Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 159 of 226
Found at i:51243177 original size:50 final size:50
Alignment explanation
Indices: 51243102--51243243 Score: 221
Period size: 50 Copynumber: 2.8 Consensus size: 50
51243092 ATTTGGGTAA
*
51243102 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* *
51243152 AGAGGTCCCATGTAAGACCATGTCTGGAACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* * * *
51243202 AGATGTCCCCTGTAAGACCATGTCTGGGATATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
51243244 TGTTATTATT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 84 1.00
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
Found at i:51245190 original size:15 final size:15
Alignment explanation
Indices: 51245170--51245199 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
51245160 ACAAATGCAG
51245170 AAAAGAAATAACAGA
1 AAAAGAAATAACAGA
51245185 AAAAGAAATAACAGA
1 AAAAGAAATAACAGA
51245200 TCGATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.07, G:0.13, T:0.07
Consensus pattern (15 bp):
AAAAGAAATAACAGA
Found at i:51246202 original size:24 final size:24
Alignment explanation
Indices: 51246170--51246233 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
51246160 ATTACTTTTT
* * *
51246170 TAAAATTATAATGTATTTTTATTA
1 TAAATTTATTATGTATTATTATTA
* * *
51246194 TAAGTTTATTACGTATTATTATTT
1 TAAATTTATTATGTATTATTATTA
51246218 TAAATTTATTATGTAT
1 TAAATTTATTATGTAT
51246234 CACTACTTAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (24 bp):
TAAATTTATTATGTATTATTATTA
Found at i:51254537 original size:17 final size:18
Alignment explanation
Indices: 51254515--51254556 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
51254505 TGAATTGGGC
51254515 CATGTGGGC-CACACAGG
1 CATGTGGGCACACACAGG
*
51254532 CATGTGGGCTACACACGGG
1 CATGTGGGC-ACACACAGG
51254551 CATGTG
1 CATGTG
51254557 AAAATATTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
19 13 0.59
ACGTcount: A:0.21, C:0.26, G:0.36, T:0.17
Consensus pattern (18 bp):
CATGTGGGCACACACAGG
Found at i:51255467 original size:19 final size:20
Alignment explanation
Indices: 51255431--51255472 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
51255421 ACATGACCTC
51255431 TTTGGATTTATATTTTTT-A
1 TTTGGATTTATATTTTTTGA
*
51255450 TTTGGGTTT-TATTGTTTTGA
1 TTTGGATTTATATT-TTTTGA
51255470 TTT
1 TTT
51255473 ATAACTGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 4 0.20
19 12 0.60
20 4 0.20
ACGTcount: A:0.14, C:0.00, G:0.17, T:0.69
Consensus pattern (20 bp):
TTTGGATTTATATTTTTTGA
Found at i:51259620 original size:13 final size:13
Alignment explanation
Indices: 51259588--51259621 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
51259578 ATCTTTGTCC
51259588 CTTTTTTTCTTCT
1 CTTTTTTTCTTCT
* *
51259601 CTCTTTTTCTTTT
1 CTTTTTTTCTTCT
51259614 CTTTTTTT
1 CTTTTTTT
51259622 TAACTCTAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
CTTTTTTTCTTCT
Found at i:51264464 original size:18 final size:18
Alignment explanation
Indices: 51264423--51264465 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
51264413 ATGAACACAT
51264423 AAATAAATATCAAATAAGA
1 AAAT-AATATCAAATAAGA
*
51264442 CAATAATATC-AATAATGA
1 AAATAATATCAAATAA-GA
51264460 AAATAA
1 AAATAA
51264466 ATTATAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 13 0.62
19 3 0.14
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAATATCAAATAAGA
Found at i:51264485 original size:6 final size:6
Alignment explanation
Indices: 51264459--51264497 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
51264449 ATCAATAATG
* *
51264459 AAAATA AATTATA AAACTA AAAATA AAAATA AAAATA AA
1 AAAATA AA-AATA AAAATA AAAATA AAAATA AAAATA AA
51264498 GATCTATGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:51264582 original size:28 final size:28
Alignment explanation
Indices: 51264551--51264611 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
51264541 AATAATATCA
* *
51264551 ATATATA-ACAAGACAAGTATGTATATAT
1 ATATATATACAA-ACAAGCATGCATATAT
* *
51264579 ATATATATATAAACATGCATGCATATAT
1 ATATATATACAAACAAGCATGCATATAT
51264607 ATATA
1 ATATA
51264612 AATTATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.34
Consensus pattern (28 bp):
ATATATATACAAACAAGCATGCATATAT
Found at i:51264973 original size:2 final size:2
Alignment explanation
Indices: 51264968--51265006 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
51264958 TATATAGAAG
51264968 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51265007 GTATGTAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51266314 original size:22 final size:22
Alignment explanation
Indices: 51266289--51266332 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
51266279 TGCGGGCTCG
*
51266289 GGCAAATTTGGGCTTCTACAAT
1 GGCAAATATGGGCTTCTACAAT
51266311 GGCAAATATGGGCTTCTACAAT
1 GGCAAATATGGGCTTCTACAAT
51266333 CGTTATAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (22 bp):
GGCAAATATGGGCTTCTACAAT
Found at i:51274094 original size:105 final size:105
Alignment explanation
Indices: 51273829--51274085 Score: 361
Period size: 105 Copynumber: 2.4 Consensus size: 105
51273819 GCCGTTGATT
* * ***
51273829 AATGCACTATAGGTAACAACATTAGGCTCAATGCCTCGCTTTATCATTGCGTCAGTGATATCCTC
1 AATGCACTATACGTGACAACATTAGGCTCAATGCCTCGCTTTATCATTGCGTCAACAATATCCTC
*
51273894 AGCTTCAAAAACCATCCCTTCCTTACAATGTGCATCAACC
66 AGCTTCAAAAACCATCCCTTCCTTACAATGCGCATCAACC
* * * *
51273934 AATGTATTATACGAGACAACATCAGGCTCAATGCCTCGCTTTATCATTGCGTCAACAATATCCTC
1 AATGCACTATACGTGACAACATTAGGCTCAATGCCTCGCTTTATCATTGCGTCAACAATATCCTC
** * *
51273999 AGCTTCTGAGACCATCCCTTCCTTGCAATGCGCATCAACC
66 AGCTTCAAAAACCATCCCTTCCTTACAATGCGCATCAACC
* * *
51274039 AATGCAGTATACGTGACAACATTAGGCTCAATGCCTTGCTTTCTCAT
1 AATGCACTATACGTGACAACATTAGGCTCAATGCCTCGCTTTATCAT
51274086 CATGTCAACG
Statistics
Matches: 132, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
105 132 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.29
Consensus pattern (105 bp):
AATGCACTATACGTGACAACATTAGGCTCAATGCCTCGCTTTATCATTGCGTCAACAATATCCTC
AGCTTCAAAAACCATCCCTTCCTTACAATGCGCATCAACC
Found at i:51276905 original size:13 final size:15
Alignment explanation
Indices: 51276886--51276918 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
51276876 CACATTTGAT
*
51276886 TTTTTTTTAAA-ATA
1 TTTTTTATAAATATA
51276900 TTTTTTATAAATATA
1 TTTTTTATAAATATA
51276915 TTTT
1 TTTT
51276919 CTACAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTTATAAATATA
Found at i:51276982 original size:16 final size:17
Alignment explanation
Indices: 51276953--51276990 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
51276943 GTGTGTAATA
51276953 ATTTA-GTATAATATAT
1 ATTTATGTATAATATAT
51276969 ATTTATGTAT-ATATAT
1 ATTTATGTATAATATAT
51276985 ATTTAT
1 ATTTAT
51276991 ATCTTTAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
ATTTATGTATAATATAT
Found at i:51278993 original size:105 final size:105
Alignment explanation
Indices: 51278900--51279151 Score: 414
Period size: 105 Copynumber: 2.4 Consensus size: 105
51278890 ACCATTAACT
* * *
51278900 AATGCACTATAGGTAACAACATTAGGCTCAATGCCTCTCTTTATCATTGCATCAACAATATCCTC
1 AATGCACTATAGGTAACAACATCAGGCTCAATGCCTCGCTTTATCATTACATCAACAATATCCTC
*
51278965 AGCTTCAGAGACCATTCCTTCCTTGCAATGCGCATCAACC
66 AGCTTCAGAGACCATCCCTTCCTTGCAATGCGCATCAACC
*
51279005 AATGCACTATAGGTAACAACATCAGGCTCAATGCCTCGCTTTATCATTACGTCAACAATATCCTC
1 AATGCACTATAGGTAACAACATCAGGCTCAATGCCTCGCTTTATCATTACATCAACAATATCCTC
51279070 AGCTTCAGAGACCATCCCTTCCTTGCAATGCGCATCAACC
66 AGCTTCAGAGACCATCCCTTCCTTGCAATGCGCATCAACC
* * * * *
51279110 AATGTACTATACGTGACAAAATCAGGCTCAATGCCTTGCTTT
1 AATGCACTATAGGTAACAACATCAGGCTCAATGCCTCGCTTT
51279152 CTCAACATGT
Statistics
Matches: 137, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
105 137 1.00
ACGTcount: A:0.30, C:0.29, G:0.13, T:0.28
Consensus pattern (105 bp):
AATGCACTATAGGTAACAACATCAGGCTCAATGCCTCGCTTTATCATTACATCAACAATATCCTC
AGCTTCAGAGACCATCCCTTCCTTGCAATGCGCATCAACC
Found at i:51279164 original size:105 final size:105
Alignment explanation
Indices: 51278900--51279233 Score: 373
Period size: 105 Copynumber: 3.2 Consensus size: 105
51278890 ACCATTAACT
* * * * * * *** *
51278900 AATGCACTATAGGTAACAACATTAGGCTCAATGCCTCTCTTTATCATTGCATCAACAATATCCTC
1 AATGTACTATACGTGACAAAATCAGGCTCAATGCCTCGCTTTATCAACACGTCAACAATATCCTC
51278965 AGCTTCAGAGACCATTCCTTCCTTGCAATGCGCATCAACC
66 AGCTTCAGAGACCATTCCTTCCTTGCAATGCGCATCAACC
* * * * **
51279005 AATGCACTATAGGTAACAACATCAGGCTCAATGCCTCGCTTTATCATTACGTCAACAATATCCTC
1 AATGTACTATACGTGACAAAATCAGGCTCAATGCCTCGCTTTATCAACACGTCAACAATATCCTC
*
51279070 AGCTTCAGAGACCATCCCTTCCTTGCAATGCGCATCAACC
66 AGCTTCAGAGACCATTCCTTCCTTGCAATGCGCATCAACC
* * * ** *
51279110 AATGTACTATACGTGACAAAATCAGGCTCAATGCCTTGCTTTCTCAACATGTCAACGGTCT-CTA
1 AATGTACTATACGTGACAAAATCAGGCTCAATGCCTCGCTTTATCAACACGTCAACAATATCCT-
* * * * * *
51279174 CAGCTTTAGAAATCGTTCCTTCCTTGCAAAGAGCATCAACC
65 CAGCTTCAGAGACCATTCCTTCCTTGCAATGCGCATCAACC
* *
51279215 AATGTATTATATGTGACAA
1 AATGTACTATACGTGACAA
51279234 TATTAAGTGA
Statistics
Matches: 202, Mismatches: 26, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
104 2 0.01
105 200 0.99
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (105 bp):
AATGTACTATACGTGACAAAATCAGGCTCAATGCCTCGCTTTATCAACACGTCAACAATATCCTC
AGCTTCAGAGACCATTCCTTCCTTGCAATGCGCATCAACC
Found at i:51280199 original size:22 final size:22
Alignment explanation
Indices: 51280156--51280230 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 22
51280146 GTTATTAATA
*
51280156 AAATTT-ATAAATCTTCCT-TTT
1 AAATTTAATAAAT-TTACTATTT
51280177 AAATTTAATAAATTTACTATTT
1 AAATTTAATAAATTTACTATTT
* *
51280199 -ATTTTAATAAAATTTATTAAATTT
1 AAATTTAAT-AAATTTACT--ATTT
51280223 AAATTTAA
1 AAATTTAA
51280231 ATTTTTAGAC
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
21 17 0.39
22 17 0.39
24 4 0.09
25 6 0.14
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATTTAATAAATTTACTATTT
Found at i:51283727 original size:18 final size:18
Alignment explanation
Indices: 51283704--51283739 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
51283694 ACTTATTTTT
51283704 ATAATTAAGTTTTAAATA
1 ATAATTAAGTTTTAAATA
51283722 ATAATTAAGTTTTAAATA
1 ATAATTAAGTTTTAAATA
51283740 TGATTAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
ATAATTAAGTTTTAAATA
Found at i:51286457 original size:13 final size:15
Alignment explanation
Indices: 51286421--51286454 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
51286411 ATCACATTTG
*
51286421 ATTTTTTTAAATATT
1 ATTTTTATAAATATT
51286436 ATTTTTATAAATA-T
1 ATTTTTATAAATATT
51286450 ATTTT
1 ATTTT
51286455 ATACATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTTTATAAATATT
Found at i:51286805 original size:10 final size:10
Alignment explanation
Indices: 51286790--51286836 Score: 67
Period size: 10 Copynumber: 4.4 Consensus size: 10
51286780 TTCATTATTG
51286790 TTTTAATATA
1 TTTTAATATA
51286800 TTTTAATATGTTA
1 TTTTAATA---TA
51286813 TTTTAATATA
1 TTTTAATATA
51286823 TTTTAATATA
1 TTTTAATATA
51286833 TTTT
1 TTTT
51286837 GTACATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 24 0.71
13 10 0.29
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTTAATATA
Found at i:51289200 original size:18 final size:18
Alignment explanation
Indices: 51289173--51289516 Score: 182
Period size: 17 Copynumber: 19.5 Consensus size: 18
51289163 CGAAAGTTTT
51289173 TTTTTG-AAACACGAGAA
1 TTTTTGAAAACACGAGAA
* *
51289190 TTTTTAAAAACACGAAAA
1 TTTTTGAAAACACGAGAA
*
51289208 TTTTTTG-AAACATGA-AA
1 -TTTTTGAAAACACGAGAA
* * *
51289225 -ATTTAAAAACACGAAAA
1 TTTTTGAAAACACGAGAA
* *
51289242 TTTTTAAAAAAACACGACAA
1 TTTTT--GAAAACACGAGAA
* ** *
51289262 TTTTTTTTAAAACATAAAAA
1 --TTTTTGAAAACACGAGAA
*
51289282 ATTTTG-AAACACG-GAAA
1 TTTTTGAAAACACGAG-AA
*
51289299 TTTGTG-AAACACGAGAA
1 TTTTTGAAAACACGAGAA
*
51289316 TTGTTGAAAACACGA-AA
1 TTTTTGAAAACACGAGAA
* *
51289333 ATTTTGAAAACACGAAAAA
1 TTTTTGAAAACACG-AGAA
*
51289352 TTTTTTGAAAACCCGA-AA
1 -TTTTTGAAAACACGAGAA
* **
51289370 TTTTGGATCAC-CG-GAA
1 TTTTTGAAAACACGAGAA
* ** *
51289386 TCTTTGAAAACATAAAAA
1 TTTTTGAAAACACGAGAA
*
51289404 TTTTTGAAATAC-TG-GAA
1 TTTTTGAAA-ACACGAGAA
*
51289421 TTTTTGAAAACACGAGGA
1 TTTTTGAAAACACGAGAA
* *
51289439 TTTTTG-AAACGCGA-AT
1 TTTTTGAAAACACGAGAA
* * *
51289455 TTTTTAAAAATACGAAAA
1 TTTTTGAAAACACGAGAA
51289473 TTTTTGAAAACAC-AGAAA
1 TTTTTGAAAACACGAG-AA
*
51289491 TTTTT-AAAACACGGGAA
1 TTTTTGAAAACACGAGAA
51289508 TTTTTGAAA
1 TTTTTGAAA
51289517 TACGAATTTT
Statistics
Matches: 249, Mismatches: 52, Indels: 51
0.71 0.15 0.14
Matches are distributed among these distances:
15 3 0.01
16 25 0.10
17 95 0.38
18 78 0.31
19 10 0.04
20 33 0.13
22 5 0.02
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.31
Consensus pattern (18 bp):
TTTTTGAAAACACGAGAA
Found at i:51289211 original size:17 final size:17
Alignment explanation
Indices: 51289179--51289355 Score: 99
Period size: 18 Copynumber: 9.9 Consensus size: 17
51289169 TTTTTTTTTG
*
51289179 AAACACGAGAATTTTTAA
1 AAACACGA-AAATTTTAA
**
51289197 AAACACGAAAATTTTTTG
1 AAACACGAAAA-TTTTAA
*
51289215 AAACATGAAAA-TTTAA
1 AAACACGAAAATTTTAA
51289231 AAACACGAAAATTTTTAAAA
1 AAACACGAAAA-TTTT--AA
* *
51289251 AAACACGACAATTTTTTTTA
1 AAACACGA-AA--ATTTTAA
** *
51289271 AAACATAAAAAATTTT-G
1 AAACA-CGAAAATTTTAA
* *
51289288 AAACACGGAAATTTGT-G
1 AAACACGAAAATTT-TAA
* *
51289305 AAACACGAGAATTGTTGA
1 AAACACGAAAATT-TTAA
*
51289323 AAACACGAAAATTTTGA
1 AAACACGAAAATTTTAA
51289340 AAACACGAAAAATTTT
1 AAACACG-AAAATTTT
51289356 TTGAAAACCC
Statistics
Matches: 126, Mismatches: 20, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
16 19 0.15
17 32 0.25
18 50 0.40
20 18 0.14
21 3 0.02
22 4 0.03
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.28
Consensus pattern (17 bp):
AAACACGAAAATTTTAA
Found at i:51289235 original size:34 final size:36
Alignment explanation
Indices: 51289172--51289361 Score: 124
Period size: 36 Copynumber: 5.3 Consensus size: 36
51289162 ACGAAAGTTT
*
51289172 TTTTTTGAAACACGAGAATTTTTAAAAACACGAAAA
1 TTTTTTGAAACACGAGAATATTTAAAAACACGAAAA
*
51289208 TTTTTTGAAACATGA-AA-ATTTAAAAACACGAAAA
1 TTTTTTGAAACACGAGAATATTTAAAAACACGAAAA
** * * * *
51289242 TTTTTAAAAAAACACGACAATTTTTTTTAAAACA-TAAAA
1 TTTTT--TGAAACACGAGAA--TATTTAAAAACACGAAAA
** ** *
51289281 AATTTTGAAACACG-GAA-ATTTGTGAAACACGAGAA
1 TTTTTTGAAACACGAGAATATTT-AAAAACACGAAAA
* * *
51289316 -TTGTTGAAAACACGAAAAT-TTTGAAAACACGAAAAA
1 TTTTTTG-AAACACGAGAATATTTAAAAACACG-AAAA
51289352 TTTTTTGAAA
1 TTTTTTGAAA
51289362 ACCCGAAATT
Statistics
Matches: 117, Mismatches: 24, Indels: 26
0.70 0.14 0.16
Matches are distributed among these distances:
33 3 0.03
34 31 0.26
35 19 0.16
36 34 0.29
37 14 0.12
39 7 0.06
40 9 0.08
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (36 bp):
TTTTTTGAAACACGAGAATATTTAAAAACACGAAAA
Found at i:51289240 original size:16 final size:16
Alignment explanation
Indices: 51289192--51289244 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
51289182 CACGAGAATT
51289192 TTTAAAAACACGAAAA
1 TTTAAAAACACGAAAA
** *
51289208 TTTTTTGAAACATGAAAA
1 --TTTAAAAACACGAAAA
51289226 TTTAAAAACACGAAAA
1 TTTAAAAACACGAAAA
51289242 TTT
1 TTT
51289245 TTAAAAAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 16 0.55
18 13 0.45
ACGTcount: A:0.53, C:0.09, G:0.08, T:0.30
Consensus pattern (16 bp):
TTTAAAAACACGAAAA
Found at i:51289275 original size:92 final size:91
Alignment explanation
Indices: 51289150--51289342 Score: 212
Period size: 92 Copynumber: 2.1 Consensus size: 91
51289140 AAGCATGAAT
* * * * *
51289150 TTTTTAAAAAAAACGAAAGTTTTTTTTTGAAACACGAGAATTTTTAAAAACACGAAAATTTTTTG
1 TTTTTAAAAAAAACGAAAG-TTTTTTTTAAAACACAAAAAATTTT-AAAACACGAAAA-TTTGTG
*
51289215 AAACATGA-AAAT-TTAAAAACACGAAAA
63 AAACACGAGAAATGTTAAAAACACGAAAA
* * *
51289242 TTTTTAAAAAAACACGACAA-TTTTTTTTAAAACATAAAAAATTTTGAAACACGGAAATTTGTGA
1 TTTTTAAAAAAA-ACGA-AAGTTTTTTTTAAAACACAAAAAATTTTAAAACACGAAAATTTGTGA
* *
51289306 AACACGAGAATTGTTGAAAACACGAAAA
64 AACACGAGAAATGTTAAAAACACGAAAA
*
51289334 TTTTGAAAA
1 TTTTTAAAA
51289343 CACGAAAAAT
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
90 12 0.14
91 13 0.15
92 54 0.64
93 4 0.05
94 2 0.02
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (91 bp):
TTTTTAAAAAAAACGAAAGTTTTTTTTAAAACACAAAAAATTTTAAAACACGAAAATTTGTGAAA
CACGAGAAATGTTAAAAACACGAAAA
Found at i:51289301 original size:16 final size:17
Alignment explanation
Indices: 51289280--51289516 Score: 105
Period size: 18 Copynumber: 13.6 Consensus size: 17
51289270 AAAACATAAA
51289280 AAATTTTG-AAACACGG
1 AAATTTTGAAAACACGG
51289296 AAATTTGTG-AAACAC-G
1 AAATTT-TGAAAACACGG
*
51289312 AGAATTGTTGAAAACACGA
1 A-AATT-TTGAAAACACGG
*
51289331 AAATTTTGAAAACACGAA
1 AAATTTTGAAAACACG-G
*
51289349 AAATTTTTTGAAAAC-CCG
1 AAA--TTTTGAAAACACGG
* *
51289367 AAATTTTG-GATCACCGG
1 AAATTTTGAAAACA-CGG
***
51289384 -AATCTTTGAAAACATAA
1 AAAT-TTTGAAAACACGG
*
51289401 AAATTTTTGAAATAC-TGG
1 AAA-TTTTGAAA-ACACGG
*
51289419 AATTTTTGAAAACACGAG
1 AAATTTTGAAAACACG-G
* * *
51289437 GATTTTTG-AAACGC-G
1 AAATTTTGAAAACACGG
* * * *
51289452 AATTTTTTAAAAATACGA
1 AA-ATTTTGAAAACACGG
*
51289470 AAATTTTTGAAAACACAG
1 AAA-TTTTGAAAACACGG
*
51289488 AAATTTTTAAAACACGGG
1 AAATTTTGAAAACAC-GG
*
51289506 AATTTTTGAAA
1 AAATTTTGAAA
51289517 TACGAATTTT
Statistics
Matches: 168, Mismatches: 31, Indels: 42
0.70 0.13 0.17
Matches are distributed among these distances:
15 4 0.02
16 23 0.14
17 60 0.36
18 66 0.39
19 5 0.03
20 10 0.06
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (17 bp):
AAATTTTGAAAACACGG
Found at i:51289335 original size:35 final size:34
Alignment explanation
Indices: 51289281--51289521 Score: 147
Period size: 35 Copynumber: 7.0 Consensus size: 34
51289271 AAACATAAAA
* *
51289281 AATTTTG-AAACACGGAAATTTGTGAAACACGAG
1 AATTTTGAAAACACGAAAATTTTTGAAACACGAG
*
51289314 AATTGTTGAAAACACGAAAA-TTTTGAAAACACGAAA
1 AATT-TTGAAAACACGAAAATTTTTG-AAACACG-AG
* * *
51289350 AATTTTTTGAAAACCCG-AAA-TTTTGGATCACCG-G
1 AA--TTTTGAAAACACGAAAATTTTTGAAACA-CGAG
** *
51289384 AATCTTTGAAAACATAAAAATTTTTGAAATACTG-G
1 AAT-TTTGAAAACACGAAAATTTTTGAAACAC-GAG
** *
51289419 AATTTTTGAAAACACGAGGATTTTTGAAACGCGA-
1 AA-TTTTGAAAACACGAAAATTTTTGAAACACGAG
* * *
51289453 ATTTTTTAAAAATACGAAAATTTTTGAAAACAC-AG
1 A-ATTTTGAAAACACGAAAATTTTTG-AAACACGAG
* ** *
51289488 AAATTTTTAAAACACGGGAATTTTTGAAATACGA
1 -AATTTTGAAAACACGAAAATTTTTGAAACACGA
51289522 ATTTTATTTA
Statistics
Matches: 159, Mismatches: 31, Indels: 34
0.71 0.14 0.15
Matches are distributed among these distances:
32 1 0.01
33 13 0.08
34 40 0.25
35 78 0.49
36 15 0.09
37 10 0.06
38 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (34 bp):
AATTTTGAAAACACGAAAATTTTTGAAACACGAG
Found at i:51289473 original size:69 final size:71
Alignment explanation
Indices: 51289400--51289535 Score: 181
Period size: 69 Copynumber: 1.9 Consensus size: 71
51289390 TGAAAACATA
* * * *
51289400 AAAATTTTTG-AAATACTGGAATTTTTGAAAACACGAGG-ATTTTTGAAACGCGAA-TTT-TTTA
1 AAAATTTTTGAAAACACAGAAATTTTT-AAAACACG-GGAATTTTTGAAACACGAATTTTATTTA
51289461 AAAATACG
64 AAAATACG
*
51289469 AAAATTTTTGAAAACACAGAAATTTTTAAAACACGGGAATTTTTGAAATACGAATTTTATTTAAA
1 AAAATTTTTGAAAACACAGAAATTTTTAAAACACGGGAATTTTTGAAACACGAATTTTATTTAAA
51289534 AA
66 AA
51289536 ACGCGGAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
68 2 0.03
69 32 0.55
70 16 0.28
71 8 0.14
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (71 bp):
AAAATTTTTGAAAACACAGAAATTTTTAAAACACGGGAATTTTTGAAACACGAATTTTATTTAAA
AATACG
Found at i:51289518 original size:52 final size:50
Alignment explanation
Indices: 51289402--51289522 Score: 129
Period size: 52 Copynumber: 2.3 Consensus size: 50
51289392 AAAACATAAA
* * *
51289402 AATTTTTGAAATACTG-GAATTTTTGAAAACACGAGGATTTTTGAAACGCG
1 AATTTTTGAAATAC-GAAAATTTTTGAAAACACGAGAATTTTTAAAACGCG
* *
51289452 AATTTTTTAAAAATACGAAAATTTTTGAAAACAC-AGAAATTTTTAAAACACGGG
1 AA-TTTTT-GAAATACGAAAATTTTTGAAAACACGAG-AATTTTT-AAA-ACGCG
51289506 AATTTTTGAAATACGAA
1 AATTTTTGAAATACGAA
51289523 TTTTATTTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
50 2 0.03
51 8 0.14
52 36 0.61
53 7 0.12
54 6 0.10
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (50 bp):
AATTTTTGAAATACGAAAATTTTTGAAAACACGAGAATTTTTAAAACGCG
Found at i:51290286 original size:14 final size:12
Alignment explanation
Indices: 51290252--51290348 Score: 68
Period size: 13 Copynumber: 7.3 Consensus size: 12
51290242 TAGCCTGCTG
*
51290252 TTTTTTATTTTT
1 TTTTTTCTTTTT
*
51290264 TTCTTTCTTTTT
1 TTTTTTCTTTTT
*
51290276 CTCTTTTTCTTCTAT
1 -T-TTTTTCTT-TTT
51290291 TTTTTTCTTTCTATT
1 TTTTTTC-TT-T-TT
51290306 TTTTCTTCTTTTT
1 TTTT-TTCTTTTT
*
51290319 TTTTTCCTTTTT
1 TTTTTTCTTTTT
*
51290331 CCTTTTTCTTCTTT
1 -TTTTTTCTT-TTT
51290345 TTTT
1 TTTT
51290349 GGGCCGAACC
Statistics
Matches: 68, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
12 17 0.25
13 23 0.34
14 16 0.24
15 9 0.13
16 3 0.04
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:51290292 original size:31 final size:30
Alignment explanation
Indices: 51290259--51290348 Score: 104
Period size: 28 Copynumber: 3.2 Consensus size: 30
51290249 CTGTTTTTTA
51290259 TTTTTTTCTTTCTTTTTCTCTTTTTCTTCT
1 TTTTTTTCTTTCTTTTTCTCTTTTTCTTCT
*
51290289 ATTTTTTTCTTTC----TAT-TTTTTCTTCT
1 -TTTTTTTCTTTCTTTTTCTCTTTTTCTTCT
*
51290315 TTTTTTT-TTCCTTTTTC-CTTTTTCTTCT
1 TTTTTTTCTTTCTTTTTCTCTTTTTCTTCT
51290343 TTTTTT
1 TTTTTT
51290349 GGGCCGAACC
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
24 3 0.06
25 7 0.14
26 10 0.20
27 2 0.04
28 17 0.33
31 12 0.24
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (30 bp):
TTTTTTTCTTTCTTTTTCTCTTTTTCTTCT
Found at i:51290293 original size:28 final size:27
Alignment explanation
Indices: 51290260--51290348 Score: 110
Period size: 27 Copynumber: 3.3 Consensus size: 27
51290250 TGTTTTTTAT
51290260 TTTTTTCTTTCTTTTTCTCTTTTTCTTC
1 TTTTTT-TTTCTTTTTCTCTTTTTCTTC
* * *
51290288 TATTTTTTTCTTTCTAT-TTTTTCTTC
1 TTTTTTTTTCTTTTTCTCTTTTTCTTC
51290314 TTTTTTTTTTCCTTTTTC-CTTTTTCTTC
1 -TTTTTTTTT-CTTTTTCTCTTTTTCTTC
51290342 TTTTTTT
1 TTTTTTT
51290349 GGGCCGAACC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
26 9 0.17
27 24 0.46
28 19 0.37
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (27 bp):
TTTTTTTTTCTTTTTCTCTTTTTCTTC
Found at i:51290348 original size:12 final size:12
Alignment explanation
Indices: 51290252--51290330 Score: 63
Period size: 12 Copynumber: 6.2 Consensus size: 12
51290242 TAGCCTGCTG
*
51290252 TTTTTTATT-TT
1 TTTTTTCTTCTT
*
51290263 TTTCTTTCTTTTT
1 TTT-TTTCTTCTT
51290276 CTCTTTTTCTTCTAT
1 -T-TTTTTCTTCT-T
*
51290291 TTTTTTCTTTCTA
1 TTTTTTC-TTCTT
51290304 TTTTTTCTTCTT
1 TTTTTTCTTCTT
51290316 TTTTTT-TTCCTT
1 TTTTTTCTT-CTT
51290328 TTT
1 TTT
51290331 CCTTTTTCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
11 5 0.09
12 21 0.37
13 15 0.26
14 13 0.23
15 3 0.05
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTCTTCTT
Found at i:51290446 original size:22 final size:22
Alignment explanation
Indices: 51290421--51290462 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
51290411 CGCGCCTCTC
51290421 TTCTCCTCCTCTATCTTTTTCT
1 TTCTCCTCCTCTATCTTTTTCT
* * *
51290443 TTCTTCTCTTCTTTCTTTTT
1 TTCTCCTCCTCTATCTTTTT
51290463 GGTTGCTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (22 bp):
TTCTCCTCCTCTATCTTTTTCT
Found at i:51290477 original size:14 final size:14
Alignment explanation
Indices: 51290458--51290489 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
51290448 CTCTTCTTTC
51290458 TTTTTGGTTGCTAT
1 TTTTTGGTTGCTAT
*
51290472 TTTTTGGTTGCTGT
1 TTTTTGGTTGCTAT
51290486 TTTT
1 TTTT
51290490 GTTTCTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.03, C:0.06, G:0.22, T:0.69
Consensus pattern (14 bp):
TTTTTGGTTGCTAT
Found at i:51292899 original size:36 final size:35
Alignment explanation
Indices: 51292822--51292899 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 35
51292812 AAAGGAAACT
*
51292822 AAAAATTTCTAATATTCATTTTCACCAAATATTTA
1 AAAAATTTCTAATATTCATTTTCACCAAATACTTA
* **
51292857 ATAAAATTTCTAATAATT-ATTTTTATTAAATGACTTA
1 A-AAAATTTCTAAT-ATTCATTTTCACCAAAT-ACTTA
51292894 AAAAAT
1 AAAAAT
51292900 ATAAATAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
35 1 0.03
36 27 0.75
37 8 0.22
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.44
Consensus pattern (35 bp):
AAAAATTTCTAATATTCATTTTCACCAAATACTTA
Found at i:51303897 original size:18 final size:18
Alignment explanation
Indices: 51303874--51303909 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
51303864 ACTTATTTTT
*
51303874 ATAATTAAGTTTTAAATA
1 ATAATTAAGTTTGAAATA
51303892 ATAATTAAGTTTGAAATA
1 ATAATTAAGTTTGAAATA
51303910 TGATTAAATG
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:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (18 bp):
ATAATTAAGTTTGAAATA
Found at i:51308853 original size:36 final size:35
Alignment explanation
Indices: 51308776--51308861 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 35
51308766 AAAGGAAACT
* *
51308776 AAAAATTTCTAATAATCATTTTCACCAAATATTTA
1 AAAAATTTATAATAATCATTTTCACCAAATACTTA
* * *
51308811 ATAAAATTTATAATAATTATTTTTACTAAATGACTTA
1 A-AAAATTTATAATAATCATTTTCACCAAAT-ACTTA
*
51308848 AAAAATATA-AATAA
1 AAAAATTTATAATAA
51308862 AAATTTATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
35 6 0.14
36 32 0.74
37 5 0.12
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.40
Consensus pattern (35 bp):
AAAAATTTATAATAATCATTTTCACCAAATACTTA
Found at i:51310138 original size:105 final size:105
Alignment explanation
Indices: 51310026--51310239 Score: 288
Period size: 105 Copynumber: 2.0 Consensus size: 105
51310016 ACTATAGGTA
* *
51310026 ACAACATCAGGCTCAATGCCTCGCTTTATCATT-TCATCAACTATATCCT-CAGCTTCAGAGACC
1 ACAACATCAGGCTCAATGCCTCGCTTTATCATTGT-ATCAACGATAT-CTACAGCTTCAGAAACC
* *
51310089 ATCCCTTCCTTGCAATGCGCATCAACCAATGTATTATACGTG
64 ATCCCTTCCTTGCAAAGAGCATCAACCAATGTATTATACGTG
* * * * * * *
51310131 ACAACATCAGGCTCAATGCCTTGCTTTCTCATTGTGTCAACGATCTCTACAGCTTTAGAAATCGT
1 ACAACATCAGGCTCAATGCCTCGCTTTATCATTGTATCAACGATATCTACAGCTTCAGAAACCAT
*
51310196 TCCTTCCTTGCAAAGAGCATCAACCAATGTATTATACGTG
66 CCCTTCCTTGCAAAGAGCATCAACCAATGTATTATACGTG
51310236 ACAA
1 ACAA
51310240 TATTAAGTGA
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
104 2 0.02
105 92 0.97
106 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.30
Consensus pattern (105 bp):
ACAACATCAGGCTCAATGCCTCGCTTTATCATTGTATCAACGATATCTACAGCTTCAGAAACCAT
CCCTTCCTTGCAAAGAGCATCAACCAATGTATTATACGTG
Found at i:51311189 original size:11 final size:11
Alignment explanation
Indices: 51311168--51311201 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
51311158 TAAAGTGAAT
51311168 AATATTTAATAA
1 AATA-TTAATAA
51311180 AATATTAATAA
1 AATATTAATAA
51311191 AATTATTAATA
1 AA-TATTAATA
51311202 TTATTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATATTAATAA
Found at i:51311208 original size:12 final size:12
Alignment explanation
Indices: 51311173--51311201 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
51311163 TGAATAATAT
51311173 TTAATAAAA-TA
1 TTAATAAAATTA
51311184 TTAATAAAATTA
1 TTAATAAAATTA
51311196 TTAATA
1 TTAATA
51311202 TTATTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TTAATAAAATTA
Found at i:51311276 original size:25 final size:26
Alignment explanation
Indices: 51311230--51311285 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
51311220 TCTTCCTTTT
*
51311230 AAATTTAATAAAATTACTATTTAATA
1 AAATTTAATAAAATTACAATTTAATA
* *
51311256 AAATTTATTAAATTTA-AATTTAATA
1 AAATTTAATAAAATTACAATTTAATA
51311281 AAATT
1 AAATT
51311286 ACTATTTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 13 0.48
26 14 0.52
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
AAATTTAATAAAATTACAATTTAATA
Found at i:51311606 original size:9 final size:9
Alignment explanation
Indices: 51311587--51311623 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
51311577 TGAGTTTTCG
51311587 AATTCGAAT
1 AATTCGAAT
51311596 AACTT-GAAT
1 AA-TTCGAAT
51311605 AATTCGAAT
1 AATTCGAAT
51311614 AATTCGAAT
1 AATTCGAAT
51311623 A
1 A
51311624 TCAAACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:51311863 original size:30 final size:31
Alignment explanation
Indices: 51311829--51311888 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
51311819 AAACCTTTTA
*
51311829 TTTTCTCCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTC-CCCTAAAACTTTTACTCCCTTCCCAC
*
51311859 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
51311889 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:51315881 original size:67 final size:67
Alignment explanation
Indices: 51315802--51315938 Score: 274
Period size: 67 Copynumber: 2.0 Consensus size: 67
51315792 ATATTTATGC
51315802 ATGTATACTAATGGTATTTGGTGTTAAGATATAATTAAAAGTATGTTTATTGAATAAATTTTAAA
1 ATGTATACTAATGGTATTTGGTGTTAAGATATAATTAAAAGTATGTTTATTGAATAAATTTTAAA
51315867 GT
66 GT
51315869 ATGTATACTAATGGTATTTGGTGTTAAGATATAATTAAAAGTATGTTTATTGAATAAATTTTAAA
1 ATGTATACTAATGGTATTTGGTGTTAAGATATAATTAAAAGTATGTTTATTGAATAAATTTTAAA
51315934 GT
66 GT
51315936 ATG
1 ATG
51315939 GATGATATTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.39, C:0.01, G:0.17, T:0.43
Consensus pattern (67 bp):
ATGTATACTAATGGTATTTGGTGTTAAGATATAATTAAAAGTATGTTTATTGAATAAATTTTAAA
GT
Found at i:51319711 original size:6 final size:6
Alignment explanation
Indices: 51319549--51319692 Score: 243
Period size: 6 Copynumber: 24.0 Consensus size: 6
51319539 CTAGACAAGG
51319549 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
* * *
51319597 GTCTAT GTCTAT GTCTAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
* *
51319645 GTCTAT GTCTAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
1 GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
51319693 AAAATTCGAA
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 134 1.00
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.50
Consensus pattern (6 bp):
GTATAT
Found at i:51319815 original size:2 final size:2
Alignment explanation
Indices: 51319810--51319842 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
51319800 TATGGTTCGA
51319810 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51319843 CACACATGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51320270 original size:41 final size:41
Alignment explanation
Indices: 51320209--51320312 Score: 129
Period size: 41 Copynumber: 2.5 Consensus size: 41
51320199 GAATACAATA
* * * * *
51320209 CAGACTTTACGTCTAACAGGCTTGATGCCGGTGATA-TAATT
1 CAGACTATACGTCTAGCAGGCTTCATGCCAGTGAAACTAA-T
51320250 CAGACTATACGTCTAGCAGGCTTCATGCCAGTGAAACTAAT
1 CAGACTATACGTCTAGCAGGCTTCATGCCAGTGAAACTAAT
* *
51320291 CGGACTATAAGTCTAGCAGGCT
1 CAGACTATACGTCTAGCAGGCT
51320313 AAAAGCCGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 52 0.95
42 3 0.05
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (41 bp):
CAGACTATACGTCTAGCAGGCTTCATGCCAGTGAAACTAAT
Found at i:51320766 original size:2 final size:2
Alignment explanation
Indices: 51320747--51320798 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
51320737 TTTGGTTGTG
* * * * *
51320747 TA TA TA TT TT TA TT TA TA TA TA TA TA TT TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
51320789 TA TA TG TA TA
1 TA TA TA TA TA
51320799 CAGTGATTCG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (2 bp):
TA
Found at i:51320766 original size:14 final size:14
Alignment explanation
Indices: 51320747--51320793 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
51320737 TTTGGTTGTG
*
51320747 TATATATTTTTATT
1 TATATATATTTATT
*
51320761 TATATATATATATT
1 TATATATATTTATT
*
51320775 TATATATATTTATA
1 TATATATATTTATT
51320789 TATAT
1 TATAT
51320794 GTATACAGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATATATATTTATT
Found at i:51320780 original size:10 final size:10
Alignment explanation
Indices: 51320747--51320798 Score: 68
Period size: 10 Copynumber: 5.2 Consensus size: 10
51320737 TTTGGTTGTG
*
51320747 TATATATTTT
1 TATATATTTA
* *
51320757 TATTTATATA
1 TATATATTTA
51320767 TATATATTTA
1 TATATATTTA
51320777 TATATATTTA
1 TATATATTTA
*
51320787 TATATATGTA
1 TATATATTTA
51320797 TA
1 TA
51320799 CAGTGATTCG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (10 bp):
TATATATTTA
Found at i:51326486 original size:21 final size:22
Alignment explanation
Indices: 51326418--51326526 Score: 134
Period size: 23 Copynumber: 5.0 Consensus size: 22
51326408 GCTTTGCCGA
*
51326418 TCAGGCACTATATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
*
51326440 ATCAGGCACTTTATGTGTTGTATT
1 -TCAGGCACTTTATGTGTCGTA-T
**
51326464 TCAGGCACTTCGTGTGTCGT-T
1 TCAGGCACTTTATGTGTCGTAT
*
51326485 TCAGGCACTTTATGTGTCGTGT
1 TCAGGCACTTTATGTGTCGTAT
51326507 T-AGGCAC-TTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
51326527 ACTGATCAGG
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
20 12 0.16
21 25 0.33
22 2 0.03
23 36 0.47
24 1 0.01
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.40
Consensus pattern (22 bp):
TCAGGCACTTTATGTGTCGTAT
Found at i:51326950 original size:19 final size:19
Alignment explanation
Indices: 51326923--51326959 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
51326913 GAAACAAGCT
*
51326923 ATTGAAATGAGATTGAAAA
1 ATTGAAATGAAATTGAAAA
*
51326942 ATTGCAATGAAATTGAAA
1 ATTGAAATGAAATTGAAA
51326960 TAGTGAAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.19, T:0.27
Consensus pattern (19 bp):
ATTGAAATGAAATTGAAAA
Found at i:51330012 original size:105 final size:105
Alignment explanation
Indices: 51329919--51330147 Score: 253
Period size: 105 Copynumber: 2.2 Consensus size: 105
51329909 ACCATTAACT
* * *
51329919 AATGCACTATAGGTAACAACATTAGGCTCAATGCCTCGCTTTATCATTGCATCAACAATATCCT-
1 AATGCACTATACGTAACAACATCAGGCTCAAAGCCTCGCTTTATCATTGCATCAACAATAT-CTA
*
51329983 CAGCTTCAGAGACCATCCCTTCCTTGCAATGCGCATCAACC
65 CAGCTTCAGAAACCATCCCTTCCTTGCAATGCGCATCAACC
* * * * * ** * *
51330024 AATGTATTATACGTGACAACATCAGGCTCAAAGCCTTGCTTTCTCATTGTGTCAACGATCTCTAC
1 AATGCACTATACGTAACAACATCAGGCTCAAAGCCTCGCTTTATCATTGCATCAACAATATCTAC
* * * * *
51330089 AGCTTTAGAAACCGTTCCTTCCTTGCAAAGAGCATCAACC
66 AGCTTCAGAAACCATCCCTTCCTTGCAATGCGCATCAACC
* * *
51330129 AATGTATTATACGTGACAA
1 AATGCACTATACGTAACAA
51330148 TATTAAGTGA
Statistics
Matches: 105, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
104 2 0.02
105 103 0.98
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.28
Consensus pattern (105 bp):
AATGCACTATACGTAACAACATCAGGCTCAAAGCCTCGCTTTATCATTGCATCAACAATATCTAC
AGCTTCAGAAACCATCCCTTCCTTGCAATGCGCATCAACC
Found at i:51345997 original size:97 final size:97
Alignment explanation
Indices: 51345890--51346106 Score: 416
Period size: 97 Copynumber: 2.2 Consensus size: 97
51345880 ATATGTATTC
51345890 ATATATACAACTATGTTCTTATAATGTACATTCTTTATATTAATGATATATGTAAGCTTACACCC
1 ATATATACAACTATGTTCTTATAATGTACATTCTTTATATTAATGATATATGTAAGCTTACACCC
51345955 TAAACGAGTATCTAATTTTATGGTAGATTATA
66 TAAACGAGTATCTAATTTTATGGTAGATTATA
51345987 ATATATACAACTATGTTCTTATAATGTACATTCTTTATATTAATGATATATGTAAGCTTACACCC
1 ATATATACAACTATGTTCTTATAATGTACATTCTTTATATTAATGATATATGTAAGCTTACACCC
51346052 TAAACGAGTATCTAATTTTATGGTAGATTATA
66 TAAACGAGTATCTAATTTTATGGTAGATTATA
*
51346084 ATATATACAACTATTTTTCTTAT
1 ATATATACAACTA-TGTTCTTAT
51346107 CTCGTGCGAT
Statistics
Matches: 118, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
97 110 0.93
98 8 0.07
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (97 bp):
ATATATACAACTATGTTCTTATAATGTACATTCTTTATATTAATGATATATGTAAGCTTACACCC
TAAACGAGTATCTAATTTTATGGTAGATTATA
Found at i:51347645 original size:2 final size:2
Alignment explanation
Indices: 51347638--51347682 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
51347628 NNNNNNNNNN
* *
51347638 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AA AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51347678 AT AT A
1 AT AT A
51347683 ATTATGAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:51350130 original size:36 final size:35
Alignment explanation
Indices: 51350053--51350130 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 35
51350043 AAAGGAAACT
*
51350053 AAAAATTTCTAATAATCATTTTCATCAAATATTTA
1 AAAAATTTCTAATAATCATTTTCATCAAATACTTA
*
51350088 ATAAAATTTCTAATAA-CTATTTTTA-CTAAATGACTTA
1 A-AAAATTTCTAATAATC-ATTTTCATC-AAAT-ACTTA
51350125 AAAAAT
1 AAAAAT
51350131 ATAAATAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
35 3 0.08
36 29 0.78
37 5 0.14
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.41
Consensus pattern (35 bp):
AAAAATTTCTAATAATCATTTTCATCAAATACTTA
Found at i:51353561 original size:105 final size:103
Alignment explanation
Indices: 51353403--51353621 Score: 226
Period size: 105 Copynumber: 2.1 Consensus size: 103
51353393 ACTATAGGTA
*
51353403 ACAACATTAGGCTCAATGCCTCGCTTTATCATTGCATCAACAAAATCCTCAGCTTCAGAGACCAT
1 ACAACATTAGGCTCAATGCCTCGCTTTATCATTG-ATCAAC-AAATCCTCAGCTTCAGAAACCAT
* * * *
51353468 CCCTTCCTTGCAATGTGAATCAACCAATGTATTATACGTG
64 CCCTTCCTTGCAAAGAGAATCAACCAATATAGTATACGTG
* * * * *
51353508 ACAACATTAGGCTCAATGCCTTGCTTTCTCATCATG-TCAAC-AGTCTCTACAGCTTTAGAAATC
1 ACAACATTAGGCTCAATGCCTCGCTTTATCAT--TGATCAACAAATC-CT-CAGCTTCAGAAACC
* * * * *
51353571 GTTCCTTCCTTGCAAAGAGCATCAATCAATATAGTATATGTG
62 ATCCCTTCCTTGCAAAGAGAATCAACCAATATAGTATACGTG
*
51353613 ACAATATTA
1 ACAACATTA
51353622 AGTGAAATAT
Statistics
Matches: 94, Mismatches: 16, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
103 3 0.03
104 2 0.02
105 87 0.93
107 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (103 bp):
ACAACATTAGGCTCAATGCCTCGCTTTATCATTGATCAACAAATCCTCAGCTTCAGAAACCATCC
CTTCCTTGCAAAGAGAATCAACCAATATAGTATACGTG
Found at i:51355764 original size:36 final size:35
Alignment explanation
Indices: 51355687--51355764 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 35
51355677 AAAGGAAACT
*
51355687 AAAAATTTCTAATAATCATTTTCACCAAATATTTA
1 AAAAATTTCTAATAATCATTTTCACCAAATACTTA
* * *
51355722 ATAAAATTTCTAATAATTATTTTTACTAAATGACTTA
1 A-AAAATTTCTAATAATCATTTTCACCAAAT-ACTTA
51355759 AAAAAT
1 AAAAAT
51355765 ATAAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 1 0.03
36 31 0.84
37 5 0.14
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.41
Consensus pattern (35 bp):
AAAAATTTCTAATAATCATTTTCACCAAATACTTA
Found at i:51356415 original size:51 final size:51
Alignment explanation
Indices: 51356339--51356467 Score: 204
Period size: 51 Copynumber: 2.5 Consensus size: 51
51356329 CTTACGTATG
* * *
51356339 ATCACTTATCACTTGTCCCTAATCAGATAAGTGTAGCTAAAACTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTT
* *
51356390 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTT
*
51356441 ATCACTTGCCACTTGTCACTGATCAGA
1 ATCACTTGTCACTTGTCACTGATCAGA
51356468 AGTACTCAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 72 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTT
Found at i:51359215 original size:17 final size:17
Alignment explanation
Indices: 51359172--51359216 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
51359162 AAGGCAGCAG
51359172 AAAAGAAGAAAAGAAAA
1 AAAAGAAGAAAAGAAAA
51359189 AAAATG-AGAAAAGAAAA
1 AAAA-GAAGAAAAGAAAA
*
51359206 AGAAGAAGAAA
1 AAAAGAAGAAA
51359217 TGGACATACC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 1 0.04
17 23 0.92
18 1 0.04
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (17 bp):
AAAAGAAGAAAAGAAAA
Found at i:51362121 original size:105 final size:105
Alignment explanation
Indices: 51361999--51362317 Score: 388
Period size: 105 Copynumber: 3.0 Consensus size: 105
51361989 ACTATAGGTA
* * * * *
51361999 ACAACATTAGGCTCAATGCCTCACTTTATCATCGCGTCAATGATATCCTCAGCTTTAAAAACCAT
1 ACAACATCAGGCTCAATGCCTCGCTTTATCATTGCGTCAACGATATCCTCAGCTTTAGAAACCAT
* *
51362064 CCCTTGCTTGCAATGTGCATCAACCAATGTATTATACGTG
66 CCCTTCCTTGCAATGAGCATCAACCAATGTATTATACGTG
* * * * *
51362104 ACAACATCAGGCTCAATGCCTCGTTTTATCATTGCATCAACAATATCCTCAGCTTCAGAGACCAT
1 ACAACATCAGGCTCAATGCCTCGCTTTATCATTGCGTCAACGATATCCTCAGCTTTAGAAACCAT
** * *
51362169 CCCTTCCTTGCAATGCCCATCAACCAATGTACTATACATG
66 CCCTTCCTTGCAATGAGCATCAACCAATGTATTATACGTG
* * * * ***
51362209 ACAACATCAGGCTCAATGCCTTGCTTTCTCATTGTGTCAACGATCT-CTACAGCTTTAGAAATTG
1 ACAACATCAGGCTCAATGCCTCGCTTTATCATTGCGTCAACGATATCCT-CAGCTTTAGAAACCA
* * *
51362273 TTCCTTCCTTGCAAAGAGCATCAACCAAAGTATTATACGTG
65 TCCCTTCCTTGCAATGAGCATCAACCAATGTATTATACGTG
51362314 ACAA
1 ACAA
51362318 TATTAAGTGA
Statistics
Matches: 179, Mismatches: 34, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
104 2 0.01
105 177 0.99
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.29
Consensus pattern (105 bp):
ACAACATCAGGCTCAATGCCTCGCTTTATCATTGCGTCAACGATATCCTCAGCTTTAGAAACCAT
CCCTTCCTTGCAATGAGCATCAACCAATGTATTATACGTG
Found at i:51363603 original size:15 final size:15
Alignment explanation
Indices: 51363583--51363623 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
51363573 AATAATTTAG
51363583 TATAATATATATTTT
1 TATAATATATATTTT
*
51363598 TATAATTTATATTTT
1 TATAATATATATTTT
*
51363613 TATAATCTATA
1 TATAATATATA
51363624 AATTATAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (15 bp):
TATAATATATATTTT
Found at i:51363629 original size:14 final size:14
Alignment explanation
Indices: 51363612--51363645 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
51363602 ATTTATATTT
*
51363612 TTATAATCTATAAA
1 TTATAAGCTATAAA
*
51363626 TTATAAGCTATAAT
1 TTATAAGCTATAAA
51363640 TTATAA
1 TTATAA
51363646 CTTCAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (14 bp):
TTATAAGCTATAAA
Found at i:51367966 original size:50 final size:50
Alignment explanation
Indices: 51367851--51368149 Score: 355
Period size: 50 Copynumber: 5.8 Consensus size: 50
51367841 GATAATAACA
* ** * *
51367851 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * *
51367902 TGCCCATGCCATGTCTCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
51367952 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCGTCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
51368002 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
51368052 TGCCCATGCCACGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATC-T-CGG
*
51368107 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
51368150 TTACCCAAAT
Statistics
Matches: 215, Mismatches: 27, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
50 140 0.65
51 32 0.15
53 2 0.01
54 1 0.00
55 2 0.01
56 38 0.18
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:51368265 original size:13 final size:13
Alignment explanation
Indices: 51368244--51368275 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
51368234 GCTTGGATCA
*
51368244 TCATCAAATAAAT
1 TCATAAAATAAAT
51368257 TCATAAAATAAAT
1 TCATAAAATAAAT
51368270 TCATAA
1 TCATAA
51368276 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:51368522 original size:29 final size:30
Alignment explanation
Indices: 51368488--51368544 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
51368478 CCTCGACTCT
51368488 AACTTTT-CAAAATTACGA-TTTTGCCCCTA
1 AACTTTTACAAAATTAC-ATTTTTGCCCCTA
*
51368517 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACATTTTTGCCCC
51368545 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (30 bp):
AACTTTTACAAAATTACATTTTTGCCCCTA
Found at i:51380613 original size:5 final size:5
Alignment explanation
Indices: 51380603--51380635 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
51380593 AGGATTAGGG
51380603 TTTTC TTTTC -TTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
51380636 TTGAAAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:51380618 original size:9 final size:9
Alignment explanation
Indices: 51380604--51380634 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
51380594 GGATTAGGGT
51380604 TTTCTTTTC
1 TTTCTTTTC
51380613 TTTCTTTTC
1 TTTCTTTTC
51380622 TTTTCTTTTC
1 -TTTCTTTTC
51380632 TTT
1 TTT
51380635 TTTGAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:51380622 original size:14 final size:15
Alignment explanation
Indices: 51380603--51380635 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
51380593 AGGATTAGGG
51380603 TTTTCTTTTC-TTTC
1 TTTTCTTTTCTTTTC
51380617 TTTTCTTTTCTTTTC
1 TTTTCTTTTCTTTTC
51380632 TTTT
1 TTTT
51380636 TTGAAAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTCTTTTC
Found at i:51381399 original size:5 final size:5
Alignment explanation
Indices: 51381389--51381425 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
51381379 TTTTGAAAGC
* *
51381389 ACGAT ACGAT ACGAT ACGAT ACGAT ATGAT ACTAT AC
1 ACGAT ACGAT ACGAT ACGAT ACGAT ACGAT ACGAT AC
51381426 TATAATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (5 bp):
ACGAT
Found at i:51382071 original size:3 final size:3
Alignment explanation
Indices: 51382055--51382087 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
51382045 GTAGGGCAAC
51382055 AGA A-A AGA AG- AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
51382088 TGTAACAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:51384619 original size:16 final size:15
Alignment explanation
Indices: 51384600--51384629 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
51384590 TCTTTGTCCC
51384600 TTTTTTTCTTCTCTTT
1 TTTTTTTCTT-TCTTT
51384616 TTTTTTTCTTTCTT
1 TTTTTTTCTTTCTT
51384630 AACTCTAGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTTTCTTTCTTT
Found at i:51387378 original size:105 final size:105
Alignment explanation
Indices: 51387269--51387623 Score: 399
Period size: 105 Copynumber: 3.4 Consensus size: 105
51387259 TATTCTGCAA
** * * * ** **
51387269 GCAATGACCATTTACTAATGCACTATATGTAACAACATTAGGCTTGATTTCTCGCTTTATCATTG
1 GCAATGACCATCAACCAATGTACTATATGTGACAACATTAGGCTCAATGCCTCGCTTTATCATTG
51387334 CGTCAACAATATCCTCAGCTTCAGAGACCATCCCTTCCTT
66 CGTCAACAATATCCTCAGCTTCAGAGACCATCCCTTCCTT
** *
51387374 GCAAT-ACGCATCAACCAATGTGTTATATGTGACAACATTAGGCCCAATGCCTCGCTTTATCATT
1 GCAATGAC-CATCAACCAATGTACTATATGTGACAACATTAGGCTCAATGCCTCGCTTTATCATT
51387438 GCGTCAACAATATCCTCAGCTTCAGAGACCATCCCTTCCTT
65 GCGTCAACAATATCCTCAGCTTCAGAGACCATCCCTTCCTT
* * * * * *
51387479 GAAATGAGCATCAACCAATGTACTATACGTGACAACATCAGGCTCAATGCCTTGCTTTCTCATTG
1 GCAATGACCATCAACCAATGTACTATATGTGACAACATTAGGCTCAATGCCTCGCTTTATCATTG
* * * * * * * *
51387544 TGTCAACGATCT-CTACAGCTTTAGAAATCGTTCCTTCCTT
66 CGTCAACAATATCCT-CAGCTTCAGAGACCATCCCTTCCTT
* * * * *
51387584 GCAAAGAGCATCAACCAATGTATTATACGTGACAATATTA
1 GCAATGACCATCAACCAATGTACTATATGTGACAACATTA
51387624 AGTGAAATAT
Statistics
Matches: 213, Mismatches: 34, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
104 4 0.02
105 208 0.98
106 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.30
Consensus pattern (105 bp):
GCAATGACCATCAACCAATGTACTATATGTGACAACATTAGGCTCAATGCCTCGCTTTATCATTG
CGTCAACAATATCCTCAGCTTCAGAGACCATCCCTTCCTT
Found at i:51391466 original size:15 final size:17
Alignment explanation
Indices: 51391446--51391480 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
51391436 TCACATATGA
51391446 TTTTTTA-AAAAATATT
1 TTTTTTATAAAAATATT
*
51391462 TTTTTTATAAATATATT
1 TTTTTTATAAAAATATT
51391479 TT
1 TT
51391481 ATACATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTTTATAAAAATATT
Found at i:51393338 original size:2 final size:2
Alignment explanation
Indices: 51393333--51393374 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
51393323 AAATTAATGT
51393333 TA TA TA TA 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 TA TA TA TA
51393375 ATAAAAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51398680 original size:58 final size:58
Alignment explanation
Indices: 51398590--51398704 Score: 194
Period size: 58 Copynumber: 2.0 Consensus size: 58
51398580 AGAAGAAGAA
* * *
51398590 GAAATGGACATACTTTAGCTGCGACCGTTTTGTTCCTCCAAGGTAGAGCCACCACTTG
1 GAAATGGACATACCTTAGATGCGACCGTTTTGTTCCTACAAGGTAGAGCCACCACTTG
*
51398648 GAAATGGACATACCTTAGATGCGACCGTTTTGTTCCTACAAGGTAGAGTCACCACTT
1 GAAATGGACATACCTTAGATGCGACCGTTTTGTTCCTACAAGGTAGAGCCACCACTT
51398705 AGTTTGCTGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (58 bp):
GAAATGGACATACCTTAGATGCGACCGTTTTGTTCCTACAAGGTAGAGCCACCACTTG
Found at i:51402435 original size:21 final size:23
Alignment explanation
Indices: 51402394--51402438 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
51402384 TCTGCCCGTT
51402394 TTTTAAATAAATACCAAAAATTTA
1 TTTTAAATAAATA-CAAAAATTTA
51402418 TTTTAAA-AAATA-AAAAATTTA
1 TTTTAAATAAATACAAAAATTTA
51402439 AAAAAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.43
23 5 0.24
24 7 0.33
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (23 bp):
TTTTAAATAAATACAAAAATTTA
Found at i:51402482 original size:39 final size:41
Alignment explanation
Indices: 51402416--51402511 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 41
51402406 ACCAAAAATT
* *
51402416 TATTTTAAAAAATAAAAAATTTAAAAAAATTATTTTAAAAA
1 TATTTTAAAAAATAAAAAAATTAAAAAAAGTATTTTAAAAA
*
51402457 TATTTT-AAAATTAAAAAAATT-AAAAAAGTATTTT--AAA
1 TATTTTAAAAAATAAAAAAATTAAAAAAAGTATTTTAAAAA
*
51402494 -ATTTAAAAAAATAAAAAA
1 TATTTTAAAAAATAAAAAA
51402512 TAAAAATATT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
36 4 0.08
37 14 0.29
39 12 0.24
40 13 0.27
41 6 0.12
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (41 bp):
TATTTTAAAAAATAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:51402488 original size:28 final size:27
Alignment explanation
Indices: 51402452--51402513 Score: 99
Period size: 28 Copynumber: 2.3 Consensus size: 27
51402442 AAATTATTTT
51402452 AAAAATATTTTAAAA-TTAAAAAAATTA
1 AAAAATATTTTAAAATTTAAAAAAA-TA
51402479 AAAAAGTATTTTAAAATTTAAAAAAATA
1 AAAAA-TATTTTAAAATTTAAAAAAATA
51402507 AAAAATA
1 AAAAATA
51402514 AAAATATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 7 0.21
28 17 0.52
29 9 0.27
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (27 bp):
AAAAATATTTTAAAATTTAAAAAAATA
Found at i:51418819 original size:105 final size:105
Alignment explanation
Indices: 51418668--51418898 Score: 390
Period size: 105 Copynumber: 2.2 Consensus size: 105
51418658 ACTATAGGTA
* *
51418668 ACAACATTAGGTTCAATGCCTCGCTTCATCATTGCGTCAACAATATCCTCAGCTTCAGAGACCAT
1 ACAACATCAGGCTCAATGCCTCGCTTCATCATTGCGTCAACAATATCCTCAGCTTCAGAGACCAT
*
51418733 CCCTTCCTTGCAATGCGCATCAACCAATGTATTATACGTG
66 CCCTTCCTTGCAATGAGCATCAACCAATGTATTATACGTG
* * * **
51418773 ACAATATCAGGCTCAATGCCTCTCTTTATCATTGCGTCAATGATATCCTCAGCTTCAGAGACCAT
1 ACAACATCAGGCTCAATGCCTCGCTTCATCATTGCGTCAACAATATCCTCAGCTTCAGAGACCAT
51418838 CCCTTCCTTGCAATGAGCATCAACCAATGTATTATACGTG
66 CCCTTCCTTGCAATGAGCATCAACCAATGTATTATACGTG
51418878 ACAACATCAGGCTCAATGCCT
1 ACAACATCAGGCTCAATGCCT
51418899 TGCATTATCA
Statistics
Matches: 117, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
105 117 1.00
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (105 bp):
ACAACATCAGGCTCAATGCCTCGCTTCATCATTGCGTCAACAATATCCTCAGCTTCAGAGACCAT
CCCTTCCTTGCAATGAGCATCAACCAATGTATTATACGTG
Found at i:51425279 original size:6 final size:6
Alignment explanation
Indices: 51425268--51425292 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
51425258 TTTTACATTT
51425268 TAATTA TAATTA TAATTA TAATTA T
1 TAATTA TAATTA TAATTA TAATTA T
51425293 TCACACTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATTA
Found at i:51426323 original size:11 final size:11
Alignment explanation
Indices: 51426304--51426346 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
51426294 ATATTTTTAT
*
51426304 AAAGTAAAAAG
1 AAAGAAAAAAG
*
51426315 AAAGAAAAAGG
1 AAAGAAAAAAG
51426326 AAAGCAAAAAAG
1 AAAG-AAAAAAG
51426338 -AAGAAAAAA
1 AAAGAAAAAA
51426347 AAGATGGGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 6 0.21
11 16 0.57
12 6 0.21
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:51436430 original size:27 final size:28
Alignment explanation
Indices: 51436394--51436446 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
51436384 TTCTAAATTT
*
51436394 TTATTTATTT-GTGTACACAAA-AAACTA
1 TTATTGATTTAGTGT-CACAAATAAACTA
51436421 TTATTGATTTAGTGTCACAAATAAAC
1 TTATTGATTTAGTGTCACAAATAAAC
51436447 ACGACATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (28 bp):
TTATTGATTTAGTGTCACAAATAAACTA
Found at i:51438723 original size:18 final size:18
Alignment explanation
Indices: 51438702--51438739 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
51438692 ATAAAATTAT
51438702 AAAATT-AAAAATTAAATA
1 AAAATTCAAAAA-TAAATA
51438720 AAAATTCAAAAATAAATA
1 AAAATTCAAAAATAAATA
51438738 AA
1 AA
51438740 GTAAGAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATTCAAAAATAAATA
Found at i:51440245 original size:18 final size:18
Alignment explanation
Indices: 51440199--51440249 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
51440189 AGCTGCCAGG
51440199 CATTCTTCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
* ***
51440217 CAGTAAGCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
51440235 CATTCTTCTCCCTTC
1 CATTCTTCTCCCTTC
51440250 CTTCATTCCT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.14, C:0.43, G:0.04, T:0.39
Consensus pattern (18 bp):
CATTCTTCTCCCTTCATC
Found at i:51447100 original size:15 final size:15
Alignment explanation
Indices: 51447065--51447100 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
51447055 TTTAGACTAA
51447065 AAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
*
51447080 CAAAAATAAAAAAAT
1 AAAAAATAAAAAAAT
51447095 AAAAAA
1 AAAAAA
51447101 ATCAAAGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.86, C:0.03, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAAAATAAAAAAAT
Found at i:51447121 original size:8 final size:8
Alignment explanation
Indices: 51447064--51447102 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
51447054 GTTTAGACTA
51447064 AAAAAAAT
1 AAAAAAAT
51447072 AAAAAAAT
1 AAAAAAAT
*
51447080 -CAAAAAT
1 AAAAAAAT
51447087 AAAAAAAT
1 AAAAAAAT
51447095 AAAAAAAT
1 AAAAAAAT
51447103 CAAAGTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAAAAT
Found at i:51447128 original size:6 final size:6
Alignment explanation
Indices: 51447119--51447162 Score: 61
Period size: 6 Copynumber: 7.0 Consensus size: 6
51447109 CAAAATAGAA
*
51447119 AAAAAG AAAAAG AAAAAA AAGAGAAG AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AA-A-AAG AAAAAG AAAAAG AAAAAG
51447163 GAGGGGTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 28 0.82
7 2 0.06
8 4 0.12
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:51447155 original size:26 final size:25
Alignment explanation
Indices: 51447110--51447161 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
51447100 AATCAAAGTC
*
51447110 AAAATAGAAAAAAAGAAAAAGAAAA
1 AAAAGAGAAAAAAAGAAAAAGAAAA
51447135 AAAAGAGAAGAAAAAGAAAAAGAAAA
1 AAAAGAGAA-AAAAAGAAAAAGAAAA
51447161 A
1 A
51447162 GGAGGGGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (25 bp):
AAAAGAGAAAAAAAGAAAAAGAAAA
Found at i:51447550 original size:13 final size:14
Alignment explanation
Indices: 51447498--51447542 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
51447488 TCAAAAAAGA
*
51447498 AAAAGATGAAGAATG
1 AAAA-ATGAAAAATG
*
51447513 -AAAATGGAAAATG
1 AAAAATGAAAAATG
51447526 AAAAATGAAAAATG
1 AAAAATGAAAAATG
51447540 AAA
1 AAA
51447543 GAGTAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 8 0.31
14 18 0.69
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (14 bp):
AAAAATGAAAAATG
Found at i:51448959 original size:88 final size:88
Alignment explanation
Indices: 51448794--51449111 Score: 426
Period size: 88 Copynumber: 3.6 Consensus size: 88
51448784 TGAAGATAGC
* * * * * *
51448794 AGATCTTGCCTTTCTGCATTAACAGTGAAGCAGATTGAAAACA-AAACCTTACCTCTCTCGGTGG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACACAAACCTTGCCTCTCTCGGTTG
*
51448858 TGATGGAGCTGGTTGAAAACAAA
66 TGATGGAGCTGGTTGAAGACAAA
*
51448881 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAAACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACACAAACCTTGCCTCTCTCGGTTG
51448946 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * *
51448969 AGATCTTGCCTTCCTGCATTGACGGCGAAGCA-AGTCGAAGACACAAACTTTGCCTCTCTCGGTT
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGA-TCGAAAACACAAACCTTGCCTCTCTCGGTT
* **
51449033 GT-AGTGGAGATGGTTGAAGACAGC
65 GTGA-TGGAGCTGGTTGAAGACAAA
* * * * *
51449057 AGATCTTGCCTTCTTGCCTTGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACACAAACCTTGCCT
51449112 TCCTGTACTG
Statistics
Matches: 206, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
87 39 0.19
88 166 0.81
89 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (88 bp):
AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACACAAACCTTGCCTCTCTCGGTTG
TGATGGAGCTGGTTGAAGACAAA
Found at i:51448977 original size:44 final size:44
Alignment explanation
Indices: 51448828--51448979 Score: 127
Period size: 44 Copynumber: 3.5 Consensus size: 44
51448818 GTGAAGCAGA
* * *
51448828 TTGAAAAC-AAA-ACCTTACCTCTCTCGGTGGTGATGGAGCTGG
1 TTGAAAACAAAAGATCTTGCCTCTCTCGGTTGTGATGGAGCTGG
** * *
51448870 TTGAAAACAAAAGATCTTGCCT-TC-CTGCAT-TGACAGCGAAGCAGG
1 TTGAAAACAAAAGATCTTGCCTCTCTC-GGTTGTGA-TG-G-AGCTGG
* * *
51448915 TCGAAAACACAA-ACCTTGCCTCTCTCGGTTGTGATGGAGCTGG
1 TTGAAAACAAAAGATCTTGCCTCTCTCGGTTGTGATGGAGCTGG
*
51448958 TTGAAGACAAAAGATCTTGCCT
1 TTGAAAACAAAAGATCTTGCCT
51448980 TCCTGCATTG
Statistics
Matches: 82, Mismatches: 18, Indels: 18
0.69 0.15 0.15
Matches are distributed among these distances:
42 12 0.15
43 21 0.26
44 25 0.30
45 20 0.24
46 4 0.05
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (44 bp):
TTGAAAACAAAAGATCTTGCCTCTCTCGGTTGTGATGGAGCTGG
Found at i:51449011 original size:45 final size:45
Alignment explanation
Indices: 51448876--51449127 Score: 123
Period size: 44 Copynumber: 5.7 Consensus size: 45
51448866 CTGGTTGAAA
*
51448876 ACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAA
1 ACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAG
* * ** * * *
51448921 ACACAA-ACCTTGCC-TCTCTCGGTTGTGA-TG-G-AGCTGGTTGAAG
1 ACAAAAGATCTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCGAAG
* *
51448964 ACAAAAGATCTTGCCTTCCTGCATTGACGGCGAAGCAAGTCGAAG
1 ACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAG
* * * * * *
51449009 ACACAA-A-CTTTGCC-TCTCT-CGGTTG-TAGTGGAG-ATGGTTGAAG
1 ACAAAAGATC-TTGCCTTC-CTGC-ATTGACAGCGAAGCA-GGTCGAAG
** * * *
51449052 ACAGCAGATCTTGCCTTCTTGCCTTGACAGCGAAGCAGATCGAAG
1 ACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAG
** * * *
51449097 ACACCAG-CCTTGCCTTCCTGTACTGACAGCG
1 ACAAAAGATCTTGCCTTCCTGCATTGACAGCG
51449128 GAGTAGAATG
Statistics
Matches: 150, Mismatches: 39, Indels: 37
0.66 0.17 0.16
Matches are distributed among these distances:
42 4 0.03
43 37 0.25
44 60 0.40
45 45 0.30
46 4 0.03
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (45 bp):
ACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAG
Found at i:51449164 original size:45 final size:44
Alignment explanation
Indices: 51449047--51449186 Score: 149
Period size: 45 Copynumber: 3.1 Consensus size: 44
51449037 TGGAGATGGT
*
51449047 TGAAGACAGCAGATCTTGCCTTCTTG-CCTTGACAGCGAAGCAGA
1 TGAAGACAGCAGATCTTGCCTTCTTGTAC-TGACAGCGAAGCAGA
* * * * *
51449091 TCGAAGACACCAG-CCTTGCCTTCCTGTACTGACAGCGGAGTAGAA
1 T-GAAGACAGCAGATCTTGCCTTCTTGTACTGACAGCGAAGCAG-A
* * *
51449136 TGAAGATAGCAGATCTTGCCTTCTTGTACTAACAACGAAGCAGA
1 TGAAGACAGCAGATCTTGCCTTCTTGTACTGACAGCGAAGCAGA
51449180 TCGAAGA
1 T-GAAGA
51449187 AACCATAGTT
Statistics
Matches: 77, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
44 35 0.45
45 42 0.55
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (44 bp):
TGAAGACAGCAGATCTTGCCTTCTTGTACTGACAGCGAAGCAGA
Found at i:51449469 original size:100 final size:98
Alignment explanation
Indices: 51449199--51449571 Score: 446
Period size: 100 Copynumber: 3.7 Consensus size: 98
51449189 CCATAGTTTT
* * *
51449199 CAATTCAAAAGATTGAAGCTACAACAGCGGATCTTACATTCCAAGCGGTGCAGCGGAACAGATTG
1 CAATT-AAAAGATTGAAGCTACAACAGCGAATCTTACTTTCC-AGCGGTGCAGTGGAACAGATTG
* *
51449264 AAGCTACAAC-GACAGATCTCACTTCCCTGACATTG
64 AAGCTACAACAG-CGGATCTTACTTCCCTGACATTG
** * * **
51449299 CAATCCAAAGATTGAGGCCACAATGGCGAATCTTA-TTTCCAGGCGGTGCAGTGGAACAGATTGA
1 CAATTAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCCA-GCGGTGCAGTGGAACAGATTGA
51449363 AGCTACAACAGCGGATCTTACTTCCCTGACATTG
65 AGCTACAACAGCGGATCTTACTTCCCTGACATTG
* * * *
51449397 CAATTAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGAGTTGCAGTGGAACATATTG
1 CAATTAA-AAGATTGAAGCTACAACAGCGAATCTTACTTTCC-AGCGGTGCAGTGGAACAGATTG
*
51449462 AAGCTACAACAACGGATCTTACTTCCCTGACATTG
64 AAGCTACAACAGCGGATCTTACTTCCCTGACATTG
* * * *
51449497 CAATTAAGAAGATTGAAGCTACATCAGCAAATCTTAC-CTCTCAGGCGGTGCAGTGGAATAGATT
1 CAATTAA-AAGATTGAAGCTACAACAGCGAATCTTACTTTC-CA-GCGGTGCAGTGGAACAGATT
* *
51449561 AAAGCCACAAC
63 GAAGCTACAAC
51449572 GGTGAATCTT
Statistics
Matches: 234, Mismatches: 32, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
97 1 0.00
98 60 0.26
99 51 0.22
100 121 0.52
101 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (98 bp):
CAATTAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCCAGCGGTGCAGTGGAACAGATTGAA
GCTACAACAGCGGATCTTACTTCCCTGACATTG
Found at i:51449498 original size:50 final size:50
Alignment explanation
Indices: 51449208--51449533 Score: 261
Period size: 50 Copynumber: 6.6 Consensus size: 50
51449198 TCAATTCAAA
** ** *
51449208 AGATTGAAGCTACAACAGCGGATCTTACATTCCAAG-CGGTGCAGCGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTAC-TTCCCTGACATTGCAGTGGAAC
* * * **
51449258 AGATTGAAGCTACAAC-GACAGATCTCACTTCCCTGACATTGCAATCCAA-
1 AGATTGAAGCTACAACAG-CGGATCTTACTTCCCTGACATTGCAGTGGAAC
* * ** * * * * **
51449307 AGATTGAGGCCACAATGGCGAATCTTA-TTTCCAGGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAGTGGAAC
* * *
51449356 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAAT-TAAGA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAGTGGAA-C
* *
51449406 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGA-GTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCT-GACATTGCAGTGGAAC
* * * * *
51449456 ATATTGAAGCTACAACAACGGATCTTACTTCCCTGACATTGCAAT-TAAGA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAGTGGAA-C
* **
51449506 AGATTGAAGCTACATCAGCAAATCTTAC
1 AGATTGAAGCTACAACAGCGGATCTTAC
51449534 CTCTCAGGCG
Statistics
Matches: 212, Mismatches: 54, Indels: 20
0.74 0.19 0.07
Matches are distributed among these distances:
48 13 0.06
49 53 0.25
50 142 0.67
51 4 0.02
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.24
Consensus pattern (50 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAGTGGAAC
Found at i:51449653 original size:25 final size:25
Alignment explanation
Indices: 51449607--51449656 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
51449597 CGGTTAAAAG
* * *
51449607 GATTAAAGCCACATCGGTGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
*
51449632 GATTAAAGCTACAACAGCGAATCTT
1 GATTAAAGCCACAACAGCGAATCTT
51449657 ACGCCCCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (25 bp):
GATTAAAGCCACAACAGCGAATCTT
Found at i:51449736 original size:125 final size:124
Alignment explanation
Indices: 51449507--51449865 Score: 470
Period size: 125 Copynumber: 2.9 Consensus size: 124
51449497 CAATTAAGAA
* * * * * * *
51449507 GATTGAAGCTACATCAGCAAATCTTAC-CTCTCAGGCGGTGCAGTGGAATAGATTAAAGCCACAA
1 GATTAAAGCTACAACAGCGAATCTTACGC-CCCAAGCGATGCAGTGGAATAGATTAAAGCCACAT
* * * *
51449571 CGGTGAATCTTGCCTT-TCTGACATTGCGGTTAAAAGGATTAAAGCCACATCGGTGAATCTT
65 CGGTGAATCTTG-CTTCCCT-ACATTGCAGTTAAAAAGATTAAAGCCACATCGATGAATCTT
* *
51449632 GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAACAGATTAAAACCACATC
1 GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCACATC
51449697 GGTGAATCTTGCTTCCCCTACATTGCAGTTAAAAAGATTAAAGCCACATCGATGAATCTT
66 GGTGAATCTTGCTT-CCCTACATTGCAGTTAAAAAGATTAAAGCCACATCGATGAATCTT
* * * *
51449757 GATTAAAGCTACAATAACGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCAAATT
1 GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCACATC
* * * *
51449822 GGCGAATCTTGTTTCTCCGATATTGCAGTTAAAAAGATTAAAGC
66 GGTGAATCTTGCTTC-CCTACATTGCAGTTAAAAAGATTAAAGC
51449866 TACAATGACG
Statistics
Matches: 207, Mismatches: 23, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
124 4 0.02
125 200 0.97
126 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (124 bp):
GATTAAAGCTACAACAGCGAATCTTACGCCCCAAGCGATGCAGTGGAATAGATTAAAGCCACATC
GGTGAATCTTGCTTCCCTACATTGCAGTTAAAAAGATTAAAGCCACATCGATGAATCTT
Found at i:51450020 original size:44 final size:44
Alignment explanation
Indices: 51449948--51450112 Score: 143
Period size: 44 Copynumber: 3.7 Consensus size: 44
51449938 ATCGAAGAAC
* * * * **
51449948 CAAAGTCTTATCCCCCTGAAGATACAGTGGGGCAAATTGAAGGTG
1 CAAA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCCG
* *
51449993 CAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCG
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCCG
* * ** * **
51450037 -ATAATCCTATCTCCCTGAAGTTGCAGAGGAGCGGATTAAAGTAG
1 CA-AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCCG
* * *
51450081 TAGATCTTATCTCCCTGAAGTTGTAGTGGAGC
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGC
51450113 GGGTTAAAAT
Statistics
Matches: 99, Mismatches: 19, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
43 1 0.01
44 93 0.94
45 5 0.05
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCCG
Found at i:51450113 original size:44 final size:44
Alignment explanation
Indices: 51449996--51450156 Score: 173
Period size: 44 Copynumber: 3.7 Consensus size: 44
51449986 GAAGGTGCAA
* * * *
51449996 ATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAG-TGATAG
* *
51450040 ATCCTATCTCCCTGAAGTTGCAGAGGAGCGGATTAAAGT-AGTAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTGA-TAG
* * * *
51450084 ATCTTATCTCCCTGAAGTTGTAGTGGAGCGGGTTAAAATGATTG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTGATAG
* * *
51450128 ATCTTATCTCTCTGAAGTTACAGTAGAGC
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGC
51450157 AGATCGCATC
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
42 1 0.01
43 2 0.02
44 94 0.96
45 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTGATAG
Found at i:51451837 original size:18 final size:19
Alignment explanation
Indices: 51451808--51451843 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
51451798 TTAAATTTTG
51451808 TTATATATATATACATATT
1 TTATATATATATACATATT
51451827 TTATA-ATATATACATAT
1 TTATATATATATACATAT
51451844 ATGGGCACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (19 bp):
TTATATATATATACATATT
Found at i:51452093 original size:2 final size:2
Alignment explanation
Indices: 51452081--51452119 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
51452071 ATTTAGATAC
* *
51452081 AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51452120 CATTTTTTCC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51473376 original size:19 final size:19
Alignment explanation
Indices: 51473352--51473398 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
51473342 TAAATCTATG
51473352 AAAAAAAGAAGATTGA-AAC
1 AAAAAAA-AAGATTGATAAC
* *
51473371 AAAAAAAAAGGTTGATAGC
1 AAAAAAAAAGATTGATAAC
51473390 AAAAAAAAA
1 AAAAAAAAA
51473399 AAAAACCTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.70, C:0.04, G:0.15, T:0.11
Consensus pattern (19 bp):
AAAAAAAAAGATTGATAAC
Found at i:51475307 original size:2 final size:2
Alignment explanation
Indices: 51475300--51475331 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
51475290 AAATTGATAA
51475300 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51475332 CACGTAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:51475319 original size:15 final size:15
Alignment explanation
Indices: 51475299--51475329 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
51475289 CAAATTGATA
51475299 AATATATATATATAT
1 AATATATATATATAT
51475314 AATATATATATATAT
1 AATATATATATATAT
51475329 A
1 A
51475330 TACACGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATATATATATAT
Found at i:51477279 original size:38 final size:38
Alignment explanation
Indices: 51477232--51477306 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
51477222 GAAAATAATA
*
51477232 AAATATTAAAAAACAT-TTTTA-TATTTTTAATTGAATTT
1 AAATATT-AAAAACATCTTTTATTA-TTTAAATTGAATTT
* *
51477270 AAATTTTAAAAATATCTTTTATTATTTAAATTGAATT
1 AAATATTAAAAACATCTTTTATTATTTAAATTGAATT
51477307 CAAGTTGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 7 0.22
38 23 0.72
39 2 0.06
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (38 bp):
AAATATTAAAAACATCTTTTATTATTTAAATTGAATTT
Found at i:51482635 original size:3 final size:3
Alignment explanation
Indices: 51482627--51482655 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
51482617 TCAATTGTAA
51482627 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
51482656 CAATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:51487074 original size:38 final size:39
Alignment explanation
Indices: 51486995--51487075 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 39
51486985 TTTTAAGGTT
51486995 TTAAAAATATATATAACTTATTTTTTAAAATTAAAATTA
1 TTAAAAATATATATAACTTATTTTTTAAAATTAAAATTA
*
51487034 TTAAAAATATATATTA-TTA-TTTTTAAAACTTTAAAA-TA
1 TTAAAAATATATATAACTTATTTTTTAAAA--TTAAAATTA
51487072 TTAA
1 TTAA
51487076 TTAAATGCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
37 9 0.23
38 9 0.23
39 21 0.54
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (39 bp):
TTAAAAATATATATAACTTATTTTTTAAAATTAAAATTA
Found at i:51488143 original size:89 final size:88
Alignment explanation
Indices: 51488046--51488219 Score: 294
Period size: 89 Copynumber: 2.0 Consensus size: 88
51488036 AGCCCGATTC
*
51488046 TGGGCCTAGTCGAAAAAGTGGTTTTGGGACCACAAATCCGACAAGGGAAAATATGATTATTATTA
1 TGGGCCTAGTCGAAAAAGTGGTTTCGGGACCACAAATCCGACAAGGG-AAATATGATTATTATTA
51488111 TATTTTTATGATCTACAATTTTTT
65 TATTTTTATGATCTACAATTTTTT
* * *
51488135 TGGGCCTAGTCGGAACAGTGGTTTCGGGACCACAAATCCGACTAGGGAAATATGATTATTATTAT
1 TGGGCCTAGTCGAAAAAGTGGTTTCGGGACCACAAATCCGACAAGGGAAATATGATTATTATTAT
*
51488200 ATTTTTATGATCTCCAATTT
66 ATTTTTATGATCTACAATTT
51488220 CACGGAAAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
88 37 0.46
89 43 0.54
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.35
Consensus pattern (88 bp):
TGGGCCTAGTCGAAAAAGTGGTTTCGGGACCACAAATCCGACAAGGGAAATATGATTATTATTAT
ATTTTTATGATCTACAATTTTTT
Found at i:51489361 original size:27 final size:27
Alignment explanation
Indices: 51489323--51489374 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
51489313 TGAATAAAAA
51489323 AGGGGTTGCTAAGTGCTGATTCCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCCG
51489350 AGGGGTTGCTAAGTGCTGATTCCCC
1 AGGGGTTGCTAAGTGCTGATTCCCC
51489375 GAACCATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.15, C:0.25, G:0.33, T:0.27
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:51489444 original size:102 final size:102
Alignment explanation
Indices: 51489324--51489551 Score: 386
Period size: 102 Copynumber: 2.2 Consensus size: 102
51489314 GAATAAAAAA
* *
51489324 GGGGTTGCTAAGTGCTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGAAC-CATTGGTGG
1 GGGGTTGCTAAGTGCTGATTCCCCCAAGGGATTGCTAAGTGCTGATTCCCCG-ACTCATTGGTGG
*
51489388 TTGCTAAGTGCTGATTCAACCGTATCTTAAATGTGAAG
65 TTGCTAAGTGCTAATTCAACCGTATCTTAAATGTGAAG
*
51489426 GGGGTTGCTAAGTGCTGATTCCCCCAAGGGATTGCTAAGTGCTGATTGCCCGACTCATTGGTGGT
1 GGGGTTGCTAAGTGCTGATTCCCCCAAGGGATTGCTAAGTGCTGATTCCCCGACTCATTGGTGGT
*
51489491 TGCTAAGTGCTAATTCCACCGTATCTTAAATGTGAAG
66 TGCTAAGTGCTAATTCAACCGTATCTTAAATGTGAAG
*
51489528 GGGGTTGCCAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
51489552 GAATCATTGG
Statistics
Matches: 119, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
101 2 0.02
102 117 0.98
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.29
Consensus pattern (102 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAAGGGATTGCTAAGTGCTGATTCCCCGACTCATTGGTGGT
TGCTAAGTGCTAATTCAACCGTATCTTAAATGTGAAG
Found at i:51489535 original size:42 final size:42
Alignment explanation
Indices: 51489488--51489624 Score: 139
Period size: 42 Copynumber: 3.5 Consensus size: 42
51489478 ACTCATTGGT
*
51489488 GGTTGCTAAGTGCTAATTCCACCGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGG
* * *
51489530 GGTTGCCAAGTGCTGATTCC-CCGAATC----AT-T---GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGG
* * *
51489563 GGTTGCTAAGTGTTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGG
*
51489605 GGTTGCTAAGTGTTGATTCC
1 GGTTGCTAAGTGCTGATTCC
51489625 CCAAATCACT
Statistics
Matches: 75, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
33 19 0.25
34 6 0.08
36 1 0.01
37 2 0.03
38 2 0.03
39 1 0.01
41 6 0.08
42 38 0.51
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGG
Found at i:51489585 original size:75 final size:75
Alignment explanation
Indices: 51489451--51489661 Score: 307
Period size: 75 Copynumber: 2.8 Consensus size: 75
51489441 TGATTCCCCC
* * * *
51489451 AAGGGATTGCTAAGTGCTGATTGCCCGACTCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTAATCCCACCGTATC
51489516 TTAAATGTGA
66 TTAAATGTGA
* * * *
51489526 AGGGGGTTGCCAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTAATCCCACCGTATC
51489591 TTAAATGTGA
66 TTAAATGTGA
* * *
51489601 AAGGGGTTGCTAAGTGTTGATTCCCCAAATCACTGGTGGTTGCTAAGTGCTGAAT-CCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCT-AATCCCACCG
51489662 ATAACGGATA
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
75 118 0.98
76 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTAATCCCACCGTATC
TTAAATGTGA
Found at i:51493266 original size:14 final size:15
Alignment explanation
Indices: 51493249--51493278 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
51493239 ATTATTTTGA
51493249 TTAAT-ATAAATATT
1 TTAATAATAAATATT
51493263 TTAATAATAAATATT
1 TTAATAATAAATATT
51493278 T
1 T
51493279 AGAAGGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAATAATAAATATT
Found at i:51502880 original size:84 final size:85
Alignment explanation
Indices: 51502773--51502943 Score: 326
Period size: 84 Copynumber: 2.0 Consensus size: 85
51502763 AATTAGATTT
*
51502773 TTTACTTTGACAAATTCTATTTTTGGAAAAATCTAATTTAGTGGTTGCTTGTTGAGCACGATTCT
1 TTTACTTTGACAAATTCTATTTTTGGAAAAATCTAATTTAGTGGTTGCTTGTTAAGCACGATTCT
51502838 AGGAGTAAAATTATGTGAAA
66 AGGAGTAAAATTATGTGAAA
51502858 TTTA-TTTGACAAATTCTATTTTTGGAAAAATCTAATTTAGTGGTTGCTTGTTAAGCACGATTCT
1 TTTACTTTGACAAATTCTATTTTTGGAAAAATCTAATTTAGTGGTTGCTTGTTAAGCACGATTCT
51502922 AGGAGTAAAATTATGTGAAA
66 AGGAGTAAAATTATGTGAAA
51502942 TT
1 TT
51502944 GATTCTTTGA
Statistics
Matches: 85, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
84 81 0.95
85 4 0.05
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (85 bp):
TTTACTTTGACAAATTCTATTTTTGGAAAAATCTAATTTAGTGGTTGCTTGTTAAGCACGATTCT
AGGAGTAAAATTATGTGAAA
Found at i:51508703 original size:3 final size:3
Alignment explanation
Indices: 51508695--51508741 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
51508685 TGCATCAAAA
* *
51508695 AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AAA AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
51508742 AAATGAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:51508752 original size:9 final size:9
Alignment explanation
Indices: 51508691--51508744 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
51508681 ACAGTGCATC
51508691 AAAA-AAGA
1 AAAAGAAGA
*
51508699 AGAAGAAGA
1 AAAAGAAGA
*
51508708 AGAAGAAGA
1 AAAAGAAGA
51508717 AAAAGAAG-
1 AAAAGAAGA
51508725 --AAGAAGA
1 AAAAGAAGA
51508732 AAAAGAAGA
1 AAAAGAAGA
51508741 AAAA
1 AAAA
51508745 TGAAAAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
6 6 0.15
8 3 0.08
9 31 0.77
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAAAGAAGA
Found at i:51510144 original size:43 final size:44
Alignment explanation
Indices: 51510079--51510184 Score: 133
Period size: 43 Copynumber: 2.4 Consensus size: 44
51510069 AAGCACCAAC
* * * * * *
51510079 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGC-AAT
1 CTTATCTCCCTAAGTAGTAGTGGAGTAGATCGAAGATGGCGAAT
51510122 CTTATCTCCCTAAGTAGTAGTGGAGTAGATCGAAGATGGCGAAT
1 CTTATCTCCCTAAGTAGTAGTGGAGTAGATCGAAGATGGCGAAT
*
51510166 CTTATCTTCCTAAGGTAGT
1 CTTATCTCCCTAA-GTAGT
51510185 GGGGAAGCAG
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
43 34 0.63
44 15 0.28
45 5 0.09
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (44 bp):
CTTATCTCCCTAAGTAGTAGTGGAGTAGATCGAAGATGGCGAAT
Found at i:51510324 original size:45 final size:45
Alignment explanation
Indices: 51510261--51510695 Score: 509
Period size: 45 Copynumber: 9.7 Consensus size: 45
51510251 GTTTTACCTC
* * * *
51510261 CCTGTACTGGCAGTGGAGCAGA-CTGAAGATAGCAGATATTGTCTT
1 CCTGTACTGGCAGCGAAGTAGATC-GAAGATAGCAGATCTTGTCTT
* * * *
51510306 TCTGTACTGGCAGCGGAGCAGA-CTGAAGATAGCAGATCTTATCTT
1 CCTGTACTGGCAGCGAAGTAGATC-GAAGATAGCAGATCTTGTCTT
* *
51510351 CCTGTATTGGCAGCGAAGTAGATCGAAGATAACAGATCTTGTCTT
1 CCTGTACTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTT
* *
51510396 CCTGTATTGGCAGCGAAGTAGATCGGAGATAGCAGATCTTGTCTT
1 CCTGTACTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTT
*
51510441 CCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTT
1 CCTGTACTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTT
*
51510486 CCTGTATTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTT
1 CCTGTACTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTT
* * * *
51510531 CCTGTATTGGTAGTGAAGTAGATCGAAGATAGCAGATCTTGCCTT
1 CCTGTACTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTT
* * * * **
51510576 CCTGTACTGGCAGCGAAGCAGATCGAAGACACCAG-CCTTACCTT
1 CCTGTACTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTT
* * * * * *
51510620 CCTGTACTGACAGCGGAGCAGA-CTTAAGATAACAGATCTTGCCTT
1 CCTGTACTGGCAGCGAAGTAGATC-GAAGATAGCAGATCTTGTCTT
* * * *
51510665 CCTGTACTGACAGCAAAGCATATCGAAGATA
1 CCTGTACTGGCAGCGAAGTAGATCGAAGATA
51510696 CCATAGTTTG
Statistics
Matches: 351, Mismatches: 35, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
43 1 0.00
44 35 0.10
45 313 0.89
46 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (45 bp):
CCTGTACTGGCAGCGAAGTAGATCGAAGATAGCAGATCTTGTCTT
Done.