Multiple sequence alignment - TraesCS4D01G235600

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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 TraesCS4D01G235600 chr4D 100.000 4680 0 0 1 4680 396739666 396744345 0.000000e+00 8643.0
1 TraesCS4D01G235600 chr4D 91.516 554 45 2 4109 4661 19347372 19346820 0.000000e+00 761.0
2 TraesCS4D01G235600 chr4D 88.527 584 57 8 4099 4680 486615577 486615002 0.000000e+00 699.0
3 TraesCS4D01G235600 chr4D 93.023 43 1 2 819 861 7905027 7905067 1.410000e-05 62.1
4 TraesCS4D01G235600 chr4B 93.373 2369 125 11 1605 3945 488694963 488697327 0.000000e+00 3476.0
5 TraesCS4D01G235600 chr4B 89.583 816 48 17 819 1609 488694081 488694884 0.000000e+00 1002.0
6 TraesCS4D01G235600 chr4B 85.903 454 39 11 1 451 488692686 488693117 1.190000e-125 460.0
7 TraesCS4D01G235600 chr4B 86.772 378 34 14 456 827 488693153 488693520 1.570000e-109 407.0
8 TraesCS4D01G235600 chr4B 86.207 290 33 4 1148 1437 534068493 534068775 1.640000e-79 307.0
9 TraesCS4D01G235600 chr4B 83.051 295 38 7 1148 1442 179436131 179436413 1.670000e-64 257.0
10 TraesCS4D01G235600 chr4B 92.857 42 1 2 819 860 14343279 14343318 5.060000e-05 60.2
11 TraesCS4D01G235600 chr4A 90.967 2026 122 22 819 2817 78250177 78252168 0.000000e+00 2671.0
12 TraesCS4D01G235600 chr4A 92.165 1187 54 11 2862 4028 78252165 78253332 0.000000e+00 1640.0
13 TraesCS4D01G235600 chr4A 89.293 467 38 7 1 460 78249235 78249696 4.060000e-160 575.0
14 TraesCS4D01G235600 chr4A 91.089 202 17 1 455 656 78249721 78249921 5.970000e-69 272.0
15 TraesCS4D01G235600 chr5D 91.697 554 41 4 4109 4658 128586683 128586131 0.000000e+00 763.0
16 TraesCS4D01G235600 chr5D 95.122 41 1 1 819 859 465039043 465039004 3.910000e-06 63.9
17 TraesCS4D01G235600 chr7D 91.336 554 44 4 4108 4658 583081392 583081944 0.000000e+00 754.0
18 TraesCS4D01G235600 chr7D 94.703 472 24 1 4099 4569 583072589 583073060 0.000000e+00 732.0
19 TraesCS4D01G235600 chr7D 90.053 563 51 4 4101 4661 635996875 635996316 0.000000e+00 725.0
20 TraesCS4D01G235600 chr6D 90.731 561 48 4 4100 4658 374103597 374104155 0.000000e+00 745.0
21 TraesCS4D01G235600 chr6D 88.265 196 20 3 4487 4680 17444605 17444411 1.010000e-56 231.0
22 TraesCS4D01G235600 chr6D 83.673 98 16 0 348 445 404229251 404229348 4.990000e-15 93.5
23 TraesCS4D01G235600 chr6D 84.146 82 13 0 346 427 446127432 446127351 3.880000e-11 80.5
24 TraesCS4D01G235600 chr6D 94.737 38 1 1 819 856 456096903 456096867 1.820000e-04 58.4
25 TraesCS4D01G235600 chr6A 90.958 553 46 4 4109 4658 346586504 346587055 0.000000e+00 741.0
26 TraesCS4D01G235600 chr6A 84.902 457 45 11 2096 2544 203223509 203223949 1.550000e-119 440.0
27 TraesCS4D01G235600 chr6A 86.257 342 40 3 1148 1489 203223172 203223506 9.570000e-97 364.0
28 TraesCS4D01G235600 chr6A 82.653 98 16 1 348 445 550745055 550745151 8.340000e-13 86.1
29 TraesCS4D01G235600 chr6A 94.737 38 1 1 819 856 602912751 602912715 1.820000e-04 58.4
30 TraesCS4D01G235600 chr3D 87.370 578 64 8 4109 4680 91683696 91684270 0.000000e+00 654.0
31 TraesCS4D01G235600 chr3D 86.047 215 23 7 4469 4680 607412734 607412944 1.690000e-54 224.0
32 TraesCS4D01G235600 chr5A 84.934 458 45 12 2099 2548 601607737 601608178 4.300000e-120 442.0
33 TraesCS4D01G235600 chr5A 86.550 342 39 2 1148 1489 705383385 705383051 2.060000e-98 370.0
34 TraesCS4D01G235600 chr5A 85.340 191 28 0 1148 1338 228897736 228897926 1.030000e-46 198.0
35 TraesCS4D01G235600 chr5A 93.478 46 1 2 819 864 585434603 585434560 3.020000e-07 67.6
36 TraesCS4D01G235600 chr5B 81.538 455 54 15 2096 2546 106273847 106274275 9.640000e-92 348.0
37 TraesCS4D01G235600 chr5B 91.667 48 2 2 819 865 572394802 572394756 1.090000e-06 65.8
38 TraesCS4D01G235600 chr7B 81.333 450 53 17 2096 2541 433802935 433803357 2.090000e-88 337.0
39 TraesCS4D01G235600 chr7B 79.851 134 25 2 461 593 722308609 722308477 3.850000e-16 97.1
40 TraesCS4D01G235600 chr7B 80.000 100 17 2 321 417 731440579 731440480 2.340000e-08 71.3
41 TraesCS4D01G235600 chr7B 100.000 28 0 0 348 375 213462306 213462333 8.000000e-03 52.8
42 TraesCS4D01G235600 chr2B 89.354 263 21 4 2286 2544 406109049 406108790 1.620000e-84 324.0
43 TraesCS4D01G235600 chr3A 82.692 364 43 12 2096 2453 493647200 493646851 5.880000e-79 305.0
44 TraesCS4D01G235600 chr3A 80.000 375 44 15 2096 2466 282157185 282157532 1.010000e-61 248.0
45 TraesCS4D01G235600 chr3B 84.407 295 39 2 1148 1442 563173199 563173486 2.760000e-72 283.0
46 TraesCS4D01G235600 chr3B 90.625 192 18 0 4486 4677 531796111 531796302 6.010000e-64 255.0
47 TraesCS4D01G235600 chr3B 89.744 195 19 1 4486 4680 141803368 141803561 1.010000e-61 248.0
48 TraesCS4D01G235600 chr3B 88.205 195 23 0 4486 4680 817797508 817797314 2.820000e-57 233.0
49 TraesCS4D01G235600 chr3B 86.000 100 12 2 346 445 254939142 254939045 6.400000e-19 106.0
50 TraesCS4D01G235600 chr3B 85.000 100 15 0 346 445 694031591 694031492 8.280000e-18 102.0
51 TraesCS4D01G235600 chr6B 88.601 193 20 2 4486 4677 124636621 124636812 2.820000e-57 233.0
52 TraesCS4D01G235600 chr6B 81.633 98 17 1 348 445 606305094 606305190 3.880000e-11 80.5
53 TraesCS4D01G235600 chr2D 88.265 196 22 1 4486 4680 89256654 89256849 2.820000e-57 233.0
54 TraesCS4D01G235600 chr2A 85.340 191 28 0 1148 1338 168430906 168431096 1.030000e-46 198.0
55 TraesCS4D01G235600 chr1A 86.364 66 7 2 321 385 306642247 306642183 2.340000e-08 71.3
56 TraesCS4D01G235600 chr1A 95.122 41 1 1 819 859 426886267 426886228 3.910000e-06 63.9
57 TraesCS4D01G235600 chr1A 94.737 38 1 1 819 856 569370712 569370748 1.820000e-04 58.4
58 TraesCS4D01G235600 chr1A 90.476 42 2 2 819 860 576619399 576619360 2.000000e-03 54.7
59 TraesCS4D01G235600 chr1D 85.075 67 7 2 321 385 245980528 245980463 1.090000e-06 65.8
60 TraesCS4D01G235600 chr1D 91.667 48 2 2 819 866 329729170 329729125 1.090000e-06 65.8
61 TraesCS4D01G235600 chr1D 90.476 42 2 2 819 860 480352063 480352024 2.000000e-03 54.7
62 TraesCS4D01G235600 chr1B 95.122 41 1 1 819 859 444686379 444686340 3.910000e-06 63.9


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 TraesCS4D01G235600 chr4D 396739666 396744345 4679 False 8643.00 8643 100.00000 1 4680 1 chr4D.!!$F2 4679
1 TraesCS4D01G235600 chr4D 19346820 19347372 552 True 761.00 761 91.51600 4109 4661 1 chr4D.!!$R1 552
2 TraesCS4D01G235600 chr4D 486615002 486615577 575 True 699.00 699 88.52700 4099 4680 1 chr4D.!!$R2 581
3 TraesCS4D01G235600 chr4B 488692686 488697327 4641 False 1336.25 3476 88.90775 1 3945 4 chr4B.!!$F4 3944
4 TraesCS4D01G235600 chr4A 78249235 78253332 4097 False 1289.50 2671 90.87850 1 4028 4 chr4A.!!$F1 4027
5 TraesCS4D01G235600 chr5D 128586131 128586683 552 True 763.00 763 91.69700 4109 4658 1 chr5D.!!$R1 549
6 TraesCS4D01G235600 chr7D 583081392 583081944 552 False 754.00 754 91.33600 4108 4658 1 chr7D.!!$F2 550
7 TraesCS4D01G235600 chr7D 635996316 635996875 559 True 725.00 725 90.05300 4101 4661 1 chr7D.!!$R1 560
8 TraesCS4D01G235600 chr6D 374103597 374104155 558 False 745.00 745 90.73100 4100 4658 1 chr6D.!!$F1 558
9 TraesCS4D01G235600 chr6A 346586504 346587055 551 False 741.00 741 90.95800 4109 4658 1 chr6A.!!$F1 549
10 TraesCS4D01G235600 chr6A 203223172 203223949 777 False 402.00 440 85.57950 1148 2544 2 chr6A.!!$F3 1396
11 TraesCS4D01G235600 chr3D 91683696 91684270 574 False 654.00 654 87.37000 4109 4680 1 chr3D.!!$F1 571

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
732 779 0.610174 TGCTGCCACACTAGGAGAAG 59.390 55.0 0.00 0.00 0.00 2.85 F
1060 1682 0.179134 CCGCCTCCTCAAGTTCTACG 60.179 60.0 0.00 0.00 0.00 3.51 F
2559 3307 0.390492 TATCCTCGTCTGCAGCATGG 59.610 55.0 9.47 8.58 35.86 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1648 2372 0.108138 ACATAGCTGTTCGCCACTCC 60.108 55.0 0.00 0.0 40.39 3.85 R
2844 3593 0.178970 TACTCCCTCTGCCCCGTATC 60.179 60.0 0.00 0.0 0.00 2.24 R
4076 4847 0.171679 CACATGTGCAATGGACGCAT 59.828 50.0 13.94 0.0 42.32 4.73 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
43 44 8.603304 ACAAGTAGATAAAAGACCCTACAACAT 58.397 33.333 0.00 0.00 35.26 2.71
91 93 5.617528 TGTTACCACACTAGGAGAAAACA 57.382 39.130 0.00 0.00 0.00 2.83
139 141 1.626654 CGCCACCGTCATCAAGTCAC 61.627 60.000 0.00 0.00 0.00 3.67
155 161 1.135746 GTCACGGAGTTCTAGTCACCG 60.136 57.143 18.15 18.15 41.61 4.94
189 195 7.861372 TCATCGAACGATCTTAGAAAATAGACC 59.139 37.037 6.74 0.00 31.62 3.85
268 274 3.896648 TCTTGCGTTTGTCAATTCTCC 57.103 42.857 0.00 0.00 0.00 3.71
297 303 5.423015 TCATCAAGTCAATGGAGTTCTAGC 58.577 41.667 0.00 0.00 34.43 3.42
305 311 5.645497 GTCAATGGAGTTCTAGCAAGTCATT 59.355 40.000 10.16 0.00 0.00 2.57
331 337 2.884012 TGCCTCATCGAACAACAACAAT 59.116 40.909 0.00 0.00 0.00 2.71
332 338 3.236816 GCCTCATCGAACAACAACAATG 58.763 45.455 0.00 0.00 0.00 2.82
336 342 5.277974 CCTCATCGAACAACAACAATGAAGT 60.278 40.000 0.00 0.00 0.00 3.01
337 343 6.073276 CCTCATCGAACAACAACAATGAAGTA 60.073 38.462 0.00 0.00 0.00 2.24
364 370 3.857157 TCAAACAAGTTGAGGTAGGCT 57.143 42.857 10.54 0.00 41.47 4.58
411 418 6.359804 TGAAGCTAACTAATGATTCTGGCAT 58.640 36.000 0.00 0.00 0.00 4.40
431 438 5.414454 GGCATGTGGATAACTAACTTTCACA 59.586 40.000 0.00 0.00 37.91 3.58
451 458 5.013704 TCACACACCCTTGTCCATAATTAGT 59.986 40.000 0.00 0.00 31.66 2.24
453 460 6.208599 CACACACCCTTGTCCATAATTAGTTT 59.791 38.462 0.00 0.00 31.66 2.66
480 518 3.070018 GGACTCCTCACATGTCAAGTTG 58.930 50.000 0.00 0.00 32.84 3.16
490 529 3.008049 ACATGTCAAGTTGAGTCTACCCC 59.992 47.826 5.62 0.00 0.00 4.95
494 533 1.893801 CAAGTTGAGTCTACCCCGACT 59.106 52.381 0.00 0.00 46.39 4.18
496 535 2.606378 AGTTGAGTCTACCCCGACTTT 58.394 47.619 0.81 0.00 43.91 2.66
498 537 4.154942 AGTTGAGTCTACCCCGACTTTTA 58.845 43.478 0.81 0.00 43.91 1.52
530 569 3.126858 TCAACACGCTTTAATCATCTGCC 59.873 43.478 0.00 0.00 0.00 4.85
540 579 6.516194 GCTTTAATCATCTGCCATGCACTAAT 60.516 38.462 0.00 0.00 33.79 1.73
559 598 1.961793 TGCTTTTAGTGGTCTGCGTT 58.038 45.000 0.00 0.00 0.00 4.84
560 599 1.601903 TGCTTTTAGTGGTCTGCGTTG 59.398 47.619 0.00 0.00 0.00 4.10
561 600 1.602377 GCTTTTAGTGGTCTGCGTTGT 59.398 47.619 0.00 0.00 0.00 3.32
562 601 2.803956 GCTTTTAGTGGTCTGCGTTGTA 59.196 45.455 0.00 0.00 0.00 2.41
708 755 7.643764 CCTACAAACAGTACAACAAAGAACATG 59.356 37.037 0.00 0.00 0.00 3.21
732 779 0.610174 TGCTGCCACACTAGGAGAAG 59.390 55.000 0.00 0.00 0.00 2.85
736 783 3.594134 CTGCCACACTAGGAGAAGAAAG 58.406 50.000 0.00 0.00 0.00 2.62
738 785 4.157246 TGCCACACTAGGAGAAGAAAGTA 58.843 43.478 0.00 0.00 0.00 2.24
739 786 4.777896 TGCCACACTAGGAGAAGAAAGTAT 59.222 41.667 0.00 0.00 0.00 2.12
741 788 5.582665 GCCACACTAGGAGAAGAAAGTATTG 59.417 44.000 0.00 0.00 0.00 1.90
743 790 6.295916 CCACACTAGGAGAAGAAAGTATTGGT 60.296 42.308 0.00 0.00 0.00 3.67
745 792 7.118390 CACACTAGGAGAAGAAAGTATTGGTTG 59.882 40.741 0.00 0.00 0.00 3.77
746 793 7.016268 ACACTAGGAGAAGAAAGTATTGGTTGA 59.984 37.037 0.00 0.00 0.00 3.18
747 794 7.332182 CACTAGGAGAAGAAAGTATTGGTTGAC 59.668 40.741 0.00 0.00 0.00 3.18
748 795 5.561679 AGGAGAAGAAAGTATTGGTTGACC 58.438 41.667 0.00 0.00 0.00 4.02
749 796 5.073144 AGGAGAAGAAAGTATTGGTTGACCA 59.927 40.000 0.00 0.00 45.94 4.02
759 806 1.518367 TGGTTGACCAGGAGGAAAGT 58.482 50.000 0.00 0.00 42.01 2.66
771 818 5.334879 CCAGGAGGAAAGTTTTGTATGAACG 60.335 44.000 0.00 0.00 36.89 3.95
773 820 6.017440 CAGGAGGAAAGTTTTGTATGAACGAA 60.017 38.462 0.00 0.00 32.38 3.85
776 823 7.272037 AGGAAAGTTTTGTATGAACGAACAT 57.728 32.000 0.00 0.00 32.38 2.71
779 826 7.114388 GGAAAGTTTTGTATGAACGAACATTCC 59.886 37.037 11.93 11.93 40.63 3.01
782 829 8.561738 AGTTTTGTATGAACGAACATTCCTAT 57.438 30.769 0.00 0.00 32.38 2.57
792 839 8.358148 TGAACGAACATTCCTATAGAATAGACC 58.642 37.037 0.00 0.00 43.63 3.85
832 1322 3.364889 AAAAAGTAGGCAAAAGGACGC 57.635 42.857 0.00 0.00 0.00 5.19
833 1323 2.271944 AAAGTAGGCAAAAGGACGCT 57.728 45.000 0.00 0.00 0.00 5.07
835 1325 0.977395 AGTAGGCAAAAGGACGCTCT 59.023 50.000 0.00 0.00 0.00 4.09
875 1493 5.178438 GGCGCCTTTGTTGAAATAAAATCAA 59.822 36.000 22.15 0.00 34.56 2.57
894 1513 9.801873 AAAATCAATCGTACCTTCATAAATTGG 57.198 29.630 0.00 0.00 0.00 3.16
916 1535 5.163099 TGGAATTCATCTATCGTCCCCAATT 60.163 40.000 7.93 0.00 0.00 2.32
922 1541 3.376636 TCTATCGTCCCCAATTACACCA 58.623 45.455 0.00 0.00 0.00 4.17
930 1549 2.620627 CCCCAATTACACCAGGTCTTCC 60.621 54.545 0.00 0.00 0.00 3.46
939 1558 5.853572 ACACCAGGTCTTCCCTTTAATAA 57.146 39.130 0.00 0.00 42.73 1.40
940 1559 6.402981 ACACCAGGTCTTCCCTTTAATAAT 57.597 37.500 0.00 0.00 42.73 1.28
941 1560 7.519347 ACACCAGGTCTTCCCTTTAATAATA 57.481 36.000 0.00 0.00 42.73 0.98
1020 1642 1.227674 GATCCAGGCGGTGATGGTC 60.228 63.158 0.00 0.00 37.84 4.02
1060 1682 0.179134 CCGCCTCCTCAAGTTCTACG 60.179 60.000 0.00 0.00 0.00 3.51
1103 1725 2.064581 AGTCGCCGCCCCTTCTTAT 61.065 57.895 0.00 0.00 0.00 1.73
1112 1734 2.945668 CGCCCCTTCTTATTTTCTCCTG 59.054 50.000 0.00 0.00 0.00 3.86
1128 1755 1.301677 CCTGACGCCCTTTCTTCAGC 61.302 60.000 0.00 0.00 35.18 4.26
1158 1785 4.269523 ACCAGCTGCTCGGCCAAA 62.270 61.111 8.66 0.00 0.00 3.28
1175 1802 2.550175 CAAATTCCCCACCCAAATCCT 58.450 47.619 0.00 0.00 0.00 3.24
1254 1884 5.235305 TCTGCACTTTGTTTTTCTCTGTC 57.765 39.130 0.00 0.00 0.00 3.51
1377 2007 4.923281 CCTTTTCTTTTCGCCCTTTGTATG 59.077 41.667 0.00 0.00 0.00 2.39
1378 2008 5.508994 CCTTTTCTTTTCGCCCTTTGTATGT 60.509 40.000 0.00 0.00 0.00 2.29
1379 2009 6.294286 CCTTTTCTTTTCGCCCTTTGTATGTA 60.294 38.462 0.00 0.00 0.00 2.29
1380 2010 6.827586 TTTCTTTTCGCCCTTTGTATGTAT 57.172 33.333 0.00 0.00 0.00 2.29
1644 2368 5.467399 TGCAAATGCTCAGAAATCTTTTTGG 59.533 36.000 6.97 0.00 42.66 3.28
1648 2372 3.828451 TGCTCAGAAATCTTTTTGGAGGG 59.172 43.478 0.00 0.00 0.00 4.30
1682 2406 2.478894 GCTATGTAACGTGTGTTGCTGT 59.521 45.455 0.00 0.00 40.83 4.40
1692 2416 4.142578 ACGTGTGTTGCTGTAAACATTTGA 60.143 37.500 0.00 0.00 41.81 2.69
1698 2422 7.860373 TGTGTTGCTGTAAACATTTGACTAATC 59.140 33.333 2.25 0.00 41.81 1.75
1719 2443 7.867445 AATCGTAAAACTAAATTTGCACCTG 57.133 32.000 0.00 0.00 0.00 4.00
1753 2485 6.434596 TGTGACGGAAACAACTGAATTATTG 58.565 36.000 0.00 0.00 0.00 1.90
1755 2487 5.765677 TGACGGAAACAACTGAATTATTGGA 59.234 36.000 0.00 0.00 0.00 3.53
1759 2491 7.446013 ACGGAAACAACTGAATTATTGGAGTAA 59.554 33.333 0.00 0.00 0.00 2.24
1801 2533 3.825908 ATGAGCTGTAAGGGGGAAAAA 57.174 42.857 0.00 0.00 0.00 1.94
1874 2606 3.621268 GCATTTGGCGACACTATACTTCA 59.379 43.478 0.00 0.00 42.67 3.02
1999 2731 0.968405 AGCCGTGTGCAATGGAAAAT 59.032 45.000 10.27 0.00 44.83 1.82
2094 2826 2.996631 TCCGTACAGAGTCTACTTCCC 58.003 52.381 0.00 0.00 0.00 3.97
2122 2854 5.874810 GTGGCTGTTTATCTCATTACTGTGA 59.125 40.000 0.00 0.00 0.00 3.58
2136 2868 8.853077 TCATTACTGTGATTCTTTCAGTTCAT 57.147 30.769 12.20 5.88 41.66 2.57
2191 2925 3.442273 TCCGTATTTCCAGTGCAAATTCC 59.558 43.478 0.00 0.00 0.00 3.01
2196 2930 3.848272 TTCCAGTGCAAATTCCGATTC 57.152 42.857 0.00 0.00 0.00 2.52
2279 3024 6.364165 CACTAAGACAAACATGCATTCCTTTG 59.636 38.462 15.20 15.20 0.00 2.77
2293 3038 6.371548 TGCATTCCTTTGTACATCTAACACTC 59.628 38.462 0.00 0.00 0.00 3.51
2343 3088 8.072567 CCTCTGTTTGTCACTTTAAGATTCTTG 58.927 37.037 9.22 0.00 0.00 3.02
2352 3100 8.660373 GTCACTTTAAGATTCTTGTATGACCTG 58.340 37.037 9.22 0.00 0.00 4.00
2500 3248 9.967451 TTTGGTATTTTATTCTGGATAGTCACA 57.033 29.630 0.00 0.00 0.00 3.58
2559 3307 0.390492 TATCCTCGTCTGCAGCATGG 59.610 55.000 9.47 8.58 35.86 3.66
2685 3433 6.882610 TCTGTTTCATTTTGCACTACTGAT 57.117 33.333 0.00 0.00 0.00 2.90
2732 3480 9.498307 TCGAAGAAACATTTTCTGACTTAAAAC 57.502 29.630 1.98 0.00 0.00 2.43
2771 3519 3.879998 TGCTGGTGTTTCACTGAAGTTA 58.120 40.909 0.06 0.00 34.40 2.24
2833 3582 5.119279 GCATGTAGCTAGATACATCCGTTTG 59.881 44.000 26.69 18.40 43.01 2.93
2834 3583 6.447162 CATGTAGCTAGATACATCCGTTTGA 58.553 40.000 26.69 1.43 43.01 2.69
2835 3584 6.073327 TGTAGCTAGATACATCCGTTTGAG 57.927 41.667 16.66 0.00 30.76 3.02
2836 3585 3.983741 AGCTAGATACATCCGTTTGAGC 58.016 45.455 0.00 0.00 0.00 4.26
2837 3586 3.384789 AGCTAGATACATCCGTTTGAGCA 59.615 43.478 0.00 0.00 0.00 4.26
2838 3587 4.039730 AGCTAGATACATCCGTTTGAGCAT 59.960 41.667 0.00 0.00 0.00 3.79
2839 3588 4.752101 GCTAGATACATCCGTTTGAGCATT 59.248 41.667 0.00 0.00 0.00 3.56
2844 3593 7.642669 AGATACATCCGTTTGAGCATTAATTG 58.357 34.615 0.00 0.00 0.00 2.32
2849 3598 6.043327 TCCGTTTGAGCATTAATTGATACG 57.957 37.500 0.00 0.00 0.00 3.06
2854 3603 3.146066 GAGCATTAATTGATACGGGGCA 58.854 45.455 0.00 0.00 0.00 5.36
2980 3729 3.064900 ACCAAATCTTCTGGAGCTGTC 57.935 47.619 0.00 0.00 37.40 3.51
3022 3771 4.528596 AGTGAGCATTAGTGTCCTGTAGTT 59.471 41.667 0.00 0.00 0.00 2.24
3023 3772 5.012148 AGTGAGCATTAGTGTCCTGTAGTTT 59.988 40.000 0.00 0.00 0.00 2.66
3234 3984 2.005370 CCTATGATGCCATTGCCCTT 57.995 50.000 0.00 0.00 36.33 3.95
3251 4001 1.438469 CTTCATGGCTCCATCCCCTA 58.562 55.000 0.00 0.00 33.90 3.53
3263 4013 5.455872 CTCCATCCCCTACTTTCTGTAGTA 58.544 45.833 0.00 0.00 45.36 1.82
3411 4179 2.996621 CGACCATTCTCTCTTGGTTCAC 59.003 50.000 0.00 0.00 46.14 3.18
3539 4307 2.082231 GCGAGGTTTTTACTCCCTTCC 58.918 52.381 0.00 0.00 0.00 3.46
3686 4454 4.443063 AGCGTTTCAGCCGTTAAAATTTTC 59.557 37.500 6.72 0.00 38.01 2.29
3698 4466 6.455780 CCGTTAAAATTTTCCGCTTGTGTTTT 60.456 34.615 6.72 0.00 0.00 2.43
3755 4523 9.770503 GAAATCAAATTGATGATCATATCTCCG 57.229 33.333 8.54 0.00 39.08 4.63
3827 4595 0.723414 CTATTGGCTGACGTGCACAG 59.277 55.000 18.64 12.16 38.27 3.66
4000 4771 7.363268 GCCAGAGATTTATTTCTGACCACATTT 60.363 37.037 10.82 0.00 42.67 2.32
4028 4799 6.957631 TGGTGATATATGAGGTGTTTGAAGT 58.042 36.000 0.00 0.00 0.00 3.01
4029 4800 7.402054 TGGTGATATATGAGGTGTTTGAAGTT 58.598 34.615 0.00 0.00 0.00 2.66
4030 4801 7.552687 TGGTGATATATGAGGTGTTTGAAGTTC 59.447 37.037 0.00 0.00 0.00 3.01
4031 4802 7.012421 GGTGATATATGAGGTGTTTGAAGTTCC 59.988 40.741 0.00 0.00 0.00 3.62
4032 4803 7.552687 GTGATATATGAGGTGTTTGAAGTTCCA 59.447 37.037 0.00 0.00 0.00 3.53
4033 4804 8.106462 TGATATATGAGGTGTTTGAAGTTCCAA 58.894 33.333 0.00 0.00 0.00 3.53
4034 4805 4.918810 ATGAGGTGTTTGAAGTTCCAAC 57.081 40.909 11.87 11.87 0.00 3.77
4035 4806 3.020984 TGAGGTGTTTGAAGTTCCAACC 58.979 45.455 15.18 10.21 0.00 3.77
4036 4807 2.361119 GAGGTGTTTGAAGTTCCAACCC 59.639 50.000 15.18 14.75 0.00 4.11
4037 4808 1.066454 GGTGTTTGAAGTTCCAACCCG 59.934 52.381 15.18 0.00 0.00 5.28
4038 4809 1.066454 GTGTTTGAAGTTCCAACCCGG 59.934 52.381 15.18 0.00 0.00 5.73
4039 4810 1.064611 TGTTTGAAGTTCCAACCCGGA 60.065 47.619 15.18 0.00 44.40 5.14
4040 4811 2.235891 GTTTGAAGTTCCAACCCGGAT 58.764 47.619 0.73 0.00 45.80 4.18
4041 4812 2.194201 TTGAAGTTCCAACCCGGATC 57.806 50.000 0.73 0.00 45.80 3.36
4042 4813 1.358152 TGAAGTTCCAACCCGGATCT 58.642 50.000 0.73 0.00 45.80 2.75
4043 4814 2.542550 TGAAGTTCCAACCCGGATCTA 58.457 47.619 0.73 0.00 45.80 1.98
4044 4815 3.112263 TGAAGTTCCAACCCGGATCTAT 58.888 45.455 0.73 0.00 45.80 1.98
4045 4816 3.118408 TGAAGTTCCAACCCGGATCTATG 60.118 47.826 0.73 0.00 45.80 2.23
4046 4817 2.478292 AGTTCCAACCCGGATCTATGT 58.522 47.619 0.73 0.00 45.80 2.29
4047 4818 2.170607 AGTTCCAACCCGGATCTATGTG 59.829 50.000 0.73 0.00 45.80 3.21
4048 4819 1.128200 TCCAACCCGGATCTATGTGG 58.872 55.000 0.73 0.00 39.64 4.17
4049 4820 1.128200 CCAACCCGGATCTATGTGGA 58.872 55.000 0.73 0.00 36.56 4.02
4050 4821 1.699634 CCAACCCGGATCTATGTGGAT 59.300 52.381 0.73 0.00 36.56 3.41
4051 4822 2.550855 CCAACCCGGATCTATGTGGATG 60.551 54.545 0.73 0.00 36.56 3.51
4052 4823 1.352083 ACCCGGATCTATGTGGATGG 58.648 55.000 0.73 0.00 0.00 3.51
4053 4824 1.352083 CCCGGATCTATGTGGATGGT 58.648 55.000 0.73 0.00 0.00 3.55
4054 4825 2.158219 ACCCGGATCTATGTGGATGGTA 60.158 50.000 0.73 0.00 0.00 3.25
4055 4826 2.233922 CCCGGATCTATGTGGATGGTAC 59.766 54.545 0.73 0.00 0.00 3.34
4070 4841 3.313012 TGGTACAATCAACTCAGTCCG 57.687 47.619 0.00 0.00 31.92 4.79
4071 4842 2.894765 TGGTACAATCAACTCAGTCCGA 59.105 45.455 0.00 0.00 31.92 4.55
4072 4843 3.322541 TGGTACAATCAACTCAGTCCGAA 59.677 43.478 0.00 0.00 31.92 4.30
4073 4844 3.927142 GGTACAATCAACTCAGTCCGAAG 59.073 47.826 0.00 0.00 0.00 3.79
4074 4845 3.753294 ACAATCAACTCAGTCCGAAGT 57.247 42.857 0.00 0.00 0.00 3.01
4075 4846 4.073293 ACAATCAACTCAGTCCGAAGTT 57.927 40.909 0.00 0.00 0.00 2.66
4076 4847 5.209818 ACAATCAACTCAGTCCGAAGTTA 57.790 39.130 0.00 0.00 0.00 2.24
4077 4848 5.794894 ACAATCAACTCAGTCCGAAGTTAT 58.205 37.500 0.00 0.00 0.00 1.89
4078 4849 5.639506 ACAATCAACTCAGTCCGAAGTTATG 59.360 40.000 0.00 0.00 0.00 1.90
4079 4850 3.585862 TCAACTCAGTCCGAAGTTATGC 58.414 45.455 0.00 0.00 0.00 3.14
4080 4851 2.279582 ACTCAGTCCGAAGTTATGCG 57.720 50.000 0.00 0.00 0.00 4.73
4081 4852 1.544691 ACTCAGTCCGAAGTTATGCGT 59.455 47.619 0.00 0.00 0.00 5.24
4082 4853 2.186076 CTCAGTCCGAAGTTATGCGTC 58.814 52.381 0.00 0.00 0.00 5.19
4083 4854 1.135199 TCAGTCCGAAGTTATGCGTCC 60.135 52.381 0.00 0.00 0.00 4.79
4084 4855 0.892755 AGTCCGAAGTTATGCGTCCA 59.107 50.000 0.00 0.00 0.00 4.02
4085 4856 1.480954 AGTCCGAAGTTATGCGTCCAT 59.519 47.619 0.00 0.00 35.44 3.41
4086 4857 2.093658 AGTCCGAAGTTATGCGTCCATT 60.094 45.455 0.00 0.00 32.85 3.16
4087 4858 2.030457 GTCCGAAGTTATGCGTCCATTG 59.970 50.000 0.00 0.00 32.85 2.82
4088 4859 1.268032 CCGAAGTTATGCGTCCATTGC 60.268 52.381 0.00 0.00 32.85 3.56
4090 4861 2.785679 GAAGTTATGCGTCCATTGCAC 58.214 47.619 0.00 0.00 46.57 4.57
4091 4862 1.819928 AGTTATGCGTCCATTGCACA 58.180 45.000 0.00 0.00 46.57 4.57
4092 4863 2.368439 AGTTATGCGTCCATTGCACAT 58.632 42.857 0.00 0.00 46.57 3.21
4093 4864 2.097954 AGTTATGCGTCCATTGCACATG 59.902 45.455 0.00 0.00 46.57 3.21
4094 4865 1.748950 TATGCGTCCATTGCACATGT 58.251 45.000 0.00 0.00 46.57 3.21
4095 4866 0.171679 ATGCGTCCATTGCACATGTG 59.828 50.000 21.83 21.83 46.57 3.21
4096 4867 0.888285 TGCGTCCATTGCACATGTGA 60.888 50.000 29.80 10.03 37.44 3.58
4097 4868 0.179181 GCGTCCATTGCACATGTGAG 60.179 55.000 29.80 14.38 0.00 3.51
4098 4869 1.159285 CGTCCATTGCACATGTGAGT 58.841 50.000 29.80 10.90 0.00 3.41
4099 4870 1.536766 CGTCCATTGCACATGTGAGTT 59.463 47.619 29.80 9.41 0.00 3.01
4103 4874 4.445385 GTCCATTGCACATGTGAGTTTTTC 59.555 41.667 29.80 10.07 0.00 2.29
4224 4995 1.956477 GCGGACATTAGAATTGCCCAT 59.044 47.619 0.00 0.00 0.00 4.00
4341 5114 0.737219 CGCAGCTACGTTAGGTACCT 59.263 55.000 20.57 20.57 34.67 3.08
4363 5136 2.546778 GCGGGATGACGATTTAGTTGA 58.453 47.619 0.00 0.00 35.47 3.18
4397 5170 3.258372 GCAGATGTAGTTATCCGGGATGA 59.742 47.826 19.82 8.74 0.00 2.92
4553 5328 1.238439 ACAGTAGTTGCCATGTGTGC 58.762 50.000 0.00 0.00 0.00 4.57
4569 5344 1.202867 TGTGCTTATCTGGTTGCCACA 60.203 47.619 0.00 0.00 0.00 4.17
4570 5345 1.200020 GTGCTTATCTGGTTGCCACAC 59.800 52.381 0.00 0.00 0.00 3.82
4639 5417 2.874086 GTGTTTACCTAGTTGCCACGTT 59.126 45.455 0.00 0.00 0.00 3.99
4671 5450 1.803334 GTTGCCATCCACAACGTAGA 58.197 50.000 0.00 0.00 38.18 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.786046 TCTACTCATGTTGTAGGGTCTTTTA 57.214 36.000 20.13 4.63 38.25 1.52
79 80 3.744660 ACTGCACCTTGTTTTCTCCTAG 58.255 45.455 0.00 0.00 0.00 3.02
91 93 0.814010 AAACGCGAGAACTGCACCTT 60.814 50.000 15.93 0.00 0.00 3.50
139 141 3.179830 CAAATCGGTGACTAGAACTCCG 58.820 50.000 20.09 20.09 42.98 4.63
143 145 2.930682 GAGGCAAATCGGTGACTAGAAC 59.069 50.000 0.00 0.00 36.83 3.01
155 161 3.126831 AGATCGTTCGATGAGGCAAATC 58.873 45.455 12.42 0.00 0.00 2.17
268 274 1.938577 CCATTGACTTGATGAGGCGAG 59.061 52.381 0.00 0.00 35.50 5.03
297 303 4.095334 TCGATGAGGCAAATCAATGACTTG 59.905 41.667 0.00 0.00 39.31 3.16
305 311 3.145286 TGTTGTTCGATGAGGCAAATCA 58.855 40.909 0.00 0.00 0.00 2.57
337 343 8.088365 GCCTACCTCAACTTGTTTGATTAAAAT 58.912 33.333 0.00 0.00 43.54 1.82
385 391 6.830324 TGCCAGAATCATTAGTTAGCTTCAAT 59.170 34.615 0.00 0.00 0.00 2.57
391 398 5.278169 CCACATGCCAGAATCATTAGTTAGC 60.278 44.000 0.00 0.00 0.00 3.09
398 405 5.452255 AGTTATCCACATGCCAGAATCATT 58.548 37.500 0.00 0.00 0.00 2.57
411 418 5.761234 GGTGTGTGAAAGTTAGTTATCCACA 59.239 40.000 0.00 0.00 0.00 4.17
431 438 7.849322 AAAAACTAATTATGGACAAGGGTGT 57.151 32.000 0.00 0.00 42.10 4.16
451 458 6.303054 TGACATGTGAGGAGTCCATTAAAAA 58.697 36.000 12.86 0.00 0.00 1.94
453 460 5.497464 TGACATGTGAGGAGTCCATTAAA 57.503 39.130 12.86 0.00 0.00 1.52
540 579 1.601903 CAACGCAGACCACTAAAAGCA 59.398 47.619 0.00 0.00 0.00 3.91
545 584 4.116961 GCATATACAACGCAGACCACTAA 58.883 43.478 0.00 0.00 0.00 2.24
559 598 6.421801 CGTCTGAGATGATTTGTGCATATACA 59.578 38.462 0.00 0.00 0.00 2.29
560 599 6.642540 TCGTCTGAGATGATTTGTGCATATAC 59.357 38.462 0.00 0.00 0.00 1.47
561 600 6.748132 TCGTCTGAGATGATTTGTGCATATA 58.252 36.000 0.00 0.00 0.00 0.86
562 601 5.604565 TCGTCTGAGATGATTTGTGCATAT 58.395 37.500 0.00 0.00 0.00 1.78
708 755 2.421424 CTCCTAGTGTGGCAGCAAATTC 59.579 50.000 0.00 0.00 0.00 2.17
732 779 4.010349 CCTCCTGGTCAACCAATACTTTC 58.990 47.826 3.03 0.00 46.97 2.62
736 783 3.713826 TTCCTCCTGGTCAACCAATAC 57.286 47.619 3.03 0.00 46.97 1.89
738 785 2.447047 ACTTTCCTCCTGGTCAACCAAT 59.553 45.455 3.03 0.00 46.97 3.16
739 786 1.850345 ACTTTCCTCCTGGTCAACCAA 59.150 47.619 3.03 0.00 46.97 3.67
741 788 2.658807 AACTTTCCTCCTGGTCAACC 57.341 50.000 0.00 0.00 34.23 3.77
743 790 3.976015 ACAAAACTTTCCTCCTGGTCAA 58.024 40.909 0.00 0.00 34.23 3.18
745 792 5.313712 TCATACAAAACTTTCCTCCTGGTC 58.686 41.667 0.00 0.00 34.23 4.02
746 793 5.319043 TCATACAAAACTTTCCTCCTGGT 57.681 39.130 0.00 0.00 34.23 4.00
747 794 5.334879 CGTTCATACAAAACTTTCCTCCTGG 60.335 44.000 0.00 0.00 0.00 4.45
748 795 5.468746 TCGTTCATACAAAACTTTCCTCCTG 59.531 40.000 0.00 0.00 0.00 3.86
749 796 5.617252 TCGTTCATACAAAACTTTCCTCCT 58.383 37.500 0.00 0.00 0.00 3.69
750 797 5.934935 TCGTTCATACAAAACTTTCCTCC 57.065 39.130 0.00 0.00 0.00 4.30
751 798 6.721321 TGTTCGTTCATACAAAACTTTCCTC 58.279 36.000 0.00 0.00 0.00 3.71
753 800 7.114388 GGAATGTTCGTTCATACAAAACTTTCC 59.886 37.037 12.49 12.49 40.99 3.13
754 801 7.860872 AGGAATGTTCGTTCATACAAAACTTTC 59.139 33.333 7.01 0.00 35.59 2.62
758 805 9.916397 CTATAGGAATGTTCGTTCATACAAAAC 57.084 33.333 7.01 0.00 28.52 2.43
759 806 9.878667 TCTATAGGAATGTTCGTTCATACAAAA 57.121 29.630 0.00 0.00 28.52 2.44
782 829 7.344871 CCCTGGAGACTTTTTAGGTCTATTCTA 59.655 40.741 0.00 0.00 43.13 2.10
827 1317 0.031449 GCTCAGTGGATAGAGCGTCC 59.969 60.000 0.00 0.00 46.53 4.79
828 1318 3.560826 GCTCAGTGGATAGAGCGTC 57.439 57.895 0.00 0.00 46.53 5.19
832 1322 2.295909 GCCTGTAGCTCAGTGGATAGAG 59.704 54.545 10.86 0.00 42.19 2.43
833 1323 2.311463 GCCTGTAGCTCAGTGGATAGA 58.689 52.381 10.86 0.00 42.19 1.98
835 1325 1.032794 CGCCTGTAGCTCAGTGGATA 58.967 55.000 10.86 0.00 42.19 2.59
875 1493 8.746052 TGAATTCCAATTTATGAAGGTACGAT 57.254 30.769 2.27 0.00 0.00 3.73
892 1511 3.313791 TGGGGACGATAGATGAATTCCA 58.686 45.455 2.27 0.00 41.38 3.53
893 1512 4.351874 TTGGGGACGATAGATGAATTCC 57.648 45.455 2.27 0.00 41.38 3.01
894 1513 6.934645 TGTAATTGGGGACGATAGATGAATTC 59.065 38.462 0.00 0.00 41.38 2.17
930 1549 5.221441 GCTTTGCAGGGGGTATTATTAAAGG 60.221 44.000 0.00 0.00 0.00 3.11
939 1558 0.034089 GACAGCTTTGCAGGGGGTAT 60.034 55.000 0.00 0.00 0.00 2.73
940 1559 1.378762 GACAGCTTTGCAGGGGGTA 59.621 57.895 0.00 0.00 0.00 3.69
941 1560 2.116125 GACAGCTTTGCAGGGGGT 59.884 61.111 0.00 0.00 0.00 4.95
1020 1642 1.654954 GCTTGCCCAGAGTGCTGATG 61.655 60.000 0.00 0.00 45.17 3.07
1060 1682 3.170360 GGTTCGGGACCTGGAAATC 57.830 57.895 0.00 0.00 45.55 2.17
1103 1725 1.420138 AGAAAGGGCGTCAGGAGAAAA 59.580 47.619 0.00 0.00 0.00 2.29
1112 1734 0.606673 AAGGCTGAAGAAAGGGCGTC 60.607 55.000 0.00 0.00 0.00 5.19
1128 1755 2.347490 CTGGTGGACGGGTGAAGG 59.653 66.667 0.00 0.00 0.00 3.46
1158 1785 1.392407 TCAGGATTTGGGTGGGGAAT 58.608 50.000 0.00 0.00 0.00 3.01
1175 1802 5.344743 AGATCTAAAGATGAAGCGGTTCA 57.655 39.130 30.00 30.00 46.81 3.18
1377 2007 9.343103 CGTAACTCAACCACATCATCTATATAC 57.657 37.037 0.00 0.00 0.00 1.47
1378 2008 8.520351 CCGTAACTCAACCACATCATCTATATA 58.480 37.037 0.00 0.00 0.00 0.86
1379 2009 7.232737 TCCGTAACTCAACCACATCATCTATAT 59.767 37.037 0.00 0.00 0.00 0.86
1380 2010 6.548251 TCCGTAACTCAACCACATCATCTATA 59.452 38.462 0.00 0.00 0.00 1.31
1599 2240 9.953565 TTTGCATACCTAGTCAATAGTTTAGTT 57.046 29.630 0.00 0.00 0.00 2.24
1611 2335 4.697514 TCTGAGCATTTGCATACCTAGTC 58.302 43.478 5.20 0.00 45.16 2.59
1644 2368 2.266055 CTGTTCGCCACTCCCCTC 59.734 66.667 0.00 0.00 0.00 4.30
1648 2372 0.108138 ACATAGCTGTTCGCCACTCC 60.108 55.000 0.00 0.00 40.39 3.85
1669 2393 4.101942 CAAATGTTTACAGCAACACACGT 58.898 39.130 0.00 0.00 39.48 4.49
1692 2416 8.789762 AGGTGCAAATTTAGTTTTACGATTAGT 58.210 29.630 0.00 0.00 0.00 2.24
1698 2422 6.435428 ACTCAGGTGCAAATTTAGTTTTACG 58.565 36.000 0.00 0.00 0.00 3.18
1715 2439 4.710324 TCCGTCACAAATTTAACTCAGGT 58.290 39.130 0.00 0.00 0.00 4.00
1719 2443 6.970613 AGTTGTTTCCGTCACAAATTTAACTC 59.029 34.615 0.00 0.00 35.91 3.01
1726 2450 4.974368 TTCAGTTGTTTCCGTCACAAAT 57.026 36.364 0.00 0.00 35.91 2.32
1767 2499 7.552687 CCTTACAGCTCATTGTAGGTAAAATGA 59.447 37.037 3.16 3.16 39.79 2.57
1815 2547 3.428534 CGTTCCCTGCAAAGCATAAAAAC 59.571 43.478 0.00 0.00 38.13 2.43
1817 2549 2.887783 TCGTTCCCTGCAAAGCATAAAA 59.112 40.909 0.00 0.00 38.13 1.52
1822 2554 0.884704 GTCTCGTTCCCTGCAAAGCA 60.885 55.000 0.00 0.00 36.92 3.91
1823 2555 0.603975 AGTCTCGTTCCCTGCAAAGC 60.604 55.000 0.00 0.00 0.00 3.51
1874 2606 7.180322 TCTCAGAGCTATCAAAGACAAAGAT 57.820 36.000 0.00 0.00 0.00 2.40
1975 2707 1.134128 TCCATTGCACACGGCTATCAT 60.134 47.619 0.00 0.00 45.15 2.45
1983 2715 2.988493 CCTCAATTTTCCATTGCACACG 59.012 45.455 0.00 0.00 0.00 4.49
2062 2794 6.540914 AGACTCTGTACGGAAACATTTCAAAA 59.459 34.615 5.76 0.00 38.92 2.44
2076 2808 2.022934 GGGGGAAGTAGACTCTGTACG 58.977 57.143 0.00 0.00 0.00 3.67
2094 2826 0.251916 TGAGATAAACAGCCACCGGG 59.748 55.000 6.32 0.00 37.18 5.73
2122 2854 9.911788 AGTGTATGGATAATGAACTGAAAGAAT 57.088 29.630 0.00 0.00 37.43 2.40
2191 2925 5.868257 TGCATAAGTGTTTAGCAAGAATCG 58.132 37.500 0.00 0.00 31.42 3.34
2196 2930 6.094048 AGTGGTATGCATAAGTGTTTAGCAAG 59.906 38.462 8.28 0.00 38.85 4.01
2245 2979 3.871006 TGTTTGTCTTAGTGCAGTGACAG 59.129 43.478 12.83 3.55 40.00 3.51
2259 2993 4.942761 ACAAAGGAATGCATGTTTGTCT 57.057 36.364 21.03 7.54 38.45 3.41
2260 2994 5.527951 TGTACAAAGGAATGCATGTTTGTC 58.472 37.500 26.29 20.32 41.16 3.18
2279 3024 7.891183 ACAATTCACTGAGTGTTAGATGTAC 57.109 36.000 12.93 0.00 34.79 2.90
2293 3038 7.174599 AGGAGAAAGAAGATGAACAATTCACTG 59.825 37.037 0.00 0.00 43.48 3.66
2343 3088 6.876257 AGTTGATCTCTTCAAACAGGTCATAC 59.124 38.462 0.00 0.00 45.71 2.39
2516 3264 5.743636 AAAACACCAATGCTATTGTGGAT 57.256 34.783 0.00 0.00 36.23 3.41
2597 3345 3.037431 TGTTACATTGGGCAATTGCAC 57.963 42.857 30.32 28.29 46.69 4.57
2732 3480 8.623903 ACACCAGCATGATTTAACAACATATAG 58.376 33.333 0.00 0.00 39.69 1.31
2771 3519 1.065418 GCCACTGCCAAGGTACTACAT 60.065 52.381 0.00 0.00 38.49 2.29
2833 3582 3.146066 TGCCCCGTATCAATTAATGCTC 58.854 45.455 0.00 0.00 0.00 4.26
2834 3583 3.149196 CTGCCCCGTATCAATTAATGCT 58.851 45.455 0.00 0.00 0.00 3.79
2835 3584 3.146066 TCTGCCCCGTATCAATTAATGC 58.854 45.455 0.00 0.00 0.00 3.56
2836 3585 3.753272 CCTCTGCCCCGTATCAATTAATG 59.247 47.826 0.00 0.00 0.00 1.90
2837 3586 3.244911 CCCTCTGCCCCGTATCAATTAAT 60.245 47.826 0.00 0.00 0.00 1.40
2838 3587 2.105821 CCCTCTGCCCCGTATCAATTAA 59.894 50.000 0.00 0.00 0.00 1.40
2839 3588 1.697432 CCCTCTGCCCCGTATCAATTA 59.303 52.381 0.00 0.00 0.00 1.40
2844 3593 0.178970 TACTCCCTCTGCCCCGTATC 60.179 60.000 0.00 0.00 0.00 2.24
2849 3598 2.104669 AATACTACTCCCTCTGCCCC 57.895 55.000 0.00 0.00 0.00 5.80
2854 3603 9.939424 AGATGTAAACTAAATACTACTCCCTCT 57.061 33.333 0.00 0.00 0.00 3.69
2980 3729 9.750125 TGCTCACTTATAGTTATATGTTGTCTG 57.250 33.333 0.00 0.00 0.00 3.51
3022 3771 0.610174 CTCTGCCAGACTGCCAGTAA 59.390 55.000 12.80 0.00 0.00 2.24
3023 3772 0.251787 TCTCTGCCAGACTGCCAGTA 60.252 55.000 12.80 0.92 0.00 2.74
3127 3877 2.541346 AGTATCGATTGTCAGCATTGCG 59.459 45.455 1.71 0.00 0.00 4.85
3234 3984 0.268869 AGTAGGGGATGGAGCCATGA 59.731 55.000 6.76 0.00 36.70 3.07
3251 4001 6.154534 TGCATGGTGTAGATACTACAGAAAGT 59.845 38.462 11.17 0.00 0.00 2.66
3263 4013 8.829373 TCTCTACATATATGCATGGTGTAGAT 57.171 34.615 29.99 13.29 45.79 1.98
3411 4179 9.770503 GTGAAGCTGCATTTCATCATATTATAG 57.229 33.333 14.55 0.00 36.96 1.31
3686 4454 1.008995 CGGTCCAAAACACAAGCGG 60.009 57.895 0.00 0.00 0.00 5.52
3698 4466 1.124780 TCTCCAAAACTGTCGGTCCA 58.875 50.000 0.00 0.00 0.00 4.02
3827 4595 1.274703 TGGGGAGGGAGACAATCTGC 61.275 60.000 0.00 0.00 33.75 4.26
3830 4598 1.127343 CTCTGGGGAGGGAGACAATC 58.873 60.000 0.00 0.00 36.03 2.67
4000 4771 8.491045 TCAAACACCTCATATATCACCATAGA 57.509 34.615 0.00 0.00 0.00 1.98
4012 4783 4.825085 GGTTGGAACTTCAAACACCTCATA 59.175 41.667 10.61 0.00 34.67 2.15
4030 4801 1.128200 TCCACATAGATCCGGGTTGG 58.872 55.000 0.00 0.00 40.09 3.77
4031 4802 2.550855 CCATCCACATAGATCCGGGTTG 60.551 54.545 0.00 0.00 0.00 3.77
4032 4803 1.699634 CCATCCACATAGATCCGGGTT 59.300 52.381 0.00 0.00 0.00 4.11
4033 4804 1.352083 CCATCCACATAGATCCGGGT 58.648 55.000 0.00 0.00 0.00 5.28
4034 4805 1.352083 ACCATCCACATAGATCCGGG 58.648 55.000 0.00 0.00 0.00 5.73
4035 4806 2.897326 TGTACCATCCACATAGATCCGG 59.103 50.000 0.00 0.00 0.00 5.14
4036 4807 4.600692 TTGTACCATCCACATAGATCCG 57.399 45.455 0.00 0.00 0.00 4.18
4037 4808 6.114187 TGATTGTACCATCCACATAGATCC 57.886 41.667 4.59 0.00 0.00 3.36
4038 4809 7.220030 AGTTGATTGTACCATCCACATAGATC 58.780 38.462 12.10 0.00 0.00 2.75
4039 4810 7.141758 AGTTGATTGTACCATCCACATAGAT 57.858 36.000 12.10 0.00 0.00 1.98
4040 4811 6.156083 TGAGTTGATTGTACCATCCACATAGA 59.844 38.462 12.10 0.00 0.00 1.98
4041 4812 6.348498 TGAGTTGATTGTACCATCCACATAG 58.652 40.000 12.10 0.00 0.00 2.23
4042 4813 6.070251 ACTGAGTTGATTGTACCATCCACATA 60.070 38.462 12.10 2.25 0.00 2.29
4043 4814 5.178096 TGAGTTGATTGTACCATCCACAT 57.822 39.130 12.10 0.49 0.00 3.21
4044 4815 4.041567 ACTGAGTTGATTGTACCATCCACA 59.958 41.667 12.10 4.16 0.00 4.17
4045 4816 4.579869 ACTGAGTTGATTGTACCATCCAC 58.420 43.478 4.59 4.08 0.00 4.02
4046 4817 4.323485 GGACTGAGTTGATTGTACCATCCA 60.323 45.833 4.59 0.00 0.00 3.41
4047 4818 4.192317 GGACTGAGTTGATTGTACCATCC 58.808 47.826 4.59 0.00 0.00 3.51
4048 4819 3.865745 CGGACTGAGTTGATTGTACCATC 59.134 47.826 0.00 0.00 0.00 3.51
4049 4820 3.513912 TCGGACTGAGTTGATTGTACCAT 59.486 43.478 0.00 0.00 0.00 3.55
4050 4821 2.894765 TCGGACTGAGTTGATTGTACCA 59.105 45.455 0.00 0.00 0.00 3.25
4051 4822 3.587797 TCGGACTGAGTTGATTGTACC 57.412 47.619 0.00 0.00 0.00 3.34
4052 4823 4.557205 ACTTCGGACTGAGTTGATTGTAC 58.443 43.478 0.00 0.00 0.00 2.90
4053 4824 4.866508 ACTTCGGACTGAGTTGATTGTA 57.133 40.909 0.00 0.00 0.00 2.41
4054 4825 3.753294 ACTTCGGACTGAGTTGATTGT 57.247 42.857 0.00 0.00 0.00 2.71
4055 4826 5.446473 GCATAACTTCGGACTGAGTTGATTG 60.446 44.000 4.27 1.90 0.00 2.67
4056 4827 4.631813 GCATAACTTCGGACTGAGTTGATT 59.368 41.667 4.27 0.00 0.00 2.57
4057 4828 4.184629 GCATAACTTCGGACTGAGTTGAT 58.815 43.478 4.27 0.00 0.00 2.57
4058 4829 3.585862 GCATAACTTCGGACTGAGTTGA 58.414 45.455 4.27 0.00 0.00 3.18
4059 4830 2.345641 CGCATAACTTCGGACTGAGTTG 59.654 50.000 4.27 0.00 0.00 3.16
4060 4831 2.029290 ACGCATAACTTCGGACTGAGTT 60.029 45.455 0.00 0.00 0.00 3.01
4061 4832 1.544691 ACGCATAACTTCGGACTGAGT 59.455 47.619 0.00 0.00 0.00 3.41
4062 4833 2.186076 GACGCATAACTTCGGACTGAG 58.814 52.381 0.00 0.00 0.00 3.35
4063 4834 1.135199 GGACGCATAACTTCGGACTGA 60.135 52.381 0.00 0.00 0.00 3.41
4064 4835 1.278238 GGACGCATAACTTCGGACTG 58.722 55.000 0.00 0.00 0.00 3.51
4065 4836 0.892755 TGGACGCATAACTTCGGACT 59.107 50.000 0.00 0.00 0.00 3.85
4066 4837 1.935933 ATGGACGCATAACTTCGGAC 58.064 50.000 0.00 0.00 0.00 4.79
4067 4838 2.276201 CAATGGACGCATAACTTCGGA 58.724 47.619 0.00 0.00 0.00 4.55
4068 4839 1.268032 GCAATGGACGCATAACTTCGG 60.268 52.381 0.00 0.00 0.00 4.30
4069 4840 1.396648 TGCAATGGACGCATAACTTCG 59.603 47.619 0.00 0.00 33.55 3.79
4070 4841 2.161410 TGTGCAATGGACGCATAACTTC 59.839 45.455 0.00 0.00 42.32 3.01
4071 4842 2.158559 TGTGCAATGGACGCATAACTT 58.841 42.857 0.00 0.00 42.32 2.66
4072 4843 1.819928 TGTGCAATGGACGCATAACT 58.180 45.000 0.00 0.00 42.32 2.24
4073 4844 2.159393 ACATGTGCAATGGACGCATAAC 60.159 45.455 0.00 0.00 42.32 1.89
4074 4845 2.090760 ACATGTGCAATGGACGCATAA 58.909 42.857 0.00 0.00 42.32 1.90
4075 4846 1.401199 CACATGTGCAATGGACGCATA 59.599 47.619 13.94 0.00 42.32 3.14
4076 4847 0.171679 CACATGTGCAATGGACGCAT 59.828 50.000 13.94 0.00 42.32 4.73
4077 4848 0.888285 TCACATGTGCAATGGACGCA 60.888 50.000 21.38 0.00 36.94 5.24
4078 4849 0.179181 CTCACATGTGCAATGGACGC 60.179 55.000 21.38 0.00 0.00 5.19
4079 4850 1.159285 ACTCACATGTGCAATGGACG 58.841 50.000 21.38 4.26 0.00 4.79
4080 4851 3.648339 AAACTCACATGTGCAATGGAC 57.352 42.857 21.38 0.00 0.00 4.02
4081 4852 4.341806 AGAAAAACTCACATGTGCAATGGA 59.658 37.500 21.38 1.54 0.00 3.41
4082 4853 4.624015 AGAAAAACTCACATGTGCAATGG 58.376 39.130 21.38 10.26 0.00 3.16
4083 4854 6.592798 AAAGAAAAACTCACATGTGCAATG 57.407 33.333 21.38 12.59 0.00 2.82
4084 4855 6.037391 CCAAAAGAAAAACTCACATGTGCAAT 59.963 34.615 21.38 5.75 0.00 3.56
4085 4856 5.350914 CCAAAAGAAAAACTCACATGTGCAA 59.649 36.000 21.38 3.89 0.00 4.08
4086 4857 4.869297 CCAAAAGAAAAACTCACATGTGCA 59.131 37.500 21.38 9.15 0.00 4.57
4087 4858 5.005682 GTCCAAAAGAAAAACTCACATGTGC 59.994 40.000 21.38 5.13 0.00 4.57
4088 4859 5.229887 CGTCCAAAAGAAAAACTCACATGTG 59.770 40.000 20.18 20.18 0.00 3.21
4089 4860 5.339990 CGTCCAAAAGAAAAACTCACATGT 58.660 37.500 0.00 0.00 0.00 3.21
4090 4861 4.207019 GCGTCCAAAAGAAAAACTCACATG 59.793 41.667 0.00 0.00 0.00 3.21
4091 4862 4.359706 GCGTCCAAAAGAAAAACTCACAT 58.640 39.130 0.00 0.00 0.00 3.21
4092 4863 3.428316 GGCGTCCAAAAGAAAAACTCACA 60.428 43.478 0.00 0.00 0.00 3.58
4093 4864 3.113322 GGCGTCCAAAAGAAAAACTCAC 58.887 45.455 0.00 0.00 0.00 3.51
4094 4865 2.223386 CGGCGTCCAAAAGAAAAACTCA 60.223 45.455 0.00 0.00 0.00 3.41
4095 4866 2.032426 TCGGCGTCCAAAAGAAAAACTC 59.968 45.455 6.85 0.00 0.00 3.01
4096 4867 2.018515 TCGGCGTCCAAAAGAAAAACT 58.981 42.857 6.85 0.00 0.00 2.66
4097 4868 2.478547 TCGGCGTCCAAAAGAAAAAC 57.521 45.000 6.85 0.00 0.00 2.43
4098 4869 4.142556 GGATATCGGCGTCCAAAAGAAAAA 60.143 41.667 6.85 0.00 34.57 1.94
4099 4870 3.375922 GGATATCGGCGTCCAAAAGAAAA 59.624 43.478 6.85 0.00 34.57 2.29
4103 4874 1.597663 GTGGATATCGGCGTCCAAAAG 59.402 52.381 17.87 0.00 45.50 2.27
4173 4944 3.958860 GTGTGGGCTGCCTCCTGT 61.959 66.667 19.68 0.00 0.00 4.00
4341 5114 0.742505 ACTAAATCGTCATCCCGCGA 59.257 50.000 8.23 0.00 41.50 5.87
4363 5136 0.700564 ACATCTGCCAACCAGGATGT 59.299 50.000 0.00 0.00 42.05 3.06
4397 5170 5.507315 GCCATGCTTTTACAACTACACTTGT 60.507 40.000 0.00 0.00 38.03 3.16
4553 5328 1.464608 CGTGTGTGGCAACCAGATAAG 59.535 52.381 0.00 0.00 32.34 1.73
4569 5344 3.202001 AACTGCAGTTGCGCGTGT 61.202 55.556 30.66 4.24 45.83 4.49
4639 5417 2.314647 GGCAACTGCAGTTACGCGA 61.315 57.895 30.67 0.00 44.36 5.87
4644 5422 1.202867 TGTGGATGGCAACTGCAGTTA 60.203 47.619 30.67 16.98 44.36 2.24


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

AutoCloner maintained by Alex Coulton.