Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold215
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: 2124891
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 4 of 16
Found at i:532460 original size:71 final size:69
Alignment explanation
Indices: 532398--533038 Score: 724
Period size: 71 Copynumber: 9.5 Consensus size: 69
532388 GGGCTTTGGG
* *
532398 AAGGAAAAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGG
1 AAGG-AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGG
532462 CTTTAA
65 CTTT-A
532468 AAGGAAAAA-GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGG
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGG
532532 CTTTA
65 CTTTA
532537 AACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGG
1 AA-GGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGG
532602 GCTTTA
64 GCTTTA
* **
532608 AACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTGG
1 AA-GGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGG
532673 GCTTTA
64 GCTTTA
* * *
532679 AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA--GAAGAAG-GTTGCCACGGAGTTGTGT
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAG-TGCCACGGAG-T-TGT
532741 GGGCTTTA
62 GGGCTTTA
* * *
532749 GGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTG
1 --AA-GGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTG
532813 GGCTTTA
63 GGCTTTA
* *
532820 AAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGC
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
532883 -TTA
66 TTTA
* * * * *
532886 AACG-----GGTGCCACGGAGTTGTGGAC-TT-AAAGATGAAAAA-AGTGCCACAGAATTGTGGG
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAG-GGAAAAAGAGTGCCACGGAGTTGTGGG
532943 CTTT-
65 CTTTA
* * * *
532947 ----AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAA-GGAACAAG-GTGCCACGGAGTTATGGGC
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
533005 TTTA
66 TTTA
* * * *
533009 AA-GAAAAA-ATGCCACTGAGTCGTGGACTTT
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT
533039 GAGACAAAAT
Statistics
Matches: 504, Mismatches: 37, Indels: 65
0.83 0.06 0.11
Matches are distributed among these distances:
59 3 0.01
60 2 0.00
61 65 0.13
62 24 0.05
63 3 0.01
64 16 0.03
65 6 0.01
66 6 0.01
67 20 0.04
68 60 0.12
69 19 0.04
70 91 0.18
71 145 0.29
72 5 0.01
73 38 0.08
74 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (69 bp):
AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
TTTA
Found at i:532557 original size:34 final size:33
Alignment explanation
Indices: 532398--533038 Score: 646
Period size: 34 Copynumber: 19.0 Consensus size: 33
532388 GGGCTTTGGG
* * *
532398 AAGGAAAAAAGATGCCACGGAGTTGTGGACTTAA
1 AAGG-AAAAAGGTGCCACGGAGTTGTGGGCTTTA
532432 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTT-A
532468 AAGGAAAAA-GTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT--A
532502 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTA
532537 AACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 AA-GGAAAAAGGTGCCACGGAGTTGTGGGCTTT--A
532573 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTA
532608 AACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 AA-GGAAAAAGGTGCCACGGAGTTGTGGGCTTT--A
**
532644 AAGGAAAAAAGAGTGCCACAAAGTTGTGGGCTTTA
1 AAGG-AAAAAG-GTGCCACGGAGTTGTGGGCTTTA
* *
532679 AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT-A
* *
532713 AAAGAAGAAGGTTGCCACGGAGTTGTGTGGGCTTTA
1 AAGGAAAAAGG-TGCCACGGAG-T-TGTGGGCTTTA
* * * *
532749 GGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTAA
1 --AA-GGAAAAAGGTGCCACGGAGTTGTGGGCTTTA
532785 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTA
* *
532820 AAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTAA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT-A
532854 AAGGAAAAAGGTGCCACGGAGTTGTGGGC-TTA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTA
* *
532886 AACG-----GGTGCCACGGAGTTGTGGAC-TTA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTA
* * *
532913 AAGATGAAAAAAGTGCCACAGAATTGTGGGCTTT-
1 AAG--GAAAAAGGTGCCACGGAGTTGTGGGCTTTA
* * *
532947 ----AAAAGGGTGCCACGGAGTTGTGGACTTAA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTA
* *
532976 AAGGAACAAGGTGCCACGGAGTTATGGGCTTTA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTA
* * * *
533009 AA-GAAAAA-ATGCCACTGAGTCGTGGACTTT
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT
533039 GAGACAAAAT
Statistics
Matches: 521, Mismatches: 50, Indels: 75
0.81 0.08 0.12
Matches are distributed among these distances:
27 24 0.05
28 22 0.04
29 1 0.00
31 17 0.03
32 9 0.02
33 92 0.18
34 133 0.26
35 97 0.19
36 34 0.07
37 75 0.14
38 12 0.02
39 5 0.01
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (33 bp):
AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTA
Found at i:532593 original size:141 final size:137
Alignment explanation
Indices: 532403--533040 Score: 771
Period size: 141 Copynumber: 4.7 Consensus size: 137
532393 TTGGGAAGGA
* *
532403 AAAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTA
* *
532467 AAAGGAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGG
64 AAAGGAAAAAGTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGG
*
532532 CTTTAAACGG
129 CTTTAAA-AG
532542 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTT
* * * *
532607 AAACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTG
63 AAAAGGAAAAA-GTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTG
532672 GGCTTTAAAAG
127 GGCTTTAAAAG
* *
532683 AAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAGAAGGTTGCCACGGAGTTGTGTGGGCTT
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGAAAAAGG-TGCCACGGAG-T-TGTGGGCTT
* * *
532747 TAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTT
62 TA--AAAGGAAAAAG-TGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACAGAGTT
532810 GTGGGCTTTAAAAG
124 GTGGGCTTTAAAAG
*
532824 AAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGC-TTAAA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
* * *
532888 CGG-----GTGCCACGGAGTTGTGGAC-TT--AAAGATGAAAAA-AGTGCCACAGAATTGTGGGC
66 AGGAAAAAGTGCCACGGAGTTGTGGACTTTGAAAAG-GGAAAAAGAGTGCCACAGAGTTGTGGGC
532944 TTTAAAAG
130 TTTAAAAG
* * *
532952 -----GGTGCCACGGAGTTGTGGAC-TTAAAAGGAACAAGGTGCCACGGAGTTATGGGCTTT-AA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
* * *
533010 A-GAAAAAATGCCACTGAGTCGTGGACTTTGA
66 AGGAAAAAGTGCCACGGAGTTGTGGACTTTGA
533041 GACAAAATGC
Statistics
Matches: 449, Mismatches: 30, Indels: 50
0.85 0.06 0.09
Matches are distributed among these distances:
121 1 0.00
122 33 0.07
123 20 0.04
126 16 0.04
127 2 0.00
128 30 0.07
129 26 0.06
130 1 0.00
135 4 0.01
137 3 0.01
138 8 0.02
139 40 0.09
140 17 0.04
141 161 0.36
142 62 0.14
143 25 0.06
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.21
Consensus pattern (137 bp):
AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
AGGAAAAAGTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCT
TTAAAAG
Found at i:532900 original size:61 final size:61
Alignment explanation
Indices: 532763--533010 Score: 327
Period size: 61 Copynumber: 3.9 Consensus size: 61
532753 GGGAGAAAGA
532763 TGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
1 TGCCACGGAGTTGTGGACTTAAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAG----
*
532828 AAG
60 -GG
* *
532831 TGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGC-TTAAACGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* * * *
532892 TGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAA-AGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* *
532954 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTATGGGCTTTAAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
533011 GAAAAAATGC
Statistics
Matches: 162, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
60 5 0.03
61 70 0.43
62 31 0.19
66 6 0.04
67 19 0.12
68 25 0.15
69 6 0.04
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.21
Consensus pattern (61 bp):
TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
Found at i:532901 original size:27 final size:26
Alignment explanation
Indices: 532863--532976 Score: 93
Period size: 27 Copynumber: 4.0 Consensus size: 26
532853 AAAGGAAAAA
*
532863 GGTGCCACGGAGTTGTGGGCTTAAACG
1 GGTGCCACGGAGTTGTGGACTTAAA-G
532890 GGTGCCACGGAGTTGTGGACTTAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAG
* * *
532916 ATGAAAAAAGTGCCACAGAATTGTGGGCTTTAAAAG
1 --G------GTGCCACGGAGTTGTGGAC-TT-AAAG
532952 GGTGCCACGGAGTTGTGGACTTAAA
1 GGTGCCACGGAGTTGTGGACTTAAA
532977 AGGAACAAGG
Statistics
Matches: 70, Mismatches: 7, Indels: 21
0.71 0.07 0.21
Matches are distributed among these distances:
26 4 0.06
27 26 0.37
28 17 0.24
34 17 0.24
35 2 0.03
36 4 0.06
ACGTcount: A:0.28, C:0.15, G:0.34, T:0.23
Consensus pattern (26 bp):
GGTGCCACGGAGTTGTGGACTTAAAG
Found at i:532959 original size:28 final size:27
Alignment explanation
Indices: 532925--532979 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
532915 GATGAAAAAA
*
532925 GTGCCACAGAATTGTGGGCTTTAAAAGG
1 GTGCCACAGAATTGTGGAC-TTAAAAGG
* *
532953 GTGCCACGGAGTTGTGGACTTAAAAGG
1 GTGCCACAGAATTGTGGACTTAAAAGG
532980 AACAAGGTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.27, C:0.15, G:0.35, T:0.24
Consensus pattern (27 bp):
GTGCCACAGAATTGTGGACTTAAAAGG
Found at i:533069 original size:122 final size:122
Alignment explanation
Indices: 532830--533072 Score: 271
Period size: 122 Copynumber: 2.0 Consensus size: 122
532820 AAAGAAAAAA
* * **
532830 GTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTAAACGGGTGC
1 GTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGGAGTTATGGGCTTAAACGAATGC
* * * *
532895 CACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTTAAAAGG
66 CACGGAGTCGTGGACTT-AAGATGAAAAAAGTGCCACAGAATCGTAGACTTTAAAAGG
*
532953 GTGCCACGGAGTTGTGGAC-TTAAAAGGAACAAGGTGCCACGGAGTTATGGGCTTTAAA-GAAAA
1 GTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGGAGTTATGGGC-TTAAACG----
* * * * *
533016 AATGCCACTGAGTCGTGGACTT-TGA-GACAAAA-TGCCACTGAGTCGTAGACTTTAAAA
61 AATGCCACGGAGTCGTGGACTTAAGATGAAAAAAGTGCCACAGAATCGTAGACTTTAAAA
533073 AGGTATTTGA
Statistics
Matches: 101, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
122 52 0.51
123 29 0.29
124 2 0.02
126 18 0.18
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (122 bp):
GTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGGAGTTATGGGCTTAAACGAATGC
CACGGAGTCGTGGACTTAAGATGAAAAAAGTGCCACAGAATCGTAGACTTTAAAAGG
Found at i:534107 original size:13 final size:14
Alignment explanation
Indices: 534096--534128 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
534086 AGATTTTCTG
534096 TTTTTTTTTTCTTC
1 TTTTTTTTTTCTTC
534110 TTTTTTTTTTC--C
1 TTTTTTTTTTCTTC
534122 TTTTTTT
1 TTTTTTT
534129 GTGTTTGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
14 11 0.58
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTCTTC
Found at i:541361 original size:52 final size:52
Alignment explanation
Indices: 541291--541411 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
541281 GAAAATTTAT
*
541291 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
541343 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
541395 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
541412 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:541424 original size:52 final size:51
Alignment explanation
Indices: 541291--541431 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
541281 GAAAATTTAT
541291 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
541343 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
541395 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
541432 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:541438 original size:13 final size:13
Alignment explanation
Indices: 541420--541444 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
541410 CAAAGATCAG
541420 TGTATCGATACAA
1 TGTATCGATACAA
541433 TGTATCGATACA
1 TGTATCGATACA
541445 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:541528 original size:13 final size:13
Alignment explanation
Indices: 541510--541534 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
541500 CAAAAAAATA
541510 TGTATCGATACAT
1 TGTATCGATACAT
541523 TGTATCGATACA
1 TGTATCGATACA
541535 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:541530 original size:33 final size:33
Alignment explanation
Indices: 541488--541554 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
541478 AGTAGCTTAA
541488 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
541521 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
541554 A
1 A
541555 GATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:542519 original size:55 final size:55
Alignment explanation
Indices: 542422--542743 Score: 266
Period size: 55 Copynumber: 5.8 Consensus size: 55
542412 AAGTGATAAA
* * * * * *
542422 GATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAG
1 GATGTCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGAAAAAG
** * *
542477 GATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT--G---AA-
1 GATGTCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGAAAAAG
* *
542526 GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAG
1 GATGTCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--AAA-GATGA-GA-AAAAG
* * * * *
542586 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAG
1 -GAT---G-T--CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGAAAAAG
** * * *
542648 GATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G-AAAAT
1 GATGTCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGAAAAAG
*
542701 G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GATGTCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
542744 GTGCCAATGT
Statistics
Matches: 213, Mismatches: 36, Indels: 39
0.74 0.12 0.14
Matches are distributed among these distances:
49 34 0.16
50 2 0.01
51 3 0.01
52 40 0.19
53 6 0.03
54 1 0.00
55 70 0.33
57 1 0.00
58 1 0.00
59 2 0.01
61 6 0.03
62 5 0.02
63 2 0.01
64 6 0.03
65 3 0.01
67 31 0.15
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (55 bp):
GATGTCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAGAAAAAG
Found at i:542566 original size:49 final size:49
Alignment explanation
Indices: 542420--542578 Score: 156
Period size: 49 Copynumber: 3.1 Consensus size: 49
542410 AAAAGTGATA
* * * *
542420 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G
* ** * * *
542471 AAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
542524 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
542573 ATGATG
1 AAGATG
542579 AGAAAAGTGA
Statistics
Matches: 86, Mismatches: 18, Indels: 7
0.77 0.16 0.06
Matches are distributed among these distances:
49 45 0.52
50 2 0.02
53 1 0.01
54 2 0.02
55 36 0.42
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
Found at i:542600 original size:171 final size:173
Alignment explanation
Indices: 542358--542742 Score: 711
Period size: 171 Copynumber: 2.2 Consensus size: 173
542348 GAGATGATAA
*
542358 GCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGATGATGAGAAAAGTGATAAAG
1 GCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAG
542423 ATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGT
66 ATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGT
*
542488 GCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT-GAAGA-T
131 GCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGT
*
542529 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAG
1 GCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAG
542594 ATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGT
66 ATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGT
542659 GCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGT
131 GCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAA-GT
*
542703 GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
1 GCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAA
542743 GGTGCCAATG
Statistics
Matches: 207, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
171 163 0.79
172 4 0.02
174 40 0.19
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.25
Consensus pattern (173 bp):
GCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAAATGATGATGAGAAAAGTGATAAAG
ATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAACGT
GCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGT
Found at i:542800 original size:49 final size:49
Alignment explanation
Indices: 542658--543028 Score: 460
Period size: 49 Copynumber: 7.7 Consensus size: 49
542648 GATGTCAACG
* *
542658 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA--TGCCAATA
* *
542710 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
542753 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * *
542802 TGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
*
542845 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * *
542894 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* *
542943 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATA
* *
542995 TGCTGATTCAAGGCCAGCTATATTGGGCTTAAAG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
543029 GGGTTGCCAC
Statistics
Matches: 279, Mismatches: 25, Indels: 30
0.84 0.07 0.09
Matches are distributed among these distances:
43 70 0.25
44 5 0.02
45 2 0.01
46 3 0.01
47 1 0.00
48 5 0.02
49 119 0.43
50 2 0.01
51 2 0.01
52 70 0.25
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
Found at i:542831 original size:92 final size:93
Alignment explanation
Indices: 542657--543029 Score: 570
Period size: 92 Copynumber: 3.9 Consensus size: 93
542647 GGATGTCAAC
* * *
542657 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAG
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAGA--TGCCAATATGCTGATTCAAG
*
542722 GCCAGCTATATTGGACTTAAAGGTGCCAAT
64 GCCAGCGATATTGGACTTAAAGGTGCCAAT
*
542752 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGATGCCAATATGCTGATTCAAGGC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAGATGCCAATATGCTGATTCAAGGC
542816 CAGCGATATTGGACTTAAAGGTGCCAAT
66 CAGCGATATTGGACTTAAAGGTGCCAAT
542844 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGATGCCAATATGCTGATTCAAGGC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAGATGCCAATATGCTGATTCAAGGC
542908 CAGCGATATTGGACTTAAAGATGAAGGTGCCAAT
66 CAGCGATATTGGACTT----A--AAGGTGCCAAT
*
542942 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAG
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG--AAGATGCCAATATGCTGATTCAAG
* *
543007 GCCAGCTATATTGGGCTTAAAGG
64 GCCAGCGATATTGGACTTAAAGG
543030 GGTTGCCACC
Statistics
Matches: 262, Mismatches: 7, Indels: 18
0.91 0.02 0.06
Matches are distributed among these distances:
92 128 0.49
94 4 0.02
95 40 0.15
96 1 0.00
97 1 0.00
98 48 0.18
99 1 0.00
101 39 0.15
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (93 bp):
GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAGATGCCAATATGCTGATTCAAGGC
CAGCGATATTGGACTTAAAGGTGCCAAT
Found at i:543154 original size:71 final size:69
Alignment explanation
Indices: 543092--543732 Score: 724
Period size: 71 Copynumber: 9.5 Consensus size: 69
543082 GGGCTTTGGG
* *
543092 AAGGAAAAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGG
1 AAGG-AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGG
543156 CTTTAA
65 CTTT-A
543162 AAGGAAAAA-GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGG
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGG
543226 CTTTA
65 CTTTA
543231 AACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGG
1 AA-GGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGG
543296 GCTTTA
64 GCTTTA
* **
543302 AACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTGG
1 AA-GGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGG
543367 GCTTTA
64 GCTTTA
* * *
543373 AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA--GAAGAAG-GTTGCCACGGAGTTGTGT
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAG-TGCCACGGAG-T-TGT
543435 GGGCTTTA
62 GGGCTTTA
* * *
543443 GGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTG
1 --AA-GGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTG
543507 GGCTTTA
63 GGCTTTA
* *
543514 AAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGC
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
543577 -TTA
66 TTTA
* * * * *
543580 AACG-----GGTGCCACGGAGTTGTGGAC-TT-AAAGATGAAAAA-AGTGCCACAGAATTGTGGG
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAG-GGAAAAAGAGTGCCACGGAGTTGTGGG
543637 CTTT-
65 CTTTA
* * * *
543641 ----AAAAGGGTGCCACGGAGTTGTGGAC-TTAAAA-GGAACAAG-GTGCCACGGAGTTATGGGC
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
543699 TTTA
66 TTTA
* * * *
543703 AA-GAAAAA-ATGCCACTGAGTCGTGGACTTT
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT
543733 GAGACAAAAT
Statistics
Matches: 504, Mismatches: 37, Indels: 65
0.83 0.06 0.11
Matches are distributed among these distances:
59 3 0.01
60 2 0.00
61 65 0.13
62 24 0.05
63 3 0.01
64 16 0.03
65 6 0.01
66 6 0.01
67 20 0.04
68 60 0.12
69 19 0.04
70 91 0.18
71 145 0.29
72 5 0.01
73 38 0.08
74 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (69 bp):
AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
TTTA
Found at i:543251 original size:34 final size:33
Alignment explanation
Indices: 543092--543732 Score: 646
Period size: 34 Copynumber: 19.0 Consensus size: 33
543082 GGGCTTTGGG
* * *
543092 AAGGAAAAAAGATGCCACGGAGTTGTGGACTTAA
1 AAGG-AAAAAGGTGCCACGGAGTTGTGGGCTTTA
543126 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTT-A
543162 AAGGAAAAA-GTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT--A
543196 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTA
543231 AACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 AA-GGAAAAAGGTGCCACGGAGTTGTGGGCTTT--A
543267 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTA
543302 AACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 AA-GGAAAAAGGTGCCACGGAGTTGTGGGCTTT--A
**
543338 AAGGAAAAAAGAGTGCCACAAAGTTGTGGGCTTTA
1 AAGG-AAAAAG-GTGCCACGGAGTTGTGGGCTTTA
* *
543373 AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT-A
* *
543407 AAAGAAGAAGGTTGCCACGGAGTTGTGTGGGCTTTA
1 AAGGAAAAAGG-TGCCACGGAG-T-TGTGGGCTTTA
* * * *
543443 GGAAGGGAGAAAGATGCCACGGAGTTGTGGACTTAA
1 --AA-GGAAAAAGGTGCCACGGAGTTGTGGGCTTTA
543479 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTA
* *
543514 AAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTAA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT-A
543548 AAGGAAAAAGGTGCCACGGAGTTGTGGGC-TTA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTA
* *
543580 AACG-----GGTGCCACGGAGTTGTGGAC-TTA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTA
* * *
543607 AAGATGAAAAAAGTGCCACAGAATTGTGGGCTTT-
1 AAG--GAAAAAGGTGCCACGGAGTTGTGGGCTTTA
* * *
543641 ----AAAAGGGTGCCACGGAGTTGTGGACTTAA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTA
* *
543670 AAGGAACAAGGTGCCACGGAGTTATGGGCTTTA
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTA
* * * *
543703 AA-GAAAAA-ATGCCACTGAGTCGTGGACTTT
1 AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTT
543733 GAGACAAAAT
Statistics
Matches: 521, Mismatches: 50, Indels: 75
0.81 0.08 0.12
Matches are distributed among these distances:
27 24 0.05
28 22 0.04
29 1 0.00
31 17 0.03
32 9 0.02
33 92 0.18
34 133 0.26
35 97 0.19
36 34 0.07
37 75 0.14
38 12 0.02
39 5 0.01
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (33 bp):
AAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTA
Found at i:543287 original size:141 final size:137
Alignment explanation
Indices: 543097--543734 Score: 771
Period size: 141 Copynumber: 4.7 Consensus size: 137
543087 TTGGGAAGGA
* *
543097 AAAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTA
* *
543161 AAAGGAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGG
64 AAAGGAAAAAGTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGG
*
543226 CTTTAAACGG
129 CTTTAAA-AG
543236 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTT
* * * *
543301 AAACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTG
63 AAAAGGAAAAA-GTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTG
543366 GGCTTTAAAAG
127 GGCTTTAAAAG
* *
543377 AAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAGAAGGTTGCCACGGAGTTGTGTGGGCTT
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGAAAAAGG-TGCCACGGAG-T-TGTGGGCTT
* * *
543441 TAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTT
62 TA--AAAGGAAAAAG-TGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACAGAGTT
543504 GTGGGCTTTAAAAG
124 GTGGGCTTTAAAAG
*
543518 AAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGC-TTAAA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
* * *
543582 CGG-----GTGCCACGGAGTTGTGGAC-TT--AAAGATGAAAAA-AGTGCCACAGAATTGTGGGC
66 AGGAAAAAGTGCCACGGAGTTGTGGACTTTGAAAAG-GGAAAAAGAGTGCCACAGAGTTGTGGGC
543638 TTTAAAAG
130 TTTAAAAG
* * *
543646 -----GGTGCCACGGAGTTGTGGAC-TTAAAAGGAACAAGGTGCCACGGAGTTATGGGCTTT-AA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
* * *
543704 A-GAAAAAATGCCACTGAGTCGTGGACTTTGA
66 AGGAAAAAGTGCCACGGAGTTGTGGACTTTGA
543735 GACAAAATGC
Statistics
Matches: 449, Mismatches: 30, Indels: 50
0.85 0.06 0.09
Matches are distributed among these distances:
121 1 0.00
122 33 0.07
123 20 0.04
126 16 0.04
127 2 0.00
128 30 0.07
129 26 0.06
130 1 0.00
135 4 0.01
137 3 0.01
138 8 0.02
139 40 0.09
140 17 0.04
141 161 0.36
142 62 0.14
143 25 0.06
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.21
Consensus pattern (137 bp):
AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
AGGAAAAAGTGCCACGGAGTTGTGGACTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCT
TTAAAAG
Found at i:543594 original size:61 final size:61
Alignment explanation
Indices: 543457--543704 Score: 327
Period size: 61 Copynumber: 3.9 Consensus size: 61
543447 GGGAGAAAGA
543457 TGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
1 TGCCACGGAGTTGTGGACTTAAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAG----
*
543522 AAG
60 -GG
* *
543525 TGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGC-TTAAACGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* * * *
543586 TGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAA-AGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
* *
543648 TGCCACGGAGTTGTGGACTTAAAAGGAACAAGGTGCCACGGAGTTATGGGCTTTAAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
543705 GAAAAAATGC
Statistics
Matches: 162, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
60 5 0.03
61 70 0.43
62 31 0.19
66 6 0.04
67 19 0.12
68 25 0.15
69 6 0.04
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.21
Consensus pattern (61 bp):
TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG
Found at i:543595 original size:27 final size:26
Alignment explanation
Indices: 543557--543670 Score: 93
Period size: 27 Copynumber: 4.0 Consensus size: 26
543547 AAAGGAAAAA
*
543557 GGTGCCACGGAGTTGTGGGCTTAAACG
1 GGTGCCACGGAGTTGTGGACTTAAA-G
543584 GGTGCCACGGAGTTGTGGACTTAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAG
* * *
543610 ATGAAAAAAGTGCCACAGAATTGTGGGCTTTAAAAG
1 --G------GTGCCACGGAGTTGTGGAC-TT-AAAG
543646 GGTGCCACGGAGTTGTGGACTTAAA
1 GGTGCCACGGAGTTGTGGACTTAAA
543671 AGGAACAAGG
Statistics
Matches: 70, Mismatches: 7, Indels: 21
0.71 0.07 0.21
Matches are distributed among these distances:
26 4 0.06
27 26 0.37
28 17 0.24
34 17 0.24
35 2 0.03
36 4 0.06
ACGTcount: A:0.28, C:0.15, G:0.34, T:0.23
Consensus pattern (26 bp):
GGTGCCACGGAGTTGTGGACTTAAAG
Found at i:543653 original size:28 final size:27
Alignment explanation
Indices: 543619--543673 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
543609 GATGAAAAAA
*
543619 GTGCCACAGAATTGTGGGCTTTAAAAGG
1 GTGCCACAGAATTGTGGAC-TTAAAAGG
* *
543647 GTGCCACGGAGTTGTGGACTTAAAAGG
1 GTGCCACAGAATTGTGGACTTAAAAGG
543674 AACAAGGTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.27, C:0.15, G:0.35, T:0.24
Consensus pattern (27 bp):
GTGCCACAGAATTGTGGACTTAAAAGG
Found at i:543763 original size:122 final size:122
Alignment explanation
Indices: 543524--543766 Score: 271
Period size: 122 Copynumber: 2.0 Consensus size: 122
543514 AAAGAAAAAA
* * **
543524 GTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTAAACGGGTGC
1 GTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGGAGTTATGGGCTTAAACGAATGC
* * * *
543589 CACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACAGAATTGTGGGCTTTAAAAGG
66 CACGGAGTCGTGGACTT-AAGATGAAAAAAGTGCCACAGAATCGTAGACTTTAAAAGG
*
543647 GTGCCACGGAGTTGTGGAC-TTAAAAGGAACAAGGTGCCACGGAGTTATGGGCTTTAAA-GAAAA
1 GTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGGAGTTATGGGC-TTAAACG----
* * * * *
543710 AATGCCACTGAGTCGTGGACTT-TGA-GACAAAA-TGCCACTGAGTCGTAGACTTTAAAA
61 AATGCCACGGAGTCGTGGACTTAAGATGAAAAAAGTGCCACAGAATCGTAGACTTTAAAA
543767 AGGTATTTGA
Statistics
Matches: 101, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
122 52 0.51
123 29 0.29
124 2 0.02
126 18 0.18
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (122 bp):
GTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGGTGCCACGGAGTTATGGGCTTAAACGAATGC
CACGGAGTCGTGGACTTAAGATGAAAAAAGTGCCACAGAATCGTAGACTTTAAAAGG
Found at i:544806 original size:16 final size:14
Alignment explanation
Indices: 544795--544827 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
544785 TTTTCTGTTG
544795 TTTTTTTTTTCTTC
1 TTTTTTTTTTCTTC
544809 TTTTTTTTTTC--C
1 TTTTTTTTTTCTTC
544821 TTTTTTT
1 TTTTTTT
544828 GTGTTTGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
14 11 0.58
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTTTTTTCTTC
Found at i:546765 original size:52 final size:52
Alignment explanation
Indices: 546695--546815 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
546685 GAAAATTTAT
*
546695 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
546747 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
546799 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
546816 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:546828 original size:52 final size:51
Alignment explanation
Indices: 546695--546835 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
546685 GAAAATTTAT
546695 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
546747 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
546799 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
546836 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:546842 original size:13 final size:13
Alignment explanation
Indices: 546824--546848 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
546814 CAAAGATCAG
546824 TGTATCGATACAA
1 TGTATCGATACAA
546837 TGTATCGATACA
1 TGTATCGATACA
546849 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:546932 original size:13 final size:13
Alignment explanation
Indices: 546914--546938 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
546904 CAAAAAAATA
546914 TGTATCGATACAT
1 TGTATCGATACAT
546927 TGTATCGATACA
1 TGTATCGATACA
546939 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:546934 original size:33 final size:33
Alignment explanation
Indices: 546892--546958 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
546882 AGTAGCTTAA
546892 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
546925 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
546958 A
1 A
546959 GATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:551788 original size:13 final size:13
Alignment explanation
Indices: 551770--551796 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
551760 CATTTTGGGA
551770 TGTATCGATACAT
1 TGTATCGATACAT
551783 TGTATCGATACAT
1 TGTATCGATACAT
551796 T
1 T
551797 TTGTGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:551811 original size:32 final size:33
Alignment explanation
Indices: 551750--551813 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
551740 TACAAGCCAA
551750 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATTTTGGGATGTATCGATACAT
*
551783 TGTATCGATACATTTTGTG-TGTATCGATACA
1 TGTATCGATACATTTTGGGATGTATCGATACA
551814 AACAGTTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 12 0.40
33 18 0.60
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTTTGGGATGTATCGATACAT
Found at i:551913 original size:13 final size:13
Alignment explanation
Indices: 551895--551919 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
551885 ACTTTTGGTC
551895 ATGTATCGATACA
1 ATGTATCGATACA
551908 ATGTATCGATAC
1 ATGTATCGATAC
551920 TGTGCAATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:554119 original size:34 final size:33
Alignment explanation
Indices: 554045--554301 Score: 259
Period size: 32 Copynumber: 7.8 Consensus size: 33
554035 ACTTTTTTCA
* * * *
554045 AAAGTCCATAACTCCGTGACACCTTTTTC-TTC
1 AAAGTCCACAACTCCATGGCACCTTTTTCTTTT
*
554077 AAAGTCCACAACTCTATGGCACCATTTTTCTTTT
1 AAAGTCCACAACTCCATGGCACC-TTTTTCTTTT
* * *
554111 TAAGTCCACAACTTCGTGGCACCTTTTTCTTTT
1 AAAGTCCACAACTCCATGGCACCTTTTTCTTTT
* * * *
554144 AAAGTCTATAACTCCATGACA-CTTTTTATTTT
1 AAAGTCCACAACTCCATGGCACCTTTTTCTTTT
* ** *
554176 AAAGTCCACAACTCCGTCACACTTTTTTCTTTT
1 AAAGTCCACAACTCCATGGCACCTTTTTCTTTT
* * *
554209 AAAGTCCATAATTCCATGGCACCTTCTTCTTTTT
1 AAAGTCCACAACTCCATGGCACCTTTTTC-TTTT
* *
554243 AAAGTCCACAACTCCGTGGCACCTTTTTC-TTC
1 AAAGTCCACAACTCCATGGCACCTTTTTCTTTT
* * *
554275 AAAGTTCATAACTCTATGGCACCTTTT
1 AAAGTCCACAACTCCATGGCACCTTTT
554302 AGTCCTCAAA
Statistics
Matches: 183, Mismatches: 38, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
32 71 0.39
33 62 0.34
34 50 0.27
ACGTcount: A:0.25, C:0.27, G:0.09, T:0.39
Consensus pattern (33 bp):
AAAGTCCACAACTCCATGGCACCTTTTTCTTTT
Found at i:554243 original size:99 final size:98
Alignment explanation
Indices: 554045--554301 Score: 279
Period size: 99 Copynumber: 2.6 Consensus size: 98
554035 ACTTTTTTCA
* *
554045 AAAGTCCATAACTCCGTGACACCTTTTTCTTCAAAGTCCACAACTCTATGGCACCATTTTTCTTT
1 AAAGTCCATAACTCCATGACACCTTTTTCTTCAAAGTCCACAACTC-ACGGCACCATTTTTCTTT
* * *
554110 TTAAGTCCACAACTTCGTGGCACCTTTTTCTTTT
65 TAAAGTCCACAACTTCATGGCACCTTCTTCTTTT
* * * * *
554144 AAAGTCTATAACTCCATGACA-CTTTTTATTTTAAAGTCCACAACTC-CGTCACACTTTTTTCTT
1 AAAGTCCATAACTCCATGACACCTTTTT-CTTCAAAGTCCACAACTCACGGCAC-CATTTTTCTT
*
554207 TTAAAGTCCATAA-TTCCATGGCACCTTCTTCTTTTT
64 TTAAAGTCCACAACTT-CATGGCACCTTCTTC-TTTT
* * * * * *
554243 AAAGTCCACAACTCCGTGGCACCTTTTTCTTCAAAGTTCATAACTCTATGGCACC-TTTT
1 AAAGTCCATAACTCCATGACACCTTTTTCTTCAAAGTCCACAACTC-ACGGCACCATTTT
554302 AGTCCTCAAA
Statistics
Matches: 130, Mismatches: 21, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
97 6 0.05
98 39 0.30
99 74 0.57
100 7 0.05
101 4 0.03
ACGTcount: A:0.25, C:0.27, G:0.09, T:0.39
Consensus pattern (98 bp):
AAAGTCCATAACTCCATGACACCTTTTTCTTCAAAGTCCACAACTCACGGCACCATTTTTCTTTT
AAAGTCCACAACTTCATGGCACCTTCTTCTTTT
Found at i:554539 original size:62 final size:62
Alignment explanation
Indices: 554423--554624 Score: 246
Period size: 62 Copynumber: 3.3 Consensus size: 62
554413 TTAGAATATC
* * * *
554423 AAAGCCCACACGAGTTGATGGCACCCTAGTCAAAG-CTCGCACATGTTGGTAGCACTCAAGTT
1 AAAGTCCACACGAGTTGATGGCACCCTAGTCAAAGCCT-GCACAAGTTGGCAGCACTCGAGTT
* * * *
554485 AAAGTCGACACAAGTTGATGGCACCCTAGTCAAAGCCTGCACAAGTTAGCAGCACCCGAGTT
1 AAAGTCCACACGAGTTGATGGCACCCTAGTCAAAGCCTGCACAAGTTGGCAGCACTCGAGTT
* * * * * * *
554547 GAAG-CCACATGAGTTGGTGGCACCCTAGTCAAAGCCTACACAAGTTGGCGGCACTTGAGTC
1 AAAGTCCACACGAGTTGATGGCACCCTAGTCAAAGCCTGCACAAGTTGGCAGCACTCGAGTT
554608 AAAGTCCACACGAGTTG
1 AAAGTCCACACGAGTTG
554625 GTGGTACCTA
Statistics
Matches: 117, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
61 50 0.43
62 65 0.56
63 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (62 bp):
AAAGTCCACACGAGTTGATGGCACCCTAGTCAAAGCCTGCACAAGTTGGCAGCACTCGAGTT
Found at i:554600 original size:31 final size:31
Alignment explanation
Indices: 554421--554628 Score: 145
Period size: 31 Copynumber: 6.7 Consensus size: 31
554411 CTTTAGAATA
* * *
554421 TCAAAGCCCACACGAGTTGATGGCACCCTAG
1 TCAAAGCCTACACAAGTTGGTGGCACCCTAG
* * * * *
554452 TCAAAG-CTCGCACATGTTGGTAGCACTCAAG
1 TCAAAGCCT-ACACAAGTTGGTGGCACCCTAG
* * * *
554483 TTAAAGTCGACACAAGTTGATGGCACCCTAG
1 TCAAAGCCTACACAAGTTGGTGGCACCCTAG
* * ** *
554514 TCAAAGCCTGCACAAGTTAGCAGCACCCGAG
1 TCAAAGCCTACACAAGTTGGTGGCACCCTAG
** **
554545 TTGAAGCC-ACATGAGTTGGTGGCACCCTAG
1 TCAAAGCCTACACAAGTTGGTGGCACCCTAG
* *
554575 TCAAAGCCTACACAAGTTGGCGGCA-CTTGAG
1 TCAAAGCCTACACAAGTTGGTGGCACCCT-AG
*
554606 TCAAAGTCC-ACACGAGTTGGTGG
1 TCAAAG-CCTACACAAGTTGGTGG
554629 TACCTAAGTT
Statistics
Matches: 130, Mismatches: 42, Indels: 10
0.71 0.23 0.05
Matches are distributed among these distances:
30 24 0.18
31 103 0.79
32 3 0.02
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (31 bp):
TCAAAGCCTACACAAGTTGGTGGCACCCTAG
Found at i:554760 original size:31 final size:30
Alignment explanation
Indices: 554695--554793 Score: 112
Period size: 31 Copynumber: 3.2 Consensus size: 30
554685 TTAGAATGTT
* *
554695 AAAGCCCACATGAGTTGATGGCACCCTAGCC
1 AAAGCCCACATGAGTTGGTGGCA-CCTAGTC
554726 AAAGCTCGCAC-T-AGTTGGTGGCACCTAAGTC
1 AAAGC-C-CACATGAGTTGGTGGCACCT-AGTC
*
554757 AAAGCCCACATGAGTTAGTGGCACCTTAGTC
1 AAAGCCCACATGAGTTGGTGGCACC-TAGTC
554788 AAAGCC
1 AAAGCC
554794 TGCATAAGCC
Statistics
Matches: 59, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
29 3 0.05
30 5 0.08
31 45 0.76
32 3 0.05
33 3 0.05
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.19
Consensus pattern (30 bp):
AAAGCCCACATGAGTTGGTGGCACCTAGTC
Found at i:554842 original size:31 final size:31
Alignment explanation
Indices: 554695--554842 Score: 111
Period size: 31 Copynumber: 4.8 Consensus size: 31
554685 TTAGAATGTT
* * * *
554695 AAAGCCCACATGAGTTGATGGCACCCTAGCC
1 AAAGCCCACATAAGTTGGTGGCACCCAAGTC
*
554726 AAAGCTCGCAC-T-AGTTGGTGGCACCTAAGTC
1 AAAGC-C-CACATAAGTTGGTGGCACCCAAGTC
* * **
554757 AAAGCCCACATGAGTTAGTGGCACCTTAGTC
1 AAAGCCCACATAAGTTGGTGGCACCCAAGTC
** ** **
554788 AAAGCCTGCATAAGCCGACGGCACCCAAGTC
1 AAAGCCCACATAAGTTGGTGGCACCCAAGTC
* *
554819 AAAGCCCACACAAGCTGGTGGCAC
1 AAAGCCCACATAAGTTGGTGGCAC
554843 TTAAGTTCGA
Statistics
Matches: 91, Mismatches: 22, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
29 3 0.03
30 2 0.02
31 81 0.89
32 2 0.02
33 3 0.03
ACGTcount: A:0.30, C:0.30, G:0.24, T:0.16
Consensus pattern (31 bp):
AAAGCCCACATAAGTTGGTGGCACCCAAGTC
Found at i:554850 original size:211 final size:210
Alignment explanation
Indices: 554497--554901 Score: 515
Period size: 211 Copynumber: 1.9 Consensus size: 210
554487 AGTCGACACA
* * **
554497 AGTTGATGGCACCCTAGTCAAAGCCTGCACAAGTTAGCAGCACCCGAGTTGAAGCCACATGAGTT
1 AGTTGATGGCACCCTAGCCAAAGCCTGCACAAGTTAGCAGCACCCAAGTCAAAGCCACATGAGTT
* ** * *** * * *
554562 GGTGGCACCCTAGTCAAAGCCTACACAAGTTGGCGGCACTTGAGTCAAAGTCCACACGAGTTGGT
66 AGTGGCACCCTAGTCAAAGCCTACACAAGCCGACGGCACCCAAGTCAAAGCCCACACAAGCTGGT
* * * * * *
554627 GGTACCTAAGTTCGAGTTAAGTCCATATTGGTTGGCACCTATCTAAGGAGGTTAAGCCTTAGAAT
131 GGCACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTATCTAAAGAGGTCAAGCCTTAGAAT
554692 GTTAAAGCCCACATG
196 GTTAAAGCCCACATG
* * ** *
554707 AGTTGATGGCACCCTAGCCAAAG-CTCGCACTAGTTGGTGGCACCTAAGTCAAAGCCCACATGAG
1 AGTTGATGGCACCCTAGCCAAAGCCT-GCACAAGTTAGCAGCACCCAAGTCAAAG-CCACATGAG
* * *
554771 TTAGTGGCACCTTAGTCAAAGCCTGCATAAGCCGACGGCACCCAAGTCAAAGCCCACACAAGCTG
64 TTAGTGGCACCCTAGTCAAAGCCTACACAAGCCGACGGCACCCAAGTCAAAGCCCACACAAGCTG
* *
554836 GTGGCACTTAAGTTCGAGTCAAGTCCGCATTAGTTGGCACCTATCTAAAGAGGTCAAGCCTTAGA
129 GTGGCACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTATCTAAAGAGGTCAAGCCTTAGA
554901 A
194 A
554902 ACCAAAACCC
Statistics
Matches: 163, Mismatches: 30, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
209 2 0.01
210 42 0.26
211 119 0.73
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (210 bp):
AGTTGATGGCACCCTAGCCAAAGCCTGCACAAGTTAGCAGCACCCAAGTCAAAGCCACATGAGTT
AGTGGCACCCTAGTCAAAGCCTACACAAGCCGACGGCACCCAAGTCAAAGCCCACACAAGCTGGT
GGCACCTAAGTTCGAGTCAAGTCCACATTAGTTGGCACCTATCTAAAGAGGTCAAGCCTTAGAAT
GTTAAAGCCCACATG
Found at i:555825 original size:20 final size:21
Alignment explanation
Indices: 555777--555830 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
555767 TTCTACAATT
*
555777 TGTATCGATACAAACAGTAAA
1 TGTATCGATACATACAGTAAA
* *
555798 TATATCGATACATA-AGTGAA
1 TGTATCGATACATACAGTAAA
555818 TGTATCGATACAT
1 TGTATCGATACAT
555831 GTTTAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATACAGTAAA
Found at i:559477 original size:2 final size:2
Alignment explanation
Indices: 559470--559499 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
559460 TCTACCTTGG
559470 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
559500 GGATTTTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:570440 original size:20 final size:19
Alignment explanation
Indices: 570394--570437 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
570384 CAAACAGATG
**
570394 AAAAACTTGAAAACCCCATA
1 AAAAAC-TGAAAAAACCATA
570414 AAAAACTGAAAAAACCATA
1 AAAAACTGAAAAAACCATA
570433 AAAAA
1 AAAAA
570438 ACTAATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.66, C:0.18, G:0.05, T:0.11
Consensus pattern (19 bp):
AAAAACTGAAAAAACCATA
Found at i:570865 original size:5 final size:5
Alignment explanation
Indices: 570851--570883 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
570841 TAATTTTTTA
570851 ATTA- ATTAT ATTAT ATTAT ATTAT ATT-T ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
570884 TTTTATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 8 0.30
5 19 0.70
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATTAT
Found at i:570889 original size:15 final size:14
Alignment explanation
Indices: 570851--570893 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
570841 TAATTTTTTA
570851 ATTA-ATTATATTAT
1 ATTATATTATATT-T
570865 ATTATATTATATTT
1 ATTATATTATATTT
*
570879 ATTATTTTTATATTT
1 ATTA-TATTATATTT
570894 TGTGAAAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATTATATTATATTT
Found at i:576182 original size:15 final size:16
Alignment explanation
Indices: 576160--576196 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
576150 TTAATTATAT
576160 TATTTTATTATTTTTA
1 TATTTTATTATTTTTA
576176 T-TTTTATTATTTTTA
1 TATTTTATTATTTTTA
576191 TATTTT
1 TATTTT
576197 GTGAAAGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (16 bp):
TATTTTATTATTTTTA
Found at i:578120 original size:20 final size:20
Alignment explanation
Indices: 578087--578158 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
578077 TTACAGTATT
*
578087 AATTA-AAATGTAATATAAA
1 AATTATAAATATAATATAAA
578106 AATTATAAATATAATATAAA
1 AATTATAAATATAATATAAA
*
578126 TATT-TAAATAT-AT-TAAA
1 AATTATAAATATAATATAAA
*
578143 ATTTATATAATATAAT
1 AATTATA-AATATAAT
578159 TTATTAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
17 6 0.13
18 4 0.09
19 17 0.38
20 18 0.40
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (20 bp):
AATTATAAATATAATATAAA
Found at i:578141 original size:49 final size:49
Alignment explanation
Indices: 578086--578219 Score: 132
Period size: 49 Copynumber: 2.7 Consensus size: 49
578076 ATTACAGTAT
578086 TAATTAAAATGTAATATAAAAATTATAAATATAATATAAA-TATTTAAATA
1 TAATTAAAAT-TAATATAAAAATTATAAATATAATA-AAATTATTTAAATA
* * *
578136 T-ATTAAAATTTATATAATATAATTTATTAATATATTAAAATTTATTTAAATA
1 TAATTAAAATTAATATAA-A-AA-TTATAAATATAATAAAA-TTATTTAAATA
* *
578188 TAATTATAATATAATA-AAATA-TATAAATATAA
1 TAATTAAAAT-TAATATAAAAATTATAAATATAA
578220 ATTACTATTT
Statistics
Matches: 69, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
48 7 0.10
49 18 0.26
50 6 0.09
51 13 0.19
52 12 0.17
53 9 0.13
54 4 0.06
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.43
Consensus pattern (49 bp):
TAATTAAAATTAATATAAAAATTATAAATATAATAAAATTATTTAAATA
Found at i:578144 original size:10 final size:10
Alignment explanation
Indices: 578107--578211 Score: 63
Period size: 10 Copynumber: 10.2 Consensus size: 10
578097 TAATATAAAA
578107 ATTATAAATAT
1 ATTA-AAATAT
*
578118 AATATAAATAT
1 ATTA-AAATAT
578129 -TT-AAATAT
1 ATTAAAATAT
*
578137 ATTAAAATTT
1 ATTAAAATAT
*
578147 A-TATAATAT
1 ATTAAAATAT
*
578156 AATTTATTAATAT
1 -A-TTA-AAATAT
*
578169 ATTAAAATTT
1 ATTAAAATAT
*
578179 ATTTAAATAT
1 ATTAAAATAT
*
578189 AATTATAATAT
1 -ATTAAAATAT
*
578200 AATAAAATAT
1 ATTAAAATAT
578210 AT
1 AT
578212 AAATATAAAT
Statistics
Matches: 73, Mismatches: 14, Indels: 15
0.72 0.14 0.15
Matches are distributed among these distances:
8 6 0.08
9 8 0.11
10 29 0.40
11 21 0.29
12 3 0.04
13 6 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:578150 original size:14 final size:14
Alignment explanation
Indices: 578133--578222 Score: 56
Period size: 14 Copynumber: 5.9 Consensus size: 14
578123 AAATATTTAA
*
578133 ATATATTAAAATTT
1 ATATAATAAAATTT
*
578147 ATATAATATAATTT
1 ATATAATAAAATTT
578161 ATTAATATATTAAAATTT
1 A-T-ATA-A-TAAAATTT
* *
578179 ATTTAAATATAATTAT
1 ATAT-AATAAAATT-T
*
578195 AATATAATAAAATAT
1 -ATATAATAAAATTT
578210 ATA-AATATAAATT
1 ATATAATA-AAATT
578223 ACTATTTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
13 4 0.07
14 20 0.34
15 8 0.14
16 13 0.22
17 6 0.10
18 8 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATATAATAAAATTT
Found at i:578156 original size:33 final size:32
Alignment explanation
Indices: 578114--578219 Score: 112
Period size: 32 Copynumber: 3.3 Consensus size: 32
578104 AAAATTATAA
578114 ATATAATATAAATATTTAAATATATTAAAATTT
1 ATATAATAT-AATATTTAAATATATTAAAATTT
*
578147 ATATAATATAAT-TTATTAATATATTAAAATTT
1 ATATAATATAATATT-TAAATATATTAAAATTT
* * * *
578179 ATTTAA-AT-ATAATTATAATATAATAAAATAT
1 ATATAATATAATATTTA-AATATATTAAAATTT
578210 ATA-AATATAA
1 ATATAATATAA
578220 ATTACTATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
30 5 0.08
31 22 0.36
32 25 0.41
33 9 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
ATATAATATAATATTTAAATATATTAAAATTT
Found at i:578168 original size:13 final size:14
Alignment explanation
Indices: 578142--578219 Score: 50
Period size: 16 Copynumber: 5.1 Consensus size: 14
578132 AATATATTAA
578142 AATTTATATAATAT
1 AATTTATATAATAT
*
578156 AATTTATTAATATATTAA
1 AATTTA-T-ATA-A-TAT
*
578174 AATTTATTTAAATAT
1 AATTTATAT-AATAT
*
578189 AATTATAATATAATAA
1 AATT-T-ATATAATAT
*
578205 AATATATA-AATAT
1 AATTTATATAATAT
578218 AA
1 AA
578220 ATTACTATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
13 6 0.12
14 9 0.18
15 8 0.16
16 13 0.26
17 6 0.12
18 8 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATTTATATAATAT
Found at i:578515 original size:22 final size:22
Alignment explanation
Indices: 578484--578528 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
578474 TAAGTAATAT
*
578484 TAATATATAAATTTTAAATTAAA
1 TAATATATAAAATTTAAA-TAAA
578507 TAATA-ATAAAATTTAAATAAA
1 TAATATATAAAATTTAAATAAA
578528 T
1 T
578529 TTAAGAGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 11 0.52
23 5 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAATATATAAAATTTAAATAAA
Found at i:578523 original size:29 final size:29
Alignment explanation
Indices: 578463--578524 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
578453 TATTTATAAA
* * *
578463 AAATTTTAAATTAAGTAATATTAATATAT
1 AAATTTTAAATTAAATAATAATAAAATAT
*
578492 AAATTTTAAATTAAATAATAATAAAATTT
1 AAATTTTAAATTAAATAATAATAAAATAT
578521 AAAT
1 AAAT
578525 AAATTTAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (29 bp):
AAATTTTAAATTAAATAATAATAAAATAT
Found at i:581239 original size:13 final size:13
Alignment explanation
Indices: 581221--581248 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
581211 ACATTATGCT
581221 TTGTATCGATACA
1 TTGTATCGATACA
581234 TTGTATCGATACA
1 TTGTATCGATACA
581247 TT
1 TT
581249 TCATTGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:581329 original size:13 final size:13
Alignment explanation
Indices: 581311--581341 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
581301 CGACACATGG
581311 TACATTGTATCCA
1 TACATTGTATCCA
*
581324 TACATTGTATCGA
1 TACATTGTATCCA
581337 TACAT
1 TACAT
581342 AGTGTAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (13 bp):
TACATTGTATCCA
Found at i:582542 original size:34 final size:35
Alignment explanation
Indices: 582494--582562 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
582484 TTTGACTTAG
* *
582494 ATTTATTTCCAAGGTC-TTGGAACTTGATCTTGAA
1 ATTTATTTCAAAGGTCTTTGAAACTTGATCTTGAA
*
582528 ATTTGTTTCAAAGGTCTTTGAAACTTGATCTTGAA
1 ATTTATTTCAAAGGTCTTTGAAACTTGATCTTGAA
582563 TCAATGAGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
34 14 0.45
35 17 0.55
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (35 bp):
ATTTATTTCAAAGGTCTTTGAAACTTGATCTTGAA
Found at i:595659 original size:79 final size:79
Alignment explanation
Indices: 595401--595647 Score: 268
Period size: 79 Copynumber: 3.1 Consensus size: 79
595391 GGCGTTTTGA
* * * * *
595401 AAATAAAATCGGGATT-GAGTATCCCTTC-GAAAATAA-TGGAGTTAGAGTATCCCCGATTGTGG
1 AAATAAAACCGGGGTTGGAGTATCCCCTCAG-AAATAACGGGA-TTAGAGTATCCCCGATTGTGA
*
595463 AAAATCGATGCTTTAG
64 AAAATCGATGTTTTAG
** * * *
595479 AAATAAGGCCGGGGTTGGAGTATCCCCACCA-AAATAACGGGGTTAGAGTATCCCCGATTGTGAG
1 AAATAAAACCGGGGTTGGAGTATCCCC-TCAGAAATAACGGGATTAGAGTATCCCCGATTGTGAA
* *
595543 AAATCAATATTTTAG
65 AAATCGATGTTTTAG
** * *
595558 AAATAAAGTCGGGGTTGGAGTATCCCCTCAGAAATAACGGGATTGGAGTATCCCCGATTATGAAA
1 AAATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGATTAGAGTATCCCCGATTGTGAAA
* *
595623 AATTGATGTTTTGG
66 AATCGATGTTTTAG
595637 AAATAAAACCG
1 AAATAAAACCG
595648 AGGCTAGAGT
Statistics
Matches: 138, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
78 14 0.10
79 121 0.88
80 3 0.02
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.26
Consensus pattern (79 bp):
AAATAAAACCGGGGTTGGAGTATCCCCTCAGAAATAACGGGATTAGAGTATCCCCGATTGTGAAA
AATCGATGTTTTAG
Found at i:595690 original size:50 final size:50
Alignment explanation
Indices: 595631--595725 Score: 136
Period size: 50 Copynumber: 1.9 Consensus size: 50
595621 AAAATTGATG
*
595631 TTTTGGAAATAAAACCGAGGCTAGAGTATACCCGAGATGAAAAATCAGTA
1 TTTTAGAAATAAAACCGAGGCTAGAGTATACCCGAGATGAAAAATCAGTA
* * * * *
595681 TTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCGAGATGAAAAAT
1 TTTTAGAAATAAAACCGAGGCTAGAGTATACCCGAGATGAAAAAT
595726 ATAGAAGTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (50 bp):
TTTTAGAAATAAAACCGAGGCTAGAGTATACCCGAGATGAAAAATCAGTA
Found at i:604522 original size:32 final size:32
Alignment explanation
Indices: 604481--604592 Score: 163
Period size: 32 Copynumber: 3.5 Consensus size: 32
604471 AAACAGTAAC
* *
604481 TGTATCGATACATAAATGTTGTATCGATGCAT
1 TGTATCGATACATAAGTGTCGTATCGATGCAT
604513 TGTATCGATACATAAGTGTCGTATCGATGCAT
1 TGTATCGATACATAAGTGTCGTATCGATGCAT
* * *
604545 TGTATCGATACATAAGTGTCGTATTGATACAA
1 TGTATCGATACATAAGTGTCGTATCGATGCAT
*
604577 TGTATCGCTACA-AAGT
1 TGTATCGATACATAAGT
604593 TACTGCCAAG
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
31 4 0.05
32 70 0.95
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTCGTATCGATGCAT
Found at i:604538 original size:19 final size:19
Alignment explanation
Indices: 604514--604575 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 19
604504 TCGATGCATT
604514 GTATCGATACATAAGTGTC
1 GTATCGATACATAAGTGTC
*
604533 GTATCGATGC---A-T-T-
1 GTATCGATACATAAGTGTC
604546 GTATCGATACATAAGTGTC
1 GTATCGATACATAAGTGTC
*
604565 GTATTGATACA
1 GTATCGATACA
604576 ATGTATCGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 12
0.69 0.06 0.24
Matches are distributed among these distances:
13 9 0.26
14 1 0.03
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 19 0.56
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.34
Consensus pattern (19 bp):
GTATCGATACATAAGTGTC
Found at i:608127 original size:20 final size:20
Alignment explanation
Indices: 608102--608154 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
608092 GTTGGGGTTA
608102 ATGTATCGATACATTTCAAC
1 ATGTATCGATACATTTCAAC
*
608122 ATGTATCGATACATTTCACC
1 ATGTATCGATACATTTCAAC
608142 ATGTATCGATACA
1 ATGTATCGATACA
608155 ATGTATCGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTTCAAC
Found at i:608160 original size:13 final size:13
Alignment explanation
Indices: 608142--608166 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
608132 ACATTTCACC
608142 ATGTATCGATACA
1 ATGTATCGATACA
608155 ATGTATCGATAC
1 ATGTATCGATAC
608167 TGAGTGAGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:608252 original size:13 final size:13
Alignment explanation
Indices: 608234--608258 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
608224 TACTATGAAC
608234 ATGTATCGATACA
1 ATGTATCGATACA
608247 ATGTATCGATAC
1 ATGTATCGATAC
608259 TAAGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:608278 original size:33 final size:32
Alignment explanation
Indices: 608216--608279 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
608206 CAATTCAATG
* *
608216 TGTATTGATACTATGAACATGTATCGATACAA
1 TGTATCGATACTAAGAACATGTATCGATACAA
* *
608248 TGTATCGATACTAAGCAATATGTATTGATACA
1 TGTATCGATACTAAG-AACATGTATCGATACA
608280 TCTAGGTGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (32 bp):
TGTATCGATACTAAGAACATGTATCGATACAA
Found at i:612278 original size:13 final size:13
Alignment explanation
Indices: 612260--612285 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
612250 ACATTTTGGG
612260 ATGTATCGATACA
1 ATGTATCGATACA
612273 ATGTATCGATACA
1 ATGTATCGATACA
612286 TATTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:612280 original size:33 final size:32
Alignment explanation
Indices: 612238--612305 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
612228 CGTTACAAGC
*
612238 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGG-TGTATCGATA
*
612271 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGGGTGTATCGATA
612303 CAA
1 CAA
612306 ATTTGGCTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCGATA
Found at i:612434 original size:20 final size:20
Alignment explanation
Indices: 612411--612451 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
612401 CTGTGCAATT
612411 TGTATCGATACATTTAAAGG
1 TGTATCGATACATTTAAAGG
* *
612431 TGTATCGATACTTTTCAAGG
1 TGTATCGATACATTTAAAGG
612451 T
1 T
612452 TTTGACCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTTAAAGG
Found at i:614797 original size:13 final size:13
Alignment explanation
Indices: 614779--614803 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
614769 TATAAACCCC
614779 TTGTATCGATACA
1 TTGTATCGATACA
614792 TTGTATCGATAC
1 TTGTATCGATAC
614804 TGAGAATGCT
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:615020 original size:8 final size:8
Alignment explanation
Indices: 615007--615032 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
614997 AACATCGTTC
615007 ATCACAAA
1 ATCACAAA
615015 ATCACAAA
1 ATCACAAA
615023 ATCACAAA
1 ATCACAAA
615031 AT
1 AT
615033 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:620993 original size:13 final size:13
Alignment explanation
Indices: 620975--621000 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
620965 ACATTTTGGG
620975 ATGTATCGATACA
1 ATGTATCGATACA
620988 ATGTATCGATACA
1 ATGTATCGATACA
621001 TATTATGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:620995 original size:33 final size:32
Alignment explanation
Indices: 620953--621020 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
620943 TGTTATAAGC
* *
620953 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTAGG-TGTATCGATA
*
620986 CAATGTATCGATACATATTATGTGTATCGATA
1 CAATGTATCGATACATATTAGGTGTATCGATA
621018 CAA
1 CAA
621021 ATTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTAGGTGTATCGATA
Found at i:621099 original size:20 final size:21
Alignment explanation
Indices: 621052--621106 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
621042 GCCAATGACC
**
621052 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
621073 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
621093 TGTATCGATACATT
1 TGTATCGATACATT
621107 GTATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:621838 original size:12 final size:12
Alignment explanation
Indices: 621821--621860 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 12
621811 GTTAGTTTTA
621821 AAATCTCTTAAG
1 AAATCTCTTAAG
621833 AAATCTCTTAAGAG
1 AAATCTCTT-A-AG
621847 AAAATCTCTTAAG
1 -AAATCTCTTAAG
621860 A
1 A
621861 GAAAATCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 3 0.12
15 9 0.36
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (12 bp):
AAATCTCTTAAG
Found at i:621853 original size:15 final size:15
Alignment explanation
Indices: 621820--621867 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
621810 CGTTAGTTTT
621820 AAAATCTCTT-A-AG
1 AAAATCTCTTAAGAG
621833 -AAATCTCTTAAGAG
1 AAAATCTCTTAAGAG
621847 AAAATCTCTTAAGAG
1 AAAATCTCTTAAGAG
621862 AAAATC
1 AAAATC
621868 CAAAATGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 9 0.28
13 1 0.03
14 2 0.06
15 20 0.62
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.27
Consensus pattern (15 bp):
AAAATCTCTTAAGAG
Found at i:622623 original size:13 final size:13
Alignment explanation
Indices: 622605--622630 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
622595 ACATAAGTGC
622605 TGTATCGATACAA
1 TGTATCGATACAA
622618 TGTATCGATACAA
1 TGTATCGATACAA
622631 AGCTACCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:625627 original size:21 final size:21
Alignment explanation
Indices: 625603--625679 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
625593 AATTTATCCA
*
625603 AATGTATCAATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
625624 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
625645 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
625666 AATGTATCGATACA
1 AATGTATCGATACA
625680 GGGTCCCAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
20 3 0.06
21 47 0.94
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:625739 original size:19 final size:19
Alignment explanation
Indices: 625715--625782 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
625705 AATTCAACAA
625715 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
625734 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
625749 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
625766 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
625783 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:625754 original size:13 final size:13
Alignment explanation
Indices: 625736--625760 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
625726 ACATAAGTTT
625736 TGTATCGATACAA
1 TGTATCGATACAA
625749 TGTATCGATACA
1 TGTATCGATACA
625761 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:625758 original size:32 final size:32
Alignment explanation
Indices: 625717--625779 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
625707 TTCAACAATT
*
625717 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
625749 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
625780 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:625840 original size:13 final size:13
Alignment explanation
Indices: 625822--625847 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
625812 CATTTTTCTG
625822 TGTATCGATACAT
1 TGTATCGATACAT
625835 TGTATCGATACAT
1 TGTATCGATACAT
625848 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:625844 original size:33 final size:33
Alignment explanation
Indices: 625802--625868 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
625792 GCCAAGGAAA
***
625802 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
625835 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
625868 T
1 T
625869 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:628325 original size:54 final size:51
Alignment explanation
Indices: 628192--628325 Score: 144
Period size: 51 Copynumber: 2.6 Consensus size: 51
628182 TTGAGTTTCT
* * * *
628192 CAATTCTCCACAATCAGGGATATTCCAACACCGATTTTATTTTCAAAACAC
1 CAATTCTTCACAATCGGGGATACTCCAACACCGATTTTATTTCCAAAACAC
* * * * *
628243 TAATT-TTCTATAATCGAGGATACTCCAACTCCGATTTTATTTCCAAAAAATAC
1 CAATTCTTC-ACAATCGGGGATACTCCAACACCGATTTTATTTCC--AAAACAC
628296 CAATTTCTTCACAATCGGGGATACTCCAAC
1 CAA-TTCTTCACAATCGGGGATACTCCAAC
628326 CCCGTTAATC
Statistics
Matches: 66, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
50 2 0.03
51 33 0.50
53 8 0.12
54 20 0.30
55 3 0.05
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.31
Consensus pattern (51 bp):
CAATTCTTCACAATCGGGGATACTCCAACACCGATTTTATTTCCAAAACAC
Found at i:628426 original size:79 final size:79
Alignment explanation
Indices: 628336--628698 Score: 401
Period size: 78 Copynumber: 4.6 Consensus size: 79
628326 CCCGTTAATC
* *
628336 ATTGGGGATACTCCAACCCCGTTATTTCCGAGGGAACACTCCAACCCCGGCTTTATTCCCAAAAT
1 ATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGGCTTTATTCCCAAAAT
*
628401 ACTGATTTCTCATA
66 ACTGATTTCTCACA
* * * * ** * * * *
628415 ATTGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAATCCTGATTTTTTTTCTAATCA
1 ATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGGCTTTATTCCCAA-AA
628480 T-C-GATTTCTCACA
65 TACTGATTTCTCACA
** * *
628493 ACCGGGGATACTCCAGCCCCGTTATTTCCGAGGGGACACTCCAACCCCGGCTTTATTCCCAAAAT
1 ATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGGCTTTATTCCCAAAAT
*
628558 ACTGATTTCTCATA
66 ACTGATTTCTCACA
* * * * * ** * *
628572 ATTGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAATCCC-GATTTTTTTTCTAATT
1 ATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGGCTTTATTCCCAAAAT
628636 A-TCGATTTCTCACA
66 ACT-GATTTCTCACA
* * * *
628650 ACTGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 ATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCG
628699 TTATTATCTC
Statistics
Matches: 230, Mismatches: 49, Indels: 10
0.80 0.17 0.03
Matches are distributed among these distances:
77 3 0.01
78 122 0.53
79 103 0.45
80 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.31
Consensus pattern (79 bp):
ATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGGCTTTATTCCCAAAAT
ACTGATTTCTCACA
Found at i:628713 original size:157 final size:157
Alignment explanation
Indices: 628338--628698 Score: 641
Period size: 157 Copynumber: 2.3 Consensus size: 157
628328 CGTTAATCAT
*
628338 TGGGGATACTCCAACCCCGTTATTTCCGAGGGAACACTCCAACCCCGGCTTTATTCCCAAAATAC
1 TGGGGATACTCCAGCCCCGTTATTTCCGAGGGAACACTCCAACCCCGGCTTTATTCCCAAAATAC
*
628403 TGATTTCTCATAATTGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAATCCTGATTT
66 TGATTTCTCATAATTGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAATCCCGATTT
628468 TTTTTCTAATCATCGATTTCTCACAAC
131 TTTTTCTAATCATCGATTTCTCACAAC
* *
628495 CGGGGATACTCCAGCCCCGTTATTTCCGAGGGGACACTCCAACCCCGGCTTTATTCCCAAAATAC
1 TGGGGATACTCCAGCCCCGTTATTTCCGAGGGAACACTCCAACCCCGGCTTTATTCCCAAAATAC
* *
628560 TGATTTCTCATAATTGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAATCCCGATTT
66 TGATTTCTCATAATTGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAATCCCGATTT
*
628625 TTTTTCTAATTATCGATTTCTCACAAC
131 TTTTTCTAATCATCGATTTCTCACAAC
* *
628652 TGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 TGGGGATACTCCAGCCCCGTTATTTCCGAGGGAACACTCCAACCCCG
628699 TTATTATCTC
Statistics
Matches: 193, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 193 1.00
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.30
Consensus pattern (157 bp):
TGGGGATACTCCAGCCCCGTTATTTCCGAGGGAACACTCCAACCCCGGCTTTATTCCCAAAATAC
TGATTTCTCATAATTGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAATCCCGATTT
TTTTTCTAATCATCGATTTCTCACAAC
Found at i:641070 original size:1 final size:1
Alignment explanation
Indices: 641064--641119 Score: 58
Period size: 1 Copynumber: 56.0 Consensus size: 1
641054 CTTTCTCTTC
* * * * * *
641064 AAAAAAAGAAAAAAAACAAAAACAAAAAAACAAAACAACAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
641120 TCTGCTTAAG
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:641077 original size:8 final size:8
Alignment explanation
Indices: 641063--641116 Score: 67
Period size: 8 Copynumber: 7.0 Consensus size: 8
641053 ACTTTCTCTT
641063 CAAAAAAA
1 CAAAAAAA
*
641071 GAAAAAAA
1 CAAAAAAA
*
641079 -ACAAAAA
1 CAAAAAAA
641086 CAAAAAAA
1 CAAAAAAA
*
641094 CAAAACAA
1 CAAAAAAA
641102 CAAAAAAA
1 CAAAAAAA
641110 -AAAAAAA
1 CAAAAAAA
641117 AAATCTGCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
7 13 0.32
8 27 0.68
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:641090 original size:22 final size:20
Alignment explanation
Indices: 641064--641119 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
641054 CTTTCTCTTC
*
641064 AAAAAAAGAAAAAAAACAAA
1 AAAAAAAAAAAAAAAACAAA
*
641084 AACAAAAAAACAAAACAACAAA
1 AA-AAAAAAA-AAAAAAACAAA
641106 AAAAAAAAAAAAAA
1 AAAAAAAAAAAAAA
641120 TCTGCTTAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 6 0.19
21 13 0.42
22 12 0.39
ACGTcount: A:0.89, C:0.09, G:0.02, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAACAAA
Found at i:642304 original size:55 final size:54
Alignment explanation
Indices: 642084--642773 Score: 795
Period size: 55 Copynumber: 12.4 Consensus size: 54
642074 TCCTTCCGCT
* *
642084 TTTCAGTCCTCAAAGAGTAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCAC
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
* * * *
642138 TTCCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACCCGAGTTGGTGGCAC
1 TT-TCAGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCAC
* * *
642198 CTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-C
* * * *
642259 TTTCAGTCCCCAAAGAGCAGGACCCCTTTCGAAGCCCACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
642313 TTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCAC
1 TTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCAC
* * *
642368 TTCCCAGTCCTCAGAGAGCAGGACGCCTTCACCTTTCAAAGCCCACACAAGTTGGTGGCAT
1 TT-TCAGTCCTCAAAGAGCAGGA------CACCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
642429 TTTCCAGTCCTCAAAGAGCAAGACACCTTTCAAAGCCCACACAAGTTGGTGGCACC
1 TTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-C
* * * *
642485 TTTCAGTCCCCAAAGAGCAGGACCCCTTTCGAAGCCCACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
642539 TTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGG---
1 TTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
* * *
642591 ---CA-TCCTCAAAGAGCAAGACACCTTTCAAAGCCTACACAAGTTGGTGGCAT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
642641 TTTCTAGTCCTCAAAGAGCAGGACATCTCTT-AAAGCCCACACAAGTTGGTGGCACC
1 TTTC-AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-C
* * *
642697 TTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCTCACACGAGTTGGTGGCAC
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
*
642751 TTTTTAGTCCTCAAAGAGCAGGA
1 -TTTCAGTCCTCAAAGAGCAGGA
642774 TACACTTTAT
Statistics
Matches: 550, Mismatches: 48, Indels: 75
0.82 0.07 0.11
Matches are distributed among these distances:
47 43 0.08
48 2 0.00
53 1 0.00
54 12 0.02
55 338 0.61
56 14 0.03
59 20 0.04
60 46 0.08
61 69 0.13
64 4 0.01
65 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.22
Consensus pattern (54 bp):
TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCAC
Found at i:642446 original size:171 final size:167
Alignment explanation
Indices: 642082--642773 Score: 842
Period size: 171 Copynumber: 4.1 Consensus size: 167
642072 TCTCCTTCCG
* * *
642082 CTTTTCAGTCCTCAAAGAGTAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTC
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTC
* * *
642147 CTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACCCGAGTTGGTGGCACCTT-CAGTCCTCAA
66 CTCAAAGAGCAGGACACC---TC--TTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAA
* * *
642211 AGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
126 AGAGCAGGACGC----ACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
642257 CCTTTCAGTCCCCAAAGAGCAGGACCCCTTTCGAAGCCCACACAAGTTGGTGGCATTTTCCAGTC
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTC
*
642322 CTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAGTCCTCAGAGAG
66 CTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTT-CCAGTCCTCAAAGAG
642386 CAGGACGCCTTCACCTTTCAAAGCCCACACAAGTTGGTGGCA
130 CAGGACG----CACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
642428 -TTTTCCAGTCCTCAAAGAGCAAGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAG
1 CTTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCCAG
* * * **
642491 TCCCCAAAGAGCAGGACCCCT-TTCGAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAG
64 TCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAG
642555 AGCAGGA--CACCTTTCAAAGCCCACACAAGTTGGTGG--
128 AGCAGGACGCACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
642591 -----CA-TCCTCAAAGAGCAAGACACCTTTCAAAGCCTACACAAGTTGGTGGCATTTTCTAGTC
1 CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTC
* *
642650 CTCAAAGAGCAGGACATCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGC
66 CTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGC
* *
642715 AGGACG--CCTTTCAAAGCTCACACGAGTTGGTGGCA
131 AGGACGCACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
642750 CTTTTTAGTCCTCAAAGAGCAGGA
1 CTTTTCAGTCCTCAAAGAGCAGGA
642774 TACACTTTAT
Statistics
Matches: 455, Mismatches: 40, Indels: 54
0.83 0.07 0.10
Matches are distributed among these distances:
156 3 0.01
157 134 0.29
158 4 0.01
164 1 0.00
165 44 0.10
169 3 0.01
170 28 0.06
171 156 0.34
172 7 0.02
175 75 0.16
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (167 bp):
CTTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCCAGTC
CTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGC
AGGACGCACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:643486 original size:13 final size:13
Alignment explanation
Indices: 643468--643506 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
643458 GCTAAGGAAA
643468 TGTATCGATACAT
1 TGTATCGATACAT
643481 TGTATCGATACAT
1 TGTATCGATACAT
643494 TGTATCGATACAT
1 TGTATCGATACAT
643507 GGATCTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:646039 original size:28 final size:27
Alignment explanation
Indices: 645972--646044 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
645962 CTTCACAATC
*
645972 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
645999 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
*
646027 GGGGACACTCCAACCCCG
1 GGGGATACTCCAACCCCG
646045 GCTTTATTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:646093 original size:79 final size:78
Alignment explanation
Indices: 645998--646358 Score: 386
Period size: 78 Copynumber: 4.6 Consensus size: 78
645988 CGTTAATCAT
*
645998 CGGGGATACTCCAACCCCGTTA-TTTCTGAGGGGACACTCCAACCCCGGCTTTATTCCCAA-AAT
1 CGGGGATACTCCAACCCCGTTATTTTC-GAGGGGACACTCCAACCCCGACTTTATTCCCAATAAT
* *
646061 ACTGATTTCTCATAAT
65 -C-GATTTCTCACAAC
* * * * * * * * *
646077 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCTGATTTTTTTTCTAATCATC
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGACTTTATTCCCAATAATC
646142 GATTTCTCACAAC
66 GATTTCTCACAAC
* * * *
646155 CGGGGATACTCCAGCCCCGTTATTTCCGAGGGGACATTCCAACCCCGGCTTTATTCCCAA-AATA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGACTTTATTCCCAATAAT-
* *
646219 CTGATTTCTCATAAT
65 C-GATTTCTCACAAC
* * * * * * * * *
646234 TGAGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTCTAATCATC
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGACTTTATTCCCAATAATC
646299 GATTTCTCACAAC
66 GATTTCTCACAAC
* * *
646312 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCG
646359 TTATTATCTC
Statistics
Matches: 228, Mismatches: 49, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
77 2 0.01
78 111 0.49
79 107 0.47
80 8 0.04
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCGACTTTATTCCCAATAATC
GATTTCTCACAAC
Found at i:646225 original size:157 final size:157
Alignment explanation
Indices: 645998--646358 Score: 650
Period size: 157 Copynumber: 2.3 Consensus size: 157
645988 CGTTAATCAT
* *
645998 CGGGGATACTCCAACCCCGTTATTTCTGAGGGGACACTCCAACCCCGGCTTTATTCCCAAAATAC
1 CGGGGATACTCCAGCCCCGTTATTTCCGAGGGGACACTCCAACCCCGGCTTTATTCCCAAAATAC
* *
646063 TGATTTCTCATAATTGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCTGATTT
66 TGATTTCTCATAATTGAGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTT
646128 TTTTTCTAATCATCGATTTCTCACAAC
131 TTTTTCTAATCATCGATTTCTCACAAC
*
646155 CGGGGATACTCCAGCCCCGTTATTTCCGAGGGGACATTCCAACCCCGGCTTTATTCCCAAAATAC
1 CGGGGATACTCCAGCCCCGTTATTTCCGAGGGGACACTCCAACCCCGGCTTTATTCCCAAAATAC
646220 TGATTTCTCATAATTGAGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTT
66 TGATTTCTCATAATTGAGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTT
646285 TTTTTCTAATCATCGATTTCTCACAAC
131 TTTTTCTAATCATCGATTTCTCACAAC
* * *
646312 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAGCCCCGTTATTTCCGAGGGGACACTCCAACCCCG
646359 TTATTATCTC
Statistics
Matches: 195, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 195 1.00
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (157 bp):
CGGGGATACTCCAGCCCCGTTATTTCCGAGGGGACACTCCAACCCCGGCTTTATTCCCAAAATAC
TGATTTCTCATAATTGAGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTT
TTTTTCTAATCATCGATTTCTCACAAC
Found at i:658434 original size:39 final size:41
Alignment explanation
Indices: 658382--658477 Score: 97
Period size: 39 Copynumber: 2.4 Consensus size: 41
658372 TAAAAGTAGT
* ** *
658382 ATTTATTAGTATATTACATTTTGATATATAATTATAAA-TAA
1 ATTTA-TAATATATTACATTTAAAAATATAATTATAAATTAA
* * **
658423 ATTT-TAATATATTATATTTAAAAATATATTTATAAATTTT
1 ATTTATAATATATTACATTTAAAAATATAATTATAAATTAA
658463 ATTTATAATATATTA
1 ATTTATAATATATTA
658478 AATTAAATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
39 26 0.58
40 5 0.11
41 14 0.31
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (41 bp):
ATTTATAATATATTACATTTAAAAATATAATTATAAATTAA
Found at i:658444 original size:21 final size:21
Alignment explanation
Indices: 658420--658526 Score: 56
Period size: 20 Copynumber: 5.3 Consensus size: 21
658410 TAATTATAAA
658420 TAAATTTTAATATATTATATT
1 TAAATTTTAATATATTATATT
658441 TAAA----AATATATTTATAAATT
1 TAAATTTTAATATA-TTAT--ATT
* *
658461 T-TATTTATAATATATTA-AAT
1 TAAATTT-TAATATATTATATT
658481 TAAA-TTTAA-A-A-TATACTT
1 TAAATTTTAATATATTATA-TT
658499 TAAATATTTCAA-ATATTATATT
1 TAAAT-TTT-AATATATTATATT
658521 TAAATT
1 TAAATT
658527 ATTTGTTTCA
Statistics
Matches: 66, Mismatches: 4, Indels: 32
0.65 0.04 0.31
Matches are distributed among these distances:
16 2 0.03
17 8 0.12
18 10 0.15
19 4 0.06
20 12 0.18
21 9 0.14
22 8 0.12
23 7 0.11
24 6 0.09
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATTTTAATATATTATATT
Found at i:658452 original size:12 final size:11
Alignment explanation
Indices: 658435--658524 Score: 60
Period size: 11 Copynumber: 7.9 Consensus size: 11
658425 TTTAATATAT
658435 TATATTTAAAAA
1 TATATTT-AAAA
658447 TATATTTATAAA
1 TATATTTA-AAA
* *
658459 TTTTATTTATAA
1 -TATATTTAAAA
*
658471 TATA-TTAAAT
1 TATATTTAAAA
*
658481 TAAATTTAAAA
1 TATATTTAAAA
658492 TATACTTT-AAA
1 TATA-TTTAAAA
*
658503 TAT-TTCAAATA
1 TATATTTAAA-A
658514 TTATATTTAAA
1 -TATATTTAAA
658525 TTATTTGTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 15
0.71 0.12 0.18
Matches are distributed among these distances:
9 2 0.03
10 9 0.15
11 19 0.32
12 18 0.30
13 12 0.20
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (11 bp):
TATATTTAAAA
Found at i:663435 original size:17 final size:18
Alignment explanation
Indices: 663394--663437 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
663384 ATTTTTGTCT
*
663394 TAAATAAATATTTATTCA
1 TAAATAAATATATATTCA
*
663412 -AATTAAATATATA-TCA
1 TAAATAAATATATATTCA
663428 TAAATAAATA
1 TAAATAAATA
663438 ATACAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAATAAATATATATTCA
Found at i:665491 original size:19 final size:19
Alignment explanation
Indices: 665444--665501 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
665434 CTGCCAGTTT
**
665444 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
665465 CTATGTATCGATACAATGAA
1 C-ATGTATCGATACAATGAA
665485 CATGTATCGATACAATG
1 CATGTATCGATACAATG
665502 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.47
20 3 0.09
21 1 0.03
22 14 0.41
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:665504 original size:13 final size:13
Alignment explanation
Indices: 665486--665538 Score: 106
Period size: 13 Copynumber: 4.1 Consensus size: 13
665476 TACAATGAAC
665486 ATGTATCGATACA
1 ATGTATCGATACA
665499 ATGTATCGATACA
1 ATGTATCGATACA
665512 ATGTATCGATACA
1 ATGTATCGATACA
665525 ATGTATCGATACA
1 ATGTATCGATACA
665538 A
1 A
665539 AGCAGCATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:669517 original size:52 final size:52
Alignment explanation
Indices: 669369--669497 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
669359 CAAAATATGA
669369 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
669421 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
669473 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
669498 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:669524 original size:13 final size:13
Alignment explanation
Indices: 669506--669530 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
669496 CAAAGATCAG
669506 TGTATCGATACAA
1 TGTATCGATACAA
669519 TGTATCGATACA
1 TGTATCGATACA
669531 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:669609 original size:32 final size:32
Alignment explanation
Indices: 669568--669635 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
669558 GGCAGTAGCT
669568 TACATTGTATCGATACAAAACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
*
669600 TACATTGTATCGATACAACACTTATGTATCGA
1 TACATTGTATCGATACAAAACTTATGTATCGA
669632 TACA
1 TACA
669636 ACACTTTATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
TACATTGTATCGATACAAAACTTATGTATCGA
Found at i:669610 original size:13 final size:13
Alignment explanation
Indices: 669592--669616 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
669582 ACAAAACTTA
669592 TGTATCGATACAT
1 TGTATCGATACAT
669605 TGTATCGATACA
1 TGTATCGATACA
669617 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:669646 original size:20 final size:19
Alignment explanation
Indices: 669573--669656 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
669563 TAGCTTACAT
*
669573 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
669592 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
669605 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
669624 TGTATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
669644 TGTATCGATACAA
1 TGTATCGATACAA
669657 ATCGTTGAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 13
0.80 0.01 0.18
Matches are distributed among these distances:
13 9 0.16
14 1 0.02
16 5 0.09
18 1 0.02
19 25 0.44
20 16 0.28
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:671955 original size:58 final size:58
Alignment explanation
Indices: 671850--672007 Score: 176
Period size: 58 Copynumber: 2.7 Consensus size: 58
671840 TTCCAACATT
* * ** *
671850 AGGGA-TTGTGATACAATTTTTTGAAT-TTGATGTCATTTAGGGCATTTTCCATGATCG
1 AGGGACTT-TGATATAATTTTATGAATGTTGGGGTCATTTAGGTCATTTTCCATGATCG
* * *
671907 AGGGACTTTGATGTAATTTTATGAATGTTGGGGTCATTTAGGTCATTTTTCATGATCT
1 AGGGACTTTGATATAATTTTATGAATGTTGGGGTCATTTAGGTCATTTTCCATGATCG
* * * * *
671965 AGGGATTTTTATATAATTTTATGAAAGTTAGGGTCACTTAGGT
1 AGGGACTTTGATATAATTTTATGAATGTTGGGGTCATTTAGGT
672008 TTTTTTTAAT
Statistics
Matches: 85, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
57 20 0.24
58 65 0.76
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.43
Consensus pattern (58 bp):
AGGGACTTTGATATAATTTTATGAATGTTGGGGTCATTTAGGTCATTTTCCATGATCG
Found at i:672014 original size:58 final size:58
Alignment explanation
Indices: 671881--672031 Score: 176
Period size: 58 Copynumber: 2.6 Consensus size: 58
671871 TGAATTTGAT
* * * * * * * *
671881 GTCATTTAGGGCATTTTCCATGATCGAGGGACTTTGATGTAATTTTATGAATGTTGGG
1 GTCACTTAGGTCATTTTTCATGATCTAGGGATTTTGATATAATTTTATGAAAGTTAGG
* *
671939 GTCATTTAGGTCATTTTTCATGATCTAGGGATTTTTATATAATTTTATGAAAGTTAGG
1 GTCACTTAGGTCATTTTTCATGATCTAGGGATTTTGATATAATTTTATGAAAGTTAGG
** * *
671997 GTCACTTAGGTTTTTTTTAATGATCTAAGGATTTT
1 GTCACTTAGGTCATTTTTCATGATCTAGGGATTTT
672032 CATGCTACTT
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 80 1.00
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.45
Consensus pattern (58 bp):
GTCACTTAGGTCATTTTTCATGATCTAGGGATTTTGATATAATTTTATGAAAGTTAGG
Found at i:676568 original size:66 final size:66
Alignment explanation
Indices: 676487--676926 Score: 404
Period size: 66 Copynumber: 6.7 Consensus size: 66
676477 ACGACACTTG
* * * *
676487 GTCAACCTCATTTTGACTTAGGTTTTGCCCTAGTCGCCTATTAGTTGACATGATGGTTTTGCTCT
1 GTCAACCTCCTTTTGACTTAGGTTTTGCCCTAGTCACCTTTTAGTTGACATGATGGTTTTGCCCT
676552 A
66 A
* * * *
676553 GTCAACCTCCTTTTGACTTAGGTTTTGCCCAAGTCACCTATTAGTTGACATGATGATTCTGCCCT
1 GTCAACCTCCTTTTGACTTAGGTTTTGCCCTAGTCACCTTTTAGTTGACATGATGGTTTTGCCCT
676618 A
66 A
*** * * * * * *
676619 GTCAACCT-CTTTTCGACTTAGGTTTCATCTTTGTCACCTTTTAGTTGACATGATGATTTCGTCT
1 GTCAACCTCCTTTT-GACTTAGGTTTTGCCCTAGTCACCTTTTAGTTGACATGATGGTTTTGCCC
*
676683 TG
65 TA
* * * * *
676685 GTCAACCTCTTTTTGACTTACGTTTT-CACCTTAGTCACCTTTTAATTGACATAATGCTTTTGCC
1 GTCAACCTCCTTTTGACTTAGGTTTTGC-CC-TAGTCACCTTTTAGTTGACATGATGGTTTTGCC
*
676749 CTG
64 CTA
** ** * *
676752 GTCAACCT-CTTCTCAACTTAGGTTTTGCCCTAGTCACCTTTTAGTTGATGTGATTGTTTCGCCC
1 GTCAACCTCCTT-TTGACTTAGGTTTTGCCCTAGTCACCTTTTAGTTGACATGATGGTTTTGCCC
676816 TA
65 TA
* * ** * * ** * *
676818 GTTAACCT-CTTCTTAACTTAGGTTTCACCCTAGTCACCTATTAGTTAATGTGAAGG-TTTGGCC
1 GTCAACCTCCTT-TTGACTTAGGTTTTGCCCTAGTCACCTTTTAGTTGACATGATGGTTTTGCCC
*
676881 TT
65 TA
* *
676883 GTTCAACCTCCTTTTAACTTAGGTTTCGCCCTAGTCACCTTTTA
1 G-TCAACCTCCTTTTGACTTAGGTTTTGCCCTAGTCACCTTTTA
676927 ATTAACTTTA
Statistics
Matches: 310, Mismatches: 56, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
65 12 0.04
66 240 0.77
67 57 0.18
68 1 0.00
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.41
Consensus pattern (66 bp):
GTCAACCTCCTTTTGACTTAGGTTTTGCCCTAGTCACCTTTTAGTTGACATGATGGTTTTGCCCT
A
Found at i:676588 original size:32 final size:32
Alignment explanation
Indices: 676487--676643 Score: 126
Period size: 34 Copynumber: 4.8 Consensus size: 32
676477 ACGACACTTG
676487 GTCAACCTCATTTTGACTTAGGTTTTGCCCTA
1 GTCAACCTCATTTTGACTTAGGTTTTGCCCTA
* * *
676519 GTC-GCCT-ATTAGTTGACATGATGGTTTTGCTCTA
1 GTCAACCTCATT--TTGAC-TTA-GGTTTTGCCCTA
* *
676553 GTCAACCTCCTTTTGACTTAGGTTTTGCCCAA
1 GTCAACCTCATTTTGACTTAGGTTTTGCCCTA
* * *
676585 GTC-ACCT-ATTAGTTGACATGATGATTCTGCCCTA
1 GTCAACCTCATT--TTGAC-TTA-GGTTTTGCCCTA
676619 GTCAACCTC-TTTTCGACTTAGGTTT
1 GTCAACCTCATTTT-GACTTAGGTTT
676644 CATCTTTGTC
Statistics
Matches: 96, Mismatches: 16, Indels: 26
0.70 0.12 0.19
Matches are distributed among these distances:
30 5 0.05
31 7 0.07
32 29 0.30
33 10 0.10
34 34 0.35
35 9 0.09
36 2 0.02
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (32 bp):
GTCAACCTCATTTTGACTTAGGTTTTGCCCTA
Found at i:676827 original size:199 final size:196
Alignment explanation
Indices: 676483--676929 Score: 495
Period size: 199 Copynumber: 2.2 Consensus size: 196
676473 AGTTACGACA
* * * * *
676483 CTTGGTCAACCTCATTTTGACTTAGGTTTTGCCCTAGTCGCCTATTAGTTGACATGATGGTTTTG
1 CTTGGTCAACCTCATTTTGACTTA-GTTTT-CCCTAGTCACCTTTTAATTGACATAATGCTTTTG
* **
676548 CTCTAGTCAACCTCCTTTTGACTTAGGTTTTGCCCAAGTCACCTATTAGTTGACATGATGATTCT
64 CCCTAGTCAACCTCCTTTCAACTTAGGTTTTGCCCAAGTCACCTATTAGTTGACATGATGATTCT
* * * * * * *
676613 GCCCTAGTCAACCTCTT-TTCGACTTAGGTTTCATCTTTGTCACCTTTTAGTTGACATGATGATT
129 GCCCTAGTCAACCTCTTCTT-AACTTAGGTTTCACCCTAGTCACCTATTAGTTAACATGAAGATT
*
676677 TCGT
193 TCGC
*
676681 CTTGGTCAACCTCTTTTTGACTTACGTTTTCACCTTAGTCACCTTTTAATTGACATAATGCTTTT
1 CTTGGTCAACCTCATTTTGACTTA-GTTTTC-CC-TAGTCACCTTTTAATTGACATAATGCTTTT
* * * ** *
676746 GCCCTGGTCAACCT-CTTCTCAACTTAGGTTTTGCCCTAGTCACCTTTTAGTTGATGTGATTGTT
63 GCCCTAGTCAACCTCCTT-TCAACTTAGGTTTTGCCCAAGTCACCTATTAGTTGACATGA-TGAT
* ** *
676810 TC-GCCCTAGTTAACCTCTTCTTAACTTAGGTTTCACCCTAGTCACCTATTAGTTAATGTGAAGG
126 TCTGCCCTAGTCAACCTCTTCTTAACTTAGGTTTCACCCTAGTCACCTATTAGTTAACATGAAGA
*
676874 TTTGGC
191 TTTCGC
* * * *
676880 CTTGTTCAACCTCCTTTTAACTTAGGTTTCGCCCTAGTCACCTTTTAATT
1 CTTGGTCAACCTCATTTTGACTTA-GTTT-TCCCTAGTCACCTTTTAATT
676930 AACTTTATGT
Statistics
Matches: 209, Mismatches: 34, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
197 1 0.00
198 49 0.23
199 151 0.72
200 8 0.04
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.41
Consensus pattern (196 bp):
CTTGGTCAACCTCATTTTGACTTAGTTTTCCCTAGTCACCTTTTAATTGACATAATGCTTTTGCC
CTAGTCAACCTCCTTTCAACTTAGGTTTTGCCCAAGTCACCTATTAGTTGACATGATGATTCTGC
CCTAGTCAACCTCTTCTTAACTTAGGTTTCACCCTAGTCACCTATTAGTTAACATGAAGATTTCG
C
Found at i:676932 original size:32 final size:32
Alignment explanation
Indices: 676766--676934 Score: 98
Period size: 32 Copynumber: 5.2 Consensus size: 32
676756 ACCTCTTCTC
* *
676766 AACTTAGGTTTTGCCCTAGTCACCTTTTAGTT
1 AACTTAGGTTTCGCCCTAGTCACCTCTTAGTT
* * * *
676798 GA-TGTGATTGTTTCGCCCTAGTTAACCTCTT-CTT
1 AACT-T-A-GGTTTCGCCCTAG-TCACCTCTTAGTT
* *
676832 AACTTAGGTTTCACCCTAGTCACCTATTAGTT
1 AACTTAGGTTTCGCCCTAGTCACCTCTTAGTT
* *
676864 AA-TGTGAAGGTTT-GGCCTTGTTCAACCTCCTT--TT
1 AACT-T--AGGTTTCGCCCTAG-TC-ACCT-CTTAGTT
* *
676898 AACTTAGGTTTCGCCCTAGTCACCTTTTAATT
1 AACTTAGGTTTCGCCCTAGTCACCTCTTAGTT
676930 AACTT
1 AACTT
676935 TATGTTTTCG
Statistics
Matches: 102, Mismatches: 19, Indels: 32
0.67 0.12 0.21
Matches are distributed among these distances:
30 2 0.02
31 13 0.13
32 33 0.32
33 11 0.11
34 28 0.27
35 13 0.13
36 2 0.02
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.41
Consensus pattern (32 bp):
AACTTAGGTTTCGCCCTAGTCACCTCTTAGTT
Found at i:676963 original size:265 final size:264
Alignment explanation
Indices: 676485--676986 Score: 600
Period size: 265 Copynumber: 1.9 Consensus size: 264
676475 TTACGACACT
** * * *
676485 TGGTCAACCTCATTTTGACTTAGGTTTTGCCCTAGTCGCCTATTAGTTGACATGATGGTTTTGCT
1 TGGTCAACCTCATTTCAACTTAGGTTTTGCCCTAGTCACCTATTAGTTGACATGATGGTTTCGCC
* ** * *
676550 CTAGTCAACCTCCTTTTGACTTAGGTTTTGCCCAAGTCACCTATTAGTTGACATGATGATTCTGC
66 CTAGTCAACCTCCTTTTAACTTAGGTTTCACCCAAGTCACCTATTAGTTAACATGAAGATTCTGC
* * * * * *
676615 CCTAGTCAACCTCTTTTCGACTTAGGTTTCATCTTTGTCACCTTTTAGTTGACATGATGATTTCG
131 CCTAGTCAACCTCTTTTCAACTTAGGTTTCACCCTAGTCACCTTTTAATTAACATGATGATTTCG
*
676680 TCTTGGTCAACCTCTTTTTGACTTACGTTTTCACCTTAGTCACCTTTTAATTGACATAATGCTTT
196 TCTTGGTCAACCTCTTTTTGACTTACGTCTT-ACCTTAGTCACCTTTTAATTGACATAATGCTTT
676745 TGCCC
260 TGCCC
* ** *
676750 TGGTCAACCTC-TTCTCAACTTAGGTTTTGCCCTAGTCACCTTTTAGTTGATGTGATTGTTTCGC
1 TGGTCAACCTCATT-TCAACTTAGGTTTTGCCCTAGTCACCTATTAGTTGACATGATGGTTTCGC
* * ** *
676814 CCTAGTTAACCT-CTTCTTAACTTAGGTTTCACCCTAGTCACCTATTAGTTAATGTGAAGGTT-T
65 CCTAGTCAACCTCCTT-TTAACTTAGGTTTCACCCAAGTCACCTATTAGTTAACATGAAGATTCT
* * * * * *
676877 GGCCTTGTTCAACCTCCTTTT-AACTTAGGTTTCGCCCTAGTCACCTTTTAATTAACTTTATGTT
129 GCCCTAG-TCAACCT-CTTTTCAACTTAGGTTTCACCCTAGTCACCTTTTAATTAACATGATGAT
* * *
676941 TTCG-CTTTGGTCAACTTCTTTTTGACTTAGGTCTTACTTTAGTCAC
192 TTCGTC-TTGGTCAACCTCTTTTTGACTTACGTCTTACCTTAGTCAC
676987 TATGTTAACC
Statistics
Matches: 197, Mismatches: 35, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
264 22 0.11
265 170 0.86
266 5 0.03
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (264 bp):
TGGTCAACCTCATTTCAACTTAGGTTTTGCCCTAGTCACCTATTAGTTGACATGATGGTTTCGCC
CTAGTCAACCTCCTTTTAACTTAGGTTTCACCCAAGTCACCTATTAGTTAACATGAAGATTCTGC
CCTAGTCAACCTCTTTTCAACTTAGGTTTCACCCTAGTCACCTTTTAATTAACATGATGATTTCG
TCTTGGTCAACCTCTTTTTGACTTACGTCTTACCTTAGTCACCTTTTAATTGACATAATGCTTTT
GCCC
Found at i:676986 original size:132 final size:132
Alignment explanation
Indices: 676483--676972 Score: 454
Period size: 132 Copynumber: 3.7 Consensus size: 132
676473 AGTTACGACA
* * * *
676483 CTTGGTCAACCTCATTTTGACTTAGGTTTTGCCCTAGTCGCCTATTAGTTGACATGATGGTTTT-
1 CTTGGTCAACCTC-TTTTAACTTAGGTTTCGCCCTAGTCACCTTTTAGTTGACATGAT-GTTTTC
* * * *
676547 GCTCTAGTCAACCTCCTTTTGACTTAGGTTTT-GCCCAAGTCACCTATTAGTTGACATGATGATT
64 GCTCTAGTCAACCTCTTTTTGACTTAGGTTTTCACCCTAGTCACCTATTAGTTGACATGAAGATT
676611 CT-GC
129 -TGGC
* * * ** * * *
676615 CCTAGTCAACCTCTTTTCGACTTAGGTTTCATCTTTGTCACCTTTTAGTTGACATGATGATTTCG
1 CTTGGTCAACCTCTTTT-AACTTAGGTTTCGCCCTAGTCACCTTTTAGTTGACATGATGTTTTCG
* * * * * *
676680 -TCTTGGTCAACCTCTTTTTGACTTACGTTTTCACCTTAGTCACCTTTTAATTGACAT-AATGCT
65 CTC-TAGTCAACCTCTTTTTGACTTAGGTTTTCACCCTAGTCACCTATTAGTTGACATGAA-GAT
*
676743 TTTGC
128 TTGGC
* * * **
676748 CCTGGTCAACCTCTTCTCAACTTAGGTTTTGCCCTAGTCACCTTTTAGTTGATGTGAT-TGTTTC
1 CTTGGTCAACCTCTT-TTAACTTAGGTTTCGCCCTAGTCACCTTTTAGTTGACATGATGT-TTTC
* * * * * ** *
676812 GCCCTAGTTAACCTCTTCTTAACTTAGG-TTTCACCCTAGTCACCTATTAGTTAATGTGAAGGTT
64 GCTCTAGTCAACCTCTTTTTGACTTAGGTTTTCACCCTAGTCACCTATTAGTTGACATGAAGATT
676876 TGGC
129 TGGC
* * * * *
676880 CTTGTTCAACCTCCTTTTAACTTAGGTTTCGCCCTAGTCACCTTTTAATTAACTTTATGTTTTCG
1 CTTGGTCAACCT-CTTTTAACTTAGGTTTCGCCCTAGTCACCTTTTAGTTGACATGATGTTTTCG
* * *
676945 CTTTGGTCAACTTCTTTTTGACTTAGGT
65 CTCTAGTCAACCTCTTTTTGACTTAGGT
676973 CTTACTTTAG
Statistics
Matches: 284, Mismatches: 61, Indels: 25
0.77 0.16 0.07
Matches are distributed among these distances:
131 10 0.04
132 171 0.60
133 101 0.36
134 2 0.01
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (132 bp):
CTTGGTCAACCTCTTTTAACTTAGGTTTCGCCCTAGTCACCTTTTAGTTGACATGATGTTTTCGC
TCTAGTCAACCTCTTTTTGACTTAGGTTTTCACCCTAGTCACCTATTAGTTGACATGAAGATTTG
GC
Found at i:680181 original size:29 final size:29
Alignment explanation
Indices: 680121--680279 Score: 156
Period size: 29 Copynumber: 5.4 Consensus size: 29
680111 AAAGTTTGTG
* *
680121 ATTTTGAAAAGTTTCAAGGGTCGAAGTGTA
1 ATTTTGAAAAGTTT-AAAGGTCAAAGTGTA
* *
680151 ATTTTGAAAAATTTAAAGGTCAAAATGTA
1 ATTTTGAAAAGTTTAAAGGTCAAAGTGTA
* * * *
680180 ATGTTGAAAAGTTCAAAGGTTAAAGCGTA
1 ATTTTGAAAAGTTTAAAGGTCAAAGTGTA
* * * ** *
680209 ACTTAGAAAAGTTCAGGGGTCAAAGAGTA
1 ATTTTGAAAAGTTTAAAGGTCAAAGTGTA
* * *
680238 ATTTTAAAAAGTTTAGAGGTCAATGTGTA
1 ATTTTGAAAAGTTTAAAGGTCAAAGTGTA
680267 ATTTTGAAAAGTT
1 ATTTTGAAAAGTT
680280 GAGGAACTTA
Statistics
Matches: 104, Mismatches: 25, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
29 91 0.88
30 13 0.12
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (29 bp):
ATTTTGAAAAGTTTAAAGGTCAAAGTGTA
Found at i:683320 original size:27 final size:27
Alignment explanation
Indices: 683290--683410 Score: 118
Period size: 27 Copynumber: 4.5 Consensus size: 27
683280 GTCTAAAAGC
*
683290 GAGTCATGGACTTAAAAGGGTACCACA
1 GAGTTATGGACTTAAAAGGGTACCACA
* *
683317 GAGTCATAGACTTAAAAGGGTACCAC-
1 GAGTTATGGACTTAAAAGGGTACCACA
* * * **
683343 GAAGTTGTGGGCTTAAAAGGGTGCCATG
1 G-AGTTATGGACTTAAAAGGGTACCACA
* * *
683371 GAGTTATGGGCTTAAAAGGGTGCCATA
1 GAGTTATGGACTTAAAAGGGTACCACA
*
683398 GAGTTGTGGACTT
1 GAGTTATGGACTT
683411 TGAAAAAAAG
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
26 1 0.01
27 79 0.98
28 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (27 bp):
GAGTTATGGACTTAAAAGGGTACCACA
Found at i:684202 original size:17 final size:17
Alignment explanation
Indices: 684180--684216 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
684170 TTCTCCCGAA
*
684180 AACTGGAAGGCATTTTC
1 AACTGGAAGGCATTGTC
684197 AACTGGAAGGCATTGTC
1 AACTGGAAGGCATTGTC
684214 AAC
1 AAC
684217 AATCTAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (17 bp):
AACTGGAAGGCATTGTC
Found at i:684898 original size:8 final size:8
Alignment explanation
Indices: 684885--684955 Score: 74
Period size: 8 Copynumber: 8.9 Consensus size: 8
684875 TTCAGACCCC
684885 TTTTTTTG
1 TTTTTTTG
684893 TTTTTTTG
1 TTTTTTTG
*
684901 TTGTTTT-
1 TTTTTTTG
* *
684908 TTGTTAT-
1 TTTTTTTG
684915 TTTTTTTG
1 TTTTTTTG
*
684923 TTTTTTTAA
1 TTTTTTT-G
684932 TTTTTTTG
1 TTTTTTTG
684940 TTTTTTTG
1 TTTTTTTG
684948 TATTTTTT
1 T-TTTTTT
684956 TGCAGAGGAC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
7 11 0.20
8 30 0.56
9 13 0.24
ACGTcount: A:0.06, C:0.00, G:0.10, T:0.85
Consensus pattern (8 bp):
TTTTTTTG
Found at i:684907 original size:10 final size:9
Alignment explanation
Indices: 684885--684957 Score: 69
Period size: 10 Copynumber: 7.9 Consensus size: 9
684875 TTCAGACCCC
684885 TTTTTTTG-
1 TTTTTTTGT
684893 TTTTTTTGT
1 TTTTTTTGT
684902 TGTTTTTTGT
1 T-TTTTTTGT
*
684912 TATTTTTTTT
1 T-TTTTTTGT
**
684922 GTTTTTTTAA
1 -TTTTTTTGT
684932 TTTTTTTG-
1 TTTTTTTGT
684940 TTTTTTTGT
1 TTTTTTTGT
684949 ATTTTTTTG
1 -TTTTTTTG
684958 CAGAGGACAC
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
8 16 0.29
9 8 0.15
10 30 0.55
11 1 0.02
ACGTcount: A:0.05, C:0.00, G:0.11, T:0.84
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:684907 original size:18 final size:18
Alignment explanation
Indices: 684886--684957 Score: 74
Period size: 18 Copynumber: 3.8 Consensus size: 18
684876 TCAGACCCCT
*
684886 TTTTTTGTTTTTTTGTTG
1 TTTTTTATTTTTTTGTTG
* *
684904 TTTTTTGTTATTTTTTTTG
1 TTTTTTATT-TTTTTGTTG
684923 TTTTTTTAATTTTTTTGTT-
1 -TTTTTT-ATTTTTTTGTTG
684942 TTTTTGTATTTTTTTG
1 TTTTT-TATTTTTTTG
684958 CAGAGGACAC
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 23 0.49
19 9 0.19
20 13 0.28
21 2 0.04
ACGTcount: A:0.06, C:0.00, G:0.11, T:0.83
Consensus pattern (18 bp):
TTTTTTATTTTTTTGTTG
Done.