Multiple sequence alignment - TraesCS3B01G398900

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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 TraesCS3B01G398900 chr3B 100.000 4813 0 0 1 4813 630008115 630003303 0.000000e+00 8889
1 TraesCS3B01G398900 chr3D 93.248 2577 99 19 7 2542 473750529 473747987 0.000000e+00 3725
2 TraesCS3B01G398900 chr3D 93.436 1691 90 15 2633 4309 473747836 473746153 0.000000e+00 2488
3 TraesCS3B01G398900 chr3D 94.000 150 5 2 4667 4813 473745685 473745537 1.740000e-54 224
4 TraesCS3B01G398900 chr3A 92.277 2538 123 35 1 2500 616254275 616251773 0.000000e+00 3533
5 TraesCS3B01G398900 chr3A 92.228 1840 100 28 2484 4309 616251586 616249776 0.000000e+00 2566
6 TraesCS3B01G398900 chr3A 91.925 161 8 2 4657 4813 616249206 616249047 2.250000e-53 220
7 TraesCS3B01G398900 chr7B 85.039 381 43 7 3782 4159 639215677 639215308 4.550000e-100 375
8 TraesCS3B01G398900 chr5D 81.524 433 62 11 3544 3970 371882009 371882429 1.660000e-89 340
9 TraesCS3B01G398900 chr5D 85.593 118 11 3 4045 4162 371882432 371882543 8.460000e-23 119
10 TraesCS3B01G398900 chr4D 81.524 433 57 10 3544 3970 333467733 333467318 7.720000e-88 335
11 TraesCS3B01G398900 chr6D 90.303 165 13 3 3999 4161 193559503 193559666 3.770000e-51 213
12 TraesCS3B01G398900 chr6B 89.697 165 12 4 3999 4161 300951529 300951368 6.310000e-49 206


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 TraesCS3B01G398900 chr3B 630003303 630008115 4812 True 8889.000000 8889 100.000000 1 4813 1 chr3B.!!$R1 4812
1 TraesCS3B01G398900 chr3D 473745537 473750529 4992 True 2145.666667 3725 93.561333 7 4813 3 chr3D.!!$R1 4806
2 TraesCS3B01G398900 chr3A 616249047 616254275 5228 True 2106.333333 3533 92.143333 1 4813 3 chr3A.!!$R1 4812
3 TraesCS3B01G398900 chr5D 371882009 371882543 534 False 229.500000 340 83.558500 3544 4162 2 chr5D.!!$F1 618

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
45 46 0.521735 CCTAGGCGTTGCTTGTTTCC 59.478 55.000 0.00 0.00 0.00 3.13 F
310 322 0.675083 TTCTGCTTGGTTGTGCATGG 59.325 50.000 0.00 0.00 38.59 3.66 F
1305 1355 2.159028 GCTGGGAGATCAACTGGTAGTC 60.159 54.545 0.00 0.00 0.00 2.59 F
1447 1502 0.392060 TGACGACGCTAGCAGTAGGA 60.392 55.000 16.45 3.27 0.00 2.94 F
1448 1503 0.945813 GACGACGCTAGCAGTAGGAT 59.054 55.000 16.45 0.00 0.00 3.24 F
1450 1505 1.065701 ACGACGCTAGCAGTAGGATTG 59.934 52.381 16.45 0.00 0.00 2.67 F
2416 2476 1.076705 GAACTCCATCCCCAAGGCC 60.077 63.158 0.00 0.00 0.00 5.19 F
3121 3477 1.330655 ACCTCCATGAGCGTACCCTG 61.331 60.000 0.00 0.00 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1433 1488 0.105039 GCCAATCCTACTGCTAGCGT 59.895 55.000 10.77 13.21 0.00 5.07 R
1434 1489 0.390860 AGCCAATCCTACTGCTAGCG 59.609 55.000 10.77 7.61 30.97 4.26 R
2398 2458 1.076705 GGCCTTGGGGATGGAGTTC 60.077 63.158 0.00 0.00 33.58 3.01 R
3334 3690 0.036105 AGTGATCTGCGGCATGTGAA 60.036 50.000 1.75 0.00 0.00 3.18 R
3391 3747 1.541310 TACAGCAGAACCACCCTCGG 61.541 60.000 0.00 0.00 0.00 4.63 R
3458 3816 5.298989 TCTAGTTCAGTTTGGGCAACTAA 57.701 39.130 0.00 0.00 44.60 2.24 R
3492 3851 0.879090 CTTCACTCTGCAGCAATGCA 59.121 50.000 9.47 2.57 43.22 3.96 R
4523 5170 0.036952 CTCACGCCAATGTCAGGTCT 60.037 55.000 0.00 0.00 0.00 3.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.007473 AGCGAAAATCCCCGGAAATTA 57.993 42.857 0.73 0.00 0.00 1.40
44 45 1.519408 TCCTAGGCGTTGCTTGTTTC 58.481 50.000 2.96 0.00 0.00 2.78
45 46 0.521735 CCTAGGCGTTGCTTGTTTCC 59.478 55.000 0.00 0.00 0.00 3.13
105 115 1.498865 GATCGATCCATGCCGCGTTT 61.499 55.000 14.76 0.00 0.00 3.60
110 120 3.736100 CCATGCCGCGTTTGAGCA 61.736 61.111 9.36 9.36 41.50 4.26
237 247 4.340617 TGCCTTTATTCGTTTTCTCCCAT 58.659 39.130 0.00 0.00 0.00 4.00
269 279 1.423395 CGTTTGTGCTCCTGTCTCTC 58.577 55.000 0.00 0.00 0.00 3.20
299 311 2.744202 ACGCACCTTTAGATTCTGCTTG 59.256 45.455 0.00 0.00 0.00 4.01
310 322 0.675083 TTCTGCTTGGTTGTGCATGG 59.325 50.000 0.00 0.00 38.59 3.66
380 392 5.054390 TGATTTTGGTTACAATTCGAGGC 57.946 39.130 0.00 0.00 36.29 4.70
479 513 2.742774 GGTTTGTTGCATGTTCCTGTC 58.257 47.619 0.00 0.00 0.00 3.51
541 575 8.937884 TCGACGTTATTGGAAAATATTTCTTCA 58.062 29.630 0.10 0.00 0.00 3.02
803 840 8.461222 TGATAAAGTATTGAAAAGGCACATCTG 58.539 33.333 0.00 0.00 0.00 2.90
854 891 8.130307 ACATAACAAAAGAAATTGAACTGCAC 57.870 30.769 0.00 0.00 34.38 4.57
905 947 8.095792 TCGTTTCCTTTGTAATTACATACAGGA 58.904 33.333 24.65 24.65 37.13 3.86
1305 1355 2.159028 GCTGGGAGATCAACTGGTAGTC 60.159 54.545 0.00 0.00 0.00 2.59
1435 1490 1.362717 ACAGAGGGTGTTGACGACG 59.637 57.895 0.00 0.00 34.94 5.12
1436 1491 2.022129 CAGAGGGTGTTGACGACGC 61.022 63.158 0.00 0.00 38.05 5.19
1437 1492 2.201022 AGAGGGTGTTGACGACGCT 61.201 57.895 6.35 0.00 39.17 5.07
1438 1493 0.892358 AGAGGGTGTTGACGACGCTA 60.892 55.000 6.35 0.00 36.79 4.26
1439 1494 0.456312 GAGGGTGTTGACGACGCTAG 60.456 60.000 6.35 0.00 36.79 3.42
1440 1495 2.092882 GGGTGTTGACGACGCTAGC 61.093 63.158 4.06 4.06 38.81 3.42
1441 1496 1.372499 GGTGTTGACGACGCTAGCA 60.372 57.895 16.45 0.00 38.81 3.49
1442 1497 1.344942 GGTGTTGACGACGCTAGCAG 61.345 60.000 16.45 10.16 38.81 4.24
1443 1498 0.663568 GTGTTGACGACGCTAGCAGT 60.664 55.000 16.45 13.49 35.85 4.40
1444 1499 0.876399 TGTTGACGACGCTAGCAGTA 59.124 50.000 16.45 0.00 0.00 2.74
1445 1500 1.135774 TGTTGACGACGCTAGCAGTAG 60.136 52.381 16.45 15.29 0.00 2.57
1446 1501 0.450583 TTGACGACGCTAGCAGTAGG 59.549 55.000 16.45 11.05 0.00 3.18
1447 1502 0.392060 TGACGACGCTAGCAGTAGGA 60.392 55.000 16.45 3.27 0.00 2.94
1448 1503 0.945813 GACGACGCTAGCAGTAGGAT 59.054 55.000 16.45 0.00 0.00 3.24
1449 1504 1.334243 GACGACGCTAGCAGTAGGATT 59.666 52.381 16.45 0.00 0.00 3.01
1450 1505 1.065701 ACGACGCTAGCAGTAGGATTG 59.934 52.381 16.45 0.00 0.00 2.67
1523 1578 4.978083 CTGGACTTCCTGGATTTCATTG 57.022 45.455 0.00 0.00 36.82 2.82
1616 1671 3.538591 AGATCTGCTGATTCATTTCGCA 58.461 40.909 7.59 0.00 32.19 5.10
1620 1675 4.190772 TCTGCTGATTCATTTCGCATACA 58.809 39.130 0.00 0.00 0.00 2.29
1653 1708 4.345288 TCGTCGATGAAGTTACATTACCG 58.655 43.478 4.45 0.00 0.00 4.02
1657 1712 3.807622 CGATGAAGTTACATTACCGCCAT 59.192 43.478 0.00 0.00 0.00 4.40
1660 1715 2.411628 AGTTACATTACCGCCATGCA 57.588 45.000 0.00 0.00 0.00 3.96
1666 1721 1.174712 ATTACCGCCATGCATGCCTC 61.175 55.000 21.69 10.93 0.00 4.70
1667 1722 2.549169 TTACCGCCATGCATGCCTCA 62.549 55.000 21.69 0.00 0.00 3.86
1767 1824 7.661536 ACTAAGCTTTGATAGATGTACAGGA 57.338 36.000 14.98 0.00 0.00 3.86
1792 1849 5.768164 TCTTGGTCTTCCATTTGAACTTACC 59.232 40.000 0.00 0.00 43.91 2.85
1795 1852 5.710099 TGGTCTTCCATTTGAACTTACCATC 59.290 40.000 0.00 0.00 39.03 3.51
1802 1859 5.943416 CCATTTGAACTTACCATCCTGTGTA 59.057 40.000 0.00 0.00 0.00 2.90
1894 1951 5.894298 ATGCACCCTATGAGATTACAGAA 57.106 39.130 0.00 0.00 0.00 3.02
2089 2146 6.998673 AGATTACCATGTGGATTAGTAAAGCC 59.001 38.462 5.96 0.00 41.79 4.35
2122 2179 5.840693 TGGGTGATCAGATATTCTCTTGCTA 59.159 40.000 0.00 0.00 29.16 3.49
2124 2181 6.014669 GGGTGATCAGATATTCTCTTGCTACT 60.015 42.308 0.00 0.00 29.16 2.57
2148 2205 8.208903 ACTTATTATTTACAGCCTTGTATCGGT 58.791 33.333 0.00 0.00 39.43 4.69
2156 2213 1.473257 GCCTTGTATCGGTGCAGATCA 60.473 52.381 0.00 0.00 32.39 2.92
2192 2249 5.490139 AATGTTTTCATGCTCATCGTAGG 57.510 39.130 0.00 0.00 40.79 3.18
2227 2285 5.823209 TGTCCATTGCAATCTTACATGAG 57.177 39.130 9.53 0.00 0.00 2.90
2302 2362 3.006430 TGTTAACGAGAATGCTGGAGTGA 59.994 43.478 0.26 0.00 0.00 3.41
2398 2458 5.255397 TGGGCAGGTATGATAATTTAGGG 57.745 43.478 0.00 0.00 0.00 3.53
2416 2476 1.076705 GAACTCCATCCCCAAGGCC 60.077 63.158 0.00 0.00 0.00 5.19
2425 2485 1.914764 CCCCAAGGCCAATGTTGCT 60.915 57.895 5.01 0.00 0.00 3.91
2430 2490 3.450457 CCCAAGGCCAATGTTGCTTATTA 59.550 43.478 5.01 0.00 0.00 0.98
2440 2500 7.765819 GCCAATGTTGCTTATTATTCTTCCTTT 59.234 33.333 0.00 0.00 0.00 3.11
2478 2538 3.308401 AGGGAACACAAAGAAAATGGCT 58.692 40.909 0.00 0.00 0.00 4.75
2536 2799 9.646427 TGTAAAAATACCATTTAATGCTTCCAC 57.354 29.630 0.00 0.00 0.00 4.02
2548 2894 7.566760 TTAATGCTTCCACTGTACCATATTG 57.433 36.000 0.00 0.00 0.00 1.90
2573 2919 9.023962 TGATCATGGTTTTAATGCTTACTCTTT 57.976 29.630 0.00 0.00 0.00 2.52
2575 2921 7.826690 TCATGGTTTTAATGCTTACTCTTTCC 58.173 34.615 0.00 0.00 0.00 3.13
2576 2922 7.450014 TCATGGTTTTAATGCTTACTCTTTCCA 59.550 33.333 0.00 0.00 0.00 3.53
2577 2923 7.214467 TGGTTTTAATGCTTACTCTTTCCAG 57.786 36.000 0.00 0.00 0.00 3.86
2578 2924 6.208599 TGGTTTTAATGCTTACTCTTTCCAGG 59.791 38.462 0.00 0.00 0.00 4.45
2580 2926 7.362142 GGTTTTAATGCTTACTCTTTCCAGGAG 60.362 40.741 0.00 0.00 36.92 3.69
2581 2927 3.922171 ATGCTTACTCTTTCCAGGAGG 57.078 47.619 0.00 0.00 35.34 4.30
2587 2937 5.512576 GCTTACTCTTTCCAGGAGGTTACAA 60.513 44.000 0.00 0.00 35.34 2.41
2591 2941 4.918588 TCTTTCCAGGAGGTTACAATTCC 58.081 43.478 0.00 0.00 35.89 3.01
2606 2956 9.705290 GGTTACAATTCCATTTTACATGTTTCT 57.295 29.630 2.30 0.00 0.00 2.52
2623 2973 6.061022 TGTTTCTATGTCAATGCCCTTCTA 57.939 37.500 0.00 0.00 0.00 2.10
2626 2976 8.271458 TGTTTCTATGTCAATGCCCTTCTATTA 58.729 33.333 0.00 0.00 0.00 0.98
2627 2977 9.289782 GTTTCTATGTCAATGCCCTTCTATTAT 57.710 33.333 0.00 0.00 0.00 1.28
2628 2978 8.853077 TTCTATGTCAATGCCCTTCTATTATG 57.147 34.615 0.00 0.00 0.00 1.90
2629 2979 7.977818 TCTATGTCAATGCCCTTCTATTATGT 58.022 34.615 0.00 0.00 0.00 2.29
2630 2980 8.097038 TCTATGTCAATGCCCTTCTATTATGTC 58.903 37.037 0.00 0.00 0.00 3.06
2631 2981 6.000246 TGTCAATGCCCTTCTATTATGTCA 58.000 37.500 0.00 0.00 0.00 3.58
2632 2982 6.422333 TGTCAATGCCCTTCTATTATGTCAA 58.578 36.000 0.00 0.00 0.00 3.18
2633 2983 7.062322 TGTCAATGCCCTTCTATTATGTCAAT 58.938 34.615 0.00 0.00 0.00 2.57
2634 2984 7.013559 TGTCAATGCCCTTCTATTATGTCAATG 59.986 37.037 0.00 0.00 0.00 2.82
2635 2985 5.972107 ATGCCCTTCTATTATGTCAATGC 57.028 39.130 0.00 0.00 0.00 3.56
2636 2986 4.144297 TGCCCTTCTATTATGTCAATGCC 58.856 43.478 0.00 0.00 0.00 4.40
2637 2987 3.507622 GCCCTTCTATTATGTCAATGCCC 59.492 47.826 0.00 0.00 0.00 5.36
2638 2988 4.751028 GCCCTTCTATTATGTCAATGCCCT 60.751 45.833 0.00 0.00 0.00 5.19
2639 2989 5.388654 CCCTTCTATTATGTCAATGCCCTT 58.611 41.667 0.00 0.00 0.00 3.95
2640 2990 5.474876 CCCTTCTATTATGTCAATGCCCTTC 59.525 44.000 0.00 0.00 0.00 3.46
2641 2991 6.302269 CCTTCTATTATGTCAATGCCCTTCT 58.698 40.000 0.00 0.00 0.00 2.85
2642 2992 7.453393 CCTTCTATTATGTCAATGCCCTTCTA 58.547 38.462 0.00 0.00 0.00 2.10
2643 2993 8.105829 CCTTCTATTATGTCAATGCCCTTCTAT 58.894 37.037 0.00 0.00 0.00 1.98
2644 2994 9.512588 CTTCTATTATGTCAATGCCCTTCTATT 57.487 33.333 0.00 0.00 0.00 1.73
2645 2995 9.866655 TTCTATTATGTCAATGCCCTTCTATTT 57.133 29.630 0.00 0.00 0.00 1.40
2652 3002 8.537728 TGTCAATGCCCTTCTATTTCATTTAT 57.462 30.769 0.00 0.00 0.00 1.40
2672 3022 9.524106 CATTTATTGAAACATATGCTCATGTGT 57.476 29.630 1.58 6.45 43.54 3.72
2766 3116 3.697045 TGTTGAGGTACCTTTTGTGGTTG 59.303 43.478 17.53 0.00 41.22 3.77
2808 3160 9.950680 TCTCAATAACTCACAAAGTTTGATTTC 57.049 29.630 22.23 0.00 46.26 2.17
2813 3165 4.202010 ACTCACAAAGTTTGATTTCGGTGG 60.202 41.667 22.23 5.21 33.03 4.61
2815 3167 3.067461 CACAAAGTTTGATTTCGGTGGGA 59.933 43.478 22.23 0.00 0.00 4.37
2832 3184 5.058490 GGTGGGATTCATATTTTGCCATTG 58.942 41.667 0.00 0.00 0.00 2.82
2837 3190 6.822676 GGGATTCATATTTTGCCATTGAACAA 59.177 34.615 0.00 0.00 0.00 2.83
2903 3256 4.236527 ACTTGGTGACTTCCTTCTTGTT 57.763 40.909 0.00 0.00 0.00 2.83
2932 3285 1.556451 TGATGACCAGTCCATCAGGTG 59.444 52.381 0.00 0.00 43.67 4.00
2945 3298 7.498900 CAGTCCATCAGGTGCTTATTTAACATA 59.501 37.037 0.00 0.00 35.89 2.29
3121 3477 1.330655 ACCTCCATGAGCGTACCCTG 61.331 60.000 0.00 0.00 0.00 4.45
3127 3483 1.899437 ATGAGCGTACCCTGGGTGTG 61.899 60.000 28.64 20.07 36.19 3.82
3130 3486 2.264794 CGTACCCTGGGTGTGCTC 59.735 66.667 28.64 11.72 36.19 4.26
3242 3598 6.023603 TCAACCTATTTCTCCTACCTGACTT 58.976 40.000 0.00 0.00 0.00 3.01
3244 3600 4.717280 ACCTATTTCTCCTACCTGACTTGG 59.283 45.833 0.00 0.00 0.00 3.61
3262 3618 5.954335 ACTTGGTAAGTTTCAAGCATATGC 58.046 37.500 20.36 20.36 42.82 3.14
3287 3643 8.552034 GCTTCCAAGAATGACTGTATTGTATAC 58.448 37.037 0.00 0.00 0.00 1.47
3289 3645 7.778083 TCCAAGAATGACTGTATTGTATACGT 58.222 34.615 0.00 0.00 0.00 3.57
3290 3646 8.255206 TCCAAGAATGACTGTATTGTATACGTT 58.745 33.333 0.00 0.00 0.00 3.99
3303 3659 5.778161 TGTATACGTTGCAGAGATGTTTG 57.222 39.130 0.00 0.00 0.00 2.93
3334 3690 3.459969 AGACCCTCACACCTTCTCTTTTT 59.540 43.478 0.00 0.00 0.00 1.94
3415 3771 1.880027 GGGTGGTTCTGCTGTAAGTTG 59.120 52.381 0.00 0.00 35.30 3.16
3425 3781 8.347035 GGTTCTGCTGTAAGTTGTTAATTACAA 58.653 33.333 0.00 0.00 44.31 2.41
3457 3815 8.598916 TGTATCCTGATGTCAAACTTACCTAAA 58.401 33.333 0.00 0.00 0.00 1.85
3458 3816 9.614792 GTATCCTGATGTCAAACTTACCTAAAT 57.385 33.333 0.00 0.00 0.00 1.40
3465 3823 9.556030 GATGTCAAACTTACCTAAATTAGTTGC 57.444 33.333 0.00 0.00 31.64 4.17
3482 3841 4.489679 GTTGCCCAAACTGAACTAGAAG 57.510 45.455 0.00 0.00 35.75 2.85
3492 3851 5.690464 ACTGAACTAGAAGCTTCATGGAT 57.310 39.130 27.57 9.68 0.00 3.41
3522 3881 3.195610 TGCAGAGTGAAGTTGATCCGTAT 59.804 43.478 0.00 0.00 0.00 3.06
3594 3953 2.442212 TAACATCTGTTTCGGTCGCA 57.558 45.000 0.20 0.00 39.31 5.10
3621 3980 7.120579 ACAAGAATAATTGATAACCACGAAGCA 59.879 33.333 0.00 0.00 34.20 3.91
3660 4022 1.284657 CAGTGCGACTTGCCTGATAG 58.715 55.000 0.00 0.00 45.60 2.08
3708 4071 9.856162 TTAGTTTGTTTAAGTCCTGTTTATCCT 57.144 29.630 0.00 0.00 0.00 3.24
3844 4209 3.429881 GGAGCTTACATTTTTGCAGCAAC 59.570 43.478 7.54 0.00 32.58 4.17
3915 4282 3.192844 AGATTGCAACAATTCCTCAGCTG 59.807 43.478 7.63 7.63 0.00 4.24
4231 4603 7.042335 ACATATACTGCTGAGAAACAACCTAC 58.958 38.462 0.00 0.00 0.00 3.18
4274 4646 7.496529 TGTTTGATTTGTCTAACCAGAGAAG 57.503 36.000 0.00 0.00 35.64 2.85
4290 4662 5.123027 CCAGAGAAGGTTATGTTCAGCTTTC 59.877 44.000 0.00 0.00 32.09 2.62
4291 4663 5.123027 CAGAGAAGGTTATGTTCAGCTTTCC 59.877 44.000 0.00 0.00 32.09 3.13
4292 4664 4.336280 AGAAGGTTATGTTCAGCTTTCCC 58.664 43.478 0.00 0.00 32.09 3.97
4293 4665 4.043435 AGAAGGTTATGTTCAGCTTTCCCT 59.957 41.667 0.00 0.00 32.09 4.20
4294 4666 4.388577 AGGTTATGTTCAGCTTTCCCTT 57.611 40.909 0.00 0.00 0.00 3.95
4295 4667 4.082125 AGGTTATGTTCAGCTTTCCCTTG 58.918 43.478 0.00 0.00 0.00 3.61
4296 4668 3.826729 GGTTATGTTCAGCTTTCCCTTGT 59.173 43.478 0.00 0.00 0.00 3.16
4297 4669 4.280929 GGTTATGTTCAGCTTTCCCTTGTT 59.719 41.667 0.00 0.00 0.00 2.83
4298 4670 5.461526 GTTATGTTCAGCTTTCCCTTGTTC 58.538 41.667 0.00 0.00 0.00 3.18
4299 4671 3.011566 TGTTCAGCTTTCCCTTGTTCA 57.988 42.857 0.00 0.00 0.00 3.18
4300 4672 3.565307 TGTTCAGCTTTCCCTTGTTCAT 58.435 40.909 0.00 0.00 0.00 2.57
4301 4673 3.960102 TGTTCAGCTTTCCCTTGTTCATT 59.040 39.130 0.00 0.00 0.00 2.57
4302 4674 4.202141 TGTTCAGCTTTCCCTTGTTCATTG 60.202 41.667 0.00 0.00 0.00 2.82
4303 4675 2.892852 TCAGCTTTCCCTTGTTCATTGG 59.107 45.455 0.00 0.00 0.00 3.16
4304 4676 2.629617 CAGCTTTCCCTTGTTCATTGGT 59.370 45.455 0.00 0.00 0.00 3.67
4305 4677 3.826157 CAGCTTTCCCTTGTTCATTGGTA 59.174 43.478 0.00 0.00 0.00 3.25
4306 4678 4.463891 CAGCTTTCCCTTGTTCATTGGTAT 59.536 41.667 0.00 0.00 0.00 2.73
4307 4679 5.047092 CAGCTTTCCCTTGTTCATTGGTATT 60.047 40.000 0.00 0.00 0.00 1.89
4308 4680 5.543790 AGCTTTCCCTTGTTCATTGGTATTT 59.456 36.000 0.00 0.00 0.00 1.40
4309 4681 6.043127 AGCTTTCCCTTGTTCATTGGTATTTT 59.957 34.615 0.00 0.00 0.00 1.82
4310 4682 6.710295 GCTTTCCCTTGTTCATTGGTATTTTT 59.290 34.615 0.00 0.00 0.00 1.94
4311 4683 7.095229 GCTTTCCCTTGTTCATTGGTATTTTTC 60.095 37.037 0.00 0.00 0.00 2.29
4337 4709 7.437748 CCTTGTTCATTGGTATTTGGTGTTAA 58.562 34.615 0.00 0.00 0.00 2.01
4338 4710 7.383843 CCTTGTTCATTGGTATTTGGTGTTAAC 59.616 37.037 0.00 0.00 0.00 2.01
4339 4711 7.589958 TGTTCATTGGTATTTGGTGTTAACT 57.410 32.000 7.22 0.00 0.00 2.24
4340 4712 7.429633 TGTTCATTGGTATTTGGTGTTAACTG 58.570 34.615 7.22 0.00 0.00 3.16
4345 4718 5.938279 TGGTATTTGGTGTTAACTGTACCA 58.062 37.500 11.26 11.26 42.40 3.25
4354 4735 0.033781 TAACTGTACCACGGTGCACC 59.966 55.000 26.78 26.78 37.84 5.01
4371 4752 1.134098 CACCGGGGATTTATCTGTGCT 60.134 52.381 6.32 0.00 0.00 4.40
4372 4753 1.141053 ACCGGGGATTTATCTGTGCTC 59.859 52.381 6.32 0.00 0.00 4.26
4402 4783 9.908152 GTCAGTAGTATTTTTACTTGCCAAAAT 57.092 29.630 0.00 0.00 36.69 1.82
4434 5081 8.565896 AAACTGTGATTCACTTGAATAGCATA 57.434 30.769 17.26 0.00 44.14 3.14
4454 5101 6.891908 AGCATATCCTTTGTACTGGTGAATTT 59.108 34.615 0.00 0.00 0.00 1.82
4460 5107 6.373216 TCCTTTGTACTGGTGAATTTAATCGG 59.627 38.462 0.00 0.00 0.00 4.18
4461 5108 5.554822 TTGTACTGGTGAATTTAATCGGC 57.445 39.130 0.00 0.00 0.00 5.54
4463 5110 2.014128 ACTGGTGAATTTAATCGGCGG 58.986 47.619 7.21 0.00 0.00 6.13
4465 5112 3.199677 CTGGTGAATTTAATCGGCGGTA 58.800 45.455 7.21 0.00 0.00 4.02
4482 5129 3.116079 GGTAGGACCGTTTGTCTTTGA 57.884 47.619 0.00 0.00 43.89 2.69
4510 5157 2.128771 TTTCCAGTCCTTGCCATAGC 57.871 50.000 0.00 0.00 40.48 2.97
4523 5170 3.658757 GCCATAGCAACAAAAGTTCCA 57.341 42.857 0.00 0.00 39.53 3.53
4524 5171 3.578688 GCCATAGCAACAAAAGTTCCAG 58.421 45.455 0.00 0.00 39.53 3.86
4525 5172 3.255642 GCCATAGCAACAAAAGTTCCAGA 59.744 43.478 0.00 0.00 39.53 3.86
4526 5173 4.798574 CCATAGCAACAAAAGTTCCAGAC 58.201 43.478 0.00 0.00 0.00 3.51
4527 5174 4.321230 CCATAGCAACAAAAGTTCCAGACC 60.321 45.833 0.00 0.00 0.00 3.85
4528 5175 3.018423 AGCAACAAAAGTTCCAGACCT 57.982 42.857 0.00 0.00 0.00 3.85
4529 5176 2.689983 AGCAACAAAAGTTCCAGACCTG 59.310 45.455 0.00 0.00 0.00 4.00
4530 5177 2.687935 GCAACAAAAGTTCCAGACCTGA 59.312 45.455 0.00 0.00 0.00 3.86
4531 5178 3.489229 GCAACAAAAGTTCCAGACCTGAC 60.489 47.826 0.00 0.00 0.00 3.51
4532 5179 3.644966 ACAAAAGTTCCAGACCTGACA 57.355 42.857 0.00 0.00 0.00 3.58
4533 5180 4.170468 ACAAAAGTTCCAGACCTGACAT 57.830 40.909 0.00 0.00 0.00 3.06
4534 5181 4.536765 ACAAAAGTTCCAGACCTGACATT 58.463 39.130 0.00 0.00 0.00 2.71
4535 5182 4.339247 ACAAAAGTTCCAGACCTGACATTG 59.661 41.667 0.00 3.25 0.00 2.82
4536 5183 2.867109 AGTTCCAGACCTGACATTGG 57.133 50.000 0.00 0.00 0.00 3.16
4537 5184 1.168714 GTTCCAGACCTGACATTGGC 58.831 55.000 0.00 0.00 0.00 4.52
4538 5185 0.321564 TTCCAGACCTGACATTGGCG 60.322 55.000 0.00 0.00 0.00 5.69
4539 5186 1.003355 CCAGACCTGACATTGGCGT 60.003 57.895 0.00 0.00 0.00 5.68
4540 5187 1.300971 CCAGACCTGACATTGGCGTG 61.301 60.000 0.00 0.00 0.00 5.34
4541 5188 0.320683 CAGACCTGACATTGGCGTGA 60.321 55.000 0.00 0.00 0.00 4.35
4542 5189 0.036952 AGACCTGACATTGGCGTGAG 60.037 55.000 0.00 0.00 0.00 3.51
4547 5194 2.416747 CTGACATTGGCGTGAGAAAGA 58.583 47.619 0.00 0.00 0.00 2.52
4548 5195 2.807967 CTGACATTGGCGTGAGAAAGAA 59.192 45.455 0.00 0.00 0.00 2.52
4560 5207 4.437390 CGTGAGAAAGAAAAGTGTTGTGCT 60.437 41.667 0.00 0.00 0.00 4.40
4561 5208 4.795278 GTGAGAAAGAAAAGTGTTGTGCTG 59.205 41.667 0.00 0.00 0.00 4.41
4563 5210 4.986622 AGAAAGAAAAGTGTTGTGCTGTC 58.013 39.130 0.00 0.00 0.00 3.51
4571 5218 2.632028 AGTGTTGTGCTGTCTCTGAGAT 59.368 45.455 11.07 0.00 0.00 2.75
4584 5231 5.070981 TGTCTCTGAGATGTTTGGAGTCTTT 59.929 40.000 11.07 0.00 0.00 2.52
4585 5232 5.994668 GTCTCTGAGATGTTTGGAGTCTTTT 59.005 40.000 11.07 0.00 0.00 2.27
4586 5233 6.484977 GTCTCTGAGATGTTTGGAGTCTTTTT 59.515 38.462 11.07 0.00 0.00 1.94
4632 5279 8.918202 AACAATGTGTATCTTTCTAAAGGACA 57.082 30.769 2.77 5.18 36.67 4.02
4639 5286 8.451748 GTGTATCTTTCTAAAGGACAATGGTTC 58.548 37.037 10.65 0.00 35.52 3.62
4662 5324 8.642020 GTTCAAATCTGCAGATGAAATTAACAC 58.358 33.333 29.34 13.62 34.49 3.32
4679 5341 3.582714 ACACGTAGTACTGGTTTAGGC 57.417 47.619 5.39 0.00 41.61 3.93
4689 5351 0.402504 TGGTTTAGGCGGTGGTGAAT 59.597 50.000 0.00 0.00 0.00 2.57
4698 5360 3.118038 AGGCGGTGGTGAATATTACATGT 60.118 43.478 2.69 2.69 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.200373 AACAAGCAACGCCTAGGAAT 57.800 45.000 14.75 0.00 0.00 3.01
110 120 4.082523 CACCTGCCCACGATCCGT 62.083 66.667 0.00 0.00 42.36 4.69
237 247 2.672714 CACAAACGGAATCACGAGAGA 58.327 47.619 0.00 0.00 37.61 3.10
269 279 0.250553 TAAAGGTGCGTGGGTCCAAG 60.251 55.000 0.00 0.00 0.00 3.61
299 311 1.005867 CAGCCAACCATGCACAACC 60.006 57.895 0.00 0.00 0.00 3.77
310 322 1.431496 AATTTTGCATCGCAGCCAAC 58.569 45.000 0.00 0.00 40.61 3.77
350 362 2.817258 TGTAACCAAAATCAAGCGAGGG 59.183 45.455 0.00 0.00 0.00 4.30
380 392 8.095792 AGCATATATGATTTCCAACTCTCTGAG 58.904 37.037 17.10 0.00 35.52 3.35
497 531 4.167268 GTCGATTGTTCAGACCACTCTAC 58.833 47.826 0.00 0.00 0.00 2.59
541 575 9.561069 ACGAGATATAGCCATAAATTTTGTTCT 57.439 29.630 0.00 0.00 0.00 3.01
558 592 5.184096 GGAGCTCAAGAATCCACGAGATATA 59.816 44.000 17.19 0.00 33.66 0.86
803 840 5.037385 GGAACAAGAAAGTGACTCAAAAGC 58.963 41.667 0.00 0.00 0.00 3.51
854 891 5.424121 AATGTCTCGTTCTCCAAACTTTG 57.576 39.130 0.00 0.00 0.00 2.77
903 945 3.117888 TCCTCATGCAAGAAAGGGTATCC 60.118 47.826 0.00 0.00 0.00 2.59
905 947 4.467769 CATCCTCATGCAAGAAAGGGTAT 58.532 43.478 0.00 0.00 0.00 2.73
970 1020 5.509840 GGTGTAGAAGTACTGCCCTGATATG 60.510 48.000 0.00 0.00 0.00 1.78
1305 1355 1.354337 CCTCATCACTGACAACGCCG 61.354 60.000 0.00 0.00 0.00 6.46
1424 1479 0.663568 ACTGCTAGCGTCGTCAACAC 60.664 55.000 10.77 0.00 0.00 3.32
1426 1481 1.536149 CTACTGCTAGCGTCGTCAAC 58.464 55.000 10.77 0.00 0.00 3.18
1427 1482 0.450583 CCTACTGCTAGCGTCGTCAA 59.549 55.000 10.77 0.00 0.00 3.18
1428 1483 0.392060 TCCTACTGCTAGCGTCGTCA 60.392 55.000 10.77 0.00 0.00 4.35
1429 1484 0.945813 ATCCTACTGCTAGCGTCGTC 59.054 55.000 10.77 0.00 0.00 4.20
1430 1485 1.065701 CAATCCTACTGCTAGCGTCGT 59.934 52.381 10.77 9.60 0.00 4.34
1431 1486 1.600663 CCAATCCTACTGCTAGCGTCG 60.601 57.143 10.77 7.18 0.00 5.12
1432 1487 1.870167 GCCAATCCTACTGCTAGCGTC 60.870 57.143 10.77 0.00 0.00 5.19
1433 1488 0.105039 GCCAATCCTACTGCTAGCGT 59.895 55.000 10.77 13.21 0.00 5.07
1434 1489 0.390860 AGCCAATCCTACTGCTAGCG 59.609 55.000 10.77 7.61 30.97 4.26
1435 1490 2.216898 CAAGCCAATCCTACTGCTAGC 58.783 52.381 8.10 8.10 32.82 3.42
1436 1491 3.118629 TGACAAGCCAATCCTACTGCTAG 60.119 47.826 0.00 0.00 32.82 3.42
1437 1492 2.837591 TGACAAGCCAATCCTACTGCTA 59.162 45.455 0.00 0.00 32.82 3.49
1438 1493 1.630369 TGACAAGCCAATCCTACTGCT 59.370 47.619 0.00 0.00 35.08 4.24
1439 1494 2.113860 TGACAAGCCAATCCTACTGC 57.886 50.000 0.00 0.00 0.00 4.40
1440 1495 3.191371 GGTTTGACAAGCCAATCCTACTG 59.809 47.826 15.56 0.00 34.60 2.74
1441 1496 3.181434 TGGTTTGACAAGCCAATCCTACT 60.181 43.478 20.20 0.00 37.02 2.57
1442 1497 3.153919 TGGTTTGACAAGCCAATCCTAC 58.846 45.455 20.20 0.00 37.02 3.18
1443 1498 3.517296 TGGTTTGACAAGCCAATCCTA 57.483 42.857 20.20 0.00 37.02 2.94
1444 1499 2.380064 TGGTTTGACAAGCCAATCCT 57.620 45.000 20.20 0.00 37.02 3.24
1445 1500 3.683365 ATTGGTTTGACAAGCCAATCC 57.317 42.857 32.15 11.91 46.52 3.01
1448 1503 3.632604 TCGTAATTGGTTTGACAAGCCAA 59.367 39.130 30.95 30.95 45.02 4.52
1449 1504 3.215151 TCGTAATTGGTTTGACAAGCCA 58.785 40.909 18.80 18.80 33.23 4.75
1450 1505 3.252458 ACTCGTAATTGGTTTGACAAGCC 59.748 43.478 13.77 13.77 33.23 4.35
1613 1668 4.549980 CGACGATATAGTTGAGTGTATGCG 59.450 45.833 0.00 0.00 0.00 4.73
1616 1671 7.668525 TCATCGACGATATAGTTGAGTGTAT 57.331 36.000 10.57 0.00 37.88 2.29
1620 1675 6.621316 ACTTCATCGACGATATAGTTGAGT 57.379 37.500 10.57 4.44 37.88 3.41
1657 1712 6.982160 AATTTATATCCTTTGAGGCATGCA 57.018 33.333 21.36 0.00 34.61 3.96
1660 1715 8.854117 GTCTGAAATTTATATCCTTTGAGGCAT 58.146 33.333 0.00 0.00 34.61 4.40
1792 1849 8.988934 GGTACAAACATACATATACACAGGATG 58.011 37.037 0.00 0.00 46.00 3.51
1795 1852 6.708949 GGGGTACAAACATACATATACACAGG 59.291 42.308 0.00 0.00 0.00 4.00
1802 1859 6.697641 CCTAGGGGGTACAAACATACATAT 57.302 41.667 0.00 0.00 0.00 1.78
1954 2011 4.061131 TCCATCAGGTAGAAGACAAGGA 57.939 45.455 0.00 0.00 35.89 3.36
2089 2146 9.347240 AGAATATCTGATCACCCAAAAATAGTG 57.653 33.333 0.00 0.00 0.00 2.74
2093 2150 8.910944 CAAGAGAATATCTGATCACCCAAAAAT 58.089 33.333 0.00 0.00 38.67 1.82
2099 2156 5.226194 AGCAAGAGAATATCTGATCACCC 57.774 43.478 0.00 0.00 38.67 4.61
2122 2179 8.208903 ACCGATACAAGGCTGTAAATAATAAGT 58.791 33.333 0.00 0.00 41.36 2.24
2124 2181 7.041644 GCACCGATACAAGGCTGTAAATAATAA 60.042 37.037 0.00 0.00 41.36 1.40
2167 2224 6.470235 CCTACGATGAGCATGAAAACATTTTC 59.530 38.462 9.68 9.68 45.13 2.29
2168 2225 6.324819 CCTACGATGAGCATGAAAACATTTT 58.675 36.000 0.00 0.00 0.00 1.82
2169 2226 5.677091 GCCTACGATGAGCATGAAAACATTT 60.677 40.000 0.00 0.00 0.00 2.32
2170 2227 4.201950 GCCTACGATGAGCATGAAAACATT 60.202 41.667 0.00 0.00 0.00 2.71
2171 2228 3.313526 GCCTACGATGAGCATGAAAACAT 59.686 43.478 0.00 0.00 0.00 2.71
2173 2230 2.285834 CGCCTACGATGAGCATGAAAAC 60.286 50.000 0.00 0.00 43.93 2.43
2188 2245 3.438781 TGGACAAACAATGAATCGCCTAC 59.561 43.478 0.00 0.00 0.00 3.18
2192 2249 3.061161 GCAATGGACAAACAATGAATCGC 59.939 43.478 0.00 0.00 0.00 4.58
2199 2257 6.757237 TGTAAGATTGCAATGGACAAACAAT 58.243 32.000 18.59 0.00 33.82 2.71
2202 2260 6.389091 TCATGTAAGATTGCAATGGACAAAC 58.611 36.000 18.59 6.80 0.00 2.93
2302 2362 5.450965 GGGTTTTCATCTGATCGCATGATTT 60.451 40.000 0.00 0.00 34.09 2.17
2398 2458 1.076705 GGCCTTGGGGATGGAGTTC 60.077 63.158 0.00 0.00 33.58 3.01
2430 2490 7.838193 AGAAGGCTGATCAAATAAAGGAAGAAT 59.162 33.333 0.00 0.00 0.00 2.40
2440 2500 5.428457 TGTTCCCTAGAAGGCTGATCAAATA 59.572 40.000 0.00 0.00 32.73 1.40
2511 2774 9.869757 AGTGGAAGCATTAAATGGTATTTTTAC 57.130 29.630 0.00 0.00 40.65 2.01
2548 2894 9.508567 GAAAGAGTAAGCATTAAAACCATGATC 57.491 33.333 0.00 0.00 28.70 2.92
2555 2901 7.362142 CCTCCTGGAAAGAGTAAGCATTAAAAC 60.362 40.741 0.00 0.00 34.57 2.43
2557 2903 6.180472 CCTCCTGGAAAGAGTAAGCATTAAA 58.820 40.000 0.00 0.00 34.57 1.52
2566 2912 6.296259 GGAATTGTAACCTCCTGGAAAGAGTA 60.296 42.308 0.00 0.00 37.04 2.59
2567 2913 5.515008 GGAATTGTAACCTCCTGGAAAGAGT 60.515 44.000 0.00 0.00 37.04 3.24
2569 2915 4.352595 TGGAATTGTAACCTCCTGGAAAGA 59.647 41.667 0.00 0.00 37.04 2.52
2570 2916 4.662278 TGGAATTGTAACCTCCTGGAAAG 58.338 43.478 0.00 0.00 37.04 2.62
2573 2919 4.946160 AATGGAATTGTAACCTCCTGGA 57.054 40.909 0.00 0.00 33.44 3.86
2575 2921 7.461182 TGTAAAATGGAATTGTAACCTCCTG 57.539 36.000 0.00 0.00 36.10 3.86
2576 2922 7.673926 ACATGTAAAATGGAATTGTAACCTCCT 59.326 33.333 0.00 0.00 36.10 3.69
2577 2923 7.836842 ACATGTAAAATGGAATTGTAACCTCC 58.163 34.615 0.00 0.00 36.10 4.30
2578 2924 9.705290 AAACATGTAAAATGGAATTGTAACCTC 57.295 29.630 0.00 0.00 36.10 3.85
2580 2926 9.705290 AGAAACATGTAAAATGGAATTGTAACC 57.295 29.630 0.00 0.00 36.10 2.85
2591 2941 8.810427 GGCATTGACATAGAAACATGTAAAATG 58.190 33.333 0.00 14.11 41.06 2.32
2606 2956 7.744733 TGACATAATAGAAGGGCATTGACATA 58.255 34.615 0.00 0.00 0.00 2.29
2607 2957 6.604171 TGACATAATAGAAGGGCATTGACAT 58.396 36.000 0.00 0.00 0.00 3.06
2608 2958 6.000246 TGACATAATAGAAGGGCATTGACA 58.000 37.500 0.00 0.00 0.00 3.58
2609 2959 6.942532 TTGACATAATAGAAGGGCATTGAC 57.057 37.500 0.00 0.00 0.00 3.18
2610 2960 6.016024 GCATTGACATAATAGAAGGGCATTGA 60.016 38.462 0.00 0.00 0.00 2.57
2611 2961 6.154445 GCATTGACATAATAGAAGGGCATTG 58.846 40.000 0.00 0.00 0.00 2.82
2612 2962 5.244626 GGCATTGACATAATAGAAGGGCATT 59.755 40.000 0.00 0.00 0.00 3.56
2623 2973 8.716674 ATGAAATAGAAGGGCATTGACATAAT 57.283 30.769 0.00 0.00 0.00 1.28
2626 2976 7.427989 AAATGAAATAGAAGGGCATTGACAT 57.572 32.000 0.00 0.00 30.35 3.06
2627 2977 6.855763 AAATGAAATAGAAGGGCATTGACA 57.144 33.333 0.00 0.00 30.35 3.58
2628 2978 9.252962 CAATAAATGAAATAGAAGGGCATTGAC 57.747 33.333 0.00 0.00 30.35 3.18
2629 2979 9.199645 TCAATAAATGAAATAGAAGGGCATTGA 57.800 29.630 0.00 0.00 34.30 2.57
2630 2980 9.820725 TTCAATAAATGAAATAGAAGGGCATTG 57.179 29.630 0.00 0.00 44.94 2.82
2645 2995 9.738832 CACATGAGCATATGTTTCAATAAATGA 57.261 29.630 13.59 0.00 39.17 2.57
2652 3002 5.963176 ACACACATGAGCATATGTTTCAA 57.037 34.783 13.59 0.00 39.17 2.69
2669 3019 1.569479 GCGAAGGAGCCTGAACACAC 61.569 60.000 0.00 0.00 0.00 3.82
2808 3160 2.692557 TGGCAAAATATGAATCCCACCG 59.307 45.455 0.00 0.00 0.00 4.94
2813 3165 7.846644 TTGTTCAATGGCAAAATATGAATCC 57.153 32.000 0.00 0.00 33.12 3.01
2851 3204 5.465056 GCACTTCTAAGGATCTGCATTAGAC 59.535 44.000 6.28 0.00 46.19 2.59
2903 3256 2.290260 GGACTGGTCATCATGAACACCA 60.290 50.000 21.93 21.93 39.52 4.17
2950 3303 6.780031 TCAACAAGTTCCCTTCATAATCCAAA 59.220 34.615 0.00 0.00 0.00 3.28
2960 3313 7.881775 AATATATGGTCAACAAGTTCCCTTC 57.118 36.000 0.00 0.00 0.00 3.46
3014 3368 9.424319 CTAACCTTATACAATACAGGCTACATG 57.576 37.037 0.00 0.00 0.00 3.21
3044 3400 5.185454 CAACTGGTTCTCATAAGCATGGTA 58.815 41.667 0.00 0.00 32.61 3.25
3045 3401 4.012374 CAACTGGTTCTCATAAGCATGGT 58.988 43.478 0.00 0.00 32.61 3.55
3211 3567 6.940867 GGTAGGAGAAATAGGTTGAAACAACT 59.059 38.462 13.05 4.05 0.00 3.16
3212 3568 6.940867 AGGTAGGAGAAATAGGTTGAAACAAC 59.059 38.462 6.13 6.13 0.00 3.32
3220 3576 5.189934 CCAAGTCAGGTAGGAGAAATAGGTT 59.810 44.000 0.00 0.00 0.00 3.50
3222 3578 4.717280 ACCAAGTCAGGTAGGAGAAATAGG 59.283 45.833 0.00 0.00 40.98 2.57
3231 3587 5.223449 TGAAACTTACCAAGTCAGGTAGG 57.777 43.478 0.00 0.00 44.48 3.18
3232 3588 5.179555 GCTTGAAACTTACCAAGTCAGGTAG 59.820 44.000 0.00 0.00 44.48 3.18
3262 3618 8.755941 CGTATACAATACAGTCATTCTTGGAAG 58.244 37.037 3.32 0.00 0.00 3.46
3268 3624 7.039270 TGCAACGTATACAATACAGTCATTCT 58.961 34.615 3.32 0.00 0.00 2.40
3269 3625 7.222031 TCTGCAACGTATACAATACAGTCATTC 59.778 37.037 3.32 0.00 0.00 2.67
3275 3631 6.697455 ACATCTCTGCAACGTATACAATACAG 59.303 38.462 3.32 5.32 0.00 2.74
3287 3643 3.338818 ACAACAAACATCTCTGCAACG 57.661 42.857 0.00 0.00 0.00 4.10
3289 3645 4.337836 TGCTAACAACAAACATCTCTGCAA 59.662 37.500 0.00 0.00 0.00 4.08
3290 3646 3.882288 TGCTAACAACAAACATCTCTGCA 59.118 39.130 0.00 0.00 0.00 4.41
3303 3659 2.143925 GTGTGAGGGTCTGCTAACAAC 58.856 52.381 0.00 0.00 0.00 3.32
3334 3690 0.036105 AGTGATCTGCGGCATGTGAA 60.036 50.000 1.75 0.00 0.00 3.18
3342 3698 3.261580 TGTTGAATGTAGTGATCTGCGG 58.738 45.455 0.00 0.00 0.00 5.69
3391 3747 1.541310 TACAGCAGAACCACCCTCGG 61.541 60.000 0.00 0.00 0.00 4.63
3457 3815 5.876357 TCTAGTTCAGTTTGGGCAACTAAT 58.124 37.500 0.00 0.00 44.60 1.73
3458 3816 5.298989 TCTAGTTCAGTTTGGGCAACTAA 57.701 39.130 0.00 0.00 44.60 2.24
3465 3823 4.389374 TGAAGCTTCTAGTTCAGTTTGGG 58.611 43.478 26.09 0.00 0.00 4.12
3478 3837 2.100916 GCAATGCATCCATGAAGCTTCT 59.899 45.455 26.09 9.99 0.00 2.85
3482 3841 1.852942 CAGCAATGCATCCATGAAGC 58.147 50.000 8.35 0.00 0.00 3.86
3492 3851 0.879090 CTTCACTCTGCAGCAATGCA 59.121 50.000 9.47 2.57 43.22 3.96
3594 3953 7.968405 GCTTCGTGGTTATCAATTATTCTTGTT 59.032 33.333 0.00 0.00 0.00 2.83
3621 3980 5.128827 CACTGTGGGAGTGTATACCTTGTAT 59.871 44.000 0.00 0.00 46.30 2.29
3708 4071 4.993028 ACCCCAAGAATGCTGTTTAGTAA 58.007 39.130 0.00 0.00 0.00 2.24
3718 4081 2.102252 TGTTCACAAACCCCAAGAATGC 59.898 45.455 0.00 0.00 34.28 3.56
3719 4082 3.636300 TCTGTTCACAAACCCCAAGAATG 59.364 43.478 0.00 0.00 34.28 2.67
3844 4209 2.026822 AGGCGCCATATATTTCCTCAGG 60.027 50.000 31.54 0.00 0.00 3.86
4151 4520 6.476378 AGTATGCAACTCTAATCACAAACCT 58.524 36.000 0.00 0.00 30.33 3.50
4152 4521 6.743575 AGTATGCAACTCTAATCACAAACC 57.256 37.500 0.00 0.00 30.33 3.27
4162 4531 8.978472 AGTACAATTAGGAAGTATGCAACTCTA 58.022 33.333 0.00 0.00 37.50 2.43
4163 4532 7.852263 AGTACAATTAGGAAGTATGCAACTCT 58.148 34.615 0.00 0.00 37.50 3.24
4164 4533 9.595823 TTAGTACAATTAGGAAGTATGCAACTC 57.404 33.333 0.00 0.00 37.50 3.01
4207 4579 7.223582 CAGTAGGTTGTTTCTCAGCAGTATATG 59.776 40.741 0.00 0.00 0.00 1.78
4231 4603 2.559668 ACAAATGCCAACAGGTCATCAG 59.440 45.455 0.00 0.00 0.00 2.90
4274 4646 3.826729 ACAAGGGAAAGCTGAACATAACC 59.173 43.478 0.00 0.00 0.00 2.85
4290 4662 5.248248 AGGGAAAAATACCAATGAACAAGGG 59.752 40.000 0.00 0.00 0.00 3.95
4291 4663 6.358974 AGGGAAAAATACCAATGAACAAGG 57.641 37.500 0.00 0.00 0.00 3.61
4292 4664 7.216494 ACAAGGGAAAAATACCAATGAACAAG 58.784 34.615 0.00 0.00 0.00 3.16
4293 4665 7.130681 ACAAGGGAAAAATACCAATGAACAA 57.869 32.000 0.00 0.00 0.00 2.83
4294 4666 6.739331 ACAAGGGAAAAATACCAATGAACA 57.261 33.333 0.00 0.00 0.00 3.18
4295 4667 7.213678 TGAACAAGGGAAAAATACCAATGAAC 58.786 34.615 0.00 0.00 0.00 3.18
4296 4668 7.366847 TGAACAAGGGAAAAATACCAATGAA 57.633 32.000 0.00 0.00 0.00 2.57
4297 4669 6.985653 TGAACAAGGGAAAAATACCAATGA 57.014 33.333 0.00 0.00 0.00 2.57
4298 4670 7.119553 CCAATGAACAAGGGAAAAATACCAATG 59.880 37.037 0.00 0.00 0.00 2.82
4299 4671 7.167535 CCAATGAACAAGGGAAAAATACCAAT 58.832 34.615 0.00 0.00 0.00 3.16
4300 4672 6.100424 ACCAATGAACAAGGGAAAAATACCAA 59.900 34.615 0.00 0.00 0.00 3.67
4301 4673 5.604650 ACCAATGAACAAGGGAAAAATACCA 59.395 36.000 0.00 0.00 0.00 3.25
4302 4674 6.109156 ACCAATGAACAAGGGAAAAATACC 57.891 37.500 0.00 0.00 0.00 2.73
4303 4675 9.719355 AAATACCAATGAACAAGGGAAAAATAC 57.281 29.630 0.00 0.00 0.00 1.89
4304 4676 9.717942 CAAATACCAATGAACAAGGGAAAAATA 57.282 29.630 0.00 0.00 0.00 1.40
4305 4677 7.665145 CCAAATACCAATGAACAAGGGAAAAAT 59.335 33.333 0.00 0.00 0.00 1.82
4306 4678 6.995091 CCAAATACCAATGAACAAGGGAAAAA 59.005 34.615 0.00 0.00 0.00 1.94
4307 4679 6.100424 ACCAAATACCAATGAACAAGGGAAAA 59.900 34.615 0.00 0.00 0.00 2.29
4308 4680 5.604650 ACCAAATACCAATGAACAAGGGAAA 59.395 36.000 0.00 0.00 0.00 3.13
4309 4681 5.011533 CACCAAATACCAATGAACAAGGGAA 59.988 40.000 0.00 0.00 0.00 3.97
4310 4682 4.526262 CACCAAATACCAATGAACAAGGGA 59.474 41.667 0.00 0.00 0.00 4.20
4311 4683 4.283212 ACACCAAATACCAATGAACAAGGG 59.717 41.667 0.00 0.00 0.00 3.95
4337 4709 2.424302 GGTGCACCGTGGTACAGT 59.576 61.111 22.49 0.00 41.80 3.55
4354 4735 2.620251 TGAGCACAGATAAATCCCCG 57.380 50.000 0.00 0.00 0.00 5.73
4357 4738 5.587844 ACTGACATTGAGCACAGATAAATCC 59.412 40.000 0.00 0.00 34.88 3.01
4371 4752 8.726988 GGCAAGTAAAAATACTACTGACATTGA 58.273 33.333 0.00 0.00 29.96 2.57
4372 4753 8.511321 TGGCAAGTAAAAATACTACTGACATTG 58.489 33.333 0.00 0.00 29.96 2.82
4405 4949 8.025445 GCTATTCAAGTGAATCACAGTTTCAAT 58.975 33.333 16.38 2.52 43.17 2.57
4408 4952 6.902341 TGCTATTCAAGTGAATCACAGTTTC 58.098 36.000 16.38 0.00 43.17 2.78
4425 5072 7.217200 TCACCAGTACAAAGGATATGCTATTC 58.783 38.462 0.00 0.00 0.00 1.75
4434 5081 7.067008 CCGATTAAATTCACCAGTACAAAGGAT 59.933 37.037 6.09 0.00 0.00 3.24
4510 5157 3.694072 TGTCAGGTCTGGAACTTTTGTTG 59.306 43.478 0.00 0.00 43.66 3.33
4511 5158 3.963129 TGTCAGGTCTGGAACTTTTGTT 58.037 40.909 0.00 0.00 46.75 2.83
4513 5160 4.261741 CCAATGTCAGGTCTGGAACTTTTG 60.262 45.833 0.00 0.68 0.00 2.44
4518 5165 1.168714 GCCAATGTCAGGTCTGGAAC 58.831 55.000 0.00 0.00 0.00 3.62
4519 5166 0.321564 CGCCAATGTCAGGTCTGGAA 60.322 55.000 0.00 0.00 0.00 3.53
4520 5167 1.296392 CGCCAATGTCAGGTCTGGA 59.704 57.895 0.00 0.00 0.00 3.86
4521 5168 1.003355 ACGCCAATGTCAGGTCTGG 60.003 57.895 0.00 0.00 0.00 3.86
4522 5169 0.320683 TCACGCCAATGTCAGGTCTG 60.321 55.000 0.00 0.00 0.00 3.51
4523 5170 0.036952 CTCACGCCAATGTCAGGTCT 60.037 55.000 0.00 0.00 0.00 3.85
4524 5171 0.037326 TCTCACGCCAATGTCAGGTC 60.037 55.000 0.00 0.00 0.00 3.85
4525 5172 0.396435 TTCTCACGCCAATGTCAGGT 59.604 50.000 0.00 0.00 0.00 4.00
4526 5173 1.466167 CTTTCTCACGCCAATGTCAGG 59.534 52.381 0.00 0.00 0.00 3.86
4527 5174 2.416747 TCTTTCTCACGCCAATGTCAG 58.583 47.619 0.00 0.00 0.00 3.51
4528 5175 2.542020 TCTTTCTCACGCCAATGTCA 57.458 45.000 0.00 0.00 0.00 3.58
4529 5176 3.896648 TTTCTTTCTCACGCCAATGTC 57.103 42.857 0.00 0.00 0.00 3.06
4530 5177 3.632145 ACTTTTCTTTCTCACGCCAATGT 59.368 39.130 0.00 0.00 0.00 2.71
4531 5178 3.976942 CACTTTTCTTTCTCACGCCAATG 59.023 43.478 0.00 0.00 0.00 2.82
4532 5179 3.632145 ACACTTTTCTTTCTCACGCCAAT 59.368 39.130 0.00 0.00 0.00 3.16
4533 5180 3.013921 ACACTTTTCTTTCTCACGCCAA 58.986 40.909 0.00 0.00 0.00 4.52
4534 5181 2.639065 ACACTTTTCTTTCTCACGCCA 58.361 42.857 0.00 0.00 0.00 5.69
4535 5182 3.181500 ACAACACTTTTCTTTCTCACGCC 60.181 43.478 0.00 0.00 0.00 5.68
4536 5183 3.786048 CACAACACTTTTCTTTCTCACGC 59.214 43.478 0.00 0.00 0.00 5.34
4537 5184 3.786048 GCACAACACTTTTCTTTCTCACG 59.214 43.478 0.00 0.00 0.00 4.35
4538 5185 4.795278 CAGCACAACACTTTTCTTTCTCAC 59.205 41.667 0.00 0.00 0.00 3.51
4539 5186 4.458989 ACAGCACAACACTTTTCTTTCTCA 59.541 37.500 0.00 0.00 0.00 3.27
4540 5187 4.986622 ACAGCACAACACTTTTCTTTCTC 58.013 39.130 0.00 0.00 0.00 2.87
4541 5188 4.702131 AGACAGCACAACACTTTTCTTTCT 59.298 37.500 0.00 0.00 0.00 2.52
4542 5189 4.986622 AGACAGCACAACACTTTTCTTTC 58.013 39.130 0.00 0.00 0.00 2.62
4547 5194 3.609853 TCAGAGACAGCACAACACTTTT 58.390 40.909 0.00 0.00 0.00 2.27
4548 5195 3.118629 TCTCAGAGACAGCACAACACTTT 60.119 43.478 0.00 0.00 0.00 2.66
4560 5207 4.155709 AGACTCCAAACATCTCAGAGACA 58.844 43.478 0.91 0.00 0.00 3.41
4561 5208 4.799564 AGACTCCAAACATCTCAGAGAC 57.200 45.455 0.91 0.00 0.00 3.36
4563 5210 6.874288 AAAAAGACTCCAAACATCTCAGAG 57.126 37.500 0.00 0.00 0.00 3.35
4608 5255 8.918202 TTGTCCTTTAGAAAGATACACATTGT 57.082 30.769 3.52 0.00 38.28 2.71
4609 5256 9.778993 CATTGTCCTTTAGAAAGATACACATTG 57.221 33.333 3.52 4.59 38.28 2.82
4610 5257 8.960591 CCATTGTCCTTTAGAAAGATACACATT 58.039 33.333 3.52 0.00 38.28 2.71
4611 5258 8.109634 ACCATTGTCCTTTAGAAAGATACACAT 58.890 33.333 3.52 3.06 38.28 3.21
4612 5259 7.458397 ACCATTGTCCTTTAGAAAGATACACA 58.542 34.615 3.52 0.00 38.28 3.72
4613 5260 7.923414 ACCATTGTCCTTTAGAAAGATACAC 57.077 36.000 3.52 0.00 38.28 2.90
4614 5261 8.160765 TGAACCATTGTCCTTTAGAAAGATACA 58.839 33.333 3.52 5.14 38.28 2.29
4615 5262 8.561738 TGAACCATTGTCCTTTAGAAAGATAC 57.438 34.615 3.52 2.82 38.28 2.24
4616 5263 9.581289 TTTGAACCATTGTCCTTTAGAAAGATA 57.419 29.630 3.52 0.00 38.28 1.98
4617 5264 8.477419 TTTGAACCATTGTCCTTTAGAAAGAT 57.523 30.769 3.52 0.00 38.28 2.40
4618 5265 7.889873 TTTGAACCATTGTCCTTTAGAAAGA 57.110 32.000 3.52 0.00 38.28 2.52
4619 5266 8.579863 AGATTTGAACCATTGTCCTTTAGAAAG 58.420 33.333 0.00 0.00 35.79 2.62
4624 5271 5.538053 TGCAGATTTGAACCATTGTCCTTTA 59.462 36.000 0.00 0.00 0.00 1.85
4631 5278 5.319140 TCATCTGCAGATTTGAACCATTG 57.681 39.130 26.70 12.93 31.21 2.82
4632 5279 5.988310 TTCATCTGCAGATTTGAACCATT 57.012 34.783 26.70 0.00 31.21 3.16
4639 5286 6.803320 ACGTGTTAATTTCATCTGCAGATTTG 59.197 34.615 26.70 18.12 31.21 2.32
4662 5324 1.474077 ACCGCCTAAACCAGTACTACG 59.526 52.381 0.00 0.00 0.00 3.51
4679 5341 9.232082 CATTAAAACATGTAATATTCACCACCG 57.768 33.333 0.00 0.00 0.00 4.94
4711 5373 7.443575 AGCACATGATGGTCTAAATATTCTGAC 59.556 37.037 0.00 10.55 31.82 3.51
4726 5388 3.119065 TGGCATAAACAAGCACATGATGG 60.119 43.478 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.