Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004042.1 Hibiscus syriacus cultivar Beakdansim tig00008831_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: 69404
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:8774 original size:12 final size:12
Alignment explanation
Indices: 8745--9036 Score: 159
Period size: 12 Copynumber: 25.2 Consensus size: 12
8735 ATTTCGCTTG
*
8745 AAGAAAAATGAT
1 AAGAAAAATGAA
*
8757 GA-AAAAATGAA
1 AAGAAAAATGAA
*
8768 AAGAAAAAGGAA
1 AAGAAAAATGAA
8780 GAA-AAAAA--AA
1 -AAGAAAAATGAA
8790 AAGAAAAATG--
1 AAGAAAAATGAA
*
8800 AAGAAAAAAGAA
1 AAGAAAAATGAA
8812 AAGAAAGAA--AA
1 AAGAAA-AATGAA
8823 AATG-AAAATGAA
1 AA-GAAAAATGAA
8835 AATG-AAAATGAA
1 AA-GAAAAATGAA
8847 AATGAAAAATGAAA
1 AA-GAAAAATG-AA
8861 AATGAAAAATGAA
1 AA-GAAAAATGAA
*
8874 AA-ATGAAATGAA
1 AAGA-AAAATGAA
8886 AATG-AAAATGAA
1 AA-GAAAAATGAA
8898 AATGAAAAATGAA
1 AA-GAAAAATGAA
8911 AATG-AAAATG--
1 AA-GAAAAATGAA
*
8921 AA-ACAAATGAAA
1 AAGAAAAATG-AA
8933 AAGAAAAA--AA
1 AAGAAAAATGAA
*
8943 ATGAAAAATGAA
1 AAGAAAAATGAA
8955 AA-AAAAA--AA
1 AAGAAAAATGAA
*
8964 AAGAAAAA-AAGA
1 AAGAAAAATGA-A
*
8976 AAGAGAAAA-GAG
1 AAGA-AAAATGAA
*
8988 AAGAAAGA-GAA
1 AAGAAAAATGAA
8999 AAGAAAAATGAA
1 AAGAAAAATGAA
*
9011 AATGAAAAA-AAA
1 AA-GAAAAATGAA
*
9023 AAAAAAAAT-AA
1 AAGAAAAATGAA
9034 AAG
1 AAG
9037 GAGGGTTCAA
Statistics
Matches: 230, Mismatches: 19, Indels: 63
0.74 0.06 0.20
Matches are distributed among these distances:
9 11 0.05
10 34 0.15
11 43 0.19
12 88 0.38
13 41 0.18
14 13 0.06
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (12 bp):
AAGAAAAATGAA
Found at i:8775 original size:6 final size:6
Alignment explanation
Indices: 8766--9035 Score: 134
Period size: 6 Copynumber: 44.5 Consensus size: 6
8756 TGAAAAAATG
* * *
8766 AAAAGA AAAAG- -GAAGA AAAAAA AAAAGA AAAATG- AAGA-A AAAAG-
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA-GA AAAAGA AAAAGA
* * * * *
8810 AAAAGA AAGAA-A AAATGA AAATGA AAATGA AAATGA AAATGA AAAATGA
1 AAAAGA AA-AAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAA-GA
* * * *
8859 AAAATGA AAAATGA AAAATG- AAATGA AAATGA AAATGA AAATGA AAAATGA
1 AAAA-GA AAAA-GA AAAA-GA AAAAGA AAAAGA AAAAGA AAAAGA AAAA-GA
* * *
8910 AAATGA AAATGAA ACAAATGA AAAAG- AAAA-A AAATGA AAAATGA AAAA-A
1 AAAAGA AAAAG-A A-AAA-GA AAAAGA AAAAGA AAAAGA AAAA-GA AAAAGA
*
8959 AAAA-A AAGAA-A AAAAGA AAGAGA AAAGAGA AGAAAGA GAAAAGA AAAATGA
1 AAAAGA AA-AAGA AAAAGA AAAAGA AAA-AGA A-AAAGA -AAAAGA AAAA-GA
* * *
9010 AAATGA AAAA-A AAAAAA AAAATA AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAA
9036 GGAGGGTTCA
Statistics
Matches: 221, Mismatches: 19, Indels: 48
0.77 0.07 0.17
Matches are distributed among these distances:
4 3 0.01
5 32 0.14
6 120 0.54
7 58 0.26
8 7 0.03
9 1 0.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (6 bp):
AAAAGA
Found at i:8786 original size:17 final size:17
Alignment explanation
Indices: 8767--9025 Score: 80
Period size: 19 Copynumber: 14.9 Consensus size: 17
8757 GAAAAAATGA
* *
8767 AAAGAAAAAGGAAGAA-
1 AAAGAAAAAAGAAAAAG
8783 AAA-AAAAAAGAAAAATG
1 AAAGAAAAAAGAAAAA-G
8800 -AAGAAAAAAG-AAAAG
1 AAAGAAAAAAGAAAAAG
*
8815 AAAGAAAAAATGAAAATG
1 AAAGAAAAAA-GAAAAAG
* *
8833 AAA-ATGAAAATGAAAATGAA
1 AAAGA--AAAAAGAAAA--AG
*
8853 AAATGAAAAATGAAAAATG
1 AAA-GAAAAAAGAAAAA-G
* *
8872 AAA-AATGAAATGAAAATG
1 AAAGAA--AAAAGAAAAAG
*
8890 AAA-ATGAAAATGAAAAATG
1 AAAGA--AAAAAGAAAAA-G
* *
8909 AAA-ATGAAAATGAAACA-
1 AAAGA--AAAAAGAAAAAG
*
8926 AATG-AAAAAGAAAAA-
1 AAAGAAAAAAGAAAAAG
*
8941 AAATGAAAAATGAAAAA-
1 AAA-GAAAAAAGAAAAAG
*
8958 AAA-AAAAAGAAAAAAAG
1 AAAGAAAAA-AGAAAAAG
* *
8975 AAAGAGAAAAG-AGAAG
1 AAAGAAAAAAGAAAAAG
*
8991 AAAGAGAAAAGAAAAATG
1 AAAGAAAAAAGAAAAA-G
9009 AAAATGAAAAAA-AAAAA
1 -AAA-GAAAAAAGAAAAA
9026 AAAAATAAAA
Statistics
Matches: 193, Mismatches: 22, Indels: 53
0.72 0.08 0.20
Matches are distributed among these distances:
15 27 0.14
16 39 0.20
17 33 0.17
18 32 0.17
19 41 0.21
20 20 0.10
22 1 0.01
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.08
Consensus pattern (17 bp):
AAAGAAAAAAGAAAAAG
Found at i:8796 original size:7 final size:7
Alignment explanation
Indices: 8766--9030 Score: 86
Period size: 7 Copynumber: 37.3 Consensus size: 7
8756 TGAAAAAATG
8766 AAAAGAA
1 AAAAGAA
*
8773 AAAGGAA
1 AAAAGAA
*
8780 GAAAAAAA
1 -AAAAGAA
8788 AAAAGAAA
1 AAAAG-AA
8796 AATGAAGAA
1 AA--AAGAA
8805 AAAAGAAA
1 AAAAG-AA
8813 AGAAAGAA
1 A-AAAGAA
8821 AAAATG-A
1 AAAA-GAA
*
8828 AAATG-A
1 AAAAGAA
*
8834 AAATG-A
1 AAAAGAA
*
8840 AAATG-A
1 AAAAGAA
*
8846 AAATGAA
1 AAAAGAA
*
8853 AAATGAA
1 AAAAGAA
*
8860 AAATGAA
1 AAAAGAA
*
8867 AAATGAA
1 AAAAGAA
*
8874 AAATGAA
1 AAAAGAA
8881 ATGAAA-ATGA
1 A--AAAGA--A
*
8891 AAATG-A
1 AAAAGAA
*
8897 AAATGAA
1 AAAAGAA
*
8904 AAATG-A
1 AAAAGAA
*
8910 AAATG-A
1 AAAAGAA
*
8916 AAATGAA
1 AAAAGAA
8923 ACAAATGAA
1 A-AAA-GAA
*
8932 AAAGAAAA
1 AAA-AGAA
8940 AAAATGAA
1 AAAA-GAA
*
8948 AAATGAA
1 AAAAGAA
*
8955 AAAAAAA
1 AAAAGAA
8962 AAAAGAA
1 AAAAGAA
8969 AAAA-AGA
1 AAAAGA-A
*
8976 AAGAGAA
1 AAAAGAA
*
8983 AAGAGAA
1 AAAAGAA
* *
8990 GAAAGAG
1 AAAAGAA
8997 AAAAGAA
1 AAAAGAA
*
9004 AAATG-A
1 AAAAGAA
*
9010 AAATGAA
1 AAAAGAA
9017 AAAA-AA
1 AAAAGAA
9023 AAAA-AA
1 AAAAGAA
9029 AA
1 AA
9031 TAAAAGGAGG
Statistics
Matches: 214, Mismatches: 22, Indels: 45
0.76 0.08 0.16
Matches are distributed among these distances:
6 54 0.25
7 106 0.50
8 34 0.16
9 15 0.07
10 5 0.02
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.08
Consensus pattern (7 bp):
AAAAGAA
Found at i:8885 original size:51 final size:50
Alignment explanation
Indices: 8759--9019 Score: 207
Period size: 51 Copynumber: 5.4 Consensus size: 50
8749 AAAATGATGA
* *
8759 AAAAATGAAAA-GAAAAAGGAAGAA--AAAAA-AAAAGAAAAATG--AA-G
1 AAAAATGAAAATGAAAAATGAAAAATGAAAAAGAAAAG-AAAATGAAAATG
* * *
8803 AAAAAAGAAAA-GAAAGA--AAAAATGAAAATGAAAATGAAAATGAAAATG
1 AAAAATGAAAATGAAAAATGAAAAATGAAAAAGAAAA-GAAAATGAAAATG
*
8851 AAAAATGAAAAATGAAAAATGAAAAATG-AAATGAAAATGAAAATGAAAATG
1 AAAAATG-AAAATGAAAAATGAAAAATGAAAAAGAAAA-GAAAATGAAAATG
8902 AAAAATGAAAATG-AAAATGAAACAAATGAAAAAGAAAA-AAAATGAAAAATG
1 AAAAATGAAAATGAAAAATG-AA-AAATGAAAAAGAAAAGAAAATG-AAAATG
** * *
8953 AAAAAAAAAAAAAGAAAAA--AAGAAA-GAGAAAAGAGAAGAAAGA-GAAAA-G
1 -AAAAATGAAAATGAAAAATGAA-AAATGA-AAAAGAAAAGAAA-ATGAAAATG
9002 AAAAATGAAAATGAAAAA
1 AAAAATGAAAATGAAAAA
9020 AAAAAAAAAA
Statistics
Matches: 182, Mismatches: 15, Indels: 36
0.78 0.06 0.15
Matches are distributed among these distances:
42 4 0.02
44 19 0.10
45 10 0.05
46 1 0.01
47 2 0.01
48 22 0.12
49 13 0.07
50 36 0.20
51 45 0.25
52 26 0.14
53 4 0.02
ACGTcount: A:0.74, C:0.00, G:0.16, T:0.09
Consensus pattern (50 bp):
AAAAATGAAAATGAAAAATGAAAAATGAAAAAGAAAAGAAAATGAAAATG
Found at i:8894 original size:57 final size:57
Alignment explanation
Indices: 8822--8956 Score: 197
Period size: 57 Copynumber: 2.4 Consensus size: 57
8812 AAGAAAGAAA
8822 AAATGAAAATGAAAATGAAAATG-AAAATGAAAAATGAAAAATG-AA-AAATGAAAAATG
1 AAATGAAAATGAAAATGAAAATGAAAAATG-AAAATG-AAAATGAAACAAATGAAAAA-G
8879 AAATGAAAATGAAAATGAAAATGAAAAATGAAAATGAAAATGAAACAAATGAAAAAG
1 AAATGAAAATGAAAATGAAAATGAAAAATGAAAATGAAAATGAAACAAATGAAAAAG
*
8936 AAA-AAAAATGAAAAATGAAAA
1 AAATGAAAATG-AAAATGAAAA
8957 AAAAAAAAAG
Statistics
Matches: 73, Mismatches: 1, Indels: 8
0.89 0.01 0.10
Matches are distributed among these distances:
56 12 0.16
57 45 0.62
58 16 0.22
ACGTcount: A:0.70, C:0.01, G:0.15, T:0.14
Consensus pattern (57 bp):
AAATGAAAATGAAAATGAAAATGAAAAATGAAAATGAAAATGAAACAAATGAAAAAG
Found at i:8991 original size:16 final size:16
Alignment explanation
Indices: 8972--9002 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
8962 AAAAGAAAAA
8972 AAGAAAGAGAAAAGAG
1 AAGAAAGAGAAAAGAG
8988 AAGAAAGAGAAAAGA
1 AAGAAAGAGAAAAGA
9003 AAAATGAAAA
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:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
AAGAAAGAGAAAAGAG
Found at i:10462 original size:55 final size:55
Alignment explanation
Indices: 10397--10541 Score: 193
Period size: 55 Copynumber: 2.6 Consensus size: 55
10387 GTTGAAGATT
* * * * *
10397 GAGTCCTATACTCTCTGAA-GGAATAGGGAGTGGACAAGTTCGTTGAAGATTGTTC
1 GAGTTCTATACTCCCTAAACGG-ATAGGGAGCGGACAAGTTCATTGAAGATTGTTC
* ** *
10452 GAGTTCTATACTCCCTAAACGGATAGGGAACGGACCCGTTTATTGAAGATTGTTC
1 GAGTTCTATACTCCCTAAACGGATAGGGAGCGGACAAGTTCATTGAAGATTGTTC
10507 GAGTTCTATACTCCCTAAACGGATAGGGAGCGGAC
1 GAGTTCTATACTCCCTAAACGGATAGGGAGCGGAC
10542 TCGTCATTCG
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
55 77 0.97
56 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (55 bp):
GAGTTCTATACTCCCTAAACGGATAGGGAGCGGACAAGTTCATTGAAGATTGTTC
Found at i:10555 original size:55 final size:55
Alignment explanation
Indices: 10434--10557 Score: 196
Period size: 55 Copynumber: 2.3 Consensus size: 55
10424 GAGTGGACAA
*
10434 GTTCGTTGAAGATTGTTCGAGTTCTATACTCCCTAAACGGATAGGGAACGGACCC
1 GTTCATTGAAGATTGTTCGAGTTCTATACTCCCTAAACGGATAGGGAACGGACCC
* * *
10489 GTTTATTGAAGATTGTTCGAGTTCTATACTCCCTAAACGGATAGGGAGCGGACTC
1 GTTCATTGAAGATTGTTCGAGTTCTATACTCCCTAAACGGATAGGGAACGGACCC
10544 G-TCATTCGAAGATT
1 GTTCATT-GAAGATT
10558 TCTCAAGTTT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
54 4 0.06
55 59 0.94
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (55 bp):
GTTCATTGAAGATTGTTCGAGTTCTATACTCCCTAAACGGATAGGGAACGGACCC
Found at i:11661 original size:16 final size:15
Alignment explanation
Indices: 11629--11684 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
11619 GTTCCACGCA
*
11629 TTAGATTAAATTTGT
1 TTAGATTTAATTTGT
*
11644 TTATATTTAATTTAGT
1 TTAGATTTAATTT-GT
*
11660 TTAGGTTTAATTTGT
1 TTAGATTTAATTTGT
11675 TTAGGATTTA
1 TTA-GATTTA
11685 TATTAAATAG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 16 0.47
16 18 0.53
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (15 bp):
TTAGATTTAATTTGT
Found at i:17360 original size:17 final size:17
Alignment explanation
Indices: 17334--17372 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
17324 AGTCGAGCTA
*
17334 GAAGAGGCAGTTAGGCG
1 GAAGAGGCAGTAAGGCG
*
17351 GAAGATGCAGTAAGGCG
1 GAAGAGGCAGTAAGGCG
17368 GAAGA
1 GAAGA
17373 AGATTCTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.44, T:0.10
Consensus pattern (17 bp):
GAAGAGGCAGTAAGGCG
Found at i:22181 original size:36 final size:36
Alignment explanation
Indices: 22130--22199 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
22120 TAAAATTATA
* *
22130 ACGAAAAAATATTAAATAC-TTAAATATTTATTTTTG
1 ACGAAAAAATATTAAA-ACATTAAAAATTAATTTTTG
*
22166 ACGAAAAAATTTTAAAACATTAAAAATTAATTTT
1 ACGAAAAAATATTAAAACATTAAAAATTAATTTT
22200 AAATATTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 2 0.07
36 28 0.93
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (36 bp):
ACGAAAAAATATTAAAACATTAAAAATTAATTTTTG
Found at i:27342 original size:111 final size:112
Alignment explanation
Indices: 26998--27570 Score: 988
Period size: 112 Copynumber: 5.1 Consensus size: 112
26988 TTGTCGGTTT
* * * *
26998 GTGTCGATACTTTATAAAAATATATTGATCTATAACAATATAACAGGTAAAAAAATAACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
27063 GATCTATAAATGACAAAACAGGTAAAGTGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
27110 GTGTCGATACTTTATAAAAATGTATCGATCCGTAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
27175 GGTCTTTAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
27222 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
27286 GGTCTTTAAATGACAAAACATGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
27333 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
27397 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
27444 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGTTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * *
27509 TGTCTATAAATGATAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
27556 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
27571 TATAAATATC
Statistics
Matches: 442, Mismatches: 18, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
111 218 0.49
112 224 0.51
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:27741 original size:179 final size:180
Alignment explanation
Indices: 27441--27889 Score: 702
Period size: 179 Copynumber: 2.5 Consensus size: 180
27431 GGATATATTG
* *
27441 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGTTAAAAAAATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* ** * * * * *
27506 ATCTGTCTATAAATGATAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTCAT
*
27571 TATAAATATCGACACTTTTGGAATTTAAAAG-AGAAGTTATAGCGCTAAT
131 TATAAATATCGACACTTTTGGAATTTAAAAGAAGAAGTTATAGCGCCAAT
27620 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* *
27685 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTCCT
66 ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTCAT
* *
27750 TATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGTGCCAAT
131 TATAAATATCGACACTTTTGGAATTTAAAAG--AAGAAGTTATAGCGCCAAT
* * * *
27802 AAACTGTCGATACTTTATCAAAATGTATCGATCTATAACAATATAACATGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
27867 ATCGGTCTCGAAATGACAAAACC
66 ATCGGTCTCGAAATGACAAAACC
27890 AGTAGTAAAC
Statistics
Matches: 247, Mismatches: 20, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
179 148 0.60
182 99 0.40
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (180 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTCAT
TATAAATATCGACACTTTTGGAATTTAAAAGAAGAAGTTATAGCGCCAAT
Found at i:33385 original size:16 final size:17
Alignment explanation
Indices: 33360--33392 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
33350 TTTTATTGAT
*
33360 TTTAATATAAA-AATAA
1 TTTAAAATAAATAATAA
33376 TTTAAAATAAATAATAA
1 TTTAAAATAAATAATAA
33393 AATAATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTTAAAATAAATAATAA
Found at i:36637 original size:88 final size:87
Alignment explanation
Indices: 36536--36703 Score: 232
Period size: 88 Copynumber: 1.9 Consensus size: 87
36526 ATTTCTTTGT
* *
36536 TAAAATCATGTGTCTGTCATGTAACATATGTTTTGGC-TTAAGAATTTTGGATGAGAATGAAGAA
1 TAAAATCATGTGTCTGTCATGTAACATATATTTTGGCATTAA-AATTTTAGATGAGAATGAAGAA
36600 TTCGAGTTGACATGTTTTCCCTGC
65 TTC-AGTTGACATGTTTTCCCTGC
* * * *
36624 TAAAATTCA-GTGTCTGTCATGTAACATATATTTTGGCATTTATATTTTAGTTGGGAATGAAGAA
1 TAAAA-TCATGTGTCTGTCATGTAACATATATTTTGGCATTAAAATTTTAGATGAGAATGAAGAA
*
36688 TTCCGTTGACATGTTT
65 TTCAGTTGACATGTTT
36704 GGGTGTTTGA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
87 12 0.17
88 53 0.75
89 6 0.08
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (87 bp):
TAAAATCATGTGTCTGTCATGTAACATATATTTTGGCATTAAAATTTTAGATGAGAATGAAGAAT
TCAGTTGACATGTTTTCCCTGC
Found at i:46313 original size:21 final size:21
Alignment explanation
Indices: 46232--46325 Score: 75
Period size: 21 Copynumber: 4.4 Consensus size: 21
46222 GATTAAGACA
46232 TTTCGATAAAAGGACTTAACCT
1 TTTC-ATAAAAGGACTTAACCT
* * **
46254 TTTGATCAAAA-GAATTCTCCT
1 TTTCAT-AAAAGGACTTAACCT
* *
46275 TTTGATGAAATGG-CTTAACCT
1 TTTCAT-AAAAGGACTTAACCT
* *
46296 TTTCATAAAAGGATTTAATCT
1 TTTCATAAAAGGACTTAACCT
46317 TTTCATAAA
1 TTTCATAAA
46326 GAGAATTGTT
Statistics
Matches: 56, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
20 5 0.09
21 43 0.77
22 8 0.14
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (21 bp):
TTTCATAAAAGGACTTAACCT
Found at i:48136 original size:31 final size:31
Alignment explanation
Indices: 48098--48158 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
48088 CCAAGAAACT
* **
48098 TAAAGTGGTAATATTTGTAACATTAGGCACC
1 TAAAGTGGTAACATTAATAACATTAGGCACC
*
48129 TAAAGTGGTAACATTAATAACGTTAGGCAC
1 TAAAGTGGTAACATTAATAACATTAGGCAC
48159 GTGGATGAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (31 bp):
TAAAGTGGTAACATTAATAACATTAGGCACC
Found at i:49354 original size:19 final size:19
Alignment explanation
Indices: 49330--49368 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
49320 GGGAAAAAAC
49330 CTTATTCGTATTTAAGATG
1 CTTATTCGTATTTAAGATG
49349 CTTATTCGTATTTAAGATG
1 CTTATTCGTATTTAAGATG
49368 C
1 C
49369 AAACATGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (19 bp):
CTTATTCGTATTTAAGATG
Done.