Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002875.1 Hibiscus syriacus cultivar Beakdansim tig00005929_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: 1473696
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:4420 original size:2 final size:2
Alignment explanation
Indices: 4413--4451 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4403 AAGTAGTTAG
4413 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4452 GGAGAGATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6173 original size:125 final size:124
Alignment explanation
Indices: 5940--6173 Score: 292
Period size: 125 Copynumber: 1.9 Consensus size: 124
5930 TTGAATTAAA
* * * * *
5940 ATGCATCTTTCTCACATTTTCTTTCAAGATTAAAAAGATTTGTTATTCCACGTTAGGACGAAAAA
1 ATGCATCTTTCTAACATTTTCTTTCAAGATTAAAAAGATATGTTATTACACGTGAGGACAAAAAA
* * *
6005 TTATCAACTCCCTATCTTTTTAATCACTTTTATTTTTTACCAAATGCACTTCAAAATTG
66 ATATCAACTCCCGATCTTTTTAATCACTTTTACTTTTTACCAAATGCACTTCAAAATTG
* * *
6064 ATGCATCTTTCTAACATTTTCTTTCAAAGGTTAAAAAGATATGTTTTTACACGTGAGGATAAAAA
1 ATGCATCTTTCTAACATTTTCTTTC-AAGATTAAAAAGATATGTTATTACACGTGAGGACAAAAA
* * * *
6129 AATATTATCTCTCGAT-TTCTTTAAATCACTTTT-CTTTTTGCCAAA
65 AATATCAACTCCCGATCTT-TTT-AATCACTTTTACTTTTTACCAAA
6174 CAAATTTTAA
Statistics
Matches: 92, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
124 26 0.28
125 56 0.61
126 10 0.11
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (124 bp):
ATGCATCTTTCTAACATTTTCTTTCAAGATTAAAAAGATATGTTATTACACGTGAGGACAAAAAA
ATATCAACTCCCGATCTTTTTAATCACTTTTACTTTTTACCAAATGCACTTCAAAATTG
Found at i:11232 original size:11 final size:11
Alignment explanation
Indices: 11214--11334 Score: 116
Period size: 11 Copynumber: 10.6 Consensus size: 11
11204 TGGGGCAATG
11214 TCGAGCTTGAA
1 TCGAGCTTGAA
*
11225 TTGAGCTTAGAA
1 TCGAGCTT-GAA
11237 TCGAGCTTGAA
1 TCGAGCTTGAA
* *
11248 TTGAGCTCAGAA
1 TCGAGCT-TGAA
11260 TCGAGCTTGAA
1 TCGAGCTTGAA
* *
11271 TTGAGCTCAGAA
1 TCGAGCT-TGAA
11283 TCGAGCTTGAA
1 TCGAGCTTGAA
* ** *
11294 TTGATATCAGAA
1 TCGAGCT-TGAA
11306 TCGAGCTTGAA
1 TCGAGCTTGAA
*
11317 TCGAGCTTCAA
1 TCGAGCTTGAA
11328 TCGAGCT
1 TCGAGCT
11335 CGAGTCTCGA
Statistics
Matches: 87, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
11 52 0.60
12 35 0.40
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:11244 original size:23 final size:23
Alignment explanation
Indices: 11214--11323 Score: 184
Period size: 23 Copynumber: 4.8 Consensus size: 23
11204 TGGGGCAATG
*
11214 TCGAGCTTGAATTGAGCTTAGAA
1 TCGAGCTTGAATTGAGCTCAGAA
11237 TCGAGCTTGAATTGAGCTCAGAA
1 TCGAGCTTGAATTGAGCTCAGAA
11260 TCGAGCTTGAATTGAGCTCAGAA
1 TCGAGCTTGAATTGAGCTCAGAA
**
11283 TCGAGCTTGAATTGATATCAGAA
1 TCGAGCTTGAATTGAGCTCAGAA
*
11306 TCGAGCTTGAATCGAGCT
1 TCGAGCTTGAATTGAGCT
11324 TCAATCGAGC
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 81 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.28
Consensus pattern (23 bp):
TCGAGCTTGAATTGAGCTCAGAA
Found at i:11585 original size:16 final size:16
Alignment explanation
Indices: 11564--11620 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
11554 CCAACGTTTA
11564 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
11580 TGTTCATTTATGTTTG
1 TGTTCATTTATGTTCG
* *
11596 TGTTCGTTTATGGTCG
1 TGTTCATTTATGTTCG
11612 T-TT-ATTTAT
1 TGTTCATTTAT
11621 TAAATGAACG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
14 5 0.14
15 2 0.06
16 29 0.81
ACGTcount: A:0.12, C:0.09, G:0.19, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:12917 original size:3 final size:3
Alignment explanation
Indices: 12909--12942 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
12899 AAACTATTTA
12909 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12943 CATTAGCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:13757 original size:30 final size:29
Alignment explanation
Indices: 13701--13757 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
13691 TGGTTTTCTG
* **
13701 GAAAATAATTTATGTAAAATGGATTACCT
1 GAAAATAATTTACGTAAAATAAATTACCT
*
13730 GAAAATTATTTTACGTAAAATAAATTAC
1 GAAAA-TAATTTACGTAAAATAAATTAC
13758 ATTTTTTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 5 0.22
30 18 0.78
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (29 bp):
GAAAATAATTTACGTAAAATAAATTACCT
Found at i:16171 original size:25 final size:25
Alignment explanation
Indices: 16143--16200 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
16133 GCTAATAGAA
16143 TTAGTGAATAAGCTGAAAATATAAG
1 TTAGTGAATAAGCTGAAAATATAAG
16168 TTAGTGAATAAGCTGAAAATATAAG
1 TTAGTGAATAAGCTGAAAATATAAG
*
16193 CTAGTGAA
1 TTAGTGAA
16201 ATATGCCCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.28
Consensus pattern (25 bp):
TTAGTGAATAAGCTGAAAATATAAG
Found at i:17271 original size:19 final size:19
Alignment explanation
Indices: 17222--17304 Score: 85
Period size: 19 Copynumber: 4.4 Consensus size: 19
17212 TGCATTGTGC
**
17222 TATGAATTTGAAAATAACA
1 TATGAATTTGAAAATAAGT
* * *
17241 TATAAATATGAAATTAAGT
1 TATGAATTTGAAAATAAGT
17260 TATGAATTTGAAAATAAGT
1 TATGAATTTGAAAATAAGT
* **
17279 TATGAGTCCGAAAATAAGT
1 TATGAATTTGAAAATAAGT
*
17298 TCTGAAT
1 TATGAAT
17305 CTGAGAATGA
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (19 bp):
TATGAATTTGAAAATAAGT
Found at i:17297 original size:38 final size:38
Alignment explanation
Indices: 17222--17304 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 38
17212 TGCATTGTGC
* *
17222 TATGAATTTGAAAATAACATATAAATATGAAATTAAGT
1 TATGAATTTGAAAATAACATATAAATACGAAAATAAGT
** * * *
17260 TATGAATTTGAAAATAAGTTATGAGTCCGAAAATAAGT
1 TATGAATTTGAAAATAACATATAAATACGAAAATAAGT
*
17298 TCTGAAT
1 TATGAAT
17305 CTGAGAATGA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (38 bp):
TATGAATTTGAAAATAACATATAAATACGAAAATAAGT
Found at i:17436 original size:39 final size:39
Alignment explanation
Indices: 17388--17470 Score: 132
Period size: 39 Copynumber: 2.1 Consensus size: 39
17378 AAAAATAATA
*
17388 TGATATGACTATTATGT-ATGATATTGTTTATCATGGCTT
1 TGATATGACTATTATGTAAT-ATATTATTTATCATGGCTT
*
17427 TGATATGACTATTATGTAATATATTATTTATCATGGTTT
1 TGATATGACTATTATGTAATATATTATTTATCATGGCTT
17466 TGATA
1 TGATA
17471 AAATCATGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 39 0.95
40 2 0.05
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (39 bp):
TGATATGACTATTATGTAATATATTATTTATCATGGCTT
Found at i:18584 original size:11 final size:11
Alignment explanation
Indices: 18568--18592 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18558 AGTAATATTT
18568 TTATTAAAATA
1 TTATTAAAATA
18579 TTATTAAAATA
1 TTATTAAAATA
18590 TTA
1 TTA
18593 AATAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTATTAAAATA
Found at i:24756 original size:18 final size:16
Alignment explanation
Indices: 24733--24778 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 16
24723 TGTTTATGAG
*
24733 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTAT--A
24751 GGAATTGGAATCTATA
1 GGAATTGGAATCTATA
24767 GGAATTGGAATC
1 GGAATTGGAATC
24779 AAATTCTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 13 0.48
18 14 0.52
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (16 bp):
GGAATTGGAATCTATA
Found at i:25422 original size:37 final size:38
Alignment explanation
Indices: 25351--25424 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 38
25341 ACCCTGAACC
* *
25351 CGACCCGAATATCACACATAAAAAAACCCGACCCGACT
1 CGACCCAAATATCACACATAAAAAAACCCAACCCGACT
*
25389 CGACCCAAATATCACAC-TTAAAAAACCCAACCCGAC
1 CGACCCAAATATCACACATAAAAAAACCCAACCCGAC
25425 CCGAATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 17 0.52
38 16 0.48
ACGTcount: A:0.43, C:0.38, G:0.08, T:0.11
Consensus pattern (38 bp):
CGACCCAAATATCACACATAAAAAAACCCAACCCGACT
Found at i:25436 original size:37 final size:38
Alignment explanation
Indices: 25358--25436 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
25348 ACCCGACCCG
* * * *
25358 AATATCACACATAAAAAAACCCGACCCGACTCGACCCA
1 AATATCACACATAAAAAAACCCAACCCGACCCGAACAA
* *
25396 AATATCACAC-TTAAAAAACCCAACCCGACCCGAATAA
1 AATATCACACATAAAAAAACCCAACCCGACCCGAACAA
25433 AATA
1 AATA
25437 AAGTTTCATT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
37 25 0.71
38 10 0.29
ACGTcount: A:0.48, C:0.33, G:0.06, T:0.13
Consensus pattern (38 bp):
AATATCACACATAAAAAAACCCAACCCGACCCGAACAA
Found at i:25632 original size:32 final size:33
Alignment explanation
Indices: 25560--25636 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
25550 TTCACCCTAA
* *
25560 ACCCGACCCGAATATCACACTTAAAAAAATCTG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG
*
25593 ACCCGACCTGAATATCACACTT-AAAAAACCCG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG
*
25625 ACTCGACCCGAA
1 ACCCGACCCGAA
25637 ATAATAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
32 18 0.46
33 21 0.54
ACGTcount: A:0.40, C:0.34, G:0.10, T:0.16
Consensus pattern (33 bp):
ACCCGACCCGAATATCACACTTAAAAAAACCCG
Found at i:25688 original size:175 final size:180
Alignment explanation
Indices: 25447--25815 Score: 572
Period size: 175 Copynumber: 2.0 Consensus size: 180
25437 AAGTTTCATT
* *
25447 CGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAATAGTGACTTAATCCTACCCG
1 CGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCG
25512 ACCCGAATTATATATATTTTCGGGTCGATCCGT-TTTTTTTCACCCT-A-AACCCGACCCGAATA
66 ACCCGAATTATATATATTTTCGGGTCGATCC-TATTTTTTT-ACCCTAACAACCCGACCCGAATA
*
25574 TCACACTTAAAAAAATCTGA-C-C-CGACCTGAATATCACACTTAAAAAACC
129 TCACACTTAAAAAAACCTGACCACTCGACCTGAATATCACACTTAAAAAACC
*
25623 CGACTCGACCCGAAATAAT-AAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCG
1 CGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCG
*
25687 ACCCGAATTATATATATTTTCGGGTCGGTCCTATTTTTTTACCCTAAACCCGAACCCGACCCGAA
66 ACCCGAATTATATATATTTTCGGGTCGATCCTATTTTTTTACCCT-AA--C-AACCCGACCCGAA
25752 TATCACACTTAAAAAAACCTGACCCGACTCGACCTGAATATCACACTTAAAAAACC
127 TATCACACTTAAAAAAACCTGA-CC-ACTCGACCTGAATATCACACTTAAAAAACC
25808 CGACCCGA
1 CGACCCGA
25816 ACAAAATAAA
Statistics
Matches: 175, Mismatches: 6, Indels: 15
0.89 0.03 0.08
Matches are distributed among these distances:
174 6 0.03
175 80 0.46
176 19 0.11
180 34 0.19
182 1 0.01
184 1 0.01
185 34 0.19
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (180 bp):
CGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCG
ACCCGAATTATATATATTTTCGGGTCGATCCTATTTTTTTACCCTAACAACCCGACCCGAATATC
ACACTTAAAAAAACCTGACCACTCGACCTGAATATCACACTTAAAAAACC
Found at i:25813 original size:37 final size:38
Alignment explanation
Indices: 25734--25815 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 38
25724 TTTACCCTAA
*
25734 ACCCGAACCCGACCCGAATATCACACTTAAAAAAACCTG
1 ACCCG-ACCCGACCCGAATATCACACTTAAAAAAACCCG
* *
25773 ACCCGACTCGACCTGAATATCACACTT-AAAAAACCCG
1 ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCG
25810 ACCCGA
1 ACCCGA
25816 ACAAAATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
37 15 0.38
38 20 0.50
39 5 0.12
ACGTcount: A:0.39, C:0.37, G:0.11, T:0.13
Consensus pattern (38 bp):
ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCG
Found at i:27982 original size:43 final size:43
Alignment explanation
Indices: 27917--28004 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
27907 AAAAAATACA
* * * *
27917 GCAAAAGGTCAATATCTATAGCGACATTTTCGATACAAACGCC
1 GCAAAAGGTCAAGATCTATAGCGACATTTTAGAAACAAACACC
* * * *
27960 GCAAAAGGTCAAGCTTTGTAGCGGCATTTTAGAAACAAACACC
1 GCAAAAGGTCAAGATCTATAGCGACATTTTAGAAACAAACACC
28003 GC
1 GC
28005 TGATTACCTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (43 bp):
GCAAAAGGTCAAGATCTATAGCGACATTTTAGAAACAAACACC
Found at i:32399 original size:34 final size:34
Alignment explanation
Indices: 32356--32460 Score: 201
Period size: 34 Copynumber: 3.1 Consensus size: 34
32346 CCATAGAAGG
32356 TTGAGTCTATTGATCGGATAATCAATTGATATGT
1 TTGAGTCTATTGATCGGATAATCAATTGATATGT
32390 TTGAGTCTATTGATCGGATAATCAATTGATATGT
1 TTGAGTCTATTGATCGGATAATCAATTGATATGT
*
32424 TTGAGTTTATTGATCGGATAATCAATTGATATGT
1 TTGAGTCTATTGATCGGATAATCAATTGATATGT
32458 TTG
1 TTG
32461 GTACATGATT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 70 1.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.43
Consensus pattern (34 bp):
TTGAGTCTATTGATCGGATAATCAATTGATATGT
Found at i:33015 original size:51 final size:51
Alignment explanation
Indices: 32896--33003 Score: 209
Period size: 51 Copynumber: 2.1 Consensus size: 51
32886 CGATCGTTGG
32896 GTGTCGGTTGTTTCCAACTTTCGATCACTTTGCTTTTGCTTAGCTTCTTTC
1 GTGTCGGTTGTTTCCAACTTTCGATCACTTTGCTTTTGCTTAGCTTCTTTC
32947 GTGTCGGTTGTTTCCAACTTTCGATCACTTTGCTTTTGCTT-GCTTCTTTC
1 GTGTCGGTTGTTTCCAACTTTCGATCACTTTGCTTTTGCTTAGCTTCTTTC
32997 GTGTCGG
1 GTGTCGG
33004 GGTGTTCCCA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 16 0.28
51 41 0.72
ACGTcount: A:0.08, C:0.23, G:0.20, T:0.48
Consensus pattern (51 bp):
GTGTCGGTTGTTTCCAACTTTCGATCACTTTGCTTTTGCTTAGCTTCTTTC
Found at i:36118 original size:21 final size:21
Alignment explanation
Indices: 36094--36142 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
36084 TATGTATTCC
36094 ACCTCTAAATAATATTTCAAG
1 ACCTCTAAATAATATTTCAAG
36115 ACCTCTAAATAATATTTCAAG
1 ACCTCTAAATAATATTTCAAG
36136 ACCTCTA
1 ACCTCTA
36143 CAATCAAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (21 bp):
ACCTCTAAATAATATTTCAAG
Found at i:41108 original size:23 final size:23
Alignment explanation
Indices: 41078--41128 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
41068 CCTAAACATG
41078 TCCATGGTTGCTGGACCACTGTT
1 TCCATGGTTGCTGGACCACTGTT
41101 TCCATGGTTGCTGGACCACTGTT
1 TCCATGGTTGCTGGACCACTGTT
41124 TCCAT
1 TCCAT
41129 CAATGTAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.14, C:0.27, G:0.24, T:0.35
Consensus pattern (23 bp):
TCCATGGTTGCTGGACCACTGTT
Found at i:57756 original size:18 final size:18
Alignment explanation
Indices: 57733--57782 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
57723 ACCTCAAATT
57733 AATTTTTGGTGTCTAAAG
1 AATTTTTGGTGTCTAAAG
**
57751 AATTTTT--TGT-TAATT
1 AATTTTTGGTGTCTAAAG
*
57766 TATTTTTGGTGTCTAAA
1 AATTTTTGGTGTCTAAA
57783 CTATAGCTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
15 9 0.36
16 3 0.12
17 3 0.12
18 10 0.40
ACGTcount: A:0.26, C:0.04, G:0.16, T:0.54
Consensus pattern (18 bp):
AATTTTTGGTGTCTAAAG
Found at i:58064 original size:31 final size:31
Alignment explanation
Indices: 58029--58095 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
58019 GAAAAAATTC
* *
58029 TTTAGACACTAAAAATCAATTTAAGGTATAG
1 TTTAGACACCAAAAATCAATTTAAGGTATAA
* * *
58060 TTTAGATACCAAAAGTTAATTTAAGGTATAA
1 TTTAGACACCAAAAATCAATTTAAGGTATAA
58091 TTTAG
1 TTTAG
58096 TAACCTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.36
Consensus pattern (31 bp):
TTTAGACACCAAAAATCAATTTAAGGTATAA
Found at i:66100 original size:15 final size:16
Alignment explanation
Indices: 66071--66107 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
66061 TTAAAATTAT
66071 TTTATAATATTAAATA
1 TTTATAATATTAAATA
66087 TTTATAAT-TTAAATA
1 TTTATAATATTAAATA
66102 TCTTAT
1 T-TTAT
66108 CTATAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTATAATATTAAATA
Found at i:72726 original size:42 final size:42
Alignment explanation
Indices: 72634--72779 Score: 222
Period size: 42 Copynumber: 3.5 Consensus size: 42
72624 TTACCTAGGC
* * * * *
72634 AGATGATACGAATACTTGTGTGAGAAT-ATTTGTAACGAGGC
1 AGATGATATGAATACTTGTGTGAGTATAATCTGTAACAAGGT
*
72675 AGATTATATGAATACTTGTGTGAGTATAATCTGTAACAAGGT
1 AGATGATATGAATACTTGTGTGAGTATAATCTGTAACAAGGT
72717 AGATGATATGAATACTTGTGTGAGTATAATCTGTAACAAGGT
1 AGATGATATGAATACTTGTGTGAGTATAATCTGTAACAAGGT
*
72759 AGAAGATATGAATACTTGTGT
1 AGATGATATGAATACTTGTGT
72780 ATCTTCAAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
41 24 0.25
42 72 0.75
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.33
Consensus pattern (42 bp):
AGATGATATGAATACTTGTGTGAGTATAATCTGTAACAAGGT
Found at i:82030 original size:21 final size:21
Alignment explanation
Indices: 82004--82043 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
81994 TCTACTGAAA
* *
82004 CTCCACCTGTTTTGGAGTATG
1 CTCCACCTGCTGTGGAGTATG
82025 CTCCACCTGCTGTGGAGTA
1 CTCCACCTGCTGTGGAGTA
82044 CTACTTGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.28, G:0.25, T:0.33
Consensus pattern (21 bp):
CTCCACCTGCTGTGGAGTATG
Found at i:85086 original size:21 final size:24
Alignment explanation
Indices: 85043--85104 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
85033 AAATACAATG
85043 AATAATATTATTTATTAACAAATT
1 AATAATATTATTTATTAACAAATT
*
85067 AATATTATTATTT-TTAA-AATATT
1 AATAATATTATTTATTAACAA-ATT
85090 AGAATAAT-TTATTTA
1 --AATAATATTATTTA
85105 ATATTATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 2 0.06
23 7 0.22
24 18 0.56
25 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
AATAATATTATTTATTAACAAATT
Found at i:85221 original size:37 final size:36
Alignment explanation
Indices: 85180--85250 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 36
85170 ATTATTATAT
*
85180 TTTATTAAAATAA-AATAATTA-TAAATTATATTAATTA
1 TTTATTAAAACAATAAT-ATTATTAAA--ATATTAATTA
85217 TTTATTAAAACAATAATATTATTAAAATATTAAT
1 TTTATTAAAACAATAATATTATTAAAATATTAAT
85251 ATAAGAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
36 8 0.26
37 16 0.52
38 7 0.23
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (36 bp):
TTTATTAAAACAATAATATTATTAAAATATTAATTA
Found at i:85429 original size:32 final size:29
Alignment explanation
Indices: 85389--85470 Score: 78
Period size: 32 Copynumber: 2.7 Consensus size: 29
85379 GTATAATAGC
85389 ATATATTATAATAATATAATTATAACAATACA
1 ATATATTATAATAATATAATTAT--CAATA-A
* *
85421 ATATATTATATATTATTAAAATTATCAATAA
1 ATATATTATA-A-TAATATAATTATCAATAA
85452 ATATAATT-TAATAAT-TAAT
1 ATAT-ATTATAATAATATAAT
85471 ATTTTTATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
28 3 0.07
29 3 0.07
30 1 0.02
31 7 0.16
32 18 0.42
33 1 0.02
34 10 0.23
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATATTATAATAATATAATTATCAATAA
Found at i:91722 original size:21 final size:22
Alignment explanation
Indices: 91698--91747 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
91688 TTTTAATTTT
** *
91698 CATTTTAGATA-ACGAAATTAA
1 CATTTTAGATAGAAAAAAATAA
*
91719 CATTTTTGATAGAAAAAAATAA
1 CATTTTAGATAGAAAAAAATAA
91741 CATTTTA
1 CATTTTA
91748 AGTAACGTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (22 bp):
CATTTTAGATAGAAAAAAATAA
Found at i:95948 original size:24 final size:24
Alignment explanation
Indices: 95920--95987 Score: 136
Period size: 24 Copynumber: 2.8 Consensus size: 24
95910 ATGCATTATA
95920 TTTAATTTAACTAGTTAAAATCTT
1 TTTAATTTAACTAGTTAAAATCTT
95944 TTTAATTTAACTAGTTAAAATCTT
1 TTTAATTTAACTAGTTAAAATCTT
95968 TTTAATTTAACTAGTTAAAA
1 TTTAATTTAACTAGTTAAAA
95988 AGAAATATAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (24 bp):
TTTAATTTAACTAGTTAAAATCTT
Found at i:98793 original size:23 final size:23
Alignment explanation
Indices: 98767--98811 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
98757 ACATGTACAA
*
98767 TAATCCGATTAAGGACTTAATAG
1 TAATCCCATTAAGGACTTAATAG
98790 TAATCCCATTAAGGACTTAATA
1 TAATCCCATTAAGGACTTAATA
98812 ATAGCATAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (23 bp):
TAATCCCATTAAGGACTTAATAG
Found at i:107989 original size:12 final size:12
Alignment explanation
Indices: 107972--107997 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
107962 CTAATCTGAG
107972 ACCGACCCCAAC
1 ACCGACCCCAAC
107984 ACCGACCCCAAC
1 ACCGACCCCAAC
107996 AC
1 AC
107998 TTAAAGCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.58, G:0.08, T:0.00
Consensus pattern (12 bp):
ACCGACCCCAAC
Found at i:113675 original size:36 final size:36
Alignment explanation
Indices: 113549--113768 Score: 133
Period size: 38 Copynumber: 5.9 Consensus size: 36
113539 AATACATAAA
* *
113549 ATTTATCTC-ACTTGAGATTGTTTTTCTTAAAACCAG
1 ATTTATCTCGA-TTGAGATAGTTTTTCTTAAAACAAG
* ** * *
113585 ATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAG
1 A-TTTATCTCGATTGAGATAGTTTTTCT-TAAA-ACAAG
* *
113624 ATTTAGCTC-ACTTGAGATTGTTTTTCTTAAAACAAG
1 ATTTATCTCGA-TTGAGATAGTTTTTCTTAAAACAAG
* ** ** *
113660 ATTCATCTCGATTGAGATAGTTTCACTCGAAACAAA
1 ATTTATCTCGATTGAGATAGTTTTTCTTAAAACAAG
* * *
113696 ATTTTTTATCTC-ACTTGAGATAGTTTCTCTCGAAACATAAG
1 A---TTTATCTCGA-TTGAGATAGTTTTTCT-TAAA-ACAAG
*
113737 ATTTATCTC-ACTTGAGATTGTTTTTCTTAAAA
1 ATTTATCTCGA-TTGAGATAGTTTTTCTTAAAA
113769 TAAACTACGC
Statistics
Matches: 141, Mismatches: 31, Indels: 24
0.72 0.16 0.12
Matches are distributed among these distances:
36 33 0.23
37 28 0.20
38 48 0.34
39 26 0.18
40 2 0.01
41 4 0.03
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.40
Consensus pattern (36 bp):
ATTTATCTCGATTGAGATAGTTTTTCTTAAAACAAG
Found at i:113709 original size:75 final size:75
Alignment explanation
Indices: 113549--113721 Score: 258
Period size: 75 Copynumber: 2.3 Consensus size: 75
113539 AATACATAAA
* * *
113549 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACCAGATTTTATCTCGCTTGAGATAGTTTCACTC
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTTCATCTCGATTGAGATAGTTTCACTC
*
113614 GAAACAGAAG
66 GAAACAAAAG
*
113624 ATTTAGCTCACTTGAGATTGTTTTTCTTAAAACAAGA-TTCATCTCGATTGAGATAGTTTCACTC
1 ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTTCATCTCGATTGAGATAGTTTCACTC
*
113688 GAAACAAAATT
66 GAAACAAAA-G
* *
113699 TTTTATCTCACTTGAGATAGTTT
1 ATTTATCTCACTTGAGATTGTTT
113722 CTCTCGAAAC
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
74 33 0.38
75 55 0.62
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (75 bp):
ATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTTCATCTCGATTGAGATAGTTTCACTC
GAAACAAAAG
Found at i:113714 original size:39 final size:38
Alignment explanation
Indices: 113587--113759 Score: 181
Period size: 38 Copynumber: 4.6 Consensus size: 38
113577 AAAACCAGAT
* *
113587 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA
1 TTTATCTCACTTGAGATAGTTTCACTCGAAACAAAAGA
* * ** * *
113625 TTTAGCTCACTTGAGATTGTTTTTCT-TAAA-ACAAGA
1 TTTATCTCACTTGAGATAGTTTCACTCGAAACAAAAGA
* **
113661 TTCATCTCGA-TTGAGATAGTTTCACTCGAAACAAAATTT
1 TTTATCTC-ACTTGAGATAGTTTCACTCGAAACAAAA-GA
* *
113700 TTTATCTCACTTGAGATAGTTTCTCTCGAAACATAAGA
1 TTTATCTCACTTGAGATAGTTTCACTCGAAACAAAAGA
*
113738 TTTATCTCACTTGAGATTGTTT
1 TTTATCTCACTTGAGATAGTTT
113760 TTCTTAAAAT
Statistics
Matches: 108, Mismatches: 22, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
36 24 0.22
37 7 0.06
38 46 0.43
39 31 0.29
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (38 bp):
TTTATCTCACTTGAGATAGTTTCACTCGAAACAAAAGA
Found at i:113848 original size:59 final size:59
Alignment explanation
Indices: 113775--114050 Score: 340
Period size: 59 Copynumber: 4.7 Consensus size: 59
113765 AAAATAAACT
* * * * * *
113775 ACGCCTCACATGAGGGATTAACATTTTATTTGCTCTATTCATAACACATCGAATCAGCA
1 ACGCCTCACTTGAGGGATCAACATTTTCTTTGCTCGATTCACAACACTTCGAATCAGCA
* * * * *
113834 ACGCCTCACGTGAGGGATTAACA-TTTCTTTTGCTCGATTTACAATACTTCGAATCAACA
1 ACGCCTCACTTGAGGGATCAACATTTTC-TTTGCTCGATTCACAACACTTCGAATCAGCA
* * * * *
113893 ATGCCTCACTTGAGGGATCAATATTTCCTTTGCTCGATTCACAACACTTCGAATTAGTA
1 ACGCCTCACTTGAGGGATCAACATTTTCTTTGCTCGATTCACAACACTTCGAATCAGCA
* * * *
113952 AAGCCTCACTTGAGAGATCAACATTTTCTTCGCTCGATTCACAGCACTTCGAATCAGCA
1 ACGCCTCACTTGAGGGATCAACATTTTCTTTGCTCGATTCACAACACTTCGAATCAGCA
*
114011 ACGCCTCACTTGAGGGATCAACATTTCCTTTGCTC-ATTCA
1 ACGCCTCACTTGAGGGATCAACATTTTCTTTGCTCGATTCA
114051 TGGTATTTCG
Statistics
Matches: 185, Mismatches: 30, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
58 8 0.04
59 174 0.94
60 3 0.02
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (59 bp):
ACGCCTCACTTGAGGGATCAACATTTTCTTTGCTCGATTCACAACACTTCGAATCAGCA
Found at i:115689 original size:16 final size:16
Alignment explanation
Indices: 115665--115695 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
115655 AATTTAGTCC
115665 TTTAATTTATTTTTAT
1 TTTAATTTATTTTTAT
*
115681 TTTATTTTATTTTTA
1 TTTAATTTATTTTTA
115696 CCCTTCATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTAATTTATTTTTAT
Found at i:116933 original size:17 final size:17
Alignment explanation
Indices: 116911--116945 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
116901 CAATCTCAAA
116911 TAATATATTATATGTAT
1 TAATATATTATATGTAT
116928 TAATATATTATATGTAT
1 TAATATATTATATGTAT
116945 T
1 T
116946 GTCTTATTTA
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:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TAATATATTATATGTAT
Found at i:120755 original size:14 final size:14
Alignment explanation
Indices: 120736--120767 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
120726 AGCTATAGTA
120736 TATTATCATAAATT
1 TATTATCATAAATT
*
120750 TATTATCATAACTT
1 TATTATCATAAATT
120764 TATT
1 TATT
120768 TCAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTATCATAAATT
Found at i:122256 original size:19 final size:19
Alignment explanation
Indices: 122228--122265 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
122218 GTGATTTTGA
*
122228 AAAATATGTTGCGATAGTT
1 AAAATATGTTGCGAGAGTT
*
122247 AAAATGTGTTGCGAGAGTT
1 AAAATATGTTGCGAGAGTT
122266 TGAAAAACGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.34
Consensus pattern (19 bp):
AAAATATGTTGCGAGAGTT
Found at i:122281 original size:25 final size:22
Alignment explanation
Indices: 122253--122301 Score: 62
Period size: 25 Copynumber: 2.1 Consensus size: 22
122243 AGTTAAAATG
122253 TGTTGCGAGAGTTTGAAAAACGTAT
1 TGTTGCGAGAG--TGAAAAA-GTAT
*
122278 TGTTGCGATAGTGAAAAAGTAT
1 TGTTGCGAGAGTGAAAAAGTAT
122300 TG
1 TG
122302 CGATAGTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 7 0.30
25 10 0.43
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.33
Consensus pattern (22 bp):
TGTTGCGAGAGTGAAAAAGTAT
Found at i:122286 original size:44 final size:41
Alignment explanation
Indices: 122223--122304 Score: 110
Period size: 44 Copynumber: 1.9 Consensus size: 41
122213 GCAACGTGAT
* * *
122223 TTTGAAAAATATGTTGCGATAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAATATGTTGCGATAGTGAAAAAGTATTGCGAGAG
122264 TTTGAAAAACGTATTGTTGCGATAGTGAAAAAGTATTGCGA
1 TTTGAAAAA--TA-TGTTGCGATAGTGAAAAAGTATTGCGA
122305 TAGTGAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 9 0.26
43 2 0.06
44 24 0.69
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.33
Consensus pattern (41 bp):
TTTGAAAAATATGTTGCGATAGTGAAAAAGTATTGCGAGAG
Found at i:122710 original size:20 final size:20
Alignment explanation
Indices: 122687--122738 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
122677 GCGATAGTCA
122687 AAATCGCGTTGCGA-ATCTGG
1 AAATCGCGTTGCGATA-CTGG
* **
122707 AAATTGATTTGCGATACTGG
1 AAATCGCGTTGCGATACTGG
*
122727 AGATCGCGTTGC
1 AAATCGCGTTGC
122739 AATTTAGAGA
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (20 bp):
AAATCGCGTTGCGATACTGG
Found at i:122750 original size:19 final size:19
Alignment explanation
Indices: 122726--122762 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
122716 TGCGATACTG
*
122726 GAGATCGCGTTGCAATTTA
1 GAGATCGCATTGCAATTTA
122745 GAGATCGCATTGCAATTT
1 GAGATCGCATTGCAATTT
122763 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCAATTTA
Found at i:128914 original size:22 final size:22
Alignment explanation
Indices: 128886--128944 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
128876 AAGGTTTACT
*
128886 ATTTTGATAATTATTTTATAAC
1 ATTTTGATAATAATTTTATAAC
* *
128908 ATTTTGATAA-AATTTAATAATT
1 ATTTTGATAATAATTTTATAA-C
128930 ATTTTG-TAATAATTT
1 ATTTTGATAATAATTT
128945 GATAGATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 11 0.34
22 21 0.66
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (22 bp):
ATTTTGATAATAATTTTATAAC
Found at i:128957 original size:31 final size:32
Alignment explanation
Indices: 128892--128968 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
128882 TACTATTTTG
*
128892 ATAATTATTTTATAACATTTTGATAAAATTTA
1 ATAATTATTTTATAACAATTTGATAAAATTTA
* * *
128924 ATAATTATTTTGTAATAATTTGAT-AGATTTA
1 ATAATTATTTTATAACAATTTGATAAAATTTA
128955 ATAATTATTTTATA
1 ATAATTATTTTATA
128969 TTTTTAAAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 19 0.47
32 21 0.52
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (32 bp):
ATAATTATTTTATAACAATTTGATAAAATTTA
Found at i:131589 original size:121 final size:116
Alignment explanation
Indices: 131320--131616 Score: 316
Period size: 115 Copynumber: 2.5 Consensus size: 116
131310 AAGTATGTAA
* * * * * * * *
131320 TTAGTACTTAAATTATCAGTTTTGATCT-TTTTAGTAACTAAACTTTCAATTTTTCCAAAATCAT
1 TTAGTACCTAAACTATCAATTTTGGTTTCTTTTAGTACCTAAACTTTAAATTTTTTCAAAATCAT
* * * **
131384 ACTTACCGTTTAGTTTCATTTTAGTACCTTGTCATTAAAAACTTAACGTGT
66 ACGTAACATTTAGTTTCATTTTAGTACCTTGTCATTAAAAAAATAACGTGT
*
131435 TTAGTACTTAAACTATCAATTTTGGTTTCTTTTAGTACCTAAACTTT-AATTTTTTCAAAATCAT
1 TTAGTACCTAAACTATCAATTTTGGTTTCTTTTAGTACCTAAACTTTAAATTTTTTCAAAATCAT
* *
131499 ACGTAACATTTAGTTTTCATTTCATTTTAGTATC-TG-CTATTAAAAAAATAACTTGT
66 ACGTAACATTTAG------TTTCATTTTAGTACCTTGTC-ATTAAAAAAATAACGTGT
* *
131555 TTAGTACCTAACCTATCAATTTTTGG-TTCATTTTAGTACCTAAACTTTAAATTTTTTTAAAA
1 TTAGTACCTAAACTATCAA-TTTTGGTTTC-TTTTAGTACCTAAACTTTAAATTTTTTCAAAA
131617 CTTAACGCTA
Statistics
Matches: 155, Mismatches: 16, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
115 50 0.32
116 17 0.11
119 1 0.01
120 37 0.24
121 38 0.25
122 12 0.08
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (116 bp):
TTAGTACCTAAACTATCAATTTTGGTTTCTTTTAGTACCTAAACTTTAAATTTTTTCAAAATCAT
ACGTAACATTTAGTTTCATTTTAGTACCTTGTCATTAAAAAAATAACGTGT
Found at i:143515 original size:2 final size:2
Alignment explanation
Indices: 143508--143539 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
143498 TAGCAATCTA
143508 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
143540 TGCCTCATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:151590 original size:17 final size:15
Alignment explanation
Indices: 151568--151611 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
151558 ATTTTTTTGA
151568 TTCGGTTCGGTTTTT
1 TTCGGTTCGGTTTTT
*
151583 TTAACGGTTCGG-ATTT
1 TT--CGGTTCGGTTTTT
151599 TTCGGTTCGGTTT
1 TTCGGTTCGGTTT
151612 GGTTTATCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 8 0.33
15 3 0.12
16 5 0.21
17 8 0.33
ACGTcount: A:0.07, C:0.14, G:0.27, T:0.52
Consensus pattern (15 bp):
TTCGGTTCGGTTTTT
Found at i:153829 original size:42 final size:42
Alignment explanation
Indices: 153777--153857 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
153767 ATTAAACGGA
* * * *
153777 GACGGGAAAAAACCGTTTATGCTAAACGGGGACGGGGACAGG
1 GACGGAAAAAAAACATTTATGCTAAACGGAGACGGGGACAGG
153819 GACGGAAAAAAAACATTTATGCTAAACGGAGACGGGGAC
1 GACGGAAAAAAAACATTTATGCTAAACGGAGACGGGGAC
153858 GGGTTTGGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.38, C:0.16, G:0.33, T:0.12
Consensus pattern (42 bp):
GACGGAAAAAAAACATTTATGCTAAACGGAGACGGGGACAGG
Found at i:153972 original size:42 final size:42
Alignment explanation
Indices: 153920--154017 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
153910 TATTAAAAAT
*
153920 AATTATTATATATATATATATAATATTAATAAATTTAATTAA
1 AATTAATATATATATATATATAATATTAATAAATTTAATTAA
* * *
153962 AATTAATATATATATATATATAATATTTATATATTTAATTTA
1 AATTAATATATATATATATATAATATTAATAAATTTAATTAA
154004 AA-T-ATATATATATA
1 AATTAATATATATATA
154018 ATCGGCCTGA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 11 0.21
41 1 0.02
42 40 0.77
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (42 bp):
AATTAATATATATATATATATAATATTAATAAATTTAATTAA
Found at i:153974 original size:2 final size:2
Alignment explanation
Indices: 153967--154017 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
153957 ATTAAAATTA
* * * *
153967 AT AT AT AT AT AT AT AT A- AT AT TT AT AT AT TT A- AT TT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
154007 AT AT AT AT AT A
1 AT AT AT AT AT A
154018 ATCGGCCTGA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:153987 original size:17 final size:17
Alignment explanation
Indices: 153965--154015 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
153955 TAATTAAAAT
153965 TAATATATATATATATA
1 TAATATATATATATATA
*
153982 TAATAT-T-TATATATT
1 TAATATATATATATATA
* *
153997 TAATTTAAATATATATA
1 TAATATATATATATATA
154014 TA
1 TA
154016 TAATCGGCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
16 1 0.04
17 15 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATATATATATATATA
Found at i:155816 original size:24 final size:24
Alignment explanation
Indices: 155787--155869 Score: 121
Period size: 24 Copynumber: 3.5 Consensus size: 24
155777 AACACAAATG
* * * *
155787 AACGAACATAAACGAACGGATGTA
1 AACGAACACAAATGAACGAACGTA
*
155811 AGCGAACACAAATGAACGAACGTA
1 AACGAACACAAATGAACGAACGTA
155835 AACGAACACAAATGAACGAACGTA
1 AACGAACACAAATGAACGAACGTA
155859 AACGAACACAA
1 AACGAACACAA
155870 TAAATGAACA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.53, C:0.20, G:0.18, T:0.08
Consensus pattern (24 bp):
AACGAACACAAATGAACGAACGTA
Found at i:155855 original size:38 final size:37
Alignment explanation
Indices: 155773--155855 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 37
155763 TTAAATGATA
**
155773 AACGAACACAAATGAACGAACATAAACGAACGGATGT
1 AACGAACACAAATGAACGAACATAAACGAACAAATGT
*
155810 AAGCGAACACAAATGAACGAACGTAAACGAACACAAATG-
1 AA-CGAACACAAATGAACGAACATAAACG-A-ACAAATGT
155849 AACGAAC
1 AACGAAC
155856 GTAAACGAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
37 2 0.05
38 30 0.75
39 3 0.08
40 5 0.12
ACGTcount: A:0.53, C:0.20, G:0.18, T:0.08
Consensus pattern (37 bp):
AACGAACACAAATGAACGAACATAAACGAACAAATGT
Found at i:155865 original size:14 final size:14
Alignment explanation
Indices: 155786--155865 Score: 50
Period size: 14 Copynumber: 6.3 Consensus size: 14
155776 GAACACAAAT
*
155786 GAACGAACATAAAC
1 GAACGAACGTAAAC
* * *
155800 GAACGGATGTAAGC
1 GAACGAACGTAAAC
*
155814 GAAC--AC--AAAT
1 GAACGAACGTAAAC
155824 GAACGAACGTAAAC
1 GAACGAACGTAAAC
*
155838 GAAC--AC--AAAT
1 GAACGAACGTAAAC
155848 GAACGAACGTAAAC
1 GAACGAACGTAAAC
155862 GAAC
1 GAAC
155866 ACAATAAATG
Statistics
Matches: 48, Mismatches: 10, Indels: 16
0.65 0.14 0.22
Matches are distributed among these distances:
10 13 0.27
12 7 0.15
14 28 0.58
ACGTcount: A:0.51, C:0.20, G:0.20, T:0.09
Consensus pattern (14 bp):
GAACGAACGTAAAC
Found at i:156090 original size:34 final size:34
Alignment explanation
Indices: 156051--156116 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
156041 AAGATTGAGC
* * *
156051 TAAACATAAATGAACGCACTTAAACGAACATAAA
1 TAAACATAAATGAACGAACATAAACAAACATAAA
*
156085 TAAACATAAATGAATGAACATAAACAAACATA
1 TAAACATAAATGAACGAACATAAACAAACATA
156117 TTACCAAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.59, C:0.15, G:0.08, T:0.18
Consensus pattern (34 bp):
TAAACATAAATGAACGAACATAAACAAACATAAA
Found at i:158667 original size:38 final size:36
Alignment explanation
Indices: 158594--158668 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 36
158584 GTTGGAAAAT
*
158594 ATTTATATATTTTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
* *
158630 ATTTATATAATTTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-A-TTTTCTTTAAAAAATT-AAAATCATAAA
158668 A
1 A
158669 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 8 0.24
37 1 0.03
38 20 0.61
39 4 0.12
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAAATTAAAATCATAAA
Found at i:159772 original size:23 final size:23
Alignment explanation
Indices: 159746--159811 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
159736 CTGAATGATT
159746 CAGTGTTGACTGATTCAGCAAAA
1 CAGTGTTGACTGATTCAGCAAAA
159769 CAGTGTTGACTGATTCAGCAAAA
1 CAGTGTTGACTGATTCAGCAAAA
* *
159792 CAGTGCTGAATGATTCAGCA
1 CAGTGTTGACTGATTCAGCA
159812 CAGAAATACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (23 bp):
CAGTGTTGACTGATTCAGCAAAA
Found at i:159835 original size:27 final size:27
Alignment explanation
Indices: 159797--159863 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
159787 CAAAACAGTG
*
159797 CTGAATGATTCAGCACAGAAATACATT
1 CTGAATGATTCAGCACAAAAATACATT
159824 CTGAATGATTCAGCACAAAAATACATT
1 CTGAATGATTCAGCACAAAAATACATT
159851 CTGAATGATTCAG
1 CTGAATGATTCAG
159864 AGCCATTATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (27 bp):
CTGAATGATTCAGCACAAAAATACATT
Found at i:160080 original size:16 final size:18
Alignment explanation
Indices: 160046--160085 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
160036 TTGGTGATTA
*
160046 AAATAGAAATACTTTAAT
1 AAATAGAAATACTTAAAT
160064 AAATAG-AATA-TTAAAT
1 AAATAGAAATACTTAAAT
160080 AAATAG
1 AAATAG
160086 TTTATTCTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
17 4 0.19
18 6 0.29
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (18 bp):
AAATAGAAATACTTAAAT
Found at i:164338 original size:31 final size:31
Alignment explanation
Indices: 164277--164343 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 31
164267 TTGAAGATCG
*
164277 TTTTATAACATTTCAATAAATTATAATGATAA
1 TTTTATAACATTTCAAGAAATTATAATGAT-A
*
164309 TTTTATAATCATTT-GAGAAATT-TAATGATA
1 TTTTATAA-CATTTCAAGAAATTATAATGATA
164339 TTTTA
1 TTTTA
164344 AAGACGAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 6 0.19
31 7 0.22
32 14 0.44
33 5 0.16
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (31 bp):
TTTTATAACATTTCAAGAAATTATAATGATA
Found at i:167644 original size:40 final size:39
Alignment explanation
Indices: 167566--167644 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
167556 TAATTTTTTG
* * *
167566 TTTTTGGGTTGTTTTGGAAGGATACTTTTAACATATAAT
1 TTTTTGGGTTGTTTTAGAAGGACACTTTTAACAGATAAT
* *
167605 TTTTTGGGGTTGTTTTAGAAGGGCACTTTTAACGGATAAT
1 TTTTT-GGGTTGTTTTAGAAGGACACTTTTAACAGATAAT
167645 CTTAGGTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
39 5 0.15
40 29 0.85
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.46
Consensus pattern (39 bp):
TTTTTGGGTTGTTTTAGAAGGACACTTTTAACAGATAAT
Found at i:168612 original size:31 final size:31
Alignment explanation
Indices: 168574--168651 Score: 86
Period size: 33 Copynumber: 2.5 Consensus size: 31
168564 AAATTACGCA
* *
168574 TTTAATATTTAAATTACCA-ATTTTGATCCGT
1 TTTAATATTTAAATTA-AATATTTTGATCCAT
*
168605 TTTAATATCTAAACTTTAAATATTTTGATCCAT
1 TTTAATATTTAAA--TTAAATATTTTGATCCAT
*
168638 TTTAGTATTTAAAT
1 TTTAATATTTAAAT
168652 ATTTCAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
31 13 0.33
32 1 0.03
33 25 0.64
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (31 bp):
TTTAATATTTAAATTAAATATTTTGATCCAT
Found at i:169098 original size:2 final size:2
Alignment explanation
Indices: 169093--169119 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
169083 TCTCTCTCTC
169093 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
169120 TTAATTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:199701 original size:105 final size:105
Alignment explanation
Indices: 199519--199805 Score: 342
Period size: 105 Copynumber: 2.6 Consensus size: 105
199509 AGGATTATTC
* *
199519 AATGATCATTCAATTTAATGTAAAGACAATGAATTGAACAAAAACTTCAATGTTAGTTTAATTTA
1 AATGATTATTCAATTCAATGTAAAGACAATGAATTGAACAAAAACTTCAATGTTAGTTTAATTTA
199584 GCTCTCAGGGTATTGTTATTTTCCCGGAAAA-CTGACACTG
66 GCTCTCAGGGTATTGTTATTTTCCCGGAAAATC-GACACTG
* * *
199624 AATGATTATTCAATTCATTGTAAAGACGATGAATTGAACAAAAACTTCAATGTTAGTTTGATTTA
1 AATGATTATTCAATTCAATGTAAAGACAATGAATTGAACAAAAACTTCAATGTTAGTTTAATTTA
* * * *
199689 GTTCTCTGGGTATTTTTATTTTCCCTGAAAATCGACACTG
66 GCTCTCAGGGTATTGTTATTTTCCCGGAAAATCGACACTG
* **
199729 AAGGATTATTCAATGATCATTCAATTCATTGTAAAGACAATGAATTGAACAAAAACTTCAAAATT
1 AATGATTATTC----A--ATTC-A---A-TGTAAAGACAATGAATTGAACAAAAACTTCAATGTT
*
199794 AGTTTAGTTTAG
55 AGTTTAATTTAG
199806 TTCAGTTCTC
Statistics
Matches: 154, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
105 104 0.68
106 1 0.01
109 1 0.01
111 4 0.03
112 1 0.01
116 43 0.28
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (105 bp):
AATGATTATTCAATTCAATGTAAAGACAATGAATTGAACAAAAACTTCAATGTTAGTTTAATTTA
GCTCTCAGGGTATTGTTATTTTCCCGGAAAATCGACACTG
Found at i:208666 original size:3 final size:3
Alignment explanation
Indices: 208660--208705 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
208650 CCCCCCCCCA
* *
208660 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC TAC TAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC C
208706 TATACATTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.33, C:0.63, G:0.00, T:0.04
Consensus pattern (3 bp):
CAC
Found at i:209455 original size:39 final size:40
Alignment explanation
Indices: 209401--209479 Score: 151
Period size: 39 Copynumber: 2.0 Consensus size: 40
209391 ACAAAGAAAA
209401 AAGACAACTGACTATCGGTAACAAATATC-AAACCGATAC
1 AAGACAACTGACTATCGGTAACAAATATCAAAACCGATAC
209440 AAGACAACTGACTATCGGTAACAAATATCAAAACCGATAC
1 AAGACAACTGACTATCGGTAACAAATATCAAAACCGATAC
209480 TACCATCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
39 29 0.74
40 10 0.26
ACGTcount: A:0.47, C:0.23, G:0.13, T:0.18
Consensus pattern (40 bp):
AAGACAACTGACTATCGGTAACAAATATCAAAACCGATAC
Found at i:210598 original size:29 final size:31
Alignment explanation
Indices: 210563--210635 Score: 96
Period size: 29 Copynumber: 2.4 Consensus size: 31
210553 TAAGTTTACC
*
210563 CCTAAAATAAAATAA-AAATCAAATTCA-CT
1 CCTAAAATAAAATAATAAATCAAATTAATCT
* *
210592 CTTAAAATAAAAAAATAAATCAAATTAATCT
1 CCTAAAATAAAATAATAAATCAAATTAATCT
*
210623 CCTAACATAAAAT
1 CCTAAAATAAAAT
210636 CATTAGTTCG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 13 0.36
30 11 0.31
31 12 0.33
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (31 bp):
CCTAAAATAAAATAATAAATCAAATTAATCT
Found at i:213857 original size:21 final size:21
Alignment explanation
Indices: 213833--213895 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
213823 CTATCGTAAT
213833 GCGATAATACAAAATCGCAAC
1 GCGATAATACAAAATCGCAAC
** * *
213854 GCGATTCTGAC--TATCGCAAT
1 GCGATAAT-ACAAAATCGCAAC
*
213874 ACGATAATACAAAATCGCAAC
1 GCGATAATACAAAATCGCAAC
213895 G
1 G
213896 ACTCGTGGTA
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
19 2 0.07
20 12 0.41
21 13 0.45
22 2 0.07
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (21 bp):
GCGATAATACAAAATCGCAAC
Found at i:213858 original size:41 final size:41
Alignment explanation
Indices: 213805--213895 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
213795 GATTTTGACT
* *
213805 ATCGCAACGCGATTCTGACTATCGTAATGCGATAATACAAA
1 ATCGCAACGCGATTCTGACTATCGCAATACGATAATACAAA
213846 ATCGCAACGCGATTCTGACTATCGCAATACGATAATACAAA
1 ATCGCAACGCGATTCTGACTATCGCAATACGATAATACAAA
213887 ATCGCAACG
1 ATCGCAACG
213896 ACTCGTGGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGATTCTGACTATCGCAATACGATAATACAAA
Found at i:213878 original size:20 final size:20
Alignment explanation
Indices: 213786--213872 Score: 95
Period size: 20 Copynumber: 4.3 Consensus size: 20
213776 GTTTCCAGAT
*
213786 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTCTGACTA
213806 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
* * ** *
213826 TCGTAATGCGATAAT-ACAAAA
1 TCGCAACGCGATTCTGAC--TA
213847 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTCTGACTA
213867 TCGCAA
1 TCGCAA
213873 TACGATAATA
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
19 2 0.04
20 37 0.70
21 12 0.23
22 2 0.04
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTA
Found at i:214302 original size:19 final size:19
Alignment explanation
Indices: 214278--214314 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
214268 TTATTTTAGA
214278 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
214297 TTTTTCACTATCGCAACA
1 TTTTTCACTATCGCAACA
214315 ACATGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:214336 original size:25 final size:25
Alignment explanation
Indices: 214303--214375 Score: 107
Period size: 25 Copynumber: 3.0 Consensus size: 25
214293 ACACTTTTTC
214303 ACTATCGCAACAACATGTTTTTCAA
1 ACTATCGCAACAACATGTTTTTCAA
*
214328 ACTATCGCAACAACATGTTTTTAAA
1 ACTATCGCAACAACATGTTTTTCAA
*
214353 ACTCTCGCAAC-ACA--TTTTTCAA
1 ACTATCGCAACAACATGTTTTTCAA
214375 A
1 A
214376 ATCGCGTTGC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
22 8 0.18
24 3 0.07
25 34 0.76
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.32
Consensus pattern (25 bp):
ACTATCGCAACAACATGTTTTTCAA
Found at i:214425 original size:20 final size:20
Alignment explanation
Indices: 214375--214431 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
214365 CATTTTTCAA
*
214375 AATCGCGTTGCGAATCTTAC
1 AATCGCGTTGTGAATCTTAC
* *
214395 AATCTCATTGTGAATCTTAC
1 AATCGCGTTGTGAATCTTAC
*
214415 AATCGCGTTGTAAATCT
1 AATCGCGTTGTGAATCT
214432 GGATATTCGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (20 bp):
AATCGCGTTGTGAATCTTAC
Found at i:216658 original size:60 final size:60
Alignment explanation
Indices: 216534--216647 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
216524 AACATAATGA
* * * *
216534 ATAGTAAAGTGATTATTTTGTAACTGTTAATAGTCGAGGGACCCAATAAAGTAGCTCCCT
1 ATAGTAAAGTGAGTATCTTGTAACTGTTAATAGTCAAGAGACCCAATAAAGTAGCTCCCT
* * * **
216594 ATAGTCAAGTGAGTATCTTGTAACTTTTAATAGTTAAGAGATTCAATAAAGTAG
1 ATAGTAAAGTGAGTATCTTGTAACTGTTAATAGTCAAGAGACCCAATAAAGTAG
216648 TATCCTATAG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (60 bp):
ATAGTAAAGTGAGTATCTTGTAACTGTTAATAGTCAAGAGACCCAATAAAGTAGCTCCCT
Found at i:228961 original size:2 final size:2
Alignment explanation
Indices: 228954--228991 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
228944 ATTCTTTCAT
228954 TA TA TA TA TA TA 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 TA TA TA TA TA TA
228992 ATTTTTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:234796 original size:35 final size:34
Alignment explanation
Indices: 234743--234808 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 34
234733 ATAAAGTTTA
* *
234743 AAAATTCAAATTACATAAT-TGAAATTAAATTTATT
1 AAAATTCAAATAAAATAATAT--AATTAAATTTATT
*
234778 AAAATTTAAATAAAATAATATAATTAAATTT
1 AAAATTCAAATAAAATAATATAATTAAATTT
234809 CAAATTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 10 0.37
35 16 0.59
36 1 0.04
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (34 bp):
AAAATTCAAATAAAATAATATAATTAAATTTATT
Found at i:234889 original size:39 final size:39
Alignment explanation
Indices: 234846--234949 Score: 115
Period size: 39 Copynumber: 2.7 Consensus size: 39
234836 TTTAAAAAAT
234846 AATTTAGAACGTTAATGTGAAATAATTTAAGAAATTAAG
1 AATTTAGAACGTTAATGTGAAATAATTTAAGAAATTAAG
* * *
234885 AATTTAGAACATT-ATGGTGTCAA-AATTTAAGAAATTAGG
1 AATTTAGAACGTTAAT-GTG-AAATAATTTAAGAAATTAAG
* *
234924 ATTTTAGAATGTTAGA-GTGAAATAAT
1 AATTTAGAACGTTA-ATGTGAAATAAT
234950 GTGAGGATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
38 4 0.08
39 46 0.87
40 2 0.04
41 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.17, T:0.35
Consensus pattern (39 bp):
AATTTAGAACGTTAATGTGAAATAATTTAAGAAATTAAG
Found at i:234997 original size:20 final size:19
Alignment explanation
Indices: 234965--235005 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
234955 GATTATGAAT
*
234965 AAAAATTTAATATAAAATA
1 AAAAATATAATATAAAATA
*
234984 AAAAATATATATATATAATA
1 AAAAATATA-ATATAAAATA
235004 AA
1 AA
235006 TCGGGTACCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATATAATATAAAATA
Found at i:235513 original size:262 final size:262
Alignment explanation
Indices: 235048--235565 Score: 1036
Period size: 262 Copynumber: 2.0 Consensus size: 262
235038 GAATATTTTG
235048 TTACCCATGCTCGACCCAGAAACTCGATCTGGTACCCGACCCAAAAAATTGAGTATTTTTATTAT
1 TTACCCATGCTCGACCCAGAAACTCGATCTGGTACCCGACCCAAAAAATTGAGTATTTTTATTAT
235113 TAATACCCGATAATTTTTAACTGGGTCAGTAGGTCGACGGGTCAGCTCAATTAGGTCGAATATTT
66 TAATACCCGATAATTTTTAACTGGGTCAGTAGGTCGACGGGTCAGCTCAATTAGGTCGAATATTT
235178 TTGAACAATCTTACTGGCATGACATGTGGCATAGTTCGATTGGAGGATTAAATTTATTTTAATTT
131 TTGAACAATCTTACTGGCATGACATGTGGCATAGTTCGATTGGAGGATTAAATTTATTTTAATTT
235243 ATTAAAAGTATGACTAAATTGAGAGAATATTTAACTGTTGTTTACGAAAGTTAACCCGGGGATTA
196 ATTAAAAGTATGACTAAATTGAGAGAATATTTAACTGTTGTTTACGAAAGTTAACCCGGGGATTA
235308 AT
261 AT
235310 TTACCCATGCTCGACCCAGAAACTCGATCTGGTACCCGACCCAAAAAATTGAGTATTTTTATTAT
1 TTACCCATGCTCGACCCAGAAACTCGATCTGGTACCCGACCCAAAAAATTGAGTATTTTTATTAT
235375 TAATACCCGATAATTTTTAACTGGGTCAGTAGGTCGACGGGTCAGCTCAATTAGGTCGAATATTT
66 TAATACCCGATAATTTTTAACTGGGTCAGTAGGTCGACGGGTCAGCTCAATTAGGTCGAATATTT
235440 TTGAACAATCTTACTGGCATGACATGTGGCATAGTTCGATTGGAGGATTAAATTTATTTTAATTT
131 TTGAACAATCTTACTGGCATGACATGTGGCATAGTTCGATTGGAGGATTAAATTTATTTTAATTT
235505 ATTAAAAGTATGACTAAATTGAGAGAATATTTAACTGTTGTTTACGAAAGTTAACCCGGGG
196 ATTAAAAGTATGACTAAATTGAGAGAATATTTAACTGTTGTTTACGAAAGTTAACCCGGGG
235566 TAAGCACATC
Statistics
Matches: 256, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
262 256 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (262 bp):
TTACCCATGCTCGACCCAGAAACTCGATCTGGTACCCGACCCAAAAAATTGAGTATTTTTATTAT
TAATACCCGATAATTTTTAACTGGGTCAGTAGGTCGACGGGTCAGCTCAATTAGGTCGAATATTT
TTGAACAATCTTACTGGCATGACATGTGGCATAGTTCGATTGGAGGATTAAATTTATTTTAATTT
ATTAAAAGTATGACTAAATTGAGAGAATATTTAACTGTTGTTTACGAAAGTTAACCCGGGGATTA
AT
Found at i:235670 original size:31 final size:31
Alignment explanation
Indices: 235570--235670 Score: 139
Period size: 31 Copynumber: 3.3 Consensus size: 31
235560 CCGGGGTAAG
**
235570 CACATCTTAATTAAATAAAAATGAAATTGAC
1 CACATCTTAATTAAATAAAAACAAAATTGAC
* * *
235601 CATATCTTAATTAAATAAAAACTAAAGTGAC
1 CACATCTTAATTAAATAAAAACAAAATTGAC
*
235632 CATATCTTAATTAAATAAAAACAAAATTGAC
1 CACATCTTAATTAAATAAAAACAAAATTGAC
*
235663 TACATCTT
1 CACATCTT
235671 GTGTTTTTCA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 62 1.00
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.31
Consensus pattern (31 bp):
CACATCTTAATTAAATAAAAACAAAATTGAC
Found at i:236728 original size:3 final size:3
Alignment explanation
Indices: 236722--236759 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
236712 GACTCTCGCA
236722 CGC CGC CGC CGC CGC CGC CGC CGC CGC CGC CGC CGC CG
1 CGC CGC CGC CGC CGC CGC CGC CGC CGC CGC CGC CGC CG
236760 TCCGTCTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.66, G:0.34, T:0.00
Consensus pattern (3 bp):
CGC
Found at i:237761 original size:23 final size:23
Alignment explanation
Indices: 237726--237771 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
237716 GCTACCAAAT
237726 GACAGAGAAAAATGTGTCATAAA
1 GACAGAGAAAAATGTGTCATAAA
* *
237749 GACATAGATAAATGTGTCATAAA
1 GACAGAGAAAAATGTGTCATAAA
237772 AGCATAAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.09, G:0.20, T:0.22
Consensus pattern (23 bp):
GACAGAGAAAAATGTGTCATAAA
Found at i:250546 original size:29 final size:28
Alignment explanation
Indices: 250490--250546 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
250480 GAACAGTTTG
* * *
250490 AAAATATAATATATTAATATTTTATTTA
1 AAAATAAAATATAATAATATTATATTTA
250518 AAAATAAAATATTAATAATATTATATTTA
1 AAAATAAAATA-TAATAATATTATATTTA
250547 TGTGTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
AAAATAAAATATAATAATATTATATTTA
Found at i:251412 original size:31 final size:32
Alignment explanation
Indices: 251368--251428 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
251358 GATTTAGAAA
251368 AAAACTAAAAGTTT-AGATACTAAA-ATATATC
1 AAAACTAAAAGTTTAAG-TACTAAACATATATC
* *
251399 AAAACTGATAGTTTAAGTACTAAACATATA
1 AAAACTAAAAGTTTAAGTACTAAACATATA
251429 ATTTACCCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.30
Consensus pattern (32 bp):
AAAACTAAAAGTTTAAGTACTAAACATATATC
Found at i:255695 original size:15 final size:16
Alignment explanation
Indices: 255670--255740 Score: 51
Period size: 15 Copynumber: 4.6 Consensus size: 16
255660 ATCATTCAAC
255670 TTTTAAATTA-TAAACA
1 TTTT-AATTATTAAACA
*
255686 TTTTAATTATTAAACG
1 TTTTAATTATTAAACA
* * *
255702 TTAT-ATCATTCAAC-
1 TTTTAATTATTAAACA
*
255716 TTTTAAATTA-TAAAAA
1 TTTT-AATTATTAAACA
255732 TTTTAATTA
1 TTTTAATTA
255741 ACCTTTTTCT
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
14 3 0.07
15 21 0.49
16 19 0.44
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.48
Consensus pattern (16 bp):
TTTTAATTATTAAACA
Found at i:280268 original size:27 final size:27
Alignment explanation
Indices: 280232--280293 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
280222 AGGTACTTTG
280232 GGTCATTTTACACTTCAGGGGCATCTT
1 GGTCATTTTACACTTCAGGGGCATCTT
* *
280259 GGTCATTTTACACTTCGGGGGCATTTT
1 GGTCATTTTACACTTCAGGGGCATCTT
280286 GGTCATTT
1 GGTCATTT
280294 CCTTCAATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.40
Consensus pattern (27 bp):
GGTCATTTTACACTTCAGGGGCATCTT
Found at i:282329 original size:31 final size:31
Alignment explanation
Indices: 282288--282378 Score: 98
Period size: 30 Copynumber: 2.9 Consensus size: 31
282278 ATCATACCTA
* *
282288 ACATTTACTTTTTGTTTTATTTTAGTA-TCC
1 ACATTAACTTTTTGTTTTATTTTAGTACCCC
282318 ATCATTAAC-TTTTGTTTCT-TTTTAGTACCCC
1 A-CATTAACTTTTTGTTT-TATTTTAGTACCCC
* *
282349 ACTGTTAACTTTTTGTTTCATTTTAGTACC
1 AC-ATTAACTTTTTGTTTTATTTTAGTACC
282379 TCAATTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
30 18 0.35
31 15 0.29
32 18 0.35
ACGTcount: A:0.20, C:0.18, G:0.08, T:0.55
Consensus pattern (31 bp):
ACATTAACTTTTTGTTTTATTTTAGTACCCC
Found at i:282758 original size:71 final size:73
Alignment explanation
Indices: 282675--282813 Score: 201
Period size: 72 Copynumber: 1.9 Consensus size: 73
282665 TAAAAATGAT
* * * * *
282675 GACCTTTTATTGTAGTTACAAATAAG-AACTAAGAATCTAAACGAGAAGTTATGAATTT-TGATA
1 GACCTCTTATTGTAATTACAAATAAGAAACTAAGAATCTAAACAAGAAATTATGAATTTCTAATA
282738 AAATCAGC
66 AAATCAGC
* *
282746 GACCTCTTATTGTAATTACACATAAGAAACTAAGAATCTAAACAATAAATTATGAATTTCTAATA
1 GACCTCTTATTGTAATTACAAATAAGAAACTAAGAATCTAAACAAGAAATTATGAATTTCTAATA
282811 AAA
66 AAA
282814 AGTGACTTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 23 0.39
72 29 0.49
73 7 0.12
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (73 bp):
GACCTCTTATTGTAATTACAAATAAGAAACTAAGAATCTAAACAAGAAATTATGAATTTCTAATA
AAATCAGC
Found at i:288172 original size:19 final size:19
Alignment explanation
Indices: 288112--288173 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
288102 ACCAGGGATG
288112 TGTTTATTTTATGTTTTGT
1 TGTTTATTTTATGTTTTGT
* * * ***
288131 TGCTTATGTAATG-GACG-
1 TGTTTATTTTATGTTTTGT
288148 TGTTTATTTTATGTTTTGT
1 TGTTTATTTTATGTTTTGT
288167 TGTTTAT
1 TGTTTAT
288174 GTAATCTGTG
Statistics
Matches: 29, Mismatches: 12, Indels: 4
0.64 0.27 0.09
Matches are distributed among these distances:
17 10 0.34
18 2 0.07
19 17 0.59
ACGTcount: A:0.15, C:0.03, G:0.19, T:0.63
Consensus pattern (19 bp):
TGTTTATTTTATGTTTTGT
Found at i:301997 original size:18 final size:18
Alignment explanation
Indices: 301974--302026 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
301964 AGAATGTTTC
301974 TGAGGGAATTGAAATCTA
1 TGAGGGAATTGAAATCTA
301992 TGAGGGAATTGAAATCTA
1 TGAGGGAATTGAAATCTA
* *
302010 TGAAGGAATTGGAATCT
1 TGAGGGAATTGAAATCT
302027 GTCAGGAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.38, C:0.06, G:0.28, T:0.28
Consensus pattern (18 bp):
TGAGGGAATTGAAATCTA
Found at i:302425 original size:26 final size:26
Alignment explanation
Indices: 302396--302456 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
302386 AAAGTTTCAC
302396 CCGACCCGAATATATAAATTAGAAAT
1 CCGACCCGAATATATAAATTAGAAAT
*
302422 CCGACCCGAATATATGAATTAGAAAT
1 CCGACCCGAATATATAAATTAGAAAT
302448 CCGACCCGA
1 CCGACCCGA
302457 CACGAAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.20
Consensus pattern (26 bp):
CCGACCCGAATATATAAATTAGAAAT
Found at i:302532 original size:18 final size:18
Alignment explanation
Indices: 302509--302553 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
302499 ACTTTAAAAA
*
302509 CCTAAACCCGACCCAAGC
1 CCTAAACCCGACCCAAAC
**
302527 CCTAAACTTGACCCAAAC
1 CCTAAACCCGACCCAAAC
*
302545 ACTAAACCC
1 CCTAAACCC
302554 TAAATCCGAC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.44, G:0.07, T:0.11
Consensus pattern (18 bp):
CCTAAACCCGACCCAAAC
Found at i:311328 original size:3 final size:3
Alignment explanation
Indices: 311320--311380 Score: 113
Period size: 3 Copynumber: 20.0 Consensus size: 3
311310 TAACAATCAT
311320 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
311368 TTA TTA TATA TTA
1 TTA TTA T-TA TTA
311381 AAGCTCGCAA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 54 0.95
4 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:316970 original size:29 final size:30
Alignment explanation
Indices: 316907--316970 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
316897 ACAATGACTA
* * *
316907 CTATTCAATTTTAAATTATTTAAATTTTTG
1 CTATTAAACTTTAAATTATGTAAATTTTTG
* *
316937 TTATTAAACTTTAAATTATGT-CATTTTTG
1 CTATTAAACTTTAAATTATGTAAATTTTTG
316966 CTATT
1 CTATT
316971 TTTAATTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (30 bp):
CTATTAAACTTTAAATTATGTAAATTTTTG
Found at i:325119 original size:4 final size:4
Alignment explanation
Indices: 325112--325171 Score: 52
Period size: 4 Copynumber: 15.5 Consensus size: 4
325102 TTTTGAGTTG
* * * * * *
325112 AATA AATA AATA AAT- TATA AATA ATTG AATA CATA AATT CA-A AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
325158 AATA AATA AATA AA
1 AATA AATA AATA AA
325172 AATTATTGTC
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
3 3 0.07
4 39 0.93
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:325142 original size:23 final size:23
Alignment explanation
Indices: 325112--325171 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
325102 TTTTGAGTTG
325112 AATAAATAAATAAATT-ATAAATA
1 AATAAATAAATAAATTCA-AAATA
* * *
325135 ATTGAATACATAAATTCAAAATA
1 AATAAATAAATAAATTCAAAATA
325158 AATAAATAAATAAA
1 AATAAATAAATAAA
325172 AATTATTGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (23 bp):
AATAAATAAATAAATTCAAAATA
Found at i:335418 original size:29 final size:30
Alignment explanation
Indices: 335349--335420 Score: 96
Period size: 29 Copynumber: 2.4 Consensus size: 30
335339 ATAATTTATA
*
335349 TAAAATAGAA-TACCTGAAAATTGTTTTACG
1 TAAAAT-GAATTACCTGAAAACTGTTTTACG
335379 TAAAATGAATTACCT-AAAACTGTTTTA-G
1 TAAAATGAATTACCTGAAAACTGTTTTACG
335407 TTAAAATGAATTAC
1 -TAAAATGAATTAC
335421 ATTTTTTTGA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
28 1 0.03
29 27 0.69
30 11 0.28
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (30 bp):
TAAAATGAATTACCTGAAAACTGTTTTACG
Found at i:335728 original size:13 final size:13
Alignment explanation
Indices: 335710--335734 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
335700 CTAAATTATT
335710 ATATAAATATTAA
1 ATATAAATATTAA
335723 ATATAAATATTA
1 ATATAAATATTA
335735 CTCATTATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATAAATATTAA
Found at i:338477 original size:172 final size:173
Alignment explanation
Indices: 338191--338535 Score: 683
Period size: 172 Copynumber: 2.0 Consensus size: 173
338181 TAGTTTAGAT
338191 ATTAAATGCGTAATTTACCCTTAAATTAAATGCTCAAACGAGAGCCGAATGTCATGTGTTTCACA
1 ATTAAATGCGTAATTTACCCTTAAATTAAATGCTCAAACGAGAGCCGAATGTCATGTGTTTCACA
338256 TTGGCAGCCTCTCAACACATTAAAAGAAAGAGGGGCCACTCCGAAAATGATTAGAGTCAAAC-AA
66 TTGGCAGCCTCTCAACACATTAAAAGAAAGAGGGGCCACTCCGAAAATGATTAGAGTCAAACAAA
338320 ACGAGTACGTTTTGGCTAAGATCGAGAGATTGGATGCTATTGA
131 ACGAGTACGTTTTGGCTAAGATCGAGAGATTGGATGCTATTGA
338363 ATTAAATGCGTAATTTACCCTTAAATTAAATGCTCAAACGAGAGCCGAATGTCATGTGTTTCACA
1 ATTAAATGCGTAATTTACCCTTAAATTAAATGCTCAAACGAGAGCCGAATGTCATGTGTTTCACA
338428 TTGGCAGCCTCTCAACACATTAAAAGAAAGAGGGGCCACTCCGAAAATGATTAGAGTCAAACAAA
66 TTGGCAGCCTCTCAACACATTAAAAGAAAGAGGGGCCACTCCGAAAATGATTAGAGTCAAACAAA
338493 ACGAGTACGTTTTGGCTAAGATCGAGAGATTGGATGCTATTGA
131 ACGAGTACGTTTTGGCTAAGATCGAGAGATTGGATGCTATTGA
338536 CACATCCGAT
Statistics
Matches: 172, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
172 127 0.74
173 45 0.26
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (173 bp):
ATTAAATGCGTAATTTACCCTTAAATTAAATGCTCAAACGAGAGCCGAATGTCATGTGTTTCACA
TTGGCAGCCTCTCAACACATTAAAAGAAAGAGGGGCCACTCCGAAAATGATTAGAGTCAAACAAA
ACGAGTACGTTTTGGCTAAGATCGAGAGATTGGATGCTATTGA
Found at i:341208 original size:6 final size:6
Alignment explanation
Indices: 341197--341221 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
341187 CGTTTAGCAT
341197 CTCTTC CTCTTC CTCTTC CTCTTC C
1 CTCTTC CTCTTC CTCTTC CTCTTC C
341222 ACTGTCCAGT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CTCTTC
Found at i:341336 original size:35 final size:35
Alignment explanation
Indices: 341290--341395 Score: 185
Period size: 35 Copynumber: 3.0 Consensus size: 35
341280 AACTTAGAAT
341290 AAAGTAACATCACAGTAATGGTATGTAACAAAAAA
1 AAAGTAACATCACAGTAATGGTATGTAACAAAAAA
341325 AAAGTAACATCACAGTAATGGTATGTAACAAAAAAA
1 AAAGTAACATCACAGTAATGGTATGTAAC-AAAAAA
* *
341361 AAAGTAATATCACAGTAATGGCATGTAACAAAAAA
1 AAAGTAACATCACAGTAATGGTATGTAACAAAAAA
341396 CCAAGGCCCT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 35 0.51
36 33 0.49
ACGTcount: A:0.55, C:0.11, G:0.14, T:0.20
Consensus pattern (35 bp):
AAAGTAACATCACAGTAATGGTATGTAACAAAAAA
Found at i:341366 original size:36 final size:36
Alignment explanation
Indices: 341290--341395 Score: 187
Period size: 36 Copynumber: 3.0 Consensus size: 36
341280 AACTTAGAAT
341290 AAAGTAACATCACAGTAATGGTATGTAAC-AAAAAA
1 AAAGTAACATCACAGTAATGGTATGTAACAAAAAAA
341325 AAAGTAACATCACAGTAATGGTATGTAACAAAAAAA
1 AAAGTAACATCACAGTAATGGTATGTAACAAAAAAA
* *
341361 AAAGTAATATCACAGTAATGGCATGTAACAAAAAA
1 AAAGTAACATCACAGTAATGGTATGTAACAAAAAA
341396 CCAAGGCCCT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 29 0.43
36 39 0.57
ACGTcount: A:0.55, C:0.11, G:0.14, T:0.20
Consensus pattern (36 bp):
AAAGTAACATCACAGTAATGGTATGTAACAAAAAAA
Found at i:342194 original size:13 final size:13
Alignment explanation
Indices: 342176--342202 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
342166 TCAAGTTCGG
342176 GTTTCCAAGTCAT
1 GTTTCCAAGTCAT
342189 GTTTCCAAGTCAT
1 GTTTCCAAGTCAT
342202 G
1 G
342203 CACGCCTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (13 bp):
GTTTCCAAGTCAT
Found at i:343349 original size:14 final size:14
Alignment explanation
Indices: 343330--343368 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
343320 TAATGTGGAG
343330 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
343344 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
343358 GAATCTCTGCA
1 TAATCCCTGCA
343369 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:346754 original size:5 final size:5
Alignment explanation
Indices: 346746--346775 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
346736 AAAATTTAAT
*
346746 TTTTA TTTTA TTTAA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
346776 GTATATCGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:346775 original size:16 final size:16
Alignment explanation
Indices: 346739--346773 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
346729 ATTATATAAA
346739 ATTTAATTTTTATTTT
1 ATTTAATTTTTATTTT
346755 ATTTAA-TTTTATTTT
1 ATTTAATTTTTATTTT
346770 ATTT
1 ATTT
346774 TAGTATATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTAATTTTTATTTT
Found at i:346828 original size:13 final size:13
Alignment explanation
Indices: 346812--346840 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
346802 ATGTTAAAAA
346812 AAATTAAAAATTT
1 AAATTAAAAATTT
346825 AAATTAAAAATTT
1 AAATTAAAAATTT
346838 AAA
1 AAA
346841 CAGTAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATTAAAAATTT
Found at i:347970 original size:17 final size:19
Alignment explanation
Indices: 347943--347987 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
347933 GTGGTAAGAA
347943 ATTTATTTTT-AT-GTTATT
1 ATTT-TTTTTAATAGTTATT
347961 ATTTTTTTTAAATAGTTATT
1 ATTTTTTTT-AATAGTTATT
347981 ATTTTTT
1 ATTTTTT
347988 ATATTAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.21
18 4 0.17
19 2 0.08
20 13 0.54
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (19 bp):
ATTTTTTTTAATAGTTATT
Found at i:348013 original size:32 final size:33
Alignment explanation
Indices: 347977--348054 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
347967 TTTAAATAGT
* *
347977 TATTATTTTTTA-TATTAAT-ATATTTATGTAAA
1 TATTATTTTTTATTA-AAATAATATTTATATAAA
*
348009 TATTATTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATTAAAATAATATTTATATAAA
348042 TATTATTTATTTA
1 TATTATTT-TTTA
348055 GAATTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 15 0.38
33 21 0.52
34 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTATTTTTTATTAAAATAATATTTATATAAA
Found at i:348216 original size:17 final size:17
Alignment explanation
Indices: 348194--348247 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
348184 AATGTTAATA
348194 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
348211 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
348228 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
348245 TTT
1 TTT
348248 TTATAATATA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:352619 original size:9 final size:9
Alignment explanation
Indices: 352605--352638 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
352595 TAAAAGGGAA
352605 AAATAAAAT
1 AAATAAAAT
352614 AAATAAAAT
1 AAATAAAAT
352623 AAAT-AAAT
1 AAATAAAAT
352631 AAGATAAA
1 AA-ATAAA
352639 GGAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:352626 original size:13 final size:13
Alignment explanation
Indices: 352604--352638 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
352594 GTAAAAGGGA
352604 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
352618 AAAATAAATAAAT
1 AAAATAAATAAAT
*
352631 AAGATAAA
1 AAAATAAA
352639 GGAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:352698 original size:2 final size:2
Alignment explanation
Indices: 352691--352715 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
352681 AAAAAGGAAA
352691 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
352716 CACATCAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:353107 original size:2 final size:2
Alignment explanation
Indices: 353100--353136 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
353090 TATTAAAGAA
353100 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
353137 ACATAAACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:353635 original size:34 final size:34
Alignment explanation
Indices: 353558--353692 Score: 216
Period size: 34 Copynumber: 3.9 Consensus size: 34
353548 ATAGTATAAC
*
353558 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCATATTTTTAGGAGTTTGAATCCT---AAAAT
*
353595 TTTATCATATTTTTAGGAGTTTGAATCCTAAAAT
1 TCTATCATATTTTTAGGAGTTTGAATCCTAAAAT
353629 TCTATCATATTTTTAGGAGTTTGAATCCTAAAAT
1 TCTATCATATTTTTAGGAGTTTGAATCCTAAAAT
*
353663 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCATATTTTTAGGAGTTTGAATCCTA
353693 GTAGGACGAA
Statistics
Matches: 94, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
34 67 0.71
37 27 0.29
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (34 bp):
TCTATCATATTTTTAGGAGTTTGAATCCTAAAAT
Done.