Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009271.1 Hibiscus syriacus cultivar Beakdansim tig00112941_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: 66580
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:5786 original size:39 final size:37
Alignment explanation
Indices: 5741--5870 Score: 124
Period size: 39 Copynumber: 3.4 Consensus size: 37
5731 ACTATGCATG
*
5741 TAAACTATACATGCATAAACTATAAAAGTATATAGTTTA
1 TAAACTATA-ATGTATAAACTATAAAAGTATATA-TTTA
* **
5780 TAAACTATAATTTATATTAA-TAT-AGTGTATATATATATA
1 TAAACTATAATGTATA--AACTATAAAAGTATATAT-T-TA
5819 TAAACTATATATGTATAAACTATAAAA-TATATATTTA
1 TAAACTATA-ATGTATAAACTATAAAAGTATATATTTA
*
5856 TAAATTATAAT-TATA
1 TAAACTATAATGTATA
5871 TTAATATAGT
Statistics
Matches: 76, Mismatches: 8, Indels: 18
0.75 0.08 0.18
Matches are distributed among these distances:
35 4 0.05
36 2 0.03
37 11 0.14
38 17 0.22
39 33 0.43
40 9 0.12
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (37 bp):
TAAACTATAATGTATAAACTATAAAAGTATATATTTA
Found at i:5827 original size:15 final size:15
Alignment explanation
Indices: 5809--5842 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5799 ATATAGTGTA
5809 TATATATATATAAAC
1 TATATATATATAAAC
*
5824 TATATATGTATAAAC
1 TATATATATATAAAC
5839 TATA
1 TATA
5843 AAATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:5877 original size:75 final size:78
Alignment explanation
Indices: 5741--5904 Score: 237
Period size: 75 Copynumber: 2.1 Consensus size: 78
5731 ACTATGCATG
*
5741 TAAACTATACATGCATAAACTATAAAAGTATATAGTTTATAAACTATAATTTATATTAATATAGT
1 TAAACTATATATGCATAAACTATAAAAGTATATAGTTTATAAACTATAATTTATATTAATATAGT
*
5806 GTATATATATATA
66 ATATATATATATA
* *
5819 TAAACTATATATGTATAAACTATAAAA-TATATA-TTTATAAATTATAA-TTATATTAATATAGT
1 TAAACTATATATGCATAAACTATAAAAGTATATAGTTTATAAACTATAATTTATATTAATATAGT
* *
5881 ATATATGTATGTA
66 ATATATATATATA
5894 T-AACTAATATA
1 TAAACT-ATATA
5905 AGTCTATATA
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
74 4 0.05
75 31 0.39
76 13 0.16
77 6 0.08
78 25 0.32
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (78 bp):
TAAACTATATATGCATAAACTATAAAAGTATATAGTTTATAAACTATAATTTATATTAATATAGT
ATATATATATATA
Found at i:6132 original size:26 final size:27
Alignment explanation
Indices: 6103--6174 Score: 69
Period size: 26 Copynumber: 2.7 Consensus size: 27
6093 ATATGTAACT
* *
6103 TATAGTACATGTA-TGTATAAACTATA
1 TATAGTACATATATTATATAAACTATA
*
6129 TATA-TATATATATTATATAAACTATA
1 TATAGTACATATATTATATAAACTATA
* *
6155 TAAAGTAAAT-TACTTATATA
1 TATAGTACATATA-TTATATA
6175 GTTATAGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
25 6 0.16
26 21 0.55
27 11 0.29
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (27 bp):
TATAGTACATATATTATATAAACTATA
Found at i:6267 original size:7 final size:7
Alignment explanation
Indices: 6257--6296 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
6247 CTTTAAATTA
6257 TAAACCC
1 TAAACCC
*
6264 TAAACTC
1 TAAACCC
*
6271 TAAACCT
1 TAAACCC
*
6278 TAGACCC
1 TAAACCC
6285 TAAACCC
1 TAAACCC
6292 TAAAC
1 TAAAC
6297 TATATATGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.42, C:0.35, G:0.03, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:6274 original size:21 final size:21
Alignment explanation
Indices: 6236--6300 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
6226 ATAGAAACCC
* * * *
6236 TAAACCTTAACCTTTAAATTA
1 TAAACCCTAAACTCTAAACTA
6257 TAAACCCTAAACTCTAAACCT-
1 TAAACCCTAAACTCTAAA-CTA
* *
6278 TAGACCCTAAACCCTAAACTA
1 TAAACCCTAAACTCTAAACTA
6299 TA
1 TA
6301 TATGTATAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 2 0.06
21 33 0.92
22 1 0.03
ACGTcount: A:0.43, C:0.28, G:0.02, T:0.28
Consensus pattern (21 bp):
TAAACCCTAAACTCTAAACTA
Found at i:6347 original size:16 final size:16
Alignment explanation
Indices: 6328--6358 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6318 GATAATTCAT
6328 ATAGTTTATATAAATA
1 ATAGTTTATATAAATA
6344 ATAGTTTATATAAAT
1 ATAGTTTATATAAAT
6359 TATATATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
ATAGTTTATATAAATA
Found at i:6596 original size:21 final size:21
Alignment explanation
Indices: 6570--6701 Score: 83
Period size: 21 Copynumber: 6.2 Consensus size: 21
6560 TAGTGTACTA
* *
6570 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAAAC
*
6591 TATAGTATATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
* **
6612 TATAGTTTAT-ATTAATGTAC
1 TATAGTTTATAATTTATAAAC
*
6632 TATAGTTGTATTAATGTTAATTAAC
1 TATAGTT-TA-TAAT-TT-ATAAAC
**
6657 T-TA-ACTATAATTTATATTAA-
1 TATAGTTTATAATTTATA--AAC
* *
6677 TATAGTATATAGTTTATAAAC
1 TATAGTTTATAATTTATAAAC
6698 TATA
1 TATA
6702 CTATATTAAT
Statistics
Matches: 85, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
19 2 0.02
20 19 0.22
21 41 0.48
22 13 0.15
23 2 0.02
24 3 0.04
25 5 0.06
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (21 bp):
TATAGTTTATAATTTATAAAC
Found at i:6645 original size:19 final size:20
Alignment explanation
Indices: 6549--6648 Score: 69
Period size: 21 Copynumber: 4.8 Consensus size: 20
6539 TTTATAAACA
*
6549 ATAGTTTATATTAGTGTACTAT
1 ATAGTTTATATTAATGTAC--T
* *
6571 ATAGTTTATACTTTAT-AACCT
1 ATAGTTTATA-TTAATGTA-CT
* * **
6592 ATAGTATATAATTTATAAACT
1 ATAGTTTAT-ATTAATGTACT
6613 ATAGTTTATATTAATGTACT
1 ATAGTTTATATTAATGTACT
*
6633 ATAG-TTGTATTAATGT
1 ATAGTTTATATTAATGT
6649 TAATTAACTT
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
19 11 0.17
20 12 0.18
21 24 0.37
22 14 0.22
23 4 0.06
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (20 bp):
ATAGTTTATATTAATGTACT
Found at i:6701 original size:14 final size:14
Alignment explanation
Indices: 6684--6743 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
6674 TAATATAGTA
6684 TATAGTTTATAAAC
1 TATAGTTTATAAAC
* * *
6698 TATACTATATTAA-
1 TATAGTTTATAAAC
* *
6711 TATTAATTTTATTAAC
1 TA-T-AGTTTATAAAC
6727 TATAGTTTATAAAC
1 TATAGTTTATAAAC
6741 TAT
1 TAT
6744 GCTATATAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
13 2 0.06
14 23 0.64
15 9 0.25
16 2 0.06
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (14 bp):
TATAGTTTATAAAC
Found at i:6845 original size:26 final size:23
Alignment explanation
Indices: 6805--6894 Score: 92
Period size: 24 Copynumber: 3.8 Consensus size: 23
6795 TTTTATATTA
*
6805 ATATTAATTACAAATTATAAAGTAT
1 ATATTAA-TATAAATTATAAA-TAT
* *
6830 ATAATTAATATAAAATATTAAT-T
1 AT-ATTAATATAAATTATAAATAT
*
6853 ATATTAATATTAATTATAAATAGT
1 ATATTAATATAAATTATAAATA-T
*
6877 TTATTAATATAAATTATA
1 ATATTAATATAAATTATA
6895 TAGGGATGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
22 16 0.30
23 3 0.06
24 18 0.33
25 12 0.22
26 5 0.09
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (23 bp):
ATATTAATATAAATTATAAATAT
Found at i:7523 original size:25 final size:25
Alignment explanation
Indices: 7494--7579 Score: 102
Period size: 25 Copynumber: 3.4 Consensus size: 25
7484 ACTAATTATT
*
7494 TAACA-CCTAATGTAACATGAATTAA
1 TAACATCC-AATGCAACATGAATTAA
*
7519 TAACATGCAATGCAACATGAATTAA
1 TAACATCCAATGCAACATGAATTAA
* * *
7544 TAACATGCAATACCACATGAATTAA
1 TAACATCCAATGCAACATGAATTAA
*
7569 TAACATGCAAT
1 TAACATCCAAT
7580 TATTATTTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
25 55 0.98
26 1 0.02
ACGTcount: A:0.48, C:0.17, G:0.09, T:0.26
Consensus pattern (25 bp):
TAACATCCAATGCAACATGAATTAA
Found at i:7524 original size:13 final size:14
Alignment explanation
Indices: 7506--7581 Score: 67
Period size: 13 Copynumber: 5.9 Consensus size: 14
7496 ACACCTAATG
7506 TAACATG-AATTAA
1 TAACATGCAATTAA
*
7519 TAACATGCAA-T-G
1 TAACATGCAATTAA
*
7531 CAACATG-AATTAA
1 TAACATGCAATTAA
7544 TAACATGCAA-T-A
1 TAACATGCAATTAA
**
7556 CCACATG-AATTAA
1 TAACATGCAATTAA
7569 TAACATGCAATTA
1 TAACATGCAATTA
7582 TTATTTAACA
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
11 4 0.08
12 14 0.29
13 21 0.44
14 9 0.19
ACGTcount: A:0.49, C:0.16, G:0.09, T:0.26
Consensus pattern (14 bp):
TAACATGCAATTAA
Found at i:8159 original size:12 final size:11
Alignment explanation
Indices: 8131--8170 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
8121 TTGAATTAAC
8131 TCAAATGTTAT
1 TCAAATGTTAT
*
8142 TCAAATTTTAT
1 TCAAATGTTAT
8153 ATCAAATGTTAT
1 -TCAAATGTTAT
*
8165 TTAAAT
1 TCAAAT
8171 TATCATTATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (11 bp):
TCAAATGTTAT
Found at i:9091 original size:47 final size:48
Alignment explanation
Indices: 9009--9107 Score: 182
Period size: 47 Copynumber: 2.1 Consensus size: 48
8999 TTGACTCTAG
*
9009 TCGGTTTTAGTCAATTTCGCAGGTCGGGTCAGCTTTTTACAACCCTAC
1 TCGGTTTTAGTCAATTTCGCAGGCCGGGTCAGCTTTTTACAACCCTAC
9057 TCGGTTTTAGTCAATTT-GCAGGCCGGGTCAGCTTTTTACAACCCTAC
1 TCGGTTTTAGTCAATTTCGCAGGCCGGGTCAGCTTTTTACAACCCTAC
9104 TCGG
1 TCGG
9108 GAGTGATGAG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 33 0.66
48 17 0.34
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.34
Consensus pattern (48 bp):
TCGGTTTTAGTCAATTTCGCAGGCCGGGTCAGCTTTTTACAACCCTAC
Found at i:10222 original size:36 final size:35
Alignment explanation
Indices: 10149--10222 Score: 87
Period size: 36 Copynumber: 2.1 Consensus size: 35
10139 CTGACTGTGC
* * *
10149 CATTTCAAATATGTTCCTTTCTTTTCAAAACAGAT
1 CATTTCAAATATGTTACTTTCATTTCAAAACAAAT
*
10184 CATTTCAAATATG-TACTTTACCATTTCAAATCAAAT
1 CATTTCAAATATGTTACTTT--CATTTCAAAACAAAT
10220 CAT
1 CAT
10223 CGTTAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 5 0.15
35 13 0.39
36 15 0.45
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (35 bp):
CATTTCAAATATGTTACTTTCATTTCAAAACAAAT
Found at i:11450 original size:24 final size:24
Alignment explanation
Indices: 11418--11470 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
11408 CTTTTGCAAA
11418 TTTCACCACTAACTTTACCAAATC
1 TTTCACCACTAACTTTACCAAATC
11442 TTTCACCACTAACTTTACCAAATC
1 TTTCACCACTAACTTTACCAAATC
11466 TTTCA
1 TTTCA
11471 ACTTTACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (24 bp):
TTTCACCACTAACTTTACCAAATC
Found at i:15249 original size:17 final size:17
Alignment explanation
Indices: 15209--15251 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
15199 AAAAAGGGTT
15209 TAGTAAAAAGGATTAAA
1 TAGTAAAAAGGATTAAA
* *
15226 TAATAAAAAGTGATTTAA
1 TAGTAAAAAG-GATTAAA
15244 -AGTAAAAA
1 TAGTAAAAA
15252 ATAAAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (17 bp):
TAGTAAAAAGGATTAAA
Found at i:15855 original size:13 final size:13
Alignment explanation
Indices: 15837--15885 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
15827 CTTAGCATGT
15837 TTAAAAATAAAAC
1 TTAAAAATAAAAC
15850 TT-AAAATAAAA-
1 TTAAAAATAAAAC
15861 -TAAAAATGAAAAC
1 TTAAAAAT-AAAAC
* *
15874 TTGAAAAGAAAA
1 TTAAAAATAAAA
15886 GAAAATAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 1 0.03
11 5 0.17
12 13 0.43
13 6 0.20
14 5 0.17
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.20
Consensus pattern (13 bp):
TTAAAAATAAAAC
Found at i:15872 original size:24 final size:24
Alignment explanation
Indices: 15838--15894 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
15828 TTAGCATGTT
*
15838 TAAAAATAAAACTT-AAAATAAAA
1 TAAAAATAAAACTTGAAAAGAAAA
15861 TAAAAATGAAAACTTGAAAAGAAAA
1 TAAAAAT-AAAACTTGAAAAGAAAA
*
15886 -GAAAATAAA
1 TAAAAATAAA
15895 GAACTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 10 0.33
24 12 0.40
25 8 0.27
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.18
Consensus pattern (24 bp):
TAAAAATAAAACTTGAAAAGAAAA
Found at i:17931 original size:22 final size:22
Alignment explanation
Indices: 17875--17919 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
17865 ATGCAAACTT
17875 AGCTAATCGACCCCCATCTTAC
1 AGCTAATCGACCCCCATCTTAC
17897 AGCTAATCGACCCCCATCTTAC
1 AGCTAATCGACCCCCATCTTAC
17919 A
1 A
17920 AGCTTATTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.40, G:0.09, T:0.22
Consensus pattern (22 bp):
AGCTAATCGACCCCCATCTTAC
Found at i:19134 original size:2 final size:2
Alignment explanation
Indices: 19129--19154 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19119 GTTTAATTAT
19129 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
19155 CATGTGATTG
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):
TA
Found at i:20503 original size:20 final size:21
Alignment explanation
Indices: 20464--20503 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
20454 TTTTACATTT
**
20464 AAATATTATTTAAATTTTAAA
1 AAATATTATTTAAAAATTAAA
20485 AAATATT-TTTAAAAATTAA
1 AAATATTATTTAAAAATTAA
20504 CTTACTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AAATATTATTTAAAAATTAAA
Found at i:22981 original size:3 final size:3
Alignment explanation
Indices: 22973--23007 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
22963 AAACTTAGTC
22973 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
23008 ACCGTGAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:24229 original size:16 final size:15
Alignment explanation
Indices: 24208--24289 Score: 79
Period size: 16 Copynumber: 5.7 Consensus size: 15
24198 AATGAAAATG
24208 GTCTATGTGAATACAT
1 GTCTATGTGAATA-AT
24224 GTCTATGTG-ATAA-
1 GTCTATGTGAATAAT
24237 G-CTATGTGAA-AAT
1 GTCTATGTGAATAAT
*
24250 GGTCTATATGAATACAT
1 -GTCTATGTGAATA-AT
24267 GTCTATGTG-ATAA-
1 GTCTATGTGAATAAT
24280 G-CTATGTGAA
1 GTCTATGTGAA
24290 ATGGTATAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 17
0.75 0.03 0.22
Matches are distributed among these distances:
12 16 0.28
13 4 0.07
14 3 0.05
15 14 0.25
16 18 0.32
17 2 0.04
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (15 bp):
GTCTATGTGAATAAT
Found at i:24243 original size:12 final size:14
Alignment explanation
Indices: 24208--24292 Score: 72
Period size: 12 Copynumber: 6.1 Consensus size: 14
24198 AATGAAAATG
24208 GTCTATGTGAATACAT
1 GTCTATGTG-ATA-AT
24224 GTCTATGTGATAA-
1 GTCTATGTGATAAT
*
24237 G-CTATGTGAAAAT
1 GTCTATGTGATAAT
*
24250 GGTCTATATGAATACAT
1 -GTCTATGTG-ATA-AT
24267 GTCTATGTGATAA-
1 GTCTATGTGATAAT
24280 G-CTATGTGA-AAT
1 GTCTATGTGATAAT
24292 G
1 G
24293 GTATAAAATA
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
11 2 0.03
12 19 0.32
13 2 0.03
14 3 0.05
15 12 0.20
16 19 0.32
17 2 0.03
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.35
Consensus pattern (14 bp):
GTCTATGTGATAAT
Found at i:24248 original size:43 final size:43
Alignment explanation
Indices: 24200--24294 Score: 174
Period size: 43 Copynumber: 2.2 Consensus size: 43
24190 TCTGTGATAA
*
24200 TGAAAATGGTCTATGTGAATACATGTCTATGTGATAAGCTATG
1 TGAAAATGGTCTATATGAATACATGTCTATGTGATAAGCTATG
24243 TGAAAATGGTCTATATGAATACATGTCTATGTGATAAGCTATG
1 TGAAAATGGTCTATATGAATACATGTCTATGTGATAAGCTATG
24286 TG-AAATGGT
1 TGAAAATGGT
24295 ATAAAATATA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 7 0.14
43 44 0.86
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (43 bp):
TGAAAATGGTCTATATGAATACATGTCTATGTGATAAGCTATG
Found at i:24417 original size:46 final size:46
Alignment explanation
Indices: 24365--24461 Score: 167
Period size: 46 Copynumber: 2.1 Consensus size: 46
24355 GAGTCGAGGG
* *
24365 TTCTACGCGGTCCTTCGGGATAATTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAATACTACGTGGTCCTTCGGGACAT
*
24411 TTCTACGCGGTCCTTCGGGACAATACTATGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAATACTACGTGGTCCTTCGGGACAT
24457 TTCTA
1 TTCTA
24462 TGTGGAACTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.16, C:0.26, G:0.25, T:0.33
Consensus pattern (46 bp):
TTCTACGCGGTCCTTCGGGACAATACTACGTGGTCCTTCGGGACAT
Found at i:24472 original size:23 final size:23
Alignment explanation
Indices: 24365--24466 Score: 132
Period size: 23 Copynumber: 4.4 Consensus size: 23
24355 GAGTCGAGGG
* *
24365 TTCTACGCGGTCCTTCGGGATAA
1 TTCTACGTGGTCCTTCGGGACAA
*
24388 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
*
24411 TTCTACGCGGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* * *
24434 TACTATGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
*
24457 TTCTATGTGG
1 TTCTACGTGG
24467 AACTTCAGTG
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.16, C:0.25, G:0.26, T:0.33
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:32868 original size:23 final size:21
Alignment explanation
Indices: 32816--32877 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
32806 TTTTGGTGTA
*
32816 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
32836 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
32857 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
32878 CCAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:32896 original size:21 final size:21
Alignment explanation
Indices: 32859--32898 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
32849 CCCCCTTTGA
*
32859 AGGGGAACCGATTCCCCCCCC
1 AGGGGAACCGATACCCCCCCC
32880 AGGGGAATCC-ATACCCCCC
1 AGGGGAA-CCGATACCCCCC
32899 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.23, C:0.45, G:0.23, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCCC
Found at i:36396 original size:9 final size:9
Alignment explanation
Indices: 36382--36406 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
36372 ATTACAAACT
36382 AAATAATAA
1 AAATAATAA
36391 AAATAATAA
1 AAATAATAA
36400 AAATAAT
1 AAATAAT
36407 TAAATACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAATAATAA
Found at i:36412 original size:23 final size:24
Alignment explanation
Indices: 36358--36412 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
36348 CTAAATTGAA
* *
36358 AATTAAATAAAAATATTACAAACT
1 AATTAAATAAAAATAATACAAAAT
*
36382 AAAT-AATAAAAATAATA-AAAAT
1 AATTAAATAAAAATAATACAAAAT
36404 AATTAAATA
1 AATTAAATA
36413 CAAACATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 7 0.27
23 16 0.62
24 3 0.12
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (24 bp):
AATTAAATAAAAATAATACAAAAT
Found at i:36423 original size:13 final size:13
Alignment explanation
Indices: 36405--36453 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
36395 AATAAAAATA
36405 ATTAAATACAAAC
1 ATTAAATACAAAC
36418 ATTAAATACAAAC
1 ATTAAATACAAAC
* *
36431 ATTATAATTCAAATA
1 ATTA-AATACAAA-C
36446 ATTAAATA
1 ATTAAATA
36454 ATAAAAACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 17 0.55
14 10 0.32
15 4 0.13
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (13 bp):
ATTAAATACAAAC
Found at i:36478 original size:21 final size:21
Alignment explanation
Indices: 36453--36519 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
36443 ATAATTAAAT
36453 AATAAAAACATTAAAAAACAA
1 AATAAAAACATTAAAAAACAA
* ** * **
36474 AATAAATA-A-TCCATAATTA
1 AATAAAAACATTAAAAAACAA
*
36493 AATAAAAACATTAAGAAACAA
1 AATAAAAACATTAAAAAACAA
36514 AATAAA
1 AATAAA
36520 GAAAAATAAG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
19 12 0.39
20 2 0.06
21 17 0.55
ACGTcount: A:0.70, C:0.09, G:0.01, T:0.19
Consensus pattern (21 bp):
AATAAAAACATTAAAAAACAA
Found at i:36949 original size:21 final size:21
Alignment explanation
Indices: 36925--36976 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
36915 ACCGTTGTGG
36925 CATCTGAAATGGTTGCGGTGA
1 CATCTGAAATGGTTGCGGTGA
* * *
36946 CATC-GAAAACGGTTGTGGTGT
1 CATCTG-AAATGGTTGCGGTGA
36967 CATCTGAAAT
1 CATCTGAAAT
36977 AGCTATAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 23 0.92
22 1 0.04
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (21 bp):
CATCTGAAATGGTTGCGGTGA
Found at i:38860 original size:6 final size:6
Alignment explanation
Indices: 38849--38893 Score: 65
Period size: 6 Copynumber: 7.5 Consensus size: 6
38839 AGATGTTTAT
*
38849 AGGGGA AGGGGA AGGGGA AGGGGA AGGGG- AGGGGG AGGCGGA AGG
1 AGGGGA AGGGGA AGGGGA AGGGGA AGGGGA AGGGGA AGG-GGA AGG
38894 ATGGTTGGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
5 5 0.14
6 26 0.72
7 5 0.14
ACGTcount: A:0.29, C:0.02, G:0.69, T:0.00
Consensus pattern (6 bp):
AGGGGA
Found at i:40547 original size:19 final size:20
Alignment explanation
Indices: 40509--40560 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
40499 AAAAAAAGAT
*
40509 AAAAATTTTGACACCACTTA
1 AAAAATATTGACACCACTTA
*
40529 AAAAATATTGACA-CTCTTA
1 AAAAATATTGACACCACTTA
40548 AAGAAA-ATTGACA
1 AA-AAATATTGACA
40561 TCGATGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.50, C:0.15, G:0.08, T:0.27
Consensus pattern (20 bp):
AAAAATATTGACACCACTTA
Found at i:40891 original size:20 final size:20
Alignment explanation
Indices: 40797--41205 Score: 486
Period size: 20 Copynumber: 20.4 Consensus size: 20
40787 GATTTTCCAT
* ** *
40797 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
40817 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
40837 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
40857 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
40877 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
40897 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
40917 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
40937 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
40957 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
40977 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
40997 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
41017 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
41037 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
41057 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
41077 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
41097 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
41117 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
41137 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
41157 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
41177 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
41197 AATCACAAC
1 AATCGCAAC
41206 ACTGAAATTT
Statistics
Matches: 337, Mismatches: 42, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.01
20 331 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:41917 original size:24 final size:24
Alignment explanation
Indices: 41878--41924 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
41868 AAATTTGGTC
41878 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
41902 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
41925 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:42116 original size:12 final size:12
Alignment explanation
Indices: 42099--42123 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42089 ATATAATCCT
42099 GAAGAAGAAAAA
1 GAAGAAGAAAAA
42111 GAAGAAGAAAAA
1 GAAGAAGAAAAA
42123 G
1 G
42124 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:44451 original size:19 final size:19
Alignment explanation
Indices: 44429--44754 Score: 405
Period size: 19 Copynumber: 18.4 Consensus size: 19
44419 CGGAAAATAC
*
44429 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
44448 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
44462 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
44482 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
44496 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
44515 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
44534 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
44548 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
44567 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
44586 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
44600 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
44619 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
44638 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
44657 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
44676 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
44695 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
44709 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
44728 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
44747 AATCGCAA
1 AATCGCAA
44755 CGAGATAATC
Statistics
Matches: 269, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 50 0.19
15 3 0.01
16 13 0.05
17 12 0.04
18 4 0.01
19 174 0.65
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:44516 original size:33 final size:34
Alignment explanation
Indices: 44429--44754 Score: 321
Period size: 33 Copynumber: 9.2 Consensus size: 34
44419 CGGAAAATAC
* *
44429 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
44462 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGATGAA
44496 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
44534 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
44567 AATCGCAATGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
*
44600 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
*
44638 AATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
44676 AATCGCAATGCGAAATGAAAATCGCAACGA--AA
1 AATCGCAATGCGAAATGAAAATCGCAACGATGAA
44708 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAA
44747 AATCGCAA
1 AATCGCAA
44755 CGAGATAATC
Statistics
Matches: 257, Mismatches: 12, Indels: 43
0.82 0.04 0.14
Matches are distributed among these distances:
32 2 0.01
33 111 0.43
34 32 0.12
35 9 0.04
36 6 0.02
37 4 0.02
38 91 0.35
39 2 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACGATGAA
Found at i:44690 original size:161 final size:157
Alignment explanation
Indices: 44457--44776 Score: 552
Period size: 161 Copynumber: 2.0 Consensus size: 157
44447 AAATCCCAAC
*
44457 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
44522 ATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
66 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
44587 ATCGCAACGAGAGAATCGCAATGCGAA
131 ATCGCAACGAGAGAATCGCAATGCGAA
*
44614 ATGAAAATCGCAATGC-GAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAA
1 ATGAAAATCGCAATGCGGAAATGAAAATCGC-A-ACG--A-GAAAATCGCAATGCGAAATGAAAA
44678 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
61 TCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAA
*
44743 TGAAAATCGCAACGAGATAATCGCAATGCGAA
126 TGAAAATCGCAACGAGAGAATCGCAATGCGAA
44775 AT
1 AT
44777 TATAAACGCA
Statistics
Matches: 154, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
156 13 0.08
157 17 0.11
158 3 0.02
160 1 0.01
161 120 0.78
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (157 bp):
ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
ATCGCAACGAGAGAATCGCAATGCGAA
Found at i:44792 original size:52 final size:52
Alignment explanation
Indices: 44457--44776 Score: 550
Period size: 52 Copynumber: 6.0 Consensus size: 52
44447 AAATCCCAAC
44457 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
44510 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
44562 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
44614 ATGAAAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A-GAGAATCGCAATGCGAA
*
44671 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
44723 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
44775 AT
1 AT
44777 TATAAACGCA
Statistics
Matches: 255, Mismatches: 7, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
52 184 0.72
53 18 0.07
54 3 0.01
55 3 0.01
56 2 0.01
57 45 0.18
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:44892 original size:19 final size:19
Alignment explanation
Indices: 44783--44884 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
44773 AAATTATAAA
44783 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
44802 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
44822 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
44838 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
44855 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
44874 CGCATTGCGAT
1 CGCATTGCGAT
44885 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:45010 original size:14 final size:14
Alignment explanation
Indices: 44991--45027 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
44981 CATCAATTAC
44991 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
45005 ACAAATCATCTTTT
1 ACAAATCAACTTTT
45019 ACAAATCAA
1 ACAAATCAA
45028 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:45039 original size:12 final size:12
Alignment explanation
Indices: 45022--45094 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
45012 ATCTTTTACA
45022 AATCAATTAAAC
1 AATCAATTAAAC
*
45034 AATCAA--AAATTG
1 AATCAATTAAA--C
**
45046 AATCAACTTTTAC
1 AATCAA-TTAAAC
45059 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
45072 AATCAA-AAAAC
1 AATCAATTAAAC
45083 AATCAATTAAAC
1 AATCAATTAAAC
45095 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:45056 original size:38 final size:38
Alignment explanation
Indices: 45008--45080 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
44998 AACTTTTACA
*
45008 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
45046 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
45081 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:46934 original size:19 final size:19
Alignment explanation
Indices: 46894--47028 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
46884 TAGTTTACTT
* *
46894 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
46914 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
46933 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
46952 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
46966 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
46985 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
46999 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
47018 TCGCAATGCGA
1 TCGCAACGCGA
47029 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:46969 original size:14 final size:14
Alignment explanation
Indices: 46950--47006 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
46940 GCGAAATGAA
*
46950 AATCGCAACGACAG
1 AATCGCAACGAAAG
46964 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
46981 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
46997 AATCGCAACG
1 AATCGCAACG
47007 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:46973 original size:33 final size:33
Alignment explanation
Indices: 46931--47023 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
46921 GCGAAACCAA
*
46931 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
46964 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
46997 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
47024 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:47020 original size:52 final size:54
Alignment explanation
Indices: 46894--47028 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
46884 TAGTTTACTT
*
46894 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
46952 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
46999 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
47029 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:47046 original size:19 final size:19
Alignment explanation
Indices: 47024--47152 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
47014 AAAATCGCAA
47024 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
47043 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
47057 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
47076 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
47090 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
47109 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
47128 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
47148 TGCGA
1 TGCGA
47153 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:47066 original size:33 final size:33
Alignment explanation
Indices: 47024--47115 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
47014 AAAATCGCAA
47024 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
47057 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
47090 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
47116 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:47358 original size:92 final size:93
Alignment explanation
Indices: 47196--47573 Score: 726
Period size: 92 Copynumber: 4.1 Consensus size: 93
47186 TTGAATGGAT
47196 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
47261 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
47289 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
47353 AGTTTAGCAGAATTGGCAGCAA-CGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
47380 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
47444 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
47472 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
47537 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
47565 AAATTTACT
1 AAATTTACT
47574 AAGCAATCTA
Statistics
Matches: 281, Mismatches: 1, Indels: 6
0.98 0.00 0.02
Matches are distributed among these distances:
91 86 0.31
92 100 0.36
93 95 0.34
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:49297 original size:14 final size:14
Alignment explanation
Indices: 49278--49367 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
49268 TTGAAATGAA
49278 AATCGCAACGAGAG
1 AATCGCAACGAGAG
49292 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
49309 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
49325 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
49344 AATCGCAACGAGAG
1 AATCGCAACGAGAG
49358 AATCGCAACG
1 AATCGCAACG
49368 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:49315 original size:33 final size:33
Alignment explanation
Indices: 49270--49384 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
49260 TCTTTTGGTT
49270 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
49303 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
49336 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
49369 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
49385 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:49316 original size:19 final size:18
Alignment explanation
Indices: 49277--49389 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
49267 GTTGAAATGA
49277 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
49292 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
49309 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
49325 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
49342 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
49358 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
49375 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
49390 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:49420 original size:14 final size:14
Alignment explanation
Indices: 49401--49455 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
49391 TTTGGTTTCG
49401 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
49415 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
49434 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
49448 CGTTGCGA
1 CGTTGCGA
49456 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:49618 original size:33 final size:33
Alignment explanation
Indices: 49576--49646 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
49566 AATACTAACT
*
49576 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
49609 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
49642 TGAAA
1 TGAAA
49647 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:49878 original size:22 final size:22
Alignment explanation
Indices: 49826--49880 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
49816 TGGTTATGAG
**
49826 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
49848 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
49870 GGATTTCTTCG
1 GGATTTCTTCG
49881 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:50051 original size:20 final size:20
Alignment explanation
Indices: 50026--50219 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
50016 CTTTAAATAT
50026 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
50046 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
50068 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
50087 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
50107 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
50127 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
50147 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
50167 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
50187 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
50207 CGCGTTGCGATTT
1 CGCGTTGCGATTT
50220 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:50213 original size:60 final size:60
Alignment explanation
Indices: 50026--50219 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
50016 CTTTAAATAT
**
50026 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
50087 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
50147 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
50207 CGCGTTGCGATTT
1 CGCGTTGCGATTT
50220 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:50236 original size:21 final size:20
Alignment explanation
Indices: 50212--50288 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
50202 ATATTCGCGT
50212 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
50233 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
50253 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
50275 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
50289 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:50299 original size:20 final size:20
Alignment explanation
Indices: 50274--50325 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
50264 AAGAATCGCG
*
50274 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
50294 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
50314 TTGCGATTCTGG
1 TTGCGATTCTGG
50326 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:50615 original size:21 final size:21
Alignment explanation
Indices: 50576--50615 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
50566 AATAAACTTC
*
50576 TATTATAAGTACTACTTTATT
1 TATTATAAGTACCACTTTATT
* *
50597 TATTATAGGTACCATTTTA
1 TATTATAAGTACCACTTTA
50616 AAAGTAATTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (21 bp):
TATTATAAGTACCACTTTATT
Found at i:50673 original size:18 final size:19
Alignment explanation
Indices: 50650--50688 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
50640 GAAATTGATA
*
50650 AAAAATATATACTAA-TTT
1 AAAAATAAATACTAAGTTT
50668 AAAAATAAATACTAAGTTT
1 AAAAATAAATACTAAGTTT
50687 AA
1 AA
50689 GAATCAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAAATAAATACTAAGTTT
Found at i:52059 original size:90 final size:90
Alignment explanation
Indices: 51938--52115 Score: 304
Period size: 90 Copynumber: 2.0 Consensus size: 90
51928 TAATCTCGAA
* * *
51938 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
52003 TAGGGTAACATGGA-TATAAAAGGAT
66 TAGGGTAAC-TCGACTATAAAAGGAT
52028 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
52093 TAGGGTAACTCGACTATAAAAGG
66 TAGGGTAACTCGACTATAAAAGG
52116 GTGTGTTAGG
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
89 3 0.04
90 80 0.96
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTCGACTATAAAAGGAT
Found at i:53549 original size:30 final size:31
Alignment explanation
Indices: 53479--53552 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
53469 AACGTCAAAG
* ** *
53479 TGACCAAAACTTAATAAAACAATAATGTAAG
1 TGACTAAAACTTAATAAAACAATAACATAAA
*
53510 TGA-TCAAAACTTAAT-AAATAATAACATAAA
1 TGACT-AAAACTTAATAAAACAATAACATAAA
53540 TGACTAAAACTTA
1 TGACTAAAACTTA
53553 TGTTTTTCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 22 0.61
31 14 0.39
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.26
Consensus pattern (31 bp):
TGACTAAAACTTAATAAAACAATAACATAAA
Found at i:64673 original size:26 final size:26
Alignment explanation
Indices: 64644--64697 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
64634 TTTTATATTA
* *
64644 TAAATATTAATTTG-TACCATATAAAT
1 TAAAAATT-ATTTGATACCATAAAAAT
*
64670 TAAAAATTATTTGATACTATAAAAAT
1 TAAAAATTATTTGATACCATAAAAAT
64696 TA
1 TA
64698 TGGATAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.41
Consensus pattern (26 bp):
TAAAAATTATTTGATACCATAAAAAT
Done.