Multiple sequence alignment - TraesCS2B01G272300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2B01G272300 chr2B 100.000 2485 0 0 1 2485 373748634 373746150 0.000000e+00 4590.0
1 TraesCS2B01G272300 chr2D 94.597 1203 28 12 707 1906 305506704 305505536 0.000000e+00 1827.0
2 TraesCS2B01G272300 chr2D 91.176 306 14 7 166 470 305507021 305506728 1.070000e-108 403.0
3 TraesCS2B01G272300 chr2D 92.857 238 15 2 2245 2480 305505246 305505009 6.580000e-91 344.0
4 TraesCS2B01G272300 chr2D 88.506 261 23 5 1909 2164 305505501 305505243 2.400000e-80 309.0
5 TraesCS2B01G272300 chr2D 86.747 249 26 5 1548 1795 305442761 305442519 1.130000e-68 270.0
6 TraesCS2B01G272300 chr2D 100.000 75 0 0 1 75 305507353 305507279 3.330000e-29 139.0
7 TraesCS2B01G272300 chr2D 86.813 91 5 4 618 708 648278391 648278474 7.320000e-16 95.3
8 TraesCS2B01G272300 chr2A 93.853 1155 49 6 755 1906 384331567 384330432 0.000000e+00 1720.0
9 TraesCS2B01G272300 chr2A 94.336 459 17 5 1 458 384332346 384331896 0.000000e+00 695.0
10 TraesCS2B01G272300 chr2A 92.975 242 16 1 2245 2485 384330145 384329904 3.930000e-93 351.0
11 TraesCS2B01G272300 chr2A 88.462 260 25 3 1909 2164 384330400 384330142 2.400000e-80 309.0
12 TraesCS2B01G272300 chr2A 92.857 42 3 0 1816 1857 605185360 605185401 7.420000e-06 62.1
13 TraesCS2B01G272300 chr4B 93.130 131 8 1 469 598 16092363 16092233 9.070000e-45 191.0
14 TraesCS2B01G272300 chr4A 93.130 131 8 1 466 595 618085163 618085033 9.070000e-45 191.0
15 TraesCS2B01G272300 chr4A 78.495 186 29 7 2294 2471 625181401 625181219 7.270000e-21 111.0
16 TraesCS2B01G272300 chr7B 91.367 139 10 2 461 598 671044754 671044617 3.260000e-44 189.0
17 TraesCS2B01G272300 chr7B 89.262 149 12 4 469 614 551815402 551815255 1.520000e-42 183.0
18 TraesCS2B01G272300 chr7B 96.552 87 3 0 2162 2248 433174776 433174862 7.160000e-31 145.0
19 TraesCS2B01G272300 chr3A 91.912 136 10 1 465 599 348834576 348834441 3.260000e-44 189.0
20 TraesCS2B01G272300 chr3A 87.097 93 7 4 616 708 26034108 26034195 1.570000e-17 100.0
21 TraesCS2B01G272300 chr1D 93.701 127 7 1 469 594 49900201 49900075 3.260000e-44 189.0
22 TraesCS2B01G272300 chr1D 97.701 87 2 0 2162 2248 10183702 10183788 1.540000e-32 150.0
23 TraesCS2B01G272300 chr5D 93.023 129 8 1 469 596 377830424 377830296 1.170000e-43 187.0
24 TraesCS2B01G272300 chr5D 96.629 89 3 0 2160 2248 496216345 496216257 5.540000e-32 148.0
25 TraesCS2B01G272300 chr5D 95.556 90 4 0 2163 2252 112955953 112955864 7.160000e-31 145.0
26 TraesCS2B01G272300 chr5D 96.512 86 3 0 2163 2248 276292518 276292433 2.580000e-30 143.0
27 TraesCS2B01G272300 chr5D 87.000 100 6 4 616 715 246339102 246339010 3.380000e-19 106.0
28 TraesCS2B01G272300 chr5D 91.489 47 3 1 2424 2469 176098728 176098774 2.060000e-06 63.9
29 TraesCS2B01G272300 chr1B 90.780 141 10 3 457 594 98990016 98989876 4.220000e-43 185.0
30 TraesCS2B01G272300 chr1B 97.619 84 2 0 2165 2248 15101274 15101191 7.160000e-31 145.0
31 TraesCS2B01G272300 chr1B 96.512 86 3 0 2163 2248 429603041 429603126 2.580000e-30 143.0
32 TraesCS2B01G272300 chr1B 78.818 203 27 10 2288 2479 625306437 625306634 3.360000e-24 122.0
33 TraesCS2B01G272300 chrUn 91.176 136 11 1 465 599 128516274 128516409 1.520000e-42 183.0
34 TraesCS2B01G272300 chrUn 86.139 101 7 4 616 716 84435465 84435372 4.370000e-18 102.0
35 TraesCS2B01G272300 chr5A 81.951 205 20 15 2281 2474 672558365 672558563 9.200000e-35 158.0
36 TraesCS2B01G272300 chr5A 78.922 204 26 14 2281 2472 445581026 445581224 3.360000e-24 122.0
37 TraesCS2B01G272300 chr5B 97.674 86 2 0 2163 2248 393069275 393069190 5.540000e-32 148.0
38 TraesCS2B01G272300 chr5B 86.316 95 6 4 615 709 461134388 461134475 2.030000e-16 97.1
39 TraesCS2B01G272300 chr5B 82.955 88 13 2 2056 2142 170618726 170618640 7.370000e-11 78.7
40 TraesCS2B01G272300 chr5B 92.857 42 1 2 1816 1857 32477187 32477226 2.670000e-05 60.2
41 TraesCS2B01G272300 chr6D 96.512 86 3 0 2163 2248 68334386 68334471 2.580000e-30 143.0
42 TraesCS2B01G272300 chr6D 86.316 95 6 4 615 709 120657575 120657662 2.030000e-16 97.1
43 TraesCS2B01G272300 chr3B 78.947 209 26 14 2289 2485 752701263 752701061 2.590000e-25 126.0
44 TraesCS2B01G272300 chr3B 86.458 96 11 2 614 709 706025371 706025464 1.220000e-18 104.0
45 TraesCS2B01G272300 chr3B 97.143 35 1 0 1817 1851 41665696 41665662 2.670000e-05 60.2
46 TraesCS2B01G272300 chr7A 77.835 194 30 8 2294 2477 10268383 10268193 9.400000e-20 108.0
47 TraesCS2B01G272300 chr7A 91.228 57 4 1 2430 2485 573081933 573081877 2.650000e-10 76.8
48 TraesCS2B01G272300 chr7A 90.698 43 2 2 1816 1857 670009234 670009275 3.450000e-04 56.5
49 TraesCS2B01G272300 chr6B 85.263 95 13 1 616 709 317882465 317882371 2.030000e-16 97.1
50 TraesCS2B01G272300 chr4D 83.838 99 12 3 616 711 313572416 313572319 9.460000e-15 91.6
51 TraesCS2B01G272300 chr4D 81.818 88 11 4 2062 2149 74597186 74597104 4.430000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G272300 chr2B 373746150 373748634 2484 True 4590.00 4590 100.0000 1 2485 1 chr2B.!!$R1 2484
1 TraesCS2B01G272300 chr2D 305505009 305507353 2344 True 604.40 1827 93.4272 1 2480 5 chr2D.!!$R2 2479
2 TraesCS2B01G272300 chr2A 384329904 384332346 2442 True 768.75 1720 92.4065 1 2485 4 chr2A.!!$R1 2484

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
147 148 1.0567 AGTGGCCCTTGTGACTCTGT 61.057 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1954 2422 1.063183 AGAAGCTCCTCAAAGCCAGT 58.937 50.0 0.0 0.0 43.56 4.0 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 4.413495 TTTTGTAGGATTTGTAGCGTGC 57.587 40.909 0.00 0.00 0.00 5.34
84 85 1.506309 TTGTAGCGTGCCAGCTTGTG 61.506 55.000 8.32 0.00 46.80 3.33
103 104 6.681368 GCTTGTGTGATCCTTTTGTTCTTCTT 60.681 38.462 0.00 0.00 0.00 2.52
104 105 6.377327 TGTGTGATCCTTTTGTTCTTCTTC 57.623 37.500 0.00 0.00 0.00 2.87
105 106 6.122277 TGTGTGATCCTTTTGTTCTTCTTCT 58.878 36.000 0.00 0.00 0.00 2.85
147 148 1.056700 AGTGGCCCTTGTGACTCTGT 61.057 55.000 0.00 0.00 0.00 3.41
216 384 5.934625 GTGAGAGAGTGGTGTTGTATTCAAT 59.065 40.000 0.00 0.00 35.92 2.57
232 400 1.132834 TCAATTACAGCTTGCGCATGG 59.867 47.619 22.96 14.79 39.10 3.66
261 429 8.073467 TGCCGTCATAATATCAGGTCATATTA 57.927 34.615 0.00 0.00 36.22 0.98
372 541 3.074412 ACCTTACAACTTGGAAGATGCG 58.926 45.455 14.53 1.50 40.80 4.73
385 554 3.123621 GGAAGATGCGTCACACACTTTAG 59.876 47.826 8.99 0.00 31.29 1.85
480 909 5.933617 AGTTATTTATTTACTCCCCCGTCC 58.066 41.667 0.00 0.00 0.00 4.79
481 910 5.668991 AGTTATTTATTTACTCCCCCGTCCT 59.331 40.000 0.00 0.00 0.00 3.85
482 911 6.845975 AGTTATTTATTTACTCCCCCGTCCTA 59.154 38.462 0.00 0.00 0.00 2.94
483 912 7.348011 AGTTATTTATTTACTCCCCCGTCCTAA 59.652 37.037 0.00 0.00 0.00 2.69
484 913 6.579850 ATTTATTTACTCCCCCGTCCTAAA 57.420 37.500 0.00 0.00 0.00 1.85
485 914 6.385766 TTTATTTACTCCCCCGTCCTAAAA 57.614 37.500 0.00 0.00 0.00 1.52
486 915 6.579850 TTATTTACTCCCCCGTCCTAAAAT 57.420 37.500 0.00 0.00 0.00 1.82
487 916 4.932911 TTTACTCCCCCGTCCTAAAATT 57.067 40.909 0.00 0.00 0.00 1.82
488 917 4.492494 TTACTCCCCCGTCCTAAAATTC 57.508 45.455 0.00 0.00 0.00 2.17
489 918 2.558974 ACTCCCCCGTCCTAAAATTCT 58.441 47.619 0.00 0.00 0.00 2.40
490 919 2.917600 ACTCCCCCGTCCTAAAATTCTT 59.082 45.455 0.00 0.00 0.00 2.52
491 920 3.279434 CTCCCCCGTCCTAAAATTCTTG 58.721 50.000 0.00 0.00 0.00 3.02
492 921 2.645797 TCCCCCGTCCTAAAATTCTTGT 59.354 45.455 0.00 0.00 0.00 3.16
493 922 3.014623 CCCCCGTCCTAAAATTCTTGTC 58.985 50.000 0.00 0.00 0.00 3.18
494 923 3.308188 CCCCCGTCCTAAAATTCTTGTCT 60.308 47.826 0.00 0.00 0.00 3.41
495 924 4.332828 CCCCGTCCTAAAATTCTTGTCTT 58.667 43.478 0.00 0.00 0.00 3.01
496 925 5.493809 CCCCGTCCTAAAATTCTTGTCTTA 58.506 41.667 0.00 0.00 0.00 2.10
497 926 5.941647 CCCCGTCCTAAAATTCTTGTCTTAA 59.058 40.000 0.00 0.00 0.00 1.85
498 927 6.431852 CCCCGTCCTAAAATTCTTGTCTTAAA 59.568 38.462 0.00 0.00 0.00 1.52
499 928 7.122204 CCCCGTCCTAAAATTCTTGTCTTAAAT 59.878 37.037 0.00 0.00 0.00 1.40
500 929 8.520351 CCCGTCCTAAAATTCTTGTCTTAAATT 58.480 33.333 0.00 0.00 0.00 1.82
501 930 9.908152 CCGTCCTAAAATTCTTGTCTTAAATTT 57.092 29.630 0.00 0.00 34.86 1.82
565 994 7.683437 ATACATCCGTATCTAGACGAATTCA 57.317 36.000 6.22 0.00 45.82 2.57
566 995 6.387041 ACATCCGTATCTAGACGAATTCAA 57.613 37.500 6.22 0.00 45.82 2.69
567 996 6.439599 ACATCCGTATCTAGACGAATTCAAG 58.560 40.000 6.22 0.00 45.82 3.02
568 997 6.262496 ACATCCGTATCTAGACGAATTCAAGA 59.738 38.462 6.22 3.07 45.82 3.02
569 998 6.057627 TCCGTATCTAGACGAATTCAAGAC 57.942 41.667 6.22 0.00 45.82 3.01
570 999 5.587443 TCCGTATCTAGACGAATTCAAGACA 59.413 40.000 6.22 0.00 45.82 3.41
571 1000 6.094464 TCCGTATCTAGACGAATTCAAGACAA 59.906 38.462 6.22 0.00 45.82 3.18
572 1001 6.415280 CCGTATCTAGACGAATTCAAGACAAG 59.585 42.308 6.22 0.00 45.82 3.16
573 1002 7.187480 CGTATCTAGACGAATTCAAGACAAGA 58.813 38.462 6.22 1.01 45.82 3.02
574 1003 7.696872 CGTATCTAGACGAATTCAAGACAAGAA 59.303 37.037 6.22 0.00 45.82 2.52
575 1004 9.522804 GTATCTAGACGAATTCAAGACAAGAAT 57.477 33.333 6.22 0.00 37.30 2.40
577 1006 8.833231 TCTAGACGAATTCAAGACAAGAATTT 57.167 30.769 6.22 0.00 43.60 1.82
578 1007 9.273016 TCTAGACGAATTCAAGACAAGAATTTT 57.727 29.630 6.22 0.00 43.60 1.82
579 1008 9.322776 CTAGACGAATTCAAGACAAGAATTTTG 57.677 33.333 6.22 0.00 43.60 2.44
580 1009 7.141363 AGACGAATTCAAGACAAGAATTTTGG 58.859 34.615 6.22 0.00 43.60 3.28
581 1010 7.013274 AGACGAATTCAAGACAAGAATTTTGGA 59.987 33.333 6.22 0.00 43.60 3.53
582 1011 7.488322 ACGAATTCAAGACAAGAATTTTGGAA 58.512 30.769 6.22 0.00 43.60 3.53
583 1012 7.435192 ACGAATTCAAGACAAGAATTTTGGAAC 59.565 33.333 6.22 0.00 43.60 3.62
584 1013 7.357532 CGAATTCAAGACAAGAATTTTGGAACG 60.358 37.037 6.22 0.00 43.60 3.95
585 1014 5.181690 TCAAGACAAGAATTTTGGAACGG 57.818 39.130 0.00 0.00 0.00 4.44
586 1015 4.037446 TCAAGACAAGAATTTTGGAACGGG 59.963 41.667 0.00 0.00 0.00 5.28
587 1016 2.890945 AGACAAGAATTTTGGAACGGGG 59.109 45.455 0.00 0.00 0.00 5.73
588 1017 1.967779 ACAAGAATTTTGGAACGGGGG 59.032 47.619 0.00 0.00 0.00 5.40
617 1046 3.879932 AACAGCAACGAAAAGAGCTAC 57.120 42.857 0.00 0.00 34.50 3.58
618 1047 3.113260 ACAGCAACGAAAAGAGCTACT 57.887 42.857 0.00 0.00 34.50 2.57
619 1048 3.060602 ACAGCAACGAAAAGAGCTACTC 58.939 45.455 0.00 0.00 34.50 2.59
620 1049 2.413453 CAGCAACGAAAAGAGCTACTCC 59.587 50.000 0.00 0.00 34.50 3.85
621 1050 1.732809 GCAACGAAAAGAGCTACTCCC 59.267 52.381 0.00 0.00 0.00 4.30
622 1051 2.613223 GCAACGAAAAGAGCTACTCCCT 60.613 50.000 0.00 0.00 0.00 4.20
623 1052 3.665190 CAACGAAAAGAGCTACTCCCTT 58.335 45.455 0.00 0.00 0.00 3.95
624 1053 3.596310 ACGAAAAGAGCTACTCCCTTC 57.404 47.619 0.00 0.00 0.00 3.46
625 1054 3.166679 ACGAAAAGAGCTACTCCCTTCT 58.833 45.455 0.00 0.00 0.00 2.85
626 1055 3.579151 ACGAAAAGAGCTACTCCCTTCTT 59.421 43.478 0.00 0.00 0.00 2.52
627 1056 4.040584 ACGAAAAGAGCTACTCCCTTCTTT 59.959 41.667 0.00 0.00 40.53 2.52
628 1057 4.998033 CGAAAAGAGCTACTCCCTTCTTTT 59.002 41.667 9.94 9.94 46.68 2.27
630 1059 5.568620 AAAGAGCTACTCCCTTCTTTTCA 57.431 39.130 0.00 0.00 36.72 2.69
631 1060 5.770685 AAGAGCTACTCCCTTCTTTTCAT 57.229 39.130 0.00 0.00 0.00 2.57
632 1061 6.875972 AAGAGCTACTCCCTTCTTTTCATA 57.124 37.500 0.00 0.00 0.00 2.15
633 1062 6.875972 AGAGCTACTCCCTTCTTTTCATAA 57.124 37.500 0.00 0.00 0.00 1.90
634 1063 7.444703 AGAGCTACTCCCTTCTTTTCATAAT 57.555 36.000 0.00 0.00 0.00 1.28
635 1064 8.554490 AGAGCTACTCCCTTCTTTTCATAATA 57.446 34.615 0.00 0.00 0.00 0.98
636 1065 9.165057 AGAGCTACTCCCTTCTTTTCATAATAT 57.835 33.333 0.00 0.00 0.00 1.28
642 1071 9.785982 ACTCCCTTCTTTTCATAATATAAGAGC 57.214 33.333 0.00 0.00 0.00 4.09
643 1072 8.833231 TCCCTTCTTTTCATAATATAAGAGCG 57.167 34.615 0.00 0.00 0.00 5.03
644 1073 8.429641 TCCCTTCTTTTCATAATATAAGAGCGT 58.570 33.333 0.00 0.00 0.00 5.07
645 1074 9.057089 CCCTTCTTTTCATAATATAAGAGCGTT 57.943 33.333 0.00 0.00 0.00 4.84
653 1082 9.982291 TTCATAATATAAGAGCGTTTTTGACAC 57.018 29.630 0.00 0.00 0.00 3.67
654 1083 9.378551 TCATAATATAAGAGCGTTTTTGACACT 57.621 29.630 0.00 0.00 0.00 3.55
657 1086 8.542497 AATATAAGAGCGTTTTTGACACTACA 57.458 30.769 0.00 0.00 0.00 2.74
658 1087 4.531659 AAGAGCGTTTTTGACACTACAC 57.468 40.909 0.00 0.00 0.00 2.90
659 1088 3.793559 AGAGCGTTTTTGACACTACACT 58.206 40.909 0.00 0.00 0.00 3.55
660 1089 4.940463 AGAGCGTTTTTGACACTACACTA 58.060 39.130 0.00 0.00 0.00 2.74
661 1090 4.982916 AGAGCGTTTTTGACACTACACTAG 59.017 41.667 0.00 0.00 0.00 2.57
662 1091 4.690122 AGCGTTTTTGACACTACACTAGT 58.310 39.130 0.00 0.00 40.28 2.57
681 1110 9.550811 ACACTAGTGTTAAAATATAAAAAGCGC 57.449 29.630 22.95 0.00 41.83 5.92
682 1111 9.769093 CACTAGTGTTAAAATATAAAAAGCGCT 57.231 29.630 15.06 2.64 0.00 5.92
683 1112 9.983804 ACTAGTGTTAAAATATAAAAAGCGCTC 57.016 29.630 12.06 0.00 0.00 5.03
695 1124 7.907214 ATAAAAAGCGCTCTTATAGTATGGG 57.093 36.000 12.06 0.00 31.02 4.00
696 1125 5.546621 AAAAGCGCTCTTATAGTATGGGA 57.453 39.130 12.06 0.00 31.02 4.37
697 1126 4.522722 AAGCGCTCTTATAGTATGGGAC 57.477 45.455 12.06 0.00 0.00 4.46
698 1127 2.488545 AGCGCTCTTATAGTATGGGACG 59.511 50.000 2.64 0.00 0.00 4.79
699 1128 2.415625 GCGCTCTTATAGTATGGGACGG 60.416 54.545 0.00 0.00 0.00 4.79
700 1129 3.079578 CGCTCTTATAGTATGGGACGGA 58.920 50.000 0.00 0.00 0.00 4.69
701 1130 3.127203 CGCTCTTATAGTATGGGACGGAG 59.873 52.174 0.00 0.00 0.00 4.63
702 1131 3.444388 GCTCTTATAGTATGGGACGGAGG 59.556 52.174 0.00 0.00 0.00 4.30
703 1132 4.017808 CTCTTATAGTATGGGACGGAGGG 58.982 52.174 0.00 0.00 0.00 4.30
704 1133 3.659195 TCTTATAGTATGGGACGGAGGGA 59.341 47.826 0.00 0.00 0.00 4.20
705 1134 2.606751 ATAGTATGGGACGGAGGGAG 57.393 55.000 0.00 0.00 0.00 4.30
722 1151 7.125356 ACGGAGGGAGTATTATTTTACTGAACT 59.875 37.037 0.00 0.00 32.59 3.01
949 1378 6.147985 ACAAGATTTAAGAAAGGAGCTCGTTC 59.852 38.462 21.09 18.81 34.71 3.95
1146 1578 1.274703 ACATCGGCTCCTCCACCAAT 61.275 55.000 0.00 0.00 34.01 3.16
1227 1662 7.599630 TTGGTTCGTTGACATAATTACTACC 57.400 36.000 0.00 0.00 0.00 3.18
1253 1688 1.602311 GGATGCAGATCATGGTGACC 58.398 55.000 0.00 0.00 35.05 4.02
1588 2023 7.119116 GTGATTTGATGATGTGGTGTAGTACAA 59.881 37.037 4.11 0.00 0.00 2.41
1589 2024 7.828717 TGATTTGATGATGTGGTGTAGTACAAT 59.171 33.333 4.11 0.00 0.00 2.71
1590 2025 6.983474 TTGATGATGTGGTGTAGTACAATG 57.017 37.500 4.11 0.00 0.00 2.82
1591 2026 6.048732 TGATGATGTGGTGTAGTACAATGT 57.951 37.500 4.11 0.00 0.00 2.71
1758 2193 8.442374 AGTCCAAAAACTAAATTAGTACTCCCA 58.558 33.333 6.04 0.00 38.26 4.37
1800 2235 9.469807 AGATCGTTTACATCAGTAATTGATCTC 57.530 33.333 17.74 5.65 45.89 2.75
1906 2341 4.200283 CCTCTCACGGCTCGAGGC 62.200 72.222 27.92 27.92 38.05 4.70
2050 2518 1.516603 GTCGGCTGGCGTTAGAGTC 60.517 63.158 23.07 3.44 0.00 3.36
2091 2562 6.670617 AGGTAGGTTATAGTTAGACTCTGCA 58.329 40.000 0.00 0.00 0.00 4.41
2093 2564 7.231722 AGGTAGGTTATAGTTAGACTCTGCATG 59.768 40.741 0.00 0.00 0.00 4.06
2099 2570 3.353557 AGTTAGACTCTGCATGGTACGA 58.646 45.455 0.00 0.00 0.00 3.43
2151 2622 9.402786 TCCTAGTAGGACTCTTGTATCCTATAA 57.597 37.037 15.33 0.00 46.75 0.98
2176 2647 2.169330 ACGAAGTACTCCCTCTGTTCC 58.831 52.381 0.00 0.00 41.94 3.62
2177 2648 2.168496 CGAAGTACTCCCTCTGTTCCA 58.832 52.381 0.00 0.00 0.00 3.53
2178 2649 2.761208 CGAAGTACTCCCTCTGTTCCAT 59.239 50.000 0.00 0.00 0.00 3.41
2179 2650 3.952323 CGAAGTACTCCCTCTGTTCCATA 59.048 47.826 0.00 0.00 0.00 2.74
2180 2651 4.585162 CGAAGTACTCCCTCTGTTCCATAT 59.415 45.833 0.00 0.00 0.00 1.78
2181 2652 5.069251 CGAAGTACTCCCTCTGTTCCATATT 59.931 44.000 0.00 0.00 0.00 1.28
2182 2653 6.264744 CGAAGTACTCCCTCTGTTCCATATTA 59.735 42.308 0.00 0.00 0.00 0.98
2183 2654 6.980416 AGTACTCCCTCTGTTCCATATTAC 57.020 41.667 0.00 0.00 0.00 1.89
2184 2655 6.684538 AGTACTCCCTCTGTTCCATATTACT 58.315 40.000 0.00 0.00 0.00 2.24
2185 2656 6.778559 AGTACTCCCTCTGTTCCATATTACTC 59.221 42.308 0.00 0.00 0.00 2.59
2186 2657 4.585162 ACTCCCTCTGTTCCATATTACTCG 59.415 45.833 0.00 0.00 0.00 4.18
2187 2658 4.543689 TCCCTCTGTTCCATATTACTCGT 58.456 43.478 0.00 0.00 0.00 4.18
2188 2659 4.583489 TCCCTCTGTTCCATATTACTCGTC 59.417 45.833 0.00 0.00 0.00 4.20
2189 2660 4.537965 CCTCTGTTCCATATTACTCGTCG 58.462 47.826 0.00 0.00 0.00 5.12
2190 2661 3.961182 TCTGTTCCATATTACTCGTCGC 58.039 45.455 0.00 0.00 0.00 5.19
2191 2662 3.630769 TCTGTTCCATATTACTCGTCGCT 59.369 43.478 0.00 0.00 0.00 4.93
2192 2663 3.702330 TGTTCCATATTACTCGTCGCTG 58.298 45.455 0.00 0.00 0.00 5.18
2193 2664 3.379057 TGTTCCATATTACTCGTCGCTGA 59.621 43.478 0.00 0.00 0.00 4.26
2194 2665 4.037565 TGTTCCATATTACTCGTCGCTGAT 59.962 41.667 0.00 0.00 0.00 2.90
2195 2666 4.848562 TCCATATTACTCGTCGCTGATT 57.151 40.909 0.00 0.00 0.00 2.57
2196 2667 5.196341 TCCATATTACTCGTCGCTGATTT 57.804 39.130 0.00 0.00 0.00 2.17
2197 2668 6.321848 TCCATATTACTCGTCGCTGATTTA 57.678 37.500 0.00 0.00 0.00 1.40
2198 2669 6.379386 TCCATATTACTCGTCGCTGATTTAG 58.621 40.000 0.00 0.00 0.00 1.85
2199 2670 6.016527 TCCATATTACTCGTCGCTGATTTAGT 60.017 38.462 0.00 0.00 0.00 2.24
2200 2671 7.173735 TCCATATTACTCGTCGCTGATTTAGTA 59.826 37.037 0.00 0.00 0.00 1.82
2201 2672 7.270793 CCATATTACTCGTCGCTGATTTAGTAC 59.729 40.741 0.00 0.00 0.00 2.73
2202 2673 5.550232 TTACTCGTCGCTGATTTAGTACA 57.450 39.130 0.00 0.00 0.00 2.90
2203 2674 4.430137 ACTCGTCGCTGATTTAGTACAA 57.570 40.909 0.00 0.00 0.00 2.41
2204 2675 4.164294 ACTCGTCGCTGATTTAGTACAAC 58.836 43.478 0.00 0.00 0.00 3.32
2205 2676 4.082895 ACTCGTCGCTGATTTAGTACAACT 60.083 41.667 0.00 0.00 0.00 3.16
2206 2677 4.801891 TCGTCGCTGATTTAGTACAACTT 58.198 39.130 0.00 0.00 0.00 2.66
2207 2678 5.224888 TCGTCGCTGATTTAGTACAACTTT 58.775 37.500 0.00 0.00 0.00 2.66
2208 2679 5.118050 TCGTCGCTGATTTAGTACAACTTTG 59.882 40.000 0.00 0.00 0.00 2.77
2209 2680 5.107607 CGTCGCTGATTTAGTACAACTTTGT 60.108 40.000 0.00 0.00 44.86 2.83
2210 2681 6.088483 CGTCGCTGATTTAGTACAACTTTGTA 59.912 38.462 0.00 0.00 42.35 2.41
2224 2695 7.173863 ACAACTTTGTACTAAATCAGTGACG 57.826 36.000 0.00 0.00 40.16 4.35
2225 2696 6.982141 ACAACTTTGTACTAAATCAGTGACGA 59.018 34.615 0.00 0.00 40.16 4.20
2226 2697 7.169308 ACAACTTTGTACTAAATCAGTGACGAG 59.831 37.037 0.00 0.00 40.16 4.18
2227 2698 6.746120 ACTTTGTACTAAATCAGTGACGAGT 58.254 36.000 0.00 1.72 38.24 4.18
2228 2699 7.208080 ACTTTGTACTAAATCAGTGACGAGTT 58.792 34.615 8.30 0.00 38.24 3.01
2229 2700 8.355169 ACTTTGTACTAAATCAGTGACGAGTTA 58.645 33.333 8.30 0.00 38.24 2.24
2230 2701 9.355215 CTTTGTACTAAATCAGTGACGAGTTAT 57.645 33.333 8.30 0.00 38.24 1.89
2233 2704 9.946165 TGTACTAAATCAGTGACGAGTTATATG 57.054 33.333 8.30 0.00 38.24 1.78
2234 2705 9.395707 GTACTAAATCAGTGACGAGTTATATGG 57.604 37.037 8.30 0.00 38.24 2.74
2235 2706 8.234136 ACTAAATCAGTGACGAGTTATATGGA 57.766 34.615 0.00 0.00 35.62 3.41
2236 2707 8.692710 ACTAAATCAGTGACGAGTTATATGGAA 58.307 33.333 0.00 0.00 35.62 3.53
2237 2708 7.772332 AAATCAGTGACGAGTTATATGGAAC 57.228 36.000 0.00 0.00 0.00 3.62
2238 2709 4.916870 TCAGTGACGAGTTATATGGAACG 58.083 43.478 0.00 0.00 34.36 3.95
2239 2710 4.042398 CAGTGACGAGTTATATGGAACGG 58.958 47.826 0.00 0.00 34.36 4.44
2240 2711 3.949754 AGTGACGAGTTATATGGAACGGA 59.050 43.478 0.00 0.00 34.36 4.69
2241 2712 4.036498 AGTGACGAGTTATATGGAACGGAG 59.964 45.833 0.00 0.00 34.36 4.63
2242 2713 3.317149 TGACGAGTTATATGGAACGGAGG 59.683 47.826 0.00 0.00 34.36 4.30
2243 2714 2.626743 ACGAGTTATATGGAACGGAGGG 59.373 50.000 0.00 0.00 34.36 4.30
2244 2715 2.889045 CGAGTTATATGGAACGGAGGGA 59.111 50.000 0.00 0.00 34.36 4.20
2245 2716 3.057456 CGAGTTATATGGAACGGAGGGAG 60.057 52.174 0.00 0.00 34.36 4.30
2246 2717 3.896272 GAGTTATATGGAACGGAGGGAGT 59.104 47.826 0.00 0.00 34.36 3.85
2247 2718 5.070823 AGTTATATGGAACGGAGGGAGTA 57.929 43.478 0.00 0.00 34.36 2.59
2345 2816 1.770658 CATCCATAGTCAAGCCCAGGA 59.229 52.381 0.00 0.00 0.00 3.86
2348 2819 2.852449 TCCATAGTCAAGCCCAGGAATT 59.148 45.455 0.00 0.00 0.00 2.17
2383 2854 4.501071 GGTGAACCTCGTTAGCAAATCTA 58.499 43.478 0.00 0.00 0.00 1.98
2388 2859 3.933332 ACCTCGTTAGCAAATCTAAGTGC 59.067 43.478 0.00 0.00 37.90 4.40
2393 2864 2.185004 AGCAAATCTAAGTGCCGTGT 57.815 45.000 0.00 0.00 41.88 4.49
2420 2892 4.931601 GTGTGATTGCTTAGTCATCAGTGA 59.068 41.667 0.00 0.00 0.00 3.41
2476 2948 3.988517 GAGTAAGTTTCAAGGAGGTCGTG 59.011 47.826 0.00 0.00 0.00 4.35
2477 2949 3.640029 AGTAAGTTTCAAGGAGGTCGTGA 59.360 43.478 0.00 0.00 32.21 4.35
2478 2950 3.771577 AAGTTTCAAGGAGGTCGTGAT 57.228 42.857 0.00 0.00 34.07 3.06
2480 2952 3.403038 AGTTTCAAGGAGGTCGTGATTG 58.597 45.455 0.00 0.00 34.07 2.67
2481 2953 3.139077 GTTTCAAGGAGGTCGTGATTGT 58.861 45.455 0.00 0.00 34.07 2.71
2482 2954 4.039973 AGTTTCAAGGAGGTCGTGATTGTA 59.960 41.667 0.00 0.00 34.07 2.41
2483 2955 3.868757 TCAAGGAGGTCGTGATTGTAG 57.131 47.619 0.00 0.00 0.00 2.74
2484 2956 3.427573 TCAAGGAGGTCGTGATTGTAGA 58.572 45.455 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 2.624838 ACAAAAGGATCACACAAGCTGG 59.375 45.455 0.00 0.00 0.00 4.85
84 85 9.057089 TCTTTAGAAGAAGAACAAAAGGATCAC 57.943 33.333 0.00 0.00 33.83 3.06
103 104 6.769512 AGCTCTTATGTGTTGGTTCTTTAGA 58.230 36.000 0.00 0.00 0.00 2.10
104 105 7.819900 ACTAGCTCTTATGTGTTGGTTCTTTAG 59.180 37.037 0.00 0.00 0.00 1.85
105 106 7.602644 CACTAGCTCTTATGTGTTGGTTCTTTA 59.397 37.037 0.00 0.00 0.00 1.85
160 161 8.877864 AAAACCCTATGTACATTTCATGAGAA 57.122 30.769 14.77 0.00 0.00 2.87
232 400 2.679837 CCTGATATTATGACGGCATGGC 59.320 50.000 15.86 9.69 35.94 4.40
341 509 5.060506 CCAAGTTGTAAGGTCACATACACA 58.939 41.667 1.45 0.00 32.07 3.72
342 510 5.302360 TCCAAGTTGTAAGGTCACATACAC 58.698 41.667 1.45 0.00 32.07 2.90
343 511 5.554437 TCCAAGTTGTAAGGTCACATACA 57.446 39.130 1.45 0.00 0.00 2.29
372 541 4.976116 GCCAATGAAACTAAAGTGTGTGAC 59.024 41.667 0.00 0.00 0.00 3.67
385 554 2.159986 CGCACGAATTTGCCAATGAAAC 60.160 45.455 0.00 0.00 39.53 2.78
468 897 3.727948 AGAATTTTAGGACGGGGGAGTA 58.272 45.455 0.00 0.00 0.00 2.59
469 898 2.558974 AGAATTTTAGGACGGGGGAGT 58.441 47.619 0.00 0.00 0.00 3.85
470 899 3.279434 CAAGAATTTTAGGACGGGGGAG 58.721 50.000 0.00 0.00 0.00 4.30
471 900 2.645797 ACAAGAATTTTAGGACGGGGGA 59.354 45.455 0.00 0.00 0.00 4.81
472 901 3.014623 GACAAGAATTTTAGGACGGGGG 58.985 50.000 0.00 0.00 0.00 5.40
473 902 3.951663 AGACAAGAATTTTAGGACGGGG 58.048 45.455 0.00 0.00 0.00 5.73
474 903 7.443259 TTTAAGACAAGAATTTTAGGACGGG 57.557 36.000 0.00 0.00 0.00 5.28
475 904 9.908152 AAATTTAAGACAAGAATTTTAGGACGG 57.092 29.630 0.00 0.00 31.00 4.79
541 970 7.683437 TGAATTCGTCTAGATACGGATGTAT 57.317 36.000 0.00 0.00 40.19 2.29
542 971 7.443272 TCTTGAATTCGTCTAGATACGGATGTA 59.557 37.037 0.00 0.00 40.19 2.29
543 972 6.262496 TCTTGAATTCGTCTAGATACGGATGT 59.738 38.462 0.00 0.00 40.19 3.06
544 973 6.579292 GTCTTGAATTCGTCTAGATACGGATG 59.421 42.308 0.00 0.00 40.19 3.51
545 974 6.262496 TGTCTTGAATTCGTCTAGATACGGAT 59.738 38.462 0.00 0.00 42.90 4.18
546 975 5.587443 TGTCTTGAATTCGTCTAGATACGGA 59.413 40.000 0.00 0.00 39.77 4.69
547 976 5.817988 TGTCTTGAATTCGTCTAGATACGG 58.182 41.667 0.00 0.00 39.77 4.02
548 977 7.187480 TCTTGTCTTGAATTCGTCTAGATACG 58.813 38.462 0.00 0.00 39.77 3.06
549 978 8.912787 TTCTTGTCTTGAATTCGTCTAGATAC 57.087 34.615 0.00 0.00 39.77 2.24
551 980 9.442047 AAATTCTTGTCTTGAATTCGTCTAGAT 57.558 29.630 0.00 0.00 41.54 1.98
552 981 8.833231 AAATTCTTGTCTTGAATTCGTCTAGA 57.167 30.769 0.04 0.00 41.54 2.43
553 982 9.322776 CAAAATTCTTGTCTTGAATTCGTCTAG 57.677 33.333 0.04 0.00 41.54 2.43
554 983 8.289618 CCAAAATTCTTGTCTTGAATTCGTCTA 58.710 33.333 0.04 0.00 41.54 2.59
555 984 7.013274 TCCAAAATTCTTGTCTTGAATTCGTCT 59.987 33.333 0.04 0.00 41.54 4.18
556 985 7.138736 TCCAAAATTCTTGTCTTGAATTCGTC 58.861 34.615 0.04 0.00 41.54 4.20
557 986 7.038154 TCCAAAATTCTTGTCTTGAATTCGT 57.962 32.000 0.04 0.00 41.54 3.85
558 987 7.357532 CGTTCCAAAATTCTTGTCTTGAATTCG 60.358 37.037 0.04 0.00 41.54 3.34
559 988 7.096065 CCGTTCCAAAATTCTTGTCTTGAATTC 60.096 37.037 0.00 0.00 41.54 2.17
560 989 6.701400 CCGTTCCAAAATTCTTGTCTTGAATT 59.299 34.615 0.00 0.00 43.44 2.17
561 990 6.215845 CCGTTCCAAAATTCTTGTCTTGAAT 58.784 36.000 0.00 0.00 35.88 2.57
562 991 5.451242 CCCGTTCCAAAATTCTTGTCTTGAA 60.451 40.000 0.00 0.00 0.00 2.69
563 992 4.037446 CCCGTTCCAAAATTCTTGTCTTGA 59.963 41.667 0.00 0.00 0.00 3.02
564 993 4.298332 CCCGTTCCAAAATTCTTGTCTTG 58.702 43.478 0.00 0.00 0.00 3.02
565 994 3.320826 CCCCGTTCCAAAATTCTTGTCTT 59.679 43.478 0.00 0.00 0.00 3.01
566 995 2.890945 CCCCGTTCCAAAATTCTTGTCT 59.109 45.455 0.00 0.00 0.00 3.41
567 996 2.029380 CCCCCGTTCCAAAATTCTTGTC 60.029 50.000 0.00 0.00 0.00 3.18
568 997 1.967779 CCCCCGTTCCAAAATTCTTGT 59.032 47.619 0.00 0.00 0.00 3.16
569 998 2.741759 CCCCCGTTCCAAAATTCTTG 57.258 50.000 0.00 0.00 0.00 3.02
585 1014 2.681344 CGTTGCTGTTAAATACTCCCCC 59.319 50.000 0.00 0.00 0.00 5.40
586 1015 3.602483 TCGTTGCTGTTAAATACTCCCC 58.398 45.455 0.00 0.00 0.00 4.81
587 1016 5.616488 TTTCGTTGCTGTTAAATACTCCC 57.384 39.130 0.00 0.00 0.00 4.30
588 1017 6.894828 TCTTTTCGTTGCTGTTAAATACTCC 58.105 36.000 0.00 0.00 0.00 3.85
589 1018 6.520104 GCTCTTTTCGTTGCTGTTAAATACTC 59.480 38.462 0.00 0.00 0.00 2.59
590 1019 6.204882 AGCTCTTTTCGTTGCTGTTAAATACT 59.795 34.615 0.00 0.00 34.19 2.12
591 1020 6.371389 AGCTCTTTTCGTTGCTGTTAAATAC 58.629 36.000 0.00 0.00 34.19 1.89
617 1046 8.930760 CGCTCTTATATTATGAAAAGAAGGGAG 58.069 37.037 0.00 0.00 0.00 4.30
618 1047 8.429641 ACGCTCTTATATTATGAAAAGAAGGGA 58.570 33.333 0.00 0.00 0.00 4.20
619 1048 8.608844 ACGCTCTTATATTATGAAAAGAAGGG 57.391 34.615 0.00 0.00 0.00 3.95
627 1056 9.982291 GTGTCAAAAACGCTCTTATATTATGAA 57.018 29.630 0.00 0.00 35.42 2.57
628 1057 9.378551 AGTGTCAAAAACGCTCTTATATTATGA 57.621 29.630 0.00 0.00 45.69 2.15
631 1060 9.642327 TGTAGTGTCAAAAACGCTCTTATATTA 57.358 29.630 0.00 0.00 45.69 0.98
632 1061 8.440833 GTGTAGTGTCAAAAACGCTCTTATATT 58.559 33.333 0.00 0.00 45.69 1.28
633 1062 7.817962 AGTGTAGTGTCAAAAACGCTCTTATAT 59.182 33.333 0.00 0.00 45.69 0.86
634 1063 7.149973 AGTGTAGTGTCAAAAACGCTCTTATA 58.850 34.615 0.00 0.00 45.69 0.98
635 1064 5.989777 AGTGTAGTGTCAAAAACGCTCTTAT 59.010 36.000 0.00 0.00 45.69 1.73
636 1065 5.353938 AGTGTAGTGTCAAAAACGCTCTTA 58.646 37.500 0.00 0.00 45.69 2.10
637 1066 4.189231 AGTGTAGTGTCAAAAACGCTCTT 58.811 39.130 0.00 0.00 45.69 2.85
638 1067 3.793559 AGTGTAGTGTCAAAAACGCTCT 58.206 40.909 0.00 0.00 45.69 4.09
639 1068 4.743644 ACTAGTGTAGTGTCAAAAACGCTC 59.256 41.667 0.00 0.00 45.69 5.03
656 1085 9.769093 AGCGCTTTTTATATTTTAACACTAGTG 57.231 29.630 21.44 21.44 0.00 2.74
657 1086 9.983804 GAGCGCTTTTTATATTTTAACACTAGT 57.016 29.630 13.26 0.00 0.00 2.57
669 1098 9.601217 CCCATACTATAAGAGCGCTTTTTATAT 57.399 33.333 23.89 14.33 35.56 0.86
670 1099 8.809066 TCCCATACTATAAGAGCGCTTTTTATA 58.191 33.333 19.12 21.61 35.56 0.98
671 1100 7.603024 GTCCCATACTATAAGAGCGCTTTTTAT 59.397 37.037 19.12 21.64 35.56 1.40
672 1101 6.927381 GTCCCATACTATAAGAGCGCTTTTTA 59.073 38.462 19.12 16.70 35.56 1.52
673 1102 5.758784 GTCCCATACTATAAGAGCGCTTTTT 59.241 40.000 19.12 15.06 35.56 1.94
674 1103 5.298347 GTCCCATACTATAAGAGCGCTTTT 58.702 41.667 17.98 17.98 35.56 2.27
675 1104 4.558898 CGTCCCATACTATAAGAGCGCTTT 60.559 45.833 13.26 1.42 35.56 3.51
676 1105 3.057456 CGTCCCATACTATAAGAGCGCTT 60.057 47.826 13.26 8.09 38.15 4.68
677 1106 2.488545 CGTCCCATACTATAAGAGCGCT 59.511 50.000 11.27 11.27 0.00 5.92
678 1107 2.415625 CCGTCCCATACTATAAGAGCGC 60.416 54.545 0.00 0.00 0.00 5.92
679 1108 3.079578 TCCGTCCCATACTATAAGAGCG 58.920 50.000 0.00 0.00 0.00 5.03
680 1109 3.444388 CCTCCGTCCCATACTATAAGAGC 59.556 52.174 0.00 0.00 0.00 4.09
681 1110 4.017808 CCCTCCGTCCCATACTATAAGAG 58.982 52.174 0.00 0.00 0.00 2.85
682 1111 3.659195 TCCCTCCGTCCCATACTATAAGA 59.341 47.826 0.00 0.00 0.00 2.10
683 1112 4.017808 CTCCCTCCGTCCCATACTATAAG 58.982 52.174 0.00 0.00 0.00 1.73
684 1113 3.400322 ACTCCCTCCGTCCCATACTATAA 59.600 47.826 0.00 0.00 0.00 0.98
685 1114 2.991713 ACTCCCTCCGTCCCATACTATA 59.008 50.000 0.00 0.00 0.00 1.31
686 1115 1.787676 ACTCCCTCCGTCCCATACTAT 59.212 52.381 0.00 0.00 0.00 2.12
687 1116 1.229131 ACTCCCTCCGTCCCATACTA 58.771 55.000 0.00 0.00 0.00 1.82
688 1117 1.229131 TACTCCCTCCGTCCCATACT 58.771 55.000 0.00 0.00 0.00 2.12
689 1118 2.305858 ATACTCCCTCCGTCCCATAC 57.694 55.000 0.00 0.00 0.00 2.39
690 1119 4.687262 ATAATACTCCCTCCGTCCCATA 57.313 45.455 0.00 0.00 0.00 2.74
691 1120 3.562108 ATAATACTCCCTCCGTCCCAT 57.438 47.619 0.00 0.00 0.00 4.00
692 1121 3.339713 AATAATACTCCCTCCGTCCCA 57.660 47.619 0.00 0.00 0.00 4.37
693 1122 4.701651 AAAATAATACTCCCTCCGTCCC 57.298 45.455 0.00 0.00 0.00 4.46
694 1123 6.041296 TCAGTAAAATAATACTCCCTCCGTCC 59.959 42.308 0.00 0.00 33.90 4.79
695 1124 7.047460 TCAGTAAAATAATACTCCCTCCGTC 57.953 40.000 0.00 0.00 33.90 4.79
696 1125 7.125356 AGTTCAGTAAAATAATACTCCCTCCGT 59.875 37.037 0.00 0.00 33.90 4.69
697 1126 7.438459 CAGTTCAGTAAAATAATACTCCCTCCG 59.562 40.741 0.00 0.00 33.90 4.63
698 1127 8.265764 ACAGTTCAGTAAAATAATACTCCCTCC 58.734 37.037 0.00 0.00 33.90 4.30
699 1128 9.668497 AACAGTTCAGTAAAATAATACTCCCTC 57.332 33.333 0.00 0.00 33.90 4.30
722 1151 0.608856 AGCATCACCGGCATGAAACA 60.609 50.000 16.49 0.00 30.82 2.83
854 1283 2.158813 GGATAGGTTTCGGATCCTTGCA 60.159 50.000 10.75 0.00 36.89 4.08
890 1319 2.046700 GGGGAATCGCGTGGTGAA 60.047 61.111 5.77 0.00 0.00 3.18
949 1378 2.985117 TTGCTCAGGCGCAATGCTG 61.985 57.895 10.83 7.47 44.30 4.41
958 1387 2.389866 GATGCTGCGATTGCTCAGGC 62.390 60.000 6.47 6.21 43.34 4.85
1080 1509 2.811317 CTCAAGGACGGCAGCGTC 60.811 66.667 6.93 6.93 38.09 5.19
1146 1578 7.225341 ACGTAGTATGTGTGTGATCTTACGATA 59.775 37.037 7.15 0.00 41.94 2.92
1253 1688 1.807165 CAGCATCAGGGTCGTCGTG 60.807 63.158 0.00 0.00 0.00 4.35
1588 2023 8.681486 ACAAAGATGCATACACATACATACAT 57.319 30.769 0.00 0.00 0.00 2.29
1589 2024 8.504812 AACAAAGATGCATACACATACATACA 57.495 30.769 0.00 0.00 0.00 2.29
1590 2025 9.438291 GAAACAAAGATGCATACACATACATAC 57.562 33.333 0.00 0.00 0.00 2.39
1591 2026 9.171877 TGAAACAAAGATGCATACACATACATA 57.828 29.630 0.00 0.00 0.00 2.29
1731 2166 9.293404 GGGAGTACTAATTTAGTTTTTGGACTT 57.707 33.333 14.00 0.00 40.14 3.01
1795 2230 9.332502 TCACTAACTGATCTAAGTAGTGAGATC 57.667 37.037 15.77 15.77 45.60 2.75
1796 2231 9.860650 ATCACTAACTGATCTAAGTAGTGAGAT 57.139 33.333 22.07 0.00 40.28 2.75
1846 2281 6.627243 TGCGCTTTTATTGTTACTCTCTCTA 58.373 36.000 9.73 0.00 0.00 2.43
1954 2422 1.063183 AGAAGCTCCTCAAAGCCAGT 58.937 50.000 0.00 0.00 43.56 4.00
2006 2474 3.072468 CACCGAGGCGACCCCTTA 61.072 66.667 0.00 0.00 46.60 2.69
2050 2518 4.270084 CCTACCTTGTACACAATATGCACG 59.730 45.833 0.00 0.00 35.02 5.34
2091 2562 2.693591 CCCTGTCTACACATCGTACCAT 59.306 50.000 0.00 0.00 0.00 3.55
2093 2564 2.097825 ACCCTGTCTACACATCGTACC 58.902 52.381 0.00 0.00 0.00 3.34
2099 2570 4.323485 CCACAACATACCCTGTCTACACAT 60.323 45.833 0.00 0.00 36.98 3.21
2151 2622 4.857679 ACAGAGGGAGTACTTCGTCTATT 58.142 43.478 22.87 12.27 0.00 1.73
2153 2624 3.996921 ACAGAGGGAGTACTTCGTCTA 57.003 47.619 22.87 0.00 0.00 2.59
2155 2626 2.164017 GGAACAGAGGGAGTACTTCGTC 59.836 54.545 14.88 14.88 0.00 4.20
2172 2643 3.961182 TCAGCGACGAGTAATATGGAAC 58.039 45.455 0.00 0.00 0.00 3.62
2173 2644 4.848562 ATCAGCGACGAGTAATATGGAA 57.151 40.909 0.00 0.00 0.00 3.53
2174 2645 4.848562 AATCAGCGACGAGTAATATGGA 57.151 40.909 0.00 0.00 0.00 3.41
2175 2646 6.150318 ACTAAATCAGCGACGAGTAATATGG 58.850 40.000 0.00 0.00 0.00 2.74
2176 2647 7.801783 TGTACTAAATCAGCGACGAGTAATATG 59.198 37.037 0.00 0.00 0.00 1.78
2177 2648 7.868775 TGTACTAAATCAGCGACGAGTAATAT 58.131 34.615 0.00 0.00 0.00 1.28
2178 2649 7.250445 TGTACTAAATCAGCGACGAGTAATA 57.750 36.000 0.00 0.00 0.00 0.98
2179 2650 6.127810 TGTACTAAATCAGCGACGAGTAAT 57.872 37.500 0.00 0.00 0.00 1.89
2180 2651 5.550232 TGTACTAAATCAGCGACGAGTAA 57.450 39.130 0.00 0.00 0.00 2.24
2181 2652 5.122869 AGTTGTACTAAATCAGCGACGAGTA 59.877 40.000 0.00 0.00 0.00 2.59
2182 2653 4.082895 AGTTGTACTAAATCAGCGACGAGT 60.083 41.667 0.00 0.00 0.00 4.18
2183 2654 4.413087 AGTTGTACTAAATCAGCGACGAG 58.587 43.478 0.00 0.00 0.00 4.18
2184 2655 4.430137 AGTTGTACTAAATCAGCGACGA 57.570 40.909 0.00 0.00 0.00 4.20
2185 2656 5.107607 ACAAAGTTGTACTAAATCAGCGACG 60.108 40.000 0.00 0.00 40.16 5.12
2186 2657 6.224420 ACAAAGTTGTACTAAATCAGCGAC 57.776 37.500 0.00 0.00 40.16 5.19
2199 2670 8.136800 TCGTCACTGATTTAGTACAAAGTTGTA 58.863 33.333 0.00 0.00 42.35 2.41
2200 2671 6.982141 TCGTCACTGATTTAGTACAAAGTTGT 59.018 34.615 1.75 1.75 44.86 3.32
2201 2672 7.169308 ACTCGTCACTGATTTAGTACAAAGTTG 59.831 37.037 0.00 0.00 37.60 3.16
2202 2673 7.208080 ACTCGTCACTGATTTAGTACAAAGTT 58.792 34.615 0.00 0.00 37.60 2.66
2203 2674 6.746120 ACTCGTCACTGATTTAGTACAAAGT 58.254 36.000 0.00 0.00 37.60 2.66
2204 2675 7.639162 AACTCGTCACTGATTTAGTACAAAG 57.361 36.000 0.00 0.00 37.60 2.77
2207 2678 9.946165 CATATAACTCGTCACTGATTTAGTACA 57.054 33.333 0.00 0.00 37.60 2.90
2208 2679 9.395707 CCATATAACTCGTCACTGATTTAGTAC 57.604 37.037 0.00 0.00 37.60 2.73
2209 2680 9.346005 TCCATATAACTCGTCACTGATTTAGTA 57.654 33.333 0.00 0.00 37.60 1.82
2210 2681 8.234136 TCCATATAACTCGTCACTGATTTAGT 57.766 34.615 0.00 0.00 41.36 2.24
2211 2682 8.969267 GTTCCATATAACTCGTCACTGATTTAG 58.031 37.037 0.00 0.00 0.00 1.85
2212 2683 7.646526 CGTTCCATATAACTCGTCACTGATTTA 59.353 37.037 0.00 0.00 0.00 1.40
2213 2684 6.475727 CGTTCCATATAACTCGTCACTGATTT 59.524 38.462 0.00 0.00 0.00 2.17
2214 2685 5.977725 CGTTCCATATAACTCGTCACTGATT 59.022 40.000 0.00 0.00 0.00 2.57
2215 2686 5.507482 CCGTTCCATATAACTCGTCACTGAT 60.507 44.000 0.00 0.00 0.00 2.90
2216 2687 4.201980 CCGTTCCATATAACTCGTCACTGA 60.202 45.833 0.00 0.00 0.00 3.41
2217 2688 4.042398 CCGTTCCATATAACTCGTCACTG 58.958 47.826 0.00 0.00 0.00 3.66
2218 2689 3.949754 TCCGTTCCATATAACTCGTCACT 59.050 43.478 0.00 0.00 0.00 3.41
2219 2690 4.288531 CTCCGTTCCATATAACTCGTCAC 58.711 47.826 0.00 0.00 0.00 3.67
2220 2691 3.317149 CCTCCGTTCCATATAACTCGTCA 59.683 47.826 0.00 0.00 0.00 4.35
2221 2692 3.305199 CCCTCCGTTCCATATAACTCGTC 60.305 52.174 0.00 0.00 0.00 4.20
2222 2693 2.626743 CCCTCCGTTCCATATAACTCGT 59.373 50.000 0.00 0.00 0.00 4.18
2223 2694 2.889045 TCCCTCCGTTCCATATAACTCG 59.111 50.000 0.00 0.00 0.00 4.18
2224 2695 3.896272 ACTCCCTCCGTTCCATATAACTC 59.104 47.826 0.00 0.00 0.00 3.01
2225 2696 3.924922 ACTCCCTCCGTTCCATATAACT 58.075 45.455 0.00 0.00 0.00 2.24
2226 2697 5.069516 TGTTACTCCCTCCGTTCCATATAAC 59.930 44.000 0.00 0.00 0.00 1.89
2227 2698 5.210430 TGTTACTCCCTCCGTTCCATATAA 58.790 41.667 0.00 0.00 0.00 0.98
2228 2699 4.806892 TGTTACTCCCTCCGTTCCATATA 58.193 43.478 0.00 0.00 0.00 0.86
2229 2700 3.649843 TGTTACTCCCTCCGTTCCATAT 58.350 45.455 0.00 0.00 0.00 1.78
2230 2701 3.104519 TGTTACTCCCTCCGTTCCATA 57.895 47.619 0.00 0.00 0.00 2.74
2231 2702 1.946984 TGTTACTCCCTCCGTTCCAT 58.053 50.000 0.00 0.00 0.00 3.41
2232 2703 1.345415 GTTGTTACTCCCTCCGTTCCA 59.655 52.381 0.00 0.00 0.00 3.53
2233 2704 1.338484 GGTTGTTACTCCCTCCGTTCC 60.338 57.143 0.00 0.00 0.00 3.62
2234 2705 1.622312 AGGTTGTTACTCCCTCCGTTC 59.378 52.381 0.00 0.00 0.00 3.95
2235 2706 1.725803 AGGTTGTTACTCCCTCCGTT 58.274 50.000 0.00 0.00 0.00 4.44
2236 2707 2.610438 TAGGTTGTTACTCCCTCCGT 57.390 50.000 0.00 0.00 0.00 4.69
2237 2708 2.483188 GCATAGGTTGTTACTCCCTCCG 60.483 54.545 0.00 0.00 0.00 4.63
2238 2709 2.158798 GGCATAGGTTGTTACTCCCTCC 60.159 54.545 0.00 0.00 0.00 4.30
2239 2710 2.504175 TGGCATAGGTTGTTACTCCCTC 59.496 50.000 0.00 0.00 0.00 4.30
2240 2711 2.557869 TGGCATAGGTTGTTACTCCCT 58.442 47.619 0.00 0.00 0.00 4.20
2241 2712 3.014623 GTTGGCATAGGTTGTTACTCCC 58.985 50.000 0.00 0.00 0.00 4.30
2242 2713 3.681593 TGTTGGCATAGGTTGTTACTCC 58.318 45.455 0.00 0.00 0.00 3.85
2243 2714 6.373216 TGTTATGTTGGCATAGGTTGTTACTC 59.627 38.462 0.00 0.00 38.64 2.59
2244 2715 6.242396 TGTTATGTTGGCATAGGTTGTTACT 58.758 36.000 0.00 0.00 38.64 2.24
2245 2716 6.404293 CCTGTTATGTTGGCATAGGTTGTTAC 60.404 42.308 0.00 0.00 38.64 2.50
2246 2717 5.650266 CCTGTTATGTTGGCATAGGTTGTTA 59.350 40.000 0.00 0.00 38.64 2.41
2247 2718 4.462483 CCTGTTATGTTGGCATAGGTTGTT 59.538 41.667 0.00 0.00 38.64 2.83
2337 2808 0.846693 ATCGGCTAAATTCCTGGGCT 59.153 50.000 0.00 0.00 0.00 5.19
2340 2811 2.287915 CGAACATCGGCTAAATTCCTGG 59.712 50.000 0.00 0.00 36.00 4.45
2393 2864 3.934457 TGACTAAGCAATCACACGAGA 57.066 42.857 0.00 0.00 0.00 4.04
2420 2892 8.184192 CACTTGTTAGAATAATTTGAGGCGATT 58.816 33.333 0.00 0.00 0.00 3.34
2457 2929 4.884668 ATCACGACCTCCTTGAAACTTA 57.115 40.909 0.00 0.00 0.00 2.24


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.