Multiple sequence alignment - TraesCS6A01G011100

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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 TraesCS6A01G011100 chr6A 100.000 2729 0 0 1 2729 5205572 5208300 0.000000e+00 5040.0
1 TraesCS6A01G011100 chr6A 75.723 346 53 17 406 721 99767470 99767814 7.880000e-31 145.0
2 TraesCS6A01G011100 chrUn 87.752 1437 103 39 843 2265 76000845 75999468 0.000000e+00 1611.0
3 TraesCS6A01G011100 chrUn 86.237 465 44 8 406 857 76001353 76000896 1.140000e-133 486.0
4 TraesCS6A01G011100 chrUn 83.176 529 42 25 1747 2265 231203661 231203170 8.970000e-120 440.0
5 TraesCS6A01G011100 chrUn 79.609 358 40 14 1 338 76001905 76001561 2.730000e-55 226.0
6 TraesCS6A01G011100 chr6D 92.720 989 59 6 928 1916 5838514 5839489 0.000000e+00 1415.0
7 TraesCS6A01G011100 chr6D 91.594 345 13 5 2335 2671 5840170 5840506 1.910000e-126 462.0
8 TraesCS6A01G011100 chr6D 91.930 285 17 3 1907 2191 5839534 5839812 7.080000e-106 394.0
9 TraesCS6A01G011100 chr6D 77.971 345 40 16 409 718 432807085 432806742 1.670000e-42 183.0
10 TraesCS6A01G011100 chr6D 91.667 84 2 3 2264 2342 5840118 5840201 7.990000e-21 111.0
11 TraesCS6A01G011100 chr6D 80.769 130 21 3 586 712 114771169 114771041 6.220000e-17 99.0
12 TraesCS6A01G011100 chr1D 87.287 527 56 5 958 1476 155346048 155345525 2.340000e-165 592.0
13 TraesCS6A01G011100 chr1D 87.126 334 43 0 1484 1817 155344492 155344159 1.980000e-101 379.0
14 TraesCS6A01G011100 chr1A 86.717 527 59 6 958 1476 204826346 204826869 2.360000e-160 575.0
15 TraesCS6A01G011100 chr1A 86.826 334 44 0 1484 1817 204828012 204828345 9.230000e-100 374.0
16 TraesCS6A01G011100 chr1B 86.974 499 55 5 985 1476 220751440 220751935 1.100000e-153 553.0
17 TraesCS6A01G011100 chr1B 86.228 334 43 2 1484 1817 220752976 220753306 2.580000e-95 359.0
18 TraesCS6A01G011100 chr1B 81.290 155 20 8 22 173 658793516 658793664 1.720000e-22 117.0
19 TraesCS6A01G011100 chr1B 85.714 63 6 3 336 396 16851924 16851985 2.270000e-06 63.9
20 TraesCS6A01G011100 chr1B 100.000 29 0 0 310 338 652429909 652429881 1.000000e-03 54.7
21 TraesCS6A01G011100 chr7D 82.101 257 32 8 482 725 64511326 64511581 9.900000e-50 207.0
22 TraesCS6A01G011100 chr7D 85.507 138 12 7 406 538 183797598 183797464 1.320000e-28 137.0
23 TraesCS6A01G011100 chr7D 87.097 93 12 0 430 522 183797658 183797566 3.720000e-19 106.0
24 TraesCS6A01G011100 chr7D 85.915 71 7 3 722 789 446421801 446421871 3.770000e-09 73.1
25 TraesCS6A01G011100 chr2D 76.847 406 56 23 406 788 552623461 552623071 7.710000e-46 195.0
26 TraesCS6A01G011100 chr2D 84.426 122 17 2 403 522 14643572 14643693 4.770000e-23 119.0
27 TraesCS6A01G011100 chr2D 84.211 95 13 2 302 396 423170158 423170066 1.040000e-14 91.6
28 TraesCS6A01G011100 chr6B 80.297 269 41 10 467 725 40437238 40437504 2.770000e-45 193.0
29 TraesCS6A01G011100 chr3D 80.524 267 39 9 467 721 116163699 116163434 2.770000e-45 193.0
30 TraesCS6A01G011100 chr3D 84.874 119 14 3 407 522 157213862 157213745 1.720000e-22 117.0
31 TraesCS6A01G011100 chr5D 79.554 269 43 9 467 724 556004327 556004060 6.000000e-42 182.0
32 TraesCS6A01G011100 chr5D 85.075 67 8 1 726 790 432846149 432846083 1.750000e-07 67.6
33 TraesCS6A01G011100 chr4A 87.838 148 15 3 580 725 709847265 709847411 1.300000e-38 171.0
34 TraesCS6A01G011100 chr2A 87.838 148 15 3 580 725 698954158 698954012 1.300000e-38 171.0
35 TraesCS6A01G011100 chr2A 100.000 29 0 0 310 338 17139953 17139981 1.000000e-03 54.7
36 TraesCS6A01G011100 chr5A 77.823 248 43 9 468 705 574860208 574859963 2.830000e-30 143.0
37 TraesCS6A01G011100 chr5A 96.970 33 1 0 340 372 470074910 470074878 3.800000e-04 56.5
38 TraesCS6A01G011100 chr4D 79.812 213 27 11 586 794 372355102 372354902 1.020000e-29 141.0
39 TraesCS6A01G011100 chr4D 85.965 114 13 2 285 396 77230388 77230500 4.770000e-23 119.0
40 TraesCS6A01G011100 chr4D 95.588 68 2 1 23 90 477539646 477539580 1.030000e-19 108.0
41 TraesCS6A01G011100 chr3B 77.255 255 46 8 482 725 171699062 171698809 3.660000e-29 139.0
42 TraesCS6A01G011100 chr3B 94.444 36 2 0 331 366 237627072 237627037 3.800000e-04 56.5
43 TraesCS6A01G011100 chr7A 82.222 135 22 2 406 539 639771661 639771528 6.180000e-22 115.0
44 TraesCS6A01G011100 chr7A 85.075 67 8 2 23 89 670162567 670162631 1.750000e-07 67.6
45 TraesCS6A01G011100 chr7B 96.667 60 2 0 2670 2729 637359052 637359111 1.730000e-17 100.0
46 TraesCS6A01G011100 chr7B 94.595 37 2 0 332 368 598901570 598901606 1.060000e-04 58.4
47 TraesCS6A01G011100 chr2B 91.071 56 5 0 341 396 728627842 728627897 2.910000e-10 76.8
48 TraesCS6A01G011100 chr2B 86.765 68 6 2 726 790 754862257 754862324 3.770000e-09 73.1
49 TraesCS6A01G011100 chr4B 78.652 89 16 2 340 425 124616918 124617006 3.800000e-04 56.5


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 TraesCS6A01G011100 chr6A 5205572 5208300 2728 False 5040.000000 5040 100.000000 1 2729 1 chr6A.!!$F1 2728
1 TraesCS6A01G011100 chrUn 75999468 76001905 2437 True 774.333333 1611 84.532667 1 2265 3 chrUn.!!$R2 2264
2 TraesCS6A01G011100 chr6D 5838514 5840506 1992 False 595.500000 1415 91.977750 928 2671 4 chr6D.!!$F1 1743
3 TraesCS6A01G011100 chr1D 155344159 155346048 1889 True 485.500000 592 87.206500 958 1817 2 chr1D.!!$R1 859
4 TraesCS6A01G011100 chr1A 204826346 204828345 1999 False 474.500000 575 86.771500 958 1817 2 chr1A.!!$F1 859
5 TraesCS6A01G011100 chr1B 220751440 220753306 1866 False 456.000000 553 86.601000 985 1817 2 chr1B.!!$F3 832

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
927 1165 0.027324 GGACGACGTACTAAGCGGAG 59.973 60.0 2.02 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2707 4453 0.109272 CGACGTATGGCAGTGAGTGT 60.109 55.0 0.0 0.0 0.0 3.55 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
47 48 2.856557 GCAACTAGTTAACGATCGGTCC 59.143 50.000 20.98 7.38 0.00 4.46
111 121 3.190849 CACATGTCGCGCTCTGGG 61.191 66.667 5.56 0.00 0.00 4.45
112 122 3.695606 ACATGTCGCGCTCTGGGT 61.696 61.111 5.56 0.00 0.00 4.51
123 133 0.110486 GCTCTGGGTGTTTCCTCCAA 59.890 55.000 0.00 0.00 36.25 3.53
125 135 2.508526 CTCTGGGTGTTTCCTCCAAAG 58.491 52.381 0.00 0.00 36.25 2.77
129 139 4.079672 TCTGGGTGTTTCCTCCAAAGTTTA 60.080 41.667 0.00 0.00 36.25 2.01
159 169 1.536149 TTTTTCCGCACGTGTTTTCG 58.464 45.000 18.38 11.76 0.00 3.46
168 178 3.413558 GCACGTGTTTTCGGCTTTATAG 58.586 45.455 18.38 0.00 34.94 1.31
169 179 3.123959 GCACGTGTTTTCGGCTTTATAGA 59.876 43.478 18.38 0.00 34.94 1.98
170 180 4.201783 GCACGTGTTTTCGGCTTTATAGAT 60.202 41.667 18.38 0.00 34.94 1.98
171 181 5.255596 CACGTGTTTTCGGCTTTATAGATG 58.744 41.667 7.58 0.00 34.94 2.90
172 182 4.331717 ACGTGTTTTCGGCTTTATAGATGG 59.668 41.667 0.00 0.00 34.94 3.51
174 184 4.638865 GTGTTTTCGGCTTTATAGATGGGT 59.361 41.667 0.00 0.00 0.00 4.51
175 185 5.124936 GTGTTTTCGGCTTTATAGATGGGTT 59.875 40.000 0.00 0.00 0.00 4.11
176 186 5.712917 TGTTTTCGGCTTTATAGATGGGTTT 59.287 36.000 0.00 0.00 0.00 3.27
177 187 6.885376 TGTTTTCGGCTTTATAGATGGGTTTA 59.115 34.615 0.00 0.00 0.00 2.01
178 188 6.930667 TTTCGGCTTTATAGATGGGTTTAC 57.069 37.500 0.00 0.00 0.00 2.01
179 189 5.881923 TCGGCTTTATAGATGGGTTTACT 57.118 39.130 0.00 0.00 0.00 2.24
180 190 5.850614 TCGGCTTTATAGATGGGTTTACTC 58.149 41.667 0.00 0.00 0.00 2.59
181 191 4.684703 CGGCTTTATAGATGGGTTTACTCG 59.315 45.833 0.00 0.00 0.00 4.18
182 192 4.995487 GGCTTTATAGATGGGTTTACTCGG 59.005 45.833 0.00 0.00 0.00 4.63
183 193 4.451435 GCTTTATAGATGGGTTTACTCGGC 59.549 45.833 0.00 0.00 0.00 5.54
184 194 5.742255 GCTTTATAGATGGGTTTACTCGGCT 60.742 44.000 0.00 0.00 0.00 5.52
195 205 4.871557 GGTTTACTCGGCTTTTTGGTTTTT 59.128 37.500 0.00 0.00 0.00 1.94
198 208 4.195225 ACTCGGCTTTTTGGTTTTTCAA 57.805 36.364 0.00 0.00 0.00 2.69
200 210 2.924290 TCGGCTTTTTGGTTTTTCAACG 59.076 40.909 0.00 0.00 33.13 4.10
201 211 2.029849 CGGCTTTTTGGTTTTTCAACGG 59.970 45.455 0.00 0.00 33.13 4.44
225 235 5.450826 GGCTTTCTTAGGTTTTGGACGAAAA 60.451 40.000 0.00 0.00 0.00 2.29
227 237 6.020121 GCTTTCTTAGGTTTTGGACGAAAAAC 60.020 38.462 2.73 2.73 45.29 2.43
233 243 6.415798 AGGTTTTGGACGAAAAACAAAATG 57.584 33.333 12.48 0.00 46.98 2.32
234 244 5.025190 GGTTTTGGACGAAAAACAAAATGC 58.975 37.500 19.58 7.16 46.98 3.56
235 245 5.390991 GGTTTTGGACGAAAAACAAAATGCA 60.391 36.000 19.58 0.00 46.98 3.96
236 246 6.254480 GTTTTGGACGAAAAACAAAATGCAT 58.746 32.000 15.76 0.00 45.33 3.96
238 248 4.942852 TGGACGAAAAACAAAATGCATCT 58.057 34.783 0.00 0.00 0.00 2.90
275 295 2.480555 GCATGTCCGTGCCTTTCG 59.519 61.111 0.00 0.00 39.18 3.46
360 414 2.036346 AGAGGCATGGTTTTGCTTTCAC 59.964 45.455 0.00 0.00 42.38 3.18
423 478 0.958822 TTTTTGCTTTCGGGAGAGGC 59.041 50.000 0.00 0.00 41.75 4.70
425 480 0.889186 TTTGCTTTCGGGAGAGGCAC 60.889 55.000 0.00 0.00 44.50 5.01
426 481 1.768684 TTGCTTTCGGGAGAGGCACT 61.769 55.000 0.00 0.00 44.50 4.40
453 531 3.244911 TGCCTCTCGGAAAGGAAAAAGAT 60.245 43.478 0.36 0.00 35.83 2.40
456 534 4.762251 CCTCTCGGAAAGGAAAAAGATTGT 59.238 41.667 0.00 0.00 35.83 2.71
486 646 2.978156 TTTCCTTCCTTGACAGGCAT 57.022 45.000 0.00 0.00 40.58 4.40
558 719 4.848562 ACTTCTCCCGGTTTCATTTTTC 57.151 40.909 0.00 0.00 0.00 2.29
559 720 3.572682 ACTTCTCCCGGTTTCATTTTTCC 59.427 43.478 0.00 0.00 0.00 3.13
560 721 2.156098 TCTCCCGGTTTCATTTTTCCG 58.844 47.619 0.00 0.00 42.22 4.30
561 722 1.883926 CTCCCGGTTTCATTTTTCCGT 59.116 47.619 0.00 0.00 41.17 4.69
562 723 1.881324 TCCCGGTTTCATTTTTCCGTC 59.119 47.619 0.00 0.00 41.17 4.79
563 724 1.068125 CCCGGTTTCATTTTTCCGTCC 60.068 52.381 0.00 0.00 41.17 4.79
565 726 1.400500 CGGTTTCATTTTTCCGTCCGG 60.400 52.381 0.00 0.00 38.45 5.14
566 727 1.610038 GGTTTCATTTTTCCGTCCGGT 59.390 47.619 0.00 0.00 36.47 5.28
567 728 2.034939 GGTTTCATTTTTCCGTCCGGTT 59.965 45.455 0.00 0.00 36.47 4.44
568 729 3.491276 GGTTTCATTTTTCCGTCCGGTTT 60.491 43.478 0.00 0.00 36.47 3.27
569 730 4.114073 GTTTCATTTTTCCGTCCGGTTTT 58.886 39.130 0.00 0.00 36.47 2.43
570 731 3.629438 TCATTTTTCCGTCCGGTTTTC 57.371 42.857 0.00 0.00 36.47 2.29
571 732 3.215975 TCATTTTTCCGTCCGGTTTTCT 58.784 40.909 0.00 0.00 36.47 2.52
572 733 3.633065 TCATTTTTCCGTCCGGTTTTCTT 59.367 39.130 0.00 0.00 36.47 2.52
573 734 4.098196 TCATTTTTCCGTCCGGTTTTCTTT 59.902 37.500 0.00 0.00 36.47 2.52
574 735 3.423996 TTTTCCGTCCGGTTTTCTTTG 57.576 42.857 0.00 0.00 36.47 2.77
575 736 1.310904 TTCCGTCCGGTTTTCTTTGG 58.689 50.000 0.00 0.00 36.47 3.28
576 737 0.535553 TCCGTCCGGTTTTCTTTGGG 60.536 55.000 0.00 0.00 36.47 4.12
577 738 0.535553 CCGTCCGGTTTTCTTTGGGA 60.536 55.000 0.00 0.00 0.00 4.37
578 739 1.310904 CGTCCGGTTTTCTTTGGGAA 58.689 50.000 0.00 0.00 0.00 3.97
581 742 3.243602 CGTCCGGTTTTCTTTGGGAATTT 60.244 43.478 0.00 0.00 33.53 1.82
584 745 3.807071 CCGGTTTTCTTTGGGAATTTGTG 59.193 43.478 0.00 0.00 33.53 3.33
598 759 5.983118 GGGAATTTGTGAAAACCTACAACAG 59.017 40.000 0.00 0.00 36.61 3.16
601 762 6.767524 ATTTGTGAAAACCTACAACAGTGA 57.232 33.333 0.00 0.00 36.61 3.41
613 774 9.490379 AACCTACAACAGTGAATCTAGTTTTAG 57.510 33.333 0.00 0.00 0.00 1.85
691 852 6.183360 ACGGTTAAAGAGCTAAAACGTTTTGA 60.183 34.615 31.26 16.51 0.00 2.69
735 896 3.501950 GAAATCTTCCACCATTTGTCGC 58.498 45.455 0.00 0.00 0.00 5.19
760 930 2.040278 CTGGGGTGGAAGTGATCTTTGA 59.960 50.000 0.00 0.00 33.64 2.69
771 941 6.937465 GGAAGTGATCTTTGAAAGGAGTACTT 59.063 38.462 4.94 10.32 35.95 2.24
780 950 9.490379 TCTTTGAAAGGAGTACTTCTCAATTAC 57.510 33.333 3.51 0.00 44.40 1.89
803 973 1.302832 CTCGGACTTTTGCTGGCCT 60.303 57.895 3.32 0.00 0.00 5.19
854 1092 9.695526 TTTGTTTTAGGTGATGATGAAGAAATG 57.304 29.630 0.00 0.00 0.00 2.32
864 1102 8.036575 GTGATGATGAAGAAATGAATTGGGAAA 58.963 33.333 0.00 0.00 0.00 3.13
871 1109 7.289782 TGAAGAAATGAATTGGGAAAGGAGAAA 59.710 33.333 0.00 0.00 0.00 2.52
873 1111 6.784473 AGAAATGAATTGGGAAAGGAGAAAGT 59.216 34.615 0.00 0.00 0.00 2.66
895 1133 6.184789 AGTTATATATTAATTGGGCCGGTGG 58.815 40.000 1.90 0.00 0.00 4.61
898 1136 1.480789 ATTAATTGGGCCGGTGGAAC 58.519 50.000 1.90 0.00 0.00 3.62
922 1160 4.678396 GGCGGACGACGTACTAAG 57.322 61.111 8.88 0.00 46.52 2.18
923 1161 1.584742 GGCGGACGACGTACTAAGC 60.585 63.158 8.88 4.29 46.52 3.09
924 1162 1.931612 GCGGACGACGTACTAAGCG 60.932 63.158 8.88 0.00 46.52 4.68
925 1163 1.297158 CGGACGACGTACTAAGCGG 60.297 63.158 8.88 0.00 37.93 5.52
926 1164 1.695893 CGGACGACGTACTAAGCGGA 61.696 60.000 8.88 0.00 37.93 5.54
927 1165 0.027324 GGACGACGTACTAAGCGGAG 59.973 60.000 2.02 0.00 0.00 4.63
934 1172 4.153117 CGACGTACTAAGCGGAGGTATATT 59.847 45.833 0.00 0.00 37.06 1.28
937 1175 5.048434 ACGTACTAAGCGGAGGTATATTTCC 60.048 44.000 0.00 0.00 37.06 3.13
951 1189 4.715523 TTCCTTTGGGCCCGAGCG 62.716 66.667 19.37 10.38 41.24 5.03
1071 1310 1.838073 CGGTACCCAAGGTGAAGGCT 61.838 60.000 6.25 0.00 36.19 4.58
1100 1345 1.203013 GGTGACCCAAAACCCTAGCTT 60.203 52.381 0.00 0.00 0.00 3.74
1371 1616 0.390472 CGAGGAGGAAGAAGTGTGGC 60.390 60.000 0.00 0.00 0.00 5.01
1374 1619 2.501723 GAGGAGGAAGAAGTGTGGCATA 59.498 50.000 0.00 0.00 0.00 3.14
1377 1622 3.559171 GGAGGAAGAAGTGTGGCATAACA 60.559 47.826 0.00 0.00 0.00 2.41
1711 3135 1.228894 AGAGAGTCCCGAAGTGCCA 60.229 57.895 0.00 0.00 0.00 4.92
1712 3136 1.216710 GAGAGTCCCGAAGTGCCAG 59.783 63.158 0.00 0.00 0.00 4.85
1770 3194 7.753132 CGTAGCTGAGCTATTCCTTTAGATAAG 59.247 40.741 18.18 0.00 43.30 1.73
1847 3272 5.351465 AGTGAATTAGTTAGAATGGTGTGCG 59.649 40.000 0.00 0.00 0.00 5.34
1849 3274 5.580691 TGAATTAGTTAGAATGGTGTGCGAG 59.419 40.000 0.00 0.00 0.00 5.03
1855 3280 3.170791 AGAATGGTGTGCGAGTAGATG 57.829 47.619 0.00 0.00 0.00 2.90
1943 3430 4.142182 TGAACAAAAAGGAACCAGAAGCAG 60.142 41.667 0.00 0.00 0.00 4.24
1965 3452 3.430453 CCTCCAAAAACTTCAGGCCATA 58.570 45.455 5.01 0.00 0.00 2.74
1966 3453 3.193479 CCTCCAAAAACTTCAGGCCATAC 59.807 47.826 5.01 0.00 0.00 2.39
1967 3454 3.826157 CTCCAAAAACTTCAGGCCATACA 59.174 43.478 5.01 0.00 0.00 2.29
1968 3455 4.415596 TCCAAAAACTTCAGGCCATACAT 58.584 39.130 5.01 0.00 0.00 2.29
1969 3456 4.837860 TCCAAAAACTTCAGGCCATACATT 59.162 37.500 5.01 0.00 0.00 2.71
1970 3457 4.931002 CCAAAAACTTCAGGCCATACATTG 59.069 41.667 5.01 0.00 0.00 2.82
1971 3458 5.511202 CCAAAAACTTCAGGCCATACATTGT 60.511 40.000 5.01 0.00 0.00 2.71
1972 3459 6.295011 CCAAAAACTTCAGGCCATACATTGTA 60.295 38.462 5.01 0.00 0.00 2.41
1973 3460 7.322664 CAAAAACTTCAGGCCATACATTGTAT 58.677 34.615 5.01 3.40 0.00 2.29
1974 3461 6.455360 AAACTTCAGGCCATACATTGTATG 57.545 37.500 24.01 24.01 0.00 2.39
1975 3462 5.116084 ACTTCAGGCCATACATTGTATGT 57.884 39.130 26.98 12.44 46.92 2.29
1976 3463 4.883585 ACTTCAGGCCATACATTGTATGTG 59.116 41.667 26.98 20.76 44.60 3.21
1977 3464 3.819368 TCAGGCCATACATTGTATGTGG 58.181 45.455 26.98 19.29 44.60 4.17
1978 3465 3.201930 TCAGGCCATACATTGTATGTGGT 59.798 43.478 26.98 13.35 44.60 4.16
2059 3560 5.856126 TCAACTACTAGCAATTTCAACCG 57.144 39.130 0.00 0.00 0.00 4.44
2125 3626 9.683069 GAGAGAGAGATAAATGAAGAATGAGAC 57.317 37.037 0.00 0.00 0.00 3.36
2132 3633 3.533606 ATGAAGAATGAGACGACCTGG 57.466 47.619 0.00 0.00 0.00 4.45
2152 3653 3.566523 GGAGATTCTACTGTAATCGCCG 58.433 50.000 9.37 0.00 41.43 6.46
2209 3740 3.627577 GGCATGTTCCATTATCGTGTCTT 59.372 43.478 0.00 0.00 0.00 3.01
2212 3743 6.092748 GCATGTTCCATTATCGTGTCTTTTT 58.907 36.000 0.00 0.00 0.00 1.94
2238 3770 7.976414 TCCACTTTGGATGGAATTAATTGAT 57.024 32.000 5.17 0.00 42.67 2.57
2300 4034 6.264832 TGTATGATATTCTTGCTTTTTGCGG 58.735 36.000 0.00 0.00 46.63 5.69
2305 4039 0.038343 TCTTGCTTTTTGCGGCATCC 60.038 50.000 2.28 0.00 46.63 3.51
2309 4048 1.202627 TGCTTTTTGCGGCATCCTTTT 60.203 42.857 2.28 0.00 46.63 2.27
2342 4081 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2343 4082 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2344 4083 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2345 4084 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2346 4085 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2347 4086 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2348 4087 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2349 4088 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2350 4089 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2351 4090 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2352 4091 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2353 4092 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2354 4093 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2355 4094 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2356 4095 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2357 4096 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2358 4097 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2359 4098 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2360 4099 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2361 4100 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2362 4101 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2363 4102 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2364 4103 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2365 4104 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2380 4119 6.369065 TGTGTGTGTGTTTGGGAAATTAAAAC 59.631 34.615 0.00 0.00 34.97 2.43
2386 4125 7.443879 GTGTGTTTGGGAAATTAAAACATGGAT 59.556 33.333 0.00 0.00 43.47 3.41
2403 4142 2.711009 TGGATGTTTGGAGACTTGGAGT 59.289 45.455 0.00 0.00 0.00 3.85
2427 4166 2.739379 CCAACGGCTTTTGTTTGTTTGT 59.261 40.909 0.00 0.00 0.00 2.83
2432 4171 7.595502 CCAACGGCTTTTGTTTGTTTGTATATA 59.404 33.333 0.00 0.00 0.00 0.86
2433 4172 9.134734 CAACGGCTTTTGTTTGTTTGTATATAT 57.865 29.630 0.00 0.00 0.00 0.86
2434 4173 8.905103 ACGGCTTTTGTTTGTTTGTATATATC 57.095 30.769 0.00 0.00 0.00 1.63
2457 4196 1.877443 GATCGACTGAGGACTAGAGGC 59.123 57.143 0.00 0.00 0.00 4.70
2458 4197 0.462225 TCGACTGAGGACTAGAGGCG 60.462 60.000 0.00 0.00 0.00 5.52
2474 4213 6.996879 ACTAGAGGCGATCACAAGTATTAGTA 59.003 38.462 0.00 0.00 0.00 1.82
2475 4214 6.902771 AGAGGCGATCACAAGTATTAGTAT 57.097 37.500 0.00 0.00 0.00 2.12
2476 4215 6.682746 AGAGGCGATCACAAGTATTAGTATG 58.317 40.000 0.00 0.00 0.00 2.39
2477 4216 6.265649 AGAGGCGATCACAAGTATTAGTATGT 59.734 38.462 0.00 0.00 0.00 2.29
2478 4217 7.447545 AGAGGCGATCACAAGTATTAGTATGTA 59.552 37.037 0.00 0.00 0.00 2.29
2501 4240 3.587923 TGTAGTATTACGCAACCACACC 58.412 45.455 0.00 0.00 32.21 4.16
2621 4367 3.575687 CCTTCTTCATTTGACCAAAGGCT 59.424 43.478 2.63 0.00 32.69 4.58
2642 4388 6.071165 AGGCTTTTGGTCCTCAATGAAATTAG 60.071 38.462 0.00 0.00 32.46 1.73
2668 4414 9.278734 GATTAATTGTGCAGCTAAAGTAACTTC 57.721 33.333 0.00 0.00 0.00 3.01
2669 4415 6.633500 AATTGTGCAGCTAAAGTAACTTCA 57.367 33.333 0.00 0.00 0.00 3.02
2670 4416 5.418310 TTGTGCAGCTAAAGTAACTTCAC 57.582 39.130 0.00 0.00 0.00 3.18
2671 4417 3.493129 TGTGCAGCTAAAGTAACTTCACG 59.507 43.478 0.00 0.00 0.00 4.35
2672 4418 3.739300 GTGCAGCTAAAGTAACTTCACGA 59.261 43.478 0.00 0.00 0.00 4.35
2673 4419 4.210537 GTGCAGCTAAAGTAACTTCACGAA 59.789 41.667 0.00 0.00 0.00 3.85
2674 4420 4.812091 TGCAGCTAAAGTAACTTCACGAAA 59.188 37.500 0.00 0.00 0.00 3.46
2675 4421 5.294799 TGCAGCTAAAGTAACTTCACGAAAA 59.705 36.000 0.00 0.00 0.00 2.29
2676 4422 6.017440 TGCAGCTAAAGTAACTTCACGAAAAT 60.017 34.615 0.00 0.00 0.00 1.82
2677 4423 6.303259 GCAGCTAAAGTAACTTCACGAAAATG 59.697 38.462 0.00 0.00 0.00 2.32
2678 4424 7.352739 CAGCTAAAGTAACTTCACGAAAATGT 58.647 34.615 0.00 0.00 0.00 2.71
2679 4425 7.855904 CAGCTAAAGTAACTTCACGAAAATGTT 59.144 33.333 0.00 0.00 0.00 2.71
2680 4426 7.855904 AGCTAAAGTAACTTCACGAAAATGTTG 59.144 33.333 0.00 0.00 0.00 3.33
2681 4427 6.806120 AAAGTAACTTCACGAAAATGTTGC 57.194 33.333 0.00 0.00 0.00 4.17
2682 4428 5.751243 AGTAACTTCACGAAAATGTTGCT 57.249 34.783 0.00 0.00 0.00 3.91
2683 4429 6.131544 AGTAACTTCACGAAAATGTTGCTT 57.868 33.333 0.00 0.00 31.53 3.91
2684 4430 7.254227 AGTAACTTCACGAAAATGTTGCTTA 57.746 32.000 0.00 0.00 31.53 3.09
2685 4431 7.352739 AGTAACTTCACGAAAATGTTGCTTAG 58.647 34.615 0.00 0.00 31.53 2.18
2686 4432 4.537015 ACTTCACGAAAATGTTGCTTAGC 58.463 39.130 0.00 0.00 0.00 3.09
2687 4433 4.036262 ACTTCACGAAAATGTTGCTTAGCA 59.964 37.500 1.39 1.39 36.47 3.49
2688 4434 3.884169 TCACGAAAATGTTGCTTAGCAC 58.116 40.909 6.34 3.04 38.71 4.40
2689 4435 2.979813 CACGAAAATGTTGCTTAGCACC 59.020 45.455 6.34 0.00 38.71 5.01
2690 4436 2.621055 ACGAAAATGTTGCTTAGCACCA 59.379 40.909 6.34 6.67 38.71 4.17
2691 4437 3.255642 ACGAAAATGTTGCTTAGCACCAT 59.744 39.130 11.45 11.45 43.19 3.55
2692 4438 3.609373 CGAAAATGTTGCTTAGCACCATG 59.391 43.478 17.53 2.01 40.62 3.66
2693 4439 3.598019 AAATGTTGCTTAGCACCATGG 57.402 42.857 17.53 11.19 40.62 3.66
2694 4440 2.220653 ATGTTGCTTAGCACCATGGT 57.779 45.000 16.21 13.00 40.03 3.55
2695 4441 1.820519 ATGTTGCTTAGCACCATGGTG 59.179 47.619 36.07 36.07 40.03 4.17
2703 4449 2.282110 CACCATGGTGCACCCGAA 60.282 61.111 31.13 15.49 39.39 4.30
2704 4450 2.282180 ACCATGGTGCACCCGAAC 60.282 61.111 32.62 8.33 35.15 3.95
2705 4451 3.061848 CCATGGTGCACCCGAACC 61.062 66.667 32.62 7.71 36.96 3.62
2706 4452 2.034066 CATGGTGCACCCGAACCT 59.966 61.111 32.62 7.81 37.36 3.50
2707 4453 1.298340 CATGGTGCACCCGAACCTA 59.702 57.895 32.62 13.06 37.36 3.08
2708 4454 1.024579 CATGGTGCACCCGAACCTAC 61.025 60.000 32.62 5.17 37.36 3.18
2709 4455 1.485294 ATGGTGCACCCGAACCTACA 61.485 55.000 32.62 11.45 37.36 2.74
2710 4456 1.670083 GGTGCACCCGAACCTACAC 60.670 63.158 26.31 0.00 33.40 2.90
2711 4457 1.370064 GTGCACCCGAACCTACACT 59.630 57.895 5.22 0.00 0.00 3.55
2712 4458 0.669625 GTGCACCCGAACCTACACTC 60.670 60.000 5.22 0.00 0.00 3.51
2713 4459 1.116536 TGCACCCGAACCTACACTCA 61.117 55.000 0.00 0.00 0.00 3.41
2714 4460 0.669625 GCACCCGAACCTACACTCAC 60.670 60.000 0.00 0.00 0.00 3.51
2715 4461 0.966920 CACCCGAACCTACACTCACT 59.033 55.000 0.00 0.00 0.00 3.41
2716 4462 0.966920 ACCCGAACCTACACTCACTG 59.033 55.000 0.00 0.00 0.00 3.66
2717 4463 0.389948 CCCGAACCTACACTCACTGC 60.390 60.000 0.00 0.00 0.00 4.40
2718 4464 0.389948 CCGAACCTACACTCACTGCC 60.390 60.000 0.00 0.00 0.00 4.85
2719 4465 0.317160 CGAACCTACACTCACTGCCA 59.683 55.000 0.00 0.00 0.00 4.92
2720 4466 1.066858 CGAACCTACACTCACTGCCAT 60.067 52.381 0.00 0.00 0.00 4.40
2721 4467 2.165641 CGAACCTACACTCACTGCCATA 59.834 50.000 0.00 0.00 0.00 2.74
2722 4468 3.522553 GAACCTACACTCACTGCCATAC 58.477 50.000 0.00 0.00 0.00 2.39
2723 4469 1.476891 ACCTACACTCACTGCCATACG 59.523 52.381 0.00 0.00 0.00 3.06
2724 4470 1.476891 CCTACACTCACTGCCATACGT 59.523 52.381 0.00 0.00 0.00 3.57
2725 4471 2.479730 CCTACACTCACTGCCATACGTC 60.480 54.545 0.00 0.00 0.00 4.34
2726 4472 0.109272 ACACTCACTGCCATACGTCG 60.109 55.000 0.00 0.00 0.00 5.12
2727 4473 0.109272 CACTCACTGCCATACGTCGT 60.109 55.000 2.21 2.21 0.00 4.34
2728 4474 0.170561 ACTCACTGCCATACGTCGTC 59.829 55.000 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 2.573009 TCAGCTCATCCCAAAGTGATCA 59.427 45.455 0.00 0.00 0.00 2.92
77 78 2.186384 GGCGTGCTCTCAGCTCAT 59.814 61.111 0.00 0.00 42.97 2.90
80 81 2.952293 ATGTGGCGTGCTCTCAGCT 61.952 57.895 0.00 0.00 42.97 4.24
107 117 2.364972 ACTTTGGAGGAAACACCCAG 57.635 50.000 0.00 0.00 40.91 4.45
150 160 4.260620 CCCATCTATAAAGCCGAAAACACG 60.261 45.833 0.00 0.00 0.00 4.49
152 162 4.850680 ACCCATCTATAAAGCCGAAAACA 58.149 39.130 0.00 0.00 0.00 2.83
159 169 4.995487 CCGAGTAAACCCATCTATAAAGCC 59.005 45.833 0.00 0.00 0.00 4.35
168 178 3.366985 CCAAAAAGCCGAGTAAACCCATC 60.367 47.826 0.00 0.00 0.00 3.51
169 179 2.560981 CCAAAAAGCCGAGTAAACCCAT 59.439 45.455 0.00 0.00 0.00 4.00
170 180 1.957877 CCAAAAAGCCGAGTAAACCCA 59.042 47.619 0.00 0.00 0.00 4.51
171 181 1.958579 ACCAAAAAGCCGAGTAAACCC 59.041 47.619 0.00 0.00 0.00 4.11
172 182 3.720949 AACCAAAAAGCCGAGTAAACC 57.279 42.857 0.00 0.00 0.00 3.27
174 184 5.721232 TGAAAAACCAAAAAGCCGAGTAAA 58.279 33.333 0.00 0.00 0.00 2.01
175 185 5.326200 TGAAAAACCAAAAAGCCGAGTAA 57.674 34.783 0.00 0.00 0.00 2.24
176 186 4.985538 TGAAAAACCAAAAAGCCGAGTA 57.014 36.364 0.00 0.00 0.00 2.59
177 187 3.878160 TGAAAAACCAAAAAGCCGAGT 57.122 38.095 0.00 0.00 0.00 4.18
178 188 3.000177 CGTTGAAAAACCAAAAAGCCGAG 60.000 43.478 0.00 0.00 0.00 4.63
179 189 2.924290 CGTTGAAAAACCAAAAAGCCGA 59.076 40.909 0.00 0.00 0.00 5.54
180 190 2.029849 CCGTTGAAAAACCAAAAAGCCG 59.970 45.455 0.00 0.00 0.00 5.52
181 191 2.353269 CCCGTTGAAAAACCAAAAAGCC 59.647 45.455 0.00 0.00 0.00 4.35
182 192 2.223157 GCCCGTTGAAAAACCAAAAAGC 60.223 45.455 0.00 0.00 0.00 3.51
183 193 3.266636 AGCCCGTTGAAAAACCAAAAAG 58.733 40.909 0.00 0.00 0.00 2.27
184 194 3.336138 AGCCCGTTGAAAAACCAAAAA 57.664 38.095 0.00 0.00 0.00 1.94
195 205 2.943036 AACCTAAGAAAGCCCGTTGA 57.057 45.000 0.00 0.00 0.00 3.18
198 208 2.158579 TCCAAAACCTAAGAAAGCCCGT 60.159 45.455 0.00 0.00 0.00 5.28
200 210 2.228103 CGTCCAAAACCTAAGAAAGCCC 59.772 50.000 0.00 0.00 0.00 5.19
201 211 3.143728 TCGTCCAAAACCTAAGAAAGCC 58.856 45.455 0.00 0.00 0.00 4.35
245 265 1.160137 GACATGCCTCTTGCGAAAGT 58.840 50.000 2.29 0.00 45.60 2.66
249 269 2.125552 CGGACATGCCTCTTGCGA 60.126 61.111 0.00 0.00 45.60 5.10
250 270 2.434884 ACGGACATGCCTCTTGCG 60.435 61.111 0.00 0.00 45.60 4.85
252 272 3.181367 GCACGGACATGCCTCTTG 58.819 61.111 0.00 0.00 39.86 3.02
344 398 3.558505 CTCTCGTGAAAGCAAAACCATG 58.441 45.455 0.00 0.00 0.00 3.66
346 400 1.946768 CCTCTCGTGAAAGCAAAACCA 59.053 47.619 0.00 0.00 0.00 3.67
440 518 8.932945 AAAGAGAACACAATCTTTTTCCTTTC 57.067 30.769 0.00 0.00 41.77 2.62
476 636 3.984838 GCAAAACCATGCCTGTCAA 57.015 47.368 0.00 0.00 40.49 3.18
551 712 3.636282 AGAAAACCGGACGGAAAAATG 57.364 42.857 18.80 0.00 38.96 2.32
552 713 4.364860 CAAAGAAAACCGGACGGAAAAAT 58.635 39.130 18.80 0.00 38.96 1.82
558 719 0.535553 TCCCAAAGAAAACCGGACGG 60.536 55.000 9.46 9.56 42.03 4.79
559 720 1.310904 TTCCCAAAGAAAACCGGACG 58.689 50.000 9.46 0.00 0.00 4.79
560 721 4.055360 CAAATTCCCAAAGAAAACCGGAC 58.945 43.478 9.46 0.00 38.21 4.79
561 722 3.707102 ACAAATTCCCAAAGAAAACCGGA 59.293 39.130 9.46 0.00 38.21 5.14
562 723 3.807071 CACAAATTCCCAAAGAAAACCGG 59.193 43.478 0.00 0.00 38.21 5.28
563 724 4.688021 TCACAAATTCCCAAAGAAAACCG 58.312 39.130 0.00 0.00 38.21 4.44
565 726 7.120579 AGGTTTTCACAAATTCCCAAAGAAAAC 59.879 33.333 15.56 15.56 46.01 2.43
566 727 7.171653 AGGTTTTCACAAATTCCCAAAGAAAA 58.828 30.769 0.00 0.00 38.21 2.29
567 728 6.716284 AGGTTTTCACAAATTCCCAAAGAAA 58.284 32.000 0.00 0.00 38.21 2.52
568 729 6.306643 AGGTTTTCACAAATTCCCAAAGAA 57.693 33.333 0.00 0.00 39.32 2.52
569 730 5.948742 AGGTTTTCACAAATTCCCAAAGA 57.051 34.783 0.00 0.00 0.00 2.52
570 731 6.578023 TGTAGGTTTTCACAAATTCCCAAAG 58.422 36.000 0.00 0.00 0.00 2.77
571 732 6.546428 TGTAGGTTTTCACAAATTCCCAAA 57.454 33.333 0.00 0.00 0.00 3.28
572 733 6.070767 TGTTGTAGGTTTTCACAAATTCCCAA 60.071 34.615 0.00 0.00 36.47 4.12
573 734 5.422331 TGTTGTAGGTTTTCACAAATTCCCA 59.578 36.000 0.00 0.00 36.47 4.37
574 735 5.908341 TGTTGTAGGTTTTCACAAATTCCC 58.092 37.500 0.00 0.00 36.47 3.97
575 736 6.475402 CACTGTTGTAGGTTTTCACAAATTCC 59.525 38.462 0.00 0.00 36.47 3.01
576 737 7.254852 TCACTGTTGTAGGTTTTCACAAATTC 58.745 34.615 0.00 0.00 36.47 2.17
577 738 7.164230 TCACTGTTGTAGGTTTTCACAAATT 57.836 32.000 0.00 0.00 36.47 1.82
578 739 6.767524 TCACTGTTGTAGGTTTTCACAAAT 57.232 33.333 0.00 0.00 36.47 2.32
581 742 6.119536 AGATTCACTGTTGTAGGTTTTCACA 58.880 36.000 0.00 0.00 0.00 3.58
584 745 7.964604 ACTAGATTCACTGTTGTAGGTTTTC 57.035 36.000 0.00 0.00 0.00 2.29
598 759 8.399425 TGTCGAGATCTCTAAAACTAGATTCAC 58.601 37.037 20.26 0.00 32.60 3.18
601 762 7.280428 TCGTGTCGAGATCTCTAAAACTAGATT 59.720 37.037 20.26 0.00 32.60 2.40
718 879 1.606668 GTTGCGACAAATGGTGGAAGA 59.393 47.619 0.00 0.00 0.00 2.87
721 882 0.179004 AGGTTGCGACAAATGGTGGA 60.179 50.000 6.39 0.00 0.00 4.02
727 888 1.152830 ACCCCAGGTTGCGACAAAT 59.847 52.632 6.39 0.00 27.29 2.32
735 896 0.405585 ATCACTTCCACCCCAGGTTG 59.594 55.000 0.00 0.00 31.02 3.77
760 930 9.041354 AGATCAGTAATTGAGAAGTACTCCTTT 57.959 33.333 0.00 0.00 40.00 3.11
771 941 6.531503 AAAGTCCGAGATCAGTAATTGAGA 57.468 37.500 0.00 0.00 39.68 3.27
780 950 2.005451 CCAGCAAAAGTCCGAGATCAG 58.995 52.381 0.00 0.00 0.00 2.90
864 1102 9.755122 GGCCCAATTAATATATAACTTTCTCCT 57.245 33.333 0.00 0.00 0.00 3.69
871 1109 6.012333 TCCACCGGCCCAATTAATATATAACT 60.012 38.462 0.00 0.00 0.00 2.24
873 1111 6.390048 TCCACCGGCCCAATTAATATATAA 57.610 37.500 0.00 0.00 0.00 0.98
913 1151 5.048434 GGAAATATACCTCCGCTTAGTACGT 60.048 44.000 0.00 0.00 0.00 3.57
914 1152 5.182760 AGGAAATATACCTCCGCTTAGTACG 59.817 44.000 0.00 0.00 36.78 3.67
915 1153 6.587206 AGGAAATATACCTCCGCTTAGTAC 57.413 41.667 0.00 0.00 36.78 2.73
916 1154 7.439381 CAAAGGAAATATACCTCCGCTTAGTA 58.561 38.462 2.48 0.00 36.67 1.82
917 1155 6.289064 CAAAGGAAATATACCTCCGCTTAGT 58.711 40.000 2.48 0.00 36.67 2.24
918 1156 5.701290 CCAAAGGAAATATACCTCCGCTTAG 59.299 44.000 2.48 0.00 36.67 2.18
919 1157 5.455612 CCCAAAGGAAATATACCTCCGCTTA 60.456 44.000 2.48 0.00 36.67 3.09
920 1158 4.461198 CCAAAGGAAATATACCTCCGCTT 58.539 43.478 2.48 0.00 36.67 4.68
921 1159 3.181443 CCCAAAGGAAATATACCTCCGCT 60.181 47.826 2.48 0.00 36.67 5.52
922 1160 3.146847 CCCAAAGGAAATATACCTCCGC 58.853 50.000 2.48 0.00 36.67 5.54
923 1161 3.146847 GCCCAAAGGAAATATACCTCCG 58.853 50.000 2.48 0.00 36.67 4.63
924 1162 3.497332 GGCCCAAAGGAAATATACCTCC 58.503 50.000 0.00 0.00 36.67 4.30
925 1163 3.497332 GGGCCCAAAGGAAATATACCTC 58.503 50.000 19.95 0.00 36.67 3.85
926 1164 2.158519 CGGGCCCAAAGGAAATATACCT 60.159 50.000 24.92 0.00 39.69 3.08
927 1165 2.158579 TCGGGCCCAAAGGAAATATACC 60.159 50.000 24.92 0.00 33.47 2.73
934 1172 4.715523 CGCTCGGGCCCAAAGGAA 62.716 66.667 24.92 0.00 33.47 3.36
937 1175 2.897350 GATCGCTCGGGCCCAAAG 60.897 66.667 24.92 19.59 34.44 2.77
951 1189 1.477014 GGGGAAAACGGAGGATGGATC 60.477 57.143 0.00 0.00 0.00 3.36
1256 1501 1.304547 AGCTCCCAGACGTACTGCT 60.305 57.895 8.85 1.89 44.52 4.24
1315 1560 4.514577 CTTCGCCTCCGATGCCGT 62.515 66.667 0.00 0.00 43.97 5.68
1371 1616 0.527565 GCACCTTGCACCCTGTTATG 59.472 55.000 0.00 0.00 44.26 1.90
1374 1619 2.906897 CGCACCTTGCACCCTGTT 60.907 61.111 0.00 0.00 45.36 3.16
1477 1722 2.175878 ATCTGTGCACCACTCTTGAC 57.824 50.000 15.69 0.00 35.11 3.18
1711 3135 0.553333 GGCTATTTCTTCCCTGCCCT 59.447 55.000 0.00 0.00 34.81 5.19
1712 3136 3.117657 GGCTATTTCTTCCCTGCCC 57.882 57.895 0.00 0.00 34.81 5.36
1744 3168 5.440234 TCTAAAGGAATAGCTCAGCTACG 57.560 43.478 9.07 0.00 44.24 3.51
1745 3169 8.581578 ACTTATCTAAAGGAATAGCTCAGCTAC 58.418 37.037 9.07 0.00 44.24 3.58
1779 3203 8.673711 GTGCCTGACATTTTCATACAGTTTATA 58.326 33.333 0.00 0.00 32.17 0.98
1866 3297 6.489022 TGATTAATCGCTAGTGGCTACTAAGA 59.511 38.462 11.41 13.16 38.85 2.10
1870 3301 5.730296 ATGATTAATCGCTAGTGGCTACT 57.270 39.130 8.18 8.18 40.99 2.57
1871 3302 6.787085 AAATGATTAATCGCTAGTGGCTAC 57.213 37.500 10.80 0.00 39.13 3.58
1872 3303 7.497579 TGAAAAATGATTAATCGCTAGTGGCTA 59.502 33.333 10.80 0.00 39.13 3.93
1873 3304 6.318648 TGAAAAATGATTAATCGCTAGTGGCT 59.681 34.615 10.80 0.00 39.13 4.75
1874 3305 6.494842 TGAAAAATGATTAATCGCTAGTGGC 58.505 36.000 10.80 0.00 37.64 5.01
1875 3306 8.909708 TTTGAAAAATGATTAATCGCTAGTGG 57.090 30.769 10.80 0.00 0.00 4.00
1943 3430 3.894257 GCCTGAAGTTTTTGGAGGC 57.106 52.632 0.00 0.00 42.37 4.70
1967 3454 7.759489 AATTGAACAGTGTACCACATACAAT 57.241 32.000 0.00 0.00 45.51 2.71
1968 3455 8.678593 TTAATTGAACAGTGTACCACATACAA 57.321 30.769 0.00 0.00 45.51 2.41
1969 3456 8.856153 ATTAATTGAACAGTGTACCACATACA 57.144 30.769 0.00 0.00 41.71 2.29
1972 3459 9.733556 TCTTATTAATTGAACAGTGTACCACAT 57.266 29.630 0.00 0.00 36.74 3.21
1973 3460 9.214957 CTCTTATTAATTGAACAGTGTACCACA 57.785 33.333 0.00 0.00 36.74 4.17
1974 3461 8.175716 GCTCTTATTAATTGAACAGTGTACCAC 58.824 37.037 0.00 0.00 34.10 4.16
1975 3462 8.100791 AGCTCTTATTAATTGAACAGTGTACCA 58.899 33.333 0.00 0.00 0.00 3.25
1976 3463 8.494016 AGCTCTTATTAATTGAACAGTGTACC 57.506 34.615 0.00 0.00 0.00 3.34
1989 3490 8.109634 TGAGAGGACCAAAAAGCTCTTATTAAT 58.890 33.333 0.00 0.00 0.00 1.40
1995 3496 3.864789 TGAGAGGACCAAAAAGCTCTT 57.135 42.857 0.00 0.00 0.00 2.85
2059 3560 9.683069 CATTCTTAATTGTCCTTATGCAATACC 57.317 33.333 0.00 0.00 34.61 2.73
2105 3606 7.168972 CAGGTCGTCTCATTCTTCATTTATCTC 59.831 40.741 0.00 0.00 0.00 2.75
2106 3607 6.983307 CAGGTCGTCTCATTCTTCATTTATCT 59.017 38.462 0.00 0.00 0.00 1.98
2107 3608 6.201806 CCAGGTCGTCTCATTCTTCATTTATC 59.798 42.308 0.00 0.00 0.00 1.75
2108 3609 6.051717 CCAGGTCGTCTCATTCTTCATTTAT 58.948 40.000 0.00 0.00 0.00 1.40
2109 3610 5.186992 TCCAGGTCGTCTCATTCTTCATTTA 59.813 40.000 0.00 0.00 0.00 1.40
2110 3611 4.020218 TCCAGGTCGTCTCATTCTTCATTT 60.020 41.667 0.00 0.00 0.00 2.32
2117 3618 3.383185 AGAATCTCCAGGTCGTCTCATTC 59.617 47.826 0.00 0.00 0.00 2.67
2118 3619 3.370104 AGAATCTCCAGGTCGTCTCATT 58.630 45.455 0.00 0.00 0.00 2.57
2125 3626 5.561145 CGATTACAGTAGAATCTCCAGGTCG 60.561 48.000 0.00 0.00 32.17 4.79
2132 3633 3.252701 TCCGGCGATTACAGTAGAATCTC 59.747 47.826 9.30 0.00 32.17 2.75
2152 3653 1.337167 GCCAAGCAAAAGGATGTGTCC 60.337 52.381 0.00 0.00 45.45 4.02
2215 3746 7.784037 TGATCAATTAATTCCATCCAAAGTGG 58.216 34.615 0.00 0.00 39.43 4.00
2238 3770 4.086457 TGCGGCTATATATTCTCACCTGA 58.914 43.478 0.00 0.00 0.00 3.86
2300 4034 2.159254 ACACACACACACAAAAGGATGC 60.159 45.455 0.00 0.00 0.00 3.91
2305 4039 2.979151 CACACACACACACACACAAAAG 59.021 45.455 0.00 0.00 0.00 2.27
2309 4048 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2342 4081 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2343 4082 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2344 4083 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2345 4084 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2346 4085 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2347 4086 1.598882 AACACACACACACACACACA 58.401 45.000 0.00 0.00 0.00 3.72
2348 4087 2.315011 CAAACACACACACACACACAC 58.685 47.619 0.00 0.00 0.00 3.82
2349 4088 1.268079 CCAAACACACACACACACACA 59.732 47.619 0.00 0.00 0.00 3.72
2350 4089 1.402194 CCCAAACACACACACACACAC 60.402 52.381 0.00 0.00 0.00 3.82
2351 4090 0.884514 CCCAAACACACACACACACA 59.115 50.000 0.00 0.00 0.00 3.72
2352 4091 1.169577 TCCCAAACACACACACACAC 58.830 50.000 0.00 0.00 0.00 3.82
2353 4092 1.911057 TTCCCAAACACACACACACA 58.089 45.000 0.00 0.00 0.00 3.72
2354 4093 3.518634 ATTTCCCAAACACACACACAC 57.481 42.857 0.00 0.00 0.00 3.82
2355 4094 5.661056 TTAATTTCCCAAACACACACACA 57.339 34.783 0.00 0.00 0.00 3.72
2356 4095 6.369065 TGTTTTAATTTCCCAAACACACACAC 59.631 34.615 0.00 0.00 35.88 3.82
2357 4096 6.464222 TGTTTTAATTTCCCAAACACACACA 58.536 32.000 0.00 0.00 35.88 3.72
2358 4097 6.969828 TGTTTTAATTTCCCAAACACACAC 57.030 33.333 0.00 0.00 35.88 3.82
2359 4098 6.540189 CCATGTTTTAATTTCCCAAACACACA 59.460 34.615 0.00 0.00 41.85 3.72
2360 4099 6.763610 TCCATGTTTTAATTTCCCAAACACAC 59.236 34.615 0.00 0.00 41.85 3.82
2361 4100 6.889198 TCCATGTTTTAATTTCCCAAACACA 58.111 32.000 0.00 0.00 41.85 3.72
2362 4101 7.443879 ACATCCATGTTTTAATTTCCCAAACAC 59.556 33.333 0.00 0.00 41.85 3.32
2363 4102 7.512992 ACATCCATGTTTTAATTTCCCAAACA 58.487 30.769 0.00 0.00 42.89 2.83
2364 4103 7.977789 ACATCCATGTTTTAATTTCCCAAAC 57.022 32.000 0.00 0.00 37.90 2.93
2380 4119 3.689347 TCCAAGTCTCCAAACATCCATG 58.311 45.455 0.00 0.00 0.00 3.66
2386 4125 3.456644 TGGTAACTCCAAGTCTCCAAACA 59.543 43.478 2.24 0.00 44.12 2.83
2403 4142 3.870633 ACAAACAAAAGCCGTTGGTAA 57.129 38.095 2.37 0.00 28.51 2.85
2432 4171 5.046591 CCTCTAGTCCTCAGTCGATCTAGAT 60.047 48.000 4.47 4.47 35.14 1.98
2433 4172 4.282449 CCTCTAGTCCTCAGTCGATCTAGA 59.718 50.000 0.00 0.00 34.68 2.43
2434 4173 4.566004 CCTCTAGTCCTCAGTCGATCTAG 58.434 52.174 0.00 0.00 0.00 2.43
2443 4182 1.606668 GTGATCGCCTCTAGTCCTCAG 59.393 57.143 0.00 0.00 0.00 3.35
2474 4213 7.010738 GTGTGGTTGCGTAATACTACATTACAT 59.989 37.037 7.65 0.00 37.92 2.29
2475 4214 6.310956 GTGTGGTTGCGTAATACTACATTACA 59.689 38.462 7.65 0.00 37.92 2.41
2476 4215 6.237915 GGTGTGGTTGCGTAATACTACATTAC 60.238 42.308 0.00 0.00 37.92 1.89
2477 4216 5.811613 GGTGTGGTTGCGTAATACTACATTA 59.188 40.000 0.00 0.00 37.92 1.90
2478 4217 4.632688 GGTGTGGTTGCGTAATACTACATT 59.367 41.667 0.00 0.00 37.92 2.71
2501 4240 5.461032 TGCTGGTTATTGGTTTGTAAAGG 57.539 39.130 0.00 0.00 0.00 3.11
2642 4388 9.278734 GAAGTTACTTTAGCTGCACAATTAATC 57.721 33.333 1.02 0.00 0.00 1.75
2668 4414 2.979813 GGTGCTAAGCAACATTTTCGTG 59.020 45.455 0.00 0.00 46.68 4.35
2669 4415 3.282831 GGTGCTAAGCAACATTTTCGT 57.717 42.857 0.00 0.00 46.68 3.85
2687 4433 2.282180 GTTCGGGTGCACCATGGT 60.282 61.111 35.78 13.00 40.22 3.55
2688 4434 2.191786 TAGGTTCGGGTGCACCATGG 62.192 60.000 35.78 23.71 40.22 3.66
2689 4435 1.024579 GTAGGTTCGGGTGCACCATG 61.025 60.000 35.78 26.74 40.22 3.66
2690 4436 1.298667 GTAGGTTCGGGTGCACCAT 59.701 57.895 35.78 16.48 40.22 3.55
2691 4437 2.141448 TGTAGGTTCGGGTGCACCA 61.141 57.895 35.78 15.44 40.22 4.17
2692 4438 1.670083 GTGTAGGTTCGGGTGCACC 60.670 63.158 28.57 28.57 0.00 5.01
2693 4439 0.669625 GAGTGTAGGTTCGGGTGCAC 60.670 60.000 8.80 8.80 0.00 4.57
2694 4440 1.116536 TGAGTGTAGGTTCGGGTGCA 61.117 55.000 0.00 0.00 0.00 4.57
2695 4441 0.669625 GTGAGTGTAGGTTCGGGTGC 60.670 60.000 0.00 0.00 0.00 5.01
2696 4442 0.966920 AGTGAGTGTAGGTTCGGGTG 59.033 55.000 0.00 0.00 0.00 4.61
2697 4443 0.966920 CAGTGAGTGTAGGTTCGGGT 59.033 55.000 0.00 0.00 0.00 5.28
2698 4444 0.389948 GCAGTGAGTGTAGGTTCGGG 60.390 60.000 0.00 0.00 0.00 5.14
2699 4445 0.389948 GGCAGTGAGTGTAGGTTCGG 60.390 60.000 0.00 0.00 0.00 4.30
2700 4446 0.317160 TGGCAGTGAGTGTAGGTTCG 59.683 55.000 0.00 0.00 0.00 3.95
2701 4447 2.770164 ATGGCAGTGAGTGTAGGTTC 57.230 50.000 0.00 0.00 0.00 3.62
2702 4448 2.094182 CGTATGGCAGTGAGTGTAGGTT 60.094 50.000 0.00 0.00 0.00 3.50
2703 4449 1.476891 CGTATGGCAGTGAGTGTAGGT 59.523 52.381 0.00 0.00 0.00 3.08
2704 4450 1.476891 ACGTATGGCAGTGAGTGTAGG 59.523 52.381 0.00 0.00 0.00 3.18
2705 4451 2.791503 CGACGTATGGCAGTGAGTGTAG 60.792 54.545 0.00 0.00 0.00 2.74
2706 4452 1.131693 CGACGTATGGCAGTGAGTGTA 59.868 52.381 0.00 0.00 0.00 2.90
2707 4453 0.109272 CGACGTATGGCAGTGAGTGT 60.109 55.000 0.00 0.00 0.00 3.55
2708 4454 0.109272 ACGACGTATGGCAGTGAGTG 60.109 55.000 0.00 0.00 0.00 3.51
2709 4455 0.170561 GACGACGTATGGCAGTGAGT 59.829 55.000 0.00 0.00 0.00 3.41
2710 4456 2.945315 GACGACGTATGGCAGTGAG 58.055 57.895 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.