Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold445
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: 297477
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
File 1 of 2
Found at i:230 original size:17 final size:16
Alignment explanation
Indices: 205--242 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
195 TTAAATATTA
*
205 ATAAATAAAAAAATAAT
1 ATAATTAAAAAAAT-AT
222 ATAATTAAAAAAATAT
1 ATAATTAAAAAAATAT
238 ATAAT
1 ATAAT
243 CGCATCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAATTAAAAAAATAT
Found at i:233 original size:16 final size:16
Alignment explanation
Indices: 193--242 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
183 AAATATTTCG
* *
193 AATTAAATATTAATA-
1 AATTAAAAAATAATAT
*
208 AATAAAAAAATAATAT
1 AATTAAAAAATAATAT
224 AATTAAAAAA-ATATAT
1 AATTAAAAAATA-ATAT
240 AAT
1 AAT
243 CGCATCTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATTAAAAAATAATAT
Found at i:5299 original size:17 final size:18
Alignment explanation
Indices: 5271--5305 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
5261 ATAAATAAAT
5271 AAATAAATAATACAATTA
1 AAATAAATAATACAATTA
*
5289 AAATAAA-AATATAATTA
1 AAATAAATAATACAATTA
5306 CATCTCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAAATAATACAATTA
Found at i:12222 original size:2 final size:2
Alignment explanation
Indices: 12210--12242 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
12200 ATTAATCTCA
12210 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12243 GAACTCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12638 original size:2 final size:2
Alignment explanation
Indices: 12633--12667 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
12623 ATGTATTATA
* *
12633 TG TG TG TG CG TG CG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
12668 AAATATATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.06, G:0.49, T:0.46
Consensus pattern (2 bp):
TG
Found at i:17537 original size:16 final size:18
Alignment explanation
Indices: 17511--17544 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
17501 ATTCAAATTA
17511 AATCGAA-TTTTATTTTT
1 AATCGAATTTTTATTTTT
17528 AATC-AATTTTTATTTTT
1 AATCGAATTTTTATTTTT
17545 TTATAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (18 bp):
AATCGAATTTTTATTTTT
Found at i:18321 original size:20 final size:21
Alignment explanation
Indices: 18296--18345 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
18286 ACGAATTATT
*
18296 AATAAATTAA-AATTTATATA
1 AATAAATTAATAATTTAAATA
18316 AATAAA-TAATAATTTAAATA
1 AATAAATTAATAATTTAAATA
18336 AATATAATTA
1 AATA-AATTA
18346 TGATATGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 3 0.12
20 19 0.73
21 2 0.08
22 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATAAATTAATAATTTAAATA
Found at i:18334 original size:32 final size:31
Alignment explanation
Indices: 18264--18328 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
18254 TGTTCATATA
* *
18264 AATATATTAAAATTTATATAATACGAATTATT
1 AATAAATTAAAATTTATATAATAC-AATTAAT
18296 AATAAATTAAAATTTATATAAATA-AA-TAAT
1 AATAAATTAAAATTTATAT-AATACAATTAAT
18326 AAT
1 AAT
18329 TTAAATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 6 0.20
31 2 0.07
32 18 0.60
33 4 0.13
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (31 bp):
AATAAATTAAAATTTATATAATACAATTAAT
Found at i:18344 original size:15 final size:16
Alignment explanation
Indices: 18314--18344 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
18304 AAAATTTATA
18314 TAAATAAATAATAATT
1 TAAATAAATAATAATT
18330 TAAATAAAT-ATAATT
1 TAAATAAATAATAATT
18345 ATGATATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATAAATAATAATT
Found at i:22290 original size:2 final size:2
Alignment explanation
Indices: 22285--22313 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22275 CGTGTGTGTG
22285 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22314 GTTCCTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23168 original size:50 final size:50
Alignment explanation
Indices: 23109--23317 Score: 339
Period size: 50 Copynumber: 4.2 Consensus size: 50
23099 TATACTTAGA
* *
23109 GTCAACAATTATGGCTACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
23159 GTCAACAATTATGGCCATCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
23209 GTCAACAATTATGGCCACTTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
23259 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAATG-ATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAATC
23309 GTCAACAAT
1 GTCAACAAT
23318 GACAATAACT
Statistics
Matches: 149, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
50 148 0.99
51 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:23353 original size:32 final size:32
Alignment explanation
Indices: 23307--23379 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
23297 TGGTGAATGA
*
23307 TAGTCAACAATGACAATAACTTTCCACCCATT
1 TAGTTAACAATGACAATAACTTTCCACCCATT
23339 TAGTTAACAATGACAATAACTTTCCACCCATT
1 TAGTTAACAATGACAATAACTTTCCACCCATT
23371 TAGTTAACA
1 TAGTTAACA
23380 TAAATTAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30
Consensus pattern (32 bp):
TAGTTAACAATGACAATAACTTTCCACCCATT
Found at i:23673 original size:2 final size:2
Alignment explanation
Indices: 23666--23698 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
23656 TATGTTGCTT
23666 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
23699 TTTTTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25092 original size:39 final size:39
Alignment explanation
Indices: 25038--25119 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
25028 AAAAGATTGT
25038 TTTCGCACATATCATTTCTTTTGTAGTCTAATAGTAGAC
1 TTTCGCACATATCATTTCTTTTGTAGTCTAATAGTAGAC
* *
25077 TTTCGCACGTATCATTTCTTTTGTAGTCTAATTGTAGAC
1 TTTCGCACATATCATTTCTTTTGTAGTCTAATAGTAGAC
25116 TTTC
1 TTTC
25120 TTAGCTGTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.46
Consensus pattern (39 bp):
TTTCGCACATATCATTTCTTTTGTAGTCTAATAGTAGAC
Found at i:27379 original size:2 final size:2
Alignment explanation
Indices: 27374--27410 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
27364 TCTCTCTCTC
*
27374 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27411 GTCACAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:36011 original size:71 final size:71
Alignment explanation
Indices: 35936--36146 Score: 194
Period size: 71 Copynumber: 2.9 Consensus size: 71
35926 TAGAGATATT
* * *
35936 ATTTATTTTTATTAGTACAAGTTTAAATTTATTTTTTATTAGATTATATAGGTTTAAATTTTTAT
1 ATTTATTTTTATTAGTAAAAATTTAAATTTATTTTTTATTAGATTATACAGGTTTAAATTTTTAT
36001 GAAATA
66 GAAATA
* * * *
36007 ATTTATTTTGATTTGTAAAAATTT-AATTGTATTTTTTATTAG-GTATGACATGAGTTAAAATTT
1 ATTTATTTTTATTAGTAAAAATTTAAATT-TATTTTTTATTAGATTAT-ACA-G-GTTTAAATTT
**
36070 TTAATGGTATA
62 TT-ATGAAATA
* * * * **
36081 ATTTAATTTTATTTA-TAAAAATTTAAGATTTATTTTTTAATTTGATTGTAGAACTTTAAATTTT
1 ATTTATTTTTA-TTAGTAAAAATTTAA-ATTTATTTTTT-ATTAGATTATACAGGTTTAAATTTT
36145 TA
63 TA
36147 AGAATGATAT
Statistics
Matches: 111, Mismatches: 19, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
70 7 0.06
71 35 0.32
72 1 0.01
73 12 0.11
74 34 0.31
75 11 0.10
76 9 0.08
77 2 0.02
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.54
Consensus pattern (71 bp):
ATTTATTTTTATTAGTAAAAATTTAAATTTATTTTTTATTAGATTATACAGGTTTAAATTTTTAT
GAAATA
Found at i:36233 original size:12 final size:13
Alignment explanation
Indices: 36195--36234 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
36185 AAGAAGGAAT
*
36195 GAAGGAAAAAAAG
1 GAAGAAAAAAAAG
*
36208 AAAGAAAAAAAAG
1 GAAGAAAAAAAAG
36221 GAA-AAAAAAAAG
1 GAAGAAAAAAAAG
36233 GA
1 GA
36235 CTAAGCGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
GAAGAAAAAAAAG
Found at i:39914 original size:21 final size:22
Alignment explanation
Indices: 39867--39927 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
39857 AATTAAAAAT
*
39867 TAATTTTTT-AATTTGTTAATA
1 TAATTTTTTAAATTTATTAATA
39888 TAATTTTTTAAATTTAATTAA-A
1 TAATTTTTTAAATTT-ATTAATA
*
39910 T-ATTTTTT-ATTTTATTAA
1 TAATTTTTTAAATTTATTAA
39928 AAATAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
19 5 0.14
20 4 0.11
21 16 0.44
22 7 0.19
23 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TAATTTTTTAAATTTATTAATA
Found at i:40363 original size:5 final size:5
Alignment explanation
Indices: 40353--40378 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40343 ACCTTATCCA
40353 AATTT AATTT AATTT AATTT AATTT A
1 AATTT AATTT AATTT AATTT AATTT A
40379 CTAAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:41973 original size:68 final size:68
Alignment explanation
Indices: 41861--41992 Score: 192
Period size: 68 Copynumber: 1.9 Consensus size: 68
41851 CAAAAAATTG
* * *
41861 CCCTAACTATCATGGAAGAATTTGTTGTGAAAAGCCATACATCTGTCACATATATAAGTTAGTGA
1 CCCTAACTATCATGGAAGAATTTGTTGTGAAAAGCCACACATCTGTCACATATACAAATTAGTGA
41926 TTT
66 TTT
* * ** *
41929 CCCTAACTATGATGGAAGAATTTGTTGTGGAAAGCCACGTATCTGTTACATATACAAATTAGTG
1 CCCTAACTATCATGGAAGAATTTGTTGTGAAAAGCCACACATCTGTCACATATACAAATTAGTG
41993 GTGAAAATTG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (68 bp):
CCCTAACTATCATGGAAGAATTTGTTGTGAAAAGCCACACATCTGTCACATATACAAATTAGTGA
TTT
Found at i:42201 original size:68 final size:68
Alignment explanation
Indices: 42092--42227 Score: 236
Period size: 68 Copynumber: 2.0 Consensus size: 68
42082 GAGGACGAAA
*
42092 TAGCAGAGCTCGTTAGCGTTTGGGACGATTGGCGTGGTTGGAAGCAACAGGCAAGGTGTGAGCGA
1 TAGCAGAGCTCGTTAGCGTTTGGGACGATTGGCGTGGTTGGAAGCAACAGGCAAGGGGTGAGCGA
42157 CAG
66 CAG
* * *
42160 TAGCAGAGCTCGTTAGCGTTTGGGACGATTGGTGTGGTTGGAAGCGACAGGCAAGGGGTGAGGGA
1 TAGCAGAGCTCGTTAGCGTTTGGGACGATTGGCGTGGTTGGAAGCAACAGGCAAGGGGTGAGCGA
42225 CAG
66 CAG
42228 CTGAGGGGTC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.23, C:0.15, G:0.42, T:0.21
Consensus pattern (68 bp):
TAGCAGAGCTCGTTAGCGTTTGGGACGATTGGCGTGGTTGGAAGCAACAGGCAAGGGGTGAGCGA
CAG
Found at i:42577 original size:13 final size:13
Alignment explanation
Indices: 42561--42630 Score: 54
Period size: 13 Copynumber: 5.2 Consensus size: 13
42551 TAGTATATTT
42561 TTAAATATAAATA
1 TTAAATATAAATA
* *
42574 TTAATTATAAATT
1 TTAAATATAAATA
*
42587 TTAAAAAATATAAAAA
1 TT---AAATATAAATA
*
42603 TT-TATATAAATA
1 TTAAATATAAATA
42615 -TAATATATAAATA
1 TTAA-ATATAAATA
42628 TTA
1 TTA
42631 TTCTTTAATG
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
11 1 0.02
12 8 0.19
13 22 0.51
14 2 0.05
16 10 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAATATAAATA
Found at i:43317 original size:2 final size:2
Alignment explanation
Indices: 43310--43341 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
43300 CTATTTCTTT
43310 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43342 AAATGGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45106 original size:19 final size:19
Alignment explanation
Indices: 45078--45121 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
45068 AAGATTAAAC
45078 AAAA-AATAA-TTTAGATTA
1 AAAATAATAATTTTA-ATTA
*
45096 AAAATAATAATTTTATTTA
1 AAAATAATAATTTTAATTA
45115 AAAATAA
1 AAAATAA
45122 ACTTATTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 15 0.65
20 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAATAATAATTTTAATTA
Found at i:54292 original size:24 final size:24
Alignment explanation
Indices: 54265--54310 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
54255 ACTCGAATAA
* *
54265 ATTTATTTGATTTAACTTGATTCG
1 ATTTATTTAATTTAACTAGATTCG
*
54289 ATTTTTTTAATTTAACTAGATT
1 ATTTATTTAATTTAACTAGATT
54311 TGATAAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.57
Consensus pattern (24 bp):
ATTTATTTAATTTAACTAGATTCG
Found at i:56223 original size:23 final size:24
Alignment explanation
Indices: 56195--56245 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
56185 TTAATGAATT
56195 AAAATTGTAA-ATTAATAATT-TTA
1 AAAATT-TAATATTAATAATTATTA
* *
56218 AAAATTTAATATTTATAGTTATTA
1 AAAATTTAATATTAATAATTATTA
56242 AAAA
1 AAAA
56246 AAGATAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 3 0.12
23 14 0.58
24 7 0.29
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
AAAATTTAATATTAATAATTATTA
Found at i:56319 original size:15 final size:14
Alignment explanation
Indices: 56301--56337 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
56291 ATTTTTATAA
56301 TATAAATTCAATACT
1 TATAAATTCAATA-T
56316 TATAAATTCAATAT
1 TATAAATTCAATAT
*
56330 TAAAAATT
1 TATAAATT
56338 AAAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (14 bp):
TATAAATTCAATAT
Found at i:60498 original size:23 final size:23
Alignment explanation
Indices: 60453--60499 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
60443 ACATATGTAT
* *
60453 ATATATAAATTTAAATATTATTA
1 ATATATAAATATAAATATAATTA
60476 ATATATCAAATATAAAT-TAATTA
1 ATATAT-AAATATAAATATAATTA
60499 A
1 A
60500 AAATACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATATAAATATAAATATAATTA
Found at i:65744 original size:27 final size:27
Alignment explanation
Indices: 65706--65779 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
65696 AAACAACGTG
*
65706 CCACCATTTTTGACAAACAAAAAAAAA
1 CCACAATTTTTGACAAACAAAAAAAAA
* **
65733 CCACAATTTTTGACAAACACAAAGTAA
1 CCACAATTTTTGACAAACAAAAAAAAA
65760 CCACAATTTTTGACAAACAA
1 CCACAATTTTTGACAAACAA
65780 TGGGTGGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.50, C:0.23, G:0.05, T:0.22
Consensus pattern (27 bp):
CCACAATTTTTGACAAACAAAAAAAAA
Found at i:67993 original size:124 final size:124
Alignment explanation
Indices: 67773--68023 Score: 459
Period size: 124 Copynumber: 2.0 Consensus size: 124
67763 CTCTGCTACA
67773 GATTATCTTCTTTGTATCTAAGCACCAAAGTCAAAATCCTTTCACTCCATGTGTGATTCCCATAA
1 GATTATCTTCTTTGTATCTAAGCACCAAAGTCAAAATCCTTTCACTCCATGTGTGATTCCCATAA
67838 AAAGAGCCTTCTTTGTTCTCGGATCAAGCTTCGATTCCTTCACGTGATAATAGGCAGTG
66 AAAGAGCCTTCTTTGTTCTCGGATCAAGCTTCGATTCCTTCACGTGATAATAGGCAGTG
* *
67897 GATTATCTTCTTTGTGTCTAAGCACCAAAGTCGAAATCCTTTCACTCCATGTGTGATTCCCATAA
1 GATTATCTTCTTTGTATCTAAGCACCAAAGTCAAAATCCTTTCACTCCATGTGTGATTCCCATAA
*
67962 AAAGAGCCTTCTTTGCTT-TCGGATCAAGCTTCGATTCCTTCACGTGATAATAGGTAGTG
66 AAAGAGCCTTCTTTG-TTCTCGGATCAAGCTTCGATTCCTTCACGTGATAATAGGCAGTG
68021 GAT
1 GAT
68024 CCAAATATAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
124 121 0.98
125 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (124 bp):
GATTATCTTCTTTGTATCTAAGCACCAAAGTCAAAATCCTTTCACTCCATGTGTGATTCCCATAA
AAAGAGCCTTCTTTGTTCTCGGATCAAGCTTCGATTCCTTCACGTGATAATAGGCAGTG
Found at i:74238 original size:2 final size:2
Alignment explanation
Indices: 74231--74260 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
74221 TGTTTAAAAG
74231 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
74261 TTCTCCTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:77328 original size:27 final size:27
Alignment explanation
Indices: 77298--77371 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
77288 AAAAGCCACT
* *
77298 CTTTGTGTTTGTAAAAAATGGTGGTTA
1 CTTTGTGTTTGTCAAAAATGGTGATTA
* * *
77325 CTTTGTATTTGTCAAAAATTGTGATTC
1 CTTTGTGTTTGTCAAAAATGGTGATTA
*
77352 CTTTTTTGTTTGTCAAAAAT
1 C-TTTGTGTTTGTCAAAAAT
77372 TATGATTGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.26, C:0.08, G:0.18, T:0.49
Consensus pattern (27 bp):
CTTTGTGTTTGTCAAAAATGGTGATTA
Found at i:78897 original size:29 final size:31
Alignment explanation
Indices: 78843--78905 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
78833 TCGTTGAGAG
* *
78843 CTTTTTTTGTCGGTGAATATTTCCAA-CTAAA
1 CTTTTGTTGCCGGTGAATA-TTCCAACCTAAA
78874 CTTTTGTTGCCGGTGAATA-TCCAACCTAAA
1 CTTTTGTTGCCGGTGAATATTCCAACCTAAA
78904 CT
1 CT
78906 ACTTTTGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 5 0.17
30 7 0.24
31 17 0.59
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (31 bp):
CTTTTGTTGCCGGTGAATATTCCAACCTAAA
Found at i:79031 original size:9 final size:9
Alignment explanation
Indices: 79017--79045 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
79007 TTCTGTTTTG
79017 TTTTTGTTT
1 TTTTTGTTT
79026 TTTTTGTTT
1 TTTTTGTTT
79035 TTTTT-TTT
1 TTTTTGTTT
79043 TTT
1 TTT
79046 GCGATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:79032 original size:15 final size:15
Alignment explanation
Indices: 79012--79046 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
79002 TGGCTTTCTG
79012 TTTTGTTTTTGTTTT
1 TTTTGTTTTTGTTTT
*
79027 TTTTGTTTTTTTTTT
1 TTTTGTTTTTGTTTT
79042 TTTTG
1 TTTTG
79047 CGATTTAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (15 bp):
TTTTGTTTTTGTTTT
Found at i:79238 original size:20 final size:20
Alignment explanation
Indices: 79213--79254 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
79203 TGATAAATAA
* *
79213 AATTAAATAATTTATCTTTT
1 AATTAAATAATTAAACTTTT
79233 AATTAAATAATTAAACTTTT
1 AATTAAATAATTAAACTTTT
79253 AA
1 AA
79255 ATTATTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTAAATAATTAAACTTTT
Found at i:79262 original size:28 final size:27
Alignment explanation
Indices: 79231--79301 Score: 88
Period size: 28 Copynumber: 2.6 Consensus size: 27
79221 AATTTATCTT
79231 TTAATTAAATAATTAAACTTTTAAATTA
1 TTAATTAAATAATTAAACTTTT-AATTA
* * *
79259 TTAATTAATTAATTTACCTTTTAATTA
1 TTAATTAAATAATTAAACTTTTAATTA
* *
79286 TTATTTATATAATTAA
1 TTAATTAAATAATTAA
79302 TTAATTTACT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 17 0.47
28 19 0.53
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (27 bp):
TTAATTAAATAATTAAACTTTTAATTA
Found at i:79263 original size:88 final size:83
Alignment explanation
Indices: 79167--79327 Score: 200
Period size: 83 Copynumber: 1.9 Consensus size: 83
79157 TTAATTATAT
*
79167 ATTATTAATTACA-TAATTTTCCTTTTAACTTTGAGTTGATAAATAAAATTAAATAATTTATCTT
1 ATTATTAATTA-ATTAATTTACCTTTTAA--TT-A-TT-ATAAATAAAATTAAATAATTTA-CTT
79231 T-TAATTAAATAATTAAACTTTTAA
59 TATAATTAAATAATTAAACTTTTAA
** * *
79255 ATTATTAATTAATTAATTTACCTTTTAATTATTATTTATATAATTAATTAATTTACTTTATAATT
1 ATTATTAATTAATTAATTTACCTTTTAATTATTATAAATAAAATTAAATAATTTACTTTATAATT
79320 AAATAATT
66 AAATAATT
79328 GTTTAGGCAT
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
82 4 0.06
83 31 0.47
84 2 0.03
85 1 0.02
86 2 0.03
87 1 0.02
88 25 0.38
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.51
Consensus pattern (83 bp):
ATTATTAATTAATTAATTTACCTTTTAATTATTATAAATAAAATTAAATAATTTACTTTATAATT
AAATAATTAAACTTTTAA
Found at i:79282 original size:20 final size:19
Alignment explanation
Indices: 79259--79327 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
79249 TTTTAAATTA
79259 TTAATTAATTAATTTACCTT
1 TTAATTAATTAATTTA-CTT
79279 TTAATT-ATT-ATTTA--T
1 TTAATTAATTAATTTACTT
*
79294 ATAATTAATTAATTTACTT
1 TTAATTAATTAATTTACTT
*
79313 TATAATTAAATAATT
1 T-TAATTAATTAATT
79328 GTTTAGGCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
15 6 0.15
16 3 0.07
17 5 0.12
18 5 0.12
19 4 0.10
20 18 0.44
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAATTAATTAATTTACTT
Found at i:79298 original size:27 final size:27
Alignment explanation
Indices: 79231--79301 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
79221 AATTTATCTT
79231 TTAATTAAATAATTAAACTTTTAAATTA
1 TTAATT-AATAATTAAACTTTTAAATTA
* *
79259 TTAATTAATTAATTTACCTTTT-AATTA
1 TTAATTAA-TAATTAAACTTTTAAATTA
*
79286 TTATTTATATAATTAA
1 TTAATTA-ATAATTAA
79302 TTAATTTACT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 19 0.51
28 18 0.49
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (27 bp):
TTAATTAATAATTAAACTTTTAAATTA
Found at i:83428 original size:30 final size:30
Alignment explanation
Indices: 83392--83453 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
83382 TTTACTTTAA
* *
83392 TTTGATT-GATTTCTTTATTAAATTTTAATT
1 TTTGATTAAATTT-TTTACTAAATTTTAATT
*
83422 TTTGATTAAATTTTTTACTAAATTTTGATT
1 TTTGATTAAATTTTTTACTAAATTTTAATT
83452 TT
1 TT
83454 GTACAATTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.63
Consensus pattern (30 bp):
TTTGATTAAATTTTTTACTAAATTTTAATT
Found at i:84719 original size:22 final size:21
Alignment explanation
Indices: 84693--84749 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
84683 AATCCAAAAA
84693 AAAATTCAAAAATTGAAAAACT
1 AAAATTCAAAAATT-AAAAACT
* * *
84715 CAAATTTCAAAAAATTTAAAATT
1 -AAAATTC-AAAAATTAAAAACT
84738 AAAATTCAAAAA
1 AAAATTCAAAAA
84750 ATTATGAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 5 0.17
22 6 0.21
23 11 0.38
24 7 0.24
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAATTCAAAAATTAAAAACT
Found at i:84750 original size:22 final size:24
Alignment explanation
Indices: 84693--84752 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 24
84683 AATCCAAAAA
84693 AAAATTC-AAAAATTGAAAAACTC
1 AAAATTCAAAAAATTGAAAAACTC
* * *
84716 AAATTTCAAAAAATT-TAAAA-TT
1 AAAATTCAAAAAATTGAAAAACTC
84738 AAAATTCAAAAAATT
1 AAAATTCAAAAAATT
84753 ATGAAGAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 15 0.47
23 10 0.31
24 7 0.22
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATTCAAAAAATTGAAAAACTC
Found at i:84771 original size:19 final size:17
Alignment explanation
Indices: 84737--84823 Score: 56
Period size: 19 Copynumber: 4.8 Consensus size: 17
84727 AATTTAAAAT
84737 TAAAATTCA-AAAAATTA
1 TAAAATT-ATAAAAATTA
84754 TGAAGAATCTAT-AAAATTA
1 T-AA-AAT-TATAAAAATTA
84773 TAAAAATTATAAAAATT-
1 T-AAAATTATAAAAATTA
*
84790 TAAATATTTTTACAAAATGTA
1 TAAA-A-TTATA-AAAAT-TA
84811 TAAAATTA-AAAAA
1 TAAAATTATAAAAA
84824 CAAAAAAAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
16 3 0.05
17 10 0.18
18 16 0.28
19 21 0.37
20 3 0.05
21 4 0.07
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAATTATAAAAATTA
Found at i:84793 original size:8 final size:9
Alignment explanation
Indices: 84746--84838 Score: 59
Period size: 9 Copynumber: 10.2 Consensus size: 9
84736 TTAAAATTCA
84746 AAAAATTAT
1 AAAAATTAT
*
84755 GAAGAATCTAT
1 -AAAAAT-TAT
84766 -AAAATTAT
1 AAAAATTAT
84774 AAAAATTAT
1 AAAAATTAT
84783 AAAAATT-T
1 AAAAATTAT
* *
84791 AAATATTTTT
1 AAA-AATTAT
84801 ACAAAATGTAT
1 A-AAAAT-TAT
84812 -AAAATTA-
1 AAAAATTAT
** *
84819 AAAAACAAA
1 AAAAATTAT
84828 AAAAATTAT
1 AAAAATTAT
84837 AA
1 AA
84839 TTTTTTTAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
8 14 0.22
9 35 0.54
10 9 0.14
11 7 0.11
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:84870 original size:9 final size:9
Alignment explanation
Indices: 84856--85058 Score: 77
Period size: 9 Copynumber: 22.6 Consensus size: 9
84846 AAATCAATAG
84856 ATTTTTTAT
1 ATTTTTTAT
*
84865 ATTTTTGA-
1 ATTTTTTAT
84873 ATTTTATTTAT
1 A-TTT-TTTAT
*
84884 ATTTTTGA-
1 ATTTTTTAT
*
84892 ATTTTTTGT
1 ATTTTTTAT
*
84901 AATTTTTGA-
1 -ATTTTTTAT
*
84910 ATTTTATAT
1 ATTTTTTAT
*
84919 ATTTTTAAT
1 ATTTTTTAT
* * *
84928 AATTTTAAA
1 ATTTTTTAT
84937 ATTTTTTAT
1 ATTTTTTAT
84946 -TATTTTTAT
1 AT-TTTTTAT
*
84955 -TATTTTAT
1 ATTTTTTAT
*
84963 AAATTTTTAT
1 -ATTTTTTAT
*
84973 AATTTTTAT
1 ATTTTTTAT
*
84982 A-ATTTT-T
1 ATTTTTTAT
84989 A-TTTTTAT
1 ATTTTTTAT
*
84997 -TTTTTGA-
1 ATTTTTTAT
85004 ATTTTTTAT
1 ATTTTTTAT
*
85013 AGTTTATTTTT
1 A-TTT-TTTAT
* *
85024 AATTTTATAG
1 -ATTTTTTAT
85034 ATTTTGTTAT
1 ATTTT-TTAT
85044 AATTTCTTTA-
1 -ATTT-TTTAT
85054 ATTTT
1 ATTTT
85059 AAATTTATTC
Statistics
Matches: 146, Mismatches: 29, Indels: 39
0.68 0.14 0.18
Matches are distributed among these distances:
7 6 0.04
8 37 0.25
9 61 0.42
10 25 0.17
11 15 0.10
12 2 0.01
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:84884 original size:19 final size:19
Alignment explanation
Indices: 84860--84924 Score: 93
Period size: 19 Copynumber: 3.6 Consensus size: 19
84850 CAATAGATTT
84860 TTTATATTTTTGAATTTTA
1 TTTATATTTTTGAATTTTA
84879 TTTATATTTTTGAATTTT-
1 TTTATATTTTTGAATTTTA
84897 TTGTA-ATTTTTGAATTTTA
1 TT-TATATTTTTGAATTTTA
84916 --TATATTTTT
1 TTTATATTTTT
84925 AATAATTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
16 2 0.05
17 6 0.14
18 15 0.35
19 20 0.47
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (19 bp):
TTTATATTTTTGAATTTTA
Found at i:84922 original size:27 final size:26
Alignment explanation
Indices: 84909--85001 Score: 86
Period size: 27 Copynumber: 3.6 Consensus size: 26
84899 GTAATTTTTG
* *
84909 AATTTTATATATTTTTAATAATTTTAA
1 AATTTT-TATATTTTTTATAATTTTTA
*
84936 AATTTTT-TATTATTTTTATTATTTTATA
1 AATTTTTATA-T-TTTTTATAATTTT-TA
*
84964 AATTTTTATAATTTTTATAATTTTT-
1 AATTTTTATATTTTTTATAATTTTTA
84989 -ATTTTTAT-TTTTT
1 AATTTTTATATTTTT
85002 GAATTTTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
23 4 0.07
24 8 0.14
25 2 0.04
26 3 0.05
27 29 0.52
28 8 0.14
29 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (26 bp):
AATTTTTATATTTTTTATAATTTTTA
Found at i:84988 original size:19 final size:19
Alignment explanation
Indices: 84911--85134 Score: 107
Period size: 18 Copynumber: 11.7 Consensus size: 19
84901 AATTTTTGAA
*
84911 TTTTATATATTTTTAATAA-
1 TTTTATA-ATTTTTTATAAT
* *
84930 TTTTAAAATTTTTTATTAT
1 TTTTATAATTTTTTATAAT
* *
84949 TTTTATTATTTTATA-AAT
1 TTTTATAATTTTTTATAAT
84967 TTTTATAA-TTTTTATAAT
1 TTTTATAATTTTTTATAAT
** *
84985 TTTTATTTTTATTTTTTGAATT
1 TTTTATAATT-TTTTAT-AA-T
* *
85007 TTTTATAGTTTATTTTTAA-
1 TTTTATAATTT-TTTATAAT
85026 TTTTATAGATTTTGTTATAAT
1 TTTTATA-ATTTT-TTATAAT
85047 TTCTT-TAA--TTTTA-AAT
1 TT-TTATAATTTTTTATAAT
*
85063 TTATTCATAATTTTTTTTTTAA-
1 TT-TT-ATAA--TTTTTTATAAT
85085 TTTT-TAA-TTTTTATAAAT
1 TTTTATAATTTTTTAT-AAT
85103 TTTT-TGAAATTTTTT-TATAT
1 TTTTAT--AATTTTTTATA-AT
85123 TTTTA-AATTTTT
1 TTTTATAATTTTT
85135 AAAATTTAAA
Statistics
Matches: 161, Mismatches: 19, Indels: 51
0.70 0.08 0.22
Matches are distributed among these distances:
16 13 0.08
17 10 0.06
18 44 0.27
19 31 0.19
20 23 0.14
21 16 0.10
22 22 0.14
23 2 0.01
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTATAATTTTTTATAAT
Found at i:85007 original size:30 final size:28
Alignment explanation
Indices: 84965--85134 Score: 105
Period size: 30 Copynumber: 5.8 Consensus size: 28
84955 TATTTTATAA
84965 ATTTTTATAATTTTTATAATTTTTATTTTT
1 ATTTTT-TAATTTTTATAATTTTT-TTTTT
* * *
84995 ATTTTTTGAATTTTTTATAGTTTATTTTTA
1 ATTTTTT-AA-TTTTTATAATTTTTTTTTT
* *
85025 ATTTTATAGATTTTGTTATAA---TTTCTTT
1 ATTTTTTA-A-TTT-TTATAATTTTTTTTTT
* *
85053 AATTTTAAATTTATTCATAATTTTTTTTTT
1 ATTTTTTAATTT-TT-ATAATTTTTTTTTT
* * ***
85083 AATTTTTAATTTTTATAAATTTTTTGAA
1 ATTTTTTAATTTTTATAATTTTTTTTTT
85111 ATTTTTTTATATTTTTA-AATTTTT
1 A-TTTTTTA-ATTTTTATAATTTTT
85135 AAAATTTAAA
Statistics
Matches: 110, Mismatches: 20, Indels: 21
0.73 0.13 0.14
Matches are distributed among these distances:
26 5 0.05
27 5 0.05
28 20 0.18
29 16 0.15
30 47 0.43
31 17 0.15
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (28 bp):
ATTTTTTAATTTTTATAATTTTTTTTTT
Found at i:85010 original size:31 final size:32
Alignment explanation
Indices: 84927--85106 Score: 97
Period size: 29 Copynumber: 5.8 Consensus size: 32
84917 ATATTTTTAA
* *
84927 TAATTTTA-AAATTTTTTATTATTTTTATTATTTT
1 TAATTTTATAGATTTTTTA-TA-ATTT-TTATTTT
84961 ATAAATTTTTATA-A-TTTTTATAATTTTTATTTT
1 -T-AA-TTTTATAGATTTTTTATAATTTTTATTTT
* *
84994 T-ATTTT-TTGAATTTTTTAT-A-GTTTATTTT
1 TAATTTTATAG-ATTTTTTATAATTTTTATTTT
*
85023 TAATTTTATAGATTTTGTTATAA---TT-TCTT
1 TAATTTTATAGATTTT-TTATAATTTTTATTTT
*
85052 TAATTTTA-A-ATTTATTCATAATTTTT-TTTT
1 TAATTTTATAGATTT-TTTATAATTTTTATTTT
85082 TAATTTT-TA-A-TTTTTATAAATTTTT
1 TAATTTTATAGATTTTTTAT-AATTTTT
85107 TGAAATTTTT
Statistics
Matches: 121, Mismatches: 8, Indels: 38
0.72 0.05 0.23
Matches are distributed among these distances:
27 9 0.07
28 7 0.06
29 33 0.27
30 29 0.24
31 13 0.11
32 2 0.02
33 7 0.06
34 3 0.02
35 3 0.02
36 8 0.07
37 6 0.05
38 1 0.01
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.68
Consensus pattern (32 bp):
TAATTTTATAGATTTTTTATAATTTTTATTTT
Found at i:85097 original size:38 final size:35
Alignment explanation
Indices: 84938--85142 Score: 94
Period size: 37 Copynumber: 5.8 Consensus size: 35
84928 AATTTTAAAA
84938 TTTTTTATTATTTTTATTATTTTATAAATTT-TT-ATAAT
1 TTTTTTA-TATTTTTA--ATTTT-TAAATTTATTCA-AAT
* **
84976 TTTTATA-ATTTTT-ATTTTT--ATTT-TTTGAA-
1 TTTTTTATATTTTTAATTTTTAAATTTATTCAAAT
* * *
85005 TTTTTTATA-GTTT-ATTTTTAATTTTA-T-AGAT
1 TTTTTTATATTTTTAATTTTTAAATTTATTCAAAT
*
85036 TTTGTTATAATTTCTTTAA-TTTTAAATTTATTCATAATT
1 TTTTTTAT-A-TT-TTTAATTTTTAAATTTATTCA-AA-T
* * *
85075 TTTTTTTTAATTTTTAATTTTTATAAATTTTTTGAAAT
1 TTTTTTAT-ATTTTTAA-TTTT-TAAATTTATTCAAAT
85113 TTTTTTATATTTTTAAATTTTTAAAATTTA
1 TTTTTTATATTTTT-AATTTTT-AAATTTA
85143 AAGGACATAT
Statistics
Matches: 130, Mismatches: 17, Indels: 41
0.69 0.09 0.22
Matches are distributed among these distances:
29 15 0.12
30 10 0.08
31 11 0.08
32 2 0.02
33 5 0.04
35 13 0.10
36 9 0.07
37 22 0.17
38 19 0.15
39 14 0.11
40 10 0.08
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.68
Consensus pattern (35 bp):
TTTTTTATATTTTTAATTTTTAAATTTATTCAAAT
Found at i:85103 original size:10 final size:9
Alignment explanation
Indices: 85076--85141 Score: 57
Period size: 10 Copynumber: 7.3 Consensus size: 9
85066 TTCATAATTT
*
85076 TTTTTTTAA
1 TTTTTTAAA
85085 -TTTTT-AA
1 TTTTTTAAA
85092 TTTTTATAAA
1 TTTTT-TAAA
85102 TTTTTTGAAA
1 TTTTTT-AAA
*
85112 TTTTTT-TA
1 TTTTTTAAA
85120 TATTTTTAAA
1 T-TTTTTAAA
*
85130 TTTTTAAAA
1 TTTTTTAAA
85139 TTT
1 TTT
85142 AAAGGACATA
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
7 2 0.04
8 11 0.23
9 17 0.35
10 18 0.38
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:85105 original size:9 final size:8
Alignment explanation
Indices: 85077--85137 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 8
85067 TCATAATTTT
*
85077 TTTTTTAA
1 TTTTTAAA
*
85085 TTTTTAAT
1 TTTTTAAA
85093 TTTTATAAA
1 TTTT-TAAA
85102 TTTTTTGAAA
1 -TTTTT-AAA
*
85112 TTTTTTTATA
1 --TTTTTAAA
85122 TTTTTAAA
1 TTTTTAAA
85130 TTTTTAAA
1 TTTTTAAA
85138 ATTTAAAGGA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
8 25 0.57
9 4 0.09
10 9 0.20
11 6 0.14
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (8 bp):
TTTTTAAA
Found at i:85133 original size:7 final size:8
Alignment explanation
Indices: 84901--85137 Score: 66
Period size: 9 Copynumber: 28.2 Consensus size: 8
84891 AATTTTTTGT
*
84901 AATTTTTG
1 AATTTTTA
84909 AATTTTATA
1 AATTTT-TA
*
84918 TATTTTTAA
1 AATTTTT-A
*
84927 TAATTTTAA
1 -AATTTTTA
84936 AATTTTTTA
1 AA-TTTTTA
*
84945 TTATTTTTA
1 -AATTTTTA
*
84954 TTATTTTATA
1 -AATTTT-TA
84964 AATTTTTA
1 AATTTTTA
84972 TAATTTTTA
1 -AATTTTTA
84981 TAATTTTT-
1 -AATTTTTA
84989 -ATTTTT-
1 AATTTTTA
* *
84995 ATTTTTTG
1 AATTTTTA
85003 AATTTTT-
1 AATTTTTA
* *
85010 TATAGTTT-
1 AAT-TTTTA
85018 -ATTTTT-
1 AATTTTTA
85024 AATTTTATA
1 AATTTT-TA
*
85033 GATTTTGTTA
1 -AATTT-TTA
*
85043 TAATTTCTTT
1 -AATTT-TTA
85053 AA-TTTTA
1 AATTTTTA
85060 AATTTATTCA
1 AATTT-TT-A
85070 TAATTTTT-
1 -AATTTTTA
85078 --TTTTT-
1 AATTTTTA
85083 AATTTTTA
1 AATTTTTA
*
85091 ATTTTTATA
1 AATTTT-TA
85100 AATTTTTTGA
1 AA-TTTTT-A
85110 AATTTTTTTA
1 AA--TTTTTA
*
85120 TATTTTTA
1 AATTTTTA
85128 AATTTTTA
1 AATTTTTA
85136 AA
1 AA
85138 ATTTAAAGGA
Statistics
Matches: 181, Mismatches: 22, Indels: 52
0.71 0.09 0.20
Matches are distributed among these distances:
5 5 0.03
6 9 0.05
7 23 0.13
8 45 0.25
9 55 0.30
10 32 0.18
11 12 0.07
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (8 bp):
AATTTTTA
Found at i:85141 original size:66 final size:66
Alignment explanation
Indices: 85018--85141 Score: 157
Period size: 66 Copynumber: 1.9 Consensus size: 66
85008 TTTATAGTTT
* *
85018 ATTTTTAATTTTATAGATTTTGTTATAATTTCTTTAATTTTAAATTTATTCATAATTTTTTTTTT
1 ATTTTTAATTTTATAAATTTTGTTATAATTTCTTTAATTTTAAATTTATTCAAAATTTTTTTTTT
85083 A
66 A
*
85084 ATTTTTAATTTTTATAAATTTT-TTGA-AATTTTTTTATATTTTTAAATTT-TT-AAAATTT
1 ATTTTTAA-TTTTATAAATTTTGTT-ATAATTTCTTTA-A-TTTTAAATTTATTCAAAATTT
85142 AAAGGACATA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
66 25 0.49
67 16 0.31
68 10 0.20
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (66 bp):
ATTTTTAATTTTATAAATTTTGTTATAATTTCTTTAATTTTAAATTTATTCAAAATTTTTTTTTT
A
Found at i:86356 original size:27 final size:27
Alignment explanation
Indices: 86311--86362 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
86301 AAATTATACA
* *
86311 AATAAAATTATGACTAATAATAATAAT
1 AATAAAATTAAGACTAATAAAAATAAT
86338 AATAAAATTAAG-CTCAATAAAAATA
1 AATAAAATTAAGACT-AATAAAAATA
86363 GCATGGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.29
Consensus pattern (27 bp):
AATAAAATTAAGACTAATAAAAATAAT
Found at i:89837 original size:16 final size:16
Alignment explanation
Indices: 89775--89837 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
89765 AACCCGAATC
*
89775 CAAAATGATCCGAACT
1 CAAAATAATCCGAACT
* *
89791 TAAAATAACCCGAACT
1 CAAAATAATCCGAACT
* *
89807 CGAAATGA-CTCGAACT
1 CAAAATAATC-CGAACT
*
89823 CAAAATAATCTGAAC
1 CAAAATAATCCGAAC
89838 CCGAAATGAC
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
15 1 0.03
16 34 0.94
17 1 0.03
ACGTcount: A:0.46, C:0.24, G:0.11, T:0.19
Consensus pattern (16 bp):
CAAAATAATCCGAACT
Found at i:89843 original size:32 final size:33
Alignment explanation
Indices: 89765--89847 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 33
89755 ACTAATCCGA
* * *
89765 AACCCGAATCCAAAATGA-TCCGAACTTAAAAT
1 AACCCGAACCCGAAATGACTCCGAACTCAAAAT
*
89797 AACCCGAACTCGAAATGACT-CGAACTCAAAAT
1 AACCCGAACCCGAAATGACTCCGAACTCAAAAT
* *
89829 AATCTGAACCCGAAATGAC
1 AACCCGAACCCGAAATGAC
89848 CCAGATAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 42 0.98
33 1 0.02
ACGTcount: A:0.45, C:0.27, G:0.12, T:0.17
Consensus pattern (33 bp):
AACCCGAACCCGAAATGACTCCGAACTCAAAAT
Found at i:90663 original size:16 final size:16
Alignment explanation
Indices: 90644--90717 Score: 71
Period size: 16 Copynumber: 4.6 Consensus size: 16
90634 GACCTGAATC
90644 CGAAATGACCCGAACT
1 CGAAATGACCCGAACT
*
90660 CGAAATAACCCGAAC-
1 CGAAATGACCCGAACT
*
90675 CTGAAATGA-TCGAAACT
1 C-GAAATGACCCG-AACT
* *
90692 CGAAATGACTCGAATT
1 CGAAATGACCCGAACT
90708 CGAAAATGAC
1 CG-AAATGAC
90718 TTAAAAATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
15 3 0.06
16 35 0.71
17 11 0.22
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (16 bp):
CGAAATGACCCGAACT
Found at i:93929 original size:24 final size:24
Alignment explanation
Indices: 93879--93938 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
93869 AGATGGTATG
* * **
93879 AAAGAAAGAAGAGAACGGAAAGGA
1 AAAGAAAGAAAAGAACAGAAAAAA
*
93903 AAAGAAAGAAAAGAACATAAAAAA
1 AAAGAAAGAAAAGAACAGAAAAAA
*
93927 AAAAAAAGAAAA
1 AAAGAAAGAAAA
93939 AAAAGGTGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (24 bp):
AAAGAAAGAAAAGAACAGAAAAAA
Found at i:96301 original size:30 final size:30
Alignment explanation
Indices: 96267--96328 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
96257 CAAATTGTAT
* *
96267 AAAATCAAAGTTTGGTAAAAAATTTAATCA
1 AAAATCAAAATTTGGTAAAAAATTCAATCA
*
96297 AAAATCAAAATTTGGTAACAAATTCAATCA
1 AAAATCAAAATTTGGTAAAAAATTCAATCA
96327 AA
1 AA
96329 TAAAAGTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (30 bp):
AAAATCAAAATTTGGTAAAAAATTCAATCA
Found at i:99183 original size:21 final size:22
Alignment explanation
Indices: 99151--99200 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
99141 TTAAAAATAT
99151 AAAAAATAAA-TTT-TTT-TTA
1 AAAAAATAAATTTTCTTTATTA
99170 AAAAAATATGAATTTTCTTTATTA
1 AAAAAATA--AATTTTCTTTATTA
99194 AAAAAAT
1 AAAAAAT
99201 TGTTCGTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 8 0.31
21 2 0.08
22 3 0.12
23 3 0.12
24 10 0.38
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AAAAAATAAATTTTCTTTATTA
Found at i:101378 original size:2 final size:2
Alignment explanation
Indices: 101371--101402 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
101361 AACTTAAACG
101371 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
101403 GACCACTCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:103947 original size:29 final size:30
Alignment explanation
Indices: 103904--103965 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
103894 ATTGTTAAAA
103904 TTAAAATAAATTATTAAAATAGTA-TTTTTT
1 TTAAAATAAATTATTAAAA-AGTACTTTTTT
*
103934 TTAAAA-AAATTATTAAAAATTACTTTTTT
1 TTAAAATAAATTATTAAAAAGTACTTTTTT
103963 TTA
1 TTA
103966 TAGTTAACTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 3 0.10
29 21 0.70
30 6 0.20
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (30 bp):
TTAAAATAAATTATTAAAAAGTACTTTTTT
Found at i:110266 original size:17 final size:16
Alignment explanation
Indices: 110238--110292 Score: 65
Period size: 18 Copynumber: 3.2 Consensus size: 16
110228 ATAATAGTAT
110238 TATAAATTAATAAGAA
1 TATAAATTAATAAGAA
*
110254 TATAAATTTAATAAAAAA
1 TATAAA-TTAAT-AAGAA
*
110272 TATAAAATTAATAAGTA
1 TAT-AAATTAATAAGAA
110289 TATA
1 TATA
110293 TTTTTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 7 0.21
17 11 0.33
18 12 0.36
19 3 0.09
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (16 bp):
TATAAATTAATAAGAA
Found at i:110366 original size:13 final size:14
Alignment explanation
Indices: 110343--110379 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
110333 ATGTGATAAA
110343 ATAATAATATTTTG
1 ATAATAATATTTTG
110357 ATAA-AATATTTT-
1 ATAATAATATTTTG
*
110369 AAAATAATATT
1 ATAATAATATT
110380 AGCTTAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 3 0.14
13 14 0.67
14 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (14 bp):
ATAATAATATTTTG
Found at i:110568 original size:2 final size:2
Alignment explanation
Indices: 110561--110591 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
110551 CTGTCATCAC
110561 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
110592 GCTTGTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:112305 original size:20 final size:20
Alignment explanation
Indices: 112252--112297 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 20
112242 GAAAGAACTG
112252 AAAATAATTAATAATTATTTTT
1 AAAA-AATTAA-AATTATTTTT
*
112274 AAAAAATAAAAATTA-TTTT
1 AAAAAATTAAAATTATTTTT
112293 AAAAA
1 AAAAA
112298 TTTTAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 5 0.22
21 5 0.22
22 4 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAAATTAAAATTATTTTT
Found at i:113632 original size:31 final size:32
Alignment explanation
Indices: 113590--113687 Score: 94
Period size: 31 Copynumber: 3.1 Consensus size: 32
113580 ACACAATAAA
**
113590 AAAAT-TAAATTATTATATGATAAAAATATAT
1 AAAATATAAATTATTATAAAATAAAAATATAT
* * **
113621 ACAATAT-AATTATAATAAAATATCAATATAT
1 AAAATATAAATTATTATAAAATAAAAATATAT
*
113652 AAAATATAAATTATTA-AAATATTTAAAATATAT
1 AAAATATAAATTATTATAAA-A-TAAAAATATAT
113685 AAA
1 AAA
113688 TAACTATGAT
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
31 32 0.62
32 9 0.17
33 11 0.21
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (32 bp):
AAAATATAAATTATTATAAAATAAAAATATAT
Found at i:113634 original size:15 final size:16
Alignment explanation
Indices: 113590--113687 Score: 71
Period size: 15 Copynumber: 6.2 Consensus size: 16
113580 ACACAATAAA
113590 AAAAT-TAAATTATTAT
1 AAAATATAAATTA-TAT
** *
113606 ATGATA-AAAATATAT
1 AAAATATAAATTATAT
*
113621 ACAATAT-AATTATAAT
1 AAAATATAAATTAT-AT
*
113637 AAAATATCAA-TATAT
1 AAAATATAAATTATAT
113652 AAAATATAAATTAT-T
1 AAAATATAAATTATAT
*
113667 AAAATATTTAAAATATAT
1 AAAATA--TAAATTATAT
113685 AAA
1 AAA
113688 TAACTATGAT
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
15 30 0.46
16 22 0.34
17 9 0.14
18 4 0.06
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (16 bp):
AAAATATAAATTATAT
Found at i:115743 original size:24 final size:25
Alignment explanation
Indices: 115693--115743 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
115683 CAAAATAACA
* * *
115693 TTATTATTTTCATATTTCTACACTT
1 TTATTATTTTCAGATATATACACTT
*
115718 TTATTATTTT-AGATATATACATTT
1 TTATTATTTTCAGATATATACACTT
115742 TT
1 TT
115744 TAATCATATC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.27, C:0.10, G:0.02, T:0.61
Consensus pattern (25 bp):
TTATTATTTTCAGATATATACACTT
Found at i:115806 original size:18 final size:19
Alignment explanation
Indices: 115771--115806 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
115761 CAAATATTTT
115771 TTCAAAATAATATTAAACG
1 TTCAAAATAATATTAAACG
*
115790 TTCAAAA-AATTTTAAAC
1 TTCAAAATAATATTAAAC
115807 CACATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (19 bp):
TTCAAAATAATATTAAACG
Found at i:128592 original size:79 final size:79
Alignment explanation
Indices: 128491--128858 Score: 393
Period size: 79 Copynumber: 4.7 Consensus size: 79
128481 TATTTTAGAG
* * *
128491 ATAAAATC-AGAGTTGAAGTATCCTTTCGAAAATAACGGGGTTGGAGTATCCCTGATTGTGAAAA
1 ATAAAATCGAG-GTTGGAGTATCCTTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAA
*
128555 GTTAATGTTTTGAAA
65 ATTAATGTTTTGAAA
* ** * * *
128570 ATTAAATCGAGGTTGGAGTATCCCCTCAAAAATAACGGGGTCGGAGTATGCCCGATTATGAAAAA
1 ATAAAATCGAGGTTGGAGTATCCTTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAA
* *
128635 TTAGTGTTTTAAAA
66 TTAATGTTTTGAAA
* *
128649 ATAAAA-CCAGGGTTGGAGTATCCTTTCGAAAATAACGGGGTTGAAGTATCCCCGATTATGAAAA
1 ATAAAATCGA-GGTTGGAGTATCCTTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAA
** *
128713 ATCGATATTTTGAAA
65 ATTAATGTTTTGAAA
* *** * * * * *
128728 ATAAAATCGGGGTCAAAGTATCCCTTTAG-AAATAACAGGGTTAGAGTATCCCCGTTTGTGAAAA
1 ATAAAATCGAGGTTGGAGTAT-CCTTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAA
* *
128792 ATTGATGTTTTGGAA
65 ATTAATGTTTTGAAA
* ** *
128807 ATAAAATCG-GGATGGAGTATCCCGTCGAAAATAATGGGGTTGGAGTATCCCC
1 ATAAAATCGAGGTTGGAGTATCCTTTCGAAAATAACGGGGTTGGAGTATCCCC
128859 ATGGAAATAA
Statistics
Matches: 235, Mismatches: 49, Indels: 11
0.80 0.17 0.04
Matches are distributed among these distances:
77 4 0.02
78 30 0.13
79 192 0.82
80 9 0.04
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (79 bp):
ATAAAATCGAGGTTGGAGTATCCTTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAA
TTAATGTTTTGAAA
Found at i:128681 original size:158 final size:158
Alignment explanation
Indices: 128491--128858 Score: 443
Period size: 158 Copynumber: 2.3 Consensus size: 158
128481 TATTTTAGAG
* * * * *
128491 ATAAAATCAGAGTTGAAGTATCCTTTCGAAAATAACGGGGTTGGAGTATCCCTGATTGTGAAAAG
1 ATAAAATCAGGGTTGGAGTATCCTTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAA
* * * *** * * *
128556 TTAATGTTTTGAAAATTAAATCGAGGTTGGAGTATCCCCTCAAAAATAACGGGGTCGGAGTATGC
66 TCAATATTTTGAAAATAAAATCGAGGTCAAAGTATCCCCTCAAAAATAACAGGGTCAGAGTATCC
128621 CCGATTATGAAAAATT-AGTGTTTTAAAA
131 CCGATTATGAAAAATTGA-TGTTTTAAAA
* *
128649 ATAAAACCAGGGTTGGAGTATCCTTTCGAAAATAACGGGGTTGAAGTATCCCCGATTATGAAAAA
1 ATAAAATCAGGGTTGGAGTATCCTTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAA
* * * * * *
128714 TCGATATTTTGAAAATAAAATCGGGGTCAAAGTATCCCTTTAGAAATAACAGGGTTAGAGTATCC
66 TCAATATTTTGAAAATAAAATCGAGGTCAAAGTATCCCCTCAAAAATAACAGGGTCAGAGTATCC
* * **
128779 CCGTTTGTGAAAAATTGATGTTTTGGAA
131 CCGATTATGAAAAATTGATGTTTTAAAA
* ** *
128807 ATAAAATC-GGGATGGAGTATCCCGTCGAAAATAATGGGGTTGGAGTATCCCC
1 ATAAAATCAGGGTTGGAGTATCCTTTCGAAAATAACGGGGTTGGAGTATCCCC
128859 ATGGAAATAA
Statistics
Matches: 177, Mismatches: 32, Indels: 3
0.83 0.15 0.01
Matches are distributed among these distances:
157 39 0.22
158 137 0.77
159 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (158 bp):
ATAAAATCAGGGTTGGAGTATCCTTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAA
TCAATATTTTGAAAATAAAATCGAGGTCAAAGTATCCCCTCAAAAATAACAGGGTCAGAGTATCC
CCGATTATGAAAAATTGATGTTTTAAAA
Found at i:128852 original size:28 final size:27
Alignment explanation
Indices: 128819--128885 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 27
128809 AAAATCGGGA
* *
128819 TGGAGTATCCCGTCGAAAATAATGGGGT
1 TGGAGTATCCCAT-GAAAATAATAGGGT
*
128847 TGGAGTATCCCCATGGAAATAATAGGGT
1 TGGAGTAT-CCCATGAAAATAATAGGGT
128875 TGGAGTATCCC
1 TGGAGTATCCC
128886 TGATCATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
27 3 0.09
28 28 0.80
29 4 0.11
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (27 bp):
TGGAGTATCCCATGAAAATAATAGGGT
Found at i:128866 original size:106 final size:106
Alignment explanation
Indices: 128756--128962 Score: 247
Period size: 106 Copynumber: 1.9 Consensus size: 106
128746 TATCCCTTTA
* ** * * *
128756 GAAATAACAGGGTTAGAGTATCCCCGTTTGTGAAAAAT-TGATGTTTTGGAAATAAAATCG-GGA
1 GAAATAACAGGGTTAGAGTATCCCCGATCATAAAAAATCAGA--TTTTGGAAATAAAACCGAGGA
* * * * *
128819 TGGAGTATCCCGTCGAAAATAATGGGGTTGGAGTATCCCCATG
64 TAGAGTAGCCCCTCGAAAATAACGAGGTTGGAGTATCCCCATG
* * *
128862 GAAATAATAGGGTTGGAGTATCCCTGATCATAAAAAATCAGCATTTTGGAAATAAAACCGAGGAT
1 GAAATAACAGGGTTAGAGTATCCCCGATCATAAAAAATCAG-ATTTTGGAAATAAAACCGAGGAT
128927 AGAGTAGCCCCTCGAAAATAACGAGGTTGGAGTATC
65 AGAGTAGCCCCTCGAAAATAACGAGGTTGGAGTATC
128963 TTCTCAAAAA
Statistics
Matches: 84, Mismatches: 14, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
106 47 0.56
107 36 0.43
108 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (106 bp):
GAAATAACAGGGTTAGAGTATCCCCGATCATAAAAAATCAGATTTTGGAAATAAAACCGAGGATA
GAGTAGCCCCTCGAAAATAACGAGGTTGGAGTATCCCCATG
Found at i:128959 original size:28 final size:28
Alignment explanation
Indices: 128928--128988 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
128918 ACCGAGGATA
* *
128928 GAGTAGCCCCTCGAAAATAACGAGGTTG
1 GAGTAGCCCCTCAAAAATAACAAGGTTG
* ** *
128956 GAGTATCTTCTCAAAAATAATAAGGTTG
1 GAGTAGCCCCTCAAAAATAACAAGGTTG
128984 GAGTA
1 GAGTA
128989 TCCTTGATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.25
Consensus pattern (28 bp):
GAGTAGCCCCTCAAAAATAACAAGGTTG
Found at i:129021 original size:107 final size:105
Alignment explanation
Indices: 128797--129027 Score: 266
Period size: 107 Copynumber: 2.2 Consensus size: 105
128787 GAAAAATTGA
* * * * * *
128797 TGTTTTGGAAATAAAATCGGGATGGAGTATCCCGTCGAAAATAATGGGGTTGGAGTATCCCCATG
1 TGTTTTGGAAATAAAACCGGGATAGAGTAGCCCCTCGAAAATAACGAGGTTGGAGTATCCCCA-G
* *
128862 GAAATAATAGGGTTGGAGTATCCCTGATCATAAAAAATCAG
65 AAAATAATAAGGTTGGAGTATCCCTGATCATAAAAAATCAG
** *
128903 CATTTTGGAAATAAAACCGAGGATAGAGTAGCCCCTCGAAAATAACGAGGTTGGAGTATCTTCTC
1 TGTTTTGGAAATAAAACCG-GGATAGAGTAGCCCCTCGAAAATAACGAGGTTGGAGTATC--CCC
* * * * *
128968 A-AAAATAATAAGGTTGGAGTATCCTTGATTATGACAAATCGG
63 AGAAAATAATAAGGTTGGAGTATCCCTGATCATAAAAAATCAG
*
129010 TGTTTTAGAAATAAAACC
1 TGTTTTGGAAATAAAACC
129028 AGGGTTACGA
Statistics
Matches: 103, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
106 16 0.16
107 84 0.82
109 3 0.03
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (105 bp):
TGTTTTGGAAATAAAACCGGGATAGAGTAGCCCCTCGAAAATAACGAGGTTGGAGTATCCCCAGA
AAATAATAAGGTTGGAGTATCCCTGATCATAAAAAATCAG
Found at i:132196 original size:61 final size:61
Alignment explanation
Indices: 132102--132737 Score: 828
Period size: 61 Copynumber: 10.4 Consensus size: 61
132092 AAAGGAAAGT
* * * *
132102 GTCCTGCTCTTTG-GAGACT-AGAAGGTGCCACCAACATGTGTGGGCTTTAAAAAGAAAAGAT
1 GTCCTACTCTTTGAG-GACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAC
* * ** * *
132163 GTCCCACTCTTTGATGACTGAAAGGTGCCACCAACTCATGTGGACTTTAAAAGGAAAAGGC
1 GTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAC
* * * *
132224 GTCTTGCTCTTTGAGGACTAAAAGGTGTCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAC
1 GTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAC
* *
132285 GTCCTACTCTTTGAGGGCTGAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGAAAAGAC
1 GTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAC
* * * *
132346 GTCCTACTCTTTGAGGGCTGAAAGGTGCCACCAACTCGTGTGGGATTTAAAAGGAAAAGAT
1 GTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAC
** * **
132407 GTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTCATGTGGGCTTTAAAAGGAGAAGGT
1 GTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAC
* * * *
132468 GCCCTACTCTTTAAGAACTGAAAGGTGCCACCAACTTGTGTGGGTTTTAAAAGGAAAAGAC
1 GTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAC
* * *
132529 GTCCTGCTCTTTGAGGACTGAAAGATACCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAC
1 GTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAC
* * * * * *
132590 ATCCTACTCTTTGGGGACTAAAAGGTGCCACCAACTTGTGTAGG-TTTTAAAGGAAAAGAAGT
1 GTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAG-A-C
* * *
132652 GTCCTACTCTTCGAGGACTAAAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGAC
1 GTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAC
* *
132713 ATCCTACTCTTTGAGGACTAAAAGG
1 GTCCTACTCTTTGAGGACTGAAAGG
132738 ATAAAAGGTT
Statistics
Matches: 503, Mismatches: 67, Indels: 10
0.87 0.12 0.02
Matches are distributed among these distances:
60 13 0.03
61 436 0.87
62 41 0.08
63 13 0.03
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (61 bp):
GTCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAC
Found at i:132303 original size:34 final size:34
Alignment explanation
Indices: 132265--132364 Score: 88
Period size: 34 Copynumber: 3.1 Consensus size: 34
132255 CAACTTGTGT
132265 GGGCTTTAAAAGGAAAAGACGTCCTACTCTTTGA
1 GGGCTTTAAAAGGAAAAGACGTCCTACTCTTTGA
* * ** * * *
132299 GGGC--TGAAAGG---TG-CCACCAACTC-GTGT
1 GGGCTTTAAAAGGAAAAGACGTCCTACTCTTTGA
132326 GGGCTTTAAAAGGAAAAGACGTCCTACTCTTTGA
1 GGGCTTTAAAAGGAAAAGACGTCCTACTCTTTGA
132360 GGGCT
1 GGGCT
132365 GAAAGGTGCC
Statistics
Matches: 45, Mismatches: 14, Indels: 14
0.62 0.19 0.19
Matches are distributed among these distances:
27 6 0.13
28 7 0.16
29 7 0.16
32 7 0.16
33 7 0.16
34 11 0.24
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (34 bp):
GGGCTTTAAAAGGAAAAGACGTCCTACTCTTTGA
Found at i:132357 original size:183 final size:185
Alignment explanation
Indices: 132043--132737 Score: 929
Period size: 183 Copynumber: 3.8 Consensus size: 185
132033 TGCGTCCTGT
* *
132043 TCTTTGAGGACAAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGGAAAGTGTCCTG
1 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGG-AAAA-G-AAGTGTCCTA
* * * *
132108 CTCTTTG-GAGACT-AGAAGGTGCCACCAACATGTGTGGGCTTTAAAAAGAAAAGATGTCCCACT
63 CTCTTTGAG-GACTGA-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCCTACT
* * * * *
132171 CTTTGATGACTGAAAGGTGCCACCAACTCATGTGGACTTTAAAAGGAAAAGGCGTCTTGC
126 CTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGACTTTAAAAGGAAAAGACGTCCTAC
* *
132231 TCTTTGAGGACTAAAAGGTGTCACCAACTTGTGTGGGCTTTAAAAGGAAAAG-A-CGTCCTACTC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAAGTGTCCTACTC
* *
132294 TTTGAGGGCTGAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGAAAAGACGTCCTACTCTTTG
66 TTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCCTACTCTTTG
* *
132359 AGGGCTGAAAGGTGCCACCAACTCGTGTGGGA-TTTAAAAGGAAAAGATGTCCTAC
131 AGGACTGAAAGGTGCCACCAACTCGTGT-GGACTTTAAAAGGAAAAGACGTCCTAC
* ** * *
132414 TCTTTGAGGACTGAAAGGTGCCACCAACTCATGTGGGCTTTAAAAGGAGAAG--GTGCCCTACTC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAAGTGTCCTACTC
* * * *
132477 TTTAAGAACTGAAAGGTGCCACCAACTTGTGTGGGTTTTAAAAGGAAAAGACGTCCTGCTCTTTG
66 TTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCCTACTCTTTG
* * * * *
132542 AGGACTGAAAGATACCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACATCCTAC
131 AGGACTGAAAGGTGCCACCAACTCGTGTGGACTTTAAAAGGAAAAGACGTCCTAC
* * *
132597 TCTTTGGGGACTAAAAGGTGCCACCAACTTGTGTAGG-TTTTAAAGGAAAAGAAGTGTCCTACTC
1 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAAGTGTCCTACTC
* * * *
132661 TTCGAGGACTAAAAGGTGCCACCAACTTGTATGGGCTTTAAAAGGAAAAGACATCCTACTCTTTG
66 TTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCCTACTCTTTG
*
132726 AGGACTAAAAGG
131 AGGACTGAAAGG
132738 ATAAAAGGTT
Statistics
Matches: 445, Mismatches: 55, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
182 14 0.03
183 298 0.67
184 83 0.19
186 1 0.00
187 4 0.01
188 45 0.10
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (185 bp):
TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGAAGTGTCCTACTC
TTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGACGTCCTACTCTTTG
AGGACTGAAAGGTGCCACCAACTCGTGTGGACTTTAAAAGGAAAAGACGTCCTAC
Found at i:139078 original size:20 final size:20
Alignment explanation
Indices: 139053--139129 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
139043 GTAAAAAGAC
139053 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
139073 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* *
139093 TA-CATGTATCGATATATTGA
1 -AGAATGTATCGATACATTGA
*
139113 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
139130 CTGGATAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:151986 original size:20 final size:20
Alignment explanation
Indices: 151963--152035 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
151953 ACAATTCAAA
151963 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
151983 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
152004 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
152024 GTATCGATACAT
1 GTATCGATACAT
152036 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:152007 original size:21 final size:21
Alignment explanation
Indices: 151981--152056 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
151971 ACATGTTGCA
151981 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
152002 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
152022 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
152043 ATGTATCAATACAT
1 ATGTATCGATACAT
152057 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:152014 original size:41 final size:41
Alignment explanation
Indices: 151963--152056 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
151953 ACAATTCAAA
*
151963 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
152004 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
152045 GTATCAATACAT
1 GTATCGATACAT
152057 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:152113 original size:13 final size:13
Alignment explanation
Indices: 152095--152120 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
152085 TACAGCAAGT
152095 ATGTATCGATACA
1 ATGTATCGATACA
152108 ATGTATCGATACA
1 ATGTATCGATACA
152121 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:156202 original size:15 final size:15
Alignment explanation
Indices: 156182--156212 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
156172 TAAAATTGTC
*
156182 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
156197 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
156212 C
1 C
156213 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:158310 original size:13 final size:13
Alignment explanation
Indices: 158292--158329 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
158282 CATTTTTATT
158292 TGTATCGATACAA
1 TGTATCGATACAA
*
158305 TGTATCGATACAC
1 TGTATCGATACAA
158318 TGTATCGATACA
1 TGTATCGATACA
158330 GGGTGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:160157 original size:31 final size:31
Alignment explanation
Indices: 160122--160182 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
160112 AATTTTGATA
160122 TGAATTACTTGATTAAGGGGGAGATTTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTTT
160153 TGAATTACTTGATTAAGGGGGAGATTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTT
160183 AATAAACGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.44
Consensus pattern (31 bp):
TGAATTACTTGATTAAGGGGGAGATTTTTTT
Found at i:160827 original size:20 final size:20
Alignment explanation
Indices: 160804--160876 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
160794 ACAATTCAAA
160804 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
160824 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
160845 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
160865 GTATCGATACAT
1 GTATCGATACAT
160877 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:160848 original size:21 final size:21
Alignment explanation
Indices: 160822--160897 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
160812 ACATGTTGCA
160822 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
160843 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
160863 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
160884 ATGTATCGATACAT
1 ATGTATCGATACAT
160898 TTCTTGGTAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:160855 original size:41 final size:41
Alignment explanation
Indices: 160804--160897 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
160794 ACAATTCAAA
*
160804 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
160845 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
160886 GTATCGATACAT
1 GTATCGATACAT
160898 TTCTTGGTAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:160954 original size:13 final size:13
Alignment explanation
Indices: 160936--160961 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
160926 TACAGCAAGT
160936 ATGTATCGATACA
1 ATGTATCGATACA
160949 ATGTATCGATACA
1 ATGTATCGATACA
160962 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:162059 original size:13 final size:13
Alignment explanation
Indices: 162041--162065 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
162031 CATAAAATGT
162041 TGTATCGATACAA
1 TGTATCGATACAA
162054 TGTATCGATACA
1 TGTATCGATACA
162066 TATTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:162063 original size:33 final size:34
Alignment explanation
Indices: 162021--162091 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
162011 TTCAACGATT
162021 TGTATCGATACATA-AAATGTTGTATCGATACAA
1 TGTATCGATACATATAAATGTTGTATCGATACAA
*** *
162054 TGTATCGATACATATTTTTTTTGTATCGATACAA
1 TGTATCGATACATATAAATGTTGTATCGATACAA
162088 TGTA
1 TGTA
162092 AGCTACTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 14 0.42
34 19 0.58
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (34 bp):
TGTATCGATACATATAAATGTTGTATCGATACAA
Found at i:162149 original size:13 final size:13
Alignment explanation
Indices: 162131--162155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
162121 ATTATTCACA
162131 TGTATCGATACAT
1 TGTATCGATACAT
162144 TGTATCGATACA
1 TGTATCGATACA
162156 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:168176 original size:156 final size:157
Alignment explanation
Indices: 167892--168243 Score: 451
Period size: 156 Copynumber: 2.2 Consensus size: 157
167882 GTTTTAAAGA
* *
167892 TATCGGGATACTTTCATATCAAAGGTATGCTCATAAGGGGCATTTAAGTAATTTTTTCTAGAGCC
1 TATCGGGATACTTTCATATCAAAGGTATACTCATAAGGGGCATTTAAGTAATTTTTTCTAAAGCC
* * * *
167957 GAGTCCTAATTAGTCACCGGGATACTTTTATGCCAAAGGTGTGCATATAGGATAAGGTTCTCTTT
66 GAGTCCTAAGTAGTCACCAGGAGACTTTTATGCCAAAGGTGTGCATATAAGATAAGGTTCTCTTT
* *
168022 CTTGTGATCTTTCCTTATCCTTTAAGGT
131 -TTATGATCTTTCCATATCCTTTAAGGT
* *
168050 TATCGGGATACTTTCATATCGAAGGTATACTCAT-AGGGGCATTTTAGTAA-TTTTTCTAAAGCC
1 TATCGGGATACTTTCATATCAAAGGTATACTCATAAGGGGCATTTAAGTAATTTTTTCTAAAGCC
* * *
168113 GAGTCCTAGGTAGTCACCAGGAGGCTTTTATGCCAAAGGTGTGCATTTAAGAT-AGGTTCCTCTT
66 GAGTCCTAAGTAGTCACCAGGAGACTTTTATGCCAAAGGTGTGCATATAAGATAAGGTT-CTCTT
* * *
168177 TTTATGATCTTTTCATGTCTTTTAAGGT
130 TTTATGATCTTTCCATATCCTTTAAGGT
* * * ** *
168205 TA-CTGAGATACTTTTATGTCAAACTTATACCCATAAGGG
1 TATC-GGGATACTTTCATATCAAAGGTATACTCATAAGGG
168244 TATTTTAGTA
Statistics
Matches: 168, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
154 1 0.01
155 52 0.31
156 68 0.40
157 15 0.09
158 32 0.19
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.37
Consensus pattern (157 bp):
TATCGGGATACTTTCATATCAAAGGTATACTCATAAGGGGCATTTAAGTAATTTTTTCTAAAGCC
GAGTCCTAAGTAGTCACCAGGAGACTTTTATGCCAAAGGTGTGCATATAAGATAAGGTTCTCTTT
TTATGATCTTTCCATATCCTTTAAGGT
Found at i:168273 original size:156 final size:156
Alignment explanation
Indices: 167892--168307 Score: 410
Period size: 155 Copynumber: 2.7 Consensus size: 156
167882 GTTTTAAAGA
* * * * * * * *
167892 TATCGGGATACTTTCATATCAAAGGTATGCTCATAAGGGGCATTTAAGTAATTTTTTCTAGAGCC
1 TATCGAGATACTTTCATATCAAACGTATACCCATAA-GGGCATTTTAGTAA-ATTTACTAAAGCC
* * * *
167957 GAGTCCTAATTAGTCACCGGGATACTTTTATGCCAAAGGTGTGCATATAGGATAAGGTTCTCTTT
64 GAGTCCTAGTTAGTCACCAGGATGCTTTTATGCCAAAGGTGTGCATATAAGATAAGGTTCTCTTT
* *
168022 CTTGTGATCTTTCCTTATCCTTTAAGGT
129 CTTATGATCTTTCCATATCCTTTAAGGT
* * * * * * *
168050 TATCGGGATACTTTCATATCGAAGGTATACTCATAGGGGCATTTTAGTAATTTTTCTAAAGCCGA
1 TATCGAGATACTTTCATATCAAACGTATACCCATAAGGGCATTTTAGTAAATTTACTAAAGCCGA
* * *
168115 GTCCTAGGTAGTCACCAGGAGGCTTTTATGCCAAAGGTGTGCATTTAAGAT-AGGTTCCTCTTT-
66 GTCCTAGTTAGTCACCAGGATGCTTTTATGCCAAAGGTGTGCATATAAGATAAGGTT-CTCTTTC
* * *
168178 TTATGATCTTTTCATGTCTTTTAAGGT
130 TTATGATCTTTCCATATCCTTTAAGGT
* * * * *
168205 TA-CTGAGATACTTTTATGTCAAACTTATACCCATAAGGGTATTTTAGTAAATTTACTTAGAA-T
1 TATC-GAGATACTTTCATATCAAACGTATACCCATAAGGGCATTTTAGTAAATTTAC-TA-AAGC
* * * * *
168268 TGAGTCTTAGTTAGTCATCA-GATGCTTTCAGGCCAAAGGT
63 CGAGTCCTAGTTAGTCACCAGGATGCTTTTATGCCAAAGGT
168308 ACATAATTAG
Statistics
Matches: 218, Mismatches: 36, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
154 1 0.00
155 87 0.40
156 82 0.38
157 15 0.07
158 33 0.15
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (156 bp):
TATCGAGATACTTTCATATCAAACGTATACCCATAAGGGCATTTTAGTAAATTTACTAAAGCCGA
GTCCTAGTTAGTCACCAGGATGCTTTTATGCCAAAGGTGTGCATATAAGATAAGGTTCTCTTTCT
TATGATCTTTCCATATCCTTTAAGGT
Found at i:168881 original size:18 final size:19
Alignment explanation
Indices: 168841--168881 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
168831 ATTTTTAAAA
* *
168841 AAATTAAAGTAATACTTTG
1 AAATTAAAATAATACTGTG
168860 -AATTAAAATAATAC-GTG
1 AAATTAAAATAATACTGTG
168877 AAATT
1 AAATT
168882 TCTCCCACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.34
Consensus pattern (19 bp):
AAATTAAAATAATACTGTG
Found at i:170216 original size:13 final size:13
Alignment explanation
Indices: 170198--170236 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
170188 CATTTTGGGA
*
170198 TGTATCAATACAT
1 TGTATCGATACAT
170211 TGTATCGATACAT
1 TGTATCGATACAT
170224 TGTATCGATACAT
1 TGTATCGATACAT
170237 AATGTGTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:170334 original size:20 final size:21
Alignment explanation
Indices: 170287--170341 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
170277 GCCAATGACC
**
170287 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
170308 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
170328 TGTATCGATACATT
1 TGTATCGATACATT
170342 GTATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:172338 original size:21 final size:21
Alignment explanation
Indices: 172307--172358 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
172297 GCTGCTAGTG
*
172307 TGGGGGCTGCCCGGTTGCGACC
1 TGGGGG-TGCCCGGTCGCGACC
172329 TGGGGGTG-CCGGTCGCGACC
1 TGGGGGTGCCCGGTCGCGACC
172349 TGGTGGGTGC
1 TGG-GGGTGC
172359 TGCCTAGGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 14 0.52
21 7 0.26
22 6 0.22
ACGTcount: A:0.04, C:0.27, G:0.50, T:0.19
Consensus pattern (21 bp):
TGGGGGTGCCCGGTCGCGACC
Found at i:177366 original size:9 final size:9
Alignment explanation
Indices: 177352--177382 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
177342 TCTGAGTTAC
*
177352 CATCATCAT
1 CATCATCTT
177361 CATCATCTT
1 CATCATCTT
177370 CATCATCTT
1 CATCATCTT
177379 CATC
1 CATC
177383 GTCCTTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.39
Consensus pattern (9 bp):
CATCATCTT
Found at i:179009 original size:13 final size:13
Alignment explanation
Indices: 178991--179016 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
178981 CATTGTGGGA
178991 TGTATCGATACAT
1 TGTATCGATACAT
179004 TGTATCGATACAT
1 TGTATCGATACAT
179017 AATGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:179013 original size:33 final size:32
Alignment explanation
Indices: 178971--179034 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
178961 TACAAGCCCA
**
178971 TGTATCGATACATTGTGGGATGTATCGATACAT
1 TGTATCGATACATAATGGG-TGTATCGATACAT
*
179004 TGTATCGATACATAATGTGTGTATCGATACA
1 TGTATCGATACATAATGGGTGTATCGATACA
179035 AATTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAATGGGTGTATCGATACAT
Found at i:179114 original size:20 final size:21
Alignment explanation
Indices: 179067--179121 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
179057 GCCAATGACC
**
179067 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
179088 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
179108 TGTATCGATACATT
1 TGTATCGATACATT
179122 GTATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:181146 original size:22 final size:23
Alignment explanation
Indices: 181101--181146 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
181091 ATTATTATGG
*
181101 TAAAAATATAACAAACTTGCTTA
1 TAAAAATATAACAAACTTGATTA
*
181124 TAAAAATATAGCAAACTT-ATTA
1 TAAAAATATAACAAACTTGATTA
181146 T
1 T
181147 TTATCTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.33
Consensus pattern (23 bp):
TAAAAATATAACAAACTTGATTA
Found at i:184586 original size:21 final size:22
Alignment explanation
Indices: 184548--184593 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
184538 ATCTGTTGAA
* **
184548 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
184569 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
184591 ACT
1 ACT
184594 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:194812 original size:22 final size:22
Alignment explanation
Indices: 194787--194855 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
194777 TTTGGGTCAT
194787 TTTGGATTAATCTTCGAATCTA
1 TTTGGATTAATCTTCGAATCTA
* ** *
194809 TTT-GAATAAT-TTTTAGGTC-A
1 TTTGGATTAATCTTCGA-ATCTA
194829 TTTTGGATTAATCTTCGAATCTA
1 -TTTGGATTAATCTTCGAATCTA
194852 TTTG
1 TTTG
194856 AGTTCAAATT
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
20 4 0.12
21 11 0.32
22 15 0.44
23 4 0.12
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.49
Consensus pattern (22 bp):
TTTGGATTAATCTTCGAATCTA
Found at i:194818 original size:43 final size:43
Alignment explanation
Indices: 194771--194856 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
194761 AAAATTATAC
*
194771 ATAATTTTTGGGTCATTTTGGATTAATCTTCGAATCTATTTGA
1 ATAATTTTTAGGTCATTTTGGATTAATCTTCGAATCTATTTGA
194814 ATAATTTTTAGGTCATTTTGGATTAATCTTCGAATCTATTTGA
1 ATAATTTTTAGGTCATTTTGGATTAATCTTCGAATCTATTTGA
194857 GTTCAAATTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.27, C:0.09, G:0.15, T:0.49
Consensus pattern (43 bp):
ATAATTTTTAGGTCATTTTGGATTAATCTTCGAATCTATTTGA
Found at i:198747 original size:8 final size:8
Alignment explanation
Indices: 198734--198765 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
198724 AGTGCAAAGC
198734 AAAAAAAT
1 AAAAAAAT
198742 AAAAAAAT
1 AAAAAAAT
198750 AAAAAAAAT
1 -AAAAAAAT
198759 AAAAAAA
1 AAAAAAA
198766 ATGAAACGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (8 bp):
AAAAAAAT
Found at i:198748 original size:9 final size:9
Alignment explanation
Indices: 198734--198767 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
198724 AGTGCAAAGC
198734 AAAAAAAT-
1 AAAAAAATA
198742 AAAAAAATA
1 AAAAAAATA
198751 AAAAAAATA
1 AAAAAAATA
198760 AAAAAAAT
1 AAAAAAAT
198768 GAAACGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAATA
Found at i:199152 original size:13 final size:14
Alignment explanation
Indices: 199136--199167 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
199126 TTAAAAATCA
199136 ATTTTATTTT-TTT
1 ATTTTATTTTATTT
199149 ATTTTATTTTATTT
1 ATTTTATTTTATTT
199163 -TTTTA
1 ATTTTA
199168 ATCTTTTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
ATTTTATTTTATTT
Found at i:199458 original size:13 final size:14
Alignment explanation
Indices: 199434--199463 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
199424 AAAATTTTTG
199434 AAAATAAAAATAAT
1 AAAATAAAAATAAT
199448 AAAAT-AAAATAAT
1 AAAATAAAAATAAT
199461 AAA
1 AAA
199464 TAGATTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAATAAAAATAAT
Found at i:200980 original size:21 final size:21
Alignment explanation
Indices: 200954--200995 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
200944 TAATTAAATT
200954 TTCATATAACACAAATCATGA
1 TTCATATAACACAAATCATGA
* *
200975 TTCATATAAGACGAATCATGA
1 TTCATATAACACAAATCATGA
200996 CAATAGTATT
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:0.45, C:0.17, G:0.10, T:0.29
Consensus pattern (21 bp):
TTCATATAACACAAATCATGA
Found at i:202711 original size:13 final size:13
Alignment explanation
Indices: 202693--202717 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
202683 CATTTTATGG
202693 TGTATCGATACAA
1 TGTATCGATACAA
202706 TGTATCGATACA
1 TGTATCGATACA
202718 TACTATGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:202733 original size:32 final size:33
Alignment explanation
Indices: 202670--202737 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
202660 CGTTACAAGC
* **
202670 CAATGTATTGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
202703 CAATGTATCGATACATACTAT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
202735 CAA
1 CAA
202738 GTTTAGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:202833 original size:20 final size:20
Alignment explanation
Indices: 202791--202840 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
202781 TCTTTTTCAA
*
202791 GTATCGATACAATGCAACAT
1 GTATCGATACAATGAAACAT
* **
202811 GTATCGATACAATTAAATGT
1 GTATCGATACAATGAAACAT
202831 GTATCGATAC
1 GTATCGATAC
202841 TTTTCAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACAATGAAACAT
Found at i:210656 original size:13 final size:13
Alignment explanation
Indices: 210638--210662 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
210628 CATTTTATGG
210638 TGTATCGATACAA
1 TGTATCGATACAA
210651 TGTATCGATACA
1 TGTATCGATACA
210663 TACTATGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Done.