Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000356.1 Hibiscus syriacus cultivar Beakdansim tig00000652_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: 63871
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:267 original size:21 final size:21
Alignment explanation
Indices: 219--269 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
209 TTCTGCAGAC
* *
219 ATTTCAGATGGCACCGTAGCT
1 ATTTCAGATGACACCATAGCT
**
240 ACATCAGATGACACCATAGCT
1 ATTTCAGATGACACCATAGCT
261 ATTTCAGAT
1 ATTTCAGAT
270 ATCCACAGCC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (21 bp):
ATTTCAGATGACACCATAGCT
Found at i:329 original size:61 final size:62
Alignment explanation
Indices: 242--359 Score: 150
Period size: 61 Copynumber: 1.9 Consensus size: 62
232 CCGTAGCTAC
* *
242 ATCAGATGACACCATAGCTATTTCAGATA-TCCACAGCCGAGTCAAACGCCACCGTTTCCAT
1 ATCAGATGACACCATAGCTATATCAGATACACCACAGCCGAGTCAAACGCCACCGTTTCCAT
* * * *
303 ATCAGATGCCACCATAAG-TATATCAGATACCACCACAGCCGGGTCAGATGCCACCGT
1 ATCAGATGACACCAT-AGCTATATCAGATA-CACCACAGCCGAGTCAAACGCCACCGT
360 CGCAGGGTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
61 24 0.50
62 2 0.04
63 22 0.46
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.20
Consensus pattern (62 bp):
ATCAGATGACACCATAGCTATATCAGATACACCACAGCCGAGTCAAACGCCACCGTTTCCAT
Found at i:829 original size:23 final size:24
Alignment explanation
Indices: 803--859 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
793 TTGTAAAGTT
*
803 TTTATTTAATTATGGA-ATTTTTA
1 TTTATTTAATTATGAATATTTTTA
** *
826 TTTATTTTTTTATTAATATTTTTA
1 TTTATTTAATTATGAATATTTTTA
850 -TTATTTAATT
1 TTTATTTAATT
860 GTTAGAATTG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (24 bp):
TTTATTTAATTATGAATATTTTTA
Found at i:4166 original size:16 final size:15
Alignment explanation
Indices: 4136--4172 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
4126 AAATTTGTTC
*
4136 AAATAATTAAATATA
1 AAATAAATAAATATA
4151 AAATAAATATAATATA
1 AAATAAATA-AATATA
4167 AAATAA
1 AAATAA
4173 TTTTACCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATAAATAAATATA
Found at i:6727 original size:29 final size:29
Alignment explanation
Indices: 6642--6714 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
6632 CCCTTTTTGA
*
6642 AATGAACATTCCAAGATTTTACCTTTACC
1 AATGAACAATCCAAGATTTTACCTTTACC
*
6671 AATTAACAATCCAAGATTTTACCTTTACC
1 AATGAACAATCCAAGATTTTACCTTTACC
6700 AATGAACAATCCAAG
1 AATGAACAATCCAAG
6715 CCTTTTTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (29 bp):
AATGAACAATCCAAGATTTTACCTTTACC
Found at i:9939 original size:6 final size:6
Alignment explanation
Indices: 9928--10170 Score: 458
Period size: 6 Copynumber: 41.2 Consensus size: 6
9918 AACCAACGAT
9928 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
9976 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
10024 ATATAC ATATAC ATATAC --ATAC ATATAC ATATAC ATATAC --ATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
10068 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
10116 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
10164 ATATAC A
1 ATATAC A
10171 GTGTTGGATT
Statistics
Matches: 233, Mismatches: 0, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.03
6 225 0.97
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:11783 original size:23 final size:23
Alignment explanation
Indices: 11753--11797 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
11743 TCCTTATAAT
11753 TGGAGGGCAACCAATAAAAAAAC
1 TGGAGGGCAACCAATAAAAAAAC
11776 TGGAGGGCAACCAATAAAAAAA
1 TGGAGGGCAACCAATAAAAAAA
11798 GTTAACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.53, C:0.16, G:0.22, T:0.09
Consensus pattern (23 bp):
TGGAGGGCAACCAATAAAAAAAC
Found at i:15848 original size:38 final size:38
Alignment explanation
Indices: 15797--15870 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
15787 TATATTTAAT
*
15797 GGATATGAACTCAACTTTTGACAGAGAATGTGAAAGGG
1 GGATATGAACTCAACTTTTGAAAGAGAATGTGAAAGGG
15835 GGATATGAACTCAACTTTTGAAAGAGAATGTGAAAG
1 GGATATGAACTCAACTTTTGAAAGAGAATGTGAAAG
15871 AGAGATCTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.39, C:0.09, G:0.27, T:0.24
Consensus pattern (38 bp):
GGATATGAACTCAACTTTTGAAAGAGAATGTGAAAGGG
Found at i:21394 original size:31 final size:31
Alignment explanation
Indices: 21356--21427 Score: 144
Period size: 31 Copynumber: 2.3 Consensus size: 31
21346 TTGATCCACT
21356 TTGGTCCATGTTGGGACAACTTGCACCAGCC
1 TTGGTCCATGTTGGGACAACTTGCACCAGCC
21387 TTGGTCCATGTTGGGACAACTTGCACCAGCC
1 TTGGTCCATGTTGGGACAACTTGCACCAGCC
21418 TTGGTCCATG
1 TTGGTCCATG
21428 CTCAATTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.28
Consensus pattern (31 bp):
TTGGTCCATGTTGGGACAACTTGCACCAGCC
Found at i:21889 original size:23 final size:22
Alignment explanation
Indices: 21846--21889 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
21836 TGAAATAATA
* **
21846 TATTTATTAAAAATATTATTTT
1 TATTTAATAAAAATAGGATTTT
21868 TATTTAATAAAAATAAGGATTT
1 TATTTAATAAAAAT-AGGATTT
21890 AATTGAACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (22 bp):
TATTTAATAAAAATAGGATTTT
Found at i:24880 original size:20 final size:20
Alignment explanation
Indices: 24841--24881 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
24831 ACAATGAACT
*
24841 GACTGAAAACCAGTAGAACC
1 GACTGAAAACCAGTAAAACC
**
24861 GACTGAAAACTGGTAAAACC
1 GACTGAAAACCAGTAAAACC
24881 G
1 G
24882 GGATGAACCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (20 bp):
GACTGAAAACCAGTAAAACC
Found at i:25149 original size:16 final size:16
Alignment explanation
Indices: 25107--25149 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
25097 ATTAAAACTT
*
25107 GAACTCGAAAAGGCTC
1 GAACTCAAAAAGGCTC
25123 GAACTCAAAAAGGCTC
1 GAACTCAAAAAGGCTC
25139 GAACTCAAAAA
1 GAACTCAAAAA
25150 ATATTTAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.12
Consensus pattern (16 bp):
GAACTCAAAAAGGCTC
Found at i:26652 original size:17 final size:19
Alignment explanation
Indices: 26617--26662 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
26607 GACCAAGTCT
26617 TATAGTTCTCCATTATATA
1 TATAGTTCTCCATTATATA
26636 TATAGTTCTCCATTATATA
1 TATAGTTCTCCATTATATA
26655 TATAGTTC
1 TATAGTTC
26663 ATGTCTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (19 bp):
TATAGTTCTCCATTATATA
Found at i:27580 original size:16 final size:17
Alignment explanation
Indices: 27559--27598 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
27549 ATATTTTATT
*
27559 ATATTTTTA-ATATTTA
1 ATATTTTAATATATTTA
27575 ATA-TTTAATATATTTA
1 ATATTTTAATATATTTA
27591 ATATTTTA
1 ATATTTTA
27599 CTTAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 13 0.62
17 4 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATTTTAATATATTTA
Found at i:32211 original size:15 final size:16
Alignment explanation
Indices: 32179--32211 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
32169 AAAATCTTTC
32179 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
32195 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
32210 TT
1 TT
32212 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:32988 original size:16 final size:17
Alignment explanation
Indices: 32961--32993 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
32951 TATCGCCGAC
32961 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
32978 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
32994 TGTGAATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:34793 original size:13 final size:13
Alignment explanation
Indices: 34752--34795 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
34742 TATTTAGTAC
*
34752 TTTTTATTGTAGT
1 TTTTTATTGTAAT
* * *
34765 TGTTTATTGGACT
1 TTTTTATTGTAAT
34778 TTTTTATTGTAAT
1 TTTTTATTGTAAT
34791 TTTTT
1 TTTTT
34796 TATTTATCAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.68
Consensus pattern (13 bp):
TTTTTATTGTAAT
Found at i:34889 original size:34 final size:34
Alignment explanation
Indices: 34834--34904 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
34824 CGTTAATATG
34834 GTTGGATTTATTTTAATTTATTTTG-TTAAATTT
1 GTTGGATTTATTTTAATTTATTTTGCTTAAATTT
*
34867 GTTGGACTTT-TTGTTAATTTATTTTGCTTAATTTT
1 GTTGGA-TTTATT-TTAATTTATTTTGCTTAAATTT
34902 GTT
1 GTT
34905 TATTACCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
33 8 0.24
34 16 0.47
35 10 0.29
ACGTcount: A:0.20, C:0.03, G:0.14, T:0.63
Consensus pattern (34 bp):
GTTGGATTTATTTTAATTTATTTTGCTTAAATTT
Found at i:39295 original size:18 final size:18
Alignment explanation
Indices: 39268--39302 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39258 TATTTTGGAG
*
39268 CTTAATTGTTTATTAACT
1 CTTAACTGTTTATTAACT
39286 CTTAACTGTTTATTAAC
1 CTTAACTGTTTATTAAC
39303 AAATAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (18 bp):
CTTAACTGTTTATTAACT
Found at i:44073 original size:21 final size:21
Alignment explanation
Indices: 43958--44073 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
43948 GCGAAATAAA
**
43958 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
43978 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
43998 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
44019 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
44039 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
44061 AATCGCAACGCGA
1 AATCGCAACGCGA
44074 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:44086 original size:20 final size:20
Alignment explanation
Indices: 44061--44253 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
44051 GATTTTCCAG
* ** *
44061 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
44081 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
44101 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
44121 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
44141 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
44161 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
44181 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
44201 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
44222 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
44242 AATCGCAACGCG
1 AATCGCAACGCG
44254 ATTTTTAAAG
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 131 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:44670 original size:33 final size:33
Alignment explanation
Indices: 44631--44701 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
44621 TTCACTTAGA
44631 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
44664 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
44697 TTTCA
1 TTTCA
44702 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:44807 original size:21 final size:20
Alignment explanation
Indices: 44781--44887 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
44771 TGCAGAAGAG
44781 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
44802 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
44822 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
44844 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
44858 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
44877 TCGCAACGAGA
1 TCGCAACGAGA
44888 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 25 0.36
22 10 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:44861 original size:14 final size:14
Alignment explanation
Indices: 44842--44898 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
44832 GAAAAATGAA
44842 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
44856 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
44875 AATCGCAACGAGAG
1 AATCGCAACGAGAG
44889 AATCGCAACG
1 AATCGCAACG
44899 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:44873 original size:33 final size:33
Alignment explanation
Indices: 44835--44914 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
44825 GCAACGAGAA
44835 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
44868 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
44901 AAACCAAAATCGCA
1 AAATGAAAATCGCA
44915 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:44932 original size:19 final size:19
Alignment explanation
Indices: 44910--45023 Score: 94
Period size: 19 Copynumber: 6.1 Consensus size: 19
44900 GAAACCAAAA
*
44910 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
44929 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
44943 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
44962 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
44982 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
45002 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
45022 TC
1 TC
45024 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.12
16 3 0.04
17 3 0.04
19 29 0.36
20 21 0.26
21 14 0.17
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:45019 original size:41 final size:40
Alignment explanation
Indices: 44940--45023 Score: 132
Period size: 41 Copynumber: 2.1 Consensus size: 40
44930 CGCGTTGCGA
***
44940 TTCTCTCGTTGCGATTTTCATTTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAGTCATTTCTCGTTGCGATTTTCAT
44980 TTCTCTCGTTGCGACAGTCATTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAGTCATT-TCTCGTTGCGATTTTCAT
45021 TTC
1 TTC
45024 AACCAAAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 19 0.47
41 21 0.52
ACGTcount: A:0.11, C:0.25, G:0.15, T:0.49
Consensus pattern (40 bp):
TTCTCTCGTTGCGACAGTCATTTCTCGTTGCGATTTTCAT
Found at i:45020 original size:20 final size:20
Alignment explanation
Indices: 44939--45021 Score: 123
Period size: 20 Copynumber: 4.2 Consensus size: 20
44929 TCGCGTTGCG
44939 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
44959 ATT-TCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
44978 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
44999 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
45019 ATT
1 ATT
45022 TCAACCAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.31
20 24 0.44
21 14 0.25
ACGTcount: A:0.12, C:0.24, G:0.16, T:0.48
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:46857 original size:93 final size:93
Alignment explanation
Indices: 46698--47013 Score: 614
Period size: 93 Copynumber: 3.4 Consensus size: 93
46688 TAGATTGCTT
*
46698 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
46763 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
46791 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
46856 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
46884 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTAAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
46949 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
46977 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
47014 AATACCCTGA
Statistics
Matches: 221, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 221 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:47169 original size:33 final size:33
Alignment explanation
Indices: 47111--47234 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
47101 TAGTTTACTT
* * *
47111 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
* **
47145 TTGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
47178 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
47211 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
47235 TTACGATTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
33 70 0.86
34 11 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.10
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:47171 original size:19 final size:18
Alignment explanation
Indices: 47147--47234 Score: 57
Period size: 19 Copynumber: 5.2 Consensus size: 18
47137 CGAGAGAATT
47147 GCAACGCGAAATGAAAATC
1 GCAACGCGAAA-GAAAATC
*
47166 GCAA--CGACAG--AATC
1 GCAACGCGAAAGAAAATC
*
47180 GCAACGCGAAACCAAAATC
1 GCAACGCGAAA-GAAAATC
*
47199 GCAA--CG--ACAAAATC
1 GCAACGCGAAAGAAAATC
*
47213 GCAACGCGAAACCAAAATC
1 GCAACGCGAAA-GAAAATC
47232 GCA
1 GCA
47235 TTACGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
14 19 0.34
15 1 0.02
16 7 0.12
17 6 0.11
18 1 0.02
19 22 0.39
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.07
Consensus pattern (18 bp):
GCAACGCGAAAGAAAATC
Found at i:47181 original size:14 final size:14
Alignment explanation
Indices: 47160--47218 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
47150 ACGCGAAATG
47160 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
47174 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
47193 AAAATCGCAACGAC
1 AAAATCGCAACGAC
47207 AAAATCGCAACG
1 AAAATCGCAACG
47219 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:47260 original size:19 final size:19
Alignment explanation
Indices: 47238--47380 Score: 114
Period size: 19 Copynumber: 8.2 Consensus size: 19
47228 AATCGCATTA
47238 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
47257 CGA--TTC---T--CGTTG
1 CGATTTTCATTTCGCGTTG
*
47269 CGA-TTTCATTTCGCATTG
1 CGATTTTCATTTCGCGTTG
*
47287 CGA--TTC-TGT--CGTTG
1 CGATTTTCATTTCGCGTTG
47301 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
** *
47320 CGATTTTGGTTTCTCGTTG
1 CGATTTTCATTTCGCGTTG
*
47339 CGATTCTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
* *
47358 CGATTTTAAGTTTCGTGTTG
1 CGATTTTCA-TTTCGCGTTG
47378 CGA
1 CGA
47381 AAGTAACTAT
Statistics
Matches: 98, Mismatches: 14, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
12 8 0.08
13 3 0.03
14 8 0.08
16 6 0.06
17 8 0.08
18 7 0.07
19 46 0.47
20 12 0.12
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.45
Consensus pattern (19 bp):
CGATTTTCATTTCGCGTTG
Found at i:47337 original size:38 final size:36
Alignment explanation
Indices: 47238--47364 Score: 146
Period size: 38 Copynumber: 3.7 Consensus size: 36
47228 AATCGCATTA
47238 CGATTTTCATTTCGCGTTGCGA-----TTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTTTGTTCTCGTTG
* *
47269 CGA-TTTCATTTCGCATTGCGATTCTG---TCGTTG
1 CGATTTTCATTTCGCGTTGCGATTTTGTTCTCGTTG
47301 CGATTTTCATTTCGCGTTGCGATTTTGGTTTCTCGTTG
1 CGATTTTCATTTCGCGTTGCGATTTT-G-TTCTCGTTG
*
47339 CGATTCTCATTTCGCGTTGCGATTTT
1 CGATTTTCATTTCGCGTTGCGATTTT
47365 AAGTTTCGTG
Statistics
Matches: 81, Mismatches: 4, Indels: 15
0.81 0.04 0.15
Matches are distributed among these distances:
30 17 0.21
31 3 0.04
32 9 0.11
33 20 0.25
34 1 0.01
38 31 0.38
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.46
Consensus pattern (36 bp):
CGATTTTCATTTCGCGTTGCGATTTTGTTCTCGTTG
Found at i:49320 original size:14 final size:14
Alignment explanation
Indices: 49301--49336 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
49291 ATTGTTTAAT
49301 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
49315 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
49329 TGATTTGT
1 TGATTTGT
49337 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:49523 original size:20 final size:19
Alignment explanation
Indices: 49443--49541 Score: 127
Period size: 20 Copynumber: 5.4 Consensus size: 19
49433 AAAAATGACT
49443 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
49462 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
49481 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
49495 ATCGTAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
49515 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
49535 ATCGCAA
1 ATCGCAA
49542 CGAGAGAATC
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 1 0.01
17 3 0.04
19 27 0.39
20 29 0.41
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:49545 original size:54 final size:53
Alignment explanation
Indices: 49443--49559 Score: 209
Period size: 54 Copynumber: 2.2 Consensus size: 53
49433 AAAAATGACT
49443 ATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
49495 ATCGTAATGCGGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
49549 ATCGCAATGCG
1 ATCGCAATGCG
49560 ATTTTCATTT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
52 9 0.15
53 19 0.31
54 33 0.54
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:49578 original size:19 final size:19
Alignment explanation
Indices: 49550--49764 Score: 262
Period size: 19 Copynumber: 11.9 Consensus size: 19
49540 AACGAGAGAA
*
49550 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
49569 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
49588 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
49605 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
49622 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
49641 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
49657 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
49674 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
49693 TCCGCATTGCGA--TTC-TC
1 T-CGCATTGCGATTTTCATT
49710 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
49727 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
49746 TCCGCATTGCGATTTTCAT
1 T-CGCATTGCGATTTTCAT
49765 GTTGGGATTT
Statistics
Matches: 171, Mismatches: 7, Indels: 35
0.80 0.03 0.16
Matches are distributed among these distances:
14 18 0.11
16 17 0.10
17 19 0.11
18 6 0.04
19 74 0.43
20 37 0.22
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:49619 original size:53 final size:53
Alignment explanation
Indices: 49556--49792 Score: 415
Period size: 53 Copynumber: 4.5 Consensus size: 53
49546 AGAATCGCAA
49556 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
49609 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
49661 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
49714 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGT
* * *
49767 TGGGATTTTCATTTCGCGTTGTGATT
1 TGCGATTTTCATTTCGCATTGCGATT
49793 CTCTCGTTGC
Statistics
Matches: 178, Mismatches: 4, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
52 52 0.29
53 125 0.70
54 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:49632 original size:33 final size:33
Alignment explanation
Indices: 49574--49739 Score: 167
Period size: 33 Copynumber: 4.8 Consensus size: 33
49564 TCATTTCGCA
49574 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
49608 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
49644 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
49679 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
49713 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
49740 TTCATTTCCG
Statistics
Matches: 108, Mismatches: 12, Indels: 25
0.74 0.08 0.17
Matches are distributed among these distances:
31 4 0.04
32 6 0.06
33 34 0.31
34 33 0.31
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.07
39 3 0.03
40 9 0.08
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:49717 original size:86 final size:84
Alignment explanation
Indices: 49627--49806 Score: 224
Period size: 86 Copynumber: 2.1 Consensus size: 84
49617 TCATTTCGCA
49627 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-TTGCGATTTTCATTTCGCATTGCGATTT
1 TTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTCA--T-G--TTGCGATTT
49688 TCATTTCCGCATTGCGATTCTCTCG
61 TCATTT-CGCATTGCGATTCTCTCG
* *
49713 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCCG-ATTGCGATTTTCATGTTGCGATTTTCA
* *
49778 TTTCGCGTTGTGATTCTCTCG
64 TTTCGCATTGCGATTCTCTCG
49799 TTGCGATT
1 TTGCGATT
49807 GTAATTTCCG
Statistics
Matches: 84, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
86 49 0.58
87 14 0.17
88 3 0.04
89 3 0.04
90 3 0.04
92 12 0.14
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.47
Consensus pattern (84 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGATTGCGATTTTCATGTTGCGATTTTCATT
TCGCATTGCGATTCTCTCG
Found at i:49718 original size:105 final size:106
Alignment explanation
Indices: 49556--49792 Score: 415
Period size: 105 Copynumber: 2.2 Consensus size: 106
49546 AGAATCGCAA
49556 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
49621 TTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
66 TTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCAT-GT
49661 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
49726 TTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATGT
66 TTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCATGT
* * *
49767 TGGGATTTTCATTTCGCGTTGTGATT
1 TGCGATTTTCATTTCGCATTGCGATT
49793 CTCTCGTTGC
Statistics
Matches: 126, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
105 86 0.68
106 39 0.31
107 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (106 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCATGT
Found at i:52308 original size:24 final size:24
Alignment explanation
Indices: 52274--52320 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
52264 CTGAAACATC
52274 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
52298 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
52321 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:53037 original size:20 final size:20
Alignment explanation
Indices: 53009--53237 Score: 235
Period size: 20 Copynumber: 11.4 Consensus size: 20
52999 AAATTTCAGT
* * *
53009 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
53029 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
53049 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
53069 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
53089 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
53109 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
53129 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
53149 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
53169 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
53189 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
53209 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
53229 GTTGCGATT
1 GTTGCGATT
53238 CTTGAAATCG
Statistics
Matches: 181, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 180 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:53248 original size:20 final size:19
Alignment explanation
Indices: 53186--53361 Score: 84
Period size: 20 Copynumber: 8.8 Consensus size: 19
53176 TTTACGGATA
***
53186 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTT-TGAAAT
* *
53206 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTTGA-AAT
53226 CGCGTTGCGATTCTTGAAAT
1 CGCGTTGCGATT-TTGAAAT
** * *
53246 CGCAATGCGAATTTGTACTAT
1 CGCGTTGCGATTTTG-A-AAT
* *
53267 CGCATTGCGATTTTCAAGAAT
1 CGCGTTGCGATTTT-GA-AAT
53288 CGCGTTGCGATTTTGGAAA-
1 CGCGTTGCGATTTT-GAAAT
** * **
53307 CTGATTTGCGATTCTGGGGAT
1 C-GCGTTGCGATT-TTGAAAT
* **
53328 CGCGTTGCGATTTTTATTT
1 CGCGTTGCGATTTTGAAAT
53347 CGCGTTGCGATTTTG
1 CGCGTTGCGATTTTG
53362 TTGGTCATTT
Statistics
Matches: 118, Mismatches: 30, Indels: 17
0.72 0.18 0.10
Matches are distributed among these distances:
19 21 0.18
20 61 0.52
21 36 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.39
Consensus pattern (19 bp):
CGCGTTGCGATTTTGAAAT
Found at i:55306 original size:14 final size:14
Alignment explanation
Indices: 55287--55316 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55277 TTTAGATTTT
*
55287 TTAAAATTACATTA
1 TTAAAAATACATTA
55301 TTAAAAATACATTA
1 TTAAAAATACATTA
55315 TT
1 TT
55317 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:55689 original size:17 final size:17
Alignment explanation
Indices: 55667--55699 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
55657 CAATTAATTC
55667 AAATAATATCTAATTAT
1 AAATAATATCTAATTAT
55684 AAATAATATCTAATTA
1 AAATAATATCTAATTA
55700 ATTTGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATAATATCTAATTAT
Found at i:55999 original size:7 final size:6
Alignment explanation
Indices: 55979--56041 Score: 63
Period size: 7 Copynumber: 9.3 Consensus size: 6
55969 TGAACACCCC
55979 TAGGTT TAGTGTT TATGGTT TAGGGTT TAGGTT TAAGGTT TAAGGTT TAGGATT
1 TAGGTT TAG-GTT TA-GGTT TA-GGTT TAGGTT T-AGGTT T-AGGTT TAGG-TT
56033 TAGGGTT TA
1 TA-GGTT TA
56042 AGTTATGCAC
Statistics
Matches: 51, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
6 11 0.22
7 37 0.73
8 3 0.06
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.48
Consensus pattern (6 bp):
TAGGTT
Found at i:56009 original size:27 final size:26
Alignment explanation
Indices: 55979--56041 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
55969 TGAACACCCC
* *
55979 TAGGTTTAGTGTTTATGGTTTAGGGTT
1 TAGGTTTAG-GTTTAAGGTTTAGGATT
56006 TAGGTTTAAGGTTTAAGGTTTAGGATT
1 TAGGTTT-AGGTTTAAGGTTTAGGATT
56033 TAGGGTTTA
1 TA-GGTTTA
56042 AGTTATGCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 25 0.78
28 7 0.22
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.48
Consensus pattern (26 bp):
TAGGTTTAGGTTTAAGGTTTAGGATT
Found at i:58199 original size:11 final size:11
Alignment explanation
Indices: 58183--58231 Score: 71
Period size: 11 Copynumber: 4.5 Consensus size: 11
58173 TTAACCTGTC
58183 GAGCTTGAATT
1 GAGCTTGAATT
58194 GAGCTTGAATT
1 GAGCTTGAATT
* * *
58205 GAGTTTTAAAT
1 GAGCTTGAATT
58216 GAGCTTGAATT
1 GAGCTTGAATT
58227 GAGCT
1 GAGCT
58232 CAGTCTCGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.37
Consensus pattern (11 bp):
GAGCTTGAATT
Found at i:60033 original size:21 final size:21
Alignment explanation
Indices: 60007--60048 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
59997 AGAATTCCTG
*
60007 GAATGTATCATTACCTAACAT
1 GAATGTAGCATTACCTAACAT
60028 GAATGTAGCATTACCTAACAT
1 GAATGTAGCATTACCTAACAT
60049 ATGATTGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (21 bp):
GAATGTAGCATTACCTAACAT
Found at i:63099 original size:17 final size:18
Alignment explanation
Indices: 63079--63114 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
63069 TTCGAATTGA
63079 TCAATTTTT-TTTAAAAT
1 TCAATTTTTATTTAAAAT
63096 TCAATTTTTATTTAAAAT
1 TCAATTTTTATTTAAAAT
63114 T
1 T
63115 TTTAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (18 bp):
TCAATTTTTATTTAAAAT
Found at i:63104 original size:18 final size:17
Alignment explanation
Indices: 63079--63114 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
63069 TTCGAATTGA
*
63079 TCAATTTTTTTTAAAAT
1 TCAATTTTATTTAAAAT
63096 TCAATTTTTATTTAAAAT
1 TCAA-TTTTATTTAAAAT
63114 T
1 T
63115 TTTAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (17 bp):
TCAATTTTATTTAAAAT
Done.