Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold152
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: 2945013
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 13 of 18
Found at i:2086213 original size:13 final size:13
Alignment explanation
Indices: 2086195--2086219 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2086185 CAAAGATCAG
2086195 TGTATCGATACAA
1 TGTATCGATACAA
2086208 TGTATCGATACA
1 TGTATCGATACA
2086220 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2086286 original size:19 final size:19
Alignment explanation
Indices: 2086258--2086346 Score: 84
Period size: 19 Copynumber: 5.0 Consensus size: 19
2086248 GCAGTAGCTT
2086258 ACAT-TGTATCGATACAAA
1 ACATATGTATCGATACAAA
*
2086276 ACATATGTATCGATACAAC
1 ACATATGTATCGATACAAA
*
2086295 ACTTATGTATCGAT-----
1 ACATATGTATCGATACAAA
*
2086309 ACAT-TGTATCGATACAAT
1 ACATATGTATCGATACAAA
*
2086327 ACTTTATGTATCGATACAAA
1 AC-ATATGTATCGATACAAA
2086347 TCGTTGAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
13 9 0.16
14 3 0.05
18 6 0.10
19 27 0.47
20 13 0.22
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (19 bp):
ACATATGTATCGATACAAA
Found at i:2086318 original size:13 final size:13
Alignment explanation
Indices: 2086300--2086324 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2086290 ACAACACTTA
2086300 TGTATCGATACAT
1 TGTATCGATACAT
2086313 TGTATCGATACA
1 TGTATCGATACA
2086325 ATACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2086322 original size:32 final size:34
Alignment explanation
Indices: 2086276--2086344 Score: 115
Period size: 33 Copynumber: 2.1 Consensus size: 34
2086266 TCGATACAAA
2086276 ACATATGTATCGATACAACAC-TTATGTATCGAT
1 ACATATGTATCGATACAACACTTTATGTATCGAT
*
2086309 ACAT-TGTATCGATACAATACTTTATGTATCGAT
1 ACATATGTATCGATACAACACTTTATGTATCGAT
2086342 ACA
1 ACA
2086345 AATCGTTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 15 0.44
33 19 0.56
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (34 bp):
ACATATGTATCGATACAACACTTTATGTATCGAT
Found at i:2090424 original size:27 final size:27
Alignment explanation
Indices: 2090386--2090456 Score: 142
Period size: 27 Copynumber: 2.6 Consensus size: 27
2090376 GGTTGAAAAC
2090386 GGGGTTGGAGTGTCCCCTCGGAGGAAT
1 GGGGTTGGAGTGTCCCCTCGGAGGAAT
2090413 GGGGTTGGAGTGTCCCCTCGGAGGAAT
1 GGGGTTGGAGTGTCCCCTCGGAGGAAT
2090440 GGGGTTGGAGTGTCCCC
1 GGGGTTGGAGTGTCCCC
2090457 GACAATGATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.13, C:0.20, G:0.45, T:0.23
Consensus pattern (27 bp):
GGGGTTGGAGTGTCCCCTCGGAGGAAT
Found at i:2092751 original size:17 final size:18
Alignment explanation
Indices: 2092729--2092768 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
2092719 AGATCAATGT
2092729 ATTG-AATGTATCGATAC
1 ATTGAAATGTATCGATAC
2092746 ATTGAATAATGTATCGATAC
1 ATTG-A-AATGTATCGATAC
2092766 ATT
1 ATT
2092769 TCCTTGGCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
20 16 0.80
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (18 bp):
ATTGAAATGTATCGATAC
Found at i:2092839 original size:21 final size:19
Alignment explanation
Indices: 2092792--2092846 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
2092782 GCAGGGCAAC
2092792 TTTGTATCGATACAACACT
1 TTTGTATCGATACAACACT
* **
2092811 TATGTATCGATACATTTACT
1 TTTGTATCGATACA-ACACT
2092831 GTTTGTATCGATACAA
1 -TTTGTATCGATACAA
2092847 AGTATGAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACAACACT
Found at i:2102283 original size:27 final size:27
Alignment explanation
Indices: 2102210--2102949 Score: 615
Period size: 27 Copynumber: 26.5 Consensus size: 27
2102200 GCAGGCTTTG
*
2102210 AAAAGGGTGCCACGGAGTTGTGGAG-TT
1 AAAAGGGTGCCACGGAGTCGTGG-GCTT
* *
2102237 AAAAGGGGTGCCACGAAGTCGTGGACTT
1 AAAA-GGGTGCCACGGAGTCGTGGGCTT
*
2102265 AAAAGGGTGCCACGGAGTCATGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
* * *
2102292 AAAAGGGTGCCACAGAGTCATGGGCTG
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
* *
2102319 AAAAGGGTGCCACGCAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
* *
2102346 AAAAGGGTGCCACGGAATCGTGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
*
2102373 AAAAGGGTGCCACAGAGTCGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
* * * * *
2102400 AGAAGGGTGCCACAGAGCCATGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
* *
2102427 AAAAGGAAAAAAGGGTGCCACAGAGTTGTGGGCTT
1 --------AAAAGGGTGCCACGGAGTCGTGGGCTT
* *
2102462 -AAAGGGAAAAAAATTGCCACGAAGAT-GTGGACTT
1 AAAAGGG--------TGCCACGGAG-TCGTGGGCTT
* *
2102496 AAAGGGGTGCCATGGAGTCGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
**
2102523 AAAAGGGTGCCATAGAGTCGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
*
2102550 AAAAGGGTGCCATGGAGTCGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
** * *
2102577 AAAAGGGTGCCATAGAGTCATGGGCTA
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
* * * *
2102604 AAAAAGGTGCCATGGAGTCATGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
* * ** *
2102631 AAAAGGGTGCCACAGAATCAAGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
**
2102658 AAAAGGGTGCCATAGAGTCGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
*
2102685 AAAAGGGTGCCACAGAGTCGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
***
2102712 AAAAGGGTGCCATAAAGTCGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
* * * *
2102739 AAAAGAGTGTCATGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
* * * * *
2102766 AAAAGGAAAAAAAATTACCACGAAGAT-GTGGACATA
1 AAAAGG--------GTGCCACGGAG-TCGTGGGC-TT
2102802 AAAAGGGTGCCACGGAGTCGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
* *
2102829 AAAAGGGTGCCACAGAGTCGTGGACTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
* * *
2102856 AAAGGGGTGCCACGCAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
2102883 AAAAGGGTGCCACGGAGTCGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
* ** *
2102910 AAAAAGGTGCCATAGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTCGTGGGCTT
*
2102937 AAAAGGATGCCAC
1 AAAAGGGTGCCAC
2102950 TGACTTATAG
Statistics
Matches: 589, Mismatches: 92, Indels: 64
0.79 0.12 0.09
Matches are distributed among these distances:
26 7 0.01
27 484 0.82
28 36 0.06
34 15 0.03
35 39 0.07
36 8 0.01
ACGTcount: A:0.30, C:0.16, G:0.35, T:0.19
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTCGTGGGCTT
Found at i:2102480 original size:34 final size:35
Alignment explanation
Indices: 2102420--2102501 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 35
2102410 CACAGAGCCA
* * *
2102420 TGGACTTAAAAGGAAAAAAGGGTGCCAC-AGAGTTG
1 TGGACTTAAAGGGAAAAAAGAGTGCCACGA-AGATG
* *
2102455 TGGGCTTAAAGGGAAAAAA-ATTGCCACGAAGATG
1 TGGACTTAAAGGGAAAAAAGAGTGCCACGAAGATG
2102489 TGGACTTAAAGGG
1 TGGACTTAAAGGG
2102502 GTGCCATGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
34 22 0.55
35 18 0.45
ACGTcount: A:0.39, C:0.11, G:0.32, T:0.18
Consensus pattern (35 bp):
TGGACTTAAAGGGAAAAAAGAGTGCCACGAAGATG
Found at i:2118420 original size:21 final size:19
Alignment explanation
Indices: 2118373--2118427 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
2118363 GCAGGGCAGC
2118373 TTTGTATCGATACAACACT
1 TTTGTATCGATACAACACT
* **
2118392 TATGTATCGATACATTTACT
1 TTTGTATCGATACA-ACACT
2118412 ATTTGTATCGATACAA
1 -TTTGTATCGATACAA
2118428 ACTATAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACAACACT
Found at i:2119146 original size:20 final size:19
Alignment explanation
Indices: 2119118--2119176 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 19
2119108 TACTAGAAAC
*
2119118 CATATGTATCGATACATTT
1 CATATGTATTGATACATTT
*
2119137 CATCATGTATTGATACATCAT
1 CAT-ATGTATTGATACAT-TT
2119158 CATATGTATTGATACATTT
1 CATATGTATTGATACATTT
2119177 GAAAAAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.11
20 27 0.77
21 4 0.11
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.42
Consensus pattern (19 bp):
CATATGTATTGATACATTT
Found at i:2119637 original size:15 final size:15
Alignment explanation
Indices: 2119617--2119665 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
2119607 TTCTTAGCAG
*
2119617 AAAAAACCAAAAAAA
1 AAAAAAACAAAAAAA
*
2119632 AAAAAAAGAAAAAAA
1 AAAAAAACAAAAAAA
* *
2119647 AGAAAAAGAAAAGAAA
1 AAAAAAACAAAA-AAA
2119663 AAA
1 AAA
2119666 TAGTGGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 24 0.83
16 5 0.17
ACGTcount: A:0.88, C:0.04, G:0.08, T:0.00
Consensus pattern (15 bp):
AAAAAAACAAAAAAA
Found at i:2119658 original size:20 final size:18
Alignment explanation
Indices: 2119625--2119665 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 18
2119615 AGAAAAAACC
2119625 AAAAAAAAAAAAAAGAAA
1 AAAAAAAAAAAAAAGAAA
2119643 AAAAAGAAAAAGAAAAGAAA
1 AAAAA-AAAAA-AAAAGAAA
2119663 AAA
1 AAA
2119666 TAGTGGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.24
19 5 0.24
20 11 0.52
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAAGAAA
Found at i:2120466 original size:59 final size:58
Alignment explanation
Indices: 2120349--2120505 Score: 152
Period size: 59 Copynumber: 2.7 Consensus size: 58
2120339 TTTTCATGCA
* * * * * * **
2120349 TTTAAGGCCATTTAGGGTGTTTTATATCATATAGGGACCATTTAGCAATATCCTTGTAT
1 TTTAAGGCCATTTA-GGTATTTTACATAATCTAGGGTCAATTTAGCAATATCAATGTAT
* * *
2120408 TTTAAAGCCATTTAGGTTATTTTACATAATCTAGGGTCAATTTAGCATTTTCAATGTAT
1 TTTAAGGCCATTTAGG-TATTTTACATAATCTAGGGTCAATTTAGCAATATCAATGTAT
* * * *
2120467 TTTAGGGCCAATTAAAGTATTTTACATAGTCTAGGGTCA
1 TTTAAGGCC-ATTTAGGTATTTTACATAATCTAGGGTCA
2120506 TTATAGGAAT
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
58 2 0.03
59 73 0.91
60 5 0.06
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (58 bp):
TTTAAGGCCATTTAGGTATTTTACATAATCTAGGGTCAATTTAGCAATATCAATGTAT
Found at i:2128672 original size:6 final size:6
Alignment explanation
Indices: 2128653--2128712 Score: 50
Period size: 6 Copynumber: 9.7 Consensus size: 6
2128643 TGTTTTTTTC
* * * *
2128653 TTTTGA TTGATGA TTTTGA TTTTGA TTTTGA TTATAA TTATGTA TTTT-A
1 TTTTGA TT-TTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTG-A TTTTGA
2128702 GTTTTGA TTTT
1 -TTTTGA TTTT
2128713 AATAATATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
5 1 0.02
6 33 0.75
7 10 0.23
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (6 bp):
TTTTGA
Found at i:2128699 original size:25 final size:24
Alignment explanation
Indices: 2128653--2128723 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
2128643 TGTTTTTTTC
* *
2128653 TTTTGATTGATGATTTTGATTTT-G
1 TTTTGATT-ATAATTATGATTTTAG
2128677 ATTTTGATTATAATTATGTATTTTAG
1 -TTTTGATTATAATTATG-ATTTTAG
* *
2128703 TTTTGATTTTAATAAT-ATTTT
1 TTTTGATTATAATTATGATTTT
2128724 TAAATGATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 5 0.12
24 7 0.17
25 27 0.68
26 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.13, T:0.62
Consensus pattern (24 bp):
TTTTGATTATAATTATGATTTTAG
Found at i:2129214 original size:20 final size:20
Alignment explanation
Indices: 2129191--2129257 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 20
2129181 CACATCTAGA
2129191 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
*
2129211 TGTATTGAT--A-TA----T
1 TGTATCGATACATTATGCTT
2129224 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
*
2129244 TGTATTGATACATT
1 TGTATCGATACATT
2129258 GTATCGATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 14
0.69 0.06 0.26
Matches are distributed among these distances:
13 9 0.24
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
20 22 0.59
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.48
Consensus pattern (20 bp):
TGTATCGATACATTATGCTT
Found at i:2129233 original size:33 final size:33
Alignment explanation
Indices: 2129191--2129266 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
2129181 CACATCTAGA
*
2129191 TGTATCGATACATTATGCTTTGTATTGATATAT
1 TGTATCGATACATTATGCTTTGTATTGATACAT
2129224 TGTATCGATACATTATGCTTTGTATTGATACAT
1 TGTATCGATACATTATGCTTTGTATTGATACAT
2129257 TGTATCGATA
1 TGTATCGATA
2129267 TATGCTCATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.46
Consensus pattern (33 bp):
TGTATCGATACATTATGCTTTGTATTGATACAT
Found at i:2129363 original size:20 final size:20
Alignment explanation
Indices: 2129335--2129390 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2129325 ACCCTAAGTG
2129335 AAATGTATCGATACATGGGA
1 AAATGTATCGATACATGGGA
* * * *
2129355 CATTGTATCAATACATGGTA
1 AAATGTATCGATACATGGGA
2129375 AAATGTATCGATACAT
1 AAATGTATCGATACAT
2129391 TGTGCCTAAC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (20 bp):
AAATGTATCGATACATGGGA
Found at i:2129748 original size:13 final size:13
Alignment explanation
Indices: 2129730--2129754 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2129720 ACATAAGTGT
2129730 TGTATCGATACAA
1 TGTATCGATACAA
2129743 TGTATCGATACA
1 TGTATCGATACA
2129755 TACGTTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2129754 original size:32 final size:32
Alignment explanation
Indices: 2129709--2129781 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
2129699 ACAAACAGAA
* *
2129709 AATGTATCAATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTATATCGATAC
* *
2129741 AATGTATCGATACATACGTTTTATATCGATAC
1 AATGTATCGATACATAAGTGTTATATCGATAC
2129773 AATGTATCG
1 AATGTATCG
2129782 CTACGAAGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTATATCGATAC
Found at i:2129824 original size:21 final size:21
Alignment explanation
Indices: 2129798--2129840 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
2129788 AGCTACTGCC
2129798 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
2129819 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
2129840 A
1 A
2129841 TATCAATACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:2132266 original size:52 final size:52
Alignment explanation
Indices: 2132198--2132332 Score: 166
Period size: 52 Copynumber: 2.6 Consensus size: 52
2132188 GTTAAGTTTC
* *
2132198 CCAATTGTT-CATAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAATA
1 CCAATT-TTCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACA
* * *
2132249 CCAATTTTCCTTTAATCGGGGATACTCCGACTCCGATTTTATTTCCAAAAACA
1 CCAATTTTCC-ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACA
* * *
2132302 CCAATTTTTCACAATCGAGGATACTCCAACC
1 CCAATTTTCCATAATCGGGGATACTCCAACC
2132333 TCATTATTTC
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
50 2 0.03
51 7 0.10
52 47 0.67
53 14 0.20
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (52 bp):
CCAATTTTCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACA
Found at i:2132524 original size:52 final size:51
Alignment explanation
Indices: 2132343--2132566 Score: 227
Period size: 51 Copynumber: 4.4 Consensus size: 51
2132333 TCATTATTTC
** ** * ***
2132343 ATCGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGA-TTTCTCATA
1 ATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTC-CATA
* * *
2132394 ATCGGGGATACTCCAACCCCGGTTTTA-TTTCTAAAACACTAATTTTCCACA
1 ATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTTCCATA
*
2132445 ATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTA
1 ATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCC-ATA
* * * * *
2132497 ATCAGGGATACTCCAACTCCGATTTTATTTCCAAAGACACCAATTTTTCACA
1 ATCGGGGATACTCCAACCCCGATTTTATTTTCAAA-ACACCAATTTTCCATA
**
2132549 ATCCAGGATACTCCAACC
1 ATCGGGGATACTCCAACC
2132567 TCATTATTTC
Statistics
Matches: 148, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
50 2 0.01
51 77 0.52
52 57 0.39
53 12 0.08
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (51 bp):
ATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCATA
Found at i:2132711 original size:79 final size:79
Alignment explanation
Indices: 2132579--2132761 Score: 197
Period size: 79 Copynumber: 2.3 Consensus size: 79
2132569 ATTATTTCAT
* ** **
2132579 CGGGGATACTCTAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAAT-A
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAACTTTATTCCC-AAATCA
** * *
2132643 TTGATTTCTCATAAT
65 TCAATTTCTCACAAC
* * * * * * *
2132658 TGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAATCTCAATTTTATTTCCTAATCAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAACTTTATTCCCAAATCAT
*
2132723 CAATTTTTCACAAC
66 CAATTTCTCACAAC
2132737 CGGGGATACTCCAACCCCGTTATTT
1 CGGGGATACTCCAACCCCGTTATTT
2132762 TCAAGGAGAT
Statistics
Matches: 85, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
78 3 0.04
79 82 0.96
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.31
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCAACTTTATTCCCAAATCAT
CAATTTCTCACAAC
Found at i:2135518 original size:13 final size:13
Alignment explanation
Indices: 2135500--2135526 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2135490 ACATCTTGCT
2135500 TTGTATCGATACA
1 TTGTATCGATACA
2135513 TTGTATCGATACA
1 TTGTATCGATACA
2135526 T
1 T
2135527 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2135523 original size:33 final size:32
Alignment explanation
Indices: 2135481--2135545 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
2135471 CACACCCAAA
*
2135481 TGTATCGATACATCTTGCTTTGTATCGATACAT
1 TGTATCGATACATCTT-CATTGTATCGATACAT
*
2135514 TGTATCGATACATGTTCATTGTATCGATACAT
1 TGTATCGATACATCTTCATTGTATCGATACAT
2135546 GGACAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATCTTCATTGTATCGATACAT
Found at i:2135556 original size:20 final size:19
Alignment explanation
Indices: 2135510--2135566 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
2135500 TTGTATCGAT
*
2135510 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
2135529 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
2135548 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
2135567 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:2141664 original size:20 final size:19
Alignment explanation
Indices: 2141630--2141667 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2141620 AATTTTGATG
2141630 TTGTATGATTGAATTATGT
1 TTGTATGATTGAATTATGT
*
2141649 TTGTTTGATATGAATTATG
1 TTGTATGAT-TGAATTATG
2141668 GTTTATAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (19 bp):
TTGTATGATTGAATTATGT
Found at i:2141808 original size:13 final size:13
Alignment explanation
Indices: 2141790--2141816 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2141780 ACAACATTCC
2141790 TTGTATCGATACA
1 TTGTATCGATACA
2141803 TTGTATCGATACA
1 TTGTATCGATACA
2141816 T
1 T
2141817 AGGGTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2144080 original size:20 final size:20
Alignment explanation
Indices: 2144039--2144090 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2144029 CAGCTAAATT
*
2144039 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
2144058 TGTATCGATACATCACAAAA
1 TGTATCGATACATCACAAAA
2144078 TGTATCGATACAT
1 TGTATCGATACAT
2144091 TAACTAGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.39
20 19 0.61
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:2150392 original size:20 final size:20
Alignment explanation
Indices: 2150357--2150397 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
2150347 CAAATTTCTT
2150357 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
2150379 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
2150398 AACAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:2150692 original size:20 final size:21
Alignment explanation
Indices: 2150660--2150711 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
2150650 CTCCTAGGCA
*
2150660 GCACCCACCAGGTCGCGACC-G
1 GCACCC-CCAGGTCGCAACCAG
2150681 GCACCCCCAGGTCGCAACCAG
1 GCACCCCCAGGTCGCAACCAG
2150702 GCAGCCCCCA
1 GCA-CCCCCA
2150712 CACTAGCAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 12 0.43
21 10 0.36
22 6 0.21
ACGTcount: A:0.21, C:0.50, G:0.25, T:0.04
Consensus pattern (21 bp):
GCACCCCCAGGTCGCAACCAG
Found at i:2152114 original size:22 final size:21
Alignment explanation
Indices: 2152089--2152132 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2152079 CGAAATTGTC
*
2152089 AAATTATTTTACTAAGGGGGAG
1 AAATT-TTTGACTAAGGGGGAG
*
2152111 AAATTTTTGATTAAGGGGGAG
1 AAATTTTTGACTAAGGGGGAG
2152132 A
1 A
2152133 GAAAAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.36, C:0.02, G:0.30, T:0.32
Consensus pattern (21 bp):
AAATTTTTGACTAAGGGGGAG
Found at i:2152811 original size:13 final size:13
Alignment explanation
Indices: 2152793--2152818 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2152783 ACACACAATA
2152793 TGTATCGATACAT
1 TGTATCGATACAT
2152806 TGTATCGATACAT
1 TGTATCGATACAT
2152819 CACAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2152814 original size:32 final size:33
Alignment explanation
Indices: 2152773--2152840 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
2152763 GTAGCTAAAT
*
2152773 TTGTATCGATACA-CACAATATGTATCGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
*
2152805 TTGTATCGATACATCACAAAATGTATTGATACA
1 TTGTATCGATACATCACAAAATGTATCGATACA
2152838 TTG
1 TTG
2152841 ACTAGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACATCACAAAATGTATCGATACA
Found at i:2154199 original size:20 final size:20
Alignment explanation
Indices: 2154174--2154291 Score: 82
Period size: 20 Copynumber: 5.8 Consensus size: 20
2154164 GTATCGATGC
2154174 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
2154194 ATTGTATCGATACAT-GA-A
1 ATTGTATCGATACATGGACA
* * *
2154212 ATTGGTAGTAGCTACCCTAT-CACTA
1 ATT-GTA-TCGATA--C-ATGGAC-A
*
2154237 TTTGTATCGATACATGGTACA
1 ATTGTATCGATACATGG-ACA
* *
2154258 A-TGTATCGATACATGAAGA
1 ATTGTATCGATACATGGACA
*
2154277 AATGTATCGATACAT
1 ATTGTATCGATACAT
2154292 AGCTTGTAAC
Statistics
Matches: 78, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
18 4 0.05
19 8 0.10
20 48 0.62
21 2 0.03
22 3 0.04
23 7 0.09
24 3 0.04
25 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:2157086 original size:20 final size:20
Alignment explanation
Indices: 2157061--2157167 Score: 97
Period size: 20 Copynumber: 4.8 Consensus size: 20
2157051 TTTTTATAAT
2157061 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
2157081 TTGTATCGATACATTCTGGGTTTTACCCA
1 TTGTATCGATACA-T-T--G--TT---CA
* *
2157110 GATGTATCGATACATTGCTCA
1 -TTGTATCGATACATTGTTCA
*
2157131 TTGTATCGATACGTTGTTCA
1 TTGTATCGATACATTGTTCA
2157151 TTGTATCGATACATTGT
1 TTGTATCGATACATTGT
2157168 ATCGATACAT
Statistics
Matches: 71, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
20 46 0.65
21 3 0.04
22 1 0.01
24 2 0.03
26 3 0.04
28 1 0.01
29 3 0.04
30 12 0.17
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:2157165 original size:13 final size:13
Alignment explanation
Indices: 2157149--2157178 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2157139 ATACGTTGTT
2157149 CATTGTATCGATA
1 CATTGTATCGATA
2157162 CATTGTATCGATA
1 CATTGTATCGATA
2157175 CATT
1 CATT
2157179 CTGGGTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:2159698 original size:79 final size:79
Alignment explanation
Indices: 2159565--2159720 Score: 231
Period size: 79 Copynumber: 2.0 Consensus size: 79
2159555 TCATTCATGT
* * * *
2159565 TTTTATTTTTAAAACACCGATTTTCCACAATCGGGGATACTCAAACCCCGTTATTTTCGAGGGGA
1 TTTTATTTTCAAAACACCAATTTTCCACAATCGGGGATACTCAAACCCCATTATTTTCGAGAGGA
*
2159630 TACTCCAACCCCAG
66 TACTCAAACCCCAG
* * * *
2159644 TTTTATTTTCAAAACATCAATTTTTCACAATCGGGGATACTCCAACCTCATTATTTTCGAGAGGA
1 TTTTATTTTCAAAACACCAATTTTCCACAATCGGGGATACTCAAACCCCATTATTTTCGAGAGGA
2159709 TACTCAAACCCC
66 TACTCAAACCCC
2159721 GTTATTTCCG
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 68 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (79 bp):
TTTTATTTTCAAAACACCAATTTTCCACAATCGGGGATACTCAAACCCCATTATTTTCGAGAGGA
TACTCAAACCCCAG
Found at i:2159718 original size:28 final size:28
Alignment explanation
Indices: 2159678--2159747 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
2159668 TCACAATCGG
*
2159678 GGATACTCCAACCTCATTATTTTCGAGA
1 GGATACTCCAACCTCATTATTTCCGAGA
* * * *
2159706 GGATACTCAAACCCCGTTATTTCCGAGG
1 GGATACTCCAACCTCATTATTTCCGAGA
2159734 GGATACTCCAACCT
1 GGATACTCCAACCT
2159748 TGGTTTTGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (28 bp):
GGATACTCCAACCTCATTATTTCCGAGA
Found at i:2159733 original size:107 final size:106
Alignment explanation
Indices: 2159599--2159935 Score: 442
Period size: 107 Copynumber: 3.2 Consensus size: 106
2159589 CCACAATCGG
*
2159599 GGATACTCAAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTTCAAAACATCAA
1 GGATACTCAAACCCCGTTATTTCCGAGGGGATACTCCAACCCC-GTTTTATTTTCAAAACATCAA
* *
2159664 TTTTTCACAATCGGGGATACTCCAACCTCATTATTTTCGAGA
65 TTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGA
** * *
2159706 GGATACTCAAACCCCGTTATTTCCGAGGGGATACTCCAACCTTGGTTTTGTTTCCAAAACATCAA
1 GGATACTCAAACCCCGTTATTTCCGAGGGGATACTCCAACC-CCGTTTTATTTTCAAAACATCAA
* * *
2159771 TTTTTCACAACCAGGGATACTCCAACCCCGTTATTTTTGA-A
65 TTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGA
* ** * * *
2159812 GGGATACTCCAACCTTGTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTTCAAAATATCG
1 -GGATACTCAAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG-TTTTATTTTCAAAACATCA
* * * *
2159877 ATTTTCCACAATCGAGGATACTCCAACCCCGTTGTTTTCGAGG
64 ATTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGA
*
2159920 GGATACTCCAACCCCG
1 GGATACTCAAACCCCG
2159936 GTTTTATTTC
Statistics
Matches: 197, Mismatches: 29, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
106 2 0.01
107 195 0.99
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (106 bp):
GGATACTCAAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGTTTTATTTTCAAAACATCAAT
TTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGA
Found at i:2159823 original size:28 final size:27
Alignment explanation
Indices: 2159783--2159856 Score: 94
Period size: 28 Copynumber: 2.7 Consensus size: 27
2159773 TTTCACAACC
**
2159783 AGGGATACTCCAACCCCGTTATTTTTG
1 AGGGATACTCCAACCCCGTTATTTCCG
**
2159810 AAGGGATACTCCAACCTTGTTATTTCCG
1 -AGGGATACTCCAACCCCGTTATTTCCG
2159838 AGGAGATACTCCAACCCCG
1 AGG-GATACTCCAACCCCG
2159857 ATTTTATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 3 0.08
28 36 0.92
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (27 bp):
AGGGATACTCCAACCCCGTTATTTCCG
Found at i:2159896 original size:79 final size:79
Alignment explanation
Indices: 2159813--2159964 Score: 214
Period size: 79 Copynumber: 1.9 Consensus size: 79
2159803 ATTTTTGAAG
** * * * *
2159813 GGATACTCCAACCTTGTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTTCAAAATATCGA
1 GGATACTCCAACCCCGTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTCCAAAACACCAA
2159878 TTTTCCACAATCGA
66 TTTTCCACAATCGA
* * * *
2159892 GGATACTCCAACCCCGTTGTTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAA
1 GGATACTCCAACCCCGTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTCCAAAACACCAA
2159957 TTTTCCAC
66 TTTTCCAC
2159965 CATTGGGGAT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
79 63 1.00
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (79 bp):
GGATACTCCAACCCCGTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTCCAAAACACCAA
TTTTCCACAATCGA
Found at i:2159975 original size:79 final size:79
Alignment explanation
Indices: 2159812--2159980 Score: 212
Period size: 79 Copynumber: 2.1 Consensus size: 79
2159802 TATTTTTGAA
** * * * *
2159812 GGGATACTCCAACCTTGTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTTCAAAATATCG
1 GGGATACTCCAACCCCGTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTCCAAAACACCA
2159877 ATTTTCCACAATCG
66 ATTTTCCACAATCG
* * * * *
2159891 AGGATACTCCAACCCCGTTGTTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCA
1 GGGATACTCCAACCCCGTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTCCAAAACACCA
* *
2159956 ATTTTCCACCATTG
66 ATTTTCCACAATCG
*
2159970 GGGATATTCCA
1 GGGATACTCCA
2159981 GCCCTGATTT
Statistics
Matches: 75, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (79 bp):
GGGATACTCCAACCCCGTTATTTCCGAGGAGATACTCCAACCCCGATTTTATTTCCAAAACACCA
ATTTTCCACAATCG
Found at i:2159992 original size:51 final size:49
Alignment explanation
Indices: 2159918--2160097 Score: 162
Period size: 51 Copynumber: 3.6 Consensus size: 49
2159908 TTGTTTTCGA
* *
2159918 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACCATT
1 GGGGATACTCCAA-CCCGATTTTATTTCCAAAACA-CAATTTTCCACCATC
* * * * * *
2159969 GGGGATATTCCAGCCCTGATTTTATTTCCAGAACATCTATTTTTCACAATC
1 GGGGATACTCCAACCC-GATTTTATTTCCAAAACA-CAATTTTCCACCATC
* * *
2160020 AGGGATACTCCAACCCCAGTTTTATTTTCAAAACACAATTTTCCACCATC
1 GGGGATACTCCAACCCGA-TTTTATTTCCAAAACACAATTTTCCACCATC
** * * *
2160070 AAGGATTCTCCATCCTTGATTTTATTTC
1 GGGGATACTCCAACC-CGATTTTATTTC
2160098 TAGACAATCG
Statistics
Matches: 102, Mismatches: 24, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
50 36 0.35
51 66 0.65
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.34
Consensus pattern (49 bp):
GGGGATACTCCAACCCGATTTTATTTCCAAAACACAATTTTCCACCATC
Found at i:2160126 original size:101 final size:102
Alignment explanation
Indices: 2159918--2160137 Score: 277
Period size: 101 Copynumber: 2.2 Consensus size: 102
2159908 TTGTTTTCGA
* ***
2159918 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACCATTGGGGATATTCCAGC
1 GGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACCATCAAGGATATTCCAGC
* *
2159983 CCTGATTTTATTTCCAGAACATCTATTTTTCACAATC
66 CCTGATTTTATTTCCAGAACATCGATTTTCCACAATC
* * *
2160020 AGGGATACTCCAACCCCAGTTTTATTTTCAAAACA-CAATTTTCCACCATCAAGGAT-TCTCCAT
1 GGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACCATCAAGGATAT-TCCAG
* *
2160083 CCTTGATTTTATTTCTAG-ACAATCGATTTTCCA-ATATC
65 CCCTGATTTTATTTCCAGAAC-ATCGATTTTCCACA-ATC
*
2160121 GGGGATACTCTAACCCC
1 GGGGATACTCCAACCCC
2160138 GTTATTTTCG
Statistics
Matches: 102, Mismatches: 13, Indels: 7
0.84 0.11 0.06
Matches are distributed among these distances:
100 4 0.04
101 66 0.65
102 32 0.31
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (102 bp):
GGGGATACTCCAACCCCAGTTTTATTTCCAAAACACCAATTTTCCACCATCAAGGATATTCCAGC
CCTGATTTTATTTCCAGAACATCGATTTTCCACAATC
Found at i:2160189 original size:79 final size:78
Alignment explanation
Indices: 2160089--2160257 Score: 191
Period size: 79 Copynumber: 2.1 Consensus size: 78
2160079 CCATCCTTGA
* * * * *
2160089 TTTTATTTCTAGACAATCGATTTTCCA-ATATCGGGGATACTCTAACCCCGTTATTT-TCGAAGG
1 TTTTATTTCCAGACAACCGATTTTCCACA-ATCAGAGATACTCCAACCCCGTTATTTCT-GAAGG
2160152 GATACTCCAACCCCAG
64 GATACTCCAACCCC-G
* *
2160168 TTTTATTTCCAGA-ACACCGATTTTCCACAATCAGAGATACTCCAGCCCCGTTATTTCTGAGGGG
1 TTTTATTTCCAGACA-ACCGATTTTCCACAATCAGAGATACTCCAACCCCGTTATTTCTGAAGGG
*
2160232 CTACTCCAACCCCG
65 ATACTCCAACCCCG
*
2160246 TCTTTATCTCCA
1 T-TTTATTTCCA
2160258 AAATATTAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
78 3 0.04
79 72 0.94
80 2 0.03
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (78 bp):
TTTTATTTCCAGACAACCGATTTTCCACAATCAGAGATACTCCAACCCCGTTATTTCTGAAGGGA
TACTCCAACCCCG
Found at i:2166019 original size:70 final size:70
Alignment explanation
Indices: 2165945--2166162 Score: 315
Period size: 70 Copynumber: 3.2 Consensus size: 70
2165935 TTTTCACAAT
*
2165945 TTGTATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTTTTGATACATT
1 TTGTATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTATTGATACATT
*
2166010 GTTCG
66 GTTCA
* * *
2166015 TTGTATCGATACGTTGTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATAAATT
1 TTGTATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTATTGATACATT
2166080 GTTCA
66 GTTCA
*
2166085 TTGTATCGAT--A-----CATTGTATCGATACATTTTGGGTTTTACCCAGATGTATTGATACATT
1 TTGTATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTATTGATACATT
*
2166143 TTTCA
66 GTTCA
*
2166148 ATGTATCGATACATT
1 TTGTATCGATACATT
2166163 CAGGCATTTT
Statistics
Matches: 133, Mismatches: 11, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
63 57 0.43
65 1 0.01
70 75 0.56
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.43
Consensus pattern (70 bp):
TTGTATCGATACATTGTTCATTGTATCGATACATTCTGGGTTTTACCCAGATGTATTGATACATT
GTTCA
Found at i:2166031 original size:20 final size:20
Alignment explanation
Indices: 2166002--2166049 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
2165992 CAGATGTTTT
*
2166002 GATACATTGTTCGTTGTATC
1 GATACATTGTTCATTGTATC
*
2166022 GATACGTTGTTCATTGTATC
1 GATACATTGTTCATTGTATC
2166042 GATACATT
1 GATACATT
2166050 CTGGGTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.44
Consensus pattern (20 bp):
GATACATTGTTCATTGTATC
Found at i:2166101 original size:13 final size:13
Alignment explanation
Indices: 2166083--2166112 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
2166073 ATAAATTGTT
2166083 CATTGTATCGATA
1 CATTGTATCGATA
2166096 CATTGTATCGATA
1 CATTGTATCGATA
2166109 CATT
1 CATT
2166113 TTGGGTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:2166132 original size:63 final size:63
Alignment explanation
Indices: 2166033--2166162 Score: 215
Period size: 63 Copynumber: 2.1 Consensus size: 63
2166023 ATACGTTGTT
*
2166033 CATTGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATAAATTGTTCATTGTATCGATA
1 CATTGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATAAATTGTTCAATGTATCGATA
* * * *
2166096 CATTGTATCGATACATTTTGGGTTTTACCCAGATGTATTGATACATTTTTCAATGTATCGATA
1 CATTGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATAAATTGTTCAATGTATCGATA
2166159 CATT
1 CATT
2166163 CAGGCATTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (63 bp):
CATTGTATCGATACATTCTGGGTTTTACCCAGATGTATCGATAAATTGTTCAATGTATCGATA
Found at i:2168609 original size:79 final size:78
Alignment explanation
Indices: 2168498--2168644 Score: 204
Period size: 79 Copynumber: 1.9 Consensus size: 78
2168488 TCATTCATGT
* * * * *
2168498 TTTTATTTCTAAAACACCGATTTTCCATAATCGGGGATACTCAAACCCCGTTATTTTCGAGGGGA
1 TTTTATTTCCAAAACACCAATTTTACACAATCGGGGATACTCAAACCCCATT-TTTTCGAGGGGA
2168563 TACTTTAACCCCAG
65 TACTTTAACCCCAG
* * * *
2168577 TTTTGTTTCCAAAACATCAATTTTACACAATCGGGGATACTCCAACCCTATTTTTTCGAGGGGAT
1 TTTTATTTCCAAAACACCAATTTTACACAATCGGGGATACTCAAACCCCATTTTTTCGAGGGGAT
2168642 ACT
66 ACT
2168645 CCAACCCCGT
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
78 16 0.27
79 43 0.73
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (78 bp):
TTTTATTTCCAAAACACCAATTTTACACAATCGGGGATACTCAAACCCCATTTTTTCGAGGGGAT
ACTTTAACCCCAG
Found at i:2168640 original size:27 final size:28
Alignment explanation
Indices: 2168609--2168681 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
2168599 TTACACAATC
* * *
2168609 GGGGATACTCCAACCCTATT-TTTTCGA
1 GGGGATACTCCAACCCCATTACTTCCGA
*
2168636 GGGGATACTCCAACCCCGTTACTTCCGA
1 GGGGATACTCCAACCCCATTACTTCCGA
*
2168664 GGGGATACTCTAACCCCA
1 GGGGATACTCCAACCCCA
2168682 GTTTTGTTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 18 0.46
28 21 0.54
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.25
Consensus pattern (28 bp):
GGGGATACTCCAACCCCATTACTTCCGA
Found at i:2168757 original size:28 final size:28
Alignment explanation
Indices: 2168718--2168788 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
2168708 CACAACCGAG
*
2168718 GATACTCCAACCTCGTTATTTTTGAGGA
1 GATACTCCAACCTCGTTATTTTCGAGGA
* *
2168746 GATACTCTAACC-CTGTTATTTTCGAGGG
1 GATACTCCAACCTC-GTTATTTTCGAGGA
*
2168774 GATACCCCAACCTCG
1 GATACTCCAACCTCG
2168789 GTTTTATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.03
28 34 0.94
29 1 0.03
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (28 bp):
GATACTCCAACCTCGTTATTTTCGAGGA
Found at i:2168812 original size:107 final size:106
Alignment explanation
Indices: 2168530--2168867 Score: 455
Period size: 107 Copynumber: 3.2 Consensus size: 106
2168520 TTCCATAATC
* *
2168530 GGGGATACTCAAACCCCGTTATTTTCGAGGGGATACTTTAACCCCAGTTTTGTTTCCAAAACATC
1 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAACCCCAGTTTTGTTTCCAAAACATC
2168595 AATTTTACACAATCGGGGATACTCCAACCC--TATTTTTTCGA
66 AATTTTACACAATCGGGGATACTCCAACCCGTTA-TTTTT-GA
* *
2168636 GGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCTAACCCCAGTTTTGTTTCCAAAACATC
1 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAACCCCAGTTTTGTTTCCAAAACATC
* * *
2168701 AATTTTTCACAACCGAGGATACTCCAACCTCGTTATTTTTGA
66 AATTTTACACAATCGGGGATACTCCAACC-CGTTATTTTTGA
* * * * * * * * *
2168743 GGAGATACTCTAACCCTGTTATTTTCGAGGGGATACCCCAACCTCGGTTTTATTTTCAAAACATC
1 GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAACCCCAGTTTTGTTTCCAAAACATC
* **
2168808 AATTTTCCACAATCGGGGATACTCCAACCCTGTTATTTCCGA
66 AATTTTACACAATCGGGGATACTCCAACCC-GTTATTTTTGA
2168850 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
2168868 ATTTTATTTT
Statistics
Matches: 202, Mismatches: 26, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
106 88 0.44
107 107 0.53
108 5 0.02
109 2 0.01
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (106 bp):
GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCTAACCCCAGTTTTGTTTCCAAAACATC
AATTTTACACAATCGGGGATACTCCAACCCGTTATTTTTGA
Found at i:2168873 original size:79 final size:79
Alignment explanation
Indices: 2168746--2168997 Score: 342
Period size: 79 Copynumber: 3.2 Consensus size: 79
2168736 TTTTTGAGGA
* * *
2168746 GATACTCTAACCCTGTTATTTTCGAGGGGATACCCCAACCTCGGTTTTATTTTCAAAACATCAAT
1 GATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTTCAAAACATCAAT
2168811 TTTCCACAATCGGG
66 TTTCCACAATCGGG
* * * * *
2168825 GATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAACCCCGATTTTATTTTTAAAATATCGAT
1 GATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTTCAAAACATCAAT
*
2168890 TTTCCACAATCGAG
66 TTTCCACAATCGGG
* * * * * *
2168904 AATACTACAACCCCGTTGTTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAAT
1 GATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTTCAAAACATCAAT
* *
2168969 TTTCCACCATTGGG
66 TTTCCACAATCGGG
*
2168983 GGTACTCCAACCCTG
1 GATACTCCAACCCTG
2168998 ACTTTATTTC
Statistics
Matches: 146, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
79 146 1.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (79 bp):
GATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTTCAAAACATCAAT
TTTCCACAATCGGG
Found at i:2168994 original size:51 final size:51
Alignment explanation
Indices: 2168929--2169047 Score: 157
Period size: 51 Copynumber: 2.3 Consensus size: 51
2168919 TTGTTTTCGA
** * *
2168929 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACCATT
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTTTCCACAATC
* * * * *
2168980 GGGGGTACTCCAACCCTGACTTTATTTCCAGAACATCGATTTTCCACAATC
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTTTCCACAATC
2169031 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
2169048 ATTATTTTTG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:2169174 original size:129 final size:130
Alignment explanation
Indices: 2168852--2169254 Score: 522
Period size: 130 Copynumber: 3.1 Consensus size: 130
2168842 ATTTCCGAGG
* ** *
2168852 GGATACTCCAACCCCGATTTTATTTTTAAAATATCGATTTTCCACAATC-GAGAATACTACAACC
1 GGATACTCCAACCCTGATTTTATTTCCAAAACATCGATTTTCCACAATCGGAG-ATACTACAACC
* * **
2168916 CCGTTGTTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACCATTG
65 CCATTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACCATCA
*
2168981 G
130 A
* * * * *
2168982 GGGTACTCCAACCCTGACTTTATTTCCAGAACATCGATTTTCCACAATCGGGGATACTCCAACCC
1 GGATACTCCAACCCTGATTTTATTTCCAAAACATCGATTTTCCACAATCGGAGATACTACAACCC
* *
2169047 CATTATTTTTGAGGGGATACTCCAACCCCGGTTTTATTTTCAAAACA-CAATTTTCCACCATCAA
66 CATTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACCATCAA
* * * * *
2169111 GGATACTTCATCCCTGATTTTATTTCCAAAACATCGATTTTTCACAATCGGAGACACTACAACCT
1 GGATACTCCAACCCTGATTTTATTTCCAAAACATCGATTTTCCACAATCGGAGATACTACAACCC
* * * ** ** *
2169176 CATTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCTAGAACACTGATTTTCCATAATCGA
66 CATTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACCATCAA
2169241 GGATACTCCAACCC
1 GGATACTCCAACCC
2169255 CGTTATTTCT
Statistics
Matches: 233, Mismatches: 38, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
129 111 0.48
130 120 0.52
131 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (130 bp):
GGATACTCCAACCCTGATTTTATTTCCAAAACATCGATTTTCCACAATCGGAGATACTACAACCC
CATTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACACCAATTTTCCACCATCAA
Found at i:2169215 original size:79 final size:78
Alignment explanation
Indices: 2169128--2169299 Score: 179
Period size: 79 Copynumber: 2.2 Consensus size: 78
2169118 TCATCCCTGA
* *
2169128 TTTTATTTCCAAAACA-TCGATTTTTCACAATCG-GAGACACTACAACCTCATTATTT-TCGAGG
1 TTTTATTTCCAAAACACT-GATTTTCCACAATCGAG-GACACTACAACCCCATTATTTCT-GAGG
*
2169190 GGATACTCCAACCCCAG
63 CGATACTCCAACCCC-G
* * * * * * *
2169207 TTTTATTTCTAGAACACTGATTTTCCATAATCGAGGATACTCCAACCCCGTTATTTCTGAGGCGC
1 TTTTATTTCCAAAACACTGATTTTCCACAATCGAGGACACTACAACCCCATTATTTCTGAGGCGA
2169272 TACTCCAACCCCG
66 TACTCCAACCCCG
*
2169285 TCTTTATCTCCAAAA
1 T-TTTATTTCCAAAA
2169300 TATTAAAATT
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
78 2 0.03
79 71 0.93
80 3 0.04
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (78 bp):
TTTTATTTCCAAAACACTGATTTTCCACAATCGAGGACACTACAACCCCATTATTTCTGAGGCGA
TACTCCAACCCCG
Found at i:2173014 original size:77 final size:78
Alignment explanation
Indices: 2172912--2173116 Score: 229
Period size: 77 Copynumber: 2.6 Consensus size: 78
2172902 GAGATAATAA
* * * * * *
2172912 CGGGGTTGGAGTGTTCCCTTGAAAATAACGAGGCTGGAGTATCCCCGATTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
2172977 -TT-AGAAAAAAAT
65 TTTGAGAAAAAAAC
* * *
2172989 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* * *
2173054 TTTGGGAATAAAGC
65 TTTGAGAAAAAAAC
2173068 CGGGGTTGGAGTATCCCCTC-AGAAATAAC-AGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGA-AAATAACGA-GGTTGGAGTATCCCCGAT
2173117 GATTAACGGG
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
76 1 0.01
77 54 0.50
78 3 0.03
79 49 0.46
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTGAGAAAAAAAC
Found at i:2173025 original size:28 final size:29
Alignment explanation
Indices: 2172980--2173034 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
2172970 TCGATGATTA
2172980 GAAAAAAATCGGGATTGGAGTATCCCCTC
1 GAAAAAAATCGGGATTGGAGTATCCCCTC
* *
2173009 GAAAATAA-CGGGGTTGGAGTATCCCC
1 GAAAAAAATCGGGATTGGAGTATCCCC
2173035 AATTATGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (29 bp):
GAAAAAAATCGGGATTGGAGTATCCCCTC
Found at i:2173131 original size:27 final size:28
Alignment explanation
Indices: 2173068--2173143 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
2173058 GGAATAAAGC
*
2173068 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
* *
2173096 CAGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
2173123 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
2173144 TGTGAAGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 25 0.58
28 18 0.42
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:2173230 original size:51 final size:51
Alignment explanation
Indices: 2173162--2173260 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
2173152 AATTGGTATT
* * *
2173162 TTTTGGAAATAAAATCGGAGTTGGAGTATCCTCGATTATAGAAAATTAGTG
1 TTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTATAGAAAATTAGTG
* *
2173213 TTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTATGGAGAATTA
1 TTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTATAGAAAATTA
2173261 AGAAACTCAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.32
Consensus pattern (51 bp):
TTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTATAGAAAATTAGTG
Found at i:2175622 original size:13 final size:13
Alignment explanation
Indices: 2175604--2175629 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2175594 ACAAAGATCC
2175604 ATGTATCGATACA
1 ATGTATCGATACA
2175617 ATGTATCGATACA
1 ATGTATCGATACA
2175630 CAAAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2175694 original size:19 final size:18
Alignment explanation
Indices: 2175670--2175736 Score: 81
Period size: 19 Copynumber: 3.9 Consensus size: 18
2175660 AGTAGCTAAA
2175670 TATGTATCGATACAATACT
1 TATGTATCGATACAA-ACT
2175689 TATGTATCGATAC--A--
1 TATGTATCGATACAAACT
2175703 T-TGTATCGATACAAAACT
1 TATGTATCGATAC-AAACT
2175721 TATGTATCGATACAAA
1 TATGTATCGATACAAA
2175737 TCGTTGAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.57
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (18 bp):
TATGTATCGATACAAACT
Found at i:2175709 original size:13 final size:13
Alignment explanation
Indices: 2175691--2175715 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2175681 ACAATACTTA
2175691 TGTATCGATACAT
1 TGTATCGATACAT
2175704 TGTATCGATACA
1 TGTATCGATACA
2175716 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2175713 original size:32 final size:32
Alignment explanation
Indices: 2175672--2175734 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2175662 TAGCTAAATA
*
2175672 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2175704 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2175735 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2176629 original size:55 final size:54
Alignment explanation
Indices: 2176534--2178355 Score: 1856
Period size: 55 Copynumber: 32.0 Consensus size: 54
2176524 ATAAAGTGTA
* * * *
2176534 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
2176589 TCTTACTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* * * * **
2176644 TCCTACTCTTTAAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGATG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
2176699 TCCTGCTCTTTGGGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGGG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
2176754 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
* * *
2176815 TCCTGCTTTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTG
1 TCCTGCTCTTTGAGGACTG-AAAGTGCCACCAACTTGTGTGGGCTTT-----G--AAAGGCG
2176877 TCCTGCTCTTTGAGGACTGGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGG-G
1 TCCTGCTCTTTGAGGACT-G-AAAGTGCCACCAACTTGTGTGGGCTTTG-AAAGGCG
* * *
2176933 TCTTGCTCTTTGGGGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTG-AAAGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
* * *
2176994 TCTTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
* * * *
2177053 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGAAAATGTG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
* ** *
2177112 TCCCGCTCTTTGAGGACTGAGGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* * *
2177166 TCCTGCTCTCTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
2177221 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
2177276 TCCTGCTCTTTAAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
* *
2177336 TCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
2177391 TCCTGCTCTTTGAGGCCTGAGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGAGGGG
1 TCCTGCTCTTTGAGGACTGA-AAGTGCCACCAACTTGTGTGGGCTTTGAAAGGC-----G
* * * *
2177451 TCCTGCTCTTTGGGGACTGGAAAATGCCACCAACTTGTGTGGCCTTTGAAGAAAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT---G--AAAGGCG
* *
2177511 TCCTGCTCTTTGGGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAGAGAAGAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT----G-A-AAGGCG
* * * **
2177572 TCCTGCTCTTTAAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGTA
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
2177627 TCCTGCTCTTTGAGGATTAGGAAGTGCCACCAACTTGGGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAA-AGGCG
* * *
2177682 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
2177737 TCCTGCTCTTTG-GGAACTGAAAGGTGCTACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGG-ACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
2177792 TCCGGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
2177847 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGGG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
2177902 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
*
2177963 TCCTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTT----G-AAAGGCG
* * *
2178022 TCCCGCTCTTTGAGGACTGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
2178076 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
2178131 TCCTGCTCTTTGAGGACTGGAGGATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAG-TGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCG
* * * * *
2178192 CCCTGCTCTTTGAGGACTGAAGGTGCCACCAACTTGGGTGGGCTTTAAAAGGCA
1 TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
2178246 TCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
2178301 TCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
2178356 AAGGCGTCCT
Statistics
Matches: 1559, Mismatches: 128, Indels: 160
0.84 0.07 0.09
Matches are distributed among these distances:
53 2 0.00
54 92 0.06
55 829 0.53
56 42 0.03
57 6 0.00
58 1 0.00
59 143 0.09
60 214 0.14
61 157 0.10
62 21 0.01
63 28 0.02
64 12 0.01
65 6 0.00
66 1 0.00
67 5 0.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:2176751 original size:29 final size:29
Alignment explanation
Indices: 2176718--2176804 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
2176708 TTGGGGACTA
2176718 AAAGGTGCCACCAACTTGTGTGGGCTTTG
1 AAAGGTGCCACCAACTTGTGTGGGCTTTG
* ** *
2176747 AAAGGGGTCCTGC-TCTT-TG-GGGAC--TG
1 AAAGGTG-CCACCAACTTGTGTGGG-CTTTG
2176773 AAAGGTGCCACCAACTTGTGTGGGCTTTG
1 AAAGGTGCCACCAACTTGTGTGGGCTTTG
2176802 AAA
1 AAA
2176805 AGAAAAAGCA
Statistics
Matches: 43, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
25 3 0.07
26 11 0.26
27 6 0.14
28 6 0.14
29 14 0.33
30 3 0.07
ACGTcount: A:0.22, C:0.20, G:0.32, T:0.26
Consensus pattern (29 bp):
AAAGGTGCCACCAACTTGTGTGGGCTTTG
Found at i:2176928 original size:29 final size:29
Alignment explanation
Indices: 2176896--2176985 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
2176886 TTGAGGACTG
2176896 GAAAAGTGCCACCAACTTGTGTGGGCTTT
1 GAAAAGTGCCACCAACTTGTGTGGGCTTT
* *** *
2176925 GAAAAGGGTCTTGC-TCTT-TG-GGGAC--T
1 GAAAAGTG-CCACCAACTTGTGTGGG-CTTT
2176951 GAAAAGTGCCACCAACTTGTGTGGGCTTT
1 GAAAAGTGCCACCAACTTGTGTGGGCTTT
2176980 GAAAAG
1 GAAAAG
2176986 AAAAAGCATC
Statistics
Matches: 44, Mismatches: 10, Indels: 14
0.65 0.15 0.21
Matches are distributed among these distances:
25 2 0.05
26 11 0.25
27 6 0.14
28 6 0.14
29 17 0.39
30 2 0.05
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.27
Consensus pattern (29 bp):
GAAAAGTGCCACCAACTTGTGTGGGCTTT
Found at i:2177869 original size:26 final size:26
Alignment explanation
Indices: 2177840--2177927 Score: 81
Period size: 26 Copynumber: 3.3 Consensus size: 26
2177830 GTGGGCTTTA
2177840 AAAGGTGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
** *
2177866 AAAGGTG-CCACCAACTTGTGTGGG-CTTTG
1 AAAGGTGTCCTGC-TCTT-TG-GGGAC--TG
*
2177895 AAAGGGGTCCTGCTCTTTGGGGACTG
1 AAAGGTGTCCTGCTCTTTGGGGACTG
2177921 AAAGGTG
1 AAAGGTG
2177928 CCACCAACTT
Statistics
Matches: 47, Mismatches: 8, Indels: 14
0.68 0.12 0.20
Matches are distributed among these distances:
25 3 0.06
26 18 0.38
27 6 0.13
28 6 0.13
29 11 0.23
30 3 0.06
ACGTcount: A:0.19, C:0.18, G:0.35, T:0.27
Consensus pattern (26 bp):
AAAGGTGTCCTGCTCTTTGGGGACTG
Found at i:2178323 original size:27 final size:27
Alignment explanation
Indices: 2178239--2178323 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
2178229 GTGGGCTTTA
2178239 AAAGGCATCCTGCTCTTTGAGGATTGG
1 AAAGGCATCCTGCTCTTTGAGGATTGG
* ** * *
2178266 AAAATGCCA-CCAACT-TGTGTG-GGCTTTG
1 -AAA-GGCATCCTGCTCT-T-TGAGGATTGG
2178294 AAAGGCATCCTGCTCTTTGAGGATTGG
1 AAAGGCATCCTGCTCTTTGAGGATTGG
2178321 AAA
1 AAA
2178324 ATGCCACCAA
Statistics
Matches: 41, Mismatches: 10, Indels: 13
0.64 0.16 0.20
Matches are distributed among these distances:
26 5 0.12
27 17 0.41
28 14 0.34
29 5 0.12
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (27 bp):
AAAGGCATCCTGCTCTTTGAGGATTGG
Found at i:2184598 original size:28 final size:29
Alignment explanation
Indices: 2184553--2184607 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
2184543 TCGATGATTA
2184553 GAAAAAAATCGGGATTGGAGTATCCCCTC
1 GAAAAAAATCGGGATTGGAGTATCCCCTC
* *
2184582 GAAAATAA-CGGGGTTGGAGTATCCCC
1 GAAAAAAATCGGGATTGGAGTATCCCC
2184608 AATTATGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (29 bp):
GAAAAAAATCGGGATTGGAGTATCCCCTC
Found at i:2184600 original size:77 final size:78
Alignment explanation
Indices: 2184485--2184689 Score: 225
Period size: 77 Copynumber: 2.6 Consensus size: 78
2184475 GAGATAATAA
* * * ** * * *
2184485 CGGGGTTGGAGTGTTCCCTTGAAAATAACGAGACTGGAGTATCCCCGGTTTTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTATGAGAAATCAAT-A
*
2184550 -TT-AGAAAAAAAT
65 TTTGAGAAAAAAAC
* * *
2184562 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTATGAGAAATCAATA-
* * *
2184627 TTTGGGAATAAAGC
65 TTTGAGAAAAAAAC
* *
2184641 CGGGGTTGGAGTATCCCCTCGGAAATAACAAGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGAT
2184690 GATTAACGGG
Statistics
Matches: 105, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
76 1 0.01
77 52 0.50
78 2 0.02
79 50 0.48
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGAGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
TTGAGAAAAAAAC
Found at i:2190373 original size:19 final size:20
Alignment explanation
Indices: 2190331--2190376 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
2190321 AGATGTTTTG
* *
2190331 ATACATTGTTCATTGTATCG
1 ATACATTGTTCACTGTATCA
*
2190351 ATACGTTGTTCACT-TATCA
1 ATACATTGTTCACTGTATCA
2190370 ATACATT
1 ATACATT
2190377 ATATCGATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.43
Consensus pattern (20 bp):
ATACATTGTTCACTGTATCA
Found at i:2196500 original size:16 final size:16
Alignment explanation
Indices: 2196479--2196515 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
2196469 TTTAATTATT
2196479 TTATTAAGGGGGAGAA
1 TTATTAAGGGGGAGAA
*
2196495 TTATTAAGGGGGAGAT
1 TTATTAAGGGGGAGAA
2196511 TTATT
1 TTATT
2196516 GAAAATTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (16 bp):
TTATTAAGGGGGAGAA
Found at i:2197181 original size:19 final size:19
Alignment explanation
Indices: 2197143--2197196 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
2197133 GTATCCATAT
* *
2197143 ATTGTATCGATATATGCTC
1 ATTGTATCGATACATACTC
*
2197162 ATTGTATCTATACATACTC
1 ATTGTATCGATACATACTC
* *
2197181 AATTGCATTGATACAT
1 -ATTGTATCGATACAT
2197197 GAGACTGGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (19 bp):
ATTGTATCGATACATACTC
Found at i:2197260 original size:13 final size:13
Alignment explanation
Indices: 2197242--2197271 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2197232 GATACATGGG
*
2197242 ACATTGTATCTAT
1 ACATTGTATCGAT
2197255 ACATTGTATCGAT
1 ACATTGTATCGAT
2197268 ACAT
1 ACAT
2197272 GGTAAAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:2197269 original size:33 final size:33
Alignment explanation
Indices: 2197226--2197294 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
2197216 CTAAGTAAAA
* * * *
2197226 TGTATGGATACATGGGACATTGTATCTATACAT
1 TGTATCGATACATGGGAAAATGTATCGATACAT
*
2197259 TGTATCGATACATGGTAAAATGTATCGATACAT
1 TGTATCGATACATGGGAAAATGTATCGATACAT
2197292 TGT
1 TGT
2197295 GCCCAACGGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATGGGAAAATGTATCGATACAT
Found at i:2198216 original size:21 final size:21
Alignment explanation
Indices: 2198192--2198232 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2198182 TATCAGTAAG
*
2198192 TTAATATAAAATTTTTAACAC
1 TTAACATAAAATTTTTAACAC
2198213 TTAACATAAAATTTTTAACA
1 TTAACATAAAATTTTTAACA
2198233 TTGTTATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAACATAAAATTTTTAACAC
Found at i:2199280 original size:22 final size:21
Alignment explanation
Indices: 2199245--2199286 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
2199235 AAAAATGATA
*
2199245 CATAATTTTATTATAATAATT
1 CATAATTATATTATAATAATT
2199266 CATACATTATATTATAATAAT
1 CATA-ATTATATTATAATAAT
2199287 ATGGTATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (21 bp):
CATAATTATATTATAATAATT
Found at i:2201242 original size:2 final size:2
Alignment explanation
Indices: 2201235--2201274 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2201225 CATGTCATGC
* *
2201235 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2201275 TTATGCATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2204321 original size:3 final size:3
Alignment explanation
Indices: 2204313--2204339 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2204303 GGAAGGATAG
2204313 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
2204340 ACAAGCACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2204636 original size:12 final size:12
Alignment explanation
Indices: 2204619--2204645 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2204609 TTTTTTAGTT
2204619 AAAAAATAAAAA
1 AAAAAATAAAAA
2204631 AAAAAATAAAAA
1 AAAAAATAAAAA
2204643 AAA
1 AAA
2204646 TTTAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAAAATAAAAA
Found at i:2204689 original size:23 final size:24
Alignment explanation
Indices: 2204662--2204726 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 24
2204652 AATTCGTATT
2204662 TTTATTATTTTTATAT-TTAA-AA
1 TTTATTATTTTTATATATTAATAA
2204684 TATTA-TATTTTTATATATTAATAA
1 T-TTATTATTTTTATATATTAATAA
*
2204708 TTTATTTTATTTTATATAT
1 TTTATTAT-TTTTATATAT
2204727 ATTTATATGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 12 0.32
23 10 0.27
24 5 0.14
25 10 0.27
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTATTATTTTTATATATTAATAA
Found at i:2204711 original size:31 final size:30
Alignment explanation
Indices: 2204644--2204711 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
2204634 AAATAAAAAA
* **
2204644 AATTTAAAAATTCGTATTTTTATTATTTTT
1 AATTTAAAAATTCATATTTTTATTATTAAT
2204674 ATATTTAAAATATT-ATATTTTTATATATTAAT
1 A-ATTTAAAA-ATTCATATTTTTAT-TATTAAT
2204706 AATTTA
1 AATTTA
2204712 TTTTATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
30 1 0.03
31 22 0.69
32 9 0.28
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (30 bp):
AATTTAAAAATTCATATTTTTATTATTAAT
Found at i:2204763 original size:3 final size:3
Alignment explanation
Indices: 2204755--2204826 Score: 53
Period size: 3 Copynumber: 23.3 Consensus size: 3
2204745 GTATTATGTG
*
2204755 TTA TTA TTA TTA TTG TT- TT- TTA TTA TCTA TTTA TT- TATA TCTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA T-TA T-TA TTA
2204800 TTTA TTA TTA TTA TTA TTA TTTA TTA T
1 -TTA TTA TTA TTA TTA TTA -TTA TTA T
2204827 CTATCTATCT
Statistics
Matches: 59, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
2 7 0.12
3 39 0.66
4 12 0.20
5 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2204803 original size:16 final size:17
Alignment explanation
Indices: 2204773--2204830 Score: 65
Period size: 16 Copynumber: 3.7 Consensus size: 17
2204763 ATTATTGTTT
2204773 TTTATTATC--TATTTA
1 TTTATTATCTATATTTA
2204788 TTTA-TATCTATATTTA
1 TTTATTATCTATATTTA
2204804 -TTATTAT-TAT-TATTA
1 TTTATTATCTATAT-TTA
2204819 TTTATTATCTAT
1 TTTATTATCTAT
2204831 CTATCTGTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 5 0.14
15 13 0.35
16 16 0.43
17 3 0.08
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTATTATCTATATTTA
Found at i:2205294 original size:2 final size:2
Alignment explanation
Indices: 2205287--2205313 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2205277 CATATAGATT
2205287 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 T
2205314 GCAAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2205920 original size:23 final size:23
Alignment explanation
Indices: 2205893--2205937 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2205883 AAAATTTACA
**
2205893 TATTTATGTTTTTTATTATTTAT
1 TATTTATAATTTTTATTATTTAT
2205916 TATTTATAATTTTTATTATTTA
1 TATTTATAATTTTTATTATTTA
2205938 AAATATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (23 bp):
TATTTATAATTTTTATTATTTAT
Found at i:2205996 original size:11 final size:11
Alignment explanation
Indices: 2205980--2206062 Score: 78
Period size: 11 Copynumber: 7.3 Consensus size: 11
2205970 AATTTTATGT
2205980 TTTTATATTTA
1 TTTTATATTTA
2205991 TTTTATATTTA
1 TTTTATATTTA
2206002 TTTTATATTTTA
1 TTTTATA-TTTA
*
2206014 TTTTA-ATTAA
1 TTTTATATTTA
*
2206024 TTTTAAATATTA
1 TTTTATAT-TTA
*
2206036 TATATATATGTTA
1 T-TTTATAT-TTA
* *
2206049 TTTTTTATATA
1 TTTTATATTTA
2206060 TTT
1 TTT
2206063 AAAATATTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
10 8 0.13
11 26 0.43
12 17 0.28
13 9 0.15
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (11 bp):
TTTTATATTTA
Found at i:2206130 original size:24 final size:26
Alignment explanation
Indices: 2206096--2206151 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
2206086 TTTGTACATA
*
2206096 TTAAT-TATTTATTTA-T-ATATTTT
1 TTAATATATTTATATATTCATATTTT
2206119 TTAATATATTTATATATTCATATTTT
1 TTAATATATTTATATATTCATATTTT
*
2206145 TTTATAT
1 TTAATAT
2206152 TATGTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 5 0.18
24 9 0.32
25 1 0.04
26 13 0.46
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (26 bp):
TTAATATATTTATATATTCATATTTT
Found at i:2207109 original size:13 final size:13
Alignment explanation
Indices: 2207091--2207115 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2207081 AAAAACTTCA
2207091 TATTTTTTATTTG
1 TATTTTTTATTTG
2207104 TATTTTTTATTT
1 TATTTTTTATTT
2207116 TTTAATTTTA
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:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (13 bp):
TATTTTTTATTTG
Found at i:2207130 original size:19 final size:20
Alignment explanation
Indices: 2207108--2207151 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
2207098 TATTTGTATT
* *
2207108 TTTTATTTTTTAATTTTA-A
1 TTTTATTTTTAAATTATATA
2207127 TTTTATTTTTAAATTATATA
1 TTTTATTTTTAAATTATATA
2207147 TTTTA
1 TTTTA
2207152 ATGTTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTATTTTTAAATTATATA
Found at i:2207131 original size:32 final size:32
Alignment explanation
Indices: 2207095--2207161 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
2207085 ACTTCATATT
** * * *
2207095 TTTTATTTGTATTTTTTATTTTTTAATTTTAA
1 TTTTATTTGTAAATTATATATTTTAATGTTAA
*
2207127 TTTTATTTTTAAATTATATATTTTAATGTTAA
1 TTTTATTTGTAAATTATATATTTTAATGTTAA
2207159 TTT
1 TTT
2207162 GCATTGTCGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (32 bp):
TTTTATTTGTAAATTATATATTTTAATGTTAA
Found at i:2207252 original size:13 final size:13
Alignment explanation
Indices: 2207231--2207279 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 13
2207221 TTTTTAGTCT
2207231 TTTATATTTTAAA
1 TTTATATTTTAAA
* *
2207244 TTTAGA-TTTAAT
1 TTTATATTTTAAA
*
2207256 TTTA-ATTTTTAA
1 TTTATATTTTAAA
2207268 TTT-TATTTTAAA
1 TTTATATTTTAAA
2207280 ATAATGTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
11 1 0.03
12 23 0.79
13 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (13 bp):
TTTATATTTTAAA
Found at i:2207257 original size:18 final size:17
Alignment explanation
Indices: 2207231--2207279 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
2207221 TTTTTAGTCT
2207231 TTTATATTTTAAATTTAGA
1 TTTA-ATTTTAAATTTA-A
*
2207250 TTTAATTTTAATTTTTAA
1 TTTAATTTTAA-ATTTAA
*
2207268 TTTTATTTTAAA
1 TTTAATTTTAAA
2207280 ATAATGTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTAATTTTAAATTTAA
Found at i:2208066 original size:19 final size:18
Alignment explanation
Indices: 2208021--2208075 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
2208011 AATTAAAAAA
*
2208021 TAAATACTAATTAATTTTT
1 TAAATA-TAATAAATTTTT
**
2208040 TATTTATAATAAATTTTT
1 TAAATATAATAAATTTTT
*
2208058 TTAA-AT-ATAAATTTTT
1 TAAATATAATAAATTTTT
2208074 TA
1 TA
2208076 TTCATTGCAC
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
16 11 0.38
17 2 0.07
18 12 0.41
19 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TAAATATAATAAATTTTT
Found at i:2210838 original size:3 final size:3
Alignment explanation
Indices: 2210823--2210854 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2210813 AACCATCAAA
*
2210823 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
2210855 AGTTGATTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (3 bp):
GAT
Found at i:2217257 original size:24 final size:24
Alignment explanation
Indices: 2217230--2217282 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2217220 AATTTTTTTT
* *
2217230 GAAAATAAATTTGAAAGAGGGGGA
1 GAAAATAAATTTGAAAAAAGGGGA
2217254 GAAAATAAATTTGAAAAAAGGGGA
1 GAAAATAAATTTGAAAAAAGGGGA
2217278 -AAAAT
1 GAAAAT
2217283 TTTTTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.57, C:0.00, G:0.26, T:0.17
Consensus pattern (24 bp):
GAAAATAAATTTGAAAAAAGGGGA
Found at i:2218105 original size:13 final size:13
Alignment explanation
Indices: 2218087--2218117 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2218077 TGATACATGG
*
2218087 TACATTGTATCGA
1 TACATTATATCGA
2218100 TACATTATATCGA
1 TACATTATATCGA
2218113 TACAT
1 TACAT
2218118 AGTGAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (13 bp):
TACATTATATCGA
Found at i:2222479 original size:21 final size:22
Alignment explanation
Indices: 2222455--2222506 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
2222445 CAATATCAAT
*
2222455 AAATGTTTTAGAG-TTATGAA-C
1 AAATGTTTTAGAGCTT-TAAATC
*
2222476 AAATGTTTTCGAGCTTTAAATC
1 AAATGTTTTAGAGCTTTAAATC
2222498 AAATGTTTT
1 AAATGTTTT
2222507 TAACTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (22 bp):
AAATGTTTTAGAGCTTTAAATC
Found at i:2224360 original size:15 final size:15
Alignment explanation
Indices: 2224340--2224374 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2224330 AACTATCAAA
2224340 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
2224355 GATGATGAGGATAAT
1 GATGATGAAGATAAT
2224370 GATGA
1 GATGA
2224375 AGTTGACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.31, T:0.26
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:2232111 original size:19 final size:19
Alignment explanation
Indices: 2232086--2232142 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
2232076 TTGTATCGAA
*
2232086 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGC
* *
2232105 TCATTGTATCGATACATAC
1 ACATTGTATCGATACATGC
2232124 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
2232143 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:2232231 original size:33 final size:33
Alignment explanation
Indices: 2232172--2232236 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
2232162 TACCACTGTT
*
2232172 TGTATCGATACATGGCACAATATATCGATACAA
1 TGTATCGATACATGGAACAATATATCGATACAA
* *
2232205 TGTATCGATACAT-GAAGAATTGTATCGATACA
1 TGTATCGATACATGGAACAA-TATATCGATACA
2232237 TGGTCTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 4 0.14
33 24 0.86
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (33 bp):
TGTATCGATACATGGAACAATATATCGATACAA
Found at i:2236966 original size:156 final size:153
Alignment explanation
Indices: 2236747--2237045 Score: 352
Period size: 156 Copynumber: 1.9 Consensus size: 153
2236737 ATTTTAAAAG
* * * * * * * * * *
2236747 GGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAGCAGACCTGGCGACGATCTAGGACTCG
1 GGATGAACCTATCCTAAATACCCACCTTCAGCAAAAAAGCAAACCTAGCGACAACCTAAGACTCA
* * *
2236812 GTTCT-AGAGAATTATAAAAATGC-CTTTAGGGGATATACCTTT-GATGTAAAAGTATCCAACAC
66 GTTCTAAGA-AATTATAAAAATGCTC-TTA--GGAGATA-CTTTCGACGTAAAAGTACCCAACAC
*
2236874 CCCTAAAGGACTTTAAAAATTTAGAAATA
126 CCATAAAGGAC-TTAAAAATTTAGAAATA
* *
2236903 GGATGAACCTATCCTAAATGCCCACCTTCAGCAAAAAAGCAAACCTAGTGACAACCTAAGACTCA
1 GGATGAACCTATCCTAAATACCCACCTTCAGCAAAAAAGCAAACCTAGCGACAACCTAAGACTCA
* * *
2236968 GTTCTAAGAAATTATGAAAATGCTCTTAGGAGATACTTTCGACGTAAAAGTACCCGATACCCATA
66 GTTCTAAGAAATTATAAAAATGCTCTTAGGAGATACTTTCGACGTAAAAGTACCCAACACCCATA
2237033 AAGGACTTAAAAA
131 AAGGACTTAAAAA
2237046 GGATAATAGA
Statistics
Matches: 121, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
153 11 0.09
154 32 0.26
156 74 0.61
157 4 0.03
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (153 bp):
GGATGAACCTATCCTAAATACCCACCTTCAGCAAAAAAGCAAACCTAGCGACAACCTAAGACTCA
GTTCTAAGAAATTATAAAAATGCTCTTAGGAGATACTTTCGACGTAAAAGTACCCAACACCCATA
AAGGACTTAAAAATTTAGAAATA
Found at i:2237965 original size:33 final size:33
Alignment explanation
Indices: 2237907--2237974 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
2237897 CCGTTGGGCT
* **
2237907 CAATGTATCGATACAATTCTTCATGTATCAATA
1 CAATGTATCGATACAATGCCCCATGTATCAATA
* *
2237940 CAATGTATCGATATAATGCCCCATGTATCGATA
1 CAATGTATCGATACAATGCCCCATGTATCAATA
2237973 CA
1 CA
2237975 TTTCTTTTAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACAATGCCCCATGTATCAATA
Found at i:2238788 original size:16 final size:16
Alignment explanation
Indices: 2238767--2238798 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2238757 CTCCCTATTT
*
2238767 TTGTTTGAATAAACTC
1 TTGTTTGAACAAACTC
2238783 TTGTTTGAACAAACTC
1 TTGTTTGAACAAACTC
2238799 CTATTTCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (16 bp):
TTGTTTGAACAAACTC
Found at i:2240173 original size:161 final size:161
Alignment explanation
Indices: 2239908--2240229 Score: 608
Period size: 161 Copynumber: 2.0 Consensus size: 161
2239898 TCGGGAGATA
* * *
2239908 GAAAAAGTTAAAAGTTTTTAAATAAGCCATGTCGATCGCTTGACATTACCTAATTGATAACTGAG
1 GAAAAAGTTAAAAGTTTTTAAATAAGCCACGCCGATCGCTTGACATTACCTAATTGATAACCGAG
*
2239973 CAAAGGTTTGGTTAAAACGTTCAAGATTTATCGAGGAAACAACCTTCAATGAAGGATTGATTTTA
66 CAAAAGTTTGGTTAAAACGTTCAAGATTTATCGAGGAAACAACCTTCAATGAAGGATTGATTTTA
2240038 GGGATTTGAAGACGAAGTGCCTCGAGTGCGT
131 GGGATTTGAAGACGAAGTGCCTCGAGTGCGT
2240069 GAAAAAGTTAAAAGTTTTTAAATAAGCCACGCCGATCGCTTGACATTACCTAATTGATAACCGAG
1 GAAAAAGTTAAAAGTTTTTAAATAAGCCACGCCGATCGCTTGACATTACCTAATTGATAACCGAG
2240134 CAAAAGTTTGGTTAAAACGTTCAAGATTTATCGAGGAAACAACCTTCAATGAAGGATTGATTTTA
66 CAAAAGTTTGGTTAAAACGTTCAAGATTTATCGAGGAAACAACCTTCAATGAAGGATTGATTTTA
2240199 GGGATTTGAAGACGAAGTGCCTCGAGTGCGT
131 GGGATTTGAAGACGAAGTGCCTCGAGTGCGT
2240230 TTTTGAGAGG
Statistics
Matches: 157, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
161 157 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (161 bp):
GAAAAAGTTAAAAGTTTTTAAATAAGCCACGCCGATCGCTTGACATTACCTAATTGATAACCGAG
CAAAAGTTTGGTTAAAACGTTCAAGATTTATCGAGGAAACAACCTTCAATGAAGGATTGATTTTA
GGGATTTGAAGACGAAGTGCCTCGAGTGCGT
Found at i:2247012 original size:20 final size:20
Alignment explanation
Indices: 2246987--2247044 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
2246977 GTTGGGCTCA
**
2246987 ATGTATCGATACAATTCTTT
1 ATGTATCGATACAATTCTGC
*
2247007 ATGTATCGATAAAATAT-TGC
1 ATGTATCGATACAAT-TCTGC
*
2247027 ATGTATCGATACATTTCT
1 ATGTATCGATACAATTCT
2247045 CTTAGGGTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACAATTCTGC
Found at i:2247256 original size:20 final size:21
Alignment explanation
Indices: 2247231--2247271 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2247221 ACTTTGAAGT
2247231 AATTTAA-CTTGAAAACATTC
1 AATTTAAGCTTGAAAACATTC
*
2247251 AATTTAAGGTTTGAAAACATT
1 AATTTAA-GCTTGAAAACATT
2247272 TATTCATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (21 bp):
AATTTAAGCTTGAAAACATTC
Found at i:2249936 original size:1 final size:1
Alignment explanation
Indices: 2249930--2250014 Score: 80
Period size: 1 Copynumber: 85.0 Consensus size: 1
2249920 AAATCTTCAC
* * ** * * *
2249930 TTTTTTTTTTGTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTTTTTTTTTCTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
2249995 TGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTT
2250015 CCAATTGCCA
Statistics
Matches: 66, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.00, C:0.07, G:0.05, T:0.88
Consensus pattern (1 bp):
T
Found at i:2249973 original size:29 final size:29
Alignment explanation
Indices: 2249929--2250016 Score: 142
Period size: 29 Copynumber: 3.0 Consensus size: 29
2249919 CAAATCTTCA
2249929 CTTTTTTTT-TTGTTTTTTTTTTCTTTTTC
1 CTTTTTTTTGTT-TTTTTTTTTTCTTTTTC
2249958 CTTTTTTTTGTTTTTTTTTTTTCTTTTTC
1 CTTTTTTTTGTTTTTTTTTTTTCTTTTTC
* *
2249987 TTTTTTTTTGTTTTGTTTTTTTCTTTTTC
1 CTTTTTTTTGTTTTTTTTTTTTCTTTTTC
2250016 C
1 C
2250017 AATTGCCATG
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 53 0.96
30 2 0.04
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.85
Consensus pattern (29 bp):
CTTTTTTTTGTTTTTTTTTTTTCTTTTTC
Found at i:2260072 original size:166 final size:160
Alignment explanation
Indices: 2259900--2260445 Score: 524
Period size: 167 Copynumber: 3.3 Consensus size: 160
2259890 ATTTATGGAA
* * **
2259900 TAGAAAACTCAGTTTTTCGAGAAAATAGAG-ATTTCAAAAAAAAATTCAAAAACTCATGAAGGTG
1 TAGAAAACTCAGTATTTCGA-AAAA-AGAGAATTTCAAGAAAAAATT-AAAAACTCATGAAAATG
* * * *
2259964 AATGAATTTTTGAAAAATGTATTAATATGAAATAAATAATGACGTTTGAGGAATTTTAAAAATTG
63 AAT-AAATTTTGAAAACTGAATTAATATGAAATAAATAAT-A--TTTGATGAATTTTAAAAATTG
2260029 AAAACCAAGAAAAATCCCCTCCAAAAAATTTACAGAG
124 AAAACCAAGAAAAATCCCCTCCAAAAAATTTACAGAG
* * * *
2260066 TAGAAAATATC-GTATTTCGAAAAAAGGGAAGTTTCAAGGAAAAAATAAAAAAACTCTTGAAAAT
1 TAGAAAA-CTCAGTATTTCGAAAAAAGAGAA-TTTCAA-GAAAAAAT-TAAAAACTCATGAAAAT
*
2260130 GAATAAAATTTTGAAAACTGAATTAATATGAAATAAATGATAATATTTGATCAATTTTAAAAATT
62 GAAT-AAATTTTGAAAACTGAATTAATATGAAAT-AA--ATAATATTTGATGAATTTTAAAAATT
* *
2260195 GAAAACCAAGAAAAATCCTCT-CAAAAAATTTTACGGAG
123 GAAAACCAAGAAAAATCCCCTCCAAAAAA-TTTACAGAG
* * * *
2260233 TAGAAAA-TATAGTATTTCAAAAAAAGAAGAATTTCAAGAAAAAACTAAAAGCTCATGAAAATGA
1 TAGAAAACT-CAGTATTTCGAAAAAAG-AGAATTTCAAGAAAAAATTAAAAACTCATGAAAATGA
* * * *
2260297 ATAAATTTTGAAAACTAAATTAATCTG-AA-AAA-AATATTTGATGAATTTTAAAAATTAAAAAT
64 ATAAATTTTGAAAACTGAATTAATATGAAATAAATAATATTTGATGAATTTTAAAAATTGAAAAC
* *
2260359 TAAGAAAAAT--CCTACCGAAAAAATTTACAGAA
129 CAAGAAAAATCCCCT-CC-AAAAAATTTACAGAG
* *
2260391 AAGAAAACCTC-GTAATTT-GAAAATAAGAGGAA-TTC-AGAAGGAAAATTAATAACTC
1 TAGAAAA-CTCAGT-ATTTCGAAAA-AAGA-GAATTTCAAGAA--AAAATTAAAAACTC
2260446 CAAAAATAAA
Statistics
Matches: 320, Mismatches: 38, Indels: 51
0.78 0.09 0.12
Matches are distributed among these distances:
156 2 0.01
157 4 0.01
158 60 0.19
159 28 0.09
160 1 0.00
161 2 0.01
163 2 0.01
164 26 0.08
165 24 0.08
166 35 0.11
167 125 0.39
168 5 0.02
169 1 0.00
170 5 0.02
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (160 bp):
TAGAAAACTCAGTATTTCGAAAAAAGAGAATTTCAAGAAAAAATTAAAAACTCATGAAAATGAAT
AAATTTTGAAAACTGAATTAATATGAAATAAATAATATTTGATGAATTTTAAAAATTGAAAACCA
AGAAAAATCCCCTCCAAAAAATTTACAGAG
Found at i:2260137 original size:19 final size:19
Alignment explanation
Indices: 2260115--2260152 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2260105 AAAAAATAAA
2260115 AAAACTCTTGAAAA-TGAAT
1 AAAA-TCTTGAAAACTGAAT
*
2260134 AAAATTTTGAAAACTGAAT
1 AAAATCTTGAAAACTGAAT
2260153 TAATATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.29
Consensus pattern (19 bp):
AAAATCTTGAAAACTGAAT
Found at i:2260157 original size:167 final size:160
Alignment explanation
Indices: 2259930--2260389 Score: 529
Period size: 167 Copynumber: 2.8 Consensus size: 160
2259920 GAAAATAGAG
* ** * * *
2259930 ATTTCAAAAAAAAATTCAAAAACTCATGAAGGTGAATGAATTTTTGAAAAATGTATTAATATGAA
1 ATTTCAAGAAAAAA-T-AAAAACTCATGAAAATGAAT-AAATTTTGAAAACTGAATTAATATGAA
*
2259995 ATAAATAATGACGTTTGAGGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCCAAAAAATTT
63 ATAAATAAT-A--TTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCCAAAAAATTT
* * *
2260060 ACAGAGTAGAAAATATCGTATTTCGAAAAAAG-GGA
125 ACAGAGTAGAAAATATAGTATTTCAAAAAAAGAAGA
*
2260095 AGTTTCAAGGAAAAAATAAAAAAACTCTTGAAAATGAATAAAATTTTGAAAACTGAATTAATATG
1 A-TTTCAA-GAAAAAAT--AAAAACTCATGAAAATGAAT-AAATTTTGAAAACTGAATTAATATG
* *
2260160 AAATAAATGATAATATTTGATCAATTTTAAAAATTGAAAACCAAGAAAAATCCTCT-CAAAAAAT
61 AAAT-AA--ATAATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCCAAAAAA-
*
2260224 TTTACGGAGTAGAAAATATAGTATTTCAAAAAAAGAAGA
122 TTTACAGAGTAGAAAATATAGTATTTCAAAAAAAGAAGA
* * *
2260263 ATTTCAAGAAAAAACTAAAAGCTCATGAAAATGAATAAATTTTGAAAACTAAATTAATCTG-AA-
1 ATTTCAAGAAAAAA-TAAAAACTCATGAAAATGAATAAATTTTGAAAACTGAATTAATATGAAAT
* **
2260326 AAA-AATATTTGATGAATTTTAAAAATTAAAAATTAAGAAAAAT--CCTACCGAAAAAATTTACA
65 AAATAATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCT-CC-AAAAAATTTACA
2260388 GA
128 GA
2260390 AAAGAAAACC
Statistics
Matches: 257, Mismatches: 26, Indels: 31
0.82 0.08 0.10
Matches are distributed among these distances:
156 2 0.01
158 44 0.17
159 7 0.03
161 2 0.01
163 2 0.01
164 23 0.09
165 19 0.07
166 21 0.08
167 126 0.49
168 5 0.02
169 1 0.00
170 5 0.02
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.27
Consensus pattern (160 bp):
ATTTCAAGAAAAAATAAAAACTCATGAAAATGAATAAATTTTGAAAACTGAATTAATATGAAATA
AATAATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCCAAAAAATTTACAGAG
TAGAAAATATAGTATTTCAAAAAAAGAAGA
Found at i:2261535 original size:35 final size:35
Alignment explanation
Indices: 2261496--2261567 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
2261486 TCTCTTGACC
2261496 CTTCTTTCCATTACCTTAGACTTTTCTGATGAAAA
1 CTTCTTTCCATTACCTTAGACTTTTCTGATGAAAA
2261531 CTTCTTTCCATTACCTTAGACTTTTCTGATGAAAA
1 CTTCTTTCCATTACCTTAGACTTTTCTGATGAAAA
2261566 CT
1 CT
2261568 GATGTGTGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.25, C:0.24, G:0.08, T:0.43
Consensus pattern (35 bp):
CTTCTTTCCATTACCTTAGACTTTTCTGATGAAAA
Found at i:2264461 original size:166 final size:165
Alignment explanation
Indices: 2264156--2264713 Score: 689
Period size: 166 Copynumber: 3.4 Consensus size: 165
2264146 GACAATATTA
* ** * * * *
2264156 GATGCATTTTAAAAATTTTAGACCGAGAAAAAT-CCCTCTAAACAAAATTACGAAGAAGAAAACA
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAA-AAATTTACGAAGAAGAAAACA
* *
2264220 CCGTATTTC---AAAA-AAAATTTCAAGGAAAAAATCCAAAACTCATGAAAATGAGTTTATTTTT
65 CCGTATTTCAAAAAAAGAAAATTTCAAGAAAAAAATCCAAAACTCATGAAAATGAATTTATTTTT
* *
2264281 TAAAATTAAATTAATAGGAAATAAATAATGATGTTT
130 TAAAAATAAATTAATATGAAATAAATAATGATGTTT
* * *
2264317 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGGAGAAGAAAATAT
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGAAGAAGAAAACAC
2264382 CGTATTTCAAAAAAAGGAAAATTTCAAGAAAAAAATCCAAAACTCATGAAAATGAATTTATTTTT
66 CGTATTTCAAAAAAA-GAAAATTTCAAGAAAAAAATCCAAAACTCATGAAAATGAATTTATTTTT
*
2264447 TAAAAATGAATTAATATGAAATAAATAATGATGTTT
130 TAAAAATAAATTAATATGAAATAAATAATGATGTTT
* * * *
2264483 TATGAATTTTAAAAATTGAAAACTAAGAAAAATCCCCTCGAAAAAATTTATGAAGTAGAAAACAC
1 GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGAAGAAGAAAACAC
* * ** **
2264548 CATATTTCAGAAAAAATGAGAATTTCAAGAAAAAAATTTAAAAACTCATGAAAATGAATAAATTT
66 CGTATTTCA-AAAAAA-GAAAATTTCAAGAAAAAAA-TCCAAAACTCATGAAAATGAATTTATTT
* * ** *
2264613 TTGAAAACTAAATTAATATGAAATAAATAAAAATATTT
128 TTTAAAAATAAATTAATATGAAATAAATAATGATGTTT
** * * *
2264651 GATGAATTTTAAAAATT-ATAAATTAAAAAAAATCCTCC-CAAAAAAATTTACGAATAAGAAAAC
1 GATGAATTTTAAAAATTGA-AAACCAAGAAAAATCC-CCTCGAAAAAATTTACGAAGAAGAAAAC
2264714 CCCATAATTT
Statistics
Matches: 345, Mismatches: 42, Indels: 13
0.86 0.10 0.03
Matches are distributed among these distances:
161 54 0.16
162 8 0.02
164 4 0.01
166 145 0.42
167 25 0.07
168 107 0.31
169 2 0.01
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.28
Consensus pattern (165 bp):
GATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTTACGAAGAAGAAAACAC
CGTATTTCAAAAAAAGAAAATTTCAAGAAAAAAATCCAAAACTCATGAAAATGAATTTATTTTTT
AAAAATAAATTAATATGAAATAAATAATGATGTTT
Found at i:2266192 original size:84 final size:83
Alignment explanation
Indices: 2266107--2266778 Score: 255
Period size: 84 Copynumber: 8.0 Consensus size: 83
2266097 ATAAAATATA
* * *
2266107 AAAGGAAGTACCTGGAACCAAGCCCACAAGTGATTGAAGGATAAAAAGTTGACCAAGATTAAACC
1 AAAGGAAGTACCTGGAACCAAGCCGACAAGTGAATGAAGGATAAAAAGTTGACCAGGATTAAACC
2266172 GACAAGTCAACGAGGGAT
66 GACAAGTCAACGAGGGAT
** * * *** * * * * ** *
2266190 AAAGGATTTACCCGGGACTGGGCCGACGAGTAAATAAAGGATAAAAAAGTTGACCGGGATTGGAT
1 AAAGGAAGTACCTGGAACCAAGCCGACAAGTGAATGAAGGAT-AAAAAGTTGACCAGGATTAAAC
* * **
2266255 CAACACA-TCAACAAAAGAT
65 CGACA-AGTCAACGAGGGAT
* * * * * *
2266274 AAAAGGAAGTACCTAGAACCAAGGCGATAGGGGAATGAAGGACAAAAAGTTGACCAGGATTAAAC
1 -AAAGGAAGTACCTGGAACCAAGCCGACAAGTGAATGAAGGATAAAAAGTTGACCAGGATTAAAC
*
2266339 TGACAAGTCAACGAGGGAT
65 CGACAAGTCAACGAGGGAT
* * * *** * ** * ** * * ** *
2266358 AAAGGAATTACCCGGGACTGGGTC-AGCGGGTAAACAAAGGATAAAGAAATTAACTGGGATTGAA
1 AAAGGAAGTACCTGGAACCAAGCCGA-CAAGTGAATGAAGGATAAA-AAGTTGACCAGGATTAAA
* **
2266422 CCGACAAGTCAACAAAAGAT
64 CCGACAAGTCAACGAGGGAT
* ** * * * * ** * *
2266442 AAAAGATTTATCC--GAGACTAAGTCGACAGGTAAAT-AAGGGATAAAAAAGTTGGTCGGGATTG
1 AAAGGAAGTA-CCTGGA-ACCAAGCCGACAAGTGAATGAA-GGAT-AAAAAGTTGACCAGGATTA
* ** ***
2266504 GACCGACAAGTCAATAAAATAT
62 AACCGACAAGTCAACGAGGGAT
* * * * *
2266526 AAA--AAGTACTTGGGACCAAGCTGACAGGTGAATGAAGGATTAAAAGTTGACC-GAGATTAAAC
1 AAAGGAAGTACCTGGAACCAAGCCGACAAGTGAATGAAGGATAAAAAGTTGACCAG-GATTAAAC
* *
2266588 CGACAAGTCAGCAAGGGAT
65 CGACAAGTCAACGAGGGAT
** * ** * * *** ** ** * **
2266607 AAAGGATTTACTTGGGGCTAGGCCGATGGGCAAACAAAGGATAAAGAAGTTGATCAGGATTGGAC
1 AAAGGAAGTACCTGGAACCAAGCCGACAAGTGAATGAAGGATAAA-AAGTTGACCAGGATTAAAC
* * ** **
2266672 CGAAAAATCAATAAAAGAT
65 CGACAAGTCAACGAGGGAT
* * * * *
2266691 AAAAGGAAATACCTGGGACCAAGCCTACAGGAGAATGAAGGATAAAAAGTTGACC-GAGATTAAA
1 -AAAGGAAGTACCTGGAACCAAGCCGACAAGTGAATGAAGGATAAAAAGTTGACCAG-GATTAAA
*
2266755 CTGACAAGTCAACGAGGGAT
64 CCGACAAGTCAACGAGGGAT
2266775 AAAG
1 AAAG
2266779 ATTTACCCAA
Statistics
Matches: 420, Mismatches: 148, Indels: 42
0.69 0.24 0.07
Matches are distributed among these distances:
80 1 0.00
81 33 0.08
82 23 0.05
83 97 0.23
84 200 0.48
85 66 0.16
ACGTcount: A:0.43, C:0.15, G:0.26, T:0.16
Consensus pattern (83 bp):
AAAGGAAGTACCTGGAACCAAGCCGACAAGTGAATGAAGGATAAAAAGTTGACCAGGATTAAACC
GACAAGTCAACGAGGGAT
Done.