Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004706.1 Hibiscus syriacus cultivar Beakdansim tig00010576_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: 124733
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:341 original size:23 final size:23
Alignment explanation
Indices: 315--359 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
305 CACCACAGCT
*
315 CGTATAATTACACCGAAGTGCCG
1 CGTAGAATTACACCGAAGTGCCG
* *
338 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTACACCGAAGTGCC
360 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTACACCGAAGTGCCG
Found at i:580 original size:147 final size:144
Alignment explanation
Indices: 327--635 Score: 523
Period size: 147 Copynumber: 2.1 Consensus size: 144
317 TATAATTACA
327 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
*
391 TTCCTTAAGAATCATACATATGTTAGGGATCAAGTATGTGTCTTTCAAGACTTCAGACATGTTCC
65 TTCCTTAAGAATCATACATATGCTAGGGATCAAGTA-GTGTCTTTCAAGACTTCAGACATGTTCC
456 ACAGAATATATATATAT
129 ACAGAATATAT-TATAT
* *
473 CCCTAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 -CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
538 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTA-TGTCTTTCAAGACTTCAGACATGTTC
65 TTCCTTAAGAATC--ATACATATGCTAGGGATCAAGTAGTGTCTTTCAAGACTTCAGACATGTTC
602 CACAGAATATATTATAT
128 CACAGAATATATTATAT
619 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
636 CCCTCGACTC
Statistics
Matches: 155, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
145 16 0.10
146 6 0.04
147 111 0.72
149 22 0.14
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (144 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATACATATGCTAGGGATCAAGTAGTGTCTTTCAAGACTTCAGACATGTTCCAC
AGAATATATTATAT
Found at i:2180 original size:63 final size:62
Alignment explanation
Indices: 2029--2187 Score: 178
Period size: 63 Copynumber: 2.5 Consensus size: 62
2019 TAATGAAGGT
* * * * *
2029 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTAATGGGG
1 ATGCATCGATGCACTCCA-TATGCATCGATGCATAAATCATATTCGATGTTTCTATTAAT-GGC
* *
2093 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT-TC
1 ATGCATCGATGCACTCCATATGCATCGATGCATAAATCATATTCGATG-TTTCTA-TT-AATGGC
* *
2157 ATGCATCGATGCA-TGCATGTGCATCGATGCA
1 ATGCATCGATGCACTCCATATGCATCGATGCA
2188 CCTTGAACAA
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
63 43 0.52
64 34 0.41
65 2 0.02
66 3 0.04
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (62 bp):
ATGCATCGATGCACTCCATATGCATCGATGCATAAATCATATTCGATGTTTCTATTAATGGC
Found at i:5309 original size:147 final size:146
Alignment explanation
Indices: 5024--5333 Score: 575
Period size: 147 Copynumber: 2.1 Consensus size: 146
5014 TATAATTACA
* *
5024 CCGAAGTACCGTGTAGAATGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATT
1 CCGAAGGACCGCGTAGAATGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATT
5089 CCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCC
66 CCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCC
5154 ACAGAATATATATATC
131 ACAGAATATATATATC
*
5170 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAA-TGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
*
5235 TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATTTGTCTTTCAAGACTTCACACATGTTC
65 TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
5300 CACAGAATATATATATC
130 CACAGAATATATATATC
5317 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
5334 CCCTCGACTC
Statistics
Matches: 159, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
146 16 0.10
147 143 0.90
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (146 bp):
CCGAAGGACCGCGTAGAATGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATT
CCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCC
ACAGAATATATATATC
Found at i:6825 original size:64 final size:63
Alignment explanation
Indices: 6727--6887 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
6717 TAATGAAGGT
* * *
6727 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATG-TTTGTATTT-AATGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAAT--
*
6790 GG
62 GC
*
6792 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
* *
6856 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
6888 CCTTGAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.67
65 24 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCATATTCGATGTTTTCTATTTAAATGC
Found at i:9245 original size:45 final size:45
Alignment explanation
Indices: 9191--9414 Score: 319
Period size: 44 Copynumber: 5.0 Consensus size: 45
9181 GTATCACATT
9191 TCATTTTCGCTCGATTCCATCACATAAGGAGTTGGATCAACATCA
1 TCATTTTCGCTCGATTCCATCACATAAGGAGTTGGATCAACATCA
9236 TCATTTTCGCTCGATTCCATCACATAAGGAGTTGGATCAACATCA
1 TCATTTTCGCTCGATTCCATCACATAAGGAGTTGGATCAACATCA
* * * * **
9281 ACATTTT-TCTCGATTCCTTCACATAGGGAGTTGGATCAGTATCA
1 TCATTTTCGCTCGATTCCATCACATAAGGAGTTGGATCAACATCA
* * * **
9325 TAATTTT-GCTCGATTCCATCGCATAAGGAATTGGATCAGTATCA
1 TCATTTTCGCTCGATTCCATCACATAAGGAGTTGGATCAACATCA
*
9369 TCA-TTTCGCTCGATTCCATAACATAAGGAGTTGGATCAACATCA
1 TCATTTTCGCTCGATTCCATCACATAAGGAGTTGGATCAACATCA
9413 TC
1 TC
9415 TTGCTTGATA
Statistics
Matches: 159, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
43 3 0.02
44 105 0.66
45 51 0.32
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.33
Consensus pattern (45 bp):
TCATTTTCGCTCGATTCCATCACATAAGGAGTTGGATCAACATCA
Found at i:9571 original size:37 final size:36
Alignment explanation
Indices: 9466--9572 Score: 142
Period size: 36 Copynumber: 2.9 Consensus size: 36
9456 TCAAGAAATA
*
9466 ATCTCACTTGATATTGTTTTTCTTAAAACGAATTTT
1 ATCTCACTTGATATTGTTTTTCTTAAAACAAATTTT
* * * *
9502 ATATCACTCGAAATTGTTTTTCTTAAAGCAAATTTT
1 ATCTCACTTGATATTGTTTTTCTTAAAACAAATTTT
* *
9538 GTCTCTCTTGATATTGTTTTTTCTTAAAACAAATT
1 ATCTCACTTGATATTG-TTTTTCTTAAAACAAATT
9573 GCATCCCTCT
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
36 42 0.71
37 17 0.29
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (36 bp):
ATCTCACTTGATATTGTTTTTCTTAAAACAAATTTT
Found at i:11339 original size:42 final size:42
Alignment explanation
Indices: 11292--11415 Score: 216
Period size: 42 Copynumber: 3.0 Consensus size: 42
11282 CATATTCGCA
*
11292 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
11334 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
11376 TTGCGATAGTCCAAGTT--CGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
11416 CAACGACGGT
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
40 23 0.29
42 57 0.71
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:11351 original size:19 final size:19
Alignment explanation
Indices: 11292--11401 Score: 103
Period size: 21 Copynumber: 5.4 Consensus size: 19
11282 CATATTCGCA
*
11292 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
*
11313 TTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCG
*
11334 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTT--CG
* *
11355 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCG
11376 TTGCGATAGTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCG
11395 TTGCGAT
1 TTGCGAT
11402 TTATTCCAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 14
0.76 0.09 0.14
Matches are distributed among these distances:
19 27 0.36
21 30 0.41
23 17 0.23
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.35
Consensus pattern (19 bp):
TTGCGATAGTCCAAGTTCG
Found at i:11377 original size:21 final size:21
Alignment explanation
Indices: 11311--11415 Score: 119
Period size: 21 Copynumber: 5.1 Consensus size: 21
11301 TCGAAGTTCG
11311 CGTTGCGATTTATTCCAAGTT
1 CGTTGCGATTTATTCCAAGTT
* *
11332 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAGTT
*
11351 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAGTT
*
11374 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAGTT
*
11393 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAGTT
11414 CG
1 CG
11416 CAACGACGGT
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
19 26 0.38
21 35 0.51
23 8 0.12
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAGTT
Found at i:12136 original size:21 final size:21
Alignment explanation
Indices: 12112--12223 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 21
12102 ATTTTGAACT
12112 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
12133 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
12154 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
12175 ATCGCAACACGAACTTCGACT--
1 ATCGC-A-ACGAATTTGGAATAA
*
12196 ATCACAACGAATTTGG-A-AA
1 ATCGCAACGAATTTGGAATAA
12215 ATCGCAACG
1 ATCGCAACG
12224 CGAACTTGGA
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
19 25 0.36
20 1 0.01
21 23 0.33
22 1 0.01
23 19 0.28
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:12168 original size:42 final size:42
Alignment explanation
Indices: 12109--12242 Score: 227
Period size: 42 Copynumber: 3.2 Consensus size: 42
12099 GCGATTTTGA
12109 ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCG
1 ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCG
*
12151 ACTATCGCAACGAATTTGGAATAAATCGCAACACGAACTTCG
1 ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCG
* *
12193 ACTATCACAACGAATTTGG-A-AAATCGCAACGCGAACTTGG
1 ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCG
12233 ACTATCGCAA
1 ACTATCGCAA
12243 TGCGAATATG
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 27 0.31
41 1 0.01
42 59 0.68
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (42 bp):
ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCG
Found at i:12232 original size:21 final size:21
Alignment explanation
Indices: 12131--12248 Score: 73
Period size: 21 Copynumber: 5.7 Consensus size: 21
12121 AATTTGGAAT
*
12131 AAATCGCAACGCGAACTTCGA
1 AAATCGCAACGCGAACTTGGA
** *
12152 CTATCGCAA--CGAATTTGGAA
1 AAATCGCAACGCGAACTTGG-A
* *
12172 TAAATCGCAACACGAACTTCGA
1 -AAATCGCAACGCGAACTTGGA
** * *
12194 CTATCACAA--CGAATTTGGA
1 AAATCGCAACGCGAACTTGGA
12213 AAATCGCAACGCGAACTTGGA
1 AAATCGCAACGCGAACTTGGA
** *
12234 CTATCGCAATGCGAA
1 AAATCGCAACGCGAA
12249 TATGTAAATC
Statistics
Matches: 71, Mismatches: 20, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
19 21 0.30
20 1 0.01
21 41 0.58
22 1 0.01
23 7 0.10
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (21 bp):
AAATCGCAACGCGAACTTGGA
Found at i:12249 original size:42 final size:42
Alignment explanation
Indices: 12109--12384 Score: 205
Period size: 42 Copynumber: 6.4 Consensus size: 42
12099 GCGATTTTGA
12109 ACTATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCG
1 ACTATCGCAATGCGAATTTGG-A-AAATCGCAACGCGAACTTCG
*
12151 ACTATCGCAA--CGAATTTGGAATAAATCGCAACACGAACTTCG
1 ACTATCGCAATGCGAATTTGG-A-AAATCGCAACGCGAACTTCG
* *
12193 ACTATCACAA--CGAATTTGGAAAATCGCAACGCGAACTTGG
1 ACTATCGCAATGCGAATTTGGAAAATCGCAACGCGAACTTCG
* * * *
12233 ACTATCGCAATGCGAATAT-GTAAATCGGAATGCAATGCGAACTTGG
1 ACTATCGCAATGCGAATTTGGAAAATC-----GCAACGCGAACTTCG
* * *
12279 ACTATCGCAATGCGAATAT-GTAAATCGCAATGCGATAGTCGAAGTTCG
1 ACTATCGCAATGCGAATTTGGAAAATCGCAA--C----G-CGAACTTCG
*
12327 -CGT-T-GCGATAGTCGAATTTGGAAAATCGCAACGCGAACTTCG
1 AC-TATCGCAAT-G-CGAATTTGGAAAATCGCAACGCGAACTTCG
12369 ACTATCGCAATGCGAA
1 ACTATCGCAATGCGAA
12385 CTTGAACTAT
Statistics
Matches: 197, Mismatches: 16, Indels: 42
0.77 0.06 0.16
Matches are distributed among these distances:
40 27 0.14
41 11 0.06
42 78 0.40
43 4 0.02
44 4 0.02
46 44 0.22
47 5 0.03
48 14 0.07
49 10 0.05
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (42 bp):
ACTATCGCAATGCGAATTTGGAAAATCGCAACGCGAACTTCG
Found at i:12276 original size:46 final size:46
Alignment explanation
Indices: 12218--12311 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
12208 TTGGAAAATC
*
12218 GCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGGAAT
1 GCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAAT
*
12264 GCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAAT
1 GCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAAT
12310 GC
1 GC
12312 GATAGTCGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.22
Consensus pattern (46 bp):
GCAACGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAAT
Found at i:12307 original size:20 final size:20
Alignment explanation
Indices: 12236--12313 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
12226 AACTTGGACT
12236 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
12256 ATCGGAATGCAATGCGAACT-TGGACT
1 ATC-----GCAATGCGAA-TATGTA-A
12282 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
12302 ATCGCAATGCGA
1 ATCGCAATGCGA
12314 TAGTCGAAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
20 16 0.35
21 13 0.28
25 13 0.28
26 4 0.09
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:12375 original size:21 final size:21
Alignment explanation
Indices: 12351--12405 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
12341 AATTTGGAAA
*
12351 ATCGCAACGCGAACTTCG-ACT
1 ATCGCAATGCGAACTT-GAACT
12372 ATCGCAATGCGAACTTGAACT
1 ATCGCAATGCGAACTTGAACT
12393 ATCGCAATGCGAA
1 ATCGCAATGCGAA
12406 TATAAATCGC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAATGCGAACTTGAACT
Found at i:13258 original size:21 final size:21
Alignment explanation
Indices: 13209--13258 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
13199 AATTTGGAAA
*
13209 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
* *
13230 ATCGCAATGTGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
13251 ATCGCAAT
1 ATCGCAAT
13259 ACGATAGTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:14044 original size:140 final size:140
Alignment explanation
Indices: 13869--14132 Score: 357
Period size: 140 Copynumber: 1.9 Consensus size: 140
13859 GATTTCTCAC
* * ** *
13869 ACTTTAGTCCCTTAATTTAGGGAATAATTCGATTTGGCTCTCGCATTAAATGTATGATGGTTCAT
1 ACTTTAGTCCCTTAATTTAGGGAATAATTCGATTTGGCTCTCGCATTAAATGCACGACAGTCCAT
** ** * *
13934 TTTGATCATTTGATTCAATAATTGATTAAAATAAATTAGAATTAATATTAGAGTCTCCACTTTAG
66 TTCCATCATTCAATTCAATAATTGAATAAAATAAATTAGAATAAATATTAGAGTCTCCACTTTAG
13999 GCTTAATTTA
131 GCTTAATTTA
* ** * *
14009 ACTTTAGTCTCTTAATTTTTGGAATAATTTGATTTGGCTCTCGCATTAAATGCCCGACAGTCCAT
1 ACTTTAGTCCCTTAATTTAGGGAATAATTCGATTTGGCTCTCGCATTAAATGCACGACAGTCCAT
* * *
14074 TTCCATTATTCAATTCAATAATTGAATAAAATGAATTAGGATAAATATTAGAGTCTCCA
66 TTCCATCATTCAATTCAATAATTGAATAAAATAAATTAGAATAAATATTAGAGTCTCCA
14133 TTTTTAGGTT
Statistics
Matches: 105, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
140 105 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (140 bp):
ACTTTAGTCCCTTAATTTAGGGAATAATTCGATTTGGCTCTCGCATTAAATGCACGACAGTCCAT
TTCCATCATTCAATTCAATAATTGAATAAAATAAATTAGAATAAATATTAGAGTCTCCACTTTAG
GCTTAATTTA
Found at i:15814 original size:428 final size:426
Alignment explanation
Indices: 14605--16433 Score: 1747
Period size: 428 Copynumber: 4.3 Consensus size: 426
14595 AAGTTTATAC
* * * *
14605 ACTAAACGTGTAATTTACCCTTAAATTACGTAAAAGTTTAAAATTTTTAGAGATAATTAACTCTT
1 ACTAAACGCGTAATTTACCCTTAAATTATGTAAAAGTTTAAAATTTTTAAAGATAATTATCTCTT
* * * * * *
14670 GTTTTCTTAATCGATCCCTCAATATAAAGAAAGAT-CTCTAACACACAAAAATAGATGAATTTAT
66 ATTTTCTCAATCGATCCCTCAATATAAAGAGAGATGC-CTAACAAAAAAAAAGAGATGAATTTAT
* * * * * *
14734 CTACGCTCTAAACAAATACGCAATGTCCAAGTTTTAATA-CCAAACTTTTTATTTTTTTAAAATC
130 CTACGCTCTAAACAAATACGTAATGTACAAGTTTTAATATCTAAACTTTTAATTTTTTCAAAATT
** * * * *
14798 ATACCTAATGTTTAGGTTTTATTTCATTTTAGTA-CCCGCCG-TAAAAATTTCATGCGTTTAATA
195 ATACCTAACATTTAGTTTTTATTTCATTTTAGTATCCCACCGTTAAAAATTTCACGCGTTTAGTA
* * * *
14861 TCTATACTATCAGTTTTGATCCGTTTTAGTACCTAAACTTTCATTTTTTTTCAAAATTTAACATT
260 TCTAAACTATCAGTTTTGATCCGTTTTAGTATCTAAACTTT--TTTTTTTTCAAAACTTAACGTT
* * *
14926 ATATTTTGAATGGGGTACAAAAATGAAACAAAAACTAAATTATAAGTATGATTTTG-AAAAATTG
323 AAATTTTGAAT-GGGTACTAAAATAAAACAAAAACTAAATT-TAAGTATGATTTTGAAAAAATTG
* * *
14990 AAACTTTAAGT-AAAGTTATAGAC-CGAAACTAACATTTTAGGT
386 AAACTTTAAGTAAAAG-TATA-ACTCG-AACTGATAGTTTAGGT
* * * * * *
15032 AGTAAATGCGTAATTTAACCTTATATTATGCAAAA-TATT---TTTTTTAAAAGAT--TTATCTC
1 ACTAAACGCGTAATTTACCCTTAAATTATGTAAAAGT-TTAAAATTTTT-AAAGATAATTATCTC
* *
15091 TTATTTTCTCAATCGATCCCTCAATATAAAGAGAGATGTCTAAC-ACAAAAAAGAGATGAATTTA
64 TTATTTTCTCAATCGATCCCTCAATATAAAGAGAGATGCCTAACAAAAAAAAAGAGATGAATTTA
* * * * * *
15155 TCTACGCTCTATA-AAACATGTAATGTAAAAGTTTTAGTATCTAAACTTTTAATATTTTCAAAA-
129 TCTACGCTCTAAACAAATACGTAATGTACAAGTTTTAATATCTAAACTTTTAATTTTTTCAAAAT
* * * * * * *
15218 TAT--CTGACATTTATTTTTTGTTTTATTTTAGTATCTCACCGATAAAAACTTCACGCGTTTAGT
194 TATACCTAACATTTAGTTTTTATTTCATTTTAGTATCCCACCGTTAAAAATTTCACGCGTTTAGT
* * * * * ** **
15281 ATCTAAACTTTTAGTTTTGATCCTTTTTAGTATCTAGACTTTCAAAAAATAATAATCAAAACTTA
259 ATCTAAACTATCAGTTTTGATCCGTTTTAGTATCTAAACTTT------TTTTTTTTCAAAACTTA
* * *
15346 ACGTTAAATTTTGAATGAGTTACTAAAATGAAACAAAAACTAAAATTTAAATATGATTTTGAAAA
318 ACGTTAAATTTTGAATG-GGTACTAAAATAAAACAAAAACT-AAATTTAAGTATGATTTTGAAAA
* * * * *
15411 AATTGAAACTTTAAGTAAAAGTACATACTAGAATTGGTGGTTTAGGT
381 AATTGAAACTTTAAGTAAAAGTATA-ACTCGAACTGATAGTTTAGGT
* *
15458 ACTAAACACGTAATATACCCTTAAATTATGTAAAAGTTT-AAATTTTTAAAGATAATTATCTCTT
1 ACTAAACGCGTAATTTACCCTTAAATTATGTAAAAGTTTAAAATTTTTAAAGATAATTATCTCTT
*
15522 ATTCTCT-AATCGATCCCTCAATATAAAGAGAGATGCCTAACATAAAAAAAGAGAGATGAATTTA
66 ATTTTCTCAATCGATCCCTCAATATAAAGAGAGATGCCTAACA-AAAAAAA-AGAGATGAATTTA
* * *
15586 TCTACACTCTAAACAAATATGTAATGTACAAGTTTTAGTATCTAAACTTTTAATTTTTCTCAAAA
129 TCTACGCTCTAAACAAATACGTAATGTACAAGTTTTAATATCTAAACTTTTAATTTTT-TCAAAA
* ** *
15651 TTATACCTAACATTTAGTTTTTATTTCATTTTAATATCAAACCGTTAAAAAATTTAACGCGTTTA
193 TTATACCTAACATTTAGTTTTTATTTCATTTTAGTATCCCACCGTT-AAAAATTTCACGCGTTTA
* * *
15716 GTATCTAAACTATCAATTCTGATCCGTTTTAGT-TCCTAAAC-TTTTTTTTTTCAAAACATAACG
257 GTATCTAAACTATCAGTTTTGATCCGTTTTAGTAT-CTAAACTTTTTTTTTTTCAAAACTTAACG
*** * * *
15779 TTAAATTTCCCCCA-GGGTACTAAAAT-AAA-AAAAACTAAATTTTAATTATGGTTTTGAGAAAA
321 TTAAATTT--TGAATGGGTACTAAAATAAAACAAAAACTAAA-TTTAAGTATGATTTTGAAAAAA
* *
15841 TTGAAACTTTAAGTAAAAATATAAATCCGAACTGATAGTTTAGGT
383 TTGAAACTTTAAGTAAAAGTATAACT-CGAACTGATAGTTTAGGT
* * * * *
15886 ATTAAATGCGCAA-TTATCCTTATATTATGTAAAAGTTTAAAATTTTTAAAGATAATTATCTCTT
1 ACTAAACGCGTAATTTACCCTTAAATTATGTAAAAGTTTAAAATTTTTAAAGATAATTATCTCTT
** * * *
15950 ATTTTCTCGTTCGATCCCTCAATATAAAGAGAGATGTCTAACACACAAAAAAGAAATGAATTTAT
66 ATTTTCTCAATCGATCCCTCAATATAAAGAGAGATGCCTAACA-AAAAAAAAGAGATGAATTTAT
* * * ** **
16015 CTATGCTCTAAACAAATACGTAATGTACAAGTTTTAATACCTTAACTTTTGTTTTTTTTTAAATT
130 CTACGCTCTAAACAAATACGTAATGTACAAGTTTTAATATCTAAACTTTTAATTTTTTCAAAATT
** * * *
16080 ATATTTAATATTTAG-TTTTATTTCATTTTAGTATTCCCACCATT-AAAATCTTCACGTGTTTAG
195 ATACCTAACATTTAGTTTTTATTTCATTTTAGTA-TCCCACCGTTAAAAAT-TTCACGCGTTTAG
* * * *
16143 TATCTAAACTATCAGTTTTGGTTCATTTAAGTATCTAAACTTCCATTTTTCTTTTCAAAACTTAA
258 TATCTAAACTATCAGTTTTGATCCGTTTTAGTATCTAAACTT---TTTTT-TTTTCAAAACTTAA
* * *
16208 CGTTAAATTTTGAATGGGTACTAAAATAAAAAAAAAACTAAATTTGAAGTATGATTTCGAAAAAC
319 CGTTAAATTTTGAATGGGTACTAAAATAAAACAAAAACTAAATTT-AAGTATGATTTTGAAAAAA
* * * * * * *
16273 TT-AAAATCTTAAGTAAAA-AATACATATCAAAATTAATAGTTTAAGT
383 TTGAAACT-TTAAGTAAAAGTATA-A-CTC-GAACTGATAGTTTAGGT
* * *** *
16319 ATTAAACGCATAATTTATAATTAAATTA--T---A---TAAATTTTTTAAAGATAATTATCTCTT
1 ACTAAACGCGTAATTTACCCTTAAATTATGTAAAAGTTTAAAATTTTTAAAGATAATTATCTCTT
* * * * ** * *
16376 CTTTTCTCGATCAATCCCTCGATATAAAGAGATG-TGTGTAACACAAAAACAGAGATGA
66 ATTTTCTCAATCGATCCCTCAATATAAAGAGA-GATGCCTAACAAAAAAAAAGAGATGA
16434 CGCTCTAAAC
Statistics
Matches: 1157, Mismatches: 191, Indels: 110
0.79 0.13 0.08
Matches are distributed among these distances:
419 23 0.02
420 5 0.00
421 76 0.07
422 47 0.04
423 45 0.04
424 6 0.01
425 81 0.07
426 192 0.17
427 97 0.08
428 201 0.17
429 58 0.05
430 55 0.05
431 61 0.05
432 81 0.07
433 31 0.03
434 14 0.01
436 35 0.03
437 49 0.04
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (426 bp):
ACTAAACGCGTAATTTACCCTTAAATTATGTAAAAGTTTAAAATTTTTAAAGATAATTATCTCTT
ATTTTCTCAATCGATCCCTCAATATAAAGAGAGATGCCTAACAAAAAAAAAGAGATGAATTTATC
TACGCTCTAAACAAATACGTAATGTACAAGTTTTAATATCTAAACTTTTAATTTTTTCAAAATTA
TACCTAACATTTAGTTTTTATTTCATTTTAGTATCCCACCGTTAAAAATTTCACGCGTTTAGTAT
CTAAACTATCAGTTTTGATCCGTTTTAGTATCTAAACTTTTTTTTTTTCAAAACTTAACGTTAAA
TTTTGAATGGGTACTAAAATAAAACAAAAACTAAATTTAAGTATGATTTTGAAAAAATTGAAACT
TTAAGTAAAAGTATAACTCGAACTGATAGTTTAGGT
Found at i:21008 original size:20 final size:20
Alignment explanation
Indices: 20983--21028 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
20973 ATACAGATTG
20983 AATATTAGGTCAATCTATTA
1 AATATTAGGTCAATCTATTA
21003 AATATTAGGTCAATCTATTA
1 AATATTAGGTCAATCTATTA
21023 AATATT
1 AATATT
21029 TATGATTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (20 bp):
AATATTAGGTCAATCTATTA
Found at i:28163 original size:17 final size:17
Alignment explanation
Indices: 28141--28178 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
28131 GGTCTGACCC
*
28141 GACCCGACCCGACCGTT
1 GACCCGACCCGACCATT
28158 GACCCGACCCGACCATT
1 GACCCGACCCGACCATT
28175 GACC
1 GACC
28179 GTGACCGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.47, G:0.21, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCATT
Found at i:31277 original size:21 final size:21
Alignment explanation
Indices: 31233--31277 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
31223 TGATTCTGGG
* * *
31233 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
31254 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
31275 CAA
1 CAA
31278 ACGAACATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:32151 original size:29 final size:30
Alignment explanation
Indices: 32057--32153 Score: 142
Period size: 30 Copynumber: 3.2 Consensus size: 30
32047 AAGGAACATA
32057 TGGATAGTTTACCGAGGATCTTTATGACCTC
1 TGGATAG-TTACCGAGGATCTTTATGACCTC
*
32088 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
* * *
32118 TGGATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
32147 TGGATAG
1 TGGATAG
32154 GTCATTCGGG
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 20 0.33
30 35 0.57
31 6 0.10
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.32
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:35422 original size:21 final size:21
Alignment explanation
Indices: 35378--35422 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35368 TGATTCTGGG
* * *
35378 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
35399 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
35420 CAA
1 CAA
35423 ACGAACATAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:36187 original size:31 final size:31
Alignment explanation
Indices: 36149--36214 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
36139 TCGAGGGTTT
**
36149 TACCTATG-TCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTAACGA-ACATATGGACAGTA
* *
36180 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTAACGAACATATGGACAGTA
36211 TACC
1 TACC
36215 GAGGATCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTAACGAACATATGGACAGTA
Found at i:36293 original size:29 final size:30
Alignment explanation
Indices: 36210--36298 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 30
36200 TATGGACAGT
* * *
36210 TTACCGAGGATCTTTATGACCTCTAGACAG
1 TTACCGAGGATCTGTATGACCTCTGGATAG
*
36240 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTGTATGACCTCTGGATAG
* *
36270 TTACCG-GGGTCTGTGTGACCTCTGGATAG
1 TTACCGAGGATCTGTATGACCTCTGGATAG
36299 GTCCTTCGGG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 20 0.37
30 34 0.63
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (30 bp):
TTACCGAGGATCTGTATGACCTCTGGATAG
Found at i:41798 original size:26 final size:26
Alignment explanation
Indices: 41755--41805 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
41745 CTGAACTGGT
*
41755 TTGACCGGTCTGACCCGACCCGACCG
1 TTGACCGATCTGACCCGACCCGACCG
41781 TTGACCCGATCTGA-CCGACCCGACC
1 TTGA-CCGATCTGACCCGACCCGACC
41806 CGACCCGACC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.18, C:0.43, G:0.24, T:0.16
Consensus pattern (26 bp):
TTGACCGATCTGACCCGACCCGACCG
Found at i:45963 original size:30 final size:31
Alignment explanation
Indices: 45907--45967 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
45897 ATAAAGCAGA
45907 GGGAATATTTTTTTAATTTAATTATAATTTT
1 GGGAATATTTTTTTAATTTAATTATAATTTT
*
45938 GGGAATATTTTTTT-GTTTCAA-TATAATTTT
1 GGGAATATTTTTTTAATTT-AATTATAATTTT
45968 AACATTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 12 0.43
31 16 0.57
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (31 bp):
GGGAATATTTTTTTAATTTAATTATAATTTT
Found at i:47617 original size:21 final size:22
Alignment explanation
Indices: 47582--47623 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
47572 TGCAAACCAC
* *
47582 TTTGAAACTTCATGTATCTTTA
1 TTTGAAACATCATGTAACTTTA
47604 TTTGAAA-ATCATGTAACTTT
1 TTTGAAACATCATGTAACTTT
47624 GTTCAAGGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (22 bp):
TTTGAAACATCATGTAACTTTA
Found at i:48767 original size:22 final size:22
Alignment explanation
Indices: 48739--48793 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
48729 AAGCCTGTAG
48739 TATCGATACTAACCTCTTATGA
1 TATCGATACTAACCTCTTATGA
48761 TATCGATACTAACCTCTTATGA
1 TATCGATACTAACCTCTTATGA
*
48783 TACCGATACTA
1 TATCGATACTA
48794 TCCCAAGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.33, C:0.24, G:0.09, T:0.35
Consensus pattern (22 bp):
TATCGATACTAACCTCTTATGA
Found at i:49965 original size:7 final size:7
Alignment explanation
Indices: 49955--50002 Score: 87
Period size: 7 Copynumber: 6.9 Consensus size: 7
49945 TCTTTTTTCT
49955 TTTTCCA
1 TTTTCCA
49962 TTTTCCA
1 TTTTCCA
49969 TTTTCCA
1 TTTTCCA
*
49976 TTTTTCA
1 TTTTCCA
49983 TTTTCCA
1 TTTTCCA
49990 TTTTCCA
1 TTTTCCA
49997 TTTTCC
1 TTTTCC
50003 TTTCTTTATC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTTCCA
Found at i:49965 original size:14 final size:14
Alignment explanation
Indices: 49948--50002 Score: 83
Period size: 14 Copynumber: 3.9 Consensus size: 14
49938 GTTTTTTTCT
*
49948 TTTTTCTTTTTCCA
1 TTTTTCATTTTCCA
*
49962 TTTTCCATTTTCCA
1 TTTTTCATTTTCCA
49976 TTTTTCATTTTCCA
1 TTTTTCATTTTCCA
*
49990 TTTTCCATTTTCC
1 TTTTTCATTTTCC
50003 TTTCTTTATC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.11, C:0.25, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTCATTTTCCA
Found at i:49972 original size:28 final size:28
Alignment explanation
Indices: 49941--50005 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
49931 TGGGATTGTT
* *
49941 TTTTTCTTTTTTCTTTTTCCATTTTCCA
1 TTTTCCTTTTTTCATTTTCCATTTTCCA
*
49969 TTTTCCATTTTTCATTTTCCATTTTCCA
1 TTTTCCTTTTTTCATTTTCCATTTTCCA
49997 TTTTCCTTT
1 TTTTCCTTT
50006 CTTTATCTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.09, C:0.23, G:0.00, T:0.68
Consensus pattern (28 bp):
TTTTCCTTTTTTCATTTTCCATTTTCCA
Found at i:51119 original size:29 final size:29
Alignment explanation
Indices: 51081--51218 Score: 114
Period size: 29 Copynumber: 4.8 Consensus size: 29
51071 TCTGATGTTG
*
51081 CATGAGATTATATCCCCGTTCTGGTTCTA
1 CATGAGATTATATCCCCGTTCTGATTCTA
* * ** *
51110 TATGATATTATATCCCTATTCTGATTCTG
1 CATGAGATTATATCCCCGTTCTGATTCTA
* ** *
51139 CATGGGATTATATCCCCACTCTGATTTTA
1 CATGAGATTATATCCCCGTTCTGATTCTA
* * ** * * *
51168 TATGATATTACGTCACTGTTTTGATTCTA
1 CATGAGATTATATCCCCGTTCTGATTCTA
*
51197 CATGAGATTTTATCCCCGTTCT
1 CATGAGATTATATCCCCGTTCT
51219 AATTATGTAT
Statistics
Matches: 77, Mismatches: 32, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
29 77 1.00
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.43
Consensus pattern (29 bp):
CATGAGATTATATCCCCGTTCTGATTCTA
Found at i:51148 original size:58 final size:58
Alignment explanation
Indices: 51071--51218 Score: 172
Period size: 58 Copynumber: 2.6 Consensus size: 58
51061 TTGATGTATA
* * *
51071 TCTGATGT-TGCATGAGATTATATCCCCGTTCTGGTTCTATATGATATTATATCCCTAT
1 TCTGAT-TCTGCATGAGATTATATCCCCGTTCTGATTCTATATGATATTACATCACTAT
* ** * * *
51129 TCTGATTCTGCATGGGATTATATCCCCACTCTGATTTTATATGATATTACGTCACTGT
1 TCTGATTCTGCATGAGATTATATCCCCGTTCTGATTCTATATGATATTACATCACTAT
* * *
51187 TTTGATTCTACATGAGATTTTATCCCCGTTCT
1 TCTGATTCTGCATGAGATTATATCCCCGTTCT
51219 AATTATGTAT
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
57 1 0.01
58 73 0.99
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (58 bp):
TCTGATTCTGCATGAGATTATATCCCCGTTCTGATTCTATATGATATTACATCACTAT
Found at i:54923 original size:29 final size:29
Alignment explanation
Indices: 54878--54951 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 29
54868 GATGCATTTC
* * *
54878 TGATTCTGCATGAGATTATATCTCTATTA
1 TGATTCTGCATGGGATTATATCCCCATTA
* *
54907 TGATTTTGCATGGGATTATATCCCCATTC
1 TGATTCTGCATGGGATTATATCCCCATTA
*
54936 TAATTCTGCATGGGAT
1 TGATTCTGCATGGGAT
54952 CCTTTACGGA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (29 bp):
TGATTCTGCATGGGATTATATCCCCATTA
Found at i:58154 original size:27 final size:26
Alignment explanation
Indices: 58123--58174 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
58113 CATTGATTGT
58123 TGACTGTTGACCGTTAACTATTGACTA
1 TGACTGTTGACCGTTAACT-TTGACTA
* * *
58150 TGACTTTTGACCTTTGACTTTGACT
1 TGACTGTTGACCGTTAACTTTGACT
58175 CGTTGAAGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (26 bp):
TGACTGTTGACCGTTAACTTTGACTA
Found at i:58776 original size:58 final size:58
Alignment explanation
Indices: 58665--58814 Score: 149
Period size: 58 Copynumber: 2.6 Consensus size: 58
58655 TTTCTAATCT
* * * * * * *
58665 TGCATGGGATTATATCCTCATTCTAATTTTGTATGAGAGTATATTCACGTTCTGATTT
1 TGCATGAGATTATATCCTCATTCTAATTCTGCATAAGAGTATATCCACATTCTGATTC
* * * * *
58723 TGTATGAGATTATATCCTCGTTCTCATTCTGCATAAGATTATATCCATATTCTGATTC
1 TGCATGAGATTATATCCTCATTCTAATTCTGCATAAGAGTATATCCACATTCTGATTC
* * *
58781 TGCATGGGATTTTATCC-CTATTCTGATTCTGCAT
1 TGCATGAGATTATATCCTC-ATTCTAATTCTGCAT
58815 GGGATCCTCT
Statistics
Matches: 74, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
57 1 0.01
58 73 0.99
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.44
Consensus pattern (58 bp):
TGCATGAGATTATATCCTCATTCTAATTCTGCATAAGAGTATATCCACATTCTGATTC
Found at i:58815 original size:29 final size:29
Alignment explanation
Indices: 58665--58819 Score: 125
Period size: 29 Copynumber: 5.3 Consensus size: 29
58655 TTTCTAATCT
* *
58665 TGCATGGGATTATATCC-TCATTCTAATTT
1 TGCATGGGATTATATCCAT-ATTCTGATTC
* * * * ** *
58694 TGTATGAGAGTATATTCACGTTCTGATTT
1 TGCATGGGATTATATCCATATTCTGATTC
* * * *
58723 TGTATGAGATTATATCC-TCGTTCTCATTC
1 TGCATGGGATTATATCCAT-ATTCTGATTC
**
58752 TGCATAAGATTATATCCATATTCTGATTC
1 TGCATGGGATTATATCCATATTCTGATTC
* *
58781 TGCATGGGATTTTATCCCTATTCTGATTC
1 TGCATGGGATTATATCCATATTCTGATTC
58810 TGCATGGGAT
1 TGCATGGGAT
58820 CCTCTACGGA
Statistics
Matches: 103, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
29 102 0.99
30 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (29 bp):
TGCATGGGATTATATCCATATTCTGATTC
Found at i:79006 original size:22 final size:22
Alignment explanation
Indices: 78981--79022 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
78971 CTCACTAGCA
78981 TTGACCATTAACCTTGACCACG
1 TTGACCATTAACCTTGACCACG
* *
79003 TTGACCATTGACTTTGACCA
1 TTGACCATTAACCTTGACCA
79023 AAAAGTCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (22 bp):
TTGACCATTAACCTTGACCACG
Found at i:85367 original size:16 final size:16
Alignment explanation
Indices: 85346--85378 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
85336 ACTCAATAAG
85346 AATAATAAGATAATTA
1 AATAATAAGATAATTA
*
85362 AATAATATGATAATTA
1 AATAATAAGATAATTA
85378 A
1 A
85379 TAAACATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (16 bp):
AATAATAAGATAATTA
Found at i:95720 original size:38 final size:36
Alignment explanation
Indices: 95643--95715 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 36
95633 TCATTAATTT
*
95643 TTTTATATTTTAAATTTTATAAAAAAATTATATAAA
1 TTTTATAATTTAAATTTTATAAAAAAATTATATAAA
95679 TTTTATGAATTTAAATTTT-TAAAGAAAA-TATATAAA
1 TTTTAT-AATTTAAATTTTATAAA-AAAATTATATAAA
95715 T
1 T
95716 ATTTTTCAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
36 19 0.56
37 15 0.44
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (36 bp):
TTTTATAATTTAAATTTTATAAAAAAATTATATAAA
Found at i:101579 original size:60 final size:59
Alignment explanation
Indices: 101462--101579 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 59
101452 CTAAATTTGT
* * *
101462 TCTTAAACTTTTAAATATTTTAATTTCATCCTTAAATTATGGTTTTCATTCTAAATTAA
1 TCTTAAACTTTTAAATATTTTAATTTCATCCTTAAACTATGATATTCATTCTAAATTAA
101521 TCTTCAAACTTTTGAAA-ATTTTAATTTCAT-CTCTAAACTATGATATTCATTCTAAATTA
1 TCTT-AAACTTTT-AAATATTTTAATTTCATCCT-TAAACTATGATATTCATTCTAAATTA
101580 GTCCCCAAAC
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
59 6 0.11
60 44 0.83
61 3 0.06
ACGTcount: A:0.35, C:0.14, G:0.03, T:0.48
Consensus pattern (59 bp):
TCTTAAACTTTTAAATATTTTAATTTCATCCTTAAACTATGATATTCATTCTAAATTAA
Found at i:101593 original size:31 final size:31
Alignment explanation
Indices: 101555--101621 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
101545 TTTCATCTCT
*
101555 AAACTATGATATTCATTCTAAATTAGTCCCC
1 AAACTATGATATTCATTCTAAATTACTCCCC
* *
101586 AAACTATGATCTTCATTCTAAATTACTCCTC
1 AAACTATGATATTCATTCTAAATTACTCCCC
101617 AAACT
1 AAACT
101622 TTTTTAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (31 bp):
AAACTATGATATTCATTCTAAATTACTCCCC
Found at i:103222 original size:31 final size:31
Alignment explanation
Indices: 103185--103259 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
103175 TTATAAAATT
103185 TTGCTTGACTCGTGCTCGTTAAGAAAATTTG
1 TTGCTTGACTCGTGCTCGTTAAGAAAATTTG
*
103216 TTGCTTGACTCATGCTCGTTAAGAAAATTTG
1 TTGCTTGACTCGTGCTCGTTAAGAAAATTTG
* *
103247 TTACTCGACTCGT
1 TTGCTTGACTCGT
103260 TGCATGTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.39
Consensus pattern (31 bp):
TTGCTTGACTCGTGCTCGTTAAGAAAATTTG
Found at i:103954 original size:23 final size:23
Alignment explanation
Indices: 103928--103972 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
103918 TGATCGTAAA
103928 GCAAAACAAATATACTAAGAACT
1 GCAAAACAAATATACTAAGAACT
*
103951 GCAAAACAAATATACTTAGAAC
1 GCAAAACAAATATACTAAGAAC
103973 CTAAAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.56, C:0.18, G:0.09, T:0.18
Consensus pattern (23 bp):
GCAAAACAAATATACTAAGAACT
Found at i:104487 original size:3 final size:3
Alignment explanation
Indices: 104479--104508 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
104469 GTTTCGATGA
104479 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
104509 CTCGACTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:114095 original size:20 final size:19
Alignment explanation
Indices: 114062--114099 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
114052 CATTTTGGGT
*
114062 AGGGGTTTCGAAACCTCTG
1 AGGGGTTTCAAAACCTCTG
114081 AGGGTGTTTCAAAACCTCT
1 AGGG-GTTTCAAAACCTCT
114100 CTAGCAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (19 bp):
AGGGGTTTCAAAACCTCTG
Done.