Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chrUn_random
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: 10571689
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.28
Warning! 1662808 characters in sequence are not A, C, G, or T
File 11 of 30
Found at i:3810213 original size:20 final size:20
Alignment explanation
Indices: 3810188--3810233 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
3810178 TTTTAACCTC
3810188 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
3810208 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
3810228 ATTTGA
1 ATTTGA
3810234 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:3832062 original size:22 final size:21
Alignment explanation
Indices: 3832022--3832062 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3832012 TGAAAGTTGC
* *
3832022 AAGAAAAAATACAAGGAAAGG
1 AAGAAAAAAAACAAAGAAAGG
3832043 AAGAAAGAAAAACAAAGAAA
1 AAGAAA-AAAAACAAAGAAA
3832063 AGATATGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.73, C:0.05, G:0.20, T:0.02
Consensus pattern (21 bp):
AAGAAAAAAAACAAAGAAAGG
Found at i:3836409 original size:18 final size:18
Alignment explanation
Indices: 3836386--3836448 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
3836376 CTCTCTAAAA
*
3836386 CTCCCATAACTCTAAGGC
1 CTCCCACAACTCTAAGGC
*
3836404 CTCCCACAAGTCTAAGGC
1 CTCCCACAACTCTAAGGC
** * * *
3836422 CTCTGACAAGTCCAATGC
1 CTCCCACAACTCTAAGGC
3836440 CTCCCACAA
1 CTCCCACAA
3836449 GTCCAAAACC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.29, C:0.40, G:0.13, T:0.19
Consensus pattern (18 bp):
CTCCCACAACTCTAAGGC
Found at i:3836449 original size:18 final size:18
Alignment explanation
Indices: 3836399--3836454 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
3836389 CCATAACTCT
*
3836399 AAGGCCTCCCACAAGTCT
1 AAGGCCTCCCACAAGTCC
**
3836417 AAGGCCTCTGACAAGTCC
1 AAGGCCTCCCACAAGTCC
*
3836435 AATGCCTCCCACAAGTCC
1 AAGGCCTCCCACAAGTCC
3836453 AA
1 AA
3836455 AACCTTTAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.30, C:0.38, G:0.16, T:0.16
Consensus pattern (18 bp):
AAGGCCTCCCACAAGTCC
Found at i:3836614 original size:41 final size:41
Alignment explanation
Indices: 3836540--3836766 Score: 231
Period size: 41 Copynumber: 5.5 Consensus size: 41
3836530 GATTATGTCG
**
3836540 CAAGACCCTAAAAGCAAAAGTTTGAAGTTCAAGAACAAATCA
1 CAAGACCCTTGAAGC-AAAGTTTGAAGTTCAAGAACAAATCA
* * * * *
3836582 CAAAACCTTTGAAGCAAATTTTGAAGTTCAAGATCAAGTCA
1 CAAGACCCTTGAAGCAAAGTTTGAAGTTCAAGAACAAATCA
* * *
3836623 CAAGACCCTTGAAGCAAAGTTCGAAGTTCAAGAACAAGTCG
1 CAAGACCCTTGAAGCAAAGTTTGAAGTTCAAGAACAAATCA
* * * * * *
3836664 CAAGACCTTTGAAGCAAATTTTAAAGTTAAAGAA-TAAGCA
1 CAAGACCCTTGAAGCAAAGTTTGAAGTTCAAGAACAAATCA
* * * * *
3836704 TAAGACCCTTGAAGCAAAGTTCGAAGTTCAATAACAAGTCG
1 CAAGACCCTTGAAGCAAAGTTTGAAGTTCAAGAACAAATCA
* *
3836745 CAAGACCCTTAAAACAAAGTTT
1 CAAGACCCTTGAAGCAAAGTTT
3836767 CCAAATCGTT
Statistics
Matches: 147, Mismatches: 37, Indels: 3
0.79 0.20 0.02
Matches are distributed among these distances:
40 29 0.20
41 107 0.73
42 11 0.07
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.22
Consensus pattern (41 bp):
CAAGACCCTTGAAGCAAAGTTTGAAGTTCAAGAACAAATCA
Found at i:3836672 original size:82 final size:81
Alignment explanation
Indices: 3836525--3836751 Score: 303
Period size: 82 Copynumber: 2.8 Consensus size: 81
3836515 TCATCATAGT
* * ** * * * *
3836525 TTCAAGATTATGTCGCAAGACCCTAAAAGCAAAAGTTTGAAGTTCAAGAACAAATCACAAAACCT
1 TTCAAGA-TAAGTCACAAGACCCTTGAAGC-AAAGTTCGAAGTTCAAGAACAAGTCGCAAGACCT
*
3836590 TTGAAGCAAATTTTGAAG
64 TTGAAGCAAATTTTAAAG
3836608 TTCAAGATCAAGTCACAAGACCCTTGAAGCAAAGTTCGAAGTTCAAGAACAAGTCGCAAGACCTT
1 TTCAAGAT-AAGTCACAAGACCCTTGAAGCAAAGTTCGAAGTTCAAGAACAAGTCGCAAGACCTT
3836673 TGAAGCAAATTTTAAAG
65 TGAAGCAAATTTTAAAG
* * *
3836690 TTAAAGAATAAG-CATAAGACCCTTGAAGCAAAGTTCGAAGTTCAATAACAAGTCGCAAGACC
1 TTCAAG-ATAAGTCACAAGACCCTTGAAGCAAAGTTCGAAGTTCAAGAACAAGTCGCAAGACC
3836752 CTTAAAACAA
Statistics
Matches: 130, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
81 48 0.37
82 56 0.43
83 26 0.20
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (81 bp):
TTCAAGATAAGTCACAAGACCCTTGAAGCAAAGTTCGAAGTTCAAGAACAAGTCGCAAGACCTTT
GAAGCAAATTTTAAAG
Found at i:3836969 original size:96 final size:96
Alignment explanation
Indices: 3836857--3837077 Score: 279
Period size: 96 Copynumber: 2.3 Consensus size: 96
3836847 AACAAGTTGC
* * * *
3836857 AAGACCCTTAAAGCGAAGTCTCCAAATTGTTCATTTAAGAGT-AATTCAAGACCCTT-AAAGTGA
1 AAGACCCTTGAAGCGAAGTCTCCAAATTGTTCATTCAAGA-TAAAGTCAAGACCCTTGAAA--AA
3836920 A-GTCTCCAAATCGTTCATTCAAGATCAAGTCAT
63 AGGTCTCCAAATCGTTCATTCAAGATCAAGTCAT
*
3836953 AAGACCCTTGAAGCGAAGTCTCCAAATTGTTCATTCAAGATAAAGTCAAGAGCCTTGAAAAAAGG
1 AAGACCCTTGAAGCGAAGTCTCCAAATTGTTCATTCAAGATAAAGTCAAGACCCTTGAAAAAAGG
* * * * *
3837018 TTTCCAAATTGTTCGTTCAATATGAAGTCAT
66 TCTCCAAATCGTTCATTCAAGATCAAGTCAT
*
3837049 AAGACCATTGAAGCGAAG-CTTCCAAATTG
1 AAGACCCTTGAAGCGAAGTC-TCCAAATTG
3837078 CATGAAGTTC
Statistics
Matches: 110, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
95 4 0.04
96 103 0.94
97 3 0.03
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (96 bp):
AAGACCCTTGAAGCGAAGTCTCCAAATTGTTCATTCAAGATAAAGTCAAGACCCTTGAAAAAAGG
TCTCCAAATCGTTCATTCAAGATCAAGTCAT
Found at i:3836976 original size:49 final size:46
Alignment explanation
Indices: 3836856--3837077 Score: 223
Period size: 47 Copynumber: 4.7 Consensus size: 46
3836846 GAACAAGTTG
* * *
3836856 CAAGACCCTTAAAGCGAAGTCTCCAAATTGTTCATTTAAGAGTAATT
1 CAAGACCCTTGAAGCGAAGTCTCCAAATTGTTCATTCAAGA-TAAGT
* * *
3836903 CAAGACCCTTAAAGTGAAGTCTCCAAATCGTTCATTCAAGATCAAGT
1 CAAGACCCTTGAAGCGAAGTCTCCAAATTGTTCATTCAAGAT-AAGT
3836950 CATAAGACCCTTGAAGCGAAGTCTCCAAATTGTTCATTCAAGATAAAGT
1 C--AAGACCCTTGAAGCGAAGTCTCCAAATTGTTCATTCAAGAT-AAGT
* ** * * *
3836999 CAAGAGCCTTGAA-AAAAGGTTTCCAAATTGTTCGTTCAATATGAAGT
1 CAAGACCCTTGAAGCGAA-GTCTCCAAATTGTTCATTCAAGAT-AAGT
*
3837046 CATAAGACCATTGAAGCGAAG-CTTCCAAATTG
1 C--AAGACCCTTGAAGCGAAGTC-TCCAAATTG
3837078 CATGAAGTTC
Statistics
Matches: 147, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
46 3 0.02
47 79 0.54
49 63 0.43
50 2 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (46 bp):
CAAGACCCTTGAAGCGAAGTCTCCAAATTGTTCATTCAAGATAAGT
Found at i:3837295 original size:22 final size:22
Alignment explanation
Indices: 3837270--3837335 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
3837260 ACAACAACAT
3837270 AAAAA-ACCTATTTGAGAACCA
1 AAAAATACCTATTTGAGAACCA
3837291 AAAAATACCTATTTGCA-AACCA
1 AAAAATACCTATTTG-AGAACCA
*
3837313 AAAAATACCTATTTG-GAAACA
1 AAAAATACCTATTTGAGAACCA
3837334 AA
1 AA
3837336 CTTCAAGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
21 11 0.27
22 29 0.71
23 1 0.02
ACGTcount: A:0.53, C:0.18, G:0.08, T:0.21
Consensus pattern (22 bp):
AAAAATACCTATTTGAGAACCA
Found at i:3840718 original size:51 final size:51
Alignment explanation
Indices: 3840632--3840736 Score: 147
Period size: 51 Copynumber: 2.1 Consensus size: 51
3840622 GGATTTCACG
* * * *
3840632 CATGACACCTCAAAGTGTCGAAGCGCAAGTGTGGAGTTTGGTATGGGCTAA
1 CATGACACCTCAAAGTGTCAAAGCGAAAGTATGGAGTTTGGTATGAGCTAA
* * *
3840683 CATGGCACCTCAAAGTGTCAAAGTGAAATTATGGAGTTTGGTATGAGCTAA
1 CATGACACCTCAAAGTGTCAAAGCGAAAGTATGGAGTTTGGTATGAGCTAA
3840734 CAT
1 CAT
3840737 TGCTAGGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (51 bp):
CATGACACCTCAAAGTGTCAAAGCGAAAGTATGGAGTTTGGTATGAGCTAA
Found at i:3846850 original size:28 final size:29
Alignment explanation
Indices: 3846792--3846855 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
3846782 GTAAATTTTT
** *
3846792 AAAAATTACACTTTTACCCCCGTAAAGTG
1 AAAAATTACACTTTTACCCCCAAAAACTG
* *
3846821 AAAAATTACATTTTTA-CCTCAAAAACTG
1 AAAAATTACACTTTTACCCCCAAAAACTG
3846849 AAAAATT
1 AAAAATT
3846856 GCCCATACAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCCAAAAACTG
Found at i:3857602 original size:69 final size:70
Alignment explanation
Indices: 3857482--3857682 Score: 176
Period size: 77 Copynumber: 2.8 Consensus size: 70
3857472 AGGAAAGTTC
* * * * **
3857482 AATGCTATCACATAACTTTAGAAATTTCTTTTAAAATA-AGAAACTAA-TTCTTATGAATGTCCC
1 AATGCTATC-CTTAATTTTAGGAATTTCTTTTAAAGTAGA-AAAC-AATTTCTTATGAATCACCC
3857545 -AAATTAA
63 AAAATTAA
*
3857552 AATGCTATCCTTAATTTTAGGAATTTCTTTTAAAGTAGAAAACAATTTCTTATTCTTTATAAATC
1 AATGCTATCCTTAATTTTAGGAATTTCTTTTAAAGTAGAAAACAA-----T-TTC-TTATGAATC
3857617 ACCCAAAATTAA
59 ACCCAAAATTAA
* * * *
3857629 AACT-ATATCCTTAATTTTAGGAATTGCTTTTAAAGTAGGAAATAATTTCTTATG
1 AA-TGCTATCCTTAATTTTAGGAATTTCTTTTAAAGTAGAAAACAATTTCTTATG
3857683 TTTTATGAAT
Statistics
Matches: 108, Mismatches: 12, Indels: 22
0.76 0.08 0.15
Matches are distributed among these distances:
68 2 0.02
69 28 0.26
70 14 0.13
71 3 0.03
72 1 0.01
75 3 0.03
76 10 0.09
77 46 0.43
78 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.39
Consensus pattern (70 bp):
AATGCTATCCTTAATTTTAGGAATTTCTTTTAAAGTAGAAAACAATTTCTTATGAATCACCCAAA
ATTAA
Found at i:3857676 original size:77 final size:77
Alignment explanation
Indices: 3857557--3857707 Score: 241
Period size: 77 Copynumber: 2.0 Consensus size: 77
3857547 ATTAAAATGC
* *
3857557 TATCCTTAATTTTAGGAATTTCTTTTAAAGTAGAAAACAATTTCTTAT-TCTTTATAAATCACCC
1 TATCCTTAATTTTAGGAATTGCTTTTAAAGTAGAAAACAATTTCTTATGT-TTTATAAATCACAC
3857621 AAAATTAAAACTA
65 AAAATTAAAACTA
* * *
3857634 TATCCTTAATTTTAGGAATTGCTTTTAAAGTAGGAAATAATTTCTTATGTTTTATGAATCACACA
1 TATCCTTAATTTTAGGAATTGCTTTTAAAGTAGAAAACAATTTCTTATGTTTTATAAATCACACA
3857699 AAATTAAAA
66 AAATTAAAA
3857708 TAGATGGCAC
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
77 67 0.99
78 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (77 bp):
TATCCTTAATTTTAGGAATTGCTTTTAAAGTAGAAAACAATTTCTTATGTTTTATAAATCACACA
AAATTAAAACTA
Found at i:3860209 original size:51 final size:50
Alignment explanation
Indices: 3860091--3860210 Score: 136
Period size: 50 Copynumber: 2.4 Consensus size: 50
3860081 CAACAAACAA
* ** *
3860091 GCACCCCAAAGTGTCAAAGTGAAATTGTGAAGTTTGGTATGGCTAACATG
1 GCACCCCAAAGTGTCGAAGCAAAATTGGGAAGTTTGGTATGGCTAACATG
* *
3860141 GCACCGCAACA-TATCGAAGCAAAATTGAGGAA-TTTGGTATGAGCTAACATG
1 GCACCCCAA-AGTGTCGAAGCAAAATTG-GGAAGTTTGGTATG-GCTAACATG
*
3860192 GCACCTCAAAGTGTCGAAG
1 GCACCCCAAAGTGTCGAAG
3860211 TGAAAGGTGG
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
50 30 0.52
51 28 0.48
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (50 bp):
GCACCCCAAAGTGTCGAAGCAAAATTGGGAAGTTTGGTATGGCTAACATG
Found at i:3860523 original size:51 final size:51
Alignment explanation
Indices: 3860432--3860638 Score: 204
Period size: 51 Copynumber: 4.1 Consensus size: 51
3860422 CCAATAAAAG
* * *
3860432 GAAAGTGTGGAGTTTAGTATGGGCTAACAAGGCA-CTCCAAAGTGTTGAAGC
1 GAAAGTGTGGAGTTTGGTATGGGCTAACATGGCAGC-CCAAAGTGTCGAAGC
* * *
3860483 GAAAGTGTGGAGTTTGGTATGGGCCAACATGGCAGCCCAAAGTGTCAAAGT
1 GAAAGTGTGGAGTTTGGTATGGGCTAACATGGCAGCCCAAAGTGTCGAAGC
* * * * * *
3860534 GAAATTGTGAAGTGTGGTAT-GGCTAACATGGCAAG-CTAACGTATCGAAGC
1 GAAAGTGTGGAGTTTGGTATGGGCTAACATGGC-AGCCCAAAGTGTCGAAGC
* * * * * * *
3860584 AAAATTATGGAATTTGGTATGAGCTAACATGGCACCCCAAAGTGTCGAAGT
1 GAAAGTGTGGAGTTTGGTATGGGCTAACATGGCAGCCCAAAGTGTCGAAGC
3860635 GAAA
1 GAAA
3860639 AGTGGCGATG
Statistics
Matches: 125, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
50 37 0.30
51 87 0.70
52 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.23
Consensus pattern (51 bp):
GAAAGTGTGGAGTTTGGTATGGGCTAACATGGCAGCCCAAAGTGTCGAAGC
Found at i:3862525 original size:43 final size:43
Alignment explanation
Indices: 3862455--3862573 Score: 177
Period size: 43 Copynumber: 2.8 Consensus size: 43
3862445 GTAATTATGT
* *
3862455 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
*
3862498 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* *
3862541 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
3862574 GAGCTGGTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.22, C:0.21, G:0.38, T:0.19
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:3862583 original size:43 final size:43
Alignment explanation
Indices: 3862465--3862586 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
3862455 TGACTCGGCT
* **
3862465 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
3862508 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
3862551 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
3862587 TGATGATGAG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 70 0.99
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:3862597 original size:20 final size:20
Alignment explanation
Indices: 3862572--3862634 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
3862562 GGGAGTGCGC
3862572 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
3862592 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
* *
3862612 ATGGGTTGGTGA-GATGATG
1 ATGAGCTGGTGATGATGATG
3862631 ATGA
1 ATGA
3862635 TGGGTATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.25, C:0.03, G:0.41, T:0.30
Consensus pattern (20 bp):
ATGAGCTGGTGATGATGATG
Found at i:3863693 original size:51 final size:51
Alignment explanation
Indices: 3863617--3863973 Score: 377
Period size: 51 Copynumber: 7.0 Consensus size: 51
3863607 CCAATAAAAG
* * *
3863617 GAAAGTGTGGAGTTTGGTTTGGGCTAACATGACACCTCAAAGTGTTGAAAT
1 GAAAGTGTGGAGTTTGGTATGGGCTAACATGGCACCTCAAAGTGTTGAAAC
*
3863668 GAAAGTGTGGAGTTTGGTATGGGCTAACATGGCA-CTCCAAAAGTGTTGAAGC
1 GAAAGTGTGGAGTTTGGTATGGGCTAACATGGCACCT-C-AAAGTGTTGAAAC
* ** * * * *
3863720 GAAAAGTGTGGAGTTTGGCATAAGCTAACATGGCATCTCGAAGTG-TCAAAGT
1 G-AAAGTGTGGAGTTTGGTATGGGCTAACATGGCACCTCAAAGTGTTGAAA-C
* *
3863772 GAAAGTGTGGAG-TTGATATGGGCTAACATGGCAGCC-CAAAGTGTTGAAGC
1 GAAAGTGTGGAGTTTGGTATGGGCTAACATGGCA-CCTCAAAGTGTTGAAAC
* * * * * *
3863822 GAAAAGTGTGGAGTTTGGCATGAGCTAACATGGCATCTCAAAGTATCGAAGC
1 G-AAAGTGTGGAGTTTGGTATGGGCTAACATGGCACCTCAAAGTGTTGAAAC
* *
3863874 GAAA-TGGTGGAGTTTGGTATGGGCTAACATGGCATCC-CAAAGTG-TCAAAGT
1 GAAAGT-GTGGAGTTTGGTATGGGCTAACATGGCA-CCTCAAAGTGTTGAAA-C
* *
3863925 GAAAGTGTGGAGTTTGATATGGGCTAACATGGCACCCCAAAGTGTTGAA
1 GAAAGTGTGGAGTTTGGTATGGGCTAACATGGCACCTCAAAGTGTTGAA
3863974 GCATTTGTTT
Statistics
Matches: 254, Mismatches: 36, Indels: 31
0.79 0.11 0.10
Matches are distributed among these distances:
50 31 0.12
51 136 0.54
52 54 0.21
53 31 0.12
54 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.25
Consensus pattern (51 bp):
GAAAGTGTGGAGTTTGGTATGGGCTAACATGGCACCTCAAAGTGTTGAAAC
Found at i:3863950 original size:154 final size:154
Alignment explanation
Indices: 3863613--3863975 Score: 511
Period size: 154 Copynumber: 2.4 Consensus size: 154
3863603 GAAACCAATA
* * * **
3863613 AAAG-GAAAGTGTGGAGTTTGGTTTGGGCTAACATGACACCTCAAAGTGTTGAAATGAAAGTGTG
1 AAAGTGAAAGTGTGGAGTTTGATATGGGCTAACATGGCACC-CAAAGTGTTGAAGCGAAAGTGTG
* * * *
3863677 GAGTTTGGTATGGGCTAACATGGCACTCCAAAAGTGTTGAAGCGAAAAGTGTGGAGTTTGGCATA
65 GAGTTTGGCATGAGCTAACATGGCACTCCAAAAGTATCGAAGCGAAAAGTGTGGAGTTTGGCATA
* *
3863742 AGCTAACATGGCATCTCGAAGTGTC
130 AGCTAACATGGCATCCCAAAGTGTC
3863767 AAAGTGAAAGTGTGGAG-TTGATATGGGCTAACATGGCAGCCCAAAGTGTTGAAGCGAAAAGTGT
1 AAAGTGAAAGTGTGGAGTTTGATATGGGCTAACATGGCA-CCCAAAGTGTTGAAGCG-AAAGTGT
* *
3863831 GGAGTTTGGCATGAGCTAACATGGCA-TCTC-AAAGTATCGAAGCGAAATG-GTGGAGTTTGGTA
64 GGAGTTTGGCATGAGCTAACATGGCACTC-CAAAAGTATCGAAGCGAAAAGTGTGGAGTTTGGCA
**
3863893 TGGGCTAACATGGCATCCCAAAGTGTC
128 TAAGCTAACATGGCATCCCAAAGTGTC
3863920 AAAGTGAAAGTGTGGAGTTTGATATGGGCTAACATGGCACCCCAAAGTGTTGAAGC
1 AAAGTGAAAGTGTGGAGTTTGATATGGGCTAACATGGCA-CCCAAAGTGTTGAAGC
3863976 ATTTGTTTGG
Statistics
Matches: 188, Mismatches: 16, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
153 52 0.28
154 90 0.48
155 46 0.24
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.25
Consensus pattern (154 bp):
AAAGTGAAAGTGTGGAGTTTGATATGGGCTAACATGGCACCCAAAGTGTTGAAGCGAAAGTGTGG
AGTTTGGCATGAGCTAACATGGCACTCCAAAAGTATCGAAGCGAAAAGTGTGGAGTTTGGCATAA
GCTAACATGGCATCCCAAAGTGTC
Found at i:3863975 original size:102 final size:103
Alignment explanation
Indices: 3863618--3863975 Score: 443
Period size: 102 Copynumber: 3.5 Consensus size: 103
3863608 CAATAAAAGG
** * * * **
3863618 AAAGTGTGGAGTTTGGTTTGGGCTAACATGACACCTCAAAGTGTTGAAATGAAAGTGTGGAGTTT
1 AAAGTGTGGAGTTTGGCATGAGCTAACATGGCACCTCAAAGTGTCGAAGCGAAAGTGTGGAGTTT
* *
3863683 GGTATGGGCTAACATGGCACTCCAAAAGTGTTGAAGCGA
66 GGTATGGGCTAACATGGCA-TCCCAAAGTGTTAAAGCGA
* * * * *
3863722 AAAGTGTGGAGTTTGGCATAAGCTAACATGGCATCTCGAAGTGTCAAAGTGAAAGTGTGGAG-TT
1 AAAGTGTGGAGTTTGGCATGAGCTAACATGGCACCTCAAAGTGTCGAAGCGAAAGTGTGGAGTTT
* * *
3863786 GATATGGGCTAACATGGCAGCCCAAAGTGTTGAAGCGA
66 GGTATGGGCTAACATGGCATCCCAAAGTGTTAAAGCGA
* *
3863824 AAAGTGTGGAGTTTGGCATGAGCTAACATGGCATCTCAAAGTATCGAAGCGAAA-TGGTGGAGTT
1 AAAGTGTGGAGTTTGGCATGAGCTAACATGGCACCTCAAAGTGTCGAAGCGAAAGT-GTGGAGTT
* *
3863888 TGGTATGGGCTAACATGGCATCCCAAAGTGTCAAAGTG-
65 TGGTATGGGCTAACATGGCATCCCAAAGTGTTAAAGCGA
** * * *
3863926 AAAGTGTGGAGTTTGATATGGGCTAACATGGCACCCCAAAGTGTTGAAGC
1 AAAGTGTGGAGTTTGGCATGAGCTAACATGGCACCTCAAAGTGTCGAAGC
3863976 ATTTGTTTGG
Statistics
Matches: 222, Mismatches: 30, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
101 1 0.00
102 115 0.52
103 54 0.24
104 52 0.23
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.25
Consensus pattern (103 bp):
AAAGTGTGGAGTTTGGCATGAGCTAACATGGCACCTCAAAGTGTCGAAGCGAAAGTGTGGAGTTT
GGTATGGGCTAACATGGCATCCCAAAGTGTTAAAGCGA
Found at i:3864503 original size:2 final size:2
Alignment explanation
Indices: 3864474--3864522 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
3864464 AGAGAAAACT
*
3864474 TA TA T- TA TA T- TA TA TGA TA T- TT TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
3864514 TA TA TA TA T
1 TA TA TA TA T
3864523 TGAGCAGGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
1 3 0.07
2 37 0.88
3 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (2 bp):
TA
Found at i:3868767 original size:29 final size:27
Alignment explanation
Indices: 3868724--3868786 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 27
3868714 GCAAATTTTA
*
3868724 AAAAATTACACTTTTACCCCGATAAAGTG
1 AAAAATTACACTTTTACCCC-A-AAACTG
*
3868753 AAAAATTACATTTTTACCCCAAAACTG
1 AAAAATTACACTTTTACCCCAAAACTG
3868780 AAAAATT
1 AAAAATT
3868787 GCCCATAGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 12 0.38
28 1 0.03
29 19 0.59
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.29
Consensus pattern (27 bp):
AAAAATTACACTTTTACCCCAAAACTG
Found at i:3874326 original size:13 final size:13
Alignment explanation
Indices: 3874308--3874332 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3874298 TTCCAGAAAA
3874308 TTTATAAAATCAT
1 TTTATAAAATCAT
3874321 TTTATAAAATCA
1 TTTATAAAATCA
3874333 CAATTTCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:3887931 original size:12 final size:11
Alignment explanation
Indices: 3887904--3887958 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
3887894 AACCAAGCTT
3887904 TTTCTTCCTTTC
1 TTTC-TCCTTTC
* *
3887916 TCTCT-TTTTC
1 TTTCTCCTTTC
3887926 TTTCTCCTTTC
1 TTTCTCCTTTC
*
3887937 TTTCT--TTCC
1 TTTCTCCTTTC
3887946 TTTCTCCTTTC
1 TTTCTCCTTTC
3887957 TT
1 TT
3887959 CCAACTGATC
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
9 8 0.24
10 8 0.24
11 15 0.44
12 3 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTCTCCTTTC
Found at i:3887950 original size:20 final size:21
Alignment explanation
Indices: 3887904--3887958 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 21
3887894 AACCAAGCTT
* *
3887904 TTTCTTCCTTTCTCTCTTTTTC
1 TTTC-TCCTTTCTTTCTTTTCC
3887926 TTTCTCCTTTCTTTC-TTTCC
1 TTTCTCCTTTCTTTCTTTTCC
3887946 TTTCTCCTTTCTT
1 TTTCTCCTTTCTT
3887959 CCAACTGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 17 0.55
21 10 0.32
22 4 0.13
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTCTCCTTTCTTTCTTTTCC
Found at i:3902553 original size:13 final size:13
Alignment explanation
Indices: 3902535--3902559 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3902525 AGAGAAATCG
3902535 TGATTTTATAAAA
1 TGATTTTATAAAA
3902548 TGATTTTATAAA
1 TGATTTTATAAA
3902560 TTTTCTGAAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:3904980 original size:2 final size:2
Alignment explanation
Indices: 3904973--3905001 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3904963 CATTCAATTT
3904973 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3905002 TATGCCTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3905572 original size:19 final size:20
Alignment explanation
Indices: 3905548--3905593 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
3905538 TTAATATTTT
*
3905548 AATATTATTTTATT-TATAA
1 AATATTATTTTATTCTAAAA
3905567 AATATTATTTTATTCTAAAA
1 AATATTATTTTATTCTAAAA
3905587 AAT-TTAT
1 AATATTAT
3905594 CTTGCCTCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
AATATTATTTTATTCTAAAA
Found at i:3906563 original size:2 final size:2
Alignment explanation
Indices: 3906556--3906592 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3906546 CTAAATTTAG
3906556 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3906593 ATCAATAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3907777 original size:20 final size:20
Alignment explanation
Indices: 3907752--3907797 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
3907742 TTTTGACCCC
3907752 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
3907772 ATTTGACTTATTGGAGTATG
1 ATTTGACTTATTGGAGTATA
3907792 ATTTGA
1 ATTTGA
3907798 GGTTTAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.04, G:0.22, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:3916169 original size:20 final size:20
Alignment explanation
Indices: 3916144--3916189 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3916134 TTTTGACCCC
*
3916144 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGAAGTATA
*
3916164 ATTTGACTTATTGAAGTATG
1 ATTTGACTTATTGAAGTATA
3916184 ATTTGA
1 ATTTGA
3916190 GGTTTAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (20 bp):
ATTTGACTTATTGAAGTATA
Found at i:3916265 original size:28 final size:27
Alignment explanation
Indices: 3916234--3916286 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
3916224 TTTGGAGTAT
*
3916234 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTT-CCACCTC
*
3916262 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
3916287 ACCAGGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCTC
Found at i:3916292 original size:28 final size:28
Alignment explanation
Indices: 3916234--3916292 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
3916224 TTTGGAGTAT
* *
3916234 AGGGGTAAAATGGTAATTTTGCCACCTC
1 AGGGGCAAAATGGTAATTTTGCCACCCC
*
3916262 AGGGGCAAAATTGTAATTTT-CCACCACC
1 AGGGGCAAAATGGTAATTTTGCCACC-CC
3916290 AGG
1 AGG
3916293 ATATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTGCCACCCC
Found at i:3919067 original size:2 final size:2
Alignment explanation
Indices: 3919060--3919094 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3919050 GCTTGTTTAT
3919060 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3919095 TGGGAAAGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3921853 original size:15 final size:14
Alignment explanation
Indices: 3921833--3921866 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
3921823 ATAGGATATT
3921833 TTAAATTTAAACAAA
1 TTAAATTTAAA-AAA
3921848 TTAAATTTAAAAAA
1 TTAAATTTAAAAAA
3921862 -TAAAT
1 TTAAAT
3921867 AATCCTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 3 0.16
15 11 0.58
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAAATTTAAAAAA
Found at i:3928235 original size:17 final size:18
Alignment explanation
Indices: 3928208--3928241 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3928198 GAAAACTTTG
3928208 AAAAAATAATAAAATAAT
1 AAAAAATAATAAAATAAT
*
3928226 AAAAAA-AATAGAATAA
1 AAAAAATAATAAAATAA
3928242 AATATGTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (18 bp):
AAAAAATAATAAAATAAT
Found at i:3930061 original size:18 final size:19
Alignment explanation
Indices: 3930038--3930076 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
3930028 ACTTAAGTTT
*
3930038 ATTTTACTTGT-CATTTGC
1 ATTTTACATGTCCATTTGC
3930056 ATTTTACATGTCCATTTGC
1 ATTTTACATGTCCATTTGC
3930075 AT
1 AT
3930077 ATATCATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.21, C:0.18, G:0.10, T:0.51
Consensus pattern (19 bp):
ATTTTACATGTCCATTTGC
Found at i:3941087 original size:20 final size:20
Alignment explanation
Indices: 3941062--3941115 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
3941052 AATTTTAAAT
*
3941062 AAATAAAAACTATAATGAA-A
1 AAATAAAAAATATAAT-AATA
3941082 AAATAAAAAATATAATAATA
1 AAATAAAAAATATAATAATA
*
3941102 TAATAAAAAA-ATAA
1 AAATAAAAAATATAA
3941116 ATTTCACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (20 bp):
AAATAAAAAATATAATAATA
Found at i:3942795 original size:47 final size:47
Alignment explanation
Indices: 3942670--3942945 Score: 412
Period size: 47 Copynumber: 5.9 Consensus size: 47
3942660 TGCATACAAG
* * *
3942670 TTTACTTAACAAATAAGTAAAATAATTGCACCATGCATTTTATAAAT
1 TTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATAAAT
* ** *
3942717 TTTGCCTTTTCAAATAAGTAAAATAATTACATTATGCATTTTATAAAT
1 TTTACC-TAACAAATAAGTAAAATAATTACATCATGCATTTTATAAAT
* * *
3942765 TTTACCTAAAAAATAAGTAAAATAAATACATCAGGCATTTTATAAAT
1 TTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATAAAT
* *
3942812 TTTACATAACAAATAAGTAAAATAATTGCATCATGCATTTTATAAAT
1 TTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATAAAT
*
3942859 TTTACCTAACAAATAAGTAAAATAAATACATCATGCATTTTATAAAT
1 TTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATAAAT
3942906 TTTACCTAACAAATAAGTAAAATAATTACAT-A-GCATTTTA
1 TTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTA
3942946 CAACATATGT
Statistics
Matches: 205, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
45 8 0.04
46 1 0.00
47 155 0.76
48 41 0.20
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.36
Consensus pattern (47 bp):
TTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATAAAT
Found at i:3943963 original size:15 final size:15
Alignment explanation
Indices: 3943940--3943971 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3943930 CAATGGATAG
*
3943940 ATAATTTAAATTTAA
1 ATAAATTAAATTTAA
3943955 ATAAATTAAATTTAA
1 ATAAATTAAATTTAA
3943970 AT
1 AT
3943972 TTATCCTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAAATTAAATTTAA
Found at i:3944424 original size:28 final size:28
Alignment explanation
Indices: 3944373--3944427 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
3944363 AGTTTTGGAC
* *
3944373 TTGGTGTGTAATATTTGTTGCTGAAGTT
1 TTGGTGTGTAACATTTGTTACTGAAGTT
3944401 TTGGTGTGTAACATCTT-TTACTGAAGT
1 TTGGTGTGTAACAT-TTGTTACTGAAGT
3944428 GTATAACATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.20, C:0.07, G:0.25, T:0.47
Consensus pattern (28 bp):
TTGGTGTGTAACATTTGTTACTGAAGTT
Found at i:3947487 original size:37 final size:37
Alignment explanation
Indices: 3947417--3947489 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 37
3947407 TACCACCATA
* ** *
3947417 TGTGCACTCCCTACTCGCACATTTCAATGTCATCATG
1 TGTGCACTCCCTACTCACACACCTCAATATCATCATG
*
3947454 TGTGCACTCCCTACTCACACACCTCATTATCATCAT
1 TGTGCACTCCCTACTCACACACCTCAATATCATCAT
3947490 ACAACATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.23, C:0.36, G:0.10, T:0.32
Consensus pattern (37 bp):
TGTGCACTCCCTACTCACACACCTCAATATCATCATG
Found at i:3950753 original size:20 final size:21
Alignment explanation
Indices: 3950707--3950761 Score: 76
Period size: 20 Copynumber: 2.6 Consensus size: 21
3950697 AACCAAGCTT
* *
3950707 TTTCTTCCTTTCGTTCTTTTTC
1 TTTC-TCCTTTCTTTCTTTTCC
3950729 TTTCTCCTTTCTTTC-TTTCC
1 TTTCTCCTTTCTTTCTTTTCC
3950749 TTTCTCCTTTCTT
1 TTTCTCCTTTCTT
3950762 CCAACTGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 17 0.55
21 10 0.32
22 4 0.13
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTCTCCTTTCTTTCTTTTCC
Found at i:3950874 original size:19 final size:19
Alignment explanation
Indices: 3950850--3950891 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3950840 GGTGGCAAGG
*
3950850 TGAAAATGGAATGGAAGCT
1 TGAAAATGGAATGGAAGCA
*
3950869 TGAAAATGGCATGGAAGCA
1 TGAAAATGGAATGGAAGCA
3950888 TGAA
1 TGAA
3950892 GGTGAGGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.43, C:0.07, G:0.31, T:0.19
Consensus pattern (19 bp):
TGAAAATGGAATGGAAGCA
Found at i:3958504 original size:35 final size:35
Alignment explanation
Indices: 3958475--3958614 Score: 190
Period size: 35 Copynumber: 4.0 Consensus size: 35
3958465 GGAGTACGTG
*
3958475 TGATGGTATTGAAATGTGCGTGCAGGGAGTGCACA
1 TGATGATATTGAAATGTGCGTGCAGGGAGTGCACA
* *
3958510 TGATGATATTGAAATGTGCATGTAGGGAGTGCACA
1 TGATGATATTGAAATGTGCGTGCAGGGAGTGCACA
* *
3958545 TGATGATATTGAAATGTGCGTGTAAGGAGTGCACA
1 TGATGATATTGAAATGTGCGTGCAGGGAGTGCACA
**** *
3958580 TGATGATATTCCCTTGTGCGTGTAGGGAGTGCACA
1 TGATGATATTGAAATGTGCGTGCAGGGAGTGCACA
3958615 AGAGCTAATG
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 95 1.00
ACGTcount: A:0.27, C:0.11, G:0.33, T:0.29
Consensus pattern (35 bp):
TGATGATATTGAAATGTGCGTGCAGGGAGTGCACA
Found at i:3964674 original size:25 final size:26
Alignment explanation
Indices: 3964616--3964675 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
3964606 GTGGTCGCAA
3964616 CCAC-GTATATCAACTCGTGGCCCAG
1 CCACTGTATATCAACTCGTGGCCCAG
* **
3964641 CCACT-TATATCATCTCGTGGCCTTG
1 CCACTGTATATCAACTCGTGGCCCAG
3964666 CCA-TGTATAT
1 CCACTGTATAT
3964676 ATATATCACA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 1 0.03
25 29 0.97
ACGTcount: A:0.22, C:0.32, G:0.17, T:0.30
Consensus pattern (26 bp):
CCACTGTATATCAACTCGTGGCCCAG
Found at i:3965982 original size:37 final size:37
Alignment explanation
Indices: 3965875--3965985 Score: 132
Period size: 37 Copynumber: 3.0 Consensus size: 37
3965865 CTTCAGCTCT
* ** * *
3965875 TGTGCACTCCCTACACACACAAGGCAATACCACCATA
1 TGTGCACTCCCTACTCACACAATTCAATATCATCATA
* * *
3965912 TGTGCACTCCCTACTCACACATTTCAATGTCATCATG
1 TGTGCACTCCCTACTCACACAATTCAATATCATCATA
* *
3965949 TGTGCACTCCCTACTCACACACTTCATTATCATCATA
1 TGTGCACTCCCTACTCACACAATTCAATATCATCATA
3965986 CAACATCATT
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.29, C:0.35, G:0.09, T:0.27
Consensus pattern (37 bp):
TGTGCACTCCCTACTCACACAATTCAATATCATCATA
Found at i:3975240 original size:22 final size:22
Alignment explanation
Indices: 3975215--3975258 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3975205 TTTAAAACAA
*
3975215 CTTTAAAACTAAAAACTTTGAT
1 CTTTAAAACCAAAAACTTTGAT
*
3975237 CTTTAAAACCAAAAGCTTTGAT
1 CTTTAAAACCAAAAACTTTGAT
3975259 ACCAATTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (22 bp):
CTTTAAAACCAAAAACTTTGAT
Found at i:3977857 original size:20 final size:20
Alignment explanation
Indices: 3977832--3977877 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
3977822 CTTCTAAACC
3977832 TCAAATCATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
*
3977852 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
3977872 TCAAAT
1 TCAAAT
3977878 GGAGTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:3988423 original size:19 final size:19
Alignment explanation
Indices: 3988399--3988441 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
3988389 TCTTCTTCTC
* *
3988399 TTTCATGCTGCTACGCCAT
1 TTTCATGCTCCCACGCCAT
*
3988418 TTTCATGCTCCCACGCTAT
1 TTTCATGCTCCCACGCCAT
3988437 TTTCA
1 TTTCA
3988442 CCTTACCCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.16, C:0.33, G:0.12, T:0.40
Consensus pattern (19 bp):
TTTCATGCTCCCACGCCAT
Found at i:3990469 original size:14 final size:14
Alignment explanation
Indices: 3990452--3990481 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
3990442 AATCGGCTTG
3990452 AAAGAAAGAAGAAA
1 AAAGAAAGAAGAAA
3990466 AAAGAAAGAAGAAA
1 AAAGAAAGAAGAAA
3990480 AA
1 AA
3990482 GGAGAAGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAAGAAA
Found at i:3990482 original size:23 final size:23
Alignment explanation
Indices: 3990456--3990503 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
3990446 GGCTTGAAAG
3990456 AAAGAAGAAAAAAGAAAGAAGAA
1 AAAGAAGAAAAAAGAAAGAAGAA
* ***
3990479 AAAGGAGAAGGGAGAAAGAAGAA
1 AAAGAAGAAAAAAGAAAGAAGAA
3990502 AA
1 AA
3990504 GCTAAAAGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (23 bp):
AAAGAAGAAAAAAGAAAGAAGAA
Found at i:3994320 original size:37 final size:37
Alignment explanation
Indices: 3994270--3994415 Score: 197
Period size: 37 Copynumber: 3.9 Consensus size: 37
3994260 TTCATCGTCA
* *
3994270 TGTGCACTTCCTACTCGCACGCTTCAACATCATCATG
1 TGTGCACTCCCTACTCGCACACTTCAACATCATCATG
*
3994307 TGTGCATTCCCTACTCGCACAC-TCTAACATCATCATG
1 TGTGCACTCCCTACTCGCACACTTC-AACATCATCATG
* * *
3994344 TGTGCACTCCTTACTTC-CACACATCAATATCATCATG
1 TGTGCACTCCCTAC-TCGCACACTTCAACATCATCATG
*
3994381 TGTCCACTCCCTACTCGCACACTTCAACATCATCA
1 TGTGCACTCCCTACTCGCACACTTCAACATCATCA
3994416 CATAACATTA
Statistics
Matches: 95, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
36 4 0.04
37 87 0.92
38 4 0.04
ACGTcount: A:0.25, C:0.36, G:0.10, T:0.29
Consensus pattern (37 bp):
TGTGCACTCCCTACTCGCACACTTCAACATCATCATG
Found at i:4002979 original size:28 final size:29
Alignment explanation
Indices: 4002938--4002997 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
4002928 GTCTATGGGC
*
4002938 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
4002966 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
4002996 AA
1 AA
4002998 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:4006081 original size:20 final size:20
Alignment explanation
Indices: 4006056--4006094 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4006046 GAAGAAGAAC
*
4006056 AAGCTGTTGGAAAAATGAGG
1 AAGCTGCTGGAAAAATGAGG
*
4006076 AAGCTGCTGGATAAATGAG
1 AAGCTGCTGGAAAAATGAG
4006095 ATATTTATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.08, G:0.33, T:0.21
Consensus pattern (20 bp):
AAGCTGCTGGAAAAATGAGG
Found at i:4010471 original size:185 final size:186
Alignment explanation
Indices: 4010124--4010482 Score: 684
Period size: 186 Copynumber: 1.9 Consensus size: 186
4010114 CAAAATTACC
4010124 ATTTTACCCCTATGCTCCGAAAAATACGAAGATTAAAAATTTTCACTTCTCAACCTCAAATCATA
1 ATTTTACCCCTATGCTCCGAAAAATACGAAGATTAAAAATTTTCACTTCTCAACCTCAAATCATA
4010189 CTCCAATAAGTCAAATATGATCAAAATCTTTTAAAAAAAAATTCCTTTCTTGTCCTCTAGTGGCA
66 CTCCAATAAGTCAAATATGATCAAAATCTTTTAAAAAAAAATTCCTTTCTTGTCCTCTAGTGGCA
4010254 AAATTACCATTTTACCCATAGATAGTAAAATTTTCGATTTGACTGGCAAAATTGTA
131 AAATTACCATTTTACCCATAGATAGTAAAATTTTCGATTTGACTGGCAAAATTGTA
*
4010310 ATTTTACCCCTATGCTCCGAAAAATACGAAGATTAAAATTTTTCACTTCTCAACCTCAAATCATA
1 ATTTTACCCCTATGCTCCGAAAAATACGAAGATTAAAAATTTTCACTTCTCAACCTCAAATCATA
*
4010375 CTCCAATAAGTCAAATATGATCAAAATC-TTTCAAAAAAAATTCCTTTCTTGTCCTCTAGTGGCA
66 CTCCAATAAGTCAAATATGATCAAAATCTTTTAAAAAAAAATTCCTTTCTTGTCCTCTAGTGGCA
*
4010439 AAATTACCATTTTACCCATAGATAGTAAAATTTTCGGTTTGACT
131 AAATTACCATTTTACCCATAGATAGTAAAATTTTCGATTTGACT
4010483 CCAAATTGAT
Statistics
Matches: 170, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
185 78 0.46
186 92 0.54
ACGTcount: A:0.37, C:0.21, G:0.09, T:0.34
Consensus pattern (186 bp):
ATTTTACCCCTATGCTCCGAAAAATACGAAGATTAAAAATTTTCACTTCTCAACCTCAAATCATA
CTCCAATAAGTCAAATATGATCAAAATCTTTTAAAAAAAAATTCCTTTCTTGTCCTCTAGTGGCA
AAATTACCATTTTACCCATAGATAGTAAAATTTTCGATTTGACTGGCAAAATTGTA
Found at i:4015823 original size:43 final size:43
Alignment explanation
Indices: 4015735--4015853 Score: 143
Period size: 43 Copynumber: 2.8 Consensus size: 43
4015725 GTAATTATAT
* *
4015735 TGACTTGGCTATGTGCGAGTAGGGAGTGTGCATAAGCCGAGGA
1 TGACCTGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAGGA
* * *
4015778 TGACCTGGTTATGTGCTAGTAGAGAGTGCGCATAA-CTCG-GTGA
1 TGACCTGGCTATGTGCGAGTAGGGAGTGCGCATAAGC-CGAG-GA
* *
4015821 TGACCTAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCTGGCTATGTGCGAGTAGGGAGTGCGCAT
4015854 NNNNNNNNNN
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 2 0.03
43 62 0.97
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.24
Consensus pattern (43 bp):
TGACCTGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAGGA
Found at i:4017398 original size:69 final size:69
Alignment explanation
Indices: 4017259--4017388 Score: 224
Period size: 69 Copynumber: 1.9 Consensus size: 69
4017249 GTGATAATAA
* *
4017259 TGACCCAGCTATGTGTGGTGTGGGAGTGCACATGAGCTGATGATGACCCATCTTTGTGCGATGTG
1 TGACCCAGCTATGTGTGGTGTGGGAGTGCACATGAGCTGATGATGACCCAGCTATGTGCGATGTG
4017324 CGAG
66 CGAG
**
4017328 TGACCCAGCTATGTGTGGTGTGGGAGTGCACATGAGCTGATGATGACCTGGCTATGTGCGA
1 TGACCCAGCTATGTGTGGTGTGGGAGTGCACATGAGCTGATGATGACCCAGCTATGTGCGA
4017389 GTAGGGAGTG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 57 1.00
ACGTcount: A:0.19, C:0.18, G:0.35, T:0.27
Consensus pattern (69 bp):
TGACCCAGCTATGTGTGGTGTGGGAGTGCACATGAGCTGATGATGACCCAGCTATGTGCGATGTG
CGAG
Found at i:4020999 original size:22 final size:22
Alignment explanation
Indices: 4020957--4020997 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
4020947 TACCTTTTGT
*
4020957 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
4020979 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
4020998 TCCACGTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:4024600 original size:20 final size:20
Alignment explanation
Indices: 4024572--4024609 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4024562 ACCTAGCTTG
4024572 TTTCCTTG-ATTTCTTCACTT
1 TTTCCTTGAATTT-TTCACTT
*
4024592 TTTCTTTGAATTTTTCAC
1 TTTCCTTGAATTTTTCAC
4024610 CTAGGTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.13, C:0.21, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTCCTTGAATTTTTCACTT
Found at i:4024914 original size:28 final size:27
Alignment explanation
Indices: 4024874--4024929 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
4024864 AATGTCCTGG
** *
4024874 TGGTGGAAAATTACTGTTTTGCCCCTA
1 TGGTGGAAAATTACCATTTTACCCCTA
4024901 TGGTGGTAAAATTACCATTTTACCCCTA
1 TGGTGG-AAAATTACCATTTTACCCCTA
4024929 T
1 T
4024930 ACTCCAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.38
Consensus pattern (27 bp):
TGGTGGAAAATTACCATTTTACCCCTA
Found at i:4029452 original size:18 final size:18
Alignment explanation
Indices: 4029418--4029451 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4029408 AACATTTAAA
*
4029418 AATAAATTAAAATAAAAT
1 AATAAAATAAAATAAAAT
4029436 AATAAAAT-AAATAAAA
1 AATAAAATAAAATAAAA
4029452 ACACCTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
AATAAAATAAAATAAAAT
Found at i:4039559 original size:263 final size:260
Alignment explanation
Indices: 4039082--4039603 Score: 633
Period size: 263 Copynumber: 2.0 Consensus size: 260
4039072 ACTTCAATTG
* *
4039082 GTGAAGAAAGGTGCACAATGGACTATTGCTCTATTTGCATATGTTTCGGTTTATCAAATATATCT
1 GTGAAGAAAGGTGCACAATGGACTATTGCTCTATTTGCATATATTTCAGTTTATCAAATATATCT
** * * * * **
4039147 CTTACTACCCAAGTCCAAATGATATGGTTTTTTAACCATTAGAAAGCTAAGAGGTAGGCTACAAC
66 CCCACTACACAAGTCCAAATGATATGATTTTTTAACCATTAGAAAGCAAAGAGGAACACTACAAC
* * *
4039212 TTTGATGTTTACCACTTTGCCCAGTTCTGGTAGGAAGGTGGTCAAAATCTTTGTTAAAGTGAAAG
131 TTTGATGTTTACCACTTTGCCCAGTTCTGATAGGAAAGTGGTCAAAATCTTTGTCAAAGTGAAAG
* * * **
4039277 TACTGCATGAGAGGAACAGAATT-TGGCAGAACATTT-ATGCGTCGCGGTGCTAGAAATTGAGAG
196 TACTGCATGAGAAGAACAG-ATTCAGACAGAACATTTGA-GCGTCGCGGCACTAGAAATTGAGAG
4039340 CC
259 CC
* * * *
4039342 NGTGAAGAAAGGTGCATAATGGGCTGTTGCTCTATTTGCATATATTTCAGTTTTTCAAGA-ATAT
1 -GTGAAGAAAGGTGCACAATGGACTATTGCTCTATTTGCATATATTTCAGTTTATCAA-ATATAT
* * * *
4039406 CTCCCACTATAGAAGTCGAAATGACT-TGATTTTTTGACCATTAGAAAGCAAAGAGGCAACACTA
64 CTCCCACTACACAAGTCCAAATGA-TATGATTTTTTAACCATTAGAAAGCAAAGAGG-AACACTA
* * * *
4039470 CAACTTTTGTTGTTTACCACTTTGCCCAGTTTTGATGGGAAAGTGGTCAAAATCTTTGTCGAAGT
127 CAAC-TTTGATGTTTACCACTTTGCCCAGTTCTGATAGGAAAGTGGTCAAAATCTTTGTCAAAGT
* *
4039535 GGAAGTACTG-A-GCTAGAAGAACAGATTCAGACAGAACATTTGAGCGTCGCGGCACTGGAAATT
191 GAAAGTACTGCATG--AGAAGAACAGATTCAGACAGAACATTTGAGCGTCGCGGCACTAGAAATT
4039598 GAGAGC
254 GAGAGC
4039604 TGCGACCCCT
Statistics
Matches: 221, Mismatches: 32, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
261 101 0.46
262 14 0.06
263 105 0.48
264 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (260 bp):
GTGAAGAAAGGTGCACAATGGACTATTGCTCTATTTGCATATATTTCAGTTTATCAAATATATCT
CCCACTACACAAGTCCAAATGATATGATTTTTTAACCATTAGAAAGCAAAGAGGAACACTACAAC
TTTGATGTTTACCACTTTGCCCAGTTCTGATAGGAAAGTGGTCAAAATCTTTGTCAAAGTGAAAG
TACTGCATGAGAAGAACAGATTCAGACAGAACATTTGAGCGTCGCGGCACTAGAAATTGAGAGCC
Found at i:4041283 original size:26 final size:26
Alignment explanation
Indices: 4041254--4041338 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
4041244 ATGTGGATCC
4041254 CCCCACATCGTGCACACAGTCGGACA
1 CCCCACATCGTGCACACAGTCGGACA
*** * * *
4041280 CCCCATC-TCACCCAACTCATGT-GCATCC
1 CCCCA-CATCGTGC-ACACA-GTCGGA-CA
4041308 CCCCACATCGTGCACACAGTCGGACA
1 CCCCACATCGTGCACACAGTCGGACA
4041334 CCCCA
1 CCCCA
4041339 TCTCACCCAA
Statistics
Matches: 41, Mismatches: 12, Indels: 12
0.63 0.18 0.18
Matches are distributed among these distances:
26 16 0.39
27 14 0.34
28 11 0.27
ACGTcount: A:0.25, C:0.47, G:0.14, T:0.14
Consensus pattern (26 bp):
CCCCACATCGTGCACACAGTCGGACA
Found at i:4041313 original size:54 final size:54
Alignment explanation
Indices: 4041231--4041431 Score: 330
Period size: 54 Copynumber: 3.7 Consensus size: 54
4041221 ACCACCACAT
* * *
4041231 TCTCATCCAGCTCATGTGGATCCCCCCACATCGTGCACACAGTCGGACACCCCA
1 TCTCACCCAACTCATGTGCATCCCCCCACATCGTGCACACAGTCGGACACCCCA
4041285 TCTCACCCAACTCATGTGCATCCCCCCACATCGTGCACACAGTCGGACACCCCA
1 TCTCACCCAACTCATGTGCATCCCCCCACATCGTGCACACAGTCGGACACCCCA
* *
4041339 TCTCACCCAACTCATGTGCATCCCCCCACATCGTGCACATAGTCGGACACCCTA
1 TCTCACCCAACTCATGTGCATCCCCCCACATCGTGCACACAGTCGGACACCCCA
* * *
4041393 TCTCAACCAGCTCGTGTGCATCCCCCCACATCGTGCACA
1 TCTCACCCAACTCATGTGCATCCCCCCACATCGTGCACA
4041432 ATTAATGCCA
Statistics
Matches: 139, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 139 1.00
ACGTcount: A:0.23, C:0.44, G:0.14, T:0.19
Consensus pattern (54 bp):
TCTCACCCAACTCATGTGCATCCCCCCACATCGTGCACACAGTCGGACACCCCA
Found at i:4043382 original size:40 final size:38
Alignment explanation
Indices: 4043284--4043386 Score: 129
Period size: 38 Copynumber: 2.7 Consensus size: 38
4043274 ATACTGCCTG
*
4043284 TGTGCACGATGTGGGGGGATGTACACGATGGCATTAAC
1 TGTGCACGATGTGGGGGGATGCACACGATGGCATTAAC
*
4043322 TGTGCACGATGTGGGGGGATGCACACGAT-G-ATTCTAGC
1 TGTGCACGATGTGGGGGGATGCACACGATGGCA-T-TAAC
*
4043360 TATGTGCACGATGTGGGTGGATGCACA
1 --TGTGCACGATGTGGGGGGATGCACA
4043387 TGAGCTGGGT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
36 1 0.02
37 2 0.03
38 31 0.53
40 24 0.41
ACGTcount: A:0.22, C:0.17, G:0.37, T:0.24
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGATGCACACGATGGCATTAAC
Found at i:4053354 original size:36 final size:36
Alignment explanation
Indices: 4053308--4053453 Score: 107
Period size: 36 Copynumber: 4.1 Consensus size: 36
4053298 CAACTTGACT
*
4053308 TTTTAATAGGATCAAACATAACCTTTACAACATGCC
1 TTTTAATAGGATCAAACATAACCTTCACAACATGCC
****
4053344 TTTTAATAGGATCAGGTGTAACCTTCACAACATGCC
1 TTTTAATAGGATCAAACATAACCTTCACAACATGCC
** * * ** * *
4053380 TTTCCACAGGATTAGGCGTAATC-TCACAACATGCC
1 TTTTAATAGGATCAAACATAACCTTCACAACATGCC
* * * ** *
4053415 TTATCACAACATCAAGCATAACC-TCACAACATGCC
1 TTTTAATAGGATCAAACATAACCTTCACAACATGCC
4053450 TTTT
1 TTTT
4053454 CACAAGATTA
Statistics
Matches: 90, Mismatches: 20, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
35 42 0.47
36 48 0.53
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.29
Consensus pattern (36 bp):
TTTTAATAGGATCAAACATAACCTTCACAACATGCC
Found at i:4053414 original size:35 final size:35
Alignment explanation
Indices: 4053334--4053475 Score: 149
Period size: 35 Copynumber: 4.0 Consensus size: 35
4053324 CATAACCTTT
* * * *
4053334 ACAACATGCCTTTTAATAGGATCAGGTGTAACCTTC
1 ACAACATGCCTTTTCACAAGATCAGGCGTAACC-TC
* * * *
4053370 ACAACATGCCTTTCCACAGGATTAGGCGTAATCTC
1 ACAACATGCCTTTTCACAAGATCAGGCGTAACCTC
* * * *
4053405 ACAACATGCCTTATCACAACATCAAGCATAACCTC
1 ACAACATGCCTTTTCACAAGATCAGGCGTAACCTC
* *
4053440 ACAACATGCCTTTTCACAAGATTAGGCTTAACCTC
1 ACAACATGCCTTTTCACAAGATCAGGCGTAACCTC
4053475 A
1 A
4053476 ACCAAAGCAC
Statistics
Matches: 87, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
35 60 0.69
36 27 0.31
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (35 bp):
ACAACATGCCTTTTCACAAGATCAGGCGTAACCTC
Found at i:4058679 original size:37 final size:37
Alignment explanation
Indices: 4058630--4058748 Score: 177
Period size: 37 Copynumber: 3.2 Consensus size: 37
4058620 AATGCAATAT
** **
4058630 CATCATCATGTGTGCACTCCCAACTTGCACACTTCAA
1 CATCATCATGTGTGCACTCCTTACTCACACACTTCAA
*
4058667 CATCATCGTGTGTGCACTCCTTACTCACACAC-TCTAA
1 CATCATCATGTGTGCACTCCTTACTCACACACTTC-AA
4058704 CATCATCATGTGTGCACTCCTTACTCACACACTTCAA
1 CATCATCATGTGTGCACTCCTTACTCACACACTTCAA
4058741 CATCATCA
1 CATCATCA
4058749 CACAACATTA
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
36 2 0.03
37 70 0.95
38 2 0.03
ACGTcount: A:0.27, C:0.35, G:0.09, T:0.29
Consensus pattern (37 bp):
CATCATCATGTGTGCACTCCTTACTCACACACTTCAA
Found at i:4060733 original size:35 final size:35
Alignment explanation
Indices: 4060667--4060894 Score: 232
Period size: 35 Copynumber: 6.6 Consensus size: 35
4060657 GAGGCTTTGA
* * *
4060667 GCTGCAAAACTTTGAGA-GGAAAAAGACAGAGTTTT
1 GCTGC-AAATTTTGAGAGGGAAATAGAGAGAGTTTT
**
4060702 GCTATAAATTTTGAGAGGGAAATAGAGAGAGTTTT
1 GCTGCAAATTTTGAGAGGGAAATAGAGAGAGTTTT
** * *
4060737 GCTGCAAATTTTG-GAAAGAAATAGAAAGAGTTGT
1 GCTGCAAATTTTGAGAGGGAAATAGAGAGAGTTTT
*
4060771 GTTGCAAATTTTGAGAGGGAAATAGAGAGAGTTTT
1 GCTGCAAATTTTGAGAGGGAAATAGAGAGAGTTTT
* * * * *
4060806 GATGCAAATTTGGAAAGGGAAAAAGAGAAAG-TTT
1 GCTGCAAATTTTGAGAGGGAAATAGAGAGAGTTTT
* * * *
4060840 GCTGTAAATTTTGAGA-GGAGAGAGAAAGAGTTTT
1 GCTGCAAATTTTGAGAGGGAAATAGAGAGAGTTTT
*
4060874 GCTGCAAA-TTTGAGAGAGAAA
1 GCTGCAAATTTTGAGAGGGAAA
4060895 ACAAGAGCTG
Statistics
Matches: 157, Mismatches: 32, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
33 17 0.11
34 67 0.43
35 73 0.46
ACGTcount: A:0.39, C:0.05, G:0.29, T:0.26
Consensus pattern (35 bp):
GCTGCAAATTTTGAGAGGGAAATAGAGAGAGTTTT
Found at i:4060785 original size:69 final size:69
Alignment explanation
Indices: 4060683--4060884 Score: 241
Period size: 69 Copynumber: 2.9 Consensus size: 69
4060673 AAACTTTGAG
* * **
4060683 AGGAAAAAGACAGAGTTTTGCTATAAATTTTGAGAGGGAAATAGAGAGAGTTTTGCTGCAAATTT
1 AGGAAAAAGAGAAAG-TTTGCTGCAAATTTTGAGAGGGAAATAGAGAGAGTTTTGCTGCAAATTT
4060748 TGGAA
65 TGGAA
* * *
4060753 A-GAAATAGA-AAGAGTTGTGTTGCAAATTTTGAGAGGGAAATAGAGAGAGTTTTGATGCAAA-T
1 AGGAAAAAGAGAA-AGTT-TGCTGCAAATTTTGAGAGGGAAATAGAGAGAGTTTTGCTGCAAATT
4060815 TTGGAA
64 TTGGAA
* * * *
4060821 AGGGAAAAAGAGAAAGTTTGCTGTAAATTTTGAGA-GGAGAGAGAAAGAGTTTTGCTGCAAATTT
1 A-GGAAAAAGAGAAAGTTTGCTGCAAATTTTGAGAGGGAAATAGAGAGAGTTTTGCTGCAAATTT
4060885 GAGAGAGAAA
Statistics
Matches: 113, Mismatches: 13, Indels: 13
0.81 0.09 0.09
Matches are distributed among these distances:
68 33 0.29
69 66 0.58
70 12 0.11
71 2 0.02
ACGTcount: A:0.39, C:0.04, G:0.29, T:0.28
Consensus pattern (69 bp):
AGGAAAAAGAGAAAGTTTGCTGCAAATTTTGAGAGGGAAATAGAGAGAGTTTTGCTGCAAATTTT
GGAA
Found at i:4061631 original size:42 final size:42
Alignment explanation
Indices: 4061505--4061668 Score: 159
Period size: 42 Copynumber: 3.9 Consensus size: 42
4061495 GGTGTGGACT
* *
4061505 CAACTATGTGCGAGTAAGAGTGTGCATAAGCTGATGATGA-C
1 CAACTATGTGCGAGTAGGAGTGCGCATAAGCTGATGATGACC
* ** * *
4061546 CAGGCTATGCACGAGTAGAAGTGCGCATAAGTTGATGATGACC
1 CA-ACTATGTGCGAGTAGGAGTGCGCATAAGCTGATGATGACC
* **
4061589 CAACTATGTGCGATTAGGAGTGCGCATAAGCCAATGATGACC
1 CAACTATGTGCGAGTAGGAGTGCGCATAAGCTGATGATGACC
* * * * * *
4061631 CAGCCATGTGCTAGTGGAGAGTGCACATGAGCTGATGA
1 CAACTATGTGCGAGTAG-GAGTGCGCATAAGCTGATGA
4061669 CGATGGGAAA
Statistics
Matches: 96, Mismatches: 24, Indels: 4
0.77 0.19 0.03
Matches are distributed among these distances:
41 2 0.02
42 75 0.78
43 19 0.20
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.22
Consensus pattern (42 bp):
CAACTATGTGCGAGTAGGAGTGCGCATAAGCTGATGATGACC
Found at i:4064349 original size:2 final size:2
Alignment explanation
Indices: 4064342--4064377 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4064332 AACCAACACG
4064342 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4064378 NCACAAGGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4064546 original size:225 final size:223
Alignment explanation
Indices: 4064156--4064580 Score: 640
Period size: 225 Copynumber: 1.9 Consensus size: 223
4064146 ACACAAAAAT
**
4064156 ACAAGGCACGAATTTTGATGCAAACATCATAAAAAGACTTGTTTCTTGATTTCTAAAACACTTTA
1 ACAAGGCACGAATTTTGATGCAAACATCATAAAAAGACTTGTTTCCCGATTTCTAAAACACTTTA
* *
4064221 CATATATAGTTATCTACAAGCATATCCAAACCAACTTTCAGAACAACTTGCATCCACAAAATACT
66 CAGATATAGTTATCTACAAGCATATCCAAACCAACTTTCAAAACAACTTGCATCCACAAAATACT
* *
4064286 GAGAATTCTACCAACTCATGCTTTCCACAATTTTGCATTTAAAGTAAACCAACACGTATATATAT
131 AAGAATTCTACCAACTCATGCTTTCCACAATTTTGCATTTAAAGTAAACCAACACATATATATAT
4064351 ATATATATATATATATATATATATATANC
196 ATATATATATATATATATATATATATA-C
* * *
4064380 ACAAGGCAC-AGATTTTGATGCAAACATCGTAATAAGGCTTGTTTCCCGATTTCTAAAACACTTT
1 ACAAGGCACGA-ATTTTGATGCAAACATCATAAAAAGACTTGTTTCCCGATTTCTAAAACACTTT
* * *
4064444 ACAGATATAGTCTATCTA-TAGATATATCCAAACCAACTTTCAAAACAACTTGCATCCACAAAGT
65 ACAGATATAGT-TATCTACAAG-CATATCCAAACCAACTTTCAAAACAACTTGCATCCACAAAAT
* * * *
4064508 ACCTAAG-ATTCTACTAGCTCATGCTTTCCACAATTTTGCGTTTAAAGTCAACCAACACATATAT
128 A-CTAAGAATTCTACCAACTCATGCTTTCCACAATTTTGCATTTAAAGTAAACCAACACATATAT
4064572 ATATATATA
192 ATATATATA
4064581 GCTTATGGAA
Statistics
Matches: 181, Mismatches: 16, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
223 1 0.01
224 69 0.38
225 107 0.59
226 4 0.02
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (223 bp):
ACAAGGCACGAATTTTGATGCAAACATCATAAAAAGACTTGTTTCCCGATTTCTAAAACACTTTA
CAGATATAGTTATCTACAAGCATATCCAAACCAACTTTCAAAACAACTTGCATCCACAAAATACT
AAGAATTCTACCAACTCATGCTTTCCACAATTTTGCATTTAAAGTAAACCAACACATATATATAT
ATATATATATATATATATATATATATAC
Found at i:4071025 original size:42 final size:42
Alignment explanation
Indices: 4070943--4071067 Score: 144
Period size: 42 Copynumber: 3.0 Consensus size: 42
4070933 CTCCCATCGT
* * * *
4070943 CATCAGC-TCATGTGCACTCCACACTAGCACATGGTTGGGTCAG
1 CATCAGCGT-ATGCGCACTCC-TACTCGCACATAGTTGGGTCAG
* * *
4070986 CATCAGCTTATGCGCACTCTTACTCGCACATAGTTGGGTCAT
1 CATCAGCGTATGCGCACTCCTACTCGCACATAGTTGGGTCAG
* *
4071028 CATCGGCGTATGCGCACTCCTACTCGCACATAGTCGGGTC
1 CATCAGCGTATGCGCACTCCTACTCGCACATAGTTGGGTC
4071068 CACATCAACA
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
42 54 0.76
43 16 0.23
44 1 0.01
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (42 bp):
CATCAGCGTATGCGCACTCCTACTCGCACATAGTTGGGTCAG
Found at i:4072485 original size:43 final size:43
Alignment explanation
Indices: 4072402--4072515 Score: 122
Period size: 43 Copynumber: 2.7 Consensus size: 43
4072392 AGCTCATGTG
* * * * *
4072402 CACTCCCTACTCGTACATGGCTGGGCCATCACCGGGTTATGCA
1 CACTCCCTACTCGCACATAGCCGGGTCATCACCGGCTTATGCA
* *
4072445 CACTCCCTACTCGCACATAACCGGGTCATC-CTCGGCTTATGCG
1 CACTCCCTACTCGCACATAGCCGGGTCATCAC-CGGCTTATGCA
* * *
4072488 CACTTCCTACTCACACATAGCCGAGTCA
1 CACTCCCTACTCGCACATAGCCGGGTCA
4072516 ATATAATTAC
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 1 0.02
43 58 0.98
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.23
Consensus pattern (43 bp):
CACTCCCTACTCGCACATAGCCGGGTCATCACCGGCTTATGCA
Found at i:4080934 original size:63 final size:62
Alignment explanation
Indices: 4080857--4080981 Score: 241
Period size: 63 Copynumber: 2.0 Consensus size: 62
4080847 CCAATTGATT
4080857 GTAAAGCCTTTAGATGACTCCAATTCCCCTAATTGTCCAAATGAGATGATGGGGCTTCCTTA
1 GTAAAGCCTTTAGATGACTCCAATTCCCCTAATTGTCCAAATGAGATGATGGGGCTTCCTTA
4080919 NGTAAAGCCTTTAGATGACTCCAATTCCCCTAATTGTCCAAATGAGATGATGGGGCTTCCTTA
1 -GTAAAGCCTTTAGATGACTCCAATTCCCCTAATTGTCCAAATGAGATGATGGGGCTTCCTTA
4080982 AAACCTAGGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.30
Consensus pattern (62 bp):
GTAAAGCCTTTAGATGACTCCAATTCCCCTAATTGTCCAAATGAGATGATGGGGCTTCCTTA
Found at i:4094079 original size:30 final size:30
Alignment explanation
Indices: 4094019--4094079 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
4094009 TTTTTTTTAT
* *
4094019 TTTTTATCAAAAAAATTATAAGATTATAAA
1 TTTTTAACAAAAAAATTATAAAATTATAAA
*
4094049 TTTTTAACAAAAAAATGTA-AAAATTTTAAA
1 TTTTTAACAAAAAAAT-TATAAAATTATAAA
4094079 T
1 T
4094080 ATCAAAACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (30 bp):
TTTTTAACAAAAAAATTATAAAATTATAAA
Found at i:4099431 original size:3 final size:3
Alignment explanation
Indices: 4099423--4099457 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4099413 TGTCATTATA
4099423 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
4099458 ATTATTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:4102114 original size:22 final size:22
Alignment explanation
Indices: 4102034--4102116 Score: 76
Period size: 22 Copynumber: 3.5 Consensus size: 22
4102024 CTTAACGAAG
* *
4102034 TTTTAGGAATTGCTTGACTAAT
1 TTTTAGGCATTGCTTGACTAGT
* * *
4102056 TTGTAGGCATTGCATGACTTGT
1 TTTTAGGCATTGCTTGACTAGT
4102078 TTTTAGTTATTGCATTGCTTGACTAGT
1 TTTTAG-----GCATTGCTTGACTAGT
4102105 TTTTAGGCATTG
1 TTTTAGGCATTG
4102117 TGTGACTGGT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
22 28 0.58
27 20 0.42
ACGTcount: A:0.20, C:0.11, G:0.22, T:0.47
Consensus pattern (22 bp):
TTTTAGGCATTGCTTGACTAGT
Found at i:4102116 original size:27 final size:27
Alignment explanation
Indices: 4102062--4102116 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
4102052 TAATTTGTAG
* **
4102062 GCATTGCATGACTTGTTTTTAGTTATT
1 GCATTGCATGACTAGTTTTTAGGCATT
*
4102089 GCATTGCTTGACTAGTTTTTAGGCATT
1 GCATTGCATGACTAGTTTTTAGGCATT
4102116 G
1 G
4102117 TGTGACTGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.18, C:0.13, G:0.22, T:0.47
Consensus pattern (27 bp):
GCATTGCATGACTAGTTTTTAGGCATT
Found at i:4102165 original size:22 final size:22
Alignment explanation
Indices: 4102097--4102166 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
4102087 TTGCATTGCT
* * *
4102097 TGACTAGTTTTTAGGCATTGTG
1 TGACTGGTTTTTATGTATTGTG
*
4102119 TGACTGGTTGTTATGTATTCG-G
1 TGACTGGTTTTTATGTATT-GTG
*
4102141 TGATTGGTTTTTATGTATTGTG
1 TGACTGGTTTTTATGTATTGTG
4102163 TGAC
1 TGAC
4102167 GTAGAGCTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 1 0.03
22 37 0.95
23 1 0.03
ACGTcount: A:0.16, C:0.07, G:0.29, T:0.49
Consensus pattern (22 bp):
TGACTGGTTTTTATGTATTGTG
Found at i:4108514 original size:16 final size:16
Alignment explanation
Indices: 4108475--4108515 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
4108465 AACAAACATT
4108475 TCACGCAATAAGTGAG
1 TCACGCAATAAGTGAG
* *
4108491 GCATGCAATAAGTGAG
1 TCACGCAATAAGTGAG
4108507 TCACGCAAT
1 TCACGCAAT
4108516 GCCTACCAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (16 bp):
TCACGCAATAAGTGAG
Found at i:4119503 original size:32 final size:32
Alignment explanation
Indices: 4119442--4119504 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
4119432 CACAAAAAAG
* *
4119442 AAGAAAGAGAGAGGGAAGGAAGGAAAAGGAAT
1 AAGAAAGAGAGAGAGAAGAAAGGAAAAGGAAT
*
4119474 AAGAAAGAGAGAGAG-AGAAAGAGAGAAGGAA
1 AAGAAAGAGAGAGAGAAGAAAG-GAAAAGGAA
4119505 AGAAACGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.59, C:0.00, G:0.40, T:0.02
Consensus pattern (32 bp):
AAGAAAGAGAGAGAGAAGAAAGGAAAAGGAAT
Found at i:4119505 original size:12 final size:14
Alignment explanation
Indices: 4119475--4119507 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
4119465 AAAAGGAATA
4119475 AGAAAGAGAGAGAG
1 AGAAAGAGAGAGAG
4119489 AGAAAGAGAGA-AG
1 AGAAAGAGAGAGAG
4119502 -GAAAGA
1 AGAAAGA
4119508 AACGATGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 2 0.11
14 11 0.58
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (14 bp):
AGAAAGAGAGAGAG
Found at i:4126844 original size:21 final size:22
Alignment explanation
Indices: 4126813--4126853 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
4126803 GCAACCTTTT
*
4126813 TCTTCTAAAACCTCCGGGTACG
1 TCTTCTAAAACCTCCAGGTACG
4126835 TCTTC-AAAACCTCCAGGTA
1 TCTTCTAAAACCTCCAGGTA
4126854 ATTAGTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.27
Consensus pattern (22 bp):
TCTTCTAAAACCTCCAGGTACG
Found at i:4126854 original size:102 final size:101
Alignment explanation
Indices: 4126671--4126981 Score: 388
Period size: 102 Copynumber: 3.1 Consensus size: 101
4126661 GAGAGAATTT
* * * * * * *
4126671 AAGTTAAGTAGCCTCATTTTGAGATGAGGAAAAACCTTTTCTTTTAAAACATCTGGGTATATTCT
1 AAGTTACGTAGCCTCATTCTGAGATGAGGAACAACCTTTTCTTCTAAAACCTCCGGGTACA-TCT
* * * * *
4126736 CCAAAACCTTCGGGTAATTAGTTTGAAGATTTCTACA
65 TCAAAACCTCCAGGTAATTAGTTTCAAGATTTCTTCA
* *
4126773 AAGTTACGTAGCCTCATTCTGAGATGAGGAGCAACCTTTTTCTTCTAAAACCTCCGGGTACGTCT
1 AAGTTACGTAGCCTCATTCTGAGATGAGGAACAACC-TTTTCTTCTAAAACCTCCGGGTACATCT
* *
4126838 TCAAAACCTCCAGGTAATTAGTTTCAAAATTTTTTCA
65 TCAAAACCTCCAGGTAATTAGTTTCAAGATTTCTTCA
* * * * * *
4126875 AAGTTACGTAGCCTTATTCTAAAATGAGGAACGACCTTTCCTTCTAAAACCTCCGGATACATCTT
1 AAGTTACGTAGCCTCATTCTGAGATGAGGAACAACCTTTTCTTCTAAAACCTCCGGGTACATCTT
* *
4126940 CAAAACCTCTAAGTAATTAGTTTCAAGATTTCTTCA
66 CAAAACCTCCAGGTAATTAGTTTCAAGATTTCTTCA
4126976 AAGTTA
1 AAGTTA
4126982 TGCAACGTCG
Statistics
Matches: 180, Mismatches: 28, Indels: 3
0.85 0.13 0.01
Matches are distributed among these distances:
101 64 0.36
102 96 0.53
103 20 0.11
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (101 bp):
AAGTTACGTAGCCTCATTCTGAGATGAGGAACAACCTTTTCTTCTAAAACCTCCGGGTACATCTT
CAAAACCTCCAGGTAATTAGTTTCAAGATTTCTTCA
Found at i:4128355 original size:16 final size:16
Alignment explanation
Indices: 4128334--4128366 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4128324 AAAAATCAAT
4128334 AAAT-AAATAGAAATAA
1 AAATAAAATA-AAATAA
4128350 AAATAAAATAAAATAA
1 AAATAAAATAAAATAA
4128366 A
1 A
4128367 TGATGTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (16 bp):
AAATAAAATAAAATAA
Found at i:4131782 original size:13 final size:13
Alignment explanation
Indices: 4131764--4131788 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4131754 TTTCAGAAAA
4131764 TTTATAAAATCAT
1 TTTATAAAATCAT
4131777 TTTATAAAATCA
1 TTTATAAAATCA
4131789 CAATTTCTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:4135534 original size:13 final size:13
Alignment explanation
Indices: 4135516--4135540 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4135506 TTTCAGAAAA
4135516 TTTATAAAATCAT
1 TTTATAAAATCAT
4135529 TTTATAAAATCA
1 TTTATAAAATCA
4135541 CAATTTCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:4136803 original size:19 final size:19
Alignment explanation
Indices: 4136779--4136815 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
4136769 CTTCTAAACT
4136779 TCAAATCATACTCCAATAC
1 TCAAATCATACTCCAATAC
4136798 TCAAATCATACTCCAATA
1 TCAAATCATACTCCAATA
4136816 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (19 bp):
TCAAATCATACTCCAATAC
Found at i:4147823 original size:20 final size:20
Alignment explanation
Indices: 4147795--4147840 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
4147785 TTTTTACCCC
*
4147795 ATTTGACTTATTGGAGTATA
1 ATTTAACTTATTGGAGTATA
*
4147815 ATTTAACTTATTGGAGTATG
1 ATTTAACTTATTGGAGTATA
4147835 ATTTAA
1 ATTTAA
4147841 GATTTAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTAACTTATTGGAGTATA
Found at i:4152693 original size:13 final size:13
Alignment explanation
Indices: 4152675--4152699 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4152665 GGAAAATGGG
4152675 ATTTTATAAAATA
1 ATTTTATAAAATA
4152688 ATTTTATAAAAT
1 ATTTTATAAAAT
4152700 TTTTGAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:4154049 original size:19 final size:19
Alignment explanation
Indices: 4154025--4154062 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4154015 CCATTTAACT
*
4154025 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
4154044 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
4154063 GGTTTGGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:4155934 original size:13 final size:13
Alignment explanation
Indices: 4155916--4155940 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4155906 AAAGAAATTG
4155916 TGATTTTATAAAA
1 TGATTTTATAAAA
4155929 TGATTTTATAAA
1 TGATTTTATAAA
4155941 TTTTCTAGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:4157183 original size:15 final size:15
Alignment explanation
Indices: 4157139--4157184 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
4157129 AGATCAGAGA
*
4157139 TTTTGATTTTAAAGC
1 TTTTGATTTTAAAGT
*
4157154 TTTGGATTTTAAAGT
1 TTTTGATTTTAAAGT
4157169 TTTTGATTTTAAAGT
1 TTTTGATTTTAAAGT
4157184 T
1 T
4157185 GTTTTAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (15 bp):
TTTTGATTTTAAAGT
Found at i:4157229 original size:5 final size:5
Alignment explanation
Indices: 4157219--4157258 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
4157209 TGCATGGCCC
*
4157219 AAGTT AAGTT AAGTT AAGTT -AGTT AAGTT AAGTC AAGTT A
1 AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT AAGTT A
4157259 GGTAGAATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.38
Consensus pattern (5 bp):
AAGTT
Found at i:4157244 original size:14 final size:15
Alignment explanation
Indices: 4157219--4157258 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
4157209 TGCATGGCCC
4157219 AAGTTAAGTTAAGTT
1 AAGTTAAGTTAAGTT
4157234 AAGTT-AGTTAAGTT
1 AAGTTAAGTTAAGTT
*
4157248 AAGTCAAGTTA
1 AAGTTAAGTTA
4157259 GGTAGAATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.38
Consensus pattern (15 bp):
AAGTTAAGTTAAGTT
Found at i:4157244 original size:19 final size:19
Alignment explanation
Indices: 4157220--4157259 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
4157210 GCATGGCCCA
*
4157220 AGTTAAGTTAAGTTAAGTT
1 AGTTAAGTTAAGTCAAGTT
4157239 AGTTAAGTTAAGTCAAGTT
1 AGTTAAGTTAAGTCAAGTT
4157258 AG
1 AG
4157260 GTAGAATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.38
Consensus pattern (19 bp):
AGTTAAGTTAAGTCAAGTT
Found at i:4160298 original size:105 final size:106
Alignment explanation
Indices: 4160187--4160388 Score: 356
Period size: 105 Copynumber: 1.9 Consensus size: 106
4160177 CTGTGCTTTT
*
4160187 TTAAAATTTTTTGTTTGATAAAGTACATGTATTTTTTATTTAAATTCTTTTAATTAAAATTTTAA
1 TTAAAATTTTTTGTTTGATAAAGTACATGTATTTTTTATTTAAATTCTTTTAATTAAAACTTTAA
4160252 AATTT-AAT-AATATTTAATTTT-ATTAAATATTACAATAAA
66 AATTTAAATAAATATTT-ATTTTAATTAAATATTACAATAAA
4160291 TTNAAAATTTTTTGTTTGATAAAGTACATGTATTTTTTATTTAAATTCTTTTAATTAAAACTTTA
1 TT-AAAATTTTTTGTTTGATAAAGTACATGTATTTTTTATTTAAATTCTTTTAATTAAAACTTTA
4160356 AAATTTAAATAAATATTTATTTTAATTAAATAT
65 AAATTTAAATAAATATTTATTTTAATTAAATAT
4160389 ATTAATTAAA
Statistics
Matches: 93, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
104 2 0.02
105 67 0.72
106 8 0.09
107 16 0.17
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (106 bp):
TTAAAATTTTTTGTTTGATAAAGTACATGTATTTTTTATTTAAATTCTTTTAATTAAAACTTTAA
AATTTAAATAAATATTTATTTTAATTAAATATTACAATAAA
Found at i:4160409 original size:20 final size:21
Alignment explanation
Indices: 4160381--4160421 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4160371 TTTATTTTAA
*
4160381 TTAAATAT-ATTAATTAAAAT
1 TTAAATATAATTAATAAAAAT
*
4160401 TTAATTATAATTAATAAAAAT
1 TTAAATATAATTAATAAAAAT
4160422 ATCACTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTAAATATAATTAATAAAAAT
Found at i:4160412 original size:30 final size:28
Alignment explanation
Indices: 4160353--4160414 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 28
4160343 AATTAAAACT
*
4160353 TTAAAATTTAAATAAATATTTATTTTAA
1 TTAAAATTTAAATAAATATTTATTATAA
*
4160381 TTAAATATATTAATTAAA-ATTTAATTATAA
1 TTAAA-AT-TTAAATAAATATTT-ATTATAA
4160411 TTAA
1 TTAA
4160415 TAAAAATATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 5 0.17
29 6 0.21
30 18 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TTAAAATTTAAATAAATATTTATTATAA
Found at i:4160418 original size:105 final size:103
Alignment explanation
Indices: 4160189--4160418 Score: 279
Period size: 105 Copynumber: 2.2 Consensus size: 103
4160179 GTGCTTTTTT
** * *
4160189 AAAATTTTTTGTTTGATAAAGTACATGTATTTTTTATTTAAATTCTTTTAATTAAAATTTTAAAA
1 AAAATTTTTTAATTAATAAAGTACATGTATTTTTTATTTAAATTCTTTTAATTAAAACTTTAAAA
*
4160254 TTTAATAATATTTAATTTTATTAAATATTACAATAAATTN
66 TTTAATAATATTTAATTTTATTAAATATT--AATAAATTA
** *
4160294 AAAATTTTTTGTTTGATAAAGTACATGTATTTTTTATTTAAATTCTTTTAATTAAAACTTTAAAA
1 AAAATTTTTTAATTAATAAAGTACATGTATTTTTTATTTAAATTCTTTTAATTAAAACTTTAAAA
*
4160359 TTTAAATAAATATTT-ATTTTAATTAAATA-T-ATTAATT-
66 TTT-AAT-AATATTTAATTTT-ATTAAATATTAATAAATTA
4160396 AAAATTTAATTATAATTAATAAA
1 AAAATTT--TT-TAATTAATAAA
4160419 AATATCACTT
Statistics
Matches: 114, Mismatches: 5, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
102 7 0.06
103 6 0.05
104 2 0.02
105 75 0.66
106 9 0.08
107 15 0.13
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (103 bp):
AAAATTTTTTAATTAATAAAGTACATGTATTTTTTATTTAAATTCTTTTAATTAAAACTTTAAAA
TTTAATAATATTTAATTTTATTAAATATTAATAAATTA
Found at i:4167369 original size:13 final size:13
Alignment explanation
Indices: 4167351--4167381 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4167341 TCAGCAGCTC
4167351 TTTTCTTATTAGA
1 TTTTCTTATTAGA
*
4167364 TTTTCTTATTCGA
1 TTTTCTTATTAGA
4167377 TTTTC
1 TTTTC
4167382 CATTGGGATT
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:0.16, C:0.13, G:0.06, T:0.65
Consensus pattern (13 bp):
TTTTCTTATTAGA
Found at i:4192063 original size:13 final size:13
Alignment explanation
Indices: 4192045--4192069 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4192035 TTTCAGAAAA
4192045 TTTATAAAATCAT
1 TTTATAAAATCAT
4192058 TTTATAAAATCA
1 TTTATAAAATCA
4192070 CAATTTCTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:4210343 original size:21 final size:21
Alignment explanation
Indices: 4210317--4210357 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4210307 TGCATCATGT
4210317 TTGGTTGCTT-TTTCCCTGCCA
1 TTGGTTG-TTCTTTCCCTGCCA
*
4210338 TTGGTTGTTCTTTCCTTGCC
1 TTGGTTGTTCTTTCCCTGCC
4210358 TCTTAGAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.02, C:0.27, G:0.20, T:0.51
Consensus pattern (21 bp):
TTGGTTGTTCTTTCCCTGCCA
Found at i:4214941 original size:2 final size:2
Alignment explanation
Indices: 4214934--4214972 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4214924 NNNNNNNNNN
4214934 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4214973 CTATGTCATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4215098 original size:61 final size:61
Alignment explanation
Indices: 4215007--4215174 Score: 246
Period size: 61 Copynumber: 2.8 Consensus size: 61
4214997 GTGACAAGTG
* *
4215007 CAACCGTGCATGTGCGGAGTGGGCAATGCACATGCCGGTAATGATGCTATTGTGATAATTA
1 CAACCGTGCATGTGCGGAGTGGGCAATGCACATGCCGGTAATGATGATATCGTGATAATTA
* * * * * *
4215068 CAATCGTGCATGTGCAGAGCGGGTAGTGCACATGCCGGTAATGATGATGTCGTGATAATTA
1 CAACCGTGCATGTGCGGAGTGGGCAATGCACATGCCGGTAATGATGATATCGTGATAATTA
* *
4215129 CAACCGTGCATGTGCGGAGTAGGCAATGCACATGCCGATAATGATG
1 CAACCGTGCATGTGCGGAGTGGGCAATGCACATGCCGGTAATGATG
4215175 TACATGAGCT
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 92 1.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (61 bp):
CAACCGTGCATGTGCGGAGTGGGCAATGCACATGCCGGTAATGATGATATCGTGATAATTA
Found at i:4219035 original size:43 final size:42
Alignment explanation
Indices: 4218940--4219082 Score: 154
Period size: 43 Copynumber: 3.5 Consensus size: 42
4218930 CCCACCACAC
*
4218940 TCAGCTCATGTGCACTCCCTACATGCACA-ATG-CA-AT-ATCA
1 TCAGCTCATGTGCACTCCCTAC-TGCACATA-GCCAGGTCATCA
4218980 TCA-C-CATGTGCACTCCCTACTCGCACATAGCCAGGTCATCA
1 TCAGCTCATGTGCACTCCCTACT-GCACATAGCCAGGTCATCA
* **
4219021 TCAGCTCATGTGCACTCCCGCACTGCACATAGCTGGGTCATCA
1 TCAGCTCATGTGCACTCCC-TACTGCACATAGCCAGGTCATCA
* *
4219064 TCAACCCATGTGCACTCCC
1 TCAGCTCATGTGCACTCCC
4219083 ACACCGCACA
Statistics
Matches: 89, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
37 1 0.01
38 22 0.25
39 4 0.04
40 4 0.04
41 7 0.08
42 1 0.01
43 47 0.53
44 3 0.03
ACGTcount: A:0.24, C:0.37, G:0.15, T:0.23
Consensus pattern (42 bp):
TCAGCTCATGTGCACTCCCTACTGCACATAGCCAGGTCATCA
Found at i:4219092 original size:43 final size:43
Alignment explanation
Indices: 4218976--4219107 Score: 153
Period size: 43 Copynumber: 3.1 Consensus size: 43
4218966 ACAATGCAAT
* **
4218976 ATCATC-A-CCATGTGCACTCCCTAC-TCGCACATAGCCAGGTC
1 ATCATCAACCCATGTGCACTCCC-ACACCGCACATAGCTGGGTC
* * * *
4219017 ATCATCAGCTCATGTGCACTCCCGCACTGCACATAGCTGGGTC
1 ATCATCAACCCATGTGCACTCCCACACCGCACATAGCTGGGTC
**
4219060 ATCATCAACCCATGTGCACTCCCACACCGCACATAATTGGGTC
1 ATCATCAACCCATGTGCACTCCCACACCGCACATAGCTGGGTC
4219103 ATCAT
1 ATCAT
4219108 TATCACACAA
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
41 6 0.08
42 1 0.01
43 68 0.91
ACGTcount: A:0.25, C:0.36, G:0.16, T:0.23
Consensus pattern (43 bp):
ATCATCAACCCATGTGCACTCCCACACCGCACATAGCTGGGTC
Found at i:4219420 original size:11 final size:11
Alignment explanation
Indices: 4219404--4219433 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4219394 GGAACCCATC
4219404 ATCACAATAGA
1 ATCACAATAGA
*
4219415 ATCACAATAGC
1 ATCACAATAGA
4219426 ATCACAAT
1 ATCACAAT
4219434 TAACTCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.23, G:0.07, T:0.20
Consensus pattern (11 bp):
ATCACAATAGA
Found at i:4225804 original size:171 final size:171
Alignment explanation
Indices: 4225515--4226320 Score: 1064
Period size: 171 Copynumber: 4.7 Consensus size: 171
4225505 NNNNNNNGTT
* * *
4225515 GCTTTAAATGGTTTTATAATCTTATAATTGCTTTTAAGTTGAATTTGTTTT-CATTTTTTGTTAA
1 GCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTT-TTTTACATTTTTGGTTAA
* * * * *
4225579 AACAGATCATAATTTAATGTTTACCTCGGGAAATGTGAAGCAAAAGCCATCCATTGACAAGAAAA
65 AACAGATTATAATTGAATGTTTACCTCGAGAAACGTGAAGCGAAAGCCATCCATTGACAAGAAAA
* * *
4225644 GTTTATTTAAAGTCACTTATGCCTTT-GAAAGCCTTATTACTC
130 GTTCATTTATAGTCACTCAT-CCTTTCGAAAGCCTTATTACTC
* * *
4225686 GCTATAAATGGTTTTAGAATCTCATAATTGATTTTAAGTTGAATTTTTTTATATTTTTGGTTAAA
1 GCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAA
* *
4225751 ACAGATTATAATAGAATGTTTACCTCGAGAAACGTGAAGTGAAAGCCATCCATTGACAAGAAAAG
66 ACAGATTATAATTGAATGTTTACCTCGAGAAACGTGAAGCGAAAGCCATCCATTGACAAGAAAAG
* * *
4225816 TTCATTTATAGTGACTCATGTCTTT-GAAAGACTTATTACTC
131 TTCATTTATAGTCACTCAT-CCTTTCGAAAGCCTTATTACTC
* * * *
4225857 ACTTTAAATGGTTTTATAATCTTATAATTGATTTTAAGTTGAATGTTTTTACACTTTTGGTTAAA
1 GCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAA
* * * * * *
4225922 ACAGATTCTAATT-AATGTTTACCTCGAGAAACATGAAGCAAAAGTCATCCGTTAACAAGAAAAG
66 ACAGATTATAATTGAATGTTTACCTCGAGAAACGTGAAGCGAAAGCCATCCATTGACAAGAAAAG
** * * *
4225986 TTCATTTATAGTCACTCATATTTTCAAAAGCTTTATTATTC
131 TTCATTTATAGTCACTCATCCTTTCGAAAGCCTTATTACTC
*
4226027 GCTTTAAATGGTTTTATAATCTCATAATTAATTTTAAGTTGAATTTTTTTTACATTTTTGGTTAA
1 GCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTTACATTTTTGGTTAA
* * * * * * * *
4226092 AACAAATTATAATTGAATGTTTAGCTTGTGAAACGTGAAGTGAAAGCTATCAATTGAGAAGAAAA
65 AACAGATTATAATTGAATGTTTACCTCGAGAAACGTGAAGCGAAAGCCATCCATTGACAAGAAAA
* * *
4226157 TTTCATTTATAGTCACTCATCCTTTCGAAAGGCTTATTTCTC
130 GTTCATTTATAGTCACTCATCCTTTCGAAAGCCTTATTACTC
* * * *
4226199 TCTTTAACTGGTTTTATAATCGCATAATTGATTTTAAGTTGAATTCTTTTACATTTTTGGTTAAA
1 GCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAA
* * *
4226264 ACAGATTATAATTGAAT-ATTGCCTCAAGAAACGTGAAGCGAAAGCCATCCATTGACA
66 ACAGATTATAATTGAATGTTTACCTCGAGAAACGTGAAGCGAAAGCCATCCATTGACA
4226321 TGAGATGTCA
Statistics
Matches: 547, Mismatches: 84, Indels: 9
0.85 0.13 0.01
Matches are distributed among these distances:
169 3 0.01
170 149 0.27
171 284 0.52
172 111 0.20
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.40
Consensus pattern (171 bp):
GCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAA
ACAGATTATAATTGAATGTTTACCTCGAGAAACGTGAAGCGAAAGCCATCCATTGACAAGAAAAG
TTCATTTATAGTCACTCATCCTTTCGAAAGCCTTATTACTC
Found at i:4226689 original size:20 final size:20
Alignment explanation
Indices: 4226643--4226702 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 20
4226633 AGATGTCTAA
*
4226643 AGTAATTATTTGAAATGAAATT
1 AGTAATTATTTG-AAT-AAAAT
*
4226665 A-TAATTGTTTGAATAAAAT
1 AGTAATTATTTGAATAAAAT
4226684 AGTAA-TATTT-AATAAAAT
1 AGTAATTATTTGAATAAAAT
4226702 A
1 A
4226703 TTTTATTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 9 0.26
19 9 0.26
20 6 0.18
21 9 0.26
22 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (20 bp):
AGTAATTATTTGAATAAAAT
Found at i:4227671 original size:13 final size:13
Alignment explanation
Indices: 4227653--4227677 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4227643 TTCCAGAAAA
4227653 TTTATAAAATCAT
1 TTTATAAAATCAT
4227666 TTTATAAAATCA
1 TTTATAAAATCA
4227678 CAATTTCTCC
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:4229318 original size:19 final size:19
Alignment explanation
Indices: 4229294--4229331 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4229284 CTGCTAAACC
*
4229294 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
4229313 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
4229332 AGTTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:4230221 original size:171 final size:172
Alignment explanation
Indices: 4229656--4231510 Score: 2030
Period size: 171 Copynumber: 10.8 Consensus size: 172
4229646 AAAACAGGGT
* * * *
4229656 TTGACATGAGAAA-TCCATTTGTAGTCACTCATGCCTTCGAAAGCCTTATTTCTTGCTTTAAATG
1 TTGACAAGA-AAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATG
* * * * *
4229720 CTTTTATAATCTCATAATTTATTTTAAG-AGAATTTTTTTACATTTTTTTGTTAAAACAGACTAT
65 GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGGTTAAAACAGATTAT
* * ** *
4229784 AATTGAATGTTTACCT-A-AAAAAAGTGAAGCGAAAGGTATCTA
130 AATTGAATGTTTACCTCAGGAAACA-TGAAGCGAAAGCCATCCA
* * * * * *
4229826 TCGAAAAGAAAAGTCCATTTGTAGTCACTCATGCCTTCGAAAGTCTCATTACTCGTTTTAAATGG
1 TTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGG
* * *
4229891 TTTTATAATGTCATAATTGATTTTAAGTTGAATTGTTTTAC-GTTTTT-GTTAAAACAGATTATA
66 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGGTTAAAACAGATTATA
* * * * * *
4229954 ATTGAATGTTTATCTTAGAAAATATGAAGCGAAAGTCACCCA
131 ATTGAATGTTTACCTCAGGAAACATGAAGCGAAAGCCATCCA
* * * * * * *
4229996 TTTACAAGAAAAGTCCATTTATAGGCACTTATGGCTTCGAAACCCTTATTACTCGCTATAAATGA
1 TTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGG
* * * *
4230061 TTTTATAATCTCTTAATTGATTTTAAGTTGAATATTTTTA-ATTTTTTGGTTAAAATAAATTATA
66 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGGTTAAAACAGATTATA
* * **
4230125 ATTGAATGTTTGCCTCAGGAAACATGAAGCAAAAGCCATCTG
131 ATTGAATGTTTACCTCAGGAAACATGAAGCGAAAGCCATCCA
* * * * *
4230167 TTTACACA-AAAAGTCCATTTGTAGTCACTCATGCCTTCAAAAGCCTTGTTACTCGCTATAAATG
1 TTGACA-AGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATG
* * * *** *
4230231 ATTTTATAACCTCATAATTGATTTTAAGTTCAATTTTTTTTTTGTATTTTTGGTTAAAACAAATT
65 GTTTTATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTTACAT-TTTTTGGTTAAAACAGATT
* ** *
4230296 ATAATTGAATGTTTACCTCAGAAAATGTGAGGCGAAAGCCATCCA
128 ATAATTGAATGTTTACCTCAGGAAACATGAAGCGAAAGCCATCCA
* ** * * * * * *
4230341 TTGATAAGAAAAGTTTATTTAAAGTCACTCATACCTTTGAAAGCGTTATTACTCACTATAAATGG
1 TTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGG
* * * *
4230406 TTTTATAATCTCGTAATTGAATTTAAGATGAATTTTTTTACATTTTTT-GTTAAAACAAATTATA
66 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGGTTAAAACAGATTATA
* **
4230470 ATTGAATGTTTACCT-TGAGAAATGTGAAGCGAAAGCCATCCA
131 ATTGAATGTTTACCTCAG-GAAACATGAAGCGAAAGCCATCCA
* * * *
4230512 TTGACAAGAAAAGTTCATTTATAGTGACTCATGCCTTTC-AAAGACTTATTACTTGCTTTAAATG
1 TTGACAAGAAAAGTCCATTTATAGTCACTCATGCC-TTCGAAAGCCTTATTACTCGCTTTAAATG
* * *
4230576 GTTTTATAAACTTATAATTGATTTTAAGTTGAATATTTTTTAC-TTTTTTGGTTAAAATAGATT-
65 GTTTTATAATCTCATAATTGATTTTAAGTTGAAT-TTTTTTACATTTTTTGGTTAAAACAGATTA
* * * *
4230639 TAATT-AATGTTTACCTCGGGAAAAATGAAGGGAAATG-CATCCG
129 TAATTGAATGTTTACCTCAGGAAACATGAAGCGAAA-GCCATCCA
* * * *
4230682 TTGATAAGAAAAATCTATTTATAGTCACTCATGCCTTCGAAAG-CTGTATTACTTGCTTTAAATG
1 TTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCT-TATTACTCGCTTTAAATG
* *
4230746 GTTATATAATCTCATAATTGATTTTAAGTTGAATTTGTTTACA-TTTTTGGTTAAAACAGATTAT
65 GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGGTTAAAACAGATTAT
* * * *
4230810 AATTGAATGTTTACCTTAGGAAACGTGAAGTGAAAGCCGTCCA
130 AATTGAATGTTTACCTCAGGAAACATGAAGCGAAAGCCATCCA
* * * * ** *
4230853 TTGAAAAGAAAAGTTCATTTATAGTCACTCATCCCTTAGAAAGGTTTATTACTCTCTTTAAATGG
1 TTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGG
* *
4230918 TTTTATAATCTCATAGTTGATTTTAAGATT-AATTTTTTTATATTTTTTGGTTAAAACAGATTAT
66 TTTTATAATCTCATAATTGATTTTAAG-TTGAATTTTTTTACATTTTTTGGTTAAAACAGATTAT
** *
4230982 AATTGAATGTTGGCCTCAGGAAACATGAAGTGAAAGCCATCCA
130 AATTGAATGTTTACCTCAGGAAACATGAAGCGAAAGCCATCCA
* * * * * * *
4231025 TTGACACGAGAAA-TCTATTTGTAGTCACTCAT-CTTTCAAAAGCCTTATAACTTGCTTTAAATG
1 TTGACAAGA-AAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATG
* * * *
4231088 GTTTTATAACCTCATAATTGATTTTAGGTTCAATTTTTTTGACA-TTTTTGGTTAAACCAGATTA
65 GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTT-ACATTTTTTGGTTAAAACAGATTA
* * * * * * * *
4231152 TAATTGAATGTTTACTTGAAGAATCGTGAGGTGAAAGCAATCCA
129 TAATTGAATGTTTACCTCAGGAAACATGAAGCGAAAGCCATCCA
* ** ** * * * * * *
4231196 TTAATGAGAAAAGTTTATTTAAAGTTACTCATGCATTCAAAAGCCTTATTAGTAGCTTTAAATGG
1 TTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGG
* ***
4231261 TTTTATAATCTCATAATTGCTTTTAAGTTGAATTTTTTTTTGTTTTTT-GTTAAAACAGATTATA
66 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGGTTAAAACAGATTATA
* *
4231325 ATTGAATGTTTACCTCTGGAAACATGAAGCGAAAGTCATCCA
131 ATTGAATGTTTACCTCAGGAAACATGAAGCGAAAGCCATCCA
* * *
4231367 TTGACAAGAAAAGTCCATTTATAGTTACTGATGCCTTCGAAAGCCTTATTACTCACTTTAAATGG
1 TTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGG
* * * * *
4231432 ATTTATAACCTCATAATTGATTTTAAGTTCAA-TTTTTTACA-TGTTTGGTTAAAATAGATTATA
66 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGGTTAAAACAGATTATA
* *
4231495 ATTGAATATTTGCCTC
131 ATTGAATGTTTACCTC
4231511 GAGAAATGTG
Statistics
Matches: 1417, Mismatches: 235, Indels: 66
0.82 0.14 0.04
Matches are distributed among these distances:
169 66 0.05
170 349 0.25
171 669 0.47
172 188 0.13
173 13 0.01
174 132 0.09
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (172 bp):
TTGACAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGG
TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTTGGTTAAAACAGATTATA
ATTGAATGTTTACCTCAGGAAACATGAAGCGAAAGCCATCCA
Found at i:4230781 original size:341 final size:342
Alignment explanation
Indices: 4229656--4231521 Score: 2057
Period size: 341 Copynumber: 5.5 Consensus size: 342
4229646 AAAACAGGGT
* * * * * *
4229656 TTGACATGAGAAATCCATTTGTAGTCACTCATGCCTTCGAAAGCCTTATTTCTTGCTTTAAATGC
1 TTGACAAGAAAAATCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGG
* * * *
4229721 TTTTATAATCTCATAATTTATTTTAAG-AGAATTTTTTTACATTTTTTTGTTAAAACAGACTATA
66 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACA-TTTTTGGTTAAAACAGATTATA
* * * ** * * * *
4229785 ATTGAATGTTTACC-TAAAAAAAGTGAAGCGAAAGGTATCTATCGAAAAGAAAAGTCCATTTGTA
130 ATTGAATGTTTACCTTGAGAAATGTGAAGCGAAAGCCATCCATTGAAAAGAAAAGTTCATTTATA
* * * * *
4229849 GTCACTCATGCCTTCGAAAGTCTCATTACTCGTTTTAAATGGTTTTATAATGTCATAATTGATTT
195 GTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * *
4229914 TAAGTTGAATTGTTTTACGTTTTT-GTTAAAACAGATTATAATTGAATGTTTATCT-TAGAAAAT
260 TAAGTTGAATTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTTTACCTCTGGAAAA-
* *
4229977 ATGAAGCGAAAGTCACCCA
324 ATGAAGCGAAAGCCATCCA
* * * * * * * *
4229996 TTTACAAGAAAAGTCCATTTATAGGCACTTATGGCTTCGAAACCCTTATTACTCGCTATAAATGA
1 TTGACAAGAAAAATCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGG
* * * *
4230061 TTTTATAATCTCTTAATTGATTTTAAGTTGAATATTTTTA-ATTTTTTGGTTAAAATAAATTATA
66 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACA-TTTTTGGTTAAAACAGATTATA
* * ** * ** * * * *
4230125 ATTGAATGTTTGCC-TCAGGAAACATGAAGCAAAAGCCATCTGTTTACACA-AAAAGTCCATTTG
130 ATTGAATGTTTACCTTGA-GAAATGTGAAGCGAAAGCCATCCATTGA-AAAGAAAAGTTCATTTA
* * * *
4230188 TAGTCACTCATGCCTTCAAAAGCCTTGTTACTCGCTATAAATGATTTTATAACCTCATAATTGAT
193 TAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGAT
* ** * *
4230253 TTTAAGTTCAATTTTTTTTTTGTATTTTTGGTTAAAACAAATTATAATTGAATGTTTACCTC-AG
258 TTTAAGTTGAA--TTTTTTTACT-TTTTTGGTTAAAACAGATTATAATTGAATGTTTACCTCTGG
* *
4230317 AAAATGTGAGGCGAAAGCCATCCA
320 AAAA-ATGAAGCGAAAGCCATCCA
* * ** * * * * * *
4230341 TTGATAAGAAAAGTTTATTTAAAGTCACTCATACCTTTGAAAGCGTTATTACTCACTATAAATGG
1 TTGACAAGAAAAATCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGG
* * * * *
4230406 TTTTATAATCTCGTAATTGAATTTAAGATGAATTTTTTTACATTTTTTGTTAAAACAAATTATAA
66 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGATTATAA
*
4230471 TTGAATGTTTACCTTGAGAAATGTGAAGCGAAAGCCATCCATTGACAAGAAAAGTTCATTTATAG
131 TTGAATGTTTACCTTGAGAAATGTGAAGCGAAAGCCATCCATTGAAAAGAAAAGTTCATTTATAG
* * * * *
4230536 TGACTCATGCCTTTC-AAAGACTTATTACTTGCTTTAAATGGTTTTATAAACTTATAATTGATTT
196 TCACTCATGCC-TTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* *
4230600 TAAGTTGAATATTTTTTACTTTTTTGGTTAAAATAGATT-TAATT-AATGTTTACCTCGGGAAAA
260 TAAGTTGAAT-TTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTTTACCTCTGGAAAA
* *
4230663 ATGAAGGGAAATG-CATCCG
324 ATGAAGCGAAA-GCCATCCA
* * *
4230682 TTGATAAGAAAAATCTATTTATAGTCACTCATGCCTTCGAAAG-CTGTATTACTTGCTTTAAATG
1 TTGACAAGAAAAATCCATTTATAGTCACTCATGCCTTCGAAAGCCT-TATTACTCGCTTTAAATG
* *
4230746 GTTATATAATCTCATAATTGATTTTAAGTTGAATTTGTTTACATTTTTGGTTAAAACAGATTATA
65 GTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGATTATA
* * *
4230811 ATTGAATGTTTACCTT-AGGAAACGTGAAGTGAAAGCCGTCCATTGAAAAGAAAAGTTCATTTAT
130 ATTGAATGTTTACCTTGA-GAAATGTGAAGCGAAAGCCATCCATTGAAAAGAAAAGTTCATTTAT
* ** * *
4230875 AGTCACTCATCCCTT-AGAAAGGTTTATTACTCTCTTTAAATGGTTTTATAATCTCATAGTTGAT
194 AGTCACTCATGCCTTCA-AAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGAT
* ** *
4230939 TTTAAGATT-AATTTTTTTATATTTTTTGGTTAAAACAGATTATAATTGAATGTTGGCCTCAGGA
258 TTTAAG-TTGAATTTTTTTA-CTTTTTTGGTTAAAACAGATTATAATTGAATGTTTACCTCTGGA
* *
4231003 AACATGAAGTGAAAGCCATCCA
321 AAAATGAAGCGAAAGCCATCCA
* * * * * * * *
4231025 TTGACACGAGAAATCTATTTGTAGTCACTCAT-CTTTCAAAAGCCTTATAACTTGCTTTAAATGG
1 TTGACAAGAAAAATCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGG
* * * *
4231089 TTTTATAACCTCATAATTGATTTTAGGTTCAATTTTTTTGACATTTTTGGTTAAACCAGATTATA
66 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTT-ACATTTTTGGTTAAAACAGATTATA
* * * * *
4231154 ATTGAATGTTTA-CTTGA-AGAATCGTGAGGTGAAAGCAATCCATT-AATGAGAAAAGTTTATTT
130 ATTGAATGTTTACCTTGAGA-AAT-GTGAAGCGAAAGCCATCCATTGAA-AAGAAAAGTTCATTT
* * * * * *
4231216 AAAGTTACTCATGCATTCAAAAGCCTTATTAGTAGCTTTAAATGGTTTTATAATCTCATAATTGC
192 ATAGTCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGA
* *
4231281 TTTTAAGTTGAATTTTTTT-TTGTTTTTTGTTAAAACAGATTATAATTGAATGTTTACCTCTGGA
257 TTTTAAGTTGAATTTTTTTACT-TTTTTGGTTAAAACAGATTATAATTGAATGTTTACCTCTGGA
* *
4231345 AACATGAAGCGAAAGTCATCCA
321 AAAATGAAGCGAAAGCCATCCA
* * * *
4231367 TTGACAAGAAAAGTCCATTTATAGTTACTGATGCCTTCGAAAGCCTTATTACTCACTTTAAATGG
1 TTGACAAGAAAAATCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGG
* * * * *
4231432 ATTTATAACCTCATAATTGATTTTAAGTTCAA-TTTTTTACATGTTTGGTTAAAATAGATTATAA
66 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGATTATAA
* * *
4231496 TTGAATATTTGCCTCGAGAAATGTGA
131 TTGAATGTTTACCTTGAGAAATGTGA
4231522 GGCAAAATGT
Statistics
Matches: 1293, Mismatches: 197, Indels: 71
0.83 0.13 0.05
Matches are distributed among these distances:
340 123 0.10
341 419 0.32
342 186 0.14
343 278 0.22
344 14 0.01
345 267 0.21
346 6 0.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (342 bp):
TTGACAAGAAAAATCCATTTATAGTCACTCATGCCTTCGAAAGCCTTATTACTCGCTTTAAATGG
TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGATTATAA
TTGAATGTTTACCTTGAGAAATGTGAAGCGAAAGCCATCCATTGAAAAGAAAAGTTCATTTATAG
TCACTCATGCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTT
AAGTTGAATTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTTTACCTCTGGAAAAAT
GAAGCGAAAGCCATCCA
Found at i:4238470 original size:9 final size:9
Alignment explanation
Indices: 4238456--4238488 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
4238446 ACCGAGACTA
4238456 CTCCACATC
1 CTCCACATC
4238465 CTCCACATC
1 CTCCACATC
*
4238474 CTCGACATC
1 CTCCACATC
4238483 CTCCAC
1 CTCCAC
4238489 CACCTACTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.21, C:0.55, G:0.03, T:0.21
Consensus pattern (9 bp):
CTCCACATC
Found at i:4249523 original size:157 final size:162
Alignment explanation
Indices: 4249053--4249839 Score: 741
Period size: 171 Copynumber: 4.7 Consensus size: 162
4249043 GACACAAAAG
* * * * * *
4249053 CCATCCATTGACAAGAAAAGTTTATTTAAAGTCACTTATGCGTTTGAAAGCCTTATTACTCA-TT
1 CCATCCATTGACAAGAAAAGTTCATTTATAGTCACTCATGCCTTCGAAAGACTTATTACTCACTT
* * * * * *
4249117 ATAAATGGTTTTAGAACCTCATAATTGATTTTTAGTTGATTTTTTTTACTTTTTTGGTT-AAA-A
66 -TAAATGGTTTTATAATCTTATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACA
*
4249180 AATTATAATTGAATGTTTACCTCA-GGAAATGTAAA
130 AATTATAATT-AATGTTTACCTTACGG-AATG-AAA
* *
4249215 GCGAAAGTCATCCATTGACAAGAAAAGTTCATTTATAGTGACTCATGCCTTCAAAAGACTTATTA
1 -C------CATCCATTGACAAGAAAAGTTCATTTATAGTCACTCATGCCTTCGAAAGACTTATTA
* * *
4249280 CTCACTTTAAATAGTTTTATAAACTTATAATTGATTTTAAGTTGAATTTTTTTTATATTTTTGGT
59 CTCACTTTAAATGGTTTTATAATCTTATAATTGATTTTAAGTTGAA-TTTTTTTACATTTTTGGT
*
4249345 TAAAACAGATTATAATTAATGTTTACC-T-C-G-A-GAAA
123 TAAAACAAATTATAATTAATGTTTACCTTACGGAATGAAA
** * * * * *
4249380 -CATCTGTTGATAAGAAAAGTCCATTTATAGTCACTCATGCCTTCGAAAGCCGTATAACTCACTT
1 CCATCCATTGACAAGAAAAGTTCATTTATAGTCACTCATGCCTTCGAAAGACTTATTACTCACTT
* * *
4249444 TAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTGTTTTACATTTTTGGTTAAAACAT
66 TAAATGGTTTTATAATCTTATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAA
4249509 ATTATAATTGAATGTTTACCTTGGGAAACGTGAATTGAAA
131 ATTATAATT-AATGTTTACCTT-----ACG-GAA-TGAAA
* * * * * *
4249549 GCCATCCATTAAGAAGAAAAATTCATTTATAGTCACTCATCCCTTCGAAAGGCTTATTACTCTCT
1 -CCATCCATTGACAAGAAAAGTTCATTTATAGTCACTCATGCCTTCGAAAGACTTATTACTCACT
*
4249614 TTAAATGGTTTTATAATCTTATAATTGATTTTAAGTTCAATTTTTTTACATTTTTTGGTTAAAAC
65 TTAAATGGTTTTATAATCTTATAATTGATTTTAAGTTGAATTTTTTTACA-TTTTTGGTTAAAAC
* * *
4249679 AAATTATAATTAAATGTTTGTCTCATGAAACGTGAAGTAAAA
129 AAATTATAATT-AATGTTT-AC-C-T--TACG-GAA-TGAAA
** * * * * * *
4249721 GCCATCCATTGACTTGAAAAATCCATTTGTAGTCACTCAT-CCTTCAAAAGCCTTATTACTCGCT
1 -CCATCCATTGACAAGAAAAGTTCATTTATAGTCACTCATGCCTTCGAAAGACTTATTACTCACT
* * ** * *
4249785 TTAAATTGTTTTATAACCCCATAATTGATTTTAAGTTCAATTTTCTTACATTTTT
65 TTAAATGGTTTTATAATCTTATAATTGATTTTAAGTTGAATTTTTTTACATTTTT
4249840 TATAAAACCT
Statistics
Matches: 525, Mismatches: 67, Indels: 57
0.81 0.10 0.09
Matches are distributed among these distances:
156 32 0.06
157 101 0.19
158 1 0.00
163 1 0.00
164 1 0.00
165 3 0.01
166 2 0.00
167 2 0.00
169 91 0.17
170 24 0.05
171 178 0.34
172 86 0.16
173 1 0.00
174 1 0.00
175 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (162 bp):
CCATCCATTGACAAGAAAAGTTCATTTATAGTCACTCATGCCTTCGAAAGACTTATTACTCACTT
TAAATGGTTTTATAATCTTATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAA
ATTATAATTAATGTTTACCTTACGGAATGAAA
Done.