Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004321.1 Hibiscus syriacus cultivar Beakdansim tig00009472_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: 106644
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:520 original size:45 final size:45
Alignment explanation
Indices: 469--793 Score: 463
Period size: 45 Copynumber: 7.2 Consensus size: 45
459 AAAATAAGAA
* *
469 ATAAATGAAAAGCATAGTGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
*
514 ATAAATGAAATTCATAATGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
* * * * *
559 ATATATGAAATGAATAACT-ATGTATTATCGGTATGAAAGGATGCC
1 ATAAATGAAATGCATAA-TGGTGCATTATCGGCATGAAAGGATGCC
* *
604 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAATGATGCC
1 ATAAATGAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
*
649 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
* * * ** *
694 ATAAATGAAATGCATAACGGTGCATTATCGACATAAAAGGACACA
1 ATAAATGAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
* *
739 ATAAATAAAATGCATAATTGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
784 ATAAATGAAA
1 ATAAATGAAA
794 ATAACGAATA
Statistics
Matches: 247, Mismatches: 31, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
45 246 1.00
46 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.25
Consensus pattern (45 bp):
ATAAATGAAATGCATAATGGTGCATTATCGGCATGAAAGGATGCC
Found at i:7593 original size:95 final size:95
Alignment explanation
Indices: 7423--7620 Score: 299
Period size: 95 Copynumber: 2.1 Consensus size: 95
7413 AATATGTTGA
* * * *
7423 ATAATATAGTAGTATCGATATTAAGAGAAATGTATTGATACCAGAGATTCCATAATGTAGAAATG
1 ATAATATAGTAGTATCAATAATAAGAGAAAGGTATCGATACCAGAGATTCCATAATGTAGAAATG
*
7488 GTATCGATACTGAAAGGGAGTATCGGTACC
66 ATATCGATACTGAAAGGGAGTATCGGTACC
*
7518 ATAATATAGTAGTATCAATAATAAGAGAAAGGTGTCGATACCATG-GATTCCATAATGTAGAAAT
1 ATAATATAGTAGTATCAATAATAAGAGAAAGGTATCGATACCA-GAGATTCCATAATGTAGAAAT
* *
7582 GATATCTATACTGAAAGGGAGTATCGTTACC
65 GATATCGATACTGAAAGGGAGTATCGGTACC
*
7613 ATAGTATA
1 ATAATATA
7621 AAAGTATTGA
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
95 92 0.99
96 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.29
Consensus pattern (95 bp):
ATAATATAGTAGTATCAATAATAAGAGAAAGGTATCGATACCAGAGATTCCATAATGTAGAAATG
ATATCGATACTGAAAGGGAGTATCGGTACC
Found at i:8083 original size:45 final size:45
Alignment explanation
Indices: 8032--8356 Score: 481
Period size: 45 Copynumber: 7.2 Consensus size: 45
8022 AAAATGAGTA
* *
8032 ATAAATGAAATGCATAATGGTGCATTATCGACATG-AAGGAATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGG-ATGCC
** *
8077 ATAAATGAAATGCATAACAATGCATTATCGGCATGAAAGGATGTC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
8122 ATAAATAAAATGCATAACAGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
8167 ATAAATGAAATGTATAATGGTGCATTATCGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* **
8212 ATAAATGAAATGCATAATGGTGCATTATCAACATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * *
8257 ATAAATAAAATGCATAACGATGCATTATCGGCATGAAAAGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
8302 ATAAATGAAATGCATAACGGTGCATTATCGACATGAAATGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
8347 ATAAATGAAA
1 ATAAATGAAA
8357 ATAACGAATA
Statistics
Matches: 254, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 250 0.98
46 4 0.02
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (45 bp):
ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:10749 original size:45 final size:45
Alignment explanation
Indices: 10621--10837 Score: 269
Period size: 47 Copynumber: 4.8 Consensus size: 45
10611 TATAAAATCT
* ** *
10621 CTTACCATTTATCCCATAAGCTTGTAAGCTTATTTTTCCAAAATA
1 CTTACCATTTATTCCATAAGCTCATAAGCTTATTTTTCCAATATA
*
10666 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTAT-CAATATA
1 CTTACCATTT--ATTCCATAAGCTCATAAGCTTATTTT-TCCAATATA
* *
10713 TTTACCATTTGTTCCATAAGCTC-TAAGCTTATTTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCATAAGCTTATTTTT-CCAATATA
* *
10758 TTTACCATTTAATACCATAAGCTCATAAGCTTATTTTTCCAATATA
1 CTTACCATTT-ATTCCATAAGCTCATAAGCTTATTTTTCCAATATA
* *
10804 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCATAAGCTTATTT
10838 GCATGGTTAC
Statistics
Matches: 154, Mismatches: 11, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.01
44 35 0.23
45 41 0.27
46 24 0.16
47 52 0.34
48 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCATAAGCTTATTTTTCCAATATA
Found at i:10788 original size:91 final size:91
Alignment explanation
Indices: 10621--10837 Score: 287
Period size: 91 Copynumber: 2.4 Consensus size: 91
10611 TATAAAATCT
* * *
10621 CTTACCATTTATCCCATAAGCTTGTAAGCTTATTTTTCCAAAATACTTACCATTTAAATTCCATA
1 CTTACCATTTATTCCATAAGC-TCTAAGCTTATTTTTCCAAAATACTTACCATTTAAATACCATA
*
10686 AGCTCGTAAGCTTATTTTAT-CAATATA
65 AGCTCATAAGCTTATTTT-TCCAATATA
* * * *
10713 TTTACCATTTGTTCCATAAGCTCTAAGCTTATTTTTACCAATATATTTACCATTT-AATACCATA
1 CTTACCATTTATTCCATAAGCTCTAAGCTTATTTTT-CCAAAATACTTACCATTTAAATACCATA
10777 AGCTCATAAGCTTATTTTTCCAATATA
65 AGCTCATAAGCTTATTTTTCCAATATA
* *
10804 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTC-TAAGCTTATTT
10838 GCATGGTTAC
Statistics
Matches: 110, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
90 14 0.13
91 62 0.56
92 34 0.31
ACGTcount: A:0.31, C:0.21, G:0.07, T:0.41
Consensus pattern (91 bp):
CTTACCATTTATTCCATAAGCTCTAAGCTTATTTTTCCAAAATACTTACCATTTAAATACCATAA
GCTCATAAGCTTATTTTTCCAATATA
Found at i:15339 original size:2 final size:2
Alignment explanation
Indices: 15332--15364 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15322 TCTTATATCT
15332 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 T
15365 CTTATACTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17518 original size:23 final size:23
Alignment explanation
Indices: 17492--17558 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
17482 GTGCCACATA
*
17492 TTGTCCCGAAGAACCATATAGTT
1 TTGTCCCGAAGAACCACATAGTT
* *
17515 TTGTCACGAAGGACCACATAGTT
1 TTGTCCCGAAGAACCACATAGTT
*
17538 TTGTCCCAAATG-ACCACATAG
1 TTGTCCCGAA-GAACCACATAG
17559 AACCCTCGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
23 37 0.97
24 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (23 bp):
TTGTCCCGAAGAACCACATAGTT
Found at i:21792 original size:19 final size:19
Alignment explanation
Indices: 21745--21814 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
21735 TTTTCAATCA
*
21745 TAGTATCGATACCTTC-CTT
1 TAGTATCGATACC-CCACTT
*
21764 TTGATATCGATACCCCACTT
1 TAG-TATCGATACCCCACTT
*
21784 TAGTATCGATACTCCACTT
1 TAGTATCGATACCCCACTT
*
21803 CAGTATCGATAC
1 TAGTATCGATAC
21815 TACTTGCATC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
19 29 0.66
20 15 0.34
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.36
Consensus pattern (19 bp):
TAGTATCGATACCCCACTT
Found at i:24141 original size:36 final size:36
Alignment explanation
Indices: 24025--24141 Score: 94
Period size: 36 Copynumber: 3.2 Consensus size: 36
24015 TTGTTTCTTC
* *
24025 TGAAACAAAGTTTCGTCTCGTTTGAGACAATTT-TCCT
1 TGAAACAAA-TTTTGTCTCGCTTGAGACAATTTCT-CT
** * ***
24062 TGAAA-AAAAATTGATCTCACTTGAGATTGTTTTCTCT
1 TGAAACAAATTTTG-TCTCGCTTGAGA-CAATTTCTCT
**
24099 AAAAACAAATTTTGTCTCGCTTGAGACAATTTCTCT
1 TGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCT
24135 TGAAACA
1 TGAAACA
24142 CAAATCCTTG
Statistics
Matches: 58, Mismatches: 18, Indels: 9
0.68 0.21 0.11
Matches are distributed among these distances:
35 2 0.03
36 25 0.43
37 24 0.41
38 7 0.12
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (36 bp):
TGAAACAAATTTTGTCTCGCTTGAGACAATTTCTCT
Found at i:25128 original size:122 final size:122
Alignment explanation
Indices: 24910--25352 Score: 500
Period size: 122 Copynumber: 3.6 Consensus size: 122
24900 CTAGAACATA
* * * * *
24910 TTCAACACCAAATTATCTTCAGATTGACCCGACTTACTTAACAAGAAGGAACAACTTCATCTTCA
1 TTCAACACCAAATTATCTCCAGATTGACCCGATTTCCTCAACAAGAAGGAACAACGTCATCTTCA
* * * * *
24975 ACAAGA-AAGTTACCTAAAAGCGGCTAGAACTCTTAAACACTTATGATCAGAGTCATC
66 ACAA-ACAATTTACCTAAAAGCAGCTAGAACTCTTCAACACTGATGAACAGAGTCATC
** * * ** * *
25032 TTCAACACCGTATTATCTCCATATTAACATGATTTCCTCAACTAGAAGGAGCAACGTCATCTTCA
1 TTCAACACCAAATTATCTCCAGATTGACCCGATTTCCTCAACAAGAAGGAACAACGTCATCTTCA
* * * * * *
25097 ACAAACAATTTATCTAAAAGCAGCCAAAACTCTTCAACA-TGGATGAGCAGTGTCGTC
66 ACAAACAATTTACCTAAAAGCAGCTAGAACTCTTCAACACT-GATGAACAGAGTCATC
* * * * *
25154 TTTAACACCAAATTATCTCCAGATTGACCCGACTTCCTCAACGAGAA-GAGACTATGTCATCTT-
1 TTCAACACCAAATTATCTCCAGATTGACCCGATTTCCTCAACAAGAAGGA-ACAACGTCATCTTC
* * * *
25217 ATGCAAATAATTTACCTGAAAGCTA-CTAGAACTCTTCAACACGGATGAACAGAGTCATC
65 A-ACAAACAATTTACCTAAAAGC-AGCTAGAACTCTTCAACACTGATGAACAGAGTCATC
*
25276 TTCAACACCAAATTATCTCCAGATTGACCCGATTTCCTTAACAAGAAGGAACAACGTCATCTTCA
1 TTCAACACCAAATTATCTCCAGATTGACCCGATTTCCTCAACAAGAAGGAACAACGTCATCTTCA
25341 ACAAACAATTTA
66 ACAAACAATTTA
25353 TCTCAAAATA
Statistics
Matches: 260, Mismatches: 53, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
121 5 0.02
122 251 0.97
123 4 0.02
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (122 bp):
TTCAACACCAAATTATCTCCAGATTGACCCGATTTCCTCAACAAGAAGGAACAACGTCATCTTCA
ACAAACAATTTACCTAAAAGCAGCTAGAACTCTTCAACACTGATGAACAGAGTCATC
Found at i:25342 original size:244 final size:245
Alignment explanation
Indices: 24913--25360 Score: 618
Period size: 244 Copynumber: 1.8 Consensus size: 245
24903 GAACATATTC
* *
24913 AACACCAAATTATCTTCAGATTGACCCGACTTACTTAACAAGAAGGAACAACTTCATCTTCAACA
1 AACACCAAATTATCTCCAGATTGACCCGACTTACTCAACAAGAAGGAACAACTTCATCTTCAACA
* ** * **
24978 AGAAAGTTACCTAAAAGCGGCTAGAACTCTTAAACACTTATGATCAGAGTCATCTTCAACACCGT
66 AGAAAGTTACCTAAAAGCGACTAGAACTCTTAAACACGGATGAACAGAGTCATCTTCAACACCAA
* * * *
25043 ATTATCTCCATATTAACATGATTTCCTCAACTAGAAGGAGCAACGTCATCTTCAACAAACAATTT
131 ATTATCTCCAGATTAACACGATTTCCTCAACAAGAAGGAACAACGTCATCTTCAACAAACAATTT
25108 ATCT-AAAAGCAGCCAAAACTCTTCAACATGGATGAGCAGTGTCGTCTTT
196 ATCTCAAAAGCAGCCAAAACTCTTCAACATGGATGAGCAGTGTCGTCTTT
* * *
25157 AACACCAAATTATCTCCAGATTGACCCGACTTCCTCAACGAGAA-GAGACTA-TGTCATCTT-AT
1 AACACCAAATTATCTCCAGATTGACCCGACTTACTCAACAAGAAGGA-ACAACT-TCATCTTCA-
* * * * *
25219 GCAA-ATAATTTACCTGAAAGCTACTAGAACTCTTCAACACGGATGAACAGAGTCATCTTCAACA
63 ACAAGA-AAGTTACCTAAAAGCGACTAGAACTCTTAAACACGGATGAACAGAGTCATCTTCAACA
* * *
25283 CCAAATTATCTCCAGATTGACCCGATTTCCTTAACAAGAAGGAACAACGTCATCTTCAACAAACA
127 CCAAATTATCTCCAGATTAACACGATTTCCTCAACAAGAAGGAACAACGTCATCTTCAACAAACA
25348 ATTTATCTCAAAA
192 ATTTATCTCAAAA
25361 TACGACCAAA
Statistics
Matches: 176, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
243 5 0.03
244 167 0.95
245 4 0.02
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (245 bp):
AACACCAAATTATCTCCAGATTGACCCGACTTACTCAACAAGAAGGAACAACTTCATCTTCAACA
AGAAAGTTACCTAAAAGCGACTAGAACTCTTAAACACGGATGAACAGAGTCATCTTCAACACCAA
ATTATCTCCAGATTAACACGATTTCCTCAACAAGAAGGAACAACGTCATCTTCAACAAACAATTT
ATCTCAAAAGCAGCCAAAACTCTTCAACATGGATGAGCAGTGTCGTCTTT
Found at i:26891 original size:32 final size:32
Alignment explanation
Indices: 26847--26937 Score: 119
Period size: 32 Copynumber: 2.8 Consensus size: 32
26837 TCACTAACTT
**
26847 ACTAACATTCTAACCTTTATTTTATTATTCGA
1 ACTAACATTCTAATATTTATTTTATTATTCGA
* **
26879 ACTAACACTCTAATATTTATTTTATCGTTCGA
1 ACTAACATTCTAATATTTATTTTATTATTCGA
*
26911 ACTAACATTCTAATTGTTTATTTTATT
1 ACTAACATTCTAA-TATTTATTTTATT
26938 TGTTCTTACT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
32 39 0.78
33 11 0.22
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.48
Consensus pattern (32 bp):
ACTAACATTCTAATATTTATTTTATTATTCGA
Found at i:36671 original size:55 final size:55
Alignment explanation
Indices: 36592--37042 Score: 688
Period size: 55 Copynumber: 8.2 Consensus size: 55
36582 TTTATTAAGA
* * * * **
36592 TGCACACGTAGTGCCTGTAAGGTTATTCATCAGCTCATGATGAATTTTGTGGTTT
1 TGCACACTTAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTT
* *
36647 TGCTCACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTT
1 TGCACACTTAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTT
*
36702 TGCACACTTAGTGCTTGTACAGTTATTCATCAACTCATGATGAATTCCGTGGTTT
1 TGCACACTTAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTT
*
36757 TGCACACTTAGTGCTTGTACAGTTATTCATCAACTCATGATGAATTCCGTGGTTT
1 TGCACACTTAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTT
* * *
36812 TGCGCACTTAGTGCATGTACGGTTATTCATCAACTCAAGATGAATTCCGTGGTTT
1 TGCACACTTAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTT
* * *
36867 TGCACATTTAGTGCTTGTACAGTTATTCATCAACTCATGATGAATTACGTGGTTT
1 TGCACACTTAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTT
* *
36922 TGCACACTTAG-GCTTGTACGGTTATTCATCAACTCATGATAAATTTCGTGGTTT
1 TGCACACTTAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTT
* * * *
36976 TGCAAACTTAGTGCATGTACGATTATTCATCAACTCATGATGACTTCCGTGGTTT
1 TGCACACTTAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTT
*
37031 TGCACATTTAGT
1 TGCACACTTAGT
37043 TCCTGTAGTA
Statistics
Matches: 364, Mismatches: 31, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
54 50 0.14
55 314 0.86
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.38
Consensus pattern (55 bp):
TGCACACTTAGTGCTTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTT
Found at i:42015 original size:18 final size:19
Alignment explanation
Indices: 41974--42015 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
41964 AATGTCATAA
41974 ATAAA-TTTAGAAGTGTTT
1 ATAAATTTTAGAAGTGTTT
41992 ATAAATTTTATGAAGT-TTT
1 ATAAATTTTA-GAAGTGTTT
42011 A-AAAT
1 ATAAAT
42016 ATTTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.41
19 8 0.36
20 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (19 bp):
ATAAATTTTAGAAGTGTTT
Found at i:42019 original size:20 final size:19
Alignment explanation
Indices: 41979--42020 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
41969 CATAAATAAA
*
41979 TTTAGAAGTGTTTATAAAT
1 TTTAGAAGTGTTTAAAAAT
41998 TTTATGAAGT-TTTAAAATAT
1 TTTA-GAAGTGTTTAAAA-AT
42018 TTT
1 TTT
42021 TTAAATATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (19 bp):
TTTAGAAGTGTTTAAAAAT
Found at i:42178 original size:44 final size:44
Alignment explanation
Indices: 42124--42208 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
42114 TTTTCTACAG
* *
42124 GTTTCGAAACCCCTGCTTCAACGGTCAAAATTTATCAAAGGCAA
1 GTTTCAAAACCCCTACTTCAACGGTCAAAATTTATCAAAGGCAA
* * * *
42168 GTTTCAAAACCCCTACTTTAATGGTTAAAATTTTTCAAAGG
1 GTTTCAAAACCCCTACTTCAACGGTCAAAATTTATCAAAGG
42209 TAGGTTTTCC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (44 bp):
GTTTCAAAACCCCTACTTCAACGGTCAAAATTTATCAAAGGCAA
Found at i:46855 original size:3 final size:3
Alignment explanation
Indices: 46847--47730 Score: 1297
Period size: 3 Copynumber: 305.7 Consensus size: 3
46837 TAGTCAATAC
46847 AGA AGA AGA AGA AGA AGA AGA AGA AG- AGA AGA A-A AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
46893 AGA A-A AGAA AGA AGA AGA AG- AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * *
46937 AGA AGA AG- AGA AGA AGA AGA CGA AGA AGA AGA CGA AGA AGA AGA CGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
46984 A-A AGA AGA AGA AG- AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
47030 AGA ATA AGA AGA AGA A-A AGA AGA AGA AGA A-A AGA A-A AGA AGA AG-
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
47074 AGA AGA AGA AAA AG- AGA AGA AGA AGA AGA AGA A-A AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
47120 AGA AGA AGA AGA AGA A-A AGA AG- AGA AGA AGA AGA A-A AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
47165 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
47213 AGA CA-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA -AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
47258 AGA AGA AGA AGA AGA AGA AGA A-A AGA AGA AGAA AGA AGA AGA AG-
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA
47302 AGA AG- AGA A-A AGA AGA AG- AGA AGA A-A AG- AGA AGA AG- AGA AG-
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* *
47343 AGA AGA AGA GGA AGA AGA A-A AGA AGA GGA AGA AGA AG- AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * *
47389 GGA AGA AGAA AGA GGA A-A GGA AGA AG- AGA AGA AG- AGA AG- AGA
1 AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * *
47431 AGA AG- AGG AGA AG- AGA AGA AGA AGA GGA GAGA AGA GGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA AGA AGA
* *
47475 GGA AGA AG- AGA AGA AG- AGA AGA AGA GGA AGA AG- AGA A-A AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
47519 AGA AGA GAGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA -AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
47565 AGA AGA A-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA GGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
47612 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
47660 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
47708 AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AG
47731 GGTCAACTGC
Statistics
Matches: 805, Mismatches: 31, Indels: 90
0.87 0.03 0.10
Matches are distributed among these distances:
2 76 0.09
3 714 0.89
4 15 0.02
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:56513 original size:22 final size:22
Alignment explanation
Indices: 56487--56557 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
56477 ACTGAAAGAG
56487 AGTATCGGTACCATAGTATAGT
1 AGTATCGGTACCATAGTATAGT
* * *
56509 AGTATCGATACTGAAAG-A-AG-
1 AGTATCGGTAC-CATAGTATAGT
*
56529 GGTATCGGTACCATAGTATAGT
1 AGTATCGGTACCATAGTATAGT
56551 AGTATCG
1 AGTATCG
56558 ATATTGGAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 3 0.08
20 10 0.27
21 4 0.11
22 17 0.46
23 3 0.08
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (22 bp):
AGTATCGGTACCATAGTATAGT
Found at i:56535 original size:20 final size:20
Alignment explanation
Indices: 56510--56581 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
56500 TAGTATAGTA
56510 GTATCGATACTGAAAGAAGG
1 GTATCGATACTGAAAGAAGG
* * * *
56530 GTATCGGTAC-CATAGTATAGTA
1 GTATCGATACTGAAAG-A-AG-G
* *
56552 GTATCGATATTGGAAGAAGG
1 GTATCGATACTGAAAGAAGG
56572 GTATCGATAC
1 GTATCGATAC
56582 CATGTAACAC
Statistics
Matches: 37, Mismatches: 11, Indels: 8
0.66 0.20 0.14
Matches are distributed among these distances:
19 3 0.08
20 19 0.51
21 4 0.11
22 9 0.24
23 2 0.05
ACGTcount: A:0.35, C:0.11, G:0.28, T:0.26
Consensus pattern (20 bp):
GTATCGATACTGAAAGAAGG
Found at i:56546 original size:42 final size:42
Alignment explanation
Indices: 56469--56584 Score: 189
Period size: 42 Copynumber: 2.8 Consensus size: 42
56459 TGTGAAAATG
*
56469 GTATCGATACTGAAAG-AGAGTATCGGTACCATAGTATAGTA
1 GTATCGATACTGAAAGAAGGGTATCGGTACCATAGTATAGTA
56510 GTATCGATACTGAAAGAAGGGTATCGGTACCATAGTATAGTA
1 GTATCGATACTGAAAGAAGGGTATCGGTACCATAGTATAGTA
* * *
56552 GTATCGATATTGGAAGAAGGGTATCGATACCAT
1 GTATCGATACTGAAAGAAGGGTATCGGTACCAT
56585 GTAACACATA
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
41 16 0.23
42 54 0.77
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (42 bp):
GTATCGATACTGAAAGAAGGGTATCGGTACCATAGTATAGTA
Found at i:57147 original size:45 final size:45
Alignment explanation
Indices: 57079--57490 Score: 515
Period size: 45 Copynumber: 9.1 Consensus size: 45
57069 AACGAATGAA
* * *
57079 CAAAATAATAATGTATATAGGTGCATTATCGGCATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
* * *
57124 TAAAATAATAATGCATATGGGTGCATTATCGGCATAAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
* * * *
57169 CAAAATAATAATGCCTATGAGTGCATTATAGGCATGAAATGAAGC
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
* * *
57214 CAAAATAATAATGTATATGAGTGCATTATATGCATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
* * *
57259 CAAAATAATAATTCATATGGGTGCATTATATGTATGAAA-GATGC
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
* * * *
57303 CAAAATAATAATGCATATCGGCGCATTATTGGCATGAAATGATGC
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
* *
57348 CAAAATAATAATGCATATGGGTGCATTATCGACATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
* *
57393 CAAAATAATAATGCATATGGGTGCATTATTGGTATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
* * * *
57438 CATAACTGA-AATGCATGAACGGATGCATTA-AGGCATGAAAGGATGC
1 CA-AAATAATAATGCAT--ATGGGTGCATTATAGGCATGAAAGGATGC
57484 CATAAAT
1 CA-AAAT
57491 GAAATGTATG
Statistics
Matches: 322, Mismatches: 41, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
44 38 0.12
45 250 0.78
46 24 0.07
47 10 0.03
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (45 bp):
CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
Found at i:57502 original size:26 final size:25
Alignment explanation
Indices: 57426--57614 Score: 120
Period size: 26 Copynumber: 7.9 Consensus size: 25
57416 CATTATTGGT
57426 ATGAAAGGATGCCATAACTGAAATGC
1 ATGAAAGGATGCCATAA-TGAAATGC
* *
57452 ATGAACGGATG-CAT--T--AAGGC
1 ATGAAAGGATGCCATAATGAAATGC
*
57472 ATGAAAGGATGCCATAAATGAAATGT
1 ATGAAAGGATGCCAT-AATGAAATGC
*
57498 ATGAAAGGAT-TCAT--T-AAA-GC
1 ATGAAAGGATGCCATAATGAAATGC
* *
57518 ATGAAAGGATTCCATAACTAAAAATGC
1 ATGAAAGGATGCCATAA-T-GAAATGC
* * *
57545 ATGAATGGATG-CAT--T--AAGGA
1 ATGAAAGGATGCCATAATGAAATGC
* *
57565 ATGAAAGGGTACCATAAATGAAATGC
1 ATGAAAGGATGCCAT-AATGAAATGC
57591 ATGAAAGGATGCCATAAATGAAAT
1 ATGAAAGGATGCCAT-AATGAAAT
57615 TAATGAATAA
Statistics
Matches: 125, Mismatches: 19, Indels: 38
0.69 0.10 0.21
Matches are distributed among these distances:
20 36 0.29
21 12 0.10
22 2 0.02
23 1 0.01
24 3 0.02
25 6 0.05
26 54 0.43
27 11 0.09
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (25 bp):
ATGAAAGGATGCCATAATGAAATGC
Found at i:57559 original size:93 final size:92
Alignment explanation
Indices: 57426--57600 Score: 278
Period size: 93 Copynumber: 1.9 Consensus size: 92
57416 CATTATTGGT
* * *
57426 ATGAAAGGATGCCATAACTGAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGCCATAAAT
1 ATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGAATGAAAGGATACCATAAAT
*
57491 GAAATGTATGAAAGGATTCATTAAAGC
66 GAAATGCATGAAAGGATTCATTAAAGC
* * *
57518 ATGAAAGGATTCCATAACTAAAAATGCATGAATGGATGCATTAAGGAATGAAAGGGTACCATAAA
1 ATGAAAGGATGCCATAACT-AAAATGCATGAACGGATGCATTAAGGAATGAAAGGATACCATAAA
57583 TGAAATGCATGAAAGGAT
65 TGAAATGCATGAAAGGAT
57601 GCCATAAATG
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
92 18 0.24
93 57 0.76
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (92 bp):
ATGAAAGGATGCCATAACTAAAATGCATGAACGGATGCATTAAGGAATGAAAGGATACCATAAAT
GAAATGCATGAAAGGATTCATTAAAGC
Found at i:57561 original size:47 final size:46
Alignment explanation
Indices: 57333--57602 Score: 246
Period size: 46 Copynumber: 5.9 Consensus size: 46
57323 GCGCATTATT
* * * * *
57333 GGCATGAAATGATGCCA-AAATAATAATGCAT--ATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAAATGA-AATGCATGAAAGGATGCATTA-A
* * * * *
57378 GACATGAAAGGATGCCA-AAATAATAATGCAT--ATGGGTGCATTATT
1 GGCATGAAAGGATGCCATAAATGA-AATGCATGAAAGGATGCATTA-A
* * *
57423 GGTATGAAAGGATGCCATAACTGAAATGCATGAACGGATGCATTAA
1 GGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAA
* *
57469 GGCATGAAAGGATGCCATAAATGAAATGTATGAAAGGATTCATTAA
1 GGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAA
* * * * *
57515 AGCATGAAAGGATTCCATAACTAAAAATGCATGAATGGATGCATTAA
1 GGCATGAAAGGATGCCATAAAT-GAAATGCATGAAAGGATGCATTAA
* * *
57562 GGAATGAAAGGGTACCATAAATGAAATGCATGAAAGGATGC
1 GGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGC
57603 CATAAATGAA
Statistics
Matches: 192, Mismatches: 29, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
45 64 0.33
46 81 0.42
47 47 0.24
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.23
Consensus pattern (46 bp):
GGCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAA
Found at i:57620 original size:26 final size:26
Alignment explanation
Indices: 57563--57621 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
57553 ATGCATTAAG
*
57563 GAATGAAAGGGTACCATAAATGAAAT
1 GAATGAAAGGATACCATAAATGAAAT
* *
57589 GCATGAAAGGATGCCATAAATGAAAT
1 GAATGAAAGGATACCATAAATGAAAT
*
57615 TAATGAA
1 GAATGAA
57622 TAATTACTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.49, C:0.08, G:0.22, T:0.20
Consensus pattern (26 bp):
GAATGAAAGGATACCATAAATGAAAT
Found at i:63002 original size:90 final size:90
Alignment explanation
Indices: 62719--63097 Score: 441
Period size: 90 Copynumber: 4.2 Consensus size: 90
62709 AACGAATGAT
* * *
62719 CAAAATAATAATGCATATGGGTGTATTATCGGCATGAAAGGATGCCAAAATAATAATGCATATGG
1 CAAACTAATAATGCATATGGGTGCATTATCAGCATGAAAGGATGCCAAAATAATAATGCATATGG
*
62784 GTGCATTATCGGCATCAAAGGATGC
66 GTGCATTATCGGCATGAAAGGATGC
*
62809 CAAAATAATAATGCATATGGGTGCATTAT-AGGCATGAAAGGATGCCAAAATAATAATGCATATG
1 CAAACTAATAATGCATATGGGTGCATTATCA-GCATGAAAGGATGCCAAAATAATAATGCATATG
*
62873 GGTGCATTATAGGCATGAAAGGATGC
65 GGTGCATTATCGGCATGAAAGGATGC
62899 CAAAAC-AATAATGCATATGGGTGCATTATCAGCATGAAAGGATGCCAAAATAATAATGCATATG
1 C-AAACTAATAATGCATATGGGTGCATTATCAGCATGAAAGGATGCCAAAATAATAATGCATATG
* * *
62963 GTTGCATTATCGACATGAAAGGATAC
65 GGTGCATTATCGGCATGAAAGGATGC
* ** * * *
62989 CATAACTGA-AATGCATGAACAGATGTATTA--AGGCATAAAAGGATGCCATAAATGAA-AA-GC
1 CA-AACTAATAATGCAT--ATGGGTGCATTATCA-GCATGAAAGGATGCCA-AAAT-AATAATGC
* *
63049 ATGAAGGGATGCATTA-AGGCATGAAAGGATGC
60 AT-ATGGG-TGCATTATCGGCATGAAAGGATGC
*
63081 CATAACTAAAAATGCAT
1 CA-AACTAATAATGCAT
63098 GAACATATGC
Statistics
Matches: 255, Mismatches: 21, Indels: 23
0.85 0.07 0.08
Matches are distributed among these distances:
89 1 0.00
90 176 0.69
91 24 0.09
92 38 0.15
93 16 0.06
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.23
Consensus pattern (90 bp):
CAAACTAATAATGCATATGGGTGCATTATCAGCATGAAAGGATGCCAAAATAATAATGCATATGG
GTGCATTATCGGCATGAAAGGATGC
Found at i:63004 original size:45 final size:45
Alignment explanation
Indices: 62719--62986 Score: 464
Period size: 45 Copynumber: 6.0 Consensus size: 45
62709 AACGAATGAT
*
62719 CAAAATAATAATGCATATGGGTGTATTATCGGCATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
*
62764 CAAAATAATAATGCATATGGGTGCATTATCGGCATCAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
*
62809 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
*
62854 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
* *
62899 CAAAACAATAATGCATATGGGTGCATTATCAGCATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
* *
62944 CAAAATAATAATGCATATGGTTGCATTATCGACATGAAAGGAT
1 CAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGAT
62987 ACCATAACTG
Statistics
Matches: 212, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 212 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.25
Consensus pattern (45 bp):
CAAAATAATAATGCATATGGGTGCATTATCGGCATGAAAGGATGC
Found at i:63032 original size:46 final size:46
Alignment explanation
Indices: 62749--63185 Score: 287
Period size: 45 Copynumber: 9.6 Consensus size: 46
62739 GTGTATTATC
* ** * *
62749 GGCATGAAAGGATGCCA-AAATAATAATGCAT--ATGGGTGCATTATC
1 GGCATGAAAGGATGCCATAAATGA-AATGCATGAACAGATGCATTA-A
* * ** *
62794 GGCATCAAAGGATGCCA-AAATAATAATGCAT--ATGGGTGCATTATA
1 GGCATGAAAGGATGCCATAAATGA-AATGCATGAACAGATGCATTA-A
* ** *
62839 GGCATGAAAGGATGCCA-AAATAATAATGCAT--ATGGGTGCATTATA
1 GGCATGAAAGGATGCCATAAATGA-AATGCATGAACAGATGCATTA-A
** ** *
62884 GGCATGAAAGGATGCCA-AAACAATAATGCAT--ATGGGTGCATTATCA
1 GGCATGAAAGGATGCCATAAATGA-AATGCATGAACAGATGCATTA--A
* ** * *
62930 -GCATGAAAGGATGCCA-AAATAATAATGCAT--ATGGTTGCATTATC
1 GGCATGAAAGGATGCCATAAATGA-AATGCATGAACAGATGCATTA-A
* * * *
62974 GACATGAAAGGATACCATAACTGAAATGCATGAACAGATGTATTAA
1 GGCATGAAAGGATGCCATAAATGAAATGCATGAACAGATGCATTAA
* * **
63020 GGCATAAAAGGATGCCATAAATGAAAAGCATGAAGGGATGCATTAA
1 GGCATGAAAGGATGCCATAAATGAAATGCATGAACAGATGCATTAA
* * *
63066 GGCATGAAAGGATGCCATAACTAAAAATGCATGAACATATGCATTAA
1 GGCATGAAAGGATGCCATAAAT-GAAATGCATGAACAGATGCATTAA
* *
63113 GGCATGAAAGGATGCCATAAATGAAATGGATGAA-AGGATGCACTAA
1 GGCATGAAAGGATGCCATAAATGAAATGCATGAACA-GATGCATTAA
* *
63159 AGCATGAAAGGATTCCATAAATGAAAT
1 GGCATGAAAGGATGCCATAAATGAAAT
63186 TAACAAATAA
Statistics
Matches: 345, Mismatches: 40, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
45 191 0.55
46 106 0.31
47 48 0.14
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.22
Consensus pattern (46 bp):
GGCATGAAAGGATGCCATAAATGAAATGCATGAACAGATGCATTAA
Found at i:63672 original size:81 final size:82
Alignment explanation
Indices: 63523--63677 Score: 186
Period size: 81 Copynumber: 1.9 Consensus size: 82
63513 ACAGTTCTAA
* * * * * * *
63523 AGTAAAAGATTAATGGCCTAGTTGTGCAATTGGGTAGAAAGGTGTCAATTATACCAGTTAGATAA
1 AGTAAAAGATTAATGGCCTAGCTATGCAAGTGGGCAGAAAAGTGTCAATCATACAAGTTAGATAA
*
63588 AAGGTTAAATACATTTG
66 AAGGCTAAATACATTTG
* * * * *
63605 AGTAAAAGATTAATGGCCTAGCTATGTAGGT-GGCAGAAAAGTGTCAATCATGCAAGTTAGGTGA
1 AGTAAAAGATTAATGGCCTAGCTATGCAAGTGGGCAGAAAAGTGTCAATCATACAAGTTAGATAA
63669 AAGGCTAAA
66 AAGGCTAAA
63678 GGCCTTTGGG
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
81 34 0.57
82 26 0.43
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (82 bp):
AGTAAAAGATTAATGGCCTAGCTATGCAAGTGGGCAGAAAAGTGTCAATCATACAAGTTAGATAA
AAGGCTAAATACATTTG
Found at i:64635 original size:40 final size:40
Alignment explanation
Indices: 64544--64649 Score: 124
Period size: 40 Copynumber: 2.6 Consensus size: 40
64534 TAAGCACTTT
* * *
64544 AGTGCATATAGTGGGCACGACCTTATGTGTAATGCAATTC
1 AGTGCATATGGTGGGCACAACCTTATGTGTAATGCAATCC
* * * * *
64584 AATGCACATGGTGTGCACAACCTTATTTGTAATGCACTCC
1 AGTGCATATGGTGGGCACAACCTTATGTGTAATGCAATCC
64624 AGTGCATATGGTGGGCACGAA-CTTAT
1 AGTGCATATGGTGGGCAC-AACCTTAT
64650 ATTTAAGCAC
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
40 52 0.96
41 2 0.04
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (40 bp):
AGTGCATATGGTGGGCACAACCTTATGTGTAATGCAATCC
Found at i:70274 original size:12 final size:13
Alignment explanation
Indices: 70235--70277 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
70225 AATTTCGTCC
70235 TTATATTATATAA
1 TTATATTATATAA
*
70248 -TATA-TATATAT
1 TTATATTATATAA
70259 TTATATTATA-AA
1 TTATATTATATAA
70271 TTATATT
1 TTATATT
70278 TACATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 6 0.23
12 16 0.62
13 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATATTATATAA
Found at i:70284 original size:24 final size:24
Alignment explanation
Indices: 70235--70284 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
70225 AATTTCGTCC
*
70235 TTATATTATATAATATATATATAT
1 TTATATTATATAATATATATACAT
*
70259 TTATATTATA-AATTATATTTACAT
1 TTATATTATATAA-TATATATACAT
70283 TT
1 TT
70285 TTTTTTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATATTATATAATATATATACAT
Found at i:71285 original size:31 final size:30
Alignment explanation
Indices: 71187--71289 Score: 84
Period size: 30 Copynumber: 3.3 Consensus size: 30
71177 CAAACTGCGT
71187 TTTGGCTCCCTCTGTTTTGAAAAACATTCAA
1 TTTGG-TCCCTCTGTTTTGAAAAACATTCAA
* * ** *
71218 TTTGGTCCC-CAAATCGGTTGGGTAAAC-TTCAT
1 TTTGGTCCCTC---T-GTTTTGAAAAACATTCAA
*
71250 TTTGGCTCCCTCTGTTTTGAAAAACATTTAA
1 TTTGG-TCCCTCTGTTTTGAAAAACATTCAA
71281 TTTGGTCCC
1 TTTGGTCCC
71290 CAAATCGGTT
Statistics
Matches: 54, Mismatches: 11, Indels: 15
0.68 0.14 0.19
Matches are distributed among these distances:
29 1 0.02
30 16 0.30
31 14 0.26
32 10 0.19
33 12 0.22
34 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (30 bp):
TTTGGTCCCTCTGTTTTGAAAAACATTCAA
Found at i:82160 original size:61 final size:61
Alignment explanation
Indices: 82061--82176 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 61
82051 AATACTTCGC
* *
82061 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAAAAAAAAAAAAAAAAAAAACGT
1 TTAGGATGAAAACCCGAGAGGGCGCCCTAAATTGAAAAAAAAAAAAAAAAAAAAAAAACGT
* *
82122 TTAGGGTGAAAACTCG-GAAGGGCGCCCTAAAATT-AAAAAAAAAAAAAAAAAAAAA
1 TTAGGATGAAAACCCGAG-AGGGCGCCCT-AAATTGAAAAAAAAAAAAAAAAAAAAA
82177 GAGAAAAGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 1 0.02
61 44 0.90
62 4 0.08
ACGTcount: A:0.57, C:0.11, G:0.19, T:0.13
Consensus pattern (61 bp):
TTAGGATGAAAACCCGAGAGGGCGCCCTAAATTGAAAAAAAAAAAAAAAAAAAAAAAACGT
Found at i:83106 original size:105 final size:105
Alignment explanation
Indices: 82924--83768 Score: 1483
Period size: 105 Copynumber: 8.0 Consensus size: 105
82914 AGGTTTTACC
82924 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
82989 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTT
*
83029 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
83094 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTT
*
83134 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
83199 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATA
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTT
*
83239 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
83304 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTT
83344 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
83409 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTT
*
83449 CATAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
83514 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ACTTCTCAATTT
* * *
83555 CAGAGTCAATTTCAACTTCACATCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
83620 GCGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ACTTCTCAATTT
* *
83661 CAGAGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
83726 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTT
83766 CAG
1 CAG
83769 CTCCACAACG
Statistics
Matches: 710, Mismatches: 29, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
105 512 0.72
106 198 0.28
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTT
Found at i:83864 original size:20 final size:20
Alignment explanation
Indices: 83826--83867 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
83816 CCAGAACTCT
*
83826 GAGTTCGATTTCAGCTTCAC
1 GAGTTCGATTTCAACTTCAC
* *
83846 GAGTTTGATTTCAATTTCAC
1 GAGTTCGATTTCAACTTCAC
83866 GA
1 GA
83868 CGAAGGATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (20 bp):
GAGTTCGATTTCAACTTCAC
Found at i:84035 original size:106 final size:106
Alignment explanation
Indices: 83905--84161 Score: 444
Period size: 106 Copynumber: 2.4 Consensus size: 106
83895 GTTTTTAACT
*
83905 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
1 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACGTCACA
* *
83970 TCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCA
66 ACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCA
*
84011 CGGCGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACGTCACA
1 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACGTCACA
*
84076 ACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCA
66 ACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCA
* *
84117 CGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCCCAATTTCAG
1 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
84162 CTCCACAACG
Statistics
Matches: 143, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
105 13 0.09
106 130 0.91
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (106 bp):
CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACGTCACA
ACGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCA
Found at i:84237 original size:393 final size:393
Alignment explanation
Indices: 83092--84298 Score: 1628
Period size: 393 Copynumber: 3.0 Consensus size: 393
83082 TTCAACTTCA
*
83092 CGACGAAGGGACCGCTGGTTGTCAACAAAC-ACTTCTCAATGTCAGAGCCAATTTCAACTTCACA
1 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
* * * *
83156 ACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
66 TCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGGTTGTCA
* * * *
83221 ACAAAC-ATTTCTCAAATACAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
131 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGACA
**
83285 ACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACACTTCTCAATTTCAGAGC
196 ACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AA-A-----C-ATTTC----C
* * * * * ** * * ** * *
83350 CAATTTCAACTTCACAACGAAGGAT-ATTGGACT-CCAGAC-AACGCAAGTTCAACTTCACGACG
249 CAATTTCAGCTCCACAACGGAGTATCTTTGG-CTAGAAGACGATC-CATGAGCTACCTC-C-A-G
* ** * * * * * *
83412 AAGGGACCGCTG-GTT-G-TCAACAAACATTTCTCAAATTCATAGCCAATTTCAACTTCACAACG
309 -A---A-CTCTGAGTTCGAT-TTC-AGC--TTCACGAGTT--T-G---ATTTCAATTTCACGACG
* * * * *
83474 AAGGATAT-TGGACTCCAGACAAC-GCAAG--TTCAACTT
359 AAGGAT-TCAGG-CT-CAGA-ATCTTCCAGTTTTTAAC-T
*
83510 CACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGTCAATTTCAACTTCA
1 --CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCA
83575 CATCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGGTTGT
64 CATCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGGTTGT
83640 CAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGA
129 CAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGA
83705 CAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGC
194 CAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGC
83770 TCCACAACGGAGTATCTTTGGCTAGAAGACGATCCATGAGCTACCTCCAGAACTCTGAGTTCGAT
259 TCCACAACGGAGTATCTTTGGCTAGAAGACGATCCATGAGCTACCTCCAGAACTCTGAGTTCGAT
83835 TTCAGCTTCACGAGTTTGATTTCAATTTCACGACGAAGGATTCAGGCTCAGAATCTTCCAGTTTT
324 TTCAGCTTCACGAGTTTGATTTCAATTTCACGACGAAGGATTCAGGCTCAGAATCTTCCAGTTTT
83900 TAACT
389 TAACT
83905 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
1 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
83970 TCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGGTTGTCA
66 TCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGGTTGTCA
84035 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGACA
131 ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGACA
84100 ACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGCTC
196 ACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGCTC
84165 CACAACGGAGTATCTTTGGCTAGAAGACGATCCATGAGCTACCTCCAGAACTCTGAGTTCGATTT
261 CACAACGGAGTATCTTTGGCTAGAAGACGATCCATGAGCTACCTCCAGAACTCTGAGTTCGATTT
84230 CAGCTTCACGAGTTTGATTTCAATTTCACGACGAAGGATTCAGGCTCAGAATCTTCCAGTTTTTA
326 CAGCTTCACGAGTTTGATTTCAATTTCACGACGAAGGATTCAGGCTCAGAATCTTCCAGTTTTTA
84295 ACT
391 ACT
84298 C
1 C
84299 AACCTCATGA
Statistics
Matches: 735, Mismatches: 40, Indels: 51
0.89 0.05 0.06
Matches are distributed among these distances:
393 395 0.54
394 7 0.01
395 4 0.01
396 28 0.04
399 1 0.00
400 1 0.00
402 7 0.01
403 4 0.01
404 6 0.01
405 2 0.00
406 1 0.00
407 1 0.00
408 1 0.00
409 1 0.00
410 25 0.03
411 16 0.02
412 2 0.00
414 5 0.01
415 1 0.00
420 31 0.04
421 101 0.14
422 95 0.13
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (393 bp):
CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
TCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGGCGAAGGGACCGCTGGTTGTCA
ACAAACAACTTCTCAATTTCAGAGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGACA
ACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTTCAGCTC
CACAACGGAGTATCTTTGGCTAGAAGACGATCCATGAGCTACCTCCAGAACTCTGAGTTCGATTT
CAGCTTCACGAGTTTGATTTCAATTTCACGACGAAGGATTCAGGCTCAGAATCTTCCAGTTTTTA
ACT
Found at i:84257 original size:20 final size:20
Alignment explanation
Indices: 84219--84260 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
84209 CCAGAACTCT
*
84219 GAGTTCGATTTCAGCTTCAC
1 GAGTTCGATTTCAACTTCAC
* *
84239 GAGTTTGATTTCAATTTCAC
1 GAGTTCGATTTCAACTTCAC
84259 GA
1 GA
84261 CGAAGGATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (20 bp):
GAGTTCGATTTCAACTTCAC
Found at i:84504 original size:22 final size:20
Alignment explanation
Indices: 84478--84517 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
84468 AATTTCGTCC
84478 TTATATTATACAATATATATAT
1 TTATATTATA-AAT-TATATAT
84500 TTATATTATAAATTATAT
1 TTATATTATAAATTATAT
84518 TTACATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATATTATAAATTATATAT
Found at i:85523 original size:31 final size:30
Alignment explanation
Indices: 85425--85527 Score: 84
Period size: 30 Copynumber: 3.3 Consensus size: 30
85415 CAAACTGCGT
85425 TTTGGCTCCCTCTGTTTTGAAAAACATTCAA
1 TTTGG-TCCCTCTGTTTTGAAAAACATTCAA
* * ** *
85456 TTTGGTCCC-CAAATCGGTTGGGTAAAC-TTCAT
1 TTTGGTCCCTC---T-GTTTTGAAAAACATTCAA
*
85488 TTTGGCTCCCTCTGTTTTGAAAAACATTTAA
1 TTTGG-TCCCTCTGTTTTGAAAAACATTCAA
85519 TTTGGTCCC
1 TTTGGTCCC
85528 CAAATCGGTT
Statistics
Matches: 54, Mismatches: 11, Indels: 15
0.68 0.14 0.19
Matches are distributed among these distances:
29 1 0.02
30 16 0.30
31 14 0.26
32 10 0.19
33 12 0.22
34 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (30 bp):
TTTGGTCCCTCTGTTTTGAAAAACATTCAA
Found at i:87122 original size:40 final size:40
Alignment explanation
Indices: 87064--87195 Score: 178
Period size: 40 Copynumber: 3.3 Consensus size: 40
87054 TATCGATTAA
* * *
87064 GCACTTCGGTGCATATGGTGGGCATGACCTTATGTGTAAT
1 GCACTTCAGTGCACATGGTGGGCACGACCTTATGTGTAAT
*
87104 GCACTTCAGTGCACATGGTGGGCACAACCTTATGTGTAAT
1 GCACTTCAGTGCACATGGTGGGCACGACCTTATGTGTAAT
* * *
87144 ACACTCCGGTGCACATGGTGGGCACGACCTTATGTGTAA-
1 GCACTTCAGTGCACATGGTGGGCACGACCTTATGTGTAAT
87183 GCACTAT-AGTGCA
1 GCACT-TCAGTGCA
87196 TATATTTGAC
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
39 9 0.11
40 71 0.89
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
GCACTTCAGTGCACATGGTGGGCACGACCTTATGTGTAAT
Found at i:89414 original size:22 final size:22
Alignment explanation
Indices: 89388--89438 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
89378 TTTGGGAATT
89388 TCTCGTTAGCAGTATTTTGCTA
1 TCTCGTTAGCAGTATTTTGCTA
89410 TCTCGTTAGCAGTATTTTGCTA
1 TCTCGTTAGCAGTATTTTGCTA
89432 TCTCGTT
1 TCTCGTT
89439 TATCTTGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.47
Consensus pattern (22 bp):
TCTCGTTAGCAGTATTTTGCTA
Found at i:91240 original size:95 final size:93
Alignment explanation
Indices: 91077--91265 Score: 333
Period size: 95 Copynumber: 2.0 Consensus size: 93
91067 TTGGGCAATG
* *
91077 AGAATGTGACATGTAACACGTTTTATTAGATATTAGTAGGAAATAATGATAATTTAGATACCATT
1 AGAATGTGACATGTAACACATTTTATTAGATATTAGTAGAAAATAATGATAATTTAGATACCATT
91142 TTTATAAAAAAAAAATTATAATTTAAGGTT
66 TTTAT-AAAAAAAAA-TATAATTTAAGGTT
91172 AGAATGTGACATGTAACACATTTTATTAGATATTAGTAGAAAATAATGATAATTTAGATACCATT
1 AGAATGTGACATGTAACACATTTTATTAGATATTAGTAGAAAATAATGATAATTTAGATACCATT
*
91237 TTTATAAAAAAAAATATAATTTGAGGTT
66 TTTATAAAAAAAAATATAATTTAAGGTT
91265 A
1 A
91266 AATTTTAGTA
Statistics
Matches: 91, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
93 14 0.15
94 9 0.10
95 68 0.75
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (93 bp):
AGAATGTGACATGTAACACATTTTATTAGATATTAGTAGAAAATAATGATAATTTAGATACCATT
TTTATAAAAAAAAATATAATTTAAGGTT
Found at i:92355 original size:29 final size:30
Alignment explanation
Indices: 92308--92380 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
92298 AATAGATTTA
92308 ATATACTATTTTTAATTTTT-TTT-AAAAAT
1 ATATA-TATTTTTAATTTTTATTTCAAAAAT
* *
92337 ATATATATATTTAATTTTTTATTTCAGAAAT
1 ATATATATTTTTAA-TTTTTATTTCAAAAAT
*
92368 TTATATATTTTTA
1 ATATATATTTTTA
92381 TTCTATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 8 0.22
29 10 0.27
30 3 0.08
31 16 0.43
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (30 bp):
ATATATATTTTTAATTTTTATTTCAAAAAT
Found at i:92428 original size:31 final size:31
Alignment explanation
Indices: 92376--92438 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
92366 ATTTATATAT
92376 TTTTATTCTATTAAACCTTTTTTTTG-CAAA
1 TTTTATTCTATTAAACCTTTTTTTTGACAAA
*
92406 TTTTATTCTATTAAACTTTTTTTTTGACAAA
1 TTTTATTCTATTAAACCTTTTTTTTGACAAA
92437 TT
1 TT
92439 AGAAGCCACT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 25 0.81
31 6 0.19
ACGTcount: A:0.27, C:0.11, G:0.03, T:0.59
Consensus pattern (31 bp):
TTTTATTCTATTAAACCTTTTTTTTGACAAA
Found at i:93561 original size:15 final size:15
Alignment explanation
Indices: 93541--93577 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
93531 TTCAAACTTT
93541 AAATATTGAATATTG
1 AAATATTGAATATTG
93556 AAATATTGAATATTG
1 AAATATTGAATATTG
93571 AAATATT
1 AAATATT
93578 ATAACAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.41
Consensus pattern (15 bp):
AAATATTGAATATTG
Found at i:93562 original size:8 final size:8
Alignment explanation
Indices: 93541--93577 Score: 60
Period size: 7 Copynumber: 4.9 Consensus size: 8
93531 TTCAAACTTT
93541 AAATATTG
1 AAATATTG
93549 -AATATTG
1 AAATATTG
93556 AAATATTG
1 AAATATTG
93564 -AATATTG
1 AAATATTG
93571 AAATATT
1 AAATATT
93578 ATAACAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 14 0.52
8 13 0.48
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.41
Consensus pattern (8 bp):
AAATATTG
Found at i:93669 original size:92 final size:92
Alignment explanation
Indices: 93476--93648 Score: 231
Period size: 92 Copynumber: 1.9 Consensus size: 92
93466 ATAATATATA
* * * *
93476 AAAATATTATATAACATTGTAAACTTAAAAAGTAATAGAATCAAACTAGATTGAGTTCAAACTTT
1 AAAATA-T-TATAACAGTATAAACTTAAAAAGTAACAGAATCAAAATAGATTGAGTTCAAACTTT
** * *
93541 AAATATTGAATATTGAAATATTGAATATT
64 AAATATTGAATATTGAAATAGCGAAGATC
*
93570 GAAATATTATAACAGTATAAACTTAAAAA-TGAACAGAATCAAAATAGATTGAGTTCAAACTTTA
1 AAAATATTATAACAGTATAAACTTAAAAAGT-AACAGAATCAAAATAGATTGAGTTCAAACTTTA
93634 AATATTGAATATTGA
65 AATATTGAATATTGA
93649 GATGCGAGCT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
91 1 0.01
92 66 0.90
93 1 0.01
94 5 0.07
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (92 bp):
AAAATATTATAACAGTATAAACTTAAAAAGTAACAGAATCAAAATAGATTGAGTTCAAACTTTAA
ATATTGAATATTGAAATAGCGAAGATC
Found at i:94713 original size:62 final size:63
Alignment explanation
Indices: 94644--94765 Score: 169
Period size: 63 Copynumber: 2.0 Consensus size: 63
94634 AGTTATTTAT
* *
94644 TATCTATTTAACTTTAAATA-TTAAAGATAAT-TATATAC-TTTGAATATTTCAAATTAAAATAA
1 TATCTATTTAACTTTAAATAGTAAAAG-GAATCTATAT-CTTTTGAATATTTCAAATTAAAATAA
* *
94706 TATCTATTTAAGTTTGAATAGTAAAAGGAATCTATATCTTTTGAATATTTCAAATTAAAA
1 TATCTATTTAACTTTAAATAGTAAAAGGAATCTATATCTTTTGAATATTTCAAATTAAAA
94766 GATATTATCA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
62 22 0.42
63 31 0.58
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.43
Consensus pattern (63 bp):
TATCTATTTAACTTTAAATAGTAAAAGGAATCTATATCTTTTGAATATTTCAAATTAAAATAA
Done.