Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 67 of 202
Found at i:19792313 original size:15 final size:16
Alignment explanation
Indices: 19792293--19792327 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
19792283 CTCCTTTTTC
19792293 TTTTCTTTTTCTCTT-
1 TTTTCTTTTTCTCTTA
19792308 TTTTCTTTTTCTCTTA
1 TTTTCTTTTTCTCTTA
19792324 TTTT
1 TTTT
19792328 TGAATTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTCTTTTTCTCTTA
Found at i:19792348 original size:26 final size:26
Alignment explanation
Indices: 19792314--19792379 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
19792304 TCTTTTTTCT
19792314 TTTTCTCTTATTTTTGAATTTGA-TTGA
1 TTTT-TCTT-TTTTTGAATTTGATTTGA
**
19792341 TTTTTCTTTTTTTGCTTTTGATTTTGA
1 TTTTTCTTTTTTTGAATTTGA-TTTGA
19792368 TTTTTCTTTTTT
1 TTTTTCTTTTTT
19792380 CGTTTCCTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 11 0.31
26 4 0.11
27 20 0.57
ACGTcount: A:0.11, C:0.08, G:0.09, T:0.73
Consensus pattern (26 bp):
TTTTTCTTTTTTTGAATTTGATTTGA
Found at i:19796978 original size:3 final size:3
Alignment explanation
Indices: 19796970--19797037 Score: 75
Period size: 3 Copynumber: 22.7 Consensus size: 3
19796960 TAAATGGGTA
* * * **
19796970 AAT AAT AAT AAT AAT AAT AA- AATT GAT TAG CTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT
19797015 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
19797038 AACGGGACTA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 52 0.95
4 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:19801030 original size:4 final size:4
Alignment explanation
Indices: 19801021--19801054 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
19801011 ATCCTTTTCT
19801021 CATA CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CA
19801055 CGCATGCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:19803426 original size:21 final size:21
Alignment explanation
Indices: 19803401--19803455 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
19803391 GCTTTTGTGG
19803401 TTGTACTTGTTTTTGATGAAC
1 TTGTACTTGTTTTTGATGAAC
19803422 TTGTACTTGTTTTTGATGAAC
1 TTGTACTTGTTTTTGATGAAC
*
19803443 TTGAACTTGTTTT
1 TTGTACTTGTTTT
19803456 CGATTTTACC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55
Consensus pattern (21 bp):
TTGTACTTGTTTTTGATGAAC
Found at i:19804664 original size:27 final size:27
Alignment explanation
Indices: 19804623--19804675 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
19804613 GGATTTGGTG
*
19804623 GTGCCTTCCTAAAAGGTGGCACCAGTT
1 GTGCCTTCCTAAAAGGCGGCACCAGTT
* *
19804650 GTGCCTTCTTGAAAGGCGGCACCAGT
1 GTGCCTTCCTAAAAGGCGGCACCAGT
19804676 CTGATTAGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.25
Consensus pattern (27 bp):
GTGCCTTCCTAAAAGGCGGCACCAGTT
Found at i:19806261 original size:13 final size:13
Alignment explanation
Indices: 19806243--19806267 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19806233 TTGGATCTGT
19806243 ACCAAAACAATCC
1 ACCAAAACAATCC
19806256 ACCAAAACAATC
1 ACCAAAACAATC
19806268 ATGAAACATA
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:0.56, C:0.36, G:0.00, T:0.08
Consensus pattern (13 bp):
ACCAAAACAATCC
Found at i:19807174 original size:44 final size:42
Alignment explanation
Indices: 19807095--19807197 Score: 125
Period size: 44 Copynumber: 2.4 Consensus size: 42
19807085 TCCCAGATAG
* *
19807095 GGTCTTACACGAAATCATATACGATGCCAATGTCCCAAACAT
1 GGTCTTACACGAAATCATAAACGATGCCAACGTCCCAAACAT
* * **
19807137 GGTCTTACACGTAAATCTTAAATCGATGCCAACGTCCCAGATGT
1 GGTCTTACACG-AAATCATAAA-CGATGCCAACGTCCCAAACAT
*
19807181 GGTCTTACACAAAATCA
1 GGTCTTACACGAAATCA
19807198 CATATCGGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
42 11 0.22
43 13 0.25
44 27 0.53
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (42 bp):
GGTCTTACACGAAATCATAAACGATGCCAACGTCCCAAACAT
Found at i:19808641 original size:12 final size:12
Alignment explanation
Indices: 19808624--19808653 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19808614 TATTATTGTA
19808624 TATTATTAATTG
1 TATTATTAATTG
*
19808636 TATTATTTATTG
1 TATTATTAATTG
19808648 TATTAT
1 TATTAT
19808654 ATTTATGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (12 bp):
TATTATTAATTG
Found at i:19808656 original size:14 final size:13
Alignment explanation
Indices: 19808616--19808659 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
19808606 TTTAATGATA
19808616 TTATTGTATATTAT
1 TTATTGTATA-TAT
*
19808630 TAATTGTAT-TAT
1 TTATTGTATATAT
19808642 TTATTGTATTATAT
1 TTATTGTA-TATAT
19808656 TTAT
1 TTAT
19808660 GTGTTTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 10 0.38
13 1 0.04
14 15 0.58
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (13 bp):
TTATTGTATATAT
Found at i:19812270 original size:3 final size:3
Alignment explanation
Indices: 19812262--19812310 Score: 82
Period size: 3 Copynumber: 16.3 Consensus size: 3
19812252 ATATGTAGGT
19812262 ATA ATA ATA TATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19812307 ATA A
1 ATA A
19812311 CAAAATTAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:19812324 original size:9 final size:8
Alignment explanation
Indices: 19812262--19812326 Score: 58
Period size: 9 Copynumber: 7.4 Consensus size: 8
19812252 ATATGTAGGT
19812262 ATAATAATA
1 ATAATAA-A
*
19812271 TATAATATA
1 -ATAATAAA
19812280 ATAATAATA
1 ATAATAA-A
19812289 ATAATAATA
1 ATAATAA-A
19812298 ATAATAATA
1 ATAATAA-A
*
19812307 ATAACAAA
1 ATAATAAA
19812315 ATTAATAAA
1 A-TAATAAA
19812324 ATA
1 ATA
19812327 GACTAAAAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
8 10 0.20
9 33 0.67
10 6 0.12
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (8 bp):
ATAATAAA
Found at i:19812774 original size:23 final size:22
Alignment explanation
Indices: 19812729--19812784 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
19812719 AAAGGGTATC
* * *
19812729 TACAAATTAAATC-TCTAATAT
1 TACAAATCATATCTTCTAAGAT
19812750 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
19812773 TACATATCATAT
1 TACAAATCATAT
19812785 TTAAGATTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 16 0.55
23 10 0.34
ACGTcount: A:0.45, C:0.16, G:0.02, T:0.38
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:19812791 original size:19 final size:19
Alignment explanation
Indices: 19812765--19812820 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
19812755 AATCATATCT
19812765 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
* *
19812784 TTTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
19812805 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
19812821 CTCGAAGATT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 13 0.43
21 17 0.57
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:19812802 original size:21 final size:21
Alignment explanation
Indices: 19812776--19812819 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
19812766 CTAAGATTAC
*
19812776 ATATCATATTTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
19812797 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
19812818 AT
1 AT
19812820 CCTCGAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:19813300 original size:44 final size:44
Alignment explanation
Indices: 19813204--19813355 Score: 140
Period size: 44 Copynumber: 3.5 Consensus size: 44
19813194 TTTAGCCTGA
*
19813204 TCCACTGCAACTTCAGGGAGATAAGA-C-TAGATGC-GT--TCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATCATAG--GCTTTAATCTGC
* * *
19813245 T-CTCTGCAACTTCAGAGAGATAAGATCCA-AGGTTTTAAT-TCGC
1 TCCACTGCAACTTCAGGGAGATAAGAT-CATAGGCTTTAATCT-GC
* * * *
19813288 TTCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATCATAGGCTTTAATCTGC
19813332 TCCACTGCAACTTCAGGGAGATAA
1 TCCACTGCAACTTCAGGGAGATAA
19813356 AATTTACCAT
Statistics
Matches: 89, Mismatches: 12, Indels: 17
0.75 0.10 0.14
Matches are distributed among these distances:
40 23 0.26
41 2 0.02
42 4 0.04
43 5 0.06
44 54 0.61
45 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (44 bp):
TCCACTGCAACTTCAGGGAGATAAGATCATAGGCTTTAATCTGC
Found at i:19813300 original size:128 final size:129
Alignment explanation
Indices: 19813104--19813355 Score: 303
Period size: 128 Copynumber: 2.0 Consensus size: 129
19813094 AGATGAATTT
* * * *
19813104 GATGCGATCTGCTCTACTGTAATTTCAGAGAGATAAGATCCATCATTCTAATCCACTCCGCTACA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
* * *
19813169 ACTTTAGGGAGATAGGATT-T-GTTTATTTAGCCTGATCCACTGCAACTTCAGGGAGATAAGACT
66 ACTTCAGGGAGATAGGATTATCG--GATTTAACCTGATCCACTGCAACTTCAGGGAGATAAGACT
19813232 A
129 A
* ** * * * * *
19813233 GATGCGTTCTGCTCT-CTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATTCGCTTCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
* * *
19813297 ACTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
66 ACTTCAGGGAGATAGGATTATCGGATTTAACCTGATCCACTGCAACTTCAGGGAGATAA
19813356 AATTTACCAT
Statistics
Matches: 103, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
128 87 0.84
129 15 0.15
130 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (129 bp):
GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
ACTTCAGGGAGATAGGATTATCGGATTTAACCTGATCCACTGCAACTTCAGGGAGATAAGACTA
Found at i:19813926 original size:126 final size:126
Alignment explanation
Indices: 19813661--19813996 Score: 467
Period size: 126 Copynumber: 2.6 Consensus size: 126
19813651 GCTATTTTCC
* * * * * * *
19813661 ACCTACTCCACTGCT-ACTCAGGGAGATAGGGTTCACAATCTTCAACCAATTTCGCTGTTGACCA
1 ACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGTTGTCCA
* * *
19813725 GGGATATAGGACCTACAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCT
65 GGGAGATAGGA--T----TCTTCAATCTATTCCACTACTACCCAGGGAGATAGAATTCTCAATCT
19813790 TCA
124 TCA
* *
19813793 ACCTATTCCACTGCTGACCAGGGAGATAAGATTCACAATCTTTAACCTATTCCACTATTGTCCAG
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGTTGTCCAG
*
19813858 GGAGATAGGATTCTTTAATCTATTCCACTACTACCCAGGGAGATAGAATTCTCAATCTTCA
66 GGAGATAGGATTCTTCAATCTATTCCACTACTACCCAGGGAGATAGAATTCTCAATCTTCA
* *
19813919 ACTTATTCCACTACTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGTTGTCCAG
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGTTGTCCAG
19813984 GGAGATAGGATTC
66 GGAGATAGGATTC
19813997 ACAATATTTA
Statistics
Matches: 186, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
126 121 0.65
130 1 0.01
132 62 0.33
133 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (126 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGTTGTCCAG
GGAGATAGGATTCTTCAATCTATTCCACTACTACCCAGGGAGATAGAATTCTCAATCTTCA
Found at i:19814036 original size:44 final size:44
Alignment explanation
Indices: 19813661--19814036 Score: 392
Period size: 44 Copynumber: 8.7 Consensus size: 44
19813651 GCTATTTTCC
* *
19813661 ACCTACTCCACTGCT-ACTCAGGGAGATAGGGTTCACAATCTTCA
1 ACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTCA
* * * * * *
19813705 ACCAATTTCGCTGTTGACCAGGGATATAGGA-CCTACAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC-ACAATCTTCA
* * * *
19813749 ATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* *
19813793 ACCTATTCCACTGCTGACCAGGGAGATAAGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
** *
19813837 ACCTATTCCACTATTGTCCAGGGAGATAGGATT--C--T-TT-A
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* * * *
19813875 ATCTATTCCACTACT-ACCCAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGA-CCAGGGAGATAGGATTCACAATCTTCA
* * *
19813919 ACTTATTCCACTACTGACCAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* * * *
19813963 ACCTATTCCACTGTTGTCCAGGGAGATAGGATTCACAATATTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
**
19814007 ACCTATAACACTGCTGACCAGGGAGATAGG
1 ACCTATTCCACTGCTGACCAGGGAGATAGG
19814037 GTTGGGGTCA
Statistics
Matches: 275, Mismatches: 46, Indels: 22
0.80 0.13 0.06
Matches are distributed among these distances:
38 29 0.11
39 2 0.01
40 2 0.01
42 2 0.01
43 3 0.01
44 233 0.85
45 4 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (44 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
Found at i:19814118 original size:88 final size:87
Alignment explanation
Indices: 19814050--19814277 Score: 314
Period size: 88 Copynumber: 2.6 Consensus size: 87
19814040 GGGGTCATCA
* * * *
19814050 ATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCTA
1 ATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCA
19814115 GGGAGGCAAGGCTGGTGTCTACG
66 GGGAGGCAAGGCTGGTGTCT-CG
* * * *
19814138 ATTTGCTTCGCTGTCAGTGCTGGAAGGAAAGATCTGCTA-TTTTAAGTCTGCTCCACTGCAACCC
1 ATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAA-CCTGCTCCACTGCAACCC
*
19814202 AGGGAGGCAAGGCTGGTGACTTCG
65 AGGGAGGCAAGGCTGGTGTC-TCG
* * *
19814226 ATCTGCTTCGTTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTCAGCCTGCT
1 ATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCT
19814278 TGTGTCACGA
Statistics
Matches: 121, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
87 6 0.05
88 110 0.91
89 5 0.04
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.28
Consensus pattern (87 bp):
ATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCACTGCAACCCA
GGGAGGCAAGGCTGGTGTCTCG
Found at i:19814539 original size:45 final size:45
Alignment explanation
Indices: 19814404--19814539 Score: 125
Period size: 44 Copynumber: 3.1 Consensus size: 45
19814394 NNNTACTTCA
* *
19814404 CTGTCGGTGCAGGACGGCAAGATCTGCTATTTTCAGCCTGCTCCG
1 CTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCG
**** * * * * * *
19814449 CTG-CAACCCAGGGAGGCAAGA-CTGGT-GTCTTCGACCTGCTTCG
1 CTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAG-CCTGCTCCG
*
19814492 CTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCG
1 CTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCG
19814537 CTG
1 CTG
19814540 CCACTGAGGG
Statistics
Matches: 64, Mismatches: 23, Indels: 8
0.67 0.24 0.08
Matches are distributed among these distances:
42 3 0.05
43 15 0.23
44 24 0.38
45 18 0.28
46 4 0.06
ACGTcount: A:0.18, C:0.28, G:0.29, T:0.26
Consensus pattern (45 bp):
CTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCG
Found at i:19814553 original size:88 final size:88
Alignment explanation
Indices: 19814399--19814614 Score: 288
Period size: 88 Copynumber: 2.5 Consensus size: 88
19814389 NNNNNNNNTA
*
19814399 CTTCACTGTCGGTGCAGGACGGCAAGATCTGCTATTTTCAGCCTGCTCCGCTGCAACCCAGGGAG
1 CTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTCAGCCTGCTCCGCTGCAACCCAGGGAG
*
19814464 GCAAGACTGGTGTCTTCGACCTG
66 GCAAGACTAGTGTCTTCGACCTG
* * * * **
19814487 CTTCGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCCACTGAGGGAG
1 CTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTCAGCCTGCTCCGCTGCAACCCAGGGAG
* *
19814552 GCAAGGCTAGTGTCTTCGATCTG
66 GCAAGACTAGTGTCTTCGACCTG
* * ** * *
19814575 GTTCACTGTCAGTATAGGAAGGCAAGATCTGTTATCTTCA
1 CTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTCA
19814615 CTGATTTGTT
Statistics
Matches: 109, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
88 109 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.27
Consensus pattern (88 bp):
CTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTCAGCCTGCTCCGCTGCAACCCAGGGAG
GCAAGACTAGTGTCTTCGACCTG
Found at i:19814554 original size:44 final size:44
Alignment explanation
Indices: 19814419--19814556 Score: 118
Period size: 44 Copynumber: 3.1 Consensus size: 44
19814409 GGTGCAGGAC
* * **
19814419 GGCAAGATCTGCTATTTTCAGCCTGCTCCGCTGCAACCCAGGGA
1 GGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCCACTGAGGGA
* * * * * * ** * *
19814463 GGCAAGA-CTGGT-GTCTTCGACCTGCTTCGCTGTCGGTGCAAGAA
1 GGCAAGATCTGCTATTTTTAG-CCTGCTCCGCTGCCACTG-AGGGA
19814507 GGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCCACTGAGGGA
1 GGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCCACTGAGGGA
19814551 GGCAAG
1 GGCAAG
19814557 GCTAGTGTCT
Statistics
Matches: 66, Mismatches: 24, Indels: 8
0.67 0.24 0.08
Matches are distributed among these distances:
42 3 0.05
43 15 0.23
44 26 0.39
45 18 0.27
46 4 0.06
ACGTcount: A:0.20, C:0.28, G:0.29, T:0.24
Consensus pattern (44 bp):
GGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCCACTGAGGGA
Found at i:19820870 original size:53 final size:51
Alignment explanation
Indices: 19820770--19820875 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 51
19820760 TTATAAAACT
* * *
19820770 TATATATATAAAATACATAATGCATTTATGAAAACAAGGAAAATATAAATA
1 TATACATATAAAATACATAATGCATTTATAAAAAAAAGGAAAATATAAATA
* * * *
19820821 TATACATATAAAATATATTCATGCATTTATAAAAAAAATGAAACATATAAGTA
1 TATACATATAAAATACA-TAATGCATTTATAAAAAAAAGGAAA-ATATAAATA
19820874 TA
1 TA
19820876 ATATAAAAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
51 15 0.33
52 21 0.46
53 10 0.22
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (51 bp):
TATACATATAAAATACATAATGCATTTATAAAAAAAAGGAAAATATAAATA
Found at i:19821148 original size:3 final size:3
Alignment explanation
Indices: 19821140--19821224 Score: 145
Period size: 3 Copynumber: 28.3 Consensus size: 3
19821130 ATATGTAGGT
19821140 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA AT- ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
*
19821185 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
19821225 CAAAATTAAT
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
2 2 0.03
3 73 0.94
4 3 0.04
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:19821238 original size:9 final size:8
Alignment explanation
Indices: 19821140--19821239 Score: 83
Period size: 9 Copynumber: 11.2 Consensus size: 8
19821130 ATATGTAGGT
19821140 ATAATAATA
1 ATAATAA-A
19821149 ATAATAATA
1 ATAATAA-A
19821158 ATAATAATA
1 ATAATAA-A
*
19821167 ATATATAAT
1 ATA-ATAAA
19821176 ATAATAATA
1 ATAATAA-A
19821185 ATAATAATA
1 ATAATAA-A
19821194 ATAATAATA
1 ATAATAA-A
19821203 ATAATAATA
1 ATAATAA-A
*
19821212 ATAGTAATA
1 ATAATAA-A
*
19821221 ATAACAAA
1 ATAATAAA
19821229 ATTAATAAA
1 A-TAATAAA
19821238 AT
1 AT
19821240 GGACTAAAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
8 7 0.09
9 71 0.87
10 4 0.05
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (8 bp):
ATAATAAA
Found at i:19821482 original size:19 final size:21
Alignment explanation
Indices: 19821444--19821482 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
19821434 CCTTTTTTAA
*
19821444 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
19821465 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
19821483 ACAGTAAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:19821664 original size:22 final size:21
Alignment explanation
Indices: 19821629--19821705 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 21
19821619 GGCGGGTATC
* *
19821629 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
19821650 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
*
19821673 TACATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
19821692 TGCATATCATATCT
1 TACAAATCATATCT
19821706 AAGATTGCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
19 18 0.38
21 4 0.08
22 15 0.31
23 11 0.23
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:19821672 original size:23 final size:22
Alignment explanation
Indices: 19821629--19821686 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
19821619 GGCGGGTATC
* *
19821629 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
19821650 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
19821673 TACATATCATATCT
1 TACAAATCATATCT
19821687 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:19821689 original size:19 final size:19
Alignment explanation
Indices: 19821642--19821718 Score: 91
Period size: 19 Copynumber: 3.8 Consensus size: 19
19821632 AAATTAAATC
*
19821642 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
19821662 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
19821684 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
19821703 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
19821719 CTCGAAGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 34 0.65
22 7 0.13
23 11 0.21
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:19822458 original size:29 final size:29
Alignment explanation
Indices: 19822416--19822488 Score: 146
Period size: 29 Copynumber: 2.5 Consensus size: 29
19822406 CTACCCACGA
19822416 AATACCATTTTGGTAAATAATGTGAGTGG
1 AATACCATTTTGGTAAATAATGTGAGTGG
19822445 AATACCATTTTGGTAAATAATGTGAGTGG
1 AATACCATTTTGGTAAATAATGTGAGTGG
19822474 AATACCATTTTGGTA
1 AATACCATTTTGGTA
19822489 TTTTTCTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (29 bp):
AATACCATTTTGGTAAATAATGTGAGTGG
Found at i:19822602 original size:7 final size:7
Alignment explanation
Indices: 19822592--19822625 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
19822582 TATATTTATT
19822592 TTTTAAA
1 TTTTAAA
19822599 TTTTAAA
1 TTTTAAA
19822606 TTTTAAA
1 TTTTAAA
19822613 TTTTAAA
1 TTTTAAA
19822620 TTTTAA
1 TTTTAA
19822626 TATTATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTAAA
Found at i:19822674 original size:13 final size:12
Alignment explanation
Indices: 19822635--19822676 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
19822625 ATATTATTAA
19822635 TTAATAAAA-TT
1 TTAATAAAATTT
*
19822646 TAAATAAAATTT
1 TTAATAAAATTT
19822658 TTAATAAAATTT
1 TTAATAAAATTT
19822670 GTTAATA
1 -TTAATA
19822677 TGGTTTCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 8 0.30
12 13 0.48
13 6 0.22
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (12 bp):
TTAATAAAATTT
Found at i:19823292 original size:22 final size:23
Alignment explanation
Indices: 19823266--19823309 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
19823256 GAAGACCTGC
*
19823266 AAACAGTCACAAA-AACAAAAAG
1 AAACAGTAACAAAGAACAAAAAG
19823288 AAACAGTAACAAAGAACAAAAA
1 AAACAGTAACAAAGAACAAAAA
19823310 AATAGTAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.70, C:0.16, G:0.09, T:0.05
Consensus pattern (23 bp):
AAACAGTAACAAAGAACAAAAAG
Found at i:19824119 original size:15 final size:15
Alignment explanation
Indices: 19824099--19824131 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
19824089 TATTTGTATC
19824099 ATTATCATTATTATT
1 ATTATCATTATTATT
19824114 ATTATCATTATTATT
1 ATTATCATTATTATT
19824129 ATT
1 ATT
19824132 GTTAATGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTATCATTATTATT
Found at i:19824162 original size:3 final size:3
Alignment explanation
Indices: 19824099--19824147 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
19824089 TATTTGTATC
* * * * *
19824099 ATT ATC ATT ATT ATT ATT ATC ATT ATT ATT ATT GTT AAT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19824147 A
1 A
19824148 CTAGTAACTA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:19826389 original size:22 final size:21
Alignment explanation
Indices: 19826359--19826399 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
19826349 GGCCTAAAAC
19826359 ACTTTTAGTGTTACGACATTG
1 ACTTTTAGTGTTACGACATTG
19826380 ACTTGTTAGTGTTACGACAT
1 ACTT-TTAGTGTTACGACAT
19826400 GCAAAATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (21 bp):
ACTTTTAGTGTTACGACATTG
Found at i:19829240 original size:31 final size:32
Alignment explanation
Indices: 19829176--19829240 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 32
19829166 AAAAAGAAGG
*
19829176 AAGAAAAAGCAAAAAAAAAATAGCAACAGAAA
1 AAGAAAAAGCAAAAAAAAAATAGCAACAAAAA
* * **
19829208 AAGAAAAAG-AGAAAAAAGATAGCAGGAAAAA
1 AAGAAAAAGCAAAAAAAAAATAGCAACAAAAA
19829239 AA
1 AA
19829241 AAGAGAGATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 19 0.68
32 9 0.32
ACGTcount: A:0.74, C:0.06, G:0.17, T:0.03
Consensus pattern (32 bp):
AAGAAAAAGCAAAAAAAAAATAGCAACAAAAA
Found at i:19830593 original size:21 final size:23
Alignment explanation
Indices: 19830560--19830604 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
19830550 TAGAATATCA
19830560 TTTTATATATATATACAA-ATTT
1 TTTTATATATATATACAATATTT
* *
19830582 TTTTAT-TTTATATATAATATTT
1 TTTTATATATATATACAATATTT
19830604 T
1 T
19830605 CCATATGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTATATATATATACAATATTT
Found at i:19831863 original size:37 final size:37
Alignment explanation
Indices: 19831808--19831912 Score: 158
Period size: 37 Copynumber: 2.8 Consensus size: 37
19831798 TGTTTTCTAT
* * *
19831808 TGGACTAGCTCTTATGAGCATCTGGTATGTTGTCGGG
1 TGGATTAGCTCTTATGAGCATCTGGCATGTTATCGGG
*
19831845 TGGATTAGCTCTTATGAGCATCTGGCGTGTTATCGGG
1 TGGATTAGCTCTTATGAGCATCTGGCATGTTATCGGG
19831882 TGGATTAGCTCTTATGAGCGAT-TGGCATGTT
1 TGGATTAGCTCTTATGAGC-ATCTGGCATGTT
19831913 TTGGTTGGAA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
37 60 0.97
38 2 0.03
ACGTcount: A:0.17, C:0.15, G:0.31, T:0.36
Consensus pattern (37 bp):
TGGATTAGCTCTTATGAGCATCTGGCATGTTATCGGG
Found at i:19832899 original size:25 final size:25
Alignment explanation
Indices: 19832871--19832928 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
19832861 CATACGGGCA
*
19832871 TGTGACACAGCTTGGCACACGAGCG
1 TGTGACACAGCCTGGCACACGAGCG
* *
19832896 TGTGACACAGCCTGGCACATGGGCG
1 TGTGACACAGCCTGGCACACGAGCG
19832921 TGTGACAC
1 TGTGACAC
19832929 GGTCTTGTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.22, C:0.28, G:0.33, T:0.17
Consensus pattern (25 bp):
TGTGACACAGCCTGGCACACGAGCG
Found at i:19833719 original size:25 final size:25
Alignment explanation
Indices: 19833663--19833719 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
19833653 CATTCCATAT
* * * *
19833663 CTTGTGTGAGCATTTACAGTTATAG
1 CTTGTGTGAGCAATTACAATTACAA
* *
19833688 CTCGTGTGATCAATTACAATTACAA
1 CTTGTGTGAGCAATTACAATTACAA
19833713 CTTGTGT
1 CTTGTGT
19833720 TAGTAATATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (25 bp):
CTTGTGTGAGCAATTACAATTACAA
Found at i:19833818 original size:41 final size:40
Alignment explanation
Indices: 19833772--19833892 Score: 138
Period size: 41 Copynumber: 3.0 Consensus size: 40
19833762 ATCAAGTGGA
19833772 AAATGAATATATAAAATGATTATATGAATCGATTATATGG
1 AAATGAATATATAAAATGATTATATGAATCGATTATATGG
* * * *
19833812 AGAATGAATATATAAAATGGTAATATGAAT-TAGTTAAATGG
1 A-AATGAATATATAAAATGATTATATGAATCGA-TTATATGG
** * *
19833853 AAATG-ATATATGGAATGATTATATAAATCGGTTATATGG
1 AAATGAATATATAAAATGATTATATGAATCGATTATATGG
19833892 A
1 A
19833893 TAGATATTTA
Statistics
Matches: 66, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
39 26 0.39
40 6 0.09
41 34 0.52
ACGTcount: A:0.46, C:0.02, G:0.18, T:0.34
Consensus pattern (40 bp):
AAATGAATATATAAAATGATTATATGAATCGATTATATGG
Found at i:19833871 original size:12 final size:14
Alignment explanation
Indices: 19833772--19833876 Score: 55
Period size: 13 Copynumber: 7.9 Consensus size: 14
19833762 ATCAAGTGGA
* *
19833772 AAATGAATATAT-A
1 AAATGATTATATGG
19833785 AAATGATTATAT-G
1 AAATGATTATATGG
19833798 -AATCGATTATATGG
1 AAAT-GATTATATGG
* *
19833812 AGAATGAATATAT-A
1 A-AATGATTATATGG
* *
19833826 AAATGGTAATAT-G
1 AAATGATTATATGG
* *
19833839 -AATTAGTTAAATGG
1 AAATGA-TTATATGG
19833853 AAATGA-TATATGG
1 AAATGATTATATGG
19833866 -AATGATTATAT
1 AAATGATTATAT
19833877 AAATCGGTTA
Statistics
Matches: 70, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
12 11 0.16
13 42 0.60
14 3 0.04
15 11 0.16
16 3 0.04
ACGTcount: A:0.48, C:0.01, G:0.17, T:0.34
Consensus pattern (14 bp):
AAATGATTATATGG
Found at i:19834731 original size:22 final size:22
Alignment explanation
Indices: 19834703--19834748 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
19834693 AATTGGGTAT
19834703 TGAATTCATGGAATGGAAGGTG
1 TGAATTCATGGAATGGAAGGTG
19834725 TGAATTCATGGAATGGAAGGTG
1 TGAATTCATGGAATGGAAGGTG
19834747 TG
1 TG
19834749 GTTAACTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.37, T:0.28
Consensus pattern (22 bp):
TGAATTCATGGAATGGAAGGTG
Found at i:19835497 original size:22 final size:22
Alignment explanation
Indices: 19835472--19835513 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
19835462 GTTTAAACAT
*
19835472 ATTTCTTTTCCCGTGCCCCCAC
1 ATTTCTTTTCCCGTCCCCCCAC
*
19835494 ATTTCTTTTCTCGTCCCCCC
1 ATTTCTTTTCCCGTCCCCCC
19835514 CACTCCCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.07, C:0.45, G:0.07, T:0.40
Consensus pattern (22 bp):
ATTTCTTTTCCCGTCCCCCCAC
Found at i:19838908 original size:9 final size:9
Alignment explanation
Indices: 19838892--19838937 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
19838882 GCTTGCAAAA
19838892 AGGACGATG
1 AGGACGATG
*
19838901 ACGACGATG
1 AGGACGATG
19838910 AGGACGATG
1 AGGACGATG
19838919 AGGACGATG
1 AGGACGATG
*
19838928 AGGATGATG
1 AGGACGATG
19838937 A
1 A
19838938 TGTTTCTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.35, C:0.11, G:0.41, T:0.13
Consensus pattern (9 bp):
AGGACGATG
Found at i:19841425 original size:26 final size:26
Alignment explanation
Indices: 19841389--19841440 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
19841379 AGAAGATGAA
19841389 TTAGAAATCTTCTCTCTACTATCACG
1 TTAGAAATCTTCTCTCTACTATCACG
19841415 TTAGAAATCTTCTCTCTACTATCACG
1 TTAGAAATCTTCTCTCTACTATCACG
19841441 CTATCTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (26 bp):
TTAGAAATCTTCTCTCTACTATCACG
Found at i:19843220 original size:27 final size:27
Alignment explanation
Indices: 19843146--19843222 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
19843136 CCTCATCCCT
* * *
19843146 ATTTTACCCCTATTAAAA-ATTTAACG
1 ATTTTACCCTTATTAAAATTTTTAACA
** *
19843172 ATTTTACCCTTGA-TAATTTTTTTTACA
1 ATTTTACCCTT-ATTAAAATTTTTAACA
19843199 ATTTTACCCTTATTAAAATTTTTA
1 ATTTTACCCTTATTAAAATTTTTA
19843223 GAAAATATGT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
26 14 0.36
27 25 0.64
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.49
Consensus pattern (27 bp):
ATTTTACCCTTATTAAAATTTTTAACA
Found at i:19851524 original size:30 final size:30
Alignment explanation
Indices: 19851490--19851553 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
19851480 TTCCCATTTT
19851490 GATACATAAATTCCTCTTTTATATATAAAA
1 GATACATAAATTCCTCTTTTATATATAAAA
19851520 GATACATAAATTCCTCTTTTATATATAAAA
1 GATACATAAATTCCTCTTTTATATATAAAA
19851550 GATA
1 GATA
19851554 TAAATATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (30 bp):
GATACATAAATTCCTCTTTTATATATAAAA
Found at i:19851751 original size:2 final size:2
Alignment explanation
Indices: 19851744--19851777 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19851734 TGGAGTATTT
19851744 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19851778 CACACACACG
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):
TA
Found at i:19859230 original size:1 final size:1
Alignment explanation
Indices: 19859224--19859250 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
19859214 GATCAAATTG
19859224 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
19859251 CTTTCCCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19862855 original size:16 final size:16
Alignment explanation
Indices: 19862834--19862880 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
19862824 GTTTGGTTCG
19862834 CTGTAATGGAATAGAA
1 CTGTAATGGAATAGAA
*
19862850 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAA
*
19862866 CTATAATGGAATAGA
1 CTGTAATGGAATAGA
19862881 GGCATAATAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.43, C:0.06, G:0.26, T:0.26
Consensus pattern (16 bp):
CTGTAATGGAATAGAA
Found at i:19866680 original size:21 final size:21
Alignment explanation
Indices: 19866650--19866708 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
19866640 AAAAATAGCG
* *
19866650 GTAGTAGTGAGATTAGTTATT
1 GTAGCAGTGAGATTAGATATT
* *
19866671 GTAGCGGTGAGATTGGATATT
1 GTAGCAGTGAGATTAGATATT
19866692 GTAGCAGTGAGATTAGA
1 GTAGCAGTGAGATTAGA
19866709 AACAATGTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.29, C:0.03, G:0.34, T:0.34
Consensus pattern (21 bp):
GTAGCAGTGAGATTAGATATT
Found at i:19868115 original size:46 final size:47
Alignment explanation
Indices: 19868036--19868127 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 47
19868026 ATCATGTCGA
19868036 ATATGGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCGC
1 ATATGGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCGC
19868083 ATATGGTTCGGTACTT-CTCGAATTGACCTTCAGTGGGTTTAATCG
1 ATATGGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCG
19868128 TGTCTATTCC
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 29 0.64
47 16 0.36
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (47 bp):
ATATGGTTCGGTACTTCCTCGAATTGACCTTCAGTGGGTTTAATCGC
Found at i:19870893 original size:27 final size:27
Alignment explanation
Indices: 19870855--19870907 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
19870845 AACTGAGAAG
*
19870855 TGAATAGAAAGCACAGAATATTCTATT
1 TGAATAGAAAGCACAGAATATGCTATT
*
19870882 TGAATAGAAAGCACCGAATATGCTAT
1 TGAATAGAAAGCACAGAATATGCTAT
19870908 AGTTTCAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (27 bp):
TGAATAGAAAGCACAGAATATGCTATT
Found at i:19871982 original size:17 final size:17
Alignment explanation
Indices: 19871960--19872001 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
19871950 GGCCCGAGGT
* *
19871960 GGCCCAAACCCAACTGA
1 GGCCCAAACCAAACAGA
19871977 GGCCCAAACCAAACAGA
1 GGCCCAAACCAAACAGA
*
19871994 AGCCCAAA
1 GGCCCAAA
19872002 GCAGATTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.43, C:0.38, G:0.17, T:0.02
Consensus pattern (17 bp):
GGCCCAAACCAAACAGA
Found at i:19873232 original size:27 final size:28
Alignment explanation
Indices: 19873173--19873229 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 28
19873163 CATACGCATA
19873173 TTTATTTTTGTAGTATAATATAATTATT
1 TTTATTTTTGTAGTATAATATAATTATT
* *
19873201 TTTATTTTT-TATTAT-ATGTAATTATT
1 TTTATTTTTGTAGTATAATATAATTATT
19873227 TTT
1 TTT
19873230 TATAACCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 13 0.48
27 5 0.19
28 9 0.33
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (28 bp):
TTTATTTTTGTAGTATAATATAATTATT
Found at i:19874055 original size:98 final size:98
Alignment explanation
Indices: 19873925--19874121 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
19873915 TTTAAAATAA
* * * *
19873925 TAAAGGAAATATTCGGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCGGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGCGTGTGATTTC
19873990 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
19874023 TAAAGGAAATATTCTGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGCGTGTGATTTC
1 TAAAGGAAATATTCGGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGCGTGTGATTTC
19874088 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
19874121 T
1 T
19874122 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCGGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACGTATTGCGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:19885572 original size:44 final size:42
Alignment explanation
Indices: 19885521--19886072 Score: 334
Period size: 44 Copynumber: 12.7 Consensus size: 42
19885511 AAATTGAGTT
19885521 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-A-AATC
* * * *
19885565 CTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTCAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGC-CAAATC
* * * *** * * *
19885609 TTATCTCTCTGAAGTTGCAG-AGAGCAAATCGCA-TCTAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAATC
* * * *
19885649 ATATCTCCCTGAGGTTGCAGTGGAGCAGAATATGTAAG-CAAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAG-AT-T-AAAGCCAAATC
* * *
19885693 TTATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATGGCAAATC
1 TTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCAAATC
19885738 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-A-AATC
* * ** * *
19885782 CTATCTCCCTGAAGTTACAGTGGAGTGGATTAAAACCCCAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAA-GCCAAATC
* * * * *** * * *
19885826 TTATCTCTCTGAAGATGCAG-AGAGTAGATCGCA-TCTAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAATC
* *
19885866 TTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGTAAAG-CAAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-T---TAAAGCCAAATC
*
19885911 TTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGGTAG-CAAATC
1 TTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA---AGCCAAATC
*
19885956 TTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCGACAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-A-AATC
* * * * *
19886000 CTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAACCTCAGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGC-CAAATC
* *
19886044 TTATCCCCCTGAAGTTGTAGTGGAGCAGA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA
19886073 CTGGTAGATC
Statistics
Matches: 393, Mismatches: 78, Indels: 74
0.72 0.14 0.14
Matches are distributed among these distances:
40 40 0.10
41 13 0.03
42 11 0.03
43 21 0.05
44 195 0.50
45 103 0.26
46 10 0.03
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (42 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAATC
Found at i:19886009 original size:218 final size:217
Alignment explanation
Indices: 19885521--19886057 Score: 894
Period size: 217 Copynumber: 2.5 Consensus size: 217
19885511 AAATTGAGTT
*
19885521 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGCAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGT
*
19885586 GGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAAATCGCATCTAGTCAT
66 GGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGATGCAGAGAGCAAATCGCATCTAGTCAT
* *
19885651 ATCTCCCTGAGGTTGCAGTGGAGCAGAATATGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGA
131 ATCTCCCTGAAGTTGCAGTGGAGCAGAATAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGA
* *
19885716 GGTAGACTGAAGATGGCAAATC
196 GGCAGACTGAAGATAGCAAATC
*
19885738 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTACAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGT
* * * * *
19885803 GGAGTGGATTAAAACCCCAGATCTTATCTCTCTGAAGATGCAGAGAGTAGATCGCATCTAGTCTT
66 GGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGATGCAGAGAGCAAATCGCATCTAGTCAT
* *
19885868 ATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGTAAAGCAAGTCTTATCCTCCTGAAGTTGCAGTG
131 ATCTCCCTGAAGTTGCAGTGGAGCAGAATAAGT-AAGCAAGTCTTATCCTCCTGAAGTTGCAGTG
*
19885933 AGGCAGACTGAAGGTAGCAAATC
195 AGGCAGACTGAAGATAGCAAATC
*
19885956 TTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGT
* * *
19886021 AGAGCGGATTAAAACCTCAGATCTTATCCCCCTGAAG
66 GGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAG
19886058 TTGTAGTGGA
Statistics
Matches: 297, Mismatches: 22, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
217 151 0.51
218 146 0.49
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (217 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGACAATCCTATCTCCCTGAAGTTGCAGT
GGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGATGCAGAGAGCAAATCGCATCTAGTCAT
ATCTCCCTGAAGTTGCAGTGGAGCAGAATAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGA
GGCAGACTGAAGATAGCAAATC
Found at i:19886365 original size:16 final size:17
Alignment explanation
Indices: 19886330--19886369 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
19886320 GCCCGAAGTG
* *
19886330 GCCCAAACCCAACTGAA
1 GCCCAAACCAAACAGAA
19886347 GCCCAAA-CAAACAGAA
1 GCCCAAACCAAACAGAA
19886363 GCCCAAA
1 GCCCAAA
19886370 GCAGATTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.47, C:0.38, G:0.12, T:0.03
Consensus pattern (17 bp):
GCCCAAACCAAACAGAA
Found at i:19887508 original size:27 final size:28
Alignment explanation
Indices: 19887474--19887530 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
19887464 TTTCATTTTC
19887474 TTTATT-TTTTT--TATT-AATTAGTTT
1 TTTATTCTTTTTCATATTAAATTAGTTT
*
19887498 TTTATTCTTTTTCATATTAAATTATTTT
1 TTTATTCTTTTTCATATTAAATTAGTTT
19887526 TTTAT
1 TTTAT
19887531 ATACATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 6 0.21
25 5 0.18
27 4 0.14
28 13 0.46
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.72
Consensus pattern (28 bp):
TTTATTCTTTTTCATATTAAATTAGTTT
Found at i:19887614 original size:28 final size:28
Alignment explanation
Indices: 19887554--19887611 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
19887544 CATACGCATA
19887554 TTTATTTTTGTAGTATAATATAATTATT
1 TTTATTTTTGTAGTATAATATAATTATT
* * *
19887582 TTTATTTTTTTATTAT-ATGTAATTATT
1 TTTATTTTTGTAGTATAATATAATTATT
19887609 TTT
1 TTT
19887612 TATAACCTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (28 bp):
TTTATTTTTGTAGTATAATATAATTATT
Found at i:19888353 original size:99 final size:98
Alignment explanation
Indices: 19888240--19888497 Score: 267
Period size: 98 Copynumber: 2.6 Consensus size: 98
19888230 ATTCAACACG
* * *
19888240 TTGTGTCCTAACGTATTGGATGTGACGTATT-GATTTCTCGA-AA-TGAAGAT-TT-TTTTAAAA
1 TTGTGCCCTAACGTATTGGATGTGACGTATTAAATCT-TCGATAAGTG--GATGTTCTTTT--AA
*
19888300 TAATAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAA
61 -AATAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAA
* ** * * *
19888339 TTGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAAGTAA
1 TTGTGCCCTAACGTATTGGATGTGACGTATTAAATCTTCGATAAGTGGATGTTCTTTTAAAATAA
*
19888404 AGGAAATATTCCGAGTTTGGGGTTCTAAAGGAA
66 AGGAAATATTCCGAGTTTGGGATTCTAAAGGAA
* ** * *
19888437 TCGTGCCCTAACGTATTGCG-TGTGATTTCTTAAATCTTGGATAAGTGGATGTTCTTTTAAA
1 TTGTGCCCTAACGTATTG-GATGTGACGTATTAAATCTTCGATAAGTGGATGTTCTTTTAAA
19888498 GTTTTATTGT
Statistics
Matches: 141, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
98 93 0.66
99 35 0.25
100 7 0.05
101 6 0.04
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (98 bp):
TTGTGCCCTAACGTATTGGATGTGACGTATTAAATCTTCGATAAGTGGATGTTCTTTTAAAATAA
AGGAAATATTCCGAGTTTGGGATTCTAAAGGAA
Found at i:19888417 original size:98 final size:98
Alignment explanation
Indices: 19888303--19888499 Score: 358
Period size: 98 Copynumber: 2.0 Consensus size: 98
19888293 TTTAAAATAA
* * *
19888303 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGCGTGTGATTTC
19888368 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
19888401 TAAAGGAAATATTCCGAGTTTGGGGTTCTAAAGGAATCGTGCCCTAACGTATTGCGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGCGTGTGATTTC
19888466 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
19888499 T
1 T
19888500 TTTATTGTAC
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGCGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:19889481 original size:22 final size:22
Alignment explanation
Indices: 19889437--19889481 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
19889427 CCAAATTGAA
*
19889437 TCAAACTCAAACCGACCTGAAC
1 TCAAACTCAAACCGACCTAAAC
*
19889459 TCAAACTCAAGA-CGATCTAAAC
1 TCAAACTCAA-ACCGACCTAAAC
19889481 T
1 T
19889482 TGAAACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.42, C:0.31, G:0.09, T:0.18
Consensus pattern (22 bp):
TCAAACTCAAACCGACCTAAAC
Found at i:19889701 original size:6 final size:6
Alignment explanation
Indices: 19889690--19889716 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
19889680 TTTTTCAACG
19889690 TATCCA TATCCA TATCCA TATCCA TAT
1 TATCCA TATCCA TATCCA TATCCA TAT
19889717 TTAAATTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (6 bp):
TATCCA
Found at i:19890211 original size:21 final size:20
Alignment explanation
Indices: 19890182--19890222 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
19890172 CTCTCTCACC
*
19890182 AAAATTTTCAAAAATATTTAT
1 AAAAATTTCAAAAAT-TTTAT
19890203 AAAAATTTCAAAAATTTTAT
1 AAAAATTTCAAAAATTTTAT
19890223 TTTTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAATTTCAAAAATTTTAT
Found at i:19892390 original size:16 final size:16
Alignment explanation
Indices: 19892366--19892403 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
19892356 TAAAAGTTAC
*
19892366 AAAAAATAAA-AAAAT
1 AAAATATAAATAAAAT
19892381 ATAAATATAAATAAAAT
1 A-AAATATAAATAAAAT
19892398 AAAATA
1 AAAATA
19892404 AATATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 13 0.65
17 6 0.30
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATATAAATAAAAT
Found at i:19892394 original size:20 final size:20
Alignment explanation
Indices: 19892369--19892408 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
19892359 AAGTTACAAA
19892369 AAATAAAA-AAATATAAATAT
1 AAATAAAATAAA-ATAAATAT
19892389 AAATAAAATAAAATAAATAT
1 AAATAAAATAAAATAAATAT
19892409 TAATTACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATAAAATAAAATAAATAT
Found at i:19894310 original size:40 final size:41
Alignment explanation
Indices: 19894232--19894312 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 41
19894222 AGGAAGCGCT
**
19894232 TGTCCACGTGGACAGAAAACACTTCCTTGAGGGCGCACTTTG
1 TGTCCACGTGGACA-AAAACACTTCCTTGAGGAAGCACTTTG
* *
19894274 TGTCCACGTGGAC-AAAGCGCTTCCTTGAGGAAGCACTTT
1 TGTCCACGTGGACAAAAACACTTCCTTGAGGAAGCACTTT
19894313 TTTCCGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 22 0.63
42 13 0.37
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (41 bp):
TGTCCACGTGGACAAAAACACTTCCTTGAGGAAGCACTTTG
Found at i:19894497 original size:95 final size:95
Alignment explanation
Indices: 19894392--19894701 Score: 439
Period size: 97 Copynumber: 3.2 Consensus size: 95
19894382 ATTTTAGGGG
* * * * * *
19894392 TTTAAGGAAAAAATTAAATAAATAAGGGTTTAGGGTTTCTTAATTAAATTAATTATAGATTTTAA
1 TTTAAGGAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATA-ATTTTAA
19894457 AAAATTAGATTAGGGTTTAGTGTTTATGGTT
65 AAAATTAGATTAGGGTTTAGTGTTTATGGTT
19894488 TTTAA-GAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAATTTTTTT
1 TTTAAGGAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAA---TTTT
*
19894552 AAAAAAATAGATTAGGGTTTAGTG-TT-TGGTT
63 AAAAAATTAGATTAGGGTTTAGTGTTTATGGTT
19894583 TTTAAGGGAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAAATTTTA
1 TTTAA-GGAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTAT-AATTTT-
* * *
19894648 AAAAAATTAGATTGGGGTTTAGTATTTAGGGTT
63 AAAAAATTAGATTAGGGTTTAGTGTTTATGGTT
19894681 TTTAAGG-AAAAATCAAATAAA
1 TTTAAGGAAAAAATCAAATAAA
19894702 GCTAGGTGTT
Statistics
Matches: 194, Mismatches: 11, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
94 1 0.01
95 59 0.30
96 42 0.22
97 81 0.42
98 11 0.06
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.39
Consensus pattern (95 bp):
TTTAAGGAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAATTTTAAA
AAATTAGATTAGGGTTTAGTGTTTATGGTT
Found at i:19895486 original size:40 final size:41
Alignment explanation
Indices: 19895429--19895510 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 41
19895419 GGAAACACTT
19895429 TGTCCACGTGGACACAAAGCGCGCCCTCAAGGAAGCGTTTTC
1 TGTCCACGTGGA-ACAAAGCGCGCCCTCAAGGAAGCGTTTTC
** **
19895471 TGTCCACGTGG-ACAAAGCGCTTCCTTGAGGAAGCGTTTTC
1 TGTCCACGTGGAACAAAGCGCGCCCTCAAGGAAGCGTTTTC
19895511 CTACTTTATC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 25 0.69
42 11 0.31
ACGTcount: A:0.22, C:0.28, G:0.27, T:0.23
Consensus pattern (41 bp):
TGTCCACGTGGAACAAAGCGCGCCCTCAAGGAAGCGTTTTC
Found at i:19897059 original size:79 final size:79
Alignment explanation
Indices: 19896921--19897066 Score: 215
Period size: 79 Copynumber: 1.8 Consensus size: 79
19896911 ACGTTTATAA
* *
19896921 GTGTTCTATCATATAGCCTATACCCTCCATGCTCTCAAACGCTAGTTAGACCGAGTGATGTTCAA
1 GTGTTCTATCAGATAGCCTATACCATCCATGCTCTCAAACGCTAGTTAGACCGAGTGATGTTCAA
19896986 TGTGGTGTATGTGT
66 TGTGGTGTATGTGT
* * *
19897000 GTGTTCTATCAGATA-CCTTATACCATCCATGTTCTCAAATGCTAGTTAGGCC-AGCTGATGTTC
1 GTGTTCTATCAGATAGCC-TATACCATCCATGCTCTCAAACGCTAGTTAGACCGAG-TGATGTTC
19897063 AATG
64 AATG
19897067 CAGTATGTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
78 4 0.07
79 56 0.93
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (79 bp):
GTGTTCTATCAGATAGCCTATACCATCCATGCTCTCAAACGCTAGTTAGACCGAGTGATGTTCAA
TGTGGTGTATGTGT
Found at i:19902044 original size:21 final size:21
Alignment explanation
Indices: 19902005--19902045 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
19901995 TACTTTATTT
*
19902005 CATTTTTCTTTATTTTTCTTC
1 CATTTTTCTTTATTATTCTTC
* *
19902026 CATTTTTTTTTCTTATTCTT
1 CATTTTTCTTTATTATTCTT
19902046 TCCTTTCTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (21 bp):
CATTTTTCTTTATTATTCTTC
Found at i:19902048 original size:22 final size:21
Alignment explanation
Indices: 19902005--19902061 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
19901995 TACTTTATTT
* * *
19902005 CATTTTTCTTTATTTTTCTTC
1 CATTTTTATTTCTTATTCTTC
*
19902026 CATTTTTTTTTCTTATTCTTTC
1 CATTTTTATTTCTTATTC-TTC
19902048 C-TTTCTTATTTCTT
1 CATTT-TTATTTCTT
19902062 TTCCTTCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (21 bp):
CATTTTTATTTCTTATTCTTC
Found at i:19902052 original size:15 final size:17
Alignment explanation
Indices: 19902034--19902067 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
19902024 TCCATTTTTT
19902034 TTTCTTA-TTC-TTTCC
1 TTTCTTATTTCTTTTCC
19902049 TTTCTTATTTCTTTTCC
1 TTTCTTATTTCTTTTCC
19902066 TT
1 TT
19902068 CATTCTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCTTATTTCTTTTCC
Found at i:19908454 original size:28 final size:28
Alignment explanation
Indices: 19908414--19908471 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
19908404 GATCTACTTC
19908414 ATGTCAATACATGAAGACAAGATCCATT
1 ATGTCAATACATGAAGACAAGATCCATT
19908442 ATGTCAATACATGAAGACAAGATCCATT
1 ATGTCAATACATGAAGACAAGATCCATT
19908470 AT
1 AT
19908472 CTTCGATCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (28 bp):
ATGTCAATACATGAAGACAAGATCCATT
Found at i:19908573 original size:44 final size:44
Alignment explanation
Indices: 19908442--19908795 Score: 493
Period size: 44 Copynumber: 8.0 Consensus size: 44
19908432 AAGATCCATT
*
19908442 ATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTC
1 ATGTCAATACATGAAGACAAGATCCACTATCTTCGATCTACTTC
* * * * * * *
19908486 A--CCACTAGTATGGGAAGACAAGATCTACCATCTTCGATATACTTA
1 ATGTCAATA-CAT--GAAGACAAGATCCACTATCTTCGATCTACTTC
19908531 ATGTCAATACATGAAGACAAGATCCACTATC-TCTGATCTACTTC
1 ATGTCAATACATGAAGACAAGATCCACTATCTTC-GATCTACTTC
*
19908575 ATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTC
1 ATGTCAATACATGAAGACAAGATCCACTATCTTCGATCTACTTC
* *
19908619 ATGTCAATACATGAAGACAAGATTCGCTATCTTCGATCTACTTC
1 ATGTCAATACATGAAGACAAGATCCACTATCTTCGATCTACTTC
19908663 ATGTCAATACATGAAGACAAGATCCACTATC-TCTGATCTACTTC
1 ATGTCAATACATGAAGACAAGATCCACTATCTTC-GATCTACTTC
**
19908707 ATGTCAATACATGAAGACAAGATCTGCTATC-TCTGATCTACTTC
1 ATGTCAATACATGAAGACAAGATCCACTATCTTC-GATCTACTTC
*
19908751 ATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTC
1 ATGTCAATACATGAAGACAAGATCCACTATCTTCGATCTACTTC
19908795 A
1 A
19908796 CCACCAGTAT
Statistics
Matches: 275, Mismatches: 26, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
42 4 0.01
43 6 0.02
44 227 0.83
45 32 0.12
46 2 0.01
47 4 0.01
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31
Consensus pattern (44 bp):
ATGTCAATACATGAAGACAAGATCCACTATCTTCGATCTACTTC
Found at i:19913201 original size:19 final size:19
Alignment explanation
Indices: 19913177--19913216 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
19913167 AATAACTACT
19913177 TGTGCAATATGGTCATGAA
1 TGTGCAATATGGTCATGAA
19913196 TGTGCAATATGGTCATGAA
1 TGTGCAATATGGTCATGAA
19913215 TG
1 TG
19913217 AGATGTAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.33
Consensus pattern (19 bp):
TGTGCAATATGGTCATGAA
Found at i:19920293 original size:25 final size:23
Alignment explanation
Indices: 19920258--19920303 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
19920248 AATACTTCGT
* *
19920258 TTTAAAATATGTATGTATATATA
1 TTTAAAATATGAATATATATATA
19920281 TTTACAAAGTATGAATATATATA
1 TTTA-AAA-TATGAATATATATA
19920304 GACATGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 3 0.16
25 12 0.63
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (23 bp):
TTTAAAATATGAATATATATATA
Found at i:19924925 original size:15 final size:17
Alignment explanation
Indices: 19924905--19924936 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
19924895 ACAAAACGAG
19924905 AATAA-TTAAT-ACAAA
1 AATAATTTAATCACAAA
19924920 AATAATTTAATCACAAA
1 AATAATTTAATCACAAA
19924937 CAAACCAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAATTTAATCACAAA
Found at i:19926553 original size:16 final size:16
Alignment explanation
Indices: 19926518--19926552 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
19926508 TGTACTGGAC
19926518 TTTTAATTTATTTGGT
1 TTTTAATTTATTTGGT
*
19926534 TTTTATTTTATTT-GT
1 TTTTAATTTATTTGGT
19926549 TTTT
1 TTTT
19926553 TTGGTAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.14, C:0.00, G:0.09, T:0.77
Consensus pattern (16 bp):
TTTTAATTTATTTGGT
Found at i:19930679 original size:21 final size:21
Alignment explanation
Indices: 19930614--19930680 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
19930604 TTATTTACTC
19930614 TAAAACCTTAAAT-CTAAAATT
1 TAAAACCTTAAATCCT-AAATT
* * *
19930635 CAAAACCCTAAATCC-AAAGCT
1 TAAAACCTTAAATCCTAAA-TT
*
19930656 TAAAATCTTAAATCCTAAATT
1 TAAAACCTTAAATCCTAAATT
19930677 TAAA
1 TAAA
19930681 CCCGTAACCC
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
20 3 0.08
21 29 0.81
22 4 0.11
ACGTcount: A:0.51, C:0.19, G:0.01, T:0.28
Consensus pattern (21 bp):
TAAAACCTTAAATCCTAAATT
Found at i:19930801 original size:28 final size:29
Alignment explanation
Indices: 19930761--19930815 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
19930751 TATGAATCCC
*
19930761 TAAATCTAAAAT-CGTAACCCCAAACCAT
1 TAAATCTAAAATCCATAACCCCAAACCAT
**
19930789 TAAATCTTGAATCCATAACCCCAAACC
1 TAAATCTAAAATCCATAACCCCAAACC
19930816 TTTGAACCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.44, C:0.31, G:0.04, T:0.22
Consensus pattern (29 bp):
TAAATCTAAAATCCATAACCCCAAACCAT
Found at i:19932793 original size:16 final size:17
Alignment explanation
Indices: 19932754--19932796 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
19932744 TTTTTTATCA
*
19932754 TTCTAATTTTTCACCTC
1 TTCTAATTTTCCACCTC
*
19932771 TTC-AATTTTCCATCT-
1 TTCTAATTTTCCACCTC
19932786 TTCTAATTTTC
1 TTCTAATTTTC
19932797 TTTCTACCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 3 0.13
16 17 0.74
17 3 0.13
ACGTcount: A:0.19, C:0.26, G:0.00, T:0.56
Consensus pattern (17 bp):
TTCTAATTTTCCACCTC
Found at i:19935495 original size:20 final size:20
Alignment explanation
Indices: 19935470--19935538 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
19935460 ACATGATATC
19935470 CTTAGAAATTTTGGTAAAAG
1 CTTAGAAATTTTGGTAAAAG
* * *
19935490 CTTAGAAAATTT-GTTAAAT
1 CTTAGAAATTTTGGTAAAAG
* *
19935509 TTATAGGAATTTTGGTAAATAG
1 CT-TAGAAATTTTGGTAAA-AG
19935531 -TTAGAAAT
1 CTTAGAAAT
19935539 AATTGAAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 6 0.16
20 25 0.68
21 5 0.14
22 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.17, T:0.39
Consensus pattern (20 bp):
CTTAGAAATTTTGGTAAAAG
Found at i:19935630 original size:20 final size:20
Alignment explanation
Indices: 19935602--19935639 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19935592 AAATTTTGAT
19935602 TTTTAATAAATGATTAGACG
1 TTTTAATAAATGATTAGACG
* *
19935622 TTTTGATAAATGCTTAGA
1 TTTTAATAAATGATTAGA
19935640 AATATTAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (20 bp):
TTTTAATAAATGATTAGACG
Found at i:19935671 original size:20 final size:20
Alignment explanation
Indices: 19935648--19935731 Score: 53
Period size: 20 Copynumber: 4.2 Consensus size: 20
19935638 GAAATATTAG
19935648 TAAATTTTTAAAAGTTTTGA
1 TAAATTTTTAAAAGTTTTGA
* ** *
19935668 TAAATTCTTGCAAGTTTTGG
1 TAAATTTTTAAAAGTTTTGA
** * * *
19935688 TAAAAGTGTAGAAGTTCTGA
1 TAAATTTTTAAAAGTTTTGA
* *
19935708 TAAATTATTAGATA-TTTTGA
1 TAAATTTTTA-AAAGTTTTGA
19935728 TAAA
1 TAAA
19935732 CCCTAATGAT
Statistics
Matches: 44, Mismatches: 19, Indels: 2
0.68 0.29 0.03
Matches are distributed among these distances:
20 43 0.98
21 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.43
Consensus pattern (20 bp):
TAAATTTTTAAAAGTTTTGA
Found at i:19937596 original size:25 final size:27
Alignment explanation
Indices: 19937545--19937599 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
19937535 TCCAAAAGAG
* *
19937545 TACAAATACAATTATATTGATAGATAAT
1 TACAAAAACAATTATATT-ATAAATAAT
19937573 TACAAAAACAA-TATATT-TAAATAAT
1 TACAAAAACAATTATATTATAAATAAT
19937598 TA
1 TA
19937600 TAAACAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.36
27 6 0.24
28 10 0.40
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.35
Consensus pattern (27 bp):
TACAAAAACAATTATATTATAAATAAT
Found at i:19943257 original size:13 final size:13
Alignment explanation
Indices: 19943212--19943262 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
19943202 ACATTCTCTC
*
19943212 AAAAT-AATAATG
1 AAAATGAATAAAG
19943224 AAAATGTAAATAAA-
1 AAAATG--AATAAAG
*
19943238 TAAATGAATAAAG
1 AAAATGAATAAAG
19943251 AAAATGAATAAA
1 AAAATGAATAAA
19943263 ATTATAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 11 0.34
13 11 0.34
14 5 0.16
15 5 0.16
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.22
Consensus pattern (13 bp):
AAAATGAATAAAG
Found at i:19943446 original size:24 final size:25
Alignment explanation
Indices: 19943419--19943471 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
19943409 ATAGGTGTGT
19943419 GTATATACATATAT-A-TTATAAAAA
1 GTATATACATATATAAGTTAT-AAAA
* *
19943443 GTATGTATATATATAAGTTATAAAA
1 GTATATACATATATAAGTTATAAAA
19943468 GTAT
1 GTAT
19943472 GTACGTGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 12 0.48
25 9 0.36
26 4 0.16
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (25 bp):
GTATATACATATATAAGTTATAAAA
Found at i:19943473 original size:25 final size:24
Alignment explanation
Indices: 19943427--19943521 Score: 73
Period size: 25 Copynumber: 3.5 Consensus size: 24
19943417 GTGTATATAC
19943427 ATATATATTATAAAAAGTATGTAT
1 ATATATATTATAAAAAGTATGTAT
19943451 ATATATAAGTTATAAAAGTATGTACGTGCATAT
1 ATATAT-A-TTATAAAA--A-GTA--TG--TAT
*
19943484 GTATATATTATAAAAATGTATGTAT
1 ATATATATTATAAAAA-GTATGTAT
*
19943509 GTATATATGTATA
1 ATATATAT-TATA
19943522 TAAATTATAA
Statistics
Matches: 60, Mismatches: 1, Indels: 18
0.76 0.01 0.23
Matches are distributed among these distances:
24 6 0.10
25 12 0.20
26 12 0.20
27 2 0.03
28 1 0.02
29 8 0.13
31 10 0.17
32 1 0.02
33 8 0.13
ACGTcount: A:0.44, C:0.02, G:0.13, T:0.41
Consensus pattern (24 bp):
ATATATATTATAAAAAGTATGTAT
Found at i:19943505 original size:33 final size:33
Alignment explanation
Indices: 19943452--19943532 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 33
19943442 AGTATGTATA
*
19943452 TATATAAGTTAT-AAAAGTATGTACGTGCATATG
1 TATATAA-TTATAAAAAGTATGTACGTACATATG
* *
19943485 TATAT-ATTATAAAAATGTATGTATGTATATATG
1 TATATAATTATAAAAA-GTATGTACGTACATATG
19943518 TATATAAATTATAAA
1 TATAT-AATTATAAA
19943533 GTATAACAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 4 0.10
32 5 0.12
33 24 0.59
35 8 0.20
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.41
Consensus pattern (33 bp):
TATATAATTATAAAAAGTATGTACGTACATATG
Found at i:19944290 original size:14 final size:14
Alignment explanation
Indices: 19944273--19944303 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
19944263 TTCCTCTTTT
*
19944273 TATTTTTTTATATA
1 TATTATTTTATATA
19944287 TATTATTTTATATA
1 TATTATTTTATATA
19944301 TAT
1 TAT
19944304 ATATACATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATTTTATATA
Found at i:19945394 original size:183 final size:183
Alignment explanation
Indices: 19945132--19945567 Score: 632
Period size: 183 Copynumber: 2.4 Consensus size: 183
19945122 TGGTTCTAGT
* *
19945132 CTGCTCCACTGCAA-TGTTAGGGAGATAAGAC-TTATTGCCTCAACCTGCTCCACTACGACCTCA
1 CTGCTCCACTGTAACT-TCAGGGAGATAAGACTTTATT-CCTCAACCTGCTCCACTACGACCTCA
* * * * * *
19945195 GGGAGATAATGTTTGATATGATAAGGTTTAATCCGACCCTTTGCAATTTCAAAGGTATAGGATTC
64 GGGAGATAAGGTTTGATACGATAAGATTTAATCCGACCCTCTACAACTTCAAAGGTATAGGATTC
* * *
19945260 ATCGTTTTAATCCGTTCCACTGCAACTTTAGGGAGATAGGATTAGTAGCTTCAGC
129 ATCATTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGAATTAGTAGCTTCAGC
* * *
19945315 CTGCTCCACTGTAACTTCAGGGAGATAAGACTTCTATT-TTCAACCTGCTCTACTGCGACCTCAG
1 CTGCTCCACTGTAACTTCAGGGAGATAAGACTT-TATTCCTCAACCTGCTCCACTACGACCTCAG
19945379 GGAGATAAGGTTTGATACGATAAGATTTAATCCGACCCTCTACAACTTCAAAGGTATAGGATTCA
65 GGAGATAAGGTTTGATACGATAAGATTTAATCCGACCCTCTACAACTTCAAAGGTATAGGATTCA
*
19945444 TCATTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGAATTAGTAGCTTCAGT
130 TCATTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGAATTAGTAGCTTCAGC
* *
19945498 CTGCTCCACTGTAACTTCAAGGAGATAAGACTTGTA-TCCTCAACTTGCTCCACTACTG--CTCA
1 CTGCTCCACTGTAACTTCAGGGAGATAAGACTT-TATTCCTCAACCTGCTCCACTAC-GACCTCA
19945560 GGGAGATA
64 GGGAGATA
19945568 GGACTAGTTT
Statistics
Matches: 227, Mismatches: 21, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
182 13 0.06
183 207 0.91
184 3 0.01
185 4 0.02
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (183 bp):
CTGCTCCACTGTAACTTCAGGGAGATAAGACTTTATTCCTCAACCTGCTCCACTACGACCTCAGG
GAGATAAGGTTTGATACGATAAGATTTAATCCGACCCTCTACAACTTCAAAGGTATAGGATTCAT
CATTTTAATCCGCTCCACTGCAACTTTAGGGAGATAGAATTAGTAGCTTCAGC
Found at i:19945741 original size:41 final size:44
Alignment explanation
Indices: 19945622--19945750 Score: 122
Period size: 41 Copynumber: 3.0 Consensus size: 44
19945612 GCTAGTACAT
* * *
19945622 GAAGACAAGATCTACAATCTTCAACCTACTCCACCGCTGCTCAG
1 GAAGACAAGATCTACAATTTTCGACCTACTCCACTGCTGCTCAG
* * *** * * * *
19945666 GGAGACAAG-GCTAGTGTTTTCGATCTGCTTCACTG-T-C-CTG
1 GAAGACAAGATCTACAATTTTCGACCTACTCCACTGCTGCTCAG
19945706 GAAGACAAGATCTACAATTTTCGACCTACTCCACTGCTGCTCAG
1 GAAGACAAGATCTACAATTTTCGACCTACTCCACTGCTGCTCAG
19945750 G
1 G
19945751 GAGATAAGGC
Statistics
Matches: 60, Mismatches: 21, Indels: 8
0.67 0.24 0.09
Matches are distributed among these distances:
40 10 0.17
41 20 0.33
42 2 0.03
43 17 0.28
44 11 0.18
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (44 bp):
GAAGACAAGATCTACAATTTTCGACCTACTCCACTGCTGCTCAG
Found at i:19945776 original size:84 final size:84
Alignment explanation
Indices: 19945622--19945780 Score: 246
Period size: 84 Copynumber: 1.9 Consensus size: 84
19945612 GCTAGTACAT
** *
19945622 GAAGACAAGATCTACAATCTTCAACCTACTCCACCGCTGCTCAGGGAGACAAGGCTAGTGTTTTC
1 GAAGACAAGATCTACAATCTTCAACCTACTCCACCGCTGCTCAGGGAGACAAGGCTAGTGGCTTA
*
19945687 GATCTGCTTCACTGTCCTG
66 AATCTGCTTCACTGTCCTG
* * * *
19945706 GAAGACAAGATCTACAATTTTCGACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTA
1 GAAGACAAGATCTACAATCTTCAACCTACTCCACCGCTGCTCAGGGAGACAAGGCTAGTGGCTTA
19945771 AATCTGCTTC
66 AATCTGCTTC
19945781 CCTACTACCT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 67 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (84 bp):
GAAGACAAGATCTACAATCTTCAACCTACTCCACCGCTGCTCAGGGAGACAAGGCTAGTGGCTTA
AATCTGCTTCACTGTCCTG
Found at i:19945954 original size:44 final size:43
Alignment explanation
Indices: 19945784--19946283 Score: 255
Period size: 44 Copynumber: 11.5 Consensus size: 43
19945774 CTGCTTCCCT
* *
19945784 ACTAC-CTT-GGGAAGATAAGATTCGCCGTCTTCGATCTGCTCC
1 ACTACTCTTAGGG-AGATAAGATTTGCCGTCTTCAATCTGCTCC
* * * *** * *
19945826 ACTACTTCTTAGGGAGACAGGATCTGCAACCTTCAACCTACTCC
1 ACTAC-TCTTAGGGAGATAAGATTTGCCGTCTTCAATCTGCTCC
* * * * * * * * *
19945870 ACTGCTGCTCAAGGAGATAGGACTTG-TGGCTTAAATCTGCTTCGT
1 ACTACT-CTTAGGGAGATAAGATTTGCCGTCTTCAATCTGC-TC-C
* *
19945915 ACTAC-CTTAGGAAGATAAGATTTGCCGTCTTCGATCTGCTCC
1 ACTACTCTTAGGGAGATAAGATTTGCCGTCTTCAATCTGCTCC
* ** * *
19945957 ACTACTTCTTAGGGAGATAAGATATGCAATCTTCAACCTACTCC
1 ACTAC-TCTTAGGGAGATAAGATTTGCCGTCTTCAATCTGCTCC
* * ** ** * * *
19946001 ACTGCTGCTCAGGGAGATAAG-GCTGGTGGCTTAAATCTGCTTCGT
1 ACTACT-CTTAGGGAGATAAGATTTGCCGTCTTCAATCTGC-TC-C
* *
19946046 ACTAC-CTTAGGAAGATAAGATTTGCCGTCTTCGATCTGCTCC
1 ACTACTCTTAGGGAGATAAGATTTGCCGTCTTCAATCTGCTCC
* ** * *
19946088 ACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCC
1 ACTACT-CTTAGGGAGATAAGATTTGCCGTCTTCAATCTGCTCC
* * * *
19946132 ACTGCTGCTCAGGGAGATAAGGATGGTG--G-CTTAAATCTGCTTCC
1 ACTACT-CTTAGGGAGATAA-GAT-TTGCCGTCTTCAATCTGC-TCC
* ** *
19946176 TACTAC-CTTAGGAAGATAAGATCCGCCGTCTTCGATCTGCTCC
1 -ACTACTCTTAGGGAGATAAGATTTGCCGTCTTCAATCTGCTCC
* * ** * * *
19946219 ACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTTC
1 ACTACT-CTTAGGGAGATAAGATTTGCCGTCTTCAATCTGCTCC
*
19946263 ACTACTGCTCAGGGAGATAAG
1 ACTACT-CTTAGGGAGATAAG
19946284 GCTTGATATG
Statistics
Matches: 339, Mismatches: 95, Indels: 46
0.71 0.20 0.10
Matches are distributed among these distances:
41 1 0.00
42 23 0.07
43 73 0.22
44 222 0.65
45 18 0.05
46 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (43 bp):
ACTACTCTTAGGGAGATAAGATTTGCCGTCTTCAATCTGCTCC
Found at i:19945970 original size:131 final size:131
Alignment explanation
Indices: 19945712--19946286 Score: 927
Period size: 131 Copynumber: 4.4 Consensus size: 131
19945702 CCTGGAAGAC
* * * *
19945712 AAGATCTACAATTTTCGACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTG
1 AAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTG
* *
19945777 CTTCCCTACTACCTTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTTCTTAGGGAG
66 CTT-CCTACTACCTTAGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAG
*
19945842 AC
130 AT
* * * *
19945844 AGGATCTGCAACCTTCAACCTACTCCACTGCTGCTCAAGGAGAT-AGGACTTGTGGCTTAAATCT
1 AAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGG-CTGGTGGCTTAAATCT
* * *
19945908 GCTTCGTACTACCTTAGGAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTTCTTAGGGAG
65 GCTTCCTACTACCTTAGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAG
19945973 AT
130 AT
*
19945975 AAGATATGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTG
1 AAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTG
* *
19946040 CTTCGTACTACCTTAGGAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
66 CTTCCTACTACCTTAGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
19946105 T
131 T
*
19946106 AAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGATGGTGGCTTAAATCTG
1 AAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTG
*
19946171 CTTCCTACTACCTTAGGAAGATAAGATCCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
66 CTTCCTACTACCTTAGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
19946236 T
131 T
* * *
19946237 AAGATCTACAATCTTCAACCTACTTCACTACTGCTCAGGGAGATAAGGCT
1 AAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCT
19946287 TGATATGATG
Statistics
Matches: 415, Mismatches: 26, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
131 355 0.86
132 60 0.14
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (131 bp):
AAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTG
CTTCCTACTACCTTAGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
T
Found at i:19946170 original size:87 final size:86
Alignment explanation
Indices: 19945817--19946239 Score: 259
Period size: 87 Copynumber: 4.8 Consensus size: 86
19945807 GCCGTCTTCG
* * ** * * * * *
19945817 ATCTGCTCCACTACTTCTTAGGGAGACAGGATCTGCAACCTTCAACCTACTCCACTGCTGCTCAA
1 ATCTGCTCCACTAC-TCTTAGGGAGATAAGATCTGCAGTCTTCAATCTGCTCCACTACTGCTTAG
*
19945882 GGAGAT-AGGACTTGTGGCTTAA
65 GGAGATAAGGA-TGGTGGCTTAA
* * * * * *
19945904 ATCTGCTTCGTACTAC-CTTAGGAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTTCTTA
1 ATCTGC-TC-CACTACTCTTAGGGAGATAAGATCTGCAGTCTTCAATCTGCTCCACTACTGCTTA
* **** *
19945968 GGGAGATAAGATATGCAATCTTCA
64 GGGAGATAAG-GATGGTGGCTTAA
* * * * * ** * * *
19945992 ACCTACTCCACTGCTGCTCAGGGAGATAAG-GCTGGTGGCTTAAATCTGCTTCGTACTAC--CTT
1 ATCTGCTCCACTACT-CTTAGGGAGATAAGATCTGCAGTCTTCAATCTGC-TC-CACTACTGCTT
* * **
19946054 AGGAAGATAA-GAT-TTGCCGTCTTCG
63 AGGGAGATAAGGATGGTG--G-CTTAA
* * * * *
19946079 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATCTTCAACCTACTCCACTGCTGCTCAG
1 ATCTGCTCCACTACT-CTTAGGGAGATAAGATCTGCAGTCTTCAATCTGCTCCACTACTGCTTAG
19946144 GGAGATAAGGATGGTGGCTTAA
65 GGAGATAAGGATGGTGGCTTAA
* * * *
19946166 ATCTGCTTCCTACTAC-CTTAGGAAGATAAGATCCGCCGTCTTCGATCTGCTCCACTACTGCTTA
1 ATCTGC-TCC-ACTACTCTTAGGGAGATAAGATCTGCAGTCTTCAATCTGCTCCACTACTGCTTA
19946230 GGGAGATAAG
64 GGGAGATAAG
19946240 ATCTACAATC
Statistics
Matches: 247, Mismatches: 71, Indels: 36
0.70 0.20 0.10
Matches are distributed among these distances:
85 2 0.01
86 8 0.03
87 163 0.66
88 53 0.21
89 19 0.08
90 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (86 bp):
ATCTGCTCCACTACTCTTAGGGAGATAAGATCTGCAGTCTTCAATCTGCTCCACTACTGCTTAGG
GAGATAAGGATGGTGGCTTAA
Found at i:19946649 original size:24 final size:24
Alignment explanation
Indices: 19946614--19946671 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
19946604 CGGATTGCCC
19946614 CCACTGTAATCTTCAAAGTTCAAT
1 CCACTGTAATCTTCAAAGTTCAAT
* * *
19946638 CCGCTGTAATCTTCAAGGTTCAGT
1 CCACTGTAATCTTCAAAGTTCAAT
19946662 CCACTGTAAT
1 CCACTGTAAT
19946672 TTTGGACATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (24 bp):
CCACTGTAATCTTCAAAGTTCAAT
Found at i:19947276 original size:48 final size:47
Alignment explanation
Indices: 19947222--19947373 Score: 123
Period size: 48 Copynumber: 3.1 Consensus size: 47
19947212 TCAAGATAGC
19947222 AAATTTTGCTAGGATAAGATGAAAAAGATTATCACAATGGATAAGATA
1 AAATTTTGCTAGGATAAGATGAAAAAGA-TATCACAATGGATAAGATA
** * * * * **
19947270 AAATTTTATTAAGAGCACAGCTCG-AAATGA-AT-A-AATTAATCAAGATA
1 AAATTTTGCTAGGA-TA-AGAT-GAAAAAGATATCACAATGGAT-AAGATA
*
19947317 GCAAATTTTGCTAGGATAAGATGAAAAAGATCATCACAATGGATAAGATG
1 --AAATTTTGCTAGGATAAGATGAAAAAGAT-ATCACAATGGATAAGATA
19947367 AAATTTT
1 AAATTTT
19947374 ATTGAGAGCA
Statistics
Matches: 76, Mismatches: 17, Indels: 22
0.66 0.15 0.19
Matches are distributed among these distances:
46 6 0.08
47 15 0.20
48 21 0.28
49 14 0.18
50 14 0.18
51 6 0.08
ACGTcount: A:0.47, C:0.09, G:0.17, T:0.28
Consensus pattern (47 bp):
AAATTTTGCTAGGATAAGATGAAAAAGATATCACAATGGATAAGATA
Found at i:19947310 original size:97 final size:97
Alignment explanation
Indices: 19947144--19947431 Score: 495
Period size: 97 Copynumber: 3.0 Consensus size: 97
19947134 GAAAAATGCT
* * *
19947144 TGAAAAAGATTATCACAATGGACAAGATGAAATTTTATTGAGAACAAAGCTCGAAATGAATAAAT
1 TGAAAAAGATTATCACAATGGATAAGATGAAATTTTATTGAGAGCACAGCTCGAAATGAATAAAT
19947209 TAATCAAGATAGCAAATTTTGCTAGGATAAGA
66 TAATCAAGATAGCAAATTTTGCTAGGATAAGA
* *
19947241 TGAAAAAGATTATCACAATGGATAAGATAAAATTTTATTAAGAGCACAGCTCGAAATGAATAAAT
1 TGAAAAAGATTATCACAATGGATAAGATGAAATTTTATTGAGAGCACAGCTCGAAATGAATAAAT
19947306 TAATCAAGATAGCAAATTTTGCTAGGATAAGA
66 TAATCAAGATAGCAAATTTTGCTAGGATAAGA
* *
19947338 TGAAAAAGATCATCACAATGGATAAGATGAAATTTTATTGAGAGCACAGCTCAAAATGAATAAAT
1 TGAAAAAGATTATCACAATGGATAAGATGAAATTTTATTGAGAGCACAGCTCGAAATGAATAAAT
* *
19947403 TAATCAAGATAGCAAATTCTGCTAAGATA
66 TAATCAAGATAGCAAATTTTGCTAGGATA
19947432 CGAAATGAAT
Statistics
Matches: 180, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 180 1.00
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.26
Consensus pattern (97 bp):
TGAAAAAGATTATCACAATGGATAAGATGAAATTTTATTGAGAGCACAGCTCGAAATGAATAAAT
TAATCAAGATAGCAAATTTTGCTAGGATAAGA
Found at i:19947491 original size:14 final size:14
Alignment explanation
Indices: 19947472--19947498 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19947462 AGATATCGTA
19947472 GCATGAGCTTCTTT
1 GCATGAGCTTCTTT
19947486 GCATGAGCTTCTT
1 GCATGAGCTTCTT
19947499 GAAGACCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (14 bp):
GCATGAGCTTCTTT
Found at i:19947779 original size:10 final size:10
Alignment explanation
Indices: 19947760--19947812 Score: 67
Period size: 10 Copynumber: 5.6 Consensus size: 10
19947750 CTCCTTTTTC
19947760 TTTT-CTTCT
1 TTTTCCTTCT
*
19947769 TCTTCCTTCT
1 TTTTCCTTCT
*
19947779 TTTTTCTTCT
1 TTTTCCTTCT
19947789 TTTTCCTTCT
1 TTTTCCTTCT
19947799 TTTT-CTT-T
1 TTTTCCTTCT
19947807 TTTTCC
1 TTTTCC
19947813 CTTTTTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
8 5 0.13
9 7 0.18
10 26 0.68
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTCCTTCT
Found at i:19947785 original size:20 final size:20
Alignment explanation
Indices: 19947760--19947802 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
19947750 CTCCTTTTTC
19947760 TTTTCTTCTTCTTCCTTCTT
1 TTTTCTTCTTCTTCCTTCTT
*
19947780 TTTTCTTCTTTTTCCTTCTT
1 TTTTCTTCTTCTTCCTTCTT
19947800 TTT
1 TTT
19947803 CTTTTTTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTCTTCTTCTTCCTTCTT
Found at i:19947921 original size:14 final size:15
Alignment explanation
Indices: 19947898--19947930 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
19947888 ATCAACGCTT
19947898 TTCCAAATAAGG-CC
1 TTCCAAATAAGGTCC
*
19947912 TTCCACATAAGGTCC
1 TTCCAAATAAGGTCC
19947927 TTCC
1 TTCC
19947931 CAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:19952876 original size:24 final size:26
Alignment explanation
Indices: 19952849--19952897 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
19952839 ATAGGTGTGT
19952849 GTATATACATATAT-A-TTATAAAAA
1 GTATATACATATATAAGTTATAAAAA
* *
19952873 GTATGTATATATATAAGTTATAAAA
1 GTATATACATATATAAGTTATAAAA
19952898 GTACGTACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 12 0.57
25 1 0.05
26 8 0.38
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (26 bp):
GTATATACATATATAAGTTATAAAAA
Found at i:19954150 original size:19 final size:20
Alignment explanation
Indices: 19954117--19954156 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
19954107 AAGTAAAAAG
*
19954117 AATTTAAAATAATGTTGATA
1 AATTTAAAATAATGTGGATA
*
19954137 AATTT-AAATCATGTGGATA
1 AATTTAAAATAATGTGGATA
19954156 A
1 A
19954157 TAATTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (20 bp):
AATTTAAAATAATGTGGATA
Found at i:19954558 original size:25 final size:25
Alignment explanation
Indices: 19954530--19954577 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
19954520 TATTAAATAC
*
19954530 TATAATATATAAAA-ATAGAATTTGT
1 TATAAT-TAAAAAACATAGAATTTGT
*
19954555 TATAATTAAAAAACATTGAATTT
1 TATAATTAAAAAACATAGAATTT
19954578 TAAGAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (25 bp):
TATAATTAAAAAACATAGAATTTGT
Found at i:19956171 original size:50 final size:50
Alignment explanation
Indices: 19956029--19956252 Score: 159
Period size: 50 Copynumber: 4.4 Consensus size: 50
19956019 CGCCATTGTA
* * * ** * *
19956029 GCTTCAATCTTTTTAACTGCACCGCCAGGGAAGTAAGATTCACCGTTATG-G
1 GCTTTAATCTGTTTCACTGCAATGCCGGGGAAGCAAGATTCACCG--ATGTG
* *
19956080 CAGCTTTAATCCT-TTT-AGCTGCAATGTCGGGGAAGCGAGATTCACCGATGTG
1 --GCTTTAAT-CTGTTTCA-CTGCAATGCCGGGGAAGCAAGATTCACCGATGTG
* * ** * * *
19956132 GCTTTAATCTGTTTCACTGCATTGCCTGGGG-AGTAAGATTTGCTGTTGTA
1 GCTTTAATCTGTTTCACTGCAATGCC-GGGGAAGCAAGATTCACCGATGTG
* * * *
19956182 GCTTTAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCACCGATGTG
1 GCTTTAATCTGTTTCACTGCAATGCCGGGGAAGCAAGATTCACCGATGTG
* *
19956232 GCTTTAATCTGCTCCACTGCA
1 GCTTTAATCTGTTTCACTGCA
19956253 CCATTTGGGA
Statistics
Matches: 132, Mismatches: 32, Indels: 17
0.73 0.18 0.09
Matches are distributed among these distances:
49 6 0.05
50 81 0.61
51 8 0.06
52 2 0.02
53 33 0.25
54 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (50 bp):
GCTTTAATCTGTTTCACTGCAATGCCGGGGAAGCAAGATTCACCGATGTG
Found at i:19956313 original size:46 final size:46
Alignment explanation
Indices: 19956262--19956361 Score: 182
Period size: 46 Copynumber: 2.2 Consensus size: 46
19956252 ACCATTTGGG
*
19956262 AGATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGG
1 AGATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGC
*
19956308 GGATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGC
1 AGATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGC
19956354 AGATAAGA
1 AGATAAGA
19956362 CCTGATGCGA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (46 bp):
AGATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGC
Found at i:19956343 original size:23 final size:23
Alignment explanation
Indices: 19956271--19956346 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
19956261 GAGATAAGAT
19956271 CTGTAATTCTTCGGTCTATTCCA
1 CTGTAATTCTTCGGTCTATTCCA
*** ***
19956294 CTGTAA-TC-TCAGGGGGATAAGA
1 CTGTAATTCTTC-GGTCTATTCCA
19956316 TCTGTAATTCTTCGGTCTATTCCA
1 -CTGTAATTCTTCGGTCTATTCCA
19956340 CTGTAAT
1 CTGTAAT
19956347 CTCAGGCAGA
Statistics
Matches: 37, Mismatches: 12, Indels: 8
0.65 0.21 0.14
Matches are distributed among these distances:
21 2 0.05
22 7 0.19
23 19 0.51
24 7 0.19
25 2 0.05
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.38
Consensus pattern (23 bp):
CTGTAATTCTTCGGTCTATTCCA
Found at i:19956443 original size:44 final size:43
Alignment explanation
Indices: 19956395--19956775 Score: 128
Period size: 44 Copynumber: 8.2 Consensus size: 43
19956385 AACTTCAGAA
*
19956395 AGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGG
1 AGATAAGAT-CTTTACTTTAATCCGCTCCACTGTAATCTCAGGG
* * * * *
19956439 AGATAGGAT-TACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGG
1 AGATAAGATCT-TTA-CTTTAATCCGCTCCACTGTAATCTCAGGG
* * *
19956483 AGATAAGAT-TTCTGGCTTCAATCTGATGCGATCTACTCTACTGTAA-CTTCAGAG
1 AGATAAGATCTT-T-ACTTTAATC-----CG--CT-C-C-ACTGTAATC-TCAGGG
*
19956537 AGATAAGATCATTTA-TCTTAATCCGCTCCACTGTAATCTAAGGG
1 AGATAAGATC-TTTACT-TTAATCCGCTCCACTGTAATCTCAGGG
* * ** *
19956581 AGATAGGAT-TACTAGCTTTAATCTACTCCGCTGTAATCTCAGGG
1 AGATAAGATCT-TTA-CTTTAATCCGCTCCACTGTAATCTCAGGG
* * * * *
19956625 AGATAAGATTTTTGGCTTCAATCTGATGTGATCTACTCTACTGTAA-CTTCAGAG
1 AGATAAGATCTTT-ACTTTAATC-----CG--CT-C-C-ACTGTAATC-TCAGGG
* * * *
19956679 AGATAATATCCTTTATTTTAATCCACTCCACTATAATCTCAGGG
1 AGATAAGAT-CTTTACTTTAATCCGCTCCACTGTAATCTCAGGG
* * * ** *
19956723 AGATAGGAT-TACTAGCTTCAATATGCTCCGCTGTAATCTCAGGG
1 AGATAAGATCT-TTA-CTTTAATCCGCTCCACTGTAATCTCAGGG
19956767 AGATAAGAT
1 AGATAAGAT
19956776 TTCTAGCTTC
Statistics
Matches: 249, Mismatches: 49, Indels: 78
0.66 0.13 0.21
Matches are distributed among these distances:
42 3 0.01
43 6 0.02
44 157 0.63
45 6 0.02
46 2 0.01
47 4 0.02
49 4 0.02
51 4 0.02
52 2 0.01
53 5 0.02
54 50 0.20
55 4 0.02
56 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (43 bp):
AGATAAGATCTTTACTTTAATCCGCTCCACTGTAATCTCAGGG
Found at i:19956838 original size:142 final size:142
Alignment explanation
Indices: 19956363--19956829 Score: 817
Period size: 142 Copynumber: 3.3 Consensus size: 142
19956353 CAGATAAGAC
*
19956363 CTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
19956428 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
19956493 TCTGGCTTCAAT
131 TCTGGCTTCAAT
* *
19956505 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATCTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * *
19956570 TAATCTAAGGGAGATAGGATTACTAGCTTTAATCTACTCCGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
*
19956635 TTTGGCTTCAAT
131 TCTGGCTTCAAT
* * * *
19956647 CTGATGTGATCTACTCTACTGTAACTTCAGAGAGATAATATCCTTTATTTTAATCCACTCCACTA
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
*
19956712 TAATCTCAGGGAGATAGGATTACTAGCTTCAATATGCTCCGCTGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
*
19956777 TCTAGCTTCAAT
131 TCTGGCTTCAAT
19956789 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGAT
1 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGAT
19956830 TCGCTATTTC
Statistics
Matches: 304, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 304 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (142 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATT
TCTGGCTTCAAT
Found at i:19966014 original size:15 final size:16
Alignment explanation
Indices: 19965976--19966016 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
19965966 ATCCAGATCC
*
19965976 TCCTCTACTTTATTCT
1 TCCTCTTCTTTATTCT
19965992 TCCTCTTCTTTATTCT
1 TCCTCTTCTTTATTCT
19966008 T-CTCTTCTT
1 TCCTCTTCTT
19966017 CCAACCACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.07, C:0.32, G:0.00, T:0.61
Consensus pattern (16 bp):
TCCTCTTCTTTATTCT
Found at i:19985468 original size:26 final size:26
Alignment explanation
Indices: 19985439--19985493 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
19985429 TCAACTTCTC
19985439 TTTTAAGTT-AATAAATTCTCATTGAG
1 TTTTAAGTTCAATAAATTCTC-TTGAG
* * *
19985465 TTTTCATTTCAATAATTTCTCTTGAG
1 TTTTAAGTTCAATAAATTCTCTTGAG
19985491 TTT
1 TTT
19985494 ATTTTAGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (26 bp):
TTTTAAGTTCAATAAATTCTCTTGAG
Found at i:19987062 original size:96 final size:96
Alignment explanation
Indices: 19986944--19987132 Score: 263
Period size: 96 Copynumber: 2.0 Consensus size: 96
19986934 AAAGGAGGAA
* * * * *
19986944 TACGATTGAGGTATCATCTTTTGTGCGATGTTATTGGTATAGTTCAAAAGATCATAAGGGTTTCC
1 TACGATTGAGATATCATCTTTTGTGCAATGTTATTGGTATAATTCAAAAGATCACAAGAGTTTCC
19987009 AATGTCCAATTAAATATCCAAATAGAGAGAC
66 AATGTCCAATTAAATATCCAAATAGAGAGAC
* * * *
19987040 TACGATTGAGATATCA-CATTTTGTGTAATGTTATTGGTGTAATTCAAAAGATTACAAGAGTTTT
1 TACGATTGAGATATCATC-TTTTGTGCAATGTTATTGGTATAATTCAAAAGATCACAAGAGTTTC
* *
19987104 CAATGTCCAGTTAAATATCCAACTAGAGA
65 CAATGTCCAATTAAATATCCAAATAGAGA
19987133 ATAAAGTAAG
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 1 0.01
96 80 0.99
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (96 bp):
TACGATTGAGATATCATCTTTTGTGCAATGTTATTGGTATAATTCAAAAGATCACAAGAGTTTCC
AATGTCCAATTAAATATCCAAATAGAGAGAC
Done.