Multiple sequence alignment - TraesCS1B01G206200

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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 TraesCS1B01G206200 chr1B 100.000 4656 0 0 1 4656 373139906 373144561 0.000000e+00 8599.0
1 TraesCS1B01G206200 chr1B 100.000 52 0 0 495 546 373140347 373140398 3.830000e-16 97.1
2 TraesCS1B01G206200 chr1B 100.000 52 0 0 442 493 373140400 373140451 3.830000e-16 97.1
3 TraesCS1B01G206200 chr1A 88.418 1606 110 36 3102 4654 345785920 345787502 0.000000e+00 1866.0
4 TraesCS1B01G206200 chr1A 88.715 1471 91 25 1656 3079 345784319 345785761 0.000000e+00 1727.0
5 TraesCS1B01G206200 chr1A 89.979 938 59 18 630 1546 345783311 345784234 0.000000e+00 1179.0
6 TraesCS1B01G206200 chr1A 90.196 510 34 7 1 495 345782638 345783146 0.000000e+00 651.0
7 TraesCS1B01G206200 chr1A 94.737 57 1 2 495 550 345783094 345783149 2.310000e-13 87.9
8 TraesCS1B01G206200 chr1A 96.078 51 2 0 1612 1662 345784255 345784305 2.990000e-12 84.2
9 TraesCS1B01G206200 chr1D 88.617 1555 98 40 3152 4655 273813868 273815394 0.000000e+00 1818.0
10 TraesCS1B01G206200 chr1D 88.954 1358 101 31 1755 3097 273812443 273813766 0.000000e+00 1631.0
11 TraesCS1B01G206200 chr1D 87.141 1252 64 43 495 1652 273811126 273812374 0.000000e+00 1330.0
12 TraesCS1B01G206200 chr1D 94.929 493 20 3 1 493 273810690 273811177 0.000000e+00 767.0


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 TraesCS1B01G206200 chr1B 373139906 373144561 4655 False 8599.000000 8599 100.000000 1 4656 1 chr1B.!!$F1 4655
1 TraesCS1B01G206200 chr1A 345782638 345787502 4864 False 932.516667 1866 91.353833 1 4654 6 chr1A.!!$F1 4653
2 TraesCS1B01G206200 chr1D 273810690 273815394 4704 False 1386.500000 1818 89.910250 1 4655 4 chr1D.!!$F1 4654

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
110 114 0.878416 TTTGAATTCTTGCCCGTCCG 59.122 50.0 7.05 0.00 0.00 4.79 F
1777 1970 0.179156 GCTGCTTGTATGTGCGCAAT 60.179 50.0 14.00 11.02 31.24 3.56 F
2068 2269 1.011451 GCTCACTGTCCAACTCGCTC 61.011 60.0 0.00 0.00 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 2135 0.108138 CCCAGTCGCTCGAGGAATTT 60.108 55.0 15.58 0.0 0.00 1.82 R
3340 3713 0.179084 AGGAACCGTGCATACCATCG 60.179 55.0 0.00 0.0 0.00 3.84 R
3728 4101 0.461961 CTTCTAGAGAAGGGGGCACG 59.538 60.0 10.88 0.0 45.79 5.34 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
25 26 8.679288 CTTTTGGATGAACTATGCTTGTTTAG 57.321 34.615 0.00 0.00 0.00 1.85
107 111 3.810310 TTTGTTTGAATTCTTGCCCGT 57.190 38.095 7.05 0.00 0.00 5.28
110 114 0.878416 TTTGAATTCTTGCCCGTCCG 59.122 50.000 7.05 0.00 0.00 4.79
178 184 2.225675 TGGAGGACACCCTAACATACCA 60.226 50.000 0.00 0.00 44.53 3.25
180 186 3.118371 GGAGGACACCCTAACATACCAAG 60.118 52.174 0.00 0.00 44.53 3.61
190 196 6.119536 CCCTAACATACCAAGTTAGCATTCA 58.880 40.000 7.40 0.00 44.37 2.57
197 203 9.407380 ACATACCAAGTTAGCATTCAATTATCA 57.593 29.630 0.00 0.00 0.00 2.15
283 289 6.757897 TCACTTGTGATAAATCCCAATGAC 57.242 37.500 0.00 0.00 0.00 3.06
351 367 9.793259 AATTTTAGACTTGATGTTGGAGTAGAA 57.207 29.630 0.00 0.00 0.00 2.10
498 514 9.420118 AGTTAGGTTTTATGATTTATGATGCCA 57.580 29.630 0.00 0.00 0.00 4.92
509 525 6.016024 TGATTTATGATGCCATAACTCAAGGC 60.016 38.462 12.63 0.00 44.62 4.35
528 544 3.447918 GCATGAGCAAATGCCATAGTT 57.552 42.857 11.48 0.00 45.93 2.24
529 545 4.572985 GCATGAGCAAATGCCATAGTTA 57.427 40.909 11.48 0.00 45.93 2.24
530 546 4.543692 GCATGAGCAAATGCCATAGTTAG 58.456 43.478 11.48 0.00 45.93 2.34
531 547 4.558095 GCATGAGCAAATGCCATAGTTAGG 60.558 45.833 11.48 0.00 45.93 2.69
532 548 4.235079 TGAGCAAATGCCATAGTTAGGT 57.765 40.909 0.94 0.00 43.38 3.08
533 549 4.599041 TGAGCAAATGCCATAGTTAGGTT 58.401 39.130 0.94 0.00 43.38 3.50
534 550 5.016173 TGAGCAAATGCCATAGTTAGGTTT 58.984 37.500 0.94 0.00 43.38 3.27
535 551 5.480073 TGAGCAAATGCCATAGTTAGGTTTT 59.520 36.000 0.94 0.00 43.38 2.43
536 552 6.661377 TGAGCAAATGCCATAGTTAGGTTTTA 59.339 34.615 0.94 0.00 43.38 1.52
537 553 7.341769 TGAGCAAATGCCATAGTTAGGTTTTAT 59.658 33.333 0.94 0.00 43.38 1.40
538 554 7.491682 AGCAAATGCCATAGTTAGGTTTTATG 58.508 34.615 0.94 0.00 43.38 1.90
539 555 7.341769 AGCAAATGCCATAGTTAGGTTTTATGA 59.658 33.333 0.94 0.00 43.38 2.15
540 556 8.143835 GCAAATGCCATAGTTAGGTTTTATGAT 58.856 33.333 0.00 0.00 34.31 2.45
587 603 4.330944 ACATCCACGACTGACTTTTACA 57.669 40.909 0.00 0.00 0.00 2.41
588 604 4.056050 ACATCCACGACTGACTTTTACAC 58.944 43.478 0.00 0.00 0.00 2.90
589 605 3.102052 TCCACGACTGACTTTTACACC 57.898 47.619 0.00 0.00 0.00 4.16
590 606 2.140717 CCACGACTGACTTTTACACCC 58.859 52.381 0.00 0.00 0.00 4.61
591 607 2.140717 CACGACTGACTTTTACACCCC 58.859 52.381 0.00 0.00 0.00 4.95
592 608 1.071228 ACGACTGACTTTTACACCCCC 59.929 52.381 0.00 0.00 0.00 5.40
595 611 1.144298 ACTGACTTTTACACCCCCACC 59.856 52.381 0.00 0.00 0.00 4.61
596 612 1.144093 CTGACTTTTACACCCCCACCA 59.856 52.381 0.00 0.00 0.00 4.17
597 613 1.133730 TGACTTTTACACCCCCACCAC 60.134 52.381 0.00 0.00 0.00 4.16
598 614 0.927767 ACTTTTACACCCCCACCACA 59.072 50.000 0.00 0.00 0.00 4.17
665 730 5.060427 TCCATCCATAAATTGTACCCCTG 57.940 43.478 0.00 0.00 0.00 4.45
671 736 4.881850 CCATAAATTGTACCCCTGTGAGTC 59.118 45.833 0.00 0.00 0.00 3.36
712 778 9.489084 GCTTTGAACTAAGGTCCAAAATAAATT 57.511 29.630 0.00 0.00 0.00 1.82
719 785 9.143155 ACTAAGGTCCAAAATAAATTTCACAGT 57.857 29.630 0.00 0.00 0.00 3.55
815 897 1.279271 TCCCAGAAAAGCTAGGAGCAC 59.721 52.381 0.64 0.00 45.56 4.40
825 907 2.159085 AGCTAGGAGCACGTGGTAAATC 60.159 50.000 21.92 7.98 45.56 2.17
868 950 5.006261 GCAACATAAACTTGCTTCCGTTTTT 59.994 36.000 0.00 0.00 40.79 1.94
869 951 6.199342 GCAACATAAACTTGCTTCCGTTTTTA 59.801 34.615 0.00 0.00 40.79 1.52
875 957 4.928601 ACTTGCTTCCGTTTTTACTTTCC 58.071 39.130 0.00 0.00 0.00 3.13
924 1006 1.658686 CCACGTCCTCTTCTCCCTCG 61.659 65.000 0.00 0.00 0.00 4.63
1049 1134 4.498520 CATCAGCCGACGCCTCGT 62.499 66.667 4.43 0.00 45.10 4.18
1190 1275 2.181021 GGACGCCGACGAAGATGT 59.819 61.111 0.00 0.00 43.93 3.06
1215 1300 2.462782 CGACGAGGACGAGGAGGAC 61.463 68.421 0.00 0.00 42.66 3.85
1354 1439 2.669229 CCATGGTGCGCACACTCA 60.669 61.111 38.60 28.11 46.57 3.41
1355 1440 2.557805 CATGGTGCGCACACTCAC 59.442 61.111 38.60 22.82 46.57 3.51
1358 1443 3.044305 GGTGCGCACACTCACCTC 61.044 66.667 38.60 17.35 46.28 3.85
1361 1446 2.203082 TGCGCACACTCACCTCTCT 61.203 57.895 5.66 0.00 0.00 3.10
1362 1447 1.735920 GCGCACACTCACCTCTCTG 60.736 63.158 0.30 0.00 0.00 3.35
1369 1454 3.570125 CACACTCACCTCTCTGTCTTACA 59.430 47.826 0.00 0.00 0.00 2.41
1383 1481 5.997746 TCTGTCTTACAGTTGCTAATTTGCT 59.002 36.000 12.99 0.00 46.03 3.91
1459 1576 4.973168 ACTCTGACAAGATTTTGGTGCTA 58.027 39.130 0.57 0.00 38.66 3.49
1463 1580 6.913170 TCTGACAAGATTTTGGTGCTATTTC 58.087 36.000 0.57 0.00 38.66 2.17
1516 1656 4.145876 CAAGTTTGACGATTGCTTGCTA 57.854 40.909 0.00 0.00 31.72 3.49
1518 1658 5.156355 CAAGTTTGACGATTGCTTGCTAAT 58.844 37.500 0.00 0.00 31.72 1.73
1522 1662 2.677836 TGACGATTGCTTGCTAATGACC 59.322 45.455 0.00 0.00 0.00 4.02
1533 1673 3.674997 TGCTAATGACCTGAGTGTTTCC 58.325 45.455 0.00 0.00 0.00 3.13
1534 1674 3.327757 TGCTAATGACCTGAGTGTTTCCT 59.672 43.478 0.00 0.00 0.00 3.36
1540 1680 4.942944 TGACCTGAGTGTTTCCTCCTATA 58.057 43.478 0.00 0.00 0.00 1.31
1550 1692 3.485463 TTCCTCCTATATTTGGCGGTG 57.515 47.619 4.17 0.00 31.72 4.94
1565 1707 1.777030 CGGTGCCAAACGTGCAACTA 61.777 55.000 11.97 0.00 44.26 2.24
1568 1710 1.064952 GTGCCAAACGTGCAACTAACT 59.935 47.619 0.04 0.00 41.06 2.24
1581 1723 5.062308 GTGCAACTAACTATCACTACACTGC 59.938 44.000 0.00 0.00 0.00 4.40
1642 1786 4.141135 TGTGGAATTGAAGGTGGTTTCCTA 60.141 41.667 0.00 0.00 37.36 2.94
1699 1863 3.057315 GCACCACAAATGCAGAATACACT 60.057 43.478 0.00 0.00 42.88 3.55
1702 1866 6.676950 CACCACAAATGCAGAATACACTTTA 58.323 36.000 0.00 0.00 0.00 1.85
1729 1906 8.818057 GCTAGTAATTGGTGTGAATAGTAACTG 58.182 37.037 0.00 0.00 0.00 3.16
1747 1924 0.895530 TGGTGTCAGGGATTCGTCTC 59.104 55.000 0.00 0.00 0.00 3.36
1777 1970 0.179156 GCTGCTTGTATGTGCGCAAT 60.179 50.000 14.00 11.02 31.24 3.56
1795 1988 8.802856 GTGCGCAATTACAATTTATTTGTCATA 58.197 29.630 14.00 0.00 45.55 2.15
1796 1989 8.802856 TGCGCAATTACAATTTATTTGTCATAC 58.197 29.630 8.16 0.00 45.55 2.39
1803 1997 9.613957 TTACAATTTATTTGTCATACGTGTTGG 57.386 29.630 0.00 0.00 45.55 3.77
1809 2003 1.139256 TGTCATACGTGTTGGTGGTGT 59.861 47.619 0.00 0.00 0.00 4.16
1903 2104 6.917533 ACTTATGAATGGTTTCTTGCTCAAG 58.082 36.000 3.32 3.32 39.71 3.02
1934 2135 2.693210 TCTCAGGCATGGTGGATGATA 58.307 47.619 0.00 0.00 33.31 2.15
1946 2147 3.748568 GGTGGATGATAAATTCCTCGAGC 59.251 47.826 6.99 0.00 32.95 5.03
2044 2245 3.322466 ACCTACAAGGCCGCTGCT 61.322 61.111 7.72 0.00 39.63 4.24
2068 2269 1.011451 GCTCACTGTCCAACTCGCTC 61.011 60.000 0.00 0.00 0.00 5.03
2208 2410 3.776969 TCAGACAATATCCTGACTGCCTT 59.223 43.478 3.02 0.00 38.48 4.35
2278 2483 4.278170 TGACATCAAACTGTTTGGATCACC 59.722 41.667 27.52 15.07 40.98 4.02
2282 2487 1.620822 AACTGTTTGGATCACCCTGC 58.379 50.000 0.00 0.00 35.38 4.85
2429 2635 5.966742 AGTTTCTTCACTAATGGCTTTCC 57.033 39.130 0.00 0.00 0.00 3.13
2430 2636 5.635120 AGTTTCTTCACTAATGGCTTTCCT 58.365 37.500 0.00 0.00 0.00 3.36
2431 2637 5.474876 AGTTTCTTCACTAATGGCTTTCCTG 59.525 40.000 0.00 0.00 0.00 3.86
2434 2640 5.003804 TCTTCACTAATGGCTTTCCTGTTC 58.996 41.667 0.00 0.00 0.00 3.18
2436 2642 5.755409 TCACTAATGGCTTTCCTGTTCTA 57.245 39.130 0.00 0.00 0.00 2.10
2437 2643 5.488341 TCACTAATGGCTTTCCTGTTCTAC 58.512 41.667 0.00 0.00 0.00 2.59
2438 2644 4.330074 CACTAATGGCTTTCCTGTTCTACG 59.670 45.833 0.00 0.00 0.00 3.51
2440 2646 3.914426 ATGGCTTTCCTGTTCTACGAT 57.086 42.857 0.00 0.00 0.00 3.73
2441 2647 3.247006 TGGCTTTCCTGTTCTACGATC 57.753 47.619 0.00 0.00 0.00 3.69
2460 2667 2.785562 TCATTGGTAAACTTGTCCGGG 58.214 47.619 0.00 0.00 0.00 5.73
2464 2671 3.124578 TGGTAAACTTGTCCGGGTTAC 57.875 47.619 0.00 0.00 0.00 2.50
2472 2679 4.016444 ACTTGTCCGGGTTACGAAGTATA 58.984 43.478 0.00 0.00 45.21 1.47
2481 2688 6.183360 CCGGGTTACGAAGTATACTTAGACAA 60.183 42.308 26.48 17.86 45.21 3.18
2508 2715 8.974060 AGTTTATGTGTTCTTTACTCTTTGGA 57.026 30.769 0.00 0.00 0.00 3.53
2550 2763 6.061022 TCCTGGAAATGTAGCAATTCACTA 57.939 37.500 0.00 0.00 0.00 2.74
2567 2780 8.734386 CAATTCACTATTTGGCTTCTTAAGAGT 58.266 33.333 5.12 0.00 0.00 3.24
2572 2785 8.821894 CACTATTTGGCTTCTTAAGAGTGTATC 58.178 37.037 5.12 0.00 0.00 2.24
2573 2786 7.988028 ACTATTTGGCTTCTTAAGAGTGTATCC 59.012 37.037 5.12 0.00 0.00 2.59
2574 2787 5.755409 TTGGCTTCTTAAGAGTGTATCCA 57.245 39.130 5.12 0.00 0.00 3.41
2575 2788 5.957771 TGGCTTCTTAAGAGTGTATCCAT 57.042 39.130 5.12 0.00 0.00 3.41
2576 2789 7.432148 TTGGCTTCTTAAGAGTGTATCCATA 57.568 36.000 5.12 0.00 0.00 2.74
2577 2790 7.618019 TGGCTTCTTAAGAGTGTATCCATAT 57.382 36.000 5.12 0.00 0.00 1.78
2578 2791 8.721133 TGGCTTCTTAAGAGTGTATCCATATA 57.279 34.615 5.12 0.00 0.00 0.86
2579 2792 9.326489 TGGCTTCTTAAGAGTGTATCCATATAT 57.674 33.333 5.12 0.00 0.00 0.86
2614 2827 9.850628 CTATGCATGGTCTTATTTGAATTATGG 57.149 33.333 10.16 0.00 0.00 2.74
2615 2828 7.894753 TGCATGGTCTTATTTGAATTATGGA 57.105 32.000 0.00 0.00 0.00 3.41
2637 2850 6.882678 TGGATATAGCATTGAGAACATCCATG 59.117 38.462 0.00 0.00 36.62 3.66
2639 2852 7.065563 GGATATAGCATTGAGAACATCCATGTC 59.934 40.741 0.00 0.00 40.80 3.06
2665 2878 9.573133 CATATCAATTTTTCCTTGGACAAGTAC 57.427 33.333 10.81 0.00 36.72 2.73
2706 2919 6.239829 CCATTTATGTAGAGATTCTCCTGGCT 60.240 42.308 10.09 0.00 0.00 4.75
2714 2927 3.037549 AGATTCTCCTGGCTCTACCTTG 58.962 50.000 0.00 0.00 40.22 3.61
2771 2984 5.652452 GGGTACATCTTCAACTTTGGCTTAT 59.348 40.000 0.00 0.00 0.00 1.73
2976 3189 2.407428 TGAGACTAGCCTCCGTGCG 61.407 63.158 3.37 0.00 36.02 5.34
2979 3192 2.678934 ACTAGCCTCCGTGCGGAA 60.679 61.111 14.53 0.00 44.66 4.30
3013 3226 7.339212 TGTTACTATGGCACTTGCAATTATCTT 59.661 33.333 0.00 0.00 44.36 2.40
3050 3264 6.661377 ACACACTCTACAGTCATAAGTCATCT 59.339 38.462 0.00 0.00 0.00 2.90
3052 3266 8.031864 CACACTCTACAGTCATAAGTCATCTTT 58.968 37.037 0.00 0.00 35.36 2.52
3060 3274 7.065085 ACAGTCATAAGTCATCTTTCATTTCCG 59.935 37.037 0.00 0.00 35.36 4.30
3063 3277 7.905493 GTCATAAGTCATCTTTCATTTCCGTTC 59.095 37.037 0.00 0.00 35.36 3.95
3066 3280 6.246420 AGTCATCTTTCATTTCCGTTCAAG 57.754 37.500 0.00 0.00 0.00 3.02
3079 3293 3.640029 TCCGTTCAAGTAACAAGAGGTCT 59.360 43.478 0.00 0.00 38.03 3.85
3080 3294 3.741344 CCGTTCAAGTAACAAGAGGTCTG 59.259 47.826 0.00 0.00 38.03 3.51
3172 3545 3.214696 AGTGCTATGTAATTCCCAGCC 57.785 47.619 0.00 0.00 0.00 4.85
3178 3551 4.021719 GCTATGTAATTCCCAGCCGTACTA 60.022 45.833 0.00 0.00 0.00 1.82
3183 3556 2.226962 TTCCCAGCCGTACTAACTCT 57.773 50.000 0.00 0.00 0.00 3.24
3208 3581 7.418378 TGGTCCTAAACATTTTCAGGGATATT 58.582 34.615 0.00 0.00 0.00 1.28
3223 3596 5.639506 CAGGGATATTGTAGGAAACTATGCG 59.360 44.000 0.00 0.00 46.56 4.73
3274 3647 4.170723 GCGTTCTGCGAGCTAACT 57.829 55.556 0.00 0.00 44.77 2.24
3322 3695 5.221521 TGCGAGATACTTGAGCCATTCTATT 60.222 40.000 0.00 0.00 0.00 1.73
3331 3704 7.069986 ACTTGAGCCATTCTATTCCTCTAGTA 58.930 38.462 0.00 0.00 37.04 1.82
3334 3707 6.665680 TGAGCCATTCTATTCCTCTAGTATCC 59.334 42.308 0.00 0.00 0.00 2.59
3340 3713 7.992754 TTCTATTCCTCTAGTATCCGTTACC 57.007 40.000 0.00 0.00 0.00 2.85
3394 3767 5.653255 AAGGTGAAGCAATATACATCCCT 57.347 39.130 0.00 0.00 0.00 4.20
3397 3770 4.202461 GGTGAAGCAATATACATCCCTCCA 60.202 45.833 0.00 0.00 0.00 3.86
3478 3851 3.925090 GGTATCCTCCGGGGTGCG 61.925 72.222 0.00 0.00 36.25 5.34
3481 3854 3.665515 TATCCTCCGGGGTGCGTCA 62.666 63.158 0.00 0.00 36.25 4.35
3496 3869 1.813513 CGTCAGACTTGAAGGGCATT 58.186 50.000 0.00 0.00 34.49 3.56
3657 4030 4.165372 GGACCAGGTTCCCAACTTATGATA 59.835 45.833 0.00 0.00 0.00 2.15
3722 4095 1.593265 GAACTACCGAGGGCCGAAA 59.407 57.895 0.00 0.00 41.76 3.46
3723 4096 0.037046 GAACTACCGAGGGCCGAAAA 60.037 55.000 0.00 0.00 41.76 2.29
3764 4137 6.442952 TCTAGAAGATCTCTTAAGCGATTGC 58.557 40.000 9.26 0.00 37.62 3.56
3821 4195 1.726853 CTAAACCAGCACCTCCTTCG 58.273 55.000 0.00 0.00 0.00 3.79
3822 4196 1.275291 CTAAACCAGCACCTCCTTCGA 59.725 52.381 0.00 0.00 0.00 3.71
3823 4197 0.472471 AAACCAGCACCTCCTTCGAA 59.528 50.000 0.00 0.00 0.00 3.71
3824 4198 0.250338 AACCAGCACCTCCTTCGAAC 60.250 55.000 0.00 0.00 0.00 3.95
3825 4199 1.371183 CCAGCACCTCCTTCGAACA 59.629 57.895 0.00 0.00 0.00 3.18
3826 4200 0.671781 CCAGCACCTCCTTCGAACAG 60.672 60.000 0.00 0.00 0.00 3.16
3827 4201 1.004440 AGCACCTCCTTCGAACAGC 60.004 57.895 0.00 0.00 0.00 4.40
3830 4204 1.593196 CACCTCCTTCGAACAGCAAA 58.407 50.000 0.00 0.00 0.00 3.68
3831 4205 1.946768 CACCTCCTTCGAACAGCAAAA 59.053 47.619 0.00 0.00 0.00 2.44
3832 4206 2.554032 CACCTCCTTCGAACAGCAAAAT 59.446 45.455 0.00 0.00 0.00 1.82
3833 4207 2.554032 ACCTCCTTCGAACAGCAAAATG 59.446 45.455 0.00 0.00 0.00 2.32
3834 4208 2.589014 CTCCTTCGAACAGCAAAATGC 58.411 47.619 0.00 0.00 45.46 3.56
3855 4234 4.471025 TGCTAGAAGGGTTCATCAGATTGA 59.529 41.667 0.00 0.00 0.00 2.57
3856 4235 5.131642 TGCTAGAAGGGTTCATCAGATTGAT 59.868 40.000 0.00 0.00 37.65 2.57
3877 4256 1.244019 CCCCTTCAACTTCAAGCCCG 61.244 60.000 0.00 0.00 0.00 6.13
3939 4319 5.772004 TCTCATTCCTTTAGTCCTAGCTCT 58.228 41.667 0.00 0.00 0.00 4.09
3947 4327 5.407407 TTTAGTCCTAGCTCTTTGTCAGG 57.593 43.478 0.00 0.00 0.00 3.86
3948 4328 1.552792 AGTCCTAGCTCTTTGTCAGGC 59.447 52.381 0.00 0.00 0.00 4.85
3969 4349 1.142748 CTCGGCCTCTGTCACCATC 59.857 63.158 0.00 0.00 0.00 3.51
3991 4371 6.909550 TCCCATTACTTACATTTTTGCACT 57.090 33.333 0.00 0.00 0.00 4.40
3993 4373 5.348451 CCCATTACTTACATTTTTGCACTGC 59.652 40.000 0.00 0.00 0.00 4.40
4014 4394 3.643763 CAAGGATGCTACATACTCCGAC 58.356 50.000 0.00 0.00 32.87 4.79
4015 4395 3.231207 AGGATGCTACATACTCCGACT 57.769 47.619 0.00 0.00 32.87 4.18
4016 4396 3.567397 AGGATGCTACATACTCCGACTT 58.433 45.455 0.00 0.00 32.87 3.01
4017 4397 3.961408 AGGATGCTACATACTCCGACTTT 59.039 43.478 0.00 0.00 32.87 2.66
4019 4399 4.508124 GGATGCTACATACTCCGACTTTTG 59.492 45.833 0.00 0.00 0.00 2.44
4020 4400 3.857052 TGCTACATACTCCGACTTTTGG 58.143 45.455 0.00 0.00 0.00 3.28
4021 4401 2.608090 GCTACATACTCCGACTTTTGGC 59.392 50.000 0.00 0.00 0.00 4.52
4022 4402 2.109425 ACATACTCCGACTTTTGGCC 57.891 50.000 0.00 0.00 0.00 5.36
4023 4403 1.006832 CATACTCCGACTTTTGGCCG 58.993 55.000 0.00 0.00 0.00 6.13
4024 4404 0.899720 ATACTCCGACTTTTGGCCGA 59.100 50.000 0.00 0.00 0.00 5.54
4025 4405 0.245539 TACTCCGACTTTTGGCCGAG 59.754 55.000 0.00 0.00 38.51 4.63
4026 4406 2.358247 TCCGACTTTTGGCCGAGC 60.358 61.111 0.00 0.00 0.00 5.03
4027 4407 2.668212 CCGACTTTTGGCCGAGCA 60.668 61.111 0.00 0.00 0.00 4.26
4028 4408 2.556287 CGACTTTTGGCCGAGCAC 59.444 61.111 0.00 0.00 0.00 4.40
4029 4409 2.250939 CGACTTTTGGCCGAGCACA 61.251 57.895 0.00 0.00 0.00 4.57
4030 4410 1.577328 CGACTTTTGGCCGAGCACAT 61.577 55.000 0.00 0.00 0.00 3.21
4031 4411 0.109597 GACTTTTGGCCGAGCACATG 60.110 55.000 0.00 0.00 0.00 3.21
4044 4424 4.261572 CCGAGCACATGGGGTATTTTTATG 60.262 45.833 0.00 0.00 0.00 1.90
4053 4436 5.433526 TGGGGTATTTTTATGTCGAAGGAG 58.566 41.667 0.00 0.00 0.00 3.69
4066 4449 5.714047 TGTCGAAGGAGCATGATATCATAC 58.286 41.667 17.77 12.60 34.26 2.39
4083 4466 9.151471 GATATCATACGTTTGGCTGTAATGTAT 57.849 33.333 6.15 0.00 37.90 2.29
4085 4468 8.896320 ATCATACGTTTGGCTGTAATGTATAA 57.104 30.769 6.15 1.19 36.20 0.98
4086 4469 8.896320 TCATACGTTTGGCTGTAATGTATAAT 57.104 30.769 6.15 0.00 36.20 1.28
4087 4470 8.769891 TCATACGTTTGGCTGTAATGTATAATG 58.230 33.333 6.15 0.00 36.20 1.90
4088 4471 5.816919 ACGTTTGGCTGTAATGTATAATGC 58.183 37.500 0.00 0.00 0.00 3.56
4089 4472 5.355630 ACGTTTGGCTGTAATGTATAATGCA 59.644 36.000 0.00 0.00 0.00 3.96
4104 4487 1.538047 ATGCACAGCCGAAAGACAAT 58.462 45.000 0.00 0.00 0.00 2.71
4109 4492 0.454957 CAGCCGAAAGACAATTGCCG 60.455 55.000 5.05 1.91 0.00 5.69
4144 4527 5.957842 ATGTGAATAAACTTCTTTCGGCA 57.042 34.783 0.00 0.00 0.00 5.69
4146 4529 4.159120 GTGAATAAACTTCTTTCGGCAGC 58.841 43.478 0.00 0.00 0.00 5.25
4147 4530 4.072131 TGAATAAACTTCTTTCGGCAGCT 58.928 39.130 0.00 0.00 0.00 4.24
4153 4536 0.108585 TTCTTTCGGCAGCTCCTGTT 59.891 50.000 0.00 0.00 33.43 3.16
4154 4537 0.603707 TCTTTCGGCAGCTCCTGTTG 60.604 55.000 0.00 0.00 33.43 3.33
4155 4538 0.886490 CTTTCGGCAGCTCCTGTTGT 60.886 55.000 0.00 0.00 33.43 3.32
4156 4539 0.884704 TTTCGGCAGCTCCTGTTGTC 60.885 55.000 0.00 0.00 33.43 3.18
4158 4541 2.431683 GGCAGCTCCTGTTGTCCA 59.568 61.111 0.00 0.00 33.43 4.02
4159 4542 1.968540 GGCAGCTCCTGTTGTCCAC 60.969 63.158 0.00 0.00 33.43 4.02
4160 4543 1.072159 GCAGCTCCTGTTGTCCACT 59.928 57.895 0.00 0.00 33.43 4.00
4161 4544 1.233285 GCAGCTCCTGTTGTCCACTG 61.233 60.000 0.00 0.00 33.43 3.66
4162 4545 1.072159 AGCTCCTGTTGTCCACTGC 59.928 57.895 0.00 0.00 0.00 4.40
4163 4546 1.968540 GCTCCTGTTGTCCACTGCC 60.969 63.158 0.00 0.00 0.00 4.85
4166 4561 1.601759 CCTGTTGTCCACTGCCCAG 60.602 63.158 0.00 0.00 0.00 4.45
4200 4595 3.848272 ATCACCAAAACTGTAATGCGG 57.152 42.857 0.00 0.00 0.00 5.69
4257 4662 2.027625 GTGGAACGTCGCCTTCAGG 61.028 63.158 8.64 0.00 38.53 3.86
4277 4682 7.159322 TCAGGAGCGAAAGGTATAATATCTC 57.841 40.000 0.00 0.00 45.11 2.75
4284 4691 7.283580 AGCGAAAGGTATAATATCTCGAGCTAT 59.716 37.037 7.81 5.09 41.99 2.97
4334 4741 2.569404 AGTTCAGTGACCCAGATTCTCC 59.431 50.000 0.00 0.00 0.00 3.71
4342 4749 4.019771 GTGACCCAGATTCTCCTCTTTCTT 60.020 45.833 0.00 0.00 0.00 2.52
4344 4751 3.265479 ACCCAGATTCTCCTCTTTCTTGG 59.735 47.826 0.00 0.00 0.00 3.61
4345 4752 3.265479 CCCAGATTCTCCTCTTTCTTGGT 59.735 47.826 0.00 0.00 0.00 3.67
4346 4753 4.471386 CCCAGATTCTCCTCTTTCTTGGTA 59.529 45.833 0.00 0.00 0.00 3.25
4347 4754 5.396213 CCCAGATTCTCCTCTTTCTTGGTAG 60.396 48.000 0.00 0.00 0.00 3.18
4349 4756 3.983044 TTCTCCTCTTTCTTGGTAGCC 57.017 47.619 0.00 0.00 0.00 3.93
4350 4757 3.191888 TCTCCTCTTTCTTGGTAGCCT 57.808 47.619 0.00 0.00 0.00 4.58
4351 4758 4.332683 TCTCCTCTTTCTTGGTAGCCTA 57.667 45.455 0.00 0.00 0.00 3.93
4451 4861 1.980844 CGTATGCTTGCTTGTTTGCAG 59.019 47.619 0.00 0.00 44.27 4.41
4452 4862 2.605338 CGTATGCTTGCTTGTTTGCAGT 60.605 45.455 0.00 0.00 44.27 4.40
4453 4863 1.860676 ATGCTTGCTTGTTTGCAGTG 58.139 45.000 0.00 0.00 44.27 3.66
4454 4864 0.806884 TGCTTGCTTGTTTGCAGTGC 60.807 50.000 8.58 8.58 44.27 4.40
4455 4865 1.493134 GCTTGCTTGTTTGCAGTGCC 61.493 55.000 13.72 0.00 44.27 5.01
4456 4866 0.179105 CTTGCTTGTTTGCAGTGCCA 60.179 50.000 13.72 0.00 44.27 4.92
4459 4869 0.863144 GCTTGTTTGCAGTGCCATTG 59.137 50.000 13.72 1.42 0.00 2.82
4460 4870 0.863144 CTTGTTTGCAGTGCCATTGC 59.137 50.000 13.72 5.08 41.86 3.56
4461 4871 0.464870 TTGTTTGCAGTGCCATTGCT 59.535 45.000 13.72 0.00 42.02 3.91
4463 4873 0.863144 GTTTGCAGTGCCATTGCTTG 59.137 50.000 13.72 0.00 42.02 4.01
4465 4875 0.464870 TTGCAGTGCCATTGCTTGTT 59.535 45.000 13.72 0.00 42.02 2.83
4466 4876 0.464870 TGCAGTGCCATTGCTTGTTT 59.535 45.000 13.72 0.00 42.02 2.83
4559 4978 4.684877 CGAGAGCTGTAGACTGTAGAGTA 58.315 47.826 0.00 0.00 30.16 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 8.787852 AGGTAGAAGTTCAAAATTTCATGAGAC 58.212 33.333 5.50 0.00 30.34 3.36
103 107 2.004733 GGTGATAAAGAAACGGACGGG 58.995 52.381 0.00 0.00 0.00 5.28
107 111 2.754946 AGCGGTGATAAAGAAACGGA 57.245 45.000 0.00 0.00 0.00 4.69
178 184 9.282569 GGAGATCTGATAATTGAATGCTAACTT 57.717 33.333 0.00 0.00 0.00 2.66
180 186 8.845413 AGGAGATCTGATAATTGAATGCTAAC 57.155 34.615 0.00 0.00 0.00 2.34
190 196 9.579932 GTTTCCCATTTAGGAGATCTGATAATT 57.420 33.333 0.00 0.00 41.22 1.40
197 203 6.581388 TCATGTTTCCCATTTAGGAGATCT 57.419 37.500 0.00 0.00 41.22 2.75
509 525 4.581824 ACCTAACTATGGCATTTGCTCATG 59.418 41.667 4.78 0.00 41.70 3.07
510 526 4.796606 ACCTAACTATGGCATTTGCTCAT 58.203 39.130 4.78 7.04 41.70 2.90
511 527 4.235079 ACCTAACTATGGCATTTGCTCA 57.765 40.909 4.78 0.00 41.70 4.26
512 528 5.582689 AAACCTAACTATGGCATTTGCTC 57.417 39.130 4.78 0.00 41.70 4.26
513 529 7.341769 TCATAAAACCTAACTATGGCATTTGCT 59.658 33.333 4.78 0.00 41.70 3.91
514 530 7.488322 TCATAAAACCTAACTATGGCATTTGC 58.512 34.615 4.78 0.00 41.14 3.68
547 563 2.426024 TGTAACGCTGCTCCTAACTAGG 59.574 50.000 0.00 0.00 45.02 3.02
548 564 3.777465 TGTAACGCTGCTCCTAACTAG 57.223 47.619 0.00 0.00 0.00 2.57
553 569 1.136305 GTGGATGTAACGCTGCTCCTA 59.864 52.381 0.00 0.00 0.00 2.94
587 603 3.018193 TGTGTGTGTGGTGGGGGT 61.018 61.111 0.00 0.00 0.00 4.95
588 604 2.518349 GTGTGTGTGTGGTGGGGG 60.518 66.667 0.00 0.00 0.00 5.40
589 605 1.077068 AAGTGTGTGTGTGGTGGGG 60.077 57.895 0.00 0.00 0.00 4.96
590 606 0.393673 TCAAGTGTGTGTGTGGTGGG 60.394 55.000 0.00 0.00 0.00 4.61
591 607 1.458398 TTCAAGTGTGTGTGTGGTGG 58.542 50.000 0.00 0.00 0.00 4.61
592 608 3.781079 ATTTCAAGTGTGTGTGTGGTG 57.219 42.857 0.00 0.00 0.00 4.17
595 611 3.064682 TCCGAATTTCAAGTGTGTGTGTG 59.935 43.478 0.00 0.00 0.00 3.82
596 612 3.275143 TCCGAATTTCAAGTGTGTGTGT 58.725 40.909 0.00 0.00 0.00 3.72
597 613 3.961477 TCCGAATTTCAAGTGTGTGTG 57.039 42.857 0.00 0.00 0.00 3.82
598 614 4.578516 TCATTCCGAATTTCAAGTGTGTGT 59.421 37.500 0.00 0.00 0.00 3.72
679 744 3.287222 ACCTTAGTTCAAAGCTGCAACA 58.713 40.909 1.02 0.00 0.00 3.33
712 778 6.764085 TCCGAATCTTAGTTCAAAACTGTGAA 59.236 34.615 2.65 0.00 42.84 3.18
815 897 3.387397 GACCGGATAAGGATTTACCACG 58.613 50.000 9.46 0.00 42.04 4.94
868 950 2.966732 CGGCCAGGCTGGGAAAGTA 61.967 63.158 33.43 0.00 38.19 2.24
869 951 4.351054 CGGCCAGGCTGGGAAAGT 62.351 66.667 33.43 0.00 38.19 2.66
924 1006 0.107165 GAGTGGATTAGGGTGTGGGC 60.107 60.000 0.00 0.00 0.00 5.36
1190 1275 3.785499 CGTCCTCGTCGTCGCTGA 61.785 66.667 0.00 0.00 36.96 4.26
1252 1337 4.767255 GTCCTCGCACCCCTGCTG 62.767 72.222 0.00 0.00 41.77 4.41
1358 1443 6.148480 AGCAAATTAGCAACTGTAAGACAGAG 59.852 38.462 13.38 6.55 42.10 3.35
1361 1446 7.606073 TGATAGCAAATTAGCAACTGTAAGACA 59.394 33.333 0.00 0.00 35.42 3.41
1362 1447 7.974675 TGATAGCAAATTAGCAACTGTAAGAC 58.025 34.615 0.00 0.00 35.42 3.01
1369 1454 5.711976 ACTGGTTGATAGCAAATTAGCAACT 59.288 36.000 12.17 0.00 44.89 3.16
1383 1481 3.519510 AGGCTTGAAGCTACTGGTTGATA 59.480 43.478 17.59 0.00 41.99 2.15
1510 1650 4.154918 GGAAACACTCAGGTCATTAGCAAG 59.845 45.833 0.00 0.00 0.00 4.01
1511 1651 4.072131 GGAAACACTCAGGTCATTAGCAA 58.928 43.478 0.00 0.00 0.00 3.91
1516 1656 2.982488 AGGAGGAAACACTCAGGTCATT 59.018 45.455 0.00 0.00 39.27 2.57
1518 1658 2.103153 AGGAGGAAACACTCAGGTCA 57.897 50.000 0.00 0.00 39.27 4.02
1522 1662 5.529060 GCCAAATATAGGAGGAAACACTCAG 59.471 44.000 0.00 0.00 39.27 3.35
1550 1692 3.187637 TGATAGTTAGTTGCACGTTTGGC 59.812 43.478 0.00 0.00 0.00 4.52
1565 1707 7.841956 AGTAGAAATGCAGTGTAGTGATAGTT 58.158 34.615 0.00 0.00 0.00 2.24
1642 1786 5.531659 TCAATGTTTCTTGCAATTTGGCATT 59.468 32.000 0.00 5.22 44.48 3.56
1702 1866 8.759782 AGTTACTATTCACACCAATTACTAGCT 58.240 33.333 0.00 0.00 0.00 3.32
1725 1902 1.002087 GACGAATCCCTGACACCAGTT 59.998 52.381 0.00 0.00 38.74 3.16
1729 1906 0.179134 CGAGACGAATCCCTGACACC 60.179 60.000 0.00 0.00 0.00 4.16
1747 1924 1.735198 CAAGCAGCAAATGGCCACG 60.735 57.895 8.16 0.00 46.50 4.94
1795 1988 1.757682 ATTTGACACCACCAACACGT 58.242 45.000 0.00 0.00 0.00 4.49
1796 1989 3.252215 ACATATTTGACACCACCAACACG 59.748 43.478 0.00 0.00 0.00 4.49
1803 1997 6.551736 GTGTCCATTACATATTTGACACCAC 58.448 40.000 8.91 0.00 44.09 4.16
1809 2003 7.625469 TGTACTGGTGTCCATTACATATTTGA 58.375 34.615 12.66 0.00 42.15 2.69
1903 2104 3.265791 CATGCCTGAGAAGTCAACCTAC 58.734 50.000 0.00 0.00 30.14 3.18
1934 2135 0.108138 CCCAGTCGCTCGAGGAATTT 60.108 55.000 15.58 0.00 0.00 1.82
1946 2147 0.390860 CCCTTCTCTATGCCCAGTCG 59.609 60.000 0.00 0.00 0.00 4.18
2044 2245 0.764369 AGTTGGACAGTGAGCCTCCA 60.764 55.000 0.00 0.00 31.94 3.86
2068 2269 1.078848 AAGCCTTGCTAGAGCCACG 60.079 57.895 0.00 0.00 38.25 4.94
2188 2390 4.225942 TCAAAGGCAGTCAGGATATTGTCT 59.774 41.667 0.00 0.00 0.00 3.41
2198 2400 3.567164 ACAACAAGATCAAAGGCAGTCAG 59.433 43.478 0.00 0.00 0.00 3.51
2200 2402 4.757149 AGTACAACAAGATCAAAGGCAGTC 59.243 41.667 0.00 0.00 0.00 3.51
2208 2410 7.390823 TGGTAGCAATAGTACAACAAGATCAA 58.609 34.615 0.00 0.00 0.00 2.57
2429 2635 7.117812 ACAAGTTTACCAATGATCGTAGAACAG 59.882 37.037 0.00 0.00 43.96 3.16
2430 2636 6.932400 ACAAGTTTACCAATGATCGTAGAACA 59.068 34.615 0.00 0.00 45.05 3.18
2431 2637 7.360575 ACAAGTTTACCAATGATCGTAGAAC 57.639 36.000 0.00 0.00 43.58 3.01
2434 2640 5.005394 CGGACAAGTTTACCAATGATCGTAG 59.995 44.000 0.00 0.00 0.00 3.51
2436 2642 3.682858 CGGACAAGTTTACCAATGATCGT 59.317 43.478 0.00 0.00 0.00 3.73
2437 2643 3.063452 CCGGACAAGTTTACCAATGATCG 59.937 47.826 0.00 0.00 0.00 3.69
2438 2644 3.377172 CCCGGACAAGTTTACCAATGATC 59.623 47.826 0.73 0.00 0.00 2.92
2440 2646 2.106857 ACCCGGACAAGTTTACCAATGA 59.893 45.455 0.73 0.00 0.00 2.57
2441 2647 2.510613 ACCCGGACAAGTTTACCAATG 58.489 47.619 0.73 0.00 0.00 2.82
2490 2697 7.148623 CCGAAGTATCCAAAGAGTAAAGAACAC 60.149 40.741 0.00 0.00 0.00 3.32
2493 2700 7.039223 ACTCCGAAGTATCCAAAGAGTAAAGAA 60.039 37.037 0.00 0.00 32.59 2.52
2508 2715 2.354805 GGAAGGCACAACTCCGAAGTAT 60.355 50.000 0.00 0.00 33.48 2.12
2550 2763 6.721318 TGGATACACTCTTAAGAAGCCAAAT 58.279 36.000 8.99 0.00 46.17 2.32
2581 2794 9.625747 TCAAATAAGACCATGCATAGTTATTCA 57.374 29.630 0.00 0.00 0.00 2.57
2588 2801 9.850628 CCATAATTCAAATAAGACCATGCATAG 57.149 33.333 0.00 0.00 0.00 2.23
2589 2802 9.585369 TCCATAATTCAAATAAGACCATGCATA 57.415 29.630 0.00 0.00 0.00 3.14
2590 2803 8.481492 TCCATAATTCAAATAAGACCATGCAT 57.519 30.769 0.00 0.00 0.00 3.96
2591 2804 7.894753 TCCATAATTCAAATAAGACCATGCA 57.105 32.000 0.00 0.00 0.00 3.96
2609 2822 8.605065 TGGATGTTCTCAATGCTATATCCATAA 58.395 33.333 0.00 0.00 38.24 1.90
2614 2827 7.605309 TGACATGGATGTTCTCAATGCTATATC 59.395 37.037 0.00 0.00 38.69 1.63
2615 2828 7.455891 TGACATGGATGTTCTCAATGCTATAT 58.544 34.615 0.00 0.00 38.69 0.86
2637 2850 8.306761 ACTTGTCCAAGGAAAAATTGATATGAC 58.693 33.333 11.45 0.00 42.53 3.06
2639 2852 9.573133 GTACTTGTCCAAGGAAAAATTGATATG 57.427 33.333 11.45 0.00 42.53 1.78
2676 2889 6.944862 GGAGAATCTCTACATAAATGGCCAAT 59.055 38.462 10.96 0.00 33.73 3.16
2694 2907 2.769095 ACAAGGTAGAGCCAGGAGAATC 59.231 50.000 0.00 0.00 40.61 2.52
2706 2919 5.663106 AGGCATCATTAGAGAACAAGGTAGA 59.337 40.000 0.00 0.00 0.00 2.59
2714 2927 7.119846 ACAAGTTACAAGGCATCATTAGAGAAC 59.880 37.037 0.00 0.00 0.00 3.01
2771 2984 4.713814 ACTATCTCTGCCAAGTCTGAATCA 59.286 41.667 0.00 0.00 0.00 2.57
2837 3050 8.523915 TGATGGCTTCAATTGTATGACTAAAT 57.476 30.769 5.13 0.00 0.00 1.40
2979 3192 5.700402 AGTGCCATAGTAACAGGAAATCT 57.300 39.130 0.00 0.00 0.00 2.40
2991 3204 5.653769 ACAAGATAATTGCAAGTGCCATAGT 59.346 36.000 10.14 0.00 41.18 2.12
3013 3226 0.463654 GAGTGTGTGCAACTGGGACA 60.464 55.000 0.00 0.00 46.42 4.02
3050 3264 7.323049 TCTTGTTACTTGAACGGAAATGAAA 57.677 32.000 0.00 0.00 41.35 2.69
3052 3266 5.468746 CCTCTTGTTACTTGAACGGAAATGA 59.531 40.000 0.00 0.00 41.35 2.57
3060 3274 5.602628 ACTCAGACCTCTTGTTACTTGAAC 58.397 41.667 0.00 0.00 38.65 3.18
3063 3277 9.706691 TTTATAACTCAGACCTCTTGTTACTTG 57.293 33.333 0.00 0.00 30.56 3.16
3066 3280 9.871238 TGATTTATAACTCAGACCTCTTGTTAC 57.129 33.333 1.60 0.00 30.56 2.50
3108 3474 6.238049 GCAAATGTACACTTGCAATCACAAAA 60.238 34.615 31.03 0.00 45.81 2.44
3149 3522 5.337250 CGGCTGGGAATTACATAGCACTATA 60.337 44.000 15.53 0.00 36.15 1.31
3151 3524 3.244078 CGGCTGGGAATTACATAGCACTA 60.244 47.826 15.53 0.00 36.15 2.74
3153 3526 1.873591 CGGCTGGGAATTACATAGCAC 59.126 52.381 15.53 6.55 36.15 4.40
3158 3531 4.407945 AGTTAGTACGGCTGGGAATTACAT 59.592 41.667 0.00 0.00 0.00 2.29
3172 3545 5.633830 TGTTTAGGACCAGAGTTAGTACG 57.366 43.478 0.00 0.00 0.00 3.67
3178 3551 5.770162 CCTGAAAATGTTTAGGACCAGAGTT 59.230 40.000 0.00 0.00 41.98 3.01
3183 3556 4.733077 TCCCTGAAAATGTTTAGGACCA 57.267 40.909 8.04 0.00 41.98 4.02
3208 3581 5.801531 ATATGTCCGCATAGTTTCCTACA 57.198 39.130 0.00 0.00 40.51 2.74
3274 3647 1.000163 GACACCGTGCTCTCTTCTGAA 60.000 52.381 0.00 0.00 0.00 3.02
3340 3713 0.179084 AGGAACCGTGCATACCATCG 60.179 55.000 0.00 0.00 0.00 3.84
3394 3767 0.756294 CAGGTATACATGCCGGTGGA 59.244 55.000 4.35 0.00 37.65 4.02
3397 3770 0.468226 CCACAGGTATACATGCCGGT 59.532 55.000 17.06 0.00 41.06 5.28
3475 3848 1.301716 GCCCTTCAAGTCTGACGCA 60.302 57.895 1.52 0.00 0.00 5.24
3478 3851 1.815003 CCAATGCCCTTCAAGTCTGAC 59.185 52.381 0.00 0.00 0.00 3.51
3481 3854 2.967270 GCCAATGCCCTTCAAGTCT 58.033 52.632 0.00 0.00 0.00 3.24
3520 3893 4.228567 TGCCCGACGACAACAGCA 62.229 61.111 0.00 0.00 0.00 4.41
3547 3920 0.541863 CATCCTTAACCCTCAGGCGT 59.458 55.000 0.00 0.00 36.11 5.68
3657 4030 1.299939 GGACTTGAGGGGGAGGAAAT 58.700 55.000 0.00 0.00 0.00 2.17
3697 4070 1.067582 CCTCGGTAGTTCCCATCGC 59.932 63.158 0.00 0.00 0.00 4.58
3728 4101 0.461961 CTTCTAGAGAAGGGGGCACG 59.538 60.000 10.88 0.00 45.79 5.34
3759 4132 6.651225 AGTCTGAGTGGTAAAACTAAGCAATC 59.349 38.462 0.00 0.00 39.25 2.67
3764 4137 6.159988 CCTGAGTCTGAGTGGTAAAACTAAG 58.840 44.000 0.00 0.00 30.65 2.18
3826 4200 4.158394 TGATGAACCCTTCTAGCATTTTGC 59.842 41.667 0.00 0.00 45.46 3.68
3827 4201 5.649395 TCTGATGAACCCTTCTAGCATTTTG 59.351 40.000 0.00 0.00 0.00 2.44
3830 4204 5.643421 ATCTGATGAACCCTTCTAGCATT 57.357 39.130 0.00 0.00 0.00 3.56
3831 4205 5.131642 TCAATCTGATGAACCCTTCTAGCAT 59.868 40.000 0.00 0.00 0.00 3.79
3832 4206 4.471025 TCAATCTGATGAACCCTTCTAGCA 59.529 41.667 0.00 0.00 0.00 3.49
3833 4207 5.028549 TCAATCTGATGAACCCTTCTAGC 57.971 43.478 0.00 0.00 0.00 3.42
3855 4234 1.260544 GCTTGAAGTTGAAGGGGCAT 58.739 50.000 4.18 0.00 0.00 4.40
3856 4235 0.827507 GGCTTGAAGTTGAAGGGGCA 60.828 55.000 4.18 0.00 0.00 5.36
3858 4237 1.244019 CGGGCTTGAAGTTGAAGGGG 61.244 60.000 4.18 0.00 0.00 4.79
3877 4256 4.208686 CCTAGGACCTGTCGCGCC 62.209 72.222 1.05 0.00 0.00 6.53
3890 4270 7.154656 TGCTATATACAAGTGAATGTGCCTAG 58.845 38.462 0.00 0.00 34.75 3.02
3969 4349 5.348451 GCAGTGCAAAAATGTAAGTAATGGG 59.652 40.000 11.09 0.00 0.00 4.00
3993 4373 3.319405 AGTCGGAGTATGTAGCATCCTTG 59.681 47.826 0.00 0.00 0.00 3.61
4009 4389 2.358247 GCTCGGCCAAAAGTCGGA 60.358 61.111 2.24 0.00 46.04 4.55
4010 4390 2.668212 TGCTCGGCCAAAAGTCGG 60.668 61.111 2.24 0.00 46.04 4.79
4014 4394 1.213537 CCATGTGCTCGGCCAAAAG 59.786 57.895 2.24 0.00 0.00 2.27
4015 4395 2.274645 CCCATGTGCTCGGCCAAAA 61.275 57.895 2.24 0.00 0.00 2.44
4016 4396 2.676121 CCCATGTGCTCGGCCAAA 60.676 61.111 2.24 0.00 0.00 3.28
4017 4397 4.738998 CCCCATGTGCTCGGCCAA 62.739 66.667 2.24 0.00 0.00 4.52
4019 4399 2.624674 AATACCCCATGTGCTCGGCC 62.625 60.000 0.00 0.00 0.00 6.13
4020 4400 0.751643 AAATACCCCATGTGCTCGGC 60.752 55.000 0.00 0.00 0.00 5.54
4021 4401 1.762708 AAAATACCCCATGTGCTCGG 58.237 50.000 0.00 0.00 0.00 4.63
4022 4402 4.338118 ACATAAAAATACCCCATGTGCTCG 59.662 41.667 0.00 0.00 0.00 5.03
4023 4403 5.505654 CGACATAAAAATACCCCATGTGCTC 60.506 44.000 0.00 0.00 30.25 4.26
4024 4404 4.338118 CGACATAAAAATACCCCATGTGCT 59.662 41.667 0.00 0.00 30.25 4.40
4025 4405 4.336993 TCGACATAAAAATACCCCATGTGC 59.663 41.667 0.00 0.00 30.25 4.57
4026 4406 6.443934 TTCGACATAAAAATACCCCATGTG 57.556 37.500 0.00 0.00 30.25 3.21
4027 4407 5.592688 CCTTCGACATAAAAATACCCCATGT 59.407 40.000 0.00 0.00 32.70 3.21
4028 4408 5.825679 TCCTTCGACATAAAAATACCCCATG 59.174 40.000 0.00 0.00 0.00 3.66
4029 4409 6.008696 TCCTTCGACATAAAAATACCCCAT 57.991 37.500 0.00 0.00 0.00 4.00
4030 4410 5.433526 CTCCTTCGACATAAAAATACCCCA 58.566 41.667 0.00 0.00 0.00 4.96
4031 4411 4.275196 GCTCCTTCGACATAAAAATACCCC 59.725 45.833 0.00 0.00 0.00 4.95
4044 4424 4.795795 CGTATGATATCATGCTCCTTCGAC 59.204 45.833 25.44 12.52 36.91 4.20
4053 4436 4.214119 ACAGCCAAACGTATGATATCATGC 59.786 41.667 25.44 22.81 37.15 4.06
4066 4449 5.681105 GTGCATTATACATTACAGCCAAACG 59.319 40.000 0.00 0.00 0.00 3.60
4083 4466 2.177394 TGTCTTTCGGCTGTGCATTA 57.823 45.000 0.00 0.00 0.00 1.90
4084 4467 1.317613 TTGTCTTTCGGCTGTGCATT 58.682 45.000 0.00 0.00 0.00 3.56
4085 4468 1.538047 ATTGTCTTTCGGCTGTGCAT 58.462 45.000 0.00 0.00 0.00 3.96
4086 4469 1.001487 CAATTGTCTTTCGGCTGTGCA 60.001 47.619 0.00 0.00 0.00 4.57
4087 4470 1.689959 CAATTGTCTTTCGGCTGTGC 58.310 50.000 0.00 0.00 0.00 4.57
4088 4471 1.666888 GGCAATTGTCTTTCGGCTGTG 60.667 52.381 7.40 0.00 0.00 3.66
4089 4472 0.598065 GGCAATTGTCTTTCGGCTGT 59.402 50.000 7.40 0.00 0.00 4.40
4093 4476 1.156736 AGACGGCAATTGTCTTTCGG 58.843 50.000 8.67 0.00 44.00 4.30
4104 4487 2.301870 ACATTCTAGACCAAGACGGCAA 59.698 45.455 0.00 0.00 39.03 4.52
4109 4492 8.779354 AGTTTATTCACATTCTAGACCAAGAC 57.221 34.615 0.00 0.00 0.00 3.01
4144 4527 1.072159 GCAGTGGACAACAGGAGCT 59.928 57.895 0.00 0.00 0.00 4.09
4146 4529 1.302832 GGGCAGTGGACAACAGGAG 60.303 63.158 0.00 0.00 0.00 3.69
4147 4530 2.055689 CTGGGCAGTGGACAACAGGA 62.056 60.000 0.00 0.00 0.00 3.86
4153 4536 2.930019 CCCTCTGGGCAGTGGACA 60.930 66.667 0.00 0.00 42.98 4.02
4163 4546 3.054802 GGTGATAAGCATATCCCCTCTGG 60.055 52.174 6.50 0.00 37.68 3.86
4166 4561 4.640771 TTGGTGATAAGCATATCCCCTC 57.359 45.455 11.06 0.00 37.08 4.30
4200 4595 1.459592 CATCCAACAAAGTCGGACGAC 59.540 52.381 16.39 16.39 44.86 4.34
4257 4662 5.740099 GCTCGAGATATTATACCTTTCGCTC 59.260 44.000 18.75 0.00 0.00 5.03
4277 4682 2.033927 TGCAGCTCTGACTAATAGCTCG 59.966 50.000 0.29 0.00 44.58 5.03
4284 4691 0.681175 TGCAGTGCAGCTCTGACTAA 59.319 50.000 25.42 6.99 35.20 2.24
4451 4861 0.532417 TGGCAAACAAGCAATGGCAC 60.532 50.000 0.00 0.00 43.60 5.01
4452 4862 0.532417 GTGGCAAACAAGCAATGGCA 60.532 50.000 0.00 0.00 45.85 4.92
4453 4863 1.229975 GGTGGCAAACAAGCAATGGC 61.230 55.000 0.00 0.00 39.81 4.40
4454 4864 0.393820 AGGTGGCAAACAAGCAATGG 59.606 50.000 0.00 0.00 35.83 3.16
4455 4865 1.068895 TCAGGTGGCAAACAAGCAATG 59.931 47.619 0.00 0.00 35.83 2.82
4456 4866 1.069049 GTCAGGTGGCAAACAAGCAAT 59.931 47.619 0.00 0.00 35.83 3.56
4459 4869 0.031178 CAGTCAGGTGGCAAACAAGC 59.969 55.000 0.00 0.00 0.00 4.01
4460 4870 1.392589 ACAGTCAGGTGGCAAACAAG 58.607 50.000 0.00 0.00 0.00 3.16
4461 4871 2.719531 TACAGTCAGGTGGCAAACAA 57.280 45.000 0.00 0.00 0.00 2.83
4463 4873 4.202111 ACATTTTACAGTCAGGTGGCAAAC 60.202 41.667 0.00 0.00 0.00 2.93
4465 4875 3.561143 ACATTTTACAGTCAGGTGGCAA 58.439 40.909 0.00 0.00 0.00 4.52
4466 4876 3.222173 ACATTTTACAGTCAGGTGGCA 57.778 42.857 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.