Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2946
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: 411495
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 2
Found at i:653 original size:27 final size:27
Alignment explanation
Indices: 623--799 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 27
613 ATATTGAGTC
* *
623 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
650 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
677 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
705 CGCACACTT-GTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
731 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
758 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
785 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
800 GTACAATTTA
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
26 12 0.09
27 102 0.80
28 13 0.10
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:734 original size:54 final size:54
Alignment explanation
Indices: 623--799 Score: 205
Period size: 54 Copynumber: 3.3 Consensus size: 54
613 ATATTGAGTC
* * * * *
623 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
677 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTT-GTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* **
731 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
785 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
800 GTACAATTTA
Statistics
Matches: 103, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
53 12 0.12
54 78 0.76
55 13 0.13
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:762 original size:81 final size:81
Alignment explanation
Indices: 644--798 Score: 224
Period size: 81 Copynumber: 1.9 Consensus size: 81
634 TGCTATATAA
* *
644 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
709 CACTT-GTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
725 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
789 CACTTAGTGC
65 CACTTAGTGC
799 TGTACAATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
80 11 0.17
81 55 0.83
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:11944 original size:27 final size:27
Alignment explanation
Indices: 11913--12090 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
11903 TAAATTGTAC
11913 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
11940 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
11966 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
11994 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
12022 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
12049 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
12076 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
12091 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:12027 original size:82 final size:81
Alignment explanation
Indices: 11914--12069 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
11904 AAATTGTACA
* *
11914 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
11978 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
11995 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
12060 TGCGAGTTGA
65 TGCGAATTGA
12070 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:12081 original size:82 final size:81
Alignment explanation
Indices: 11910--12090 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
11900 GATTAAATTG
* *
11910 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
11975 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
11991 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
12055 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
12073 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
12091 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:14952 original size:318 final size:317
Alignment explanation
Indices: 14359--15082 Score: 1144
Period size: 318 Copynumber: 2.3 Consensus size: 317
14349 GGGTGTTACA
* * *
14359 AAGCCTAATGACGAACCTATGTAGCTACCATTAGGGCCAATCACTCGAGCCCGTGCCAAGAGATT
1 AAGCCTAATGACGAACCTATGGAGCTGCCATCAGGGCCAATCACTCGAG-CCGTGCCAAGAGATT
* *
14424 TCAAGAAGTCATGGGTAGCCACATGCATAAAGAACGGTTTCTCAAGCAAAGGAAATCCAAGCTTC
65 TCAAGAAGTCATGGGTAGCCACATGCATAAAGAACGATTTCTCAAGAAAAGGAAATCCAAGCTTC
* * * *
14489 AACCAAGGGGTGATGGTCCATTCCATGTATTGAAACGGATCAACGACAACGTCTAAAAAATCGAT
130 AACAAAGGGGTGATGGTCCATTCCAAGTATTGAAACGGATCAACAACAACATCTAAAAAATCGAT
* * * *
14554 TTACCAGGTGAGTATGGAGTGAGTGCAAGTTTTAACGTTCCTGATCTCTTTCTTTTTGATGTAGG
195 TTACCAGGTGAGTATGGAGTGAGCGCAAGTTTTAACATTCCTGATCTCTCTCTTTTTGATGTAGC
* *
14619 TGACGATTTGAGGACGAATCACCTTGAAGAGAGGGGGGATGATGTGAGCTCGCCCATC
260 TGACGATTCGAGGACGAATCACCTTGAAGAGAGGGAGGATGATGTGAGCTCGCCCATC
14677 AAGCCTAATGACGAACCTATGGAGCTGCCATCAGGGCCAATCACTCGAGCTCGTGCCAAGAGATT
1 AAGCCTAATGACGAACCTATGGAGCTGCCATCAGGGCCAATCACTCGAGC-CGTGCCAAGAGATT
* *
14742 TCAAGAAGTCATGGGTAGCCACATGCGTAAAGAACGATTTCTCGAGAAAAGGAAATCCAAGCTTC
65 TCAAGAAGTCATGGGTAGCCACATGCATAAAGAACGATTTCTCAAGAAAAGGAAATCCAAGCTTC
* **
14807 AACAAAGGGGTGATGGTCCATTCCAAGTATTGGAACGGATCAACAACAACATCTTCAAAATCGAT
130 AACAAAGGGGTGATGGTCCATTCCAAGTATTGAAACGGATCAACAACAACATCTAAAAAATCGAT
**
14872 TTACCAGGTGAGTATGGAGTGAGCGCAAGTTTTAACATTGTTGATCTCTCTCTTTTTGATGTAGC
195 TTACCAGGTGAGTATGGAGTGAGCGCAAGTTTTAACATTCCTGATCTCTCTCTTTTTGATGTAGC
*
14937 TGATGATTCGAGGACGAATCACCTTGAAGAGAGGGAGGATGATGTGAGCTCGCCCATC
260 TGACGATTCGAGGACGAATCACCTTGAAGAGAGGGAGGATGATGTGAGCTCGCCCATC
* * * *
14995 AAGCCTAATGACGATCCTATGGAGCTG-AATCAAGGCTAATCACTCGAGCCTGTGCCAAGAGATT
1 AAGCCTAATGACGAACCTATGGAGCTGCCATCAGGGCCAATCACTCGAGCC-GTGCCAAGAGATT
* * *
15059 TCAAAAAGTCGTGGGTAGCTACAT
65 TCAAGAAGTCATGGGTAGCCACAT
15083 TGCTCGAGTT
Statistics
Matches: 374, Mismatches: 30, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
316 1 0.00
317 54 0.14
318 319 0.85
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.24
Consensus pattern (317 bp):
AAGCCTAATGACGAACCTATGGAGCTGCCATCAGGGCCAATCACTCGAGCCGTGCCAAGAGATTT
CAAGAAGTCATGGGTAGCCACATGCATAAAGAACGATTTCTCAAGAAAAGGAAATCCAAGCTTCA
ACAAAGGGGTGATGGTCCATTCCAAGTATTGAAACGGATCAACAACAACATCTAAAAAATCGATT
TACCAGGTGAGTATGGAGTGAGCGCAAGTTTTAACATTCCTGATCTCTCTCTTTTTGATGTAGCT
GACGATTCGAGGACGAATCACCTTGAAGAGAGGGAGGATGATGTGAGCTCGCCCATC
Found at i:20405 original size:18 final size:18
Alignment explanation
Indices: 20363--20399 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20353 TTTCACTTAC
*
20363 TTCTTTTTCAATTTCTTT
1 TTCTTTTTCAATCTCTTT
*
20381 TTCTTTTTCACTCTCTTT
1 TTCTTTTTCAATCTCTTT
20399 T
1 T
20400 GTTTTTGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.70
Consensus pattern (18 bp):
TTCTTTTTCAATCTCTTT
Found at i:22419 original size:11 final size:11
Alignment explanation
Indices: 22403--22446 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
22393 GAATGGAAAT
22403 AATTTTTTTTGA
1 AATTTTTTTT-A
*
22415 ATTTTTTTTTCA
1 AATTTTTTTT-A
*
22427 AATTTTTTTCA
1 AATTTTTTTTA
22438 AATTTTTTT
1 AATTTTTTT
22447 CGAAGAAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (11 bp):
AATTTTTTTTA
Found at i:22423 original size:13 final size:13
Alignment explanation
Indices: 22405--22446 Score: 54
Period size: 11 Copynumber: 3.5 Consensus size: 13
22395 ATGGAAATAA
*
22405 TTTTTTTT-GAAT
1 TTTTTTTTCAAAT
22417 TTTTTTTTCAAA-
1 TTTTTTTTCAAAT
22429 -TTTTTTTCAAAT
1 TTTTTTTTCAAAT
22441 TTTTTT
1 TTTTTT
22447 CGAAGAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 11 0.42
12 8 0.31
13 7 0.27
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTTTTTTCAAAT
Found at i:22447 original size:11 final size:11
Alignment explanation
Indices: 22418--22447 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
22408 TTTTTGAATT
22418 TTTTTTTCAAA
1 TTTTTTTCAAA
22429 TTTTTTTCAAA
1 TTTTTTTCAAA
22440 TTTTTTTC
1 TTTTTTTC
22448 GAAGAAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTTTCAAA
Found at i:25017 original size:20 final size:20
Alignment explanation
Indices: 24992--25057 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
24982 TCCATGCGGT
24992 TCAGCTCACTCGAGCTCAAG
1 TCAGCTCACTCGAGCTCAAG
*
25012 TCAGCTCATTCGAGCTCAAG
1 TCAGCTCACTCGAGCTCAAG
* * *
25032 TTAGCTCACACGAGCTCAAT
1 TCAGCTCACTCGAGCTCAAG
25052 TCAGCT
1 TCAGCT
25058 TATTGAGCTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (20 bp):
TCAGCTCACTCGAGCTCAAG
Found at i:30012 original size:12 final size:12
Alignment explanation
Indices: 29995--30029 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
29985 TAATTGAAAG
29995 AAAAAAATCAAT
1 AAAAAAATCAAT
30007 AAAAAAATCAA-
1 AAAAAAATCAAT
*
30018 AAAAAATTCAAT
1 AAAAAAATCAAT
30030 TTCTCCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAAAATCAAT
Found at i:52417 original size:16 final size:16
Alignment explanation
Indices: 52396--52446 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
52386 TTTCTAGTAT
*
52396 TTTATTTACTAGCGTG
1 TTTATTTACTAGCGTA
52412 TTTATTTACTAGCGTA
1 TTTATTTACTAGCGTA
52428 TTTATTTACTAGCGTA
1 TTTATTTACTAGCGTA
52444 TTT
1 TTT
52447 GCTCTTTCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.53
Consensus pattern (16 bp):
TTTATTTACTAGCGTA
Found at i:57727 original size:36 final size:33
Alignment explanation
Indices: 57662--57728 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 33
57652 GTGAATAAAG
*
57662 TGAGTGAAAAAGAGAGAGAGCTTAAACAAGGAA
1 TGAGTGAAAAAGAGAGAGAGCTAAAACAAGGAA
* *
57695 TGAGTGAAGAAGAAGAGAGTGCTCAAATACAAGG
1 TGAGTGAAAAAG-AGAGAGAGCT-AAA-ACAAGG
57729 GAGGAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 11 0.39
34 9 0.32
35 2 0.07
36 6 0.21
ACGTcount: A:0.48, C:0.07, G:0.31, T:0.13
Consensus pattern (33 bp):
TGAGTGAAAAAGAGAGAGAGCTAAAACAAGGAA
Found at i:65590 original size:14 final size:14
Alignment explanation
Indices: 65571--65597 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
65561 TTTGAGAGAT
65571 TTGTGAGGTTTTTG
1 TTGTGAGGTTTTTG
65585 TTGTGAGGTTTTT
1 TTGTGAGGTTTTT
65598 ATTTTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.00, G:0.33, T:0.59
Consensus pattern (14 bp):
TTGTGAGGTTTTTG
Found at i:67350 original size:24 final size:23
Alignment explanation
Indices: 67318--67368 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
67308 AAATGAGAGA
*
67318 AAAAGAAAA-GAGTGAAAACAAAG
1 AAAAGAAAATGAG-AAAAACAAAG
*
67341 AAAAGAAAAATGAGAAAAAGAAAG
1 AAAAG-AAAATGAGAAAAACAAAG
67365 AAAA
1 AAAA
67369 TCTGAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 5 0.21
24 16 0.67
25 3 0.12
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.04
Consensus pattern (23 bp):
AAAAGAAAATGAGAAAAACAAAG
Found at i:67378 original size:20 final size:20
Alignment explanation
Indices: 67318--67378 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 20
67308 AAATGAGAGA
67318 AAAAGAAAAGAGTGAAAACAAAG
1 AAAAGAAAA-A-TGAAAA-AAAG
*
67341 AAAAGAAAAATGAGAAAAAG
1 AAAAGAAAAATGAAAAAAAG
*
67361 -AAAGAAAATCTGAAAAAA
1 AAAAGAAAA-ATGAAAAAA
67379 GAGAGTGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 8 0.24
20 11 0.32
21 5 0.15
22 1 0.03
23 9 0.26
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAATGAAAAAAAG
Found at i:71656 original size:6 final size:6
Alignment explanation
Indices: 71645--71671 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
71635 TCCATTCCTT
71645 ACCTAA ACCTAA ACCTAA ACCTAA ACC
1 ACCTAA ACCTAA ACCTAA ACCTAA ACC
71672 AAATTTGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.37, G:0.00, T:0.15
Consensus pattern (6 bp):
ACCTAA
Found at i:77063 original size:20 final size:21
Alignment explanation
Indices: 77019--77064 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
77009 CAATGTGTCT
77019 TGTCTTAACCGAATTAATTAG
1 TGTCTTAACCGAATTAATTAG
**
77040 -GTCTTAACTTAATTAATT-G
1 TGTCTTAACCGAATTAATTAG
77059 TGTCTT
1 TGTCTT
77065 GTTTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (21 bp):
TGTCTTAACCGAATTAATTAG
Found at i:87625 original size:18 final size:18
Alignment explanation
Indices: 87604--87642 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
87594 AAAGGAAGAC
87604 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
87622 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
87640 AGA
1 AGA
87643 GCAAAAAGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:94202 original size:50 final size:52
Alignment explanation
Indices: 94047--94207 Score: 158
Period size: 50 Copynumber: 3.2 Consensus size: 52
94037 ATGATGCTTA
** * *
94047 AATGCATGATTTAA-TTAA-GATGCAAAC-TAAA-TGAACA-AATGAGTTACTT
1 AATGCATGACATAATTTAATGATGCAAACTTAAACT-AACATGA-GAGTTACAT
* * * *
94096 AATGCATGACTTAATTTAATGATGTAGACTTAAACTAACATGGGAGTTACGA-
1 AATGCATGACATAATTTAATGATGCAAACTTAAACTAACATGAGAGTTAC-AT
*
94148 AATGCATGTCATAATTT-ATGATGCAAACTT-AACTAACATGAGAGTTACAT
1 AATGCATGACATAATTTAATGATGCAAACTTAAACTAACATGAGAGTTACAT
94198 AATGCATGAC
1 AATGCATGAC
94208 TTTATTAAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
49 14 0.15
50 30 0.32
51 18 0.19
52 30 0.32
53 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.30
Consensus pattern (52 bp):
AATGCATGACATAATTTAATGATGCAAACTTAAACTAACATGAGAGTTACAT
Found at i:98409 original size:20 final size:20
Alignment explanation
Indices: 98386--98433 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
98376 TTAACTTAGT
*
98386 TCAGCTCACTCGAGCTTAAG
1 TCAGCTCACTCGAGCTCAAG
* *
98406 TCAGCTCATTCGAGCTCAAT
1 TCAGCTCACTCGAGCTCAAG
98426 TCAGCTCA
1 TCAGCTCA
98434 ATCTTAACCC
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:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (20 bp):
TCAGCTCACTCGAGCTCAAG
Found at i:100667 original size:22 final size:21
Alignment explanation
Indices: 100638--100685 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
100628 AAGCATGAAC
*
100638 TGAA-ATTTTAATGATTTAGTG
1 TGAACATTTTAATGAATT-GTG
* *
100659 TGAACATTTTTATTAATTGTG
1 TGAACATTTTAATGAATTGTG
100680 TGAACA
1 TGAACA
100686 CATAGATGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (21 bp):
TGAACATTTTAATGAATTGTG
Found at i:101079 original size:19 final size:17
Alignment explanation
Indices: 101043--101081 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
101033 TCAGTTGCTG
101043 ATTAGTTAAATAAATTA
1 ATTAGTTAAATAAATTA
*
101060 ATTAGCTTAAGATTAATTA
1 ATTAG-TTAA-ATAAATTA
101079 ATT
1 ATT
101082 TTATAAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (17 bp):
ATTAGTTAAATAAATTA
Found at i:111113 original size:13 final size:13
Alignment explanation
Indices: 111095--111130 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
111085 ACGAGATTGT
111095 AAAAAAATTTGAA
1 AAAAAAATTTGAA
111108 AAAAAAATTTGAA
1 AAAAAAATTTGAA
111121 AAAAAAATTT
1 AAAAAAATTT
111131 ATTTTGTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (13 bp):
AAAAAAATTTGAA
Found at i:113222 original size:15 final size:14
Alignment explanation
Indices: 113186--113230 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
113176 TCTATTGAGC
113186 GAGAAAAACAAAAA
1 GAGAAAAACAAAAA
113200 GAGAAAAACAAAAA
1 GAGAAAAACAAAAA
* *
113214 GAGTGAAAAGAAAAA
1 GAG-AAAAACAAAAA
113229 GA
1 GA
113231 AAGAAACGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.73, C:0.04, G:0.20, T:0.02
Consensus pattern (14 bp):
GAGAAAAACAAAAA
Found at i:113236 original size:15 final size:15
Alignment explanation
Indices: 113186--113236 Score: 61
Period size: 14 Copynumber: 3.5 Consensus size: 15
113176 TCTATTGAGC
113186 GAGA-AAAACAAAAA
1 GAGAGAAAACAAAAA
113200 GAGA-AAAACAAAAA
1 GAGAGAAAACAAAAA
* *
113214 GAGTGAAAAGAAAAA
1 GAGAGAAAACAAAAA
*
113229 GAAAGAAA
1 GAGAGAAA
113237 CGAATGATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 17 0.53
15 15 0.47
ACGTcount: A:0.75, C:0.04, G:0.20, T:0.02
Consensus pattern (15 bp):
GAGAGAAAACAAAAA
Found at i:123188 original size:27 final size:26
Alignment explanation
Indices: 123152--123202 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
123142 ACAAGAAATC
123152 AAAAAAGAAAATGAGAGTGAGAAAAAG
1 AAAAAAGAAAATGAGAGTGA-AAAAAG
* *
123179 AAAAAAGAAATTGAGATTGAAAAA
1 AAAAAAGAAAATGAGAGTGAAAAA
123203 GGATGTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.12
Consensus pattern (26 bp):
AAAAAAGAAAATGAGAGTGAAAAAAG
Found at i:123193 original size:21 final size:19
Alignment explanation
Indices: 123120--123194 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 19
123110 CGAGAAACGA
123120 AAAAAGAAATGAAAGAAAAAG
1 AAAAAGAAATG--AGAAAAAG
* *
123141 AACAAGAAATCA-AAAAAG
1 AAAAAGAAATGAGAAAAAG
* *
123159 AAAATGAGAGTGAGAAAAAG
1 AAAAAGA-AATGAGAAAAAG
123179 AAAAAAGAAATTGAGA
1 -AAAAAGAAA-TGAGA
123195 TTGAAAAAGG
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
18 11 0.26
19 4 0.10
20 7 0.17
21 20 0.48
ACGTcount: A:0.69, C:0.03, G:0.20, T:0.08
Consensus pattern (19 bp):
AAAAAGAAATGAGAAAAAG
Found at i:125156 original size:20 final size:21
Alignment explanation
Indices: 125133--125178 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
125123 TAAATAAAAC
125133 AAGACAC-AATTAATTAAGTT
1 AAGACACTAATTAATTAAGTT
**
125153 AAGAC-CTAATTAATTCGGTT
1 AAGACACTAATTAATTAAGTT
125173 AAGACA
1 AAGACA
125179 AGACACATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (21 bp):
AAGACACTAATTAATTAAGTT
Found at i:128628 original size:20 final size:21
Alignment explanation
Indices: 128595--128658 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 21
128585 CAACTCCTTT
* *
128595 AGCTCGTTTCAGCTCCAA-TC
1 AGCTCATTTGAGCTCCAATTC
128615 AGCTCATTTGAGCT-CAATTC
1 AGCTCATTTGAGCTCCAATTC
* *
128635 AGCTCATTCGAGCT-CAATTT
1 AGCTCATTTGAGCTCCAATTC
128655 AGCT
1 AGCT
128659 TTCTATCAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 3 0.08
20 36 0.92
ACGTcount: A:0.23, C:0.28, G:0.16, T:0.33
Consensus pattern (21 bp):
AGCTCATTTGAGCTCCAATTC
Found at i:128649 original size:30 final size:30
Alignment explanation
Indices: 128592--128658 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
128582 TTCCAACTCC
**
128592 TTTAGCTCGTTTCAGCTCCAATCAGCTC-A
1 TTTAGCTCAATTCAGCTCCAATCAGCTCAA
*
128621 TTTGAGCTCAATTCAGCT-CATTCGAGCTCAA
1 TTT-AGCTCAATTCAGCTCCAATC-AGCTCAA
128652 TTTAGCT
1 TTTAGCT
128659 TTCTATCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 7 0.22
30 21 0.66
31 4 0.12
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (30 bp):
TTTAGCTCAATTCAGCTCCAATCAGCTCAA
Found at i:129949 original size:18 final size:19
Alignment explanation
Indices: 129928--129963 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
129918 ATACATTCAA
129928 TTTTTCA-CTTGCTTTTTC
1 TTTTTCATCTTGCTTTTTC
*
129946 TTTTTCATCTTTCTTTTT
1 TTTTTCATCTTGCTTTTT
129964 TCTCGCTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.06, C:0.19, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTTTCATCTTGCTTTTTC
Found at i:134791 original size:19 final size:20
Alignment explanation
Indices: 134753--134790 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
134743 TTATTAATAA
134753 TGTAATTAAAAAAATAAAAT
1 TGTAATTAAAAAAATAAAAT
134773 TGTAA-TAAAAAAACTAAA
1 TGTAATTAAAAAAA-TAAA
134791 TAATAGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (20 bp):
TGTAATTAAAAAAATAAAAT
Found at i:137593 original size:100 final size:100
Alignment explanation
Indices: 137415--137614 Score: 310
Period size: 100 Copynumber: 2.0 Consensus size: 100
137405 TTTGATCAAA
* *
137415 GTAGCTTTGTTTCCACACACAAACAGTTCATTTCTTAGATTATCTTGAATCCCTTCAAAGCAAAA
1 GTAGCTTTGTTTCCACACACAAACAATTCATTTCTCAGATTATCTTGAATCCCTTCAAAGCAAAA
137480 CATTTTCTCAAACATAATCAATAAAATTGAAAATG
66 CATTTTCTCAAACATAATCAATAAAATTGAAAATG
* ** * *
137515 GTAGCTTTGTTTCCACACACAAACAATTTATTTCTCCTATTATCTTGGATCCCTTCAAAGGAAAA
1 GTAGCTTTGTTTCCACACACAAACAATTCATTTCTCAGATTATCTTGAATCCCTTCAAAGCAAAA
* **
137580 CATTTTCTGAAACATAATTGATAAAATTGAAAATG
66 CATTTTCTCAAACATAATCAATAAAATTGAAAATG
137615 ATCAAAACAA
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 90 1.00
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (100 bp):
GTAGCTTTGTTTCCACACACAAACAATTCATTTCTCAGATTATCTTGAATCCCTTCAAAGCAAAA
CATTTTCTCAAACATAATCAATAAAATTGAAAATG
Found at i:140678 original size:10 final size:11
Alignment explanation
Indices: 140651--140677 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
140641 CGGTATTGTA
140651 AAAAAATCAAT
1 AAAAAATCAAT
140662 AAAAAATCAAT
1 AAAAAATCAAT
140673 AAAAA
1 AAAAA
140678 TTTCGTGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAATCAAT
Found at i:147235 original size:20 final size:20
Alignment explanation
Indices: 147189--147235 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
147179 AGCTCGTTTC
*
147189 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
147209 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
147229 CAGCTCA
1 CAGCTCA
147236 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:148243 original size:18 final size:17
Alignment explanation
Indices: 148160--148288 Score: 61
Period size: 18 Copynumber: 7.4 Consensus size: 17
148150 GGAACAAGAA
*
148160 ATTGAAAAAGAGAGTGAG
1 ATTGAAAAAGA-AATGAG
*
148178 ATTGAAGAAAGAAACGAG
1 ATTGAA-AAAGAAATGAG
* * *
148196 AGTGTAAAAGAAACGAGTG
1 ATTGAAAAAGAAATGA--G
*
148215 TCATGGAAAAAGAAATTGAG
1 --ATTGAAAAAGAAA-TGAG
*
148235 ATTGAAAAAG-GAT--G
1 ATTGAAAAAGAAATGAG
* *
148249 --TGAAAAAGAGAAAGAA
1 ATTGAAAAAGA-AATGAG
148265 ATTGAAAAAGAAATTGAG
1 ATTGAAAAAGAAA-TGAG
148283 ATTGAA
1 ATTGAA
148289 CAAAAGTGTG
Statistics
Matches: 83, Mismatches: 15, Indels: 26
0.67 0.12 0.21
Matches are distributed among these distances:
12 8 0.10
14 2 0.02
16 1 0.01
17 13 0.16
18 40 0.48
19 6 0.07
20 1 0.01
21 10 0.12
22 2 0.02
ACGTcount: A:0.53, C:0.02, G:0.27, T:0.17
Consensus pattern (17 bp):
ATTGAAAAAGAAATGAG
Found at i:148278 original size:48 final size:47
Alignment explanation
Indices: 148220--148325 Score: 144
Period size: 48 Copynumber: 2.2 Consensus size: 47
148210 GAGTGTCATG
*
148220 GAAAAAGAAATTGAGATTGAA-AAAGGATGTGA-AAAAGAGAAAGAAATT
1 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGAAAA-AGAAA-AAATT
*
148268 GAAAAAGAAATTGAGATTGAACAAAAGTGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAACAAAAGTGTGA-GAAAAAGAAAAAATT
148316 GAAAAAGAAA
1 GAAAAAGAAA
148326 GAAAAGACAA
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
48 41 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.01, G:0.25, T:0.15
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAACAAAAGTGTGAGAAAAAGAAAAAATT
Found at i:150040 original size:20 final size:20
Alignment explanation
Indices: 149994--150040 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
149984 AGCTCGTTTC
*
149994 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
150014 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
150034 CAGCTCA
1 CAGCTCA
150041 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:157096 original size:13 final size:12
Alignment explanation
Indices: 157064--157093 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
157054 TTTTCTTTTC
157064 TTTTTTT-ACAA
1 TTTTTTTCACAA
157075 TTTTTTTCACAA
1 TTTTTTTCACAA
157087 TTTTTTT
1 TTTTTTT
157094 TCAACTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTTTCACAA
Found at i:157155 original size:14 final size:13
Alignment explanation
Indices: 157134--157180 Score: 71
Period size: 13 Copynumber: 3.7 Consensus size: 13
157124 ATGGAAACTA
157134 AATTTTTTTTT-G
1 AATTTTTTTTTCG
157146 AA-TTTTTTTTCG
1 AATTTTTTTTTCG
157158 AAATTTTTTTTTCG
1 -AATTTTTTTTTCG
157172 AATTTTTTT
1 AATTTTTTT
157181 CAAAGAACCT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.25
12 3 0.09
13 11 0.34
14 10 0.31
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.70
Consensus pattern (13 bp):
AATTTTTTTTTCG
Found at i:166298 original size:19 final size:20
Alignment explanation
Indices: 166274--166311 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
166264 TGAGTTGATT
166274 GGAGCTGAAA-TGAGCTAAG
1 GGAGCTGAAATTGAGCTAAG
166293 GGAGCTGAAATTGAGCTAA
1 GGAGCTGAAATTGAGCTAA
166312 AGTCAGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.37, C:0.11, G:0.34, T:0.18
Consensus pattern (20 bp):
GGAGCTGAAATTGAGCTAAG
Found at i:168197 original size:21 final size:22
Alignment explanation
Indices: 168172--168217 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
168162 TTAAAAACAA
168172 ATTAAACACTT-AACTAAATTT
1 ATTAAACACTTAAACTAAATTT
* *
168193 ATTAAATACTTAAACTAATTTT
1 ATTAAACACTTAAACTAAATTT
168215 ATT
1 ATT
168218 CCAACAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTAAACACTTAAACTAAATTT
Found at i:174139 original size:13 final size:13
Alignment explanation
Indices: 174123--174149 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
174113 TTTTTTAACA
174123 CATAATTTTTTTT
1 CATAATTTTTTTT
174136 CATAATTTTTTTT
1 CATAATTTTTTTT
174149 C
1 C
174150 CTTTTTTTTG
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:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (13 bp):
CATAATTTTTTTT
Found at i:178711 original size:21 final size:18
Alignment explanation
Indices: 178669--178713 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
178659 TTTTTCAAAC
178669 TCTTTTTCAAATCCTCTT
1 TCTTTTTCAAATCCTCTT
*
178687 TCTTTTATCACATCACTCATT
1 TCTTTT-TCAAATC-CTC-TT
178708 TCTTTT
1 TCTTTT
178714 GTACTCTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 6 0.26
20 3 0.13
21 8 0.35
ACGTcount: A:0.18, C:0.27, G:0.00, T:0.56
Consensus pattern (18 bp):
TCTTTTTCAAATCCTCTT
Found at i:178847 original size:15 final size:16
Alignment explanation
Indices: 178822--178851 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
178812 TATCTCACAC
178822 TCATCTTCTTTTTCTG
1 TCATCTTCTTTTTCTG
178838 TCAT-TTCTTTTTCT
1 TCATCTTCTTTTTCT
178852 TTTTCATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.07, C:0.23, G:0.03, T:0.67
Consensus pattern (16 bp):
TCATCTTCTTTTTCTG
Found at i:179743 original size:32 final size:31
Alignment explanation
Indices: 179707--179776 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 31
179697 TCAATCACTC
* *
179707 TCTTTTTTTTTTCAATTTCAATTTTTTTTTCT
1 TCTTTTTTTTTT-AATTCCAAATTTTTTTTCT
179739 TCTTTTTTTTTTAATTCCAAATTTTTTTTCT
1 TCTTTTTTTTTTAATTCCAAATTTTTTTTCT
179770 TCTTTTT
1 TCTTTTT
179777 CTTCCTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (31 bp):
TCTTTTTTTTTTAATTCCAAATTTTTTTTCT
Found at i:179841 original size:12 final size:13
Alignment explanation
Indices: 179824--179869 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
179814 GAATACAAAC
*
179824 TTTTTTTTGAATT
1 TTTTTTTTGAAGT
*
179837 TTTTTTTTG-ATT
1 TTTTTTTTGAAGT
*
179849 TTTTTTTTCAAGT
1 TTTTTTTTGAAGT
179862 TTTTTTTT
1 TTTTTTTT
179870 ACAATACCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (13 bp):
TTTTTTTTGAAGT
Found at i:179842 original size:13 final size:13
Alignment explanation
Indices: 179824--179869 Score: 67
Period size: 12 Copynumber: 3.5 Consensus size: 13
179814 GAATACAAAC
179824 TTTTTTTTGAATT
1 TTTTTTTTGAATT
179837 TTTTTTTTG-ATT
1 TTTTTTTTGAATT
*
179849 TTTTTTTTCAAGTT
1 TTTTTTTTGAA-TT
179863 TTTTTTT
1 TTTTTTT
179870 ACAATACCGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 11 0.37
13 10 0.33
14 9 0.30
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:185606 original size:11 final size:12
Alignment explanation
Indices: 185582--185609 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
185572 ATACTTTGAA
185582 TTTTTGAAATTT
1 TTTTTGAAATTT
185594 TTTTTGAAATTT
1 TTTTTGAAATTT
185606 TTTT
1 TTTT
185610 ACAAACTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (12 bp):
TTTTTGAAATTT
Found at i:187385 original size:13 final size:12
Alignment explanation
Indices: 187353--187384 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
187343 TTGTAAATCC
*
187353 AAAAAAAATTTG
1 AAAAAAAATTCG
187365 AAAAAAAATTCG
1 AAAAAAAATTCG
187377 AAAAAAAA
1 AAAAAAAA
187385 AGAAGAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTCG
Found at i:188822 original size:21 final size:23
Alignment explanation
Indices: 188777--188823 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
188767 TCACCTGCAA
* *
188777 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
188800 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
188821 TAA
1 TAA
188824 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:192897 original size:16 final size:15
Alignment explanation
Indices: 192871--192900 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
192861 TTTCAATCCA
192871 TCATCCCAATCAAAG
1 TCATCCCAATCAAAG
192886 TCATCACCAATCAAA
1 TCATC-CCAATCAAA
192901 AATTGATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
TCATCCCAATCAAAG
Found at i:194467 original size:11 final size:11
Alignment explanation
Indices: 194451--194490 Score: 66
Period size: 10 Copynumber: 3.8 Consensus size: 11
194441 TTTTGAATAC
194451 AATTTTTTTTG
1 AATTTTTTTTG
194462 AA-TTTTTTT-
1 AATTTTTTTTG
194471 AATTTTTTTTG
1 AATTTTTTTTG
194482 AATTTTTTT
1 AATTTTTTT
194491 CCTTTGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 2 0.07
10 14 0.52
11 11 0.41
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (11 bp):
AATTTTTTTTG
Found at i:194476 original size:20 final size:20
Alignment explanation
Indices: 194451--194490 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
194441 TTTTGAATAC
194451 AATTTTTTTTGAATTTTTTT
1 AATTTTTTTTGAATTTTTTT
194471 AATTTTTTTTGAATTTTTTT
1 AATTTTTTTTGAATTTTTTT
194491 CCTTTGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (20 bp):
AATTTTTTTTGAATTTTTTT
Found at i:194500 original size:20 final size:20
Alignment explanation
Indices: 194451--194500 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
194441 TTTTGAATAC
*
194451 AATTTTTTTTGAATTTTTTT
1 AATTTGTTTTGAATTTTTTT
*
194471 AATTTTTTTTGAATTTTTTT
1 AATTTGTTTTGAATTTTTTT
**
194491 CCTTTGTTTT
1 AATTTGTTTT
194501 TACAATACCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.74
Consensus pattern (20 bp):
AATTTGTTTTGAATTTTTTT
Found at i:199932 original size:16 final size:15
Alignment explanation
Indices: 199893--199929 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
199883 TAGCTTCTTC
199893 TTTTTTTCACGAATT
1 TTTTTTTCACGAATT
199908 TTTTTTTCACGAATT
1 TTTTTTTCACGAATT
199923 TTTTTTT
1 TTTTTTT
199930 TCAACTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.16, C:0.11, G:0.05, T:0.68
Consensus pattern (15 bp):
TTTTTTTCACGAATT
Found at i:199986 original size:12 final size:13
Alignment explanation
Indices: 199966--200001 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
199956 TTGAATGGAA
199966 AATTTTTTTTTTG
1 AATTTTTTTTTTG
199979 AATTTTTTTTTTG
1 AATTTTTTTTTTG
199992 AATTTTTTTT
1 AATTTTTTTT
200002 GAAAAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78
Consensus pattern (13 bp):
AATTTTTTTTTTG
Found at i:204614 original size:12 final size:12
Alignment explanation
Indices: 204597--204653 Score: 87
Period size: 12 Copynumber: 4.8 Consensus size: 12
204587 AGTTTCTTTG
204597 AAAAAAATTCAA
1 AAAAAAATTCAA
**
204609 AAAAAAATTTGA
1 AAAAAAATTCAA
204621 AAAAAAATTCAA
1 AAAAAAATTCAA
*
204633 AAAAAAATTCGA
1 AAAAAAATTCAA
204645 AAAAAAATT
1 AAAAAAATT
204654 TAGTTTCTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 40 1.00
ACGTcount: A:0.72, C:0.05, G:0.04, T:0.19
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:204629 original size:24 final size:24
Alignment explanation
Indices: 204593--204653 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
204583 TAGTAGTTTC
204593 TTTG-AAAAAAATTCAAAAAAAAA
1 TTTGAAAAAAAATTCAAAAAAAAA
204616 TTTGAAAAAAAATTCAAAAAAAAA
1 TTTGAAAAAAAATTCAAAAAAAAA
*
204640 TTCGAAAAAAAATT
1 TTTGAAAAAAAATT
204654 TAGTTTCTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 4 0.11
24 32 0.89
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (24 bp):
TTTGAAAAAAAATTCAAAAAAAAA
Found at i:209827 original size:12 final size:12
Alignment explanation
Indices: 209812--209857 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
209802 GAAAAAATTC
209812 AAAAAAATTTGA
1 AAAAAAATTTGA
* *
209824 AAAAAAAATTCA
1 AAAAAAATTTGA
*
209836 AAAAAAATTCGA
1 AAAAAAATTTGA
209848 AAAAAAATTT
1 AAAAAAATTT
209858 AGTTTCTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (12 bp):
AAAAAAATTTGA
Found at i:209833 original size:23 final size:24
Alignment explanation
Indices: 209803--209854 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
209793 AGTTTCTTTG
*
209803 AAAAAATTC-AAAAAAATTTGAAA
1 AAAAAATTCAAAAAAAATTCGAAA
209826 AAAAAATTCAAAAAAAATTCGAAA
1 AAAAAATTCAAAAAAAATTCGAAA
209850 AAAAA
1 AAAAA
209855 TTTAGTTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.17
Consensus pattern (24 bp):
AAAAAATTCAAAAAAAATTCGAAA
Found at i:222838 original size:79 final size:81
Alignment explanation
Indices: 222699--222883 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
222689 TTGAATGATG
*
222699 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCAAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCAAAGGCATT
222763 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * ** *
222778 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCAAAGGCA
*
222840 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
222858 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
222884 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCAAAGGCATT
TGTGCGAGATACTATA
Found at i:222890 original size:40 final size:40
Alignment explanation
Indices: 222699--222883 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
222689 TTGAATGATG
* * * *
222699 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
222739 TCCGGACTAAGAT-CCAAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
222779 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
222818 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
222859 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
222884 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
39 34 0.27
40 81 0.65
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:222905 original size:79 final size:79
Alignment explanation
Indices: 222755--222916 Score: 204
Period size: 79 Copynumber: 2.1 Consensus size: 79
222745 CTAAGATCCA
* **
222755 AAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATC
1 AAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAATC
*
222820 CGGGTTAAGTCCCG
66 CGGGTTAAATCCCG
* * *
222834 AAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTAT
1 AAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CTAA
*
222897 ATCC-GGTTAAATTCCG
63 ATCCGGGTTAAATCCCG
222913 AAGG
1 AAGG
222917 TACGTGACTT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 45 0.62
80 25 0.35
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (79 bp):
AAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAATC
CGGGTTAAATCCCG
Found at i:239790 original size:56 final size:55
Alignment explanation
Indices: 239674--239791 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
239664 TGCATGCTTT
* * * *
239674 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
239728 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
239784 CATTAAAT
1 CATTAAAT
239792 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:240440 original size:20 final size:20
Alignment explanation
Indices: 240415--240469 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
240405 ACGAGTTAAA
* *
240415 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
240435 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
240455 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
240470 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:241380 original size:16 final size:15
Alignment explanation
Indices: 241354--241383 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
241344 TTTCAATCCA
241354 TCATCCCAATCAAAG
1 TCATCCCAATCAAAG
241369 TCATCACCAATCAAA
1 TCATC-CCAATCAAA
241384 AATTGATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.20
Consensus pattern (15 bp):
TCATCCCAATCAAAG
Found at i:242830 original size:26 final size:28
Alignment explanation
Indices: 242791--242854 Score: 96
Period size: 27 Copynumber: 2.3 Consensus size: 28
242781 CAATCACTCT
*
242791 TTTTTTTTTCAATTTCG-ATTTTTTTTC
1 TTTTTTTTTCAATTCCGAATTTTTTTTC
242818 TTTTTTTTT-AATTCCGAATTTTTTTTC
1 TTTTTTTTTCAATTCCGAATTTTTTTTC
242845 TTCTTTTTTT
1 TT-TTTTTTT
242855 TTCTTCAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
26 6 0.18
27 21 0.62
28 7 0.21
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.75
Consensus pattern (28 bp):
TTTTTTTTTCAATTCCGAATTTTTTTTC
Found at i:242852 original size:13 final size:13
Alignment explanation
Indices: 242836--242860 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
242826 TAATTCCGAA
242836 TTTTTTTTCTTCT
1 TTTTTTTTCTTCT
242849 TTTTTTTTCTTC
1 TTTTTTTTCTTC
242861 AATACTAAAT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTTCTTCT
Found at i:242941 original size:11 final size:11
Alignment explanation
Indices: 242902--242941 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
242892 AATACAAACT
242902 TTTTTTTTGAA
1 TTTTTTTTGAA
*
242913 TTGTTTTTGAA
1 TTTTTTTTGAA
*
242924 TTTTTTTT-TA
1 TTTTTTTTGAA
242934 TTTTTTTT
1 TTTTTTTT
242942 ATAATACCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.12, C:0.00, G:0.07, T:0.80
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:244101 original size:56 final size:56
Alignment explanation
Indices: 243996--244102 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
243986 ATTAATGCCG
* * * * *
243996 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGTCGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGTCGT
244052 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
244103 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGTCGT
Found at i:244434 original size:23 final size:22
Alignment explanation
Indices: 244408--244456 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
244398 AACATCAATA
*
244408 AATTCGGCA-ACTAAGACATAGTT
1 AATTCAGCATACT-AGACA-AGTT
*
244431 AATTCAGCATCCTAGACAAGTT
1 AATTCAGCATACTAGACAAGTT
244453 AATT
1 AATT
244457 AAATTTGGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.35
23 13 0.57
24 2 0.09
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (22 bp):
AATTCAGCATACTAGACAAGTT
Found at i:246218 original size:20 final size:20
Alignment explanation
Indices: 246193--246247 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
246183 ACGAGTTAAA
* *
246193 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
246213 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
246233 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
246248 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:246445 original size:21 final size:23
Alignment explanation
Indices: 246400--246446 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
246390 TCACCTGCAA
* *
246400 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
246423 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
246444 TAA
1 TAA
246447 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:259833 original size:16 final size:15
Alignment explanation
Indices: 259812--259867 Score: 103
Period size: 15 Copynumber: 3.7 Consensus size: 15
259802 TAGCTTCTTC
259812 TTTTTTTTCACGAAAT
1 TTTTTTTTCACG-AAT
259828 TTTTTTTTCACGAAT
1 TTTTTTTTCACGAAT
259843 TTTTTTTTCACGAAT
1 TTTTTTTTCACGAAT
259858 TTTTTTTTCA
1 TTTTTTTTCA
259868 ACTTGATATC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
15 28 0.70
16 12 0.30
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.62
Consensus pattern (15 bp):
TTTTTTTTCACGAAT
Found at i:259925 original size:13 final size:12
Alignment explanation
Indices: 259905--259942 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
259895 ATGGAAACCA
259905 AATTTTTTTTTG
1 AATTTTTTTTTG
259917 AATTTTTTTTTG
1 AATTTTTTTTTG
259929 AATTTTTTTTTG
1 AATTTTTTTTTG
259941 AA
1 AA
259943 GAAACTACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:260973 original size:21 final size:23
Alignment explanation
Indices: 260928--260974 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
260918 TCACCTGCAA
* *
260928 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
260951 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
260972 TAA
1 TAA
260975 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:265491 original size:29 final size:27
Alignment explanation
Indices: 265458--265512 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
265448 GTGATTAAAT
265458 AAAATCGACA-CAAGCAGAACTTAAAAGAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAA
*
265487 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
265513 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 2 0.08
29 10 0.42
30 4 0.17
ACGTcount: A:0.60, C:0.13, G:0.15, T:0.13
Consensus pattern (27 bp):
AAAATCGACAGCAAGAAATTAAAAGAA
Found at i:266621 original size:247 final size:247
Alignment explanation
Indices: 266174--266668 Score: 810
Period size: 247 Copynumber: 2.0 Consensus size: 247
266164 TTTCTTGATT
* * **
266174 CTTGAAATCGTTCCAAACAACAAGATTGGGCCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAG
1 CTTGAAATCGCTCCAAACAACAAAATTGAACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAG
266239 AAAGTGAATCTTGATTTTCTCTTTCTTTCATGTACGCATCTAAGGCCTTGCTAACAAACTCCTAA
66 AAAGTGAATCTTGATTTTCTCTTTCTTTCATGTACGCATCTAAGGCCTTGCTAACAAACTCCTAA
*
266304 ATGATCCCATTTAGTTTGGAACGCATCTGTCGGGCCTTTGATCTCGTTATTGGGCCTTGTGGTAA
131 ATGATCCCATTTAGTTTGGAACGCATCTGTCGGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAA
* * * *
266369 TTTGAGCCCATCACGTTCTTGGGCTTGGGTTGGGCTTTTGTGACTTGTATCA
196 TTTGAGCCCATCACGTTCTTGAGATTGGGTTGGGCCTTTGTGACTCGTATCA
**
266421 CTTGAAATCGCTCCAAACAGTAAAATTGAACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAG
1 CTTGAAATCGCTCCAAACAACAAAATTGAACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAG
* * *
266486 AAAGTGAATCTTGATTTTCTCTTTCTTTCGTGTACGCATCTAAGGCCTTGCTAACAAATTCCTGA
66 AAAGTGAATCTTGATTTTCTCTTTCTTTCATGTACGCATCTAAGGCCTTGCTAACAAACTCCTAA
* * * * * *
266551 ATGGTCCCATTTAGTTTGGAACGCATTTTTCTGGCCTTTGACCTCGTTATTGGGCCTTTTGGTGA
131 ATGATCCCATTTAGTTTGGAACGCATCTGTCGGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAA
266616 TTTGAGCCCATCACGTTCTTGAGATTGGGTTGGGCCTTTGTGACTCGTATCA
196 TTTGAGCCCATCACGTTCTTGAGATTGGGTTGGGCCTTTGTGACTCGTATCA
266668 C
1 C
266669 ATTCCATAAC
Statistics
Matches: 228, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
247 228 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (247 bp):
CTTGAAATCGCTCCAAACAACAAAATTGAACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAG
AAAGTGAATCTTGATTTTCTCTTTCTTTCATGTACGCATCTAAGGCCTTGCTAACAAACTCCTAA
ATGATCCCATTTAGTTTGGAACGCATCTGTCGGGCCTTTGACCTCGTTATTGGGCCTTGTGGTAA
TTTGAGCCCATCACGTTCTTGAGATTGGGTTGGGCCTTTGTGACTCGTATCA
Found at i:266900 original size:11 final size:10
Alignment explanation
Indices: 266868--266899 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
266858 ACGATATTGT
*
266868 AATTTAAAAA
1 AATTCAAAAA
266878 AATTCAAAAA
1 AATTCAAAAA
266888 AATTCAAAAA
1 AATTCAAAAA
266898 AA
1 AA
266900 AAGTTTGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (10 bp):
AATTCAAAAA
Found at i:269814 original size:10 final size:10
Alignment explanation
Indices: 269788--269855 Score: 59
Period size: 10 Copynumber: 6.8 Consensus size: 10
269778 TTTCATGTGG
*
269788 TTCAGCTCAC
1 TTCAGCTCAA
*
269798 TTGAGCTCAA
1 TTCAGCTCAA
*
269808 GTCAGCTC-A
1 TTCAGCTCAA
*
269817 TTCGAGTTCAA
1 TTC-AGCTCAA
*
269828 GTCAGCTC-A
1 TTCAGCTCAA
269837 TTCAAGCTCAA
1 TTC-AGCTCAA
269848 TTCAGCTC
1 TTCAGCTC
269856 GTTATTAGCT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
9 6 0.13
10 32 0.71
11 7 0.16
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (10 bp):
TTCAGCTCAA
Found at i:269814 original size:20 final size:20
Alignment explanation
Indices: 269789--269855 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
269779 TTCATGTGGT
269789 TCAGCTCACTT-GAGCTCAAG
1 TCAGCTCA-TTCGAGCTCAAG
*
269809 TCAGCTCATTCGAGTTCAAG
1 TCAGCTCATTCGAGCTCAAG
* *
269829 TCAGCTCATTCAAGCTCAAT
1 TCAGCTCATTCGAGCTCAAG
269849 TCAGCTC
1 TCAGCTC
269856 GTTATTAGCT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 2 0.05
20 40 0.95
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.28
Consensus pattern (20 bp):
TCAGCTCATTCGAGCTCAAG
Found at i:270045 original size:28 final size:28
Alignment explanation
Indices: 270020--270074 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
270010 TATAACATAG
* *
270020 CATAAATGTGTTTTATTTTATTACATGT
1 CATAAATGTGTCTAATTTTATTACATGT
* *
270048 TATTAATGTGTCTAATTTTATTACATG
1 CATAAATGTGTCTAATTTTATTACATG
270075 CTTTAATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.53
Consensus pattern (28 bp):
CATAAATGTGTCTAATTTTATTACATGT
Found at i:270087 original size:28 final size:28
Alignment explanation
Indices: 270034--270090 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
270024 AATGTGTTTT
* *
270034 ATTTTATTACATGTTATTAATGTGTCTA
1 ATTTTATTACATGCTATTAATATGTCTA
270062 ATTTTATTACATGCT-TTAATAATGTCTA
1 ATTTTATTACATGCTATTAAT-ATGTCTA
270090 A
1 A
270091 GTCTAGCTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.51
Consensus pattern (28 bp):
ATTTTATTACATGCTATTAATATGTCTA
Found at i:273036 original size:15 final size:16
Alignment explanation
Indices: 273016--273047 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
273006 AGAAAATGAA
273016 AAAGAAAAAGAA-ATG
1 AAAGAAAAAGAAGATG
273031 AAAGAAAAAGAAGATG
1 AAAGAAAAAGAAGATG
273047 A
1 A
273048 GCGTGAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGAAGATG
Found at i:279648 original size:40 final size:40
Alignment explanation
Indices: 279593--279673 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
279583 TCATACACTT
279593 AAATAGCTGAATTTTTTTACTTTGTAAAGGGACTTTTGAC
1 AAATAGCTGAATTTTTTTACTTTGTAAAGGGACTTTTGAC
279633 AAATAGCTGAATTTTTTTACTTTGTAAAGGGACTTTTGAC
1 AAATAGCTGAATTTTTTTACTTTGTAAAGGGACTTTTGAC
279673 A
1 A
279674 TTTTAATTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (40 bp):
AAATAGCTGAATTTTTTTACTTTGTAAAGGGACTTTTGAC
Found at i:280001 original size:21 final size:21
Alignment explanation
Indices: 279975--280018 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
279965 ATACAAAATA
279975 CCATACCATTTCATACCAATT
1 CCATACCATTTCATACCAATT
*
279996 CCATACCATTTCGTACCAATT
1 CCATACCATTTCATACCAATT
280017 CC
1 CC
280019 CAAATACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.32
Consensus pattern (21 bp):
CCATACCATTTCATACCAATT
Found at i:280350 original size:12 final size:12
Alignment explanation
Indices: 280333--280367 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
280323 AAAGGAGTTC
280333 GAAAAAAAAATTT
1 GAAAAAAAAA-TT
280346 GAAAAAAAAATT
1 GAAAAAAAAATT
280358 GAAAAAAAAA
1 GAAAAAAAAA
280368 ATTGCATACG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (12 bp):
GAAAAAAAAATT
Found at i:280368 original size:13 final size:13
Alignment explanation
Indices: 280333--280371 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
280323 AAAGGAGTTC
*
280333 GAAAAAAAAATTT
1 GAAAAAAAAAATT
280346 G-AAAAAAAAATT
1 GAAAAAAAAAATT
280358 GAAAAAAAAAATT
1 GAAAAAAAAAATT
280371 G
1 G
280372 CATACGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (13 bp):
GAAAAAAAAAATT
Found at i:281172 original size:15 final size:15
Alignment explanation
Indices: 281140--281173 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
281130 GTTCAACGAA
*
281140 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
281155 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
281170 GAGG
1 GAGG
281174 GAGGTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:285909 original size:10 final size:10
Alignment explanation
Indices: 285894--285955 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
285884 TTTGAACCAT
*
285894 TACCAATTCG
1 TACCAATTCA
*
285904 TACCAAATACCA
1 TACC-AAT-TCA
*
285916 TACCATTTCA
1 TACCAATTCA
285926 TACCAATTCCA
1 TACCAATT-CA
* *
285937 TACCATTTCG
1 TACCAATTCA
285947 TACCAATTC
1 TACCAATTC
285956 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:285939 original size:21 final size:21
Alignment explanation
Indices: 285894--285956 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
285884 TTTGAACCAT
* *
285894 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
285916 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
285937 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
285957 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:295331 original size:23 final size:22
Alignment explanation
Indices: 295280--295331 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
295270 CCTCGTCTTT
*
295280 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
295302 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
295325 TTCTTTT
1 TTCTTTT
295332 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:304950 original size:20 final size:19
Alignment explanation
Indices: 304919--304956 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
304909 GAGCTAATAC
304919 GAGCTCAATGAGCTGAATT
1 GAGCTCAATGAGCTGAATT
304938 GAGCTCGAATGAGCTGAAT
1 GAGCTC-AATGAGCTGAAT
304957 CGAAAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:306677 original size:15 final size:14
Alignment explanation
Indices: 306658--306708 Score: 66
Period size: 15 Copynumber: 3.5 Consensus size: 14
306648 CTCACTCTCA
306658 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
306672 TATTTCTTTTTCTTT
1 T-TTTCTTTTTCTTT
* *
306687 TTCTCTCATTTCTTT
1 TTTTCT-TTTTCTTT
306702 TTTTCTT
1 TTTTCTT
306709 CTCTCAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 5 0.16
15 26 0.84
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTCTTTTTCTTT
Found at i:306713 original size:22 final size:21
Alignment explanation
Indices: 306637--306719 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
306627 CTCAAATTCT
* *
306637 TTTTTCTTTTTCTCAC-TCTC
1 TTTTTCTTTTTCTCTCATTTC
* * *
306657 ATTTTCTTTTTCTTTTATTTC
1 TTTTTCTTTTTCTCTCATTTC
306678 TTTTTCTTTTTCTCTCATTTC
1 TTTTTCTTTTTCTCTCATTTC
*
306699 TTTTT-TTCTTCTCTCAATTTC
1 TTTTTCTTTTTCTCTC-ATTTC
306720 ATTCAAGATT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
20 21 0.40
21 31 0.60
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTCTTTTTCTCTCATTTC
Found at i:309537 original size:20 final size:19
Alignment explanation
Indices: 309506--309543 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
309496 GAGCTAATAC
309506 GAGCTCAATGAGCTGAATT
1 GAGCTCAATGAGCTGAATT
309525 GAGCTCGAATGAGCTGAAT
1 GAGCTC-AATGAGCTGAAT
309544 CGAAAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:310093 original size:20 final size:19
Alignment explanation
Indices: 310029--310093 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
310019 TATAAACGCA
310029 AATGAGCTTAAAATGAGCTG
1 AATGAGC-TAAAATGAGCTG
* *
310049 ATTGAGCTAAGAGTGAGCTCG
1 AATGAGCTAA-AATGAGCT-G
310070 -ATGAGCTAAAATTGAGCTG
1 AATGAGCTAAAA-TGAGCTG
310089 AATGA
1 AATGA
310094 ACTTAAAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 5 0.14
20 31 0.84
21 1 0.03
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.25
Consensus pattern (19 bp):
AATGAGCTAAAATGAGCTG
Found at i:319965 original size:28 final size:28
Alignment explanation
Indices: 319910--319963 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
319900 TGAAATGAAA
* *
319910 AGGGGTTGCTGATGTGCTGATTCCCCCG
1 AGGGGTTGCTGAAGTGATGATTCCCCCG
319938 AGGGGTTGCT-AAGTGATGATTCCCCC
1 AGGGGTTGCTGAAGTGATGATTCCCCC
319964 CGTTCAGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.15, C:0.24, G:0.33, T:0.28
Consensus pattern (28 bp):
AGGGGTTGCTGAAGTGATGATTCCCCCG
Found at i:322703 original size:21 final size:21
Alignment explanation
Indices: 322679--322731 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 21
322669 GGTGCGAGCG
322679 AGAAAAAGAAATCGAAAGAA-A
1 AGAAAAAGAAATCGAAA-AAGA
*
322700 AGAAAAAGAAATTGAAAAAGA
1 AGAAAAAGAAATCGAAAAAGA
322721 AGAAAAAGAAA
1 AGAAAAAGAAA
322732 GATTGGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.06
Consensus pattern (21 bp):
AGAAAAAGAAATCGAAAAAGA
Found at i:322753 original size:25 final size:23
Alignment explanation
Indices: 322725--322770 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
322715 AAAAGAAGAA
322725 AAAGAAAGATTGGAAAAAGAAATTG
1 AAAGAAAGATT-G-AAAAGAAATTG
* *
322750 AAAGAGAGCTTGAAAAGAAAT
1 AAAGAAAGATTGAAAAGAAAT
322771 CGAGTGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
24 1 0.05
25 9 0.47
ACGTcount: A:0.59, C:0.02, G:0.24, T:0.15
Consensus pattern (23 bp):
AAAGAAAGATTGAAAAGAAATTG
Found at i:328785 original size:36 final size:35
Alignment explanation
Indices: 328733--328822 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 35
328723 TCACCTTTTT
* *
328733 TTTTCTTTTCTTTTTTTTTGC-TCGATTTCTTTTTCA
1 TTTT-TTTTCATTTTTTTT-CATCAATTTCTTTTTCA
* *
328769 CTTTTTTTTCATTTTTTTTCAATCAATTTTTTTTTGA
1 -TTTTTTTTCATTTTTTTTC-ATCAATTTCTTTTTCA
*
328806 TTTTTTTTGATTTTTTT
1 TTTTTTTTCATTTTTTT
328823 GTTACTCCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
35 1 0.02
36 29 0.63
37 16 0.35
ACGTcount: A:0.10, C:0.11, G:0.04, T:0.74
Consensus pattern (35 bp):
TTTTTTTTCATTTTTTTTCATCAATTTCTTTTTCA
Found at i:328823 original size:9 final size:10
Alignment explanation
Indices: 328796--328822 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
328786 TTCAATCAAT
328796 TTTTTTTTGA
1 TTTTTTTTGA
328806 TTTTTTTTGA
1 TTTTTTTTGA
328816 TTTTTTT
1 TTTTTTT
328823 GTTACTCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.85
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:336771 original size:15 final size:15
Alignment explanation
Indices: 336724--336763 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
336714 TATAAGCAAC
336724 AAAACATAGTAATTA
1 AAAACATAGTAATTA
* *
336739 AAAAAATAATTAATTA
1 AAAACAT-AGTAATTA
336755 AAAACATAG
1 AAAACATAG
336764 CTATTAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (15 bp):
AAAACATAGTAATTA
Found at i:344734 original size:22 final size:21
Alignment explanation
Indices: 344709--344750 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
344699 TTTGAACCAT
344709 TACCAATT-CGTACCAACTTCCA
1 TACC-ATTACGTACCAA-TTCCA
344731 TACCATTACGTACCAATTCC
1 TACCATTACGTACCAATTCC
344751 TAAATACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.31, C:0.36, G:0.05, T:0.29
Consensus pattern (21 bp):
TACCATTACGTACCAATTCCA
Found at i:349834 original size:22 final size:22
Alignment explanation
Indices: 349806--349849 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
349796 TTTTGAACCA
349806 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
349828 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
349850 AAATACCAAA
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:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:353078 original size:22 final size:22
Alignment explanation
Indices: 353050--353093 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
353040 TTTTGAACCA
353050 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
353072 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
353094 AAATACCAAA
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:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:359890 original size:22 final size:22
Alignment explanation
Indices: 359862--359905 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
359852 TTTTGAACCA
359862 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
359884 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
359906 AAATACCAAA
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:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:362268 original size:23 final size:23
Alignment explanation
Indices: 362227--362270 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
362217 GCTATGTATG
*
362227 AAATAAGACACATTAAAAACATA
1 AAATAAAACACATTAAAAACATA
* *
362250 AAATAAAACATATTTAAAACA
1 AAATAAAACACATTAAAAACA
362271 CCTAATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.66, C:0.11, G:0.02, T:0.20
Consensus pattern (23 bp):
AAATAAAACACATTAAAAACATA
Found at i:367421 original size:13 final size:13
Alignment explanation
Indices: 367403--367428 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
367393 ACCTGAAAGC
367403 AATTTAATTCATA
1 AATTTAATTCATA
367416 AATTTAATTCATA
1 AATTTAATTCATA
367429 TTAGGACACA
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
AATTTAATTCATA
Found at i:367843 original size:20 final size:21
Alignment explanation
Indices: 367818--367856 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
367808 TCAAACAAGC
367818 AAATGAGCTCAA-TGAGCTGG
1 AAATGAGCTCAATTGAGCTGG
*
367838 AAATGAGCTGAATTGAGCT
1 AAATGAGCTCAATTGAGCT
367857 CAACGAGCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (21 bp):
AAATGAGCTCAATTGAGCTGG
Found at i:369134 original size:17 final size:17
Alignment explanation
Indices: 369114--369167 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
369104 CTTCACTCGT
369114 TTTCTTTTCAAACTCTC
1 TTTCTTTTCAAACTCTC
*
369131 TTTCTTTTTCAATCTCAT-
1 TTTC-TTTTCAAACTC-TC
369149 TTTGCTTTTC--ACTCTC
1 TTT-CTTTTCAAACTCTC
369165 TTT
1 TTT
369168 TGTTTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 1 0.03
16 6 0.19
17 4 0.13
18 18 0.58
19 2 0.06
ACGTcount: A:0.13, C:0.26, G:0.02, T:0.59
Consensus pattern (17 bp):
TTTCTTTTCAAACTCTC
Found at i:369157 original size:18 final size:18
Alignment explanation
Indices: 369136--369187 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
369126 CTCTCTTTCT
369136 TTTTCAATCTCATTTTGC
1 TTTTCAATCTCATTTTGC
* *
369154 TTTTCACTCTC-TTTTGT
1 TTTTCAATCTCATTTTGC
*
369171 TTTTGAAATCTCATTTT
1 TTTT-CAATCTCATTTT
369188 CATATTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 9 0.32
18 15 0.54
19 4 0.14
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.60
Consensus pattern (18 bp):
TTTTCAATCTCATTTTGC
Found at i:369201 original size:6 final size:6
Alignment explanation
Indices: 369192--369290 Score: 65
Period size: 6 Copynumber: 16.0 Consensus size: 6
369182 CATTTTCATA
* * * **
369192 TTTTTC TTTTTC AATTTTC TTTTCTTC ATTTTC TTTTTC TCTCAC TTTTTC
1 TTTTTC TTTTTC -TTTTTC -TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC
* * * **
369243 GTTTTC GTTTTC TTTTT- TGTTTTC TTTTTC TTCTTC ACTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TTTTTC
369291 GAATTCATTA
Statistics
Matches: 70, Mismatches: 19, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
5 1 0.01
6 56 0.80
7 10 0.14
8 3 0.04
ACGTcount: A:0.05, C:0.20, G:0.03, T:0.72
Consensus pattern (6 bp):
TTTTTC
Found at i:370601 original size:21 final size:21
Alignment explanation
Indices: 370575--370637 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
370565 TTGGTATTTG
370575 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
370596 GGAATTGGTATGAAACGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
370617 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
370638 ATGGTTCAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
21 21 0.60
22 14 0.40
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.32
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:374225 original size:12 final size:12
Alignment explanation
Indices: 374208--374245 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
374198 TAGTAGTTTC
374208 TTCAAAAAAAAA
1 TTCAAAAAAAAA
374220 TTCAAAAAAAAA
1 TTCAAAAAAAAA
*
374232 ATCAAAAAAAAA
1 TTCAAAAAAAAA
374244 TT
1 TT
374246 GATTTCCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:374301 original size:14 final size:14
Alignment explanation
Indices: 374282--374318 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
374272 GATATCAAGT
374282 TGAAAAAAAATTCA
1 TGAAAAAAAATTCA
*
374296 TG-AAAAAAATTCG
1 TGAAAAAAAATTCA
374309 TGAAAAAAAA
1 TGAAAAAAAA
374319 AGAAGAAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.65, C:0.05, G:0.11, T:0.19
Consensus pattern (14 bp):
TGAAAAAAAATTCA
Done.