Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006677.1 Hibiscus syriacus cultivar Beakdansim tig00016556_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: 59918
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3197 original size:37 final size:37
Alignment explanation
Indices: 3146--3250 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
3136 CCTTTTCGTC
3146 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
3183 TTACTAGGATTCAAACTCCTTAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
3220 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
3251 TCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:3808 original size:2 final size:2
Alignment explanation
Indices: 3788--3841 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
3778 TTTTTAATAC
* *
3788 TA TA TT TA T- TA TT TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3828 T- TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
3842 TTTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
1 3 0.07
2 42 0.93
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:3864 original size:14 final size:14
Alignment explanation
Indices: 3793--3875 Score: 59
Period size: 14 Copynumber: 5.8 Consensus size: 14
3783 AATACTATAT
3793 TTATTATT-T-ATA
1 TTATTATTATAATA
3805 -TATATATATATATATA
1 TTAT-TAT-TATA-ATA
3821 TTATATATTATATATA
1 TTAT-TATTATA-ATA
*
3837 TATATT-TTAAAATA
1 T-TATTATTATAATA
3851 TT-TTACTTATAATA
1 TTATTA-TTATAATA
3865 TTATTATTATA
1 TTATTATTATA
3876 TATAGATGTA
Statistics
Matches: 59, Mismatches: 2, Indels: 18
0.75 0.03 0.23
Matches are distributed among these distances:
11 3 0.05
12 5 0.08
13 2 0.03
14 19 0.32
15 7 0.12
16 13 0.22
17 10 0.17
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATTATTATAATA
Found at i:4059 original size:20 final size:22
Alignment explanation
Indices: 4031--4071 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
4021 GTTTTTGGTT
*
4031 TTTTTATATTA-TA-TATTATA
1 TTTTCATATTACTATTATTATA
4051 TTTTCATATTACTATTATTAT
1 TTTTCATATTACTATTATTAT
4072 TGTTATGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTCATATTACTATTATTATA
Found at i:4147 original size:17 final size:17
Alignment explanation
Indices: 4125--4160 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4115 TATATATTAA
4125 TATTTCATTTATTTATT
1 TATTTCATTTATTTATT
* *
4142 TATTTCCTTTATTTTTT
1 TATTTCATTTATTTATT
4159 TA
1 TA
4161 CTTATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.72
Consensus pattern (17 bp):
TATTTCATTTATTTATT
Found at i:5146 original size:18 final size:19
Alignment explanation
Indices: 5111--5146 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5101 ACCTTACTAA
*
5111 CTCTTTTCATTTTTTTCCT
1 CTCTTTTCATTTTATTCCT
5130 CTCTTTT-ATTTTATTCC
1 CTCTTTTCATTTTATTCC
5147 ATCATCTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.08, C:0.25, G:0.00, T:0.67
Consensus pattern (19 bp):
CTCTTTTCATTTTATTCCT
Found at i:8560 original size:17 final size:17
Alignment explanation
Indices: 8511--8551 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
8501 AGATCCAATC
8511 AAGAACAAAAAAGA-AAAG
1 AAGAA-AAAAAA-ACAAAG
8529 AAGAAAAAAAAACAAAG
1 AAGAAAAAAAAACAAAG
8546 AA-AAAA
1 AAGAAAA
8552 GAGAAACAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.23
17 12 0.55
18 5 0.23
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAACAAAG
Found at i:8577 original size:31 final size:29
Alignment explanation
Indices: 8507--8581 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 29
8497 GCGAAGATCC
* * *
8507 AATCAAGAACAAAAAAGAAAAGAAGAAAA
1 AATCAAAAAGAAAAAAGAAAACAAGAAAA
*
8536 AA-AAACAAAGAAAAAAGAGAAACAAGAATAA
1 AATCAA-AAAGAAAAAAGA-AAACAAGAA-AA
8567 AATCAAAAAGAAAAA
1 AATCAAAAAGAAAAA
8582 GGGACAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
28 2 0.05
29 12 0.32
30 8 0.22
31 13 0.35
32 2 0.05
ACGTcount: A:0.77, C:0.07, G:0.12, T:0.04
Consensus pattern (29 bp):
AATCAAAAAGAAAAAAGAAAACAAGAAAA
Found at i:9431 original size:22 final size:22
Alignment explanation
Indices: 9357--9433 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
9347 GCTACCCCAT
*
9357 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
9379 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
9401 CAAACCTTTAAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
9423 CAAACCTTTGA
1 CAAACCTTTGA
9434 CCAAACATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:10532 original size:106 final size:106
Alignment explanation
Indices: 10243--11918 Score: 2568
Period size: 106 Copynumber: 15.9 Consensus size: 106
10233 CAAGATAAGA
* * *
10243 CAAGTTCAACTTCACAATGAAGGGACCACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
*
10308 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* *
10349 CAAGTTCAACTTCACGACGAA-GGACCGCTGGTTGTCAATAAACAATTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
10413 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* *
10454 CAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACGACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
* **
10519 CTTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* *
10560 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
*
10625 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* *
10666 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
10731 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
*
10772 CAAGTTCAACTTCACGACGAAGAGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
* *
10837 ATTTCAACTTTACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * * * *
10878 CAAGTTCATCTTCACGATGAAGGGACTGCTGGTTGTCAATAAACAATTTC-CCATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
* * *
10942 ATTTAAACTTCACAGCGTAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * *
10983 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAATAAATAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
*
11048 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
11089 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
11154 ATTTCAACTTCACAGCGAAGGATATTGGAC-CCAAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACG
* *
11195 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
* *
11260 ATTTCAACTTCACAGCAAAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * *
11301 CAAGTTCAACTTCACGACAAAGGGACCGATGGTTGTCAACAAACAAATTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
11366 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* *
11407 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTTAGAGTCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
* * *
11472 ATTTTAACTTCACAACGAAGGATATTGGACTCCAGAAAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * *
11513 CAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
* *
11578 ATTTCAACTTCACAGCGTAGGATATTGGACTCAAGACAACG
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * *
11619 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGTCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
* * * *
11684 ATTTCAACTTCTCAACGAAGGATCTTGGAC-CCAAGACAACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACG
* * * *
11725 CAAGCTCAACTTCACGACGAAGGG-CGGCTGATTGTCAAC--A-AA-TT-TC-A-TTCAGAGTCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
* *
11782 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACA
66 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * * * * ** *
11823 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCGGTTCCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
*
11888 ATTTCAACTTCAC-GACGGAGGATATTGGACT
66 ATTTCAACTTCACAG-CGAAGGATATTGGACT
11919 TAGAACAATG
Statistics
Matches: 1445, Mismatches: 110, Indels: 30
0.91 0.07 0.02
Matches are distributed among these distances:
98 67 0.05
99 16 0.01
100 1 0.00
101 3 0.00
102 4 0.00
103 3 0.00
104 1 0.00
105 208 0.14
106 1141 0.79
107 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
Found at i:12704 original size:37 final size:37
Alignment explanation
Indices: 12651--12755 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
12641 CTTTTTGTCC
12651 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
12688 TTGCTAGGATTCAAACTCCTTAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
12725 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
12756 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:13280 original size:19 final size:19
Alignment explanation
Indices: 13256--13319 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
13246 TATATGTACA
13256 TATATTTTTTTTATTTATT
1 TATATTTTTTTTATTTATT
13275 TATATTAATTTGTTTATTT-TT
1 TATATT--TTT-TTTATTTATT
* * *
13296 TAATACTATATTTA-TTATT
1 T-ATATTTTTTTTATTTATT
13315 TATAT
1 TATAT
13320 ATATATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
18 5 0.14
19 13 0.36
20 1 0.03
21 6 0.17
22 11 0.31
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
TATATTTTTTTTATTTATT
Found at i:13292 original size:22 final size:22
Alignment explanation
Indices: 13262--13329 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
13252 TACATATATT
13262 TTTTTTATTTATTTATATTA-A
1 TTTTTTATTTATTTATATTATA
*
13283 TTTGTTTATTT-TTTAATACTATA
1 TTT-TTTATTTATTT-ATATTATA
* *
13306 TTTATTATTTATATATATATATA
1 TTTTTTATTTATTTATAT-TATA
13329 T
1 T
13330 ATACTTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 6 0.16
22 21 0.55
23 11 0.29
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (22 bp):
TTTTTTATTTATTTATATTATA
Found at i:13324 original size:19 final size:19
Alignment explanation
Indices: 13287--13325 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
13277 TATTAATTTG
*
13287 TTTATTTTTTAATACTATA
1 TTTATTATTTAATACTATA
13306 TTTATTATTTATATA-TATA
1 TTTATTATTTA-ATACTATA
13325 T
1 T
13326 ATATATACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATTATTTAATACTATA
Found at i:13717 original size:16 final size:16
Alignment explanation
Indices: 13681--13716 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
13671 TTTGTACTTA
13681 TTTTT-ATTTTTCATT
1 TTTTTCATTTTTCATT
13696 TTTTTCATTTATTCATT
1 TTTTTCATTT-TTCATT
13713 TTTT
1 TTTT
13717 CCCTCTGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 4 0.21
17 10 0.53
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCATTTTTCATT
Found at i:17700 original size:2 final size:2
Alignment explanation
Indices: 17693--17740 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
17683 TCCATACAGC
17693 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17735 TA TA TA
1 TA TA TA
17741 GAAAATGTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31005 original size:19 final size:19
Alignment explanation
Indices: 30981--31026 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
30971 ACTTGAGACC
30981 TTGCTTAAGCGATATCAAG
1 TTGCTTAAGCGATATCAAG
31000 TTGCTTAAGCGATATCAAG
1 TTGCTTAAGCGATATCAAG
*
31019 CTGCTTAA
1 TTGCTTAA
31027 CACTTGAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (19 bp):
TTGCTTAAGCGATATCAAG
Found at i:33835 original size:45 final size:42
Alignment explanation
Indices: 33736--33836 Score: 112
Period size: 45 Copynumber: 2.3 Consensus size: 42
33726 TCATTGCCGT
* **
33736 CTTCTCCAGCCAAGCCAGTGGCGGCTACTGCCTCCGTTCCCT
1 CTTCTCCAGCCAAGCCAGTGGCGACTACTGCCTCCGTTCCAA
* * *
33778 CTTCTCCTGCCAAGCCAGTGGCGACTACTACTTCCTCGGTTCCAA
1 CTTCTCCAGCCAAGCCAGTGGCG---ACTACTGCCTCCGTTCCAA
*
33823 CTTCACCAGCCAAG
1 CTTCTCCAGCCAAG
33837 ACAGCCCCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 22 0.46
45 26 0.54
ACGTcount: A:0.17, C:0.41, G:0.19, T:0.24
Consensus pattern (42 bp):
CTTCTCCAGCCAAGCCAGTGGCGACTACTGCCTCCGTTCCAA
Found at i:40045 original size:31 final size:31
Alignment explanation
Indices: 39985--40062 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
39975 ACGGATCGGG
* *
39985 TAACGAGCATG-GTCGAGCAACAAATTTTTT
1 TAACGAGCACGAGTCGAGCAACAAAATTTTT
* *
40015 TAACGAGCACGAGTTGAGTAACAAAATTTTT
1 TAACGAGCACGAGTCGAGCAACAAAATTTTT
*
40046 TAACAAGCACGAGTCGA
1 TAACGAGCACGAGTCGA
40063 ACACTACTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 10 0.24
31 31 0.76
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.26
Consensus pattern (31 bp):
TAACGAGCACGAGTCGAGCAACAAAATTTTT
Found at i:48145 original size:20 final size:20
Alignment explanation
Indices: 48120--48232 Score: 136
Period size: 20 Copynumber: 5.5 Consensus size: 20
48110 TTTTCCCAAT
48120 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
48140 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
48161 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
48181 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
48201 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
48222 TCGCAATGCGA
1 TCGCAATGCGA
48233 TACTGACTAT
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
20 47 0.60
21 31 0.40
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:48246 original size:20 final size:19
Alignment explanation
Indices: 48221--48335 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 19
48211 AATTGGGAAA
48221 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACT-ACT
* *
48241 ATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATACTAC--T
*
48262 ATCGCAACT-AGATACTTACT
1 ATCGCAA-TGCGATAC-TACT
* *
48282 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATACT-ACT
* * *
48302 TTCGCAACGCGATAATACAT
1 ATCGCAATGCGATACTAC-T
48322 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
48336 TTTCAAAGCG
Statistics
Matches: 76, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
19 5 0.07
20 45 0.59
21 22 0.29
22 4 0.05
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
ATCGCAATGCGATACTACT
Found at i:48263 original size:41 final size:41
Alignment explanation
Indices: 48218--48295 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
48208 GCGAATTGGG
* *
48218 AAAATCGCAA-TGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACT-AGATACTGACTATCGCAACGCGATAATAC
* *
48259 AAAATCGCAACTAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACTAGATACTGACTATCGCAACGCGATA
48296 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 31 0.97
42 1 0.03
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACTAGATACTGACTATCGCAACGCGATAATAC
Found at i:48531 original size:22 final size:22
Alignment explanation
Indices: 48503--48546 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
48493 CACTCTCTCA
48503 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
48525 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
48547 TATCTCTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:50190 original size:17 final size:18
Alignment explanation
Indices: 50165--50208 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
50155 TCCACTTCGG
*
50165 GAGCCATCACCTC-GCCA
1 GAGCCATCACCTCACCCA
*
50182 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
50200 GAGCCATCA
1 GAGCCATCA
50209 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.27, C:0.43, G:0.16, T:0.14
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:50713 original size:20 final size:20
Alignment explanation
Indices: 50688--50733 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
50678 ATAGTTACTT
50688 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
50708 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
50728 TCGCAA
1 TCGCAA
50734 TGCGAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:50762 original size:14 final size:14
Alignment explanation
Indices: 50743--50832 Score: 81
Period size: 14 Copynumber: 5.9 Consensus size: 14
50733 ATGCGAAATA
50743 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
50757 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
50773 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
* *
50789 AAAATCGTAATGCGAA
1 AAAATCGCAA--CGAC
50805 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
50821 AAAATCGCAACG
1 AAAATCGCAACG
50833 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
14 29 0.47
16 16 0.26
18 17 0.27
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:50785 original size:32 final size:32
Alignment explanation
Indices: 50727--50849 Score: 201
Period size: 32 Copynumber: 3.8 Consensus size: 32
50717 GGAAATGGCT
*
50727 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAAT-GAAATCGCAACGACAAA
50760 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
*
50792 ATCGTAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
*
50824 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATG-AAATCGCAA
50850 TGCGATTTGT
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
32 61 0.72
33 24 0.28
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:50885 original size:14 final size:14
Alignment explanation
Indices: 50866--50923 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
50856 TTGTGTTTCG
50866 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
50880 CGTTGCGATTTCATTTCT
1 CGTTGCGA--T--TTTGT
*
50898 CGTTGTGATTTTGT
1 CGTTGCGATTTTGT
50912 CGTTGCGATTTT
1 CGTTGCGATTTT
50924 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 23 0.64
16 2 0.06
18 11 0.31
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.52
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:50908 original size:32 final size:33
Alignment explanation
Indices: 50861--50939 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
50851 GCGATTTGTG
50861 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
* *
50893 TTTCTCGTTGTGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
50926 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
50940 AGCCATTTCC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 25 0.61
33 16 0.39
ACGTcount: A:0.10, C:0.18, G:0.23, T:0.49
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:50938 original size:19 final size:19
Alignment explanation
Indices: 50912--50978 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
50902 GTGATTTTGT
**
50912 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
50931 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
50951 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
50970 CGTTGCGAT
1 CGTTGCGAT
50979 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:50958 original size:20 final size:19
Alignment explanation
Indices: 50924--50978 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
50914 TTGCGATTTT
*
50924 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
50943 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
50963 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
50979 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:51888 original size:14 final size:14
Alignment explanation
Indices: 51869--51904 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
51859 ATTGTTTAAT
51869 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
51883 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
51897 TGATTTGT
1 TGATTTGT
51905 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:52014 original size:19 final size:19
Alignment explanation
Indices: 51992--52093 Score: 168
Period size: 19 Copynumber: 5.4 Consensus size: 19
51982 AAAACAGACT
* ***
51992 ATCGCAACGCGAAATGGCT
1 ATCGCAATGCGAAATGAAA
52011 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
52030 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
52049 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
52068 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
52087 ATCGCAA
1 ATCGCAA
52094 CGATTTTCTC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 79 1.00
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:52153 original size:20 final size:20
Alignment explanation
Indices: 52096--52153 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
52086 AATCGCAACG
* *
52096 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
*
52116 ATTTTCGCATTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
52136 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
52154 TCAAATGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:53237 original size:24 final size:24
Alignment explanation
Indices: 53210--53263 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
53200 GTATTCGAAA
* *
53210 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
53234 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
53258 TTTGAT
1 TTTGAT
53264 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:53455 original size:12 final size:12
Alignment explanation
Indices: 53438--53462 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53428 ATATAATCCT
53438 GAAGAAGAAAAA
1 GAAGAAGAAAAA
53450 GAAGAAGAAAAA
1 GAAGAAGAAAAA
53462 G
1 G
53463 TCCTCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:55772 original size:19 final size:19
Alignment explanation
Indices: 55750--55880 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
55740 GGAAATTACT
55750 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
55769 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
55783 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
55802 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
55816 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
55835 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
55849 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
55868 ATCGCAACGCGAA
1 ATCGCAATGCGAA
55881 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:55792 original size:33 final size:33
Alignment explanation
Indices: 55750--55876 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
55740 GGAAATTACT
55750 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
55783 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
55815 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
55849 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
55877 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:55857 original size:66 final size:66
Alignment explanation
Indices: 55751--55883 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
55741 GAAATTACTA
*
55751 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
55816 T
66 T
*
55817 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
55882 T
66 T
55883 T
1 T
55884 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:56058 original size:14 final size:14
Alignment explanation
Indices: 56039--56075 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
56029 CATCAATTAA
*
56039 ACAAATTAACTTTT
1 ACAAATCAACTTTT
*
56053 ACAAATCACCTTTT
1 ACAAATCAACTTTT
56067 ACAAATCAA
1 ACAAATCAA
56076 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:57489 original size:21 final size:21
Alignment explanation
Indices: 57423--57489 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
57413 GTGAATCGGG
*
57423 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
57443 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
57465 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
57486 CTCT
1 CTCT
57490 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:57508 original size:42 final size:41
Alignment explanation
Indices: 57423--57545 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
57413 GTGAATCGGG
* * * * *
57423 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
57465 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
57507 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
57546 CGATTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:58229 original size:21 final size:21
Alignment explanation
Indices: 58205--58272 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
58195 GTGACGGGAT
58205 AGGTGATGGCTCTCGTTGTAG
1 AGGTGATGGCTCTCGTTGTAG
* ** * *
58226 AGGTGTATAG-TCGGGTCG-ATC
1 AGGTG-ATGGCTCTCGTTGTA-G
58247 AGGTGATGGCTCTCGTTGTAG
1 AGGTGATGGCTCTCGTTGTAG
58268 AGGTG
1 AGGTG
58273 TATAGTCGGG
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
20 4 0.12
21 25 0.76
22 4 0.12
ACGTcount: A:0.16, C:0.13, G:0.40, T:0.31
Consensus pattern (21 bp):
AGGTGATGGCTCTCGTTGTAG
Found at i:58264 original size:42 final size:42
Alignment explanation
Indices: 58205--58301 Score: 194
Period size: 42 Copynumber: 2.3 Consensus size: 42
58195 GTGACGGGAT
58205 AGGTGATGGCTCTCGTTGTAGAGGTGTATAGTCGGGTCGATC
1 AGGTGATGGCTCTCGTTGTAGAGGTGTATAGTCGGGTCGATC
58247 AGGTGATGGCTCTCGTTGTAGAGGTGTATAGTCGGGTCGATC
1 AGGTGATGGCTCTCGTTGTAGAGGTGTATAGTCGGGTCGATC
58289 AGGTGATGGCTCT
1 AGGTGATGGCTCT
58302 GGGTGAGGTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.16, C:0.14, G:0.38, T:0.31
Consensus pattern (42 bp):
AGGTGATGGCTCTCGTTGTAGAGGTGTATAGTCGGGTCGATC
Found at i:58292 original size:21 final size:21
Alignment explanation
Indices: 58226--58293 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
58216 CTCGTTGTAG
58226 AGGTGTATAGTCGGGTCGATC
1 AGGTGTATAGTCGGGTCGATC
* ** * *
58247 AGGTG-ATGGCTCTCGTTG-TAG
1 AGGTGTATAG-TCGGGTCGAT-C
58268 AGGTGTATAGTCGGGTCGATC
1 AGGTGTATAGTCGGGTCGATC
58289 AGGTG
1 AGGTG
58294 ATGGCTCTGG
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
20 4 0.12
21 25 0.76
22 4 0.12
ACGTcount: A:0.18, C:0.13, G:0.40, T:0.29
Consensus pattern (21 bp):
AGGTGTATAGTCGGGTCGATC
Found at i:59596 original size:20 final size:19
Alignment explanation
Indices: 59565--59744 Score: 119
Period size: 19 Copynumber: 9.8 Consensus size: 19
59555 GTCTTTGGTT
59565 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
59584 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
59605 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
59624 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
59638 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
59654 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
* *
59671 CAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGA
* *
59691 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
59710 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
59729 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
59745 TGCGATTTGG
Statistics
Matches: 129, Mismatches: 19, Indels: 26
0.74 0.11 0.15
Matches are distributed among these distances:
14 17 0.13
15 1 0.01
16 4 0.03
17 4 0.03
18 1 0.01
19 54 0.42
20 46 0.36
21 2 0.02
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:59647 original size:33 final size:33
Alignment explanation
Indices: 59590--59688 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
59580 ACGAGATAAT
*
59590 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
59624 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* * **
59657 GACAATCGCAACGCCAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
59689 GCGAAATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.27, G:0.22, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:59684 original size:19 final size:19
Alignment explanation
Indices: 59660--59749 Score: 144
Period size: 19 Copynumber: 4.7 Consensus size: 19
59650 GCGACCAGAC
*
59660 AATCGCAACGCCAAATGAA
1 AATCGCAACGCGAAATGAA
*
59679 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
59699 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
59718 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
59737 AATCGCAATGCGA
1 AATCGCAACGCGA
59750 TTTGGTTTCG
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
19 49 0.74
20 17 0.26
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:59703 original size:39 final size:38
Alignment explanation
Indices: 59660--59744 Score: 143
Period size: 39 Copynumber: 2.2 Consensus size: 38
59650 GCGACCAGAC
59660 AATCGCAACGCCAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCCAAATGAAAATCGCAA-CGCGAAATAAA
* *
59699 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCCAAATGAAAATCGCAACGCGAAATAAA
59737 AATCGCAA
1 AATCGCAA
59745 TGCGATTTGG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 18 0.41
39 26 0.59
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCCAAATGAAAATCGCAACGCGAAATAAA
Found at i:59766 original size:18 final size:18
Alignment explanation
Indices: 59745--59787 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
59735 AAAATCGCAA
*
59745 TGCGATTTGGTTTCGCGT
1 TGCGATTTGATTTCGCGT
*
59763 TGCGATTTTATTTCGCGT
1 TGCGATTTGATTTCGCGT
59781 TGCGATT
1 TGCGATT
59788 ATCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTGATTTCGCGT
Done.