Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 94 of 125
Found at i:28266201 original size:117 final size:116
Alignment explanation
Indices: 28266054--28266360 Score: 332
Period size: 117 Copynumber: 2.6 Consensus size: 116
28266044 CACCGTCAGT
* * * *
28266054 TCAAAATAACATTGCAGTGTTTACAGTGTCACTACTAAGTCAGTATAGCTTCGCAGTGTTTACAG
1 TCAATATAACTTTGCAGTGTTTACAATGTCACTACTAAGTCAGTATAGCTTCGCAATGTTTACAG
* *
28266119 TGTCACTACTAAG-TCAGTATAGCTTCGTAGTGTTTGCAGTGTCACTACTGGC
66 TGTCACTACTAAGTTCAGTATAGCTTCGCAGTGTTTACAGTGTCACTACT--C
* ** * * * *
28266171 TCAGTATAGTTTTGCGGTGTTTACAATGTCACTGCTAAGTCAATATAGCTTCGTAATGTTTACAG
1 TCAATATAACTTTGCAGTGTTTACAATGTCACTACTAAGTCAGTATAGCTTCGCAATGTTTACAG
* ** * *
28266236 TGTCACTGC-CGGTTCAGTATAGTTTCGCAGTGTTTACAGTGTCACTACTT
66 TGTCACTACTAAGTTCAGTATAGCTTCGCAGTGTTTACAGTGTCACTACTC
* ** * * * *
28266286 TCAATATAACTTCGCAGTGTTTACAATGTCACTA-TCGGTTTAGTATAGTTTTGCATTGTTTACA
1 TCAATATAACTTTGCAGTGTTTACAATGTCACTACTAAG-TCAGTATAGCTTCGCAATGTTTACA
*
28266350 ATGTCACTACT
65 GTGTCACTACT
28266361 TACTTAGTAT
Statistics
Matches: 153, Mismatches: 34, Indels: 7
0.79 0.18 0.04
Matches are distributed among these distances:
114 2 0.01
115 55 0.36
116 1 0.01
117 95 0.62
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (116 bp):
TCAATATAACTTTGCAGTGTTTACAATGTCACTACTAAGTCAGTATAGCTTCGCAATGTTTACAG
TGTCACTACTAAGTTCAGTATAGCTTCGCAGTGTTTACAGTGTCACTACTC
Found at i:28266370 original size:39 final size:39
Alignment explanation
Indices: 28266067--28266360 Score: 292
Period size: 39 Copynumber: 7.6 Consensus size: 39
28266057 AAATAACATT
28266067 GCAGTGTTTACAGTGTCACTACTAAGTCAGTATAGCTTC
1 GCAGTGTTTACAGTGTCACTACTAAGTCAGTATAGCTTC
28266106 GCAGTGTTTACAGTGTCACTACTAAGTCAGTATAGCTTC
1 GCAGTGTTTACAGTGTCACTACTAAGTCAGTATAGCTTC
* * * * *
28266145 GTAGTGTTTGCAGTGTCACTACT-GGCTCAGTATAGTTTT
1 GCAGTGTTTACAGTGTCACTACTAAG-TCAGTATAGCTTC
* * * *
28266184 GCGGTGTTTACAATGTCACTGCTAAGTCAATATAGCTTC
1 GCAGTGTTTACAGTGTCACTACTAAGTCAGTATAGCTTC
* * * ** *
28266223 GTAATGTTTACAGTGTCACTGC-CGGTTCAGTATAGTTTC
1 GCAGTGTTTACAGTGTCACTACTAAG-TCAGTATAGCTTC
* * *
28266262 GCAGTGTTTACAGTGTCACTACT--TTCAATATAACTTC
1 GCAGTGTTTACAGTGTCACTACTAAGTCAGTATAGCTTC
* ** * * *
28266299 GCAGTGTTTACAATGTCACTA-TCGGTTTAGTATAGTTTT
1 GCAGTGTTTACAGTGTCACTACTAAG-TCAGTATAGCTTC
* *
28266338 GCATTGTTTACAATGTCACTACT
1 GCAGTGTTTACAGTGTCACTACT
28266361 TACTTAGTAT
Statistics
Matches: 210, Mismatches: 37, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
36 1 0.00
37 30 0.14
38 2 0.01
39 175 0.83
40 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (39 bp):
GCAGTGTTTACAGTGTCACTACTAAGTCAGTATAGCTTC
Found at i:28266547 original size:12 final size:12
Alignment explanation
Indices: 28266530--28266554 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28266520 AAATGGTATG
28266530 GGCACACGGTCT
1 GGCACACGGTCT
28266542 GGCACACGGTCT
1 GGCACACGGTCT
28266554 G
1 G
28266555 AACTCTCAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (12 bp):
GGCACACGGTCT
Found at i:28272869 original size:22 final size:22
Alignment explanation
Indices: 28272811--28272871 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
28272801 TTAAAATAAT
* * *
28272811 AAAATTTTAATTTAATTTTTTA
1 AAAATTATAATTTAATATTATA
* *
28272833 AAAATTATATTTTTACTATTATA
1 AAAATTATA-ATTTAATATTATA
28272856 AAAATTATAATTTAAT
1 AAAATTATAATTTAAT
28272872 TTTGATCCCT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
AAAATTATAATTTAATATTATA
Found at i:28273458 original size:16 final size:18
Alignment explanation
Indices: 28273430--28273463 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28273420 ATGAAAATGG
28273430 TTTTAATTAAAAT-ATTA
1 TTTTAATTAAAATGATTA
28273447 TTTTAA-TAAAATGATTA
1 TTTTAATTAAAATGATTA
28273464 AATTTCACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTTAATTAAAATGATTA
Found at i:28278327 original size:20 final size:21
Alignment explanation
Indices: 28278302--28278350 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
28278292 ATACAGAATA
28278302 GAATAAAA-CATTGTCGAAGC
1 GAATAAAAGCATTGTCGAAGC
*
28278322 GAATAACAAAGTATTGTCGAAGC
1 GAAT-A-AAAGCATTGTCGAAGC
*
28278345 GGATAA
1 GAATAA
28278351 TAGTAAGCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 4 0.17
21 2 0.08
22 4 0.17
23 14 0.58
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.20
Consensus pattern (21 bp):
GAATAAAAGCATTGTCGAAGC
Found at i:28280048 original size:23 final size:25
Alignment explanation
Indices: 28279999--28280052 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
28279989 CAAAAAATAT
* *
28279999 AAATTCAAAAATTAACAAAGACGAA
1 AAATTAAAAAATTAACAAAGACAAA
*
28280024 AAATTAAAAAATT-A-AAGGACAAA
1 AAATTAAAAAATTAACAAAGACAAA
28280047 AAATTA
1 AAATTA
28280053 TTATGCAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 13 0.50
24 1 0.04
25 12 0.46
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.19
Consensus pattern (25 bp):
AAATTAAAAAATTAACAAAGACAAA
Found at i:28286278 original size:20 final size:20
Alignment explanation
Indices: 28286241--28286278 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28286231 CAATTTGTTC
*
28286241 GAAAAATAAAAGTGTACATA
1 GAAAAATAAAAGTCTACATA
28286261 GAAAAA-AAAAGTACTACA
1 GAAAAATAAAAGT-CTACA
28286279 CTTAGGGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.63, C:0.08, G:0.13, T:0.16
Consensus pattern (20 bp):
GAAAAATAAAAGTCTACATA
Found at i:28289538 original size:17 final size:18
Alignment explanation
Indices: 28289506--28289539 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28289496 AATTTCTATC
28289506 CAATTTATACCCTAATTT
1 CAATTTATACCCTAATTT
*
28289524 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
28289540 AACTCATTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (18 bp):
CAATTTATACCCTAATTT
Found at i:28295331 original size:59 final size:59
Alignment explanation
Indices: 28295143--28295578 Score: 434
Period size: 58 Copynumber: 7.4 Consensus size: 59
28295133 CTTTGGATGC
* * *
28295143 TCGAGGGTAAAACGGTAATTTTTGGTGAAATCGGGGTTAGAAAATGGGATTTTGGTAAGT
1 TCGAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTA-AAAATGGGATTTTGGAAAGT
* * ** * * * *
28295203 TTGGGGGTAAAATGGTGGTTTTTGGTTTAAATC-GAGGTTAAATATAGGATTTTGGAGAGTT
1 TCGAGGGTAAAATGGTAATTTTTGG-TGAAATCAG-GGTTAAAAATGGGATTTTGGAAAG-T
* * *** *
28295264 TC-AAGGTAAAATGATAATTTTCAATGAAATCAGGGTTAAAAATGGGATTTTGAAAAGT
1 TCGAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAGT
* * * *
28295322 TCGAGGGTAAAATGGTAATTTTTGGTAAAATCGGGGATAAAAATAGGATTTTGGAAAGT
1 TCGAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAGT
* * * * * *
28295381 T-TAGGGTAAAATGGTAATATTTGGTAAAATCAGGGTTAAAAGTGGAATTTTAGAAAGT
1 TCGAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAGT
** * * *
28295439 TCG-GGGGGAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAGATTTTAGAAAGT
1 TCGAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAGT
* * * *
28295497 TCGAGGGTAAAATGGTGATTTTTGGTG-AATCAGGGTTGAAAATAGAATTTTGGAAAGT
1 TCGAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAGT
* * *
28295555 TTGGGGGTCAAAAT-ATAATTTTTG
1 TCGAGGGT-AAAATGGTAATTTTTG
28295579 AAAAGTTTAA
Statistics
Matches: 304, Mismatches: 64, Indels: 18
0.79 0.17 0.05
Matches are distributed among these distances:
58 142 0.47
59 98 0.32
60 51 0.17
61 13 0.04
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.33
Consensus pattern (59 bp):
TCGAGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAGT
Found at i:28295516 original size:29 final size:29
Alignment explanation
Indices: 28295302--28295518 Score: 104
Period size: 29 Copynumber: 7.5 Consensus size: 29
28295292 ATCAGGGTTA
* *
28295302 AAAATGG-GATTTTGAAAAGTTCGAGGGT
1 AAAATGGTAATTTTGGAAAGTTCGAGGGT
*
28295330 AAAATGGTAATTTTTGGTAAA-ATCG-GGGAT
1 AAAATGGTAA-TTTTGG-AAAGTTCGAGGG-T
*
28295360 AAAAATAGG--ATTTTGGAAAGTT-TAGGGT
1 -AAAAT-GGTAATTTTGGAAAGTTCGAGGGT
*
28295388 AAAATGGTAATATTTGGTAAA-ATC-AGGGTT
1 AAAATGGTAAT-TTTGG-AAAGTTCGAGGG-T
* *
28295418 AAAAGTGG-AATTTTAGAAAGTTCG-GGGG
1 AAAA-TGGTAATTTTGGAAAGTTCGAGGGT
*
28295446 GAAATGGTAATTTTTGGTGAAA--TCG-GGGTT
1 AAAATGGTAA-TTTT-G-GAAAGTTCGAGGG-T
*
28295476 AAAAAT-G-AGATTTTAGAAAGTTCGAGGGT
1 -AAAATGGTA-ATTTTGGAAAGTTCGAGGGT
*
28295505 AAAATGGTGATTTT
1 AAAATGGTAATTTT
28295519 TGGTGAATCA
Statistics
Matches: 145, Mismatches: 15, Indels: 57
0.67 0.07 0.26
Matches are distributed among these distances:
26 2 0.01
27 12 0.08
28 26 0.18
29 58 0.40
30 26 0.18
31 19 0.13
32 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAAAGTTCGAGGGT
Found at i:28296366 original size:18 final size:18
Alignment explanation
Indices: 28296339--28296373 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28296329 TTTTGTTTTA
28296339 TTTTTAAACCAGATCTGG
1 TTTTTAAACCAGATCTGG
*
28296357 TTTTTGAACCAGATCTG
1 TTTTTAAACCAGATCTG
28296374 AGCATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (18 bp):
TTTTTAAACCAGATCTGG
Found at i:28299522 original size:14 final size:14
Alignment explanation
Indices: 28299503--28299529 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28299493 AAATCGAATT
28299503 TCGAATTATTCGAA
1 TCGAATTATTCGAA
28299517 TCGAATTATTCGA
1 TCGAATTATTCGA
28299530 GTTATTCGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (14 bp):
TCGAATTATTCGAA
Found at i:28299528 original size:23 final size:21
Alignment explanation
Indices: 28299494--28299538 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
28299484 ATTCAAAAAA
28299494 AATCGAATTTCGAATTATTCG
1 AATCGAATTTCGAATTATTCG
*
28299515 AATCGAATTATTCGAGTTATTCG
1 AATCGAA-T-TTCGAATTATTCG
28299538 A
1 A
28299539 GTTAAACGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 1 0.05
23 13 0.62
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (21 bp):
AATCGAATTTCGAATTATTCG
Found at i:28299866 original size:58 final size:57
Alignment explanation
Indices: 28299775--28299950 Score: 246
Period size: 58 Copynumber: 3.0 Consensus size: 57
28299765 ACTCATCAAC
* * *
28299775 AAACTAAATCCAAATATTTTTAAACGCACATATAATTTCATTATTCAAAAACACTCAT
1 AAACTAAA-CCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAAAACACTCAT
28299833 AAACTAAACCTAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAAAACACTCAT
1 AAACTAAACC-AAATATTTTTAAACCCAAATATAATTTCATTCTTCAAAAACACTCAT
* * * *
28299891 AAATTAAGCCCAAATATTTTTAAACCCAAATATAATTTTATTCCT-AAATAACACTCAT
1 AAACTAA-ACCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAA-AACACTCAT
28299949 AA
1 AA
28299951 GCAACTCCTT
Statistics
Matches: 108, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
57 5 0.05
58 101 0.94
59 2 0.02
ACGTcount: A:0.47, C:0.19, G:0.01, T:0.33
Consensus pattern (57 bp):
AAACTAAACCAAATATTTTTAAACCCAAATATAATTTCATTCTTCAAAAACACTCAT
Found at i:28301542 original size:17 final size:18
Alignment explanation
Indices: 28301508--28301543 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28301498 TGAATTTCTA
28301508 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
28301526 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
28301543 T
1 T
28301544 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:28307872 original size:90 final size:88
Alignment explanation
Indices: 28307692--28307877 Score: 234
Period size: 90 Copynumber: 2.1 Consensus size: 88
28307682 AATATTTAAT
* *
28307692 AAATTTAGGTA-CAAAATTGAATCTAAAAAAAATTTAGGTACCAAATTAGGAAAAAAATATCAAG
1 AAATTTAAGTATC-AAATTGAATCTAAAAAAAACTTAGGTACCAAATTAGG-AAAAAATATCAAG
* **
28307756 TTTAGTTACTAAATTGGGTTTAAAA
64 TTTAGGTACTAAATTGGGTCCAAAA
*
28307781 AAAGTTTAAGTATCAAATTGAATCTAAAAAAAAAGCTTAGGTACTAAATTAGG-AAAAATATCAA
1 AAA-TTTAAGTATCAAATTGAATCT-AAAAAAAA-CTTAGGTACCAAATTAGGAAAAAATATCAA
*
28307845 GTTTAGGTA-TCAAATTGGGTCCCAAA
63 GTTTAGGTACT-AAATTGGGTCCAAAA
28307871 AAATTTA
1 AAATTTA
28307878 GATATTAAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
89 8 0.09
90 52 0.61
91 9 0.11
92 16 0.19
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (88 bp):
AAATTTAAGTATCAAATTGAATCTAAAAAAAACTTAGGTACCAAATTAGGAAAAAATATCAAGTT
TAGGTACTAAATTGGGTCCAAAA
Found at i:28311168 original size:39 final size:39
Alignment explanation
Indices: 28311121--28311198 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
28311111 TTTATGTGAA
* * *
28311121 AATAATCACATTTATTTGGTCTCCATTTCTAGTTATGAT
1 AATAATCACATATATTTGCTCTCCATTTCTACTTATGAT
*
28311160 AATAATCACGTATATTTGCTCTCCATTTCTACTTATGAT
1 AATAATCACATATATTTGCTCTCCATTTCTACTTATGAT
28311199 GGCATATGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.45
Consensus pattern (39 bp):
AATAATCACATATATTTGCTCTCCATTTCTACTTATGAT
Found at i:28315887 original size:19 final size:19
Alignment explanation
Indices: 28315863--28315904 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
28315853 TTTTCTATTA
28315863 AAAATCATAAAAATTATAT
1 AAAATCATAAAAATTATAT
*
28315882 AAAATCATAAAATTTATAT
1 AAAATCATAAAAATTATAT
28315901 AAAA
1 AAAA
28315905 ATATTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAATCATAAAAATTATAT
Found at i:28315935 original size:18 final size:18
Alignment explanation
Indices: 28315914--28315961 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
28315904 AATATTTAAT
28315914 AATTACAAAAAT-TATGAA
1 AATTACAAAAATATA-GAA
28315932 AATTATC-AAAATATAGAA
1 AATTA-CAAAAATATAGAA
28315950 AATTACAGAAAA
1 AATTACA-AAAA
28315962 ATTCAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 1 0.04
18 18 0.69
19 7 0.27
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.25
Consensus pattern (18 bp):
AATTACAAAAATATAGAA
Found at i:28316004 original size:18 final size:17
Alignment explanation
Indices: 28315983--28316017 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28315973 TAAGATTACT
28315983 CAAAAAGATAGAAAATTA
1 CAAAAAGATA-AAAATTA
*
28316001 CAAAAATATAAAAATTA
1 CAAAAAGATAAAAATTA
28316018 TATAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.20
Consensus pattern (17 bp):
CAAAAAGATAAAAATTA
Found at i:28316014 original size:27 final size:27
Alignment explanation
Indices: 28315984--28316042 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
28315974 AAGATTACTC
28315984 AAAAAGATAGAAAATTACA-AAAATATA
1 AAAAAGATAGAAAATTACACAAAA-ATA
** *
28316011 AAAATTATATAAAATTACACAAAAATA
1 AAAAAGATAGAAAATTACACAAAAATA
28316038 AAAAA
1 AAAAA
28316043 TATTTACAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.20
Consensus pattern (27 bp):
AAAAAGATAGAAAATTACACAAAAATA
Found at i:28316534 original size:32 final size:31
Alignment explanation
Indices: 28316498--28316579 Score: 74
Period size: 36 Copynumber: 2.4 Consensus size: 31
28316488 TTTTTCCATT
**
28316498 TATAATAATTTTTTAATTTATTTCTATATTTC
1 TATAATAATTTTTTAATTT-TTTAAATATTTC
28316530 TATAATTTTATAGTTTTTTAATTTTTTAAATATTTC
1 TATAA---TA-A-TTTTTTAATTTTTTAAATATTTC
*
28316566 TTTATATAATTTTT
1 TATA-ATAATTTTT
28316580 ATTTTTAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
32 10 0.24
33 1 0.02
34 2 0.05
35 2 0.05
36 14 0.34
37 12 0.29
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (31 bp):
TATAATAATTTTTTAATTTTTTAAATATTTC
Found at i:28316944 original size:25 final size:24
Alignment explanation
Indices: 28316911--28316957 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
28316901 GGGGGAATTT
* *
28316911 TTATTTTATTTGATATTAATATCA
1 TTATTTTATTTAATATAAATATCA
28316935 TTATATTTATTTAATATAAATAT
1 TTAT-TTTATTTAATATAAATAT
28316958 AAAATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATTTTATTTAATATAAATATCA
Found at i:28322204 original size:12 final size:12
Alignment explanation
Indices: 28322187--28322213 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28322177 TGTCTAGACC
28322187 TAAAAATATGAT
1 TAAAAATATGAT
28322199 TAAAAATATGAT
1 TAAAAATATGAT
28322211 TAA
1 TAA
28322214 GCTTGCAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (12 bp):
TAAAAATATGAT
Found at i:28324518 original size:28 final size:29
Alignment explanation
Indices: 28324454--28324518 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 29
28324444 ATTTAGATTT
* *
28324454 ATTTGATTCTTTTTAATAGTATAGGGATTA
1 ATTTGATTCTATTTAATAG-ATAGGGACTA
*
28324484 AATTGATTC-ATTTAATA-ATAGGGGACTA
1 ATTTGATTCTATTTAATAGATA-GGGACTA
28324512 ATTTGAT
1 ATTTGAT
28324519 ACAACCCCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 3 0.10
28 12 0.40
29 7 0.23
30 8 0.27
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.45
Consensus pattern (29 bp):
ATTTGATTCTATTTAATAGATAGGGACTA
Found at i:28325310 original size:18 final size:18
Alignment explanation
Indices: 28325289--28325335 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
28325279 TTATAAAACA
28325289 ATATTATATTAATTATAT
1 ATATTATATTAATTATAT
*
28325307 ATATTAAATAATAATTATAT
1 ATATT--ATATTAATTATAT
28325327 AT-TTATATT
1 ATATTATATT
28325336 GTCTTAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 4 0.16
18 5 0.20
19 2 0.08
20 14 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTATATTAATTATAT
Found at i:28326929 original size:24 final size:24
Alignment explanation
Indices: 28326878--28326923 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
28326868 AGGTTGTAAC
28326878 AAATAAATTATACTAATAAATAAA
1 AAATAAATTATACTAATAAATAAA
*
28326902 AAATATATTATACTAATAAATA
1 AAATAAATTATACTAATAAATA
28326924 CTAAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATAAA
Found at i:28327275 original size:27 final size:29
Alignment explanation
Indices: 28327201--28327276 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 29
28327191 TAAAGCTAAT
28327201 TATA-ATTTTAATGTATTAA-AAGTATACA
1 TATATATTTTAATGTATTAATAAG-ATACA
*
28327229 -ATTATATTTTTAT-TATTTAATAA-A-ACA
1 TA-TATATTTTAATGTA-TTAATAAGATACA
28327256 TATATATTTTAATGTATTAAT
1 TATATATTTTAATGTATTAAT
28327277 GTTAAAATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
27 19 0.47
28 8 0.20
29 11 0.28
30 2 0.05
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (29 bp):
TATATATTTTAATGTATTAATAAGATACA
Found at i:28327601 original size:23 final size:25
Alignment explanation
Indices: 28327574--28327629 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
28327564 AATAAATACT
*
28327574 AATAATATTACAAA-TA-TATTTAA
1 AATAATATTACAAATTAGTAGTTAA
28327597 AATAA-ATT-CAAATTAGTAGTTAA
1 AATAATATTACAAATTAGTAGTTAA
*
28327620 ATTAATATTA
1 AATAATATTA
28327630 ATTCAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 4 0.15
22 5 0.19
23 15 0.56
24 3 0.11
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (25 bp):
AATAATATTACAAATTAGTAGTTAA
Found at i:28330267 original size:7 final size:7
Alignment explanation
Indices: 28330252--28330291 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
28330242 AATTAAATAA
28330252 AACCCTG
1 AACCCTG
*
28330259 AACCATG
1 AACCCTG
28330266 AACCCTG
1 AACCCTG
*
28330273 AACTCTG
1 AACCCTG
*
28330280 AACCTTG
1 AACCCTG
28330287 AACCC
1 AACCC
28330292 GTCAAATATC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.33, C:0.38, G:0.12, T:0.17
Consensus pattern (7 bp):
AACCCTG
Found at i:28331995 original size:15 final size:15
Alignment explanation
Indices: 28331975--28332045 Score: 51
Period size: 15 Copynumber: 4.9 Consensus size: 15
28331965 AGATATTTTT
28331975 TTTAATATTTTAATA
1 TTTAATATTTTAATA
* *
28331990 TTTAATATTAT-ATT
1 TTTAATATTTTAATA
* *
28332004 TTTCTATTTTTTAA-A
1 TTT-AATATTTTAATA
28332019 TTTAA-A-TTTAATA
1 TTTAATATTTTAATA
**
28332032 TTTTTTATTTTAAT
1 TTTAATATTTTAAT
28332046 TGTCACATGA
Statistics
Matches: 41, Mismatches: 10, Indels: 10
0.67 0.16 0.16
Matches are distributed among these distances:
12 5 0.12
13 4 0.10
14 7 0.17
15 24 0.59
16 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTAATATTTTAATA
Found at i:28332021 original size:29 final size:30
Alignment explanation
Indices: 28331973--28332042 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
28331963 AAAGATATTT
* *
28331973 TTTTTAATATTTTAATATTT-AATATT-ATA
1 TTTTTTATTTTTTAATATTTAAAT-TTAATA
28332002 TTTTTCTATTTTTTAA-ATTTAAATTTAATA
1 TTTTT-TATTTTTTAATATTTAAATTTAATA
28332032 TTTTTTATTTT
1 TTTTTTATTTT
28332043 AATTGTCACA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (30 bp):
TTTTTTATTTTTTAATATTTAAATTTAATA
Found at i:28343469 original size:17 final size:16
Alignment explanation
Indices: 28343434--28343466 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28343424 ATGATTTTAA
28343434 TGTTAAAGAACTAAAT
1 TGTTAAAGAACTAAAT
28343450 TGTTAAAAGAA-TAAAT
1 TGTT-AAAGAACTAAAT
28343466 T
1 T
28343467 TGTAAGGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (16 bp):
TGTTAAAGAACTAAAT
Found at i:28344547 original size:52 final size:52
Alignment explanation
Indices: 28344450--28344684 Score: 334
Period size: 52 Copynumber: 4.6 Consensus size: 52
28344440 TAAATGCAAA
*
28344450 AGGTCCGATGACTATGTGTCA---T-AGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
* *
28344498 AGGTCCGATGACTATGTGTCATTGTGAGTATATGAATCCTTTATAGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
* * * * *
28344550 AGGTCCGATGACTATATGTTATCGTGAGTATATGAATCCTTTACGAATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
* * *
28344602 AGGTCCAATGACTATGTGTCATCGTGAGCATATGAATCCTTTTTGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
*
28344654 AGGTCCGATGACTATGTGTTATCGTGAGTAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTAT
28344685 CAAATGAGAA
Statistics
Matches: 163, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
48 21 0.13
51 1 0.01
52 141 0.87
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
Found at i:28349610 original size:31 final size:31
Alignment explanation
Indices: 28349574--28349633 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
28349564 AACAATTCGA
* *
28349574 CTCTTTCGAAAAGATTGATGGTCAAATTTCT
1 CTCTTTCGAAAAGATTGAAGGGCAAATTTCT
* *
28349605 CTCTTTTGAAAAGGTTGAAGGGCAAATTT
1 CTCTTTCGAAAAGATTGAAGGGCAAATTT
28349634 AACTCTAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (31 bp):
CTCTTTCGAAAAGATTGAAGGGCAAATTTCT
Found at i:28349920 original size:9 final size:9
Alignment explanation
Indices: 28349908--28349941 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
28349898 AAAAAAAACC
28349908 TTTAAAATA
1 TTTAAAATA
*
28349917 TTTAAAACA
1 TTTAAAATA
*
28349926 TTAAAAATA
1 TTTAAAATA
28349935 TTTAAAA
1 TTTAAAA
28349942 AATCCAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (9 bp):
TTTAAAATA
Found at i:28349950 original size:19 final size:19
Alignment explanation
Indices: 28349911--28349984 Score: 80
Period size: 19 Copynumber: 3.8 Consensus size: 19
28349901 AAAAACCTTT
* *
28349911 AAAATATTTAAAACAT-TA
1 AAAATATTTAAAAAATCCA
28349929 AAAATATTTAAAAAATCCA
1 AAAATATTTAAAAAATCCA
28349948 AAAAT-TATTAAAAAATCCA
1 AAAATAT-TTAAAAAATCCA
*
28349967 AGAAATTATTTAAGAAAT
1 A-AAA-TATTTAAAAAAT
28349985 TATTAAAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
18 16 0.33
19 19 0.40
20 3 0.06
21 9 0.19
22 1 0.02
ACGTcount: A:0.61, C:0.07, G:0.03, T:0.30
Consensus pattern (19 bp):
AAAATATTTAAAAAATCCA
Found at i:28349951 original size:20 final size:20
Alignment explanation
Indices: 28349911--28349984 Score: 73
Period size: 18 Copynumber: 3.8 Consensus size: 20
28349901 AAAAACCTTT
* *
28349911 AAAATATTTAAAACAT--TA
1 AAAATATTTAAAAAATCCAA
28349929 AAAATATTTAAAAAATCCAA
1 AAAATATTTAAAAAATCCAA
*
28349949 AAATTA-TTAAAAAATCCAA
1 AAAATATTTAAAAAATCCAA
* *
28349968 GAAATTATTTAAGAAAT
1 -AAAATATTTAAAAAAT
28349985 TATTAAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
18 15 0.31
19 13 0.27
20 12 0.25
21 8 0.17
ACGTcount: A:0.61, C:0.07, G:0.03, T:0.30
Consensus pattern (20 bp):
AAAATATTTAAAAAATCCAA
Found at i:28350034 original size:19 final size:19
Alignment explanation
Indices: 28349989--28350035 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
28349979 AGAAATTATT
*
28349989 AAAATAAAAAATAATTATA
1 AAAATAAAAAATAAATATA
**
28350008 AAGTTAAAAAA-ACAATATA
1 AAAATAAAAAATA-AATATA
28350027 AAAATAAAA
1 AAAATAAAA
28350036 TTTACTAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
AAAATAAAAAATAAATATA
Found at i:28350087 original size:17 final size:19
Alignment explanation
Indices: 28350057--28350091 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
28350047 TATTAATATA
28350057 TTAATATATATTATAAATT
1 TTAATATATATTATAAATT
28350076 TTAATAT-T-TTATAAAT
1 TTAATATATATTATAAAT
28350092 CACATATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTAATATATATTATAAATT
Found at i:28360137 original size:30 final size:31
Alignment explanation
Indices: 28360070--28360140 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
28360060 GATTTCATTT
*
28360070 ACTGTTTTGTCACTTTTTGATAATGTTAGTG
1 ACTGTTTTGTCACATTTTGATAATGTTAGTG
*
28360101 ACTGTTTTGTCACATTTT-CTAA-GTTGAGTG
1 ACTGTTTTGTCACATTTTGATAATGTT-AGTG
*
28360131 ATTGTTTTGT
1 ACTGTTTTGT
28360141 TAAATGTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.08
30 16 0.44
31 17 0.47
ACGTcount: A:0.18, C:0.10, G:0.20, T:0.52
Consensus pattern (31 bp):
ACTGTTTTGTCACATTTTGATAATGTTAGTG
Found at i:28363062 original size:23 final size:24
Alignment explanation
Indices: 28363035--28363080 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
28363025 TTTATCTTTA
*
28363035 AATATAACTATAAAA-TAAAAAAT
1 AATATAACTAAAAAATTAAAAAAT
28363058 AATATAACTAAAAAATTAAAAAA
1 AATATAACTAAAAAATTAAAAAA
28363081 AAAACTGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (24 bp):
AATATAACTAAAAAATTAAAAAAT
Found at i:28363367 original size:21 final size:19
Alignment explanation
Indices: 28363315--28363369 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 19
28363305 CAATTAAATT
28363315 AATATTATAAAATATAATATA
1 AATA-TATAAAATA-AATATA
*
28363336 AAT-TTTAAAATAAATACATA
1 AATATATAAAATAAAT--ATA
28363356 AATATATAAAATAA
1 AATATATAAAATAA
28363370 TATCATGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 3 0.10
19 8 0.28
20 6 0.21
21 12 0.41
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
AATATATAAAATAAATATA
Found at i:28365822 original size:28 final size:27
Alignment explanation
Indices: 28365791--28365853 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
28365781 CATCAATACA
* **
28365791 TAAATGTAGGGAAAAGGCATTAAAACAT
1 TAAATGCAGGGAAAAACCATT-AAACAT
* *
28365819 TAAATGCATGGAAAAACCATTAAGCAT
1 TAAATGCAGGGAAAAACCATTAAACAT
28365846 TAAATGCA
1 TAAATGCA
28365854 AAGAAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 13 0.43
28 17 0.57
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.22
Consensus pattern (27 bp):
TAAATGCAGGGAAAAACCATTAAACAT
Found at i:28371889 original size:20 final size:17
Alignment explanation
Indices: 28371855--28371929 Score: 55
Period size: 17 Copynumber: 4.2 Consensus size: 17
28371845 AAAACATTCC
*
28371855 AAATTA-AAAATTAATA
1 AAATTATAATATTAATA
28371871 TAAATATAATAATATTAATA
1 -AAAT-T-ATAATATTAATA
*
28371891 AAATTTTAATATTAATAGA
1 AAATTATAATATTAAT--A
*
28371910 AACATTA-AACATTAATA
1 AA-ATTATAATATTAATA
28371927 AAA
1 AAA
28371930 AAAACAAAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
16 1 0.02
17 17 0.35
18 2 0.04
19 16 0.33
20 12 0.25
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (17 bp):
AAATTATAATATTAATA
Found at i:28380260 original size:43 final size:43
Alignment explanation
Indices: 28380175--28380258 Score: 138
Period size: 40 Copynumber: 2.0 Consensus size: 43
28380165 CTATATATCC
*
28380175 ATTTTTTTAAATTTAATAGAAAATAATATTTTAAAATTATAAT
1 ATTTTTTTAAATTTAATAGAAAATAATATCTTAAAATTATAAT
28380218 ATTTTTTTAAA-TTAATAGAAAAT-A-ATCTTAAAATTATAAT
1 ATTTTTTTAAATTTAATAGAAAATAATATCTTAAAATTATAAT
28380258 A
1 A
28380259 ATTAGATGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
40 16 0.40
41 1 0.03
42 12 0.30
43 11 0.28
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.46
Consensus pattern (43 bp):
ATTTTTTTAAATTTAATAGAAAATAATATCTTAAAATTATAAT
Found at i:28380597 original size:20 final size:20
Alignment explanation
Indices: 28380572--28380610 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
28380562 AATCACTGAT
28380572 TTAAAAATGATAAAAAAAAA
1 TTAAAAATGATAAAAAAAAA
28380592 TTAAAAATGATAAAAAAAA
1 TTAAAAATGATAAAAAAAA
28380611 TGAACCGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (20 bp):
TTAAAAATGATAAAAAAAAA
Found at i:28382356 original size:63 final size:60
Alignment explanation
Indices: 28382263--28382438 Score: 183
Period size: 63 Copynumber: 2.8 Consensus size: 60
28382253 AATATAATTT
28382263 AATATAAAAATAAAAAAATCTTTTAATATAATTTAATATAAAATATTATTTTCAAATTTCAA-AA
1 AATAT-AAAA-AAAAAAATCTTTTAATATAATTTAATATAAAATATTATTTT---ATTTCAATAA
* * ** * *
28382327 AATATAAAAAAATAAAATGTTTTAATATAATTTAATGTAAAATATTAAATTATTTTAATAT
1 AATATAAAAAAA-AAAATCTTTTAATATAATTTAATATAAAATATTATTTTATTTCAATAA
* * *
28382388 AATTTAATATAAAAAATAATTTTTTAATGTAATTTAATATAAAATATTATT
1 AATATAA-A-AAAAAA-AATCTTTTAATATAATTTAATATAAAATATTATT
28382439 CTTTTGATAG
Statistics
Matches: 95, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
60 6 0.06
61 7 0.07
62 6 0.06
63 71 0.75
64 5 0.05
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (60 bp):
AATATAAAAAAAAAAATCTTTTAATATAATTTAATATAAAATATTATTTTATTTCAATAA
Found at i:28386435 original size:72 final size:72
Alignment explanation
Indices: 28386355--28386501 Score: 258
Period size: 72 Copynumber: 2.0 Consensus size: 72
28386345 ACTTTAATCC
*
28386355 AAATATATTAATTGTGTAAATTATTTGAACTAATTAATAAAATTAATTTATCTAAAAAGAAAATG
1 AAATATATTAATTGTGTAAACTATTTGAACTAATTAATAAAATTAATTTATCTAAAAAGAAAATG
28386420 ATATTAT
66 ATATTAT
* * *
28386427 AAATATATTAATTGTGTAAACTATTTGAATTAATTAATAATATTAATTTATCTAAAAAGCAAATG
1 AAATATATTAATTGTGTAAACTATTTGAACTAATTAATAAAATTAATTTATCTAAAAAGAAAATG
28386492 ATATTAT
66 ATATTAT
28386499 AAA
1 AAA
28386502 AATAAAGATA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (72 bp):
AAATATATTAATTGTGTAAACTATTTGAACTAATTAATAAAATTAATTTATCTAAAAAGAAAATG
ATATTAT
Found at i:28390294 original size:6 final size:6
Alignment explanation
Indices: 28390283--28390307 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
28390273 TTTTTCAGCC
28390283 TGGTCA TGGTCA TGGTCA TGGTCA T
1 TGGTCA TGGTCA TGGTCA TGGTCA T
28390308 TTTTATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.36
Consensus pattern (6 bp):
TGGTCA
Found at i:28390908 original size:12 final size:12
Alignment explanation
Indices: 28390871--28390909 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
28390861 TCAAGTTGCG
*
28390871 TTTTGTTCGAAA
1 TTTTGTTCAAAA
*
28390883 TTTGGTTCAGAAA
1 TTTTGTTCA-AAA
28390896 TTTTGTTCAAAA
1 TTTTGTTCAAAA
28390908 TT
1 TT
28390910 GCCTTATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (12 bp):
TTTTGTTCAAAA
Found at i:28391968 original size:2 final size:2
Alignment explanation
Indices: 28391961--28391991 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28391951 AAAGACAAAC
28391961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28391992 AAGAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28397607 original size:18 final size:18
Alignment explanation
Indices: 28397570--28397626 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
28397560 TTTATAATAC
*
28397570 ATAAGTTTTTATGATTTTTT
1 ATAAGTTTATAT--TTTTTT
**
28397590 ATACTTTTATATTTTTTT
1 ATAAGTTTATATTTTTTT
28397608 ATAAGTTTATATTTATTTT
1 ATAAGTTTATATTT-TTTT
28397627 TTTTAATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 18 0.58
19 4 0.13
20 9 0.29
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (18 bp):
ATAAGTTTATATTTTTTT
Found at i:28406530 original size:42 final size:42
Alignment explanation
Indices: 28406471--28406550 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
28406461 AAAGCATATG
28406471 AATTTAATCCAAGTTTTAGCATAGTAGAGGAGCTAAAATTGA
1 AATTTAATCCAAGTTTTAGCATAGTAGAGGAGCTAAAATTGA
* *
28406513 AATTTAATCCAAGTTTTAGCATAGTATAGGGGCTAAAA
1 AATTTAATCCAAGTTTTAGCATAGTAGAGGAGCTAAAA
28406551 GAAAGTAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (42 bp):
AATTTAATCCAAGTTTTAGCATAGTAGAGGAGCTAAAATTGA
Found at i:28407995 original size:24 final size:24
Alignment explanation
Indices: 28407966--28408015 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
28407956 ACGAGATTAA
28407966 TTAACAAAATTTCACATAAAAAAT
1 TTAACAAAATTTCACATAAAAAAT
* *
28407990 TTAACAAAATTTGACATAACAAAT
1 TTAACAAAATTTCACATAAAAAAT
28408014 TT
1 TT
28408016 TAAAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.32
Consensus pattern (24 bp):
TTAACAAAATTTCACATAAAAAAT
Found at i:28408171 original size:17 final size:16
Alignment explanation
Indices: 28408145--28408176 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
28408135 TGAATATCTT
28408145 TTAAATAAAATTTGGC
1 TTAAATAAAATTTGGC
28408161 TTAATATAAAATTTGG
1 TTAA-ATAAAATTTGG
28408177 TACCTAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.44, C:0.03, G:0.12, T:0.41
Consensus pattern (16 bp):
TTAAATAAAATTTGGC
Found at i:28408273 original size:32 final size:30
Alignment explanation
Indices: 28408228--28408307 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
28408218 TTTTTGGCCC
*
28408228 AATTTGGTACTAAAACTTGACA-TTTTTTCTT
1 AATTTGATACT-AAACTTGACACTTTTTT-TT
28408259 AATTTGATACCTAAACTTGACACTTTTTTTT
1 AATTTGATA-CTAAACTTGACACTTTTTTTT
* *
28408290 AAGTTGGTACTTAAACTT
1 AATTTGATAC-TAAACTT
28408308 TTTGGGGTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
30 1 0.02
31 34 0.79
32 8 0.19
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (30 bp):
AATTTGATACTAAACTTGACACTTTTTTTT
Found at i:28408275 original size:31 final size:31
Alignment explanation
Indices: 28408240--28408307 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
28408230 TTTGGTACTA
*
28408240 AAACTTGACA-TTTTTTCTTAATTTGATACCT
1 AAACTTGACACTTTTTT-TTAAGTTGATACCT
* *
28408271 AAACTTGACACTTTTTTTTAAGTTGGTACTT
1 AAACTTGACACTTTTTTTTAAGTTGATACCT
28408302 AAACTT
1 AAACTT
28408308 TTTGGGGTCC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 27 0.82
32 6 0.18
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (31 bp):
AAACTTGACACTTTTTTTTAAGTTGATACCT
Found at i:28408603 original size:57 final size:58
Alignment explanation
Indices: 28408530--28408696 Score: 187
Period size: 58 Copynumber: 2.9 Consensus size: 58
28408520 ATTGAATATT
* * * * * *
28408530 AAAAAAAGCTTGGGTACCAAATTAGGAAAACA-TGTCAAGTTTAGGTA-CAAATTGGGTC
1 AAAAAAAGTTTAGGTACCAAATTA--AAAAAAGTGTCAAGTTCAAGTACCAAATTAGGTC
*
28408588 -AAAAAAGTTTAGGTACCAAATTAAAAAAAGTGTCTAGTTCAAGTACCAAATTAGGTC
1 AAAAAAAGTTTAGGTACCAAATTAAAAAAAGTGTCAAGTTCAAGTACCAAATTAGGTC
** * * *
28408645 AAAAAAAGTTTAAATATCAAATTATAAAAAGTGTCAAGTTCAAGTACTAAAT
1 AAAAAAAGTTTAGGTACCAAATTAAAAAAAGTGTCAAGTTCAAGTACCAAAT
28408697 GTTATATTAA
Statistics
Matches: 93, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
55 5 0.05
56 12 0.13
57 31 0.33
58 45 0.48
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (58 bp):
AAAAAAAGTTTAGGTACCAAATTAAAAAAAGTGTCAAGTTCAAGTACCAAATTAGGTC
Found at i:28410068 original size:2 final size:2
Alignment explanation
Indices: 28410061--28410092 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28410051 GAGTACGCGC
28410061 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28410093 ATCTATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:28410101 original size:2 final size:2
Alignment explanation
Indices: 28410096--28410129 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
28410086 TCTCTCTATC
*
28410096 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28410130 GAAAAGTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:28413532 original size:7 final size:7
Alignment explanation
Indices: 28413516--28413553 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
28413506 GGGATACTAG
28413516 TTTTTA-
1 TTTTTAT
28413522 TTTTTAT
1 TTTTTAT
28413529 TTTTTAT
1 TTTTTAT
28413536 TTTTTAT
1 TTTTTAT
*
28413543 TCTTTTCT
1 T-TTTTAT
28413551 TTT
1 TTT
28413554 GGGTTTGGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 6 0.21
7 17 0.59
8 6 0.21
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTAT
Found at i:28415750 original size:81 final size:82
Alignment explanation
Indices: 28415642--28415795 Score: 222
Period size: 81 Copynumber: 1.9 Consensus size: 82
28415632 TGAACATTCC
* * * * *
28415642 GTTTGATTTAAAAAGGAAACTAGAGAAGATGATTTTTTG-A-AAAAAAGATGAACGGTTTATATT
1 GTTTGATTAAAAAAGGAAACTAGAGAAGATGATTTTCTGAAGAAAAAAAATGAACGGTTCACATT
28415705 TCAAAGTGTGAGGGAGA
66 TCAAAGTGTGAGGGAGA
* *
28415722 GTTTGAATTAAAAAAGGAAATTAGAGAAGATGATTTTCTGAAGAAAAAAAATGAACGGTTCACCT
1 GTTTG-ATTAAAAAAGGAAACTAGAGAAGATGATTTTCTGAAGAAAAAAAATGAACGGTTCACAT
28415787 TTCAAAGTG
65 TTCAAAGTG
28415796 AGAGAGAGCA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
80 5 0.08
81 31 0.48
82 1 0.02
83 27 0.42
ACGTcount: A:0.43, C:0.06, G:0.23, T:0.29
Consensus pattern (82 bp):
GTTTGATTAAAAAAGGAAACTAGAGAAGATGATTTTCTGAAGAAAAAAAATGAACGGTTCACATT
TCAAAGTGTGAGGGAGA
Found at i:28415989 original size:23 final size:23
Alignment explanation
Indices: 28415963--28416007 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
28415953 ATAATAATTA
28415963 TATTAAATTATGATTAAATTATT
1 TATTAAATTATGATTAAATTATT
** * *
28415986 TATTTTATTTTTATTAAATTAT
1 TATTAAATTATGATTAAATTAT
28416008 ATTTAATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TATTAAATTATGATTAAATTATT
Found at i:28416207 original size:45 final size:44
Alignment explanation
Indices: 28416126--28416215 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 44
28416116 AATCTATTCT
*
28416126 ATTCAACCAAACACAATAATTCTATTACAATTCTATTCCATTAC
1 ATTCAACCAAACACAATAATTCTATTACAACTCTATTCCATTAC
28416170 ATTCAACC-AA-ACAATGAATTACTAATTACAACTCTATTCCATTAC
1 ATTCAACCAAACACAAT-AATT-CT-ATTACAACTCTATTCCATTAC
28416215 A
1 A
28416216 GCTTTATTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
42 5 0.12
43 6 0.14
44 10 0.24
45 21 0.50
ACGTcount: A:0.42, C:0.24, G:0.01, T:0.32
Consensus pattern (44 bp):
ATTCAACCAAACACAATAATTCTATTACAACTCTATTCCATTAC
Found at i:28416215 original size:16 final size:16
Alignment explanation
Indices: 28416194--28416260 Score: 80
Period size: 16 Copynumber: 4.2 Consensus size: 16
28416184 TGAATTACTA
28416194 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
* * *
28416210 ATTACAGCTTTATTTC
1 ATTACAACTCTATTCC
* *
28416226 ATTACAACTATATTCT
1 ATTACAACTCTATTCC
*
28416242 ATTACAACCCTATTCC
1 ATTACAACTCTATTCC
28416258 ATT
1 ATT
28416261 CCAGTGAACC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.31, C:0.25, G:0.01, T:0.42
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:28427149 original size:17 final size:18
Alignment explanation
Indices: 28427131--28427173 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
28427121 CCCAAAAAAA
* *
28427131 TTTAAATGTTTTTTTAAT
1 TTTAAATATTTTTTTAAG
*
28427149 TTTAATTATTTTTTTAAG
1 TTTAAATATTTTTTTAAG
28427167 TTTAAAT
1 TTTAAAT
28427174 TCATTTGCTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTAAATATTTTTTTAAG
Found at i:28427174 original size:19 final size:19
Alignment explanation
Indices: 28427139--28427179 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
28427129 AATTTAAATG
*
28427139 TTTTTTTAATTTTAATT-A
1 TTTTTTTAATTTAAATTCA
28427157 TTTTTTTAAGTTTAAATTCA
1 TTTTTTTAA-TTTAAATTCA
28427177 TTT
1 TTT
28427180 GCTGACGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 9 0.45
19 7 0.35
20 4 0.20
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTTTTAATTTAAATTCA
Found at i:28429331 original size:20 final size:20
Alignment explanation
Indices: 28429306--28429343 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28429296 GGTTTTTCGA
28429306 AAAAAGTCAACAGTCAACCC
1 AAAAAGTCAACAGTCAACCC
* *
28429326 AAAAAGTTAACGGTCAAC
1 AAAAAGTCAACAGTCAAC
28429344 TGTTAATGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.24, G:0.13, T:0.13
Consensus pattern (20 bp):
AAAAAGTCAACAGTCAACCC
Found at i:28440399 original size:90 final size:88
Alignment explanation
Indices: 28440237--28440402 Score: 233
Period size: 90 Copynumber: 1.9 Consensus size: 88
28440227 ATTTCAAAAG
* * ***
28440237 TGAAGTTATTAAAGTATTAGTATTGTCTTAATTGGATTTCTCTCAATTTAAATATTAATTGGAGT
1 TGAAGATATTAAAATATTAGTATTGTCTTAATCAAATTTCTCTCAATTTAAATATTAATTGGAGT
28440302 GTTAAATATTAGTTCGAATAAAT
66 GTTAAATATTAGTTCGAATAAAT
* * * *
28440325 TGAAGATATTAAAATATTAGTATTGTTTTAATCAAATTTATCTGTCAATTTAACTATTAGTTGGA
1 TGAAGATATTAAAATATTAGTATTGTCTTAATCAAA-TT-TCTCTCAATTTAAATATTAATTGGA
28440390 GTGTTAAATATTA
64 GTGTTAAATATTA
28440403 ACTTAAATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
88 30 0.45
89 2 0.03
90 35 0.52
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (88 bp):
TGAAGATATTAAAATATTAGTATTGTCTTAATCAAATTTCTCTCAATTTAAATATTAATTGGAGT
GTTAAATATTAGTTCGAATAAAT
Found at i:28450883 original size:21 final size:20
Alignment explanation
Indices: 28450830--28450884 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
28450820 AATAGCAGTT
28450830 AAAACAGTAAAAATAACACC
1 AAAACAGTAAAAATAACACC
* ** *
28450850 AAGACAACAAAAAATAGCAACC
1 AAAAC-AGTAAAAATAAC-ACC
28450872 AAAACAGTAAAAA
1 AAAACAGTAAAAA
28450885 AAGAGAATCA
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
20 4 0.15
21 15 0.58
22 7 0.27
ACGTcount: A:0.67, C:0.18, G:0.07, T:0.07
Consensus pattern (20 bp):
AAAACAGTAAAAATAACACC
Found at i:28450883 original size:22 final size:21
Alignment explanation
Indices: 28450830--28450885 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
28450820 AATAGCAGTT
28450830 AAAACAGT-AAAAATAACACC
1 AAAACAGTAAAAAATAACACC
* ** *
28450850 AAGACAACAAAAAATAGCAACC
1 AAAACAGTAAAAAATAAC-ACC
28450872 AAAACAGTAAAAAA
1 AAAACAGTAAAAAA
28450886 AGAGAATCAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 5 0.19
21 8 0.30
22 14 0.52
ACGTcount: A:0.68, C:0.18, G:0.07, T:0.07
Consensus pattern (21 bp):
AAAACAGTAAAAAATAACACC
Found at i:28451518 original size:23 final size:23
Alignment explanation
Indices: 28451492--28451562 Score: 83
Period size: 22 Copynumber: 3.2 Consensus size: 23
28451482 AAACAGCACC
**
28451492 AAAATAACAATTAAAACAGTAAA
1 AAAATAACAACCAAAACAGTAAA
* *
28451515 AAAATAAC-ACCAAGACAGCAAA
1 AAAATAACAACCAAAACAGTAAA
*
28451537 AAAA-AGCAACCAAAACAGTAAA
1 AAAATAACAACCAAAACAGTAAA
28451559 AAAA
1 AAAA
28451563 GAGAGCACCA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 2 0.05
22 30 0.75
23 8 0.20
ACGTcount: A:0.69, C:0.15, G:0.07, T:0.08
Consensus pattern (23 bp):
AAAATAACAACCAAAACAGTAAA
Found at i:28451561 original size:24 final size:23
Alignment explanation
Indices: 28451504--28451577 Score: 73
Period size: 22 Copynumber: 3.3 Consensus size: 23
28451494 AATAACAATT
*
28451504 AAAACAGTAAAAAAATAA-CACC
1 AAAACAGTAAAAAAAAAAGCACC
* *
28451526 AAGACAG--CAAAAAAAAGCAACC
1 AAAACAGTAAAAAAAAAAGC-ACC
*
28451548 AAAACAGTAAAAAAAGAGAGCACC
1 AAAACAGTAAAAAAA-AAAGCACC
28451572 AAAACA
1 AAAACA
28451578 ACTATATAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
20 7 0.17
21 1 0.02
22 15 0.37
24 14 0.34
25 4 0.10
ACGTcount: A:0.66, C:0.19, G:0.11, T:0.04
Consensus pattern (23 bp):
AAAACAGTAAAAAAAAAAGCACC
Found at i:28451823 original size:17 final size:17
Alignment explanation
Indices: 28451801--28451836 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28451791 TTGAAGCTCA
28451801 ATATTTTAAATATATTT
1 ATATTTTAAATATATTT
* *
28451818 ATATTTTTAATATTTTT
1 ATATTTTAAATATATTT
28451835 AT
1 AT
28451837 TATAACATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTTTAAATATATTT
Found at i:28458601 original size:29 final size:29
Alignment explanation
Indices: 28458551--28458607 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
28458541 TTTATGATTA
* * *
28458551 ATATTTTAATAATTTTATTGTTAAATTTT
1 ATATTTTAATAATATAAATGTTAAATTTT
* *
28458580 ATATTTTAATCATATAAATGTTTAATTT
1 ATATTTTAATAATATAAATGTTAAATTT
28458608 GACGTAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (29 bp):
ATATTTTAATAATATAAATGTTAAATTTT
Found at i:28465374 original size:17 final size:18
Alignment explanation
Indices: 28465352--28465395 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
28465342 TGCGATTATC
28465352 ATAATT-TTTATTAAAT-T
1 ATAATTATTT-TTAAATAT
*
28465369 ATAATTATTTTTGAATAT
1 ATAATTATTTTTAAATAT
28465387 ATAATTATT
1 ATAATTATT
28465396 AAAACTTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
ATAATTATTTTTAAATAT
Found at i:28466285 original size:20 final size:20
Alignment explanation
Indices: 28466257--28466297 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
28466247 TTTTAAAAAA
*
28466257 TTTAAAAAATTCAAAATTAT
1 TTTAAAAAATTAAAAATTAT
*
28466277 TTTACAAAATTAAAAATTAT
1 TTTAAAAAATTAAAAATTAT
28466297 T
1 T
28466298 AAAGTTATAA
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:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTAAAAAATTAAAAATTAT
Found at i:28468023 original size:91 final size:91
Alignment explanation
Indices: 28467909--28468089 Score: 362
Period size: 91 Copynumber: 2.0 Consensus size: 91
28467899 GGGGATGAAG
28467909 ATATGTAATTTTGACTGAATATAGATTCTACTAGCTATTGCCAAATACCAGCATCCGCAATTAAC
1 ATATGTAATTTTGACTGAATATAGATTCTACTAGCTATTGCCAAATACCAGCATCCGCAATTAAC
28467974 TGATTTTTTCCCATCATTTCTAATGA
66 TGATTTTTTCCCATCATTTCTAATGA
28468000 ATATGTAATTTTGACTGAATATAGATTCTACTAGCTATTGCCAAATACCAGCATCCGCAATTAAC
1 ATATGTAATTTTGACTGAATATAGATTCTACTAGCTATTGCCAAATACCAGCATCCGCAATTAAC
28468065 TGATTTTTTCCCATCATTTCTAATG
66 TGATTTTTTCCCATCATTTCTAATG
28468090 GTGTATAAAT
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (91 bp):
ATATGTAATTTTGACTGAATATAGATTCTACTAGCTATTGCCAAATACCAGCATCCGCAATTAAC
TGATTTTTTCCCATCATTTCTAATGA
Found at i:28475812 original size:18 final size:17
Alignment explanation
Indices: 28475789--28475830 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
28475779 ATAGATCTTT
28475789 TTAAAAGCATTTTTAATA
1 TTAAAAGCATTTTTAA-A
**
28475807 TTAAAAATATTTTTAAA
1 TTAAAAGCATTTTTAAA
28475824 TTAAAAG
1 TTAAAAG
28475831 TAATGTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (17 bp):
TTAAAAGCATTTTTAAA
Found at i:28476234 original size:13 final size:13
Alignment explanation
Indices: 28476212--28476274 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
28476202 TTAAATCAAG
28476212 TTTTTCAAAAATAC
1 TTTTT-AAAAATAC
* *
28476226 TTTTTAAAATTAT
1 TTTTTAAAAATAC
* **
28476239 TTTTTTAAAGCAC
1 TTTTTAAAAATAC
28476252 TTTTTAAAAATAC
1 TTTTTAAAAATAC
*
28476265 TTCTTAAAAA
1 TTTTTAAAAA
28476275 CAATGCTAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
13 34 0.87
14 5 0.13
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.48
Consensus pattern (13 bp):
TTTTTAAAAATAC
Found at i:28477809 original size:32 final size:31
Alignment explanation
Indices: 28477761--28477829 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 31
28477751 CACGTTGAAG
*
28477761 ACATTTTATTTTTTTATT-AAAATTGTAATCA
1 ACATTTGATTTTTTTATTAAAAATT-TAATCA
*
28477792 ACATTTGATTTCTTTTATTAAAAATTTAATTA
1 ACATTTGATTT-TTTTATTAAAAATTTAATCA
28477824 ACATTT
1 ACATTT
28477830 TAAGTGAGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 10 0.29
32 18 0.53
33 6 0.18
ACGTcount: A:0.36, C:0.07, G:0.03, T:0.54
Consensus pattern (31 bp):
ACATTTGATTTTTTTATTAAAAATTTAATCA
Found at i:28478089 original size:20 final size:19
Alignment explanation
Indices: 28478051--28478090 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
28478041 GTATACCATG
*
28478051 TTATAAAATCTTATAAAAA
1 TTATAAAATCTAATAAAAA
*
28478070 TTATAAATATCTAATTAAAA
1 TTATAAA-ATCTAATAAAAA
28478090 T
1 T
28478091 ATGCAAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
TTATAAAATCTAATAAAAA
Found at i:28480580 original size:23 final size:23
Alignment explanation
Indices: 28480532--28480581 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
28480522 AAAGCATACT
* *
28480532 TCCTTTGATTCATAAATATTTCA
1 TCCTTGGATTCATAAATATTTAA
*
28480555 TCCTTGGATCTCAT-AATTTTTAA
1 TCCTTGGAT-TCATAAATATTTAA
28480578 TCCT
1 TCCT
28480582 AAAGAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (23 bp):
TCCTTGGATTCATAAATATTTAA
Found at i:28486826 original size:40 final size:40
Alignment explanation
Indices: 28486782--28486868 Score: 165
Period size: 40 Copynumber: 2.2 Consensus size: 40
28486772 TAAGAAAAAT
28486782 GGTGCAATCGGAGTTAAAAATGAGACTTTTTAGATACCCG
1 GGTGCAATCGGAGTTAAAAATGAGACTTTTTAGATACCCG
28486822 GGTGCAATCGGAGTTAAAAATGAGACTTTTTAGATACCCG
1 GGTGCAATCGGAGTTAAAAATGAGACTTTTTAGATACCCG
*
28486862 GGGGCAA
1 GGTGCAA
28486869 AATGGTAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.25
Consensus pattern (40 bp):
GGTGCAATCGGAGTTAAAAATGAGACTTTTTAGATACCCG
Found at i:28486880 original size:29 final size:30
Alignment explanation
Indices: 28486848--28486906 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 30
28486838 AAAATGAGAC
*
28486848 TTTTTAGA-TACCCGGGGGC-AAAATGGTAA
1 TTTTTAGACT-CCCAGGGGCAAAAATGGTAA
*
28486877 -TTTTAGACTCTCAGGGGCAAAAATGGTAA
1 TTTTTAGACTCCCAGGGGCAAAAATGGTAA
28486906 T
1 T
28486907 CTTGGGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (30 bp):
TTTTTAGACTCCCAGGGGCAAAAATGGTAA
Found at i:28487042 original size:30 final size:30
Alignment explanation
Indices: 28486982--28487106 Score: 112
Period size: 30 Copynumber: 4.2 Consensus size: 30
28486972 AAAATAGGGA
28486982 TCAAAAATGAAATTTTTGGAAGTTTCGGGG
1 TCAAAAATGAAATTTTTGGAAGTTTCGGGG
* *
28487012 TTAAAAATGGAATTTTTGGAAG-TTCGGGGG
1 TCAAAAATGAAATTTTTGGAAGTTTC-GGGG
* * ***
28487042 TC-AAAAT-ATATTTTTTAGAAGTTTTAAGG
1 TCAAAAATGA-AATTTTTGGAAGTTTCGGGG
* * * *
28487071 TCAATAATGTAATTTTTGAAAGTTTCAGGG
1 TCAAAAATGAAATTTTTGGAAGTTTCGGGG
28487101 TCAAAA
1 TCAAAA
28487107 TATAATTTCT
Statistics
Matches: 73, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
29 22 0.30
30 51 0.70
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (30 bp):
TCAAAAATGAAATTTTTGGAAGTTTCGGGG
Found at i:28487128 original size:59 final size:59
Alignment explanation
Indices: 28487017--28487129 Score: 131
Period size: 59 Copynumber: 1.9 Consensus size: 59
28487007 CGGGGTTAAA
* * * * *
28487017 AATGGAATTTTTGGAAGTTCGGGGGTCAAAATATATTTTTTAGAAGTTTTAAGGTCAAT
1 AATGGAATTTTTGAAAGTTCGAGGGTCAAAATATAATTTCTAGAAGTCTTAAGGTCAAT
* *
28487076 AATGTAATTTTTGAAAGTTTC-AGGGTCAAAATATAATTTCTGGACAG-CTTAAGG
1 AATGGAATTTTTGAAAG-TTCGAGGGTCAAAATATAATTTCTAGA-AGTCTTAAGG
28487130 ACCTTCAGGG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
59 40 0.89
60 5 0.11
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.37
Consensus pattern (59 bp):
AATGGAATTTTTGAAAGTTCGAGGGTCAAAATATAATTTCTAGAAGTCTTAAGGTCAAT
Found at i:28488938 original size:6 final size:6
Alignment explanation
Indices: 28488927--28488978 Score: 52
Period size: 6 Copynumber: 8.8 Consensus size: 6
28488917 TCAAATTTAG
** * * *
28488927 TTAAAT TTAAAT TTAAA- ACAAAT CTAAAT TTAAAT TTAAAA ATAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
28488974 TTAAA
1 TTAAA
28488979 ACCAATCTAA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
5 3 0.08
6 33 0.92
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (6 bp):
TTAAAT
Found at i:28489010 original size:35 final size:35
Alignment explanation
Indices: 28488934--28489001 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
28488924 TAGTTAAATT
*
28488934 TAAATTTAAAACAAATCTAAATTTAAATTTAAAAA
1 TAAATTTAAAACAAATCTAAACTTAAATTTAAAAA
*
28488969 TAAATTTAAAACCAATCTAAACTT-AATTTAAAA
1 TAAATTTAAAACAAATCTAAACTTAAATTTAAAA
28489002 TCAAAATTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 9 0.29
35 22 0.71
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (35 bp):
TAAATTTAAAACAAATCTAAACTTAAATTTAAAAA
Found at i:28489677 original size:119 final size:120
Alignment explanation
Indices: 28489518--28489757 Score: 401
Period size: 119 Copynumber: 2.0 Consensus size: 120
28489508 GCTGGGGTTC
*
28489518 GAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGA-
1 GAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGAT
* *
28489582 GACCGCATCGTTTGTTTCAATCCGTTTCTCTGTATCTAATCAGGAAGACGAATTT
66 GACCGCATCGTTTGTTTCAATCCGCTTCTCTGTATCTAATCAGGAAGACAAATTT
* *
28489637 GAAGATTTACTCATATCGAGTGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGAT
1 GAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGAT
* * *
28489702 GACCGCATCGTTTGTTTTAATTCGCTTCTCTGTATCTCATCAGGAAGACAAATTT
66 GACCGCATCGTTTGTTTCAATCCGCTTCTCTGTATCTAATCAGGAAGACAAATTT
28489757 G
1 G
28489758 GTCCATTTCT
Statistics
Matches: 112, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
119 61 0.54
120 51 0.46
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (120 bp):
GAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAAGAAGAT
GACCGCATCGTTTGTTTCAATCCGCTTCTCTGTATCTAATCAGGAAGACAAATTT
Found at i:28501389 original size:29 final size:28
Alignment explanation
Indices: 28501347--28501407 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
28501337 ATCGGAGTTA
* *
28501347 AAAATGAGACTTTTTGGA-TACTCGTGGGC
1 AAAATGAGA-ATTTTGGACT-CTCGGGGGC
*
28501376 AAAATGATAATTTTGGACTCTCGGGGGC
1 AAAATGAGAATTTTGGACTCTCGGGGGC
28501404 AAAA
1 AAAA
28501408 ATGGTAATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (28 bp):
AAAATGAGAATTTTGGACTCTCGGGGGC
Found at i:28501572 original size:59 final size:59
Alignment explanation
Indices: 28501505--28501646 Score: 182
Period size: 59 Copynumber: 2.4 Consensus size: 59
28501495 AAATGTCCGG
*
28501505 GGGTAAAATGGTAATTTTTAGAAA-AATTAGGATCAAAAACGGAATTTTTGGATA-TTCGA
1 GGGTAAAATGGTAATTTTT-GAAAGAATTAGGATCAAAAACGAAATTTTTGGA-AGTTCGA
* ** * *
28501564 GGGTAAAATGATAATTTTTGAAAGGCTTAGGGTCAAAAATGAAATTTTTGGAAGTTCGA
1 GGGTAAAATGGTAATTTTTGAAAGAATTAGGATCAAAAACGAAATTTTTGGAAGTTCGA
28501623 GGGTAAAAAT-GTAATTTTTGAAAG
1 GGGT-AAAATGGTAATTTTTGAAAG
28501647 TTTTGGGTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
58 5 0.07
59 63 0.86
60 5 0.07
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGAAAGAATTAGGATCAAAAACGAAATTTTTGGAAGTTCGA
Found at i:28501579 original size:29 final size:29
Alignment explanation
Indices: 28501547--28501642 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
28501537 TCAAAAACGG
28501547 AATTTTTGGATATTCGAGGGT-AAAATGAT
1 AATTTTTGGA-ATTCGAGGGTAAAAATGAT
* ** *
28501576 AATTTTTGAAAGGCTTAGGGTCAAAAATGA-
1 AATTTTTGGAATTC-GAGGGT-AAAAATGAT
28501606 AATTTTTGGAAGTTCGAGGGTAAAAATG-T
1 AATTTTTGGAA-TTCGAGGGTAAAAATGAT
28501635 AATTTTTG
1 AATTTTTG
28501643 AAAGTTTTGG
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
28 2 0.04
29 29 0.54
30 15 0.28
31 8 0.15
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.36
Consensus pattern (29 bp):
AATTTTTGGAATTCGAGGGTAAAAATGAT
Found at i:28501647 original size:29 final size:30
Alignment explanation
Indices: 28501559--28501760 Score: 150
Period size: 30 Copynumber: 6.8 Consensus size: 30
28501549 TTTTTGGATA
*
28501559 TTCGAGGGT-AAAATGATAATTTTTGAAAGGC
1 TTCGAGGGTAAAAATG-TAATTTTTGAAA-GT
* *
28501590 TT--AGGGTCAAAAATGAAATTTTTGGAAG-
1 TTCGAGGGT-AAAAATGTAATTTTTGAAAGT
28501618 TTCGAGGGTAAAAATGTAATTTTTGAAAGT
1 TTCGAGGGTAAAAATGTAATTTTTGAAAGT
* * * ** *
28501648 TTTG-GGTTTAATAATGGCATTTTTGGAAGT
1 TTCGAGG-GTAAAAATGTAATTTTTGAAAGT
* * *
28501678 TTAG-GGGTGAAAATGTAATTTTTGGAAGT
1 TTCGAGGGTAAAAATGTAATTTTTGAAAGT
* * *
28501707 TT-TAGGGTTAATAATGTAAGTTTTGAAAGT
1 TTCGAGGG-TAAAAATGTAATTTTTGAAAGT
* *
28501737 TTCGA-GGTCAAAATATAATTTTTG
1 TTCGAGGGTAAAAATGTAATTTTTG
28501761 GACAGCTTAG
Statistics
Matches: 136, Mismatches: 26, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
28 2 0.01
29 62 0.46
30 63 0.46
31 9 0.07
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.39
Consensus pattern (30 bp):
TTCGAGGGTAAAAATGTAATTTTTGAAAGT
Found at i:28501672 original size:30 final size:29
Alignment explanation
Indices: 28501570--28501760 Score: 127
Period size: 29 Copynumber: 6.4 Consensus size: 29
28501560 TCGAGGGTAA
* * * *
28501570 AATGATAATTTTTGAAAGGCTTAGGGTCAAA
1 AATG-TAATTTTTGAAA-GTTTTGGGTTAAT
* * * * *
28501601 AATGAAATTTTTGGAAG-TTCGAGGGTAAA
1 AATGTAATTTTTGAAAGTTTTG-GGTTAAT
28501630 AATGTAATTTTTGAAAGTTTTGGGTTTAAT
1 AATGTAATTTTTGAAAGTTTTGGG-TTAAT
** * * *
28501660 AATGGCATTTTTGGAAGTTTAGGGGTGAA-
1 AATGTAATTTTTGAAAGTTT-TGGGTTAAT
*
28501689 AATGTAATTTTTGGAAGTTTTAGGGTTAAT
1 AATGTAATTTTTGAAAGTTTT-GGGTTAAT
* * *
28501719 AATGTAAGTTTTGAAAGTTTCGAGGTCAA-
1 AATGTAATTTTTGAAAGTTTTG-GGTTAAT
*
28501748 AATATAATTTTTG
1 AATGTAATTTTTG
28501761 GACAGCTTAG
Statistics
Matches: 128, Mismatches: 25, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
28 3 0.02
29 59 0.46
30 59 0.46
31 7 0.05
ACGTcount: A:0.34, C:0.03, G:0.24, T:0.39
Consensus pattern (29 bp):
AATGTAATTTTTGAAAGTTTTGGGTTAAT
Found at i:28501762 original size:59 final size:59
Alignment explanation
Indices: 28501547--28501760 Score: 215
Period size: 59 Copynumber: 3.6 Consensus size: 59
28501537 TCAAAAACGG
** * *
28501547 AATTTTTGG-A-TATTCGAGGGTAAAATGATAATTTTTGAAAGGCTTAGGGTCAAAAATGA
1 AATTTTTGGAAGT-TTCGAGGGTAAAAT-ATAATTTTTGAAAGTTTTAGGGTTAATAATGA
* *
28501606 AATTTTTGGAAG-TTCGAGGGTAAAAATGTAATTTTTGAAAGTTTT-GGGTTTAATAATGG
1 AATTTTTGGAAGTTTCGAGGGT-AAAATATAATTTTTGAAAGTTTTAGGG-TTAATAATGA
* * * * *
28501665 CATTTTTGGAAGTTTAG-GGGTGAAAATGTAATTTTTGGAAGTTTTAGGGTTAATAATGT
1 AATTTTTGGAAGTTTCGAGGGT-AAAATATAATTTTTGAAAGTTTTAGGGTTAATAATGA
* *
28501724 AAGTTTTGAAAGTTTCGA-GGTCAAAATATAATTTTTG
1 AATTTTTGGAAGTTTCGAGGGT-AAAATATAATTTTTG
28501761 GACAGCTTAG
Statistics
Matches: 131, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
58 3 0.02
59 116 0.89
60 12 0.09
ACGTcount: A:0.33, C:0.03, G:0.24, T:0.39
Consensus pattern (59 bp):
AATTTTTGGAAGTTTCGAGGGTAAAATATAATTTTTGAAAGTTTTAGGGTTAATAATGA
Found at i:28503604 original size:6 final size:6
Alignment explanation
Indices: 28503590--28503682 Score: 73
Period size: 6 Copynumber: 15.8 Consensus size: 6
28503580 TCAAATTTAG
* ** * * * *
28503590 TTAATT TTAAAT TTAAA- ACAAAT CTAAAT TTAAAT TTAAAA ATAAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * *
28503637 ATAAAT TTAAAT TTAAA- ATAAAT TTAAAT TTAAAA ATAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
28503683 AACAATCTAA
Statistics
Matches: 69, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
5 7 0.10
6 62 0.90
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:28503623 original size:23 final size:23
Alignment explanation
Indices: 28503595--28503670 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
28503585 TTTAGTTAAT
* *
28503595 TTTAAATTTAAAACAAATCTAAA
1 TTTAAATTTAAAATAAATATAAA
*
28503618 TTTAAATTTAAAAATAAAAATAAA
1 TTTAAATTT-AAAATAAATATAAA
*
28503642 TTTAAATTTAAAATAAATTTAAA
1 TTTAAATTTAAAATAAATATAAA
28503665 TTTAAA
1 TTTAAA
28503671 AATAAATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 27 0.57
24 20 0.43
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (23 bp):
TTTAAATTTAAAATAAATATAAA
Found at i:28503641 original size:18 final size:18
Alignment explanation
Indices: 28503620--28503684 Score: 87
Period size: 18 Copynumber: 3.7 Consensus size: 18
28503610 AATCTAAATT
28503620 TAAATTTAAAAATAAAAA
1 TAAATTTAAAAATAAAAA
* *
28503638 TAAATTT-AAATTTAAAA
1 TAAATTTAAAAATAAAAA
**
28503655 TAAATTTAAATTTAAAAA
1 TAAATTTAAAAATAAAAA
28503673 TAAATTTAAAAA
1 TAAATTTAAAAA
28503685 CAATCTAAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
17 15 0.38
18 25 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAATTTAAAAATAAAAA
Found at i:28503645 original size:41 final size:41
Alignment explanation
Indices: 28503597--28503676 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
28503587 TAGTTAATTT
*
28503597 TAAATTTAAA-ACAAATCTAAATTTAAATTTAAAAATAAAAA
1 TAAATTTAAATACAAA-ATAAATTTAAATTTAAAAATAAAAA
**
28503638 TAAATTTAAATTTAAAATAAATTTAAATTTAAAAATAAA
1 TAAATTTAAATACAAAATAAATTTAAATTTAAAAATAAA
28503677 TTTAAAAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 32 0.91
42 3 0.09
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (41 bp):
TAAATTTAAATACAAAATAAATTTAAATTTAAAAATAAAAA
Found at i:28503670 original size:29 final size:29
Alignment explanation
Indices: 28503614--28503704 Score: 79
Period size: 29 Copynumber: 3.3 Consensus size: 29
28503604 AAAACAAATC
*
28503614 TAAATTTAAATTTAAAAATAA---AAA--
1 TAAATTTAAATTTAAAAACAATCTAAACT
* *
28503638 TAAATTTAAATTTAAAATA-AATTTAAATT
1 TAAATTTAAATTTAAAA-ACAATCTAAACT
**
28503667 TAAAAATAAATTTAAAAACAATCTAAACT
1 TAAATTTAAATTTAAAAACAATCTAAACT
28503696 T-AATTTAAA
1 TAAATTTAAA
28503705 ATCAAAATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
24 19 0.35
25 1 0.02
27 3 0.06
28 7 0.13
29 24 0.44
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (29 bp):
TAAATTTAAATTTAAAAACAATCTAAACT
Found at i:28507227 original size:18 final size:18
Alignment explanation
Indices: 28507187--28507230 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28507177 TTCTTGTCCC
28507187 TTTTTTTTATATTCAGTT
1 TTTTTTTTATATTCAGTT
* **
28507205 CTTTTTTTATATTTTGTT
1 TTTTTTTTATATTCAGTT
28507223 TTTTTTTT
1 TTTTTTTT
28507231 TAATTTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.11, C:0.05, G:0.05, T:0.80
Consensus pattern (18 bp):
TTTTTTTTATATTCAGTT
Found at i:28507238 original size:19 final size:20
Alignment explanation
Indices: 28507206--28507248 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
28507196 TATTCAGTTC
*
28507206 TTTTTTTATATTTTGTTT-T
1 TTTTTTTATATTTTATTTGT
28507225 TTTTTTTA-ATTTTTATTTGT
1 TTTTTTTATA-TTTTATTTGT
28507245 TTTT
1 TTTT
28507249 GTGGCACGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 15 0.71
20 5 0.24
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.84
Consensus pattern (20 bp):
TTTTTTTATATTTTATTTGT
Found at i:28507247 original size:18 final size:19
Alignment explanation
Indices: 28507189--28507248 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 19
28507179 CTTGTCCCTT
** *
28507189 TTTTTTATATTCAGTTCT-
1 TTTTTTATATTTTGTTTTG
*
28507207 TTTTTTATATTTTGTTTTT
1 TTTTTTATATTTTGTTTTG
28507226 TTTTTTA-ATTTT-TATTTG
1 TTTTTTATATTTTGT-TTTG
28507244 TTTTT
1 TTTTT
28507249 GTGGCACGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 1 0.03
18 28 0.78
19 7 0.19
ACGTcount: A:0.13, C:0.03, G:0.05, T:0.78
Consensus pattern (19 bp):
TTTTTTATATTTTGTTTTG
Found at i:28507753 original size:20 final size:21
Alignment explanation
Indices: 28507719--28507759 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
28507709 AATTATATAA
28507719 TATACAAAATAAAAAT-AATT
1 TATACAAAATAAAAATGAATT
28507739 TATA-AAAATATAAAATGAATT
1 TATACAAAATA-AAAATGAATT
28507760 GGGTTCGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 9 0.47
21 4 0.21
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
TATACAAAATAAAAATGAATT
Found at i:28507961 original size:58 final size:59
Alignment explanation
Indices: 28507888--28508001 Score: 203
Period size: 58 Copynumber: 1.9 Consensus size: 59
28507878 GTAAGAAATT
* *
28507888 TTAATTTCTTAAATCTAACTAGCAAAGTGAAATTATGTAGCTGCAAGAATAACACTTTG
1 TTAATTTCTTAAATCTAACTAGCAAAATGAAATTATATAGCTGCAAGAATAACACTTTG
28507947 TTAA-TTCTTAAATCTAACTAGCAAAATGAAATTATATAGCTGCAAGAATAACACT
1 TTAATTTCTTAAATCTAACTAGCAAAATGAAATTATATAGCTGCAAGAATAACACT
28508002 GTAAAGCTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
58 49 0.92
59 4 0.08
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.32
Consensus pattern (59 bp):
TTAATTTCTTAAATCTAACTAGCAAAATGAAATTATATAGCTGCAAGAATAACACTTTG
Found at i:28517268 original size:33 final size:33
Alignment explanation
Indices: 28517226--28517295 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
28517216 GATGGTGTGT
28517226 ATGTCAACCATTTCATCGGTAAAGGAGAGAGGC
1 ATGTCAACCATTTCATCGGTAAAGGAGAGAGGC
*
28517259 ATGTCAACCATTTCATCGGTAGAGGAGAGAGGC
1 ATGTCAACCATTTCATCGGTAAAGGAGAGAGGC
28517292 ATGT
1 ATGT
28517296 TCTCTAAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (33 bp):
ATGTCAACCATTTCATCGGTAAAGGAGAGAGGC
Found at i:28524722 original size:17 final size:17
Alignment explanation
Indices: 28524700--28524733 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28524690 TAGGCTAATT
28524700 TTATACAATTATATATA
1 TTATACAATTATATATA
*
28524717 TTATACAATTTTATATA
1 TTATACAATTATATATA
28524734 CAAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATACAATTATATATA
Found at i:28526971 original size:44 final size:44
Alignment explanation
Indices: 28526920--28527007 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
28526910 ATGACATGGC
*
28526920 TTAGACTTCATGGCCAGTCATATCTATTTTTGGAGGAGGAAAAG
1 TTAGACTTCATGGCCAGTCATATCTATTTGTGGAGGAGGAAAAG
28526964 TTAGACTTCATGGCCAGTCATATCTATTTGTGGAGGAGGAAAAG
1 TTAGACTTCATGGCCAGTCATATCTATTTGTGGAGGAGGAAAAG
28527008 AGTAGACAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.31
Consensus pattern (44 bp):
TTAGACTTCATGGCCAGTCATATCTATTTGTGGAGGAGGAAAAG
Found at i:28527026 original size:41 final size:43
Alignment explanation
Indices: 28526932--28527018 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 43
28526922 AGACTTCATG
* * **
28526932 GCCAGTCATATCTATTTTTGGAGGAGGAAAAGTTAGACTTCAT
1 GCCAGTCATATCTATTTGTGGAGGAGGAAAAGGTAGACTAAAT
28526975 GGCCAGTCATATCTATTTGTGGAGGAGGAAAAGAGTAGAC-AAAT
1 -GCCAGTCATATCTATTTGTGGAGGAGGAAAAG-GTAGACTAAAT
28527019 TCGTCATAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 33 0.87
45 5 0.13
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (43 bp):
GCCAGTCATATCTATTTGTGGAGGAGGAAAAGGTAGACTAAAT
Found at i:28530226 original size:50 final size:50
Alignment explanation
Indices: 28530083--28530229 Score: 197
Period size: 50 Copynumber: 2.9 Consensus size: 50
28530073 AGTTTGTGTA
* * * *
28530083 AAACCTTTGTGGCAGGTTACTTGAAAAGCCTATGTGGCGTAATATCTTGT
1 AAACCTTTGTGGCAGGTTACCTGTAAAGCCTATGTGGCGTAATGTCTTGG
* * * *
28530133 AAGCCTTTGTGGCAGGTTGCCTGTAAATCCTATGTGGTGTAATGT-TTAGG
1 AAACCTTTGTGGCAGGTTACCTGTAAAGCCTATGTGGCGTAATGTCTT-GG
*
28530183 AAACCTTTGTGGCAGGTTACCTGTAAAGCATATGTGGCGTAATGTCT
1 AAACCTTTGTGGCAGGTTACCTGTAAAGCCTATGTGGCGTAATGTCT
28530230 AGAAAGTCAG
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
49 2 0.02
50 79 0.96
51 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.34
Consensus pattern (50 bp):
AAACCTTTGTGGCAGGTTACCTGTAAAGCCTATGTGGCGTAATGTCTTGG
Found at i:28532174 original size:31 final size:31
Alignment explanation
Indices: 28532136--28532202 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
28532126 CATAGAATGT
28532136 GTTTTTATTGAAAGCGTGTCCTATATGACAC
1 GTTTTTATTGAAAGCGTGTCCTATATGACAC
28532167 GTTTTTATTGAAAGCGTGTCCTATATGACAC
1 GTTTTTATTGAAAGCGTGTCCTATATGACAC
28532198 GTTTT
1 GTTTT
28532203 CACTCTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (31 bp):
GTTTTTATTGAAAGCGTGTCCTATATGACAC
Found at i:28533947 original size:2 final size:2
Alignment explanation
Indices: 28533940--28533971 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28533930 TGTATAAATA
28533940 AT 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 AT
28533972 TTGATTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28549753 original size:20 final size:20
Alignment explanation
Indices: 28549728--28549769 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
28549718 ATCACATTGA
28549728 TGTGGATATTCAGAAGGATG
1 TGTGGATATTCAGAAGGATG
28549748 TGTGGATATTCAGAAGGATG
1 TGTGGATATTCAGAAGGATG
28549768 TG
1 TG
28549770 GCGAATGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.31
Consensus pattern (20 bp):
TGTGGATATTCAGAAGGATG
Found at i:28551573 original size:28 final size:28
Alignment explanation
Indices: 28551530--28551586 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
28551520 TTTTTATAAA
28551530 TTTTTTAAAGACTAAA-TCAAAATTTTAT
1 TTTTTTAAAGACTAAAGT-AAAATTTTAT
* * *
28551558 TTTTTTAAGGATTAAAGTACAATTTTAT
1 TTTTTTAAAGACTAAAGTAAAATTTTAT
28551586 T
1 T
28551587 ATGCACTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (28 bp):
TTTTTTAAAGACTAAAGTAAAATTTTAT
Found at i:28555737 original size:22 final size:22
Alignment explanation
Indices: 28555712--28555757 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
28555702 TTCAAAATTA
28555712 TTCTAATGAATTAATTAAAGAG
1 TTCTAATGAATTAATTAAAGAG
28555734 TTCTAATGAATTAATTAAAGAG
1 TTCTAATGAATTAATTAAAGAG
28555756 TT
1 TT
28555758 AAATCGCTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.39
Consensus pattern (22 bp):
TTCTAATGAATTAATTAAAGAG
Found at i:28561659 original size:13 final size:13
Alignment explanation
Indices: 28561641--28561665 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28561631 TTAAAACTAA
28561641 AATTAACTAATTT
1 AATTAACTAATTT
28561654 AATTAACTAATT
1 AATTAACTAATT
28561666 GTCGAAACGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTAACTAATTT
Found at i:28562880 original size:59 final size:58
Alignment explanation
Indices: 28562812--28562952 Score: 155
Period size: 58 Copynumber: 2.4 Consensus size: 58
28562802 ATTTTAGTCA
* *
28562812 TTCGGGGGTAAAATGGTAATTTTTACAAGTTTTG-GGGTCAAAAATGA-AATTTTTTAAAG-
1 TTCGAGGGTAAAATGG-AATTTTTACAAG-TTTGAGGGT-AAAAAT-ATAATTTTTAAAAGT
**
28562871 TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATATAATTTTTAAAAGT
1 TTCGAGGGT-AAAATGGAATTTTTACAAGTTTGAGGGTAAAAATATAATTTTTAAAAGT
*
28562930 TTC-AGGAGTAAAATGGATTTTTT
1 TTCGAGG-GTAAAATGGAATTTTT
28562953 GGATAATTTA
Statistics
Matches: 72, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
57 1 0.01
58 37 0.51
59 27 0.38
60 7 0.10
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (58 bp):
TTCGAGGGTAAAATGGAATTTTTACAAGTTTGAGGGTAAAAATATAATTTTTAAAAGT
Done.