Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003696.1 Hibiscus syriacus cultivar Beakdansim tig00007902_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: 251402
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
File 2 of 4
Found at i:178898 original size:41 final size:40
Alignment explanation
Indices: 178853--178983 Score: 111
Period size: 41 Copynumber: 3.1 Consensus size: 40
178843 TTAGGTTTCA
**
178853 GGTTTTAGGTTTTTACCTTTAAATTTTGGGTTTCAAGTTTT
1 GGTTTTAGG-TTTTAGATTTAAATTTTGGGTTTCAAGTTTT
* * * *
178894 GGTTTTCTGGTTTTAGGATTCAAATTTTGGGTTTTAAGGTTT
1 GGTTTT-AGGTTTTA-GATTTAAATTTTGGGTTTCAAGTTTT
* * * *
178936 GAGTTTCA-GTTTTAGGTTTCAAATTTTGAGTTTCAGGTTTT
1 G-GTTTTAGGTTTTAGATTT-AAATTTTGGGTTTCAAGTTTT
178977 AGGTTTT
1 -GGTTTT
178984 GGGCTTTAAA
Statistics
Matches: 70, Mismatches: 15, Indels: 10
0.74 0.16 0.11
Matches are distributed among these distances:
40 3 0.04
41 38 0.54
42 25 0.36
43 4 0.06
ACGTcount: A:0.18, C:0.06, G:0.23, T:0.53
Consensus pattern (40 bp):
GGTTTTAGGTTTTAGATTTAAATTTTGGGTTTCAAGTTTT
Found at i:178991 original size:14 final size:13
Alignment explanation
Indices: 178974--179038 Score: 76
Period size: 14 Copynumber: 4.7 Consensus size: 13
178964 AGTTTCAGGT
178974 TTTAGGTTTTGGG
1 TTTAGGTTTTGGG
**
178987 CTTTAAATTTTGGG
1 -TTTAGGTTTTGGG
179001 TTTAAGGTTTTGGG
1 TTT-AGGTTTTGGG
179015 TTTAGGGTTTTGGG
1 TTTA-GGTTTTGGG
179029 TTTTAGGTTT
1 -TTTAGGTTT
179039 CAAATTTCTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
13 4 0.09
14 36 0.82
15 4 0.09
ACGTcount: A:0.12, C:0.02, G:0.32, T:0.54
Consensus pattern (13 bp):
TTTAGGTTTTGGG
Found at i:179002 original size:28 final size:28
Alignment explanation
Indices: 178971--179038 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
178961 TTGAGTTTCA
178971 GGTTTTAGGTTTTGGGCTTTA-AATTTTG
1 GGTTTTAGGTTTTGGG-TTTAGAATTTTG
* **
178999 GGTTTAAGGTTTTGGGTTTAGGGTTTTG
1 GGTTTTAGGTTTTGGGTTTAGAATTTTG
179027 GGTTTTAGGTTT
1 GGTTTTAGGTTT
179039 CAAATTTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 4 0.11
28 31 0.89
ACGTcount: A:0.12, C:0.01, G:0.34, T:0.53
Consensus pattern (28 bp):
GGTTTTAGGTTTTGGGTTTAGAATTTTG
Found at i:179054 original size:56 final size:56
Alignment explanation
Indices: 178994--179115 Score: 158
Period size: 56 Copynumber: 2.2 Consensus size: 56
178984 GGGCTTTAAA
** * * * *
178994 TTTTGGGTTTAAGGTTTTGGGTT-TAGGGTTTTGGGTTTTAGGTTTCAAATTTCT-AT
1 TTTTGGGTTTAAAATTTCGGGTTAT-GGGTTTTGAGTTTCAGGTTTCAAATTT-TGAG
179050 TTTTGGGTTTAAAATTTCGGGTTATGGGTTTTGAGTTTCAGGTTTCAAATTTTGAG
1 TTTTGGGTTTAAAATTTCGGGTTATGGGTTTTGAGTTTCAGGTTTCAAATTTTGAG
179106 TTTTGGGTTT
1 TTTTGGGTTT
179116 CGAGTTTCAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
55 1 0.02
56 56 0.97
57 1 0.02
ACGTcount: A:0.16, C:0.04, G:0.28, T:0.52
Consensus pattern (56 bp):
TTTTGGGTTTAAAATTTCGGGTTATGGGTTTTGAGTTTCAGGTTTCAAATTTTGAG
Found at i:179101 original size:35 final size:35
Alignment explanation
Indices: 179055--179124 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
179045 TCTATTTTTG
* *
179055 GGTTTAAAATTTCGGGTTATGGGTTTTGAGTTTCA
1 GGTTTAAAATTTCGAGTTATGGGTTTCGAGTTTCA
* * *
179090 GGTTTCAAATTTTGAGTTTTGGGTTTCGAGTTTCA
1 GGTTTAAAATTTCGAGTTATGGGTTTCGAGTTTCA
179125 AATTCTAGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.19, C:0.07, G:0.27, T:0.47
Consensus pattern (35 bp):
GGTTTAAAATTTCGAGTTATGGGTTTCGAGTTTCA
Found at i:179136 original size:28 final size:27
Alignment explanation
Indices: 179076--179171 Score: 86
Period size: 28 Copynumber: 3.4 Consensus size: 27
179066 TCGGGTTATG
* *
179076 GGTTTTGAGTTTC-AGGTTTCAAATTTT
1 GGTTTTGGGTTTCGA-GTTTCAAATTTA
179103 GAGTTTTGGGTTTCGAGTTTCAAATTCTA
1 G-GTTTTGGGTTTCGAGTTTCAAATT-TA
* * * * *
179132 GGTTTTAGGTTTTGGGTTTTGAATTTTA
1 GGTTTTGGGTTTCGAG-TTTCAAATTTA
179160 GGTTTTGGGTTT
1 GGTTTTGGGTTT
179172 TGTATTTAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
27 1 0.02
28 46 0.81
29 10 0.18
ACGTcount: A:0.16, C:0.05, G:0.27, T:0.52
Consensus pattern (27 bp):
GGTTTTGGGTTTCGAGTTTCAAATTTA
Found at i:179149 original size:14 final size:14
Alignment explanation
Indices: 179130--179172 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
179120 TTTCAAATTC
*
179130 TAGGTTTTAGGTTT
1 TAGGTTTTGGGTTT
* **
179144 TGGGTTTTGAATTT
1 TAGGTTTTGGGTTT
179158 TAGGTTTTGGGTTT
1 TAGGTTTTGGGTTT
179172 T
1 T
179173 GTATTTAAAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.12, C:0.00, G:0.30, T:0.58
Consensus pattern (14 bp):
TAGGTTTTGGGTTT
Found at i:179158 original size:21 final size:21
Alignment explanation
Indices: 179134--179178 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
179124 AAATTCTAGG
179134 TTTTAGGTTTTGGGTTTTGAA
1 TTTTAGGTTTTGGGTTTTGAA
*
179155 TTTTAGGTTTTGGGTTTTGTA
1 TTTTAGGTTTTGGGTTTTGAA
179176 TTT
1 TTT
179179 AAAATTTCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.11, C:0.00, G:0.27, T:0.62
Consensus pattern (21 bp):
TTTTAGGTTTTGGGTTTTGAA
Found at i:179172 original size:28 final size:28
Alignment explanation
Indices: 179097--179444 Score: 87
Period size: 28 Copynumber: 11.9 Consensus size: 28
179087 TCAGGTTTCA
* * **
179097 AATTTT-GAGTTTTGGGTTTCGAGTTTCA
1 AATTTTAG-GTTTTGGGTTTTGGGTTTTG
* *
179125 AATTCTAGGTTTTAGGTTTTGGGTTTTG
1 AATTTTAGGTTTTGGGTTTTGGGTTTTG
** **
179153 AATTTTAGGTTTTGGGTTTTGTATTTAA
1 AATTTTAGGTTTTGGGTTTTGGGTTTTG
*
179181 AATTTCAGGTTACAGGTTTTGGGTTTTAGGTTTTG
1 AA-TT----TT--AGGTTTTGGGTTTTGGGTTTTG
** * * * * * *
179216 GGTTTCAAGTTTCGAG-TTTCGGTTTTCA
1 AATTTTAGGTTTTGGGTTTTGGGTTTT-G
* * *
179244 AATTTTGGGTTTCGGGTTTCT-GG-TTTC
1 AATTTTAGGTTTTGGGTTT-TGGGTTTTG
* * * *
179271 AAATTTCGGTTTTCGGTTTTCGGGTTTCG
1 AATTTTAGGTTTTGGGTTTT-GGGTTTTG
* * * *
179300 AGTTTT-GAGTTTCGGGATTTGGGTTTCG
1 AATTTTAG-GTTTTGGGTTTTGGGTTTTG
* * * * * *
179328 AGA-TTCAGGTTTAGGTTTTTTGTTTTTA
1 A-ATTTTAGGTTTTGGGTTTTGGGTTTTG
*
179356 AATTTTGAGTTTCTTGTTTCGAGTTTTGGGTTTTG
1 AATTTT-AGGTT-TTG----G-GTTTTGGGTTTTG
** * * *
179391 GGTTTTAAGTTTTGGGTCTTGGGTTTCG
1 AATTTTAGGTTTTGGGTTTTGGGTTTTG
*
179419 AATTTTGGGTTTTGGGTTTTGGGTTT
1 AATTTTAGGTTTTGGGTTTTGGGTTT
179445 CGGGTTTCAG
Statistics
Matches: 225, Mismatches: 70, Indels: 50
0.65 0.20 0.14
Matches are distributed among these distances:
26 1 0.00
27 25 0.11
28 126 0.56
29 28 0.12
30 4 0.02
33 5 0.02
34 6 0.03
35 30 0.13
ACGTcount: A:0.13, C:0.07, G:0.28, T:0.52
Consensus pattern (28 bp):
AATTTTAGGTTTTGGGTTTTGGGTTTTG
Found at i:179184 original size:56 final size:56
Alignment explanation
Indices: 179097--179207 Score: 138
Period size: 56 Copynumber: 2.0 Consensus size: 56
179087 TCAGGTTTCA
* **
179097 AATTTTGAGTTTTGGGTTTCGAGTTTCAAA-TTCTAGGTTTTAGGTTTTGGGTTTTG
1 AATTTTGAGTTTTGGGTTTCGAGTTTAAAATTTC-AGGTTACAGGTTTTGGGTTTTG
*
179153 AATTTT-AGGTTTTGGGTTTTGTA-TTTAAAATTTCAGGTTACAGGTTTTGGGTTTT
1 AATTTTGA-GTTTTGGGTTTCG-AGTTTAAAATTTCAGGTTACAGGTTTTGGGTTTT
179208 AGGTTTTGGG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
55 1 0.02
56 43 0.90
57 4 0.08
ACGTcount: A:0.18, C:0.05, G:0.25, T:0.52
Consensus pattern (56 bp):
AATTTTGAGTTTTGGGTTTCGAGTTTAAAATTTCAGGTTACAGGTTTTGGGTTTTG
Found at i:179211 original size:14 final size:14
Alignment explanation
Indices: 179194--179220 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
179184 TTCAGGTTAC
179194 AGGTTTTGGGTTTT
1 AGGTTTTGGGTTTT
179208 AGGTTTTGGGTTT
1 AGGTTTTGGGTTT
179221 CAAGTTTCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.00, G:0.37, T:0.56
Consensus pattern (14 bp):
AGGTTTTGGGTTTT
Found at i:179227 original size:21 final size:21
Alignment explanation
Indices: 179203--179263 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
179193 CAGGTTTTGG
*
179203 GTTTTAGGTTTTGGGTTTCAA
1 GTTTTAGGTTTCGGGTTTCAA
* *
179224 G-TTTCGAGTTTCGGTTTTCAA
1 GTTTTAG-GTTTCGGGTTTCAA
* *
179245 ATTTTGGGTTTCGGGTTTC
1 GTTTTAGGTTTCGGGTTTC
179264 TGGTTTCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 4 0.12
21 24 0.75
22 4 0.12
ACGTcount: A:0.11, C:0.10, G:0.28, T:0.51
Consensus pattern (21 bp):
GTTTTAGGTTTCGGGTTTCAA
Found at i:179242 original size:14 final size:14
Alignment explanation
Indices: 179224--179339 Score: 74
Period size: 14 Copynumber: 8.3 Consensus size: 14
179214 TGGGTTTCAA
179224 GTTTCGAGTTTCGG
1 GTTTCGAGTTTCGG
* * * *
179238 TTTTCAAATTTTGG
1 GTTTCGAGTTTCGG
* *
179252 GTTTCGGGTTTCTG
1 GTTTCGAGTTTCGG
* *
179266 GTTTCAAATTTCGG
1 GTTTCGAGTTTCGG
*
179280 TTTTCG-GTTTTCGG
1 GTTTCGAG-TTTCGG
* *
179294 GTTTCGAGTTTTGA
1 GTTTCGAGTTTCGG
*
179308 GTTTCGGGATTT-GG
1 GTTTCGAG-TTTCGG
* *
179322 GTTTCGAGATTCAG
1 GTTTCGAGTTTCGG
179336 GTTT
1 GTTT
179340 AGGTTTTTTG
Statistics
Matches: 73, Mismatches: 25, Indels: 8
0.69 0.24 0.08
Matches are distributed among these distances:
13 2 0.03
14 67 0.92
15 4 0.05
ACGTcount: A:0.11, C:0.11, G:0.29, T:0.48
Consensus pattern (14 bp):
GTTTCGAGTTTCGG
Found at i:179250 original size:49 final size:49
Alignment explanation
Indices: 179197--179291 Score: 131
Period size: 49 Copynumber: 1.9 Consensus size: 49
179187 AGGTTACAGG
* *
179197 TTTTGGGTTTTAGGTTT-TGGGTTTCAAGTTTCGAG-TTTCGGTTTTCAAA
1 TTTTGGGTTTCAGGTTTCT-GGTTTCAAATTTCG-GTTTTCGGTTTTCAAA
*
179246 TTTTGGGTTTCGGGTTTCTGGTTTCAAATTTCGGTTTTCGGTTTTC
1 TTTTGGGTTTCAGGTTTCTGGTTTCAAATTTCGGTTTTCGGTTTTC
179292 GGGTTTCGAG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
48 1 0.02
49 39 0.95
50 1 0.02
ACGTcount: A:0.11, C:0.11, G:0.26, T:0.53
Consensus pattern (49 bp):
TTTTGGGTTTCAGGTTTCTGGTTTCAAATTTCGGTTTTCGGTTTTCAAA
Found at i:179255 original size:42 final size:42
Alignment explanation
Indices: 179204--179284 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
179194 AGGTTTTGGG
* * *
179204 TTTTAGGTTTTGGGTTTCAAGTTTCGAGTTTCGGTTTTCAAA
1 TTTTAGGTTTCGGGTTTCAAGTTTCAAATTTCGGTTTTCAAA
* **
179246 TTTTGGGTTTCGGGTTTCTGGTTTCAAATTTCGGTTTTC
1 TTTTAGGTTTCGGGTTTCAAGTTTCAAATTTCGGTTTTC
179285 GGTTTTCGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.12, C:0.11, G:0.25, T:0.52
Consensus pattern (42 bp):
TTTTAGGTTTCGGGTTTCAAGTTTCAAATTTCGGTTTTCAAA
Found at i:179388 original size:7 final size:7
Alignment explanation
Indices: 179378--179466 Score: 88
Period size: 7 Copynumber: 12.7 Consensus size: 7
179368 CTTGTTTCGA
179378 GTTTTGG
1 GTTTTGG
179385 GTTTTGG
1 GTTTTGG
**
179392 GTTTTAA
1 GTTTTGG
179399 GTTTTGG
1 GTTTTGG
*
179406 GTCTTGG
1 GTTTTGG
* *
179413 GTTTCGA
1 GTTTTGG
*
179420 ATTTTGG
1 GTTTTGG
179427 GTTTTGG
1 GTTTTGG
179434 GTTTTGG
1 GTTTTGG
*
179441 GTTTCGG
1 GTTTTGG
**
179448 GTTTCAG
1 GTTTTGG
*
179455 TTTTTGG
1 GTTTTGG
179462 GTTTT
1 GTTTT
179467 TAAATTCAGG
Statistics
Matches: 64, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 64 1.00
ACGTcount: A:0.06, C:0.04, G:0.35, T:0.55
Consensus pattern (7 bp):
GTTTTGG
Found at i:179388 original size:21 final size:21
Alignment explanation
Indices: 179358--179430 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 21
179348 TGTTTTTAAA
*
179358 TTTTGAGTTTCTTGTTTCGAG
1 TTTTGGGTTTCTTGTTTCGAG
* **
179379 TTTTGGGTTT-TGGGTTTTAAG
1 TTTTGGGTTTCT-TGTTTCGAG
*
179400 TTTTGGG--TCTTGGGTTTCGAA
1 TTTTGGGTTTCTT--GTTTCGAG
179421 TTTTGGGTTT
1 TTTTGGGTTT
179431 TGGGTTTTGG
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
19 1 0.03
20 2 0.05
21 34 0.89
23 1 0.03
ACGTcount: A:0.08, C:0.05, G:0.30, T:0.56
Consensus pattern (21 bp):
TTTTGGGTTTCTTGTTTCGAG
Found at i:179398 original size:42 final size:41
Alignment explanation
Indices: 179351--179438 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 41
179341 GGTTTTTTGT
* *
179351 TTTTAAATTTTGAGTTTCTT-GTTTCGAGTTTTGGGTTTTGGG
1 TTTTAAATTTTG-G-GTCTTGGTTTCGAATTTTGGGTTTTGGG
*
179393 TTTTAAGTTTTGGGTCTTGGGTTTCGAATTTTGGGTTTTGGG
1 TTTTAAATTTTGGGTCTT-GGTTTCGAATTTTGGGTTTTGGG
179435 TTTT
1 TTTT
179439 GGGTTTCGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
40 4 0.10
41 1 0.02
42 36 0.88
ACGTcount: A:0.10, C:0.05, G:0.28, T:0.57
Consensus pattern (41 bp):
TTTTAAATTTTGGGTCTTGGTTTCGAATTTTGGGTTTTGGG
Found at i:179433 original size:21 final size:21
Alignment explanation
Indices: 179371--179437 Score: 91
Period size: 21 Copynumber: 3.2 Consensus size: 21
179361 TGAGTTTCTT
*
179371 GTTTCGAGTTTTGGGTTTTGG
1 GTTTCGAATTTTGGGTTTTGG
* *
179392 GTTT-TAAGTTTTGGGTCTTGG
1 GTTTCGAA-TTTTGGGTTTTGG
179413 GTTTCGAATTTTGGGTTTTGG
1 GTTTCGAATTTTGGGTTTTGG
179434 GTTT
1 GTTT
179438 TGGGTTTCGG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
20 1 0.03
21 36 0.92
22 2 0.05
ACGTcount: A:0.07, C:0.04, G:0.34, T:0.54
Consensus pattern (21 bp):
GTTTCGAATTTTGGGTTTTGG
Found at i:179499 original size:21 final size:21
Alignment explanation
Indices: 179475--179514 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
179465 TTTAAATTCA
179475 GGTTT-TAGCTTTCAAATTTAT
1 GGTTTCTAG-TTTCAAATTTAT
*
179496 GGTTTCTAGTTTTAAATTT
1 GGTTTCTAGTTTCAAATTT
179515 TGATTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.23, C:0.07, G:0.15, T:0.55
Consensus pattern (21 bp):
GGTTTCTAGTTTCAAATTTAT
Found at i:179529 original size:14 final size:14
Alignment explanation
Indices: 179512--179550 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
179502 TAGTTTTAAA
*
179512 TTTTGATTTTTTGT
1 TTTTGATTTTTTGG
*
179526 TTTTGAGTTTTTGG
1 TTTTGATTTTTTGG
179540 TTTTGATTTTT
1 TTTTGATTTTT
179551 GAATTTAGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.08, C:0.00, G:0.18, T:0.74
Consensus pattern (14 bp):
TTTTGATTTTTTGG
Found at i:179562 original size:21 final size:20
Alignment explanation
Indices: 179520--179563 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
179510 AATTTTGATT
* **
179520 TTTTGTTTTTGAGTTTTTGG
1 TTTTGTTTTTGAATTTAGGG
179540 TTTTGATTTTTGAATTTAGGG
1 TTTTG-TTTTTGAATTTAGGG
179561 TTT
1 TTT
179564 CTAGTTTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.11, C:0.00, G:0.23, T:0.66
Consensus pattern (20 bp):
TTTTGTTTTTGAATTTAGGG
Found at i:179606 original size:20 final size:20
Alignment explanation
Indices: 179581--179618 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
179571 CAAATTTCAA
*
179581 ATTTTAGGTTTCAGGTTTTT
1 ATTTTAAGTTTCAGGTTTTT
*
179601 ATTTTAAGTTTTAGGTTT
1 ATTTTAAGTTTCAGGTTT
179619 CAAAATTCTA
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:0.18, C:0.03, G:0.18, T:0.61
Consensus pattern (20 bp):
ATTTTAAGTTTCAGGTTTTT
Found at i:179657 original size:34 final size:33
Alignment explanation
Indices: 179595--179675 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 33
179585 TAGGTTTCAG
*
179595 GTTTTTA-TTTTAAGTTTTAGGTTTCAAAATTCT-A
1 GTTTTTAGTTTT--GTTTTAGGTTCCAAAATT-TGA
179629 GTTTTTAGTTTTGTTTTAGGGTTCCAAAATTTGA
1 GTTTTTAGTTTTGTTTTA-GGTTCCAAAATTTGA
*
179663 GTTTTTGGTTTTG
1 GTTTTTAGTTTTG
179676 AGTTTCAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 7 0.17
34 31 0.74
35 4 0.10
ACGTcount: A:0.20, C:0.05, G:0.19, T:0.57
Consensus pattern (33 bp):
GTTTTTAGTTTTGTTTTAGGTTCCAAAATTTGA
Found at i:179695 original size:21 final size:21
Alignment explanation
Indices: 179671--179710 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
179661 GAGTTTTTGG
179671 TTTTGAGTTTCAAGTTTCATA
1 TTTTGAGTTTCAAGTTTCATA
* *
179692 TTTTGGGTTTCAGGTTTCA
1 TTTTGAGTTTCAAGTTTCA
179711 GGTTTCGGTT
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:0.17, C:0.10, G:0.20, T:0.53
Consensus pattern (21 bp):
TTTTGAGTTTCAAGTTTCATA
Found at i:179723 original size:21 final size:21
Alignment explanation
Indices: 179699--179765 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
179689 ATATTTTGGG
179699 TTTCAGGTTTCAGGTTTCGGT
1 TTTCAGGTTTCAGGTTTCGGT
* ** *
179720 TTTCAAGTTTTGGGTTTCGAAT
1 TTTCAGGTTTCAGGTTTCG-GT
*
179742 TTT-AGGTTTCAGTTTTCGGGT
1 TTTCAGGTTTCAGGTTTC-GGT
179763 TTT
1 TTT
179766 GTTTTTTGTG
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
21 30 0.86
22 5 0.14
ACGTcount: A:0.12, C:0.10, G:0.25, T:0.52
Consensus pattern (21 bp):
TTTCAGGTTTCAGGTTTCGGT
Found at i:179737 original size:14 final size:14
Alignment explanation
Indices: 179704--179764 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
179694 TTGGGTTTCA
* *
179704 GGTTTCAGGTTTCG
1 GGTTTCAAGTTTTG
*
179718 GTTTTCAAGTTTTG
1 GGTTTCAAGTTTTG
*
179732 GGTTTCGAA-TTTTA
1 GGTTTC-AAGTTTTG
179746 GGTTTC-AGTTTTCG
1 GGTTTCAAGTTTT-G
179760 GGTTT
1 GGTTT
179765 TGTTTTTTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 1 0.03
13 4 0.11
14 31 0.82
15 2 0.05
ACGTcount: A:0.11, C:0.10, G:0.28, T:0.51
Consensus pattern (14 bp):
GGTTTCAAGTTTTG
Found at i:179766 original size:35 final size:35
Alignment explanation
Indices: 179692--179758 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
179682 AAGTTTCATA
* *
179692 TTTTGGGTTTCAGGTTTCAGGTTTCGGTTTTCAAG
1 TTTTGGGTTTCAGATTTCAGGTTTCAGTTTTCAAG
*
179727 TTTTGGGTTTC-GAATTTTAGGTTTCAGTTTTC
1 TTTTGGGTTTCAG-ATTTCAGGTTTCAGTTTTC
179759 GGGTTTTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 1 0.04
35 27 0.96
ACGTcount: A:0.12, C:0.10, G:0.25, T:0.52
Consensus pattern (35 bp):
TTTTGGGTTTCAGATTTCAGGTTTCAGTTTTCAAG
Found at i:179771 original size:14 final size:14
Alignment explanation
Indices: 179753--179806 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
179743 TTAGGTTTCA
179753 GTTTTCGGGTTTTGT
1 GTTTT-GGGTTTTGT
* *
179768 TTTTTGTGTTTTGT
1 GTTTTGGGTTTTGT
*
179782 GTTTTGGGTTTTGG
1 GTTTTGGGTTTTGT
*
179796 GTTTTAGGTTT
1 GTTTTGGGTTT
179807 CAAATTTCGG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 29 0.88
15 4 0.12
ACGTcount: A:0.02, C:0.02, G:0.31, T:0.65
Consensus pattern (14 bp):
GTTTTGGGTTTTGT
Found at i:179862 original size:35 final size:34
Alignment explanation
Indices: 179804--179931 Score: 107
Period size: 35 Copynumber: 3.7 Consensus size: 34
179794 GGGTTTTAGG
*** *
179804 TTTCAAATTTC-GGTTTTTAGTTTTTGGGTTCAT
1 TTTCAAATTTCAGGTTTCGGGTTTTTGGTTTCAT
**
179837 ATTTCAAATTTCAGGTTTCGGGTTTTAT-GTTTCGGG
1 -TTTCAAATTTCAGGTTTCGGGTTTT-TGGTTTC-AT
* *
179873 TTTAAAATTTCAGGTTTCGGGTTTTTGTTTTCGAT
1 TTTCAAATTTCAGGTTTCGGGTTTTTGGTTTC-AT
* * *
179908 TTTTAAATTTCGGGTTTTGGGTTT
1 TTTCAAATTTCAGGTTTCGGGTTT
179932 CAAGTTTCAA
Statistics
Matches: 77, Mismatches: 13, Indels: 7
0.79 0.13 0.07
Matches are distributed among these distances:
34 12 0.16
35 64 0.83
36 1 0.01
ACGTcount: A:0.16, C:0.09, G:0.22, T:0.54
Consensus pattern (34 bp):
TTTCAAATTTCAGGTTTCGGGTTTTTGGTTTCAT
Found at i:179943 original size:28 final size:28
Alignment explanation
Indices: 179887--179944 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
179877 AAATTTCAGG
* * * * *
179887 TTTCGGGTTTTTGTTTTCGATTTTTAAA
1 TTTCGGGTTTTGGGTTTCAAGTTTCAAA
179915 TTTCGGGTTTTGGGTTTCAAGTTTCAAA
1 TTTCGGGTTTTGGGTTTCAAGTTTCAAA
179943 TT
1 TT
179945 CTGCTGCTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.16, C:0.09, G:0.21, T:0.55
Consensus pattern (28 bp):
TTTCGGGTTTTGGGTTTCAAGTTTCAAA
Found at i:180025 original size:21 final size:21
Alignment explanation
Indices: 180001--180206 Score: 87
Period size: 21 Copynumber: 9.8 Consensus size: 21
179991 AGGTATCAGG
*
180001 TTTTGAGTTTTGGGTTTTAAA
1 TTTTGAGTTTTGGGTTTCAAA
* * *
180022 TTTTGGGTTTAGGGTTTCAAG
1 TTTTGAGTTTTGGGTTTCAAA
* *
180043 TTTT-AGATTTTAGGTTTCAAG
1 TTTTGAG-TTTTGGGTTTCAAA
**
180064 TTTCAAGTTTTGGGTTTCAAA
1 TTTTGAGTTTTGGGTTTCAAA
* * ***
180085 TTTCGGGTAAAGGGTTTCAAA
1 TTTTGAGTTTTGGGTTTCAAA
* * *
180106 TTTT-AGGTTTCGAGATTCAAA
1 TTTTGA-GTTTTGGGTTTCAAA
* * * * **
180127 TTTCGGGTTTTAGGTTTTATG
1 TTTTGAGTTTTGGGTTTCAAA
** ***
180148 TTTT-AGATTTTATGTTTCGGG
1 TTTTGAG-TTTTGGGTTTCAAA
*
180169 TTTTGGGTTTTGGGTTTCAAA
1 TTTTGAGTTTTGGGTTTCAAA
*
180190 TTTT-AGATTTTGAGTTT
1 TTTTGAG-TTTTGGGTTT
180207 TGGGTTTTAG
Statistics
Matches: 133, Mismatches: 45, Indels: 14
0.69 0.23 0.07
Matches are distributed among these distances:
20 3 0.02
21 127 0.95
22 3 0.02
ACGTcount: A:0.19, C:0.05, G:0.24, T:0.51
Consensus pattern (21 bp):
TTTTGAGTTTTGGGTTTCAAA
Found at i:180045 original size:28 final size:28
Alignment explanation
Indices: 180014--180074 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
180004 TGAGTTTTGG
* *
180014 GTTTTAAATTTTGGGTTT-AGGGTTTCAA
1 GTTTTAAATTTTAGGTTTCA-AGTTTCAA
*
180042 GTTTTAGATTTTAGGTTTCAAGTTTCAA
1 GTTTTAAATTTTAGGTTTCAAGTTTCAA
180070 GTTTT
1 GTTTT
180075 GGGTTTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.52
Consensus pattern (28 bp):
GTTTTAAATTTTAGGTTTCAAGTTTCAA
Found at i:180099 original size:63 final size:63
Alignment explanation
Indices: 179986--180111 Score: 171
Period size: 63 Copynumber: 2.0 Consensus size: 63
179976 AAGGTTTCAA
* ** * * ** *
179986 ATTTTAGGTATCAGGTTTTGAGTTTTGGGTTTTAAATTTTGGGTTTAGGGTTTCAAGTTTTAG
1 ATTTTAGGTATCAAGTTTCAAGTTTTGGGTTTCAAATTTCGGGTAAAGGGTTTCAAATTTTAG
*
180049 ATTTTAGGTTTCAAGTTTCAAGTTTTGGGTTTCAAATTTCGGGTAAAGGGTTTCAAATTTTAG
1 ATTTTAGGTATCAAGTTTCAAGTTTTGGGTTTCAAATTTCGGGTAAAGGGTTTCAAATTTTAG
180112 GTTTCGAGAT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.22, C:0.06, G:0.25, T:0.48
Consensus pattern (63 bp):
ATTTTAGGTATCAAGTTTCAAGTTTTGGGTTTCAAATTTCGGGTAAAGGGTTTCAAATTTTAG
Found at i:180101 original size:42 final size:42
Alignment explanation
Indices: 180055--180134 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
180045 TTAGATTTTA
* * * *
180055 GGTTTCAAGTTTCAAGTTTTGGGTTTCAAATTTCGGGTAAAG
1 GGTTTCAAATTTCAAGTTTCGAGATTCAAATTTCGGGTAAAG
* *
180097 GGTTTCAAATTTTAGGTTTCGAGATTCAAATTTCGGGT
1 GGTTTCAAATTTCAAGTTTCGAGATTCAAATTTCGGGT
180135 TTTAGGTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.41
Consensus pattern (42 bp):
GGTTTCAAATTTCAAGTTTCGAGATTCAAATTTCGGGTAAAG
Found at i:180125 original size:63 final size:63
Alignment explanation
Indices: 180006--180130 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
179996 TCAGGTTTTG
* * ** * * * *
180006 AGTTTTGGGTTTTAAATTTTGGGTTTAGGGTTTCAAGTTTTAGATTTTAGGTTTCAAGTTTCA
1 AGTTTTGGGTTTCAAATTTCGGGTAAAGGGTTTCAAATTTTAGATTTGAGGATTCAAATTTCA
*
180069 AGTTTTGGGTTTCAAATTTCGGGTAAAGGGTTTCAAATTTTAGGTTTCGA-GATTCAAATTTC
1 AGTTTTGGGTTTCAAATTTCGGGTAAAGGGTTTCAAATTTTAGATTT-GAGGATTCAAATTTC
180131 GGGTTTTAGG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 51 0.98
64 1 0.02
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.46
Consensus pattern (63 bp):
AGTTTTGGGTTTCAAATTTCGGGTAAAGGGTTTCAAATTTTAGATTTGAGGATTCAAATTTCA
Found at i:180143 original size:42 final size:42
Alignment explanation
Indices: 180050--180143 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 42
180040 AAGTTTTAGA
* * * *
180050 TTTTAGGTTTCAAGTTTCAAGTTTTGGGTTTCAAATTTCGGG
1 TTTTAGGTTTCAAATTTCAAGTTTCGAGATTCAAATTTCGGG
** * *
180092 -TAAAGGGTTTCAAATTTTAGGTTTCGAGATTCAAATTTCGGG
1 TTTTA-GGTTTCAAATTTCAAGTTTCGAGATTCAAATTTCGGG
180134 TTTTAGGTTT
1 TTTTAGGTTT
180144 TATGTTTTAG
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
41 2 0.05
42 36 0.90
43 2 0.05
ACGTcount: A:0.22, C:0.09, G:0.23, T:0.46
Consensus pattern (42 bp):
TTTTAGGTTTCAAATTTCAAGTTTCGAGATTCAAATTTCGGG
Found at i:180144 original size:7 final size:7
Alignment explanation
Indices: 180132--180297 Score: 75
Period size: 7 Copynumber: 23.7 Consensus size: 7
180122 TCAAATTTCG
180132 GGTTTTA
1 GGTTTTA
180139 GGTTTTA
1 GGTTTTA
*
180146 TGTTTTA
1 GGTTTTA
*
180153 GATTTTA
1 GGTTTTA
* **
180160 TGTTTCG
1 GGTTTTA
*
180167 GGTTTTG
1 GGTTTTA
*
180174 GGTTTTG
1 GGTTTTA
*
180181 GGTTTCA
1 GGTTTTA
**
180188 AATTTTA
1 GGTTTTA
*
180195 GATTTT-
1 GGTTTTA
*
180201 GAGTTTTG
1 G-GTTTTA
180209 GGTTTTA
1 GGTTTTA
*
180216 GGGTTCTA
1 -GGTTTTA
*
180224 -GTTTCA
1 GGTTTTA
*
180230 AGTTTTA
1 GGTTTTA
*
180237 GGTTTCA
1 GGTTTTA
*
180244 GGTTTTG
1 GGTTTTA
*
180251 GGTTTCA
1 GGTTTTA
**
180258 AATTTTA
1 GGTTTTA
*
180265 GATTTTA
1 GGTTTTA
*
180272 GGTTTCA
1 GGTTTTA
**
180279 AATTTTA
1 GGTTTTA
*
180286 GGTTTCA
1 GGTTTTA
180293 GGTTT
1 GGTTT
180298 CGAGTTTTAA
Statistics
Matches: 116, Mismatches: 39, Indels: 8
0.71 0.24 0.05
Matches are distributed among these distances:
6 5 0.04
7 104 0.90
8 7 0.06
ACGTcount: A:0.17, C:0.05, G:0.25, T:0.54
Consensus pattern (7 bp):
GGTTTTA
Found at i:180145 original size:35 final size:36
Alignment explanation
Indices: 180106--180256 Score: 94
Period size: 35 Copynumber: 4.3 Consensus size: 36
180096 GGGTTTCAAA
180106 TTTTAGGTTTCGAGA-TTCAAATTTCGGGTTTTAGG
1 TTTTAGGTTTCGAGATTTCAAATTTCGGGTTTTAGG
* * * ** *
180141 TTTTATGTTT-TAGATTTTATGTTTCGGGTTTTGGG
1 TTTTAGGTTTCGAGATTTCAAATTTCGGGTTTTAGG
* * * * * * *
180176 TTTTGGGTTTC-AAATTTTAGATTTTGAGTTTTGGG
1 TTTTAGGTTTCGAGATTTCAAATTTCGGGTTTTAGG
* * * ** *
180211 TTTTAGGGTTCTAG-TTTCAAGTTTTAGGTTTCAGG
1 TTTTAGGTTTCGAGATTTCAAATTTCGGGTTTTAGG
*
180246 TTTTGGGTTTC
1 TTTTAGGTTTC
180257 AAATTTTAGA
Statistics
Matches: 88, Mismatches: 25, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
34 3 0.03
35 84 0.95
36 1 0.01
ACGTcount: A:0.15, C:0.06, G:0.26, T:0.53
Consensus pattern (36 bp):
TTTTAGGTTTCGAGATTTCAAATTTCGGGTTTTAGG
Found at i:180177 original size:42 final size:42
Alignment explanation
Indices: 180131--180255 Score: 137
Period size: 42 Copynumber: 3.0 Consensus size: 42
180121 TTCAAATTTC
* * *
180131 GGGTTTTAGGTTTTATGTTTTAGATTTTATGTTTCGGGTTTT-
1 GGGTTTTAGGTTTCAAGTTTTAGATTTTA-GTTTTGGGTTTTA
* *
180173 GGGTTTTGGGTTTCAAATTTTAGATTTTGAGTTTTGGGTTTTA
1 GGGTTTTAGGTTTCAAGTTTTAGATTTT-AGTTTTGGGTTTTA
* * *
180216 GGGTTCTA-GTTTCAAGTTTTAGGTTTCAGGTTTTGGGTTT
1 GGGTTTTAGGTTTCAAGTTTTAGATTTTA-GTTTTGGGTTT
180256 CAAATTTTAG
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.01
42 62 0.89
43 7 0.10
ACGTcount: A:0.14, C:0.04, G:0.28, T:0.54
Consensus pattern (42 bp):
GGGTTTTAGGTTTCAAGTTTTAGATTTTAGTTTTGGGTTTTA
Found at i:180285 original size:70 final size:70
Alignment explanation
Indices: 180174--180306 Score: 180
Period size: 70 Copynumber: 1.9 Consensus size: 70
180164 TCGGGTTTTG
****
180174 GGTTTTGGGTTTCAAATTTTAGATTTTGAGTTTTGGGTTTTAGGGTTCTA-GTTTCAAGTTTTAG
1 GGTTTTGGGTTTCAAATTTTAGATTTTGAGTTTCAAATTTTAGGGTTC-AGGTTTCAAGTTTTAG
180238 GTTTCA
65 GTTTCA
* *
180244 GGTTTTGGGTTTCAAATTTTAGATTTT-AGGTTTCAAATTTTAGGTTTCAGGTTTCGAGTTTTA
1 GGTTTTGGGTTTCAAATTTTAGATTTTGA-GTTTCAAATTTTAGGGTTCAGGTTTCAAGTTTTA
180307 AATTTTGGGT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
69 2 0.04
70 53 0.96
ACGTcount: A:0.19, C:0.06, G:0.24, T:0.51
Consensus pattern (70 bp):
GGTTTTGGGTTTCAAATTTTAGATTTTGAGTTTCAAATTTTAGGGTTCAGGTTTCAAGTTTTAGG
TTTCA
Found at i:180317 original size:28 final size:28
Alignment explanation
Indices: 180273--180339 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
180263 TAGATTTTAG
*
180273 GTTTCAAATTTTAGGTTTC-AGGTTTCGA
1 GTTTCAAATTTTAGGTTTCGA-GTTTCAA
* *
180301 GTTTTAAATTTTGGGTTTCGAGTTTCAA
1 GTTTCAAATTTTAGGTTTCGAGTTTCAA
180329 GTTTCAAATTT
1 GTTTCAAATTT
180340 CGATTTTCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 33 0.97
29 1 0.03
ACGTcount: A:0.22, C:0.09, G:0.19, T:0.49
Consensus pattern (28 bp):
GTTTCAAATTTTAGGTTTCGAGTTTCAA
Found at i:180325 original size:21 final size:21
Alignment explanation
Indices: 180246--180319 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
180236 AGGTTTCAGG
*
180246 TTTTGGGTTTCAAATTTTAGA
1 TTTTAGGTTTCAAATTTTAGA
*
180267 TTTTAGGTTTCAAATTTTAGG
1 TTTTAGGTTTCAAATTTTAGA
* * * *
180288 TTTCAGGTTTCGAGTTTTAAA
1 TTTTAGGTTTCAAATTTTAGA
*
180309 TTTTGGGTTTC
1 TTTTAGGTTTC
180320 GAGTTTCAAG
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.53
Consensus pattern (21 bp):
TTTTAGGTTTCAAATTTTAGA
Found at i:180340 original size:21 final size:21
Alignment explanation
Indices: 180316--180374 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
180306 AAATTTTGGG
180316 TTTCGAGTTTCAAGTTTCAAA
1 TTTCGAGTTTCAAGTTTCAAA
* ** *
180337 TTTCGATTTTCTGGTTTCAAT
1 TTTCGAGTTTCAAGTTTCAAA
*
180358 TTTC-ATGTTTCATGTTT
1 TTTCGA-GTTTCAAGTTT
180375 TGGTATTTCA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.54
Consensus pattern (21 bp):
TTTCGAGTTTCAAGTTTCAAA
Found at i:180411 original size:14 final size:14
Alignment explanation
Indices: 180394--180445 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
180384 AGGTTTTGAT
*
180394 TTTTGGGTTTCAAA
1 TTTTAGGTTTCAAA
****
180408 TTTTAGGTTTTGGG
1 TTTTAGGTTTCAAA
*
180422 TTTTGGGTTTCAAA
1 TTTTAGGTTTCAAA
180436 TTTTAGGTTT
1 TTTTAGGTTT
180446 TCGGTTTCCG
Statistics
Matches: 27, Mismatches: 11, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.15, C:0.04, G:0.25, T:0.56
Consensus pattern (14 bp):
TTTTAGGTTTCAAA
Found at i:180415 original size:28 final size:28
Alignment explanation
Indices: 180379--180536 Score: 129
Period size: 28 Copynumber: 5.4 Consensus size: 28
180369 ATGTTTTGGT
* *
180379 ATTTCAGGTTTTGATTTTTGGGTTTCAA
1 ATTTTAGGTTTTGAGTTTTGGGTTTCAA
*
180407 ATTTTAGGTTTTGGGTTTTGGGTTTCAA
1 ATTTTAGGTTTTGAGTTTTGGGTTTCAA
**
180435 ATTTTAGGTTTTCG-GTTTCCGGTTTCAA
1 ATTTTAGGTTTT-GAGTTTTGGGTTTCAA
* * *
180463 GTTTTGGGTTTTGAATTTAAGATTTTGAGTTTCAA
1 ATTTTAGGTTTTG------AG-TTTTGGGTTTCAA
* * *
180498 ATTTCAGGTTTTAAGTTTCGGGTTTCAA
1 ATTTTAGGTTTTGAGTTTTGGGTTTCAA
*
180526 ATTTTGGGTTT
1 ATTTTAGGTTT
180537 CAAATTTTAG
Statistics
Matches: 103, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
27 1 0.01
28 79 0.77
29 3 0.03
34 1 0.01
35 19 0.18
ACGTcount: A:0.18, C:0.07, G:0.23, T:0.52
Consensus pattern (28 bp):
ATTTTAGGTTTTGAGTTTTGGGTTTCAA
Found at i:180501 original size:14 final size:14
Alignment explanation
Indices: 180471--180544 Score: 53
Period size: 14 Copynumber: 5.3 Consensus size: 14
180461 AAGTTTTGGG
*
180471 TTTTGAATTT-AAGA
1 TTTTGAGTTTCAA-A
180485 TTTTGAGTTTCAAA
1 TTTTGAGTTTCAAA
* * *
180499 -TTTCAGGTTTTAAG
1 TTTTGA-GTTTCAAA
* *
180513 TTTCGGGTTTCAAA
1 TTTTGAGTTTCAAA
*
180527 TTTTGGGTTTCAAA
1 TTTTGAGTTTCAAA
180541 TTTT
1 TTTT
180545 AGGTTTCGGG
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
13 4 0.09
14 39 0.83
15 4 0.09
ACGTcount: A:0.24, C:0.07, G:0.18, T:0.51
Consensus pattern (14 bp):
TTTTGAGTTTCAAA
Found at i:180538 original size:35 final size:35
Alignment explanation
Indices: 180506--180606 Score: 139
Period size: 35 Copynumber: 2.9 Consensus size: 35
180496 AAATTTCAGG
*
180506 TTTTAAGTTTCGGGTTTCAAATTTTGGGTTTCAAA
1 TTTTAGGTTTCGGGTTTCAAATTTTGGGTTTCAAA
* **
180541 TTTTAGGTTTCGGGTTTTAGTTTTTGGGTTTCAAA
1 TTTTAGGTTTCGGGTTTCAAATTTTGGGTTTCAAA
* * *
180576 TTTTGGGTTTTGGGTTTCAAATTTCGGGTTT
1 TTTTAGGTTTCGGGTTTCAAATTTTGGGTTT
180607 TCAGTTTCGA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.16, C:0.07, G:0.25, T:0.52
Consensus pattern (35 bp):
TTTTAGGTTTCGGGTTTCAAATTTTGGGTTTCAAA
Found at i:180549 original size:14 final size:14
Alignment explanation
Indices: 180491--180551 Score: 68
Period size: 14 Copynumber: 4.4 Consensus size: 14
180481 AAGATTTTGA
180491 GTTTCAAATTTCAG
1 GTTTCAAATTTCAG
* * *
180505 GTTTTAAGTTTCGG
1 GTTTCAAATTTCAG
**
180519 GTTTCAAATTTTGG
1 GTTTCAAATTTCAG
*
180533 GTTTCAAATTTTAG
1 GTTTCAAATTTCAG
180547 GTTTC
1 GTTTC
180552 GGGTTTTAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 40 1.00
ACGTcount: A:0.21, C:0.10, G:0.20, T:0.49
Consensus pattern (14 bp):
GTTTCAAATTTCAG
Found at i:180555 original size:21 final size:21
Alignment explanation
Indices: 180415--180599 Score: 105
Period size: 21 Copynumber: 9.1 Consensus size: 21
180405 AAATTTTAGG
*
180415 TTTTGGGTTTTGGGTTTCAAA
1 TTTTAGGTTTTGGGTTTCAAA
* ***
180436 TTTTAGGTTTTCGGTTTCCGG
1 TTTTAGGTTTTGGGTTTCAAA
* * **
180457 TTTCAAGTTTTGGGTTTTGAA
1 TTTTAGGTTTTGGGTTTCAAA
* * *
180478 TTTAAGATTTTGAGTTTCAAA
1 TTTTAGGTTTTGGGTTTCAAA
* ** ***
180499 TTTCAGGTTTTAAGTTTCGGG
1 TTTTAGGTTTTGGGTTTCAAA
* **
180520 TTTCAAATTTTGGGTTTCAAA
1 TTTTAGGTTTTGGGTTTCAAA
*
180541 TTTTAGGTTTCGGG-------
1 TTTTAGGTTTTGGGTTTCAAA
*
180555 TTTTAGTTTTTGGGTTTCAAA
1 TTTTAGGTTTTGGGTTTCAAA
*
180576 TTTTGGGTTTTGGGTTTCAAA
1 TTTTAGGTTTTGGGTTTCAAA
180597 TTT
1 TTT
180600 CGGGTTTTCA
Statistics
Matches: 118, Mismatches: 39, Indels: 14
0.69 0.23 0.08
Matches are distributed among these distances:
14 12 0.10
21 106 0.90
ACGTcount: A:0.17, C:0.07, G:0.24, T:0.52
Consensus pattern (21 bp):
TTTTAGGTTTTGGGTTTCAAA
Found at i:180604 original size:21 final size:21
Alignment explanation
Indices: 180562--180607 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
180552 GGGTTTTAGT
*
180562 TTTTGGGTTTCAAATTTTGGG
1 TTTTGGGTTTCAAATTTCGGG
180583 TTTTGGGTTTCAAATTTCGGG
1 TTTTGGGTTTCAAATTTCGGG
180604 TTTT
1 TTTT
180608 CAGTTTCGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.07, G:0.26, T:0.54
Consensus pattern (21 bp):
TTTTGGGTTTCAAATTTCGGG
Found at i:180613 original size:21 final size:21
Alignment explanation
Indices: 180568--180671 Score: 75
Period size: 21 Copynumber: 4.9 Consensus size: 21
180558 TAGTTTTTGG
* **
180568 GTTTCAAATTTTGGGTTTTGG
1 GTTTCAAATTTCGGGTTTTCA
180589 GTTTCAAATTTCGGGTTTTCA
1 GTTTCAAATTTCGGGTTTTCA
* * * *
180610 GTTTCGAGTTTCAGGTTTTAAA
1 GTTTCAAATTTCGGGTTTT-CA
* * * *
180632 CTTTCAAGTTTCGGTTTTTCG
1 GTTTCAAATTTCGGGTTTTCA
*
180653 GTTTTC-AATTTCAGGTTTT
1 G-TTTCAAATTTCGGGTTTT
180672 ATGTTTTAGT
Statistics
Matches: 64, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
21 44 0.69
22 20 0.31
ACGTcount: A:0.16, C:0.12, G:0.21, T:0.51
Consensus pattern (21 bp):
GTTTCAAATTTCGGGTTTTCA
Found at i:180638 original size:43 final size:43
Alignment explanation
Indices: 180590--180672 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
180580 GGGTTTTGGG
*
180590 TTTCAAATTTCGGGTTTTCAG-TTTCGAGTTTCAGGTTTTAAAC
1 TTTCAAATTTCGGGTTTTCAGTTTTC-AATTTCAGGTTTTAAAC
* * *
180633 TTTCAAGTTTCGGTTTTTCGGTTTTCAATTTCAGGTTTTA
1 TTTCAAATTTCGGGTTTTCAGTTTTCAATTTCAGGTTTTA
180673 TGTTTTAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 31 0.89
44 4 0.11
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (43 bp):
TTTCAAATTTCGGGTTTTCAGTTTTCAATTTCAGGTTTTAAAC
Found at i:180774 original size:7 final size:7
Alignment explanation
Indices: 180759--180941 Score: 73
Period size: 7 Copynumber: 26.3 Consensus size: 7
180749 TTGGTTCAAA
*
180759 TTTTAGG
1 TTTTGGG
180766 TTTTGGG
1 TTTTGGG
* **
180773 TTTCGAT
1 TTTTGGG
*
180780 TTTTAGG
1 TTTTGGG
180787 TTTTGGG
1 TTTTGGG
180794 TTTTGGG
1 TTTTGGG
**
180801 TTTCAGG
1 TTTTGGG
180808 TTTTGGG
1 TTTTGGG
**
180815 TTTCAGG
1 TTTTGGG
*
180822 TTTTGAG
1 TTTTGGG
**
180829 TTTTAAG
1 TTTTGGG
*
180836 TTTTAGG
1 TTTTGGG
*
180843 TTTTAGG
1 TTTTGGG
180850 TTTT-GG
1 TTTTGGG
****
180856 -TTCACA
1 TTTTGGG
**
180862 TTTTTTG
1 TTTTGGG
* *
180869 TTTTTGA
1 TTTTGGG
180876 TTTTGGG
1 TTTTGGG
180883 TTTTGGG
1 TTTTGGG
*
180890 TTTCGGG
1 TTTTGGG
* **
180897 TTTCGAA
1 TTTTGGG
**
180904 TTTCAGG
1 TTTTGGG
180911 TTTTGGG
1 TTTTGGG
*
180918 TTTTGAG
1 TTTTGGG
180925 TTTTAGGG
1 TTTT-GGG
*
180933 TTTAGGG
1 TTTTGGG
180940 TT
1 TT
180942 CAATTTTTAA
Statistics
Matches: 131, Mismatches: 42, Indels: 6
0.73 0.23 0.03
Matches are distributed among these distances:
5 2 0.02
6 2 0.02
7 122 0.93
8 5 0.04
ACGTcount: A:0.10, C:0.04, G:0.30, T:0.55
Consensus pattern (7 bp):
TTTTGGG
Found at i:180783 original size:21 final size:21
Alignment explanation
Indices: 180759--180941 Score: 99
Period size: 21 Copynumber: 8.8 Consensus size: 21
180749 TTGGTTCAAA
*
180759 TTTTAGGTTTTGGGTTTCGAT
1 TTTTAGGTTTTGGGTTTCGAG
* *
180780 TTTTAGGTTTTGGGTTTTGGG
1 TTTTAGGTTTTGGGTTTCGAG
*
180801 TTTCAGGTTTTGGGTTTC-AGG
1 TTTTAGGTTTTGGGTTTCGA-G
** *
180822 TTTT-GAGTTTTAAGTTT-TAGG
1 TTTTAG-GTTTTGGGTTTCGA-G
*
180843 TTTTAGGTTTT-GG-TTC-ACA
1 TTTTAGGTTTTGGGTTTCGA-G
** * * * *
180862 TTTTTTGTTTTTGATTTTGGG
1 TTTTAGGTTTTGGGTTTCGAG
* * *
180883 TTTTGGGTTTCGGGTTTCGAA
1 TTTTAGGTTTTGGGTTTCGAG
* *
180904 TTTCAGGTTTTGGGTTTTGAG
1 TTTTAGGTTTTGGGTTTCGAG
*
180925 TTTTAGGGTTTAGGGTT
1 TTTTA-GGTTTTGGGTT
180942 CAATTTTTAA
Statistics
Matches: 120, Mismatches: 33, Indels: 17
0.71 0.19 0.10
Matches are distributed among these distances:
19 12 0.10
20 3 0.03
21 94 0.78
22 11 0.09
ACGTcount: A:0.10, C:0.04, G:0.30, T:0.55
Consensus pattern (21 bp):
TTTTAGGTTTTGGGTTTCGAG
Found at i:180797 original size:14 final size:14
Alignment explanation
Indices: 180780--180855 Score: 89
Period size: 14 Copynumber: 5.4 Consensus size: 14
180770 GGGTTTCGAT
* *
180780 TTTTAGGTTTTGGG
1 TTTTGGGTTTTAGG
*
180794 TTTTGGGTTTCAGG
1 TTTTGGGTTTTAGG
*
180808 TTTTGGGTTTCAGG
1 TTTTGGGTTTTAGG
* *
180822 TTTTGAGTTTTAAG
1 TTTTGGGTTTTAGG
*
180836 TTTTAGGTTTTAGG
1 TTTTGGGTTTTAGG
180850 TTTTGG
1 TTTTGG
180856 TTCACATTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 52 1.00
ACGTcount: A:0.11, C:0.03, G:0.32, T:0.55
Consensus pattern (14 bp):
TTTTGGGTTTTAGG
Found at i:181013 original size:21 final size:21
Alignment explanation
Indices: 180987--181144 Score: 72
Period size: 21 Copynumber: 7.6 Consensus size: 21
180977 CAAGCTTCGG
*
180987 GGGTTTTAGGTTTCATATTTT
1 GGGTTTTAGGTTTCAAATTTT
* *
181008 GGGTTTTGGGTTTTAAATTTT
1 GGGTTTTAGGTTTCAAATTTT
* * * * *
181029 GTG-TTTCGAATTTTAAATTTC
1 GGGTTTTAG-GTTTCAAATTTT
* * *
181050 CGGTTTTAGGTTTTAAATTTC
1 GGGTTTTAGGTTTCAAATTTT
* * **
181071 GGGTTTTGGGTTT-TAGGTTT
1 GGGTTTTAGGTTTCAAATTTT
**
181091 CAGTTTT-GTGTTTCAAATTTT
1 GGGTTTTAG-GTTTCAAATTTT
* *
181112 AGGTTTT-GAGTTTAAAATTTT
1 GGGTTTTAG-GTTTCAAATTTT
* *
181133 TGGTTTTGGGTT
1 GGGTTTTAGGTT
181145 CGGGTTTTAA
Statistics
Matches: 105, Mismatches: 27, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
19 1 0.01
20 16 0.15
21 83 0.79
22 5 0.05
ACGTcount: A:0.16, C:0.04, G:0.24, T:0.55
Consensus pattern (21 bp):
GGGTTTTAGGTTTCAAATTTT
Found at i:181232 original size:28 final size:28
Alignment explanation
Indices: 181177--181249 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
181167 GGGTTTCGGG
* *
181177 TTTCAGGCTTCGGGAGTTTTAGGTTTCAAA
1 TTTCAGGTTTC-GG-GTTTTAGGATTCAAA
** *
181207 TTTTGGGTTTCGGGTTTTGGGATTCAAA
1 TTTCAGGTTTCGGGTTTTAGGATTCAAA
181235 TTTCAGGTTTCGGGT
1 TTTCAGGTTTCGGGT
181250 CTCGGGTTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 26 0.72
29 2 0.06
30 8 0.22
ACGTcount: A:0.15, C:0.11, G:0.30, T:0.44
Consensus pattern (28 bp):
TTTCAGGTTTCGGGTTTTAGGATTCAAA
Found at i:181294 original size:14 final size:14
Alignment explanation
Indices: 181277--181307 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
181267 TTGTTTTAAA
*
181277 TTTCAAATTTTGGG
1 TTTCAAATTTCGGG
181291 TTTCAAATTTCGGG
1 TTTCAAATTTCGGG
181305 TTT
1 TTT
181308 TAGGTTTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (14 bp):
TTTCAAATTTCGGG
Found at i:181308 original size:21 final size:21
Alignment explanation
Indices: 181214--181350 Score: 62
Period size: 21 Copynumber: 6.5 Consensus size: 21
181204 AAATTTTGGG
*
181214 TTTCGGGTTTTGGGATTCAAA
1 TTTCGGGTTTTGGGTTTCAAA
* * * ***
181235 TTTCAGGTTTCGGGTCTCGGG
1 TTTCGGGTTTTGGGTTTCAAA
* *
181256 TTTCGAGTTACTT--GTTTTAAA
1 TTTCGGGTT--TTGGGTTTCAAA
***
181277 TTTCAAATTTTGGGTTTCAAA
1 TTTCGGGTTTTGGGTTTCAAA
* **
181298 TTTCGGGTTTTAGGTTTCAGG
1 TTTCGGGTTTTGGGTTTCAAA
* * * *
181319 TTTTGGGTTTGGGGTTTTAAG
1 TTTCGGGTTTTGGGTTTCAAA
*
181340 TTTCAGGTTTT
1 TTTCGGGTTTT
181351 AAATTTCATG
Statistics
Matches: 80, Mismatches: 32, Indels: 8
0.67 0.27 0.07
Matches are distributed among these distances:
19 2 0.03
21 77 0.96
23 1 0.01
ACGTcount: A:0.15, C:0.09, G:0.27, T:0.48
Consensus pattern (21 bp):
TTTCGGGTTTTGGGTTTCAAA
Found at i:181315 original size:14 final size:14
Alignment explanation
Indices: 181298--181351 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
181288 GGGTTTCAAA
*
181298 TTTCGGGTTTTAGG
1 TTTCAGGTTTTAGG
*
181312 TTTCAGGTTTTGGG
1 TTTCAGGTTTTAGG
** *
181326 TTTGGGGTTTTAAG
1 TTTCAGGTTTTAGG
181340 TTTCAGGTTTTA
1 TTTCAGGTTTTA
181352 AATTTCATGG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.11, C:0.06, G:0.31, T:0.52
Consensus pattern (14 bp):
TTTCAGGTTTTAGG
Found at i:181352 original size:14 final size:14
Alignment explanation
Indices: 181298--181364 Score: 62
Period size: 14 Copynumber: 4.7 Consensus size: 14
181288 GGGTTTCAAA
* *
181298 TTTCGGGTTTTAGG
1 TTTCAGGTTTTAAG
**
181312 TTTCAGGTTTTGGG
1 TTTCAGGTTTTAAG
**
181326 TTTGGGGTTTTAAG
1 TTTCAGGTTTTAAG
*
181340 TTTCAGGTTTTAAA
1 TTTCAGGTTTTAAG
181354 TTTCATGGTTT
1 TTTCA-GGTTT
181365 GGGTTTTAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
14 38 0.88
15 5 0.12
ACGTcount: A:0.13, C:0.06, G:0.28, T:0.52
Consensus pattern (14 bp):
TTTCAGGTTTTAAG
Found at i:181369 original size:35 final size:35
Alignment explanation
Indices: 181324--181420 Score: 106
Period size: 35 Copynumber: 2.8 Consensus size: 35
181314 TCAGGTTTTG
* *
181324 GGTTTGGGGTTTTAAGTTTCAGGTTTTAAATTTCAT
1 GGTTTCGGGTTTTAAATTTCAGGTTTTAAATTT-AT
** * * *
181360 GGTTT-GGGTTTTAAATTTCAAATTTTGAGTTTTT
1 GGTTTCGGGTTTTAAATTTCAGGTTTTAAATTTAT
*
181394 GGTTTCGGGTTTCAAATTTCAGGTTTT
1 GGTTTCGGGTTTTAAATTTCAGGTTTT
181421 TGGTTTCGAG
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
34 6 0.12
35 40 0.78
36 5 0.10
ACGTcount: A:0.19, C:0.06, G:0.24, T:0.52
Consensus pattern (35 bp):
GGTTTCGGGTTTTAAATTTCAGGTTTTAAATTTAT
Found at i:181386 original size:21 final size:21
Alignment explanation
Indices: 181345--181392 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
181335 TTAAGTTTCA
**
181345 GGTTTTAAATTTCATGGTTTG
1 GGTTTTAAATTTCAAAGTTTG
*
181366 GGTTTTAAATTTCAAATTTTG
1 GGTTTTAAATTTCAAAGTTTG
*
181387 AGTTTT
1 GGTTTT
181393 TGGTTTCGGG
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:0.23, C:0.04, G:0.19, T:0.54
Consensus pattern (21 bp):
GGTTTTAAATTTCAAAGTTTG
Found at i:181406 original size:28 final size:28
Alignment explanation
Indices: 181375--181447 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
181365 GGGTTTTAAA
*
181375 TTTCAAATTTTGAGTTTTTGGTTTCGGG
1 TTTCAAATTTTGAGTTTTTGGTTTCGAG
*
181403 TTTCAAA-TTTCAGGTTTTTGGTTTCGAG
1 TTTCAAATTTTGA-GTTTTTGGTTTCGAG
* *
181431 TATCAAATTTTGGGTTT
1 TTTCAAATTTTGAGTTT
181448 CAAATTTTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
27 4 0.11
28 31 0.82
29 3 0.08
ACGTcount: A:0.18, C:0.08, G:0.22, T:0.52
Consensus pattern (28 bp):
TTTCAAATTTTGAGTTTTTGGTTTCGAG
Found at i:181425 original size:21 final size:21
Alignment explanation
Indices: 181401--181496 Score: 59
Period size: 21 Copynumber: 4.6 Consensus size: 21
181391 TTTGGTTTCG
181401 GGTTTCAAATTTCAGGTTTTT
1 GGTTTCAAATTTCAGGTTTTT
* * * ** *
181422 GGTTTCGAGTATCAAATTTTG
1 GGTTTCAAATTTCAGGTTTTT
** *
181443 GGTTTCAAATTTTTGGTTTAT
1 GGTTTCAAATTTCAGGTTTTT
*** *
181464 GGTTTCTTGTTTC-TGTTTTT
1 GGTTTCAAATTTCAGGTTTTT
181484 GAGTTTCAAATTT
1 G-GTTTCAAATTT
181497 TGGGTTTCAA
Statistics
Matches: 50, Mismatches: 24, Indels: 2
0.66 0.32 0.03
Matches are distributed among these distances:
20 6 0.12
21 44 0.88
ACGTcount: A:0.18, C:0.08, G:0.20, T:0.54
Consensus pattern (21 bp):
GGTTTCAAATTTCAGGTTTTT
Found at i:181509 original size:21 final size:21
Alignment explanation
Indices: 181500--181552 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
181490 CAAATTTTGG
* * *
181500 GTTTCAAGTTTAGGGTTTTAA
1 GTTTCAAATTTAAGGTTTCAA
* *
181521 GTTTCAAATTTTAGGTTTCAT
1 GTTTCAAATTTAAGGTTTCAA
181542 GTTTCAAATTT
1 GTTTCAAATTT
181553 CAATTTTTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.51
Consensus pattern (21 bp):
GTTTCAAATTTAAGGTTTCAA
Found at i:181515 original size:14 final size:14
Alignment explanation
Indices: 181486--181524 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
181476 CTGTTTTTGA
* *
181486 GTTTCAAATTTTGG
1 GTTTCAAGTTTAGG
181500 GTTTCAAGTTTAGG
1 GTTTCAAGTTTAGG
*
181514 GTTTTAAGTTT
1 GTTTCAAGTTT
181525 CAAATTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.21, C:0.05, G:0.23, T:0.51
Consensus pattern (14 bp):
GTTTCAAGTTTAGG
Found at i:181743 original size:21 final size:21
Alignment explanation
Indices: 181717--181769 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
181707 TTGCGTTTTA
181717 GTTTCGGGTTTCAAATTTCGG
1 GTTTCGGGTTTCAAATTTCGG
* *
181738 GTTTCGAGTTTCAAATTTTGG
1 GTTTCGGGTTTCAAATTTCGG
*
181759 GTTTTGGGTTT
1 GTTTCGGGTTT
181770 TGGGTTTTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.13, C:0.09, G:0.28, T:0.49
Consensus pattern (21 bp):
GTTTCGGGTTTCAAATTTCGG
Found at i:181749 original size:14 final size:14
Alignment explanation
Indices: 181608--181749 Score: 54
Period size: 14 Copynumber: 10.2 Consensus size: 14
181598 GTAAAAAAAA
*
181608 TTCGGGTTTCAGGT
1 TTCGGGTTTCAAGT
* *
181622 TT-GGACTTTCAAAT
1 TTCGG-GTTTCAAGT
* *
181636 TTTGGGTTTCACGT
1 TTCGGGTTTCAAGT
* *
181650 TTCAGGTTTCAAAT
1 TTCGGGTTTCAAGT
* * *
181664 TTCAGTTTTCTAGT
1 TTCGGGTTTCAAGT
** *
181678 TTCGAATTTCAAAT
1 TTCGGGTTTCAAGT
* * ***
181692 TTTGGATTTTGGGT
1 TTCGGGTTTCAAGT
* * *
181706 TTTGCGTTT-TAGT
1 TTCGGGTTTCAAGT
*
181719 TTCGGGTTTCAAAT
1 TTCGGGTTTCAAGT
*
181733 TTCGGGTTTCGAGT
1 TTCGGGTTTCAAGT
181747 TTC
1 TTC
181750 AAATTTTGGG
Statistics
Matches: 91, Mismatches: 34, Indels: 6
0.69 0.26 0.05
Matches are distributed among these distances:
13 11 0.12
14 78 0.86
15 2 0.02
ACGTcount: A:0.16, C:0.13, G:0.23, T:0.49
Consensus pattern (14 bp):
TTCGGGTTTCAAGT
Found at i:181763 original size:7 final size:7
Alignment explanation
Indices: 181753--181785 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
181743 GAGTTTCAAA
181753 TTTTGGG
1 TTTTGGG
181760 TTTTGGG
1 TTTTGGG
181767 TTTTGGG
1 TTTTGGG
*
181774 TTTTAGG
1 TTTTGGG
181781 TTTTG
1 TTTTG
181786 AGATTCAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.03, C:0.00, G:0.36, T:0.61
Consensus pattern (7 bp):
TTTTGGG
Found at i:181770 original size:14 final size:14
Alignment explanation
Indices: 181753--181979 Score: 76
Period size: 14 Copynumber: 16.2 Consensus size: 14
181743 GAGTTTCAAA
*
181753 TTTTGGGTTTTGGG
1 TTTTGGGTTTTAGG
181767 TTTTGGGTTTTAGG
1 TTTTGGGTTTTAGG
* * *
181781 TTTTGAGATTCAGG
1 TTTTGGGTTTTAGG
* * *
181795 TTTAGGGTTTCATG
1 TTTTGGGTTTTAGG
* *** * *
181809 TATTAAATTCTAAG
1 TTTTGGGTTTTAGG
*
181823 TTTTGGGTTTTAGA
1 TTTTGGGTTTTAGG
* * * **
181837 CTCTGGGTTTCAAT
1 TTTTGGGTTTTAGG
**
181851 TTTTGGGTTTGGGG
1 TTTTGGGTTTTAGG
* * **
181865 TTTAGGGTTTCAAA
1 TTTTGGGTTTTAGG
*
181879 TTTTGGGTTTTGGG
1 TTTTGGGTTTTAGG
**** * *
181893 TTTCAAATCTCAGG
1 TTTTGGGTTTTAGG
*
181907 TTTTGAGTTTTAGG
1 TTTTGGGTTTTAGG
* **
181921 TTTTGGGTTTCAAA
1 TTTTGGGTTTTAGG
**
181935 TTTTGGGTTTTAAT
1 TTTTGGGTTTTAGG
* * *
181949 TTTTAGGTTTCAAG
1 TTTTGGGTTTTAGG
*
181963 TTTTAGGTTTTAGG
1 TTTTGGGTTTTAGG
181977 TTT
1 TTT
181980 CAAATTTTGG
Statistics
Matches: 146, Mismatches: 67, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
14 146 1.00
ACGTcount: A:0.16, C:0.05, G:0.27, T:0.52
Consensus pattern (14 bp):
TTTTGGGTTTTAGG
Found at i:181796 original size:28 final size:28
Alignment explanation
Indices: 181766--182120 Score: 131
Period size: 28 Copynumber: 12.7 Consensus size: 28
181756 TGGGTTTTGG
* *
181766 GTTTTGGGTTTTAGGTTTTGAGATTCAG
1 GTTTTGGGTTTTAGGTTTTGAGTTTCAA
* * * * **
181794 GTTTAGGGTTTCATGTATT-AAATTCTAA
1 GTTTTGGGTTTTAGGTTTTGAGTTTC-AA
** * *
181822 GTTTTGGGTTTTAGACTCTGGGTTTCAA
1 GTTTTGGGTTTTAGGTTTTGAGTTTCAA
* ** * *
181850 TTTTTGGGTTTGGGGTTTAGGGTTTCAA
1 GTTTTGGGTTTTAGGTTTTGAGTTTCAA
* * ** * * *
181878 ATTTTGGGTTTTGGGTTTCAAATCTCAG
1 GTTTTGGGTTTTAGGTTTTGAGTTTCAA
* *
181906 GTTTTGAGTTTTAGGTTTTGGGTTTCAA
1 GTTTTGGGTTTTAGGTTTTGAGTTTCAA
* * *
181934 ATTTTGGGTTTTA-ATTTTTAGGTTTCAA
1 GTTTTGGGTTTTAGGTTTTGA-GTTTCAA
*
181962 GTTTTAGGTTTTA------G-GTTTCAA
1 GTTTTGGGTTTTAGGTTTTGAGTTTCAA
* *
181983 ATTTTGGGTTTCT-GGTTTCGAGTTTCAA
1 GTTTTGGGTTT-TAGGTTTTGAGTTTCAA
* ** *
182011 ATTTTGGGTTTCGGGTTTTGAATTTCAAATTTCAA
1 GTTTTGGGTTTTAGGTTTTG-------AGTTTCAA
* * *
182046 ATTTTGGGTTTTAGGTTTTGGGTTTTAA
1 GTTTTGGGTTTTAGGTTTTGAGTTTCAA
* * *
182074 ATTTTGGGTTTT-GGTTTTTGAGTTTTAG
1 GTTTTGGGTTTTAGG-TTTTGAGTTTCAA
*
182102 GCTTTGGGTTTCT-GGTTTT
1 GTTTTGGGTTT-TAGGTTTT
182121 TGAATTTTGG
Statistics
Matches: 244, Mismatches: 62, Indels: 42
0.70 0.18 0.12
Matches are distributed among these distances:
21 16 0.07
22 1 0.00
27 12 0.05
28 184 0.75
29 6 0.02
35 25 0.10
ACGTcount: A:0.16, C:0.06, G:0.26, T:0.52
Consensus pattern (28 bp):
GTTTTGGGTTTTAGGTTTTGAGTTTCAA
Found at i:181908 original size:21 final size:21
Alignment explanation
Indices: 181863--181916 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
181853 TTGGGTTTGG
* * **
181863 GGTTTAGGGTTTCAAATTTTG
1 GGTTTTGGGTTTCAAATCTCA
181884 GGTTTTGGGTTTCAAATCTCA
1 GGTTTTGGGTTTCAAATCTCA
*
181905 GGTTTTGAGTTT
1 GGTTTTGGGTTT
181917 TAGGTTTTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (21 bp):
GGTTTTGGGTTTCAAATCTCA
Found at i:181923 original size:7 final size:7
Alignment explanation
Indices: 181904--181979 Score: 55
Period size: 7 Copynumber: 10.9 Consensus size: 7
181894 TTCAAATCTC
181904 AGGTTTT
1 AGGTTTT
181911 -GAGTTTT
1 AG-GTTTT
181918 AGGTTTT
1 AGGTTTT
* *
181925 GGGTTTC
1 AGGTTTT
**
181932 AAATTTT
1 AGGTTTT
*
181939 GGGTTTT
1 AGGTTTT
**
181946 AATTTTT
1 AGGTTTT
*
181953 AGGTTTC
1 AGGTTTT
*
181960 AAGTTTT
1 AGGTTTT
181967 AGGTTTT
1 AGGTTTT
181974 AGGTTT
1 AGGTTT
181980 CAAATTTTGG
Statistics
Matches: 49, Mismatches: 18, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
6 1 0.02
7 47 0.96
8 1 0.02
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.55
Consensus pattern (7 bp):
AGGTTTT
Found at i:181944 original size:35 final size:35
Alignment explanation
Indices: 181870--181958 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
181860 TGGGGTTTAG
* * *
181870 GGTTTCAAATTTTGGGTTTTGGGTTTCAAATCTCA
1 GGTTTTAAGTTTTAGGTTTTGGGTTTCAAATCTCA
* * **
181905 GGTTTTGAGTTTTAGGTTTTGGGTTTCAAATTTTG
1 GGTTTTAAGTTTTAGGTTTTGGGTTTCAAATCTCA
*
181940 GGTTTTAATTTTTAGGTTT
1 GGTTTTAAGTTTTAGGTTT
181959 CAAGTTTTAG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.17, C:0.06, G:0.25, T:0.53
Consensus pattern (35 bp):
GGTTTTAAGTTTTAGGTTTTGGGTTTCAAATCTCA
Found at i:181965 original size:21 final size:21
Alignment explanation
Indices: 181941--182022 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 21
181931 CAAATTTTGG
*
181941 GTTTTAATTTTTAGGTTTCAA
1 GTTTTAAGTTTTAGGTTTCAA
*
181962 GTTTTAGGTTTTAGGTTTCAA
1 GTTTTAAGTTTTAGGTTTCAA
* ** *
181983 ATTTTGGGTTTCT-GGTTTCGA
1 GTTTTAAGTTT-TAGGTTTCAA
* * *
182004 GTTTCAAATTTTGGGTTTC
1 GTTTTAAGTTTTAGGTTTC
182023 GGGTTTTGAA
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
20 1 0.02
21 47 0.96
22 1 0.02
ACGTcount: A:0.17, C:0.07, G:0.22, T:0.54
Consensus pattern (21 bp):
GTTTTAAGTTTTAGGTTTCAA
Found at i:181992 original size:14 final size:14
Alignment explanation
Indices: 181921--182022 Score: 60
Period size: 14 Copynumber: 6.8 Consensus size: 14
181911 GAGTTTTAGG
181921 TTTTGGGTTTCAAA
1 TTTTGGGTTTCAAA
* *
181935 TTTTGGGTTTTAAT
1 TTTTGGGTTTCAAA
*
181949 TTTTAGGTTTCAAGTTTTA
1 TTTTGGGTTTCAA-----A
*
181968 GGTTTTAGGTTTCAAA
1 --TTTTGGGTTTCAAA
***
181984 TTTTGGGTTTCTGG
1 TTTTGGGTTTCAAA
* *
181998 TTTCGAGTTTCAAA
1 TTTTGGGTTTCAAA
182012 TTTTGGGTTTC
1 TTTTGGGTTTC
182023 GGGTTTTGAA
Statistics
Matches: 65, Mismatches: 16, Indels: 14
0.68 0.17 0.15
Matches are distributed among these distances:
14 51 0.78
16 1 0.02
21 13 0.20
ACGTcount: A:0.17, C:0.07, G:0.23, T:0.54
Consensus pattern (14 bp):
TTTTGGGTTTCAAA
Found at i:182057 original size:7 final size:7
Alignment explanation
Indices: 182047--182142 Score: 75
Period size: 7 Copynumber: 13.6 Consensus size: 7
182037 AAATTTCAAA
182047 TTTTGGG
1 TTTTGGG
*
182054 TTTTAGG
1 TTTTGGG
182061 TTTTGGG
1 TTTTGGG
***
182068 TTTTAAA
1 TTTTGGG
182075 TTTTGGG
1 TTTTGGG
*
182082 TTTTGGT
1 TTTTGGG
*
182089 TTTTGAG
1 TTTTGGG
*
182096 TTTTAGG
1 TTTTGGG
*
182103 CTTTGGG
1 TTTTGGG
*
182110 TTTCTGGT
1 TTT-TGGG
**
182118 TTTTGAA
1 TTTTGGG
182125 TTTTGGG
1 TTTTGGG
*
182132 TTTTAGG
1 TTTTGGG
182139 TTTT
1 TTTT
182143 AAATTTTGAG
Statistics
Matches: 66, Mismatches: 22, Indels: 2
0.73 0.24 0.02
Matches are distributed among these distances:
7 60 0.91
8 6 0.09
ACGTcount: A:0.09, C:0.02, G:0.29, T:0.59
Consensus pattern (7 bp):
TTTTGGG
Found at i:182064 original size:14 final size:14
Alignment explanation
Indices: 182047--182169 Score: 90
Period size: 14 Copynumber: 8.7 Consensus size: 14
182037 AAATTTCAAA
182047 TTTTGGGTTTTAGG
1 TTTTGGGTTTTAGG
**
182061 TTTTGGGTTTTAAA
1 TTTTGGGTTTTAGG
182075 TTTTGGGTTTT-GG
1 TTTTGGGTTTTAGG
*
182088 TTTTTGAGTTTTAGG
1 -TTTTGGGTTTTAGG
*
182103 CTTTGGGTTTCT-GG
1 TTTTGGGTTT-TAGG
** *
182117 TTTTTGAATTTTGGG
1 -TTTTGGGTTTTAGG
* **
182132 TTTTAGGTTTTAAA
1 TTTTGGGTTTTAGG
182146 TTTTGAGG-TTTAGG
1 TTTTG-GGTTTTAGG
*
182160 TTTAGGGTTT
1 TTTTGGGTTT
182170 CAAATTTTGG
Statistics
Matches: 82, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
13 2 0.02
14 66 0.80
15 14 0.17
ACGTcount: A:0.12, C:0.02, G:0.29, T:0.57
Consensus pattern (14 bp):
TTTTGGGTTTTAGG
Found at i:182143 original size:7 final size:7
Alignment explanation
Indices: 182047--182162 Score: 58
Period size: 7 Copynumber: 16.4 Consensus size: 7
182037 AAATTTCAAA
*
182047 TTTTGGG
1 TTTTAGG
182054 TTTTAGG
1 TTTTAGG
*
182061 TTTTGGG
1 TTTTAGG
**
182068 TTTTAAA
1 TTTTAGG
*
182075 TTTTGGG
1 TTTTAGG
182082 TTTT-GG
1 TTTTAGG
*
182088 TTTTTGAG
1 TTTTAG-G
182096 TTTTAGG
1 TTTTAGG
* *
182103 CTTTGGG
1 TTTTAGG
182110 TTTCT-GG
1 TTT-TAGG
* *
182117 TTTTTGAA
1 TTTTAG-G
*
182125 TTTTGGG
1 TTTTAGG
182132 TTTTAGG
1 TTTTAGG
**
182139 TTTTAAA
1 TTTTAGG
182146 TTTTGAGG
1 TTTT-AGG
182154 -TTTAGG
1 TTTTAGG
182160 TTT
1 TTT
182163 AGGGTTTCAA
Statistics
Matches: 82, Mismatches: 20, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
6 10 0.12
7 59 0.72
8 13 0.16
ACGTcount: A:0.12, C:0.02, G:0.28, T:0.58
Consensus pattern (7 bp):
TTTTAGG
Found at i:182147 original size:21 final size:21
Alignment explanation
Indices: 182104--182162 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
182094 AGTTTTAGGC
*
182104 TTTGGGTTTCT-GGTTTTTGAAT
1 TTTGGGTTT-TAGG-TTTTAAAT
182126 TTTGGGTTTTAGGTTTTAAAT
1 TTTGGGTTTTAGGTTTTAAAT
182147 TTTGAGG-TTTAGGTTT
1 TTTG-GGTTTTAGGTTT
182163 AGGGTTTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
21 21 0.62
22 13 0.38
ACGTcount: A:0.14, C:0.02, G:0.27, T:0.58
Consensus pattern (21 bp):
TTTGGGTTTTAGGTTTTAAAT
Found at i:182186 original size:14 final size:14
Alignment explanation
Indices: 182167--182213 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
182157 AGGTTTAGGG
182167 TTTCAAATTTTGGA
1 TTTCAAATTTTGGA
***
182181 TTTCAAATTTCAAA
1 TTTCAAATTTTGGA
*
182195 TTTCAAATTTTGGG
1 TTTCAAATTTTGGA
182209 TTTCA
1 TTTCA
182214 GGTTTTGGGT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (14 bp):
TTTCAAATTTTGGA
Found at i:182190 original size:7 final size:7
Alignment explanation
Indices: 182180--182204 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
182170 CAAATTTTGG
182180 ATTTCAA
1 ATTTCAA
182187 ATTTCAA
1 ATTTCAA
182194 ATTTCAA
1 ATTTCAA
182201 ATTT
1 ATTT
182205 TGGGTTTCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (7 bp):
ATTTCAA
Found at i:182224 original size:7 final size:7
Alignment explanation
Indices: 182202--182268 Score: 64
Period size: 7 Copynumber: 9.6 Consensus size: 7
182192 AAATTTCAAA
182202 TTTTGGG
1 TTTTGGG
**
182209 TTTCAGG
1 TTTTGGG
182216 TTTTGGG
1 TTTTGGG
182223 TTTTGGG
1 TTTTGGG
* *
182230 TTTCGAG
1 TTTTGGG
182237 TTTTGGG
1 TTTTGGG
182244 TTTCT-GG
1 TTT-TGGG
* *
182251 TTTCGAG
1 TTTTGGG
182258 TTTTGGG
1 TTTTGGG
182265 TTTT
1 TTTT
182269 AAATTTCAAA
Statistics
Matches: 46, Mismatches: 12, Indels: 4
0.74 0.19 0.06
Matches are distributed among these distances:
7 45 0.98
8 1 0.02
ACGTcount: A:0.04, C:0.06, G:0.34, T:0.55
Consensus pattern (7 bp):
TTTTGGG
Found at i:182226 original size:21 final size:21
Alignment explanation
Indices: 182202--182268 Score: 102
Period size: 21 Copynumber: 3.2 Consensus size: 21
182192 AAATTTCAAA
182202 TTTTGGGTTTC-AGGTTTTGGG
1 TTTTGGGTTTCGA-GTTTTGGG
182223 TTTTGGGTTTCGAGTTTTGGG
1 TTTTGGGTTTCGAGTTTTGGG
182244 TTTCT-GGTTTCGAGTTTTGGG
1 TTT-TGGGTTTCGAGTTTTGGG
182265 TTTT
1 TTTT
182269 AAATTTCAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.02
21 41 0.93
22 2 0.05
ACGTcount: A:0.04, C:0.06, G:0.34, T:0.55
Consensus pattern (21 bp):
TTTTGGGTTTCGAGTTTTGGG
Found at i:182317 original size:21 final size:21
Alignment explanation
Indices: 182290--182344 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
182280 TTCGGGTTTC
*
182290 AGGTTTTGAGTTTAAAATTTT
1 AGGTTTTGGGTTTAAAATTTT
* *
182311 GGGTTTTGGGTTTCAAATTTT
1 AGGTTTTGGGTTTAAAATTTT
182332 AGGTTTTGGGTTT
1 AGGTTTTGGGTTT
182345 TTTGTTTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.18, C:0.02, G:0.27, T:0.53
Consensus pattern (21 bp):
AGGTTTTGGGTTTAAAATTTT
Found at i:182322 original size:35 final size:35
Alignment explanation
Indices: 182199--182325 Score: 112
Period size: 35 Copynumber: 3.6 Consensus size: 35
182189 TTCAAATTTC
* ** *
182199 AAATTTTGGGTTTCAGGTTTTGGGTTTTGGGTTTC
1 AAATTTTGGGTTTCGGGTTTCAGGTTTTGGGTTTA
* * * *
182234 GAGTTTTGGGTTTCTGGTTTC-GAGTTTTGGGTTTT
1 AAATTTTGGGTTTCGGGTTTCAG-GTTTTGGGTTTA
**** *
182269 AAATTTCAAATTTCGGGTTTCAGGTTTTGAGTTTA
1 AAATTTTGGGTTTCGGGTTTCAGGTTTTGGGTTTA
*
182304 AAATTTTGGGTTTTGGGTTTCA
1 AAATTTTGGGTTTCGGGTTTCA
182326 AATTTTAGGT
Statistics
Matches: 71, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
34 1 0.01
35 69 0.97
36 1 0.01
ACGTcount: A:0.15, C:0.06, G:0.28, T:0.50
Consensus pattern (35 bp):
AAATTTTGGGTTTCGGGTTTCAGGTTTTGGGTTTA
Found at i:182352 original size:35 final size:35
Alignment explanation
Indices: 182313--182379 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
182303 AAAATTTTGG
182313 GTTTTGGGTTTCAAATTTTAGGTTTTGGGTTTTTT
1 GTTTTGGGTTTCAAATTTTAGGTTTTGGGTTTTTT
* *
182348 GTTTTTGGTTTCAAATTTTGGGTTTTGGGTTT
1 GTTTTGGGTTTCAAATTTTAGGTTTTGGGTTT
182380 CGGATTTAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.10, C:0.03, G:0.27, T:0.60
Consensus pattern (35 bp):
GTTTTGGGTTTCAAATTTTAGGTTTTGGGTTTTTT
Found at i:182421 original size:21 final size:21
Alignment explanation
Indices: 182390--182449 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
182380 CGGATTTAGG
* *
182390 TTTCAAGTTTCGGGTTTCGAGT
1 TTTCAAATTTCAGGTTTCGA-T
182412 TTT-AAATTTCAGGTTTCGAT
1 TTTCAAATTTCAGGTTTCGAT
*
182432 TTTCAAATTTTAGGTTTC
1 TTTCAAATTTCAGGTTTC
182450 TGGTTTCGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.12
21 27 0.79
22 3 0.09
ACGTcount: A:0.20, C:0.12, G:0.18, T:0.50
Consensus pattern (21 bp):
TTTCAAATTTCAGGTTTCGAT
Found at i:182435 original size:28 final size:28
Alignment explanation
Indices: 182390--182465 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
182380 CGGATTTAGG
* * * *
182390 TTTCAAGTTTCGGGTTTCGAGTTTTAAA
1 TTTCAGGTTTCGAGTTTCAAATTTTAAA
* **
182418 TTTCAGGTTTCGATTTTCAAATTTTAGG
1 TTTCAGGTTTCGAGTTTCAAATTTTAAA
*
182446 TTTCTGGTTTCGAGTTTCAA
1 TTTCAGGTTTCGAGTTTCAA
182466 GGCTATGGGT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.49
Consensus pattern (28 bp):
TTTCAGGTTTCGAGTTTCAAATTTTAAA
Found at i:182507 original size:7 final size:7
Alignment explanation
Indices: 182495--182541 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
182485 AAGGCTTTGG
182495 GTTTCGA
1 GTTTCGA
182502 GTTTCGA
1 GTTTCGA
*
182509 GTTTCAA
1 GTTTCGA
* *
182516 ATTTCGG
1 GTTTCGA
*
182523 GTTTTGA
1 GTTTCGA
182530 GTTTCGA
1 GTTTCGA
182537 GTTTC
1 GTTTC
182542 AAATTTTGTG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.47
Consensus pattern (7 bp):
GTTTCGA
Found at i:182513 original size:35 final size:33
Alignment explanation
Indices: 182474--182604 Score: 112
Period size: 35 Copynumber: 3.9 Consensus size: 33
182464 AAGGCTATGG
182474 GTTTCAAATTTAAGGCTTTGGGTTTCGAGTTTCGA
1 GTTTCAAATTT-AGG-TTTGGGTTTCGAGTTTCGA
* *
182509 GTTTCAAA--T---TTCGGGTTTTGAGTTTCGA
1 GTTTCAAATTTAGGTTTGGGTTTCGAGTTTCGA
* * *
182537 GTTTCAAATTTTGTGTTACGGGTTT-GCAGTTTTGA
1 GTTTCAAATTTAG-GTT-TGGGTTTCG-AGTTTCGA
182572 GTTTCAAATTTTAGGTTTCGGGTTTCGAGTTTC
1 GTTTCAAA-TTTAGGTTT-GGGTTTCGAGTTTC
182605 AAATTTTAGT
Statistics
Matches: 79, Mismatches: 6, Indels: 22
0.74 0.06 0.21
Matches are distributed among these distances:
28 25 0.32
30 1 0.01
33 1 0.01
34 3 0.04
35 44 0.56
36 5 0.06
ACGTcount: A:0.18, C:0.11, G:0.25, T:0.47
Consensus pattern (33 bp):
GTTTCAAATTTAGGTTTGGGTTTCGAGTTTCGA
Found at i:182520 original size:14 final size:14
Alignment explanation
Indices: 182503--182547 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
182493 GGGTTTCGAG
182503 TTTCGAGTTTCAAA
1 TTTCGAGTTTCAAA
* ** *
182517 TTTCGGGTTTTGAG
1 TTTCGAGTTTCAAA
182531 TTTCGAGTTTCAAA
1 TTTCGAGTTTCAAA
182545 TTT
1 TTT
182548 TGTGTTACGG
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.49
Consensus pattern (14 bp):
TTTCGAGTTTCAAA
Found at i:182524 original size:28 final size:28
Alignment explanation
Indices: 182493--182610 Score: 112
Period size: 28 Copynumber: 4.0 Consensus size: 28
182483 TTAAGGCTTT
182493 GGGTTTCGAGTTTCGAGTTTCAAATTTC
1 GGGTTTCGAGTTTCGAGTTTCAAATTTC
*
182521 GGGTTTTGAGTTTCGAGTTTCAAATTTTGTGTTAC
1 GGGTTTCGAGTTTCGAGTTTCAAA-----T-TT-C
* *
182556 GGGTTT-GCAGTTTTGAGTTTCAAATTTT
1 GGGTTTCG-AGTTTCGAGTTTCAAATTTC
* *
182584 AGGTTTCGGGTTTCGAGTTTCAAATTT
1 GGGTTTCGAGTTTCGAGTTTCAAATTT
182611 TAGTTTTCGG
Statistics
Matches: 75, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
28 45 0.60
29 3 0.04
30 1 0.01
33 1 0.01
34 3 0.04
35 22 0.29
ACGTcount: A:0.18, C:0.10, G:0.25, T:0.47
Consensus pattern (28 bp):
GGGTTTCGAGTTTCGAGTTTCAAATTTC
Found at i:182548 original size:21 final size:21
Alignment explanation
Indices: 182524--182633 Score: 71
Period size: 21 Copynumber: 5.2 Consensus size: 21
182514 AAATTTCGGG
182524 TTTTGAGTTTCGAGTTTCAAA
1 TTTTGAGTTTCGAGTTTCAAA
* * * *
182545 TTTTGTGTTACGGGTTTGC-AG
1 TTTTGAGTTTCGAGTTT-CAAA
* * * **
182566 TTTTGAGTTTCAAATTTTAGG
1 TTTTGAGTTTCGAGTTTCAAA
* *
182587 TTTCGGGTTTCGAGTTTCAAA
1 TTTTGAGTTTCGAGTTTCAAA
* *
182608 TTTT-AGTTTTCGGGTTTAAAA
1 TTTTGAG-TTTCGAGTTTCAAA
182629 TTTTG
1 TTTTG
182634 GGTTATGGGT
Statistics
Matches: 63, Mismatches: 22, Indels: 7
0.68 0.24 0.08
Matches are distributed among these distances:
20 1 0.02
21 61 0.97
22 1 0.02
ACGTcount: A:0.19, C:0.08, G:0.23, T:0.50
Consensus pattern (21 bp):
TTTTGAGTTTCGAGTTTCAAA
Found at i:182560 original size:63 final size:63
Alignment explanation
Indices: 182493--182624 Score: 178
Period size: 63 Copynumber: 2.1 Consensus size: 63
182483 TTAAGGCTTT
* *
182493 GGGTTT-CGAGTTTCGAGTTTCAAATTTCGGGTTTTGAGTTTCGAGTTTCAAATTTT-GTGTTAC
1 GGGTTTGC-AGTTTCGAGTTTCAAATTTCAGGTTTCGAGTTTCGAGTTTCAAATTTTAGT-TTAC
* * * *
182556 GGGTTTGCAGTTTTGAGTTTCAAATTTTAGGTTTCGGGTTTCGAGTTTCAAATTTTAGTTTTC
1 GGGTTTGCAGTTTCGAGTTTCAAATTTCAGGTTTCGAGTTTCGAGTTTCAAATTTTAGTTTAC
182619 GGGTTT
1 GGGTTT
182625 AAAATTTTGG
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
63 58 0.95
64 3 0.05
ACGTcount: A:0.17, C:0.10, G:0.26, T:0.48
Consensus pattern (63 bp):
GGGTTTGCAGTTTCGAGTTTCAAATTTCAGGTTTCGAGTTTCGAGTTTCAAATTTTAGTTTAC
Found at i:182611 original size:28 final size:28
Alignment explanation
Indices: 182565--182624 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
182555 CGGGTTTGCA
*
182565 GTTTTGAGTTTCAAATTTTAGGTTTCGG
1 GTTTCGAGTTTCAAATTTTAGGTTTCGG
*
182593 GTTTCGAGTTTCAAATTTTAGTTTTCGG
1 GTTTCGAGTTTCAAATTTTAGGTTTCGG
182621 GTTT
1 GTTT
182625 AAAATTTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.17, C:0.08, G:0.23, T:0.52
Consensus pattern (28 bp):
GTTTCGAGTTTCAAATTTTAGGTTTCGG
Found at i:182624 original size:35 final size:34
Alignment explanation
Indices: 182490--182624 Score: 113
Period size: 35 Copynumber: 4.1 Consensus size: 34
182480 AATTTAAGGC
* * * * **
182490 TTTGGGTTTCGAGTTTCGAGTTTCAAATTTCGGG
1 TTTGAGTTTCGAGTTTCAAATTTTAGTTTTCGGG
*
182524 TTTTGAGTTTCGAGTTTCAAATTTT-GTGTTACGGG
1 -TTTGAGTTTCGAGTTTCAAATTTTAGT-TTTCGGG
* *
182559 TTTGCAGTTTTGAGTTTCAAATTTTAGGTTTC--G
1 TTTG-AGTTTCGAGTTTCAAATTTTAGTTTTCGGG
182592 ---G-GTTTCGAGTTTCAAATTTTAGTTTTCGGG
1 TTTGAGTTTCGAGTTTCAAATTTTAGTTTTCGGG
182622 TTT
1 TTT
182625 AAAATTTTGG
Statistics
Matches: 80, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
28 24 0.30
30 2 0.03
33 1 0.01
34 4 0.05
35 48 0.60
36 1 0.01
ACGTcount: A:0.16, C:0.10, G:0.25, T:0.49
Consensus pattern (34 bp):
TTTGAGTTTCGAGTTTCAAATTTTAGTTTTCGGG
Found at i:182630 original size:49 final size:48
Alignment explanation
Indices: 182564--182673 Score: 132
Period size: 49 Copynumber: 2.2 Consensus size: 48
182554 ACGGGTTTGC
*
182564 AGTTTTGAGTTTCAAATTTTAGGTT-TCGGGTTTCGAGTTTCAAATTTT
1 AGTTTTGAGTTTAAAATTTTAGGTTAT-GGGTTTCGAGTTTCAAATTTT
* * * *
182612 AGTTTTCGGGTTTAAAATTTTGGGTTATGGGTTTCGAGTTTCGAATTTCA
1 AGTTTT-GAGTTTAAAATTTTAGGTTATGGGTTTCGAGTTTCAAATTT-T
*
182662 AATTTTGAGTTT
1 AGTTTTGAGTTT
182674 TAGGTTTCAG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
48 6 0.12
49 40 0.77
50 6 0.12
ACGTcount: A:0.21, C:0.07, G:0.23, T:0.49
Consensus pattern (48 bp):
AGTTTTGAGTTTAAAATTTTAGGTTATGGGTTTCGAGTTTCAAATTTT
Found at i:182673 original size:28 final size:28
Alignment explanation
Indices: 182500--182673 Score: 75
Period size: 28 Copynumber: 6.2 Consensus size: 28
182490 TTTGGGTTTC
***
182500 GAGTTTCGAGTTTCAAATTTCGGGTTTT
1 GAGTTTCGAGTTTCAAATTTCAAATTTT
**** **
182528 GAGTTTCGAGTTTCAAATTTTGTGTTAC
1 GAGTTTCGAGTTTCAAATTTCAAATTTT
* ** *
182556 GGGTTT-GCAGTTTTGAGTTTCAAATTTT
1 GAGTTTCG-AGTTTCAAATTTCAAATTTT
* * *
182584 -AGGTTTCGGGTTTCGAGTTTCAAATTTT
1 GA-GTTTCGAGTTTCAAATTTCAAATTTT
* * **** *
182612 -AGTTTTCGGGTTTAAAATTTTGGGTTAT
1 GAG-TTTCGAGTTTCAAATTTCAAATTTT
* *
182640 GGGTTTCGAGTTTCGAATTTCAAATTTT
1 GAGTTTCGAGTTTCAAATTTCAAATTTT
182668 GAGTTT
1 GAGTTT
182674 TAGGTTTCAG
Statistics
Matches: 106, Mismatches: 35, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
27 2 0.02
28 102 0.96
29 2 0.02
ACGTcount: A:0.20, C:0.09, G:0.24, T:0.48
Consensus pattern (28 bp):
GAGTTTCGAGTTTCAAATTTCAAATTTT
Found at i:182680 original size:35 final size:34
Alignment explanation
Indices: 182626--182724 Score: 92
Period size: 35 Copynumber: 2.8 Consensus size: 34
182616 TTCGGGTTTA
* *
182626 AAATTTTGGGTTATGGGTTTCGAGTTTCGA-ATTT
1 AAATTTTGGGTTTTAGGTTTC-AGTTTCGACATTT
* * *
182660 CAAATTTTGAGTTTTAGGTTTCAGGTTTTGACCTTT
1 -AAATTTTGGGTTTTAGGTTTCA-GTTTCGACATTT
* *
182696 AAATTTTGGGTTTCAAGTTTCAAGTTTCG
1 AAATTTTGGGTTTTAGGTTTC-AGTTTCG
182725 GTTTTCTGGT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
34 1 0.02
35 47 0.90
36 4 0.08
ACGTcount: A:0.21, C:0.09, G:0.22, T:0.47
Consensus pattern (34 bp):
AAATTTTGGGTTTTAGGTTTCAGTTTCGACATTT
Found at i:182688 original size:21 final size:21
Alignment explanation
Indices: 182664--182814 Score: 60
Period size: 21 Copynumber: 7.2 Consensus size: 21
182654 GAATTTCAAA
182664 TTTTGAGTTTTAGGTTTCAGG
1 TTTTGAGTTTTAGGTTTCAGG
** ** **
182685 TTTTGACCTTTAAATTTTGGG
1 TTTTGAGTTTTAGGTTTCAGG
** * *
182706 TTTCAAGTTTCAAGTTTC-GG
1 TTTTGAGTTTTAGGTTTCAGG
* **
182726 TTTTCTG-GTTTTAGGATTCAAA
1 -TTT-TGAGTTTTAGGTTTCAGG
* *
182748 TTTT-AGGTTTTGGGGTTTGA-G
1 TTTTGA-GTTTT-AGGTTTCAGG
* **
182769 -TTTCAGTTTTAGGTTTCAAA
1 TTTTGAGTTTTAGGTTTCAGG
*
182789 TTTTGAGTTTTAGGTTTTAGG
1 TTTTGAGTTTTAGGTTTCAGG
182810 TTTTG
1 TTTTG
182815 GGCTTTAAAT
Statistics
Matches: 90, Mismatches: 31, Indels: 18
0.65 0.22 0.13
Matches are distributed among these distances:
19 6 0.07
20 11 0.12
21 68 0.76
22 5 0.06
ACGTcount: A:0.17, C:0.07, G:0.24, T:0.52
Consensus pattern (21 bp):
TTTTGAGTTTTAGGTTTCAGG
Found at i:182784 original size:7 final size:7
Alignment explanation
Indices: 182748--182868 Score: 68
Period size: 7 Copynumber: 17.4 Consensus size: 7
182738 AGGATTCAAA
182748 TTTTAGG
1 TTTTAGG
*
182755 TTTTGGG
1 TTTTAGG
*
182762 GTTT-GAG
1 TTTTAG-G
*
182769 TTTCA-G
1 TTTTAGG
182775 TTTTAGG
1 TTTTAGG
* **
182782 TTTCAAA
1 TTTTAGG
182789 TTTT-GAG
1 TTTTAG-G
182796 TTTTAGG
1 TTTTAGG
182803 TTTTAGG
1 TTTTAGG
*
182810 TTTTGGG
1 TTTTAGG
* **
182817 CTTTAAA
1 TTTTAGG
**
182824 TTTCGGG
1 TTTTAGG
*
182831 TTTAAGG
1 TTTTAGG
*
182838 TTTTTGG
1 TTTTAGG
*
182845 TTTTGGG
1 TTTTAGG
182852 TTTTAGG
1 TTTTAGG
182859 TTTTAGG
1 TTTTAGG
182866 TTT
1 TTT
182869 CAAATTTCTA
Statistics
Matches: 82, Mismatches: 27, Indels: 10
0.69 0.23 0.08
Matches are distributed among these distances:
6 6 0.07
7 75 0.91
8 1 0.01
ACGTcount: A:0.14, C:0.03, G:0.28, T:0.55
Consensus pattern (7 bp):
TTTTAGG
Found at i:182813 original size:35 final size:34
Alignment explanation
Indices: 182774--182854 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 34
182764 TTGAGTTTCA
* * *
182774 GTTTTAGGTTTCAAATTTTGAGTTTTAGGTTTTAG
1 GTTTTGGGTTT-AAATTTCGAGTTTAAGGTTTTAG
* *
182809 GTTTTGGGCTTTAAATTTCGGGTTTAAGGTTTTTG
1 GTTTTGGG-TTTAAATTTCGAGTTTAAGGTTTTAG
182844 GTTTTGGGTTT
1 GTTTTGGGTTT
182855 TAGGTTTTAG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
34 3 0.08
35 34 0.85
36 3 0.08
ACGTcount: A:0.15, C:0.04, G:0.27, T:0.54
Consensus pattern (34 bp):
GTTTTGGGTTTAAATTTCGAGTTTAAGGTTTTAG
Found at i:182867 original size:21 final size:21
Alignment explanation
Indices: 182795--182868 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
182785 CAAATTTTGA
* *
182795 GTTTTAGGTTTTAGGTTTTGG
1 GTTTTAGGTTTTGGGTTTTAG
* ** * *
182816 GCTTTAAATTTCGGGTTTAAG
1 GTTTTAGGTTTTGGGTTTTAG
*
182837 GTTTTTGGTTTTGGGTTTTAG
1 GTTTTAGGTTTTGGGTTTTAG
182858 GTTTTAGGTTT
1 GTTTTAGGTTT
182869 CAAATTTCTA
Statistics
Matches: 39, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.12, C:0.03, G:0.30, T:0.55
Consensus pattern (21 bp):
GTTTTAGGTTTTGGGTTTTAG
Found at i:182888 original size:56 final size:56
Alignment explanation
Indices: 182828--182965 Score: 172
Period size: 56 Copynumber: 2.5 Consensus size: 56
182818 TTTAAATTTC
* * * * *
182828 GGGTTTAAGGTTTTTGGTTTTGGGTTTTAG-GTTTTAGGTTTCAAATTTCTATTTTT
1 GGGTTTAA-ATTTTGGGTTTTGGGTTTTAGAGTTTCAGGTTTCAAATTTCGAGTTTT
* *
182884 GGGTTTAAAATTTTGGGTTATGGG-TTTGGAGTTTCAGGTTTCAAATTTCGAGTTTT
1 GGGTTT-AAATTTTGGGTTTTGGGTTTTAGAGTTTCAGGTTTCAAATTTCGAGTTTT
*
182940 GGGTTTAAATTTTGGGTTTCGGGTTT
1 GGGTTTAAATTTTGGGTTTTGGGTTT
182966 CAAATTCTAG
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
55 19 0.27
56 49 0.70
57 2 0.03
ACGTcount: A:0.16, C:0.04, G:0.28, T:0.51
Consensus pattern (56 bp):
GGGTTTAAATTTTGGGTTTTGGGTTTTAGAGTTTCAGGTTTCAAATTTCGAGTTTT
Found at i:182951 original size:20 final size:21
Alignment explanation
Indices: 182912--182971 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
182902 TATGGGTTTG
*
182912 GAGTTTCAGGTTTCAAATTTC
1 GAGTTTCGGGTTTCAAATTTC
* *
182933 GAGTTTTGGGTTT-AAATTTT
1 GAGTTTCGGGTTTCAAATTTC
*
182953 GGGTTTCGGGTTTCAAATT
1 GAGTTTCGGGTTTCAAATT
182972 CTAGGTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.20, C:0.08, G:0.25, T:0.47
Consensus pattern (21 bp):
GAGTTTCGGGTTTCAAATTTC
Found at i:182978 original size:21 final size:20
Alignment explanation
Indices: 182914--182979 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
182904 TGGGTTTGGA
* *
182914 GTTTCAGGTTTCAAATTTCG
1 GTTTCGGGTTTCAAATTTAG
* *
182934 AGTTTTGGGTTT-AAATTTTGG
1 -GTTTCGGGTTTCAAA-TTTAG
182955 GTTTCGGGTTTCAAATTCTAG
1 GTTTCGGGTTTCAAATT-TAG
182976 GTTT
1 GTTT
182980 TAGGTTTTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 15 0.41
21 22 0.59
ACGTcount: A:0.18, C:0.09, G:0.24, T:0.48
Consensus pattern (20 bp):
GTTTCGGGTTTCAAATTTAG
Found at i:182980 original size:41 final size:42
Alignment explanation
Indices: 182908--182986 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
182898 GGGTTATGGG
* *
182908 TTTGGAGTTTCAGGTTTCAAATTTCGAGTTTTGGGTTTAAAT
1 TTTGGAGTTTCAGGTTTCAAATTTAGAGTTTTAGGTTTAAAT
*
182950 TTTGG-GTTTCGGGTTTCAAATTCTAG-GTTTTAGGTTT
1 TTTGGAGTTTCAGGTTTCAAATT-TAGAGTTTTAGGTTT
182987 TGGGTTTCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 26 0.79
42 7 0.21
ACGTcount: A:0.18, C:0.08, G:0.25, T:0.49
Consensus pattern (42 bp):
TTTGGAGTTTCAGGTTTCAAATTTAGAGTTTTAGGTTTAAAT
Found at i:182986 original size:28 final size:28
Alignment explanation
Indices: 182949--183008 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
182939 TGGGTTTAAA
*
182949 TTTTGGGTTTCGGGTTTCAAATTCTAGG
1 TTTTAGGTTTCGGGTTTCAAATTCTAGG
* * *
182977 TTTTAGGTTTTGGGTTTCGAATTTTAGG
1 TTTTAGGTTTCGGGTTTCAAATTCTAGG
183005 TTTT
1 TTTT
183009 GTATTTCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.13, C:0.07, G:0.27, T:0.53
Consensus pattern (28 bp):
TTTTAGGTTTCGGGTTTCAAATTCTAGG
Found at i:183001 original size:21 final size:21
Alignment explanation
Indices: 182977--183027 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
182967 AAATTCTAGG
* *
182977 TTTTAGGTTTTGGGTTTCGAA
1 TTTTAGGTTTTGGATTTCAAA
*
182998 TTTTAGGTTTTGTATTTCAAA
1 TTTTAGGTTTTGGATTTCAAA
183019 TTTTAGGTT
1 TTTTAGGTT
183028 ACAGGTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.04, G:0.22, T:0.57
Consensus pattern (21 bp):
TTTTAGGTTTTGGATTTCAAA
Found at i:183016 original size:49 final size:49
Alignment explanation
Indices: 182935--183044 Score: 141
Period size: 49 Copynumber: 2.3 Consensus size: 49
182925 CAAATTTCGA
* * **
182935 GTTTTGGGTTT-AAATTTTGGGTTTCGGGTTTCAAATTCTAGGTTTTAG
1 GTTTTGGGTTTCAAATTTTAGGTTTCGGATTTCAAATTCTAGGTTACAG
* * * *
182983 GTTTTGGGTTTCGAATTTTAGGTTTTGTATTTCAAATTTTAGGTTACAG
1 GTTTTGGGTTTCAAATTTTAGGTTTCGGATTTCAAATTCTAGGTTACAG
183032 GTTTTGGGTTTCA
1 GTTTTGGGTTTCA
183045 GGTTTCGAGT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
48 11 0.21
49 41 0.79
ACGTcount: A:0.17, C:0.06, G:0.25, T:0.51
Consensus pattern (49 bp):
GTTTTGGGTTTCAAATTTTAGGTTTCGGATTTCAAATTCTAGGTTACAG
Found at i:183056 original size:21 final size:21
Alignment explanation
Indices: 183032--183123 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 21
183022 TAGGTTACAG
* **
183032 GTTTTGGGTTTCAGGTTTCGA
1 GTTTCGGGTTTCAAATTTCGA
* *
183053 GTTTCGGTTTTCAAATTTCGG
1 GTTTCGGGTTTCAAATTTCGA
*
183074 GTTTCGGGTTTCAAATTTTG-
1 GTTTCGGGTTTCAAATTTCGA
* * *
183094 GTTTTTGGGTTTCGAGTTTCGA
1 G-TTTCGGGTTTCAAATTTCGA
183116 GTTTCGGG
1 GTTTCGGG
183124 AATTGTGTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
20 1 0.02
21 55 0.96
22 1 0.02
ACGTcount: A:0.11, C:0.11, G:0.30, T:0.48
Consensus pattern (21 bp):
GTTTCGGGTTTCAAATTTCGA
Found at i:183065 original size:49 final size:49
Alignment explanation
Indices: 182935--183070 Score: 134
Period size: 49 Copynumber: 2.8 Consensus size: 49
182925 CAAATTTCGA
* * * * * **
182935 GTTTTGGGTTT-AAATTTTGGGTTTCGGGTTTCAAATTCTAGGTTTTAG
1 GTTTTGGGTTTCGAAGTTTAGGTTTCGGTTTTCAAATTTTAGGTTACAG
* *
182983 GTTTTGGGTTTCGAATTTTAGGTTT-TGTATTTCAAATTTTAGGTTACAG
1 GTTTTGGGTTTCGAAGTTTAGGTTTCGGT-TTTCAAATTTTAGGTTACAG
* *
183032 GTTTTGGGTTTC-AGGTTTCGAGTTTCGGTTTTCAAATTT
1 GTTTTGGGTTTCGAAGTTTAG-GTTTCGGTTTTCAAATTT
183071 CGGGTTTCGG
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
48 17 0.23
49 54 0.74
50 2 0.03
ACGTcount: A:0.17, C:0.07, G:0.25, T:0.51
Consensus pattern (49 bp):
GTTTTGGGTTTCGAAGTTTAGGTTTCGGTTTTCAAATTTTAGGTTACAG
Found at i:183196 original size:7 final size:7
Alignment explanation
Indices: 183186--183267 Score: 74
Period size: 7 Copynumber: 11.7 Consensus size: 7
183176 CTTGTTTCGA
183186 GTTTTGG
1 GTTTTGG
183193 GTTTTGG
1 GTTTTGG
**
183200 GTTTTAA
1 GTTTTGG
183207 GTTTTGG
1 GTTTTGG
* *
183214 GTCTCGG
1 GTTTTGG
***
183221 GTTTCAA
1 GTTTTGG
*
183228 ATTTTGG
1 GTTTTGG
183235 GTTTTGG
1 GTTTTGG
183242 GTTTTGG
1 GTTTTGG
*
183249 GTTTTAG
1 GTTTTGG
*
183256 TTTTTGG
1 GTTTTGG
183263 GTTTT
1 GTTTT
183268 TAAATTCAGG
Statistics
Matches: 57, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 57 1.00
ACGTcount: A:0.07, C:0.04, G:0.33, T:0.56
Consensus pattern (7 bp):
GTTTTGG
Found at i:183196 original size:14 final size:14
Alignment explanation
Indices: 183166--183267 Score: 64
Period size: 14 Copynumber: 7.3 Consensus size: 14
183156 CGTTTTCAAA
*
183166 TTTTGAGTTTCT-TG
1 TTTTGAGTTT-TGGG
*
183180 TTTCGAGTTTTGGG
1 TTTTGAGTTTTGGG
* **
183194 TTTTGGGTTTTAAG
1 TTTTGAGTTTTGGG
* * *
183208 TTTTGGGTCTCGGG
1 TTTTGAGTTTTGGG
** *
183222 TTTCAAATTTTGGG
1 TTTTGAGTTTTGGG
*
183236 TTTTGGGTTTTGGG
1 TTTTGAGTTTTGGG
183250 TTTT-AGTTTTTGGG
1 TTTTGAG-TTTTGGG
183264 TTTT
1 TTTT
183268 TAAATTCAGG
Statistics
Matches: 65, Mismatches: 21, Indels: 4
0.72 0.23 0.04
Matches are distributed among these distances:
13 2 0.03
14 63 0.97
ACGTcount: A:0.08, C:0.05, G:0.30, T:0.57
Consensus pattern (14 bp):
TTTTGAGTTTTGGG
Found at i:183253 original size:21 final size:21
Alignment explanation
Indices: 183185--183267 Score: 94
Period size: 21 Copynumber: 4.0 Consensus size: 21
183175 TCTTGTTTCG
183185 AGTTTTGGGTTTTGGGTTTTA
1 AGTTTTGGGTTTTGGGTTTTA
* * *
183206 AGTTTTGGGTCTCGGGTTTCA
1 AGTTTTGGGTTTTGGGTTTTA
* *
183227 AATTTTGGGTTTTGGGTTTTG
1 AGTTTTGGGTTTTGGGTTTTA
* * *
183248 GGTTTTAGTTTTTGGGTTTT
1 AGTTTTGGGTTTTGGGTTTT
183268 TAAATTCAGG
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.08, C:0.04, G:0.33, T:0.55
Consensus pattern (21 bp):
AGTTTTGGGTTTTGGGTTTTA
Found at i:183300 original size:21 final size:21
Alignment explanation
Indices: 183276--183315 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
183266 TTTAAATTCA
183276 GGTTT-TAGCTTTCAAATTTAG
1 GGTTTCTAG-TTTCAAATTTAG
*
183297 GGTTTCTAGTTTTAAATTT
1 GGTTTCTAGTTTCAAATTT
183316 CGATTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.23, C:0.07, G:0.17, T:0.53
Consensus pattern (21 bp):
GGTTTCTAGTTTCAAATTTAG
Found at i:183323 original size:63 final size:64
Alignment explanation
Indices: 183256--183393 Score: 138
Period size: 63 Copynumber: 2.2 Consensus size: 64
183246 TGGGTTTTAG
* * *
183256 TTTTTGGGTTTTT-AAATTCAGGTTTT-AGCTTTCAAATTTAGGGTTTCTAGTTTTAAATTTCGA
1 TTTTTGGGTTTTTGAAATTCAGGTTTTGA-CTTTCAAATATAAGGTTTCTAGTTTTAAATTTCAA
* ** ** * **
183319 TTTTT-TGTTTTTGAGTTTTTGGTTTTGATTTTTGAATATAAGGTTTCTAGTTTTAAATTTCAA
1 TTTTTGGGTTTTTGAAATTCAGGTTTTGACTTTCAAATATAAGGTTTCTAGTTTTAAATTTCAA
*
183382 ATTTTGGGTTTT
1 TTTTTGGGTTTT
183394 AGATTTTTGT
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
62 6 0.10
63 47 0.80
64 6 0.10
ACGTcount: A:0.20, C:0.05, G:0.17, T:0.57
Consensus pattern (64 bp):
TTTTTGGGTTTTTGAAATTCAGGTTTTGACTTTCAAATATAAGGTTTCTAGTTTTAAATTTCAA
Done.