Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002903.1 Hibiscus syriacus cultivar Beakdansim tig00005994_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: 86523
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:218 original size:71 final size:69
Alignment explanation
Indices: 140--281 Score: 232
Period size: 71 Copynumber: 2.0 Consensus size: 69
130 TATAACAGGC
*
140 GTTCCTTAACTGCCTTAG-CCCTCATTACCGAAAATTTCTTGTTTAGATAAATTTTGATTTAATT
1 GTTCCTTAACTGCC-TAGTCCATCATTACCGAAAATTTCTTGTTTAGAT-AA-TTTGATTTAATT
204 TACCATT
63 TACCATT
*
211 GTTCCTTAACTGCCTAGTCCATCATTACCGAAAATTTCTTGTTTTGATAATTTGATTTAATTTAC
1 GTTCCTTAACTGCCTAGTCCATCATTACCGAAAATTTCTTGTTTAGATAATTTGATTTAATTTAC
276 CATT
66 CATT
280 GT
1 GT
282 CTGGCTAGCC
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
69 21 0.31
70 5 0.07
71 42 0.62
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (69 bp):
GTTCCTTAACTGCCTAGTCCATCATTACCGAAAATTTCTTGTTTAGATAATTTGATTTAATTTAC
CATT
Found at i:4615 original size:17 final size:17
Alignment explanation
Indices: 4593--4642 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
4583 AAATTCTTCT
4593 AACATTCATAGAAATCA
1 AACATTCATAGAAATCA
* *
4610 AACATTGAT---ACTCA
1 AACATTCATAGAAATCA
*
4624 AACATTCATAGAAACCA
1 AACATTCATAGAAATCA
4641 AA
1 AA
4643 ACATGAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 6
0.69 0.14 0.17
Matches are distributed among these distances:
14 12 0.48
17 13 0.52
ACGTcount: A:0.52, C:0.20, G:0.06, T:0.22
Consensus pattern (17 bp):
AACATTCATAGAAATCA
Found at i:6101 original size:12 final size:13
Alignment explanation
Indices: 6076--6108 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
6066 AATTTAATAA
*
6076 ATAATTTATTTTT
1 ATAATTTATATTT
6089 ATAATTT-TATTT
1 ATAATTTATATTT
6101 ATAATTTA
1 ATAATTTA
6109 AATTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATAATTTATATTT
Found at i:6626 original size:31 final size:32
Alignment explanation
Indices: 6591--6658 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
6581 TCGAATGATT
* * *
6591 TGATACCGATCCGACCC-GAAATCAACCGATC
1 TGATACCGACCCAACCCAAAAATCAACCGATC
**
6622 TGATATTGACCCAACCCAAAAATCAACCGATC
1 TGATACCGACCCAACCCAAAAATCAACCGATC
6654 TGATA
1 TGATA
6659 TTAATTAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.37, C:0.31, G:0.13, T:0.19
Consensus pattern (32 bp):
TGATACCGACCCAACCCAAAAATCAACCGATC
Found at i:7214 original size:25 final size:24
Alignment explanation
Indices: 7173--7233 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 24
7163 TGATTTTATG
*
7173 TTAAGAGAATAAGTTTATAAAATT
1 TTAAGAGAATAAATTTATAAAATT
*
7197 TTAAGGAGGATAAATTTATAAAATT
1 TTAA-GAGAATAAATTTATAAAATT
*
7222 TTAA-AAAATAAA
1 TTAAGAGAATAAA
7234 AATAAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 6 0.19
24 4 0.12
25 22 0.69
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.34
Consensus pattern (24 bp):
TTAAGAGAATAAATTTATAAAATT
Found at i:13546 original size:3 final size:3
Alignment explanation
Indices: 13538--13577 Score: 53
Period size: 3 Copynumber: 12.7 Consensus size: 3
13528 TTTTTCACTA
*
13538 TAT TAT TAT TAT TAT TAT TAT ATAT ATAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TAT TAT TA
13578 AATTAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 27 0.79
4 7 0.21
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:13559 original size:20 final size:21
Alignment explanation
Indices: 13536--13589 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
13526 ATTTTTTCAC
*
13536 TATATTAT-TATTATTATTAT
1 TATATTATATATTAATATTAT
13556 TATA-TATATATTAATATTAT
1 TATATTATATATTAATATTAT
* *
13576 TAAATTAAATATTA
1 TATATTATATATTA
13590 CAAAACCCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.10
20 18 0.62
21 8 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATTATATATTAATATTAT
Found at i:13578 original size:9 final size:9
Alignment explanation
Indices: 13541--13582 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
13531 TTCACTATAT
*
13541 TATTATTAT
1 TATTATTAA
13550 TATTATTATA
1 TATTATTA-A
13560 TATATATTAA
1 TAT-TATTAA
13570 TATTATTAA
1 TATTATTAA
13579 -ATTA
1 TATTA
13583 AATATTACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 4 0.13
9 14 0.47
10 7 0.23
11 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TATTATTAA
Found at i:14829 original size:17 final size:17
Alignment explanation
Indices: 14797--14844 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
14787 TAATAATTGG
*
14797 ATATTTTTCA-TTTAAT
1 ATATTTTGCATTTTAAT
14813 ATATTTTGCATTTTAAT
1 ATATTTTGCATTTTAAT
*
14830 AT-TATTGC-TTTTAAT
1 ATATTTTGCATTTTAAT
14845 TTCTTTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.24
16 14 0.48
17 8 0.28
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.60
Consensus pattern (17 bp):
ATATTTTGCATTTTAAT
Found at i:15233 original size:135 final size:136
Alignment explanation
Indices: 15051--15400 Score: 412
Period size: 135 Copynumber: 2.6 Consensus size: 136
15041 TATCATATTT
* * *
15051 TAATATATATTTA-TTTTTCAATATTAAGAAAGGGCAGTCTTAAAGCAACTAGATGTCCATTTTA
1 TAATATATATTTATTTTTTCAATATTAAGAAATGACAGTCTTAAAGCAACTAGATGTCCATTTTC
* *
15115 TGATATTTTTAAATAAATATTTTATTTTTATAAATTATATATATTAATC-TATTT-TTAGA-AAT
66 TGATATTTTTAAATAAATATTTTACTTTTATAAATTATA-ATATTAATCATATTTATTAGATAAA
*
15177 TTTTTTA
130 TGTTTTA
* * *
15184 TCAATATATATTTATTTTTTCAATATTAGGAAATGACAGTCTTAAAGCAACTGGATGTCTATTTT
1 T-AATATATATTTATTTTTTCAATATTAAGAAATGACAGTCTTAAAGCAACTAGATGTCCATTTT
* * *
15249 CTGATATTTTTTTAATAAATATTTTACTTTTATAAATTTTAATATTAATCAAATTTTTTATTAGA
65 CTGATA-TTTTTAAATAAATATTTTACTTTTATAAATTATAATATTAATC--A-TATTTATTAGA
15314 TAAATGTTTTA
126 TAAATGTTTTA
* * * * *
15325 T--TA-ATATTTATTTTTT-AATATTAAGAAATGAACTGTCTTAAAGTACCTAGAAG-CCCTTTT
1 TAATATATATTTATTTTTTCAATATTAAGAAATG-ACAGTCTTAAAGCAACTAGATGTCCATTTT
*
15385 CTGATATTTCTAAATA
65 CTGATATTTTTAAATA
15401 TATAATTATC
Statistics
Matches: 185, Mismatches: 22, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
133 1 0.01
134 12 0.06
135 67 0.36
136 55 0.30
137 30 0.16
138 2 0.01
139 4 0.02
140 5 0.03
141 9 0.05
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (136 bp):
TAATATATATTTATTTTTTCAATATTAAGAAATGACAGTCTTAAAGCAACTAGATGTCCATTTTC
TGATATTTTTAAATAAATATTTTACTTTTATAAATTATAATATTAATCATATTTATTAGATAAAT
GTTTTA
Found at i:15318 original size:16 final size:15
Alignment explanation
Indices: 15255--15330 Score: 64
Period size: 16 Copynumber: 4.8 Consensus size: 15
15245 TTTTCTGATA
15255 TTTTT-TTAATAAAT
1 TTTTTATTAATAAAT
* *
15269 ATTTTACTTTTATAAAT
1 TTTTTA--TTAATAAAT
*
15286 TTTAATATTAATCAAAT
1 TTT-TTATTAAT-AAAT
15303 TTTTTATTAGATAAAT
1 TTTTTATTA-ATAAAT
*
15319 GTTTTATTAATA
1 TTTTTATTAATA
15331 TTTATTTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 4 0.08
15 3 0.06
16 21 0.43
17 19 0.39
18 2 0.04
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (15 bp):
TTTTTATTAATAAAT
Found at i:20816 original size:7 final size:7
Alignment explanation
Indices: 20814--20887 Score: 89
Period size: 7 Copynumber: 10.7 Consensus size: 7
20804 AAAAAAGAAA
20814 AAAAAAGG
1 AAAAAA-G
20822 AAAAAAG
1 AAAAAAG
*
20829 AAAAAGG
1 AAAAAAG
20836 AAAAAAG
1 AAAAAAG
20843 AAAAAA-
1 AAAAAAG
*
20849 AAAGAA-
1 AAAAAAG
*
20855 AAAAAGG
1 AAAAAAG
*
20862 AAAAAGG
1 AAAAAAG
20869 AAAAAAG
1 AAAAAAG
20876 AAAAAAG
1 AAAAAAG
20883 AAAAA
1 AAAAA
20888 TTGAATCAAG
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
6 9 0.15
7 44 0.75
8 6 0.10
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:20825 original size:6 final size:6
Alignment explanation
Indices: 20805--20887 Score: 62
Period size: 7 Copynumber: 12.8 Consensus size: 6
20795 TATACTCATA
* *
20805 AAAAAG AAAAA- AAAAGG AAAAAAG AAAAAGG AAAAAAG AAAAA- AAAAGAA
1 AAAAAG AAAAAG AAAAAG -AAAAAG AAAAA-G -AAAAAG AAAAAG AAAA-AG
20855 AAAAAGG AAAAAGG AAAAAAG AAAAAAG AAAAA
1 AAAAA-G AAAAA-G -AAAAAG -AAAAAG AAAAA
20888 TTGAATCAAG
Statistics
Matches: 66, Mismatches: 3, Indels: 16
0.78 0.04 0.19
Matches are distributed among these distances:
5 8 0.12
6 22 0.33
7 26 0.39
8 10 0.15
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:20848 original size:33 final size:33
Alignment explanation
Indices: 20804--20881 Score: 140
Period size: 32 Copynumber: 2.4 Consensus size: 33
20794 CTATACTCAT
*
20804 AAAAAAGAAAAAAAAAGGAAAAAA-GAAAAAGG
1 AAAAAAGAAAAAAAAAGAAAAAAAGGAAAAAGG
20836 AAAAAAGAAAAAAAAAGAAAAAAAGGAAAAAGG
1 AAAAAAGAAAAAAAAAGAAAAAAAGGAAAAAGG
20869 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
20882 GAAAAATTGA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 23 0.52
33 21 0.48
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (33 bp):
AAAAAAGAAAAAAAAAGAAAAAAAGGAAAAAGG
Found at i:20849 original size:40 final size:40
Alignment explanation
Indices: 20804--20887 Score: 134
Period size: 40 Copynumber: 2.1 Consensus size: 40
20794 CTATACTCAT
* *
20804 AAAAAAGAA-AAAAAAAGGAAAAAAGAAAAAGGAAAAAAG
1 AAAAAAAAAGAAAAAAAGGAAAAAAGAAAAAAGAAAAAAG
*
20843 AAAAAAAAAGAAAAAAAGGAAAAAGGAAAAAAGAAAAAAG
1 AAAAAAAAAGAAAAAAAGGAAAAAAGAAAAAAGAAAAAAG
20883 AAAAA
1 AAAAA
20888 TTGAATCAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 8 0.20
40 33 0.80
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (40 bp):
AAAAAAAAAGAAAAAAAGGAAAAAAGAAAAAAGAAAAAAG
Found at i:25321 original size:22 final size:22
Alignment explanation
Indices: 25295--25352 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
25285 TACATCTATA
25295 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
25317 CTCTTTAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
25339 TTTTTCAAAGATGA
1 CTCTTCAAAGATGA
25353 AAGCTTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:27935 original size:23 final size:23
Alignment explanation
Indices: 27901--27969 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
27891 CAATCTTATA
27901 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* *
27924 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
27947 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
27970 AGTTGTGGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:29462 original size:45 final size:46
Alignment explanation
Indices: 29317--29773 Score: 721
Period size: 46 Copynumber: 10.0 Consensus size: 46
29307 TTGTTTCCCA
* * * *
29317 CATCTGTAAGACCTTCAGTGCATGACGTTTTCAAAAACCTTCGAGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* *
29363 CATTTGTAAGCCCTTCAGTG-TAAGATGTTTTCAAAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCT-TGATGTTTTC--AAAAACCTTCGGGT
29411 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
29456 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
29502 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
29547 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
29592 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
29638 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* * *
29684 CATCTGTAATCCCTTCAGTGCATG-TGTTTTC-AAAACATTCGGGT
1 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
* *
29728 CATCTGTAAGCCCTTCAGTGCATG-TAGTTTTCAAAAAGCCATCGGG
1 CATCTGTAAGCCCTTCAGTGCTTGAT-GTTTTCAAAAA-CCTTCGGG
29774 AGCTTTTTGA
Statistics
Matches: 388, Mismatches: 14, Indels: 17
0.93 0.03 0.04
Matches are distributed among these distances:
44 36 0.09
45 148 0.38
46 156 0.40
47 6 0.02
48 41 0.11
49 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (46 bp):
CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
Found at i:29604 original size:136 final size:137
Alignment explanation
Indices: 29317--29773 Score: 742
Period size: 136 Copynumber: 3.3 Consensus size: 137
29307 TTGTTTCCCA
* * * *
29317 CATCTGTAAGACCTTCAGTGCATGACGTTTTCAAAAACCTTCGAGTCATTTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
*
29382 G-TAAGATGTTTTCAAAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAA
66 GCT-TGATGTTTTC--AAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAA
29446 ACCTTCGGGT
128 ACCTTCGGGT
*
29456 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
29521 GCTTGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACC
66 GCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACC
29585 TTCGGGT
131 TTCGGGT
*
29592 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
* * *
29657 GCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAATCCCTTCAGTGCATG-TGTTTTCAAAACA
66 GCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACC
29721 TTCGGGT
131 TTCGGGT
*
29728 CATCTGTAAGCCCTTCAGTGCATG-TAGTTTTCAAAAAGCCATCGGG
1 CATCTGTAAGCCCTTCAGTGCATGAT-GTTTTCAAAAA-CCTTCGGG
29774 AGCTTTTTGA
Statistics
Matches: 303, Mismatches: 11, Indels: 10
0.94 0.03 0.03
Matches are distributed among these distances:
135 1 0.00
136 189 0.62
137 42 0.14
139 70 0.23
140 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (137 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
GCTTGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAACC
TTCGGGT
Found at i:29848 original size:73 final size:73
Alignment explanation
Indices: 29724--29973 Score: 430
Period size: 73 Copynumber: 3.4 Consensus size: 73
29714 CAAAACATTC
* * *
29724 GGGTCATCTGTAAGCCCTTCAGTGCATG-TAGTTTTCAAAAAGCCATCGGGAGCTTTTTGATTTT
1 GGGTCATCTGTAAGACCTACAGTGCATGAT-GTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTT
*
29788 AAAGCATCA
65 AAAGCCTCA
*
29797 GGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTAGGGAGCTTTTTGATTTTA
1 GGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTA
29862 AAGCCTCA
66 AAGCCTCA
29870 GGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTA
1 GGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTA
29935 AAGCCTCA
66 AAGCCTCA
*
29943 GGGTCATCTGTAAGACCTACAGTGCAAGATG
1 GGGTCATCTGTAAGACCTACAGTGCATGATG
29974 ATAAGACATT
Statistics
Matches: 169, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
73 168 0.99
74 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (73 bp):
GGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATTTTA
AAGCCTCA
Found at i:30158 original size:24 final size:24
Alignment explanation
Indices: 30107--30160 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
30097 TTTTTTCACC
* *
30107 ATATTATTATTATTATTATAATAT
1 ATATTATTAATATTATTATAATAA
30131 ATATTATTAATATTATTA-AATTAA
1 ATATTATTAATATTATTATAA-TAA
30155 ATATTA
1 ATATTA
30161 AAAAACCCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 2 0.07
24 25 0.93
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
ATATTATTAATATTATTATAATAA
Found at i:31451 original size:19 final size:19
Alignment explanation
Indices: 31420--31459 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
31410 AATTTCTTTC
31420 ATTTTGATTATTATTATTTT
1 ATTTTGATTATTATT-TTTT
31440 ATTTTG-TTATTATTTTTT
1 ATTTTGATTATTATTTTTT
31458 AT
1 AT
31460 ATATGTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.30
19 8 0.40
20 6 0.30
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (19 bp):
ATTTTGATTATTATTTTTT
Found at i:31452 original size:11 final size:11
Alignment explanation
Indices: 31426--31501 Score: 66
Period size: 11 Copynumber: 6.5 Consensus size: 11
31416 TTTCATTTTG
31426 ATTATTATTATT
1 ATTATT-TTATT
*
31438 -TTATTTTGTT
1 ATTATTTTATT
31448 ATTATTTT-TT
1 ATTATTTTATT
31458 ATATATGTTTAAATT
1 AT-TAT-TTT--ATT
31473 ATTATTTTCATT
1 ATTATTTT-ATT
*
31485 ATCATTTTATT
1 ATTATTTTATT
31496 ATTATT
1 ATTATT
31502 ATCTTAAGTC
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
10 8 0.15
11 23 0.43
12 13 0.24
13 3 0.06
14 3 0.06
15 4 0.07
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:31466 original size:19 final size:19
Alignment explanation
Indices: 31427--31486 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 19
31417 TTCATTTTGA
*
31427 TTATTATTATTTTATTTTG
1 TTATTATTATTTTATTATG
31446 TTATTATT-TTTTATATATG
1 TTATTATTATTTTAT-TATG
31465 TTTAAATTATTATTTTCATTAT
1 -TT--ATTATTATTTT-ATTAT
31487 CATTTTATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
18 6 0.18
19 11 0.32
20 2 0.06
22 6 0.18
23 7 0.21
24 2 0.06
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (19 bp):
TTATTATTATTTTATTATG
Found at i:31772 original size:136 final size:136
Alignment explanation
Indices: 31612--31964 Score: 456
Period size: 135 Copynumber: 2.6 Consensus size: 136
31602 TATCATATTT
*
31612 TAATATATATTTA-TTTTTCAATATTAAGAAATGGCAGTCTTAAAGCAACTAGATGTCCATTTTT
1 TAATATATATTTATTTTTTCAATATTAAGAAATGGCAGTCTTAAAGCAACTAGATGTCCATTTTC
*
31676 TGATATTTTTAAATAAATATTTTATTTTTATAAATTATATATATTAATC-TATTT-TTAGATAAA
66 TGATATTTTTAAATAAATATTTTACTTTTATAAATTATA-ATATTAATCATATTTATTAGATAAA
*
31739 TGTTTTA
130 TGTGTTA
* * *
31746 TCAATATATATTTATTTTTTCAATATTAGGAAAGGGCAGTCTTAAAGCAACTGGATGTCCATTTT
1 T-AATATATATTTATTTTTTCAATATTAAGAAATGGCAGTCTTAAAGCAACTAGATGTCCATTTT
* *
31811 CTGAT-TTTTTTAATAAATATTTTACTTTTATAAATTATAATATTAATCAAATTTTTTATTAGAT
65 CTGATATTTTTAAATAAATATTTTACTTTTATAAATTATAATATTAATC--A-TATTTATTAGAT
31875 AAATGTGTTA
127 AAATGTGTTA
* * * *
31885 T--TA-ATATTTATTTTTT-AATATTAAGAAATGAACTGTTTTAAAGC-ACATAGAAG-CCATTT
1 TAATATATATTTATTTTTTCAATATTAAGAAATG-GCAGTCTTAAAGCAAC-TAGATGTCCATTT
*
31944 TCTGATATTTCTAAATAAATA
64 TCTGATATTTTTAAATAAATA
31965 AATATCTTAT
Statistics
Matches: 192, Mismatches: 17, Indels: 19
0.84 0.07 0.08
Matches are distributed among these distances:
134 36 0.19
135 83 0.43
136 53 0.28
138 4 0.02
139 16 0.08
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (136 bp):
TAATATATATTTATTTTTTCAATATTAAGAAATGGCAGTCTTAAAGCAACTAGATGTCCATTTTC
TGATATTTTTAAATAAATATTTTACTTTTATAAATTATAATATTAATCATATTTATTAGATAAAT
GTGTTA
Found at i:31986 original size:21 final size:20
Alignment explanation
Indices: 31962--32009 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
31952 TTCTAAATAA
31962 ATAAATATCTTAT-TTAAAAAT
1 ATAAATAT-TT-TCTTAAAAAT
*
31983 ATAATATATTTTCTTAAAATT
1 ATAA-ATATTTTCTTAAAAAT
32004 ATAAAT
1 ATAAAT
32010 TTGAAATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 3 0.12
21 17 0.71
22 4 0.17
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAAATATTTTCTTAAAAAT
Found at i:37656 original size:53 final size:53
Alignment explanation
Indices: 37553--37657 Score: 147
Period size: 53 Copynumber: 2.0 Consensus size: 53
37543 TAGGTGGTAT
* * * *
37553 GATACTACTAACATTGATCAAATTCCATAATGTAAAAATGGTACCGATACCCC
1 GATACTACCAACATTGATCAAATTCCAGAATGCAAAAATGGTACCAATACCCC
* * *
37606 GATACTACCAACATTGCTCAAATTTCAGAATGCAAAAATGGTACTAATACCC
1 GATACTACCAACATTGATCAAATTCCAGAATGCAAAAATGGTACCAATACCC
37658 AAAGGGGTAC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (53 bp):
GATACTACCAACATTGATCAAATTCCAGAATGCAAAAATGGTACCAATACCCC
Found at i:42507 original size:338 final size:339
Alignment explanation
Indices: 41890--42569 Score: 1299
Period size: 338 Copynumber: 2.0 Consensus size: 339
41880 TAACTGCTCT
41890 TCAACTTCTCCTGTGAAAGAAGACCAAAGACATAGTTCAGCTAATGTTTTCCCGATCCAATCAAA
1 TCAACTTCTCCTGTGAAAGAAGACCAAAGACATAGTTCAGCTAATGTTTTCCCGATCCAATCAAA
*
41955 TATCATGAGATGCAAACTGTAGCTAAAAGGTTTACATCTATCTATAATATCACAGTGACCAGCAA
66 TATCATGAGATGCAAACTGTAGCTAAAAGGTTTACATCTATCTACAATATCACAGTGACCAGCAA
*
42020 TTAGTTTGTGCATAAGCTCCTCTTTTGTAATAACCGACTGATTTATGGACTGGAAAAAATAGTGA
131 TTAGTTTGTGCATAAGCTCCGCTTTTGTAATAACCGACTGATTTATGGACTGGAAAAAATAGTGA
*
42085 ATCATGTTGAAGAGCTTAGGTAGGCAGGCAATCATTGGTTGCCGTCTCTTTGCTTGTGAGATTGC
196 ATCATGTTGAAGAGCTTAGGAAGGCAGGCAATCATTGGTTGCCGTCTCTTTGCTTGTGAGATTGC
42150 TGGATCTCGCTCCTCCAATGCTTTCCTCTCTTTCTCCCTTATCTGCAAGGATAATGAACGATTAC
261 TGGATCTCGCTCCTCCAATGCTTTCCTCTCTTTCTCCCTTATCTGCAAGGATAATGAACGATTAC
42215 CTAATGCTTTTTAC
326 CTAATGCTTTTTAC
42229 TCAACTTCTCCTGTGAAAGAAGACCAAAGACATAGTTCAGCTAA-GTTTTCCCGATCCAATCAAA
1 TCAACTTCTCCTGTGAAAGAAGACCAAAGACATAGTTCAGCTAATGTTTTCCCGATCCAATCAAA
* *
42293 TATCATGAGATGCAAACTGTAGCTAAAAGGTTTACCTCTATCTGCAATATCACAGTGACCAGCAA
66 TATCATGAGATGCAAACTGTAGCTAAAAGGTTTACATCTATCTACAATATCACAGTGACCAGCAA
42358 TTAGTTTGTGCATAAGCTCCGCTTTTGTAATAACCGACTGATTTATGGACTGGAAAAAATAGTGA
131 TTAGTTTGTGCATAAGCTCCGCTTTTGTAATAACCGACTGATTTATGGACTGGAAAAAATAGTGA
*
42423 ATCATGTTGAAGAGCTTAGGAATGCAGGCAATCATTGGTTGCCGTCTCTTTGCTTGTGAGATTGC
196 ATCATGTTGAAGAGCTTAGGAAGGCAGGCAATCATTGGTTGCCGTCTCTTTGCTTGTGAGATTGC
42488 TGGATCTCGCTCCTCCAATGCTTTCCTCTCTTTCTCCCTTATCTGCAAGGATAATGAACGATTAC
261 TGGATCTCGCTCCTCCAATGCTTTCCTCTCTTTCTCCCTTATCTGCAAGGATAATGAACGATTAC
42553 CTAATGCTTTTTAC
326 CTAATGCTTTTTAC
42567 TCA
1 TCA
42570 TGCAGCAATC
Statistics
Matches: 335, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
338 291 0.87
339 44 0.13
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (339 bp):
TCAACTTCTCCTGTGAAAGAAGACCAAAGACATAGTTCAGCTAATGTTTTCCCGATCCAATCAAA
TATCATGAGATGCAAACTGTAGCTAAAAGGTTTACATCTATCTACAATATCACAGTGACCAGCAA
TTAGTTTGTGCATAAGCTCCGCTTTTGTAATAACCGACTGATTTATGGACTGGAAAAAATAGTGA
ATCATGTTGAAGAGCTTAGGAAGGCAGGCAATCATTGGTTGCCGTCTCTTTGCTTGTGAGATTGC
TGGATCTCGCTCCTCCAATGCTTTCCTCTCTTTCTCCCTTATCTGCAAGGATAATGAACGATTAC
CTAATGCTTTTTAC
Found at i:45698 original size:16 final size:16
Alignment explanation
Indices: 45658--45714 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
45648 GGAACGTTTG
* *
45658 CTCTCTGTTTCTGTCT
1 CTCTCTGTCTCTGTAT
* *
45674 CTCTTTGTCTCTGTGT
1 CTCTCTGTCTCTGTAT
* *
45690 GTCTCTGTCTGTGTAT
1 CTCTCTGTCTCTGTAT
45706 CTCTCTGTC
1 CTCTCTGTC
45715 CTCTTTTTTT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.02, C:0.28, G:0.18, T:0.53
Consensus pattern (16 bp):
CTCTCTGTCTCTGTAT
Found at i:46079 original size:3 final size:3
Alignment explanation
Indices: 46071--46130 Score: 84
Period size: 3 Copynumber: 20.0 Consensus size: 3
46061 TTAATATATT
* * * *
46071 TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA TAA TTA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
46119 TAA TAA TAA TAA
1 TAA TAA TAA TAA
46131 ATAAATCAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:46087 original size:21 final size:21
Alignment explanation
Indices: 46062--46130 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
46052 TATATATATT
46062 TAAT-ATATTTAATAATAATAA
1 TAATAATATTT-ATAATAATAA
46083 TAATAATATTTATAATAATAA
1 TAATAATATTTATAATAATAA
* *
46104 TAATAATAATTATTATAATAA
1 TAATAATATTTATAATAATAA
46125 TAATAA
1 TAATAA
46131 ATAAATCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 39 0.87
22 6 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAATAATATTTATAATAATAA
Found at i:46090 original size:24 final size:25
Alignment explanation
Indices: 46062--46130 Score: 117
Period size: 24 Copynumber: 2.9 Consensus size: 25
46052 TATATATATT
46062 TAATATATT-TAATAATAATAATAA
1 TAATATATTATAATAATAATAATAA
46086 TAATAT-TTATAATAATAATAATAA
1 TAATATATTATAATAATAATAATAA
46110 TAAT-TATTATAATAATAATAA
1 TAATATATTATAATAATAATAA
46131 ATAAATCAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
23 3 0.07
24 40 0.93
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
TAATATATTATAATAATAATAATAA
Found at i:46623 original size:135 final size:133
Alignment explanation
Indices: 46450--46719 Score: 497
Period size: 135 Copynumber: 2.0 Consensus size: 133
46440 ACGGTTGGGG
46450 AGCCGGGAGGAGTTCTTTTCCGGGGTTTTGGAAACCGGAGATTTCGAGGTTAGGCTCCGAGAAAC
1 AGCCGGGAGGAGTTCTTTTCCGGGGTTTTGGAAACCGGAGATTTCGAGGTTAGGCTCCGAGAAAC
46515 CTTGGATTTCAAA-GGTTGATTTGAGAGAGAATCTGAGGAGCTCATAGCTTAAAACTTACAGAGC
66 CTTGGATTTCAAAGGGTTGATTT--GAGAGAATCTGAGGAGCTCATAGCTTAAAACTTACAGAGC
46579 AGACA
129 AGACA
46584 AGCCGGGAGGGAGTTCTTTTCCGGGGTTTTGGAAACCGGAGATTTCGAGGTTAGGCTCCGAGAAA
1 AGCCGGGA-GGAGTTCTTTTCCGGGGTTTTGGAAACCGGAGATTTCGAGGTTAGGCTCCGAGAAA
46649 CCTTGGATTTCAAAGGGGTTGATTTGAGAGAATCTGAGGAGCTCATAGCTTAAAACTTACAGAGC
65 CCTTGGATTTCAAA-GGGTTGATTTGAGAGAATCTGAGGAGCTCATAGCTTAAAACTTACAGAGC
46714 AGACA
129 AGACA
46719 A
1 A
46720 AAAAATAGGC
Statistics
Matches: 133, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
134 8 0.06
135 116 0.87
137 9 0.07
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (133 bp):
AGCCGGGAGGAGTTCTTTTCCGGGGTTTTGGAAACCGGAGATTTCGAGGTTAGGCTCCGAGAAAC
CTTGGATTTCAAAGGGTTGATTTGAGAGAATCTGAGGAGCTCATAGCTTAAAACTTACAGAGCAG
ACA
Found at i:47134 original size:16 final size:16
Alignment explanation
Indices: 47113--47173 Score: 68
Period size: 16 Copynumber: 3.8 Consensus size: 16
47103 CTTCAGAAGA
47113 TTAAATATTGAATTAT
1 TTAAATATTGAATTAT
* *
47129 TTAAATGTTAAATTAT
1 TTAAATATTGAATTAT
* *
47145 TTAAATACTGAATGAT
1 TTAAATATTGAATTAT
* *
47161 TCAAATGTTGAAT
1 TTAAATATTGAAT
47174 GATTCAGATG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (16 bp):
TTAAATATTGAATTAT
Found at i:47191 original size:18 final size:16
Alignment explanation
Indices: 47111--47195 Score: 64
Period size: 16 Copynumber: 5.2 Consensus size: 16
47101 TACTTCAGAA
*
47111 GATT-AAATATTGAAT
1 GATTCAAATGTTGAAT
* * *
47126 TATTTAAATGTTAAAT
1 GATTCAAATGTTGAAT
* * **
47142 TATTTAAATACTGAAT
1 GATTCAAATGTTGAAT
47158 GATTCAAATGTTGAAT
1 GATTCAAATGTTGAAT
*
47174 GATTCAGATGTTTTGAAT
1 GATTCAAATG--TTGAAT
47192 GATT
1 GATT
47196 TAACTCTGAA
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
15 3 0.05
16 43 0.77
18 10 0.18
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.44
Consensus pattern (16 bp):
GATTCAAATGTTGAAT
Found at i:51802 original size:34 final size:34
Alignment explanation
Indices: 51762--51867 Score: 104
Period size: 34 Copynumber: 3.1 Consensus size: 34
51752 CAAATGATAA
51762 ATGAACACTAAATGAACGCTAAACGAACATGTTC
1 ATGAACACTAAATGAACGCTAAACGAACATGTTC
*** ** * *
51796 ATGAACACATTCGTGAACATATAAATGAACACGTTC
1 ATGAACAC-TAAATGAAC-GCTAAACGAACATGTTC
* * *
51832 GTGGACATTAAATGAACGCTAAACGAACATGTTC
1 ATGAACACTAAATGAACGCTAAACGAACATGTTC
51866 AT
1 AT
51868 TGTCAAAACT
Statistics
Matches: 52, Mismatches: 18, Indels: 4
0.70 0.24 0.05
Matches are distributed among these distances:
34 22 0.42
35 12 0.23
36 18 0.35
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.24
Consensus pattern (34 bp):
ATGAACACTAAATGAACGCTAAACGAACATGTTC
Found at i:51847 original size:23 final size:24
Alignment explanation
Indices: 51796--51848 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
51786 GAACATGTTC
51796 ATGAACACATTCGTGAACATATAA
1 ATGAACACATTCGTGAACATATAA
* *
51820 ATGAACACGTTCGTGGACAT-TAA
1 ATGAACACATTCGTGAACATATAA
51843 ATGAAC
1 ATGAAC
51849 GCTAAACGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (24 bp):
ATGAACACATTCGTGAACATATAA
Found at i:54293 original size:168 final size:168
Alignment explanation
Indices: 54013--54352 Score: 653
Period size: 168 Copynumber: 2.0 Consensus size: 168
54003 CATTTGTAGC
54013 CTTTTGGAGTGGAGGAATAGCAAATAAATATACATTTTGGTGCCCTTGGATCAAGTTTTCCCCTT
1 CTTTTGGAGTGGAGGAATAGCAAATAAATATACATTTTGGTGCCCTTGGATCAAGTTTTCCCCTT
* *
54078 CCTTGAGAATGTATGAACAAAAGCAACACACCCAAATATTATAAGTTTTAAGTTAAGAAATGGTC
66 CCCTGAGAATGTATAAACAAAAGCAACACACCCAAATATTATAAGTTTTAAGTTAAGAAATGGTC
54143 TAAAATTTGGATAGAATTTTGTGAGGACTTGAAGAGGA
131 TAAAATTTGGATAGAATTTTGTGAGGACTTGAAGAGGA
54181 CTTTTGGAGTGGAGGAATAGCAAATAAATATACATTTTGGTGCCCTTGGATCAAGTTTTCCCCTT
1 CTTTTGGAGTGGAGGAATAGCAAATAAATATACATTTTGGTGCCCTTGGATCAAGTTTTCCCCTT
*
54246 CCCTGAGAATGTATAAACAAAAGCAACACACCCAAATATTCTAAGTTTTAAGTTAAGAAATGGTC
66 CCCTGAGAATGTATAAACAAAAGCAACACACCCAAATATTATAAGTTTTAAGTTAAGAAATGGTC
54311 TAAAATTTGGATAGAATTTTGTGAGGACTTGAAGAGGA
131 TAAAATTTGGATAGAATTTTGTGAGGACTTGAAGAGGA
54349 CTTT
1 CTTT
54353 GGGATTCAAG
Statistics
Matches: 169, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
168 169 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (168 bp):
CTTTTGGAGTGGAGGAATAGCAAATAAATATACATTTTGGTGCCCTTGGATCAAGTTTTCCCCTT
CCCTGAGAATGTATAAACAAAAGCAACACACCCAAATATTATAAGTTTTAAGTTAAGAAATGGTC
TAAAATTTGGATAGAATTTTGTGAGGACTTGAAGAGGA
Found at i:56828 original size:15 final size:15
Alignment explanation
Indices: 56808--56836 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
56798 TGTTGAAATC
56808 AGCAGATTGTTCTTG
1 AGCAGATTGTTCTTG
56823 AGCAGATTGTTCTT
1 AGCAGATTGTTCTT
56837 CAGCCTCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.24, T:0.41
Consensus pattern (15 bp):
AGCAGATTGTTCTTG
Found at i:58185 original size:22 final size:23
Alignment explanation
Indices: 58129--58230 Score: 152
Period size: 23 Copynumber: 4.5 Consensus size: 23
58119 TGACATTCAT
* * *
58129 GAACACTAAACGAACACGTTCGC
1 GAACATTAAATGAACATGTTCGC
58152 GAACATTAAATGAACATGTTCGC
1 GAACATTAAATGAACATGTTCGC
58175 GAAC-TTAAATGAACATGTTCGC
1 GAACATTAAATGAACATGTTCGC
*
58197 GAACATTAAATGAACATGTTCGT
1 GAACATTAAATGAACATGTTCGC
*
58220 GAACAATAAAT
1 GAACATTAAAT
58231 AAACGAACAC
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
22 22 0.30
23 51 0.70
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (23 bp):
GAACATTAAATGAACATGTTCGC
Found at i:58204 original size:45 final size:45
Alignment explanation
Indices: 58135--58223 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
58125 TCATGAACAC
58135 TAAACGAACACGTTCGCGAACATTAAATGAACATGTTCGCGAACT
1 TAAACGAACACGTTCGCGAACATTAAATGAACATGTTCGCGAACT
* * *
58180 TAAATGAACATGTTCGCGAACATTAAATGAACATGTTCGTGAAC
1 TAAACGAACACGTTCGCGAACATTAAATGAACATGTTCGCGAAC
58224 AATAAATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (45 bp):
TAAACGAACACGTTCGCGAACATTAAATGAACATGTTCGCGAACT
Found at i:58265 original size:30 final size:30
Alignment explanation
Indices: 58224--58294 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
58214 GTTCGTGAAC
*
58224 AATAAATAAACGAACACAAACACCTTTAAA
1 AATAAATAAACGAACACAAACACCTTCAAA
* * *
58254 AATAAACAAACGAATACGAACACCTTCAAA
1 AATAAATAAACGAACACAAACACCTTCAAA
58284 AATAAATAAAC
1 AATAAATAAAC
58295 AGCCTTGTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.61, C:0.20, G:0.04, T:0.15
Consensus pattern (30 bp):
AATAAATAAACGAACACAAACACCTTCAAA
Found at i:64192 original size:30 final size:30
Alignment explanation
Indices: 64138--64253 Score: 200
Period size: 30 Copynumber: 3.9 Consensus size: 30
64128 AATGAATAAT
64138 AGCTTAGCAAAGCTATT--AGAGAGGGTAA
1 AGCTTAGCAAAGCTATTAGAGAGAGGGTAA
* *
64166 AGCTTAGCAAAGCTATTAGTGAGAGGGTGA
1 AGCTTAGCAAAGCTATTAGAGAGAGGGTAA
64196 AGCTTAGCAAAGCTATTAGAGAGAGGGTAA
1 AGCTTAGCAAAGCTATTAGAGAGAGGGTAA
64226 AGCTTAGCAAAGCTATTAGAGAGAGGGT
1 AGCTTAGCAAAGCTATTAGAGAGAGGGT
64254 GAGGTTGTGT
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 17 0.21
30 65 0.79
ACGTcount: A:0.37, C:0.10, G:0.31, T:0.22
Consensus pattern (30 bp):
AGCTTAGCAAAGCTATTAGAGAGAGGGTAA
Found at i:73430 original size:23 final size:23
Alignment explanation
Indices: 73404--73451 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
73394 ATTTATGTTT
*
73404 TAAAAATTTAAGGTAA-AAAATTA
1 TAAAAATTTAA-GAAATAAAATTA
*
73427 TAAAATTTTAAGAAATAAAATTA
1 TAAAAATTTAAGAAATAAAATTA
73450 TA
1 TA
73452 TAATCAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.33
Consensus pattern (23 bp):
TAAAAATTTAAGAAATAAAATTA
Found at i:73827 original size:41 final size:42
Alignment explanation
Indices: 73723--73937 Score: 226
Period size: 41 Copynumber: 5.2 Consensus size: 42
73713 TAAAAAAAAT
* * *
73723 GCCGTTAAA-ACTCATATTTTAGTGGCGTTTTAAGCATAAAC
1 GCCGCTAAAGACTCATACTTTAGTGGCGTTTTAAGCACAAAC
* * *
73764 GCCACTAAAGACTCATACTTTAGTGGCGTTTT-TGTACAAAC
1 GCCGCTAAAGACTCATACTTTAGTGGCGTTTTAAGCACAAAC
* * *
73805 GCCGCTAAAAACT-AGTAATTTAGTGGCGTTTTAAGCA-AAAA
1 GCCGCTAAAGACTCA-TACTTTAGTGGCGTTTTAAGCACAAAC
* * *
73846 GCCGCTAAATACTCATACTTTAGAGGCGTTTT--TCTACAAAC
1 GCCGCTAAAGACTCATACTTTAGTGGCGTTTTAAGC-ACAAAC
* * *
73887 GCCGCTAAAGACTCGTACTTTAGTGGTGTTTTAAGCACAAAT
1 GCCGCTAAAGACTCATACTTTAGTGGCGTTTTAAGCACAAAC
*
73929 GCCACTAAA
1 GCCGCTAAA
73938 ATACTACTCT
Statistics
Matches: 142, Mismatches: 24, Indels: 15
0.78 0.13 0.08
Matches are distributed among these distances:
39 1 0.01
40 2 0.01
41 101 0.71
42 37 0.26
43 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (42 bp):
GCCGCTAAAGACTCATACTTTAGTGGCGTTTTAAGCACAAAC
Found at i:73874 original size:82 final size:83
Alignment explanation
Indices: 73740--73942 Score: 291
Period size: 82 Copynumber: 2.4 Consensus size: 83
73730 AAACTCATAT
* * * * *
73740 TTTAGTGGCGTTTTAAGCATAAACGCCACTAAAGACTCATACTTTAGTGGCGTTTTTGTACAAAC
1 TTTAGTGGCGTTTTAAGCACAAAAGCCACTAAATACTCATACTTTAGAGGCGTTTTTCTACAAAC
73805 GCCGCTAAAAACTAGTAA
66 GCCGCTAAAAACTAGTAA
*
73823 TTTAGTGGCGTTTTAAGCA-AAAAGCCGCTAAATACTCATACTTTAGAGGCGTTTTTCTACAAAC
1 TTTAGTGGCGTTTTAAGCACAAAAGCCACTAAATACTCATACTTTAGAGGCGTTTTTCTACAAAC
* * *
73887 GCCGCTAAAGACTCGTAC
66 GCCGCTAAAAACTAGTAA
* *
73905 TTTAGTGGTGTTTTAAGCACAAATGCCACTAAAATACT
1 TTTAGTGGCGTTTTAAGCACAAAAGCCACT-AAATACT
73943 ACTCTATTGC
Statistics
Matches: 107, Mismatches: 11, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
82 73 0.68
83 27 0.25
84 7 0.07
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (83 bp):
TTTAGTGGCGTTTTAAGCACAAAAGCCACTAAATACTCATACTTTAGAGGCGTTTTTCTACAAAC
GCCGCTAAAAACTAGTAA
Found at i:73978 original size:83 final size:81
Alignment explanation
Indices: 73740--73970 Score: 227
Period size: 82 Copynumber: 2.8 Consensus size: 81
73730 AAACTCATAT
* * * *
73740 TTTAGTGGCGTTTTAAGCATAAACGCCACTAAAGACT-CATACT-TTAGTGGCGTTTTTGTACAA
1 TTTAGTGGCGTTTTAAGCA-AAAAGCCACTAAA-A-TAC-TACTCTTTGAGGCGTTTTTATACAA
73803 ACGCCGCTAAAAACTAGTAA
62 ACGCCGCTAAAAACTAGTAA
* *
73823 TTTAGTGGCGTTTTAAGCAAAAAGCCGCT-AAATACT-CATACTTTAGAGGCGTTTTTCTACAAA
1 TTTAGTGGCGTTTTAAGCAAAAAGCCACTAAAATACTAC-T-CTTT-GAGGCGTTTTTATACAAA
* * *
73886 CGCCGCTAAAGACTCGTAC
63 CGCCGCTAAAAACTAGTAA
* * * * *
73905 TTTAGTGGTGTTTTAAGCACAAATGCCACTAAAATACTACTCTATTGCGGCGTTTATATAAAAAC
1 TTTAGTGGCGTTTTAAGCA-AAAAGCCACTAAAATACTACTCT-TTGAGGCGTTTTTATACAAAC
73970 G
64 G
73971 ACACTAAATA
Statistics
Matches: 124, Mismatches: 15, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
78 1 0.01
79 3 0.02
80 2 0.02
81 4 0.03
82 58 0.47
83 45 0.36
84 10 0.08
85 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (81 bp):
TTTAGTGGCGTTTTAAGCAAAAAGCCACTAAAATACTACTCTTTGAGGCGTTTTTATACAAACGC
CGCTAAAAACTAGTAA
Found at i:74002 original size:41 final size:41
Alignment explanation
Indices: 73957--74035 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 41
73947 TATTGCGGCG
73957 TTTAT-ATAAAAACGACACT-AAATAACGAGTCTTTAGCGACA
1 TTTATGATAAAAACGACACTAAAAT-ACGAGT-TTTAGCGACA
* * *
73998 TTTATGCTTAAAACGCCACTAAAATACGAGTTTTAGCG
1 TTTATGATAAAAACGACACTAAAATACGAGTTTTAGCG
74036 GTGCTTGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 12 0.36
42 17 0.52
43 4 0.12
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (41 bp):
TTTATGATAAAAACGACACTAAAATACGAGTTTTAGCGACA
Found at i:75560 original size:34 final size:34
Alignment explanation
Indices: 75495--75564 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 34
75485 AATCGATACC
**
75495 TTTTACATTTGTATATGTATTTGCATCTTTGCAT
1 TTTTACATTTGTATATACATTTGCATCTTTGCAT
* * * *
75529 TTTTACGTTTGTATTTACATTTTCATTTTTGCAT
1 TTTTACATTTGTATATACATTTGCATCTTTGCAT
75563 TT
1 TT
75565 ACATCTTTGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.19, C:0.11, G:0.10, T:0.60
Consensus pattern (34 bp):
TTTTACATTTGTATATACATTTGCATCTTTGCAT
Found at i:80775 original size:22 final size:21
Alignment explanation
Indices: 80750--80820 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
80740 CATTTGACTA
80750 AAGATTGTTTTCCTTGAAACAG
1 AAGATT-TTTTCCTTGAAACAG
* *
80772 AAGATTTTATTTCATT--CA-AG
1 AAGA-TTT-TTTCCTTGAAACAG
**
80792 ATTATTTTTTCCTTGAAACAG
1 AAGATTTTTTCCTTGAAACAG
80813 AAGATTTT
1 AAGATTTT
80821 ATCTCATTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 11
0.65 0.15 0.20
Matches are distributed among these distances:
18 6 0.17
19 3 0.08
20 5 0.14
21 9 0.25
22 5 0.14
23 8 0.22
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (21 bp):
AAGATTTTTTCCTTGAAACAG
Found at i:81017 original size:23 final size:23
Alignment explanation
Indices: 80991--81059 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
80981 TATCTCACTC
80991 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
* * **
81014 AAGA-T-TTTAT-C-T--CACTC
1 AAGATTGTTTTTCCTTGAAACAG
81031 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
81054 AAGATT
1 AAGATT
81060 CTATCTCACT
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 6 0.19
18 1 0.03
19 5 0.16
20 2 0.06
21 5 0.16
22 1 0.03
23 12 0.38
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (23 bp):
AAGATTGTTTTTCCTTGAAACAG
Found at i:81177 original size:23 final size:23
Alignment explanation
Indices: 81151--81219 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 23
81141 TATCTCACTC
81151 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
* *
81174 AAGATT-TTATCTCATT----C--
1 AAGATTGTT-TTTCCTTGAAACAG
81191 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
81214 AAGATT
1 AAGATT
81220 TTATCTCACT
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
17 11 0.32
18 2 0.06
19 1 0.03
21 1 0.03
22 2 0.06
23 17 0.50
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (23 bp):
AAGATTGTTTTTCCTTGAAACAG
Found at i:81332 original size:40 final size:40
Alignment explanation
Indices: 80750--81306 Score: 911
Period size: 40 Copynumber: 13.9 Consensus size: 40
80740 CATTTGACTA
* *
80750 AAGATTG-TTTTCCTTGAAACAGAAGATTTTATTTCATTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
* *
80789 AAGATTATTTTTTCCTTGAAACAGAAGATTTTATCTCATTC
1 AAGATT-GTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
*
80830 AAGATTGTTTTTCCTTGAAATAGAAGATTTTATCTCACTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
* *
80870 AAGATTATTTTTTCCTTGAAACAGAAGATTTTATCTCATTC
1 AAGATT-GTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
* *
80911 AATATTGTTTTTCCTTGAAACAGAAGATTCTATCTCACTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
*
80951 AAGATTATTTTTCCTTGAAACAGAAGATTTTATCTCACTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
80991 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
*
81031 AAGATTGTTTTTCCTTGAAACAGAAGATTCTATCTCACTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
* *
81071 AAGATTGTTTTTCCTTGAAACAGAAGATTCTATCTCATTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
* *
81111 AAGATTGTTTTTTCTTGATACAGAAGATTTTATCTCACTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
*
81151 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCATTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
81191 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
*
81231 AATATTGTTTTTCCTTGAAACCA-AAGATTTTATCTCACTC
1 AAGATTGTTTTTCCTTGAAA-CAGAAGATTTTATCTCACTC
*
81271 AATATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
1 AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
81307 GCTTGAGATA
Statistics
Matches: 486, Mismatches: 27, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
39 8 0.02
40 403 0.83
41 75 0.15
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (40 bp):
AAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTCACTC
Found at i:81430 original size:28 final size:28
Alignment explanation
Indices: 81344--81429 Score: 136
Period size: 28 Copynumber: 3.0 Consensus size: 28
81334 ATTGTCTCCC
*
81344 TTGAGATAGTTTCTCTTGAAACAAGTTT
1 TTGATATAGTTTCTCTTGAAACAAGTTT
*
81372 TTGATACAGTTTCTCTTGAAACAAGTTT
1 TTGATATAGTTTCTCTTGAAACAAGTTT
*
81400 TTGATATAGTTTCTCTTGAAAAAAAGTTT
1 TTGATATAGTTTCTCTTG-AAACAAGTTT
81429 T
1 T
81430 GTCTCCCTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 43 0.81
29 10 0.19
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.44
Consensus pattern (28 bp):
TTGATATAGTTTCTCTTGAAACAAGTTT
Found at i:81470 original size:36 final size:37
Alignment explanation
Indices: 81430--81605 Score: 110
Period size: 36 Copynumber: 4.8 Consensus size: 37
81420 AAAAAGTTTT
* ** *
81430 GTCTCCCTTGAGATGGTTTTTCTTAAAACCAAGCT-C
1 GTCTCACTTGAGATGGTTTTTCTTAAAACCAAAATAA
** * *
81466 GTCTCACTTGAGACAGTTTTCCCTTGAAA-CAAAATAA
1 GTCTCACTTGAGATGGTTTT-TCTTAAAACCAAAATAA
* * * **
81503 ATCTCACTTGAGATGGTTTTTCTTAAAACC-TACTTC
1 GTCTCACTTGAGATGGTTTTTCTTAAAACCAAAATAA
** ** * * *
81539 GTCTGGCTTGAGACAGTTTTCCTTTTAAA-CAAAATGTA
1 GTCTCACTTGAGATGGTTTTTC-TTAAAACCAAAAT-AA
81577 -TCTCACTTGAGATGGTTTTTCTTAAAACC
1 GTCTCACTTGAGATGGTTTTTCTTAAAACC
81606 TACTTCGTCT
Statistics
Matches: 100, Mismatches: 33, Indels: 13
0.68 0.23 0.09
Matches are distributed among these distances:
36 51 0.51
37 48 0.48
38 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (37 bp):
GTCTCACTTGAGATGGTTTTTCTTAAAACCAAAATAA
Found at i:81513 original size:73 final size:73
Alignment explanation
Indices: 81431--81677 Score: 311
Period size: 73 Copynumber: 3.4 Consensus size: 73
81421 AAAAGTTTTG
* * *
81431 TCTCCCTTGAGATGGTTTTTCTTAAAACCAAGC-TCGTCTCACTTGAGACAGTTTTCCCTTGAAA
1 TCTCACTTGAGATGGTTTTTCTTAAAACCTA-CTTCGTCTCGCTTGAGACAGTTTTCCCTTGAAA
*
81495 CAAAATAAA
65 CAAAATATA
* * *
81504 TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCGTCTGGCTTGAGACAGTTTTCCTTTTAAAC
1 TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCGTCTCGCTTGAGACAGTTTTCCCTTGAAAC
*
81569 AAAATGTA
66 AAAATATA
* * * *
81577 TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCGTCTTGCTTAAGACAATTTT-CCTTCGGAA
1 TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCGTCTCGCTTGAGACAGTTTTCCCTT-GAAA
* *
81641 TAAAATTTA
65 CAAAATATA
*
81650 TCTCACTTGAGA-GTGCTTTTCTTAAAAC
1 TCTCACTTGAGATG-GTTTTTCTTAAAAC
81678 AATTTTCTTA
Statistics
Matches: 154, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
72 5 0.03
73 149 0.97
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (73 bp):
TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCGTCTCGCTTGAGACAGTTTTCCCTTGAAAC
AAAATATA
Found at i:81587 original size:37 final size:35
Alignment explanation
Indices: 81467--81604 Score: 96
Period size: 37 Copynumber: 3.8 Consensus size: 35
81457 ACCAAGCTCG
* *
81467 TCTCACTTGAGACAGTTTTCCCTTGAAACAAAATAAA
1 TCTCACTTGAGACAGTTTT-CCTTAAAACAAAAT-TA
** * ** * *
81504 TCTCACTTGAGATGGTTTTTCTTAAAACCTACTTCG
1 TCTCACTTGAGACAGTTTTCCTTAAAACAAAATT-A
** *
81540 TCTGGCTTGAGACAGTTTTCCTTTTAAACAAAATGTA
1 TCTCACTTGAGACAGTTTTCC-TTAAAACAAAAT-TA
** *
81577 TCTCACTTGAGATGGTTTTTCTTAAAAC
1 TCTCACTTGAGACAGTTTTCCTTAAAAC
81605 CTACTTCGTC
Statistics
Matches: 73, Mismatches: 25, Indels: 7
0.70 0.24 0.07
Matches are distributed among these distances:
36 31 0.42
37 41 0.56
38 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (35 bp):
TCTCACTTGAGACAGTTTTCCTTAAAACAAAATTA
Found at i:82230 original size:105 final size:105
Alignment explanation
Indices: 82060--82339 Score: 357
Period size: 105 Copynumber: 2.6 Consensus size: 105
82050 AGGGATCGAA
82060 ATTTCCAATGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAATTCATAATAAGAAGA
1 ATTTCC-A-GAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAATTCATAATAAGAAGA
* * * *
82125 AATTGTTCCTTTCAAATTCACCACATAATGAGGTGAACCAAC
64 AATTGCTCCTTTCAAATCCACCACAGAAGGAGGTGAACCAAC
* * *
82167 ATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAATGA-AAAAGTTTATAATGAGAAGAA
1 ATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAA-TTCATAATAAGAAGAA
* * * *
82231 CTTGCTCTTTTCAAGTCCACCGCAGAAGGAGGTGAACCAAC
65 ATTGCTCCTTTCAAATCCACCACAGAAGGAGGTGAACCAAC
* *
82272 ATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCC-AATGAGGAAGAAGAAGTTCATAATGAGA
1 ATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAA--AGG-AGAA-AA-TTCATAATAAGA
82336 AGAA
61 AGAA
82340 CTTGTTCAAC
Statistics
Matches: 153, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
104 6 0.04
105 117 0.76
106 3 0.02
107 7 0.05
108 2 0.01
109 18 0.12
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (105 bp):
ATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAATTCATAATAAGAAGAAA
TTGCTCCTTTCAAATCCACCACAGAAGGAGGTGAACCAAC
Found at i:82430 original size:117 final size:118
Alignment explanation
Indices: 82173--82587 Score: 468
Period size: 117 Copynumber: 3.6 Consensus size: 118
82163 CAACATTTCC
* * *
82173 AGAAGAGTTCATAATGAGAAGAACTCGTCC--T-A--AATGAAAAAGTTTATAATGAGAAGAACT
1 AGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAA-GAAGAAGTTCATAATGAGAAGAACT
* * * ** * * *
82233 TG--C-TC-TT--TTCAAGTCCACCGCAGAAGGAGGTGAACCAACATTTCC---
65 TGTTCAACATTGGTTCAATTCCATCAAAGAAGAAGGTGGATCAACATTTCCAGT
82278 AGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
1 AGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
** *
82343 GTTCAACATTGGTTTGATTCCATCAAAGAA-AGAGGTGGATCAACATTTTCAGT
66 GTTCAACATTGGTTCAATTCCATCAAAGAAGA-AGGTGGATCAACATTTCCAGT
* *
82396 AGAA-AGTTCATAATGAGAAAAACTCATCCAATGAGTAAGAAGAAGTTCATAATGAGAAGAACTT
1 AGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
* * * *
82460 GTTCAACCTTGGTTCAATTCCATCACAGAAGAAGGTGGATTAATATTTCCAGT
66 GTTCAACATTGGTTCAATTCCATCAAAGAAGAAGGTGGATCAACATTTCCAGT
* * * * *
82513 -GAAGAGTTCATAATGAGAAGAACTCATCTAACGAGGAATAAGAAGTTCATAATGAGAAAAACTC
1 AGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
82577 GTTCAACATTG
66 GTTCAACATTG
82588 CATTAACATT
Statistics
Matches: 262, Mismatches: 31, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
105 29 0.11
107 1 0.00
108 1 0.00
109 25 0.10
110 2 0.01
111 1 0.00
112 1 0.00
113 2 0.01
115 27 0.10
116 3 0.01
117 165 0.63
118 5 0.02
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (118 bp):
AGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
GTTCAACATTGGTTCAATTCCATCAAAGAAGAAGGTGGATCAACATTTCCAGT
Found at i:82610 original size:91 final size:91
Alignment explanation
Indices: 82498--82673 Score: 273
Period size: 91 Copynumber: 1.9 Consensus size: 91
82488 AAGAAGGTGG
* * * *
82498 ATTAATATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCTAACGAG-GAATAAGAAGTTCA
1 ATTAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAACAAGAG-AGAAGAAGTTCA
82562 TAATGAGAAAAACTCGTTCAACATTGC
65 TAATGAGAAAAACTCGTTCAACATTGC
*
82589 ATTAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACAAGAGAGAAGAAGTTCAT
1 ATTAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAACAAGAGAGAAGAAGTTCAT
* *
82654 AATGAGAAGAACTTGTTCAA
66 AATGAGAAAAACTCGTTCAA
82674 TTCAACACTT
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
91 76 0.99
92 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (91 bp):
ATTAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCAACAAGAGAGAAGAAGTTCAT
AATGAGAAAAACTCGTTCAACATTGC
Found at i:86391 original size:35 final size:36
Alignment explanation
Indices: 86319--86392 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
86309 ATTGGTCACT
86319 TAATTTATGTAATATTTTATGATAACATATACATTA
1 TAATTTATGTAATATTTTATGATAACATATACATTA
86355 TAATTTATGTAATATTTTAT-A-AACGATATACATTA
1 TAATTTATGTAATATTTTATGATAAC-ATATACATTA
86390 TAA
1 TAA
86393 GTATGTGCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
34 3 0.08
35 14 0.38
36 20 0.54
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (36 bp):
TAATTTATGTAATATTTTATGATAACATATACATTA
Done.