Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004104.1 Hibiscus syriacus cultivar Beakdansim tig00008977_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: 67091
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:46 original size:34 final size:35
Alignment explanation
Indices: 3--71 Score: 131
Period size: 34 Copynumber: 2.0 Consensus size: 35
1 GG
3 GGGAATCGATACCCCCCAGGGG-GAATCTGTTCCC
1 GGGAATCGATACCCCCCAGGGGAGAATCTGTTCCC
37 GGGAATCGATACCCCCCAGGGGAGAATCTGTTCCC
1 GGGAATCGATACCCCCCAGGGGAGAATCTGTTCCC
72 CCTGTACATA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 22 0.65
35 12 0.35
ACGTcount: A:0.22, C:0.32, G:0.29, T:0.17
Consensus pattern (35 bp):
GGGAATCGATACCCCCCAGGGGAGAATCTGTTCCC
Found at i:3777 original size:30 final size:30
Alignment explanation
Indices: 3741--3892 Score: 243
Period size: 30 Copynumber: 5.0 Consensus size: 30
3731 CCCGAAGGAC
* *
3741 CAGTCCATA-GATCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCGAAGAACATAGGTAAA
3771 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGT-CCGAAGAACATAGGTAAA
*
3802 CAATCCATATGTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCGAAGAACATAGGTAAA
*
3832 CAGTCCATATGTCCGAAGAACAGAGGTAAA
1 CAGTCCATATGTCCGAAGAACATAGGTAAA
3862 CAGTCCATATGTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCGAAGAACATAGGTAAA
3892 C
1 C
3893 CCTCACCCTT
Statistics
Matches: 114, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
30 86 0.75
31 28 0.25
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (30 bp):
CAGTCCATATGTCCGAAGAACATAGGTAAA
Found at i:4485 original size:34 final size:34
Alignment explanation
Indices: 4442--4509 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
4432 TTTCATTTAG
4442 GGGGAATCGATACCCCCTA-AGGGAATCTGTTCCC
1 GGGGAATCGATACCCCC-AGAGGGAATCTGTTCCC
*
4476 GGGGAATCGATACCCCCAGTGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCAGAGGGAATCTGTTCCC
4510 CCTGTACATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 1 0.03
34 31 0.97
ACGTcount: A:0.22, C:0.29, G:0.28, T:0.21
Consensus pattern (34 bp):
GGGGAATCGATACCCCCAGAGGGAATCTGTTCCC
Found at i:10280 original size:45 final size:44
Alignment explanation
Indices: 10205--10302 Score: 112
Period size: 45 Copynumber: 2.2 Consensus size: 44
10195 TTGTGCATAA
*
10205 TGCATCGATACACTATGAAAGTGCATCGATGAATC-CCTTTGAATG
1 TGCATCGATACACTATGAAAGTGCACCGATGAA-CGCC-TTGAATG
* *
10250 TGCATTGATACA-TCATG-AAGATGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACT-ATGAAAG-TGCACCGATGAACGCCTTGAATG
10294 TGCATCGAT
1 TGCATCGAT
10303 CCACAGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
44 20 0.43
45 26 0.57
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (44 bp):
TGCATCGATACACTATGAAAGTGCACCGATGAACGCCTTGAATG
Found at i:13146 original size:19 final size:20
Alignment explanation
Indices: 13122--13161 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
13112 AGGTATGTAC
13122 AAATGAT-AATGTTGTGGAA
1 AAATGATGAATGTTGTGGAA
*
13141 AAATGATGGATGTTGTGGAA
1 AAATGATGAATGTTGTGGAA
13161 A
1 A
13162 TGGAATGGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (20 bp):
AAATGATGAATGTTGTGGAA
Found at i:13287 original size:2 final size:2
Alignment explanation
Indices: 13280--13336 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
13270 ATTGGATTTA
13280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
13322 AC AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
13337 CATGACTTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:25307 original size:65 final size:64
Alignment explanation
Indices: 25238--25393 Score: 244
Period size: 65 Copynumber: 2.4 Consensus size: 64
25228 AAATTGAATT
*
25238 TCGAATGCATTTTATGCATCGATGCACATA-CCATGCATCGATGCACTC-CGATTTTTATGAAAA
1 TCGAATGCATTTTATGCATCGATGCACA-AGCCATGCATCGATGCACTCACGATATTT-T-AAAA
25301 CA
63 CA
* *
25303 TCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTAAAACA
1 TCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCACGATATTTTAAAACA
25367 TCGAATGCATTTTATGCATCGATGCAC
1 TCGAATGCATTTTATGCATCGATGCAC
25394 CCTTAGTGCA
Statistics
Matches: 86, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
64 34 0.40
65 47 0.55
66 5 0.06
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (64 bp):
TCGAATGCATTTTATGCATCGATGCACAAGCCATGCATCGATGCACTCACGATATTTTAAAACA
Found at i:26549 original size:23 final size:23
Alignment explanation
Indices: 26523--26567 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
26513 CACCACAGCT
*
26523 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
26546 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
26568 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:26805 original size:149 final size:149
Alignment explanation
Indices: 26546--26849 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
26536 CGAAGTGCCC
*
26546 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
26611 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
26676 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
26695 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
*
26760 CATATACATATTCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
26825 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
26844 CGTAGA
1 CGTAGA
26850 CCCTCGACTC
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:27747 original size:18 final size:18
Alignment explanation
Indices: 27726--27760 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
27716 TCCCATCTAG
27726 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
27744 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
27761 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:28367 original size:21 final size:21
Alignment explanation
Indices: 28343--28387 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
28333 TCTTGTTCGT
* *
28343 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
28364 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
28385 TTG
1 TTG
28388 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:31832 original size:17 final size:17
Alignment explanation
Indices: 31812--31845 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31802 AACAAAATCA
*
31812 AATTAAACCTTTTCAAC
1 AATTAAACCTCTTCAAC
31829 AATTAAACCTCTTCAAC
1 AATTAAACCTCTTCAAC
31846 TTTTATCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.32
Consensus pattern (17 bp):
AATTAAACCTCTTCAAC
Found at i:32987 original size:220 final size:225
Alignment explanation
Indices: 32597--33042 Score: 857
Period size: 220 Copynumber: 2.0 Consensus size: 225
32587 ATGTTGGGAT
32597 TGATCAACACTTAGTCCCTCCTTTAGATATTTATGATCCTAGAAATTGGGGTAATCTTCATAATA
1 TGATCAACACTTAGTCCCTCCTTTAGATATTTATGATCCTAGAAATTGGGGTAATCTTCATAATA
32662 AATCTAGAGTTATTTTAGTTGAAAAATGACCTATAAGAGAATTGAATTTGAAATTTCCCTTAACC
66 AATCTAGAGTTATTTTAGTTGAAAAATGACCTATAAGAGAATTGAATTTGAAATTTCCCTTAACC
32727 AATAATTCTAGGCATTTTTCATATGCTTATTTTTCTAGAAAATTAAGTAATGGAG-AAACTATTG
131 AATAATTCTAGGCATTTTTCATATGCTTATTTTTCTAGAAAATTAAGTAATGGAGAAAACTATTG
32791 ATAGAAAATGGTTGG-TT-TTCTAAACATG
196 ATAGAAAATGGTTGGTTTATTCTAAACATG
32819 TGATCAACACTTAGTCCCTCCTTTAGATATTTATGATCCTAGAAATTGGGGTAATCTTCATAAT-
1 TGATCAACACTTAGTCCCTCCTTTAGATATTTATGATCCTAGAAATTGGGGTAATCTTCATAATA
32883 AATCTAGAGTTATTTTAGTTGAAAAATGACCTATAAGAG-ATTGAATTTGAAATTTCCCTTAACC
66 AATCTAGAGTTATTTTAGTTGAAAAATGACCTATAAGAGAATTGAATTTGAAATTTCCCTTAACC
32947 AATAATTCTAGGCATTTTTCATATGCTTATTTTTCTAGAAAATTAAGTAATGGAGAAAACTATTG
131 AATAATTCTAGGCATTTTTCATATGCTTATTTTTCTAGAAAATTAAGTAATGGAGAAAACTATTG
33012 ATAGAAAATGGTTGGTTTATTCTAAACATG
196 ATAGAAAATGGTTGGTTTATTCTAAACATG
33042 T
1 T
33043 AGACAAGGTT
Statistics
Matches: 221, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
220 80 0.36
221 63 0.29
222 66 0.30
223 12 0.05
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (225 bp):
TGATCAACACTTAGTCCCTCCTTTAGATATTTATGATCCTAGAAATTGGGGTAATCTTCATAATA
AATCTAGAGTTATTTTAGTTGAAAAATGACCTATAAGAGAATTGAATTTGAAATTTCCCTTAACC
AATAATTCTAGGCATTTTTCATATGCTTATTTTTCTAGAAAATTAAGTAATGGAGAAAACTATTG
ATAGAAAATGGTTGGTTTATTCTAAACATG
Found at i:34267 original size:7 final size:7
Alignment explanation
Indices: 34257--34283 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
34247 TATATATATT
34257 ATATTTA
1 ATATTTA
34264 ATATTTA
1 ATATTTA
34271 ATATTTA
1 ATATTTA
34278 ATATTT
1 ATATTT
34284 TTAGTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATATTTA
Found at i:34375 original size:11 final size:12
Alignment explanation
Indices: 34361--34399 Score: 64
Period size: 11 Copynumber: 3.4 Consensus size: 12
34351 CCATTTGTTT
34361 TTATTTATATT-
1 TTATTTATATTA
34372 TTATTTATATTA
1 TTATTTATATTA
34384 TTA-TTATATTA
1 TTATTTATATTA
34395 TTATT
1 TTATT
34400 AAATAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 22 0.85
12 4 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTTATATTA
Found at i:35556 original size:17 final size:16
Alignment explanation
Indices: 35518--35552 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
35508 TAGGTCATTA
*
35518 ATTT-ATATATTTTTC
1 ATTTAATATATTTTGC
35533 ATTTAATATATTTTGC
1 ATTTAATATATTTTGC
35549 ATTT
1 ATTT
35553 TAATTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (16 bp):
ATTTAATATATTTTGC
Found at i:35804 original size:2 final size:2
Alignment explanation
Indices: 35792--35884 Score: 107
Period size: 2 Copynumber: 51.5 Consensus size: 2
35782 ATATCCTGCT
*
35792 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35832 TA TA -A TA TA TA TA TA T- TA TA -A TA TA TA -A TA TA T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35868 TA T- TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA T
35885 TATTTTTATT
Statistics
Matches: 79, Mismatches: 2, Indels: 20
0.78 0.02 0.20
Matches are distributed among these distances:
1 10 0.13
2 69 0.87
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35810 original size:10 final size:10
Alignment explanation
Indices: 35792--35884 Score: 107
Period size: 9 Copynumber: 10.3 Consensus size: 10
35782 ATATCCTGCT
*
35792 TATAAATATA
1 TATATATATA
35802 TATATATATA
1 TATATATATA
35812 TATATATATA
1 TATATATATA
35822 TATAT-TATA
1 TATATATATA
35831 T-TATA-ATA
1 TATATATATA
35839 TATATATAT-
1 TATATATATA
35848 TATA-ATATA
1 TATATATATA
35857 TA-ATATAT-
1 TATATATATA
35865 TAT-TAT-TA
1 TATATATATA
35873 TATATAT-TA
1 TATATATATA
35882 TAT
1 TAT
35885 TATTTTTATT
Statistics
Matches: 74, Mismatches: 1, Indels: 17
0.80 0.01 0.18
Matches are distributed among these distances:
7 1 0.01
8 20 0.27
9 27 0.36
10 26 0.35
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TATATATATA
Found at i:35893 original size:23 final size:24
Alignment explanation
Indices: 35797--35895 Score: 80
Period size: 25 Copynumber: 4.0 Consensus size: 24
35787 CTGCTTATAA
*
35797 ATATATA-TATA-TATA-TATATAT
1 ATATATATTATATTATATTTTAT-T
* *
35819 ATATATATTATATTATAATATATAT
1 ATATATATTATATTATATTTTAT-T
*
35844 ATATTATAATATATAATATATTATTATT
1 ATA-TAT-AT-TATATTATATT-TTATT
35872 ATATATATTATATTAT-TTTTATT
1 ATATATATTATATTATATTTTATT
35895 A
1 A
35896 AAAATTATAT
Statistics
Matches: 66, Mismatches: 4, Indels: 13
0.80 0.05 0.16
Matches are distributed among these distances:
22 7 0.11
23 10 0.15
24 6 0.09
25 17 0.26
26 5 0.08
27 5 0.08
28 13 0.20
29 3 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATATATATTATATTATATTTTATT
Found at i:40960 original size:19 final size:19
Alignment explanation
Indices: 40936--40986 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
40926 ACCAACAAAA
40936 TCGCAATGCGATCGCTAAT
1 TCGCAATGCGATCGCTAAT
40955 TCGCAATGCGATCGCTAAT
1 TCGCAATGCGATCGCTAAT
*
40974 TCGCAACGCGATC
1 TCGCAATGCGATC
40987 TCCATTATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (19 bp):
TCGCAATGCGATCGCTAAT
Found at i:41108 original size:41 final size:41
Alignment explanation
Indices: 41078--41170 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 41
41068 TTTTCCCAAT
**
41078 TCGCAATGCGAATAAGTAAATCACAATGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCACAATGCGAATTGCCAAAA
* * **
41119 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCACAATGCGAATTGCCAAAA
41160 TCGCAATGCGA
1 TCGCAATGCGA
41171 TACTGACTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCACAATGCGAATTGCCAAAA
Found at i:41125 original size:21 final size:20
Alignment explanation
Indices: 41078--41170 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
41068 TTTTCCCAAT
*
41078 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
41098 TCACAATGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
*
41119 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
41139 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
41160 TCGCAATGCGA
1 TCGCAATGCGA
41171 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:41183 original size:41 final size:41
Alignment explanation
Indices: 41105--41231 Score: 116
Period size: 41 Copynumber: 3.1 Consensus size: 41
41095 AAATCACAAT
* *
41105 GCGAATTGGGAAAATCGCAATGCGAATA-AGTA-AATCGCAAC
1 GCGAATTGGGAAAATCGCAATGCG-ATACTG-ACTATCGCAAC
*
41146 GCGAATTGGGAAAATCGCAATGCGATACTGACTATCGCAAT
1 GCGAATTGGGAAAATCGCAATGCGATACTGACTATCGCAAC
* ** * * * *
41187 GCGATAAT-ACAAAATCGCAACGAGATACTTACTTTCGCAAC
1 GCGA-ATTGGGAAAATCGCAATGCGATACTGACTATCGCAAC
41228 GCGA
1 GCGA
41232 TACTGACTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
40 4 0.06
41 66 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (41 bp):
GCGAATTGGGAAAATCGCAATGCGATACTGACTATCGCAAC
Found at i:41184 original size:20 final size:20
Alignment explanation
Indices: 41159--41273 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
41149 AATTGGGAAA
*
41159 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
41179 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
41200 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
41220 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
41240 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
41260 TTCGCAACGCGATA
1 ATCGCAACGCGATA
41274 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:41232 original size:41 final size:41
Alignment explanation
Indices: 41156--41293 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
41146 GCGAATTGGG
* * *
41156 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
41197 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
41239 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
41278 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
41294 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.39
41 44 0.56
42 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:41484 original size:22 final size:22
Alignment explanation
Indices: 41456--41499 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
41446 CACTCTCTCA
*
41456 CCCATCTCCGATGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
41478 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
41500 TATCTTCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:43160 original size:18 final size:18
Alignment explanation
Indices: 43139--43183 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
43129 TCCACTTCGG
*
43139 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
43157 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
43175 GAGCCATCA
1 GAGCCATCA
43184 TCTGATTGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:43715 original size:20 final size:20
Alignment explanation
Indices: 43665--43717 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
43655 TAGTTTACTT
*
43665 TCGCAACACGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
43685 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGACTA
*
43705 TCGCAATGCGAAA
1 TCGCAACGCGAAA
43718 TGAAAATCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:43746 original size:33 final size:33
Alignment explanation
Indices: 43704--43796 Score: 161
Period size: 32 Copynumber: 2.8 Consensus size: 33
43694 GAAAATGGCT
43704 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
*
43737 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
*
43769 ATCGCAACGCGAAATGAAAATCGCAATG
1 ATCGCAATGCGAAATGAAAATCGCAATG
43797 CGATTTGTGT
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.54
33 26 0.46
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAATGACAAA
Found at i:43776 original size:14 final size:14
Alignment explanation
Indices: 43720--43777 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
43710 ATGCGAAATG
*
43720 AAAATCGCAATGAC
1 AAAATCGCAACGAC
*
43734 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
43750 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
43766 AAAATCGCAACG
1 AAAATCGCAACG
43778 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.57
16 7 0.19
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:43857 original size:20 final size:19
Alignment explanation
Indices: 43806--43877 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
43796 GCGATTTGTG
**
43806 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATAGTCA
* *
43825 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATAGTCA
43844 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATAGTCA
43864 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
43878 TTTAAGTTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 29 0.63
20 17 0.37
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.39
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:45890 original size:19 final size:19
Alignment explanation
Indices: 45868--45916 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
45858 ATCGCAACGA
45868 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
45887 GAAAATCACAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
45906 GAAAATCGCAA
1 GAAAATCGCAA
45917 CGAAAATCGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:45977 original size:20 final size:20
Alignment explanation
Indices: 45952--46009 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
45942 TCGCATTGCG
*
45952 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
45972 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
45992 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
46010 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:47092 original size:24 final size:24
Alignment explanation
Indices: 47065--47118 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
47055 GTATTCGAAA
* *
47065 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
47089 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
47113 TTTGAT
1 TTTGAT
47119 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:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:49624 original size:33 final size:33
Alignment explanation
Indices: 49582--49708 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
49572 GGAAATTACT
*
49582 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
49615 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
49647 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
49681 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
49709 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:49665 original size:66 final size:66
Alignment explanation
Indices: 49583--49715 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
49573 GAAATTACTA
*
49583 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
49648 T
66 T
* *
49649 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
49714 T
66 T
49715 T
1 T
49716 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCACAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:49730 original size:19 final size:20
Alignment explanation
Indices: 49708--49750 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
49698 AAATCGCAAC
49708 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
49727 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
49747 GCGA
1 GCGA
49751 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:49735 original size:14 final size:14
Alignment explanation
Indices: 49736--49769 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
49726 TGCGATTTTC
49736 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
49750 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
49764 ATTTTC
1 ATTTTC
49770 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:49910 original size:14 final size:14
Alignment explanation
Indices: 49891--49927 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
49881 CATCAATTAA
49891 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
49905 ACAAATCACCTTTT
1 ACAAATCAACTTTT
49919 ACAAATCAA
1 ACAAATCAA
49928 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:51362 original size:41 final size:42
Alignment explanation
Indices: 51317--51395 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
51307 CGATGACAGT
* *
51317 GGCCTCTTGAACG-TGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
51358 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
51396 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
41 12 0.38
42 20 0.62
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.22
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:53445 original size:20 final size:19
Alignment explanation
Indices: 53400--53458 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
53390 TCTTTTGGTT
53400 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
53419 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
53440 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
53459 TAGAATCGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 2 0.06
20 29 0.88
21 2 0.06
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:53468 original size:14 final size:14
Alignment explanation
Indices: 53449--53485 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
53439 GGAAATGACT
*
53449 ATCGCAACGATAGA
1 ATCGCAACGAGAGA
53463 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
53477 ATCGCAACG
1 ATCGCAACG
53486 CGAAATGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:53513 original size:47 final size:48
Alignment explanation
Indices: 53425--53518 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 48
53415 ACGAGATAAT
* * *
53425 GAGAATCGCAACGCGGAAATGACTATCGCAACGATAGAATCGCAACGA
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAACGA
*
53473 GAGAATCGCAACGC-GAAATGACTATCGCGACCAGACAATCGCAACG
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAACG
53519 CGAAATGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 28 0.67
48 14 0.33
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.12
Consensus pattern (48 bp):
GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAACGA
Found at i:53531 original size:19 final size:19
Alignment explanation
Indices: 53509--53597 Score: 144
Period size: 19 Copynumber: 4.7 Consensus size: 19
53499 GCGACCAGAC
53509 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
53528 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
53548 AATCGCAACGCGAAATG-A
1 AATCGCAACGCGAAATGAA
53566 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
53585 AATCGCAATGCGA
1 AATCGCAACGCGA
53598 TTTTGTTTCG
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
18 18 0.28
19 29 0.45
20 18 0.28
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:53533 original size:33 final size:33
Alignment explanation
Indices: 53462--53537 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
53452 GCAACGATAG
* * *
53462 AATCGCAACGAGAGAATCGCAACGCGAAATGAC
1 AATCGCAACCAGACAATCGCAACGCGAAATGAA
* *
53495 TATCGCGACCAGACAATCGCAACGCGAAATGAA
1 AATCGCAACCAGACAATCGCAACGCGAAATGAA
53528 AATCGCAACC
1 AATCGCAACC
53538 GCGAAATAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.28, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACCAGACAATCGCAACGCGAAATGAA
Found at i:53552 original size:39 final size:37
Alignment explanation
Indices: 53509--53597 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
53499 GCGACCAGAC
53509 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATG-AAATCGCAA-CGCGAAATAAA
*
53548 AATCGCAACGCGAAATGAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAATCGCAACGCGAAATAAA
*
53585 AATCGCAATGCGA
1 AATCGCAACGCGA
53598 TTTTGTTTCG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 22 0.46
38 9 0.19
39 17 0.35
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.11
Consensus pattern (37 bp):
AATCGCAACGCGAAATGAAATCGCAACGCGAAATAAA
Found at i:53625 original size:19 final size:19
Alignment explanation
Indices: 53598--53658 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
53588 CGCAATGCGA
*
53598 TTTTGTTTCGCGTTGCGTT
1 TTTTATTTCGCGTTGCGTT
*
53617 TTTTATTTCGCGTTGCGAT
1 TTTTATTTCGCGTTGCGTT
**
53636 AGTTATTTCCGCGTTGCGATT
1 TTTTATTT-CGCGTTGCG-TT
53657 TT
1 TT
53659 CATTCTCGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
19 23 0.70
20 9 0.27
21 1 0.03
ACGTcount: A:0.08, C:0.16, G:0.23, T:0.52
Consensus pattern (19 bp):
TTTTATTTCGCGTTGCGTT
Found at i:53650 original size:20 final size:19
Alignment explanation
Indices: 53603--53655 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
53593 TGCGATTTTG
* **
53603 TTTCGCGTTGCGTTTTTTA
1 TTTCGCGTTGCGATAGTTA
53622 TTTCGCGTTGCGATAGTTA
1 TTTCGCGTTGCGATAGTTA
53641 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
53656 TTTCATTCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 19 0.63
20 11 0.37
ACGTcount: A:0.09, C:0.19, G:0.25, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTTA
Found at i:54200 original size:20 final size:20
Alignment explanation
Indices: 54175--54227 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
54165 GCGCTATGTA
54175 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
54195 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
54215 TATCTCGTTGCGA
1 AATCGCGTTGCGA
54228 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:54261 original size:20 final size:20
Alignment explanation
Indices: 54236--54289 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
54226 GATTTTGTAT
54236 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
54256 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
*
54276 CATCGCATTGCGAT
1 TATCGCATTGCGAT
54290 TTTCCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:54274 original size:61 final size:61
Alignment explanation
Indices: 54176--54292 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
54166 CGCTATGTAA
* * * * * *
54176 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGCATCGCATTGCGATTTTGTATT
* * *
54237 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGCATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGCATCGCATTGCGATTTT
54293 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGCATCGCATTGCGATTTTGTATT
Found at i:54308 original size:61 final size:61
Alignment explanation
Indices: 54176--54310 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
54166 CGCTATGTAA
* * * * * * ** *
54176 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGCATCGCATTGCGATTTTCCAAT
* * *
54237 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGCATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGCATCGCATTGCGATTTT-CCAAT
54299 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
54311 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGCATCGCATTGCGATTTTCCAAT
Found at i:58880 original size:3 final size:3
Alignment explanation
Indices: 58872--58897 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
58862 TCATGTGTAG
58872 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
58898 TTTTAGCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:60365 original size:63 final size:63
Alignment explanation
Indices: 60284--60528 Score: 259
Period size: 63 Copynumber: 3.8 Consensus size: 63
60274 TGACCAAAAC
60284 ATAAATTAAATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAAAAATATATATGAA
1 ATAAATTAAATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAAAAATATATATGAA
* * * * ** *
60347 TTATATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGA-GTGACCA
1 ATAAATTAAATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAAAAATATATATGA--A
*
60411 A-AACA-TAAATTAGATATATAAGTGACCGAAA-AGGTAGTTTACCCTAAATAATAATAGT-TAC
1 ATAA-ATTAAA-TA-ATATATAAGTGACC-AAATAGGTAGTTTACCCTAAATAAAAATA-TATA-
**
60472 CAAAA
60 -TGAA
*
60477 CATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAA-AAAA
1 -ATAAATTAAATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAAAA
60529 TCCCTAACCG
Statistics
Matches: 151, Mismatches: 17, Indels: 26
0.78 0.09 0.13
Matches are distributed among these distances:
62 3 0.02
63 55 0.36
64 4 0.03
65 44 0.29
66 35 0.23
67 4 0.03
68 6 0.04
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.29
Consensus pattern (63 bp):
ATAAATTAAATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAAAAATATATATGAA
Found at i:60411 original size:131 final size:130
Alignment explanation
Indices: 60260--60524 Score: 394
Period size: 131 Copynumber: 2.0 Consensus size: 130
60250 TTTTGAAAAA
60260 AAATAATAATCGAGTGACCAAAACATAAATTAAATAATATATAAGTGACC-AAATAGGTAGTTTA
1 AAATAATAATCGAGTGACCAAAACATAAATT--A-AATATATAAGTGACCGAAA-AGGTAGTTTA
** * *
60324 CCCTAAATAAAAATA-TATA-TGAA-TTATATTAGATAATATATAAGTGACCAAATAGGTAGTTT
62 CCCTAAATAAAAATAGT-TACAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTT
60386 ACCCT
126 ACCCT
*
60391 AAATAATAATCGAGTGACCAAAACATAAATTAGATATATAAGTGACCGAAAAGGTAGTTTACCCT
1 AAATAATAATCGAGTGACCAAAACATAAATTAAATATATAAGTGACCGAAAAGGTAGTTTACCCT
*
60456 AAATAATAATAGTTACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCC
66 AAATAAAAATAGTTA-CAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCC
60521 T
130 T
60522 AAA
1 AAA
60525 AAAATCCCTA
Statistics
Matches: 123, Mismatches: 6, Indels: 10
0.88 0.04 0.07
Matches are distributed among these distances:
128 40 0.33
129 5 0.04
130 2 0.02
131 76 0.62
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (130 bp):
AAATAATAATCGAGTGACCAAAACATAAATTAAATATATAAGTGACCGAAAAGGTAGTTTACCCT
AAATAAAAATAGTTACAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCT
Found at i:62102 original size:30 final size:30
Alignment explanation
Indices: 62063--62127 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
62053 TTGCTACAGT
* * *
62063 GACCACCATAGGTCTCCAGGAGTACACGGC
1 GACCTCCATAGGTCTCCAGGAGCACACGAC
62093 GACCTCCATAGGTCTCCAGGAGCACACGAC
1 GACCTCCATAGGTCTCCAGGAGCACACGAC
62123 GACCT
1 GACCT
62128 ATGGAGCACT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.35, G:0.25, T:0.14
Consensus pattern (30 bp):
GACCTCCATAGGTCTCCAGGAGCACACGAC
Found at i:62175 original size:7 final size:7
Alignment explanation
Indices: 62163--62193 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
62153 CTGCAACAGC
62163 GAGGGAA
1 GAGGGAA
62170 GAGGGAA
1 GAGGGAA
62177 GAGGGAA
1 GAGGGAA
*
62184 GAGAGAA
1 GAGGGAA
62191 GAG
1 GAG
62194 TTACTGCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (7 bp):
GAGGGAA
Found at i:62250 original size:19 final size:19
Alignment explanation
Indices: 62223--62261 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
62213 TTTGTCGCAA
62223 GGAGCACTTAGCGACCTAT
1 GGAGCACTTAGCGACCTAT
* *
62242 GGAGTACTTGGCGACCTAT
1 GGAGCACTTAGCGACCTAT
62261 G
1 G
62262 TAACACATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (19 bp):
GGAGCACTTAGCGACCTAT
Found at i:62990 original size:20 final size:20
Alignment explanation
Indices: 62944--62996 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
62934 TTTTATTAAG
* *
62944 ATAAAATTGTTTACAAAGTA
1 ATAAAATTATTTACAAACTA
*
62964 A-AAAATTATTTACAATCTA
1 ATAAAATTATTTACAAACTA
62983 ATAAAATTAATTTA
1 ATAAAATT-ATTTA
62997 ATATTTCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 16 0.57
20 7 0.25
21 5 0.18
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.38
Consensus pattern (20 bp):
ATAAAATTATTTACAAACTA
Found at i:64076 original size:15 final size:15
Alignment explanation
Indices: 64055--64096 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
64045 ATGGCGCCAT
*
64055 CTAAAAATATTTAAAA
1 CTAAAAA-AATTAAAA
64071 -TAAAAAAATTAAAA
1 CTAAAAAAATTAAAA
64085 CT-AAAAAATTAA
1 CTAAAAAAATTAA
64097 TAAAGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (15 bp):
CTAAAAAAATTAAAA
Done.