Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 60 of 290
Found at i:18476471 original size:11 final size:11
Alignment explanation
Indices: 18476455--18476493 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
18476445 CCAGCCCAGC
18476455 AGAAAAAAAAG
1 AGAAAAAAAAG
*
18476466 AGAAAAAAAAA
1 AGAAAAAAAAG
*
18476477 AG-AAAAAGAG
1 AGAAAAAAAAG
18476487 AGAAAAA
1 AGAAAAA
18476494 GAAAAAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAG
Found at i:18476473 original size:10 final size:9
Alignment explanation
Indices: 18476455--18476510 Score: 60
Period size: 10 Copynumber: 5.9 Consensus size: 9
18476445 CCAGCCCAGC
18476455 AGAAAAAAA
1 AGAAAAAAA
18476464 AGAGAAAAAA
1 AGA-AAAAAA
18476474 A-AAAGAAAA
1 AGAAA-AAAA
*
18476483 AGAGAGAAAA
1 AGA-AAAAAA
18476493 AGAAAAAACA
1 AGAAAAAA-A
18476503 AGAAAAAA
1 AGAAAAAA
18476511 GGGGTTCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 2 0.05
9 13 0.32
10 24 0.60
11 1 0.03
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:18476488 original size:21 final size:22
Alignment explanation
Indices: 18476458--18476499 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
18476448 GCCCAGCAGA
18476458 AAAAAAAGAGAAAAA-AAAAAG
1 AAAAAAAGAGAAAAAGAAAAAG
*
18476479 AAAAAGAGAGAAAAAGAAAAA
1 AAAAAAAGAGAAAAAGAAAAA
18476500 ACAAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAAAAGAGAAAAAGAAAAAG
Found at i:18476506 original size:16 final size:16
Alignment explanation
Indices: 18476455--18476509 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
18476445 CCAGCCCAGC
*
18476455 AGAAAAA-AAAGAGAAA
1 AGAAAAAGAAAAAG-AA
* *
18476471 AAAAAAAGAAAAAGAG
1 AGAAAAAGAAAAAGAA
18476487 AGAAAAAGAAAAA-ACA
1 AGAAAAAGAAAAAGA-A
18476503 AGAAAAA
1 AGAAAAA
18476510 AGGGGTTCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 1 0.03
16 26 0.81
17 5 0.16
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (16 bp):
AGAAAAAGAAAAAGAA
Found at i:18476893 original size:21 final size:20
Alignment explanation
Indices: 18476861--18476902 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
18476851 TCGCGTTTCG
18476861 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTCAAAA
*
18476881 AAATTTCTCGTGTTTTCAAAA
1 AAATTT-TCGTGTCTTCAAAA
18476902 A
1 A
18476903 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
AAATTTTCGTGTCTTCAAAA
Found at i:18476903 original size:19 final size:19
Alignment explanation
Indices: 18476861--18476902 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
18476851 TCGCGTTTCG
18476861 AAATTTTCGTGTCTTCAAAA
1 AAATTTTCGTGTCTTC-AAA
*
18476881 AAATTTCTCGTGTTTTCAAA
1 AAATTT-TCGTGTCTTCAAA
18476901 AA
1 AA
18476903 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (19 bp):
AAATTTTCGTGTCTTCAAA
Found at i:18477074 original size:38 final size:38
Alignment explanation
Indices: 18477008--18477095 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 38
18476998 AAAAATCAGA
*
18477008 AAAATTTTCGTG---TTTTCAAAAAATTCCATTTTTC-
1 AAAATTTTCGTGTTTTTTTCAAAAAATTCCATATTTCT
*
18477042 AAAATTTTTCGTGTTTTTTTTAAAAAATTCCATATTTCT
1 AAAA-TTTTCGTGTTTTTTTCAAAAAATTCCATATTTCT
18477081 AAAATTTTCGTGTTT
1 AAAATTTTCGTGTTT
18477096 AAAAAATTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
34 4 0.09
35 8 0.17
38 31 0.66
39 4 0.09
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (38 bp):
AAAATTTTCGTGTTTTTTTCAAAAAATTCCATATTTCT
Found at i:18477240 original size:34 final size:35
Alignment explanation
Indices: 18477007--18477352 Score: 201
Period size: 35 Copynumber: 9.7 Consensus size: 35
18476997 GAAAAATCAG
*
18477007 AAAAATTTTCGTGTTTTCAAAAAATTC-CATTTTTC
1 AAAAATTTTCGTGTTTTC-AAAAATTCTCATGTTTC
* * *
18477042 AAAATTTTTCGTGTTTTTTTTAAAAAATTC-CATATTTC
1 AAAAATTTTCGTG----TTTTCAAAAATTCTCATGTTTC
* *
18477080 TAAAATTTTCGTG-TTTAAAAAATT-TCGTAT-TTTC
1 AAAAATTTTCGTGTTTTCAAAAATTCTC--ATGTTTC
* ** * * *
18477114 AAAATTTTTTATTTTTTTCAACAATTCTCGTGTTTC
1 AAAA-ATTTTCGTGTTTTCAAAAATTCTCATGTTTC
* * * * * * *
18477150 ACAAATTCTCGTATTTT-AAAATTTTTTATGTTTTA
1 AAAAATTTTCGTGTTTTCAAAAATTCTCATG-TTTC
* *
18477185 AAAAATAAATTTC-TCGTGTTTCAAAAATTGTCATGTTTT
1 AAAAAT---TTTCGT-GT-TTTCAAAAATTCTCATGTTTC
* * * *
18477224 AAAAATTTTCATG-TTTCTAAAATGT-TCGTATTTC
1 AAAAATTTTCGTGTTTTCAAAAAT-TCTCATGTTTC
**
18477258 AAAAAATCCTCGTGTTTTCAAAAATTCTCATGTTTC
1 -AAAAATTTTCGTGTTTTCAAAAATTCTCATGTTTC
*
18477294 AAAAATCTTCGTGTTTTC-AAAATTCT-AGTGTTTC
1 AAAAATTTTCGTGTTTTCAAAAATTCTCA-TGTTTC
*
18477328 AAAAATTTTCATGTTTTCAAAAATT
1 AAAAATTTTCGTGTTTTCAAAAATT
18477353 TCCCCTGTTT
Statistics
Matches: 241, Mismatches: 45, Indels: 50
0.72 0.13 0.15
Matches are distributed among these distances:
33 13 0.05
34 60 0.25
35 71 0.29
36 37 0.15
37 4 0.02
38 30 0.12
39 16 0.07
40 10 0.04
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.48
Consensus pattern (35 bp):
AAAAATTTTCGTGTTTTCAAAAATTCTCATGTTTC
Found at i:18477308 original size:161 final size:160
Alignment explanation
Indices: 18477059--18477351 Score: 358
Period size: 161 Copynumber: 1.8 Consensus size: 160
18477049 TTCGTGTTTT
* * * * * *
18477059 TTTTAAAAAATTCCATATTTCTAAAATTTTCGTGTTTAAAAAATTTCGTATTTTCAAAATTTTTT
1 TTTTAAAAAATTCCATATTTCTAAAATGTTCGTATTTAAAAAATCTCGTATTTTCAAAAATTCTC
* * * * * *
18477124 ATTTTTTTCAACAATTCTCGTG-TTTCACAAATTCTCGTATTTTAAAATTTTTTATGTTTTAAAA
66 A-TTGTTTCAAAAATTCTCGTGTTTTCA-AAATTCTAGTATTTCAAAAATTTTCATGTTTTAAAA
18477188 AATAAATTTCTCGTGTTTCAAAAATTGTCATG
129 AATAAATTTCTCGTGTTTCAAAAATTGTCATG
* * * *
18477220 TTTTAAAAATTTTCATGTTTCTAAAATGTTCGTATTTCAAAAAATCCTCGTGTTTTCAAAAATTC
1 TTTTAAAAAATTCCATATTTCTAAAATGTTCGTATTT-AAAAAAT-CTCGTATTTTCAAAAATTC
* *
18477285 TCA-TGTTTCAAAAA-TCTTCGTGTTTTCAAAATTCTAGTGTTTCAAAAATTTTCATGTTTTCAA
64 TCATTGTTTCAAAAATTC-TCGTGTTTTCAAAATTCTAGTATTTCAAAAATTTTCATGTTTTAAA
18477348 AAAT
128 AAAT
18477352 TTCCCCTGTT
Statistics
Matches: 110, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
160 2 0.02
161 79 0.72
162 12 0.11
163 17 0.15
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (160 bp):
TTTTAAAAAATTCCATATTTCTAAAATGTTCGTATTTAAAAAATCTCGTATTTTCAAAAATTCTC
ATTGTTTCAAAAATTCTCGTGTTTTCAAAATTCTAGTATTTCAAAAATTTTCATGTTTTAAAAAA
TAAATTTCTCGTGTTTCAAAAATTGTCATG
Found at i:18477329 original size:16 final size:16
Alignment explanation
Indices: 18477273--18477331 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 16
18477263 ATCCTCGTGT
18477273 TTTCAAAAATTCTCA-TG
1 TTTC-AAAATTCT-AGTG
* *
18477290 TTTCAAAAATCTTCGTG
1 TTTCAAAATTC-TAGTG
18477307 TTTTCAAAATTCTAGTG
1 -TTTCAAAATTCTAGTG
18477324 TTTCAAAA
1 TTTCAAAA
18477332 ATTTTCATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 14 0.40
17 11 0.31
18 10 0.29
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (16 bp):
TTTCAAAATTCTAGTG
Found at i:18477353 original size:18 final size:18
Alignment explanation
Indices: 18477007--18477368 Score: 151
Period size: 17 Copynumber: 20.2 Consensus size: 18
18476997 GAAAAATCAG
*
18477007 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCATGTTTTC
* *
18477025 AAAAAATTCCAT-TTTTC
1 AAAAATTTTCATGTTTTC
* * *
18477042 AAAATTTTTCGTGTTTTTTTT
1 AAAAATTTTCATG---TTTTC
* * *
18477063 AAAAAATTCCAT-ATTTC
1 AAAAATTTTCATGTTTTC
* *
18477080 TAAAATTTTCGTG-TTT-
1 AAAAATTTTCATGTTTTC
* * *
18477096 AAAAAATTTCGTATTTTC
1 AAAAATTTTCATGTTTTC
* * *
18477114 AAAATTTTTTATTTTTTTC
1 AAAAATTTTCA-TGTTTTC
* * *
18477133 AACAATTCTCGTG-TTTC
1 AAAAATTTTCATGTTTTC
* * * *
18477150 ACAAATTCTCGTATTTT-
1 AAAAATTTTCATGTTTTC
* * *
18477167 AAAATTTTTTATGTTTTA
1 AAAAATTTTCATGTTTTC
18477185 AAAAATAAATTTC-TCGTGTTTC
1 AAAAAT---TTTCAT-GT-TTTC
*
18477207 AAAAATTGTCATGTTTT-
1 AAAAATTTTCATGTTTTC
18477224 AAAAATTTTCATG-TTTC
1 AAAAATTTTCATGTTTTC
* *
18477241 TAAAATGTTC--GTATTTC
1 AAAAATTTTCATGT-TTTC
** *
18477258 AAAAAATCCTCGTGTTTTC
1 -AAAAATTTTCATGTTTTC
*
18477277 AAAAATTCTCATG-TTTC
1 AAAAATTTTCATGTTTTC
* *
18477294 AAAAATCTTCGTGTTTTC
1 AAAAATTTTCATGTTTTC
*
18477312 -AAAATTCT-A-GTGTTTC
1 AAAAATTTTCATGT-TTTC
18477328 AAAAATTTTCATGTTTTC
1 AAAAATTTTCATGTTTTC
* *
18477346 AAAAATTTCCCCTGTTTTC
1 AAAAATTT-TCATGTTTTC
18477365 AAAA
1 AAAA
18477369 TTCTCGTATT
Statistics
Matches: 254, Mismatches: 62, Indels: 55
0.68 0.17 0.15
Matches are distributed among these distances:
15 3 0.01
16 17 0.07
17 106 0.42
18 63 0.25
19 35 0.14
20 4 0.02
21 17 0.07
22 9 0.04
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.47
Consensus pattern (18 bp):
AAAAATTTTCATGTTTTC
Found at i:18477390 original size:53 final size:52
Alignment explanation
Indices: 18477098--18477404 Score: 180
Period size: 53 Copynumber: 5.8 Consensus size: 52
18477088 TCGTGTTTAA
* * * * *
18477098 AAAATT-TCGTATTTTCAAAATTTTTTATTTTTTTCAACAAT-TCTCGTG-TTTC
1 AAAATTCTCGTA-TTTCAAAAATTTTCA-TGTTTTCAAAAATAT-TCCTGTTTTC
* * * * *
18477150 ACAAATTCTCGTATTTTAAAATTTTTTATGTTTTAAAAAATAAATTTCTCGTGTTTC
1 A-AAATTCTCGTATTTCAAAAATTTTCATGTTTTCAAAAAT--ATTCCT-GT-TTTC
* * * * * *
18477207 AAAAATTGTCATGTTTTAAAAATTTTCATG-TTTCTAAAATGTT-C-GTATTTC
1 -AAAATTCTCGTATTTCAAAAATTTTCATGTTTTCAAAAATATTCCTGT-TTTC
* * * * *
18477258 AAAAAATCCTCGTGTTTTCAAAAATTCTCATG-TTTCAAAAATCTTCGTGTTTTC
1 --AAAATTCTCGT-ATTTCAAAAATTTTCATGTTTTCAAAAATATTCCTGTTTTC
* *
18477312 AAAATTCTAGTGTTTCAAAAATTTTCATGTTTTCAAAAAT-TTCCCCTGTTTTC
1 AAAATTCTCGTATTTCAAAAATTTTCATGTTTTCAAAAATATT--CCTGTTTTC
* * *
18477365 AAAATTCTCGTATTTCAAAATTTTTCTTTTTTTTCAAAAA
1 AAAATTCTCGTATTTCAAAAATTTTC-ATGTTTTCAAAAA
18477405 AAAACTTCCG
Statistics
Matches: 204, Mismatches: 34, Indels: 32
0.76 0.13 0.12
Matches are distributed among these distances:
51 24 0.12
52 39 0.19
53 77 0.38
54 24 0.12
55 4 0.02
56 8 0.04
57 27 0.13
58 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.48
Consensus pattern (52 bp):
AAAATTCTCGTATTTCAAAAATTTTCATGTTTTCAAAAATATTCCTGTTTTC
Found at i:18477458 original size:18 final size:18
Alignment explanation
Indices: 18477435--18477482 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
18477425 ATCTCCGTGT
18477435 TTTCAAAAAATTCTCG-AC
1 TTTCAAAAAATT-TCGTAC
**
18477453 TTTCAAAAAATTTCGTGT
1 TTTCAAAAAATTTCGTAC
18477471 TTTCAAAAAATT
1 TTTCAAAAAATT
18477483 GACATTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 3 0.11
18 24 0.89
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (18 bp):
TTTCAAAAAATTTCGTAC
Found at i:18477478 original size:17 final size:17
Alignment explanation
Indices: 18477198--18477479 Score: 118
Period size: 17 Copynumber: 15.9 Consensus size: 17
18477188 AATAAATTTC
18477198 TCGTG-TTTCAAAAATT
1 TCGTGTTTTCAAAAATT
*
18477214 GTCATGTTTT-AAAAATTT
1 -TCGTGTTTTCAAAAA-TT
* *
18477232 TCATG-TTTCTAAAATGT
1 TCGTGTTTTCAAAAAT-T
* *
18477249 TCGT-ATTTCAAAAAATCC
1 TCGTGTTTTC-AAAAAT-T
18477267 TCGTGTTTTCAAAAATT
1 TCGTGTTTTCAAAAATT
*
18477284 CTCATG-TTTCAAAAATCT
1 -TCGTGTTTTCAAAAAT-T
18477302 TCGTGTTTTC-AAAATT
1 TCGTGTTTTCAAAAATT
*
18477318 CTAGTG-TTTCAAAAATTT
1 -TCGTGTTTTCAAAAA-TT
*
18477336 TCATGTTTTCAAAAATT
1 TCGTGTTTTCAAAAATT
*
18477353 TCCCCTGTTTTC-AAAATT
1 T--CGTGTTTTCAAAAATT
* *
18477371 CTCGT-ATTTCAAAATTTT
1 -TCGTGTTTTCAAAA-ATT
* *
18477389 TCTTTTTTTTCAAAAAAAAACTT
1 TC-GTGTTTTC----AAAAA-TT
* *
18477412 CCGTGTTTT-ATAAATCT
1 TCGTGTTTTCAAAAAT-T
*
18477429 CCGTGTTTTCAAAAAATT
1 TCGTGTTTTC-AAAAATT
**
18477447 CTCG-ACTTTCAAAAAATT
1 -TCGTGTTTTC-AAAAATT
18477465 TCGTGTTTTCAAAAA
1 TCGTGTTTTCAAAAA
18477480 ATTGACATTG
Statistics
Matches: 204, Mismatches: 30, Indels: 62
0.69 0.10 0.21
Matches are distributed among these distances:
16 14 0.07
17 88 0.43
18 66 0.32
19 24 0.12
22 5 0.02
23 7 0.03
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.44
Consensus pattern (17 bp):
TCGTGTTTTCAAAAATT
Found at i:18477572 original size:19 final size:19
Alignment explanation
Indices: 18477548--18477622 Score: 96
Period size: 19 Copynumber: 3.8 Consensus size: 19
18477538 ATCAAAATTT
18477548 TTGTGTTTTCAAAATAAAA
1 TTGTGTTTTCAAAATAAAA
*
18477567 TTGTGTTTTAAAAATAAAA
1 TTGTGTTTTCAAAATAAAA
*
18477586 TTCGTGTTTTCAAAAAAAAA
1 TT-GTGTTTTCAAAATAAAA
*
18477606 TTCTCGTGTTTCAAAAT
1 TTGT-GT-TTTCAAAAT
18477623 TTTCGTGTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 21 0.44
20 19 0.40
21 8 0.17
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (19 bp):
TTGTGTTTTCAAAATAAAA
Found at i:18477621 original size:18 final size:17
Alignment explanation
Indices: 18477600--18477723 Score: 60
Period size: 17 Copynumber: 7.1 Consensus size: 17
18477590 TGTTTTCAAA
18477600 AAAAAATTCTCGTGTTTC
1 AAAAAATT-TCGTGTTTC
* *
18477618 -AAAATTTTCGTGTTTTTTT
1 AAAAAATTTCGTG---TTTC
*
18477637 AAAAAAATTCGTGTTTC
1 AAAAAATTTCGTGTTTC
* * * *
18477654 -TAAAATTCTTGTATTTT
1 AAAAAATT-TCGTGTTTC
*
18477671 AAAATATTTCGTGTTTC
1 AAAAAATTTCGTGTTTC
*
18477688 GAAAAAAGGTT-GTGTTTC
1 -AAAAAA-TTTCGTGTTTC
18477706 --AAAATTCTCGTGTTTC
1 AAAAAATT-TCGTGTTTC
18477722 AA
1 AA
18477724 TTGGATCACG
Statistics
Matches: 76, Mismatches: 18, Indels: 24
0.64 0.15 0.20
Matches are distributed among these distances:
14 1 0.01
15 5 0.07
16 17 0.22
17 21 0.28
18 17 0.22
19 5 0.07
20 10 0.13
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (17 bp):
AAAAAATTTCGTGTTTC
Found at i:18477621 original size:20 final size:19
Alignment explanation
Indices: 18477496--18477621 Score: 60
Period size: 20 Copynumber: 5.9 Consensus size: 19
18477486 ATTGTTTCAT
18477496 AAATTTCCGTGTTTCAAAAA
1 AAATTT-CGTGTTTCAAAAA
18477516 AAATCCTT-GTGTTTCATAATTTATCA
1 AAAT--TTCGTGTTTCA-AA---A--A
*
18477542 AAATTTTTGTGTTTTCAAAATA
1 AAA-TTTCGTG-TTTCAAAA-A
*
18477564 AAA-TT-GTGTTTTAAAAA
1 AAATTTCGTGTTTCAAAAA
*
18477581 TAAAATTCGTGTTTTCAAAAAA
1 -AAATTTCGTG-TTTC-AAAAA
18477603 AAATTCTCGTGTTTCAAAA
1 AAATT-TCGTGTTTCAAAA
18477622 TTTTCGTGTT
Statistics
Matches: 85, Mismatches: 4, Indels: 34
0.69 0.03 0.28
Matches are distributed among these distances:
17 1 0.01
18 10 0.12
19 5 0.06
20 21 0.25
21 13 0.15
22 16 0.19
23 1 0.01
24 1 0.01
25 2 0.02
26 9 0.11
27 6 0.07
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (19 bp):
AAATTTCGTGTTTCAAAAA
Found at i:18477623 original size:16 final size:16
Alignment explanation
Indices: 18477602--18477723 Score: 57
Period size: 16 Copynumber: 7.1 Consensus size: 16
18477592 TTTTCAAAAA
18477602 AAAATTCTCGTGTTTC
1 AAAATTCTCGTGTTTC
* *
18477618 AAAATTTTCGTGTTTTTTTAA
1 AAAATTCTCGTG----TTT-C
*
18477639 AAAAAT-TCGTGTTTC
1 AAAATTCTCGTGTTTC
* * *
18477654 TAAAATTCTTGTATTTT
1 -AAAATTCTCGTGTTTC
*
18477671 AAAATATTTCGTGTTTC
1 AAAAT-TCTCGTGTTTC
*** *
18477688 GAAAAAAGGTTGTGTTTC
1 --AAAATTCTCGTGTTTC
18477706 AAAATTCTCGTGTTTC
1 AAAATTCTCGTGTTTC
18477722 AA
1 AA
18477724 TTGGATCACG
Statistics
Matches: 76, Mismatches: 20, Indels: 20
0.66 0.17 0.17
Matches are distributed among these distances:
16 38 0.50
17 13 0.17
18 8 0.11
19 4 0.05
20 8 0.11
21 5 0.07
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.46
Consensus pattern (16 bp):
AAAATTCTCGTGTTTC
Found at i:18486760 original size:20 final size:20
Alignment explanation
Indices: 18486735--18486773 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
18486725 CAGAATAGAA
18486735 TCCGAGTCATCAAAAGAGAG
1 TCCGAGTCATCAAAAGAGAG
18486755 TCCGAGTCATCAAAAGAGA
1 TCCGAGTCATCAAAAGAGA
18486774 AGTCATGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (20 bp):
TCCGAGTCATCAAAAGAGAG
Found at i:18489678 original size:122 final size:122
Alignment explanation
Indices: 18489460--18489686 Score: 296
Period size: 122 Copynumber: 1.9 Consensus size: 122
18489450 ATTTTAAAAA
* ** * * *
18489460 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTTTAT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCCGAGGTATTTTAAATTTAT
* ** *
18489525 GTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
66 GTTTAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
* **
18489582 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGTTGAGGTATTTTAAATTT-T
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCCGAGGTATTTTAAATTTAT
*
18489646 -TTTAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
66 GTTT--AAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCT
18489687 CGGGGCACGC
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
120 3 0.03
121 1 0.01
122 85 0.96
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (122 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCCGAGGTATTTTAAATTTAT
GTTTAAAATCAACTCATATTGCGAGAAGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:18489967 original size:194 final size:194
Alignment explanation
Indices: 18489390--18490194 Score: 1412
Period size: 191 Copynumber: 4.2 Consensus size: 194
18489380 CTTTCCAAGG
18489390 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAA--TT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
* *
18489453 TTAAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT
66 TTTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTT
18489518 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
*
18489582 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGTTGAGGTA-TTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
18489646 TTT--AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTT
66 TTTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTT
18489709 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
18489773 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
*
18489838 TTTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATGTTT
66 TTTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTT
*
18489903 AGTTTATGTTTTAAATTGACTCATGTTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
131 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
** *
18489967 AAAATCAACTCATATTGCGAGAAATGAGTTGAG-CTCATCACATGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
* * *
18490031 TTTAAAAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTT
66 TTTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTT
18490096 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAA--CTTTTAA-TTTTGTTTTTC
131 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
* **
18490157 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC
1 -AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
18490195 GAGCTCACAT
Statistics
Matches: 589, Mismatches: 17, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
190 11 0.02
191 219 0.37
192 69 0.12
193 135 0.23
194 155 0.26
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (194 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
TTTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTT
AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC
Found at i:18490145 original size:385 final size:382
Alignment explanation
Indices: 18489390--18490194 Score: 1427
Period size: 385 Copynumber: 2.1 Consensus size: 382
18489380 CTTTCCAAGG
18489390 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
*
18489455 AAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAG
66 AAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTTAG
18489520 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAA
131 TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAA
*
18489585 ATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGTTGAGGTATTTTAAATTTTTTTA
196 ATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAACACATGTTGAGGTATTTTAAATTTTTTTA
*
18489650 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTTAGTTTA
261 AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTTAGTTTA
18489715 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC-
326 TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAA-CCTTTTAA-TTTTGTTTTTCA
18489773 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAA--TT
* *
18489838 TTTAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATGTTT
64 TTAAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTT
*
18489903 AGTTTATGTTTTAAATTGACTCATGTTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCA
129 AGTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCA
*
18489968 AAATCAACTCATATTGCGAGAAATGAGTTGAG-CTCATCACATGTTGAGGTATTTTTAAATTTTT
194 AAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAACACATGTTGAGGTA-TTTTAAATTTTT
*
18490032 TTAAAAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTA
258 TT-AAAAAA-TCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTTA
18490097 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAA-CTTTTAATTTTGTTTTTCA
321 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAACCTTTTAATTTTGTTTTTCA
* **
18490158 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
18490195 GAGCTCACAT
Statistics
Matches: 405, Mismatches: 11, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
383 61 0.15
384 28 0.07
385 215 0.53
386 6 0.01
387 95 0.23
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (382 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
AAAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTTAG
TTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCAAA
ATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAACACATGTTGAGGTATTTTAAATTTTTTTA
AAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTATGTTTAGTTTA
TGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAACCTTTTAATTTTGTTTTTCA
Found at i:18490234 original size:15 final size:16
Alignment explanation
Indices: 18490214--18490246 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
18490204 TGCTGAGGTA
*
18490214 TTTTCAATTTATG-TT
1 TTTTCAATCTATGCTT
18490229 TTTTCAATCTATGCTT
1 TTTTCAATCTATGCTT
18490245 TT
1 TT
18490247 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (16 bp):
TTTTCAATCTATGCTT
Found at i:18490410 original size:85 final size:88
Alignment explanation
Indices: 18490152--18490410 Score: 300
Period size: 91 Copynumber: 2.9 Consensus size: 88
18490142 TTAATTTTGT
*
18490152 TTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GAGCTCACATGCTGAGGTATT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAG-GC-CACACGCTGAGGTATT
* *
18490216 TTCAATTTATGTTTTTTCAA-TCTATGC
63 TTCAATTTCTGATTTTT-AATTCTA-GC
* *
18490243 TTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGG---CACGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGCCACACGCTGAGGTATTT
* *
18490305 TCAATTTCTGCTTTACTAATTCTA-C
64 TCAATTTCTGATTT-TTAATTCTAGC
* *
18490330 TTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACACGCTGAGGTCTTTTC
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
*
18490394 AAATTCT-ATTTTTAATT
66 AATTTCTGATTTTTAATT
18490411 TCAATTTCTG
Statistics
Matches: 148, Mismatches: 13, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
84 3 0.02
85 38 0.26
86 3 0.02
87 28 0.19
88 28 0.19
89 5 0.03
91 41 0.28
92 1 0.01
93 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (88 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACACGCTGAGGTATTTTC
AATTTCTGATTTTTAATTCTAGC
Found at i:18490498 original size:53 final size:54
Alignment explanation
Indices: 18490429--18490572 Score: 194
Period size: 53 Copynumber: 2.7 Consensus size: 54
18490419 TGTGTTTCAA
*
18490429 AAAAAAATCAA-T-ATATTGCGAGAGGTGAGTTGAGCCTTTT-TTTCTATTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTCTATTTTC
*
18490480 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG-CTTTTGCAAATTCTGTTTTC
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTT---AATTCTATTTTC
18490536 ---AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
1 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
18490573 GGCTCACGTG
Statistics
Matches: 84, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
51 11 0.13
52 6 0.07
53 55 0.65
54 3 0.04
56 9 0.11
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (54 bp):
AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTCTATTTTC
Found at i:18490879 original size:30 final size:31
Alignment explanation
Indices: 18490845--18490946 Score: 113
Period size: 30 Copynumber: 3.4 Consensus size: 31
18490835 TAAAAAATAG
*
18490845 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* * *
18490875 AAATTTCATTTTAACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
18490905 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
18490935 AAATTTCATTTT
1 AAATTTCATTTT
18490947 AATCCTAAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 4 0.07
30 55 0.92
31 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:18490909 original size:60 final size:59
Alignment explanation
Indices: 18490845--18490961 Score: 155
Period size: 60 Copynumber: 2.0 Consensus size: 59
18490835 TAAAAAATAG
* *
18490845 AAATTGCATTTTGACCCCTAAACTTTTC-CTAAATTTCATTTTAACCCTTAAACTTTCTTT
1 AAATTGCACTTAGACCCCTAAAC-TTTCACTAAATTTCATTTTAACCC-TAAACTTTCTTT
* * * *
18490905 AAATTTCACTTAGACCCCTAAACTTTCATTAAATTTCATTTTAATCCTAAATTTTCT
1 AAATTGCACTTAGACCCCTAAACTTTCACTAAATTTCATTTTAACCCTAAACTTTCT
18490962 AAAAATTACA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
59 13 0.26
60 37 0.74
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (59 bp):
AAATTGCACTTAGACCCCTAAACTTTCACTAAATTTCATTTTAACCCTAAACTTTCTTT
Found at i:18491354 original size:14 final size:14
Alignment explanation
Indices: 18491335--18491393 Score: 68
Period size: 14 Copynumber: 4.1 Consensus size: 14
18491325 GAAGAAGAAG
18491335 AAAAGAAAGAAAAA
1 AAAAGAAAGAAAAA
18491349 AAAAGAAA-AAAGAA
1 AAAAGAAAGAAA-AA
18491363 AAAAGGGGAAAG-AAAA
1 AAAA---GAAAGAAAAA
18491379 AAAAGAAAGAAAAA
1 AAAAGAAAGAAAAA
18491393 A
1 A
18491394 TAAAAAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 8 0.21
14 19 0.49
16 6 0.15
17 6 0.15
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAGAAAGAAAAA
Found at i:18491536 original size:23 final size:24
Alignment explanation
Indices: 18491499--18491552 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
18491489 AGCAAAAAAA
18491499 AAGCAGCAAAAAAGAAGAAGAAAG
1 AAGCAGCAAAAAAGAAGAAGAAAG
18491523 AAGCAG-AAAAAAGAAGAAGAAAG
1 AAGCAGCAAAAAAGAAGAAGAAAG
18491546 AAGCAGC
1 AAGCAGC
18491553 CCAAATGCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.65, C:0.09, G:0.26, T:0.00
Consensus pattern (24 bp):
AAGCAGCAAAAAAGAAGAAGAAAG
Found at i:18491705 original size:11 final size:10
Alignment explanation
Indices: 18491672--18491705 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
18491662 GCCCAGCAGA
18491672 AAAAAAAGAG
1 AAAAAAAGAG
18491682 AAAAAAA-AG
1 AAAAAAAGAG
*
18491691 AAAAAGAGAG
1 AAAAAAAGAG
18491701 AAAAA
1 AAAAA
18491706 GAAAAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:18491712 original size:17 final size:17
Alignment explanation
Indices: 18491671--18491722 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
18491661 AGCCCAGCAG
18491671 AAAAAAAAGAGA-AAAA
1 AAAAAAAAGAGAGAAAA
18491687 AAAGAAAAAGAGAGAAAA
1 AAA-AAAAAGAGAGAAAA
* *
18491705 AGAAAAAACA-AGAAAA
1 AAAAAAAAGAGAGAAAA
18491721 AA
1 AA
18491723 GGGGTTCAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 10 0.32
17 15 0.48
18 6 0.19
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAGAGAAAA
Found at i:18491718 original size:16 final size:16
Alignment explanation
Indices: 18491669--18491721 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
18491659 CCAGCCCAGC
*
18491669 AGAAAAA-AAAGAGAA
1 AGAAAAAGAAAAAGAA
*
18491684 A-AAAAAGAAAAAGAG
1 AGAAAAAGAAAAAGAA
18491699 AGAAAAAGAAAAA-ACA
1 AGAAAAAGAAAAAGA-A
18491715 AGAAAAA
1 AGAAAAA
18491722 AGGGGTTCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
14 5 0.16
15 9 0.28
16 18 0.56
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (16 bp):
AGAAAAAGAAAAAGAA
Found at i:18491723 original size:17 final size:17
Alignment explanation
Indices: 18491669--18491723 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 17
18491659 CCAGCCCAGC
18491669 AGAAAAAAAAGAGAAAA
1 AGAAAAAAAAGAGAAAA
*
18491686 AAAAGAAAAAGAGAGAAAA
1 AGAA-AAAAA-AGAGAAAA
18491705 AGAAAAAACAAGA-AAAA
1 AGAAAAAA-AAGAGAAAA
18491722 AG
1 AG
18491724 GGGTTCAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 9 0.27
18 12 0.36
19 12 0.36
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAAGAGAAAA
Found at i:18492107 original size:19 final size:20
Alignment explanation
Indices: 18492083--18492123 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
18492073 TCGCGTTTCG
18492083 AAATTT-TCGTGTCTTCAAA
1 AAATTTCTCGTGTCTTCAAA
*
18492102 AAATTTCTCGTGTTTTCAAA
1 AAATTTCTCGTGTCTTCAAA
18492122 AA
1 AA
18492124 TAAGGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (20 bp):
AAATTTCTCGTGTCTTCAAA
Found at i:18492267 original size:17 final size:18
Alignment explanation
Indices: 18492228--18492720 Score: 226
Period size: 17 Copynumber: 27.3 Consensus size: 18
18492218 GAAAAATCAG
18492228 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
18492246 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* * *
18492264 AAAAAATTCCAT-TTTTC
1 AAAAATTTTCGTGTTTTC
* *
18492281 AAAATTTTTCGTGTTTTTTTA
1 AAAAATTTTCGTG---TTTTC
* * * *
18492302 AAAAAATTCCAT-ATTTC
1 AAAAATTTTCGTGTTTTC
*
18492319 TAAAATTTTCGTG-TTT-
1 AAAAATTTTCGTGTTTTC
* *
18492335 AAAAAATTTCGTATTTTC
1 AAAAATTTTCGTGTTTTC
* ** *
18492353 AAAATTTTTTTATTTTTTTC
1 AAAA--ATTTTCGTGTTTTC
* *
18492373 AACAATTCTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
* * *
18492390 ACAAATTCTCGTATTTT-
1 AAAAATTTTCGTGTTTTC
* ** *
18492407 AAAATTTTTTATGTTTTA
1 AAAAATTTTCGTGTTTTC
18492425 AAAAATAAATTTC-TCGTGTTTC
1 AAAAAT---TTTCGT-GT-TTTC
* *
18492447 AAAAATTGTCATGTTTT-
1 AAAAATTTTCGTGTTTTC
*
18492464 AAAAATTTTCATG-TTTC
1 AAAAATTTTCGTGTTTTC
* * *
18492481 TAAAATGTTCGT-ATTTC
1 AAAAATTTTCGTGTTTTC
**
18492498 AAAAAATCCTCGTGTTTTC
1 -AAAAATTTTCGTGTTTTC
* *
18492517 AAAAATTCTCATG-TTTC
1 AAAAATTTTCGTGTTTTC
*
18492534 AAAAATCTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
18492552 -AAAATTCTAGTG-TTTC
1 AAAAATTTTCGTGTTTTC
*
18492568 AAAAATTTTCATGTTTTC
1 AAAAATTTTCGTGTTTTC
* *
18492586 AAAAATTTCCCCTGTTTTC
1 AAAAATTT-TCGTGTTTTC
* *
18492605 AAAAATTCTCGT-ATTTC
1 AAAAATTTTCGTGTTTTC
* *
18492622 AAAAATTTTCTTTTTTTC
1 AAAAATTTTCGTGTTTTC
* *
18492640 AAAAAAAAAACTTCCGTGTTTT-
1 -----AAAAATTTTCGTGTTTTC
* * *
18492662 ATAAATCTCCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
* **
18492680 AAAAAATTCTCG-ACTTTC
1 -AAAAATTTTCGTGTTTTC
*
18492698 AAAAAATTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
18492716 AAAAA
1 AAAAA
18492721 ATTGACATTG
Statistics
Matches: 351, Mismatches: 90, Indels: 68
0.69 0.18 0.13
Matches are distributed among these distances:
16 17 0.05
17 149 0.42
18 101 0.29
19 31 0.09
20 14 0.04
21 17 0.05
22 9 0.03
23 13 0.04
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.46
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:18492328 original size:38 final size:37
Alignment explanation
Indices: 18492242--18492334 Score: 120
Period size: 38 Copynumber: 2.5 Consensus size: 37
18492232 ATTTTCGTGT
* *
18492242 TTTCAAAAATTTTCGTG---TTTTCAAAAAATTCCATT
1 TTTC-AAAATTTTCGTGTTTTTTTAAAAAAATTCCATA
18492277 TTTCAAAATTTTTCGTGTTTTTTTAAAAAAATTCCATA
1 TTTCAAAA-TTTTCGTGTTTTTTTAAAAAAATTCCATA
18492315 TTTCTAAAATTTTCGTGTTT
1 TTTC-AAAATTTTCGTGTTT
18492335 AAAAAATTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
34 4 0.08
35 12 0.24
38 31 0.61
39 4 0.08
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.51
Consensus pattern (37 bp):
TTTCAAAATTTTCGTGTTTTTTTAAAAAAATTCCATA
Found at i:18492453 original size:57 final size:55
Alignment explanation
Indices: 18492320--18492485 Score: 160
Period size: 57 Copynumber: 3.0 Consensus size: 55
18492310 CCATATTTCT
* ***
18492320 AAAATTT-TCGTGTTTAAAAAATTTCGTATTTTCAAAATTTTTTTAT-TTTT-TTCA
1 AAAATTTCTCGTGTTTCAAAAATTTCGTATTTT-AAAA-TTTTTTATGTTTTAAAAA
* *
18492374 ACAA-TTCTCGTGTTTCACAAATTCTCGTATTTTAAAATTTTTTATGTTTTAAAAA
1 AAAATTTCTCGTGTTTCAAAAATT-TCGTATTTTAAAATTTTTTATGTTTTAAAAA
* * * *
18492429 ATAAATTTCTCGTGTTTCAAAAATTGTCATGTTTTAAAAATTTTCATGTTTCTAAAA
1 A-AAATTTCTCGTGTTTCAAAAATT-TCGTATTTTAAAATTTTTTATGTTT-TAAAA
18492486 TGTTCGTATT
Statistics
Matches: 92, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
53 10 0.11
54 25 0.27
55 11 0.12
56 2 0.02
57 39 0.42
58 5 0.05
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.49
Consensus pattern (55 bp):
AAAATTTCTCGTGTTTCAAAAATTTCGTATTTTAAAATTTTTTATGTTTTAAAAA
Found at i:18492569 original size:16 final size:16
Alignment explanation
Indices: 18492513--18492571 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 16
18492503 ATCCTCGTGT
18492513 TTTCAAAAATTCTCA-TG
1 TTTC-AAAATTCT-AGTG
* *
18492530 TTTCAAAAATCTTCGTG
1 TTTCAAAATTC-TAGTG
18492547 TTTTCAAAATTCTAGTG
1 -TTTCAAAATTCTAGTG
18492564 TTTCAAAA
1 TTTCAAAA
18492572 ATTTTCATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 14 0.40
17 11 0.31
18 10 0.29
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (16 bp):
TTTCAAAATTCTAGTG
Found at i:18492721 original size:18 final size:18
Alignment explanation
Indices: 18492228--18492723 Score: 144
Period size: 18 Copynumber: 27.4 Consensus size: 18
18492218 GAAAAATCAG
*
18492228 AAAAATTTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
*
18492246 AAAAATTTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
* *
18492264 AAAAAATTCCAT-TTTTC
1 AAAAAATTTCGTGTTTTC
** *
18492281 AAAATTTTTCGTGTTTTTTTA
1 AAAAAATTTCGTG---TTTTC
* * *
18492302 AAAAAATTCCAT-ATTTC
1 AAAAAATTTCGTGTTTTC
* *
18492319 TAAAATTTTCGTG-TTT-
1 AAAAAATTTCGTGTTTTC
*
18492335 AAAAAATTTCGTATTTTC
1 AAAAAATTTCGTGTTTTC
** ** *
18492353 AAAATTTTTTTATTTTTTTC
1 AAAA--AATTTCGTGTTTTC
*
18492373 -AACAATTCTCGTG-TTTC
1 AAAAAATT-TCGTGTTTTC
* *
18492390 -ACAAATTCTCGTATTTT-
1 AAAAAATT-TCGTGTTTTC
** ** *
18492407 AAAATTTTTTATGTTTTAAA
1 AAAAAATTTCGTGTTTT--C
18492427 AAATAAATTTC-TCGTGTTTC
1 AAA-AAATTTCGT-GT-TTTC
*
18492447 -AAAAATTGTCATGTTTT-
1 AAAAAATT-TCGTGTTTTC
* *
18492464 AAAAATTTTCATG-TTTC
1 AAAAAATTTCGTGTTTTC
* *
18492481 -TAAAATGTTCGT-ATTTC
1 AAAAAAT-TTCGTGTTTTC
*
18492498 AAAAAATCCTCGTGTTTTC
1 AAAAAAT-TTCGTGTTTTC
*
18492517 -AAAAATTCTCATG-TTTC
1 AAAAAATT-TCGTGTTTTC
18492534 -AAAAATCTTCGTGTTTTC
1 AAAAAAT-TTCGTGTTTTC
*
18492552 --AAAATTCTAGTG-TTTC
1 AAAAAATT-TCGTGTTTTC
* *
18492568 AAAAATTTTCATGTTTTC
1 AAAAAATTTCGTGTTTTC
*
18492586 -AAAAATTTCCCCTGTTTTC
1 AAAAAATTT--CGTGTTTTC
*
18492605 -AAAAATTCTCGT-ATTTC
1 AAAAAATT-TCGTGTTTTC
* * *
18492622 AAAAATTTTCTTTTTTTC
1 AAAAAATTTCGTGTTTTC
*
18492640 AAAAAAAAAACTTCCGTGTTTT-
1 ----AAAAAA-TTTCGTGTTTTC
* *
18492662 -ATAAATCTCCGTGTTTTC
1 AAAAAAT-TTCGTGTTTTC
**
18492680 AAAAAATTCTCG-ACTTTC
1 AAAAAATT-TCGTGTTTTC
18492698 AAAAAATTTCGTGTTTTC
1 AAAAAATTTCGTGTTTTC
18492716 AAAAAATT
1 AAAAAATT
18492724 GACATTGTTT
Statistics
Matches: 352, Mismatches: 78, Indels: 96
0.67 0.15 0.18
Matches are distributed among these distances:
16 23 0.07
17 122 0.35
18 124 0.35
19 34 0.10
20 15 0.04
21 18 0.05
22 8 0.02
23 8 0.02
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (18 bp):
AAAAAATTTCGTGTTTTC
Found at i:18492847 original size:21 final size:21
Alignment explanation
Indices: 18492791--18492863 Score: 91
Period size: 19 Copynumber: 3.6 Consensus size: 21
18492781 CAAAATTTTT
18492791 GTGTTTTC-AAAATAAAATT-
1 GTGTTTTCAAAAATAAAATTC
18492810 GTGTTTT-AAAAATAAAATTC
1 GTGTTTTCAAAAATAAAATTC
*
18492830 GTGTTTTCAAAAAAAAAATTC
1 GTGTTTTCAAAAATAAAATTC
18492851 -TCGTGTTTCAAAA
1 GT-GT-TTTCAAAA
18492864 TTTTCGTGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
19 18 0.38
20 8 0.17
21 14 0.29
22 8 0.17
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.38
Consensus pattern (21 bp):
GTGTTTTCAAAAATAAAATTC
Found at i:18492859 original size:22 final size:20
Alignment explanation
Indices: 18492795--18492863 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
18492785 ATTTTTGTGT
*
18492795 TTTC-AAAATAAAATT-GTG
1 TTTCAAAAAAAAAATTCGTG
* *
18492813 TTTTAAAAATAAAATTCGTG
1 TTTCAAAAAAAAAATTCGTG
18492833 TTTTCAAAAAAAAAATTCTCGTG
1 -TTTCAAAAAAAAAA-T-TCGTG
18492856 TTTCAAAA
1 TTTCAAAA
18492864 TTTTCGTGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
18 3 0.07
19 11 0.26
20 3 0.07
21 12 0.28
22 9 0.21
23 5 0.12
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (20 bp):
TTTCAAAAAAAAAATTCGTG
Found at i:18492863 original size:18 final size:17
Alignment explanation
Indices: 18492842--18492966 Score: 53
Period size: 17 Copynumber: 7.1 Consensus size: 17
18492832 GTTTTCAAAA
18492842 AAAAAATTCTCGTGTTTC
1 AAAAAATT-TCGTGTTTC
* *
18492860 -AAAATTTTCGTGTTTTTTTA
1 AAAAAATTTCGTG----TTTC
*
18492880 AAAAAAATTCGTGTTTC
1 AAAAAATTTCGTGTTTC
* * * *
18492897 -TAAAATTCTTGTATTTT
1 AAAAAATT-TCGTGTTTC
*
18492914 AAAATATTTCGTGTTTC
1 AAAAAATTTCGTGTTTC
*
18492931 GAAAAAAGGTT-GTGTTTC
1 -AAAAAA-TTTCGTGTTTC
18492949 --AAAATTCTCGTGTTTC
1 AAAAAATT-TCGTGTTTC
18492965 AA
1 AA
18492967 TTGGATCACG
Statistics
Matches: 76, Mismatches: 18, Indels: 26
0.63 0.15 0.22
Matches are distributed among these distances:
14 1 0.01
15 5 0.07
16 17 0.22
17 21 0.28
18 17 0.22
19 2 0.03
20 3 0.04
21 10 0.13
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (17 bp):
AAAAAATTTCGTGTTTC
Found at i:18492863 original size:20 final size:19
Alignment explanation
Indices: 18492737--18492863 Score: 60
Period size: 20 Copynumber: 5.9 Consensus size: 19
18492727 ATTGTTTCAT
18492737 AAATTTCCGTGTTTCAAAAA
1 AAATTT-CGTGTTTCAAAAA
*
18492757 AAATCCTCGTGTTTCATAATTTATCA
1 AAAT-TTCGTGTTTCA-AA---A--A
*
18492783 AAATTTTTGTGTTTTCAAAATA
1 AAA-TTTCGTG-TTTCAAAA-A
*
18492805 AAA-TT-GTGTTTTAAAAA
1 AAATTTCGTGTTTCAAAAA
*
18492822 TAAAATTCGTGTTTTCAAAAAAA
1 -AAATTTCGTG-TTTC--AAAAA
18492845 AAATTCTCGTGTTTCAAAA
1 AAATT-TCGTGTTTCAAAA
18492864 TTTTCGTGTT
Statistics
Matches: 84, Mismatches: 7, Indels: 32
0.68 0.06 0.26
Matches are distributed among these distances:
17 1 0.01
18 10 0.12
19 5 0.06
20 22 0.26
21 6 0.07
22 12 0.14
23 11 0.13
24 1 0.01
26 10 0.12
27 6 0.07
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.40
Consensus pattern (19 bp):
AAATTTCGTGTTTCAAAAA
Found at i:18492865 original size:16 final size:16
Alignment explanation
Indices: 18492844--18492874 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18492834 TTTCAAAAAA
18492844 AAAATTCTCGTGTTTC
1 AAAATTCTCGTGTTTC
*
18492860 AAAATTTTCGTGTTT
1 AAAATTCTCGTGTTT
18492875 TTTTAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (16 bp):
AAAATTCTCGTGTTTC
Found at i:18492870 original size:39 final size:37
Alignment explanation
Indices: 18492780--18492903 Score: 101
Period size: 39 Copynumber: 3.2 Consensus size: 37
18492770 TCATAATTTA
* *
18492780 TCAAAATTTTTGTGTTTTCAAAATAAAA-TT-GTGTTT
1 TCAAAATTTTCGTGTTTTCAAAAAAAAATTTCGTG-TT
* *
18492816 TAAAAATAAAATTCGTGTTTTCAAAAAAAAAATTCTCGTGTT
1 TCAAAAT---TTTCGTGTTTTC-AAAAAAAAATT-TCGTGTT
**
18492858 TCAAAATTTTCGTGTTTTTTTAAAAAAAA-TTCGTGTT
1 TCAAAATTTTCGTG-TTTTCAAAAAAAAATTTCGTGTT
18492895 TCTAAAATT
1 TC-AAAATT
18492904 CTTGTATTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
36 6 0.08
37 9 0.13
38 7 0.10
39 24 0.34
40 12 0.17
41 1 0.01
42 9 0.13
43 3 0.04
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (37 bp):
TCAAAATTTTCGTGTTTTCAAAAAAAAATTTCGTGTT
Found at i:18492900 original size:19 final size:19
Alignment explanation
Indices: 18492795--18492901 Score: 55
Period size: 19 Copynumber: 5.5 Consensus size: 19
18492785 ATTTTTGTGT
18492795 TTTC-AAAATAAAATT-GTG
1 TTTCTAAAA-AAAATTCGTG
18492813 TTT-TAAAAATAAAATTCGTG
1 TTTCT-AAAA-AAAATTCGTG
*
18492833 TTTTCAAAAAAAAAATTCTCGTG
1 -TTTC-TAAAAAAAA-T-TCGTG
**
18492856 TTTC---AAAATTTTCGTG
1 TTTCTAAAAAAAATTCGTG
*
18492872 TTTTTTTAAAAAAAATTCGTG
1 --TTTCTAAAAAAAATTCGTG
18492893 TTTCTAAAA
1 TTTCTAAAA
18492902 TTCTTGTATT
Statistics
Matches: 69, Mismatches: 7, Indels: 25
0.68 0.07 0.25
Matches are distributed among these distances:
16 5 0.07
17 1 0.01
18 10 0.14
19 19 0.28
20 3 0.04
21 17 0.25
22 9 0.13
23 5 0.07
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.42
Consensus pattern (19 bp):
TTTCTAAAAAAAATTCGTG
Found at i:18498362 original size:20 final size:20
Alignment explanation
Indices: 18498337--18498398 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 20
18498327 AATTAAATTC
18498337 TAAAAGATAAATACAAATAAA
1 TAAAAGATAAATA-AAATAAA
*
18498358 T-AAAGATAATTAAAGAT-AA
1 TAAAAGATAAATAAA-ATAAA
18498377 TAAAAGATAAATGAAAATAAA
1 TAAAAGATAAAT-AAAATAAA
18498398 T
1 T
18498399 CCTAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
19 5 0.14
20 23 0.66
21 7 0.20
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.23
Consensus pattern (20 bp):
TAAAAGATAAATAAAATAAA
Found at i:18498366 original size:10 final size:10
Alignment explanation
Indices: 18498339--18498398 Score: 63
Period size: 10 Copynumber: 6.0 Consensus size: 10
18498329 TTAAATTCTA
18498339 AAAGATAAAT
1 AAAGATAAAT
18498349 ACAA-ATAAAT
1 A-AAGATAAAT
*
18498359 AAAGATAATT
1 AAAGATAAAT
18498369 AAAGAT-AAT
1 AAAGATAAAT
18498378 AAAAGATAAAT
1 -AAAGATAAAT
18498389 GAAA-ATAAAT
1 -AAAGATAAAT
18498399 CCTAAAATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
9 4 0.09
10 31 0.72
11 8 0.19
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:18498387 original size:30 final size:30
Alignment explanation
Indices: 18498339--18498396 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
18498329 TTAAATTCTA
*
18498339 AAAGATAAATACAAATAAAT-AAAGATAATT
1 AAAGATAAATAAAAATAAATGAAA-ATAATT
18498369 AAAGAT-AATAAAAGATAAATGAAAATAA
1 AAAGATAAATAAAA-ATAAATGAAAATAA
18498397 ATCCTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 6 0.24
30 16 0.64
31 3 0.12
ACGTcount: A:0.69, C:0.02, G:0.09, T:0.21
Consensus pattern (30 bp):
AAAGATAAATAAAAATAAATGAAAATAATT
Found at i:18499232 original size:96 final size:97
Alignment explanation
Indices: 18499046--18499233 Score: 297
Period size: 96 Copynumber: 1.9 Consensus size: 97
18499036 TAATTAATTA
* * * *
18499046 ATTTTTGCTTAGGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCGAGCACCTCACCC
1 ATTTTTGCTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCTCACCC
* *
18499111 TGGTTATTCAGCCCAACACACTCTTAATTTTT
66 CGGTTACTCAGCCCAACACACTCTTAATTTTT
*
18499143 ATTTTT-CTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCTTACCC
1 ATTTTTGCTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCTCACCC
*
18499207 CGGTTACTCAGCCCAACACATTCTTAA
66 CGGTTACTCAGCCCAACACACTCTTAA
18499234 AAATTAATTC
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
96 77 0.93
97 6 0.07
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (97 bp):
ATTTTTGCTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCTCACCC
CGGTTACTCAGCCCAACACACTCTTAATTTTT
Found at i:18502965 original size:29 final size:28
Alignment explanation
Indices: 18502907--18502995 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 28
18502897 GAACTTGAAT
*
18502907 TTTTAAAATATAAAAAGTAGAAAAACTAAA
1 TTTTAAAA-ATAAAAA-TAAAAAAACTAAA
* *
18502937 TCTTTAAAAATAAGAATAAAAAAATTAAA
1 T-TTTAAAAATAAAAATAAAAAAACTAAA
*
18502966 TTGTTGAAAATAAAAAT-AAAAAA-TAAA
1 TT-TTAAAAATAAAAATAAAAAAACTAAA
18502993 TTT
1 TTT
18502996 CAAATATACG
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
26 1 0.02
27 6 0.12
28 7 0.13
29 24 0.46
30 7 0.13
31 7 0.13
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (28 bp):
TTTTAAAAATAAAAATAAAAAAACTAAA
Found at i:18515050 original size:45 final size:45
Alignment explanation
Indices: 18514993--18515084 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
18514983 GTAGAGAAAA
* *
18514993 TTAATGTCAATGAGGAGGTTGATAGCCAGCTAGCAAGTGAGAAGC
1 TTAATGTCAATGAGGAGGTTAACAGCCAGCTAGCAAGTGAGAAGC
*
18515038 TTAATGTCAATGAGGAGGTTAACAGTCAGCTAGCAAGTGAGAAGC
1 TTAATGTCAATGAGGAGGTTAACAGCCAGCTAGCAAGTGAGAAGC
18515083 TT
1 TT
18515085 TGTTCTGCAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.24
Consensus pattern (45 bp):
TTAATGTCAATGAGGAGGTTAACAGCCAGCTAGCAAGTGAGAAGC
Found at i:18520739 original size:27 final size:28
Alignment explanation
Indices: 18520699--18520767 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 28
18520689 GTTATGAAAG
18520699 TATATGAAAT-TAATTTAATTT-T-TACAT
1 TATAT-AAATATAATTT-ATTTGTATACAT
*
18520726 TATATAAATATAA-TTATTTGTATATAT
1 TATATAAATATAATTTATTTGTATACAT
*
18520753 AATATAAATATAATT
1 TATATAAATATAATT
18520768 ATTATATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
25 4 0.11
26 7 0.19
27 24 0.67
28 1 0.03
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (28 bp):
TATATAAATATAATTTATTTGTATACAT
Found at i:18521190 original size:15 final size:16
Alignment explanation
Indices: 18521160--18521198 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
18521150 TAGTAAAAAT
18521160 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
18521177 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
18521192 ATAATTT
1 ATAATTT
18521199 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:18522328 original size:20 final size:20
Alignment explanation
Indices: 18522276--18522330 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
18522266 AACTTTTTAT
18522276 GTATTTA-TATAATTTTCTAA
1 GTATTTATTAT-ATTTTCTAA
* *
18522296 ATTTTTATT-TATTTTC-AA
1 GTATTTATTATATTTTCTAA
18522314 GTATTTATGTATATTTT
1 GTATTTAT-TATATTTT
18522331 TTATTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
18 8 0.29
19 7 0.25
20 12 0.43
21 1 0.04
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (20 bp):
GTATTTATTATATTTTCTAA
Found at i:18522381 original size:15 final size:16
Alignment explanation
Indices: 18522343--18522380 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
18522333 ATTTTTTATA
18522343 ATTTTTTAAAAAATTG
1 ATTTTTTAAAAAATTG
18522359 ATTTTTTAAAAAATTG
1 ATTTTTTAAAAAATTG
18522375 ATTTTT
1 ATTTTT
18522381 ATATATAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (16 bp):
ATTTTTTAAAAAATTG
Found at i:18523985 original size:23 final size:23
Alignment explanation
Indices: 18523956--18524175 Score: 151
Period size: 23 Copynumber: 9.3 Consensus size: 23
18523946 CTGTTTACAA
18523956 AAGGGGTTCACATATCATTCACT
1 AAGGGGTTCACATATCATTCACT
** *
18523979 AAGGGGTTCGTATAACATTCACT
1 AAGGGGTTCACATATCATTCACT
* *
18524002 AAGGGGTTCACACAACATTCACT
1 AAGGGGTTCACATATCATTCACT
* *
18524025 AAGGGGTTGGCACAAAT-ATTCATT
1 AAGGGGTT--CACATATCATTCACT
* *
18524049 AAGGGGTTGGCATAAAT-ATTCACT
1 AAGGGGTT--CACATATCATTCACT
* * *
18524073 GAGGGGTTCGCATAACATTCACT
1 AAGGGGTTCACATATCATTCACT
* * *
18524096 GAGGGGTTCGCATAAAT-ATTCATT
1 AAGGGGTTCACAT--ATCATTCACT
** *
18524120 AAGGGGTTTGCATAACATTCACT
1 AAGGGGTTCACATATCATTCACT
* *
18524143 AAGGGGGTTTGCATAAAT-ATTCACT
1 AA-GGGG-TT-CACATATCATTCACT
18524168 AAGGGGTT
1 AAGGGGTT
18524176 GGGCTTATCC
Statistics
Matches: 161, Mismatches: 27, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
22 4 0.02
23 78 0.48
24 60 0.37
25 17 0.11
26 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (23 bp):
AAGGGGTTCACATATCATTCACT
Found at i:18524051 original size:24 final size:24
Alignment explanation
Indices: 18523972--18524177 Score: 215
Period size: 24 Copynumber: 8.7 Consensus size: 24
18523962 TTCACATATC
* * *
18523972 ATTCACTAAGGGGTTCGTAT-AAC
1 ATTCACTAAGGGGTTGGCATAAAT
* *
18523995 ATTCACTAAGGGGTT--CACACAAC
1 ATTCACTAAGGGGTTGGCATA-AAT
*
18524018 ATTCACTAAGGGGTTGGCACAAAT
1 ATTCACTAAGGGGTTGGCATAAAT
*
18524042 ATTCATTAAGGGGTTGGCATAAAT
1 ATTCACTAAGGGGTTGGCATAAAT
* * *
18524066 ATTCACTGAGGGGTTCGCAT-AAC
1 ATTCACTAAGGGGTTGGCATAAAT
* *
18524089 ATTCACTGAGGGGTTCGCATAAAT
1 ATTCACTAAGGGGTTGGCATAAAT
* * *
18524113 ATTCATTAAGGGGTTTGCAT-AAC
1 ATTCACTAAGGGGTTGGCATAAAT
*
18524136 ATTCACTAAGGGGGTTTGCATAAAT
1 ATTCACTAA-GGGGTTGGCATAAAT
18524161 ATTCACTAAGGGGTTGG
1 ATTCACTAAGGGGTTGG
18524178 GCTTATCCGA
Statistics
Matches: 159, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
21 1 0.01
23 65 0.41
24 78 0.49
25 15 0.09
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (24 bp):
ATTCACTAAGGGGTTGGCATAAAT
Found at i:18524078 original size:71 final size:69
Alignment explanation
Indices: 18523956--18524177 Score: 250
Period size: 71 Copynumber: 3.1 Consensus size: 69
18523946 CTGTTTACAA
* * *
18523956 AAGGGGTT--CACATATCATTCACTAAGGGGTTCGTATAACATTCACTAAGGGGTTCACACAACA
1 AAGGGGTTGGCACAAAT-ATTCATTAAGGGGTTCGCATAACATTCACTAAGGGGTTCACA-AACA
18524019 TTCACT
64 TTCACT
* * * *
18524025 AAGGGGTTGGCACAAATATTCATTAAGGGGTTGGCATAAATATTCACTGAGGGGTTCGCATAACA
1 AAGGGGTTGGCACAAATATTCATTAAGGGGTTCGCAT-AACATTCACTAAGGGGTTCACA-AACA
18524090 TTCACT
64 TTCACT
* * * * * *
18524096 GAGGGGTTCGCATAAATATTCATTAAGGGGTTTGCATAACATTCACTAAGGGGGTTTGCATAAAT
1 AAGGGGTTGGCACAAATATTCATTAAGGGGTTCGCATAACATTCACTAA-GGGG-TT-CACAAAC
18524161 ATTCACT
63 ATTCACT
18524168 AAGGGGTTGG
1 AAGGGGTTGG
18524178 GCTTATCCGA
Statistics
Matches: 128, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
69 8 0.06
70 27 0.21
71 72 0.56
72 19 0.15
73 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (69 bp):
AAGGGGTTGGCACAAATATTCATTAAGGGGTTCGCATAACATTCACTAAGGGGTTCACAAACATT
CACT
Found at i:18524259 original size:43 final size:43
Alignment explanation
Indices: 18524180--18524303 Score: 167
Period size: 43 Copynumber: 2.8 Consensus size: 43
18524170 GGGGTTGGGC
*
18524180 TTATCCGATGATGCATTGTGTGTATGCCAATATAGTTGCTCCGAT
1 TTATCCGATGATGCA--ATGTGTATGCCAATATAGTTGCTCCGAT
* * ** *
18524225 TTATCTGATGATGCAATGTGTATACCAATATAGTTGCTTTGGT
1 TTATCCGATGATGCAATGTGTATGCCAATATAGTTGCTCCGAT
*
18524268 TTATCCGATGATGCACTGTGTATGCCAATATAGTTG
1 TTATCCGATGATGCAATGTGTATGCCAATATAGTTG
18524304 TTCCAGTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
43 56 0.80
45 14 0.20
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (43 bp):
TTATCCGATGATGCAATGTGTATGCCAATATAGTTGCTCCGAT
Found at i:18524323 original size:43 final size:42
Alignment explanation
Indices: 18524180--18524329 Score: 156
Period size: 43 Copynumber: 3.5 Consensus size: 42
18524170 GGGGTTGGGC
* * *
18524180 TTATCCGATGATGCATTGTGTGTATGCCAATATAGTTGCTCCGAT
1 TTATCTGATGATGCA--CTGTGTATGCCAATATAGTTGTTCCG-T
* * **
18524225 TTATCTGATGATGCAATGTGTATACCAATATAGTTGCTTTGGT
1 TTATCTGATGATGCACTGTGTATGCCAATATAGTTG-TTCCGT
*
18524268 TTATCCGATGATGCACTGTGTATGCCAATATAGTTGTTCCAGT
1 TTATCTGATGATGCACTGTGTATGCCAATATAGTTGTTCC-GT
* * *
18524311 ATATTTGGTGATGCACTGT
1 TTATCTGATGATGCACTGT
18524330 ATGTGCTAGC
Statistics
Matches: 88, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
42 2 0.02
43 70 0.80
44 2 0.02
45 14 0.16
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.39
Consensus pattern (42 bp):
TTATCTGATGATGCACTGTGTATGCCAATATAGTTGTTCCGT
Found at i:18524344 original size:86 final size:87
Alignment explanation
Indices: 18524180--18524365 Score: 196
Period size: 86 Copynumber: 2.1 Consensus size: 87
18524170 GGGGTTGGGC
* * *
18524180 TTATCCGATGATGCATTGTGTGTATGCCAATATAGTTGCTCCGATTTATCTGATGATGCAATGTG
1 TTATCCGATGATGCA-TCTGTGTATGCCAATATAGTTGCTCCGATATATCTGATGATGCAATGTA
* * *
18524245 TATACCAATATAGTTGCTTTGGT
65 TATACCAACATAGTTGATTCGGT
* * * *
18524268 TTATCCGATGATGCA-CTGTGTATGCCAATATAGTTGTTCC-AGTATATTTGGTGATGCACTGTA
1 TTATCCGATGATGCATCTGTGTATGCCAATATAGTTGCTCCGA-TATATCTGATGATGCAATGTA
* * * * *
18524331 TGTGCTAGCATAGTTTATTCGGT
65 TATACCAACATAGTTGATTCGGT
*
18524354 TTATCCAATGAT
1 TTATCCGATGAT
18524366 TCATTATTTG
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
85 1 0.01
86 65 0.80
88 15 0.19
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.40
Consensus pattern (87 bp):
TTATCCGATGATGCATCTGTGTATGCCAATATAGTTGCTCCGATATATCTGATGATGCAATGTAT
ATACCAACATAGTTGATTCGGT
Found at i:18524453 original size:44 final size:43
Alignment explanation
Indices: 18524348--18524460 Score: 127
Period size: 43 Copynumber: 2.6 Consensus size: 43
18524338 GCATAGTTTA
* * * *
18524348 TTCGGTTTATCCAATGATTCATTATTTGTGACAGTATAATTGT
1 TTCGATTTATCCAATGATGCATTATGTGTGACAATATAATTGT
* * * * *
18524391 TTCGATATATTCAATGATGCATTGTGTGTGCCAATATGATTGT
1 TTCGATTTATCCAATGATGCATTATGTGTGACAATATAATTGT
*
18524434 TTCAGTTTTATCCAATGATGCATTATG
1 TTC-GATTTATCCAATGATGCATTATG
18524461 ATGCTAGATT
Statistics
Matches: 56, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
43 37 0.66
44 19 0.34
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (43 bp):
TTCGATTTATCCAATGATGCATTATGTGTGACAATATAATTGT
Found at i:18536454 original size:2 final size:2
Alignment explanation
Indices: 18536447--18536480 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18536437 AAATATTTGA
18536447 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18536481 TACCACTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18553401 original size:6 final size:6
Alignment explanation
Indices: 18553383--18553414 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
18553373 CTATTAGTGT
18553383 ATGTAA TATGTAA ATGTAA ATGTAA ATGTAA A
1 ATGTAA -ATGTAA ATGTAA ATGTAA ATGTAA A
18553415 ATGGTGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
ATGTAA
Found at i:18556527 original size:24 final size:24
Alignment explanation
Indices: 18556511--18556557 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
18556501 AATGAATTGT
18556511 TAATT-TAAAA-TTAAAATATTTA
1 TAATTATAAAATTTAAAATATTTA
18556533 TAATTATAAAATTTAAAATTATTTA
1 TAATTATAAAATTTAAAA-TATTTA
18556558 AATCTGTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.23
23 5 0.23
24 6 0.27
25 6 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATTATAAAATTTAAAATATTTA
Found at i:18556537 original size:15 final size:15
Alignment explanation
Indices: 18556512--18556554 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
18556502 ATGAATTGTT
18556512 AATTTAAAATTA-AA
1 AATTTAAAATTATAA
*
18556526 ATATTTATAATTATAA
1 A-ATTTAAAATTATAA
18556542 AATTTAAAATTAT
1 AATTTAAAATTAT
18556555 TTAAATCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 1 0.04
15 21 0.84
16 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTTAAAATTATAA
Found at i:18558975 original size:30 final size:31
Alignment explanation
Indices: 18558919--18558977 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
18558909 TTATAACTTT
18558919 ATTTTTAAAAATCATTTTTTATAATTTTATG
1 ATTTTTAAAAATCATTTTTTATAATTTTATG
*
18558950 ATTTTTAAATAAT-TTTTTTTA-AATTTTA
1 ATTTTTAAA-AATCATTTTTTATAATTTTA
18558978 AAATGACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 7 0.27
31 16 0.62
32 3 0.12
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (31 bp):
ATTTTTAAAAATCATTTTTTATAATTTTATG
Found at i:18561229 original size:2 final size:2
Alignment explanation
Indices: 18561222--18561255 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18561212 TGTTCTTCAA
18561222 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18561256 GAAGTTGCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18564537 original size:27 final size:27
Alignment explanation
Indices: 18564507--18564558 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
18564497 AAATTTTCAA
18564507 TTTT-TAAAATATAGAAAAT-GAAAATTG
1 TTTTCTAAAA-AT-GAAAATGGAAAATTG
18564534 TTTTCTAAAAATGAAAATGGAAAAT
1 TTTTCTAAAAATGAAAATGGAAAAT
18564559 GAAATAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 6 0.26
27 12 0.52
28 5 0.22
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.35
Consensus pattern (27 bp):
TTTTCTAAAAATGAAAATGGAAAATTG
Found at i:18566494 original size:24 final size:24
Alignment explanation
Indices: 18566467--18566513 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
18566457 TTATTAATTT
18566467 TATG-TTATTT-TAATTTCTTTTAAA
1 TATGTTTATTTGT-ATTT-TTTTAAA
18566491 TATGTTTATTTGTATTTTTTTAA
1 TATGTTTATTTGTATTTTTTTAA
18566514 CAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 10 0.48
25 10 0.48
26 1 0.05
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (24 bp):
TATGTTTATTTGTATTTTTTTAAA
Found at i:18573879 original size:24 final size:24
Alignment explanation
Indices: 18573851--18573902 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
18573841 TTCATAGATA
* *
18573851 AAATAAATTGTGCTAACAAATACT
1 AAATAAATTATACTAACAAATACT
* * *
18573875 AAATATATTATACTAATACATACT
1 AAATAAATTATACTAACAAATACT
18573899 AAAT
1 AAAT
18573903 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAACAAATACT
Found at i:18574643 original size:7 final size:8
Alignment explanation
Indices: 18574620--18574648 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
18574610 TTAAATTAAA
18574620 TTAATTTT
1 TTAATTTT
18574628 TTAATTTT
1 TTAATTTT
18574636 TTAATTTT
1 TTAATTTT
18574644 TTAAT
1 TTAAT
18574649 CGCTAATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TTAATTTT
Found at i:18575357 original size:29 final size:29
Alignment explanation
Indices: 18575309--18575386 Score: 84
Period size: 30 Copynumber: 2.7 Consensus size: 29
18575299 AAATTAGTAT
**
18575309 ATAATAAAATTATACTTTAATCTATTAAA
1 ATAATAAAATTATAAATTAATCTATTAAA
* * *
18575338 ATAATAAAATTTTAAATTAAATTTTTTAAA
1 ATAATAAAATTATAAATT-AATCTATTAAA
* *
18575368 ATTATAAAAATATAAATTA
1 ATAATAAAATTATAAATTA
18575387 TTGAAATGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 16 0.40
30 24 0.60
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (29 bp):
ATAATAAAATTATAAATTAATCTATTAAA
Found at i:18589170 original size:12 final size:12
Alignment explanation
Indices: 18589153--18589178 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18589143 TCACTCAACC
18589153 AAAATTCAAAAA
1 AAAATTCAAAAA
18589165 AAAATTCAAAAA
1 AAAATTCAAAAA
18589177 AA
1 AA
18589179 TTTAAAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATTCAAAAA
Found at i:18589469 original size:15 final size:15
Alignment explanation
Indices: 18589445--18589474 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18589435 AATTTCACTT
*
18589445 GATTTGATTCGATTC
1 GATTTAATTCGATTC
18589460 GATTTAATTCGATTC
1 GATTTAATTCGATTC
18589475 AACTCGGATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (15 bp):
GATTTAATTCGATTC
Found at i:18591204 original size:13 final size:13
Alignment explanation
Indices: 18591185--18591245 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
18591175 AATCAAAATA
18591185 ATTAAAAAATATT
1 ATTAAAAAATATT
* *
18591198 TTTAAAAAATATG
1 ATTAAAAAATATT
* *
18591211 AAT-CAAAATA--
1 ATTAAAAAATATT
18591221 ATTAAAAAATATT
1 ATTAAAAAATATT
*
18591234 TTTAAAAAATAT
1 ATTAAAAAATAT
18591246 ATAAATTAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
10 2 0.05
11 6 0.16
12 6 0.16
13 23 0.62
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (13 bp):
ATTAAAAAATATT
Found at i:18591216 original size:36 final size:36
Alignment explanation
Indices: 18591169--18591245 Score: 154
Period size: 36 Copynumber: 2.1 Consensus size: 36
18591159 CCAATAACCC
18591169 AATATGAATCAAAATAATTAAAAAATATTTTTAAAA
1 AATATGAATCAAAATAATTAAAAAATATTTTTAAAA
18591205 AATATGAATCAAAATAATTAAAAAATATTTTTAAAA
1 AATATGAATCAAAATAATTAAAAAATATTTTTAAAA
18591241 AATAT
1 AATAT
18591246 ATAAATTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (36 bp):
AATATGAATCAAAATAATTAAAAAATATTTTTAAAA
Found at i:18591436 original size:28 final size:28
Alignment explanation
Indices: 18591387--18591441 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
18591377 CTTATTAAAA
* *
18591387 TAAAATTCAAAGATGTATTAATATCAAC
1 TAAAATTAAAAGATATATTAATATCAAC
*
18591415 TAAAATGTAAAAGATATA-TAATTTCAA
1 TAAAAT-TAAAAGATATATTAATATCAA
18591442 AAATTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (28 bp):
TAAAATTAAAAGATATATTAATATCAAC
Found at i:18591652 original size:18 final size:17
Alignment explanation
Indices: 18591629--18591668 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
18591619 TTTAGGGTTT
18591629 TTTTTTTCAATTTTGATA
1 TTTTTTTCAATTTTGA-A
*
18591647 TTTTTTTGAATTTTGAA
1 TTTTTTTCAATTTTGAA
18591664 TTTTT
1 TTTTT
18591669 ATTTTTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (17 bp):
TTTTTTTCAATTTTGAA
Found at i:18594042 original size:3 final size:3
Alignment explanation
Indices: 18594034--18594072 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
18594024 ACAAGGATAT
18594034 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18594073 TTGAAACACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:18594179 original size:3 final size:3
Alignment explanation
Indices: 18594171--18594208 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
18594161 ACTAATGTAC
*
18594171 AAT AAT AAT AAT AAAT AAT AAT AAT AAT ATT AAT AAT A
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT A
18594209 TGAAAATAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:18595098 original size:35 final size:35
Alignment explanation
Indices: 18595052--18595120 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
18595042 GGGTGTGTGA
*
18595052 TGGTGCTGGTGGCAGACAGCATGGGAGAGTGGGAG
1 TGGTGCTGGTGGCAGACAGCATGAGAGAGTGGGAG
18595087 TGGTGCTGGTGGCAGACAGCATGAGAGAGTGGGA
1 TGGTGCTGGTGGCAGACAGCATGAGAGAGTGGGA
18595121 AGAGGCAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.22, C:0.12, G:0.49, T:0.17
Consensus pattern (35 bp):
TGGTGCTGGTGGCAGACAGCATGAGAGAGTGGGAG
Found at i:18595360 original size:20 final size:19
Alignment explanation
Indices: 18595335--18595393 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
18595325 AAAAAAAATT
18595335 TCTTAAAAATAATTCTAAAA
1 TCTTAAAAATAATT-TAAAA
*
18595355 TCTTAAAAATAATTAAAAA
1 TCTTAAAAATAATTTAAAA
* *
18595374 TATTAAAAATATTTTAAAA
1 TCTTAAAAATAATTTAAAA
18595393 T
1 T
18595394 AATTTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 21 0.60
20 14 0.40
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TCTTAAAAATAATTTAAAA
Found at i:18595372 original size:10 final size:10
Alignment explanation
Indices: 18595337--18595407 Score: 65
Period size: 10 Copynumber: 7.0 Consensus size: 10
18595327 AAAAAATTTC
18595337 TTAAAAATAA
1 TTAAAAATAA
* *
18595347 TTCTAAAAT-C
1 TT-AAAAATAA
18595357 TTAAAAATAA
1 TTAAAAATAA
18595367 TTAAAAAT-A
1 TTAAAAATAA
*
18595376 TTAAAAATAT
1 TTAAAAATAA
*
18595386 TTTAAAATAA
1 TTAAAAATAA
18595396 TTTTAAAAATAA
1 --TTAAAAATAA
18595408 AAATTCAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
9 14 0.29
10 20 0.42
11 5 0.10
12 9 0.19
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (10 bp):
TTAAAAATAA
Found at i:18597021 original size:22 final size:22
Alignment explanation
Indices: 18596959--18597023 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
18596949 CTCCGATTAT
* * * *
18596959 TAGCACCTTAGTACTCTCCGTT
1 TAGCACATTAGTGCTCTCTGTA
*
18596981 TAGCACATTCGTGCTCTCTGTA
1 TAGCACATTAGTGCTCTCTGTA
*
18597003 TAGCACTTTAGTGCTCTCTGT
1 TAGCACATTAGTGCTCTCTGT
18597024 TCAATAGTGC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (22 bp):
TAGCACATTAGTGCTCTCTGTA
Found at i:18598480 original size:13 final size:13
Alignment explanation
Indices: 18598462--18598519 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
18598452 TGGCAATACC
18598462 TTTGAAAAGTACT
1 TTTGAAAAGTACT
*
18598475 TTTGAAAAGTGCT
1 TTTGAAAAGTACT
* * * *
18598488 GTGGAAAAATGCT
1 TTTGAAAAGTACT
18598501 TTTGAAAAGTACT
1 TTTGAAAAGTACT
18598514 TTTGAA
1 TTTGAA
18598520 GTTTGGTTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (13 bp):
TTTGAAAAGTACT
Found at i:18599919 original size:27 final size:27
Alignment explanation
Indices: 18599830--18599937 Score: 93
Period size: 27 Copynumber: 4.1 Consensus size: 27
18599820 AGCATGGCTG
* * * *
18599830 CCAGAACAGATA-ATGTGACAGAGTCA
1 CCAGATCAGATATATATGGCAGAGCCA
18599856 CCAGATACA-A-ATA-AT-GCAGAGCCA
1 CCAGAT-CAGATATATATGGCAGAGCCA
*
18599880 CCAGAAT-AGATATATGTGGCAGAGCCA
1 CCAG-ATCAGATATATATGGCAGAGCCA
* *
18599907 CCAGATCAGATATTTATGGCATAGCCA
1 CCAGATCAGATATATATGGCAGAGCCA
18599934 CCAG
1 CCAG
18599938 GACGCTTCCT
Statistics
Matches: 66, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
23 1 0.02
24 12 0.18
25 7 0.11
26 10 0.15
27 36 0.55
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.18
Consensus pattern (27 bp):
CCAGATCAGATATATATGGCAGAGCCA
Found at i:18600344 original size:8 final size:8
Alignment explanation
Indices: 18600328--18600357 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
18600318 CTCAAAATAC
18600328 CGGCTTTT
1 CGGCTTTT
*
18600336 CGGCATTT
1 CGGCTTTT
18600344 CGGCTTTT
1 CGGCTTTT
18600352 CGGCTT
1 CGGCTT
18600358 GTGTCGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.27, G:0.27, T:0.43
Consensus pattern (8 bp):
CGGCTTTT
Found at i:18604718 original size:44 final size:44
Alignment explanation
Indices: 18604655--18604745 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
18604645 ACTATTTTTC
18604655 TTATTTTAATATGTCACATGGGTTAGTCATTGGGTTATAAAGGG
1 TTATTTTAATATGTCACATGGGTTAGTCATTGGGTTATAAAGGG
18604699 TTATTTTAATATGTCACATGGGTTAGTCATTGGGTTATAAAGGG
1 TTATTTTAATATGTCACATGGGTTAGTCATTGGGTTATAAAGGG
18604743 TTA
1 TTA
18604746 AAAATGGTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.42
Consensus pattern (44 bp):
TTATTTTAATATGTCACATGGGTTAGTCATTGGGTTATAAAGGG
Found at i:18614699 original size:20 final size:20
Alignment explanation
Indices: 18614674--18614713 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
18614664 TTGATGCTGC
18614674 CTGTGAGATTGGCGTCACCG
1 CTGTGAGATTGGCGTCACCG
18614694 CTGTGAGATTGGCGTCACCG
1 CTGTGAGATTGGCGTCACCG
18614714 GGCTGCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.25, G:0.35, T:0.25
Consensus pattern (20 bp):
CTGTGAGATTGGCGTCACCG
Found at i:18624234 original size:13 final size:13
Alignment explanation
Indices: 18624216--18624240 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18624206 AATAAAAAAA
18624216 AAATTTGAAATTC
1 AAATTTGAAATTC
18624229 AAATTTGAAATT
1 AAATTTGAAATT
18624241 TCTCCCGCTT
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:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (13 bp):
AAATTTGAAATTC
Found at i:18637582 original size:14 final size:15
Alignment explanation
Indices: 18637558--18637587 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
18637548 GGATATCAAA
18637558 ACAAGAATTAAGAAC
1 ACAAGAATTAAGAAC
18637573 ACAA-AATTAAGAAC
1 ACAAGAATTAAGAAC
18637587 A
1 A
18637588 AGTTAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.63, C:0.13, G:0.10, T:0.13
Consensus pattern (15 bp):
ACAAGAATTAAGAAC
Found at i:18646869 original size:36 final size:37
Alignment explanation
Indices: 18646815--18646888 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
18646805 ATCCTACAAA
*
18646815 CTAGATAAAACCACTAAAATGCGAGT-AAATGCAATG
1 CTAGATAAAACCACTAAAAAGCGAGTAAAATGCAATG
** * *
18646851 CTAGATAAAAGTATTAAAAAGTGAGTAAAATGCAATG
1 CTAGATAAAACCACTAAAAAGCGAGTAAAATGCAATG
18646888 C
1 C
18646889 AGAAACTATC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
36 21 0.66
37 11 0.34
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.22
Consensus pattern (37 bp):
CTAGATAAAACCACTAAAAAGCGAGTAAAATGCAATG
Found at i:18653085 original size:32 final size:32
Alignment explanation
Indices: 18653019--18653086 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
18653009 TAGAACTAGA
* *
18653019 AACTTATGTTCAAATTTCATATTACATAATAG
1 AACTTATGTTCAAATTTCATAGTACATAAAAG
*
18653051 AACTTATGTTTCAGATTTCA-AGTAGC-TAAAAG
1 AACTTATG-TTCAAATTTCATAGTA-CATAAAAG
18653083 AACT
1 AACT
18653087 ACTATCTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
32 20 0.65
33 11 0.35
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (32 bp):
AACTTATGTTCAAATTTCATAGTACATAAAAG
Found at i:18655062 original size:23 final size:23
Alignment explanation
Indices: 18654990--18655076 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
18654980 CCTGATCAGT
18654990 ATACGACACATAAAGTGCCT-AA
1 ATACGACACATAAAGTGCCTGAA
* ** * *
18655012 A-ATGACACACGAGGTGCTTG--
1 ATACGACACATAAAGTGCCTGAA
* *
18655032 ATACGACACATGAGGTGCCTGAA
1 ATACGACACATAAAGTGCCTGAA
18655055 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
18655077 TCAGTAAAGT
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
20 1 0.02
21 29 0.57
22 1 0.02
23 20 0.39
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAA
Found at i:18658300 original size:22 final size:22
Alignment explanation
Indices: 18658258--18658307 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
18658248 TCTGAGCTGA
*
18658258 TAAACGGTAAGCTCTGAAGAGC
1 TAAACGGTAAGCTCTCAAGAGC
18658280 TAAACGGTAAGCTC-CATAGAGC
1 TAAACGGTAAGCTCTCA-AGAGC
18658302 TGAAAC
1 T-AAAC
18658308 AGAAACAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 20 0.80
23 4 0.16
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (22 bp):
TAAACGGTAAGCTCTCAAGAGC
Found at i:18663092 original size:79 final size:79
Alignment explanation
Indices: 18663004--18663162 Score: 264
Period size: 79 Copynumber: 2.0 Consensus size: 79
18662994 CCCTTTTCTG
* * * * *
18663004 GCTAAAAAATATTAAAGCCTGATCATGTGTCCCCAACAAAAAGATCAACCTTTTAGCTTAAAGCT
1 GCTAAAAAATACTAAAGCCTGATCAAGCGTCCCCAACAAAAAGATCAACCTTGTAGATTAAAGCT
18663069 CTACTCTTCTATCT
66 CTACTCTTCTATCT
*
18663083 GCTAAAAAATACTAAAGCCTGATCAAGCGTCCCCAATAAAAAGATCAACCTTGTAGATTAAAGCT
1 GCTAAAAAATACTAAAGCCTGATCAAGCGTCCCCAACAAAAAGATCAACCTTGTAGATTAAAGCT
18663148 CTACTCTTCTATCT
66 CTACTCTTCTATCT
18663162 G
1 G
18663163 TTGAGGAACT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
79 74 1.00
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.28
Consensus pattern (79 bp):
GCTAAAAAATACTAAAGCCTGATCAAGCGTCCCCAACAAAAAGATCAACCTTGTAGATTAAAGCT
CTACTCTTCTATCT
Found at i:18669556 original size:95 final size:95
Alignment explanation
Indices: 18669451--18669641 Score: 382
Period size: 95 Copynumber: 2.0 Consensus size: 95
18669441 ATGCCCTCAA
18669451 AAATTTCATAATATATGGCATCTCATAACTAATCTTTTTCACCATAACTTACCAACTACTTGTTT
1 AAATTTCATAATATATGGCATCTCATAACTAATCTTTTTCACCATAACTTACCAACTACTTGTTT
18669516 TAACATAATTAAGCCATGATGACTATACAT
66 TAACATAATTAAGCCATGATGACTATACAT
18669546 AAATTTCATAATATATGGCATCTCATAACTAATCTTTTTCACCATAACTTACCAACTACTTGTTT
1 AAATTTCATAATATATGGCATCTCATAACTAATCTTTTTCACCATAACTTACCAACTACTTGTTT
18669611 TAACATAATTAAGCCATGATGACTATACAT
66 TAACATAATTAAGCCATGATGACTATACAT
18669641 A
1 A
18669642 TTTGTCTCAT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.37
Consensus pattern (95 bp):
AAATTTCATAATATATGGCATCTCATAACTAATCTTTTTCACCATAACTTACCAACTACTTGTTT
TAACATAATTAAGCCATGATGACTATACAT
Found at i:18669743 original size:17 final size:17
Alignment explanation
Indices: 18669721--18669753 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
18669711 AAAGTAAGGT
18669721 TATCCAATGGTGTTTAC
1 TATCCAATGGTGTTTAC
18669738 TATCCAATGGTGTTTA
1 TATCCAATGGTGTTTA
18669754 TCTCTTGGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.42
Consensus pattern (17 bp):
TATCCAATGGTGTTTAC
Found at i:18670009 original size:20 final size:20
Alignment explanation
Indices: 18669970--18670009 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
18669960 CTTGATGAAG
*
18669970 CTTTCTCTCTCAAGATTTAA
1 CTTTCTCTCTCAAGACTTAA
*
18669990 CTTTCTCTCTCTAGACTTAA
1 CTTTCTCTCTCAAGACTTAA
18670010 GAAAAACCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.28, G:0.05, T:0.45
Consensus pattern (20 bp):
CTTTCTCTCTCAAGACTTAA
Found at i:18673722 original size:20 final size:20
Alignment explanation
Indices: 18673699--18673738 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
18673689 TAATTTTCCT
18673699 CATCTAAAAAGCATTTCTAA
1 CATCTAAAAAGCATTTCTAA
18673719 CATCTAAAAAGCATTTCTAA
1 CATCTAAAAAGCATTTCTAA
18673739 TTTCTTATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (20 bp):
CATCTAAAAAGCATTTCTAA
Found at i:18680272 original size:15 final size:15
Alignment explanation
Indices: 18680254--18680284 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18680244 ATATATATGC
18680254 TAATAAATAATAAAA
1 TAATAAATAATAAAA
*
18680269 TAATATATAATAAAA
1 TAATAAATAATAAAA
18680284 T
1 T
18680285 GAAGATAATA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAATAAATAATAAAA
Found at i:18686350 original size:14 final size:14
Alignment explanation
Indices: 18686308--18686350 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
18686298 TTTTAAATAT
18686308 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
*
18686321 TCATAATGGTTTAA
1 TTATAATGGTTTAA
18686335 TTATAATGGTTTAA
1 TTATAATGGTTTAA
18686349 TT
1 TT
18686351 CATCGTTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 6 0.22
14 21 0.78
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:18687129 original size:43 final size:43
Alignment explanation
Indices: 18687066--18687218 Score: 207
Period size: 43 Copynumber: 3.6 Consensus size: 43
18687056 TGAGAAATGC
* * * * *
18687066 GCCGTTAAAAGTCAAGTTCTTTAGCGGGGTTTGTATGAAAAGC
1 GCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTGTATGAAAAGT
* * * * *
18687109 GCCTCTAAAGGTCCCGTTCTTTGGCGGCGTTTGTTTGAGAAGT
1 GCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTGTATGAAAAGT
*
18687152 GCCGCTAAAGGTCACGTTCTTTAGCTGCGTTTGTATGAAAAGT
1 GCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTGTATGAAAAGT
18687195 GCCGCTAAAGGTCACGTTCTTTAG
1 GCCGCTAAAGGTCACGTTCTTTAG
18687219 AGACGCTTTC
Statistics
Matches: 94, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 94 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (43 bp):
GCCGCTAAAGGTCACGTTCTTTAGCGGCGTTTGTATGAAAAGT
Found at i:18691386 original size:13 final size:13
Alignment explanation
Indices: 18691370--18691402 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
18691360 TTTAATTAAA
*
18691370 TTAGTTAATTAGT
1 TTAGATAATTAGT
18691383 TTAGATAATTAGT
1 TTAGATAATTAGT
18691396 TTA-ATAA
1 TTAGATAA
18691403 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:18697552 original size:16 final size:16
Alignment explanation
Indices: 18697531--18697568 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
18697521 CCATTGTTCT
*
18697531 AAAAAAATGAA-TGAA
1 AAAAAAAAGAAGTGAA
18697546 AAAAAAAAGAAGTGAA
1 AAAAAAAAGAAGTGAA
18697562 AAAAAAA
1 AAAAAAA
18697569 CATTTATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (16 bp):
AAAAAAAAGAAGTGAA
Found at i:18698409 original size:30 final size:30
Alignment explanation
Indices: 18698373--18698433 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
18698363 GAGTTTTCAG
* *
18698373 GATCCACACGGGCTGGGC-ACACGCCCATGT
1 GATCCACACAGGC-AGGCAACACGCCCATGT
*
18698403 GATCCACACAGGCAGGCAATACGCCCATGT
1 GATCCACACAGGCAGGCAACACGCCCATGT
18698433 G
1 G
18698434 CCAGCCCCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 3 0.11
30 24 0.89
ACGTcount: A:0.25, C:0.34, G:0.28, T:0.13
Consensus pattern (30 bp):
GATCCACACAGGCAGGCAACACGCCCATGT
Found at i:18701596 original size:5 final size:5
Alignment explanation
Indices: 18701586--18701610 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
18701576 AATGAAATTC
18701586 TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA
18701611 AAAAAACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:18709468 original size:16 final size:16
Alignment explanation
Indices: 18709443--18709488 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
18709433 CCAGAAAAAC
18709443 ACAA-TTGTTCTAAAT
1 ACAAGTTGTTCTAAAT
18709458 ACAAGTTGTTCTAAAT
1 ACAAGTTGTTCTAAAT
*
18709474 A-ATGGTTGTTCTAAA
1 ACA-AGTTGTTCTAAA
18709489 CATAGTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 5 0.18
16 23 0.82
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (16 bp):
ACAAGTTGTTCTAAAT
Found at i:18711176 original size:32 final size:33
Alignment explanation
Indices: 18711146--18711324 Score: 168
Period size: 33 Copynumber: 5.5 Consensus size: 33
18711136 GGTGTACATT
**
18711146 CCTTTCCAAGTGGTACACACAAAGTATACATTT
1 CCTTTCCAAGTGGTACACACAAAGTATACATAA
* * * *
18711179 CCTTTTCATA-TGGTATACACTAAGTATACCTAA
1 CCTTTCCA-AGTGGTACACACAAAGTATACATAA
* * **
18711212 CCTTTCCAAGT-GTACACATAAAGTATACCTTT
1 CCTTTCCAAGTGGTACACACAAAGTATACATAA
* * * *
18711244 CCTTTTCATA-TGGTATACACTAAGTATACCTAA
1 CCTTTCCA-AGTGGTACACACAAAGTATACATAA
*
18711277 CCTTTCCAAGT-GTACACACAAAGTGTACATAA
1 CCTTTCCAAGTGGTACACACAAAGTATACATAA
*
18711309 CCTTTCCAAGTTGTAC
1 CCTTTCCAAGTGGTAC
18711325 CATTTGGGTA
Statistics
Matches: 117, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
32 54 0.46
33 62 0.53
34 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (33 bp):
CCTTTCCAAGTGGTACACACAAAGTATACATAA
Found at i:18711313 original size:65 final size:65
Alignment explanation
Indices: 18711146--18711306 Score: 286
Period size: 65 Copynumber: 2.5 Consensus size: 65
18711136 GGTGTACATT
18711146 CCTTTCCAAGTGGTACACACAAAGTATACATTTCCTTTTCATATGGTATACACTAAGTATACCTA
1 CCTTTCCAAGT-GTACACACAAAGTATACATTTCCTTTTCATATGGTATACACTAAGTATACCTA
18711211 A
65 A
* *
18711212 CCTTTCCAAGTGTACACATAAAGTATACCTTTCCTTTTCATATGGTATACACTAAGTATACCTAA
1 CCTTTCCAAGTGTACACACAAAGTATACATTTCCTTTTCATATGGTATACACTAAGTATACCTAA
*
18711277 CCTTTCCAAGTGTACACACAAAGTGTACAT
1 CCTTTCCAAGTGTACACACAAAGTATACAT
18711307 AACCTTTCCA
Statistics
Matches: 90, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
65 79 0.88
66 11 0.12
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.33
Consensus pattern (65 bp):
CCTTTCCAAGTGTACACACAAAGTATACATTTCCTTTTCATATGGTATACACTAAGTATACCTAA
Found at i:18712503 original size:13 final size:13
Alignment explanation
Indices: 18712485--18712509 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18712475 CACATATTTG
18712485 ATAAAAATTTTCT
1 ATAAAAATTTTCT
18712498 ATAAAAATTTTC
1 ATAAAAATTTTC
18712510 ATGCAATATT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAAATTTTCT
Found at i:18717918 original size:3 final size:3
Alignment explanation
Indices: 18717910--18717937 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
18717900 TTTGACCTCG
18717910 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
18717938 CATCTTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:18722047 original size:34 final size:35
Alignment explanation
Indices: 18722003--18722069 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
18721993 CAGTAAAATA
18722003 TTTTCCGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
18722037 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
18722070 CTGGTGTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:18737154 original size:25 final size:25
Alignment explanation
Indices: 18737126--18737177 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
18737116 AAATTAACTT
18737126 ACCATTTATTTCACATTTAAGGTAA
1 ACCATTTATTTCACATTTAAGGTAA
18737151 ACCATTTATTTCACATTTAAGGTAA
1 ACCATTTATTTCACATTTAAGGTAA
18737176 AC
1 AC
18737178 TAACTAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (25 bp):
ACCATTTATTTCACATTTAAGGTAA
Found at i:18737626 original size:25 final size:24
Alignment explanation
Indices: 18737544--18737639 Score: 61
Period size: 25 Copynumber: 3.9 Consensus size: 24
18737534 CCCTCTCTCA
* *
18737544 AGCCATATAACAAGAAGTTCATGT
1 AGCCATATAACAAGAAGCTCATAT
* * *
18737568 GAGCCATGTAACAGGAAGCTTAT-T
1 -AGCCATATAACAAGAAGCTCATAT
* * *
18737592 CGGGCTATATAACAGGAAGCTCATAAT
1 --AGCCATATAACAAGAAGCTCAT-AT
*
18737619 AGCCATAT-TCAAGAAGCTCAT
1 AGCCATATAACAAGAAGCTCAT
18737640 GCGAGCCATT
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
24 12 0.21
25 43 0.77
27 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.24
Consensus pattern (24 bp):
AGCCATATAACAAGAAGCTCATAT
Found at i:18745556 original size:32 final size:33
Alignment explanation
Indices: 18745448--18745561 Score: 124
Period size: 33 Copynumber: 3.5 Consensus size: 33
18745438 GGTGTACGTT
* **
18745448 CCTTTTCAACTGGTACACACAAAGTATACATTT
1 CCTTTTCAAGTGGTACACACAAAGTATACATAA
* *
18745481 CCTTTTCATA-TGGTATACACAAAGTATACCTAA
1 CCTTTTCA-AGTGGTACACACAAAGTATACATAA
* *
18745514 CCTTTCCAAGT-GTACACACAAAGTGTACATAA
1 CCTTTTCAAGTGGTACACACAAAGTATACATAA
* *
18745546 CTTTTTCAAGTTGTAC
1 CCTTTTCAAGTGGTAC
18745562 CATTTGGGTA
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
32 28 0.41
33 39 0.57
34 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (33 bp):
CCTTTTCAAGTGGTACACACAAAGTATACATAA
Found at i:18746757 original size:13 final size:13
Alignment explanation
Indices: 18746739--18746763 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18746729 CACATATTTG
18746739 ATAAAAATTTTCT
1 ATAAAAATTTTCT
18746752 ATAAAAATTTTC
1 ATAAAAATTTTC
18746764 ATGAAATATT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAAATTTTCT
Found at i:18748631 original size:29 final size:31
Alignment explanation
Indices: 18748583--18748646 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
18748573 TTTATAATTA
*
18748583 TTTAATTAGATAATTATTATT-TATTTAATAT
1 TTTAATAAGATAATTATTATTAT-TTTAATAT
*
18748614 TTTAATAAGAT-ATT-TTATTATTTTATTAT
1 TTTAATAAGATAATTATTATTATTTTAATAT
18748643 TTTA
1 TTTA
18748647 TTTAGTCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.53
30 4 0.13
31 10 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (31 bp):
TTTAATAAGATAATTATTATTATTTTAATAT
Done.