGAATTCGAAAATTGTGTTTCAAATTTGAC
1 -AATTCGTGTTGCGAATTCGAAAATTGAGTTGCGAATTTGAC
* * *
673788 -TTTCGTGTTCCGAATTCG-AAATTGAATTGCGAATT
1 AATTCGTGTTGCGAATTCGAAAATTGAGTTGCGAATT
673823 CGTTGGTTAT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
39 13 0.20
40 16 0.25
42 36 0.55
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (41 bp):
AATTCGTGTTGCGAATTCGAAAATTGAGTTGCGAATTTGAC
Found at i:673783 original size:20 final size:20
Alignment explanation
Indices: 673712--673786 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
673702 CCGAATTCGA
*
673712 GTTGCGAATTTGAAAATTGA
1 GTTGCGAATTTGAAAATTGT
673732 GTTGCGAATTTGACAAATTCGT
1 GTTGCGAATTTGA-AAATT-GT
*
673754 GTTGCGAATTCGAAAATTGT
1 GTTGCGAATTTGAAAATTGT
* *
673774 GTTTCAAATTTGA
1 GTTGCGAATTTGA
673787 CTTTCGTGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
20 25 0.52
21 10 0.21
22 13 0.27
ACGTcount: A:0.31, C:0.09, G:0.23, T:0.37
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATTGT
Found at i:674699 original size:85 final size:85
Alignment explanation
Indices: 674556--674810 Score: 510
Period size: 85 Copynumber: 3.0 Consensus size: 85
674546 ATATTTTGTA
674556 AGGGTATAAATACACCTAATTAGCGAATCAAAGGAAGTTAGGTGTTAGGTAGGGCCCAAACATAT
1 AGGGTATAAATACACCTAATTAGCGAATCAAAGGAAGTTAGGTGTTAGGTAGGGCCCAAACATAT
674621 GAACCCGAATGAGTAGCATG
66 GAACCCGAATGAGTAGCATG
674641 AGGGTATAAATACACCTAATTAGCGAATCAAAGGAAGTTAGGTGTTAGGTAGGGCCCAAACATAT
1 AGGGTATAAATACACCTAATTAGCGAATCAAAGGAAGTTAGGTGTTAGGTAGGGCCCAAACATAT
674706 GAACCCGAATGAGTAGCATG
66 GAACCCGAATGAGTAGCATG
674726 AGGGTATAAATACACCTAATTAGCGAATCAAAGGAAGTTAGGTGTTAGGTAGGGCCCAAACATAT
1 AGGGTATAAATACACCTAATTAGCGAATCAAAGGAAGTTAGGTGTTAGGTAGGGCCCAAACATAT
674791 GAACCCGAATGAGTAGCATG
66 GAACCCGAATGAGTAGCATG
674811 TATTAATGTG
Statistics
Matches: 170, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 170 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (85 bp):
AGGGTATAAATACACCTAATTAGCGAATCAAAGGAAGTTAGGTGTTAGGTAGGGCCCAAACATAT
GAACCCGAATGAGTAGCATG
Found at i:678666 original size:33 final size:33
Alignment explanation
Indices: 678623--678721 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
678613 AGTTTACGAT
* *
678623 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
678656 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
*
678689 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
678721 A
1 A
678722 TTGGAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTTGATA
Found at i:678741 original size:21 final size:21
Alignment explanation
Indices: 678716--678757 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
678706 ACTTCAAGTT
*
678716 CGATAATTGGAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
678737 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
678758 AAAATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:681105 original size:26 final size:27
Alignment explanation
Indices: 681069--681125 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
681059 AAAAAACCGG
681069 TTTTTCCC-AAATCCGAT-TTCGGATAT
1 TTTTTCCCAAAATCCGATATTCGGAT-T
* *
681095 TTTTTCGCAAAATCGGATATTCGGATT
1 TTTTTCCCAAAATCCGATATTCGGATT
681122 TTTT
1 TTTT
681126 GTGCACCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 7 0.26
27 13 0.48
28 7 0.26
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.46
Consensus pattern (27 bp):
TTTTTCCCAAAATCCGATATTCGGATT
Found at i:681442 original size:14 final size:13
Alignment explanation
Indices: 681379--681429 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 13
681369 TTCATTGAAA
681379 AACCGAAAAACCG
1 AACCGAAAAACCG
681392 AACCGAAAAACTCG
1 AACCGAAAAAC-CG
681406 AACCGTTAAAAAACCCG
1 AACCG---AAAAA-CCG
681423 AACCGAA
1 AACCGAA
681430 CCGAAAAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 11 0.33
14 9 0.27
17 12 0.36
18 1 0.03
ACGTcount: A:0.51, C:0.29, G:0.14, T:0.06
Consensus pattern (13 bp):
AACCGAAAAACCG
Found at i:681547 original size:5 final size:5
Alignment explanation
Indices: 681537--681563 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
681527 TTTGGTAAAA
681537 AACCG AACCG AACCG AACCG AACCG AA
1 AACCG AACCG AACCG AACCG AACCG AA
681564 TATACCCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.37, G:0.19, T:0.00
Consensus pattern (5 bp):
AACCG
Found at i:682456 original size:6 final size:6
Alignment explanation
Indices: 682445--682477 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
682435 ACATAATTAA
682445 AAAATT AAAATT AAAAATT AAAATT -AAATT AAA
1 AAAATT AAAATT -AAAATT AAAATT AAAATT AAA
682478 TTTCAAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
6 14 0.56
7 6 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:682462 original size:13 final size:13
Alignment explanation
Indices: 682439--682472 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
682429 CAAATTACAT
682439 AATTAAAAAATTAA
1 AATT-AAAAATTAA
682453 AATTAAAAATTAA
1 AATTAAAAATTAA
682466 AATTAAA
1 AATTAAA
682473 TTAAATTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATTAAAAATTAA
Found at i:682567 original size:39 final size:40
Alignment explanation
Indices: 682518--682608 Score: 98
Period size: 39 Copynumber: 2.3 Consensus size: 40
682508 TTAAAAAATG
* *
682518 ATTTTGAATGTTAAT-AT-GAAATAATCTAATAAATTAAGA
1 ATTTAGAATGTTAATGATGGAAA-AATCTAAGAAATTAAGA
* * *
682557 ATTTAGAATGTT-ATGGTGGCAAAATTTAAGAAATTAAGA
1 ATTTAGAATGTTAATGATGGAAAAATCTAAGAAATTAAGA
*
682596 ATTTAAAATGTTA
1 ATTTAGAATGTTA
682609 GAGTGAATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
38 2 0.05
39 38 0.88
40 3 0.07
ACGTcount: A:0.46, C:0.02, G:0.14, T:0.37
Consensus pattern (40 bp):
ATTTAGAATGTTAATGATGGAAAAATCTAAGAAATTAAGA
Found at i:682672 original size:18 final size:17
Alignment explanation
Indices: 682640--682673 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
682630 ATGAATAAAT
*
682640 AAATAAATATAAAATAG
1 AAATAAAAATAAAATAG
682657 AAATAAAAAGTAAAATA
1 AAATAAAAA-TAAAATA
682674 TATATATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
AAATAAAAATAAAATAG
Found at i:683853 original size:19 final size:20
Alignment explanation
Indices: 683831--683868 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
683821 TCTGCATCAA
683831 AGAATGCTC-GAAGCATGAT
1 AGAATGCTCAGAAGCATGAT
* *
683850 AGAATTCTCAGAGGCATGA
1 AGAATGCTCAGAAGCATGA
683869 AACAAGATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (20 bp):
AGAATGCTCAGAAGCATGAT
Found at i:688915 original size:14 final size:13
Alignment explanation
Indices: 688896--688928 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
688886 TCATTACTTA
688896 ATTTTATTTTATTT
1 ATTTTATTTTA-TT
688910 ATTTTATTTTATT
1 ATTTTATTTTATT
688923 ATTTTA
1 ATTTTA
688929 AACCCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTATTTTATT
Found at i:691114 original size:21 final size:22
Alignment explanation
Indices: 691057--691134 Score: 74
Period size: 21 Copynumber: 3.6 Consensus size: 22
691047 ATAAAATACA
*
691057 CCGAAGTG-CCACATAGAATGTC
1 CCGAAGAGACCACATA-AATGTC
*
691079 CCGAA-AGACCACATAAATGTT
1 CCGAAGAGACCACATAAATGTC
*
691100 CCGAAGA-ACCGCATAGAAATGTC
1 CCGAAGAGACCACAT--AAATGTC
691123 CCGAAG-GACCAC
1 CCGAAGAGACCAC
691135 GTAGAATTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
21 17 0.37
22 13 0.28
23 16 0.35
ACGTcount: A:0.37, C:0.28, G:0.21, T:0.14
Consensus pattern (22 bp):
CCGAAGAGACCACATAAATGTC
Found at i:691126 original size:23 final size:24
Alignment explanation
Indices: 691057--691140 Score: 83
Period size: 23 Copynumber: 3.8 Consensus size: 24
691047 ATAAAATACA
*
691057 CCGAAGTG-CCACATAG-AATGTC
1 CCGAAGAGACCACATAGAAATGTC
*
691079 CCGAA-AGACCACAT--AAATGTT
1 CCGAAGAGACCACATAGAAATGTC
*
691100 CCGAAGA-ACCGCATAGAAATGTC
1 CCGAAGAGACCACATAGAAATGTC
*
691123 CCGAAG-GACCACGTAGAA
1 CCGAAGAGACCACATAGAA
691141 TTGTTCCAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
21 17 0.34
22 12 0.24
23 21 0.42
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.14
Consensus pattern (24 bp):
CCGAAGAGACCACATAGAAATGTC
Found at i:691359 original size:44 final size:46
Alignment explanation
Indices: 691282--691379 Score: 112
Period size: 44 Copynumber: 2.2 Consensus size: 46
691272 ATAGGTTATG
* *
691282 TCACATAGCTTATATCCTATGTTCATGTATTCACGTAGA-T-CATA
1 TCACATAGCTTATATCCTATGTTCATATATTCACATAGATTACATA
* * *
691326 TCACATAGCTTATATCGTGT-TCTCATATGTTCACATAGATTACATA
1 TCACATAGCTTATATCCTATGT-TCATATATTCACATAGATTACATA
*
691372 ACACATAG
1 TCACATAG
691380 AATTACATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 1 0.02
44 32 0.71
45 1 0.02
46 11 0.24
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (46 bp):
TCACATAGCTTATATCCTATGTTCATATATTCACATAGATTACATA
Found at i:691378 original size:16 final size:17
Alignment explanation
Indices: 691357--691388 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
691347 CTCATATGTT
691357 CACATAG-ATTACATAA
1 CACATAGAATTACATAA
691373 CACATAGAATTACATA
1 CACATAGAATTACATA
691389 TAACTCCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (17 bp):
CACATAGAATTACATAA
Found at i:696761 original size:23 final size:23
Alignment explanation
Indices: 696666--696775 Score: 73
Period size: 23 Copynumber: 4.8 Consensus size: 23
696656 ATAAAATACA
*
696666 CCGAAGTACCACGTAGAAATCTG-C
1 CCGAAGGACCACGTAG-AAT-TGTC
* * *
696690 ACCGAAGAACTACATAG-A-TGTC
1 -CCGAAGGACCACGTAGAATTGTC
* * * * *
696712 CTGAAGGACCACATATAAATGTA
1 CCGAAGGACCACGTAGAATTGTC
696735 CCGAAGGACCACGTAGAATTGTC
1 CCGAAGGACCACGTAGAATTGTC
* *
696758 CCGAATGACCGCGTAGAA
1 CCGAAGGACCACGTAGAA
696776 CCCTCGACTC
Statistics
Matches: 67, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
21 14 0.21
22 2 0.03
23 38 0.57
25 13 0.19
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (23 bp):
CCGAAGGACCACGTAGAATTGTC
Found at i:696952 original size:43 final size:44
Alignment explanation
Indices: 696850--696979 Score: 194
Period size: 44 Copynumber: 3.0 Consensus size: 44
696840 TTTAGGTTAC
*
696850 GTCACATAACTTATATCCTATGTTCATGTATTCACGTAGATCAT
1 GTCACATAGCTTATATCCTATGTTCATGTATTCACGTAGATCAT
696894 GTCACATAGCTTATATCCTATGTTCATGTATTCACGTAGA-CAT
1 GTCACATAGCTTATATCCTATGTTCATGTATTCACGTAGATCAT
* *
696937 GTCACATAGCTTATAT-CT-TGTTCTCATATATTCACATAGATCA
1 GTCACATAGCTTATATCCTATG-T-TCATGTATTCACGTAGATCA
696980 CATAGCACAT
Statistics
Matches: 80, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
41 2 0.03
42 3 0.04
43 34 0.43
44 41 0.51
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (44 bp):
GTCACATAGCTTATATCCTATGTTCATGTATTCACGTAGATCAT
Found at i:699693 original size:23 final size:22
Alignment explanation
Indices: 699645--699716 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 22
699635 CCACTAGGGG
* *
699645 CTATGAATTTGTCCCGAATGACCA
1 CTATGAA-ATGTCCCGAAGGA-CA
699669 CTATGAAATGTCCCGAAGGATCA
1 CTATGAAATGTCCCGAAGGA-CA
*
699692 C--TG-TATGTCCCGAAGGAC-
1 CTATGAAATGTCCCGAAGGACA
699710 CTATGAA
1 CTATGAA
699717 CCCTCGACTC
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 15 0.38
21 2 0.05
23 14 0.35
24 7 0.17
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (22 bp):
CTATGAAATGTCCCGAAGGACA
Found at i:700422 original size:24 final size:20
Alignment explanation
Indices: 700365--700442 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
700355 TTCCCCTTGA
*
700365 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
700385 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
*
700408 ATGTGCATCGATGCACTCCT-T
1 A-GTGCATCGATGCA-TCCTAC
700429 A-TGCATCGATGCAT
1 AGTGCATCGATGCAT
700443 TAATTGCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
18 1 0.02
19 12 0.24
20 14 0.29
21 2 0.04
22 1 0.02
23 4 0.08
24 14 0.29
25 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:703876 original size:20 final size:21
Alignment explanation
Indices: 703829--703885 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 21
703819 GCTATGAATT
703829 TGTCCCGAATGACCACTATAAAA
1 TGTCCCGAATGACCACTAT--AA
*
703852 TGTCCCGAATGACCACTGT-A
1 TGTCCCGAATGACCACTATAA
*
703872 TGTCCCGAAGGACC
1 TGTCCCGAATGACC
703886 TATAAACCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 14 0.44
23 18 0.56
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (21 bp):
TGTCCCGAATGACCACTATAA
Found at i:704569 original size:20 final size:20
Alignment explanation
Indices: 704538--704592 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
704528 TTCCCCTTGA
*
704538 AGTGCATCGATGCATTCTAC
1 AGTGTATCGATGCATTCTAC
*
704558 AGTGTATTGATGCATTCTAC
1 AGTGTATCGATGCATTCTAC
704578 AGTGTATCGATGCAT
1 AGTGTATCGATGCAT
704593 CCCTTAACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (20 bp):
AGTGTATCGATGCATTCTAC
Found at i:706019 original size:57 final size:57
Alignment explanation
Indices: 705952--706406 Score: 754
Period size: 57 Copynumber: 8.0 Consensus size: 57
705942 ATTACCAAAT
* *
705952 GGCATTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
*
706009 GGCACTTTGTGTGCAAAAAGTTAAGAAGTTCATACTAAGTGTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
* *
706066 GGCACTTTGTGTGCAAAAAGTTAAGAAGTTCATACTAAGTGTATGAATTTCTGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
* *
706123 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGATTTTCTGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
* *
706180 GGCACTTTGTGTGTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
706237 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT-
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
* * *
706293 GGCACTTTGTGTGCAAAAAGTTAAGAAGTTCATACTAAGTGTATGAATTTTCGTATA
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
** *
706350 GGCACAATGTGTGC-AAAA-TTAAGAAATTCATACTAAGTGTATGAATTTCTGTATG
1 GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
706405 GG
1 GG
706407 AACTATATGT
Statistics
Matches: 377, Mismatches: 20, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
55 35 0.09
56 58 0.15
57 284 0.75
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (57 bp):
GGCACTTTGTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
Found at i:720796 original size:53 final size:53
Alignment explanation
Indices: 720729--720837 Score: 128
Period size: 53 Copynumber: 2.1 Consensus size: 53
720719 TGTGTAGGTA
* * ** * * *
720729 TTAAGATATTGAGAGATGTATGTATTTACACCGATGTAACTATGAGTTAATTG
1 TTAAGATACTGAGAGATATACATACTTACACCAATGTAACTATGAGCTAATTG
* * *
720782 TTAAGTTACTGAGAGATATACATACTTACACCAATGTAAGTATGCGCTAATTG
1 TTAAGATACTGAGAGATATACATACTTACACCAATGTAACTATGAGCTAATTG
720835 TTA
1 TTA
720838 CACTTTTTTT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (53 bp):
TTAAGATACTGAGAGATATACATACTTACACCAATGTAACTATGAGCTAATTG
Found at i:723342 original size:12 final size:12
Alignment explanation
Indices: 723325--723356 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
723315 GACACTTTGA
723325 ATGGATGTGGGC
1 ATGGATGTGGGC
723337 ATGGATGTGGGC
1 ATGGATGTGGGC
723349 ATGGATGT
1 ATGGATGT
723357 TCCACTCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.19, C:0.06, G:0.47, T:0.28
Consensus pattern (12 bp):
ATGGATGTGGGC
Found at i:726322 original size:3 final size:3
Alignment explanation
Indices: 726314--726352 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
726304 ACAAGTTAAT
*
726314 TTC TTC TTC TTC TTA TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
726353 ATCATCGTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:728052 original size:12 final size:12
Alignment explanation
Indices: 728022--728054 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
728012 AAGCCTAATC
728022 ATAAAA-TACAA
1 ATAAAATTACAA
728033 AT-AAATTACAA
1 ATAAAATTACAA
728044 ATAAAATTACA
1 ATAAAATTACA
728055 CTTTTAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 3 0.15
11 9 0.45
12 8 0.40
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAAATTACAA
Found at i:730611 original size:14 final size:14
Alignment explanation
Indices: 730592--730621 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
730582 TGACCTACAC
730592 TTCAAGAAATTTGG
1 TTCAAGAAATTTGG
730606 TTCAAGAAATTTGG
1 TTCAAGAAATTTGG
730620 TT
1 TT
730622 TTCTTGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (14 bp):
TTCAAGAAATTTGG
Found at i:731745 original size:151 final size:151
Alignment explanation
Indices: 731427--731735 Score: 548
Period size: 151 Copynumber: 2.0 Consensus size: 151
731417 AGTTGTCCAT
731427 CCTATTTACCTCATCTATCAGAACTTTTGGCTTGAAAACGAATAGGCAAAGGCTCTTCTAATATC
1 CCTATTTA-CTCATCTATCAGAACTTTTGGCTTGAAAACGAATAGGCAAAGGCTCTTCTAATATC
731492 ATTTACTATGGATCATTAGCCTCTTCTCAAAGCCTTCCCTTATAAAATTTCATCCATTCTCATTC
65 ATTTACTATGGATCATTAGCCTCTTCTCAAAGCCTTCCCTTATAAAATTTCATCCATTCTCATTC
731557 TTCGTCCATATATTATGGTCCC
130 TTCGTCCATATATTATGGTCCC
731579 CCTATTTACCTCATCTATCAGAACTTTTGGC-TGAAAACGAATAGGCAAAGGCTCTTCTAATATC
1 CCTATTTA-CTCATCTATCAGAACTTTTGGCTTGAAAACGAATAGGCAAAGGCTCTTCTAATATC
*
731643 ATTTATTATGGATCATTAGCCTCTTCTCAAAAGCCTTCCCTTATAAAATTTCATCCATTTCTCAT
65 ATTTACTATGGATCATTAGCCTCTTCTC-AAAGCCTTCCCTTATAAAATTTCATCCA-TTCTCAT
731708 TCTTCTCGTCCATATATTATGGTCCC
128 TC-T-TCGTCCATATATTATGGTCCC
731734 CC
1 CC
731736 GTTTCCATCT
Statistics
Matches: 152, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
151 60 0.39
152 59 0.39
153 9 0.06
154 1 0.01
155 23 0.15
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (151 bp):
CCTATTTACTCATCTATCAGAACTTTTGGCTTGAAAACGAATAGGCAAAGGCTCTTCTAATATCA
TTTACTATGGATCATTAGCCTCTTCTCAAAGCCTTCCCTTATAAAATTTCATCCATTCTCATTCT
TCGTCCATATATTATGGTCCC
Found at i:734096 original size:34 final size:35
Alignment explanation
Indices: 734045--734116 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 35
734035 TATAGCTAAA
*
734045 AAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAATCGTCATTATTCGAATTTTGCCAAAAATAGC
734080 AAAATCGT-ATTATTCGAATTTTGCCAAAAATAGC
1 AAAATCGTCATTATTCGAATTTTGCCAAAAATAGC
734114 AAA
1 AAA
734117 TCCGAAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 28 0.78
35 8 0.22
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (35 bp):
AAAATCGTCATTATTCGAATTTTGCCAAAAATAGC
Found at i:735279 original size:18 final size:18
Alignment explanation
Indices: 735256--735318 Score: 81
Period size: 18 Copynumber: 3.3 Consensus size: 18
735246 TTCAGTATTC
735256 GTCCCGTAGGACCACTAT
1 GTCCCGTAGGACCACTAT
*
735274 GTCCCGAAGGACCACTGTATAT
1 GTCCCGTAGGACCAC----TAT
735296 GTCCCGTAGGACCACTAT
1 GTCCCGTAGGACCACTAT
735314 GTCCC
1 GTCCC
735319 AAAGGACTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 22 0.56
22 17 0.44
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (18 bp):
GTCCCGTAGGACCACTAT
Found at i:736918 original size:64 final size:62
Alignment explanation
Indices: 736813--736969 Score: 156
Period size: 64 Copynumber: 2.5 Consensus size: 62
736803 TAATGAAGGT
* * * **
736813 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATG-TTGTATTATTATAGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTTCTATT-TTA-AAAG
* * *
736877 ATGCATCGATGCATGACTTATGCATCGATTCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATGTTTCTATTTTAAAAG
*
736940 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
736970 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 4 0.05
64 67 0.85
65 8 0.10
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTTCTATTTTAAAAG
Found at i:740212 original size:18 final size:18
Alignment explanation
Indices: 740189--740251 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
740179 TTCAGTATTC
740189 GTCCCGTAGGACCACTAT
1 GTCCCGTAGGACCACTAT
*
740207 GTCCCGAAGGACCACTGTATAT
1 GTCCCGTAGGACCAC----TAT
*
740229 GTCCCGTATGACCACTAT
1 GTCCCGTAGGACCACTAT
740247 GTCCC
1 GTCCC
740252 AAAGGACTAC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 22 0.58
22 16 0.42
ACGTcount: A:0.22, C:0.33, G:0.21, T:0.24
Consensus pattern (18 bp):
GTCCCGTAGGACCACTAT
Found at i:741866 original size:64 final size:63
Alignment explanation
Indices: 741761--741922 Score: 159
Period size: 64 Copynumber: 2.5 Consensus size: 63
741751 TAATGAAGGT
* * * * **
741761 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGCATTCGATG-TTGTATTATTATAGG
1 ATGCATCGATGCA-TACTAATGCATCGATACACTAAAATGCATTCGATGTTTCTATT-TTA-AAA
741824 G
63 G
* * *
741825 ATGCATCGATGCATGACTTATGCATCGATTCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCAT-ACTAATGCATCGATACACTAAAATGCATTCGATGTTTCTATTTTAAAAG
*
741888 AGTGCATCGATGCATTACCAATGCATCGATACACT
1 A-TGCATCGATGCA-TACTAATGCATCGATACACT
741923 TTCAAACAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
63 4 0.05
64 71 0.86
65 8 0.10
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATACACTAAAATGCATTCGATGTTTCTATTTTAAAAG
Found at i:746970 original size:28 final size:29
Alignment explanation
Indices: 746901--746981 Score: 94
Period size: 28 Copynumber: 2.8 Consensus size: 29
746891 TATATCTAAA
* *
746901 TAAA-TTATATATTTTAAAAATGTAATCAAT
1 TAAATTTA-ATATTTTAAAATTTTAA-CAAT
*
746931 GAAATTTAATATTTTAAAATTTTAA-AAT
1 TAAATTTAATATTTTAAAATTTTAACAAT
*
746959 TAAATTTAATATTTTAATATTTT
1 TAAATTTAATATTTTAAAATTTT
746982 TATAATTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
28 24 0.53
30 18 0.40
31 3 0.07
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (29 bp):
TAAATTTAATATTTTAAAATTTTAACAAT
Found at i:746974 original size:8 final size:8
Alignment explanation
Indices: 746935--747000 Score: 61
Period size: 8 Copynumber: 8.9 Consensus size: 8
746925 ATCAATGAAA
746935 TTTAATAT
1 TTTAATAT
*
746943 TTTAAAAT
1 TTTAATAT
746951 TTTAA-A-
1 TTTAATAT
*
746957 ATTAA-A-
1 TTTAATAT
746963 TTTAATAT
1 TTTAATAT
746971 TTTAATAT
1 TTTAATAT
* *
746979 TTTTATAA
1 TTTAATAT
746987 TTT-ATAT
1 TTTAATAT
746994 TTTAATA
1 TTTAATA
747001 CCAATTAGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
6 9 0.18
7 8 0.16
8 32 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TTTAATAT
Found at i:747127 original size:16 final size:15
Alignment explanation
Indices: 747097--747132 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
747087 TTTTTATTTT
*
747097 TAAAAATTAAATATA
1 TAAAAATGAAATATA
747112 TAAAAATGAAAT-TA
1 TAAAAATGAAATATA
747126 TAAAAAT
1 TAAAAAT
747133 ATTAAATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
TAAAAATGAAATATA
Found at i:747139 original size:16 final size:16
Alignment explanation
Indices: 747097--747139 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
747087 TTTTTATTTT
747097 TAAAAATTAAA-TATA
1 TAAAAATTAAATTATA
*
747112 TAAAAATGAAATTATA
1 TAAAAATTAAATTATA
747128 -AAAATATTAAAT
1 TAAAA-ATTAAAT
747140 CTAAGATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (16 bp):
TAAAAATTAAATTATA
Found at i:750106 original size:16 final size:16
Alignment explanation
Indices: 750081--750116 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
750071 GGATGATTAA
* *
750081 TTTTATTTTAATTTAT
1 TTTTAATTTAATATAT
750097 TTTTAATTTAATATAT
1 TTTTAATTTAATATAT
750113 TTTT
1 TTTT
750117 TCACCAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTAATTTAATATAT
Found at i:750341 original size:24 final size:25
Alignment explanation
Indices: 750314--750369 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
750304 TATTAAATTA
750314 ATTTTACATCTTAAC-ATTAAAAAT
1 ATTTTACATCTTAACTATTAAAAAT
** *
750338 ATTTTTTATCTTAACTTATTAAATAT
1 ATTTTACATCTTAAC-TATTAAAAAT
750364 ATTTTA
1 ATTTTA
750370 TTCTTTGCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 13 0.50
26 13 0.50
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTTTACATCTTAACTATTAAAAAT
Found at i:750344 original size:26 final size:25
Alignment explanation
Indices: 750321--750368 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
750311 TTAATTTTAC
750321 ATCTTAAC-ATTAAAAATATTTTTT
1 ATCTTAACTATTAAAAATATTTTTT
*
750345 ATCTTAACTTATTAAATATATTTT
1 ATCTTAAC-TATTAAAAATATTTT
750369 ATTCTTTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
26 13 0.62
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (25 bp):
ATCTTAACTATTAAAAATATTTTTT
Found at i:750370 original size:24 final size:25
Alignment explanation
Indices: 750304--750370 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 25
750294 TAAATTCACA
750304 TATTAAAT-TAATTTTACATCTTAACAT
1 TATTAAATAT-ATTTT--ATCTTAACAT
* *
750331 TA-AAAATATTTTTTATCTTAAC-T
1 TATTAAATATATTTTATCTTAACAT
750354 TATTAAATATATTTTAT
1 TATTAAATATATTTTAT
750371 TCTTTGCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
23 3 0.09
24 20 0.59
26 8 0.24
27 3 0.09
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (25 bp):
TATTAAATATATTTTATCTTAACAT
Found at i:750397 original size:29 final size:29
Alignment explanation
Indices: 750343--750475 Score: 142
Period size: 29 Copynumber: 4.5 Consensus size: 29
750333 AAAATATTTT
* *
750343 TTATCTTAACTTATTAAATATATTTTATTC
1 TTATCTTAACTTA-AAAAAATATTTTATTC
* *
750373 TT-TGCATAACTTAAAAAAATATTTTATTT
1 TTAT-CTTAACTTAAAAAAATATTTTATTC
* * *
750402 TTATTTTAATTTAAAAAATATATTTTAATC
1 TTATCTTAACTTAAAAAA-ATATTTTATTC
* * *
750432 TTATCTTAAATTAAAAATATAATTTATTC
1 TTATCTTAACTTAAAAAAATATTTTATTC
750461 TTATCTTAACTTAAA
1 TTATCTTAACTTAAA
750476 TATTTATATA
Statistics
Matches: 85, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
29 50 0.59
30 35 0.41
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.51
Consensus pattern (29 bp):
TTATCTTAACTTAAAAAAATATTTTATTC
Found at i:750404 original size:59 final size:59
Alignment explanation
Indices: 750340--750475 Score: 166
Period size: 59 Copynumber: 2.3 Consensus size: 59
750330 TTAAAAATAT
** * * *
750340 TTTTTATCTTAACTTATTAAATATATTTTATTCTT-TGCATAACTTAAAAAAATATTTTA
1 TTTTTATCTTAACTTAAAAAATATATTTTAATCTTAT-CATAAATTAAAAAAATAATTTA
* * * *
750399 TTTTTATTTTAATTTAAAAAATATATTTTAATCTTATCTTAAATTAAAAATATAATTTA
1 TTTTTATCTTAACTTAAAAAATATATTTTAATCTTATCATAAATTAAAAAAATAATTTA
*
750458 TTCTTATCTTAACTTAAA
1 TTTTTATCTTAACTTAAA
750476 TATTTATATA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 63 0.98
60 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (59 bp):
TTTTTATCTTAACTTAAAAAATATATTTTAATCTTATCATAAATTAAAAAAATAATTTA
Found at i:750542 original size:31 final size:30
Alignment explanation
Indices: 750507--750582 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
750497 CATTTTAAAT
*
750507 TTAAGATAAAAATATAATATATTTTTTGTAG
1 TTAAGATAAAAATATAATATA-TTTGTGTAG
*
750538 TTAAGATAAAAATAAAATATATTTGTGTAG
1 TTAAGATAAAAATATAATATATTTGTGTAG
* *
750568 CTAAAATAAAAATAT
1 TTAAGATAAAAATAT
750583 GATTTTAAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 20 0.50
31 20 0.50
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (30 bp):
TTAAGATAAAAATATAATATATTTGTGTAG
Found at i:750606 original size:30 final size:30
Alignment explanation
Indices: 750572--750634 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
750562 GTGTAGCTAA
*
750572 AATAAAA-ATATGATTTTAAGTTAAGATAAG
1 AATAAAAGATAT-ATTTTAAGTTAAAATAAG
750602 AATAAAAGATATATTTTAAGTTAAAATAAG
1 AATAAAAGATATATTTTAAGTTAAAATAAG
750632 AAT
1 AAT
750635 TAATTATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 27 0.87
31 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (30 bp):
AATAAAAGATATATTTTAAGTTAAAATAAG
Found at i:750670 original size:25 final size:25
Alignment explanation
Indices: 750639--750695 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
750629 AAGAATTAAT
750639 TATATTTAATAATTAAAGGAT-AAAA
1 TATATTTAATAATTAAA-GATAAAAA
* *
750664 TATATTTAATAATTTAAGTTAAAAA
1 TATATTTAATAATTAAAGATAAAAA
750689 TATATTT
1 TATATTT
750696 TATGTAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 2 0.07
25 27 0.93
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (25 bp):
TATATTTAATAATTAAAGATAAAAA
Found at i:750765 original size:33 final size:29
Alignment explanation
Indices: 750712--750802 Score: 121
Period size: 32 Copynumber: 3.0 Consensus size: 29
750702 ATAAATTAAG
750712 ATAAGAATAAAATATATTTTTTAAGTAAA
1 ATAAGAATAAAATATATTTTTTAAGTAAA
*
750741 TATAAAGATTAAAATATATATTTTTAAAGTTAAA
1 -AT-AAGAATAAAATATAT-TTTTT-AAG-TAAA
750775 ATAAGAATAAAATATA-TTTTTAAGTAAA
1 ATAAGAATAAAATATATTTTTTAAGTAAA
750803 GATGTAAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
28 4 0.07
29 3 0.05
30 7 0.13
31 14 0.25
32 18 0.33
33 5 0.09
34 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (29 bp):
ATAAGAATAAAATATATTTTTTAAGTAAA
Found at i:750792 original size:30 final size:30
Alignment explanation
Indices: 750703--750797 Score: 113
Period size: 33 Copynumber: 3.1 Consensus size: 30
750693 TTTTATGTAA
*
750703 TAAA-TTAAGATAAGAATAAAATATATTTT
1 TAAAGTTAAAATAAGAATAAAATATATTTT
* *
750732 TTAAG-TAAATATAAAGATTAAAATATATATTTT
1 TAAAGTTAAA-AT-AAGAAT-AAA-ATATATTTT
750765 TAAAGTTAAAATAAGAATAAAATATATTTT
1 TAAAGTTAAAATAAGAATAAAATATATTTT
750795 TAA
1 TAA
750798 GTAAAGATGT
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
29 6 0.11
30 14 0.25
31 8 0.15
32 8 0.15
33 15 0.27
34 4 0.07
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (30 bp):
TAAAGTTAAAATAAGAATAAAATATATTTT
Found at i:751126 original size:16 final size:16
Alignment explanation
Indices: 751105--751135 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
751095 ACATGTTATC
751105 ACACTTGGTATCATTG
1 ACACTTGGTATCATTG
751121 ACACTTGGTATCATT
1 ACACTTGGTATCATT
751136 TGATTTGAGG
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:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (16 bp):
ACACTTGGTATCATTG
Found at i:751322 original size:33 final size:32
Alignment explanation
Indices: 751257--751323 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 32
751247 TCAGCTTCTC
* *
751257 TGTTAAATATTAATGCAAGTTGCTTAACTGAA
1 TGTTAAATATTAACGCAAGTCGCTTAACTGAA
* *
751289 TGTTAAATATTAACGACAAGTCGTTTAATTGAA
1 TGTTAAATATTAACG-CAAGTCGCTTAACTGAA
751322 TG
1 TG
751324 CATTTAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTTAAATATTAACGCAAGTCGCTTAACTGAA
Found at i:763810 original size:21 final size:21
Alignment explanation
Indices: 763762--763811 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
763752 ATGACTATCG
*
763762 CAATGCGATTTTCCAATTTCG
1 CAATGCGATTTTCCAATTTCA
**
763783 CGTTGCGATTTTCCCAA-TTCA
1 CAATGCGATTTT-CCAATTTCA
763804 CAATGCGA
1 CAATGCGA
763812 ATAAGTAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (21 bp):
CAATGCGATTTTCCAATTTCA
Found at i:763843 original size:20 final size:20
Alignment explanation
Indices: 763820--763947 Score: 143
Period size: 20 Copynumber: 6.3 Consensus size: 20
763810 GAATAAGTAA
*
763820 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
763840 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
763861 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
763881 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
763901 TTCGCAACGCGATTA-TGACT
1 ATCGCAACGCGA-TACTGACT
* *
763921 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
763941 ATCGCAA
1 ATCGCAA
763948 TGAGATAATA
Statistics
Matches: 93, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.03
20 72 0.77
21 16 0.17
22 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:763920 original size:40 final size:40
Alignment explanation
Indices: 763820--763947 Score: 161
Period size: 40 Copynumber: 3.2 Consensus size: 40
763810 GAATAAGTAA
* * ** *
763820 ATCGCAATGCGATACTGACTATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGACTTTCGCAACGCGATTCTGAC--T
763861 ATCGCAACGCGATACTGACTTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACTTTCGCAACGCGATTCTGACT
*
763901 TTCGCAACGCGATTA-TGACTTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGA-TACTGACTTTCGCAACGCGATTCTGACT
763941 ATCGCAA
1 ATCGCAA
763948 TGAGATAATA
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
40 42 0.54
41 34 0.44
42 2 0.03
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (40 bp):
ATCGCAACGCGATACTGACTTTCGCAACGCGATTCTGACT
Found at i:764127 original size:12 final size:12
Alignment explanation
Indices: 764108--764141 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
764098 CTCTCTGGCG
764108 ACATCCGTTCCT
1 ACATCCGTTCCT
*
764120 ATATCCGTTCCT
1 ACATCCGTTCCT
764132 ACATCC-TTCC
1 ACATCCGTTCC
764142 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:764721 original size:24 final size:24
Alignment explanation
Indices: 764694--764747 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
764684 GTATTCGAAA
*
764694 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
764718 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
764742 TTTGAT
1 TTTGAT
764748 GATGTTTCAG
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:767248 original size:20 final size:20
Alignment explanation
Indices: 767223--767318 Score: 140
Period size: 20 Copynumber: 4.8 Consensus size: 20
767213 CAACGGGGAA
767223 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
767243 ATCGCAACGCGAAAATGGA-T
1 ATCGCAACGCGAAAAT-GACT
* *
767263 ATCGCAACGCAAAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
767283 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
767303 ATCGCAGCGCGAAAAT
1 ATCGCAACGCGAAAAT
767319 TGCAATGCGA
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
19 1 0.01
20 67 0.96
21 2 0.03
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Done.