Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004012.1 Hibiscus syriacus cultivar Beakdansim tig00008750_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: 55624
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:7866 original size:6 final size:6
Alignment explanation
Indices: 7857--8156 Score: 152
Period size: 7 Copynumber: 47.3 Consensus size: 6
7847 TGAAAAAATG
** * *
7857 AAAAGA AAAA-A GGAAGA AAAGAAA AAAAGA AAAA-A ATGAAG- AAAAG-
1 AAAAGA AAAAGA AAAAGA AAA-AGA AAAAGA AAAAGA A-AAAGA AAAAGA
* *
7903 AAAAG- AAAAGAA AAAATGA AAAATGA AAATGA AAATGA AAAATGA AAAATGA
1 AAAAGA AAAAG-A AAAA-GA AAAA-GA AAAAGA AAAAGA AAAA-GA AAAA-GA
* *
7955 AAAATGA AAAATGA AAAATGA AAAATGA AAAATGA AAACTGA AAATGA
1 AAAA-GA AAAA-GA AAAA-GA AAAA-GA AAAA-GA AAA-AGA AAAAGA
* * *
8003 AAATGA AAATGAA AAAATGA AAAAGA AAAATGA AAATGA AAAATGA AAAATGAA
1 AAAAGA AAAAG-A AAAA-GA AAAAGA AAAA-GA AAAAGA AAAA-GA AAAA-G-A
* * *
8057 AAAAGA AAAA-A AGAA-A AAAAGA AAAA-A AGAAGA AAGAGA AGAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA A-AAAGA
* *
8103 GAAGAA-A GAGAAGA AAGAGA AAAATGA AAAATGA AAAATGA AAAA-A
1 -AA-AAGA -AAAAGA AAAAGA AAAA-GA AAAA-GA AAAA-GA AAAAGA
8149 AAAAGA AA
1 AAAAGA AA
8157 TAAAAGGAGG
Statistics
Matches: 248, Mismatches: 24, Indels: 44
0.78 0.08 0.14
Matches are distributed among these distances:
5 35 0.14
6 79 0.32
7 124 0.50
8 10 0.04
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.08
Consensus pattern (6 bp):
AAAAGA
Found at i:7878 original size:5 final size:5
Alignment explanation
Indices: 7851--7916 Score: 57
Period size: 5 Copynumber: 12.8 Consensus size: 5
7841 AAATGATGAA
*
7851 AAAATG AAAAG AAAA- AAGGAAG AAAAG -AAA- AAAAG AAAAA AATGAAG
1 AAAA-G AAAAG AAAAG AA--AAG AAAAG AAAAG AAAAG AAAAG AA--AAG
7898 AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAA
7917 AATGAAAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
4 8 0.16
5 31 0.61
6 6 0.12
7 6 0.12
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:7884 original size:17 final size:17
Alignment explanation
Indices: 7856--7918 Score: 67
Period size: 16 Copynumber: 3.7 Consensus size: 17
7846 ATGAAAAAAT
7856 GAAAAG-AAAAAAGGAA
1 GAAAAGAAAAAAAGGAA
7872 GAAAAGAAAAAAA-GAA
1 GAAAAGAAAAAAAGGAA
* * *
7888 AAAAATGAAGAAAAGAAAA
1 GAAAA-GAAAAAAAG-GAA
7907 GAAAAGAAAAAA
1 GAAAAGAAAAAA
7919 TGAAAAATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 13 0.34
17 13 0.34
18 6 0.16
19 6 0.16
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (17 bp):
GAAAAGAAAAAAAGGAA
Found at i:7889 original size:7 final size:7
Alignment explanation
Indices: 7888--8066 Score: 227
Period size: 7 Copynumber: 26.7 Consensus size: 7
7878 AAAAAAAGAA
7888 AAAAATG
1 AAAAATG
*
7895 AAGAAAAG
1 AA-AAATG
7903 -AAAA-G
1 AAAAATG
7908 -AAAA-G
1 AAAAATG
7913 AAAAAATG
1 AA-AAATG
7921 AAAAATG
1 AAAAATG
7928 -AAAATG
1 AAAAATG
7934 -AAAATG
1 AAAAATG
7940 AAAAATG
1 AAAAATG
7947 AAAAATG
1 AAAAATG
7954 AAAAATG
1 AAAAATG
7961 AAAAATG
1 AAAAATG
7968 AAAAATG
1 AAAAATG
7975 AAAAATG
1 AAAAATG
7982 AAAAATG
1 AAAAATG
*
7989 AAAACTG
1 AAAAATG
7996 -AAAATG
1 AAAAATG
8002 -AAAATG
1 AAAAATG
8008 -AAAATG
1 AAAAATG
8014 AAAAAATG
1 -AAAAATG
8022 AAAAA-G
1 AAAAATG
8028 AAAAATG
1 AAAAATG
8035 -AAAATG
1 AAAAATG
8041 AAAAATG
1 AAAAATG
8048 AAAAATG
1 AAAAATG
*
8055 AAAAAAG
1 AAAAATG
8062 AAAAA
1 AAAAA
8067 AAGAAAAAAA
Statistics
Matches: 159, Mismatches: 4, Indels: 18
0.88 0.02 0.10
Matches are distributed among these distances:
5 6 0.04
6 45 0.28
7 95 0.60
8 13 0.08
ACGTcount: A:0.73, C:0.01, G:0.15, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:7890 original size:25 final size:27
Alignment explanation
Indices: 7851--7944 Score: 99
Period size: 25 Copynumber: 3.6 Consensus size: 27
7841 AAATGATGAA
7851 AAAATGAAAAG-AAAAAAGGAAGAAAAG
1 AAAA-GAAAAGAAAAAAAGGAAGAAAAG
*
7878 -AAA-AAAAGAAAAAAATGAAGAAAAG
1 AAAAGAAAAGAAAAAAAGGAAGAAAAG
* *
7903 AAAAGAAAAG-AAAAAATGAA-AAATG
1 AAAAGAAAAGAAAAAAAGGAAGAAAAG
7928 AAAATGAAAATGAAAAA
1 AAAA-GAAAA-GAAAAA
7945 TGAAAAATGA
Statistics
Matches: 59, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
24 5 0.08
25 23 0.39
26 21 0.36
27 6 0.10
28 4 0.07
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (27 bp):
AAAAGAAAAGAAAAAAAGGAAGAAAAG
Found at i:8067 original size:9 final size:9
Alignment explanation
Indices: 8055--8126 Score: 51
Period size: 9 Copynumber: 8.3 Consensus size: 9
8045 ATGAAAAATG
8055 AAAAAAG-A
1 AAAAAAGAA
8063 AAAAAAG-A
1 AAAAAAGAA
8071 AAAAAAG-A
1 AAAAAAGAA
8079 AAAAAAGAA
1 AAAAAAGAA
* *
8088 GAAAGAGAA
1 AAAAAAGAA
* *
8097 GAAAGAGAA
1 AAAAAAGAA
* *
8106 GAAAGAGAA
1 AAAAAAGAA
* *
8115 GAAAGAGAA
1 AAAAAAGAA
8124 AAA
1 AAA
8127 TGAAAAATGA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
8 23 0.38
9 37 0.62
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:8083 original size:7 final size:7
Alignment explanation
Indices: 7914--8066 Score: 230
Period size: 7 Copynumber: 22.7 Consensus size: 7
7904 AAAGAAAAGA
7914 AAAAATG
1 AAAAATG
7921 AAAAATG
1 AAAAATG
7928 -AAAATG
1 AAAAATG
7934 -AAAATG
1 AAAAATG
7940 AAAAATG
1 AAAAATG
7947 AAAAATG
1 AAAAATG
7954 AAAAATG
1 AAAAATG
7961 AAAAATG
1 AAAAATG
7968 AAAAATG
1 AAAAATG
7975 AAAAATG
1 AAAAATG
7982 AAAAATG
1 AAAAATG
*
7989 AAAACTG
1 AAAAATG
7996 -AAAATG
1 AAAAATG
8002 -AAAATG
1 AAAAATG
8008 -AAAATG
1 AAAAATG
8014 AAAAAATG
1 -AAAAATG
8022 AAAAA-G
1 AAAAATG
8028 AAAAATG
1 AAAAATG
8035 -AAAATG
1 AAAAATG
8041 AAAAATG
1 AAAAATG
8048 AAAAATG
1 AAAAATG
*
8055 AAAAAAG
1 AAAAATG
8062 AAAAA
1 AAAAA
8067 AAGAAAAAAA
Statistics
Matches: 138, Mismatches: 3, Indels: 10
0.91 0.02 0.07
Matches are distributed among these distances:
6 41 0.30
7 91 0.66
8 6 0.04
ACGTcount: A:0.72, C:0.01, G:0.14, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:8083 original size:18 final size:18
Alignment explanation
Indices: 8055--8133 Score: 54
Period size: 16 Copynumber: 4.1 Consensus size: 18
8045 ATGAAAAATG
8055 AAAAAAGAAAAAAAG--A
1 AAAAAAGAAAAAAAGAAA
8071 AAAAAAGAAAAAAAGAAGA
1 AAAAAAGAAAAAAAGAA-A
* *
8090 AAGAGAAGAAAGAGAAGAAA
1 AA-AAAAGAAA-AAAAGAAA
*
8110 GAGAAGAAAGAGAAAAATGAAA
1 -A-AA-AAAGA-AAAAAAGAAA
8132 AA
1 AA
8134 TGAAAAATGA
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
16 15 0.31
19 3 0.06
20 9 0.18
21 9 0.18
22 11 0.22
23 2 0.04
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (18 bp):
AAAAAAGAAAAAAAGAAA
Found at i:8208 original size:45 final size:45
Alignment explanation
Indices: 8153--8238 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
8143 AAAAAAAAAA
*
8153 GAAATAAAAGGAGGGTTCAAGA-TGAAAACCCGAAAAGGGCGTCTT
1 GAAATAAAAGGAGGGCTCAA-ATTGAAAACCCGAAAAGGGCGTCTT
* *
8198 GAAATCAAAGGAGGGCTCAAATTGAAAACCCGCAAAGGGCG
1 GAAATAAAAGGAGGGCTCAAATTGAAAACCCGAAAAGGGCG
8239 ACTTAAGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 1 0.03
45 36 0.97
ACGTcount: A:0.42, C:0.16, G:0.29, T:0.13
Consensus pattern (45 bp):
GAAATAAAAGGAGGGCTCAAATTGAAAACCCGAAAAGGGCGTCTT
Found at i:9594 original size:55 final size:55
Alignment explanation
Indices: 9529--9673 Score: 193
Period size: 55 Copynumber: 2.6 Consensus size: 55
9519 GTTGAAGATT
* * * * *
9529 GAGTCCTATACTCTCTGAA-GGAATAGGGAGTGGACAAGTTCGTTGAAGATTGTTC
1 GAGTTCTATACTCCCTAAACGG-ATAGGGAGCGGACAAGTTCATTGAAGATTGTTC
* ** *
9584 GAGTTCTATACTCCCTAAACGGATAGGGAACGGACCCGTTTATTGAAGATTGTTC
1 GAGTTCTATACTCCCTAAACGGATAGGGAGCGGACAAGTTCATTGAAGATTGTTC
9639 GAGTTCTATACTCCCTAAACGGATAGGGAGCGGAC
1 GAGTTCTATACTCCCTAAACGGATAGGGAGCGGAC
9674 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:9687 original size:55 final size:55
Alignment explanation
Indices: 9566--9689 Score: 196
Period size: 55 Copynumber: 2.3 Consensus size: 55
9556 GAGTGGACAA
*
9566 GTTCGTTGAAGATTGTTCGAGTTCTATACTCCCTAAACGGATAGGGAACGGACCC
1 GTTCATTGAAGATTGTTCGAGTTCTATACTCCCTAAACGGATAGGGAACGGACCC
* * *
9621 GTTTATTGAAGATTGTTCGAGTTCTATACTCCCTAAACGGATAGGGAGCGGACTC
1 GTTCATTGAAGATTGTTCGAGTTCTATACTCCCTAAACGGATAGGGAACGGACCC
9676 G-TCATTCGAAGATT
1 GTTCATT-GAAGATT
9690 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:10806 original size:16 final size:15
Alignment explanation
Indices: 10774--10829 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
10764 GTTCCACGCA
*
10774 TTAGATTAAATTTGT
1 TTAGATTTAATTTGT
*
10789 TTATATTTAATTTAGT
1 TTAGATTTAATTT-GT
*
10805 TTAGGTTTAATTTGT
1 TTAGATTTAATTTGT
10820 TTAGGATTTA
1 TTA-GATTTA
10830 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:11144 original size:17 final size:18
Alignment explanation
Indices: 11109--11146 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
11099 TGGTTTAATT
11109 TTTTATTTGTATATTAAA
1 TTTTATTTGTATATTAAA
11127 TTTTATATT-TAT-TTAAA
1 TTTTAT-TTGTATATTAAA
11144 TTT
1 TTT
11147 AATCATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 9 0.47
19 2 0.11
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTTATTTGTATATTAAA
Found at i:12014 original size:23 final size:24
Alignment explanation
Indices: 11987--12034 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
11977 AATGTATACC
*
11987 TTAA-TTTGTTGTTTTAATTAAAA
1 TTAATTTTGTTATTTTAATTAAAA
* *
12010 TTAATTTTTTTATTTTATTTAAAA
1 TTAATTTTGTTATTTTAATTAAAA
12034 T
1 T
12035 AACAAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (24 bp):
TTAATTTTGTTATTTTAATTAAAA
Found at i:16500 original size:17 final size:17
Alignment explanation
Indices: 16474--16512 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
16464 AGTCGAGCTA
*
16474 GAAGAGGCAGTTAGGCG
1 GAAGAGGCAGTAAGGCG
*
16491 GAAGATGCAGTAAGGCG
1 GAAGAGGCAGTAAGGCG
16508 GAAGA
1 GAAGA
16513 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:26345 original size:112 final size:112
Alignment explanation
Indices: 26148--26722 Score: 1015
Period size: 112 Copynumber: 5.1 Consensus size: 112
26138 TTGTCGGTTT
* *
26148 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
26213 GATCTATAAATGACAAAACAGGTAAAGTGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
26260 GTGTCGATACTTTATAAAAATGTATCGATCCGTAATAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
26325 GGTCTTTAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
26372 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
26437 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTAAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
26484 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAAAATGACAAAACT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
26549 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
26596 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGTTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
26661 GGTCTATAAATGACAAAACAGGTAAAGGGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
26708 GTGTCGATATTTTAT
1 GTGTCGATACTTTAT
26723 TATAAATATC
Statistics
Matches: 442, Mismatches: 21, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 442 1.00
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:26917 original size:182 final size:183
Alignment explanation
Indices: 26593--27046 Score: 732
Period size: 182 Copynumber: 2.5 Consensus size: 183
26583 GGATATATTG
* *
26593 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGTTAAAAAAATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
** * * * *
26658 ACCGGTCTATAAATGACAAAA-CAGGTAAAGGGCTACCGGATATGTTGATAGTGTCGATATTTTA
66 ACCGGTCTCGAAATGACAAAACCAGATAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTA
* **
26722 TTATAAATATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGTTAAT
131 TTATAAATATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
26775 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
*
26840 ACCGGTCTCGAAATGACAAAACCA-ATAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTC
66 ACCGGTCTCGAAATGACAAAACCAGATAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTA
*
26904 TTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
131 TTATAAATATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
* * *
26957 AAAGTGTCGATACTTTATTAAAATGTATCTATCTATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
**
27022 ATTGGTCTCGAAATGACAAAACCAG
66 ACCGGTCTCGAAATGACAAAACCAG
27047 TAGTAAACTT
Statistics
Matches: 252, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
182 250 0.99
183 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (183 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACCAGATAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTA
TTATAAATATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAAT
Found at i:27508 original size:181 final size:181
Alignment explanation
Indices: 27237--27599 Score: 708
Period size: 181 Copynumber: 2.0 Consensus size: 181
27227 TTACAATGTA
27237 ACCGGTAAAAATATACTGATTAATTAGCAAATAGGTTTACATTATGTATCGACACTCTTTAAATA
1 ACCGGTAAAAATATACTGATTAATTAGCAAATAGGTTTACATTATGTATCGACACTCTTTAAATA
27302 TGTGTCGATACTTTTTTTCCCAAAATGAAAGCACAACGAGGTGCACGCATAAAGTGTCGATACAT
66 TGTGTCGATACTTTTTTTCCCAAAATGAAAGCACAACGAGGTGCACGCATAAAGTGTCGATACAT
27367 TTAAAATTGTATCAATCCCAAAAACATCAAAACCGATAATTATAATGTAAT
131 TTAAAATTGTATCAATCCCAAAAACATCAAAACCGATAATTATAATGTAAT
*
27418 ACCGGTAAAAATATACTGGTTAATTAGCAAATAGGTTTACATTATGTATCGACACTCTTTAAATA
1 ACCGGTAAAAATATACTGATTAATTAGCAAATAGGTTTACATTATGTATCGACACTCTTTAAATA
*
27483 TGTGTCGATACTTTTTTTCCCAAAATGAAAGCACAACGAGGTGCACGGATAAAGTGTCGATACAT
66 TGTGTCGATACTTTTTTTCCCAAAATGAAAGCACAACGAGGTGCACGCATAAAGTGTCGATACAT
27548 TTAAAATTGTATCAATCCCAAAAACATCAAAACCGATAATTATAATGTAAT
131 TTAAAATTGTATCAATCCCAAAAACATCAAAACCGATAATTATAATGTAAT
27599 A
1 A
27600 GGTAAATTTG
Statistics
Matches: 180, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
181 180 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (181 bp):
ACCGGTAAAAATATACTGATTAATTAGCAAATAGGTTTACATTATGTATCGACACTCTTTAAATA
TGTGTCGATACTTTTTTTCCCAAAATGAAAGCACAACGAGGTGCACGCATAAAGTGTCGATACAT
TTAAAATTGTATCAATCCCAAAAACATCAAAACCGATAATTATAATGTAAT
Found at i:27701 original size:23 final size:23
Alignment explanation
Indices: 27655--27702 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
27645 AAATATGTCA
* *
27655 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACATAATACATT
*
27678 ATATAAGCGCTACATAATATATT
1 ATATAAGCGCTACATAATACATT
27701 AT
1 AT
27703 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACATAATACATT
Found at i:52657 original size:88 final size:84
Alignment explanation
Indices: 52556--52720 Score: 217
Period size: 88 Copynumber: 1.9 Consensus size: 84
52546 ATTTCTTTGT
*
52556 TAAAATCATGTGTCTGTCATGTAACATATGTTTTGGC-TTAAGAATTTTGGATGAGAATGAAGAA
1 TAAAATCATGTGTCTGTCATGTAACATA--TTTTGGCATT-A-AATTTTAGATGAGAATGAAGAA
52620 TTCGAGTTGACATGTTTTCCCTGC
62 TTC-AGTTGACATGTTTTCCCTGC
* * *
52644 TAAAATTCA-GTGTCTGTCATGTAACATATTTTGGCATTATATTTTAGTTGGGAATGAAGAATTC
1 TAAAA-TCATGTGTCTGTCATGTAACATATTTTGGCATTAAATTTTAGATGAGAATGAAGAATTC
*
52708 CGTTGACATGTTT
65 AGTTGACATGTTT
52721 GGGTGTTTGA
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
84 12 0.17
85 21 0.30
86 8 0.11
87 2 0.03
88 24 0.34
89 3 0.04
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (84 bp):
TAAAATCATGTGTCTGTCATGTAACATATTTTGGCATTAAATTTTAGATGAGAATGAAGAATTCA
GTTGACATGTTTTCCCTGC
Done.