Multiple sequence alignment - TraesCS5D01G416900

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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 TraesCS5D01G416900 chr5D 100.000 3317 0 0 1 3317 479128018 479124702 0.000000e+00 6126.0
1 TraesCS5D01G416900 chr5D 86.937 222 21 5 3 216 458453319 458453540 3.310000e-60 243.0
2 TraesCS5D01G416900 chr5B 88.188 2760 174 72 619 3285 586866637 586863937 0.000000e+00 3151.0
3 TraesCS5D01G416900 chr5B 90.803 685 33 11 1795 2458 625120718 625120043 0.000000e+00 889.0
4 TraesCS5D01G416900 chr5B 90.803 685 33 11 1795 2458 628700267 628699592 0.000000e+00 889.0
5 TraesCS5D01G416900 chr5B 79.856 278 19 16 2841 3104 625120050 625119796 5.690000e-38 169.0
6 TraesCS5D01G416900 chr5B 79.856 278 19 16 2841 3104 628699599 628699345 5.690000e-38 169.0
7 TraesCS5D01G416900 chr5A 88.535 2512 130 78 876 3294 597841814 597839368 0.000000e+00 2898.0
8 TraesCS5D01G416900 chr5A 84.163 221 25 5 5 217 597843142 597842924 4.340000e-49 206.0
9 TraesCS5D01G416900 chr2D 86.632 1354 84 48 1795 3104 81516751 81515451 0.000000e+00 1408.0
10 TraesCS5D01G416900 chr2D 77.896 656 115 20 1001 1644 309576862 309577499 6.710000e-102 381.0
11 TraesCS5D01G416900 chr2D 77.463 670 114 24 1676 2317 309577673 309578333 1.880000e-97 366.0
12 TraesCS5D01G416900 chr6B 84.242 1358 97 52 1795 3104 507371888 507373176 0.000000e+00 1214.0
13 TraesCS5D01G416900 chr6B 92.213 732 32 6 1795 2510 615609089 615608367 0.000000e+00 1013.0
14 TraesCS5D01G416900 chr6B 77.148 582 60 36 2545 3097 615608369 615607832 1.520000e-68 270.0
15 TraesCS5D01G416900 chr6D 88.191 940 80 15 925 1861 5800685 5799774 0.000000e+00 1092.0
16 TraesCS5D01G416900 chr7A 91.202 682 30 10 1795 2455 487477319 487477991 0.000000e+00 900.0
17 TraesCS5D01G416900 chr7A 80.153 262 17 14 2841 3090 487477987 487478225 2.650000e-36 163.0
18 TraesCS5D01G416900 chr2B 77.508 658 120 18 1001 1647 362694158 362693518 1.450000e-98 370.0
19 TraesCS5D01G416900 chr2A 77.356 658 121 18 1001 1647 429718844 429718204 6.760000e-97 364.0
20 TraesCS5D01G416900 chr6A 83.529 170 23 5 1 167 373975563 373975730 1.590000e-33 154.0
21 TraesCS5D01G416900 chr6A 81.765 170 25 6 1 167 145647767 145647933 1.600000e-28 137.0
22 TraesCS5D01G416900 chr6A 94.286 35 1 1 1858 1891 98355176 98355210 6.000000e-03 52.8
23 TraesCS5D01G416900 chr3A 83.529 170 23 5 1 167 728515635 728515802 1.590000e-33 154.0
24 TraesCS5D01G416900 chr3B 78.603 229 36 8 1 217 794882734 794882507 4.460000e-29 139.0


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 TraesCS5D01G416900 chr5D 479124702 479128018 3316 True 6126.0 6126 100.0000 1 3317 1 chr5D.!!$R1 3316
1 TraesCS5D01G416900 chr5B 586863937 586866637 2700 True 3151.0 3151 88.1880 619 3285 1 chr5B.!!$R1 2666
2 TraesCS5D01G416900 chr5B 625119796 625120718 922 True 529.0 889 85.3295 1795 3104 2 chr5B.!!$R2 1309
3 TraesCS5D01G416900 chr5B 628699345 628700267 922 True 529.0 889 85.3295 1795 3104 2 chr5B.!!$R3 1309
4 TraesCS5D01G416900 chr5A 597839368 597843142 3774 True 1552.0 2898 86.3490 5 3294 2 chr5A.!!$R1 3289
5 TraesCS5D01G416900 chr2D 81515451 81516751 1300 True 1408.0 1408 86.6320 1795 3104 1 chr2D.!!$R1 1309
6 TraesCS5D01G416900 chr2D 309576862 309578333 1471 False 373.5 381 77.6795 1001 2317 2 chr2D.!!$F1 1316
7 TraesCS5D01G416900 chr6B 507371888 507373176 1288 False 1214.0 1214 84.2420 1795 3104 1 chr6B.!!$F1 1309
8 TraesCS5D01G416900 chr6B 615607832 615609089 1257 True 641.5 1013 84.6805 1795 3097 2 chr6B.!!$R1 1302
9 TraesCS5D01G416900 chr6D 5799774 5800685 911 True 1092.0 1092 88.1910 925 1861 1 chr6D.!!$R1 936
10 TraesCS5D01G416900 chr7A 487477319 487478225 906 False 531.5 900 85.6775 1795 3090 2 chr7A.!!$F1 1295
11 TraesCS5D01G416900 chr2B 362693518 362694158 640 True 370.0 370 77.5080 1001 1647 1 chr2B.!!$R1 646
12 TraesCS5D01G416900 chr2A 429718204 429718844 640 True 364.0 364 77.3560 1001 1647 1 chr2A.!!$R1 646

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
566 779 0.035739 GTGGAACCCGAGCTAAACCA 59.964 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2331 3072 0.248215 CGGAATGAGATGTTTGCCGC 60.248 55.0 0.0 0.0 0.0 6.53 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
32 33 9.833182 GATAAAGGAGATGAAAGAAAGTTTGAC 57.167 33.333 0.00 0.00 0.00 3.18
37 38 3.963383 TGAAAGAAAGTTTGACCGAGC 57.037 42.857 0.00 0.00 0.00 5.03
41 42 3.102052 AGAAAGTTTGACCGAGCGTAA 57.898 42.857 0.00 0.00 0.00 3.18
59 60 7.167635 CGAGCGTAATTCTTGTATTACTCATGT 59.832 37.037 0.00 0.00 38.34 3.21
70 71 5.467063 TGTATTACTCATGTTTGACGCACAA 59.533 36.000 0.00 0.00 36.65 3.33
121 122 2.488204 TGGAAGATCACAATGCCGAA 57.512 45.000 0.00 0.00 0.00 4.30
122 123 2.358957 TGGAAGATCACAATGCCGAAG 58.641 47.619 0.00 0.00 0.00 3.79
138 139 0.954452 GAAGAGTTGTGTGGCTTGGG 59.046 55.000 0.00 0.00 0.00 4.12
139 140 0.258774 AAGAGTTGTGTGGCTTGGGT 59.741 50.000 0.00 0.00 0.00 4.51
140 141 0.258774 AGAGTTGTGTGGCTTGGGTT 59.741 50.000 0.00 0.00 0.00 4.11
141 142 1.111277 GAGTTGTGTGGCTTGGGTTT 58.889 50.000 0.00 0.00 0.00 3.27
159 160 5.010922 TGGGTTTGATCCAAATGAACTTCTG 59.989 40.000 0.00 0.00 35.74 3.02
161 162 5.243730 GGTTTGATCCAAATGAACTTCTGGA 59.756 40.000 1.72 1.72 42.04 3.86
163 164 4.984295 TGATCCAAATGAACTTCTGGACA 58.016 39.130 1.32 0.91 40.69 4.02
167 168 5.139727 TCCAAATGAACTTCTGGACATTGT 58.860 37.500 0.00 0.00 32.97 2.71
169 170 5.009911 CCAAATGAACTTCTGGACATTGTCA 59.990 40.000 18.09 4.30 34.02 3.58
180 188 6.533730 TCTGGACATTGTCAGTGTAATTCTT 58.466 36.000 18.09 0.00 33.68 2.52
185 193 7.752239 GGACATTGTCAGTGTAATTCTTGATTG 59.248 37.037 18.09 0.00 33.68 2.67
189 197 7.425577 TGTCAGTGTAATTCTTGATTGTGAG 57.574 36.000 0.00 0.00 0.00 3.51
192 200 8.988934 GTCAGTGTAATTCTTGATTGTGAGTAA 58.011 33.333 0.00 0.00 0.00 2.24
198 206 9.624697 GTAATTCTTGATTGTGAGTAATGCAAA 57.375 29.630 0.00 0.00 0.00 3.68
207 215 9.546909 GATTGTGAGTAATGCAAATATTATCCG 57.453 33.333 0.00 0.00 0.00 4.18
208 216 8.669946 TTGTGAGTAATGCAAATATTATCCGA 57.330 30.769 0.00 0.00 0.00 4.55
209 217 8.669946 TGTGAGTAATGCAAATATTATCCGAA 57.330 30.769 0.00 0.00 0.00 4.30
236 265 1.464997 GCTAGGGTTTGAACTCTTGCG 59.535 52.381 12.94 0.33 45.42 4.85
256 285 4.098807 TGCGACAAGGAAGTGCTATATGTA 59.901 41.667 0.00 0.00 0.00 2.29
258 287 6.015772 TGCGACAAGGAAGTGCTATATGTATA 60.016 38.462 0.00 0.00 0.00 1.47
260 289 7.368059 CGACAAGGAAGTGCTATATGTATACA 58.632 38.462 8.27 8.27 0.00 2.29
262 291 9.360093 GACAAGGAAGTGCTATATGTATACATC 57.640 37.037 21.49 8.32 37.76 3.06
267 296 9.885934 GGAAGTGCTATATGTATACATCTATCG 57.114 37.037 21.49 8.39 37.76 2.92
288 331 5.101628 TCGATATTTTTGCACATCCTTTGC 58.898 37.500 0.00 0.00 40.63 3.68
315 358 6.916360 TTTGTAGAAATGGCCAGAGAATTT 57.084 33.333 13.05 6.23 0.00 1.82
405 594 7.733402 ACCCAATGTTTTCTTGATCAATTTG 57.267 32.000 8.96 0.00 0.00 2.32
406 595 6.711645 ACCCAATGTTTTCTTGATCAATTTGG 59.288 34.615 8.96 12.24 0.00 3.28
407 596 6.348704 CCCAATGTTTTCTTGATCAATTTGGC 60.349 38.462 8.96 0.97 30.88 4.52
408 597 6.301108 CAATGTTTTCTTGATCAATTTGGCG 58.699 36.000 8.96 0.00 0.00 5.69
409 598 4.942852 TGTTTTCTTGATCAATTTGGCGT 58.057 34.783 8.96 0.00 0.00 5.68
410 599 6.078202 TGTTTTCTTGATCAATTTGGCGTA 57.922 33.333 8.96 0.00 0.00 4.42
411 600 5.918011 TGTTTTCTTGATCAATTTGGCGTAC 59.082 36.000 8.96 1.06 0.00 3.67
412 601 4.695217 TTCTTGATCAATTTGGCGTACC 57.305 40.909 8.96 0.00 0.00 3.34
413 602 3.013921 TCTTGATCAATTTGGCGTACCC 58.986 45.455 8.96 0.00 33.59 3.69
414 603 2.498644 TGATCAATTTGGCGTACCCA 57.501 45.000 0.00 0.00 43.51 4.51
434 623 4.191033 CAATGTTTTGGAGCATTAGCCA 57.809 40.909 0.00 0.00 43.56 4.75
435 624 4.761975 CAATGTTTTGGAGCATTAGCCAT 58.238 39.130 0.00 0.00 43.56 4.40
436 625 3.872511 TGTTTTGGAGCATTAGCCATG 57.127 42.857 0.00 0.00 43.56 3.66
437 626 3.429492 TGTTTTGGAGCATTAGCCATGA 58.571 40.909 0.00 0.00 43.56 3.07
438 627 3.193267 TGTTTTGGAGCATTAGCCATGAC 59.807 43.478 0.00 0.00 43.56 3.06
439 628 2.804986 TTGGAGCATTAGCCATGACA 57.195 45.000 0.00 0.00 43.56 3.58
440 629 3.301794 TTGGAGCATTAGCCATGACAT 57.698 42.857 0.00 0.00 43.56 3.06
441 630 3.301794 TGGAGCATTAGCCATGACATT 57.698 42.857 0.00 0.00 43.56 2.71
442 631 2.953648 TGGAGCATTAGCCATGACATTG 59.046 45.455 0.00 0.00 43.56 2.82
443 632 2.288030 GGAGCATTAGCCATGACATTGC 60.288 50.000 3.31 3.31 43.56 3.56
444 633 2.621998 GAGCATTAGCCATGACATTGCT 59.378 45.455 17.28 17.28 43.56 3.91
445 634 3.817084 GAGCATTAGCCATGACATTGCTA 59.183 43.478 15.37 15.37 43.56 3.49
446 635 4.404640 AGCATTAGCCATGACATTGCTAT 58.595 39.130 18.91 8.97 43.56 2.97
447 636 4.831155 AGCATTAGCCATGACATTGCTATT 59.169 37.500 18.91 13.77 43.56 1.73
448 637 5.303589 AGCATTAGCCATGACATTGCTATTT 59.696 36.000 18.91 9.43 43.56 1.40
449 638 5.987347 GCATTAGCCATGACATTGCTATTTT 59.013 36.000 18.91 7.42 37.43 1.82
450 639 6.145048 GCATTAGCCATGACATTGCTATTTTC 59.855 38.462 18.91 8.50 37.43 2.29
451 640 7.431249 CATTAGCCATGACATTGCTATTTTCT 58.569 34.615 18.91 3.34 37.43 2.52
452 641 5.927281 AGCCATGACATTGCTATTTTCTT 57.073 34.783 12.11 0.00 32.56 2.52
453 642 5.899299 AGCCATGACATTGCTATTTTCTTC 58.101 37.500 12.11 0.00 32.56 2.87
454 643 5.655532 AGCCATGACATTGCTATTTTCTTCT 59.344 36.000 12.11 0.00 32.56 2.85
455 644 6.830324 AGCCATGACATTGCTATTTTCTTCTA 59.170 34.615 12.11 0.00 32.56 2.10
456 645 6.914757 GCCATGACATTGCTATTTTCTTCTAC 59.085 38.462 4.29 0.00 0.00 2.59
457 646 7.128331 CCATGACATTGCTATTTTCTTCTACG 58.872 38.462 0.00 0.00 0.00 3.51
458 647 7.011389 CCATGACATTGCTATTTTCTTCTACGA 59.989 37.037 0.00 0.00 0.00 3.43
487 696 7.719689 ACGAGTAAAAATGTAAAATGCATCG 57.280 32.000 0.00 0.00 0.00 3.84
491 700 9.123709 GAGTAAAAATGTAAAATGCATCGACAA 57.876 29.630 0.00 0.00 0.00 3.18
493 702 7.706281 AAAAATGTAAAATGCATCGACAACA 57.294 28.000 0.00 1.18 0.00 3.33
507 716 5.900339 TCGACAACATTGTAGAAAGACAC 57.100 39.130 5.24 0.00 42.43 3.67
508 717 5.597806 TCGACAACATTGTAGAAAGACACT 58.402 37.500 5.24 0.00 42.43 3.55
509 718 5.462068 TCGACAACATTGTAGAAAGACACTG 59.538 40.000 5.24 0.00 42.43 3.66
519 728 5.362717 TGTAGAAAGACACTGTTCCTCTCAA 59.637 40.000 0.00 0.00 0.00 3.02
521 730 5.745227 AGAAAGACACTGTTCCTCTCAAAA 58.255 37.500 0.00 0.00 0.00 2.44
522 731 6.360618 AGAAAGACACTGTTCCTCTCAAAAT 58.639 36.000 0.00 0.00 0.00 1.82
523 732 7.509546 AGAAAGACACTGTTCCTCTCAAAATA 58.490 34.615 0.00 0.00 0.00 1.40
524 733 7.442666 AGAAAGACACTGTTCCTCTCAAAATAC 59.557 37.037 0.00 0.00 0.00 1.89
525 734 6.174720 AGACACTGTTCCTCTCAAAATACA 57.825 37.500 0.00 0.00 0.00 2.29
526 735 6.226787 AGACACTGTTCCTCTCAAAATACAG 58.773 40.000 0.00 0.00 39.03 2.74
527 736 5.930135 ACACTGTTCCTCTCAAAATACAGT 58.070 37.500 0.00 0.00 44.94 3.55
528 737 7.015292 AGACACTGTTCCTCTCAAAATACAGTA 59.985 37.037 0.00 0.00 42.94 2.74
530 739 6.369065 CACTGTTCCTCTCAAAATACAGTACC 59.631 42.308 0.00 0.00 42.94 3.34
556 769 4.361253 CACTGACAGTGGAACCCG 57.639 61.111 25.22 0.14 42.35 5.28
561 774 0.541063 TGACAGTGGAACCCGAGCTA 60.541 55.000 0.00 0.00 37.80 3.32
566 779 0.035739 GTGGAACCCGAGCTAAACCA 59.964 55.000 0.00 0.00 0.00 3.67
576 789 1.586541 GCTAAACCAGCCACTTGCC 59.413 57.895 0.00 0.00 45.23 4.52
577 790 1.875963 CTAAACCAGCCACTTGCCG 59.124 57.895 0.00 0.00 42.71 5.69
578 791 1.586154 CTAAACCAGCCACTTGCCGG 61.586 60.000 0.00 0.00 43.70 6.13
601 814 1.165907 GCCCAGCTATTGCGTGCATA 61.166 55.000 0.00 0.00 45.42 3.14
603 816 0.870393 CCAGCTATTGCGTGCATAGG 59.130 55.000 0.00 0.00 45.42 2.57
627 840 1.420138 ACTCCCAGCCGAGAAAAAGAA 59.580 47.619 0.39 0.00 33.83 2.52
656 869 3.342377 ACCAAACCAAACCAAACCAAG 57.658 42.857 0.00 0.00 0.00 3.61
696 909 2.022129 CGCACAACCACTCTCGGAC 61.022 63.158 0.00 0.00 0.00 4.79
703 916 1.685765 CCACTCTCGGACCCATCCA 60.686 63.158 0.00 0.00 46.67 3.41
903 1436 0.758685 CGCCAATCTCTCTCCCTCCT 60.759 60.000 0.00 0.00 0.00 3.69
940 1474 1.302511 GTCTCCAAGCCGAGCCAAA 60.303 57.895 0.00 0.00 0.00 3.28
941 1475 1.302511 TCTCCAAGCCGAGCCAAAC 60.303 57.895 0.00 0.00 0.00 2.93
987 1538 2.276740 GGATCCAACCCTGCCTGG 59.723 66.667 6.95 0.00 0.00 4.45
1059 1610 2.825836 GCCCTCAGAATGCCGGTG 60.826 66.667 1.90 0.00 34.76 4.94
2112 2853 2.046604 GGGAACTACCGCGGCTTT 60.047 61.111 28.58 16.20 40.11 3.51
2347 3095 1.656818 CGGGCGGCAAACATCTCATT 61.657 55.000 12.47 0.00 0.00 2.57
2348 3096 0.101219 GGGCGGCAAACATCTCATTC 59.899 55.000 12.47 0.00 0.00 2.67
2349 3097 0.101219 GGCGGCAAACATCTCATTCC 59.899 55.000 3.07 0.00 0.00 3.01
2350 3098 0.248215 GCGGCAAACATCTCATTCCG 60.248 55.000 0.00 0.00 38.51 4.30
2351 3099 1.368641 CGGCAAACATCTCATTCCGA 58.631 50.000 0.00 0.00 37.79 4.55
2418 3185 4.097863 GTTGGTTGCGGCCGTAGC 62.098 66.667 28.70 24.85 38.76 3.58
2427 3194 1.944676 CGGCCGTAGCAGTTCGATC 60.945 63.158 19.50 0.00 42.56 3.69
2544 3316 0.035630 AGCCTCCTTTGCTAGCTGTG 60.036 55.000 17.23 5.42 37.28 3.66
2545 3317 0.322008 GCCTCCTTTGCTAGCTGTGT 60.322 55.000 17.23 0.00 0.00 3.72
2556 3329 3.133003 TGCTAGCTGTGTTTCCCTCTATC 59.867 47.826 17.23 0.00 0.00 2.08
2560 3333 4.521146 AGCTGTGTTTCCCTCTATCAATG 58.479 43.478 0.00 0.00 0.00 2.82
2586 3359 2.100605 AACCGAGAGCCTTTGTGATC 57.899 50.000 0.00 0.00 0.00 2.92
2587 3360 1.270907 ACCGAGAGCCTTTGTGATCT 58.729 50.000 0.00 0.00 0.00 2.75
2588 3361 2.457598 ACCGAGAGCCTTTGTGATCTA 58.542 47.619 0.00 0.00 0.00 1.98
2589 3362 2.166664 ACCGAGAGCCTTTGTGATCTAC 59.833 50.000 0.00 0.00 0.00 2.59
2590 3363 2.428890 CCGAGAGCCTTTGTGATCTACT 59.571 50.000 0.00 0.00 0.00 2.57
2591 3364 3.632604 CCGAGAGCCTTTGTGATCTACTA 59.367 47.826 0.00 0.00 0.00 1.82
2592 3365 4.498345 CCGAGAGCCTTTGTGATCTACTAC 60.498 50.000 0.00 0.00 0.00 2.73
2593 3366 4.336993 CGAGAGCCTTTGTGATCTACTACT 59.663 45.833 0.00 0.00 0.00 2.57
2594 3367 5.504994 CGAGAGCCTTTGTGATCTACTACTC 60.505 48.000 0.00 0.00 0.00 2.59
2595 3368 4.647399 AGAGCCTTTGTGATCTACTACTCC 59.353 45.833 0.00 0.00 0.00 3.85
2596 3369 4.615513 AGCCTTTGTGATCTACTACTCCT 58.384 43.478 0.00 0.00 0.00 3.69
2597 3370 4.647399 AGCCTTTGTGATCTACTACTCCTC 59.353 45.833 0.00 0.00 0.00 3.71
2598 3371 4.202172 GCCTTTGTGATCTACTACTCCTCC 60.202 50.000 0.00 0.00 0.00 4.30
2601 3374 4.440826 TGTGATCTACTACTCCTCCCTC 57.559 50.000 0.00 0.00 0.00 4.30
2617 3397 4.547671 CTCCCTCCTACTACTCCATTTCA 58.452 47.826 0.00 0.00 0.00 2.69
2638 3418 6.431198 TCAAGTTTGACCTTTGTAGAACAC 57.569 37.500 0.00 0.00 31.01 3.32
2639 3419 5.941058 TCAAGTTTGACCTTTGTAGAACACA 59.059 36.000 0.00 0.00 30.95 3.72
2640 3420 6.431543 TCAAGTTTGACCTTTGTAGAACACAA 59.568 34.615 0.00 0.00 37.55 3.33
2684 3492 4.820897 AGTACTCATTTGCGATTGAGACA 58.179 39.130 25.69 13.77 41.53 3.41
2685 3493 5.423015 AGTACTCATTTGCGATTGAGACAT 58.577 37.500 25.69 11.15 41.53 3.06
2688 3496 3.011818 TCATTTGCGATTGAGACATGCT 58.988 40.909 0.00 0.00 0.00 3.79
2689 3497 3.441222 TCATTTGCGATTGAGACATGCTT 59.559 39.130 0.00 0.00 0.00 3.91
2690 3498 3.921119 TTTGCGATTGAGACATGCTTT 57.079 38.095 0.00 0.00 0.00 3.51
2692 3500 3.206034 TGCGATTGAGACATGCTTTTG 57.794 42.857 0.00 0.00 0.00 2.44
2730 3561 7.019656 AGGATAAACCAAAATCCAAAGCATT 57.980 32.000 4.31 0.00 43.55 3.56
2744 3575 3.942796 GCATTATTGCCATGCGACA 57.057 47.368 0.00 0.00 43.38 4.35
2766 3613 3.302365 GCTTTTGCAAATGGTAGCAGA 57.698 42.857 22.61 2.15 46.58 4.26
2767 3614 3.652274 GCTTTTGCAAATGGTAGCAGAA 58.348 40.909 22.61 1.49 46.58 3.02
2768 3615 4.057432 GCTTTTGCAAATGGTAGCAGAAA 58.943 39.130 22.61 1.03 46.58 2.52
2769 3616 4.084380 GCTTTTGCAAATGGTAGCAGAAAC 60.084 41.667 22.61 3.43 46.58 2.78
2770 3617 2.987413 TGCAAATGGTAGCAGAAACG 57.013 45.000 0.00 0.00 35.51 3.60
2771 3618 2.499197 TGCAAATGGTAGCAGAAACGA 58.501 42.857 0.00 0.00 35.51 3.85
2772 3619 2.225491 TGCAAATGGTAGCAGAAACGAC 59.775 45.455 0.00 0.00 35.51 4.34
2773 3620 2.484264 GCAAATGGTAGCAGAAACGACT 59.516 45.455 0.00 0.00 0.00 4.18
2774 3621 3.667960 GCAAATGGTAGCAGAAACGACTG 60.668 47.826 0.00 0.00 40.43 3.51
2775 3622 3.402628 AATGGTAGCAGAAACGACTGT 57.597 42.857 0.00 0.00 39.73 3.55
2776 3623 2.433868 TGGTAGCAGAAACGACTGTC 57.566 50.000 0.00 0.00 39.73 3.51
2777 3624 1.000506 TGGTAGCAGAAACGACTGTCC 59.999 52.381 1.55 2.11 39.73 4.02
2807 3670 4.320608 GGTTTTCAGATGAACCAAAGCA 57.679 40.909 10.11 0.00 43.75 3.91
2867 3730 4.705482 AACCCTGCAAGCAAGGTT 57.295 50.000 19.57 19.57 43.62 3.50
2902 3770 3.632145 TGAAGGAAAAGGACTTGTGAAGC 59.368 43.478 0.00 0.00 0.00 3.86
2977 3855 2.118076 AATGGCAGGTGTGGTGGG 59.882 61.111 0.00 0.00 0.00 4.61
2994 3873 3.525545 GGGAGTACGGCCGGTCTC 61.526 72.222 31.76 30.90 0.00 3.36
2995 3874 3.525545 GGAGTACGGCCGGTCTCC 61.526 72.222 36.45 36.45 36.49 3.71
2996 3875 3.525545 GAGTACGGCCGGTCTCCC 61.526 72.222 31.76 11.87 0.00 4.30
2997 3876 4.057943 AGTACGGCCGGTCTCCCT 62.058 66.667 31.76 9.01 0.00 4.20
2998 3877 3.834799 GTACGGCCGGTCTCCCTG 61.835 72.222 31.76 0.00 0.00 4.45
3060 3955 4.082523 GCGAGGCCAGCACCAGTA 62.083 66.667 16.97 0.00 34.19 2.74
3121 4016 1.304962 TGAGCCTAGCGTTGGAGGA 60.305 57.895 0.00 0.00 34.46 3.71
3137 4059 2.046285 GGAGGTGTTGGGATTGGCG 61.046 63.158 0.00 0.00 0.00 5.69
3138 4060 2.676471 AGGTGTTGGGATTGGCGC 60.676 61.111 0.00 0.00 0.00 6.53
3139 4061 3.758931 GGTGTTGGGATTGGCGCC 61.759 66.667 22.73 22.73 0.00 6.53
3140 4062 3.758931 GTGTTGGGATTGGCGCCC 61.759 66.667 26.77 8.57 46.22 6.13
3154 4076 2.436824 GCCCAGCGACTTCCTTCC 60.437 66.667 0.00 0.00 0.00 3.46
3155 4077 2.960688 GCCCAGCGACTTCCTTCCT 61.961 63.158 0.00 0.00 0.00 3.36
3156 4078 1.679898 CCCAGCGACTTCCTTCCTT 59.320 57.895 0.00 0.00 0.00 3.36
3157 4079 0.391793 CCCAGCGACTTCCTTCCTTC 60.392 60.000 0.00 0.00 0.00 3.46
3158 4080 0.391793 CCAGCGACTTCCTTCCTTCC 60.392 60.000 0.00 0.00 0.00 3.46
3159 4081 0.610687 CAGCGACTTCCTTCCTTCCT 59.389 55.000 0.00 0.00 0.00 3.36
3160 4082 0.899019 AGCGACTTCCTTCCTTCCTC 59.101 55.000 0.00 0.00 0.00 3.71
3161 4083 0.458716 GCGACTTCCTTCCTTCCTCG 60.459 60.000 0.00 0.00 0.00 4.63
3162 4084 0.173708 CGACTTCCTTCCTTCCTCGG 59.826 60.000 0.00 0.00 0.00 4.63
3163 4085 0.108089 GACTTCCTTCCTTCCTCGGC 60.108 60.000 0.00 0.00 0.00 5.54
3294 4229 5.070580 ACCTTTCTTTCGAAAAGGAGAGAGA 59.929 40.000 26.46 10.27 38.58 3.10
3295 4230 5.992217 CCTTTCTTTCGAAAAGGAGAGAGAA 59.008 40.000 18.42 10.15 38.58 2.87
3296 4231 6.147000 CCTTTCTTTCGAAAAGGAGAGAGAAG 59.853 42.308 18.42 9.74 38.34 2.85
3297 4232 4.561105 TCTTTCGAAAAGGAGAGAGAAGC 58.439 43.478 12.41 0.00 0.00 3.86
3298 4233 2.638556 TCGAAAAGGAGAGAGAAGCG 57.361 50.000 0.00 0.00 0.00 4.68
3299 4234 1.202582 TCGAAAAGGAGAGAGAAGCGG 59.797 52.381 0.00 0.00 0.00 5.52
3300 4235 1.067495 CGAAAAGGAGAGAGAAGCGGT 60.067 52.381 0.00 0.00 0.00 5.68
3301 4236 2.610727 CGAAAAGGAGAGAGAAGCGGTT 60.611 50.000 0.00 0.00 0.00 4.44
3302 4237 2.753055 AAAGGAGAGAGAAGCGGTTC 57.247 50.000 19.40 19.40 0.00 3.62
3303 4238 0.528470 AAGGAGAGAGAAGCGGTTCG 59.472 55.000 20.64 0.00 37.79 3.95
3304 4239 0.609681 AGGAGAGAGAAGCGGTTCGT 60.610 55.000 20.64 12.77 37.79 3.85
3305 4240 0.244178 GGAGAGAGAAGCGGTTCGTT 59.756 55.000 20.64 13.23 37.79 3.85
3306 4241 1.336980 GGAGAGAGAAGCGGTTCGTTT 60.337 52.381 20.64 10.80 37.79 3.60
3307 4242 2.405172 GAGAGAGAAGCGGTTCGTTTT 58.595 47.619 20.64 8.96 37.79 2.43
3308 4243 2.405172 AGAGAGAAGCGGTTCGTTTTC 58.595 47.619 20.64 13.03 37.79 2.29
3309 4244 1.124477 GAGAGAAGCGGTTCGTTTTCG 59.876 52.381 20.64 0.00 45.64 3.46
3310 4245 0.163146 GAGAAGCGGTTCGTTTTCGG 59.837 55.000 20.64 0.00 44.25 4.30
3311 4246 0.249573 AGAAGCGGTTCGTTTTCGGA 60.250 50.000 20.64 0.00 44.25 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.287103 ACGCTCGGTCAAACTTTCTTTC 59.713 45.455 0.00 0.00 0.00 2.62
22 23 4.151867 AGAATTACGCTCGGTCAAACTTTC 59.848 41.667 0.00 0.00 0.00 2.62
32 33 5.975344 TGAGTAATACAAGAATTACGCTCGG 59.025 40.000 10.41 0.00 43.87 4.63
41 42 7.119116 TGCGTCAAACATGAGTAATACAAGAAT 59.881 33.333 0.00 0.00 0.00 2.40
81 82 4.053295 CAAAACTTGCCAGGAAATGACTG 58.947 43.478 0.00 0.00 35.74 3.51
88 89 3.025322 TCTTCCAAAACTTGCCAGGAA 57.975 42.857 0.00 0.00 36.92 3.36
121 122 0.258774 AACCCAAGCCACACAACTCT 59.741 50.000 0.00 0.00 0.00 3.24
122 123 1.111277 AAACCCAAGCCACACAACTC 58.889 50.000 0.00 0.00 0.00 3.01
138 139 6.152379 GTCCAGAAGTTCATTTGGATCAAAC 58.848 40.000 13.71 0.75 41.41 2.93
139 140 5.832595 TGTCCAGAAGTTCATTTGGATCAAA 59.167 36.000 13.71 0.00 41.41 2.69
140 141 5.384336 TGTCCAGAAGTTCATTTGGATCAA 58.616 37.500 13.71 3.26 41.41 2.57
141 142 4.984295 TGTCCAGAAGTTCATTTGGATCA 58.016 39.130 13.71 11.08 41.41 2.92
159 160 6.801539 TCAAGAATTACACTGACAATGTCC 57.198 37.500 11.24 0.00 0.00 4.02
161 162 8.077991 CACAATCAAGAATTACACTGACAATGT 58.922 33.333 0.00 0.00 0.00 2.71
163 164 8.394971 TCACAATCAAGAATTACACTGACAAT 57.605 30.769 0.00 0.00 0.00 2.71
167 168 9.725019 ATTACTCACAATCAAGAATTACACTGA 57.275 29.630 0.00 0.00 0.00 3.41
169 170 8.454106 GCATTACTCACAATCAAGAATTACACT 58.546 33.333 0.00 0.00 0.00 3.55
185 193 9.944663 TTTTCGGATAATATTTGCATTACTCAC 57.055 29.630 0.00 0.00 0.00 3.51
216 224 1.464997 CGCAAGAGTTCAAACCCTAGC 59.535 52.381 0.00 0.00 43.02 3.42
236 265 9.360093 GATGTATACATATAGCACTTCCTTGTC 57.640 37.037 18.28 0.00 36.57 3.18
262 291 8.498192 CAAAGGATGTGCAAAAATATCGATAG 57.502 34.615 11.41 0.00 0.00 2.08
282 325 5.812127 GGCCATTTCTACAAAATAGCAAAGG 59.188 40.000 0.00 0.00 0.00 3.11
288 331 7.630242 TTCTCTGGCCATTTCTACAAAATAG 57.370 36.000 5.51 0.00 0.00 1.73
379 568 9.439500 CAAATTGATCAAGAAAACATTGGGTAT 57.561 29.630 14.54 0.00 0.00 2.73
380 569 7.877097 CCAAATTGATCAAGAAAACATTGGGTA 59.123 33.333 14.54 0.00 32.07 3.69
381 570 6.711645 CCAAATTGATCAAGAAAACATTGGGT 59.288 34.615 14.54 0.00 32.07 4.51
383 572 6.604930 GCCAAATTGATCAAGAAAACATTGG 58.395 36.000 14.54 16.87 37.29 3.16
384 573 6.073657 ACGCCAAATTGATCAAGAAAACATTG 60.074 34.615 14.54 9.34 0.00 2.82
385 574 5.990996 ACGCCAAATTGATCAAGAAAACATT 59.009 32.000 14.54 0.00 0.00 2.71
386 575 5.540911 ACGCCAAATTGATCAAGAAAACAT 58.459 33.333 14.54 0.00 0.00 2.71
387 576 4.942852 ACGCCAAATTGATCAAGAAAACA 58.057 34.783 14.54 0.00 0.00 2.83
389 578 5.465935 GGTACGCCAAATTGATCAAGAAAA 58.534 37.500 14.54 0.00 34.09 2.29
390 579 4.082463 GGGTACGCCAAATTGATCAAGAAA 60.082 41.667 14.54 0.00 36.17 2.52
391 580 3.442273 GGGTACGCCAAATTGATCAAGAA 59.558 43.478 14.54 0.00 36.17 2.52
392 581 3.013921 GGGTACGCCAAATTGATCAAGA 58.986 45.455 14.54 0.00 36.17 3.02
393 582 2.752354 TGGGTACGCCAAATTGATCAAG 59.248 45.455 14.54 1.10 36.17 3.02
394 583 2.796557 TGGGTACGCCAAATTGATCAA 58.203 42.857 11.26 11.26 36.17 2.57
395 584 2.498644 TGGGTACGCCAAATTGATCA 57.501 45.000 7.55 0.00 36.17 2.92
396 585 3.130340 ACATTGGGTACGCCAAATTGATC 59.870 43.478 16.60 0.00 36.26 2.92
397 586 3.096092 ACATTGGGTACGCCAAATTGAT 58.904 40.909 16.60 1.56 36.26 2.57
398 587 2.520069 ACATTGGGTACGCCAAATTGA 58.480 42.857 16.60 0.00 36.26 2.57
399 588 3.311486 AACATTGGGTACGCCAAATTG 57.689 42.857 16.60 14.00 36.26 2.32
401 590 3.556004 CCAAAACATTGGGTACGCCAAAT 60.556 43.478 16.60 5.09 38.95 2.32
402 591 2.224066 CCAAAACATTGGGTACGCCAAA 60.224 45.455 16.60 3.05 38.42 3.28
404 593 0.962489 CCAAAACATTGGGTACGCCA 59.038 50.000 7.55 3.19 38.42 5.69
405 594 1.201414 CTCCAAAACATTGGGTACGCC 59.799 52.381 7.55 0.31 42.32 5.68
406 595 1.402325 GCTCCAAAACATTGGGTACGC 60.402 52.381 7.69 2.35 42.32 4.42
407 596 1.883275 TGCTCCAAAACATTGGGTACG 59.117 47.619 7.69 0.00 42.32 3.67
408 597 4.535526 AATGCTCCAAAACATTGGGTAC 57.464 40.909 7.69 0.00 42.32 3.34
409 598 4.159506 GCTAATGCTCCAAAACATTGGGTA 59.840 41.667 7.69 0.00 42.32 3.69
410 599 3.055891 GCTAATGCTCCAAAACATTGGGT 60.056 43.478 7.69 0.00 42.32 4.51
411 600 3.524541 GCTAATGCTCCAAAACATTGGG 58.475 45.455 7.69 0.75 42.32 4.12
412 601 3.055963 TGGCTAATGCTCCAAAACATTGG 60.056 43.478 1.10 1.10 37.11 3.16
413 602 4.191033 TGGCTAATGCTCCAAAACATTG 57.809 40.909 0.00 0.00 37.11 2.82
414 603 4.467082 TCATGGCTAATGCTCCAAAACATT 59.533 37.500 0.00 0.00 39.69 2.71
415 604 4.025360 TCATGGCTAATGCTCCAAAACAT 58.975 39.130 0.00 0.00 39.59 2.71
416 605 3.193267 GTCATGGCTAATGCTCCAAAACA 59.807 43.478 0.00 0.00 39.59 2.83
417 606 3.193267 TGTCATGGCTAATGCTCCAAAAC 59.807 43.478 0.00 0.00 39.59 2.43
418 607 3.429492 TGTCATGGCTAATGCTCCAAAA 58.571 40.909 0.00 0.00 39.59 2.44
419 608 3.084536 TGTCATGGCTAATGCTCCAAA 57.915 42.857 0.00 0.00 39.59 3.28
420 609 2.804986 TGTCATGGCTAATGCTCCAA 57.195 45.000 0.00 0.00 39.59 3.53
421 610 2.953648 CAATGTCATGGCTAATGCTCCA 59.046 45.455 0.00 0.00 39.59 3.86
423 612 2.621998 AGCAATGTCATGGCTAATGCTC 59.378 45.455 13.36 0.00 38.16 4.26
424 613 2.662866 AGCAATGTCATGGCTAATGCT 58.337 42.857 13.36 15.93 37.80 3.79
425 614 4.778534 ATAGCAATGTCATGGCTAATGC 57.221 40.909 22.94 10.79 42.76 3.56
426 615 7.431249 AGAAAATAGCAATGTCATGGCTAATG 58.569 34.615 22.94 1.11 42.76 1.90
427 616 7.592885 AGAAAATAGCAATGTCATGGCTAAT 57.407 32.000 22.94 13.97 42.76 1.73
428 617 7.340232 AGAAGAAAATAGCAATGTCATGGCTAA 59.660 33.333 22.94 9.28 42.76 3.09
429 618 6.830324 AGAAGAAAATAGCAATGTCATGGCTA 59.170 34.615 21.69 21.69 43.55 3.93
430 619 5.655532 AGAAGAAAATAGCAATGTCATGGCT 59.344 36.000 18.76 18.76 41.51 4.75
432 621 7.011389 TCGTAGAAGAAAATAGCAATGTCATGG 59.989 37.037 0.00 0.00 0.00 3.66
433 622 7.909267 TCGTAGAAGAAAATAGCAATGTCATG 58.091 34.615 0.00 0.00 0.00 3.07
434 623 8.492673 TTCGTAGAAGAAAATAGCAATGTCAT 57.507 30.769 0.00 0.00 45.90 3.06
435 624 7.899178 TTCGTAGAAGAAAATAGCAATGTCA 57.101 32.000 0.00 0.00 45.90 3.58
440 629 9.955208 TCGTATATTCGTAGAAGAAAATAGCAA 57.045 29.630 1.52 0.00 45.90 3.91
441 630 9.608617 CTCGTATATTCGTAGAAGAAAATAGCA 57.391 33.333 1.52 0.00 45.90 3.49
442 631 9.609950 ACTCGTATATTCGTAGAAGAAAATAGC 57.390 33.333 1.52 0.00 45.90 2.97
473 662 6.389091 ACAATGTTGTCGATGCATTTTACAT 58.611 32.000 0.00 4.52 36.50 2.29
474 663 5.767269 ACAATGTTGTCGATGCATTTTACA 58.233 33.333 0.00 3.02 36.50 2.41
482 691 5.107104 TGTCTTTCTACAATGTTGTCGATGC 60.107 40.000 0.99 0.00 42.35 3.91
485 694 5.462068 CAGTGTCTTTCTACAATGTTGTCGA 59.538 40.000 0.99 0.00 39.84 4.20
493 702 6.042093 TGAGAGGAACAGTGTCTTTCTACAAT 59.958 38.462 0.00 0.00 0.00 2.71
507 716 6.702329 AGGTACTGTATTTTGAGAGGAACAG 58.298 40.000 0.00 0.00 37.18 3.16
508 717 6.681729 AGGTACTGTATTTTGAGAGGAACA 57.318 37.500 0.00 0.00 37.18 3.18
509 718 7.224949 GCATAGGTACTGTATTTTGAGAGGAAC 59.775 40.741 0.00 0.00 41.52 3.62
519 728 6.610020 TCAGTGGTAGCATAGGTACTGTATTT 59.390 38.462 0.00 0.00 41.52 1.40
521 730 5.535406 GTCAGTGGTAGCATAGGTACTGTAT 59.465 44.000 0.00 0.00 41.52 2.29
522 731 4.885907 GTCAGTGGTAGCATAGGTACTGTA 59.114 45.833 0.00 0.00 41.52 2.74
523 732 3.700038 GTCAGTGGTAGCATAGGTACTGT 59.300 47.826 0.00 0.00 41.52 3.55
524 733 3.699538 TGTCAGTGGTAGCATAGGTACTG 59.300 47.826 0.00 0.00 41.52 2.74
525 734 3.954904 CTGTCAGTGGTAGCATAGGTACT 59.045 47.826 0.00 0.00 46.37 2.73
526 735 3.700038 ACTGTCAGTGGTAGCATAGGTAC 59.300 47.826 4.21 0.00 36.00 3.34
527 736 3.699538 CACTGTCAGTGGTAGCATAGGTA 59.300 47.826 23.09 0.00 42.35 3.08
528 737 2.497675 CACTGTCAGTGGTAGCATAGGT 59.502 50.000 23.09 0.00 42.35 3.08
579 792 2.124570 ACGCAATAGCTGGGCCAG 60.125 61.111 29.44 29.44 41.66 4.85
580 793 2.438254 CACGCAATAGCTGGGCCA 60.438 61.111 5.85 5.85 41.66 5.36
581 794 3.892581 GCACGCAATAGCTGGGCC 61.893 66.667 0.00 0.00 41.66 5.80
582 795 1.165907 TATGCACGCAATAGCTGGGC 61.166 55.000 0.00 0.00 41.66 5.36
583 796 0.870393 CTATGCACGCAATAGCTGGG 59.130 55.000 0.00 0.00 43.53 4.45
584 797 0.870393 CCTATGCACGCAATAGCTGG 59.130 55.000 0.00 0.00 39.10 4.85
585 798 0.236711 GCCTATGCACGCAATAGCTG 59.763 55.000 0.00 0.00 36.53 4.24
586 799 0.886490 GGCCTATGCACGCAATAGCT 60.886 55.000 0.00 0.00 40.13 3.32
587 800 1.576421 GGCCTATGCACGCAATAGC 59.424 57.895 0.00 0.00 40.13 2.97
588 801 0.534877 TGGGCCTATGCACGCAATAG 60.535 55.000 4.53 0.00 46.93 1.73
589 802 1.529309 TGGGCCTATGCACGCAATA 59.471 52.632 4.53 0.00 46.93 1.90
590 803 2.275089 TGGGCCTATGCACGCAAT 59.725 55.556 4.53 0.00 46.93 3.56
627 840 3.777522 TGGTTTGGTTTGGTTTCATTCCT 59.222 39.130 0.00 0.00 0.00 3.36
696 909 2.065470 CTGGAGCCTGGATGGATGGG 62.065 65.000 0.00 0.00 38.35 4.00
703 916 3.859414 GCGAGCTGGAGCCTGGAT 61.859 66.667 0.00 0.00 43.38 3.41
838 1091 3.473647 CAGGCTGGATCCCGCTGA 61.474 66.667 25.11 0.00 0.00 4.26
871 1124 0.404040 ATTGGCGGGTGTATATGGGG 59.596 55.000 0.00 0.00 0.00 4.96
903 1436 0.693092 CCCGGGAGATAAGGTGGGAA 60.693 60.000 18.48 0.00 39.03 3.97
976 1527 4.115199 GATCGGCCAGGCAGGGTT 62.115 66.667 15.19 0.00 38.09 4.11
1893 2608 4.988716 AGGCTGTCGGACGACCCA 62.989 66.667 20.57 3.85 43.97 4.51
2112 2853 1.293179 CACCGAGGCTGACATGACA 59.707 57.895 0.00 0.00 0.00 3.58
2331 3072 0.248215 CGGAATGAGATGTTTGCCGC 60.248 55.000 0.00 0.00 0.00 6.53
2347 3095 1.153901 GTTTGCTCGTCGGATCGGA 60.154 57.895 0.00 0.00 0.00 4.55
2348 3096 1.153823 AGTTTGCTCGTCGGATCGG 60.154 57.895 0.00 0.00 0.00 4.18
2349 3097 0.732880 ACAGTTTGCTCGTCGGATCG 60.733 55.000 0.00 0.00 0.00 3.69
2350 3098 1.918609 GTACAGTTTGCTCGTCGGATC 59.081 52.381 0.00 0.00 0.00 3.36
2351 3099 1.271379 TGTACAGTTTGCTCGTCGGAT 59.729 47.619 0.00 0.00 0.00 4.18
2418 3185 0.933097 CCATCGCCAAGATCGAACTG 59.067 55.000 0.00 0.00 39.54 3.16
2427 3194 2.981859 ACTACTAACCCATCGCCAAG 57.018 50.000 0.00 0.00 0.00 3.61
2544 3316 7.976175 GGTTTCATTTCATTGATAGAGGGAAAC 59.024 37.037 0.00 0.00 39.50 2.78
2545 3317 7.148086 CGGTTTCATTTCATTGATAGAGGGAAA 60.148 37.037 0.00 0.00 32.66 3.13
2556 3329 3.441572 AGGCTCTCGGTTTCATTTCATTG 59.558 43.478 0.00 0.00 0.00 2.82
2560 3333 3.253432 ACAAAGGCTCTCGGTTTCATTTC 59.747 43.478 0.00 0.00 0.00 2.17
2586 3359 5.157395 AGTAGTAGGAGGGAGGAGTAGTAG 58.843 50.000 0.00 0.00 0.00 2.57
2587 3360 5.154418 GAGTAGTAGGAGGGAGGAGTAGTA 58.846 50.000 0.00 0.00 0.00 1.82
2588 3361 3.975982 GAGTAGTAGGAGGGAGGAGTAGT 59.024 52.174 0.00 0.00 0.00 2.73
2589 3362 3.328637 GGAGTAGTAGGAGGGAGGAGTAG 59.671 56.522 0.00 0.00 0.00 2.57
2590 3363 3.311928 TGGAGTAGTAGGAGGGAGGAGTA 60.312 52.174 0.00 0.00 0.00 2.59
2591 3364 2.137702 GGAGTAGTAGGAGGGAGGAGT 58.862 57.143 0.00 0.00 0.00 3.85
2592 3365 2.136863 TGGAGTAGTAGGAGGGAGGAG 58.863 57.143 0.00 0.00 0.00 3.69
2593 3366 2.298619 TGGAGTAGTAGGAGGGAGGA 57.701 55.000 0.00 0.00 0.00 3.71
2594 3367 3.621682 AATGGAGTAGTAGGAGGGAGG 57.378 52.381 0.00 0.00 0.00 4.30
2595 3368 4.547671 TGAAATGGAGTAGTAGGAGGGAG 58.452 47.826 0.00 0.00 0.00 4.30
2596 3369 4.620086 TGAAATGGAGTAGTAGGAGGGA 57.380 45.455 0.00 0.00 0.00 4.20
2597 3370 4.717280 ACTTGAAATGGAGTAGTAGGAGGG 59.283 45.833 0.00 0.00 0.00 4.30
2598 3371 5.941555 ACTTGAAATGGAGTAGTAGGAGG 57.058 43.478 0.00 0.00 0.00 4.30
2601 3374 6.371825 GGTCAAACTTGAAATGGAGTAGTAGG 59.628 42.308 0.00 0.00 39.21 3.18
2617 3397 6.827586 TTGTGTTCTACAAAGGTCAAACTT 57.172 33.333 0.00 0.00 45.86 2.66
2638 3418 9.429359 ACTACTAGTTCATCTTTTCACATCTTG 57.571 33.333 0.00 0.00 0.00 3.02
2684 3492 3.258872 TCTGCTACCATTTGCAAAAGCAT 59.741 39.130 27.62 13.42 39.09 3.79
2685 3493 2.627221 TCTGCTACCATTTGCAAAAGCA 59.373 40.909 26.39 26.39 38.81 3.91
2688 3496 3.495331 TCCTCTGCTACCATTTGCAAAA 58.505 40.909 17.19 0.00 38.81 2.44
2689 3497 3.153369 TCCTCTGCTACCATTTGCAAA 57.847 42.857 15.44 15.44 38.81 3.68
2690 3498 2.877097 TCCTCTGCTACCATTTGCAA 57.123 45.000 0.00 0.00 38.81 4.08
2692 3500 4.036852 GGTTTATCCTCTGCTACCATTTGC 59.963 45.833 0.00 0.00 0.00 3.68
2693 3501 5.192927 TGGTTTATCCTCTGCTACCATTTG 58.807 41.667 0.00 0.00 37.07 2.32
2694 3502 5.450818 TGGTTTATCCTCTGCTACCATTT 57.549 39.130 0.00 0.00 37.07 2.32
2697 3505 4.919774 TTTGGTTTATCCTCTGCTACCA 57.080 40.909 0.00 0.00 37.07 3.25
2698 3506 5.299531 GGATTTTGGTTTATCCTCTGCTACC 59.700 44.000 0.00 0.00 37.83 3.18
2699 3507 5.885912 TGGATTTTGGTTTATCCTCTGCTAC 59.114 40.000 0.00 0.00 40.80 3.58
2700 3508 6.073447 TGGATTTTGGTTTATCCTCTGCTA 57.927 37.500 0.00 0.00 40.80 3.49
2701 3509 4.934356 TGGATTTTGGTTTATCCTCTGCT 58.066 39.130 0.00 0.00 40.80 4.24
2730 3561 1.391577 AAGCATGTCGCATGGCAATA 58.608 45.000 17.53 0.00 46.13 1.90
2744 3575 3.258872 TCTGCTACCATTTGCAAAAGCAT 59.741 39.130 27.62 13.42 39.09 3.79
2758 3589 1.000506 TGGACAGTCGTTTCTGCTACC 59.999 52.381 0.00 0.00 38.84 3.18
2764 3611 2.093658 ACAGTTGTGGACAGTCGTTTCT 60.094 45.455 0.00 0.00 0.00 2.52
2765 3612 2.030457 CACAGTTGTGGACAGTCGTTTC 59.970 50.000 4.34 0.00 42.10 2.78
2766 3613 2.006888 CACAGTTGTGGACAGTCGTTT 58.993 47.619 4.34 0.00 42.10 3.60
2767 3614 1.651987 CACAGTTGTGGACAGTCGTT 58.348 50.000 4.34 0.00 42.10 3.85
2768 3615 3.362581 CACAGTTGTGGACAGTCGT 57.637 52.632 4.34 0.00 42.10 4.34
2777 3624 4.898829 TCATCTGAAAACCACAGTTGTG 57.101 40.909 5.28 5.28 45.23 3.33
2787 3634 4.687483 CCATGCTTTGGTTCATCTGAAAAC 59.313 41.667 0.00 0.00 40.99 2.43
2824 3687 1.062488 ACCAGTTGCTCCTCCAAGGT 61.062 55.000 0.00 0.00 36.53 3.50
2902 3770 2.434359 GCGTTCCCTGTTCCTCCG 60.434 66.667 0.00 0.00 0.00 4.63
2931 3799 1.611419 CACCCCTCATGCACCTCAT 59.389 57.895 0.00 0.00 35.31 2.90
2932 3800 2.605607 CCACCCCTCATGCACCTCA 61.606 63.158 0.00 0.00 0.00 3.86
2977 3855 3.525545 GAGACCGGCCGTACTCCC 61.526 72.222 27.32 12.45 0.00 4.30
3057 3952 1.305802 TCCCATCGCACACCCTACT 60.306 57.895 0.00 0.00 0.00 2.57
3060 3955 2.607750 ACTCCCATCGCACACCCT 60.608 61.111 0.00 0.00 0.00 4.34
3121 4016 2.676471 GCGCCAATCCCAACACCT 60.676 61.111 0.00 0.00 0.00 4.00
3137 4059 2.436824 GGAAGGAAGTCGCTGGGC 60.437 66.667 0.00 0.00 0.00 5.36
3138 4060 0.391793 GAAGGAAGGAAGTCGCTGGG 60.392 60.000 0.00 0.00 0.00 4.45
3139 4061 0.391793 GGAAGGAAGGAAGTCGCTGG 60.392 60.000 0.00 0.00 0.00 4.85
3140 4062 0.610687 AGGAAGGAAGGAAGTCGCTG 59.389 55.000 0.00 0.00 0.00 5.18
3141 4063 0.899019 GAGGAAGGAAGGAAGTCGCT 59.101 55.000 0.00 0.00 0.00 4.93
3142 4064 0.458716 CGAGGAAGGAAGGAAGTCGC 60.459 60.000 0.00 0.00 0.00 5.19
3143 4065 0.173708 CCGAGGAAGGAAGGAAGTCG 59.826 60.000 0.00 0.00 0.00 4.18
3144 4066 0.108089 GCCGAGGAAGGAAGGAAGTC 60.108 60.000 0.00 0.00 0.00 3.01
3145 4067 0.545548 AGCCGAGGAAGGAAGGAAGT 60.546 55.000 0.00 0.00 0.00 3.01
3146 4068 0.107945 CAGCCGAGGAAGGAAGGAAG 60.108 60.000 0.00 0.00 0.00 3.46
3147 4069 0.836400 ACAGCCGAGGAAGGAAGGAA 60.836 55.000 0.00 0.00 0.00 3.36
3148 4070 1.229209 ACAGCCGAGGAAGGAAGGA 60.229 57.895 0.00 0.00 0.00 3.36
3149 4071 1.219393 GACAGCCGAGGAAGGAAGG 59.781 63.158 0.00 0.00 0.00 3.46
3150 4072 1.153745 CGACAGCCGAGGAAGGAAG 60.154 63.158 0.00 0.00 41.76 3.46
3151 4073 1.874345 GACGACAGCCGAGGAAGGAA 61.874 60.000 0.00 0.00 41.76 3.36
3152 4074 2.282958 ACGACAGCCGAGGAAGGA 60.283 61.111 0.00 0.00 41.76 3.36
3153 4075 2.182030 GACGACAGCCGAGGAAGG 59.818 66.667 0.00 0.00 41.76 3.46
3154 4076 1.153939 CAGACGACAGCCGAGGAAG 60.154 63.158 0.00 0.00 41.76 3.46
3155 4077 2.962569 CAGACGACAGCCGAGGAA 59.037 61.111 0.00 0.00 41.76 3.36
3156 4078 3.749064 GCAGACGACAGCCGAGGA 61.749 66.667 0.00 0.00 41.76 3.71
3157 4079 3.691744 GAGCAGACGACAGCCGAGG 62.692 68.421 0.00 0.00 41.76 4.63
3158 4080 2.202544 GAGCAGACGACAGCCGAG 60.203 66.667 0.00 0.00 41.76 4.63
3159 4081 2.673341 AGAGCAGACGACAGCCGA 60.673 61.111 0.00 0.00 41.76 5.54
3160 4082 2.505777 CAGAGCAGACGACAGCCG 60.506 66.667 0.00 0.00 45.44 5.52
3161 4083 2.813042 GCAGAGCAGACGACAGCC 60.813 66.667 0.00 0.00 0.00 4.85
3162 4084 1.805134 GAGCAGAGCAGACGACAGC 60.805 63.158 0.00 0.00 0.00 4.40
3163 4085 1.153862 GGAGCAGAGCAGACGACAG 60.154 63.158 0.00 0.00 0.00 3.51
3263 4198 2.074547 TCGAAAGAAAGGTACAGCGG 57.925 50.000 0.00 0.00 37.03 5.52
3294 4229 1.824272 CGTCCGAAAACGAACCGCTT 61.824 55.000 0.00 0.00 45.37 4.68
3295 4230 2.305127 CGTCCGAAAACGAACCGCT 61.305 57.895 0.00 0.00 45.37 5.52
3296 4231 2.169327 CGTCCGAAAACGAACCGC 59.831 61.111 0.00 0.00 45.37 5.68
3297 4232 1.199859 CACGTCCGAAAACGAACCG 59.800 57.895 11.06 0.00 45.37 4.44
3298 4233 1.566077 CCACGTCCGAAAACGAACC 59.434 57.895 11.06 0.00 45.37 3.62


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

AutoCloner maintained by Alex Coulton.