Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008803.1 Hibiscus syriacus cultivar Beakdansim tig00111954_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: 1826237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 9
Found at i:8329 original size:36 final size:36
Alignment explanation
Indices: 8281--8352 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
8271 GCTTTTAAAG
8281 AAAGGGTCTCTTTCGTAAGGATAAGAGAAGGTTGTT
1 AAAGGGTCTCTTTCGTAAGGATAAGAGAAGGTTGTT
*
8317 AAAGGGTTTCTTTCGTAAGGATAAGAGAAGGTTGTT
1 AAAGGGTCTCTTTCGTAAGGATAAGAGAAGGTTGTT
8353 TTTTATTGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.31, C:0.07, G:0.31, T:0.32
Consensus pattern (36 bp):
AAAGGGTCTCTTTCGTAAGGATAAGAGAAGGTTGTT
Found at i:8959 original size:23 final size:20
Alignment explanation
Indices: 8916--8964 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
8906 ATAAATAAAA
*
8916 TATTTTATTGAAGAAGATAT
1 TATTTTATTGAAAAAGATAT
8936 TATTTTATTGAAAAAGATAT
1 TATTTTATTGAAAAAGATAT
*
8956 TATTATATT
1 TATTTTATT
8965 TTTTAACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (20 bp):
TATTTTATTGAAAAAGATAT
Found at i:9633 original size:21 final size:21
Alignment explanation
Indices: 9609--9678 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
9599 TACCCTTAAC
* * *
9609 TTTAATCCTTAAATTATAAAT
1 TTTAAACCCTAAACTATAAAT
9630 TTTAAACCCTAAACTAT-AAT
1 TTTAAACCCTAAACTATAAAT
*
9650 TTCTAAACCCTAAACCAT-AAT
1 TT-TAAACCCTAAACTATAAAT
9671 TTTAAACC
1 TTTAAACC
9679 ATGAACTCTA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 11 0.25
21 33 0.75
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.37
Consensus pattern (21 bp):
TTTAAACCCTAAACTATAAAT
Found at i:9678 original size:20 final size:20
Alignment explanation
Indices: 9627--9678 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 20
9617 TTAAATTATA
*
9627 AATTTTAAACCCTAAACTAT
1 AATTTTAAACCCTAAACCAT
9647 AATTTCTAAACCCTAAACCAT
1 AATTT-TAAACCCTAAACCAT
9668 AATTTTAAACC
1 AATTTTAAACC
9679 ATGAACTCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 11 0.37
21 19 0.63
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTTTAAACCCTAAACCAT
Found at i:10356 original size:64 final size:63
Alignment explanation
Indices: 10277--10399 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 63
10267 GGTATTTATC
* *
10277 ATCTATTTAACTTTGAATATTAAAATATAA-TTATATACTTTTGAATATTTCAAATTAAAATAAT
1 ATCTATTTAACTTTGAATAGTAAAAGA-AATTTATAT-CTTTTGAATATTTCAAATTAAAATAAT
* * *
10341 ATCTATTTAAGTTTGAATAGTAAAAGAAGTTTATATCTTTTGAATATTTTAAATTAAAA
1 ATCTATTTAACTTTGAATAGTAAAAGAAATTTATATCTTTTGAATATTTCAAATTAAAA
10400 GATATTTATT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
63 23 0.43
64 30 0.57
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (63 bp):
ATCTATTTAACTTTGAATAGTAAAAGAAATTTATATCTTTTGAATATTTCAAATTAAAATAAT
Found at i:10408 original size:34 final size:34
Alignment explanation
Indices: 10237--10473 Score: 111
Period size: 34 Copynumber: 7.0 Consensus size: 34
10227 ATTAGTAGGA
* ** *
10237 TATATTCTTTTAAATATACCAAATTAAATAGGTATT
1 TATA-TCTTTTGAATATTTCAAATTAAA-AGATATT
* * * *
10273 TATCATCTATTT-AA-CTTTGAATATTAAAATATAAT
1 TAT-ATCT-TTTGAATATTTCAA-ATTAAAAGATATT
10308 TATATACTTTTGAATATTTCAAATT-AAA-ATA--
1 TATAT-CTTTTGAATATTTCAAATTAAAAGATATT
* * *
10339 -ATATCTATTT-AA-GTTTGAATAGTAAAAGA-AGTT
1 TATATCT-TTTGAATATTTCAA-ATTAAAAGATA-TT
*
10372 TATATCTTTTGAATATTTTAAATTAAAAGATATT
1 TATATCTTTTGAATATTTCAAATTAAAAGATATT
* * * *
10406 TATTGTCTTTTTAA-ATTT-AAATATTAAAGATATC
1 TA-TATCTTTTGAATATTTCAAAT-TAAAAGATATT
* * * *
10440 AATATCTTTTAAATATATCGAATTAAAAGATATT
1 TATATCTTTTGAATATTTCAAATTAAAAGATATT
10474 GTCTTTAGAG
Statistics
Matches: 154, Mismatches: 26, Indels: 44
0.69 0.12 0.20
Matches are distributed among these distances:
28 5 0.03
29 6 0.04
30 11 0.07
31 1 0.01
33 19 0.12
34 54 0.35
35 35 0.23
36 19 0.12
37 4 0.03
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (34 bp):
TATATCTTTTGAATATTTCAAATTAAAAGATATT
Found at i:11819 original size:26 final size:26
Alignment explanation
Indices: 11770--11819 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
11760 ATGCGTGAGC
* *
11770 ATTAATTATGACATTTTAATATAAAT
1 ATTAAATATGACATATTAATATAAAT
11796 ATTAAATATGACATGATTAA-ATAA
1 ATTAAATATGACAT-ATTAATATAA
11820 TATCTTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (26 bp):
ATTAAATATGACATATTAATATAAAT
Found at i:12405 original size:56 final size:55
Alignment explanation
Indices: 12259--12408 Score: 167
Period size: 56 Copynumber: 2.7 Consensus size: 55
12249 GAACAATTTC
* * ** **
12259 ATTTTGTAGAAGAAATAAATTGTTAAATTTATTT-TCACAGAATCTTGTATGATTCT
1 ATTTTGTAAAAGAAATAAATCGTTAAA-TTATTTCT-TGAGAATCAAGTATGATTCT
* * * *
12315 ATTTTGCAAAAGAATTAAATCATTGAATTTATTTCTTGAGAATCAAGTATGATTCT
1 ATTTTGTAAAAGAAATAAATCGTT-AAATTATTTCTTGAGAATCAAGTATGATTCT
12371 ATTTTGTAAAAAGAAATAAATCGTTAAATTATTTCTTG
1 ATTTTGT-AAAAGAAATAAATCGTTAAATTATTTCTTG
12409 GAAGTATCGA
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
56 59 0.77
57 18 0.23
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (55 bp):
ATTTTGTAAAAGAAATAAATCGTTAAATTATTTCTTGAGAATCAAGTATGATTCT
Found at i:14205 original size:130 final size:130
Alignment explanation
Indices: 13972--14208 Score: 357
Period size: 130 Copynumber: 1.8 Consensus size: 130
13962 ATTTAAGAGA
* * * *
13972 TAATTATTTTCAATCGAGAATAAACAACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATC
1 TAATTATTTCCAATCGAGAATAAACAACCTCTCATGCCTTAAAGCAATCATTTATCACTCCAACC
* * *
14037 GAAATGAAGAGATATAACTATTTCATCTTAAAATTCAATATTGATTTAGAGAAAATGATAATATC
66 AAAATGAAAAGATATAACTATTTCATCCTAAAATTCAATATTGATTTAGAGAAAATGATAATATC
* *
14102 TAATTATTTCCAATCGAGAATAAATAACCTCTCATTCCTTAAAGCAATCATTTATCACTCCAACC
1 TAATTATTTCCAATCGAGAATAAACAACCTCTCATGCCTTAAAGCAATCATTTATCACTCCAACC
* * * *
14167 AAAATGAAAATATATTATTATTTCGTCCTAAAATTCAATATT
66 AAAATGAAAAGATATAACTATTTCATCCTAAAATTCAATATT
14209 AATTCGAGTG
Statistics
Matches: 94, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
130 94 1.00
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.35
Consensus pattern (130 bp):
TAATTATTTCCAATCGAGAATAAACAACCTCTCATGCCTTAAAGCAATCATTTATCACTCCAACC
AAAATGAAAAGATATAACTATTTCATCCTAAAATTCAATATTGATTTAGAGAAAATGATAATATC
Found at i:17265 original size:192 final size:193
Alignment explanation
Indices: 16937--17305 Score: 578
Period size: 192 Copynumber: 1.9 Consensus size: 193
16927 CATTTTTCGA
* * * * *
16937 AAAACATATGAAAACATCCTGCTCGAAGGTCTTATGTATGGCCCGAAGGACTTATCCTCTTGCTC
1 AAAACATATGAAAACATCCTGCCCGAAGGTCTTATGTATGCCCCAAAGGACTTATCATCTTGATC
* * *
17002 GAAAGACTCATAGATGACCTGAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCTCGAA
66 GAAAGACTCATAGATGACCCGAAAGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAA
* *
17067 GGACTTACCAATTTTAGAAATAGTTTACTAGGTAATAAACTTTGGAAATCGAAAGTCTTTATG
131 GGACTTACCAATTTGAGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGAAAGTCTTTATG
* *
17130 AAAACATATGAAAACATCCTGCCCGAAGGTCTTATG-GTGCCCCAAAGGACTTATCATCTTTATC
1 AAAACATATGAAAACATCCTGCCCGAAGGTCTTATGTATGCCCCAAAGGACTTATCATCTTGATC
* * *
17194 GAAAGGCTTATAGATGACCCGAAAGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCGAA
66 GAAAGACTCATAGATGACCCGAAAGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAA
* *
17259 GGACTTATCAATTTGGGAAATAGTTTACTAGGTAAGAAACTTTGGAA
131 GGACTTACCAATTTGAGAAATAGTTTACTAGGTAAGAAACTTTGGAA
17306 TTTTTCTTAC
Statistics
Matches: 159, Mismatches: 17, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
192 124 0.78
193 35 0.22
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (193 bp):
AAAACATATGAAAACATCCTGCCCGAAGGTCTTATGTATGCCCCAAAGGACTTATCATCTTGATC
GAAAGACTCATAGATGACCCGAAAGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAA
GGACTTACCAATTTGAGAAATAGTTTACTAGGTAAGAAACTTTGGAAATCGAAAGTCTTTATG
Found at i:17913 original size:177 final size:176
Alignment explanation
Indices: 17644--17992 Score: 504
Period size: 177 Copynumber: 2.0 Consensus size: 176
17634 TTTTTTTTCA
* * * * * * *
17644 AAAAACATGTGAAAACATCCTACTCGAAGGTCTTATGAATGGCCCGAATGACTATTATCCTGCTC
1 AAAAACATATAAAAACATCCTACCCGAAGGCCTTATGAATGGCCCAAAGGACTATCATCCTGCTC
* * *
17709 GAAAGGCTTATAGATGACCTGAAGGATTTAATCATCATGCTC-AAAAGACTTACTGATGTCTCGA
66 AAAAGGCTTATAGATGACCTGAAGGATTTAATCATCATGCTCGAAAA-ACTTACTGATGGCCCGA
17773 AGGACTTACTAAGTAAGAAACTTTGGAAAACAACTTCTTACTTTTTG
130 AGGACTTACTAAGTAAGAAACTTTGGAAAACAACTTCTTACTTTTTG
* * *
17820 AAAAACATATAAAAACATCCTGCCCGAAGGCCTTATGGATGGCCCAAAGGACTTATCATCTTGCT
1 AAAAACATATAAAAACATCCTACCCGAAGGCCTTATGAATGGCCCAAAGGAC-TATCATCCTGCT
*
17885 CAAAAGGCTTATAGATGA-CTCGAAGGATTTAATCATCATGCTCGAATAACTTACTGATGGCCCG
65 CAAAAGGCTTATAGATGACCT-GAAGGATTTAATCATCATGCTCGAAAAACTTACTGATGGCCCG
* **
17949 AAGGACTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTACTT
129 AAGGACTTACTAAGTAAGAAACTTTGGAAAACAACTTCTTACTT
17993 CTTAACTTAT
Statistics
Matches: 153, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
176 46 0.30
177 104 0.68
178 3 0.02
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (176 bp):
AAAAACATATAAAAACATCCTACCCGAAGGCCTTATGAATGGCCCAAAGGACTATCATCCTGCTC
AAAAGGCTTATAGATGACCTGAAGGATTTAATCATCATGCTCGAAAAACTTACTGATGGCCCGAA
GGACTTACTAAGTAAGAAACTTTGGAAAACAACTTCTTACTTTTTG
Found at i:25827 original size:130 final size:128
Alignment explanation
Indices: 25585--25841 Score: 329
Period size: 130 Copynumber: 2.0 Consensus size: 128
25575 GGATTTTAAG
* *
25585 AGAGAAAATGATAATATAATTATTTCCAATGAGAATAAACAACCTCATATGTCTTAAAGCAGTCA
1 AGAGAAAATGATAATATAATTATTTCCAATGAGAATAAACAACCTCATATGACCTAAAGCAGTCA
* * * * *
25650 TTTATTACTCCAATCGAAATGAAGAGATATCACTATGTCGTCTTAAAATTCAATATTGATTCA
66 TTTATTACTCCAATCGAAATGAAAAGAAATCACTATGTCATCCTAAAATTCAATATTAATTCA
**
25713 AGAGAAAATGATAATAACTAATTATTTCCAATCGAGAATAAATGACCTC-TCAT-ACCTAAAGCA
1 AGAGAAAATGATAAT-A-TAATTATTTCCAAT-GAGAATAAACAACCTCAT-ATGACCTAAAGCA
* * * * * *
25776 TTCATTTATTACTCCAATTGAAATGAAAATAAATTACTTTTTCATCCTAAAATTCAATATTAATT
62 GTCATTTATTACTCCAATCGAAATGAAAAGAAATCACTATGTCATCCTAAAATTCAATATTAATT
25841 C
127 C
25842 GAGTGTTGCT
Statistics
Matches: 110, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
128 15 0.14
129 1 0.01
130 78 0.71
131 16 0.15
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (128 bp):
AGAGAAAATGATAATATAATTATTTCCAATGAGAATAAACAACCTCATATGACCTAAAGCAGTCA
TTTATTACTCCAATCGAAATGAAAAGAAATCACTATGTCATCCTAAAATTCAATATTAATTCA
Found at i:27610 original size:15 final size:16
Alignment explanation
Indices: 27590--27619 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
27580 TGACGGCTGG
27590 AAACCCTAGG-GTTTT
1 AAACCCTAGGTGTTTT
27605 AAACCCTAGGTGTTT
1 AAACCCTAGGTGTTT
27620 AGTTTAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (16 bp):
AAACCCTAGGTGTTTT
Found at i:27752 original size:6 final size:6
Alignment explanation
Indices: 27741--27786 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
27731 AAGGCTTGTA
* *
27741 AAAAAT AAAAAT AAAAAT AAAAAT AAACAAAT AATAAT AATAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT -AA-AAAT AAAAAT AAAAAT AA
27787 TTAATAATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
6 29 0.78
7 4 0.11
8 4 0.11
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:28581 original size:36 final size:36
Alignment explanation
Indices: 28541--28611 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
28531 CATGATATGA
*
28541 GATTAG-TCGATACAATTTTGGACATCCAAATTAAAC
1 GATTAGCT-GATACAATTCTGGACATCCAAATTAAAC
* *
28577 GATTAGCTTATACAATTCTGGGCATCCAAATTAAA
1 GATTAGCTGATACAATTCTGGACATCCAAATTAAA
28612 AGGTCATCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 30 0.97
37 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (36 bp):
GATTAGCTGATACAATTCTGGACATCCAAATTAAAC
Found at i:30613 original size:34 final size:32
Alignment explanation
Indices: 30575--30709 Score: 99
Period size: 34 Copynumber: 4.3 Consensus size: 32
30565 AAGCCTATTT
30575 ATGCATGTATGTACATATGTATGATGTATGCATG
1 ATGCATGTATGTA-ATATGTATGATGTATG-ATG
* **
30609 ATGCATGTATATAATTATGTATGATCAATGATG
1 ATGCATGTATGTAA-TATGTATGATGTATGATG
* *
30642 TATG--TTTATGT-ATA--TAT-ATATAT-AT-
1 -ATGCATGTATGTAATATGTATGATGTATGATG
*
30667 ATGCAT-TATGTACATATGTATTATGTATGTATG
1 ATGCATGTATGTA-ATATGTATGATGTATG-ATG
30700 ATGCATGTAT
1 ATGCATGTAT
30710 ACACATATAT
Statistics
Matches: 80, Mismatches: 8, Indels: 26
0.70 0.07 0.23
Matches are distributed among these distances:
24 3 0.04
25 5 0.06
26 3 0.04
27 7 0.09
28 3 0.04
29 3 0.04
30 7 0.09
31 1 0.01
32 7 0.09
33 10 0.12
34 31 0.39
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.44
Consensus pattern (32 bp):
ATGCATGTATGTAATATGTATGATGTATGATG
Found at i:30702 original size:91 final size:94
Alignment explanation
Indices: 30523--30710 Score: 267
Period size: 91 Copynumber: 2.0 Consensus size: 94
30513 TATATATATT
* *
30523 TAATTATGTATGATCAATAATGTATGTTTTATAGGTGTATATAAGCCTATTTATGCATGTATGTA
1 TAATTATGTATGATCAATAATGTATGTTTTATA-GTATATATAA--CTATATATGCATGTATGTA
30588 CATATGTATGATGTATGCATGATGCATGTATA
63 CATATGTATGATGTATGCATGATGCATGTATA
*
30620 TAATTATGTATGATCAATGATGTATG-TTTAT-GTATATATATA-TATATATGCAT-TATGTACA
1 TAATTATGTATGATCAATAATGTATGTTTTATAGTATATATA-ACTATATATGCATGTATGTACA
* *
30681 TATGTATTATGTATGTATGATGCATGTATA
65 TATGTATGATGTATGCATGATGCATGTATA
30711 CACATATATA
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
91 36 0.42
92 10 0.12
94 8 0.09
95 1 0.01
96 5 0.06
97 25 0.29
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (94 bp):
TAATTATGTATGATCAATAATGTATGTTTTATAGTATATATAACTATATATGCATGTATGTACAT
ATGTATGATGTATGCATGATGCATGTATA
Found at i:30780 original size:2 final size:2
Alignment explanation
Indices: 30773--30872 Score: 64
Period size: 2 Copynumber: 50.0 Consensus size: 2
30763 TAATTAATGT
* * *
30773 TA TA TA TA TA TA TA TA TA GT- TA TA CA CA TA TA -A GTA TA TG TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA
* * * * *
30815 TGA TG TGA TG TA TG TA CA TA AA TA TA TA TA TA TA TA TA TA TA TA
1 T-A TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30859 TA TA TA -A T- TA TA TA
1 TA TA TA TA TA TA TA TA
30873 CATTATACGC
Statistics
Matches: 76, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
1 4 0.05
2 67 0.88
3 5 0.07
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (2 bp):
TA
Found at i:33811 original size:20 final size:21
Alignment explanation
Indices: 33766--33815 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
33756 AGTCCAATCG
33766 TTTGTAACTCATGCAATTACC
1 TTTGTAACTCATGCAATTACC
* *
33787 TTTGTAACTCTTGCATTTA-C
1 TTTGTAACTCATGCAATTACC
33807 TTTGTAACT
1 TTTGTAACT
33816 GGCAGAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (21 bp):
TTTGTAACTCATGCAATTACC
Found at i:39325 original size:172 final size:171
Alignment explanation
Indices: 39040--39382 Score: 677
Period size: 172 Copynumber: 2.0 Consensus size: 171
39030 CGCCAATGAT
39040 GTACATTTTGATGCTTGCATCATCAGCGCCATACTTCTTCTCCAACGTGTCCAAATCGTCTTGGT
1 GTACATTTTGATGCTTGCATCATCAGCGCCATACTTCTTCTCCAACGTGTCCAAATCGTCTTGGT
39105 GTTTCTTTCTTTGAGGAACATGTCAAACATCTTGTTAGACATATGACTTAAGATATGGTATCACA
66 GTTTCTTTCTTTGAGGAACATGTCAAACATCTTGTTAGACATATGACTTAAGATATGGTATCACA
39170 TAATGTTGTTGTCTTTCTTGTACTTTTTGACTACAACGACA
131 TAATGTTGTTGTCTTTCTTGTACTTTTTGACTACAACGACA
39211 GTACATTTTGATGCTTGCATCATCAGCGCCATACTTCTTCTCCAACGTGTCCCAAATCGTCTTGG
1 GTACATTTTGATGCTTGCATCATCAGCGCCATACTTCTTCTCCAACGTGT-CCAAATCGTCTTGG
39276 TGTTTCTTTCTTTGAGGAACATGTCAAACATCTTGTTAGACATATGACTTAAGATATGGTATCAC
65 TGTTTCTTTCTTTGAGGAACATGTCAAACATCTTGTTAGACATATGACTTAAGATATGGTATCAC
39341 ATAATGTTGTTGTCTTTCTTGTACTTTTTGACTACAACGACA
130 ATAATGTTGTTGTCTTTCTTGTACTTTTTGACTACAACGACA
39383 ACTGTAATAA
Statistics
Matches: 171, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
171 50 0.29
172 121 0.71
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.38
Consensus pattern (171 bp):
GTACATTTTGATGCTTGCATCATCAGCGCCATACTTCTTCTCCAACGTGTCCAAATCGTCTTGGT
GTTTCTTTCTTTGAGGAACATGTCAAACATCTTGTTAGACATATGACTTAAGATATGGTATCACA
TAATGTTGTTGTCTTTCTTGTACTTTTTGACTACAACGACA
Found at i:39744 original size:18 final size:18
Alignment explanation
Indices: 39715--39771 Score: 96
Period size: 18 Copynumber: 3.1 Consensus size: 18
39705 GTTAATGAAT
39715 TTTAAGATTTTATATTCGA
1 TTTAA-ATTTTATATTCGA
39734 TTTAAATTTTATATTCGA
1 TTTAAATTTTATATTCGA
*
39752 TTTAAATATTATATTCGA
1 TTTAAATTTTATATTCGA
39770 TT
1 TT
39772 CAATTATTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
18 32 0.86
19 5 0.14
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.54
Consensus pattern (18 bp):
TTTAAATTTTATATTCGA
Found at i:39779 original size:18 final size:18
Alignment explanation
Indices: 39724--39779 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
39714 TTTTAAGATT
39724 TTATATTCGATTTAAATT-
1 TTATATTCGA-TTAAATTA
39742 TTATATTCGATTTAAA-TA
1 TTATATTCGA-TTAAATTA
*
39760 TTATATTCGATTCAATTA
1 TTATATTCGATTAAATTA
39778 TT
1 TT
39780 CGAATATCAC
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
17 5 0.14
18 30 0.86
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (18 bp):
TTATATTCGATTAAATTA
Found at i:50793 original size:21 final size:21
Alignment explanation
Indices: 50767--50808 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
50757 CAATTAAGAA
*
50767 TCAAGGAGCTTTACTTCAAAG
1 TCAAGGAGCCTTACTTCAAAG
*
50788 TCAAGGCGCCTTACTTCAAAG
1 TCAAGGAGCCTTACTTCAAAG
50809 CCATAGCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (21 bp):
TCAAGGAGCCTTACTTCAAAG
Found at i:59929 original size:17 final size:17
Alignment explanation
Indices: 59907--59941 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
59897 AATATTTGGA
59907 TGTTTGTTTTGAATATT
1 TGTTTGTTTTGAATATT
*
59924 TGTTTGTTTTGGATATT
1 TGTTTGTTTTGAATATT
59941 T
1 T
59942 TGTGATTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.20, T:0.66
Consensus pattern (17 bp):
TGTTTGTTTTGAATATT
Found at i:62930 original size:10 final size:10
Alignment explanation
Indices: 62897--62939 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
62887 AGCAAGAAAG
62897 AAAATAACAAA
1 AAAATAA-AAA
*
62908 GAAAA-ATAAA
1 -AAAATAAAAA
62918 AAAATAAAAA
1 AAAATAAAAA
62928 AAAATAAAAA
1 AAAATAAAAA
62938 AA
1 AA
62940 TCTCAAGACC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 4 0.14
10 19 0.68
11 1 0.04
12 4 0.14
ACGTcount: A:0.86, C:0.02, G:0.02, T:0.09
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:63262 original size:24 final size:24
Alignment explanation
Indices: 63230--63283 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
63220 ACACCATGCG
63230 GTCACCACCAACTCATCATCAACA
1 GTCACCACCAACTCATCATCAACA
63254 GTCACCACCAACTCATCATCAACA
1 GTCACCACCAACTCATCATCAACA
63278 GTCACC
1 GTCACC
63284 GTCTGCTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.35, C:0.43, G:0.06, T:0.17
Consensus pattern (24 bp):
GTCACCACCAACTCATCATCAACA
Found at i:66087 original size:14 final size:15
Alignment explanation
Indices: 66068--66096 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
66058 TTAAATTAAT
66068 CATGTAT-TAGTATG
1 CATGTATGTAGTATG
66082 CATGTATGTAGTATG
1 CATGTATGTAGTATG
66097 AAATAACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (15 bp):
CATGTATGTAGTATG
Found at i:67889 original size:21 final size:21
Alignment explanation
Indices: 67863--67905 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
67853 TCGAGATTTT
67863 TGAAGGTTC-AGAGTTGTGGTG
1 TGAAGGTTCGA-AGTTGTGGTG
67884 TGAAGGTTCGAAGTTGTGGTG
1 TGAAGGTTCGAAGTTGTGGTG
67905 T
1 T
67906 ATCGCTATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.19, C:0.05, G:0.42, T:0.35
Consensus pattern (21 bp):
TGAAGGTTCGAAGTTGTGGTG
Found at i:71275 original size:98 final size:98
Alignment explanation
Indices: 71106--71302 Score: 358
Period size: 98 Copynumber: 2.0 Consensus size: 98
71096 GATATTTTGA
* *
71106 TATACCAAAAATTGTTAAATAGATTTTACAAATTTTAAGATTATATTCGATTCAGTCATTTAAAT
1 TATACCAAAAATTGTTAAATAGATTTTACAAATTTTAAGATTATATTAGATTCAGTCATTCAAAT
*
71171 ATATAAATTATTCTTTAAAGTTAAAAAGTCAAT
66 ATATAAATTATTCTTTAAAGTTAAAAACTCAAT
*
71204 TATACCAAAAATTGTTAAATAGTTTTTACAAATTTTAAGATTATATTAGATTCAGTCATTCAAAT
1 TATACCAAAAATTGTTAAATAGATTTTACAAATTTTAAGATTATATTAGATTCAGTCATTCAAAT
71269 ATATAAATTATTCTTTAAAGTTAAAAACTCAAT
66 ATATAAATTATTCTTTAAAGTTAAAAACTCAAT
71302 T
1 T
71303 TTACTCATCA
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.41
Consensus pattern (98 bp):
TATACCAAAAATTGTTAAATAGATTTTACAAATTTTAAGATTATATTAGATTCAGTCATTCAAAT
ATATAAATTATTCTTTAAAGTTAAAAACTCAAT
Found at i:71452 original size:22 final size:21
Alignment explanation
Indices: 71427--71481 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
71417 AGATACTACT
71427 AGAACAATATCGATATTGTTCA
1 AGAA-AATATCGATATTGTTCA
*
71449 AG-AAGTATCGATATTGTTCA
1 AGAAAATATCGATATTGTTCA
*
71469 AG-AAGTATCGATA
1 AGAAAATATCGATA
71482 CAGATTCGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 29 0.91
21 1 0.03
22 2 0.06
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (21 bp):
AGAAAATATCGATATTGTTCA
Found at i:71457 original size:20 final size:20
Alignment explanation
Indices: 71434--71481 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
71424 ACTAGAACAA
71434 TATCGATATTGTTCAAGAAG
1 TATCGATATTGTTCAAGAAG
71454 TATCGATATTGTTCAAGAAG
1 TATCGATATTGTTCAAGAAG
71474 TATCGATA
1 TATCGATA
71482 CAGATTCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (20 bp):
TATCGATATTGTTCAAGAAG
Found at i:71620 original size:24 final size:22
Alignment explanation
Indices: 71593--71644 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
71583 TACGGCATCA
*
71593 ATACTACTTAGTATAGTAGTATCG
1 ATACTACTTAGT-T-GTAGTACCG
*
71617 ATACT-CTTAGTTGTGGTACCG
1 ATACTACTTAGTTGTAGTACCG
71638 ATACTAC
1 ATACTAC
71645 CTTTTTGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 12 0.48
22 2 0.08
23 6 0.24
24 5 0.20
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (22 bp):
ATACTACTTAGTTGTAGTACCG
Found at i:79512 original size:2 final size:2
Alignment explanation
Indices: 79505--79543 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
79495 TTGGATTATC
79505 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
79544 TTCACATGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:93180 original size:21 final size:22
Alignment explanation
Indices: 93148--93190 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
93138 AATTTCATAA
93148 AAAATCTCAATT-TTCTAAAAT
1 AAAATCTCAATTATTCTAAAAT
*
93169 AAAATCAT-AATTATTTTAAAAT
1 AAAATC-TCAATTATTCTAAAAT
93191 TAATCTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATCTCAATTATTCTAAAAT
Found at i:96689 original size:13 final size:13
Alignment explanation
Indices: 96667--96718 Score: 68
Period size: 13 Copynumber: 4.0 Consensus size: 13
96657 AATGACGCTC
*
96667 AATGAACGTCATA
1 AATGAGCGTCATA
96680 AATGAGCGTCATA
1 AATGAGCGTCATA
* *
96693 AATGTGTGTCATA
1 AATGAGCGTCATA
*
96706 AATGCGCGTCATA
1 AATGAGCGTCATA
96719 GATTTATGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (13 bp):
AATGAGCGTCATA
Found at i:102933 original size:28 final size:27
Alignment explanation
Indices: 102902--102963 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
102892 TTTGTTGTTC
102902 TTTAATTATCGAATGAATTACAAATTCT
1 TTTAATTATCGAA-GAATTACAAATTCT
* **
102930 TTTAATTCTTTAAGAATTACAAATTCT
1 TTTAATTATCGAAGAATTACAAATTCT
102957 TTTAATT
1 TTTAATT
102964 CTTTAAGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 21 0.68
28 10 0.32
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (27 bp):
TTTAATTATCGAAGAATTACAAATTCT
Found at i:102964 original size:27 final size:27
Alignment explanation
Indices: 102916--102974 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
102906 ATTATCGAAT
102916 GAATTACAAATTCTTTTAATTCTTTAA
1 GAATTACAAATTCTTTTAATTCTTTAA
102943 GAATTACAAATTCTTTTAATTCTTTAA
1 GAATTACAAATTCTTTTAATTCTTTAA
102970 GAATT
1 GAATT
102975 TTAGATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.47
Consensus pattern (27 bp):
GAATTACAAATTCTTTTAATTCTTTAA
Found at i:108295 original size:20 final size:21
Alignment explanation
Indices: 108266--108338 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 21
108256 GCAGCCTTCG
*
108266 TGCATGGATGCACA-ACAGGA
1 TGCATCGATGCACAGACAGGA
** **
108286 TGCATCGATGCACATTC-TTA
1 TGCATCGATGCACAGACAGGA
108306 TGCATCGATGCACAGA-AGGA
1 TGCATCGATGCACAGACAGGA
108326 TGCATCGATGCAC
1 TGCATCGATGCAC
108339 TAATTGCATT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 42 0.98
21 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.22
Consensus pattern (21 bp):
TGCATCGATGCACAGACAGGA
Found at i:108406 original size:21 final size:21
Alignment explanation
Indices: 108359--108416 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 21
108349 CGGTGTTTGA
108359 GTGCATGGATGCACTAGTGCAG
1 GTGCATGGATGCACTAGTG-AG
108381 GTGCATGGATGCACTGCAG-G-G
1 GTGCATGGATGCACT--AGTGAG
108402 GTGCATGGATGCACT
1 GTGCATGGATGCACT
108417 TTGACACCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
21 16 0.47
22 15 0.44
23 1 0.03
24 2 0.06
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.22
Consensus pattern (21 bp):
GTGCATGGATGCACTAGTGAG
Found at i:109804 original size:20 final size:20
Alignment explanation
Indices: 109769--109806 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
109759 TCTAAATCCT
* *
109769 TTTCAAAATTTCATTTTGGC
1 TTTCAAAATCTAATTTTGGC
109789 TTTCAAAATCTAATTTTG
1 TTTCAAAATCTAATTTTG
109807 TTTTAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.50
Consensus pattern (20 bp):
TTTCAAAATCTAATTTTGGC
Found at i:111082 original size:21 final size:20
Alignment explanation
Indices: 111038--111111 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
111028 GCAGCCTTCG
*
111038 TGCATGGATGCACAACAGGA
1 TGCATCGATGCACAACAGGA
**
111058 TGCATCGATGCACAACCTTGA
1 TGCATCGATGCACAA-CAGGA
*
111079 TGCATCGATGCATAGA-AGGA
1 TGCATCGATGCACA-ACAGGA
111099 TGCATCGATGCAC
1 TGCATCGATGCAC
111112 TAATTGCATT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
20 28 0.62
21 16 0.36
22 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAACAGGA
Found at i:111179 original size:22 final size:23
Alignment explanation
Indices: 111146--111188 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
111136 ATGGATACAC
111146 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
111169 TGCAT-GTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
111189 GTAGGGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:111201 original size:21 final size:21
Alignment explanation
Indices: 111175--111230 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
111165 CTAGTGCATG
*
111175 TGCATGGATGCACTGTAGGGA
1 TGCATGGATGCACTGCAGGGA
* *
111196 TGCATGGATGCATTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
111217 TGCATGGATGCACT
1 TGCATGGATGCACT
111231 TTGACGCCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.16, G:0.38, T:0.25
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:113680 original size:16 final size:15
Alignment explanation
Indices: 113659--113690 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
113649 GATGGATAAA
113659 ATAAAGATAAGAATAG
1 ATAAAGATAA-AATAG
113675 ATAAAGATAAAATAG
1 ATAAAGATAAAATAG
113690 A
1 A
113691 GATATGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.19
Consensus pattern (15 bp):
ATAAAGATAAAATAG
Found at i:114303 original size:8 final size:8
Alignment explanation
Indices: 114290--114329 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
114280 GATCATACAT
114290 ATACGTAC
1 ATACGTAC
*
114298 ATACGTAT
1 ATACGTAC
114306 ATACGTAC
1 ATACGTAC
*
114314 ATACATAC
1 ATACGTAC
114322 ATACGTAC
1 ATACGTAC
114330 GGAGTTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.28
Consensus pattern (8 bp):
ATACGTAC
Found at i:114860 original size:21 final size:22
Alignment explanation
Indices: 114828--114870 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
114818 AATTTCATAA
114828 AAAATCTCAATT-TTCTAAAAT
1 AAAATCTCAATTATTCTAAAAT
*
114849 AAAATCAT-AATTATTTTAAAAT
1 AAAATC-TCAATTATTCTAAAAT
114871 CCATTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATCTCAATTATTCTAAAAT
Found at i:115548 original size:60 final size:59
Alignment explanation
Indices: 115429--115576 Score: 167
Period size: 60 Copynumber: 2.5 Consensus size: 59
115419 AAAATTCGGA
* * *
115429 GATTAATTTAGAACGAGAGTCGTAGTCT-GGGATGAATTTGATATGTTAAAATGTATAAG
1 GATTAATTTAGAATGA-AGTCATAGTTTGGGGATGAATTTGATATGTTAAAATGTATAAG
*
115488 GATTAATTTAGAATGACAGTCATAGTTTGGGGATGAATTTAGAATAT-TTAAAA-GTTTAAG
1 GATTAATTTAGAATGA-AGTCATAGTTTGGGGATGAATTT-G-ATATGTTAAAATGTATAAG
* * *
115548 GACTAATTTAAAATGAATATCATAGTTTG
1 GATTAATTTAGAATGAA-GTCATAGTTTG
115577 AGTATGTATC
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
59 25 0.32
60 41 0.53
61 7 0.09
62 4 0.05
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.36
Consensus pattern (59 bp):
GATTAATTTAGAATGAAGTCATAGTTTGGGGATGAATTTGATATGTTAAAATGTATAAG
Found at i:121392 original size:23 final size:25
Alignment explanation
Indices: 121346--121393 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
121336 AGTGTATCGA
**
121346 TAAAAGATATTATTTTAATTTTAAT
1 TAAAAGATATTATTTTAAAATTAAT
121371 TAAAA-ATA-TATTTTAAAATTAAT
1 TAAAAGATATTATTTTAAAATTAAT
121394 GTTATACTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.62
24 3 0.14
25 5 0.24
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
TAAAAGATATTATTTTAAAATTAAT
Found at i:128575 original size:18 final size:17
Alignment explanation
Indices: 128548--128586 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
128538 TACTACTTTA
**
128548 CATAGTAGTATTGATAC
1 CATAGTAGTACCGATAC
128565 CATATGTAGTACCGATAC
1 CATA-GTAGTACCGATAC
128583 CATA
1 CATA
128587 AGGCCCAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (17 bp):
CATAGTAGTACCGATAC
Found at i:130494 original size:19 final size:19
Alignment explanation
Indices: 130458--130494 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
130448 TGAAAATGAT
*
130458 TTGATTTTGAAAGCCAAAG
1 TTGATTTTGAAAACCAAAG
*
130477 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAACCAAA
130495 ATGAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACCAAAG
Found at i:138838 original size:23 final size:23
Alignment explanation
Indices: 138806--138855 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
138796 TCATCTTGTA
138806 AAACCACCAAGGAGATATAAGAT
1 AAACCACCAAGGAGATATAAGAT
* *
138829 AAACCGCCAAGGAGATATGAGAT
1 AAACCACCAAGGAGATATAAGAT
138852 AAAC
1 AAAC
138856 TATAAGTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.50, C:0.18, G:0.20, T:0.12
Consensus pattern (23 bp):
AAACCACCAAGGAGATATAAGAT
Found at i:142945 original size:21 final size:22
Alignment explanation
Indices: 142899--142975 Score: 86
Period size: 21 Copynumber: 3.5 Consensus size: 22
142889 TTTGTGCAAA
* *
142899 GTGTATCGATACCTCCTTG-CT
1 GTGTATCGATACATCCTTGAAT
* *
142920 ATGTATTGATACA-CCTTGAAT
1 GTGTATCGATACATCCTTGAAT
*
142941 GTGTACCGATACATTCCTTGAAT
1 GTGTATCGATACA-TCCTTGAAT
142964 GTGTATCGATAC
1 GTGTATCGATAC
142976 GTCCCCTAGG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 5 0.11
21 21 0.47
23 19 0.42
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (22 bp):
GTGTATCGATACATCCTTGAAT
Found at i:147746 original size:13 final size:13
Alignment explanation
Indices: 147730--147759 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
147720 TGCTTTTCAG
*
147730 TTTTTTCTTTGTT
1 TTTTTTCCTTGTT
147743 TTTTTTCCTTGTT
1 TTTTTTCCTTGTT
147756 TTTT
1 TTTT
147760 CTTTTTTCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (13 bp):
TTTTTTCCTTGTT
Found at i:161289 original size:21 final size:21
Alignment explanation
Indices: 161263--161315 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
161253 ATTCTGACTA
161263 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
161284 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
161305 TCGCAATGCGA
1 TCGCATTGCGA
161316 ATACGTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:161330 original size:20 final size:19
Alignment explanation
Indices: 161305--161355 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
161295 TTTTCCTAAT
161305 TCGCAATGCGAATACGTAA-A
1 TCGCAATGCGAAT-C-TAACA
161325 TCGCAATGCGAATCTAACTA
1 TCGCAATGCGAATCTAAC-A
161345 TCGCAATGCGA
1 TCGCAATGCGA
161356 TTTACATAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.10
19 1 0.03
20 25 0.86
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (19 bp):
TCGCAATGCGAATCTAACA
Found at i:161559 original size:22 final size:22
Alignment explanation
Indices: 161534--161599 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
161524 GGCGACATCC
161534 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
161556 GTCCCCAGCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* **
161578 GTCTCCATCTCCGGTGAAATCA
1 GTCCCCATCTCCGACGAAATCA
161600 TTCACGGTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.24, C:0.38, G:0.17, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:162007 original size:21 final size:20
Alignment explanation
Indices: 161926--162016 Score: 87
Period size: 19 Copynumber: 4.6 Consensus size: 20
161916 GCGATTCTGT
161926 TGTTGCGATTTTCA-TTTCG
1 TGTTGCGATTTTCATTTTCG
** **
161945 TGTTGCGATAGTCAAATTCG
1 TGTTGCGATTTTCATTTTCG
* * **
161965 CGTTG-AATAGTCATTTTCG
1 TGTTGCGATTTTCATTTTCG
161984 TGTTGCGATTTTCATTTCTCG
1 TGTTGCGATTTTCATTT-TCG
162005 TGTTGCGATTTT
1 TGTTGCGATTTT
162017 AAGTTTCAGA
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
19 27 0.47
20 16 0.28
21 15 0.26
ACGTcount: A:0.15, C:0.15, G:0.22, T:0.47
Consensus pattern (20 bp):
TGTTGCGATTTTCATTTTCG
Found at i:163910 original size:20 final size:20
Alignment explanation
Indices: 163885--163992 Score: 159
Period size: 20 Copynumber: 5.5 Consensus size: 20
163875 AGAATAGTTT
163885 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
163905 ACTATCACCAATGCG-AAATG
1 ACTATC-GCAATGCGAAAATG
*
163925 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
163943 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
163963 ACTATCGCAATGCAAAAATG
1 ACTATCGCAATGCGAAAATG
163983 ACTATCGCAA
1 ACTATCGCAA
163993 CGAAAGAATC
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.08
18 9 0.11
20 57 0.72
21 7 0.09
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:163939 original size:38 final size:37
Alignment explanation
Indices: 163888--164013 Score: 168
Period size: 38 Copynumber: 3.4 Consensus size: 37
163878 ATAGTTTACT
*
163888 ATCGCAATGCGAAAATGACTATCACCAATGCGAAATGA
1 ATCGCAATGCGAAAATGACTATC-GCAATGCGAAATGA
*
163926 ATCGCAACGCGAAAATGACTATCGCAATGCGAAAATGA
1 ATCGCAATGCGAAAATGACTATCGCAATGCG-AAATGA
*
163964 CTATCGCAATGCAAAAATGACTATCGCAA--CGAAA-GA
1 --ATCGCAATGCGAAAATGACTATCGCAATGCGAAATGA
164000 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
164014 TAAAAATCGC
Statistics
Matches: 80, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
34 13 0.16
36 2 0.03
37 10 0.12
38 30 0.38
40 25 0.31
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (37 bp):
ATCGCAATGCGAAAATGACTATCGCAATGCGAAATGA
Found at i:163997 original size:58 final size:55
Alignment explanation
Indices: 163885--164013 Score: 158
Period size: 58 Copynumber: 2.3 Consensus size: 55
163875 AGAATAGTTT
*
163885 ACTATCGCAATGCGAAAATGACTATCACCAATGCGAAATGAATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCACCAATGCAAAATGAATCGCAAC-CG-AAA-G
*
163943 ACTATCGCAATGCGAAAATGACTATC-GCAATGCAAAAATGACTATCGCAA-CGAAAG
1 ACTATCGCAATGCGAAAATGACTATCACCAATGC-AAAATGA--ATCGCAACCGAAAG
163999 A--ATCGCAATGCGAAA
1 ACTATCGCAATGCGAAA
164014 TAAAAATCGC
Statistics
Matches: 66, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
54 14 0.21
56 2 0.03
57 9 0.14
58 34 0.52
60 7 0.11
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.17
Consensus pattern (55 bp):
ACTATCGCAATGCGAAAATGACTATCACCAATGCAAAATGAATCGCAACCGAAAG
Found at i:164067 original size:20 final size:20
Alignment explanation
Indices: 164042--164199 Score: 98
Period size: 20 Copynumber: 8.2 Consensus size: 20
164032 TCTCTCGTTA
*
164042 CGATAGTAATTTTTGCATTG
1 CGATAGTCATTTTTGCATTG
** *
164062 CGATAGTCATTTTCACGTTG
1 CGATAGTCATTTTTGCATTG
*
164082 CGATAGCCATTTTCGTGCATTG
1 CGATAGTCATTTT--TGCATTG
*
164104 CGAT--TC---TCT-CATTG
1 CGATAGTCATTTTTGCATTG
** **
164118 CGATAGTCAAATTCACATTG
1 CGATAGTCATTTTTGCATTG
* *
164138 TGATAGTCATTTTCGCATTG
1 CGATAGTCATTTTTGCATTG
* *
164158 CG--AGTCATTTTCGCGTTG
1 CGATAGTCATTTTTGCATTG
* *
164176 CGATAGTCATTTTCGCGTTG
1 CGATAGTCATTTTTGCATTG
164196 CGAT
1 CGAT
164200 TTTAAGTTTC
Statistics
Matches: 110, Mismatches: 18, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
14 9 0.08
15 1 0.01
16 2 0.02
17 1 0.01
18 17 0.15
19 1 0.01
20 71 0.65
22 8 0.07
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (20 bp):
CGATAGTCATTTTTGCATTG
Found at i:164122 original size:56 final size:56
Alignment explanation
Indices: 164056--164199 Score: 157
Period size: 56 Copynumber: 2.5 Consensus size: 56
164046 AGTAATTTTT
164056 GCATTGCGATAGTCATTTTCACGTTGCGATAGCCATTTTCGTGCATTGC-G-ATTCTC
1 GCATTGCGATAGTCATTTTCACGTTGCGATAGCCATTTTC--GCATTGCAGCATTCTC
* ** * * * *
164112 TCATTGCGATAGTCAAATTCACATTGTGATAGTCATTTTCGCATTGCGAGTCATTTTC
1 GCATTGCGATAGTCATTTTCACGTTGCGATAGCCATTTTCGCATTGC-AG-CATTCTC
* *
164170 GCGTTGCGATAGTCATTTTCGCGTTGCGAT
1 GCATTGCGATAGTCATTTTCACGTTGCGAT
164200 TTTAAGTTTC
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
54 7 0.10
56 35 0.50
58 28 0.40
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (56 bp):
GCATTGCGATAGTCATTTTCACGTTGCGATAGCCATTTTCGCATTGCAGCATTCTC
Found at i:164165 original size:18 final size:18
Alignment explanation
Indices: 164142--164198 Score: 87
Period size: 18 Copynumber: 3.1 Consensus size: 18
164132 ACATTGTGAT
*
164142 AGTCATTTTCGCATTGCG
1 AGTCATTTTCGCGTTGCG
164160 AGTCATTTTCGCGTTGCG
1 AGTCATTTTCGCGTTGCG
164178 ATAGTCATTTTCGCGTTGCG
1 --AGTCATTTTCGCGTTGCG
164198 A
1 A
164199 TTTTAAGTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 18 0.50
20 18 0.50
ACGTcount: A:0.16, C:0.21, G:0.25, T:0.39
Consensus pattern (18 bp):
AGTCATTTTCGCGTTGCG
Found at i:164209 original size:20 final size:20
Alignment explanation
Indices: 164166--164209 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
164156 TGCGAGTCAT
* *
164166 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTAAG
**
164186 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATAGTAAG
164206 TTTC
1 TTTC
164210 AGATTATATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTAAG
Found at i:164775 original size:21 final size:21
Alignment explanation
Indices: 164681--164787 Score: 81
Period size: 21 Copynumber: 5.1 Consensus size: 21
164671 CCTGACGCAT
* *
164681 CTGTCATCGTTCAATAGGCCT
1 CTGTCATCGTTCAAGAGGCCC
*
164702 CT-CCTATCGTTCAAGAGGCCC
1 CTGTC-ATCGTTCAAGAGGCCC
* ** *
164723 CTATCATCCCTCAAGAGTCCC
1 CTGTCATCGTTCAAGAGGCCC
** * *
164744 CTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGGCCC
* *
164765 CTGTCATCGTTGAAGAGGTCC
1 CTGTCATCGTTCAAGAGGCCC
164786 CT
1 CT
164788 CCCAACATTC
Statistics
Matches: 64, Mismatches: 20, Indels: 4
0.73 0.23 0.05
Matches are distributed among these distances:
20 1 0.02
21 62 0.97
22 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.25
Consensus pattern (21 bp):
CTGTCATCGTTCAAGAGGCCC
Found at i:164781 original size:42 final size:42
Alignment explanation
Indices: 164681--164791 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
164671 CCTGACGCAT
* * * * * *
164681 CTGTCATCGTTCAATAGGCCTCTCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
* **
164723 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
164765 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
164792 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 13, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
42 53 0.96
43 2 0.04
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.24
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:166189 original size:14 final size:14
Alignment explanation
Indices: 166170--166205 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
166160 ATTGTTTAAT
166170 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
166184 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
166198 TGATTTGT
1 TGATTTGT
166206 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:166350 original size:14 final size:14
Alignment explanation
Indices: 166331--166384 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
166321 GGAAATGACT
166331 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
166345 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
166364 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
166378 ATCGCAA
1 ATCGCAA
166385 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:166399 original size:34 final size:33
Alignment explanation
Indices: 166311--166406 Score: 147
Period size: 33 Copynumber: 2.8 Consensus size: 33
166301 AAAACAGACT
* **
166311 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
166345 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
166378 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
166407 CAAAACGCGT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 32 0.55
34 26 0.45
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:166440 original size:20 final size:20
Alignment explanation
Indices: 166412--166467 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
166402 CAACGCAAAA
166412 CGCGTTGCGATAGTCAT-TT
1 CGCGTTGCGATAGTCATATT
*
166431 CCGTGTTGCGATAGTCATATT
1 -CGCGTTGCGATAGTCATATT
166452 CGCGTTGCGATAGTCA
1 CGCGTTGCGATAGTCA
166468 AATGAATGTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 31 0.94
21 2 0.06
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATAGTCATATT
Found at i:167611 original size:20 final size:20
Alignment explanation
Indices: 167586--167652 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
167576 AAATTCAGTA
*
167586 TTGCGATAGTCAAAATCTCG
1 TTGCGATAGTCAGAATCTCG
167606 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
167626 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCTCG
167646 TTGCGAT
1 TTGCGAT
167653 TTACGTATTC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:167662 original size:20 final size:20
Alignment explanation
Indices: 167639--167730 Score: 159
Period size: 20 Copynumber: 4.7 Consensus size: 20
167629 CGATAGTCAG
*
167639 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
167659 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
167679 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
167699 ATTC-CATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
167718 ATTCGCATTGCGA
1 ATTCGCATTGCGA
167731 ATTAGGAAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 19 0.28
20 49 0.72
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:167718 original size:39 final size:40
Alignment explanation
Indices: 167639--167730 Score: 168
Period size: 39 Copynumber: 2.3 Consensus size: 40
167629 CGATAGTCAG
*
167639 ATTCGCGTTGCGATTTACGTATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTATTCACATTGCGATTTACGT
167679 ATTCGCATTGCGATTTACGTATTC-CATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGTATTCACATTGCGATTTACGT
167718 ATTCGCATTGCGA
1 ATTCGCATTGCGA
167731 ATTAGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 28 0.55
40 23 0.45
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.39
Consensus pattern (40 bp):
ATTCGCATTGCGATTTACGTATTCACATTGCGATTTACGT
Found at i:167751 original size:21 final size:21
Alignment explanation
Indices: 167727--167772 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
167717 TATTCGCATT
167727 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
167748 GCGAATTTGGAAAATTGCAAT
1 GCGAATTAGGAAAATCGCAAC
167769 GCGA
1 GCGA
167773 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.15, G:0.26, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:168107 original size:31 final size:31
Alignment explanation
Indices: 168034--168108 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 31
168024 TTCAAAATCA
* *
168034 TAAGATATGATCACTTTTGTTCTTATTTAAT
1 TAAGATATGGTCACTTTCGTTCTTATTTAAT
168065 TAAGATATGGTCACTTTCGCTT-TTATTTAAT
1 TAAGATATGGTCACTTTCG-TTCTTATTTAAT
*
168096 TAAGATGTGGTCA
1 TAAGATATGGTCA
168109 TCACAGGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 38 0.95
32 2 0.05
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.47
Consensus pattern (31 bp):
TAAGATATGGTCACTTTCGTTCTTATTTAAT
Found at i:168297 original size:23 final size:23
Alignment explanation
Indices: 168231--168303 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 23
168221 AATGAAAAGT
*
168231 AAAAATATTTTAAATTAAATTAATA
1 AAAAATATTTT--ATTAAGTTAATA
*
168256 ATAAAATATATTTAATAAGTTAATA
1 A-AAAATAT-TTTATTAAGTTAATA
168281 GAAAAATATTTT-TTAAGTTAATA
1 -AAAAATATTTTATTAAGTTAATA
168304 TATATATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.24
24 3 0.07
25 18 0.43
26 8 0.19
27 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (23 bp):
AAAAATATTTTATTAAGTTAATA
Found at i:168312 original size:23 final size:23
Alignment explanation
Indices: 168254--168312 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
168244 ATTAAATTAA
168254 TAATA-AAATATATTTAATAAGT
1 TAATAGAAATATATTTAATAAGT
* **
168276 TAATAGAAAAATATTTTTTAAGT
1 TAATAGAAATATATTTAATAAGT
* *
168299 TAATATATATATAT
1 TAATAGAAATATAT
168313 AATATTATGA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (23 bp):
TAATAGAAATATATTTAATAAGT
Found at i:172218 original size:26 final size:26
Alignment explanation
Indices: 172167--172220 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
172157 AAAAGGTCGA
* * *
172167 AAATATTAGATAGAAAATTAATAAAT
1 AAATATTAAATAGAAAATAAAAAAAT
172193 AAATATTAAATA-AAAATAAACAAAAT
1 AAATATTAAATAGAAAATAAA-AAAAT
172219 AA
1 AA
172221 TAGAATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.26
Consensus pattern (26 bp):
AAATATTAAATAGAAAATAAAAAAAT
Found at i:172229 original size:8 final size:8
Alignment explanation
Indices: 172214--172270 Score: 53
Period size: 8 Copynumber: 6.9 Consensus size: 8
172204 AAAAATAAAC
172214 AAAATAAT
1 AAAATAAT
*
172222 AGAATAAT
1 AAAATAAT
172230 AAAATAAT
1 AAAATAAT
* *
172238 AAATCAAAAG
1 AAA--ATAAT
172248 AAAATAAT
1 AAAATAAT
172256 AATAATAA-
1 AA-AATAAT
172264 AAAATAA
1 AAAATAA
172271 ACCAGACAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
7 5 0.12
8 24 0.60
9 5 0.12
10 6 0.15
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (8 bp):
AAAATAAT
Found at i:172239 original size:34 final size:31
Alignment explanation
Indices: 172200--172271 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 31
172190 AATAAATATT
172200 AAATAAA-AATAAACAAAATAATAGAATAATAAA
1 AAATAAATAA-AAACAAAATAAT--AATAATAAA
* *
172233 ATAATAAATCAAAAGAAAATAATAATAATAAA
1 A-AATAAATAAAAACAAAATAATAATAATAAA
172265 AAATAAA
1 AAATAAA
172272 CCAGACAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 6 0.17
32 10 0.29
33 1 0.03
34 17 0.49
35 1 0.03
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (31 bp):
AAATAAATAAAAACAAAATAATAATAATAAA
Found at i:172291 original size:31 final size:31
Alignment explanation
Indices: 172211--172291 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 31
172201 AATAAAAATA
* *
172211 AACAAAATAATAGAATAATAAAATAATAAATC
1 AACAAAA-AAAAGAATAATAAAATAATAAACC
*
172243 AA-AAGAAAATAATAATAATAAAA-AATAAACC
1 AACAA-AAAA-AAGAATAATAAAATAATAAACC
172274 AGACAAAAAAAAGAATAA
1 A-ACAAAAAAAAGAATAA
172292 GTCAAAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
31 19 0.46
32 20 0.49
33 2 0.05
ACGTcount: A:0.73, C:0.06, G:0.05, T:0.16
Consensus pattern (31 bp):
AACAAAAAAAAGAATAATAAAATAATAAACC
Found at i:172337 original size:25 final size:23
Alignment explanation
Indices: 172279--172339 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
172269 AAACCAGACA
*
172279 AAAAAAAGAATAAGTCAAAGAAA-
1 AAAAAAAGAA-AAATCAAAGAAAC
*
172302 AAATAAA-AAAAATCAAAGAACAC
1 AAAAAAAGAAAAATCAAAGAA-AC
172325 AAAAAAGAGAAAAAT
1 AAAAAA-AGAAAAAT
172340 AAAAATATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 10 0.32
22 3 0.10
23 11 0.35
24 1 0.03
25 6 0.19
ACGTcount: A:0.75, C:0.07, G:0.10, T:0.08
Consensus pattern (23 bp):
AAAAAAAGAAAAATCAAAGAAAC
Found at i:172379 original size:50 final size:50
Alignment explanation
Indices: 172306--172400 Score: 131
Period size: 50 Copynumber: 1.9 Consensus size: 50
172296 AAGAAAAAAT
172306 AAAAAAAATCAAAGAACACAAAAAAGAGAA-AAATAAAAATATAAATTTTA
1 AAAAAAAATCAAAGAACACAAAAAA-AGAATAAATAAAAATATAAATTTTA
* * *
172356 AAAAAAATATTAAAGAA-ATAAAAAAAGAATAAATAAGAATATAAA
1 AAAAAAA-ATCAAAGAACACAAAAAAAGAATAAATAAAAATATAAA
172401 AAGAAAACAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
49 4 0.10
50 28 0.70
51 8 0.20
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (50 bp):
AAAAAAAATCAAAGAACACAAAAAAAGAATAAATAAAAATATAAATTTTA
Found at i:172620 original size:36 final size:36
Alignment explanation
Indices: 172545--172620 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
172535 TTAATAAGTA
* * * * *
172545 AAAAAAAGATACAAAATAAATAAATAAATAAATAGT
1 AAAAAAAGATAAAAAATAAAGAAATAAACAAAAACT
172581 AAAAAAAGA-AAAAAATAATAGAAATAAACAAAAACT
1 AAAAAAAGATAAAAAATAA-AGAAATAAACAAAAACT
172617 AAAA
1 AAAA
172621 TATATATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 8 0.24
36 26 0.76
ACGTcount: A:0.76, C:0.04, G:0.05, T:0.14
Consensus pattern (36 bp):
AAAAAAAGATAAAAAATAAAGAAATAAACAAAAACT
Found at i:174464 original size:85 final size:85
Alignment explanation
Indices: 174338--175352 Score: 1126
Period size: 85 Copynumber: 11.9 Consensus size: 85
174328 CATATAGCTT
* * ** * * *
174338 TTCTCGACTTAAGCTATGCTGTGAAA-TTGACATGCCATTGAGCTAAATGTAATCGAACTCGAAG
1 TTCTCGCCTTGAGCTATGCTGT-AAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAG
*
174402 GTATTTGTTGACAGATATCCC
65 GTATTTGTTGACAGATAACCC
* * * * *
174423 TTCTTGCCTTGAGTTATGCTTTAAATTTGATATTCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* * **
174488 TCTTGGTTGACAGATAGTCC
66 TATTTGTTGACAGATAACCC
* * * * *
174508 TTCTCGCCTTGAGCTATTCTGCAAATTTGATATGCCTTTGAGCTGAATGTAATCAAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* *
174573 TCTTTTGTTGACATATAACCC
66 T-ATTTGTTGACAGATAACCC
* * * * * * * *
174594 TTCTCGCCTTGAGTTATGTTGT--ACTGGATATGCCTTTGAGTTGAATGTAATCAAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* *
174657 TCTTTTGTTGACAGATAGA-CA
66 T-ATTTGTTGACAGATA-ACCC
* * * * *
174678 TTCTTGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTAACTGTAATCAAACTCAAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* * * *
174743 TCTTGGTTAACAGATAGCCC
66 TATTTGTTGACAGATAACCC
*
174763 TTCTCGCCTTGAGCTATGCTGTAAATTGGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* *
174828 TCTTGGTTGACAGATAACCC
66 TATTTGTTGACAGATAACCC
* * * * *
174848 TTCTCGCCTTTAGTTATGCTGTAAATTGGATGTCCCATTGAGCTGAGTGTAATCGAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
** *
174913 TATTTTGTTGGTAGATAAACC
66 TA-TTTGTTGACAGATAACCC
* * * * *
174934 TTCTCGCCTTGAGCTATACTGCAAA--TGGTGTACCTTTGAGCTGAGTGTAATCGAACTTGAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* * * *
174997 TCTTGGTTGATAGATAACCA
66 TATTTGTTGACAGATAACCC
* * * * * * * * *
175017 TTCTCGTCTTGAGTTATACTGTGAATTGGATGTGCCTTTAAGTTGAATGTAATCGAACTCAAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
*
175082 TCTTTCGTTGACAGATAACCC
66 TATTT-GTTGACAGATAACCC
*
175103 TTCTCGCCTTGAGCTATGTTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* *
175168 TATTTTGTTGACAAATAGCCC
66 TA-TTTGTTGACAGATAACCC
* * * *
175189 TTCTAGCCTTGAGTTATG-TATAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAATG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* *
175253 TATTTTTTGACAGATAGCCC
66 TATTTGTTGACAGATAACCC
* * * * *
175273 TTCTTGCCTTGAGCTATGCTATAAATTTGGTGTGCCTTTGAGCTGAATGTAATCAAACTCGAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
*
175338 TATTTGTTGGCAGAT
66 TATTTGTTGACAGAT
175353 GATTTTGAAT
Statistics
Matches: 794, Mismatches: 124, Indels: 24
0.84 0.13 0.03
Matches are distributed among these distances:
83 35 0.04
84 143 0.18
85 413 0.52
86 200 0.25
87 3 0.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (85 bp):
TTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGG
TATTTGTTGACAGATAACCC
Found at i:174972 original size:340 final size:337
Alignment explanation
Indices: 174338--175352 Score: 1264
Period size: 340 Copynumber: 3.0 Consensus size: 337
174328 CATATAGCTT
* * ** * *
174338 TTCTCGACTTAAGCTATGCTGTGAAA-TTGACATGCCATTGAGCTAAATGTAATCGAACTCGAAG
1 TTCTCGCCTTGAGCTATGCTGT-AAATTTGATGTGCCTTTGAGCT-AATGTAATCGAACTCAAAG
* * * * * * * *
174402 GTATTTGTTGACAGATATCCCTTCTTGCCTTGAGTTATGCTTTAAATTTGATATTCCTTTGAGCT
64 GTCTTCGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCT
* * * *
174467 GAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGTCCTTCTCGCCTTGAGCTATTCTGCAA
129 GAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGCTGTAA
* * * * *
174532 ATTTGATATGCCTTTGAGCTGAATGTAATCAAACTCGAAGGTCTTTTGTTGACATATAACCCTTC
194 ATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTTGTTGACAGATAACCCTTC
* * * * * *
174597 TCGCCTTGAGTTATGTTGTACTGGATATGCCTTTGAGTTGAATGTAATCAAACTCGAAGGTCTTT
259 TCGCCTTGAGCTATGCTGAAATGG-TGTGCCTTTGAGCTGAATGTAATCAAACTCGAAGGTC-TT
174662 TGTTGACAGATAGA-CA
322 TGTTGACAGATA-ACCA
* *
174678 TTCTTGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTAACTGTAATCAAACTCAAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTAA-TGTAATCGAACTCAAAGG
* * * *
174743 TCTTGGTTAACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTGGATGTGCCTTTGAGCTG
65 TCTTCGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTG
* *
174808 AGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTTAGTTATGCTGTAAA
130 AGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGCTGTAAA
* * * ** *
174873 TTGGATGTCCCATTGAGCTGAGTGTAATCGAACTCGAAGGTATTTTGTTGGTAGATAAACCTTCT
195 TTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTTGTTGACAGATAACCCTTCT
* * * * * *
174938 CGCCTTGAGCTATACTGCAAATGGTGTACCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTGG
260 CGCCTTGAGCTATGCTG-AAATGGTGTGCCTTTGAGCTGAATGTAATCAAACTCGAAGGTCTTTG
*
175003 TTGATAGATAACCA
324 TTGACAGATAACCA
* * * * * * *
175017 TTCTCGTCTTGAGTTATACTGTGAATTGGATGTGCCTTTAAGTTGAATGTAATCGAACTCAAAGG
1 TTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCT-AATGTAATCGAACTCAAAGG
*
175082 TCTTTCGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATGTGCCTTTGAGCT
65 TC-TTCGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCT
* * * * *
175147 GAGTGTAATCGAACTCGAAGGTATTTTGTTGACAAATAGCCCTTCTAGCCTTGAGTTATG-TATA
129 GAGTGTAATCGAACTCGAAGGT-CTTGGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGCTGTA
* *
175211 AATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAATGTATTTT-TTGACAGATAGCCCTT
193 AATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTTGTTGACAGATAACCCTT
* * *
175275 CTTGCCTTGAGCTATGCTATAAATTTGGTGTGCCTTTGAGCTGAATGTAATCAAACTCGAAGGTA
258 CTCGCCTTGAGCTATGCT-GAAA--TGGTGTGCCTTTGAGCTGAATGTAATCAAACTCGAAGGTC
*
175340 TTTGTTGGCAGAT
320 TTTGTTGACAGAT
175353 GATTTTGAAT
Statistics
Matches: 577, Mismatches: 88, Indels: 19
0.84 0.13 0.03
Matches are distributed among these distances:
338 1 0.00
339 105 0.18
340 391 0.68
341 80 0.14
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (337 bp):
TTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTAATGTAATCGAACTCAAAGGT
CTTCGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCTTTGAGCTGA
GTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGCTGTAAAT
TTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTTGTTGACAGATAACCCTTCTC
GCCTTGAGCTATGCTGAAATGGTGTGCCTTTGAGCTGAATGTAATCAAACTCGAAGGTCTTTGTT
GACAGATAACCA
Found at i:175084 original size:425 final size:423
Alignment explanation
Indices: 174290--175352 Score: 1348
Period size: 425 Copynumber: 2.5 Consensus size: 423
174280 TGATAGGCCC
* * * ** * *
174290 TTGAGCTGAAC-GAAATCGAACTCAAAAGTCTTCGTTAACATATAGCTTTTCTCGACTTAAGCTA
1 TTGAGCT-AACTGTAATCGAACTCAAAGGTCTTCGTTAACAAATAGCCCTTCTCGCCTTGAGCTA
** * * *
174354 TGCTGTGAAATTGACATGCCATTGAGCTAAATGTAATCGAACTCGAAGGTATTTGTTGACAGATA
65 TGCTGT-AAATTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTGTTGACAGATA
* * * * *
174419 TCCCTTCTTGCCTTGAGTTATGCTTTAAATTTGATATTCCTTTGAGCTGAGTGTAATCGAACTCG
129 ACCCTTCTTGCCTTGAGTTATGCTATAAATTGGATGTCCCTTTGAGCTGAGTGTAATCGAACTCG
* * * ** * *
174484 AAGGTCTTGGTTGACAGATAGTCCTTCTCGCCTTGAGCTATTCTGCAAATTTGATATGCCTTTGA
194 AAGGTATTTGTTGGCAGATAAACCTTCTCGCCTTGAGCTATACTGCAAATGTGATA-GCCTTTGA
* * * *
174549 GCTGAATGTAATCAAACTCGAAGGTCTTTTGTTGACATATAACCCTTCTCGCCTTGAGTTATGTT
258 GCTGAATGTAATCAAACTCGAAGGTCTTTGGTTGACAGATAACCATTCTCGCCTTGAGTTATCTT
* * * *
174614 GTACTGGATATGCCTTTGAGTTGAATGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGA-CA
323 GAACTGGATATGCCTTTAAGTTGAATGTAATCAAACTCAAAGGTCTTTCGTTGACAGATA-ACCA
*
174678 TTCTTGCCTTGAGCTATGCTGTAAATTTGATGTGCCT
387 TTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCT
* * *
174715 TTGAGCTAACTGTAATCAAACTCAAAGGTCTTGGTTAACAGATAGCCCTTCTCGCCTTGAGCTAT
1 TTGAGCTAACTGTAATCGAACTCAAAGGTCTTCGTTAACAAATAGCCCTTCTCGCCTTGAGCTAT
* *
174780 GCTGTAAATTGGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAA
66 GCTGTAAATT-GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTGTTGACAGATAA
* * * *
174845 CCCTTCTCGCCTTTAGTTATGCTGTAAATTGGATGTCCCATTGAGCTGAGTGTAATCGAACTCGA
130 CCCTTCTTGCCTTGAGTTATGCTATAAATTGGATGTCCCTTTGAGCTGAGTGTAATCGAACTCGA
*
174910 AGGTATTTTGTTGGTAGATAAACCTTCTCGCCTTGAGCTATACTGCAAATGGTG-TA-CCTTTGA
195 AGGTA-TTTGTTGGCAGATAAACCTTCTCGCCTTGAGCTATACTGCAAAT-GTGATAGCCTTTGA
* * * * *
174973 GCTGAGTGTAATCGAACTTGAAGGTC-TTGGTTGATAGATAACCATTCTCGTCTTGAGTTATACT
258 GCTGAATGTAATCAAACTCGAAGGTCTTTGGTTGACAGATAACCATTCTCGCCTTGAGTTAT-CT
* * *
175037 GTGAATTGGATGTGCCTTTAAGTTGAATGTAATCGAACTCAAAGGTCTTTCGTTGACAGATAACC
322 -TGAACTGGATATGCCTTTAAGTTGAATGTAATCAAACTCAAAGGTCTTTCGTTGACAGATAACC
* *
175102 CTTCTCGCCTTGAGCTATGTTGTAAATTTGATGTGCCT
386 ATTCTCGCCTTGAGCTATGCTGTAAATTTGATGTGCCT
* * * * * * * *
175140 TTGAGCTGAGTGTAATCGAACTCGAAGGTATTTTGTTGACAAATAGCCCTTCTAGCCTTGAGTTA
1 TTGAGCTAACTGTAATCGAACTCAAAGGT-CTTCGTTAACAAATAGCCCTTCTCGCCTTGAGCTA
* * *
175205 TG-TATAAATTTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAATGTATTTTTTGACAGATA
65 TGCTGTAAA-TTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTGTTGACAGATA
* * * * *
175269 GCCCTTCTTGCCTTGAGCTATGCTATAAATTTGG-TGTGCCTTTGAGCTGAATGTAATCAAACTC
129 ACCCTTCTTGCCTTGAGTTATGCTATAAA-TTGGATGTCCCTTTGAGCTGAGTGTAATCGAACTC
175333 GAAGGTATTTGTTGGCAGAT
193 GAAGGTATTTGTTGGCAGAT
175353 GATTTTGAAT
Statistics
Matches: 552, Mismatches: 76, Indels: 21
0.85 0.12 0.03
Matches are distributed among these distances:
423 30 0.05
424 52 0.09
425 391 0.71
426 77 0.14
427 2 0.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (423 bp):
TTGAGCTAACTGTAATCGAACTCAAAGGTCTTCGTTAACAAATAGCCCTTCTCGCCTTGAGCTAT
GCTGTAAATTGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTATTTGTTGACAGATAAC
CCTTCTTGCCTTGAGTTATGCTATAAATTGGATGTCCCTTTGAGCTGAGTGTAATCGAACTCGAA
GGTATTTGTTGGCAGATAAACCTTCTCGCCTTGAGCTATACTGCAAATGTGATAGCCTTTGAGCT
GAATGTAATCAAACTCGAAGGTCTTTGGTTGACAGATAACCATTCTCGCCTTGAGTTATCTTGAA
CTGGATATGCCTTTAAGTTGAATGTAATCAAACTCAAAGGTCTTTCGTTGACAGATAACCATTCT
CGCCTTGAGCTATGCTGTAAATTTGATGTGCCT
Found at i:176459 original size:161 final size:161
Alignment explanation
Indices: 176194--176516 Score: 646
Period size: 161 Copynumber: 2.0 Consensus size: 161
176184 AGGGTTCATC
176194 TCATCACAAAGTCTTCGGCCTGACAATAGTAGTAGAGCAAACATCAAATTGCCAGGTGTTCGAAT
1 TCATCACAAAGTCTTCGGCCTGACAATAGTAGTAGAGCAAACATCAAATTGCCAGGTGTTCGAAT
176259 AATTTCATAGTTTGAATGCAATATATTCATAAAGCCAGGGCTTTCGAGCTTCCTCTATAACCAAT
66 AATTTCATAGTTTGAATGCAATATATTCATAAAGCCAGGGCTTTCGAGCTTCCTCTATAACCAAT
176324 TGCCTTAGTGGAATAGCTCAACTTTACGGAT
131 TGCCTTAGTGGAATAGCTCAACTTTACGGAT
176355 TCATCACAAAGTCTTCGGCCTGACAATAGTAGTAGAGCAAACATCAAATTGCCAGGTGTTCGAAT
1 TCATCACAAAGTCTTCGGCCTGACAATAGTAGTAGAGCAAACATCAAATTGCCAGGTGTTCGAAT
176420 AATTTCATAGTTTGAATGCAATATATTCATAAAGCCAGGGCTTTCGAGCTTCCTCTATAACCAAT
66 AATTTCATAGTTTGAATGCAATATATTCATAAAGCCAGGGCTTTCGAGCTTCCTCTATAACCAAT
176485 TGCCTTAGTGGAATAGCTCAACTTTACGGAT
131 TGCCTTAGTGGAATAGCTCAACTTTACGGAT
176516 T
1 T
176517 TAATTTCTTA
Statistics
Matches: 162, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
161 162 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (161 bp):
TCATCACAAAGTCTTCGGCCTGACAATAGTAGTAGAGCAAACATCAAATTGCCAGGTGTTCGAAT
AATTTCATAGTTTGAATGCAATATATTCATAAAGCCAGGGCTTTCGAGCTTCCTCTATAACCAAT
TGCCTTAGTGGAATAGCTCAACTTTACGGAT
Found at i:179470 original size:18 final size:18
Alignment explanation
Indices: 179444--179486 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
179434 AACAGAAAAT
179444 AAAGCAGGAAATAATATC
1 AAAGCAGGAAATAATATC
*
179462 AAAGTAGGAAATAATATC
1 AAAGCAGGAAATAATATC
179480 AAAGCAG
1 AAAGCAG
179487 CCTAGGGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.56, C:0.09, G:0.19, T:0.16
Consensus pattern (18 bp):
AAAGCAGGAAATAATATC
Found at i:180800 original size:18 final size:18
Alignment explanation
Indices: 180777--180849 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
180767 ACTGAATATT
*
180777 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
180795 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
180814 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
180833 TGTCCTGAAGGACCACT
1 TGTCCCGAAGGACCACT
180850 GTATATATCC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 30 0.64
19 2 0.04
20 15 0.32
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:180830 original size:38 final size:40
Alignment explanation
Indices: 180779--180871 Score: 129
Period size: 38 Copynumber: 2.4 Consensus size: 40
180769 TGAATATTTG
*
180779 TCCCGAATG-ACCACTATGTCCCGAAGGACCACTG-AT-TG
1 TCCCGAA-GAACCACTATGTCCCGAAGGACCACTGTATATA
* *
180817 TTCCGAAGAACCACTATGTCCTGAAGGACCACTGTATATA
1 TCCCGAAGAACCACTATGTCCCGAAGGACCACTGTATATA
180857 TCCCGAAGAACCACT
1 TCCCGAAGAACCACT
180872 CCTTAAGAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
37 1 0.02
38 30 0.62
39 2 0.04
40 15 0.31
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (40 bp):
TCCCGAAGAACCACTATGTCCCGAAGGACCACTGTATATA
Found at i:181640 original size:19 final size:19
Alignment explanation
Indices: 181612--181663 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
181602 TTTAAGTAGG
181612 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
*
181631 TGCATTGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
*
181650 TGCATCGATACACT
1 TGCATCGATGCACT
181664 AATTGCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.33
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:181780 original size:12 final size:12
Alignment explanation
Indices: 181763--181796 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
181753 CCGAAAATCA
181763 TCAATTCTTCAC
1 TCAATTCTTCAC
181775 TCAATTCTTCAC
1 TCAATTCTTCAC
181787 TCAATTCTTC
1 TCAATTCTTC
181797 TATTTAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (12 bp):
TCAATTCTTCAC
Found at i:186550 original size:60 final size:60
Alignment explanation
Indices: 186457--186576 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
186447 CTATTTCAGT
186457 TCTGCTCGATTCTTGGTACCTACGTGTAAATCACTTACACACTAAGTCATAGACTTAGTG
1 TCTGCTCGATTCTTGGTACCTACGTGTAAATCACTTACACACTAAGTCATAGACTTAGTG
186517 TCTGCTCGATTCTTGGTACCTACGTGTAAATCACTTACACACTAAGTCATAGACTTAGTG
1 TCTGCTCGATTCTTGGTACCTACGTGTAAATCACTTACACACTAAGTCATAGACTTAGTG
186577 AGGCATAACA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (60 bp):
TCTGCTCGATTCTTGGTACCTACGTGTAAATCACTTACACACTAAGTCATAGACTTAGTG
Found at i:186911 original size:18 final size:20
Alignment explanation
Indices: 186860--186933 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 20
186850 TGAATATTTA
186860 TCCCGAAGGACCACTGATTG
1 TCCCGAAGGACCACTGATTG
* * *
186880 T-TCGTAGAACCACT-A-TG
1 TCCCGAAGGACCACTGATTG
186897 TCCCGAAGGACCACTGTATATG
1 TCCCGAAGGACCACTG-AT-TG
*
186919 ACCCGAAGGACCACT
1 TCCCGAAGGACCACT
186934 CCTTAAGAAC
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
17 3 0.07
18 11 0.26
19 10 0.24
20 2 0.05
22 16 0.38
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (20 bp):
TCCCGAAGGACCACTGATTG
Found at i:187155 original size:23 final size:24
Alignment explanation
Indices: 187128--187184 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
187118 ATATCTTCTC
187128 ATCACTTTCATATA-A-ACATGT-
1 ATCACTTTCATATACACACATGTG
187149 ATTTCAC-TTCATATACACACATGTG
1 A--TCACTTTCATATACACACATGTG
187174 ATCACTTTCAT
1 ATCACTTTCAT
187185 TATTTCACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
21 1 0.03
22 8 0.27
23 9 0.30
24 11 0.37
25 1 0.03
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.39
Consensus pattern (24 bp):
ATCACTTTCATATACACACATGTG
Found at i:188681 original size:6 final size:6
Alignment explanation
Indices: 188650--188786 Score: 54
Period size: 6 Copynumber: 22.0 Consensus size: 6
188640 GACAAAATAT
*
188650 AATAAA AATAAT AATCAAA AGA-AAA AAT-AA AAT-AA AATAATA TAAT-AA
1 AATAAA AATAAA AAT-AAA A-ATAAA AATAAA AATAAA AATAA-A -AATAAA
* * * * * *
188698 TATAAA AATAAC CAGAAA AAT-TA AATAAA AATTGAAAA AAAAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AA-T--AAA AATAAA AATAAA
188748 AA-AGAA TAAGTAAA AGA-AAA AATAATA AATAAA AATAAA
1 AATA-AA -AA-TAAA A-ATAAA AATAA-A AATAAA AATAAA
188787 TCAAAGAACA
Statistics
Matches: 99, Mismatches: 14, Indels: 36
0.66 0.09 0.24
Matches are distributed among these distances:
5 19 0.19
6 52 0.53
7 15 0.15
8 7 0.07
9 6 0.06
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:188699 original size:11 final size:11
Alignment explanation
Indices: 188618--188699 Score: 57
Period size: 11 Copynumber: 7.6 Consensus size: 11
188608 TAGATAGAAA
188618 AATAATAATAT
1 AATAATAATAT
188629 AATAA-AATAT
1 AATAATAATAT
*
188639 AGACAA-AATAT
1 A-ATAATAATAT
188650 AATAA-AA-AT
1 AATAATAATAT
* *
188659 AATAATCAAAAGA
1 AATAAT-AATA-T
* *
188672 AAAAATAAAAT
1 AATAATAATAT
188683 AA-AATAATAT
1 AATAATAATAT
188693 AATAATA
1 AATAATA
188700 TAAAAATAAC
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
9 7 0.12
10 20 0.34
11 22 0.37
12 5 0.08
13 5 0.08
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (11 bp):
AATAATAATAT
Found at i:188705 original size:30 final size:30
Alignment explanation
Indices: 188616--188705 Score: 80
Period size: 30 Copynumber: 2.9 Consensus size: 30
188606 GTTAGATAGA
188616 AAAAT-AATAATATAATAAAATATAGACAAAAT
1 AAAATAAATAATATAAT-AAATATA-A-AAAAT
* *
188648 ATAATAAA-AATAATAATCAAA-AGAAAAAAT
1 AAAATAAATAAT-ATAAT-AAATATAAAAAAT
188678 AAAATAAAATAATATAAT-AATATAAAAA
1 AAAAT-AAATAATATAATAAATATAAAAA
188706 TAACCAGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
29 2 0.04
30 15 0.31
31 9 0.19
32 12 0.25
33 10 0.21
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (30 bp):
AAAATAAATAATATAATAAATATAAAAAAT
Found at i:188767 original size:19 final size:19
Alignment explanation
Indices: 188740--188781 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
188730 TGAAAAAAAA
* *
188740 AAAATAAAAAAGAATAAGT
1 AAAAGAAAAAAGAATAAAT
*
188759 AAAAGAAAAAATAATAAAT
1 AAAAGAAAAAAGAATAAAT
188778 AAAA
1 AAAA
188782 ATAAATCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (19 bp):
AAAAGAAAAAAGAATAAAT
Found at i:188784 original size:29 final size:28
Alignment explanation
Indices: 188713--188794 Score: 82
Period size: 29 Copynumber: 3.0 Consensus size: 28
188703 AAATAACCAG
* *
188713 AAAAATTAAATAAAAAT-TG-AAAA-AA
1 AAAAAATAAATAAAAATAAGTAAAAGAA
188738 AAAAAATAAA-AAAGAATAAGTAAAAGAA
1 AAAAAATAAATAAA-AATAAGTAAAAGAA
* *
188766 AAAATAATAAATAAAAATAAATCAAAGAA
1 AAAA-AATAAATAAAAATAAGTAAAAGAA
188795 CACAAAAAAG
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
24 3 0.06
25 12 0.26
26 1 0.02
27 4 0.09
28 6 0.13
29 18 0.38
30 3 0.06
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.16
Consensus pattern (28 bp):
AAAAAATAAATAAAAATAAGTAAAAGAA
Found at i:188825 original size:6 final size:7
Alignment explanation
Indices: 188808--188833 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
188798 AAAAAAGAGG
188808 AAAAATT
1 AAAAATT
188815 AAAAATT
1 AAAAATT
188822 AAAAATT
1 AAAAATT
188829 AAAAA
1 AAAAA
188834 AAAAACTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAAATT
Found at i:188868 original size:31 final size:29
Alignment explanation
Indices: 188812--188869 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
188802 AAGAGGAAAA
* *
188812 ATTAAAAATTAAAAATTAAAAAAAAAACT
1 ATTAAAAAATAAAAAATAAAAAAAAAACT
*
188841 ATTAAAGAAATAAAAAATAGAATAAAAAA
1 ATTAAA-AAATAAAAAATA-AAAAAAAAA
188870 GAAAACAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.25
30 10 0.42
31 8 0.33
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (29 bp):
ATTAAAAAATAAAAAATAAAAAAAAAACT
Found at i:189040 original size:9 final size:9
Alignment explanation
Indices: 189028--189082 Score: 58
Period size: 9 Copynumber: 6.1 Consensus size: 9
189018 AGATAAAAAT
189028 AAAAAAT-A
1 AAAAAATAA
*
189036 AAAAAATAGT
1 AAAAAATA-A
189046 AAAAAATAA
1 AAAAAATAA
189055 AAAAAATAA
1 AAAAAATAA
* *
189064 TAGAAATAA
1 AAAAAATAA
*
189073 AAAAACTAA
1 AAAAAATAA
189082 A
1 A
189083 TATATATAGC
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
8 7 0.18
9 23 0.61
10 8 0.21
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.15
Consensus pattern (9 bp):
AAAAAATAA
Found at i:189048 original size:18 final size:16
Alignment explanation
Indices: 189022--189082 Score: 77
Period size: 18 Copynumber: 3.6 Consensus size: 16
189012 AGAAAAAGAT
189022 AAAAATAAAAAATAAA
1 AAAAATAAAAAATAAA
189038 AAAATAGTAAAAAATAAA
1 AAAA-A-TAAAAAATAAA
189056 AAAAATAATAGAAATAAA
1 AAAAATAA-A-AAATAAA
*
189074 AAAACTAAA
1 AAAAATAAA
189083 TATATATAGC
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
16 7 0.17
17 4 0.10
18 29 0.73
ACGTcount: A:0.80, C:0.02, G:0.03, T:0.15
Consensus pattern (16 bp):
AAAAATAAAAAATAAA
Found at i:189199 original size:38 final size:38
Alignment explanation
Indices: 189157--189278 Score: 88
Period size: 38 Copynumber: 3.2 Consensus size: 38
189147 AAATGTTATG
189157 TAAAAAAGACAAAAAACAAATAAAATAAAATATATAAA
1 TAAAAAAGACAAAAAACAAATAAAATAAAATATATAAA
* * * * * * *
189195 TAAAACACA-AGAAAAACAAGTAATATAAAAACAAAAAAA
1 TAAAAAAGACA-AAAAACAAATAAAAT-AAAATATATAAA
* * * *
189234 TAAAAATAGTACAAAAAAAAAAAAAAATGATAT-TAT-AA
1 TAAAAA-AG-ACAAAAAACAAATAAAATAAAATATATAAA
189272 TAAAAAA
1 TAAAAAA
189279 AAGGTAAAAG
Statistics
Matches: 61, Mismatches: 18, Indels: 11
0.68 0.20 0.12
Matches are distributed among these distances:
37 2 0.03
38 28 0.46
39 15 0.25
40 3 0.05
41 12 0.20
42 1 0.02
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.16
Consensus pattern (38 bp):
TAAAAAAGACAAAAAACAAATAAAATAAAATATATAAA
Found at i:190013 original size:33 final size:33
Alignment explanation
Indices: 189976--190041 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
189966 TCGTATTTCT
189976 TTTGTAAAAAATCCTCCCTTTCGAATCAATTTA
1 TTTGTAAAAAATCCTCCCTTTCGAATCAATTTA
190009 TTTGTAAAAAATCCTCCCTTTCGAATCAATTTA
1 TTTGTAAAAAATCCTCCCTTTCGAATCAATTTA
190042 CATGCCTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.39
Consensus pattern (33 bp):
TTTGTAAAAAATCCTCCCTTTCGAATCAATTTA
Found at i:192655 original size:16 final size:16
Alignment explanation
Indices: 192634--192664 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
192624 CTTTTAATTA
192634 TTTTTTTGTTTCCATT
1 TTTTTTTGTTTCCATT
192650 TTTTTTTGTTTCCAT
1 TTTTTTTGTTTCCAT
192665 AAGCTTCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTTTTTGTTTCCATT
Found at i:196016 original size:21 final size:20
Alignment explanation
Indices: 195979--196017 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
195969 ACTCGTAATT
*
195979 TTAATTTTTTTTAAAATAGA
1 TTAATTTTTATTAAAATAGA
*
195999 TTAATATTTTATTCAAATA
1 TTAAT-TTTTATTAAAATA
196018 TAAGGATTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (20 bp):
TTAATTTTTATTAAAATAGA
Found at i:199013 original size:21 final size:21
Alignment explanation
Indices: 198987--199032 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
198977 GGACTTGTTT
*
198987 TTTTGAACTTTCTCATATTTC
1 TTTTGAACTTTCACATATTTC
*
199008 TTTTGAACTTTGACATATTTC
1 TTTTGAACTTTCACATATTTC
199029 TTTT
1 TTTT
199033 TATCAGGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.59
Consensus pattern (21 bp):
TTTTGAACTTTCACATATTTC
Found at i:200020 original size:35 final size:36
Alignment explanation
Indices: 199974--200042 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
199964 TATGTGCAGG
199974 GGGAACAGATTCCCCCT-GGGGGGTATCAATTCCTT
1 GGGAACAGATTCCCCCTGGGGGGGTATCAATTCCTT
*
200009 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCC
1 GGGAACAGATTCCCCCTGGGGGGGTATCAATTCC
200043 CCCTAAATGA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 17 0.53
36 15 0.47
ACGTcount: A:0.19, C:0.26, G:0.32, T:0.23
Consensus pattern (36 bp):
GGGAACAGATTCCCCCTGGGGGGGTATCAATTCCTT
Found at i:200648 original size:31 final size:31
Alignment explanation
Indices: 200610--200751 Score: 214
Period size: 31 Copynumber: 4.6 Consensus size: 31
200600 GGGTCGAGGG
*
200610 TTTACCTATGTTCTTCGGGACATATGGATTA
1 TTTACCTATGTTCTTCGGGACATATGGACTA
* *
200641 TTTACCTATGTTCTTAGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTA
* *
200672 TTTACCTATGATCTTCGGGACATATGGACTG
1 TTTACCTATGTTCTTCGGGACATATGGACTA
200703 TTTACCTATGTTCTTCGGGACATATGGACTGA
1 TTTACCTATGTTCTTCGGGACATATGGACT-A
*
200735 -TTACCTAGGTTCTTCGG
1 TTTACCTATGTTCTTCGG
200752 AATCTATGGA
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 102 1.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATGGACTA
Found at i:201940 original size:95 final size:95
Alignment explanation
Indices: 201824--202024 Score: 285
Period size: 95 Copynumber: 2.1 Consensus size: 95
201814 CCATATATAA
* *
201824 ATTATATATATACAATAAAGCTTGAGGTGTCCCTCTAAAGAAATTGGTTAAACGCCCCGGCTTTA
1 ATTATA-ATATACAATAAAGCTTGAGGTGTCCCTCTAAAGAAATTGGTTAAACACCCCAGCTTTA
*
201889 TGGATAAGATTCAGCTAGCCTAATAAAGGTG
65 TGGATAAGATTCAGCTAGCCTAATAAAGGCG
* * * * *
201920 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTGAACACCCTAGCTTTAT
1 ATTATAATATACAATAAAGCTTGAGGTGTCCCTCTAAAGAAATTGGTTAAACACCCCAGCTTTAT
* * *
201985 GGATAATATTTAGCTAGCCTGATAAAGGCG
66 GGATAAGATTCAGCTAGCCTAATAAAGGCG
*
202015 ATCATAATAT
1 ATTATAATAT
202025 CTATACAATG
Statistics
Matches: 93, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
95 87 0.94
96 6 0.06
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (95 bp):
ATTATAATATACAATAAAGCTTGAGGTGTCCCTCTAAAGAAATTGGTTAAACACCCCAGCTTTAT
GGATAAGATTCAGCTAGCCTAATAAAGGCG
Found at i:202085 original size:98 final size:95
Alignment explanation
Indices: 201831--202086 Score: 271
Period size: 95 Copynumber: 2.7 Consensus size: 95
201821 TAAATTATAT
* * ** * * *
201831 ATATACAATAAAGCTTGAGGTGTCCCTCTAAAGAAATTGGTTAAACGCCCCGGCTTTATGGATAA
1 ATATACAATAAAGATTAAATTGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATGGATAA
* *
201896 GATTCAGCTAGCCTAATAAAGGTGATTATA
66 GATTCAGCTAGCCTAATAAAGGCGATCATA
* * * * **
201926 ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTGAACACCCTAGCTTTATGGATAA
1 ATATACAATAAAGATTAAATTGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATGGATAA
* * *
201991 TATTTAGCTAGCCTGATAAAGGCGATCATA
66 GATTCAGCTAGCCTAATAAAGGCGATCATA
* ** *
202021 ATAT-CTATACAATGATATTAAATTGTCCCTCTAGAGCAATTGGTTAAATTCCCCGGATTTATGG
1 ATATACAATA-AA-G--ATTAAATTGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATGG
202085 AT
62 AT
202087 TCAGCTAGCC
Statistics
Matches: 135, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
94 4 0.03
95 89 0.66
96 1 0.01
98 41 0.30
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (95 bp):
ATATACAATAAAGATTAAATTGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATGGATAA
GATTCAGCTAGCCTAATAAAGGCGATCATA
Found at i:203216 original size:55 final size:55
Alignment explanation
Indices: 203134--203280 Score: 181
Period size: 53 Copynumber: 2.7 Consensus size: 55
203124 TTTGTTTGAA
* * * * * * **
203134 ATTGGATTTCAACTCCACGGCGGAGGATATCCAACTCAAAATCAACTTTCTCGAG
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAAGCAACATACAAGAG
*
203189 ATTGGATTTCAACTTCACGACGAAGGATATCCAACTC-AAAGCAACATACAATAG
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAAGCAACATACAAGAG
* *
203243 -TTGGATTTCAACTTCACGACGAAGGATATTCAAGTCAA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAA
203281 GGCTCAACTT
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
53 34 0.43
54 12 0.15
55 34 0.43
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.25
Consensus pattern (55 bp):
ATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAAGCAACATACAAGAG
Found at i:203776 original size:84 final size:84
Alignment explanation
Indices: 203635--204226 Score: 758
Period size: 84 Copynumber: 7.0 Consensus size: 84
203625 GATATCGTCT
* * *
203635 TCATTTGCAGCATAACTCAGGGCTAGAAAGGTTATCTGCCATCC-AAAGACCTTCGAGTTCTACT
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCA-CCAAAAGACCTTCGAGTTCGACT
* * *
203699 ATGCTTAGCTCCAAGACACA
65 ACGCTCAGCTCCAAGGCACA
* *
203719 TCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTTGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTA
*
203784 TGCTCAGCTCCAAGGCACA
66 CGCTCAGCTCCAAGGCACA
* * *
203803 TCATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCACTAAAAGACCTTCGAGTTTGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACT-
* *
203868 ACGCTCAGTTCCAAGACACA
65 ACGCTCAGCTCCAAGGCACA
* * * *
203888 TCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTACTAACC-AAATACCTTCGAGTTCGACT
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGC-CACCAAAAGACCTTCGAGTTCGACT
*
203952 ACGCTCAACTCCAAGGCACA
65 ACGCTCAGCTCCAAGGCACA
* * * *
203972 TCATTTGTAGCATAACTCAAGGCTAGAAGGGCTATCTACCACCAGAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTA
*
204037 CGCTCAACTCCAAGGCACA
66 CGCTCAGCTCCAAGGCACA
* * * * *
204056 TCATTTGCAACATAACTCAAGGCTAGAAGGGTTATCTGCTAACCAAAA-TCCTTCAAATTCGACT
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGC-CACCAAAAGACCTTCGAGTTCGACT
***
204120 ACGCTCAGCTCCAAGGCGTT
65 ACGCTCAGCTCCAAGGCACA
* * * * * *
204140 TCATTTGCAGCATATCTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTA
* * *
204205 CACTCAGCTCAAAGGCATA
66 CGCTCAGCTCCAAGGCACA
204224 TCA
1 TCA
204227 AAATTTACAG
Statistics
Matches: 445, Mismatches: 57, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
83 11 0.02
84 355 0.80
85 77 0.17
86 2 0.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (84 bp):
TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACA
Found at i:204083 original size:253 final size:252
Alignment explanation
Indices: 203635--204226 Score: 781
Period size: 253 Copynumber: 2.3 Consensus size: 252
203625 GATATCGTCT
* * * *
203635 TCATTTGCAGCATAACTCAGGGCTAGAAAGGTTATCTGCCATCCAAAGACCTTCGAGTTCTACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* * * * *
203700 TGCTTAGCTCCAAGACACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACCAAA
66 CGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTACCACCAAA
* * * *
203765 AGACCTTCGAGTTTGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGA
131 AGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGA
* * * * * *
203830 AGGGCTATCTGC-CACTAAAAGACCTTCGAGTTTGACTAACGCTCAGTTCCAAGACACA
196 AGGGCTATCTGCTAACCAAAA-ACCTTCAAATTCGACT-ACGCTCAGCTCCAAGACACA
* * * *
203888 TCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTACTAACCAAATACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* ** *
203953 CGCTCAACTCCAAGGCACATCATTTGTAGCATAACTCAAGGCTAGAAGGGCTATCTACCACCAGA
66 CGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTACCACCAAA
204018 AGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGA
131 AGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGA
* * * ***
204083 AGGGTTATCTGCTAACCAAAATCCTTCAAATTCGACTACGCTCAGCTCCAAGGCGTT
196 AGGGCTATCTGCTAACCAAAAACCTTCAAATTCGACTACGCTCAGCTCCAAGACACA
* * * * * *
204140 TCATTTGCAGCATATCTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTA
1 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* * *
204205 CACTCAGCTCAAAGGCATATCA
66 CGCTCAGCTCCAAGGCACATCA
204227 AAATTTACAG
Statistics
Matches: 291, Mismatches: 47, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
252 88 0.30
253 197 0.68
254 6 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (252 bp):
TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGCTATCTACCACCAAA
AGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAACATAACTCAAGGCTAGA
AGGGCTATCTGCTAACCAAAAACCTTCAAATTCGACTACGCTCAGCTCCAAGACACA
Found at i:205226 original size:63 final size:64
Alignment explanation
Indices: 205116--205244 Score: 235
Period size: 63 Copynumber: 2.0 Consensus size: 64
205106 GTTTAATTTT
205116 TTTTTGGCTTTTATACTAAAGCCCAAGACCGACCCGACCCGTATATTCGATTAAAACATTTAAAA
1 TTTTTGGCTTTTATACTAAAGCCCAAGACCGACCCGACCCGTATATTCGATT-AAACATTTAAAA
205181 TTTTTGGCTTTTATACTAAAG-CC-AGACCGACCCGACCCGTATATTCGATTAAACATTTAAAA
1 TTTTTGGCTTTTATACTAAAGCCCAAGACCGACCCGACCCGTATATTCGATTAAACATTTAAAA
205243 TT
1 TT
205245 GGGATTAAAC
Statistics
Matches: 64, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
62 14 0.22
63 27 0.42
64 2 0.03
65 21 0.33
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (64 bp):
TTTTTGGCTTTTATACTAAAGCCCAAGACCGACCCGACCCGTATATTCGATTAAACATTTAAAA
Found at i:205348 original size:14 final size:15
Alignment explanation
Indices: 205312--205385 Score: 82
Period size: 15 Copynumber: 5.0 Consensus size: 15
205302 ATCCCCTTTG
*
205312 ATTAATTAT-TATTAT
1 ATTATTTATATATT-T
* *
205327 ATTTTTTATATATCT
1 ATTATTTATATATTT
205342 ATT-TTTATATATTT
1 ATTATTTATATATTT
205356 ATATATTTATATATTT
1 AT-TATTTATATATTT
205372 ATTATTTAT-TATTT
1 ATTATTTATATATTT
205386 TGGATTTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
14 17 0.33
15 19 0.37
16 16 0.31
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTATTTATATATTT
Found at i:205352 original size:16 final size:16
Alignment explanation
Indices: 205324--205383 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
205314 TAATTATTAT
205324 TATATTTTT-TATATA
1 TATATTTTTATATATA
* *
205339 TCTATTTTTATATATT
1 TATATTTTTATATATA
* *
205355 TATATATTTATATATT
1 TATATTTTTATATATA
205371 TATTATTTATTAT
1 TA-TATTT-TTAT
205384 TTTGGATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
15 8 0.22
16 21 0.57
17 4 0.11
18 4 0.11
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TATATTTTTATATATA
Done.