Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold261
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: 750797
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 32985 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:389086 original size:54 final size:53
Alignment explanation
Indices: 389028--389278 Score: 247
Period size: 54 Copynumber: 4.6 Consensus size: 53
389018 GGGGTATAAT
**
389028 AGTCATTTTACCCTATGAGGGTATTTTAATCATTTTATCC-TTCGAGGGTATTTC
1 AGTCATTTTACCCT-TGAGGGTATTTTGGTCATTTTA-CCATTCGAGGGTATTTC
* * * ** * *
389082 AGTCATTTTACCCTTCAGGGGTATTTCGATTGTTTTACCCTTCGAGGATATTTC
1 AGTCATTTTACCCTTGA-GGGTATTTTGGTCATTTTACCATTCGAGGGTATTTC
* * * *
389136 GGCCATTTTACCCTTGGAGAGTATTTCGGTCATTTTACCATTC-AGGGGTATTTC
1 AGTCATTTTACCCTT-GAGGGTATTTTGGTCATTTTACCATTCGA-GGGTATTTC
* * *
389190 AATCATTTTTCCCTTTGAGGGTATTTTGGTCATTTTACCTTTCGAGGGTATTTC
1 AGTCATTTTACCC-TTGAGGGTATTTTGGTCATTTTACCATTCGAGGGTATTTC
* *
389244 -GATCATTTTTCCCTTCGAGGGTATTTTAGTCATTT
1 AG-TCATTTTACCCTT-GAGGGTATTTTGGTCATTT
389279 GCCCACGAAT
Statistics
Matches: 165, Mismatches: 24, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
53 7 0.04
54 154 0.93
55 4 0.02
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (53 bp):
AGTCATTTTACCCTTGAGGGTATTTTGGTCATTTTACCATTCGAGGGTATTTC
Found at i:389143 original size:81 final size:79
Alignment explanation
Indices: 389058--389278 Score: 246
Period size: 81 Copynumber: 2.7 Consensus size: 79
389048 GTATTTTAAT
* **
389058 CATTTTATCCTTCGAGGGTATTTCAGTCATTTTACCCTTCAGGGGTATTTCGATTGTTTTACCCT
1 CATTTTA-CCTTCGAGGGTATTTC-GTCATTTTACCCTTCAGGGGTATTTCAATCATTTTACCCT
389123 TCGAGGATATTTCGGC
64 TCGAGGATATTTCGGC
* * * *
389139 CATTTTACCCTTGGAGAGTATTTCGGTCATTTTACCATTCAGGGGTATTTCAATCATTTTTCCCT
1 CATTTTA-CCTTCGAGGGTATTTC-GTCATTTTACCCTTCAGGGGTATTTCAATCATTTTACCCT
* * * *
389204 TTGAGGGTATTTTGGT
64 TCGAGGATATTTCGGC
* * *
389220 CATTTTACCTTTCGAGGGTATTTCGATCATTTTTCCCTTC-GAGGGTATTTTAGTCATTT
1 CATTTTACC-TTCGAGGGTATTTCG-TCATTTTACCCTTCAG-GGGTATTTCAATCATTT
389279 GCCCACGAAT
Statistics
Matches: 118, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
80 4 0.03
81 114 0.97
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (79 bp):
CATTTTACCTTCGAGGGTATTTCGTCATTTTACCCTTCAGGGGTATTTCAATCATTTTACCCTTC
GAGGATATTTCGGC
Found at i:399502 original size:42 final size:42
Alignment explanation
Indices: 399456--399622 Score: 334
Period size: 42 Copynumber: 4.0 Consensus size: 42
399446 GTGTACATAG
399456 ATTTTATCTTTGTGTGTTTTGTTTGCATATTTTCTATTTTTT
1 ATTTTATCTTTGTGTGTTTTGTTTGCATATTTTCTATTTTTT
399498 ATTTTATCTTTGTGTGTTTTGTTTGCATATTTTCTATTTTTT
1 ATTTTATCTTTGTGTGTTTTGTTTGCATATTTTCTATTTTTT
399540 ATTTTATCTTTGTGTGTTTTGTTTGCATATTTTCTATTTTTT
1 ATTTTATCTTTGTGTGTTTTGTTTGCATATTTTCTATTTTTT
399582 ATTTTATCTTTGTGTGTTTTGTTTGCATATTTTCTATTTTT
1 ATTTTATCTTTGTGTGTTTTGTTTGCATATTTTCTATTTTT
399623 GTACAATTTT
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 125 1.00
ACGTcount: A:0.12, C:0.07, G:0.12, T:0.69
Consensus pattern (42 bp):
ATTTTATCTTTGTGTGTTTTGTTTGCATATTTTCTATTTTTT
Found at i:405496 original size:21 final size:21
Alignment explanation
Indices: 405451--405606 Score: 131
Period size: 21 Copynumber: 7.6 Consensus size: 21
405441 ATGTTTTACT
* * * *
405451 TTCTGTTTAGCTCTTTCGATC
1 TTCTGTTCAACTCTTACGAGC
* * *
405472 TTCTGTTCAACTGTTATGAGT
1 TTCTGTTCAACTCTTACGAGC
405493 TTCTGTT-AAGCTCTTACGAGC
1 TTCTGTTCAA-CTCTTACGAGC
* *
405514 TTCTGTTCAACTCTTATGAGT
1 TTCTGTTCAACTCTTACGAGC
* *
405535 TTCTGTCCAGCTCTTACGAGC
1 TTCTGTTCAACTCTTACGAGC
*
405556 TTCTGTTCAACTC-T--GAGT
1 TTCTGTTCAACTCTTACGAGC
* * * *
405574 TTATGTTTAGCTCTTAAGAGC
1 TTCTGTTCAACTCTTACGAGC
405595 TTCTGTTCAACT
1 TTCTGTTCAACT
405607 TTTGAGCTTC
Statistics
Matches: 104, Mismatches: 26, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
18 13 0.12
19 1 0.01
20 3 0.03
21 85 0.82
22 2 0.02
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (21 bp):
TTCTGTTCAACTCTTACGAGC
Found at i:405517 original size:42 final size:41
Alignment explanation
Indices: 405450--405617 Score: 216
Period size: 42 Copynumber: 4.1 Consensus size: 41
405440 CATGTTTTAC
* *
405450 TTTCTGTTTAGCTCTTTCGATCTTCTGTTCAACTGTTATGAG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACT-TTATGAG
*
405492 TTTCTGTTAAGCTCTTACGAGCTTCTGTTCAACTCTTATGAG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACT-TTATGAG
** *
405534 TTTCTGTCCAGCTCTTACGAGCTTCTGTTCAAC--TCTGAG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACTTTATGAG
* *
405573 TTTATGTTTAGCTCTTAAGAGCTTCTGTTCAACTTT-TGAG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACTTTATGAG
*
405613 CTTCT
1 TTTCT
405618 ATTGGCGTAT
Statistics
Matches: 111, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
39 34 0.31
40 7 0.06
41 1 0.01
42 69 0.62
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (41 bp):
TTTCTGTTTAGCTCTTACGAGCTTCTGTTCAACTTTATGAG
Found at i:405602 original size:81 final size:82
Alignment explanation
Indices: 405450--405606 Score: 217
Period size: 81 Copynumber: 1.9 Consensus size: 82
405440 CATGTTTTAC
** * * * *
405450 TTTCTGTTTAGCTCTTTCGATCTTCTGTTCAACTGTTATGAGTTTCTGTTAAGCTCTTACGAGCT
1 TTTCTGTCCAGCTCTTACGAGCTTCTGTTCAAC--TTATGAGTTTATGTTAAGCTCTTAAGAGCT
405515 TCTGTTCAACTCTTATGAG
64 TCTGTTCAACTCTTATGAG
* *
405534 TTTCTGTCCAGCTCTTACGAGCTTCTGTTCAAC-TCTGAGTTTATGTTTAGCTCTTAAGAGCTTC
1 TTTCTGTCCAGCTCTTACGAGCTTCTGTTCAACTTATGAGTTTATGTTAAGCTCTTAAGAGCTTC
405598 TGTTCAACT
66 TGTTCAACT
405607 TTTGAGCTTC
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 36 0.55
84 29 0.45
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.45
Consensus pattern (82 bp):
TTTCTGTCCAGCTCTTACGAGCTTCTGTTCAACTTATGAGTTTATGTTAAGCTCTTAAGAGCTTC
TGTTCAACTCTTATGAG
Found at i:405866 original size:10 final size:8
Alignment explanation
Indices: 405851--405877 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
405841 TGATGGCACA
405851 TGATATAT
1 TGATATAT
405859 TGATATAT
1 TGATATAT
405867 TGATATAT
1 TGATATAT
405875 TGA
1 TGA
405878 AATGGATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (8 bp):
TGATATAT
Found at i:411059 original size:114 final size:114
Alignment explanation
Indices: 410841--411284 Score: 642
Period size: 114 Copynumber: 4.0 Consensus size: 114
410831 ATTAGAAGAT
* * * * * *
410841 TTTGAGATCGATTGTAACTACATTTAGATGTTGTTAGCGCCGCGTGCATGTGGACTGCAGTTGAA
1 TTTGCGATCGATTCTAATTACATTTAGATGTTGTTAGCGCCACGTGTATGTGGACTGCAGTGGAA
* * * *
410906 TCTTTGTTCATAGCATAGTTGACAGTTAAAGGACTCATCATCCAATCGA
66 CCTTTGTTAATAGCATAGTTGACGGTTAAAGGACTCATCATCCAATCAA
* *
410955 TTTGTGA-CAGATTCTAATTACATTTAGATGTTGTTAGTGCCACGTGTATGTGGACTGCAGTGGA
1 TTTGCGATC-GATTCTAATTACATTTAGATGTTGTTAGCGCCACGTGTATGTGGACTGCAGTGGA
* **
411019 ACCTTTGTTAATAGCGTAGTTGACGGTTACGGGACTCATCATCCAATCAA
65 ACCTTTGTTAATAGCATAGTTGACGGTTAAAGGACTCATCATCCAATCAA
411069 TTTGCGATCGATTCTAATTACATTTAGATGTTGTTAGCGCCACGTGTATGTGGACTGCAGTGGAA
1 TTTGCGATCGATTCTAATTACATTTAGATGTTGTTAGCGCCACGTGTATGTGGACTGCAGTGGAA
411134 CCTTTGTTAATAGCATAGTTGACGGTTAAAGGACTCATCA-CCGAATCAA
66 CCTTTGTTAATAGCATAGTTGACGGTTAAAGGACTCATCATCC-AATCAA
*
411183 TTTGCGATCGATTCTAATTACATTTAGATGTTGTTAGCGCCACGTGTATGTGAACTGCAGTGGAA
1 TTTGCGATCGATTCTAATTACATTTAGATGTTGTTAGCGCCACGTGTATGTGGACTGCAGTGGAA
411248 -------T--T-GCATAGTTGACGGTTAAAGGACTCATCATCCAATC
66 CCTTTGTTAATAGCATAGTTGACGGTTAAAGGACTCATCATCCAATC
411285 GATTATGATT
Statistics
Matches: 306, Mismatches: 20, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
104 32 0.10
105 3 0.01
107 1 0.00
113 3 0.01
114 266 0.87
115 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.33
Consensus pattern (114 bp):
TTTGCGATCGATTCTAATTACATTTAGATGTTGTTAGCGCCACGTGTATGTGGACTGCAGTGGAA
CCTTTGTTAATAGCATAGTTGACGGTTAAAGGACTCATCATCCAATCAA
Found at i:420711 original size:30 final size:29
Alignment explanation
Indices: 420667--420797 Score: 93
Period size: 30 Copynumber: 4.8 Consensus size: 29
420657 AATTGAAAGG
420667 GAAAG-GAAG-GAGGAGGAAGAGGAGGCCA
1 GAAAGAGAAGAGAGGAGGAAGA-GAGGCCA
*
420695 GAAAGAGAAGAGAGGAGGAAGA-A-GCTA
1 GAAAGAGAAGAGAGGAGGAAGAGAGGCCA
* * *
420722 -AGAG-GAA-AGAGGAAGAAGAG-GCCCA
1 GAAAGAGAAGAGAGGAGGAAGAGAGGCCA
* *
420747 -AAAGAGAAGGGAAGAGGAAGAGGAGGCCA
1 GAAAGAGAAGAGAGGAGGAAGA-GAGGCCA
* *
420776 GAAGGAG-AGAGGAAGAGGAAGA
1 GAAAGAGAAGA-GAGGAGGAAGA
420798 AGCTAAGAGA
Statistics
Matches: 81, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
24 11 0.14
25 8 0.10
26 6 0.07
27 12 0.15
28 7 0.09
29 10 0.12
30 27 0.33
ACGTcount: A:0.48, C:0.06, G:0.45, T:0.01
Consensus pattern (29 bp):
GAAAGAGAAGAGAGGAGGAAGAGAGGCCA
Found at i:420778 original size:24 final size:24
Alignment explanation
Indices: 420751--420973 Score: 114
Period size: 24 Copynumber: 8.8 Consensus size: 24
420741 GGCCCAAAAG
420751 AGAAGGGAAGAGGAAGAGGAGGCC
1 AGAAGGGAAGAGGAAGAGGAGGCC
* *
420775 AGAA-GGAGAGAGGAAGAGGAAG-A
1 AGAAGGGA-AGAGGAAGAGGAGGCC
* *
420798 AGCTAAGAGAAGGGAAGAAGAGGAGGCC
1 AG--AAGGGAA--GAGGAAGAGGAGGCC
* *
420826 AGAA-GGAGAGAGGAAGAGGAAG-A
1 AGAAGGGA-AGAGGAAGAGGAGGCC
* * *
420849 AGCTAAGAGAAGAGAAGAAAAAGAGGCC
1 AG--AAGGGAAGAG--GAAGAGGAGGCC
* * * *
420877 AGGAGGAGAGAGGAGGAAGAAGAAGCT
1 AGAAGG-GA-A-GAGGAAGAGGAGGCC
*
420904 AGGAGGGAAGAGGAAGAGGAGGCC
1 AGAAGGGAAGAGGAAGAGGAGGCC
*
420928 AGAA-GGAGAGAGGAAGAGGATGCTC
1 AGAAGGGA-AGAGGAAGAGGAGGC-C
*
420953 GGAGGAGGGAAGAGGAAGAGG
1 --AGAAGGGAAGAGGAAGAGG
420974 GAGCTACCAG
Statistics
Matches: 151, Mismatches: 26, Indels: 41
0.69 0.12 0.19
Matches are distributed among these distances:
23 10 0.07
24 57 0.38
25 13 0.09
26 11 0.07
27 49 0.32
28 8 0.05
29 3 0.02
ACGTcount: A:0.45, C:0.06, G:0.47, T:0.02
Consensus pattern (24 bp):
AGAAGGGAAGAGGAAGAGGAGGCC
Found at i:420824 original size:81 final size:81
Alignment explanation
Indices: 420674--420848 Score: 223
Period size: 81 Copynumber: 2.2 Consensus size: 81
420664 AGGGAAAGGA
* * *
420674 AGGAGGAGGAAGAGGAGGCCAGAAAGAGAAGAGAGGAGGAAGAAGCTAAGAGGAAAGAGGAAGAA
1 AGGAAGAGGAAGAGGAGGCCAGAAAGAGAAGAGAAGAGGAAGAAGCTAAGAGGAAAGAAGAAGAA
420739 GAGGCCCAAAA-GAGA-
66 GAGG-CCAAAAGGAGAG
* *
420754 AGGGAAGAGGAAGAGGAGGCCAGAAGGAG-AGAGGAAGAGGAAGAAGCTAAGA-GAAGGGAAGAA
1 A-GGAAGAGGAAGAGGAGGCCAGAAAGAGAAGA-GAAGAGGAAGAAGCTAAGAGGAA-AGAAGAA
* *
420817 GAGGAGGCCAGAAGGAGAG
63 GAAGAGGCCAAAAGGAGAG
420836 AGGAAGAGGAAGA
1 AGGAAGAGGAAGA
420849 AGCTAAGAGA
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
80 12 0.14
81 70 0.84
82 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.45, T:0.01
Consensus pattern (81 bp):
AGGAAGAGGAAGAGGAGGCCAGAAAGAGAAGAGAAGAGGAAGAAGCTAAGAGGAAAGAAGAAGAA
GAGGCCAAAAGGAGAG
Found at i:420959 original size:51 final size:53
Alignment explanation
Indices: 420748--420973 Score: 267
Period size: 51 Copynumber: 4.4 Consensus size: 53
420738 AGAGGCCCAA
420748 AAGAGAAGGGAAGAGGAAGAGGAGGCCAGAAGGAGAGAGGAAGAGGAAGAAGCT
1 AAGAGAAGGGAAGAGGAAGAGGAGGCCAGAAGGAGAGAGGAAGAGG-AGAAGCT
420802 AAGAGAAGGG-A-A-GAAGAGGAGGCCAGAAGGAGAGAGGAAGAGGAAGAAGCT
1 AAGAGAAGGGAAGAGGAAGAGGAGGCCAGAAGGAGAGAGGAAGAGG-AGAAGCT
* * * * *
420853 AAGAGAAGAGAAGA--AA-AAGAGGCCAGGAGGAGAGAGGAGGAAGAAGAAGCT
1 AAGAGAAGGGAAGAGGAAGAGGAGGCCAGAAGGAGAGAGGAAG-AGGAGAAGCT
*
420904 -AG-G-AGGGAAGAGGAAGAGGAGGCCAGAAGGAGAGAGGAAGA-G-GATGCT
1 AAGAGAAGGGAAGAGGAAGAGGAGGCCAGAAGGAGAGAGGAAGAGGAGAAGCT
** *
420952 CGGAGGAGGGAAGAGGAAGAGG
1 AAGAGAAGGGAAGAGGAAGAGG
420974 GAGCTACCAG
Statistics
Matches: 151, Mismatches: 12, Indels: 21
0.82 0.07 0.11
Matches are distributed among these distances:
48 12 0.08
49 2 0.01
50 6 0.04
51 113 0.75
52 6 0.04
53 2 0.01
54 10 0.07
ACGTcount: A:0.45, C:0.06, G:0.47, T:0.02
Consensus pattern (53 bp):
AAGAGAAGGGAAGAGGAAGAGGAGGCCAGAAGGAGAGAGGAAGAGGAGAAGCT
Found at i:420988 original size:27 final size:25
Alignment explanation
Indices: 420907--420989 Score: 80
Period size: 27 Copynumber: 3.2 Consensus size: 25
420897 AGAAGCTAGG
*
420907 AGGGAAGAGGAAGAGGAG-GCCAGA
1 AGGGAAGAGGAAGAGGAGCTCCAGA
* *
420931 A-GGAGAGAGGAAGAGGATGCTCGGAGG
1 AGGGA-AGAGGAAGAGGA-GCTC-CAGA
420958 AGGGAAGAGGAAGAGGGAGCTACCAGA
1 AGGGAAGAGGAAGA-GGAGCT-CCAGA
420985 AGGGA
1 AGGGA
420990 GACAAAGAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
23 3 0.06
24 13 0.28
25 1 0.02
26 1 0.02
27 22 0.47
28 7 0.15
ACGTcount: A:0.39, C:0.08, G:0.49, T:0.04
Consensus pattern (25 bp):
AGGGAAGAGGAAGAGGAGCTCCAGA
Found at i:425171 original size:14 final size:14
Alignment explanation
Indices: 425154--425182 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
425144 CGGAGCTTCT
425154 TCTCTCCCTCTCCC
1 TCTCTCCCTCTCCC
425168 TCTCTCCCTCTCCC
1 TCTCTCCCTCTCCC
425182 T
1 T
425183 TCGGCTCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (14 bp):
TCTCTCCCTCTCCC
Found at i:425955 original size:14 final size:14
Alignment explanation
Indices: 425932--425965 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
425922 TGGTATGAGT
425932 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
425945 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
425959 TTATAGG
1 TTATAGG
425966 CAAACGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:428635 original size:11 final size:11
Alignment explanation
Indices: 428619--428656 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
428609 TCCTCCTGAT
428619 TCTTTCACATG
1 TCTTTCACATG
**
428630 TCTTTCTGAT-
1 TCTTTCACATG
428640 TCTTTCACATG
1 TCTTTCACATG
428651 TCTTTC
1 TCTTTC
428657 CAAGCCCTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.13, C:0.26, G:0.08, T:0.53
Consensus pattern (11 bp):
TCTTTCACATG
Found at i:428640 original size:21 final size:21
Alignment explanation
Indices: 428614--428656 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
428604 GGACCTCCTC
428614 CTGATTCTTTCACATGTCTTT
1 CTGATTCTTTCACATGTCTTT
428635 CTGATTCTTTCACATGTCTTT
1 CTGATTCTTTCACATGTCTTT
428656 C
1 C
428657 CAAGCCCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.26, G:0.09, T:0.51
Consensus pattern (21 bp):
CTGATTCTTTCACATGTCTTT
Found at i:435796 original size:3 final size:3
Alignment explanation
Indices: 435788--435825 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
435778 AGTTGGTTTT
435788 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
435826 GTTCCTAGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:437241 original size:20 final size:20
Alignment explanation
Indices: 437218--437269 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
437208 AATCAAGTGC
437218 AAATGATTTTAACCAAGTCA
1 AAATGATTTTAACCAAGTCA
* * *
437238 AAATGATTTCAATCAAGTTA
1 AAATGATTTTAACCAAGTCA
*
437258 AAATCATTTTAA
1 AAATGATTTTAA
437270 ATGATTTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.35
Consensus pattern (20 bp):
AAATGATTTTAACCAAGTCA
Found at i:437455 original size:20 final size:22
Alignment explanation
Indices: 437432--437471 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
437422 TATTTTCGGT
437432 ATCGATA-CTTT-TTAAAAATA
1 ATCGATACCTTTCTTAAAAATA
437452 ATCGATACCTTTCTTAAAAA
1 ATCGATACCTTTCTTAAAAA
437472 CGATACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (22 bp):
ATCGATACCTTTCTTAAAAATA
Found at i:439699 original size:19 final size:19
Alignment explanation
Indices: 439662--439700 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
439652 TTAATTTTAA
*
439662 TTGATTTAAATATTAAAAT
1 TTGATTTAAATAGTAAAAT
* *
439681 TTGATTTAGATAGTGAAAT
1 TTGATTTAAATAGTAAAAT
439700 T
1 T
439701 AATAATTTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (19 bp):
TTGATTTAAATAGTAAAAT
Found at i:454667 original size:25 final size:25
Alignment explanation
Indices: 454624--454735 Score: 100
Period size: 25 Copynumber: 4.5 Consensus size: 25
454614 GAGCTGTAAA
* * * *
454624 CGGGAAGCTCCTCCGAGCTGAATAAT
1 CGGGAAGCTCATGCAAGCTAAAT-AT
** *
454650 -GGGAAGCTCATGCAAGCTGTATAA
1 CGGGAAGCTCATGCAAGCTAAATAT
* *
454674 CAGGAAGCTCATGCAAGCCAAATAT
1 CGGGAAGCTCATGCAAGCTAAATAT
* *
454699 CAGGAAGCTCATGCGAGCTAAATAT
1 CGGGAAGCTCATGCAAGCTAAATAT
*
454724 GGGGAAGCTCAT
1 CGGGAAGCTCAT
454736 AAGAGCTGTG
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
24 1 0.01
25 70 0.99
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (25 bp):
CGGGAAGCTCATGCAAGCTAAATAT
Found at i:459257 original size:66 final size:66
Alignment explanation
Indices: 459147--459283 Score: 159
Period size: 66 Copynumber: 2.1 Consensus size: 66
459137 TCATATTCTA
* * * * *
459147 AAGTTGTAGCTGGAGTACGTCGTACTTTCTGTTCTACTCTGCTTCCCTCGCTGCTGCCTTCGCTT
1 AAGTTGTAGCTGGAGTACGTCATACTTTCTGTTCAACTCAGCTTCCCTCGATGCTGCCTCCGCTT
459212 T
66 T
* * * * * *
459213 AAGTTGTAGCTGGAGTTCTTCATATTTTCT-TTGAACCTCAGCTTCTCTCGATGCTGCCTCCGGT
1 AAGTTGTAGCTGGAGTACGTCATACTTTCTGTTCAA-CTCAGCTTCCCTCGATGCTGCCTCCGCT
459277 TT
65 TT
459279 AAGTT
1 AAGTT
459284 CAATAGGTGC
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 3 0.05
66 56 0.95
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (66 bp):
AAGTTGTAGCTGGAGTACGTCATACTTTCTGTTCAACTCAGCTTCCCTCGATGCTGCCTCCGCTT
T
Found at i:460794 original size:7 final size:7
Alignment explanation
Indices: 460784--460864 Score: 63
Period size: 7 Copynumber: 11.3 Consensus size: 7
460774 TCCCCTATCG
460784 CCTAAAC
1 CCTAAAC
*
460791 CCTAAAT
1 CCTAAAC
* *
460798 CATAAAAT
1 CCT-AAAC
*
460806 CATAAAC
1 CCTAAAC
460813 CCTAAAC
1 CCTAAAC
*
460820 CCTTAACC
1 CC-TAAAC
460828 CCTAAAC
1 CCTAAAC
*
460835 CTTAAAC
1 CCTAAAC
*
460842 CATAAAC
1 CCTAAAC
* *
460849 CATAATC
1 CCTAAAC
460856 CCTAAAC
1 CCTAAAC
460863 CC
1 CC
460865 ATAATCCATG
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
7 48 0.79
8 13 0.21
ACGTcount: A:0.44, C:0.36, G:0.00, T:0.20
Consensus pattern (7 bp):
CCTAAAC
Found at i:460803 original size:14 final size:14
Alignment explanation
Indices: 460786--460920 Score: 58
Period size: 14 Copynumber: 9.4 Consensus size: 14
460776 CCCTATCGCC
*
460786 TAAACCCTAAATCA
1 TAAACCCTAAACCA
* * *
460800 TAAAATCATAAACCC
1 T-AAACCCTAAACCA
* *
460815 TAAACCCTTAACCCC
1 TAAACCC-TAAACCA
*
460830 TAAACCTTAAACCA
1 TAAACCCTAAACCA
* * *
460844 TAAACCATAATCCC
1 TAAACCCTAAACCA
*
460858 TAAACCCATAATCCA
1 TAAACCC-TAAACCA
* *
460873 TGAACCTTAAA--A
1 TAAACCCTAAACCA
*
460885 TAGTAACTCCTAAACCT
1 TA--AAC-CCTAAACCA
* *
460902 TAAACCGTAAACCC
1 TAAACCCTAAACCA
460916 TAAAC
1 TAAAC
460921 TATAATGATA
Statistics
Matches: 90, Mismatches: 23, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
12 2 0.02
14 45 0.50
15 41 0.46
17 2 0.02
ACGTcount: A:0.45, C:0.31, G:0.02, T:0.21
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:460833 original size:22 final size:22
Alignment explanation
Indices: 460786--460883 Score: 83
Period size: 22 Copynumber: 4.5 Consensus size: 22
460776 CCCTATCGCC
* *
460786 TAAACCCTAAA-TCATAAAATCA
1 TAAACCCTAAACCCAT-AAACCA
* * *
460808 TAAACCCTAAACCCTTAACCCC
1 TAAACCCTAAACCCATAAACCA
*
460830 TAAACCTTAAA-CCATAAACCA
1 TAAACCCTAAACCCATAAACCA
* *
460851 TAATCCCTAAACCCATAATCCA
1 TAAACCCTAAACCCATAAACCA
* *
460873 TGAACCTTAAA
1 TAAACCCTAAA
460884 ATAGTAACTC
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
21 16 0.27
22 41 0.69
23 2 0.03
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.21
Consensus pattern (22 bp):
TAAACCCTAAACCCATAAACCA
Found at i:460841 original size:51 final size:50
Alignment explanation
Indices: 460753--460853 Score: 123
Period size: 51 Copynumber: 2.0 Consensus size: 50
460743 AACACTAATT
* * * * *
460753 AATCTAAACCTTAAACCCTTATCCCCTATCGCCTAAACCCTAAATCATAA
1 AATCTAAACCCTAAACCCTTAACCCCTAACGCCTAAACCATAAACCATAA
*
460803 AATCATAAACCCTAAACCCTTAACCCCTAAAC-CTTAAACCATAAACCATAA
1 AATC-TAAACCCTAAACCCTTAACCCCT-AACGCCTAAACCATAAACCATAA
460854 TCCCTAAACC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
50 4 0.09
51 37 0.86
52 2 0.05
ACGTcount: A:0.43, C:0.34, G:0.01, T:0.23
Consensus pattern (50 bp):
AATCTAAACCCTAAACCCTTAACCCCTAACGCCTAAACCATAAACCATAA
Found at i:460878 original size:15 final size:15
Alignment explanation
Indices: 460841--460878 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
460831 AAACCTTAAA
460841 CCATAAA-CCATAAT
1 CCATAAACCCATAAT
*
460855 CCCTAAACCCATAAT
1 CCATAAACCCATAAT
*
460870 CCATGAACC
1 CCATAAACC
460879 TTAAAATAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.42, C:0.37, G:0.03, T:0.18
Consensus pattern (15 bp):
CCATAAACCCATAAT
Found at i:461541 original size:40 final size:40
Alignment explanation
Indices: 461479--461583 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
461469 TTTTTGCGGC
* * *
461479 TTTTTTCAAAAAGTGGCACTAATGGTCGACCTATAGCAGCA
1 TTTTTT-AAAAAGCGCCACTAATGCTCGACCTATAGCAGCA
* * * *
461520 TTTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGCTGCG
1 TTTTTTAAAAAGCGCCACTAATGCTCGACCTATAGCAGCA
*
461560 TTTTTCAAAAAGCGCCACTAATGC
1 TTTTTTAAAAAGCGCCACTAATGC
461584 CACTAAAGCT
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
40 49 0.89
41 6 0.11
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (40 bp):
TTTTTTAAAAAGCGCCACTAATGCTCGACCTATAGCAGCA
Found at i:461656 original size:155 final size:155
Alignment explanation
Indices: 461364--461738 Score: 500
Period size: 155 Copynumber: 2.4 Consensus size: 155
461354 CGCAGCGGCG
* * * * ** * **
461364 TTTTTAAAGAAACGCCTCTAATGCTCGACCTATAACGGTATTTTTCAAAAAAGCACTGTTAATGC
1 TTTTTAAA-AAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTC-AAAAAGCGCCATTAATGC
* * * *
461429 CACTAAAGCTCAACATAAAACGACGGCGTTGTGCTTAATTTTTTTGCGGCTTTTTTCAAAAAGTG
64 CACTAAAGCTCAACATAAAACGACGACATTGTGCTTAATTTTTTTGCGGCATTTTTCAAAAAGCG
*
461494 GCACTAATGGTCGACCTATAGCAGCAT
129 CCACTAATGGTCGACCTATAGCAGCAT
* *
461521 TTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGCTGCGTTTTTCAAAAAGCGCCACTAATGCCA
1 TTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCATTAATGCCA
*
461586 CTAAAGCTTAACATAAAACGACGACATTGTGCTT-ATTTTTTTGGCGGCATTTTTCAAAAAGCGC
66 CTAAAGCTCAACATAAAACGACGACATTGTGCTTAATTTTTTT-GCGGCATTTTTCAAAAAGCGC
* * * *
461650 CGCTAATGGTTGACCTATAGCGGCGT
130 CACTAATGGTCGACCTATAGCAGCAT
* * *
461676 TTTTCAAAAAGCACCGCTAATGGTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCATTAATGC
1 TTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCATTAATGC
461739 TCGATCTATA
Statistics
Matches: 191, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
154 8 0.04
155 145 0.76
156 30 0.16
157 8 0.04
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (155 bp):
TTTTTAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCGCCATTAATGCCA
CTAAAGCTCAACATAAAACGACGACATTGTGCTTAATTTTTTTGCGGCATTTTTCAAAAAGCGCC
ACTAATGGTCGACCTATAGCAGCAT
Found at i:461684 original size:40 final size:40
Alignment explanation
Indices: 461629--461759 Score: 172
Period size: 40 Copynumber: 3.3 Consensus size: 40
461619 TATTTTTTTG
* *
461629 GCGGCATTTTTCAAAAAGCGCCGCTAATGGTTGACCTATA
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGGTCGACCTATA
* *
461669 GCGGCGTTTTTCAAAAAGCACCGCTAATGGTCGATCTATA
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGGTCGACCTATA
** * *
461709 GCGGCGTTTTTCAAAAAGCGCCATTAATGCTCGATCTATA
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGGTCGACCTATA
* *
461749 GCAGCATTTTT
1 GCGGCGTTTTT
461760 TATCCAAACG
Statistics
Matches: 81, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (40 bp):
GCGGCGTTTTTCAAAAAGCGCCGCTAATGGTCGACCTATA
Found at i:463313 original size:14 final size:15
Alignment explanation
Indices: 463286--463330 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
463276 GAATCTCAGG
*
463286 TATATTTTACTATAAT
1 TATA-TTTATTATAAT
463302 T-TATTTATTAT-AT
1 TATATTTATTATAAT
463315 TATATTTATTATAAT
1 TATATTTATTATAAT
463330 T
1 T
463331 GGAGACTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 3 0.12
14 17 0.65
15 5 0.19
16 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATTTATTATAAT
Found at i:465307 original size:21 final size:21
Alignment explanation
Indices: 465240--465294 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
465230 GTAGGGGTCT
*
465240 ACACGCCCATGTGAAGGCCAC
1 ACACGCCCGTGTGAAGGCCAC
*
465261 ATACGCCCGTGTGAAGGCCAC
1 ACACGCCCGTGTGAAGGCCAC
465282 ACACGCCCGTGTG
1 ACACGCCCGTGTG
465295 GAGGGGACAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.36, G:0.27, T:0.13
Consensus pattern (21 bp):
ACACGCCCGTGTGAAGGCCAC
Found at i:468935 original size:18 final size:18
Alignment explanation
Indices: 468881--468932 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
468871 TTACTCTTTG
* *
468881 TTTATTTATTTTATAACATA
1 TTTATATATTTT-TAATA-A
468901 TTTATATATTTTTAATAA
1 TTTATATATTTTTAATAA
468919 TTTATA-ATTTTTAA
1 TTTATATATTTTTAA
468933 ATATTTTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 8 0.27
18 7 0.23
19 4 0.13
20 11 0.37
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATATATTTTTAATAA
Found at i:477162 original size:19 final size:19
Alignment explanation
Indices: 477132--477198 Score: 64
Period size: 19 Copynumber: 3.3 Consensus size: 19
477122 AATTACAAAA
477132 AAAATATCAAAATAATTTTT
1 AAAAT-TCAAAATAATTTTT
*
477152 AAAATTCAAAAT-ATTTATA
1 AAAATTCAAAATAATTT-TT
477171 AAAATTCCAAAATTTATATTTTT
1 AAAATT-CAAAA--TA-ATTTTT
477194 AAAAT
1 AAAAT
477199 ATTATAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 4 0.10
19 14 0.36
20 10 0.26
22 1 0.03
23 6 0.15
24 4 0.10
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:478489 original size:20 final size:20
Alignment explanation
Indices: 478464--478503 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
478454 CGGAAAATGA
*
478464 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
478484 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
478504 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:478519 original size:14 final size:15
Alignment explanation
Indices: 478443--478519 Score: 61
Period size: 14 Copynumber: 5.0 Consensus size: 15
478433 GATTACTAGT
*
478443 AAAATGTTTTTC-GG
1 AAAATGATTTTCTGG
478457 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
478471 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
478491 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
478506 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
478520 TGTTTGATTG
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
13 4 0.08
14 22 0.43
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:483999 original size:44 final size:44
Alignment explanation
Indices: 483936--484026 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 44
483926 GTACGTCAAA
* * *
483936 TAATATTAAAATAACCTACACTAATTAGAGTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAGAGCTTAAGTAGGAAAC
*
483980 TAATATTAAAATAACCTACACTAATCAGAGCTTAAGTAGGAAGC
1 TAATATTAAAATAACCTACACTAATCAGAGCTTAAGTAGGAAAC
484024 TAA
1 TAA
484027 AAATAAAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.27
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAGAGCTTAAGTAGGAAAC
Found at i:485921 original size:69 final size:69
Alignment explanation
Indices: 485839--485975 Score: 211
Period size: 69 Copynumber: 2.0 Consensus size: 69
485829 GTAGGTCAAA
* *
485839 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGAAAAACTAAAAACAGAGTTTAACTGGG
1 TAATATTAAAATAACCTACACTAATCAAAGTGTAAGTGAAAAACTAAAAACAGAGTTTAACTGGG
485904 AAAC
66 AAAC
* * ** *
485908 TAATATTAAAATAACCTGCACTAATGAAAGTGTAAGTGGGAAACTAAAAATAGAGTTTAACTGGG
1 TAATATTAAAATAACCTACACTAATCAAAGTGTAAGTGAAAAACTAAAAACAGAGTTTAACTGGG
485973 AAA
66 AAA
485976 AAAATCGAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (69 bp):
TAATATTAAAATAACCTACACTAATCAAAGTGTAAGTGAAAAACTAAAAACAGAGTTTAACTGGG
AAAC
Found at i:487395 original size:31 final size:32
Alignment explanation
Indices: 487360--487432 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 32
487350 TGTCTGGGTC
* *
487360 AGGACTAATATTTTA-AAATTTGAAAAGTATA
1 AGGACTAATAATTGACAAATTTGAAAAGTATA
*
487391 AGGACTAA-AATTGACTAATTTGAAAAGTATA
1 AGGACTAATAATTGACAAATTTGAAAAGTATA
*
487422 GGGACTAATAA
1 AGGACTAATAA
487433 AAAATTTAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 4 0.11
31 30 0.83
32 2 0.06
ACGTcount: A:0.48, C:0.05, G:0.16, T:0.30
Consensus pattern (32 bp):
AGGACTAATAATTGACAAATTTGAAAAGTATA
Found at i:488339 original size:29 final size:27
Alignment explanation
Indices: 488314--488370 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
488304 ACCAAAATGT
488314 TATAACTTTTTTTTATTTACCAAAAAATA
1 TATAA-TTTTTTTTATTTACC-AAAAATA
488343 TATAATTTTTTTTATTTACC-AAAATA
1 TATAATTTTTTTTATTTACCAAAAATA
488369 TA
1 TA
488371 AAAAAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 8 0.29
28 15 0.54
29 5 0.18
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (27 bp):
TATAATTTTTTTTATTTACCAAAAATA
Found at i:488460 original size:27 final size:27
Alignment explanation
Indices: 488427--488501 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
488417 ACCTTGGTCA
488427 TGCCAATGGCATTGGCGGCACCAATGG
1 TGCCAATGGCATTGGCGGCACCAATGG
*
488454 TGCCAATGCCATTGGCGGCACCAATGG
1 TGCCAATGGCATTGGCGGCACCAATGG
488481 TGCCATACT-G-ATTGGCGGCAC
1 TGCCA-A-TGGCATTGGCGGCAC
488502 TATTCGTATT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 42 0.95
28 1 0.02
29 1 0.02
ACGTcount: A:0.21, C:0.28, G:0.31, T:0.20
Consensus pattern (27 bp):
TGCCAATGGCATTGGCGGCACCAATGG
Found at i:488675 original size:19 final size:21
Alignment explanation
Indices: 488637--488675 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
488627 AATAATTGAT
*
488637 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
488658 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
488676 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:489602 original size:18 final size:18
Alignment explanation
Indices: 489579--489616 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
489569 GGTTGGTGGT
489579 GAAGAAGAAGGTGCTGGC
1 GAAGAAGAAGGTGCTGGC
*
489597 GAAGAAGAAGGTGGTGGC
1 GAAGAAGAAGGTGCTGGC
489615 GA
1 GA
489617 TCATTGGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.08, G:0.47, T:0.11
Consensus pattern (18 bp):
GAAGAAGAAGGTGCTGGC
Found at i:492928 original size:159 final size:153
Alignment explanation
Indices: 492537--493631 Score: 876
Period size: 159 Copynumber: 6.9 Consensus size: 153
492527 TGCAAGTTGA
* * * *
492537 AAAAAAGTTAGTAAAAAAATCTTACTTCGGCCATTTATTCGTATTTTTTTCTCCGCATTTTATTC
1 AAAAAAGTTAGTAAAAAACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
* *
492602 CTTT--AAAAATATCATAATTTC-TAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGA
66 CTTTAAAAAAATAT-ATAATTTCGT-ATTTTATAATTTTACATTATTTCAGTACATAATCTTTGA
* *
492664 AATTTATTAATCTAGTGTGTTATTT
129 AATTTATTAATCTAGTCTGATATTT
* * * * ** * * *
492689 AAATTAATTTGGTGTAAAAAAACCCTTACCCCTGCCCTTTGCTCGTATTATTTTCT-CG-ATTTT
1 AAA-AAAGTT--AGT-AAAAAACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCA-TTT
* * * **
492752 TATTACTTTAAATAAAAATATATTATTCTCGTATTTTATTATTTTATATTATTTCAGTACATTTT
61 TATTACTTT-AA-AAAAATATATAATT-TCGTATTTTATAATTTTACATTATTTCAGTACATAAT
*
492817 CTTTGAAATATTTTGTATTAAT-TATTTCTGA-ATTTT
123 CTTTG-AA-A--TT-TATTAATCTA-GTCTGATA-TTT
* *
492853 AAAAAAGTTAGTAATACACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
1 AAAAAAGTTAGTAAAAAACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
* * * * *
492918 CTTTAAAAAAATCATA-AACTTAGTCTTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAA
66 CTTTAAAAAAAT-ATATAATTTCGTATTTTATAATTTTACATTATTTCAGTACATAATCTTTGAA
* *
492982 ATTTATTAATCTAGTGTGTTATTT
130 ATTTATTAATCTAGTCTGATATTT
* * * * ** * * *
493006 AAATTAATTTGGTGTAAAAAAACCCTTACCCCTGCCCTTTGCTCGTATTATTTTCT-CG-ATTTT
1 AAA-AAAGTT--AGT-AAAAAACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCA-TTT
* * * **
493069 TATTACTTTAAATAAAAATATATTATTCTCGTATTTTATTATTTTATATTATTTCAGTACATTTT
61 TATTACTTT-AA-AAAAATATATAATT-TCGTATTTTATAATTTTACATTATTTCAGTACATAAT
*
493134 CTTTGAAATATTTTGTATTAAT-TATTTCTGA-ATTTT
123 CTTTG-AA-A--TT-TATTAATCTA-GTCTGATA-TTT
* *
493170 AAAAAAGTTAGTAATACACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
1 AAAAAAGTTAGTAAAAAACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
* * * * *
493235 CTTTAAAAAAATCATA-AACTTAGTCTTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAA
66 CTTTAAAAAAAT-ATATAATTTCGTATTTTATAATTTTACATTATTTCAGTACATAATCTTTGAA
* *
493299 ATTTATTAATCTAGTGTGTTATTT
130 ATTTATTAATCTAGTCTGATATTT
* * * * ** * * *
493323 AAATTAATTTGGTGTAAAAAAACCCTTACCCCTGCCCTTTGCTCGTATTATTTTCT-CG-ATTTT
1 AAA-AAAGTT--AGT-AAAAAACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCA-TTT
* ** * **
493386 TATTACTTTAAATAAAAATATATTATTCTCGTATTTTATTGTTTTAAATTATTTCAGTACATTTT
61 TATTACTTT-AA-AAAAATATATAATT-TCGTATTTTATAATTTTACATTATTTCAGTACATAAT
*
493451 CTTTGAAATATTTTGTATTAAT-TATTTCTGA-ATTTT
123 CTTTG-AA-A--TT-TATTAATCTA-GTCTGATA-TTT
* *
493487 AAAAAAGTTAGTAATACACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
1 AAAAAAGTTAGTAAAAAACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
* * * * * *
493552 CTTT-AAAAAATATCATAAACTTAGTCTTTTATAATTTTACATTATTTCAGTGCATCATGTTTGA
66 CTTTAAAAAAATAT-AT-AATTTCGTATTTTATAATTTTACATTATTTCAGTACATAATCTTTGA
*
493616 AATTTATTAATTTAGT
129 AATTTATTAATCTAGT
493632 GTGTTAAGGG
Statistics
Matches: 735, Mismatches: 143, Indels: 128
0.73 0.14 0.13
Matches are distributed among these distances:
152 3 0.00
153 36 0.05
154 27 0.04
155 21 0.03
156 65 0.09
157 79 0.11
158 99 0.13
159 161 0.22
160 115 0.16
161 51 0.07
162 3 0.00
163 27 0.04
164 48 0.07
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (153 bp):
AAAAAAGTTAGTAAAAAACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
CTTTAAAAAAATATATAATTTCGTATTTTATAATTTTACATTATTTCAGTACATAATCTTTGAAA
TTTATTAATCTAGTCTGATATTT
Found at i:493111 original size:317 final size:317
Alignment explanation
Indices: 492537--493637 Score: 2044
Period size: 317 Copynumber: 3.5 Consensus size: 317
492527 TGCAAGTTGA
* * * * * *
492537 AAAAAAGTTAGTAAAAAAATCTTACTTCGGCCATTTATTCGTATTTTTTTCTCCGCATTTTATTC
1 AAAAAAGTTAGTAATACACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
* ** *
492602 CTTTAAAAATATCAT-AA-TTTCTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAA
66 CTTTAAAAAAATCATAAACTTAGT-CTTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAA
492665 ATTTATTAATCTAGTGTGTTATTTAAATTAATTTGGTGTAAAAAAACCCTTACCCCTGCCCTTTG
130 ATTTATTAATCTAGTGTGTTATTTAAATTAATTTGGTGTAAAAAAACCCTTACCCCTGCCCTTTG
492730 CTCGTATTATTTTCTCGATTTTTATTACTTTAAATAAAAATATATTATTCTCGTATTTTATTATT
195 CTCGTATTATTTTCTCGATTTTTATTACTTTAAATAAAAATATATTATTCTCGTATTTTATTATT
492795 TTATATTATTTCAGTACATTTTCTTTGAAATATTTTGTATTAATTATTTCTGAATTTT
260 TTATATTATTTCAGTACATTTTCTTTGAAATATTTTGTATTAATTATTTCTGAATTTT
492853 AAAAAAGTTAGTAATACACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
1 AAAAAAGTTAGTAATACACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
492918 CTTTAAAAAAATCATAAACTTAGTCTTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAA
66 CTTTAAAAAAATCATAAACTTAGTCTTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAA
492983 TTTATTAATCTAGTGTGTTATTTAAATTAATTTGGTGTAAAAAAACCCTTACCCCTGCCCTTTGC
131 TTTATTAATCTAGTGTGTTATTTAAATTAATTTGGTGTAAAAAAACCCTTACCCCTGCCCTTTGC
493048 TCGTATTATTTTCTCGATTTTTATTACTTTAAATAAAAATATATTATTCTCGTATTTTATTATTT
196 TCGTATTATTTTCTCGATTTTTATTACTTTAAATAAAAATATATTATTCTCGTATTTTATTATTT
493113 TATATTATTTCAGTACATTTTCTTTGAAATATTTTGTATTAATTATTTCTGAATTTT
261 TATATTATTTCAGTACATTTTCTTTGAAATATTTTGTATTAATTATTTCTGAATTTT
493170 AAAAAAGTTAGTAATACACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
1 AAAAAAGTTAGTAATACACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
493235 CTTTAAAAAAATCATAAACTTAGTCTTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAA
66 CTTTAAAAAAATCATAAACTTAGTCTTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAA
493300 TTTATTAATCTAGTGTGTTATTTAAATTAATTTGGTGTAAAAAAACCCTTACCCCTGCCCTTTGC
131 TTTATTAATCTAGTGTGTTATTTAAATTAATTTGGTGTAAAAAAACCCTTACCCCTGCCCTTTGC
*
493365 TCGTATTATTTTCTCGATTTTTATTACTTTAAATAAAAATATATTATTCTCGTATTTTATTGTTT
196 TCGTATTATTTTCTCGATTTTTATTACTTTAAATAAAAATATATTATTCTCGTATTTTATTATTT
*
493430 TAAATTATTTCAGTACATTTTCTTTGAAATATTTTGTATTAATTATTTCTGAATTTT
261 TATATTATTTCAGTACATTTTCTTTGAAATATTTTGTATTAATTATTTCTGAATTTT
493487 AAAAAAGTTAGTAATACACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
1 AAAAAAGTTAGTAATACACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
*
493552 CTTTAAAAAATATCATAAACTTAGTCTTTTATAATTTTACATTATTTCAGTGCATCATGTTTGAA
66 CTTTAAAAAA-ATCATAAACTTAGTCTTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAA
*
493617 ATTTATTAATTTAGTGTGTTA
130 ATTTATTAATCTAGTGTGTTA
493638 AGGGGGAATA
Statistics
Matches: 768, Mismatches: 14, Indels: 4
0.98 0.02 0.01
Matches are distributed among these distances:
316 73 0.10
317 619 0.81
318 76 0.10
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (317 bp):
AAAAAAGTTAGTAATACACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTA
CTTTAAAAAAATCATAAACTTAGTCTTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAA
TTTATTAATCTAGTGTGTTATTTAAATTAATTTGGTGTAAAAAAACCCTTACCCCTGCCCTTTGC
TCGTATTATTTTCTCGATTTTTATTACTTTAAATAAAAATATATTATTCTCGTATTTTATTATTT
TATATTATTTCAGTACATTTTCTTTGAAATATTTTGTATTAATTATTTCTGAATTTT
Found at i:495491 original size:40 final size:39
Alignment explanation
Indices: 495447--495557 Score: 143
Period size: 40 Copynumber: 2.8 Consensus size: 39
495437 GCTTGGACAA
*
495447 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCATTAC-GT
1 AAAACGCCGCTAAAAATC-AGCATTAGCGGCGC-TTACAGG
* *
495487 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTCAGG
1 AAAACGCCGCTAAAAATC-AGCATTAGCGGCGCTTACAGG
* *
495527 AAAGCGTCGCTAAAAATCAGCATTAGCGGCG
1 AAAACGCCGCTAAAAATCAGCATTAGCGGCG
495558 TTTTTCTAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
39 16 0.25
40 47 0.75
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (39 bp):
AAAACGCCGCTAAAAATCAGCATTAGCGGCGCTTACAGG
Found at i:495581 original size:39 final size:39
Alignment explanation
Indices: 495447--495582 Score: 141
Period size: 40 Copynumber: 3.4 Consensus size: 39
495437 GCTTGGACAA
*
495447 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCATTAC-G
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCG-ATTTCAG
* * *
495486 TAAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTCAGG
1 -AAAACGCCGCTAAAAATCAAGCATTAGCGGCGATTTCA-G
* * *
495527 AAAGCGTCGCTAAAAATC-AGCATTAGCGGCGTTTTTCTAG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCG-ATTTC-AG
*
495567 AAAACGCCGCAAAAAA
1 AAAACGCCGCTAAAAA
495583 CCTAAGCCAA
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
39 16 0.20
40 63 0.78
41 2 0.02
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (39 bp):
AAAACGCCGCTAAAAATCAAGCATTAGCGGCGATTTCAG
Found at i:495681 original size:41 final size:41
Alignment explanation
Indices: 495619--495770 Score: 225
Period size: 41 Copynumber: 3.7 Consensus size: 41
495609 CCTTTCGGGG
*
495619 CTTTAGCGGCGTTTTTGAAGAAGCACCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCAGAT
* * *
495660 CTTTAACGACGTTTTTTAAGAAGCGCCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCAGAT
* *
495701 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTGATGCTCAGAT
1 CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCAGAT
*
495742 CTGTAGCGGCGTTTTTGGAA-AAGCGCCGC
1 CTTTAGCGGCGTTTTT-GAAGAAGCGCCGC
495771 AAAAACATTT
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 97 0.97
42 3 0.03
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCAGAT
Found at i:495968 original size:41 final size:41
Alignment explanation
Indices: 495921--496000 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
495911 ATAGAAAAAT
*
495921 ATGCTCAGATCTGTAGCGGCGTTTTTAAAAAAGCGCCGCTG
1 ATGCTCAGATCTATAGCGGCGTTTTTAAAAAAGCGCCGCTG
*
495962 ATGCTCAGATCTATAGCGGCGTTTTTAGAAAAGCGCCGC
1 ATGCTCAGATCTATAGCGGCGTTTTTAAAAAAGCGCCGC
496001 AAAAATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (41 bp):
ATGCTCAGATCTATAGCGGCGTTTTTAAAAAAGCGCCGCTG
Found at i:496049 original size:20 final size:19
Alignment explanation
Indices: 496005--496049 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
495995 CGCCGCAAAA
496005 ATATTTTATCTGTCTATTT
1 ATATTTTATCTGTCTATTT
* *
496024 ACTATTTTATTTTGTTTATTT
1 A-TATTTTA-TCTGTCTATTT
496045 ATATT
1 ATATT
496050 AATTAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 11 0.50
21 10 0.45
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (19 bp):
ATATTTTATCTGTCTATTT
Found at i:496094 original size:230 final size:230
Alignment explanation
Indices: 495691--496152 Score: 879
Period size: 230 Copynumber: 2.0 Consensus size: 230
495681 AGCGCCGCTA
* * *
495691 ATGCTCAGATCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTGATGCTCAGATCTGTAGCGGCGTTT
1 ATGCTCAGATCTGTAGCGGCGTTTTTAAAAAAGCGCCGCTGATGCTCAGATCTATAGCGGCGTTT
*
495756 TTGGAAAAGCGCCGCAAAAACATTTTATCTGTCTATTTACTATTTTATTTTGTTTATTTATATTA
66 TTAGAAAAGCGCCGCAAAAACATTTTATCTGTCTATTTACTATTTTATTTTGTTTATTTATATTA
495821 ATTAAAATTCAATTTATTTTTAATTGAATATTTGTTAAAAATGGATAAATTTGAAATAATGACAC
131 ATTAAAATTCAATTTATTTTTAATTGAATATTTGTTAAAAATGGATAAATTTGAAATAATGACAC
495886 GTAGAAATAATTTGAAATAAAAAATATAGAAAAAT
196 GTAGAAATAATTTGAAATAAAAAATATAGAAAAAT
495921 ATGCTCAGATCTGTAGCGGCGTTTTTAAAAAAGCGCCGCTGATGCTCAGATCTATAGCGGCGTTT
1 ATGCTCAGATCTGTAGCGGCGTTTTTAAAAAAGCGCCGCTGATGCTCAGATCTATAGCGGCGTTT
*
495986 TTAGAAAAGCGCCGCAAAAATATTTTATCTGTCTATTTACTATTTTATTTTGTTTATTTATATTA
66 TTAGAAAAGCGCCGCAAAAACATTTTATCTGTCTATTTACTATTTTATTTTGTTTATTTATATTA
496051 ATTAAAATTCAATTTATTTTTAATTGAATATTTGTTAAAAATGGATAAATTTGAAATAATGACAC
131 ATTAAAATTCAATTTATTTTTAATTGAATATTTGTTAAAAATGGATAAATTTGAAATAATGACAC
496116 GTAGAAATAATTTGAAATAAAAAATATAGAAAAAT
196 GTAGAAATAATTTGAAATAAAAAATATAGAAAAAT
496151 AT
1 AT
496153 TTGTTAAAAA
Statistics
Matches: 227, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
230 227 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.38
Consensus pattern (230 bp):
ATGCTCAGATCTGTAGCGGCGTTTTTAAAAAAGCGCCGCTGATGCTCAGATCTATAGCGGCGTTT
TTAGAAAAGCGCCGCAAAAACATTTTATCTGTCTATTTACTATTTTATTTTGTTTATTTATATTA
ATTAAAATTCAATTTATTTTTAATTGAATATTTGTTAAAAATGGATAAATTTGAAATAATGACAC
GTAGAAATAATTTGAAATAAAAAATATAGAAAAAT
Found at i:496511 original size:21 final size:21
Alignment explanation
Indices: 496459--496512 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
496449 TAAGGGTTGT
* *
496459 GATTTAAGGTTTATGGGTTAGG
1 GATTTAAGG-TTAAGAGTTAGG
*
496481 G-GTTAGAGGTTAAGAGTTAGG
1 GATTTA-AGGTTAAGAGTTAGG
496502 GATTTAAGGTT
1 GATTTAAGGTT
496513 TATGAATTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (21 bp):
GATTTAAGGTTAAGAGTTAGG
Found at i:499733 original size:43 final size:43
Alignment explanation
Indices: 499672--502077 Score: 4778
Period size: 43 Copynumber: 56.0 Consensus size: 43
499662 TTGTCTATTG
499672 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
499715 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
499758 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
499801 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
499844 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
499887 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
499930 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
499973 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500016 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500059 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500102 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500145 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500188 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500231 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500274 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500317 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500360 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500403 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500446 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500489 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500532 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500575 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500618 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500661 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500704 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500747 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500790 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500833 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500876 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500919 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
500962 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501005 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501048 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501091 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501134 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501177 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501220 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501263 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501306 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501349 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501392 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501435 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501478 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501521 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501564 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501607 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501650 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501693 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501736 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501779 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501822 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501865 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501908 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
501951 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
* *
501994 GTGCTAAAAGCGCCGCTAAAGGTCCTGCTCTATAGCGGCGTTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
*
502037 GTG-GAAAAGCGCCGCTAAAGGTCCTGCTCTATAGCGGCGTT
1 GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTT
502078 CACAACAGCG
Statistics
Matches: 2360, Mismatches: 3, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
42 37 0.02
43 2323 0.98
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.23
Consensus pattern (43 bp):
GTGCGAAAAGCGCCGCTAAAGGTCCTGGTCTATAGCGGCGTTT
Found at i:507042 original size:22 final size:22
Alignment explanation
Indices: 506991--507043 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
506981 ACATGGTATG
* *
506991 TCAGATACAGATGCAGAACATA
1 TCAGATTCAGATGCAGAACAAA
* * *
507013 TTATATTCAGATGCAGAATAAA
1 TCAGATTCAGATGCAGAACAAA
507035 TCAGATTCA
1 TCAGATTCA
507044 AATATAGATT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (22 bp):
TCAGATTCAGATGCAGAACAAA
Found at i:508244 original size:10 final size:10
Alignment explanation
Indices: 508229--508277 Score: 71
Period size: 10 Copynumber: 4.9 Consensus size: 10
508219 CAAAAAAAGA
508229 AAGAAAGAAG
1 AAGAAAGAAG
*
508239 AAGAAAAAAG
1 AAGAAAGAAG
*
508249 AAGAAAAAAG
1 AAGAAAGAAG
*
508259 AAGAAAGAAA
1 AAGAAAGAAG
508269 AAGAAAGAA
1 AAGAAAGAA
508278 TGTTACTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (10 bp):
AAGAAAGAAG
Found at i:508252 original size:20 final size:20
Alignment explanation
Indices: 508221--508277 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
508211 TCAAACAACA
508221 AAAAAAGAAAGAAAGAAGAAG
1 AAAAAAG-AAGAAAGAAGAAG
*
508242 AAAAAAGAAGAAAAAAGAAG
1 AAAAAAGAAGAAAGAAGAAG
508262 AAAGAAA-AAGAAAGAA
1 AAA-AAAGAAGAAAGAA
508278 TGTTACTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 23 0.70
21 10 0.30
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAGAAAGAAGAAG
Found at i:508275 original size:17 final size:17
Alignment explanation
Indices: 508225--508277 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
508215 ACAACAAAAA
508225 AAGAAAGAAAGAAG-AAG
1 AAGAAAGAAA-AAGAAAG
*
508242 AAAAAAGAAGAAA-AAAG
1 AAGAAAGAA-AAAGAAAG
508259 AAGAAAGAAAAAGAAAG
1 AAGAAAGAAAAAGAAAG
508276 AA
1 AA
508278 TGTTACTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAGAAAGAAAAAGAAAG
Found at i:508908 original size:18 final size:18
Alignment explanation
Indices: 508887--508921 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
508877 TAATATTATA
508887 AAATAAAATAATTATTTC
1 AAATAAAATAATTATTTC
* *
508905 AAATACAATTATTATTT
1 AAATAAAATAATTATTT
508922 TTATATGTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATAAAATAATTATTTC
Found at i:510803 original size:16 final size:16
Alignment explanation
Indices: 510782--510814 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
510772 CTTTTGAATC
510782 CGTTTGTGAATTACTT
1 CGTTTGTGAATTACTT
510798 CGTTTGTGAATTACTT
1 CGTTTGTGAATTACTT
510814 C
1 C
510815 ACTTGTGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.48
Consensus pattern (16 bp):
CGTTTGTGAATTACTT
Found at i:510820 original size:16 final size:16
Alignment explanation
Indices: 510785--510822 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
510775 TTGAATCCGT
**
510785 TTGTGAATTACTTCGT
1 TTGTGAATTACTTCAC
510801 TTGTGAATTACTTCAC
1 TTGTGAATTACTTCAC
510817 TTGTGA
1 TTGTGA
510823 CATTTATGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.47
Consensus pattern (16 bp):
TTGTGAATTACTTCAC
Found at i:516889 original size:25 final size:25
Alignment explanation
Indices: 516846--516915 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
516836 CAGGCCCATT
*
516846 TTCACAGA-TCATGTAAGCATTCTGA
1 TTCACA-ACTCATGTGAGCATTCTGA
*
516871 TTTACAACTCATGTGAGCATTCTGA
1 TTCACAACTCATGTGAGCATTCTGA
* *
516896 TTCACAGCTCGTGTGAGCAT
1 TTCACAACTCATGTGAGCAT
516916 ACATGTACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
24 1 0.03
25 38 0.97
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (25 bp):
TTCACAACTCATGTGAGCATTCTGA
Found at i:518073 original size:15 final size:16
Alignment explanation
Indices: 518053--518082 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
518043 TGGTGCCTTG
518053 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
518068 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
518083 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:525893 original size:16 final size:16
Alignment explanation
Indices: 525872--525921 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
525862 AAAAATTTTA
525872 TAAGTTATGTATTATG
1 TAAGTTATGTATTATG
*
525888 TAAGTTA---A-CATG
1 TAAGTTATGTATTATG
525900 TAAGTTATGTATTATG
1 TAAGTTATGTATTATG
525916 TAAGTT
1 TAAGTT
525922 TACATATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
12 10 0.36
13 1 0.04
15 1 0.04
16 16 0.57
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (16 bp):
TAAGTTATGTATTATG
Found at i:525904 original size:28 final size:28
Alignment explanation
Indices: 525870--525938 Score: 111
Period size: 28 Copynumber: 2.4 Consensus size: 28
525860 AAAAAAATTT
525870 TATAAGTTATGTATTATGTAAGTTAACA
1 TATAAGTTATGTATTATGTAAGTTAACA
* *
525898 TGTAAGTTATGTATTATGTAAGTTTACA
1 TATAAGTTATGTATTATGTAAGTTAACA
525926 TATAAGTTTATGT
1 TATAAG-TTATGT
525939 GACAGTTATG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
28 31 0.84
29 6 0.16
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (28 bp):
TATAAGTTATGTATTATGTAAGTTAACA
Found at i:526111 original size:13 final size:13
Alignment explanation
Indices: 526095--526136 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
526085 TTAATTTTAG
*
526095 TAAGTAATGTATT
1 TAAGTAATATATT
*
526108 TAAGTAACATATT
1 TAAGTAATATATT
*
526121 TAAGTAATAAATT
1 TAAGTAATATATT
526134 TAA
1 TAA
526137 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:526962 original size:15 final size:15
Alignment explanation
Indices: 526942--526973 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
526932 TTGATAACAG
526942 TAAATTAGTACCAAA
1 TAAATTAGTACCAAA
*
526957 TAAATTAGTATCAAA
1 TAAATTAGTACCAAA
526972 TA
1 TA
526974 CTTCAACCCT
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:0.53, C:0.09, G:0.06, T:0.31
Consensus pattern (15 bp):
TAAATTAGTACCAAA
Found at i:528628 original size:147 final size:146
Alignment explanation
Indices: 528328--528774 Score: 420
Period size: 147 Copynumber: 3.0 Consensus size: 146
528318 TAAATAAGAA
* * * * *
528328 CCACTAACTATAAGTCAAAACGAAG-CTGTTTCATCAACAAATAGCTCACACCTGTGGCGTTTTT
1 CCACTAACTATAAATCAAAACGAAGTC-GTTTCATCAACAATTAACTCAAACCTGTGGCGTTTTC
* ** * * *
528392 GAATAAACGCCACTAAT-A-ATACAACAAAACGGCCTCGTATCAATAAATGTTAAAATATTTTTG
65 GAAAAAACGCCACTAATAACATA-AACAAAACGGCAACGTTTCAATAAATGTTAAAACAATTTTG
***
528455 CGGCGTTTGAACCGAAGCG
129 CGGCGTTTG-AGTAAAGCG
* * * * * *
528474 CCACTAACTGTAAATCAAAACGCAGTCGATTCATCAACACTTACCTCAAACCCGTGGCGTTTTCG
1 CCACTAACTATAAATCAAAACGAAGTCGTTTCATCAACAATTAACTCAAACCTGTGGCGTTTTCG
** * * *
528539 AAAAAACGCCACTAATAACATTTACAAAACGGCAGCGTTTCTATAAATGTTAGAACAATTTTGCG
66 AAAAAACGCCACTAATAACATAAACAAAACGGCAACGTTTCAATAAATGTTAAAACAATTTTGCG
528604 GCGTTTTGAGTAAAGCG
131 GCG-TTTGAGTAAAGCG
* ** * * *
528621 CCACTAACTATAAGCTC-AAACGAAGTCGTTTCCCCAACAGTTAACTCAAGCTTGTGGCGTTTTC
1 CCACTAACTATAA-ATCAAAACGAAGTCGTTTCATCAACAATTAACTCAAACCTGTGGCGTTTTC
* * * * * ** *
528685 -ATAAAAACACCACTAATACCATAGACAAAACGACAACATTTCAATAAA-CATAATTACAATTTT
65 GA-AAAAACGCCACTAATAACATAAACAAAACGGCAACGTTTCAATAAATGTTAA-AACAATTTT
*
528748 GCAGCGTTTGATGTAAAGCG
128 GCGGCGTTTGA-GTAAAGCG
528768 CCACTAA
1 CCACTAA
528775 TAGCAACGTA
Statistics
Matches: 246, Mismatches: 47, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
146 76 0.31
147 162 0.66
148 8 0.03
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (146 bp):
CCACTAACTATAAATCAAAACGAAGTCGTTTCATCAACAATTAACTCAAACCTGTGGCGTTTTCG
AAAAAACGCCACTAATAACATAAACAAAACGGCAACGTTTCAATAAATGTTAAAACAATTTTGCG
GCGTTTGAGTAAAGCG
Found at i:529636 original size:19 final size:20
Alignment explanation
Indices: 529612--529653 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
529602 ACAACAACCA
529612 AACCCCAAAATCC-AACCCC
1 AACCCCAAAATCCAAACCCC
*
529631 AACCCCTAAATCCTAAACCCC
1 AACCCCAAAATCC-AAACCCC
529652 AA
1 AA
529654 ATCACAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
21 8 0.40
ACGTcount: A:0.43, C:0.48, G:0.00, T:0.10
Consensus pattern (20 bp):
AACCCCAAAATCCAAACCCC
Found at i:530547 original size:19 final size:18
Alignment explanation
Indices: 530521--530560 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
530511 ATTGAATTTT
530521 AATTAATA-TAAATAAACA
1 AATTAATAGTAAAT-AACA
530539 AATTAAATAGTAAATAACA
1 AATT-AATAGTAAATAACA
530558 AAT
1 AAT
530561 AAAAGGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 11 0.55
20 5 0.25
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (18 bp):
AATTAATAGTAAATAACA
Found at i:530774 original size:114 final size:114
Alignment explanation
Indices: 530625--531222 Score: 701
Period size: 114 Copynumber: 5.3 Consensus size: 114
530615 AAATGACGCC
* * * * *
530625 GTTGGGCTTAGGTTTTTTTGCGGCGC-TTCAACAAAAAAGCCGCTAAAGCCTTAAGCATTGGCGG
1 GTTGGGCTTAGGTTTTTTTGCGGCGCTTTC-TCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGG
* * * * *
530689 CGCATT-CTT-AAAACGCCGCTAAAGCCCACGAATTG-TCAGAAAGCGGTGTA
65 CGC-TTACTTAAAAACGCCACTAAATCCC-CGAA-AGCTCAGAAAACGGCGTA
*
530739 GTTGGGCTTA-GTTTTTATTGCAGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGG
1 GTTGGGCTTAGGTTTTT-TTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGG
* * *
530803 CGCTTACTTAAAAACGCCACTAAATCCCCAAAAGCTCAAAAAACAGCGTCA
65 CGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGT-A
* * * *
530854 -TTGAGCTTTGGTTTTTTTGTGGCGCTTTCTCAAAAACGCTGCTAAAGCCCTGAGCATTAGCGGC
1 GTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGC
* *
530918 GCTTACTTAAAAATGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTC
66 GCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTA
* *
530967 GTTGGGCTTAGGTATCTTTT-CGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGG
1 GTTGGGCTTAGGT-TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGG
* ** * * * *
531031 CGTTTACTTAAAAGTGCCACTAAATCCCTGAACGCTCAAAAAATGGCGTA
65 CGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTA
* * * * * *
531081 GTTAGGCTTTGGTTTTTTTGTGGCGCTTTCTCGAAAACGCAGCGAAAGCCCTGAGCATTAGCGGC
1 GTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGC
* ** *
531146 GCTTTCTTAAAAACGCCGTTAAATCCCCGAAAGCT-AGAAAAACGGCGTC
66 GCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAG-AAAACGGCGTA
*
531195 GTTGGGCTTAGG-TATTTTGCGGCGCTTT
1 GTTGGGCTTAGGTTTTTTTGCGGCGCTTT
531223 ATGGAAACAC
Statistics
Matches: 413, Mismatches: 60, Indels: 23
0.83 0.12 0.05
Matches are distributed among these distances:
113 29 0.07
114 353 0.85
115 31 0.08
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (114 bp):
GTTGGGCTTAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGC
GCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAACGGCGTA
Found at i:536437 original size:13 final size:13
Alignment explanation
Indices: 536419--536443 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
536409 ATTTTTAATA
536419 TTATTTTGTGTGT
1 TTATTTTGTGTGT
536432 TTATTTTGTGTG
1 TTATTTTGTGTG
536444 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:539283 original size:39 final size:37
Alignment explanation
Indices: 539216--539308 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
539206 CACAAAATGG
* *
539216 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
539255 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
539292 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
539309 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:540817 original size:3 final size:3
Alignment explanation
Indices: 540809--540875 Score: 52
Period size: 3 Copynumber: 23.7 Consensus size: 3
540799 TTACTTTATT
** ** *
540809 TAA TAA TAA TAA TAA TAA T-A TAA -AA CCA TAA TAA TGG T-T TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
540854 TTA TAA TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
540876 TTTATGTATA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
2 7 0.14
3 44 0.86
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:542282 original size:25 final size:26
Alignment explanation
Indices: 542254--542314 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 26
542244 CAAATTTTGC
542254 ATATTTAATT-ATTGTCTAAAAATAA
1 ATATTTAATTCATTGTCTAAAAATAA
* *
542279 ATATTAAATTGGCCATTGTCTAAGAATAA
1 ATATTTAATT---CATTGTCTAAAAATAA
542308 ATATTTA
1 ATATTTA
542315 TTTGCTGCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 9 0.31
29 20 0.69
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (26 bp):
ATATTTAATTCATTGTCTAAAAATAA
Found at i:552567 original size:22 final size:23
Alignment explanation
Indices: 552533--552576 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
552523 GTACCCCTTC
*
552533 TTCCGTCTCTCTTTTATCATTCT
1 TTCCGTCTCTCTTCTATCATTCT
* *
552556 TTCC-TCTTTCTTCTCTCATTC
1 TTCCGTCTCTCTTCTATCATTC
552577 CTTATGTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.07, C:0.34, G:0.02, T:0.57
Consensus pattern (23 bp):
TTCCGTCTCTCTTCTATCATTCT
Found at i:552793 original size:12 final size:14
Alignment explanation
Indices: 552761--552796 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
552751 ACCATTTCTT
552761 TTCTTTCCCCTATA
1 TTCTTTCCCCTATA
552775 TTCTTTCCCCTAT-
1 TTCTTTCCCCTATA
552788 TT-TTTCCCC
1 TTCTTTCCCC
552797 ATTATCTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 7 0.32
13 2 0.09
14 13 0.59
ACGTcount: A:0.08, C:0.39, G:0.00, T:0.53
Consensus pattern (14 bp):
TTCTTTCCCCTATA
Found at i:558497 original size:34 final size:35
Alignment explanation
Indices: 558431--558497 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
558421 TGTCTCATGA
558431 AAATGTATCCATTGAATGATAAATTATCACTTTCT
1 AAATGTATCCATTGAATGATAAATTATCACTTTCT
* *
558466 AAATGTATCTATTGAATGAT-AATTATTACTTT
1 AAATGTATCCATTGAATGATAAATTATCACTTT
558498 TCAAAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 11 0.37
35 19 0.63
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.43
Consensus pattern (35 bp):
AAATGTATCCATTGAATGATAAATTATCACTTTCT
Found at i:563483 original size:12 final size:12
Alignment explanation
Indices: 563466--563506 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
563456 TGATGAGGAG
*
563466 GAAGAGGAAGAT
1 GAAGAGGATGAT
*
563478 GAAGAGGATGAG
1 GAAGAGGATGAT
*
563490 GATGAGGATGAT
1 GAAGAGGATGAT
563502 GAAGA
1 GAAGA
563507 TGATCCTGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.12
Consensus pattern (12 bp):
GAAGAGGATGAT
Found at i:563484 original size:18 final size:18
Alignment explanation
Indices: 563457--563491 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
563447 AGAATCGGAT
*
563457 GATGAGGAGGAAGAGGAA
1 GATGAAGAGGAAGAGGAA
*
563475 GATGAAGAGGATGAGGA
1 GATGAAGAGGAAGAGGA
563492 TGAGGATGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.49, T:0.09
Consensus pattern (18 bp):
GATGAAGAGGAAGAGGAA
Found at i:563834 original size:27 final size:26
Alignment explanation
Indices: 563804--563884 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 26
563794 TTCATGATAT
563804 TGGGGATAGTGATGATGATGAGGAAGA
1 TGGGGATAG-GATGATGATGAGGAAGA
* *
563831 TGGGGTAGAGGATGATGATGAGGAGGA
1 TGGGG-ATAGGATGATGATGAGGAAGA
* *
563858 -GGAGGATGAGGATGAAGAGGAGGAAGA
1 TGG-GGAT-AGGATGATGATGAGGAAGA
563885 GGTAGATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
26 3 0.07
27 39 0.87
28 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.49, T:0.16
Consensus pattern (26 bp):
TGGGGATAGGATGATGATGAGGAAGA
Found at i:563862 original size:21 final size:21
Alignment explanation
Indices: 563838--563881 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
563828 AGATGGGGTA
* *
563838 GAGGATGATGATGAGGAGGAG
1 GAGGATGAGGATGAAGAGGAG
563859 GAGGATGAGGATGAAGAGGAG
1 GAGGATGAGGATGAAGAGGAG
563880 GA
1 GA
563882 AGAGGTAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.52, T:0.11
Consensus pattern (21 bp):
GAGGATGAGGATGAAGAGGAG
Found at i:571686 original size:44 final size:44
Alignment explanation
Indices: 571619--571724 Score: 158
Period size: 44 Copynumber: 2.4 Consensus size: 44
571609 AATGAAATTG
*
571619 CTCACACGAGCTATGAATTAGACATTAACCAGTACACGATGCTA
1 CTCACACGAGCTATGAATCAGACATTAACCAGTACACGATGCTA
* *
571663 CTCACATGAGCTATGAATCAGACATTAACCATTACACGATGCTA
1 CTCACACGAGCTATGAATCAGACATTAACCAGTACACGATGCTA
* * *
571707 CTCATAGGAGCTGTGAAT
1 CTCACACGAGCTATGAAT
571725 AATCCGCAAC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (44 bp):
CTCACACGAGCTATGAATCAGACATTAACCAGTACACGATGCTA
Found at i:572379 original size:122 final size:122
Alignment explanation
Indices: 572162--572401 Score: 349
Period size: 122 Copynumber: 2.0 Consensus size: 122
572152 GTTATATCGA
* * *
572162 TACCTTGAGGACTTCTACCGAAACAAGTCAAAAAAGTAGCCAAAGTTCAGCCTCTCCTGTACTTT
1 TACCTTGAGGACTTCTACCGAAACAAGTCAAAAAAGTAGCCAAAGTTCAGCCTATCCTGCACTTC
* * **
572227 TACCGATACTTTGTTGGATTCTATCGATACCAGTTGAAACCA-CTAGAGTTCTACCGC
66 TACCGATACTCTGATGGATTCTATCGATACCAAATGAAACCATC-AGAGTTCTACCGC
*
572284 TACCTTGAGGACTTCTACCGAAACAAGTCAAAACAGTAGCCAAAG-TCTAGCCTATCCTGCACTT
1 TACCTTGAGGACTTCTACCGAAACAAGTCAAAAAAGTAGCCAAAGTTC-AGCCTATCCTGCACTT
* * *
572348 CTACTGATACTCTGATGGGTTCTATTGATACCAAATGAAACCATCAGAGTTCTA
65 CTACCGATACTCTGATGGATTCTATCGATACCAAATGAAACCATCAGAGTTCTA
572402 TTGATAGAAC
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
121 2 0.02
122 102 0.97
123 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (122 bp):
TACCTTGAGGACTTCTACCGAAACAAGTCAAAAAAGTAGCCAAAGTTCAGCCTATCCTGCACTTC
TACCGATACTCTGATGGATTCTATCGATACCAAATGAAACCATCAGAGTTCTACCGC
Found at i:578799 original size:19 final size:19
Alignment explanation
Indices: 578775--578812 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
578765 ACATGTCTAC
578775 CTAACCTCTAATGTCCATG
1 CTAACCTCTAATGTCCATG
578794 CTAACCTCTAATGTCCATG
1 CTAACCTCTAATGTCCATG
578813 GCCTAACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.32, G:0.11, T:0.32
Consensus pattern (19 bp):
CTAACCTCTAATGTCCATG
Found at i:583041 original size:3 final size:3
Alignment explanation
Indices: 583033--583074 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
583023 TATTTAAAAT
*
583033 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
583075 GGTGTAGTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:583363 original size:168 final size:169
Alignment explanation
Indices: 583078--583405 Score: 516
Period size: 168 Copynumber: 1.9 Consensus size: 169
583068 CTAATAAGGT
* **
583078 GTAGTCTCAAGATTATTTTCCATACCCTATCACATTGATTACAATAACAACCTTTAGTGTTTTTT
1 GTAGTCTCAAGATTATTTTCCATACCCTATCACACTGATTACAATAACAACCCCTAGTGTTTTTT
* *
583143 TTAAAGAGACTTAGGATTTTCAAAAAAGTATCCCCTACCCTCTGCCAAATTAGGATATTGTCCTC
66 TTAAAGAGACTTAGGATTTTCAAAAAAGTATCCCCTACCCCCTGCCAAATTAGGACATTGTCCTC
583208 AATATCAAAATCATAAGTGAAGTTTAGAGGTGATAGTTG
131 AATATCAAAATCATAAGTGAAGTTTAGAGGTGATAGTTG
* * *
583247 GTAGTTTCAAGATTATTTTCCATACTCTATCAC-CTGATTACAATAACAACCCCTAGTTTTTTTT
1 GTAGTCTCAAGATTATTTTCCATACCCTATCACACTGATTACAATAACAACCCCTAG-TGTTTTT
* * *
583311 TTTAAA-AGACTTAGGATTTTCACAAAAGTATTCCCTACCCCCTGCCAAATTAGGACATTGTCTT
65 TTTAAAGAGACTTAGGATTTTCAAAAAAGTATCCCCTACCCCCTGCCAAATTAGGACATTGTCCT
* *
583375 CAATGTCAAAATCATGAGTGAAGTTTAGAGG
130 CAATATCAAAATCATAAGTGAAGTTTAGAGG
583406 ATATCACCTG
Statistics
Matches: 145, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
168 102 0.70
169 43 0.30
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (169 bp):
GTAGTCTCAAGATTATTTTCCATACCCTATCACACTGATTACAATAACAACCCCTAGTGTTTTTT
TTAAAGAGACTTAGGATTTTCAAAAAAGTATCCCCTACCCCCTGCCAAATTAGGACATTGTCCTC
AATATCAAAATCATAAGTGAAGTTTAGAGGTGATAGTTG
Found at i:590209 original size:34 final size:35
Alignment explanation
Indices: 590029--590209 Score: 239
Period size: 34 Copynumber: 5.3 Consensus size: 35
590019 TATTCAGTGC
*
590029 GTTGGCTGGATTGGCTCATACGAGCATTCAT--TGT
1 GTTGGCTGGTTTGGCTCATACGAGCATTC-TGGTGT
590063 GTTGGCTGGTTTGGCTCATACGAGCATTC-GGTGT
1 GTTGGCTGGTTTGGCTCATACGAGCATTCTGGTGT
590097 GTTGGCTGGTTTGGCTCATACGAGCATTC-GGTGT
1 GTTGGCTGGTTTGGCTCATACGAGCATTCTGGTGT
* * *
590131 GTTGGTTGGTTTGGCTTATACGAGCATT-TGATGT
1 GTTGGCTGGTTTGGCTCATACGAGCATTCTGGTGT
* * *
590165 ATTGGTTGGTTTGGCTCATACGAG-TTTCTGGTGT
1 GTTGGCTGGTTTGGCTCATACGAGCATTCTGGTGT
*
590199 GTTGGATGGTT
1 GTTGGCTGGTT
590210 AACCGTATAC
Statistics
Matches: 133, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
33 2 0.02
34 131 0.98
ACGTcount: A:0.13, C:0.14, G:0.34, T:0.39
Consensus pattern (35 bp):
GTTGGCTGGTTTGGCTCATACGAGCATTCTGGTGT
Found at i:595087 original size:44 final size:45
Alignment explanation
Indices: 594907--595125 Score: 194
Period size: 43 Copynumber: 5.1 Consensus size: 45
594897 TTTATATGTT
*
594907 ATCACATAT-T-GATGCCAATAGCCCA-ACTATGGTCTTACACG-A
1 ATCACATATATCGATGCCAATATCCCAGAC-ATGGTCTTACACGAA
* * *
594949 AT--CATATATCGATGCCAATGTCCCATACATGGTCTTACTCGAA
1 ATCACATATATCGATGCCAATATCCCAGACATGGTCTTACACGAA
* * *
594992 ATCACATA-A-CGATGCCAATGTCCCAGACATGGTATTACACGTA
1 ATCACATATATCGATGCCAATATCCCAGACATGGTCTTACACGAA
* *
595035 ATCACATATATCGATGCC-ATATCCCAGATAAGGTCTTACAC-AA
1 ATCACATATATCGATGCCAATATCCCAGACATGGTCTTACACGAA
* * * * *
595078 AGTCTCATATATTGATTCC-ATAGCCCAG-CTATGGTC-TATACGAA
1 A-TCACATATATCGATGCCAATATCCCAGAC-ATGGTCTTACACGAA
595122 ATCA
1 ATCA
595126 TGTAATGCCA
Statistics
Matches: 146, Mismatches: 20, Indels: 21
0.78 0.11 0.11
Matches are distributed among these distances:
40 5 0.03
41 1 0.01
42 27 0.18
43 51 0.35
44 51 0.35
45 11 0.08
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.27
Consensus pattern (45 bp):
ATCACATATATCGATGCCAATATCCCAGACATGGTCTTACACGAA
Found at i:597596 original size:22 final size:22
Alignment explanation
Indices: 597568--597622 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
597558 GCCTACTAGG
* *
597568 CACTAAGCCTGAACAACATCGA
1 CACTAAGCCTGAACAACACCAA
*
597590 CACTAAGCCTGAATAACACCAA
1 CACTAAGCCTGAACAACACCAA
597612 CACTAAGCCTG
1 CACTAAGCCTG
597623 CTAGGCACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.33, G:0.13, T:0.15
Consensus pattern (22 bp):
CACTAAGCCTGAACAACACCAA
Found at i:602562 original size:21 final size:23
Alignment explanation
Indices: 602538--602582 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
602528 TTTACTTCAT
*
602538 AAAAGTTCA-AAAA-TTTAAAAA
1 AAAAGTTCATAAAAGGTTAAAAA
602559 AAAAGTTCATAAAAGGTTAAAAA
1 AAAAGTTCATAAAAGGTTAAAAA
602582 A
1 A
602583 GCTATTCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 4 0.19
23 8 0.38
ACGTcount: A:0.64, C:0.04, G:0.09, T:0.22
Consensus pattern (23 bp):
AAAAGTTCATAAAAGGTTAAAAA
Found at i:603200 original size:16 final size:16
Alignment explanation
Indices: 603164--603202 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
603154 AATCATCTAT
603164 ATATTATATCATTTTC
1 ATATTATATCATTTTC
*
603180 ATATTATATTTATTTTC
1 ATATTATA-TCATTTTC
603197 -TATTAT
1 ATATTAT
603203 TTTGTTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (16 bp):
ATATTATATCATTTTC
Found at i:615784 original size:24 final size:24
Alignment explanation
Indices: 615733--615812 Score: 90
Period size: 24 Copynumber: 3.4 Consensus size: 24
615723 ATTGTTCAGG
* ** *
615733 AACACTAAACAAACATATTTGT-G
1 AACACTAAACAAACATGTTCCTAA
* *
615756 AACACTCAACAAGCATGTTCCTAA
1 AACACTAAACAAACATGTTCCTAA
615780 AACACTAAACAAACATGTTCCTAA
1 AACACTAAACAAACATGTTCCTAA
*
615804 AATACTAAA
1 AACACTAAA
615813 TGAATCGTTC
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 17 0.36
24 30 0.64
ACGTcount: A:0.49, C:0.23, G:0.06, T:0.23
Consensus pattern (24 bp):
AACACTAAACAAACATGTTCCTAA
Found at i:617740 original size:15 final size:15
Alignment explanation
Indices: 617722--617752 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
617712 CACCGTACCA
617722 CACCGCACCCAATCG
1 CACCGCACCCAATCG
617737 CACCGCACCCAATCG
1 CACCGCACCCAATCG
617752 C
1 C
617753 CTATCCAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.55, G:0.13, T:0.06
Consensus pattern (15 bp):
CACCGCACCCAATCG
Found at i:621449 original size:24 final size:26
Alignment explanation
Indices: 621422--621481 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 26
621412 AGGACTACTT
*
621422 TTTA-TCTTTAATT-TTTCTGTTTTA
1 TTTATTCTTTAATTCTTTCTATTTTA
621446 TTTATTTCTTTAATTCCTTTCTATTTTA
1 TTTA-TTCTTTAATT-CTTTCTATTTTA
*
621474 TTAATTCT
1 TTTATTCT
621482 AATTTTGGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 4 0.13
26 9 0.30
27 4 0.13
28 13 0.43
ACGTcount: A:0.18, C:0.12, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTATTCTTTAATTCTTTCTATTTTA
Found at i:622691 original size:24 final size:24
Alignment explanation
Indices: 622654--622699 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
622644 TGCCACACAT
*
622654 GCTCGTGTGCCAGGCCGTGTGACA
1 GCTCGTGTGCCAGGCCATGTGACA
622678 GCTCGTGT-CTCAGGCCATGTGA
1 GCTCGTGTGC-CAGGCCATGTGA
622700 ACCCAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.13, C:0.28, G:0.35, T:0.24
Consensus pattern (24 bp):
GCTCGTGTGCCAGGCCATGTGACA
Found at i:623886 original size:16 final size:16
Alignment explanation
Indices: 623865--623896 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
623855 TCATCATAGC
623865 ATTGATACATTTATAT
1 ATTGATACATTTATAT
*
623881 ATTGATTCATTTATAT
1 ATTGATACATTTATAT
623897 TAAAACAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (16 bp):
ATTGATACATTTATAT
Found at i:631183 original size:5 final size:5
Alignment explanation
Indices: 631173--631204 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
631163 ATAATTTGAT
*
631173 AATTA AATTA AATTA AATTA AATTA AACTA AA
1 AATTA AATTA AATTA AATTA AATTA AATTA AA
631205 ATGTTTTGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (5 bp):
AATTA
Found at i:633354 original size:15 final size:16
Alignment explanation
Indices: 633334--633363 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
633324 TGGTGCCTTG
633334 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
633349 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
633364 AACATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:636493 original size:24 final size:24
Alignment explanation
Indices: 636435--636509 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 24
636425 AAAATTATAT
* ** *
636435 TAAAATTGTTAAAATAATAAAATAA
1 TAAAATTATTAAAATCTTACAA-AA
*
636460 TAAAAATTATTGAAATCTTACAAAA
1 TAAAA-TTATTAAAATCTTACAAAA
* *
636485 TAAAATTATTAAAATTTTATAAAA
1 TAAAATTATTAAAATCTTACAAAA
636509 T
1 T
636510 GATANNNNNN
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
24 17 0.41
25 12 0.29
26 12 0.29
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (24 bp):
TAAAATTATTAAAATCTTACAAAA
Found at i:638404 original size:25 final size:27
Alignment explanation
Indices: 638366--638415 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
638356 ACATAGAAAT
*
638366 AATATATAACATTTATATATTTTTATG
1 AATATATAACATTTACATATTTTTATG
*
638393 AATA-ATAA-ATTTACCTATTTTTA
1 AATATATAACATTTACATATTTTTA
638416 ATAATTTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 4 0.19
27 4 0.19
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (27 bp):
AATATATAACATTTACATATTTTTATG
Found at i:644567 original size:89 final size:90
Alignment explanation
Indices: 644434--645791 Score: 570
Period size: 89 Copynumber: 14.7 Consensus size: 90
644424 TTGTCGCTTC
* * *** *
644434 AATCTACTCCACTGCAACTTCAGAGAGATAAGGCATGTAGCTTCAATCTGTTCCACTGCAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTC
*
644499 AGGGAAATAAGATT-CACTACCTTT
66 AGGGAGATAAGATTACACTACCTTT
* * * * * * *
644523 GATTTGCTCCACTGCCACTTTAGGGAGATAAGATTTGTAACTTCAACCTACTCCACTGCAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTC
* *
644588 AGGGGGATAAGATTTATAACACGTAGCTTT
66 AGGGAGATAAGA--T-T-ACAC-TACCTTT
* * * * * *
644618 AATATGTTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTGTAGCTTTAGTCTGTTCCACTA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAG---A-T---TTGTAGCTTCAATCTGCTCCACTG
* * * * **
644683 CAACTTCAGGGAAATAGGACTTGCTATAATAAATTT
59 CAACTTCAGGGAGATAAGA--T--TACACTACCTTT
* * * * * *
644719 AATCCGAC-CCACTGCAACTTCAGAGG-TATAAGATTTTTTGCTTCAATCTACTCCATTGCAACT
1 AATCTG-CTCCACTGCAACTTCAG-GGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACT
* *
644782 TCAGAGAGATAAGATT-CACTACCTTC
64 TCAGGGAGATAAGATTACACTACCTTT
* * * * * *
644808 AATCTACTCCACTACCACTTTAGGGAGATAAGATTTGTAACTTCAACCTGCTCCACTGCAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTC
* *
644873 AGGGAGATAAGATTTATAACTCGTAGCTTT
66 AGGGAGATAAGA--T-T-ACAC-TACCTTT
* * * * * *
644903 AATCTGTTCCACTGCAACTTTAAGGAGATAAGATTAGTAGCTTGTAACTTTAGTCCATTCCACTG
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTT-CAA-TCT-G--C--TCCACTG
* * * **
644968 CAACTTCAGGGAAAT-AGAACTTGCTATAGTAGATTT
59 CAACTTCAGGGAGATAAG-A--T--TACACTACCTTT
* * * * * *
645004 AAT-TCGACT-CACTACAACTTCAGAGG-TATAGGATTTGTCGCTTCAATCTACTCTACTGCAAC
1 AATCT-G-CTCCACTGCAACTTCAG-GGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAAC
* * *
645066 TTCAGGGAGATAAG-GT-CTA-TAGCTTC
63 TTCAGGGAGATAAGATTAC-ACTACCTTT
* * * * * * *
645092 AATCTGTTCCACTGCCACTTCAGGGAGACAAGATTTGTAACTTCAATATGCTCCACTGTAACTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTC
* * *
645157 AGGGATATAAGATTTATAACTCGTAGCTTT
66 AGGGAGATAAGA--T-T-ACAC-TACCTTT
* * * * * * * * *
645187 AATCTGTTCCACTACAACTTTAGGGAAATGAGATTTGCTATCTTCAATCTGCTTCATTGAAACTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTCAATCTGCTCCACTGCAACTT
*
645252 CAGGGAGATAAGACTTGTA-ACTTGTAGCTTT
65 CAGGGAGATAAGA--T-TACAC---TACCTTT
* * * * * * *
645283 AATCTGTTCCACCGTAACTTTAGGGAAATACGATTTGTAGCTTTAA-CTTGCTCCACTGCAACTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATC-TGCTCCACTGCAACTT
* * ** *
645347 CAGGAAAATGAA-ATT--TGTGA-ATTT
65 CAGGGAGAT-AAGATTACACT-ACCTTT
* ** * * * * ** *
645371 AATTTTTTCCACTGCCACTTCAGGG-GCATAGAATTTGTGACTTGTAGCTTTAGTCTATTCCATT
1 AATCTGCTCCACTGCAACTTCAGGGAG-AT--AA-----GATTTGTAGCTTCAATCTGCTCCACT
* * * * * *
645435 GTAGCTTTAGGGAAATAAGATTTGCA-T--CTTC
58 GCAACTTCAGGGAGATAAGA-TTACACTACCTTT
* * ** * * * * * * *
645466 AACCTGTTCCACTGCAGTTTCAGGGAGATAAGATTTATATCTTTAATTTTCTCTACTGCAACTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTC
* * *
645531 AGAGAGATAAGATTTGC-C-ATCTTT
66 AGGGAGATAAGA-TTACACTACCTTT
** * * * * *
645555 AATCTTTTCCACTGCAACTTCAGGGAGATAAGATTTATATCTTTAATCTACTCTACTGCAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTC
* ** * *
645620 AGAGAGATAAGATT-TGCTATCTTC
66 AGGGAGATAAGATTACACTACCTTT
** * * * * * *
645644 AATCTTTTCCACTGCAACTTCAAGGAGATAAGATTTATAGCTTTAATCTGCTCTACTGTAACTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTC
* ** * *
645709 AGAGAGATAAGATT-TGCTATCTTC
66 AGGGAGATAAGATTACACTACCTTT
* * * *
645733 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTTAGTCTACTCCACTGC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGC
645792 CATTTCAATG
Statistics
Matches: 977, Mismatches: 218, Indels: 148
0.73 0.16 0.11
Matches are distributed among these distances:
87 3 0.00
88 129 0.13
89 342 0.35
90 2 0.00
91 2 0.00
92 5 0.01
93 3 0.00
94 62 0.06
95 197 0.20
96 85 0.09
97 3 0.00
98 3 0.00
99 3 0.00
100 4 0.00
101 65 0.07
102 67 0.07
103 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (90 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTC
AGGGAGATAAGATTACACTACCTTT
Found at i:644599 original size:44 final size:44
Alignment explanation
Indices: 644390--645858 Score: 579
Period size: 44 Copynumber: 31.9 Consensus size: 44
644380 TAGTAGATGT
* * * *
644390 AATCTGAC-CCACTGCAACTTCAGAGG-TATAGGGTTTGTCGCTTC
1 AATCT-ACTCCACTGCAACTTCAG-GGAGATAAGATTTGTAGCTTC
* ***
644434 AATCTACTCCACTGCAACTTCAGAGAGATAAGGCATGTAGCTTC
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTC
** * ** * *
644478 AATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCACTACCTTT
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATT-TGTAGCTTC
* * * * * *
644523 GATTTGCTCCACTGCCACTTTAGGGAGATAAGATTTGTAACTTC
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTC
* * *
644567 AACCTACTCCACTGCAACTTCAGGGGGATAAGATTTATAACACGTAGCTTT
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGA-TT-T-----GTAGCTTC
* ** *
644618 AATATGTTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTGTAGCTTT
1 AATCTACTCCACTGCAACTTCAGGGAGATAAG---A-T---TTGTAGCTTC
* ** * * * * ** *
644669 AGTCTGTTCCACTACAACTTCAGGGAAATAGGACTTGCTATAATAAATTT
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGA--T--T-T-GTAGCTTC
* * * *
644719 AATCCGAC-CCACTGCAACTTCAGAGG-TATAAGATTTTTTGCTTC
1 AAT-CTACTCCACTGCAACTTCAG-GGAGATAAGATTTGTAGCTTC
* * ** *
644763 AATCTACTCCATTGCAACTTCAGAGAGATAAGATTCACTACCTTC
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATT-TGTAGCTTC
* * * *
644808 AATCTACTCCACTACCACTTTAGGGAGATAAGATTTGTAACTTC
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTC
* * *
644852 AACCTGCTCCACTGCAACTTCAGGGAGATAAGATTTATAACTCGTAGCTTT
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGA--T-T---T-GTAGCTTC
** * * * *
644903 AATCTGTTCCACTGCAACTTTAAGGAGATAAGATTAGTAGCTTGT
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTT-C
* * * *
644948 AACTTTAGTCCATTCCACTGCAACTTCAGGGAAAT-AGAACTTGCTATAGTAGATTT
1 AA-TCTA---C--TCCACTGCAACTTCAGGGAGATAAG-A--T--T-T-GTAGCTTC
* * * * *
645004 AATTCGACT-CACTACAACTTCAGAGG-TATAGGATTTGTCGCTTC
1 AA-TCTACTCCACTGCAACTTCAG-GGAGATAAGATTTGTAGCTTC
* * * *
645048 AATCTACTCTACTGCAACTTCAGGGAGATAAGGTCTATAGCTTC
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTC
** * * *
645092 AATCTGTTCCACTGCCACTTCAGGGAGACAAGATTTGTAACTTC
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTC
* * * * * *
645136 AATATGCTCCACTGTAACTTTAGGGATATAAGATTTATAACTCGTAGCTTT
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGA--T-T---T-GTAGCTTC
** * * * * *
645187 AATCTGTTCCACTACAACTTTAGGGAAATGAGATTTGCTATCTTC
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTC
* * * * *
645232 AATCTGCTTCATTGAAACTTCAGGGAGATAAGACTTGTAACTTGTAGCTTT
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGA----T---TTGTAGCTTC
** * * * * * *
645283 AATCTGTTCCACCGTAACTTTAGGGAAATACGATTTGTAGCTTT
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTC
* * * * *
645327 AA-CTTGCTCCACTGCAACTTCAGGAAAATGAA-ATTTGT-GAATTT
1 AATC-TACTCCACTGCAACTTCAGGGAGAT-AAGATTTGTAG-CTTC
* ** * * *
645371 AATTTTTTCCACTGCCACTTCAGGG-GCATAGAATTTGTGACTTGTAGCTTT
1 AATCTACTCCACTGCAACTTCAGGGAG-AT--AA-----GATTTGTAGCTTC
* * * * * * * * *
645422 AGTCTATTCCATTGTAGCTTTAGGGAAATAAGATTTGCATCTTC
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTC
* ** ** * * *
645466 AACCTGTTCCACTGCAGTTTCAGGGAGATAAGATTTATATCTTT
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTC
* * * * * * * *
645510 AATTTTCTCTACTGCAACTTTAGAGAGATAAGATTTGCCATCTTT
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTC
** * * *
645555 AATCTTTTCCACTGCAACTTCAGGGAGATAAGATTTATATCTTT
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTC
* * *
645599 AATCTACTCTACTGCAACTTCAGAGAGATAAGATTTGCTATCTTC
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTC
** * * *
645644 AATCTTTTCCACTGCAACTTCAAGGAGATAAGATTTATAGCTTT
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTC
* * * * * *
645688 AATCTGCTCTACTGTAACTTTAGAGAGATAAGATTTGCTATCTTC
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGCTTC
* * *
645733 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTATCTTT
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTC
* * * ** *
645777 AGTCTACTCCACTGCCATTTCAATGAGATGAA-ATTTGT-GACTTT
1 AATCTACTCCACTGCAACTTCAGGGAGAT-AAGATTTGTAG-CTTC
** **
645821 AATCTTTTCCACTGCAACTTCAAAGAGATAAGATTTGT
1 AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGT
645859 CACGGTGACC
Statistics
Matches: 1081, Mismatches: 260, Indels: 168
0.72 0.17 0.11
Matches are distributed among these distances:
43 18 0.02
44 525 0.49
45 225 0.21
46 7 0.01
47 3 0.00
48 8 0.01
49 7 0.01
50 46 0.04
51 220 0.20
52 4 0.00
53 2 0.00
54 2 0.00
55 1 0.00
56 6 0.01
57 7 0.01
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (44 bp):
AATCTACTCCACTGCAACTTCAGGGAGATAAGATTTGTAGCTTC
Found at i:644650 original size:51 final size:51
Alignment explanation
Indices: 644574--644694 Score: 163
Period size: 51 Copynumber: 2.4 Consensus size: 51
644564 TTCAACCTAC
*
644574 TCCACTGCAACTTCAGGGGGATAAGATTTA-TAACACGTAGCTTTAATATGT
1 TCCACTGCAACTTCAGGGAGATAAGA-TTAGTAACACGTAGCTTTAATATGT
* ** * *
644625 TCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTGTAGCTTTAGTCTGT
1 TCCACTGCAACTTCAGGGAGATAAGATTAGTAACACGTAGCTTTAATATGT
*
644676 TCCACTACAACTTCAGGGA
1 TCCACTGCAACTTCAGGGA
644695 AATAGGACTT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 3 0.05
51 59 0.95
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (51 bp):
TCCACTGCAACTTCAGGGAGATAAGATTAGTAACACGTAGCTTTAATATGT
Found at i:644781 original size:285 final size:285
Alignment explanation
Indices: 644442--645221 Score: 1098
Period size: 285 Copynumber: 2.7 Consensus size: 285
644432 TCAATCTACT
*** ** *
644442 CCACTGCAACTTCAGAGAG-ATAAGGCATGTAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAA
1 CCACTGCAACTTCAGAG-GTATAAGATTTGTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGA
** *
644506 TAAGATTCACTACCTTTGATTTGCTCCACTGCCACTTTAGGGAGATAAGATTTGTAACTTCAACC
65 TAAGATTCACTACCTTCAATCTGCTCCACTGCCACTTTAGGGAGATAAGATTTGTAACTTCAACC
* * * *
644571 TACTCCACTGCAACTTCAGGGGGATAAGATTTATAACACGTAGCTTTAATATGTTCCACTGCAAC
130 TGCTCCACTGCAACTTCAGGGAGATAAGATTTATAACTCGTAGCTTTAATCTGTTCCACTGCAAC
* * ** *
644636 TTCAGGGAGATAAGATTAGTAGCTTGTAGCTTTAGTCTGTTCCACTACAACTTCAGGGAAATAGG
195 TTTAGGGAGATAAGATTAGTAGCTTGTAACTTTAGTCCATTCCACTACAACTTCAGGGAAATAGA
644701 ACTTGCTATAATAAATTTAATCCGAC
260 ACTTGCTATAATAAATTTAATCCGAC
* * * *
644727 CCACTGCAACTTCAGAGGTATAAGATTTTTTGCTTCAATCTACTCCATTGCAACTTCAGAGAGAT
1 CCACTGCAACTTCAGAGGTATAAGATTTGTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGAT
* *
644792 AAGATTCACTACCTTCAATCTACTCCACTACCACTTTAGGGAGATAAGATTTGTAACTTCAACCT
66 AAGATTCACTACCTTCAATCTGCTCCACTGCCACTTTAGGGAGATAAGATTTGTAACTTCAACCT
644857 GCTCCACTGCAACTTCAGGGAGATAAGATTTATAACTCGTAGCTTTAATCTGTTCCACTGCAACT
131 GCTCCACTGCAACTTCAGGGAGATAAGATTTATAACTCGTAGCTTTAATCTGTTCCACTGCAACT
* *
644922 TTAAGGAGATAAGATTAGTAGCTTGTAACTTTAGTCCATTCCACTGCAACTTCAGGGAAATAGAA
196 TTAGGGAGATAAGATTAGTAGCTTGTAACTTTAGTCCATTCCACTACAACTTCAGGGAAATAGAA
* * *
644987 CTTGCTATAGTAGATTTAATTCGAC
261 CTTGCTATAATAAATTTAATCCGAC
* * * * *
645012 TCACTACAACTTCAGAGGTATAGGATTTGTCGCTTCAATCTACTCTACTGCAACTTCAGGGAGAT
1 CCACTGCAACTTCAGAGGTATAAGATTTGTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGAT
* * * * * **
645077 AAG-GTCTA-TAGCTTCAATCTGTTCCACTGCCACTTCAGGGAGACAAGATTTGTAACTTCAATA
66 AAGATTC-ACTACCTTCAATCTGCTCCACTGCCACTTTAGGGAGATAAGATTTGTAACTTCAACC
* * * *
645140 TGCTCCACTGTAACTTTAGGGATATAAGATTTATAACTCGTAGCTTTAATCTGTTCCACTACAAC
130 TGCTCCACTGCAACTTCAGGGAGATAAGATTTATAACTCGTAGCTTTAATCTGTTCCACTGCAAC
* *
645205 TTTAGGGAAATGAGATT
195 TTTAGGGAGATAAGATT
645222 TGCTATCTTC
Statistics
Matches: 440, Mismatches: 53, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
284 125 0.28
285 315 0.72
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (285 bp):
CCACTGCAACTTCAGAGGTATAAGATTTGTAGCTTCAATCTACTCCACTGCAACTTCAGGGAGAT
AAGATTCACTACCTTCAATCTGCTCCACTGCCACTTTAGGGAGATAAGATTTGTAACTTCAACCT
GCTCCACTGCAACTTCAGGGAGATAAGATTTATAACTCGTAGCTTTAATCTGTTCCACTGCAACT
TTAGGGAGATAAGATTAGTAGCTTGTAACTTTAGTCCATTCCACTACAACTTCAGGGAAATAGAA
CTTGCTATAATAAATTTAATCCGAC
Found at i:644935 original size:51 final size:51
Alignment explanation
Indices: 644859--644975 Score: 146
Period size: 51 Copynumber: 2.3 Consensus size: 51
644849 TTCAACCTGC
* * **
644859 TCCACTGCAACTTCAGGGAGATAAGATTTA-TAACTCGTAGCTTTAATCTGT
1 TCCACTGCAACTTCAAGGAGATAAGA-TTAGTAACTCGTAACTTTAATCCAT
* * * *
644910 TCCACTGCAACTTTAAGGAGATAAGATTAGTAGCTTGTAACTTTAGTCCAT
1 TCCACTGCAACTTCAAGGAGATAAGATTAGTAACTCGTAACTTTAATCCAT
644961 TCCACTGCAACTTCA
1 TCCACTGCAACTTCA
644976 GGGAAATAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
50 3 0.05
51 53 0.95
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.32
Consensus pattern (51 bp):
TCCACTGCAACTTCAAGGAGATAAGATTAGTAACTCGTAACTTTAATCCAT
Found at i:644945 original size:329 final size:326
Alignment explanation
Indices: 644296--644893 Score: 815
Period size: 329 Copynumber: 1.8 Consensus size: 326
644286 TTCAATCTGC
* *
644296 TCCACTAGAACTTTAGGGAAATAAGATTAGTAGCTTGTAGCTTTAGTCTGTTCCACTACAACTTT
1 TCCACTAGAACTTCAGGGAAATAAGATTAGTAGCTTGTAGCTTTAGTCTGTTCCACTACAACTTC
* * * * * *
644361 AGGGGAATAGGACTTGCTATAGTAGATGTAATCTGACCCACTGCAACTTCAGAGGTATAGGGTTT
66 AGGGAAATAGGACTTGCTATAATAAATGTAATCCGACCCACTGCAACTTCAGAGGTATAAGATTT
* * **
644426 GTCGCTTCAATCTACTCCACTGCAACTTCAGAGAGATAAGGCATGTAGCTTCAATCTGTTCCACT
131 GTCGCTTCAATCTACTCCACTGCAACTTCAGAGAGATAAGGCATCTACCTTCAATCTACTCCACT
* * ** ** * *
644491 GCAACTTCAGGGAAATAAGATTCACTACCTTTGATTTGCTCCACTGCCACTTTAGGGAGATAAGA
196 ACAACTTCAGGGAAATAAGATTCACTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGA
* * *
644556 TTTGTAACTTCAACCTACTCCACTGCAACTTCAGGGGGATAAGATTTATAACACGTAGCTTTAAT
261 TTTATAACTTCAACCTACTCCACTGCAACTTCAAGGAGATAAGA-TTAT-A-ACGTAGCTTTAAT
644621 ATGT
323 ATGT
*
644625 TCCACT-GCAACTTCAGGGAGATAAGATTAGTAGCTTGTAGCTTTAGTCTGTTCCACTACAACTT
1 TCCACTAG-AACTTCAGGGAAATAAGATTAGTAGCTTGTAGCTTTAGTCTGTTCCACTACAACTT
*
644689 CAGGGAAATAGGACTTGCTATAATAAATTTAATCCGACCCACTGCAACTTCAGAGGTATAAGATT
65 CAGGGAAATAGGACTTGCTATAATAAATGTAATCCGACCCACTGCAACTTCAGAGGTATAAGATT
* * * *
644754 TTTTGCTTCAATCTACTCCATTGCAACTTCAGAGAGATAAGATTCA-CTACCTTCAATCTACTCC
130 TGTCGCTTCAATCTACTCCACTGCAACTTCAGAGAGATAAG--GCATCTACCTTCAATCTACTCC
* * * **
644818 ACTACCACTTTAGGGAGATAAGATT-TGTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATA
193 ACTACAACTTCAGGGAAATAAGATTCACTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATA
644882 AGATTTATAACT
258 AGATTTATAACT
644894 CGTAGCTTTA
Statistics
Matches: 234, Mismatches: 32, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
328 1 0.00
329 196 0.84
330 35 0.15
331 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (326 bp):
TCCACTAGAACTTCAGGGAAATAAGATTAGTAGCTTGTAGCTTTAGTCTGTTCCACTACAACTTC
AGGGAAATAGGACTTGCTATAATAAATGTAATCCGACCCACTGCAACTTCAGAGGTATAAGATTT
GTCGCTTCAATCTACTCCACTGCAACTTCAGAGAGATAAGGCATCTACCTTCAATCTACTCCACT
ACAACTTCAGGGAAATAAGATTCACTAACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGA
TTTATAACTTCAACCTACTCCACTGCAACTTCAAGGAGATAAGATTATAACGTAGCTTTAATATG
T
Found at i:645279 original size:96 final size:94
Alignment explanation
Indices: 645085--645350 Score: 293
Period size: 96 Copynumber: 2.8 Consensus size: 94
645075 ATAAGGTCTA
* * *
645085 TAGCTTCAATCTGTTCCACTGCCACTTCAGGGAGACA-AGATTTGTAACTTCAATATGCTCCACT
1 TAGCTTTAATCTGTTCCACTGCAACTTTAGGGA-A-ATAGATTTGTAACTTCAATATGCTCCACT
* * * *
645149 GTAACTTTAGGGATATAAGATTTATAACTCG
64 GAAACTTCAGGGAGATAAGACTTATAACTCG
* * * * *
645180 TAGCTTTAATCTGTTCCACTACAACTTTAGGGAAATGAGATTTGCTATCTTCAATCTGCTTCATT
1 TAGCTTTAATCTGTTCCACTGCAACTTTAGGGAAAT-AGATTTG-TAACTTCAATATGCTCCACT
* *
645245 GAAACTTCAGGGAGATAAGACTTGTAACTTG
64 GAAACTTCAGGGAGATAAGACTTATAACTCG
* * * *
645276 TAGCTTTAATCTGTTCCACCGTAACTTTAGGGAAATACGATTTGTAGCTTTAACT-TGCTCCACT
1 TAGCTTTAATCTGTTCCACTGCAACTTTAGGGAAATA-GATTTGTAACTTCAA-TATGCTCCACT
*
645340 GCAACTTCAGG
64 GAAACTTCAGG
645351 AAAATGAAAT
Statistics
Matches: 144, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
93 1 0.01
94 1 0.01
95 61 0.42
96 81 0.56
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (94 bp):
TAGCTTTAATCTGTTCCACTGCAACTTTAGGGAAATAGATTTGTAACTTCAATATGCTCCACTGA
AACTTCAGGGAGATAAGACTTATAACTCG
Found at i:645321 original size:51 final size:50
Alignment explanation
Indices: 645085--645321 Score: 165
Period size: 51 Copynumber: 4.9 Consensus size: 50
645075 ATAAGGTCTA
* ** * * *
645085 TAGCTTCAATCTGTTCCACTGCCACTTCAGGGAGACAAGATTTGTAACT-
1 TAGCTTTAATCTGTTCCACTGTAACTTTAGGGAAATAAGATTTGTAACTG
* * * *
645134 T--C---AATATGCTCCACTGTAACTTTAGGGATATAAGATTTATAACTCG
1 TAGCTTTAATCTGTTCCACTGTAACTTTAGGGAAATAAGATTTGTAACT-G
** *
645180 TAGCTTTAATCTGTTCCACTACAACTTTAGGGAAATGAGATTTG---C--
1 TAGCTTTAATCTGTTCCACTGTAACTTTAGGGAAATAAGATTTGTAACTG
* * * * * * *
645225 TATCTTCAATCTGCTT-CATTGAAACTTCAGGGAGATAAGACTTGTAACTTG
1 TAGCTTTAATCTG-TTCCACTGTAACTTTAGGGAAATAAGATTTGTAAC-TG
* *
645276 TAGCTTTAATCTGTTCCACCGTAACTTTAGGGAAATACGATTTGTA
1 TAGCTTTAATCTGTTCCACTGTAACTTTAGGGAAATAAGATTTGTA
645322 GCTTTAACTT
Statistics
Matches: 140, Mismatches: 33, Indels: 28
0.70 0.16 0.14
Matches are distributed among these distances:
44 34 0.24
45 32 0.23
46 3 0.02
47 1 0.01
48 3 0.02
49 1 0.01
50 2 0.01
51 64 0.46
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (50 bp):
TAGCTTTAATCTGTTCCACTGTAACTTTAGGGAAATAAGATTTGTAACTG
Found at i:645546 original size:139 final size:138
Alignment explanation
Indices: 645247--645756 Score: 315
Period size: 139 Copynumber: 3.7 Consensus size: 138
645237 GCTTCATTGA
* *
645247 AACTTCAGGGAGATAAGACTTGTAACTTGTAGCTTTAATCTGTTCCACCGTAACTTTAGGGAAAT
1 AACTTCA-GGAGATAAGATTTGTAACTTGTAGCTTTAATCTATTCCACCGTAACTTTAGGGAAAT
* * * * *
645312 ACGATTTGTAGCTTTAACTTGCTCCACTGCAACTTCAGGAAAATGAAATTTGTGAATTTAATTTT
65 AAGATTTGCAGCTTCAACCTGCTCCACTGCAACTTCAGGAAAATGAAATTTATGAATTTAATTTT
*
645377 TTCCACTGC
130 CTCCACTGC
* * * * ** *
645386 CACTTCAGGGGCAT-AGAATTTGTGACTTGTAGCTTTAGTCTATTCCATTGTAGCTTTAGGGAAA
1 AACTTCAGGAG-ATAAG-ATTTGTAACTTGTAGCTTTAATCTATTCCACCGTAACTTTAGGGAAA
* * ** * * *
645450 TAAGATTTGCATCTTCAACCTGTTCCACTGCAGTTTCAGGGAGAT-AAGATTTAT-ATCTTTAAT
64 TAAGATTTGCAGCTTCAACCTGCTCCACTGCAACTTCAGGAAAATGAA-ATTTATGA-ATTTAAT
*
645513 TTTCTCTACTGC
127 TTTCTCCACTGC
* * * * * * * *
645525 AACTTTAGAGAGATAAGATTTG---C---CATCTTTAATCTTTTCCACTGCAACTTCAGGGAGAT
1 AACTTCAG-GAGATAAGATTTGTAACTTGTAGCTTTAATCTATTCCACCGTAACTTTAGGGAAAT
** * * * * * * *
645584 AAGATTTATATCTTTAATCTACTCTACTGCAACTTCA-GAGAGAT-AAGA-TT-TGCTATCTTCA
65 AAGATTTGCAGCTTCAACCTGCTCCACTGCAACTTCAGGA-AAATGAA-ATTTATG-AAT-TT-A
645645 ATCTTT-TCCACTGC
125 AT-TTTCTCCACTGC
** * * * *
645659 AACTTCAAGGAGATAAGA-TT-T-A----TAGCTTTAATCTGCTCTACTGTAACTTTAGAGAGAT
1 AACTTC-AGGAGATAAGATTTGTAACTTGTAGCTTTAATCTATTCCACCGTAACTTTAGGGAAAT
* *
645717 AAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGG
65 AAGATTTGC-AGCTTCAACCTGCTCCACTGCAACTTCAGG
645757 GAGATAAGAT
Statistics
Matches: 292, Mismatches: 62, Indels: 38
0.74 0.16 0.10
Matches are distributed among these distances:
131 1 0.00
132 4 0.01
133 102 0.35
134 49 0.17
135 6 0.02
136 1 0.00
138 8 0.03
139 117 0.40
140 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (138 bp):
AACTTCAGGAGATAAGATTTGTAACTTGTAGCTTTAATCTATTCCACCGTAACTTTAGGGAAATA
AGATTTGCAGCTTCAACCTGCTCCACTGCAACTTCAGGAAAATGAAATTTATGAATTTAATTTTC
TCCACTGC
Found at i:645805 original size:89 final size:89
Alignment explanation
Indices: 645439--645856 Score: 542
Period size: 89 Copynumber: 4.7 Consensus size: 89
645429 TCCATTGTAG
* * * * **
645439 CTTTAGGGAAATAAGATTTGC-ATCTTCAACCTGTTCCACTGCAGTTTCAGGGAGATAAGATTTA
1 CTTTAGAGAGATAAGATTTGCTATCTTCAATCTTTTCCACTGCAACTTCAGGGAGATAAGATTTA
* *
645503 TATCTTTAATTTTCTCTACTGCAA
66 TATCTTTAATCTACTCTACTGCAA
* *
645527 CTTTAGAGAGATAAGATTTGCCATCTTTAATCTTTTCCACTGCAACTTCAGGGAGATAAGATTTA
1 CTTTAGAGAGATAAGATTTGCTATCTTCAATCTTTTCCACTGCAACTTCAGGGAGATAAGATTTA
645592 TATCTTTAATCTACTCTACTGCAA
66 TATCTTTAATCTACTCTACTGCAA
* *
645616 CTTCAGAGAGATAAGATTTGCTATCTTCAATCTTTTCCACTGCAACTTCAAGGAGATAAGATTTA
1 CTTTAGAGAGATAAGATTTGCTATCTTCAATCTTTTCCACTGCAACTTCAGGGAGATAAGATTTA
* * *
645681 TAGCTTTAATCTGCTCTACTGTAA
66 TATCTTTAATCTACTCTACTGCAA
** *
645705 CTTTAGAGAGATAAGATTTGCTATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTG
1 CTTTAGAGAGATAAGATTTGCTATCTTCAATCTTTTCCACTGCAACTTCAGGGAGATAAGATTTA
* * *
645770 TATCTTTAGTCTACTCCACTGCCA
66 TATCTTTAATCTACTCTACTGCAA
* **
645794 -TTTCA-ATGAGATGAA-ATTTG-TGA-CTTTAATCTTTTCCACTGCAACTTCAAAGAGATAAGA
1 CTTT-AGA-GAGAT-AAGATTTGCT-ATCTTCAATCTTTTCCACTGCAACTTCAGGGAGATAAGA
645854 TTT
62 TTT
645857 GTCACGGTGA
Statistics
Matches: 293, Mismatches: 32, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
88 59 0.20
89 232 0.79
90 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (89 bp):
CTTTAGAGAGATAAGATTTGCTATCTTCAATCTTTTCCACTGCAACTTCAGGGAGATAAGATTTA
TATCTTTAATCTACTCTACTGCAA
Found at i:655237 original size:19 final size:19
Alignment explanation
Indices: 655213--655254 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
655203 ACAAAACGAA
655213 ACAAGTTAGTACATTTCAT
1 ACAAGTTAGTACATTTCAT
* *
655232 ACAAGTTAGTCCATTTTAT
1 ACAAGTTAGTACATTTCAT
655251 ACAA
1 ACAA
655255 AGCTAGAATT
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:0.38, C:0.17, G:0.10, T:0.36
Consensus pattern (19 bp):
ACAAGTTAGTACATTTCAT
Found at i:660425 original size:42 final size:42
Alignment explanation
Indices: 660360--660444 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
660350 GCATCAATCA
* *
660360 TCATCTATTCTAGCACATCTTATATCTGTTGTGCGTATGGAG
1 TCATCTATTCTACCACATCTTATATCTATTGTGCGTATGGAG
* * *
660402 TCATCTATTCTACCAGATTTTATATCTATTGTGTGTATGGAG
1 TCATCTATTCTACCACATCTTATATCTATTGTGCGTATGGAG
660444 T
1 T
660445 AGAAGAGAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (42 bp):
TCATCTATTCTACCACATCTTATATCTATTGTGCGTATGGAG
Found at i:676143 original size:17 final size:19
Alignment explanation
Indices: 676114--676154 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
676104 CTTTAGTAAT
*
676114 TTTTTTATAAAATT-TATA
1 TTTTTTATAAAATTCTACA
676132 TTTTTTAT-AAATTCTACA
1 TTTTTTATAAAATTCTACA
676150 TTTTT
1 TTTTT
676155 AAAAATATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTTATAAAATTCTACA
Found at i:676160 original size:17 final size:17
Alignment explanation
Indices: 676114--676160 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
676104 CTTTAGTAAT
*
676114 TTTTTTATAAAATTTATA
1 TTTTTTA-AAAATTTACA
*
676132 TTTTTTATAAATTCTACA
1 TTTTTTAAAAATT-TACA
676150 -TTTTTAAAAAT
1 TTTTTTAAAAAT
676161 ATTCATAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTTTTAAAAATTTACA
Found at i:676208 original size:25 final size:25
Alignment explanation
Indices: 676170--676217 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
676160 TATTCATAAC
* *
676170 TTTTTTATGATTTTCTATTTTTAGT
1 TTTTTTATGATTTTATATATTTAGT
676195 TTTTTTA-GATTTTTATATATTTA
1 TTTTTTATGA-TTTTATATATTTA
676218 AAAAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.21, C:0.02, G:0.06, T:0.71
Consensus pattern (25 bp):
TTTTTTATGATTTTATATATTTAGT
Found at i:679684 original size:21 final size:22
Alignment explanation
Indices: 679637--679687 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
679627 TTTATTCAAT
*
679637 TCATTTATGTTCACAAACAAGC
1 TCATTTATGTTCACAAACAACC
* *
679659 TCATTTATGTTCATATA-AACC
1 TCATTTATGTTCACAAACAACC
679680 TCATTTAT
1 TCATTTAT
679688 TATGTGTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (22 bp):
TCATTTATGTTCACAAACAACC
Found at i:687627 original size:27 final size:28
Alignment explanation
Indices: 687571--687644 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 28
687561 TATTTTCTCG
*
687571 AAATTTTA-CGAAGGGTATAATCATAAA
1 AAATTTTATCGAAGGGTAAAATCATAAA
* * *
687598 AAATTTTATCGATGGGTAAAATCGT-TA
1 AAATTTTATCGAAGGGTAAAATCATAAA
687625 AAATTTTAT--AAGGGTAAAAT
1 AAATTTTATCGAAGGGTAAAAT
687645 AGGGATGAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
25 10 0.24
27 18 0.44
28 13 0.32
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (28 bp):
AAATTTTATCGAAGGGTAAAATCATAAA
Found at i:696712 original size:18 final size:18
Alignment explanation
Indices: 696683--696729 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
696673 ACTAATTAAT
696683 TTTATCATTGTATCGA-ACA
1 TTTAT-ATTGTATCGATA-A
696702 TTTATATTGTATCGATAA
1 TTTATATTGTATCGATAA
*
696720 TTTTTATTGT
1 TTTATATTGT
696730 TATGTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.53
Consensus pattern (18 bp):
TTTATATTGTATCGATAA
Found at i:696802 original size:31 final size:31
Alignment explanation
Indices: 696767--696856 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 31
696757 CATACCAATT
*
696767 TAGTATTTGTTATCATTTCACAAAATTAAAG-
1 TAGTATTTGTTAT-ATTTCACAAAATGAAAGC
*
696798 TAGTAATTTGTTAATATTTCACAAAAAGAAAGC
1 TAGT-ATTTGTT-ATATTTCACAAAATGAAAGC
696831 T-GATATTTGTTATTATTTCACAAAAT
1 TAG-TATTTGTTA-TATTTCACAAAAT
696857 CGCGCGTTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
31 5 0.10
32 42 0.82
33 4 0.08
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (31 bp):
TAGTATTTGTTATATTTCACAAAATGAAAGC
Done.