Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006881.1 Hibiscus syriacus cultivar Beakdansim tig00017542_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: 83030
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:424 original size:20 final size:20
Alignment explanation
Indices: 395--606 Score: 164
Period size: 20 Copynumber: 10.6 Consensus size: 20
385 CTTTAAAAAT
395 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
415 CGCTTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
435 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
456 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
476 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
** * * *
496 CATGTTGCAAATTTACGTATT
1 CGCGTTGC-GATTTACGGATA
*
517 CTCGTTGCGATTTAC-GATA
1 CGCGTTGCGATTTACGGATA
* *
536 --CGTTGCAATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
554 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
575 CGCGTTGCGATTTTACAGATA
1 CGCGTTGCGA-TTTACGGATA
*
596 CTCGTTGCGAT
1 CGCGTTGCGAT
607 AATCAAAATC
Statistics
Matches: 149, Mismatches: 32, Indels: 22
0.73 0.16 0.11
Matches are distributed among these distances:
17 7 0.05
18 5 0.03
19 4 0.03
20 77 0.52
21 56 0.38
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:454 original size:41 final size:41
Alignment explanation
Indices: 397--606 Score: 270
Period size: 41 Copynumber: 5.2 Consensus size: 41
387 TTAAAAATCG
*
397 CGTTGCGATTTACGGATACGCTTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCTTTGCGATTTTACGTATTCT
*
438 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCTTTGCGATTTTACGTATTCT
* * * *
478 CGTTGCGATTTACAGATAC-ATGTTGCAAATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCT-TTGCGATTTTACGTATTCT
* *
519 CGTTGCGATTTAC-GATACG--TTGCAATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCTTTGCGATTTTACGTATTCT
* *
557 CGTTGCGATTTACGGATACGCGTTGCGATTTTACAG-ATACT
1 CGTTGCGATTTACGGATACGCTTTGCGATTTTAC-GTATTCT
598 CGTTGCGAT
1 CGTTGCGAT
607 AATCAAAATC
Statistics
Matches: 151, Mismatches: 11, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
38 30 0.20
39 6 0.04
40 39 0.26
41 75 0.50
42 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCTTTGCGATTTTACGTATTCT
Found at i:646 original size:19 final size:19
Alignment explanation
Indices: 615--666 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
605 ATAATCAAAA
*
615 TCGCGTCGCGATTTAT-ATGT
1 TCGCGT-GCGATTT-TCATAT
635 TCGCGTGCGATTTTCATAT
1 TCGCGTGCGATTTTCATAT
654 TCGCGTTGCGATT
1 TCGCG-TGCGATT
667 CTGGAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 15 0.52
20 13 0.45
ACGTcount: A:0.13, C:0.21, G:0.25, T:0.40
Consensus pattern (19 bp):
TCGCGTGCGATTTTCATAT
Found at i:767 original size:20 final size:19
Alignment explanation
Indices: 718--771 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
708 TCTCTTCATA
718 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
737 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
758 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
772 TTTTCGCATT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:5633 original size:42 final size:42
Alignment explanation
Indices: 5586--5700 Score: 198
Period size: 42 Copynumber: 2.8 Consensus size: 42
5576 TCCCCGAATT
*
5586 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTC
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTC
5628 CCGTGTTTGTTTCACGTAATTCGTTTTCCGG-AAACGTTTTC
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTC
*
5669 CCGTG-TTATTTCACGTAATTCGTTTTCCGGAA
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
5701 TATAATTCAT
Statistics
Matches: 70, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
40 24 0.34
41 15 0.21
42 31 0.44
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (42 bp):
CCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTC
Found at i:5905 original size:22 final size:22
Alignment explanation
Indices: 5869--5914 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5859 ATTTTCATCA
5869 AAATATTAATTATTAAAATATTT
1 AAATATTAATTATTAAAAT-TTT
* *
5892 AAATA-TATTTATTAATATTTT
1 AAATATTAATTATTAAAATTTT
5913 AA
1 AA
5915 TAATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 11 0.52
23 5 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATATTAATTATTAAAATTTT
Found at i:5920 original size:21 final size:22
Alignment explanation
Indices: 5885--5943 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
5875 TAATTATTAA
* *
5885 AATATTTAAAT-ATAT-TTATT
1 AATATTTTAATAATATAATATT
5905 AATATTTTAATAATATAATATT
1 AATATTTTAATAATATAATATT
*
5927 -ATATTTTAATATTATAA
1 AATATTTTAATAATATAA
5944 AATAATCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.29
21 20 0.59
22 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATATTTTAATAATATAATATT
Found at i:5949 original size:13 final size:13
Alignment explanation
Indices: 5914--5964 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
5904 TAATATTTTA
5914 ATAATATAATATT
1 ATAATATAATATT
* *
5927 ATATTTTAATATT
1 ATAATATAATATT
*
5940 ATAAAATAATCAATT
1 ATAATATAAT--ATT
5955 AT-ATATAATA
1 ATAATATAATA
5965 ATAGATATTA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
12 1 0.03
13 18 0.60
14 6 0.20
15 5 0.17
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (13 bp):
ATAATATAATATT
Found at i:6287 original size:20 final size:20
Alignment explanation
Indices: 6209--6278 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
6199 TTTCCAGATG
6209 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
6229 TTTTTCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
6249 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
6269 TTTTCCAGAA
1 TTTTCCAGAA
6279 TTCAAATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:6287 original size:40 final size:40
Alignment explanation
Indices: 6209--6287 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
6199 TTTCCAGATG
* * **
6209 TTTTCCAGAAATGTAATTCATTTTTCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
6249 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
6288 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:6297 original size:15 final size:15
Alignment explanation
Indices: 6261--6327 Score: 91
Period size: 15 Copynumber: 4.5 Consensus size: 15
6251 TTACAGAAAT
**
6261 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
6276 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
6290 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
6305 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
6320 GTAATTCA
1 GTAATTCA
6328 TTTTCTGGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 12 0.27
15 33 0.73
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:6303 original size:29 final size:30
Alignment explanation
Indices: 6261--6332 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
6251 TTACAGAAAT
6261 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
6290 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
6320 GTAATTCATTTTC
1 GTAATTCATTTTC
6333 TGGAAAACCA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:19817 original size:26 final size:25
Alignment explanation
Indices: 19795--19843 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
19785 TTTATTTTAT
19795 AAAATGGGATCGGGTCAGGATTTAAA
1 AAAATGGGATCGGGTCA-GATTTAAA
*
19821 AAAATGGGATTGGGTCAGATTTA
1 AAAATGGGATCGGGTCAGATTTA
19844 GGTTTAGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.37, C:0.06, G:0.31, T:0.27
Consensus pattern (25 bp):
AAAATGGGATCGGGTCAGATTTAAA
Found at i:23011 original size:12 final size:12
Alignment explanation
Indices: 22994--23019 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
22984 ACCTGAAAGT
22994 AACTCAAACCAA
1 AACTCAAACCAA
23006 AACTCAAACCAA
1 AACTCAAACCAA
23018 AA
1 AA
23020 GTAACTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.31, G:0.00, T:0.08
Consensus pattern (12 bp):
AACTCAAACCAA
Found at i:23719 original size:39 final size:38
Alignment explanation
Indices: 23610--23743 Score: 113
Period size: 39 Copynumber: 3.6 Consensus size: 38
23600 TTAAATGTTT
* *
23610 ATTTTAAATTTTCAAATTATTTCA-TTCTAACATTCTAA
1 ATTTTAAATTTTTAAATTATTTCACAT-TAACATTCTAA
* * *
23648 ATTCCT-AATTTTTAAA-AATTTTCTACCA-TAACATTTTAA
1 ATT-TTAAATTTTTAAATTA-TTTC-A-CATTAACATTCTAA
23687 ATTTTAAATTTCTTAAATTATTTCACATTAACATTCTAA
1 ATTTTAAATTT-TTAAATTATTTCACATTAACATTCTAA
23726 A--TT--ATTTTTAAATTATTT
1 ATTTTAAATTTTTAAATTATTT
23744 ATTTTAACTT
Statistics
Matches: 79, Mismatches: 8, Indels: 22
0.72 0.07 0.20
Matches are distributed among these distances:
34 11 0.14
35 4 0.05
37 3 0.04
38 19 0.24
39 32 0.41
40 9 0.11
41 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.00, T:0.51
Consensus pattern (38 bp):
ATTTTAAATTTTTAAATTATTTCACATTAACATTCTAA
Found at i:24889 original size:32 final size:31
Alignment explanation
Indices: 24811--24902 Score: 150
Period size: 31 Copynumber: 2.9 Consensus size: 31
24801 ATCATACATA
*
24811 ATGTTTACTTTTTGTTTCATTTTAGTACCCG
1 ATGTTTACTTTTTGTTTCATTTTAGTACCCC
24842 ATGTTTACTTTTTGTTTCATTTTAGTACCCC
1 ATGTTTACTTTTTGTTTCATTTTAGTACCCC
24873 AT-TATTAACTTTTTGTTTCATTTTAGTACC
1 ATGT-TT-ACTTTTTGTTTCATTTTAGTACC
24903 TAATTTTTTA
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
30 1 0.02
31 34 0.59
32 23 0.40
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.55
Consensus pattern (31 bp):
ATGTTTACTTTTTGTTTCATTTTAGTACCCC
Found at i:28234 original size:22 final size:23
Alignment explanation
Indices: 28208--28255 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
28198 GGATTTCAAT
28208 AAAAT-AAGTAACTTAACAAAGA
1 AAAATCAAGTAACTTAACAAAGA
*
28230 AAAATCGAGTAACTTAACAAAGA
1 AAAATCAAGTAACTTAACAAAGA
28253 AAA
1 AAA
28256 TTCGAGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.62, C:0.10, G:0.10, T:0.17
Consensus pattern (23 bp):
AAAATCAAGTAACTTAACAAAGA
Found at i:28241 original size:23 final size:23
Alignment explanation
Indices: 28214--28262 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
28204 CAATAAAATA
28214 AGTAACTTAACAAAGAAAAATCG
1 AGTAACTTAACAAAGAAAAATCG
*
28237 AGTAACTTAACAAAGAAAATTCG
1 AGTAACTTAACAAAGAAAAATCG
28260 AGT
1 AGT
28263 TTTAGAGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.20
Consensus pattern (23 bp):
AGTAACTTAACAAAGAAAAATCG
Found at i:28879 original size:32 final size:30
Alignment explanation
Indices: 28836--28910 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
28826 TACGTGTCAT
28836 ATCGGAATCGGGTGGAAGATATATAATTTTTGG
1 ATCGG-ATCGGGTGG--GATATATAATTTTTGG
* * *
28869 ATCGGGTCGGGTTGTATATATAATTTTTGG
1 ATCGGATCGGGTGGGATATATAATTTTTGG
*
28899 GTCGGATCGGGT
1 ATCGGATCGGGT
28911 TCAGGTAGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 25 0.68
32 7 0.19
33 5 0.14
ACGTcount: A:0.23, C:0.08, G:0.33, T:0.36
Consensus pattern (30 bp):
ATCGGATCGGGTGGGATATATAATTTTTGG
Found at i:28890 original size:30 final size:30
Alignment explanation
Indices: 28854--28911 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
28844 CGGGTGGAAG
*
28854 ATATATAATTTTTGGATCGGGTCGGGTTGT
1 ATATATAATTTTTGGATCGGATCGGGTTGT
*
28884 ATATATAATTTTTGGGTCGGATCGGGTT
1 ATATATAATTTTTGGATCGGATCGGGTT
28912 CAGGTAGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.21, C:0.07, G:0.29, T:0.43
Consensus pattern (30 bp):
ATATATAATTTTTGGATCGGATCGGGTTGT
Found at i:29047 original size:2 final size:2
Alignment explanation
Indices: 29040--29065 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29030 ATGTTGAAAG
29040 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
29066 CTTTAATCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30439 original size:29 final size:29
Alignment explanation
Indices: 30386--30444 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
30376 CTTCCCAGCA
*
30386 TAGGTCGCCATGCCCTCCGGACGACCTTG
1 TAGGTCGCCATGCCCTCAGGACGACCTTG
*
30415 TAGGTCGCCATGCACGTCAGG-CGACCTTG
1 TAGGTCGCCATGC-CCTCAGGACGACCTTG
30444 T
1 T
30445 CCTGCGCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.15, C:0.34, G:0.29, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCAGGACGACCTTG
Found at i:30511 original size:21 final size:22
Alignment explanation
Indices: 30454--30535 Score: 130
Period size: 22 Copynumber: 3.8 Consensus size: 22
30444 TCCTGCGCCT
*
30454 TGCTCCCCGCTGCATGCTCGCC
1 TGCTCCCCGCTGCATGCTTGCC
30476 TGCTCCCCGCTGCATGCTTGCC
1 TGCTCCCCGCTGCATGCTTGCC
30498 TGCTCCCC-CTGCATGCTTGCC
1 TGCTCCCCGCTGCATGCTTGCC
* *
30519 TGCTCCCCACTACATGC
1 TGCTCCCCGCTGCATGC
30536 AGGCAACCTC
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
21 21 0.37
22 36 0.63
ACGTcount: A:0.07, C:0.48, G:0.20, T:0.26
Consensus pattern (22 bp):
TGCTCCCCGCTGCATGCTTGCC
Found at i:36999 original size:22 final size:22
Alignment explanation
Indices: 36971--37034 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
36961 ACTGTTTCAT
36971 CTCTAGAGTAGAGATAGAGATA
1 CTCTAGAGTAGAGATAGAGATA
* * *
36993 CTCTAGAATAGAGATATAAATA
1 CTCTAGAGTAGAGATAGAGATA
37015 CTCTAGAGTAGAGATGAGAG
1 CTCTAGAGTAGAGAT-AGAG
37035 CTGAAGATGA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
22 33 0.94
23 2 0.06
ACGTcount: A:0.42, C:0.09, G:0.25, T:0.23
Consensus pattern (22 bp):
CTCTAGAGTAGAGATAGAGATA
Found at i:41580 original size:18 final size:18
Alignment explanation
Indices: 41546--41583 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
41536 TACATCCGCA
*
41546 AATAAATAAATATATTTT
1 AATAAATAAATAAATTTT
41564 AATAAA-AAATAAAATTTT
1 AATAAATAAAT-AAATTTT
41582 AA
1 AA
41584 GATGAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAATAAATAAATTTT
Found at i:44902 original size:34 final size:36
Alignment explanation
Indices: 44862--44934 Score: 123
Period size: 37 Copynumber: 2.1 Consensus size: 36
44852 ATTTGTATTT
44862 AACCT-AAAAAA-ATAGTTATTAATCATTGTTATGA
1 AACCTAAAAAAAGATAGTTATTAATCATTGTTATGA
44896 AACCTAAAAAAAAGATAGTTATTAATCATTGTTATGA
1 AACCT-AAAAAAAGATAGTTATTAATCATTGTTATGA
44933 AA
1 AA
44935 TTATCAGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
34 5 0.14
36 6 0.17
37 25 0.69
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (36 bp):
AACCTAAAAAAAGATAGTTATTAATCATTGTTATGA
Found at i:46558 original size:45 final size:45
Alignment explanation
Indices: 46508--46655 Score: 156
Period size: 45 Copynumber: 3.3 Consensus size: 45
46498 GGGTAGACCA
**
46508 GGGTCACACAACATCAACTTCTCCCAAGTATCTCAGGTGAGGTCC
1 GGGTCACACAACATCAACACCTCCCAAGTATCTCAGGTGAGGTCC
* ** *
46553 GGGTCACATAACATCGGCACCTCCCAAGTATCTCAGGTGAGGTTC
1 GGGTCACACAACATCAACACCTCCCAAGTATCTCAGGTGAGGTCC
* * * * * *
46598 GGGTCACATAGCATCGACACCTCCCAA-TACCTTATGCT-AGGTCC
1 GGGTCACACAACATCAACACCTCCCAAGTATCTCA-GGTGAGGTCC
*
46642 GGGTCACATAACAT
1 GGGTCACACAACAT
46656 TGGTACCTTG
Statistics
Matches: 89, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
44 23 0.26
45 66 0.74
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.22
Consensus pattern (45 bp):
GGGTCACACAACATCAACACCTCCCAAGTATCTCAGGTGAGGTCC
Found at i:47702 original size:20 final size:20
Alignment explanation
Indices: 47679--47728 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
47669 AAATAAGGGA
*
47679 TCGATCCTTTTGAAAAGGAG
1 TCGATCCTTTTAAAAAGGAG
*
47699 TCGATCCTTTTAAAAAGGGG
1 TCGATCCTTTTAAAAAGGAG
*
47719 TCAATCCTTT
1 TCGATCCTTT
47729 ACTGGAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (20 bp):
TCGATCCTTTTAAAAAGGAG
Found at i:52169 original size:37 final size:37
Alignment explanation
Indices: 52093--52169 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
52083 TTTTTATATT
*
52093 TTTAATTTTGTAAAAAATATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAATATTATATAAATATTATCAA
* *
52130 TTTAATTTTTTAAATAAA-A-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAATATTATATAAATATTAT-CAA
52167 TTT
1 TTT
52170 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 19 0.54
38 3 0.09
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAATATTATATAAATATTATCAA
Found at i:67880 original size:19 final size:19
Alignment explanation
Indices: 67835--67870 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
67825 TTTTACCAGA
67835 GCAT-TTTATTTTTTTTTT
1 GCATGTTTATTTTTTTTTT
*
67853 GCATTTTTATTTTTTTTT
1 GCATGTTTATTTTTTTTT
67871 GTATAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.78
Consensus pattern (19 bp):
GCATGTTTATTTTTTTTTT
Found at i:78579 original size:35 final size:34
Alignment explanation
Indices: 78494--78580 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
78484 ATTTGATATT
*
78494 TAAATACAACAAACTTACAATAAGAATTAAATAG
1 TAAATACAACAAAATTACAATAAGAATTAAATAG
* * *
78528 TAAATGATAACCAAATTACAATAATTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATAG
78566 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
78581 ACTAAAATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.55
36 1 0.02
37 5 0.11
38 9 0.20
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATAG
Found at i:79199 original size:18 final size:18
Alignment explanation
Indices: 79176--79215 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
79166 AAAGGCGATA
79176 GCGGCATCATATATGGTT
1 GCGGCATCATATATGGTT
79194 GCGGCATCATATATGGTT
1 GCGGCATCATATATGGTT
79212 GCGG
1 GCGG
79216 TGGCTGCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (18 bp):
GCGGCATCATATATGGTT
Found at i:80866 original size:111 final size:113
Alignment explanation
Indices: 80725--80932 Score: 357
Period size: 111 Copynumber: 1.8 Consensus size: 113
80715 CAAAAATTAA
* *
80725 TTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAA-T-TTAAATTAAATTA
1 TTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTATTAAATTAAATTA
80788 AAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATATTTAATTC
66 AAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATATTTAATTC
80836 TTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTAAATTAAA
1 TTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAA-TT--ATTAAATTAAA
80901 TTAAAACGTTAAAATGTTACCGTATCAGCAAA
63 TTAAAACGTTAAAATGTTACCGTATCAGCAAA
80933 ATGTAGAAAT
Statistics
Matches: 90, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
111 47 0.52
113 1 0.01
116 42 0.47
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (113 bp):
TTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTATTAAATTAAATTA
AAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATATTTAATTC
Found at i:82046 original size:22 final size:22
Alignment explanation
Indices: 82021--82064 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
82011 ATTTTAAACT
82021 TTTTAGGGT-TTTTTTAAAATAA
1 TTTTA-GGTATTTTTTAAAATAA
*
82043 TTTTATGTATTTTTTAAAATAA
1 TTTTAGGTATTTTTTAAAATAA
82065 AAATTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (22 bp):
TTTTAGGTATTTTTTAAAATAA
Found at i:82356 original size:20 final size:20
Alignment explanation
Indices: 82328--82372 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
82318 ATATTTAACA
82328 AGAAAATATAAAAATAATTT
1 AGAAAATATAAAAATAATTT
* * *
82348 AGAATATATAATAATTATTT
1 AGAAAATATAAAAATAATTT
82368 A-AAAA
1 AGAAAA
82373 AAAGAAACCC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (20 bp):
AGAAAATATAAAAATAATTT
Done.