Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001945.1 Hibiscus syriacus cultivar Beakdansim tig00003939_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: 113740
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:280 original size:34 final size:34
Alignment explanation
Indices: 237--303 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
227 CAACGATAAT
*
237 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAAATGACTATCGCAACGA
271 GAGAATCGCAACGCGAAAATGACTATCGCAACG
1 GAGAATCGCAACGCGAAAATGACTATCGCAACG
304 CGAAATGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.39, C:0.24, G:0.25, T:0.12
Consensus pattern (34 bp):
GAGAATCGCAACGCGAAAATGACTATCGCAACGA
Found at i:292 original size:54 final size:51
Alignment explanation
Indices: 222--322 Score: 130
Period size: 54 Copynumber: 1.9 Consensus size: 51
212 TTGAAATGAA
* * **
222 AATCGCAACGATAATGAGAATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGAAAATGACAATCGCAACGC-GAAATGAAAATCGCAACGAGAG
*
274 AATCGCAACGCGAAAATGACTATCGCAACGCGAAATGAAAATCGCAACG
1 AATCGCAA--CGAAAATGACAATCGCAACGCGAAATGAAAATCGCAACG
323 CGAAATGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
52 8 0.19
53 16 0.38
54 18 0.43
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.13
Consensus pattern (51 bp):
AATCGCAACGAAAATGACAATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:311 original size:19 final size:19
Alignment explanation
Indices: 214--344 Score: 123
Period size: 19 Copynumber: 7.1 Consensus size: 19
204 TCTTTTGGTT
214 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
231 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
251 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
269 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
285 GAAAATGACTATCGCAACGC
1 G-AAATGAAAATCGCAACGC
305 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
324 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
343 GA
1 GA
345 TTTTGGTTTC
Statistics
Matches: 94, Mismatches: 10, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
14 9 0.10
15 1 0.01
16 2 0.02
17 3 0.03
18 14 0.15
19 37 0.39
20 26 0.28
21 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:373 original size:19 final size:19
Alignment explanation
Indices: 340--384 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
330 AAAATCGCAA
*
340 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
359 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
378 TGCGATT
1 TGCGATT
385 CTCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:2943 original size:2 final size:2
Alignment explanation
Indices: 2936--2961 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2926 TGTGGCTCAG
2936 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
2962 AACAAACTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3504 original size:21 final size:21
Alignment explanation
Indices: 3460--3507 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3450 TGTAATTCGA
* ** *
3460 TTATTTTCATTATATATTTTT
1 TTATTTTAATTATATACATAT
3481 TTATTTTAATTATATACATAT
1 TTATTTTAATTATATACATAT
3502 TTATTT
1 TTATTT
3508 ATTCAAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATTTTAATTATATACATAT
Found at i:10754 original size:20 final size:20
Alignment explanation
Indices: 10726--10763 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10716 TCATTTGTTT
10726 ATTTATTAATTTAATCTTTA
1 ATTTATTAATTTAATCTTTA
* *
10746 ATTTTTTAATTTATTCTT
1 ATTTATTAATTTAATCTT
10764 CGTAATTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTTATTAATTTAATCTTTA
Found at i:11757 original size:16 final size:16
Alignment explanation
Indices: 11736--11766 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11726 TTACCCGACT
*
11736 TGTTATCAACCTGACC
1 TGTTATAAACCTGACC
11752 TGTTATAAACCTGAC
1 TGTTATAAACCTGAC
11767 TTGTAATTGA
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:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (16 bp):
TGTTATAAACCTGACC
Found at i:12256 original size:14 final size:14
Alignment explanation
Indices: 12224--12265 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
12214 ATTGCAAAAC
*
12224 CCTAAATCCTAAA-
1 CCTACATCCTAAAT
12237 CCTACATCCTAAAT
1 CCTACATCCTAAAT
* *
12251 CTTACATTCTAAAT
1 CCTACATCCTAAAT
12265 C
1 C
12266 ATAAACTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (14 bp):
CCTACATCCTAAAT
Found at i:12561 original size:2 final size:2
Alignment explanation
Indices: 12556--12599 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
12546 ACACACAAAC
12556 AT AT AT AT AT 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 AT AT AT AT AT
12598 AT
1 AT
12600 GCATATACTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12776 original size:28 final size:26
Alignment explanation
Indices: 12710--12776 Score: 62
Period size: 27 Copynumber: 2.4 Consensus size: 26
12700 TAGTGTAAGA
* *
12710 TTTAGGGTTTAAGATTTGGATTTGGGG
1 TTTAGGGTTT-AGAATTGGATTTGGAG
* *
12737 TTTGGGGTTTTAGAATTGGCATTTAGGAT
1 TTTAGGG-TTTAGAATTGG-ATTT-GGAG
12766 TTTAGGGTTTA
1 TTTAGGGTTTA
12777 AGGATTAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
27 13 0.41
28 11 0.34
29 8 0.25
ACGTcount: A:0.19, C:0.01, G:0.33, T:0.46
Consensus pattern (26 bp):
TTTAGGGTTTAGAATTGGATTTGGAG
Found at i:13082 original size:20 final size:22
Alignment explanation
Indices: 13046--13089 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
13036 CCTAAATTCC
13046 AATCTCAAAACTTCAAATCCTA
1 AATCTCAAAACTTCAAATCCTA
*
13068 AATCTC-AAA-TTCAAATCTTA
1 AATCTCAAAACTTCAAATCCTA
13088 AA
1 AA
13090 CTTTAAACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 3 0.14
22 6 0.29
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.30
Consensus pattern (22 bp):
AATCTCAAAACTTCAAATCCTA
Found at i:13102 original size:34 final size:35
Alignment explanation
Indices: 13037--13112 Score: 93
Period size: 34 Copynumber: 2.2 Consensus size: 35
13027 TCCTAAAACC
* *
13037 CTAAATTCCAATCTCAAAACTTCAAATCCTAAA-T
1 CTAAATTCAAATCTCAAAACTTCAAACCCTAAATT
* *
13071 CTCAAATTCAAATCT-TAAACTTTAAACCCTAAATT
1 CT-AAATTCAAATCTCAAAACTTCAAACCCTAAATT
13106 CTAAATT
1 CTAAATT
13113 TTAAACTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 22 0.61
35 14 0.39
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (35 bp):
CTAAATTCAAATCTCAAAACTTCAAACCCTAAATT
Found at i:13104 original size:21 final size:21
Alignment explanation
Indices: 13080--13132 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
13070 TCTCAAATTC
13080 AAATCTTAAACTTTAAACCCT
1 AAATCTTAAACTTTAAACCCT
* **
13101 AAAT-TCTAAATTTTAAACTTT
1 AAATCT-TAAACTTTAAACCCT
*
13122 AATTCTTAAAC
1 AAATCTTAAAC
13133 CATAACTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 1 0.04
21 23 0.92
22 1 0.04
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATCTTAAACTTTAAACCCT
Found at i:13618 original size:30 final size:30
Alignment explanation
Indices: 13584--13679 Score: 165
Period size: 30 Copynumber: 3.2 Consensus size: 30
13574 CGAATATAGA
*
13584 TCGCCAGGTGATCTGGGCGACCAATGAAGG
1 TCGCCAGGTGGTCTGGGCGACCAATGAAGG
*
13614 TCGCCAGGTGGTTTGGGCGACCAATGAAGG
1 TCGCCAGGTGGTCTGGGCGACCAATGAAGG
*
13644 TCGTCAGGTGGTCTGGGCGACCAATGAAGG
1 TCGCCAGGTGGTCTGGGCGACCAATGAAGG
13674 TCGCCA
1 TCGCCA
13680 TGTATGTTGG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.21, C:0.23, G:0.38, T:0.19
Consensus pattern (30 bp):
TCGCCAGGTGGTCTGGGCGACCAATGAAGG
Found at i:14294 original size:50 final size:50
Alignment explanation
Indices: 14233--14334 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
14223 AAAATTATTG
14233 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
14283 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
14333 AA
1 AA
14335 ATAGGATAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.25
Consensus pattern (50 bp):
AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
Found at i:18092 original size:22 final size:21
Alignment explanation
Indices: 18045--18092 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
18035 ATACTAATAT
* *
18045 CTAAAATATTAATTATAAATT
1 CTAAAATATTAACTATAAATC
* *
18066 ATAAAATTTTAAACTATAAATC
1 CTAAAATATT-AACTATAAATC
18088 CTAAA
1 CTAAA
18093 TTGTAAAACT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (21 bp):
CTAAAATATTAACTATAAATC
Found at i:18621 original size:3 final size:3
Alignment explanation
Indices: 18613--18660 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
18603 TGCGTTTTGG
18613 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
18661 GAGAGAAACG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:19487 original size:20 final size:19
Alignment explanation
Indices: 19464--19507 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
19454 TCTAACTTAA
*
19464 AAACCTATATTCTAAACCCT
1 AAACCTATATT-AAAACCCT
*
19484 AAACCCTATCTTAAAACCCT
1 AAA-CCTATATTAAAACCCT
19504 AAAC
1 AAAC
19508 GATAGTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 1 0.05
20 13 0.62
21 7 0.33
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.25
Consensus pattern (19 bp):
AAACCTATATTAAAACCCT
Found at i:29526 original size:60 final size:60
Alignment explanation
Indices: 29456--29636 Score: 213
Period size: 60 Copynumber: 3.0 Consensus size: 60
29446 TCATATGTCT
* * *
29456 CCAAACTATGACCCTCATTTTAAATTGGTCCCTAAACTTTTAAATATTTCAATTTCATTC
1 CCAAACTATGACTCTCATTCTAAATTGGTCCCTAAACTTTTAAATATTTCAATTTCATCC
** * * * *
29516 TTAAACTATGACTATCATTCTAAATTGAT-CCTCAAACTTTTGAACA-TTCAATTTTCATCC
1 CCAAACTATGACTCTCATTCTAAATTGGTCCCT-AAACTTTTAAATATTTCAA-TTTCATCC
* * * *
29576 CCAAACTATGAATCTCATTCTAAATTGGTCCTTAAACTTTTAGATCTTTCAATTTCATCC
1 CCAAACTATGACTCTCATTCTAAATTGGTCCCTAAACTTTTAAATATTTCAATTTCATCC
29636 C
1 C
29637 TAAATTCATC
Statistics
Matches: 98, Mismatches: 19, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
59 8 0.08
60 83 0.85
61 7 0.07
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (60 bp):
CCAAACTATGACTCTCATTCTAAATTGGTCCCTAAACTTTTAAATATTTCAATTTCATCC
Found at i:29564 original size:29 final size:30
Alignment explanation
Indices: 29529--29616 Score: 74
Period size: 29 Copynumber: 2.9 Consensus size: 30
29519 AACTATGACT
29529 ATCATTCTAAATTGATCCTCAAACTTTTGA
1 ATCATTCTAAATTGATCCTCAAACTTTTGA
* * * *
29559 A-CATTC-AATTTTCATCCCCAAAC-TATGA
1 ATCATTCTAA-ATTGATCCTCAAACTTTTGA
* *
29587 ATCTCATTCTAAATTGGTCCTTAAACTTTT
1 A--TCATTCTAAATTGATCCTCAAACTTTT
29617 AGATCTTTCA
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
28 7 0.17
29 16 0.38
30 1 0.02
31 14 0.33
32 4 0.10
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.40
Consensus pattern (30 bp):
ATCATTCTAAATTGATCCTCAAACTTTTGA
Found at i:29872 original size:57 final size:57
Alignment explanation
Indices: 29811--29991 Score: 195
Period size: 57 Copynumber: 3.1 Consensus size: 57
29801 ATAATTTGGT
29811 GATGAAAATGAAATGTGTAGTTTGAGGATTGATTTAGAATAATAGTCATAGTTTAAG
1 GATGAAAATGAAATGTGTAGTTTGAGGATTGATTTAGAATAATAGTCATAGTTTAAG
* * * * *** * **
29868 GATGAAATTAAAACGTTTAAAAGTTT-AGGGACCAATTTTGAATGAATA-TCATAGTTTGGG
1 GATGAAAATGAAATGTGT---AGTTTGA-GGATTGATTTAGAAT-AATAGTCATAGTTTAAG
* *
29928 GATGAAAATGAAGTGTGCAGTTTGAGGATTGATTTAGAATAATAGTCATAGTTTAAG
1 GATGAAAATGAAATGTGTAGTTTGAGGATTGATTTAGAATAATAGTCATAGTTTAAG
29985 GATGAAA
1 GATGAAA
29992 TTAAATTTTT
Statistics
Matches: 95, Mismatches: 22, Indels: 14
0.73 0.17 0.11
Matches are distributed among these distances:
56 4 0.04
57 47 0.49
58 1 0.01
59 1 0.01
60 38 0.40
61 4 0.04
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (57 bp):
GATGAAAATGAAATGTGTAGTTTGAGGATTGATTTAGAATAATAGTCATAGTTTAAG
Found at i:29922 original size:60 final size:59
Alignment explanation
Indices: 29770--30019 Score: 167
Period size: 57 Copynumber: 4.3 Consensus size: 59
29760 GATATATTTA
* * * *
29770 AAAAGTTTGGGACCAATTTTGAATGAATA-TCATAATTT-GGTGATGAAAATGAAATGTGT
1 AAAAGTTTGGGACCAATTTAGAAT-AATAGTCATAGTTTAAG-GATGAAAATAAAATGTGT
*** * * *
29829 ---AGTTTGAGGATTGATTTAGAATAATAGTCATAGTTTAAGGATGAAATTAAAACGTTT
1 AAAAGTTTG-GGACCAATTTAGAATAATAGTCATAGTTTAAGGATGAAAATAAAATGTGT
* ** *
29886 AAAAGTTTAGGGACCAATTTTGAATGAATA-TCATAGTTTGGGGATGAAAAT-GAA-GTGT
1 AAAAGTTT-GGGACCAATTTAGAAT-AATAGTCATAGTTTAAGGATGAAAATAAAATGTGT
** *** * * * *
29944 -GCAGTTTGAGGATTGATTTAGAATAATAGTCATAGTTTAAGGATGAAATTAAATTTTTT
1 AAAAGTTTG-GGACCAATTTAGAATAATAGTCATAGTTTAAGGATGAAAATAAAATGTGT
30003 AAAAGTTTAGGGACCAA
1 AAAAGTTT-GGGACCAA
30020 CATGGAATGA
Statistics
Matches: 140, Mismatches: 37, Indels: 27
0.69 0.18 0.13
Matches are distributed among these distances:
56 15 0.11
57 67 0.48
58 5 0.04
59 4 0.03
60 43 0.31
61 6 0.04
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.34
Consensus pattern (59 bp):
AAAAGTTTGGGACCAATTTAGAATAATAGTCATAGTTTAAGGATGAAAATAAAATGTGT
Found at i:30038 original size:117 final size:117
Alignment explanation
Indices: 29770--30019 Score: 430
Period size: 117 Copynumber: 2.1 Consensus size: 117
29760 GATATATTTA
* * *
29770 AAAAGTTT-GGGACCAATTTTGAATGAATATCATAATTTGGTGATGAAAATGAAATGTGTAGTTT
1 AAAAGTTTAGGGACCAATTTTGAATGAATATCATAGTTTGGGGATGAAAATGAAATGTGCAGTTT
29834 GAGGATTGATTTAGAATAATAGTCATAGTTTAAGGATGAAATTAAAACGTTT
66 GAGGATTGATTTAGAATAATAGTCATAGTTTAAGGATGAAATTAAAACGTTT
*
29886 AAAAGTTTAGGGACCAATTTTGAATGAATATCATAGTTTGGGGATGAAAATGAAGTGTGCAGTTT
1 AAAAGTTTAGGGACCAATTTTGAATGAATATCATAGTTTGGGGATGAAAATGAAATGTGCAGTTT
***
29951 GAGGATTGATTTAGAATAATAGTCATAGTTTAAGGATGAAATTAAATTTTTT
66 GAGGATTGATTTAGAATAATAGTCATAGTTTAAGGATGAAATTAAAACGTTT
30003 AAAAGTTTAGGGACCAA
1 AAAAGTTTAGGGACCAA
30020 CATGGAATGA
Statistics
Matches: 126, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
116 8 0.06
117 118 0.94
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.34
Consensus pattern (117 bp):
AAAAGTTTAGGGACCAATTTTGAATGAATATCATAGTTTGGGGATGAAAATGAAATGTGCAGTTT
GAGGATTGATTTAGAATAATAGTCATAGTTTAAGGATGAAATTAAAACGTTT
Found at i:34039 original size:23 final size:23
Alignment explanation
Indices: 34013--34070 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
34003 TTTATATTCA
* *
34013 ATTCGTTTAGTATTTGTGAATAT
1 ATTCGTTTAGTATTTGCGAACAT
*
34036 ATTCGTTTAATATTTGCGAACAT
1 ATTCGTTTAGTATTTGCGAACAT
*
34059 ATTCATTTAGTA
1 ATTCGTTTAGTA
34071 CTCACGAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.29, C:0.09, G:0.14, T:0.48
Consensus pattern (23 bp):
ATTCGTTTAGTATTTGCGAACAT
Found at i:37672 original size:79 final size:79
Alignment explanation
Indices: 37466--37677 Score: 216
Period size: 79 Copynumber: 2.7 Consensus size: 79
37456 CCTTGTATTT
* * * ** * *
37466 GGTAGATTTTGAA-TGAGAGACGTTAGAGGTATATGACAATAAAGTTTTAGGAGATAACACAGTT
1 GGTAGGTTTT-AATTGAGAGACTTTAGAGATATAAAACAATAAAGTTTTATGAGATAACACAATT
*
37530 GATCTTGTTGTGTTT
65 GATCTTGTTGTGTTC
* * * * *
37545 GGT-GGATTTTAATTGAAAGACTTTAGA-AT-TACAAGGCAATAAAATTTTATGAGATGACTCAA
1 GGTAGG-TTTTAATTGAGAGACTTTAGAGATATA-AA-ACAATAAAGTTTTATGAGATAACACAA
*
37607 TTTATCTTGTTGTGTTC
63 TTGATCTTGTTGTGTTC
* *
37624 GGTAGGTTTTAATTGAGAGACTTTAGAGATATAAAACGATGAAGTTTTATGAGA
1 GGTAGGTTTTAATTGAGAGACTTTAGAGATATAAAACAATAAAGTTTTATGAGA
37678 CTTTAGAGGT
Statistics
Matches: 107, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
77 2 0.02
78 4 0.04
79 93 0.87
80 6 0.06
81 2 0.02
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (79 bp):
GGTAGGTTTTAATTGAGAGACTTTAGAGATATAAAACAATAAAGTTTTATGAGATAACACAATTG
ATCTTGTTGTGTTC
Found at i:41847 original size:21 final size:20
Alignment explanation
Indices: 41806--41854 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
41796 CTGACTATCT
*
41806 CATTGCGATTTACGTATTCG
1 CATTGCGATTTACCTATTCG
*
41826 CATTGCGATTTTCCTAATTCG
1 CATTGCGATTTACCT-ATTCG
*
41847 CAATGCGA
1 CATTGCGA
41855 ATACGTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.37
Consensus pattern (20 bp):
CATTGCGATTTACCTATTCG
Found at i:41868 original size:41 final size:40
Alignment explanation
Indices: 41844--41957 Score: 165
Period size: 41 Copynumber: 2.8 Consensus size: 40
41834 TTTTCCTAAT
*
41844 TCGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAA
* * * *
41884 TCACAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAA-TACGTAAATCGCAATGCGATTACGTAAA
*
41925 TCGCAATGCGATTACGTAAATCGCAATGCGATT
1 TCGCAATGCGAATACGTAAATCGCAATGCGATT
41958 TACATAGCGC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 29 0.46
41 34 0.54
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAA
Found at i:41894 original size:61 final size:61
Alignment explanation
Indices: 41829--41960 Score: 192
Period size: 61 Copynumber: 2.2 Consensus size: 61
41819 GTATTCGCAT
* * *
41829 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAATCACAA
1 TGCGATTTACCAAAATCGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAATCACAA
* ** * *
41890 TGCGAATTAGGAAAATCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAATCGCAA
1 TGCGATTTACCAAAATCGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAATCACAA
41951 TGCGATTTAC
1 TGCGATTTAC
41961 ATAGCGCCAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (61 bp):
TGCGATTTACCAAAATCGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAATCACAA
Found at i:41956 original size:20 final size:20
Alignment explanation
Indices: 41844--41957 Score: 165
Period size: 20 Copynumber: 5.7 Consensus size: 20
41834 TTTTCCTAAT
*
41844 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
*
41864 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
* * *
41884 TCACAATGCGAATTAGGAAAA
1 TCGCAATGCG-ATTACGTAAA
*
41905 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
41925 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
41945 TCGCAATGCGATT
1 TCGCAATGCGATT
41958 TACATAGCGC
Statistics
Matches: 82, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 65 0.79
21 17 0.21
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:43628 original size:24 final size:24
Alignment explanation
Indices: 43594--43647 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
43584 CTGAAAAATC
43594 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
43618 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
43642 ATCAAA
1 ATCAAA
43648 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:43661 original size:24 final size:24
Alignment explanation
Indices: 43594--43661 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
43584 CTGAAAAATC
* * *
43594 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
43618 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
43642 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
43662 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:44567 original size:21 final size:21
Alignment explanation
Indices: 44521--44639 Score: 188
Period size: 21 Copynumber: 5.8 Consensus size: 21
44511 GCGATTTATT
* *
44521 AAATCGCAATGCGAA-TACGT
1 AAATCGCAATGCGAATTAGGA
44541 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
44562 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
44583 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
* *
44604 AAATCGCAATGCG-ATTACGT
1 AAATCGCAATGCGAATTAGGA
44624 AAATCGCAATGCGAAT
1 AAATCGCAATGCGAAT
44640 ACGTAATCGC
Statistics
Matches: 93, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
20 33 0.35
21 60 0.65
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGA
Found at i:44642 original size:20 final size:21
Alignment explanation
Indices: 44520--44736 Score: 185
Period size: 21 Copynumber: 10.6 Consensus size: 21
44510 TGCGATTTAT
44520 TAAATCGCAATGCGAA-TACG
1 TAAATCGCAATGCGAATTACG
*
44540 TAAATCGCAATGCGAATTAGG
1 TAAATCGCAATGCGAATTACG
* *
44561 AAAATCGCAATGCGAATTAGG
1 TAAATCGCAATGCGAATTACG
* *
44582 AAAATCGCAATGCGAATTAGG
1 TAAATCGCAATGCGAATTACG
*
44603 AAAATCGCAATGCG-ATTACG
1 TAAATCGCAATGCGAATTACG
44623 TAAATCGCAATGCGAA-TACG
1 TAAATCGCAATGCGAATTACG
* * * *
44643 T-AATCGCATTGCGATTTTCC
1 TAAATCGCAATGCGAATTACG
* * *
44663 TAATTAGCATTGC-AATTTACG
1 TAAATCGCAATGCGAA-TTACG
* * * *
44684 T-ATTCGCATTGCGATTTAGG
1 TAAATCGCAATGCGAATTACG
* * **
44704 AAAATCGCAACGCGAATTTGG
1 TAAATCGCAATGCGAATTACG
*
44725 GAAATCGCAATG
1 TAAATCGCAATG
44737 TGATAGTCAG
Statistics
Matches: 166, Mismatches: 24, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.07
20 57 0.34
21 97 0.58
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (21 bp):
TAAATCGCAATGCGAATTACG
Found at i:44673 original size:21 final size:20
Alignment explanation
Indices: 44648--44701 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
44638 ATACGTAATC
*
44648 GCATTGCGATTTTCCTAATTA
1 GCATTGCGATTTACCT-ATTA
* * *
44669 GCATTGCAATTTACGTATTC
1 GCATTGCGATTTACCTATTA
44689 GCATTGCGATTTA
1 GCATTGCGATTTA
44702 GGAAAATCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.41
Consensus pattern (20 bp):
GCATTGCGATTTACCTATTA
Found at i:46318 original size:20 final size:19
Alignment explanation
Indices: 46276--46322 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
46266 CCTTGAACTG
*
46276 TTGACTTTAACCAGAGCCG
1 TTGACTTTAACCAGAGCCA
46295 TTGACTTTAACCCAGA-CCAA
1 TTGACTTTAA-CCAGAGCC-A
46315 TTGACTTT
1 TTGACTTT
46323 GATTTGGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (19 bp):
TTGACTTTAACCAGAGCCA
Found at i:48035 original size:46 final size:46
Alignment explanation
Indices: 47982--48073 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
47972 CCCTAAAATA
47982 ATAAGAAAAATATCTTATATTGTGTGGTCCAATATTAATAGTAGGT
1 ATAAGAAAAATATCTTATATTGTGTGGTCCAATATTAATAGTAGGT
48028 ATAAGAAAAATATCTTATATTGTGTGGTCCAATATTAATAGTAGGT
1 ATAAGAAAAATATCTTATATTGTGTGGTCCAATATTAATAGTAGGT
48074 TATCTTAGGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (46 bp):
ATAAGAAAAATATCTTATATTGTGTGGTCCAATATTAATAGTAGGT
Found at i:49515 original size:31 final size:31
Alignment explanation
Indices: 49472--49532 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
49462 GATAATATAA
* *
49472 TAATTATTTTATAGT-ATTTAGATAAATTTAT
1 TAATAATTTTATAATCATTTA-ATAAATTTAT
*
49503 TAATAATTTTATAATCTTTTAATAAATTTA
1 TAATAATTTTATAATCATTTAATAAATTTA
49533 ACAAGTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (31 bp):
TAATAATTTTATAATCATTTAATAAATTTAT
Found at i:50319 original size:31 final size:30
Alignment explanation
Indices: 50277--50363 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
50267 TCAATAAAAT
50277 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
50308 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
50339 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
50364 TATTATCGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:52745 original size:20 final size:22
Alignment explanation
Indices: 52722--52765 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
52712 TATGTGGAAA
52722 ATAAAAT-TTTA-TTTTAAAAT
1 ATAAAATATTTATTTTTAAAAT
52742 ATAAAATATTTATTTTTAAAAT
1 ATAAAATATTTATTTTTAAAAT
52764 AT
1 AT
52766 GTTTGTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.32
21 4 0.18
22 11 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTTATTTTTAAAAT
Found at i:53840 original size:24 final size:22
Alignment explanation
Indices: 53776--53849 Score: 64
Period size: 23 Copynumber: 3.4 Consensus size: 22
53766 AATATTTGAA
* *
53776 TTTTAAAAAATTAATA-AATAT
1 TTTTATAATATTAATATAATAT
* *
53797 TTTCATAATATTATAAATAATAT
1 TTTTATAATATTA-ATATAATAT
53820 TTTTATAATTATTCAATATAA-A-
1 TTTTATAA-TATT-AATATAATAT
53842 TTTTATAA
1 TTTTATAA
53850 ATATATAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
21 10 0.23
22 10 0.23
23 13 0.30
24 9 0.21
25 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTATAATATTAATATAATAT
Found at i:57796 original size:27 final size:27
Alignment explanation
Indices: 57753--57819 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
57743 TTCCTCCTAT
*
57753 ATTCATCTATTTTCAACATTAGTGAAA
1 ATTCTTCTATTTTCAACATTAGTGAAA
* *
57780 TTTTTTCTATTTTCAACATTAGTGAAA
1 ATTCTTCTATTTTCAACATTAGTGAAA
57807 ATTCTTCTATTTT
1 ATTCTTCTATTTT
57820 GTCGGTAGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.51
Consensus pattern (27 bp):
ATTCTTCTATTTTCAACATTAGTGAAA
Found at i:63732 original size:227 final size:226
Alignment explanation
Indices: 63332--63777 Score: 754
Period size: 227 Copynumber: 2.0 Consensus size: 226
63322 GTAAATTATC
* * *
63332 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
* *
63397 TAATATTGTTAAATTTAAAATCTAAATAATATTTATAAAATATCAAAACAATCAAATAATTTTTT
66 TAATATTGTTAAATTTAAAATCGAAATAATATTTATAAAATATCAAAACAATCAAATAATATTTT
63462 GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
131 GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
63527 AACATAAATTACATAACTTTCAAAAAAGTATA
196 AACATAAATTACATAACTTT-AAAAAAGTATA
*
63559 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATA-TTATTA-TATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
63622 TTAATATTGTTAAATTTAAATTCGAAATAATATTTTATAAAATATCAAAACAATCAAAT-ATAAT
65 TTAATATTGTTAAATTTAAAATCGAAATAATA-TTTATAAAATATCAAAACAATCAAATAAT-AT
* *
63686 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
128 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
63751 TGAAACATAAATTACATAACTTTAAAA
193 TGAAACATAAATTACATAACTTTAAAA
63778 GCAGTTTTAA
Statistics
Matches: 207, Mismatches: 9, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
226 43 0.21
227 155 0.75
228 9 0.04
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (226 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCGAAATAATATTTATAAAATATCAAAACAATCAAATAATATTTT
GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
AACATAAATTACATAACTTTAAAAAAGTATA
Found at i:63866 original size:20 final size:19
Alignment explanation
Indices: 63843--63888 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
63833 CGATATACCA
63843 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
63863 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
63883 GGTAAA
1 GGTAAA
63889 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:64033 original size:20 final size:21
Alignment explanation
Indices: 64010--64058 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
64000 CGATATAACA
*
64010 GGTAAAATTATGA-TAAAACC
1 GGTAAAATAATGATTAAAACC
64030 GGTAACAA-AATGATTAAAACC
1 GGTAA-AATAATGATTAAAACC
64051 GGTAAAAT
1 GGTAAAAT
64059 GATACCGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.51, C:0.10, G:0.16, T:0.22
Consensus pattern (21 bp):
GGTAAAATAATGATTAAAACC
Found at i:88392 original size:22 final size:21
Alignment explanation
Indices: 88367--88407 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
88357 TATAAAAATA
88367 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
88389 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
88408 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:91485 original size:2 final size:2
Alignment explanation
Indices: 91478--91510 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
91468 TTTTTCCTTT
91478 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
91511 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:91515 original size:2 final size:2
Alignment explanation
Indices: 91510--91548 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
91500 TCTCTCTCTC
91510 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
91549 CAACTCTATT
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:96185 original size:21 final size:20
Alignment explanation
Indices: 96146--96185 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
96136 TACGCATTTA
*
96146 GTACCTAACTATCAGTTTTG
1 GTACCTAACTATCAATTTTG
*
96166 GTACCTAAACTTTCAATTTT
1 GTACCT-AACTATCAATTTT
96186 TTCAAAACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (20 bp):
GTACCTAACTATCAATTTTG
Found at i:109944 original size:16 final size:15
Alignment explanation
Indices: 109907--109937 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
109897 TTATTTATTG
109907 CGTTCCAAACTTTTT
1 CGTTCCAAACTTTTT
109922 CGTTCCAAACTTTTT
1 CGTTCCAAACTTTTT
109937 C
1 C
109938 TTTTCCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.45
Consensus pattern (15 bp):
CGTTCCAAACTTTTT
Found at i:110062 original size:30 final size:30
Alignment explanation
Indices: 110026--110108 Score: 148
Period size: 30 Copynumber: 2.8 Consensus size: 30
110016 TAATGCTAAA
*
110026 CTTAGAATAGTGTCAGTTTTTTACGTTTAG
1 CTTAGAATAGTGTCAGTTTTTTACATTTAG
*
110056 CTTAGAATAATGTCAGTTTTTTACATTTAG
1 CTTAGAATAGTGTCAGTTTTTTACATTTAG
110086 CTTAGAATAGTGTCAGTTTTTTA
1 CTTAGAATAGTGTCAGTTTTTTA
110109 TTAAGCTAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.47
Consensus pattern (30 bp):
CTTAGAATAGTGTCAGTTTTTTACATTTAG
Found at i:110779 original size:2 final size:2
Alignment explanation
Indices: 110735--110768 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
110725 TTATCTTATG
110735 AT 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 AT
110769 CATCCATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.