Multiple sequence alignment - TraesCS7D01G341200

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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 TraesCS7D01G341200 chr7D 100.000 6527 0 0 1 6527 436966257 436959731 0.000000e+00 12054.0
1 TraesCS7D01G341200 chr7D 94.231 156 8 1 4309 4464 593035162 593035316 3.040000e-58 237.0
2 TraesCS7D01G341200 chr7A 96.221 2117 71 8 2626 4738 486931774 486929663 0.000000e+00 3458.0
3 TraesCS7D01G341200 chr7A 91.792 1060 55 12 1595 2627 486933066 486932012 0.000000e+00 1447.0
4 TraesCS7D01G341200 chr7A 95.250 779 24 8 4946 5720 486929690 486928921 0.000000e+00 1221.0
5 TraesCS7D01G341200 chr7A 87.485 815 39 26 827 1599 486933893 486933100 0.000000e+00 881.0
6 TraesCS7D01G341200 chr7A 94.872 156 7 1 4309 4464 462978740 462978586 6.540000e-60 243.0
7 TraesCS7D01G341200 chr7A 93.671 158 9 1 4306 4463 609383568 609383412 1.090000e-57 235.0
8 TraesCS7D01G341200 chr7A 86.301 73 6 4 5884 5953 167905075 167905146 7.020000e-10 76.8
9 TraesCS7D01G341200 chr7A 95.238 42 2 0 673 714 487025349 487025308 4.220000e-07 67.6
10 TraesCS7D01G341200 chr7B 96.993 1829 41 7 4073 5895 453623678 453621858 0.000000e+00 3061.0
11 TraesCS7D01G341200 chr7B 92.543 1046 42 12 1618 2640 453627380 453626348 0.000000e+00 1467.0
12 TraesCS7D01G341200 chr7B 98.439 833 11 1 3213 4045 453624508 453623678 0.000000e+00 1465.0
13 TraesCS7D01G341200 chr7B 93.052 734 28 9 866 1599 453628483 453627773 0.000000e+00 1051.0
14 TraesCS7D01G341200 chr7B 97.302 593 13 3 2638 3228 453626266 453625675 0.000000e+00 1003.0
15 TraesCS7D01G341200 chr7B 84.737 570 75 8 4 563 453629468 453628901 1.590000e-155 560.0
16 TraesCS7D01G341200 chr7B 93.671 158 9 1 4306 4463 567999019 567998863 1.090000e-57 235.0
17 TraesCS7D01G341200 chr7B 90.062 161 14 2 636 794 453628835 453628675 2.390000e-49 207.0
18 TraesCS7D01G341200 chr2D 90.317 537 47 4 5994 6527 67960918 67961452 0.000000e+00 699.0
19 TraesCS7D01G341200 chr2D 91.220 205 10 4 4738 4938 128025767 128025967 8.340000e-69 272.0
20 TraesCS7D01G341200 chr2D 94.937 158 7 1 4307 4463 88290212 88290055 5.050000e-61 246.0
21 TraesCS7D01G341200 chr2D 95.833 48 2 0 5905 5952 228434217 228434170 1.950000e-10 78.7
22 TraesCS7D01G341200 chr2D 94.000 50 3 0 5904 5953 467240373 467240422 7.020000e-10 76.8
23 TraesCS7D01G341200 chr6D 89.150 553 54 5 5981 6527 140141352 140140800 0.000000e+00 684.0
24 TraesCS7D01G341200 chr6D 88.848 538 56 3 5993 6527 428671873 428672409 0.000000e+00 658.0
25 TraesCS7D01G341200 chr6D 93.750 48 3 0 5906 5953 283795856 283795809 9.080000e-09 73.1
26 TraesCS7D01G341200 chr1A 89.071 549 57 2 5982 6527 418031049 418030501 0.000000e+00 678.0
27 TraesCS7D01G341200 chr1A 90.000 210 15 4 4735 4941 440899061 440899267 3.880000e-67 267.0
28 TraesCS7D01G341200 chr1A 89.372 207 15 4 4735 4938 449413873 449414075 3.020000e-63 254.0
29 TraesCS7D01G341200 chr1D 88.727 550 58 3 5982 6527 325694188 325694737 0.000000e+00 669.0
30 TraesCS7D01G341200 chr1D 87.993 558 60 6 5975 6527 309587387 309587942 0.000000e+00 652.0
31 TraesCS7D01G341200 chr5D 88.342 549 61 2 5982 6527 320814488 320815036 0.000000e+00 656.0
32 TraesCS7D01G341200 chr5D 87.619 210 22 2 4735 4942 7682471 7682264 2.350000e-59 241.0
33 TraesCS7D01G341200 chr4A 88.288 555 53 11 5981 6527 515450350 515449800 0.000000e+00 654.0
34 TraesCS7D01G341200 chr2B 88.267 554 53 12 5982 6527 264568808 264568259 0.000000e+00 652.0
35 TraesCS7D01G341200 chr6B 89.474 209 16 4 4735 4940 612537304 612537099 6.490000e-65 259.0
36 TraesCS7D01G341200 chr6B 91.071 56 4 1 5898 5953 691135698 691135644 2.520000e-09 75.0
37 TraesCS7D01G341200 chr6A 89.423 208 16 4 4736 4940 549989982 549989778 2.340000e-64 257.0
38 TraesCS7D01G341200 chr6A 94.118 51 3 0 5903 5953 31750250 31750200 1.950000e-10 78.7
39 TraesCS7D01G341200 chr2A 89.806 206 13 6 4736 4936 117393214 117393012 2.340000e-64 257.0
40 TraesCS7D01G341200 chr3D 89.899 198 14 4 4742 4936 436020076 436020270 3.910000e-62 250.0
41 TraesCS7D01G341200 chr3D 93.038 158 11 0 4306 4463 288550615 288550458 1.420000e-56 231.0
42 TraesCS7D01G341200 chr3D 94.000 50 3 0 5904 5953 505557397 505557348 7.020000e-10 76.8
43 TraesCS7D01G341200 chr5B 94.194 155 8 1 4309 4463 98663177 98663330 1.090000e-57 235.0
44 TraesCS7D01G341200 chr3A 90.323 62 3 2 5894 5953 520437431 520437491 1.950000e-10 78.7
45 TraesCS7D01G341200 chr4B 91.071 56 5 0 5898 5953 498375476 498375531 7.020000e-10 76.8


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 TraesCS7D01G341200 chr7D 436959731 436966257 6526 True 12054.000000 12054 100.000 1 6527 1 chr7D.!!$R1 6526
1 TraesCS7D01G341200 chr7A 486928921 486933893 4972 True 1751.750000 3458 92.687 827 5720 4 chr7A.!!$R4 4893
2 TraesCS7D01G341200 chr7B 453621858 453629468 7610 True 1259.142857 3061 93.304 4 5895 7 chr7B.!!$R2 5891
3 TraesCS7D01G341200 chr2D 67960918 67961452 534 False 699.000000 699 90.317 5994 6527 1 chr2D.!!$F1 533
4 TraesCS7D01G341200 chr6D 140140800 140141352 552 True 684.000000 684 89.150 5981 6527 1 chr6D.!!$R1 546
5 TraesCS7D01G341200 chr6D 428671873 428672409 536 False 658.000000 658 88.848 5993 6527 1 chr6D.!!$F1 534
6 TraesCS7D01G341200 chr1A 418030501 418031049 548 True 678.000000 678 89.071 5982 6527 1 chr1A.!!$R1 545
7 TraesCS7D01G341200 chr1D 325694188 325694737 549 False 669.000000 669 88.727 5982 6527 1 chr1D.!!$F2 545
8 TraesCS7D01G341200 chr1D 309587387 309587942 555 False 652.000000 652 87.993 5975 6527 1 chr1D.!!$F1 552
9 TraesCS7D01G341200 chr5D 320814488 320815036 548 False 656.000000 656 88.342 5982 6527 1 chr5D.!!$F1 545
10 TraesCS7D01G341200 chr4A 515449800 515450350 550 True 654.000000 654 88.288 5981 6527 1 chr4A.!!$R1 546
11 TraesCS7D01G341200 chr2B 264568259 264568808 549 True 652.000000 652 88.267 5982 6527 1 chr2B.!!$R1 545

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
172 176 0.104120 ACGCACTTTCAAAAAGGGGC 59.896 50.000 4.03 6.17 37.52 5.80 F
181 185 0.382515 CAAAAAGGGGCGACGAAACA 59.617 50.000 0.00 0.00 0.00 2.83 F
184 188 0.464916 AAAGGGGCGACGAAACAAGT 60.465 50.000 0.00 0.00 0.00 3.16 F
753 790 0.555769 TTGGCTCACCCCTGACTTTT 59.444 50.000 0.00 0.00 33.59 2.27 F
1419 1573 1.056700 TAGCCTGGGATTCCCTCTGC 61.057 60.000 22.38 19.66 45.70 4.26 F
1695 2269 1.106285 CAAGCTACCCCAATTCCTGC 58.894 55.000 0.00 0.00 0.00 4.85 F
3719 5761 1.003580 ACGTGGCAATCAAGAGATGGT 59.996 47.619 0.00 0.00 33.90 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1360 1514 1.488812 CAGGTGGGGAAACGATATGGA 59.511 52.381 0.00 0.0 0.00 3.41 R
1553 1716 1.541588 GTTCTGATTGCAGGGTTGACC 59.458 52.381 0.00 0.0 42.53 4.02 R
1967 2563 2.531206 AGAGAGTCGCGTAGAAAATGC 58.469 47.619 5.77 0.0 36.70 3.56 R
2450 3052 6.569179 TGGGCAAAAGATTGTCTAACTAAC 57.431 37.500 0.00 0.0 41.02 2.34 R
3405 5447 1.000896 ACATGTAGCACCCAAGGGC 60.001 57.895 4.70 0.0 39.32 5.19 R
3857 5899 1.213182 TGTGCCCTGTAGTGGACAAAA 59.787 47.619 0.00 0.0 37.70 2.44 R
5848 7926 0.825425 TCTTTGGTGGCATTCCGCAA 60.825 50.000 0.00 0.0 44.64 4.85 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
20 21 1.171308 TCGCTAGACACTACGCCTTT 58.829 50.000 0.00 0.00 0.00 3.11
21 22 1.131883 TCGCTAGACACTACGCCTTTC 59.868 52.381 0.00 0.00 0.00 2.62
22 23 1.135489 CGCTAGACACTACGCCTTTCA 60.135 52.381 0.00 0.00 0.00 2.69
23 24 2.260481 GCTAGACACTACGCCTTTCAC 58.740 52.381 0.00 0.00 0.00 3.18
55 56 2.233676 GGGGTCAACCATTTCCACATTC 59.766 50.000 0.89 0.00 42.91 2.67
61 62 7.069331 GGGTCAACCATTTCCACATTCAATATA 59.931 37.037 0.89 0.00 39.85 0.86
65 66 9.687210 CAACCATTTCCACATTCAATATATGAG 57.313 33.333 0.00 0.00 39.77 2.90
110 114 7.687941 AACTTAATAACCACCATCAGTTCTG 57.312 36.000 0.00 0.00 0.00 3.02
129 133 5.673337 TCTGCTAAACACATTGTCTTCAC 57.327 39.130 0.00 0.00 0.00 3.18
130 134 5.122519 TCTGCTAAACACATTGTCTTCACA 58.877 37.500 0.00 0.00 0.00 3.58
132 136 6.934083 TCTGCTAAACACATTGTCTTCACATA 59.066 34.615 0.00 0.00 30.55 2.29
171 175 2.595124 AACGCACTTTCAAAAAGGGG 57.405 45.000 4.03 4.35 0.00 4.79
172 176 0.104120 ACGCACTTTCAAAAAGGGGC 59.896 50.000 4.03 6.17 37.52 5.80
181 185 0.382515 CAAAAAGGGGCGACGAAACA 59.617 50.000 0.00 0.00 0.00 2.83
184 188 0.464916 AAAGGGGCGACGAAACAAGT 60.465 50.000 0.00 0.00 0.00 3.16
224 228 1.387756 CATGTTACCCGAACGAACGAC 59.612 52.381 0.14 0.00 41.35 4.34
239 243 3.827898 GACGCGGGGTCCTCTCAG 61.828 72.222 12.47 0.00 39.90 3.35
242 246 2.363147 GCGGGGTCCTCTCAGAGT 60.363 66.667 0.00 0.00 0.00 3.24
243 247 2.716017 GCGGGGTCCTCTCAGAGTG 61.716 68.421 0.00 0.00 0.00 3.51
258 262 6.691508 TCTCAGAGTGATTTTTGATTCTCGA 58.308 36.000 0.00 0.00 0.00 4.04
263 267 8.063038 CAGAGTGATTTTTGATTCTCGATCATC 58.937 37.037 0.00 0.00 44.01 2.92
266 270 8.954350 AGTGATTTTTGATTCTCGATCATCTTT 58.046 29.630 0.00 0.00 44.01 2.52
289 293 7.618502 TTTTTATGCTATAAACAAGAGCGGA 57.381 32.000 0.00 0.00 45.78 5.54
304 308 4.600062 AGAGCGGAAAAATGAAAGGGTAT 58.400 39.130 0.00 0.00 0.00 2.73
305 309 4.399303 AGAGCGGAAAAATGAAAGGGTATG 59.601 41.667 0.00 0.00 0.00 2.39
306 310 3.447229 AGCGGAAAAATGAAAGGGTATGG 59.553 43.478 0.00 0.00 0.00 2.74
310 314 5.269189 GGAAAAATGAAAGGGTATGGGAGA 58.731 41.667 0.00 0.00 0.00 3.71
320 324 1.152819 TATGGGAGAGGGACGGACG 60.153 63.158 0.00 0.00 0.00 4.79
328 332 3.703127 GGGACGGACGGGCTCTTT 61.703 66.667 0.00 0.00 0.00 2.52
335 339 2.966309 GACGGGCTCTTTGTTGCGG 61.966 63.158 0.00 0.00 0.00 5.69
336 340 4.404654 CGGGCTCTTTGTTGCGGC 62.405 66.667 0.00 0.00 0.00 6.53
339 343 2.429739 GCTCTTTGTTGCGGCTGC 60.430 61.111 11.65 11.65 43.20 5.25
340 344 2.912624 GCTCTTTGTTGCGGCTGCT 61.913 57.895 20.27 0.00 43.34 4.24
345 349 0.955428 TTTGTTGCGGCTGCTAGGAG 60.955 55.000 20.27 6.94 43.34 3.69
349 353 0.676184 TTGCGGCTGCTAGGAGATAG 59.324 55.000 20.27 6.09 43.34 2.08
364 368 7.717436 GCTAGGAGATAGGTGCTTATTCTTTTT 59.283 37.037 0.00 0.00 31.55 1.94
390 394 0.882474 ACACTGTCTCAGGCGTCTAC 59.118 55.000 0.00 0.00 35.51 2.59
391 395 1.169577 CACTGTCTCAGGCGTCTACT 58.830 55.000 0.00 0.00 35.51 2.57
394 398 3.190744 CACTGTCTCAGGCGTCTACTTAA 59.809 47.826 0.00 0.00 35.51 1.85
397 401 3.825014 TGTCTCAGGCGTCTACTTAAAGT 59.175 43.478 0.00 0.00 0.00 2.66
425 430 7.683746 TGCTTATTGTTCTTTTTGCAAAAGAC 58.316 30.769 22.78 20.93 36.14 3.01
436 441 9.444534 TCTTTTTGCAAAAGACAAAAGAAAAAC 57.555 25.926 22.78 0.00 45.02 2.43
438 443 9.741647 TTTTTGCAAAAGACAAAAGAAAAACAT 57.258 22.222 22.78 0.00 45.02 2.71
439 444 8.947304 TTTGCAAAAGACAAAAGAAAAACATC 57.053 26.923 10.02 0.00 34.22 3.06
440 445 7.071014 TGCAAAAGACAAAAGAAAAACATCC 57.929 32.000 0.00 0.00 0.00 3.51
441 446 6.878389 TGCAAAAGACAAAAGAAAAACATCCT 59.122 30.769 0.00 0.00 0.00 3.24
442 447 8.037758 TGCAAAAGACAAAAGAAAAACATCCTA 58.962 29.630 0.00 0.00 0.00 2.94
443 448 8.542953 GCAAAAGACAAAAGAAAAACATCCTAG 58.457 33.333 0.00 0.00 0.00 3.02
444 449 8.542953 CAAAAGACAAAAGAAAAACATCCTAGC 58.457 33.333 0.00 0.00 0.00 3.42
447 452 4.825085 ACAAAAGAAAAACATCCTAGCGGA 59.175 37.500 0.00 0.00 45.16 5.54
461 469 3.782443 CGGAGGTAGGGTGGCCAC 61.782 72.222 28.57 28.57 0.00 5.01
545 556 6.899393 AACTGGATTAGAATTGTTCTGCAA 57.101 33.333 2.60 0.00 40.94 4.08
547 558 6.006449 ACTGGATTAGAATTGTTCTGCAAGT 58.994 36.000 2.60 0.00 40.94 3.16
550 561 6.599244 TGGATTAGAATTGTTCTGCAAGTAGG 59.401 38.462 2.60 0.00 40.94 3.18
563 574 3.908103 TGCAAGTAGGGGACTAAGAAGTT 59.092 43.478 0.00 0.00 46.54 2.66
564 575 4.349930 TGCAAGTAGGGGACTAAGAAGTTT 59.650 41.667 0.00 0.00 46.54 2.66
565 576 4.695928 GCAAGTAGGGGACTAAGAAGTTTG 59.304 45.833 0.00 0.00 46.54 2.93
566 577 5.246307 CAAGTAGGGGACTAAGAAGTTTGG 58.754 45.833 0.00 0.00 46.54 3.28
569 580 4.904895 AGGGGACTAAGAAGTTTGGTAC 57.095 45.455 0.00 0.00 40.61 3.34
578 615 9.918630 GACTAAGAAGTTTGGTACAGTACATAA 57.081 33.333 12.89 4.53 36.02 1.90
614 651 8.728596 AACACCTTATTCTATATAGTGAGGCT 57.271 34.615 9.58 0.00 0.00 4.58
615 652 8.728596 ACACCTTATTCTATATAGTGAGGCTT 57.271 34.615 9.58 2.21 0.00 4.35
616 653 8.589338 ACACCTTATTCTATATAGTGAGGCTTG 58.411 37.037 9.58 9.62 0.00 4.01
617 654 8.589338 CACCTTATTCTATATAGTGAGGCTTGT 58.411 37.037 9.58 0.00 0.00 3.16
618 655 8.808092 ACCTTATTCTATATAGTGAGGCTTGTC 58.192 37.037 9.58 0.00 0.00 3.18
619 656 9.030452 CCTTATTCTATATAGTGAGGCTTGTCT 57.970 37.037 9.58 0.00 0.00 3.41
641 678 3.353370 TTTTTCCGGACGGGATATTGT 57.647 42.857 1.83 0.00 46.62 2.71
642 679 2.319136 TTTCCGGACGGGATATTGTG 57.681 50.000 1.83 0.00 46.62 3.33
643 680 1.487300 TTCCGGACGGGATATTGTGA 58.513 50.000 1.83 0.00 46.62 3.58
649 686 1.599542 GACGGGATATTGTGAGCTTGC 59.400 52.381 0.00 0.00 0.00 4.01
704 741 7.772757 TGGTTGCAAGGTTTAAGAAAATGAAAT 59.227 29.630 0.00 0.00 0.00 2.17
705 742 8.282592 GGTTGCAAGGTTTAAGAAAATGAAATC 58.717 33.333 0.00 0.00 0.00 2.17
753 790 0.555769 TTGGCTCACCCCTGACTTTT 59.444 50.000 0.00 0.00 33.59 2.27
781 818 6.055588 TCAAAACAGCTCAGCTACTACTTTT 58.944 36.000 0.00 0.00 36.40 2.27
878 971 5.543714 TGCACAGCTGATTTTTCATGAAAT 58.456 33.333 23.35 7.85 32.16 2.17
891 985 9.842444 ATTTTTCATGAAATTTTGTACGTTTCG 57.158 25.926 21.10 0.00 35.23 3.46
892 986 7.972623 TTTCATGAAATTTTGTACGTTTCGT 57.027 28.000 16.91 0.00 44.35 3.85
893 987 7.972623 TTCATGAAATTTTGTACGTTTCGTT 57.027 28.000 5.45 0.00 41.54 3.85
894 988 7.972623 TCATGAAATTTTGTACGTTTCGTTT 57.027 28.000 0.00 0.00 41.54 3.60
895 989 8.395940 TCATGAAATTTTGTACGTTTCGTTTT 57.604 26.923 0.00 0.00 41.54 2.43
977 1122 3.246112 TCCACCCCCGTGTCTTGG 61.246 66.667 0.00 0.00 38.41 3.61
978 1123 3.566210 CCACCCCCGTGTCTTGGT 61.566 66.667 0.00 0.00 38.41 3.67
979 1124 2.032071 CACCCCCGTGTCTTGGTC 59.968 66.667 0.00 0.00 35.10 4.02
980 1125 2.122547 ACCCCCGTGTCTTGGTCT 60.123 61.111 0.00 0.00 0.00 3.85
981 1126 2.214920 ACCCCCGTGTCTTGGTCTC 61.215 63.158 0.00 0.00 0.00 3.36
982 1127 2.261671 CCCCGTGTCTTGGTCTCG 59.738 66.667 0.00 0.00 0.00 4.04
983 1128 2.261671 CCCGTGTCTTGGTCTCGG 59.738 66.667 0.00 0.00 40.26 4.63
984 1129 2.432628 CCGTGTCTTGGTCTCGGC 60.433 66.667 0.00 0.00 35.72 5.54
1092 1245 1.878522 ATTAACCTCGCGCGCTCTG 60.879 57.895 30.48 18.57 0.00 3.35
1373 1527 4.778534 TCGAGGTATCCATATCGTTTCC 57.221 45.455 0.00 0.00 36.58 3.13
1376 1530 3.581332 GAGGTATCCATATCGTTTCCCCA 59.419 47.826 0.00 0.00 0.00 4.96
1400 1554 6.310224 CACCTGTCTTTTCGTTGAATTTTTGT 59.690 34.615 0.00 0.00 0.00 2.83
1419 1573 1.056700 TAGCCTGGGATTCCCTCTGC 61.057 60.000 22.38 19.66 45.70 4.26
1433 1587 4.366267 TCCCTCTGCTCTTCCTTAGATTT 58.634 43.478 0.00 0.00 30.92 2.17
1434 1596 4.163078 TCCCTCTGCTCTTCCTTAGATTTG 59.837 45.833 0.00 0.00 30.92 2.32
1441 1603 4.142004 GCTCTTCCTTAGATTTGTACGGGA 60.142 45.833 0.00 0.00 30.92 5.14
1582 1745 3.503363 CCTGCAATCAGAACAAGTAAGCA 59.497 43.478 0.00 0.00 42.95 3.91
1607 1808 7.867403 CACTAAAACTGCTCATTGTTTGGTAAT 59.133 33.333 0.00 0.00 36.63 1.89
1619 1820 9.066892 TCATTGTTTGGTAATATGGAAGCTATC 57.933 33.333 0.00 0.00 0.00 2.08
1683 2257 6.021596 CACGTTCATACCATTTTCAAGCTAC 58.978 40.000 0.00 0.00 0.00 3.58
1695 2269 1.106285 CAAGCTACCCCAATTCCTGC 58.894 55.000 0.00 0.00 0.00 4.85
1744 2318 8.435187 AGGAATAGATTTCTGCTATGTCAATGA 58.565 33.333 0.00 0.00 0.00 2.57
1760 2334 6.115446 TGTCAATGATTCCTTCGCTTCTATT 58.885 36.000 0.00 0.00 0.00 1.73
1770 2344 6.055588 TCCTTCGCTTCTATTAAGGAATTGG 58.944 40.000 0.00 0.00 43.43 3.16
1774 2359 5.367352 TCGCTTCTATTAAGGAATTGGGGTA 59.633 40.000 0.00 0.00 0.00 3.69
1902 2493 6.314917 AGGTTTTGTGAAATCAGTATTCCCT 58.685 36.000 0.00 0.00 0.00 4.20
1912 2503 4.895668 TCAGTATTCCCTTGGTACGTTT 57.104 40.909 0.00 0.00 0.00 3.60
1967 2563 4.820897 TGCATGGTAGAAGAACTGTAGTG 58.179 43.478 0.00 0.00 0.00 2.74
2162 2760 2.530177 CACAGTCCACACTAGTATGCG 58.470 52.381 0.00 0.00 0.00 4.73
2165 2763 3.181486 ACAGTCCACACTAGTATGCGATG 60.181 47.826 0.00 0.00 0.00 3.84
2433 3032 7.462571 AGTCTTTTAATATTTTCGGCTTGGT 57.537 32.000 0.00 0.00 0.00 3.67
3353 5395 9.109393 TGTGCTATCAGGAAATAAAGTATTGTC 57.891 33.333 0.00 0.00 0.00 3.18
3375 5417 3.188460 CGACACGGATTTCTTTTGTCCAT 59.812 43.478 0.00 0.00 34.33 3.41
3719 5761 1.003580 ACGTGGCAATCAAGAGATGGT 59.996 47.619 0.00 0.00 33.90 3.55
3857 5899 3.710722 CCTCCTTGCGCACCTCCT 61.711 66.667 11.12 0.00 0.00 3.69
3977 6019 0.480690 TCCTGGGCTTTGCTTGGTAA 59.519 50.000 0.00 0.00 0.00 2.85
3999 6041 2.816672 TGTCGCCAAATCTTGTGCATTA 59.183 40.909 0.00 0.00 0.00 1.90
4044 6086 7.936496 TGGTATAGACAAGAATGCATCAAAA 57.064 32.000 0.00 0.00 0.00 2.44
4045 6087 7.988737 TGGTATAGACAAGAATGCATCAAAAG 58.011 34.615 0.00 0.00 0.00 2.27
4046 6088 7.828717 TGGTATAGACAAGAATGCATCAAAAGA 59.171 33.333 0.00 0.00 0.00 2.52
4047 6089 8.677300 GGTATAGACAAGAATGCATCAAAAGAA 58.323 33.333 0.00 0.00 0.00 2.52
4149 6219 3.881688 GCCTATGCATCTGTGTTGAATCT 59.118 43.478 0.19 0.00 37.47 2.40
4161 6231 7.445121 TCTGTGTTGAATCTGAGTTCTGTTAT 58.555 34.615 0.00 0.00 0.00 1.89
4422 6492 9.793259 ATTTCAATCCGTATGTAGTCCATATTT 57.207 29.630 0.00 0.00 38.29 1.40
4483 6553 6.174049 AGTAGCTCTTAAGGTGGTCAAAATC 58.826 40.000 1.85 0.00 34.40 2.17
4753 6825 1.546029 GCTTAGGGCCAGTTCTTTTGG 59.454 52.381 6.18 0.00 38.78 3.28
4793 6865 2.044946 CCTCCCCAGCTTTTCCCG 60.045 66.667 0.00 0.00 0.00 5.14
4795 6867 1.675641 CTCCCCAGCTTTTCCCGTG 60.676 63.158 0.00 0.00 0.00 4.94
4861 6933 9.753674 TGGGATAACTGATTTAGAAGTCAAAAT 57.246 29.630 0.00 0.00 0.00 1.82
4873 6945 6.160576 AGAAGTCAAAATTTTTAGCAGGCA 57.839 33.333 0.00 0.00 0.00 4.75
4934 7006 1.115326 AGCCACCCAAAAGAACTGGC 61.115 55.000 0.00 0.00 46.65 4.85
5143 7215 2.006888 ACGCATTATGTTCTCGGGTTG 58.993 47.619 0.00 0.00 0.00 3.77
5151 7223 2.151202 TGTTCTCGGGTTGCTTTGATC 58.849 47.619 0.00 0.00 0.00 2.92
5180 7252 8.377799 TCTGGCAATCTTGAGATATTTATAGCA 58.622 33.333 0.00 0.00 33.73 3.49
5213 7285 2.837498 TCCCATGATATGCGTGTCTTG 58.163 47.619 10.50 10.50 0.00 3.02
5214 7286 2.170397 TCCCATGATATGCGTGTCTTGT 59.830 45.455 14.67 0.00 0.00 3.16
5215 7287 2.545526 CCCATGATATGCGTGTCTTGTC 59.454 50.000 14.67 0.00 0.00 3.18
5216 7288 3.461061 CCATGATATGCGTGTCTTGTCT 58.539 45.455 14.67 0.00 0.00 3.41
5217 7289 3.873361 CCATGATATGCGTGTCTTGTCTT 59.127 43.478 14.67 0.00 0.00 3.01
5757 7835 1.477105 GAAGCAAGTGGAAACGCAAC 58.523 50.000 0.00 0.00 45.56 4.17
5762 7840 2.874849 CAAGTGGAAACGCAACTGTTT 58.125 42.857 0.00 0.00 44.36 2.83
5779 7857 5.660460 ACTGTTTCAACTTTTTGGGTCATC 58.340 37.500 0.00 0.00 33.06 2.92
5786 7864 2.299867 ACTTTTTGGGTCATCCATGTGC 59.700 45.455 0.00 0.00 46.52 4.57
5790 7868 0.323633 TGGGTCATCCATGTGCTTGG 60.324 55.000 0.00 0.00 41.46 3.61
5857 7935 2.820330 AGTGTTTGGTTTTGCGGAATG 58.180 42.857 0.00 0.00 0.00 2.67
5884 7962 6.004574 ACCAAAGAAAATACTTCCTCTGTCC 58.995 40.000 0.00 0.00 0.00 4.02
5895 7973 5.799213 ACTTCCTCTGTCCAGAATTAGTTG 58.201 41.667 0.00 0.00 36.94 3.16
5896 7974 5.308237 ACTTCCTCTGTCCAGAATTAGTTGT 59.692 40.000 0.00 0.00 36.94 3.32
5897 7975 5.407407 TCCTCTGTCCAGAATTAGTTGTC 57.593 43.478 0.00 0.00 36.94 3.18
5898 7976 4.838423 TCCTCTGTCCAGAATTAGTTGTCA 59.162 41.667 0.00 0.00 36.94 3.58
5899 7977 4.932200 CCTCTGTCCAGAATTAGTTGTCAC 59.068 45.833 0.00 0.00 36.94 3.67
5900 7978 5.279708 CCTCTGTCCAGAATTAGTTGTCACT 60.280 44.000 0.00 0.00 36.94 3.41
5901 7979 5.784177 TCTGTCCAGAATTAGTTGTCACTC 58.216 41.667 0.00 0.00 33.91 3.51
5902 7980 5.540337 TCTGTCCAGAATTAGTTGTCACTCT 59.460 40.000 0.00 0.00 33.91 3.24
5903 7981 6.719829 TCTGTCCAGAATTAGTTGTCACTCTA 59.280 38.462 0.00 0.00 33.91 2.43
5904 7982 7.232737 TCTGTCCAGAATTAGTTGTCACTCTAA 59.767 37.037 0.00 0.00 33.91 2.10
5905 7983 7.907389 TGTCCAGAATTAGTTGTCACTCTAAT 58.093 34.615 4.54 4.54 38.14 1.73
5906 7984 7.819415 TGTCCAGAATTAGTTGTCACTCTAATG 59.181 37.037 9.07 2.07 37.08 1.90
5907 7985 7.819900 GTCCAGAATTAGTTGTCACTCTAATGT 59.180 37.037 9.07 3.00 37.08 2.71
5908 7986 9.031537 TCCAGAATTAGTTGTCACTCTAATGTA 57.968 33.333 9.07 0.00 37.08 2.29
5909 7987 9.823647 CCAGAATTAGTTGTCACTCTAATGTAT 57.176 33.333 9.07 0.00 37.08 2.29
5916 7994 7.777095 AGTTGTCACTCTAATGTATTCTCTCC 58.223 38.462 0.00 0.00 0.00 3.71
5917 7995 6.378710 TGTCACTCTAATGTATTCTCTCCG 57.621 41.667 0.00 0.00 0.00 4.63
5918 7996 5.886474 TGTCACTCTAATGTATTCTCTCCGT 59.114 40.000 0.00 0.00 0.00 4.69
5919 7997 7.052248 TGTCACTCTAATGTATTCTCTCCGTA 58.948 38.462 0.00 0.00 0.00 4.02
5920 7998 7.555195 TGTCACTCTAATGTATTCTCTCCGTAA 59.445 37.037 0.00 0.00 0.00 3.18
5921 7999 8.404000 GTCACTCTAATGTATTCTCTCCGTAAA 58.596 37.037 0.00 0.00 0.00 2.01
5922 8000 8.404000 TCACTCTAATGTATTCTCTCCGTAAAC 58.596 37.037 0.00 0.00 0.00 2.01
5923 8001 8.188799 CACTCTAATGTATTCTCTCCGTAAACA 58.811 37.037 0.00 0.00 0.00 2.83
5924 8002 8.746530 ACTCTAATGTATTCTCTCCGTAAACAA 58.253 33.333 0.00 0.00 0.00 2.83
5925 8003 9.582431 CTCTAATGTATTCTCTCCGTAAACAAA 57.418 33.333 0.00 0.00 0.00 2.83
5935 8013 9.582431 TTCTCTCCGTAAACAAATATAAGAGTG 57.418 33.333 0.00 0.00 31.80 3.51
5936 8014 8.746530 TCTCTCCGTAAACAAATATAAGAGTGT 58.253 33.333 0.00 0.00 31.80 3.55
5937 8015 9.367444 CTCTCCGTAAACAAATATAAGAGTGTT 57.633 33.333 0.00 0.00 35.77 3.32
5938 8016 9.715121 TCTCCGTAAACAAATATAAGAGTGTTT 57.285 29.630 5.98 5.98 44.23 2.83
5954 8032 8.967552 AAGAGTGTTTAGATCACTACTTTACG 57.032 34.615 0.00 0.00 44.68 3.18
5955 8033 7.536855 AGAGTGTTTAGATCACTACTTTACGG 58.463 38.462 0.00 0.00 44.68 4.02
5956 8034 7.392673 AGAGTGTTTAGATCACTACTTTACGGA 59.607 37.037 0.00 0.00 44.68 4.69
5957 8035 7.536855 AGTGTTTAGATCACTACTTTACGGAG 58.463 38.462 0.00 0.00 43.17 4.63
5958 8036 6.750963 GTGTTTAGATCACTACTTTACGGAGG 59.249 42.308 0.00 0.00 33.59 4.30
5959 8037 6.127535 TGTTTAGATCACTACTTTACGGAGGG 60.128 42.308 0.00 0.00 0.00 4.30
5960 8038 4.246712 AGATCACTACTTTACGGAGGGA 57.753 45.455 0.00 0.00 0.00 4.20
5961 8039 4.208746 AGATCACTACTTTACGGAGGGAG 58.791 47.826 0.00 0.00 0.00 4.30
5962 8040 3.446442 TCACTACTTTACGGAGGGAGT 57.554 47.619 0.00 0.00 0.00 3.85
5963 8041 4.574674 TCACTACTTTACGGAGGGAGTA 57.425 45.455 0.00 0.00 0.00 2.59
5964 8042 4.521146 TCACTACTTTACGGAGGGAGTAG 58.479 47.826 11.32 11.32 44.40 2.57
5965 8043 3.066481 CACTACTTTACGGAGGGAGTAGC 59.934 52.174 12.32 0.00 43.27 3.58
5966 8044 2.226962 ACTTTACGGAGGGAGTAGCA 57.773 50.000 0.00 0.00 0.00 3.49
5967 8045 1.823610 ACTTTACGGAGGGAGTAGCAC 59.176 52.381 0.00 0.00 0.00 4.40
5968 8046 1.136500 CTTTACGGAGGGAGTAGCACC 59.864 57.143 0.00 0.00 0.00 5.01
5969 8047 0.333993 TTACGGAGGGAGTAGCACCT 59.666 55.000 0.00 0.00 40.54 4.00
5970 8048 0.333993 TACGGAGGGAGTAGCACCTT 59.666 55.000 0.00 0.00 37.18 3.50
5971 8049 0.333993 ACGGAGGGAGTAGCACCTTA 59.666 55.000 0.00 0.00 37.18 2.69
5972 8050 1.063114 ACGGAGGGAGTAGCACCTTAT 60.063 52.381 0.00 0.00 37.18 1.73
5973 8051 1.341531 CGGAGGGAGTAGCACCTTATG 59.658 57.143 0.00 0.00 37.18 1.90
6060 8140 4.482030 AGACTATGAGATCATGCCACTCT 58.518 43.478 5.58 2.25 37.15 3.24
6061 8141 4.900652 AGACTATGAGATCATGCCACTCTT 59.099 41.667 5.58 9.56 37.15 2.85
6066 8146 4.747009 ATGAGATCATGCCACTCTTGGATG 60.747 45.833 0.00 0.00 45.91 3.51
6078 8158 4.030913 ACTCTTGGATGTCGGAGGAATAA 58.969 43.478 0.00 0.00 0.00 1.40
6150 8232 7.230849 TCTACAGGTATTTTCGAAGGTGTTA 57.769 36.000 0.00 0.00 0.00 2.41
6167 8251 4.013728 GTGTTAGTTGGGTTGCATGGATA 58.986 43.478 0.00 0.00 0.00 2.59
6178 8262 2.763039 TGCATGGATAGAGACTGGGAA 58.237 47.619 0.00 0.00 0.00 3.97
6210 8295 7.255766 GCTCTGTGTGATGGAGAGATATCTTTA 60.256 40.741 6.70 0.00 36.14 1.85
6241 8326 7.156000 TCTCGGTAATACAACATCACAAGAAA 58.844 34.615 0.00 0.00 0.00 2.52
6304 8390 8.292448 TCTTGTATTACGAAACGAGTAAAGAGT 58.708 33.333 0.00 0.00 37.57 3.24
6383 8471 2.684001 AACATATCGCCGGACAAAGA 57.316 45.000 5.05 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.171308 AAGGCGTAGTGTCTAGCGAA 58.829 50.000 0.00 0.00 0.00 4.70
1 2 1.131883 GAAAGGCGTAGTGTCTAGCGA 59.868 52.381 0.00 0.00 0.00 4.93
2 3 1.135489 TGAAAGGCGTAGTGTCTAGCG 60.135 52.381 0.00 0.00 0.00 4.26
17 18 5.070001 TGACCCCTTACTTCAATGTGAAAG 58.930 41.667 0.00 0.00 35.73 2.62
20 21 4.394729 GTTGACCCCTTACTTCAATGTGA 58.605 43.478 0.00 0.00 32.10 3.58
21 22 3.506067 GGTTGACCCCTTACTTCAATGTG 59.494 47.826 0.00 0.00 32.10 3.21
22 23 3.139397 TGGTTGACCCCTTACTTCAATGT 59.861 43.478 0.00 0.00 32.10 2.71
23 24 3.761897 TGGTTGACCCCTTACTTCAATG 58.238 45.455 0.00 0.00 32.10 2.82
99 100 5.048504 ACAATGTGTTTAGCAGAACTGATGG 60.049 40.000 5.97 0.00 0.00 3.51
103 104 5.679734 AGACAATGTGTTTAGCAGAACTG 57.320 39.130 0.00 0.00 0.00 3.16
110 114 8.795786 TTTTATGTGAAGACAATGTGTTTAGC 57.204 30.769 0.00 0.00 35.11 3.09
138 142 7.087639 TGAAAGTGCGTTTATCTTTAAATGGG 58.912 34.615 0.00 0.00 35.65 4.00
146 150 5.983118 CCCTTTTTGAAAGTGCGTTTATCTT 59.017 36.000 0.37 0.00 0.00 2.40
154 158 0.939106 CGCCCCTTTTTGAAAGTGCG 60.939 55.000 15.21 15.21 32.95 5.34
168 172 2.613506 CCACTTGTTTCGTCGCCCC 61.614 63.158 0.00 0.00 0.00 5.80
171 175 1.596220 GGTTTCCACTTGTTTCGTCGC 60.596 52.381 0.00 0.00 0.00 5.19
172 176 1.003223 GGGTTTCCACTTGTTTCGTCG 60.003 52.381 0.00 0.00 0.00 5.12
181 185 1.203013 GGGCAACTAGGGTTTCCACTT 60.203 52.381 0.00 0.00 39.84 3.16
184 188 1.771646 GGGGCAACTAGGGTTTCCA 59.228 57.895 0.00 0.00 39.84 3.53
201 205 0.036199 TTCGTTCGGGTAACATGGGG 60.036 55.000 0.00 0.00 38.03 4.96
209 213 2.126888 GCGTCGTTCGTTCGGGTA 60.127 61.111 0.00 0.00 42.13 3.69
224 228 3.522731 CTCTGAGAGGACCCCGCG 61.523 72.222 0.36 0.00 0.00 6.46
230 234 6.878389 AGAATCAAAAATCACTCTGAGAGGAC 59.122 38.462 14.83 0.00 33.35 3.85
231 235 7.013823 AGAATCAAAAATCACTCTGAGAGGA 57.986 36.000 14.83 8.62 33.35 3.71
232 236 6.035866 CGAGAATCAAAAATCACTCTGAGAGG 59.964 42.308 14.83 3.08 31.45 3.69
266 270 7.618502 TTCCGCTCTTGTTTATAGCATAAAA 57.381 32.000 0.00 0.00 35.98 1.52
288 292 5.360999 CCTCTCCCATACCCTTTCATTTTTC 59.639 44.000 0.00 0.00 0.00 2.29
289 293 5.272402 CCTCTCCCATACCCTTTCATTTTT 58.728 41.667 0.00 0.00 0.00 1.94
304 308 4.753662 CCGTCCGTCCCTCTCCCA 62.754 72.222 0.00 0.00 0.00 4.37
310 314 4.698625 AAGAGCCCGTCCGTCCCT 62.699 66.667 0.00 0.00 0.00 4.20
320 324 2.985847 AGCCGCAACAAAGAGCCC 60.986 61.111 0.00 0.00 0.00 5.19
328 332 1.617018 ATCTCCTAGCAGCCGCAACA 61.617 55.000 0.00 0.00 42.27 3.33
335 339 1.337118 AGCACCTATCTCCTAGCAGC 58.663 55.000 0.00 0.00 0.00 5.25
336 340 5.480073 AGAATAAGCACCTATCTCCTAGCAG 59.520 44.000 0.00 0.00 0.00 4.24
349 353 8.135529 AGTGTCTGTTTAAAAAGAATAAGCACC 58.864 33.333 9.73 0.00 0.00 5.01
364 368 2.288213 CGCCTGAGACAGTGTCTGTTTA 60.288 50.000 30.12 12.24 45.44 2.01
368 372 0.387878 GACGCCTGAGACAGTGTCTG 60.388 60.000 30.12 17.06 43.53 3.51
370 374 1.135632 GTAGACGCCTGAGACAGTGTC 60.136 57.143 15.78 15.78 36.14 3.67
371 375 0.882474 GTAGACGCCTGAGACAGTGT 59.118 55.000 0.00 0.00 0.00 3.55
394 398 8.885494 TGCAAAAAGAACAATAAGCATAACTT 57.115 26.923 0.00 0.00 42.76 2.66
410 414 9.444534 GTTTTTCTTTTGTCTTTTGCAAAAAGA 57.555 25.926 23.92 18.86 42.77 2.52
411 415 9.230932 TGTTTTTCTTTTGTCTTTTGCAAAAAG 57.769 25.926 23.92 17.05 42.77 2.27
425 430 5.371115 TCCGCTAGGATGTTTTTCTTTTG 57.629 39.130 0.00 0.00 42.75 2.44
440 445 2.499827 GCCACCCTACCTCCGCTAG 61.500 68.421 0.00 0.00 0.00 3.42
441 446 2.443390 GCCACCCTACCTCCGCTA 60.443 66.667 0.00 0.00 0.00 4.26
444 449 3.782443 GTGGCCACCCTACCTCCG 61.782 72.222 26.31 0.00 0.00 4.63
447 452 2.610859 CCAGTGGCCACCCTACCT 60.611 66.667 32.29 10.03 0.00 3.08
518 529 8.677300 TGCAGAACAATTCTAATCCAGTTTATC 58.323 33.333 0.00 0.00 38.11 1.75
520 531 7.994425 TGCAGAACAATTCTAATCCAGTTTA 57.006 32.000 0.00 0.00 38.11 2.01
525 536 6.599244 CCTACTTGCAGAACAATTCTAATCCA 59.401 38.462 0.00 0.00 38.11 3.41
526 537 6.038714 CCCTACTTGCAGAACAATTCTAATCC 59.961 42.308 0.00 0.00 38.11 3.01
532 543 3.440522 GTCCCCTACTTGCAGAACAATTC 59.559 47.826 0.00 0.00 37.72 2.17
541 552 3.517612 ACTTCTTAGTCCCCTACTTGCA 58.482 45.455 0.00 0.00 39.80 4.08
545 556 4.500452 ACCAAACTTCTTAGTCCCCTACT 58.500 43.478 0.00 0.00 42.62 2.57
547 558 5.405279 TGTACCAAACTTCTTAGTCCCCTA 58.595 41.667 0.00 0.00 31.99 3.53
550 561 5.224821 ACTGTACCAAACTTCTTAGTCCC 57.775 43.478 0.00 0.00 31.99 4.46
621 658 3.011119 CACAATATCCCGTCCGGAAAAA 58.989 45.455 5.23 0.00 46.47 1.94
622 659 2.236644 TCACAATATCCCGTCCGGAAAA 59.763 45.455 5.23 0.00 46.47 2.29
623 660 1.832366 TCACAATATCCCGTCCGGAAA 59.168 47.619 5.23 0.00 46.47 3.13
624 661 1.411246 CTCACAATATCCCGTCCGGAA 59.589 52.381 5.23 0.00 46.47 4.30
626 663 0.600255 GCTCACAATATCCCGTCCGG 60.600 60.000 0.00 0.00 0.00 5.14
627 664 0.389391 AGCTCACAATATCCCGTCCG 59.611 55.000 0.00 0.00 0.00 4.79
628 665 2.213499 CAAGCTCACAATATCCCGTCC 58.787 52.381 0.00 0.00 0.00 4.79
629 666 1.599542 GCAAGCTCACAATATCCCGTC 59.400 52.381 0.00 0.00 0.00 4.79
630 667 1.210478 AGCAAGCTCACAATATCCCGT 59.790 47.619 0.00 0.00 0.00 5.28
631 668 1.959042 AGCAAGCTCACAATATCCCG 58.041 50.000 0.00 0.00 0.00 5.14
668 705 2.443887 CTTGCAACCAAGGGTGAATG 57.556 50.000 8.65 0.00 43.75 2.67
723 760 3.769300 GGGGTGAGCCAATACTGAAAATT 59.231 43.478 1.97 0.00 36.17 1.82
724 761 3.011708 AGGGGTGAGCCAATACTGAAAAT 59.988 43.478 1.97 0.00 36.17 1.82
731 768 0.912486 AGTCAGGGGTGAGCCAATAC 59.088 55.000 1.97 0.00 36.17 1.89
753 790 7.386851 AGTAGTAGCTGAGCTGTTTTGATAAA 58.613 34.615 18.79 0.00 40.10 1.40
756 793 5.413309 AGTAGTAGCTGAGCTGTTTTGAT 57.587 39.130 18.79 0.00 40.10 2.57
758 795 5.931441 AAAGTAGTAGCTGAGCTGTTTTG 57.069 39.130 18.79 0.00 40.10 2.44
759 796 6.944234 AAAAAGTAGTAGCTGAGCTGTTTT 57.056 33.333 18.79 11.42 40.10 2.43
897 991 4.053295 CGTAGGACTTTCGGTCTCAAAAA 58.947 43.478 0.00 0.00 43.97 1.94
899 993 2.608752 GCGTAGGACTTTCGGTCTCAAA 60.609 50.000 0.00 0.00 43.97 2.69
902 996 0.522915 CGCGTAGGACTTTCGGTCTC 60.523 60.000 0.00 0.00 43.97 3.36
903 997 1.239968 ACGCGTAGGACTTTCGGTCT 61.240 55.000 11.67 0.00 43.97 3.85
904 998 0.387750 AACGCGTAGGACTTTCGGTC 60.388 55.000 14.46 0.00 43.79 4.79
905 999 0.665369 CAACGCGTAGGACTTTCGGT 60.665 55.000 14.46 0.00 0.00 4.69
906 1000 0.387622 TCAACGCGTAGGACTTTCGG 60.388 55.000 14.46 0.00 0.00 4.30
907 1001 0.982673 CTCAACGCGTAGGACTTTCG 59.017 55.000 14.46 0.00 0.00 3.46
908 1002 1.984297 GTCTCAACGCGTAGGACTTTC 59.016 52.381 14.46 0.00 0.00 2.62
910 1004 0.956633 TGTCTCAACGCGTAGGACTT 59.043 50.000 26.88 6.85 0.00 3.01
980 1125 0.601841 GTGTTTCCCTCGAAAGCCGA 60.602 55.000 0.00 0.00 46.35 5.54
981 1126 1.866925 GTGTTTCCCTCGAAAGCCG 59.133 57.895 0.00 0.00 38.66 5.52
982 1127 0.601841 TCGTGTTTCCCTCGAAAGCC 60.602 55.000 0.00 0.00 38.66 4.35
983 1128 0.790814 CTCGTGTTTCCCTCGAAAGC 59.209 55.000 0.00 0.00 38.66 3.51
984 1129 2.150397 ACTCGTGTTTCCCTCGAAAG 57.850 50.000 0.00 0.00 38.66 2.62
1092 1245 2.437651 AGAAGCAAAGAGGGATAGAGGC 59.562 50.000 0.00 0.00 0.00 4.70
1291 1445 3.399181 GATGCAGGTGGGGTCGGA 61.399 66.667 0.00 0.00 0.00 4.55
1360 1514 1.488812 CAGGTGGGGAAACGATATGGA 59.511 52.381 0.00 0.00 0.00 3.41
1373 1527 1.961793 TCAACGAAAAGACAGGTGGG 58.038 50.000 0.00 0.00 0.00 4.61
1376 1530 6.394809 ACAAAAATTCAACGAAAAGACAGGT 58.605 32.000 0.00 0.00 0.00 4.00
1419 1573 5.127356 ACTCCCGTACAAATCTAAGGAAGAG 59.873 44.000 0.00 0.00 37.74 2.85
1433 1587 2.369203 TCCAAACATCAACTCCCGTACA 59.631 45.455 0.00 0.00 0.00 2.90
1434 1596 2.740447 GTCCAAACATCAACTCCCGTAC 59.260 50.000 0.00 0.00 0.00 3.67
1441 1603 4.460382 CCATAAGCAGTCCAAACATCAACT 59.540 41.667 0.00 0.00 0.00 3.16
1553 1716 1.541588 GTTCTGATTGCAGGGTTGACC 59.458 52.381 0.00 0.00 42.53 4.02
1582 1745 5.852282 ACCAAACAATGAGCAGTTTTAGT 57.148 34.783 0.00 0.00 35.90 2.24
1683 2257 2.799176 GCACTAGCAGGAATTGGGG 58.201 57.895 0.00 0.00 41.58 4.96
1760 2334 7.519347 ACATCTTTAGTACCCCAATTCCTTA 57.481 36.000 0.00 0.00 0.00 2.69
1767 2341 9.049050 TGATAAGTAACATCTTTAGTACCCCAA 57.951 33.333 0.00 0.00 0.00 4.12
1768 2342 8.480501 GTGATAAGTAACATCTTTAGTACCCCA 58.519 37.037 0.00 0.00 0.00 4.96
1769 2343 7.650903 CGTGATAAGTAACATCTTTAGTACCCC 59.349 40.741 0.00 0.00 0.00 4.95
1770 2344 8.408601 TCGTGATAAGTAACATCTTTAGTACCC 58.591 37.037 0.00 0.00 0.00 3.69
1774 2359 7.773149 AGCTCGTGATAAGTAACATCTTTAGT 58.227 34.615 0.00 0.00 0.00 2.24
1833 2424 7.718753 AGTTGCATGGAACCAAAATTAAATTCA 59.281 29.630 24.50 0.00 0.00 2.57
1902 2493 6.592607 GGAGAATCAACATCTAAACGTACCAA 59.407 38.462 0.00 0.00 36.25 3.67
1967 2563 2.531206 AGAGAGTCGCGTAGAAAATGC 58.469 47.619 5.77 0.00 36.70 3.56
2162 2760 7.885399 ACTTAATTAAGATGGCCCATAGTCATC 59.115 37.037 27.92 0.00 37.97 2.92
2450 3052 6.569179 TGGGCAAAAGATTGTCTAACTAAC 57.431 37.500 0.00 0.00 41.02 2.34
2510 3112 7.771183 TCCATTAAAATGAAAGTATGCCTCAC 58.229 34.615 4.25 0.00 38.70 3.51
3185 4045 3.826157 TGCTCCAAAACTCATTTACCAGG 59.174 43.478 0.00 0.00 0.00 4.45
3353 5395 2.546368 TGGACAAAAGAAATCCGTGTCG 59.454 45.455 0.00 0.00 39.58 4.35
3405 5447 1.000896 ACATGTAGCACCCAAGGGC 60.001 57.895 4.70 0.00 39.32 5.19
3857 5899 1.213182 TGTGCCCTGTAGTGGACAAAA 59.787 47.619 0.00 0.00 37.70 2.44
3977 6019 1.246649 TGCACAAGATTTGGCGACAT 58.753 45.000 0.00 0.00 42.32 3.06
3999 6041 7.961326 ACCAAGATGGACTAAATAAAAGCAT 57.039 32.000 2.85 0.00 40.96 3.79
4049 6091 9.717942 GCATCAAGGATAACTGAAGATAAGTAT 57.282 33.333 0.00 0.00 0.00 2.12
4050 6092 8.928448 AGCATCAAGGATAACTGAAGATAAGTA 58.072 33.333 0.00 0.00 0.00 2.24
4051 6093 7.714377 CAGCATCAAGGATAACTGAAGATAAGT 59.286 37.037 0.00 0.00 31.30 2.24
4052 6094 7.714377 ACAGCATCAAGGATAACTGAAGATAAG 59.286 37.037 12.63 0.00 32.91 1.73
4053 6095 7.568349 ACAGCATCAAGGATAACTGAAGATAA 58.432 34.615 12.63 0.00 32.91 1.75
4054 6096 7.129457 ACAGCATCAAGGATAACTGAAGATA 57.871 36.000 12.63 0.00 32.91 1.98
4055 6097 5.999044 ACAGCATCAAGGATAACTGAAGAT 58.001 37.500 12.63 0.00 32.91 2.40
4056 6098 5.426689 ACAGCATCAAGGATAACTGAAGA 57.573 39.130 12.63 0.00 32.91 2.87
4057 6099 8.893219 TTATACAGCATCAAGGATAACTGAAG 57.107 34.615 12.63 0.00 32.91 3.02
4061 6103 9.896645 CCATATTATACAGCATCAAGGATAACT 57.103 33.333 0.00 0.00 0.00 2.24
4062 6104 8.616076 GCCATATTATACAGCATCAAGGATAAC 58.384 37.037 0.00 0.00 0.00 1.89
4063 6105 8.551440 AGCCATATTATACAGCATCAAGGATAA 58.449 33.333 0.00 0.00 0.00 1.75
4064 6106 8.094284 AGCCATATTATACAGCATCAAGGATA 57.906 34.615 0.00 0.00 0.00 2.59
4065 6107 6.966751 AGCCATATTATACAGCATCAAGGAT 58.033 36.000 0.00 0.00 0.00 3.24
4066 6108 6.378661 AGCCATATTATACAGCATCAAGGA 57.621 37.500 0.00 0.00 0.00 3.36
4067 6109 7.334090 ACTAGCCATATTATACAGCATCAAGG 58.666 38.462 0.00 0.00 0.00 3.61
4068 6110 8.783833 AACTAGCCATATTATACAGCATCAAG 57.216 34.615 0.00 0.00 0.00 3.02
4069 6111 9.002600 CAAACTAGCCATATTATACAGCATCAA 57.997 33.333 0.00 0.00 0.00 2.57
4070 6112 8.374743 TCAAACTAGCCATATTATACAGCATCA 58.625 33.333 0.00 0.00 0.00 3.07
4071 6113 8.777865 TCAAACTAGCCATATTATACAGCATC 57.222 34.615 0.00 0.00 0.00 3.91
4202 6272 8.669243 AGCTCTACTTAACAGCAAATACAATTC 58.331 33.333 0.00 0.00 35.46 2.17
4483 6553 6.223852 ACAGCCATGTTTATCCTATTAGACG 58.776 40.000 0.00 0.00 35.63 4.18
4772 6844 1.379176 GAAAAGCTGGGGAGGAGGC 60.379 63.158 0.00 0.00 0.00 4.70
4773 6845 1.304617 GGAAAAGCTGGGGAGGAGG 59.695 63.158 0.00 0.00 0.00 4.30
4793 6865 3.129638 ACTGAATAAGAGAGACGGCTCAC 59.870 47.826 22.94 15.41 43.81 3.51
4795 6867 3.490078 CCACTGAATAAGAGAGACGGCTC 60.490 52.174 11.39 11.39 41.62 4.70
4934 7006 1.097547 CCGCTGAATGGCACTAAGGG 61.098 60.000 0.00 0.00 0.00 3.95
5143 7215 3.015327 AGATTGCCAGACAGATCAAAGC 58.985 45.455 0.00 0.00 0.00 3.51
5151 7223 6.939132 AAATATCTCAAGATTGCCAGACAG 57.061 37.500 0.00 0.00 36.05 3.51
5180 7252 6.375455 GCATATCATGGGAAATATCCTTTCGT 59.625 38.462 0.00 0.00 45.77 3.85
5213 7285 6.253512 GGACAGACAAAAACATGTTCAAAGAC 59.746 38.462 12.39 3.49 32.57 3.01
5214 7286 6.152661 AGGACAGACAAAAACATGTTCAAAGA 59.847 34.615 12.39 0.00 32.57 2.52
5215 7287 6.332630 AGGACAGACAAAAACATGTTCAAAG 58.667 36.000 12.39 5.24 32.57 2.77
5216 7288 6.279513 AGGACAGACAAAAACATGTTCAAA 57.720 33.333 12.39 0.00 32.57 2.69
5217 7289 5.913137 AGGACAGACAAAAACATGTTCAA 57.087 34.783 12.39 0.00 32.57 2.69
5712 7789 5.972382 GGCGACAAAACACACACTTAAATTA 59.028 36.000 0.00 0.00 0.00 1.40
5713 7790 4.801516 GGCGACAAAACACACACTTAAATT 59.198 37.500 0.00 0.00 0.00 1.82
5757 7835 5.049828 GGATGACCCAAAAAGTTGAAACAG 58.950 41.667 0.00 0.00 36.83 3.16
5779 7857 0.945265 CCGCAAAACCAAGCACATGG 60.945 55.000 0.00 2.02 46.38 3.66
5848 7926 0.825425 TCTTTGGTGGCATTCCGCAA 60.825 50.000 0.00 0.00 44.64 4.85
5857 7935 4.767409 AGAGGAAGTATTTTCTTTGGTGGC 59.233 41.667 0.00 0.00 0.00 5.01
5895 7973 6.380095 ACGGAGAGAATACATTAGAGTGAC 57.620 41.667 0.00 0.00 0.00 3.67
5896 7974 8.404000 GTTTACGGAGAGAATACATTAGAGTGA 58.596 37.037 0.00 0.00 0.00 3.41
5897 7975 8.188799 TGTTTACGGAGAGAATACATTAGAGTG 58.811 37.037 0.00 0.00 0.00 3.51
5898 7976 8.289939 TGTTTACGGAGAGAATACATTAGAGT 57.710 34.615 0.00 0.00 0.00 3.24
5899 7977 9.582431 TTTGTTTACGGAGAGAATACATTAGAG 57.418 33.333 0.00 0.00 0.00 2.43
5909 7987 9.582431 CACTCTTATATTTGTTTACGGAGAGAA 57.418 33.333 0.00 0.00 33.96 2.87
5910 7988 8.746530 ACACTCTTATATTTGTTTACGGAGAGA 58.253 33.333 0.00 0.00 33.96 3.10
5911 7989 8.928270 ACACTCTTATATTTGTTTACGGAGAG 57.072 34.615 0.00 0.00 35.45 3.20
5912 7990 9.715121 AAACACTCTTATATTTGTTTACGGAGA 57.285 29.630 0.00 0.00 39.74 3.71
5929 8007 8.027771 CCGTAAAGTAGTGATCTAAACACTCTT 58.972 37.037 0.00 0.00 45.58 2.85
5930 8008 7.392673 TCCGTAAAGTAGTGATCTAAACACTCT 59.607 37.037 0.00 0.00 45.58 3.24
5931 8009 7.533426 TCCGTAAAGTAGTGATCTAAACACTC 58.467 38.462 0.00 0.00 45.58 3.51
5933 8011 6.750963 CCTCCGTAAAGTAGTGATCTAAACAC 59.249 42.308 0.00 0.00 38.38 3.32
5934 8012 6.127535 CCCTCCGTAAAGTAGTGATCTAAACA 60.128 42.308 0.00 0.00 0.00 2.83
5935 8013 6.096001 TCCCTCCGTAAAGTAGTGATCTAAAC 59.904 42.308 0.00 0.00 0.00 2.01
5936 8014 6.189859 TCCCTCCGTAAAGTAGTGATCTAAA 58.810 40.000 0.00 0.00 0.00 1.85
5937 8015 5.759059 TCCCTCCGTAAAGTAGTGATCTAA 58.241 41.667 0.00 0.00 0.00 2.10
5938 8016 5.104193 ACTCCCTCCGTAAAGTAGTGATCTA 60.104 44.000 0.00 0.00 0.00 1.98
5939 8017 4.208746 CTCCCTCCGTAAAGTAGTGATCT 58.791 47.826 0.00 0.00 0.00 2.75
5940 8018 3.952967 ACTCCCTCCGTAAAGTAGTGATC 59.047 47.826 0.00 0.00 0.00 2.92
5941 8019 3.978610 ACTCCCTCCGTAAAGTAGTGAT 58.021 45.455 0.00 0.00 0.00 3.06
5942 8020 3.446442 ACTCCCTCCGTAAAGTAGTGA 57.554 47.619 0.00 0.00 0.00 3.41
5943 8021 3.066481 GCTACTCCCTCCGTAAAGTAGTG 59.934 52.174 9.42 0.00 41.99 2.74
5944 8022 3.286353 GCTACTCCCTCCGTAAAGTAGT 58.714 50.000 9.42 0.00 41.99 2.73
5945 8023 3.066481 GTGCTACTCCCTCCGTAAAGTAG 59.934 52.174 4.44 4.44 42.57 2.57
5946 8024 3.019564 GTGCTACTCCCTCCGTAAAGTA 58.980 50.000 0.00 0.00 0.00 2.24
5947 8025 1.823610 GTGCTACTCCCTCCGTAAAGT 59.176 52.381 0.00 0.00 0.00 2.66
5948 8026 1.136500 GGTGCTACTCCCTCCGTAAAG 59.864 57.143 0.00 0.00 0.00 1.85
5949 8027 1.188863 GGTGCTACTCCCTCCGTAAA 58.811 55.000 0.00 0.00 0.00 2.01
5950 8028 0.333993 AGGTGCTACTCCCTCCGTAA 59.666 55.000 0.00 0.00 0.00 3.18
5951 8029 0.333993 AAGGTGCTACTCCCTCCGTA 59.666 55.000 0.00 0.00 0.00 4.02
5952 8030 0.333993 TAAGGTGCTACTCCCTCCGT 59.666 55.000 0.00 0.00 0.00 4.69
5953 8031 1.341531 CATAAGGTGCTACTCCCTCCG 59.658 57.143 0.00 0.00 0.00 4.63
5954 8032 2.630580 CTCATAAGGTGCTACTCCCTCC 59.369 54.545 0.00 0.00 0.00 4.30
5955 8033 2.630580 CCTCATAAGGTGCTACTCCCTC 59.369 54.545 0.00 0.00 37.94 4.30
5956 8034 2.247635 TCCTCATAAGGTGCTACTCCCT 59.752 50.000 0.00 0.00 43.82 4.20
5957 8035 2.679082 TCCTCATAAGGTGCTACTCCC 58.321 52.381 0.00 0.00 43.82 4.30
5958 8036 3.181464 GGTTCCTCATAAGGTGCTACTCC 60.181 52.174 0.00 0.00 43.82 3.85
5959 8037 3.491104 CGGTTCCTCATAAGGTGCTACTC 60.491 52.174 0.00 0.00 43.82 2.59
5960 8038 2.431057 CGGTTCCTCATAAGGTGCTACT 59.569 50.000 0.00 0.00 43.82 2.57
5961 8039 2.429610 TCGGTTCCTCATAAGGTGCTAC 59.570 50.000 0.00 0.00 43.82 3.58
5962 8040 2.742348 TCGGTTCCTCATAAGGTGCTA 58.258 47.619 0.00 0.00 43.82 3.49
5963 8041 1.568504 TCGGTTCCTCATAAGGTGCT 58.431 50.000 0.00 0.00 43.82 4.40
5964 8042 2.484889 GATCGGTTCCTCATAAGGTGC 58.515 52.381 0.00 0.00 43.82 5.01
5965 8043 2.100916 ACGATCGGTTCCTCATAAGGTG 59.899 50.000 20.98 0.00 43.82 4.00
5966 8044 2.385803 ACGATCGGTTCCTCATAAGGT 58.614 47.619 20.98 0.00 43.82 3.50
5967 8045 4.217767 TGATACGATCGGTTCCTCATAAGG 59.782 45.833 20.98 0.00 44.89 2.69
5968 8046 5.048643 AGTGATACGATCGGTTCCTCATAAG 60.049 44.000 20.98 0.00 0.00 1.73
5969 8047 4.825634 AGTGATACGATCGGTTCCTCATAA 59.174 41.667 20.98 0.00 0.00 1.90
5970 8048 4.395625 AGTGATACGATCGGTTCCTCATA 58.604 43.478 20.98 0.00 0.00 2.15
5971 8049 3.223435 AGTGATACGATCGGTTCCTCAT 58.777 45.455 20.98 0.00 0.00 2.90
5972 8050 2.651455 AGTGATACGATCGGTTCCTCA 58.349 47.619 20.98 11.05 0.00 3.86
5973 8051 3.712091 AAGTGATACGATCGGTTCCTC 57.288 47.619 20.98 8.63 0.00 3.71
5976 8054 8.571461 AATAAACTAAGTGATACGATCGGTTC 57.429 34.615 20.98 15.46 0.00 3.62
6042 8122 3.969312 TCCAAGAGTGGCATGATCTCATA 59.031 43.478 0.00 0.00 45.54 2.15
6060 8140 5.356751 CACAAATTATTCCTCCGACATCCAA 59.643 40.000 0.00 0.00 0.00 3.53
6061 8141 4.881273 CACAAATTATTCCTCCGACATCCA 59.119 41.667 0.00 0.00 0.00 3.41
6066 8146 3.689649 AGCACACAAATTATTCCTCCGAC 59.310 43.478 0.00 0.00 0.00 4.79
6078 8158 6.072508 ACGAAGTGATTTGATAGCACACAAAT 60.073 34.615 12.35 12.35 45.37 2.32
6150 8232 2.846206 TCTCTATCCATGCAACCCAACT 59.154 45.455 0.00 0.00 0.00 3.16
6167 8251 3.450457 CAGAGCTACAATTCCCAGTCTCT 59.550 47.826 0.00 0.00 0.00 3.10
6178 8262 3.771479 TCTCCATCACACAGAGCTACAAT 59.229 43.478 0.00 0.00 0.00 2.71
6241 8326 4.074259 TCATTAGTCACATGCTTGCAAGT 58.926 39.130 26.55 6.01 0.00 3.16
6304 8390 1.546923 TCAATCTCGTTACCGGCAAGA 59.453 47.619 0.00 0.00 33.95 3.02
6383 8471 6.479972 TCTGTCAATCCCGTATACAATTCT 57.520 37.500 3.32 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.