Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005442.1 Hibiscus syriacus cultivar Beakdansim tig00012475_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: 112145
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:6854 original size:13 final size:13
Alignment explanation
Indices: 6835--6864 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
6825 ACAAATAAGC
6835 AAAAAAAGAAACAG
1 AAAAAAA-AAACAG
6849 AAAAAAAAAACAG
1 AAAAAAAAAACAG
6862 AAA
1 AAA
6865 CTTTCTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAG
Found at i:9249 original size:6 final size:6
Alignment explanation
Indices: 9240--9264 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9230 TATCTATATG
9240 TATAAA TATAAA TATAAA TATAAA T
1 TATAAA TATAAA TATAAA TATAAA T
9265 TGTTAGTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TATAAA
Found at i:9655 original size:25 final size:24
Alignment explanation
Indices: 9627--9675 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
9617 ATTGTTGATC
9627 TAATTTCACATCCTTTAAAATTTTA
1 TAATTTCACA-CCTTTAAAATTTTA
* *
9652 TAATTTCACACTTTTTAAATTTTA
1 TAATTTCACACCTTTAAAATTTTA
9676 GTATGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.35, C:0.14, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATTTCACACCTTTAAAATTTTA
Found at i:10747 original size:31 final size:32
Alignment explanation
Indices: 10705--10790 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 32
10695 TTAAATAATG
*
10705 ATAA-ATTTTGATAAGTTTAATGATT-ATTTT
1 ATAATATTTTGATAAATTTAATGATTCATTTT
*
10735 ATAATATTTTGATAATTTTAATG-TTCATTTT
1 ATAATATTTTGATAAATTTAATGATTCATTTT
* *
10766 ATACTAATTTGATAGAATTTAATGA
1 ATAATATTTTGATA-AATTTAATGA
10791 CGATTTTGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 6 0.12
31 34 0.71
32 8 0.17
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (32 bp):
ATAATATTTTGATAAATTTAATGATTCATTTT
Found at i:10797 original size:32 final size:30
Alignment explanation
Indices: 10711--10832 Score: 93
Period size: 31 Copynumber: 3.9 Consensus size: 30
10701 AATGATAAAT
* * *
10711 TTTGATAAGTTTAATGATTATTTTATAATAT
1 TTTGATAAATTTAATGA-CATTTTATAATAA
* * *
10742 TTTGATAATTTTAATGTTCATTTTATACTAA
1 TTTGATAAATTTAATG-ACATTTTATAATAA
* *
10773 TTTGATAGAATTTAATGACGATTTTGTAATCA
1 TTTGATA-AATTTAATGAC-ATTTTATAATAA
* * *
10805 -TTGAGAACTATAATGACCATTTTATAAT
1 TTTGATAAATTTAATGA-CATTTTATAAT
10833 TTTTAAAAAT
Statistics
Matches: 73, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
30 17 0.23
31 39 0.53
32 17 0.23
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (30 bp):
TTTGATAAATTTAATGACATTTTATAATAA
Found at i:21841 original size:31 final size:31
Alignment explanation
Indices: 21806--21866 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
21796 TTTTTGATAA
* *
21806 ATTTAGTGATTATTTTGTAATAGTTTAATAT
1 ATTTAATGATTATTTTATAATAGTTTAATAT
* *
21837 ATTTAATGATTATTTTATACTATTTTAATA
1 ATTTAATGATTATTTTATAATAGTTTAATA
21867 AGACTAACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (31 bp):
ATTTAATGATTATTTTATAATAGTTTAATAT
Found at i:22224 original size:21 final size:20
Alignment explanation
Indices: 22197--22295 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
22187 AATCAGTTTC
*
22197 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAATGCGATT-TT
* * *
22218 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAATGCGAT-TTT
* *
22239 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAATGCGATTTT
* *
22259 CCAAAATCGCAATGCGAATAT
1 -CAAAATCGCAATGCGATTTT
* *
22280 GAAAATCGCAACGCGA
1 CAAAATCGCAATGCGA
22296 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 15 0.25
21 46 0.75
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
CAAAATCGCAATGCGATTTT
Found at i:22346 original size:60 final size:60
Alignment explanation
Indices: 22282--22531 Score: 245
Period size: 60 Copynumber: 4.2 Consensus size: 60
22272 GCGAATATGA
* * * *
22282 AAATCGCAACGCGAA-CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCTGT
1 AAATCGCAACGAGAATC-CGTAAATCGCAACGCGTATCCGTAAATCGCAACGTGAATCCGT
* * ** * * * * * *
22342 AAATCGCAACGCGTATGGGTAAATCGTAATGCGTATCCGTATATCGCAATGCGTATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGTGAATCCGT
* * * *
22402 AAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGAT-AATCCGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACG-TGAATCCGT
* * * *
22462 AAATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGTAAATCGCAACGCGT-ATCCGTAAATCGCAACGTGAATCCGT
*
22522 AAATCACAAC
1 AAATCGCAAC
22532 ACTGAAATTT
Statistics
Matches: 154, Mismatches: 32, Indels: 8
0.79 0.16 0.04
Matches are distributed among these distances:
60 154 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (60 bp):
AAATCGCAACGAGAATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGTGAATCCGT
Found at i:22513 original size:20 final size:20
Alignment explanation
Indices: 22301--22531 Score: 215
Period size: 20 Copynumber: 11.6 Consensus size: 20
22291 CGCGAACACA
*
22301 TAAATCGCAACGCGT-ATCCG
1 TAAATCGCAACG-ATAATCCG
* *
22321 TAAATCGCAACG-TGTATCTG
1 TAAATCGCAACGAT-AATCCG
* **
22341 TAAATCGCAACGCGT-ATGGG
1 TAAATCGCAACG-ATAATCCG
*
22361 TAAATCGTAATGCG-T-ATCCG
1 TAAATCGCAA--CGATAATCCG
*
22381 TATATCGCAATGCG-T-ATCCG
1 TAAATCGCAA--CGATAATCCG
22401 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGATAATCCG
* *
22421 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGATAATCCG
22441 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGATAATCCG
* *
22461 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGATAATCCG
22481 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGATAATCCG
* *
22501 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGATAATCCG
*
22521 TAAATCACAAC
1 TAAATCGCAAC
22532 ACTGAAATTT
Statistics
Matches: 183, Mismatches: 20, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
18 3 0.02
19 1 0.01
20 176 0.96
22 3 0.02
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
TAAATCGCAACGATAATCCG
Found at i:23253 original size:24 final size:24
Alignment explanation
Indices: 23214--23260 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
23204 AAATTTGGTC
23214 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
23238 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
23261 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:23452 original size:12 final size:12
Alignment explanation
Indices: 23435--23459 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23425 ATATAATCCT
23435 GAAGAAGAAAAA
1 GAAGAAGAAAAA
23447 GAAGAAGAAAAA
1 GAAGAAGAAAAA
23459 G
1 G
23460 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:25835 original size:33 final size:33
Alignment explanation
Indices: 25740--25972 Score: 269
Period size: 33 Copynumber: 6.9 Consensus size: 33
25730 CGGAAATTAC
25740 AATCGCAACGAGAGAATCGCAATGCGAAATG-A
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
25772 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
25806 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* * * * *
25839 AATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGA
1 AATCGCAACGAGAGAATCG-CAATGCGAAATGA-A
*
25871 GAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
25910 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
25943 AATCGCAACGAGAGAATCGCAATGCGAAAT
1 AATCGCAACGAGAGAATCGCAATGCGAAAT
25973 TATAAACGCA
Statistics
Matches: 171, Mismatches: 15, Indels: 29
0.80 0.07 0.13
Matches are distributed among these distances:
31 8 0.05
32 28 0.16
33 84 0.49
34 23 0.13
35 2 0.01
36 2 0.01
38 10 0.06
39 7 0.04
40 7 0.04
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:25844 original size:19 final size:19
Alignment explanation
Indices: 25754--25950 Score: 202
Period size: 19 Copynumber: 11.4 Consensus size: 19
25744 GCAACGAGAG
25754 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
25772 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
25786 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
25806 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
25820 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
25839 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
25858 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
25872 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
25891 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
25910 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
25924 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
25943 AATCGCAA
1 AATCGCAA
25951 CGAGAGAATC
Statistics
Matches: 149, Mismatches: 8, Indels: 43
0.75 0.04 0.22
Matches are distributed among these distances:
13 3 0.02
14 38 0.26
15 3 0.02
16 8 0.05
17 5 0.03
18 11 0.07
19 68 0.46
20 13 0.09
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:25857 original size:52 final size:52
Alignment explanation
Indices: 25781--25950 Score: 331
Period size: 52 Copynumber: 3.2 Consensus size: 52
25771 AAATCCCAAC
25781 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
25834 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
25886 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
25938 ATGAAAATCGCAA
1 ATGAAAATCGCAA
25951 CGAGAGAATC
Statistics
Matches: 117, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 101 0.86
53 16 0.14
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:25929 original size:14 final size:14
Alignment explanation
Indices: 25910--25964 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
25900 GCGAAATGAA
25910 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
25924 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
25943 AATCGCAACGAGAG
1 AATCGCAACGAGAG
25957 AATCGCAA
1 AATCGCAA
25965 TGCGAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:25988 original size:85 final size:86
Alignment explanation
Indices: 25740--25972 Score: 325
Period size: 85 Copynumber: 2.7 Consensus size: 86
25730 CGGAAATTAC
* *
25740 AATCGCAACGAGAGAATCGCAATGCGAAATG-AAATCCCAAC-ATGAAAATCGCAATGCGGAAAT
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAAT
* * *
25803 GAAAATCGCAACGAGAGAATCGC
64 GAAAATCGCAATGCGAGAATCGA
* *
25826 AATGCGAAATGA-A-AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
1 AAT-CGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
25889 AAAATCGCAATGCGA-AAT-GAA
65 AAAATCGCAATGCGAGAATCG-A
25910 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
25973 TATAAACGCA
Statistics
Matches: 132, Mismatches: 9, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
83 7 0.05
84 7 0.05
85 85 0.64
86 26 0.20
87 7 0.05
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.13
Consensus pattern (86 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGA
AAATCGCAATGCGAGAATCGA
Found at i:26091 original size:52 final size:53
Alignment explanation
Indices: 25979--26094 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
25969 AAATTATAAA
25979 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
26032 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
26084 CGCATTGCGAT
1 CGCATTGCGAT
26095 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
Found at i:26102 original size:19 final size:19
Alignment explanation
Indices: 25997--26094 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
25987 GATTCTCTCG
25997 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
26017 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
26036 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
26050 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
26069 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
26088 TTGCGAT
1 TTGCGAT
26095 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:26220 original size:14 final size:14
Alignment explanation
Indices: 26201--26237 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
26191 CATCAATTAC
26201 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
26215 ACAAATCATCTTTT
1 ACAAATCAACTTTT
26229 ACAAATCAA
1 ACAAATCAA
26238 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:28235 original size:14 final size:14
Alignment explanation
Indices: 28216--28272 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
28206 GCGAAATGAA
*
28216 AATCGCAACGACAG
1 AATCGCAACGAAAG
28230 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
28247 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
28263 AATCGCAACG
1 AATCGCAACG
28273 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:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:28243 original size:33 final size:33
Alignment explanation
Indices: 28197--28286 Score: 162
Period size: 33 Copynumber: 2.7 Consensus size: 33
28187 GCGAAACCAA
*
28197 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
28230 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
28263 AATCGCAACGCGAAATGAAAATCG
1 AATCGCAACGCGAAATGAAAATCG
28287 GAGATGGGGA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:28254 original size:19 final size:19
Alignment explanation
Indices: 28160--28286 Score: 121
Period size: 19 Copynumber: 7.2 Consensus size: 19
28150 TAGTTTACTT
* *
28160 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
28180 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
28199 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
28218 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
28232 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
28251 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
28265 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
28284 TCG
1 TCG
28287 GAGATGGGGA
Statistics
Matches: 90, Mismatches: 7, Indels: 21
0.76 0.06 0.18
Matches are distributed among these distances:
14 16 0.18
16 11 0.12
17 11 0.12
19 40 0.44
20 12 0.13
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:28479 original size:20 final size:20
Alignment explanation
Indices: 28454--28647 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
28444 CTTTAAATAT
28454 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
28474 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
28496 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
28515 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
28535 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
28555 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
28575 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
28595 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
28615 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
28635 CGCGTTGCGATTT
1 CGCGTTGCGATTT
28648 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:28641 original size:60 final size:60
Alignment explanation
Indices: 28454--28647 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
28444 CTTTAAATAT
**
28454 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
28515 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
28575 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
28635 CGCGTTGCGATTT
1 CGCGTTGCGATTT
28648 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:28664 original size:21 final size:21
Alignment explanation
Indices: 28634--28716 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
28624 ATTTTCATAT
*
28634 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
28655 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
28676 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
28697 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
28717 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:28707 original size:42 final size:43
Alignment explanation
Indices: 28614--28712 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
28604 ATTTATGTGT
* *
28614 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
28655 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
28697 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
28713 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:33789 original size:54 final size:54
Alignment explanation
Indices: 33725--33901 Score: 191
Period size: 54 Copynumber: 3.3 Consensus size: 54
33715 AGCGCTCACA
* * *
33725 TAAGGCGTGGGCACGACTTTTTCATCCAGACCTAACGAAGAAGAAGTCTTCAGT
1 TAAGGCGTGGGCACGACTTATTCATCCAGAACTAACGCAGAAGAAGTCTTCAGT
* * *
33779 TAAGGCGTGGGCACAACTTATCCAT-CATGAGA-T-ACTGCAGAAGAAGTCTCCAGT
1 TAAGGCGTGGGCACGACTTATTCATCCA-GA-ACTAAC-GCAGAAGAAGTCTTCAGT
* * * *
33833 TAAGGCGTAGGCACGGCTTATTCATCCAAAACTACCGCAGAAGAA-TCCTTCAGT
1 TAAGGCGTGGGCACGACTTATTCATCCAGAACTAACGCAGAAGAAGT-CTTCAGT
*
33887 TAAGGCGTGAGCACG
1 TAAGGCGTGGGCACG
33902 CCATCTATTG
Statistics
Matches: 101, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
53 6 0.06
54 92 0.91
55 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.22
Consensus pattern (54 bp):
TAAGGCGTGGGCACGACTTATTCATCCAGAACTAACGCAGAAGAAGTCTTCAGT
Found at i:34899 original size:21 final size:20
Alignment explanation
Indices: 34873--34931 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
34863 AAAAGGCAAC
*
34873 CTTCTTCATTTTGTTCTTCTT
1 CTTCTTC-TTTTCTTCTTCTT
*
34894 CTTCTTCTCTTTCTTCTTTTT
1 CTTCTTCT-TTTCTTCTTCTT
34915 CTTCTTCTTTTTCTTCT
1 CTTCTTC-TTTTCTTCT
34932 GTTTTGGTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (20 bp):
CTTCTTCTTTTCTTCTTCTT
Found at i:34900 original size:9 final size:9
Alignment explanation
Indices: 34873--34931 Score: 59
Period size: 9 Copynumber: 6.6 Consensus size: 9
34863 AAAAGGCAAC
34873 CTTCTTCATT
1 CTTCTTC-TT
*
34883 -TTGTTCTT
1 CTTCTTCTT
34891 CTTCTTCTT
1 CTTCTTCTT
34900 C-TCTTTCTT
1 CTTC-TTCTT
*
34909 CTTTTTCTT
1 CTTCTTCTT
*
34918 CTTCTTTTT
1 CTTCTTCTT
34927 CTTCT
1 CTTCT
34932 GTTTTGGTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
8 4 0.10
9 36 0.88
10 1 0.02
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (9 bp):
CTTCTTCTT
Found at i:34901 original size:12 final size:12
Alignment explanation
Indices: 34873--34931 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
34863 AAAAGGCAAC
34873 CTTCTTCATT-TT
1 CTTCTTC-TTCTT
*
34885 GTTCTTCTTCTT
1 CTTCTTCTTCTT
34897 CTTC-TCTTTCTT
1 CTTCTTC-TTCTT
*
34909 CTTTTTCTTCTT
1 CTTCTTCTTCTT
*
34921 CTTTTTCTTCT
1 CTTCTTCTTCT
34932 GTTTTGGTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 4 0.10
12 35 0.85
13 2 0.05
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (12 bp):
CTTCTTCTTCTT
Found at i:36554 original size:6 final size:6
Alignment explanation
Indices: 36519--36552 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
36509 AAGTTAAAAA
* *
36519 AACCCA AACCCT AACCCT AACCCT AACCTT AACC
1 AACCCT AACCCT AACCCT AACCCT AACCCT AACC
36553 TTGACCTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.38, C:0.47, G:0.00, T:0.15
Consensus pattern (6 bp):
AACCCT
Found at i:38851 original size:55 final size:55
Alignment explanation
Indices: 38739--38868 Score: 154
Period size: 55 Copynumber: 2.4 Consensus size: 55
38729 AGGGAACTCA
* ** *
38739 AACTC-GGGTGGTGTCGGACACACGTATCAAACTCGATTAACAAAGCATTTCACG
1 AACTCGGGGTGGTGTCGGACACACGTATCAAACACGAGAAACAAAGCATTCCACG
* * **
38793 AACTCGGGGTGGTGTCGGACACACGTGTCAAACACGAGAAACAATGCATTCCTTG
1 AACTCGGGGTGGTGTCGGACACACGTATCAAACACGAGAAACAAAGCATTCCACG
***
38848 AACTCGATTTGGTGTCGGACA
1 AACTCGGGGTGGTGTCGGACA
38869 TACGAGTAAC
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
54 5 0.08
55 59 0.92
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.22
Consensus pattern (55 bp):
AACTCGGGGTGGTGTCGGACACACGTATCAAACACGAGAAACAAAGCATTCCACG
Found at i:44067 original size:20 final size:20
Alignment explanation
Indices: 44030--44069 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
44020 ATGGAATCTG
*
44030 CTTTTCTTAATAAAAATAAT
1 CTTTTATTAATAAAAATAAT
* *
44050 CTTTTATTATTAATAATAAT
1 CTTTTATTAATAAAAATAAT
44070 ATAATTTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (20 bp):
CTTTTATTAATAAAAATAAT
Found at i:45322 original size:12 final size:12
Alignment explanation
Indices: 45305--45329 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45295 AAATGTAATG
45305 AATTATTAATTT
1 AATTATTAATTT
45317 AATTATTAATTT
1 AATTATTAATTT
45329 A
1 A
45330 CTAATTATTA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AATTATTAATTT
Found at i:45325 original size:7 final size:7
Alignment explanation
Indices: 45305--45350 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
45295 AAATGTAATG
45305 AATTATT
1 AATTATT
45312 AA-T-TT
1 AATTATT
45317 AATTATT
1 AATTATT
*
45324 AATTTACT
1 AA-TTATT
45332 AATTATT
1 AATTATT
*
45339 AATAATT
1 AATTATT
45346 AATTA
1 AATTA
45351 CTATATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
5 4 0.12
6 2 0.06
7 20 0.62
8 6 0.19
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (7 bp):
AATTATT
Found at i:45334 original size:15 final size:13
Alignment explanation
Indices: 45305--45370 Score: 53
Period size: 15 Copynumber: 4.7 Consensus size: 13
45295 AAATGTAATG
45305 AATTATTAA-TTT
1 AATTATTAATTTT
45317 AATTATTAATTTACT
1 AATTATTAATTT--T
*
45332 AATTATTAATAATT
1 AATTATTAAT-TTT
*
45346 AATTACTATATTTT
1 AATTATTA-ATTTT
45360 ATATCTATTAA
1 A-AT-TATTAA
45371 AAGACAAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
12 9 0.21
13 2 0.05
14 11 0.26
15 16 0.37
16 5 0.12
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (13 bp):
AATTATTAATTTT
Found at i:45341 original size:22 final size:21
Alignment explanation
Indices: 45314--45370 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
45304 GAATTATTAA
45314 TTTAATTATTAATTTACTA-AT
1 TTTAATTATTAA-TTACTATAT
*
45335 TATTAATAATTAATTACTATAT
1 T-TTAATTATTAATTACTATAT
45357 TTTATATCTATTAA
1 TTTA-AT-TATTAA
45371 AAGACAAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 10 0.33
22 15 0.50
23 5 0.17
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAATTATTAATTACTATAT
Found at i:57516 original size:113 final size:113
Alignment explanation
Indices: 57318--57893 Score: 679
Period size: 113 Copynumber: 5.0 Consensus size: 113
57308 CACATTCCAC
* *
57318 CAGTAGGGTTAGGATTACACATGTTGTACACAGTTCTAACAATTAGTTAAGGAAACCTACCATTT
1 CAGTAGGGTTAGGCTTACACATGTTGTACACAGTTCTAGCAATTAGTTAAGGAAACCTACCATTT
* * * *
57383 TTACGATCTGAAAGTATCAACCGAGCAAAGACTCAATCAACTATTGAT
66 TTACGATCCGAATGTATCAACCGAGCTAAGACTCAATCGACTATTGAT
* *
57431 CAGTAGGATTAGGCTTACACATGTTGTACACAGTTCTAGCAATCAGTTAAGGAAACCTACCATTT
1 CAGTAGGGTTAGGCTTACACATGTTGTACACAGTTCTAGCAATTAGTTAAGGAAACCTACCATTT
* *
57496 TTACTATCGGAATGTATCAACTATTAACCGATCGCTAAGACTCAATCGACTATTGA-
66 TTACGATCCGAATGTAT---C----AACCGA--GCTAAGACTCAATCGACTATTGAT
* * *
57552 CTAGTAGGGTTAGACTTACACATGTTGTACATAGTTCTAGCAATTAGTTAAGGAAGCCTACCATT
1 C-AGTAGGGTTAGGCTTACACATGTTGTACACAGTTCTAGCAATTAGTTAAGGAAACCTACCATT
* *
57617 TTTACGATCCGAATGTATCAACCGAGTTAAGACTCAATCAACTATTGAT
65 TTTACGATCCGAATGTATCAACCGAGCTAAGACTCAATCGACTATTGAT
* * * * *
57666 CAGTAGAGTTAGGCATACACATGTTGTACACAGTTCTTGCAATTAGTTAAGCAGAACCCACCAAT
1 CAGTAGGGTTAGGCTTACACATGTTGTACACAGTTCTAGCAATTAGTTAAGGA-AACCTACC-AT
* * * * * *
57731 TTTTACGATCTGAATGTATCAACTGAACTAAGTCTCGATTGACTATTGAT
64 TTTTACGATCCGAATGTATCAACCGAGCTAAGACTCAATCGACTATTGAT
** * * * *
57781 CAAAAGGGTTAGGCTTACAGATGTTGTACACAGTTCAAGCAATCAGTTAA-GAAAACTCACCATT
1 CAGTAGGGTTAGGCTTACACATGTTGTACACAGTTCTAGCAATTAGTTAAGGAAACCT-ACCA-T
* * * * *
57845 TTTTACTATCCGAATATATCAACTGAGCTTAGACTCGATCGACTATTGA
64 TTTTACGATCCGAATGTATCAACCGAGCTAAGACTCAATCGACTATTGA
57894 CGTTAAAATC
Statistics
Matches: 396, Mismatches: 52, Indels: 29
0.83 0.11 0.06
Matches are distributed among these distances:
113 146 0.37
114 54 0.14
115 92 0.23
116 1 0.00
119 1 0.00
120 6 0.02
121 1 0.00
122 95 0.24
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (113 bp):
CAGTAGGGTTAGGCTTACACATGTTGTACACAGTTCTAGCAATTAGTTAAGGAAACCTACCATTT
TTACGATCCGAATGTATCAACCGAGCTAAGACTCAATCGACTATTGAT
Found at i:57816 original size:115 final size:114
Alignment explanation
Indices: 57529--57893 Score: 430
Period size: 115 Copynumber: 3.2 Consensus size: 114
57519 TTAACCGATC
* ** * *
57529 GCTAAGACTCAATCGACTATTGA-CTAGTAGGGTTAGACTTACACATGTTGTACATAGTTCTAGC
1 GCTAAGACTCGATCGACTATTGATC-AAAAGGGTTAGGCTTACACATGTTGTACACAGTTCTAGC
* *
57593 AATTAGTTAAG-GAAGCCTACC-ATTTTTACGATCCGAATGTATCAACCGA
65 AATTAGTTAAGAGAA-CCCACCAATTTTTACGATCCGAATGTATCAACTGA
* * * ** * * *
57642 GTTAAGACTCAATCAACTATTGATCAGTAGAGTTAGGCATACACATGTTGTACACAGTTCTTGCA
1 GCTAAGACTCGATCGACTATTGATCAAAAGGGTTAGGCTTACACATGTTGTACACAGTTCTAGCA
*
57707 ATTAGTTAAGCAGAACCCACCAATTTTTACGATCTGAATGTATCAACTGA
66 ATTAGTTAAG-AGAACCCACCAATTTTTACGATCCGAATGTATCAACTGA
* * * * *
57757 ACTAAGTCTCGATTGACTATTGATCAAAAGGGTTAGGCTTACAGATGTTGTACACAGTTCAAGCA
1 GCTAAGACTCGATCGACTATTGATCAAAAGGGTTAGGCTTACACATGTTGTACACAGTTCTAGCA
* * * * * *
57822 ATCAGTTAAGAAAACTCACCATTTTTTACTATCCGAATATATCAACTGA
66 ATTAGTTAAGAGAACCCACCAATTTTTACGATCCGAATGTATCAACTGA
*
57871 GCTTAGACTCGATCGACTATTGA
1 GCTAAGACTCGATCGACTATTGA
57894 CGTTAAAATC
Statistics
Matches: 214, Mismatches: 34, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
113 66 0.31
114 58 0.27
115 90 0.42
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (114 bp):
GCTAAGACTCGATCGACTATTGATCAAAAGGGTTAGGCTTACACATGTTGTACACAGTTCTAGCA
ATTAGTTAAGAGAACCCACCAATTTTTACGATCCGAATGTATCAACTGA
Found at i:58460 original size:27 final size:28
Alignment explanation
Indices: 58430--58487 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
58420 TCGATAAATT
* *
58430 TTAATCATCATTTTAT-AATTTA-AAAGA
1 TTAATAAT-ATTTTATAAAATTAGAAAGA
*
58457 TTAATAATATTTTTTAAAATTAGAAAGA
1 TTAATAATATTTTATAAAATTAGAAAGA
58485 TTA
1 TTA
58488 TTGACCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 6 0.23
27 12 0.46
28 8 0.31
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (28 bp):
TTAATAATATTTTATAAAATTAGAAAGA
Found at i:59598 original size:21 final size:20
Alignment explanation
Indices: 59558--59599 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
59548 TAAAAATATT
*
59558 AAAAAATAATATTTTAAATA
1 AAAAAATAATATTATAAATA
*
59578 AAAATAATAATATTATCAATA
1 AAAA-AATAATATTATAAATA
59599 A
1 A
59600 TTTTTATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATAATATTATAAATA
Found at i:60255 original size:33 final size:33
Alignment explanation
Indices: 60208--60314 Score: 196
Period size: 33 Copynumber: 3.2 Consensus size: 33
60198 ATTTTAGTGA
*
60208 ATAACAGTTAATTCAAAAAGGTAATTTATAGCT
1 ATAATAGTTAATTCAAAAAGGTAATTTATAGCT
*
60241 GTAATAGTTAATTCAAAAAGGTAATTTATAGCT
1 ATAATAGTTAATTCAAAAAGGTAATTTATAGCT
60274 ATAATAGTTAATTCAAAAAGGTAATTTATAGCT
1 ATAATAGTTAATTCAAAAAGGTAATTTATAGCT
60307 ATAATAGT
1 ATAATAGT
60315 GTTCGATAGA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 71 1.00
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.36
Consensus pattern (33 bp):
ATAATAGTTAATTCAAAAAGGTAATTTATAGCT
Found at i:61258 original size:21 final size:20
Alignment explanation
Indices: 61218--61259 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
61208 TAAAAATATT
*
61218 AAAAAATAATATTTTAAATA
1 AAAAAATAATATTATAAATA
*
61238 AAAATAATAATATTATCAATA
1 AAAA-AATAATATTATAAATA
61259 A
1 A
61260 TTTTGATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATAATATTATAAATA
Found at i:61916 original size:33 final size:33
Alignment explanation
Indices: 61869--61942 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
61859 ATTTTAGTGA
*
61869 ATAACAGTTAATTCAAAAAGGTAATTTATAGCT
1 ATAATAGTTAATTCAAAAAGGTAATTTATAGCT
*
61902 GTAATAGTTAATTCAAAAAGGTAATTTATAGCT
1 ATAATAGTTAATTCAAAAAGGTAATTTATAGCT
61935 ATAATAGT
1 ATAATAGT
61943 GTTCGATAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.35
Consensus pattern (33 bp):
ATAATAGTTAATTCAAAAAGGTAATTTATAGCT
Found at i:78320 original size:101 final size:101
Alignment explanation
Indices: 78130--78341 Score: 354
Period size: 101 Copynumber: 2.1 Consensus size: 101
78120 TGCAGCATTG
* * *
78130 CAAACTAAACTCCTTGAATTCACCAAACATCCTACGAAGCCTAACAACCTGTTCTCTAAGATTTT
1 CAAAGTAAACTCATTGAATTCACCAAACACCCTACGAAGCCTAACAACCTGTTCTCTAAGATTTT
*
78195 GCTAGGTAGCAAGGCTGGAGAAAACTTGTAAAGCTA
66 GCTAGGTAGCAAGGATGGAGAAAACTTGTAAAGCTA
78231 CAAAGTAAACTCATTGAATTCACCAAACACCCTACGAAGCCTAACAACCTGTTCTCTAAGATTTT
1 CAAAGTAAACTCATTGAATTCACCAAACACCCTACGAAGCCTAACAACCTGTTCTCTAAGATTTT
*
78296 GTTAGGTAGCAAGGATGG-GAAAAACTTGTAAAGCTA
66 GCTAGGTAGCAAGGATGGAG-AAAACTTGTAAAGCTA
*
78332 CGAAGTAAAC
1 CAAAGTAAAC
78342 ATATAATACG
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
100 1 0.01
101 103 0.99
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (101 bp):
CAAAGTAAACTCATTGAATTCACCAAACACCCTACGAAGCCTAACAACCTGTTCTCTAAGATTTT
GCTAGGTAGCAAGGATGGAGAAAACTTGTAAAGCTA
Found at i:80187 original size:55 final size:55
Alignment explanation
Indices: 80120--80230 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
80110 ACTTGCATCG
* * *
80120 CTAAATTATTCACCGTTGTTTATCTTTTTTGTTATTGGAATTCATTGATTGATCA
1 CTAAATCATTCACCATTGTTTATCTTTTTCGTTATTGGAATTCATTGATTGATCA
80175 CTAAATCATTCACCATTGTTTATCTTTTTCGTTATTGGAATTCATTGATTGATCA
1 CTAAATCATTCACCATTGTTTATCTTTTTCGTTATTGGAATTCATTGATTGATCA
80230 C
1 C
80231 CTCTTTATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (55 bp):
CTAAATCATTCACCATTGTTTATCTTTTTCGTTATTGGAATTCATTGATTGATCA
Found at i:84764 original size:11 final size:11
Alignment explanation
Indices: 84731--84764 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
84721 AATTGTAATA
*
84731 AAAATATATAC
1 AAAATATATAT
*
84742 AAAATATTTAT
1 AAAATATATAT
84753 AAAATATATAT
1 AAAATATATAT
84764 A
1 A
84765 TTAATATGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAATATATAT
Found at i:85013 original size:22 final size:21
Alignment explanation
Indices: 84985--85043 Score: 102
Period size: 22 Copynumber: 2.8 Consensus size: 21
84975 TATTACACTA
84985 TTAGTATATAATATATAATTTT
1 TTAGTATATAATATATAA-TTT
85007 TTAGTATATAATATATAATTT
1 TTAGTATATAATATATAATTT
85028 TTAGTATAT-ATATATA
1 TTAGTATATAATATATA
85044 CACACATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.19
21 12 0.32
22 18 0.49
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (21 bp):
TTAGTATATAATATATAATTT
Found at i:86068 original size:12 final size:13
Alignment explanation
Indices: 86048--86085 Score: 62
Period size: 12 Copynumber: 3.1 Consensus size: 13
86038 GTTCATGAAC
86048 AAGCTCGTTTATG
1 AAGCTCGTTTATG
86061 AA-CTCGTTTAT-
1 AAGCTCGTTTATG
86072 AAGCTCGTTTATG
1 AAGCTCGTTTATG
86085 A
1 A
86086 GATCATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.09
12 18 0.78
13 3 0.13
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (13 bp):
AAGCTCGTTTATG
Found at i:86094 original size:24 final size:24
Alignment explanation
Indices: 86048--86095 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
86038 GTTCATGAAC
*
86048 AAGCTCGTTTATGAACTCGTTTAT
1 AAGCTCGTTTATGAACTCATTTAT
86072 AAGCTCGTTTATGAGA-TCATTTAT
1 AAGCTCGTTTATGA-ACTCATTTAT
86096 CAATTCATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.42
Consensus pattern (24 bp):
AAGCTCGTTTATGAACTCATTTAT
Found at i:86536 original size:17 final size:18
Alignment explanation
Indices: 86514--86553 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
86504 TTACACTCCT
86514 ACCTTAAAC-CCGATCCA
1 ACCTTAAACTCCGATCCA
*
86531 ACCTT-ACCTCCGATCCA
1 ACCTTAAACTCCGATCCA
86548 ACCTTA
1 ACCTTA
86554 CCTCATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.30, C:0.42, G:0.05, T:0.23
Consensus pattern (18 bp):
ACCTTAAACTCCGATCCA
Found at i:86554 original size:17 final size:17
Alignment explanation
Indices: 86523--86557 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
86513 TACCTTAAAC
86523 CCGATCCAACCTTACCT
1 CCGATCCAACCTTACCT
86540 CCGATCCAACCTTACCT
1 CCGATCCAACCTTACCT
86557 C
1 C
86558 ATTTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.49, G:0.06, T:0.23
Consensus pattern (17 bp):
CCGATCCAACCTTACCT
Found at i:87204 original size:10 final size:10
Alignment explanation
Indices: 87189--87216 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
87179 GAAAACACGA
87189 TGCTTCTCGC
1 TGCTTCTCGC
87199 TGCTTCTCGC
1 TGCTTCTCGC
87209 TGCTTCTC
1 TGCTTCTC
87217 TGGCCTCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.39, G:0.18, T:0.43
Consensus pattern (10 bp):
TGCTTCTCGC
Found at i:87923 original size:260 final size:259
Alignment explanation
Indices: 87463--87984 Score: 1019
Period size: 260 Copynumber: 2.0 Consensus size: 259
87453 AGAAGAGGTA
87463 AAGGAGCAATGGAGTTAACCAGCGCCGTCAGACTTATCGGCTTCTTCGCACACGAACTTCTTGTC
1 AAGGAGCAATGGAGTTAACCAGCGCCGTCAGACTTATCGGCTTCTTCGCACACGAACTTCTTGTC
87528 TTGAGAAGCTTTCAATAACAACTGCAATAACTGTAAATCCACACCGCGAGATTAGAATCATTTCC
66 TTGAGAAGCTTTCAATAACAACTGCAATAACTGTAAATCCACACCGCGAGATTAGAATCATTTCC
87593 AACACATGAAAACGAAAACTTGTAAACCTGACAAGAGAGATGATAATCAGGGTCAAGTTGGATTA
131 AACACATGAAAACGAAAACTTGTAAACCTGACAAGAGAGATGATAATCAGGGTCAAGTTGGATTA
87658 CCCACCAACTGATCAAATGCACTAGAATCAAGCATCTTTTCACCAAAGGAACCGAAGATATCCG
196 CCCACCAACTGATCAAATGCACTAGAATCAAGCATCTTTTCACCAAAGGAACCGAAGATATCCG
87722 AAGGAGCAATGGAGTTAACCAGCGCCGTCAGAGACTTATCGGCTTCTTCGCACACGAAC-TCTTG
1 AAGGAGCAATGGAGTTAACCAGCGCCGTC--AGACTTATCGGCTTCTTCGCACACGAACTTCTTG
87786 TCTTGAGAAGCTTTCAATAACAACTGCAATAACTGTAAATCCACACCGCGAGATTAGAATCATTT
64 TCTTGAGAAGCTTTCAATAACAACTGCAATAACTGTAAATCCACACCGCGAGATTAGAATCATTT
87851 CCAACACATGAAAACGAAAACTTGTAAACCTGACAAGAGAGATGATAATCAGGGTCAAGTTGGAT
129 CCAACACATGAAAACGAAAACTTGTAAACCTGACAAGAGAGATGATAATCAGGGTCAAGTTGGAT
87916 TACCCACCAACTGATCAAATGCACTAGAATCAAGCATCTTTTCACCAAAGGAACCGAAGATATCC
194 TACCCACCAACTGATCAAATGCACTAGAATCAAGCATCTTTTCACCAAAGGAACCGAAGATATCC
87981 G
259 G
87982 AAG
1 AAG
87985 CAGCCATAAT
Statistics
Matches: 261, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
259 29 0.11
260 204 0.78
261 28 0.11
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (259 bp):
AAGGAGCAATGGAGTTAACCAGCGCCGTCAGACTTATCGGCTTCTTCGCACACGAACTTCTTGTC
TTGAGAAGCTTTCAATAACAACTGCAATAACTGTAAATCCACACCGCGAGATTAGAATCATTTCC
AACACATGAAAACGAAAACTTGTAAACCTGACAAGAGAGATGATAATCAGGGTCAAGTTGGATTA
CCCACCAACTGATCAAATGCACTAGAATCAAGCATCTTTTCACCAAAGGAACCGAAGATATCCG
Found at i:89063 original size:21 final size:21
Alignment explanation
Indices: 89037--89081 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
89027 GATTTCTGGG
* *
89037 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
89058 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
89079 CAA
1 CAA
89082 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:89689 original size:18 final size:18
Alignment explanation
Indices: 89666--89700 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
89656 CTAGGAGATT
89666 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
89684 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
89701 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:90631 original size:32 final size:32
Alignment explanation
Indices: 90590--90686 Score: 128
Period size: 32 Copynumber: 3.1 Consensus size: 32
90580 GAGTCGAGGG
90590 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
90622 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
90653 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
90685 TT
1 TT
90687 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:90662 original size:31 final size:31
Alignment explanation
Indices: 90589--90689 Score: 125
Period size: 31 Copynumber: 3.2 Consensus size: 31
90579 AGAGTCGAGG
90589 GTTTACCTATGTTCT-ACGGAACATATGGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
90620 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
90652 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
90683 GTTTACC
1 GTTTACC
90690 GAGGATCTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 32 0.53
32 28 0.47
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:90747 original size:28 final size:30
Alignment explanation
Indices: 90677--90768 Score: 118
Period size: 30 Copynumber: 3.1 Consensus size: 30
90667 AAGGAACATA
90677 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
*
90708 TGGACAGTTACCGATGATCTTTATGA-C-C
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
90736 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
90765 TGGA
1 TGGA
90769 TAGGTCCTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
27 9 0.17
28 14 0.26
29 6 0.11
30 18 0.33
31 7 0.13
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.33
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:92709 original size:17 final size:19
Alignment explanation
Indices: 92683--92737 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 19
92673 TAATTTAAGG
92683 ATTAAAATTATTGTTATAT
1 ATTAAAATTATTGTTATAT
92702 A-T-AAATTAATT-TTA-AGT
1 ATTAAAATT-ATTGTTATA-T
92719 ATTAAAATTATTGTTATAT
1 ATTAAAATTATTGTTATAT
92738 TCTATAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
16 1 0.03
17 10 0.33
18 8 0.27
19 10 0.33
20 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
ATTAAAATTATTGTTATAT
Found at i:92716 original size:36 final size:34
Alignment explanation
Indices: 92664--92737 Score: 112
Period size: 36 Copynumber: 2.1 Consensus size: 34
92654 CAAATTAAAA
*
92664 ATATATATATAATTTAAGGATTAAAATTATTGTT
1 ATATATAAATAATTTAAGGATTAAAATTATTGTT
*
92698 ATATATAAATTAATTTTAAGTATTAAAATTATTGTT
1 ATATATAAA-TAA-TTTAAGGATTAAAATTATTGTT
92734 ATAT
1 ATAT
92738 TCTATAATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 8 0.22
35 3 0.08
36 25 0.69
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.49
Consensus pattern (34 bp):
ATATATAAATAATTTAAGGATTAAAATTATTGTT
Found at i:92728 original size:19 final size:19
Alignment explanation
Indices: 92676--92728 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
92666 ATATATATAA
*
92676 TTTAAGGATTAAAATT-AT
1 TTTAAGTATTAAAATTAAT
92694 TGTT-A-TA-TATAAATTAAT
1 T-TTAAGTATTA-AAATTAAT
92712 TTTAAGTATTAAAATTA
1 TTTAAGTATTAAAATTA
92729 TTGTTATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 11
0.70 0.03 0.28
Matches are distributed among these distances:
16 2 0.07
17 8 0.29
18 6 0.21
19 10 0.36
20 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (19 bp):
TTTAAGTATTAAAATTAAT
Found at i:105420 original size:2 final size:2
Alignment explanation
Indices: 105413--105449 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
105403 ACTGAATTTA
*
105413 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
105450 CAAATATGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:108793 original size:18 final size:18
Alignment explanation
Indices: 108772--108817 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
108762 TTTTAAATCA
108772 AAATAAAATTAGAATTTT
1 AAATAAAATTAGAATTTT
* *
108790 AAATTAAATTTATAATTTT
1 AAA-TAAAATTAGAATTTT
108809 AAATAAAAT
1 AAATAAAAT
108818 ATAAAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
AAATAAAATTAGAATTTT
Done.