Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 125 of 221
Found at i:38544862 original size:40 final size:42
Alignment explanation
Indices: 38544786--38544864 Score: 117
Period size: 40 Copynumber: 1.9 Consensus size: 42
38544776 CCGAATATAA
* *
38544786 TAAATATATTTTTTATTTTTATTTTTTAATTTTAAAATACTT
1 TAAAAATATTTTTTATTTATATTTTTTAATTTTAAAATACTT
*
38544828 TAAAAATATTTTTT-TTTAT-TTTTTTATTTTTAAAATA
1 TAAAAATATTTTTTATTTATATTTTTTAATTTTAAAATA
38544865 ATTTTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 17 0.50
41 4 0.12
42 13 0.38
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (42 bp):
TAAAAATATTTTTTATTTATATTTTTTAATTTTAAAATACTT
Found at i:38549387 original size:22 final size:21
Alignment explanation
Indices: 38549353--38549421 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 21
38549343 AGGCAACCCA
38549353 ATTTTTATTTTTATTATTTACT
1 ATTTTT-TTTTTATTATTTACT
*
38549375 ATTTTTTTCTTTACTTTATTTATT
1 ATTTTTTT-TTTA--TTATTTACT
38549399 ACTTTATTTTATTTTATTATTTA
1 A--TT-TTTT-TTTTATTATTTA
38549422 TTACTTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
21 2 0.05
22 10 0.26
24 9 0.23
25 7 0.18
26 2 0.05
27 8 0.21
28 1 0.03
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (21 bp):
ATTTTTTTTTTATTATTTACT
Found at i:38549402 original size:12 final size:12
Alignment explanation
Indices: 38549385--38549431 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
38549375 ATTTTTTTCT
38549385 TTACTTTATTTA
1 TTACTTTATTTA
38549397 TTACTTTATTTTA
1 TTACTTTA-TTTA
*
38549410 TT-TTATTATTTA
1 TTACT-TTATTTA
38549422 TTAC-TTATTT
1 TTACTTTATTT
38549432 GGATATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
11 6 0.20
12 15 0.50
13 9 0.30
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (12 bp):
TTACTTTATTTA
Found at i:38549421 original size:17 final size:17
Alignment explanation
Indices: 38549355--38549423 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 17
38549345 GCAACCCAAT
38549355 TTTTATTTTTATTATTTA
1 TTTTA-TTTTATTATTTA
* * *
38549373 --CTATTTTTTTCTTTA
1 TTTTATTTTATTATTTA
*
38549388 CTTTA-TTTATTACTTTA
1 TTTTATTTTATTA-TTTA
38549405 TTTTATTTTATTATTTA
1 TTTTATTTTATTATTTA
38549422 TT
1 TT
38549424 ACTTATTTGG
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
15 10 0.25
16 7 0.17
17 16 0.40
18 7 0.17
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTATTTTATTATTTA
Found at i:38549424 original size:25 final size:25
Alignment explanation
Indices: 38549355--38549431 Score: 81
Period size: 24 Copynumber: 3.1 Consensus size: 25
38549345 GCAACCCAAT
*
38549355 TTTTATTTTTATTATTTACTA-TTT-
1 TTTTA-TTTTATTATTTATTACTTTA
*
38549379 TTTT-CTTTACTTTATTTATTACTTTA
1 TTTTATTTTA--TTATTTATTACTTTA
38549405 TTTTATTTTATTATTTATTAC-TTA
1 TTTTATTTTATTATTTATTACTTTA
38549429 TTT
1 TTT
38549432 GGATATTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.09
24 19 0.42
25 14 0.31
26 4 0.09
27 4 0.09
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTATTTTATTATTTATTACTTTA
Found at i:38550368 original size:101 final size:100
Alignment explanation
Indices: 38550180--38550366 Score: 241
Period size: 101 Copynumber: 1.8 Consensus size: 100
38550170 GAACATGTTG
* * * *
38550180 GGCTGAGTAACCAATGTGGGGTGCTTGGCTGTCATCTCTTTTCGCATCAAAAGGTTCGATGTGTT
1 GGCTGAGTAACCAAGGTGGGGTGCTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTCGATATGTC
*
38550245 CTTAAGAAAAAATTATAATAAATTAGGAGTCTGCTT
66 CTAAAGAAAAAA-TATAATAAATTAGGAGTCTGCTT
** *
38550281 GGCTGAGTAACCGGGGTGGGGTGCTTGGCTGTCATCTCTCTTCGCGTCAAAAGGTTCAGTATAT-
1 GGCTGAGTAACCAAGGTGGGGTGCTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTC-G-ATATG
38550345 TCCTAAAGCATAAAAAATATAA
64 TCCTAAAG---AAAAAATATAA
38550367 ATAATAAATA
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
101 52 0.71
102 7 0.10
103 3 0.04
104 5 0.07
105 6 0.08
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (100 bp):
GGCTGAGTAACCAAGGTGGGGTGCTTGGCTGTCATCTCTCTTCGCATCAAAAGGTTCGATATGTC
CTAAAGAAAAAATATAATAAATTAGGAGTCTGCTT
Found at i:38550385 original size:17 final size:16
Alignment explanation
Indices: 38550354--38550403 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
38550344 TTCCTAAAGC
*
38550354 ATAAAAAATATAAATA
1 ATAAAAAATAAAAATA
38550370 ATAAATAAATAAAAATA
1 ATAAA-AAATAAAAATA
*
38550387 A-AAAAAGACAAAAATA
1 ATAAAAA-ATAAAAATA
38550403 A
1 A
38550404 AGAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 2 0.07
16 17 0.57
17 11 0.37
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (16 bp):
ATAAAAAATAAAAATA
Found at i:38558027 original size:44 final size:44
Alignment explanation
Indices: 38557979--38558559 Score: 167
Period size: 44 Copynumber: 13.2 Consensus size: 44
38557969 TATCTTGGAA
*
38557979 AGATAAGATTTGTCATCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGTCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * * *
38558023 AGATAAGATCT-ACAATCTTCAACCTACTCCTCTGCTGCTCAGGG
1 AGATAAGATTTGTC-ATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * ** * *
38558067 AGACAAGGCTTGGT-GGCTTAAATCTGCTTCCAACTA-T-CTT-GGAA
1 AGATAA-GATTTGTCATCTTTAATCTGC-TCC-ACTACTGCTTAGG-G
*
38558111 AGATAAGATTTGTCATCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGTCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * * *
38558155 AGATAAGATCT-ACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGTC-ATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * ** * *
38558199 AGACAAGGCTTGGT-GGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTTGTCATCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* * *
38558243 AGATAAGATTTGCCATCTTTGATCTGCTCCACTACTGCCTAGGG
1 AGATAAGATTTGTCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * ** * ** * *
38558287 AGATAAGATCT-ACAATCTTCAGCCTACTCTGCTGCTGCTCAGGG
1 AGATAAGATTTGTC-ATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * ** * * *
38558331 AGACAAGGCTTGGT-GGCTTAAATATGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTTGTCATCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* * * **
38558375 AGATAATATTTGTCGTCTTTGATCTGCTCCACTACTGCTTACAG
1 AGATAAGATTTGTCATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * *
38558419 AGATAAGATAT-ACAATCTTCAACCTACTCCGCTACTGCTCAGGG
1 AGATAAGATTTGTC-ATCTTTAATCTGCTCCACTACTGCTTAGGG
* * * ** * *
38558463 AGACAAGGCTTGGT-GGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTTGTCATCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* * *
38558507 AGATAAGATTTGTCGTCTTTGATCTGCTCCATTACTGCTTAGGG
1 AGATAAGATTTGTCATCTTTAATCTGCTCCACTACTGCTTAGGG
38558551 AGATAAGAT
1 AGATAAGAT
38558560 CTACAATATT
Statistics
Matches: 360, Mismatches: 137, Indels: 80
0.62 0.24 0.14
Matches are distributed among these distances:
42 21 0.06
43 40 0.11
44 261 0.73
45 24 0.07
46 14 0.04
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (44 bp):
AGATAAGATTTGTCATCTTTAATCTGCTCCACTACTGCTTAGGG
Found at i:38558103 original size:132 final size:132
Alignment explanation
Indices: 38557931--38558665 Score: 1308
Period size: 132 Copynumber: 5.6 Consensus size: 132
38557921 CTGCAACTTT
*
38557931 AGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCAACTATCTTGGAAAGATAAGATTTGTCATC
1 AGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCATC
*
38557996 TTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCTCTGCTGC
66 TTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGC
38558061 TC
131 TC
*
38558063 AGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCAACTATCTTGGAAAGATAAGATTTGTCATC
1 AGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCATC
38558128 TTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGC
66 TTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGC
38558193 TC
131 TC
*
38558195 AGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATC
1 AGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCATC
* * *
38558260 TTTGATCTGCTCCACTACTGCCTAGGGAGATAAGATCTACAATCTTCAGCCTACTCTGCTGCTGC
66 TTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGC
38558325 TC
131 TC
* * *
38558327 AGGGAGACAAGGCTTGGTGGCTTAAATATGCTTCCCACTATCTTGGAAAGATAATATTTGTCGTC
1 AGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCATC
** * *
38558392 TTTGATCTGCTCCACTACTGCTTACAGAGATAAGATATACAATCTTCAACCTACTCCGCTACTGC
66 TTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGC
38558457 TC
131 TC
*
38558459 AGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTC
1 AGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCATC
* *
38558524 TTTGATCTGCTCCATTACTGCTTAGGGAGATAAGATCTACAATATTCAACCTACTCCGCTGCTGC
66 TTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGC
38558589 TC
131 TC
*
38558591 AGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCATC
1 AGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCATC
38558656 TTTGATCTGC
66 TTTGATCTGC
38558666 CTCGCTGTCA
Statistics
Matches: 576, Mismatches: 27, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 576 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (132 bp):
AGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCATC
TTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGC
TC
Found at i:38566736 original size:24 final size:24
Alignment explanation
Indices: 38566707--38566752 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
38566697 ATCATCTTTT
* *
38566707 GCTGCTCATTCATTTGCTTTTGAA
1 GCTGCTCATGCATTTCCTTTTGAA
*
38566731 GCTGCTCCTGCATTTCCTTTTG
1 GCTGCTCATGCATTTCCTTTTG
38566753 GGATTGTTCT
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:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (24 bp):
GCTGCTCATGCATTTCCTTTTGAA
Found at i:38570831 original size:16 final size:17
Alignment explanation
Indices: 38570793--38570835 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
38570783 TAGAAAGTAT
38570793 AATATATATACGTACATA
1 AATATATA-ACGTACATA
* *
38570811 TATATATAAGGTA-ATA
1 AATATATAACGTACATA
38570827 AATATATAA
1 AATATATAA
38570836 ATCATAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 11 0.50
17 4 0.18
18 7 0.32
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (17 bp):
AATATATAACGTACATA
Found at i:38571420 original size:19 final size:20
Alignment explanation
Indices: 38571393--38571436 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
38571383 CGGGCATCGA
*
38571393 CCGGTCGTCGACCACC-GCG
1 CCGGCCGTCGACCACCAGCG
* *
38571412 CCGGCCGTCGATCTCCAGCG
1 CCGGCCGTCGACCACCAGCG
38571432 CCGGC
1 CCGGC
38571437 ACCGCCGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.09, C:0.48, G:0.32, T:0.11
Consensus pattern (20 bp):
CCGGCCGTCGACCACCAGCG
Found at i:38573487 original size:15 final size:14
Alignment explanation
Indices: 38573462--38573497 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
38573452 GACTCTATTT
*
38573462 TAATTATATTAGGA
1 TAATTATATTAAGA
38573476 TAATTGATATTAAGA
1 TAATT-ATATTAAGA
38573491 TAATTAT
1 TAATTAT
38573498 TAAGGATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (14 bp):
TAATTATATTAAGA
Found at i:38576815 original size:13 final size:13
Alignment explanation
Indices: 38576789--38576874 Score: 52
Period size: 13 Copynumber: 6.5 Consensus size: 13
38576779 ATCGAGTGAA
* *
38576789 AAATGAATAAATG
1 AAATGATTATATG
38576802 AAATGATTATATG
1 AAATGATTATATG
*
38576815 -AATCGGTTATATGG
1 AAAT-GATTATAT-G
*
38576829 AAGTAGA-TATATG
1 AAAT-GATTATATG
*
38576842 AAATGGTTATATGG
1 AAATGATTATAT-G
*
38576856 AACTAGA-TATATG
1 AAAT-GATTATATG
38576869 AAATGA
1 AAATGA
38576875 AATATTGGAT
Statistics
Matches: 56, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
12 6 0.11
13 31 0.55
14 15 0.27
15 4 0.07
ACGTcount: A:0.45, C:0.02, G:0.21, T:0.31
Consensus pattern (13 bp):
AAATGATTATATG
Found at i:38576841 original size:14 final size:14
Alignment explanation
Indices: 38576822--38576872 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
38576812 ATGAATCGGT
*
38576822 TATATGGAAGTAGA
1 TATATGGAAATAGA
* *
38576836 TATAT-GAAATGGT
1 TATATGGAAATAGA
*
38576849 TATATGGAACTAGA
1 TATATGGAAATAGA
38576863 TATAT-GAAAT
1 TATATGGAAAT
38576873 GAAATATTGG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
13 14 0.48
14 15 0.52
ACGTcount: A:0.43, C:0.02, G:0.22, T:0.33
Consensus pattern (14 bp):
TATATGGAAATAGA
Found at i:38576871 original size:27 final size:27
Alignment explanation
Indices: 38576809--38576873 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
38576799 ATGAAATGAT
*
38576809 TATATG-AATCGGTTATATGGAAGTAGA
1 TATATGAAAT-GGTTATATGGAACTAGA
38576836 TATATGAAATGGTTATATGGAACTAGA
1 TATATGAAATGGTTATATGGAACTAGA
38576863 TATATGAAATG
1 TATATGAAATG
38576874 AAATATTGGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 33 0.92
28 3 0.08
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (27 bp):
TATATGAAATGGTTATATGGAACTAGA
Found at i:38576883 original size:27 final size:27
Alignment explanation
Indices: 38576822--38576904 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
38576812 ATGAATCGGT
* **
38576822 TATATGGAAGTAGATATATGAAATGGT
1 TATATGGAACTAGATATATGAAATGAA
38576849 TATATGGAACTAGATATATGAAATGAA
1 TATATGGAACTAGATATATGAAATGAA
* *
38576876 -ATATTGGATA-TAAATATTTGAAAT-AA
1 TATA-TGGA-ACTAGATATATGAAATGAA
38576902 TAT
1 TAT
38576905 GTGAATTGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
26 5 0.10
27 42 0.88
28 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.18, T:0.35
Consensus pattern (27 bp):
TATATGGAACTAGATATATGAAATGAA
Found at i:38580566 original size:28 final size:28
Alignment explanation
Indices: 38580534--38580588 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
38580524 CCTTTTTACA
*
38580534 ATTTAGTTTTTTTCACCTAATTAACCAG
1 ATTTAGTCTTTTTCACCTAATTAACCAG
38580562 ATTTAGTCTTTTTCACCTAATTAACCA
1 ATTTAGTCTTTTTCACCTAATTAACCA
38580589 TTTAAACTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.45
Consensus pattern (28 bp):
ATTTAGTCTTTTTCACCTAATTAACCAG
Found at i:38589826 original size:31 final size:30
Alignment explanation
Indices: 38589786--38589861 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 30
38589776 ATAAAATTTG
* * *
38589786 AAAAGTTAAAATAA-TATATAATTTTTTTATA
1 AAAATTTAAAAAAAGTATATAA-ATTTTTA-A
*
38589817 AAAATTTAAAAAAAGTATTTAAATTTTTAA
1 AAAATTTAAAAAAAGTATATAAATTTTTAA
**
38589847 AAAATTGCAAAAAAG
1 AAAATTTAAAAAAAG
38589862 AAAACTTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 14 0.37
31 18 0.47
32 6 0.16
ACGTcount: A:0.57, C:0.01, G:0.05, T:0.37
Consensus pattern (30 bp):
AAAATTTAAAAAAAGTATATAAATTTTTAA
Found at i:38590027 original size:17 final size:17
Alignment explanation
Indices: 38590007--38590053 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
38589997 ATTTAAGGTT
38590007 TTTTTAATATTTTTTAA
1 TTTTTAATATTTTTTAA
* * * *
38590024 TTTTAAATAATTTATAT
1 TTTTTAATATTTTTTAA
38590041 TTTTTAA-ATTTTT
1 TTTTTAATATTTTT
38590054 ATATATTATT
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTAATATTTTTTAA
Found at i:38590054 original size:17 final size:17
Alignment explanation
Indices: 38590006--38590057 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
38589996 AATTTAAGGT
38590006 TTTTTTAATATTTTT-TA
1 TTTTTTAA-ATTTTTATA
* *
38590023 -ATTTTAAATAATTTATA
1 TTTTTTAAAT-TTTTATA
38590040 TTTTTTAAATTTTTATA
1 TTTTTTAAATTTTTATA
38590057 T
1 T
38590058 ATTATTTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 2 0.07
16 9 0.32
17 9 0.32
18 8 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTTAAATTTTTATA
Found at i:38591745 original size:25 final size:25
Alignment explanation
Indices: 38591717--38591795 Score: 95
Period size: 25 Copynumber: 3.2 Consensus size: 25
38591707 GATAATCGAT
*
38591717 TTAAGGATCCCTTGATGGATTTGAA
1 TTAAGAATCCCTTGATGGATTTGAA
* * *
38591742 TTAATAATCCCTTAAAGGATTTGAA
1 TTAAGAATCCCTTGATGGATTTGAA
* * *
38591767 TCAAGAATCCCCTGATGGATTTGAG
1 TTAAGAATCCCTTGATGGATTTGAA
38591792 TTAA
1 TTAA
38591796 TGATATTGTT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (25 bp):
TTAAGAATCCCTTGATGGATTTGAA
Found at i:38595011 original size:50 final size:50
Alignment explanation
Indices: 38594900--38595196 Score: 294
Period size: 50 Copynumber: 5.8 Consensus size: 50
38594890 ATTTGGGTAA
* *
38594900 AGAGATCCCATGTAAGACCATGTTTGGGACATGGCATTGGTATCCTTGAGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* *
38594956 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
38595006 AGAGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
38595056 AGAGGTCTCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGATC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * * * *
38595106 AGAAATCTCATGTAAGACCATATCTGAGATATGACATTGGCA--GTACATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* * ** *
38595155 AAACATCTTATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
38595197 TGTTATTATC
Statistics
Matches: 210, Mismatches: 28, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
48 1 0.00
49 39 0.19
50 125 0.60
51 2 0.01
53 3 0.01
55 2 0.01
56 38 0.18
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:38597742 original size:31 final size:31
Alignment explanation
Indices: 38597706--38597768 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
38597696 AAATAATGGC
38597706 AGGACATATGATAATATTATTAACTCAGAAG
1 AGGACATATGATAATATTATTAACTCAGAAG
38597737 AGGACATATGATAATATTATTAACTCAGAAG
1 AGGACATATGATAATATTATTAACTCAGAAG
38597768 A
1 A
38597769 TGTACATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.29
Consensus pattern (31 bp):
AGGACATATGATAATATTATTAACTCAGAAG
Found at i:38602372 original size:23 final size:23
Alignment explanation
Indices: 38602346--38602389 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
38602336 TCATATTATA
38602346 CAATTAAAACAATTCATCTTGTG
1 CAATTAAAACAATTCATCTTGTG
38602369 CAATTAAAACAATTCATCTTG
1 CAATTAAAACAATTCATCTTG
38602390 CTAATGCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (23 bp):
CAATTAAAACAATTCATCTTGTG
Found at i:38604209 original size:28 final size:29
Alignment explanation
Indices: 38604159--38604216 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
38604149 TAAAATACGG
*
38604159 ACTAAAATAATAATTTATTACATT-TTAA
1 ACTAAAATAATAATTTATAACATTATTAA
*
38604187 ACTATAATAATAAATTTA-AACATTATTAA
1 ACTAAAATAAT-AATTTATAACATTATTAA
38604216 A
1 A
38604217 ATTAAATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (29 bp):
ACTAAAATAATAATTTATAACATTATTAA
Found at i:38615491 original size:25 final size:25
Alignment explanation
Indices: 38615462--38615511 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
38615452 ATTATTTAAT
38615462 ATAAAAA-TATACAAAAAAAATAAAA
1 ATAAAAAGTA-ACAAAAAAAATAAAA
* *
38615487 ATAAAAAGTAACTAAACAAATAAAA
1 ATAAAAAGTAACAAAAAAAATAAAA
38615512 TAATGTAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.16
Consensus pattern (25 bp):
ATAAAAAGTAACAAAAAAAATAAAA
Found at i:38616069 original size:21 final size:21
Alignment explanation
Indices: 38616031--38616070 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
38616021 TCTTTTTTTT
*
38616031 TATGTATTCCGGCTTGTCCAG
1 TATGTATTCCGGCATGTCCAG
38616052 TATGTA-TCCGGGCATGTCC
1 TATGTATTCC-GGCATGTCC
38616071 GACGAGTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (21 bp):
TATGTATTCCGGCATGTCCAG
Found at i:38620535 original size:40 final size:40
Alignment explanation
Indices: 38620480--38620562 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
38620470 TTTTTCTTAA
38620480 GTTAGAATTACAACCCAAGCAATTGACTCTGACGATTTGG
1 GTTAGAATTACAACCCAAGCAATTGACTCTGACGATTTGG
38620520 GTTAGAATTACAACCCAAGCAATTGACTCTGACGATTTGG
1 GTTAGAATTACAACCCAAGCAATTGACTCTGACGATTTGG
38620560 GTT
1 GTT
38620563 TTCTTTTGGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (40 bp):
GTTAGAATTACAACCCAAGCAATTGACTCTGACGATTTGG
Found at i:38624356 original size:39 final size:39
Alignment explanation
Indices: 38624302--38624382 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
38624292 ATGCAATCGA
38624302 TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
1 TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
38624341 TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
1 TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
38624380 TTT
1 TTT
38624383 TCATTTTAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (39 bp):
TTTGTTCATCTTTAAAGCTTTACTTGAACTATTGTTTTC
Found at i:38624768 original size:29 final size:29
Alignment explanation
Indices: 38624693--38625556 Score: 1478
Period size: 29 Copynumber: 29.3 Consensus size: 29
38624683 CGAATAAACC
38624693 AAATACACTACATATATTTTTTTATTTTTA
1 AAATACACTACATATA-TTTTTTATTTTTA
38624723 AAATACACT-CAATATATTTTTTTTATTTTTA
1 AAATACACTAC-ATATA--TTTTTTATTTTTA
38624754 AAATACACTACATATATTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
38624783 AAATACACTACATATATTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
*
38624812 AAATACACTACATATTTTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
*
38624841 AAGTACACTACATATATTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
* * *
38624870 AAATACACAACATACATTTTTTACTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
38624899 AAATACACTACATATATATTTTTATTTTTA
1 AAATACACTACATATAT-TTTTTATTTTTA
38624929 AAATACACTACATATATTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
38624958 AAATACACTACATATATTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
38624987 AAATACACTACATATATTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
38625016 AAATACACTACATATATATTTTTTTATTTTTA
1 AAATACACTAC--ATATA-TTTTTTATTTTTA
*
38625048 AAGTACACTACATATATTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
38625077 AAATACACTACATATATTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
38625106 AAATACACTACATATATTTTTTTATTTTTA
1 AAATACACTACATATA-TTTTTTATTTTTA
38625136 AAATACACTACATATATTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
38625165 AAATACACTACATATATATTTTTTTATTTTTA
1 AAATACACTAC--ATATA-TTTTTTATTTTTA
38625197 AAATACACTACATATATTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
*
38625226 AAATACACTACATATTTTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
* *
38625255 AAATATACTACATATTTTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
38625284 AAATACACTACATATATTTTTTTATTTTTA
1 AAATACACTACATATA-TTTTTTATTTTTA
*
38625314 AAATACACTACATATAGTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
38625343 AAATACACTACATATATTTTTTTATTTTTA
1 AAATACACTACATATA-TTTTTTATTTTTA
38625373 AAATACACTACATATATTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
38625402 AAATACACTACATATATTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
38625431 AAATACACTACATATATTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
38625460 AAATACACTACATATATTTTTTATTTTTA
1 AAATACACTACATATATTTTTTATTTTTA
38625489 AAATACACTACATATATTTCTTTATTTTTA
1 AAATACACTACATATATTT-TTTATTTTTA
*
38625519 AAATACATTACATATATTTTTTTATTTTTA
1 AAATACACTACATATA-TTTTTTATTTTTA
38625549 AAATACAC
1 AAATACAC
38625557 AAATACAATA
Statistics
Matches: 799, Mismatches: 20, Indels: 30
0.94 0.02 0.04
Matches are distributed among these distances:
29 530 0.66
30 180 0.23
31 41 0.05
32 48 0.06
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.52
Consensus pattern (29 bp):
AAATACACTACATATATTTTTTATTTTTA
Found at i:38624940 original size:88 final size:88
Alignment explanation
Indices: 38624693--38625556 Score: 1497
Period size: 88 Copynumber: 9.8 Consensus size: 88
38624683 CGAATAAACC
38624693 AAATACACTACATATATTTTTTTATTTTTAAAATACACT-CAATATATTTTTTTTATTTTTAAAA
1 AAATACACTACATATA-TTTTTTATTTTTAAAATACACTAC-ATATA-TTTTTTTATTTTTAAAA
38624757 TACACTACATATATTTTTTATTTTTA
63 TACACTACATATATTTTTTATTTTTA
*
38624783 AAATACACTACATATATTTTTTATTTTTAAAATACACTACATAT-TTTTTTTATTTTTAAAGTAC
1 AAATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATAC
38624847 ACTACATATATTTTTTATTTTTA
66 ACTACATATATTTTTTATTTTTA
* * * *
38624870 AAATACACAACATACATTTTTTACTTTTAAAATACACTACATATATATTTTTATTTTTAAAATAC
1 AAATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATAC
38624935 ACTACATATATTTTTTATTTTTA
66 ACTACATATATTTTTTATTTTTA
38624958 AAATACACTACATATATTTTTTATTTTTAAAATACACTACATATA-TTTTTTATTTTTAAAATAC
1 AAATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATAC
38625022 ACTACATATATATTTTTTTATTTTTA
66 ACTAC--ATATA-TTTTTTATTTTTA
*
38625048 AAGTACACTACATATATTTTTTATTTTTAAAATACACTACATATA-TTTTTTATTTTTAAAATAC
1 AAATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATAC
38625112 ACTACATATATTTTTTTATTTTTA
66 ACTACATATA-TTTTTTATTTTTA
38625136 AAATACACTACATATATTTTTTATTTTTAAAATACACTACATATATATTTTTTTATTTTTAAAAT
1 AAATACACTACATATATTTTTTATTTTTAAAATACACTAC--ATATATTTTTTTATTTTTAAAAT
38625201 ACACTACATATATTTTTTATTTTTA
64 ACACTACATATATTTTTTATTTTTA
* *
38625226 AAATACACTACATATTTTTTTTATTTTTAAAATATACTACATAT-TTTTTTTATTTTTAAAATAC
1 AAATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATAC
38625290 ACTACATATATTTTTTTATTTTTA
66 ACTACATATA-TTTTTTATTTTTA
*
38625314 AAATACACTACATATAGTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATAC
1 AAATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATAC
38625379 ACTACATATATTTTTTATTTTTA
66 ACTACATATATTTTTTATTTTTA
38625402 AAATACACTACATATATTTTTTATTTTTAAAATACACTACATATA-TTTTTTATTTTTAAAATAC
1 AAATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATAC
38625466 ACTACATATATTTTTTATTTTTA
66 ACTACATATATTTTTTATTTTTA
*
38625489 AAATACACTACATATATTTCTTTATTTTTAAAATACATTACATATATTTTTTTATTTTTAAAATA
1 AAATACACTACATATATTT-TTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATA
38625554 CAC
65 CAC
38625557 AAATACAATA
Statistics
Matches: 743, Mismatches: 19, Indels: 25
0.94 0.02 0.03
Matches are distributed among these distances:
87 197 0.27
88 281 0.38
89 82 0.11
90 154 0.21
91 29 0.04
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.52
Consensus pattern (88 bp):
AAATACACTACATATATTTTTTATTTTTAAAATACACTACATATATTTTTTTATTTTTAAAATAC
ACTACATATATTTTTTATTTTTA
Found at i:38625649 original size:42 final size:44
Alignment explanation
Indices: 38625602--38625690 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 44
38625592 CTTCTATCGA
*
38625602 TTCCCCTCTTCCACCG-TGCCCTCCTCCCATTTCCCA-TCCCAT
1 TTCCCCTCTTCCACCGATCCCCTCCTCCCATTTCCCATTCCCAT
* *
38625644 TTCCCCTCTTCCATCGATTCCCCTCCTCTCATTTCCCATTCCCAT
1 TTCCCCTCTTCCACCGA-TCCCCTCCTCCCATTTCCCATTCCCAT
38625689 TT
1 TT
38625691 ACGGTTACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
42 15 0.37
44 18 0.44
45 8 0.20
ACGTcount: A:0.10, C:0.51, G:0.03, T:0.36
Consensus pattern (44 bp):
TTCCCCTCTTCCACCGATCCCCTCCTCCCATTTCCCATTCCCAT
Found at i:38627581 original size:19 final size:21
Alignment explanation
Indices: 38627500--38627575 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
38627490 ATCTTCGAGG
*
38627500 ATATGCCATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
38627519 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
38627540 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
38627561 ATATGCAATCTTAGA
1 ATATGCAATCTTAGA
38627576 AGATATGATT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
19 18 0.33
21 36 0.67
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:38627597 original size:23 final size:24
Alignment explanation
Indices: 38627512--38627598 Score: 93
Period size: 21 Copynumber: 4.0 Consensus size: 24
38627502 ATGCCATCTT
38627512 AGATATG--ATATGCAATCTT---
1 AGATATGATATATGCAATCTTAGA
38627531 AGATATGATATATGCAATCTT---
1 AGATATGATATATGCAATCTTAGA
38627552 AGATATGATATATGCAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
* *
38627576 AGATATGAT-TTTGTAATCTTAGA
1 AGATATGATATATGCAATCTTAGA
38627599 GATTTAATTT
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
19 7 0.11
21 33 0.54
23 12 0.20
24 9 0.15
ACGTcount: A:0.38, C:0.08, G:0.16, T:0.38
Consensus pattern (24 bp):
AGATATGATATATGCAATCTTAGA
Found at i:38628047 original size:18 final size:18
Alignment explanation
Indices: 38628022--38628065 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
38628012 GTTTTTAGTC
*
38628022 TATT-TTATTA-ATTTTA
1 TATTATTATTATATTATA
38628038 TTATTATTATTATATTATA
1 -TATTATTATTATATTATA
38628057 TATTATTAT
1 TATTATTAT
38628066 ACCTACATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 15 0.62
19 5 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTATTATTATATTATA
Found at i:38628062 original size:15 final size:14
Alignment explanation
Indices: 38628022--38628066 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
38628012 GTTTTTAGTC
*
38628022 TATT-TTATTAATTT
1 TATTATTATT-ATTA
38628036 TATTATTATTATTA
1 TATTATTATTATTA
38628050 TATTATATATTATTA
1 TATTAT-TATTATTA
38628065 TA
1 TA
38628067 CCTACATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 13 0.46
15 15 0.54
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:38634708 original size:44 final size:44
Alignment explanation
Indices: 38634660--38634799 Score: 131
Period size: 44 Copynumber: 3.2 Consensus size: 44
38634650 AAGTTACCAG
*
38634660 CCTTGCCTCCCTGGGTTGCAGTGGAGCAGGCTAAAAATAGTAGA
1 CCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAGTAGA
* **** * * * * * *
38634704 CCTTGCCTTCCTGCACCGACAGCGAAGCA-GATCGAAGACACTAG-
1 CCTTGCCTCCCTGGGTTG-CAGCGGAGCAGGCT-AAAAATAGTAGA
38634748 CCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAGTAGA
1 CCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAGTAGA
*
38634792 TCTTGCCT
1 CCTTGCCT
38634800 TCTTACACCG
Statistics
Matches: 68, Mismatches: 24, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
43 16 0.24
44 37 0.54
45 15 0.22
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.21
Consensus pattern (44 bp):
CCTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTAAAAATAGTAGA
Found at i:38634776 original size:43 final size:43
Alignment explanation
Indices: 38634634--38634776 Score: 117
Period size: 43 Copynumber: 3.3 Consensus size: 43
38634624 TCCTGTACTG
* *
38634634 GCAGCGAAGCAGATCGAAGTTACCAGCCTTGCCTCCCTGGGTT
1 GCAGCGAAGCAGATCGAAGATACTAGCCTTGCCTCCCTGGGTT
* * * * * * * ****
38634677 GCAGTGGAGCAG-GCTAAAAATAGTAGACCTTGCCTTCCTGCACC
1 GCAGCGAAGCAGATC-GAAGATACTAG-CCTTGCCTCCCTGGGTT
*
38634721 GACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTGGGTT
1 G-CAGCGAAGCAGATCGAAGATACTAGCCTTGCCTCCCTGGGTT
*
38634765 GCAGCGGAGCAG
1 GCAGCGAAGCAG
38634777 GCTAAAAATA
Statistics
Matches: 70, Mismatches: 26, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
42 1 0.01
43 26 0.37
44 26 0.37
45 16 0.23
46 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.18
Consensus pattern (43 bp):
GCAGCGAAGCAGATCGAAGATACTAGCCTTGCCTCCCTGGGTT
Found at i:38635111 original size:88 final size:88
Alignment explanation
Indices: 38634612--38635101 Score: 667
Period size: 88 Copynumber: 5.6 Consensus size: 88
38634602 GTGAAGATAA
* * * **
38634612 CAGATCTTGCCTTCCTGTACTGGCAGCGAAGCAGATCGAAGTTACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
38634677 GCAGTGGAGCAGGCTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * *
38634700 TAGACCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
38634765 GCAGCGGAGCAGGCTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
* * * * * *
38634788 TAGATCTTGCCTTCTTACACCGACAACGAAACAGATCGAAGTCACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
38634853 GCAGAGGAGCAGGCTAAAAATAA
66 GCAGCGGAGCAGGCTAAAAATAG
* * * *
38634876 CAGATATTGCCTTCTTGCACCAACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
38634941 GCAGCGGAGTAGGC-AGAAAATAG
66 GCAGCGGAGCAGGCTA-AAAATAG
* * *
38634964 CAGATCTTGCCTTTCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTACCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
38635029 GTAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGCTAAAAATAG
** * * * *
38635052 CAGATCTTGCCTTCCTGCACATACAACGAAGCAGATTGATGACCCCAGCC
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
38635102 CTATCTCCCT
Statistics
Matches: 354, Mismatches: 46, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
87 1 0.00
88 352 0.99
89 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGCTAAAAATAG
Found at i:38635167 original size:44 final size:44
Alignment explanation
Indices: 38635103--38635455 Score: 384
Period size: 44 Copynumber: 8.2 Consensus size: 44
38635093 ACCCCAGCCC
* *
38635103 TATCTCCCTGGTCAGTAGTGGAATAGGTTAAAGATTGTGAATCT
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCT
* * *
38635147 TATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCT
* *
38635191 TATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGAGAAT-T
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCT
* *
38635234 CTATCTCCCTAGG-CAGCAGCGGAATAGATT-AA-A----GAATCT
1 -TATCTCCCT-GGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCT
* * * * * * *
38635273 TATTTCCTTGGACAACAGCGGAATAGGTTAAAGATTGTGAATCA
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCT
*
38635317 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAAT-T
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCT
* * * *
38635360 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGT-AGGTCC
1 -TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGA-ATCT
* * *
38635405 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATGGTGAACCC
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCT
38635449 TATCTCC
1 TATCTCC
38635456 TTGAGCAGTA
Statistics
Matches: 261, Mismatches: 34, Indels: 28
0.81 0.11 0.09
Matches are distributed among these distances:
37 2 0.01
38 26 0.10
39 3 0.01
40 1 0.00
42 1 0.00
43 3 0.01
44 223 0.85
45 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAATCT
Found at i:38635308 original size:126 final size:126
Alignment explanation
Indices: 38635141--38635394 Score: 427
Period size: 126 Copynumber: 2.0 Consensus size: 126
38635131 TAAAGATTGT
* * *
38635141 GAATCTTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTAGTCAG
1 GAATCTTATCTCCCTGGACAACAGCGGAATAGGTTAAAGATTGTGAATCATATCTCCCTAGTCAG
38635206 CAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTAGGCAGCAGCGGAATAGATTAAA
66 CAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTAGGCAGCAGCGGAATAGATTAAA
* * *
38635267 GAATCTTATTTCCTTGGACAACAGCGGAATAGGTTAAAGATTGTGAATCATATCTCCCTGGTCAG
1 GAATCTTATCTCCCTGGACAACAGCGGAATAGGTTAAAGATTGTGAATCATATCTCCCTAGTCAG
* * *
38635332 CAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAA
66 CAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTAGGCAGCAGCGGAATAGATTAAA
38635393 GA
1 GA
38635395 TTGTAGGTCC
Statistics
Matches: 119, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
126 119 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.28
Consensus pattern (126 bp):
GAATCTTATCTCCCTGGACAACAGCGGAATAGGTTAAAGATTGTGAATCATATCTCCCTAGTCAG
CAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTAGGCAGCAGCGGAATAGATTAAA
Found at i:38635410 original size:170 final size:170
Alignment explanation
Indices: 38635122--38635430 Score: 487
Period size: 170 Copynumber: 1.8 Consensus size: 170
38635112 GGTCAGTAGT
* *
38635122 GGAATAGGTTAAAGATTGTGAATCTTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGA
1 GGAATAGGTTAAAGATTGTGAATCATATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGA
* * *
38635187 ATCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGAGAATTCTATCTCCCTAGG-CAGC
66 ATCCTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTGAGAATCCTATCTCCCT-GGTCAGC
38635251 AGCGGAATAGATTAAAGAATCTTATTTCCTTGGACAACAGC
130 AGCGGAATAGATTAAAGAATCTTATTTCCTTGGACAACAGC
* *
38635292 GGAATAGGTTAAAGATTGTGAATCATATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGA
1 GGAATAGGTTAAAGATTGTGAATCATATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGA
* * *
38635357 ATTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGTAG-GTCCTATCTCCCTGGTCAGC
66 ATCCTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTG-AGAATCCTATCTCCCTGGTCAGC
*
38635421 AGTGGAATAG
130 AGCGGAATAG
38635431 GTTGAAGATG
Statistics
Matches: 126, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
169 2 0.02
170 122 0.97
171 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (170 bp):
GGAATAGGTTAAAGATTGTGAATCATATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGAGA
ATCCTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTGAGAATCCTATCTCCCTGGTCAGCA
GCGGAATAGATTAAAGAATCTTATTTCCTTGGACAACAGC
Found at i:38635876 original size:44 final size:44
Alignment explanation
Indices: 38635783--38635890 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 44
38635773 ATGGAAAATT
* *
38635783 TTATCTCCCTGAAGTTGCAATGAAGAAGATTAAAGCCGATAATC
1 TTATCTCCCTGAAGTTGCAGTGAAGAAGATTAAAACCGATAATC
* ** * *
38635827 CTATCTCCCTGAAGTTGCAGTGAAGCGGATTAAAACC-TTGGATC
1 TTATCTCCCTGAAGTTGCAGTGAAGAAGATTAAAACCGAT-AATC
* *
38635871 TTATCTCTCTAAAGTTGCAG
1 TTATCTCCCTGAAGTTGCAG
38635891 AGAGCAAAAC
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 1 0.02
44 52 0.98
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGAAGAAGATTAAAACCGATAATC
Found at i:38636344 original size:21 final size:21
Alignment explanation
Indices: 38636319--38636383 Score: 121
Period size: 21 Copynumber: 3.1 Consensus size: 21
38636309 ATCTTCGAGG
38636319 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
*
38636340 ATATGCAATCTTAGATATTAT
1 ATATGCAATCTTAGATATGAT
38636361 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
38636382 AT
1 AT
38636384 GTAATCTTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.40
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:38636389 original size:19 final size:19
Alignment explanation
Indices: 38636318--38636394 Score: 100
Period size: 21 Copynumber: 3.8 Consensus size: 19
38636308 AATCTTCGAG
38636318 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
38636337 GATATATGCAATCTTAGATATT
1 G--ATATGCAATCTTAGATA-T
*
38636359 ATATATGCAATCTTAGATAT
1 -GATATGCAATCTTAGATAT
*
38636379 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
38636395 AGATATGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
19 15 0.29
20 1 0.02
21 34 0.67
22 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:38636401 original size:22 final size:23
Alignment explanation
Indices: 38636373--38636417 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
38636363 ATGCAATCTT
*
38636373 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATATTAGA
*
38636395 AGATATGATTTTGTAATATTAGA
1 AGATATGATTATGTAATATTAGA
38636418 GATTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.40, C:0.02, G:0.18, T:0.40
Consensus pattern (23 bp):
AGATATGATTATGTAATATTAGA
Found at i:38636427 original size:22 final size:23
Alignment explanation
Indices: 38636383--38636427 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
38636373 AGATATGATA
* *
38636383 TGTAATCTTAGAAGATATGATTT
1 TGTAATATTAGAAGATATAATTT
*
38636406 TGTAATATTAG-AGATTTAATTT
1 TGTAATATTAGAAGATATAATTT
38636428 GTAGATACGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATATTAGAAGATATAATTT
Found at i:38636869 original size:12 final size:13
Alignment explanation
Indices: 38636849--38636890 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
38636839 ATTTTATTAA
*
38636849 ATTTGTTATTATT
1 ATTTATTATTATT
38636862 ATTT-TTATTATT
1 ATTTATTATTATT
38636874 ATATTATATATTATT
1 AT-TTAT-TATTATT
38636889 AT
1 AT
38636891 ACCTACATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 10 0.38
13 6 0.23
14 1 0.04
15 9 0.35
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (13 bp):
ATTTATTATTATT
Found at i:38636890 original size:15 final size:13
Alignment explanation
Indices: 38636854--38636891 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
38636844 ATTAAATTTG
38636854 TTATTATTAT-TT
1 TTATTATTATATT
38636866 TTATTATTATATT
1 TTATTATTATATT
38636879 ATATATTATTATA
1 -T-TATTATTATA
38636892 CCTACATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.43
13 2 0.09
14 1 0.04
15 10 0.43
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTATTATATT
Found at i:38638726 original size:21 final size:22
Alignment explanation
Indices: 38638685--38638729 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
38638675 CCAAGAACAA
*
38638685 AGCAAAAAAGAGAGGAGAAACC
1 AGCAAAAAAGAGAGGACAAACC
*
38638707 AGCAAAAATGAG-GGACAAACC
1 AGCAAAAAAGAGAGGACAAACC
38638728 AG
1 AG
38638730 TAAGAACAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.56, C:0.16, G:0.27, T:0.02
Consensus pattern (22 bp):
AGCAAAAAAGAGAGGACAAACC
Found at i:38638755 original size:21 final size:21
Alignment explanation
Indices: 38638698--38638769 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
38638688 AAAAAAGAGA
* **
38638698 GGAGAAACCAGCAAAAATGAG
1 GGAGAAACCAGCAAGAACAAG
* *
38638719 GGACAAACCAGTAAGAACAAG
1 GGAGAAACCAGCAAGAACAAG
* *
38638740 GGAGAAACCAACAAGAACTAGG
1 GGAGAAACCAGCAAGAAC-AAG
38638762 GGAGAAAC
1 GGAGAAAC
38638770 TGCTGTTTTG
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 31 0.76
22 10 0.24
ACGTcount: A:0.51, C:0.17, G:0.28, T:0.04
Consensus pattern (21 bp):
GGAGAAACCAGCAAGAACAAG
Found at i:38646513 original size:19 final size:19
Alignment explanation
Indices: 38646464--38646502 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
38646454 GTGACCCTTA
38646464 TTTTC-AAAATTTTCCTAT
1 TTTTCTAAAATTTTCCTAT
38646482 TTTTCTAAAATTTT-CTAT
1 TTTTCTAAAATTTTCCTAT
38646500 TTT
1 TTT
38646503 GTTTGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTCTAAAATTTTCCTAT
Found at i:38652274 original size:13 final size:13
Alignment explanation
Indices: 38652256--38652285 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
38652246 TGACGAGATG
38652256 CAAAAGTGCAAGC
1 CAAAAGTGCAAGC
*
38652269 CAAAAGTTCAAGC
1 CAAAAGTGCAAGC
38652282 CAAA
1 CAAA
38652286 TGGGGGATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.23, G:0.17, T:0.10
Consensus pattern (13 bp):
CAAAAGTGCAAGC
Found at i:38658590 original size:23 final size:23
Alignment explanation
Indices: 38658563--38658719 Score: 160
Period size: 23 Copynumber: 7.0 Consensus size: 23
38658553 GGCTTTGCCG
38658563 ATCAGGCACTTTATGTGTCGTAC
1 ATCAGGCACTTTATGTGTCGTAC
*
38658586 ATCAGACACTTTATGTGTCGTATC
1 ATCAGGCACTTTATGTGTCGTA-C
* *
38658610 -TTAGGCACATTATGTGTCGTAC
1 ATCAGGCACTTTATGTGTCGTAC
*
38658632 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAC
* * ** *
38658655 TTCAGGCACCTCGTGTGTCGTAT
1 ATCAGGCACTTTATGTGTCGTAC
* * * *
38658678 TTCAGGCACCTTGTGTGTC--AT
1 ATCAGGCACTTTATGTGTCGTAC
38658699 ATCAGGCAC-TTATGTGTCGTA
1 ATCAGGCACTTTATGTGTCGTA
38658720 TACTGATCAG
Statistics
Matches: 116, Mismatches: 14, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
20 8 0.07
21 10 0.09
22 2 0.02
23 95 0.82
24 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.36
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAC
Found at i:38658623 original size:46 final size:45
Alignment explanation
Indices: 38658566--38658719 Score: 179
Period size: 46 Copynumber: 3.4 Consensus size: 45
38658556 TTTGCCGATC
*
38658566 AGGCACTTTATGTGTCGTACATCAGACACTTTATGTGTCGTATCTT
1 AGGCAC-TTATGTGTCGTACATCAGGCACTTTATGTGTCGTATCTT
38658612 AGGCACATTATGTGTCGTACATCAGGCACTTTATGTGTCGTAT-TT
1 AGGCAC-TTATGTGTCGTACATCAGGCACTTTATGTGTCGTATCTT
** ** * * *
38658657 CAGGCACCTCGTGTGTCGTATTTCAGGCACCTTGTGTGTCATATC--
1 -AGGCA-CTTATGTGTCGTACATCAGGCACTTTATGTGTCGTATCTT
38658702 AGGCACTTATGTGTCGTA
1 AGGCACTTATGTGTCGTA
38658720 TACTGATCAG
Statistics
Matches: 94, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
43 11 0.12
44 5 0.05
45 2 0.02
46 75 0.80
47 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (45 bp):
AGGCACTTATGTGTCGTACATCAGGCACTTTATGTGTCGTATCTT
Found at i:38658674 original size:69 final size:67
Alignment explanation
Indices: 38658563--38658721 Score: 196
Period size: 69 Copynumber: 2.4 Consensus size: 67
38658553 GGCTTTGCCG
* * *
38658563 ATCAGGCACTTTATGTGTCGTACATCAGACACTTTATGTGTCGTATCTT-AGGCACATTATGTGT
1 ATCAGGCACTTTATGTGTCGTATATCAGACACCTCATGTGTCGTAT-TTCAGGCACATTATGTGT
38658627 CGTAC
65 C--AC
* * * * *
38658632 ATCAGGCACTTTATGTGTCGTATTTCAGGCACCTCGTGTGTCGTATTTCAGGCACCTTGTGTGTC
1 ATCAGGCACTTTATGTGTCGTATATCAGACACCTCATGTGTCGTATTTCAGGCACATTATGTGTC
*
38658697 AT
66 AC
38658699 ATCAGGCAC-TTATGTGTCGTATA
1 ATCAGGCACTTTATGTGTCGTATA
38658722 CTGATCAGGT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
66 13 0.16
67 10 0.13
68 2 0.03
69 54 0.68
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (67 bp):
ATCAGGCACTTTATGTGTCGTATATCAGACACCTCATGTGTCGTATTTCAGGCACATTATGTGTC
AC
Found at i:38661434 original size:28 final size:28
Alignment explanation
Indices: 38661378--38661434 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
38661368 ACGGTTAAAT
* *
38661378 AGTTTAGGTACCAATTCTAACAAAAAAA
1 AGTTTAGATACCAATTCTAAAAAAAAAA
38661406 AGTTTAGATACCAATT-TAAAAAAACAAA
1 AGTTTAGATACCAATTCTAAAAAAA-AAA
38661434 A
1 A
38661435 ACTAGTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.54, C:0.12, G:0.09, T:0.25
Consensus pattern (28 bp):
AGTTTAGATACCAATTCTAAAAAAAAAA
Found at i:38662753 original size:19 final size:17
Alignment explanation
Indices: 38662731--38662771 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
38662721 ACTTTAGACT
38662731 TTTTTTCATTTTCTATATA
1 TTTTTTCATTTTCT-TA-A
*
38662750 TTTTTTTATTTTCTTAA
1 TTTTTTCATTTTCTTAA
38662767 TTTTT
1 TTTTT
38662772 AATTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 2 0.10
19 13 0.62
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTTCATTTTCTTAA
Found at i:38664738 original size:18 final size:18
Alignment explanation
Indices: 38664715--38664750 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
38664705 ATTAATAATG
*
38664715 TTATATATTATGTTATTT
1 TTATATATTATGTAATTT
38664733 TTATATATTATGTAATTT
1 TTATATATTATGTAATTT
38664751 ATAACATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (18 bp):
TTATATATTATGTAATTT
Found at i:38664751 original size:16 final size:17
Alignment explanation
Indices: 38664710--38664753 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
38664700 TTTAAATTAA
38664710 TAATGTTATATATTATGT
1 TAAT-TTATATATTATGT
*
38664728 TATTTTTATATATTATG-
1 TA-ATTTATATATTATGT
38664745 TAATTTATA
1 TAATTTATA
38664754 ACATATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 6 0.26
17 2 0.09
18 14 0.61
19 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (17 bp):
TAATTTATATATTATGT
Found at i:38671590 original size:28 final size:29
Alignment explanation
Indices: 38671532--38671597 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
38671522 TTTAAATAAA
*
38671532 AAAATTATAGGGACTTAAATATTAAAATT
1 AAAAGTATAGGGACTTAAATATTAAAATT
* *
38671561 AAAA-TATAGGGA-TTAAATTTTAAATTTT
1 AAAAGTATAGGGACTTAAATATTAAA-ATT
38671589 AAAAGTATA
1 AAAAGTATA
38671598 CAAGAACCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 11 0.33
28 14 0.42
29 8 0.24
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.36
Consensus pattern (29 bp):
AAAAGTATAGGGACTTAAATATTAAAATT
Found at i:38672329 original size:25 final size:24
Alignment explanation
Indices: 38672276--38672335 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
38672266 TTATTTTACA
38672276 TTTTTA-ATAAATTTTAAATTGTT
1 TTTTTAGATAAATTTTAAATTGTT
*
38672299 TATTTTAGATAATATTTTATGATT-TT
1 T-TTTTAGATAA-ATTTTA-AATTGTT
38672325 TTTTTAG-TAAA
1 TTTTTAGATAAA
38672336 GTAGGCTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
23 2 0.06
24 8 0.25
25 10 0.31
26 9 0.28
27 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (24 bp):
TTTTTAGATAAATTTTAAATTGTT
Found at i:38675224 original size:12 final size:12
Alignment explanation
Indices: 38675207--38675240 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
38675197 AAATTTGACA
38675207 TTATTATTATTG
1 TTATTATTATTG
*
38675219 TTATTATTGTTG
1 TTATTATTATTG
38675231 TTATTTATTA
1 TTA-TTATTA
38675241 GTTTTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (12 bp):
TTATTATTATTG
Found at i:38675432 original size:14 final size:15
Alignment explanation
Indices: 38675415--38675455 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
38675405 TTACTATATT
38675415 TTATTTATATTT-AC
1 TTATTTATATTTGAC
*
38675429 TTATTTATATTTGTC
1 TTATTTATATTTGAC
38675444 TTATTATATATT
1 TTATT-TATATT
38675456 ATTATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.50
15 6 0.25
16 6 0.25
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (15 bp):
TTATTTATATTTGAC
Found at i:38675459 original size:10 final size:10
Alignment explanation
Indices: 38675444--38675477 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
38675434 TATATTTGTC
38675444 TTATTATATA
1 TTATTATATA
38675454 TTATTATATAA
1 TTATTATAT-A
38675465 TTATTTATATA
1 TTA-TTATATA
38675476 TT
1 TT
38675478 CTTTTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.41
11 7 0.32
12 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATTATATA
Found at i:38683918 original size:27 final size:27
Alignment explanation
Indices: 38683879--38683938 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
38683869 TATTGTGCTT
38683879 TGTTGCCCAACAAAGCTCACAGTACAA
1 TGTTGCCCAACAAAGCTCACAGTACAA
*
38683906 TGTTGCCCGACAAAGCTCACAGTACAA
1 TGTTGCCCAACAAAGCTCACAGTACAA
38683933 TGTTGC
1 TGTTGC
38683939 TAATACTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (27 bp):
TGTTGCCCAACAAAGCTCACAGTACAA
Found at i:38685860 original size:109 final size:108
Alignment explanation
Indices: 38685662--38686140 Score: 357
Period size: 109 Copynumber: 4.5 Consensus size: 108
38685652 GTATACAGGG
* * * ******
38685662 AAAAAAAAT-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCACCTTTATGT-AATTTTTTTTTAC
1 AAAAAAAATATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAGAATTTAC
* * *
38685725 ATTTTGAGTTGTCATTGGCTGACACCAGTATACAAAAAATTCA
66 ATTTTGGGTTGTCATTGGCCGGCACCAGTATACAAAAAATTCA
**
38685768 AAAAAAGAATATTTTGGTGGTGGCCTGGCAATGGTTGGCACCACCTTTATGTAAAAAAGAATTTA
1 AAAAAA-AATATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAGAATTTA
38685833 CATTTTGGGTTGTCATTGGCCGGCACCAGTATACGAAAAAATTC-
65 CATTTTGGGTTGTCATTGGCCGGCACCAGTATAC-AAAAAATTCA
* *****
38685877 AAAAAAAA-A--TT--T--T----TGGCAATGGCCGGCACCACCTTTATG--CAATTTTTTTTAA
1 AAAAAAAATATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAGAATTT-A
* * * * *
38685929 CATTTTGGGCTGTCATTAGCCGGTACCAGTATACGAAAAATTTAA
65 CATTTTGGGTTGTCATTGGCCGGCACCAGTATAC-AAAAAATTCA
* * *****
38685974 AAAAAAAATTTTTTTGGTGGTGGCCTGGCAATAGCCGGCACCACCTTTATGTAAATTTCTTTTTT
1 AAAAAAAA-TATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAA-----AAAGA
* * **
38686039 TTTTACATTTTGGGCTGTCATTGGCCAACACCAGTATACGAAAACAATTC-
60 ATTTACATTTTGGGTTGTCATTGGCCGGCACCAGTATAC-AAAA-AATTCA
** * *
38686089 --AAAATTTTTTTTGGTGGTGGCCTGGCAATGGCCGGCATCACCTTTATGTAAA
1 AAAAAAAATATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAA
38686141 TTTTTGGTGG
Statistics
Matches: 306, Mismatches: 41, Indels: 46
0.78 0.10 0.12
Matches are distributed among these distances:
95 5 0.02
96 40 0.13
97 32 0.10
101 3 0.01
103 2 0.01
105 3 0.01
106 6 0.02
107 4 0.01
108 38 0.12
109 68 0.22
110 9 0.03
111 1 0.00
112 44 0.14
113 4 0.01
115 36 0.12
116 11 0.04
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (108 bp):
AAAAAAAATATTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAGAATTTAC
ATTTTGGGTTGTCATTGGCCGGCACCAGTATACAAAAAATTCA
Found at i:38686134 original size:112 final size:112
Alignment explanation
Indices: 38685919--38686143 Score: 317
Period size: 112 Copynumber: 2.0 Consensus size: 112
38685909 CTTTATGCAA
*** *
38685919 TTTTTTTTAACATTTTGGGCTGTCATTAGCCGGTACCAGTATACGAAAAATTTAAAAAAAAAATT
1 TTTTTTTTAACATTTTGGGCTGTCATTAGCCAACACCAGTATACGAAAAAATT---AAAAAAATT
38685984 TTTTTGGTGGTGGCCTGGCAATAGCCGGCACCACCTTTATGTAAATTTCT
63 TTTTTGGTGGTGGCCTGGCAATAGCCGGCACCACCTTTATGTAAATTTCT
* * * *
38686034 TTTTTTTTTACATTTTGGGCTGTCATTGGCCAACACCAGTATACGAAAACAATT-CAAAATTTTT
1 TTTTTTTTAACATTTTGGGCTGTCATTAGCCAACACCAGTATACGAAAA-AATTAAAAAAATTTT
* *
38686098 TTTGGTGGTGGCCTGGCAATGGCCGGCATCACCTTTATGTAAATTT
65 TTTGGTGGTGGCCTGGCAATAGCCGGCACCACCTTTATGTAAATTT
38686144 TTGGTGGTGG
Statistics
Matches: 99, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
112 52 0.53
115 44 0.44
116 3 0.03
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (112 bp):
TTTTTTTTAACATTTTGGGCTGTCATTAGCCAACACCAGTATACGAAAAAATTAAAAAAATTTTT
TTGGTGGTGGCCTGGCAATAGCCGGCACCACCTTTATGTAAATTTCT
Found at i:38686150 original size:45 final size:45
Alignment explanation
Indices: 38686096--38686185 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
38686086 TTCAAAATTT
*
38686096 TTTTTGGTGGTGGCCTGGCAATGGCCGGCATCACCTTTATGTAAA
1 TTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAA
*
38686141 TTTTTGGTGGTGGCCTGGCAATGGCTGGCACCACCTTTATGTAAA
1 TTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAA
38686186 AAAATTATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (45 bp):
TTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAA
Found at i:38686154 original size:157 final size:155
Alignment explanation
Indices: 38685984--38686295 Score: 428
Period size: 158 Copynumber: 2.0 Consensus size: 155
38685974 AAAAAAAATT
****
38685984 TTTTTGGTGGTGGCCTGGCAATAGCCGGCACCACCTTTATGTAAATTTCTT-TTTTTTTTACATT
1 TTTTTGGTGGTGGCCTGGCAATAGCCGGCACCACCTTTATGTAAAAAAATTATTTTTTTTACATT
* * ** *
38686048 TTGGGCTGTCATTGGCCAACACCAGTATACGAAAACAATTCAAAATTTTTTTTGGTGGTGGCCTG
66 TTGAGCTGTCATTGGCCAACACCAGTATACGAAAAAAATT--AAA-TTTTTTTCATGGTGGCCCG
* *
38686113 GCAATGGCCGGCATCACCTTTATGTAAA
128 GCAATGGCCGACACCACCTTTATGTAAA
* *
38686141 TTTTTGGTGGTGGCCTGGCAATGGCTGGCACCACCTTTATGTAAAAAAATTATTTTTTTTACATT
1 TTTTTGGTGGTGGCCTGGCAATAGCCGGCACCACCTTTATGTAAAAAAATTATTTTTTTTACATT
** * *
38686206 TTGAGCTGTCATTGGCCTGCACTAGTATATGAAAAAAATTAAATTTTTTTCATGGTGGCCCGGCA
66 TTGAGCTGTCATTGGCCAACACCAGTATACGAAAAAAATTAAATTTTTTTCATGGTGGCCCGGCA
*
38686271 ATGGCCGACACCACTTTTATGTAAA
131 ATGGCCGACACCACCTTTATGTAAA
38686296 AAAATTTACA
Statistics
Matches: 136, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
155 41 0.30
156 3 0.02
157 45 0.33
158 47 0.35
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (155 bp):
TTTTTGGTGGTGGCCTGGCAATAGCCGGCACCACCTTTATGTAAAAAAATTATTTTTTTTACATT
TTGAGCTGTCATTGGCCAACACCAGTATACGAAAAAAATTAAATTTTTTTCATGGTGGCCCGGCA
ATGGCCGACACCACCTTTATGTAAA
Found at i:38689454 original size:54 final size:55
Alignment explanation
Indices: 38689375--38689493 Score: 143
Period size: 56 Copynumber: 2.2 Consensus size: 55
38689365 ATATTCTTGT
* * *
38689375 AAAAATAAATTTGCATTGAAAATAG-AAAT-TTTAAATATAAAATGAAATGAGAA
1 AAAAATAAATTTCCATTGAAAATAGAAAATATGTAAATATAAAATAAAATGAGAA
* * * **
38689428 AAAAATTAAATTTCCTTTGGAAATAGAAAATATGTAGATATAAAATAAAATGAGGT
1 AAAAA-TAAATTTCCATTGAAAATAGAAAATATGTAAATATAAAATAAAATGAGAA
38689484 AAAAATAAAT
1 AAAAATAAAT
38689494 GTTATCAGGC
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
53 5 0.09
54 17 0.31
55 9 0.16
56 24 0.44
ACGTcount: A:0.57, C:0.03, G:0.12, T:0.29
Consensus pattern (55 bp):
AAAAATAAATTTCCATTGAAAATAGAAAATATGTAAATATAAAATAAAATGAGAA
Found at i:38693700 original size:33 final size:33
Alignment explanation
Indices: 38693653--38693720 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
38693643 AAGCTGCACA
*
38693653 TAAGGTATCTGGGCACCAAAGACCTGACGAGCC
1 TAAGGTATCCGGGCACCAAAGACCTGACGAGCC
38693686 TAAGGTATCCGGGCACCAAAGACCTGACGAGCC
1 TAAGGTATCCGGGCACCAAAGACCTGACGAGCC
38693719 TA
1 TA
38693721 TTCGGAGTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.15
Consensus pattern (33 bp):
TAAGGTATCCGGGCACCAAAGACCTGACGAGCC
Found at i:38694975 original size:17 final size:17
Alignment explanation
Indices: 38694953--38694987 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
38694943 GGTGTTTATA
38694953 ATCAAGTCCCACACTGT
1 ATCAAGTCCCACACTGT
38694970 ATCAAGTCCCACACTGT
1 ATCAAGTCCCACACTGT
38694987 A
1 A
38694988 AAAGGTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.34, G:0.11, T:0.23
Consensus pattern (17 bp):
ATCAAGTCCCACACTGT
Found at i:38697128 original size:27 final size:27
Alignment explanation
Indices: 38697090--38697141 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
38697080 TTTTTTTTAC
*
38697090 TTTTTTTATAATTGGATATAAGTAGAT
1 TTTTTTTATAATGGGATATAAGTAGAT
*
38697117 TTTTTTTATAATGGGTTATAAGTAG
1 TTTTTTTATAATGGGATATAAGTAG
38697142 TGAGATTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (27 bp):
TTTTTTTATAATGGGATATAAGTAGAT
Found at i:38708687 original size:32 final size:32
Alignment explanation
Indices: 38708651--38708715 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
38708641 TTTGTTAGAT
*
38708651 ATTTATTATGTTTTAAGCTTGTTAGATTTTGA
1 ATTTATTATGTTTTAAGCTTGTTAGATATTGA
*
38708683 ATTTATTATGTTTTAAGCTTGTTGGATATTGA
1 ATTTATTATGTTTTAAGCTTGTTAGATATTGA
38708715 A
1 A
38708716 ATGATTGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.26, C:0.03, G:0.17, T:0.54
Consensus pattern (32 bp):
ATTTATTATGTTTTAAGCTTGTTAGATATTGA
Found at i:38710132 original size:20 final size:20
Alignment explanation
Indices: 38710103--38710142 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38710093 AAATATTTTC
* *
38710103 AGTAAGTCATTTTTCAGAAA
1 AGTAAATCATTTTCCAGAAA
38710123 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
38710143 TTATTATAAA
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:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:38714185 original size:13 final size:13
Alignment explanation
Indices: 38714161--38714197 Score: 53
Period size: 11 Copynumber: 3.1 Consensus size: 13
38714151 ATATATTTTT
38714161 TAAAAAATT-ATA
1 TAAAAAATTAATA
38714173 T-AAAAA-TAATA
1 TAAAAAATTAATA
38714184 TAAAAAATTAATA
1 TAAAAAATTAATA
38714197 T
1 T
38714198 GGGGGCTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.05
11 9 0.41
12 6 0.27
13 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAAAATTAATA
Found at i:38715459 original size:9 final size:9
Alignment explanation
Indices: 38715431--38715470 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
38715421 CATCCATCTT
38715431 TCAACTCTC
1 TCAACTCTC
*
38715440 TCAAACCCTC
1 TC-AACTCTC
*
38715450 TCAAGTCTC
1 TCAACTCTC
38715459 TCAACTCTC
1 TCAACTCTC
38715468 TCA
1 TCA
38715471 TTTTAAAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.25, C:0.42, G:0.03, T:0.30
Consensus pattern (9 bp):
TCAACTCTC
Found at i:38717404 original size:37 final size:33
Alignment explanation
Indices: 38717362--38717469 Score: 90
Period size: 37 Copynumber: 3.0 Consensus size: 33
38717352 CAAGATAAAC
38717362 ATTAAATTTAATTTAATATTAAGATAATCACATTAA
1 ATTAAATTTAATTTAATATTAAGATAAT---ATTAA
** *
38717398 TATTAAATTAATAAAATACTATTAAGATAAGTATTAA
1 -ATTAAATT--TAATTTAATATTAAGATAA-TATTAA
*
38717435 ATTAAATTTAATATTAAACTATTAAAATAATATTA
1 ATTAAATTTAAT-TT-AA-TATTAAGATAATATTA
38717470 TTTTTGGAGT
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
34 3 0.05
35 1 0.02
36 14 0.24
37 23 0.40
39 16 0.28
40 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.41
Consensus pattern (33 bp):
ATTAAATTTAATTTAATATTAAGATAATATTAA
Found at i:38717409 original size:31 final size:29
Alignment explanation
Indices: 38717353--38717410 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 29
38717343 ATTTATATAC
*
38717353 AAGATAAACATTAAATTTAATTTAATATT
1 AAGATAAACATTAAATTTAAATTAATATT
38717382 AAGATAATCACATT-AATATTAAATTAATA
1 AAGATAA--ACATTAAAT-TTAAATTAATA
38717411 AAATACTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 7 0.28
30 3 0.12
31 15 0.60
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (29 bp):
AAGATAAACATTAAATTTAAATTAATATT
Found at i:38718361 original size:21 final size:21
Alignment explanation
Indices: 38718344--38718399 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 21
38718334 ACCAAAAATT
38718344 TATTTTAAAAATGAAAAAAAG
1 TATTTTAAAAATGAAAAAAAG
*
38718365 TATTTTAAAAAT-ATTTTAAAAAG
1 TATTTTAAAAATGA---AAAAAAG
38718388 TATTTTAAAAAT
1 TATTTTAAAAAT
38718400 ATTTTAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 1 0.03
21 12 0.39
23 18 0.58
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (21 bp):
TATTTTAAAAATGAAAAAAAG
Found at i:38718379 original size:11 final size:12
Alignment explanation
Indices: 38718359--38718408 Score: 86
Period size: 11 Copynumber: 4.3 Consensus size: 12
38718349 TAAAAATGAA
38718359 AAAAAGTATTTT
1 AAAAAGTATTTT
38718371 AAAAA-TATTTT
1 AAAAAGTATTTT
38718382 AAAAAGTATTTT
1 AAAAAGTATTTT
38718394 AAAAA-TATTTT
1 AAAAAGTATTTT
38718405 AAAA
1 AAAA
38718409 TTAAAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
11 21 0.57
12 16 0.43
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (12 bp):
AAAAAGTATTTT
Found at i:38718385 original size:23 final size:23
Alignment explanation
Indices: 38718359--38718449 Score: 102
Period size: 23 Copynumber: 4.2 Consensus size: 23
38718349 TAAAAATGAA
38718359 AAAAAGTATTTTAAAAATATTTT
1 AAAAAGTATTTTAAAAATATTTT
38718382 AAAAAGTATTTTAAAAATATTTT
1 AAAAAGTATTTTAAAAATATTTT
* * **
38718405 --AAA--A-TTAAAAAATAATAA
1 AAAAAGTATTTTAAAAATATTTT
*
38718423 AAAAAGGATTTTAAAAATATTTT
1 AAAAAGTATTTTAAAAATATTTT
38718446 AAAA
1 AAAA
38718450 TTAAAAAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
18 10 0.18
19 1 0.02
20 3 0.05
21 3 0.05
22 1 0.02
23 37 0.67
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.36
Consensus pattern (23 bp):
AAAAAGTATTTTAAAAATATTTT
Found at i:38718386 original size:12 final size:12
Alignment explanation
Indices: 38718358--38718408 Score: 70
Period size: 12 Copynumber: 4.3 Consensus size: 12
38718348 TTAAAAATGA
38718358 AAAAAAGTATTTT
1 AAAAAA-TATTTT
38718371 -AAAAATATTTT
1 AAAAAATATTTT
*
38718382 AAAAAGTATTTT
1 AAAAAATATTTT
38718394 -AAAAATATTTT
1 AAAAAATATTTT
38718405 AAAA
1 AAAA
38718409 TTAAAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 16 0.47
12 18 0.53
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (12 bp):
AAAAAATATTTT
Found at i:38718455 original size:17 final size:17
Alignment explanation
Indices: 38718433--38718478 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
38718423 AAAAAGGATT
38718433 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
* *
38718450 TTAAAAAAAATTTAAAA
1 TTAAAAATATTTTAAAA
* *
38718467 ATAAATATATTT
1 TTAAAAATATTT
38718479 ATTATATCGG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:38718467 original size:41 final size:41
Alignment explanation
Indices: 38718371--38718467 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
38718361 AAAGTATTTT
* * *
38718371 AAAAATATTTTAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAAAATTTAAAAAAGGATTTTAAAAATATTTTAAAATTA
*
38718412 AAAAATAA-TAAAAAAAGGATTTTAAAAATATTTTAAAATTA
1 AAAAA-AATTTAAAAAAGGATTTTAAAAATATTTTAAAATTA
38718453 AAAAAAATTTAAAAA
1 AAAAAAATTTAAAAA
38718468 TAAATATATT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 2 0.04
41 46 0.94
42 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (41 bp):
AAAAAAATTTAAAAAAGGATTTTAAAAATATTTTAAAATTA
Found at i:38719828 original size:20 final size:20
Alignment explanation
Indices: 38719803--38719842 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
38719793 GAGGAGCACA
*
38719803 TCGTAGGATGTAACCTTTAC
1 TCGTAGGATGCAACCTTTAC
38719823 TCGTAGGATGCAACCTTTAC
1 TCGTAGGATGCAACCTTTAC
38719843 CCGTTTGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (20 bp):
TCGTAGGATGCAACCTTTAC
Found at i:38723503 original size:52 final size:52
Alignment explanation
Indices: 38723442--38723542 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
38723432 CATGTACATA
*
38723442 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTATTG
*
38723494 TTTGAGCTTCAACCGAGCTGGAAATGAGGTCTTAAGCTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTA
38723543 CGTTTCCTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTATTG
Found at i:38737251 original size:14 final size:14
Alignment explanation
Indices: 38737225--38737283 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
38737215 ACTGTTGAAC
38737225 TTAAAATATAAAATT
1 TTAAAA-ATAAAATT
38737240 TTAAAAATAAAATT
1 TTAAAAATAAAATT
38737254 TATAAAAATAAGAA-T
1 T-TAAAAATAA-AATT
* *
38737269 ATAAAAATTAAATT
1 TTAAAAATAAAATT
38737283 T
1 T
38737284 CAAATATGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 2 0.05
14 18 0.47
15 16 0.42
16 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
TTAAAAATAAAATT
Found at i:38737589 original size:26 final size:28
Alignment explanation
Indices: 38737554--38737620 Score: 95
Period size: 30 Copynumber: 2.4 Consensus size: 28
38737544 AAAAATAATC
38737554 AAAATATTATAA-TTTTT-TTATTTACT
1 AAAATATTATAATTTTTTATTATTTACT
38737580 AAAATATTATAATTTTTTTTATTATTTACT
1 AAAATATTATAA--TTTTTTATTATTTACT
38737610 AAAATA-TATAA
1 AAAATATTATAA
38737621 AAAAACAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
26 12 0.32
29 10 0.27
30 15 0.41
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (28 bp):
AAAATATTATAATTTTTTATTATTTACT
Found at i:38737785 original size:4 final size:4
Alignment explanation
Indices: 38737776--38737911 Score: 58
Period size: 4 Copynumber: 34.0 Consensus size: 4
38737766 GAAGGAGAGG
* * * *
38737776 GAAA GAAA GAAA GAAA GGAAG GAAG GAGAG GAAA GAAA G-AA -AAA GAAG
1 GAAA GAAA GAAA GAAA -GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA
*
38737824 GAAA GAAAA GGAAA G-GA GAAGA GAAA -AAA -AAA GGAAA G-AA GAAA
1 GAAA G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA -GAAA GAAA GAAA
*
38737868 -AAGA GGAAA GGAGAA GAAA -AAA GAAA G-AA -AAA GAAG GAAA GAAA
1 GAA-A -GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
38737912 AGGAAAGGAG
Statistics
Matches: 106, Mismatches: 8, Indels: 36
0.71 0.05 0.24
Matches are distributed among these distances:
3 24 0.23
4 51 0.48
5 26 0.25
6 5 0.05
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:38737802 original size:31 final size:31
Alignment explanation
Indices: 38737766--38737826 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
38737756 GTGGGGGGGA
*
38737766 GAAGGAGAGGGAAAGAAAGAAAGA-AAGGAAG
1 GAAGGAGA-GGAAAGAAAGAAAAAGAAGGAAG
38737797 GAAGGAGAGGAAAGAAAGAAAAAGAAGGAA
1 GAAGGAGAGGAAAGAAAGAAAAAGAAGGAA
38737827 AGAAAAGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (31 bp):
GAAGGAGAGGAAAGAAAGAAAAAGAAGGAAG
Found at i:38737825 original size:18 final size:18
Alignment explanation
Indices: 38737804--38737911 Score: 78
Period size: 18 Copynumber: 6.6 Consensus size: 18
38737794 AAGGAAGGAG
38737804 AGGAAAGAAAGAAAAAGA
1 AGGAAAGAAAGAAAAAGA
**
38737822 AGGAAAG-AA-AAGGA-A
1 AGGAAAGAAAGAAAAAGA
38737837 AGGAGAAGAGAA-AAAAA-A
1 AGGA-AAGA-AAGAAAAAGA
38737855 AGGAAAG-AAGAAAAAG-
1 AGGAAAGAAAGAAAAAGA
*
38737871 AGGAAAG---G-AGAAGA
1 AGGAAAGAAAGAAAAAGA
*
38737885 A-AAAAGAAAGAAAAAGA
1 AGGAAAGAAAGAAAAAGA
38737902 AGGAAAGAAA
1 AGGAAAGAAA
38737912 AGGAAAGGAG
Statistics
Matches: 71, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
13 8 0.11
14 2 0.03
15 7 0.10
16 19 0.27
17 11 0.15
18 24 0.34
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (18 bp):
AGGAAAGAAAGAAAAAGA
Found at i:38737828 original size:36 final size:39
Alignment explanation
Indices: 38737781--38737955 Score: 177
Period size: 39 Copynumber: 4.5 Consensus size: 39
38737771 AGAGGGAAAG
*
38737781 AAAGAAAGAAAG-GAAGG-AAGGAG-AG-GAAAGAAAGAA
1 AAAGAAGGAAAGAGAAGGAAAGGAGAAGAGAAA-AAAGAA
* *
38737817 AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAAAAA
1 AAAGAAGGAAAGAGAAGGAAAGGAGAAGAGAAAAAAGAA
* *
38737856 GGAAAGAA-GAAAAAG-AGGAAAGGAGAAGAAAAAAGAAAGAA
1 --AAAGAAGGAAAGAGAAGGAAAGGAGAAG-AGAAA-AAAGAA
*
38737897 AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAA-AA
1 AAAGAAGGAAAGAGAAGGAAAGGAGAAGAGAAAAAAGAA
38737935 AGAAGAA-GAAGAGAGAAGGAA
1 A-AAGAAGGAA-AGAGAAGGAA
38737956 GAAAAAAAAG
Statistics
Matches: 116, Mismatches: 11, Indels: 21
0.78 0.07 0.14
Matches are distributed among these distances:
36 11 0.09
37 4 0.03
38 12 0.10
39 43 0.37
40 22 0.19
41 24 0.21
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (39 bp):
AAAGAAGGAAAGAGAAGGAAAGGAGAAGAGAAAAAAGAA
Found at i:38737918 original size:18 final size:18
Alignment explanation
Indices: 38737780--38737918 Score: 70
Period size: 18 Copynumber: 7.3 Consensus size: 18
38737770 GAGAGGGAAA
* *
38737780 GAAAGAAAGAAAG-GAAG
1 GAAAGAAGGAAAGAAAAG
*
38737797 GAAGGAGAGGAAAG-AAAG
1 GAAAGA-AGGAAAGAAAAG
*
38737815 AAAAAGAAGGAAAGAAAAG
1 -GAAAGAAGGAAAGAAAAG
*
38737834 GAAAGGAGAAGAGAAAAAAAAAG
1 G-AA--AGAAG-G-AAAGAAAAG
*
38737857 GAAAGAAGAAAAAGAGGAAAG
1 GAAAGAAG-GAAAGA--AAAG
*
38737878 GAGAAGAA-AAAAG-AAAG
1 GA-AAGAAGGAAAGAAAAG
*
38737895 AAAAAGAAGGAAAGAAAAG
1 -GAAAGAAGGAAAGAAAAG
38737914 GAAAG
1 GAAAG
38737919 GAGAAGAGAA
Statistics
Matches: 96, Mismatches: 12, Indels: 27
0.71 0.09 0.20
Matches are distributed among these distances:
17 14 0.15
18 25 0.26
19 18 0.19
20 11 0.11
21 11 0.11
22 8 0.08
23 9 0.09
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (18 bp):
GAAAGAAGGAAAGAAAAG
Found at i:38737936 original size:18 final size:18
Alignment explanation
Indices: 38737835--38737943 Score: 78
Period size: 18 Copynumber: 5.6 Consensus size: 18
38737825 AAAGAAAAGG
38737835 AAAGGAGAAGAGAAAAAA
1 AAAGGAGAAGAGAAAAAA
38737853 AAAGGA-AAGAAGAAAAAGA
1 AAAGGAGAAG-AGAAAAA-A
*
38737872 GGAAAGGAGAAGA-AAAAAG
1 --AAAGGAGAAGAGAAAAAA
* *
38737891 AAAGAAAAAGAAGGAAAGAAAA
1 AAAGGAGAAG-A-G-AA-AAAA
38737913 GGAAAGGAGAAGAGAAAAAA
1 --AAAGGAGAAGAGAAAAAA
*
38737933 AAAGAAGAAGA
1 AAAGGAGAAGA
38737944 AGAGAGAAGG
Statistics
Matches: 72, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
17 11 0.15
18 24 0.33
19 1 0.01
20 9 0.12
21 11 0.15
22 7 0.10
23 1 0.01
24 8 0.11
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (18 bp):
AAAGGAGAAGAGAAAAAA
Found at i:38737944 original size:21 final size:21
Alignment explanation
Indices: 38737882--38737948 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
38737872 GGAAAGGAGA
*
38737882 AGAAAAAAGAAAGAAAAAGAAG
1 AGAAAAAA-AAAGAAGAAGAAG
* * *
38737904 -GAAAGAAAAGGAAAGGAGAAG
1 AGAAAAAAAAAG-AAGAAGAAG
38737925 AGAAAAAAAAAGAAGAAGAAG
1 AGAAAAAAAAAGAAGAAGAAG
38737946 AGA
1 AGA
38737949 GAAGGAAGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
20 3 0.08
21 24 0.67
22 9 0.25
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (21 bp):
AGAAAAAAAAAGAAGAAGAAG
Found at i:38743791 original size:18 final size:19
Alignment explanation
Indices: 38743751--38743792 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
38743741 CCAATGATCG
38743751 CCACCACCTTCTTCTTCGA
1 CCACCACCTTCTTCTTCGA
38743770 -CACCACCTTCTTCTTC-A
1 CCACCACCTTCTTCTTCGA
38743787 CCACCA
1 CCACCA
38743793 ACCATATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.19, C:0.50, G:0.02, T:0.29
Consensus pattern (19 bp):
CCACCACCTTCTTCTTCGA
Found at i:38744563 original size:3 final size:3
Alignment explanation
Indices: 38744555--38744656 Score: 102
Period size: 3 Copynumber: 33.7 Consensus size: 3
38744545 TCTTAATACT
* * *
38744555 AAC AAC AAC AAC AAC AAC AAC AAC TAA- AAC TAT AAC AAC AAT ATA-
1 AAC AAC AAC AAC AAC AAC AAC AAC -AAC AAC AAC AAC AAC AAC A-AC
* *
38744600 ATC AAC AAT ATA- AAC AAC ACAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC A-AC AAC AAC A-AC AAC AAC AAC AAC AAC AAC AAC AAC
38744646 AAC AAC AAC AA
1 AAC AAC AAC AA
38744657 TAATAATAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
2 3 0.04
3 74 0.88
4 7 0.08
ACGTcount: A:0.65, C:0.27, G:0.00, T:0.08
Consensus pattern (3 bp):
AAC
Found at i:38744952 original size:27 final size:27
Alignment explanation
Indices: 38744906--38744998 Score: 109
Period size: 27 Copynumber: 3.4 Consensus size: 27
38744896 AACACGAGTA
38744906 GTGCCGCCAAT--CTGTATGGCACCATTG
1 GTGCCGCCAATGGCT-T-TGGCACCATTG
*
38744933 GTGTCGCCAATGGCTTTGGCACCATTG
1 GTGCCGCCAATGGCTTTGGCACCATTG
** *
38744960 GTGCCGCCAATGGCTTTGGTGCCTTTG
1 GTGCCGCCAATGGCTTTGGCACCATTG
*
38744987 GTGCCGGCAATG
1 GTGCCGCCAATG
38744999 CCATTGGCCT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
27 55 0.95
28 1 0.02
29 2 0.03
ACGTcount: A:0.14, C:0.27, G:0.31, T:0.28
Consensus pattern (27 bp):
GTGCCGCCAATGGCTTTGGCACCATTG
Found at i:38745114 original size:26 final size:29
Alignment explanation
Indices: 38745054--38745125 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 29
38745044 CAGGTTTTTT
38745054 TTATATATATTTTGGTAAATAATAAAAATAA
1 TTATA-ATATTTTGGT-AATAATAAAAATAA
*
38745085 TTATAATATTTTGGT-A-AATAAAAA-AG
1 TTATAATATTTTGGTAATAATAAAAATAA
38745111 TTATAATATTTTGGT
1 TTATAATATTTTGGT
38745126 TATTTTTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
26 16 0.40
27 8 0.20
28 1 0.03
30 10 0.25
31 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (29 bp):
TTATAATATTTTGGTAATAATAAAAATAA
Found at i:38747827 original size:20 final size:19
Alignment explanation
Indices: 38747796--38747849 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 19
38747786 TCTCTCAACA
38747796 AAAAATTACAAAATAATTTT
1 AAAAATT-CAAAATAATTTT
*
38747816 CAAAAATTCAAAATCATTTT
1 -AAAAATTCAAAATAATTTT
*
38747836 TAAAATTCAAAATA
1 AAAAATTCAAAATA
38747850 TTTATATAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 12 0.40
20 11 0.37
21 7 0.23
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:38748009 original size:3 final size:3
Alignment explanation
Indices: 38748001--38748026 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
38747991 AGTATCTTAT
38748001 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
38748027 TGCTTTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:38751379 original size:30 final size:29
Alignment explanation
Indices: 38751340--38751428 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 29
38751330 ACAGGCTGGC
* *
38751340 ACATGGGCGTGTGTCCAGCCTGTGTGGCTT
1 ACAT-GGCGTGTGCCCAGCCCGTGTGGCTT
* * *
38751370 ACATAGGCGTGTGCCCAACCCCTGTGGGTT
1 ACAT-GGCGTGTGCCCAGCCCGTGTGGCTT
38751400 ACATGAGCGTGTGCCCAGCCCGTGTGGCT
1 ACATG-GCGTGTGCCCAGCCCGTGTGGCT
38751429 CTTGAAATCT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 1 0.02
30 48 0.98
ACGTcount: A:0.13, C:0.28, G:0.34, T:0.25
Consensus pattern (29 bp):
ACATGGCGTGTGCCCAGCCCGTGTGGCTT
Found at i:38753216 original size:6 final size:6
Alignment explanation
Indices: 38753156--38753209 Score: 99
Period size: 6 Copynumber: 9.0 Consensus size: 6
38753146 ACAACTCAAT
*
38753156 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAC
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
38753204 TAAAAA
1 TAAAAA
38753210 AAGAAAACAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:38754893 original size:22 final size:21
Alignment explanation
Indices: 38754845--38754964 Score: 73
Period size: 22 Copynumber: 5.2 Consensus size: 21
38754835 GTTAAATAAC
* *
38754845 ATAACAATAATAAGAACAAAAATA
1 ATAA-AATAATAATAA-AAACA-A
38754869 ATAAACATAATAATAAAAACAA
1 ATAAA-ATAATAATAAAAACAA
*
38754891 ATAGAAAGAATAATAATAAAACAA
1 ATA-AAATAATAAT-A-AAAACAA
*
38754915 ATGATAATAAATAAT-AAAACAA
1 AT-AAAAT-AATAATAAAAACAA
*
38754937 ATAATAATTAA-AATAAAATAAAA
1 ATAA-AA-TAATAATAAAA-ACAA
38754960 ATAAA
1 ATAAA
38754965 GAGCAAGGGT
Statistics
Matches: 79, Mismatches: 7, Indels: 22
0.73 0.06 0.20
Matches are distributed among these distances:
21 4 0.05
22 28 0.35
23 16 0.20
24 24 0.30
25 7 0.09
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (21 bp):
ATAAAATAATAATAAAAACAA
Found at i:38754909 original size:37 final size:36
Alignment explanation
Indices: 38754853--38754960 Score: 100
Period size: 37 Copynumber: 3.0 Consensus size: 36
38754843 ACATAACAAT
38754853 AATAAGAACAAA-AATAATAAACATAATAATAAAAACA
1 AATAA-AACAAATAATAATAAACATAATAATAAAAA-A
* * *
38754890 AATAGAAA-GAATAATAATAAAACA-AATGATAATAAAT
1 AATA-AAACAAATAATAAT-AAACATAATAATAA-AAAA
38754927 AATAAAACAAATAATAATTAAA-ATAA-AATAAAAA
1 AATAAAACAAATAATAA-TAAACATAATAATAAAAA
38754961 TAAAGAGCAA
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
35 3 0.05
36 10 0.17
37 36 0.61
38 10 0.17
ACGTcount: A:0.72, C:0.05, G:0.04, T:0.19
Consensus pattern (36 bp):
AATAAAACAAATAATAATAAACATAATAATAAAAAA
Found at i:38754921 original size:12 final size:12
Alignment explanation
Indices: 38754850--38754943 Score: 63
Period size: 12 Copynumber: 7.7 Consensus size: 12
38754840 ATAACATAAC
38754850 AATAATAAGAACA
1 AATAATAA-AACA
38754863 AA-AATAATAAACA
1 AATAAT-A-AAACA
38754876 TAATAATAAAAACA
1 -AATAAT-AAAACA
*
38754890 AATAGA-AAGAA-T
1 AATA-ATAA-AACA
38754902 AATAATAAAACA
1 AATAATAAAACA
* *
38754914 AATGAT--AATA
1 AATAATAAAACA
38754924 AATAATAAAACA
1 AATAATAAAACA
38754936 AATAATAA
1 AATAATAA
38754944 TTAAAATAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 21
0.71 0.07 0.23
Matches are distributed among these distances:
10 8 0.12
11 3 0.05
12 27 0.42
13 13 0.20
14 9 0.14
15 5 0.08
ACGTcount: A:0.71, C:0.05, G:0.04, T:0.19
Consensus pattern (12 bp):
AATAATAAAACA
Found at i:38758754 original size:5 final size:5
Alignment explanation
Indices: 38758746--38758772 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
38758736 AACTAAAAAT
38758746 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
38758773 ATGGCTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:38762072 original size:3 final size:3
Alignment explanation
Indices: 38762064--38762094 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
38762054 CCAATGTCAG
38762064 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
38762095 AGATGGAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:38763403 original size:19 final size:19
Alignment explanation
Indices: 38763371--38763412 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
38763361 TCTTATTTAT
38763371 TATATGTTATTTTTAAATA
1 TATATGTTATTTTTAAATA
*
38763390 TATAT-TTATATTTTAAATT
1 TATATGTTAT-TTTTAAATA
38763409 TATA
1 TATA
38763413 ATTTCAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TATATGTTATTTTTAAATA
Found at i:38763959 original size:12 final size:13
Alignment explanation
Indices: 38763944--38763976 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
38763934 TTTGTAATAT
38763944 TTTTATTTTTC-A
1 TTTTATTTTTCTA
38763956 TTTTATTTTTCTA
1 TTTTATTTTTCTA
*
38763969 TTTAATTT
1 TTTTATTT
38763977 CTAATTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTTTTCTA
Found at i:38771323 original size:28 final size:28
Alignment explanation
Indices: 38771283--38771336 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
38771273 TGTATACTTT
*
38771283 TATTTTTTGAACAAATTGGTTTAACATG
1 TATTTTTTGAACAAATTAGTTTAACATG
38771311 TATTTTTTGAACAAATTAGTTTAACA
1 TATTTTTTGAACAAATTAGTTTAACA
38771337 ATAACATCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.46
Consensus pattern (28 bp):
TATTTTTTGAACAAATTAGTTTAACATG
Found at i:38773589 original size:18 final size:21
Alignment explanation
Indices: 38773566--38773603 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 21
38773556 TGGGAGTAAA
38773566 TTTAGG-TTT-TA-TTAAATT
1 TTTAGGATTTGTAGTTAAATT
38773584 TTTAGGATTTGTAGTTAAAT
1 TTTAGGATTTGTAGTTAAAT
38773604 CATGGACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 2 0.12
21 6 0.35
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
TTTAGGATTTGTAGTTAAATT
Found at i:38782340 original size:27 final size:26
Alignment explanation
Indices: 38782304--38782557 Score: 219
Period size: 27 Copynumber: 9.5 Consensus size: 26
38782294 CCCTAAAATA
38782304 GGTAAAATAACTGAAATACCCCTATAG
1 GGTAAAATAACTGAAATACCCC-ATAG
*
38782331 GGTAAAATAACCGAAATATCCCCATAG
1 GGTAAAATAACTGAAATA-CCCCATAG
* * * * *
38782358 GATAAAATGACTAAAATAGCCCGTAG
1 GGTAAAATAACTGAAATACCCCATAG
*
38782384 GGTAAAATGAAC-AAAATACCCCTATAG
1 GGTAAAAT-AACTGAAATACCCC-ATAG
* *
38782411 GGTAAAATAA-TCGAAGTACCCCTATAT
1 GGTAAAATAACT-GAAATACCCC-ATAG
*
38782438 GGTAAAATGAC-GTAAATAACCCCATAG
1 GGTAAAATAACTG-AAAT-ACCCCATAG
* *
38782465 GATAAAATGAAC-GAAATACCCTTATAG
1 GGTAAAAT-AACTGAAATACCC-CATAG
* * *
38782492 GGTAAAATGACCGAAATTCCCCCATAG
1 GGTAAAATAACTGAAA-TACCCCATAG
* *
38782519 GGTAAAATGACCGAAATACCCCATAG
1 GGTAAAATAACTGAAATACCCCATAG
*
38782545 GGTAAAATGACTG
1 GGTAAAATAACTG
38782558 TTATACCCTT
Statistics
Matches: 189, Mismatches: 26, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
26 52 0.28
27 121 0.64
28 16 0.08
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (26 bp):
GGTAAAATAACTGAAATACCCCATAG
Found at i:38782444 original size:80 final size:77
Alignment explanation
Indices: 38782304--38782554 Score: 306
Period size: 80 Copynumber: 3.1 Consensus size: 77
38782294 CCCTAAAATA
38782304 GGTAAAAT-AACTGAAATACCCCTATAGGGTAAAATAACCGAAATATCCCCATAGGATAAAATGA
1 GGTAAAATGAAC-GAAATACCCCTATAGGGTAAAATAACCGAAATA-CCCCATAGG-TAAAATGA
* *
38782368 CTAAAATAGCCCGTAG
63 CT-AAATACCCCATAG
* * *
38782384 GGTAAAATGAACAAAATACCCCTATAGGGTAAAATAATCGAAGTACCCCTATATGGTAAAATGAC
1 GGTAAAATGAACGAAATACCCCTATAGGGTAAAATAACCGAAATACCCC-ATA-GGTAAAATGAC
38782449 GTAAATAACCCCATAG
64 -TAAAT-ACCCCATAG
* * * *
38782465 GATAAAATGAACGAAATACCCTTATAGGGTAAAATGACCGAAATTCCCCCATAGGGTAAAATGAC
1 GGTAAAATGAACGAAATACCCCTATAGGGTAAAATAACCGAAA-TACCCCATA-GGTAAAATGA-
*
38782530 CGAAATACCCCATAG
63 CTAAATACCCCATAG
38782545 GGTAAAATGA
1 GGTAAAATGA
38782555 CTGTTATACC
Statistics
Matches: 149, Mismatches: 15, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
79 4 0.03
80 72 0.48
81 67 0.45
82 6 0.04
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (77 bp):
GGTAAAATGAACGAAATACCCCTATAGGGTAAAATAACCGAAATACCCCATAGGTAAAATGACTA
AATACCCCATAG
Found at i:38782455 original size:54 final size:51
Alignment explanation
Indices: 38782304--38782555 Score: 256
Period size: 54 Copynumber: 4.7 Consensus size: 51
38782294 CCCTAAAATA
*
38782304 GGTAAAATAACTGAAATACCCCTATAGGGTAAAATAACCGAAATATCCCCATAG
1 GGTAAAATAAC-GAAATACCCCTATAGGGTAAAATGA-CGAAATA-CCCCATAG
* * * * * *
38782358 GATAAAATGACTAAAATAGCCC-GTAGGGTAAAATGAACAAAATACCCCTATAG
1 GGTAAAATAAC-GAAATACCCCTATAGGGTAAAATG-ACGAAATACCCC-ATAG
* *
38782411 GGTAAAATAATCGAAGTACCCCTATATGGTAAAATGACGTAAATAACCCCATAG
1 GGTAAAATAA-CGAAATACCCCTATAGGGTAAAATGACG-AAAT-ACCCCATAG
* * *
38782465 GATAAAATGAACGAAATACCCTTATAGGGTAAAATGACCGAAATTCCCCCATAG
1 GGTAAAAT-AACGAAATACCCCTATAGGGTAAAATGA-CGAAA-TACCCCATAG
*
38782519 GGTAAAATGACCGAAATACCCC-ATAGGGTAAAATGAC
1 GGTAAAAT-AACGAAATACCCCTATAGGGTAAAATGAC
38782556 TGTTATACCC
Statistics
Matches: 166, Mismatches: 23, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
52 5 0.03
53 52 0.31
54 99 0.60
55 10 0.06
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (51 bp):
GGTAAAATAACGAAATACCCCTATAGGGTAAAATGACGAAATACCCCATAG
Found at i:38789490 original size:59 final size:59
Alignment explanation
Indices: 38789417--38789659 Score: 218
Period size: 59 Copynumber: 4.1 Consensus size: 59
38789407 TAGATACCCG
* * * * **
38789417 ACAAAGGTTTTCCTTTTAGATATTTTCCACAAAGGCATCCTTTTCTTTCAGTATTCATC
1 ACAAAGGCTTTCCTTTTAAATATTTTCCACAAAGGCATCATTTTCTTTCAGTACTCGCC
* ** ** ** *
38789476 ACAAAAGCTTTCCTTTTGGATATTCGCCACAAACACATCATTTTCTTTCAATACTCGCC
1 ACAAAGGCTTTCCTTTTAAATATTTTCCACAAAGGCATCATTTTCTTTCAGTACTCGCC
* * * * * * * *
38789535 ATAAAGGCTTTCCATTAAAAAAGTTTCTATAAAGGCATCCTTTTCATTT-AGTACTCGCC
1 ACAAAGGCTTTCCTTTTAAATATTTTCCACAAAGGCATCATTTTC-TTTCAGTACTCGCC
* * * * **
38789594 ACAAAGGCTTTCCTTTTAAAGATTTTCAATAAAGGAATCATTTTCTTTCAGTACTCGAA
1 ACAAAGGCTTTCCTTTTAAATATTTTCCACAAAGGCATCATTTTCTTTCAGTACTCGCC
38789653 ACAAAGG
1 ACAAAGG
38789660 TATCCTTCCG
Statistics
Matches: 144, Mismatches: 38, Indels: 4
0.77 0.20 0.02
Matches are distributed among these distances:
58 3 0.02
59 138 0.96
60 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (59 bp):
ACAAAGGCTTTCCTTTTAAATATTTTCCACAAAGGCATCATTTTCTTTCAGTACTCGCC
Found at i:38793496 original size:19 final size:21
Alignment explanation
Indices: 38793472--38793514 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38793462 GCACCTAGGA
38793472 TGATTGT-TTTGA-CATGTTT
1 TGATTGTATTTGATCATGTTT
*
38793491 TGATTGTATTTGATCGTGTTT
1 TGATTGTATTTGATCATGTTT
38793512 TGA
1 TGA
38793515 ACTGGTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.16, C:0.05, G:0.23, T:0.56
Consensus pattern (21 bp):
TGATTGTATTTGATCATGTTT
Done.