Multiple sequence alignment - TraesCS3D01G478700

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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 TraesCS3D01G478700 chr3D 100.000 6290 0 0 1 6290 578110272 578103983 0.000000e+00 11616.0
1 TraesCS3D01G478700 chr3D 94.279 1748 80 9 2151 3889 577859787 577861523 0.000000e+00 2656.0
2 TraesCS3D01G478700 chr3D 90.081 1361 71 30 805 2145 577858273 577859589 0.000000e+00 1707.0
3 TraesCS3D01G478700 chr3D 85.427 1640 171 34 1868 3459 578220324 578218705 0.000000e+00 1642.0
4 TraesCS3D01G478700 chr3D 81.605 1109 130 30 2130 3190 578166945 578165863 0.000000e+00 850.0
5 TraesCS3D01G478700 chr3D 77.402 1655 225 87 3932 5523 578219197 578217629 0.000000e+00 846.0
6 TraesCS3D01G478700 chr3D 96.614 443 14 1 4140 4581 577863098 577863540 0.000000e+00 734.0
7 TraesCS3D01G478700 chr3D 81.514 898 100 33 4656 5526 578143493 578142635 0.000000e+00 678.0
8 TraesCS3D01G478700 chr3D 87.326 576 34 9 8 561 577846455 577847013 1.930000e-174 623.0
9 TraesCS3D01G478700 chr3D 82.934 709 95 16 1138 1831 578221014 578220317 3.220000e-172 616.0
10 TraesCS3D01G478700 chr3D 95.798 357 15 0 3792 4148 577861522 577861878 1.520000e-160 577.0
11 TraesCS3D01G478700 chr3D 80.392 663 113 14 3932 4584 578144160 578143505 7.330000e-134 488.0
12 TraesCS3D01G478700 chr3D 82.429 387 48 13 1549 1928 578167474 578167101 2.830000e-83 320.0
13 TraesCS3D01G478700 chr3D 89.919 248 22 3 565 810 577857894 577858140 3.660000e-82 316.0
14 TraesCS3D01G478700 chr3D 80.607 428 64 14 1154 1578 578167889 578167478 4.730000e-81 313.0
15 TraesCS3D01G478700 chr3D 77.903 534 87 15 4836 5354 577872670 577873187 2.850000e-78 303.0
16 TraesCS3D01G478700 chr3D 80.601 366 66 3 4154 4517 578158785 578158423 1.730000e-70 278.0
17 TraesCS3D01G478700 chr3D 77.910 335 56 5 3536 3866 578144612 578144292 6.440000e-45 193.0
18 TraesCS3D01G478700 chr3D 75.000 412 94 9 3465 3872 578066017 578065611 1.390000e-41 182.0
19 TraesCS3D01G478700 chr3D 94.595 74 4 0 5617 5690 436676985 436676912 1.430000e-21 115.0
20 TraesCS3D01G478700 chr3D 72.055 365 70 14 2613 2950 577871336 577871695 5.230000e-11 80.5
21 TraesCS3D01G478700 chr3D 90.323 62 3 1 4836 4897 578207428 578207486 1.880000e-10 78.7
22 TraesCS3D01G478700 chr3A 83.628 2547 295 64 1011 3457 713666999 713664475 0.000000e+00 2281.0
23 TraesCS3D01G478700 chr3A 85.784 1639 170 28 1868 3459 713843478 713841856 0.000000e+00 1677.0
24 TraesCS3D01G478700 chr3A 82.891 1695 231 36 3946 5619 713664962 713663306 0.000000e+00 1469.0
25 TraesCS3D01G478700 chr3A 81.923 1654 226 47 3922 5526 713681543 713679914 0.000000e+00 1330.0
26 TraesCS3D01G478700 chr3A 81.931 1284 176 34 2592 3835 713705655 713704388 0.000000e+00 1035.0
27 TraesCS3D01G478700 chr3A 76.190 1659 244 80 3932 5523 713842356 713840782 0.000000e+00 736.0
28 TraesCS3D01G478700 chr3A 86.528 527 62 7 1138 1657 713844110 713843586 7.070000e-159 571.0
29 TraesCS3D01G478700 chr3A 80.323 742 101 22 1816 2543 713706379 713705669 2.600000e-143 520.0
30 TraesCS3D01G478700 chr3A 83.196 363 30 15 5686 6021 713663280 713662922 2.850000e-78 303.0
31 TraesCS3D01G478700 chr3A 80.233 430 64 9 1154 1578 713707274 713706861 2.850000e-78 303.0
32 TraesCS3D01G478700 chr3A 87.783 221 20 5 5699 5912 713679700 713679480 1.050000e-62 252.0
33 TraesCS3D01G478700 chr3A 77.660 376 76 8 4146 4517 713703629 713703258 8.210000e-54 222.0
34 TraesCS3D01G478700 chr3A 78.649 370 50 14 4958 5318 713833000 713832651 1.060000e-52 219.0
35 TraesCS3D01G478700 chr3A 75.060 417 97 7 3459 3872 713632507 713632095 2.990000e-43 187.0
36 TraesCS3D01G478700 chr3A 90.323 124 12 0 4836 4959 713833380 713833257 5.050000e-36 163.0
37 TraesCS3D01G478700 chr3A 78.537 205 29 11 5171 5368 713555876 713555680 3.080000e-23 121.0
38 TraesCS3D01G478700 chr3A 98.305 59 1 0 6053 6111 713662917 713662859 3.100000e-18 104.0
39 TraesCS3D01G478700 chr3B 85.183 1802 180 44 3861 5619 771388588 771386831 0.000000e+00 1768.0
40 TraesCS3D01G478700 chr3B 85.793 1640 169 39 1868 3451 771520234 771518603 0.000000e+00 1679.0
41 TraesCS3D01G478700 chr3B 85.469 1631 167 39 805 2401 771392918 771391324 0.000000e+00 1635.0
42 TraesCS3D01G478700 chr3B 81.413 1797 246 36 2130 3866 771442442 771440674 0.000000e+00 1387.0
43 TraesCS3D01G478700 chr3B 81.335 1618 238 41 3951 5526 771401511 771399916 0.000000e+00 1256.0
44 TraesCS3D01G478700 chr3B 82.231 1497 147 47 2426 3870 771391327 771389898 0.000000e+00 1181.0
45 TraesCS3D01G478700 chr3B 86.797 462 40 7 5829 6289 771384027 771383586 4.380000e-136 496.0
46 TraesCS3D01G478700 chr3B 78.912 735 93 28 4640 5339 771518419 771517712 5.790000e-120 442.0
47 TraesCS3D01G478700 chr3B 83.944 355 56 1 3099 3453 771388370 771388017 7.810000e-89 339.0
48 TraesCS3D01G478700 chr3B 81.622 370 65 3 4149 4517 771439965 771439598 2.850000e-78 303.0
49 TraesCS3D01G478700 chr3B 78.528 489 82 12 4883 5354 771342882 771342400 3.690000e-77 300.0
50 TraesCS3D01G478700 chr3B 80.580 345 41 15 1502 1830 771520562 771520228 6.300000e-60 243.0
51 TraesCS3D01G478700 chr3B 77.955 313 50 6 3585 3893 771402099 771401802 1.800000e-40 178.0
52 TraesCS3D01G478700 chr3B 86.250 160 21 1 3714 3872 771325860 771325701 8.380000e-39 172.0
53 TraesCS3D01G478700 chr3B 84.416 77 7 4 11 85 148495290 148495217 3.150000e-08 71.3
54 TraesCS3D01G478700 chr2A 76.391 593 120 13 101 689 749454568 749453992 1.020000e-77 302.0
55 TraesCS3D01G478700 chr2A 93.243 74 5 0 5617 5690 617636119 617636046 6.670000e-20 110.0
56 TraesCS3D01G478700 chr2B 75.282 708 134 26 1 686 374203002 374203690 3.690000e-77 300.0
57 TraesCS3D01G478700 chr4B 80.223 359 53 11 1218 1563 514747889 514747536 2.910000e-63 254.0
58 TraesCS3D01G478700 chr4B 79.032 248 48 4 95 340 344463860 344464105 3.900000e-37 167.0
59 TraesCS3D01G478700 chr4D 78.398 412 68 13 1168 1563 418398317 418397911 1.350000e-61 248.0
60 TraesCS3D01G478700 chr4D 77.494 431 86 8 1144 1567 419461402 419461828 1.350000e-61 248.0
61 TraesCS3D01G478700 chr4D 78.629 248 49 4 95 340 176779862 176780107 1.810000e-35 161.0
62 TraesCS3D01G478700 chr1A 76.054 522 99 23 159 675 449816045 449816545 1.350000e-61 248.0
63 TraesCS3D01G478700 chr2D 74.551 613 115 30 93 691 639681347 639681932 4.900000e-56 230.0
64 TraesCS3D01G478700 chr5B 74.206 535 120 13 155 685 548097962 548097442 2.300000e-49 207.0
65 TraesCS3D01G478700 chr4A 81.395 172 29 3 127 297 410394354 410394185 3.060000e-28 137.0
66 TraesCS3D01G478700 chr4A 95.775 71 3 0 5617 5687 379040947 379041017 1.430000e-21 115.0
67 TraesCS3D01G478700 chr4A 93.151 73 5 0 5618 5690 9380759 9380687 2.400000e-19 108.0
68 TraesCS3D01G478700 chr7B 95.890 73 2 1 5614 5686 529956296 529956367 3.980000e-22 117.0
69 TraesCS3D01G478700 chr7B 93.590 78 4 1 5613 5690 639796287 639796211 1.430000e-21 115.0
70 TraesCS3D01G478700 chr1B 93.671 79 3 2 5609 5687 7291980 7292056 3.980000e-22 117.0
71 TraesCS3D01G478700 chr7A 94.595 74 4 0 5618 5691 231553731 231553658 1.430000e-21 115.0
72 TraesCS3D01G478700 chr6B 93.506 77 4 1 5614 5690 551951957 551951882 5.150000e-21 113.0


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 TraesCS3D01G478700 chr3D 578103983 578110272 6289 True 11616.000000 11616 100.000000 1 6290 1 chr3D.!!$R3 6289
1 TraesCS3D01G478700 chr3D 577857894 577863540 5646 False 1198.000000 2656 93.338200 565 4581 5 chr3D.!!$F3 4016
2 TraesCS3D01G478700 chr3D 578217629 578221014 3385 True 1034.666667 1642 81.921000 1138 5523 3 chr3D.!!$R7 4385
3 TraesCS3D01G478700 chr3D 577846455 577847013 558 False 623.000000 623 87.326000 8 561 1 chr3D.!!$F1 553
4 TraesCS3D01G478700 chr3D 578165863 578167889 2026 True 494.333333 850 81.547000 1154 3190 3 chr3D.!!$R6 2036
5 TraesCS3D01G478700 chr3D 578142635 578144612 1977 True 453.000000 678 79.938667 3536 5526 3 chr3D.!!$R5 1990
6 TraesCS3D01G478700 chr3A 713662859 713666999 4140 True 1039.250000 2281 87.005000 1011 6111 4 chr3A.!!$R3 5100
7 TraesCS3D01G478700 chr3A 713840782 713844110 3328 True 994.666667 1677 82.834000 1138 5523 3 chr3A.!!$R7 4385
8 TraesCS3D01G478700 chr3A 713679480 713681543 2063 True 791.000000 1330 84.853000 3922 5912 2 chr3A.!!$R4 1990
9 TraesCS3D01G478700 chr3A 713703258 713707274 4016 True 520.000000 1035 80.036750 1154 4517 4 chr3A.!!$R5 3363
10 TraesCS3D01G478700 chr3B 771383586 771392918 9332 True 1083.800000 1768 84.724800 805 6289 5 chr3B.!!$R4 5484
11 TraesCS3D01G478700 chr3B 771439598 771442442 2844 True 845.000000 1387 81.517500 2130 4517 2 chr3B.!!$R6 2387
12 TraesCS3D01G478700 chr3B 771517712 771520562 2850 True 788.000000 1679 81.761667 1502 5339 3 chr3B.!!$R7 3837
13 TraesCS3D01G478700 chr3B 771399916 771402099 2183 True 717.000000 1256 79.645000 3585 5526 2 chr3B.!!$R5 1941
14 TraesCS3D01G478700 chr2A 749453992 749454568 576 True 302.000000 302 76.391000 101 689 1 chr2A.!!$R2 588
15 TraesCS3D01G478700 chr2B 374203002 374203690 688 False 300.000000 300 75.282000 1 686 1 chr2B.!!$F1 685
16 TraesCS3D01G478700 chr1A 449816045 449816545 500 False 248.000000 248 76.054000 159 675 1 chr1A.!!$F1 516
17 TraesCS3D01G478700 chr2D 639681347 639681932 585 False 230.000000 230 74.551000 93 691 1 chr2D.!!$F1 598
18 TraesCS3D01G478700 chr5B 548097442 548097962 520 True 207.000000 207 74.206000 155 685 1 chr5B.!!$R1 530

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
365 393 1.139853 GAGGTCATCGATGCCTCCTTT 59.860 52.381 34.92 19.81 41.28 3.11 F
1072 1263 1.075374 TGGTATGGCAGCCAGTTTCTT 59.925 47.619 21.51 4.00 36.75 2.52 F
1722 2007 0.120377 TCCCCCTTGGACCATGTACT 59.880 55.000 0.00 0.00 38.61 2.73 F
2473 3288 0.242017 AACGGCATGAGCTTTGCTTC 59.758 50.000 18.54 5.89 39.88 3.86 F
2702 3525 1.362224 AGTTACCCTCCAGCACATGT 58.638 50.000 0.00 0.00 0.00 3.21 F
2709 3533 2.229784 CCCTCCAGCACATGTTTTTCTC 59.770 50.000 0.00 0.00 0.00 2.87 F
4629 9925 2.422597 TCCCATGAAAAGTACTGTGCG 58.577 47.619 0.00 0.00 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1175 1373 0.178992 CCTTGGTGAACTTGCCTGGA 60.179 55.000 0.00 0.0 0.00 3.86 R
2452 3267 0.242017 AGCAAAGCTCATGCCGTTTC 59.758 50.000 17.97 0.0 44.91 2.78 R
2682 3505 1.705186 ACATGTGCTGGAGGGTAACTT 59.295 47.619 0.00 0.0 0.00 2.66 R
3794 6939 0.811281 CAAGAACGGGGATTTCAGGC 59.189 55.000 0.00 0.0 0.00 4.85 R
3871 7119 3.054728 TGTGGGAGAAACAGAACACAGAA 60.055 43.478 0.00 0.0 34.31 3.02 R
4687 10004 4.081198 ACATGAAGAGATTCTCGGAAGCTT 60.081 41.667 0.00 0.0 35.36 3.74 R
6202 14335 0.039618 GGAGTTGAAGGGGCCATGAA 59.960 55.000 4.39 0.0 0.00 2.57 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 27 3.007290 TGACTGGTTCCTCTTGATCACAG 59.993 47.826 0.00 0.00 0.00 3.66
85 87 7.391148 TGCAAGATTATCTTTGGTAAGAACC 57.609 36.000 4.51 0.00 43.32 3.62
186 209 5.934625 AGATCCACAAACATAGACTTCACAC 59.065 40.000 0.00 0.00 0.00 3.82
297 321 6.134535 TCCACTTAGTCCATTTAACACCAT 57.865 37.500 0.00 0.00 0.00 3.55
344 368 2.883386 CAATGAGCTAGCCCCAAGAATC 59.117 50.000 12.13 0.00 0.00 2.52
365 393 1.139853 GAGGTCATCGATGCCTCCTTT 59.860 52.381 34.92 19.81 41.28 3.11
421 450 2.375174 AGCTAATGGAGTGTCACCCAAA 59.625 45.455 14.71 7.57 35.85 3.28
453 485 5.414789 TCTCAAAACCTCATCGATTGGTA 57.585 39.130 17.23 4.47 33.17 3.25
454 486 5.175859 TCTCAAAACCTCATCGATTGGTAC 58.824 41.667 17.23 0.00 33.17 3.34
458 490 4.503714 AACCTCATCGATTGGTACCATT 57.496 40.909 17.17 12.78 33.17 3.16
472 504 5.413969 GGTACCATTACCAACGATAAAGC 57.586 43.478 7.15 0.00 46.59 3.51
480 514 3.074412 ACCAACGATAAAGCAACCTCTG 58.926 45.455 0.00 0.00 0.00 3.35
622 661 6.424812 GCCAAACAACTTTCTCAATAAGCAAT 59.575 34.615 0.00 0.00 0.00 3.56
679 719 4.761739 TCTGATTTCGAGGTTTTCAATGCT 59.238 37.500 0.00 0.00 0.00 3.79
699 739 2.965147 CTCAACCCACCTTCAAAATGGT 59.035 45.455 0.00 0.00 36.96 3.55
701 741 4.148838 TCAACCCACCTTCAAAATGGTAG 58.851 43.478 0.00 0.00 34.79 3.18
729 770 2.552743 GGACTGTGTGCTTTTAGGGAAC 59.447 50.000 0.00 0.00 0.00 3.62
751 792 7.093684 GGAACCTTCTAGAGTTATCTCAACACT 60.094 40.741 3.70 0.00 42.66 3.55
753 794 9.482175 AACCTTCTAGAGTTATCTCAACACTAT 57.518 33.333 3.70 0.00 42.66 2.12
764 805 9.046296 GTTATCTCAACACTATGTAAATCCCTG 57.954 37.037 0.00 0.00 0.00 4.45
770 811 6.500589 ACACTATGTAAATCCCTGCTGTAT 57.499 37.500 0.00 0.00 0.00 2.29
863 1044 3.194005 ACACCAACACACAGGTAAGAG 57.806 47.619 0.00 0.00 36.07 2.85
879 1060 3.761311 AAGAGCGTAAGAGTTACTCCG 57.239 47.619 8.96 6.93 43.02 4.63
884 1065 2.913590 GCGTAAGAGTTACTCCGTTCAC 59.086 50.000 8.96 0.00 43.02 3.18
927 1108 3.809832 TCTCTTTGCCTTTCAGTTCGAAG 59.190 43.478 0.00 0.00 34.32 3.79
964 1145 5.449553 AGAAACTTTGGAAGGACATTCTGT 58.550 37.500 0.00 0.00 38.07 3.41
1062 1247 4.326826 TCTTGAAGAAACTGGTATGGCAG 58.673 43.478 0.00 0.00 0.00 4.85
1063 1248 2.436417 TGAAGAAACTGGTATGGCAGC 58.564 47.619 0.00 0.00 0.00 5.25
1072 1263 1.075374 TGGTATGGCAGCCAGTTTCTT 59.925 47.619 21.51 4.00 36.75 2.52
1107 1299 8.947115 ACATTCTATTTCTACGCTTAAGCTTTT 58.053 29.630 24.33 11.43 39.32 2.27
1112 1304 4.985044 TCTACGCTTAAGCTTTTGTCAC 57.015 40.909 24.33 0.00 39.32 3.67
1118 1310 3.315191 GCTTAAGCTTTTGTCACTGGTCA 59.685 43.478 20.38 0.00 38.21 4.02
1119 1311 4.022849 GCTTAAGCTTTTGTCACTGGTCAT 60.023 41.667 20.38 0.00 38.21 3.06
1166 1364 1.202698 ACCGCTGCTTAATCCTCATCC 60.203 52.381 0.00 0.00 0.00 3.51
1201 1400 1.798813 CAAGTTCACCAAGGTACTCGC 59.201 52.381 0.00 0.00 38.49 5.03
1497 1709 1.677052 CCTTCCTCTCAGTACGGTAGC 59.323 57.143 0.00 0.00 0.00 3.58
1675 1946 9.754382 GTGTTGATTTTAGCCATATTCATGAAT 57.246 29.630 23.75 23.75 33.67 2.57
1677 1948 8.706035 GTTGATTTTAGCCATATTCATGAATGC 58.294 33.333 27.59 22.06 33.67 3.56
1722 2007 0.120377 TCCCCCTTGGACCATGTACT 59.880 55.000 0.00 0.00 38.61 2.73
1755 2042 2.573009 TGACATGGATCTTCTTGCCTCA 59.427 45.455 0.00 0.00 0.00 3.86
1832 2148 2.175931 TCCTTTGCCTAGTTTCCCACAA 59.824 45.455 0.00 0.00 0.00 3.33
2016 2599 2.874701 CTCTTGCTAGTTGTGCACTGTT 59.125 45.455 19.41 5.62 40.40 3.16
2081 2667 8.613060 AGTGTATATATGCTGTCAAATCAAGG 57.387 34.615 2.37 0.00 0.00 3.61
2095 2681 2.936919 TCAAGGTCTGATGCACAGTT 57.063 45.000 13.59 2.09 45.86 3.16
2225 3034 1.735360 CAGGGGGCACATAATTGCG 59.265 57.895 0.00 0.00 44.00 4.85
2243 3052 1.864711 GCGAGTTGCTTAACTGTCACA 59.135 47.619 0.00 0.00 41.73 3.58
2255 3064 1.004595 CTGTCACATGCAGACATCCG 58.995 55.000 18.49 7.01 44.27 4.18
2409 3223 6.401796 CGACTTACAAACTAAAGTGGGCATAC 60.402 42.308 0.00 0.00 36.10 2.39
2473 3288 0.242017 AACGGCATGAGCTTTGCTTC 59.758 50.000 18.54 5.89 39.88 3.86
2653 3470 7.120432 CAGAAGGAAAGATCTTTTTCTTCCGAT 59.880 37.037 33.20 23.78 40.18 4.18
2674 3497 5.336531 CGATCCAGGTTAAGTTGTGTACTCT 60.337 44.000 0.00 0.00 35.54 3.24
2702 3525 1.362224 AGTTACCCTCCAGCACATGT 58.638 50.000 0.00 0.00 0.00 3.21
2709 3533 2.229784 CCCTCCAGCACATGTTTTTCTC 59.770 50.000 0.00 0.00 0.00 2.87
2716 3540 5.048504 CCAGCACATGTTTTTCTCACTGTAT 60.049 40.000 0.00 0.00 0.00 2.29
2812 3654 6.654582 TCAGTGCAATGCTATCTTACAAAAGA 59.345 34.615 9.79 0.00 45.63 2.52
2820 3662 9.507329 AATGCTATCTTACAAAAGAACAGAAGA 57.493 29.630 0.00 0.00 44.75 2.87
2848 3690 6.777526 AATAGATGCGCTCATAGAGAAAAC 57.222 37.500 9.73 0.00 31.96 2.43
3232 4112 6.182627 TCAAGCACTTTCCATGTGAAGATAT 58.817 36.000 11.09 0.00 37.60 1.63
3866 7114 4.694339 GGGCTACTCTGGTATGTTAGTTG 58.306 47.826 0.00 0.00 0.00 3.16
3867 7115 4.161754 GGGCTACTCTGGTATGTTAGTTGT 59.838 45.833 0.00 0.00 0.00 3.32
3871 7119 7.417570 GGCTACTCTGGTATGTTAGTTGTACAT 60.418 40.741 0.00 0.00 39.44 2.29
4024 7929 4.651994 GTCTGAAGGATATGTTTGCAACG 58.348 43.478 0.00 0.00 0.00 4.10
4094 8012 6.042093 TGGAACAATTTAGGGCAATGTTAACA 59.958 34.615 11.41 11.41 31.92 2.41
4124 8066 3.386078 TCCTTAGTGCTTCAGCTATCAGG 59.614 47.826 0.00 1.50 42.66 3.86
4338 9508 3.193903 GGCGCACCCTTTATTTAGGAAAA 59.806 43.478 10.83 0.00 37.50 2.29
4601 9862 5.589855 TGTGCACTTGAGTTCCCATTATATG 59.410 40.000 19.41 0.00 0.00 1.78
4602 9863 5.822519 GTGCACTTGAGTTCCCATTATATGA 59.177 40.000 10.32 0.00 0.00 2.15
4604 9865 6.889177 TGCACTTGAGTTCCCATTATATGAAA 59.111 34.615 0.00 0.00 0.00 2.69
4605 9866 7.395772 TGCACTTGAGTTCCCATTATATGAAAA 59.604 33.333 0.00 0.00 0.00 2.29
4606 9867 7.702348 GCACTTGAGTTCCCATTATATGAAAAC 59.298 37.037 0.00 0.00 0.00 2.43
4607 9868 8.960591 CACTTGAGTTCCCATTATATGAAAACT 58.039 33.333 0.00 0.00 37.46 2.66
4611 9872 9.793259 TGAGTTCCCATTATATGAAAACTATCC 57.207 33.333 0.00 0.00 36.01 2.59
4612 9873 9.232473 GAGTTCCCATTATATGAAAACTATCCC 57.768 37.037 0.00 0.00 36.01 3.85
4613 9874 8.732854 AGTTCCCATTATATGAAAACTATCCCA 58.267 33.333 0.00 0.00 34.94 4.37
4614 9875 9.533831 GTTCCCATTATATGAAAACTATCCCAT 57.466 33.333 0.00 0.00 0.00 4.00
4615 9876 9.532494 TTCCCATTATATGAAAACTATCCCATG 57.468 33.333 0.00 0.00 0.00 3.66
4616 9877 8.899765 TCCCATTATATGAAAACTATCCCATGA 58.100 33.333 0.00 0.00 0.00 3.07
4625 9886 8.335532 TGAAAACTATCCCATGAAAAGTACTG 57.664 34.615 0.00 0.00 0.00 2.74
4628 9924 5.186198 ACTATCCCATGAAAAGTACTGTGC 58.814 41.667 0.00 0.00 0.00 4.57
4629 9925 2.422597 TCCCATGAAAAGTACTGTGCG 58.577 47.619 0.00 0.00 0.00 5.34
4651 9947 6.257849 TGCGTAATCTATGTGAAATCTTGTCC 59.742 38.462 0.00 0.00 0.00 4.02
4687 10004 1.566703 AGTCTCTGAGGATTCCGAGGA 59.433 52.381 4.59 0.00 35.91 3.71
4712 10029 4.269844 GCTTCCGAGAATCTCTTCATGTTC 59.730 45.833 8.77 0.00 33.56 3.18
4728 10045 3.446310 TGTTCGCTGACAGAGTTTGTA 57.554 42.857 6.65 0.00 41.05 2.41
4742 10059 5.238432 CAGAGTTTGTATAACACCAGCACAA 59.762 40.000 0.00 0.00 0.00 3.33
4743 10060 5.470098 AGAGTTTGTATAACACCAGCACAAG 59.530 40.000 0.00 0.00 31.34 3.16
4746 10063 3.334691 TGTATAACACCAGCACAAGAGC 58.665 45.455 0.00 0.00 0.00 4.09
4803 10120 1.173913 ACCGCCCTTTTATGTTGCTC 58.826 50.000 0.00 0.00 0.00 4.26
4944 10284 5.866207 AGGAACAAACTTCCGAAGTATCTT 58.134 37.500 14.19 2.77 41.91 2.40
4969 10313 9.979578 TTTGCATCTGTGTTATTCTAACATTTT 57.020 25.926 3.29 0.00 32.23 1.82
4983 10328 3.848272 ACATTTTCCCTGCGTTATGTG 57.152 42.857 0.00 0.00 0.00 3.21
4995 10340 3.927758 TGCGTTATGTGTATAAACAGCGT 59.072 39.130 14.64 0.00 35.91 5.07
5030 10375 1.869767 CGCAGCCAGATATCTTGTTCC 59.130 52.381 1.33 0.00 0.00 3.62
5037 10382 4.271291 GCCAGATATCTTGTTCCGAAGTTC 59.729 45.833 1.33 0.00 0.00 3.01
5045 10390 2.317609 TTCCGAAGTTCGCTGCTGC 61.318 57.895 19.86 5.34 38.82 5.25
5047 10392 2.740055 CGAAGTTCGCTGCTGCCT 60.740 61.111 13.08 0.00 35.36 4.75
5048 10393 2.734673 CGAAGTTCGCTGCTGCCTC 61.735 63.158 13.08 0.97 35.36 4.70
5135 10480 1.597742 ACCAAGCTGCAATATAGGCG 58.402 50.000 1.02 0.00 0.00 5.52
5193 10538 1.586154 AAGGATGGCCGTCTTTTGCG 61.586 55.000 24.11 0.00 39.96 4.85
5215 10560 2.847234 ACAACCACCTGCGGGAGA 60.847 61.111 21.41 0.00 36.25 3.71
5334 10697 4.097892 TGCTGCTACGATGATCTTGAACTA 59.902 41.667 0.00 0.00 0.00 2.24
5386 10760 1.726265 GAGGGGCTCGTACGTACAG 59.274 63.158 24.50 19.75 0.00 2.74
5387 10761 1.001641 AGGGGCTCGTACGTACAGT 60.002 57.895 24.50 3.96 0.00 3.55
5396 10770 4.785561 GCTCGTACGTACAGTAAGAAACTC 59.214 45.833 24.50 3.21 41.85 3.01
5583 11027 1.266175 CCTTGCATGCTGCTACTATGC 59.734 52.381 20.33 13.80 45.31 3.14
5584 11028 2.219458 CTTGCATGCTGCTACTATGCT 58.781 47.619 20.33 0.00 45.31 3.79
5598 11042 6.127980 TGCTACTATGCTATACGGTGATCTTC 60.128 42.308 0.00 0.00 0.00 2.87
5599 11043 5.298197 ACTATGCTATACGGTGATCTTCG 57.702 43.478 6.70 6.70 0.00 3.79
5619 11063 5.171147 TCGACTCTCGGAATGAAAGATAC 57.829 43.478 0.00 0.00 40.88 2.24
5620 11064 4.882427 TCGACTCTCGGAATGAAAGATACT 59.118 41.667 0.00 0.00 40.88 2.12
5621 11065 5.007823 TCGACTCTCGGAATGAAAGATACTC 59.992 44.000 0.00 0.00 40.88 2.59
5622 11066 5.523438 ACTCTCGGAATGAAAGATACTCC 57.477 43.478 0.00 0.00 0.00 3.85
5623 11067 4.342665 ACTCTCGGAATGAAAGATACTCCC 59.657 45.833 0.00 0.00 0.00 4.30
5629 11073 5.302059 CGGAATGAAAGATACTCCCTCTGTA 59.698 44.000 0.00 0.00 0.00 2.74
5630 11074 6.183360 CGGAATGAAAGATACTCCCTCTGTAA 60.183 42.308 0.00 0.00 0.00 2.41
5631 11075 7.565680 GGAATGAAAGATACTCCCTCTGTAAA 58.434 38.462 0.00 0.00 0.00 2.01
5632 11076 7.713073 GGAATGAAAGATACTCCCTCTGTAAAG 59.287 40.741 0.00 0.00 0.00 1.85
5644 11088 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
5645 11089 8.554490 TCCCTCTGTAAAGAAATATAAGAGCT 57.446 34.615 0.00 0.00 0.00 4.09
5646 11090 8.993424 TCCCTCTGTAAAGAAATATAAGAGCTT 58.007 33.333 0.00 0.00 0.00 3.74
5678 11122 7.393841 ACTAAAGTAGTGATCTTAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
5679 11123 7.828712 ACTAAAGTAGTGATCTTAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
5680 11124 8.954350 ACTAAAGTAGTGATCTTAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
5681 11125 9.953697 CTAAAGTAGTGATCTTAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
5753 11225 5.977635 TGTTATTGAGAGTGATTCGGATGT 58.022 37.500 0.00 0.00 0.00 3.06
5771 11259 5.872617 CGGATGTATCAGTTTGAACAACCTA 59.127 40.000 13.27 0.00 33.11 3.08
5877 14001 1.998315 GAGATACTGCTGCTGTGTGTG 59.002 52.381 20.53 0.00 0.00 3.82
5908 14032 2.094545 GCACCGAAAGAATTTGAGGCAT 60.095 45.455 0.00 0.00 39.27 4.40
5974 14106 7.122353 AGGTACTCTCGTATGAACTGTATTTGT 59.878 37.037 0.00 0.00 0.00 2.83
5986 14118 6.420903 TGAACTGTATTTGTTCTCAACTCTCG 59.579 38.462 7.89 0.00 42.86 4.04
5999 14131 3.509967 TCAACTCTCGACCAATTGAGCTA 59.490 43.478 7.12 0.00 36.40 3.32
6017 14149 3.518303 AGCTATATGATGATGCAGGCAGA 59.482 43.478 0.00 0.00 0.00 4.26
6026 14158 4.339872 TGATGCAGGCAGAAAATGTTTT 57.660 36.364 0.00 0.00 0.00 2.43
6030 14162 4.630111 TGCAGGCAGAAAATGTTTTTAGG 58.370 39.130 0.00 0.00 0.00 2.69
6119 14251 1.685224 CAGCAGGGCCCTGTTTAGA 59.315 57.895 44.45 0.00 45.24 2.10
6122 14254 1.994463 CAGGGCCCTGTTTAGAGCT 59.006 57.895 39.52 5.15 39.10 4.09
6132 14264 5.450826 GCCCTGTTTAGAGCTTCTCTAGTAC 60.451 48.000 4.07 7.21 42.92 2.73
6148 14280 8.307582 TCTCTAGTACCTCCCTTATTTCAAAG 57.692 38.462 0.00 0.00 0.00 2.77
6149 14281 7.899709 TCTCTAGTACCTCCCTTATTTCAAAGT 59.100 37.037 0.00 0.00 0.00 2.66
6154 14286 3.119495 CCTCCCTTATTTCAAAGTTGGCG 60.119 47.826 0.00 0.00 0.00 5.69
6168 14300 2.675844 AGTTGGCGCAAAAAGAAAAACC 59.324 40.909 10.83 0.00 0.00 3.27
6170 14302 0.579630 GGCGCAAAAAGAAAAACCCG 59.420 50.000 10.83 0.00 0.00 5.28
6175 14307 2.124122 CAAAAAGAAAAACCCGCTCCG 58.876 47.619 0.00 0.00 0.00 4.63
6220 14353 1.923356 TTTCATGGCCCCTTCAACTC 58.077 50.000 0.00 0.00 0.00 3.01
6227 14360 1.750399 CCCCTTCAACTCCATGCCG 60.750 63.158 0.00 0.00 0.00 5.69
6234 14367 2.852449 TCAACTCCATGCCGTAAAACA 58.148 42.857 0.00 0.00 0.00 2.83
6235 14368 3.215151 TCAACTCCATGCCGTAAAACAA 58.785 40.909 0.00 0.00 0.00 2.83
6236 14369 3.632604 TCAACTCCATGCCGTAAAACAAA 59.367 39.130 0.00 0.00 0.00 2.83
6237 14370 4.098044 TCAACTCCATGCCGTAAAACAAAA 59.902 37.500 0.00 0.00 0.00 2.44
6238 14371 4.657436 ACTCCATGCCGTAAAACAAAAA 57.343 36.364 0.00 0.00 0.00 1.94
6260 14393 0.798776 CCGTCACTTCACCTCATTGC 59.201 55.000 0.00 0.00 0.00 3.56
6272 14405 3.814268 CATTGCCGTCGCCCCTTG 61.814 66.667 0.00 0.00 0.00 3.61
6279 14412 2.112297 GTCGCCCCTTGAACACCA 59.888 61.111 0.00 0.00 0.00 4.17
6289 14422 1.225376 TTGAACACCATGCCGTCGTC 61.225 55.000 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 11 5.702670 TGTTGATTCTGTGATCAAGAGGAAC 59.297 40.000 0.00 7.56 44.29 3.62
25 27 6.223120 ACAGGGTAGCAAAAATTGTTGATTC 58.777 36.000 12.75 3.61 0.00 2.52
85 87 8.558700 CCCTTCCAAAATTAAAGTTTTGACATG 58.441 33.333 13.45 0.00 46.78 3.21
87 89 7.852263 TCCCTTCCAAAATTAAAGTTTTGACA 58.148 30.769 13.45 0.91 46.78 3.58
88 90 8.902540 ATCCCTTCCAAAATTAAAGTTTTGAC 57.097 30.769 13.45 0.00 46.78 3.18
147 170 4.657504 TGTGGATCTCATGAATTCTAGGCT 59.342 41.667 7.05 0.00 0.00 4.58
186 209 6.600822 AGGTTGAATATCAATGGTGTCTTCAG 59.399 38.462 0.00 0.00 38.79 3.02
297 321 2.956132 TCAAATCTGTTGGGCTTTCCA 58.044 42.857 0.00 0.00 45.43 3.53
365 393 8.356657 CCCGAACCTTTATTATATTGCATCAAA 58.643 33.333 0.00 0.00 0.00 2.69
386 415 6.952358 ACTCCATTAGCTCTATAATACCCGAA 59.048 38.462 0.00 0.00 0.00 4.30
421 450 5.825593 TGAGGTTTTGAGAAGATACCTGT 57.174 39.130 0.00 0.00 39.25 4.00
453 485 4.157105 GGTTGCTTTATCGTTGGTAATGGT 59.843 41.667 0.00 0.00 0.00 3.55
454 486 4.398044 AGGTTGCTTTATCGTTGGTAATGG 59.602 41.667 0.00 0.00 0.00 3.16
458 490 4.250464 CAGAGGTTGCTTTATCGTTGGTA 58.750 43.478 0.00 0.00 0.00 3.25
643 682 4.690748 TCGAAATCAGAAACTAAGTGCTGG 59.309 41.667 0.00 0.00 0.00 4.85
644 683 5.163913 CCTCGAAATCAGAAACTAAGTGCTG 60.164 44.000 0.00 0.00 0.00 4.41
679 719 3.039252 ACCATTTTGAAGGTGGGTTGA 57.961 42.857 3.53 0.00 36.60 3.18
699 739 7.227910 CCTAAAAGCACACAGTCCTTTAAACTA 59.772 37.037 0.00 0.00 0.00 2.24
701 741 6.206498 CCTAAAAGCACACAGTCCTTTAAAC 58.794 40.000 0.00 0.00 0.00 2.01
724 765 6.154706 TGTTGAGATAACTCTAGAAGGTTCCC 59.845 42.308 0.92 0.00 42.99 3.97
729 770 8.908903 ACATAGTGTTGAGATAACTCTAGAAGG 58.091 37.037 1.39 0.00 42.99 3.46
742 783 5.189736 AGCAGGGATTTACATAGTGTTGAGA 59.810 40.000 0.00 0.00 0.00 3.27
751 792 5.071250 ACGGAATACAGCAGGGATTTACATA 59.929 40.000 0.00 0.00 0.00 2.29
753 794 3.199071 ACGGAATACAGCAGGGATTTACA 59.801 43.478 0.00 0.00 0.00 2.41
764 805 5.353123 TGTTTTCCTAATGACGGAATACAGC 59.647 40.000 9.85 0.00 43.08 4.40
770 811 5.010213 CCCTTTTGTTTTCCTAATGACGGAA 59.990 40.000 0.00 0.00 38.71 4.30
846 1027 1.148310 CGCTCTTACCTGTGTGTTGG 58.852 55.000 0.00 0.00 0.00 3.77
863 1044 2.913590 GTGAACGGAGTAACTCTTACGC 59.086 50.000 0.00 0.00 45.00 4.42
879 1060 2.673368 CCGAGGCTAGTCATTTGTGAAC 59.327 50.000 0.00 0.00 0.00 3.18
884 1065 0.179000 AGGCCGAGGCTAGTCATTTG 59.821 55.000 14.33 0.00 41.60 2.32
927 1108 3.596310 AGTTTCTCTTACGAAGGGAGC 57.404 47.619 0.00 0.00 39.64 4.70
964 1145 4.574674 AGGATCAAATGTAGCAGGAACA 57.425 40.909 0.00 0.00 0.00 3.18
1062 1247 8.593492 AGAATGTAAATGAAAAAGAAACTGGC 57.407 30.769 0.00 0.00 0.00 4.85
1100 1291 5.111293 CAAAATGACCAGTGACAAAAGCTT 58.889 37.500 0.00 0.00 0.00 3.74
1107 1299 2.692557 CCAACCAAAATGACCAGTGACA 59.307 45.455 0.00 0.00 0.00 3.58
1112 1304 4.119136 GTTGAACCAACCAAAATGACCAG 58.881 43.478 0.00 0.00 38.30 4.00
1118 1310 4.779696 AGCATTGTTGAACCAACCAAAAT 58.220 34.783 7.29 0.00 42.96 1.82
1119 1311 4.213564 AGCATTGTTGAACCAACCAAAA 57.786 36.364 7.29 0.00 42.96 2.44
1166 1364 1.378250 CTTGCCTGGAAGCCTCTGG 60.378 63.158 0.00 0.00 0.00 3.86
1175 1373 0.178992 CCTTGGTGAACTTGCCTGGA 60.179 55.000 0.00 0.00 0.00 3.86
1213 1412 2.383527 CGCAGCTTCACTTCCCGAC 61.384 63.158 0.00 0.00 0.00 4.79
1319 1518 2.125552 TCATGAGCGTGGGCGAAG 60.126 61.111 0.00 0.00 46.35 3.79
1675 1946 2.779755 TCCATAGCGGAAAAAGAGCA 57.220 45.000 0.00 0.00 42.52 4.26
1722 2007 3.855255 TCCATGTCAAACTGAAGTGGA 57.145 42.857 7.01 7.01 38.83 4.02
1860 2183 5.220557 TGTACATGATGAGAAAACATGCG 57.779 39.130 0.00 0.00 43.21 4.73
1948 2530 4.065281 CGCCCCGTCGTCTTCCTT 62.065 66.667 0.00 0.00 0.00 3.36
2016 2599 2.097036 CTGGGCAGAAGCATGAATTGA 58.903 47.619 0.00 0.00 44.61 2.57
2069 2654 3.503363 GTGCATCAGACCTTGATTTGACA 59.497 43.478 0.00 0.00 44.14 3.58
2081 2667 9.703892 ATCTAATATCTAAACTGTGCATCAGAC 57.296 33.333 19.01 0.00 46.27 3.51
2145 2758 8.681486 TGCACTGCTATATGATTCTTACATTT 57.319 30.769 1.98 0.00 0.00 2.32
2152 2957 8.975295 TCTACATATGCACTGCTATATGATTCT 58.025 33.333 24.87 13.89 38.80 2.40
2225 3034 3.250762 TGCATGTGACAGTTAAGCAACTC 59.749 43.478 0.00 0.00 43.30 3.01
2243 3052 3.396560 CATGTATGTCGGATGTCTGCAT 58.603 45.455 0.00 4.85 38.18 3.96
2255 3064 5.967674 GCAATGTACTCAAAGCATGTATGTC 59.032 40.000 0.00 0.00 0.00 3.06
2323 3136 6.243811 AGAAACTTTGACGTACAACAAACA 57.756 33.333 9.41 0.00 38.29 2.83
2334 3147 9.382244 CTTGGTAAATCTTAAGAAACTTTGACG 57.618 33.333 9.71 0.00 0.00 4.35
2370 3183 7.333672 AGTTTGTAAGTCGATCTTAACCCATTC 59.666 37.037 8.43 0.00 39.88 2.67
2409 3223 3.508744 CCTTTTGGTGGGATTTGATCG 57.491 47.619 0.00 0.00 34.07 3.69
2452 3267 0.242017 AGCAAAGCTCATGCCGTTTC 59.758 50.000 17.97 0.00 44.91 2.78
2473 3288 1.407979 GATGCCCTCTTCCAAATGCAG 59.592 52.381 0.00 0.00 31.53 4.41
2585 3402 5.096521 TGGATTACTCATCTGGGATATGCT 58.903 41.667 0.00 0.00 31.67 3.79
2653 3470 4.897076 TCAGAGTACACAACTTAACCTGGA 59.103 41.667 0.00 0.00 39.07 3.86
2674 3497 6.069905 TGTGCTGGAGGGTAACTTAATAATCA 60.070 38.462 0.00 0.00 0.00 2.57
2682 3505 1.705186 ACATGTGCTGGAGGGTAACTT 59.295 47.619 0.00 0.00 0.00 2.66
2716 3540 8.783093 CAGGATCTTCTGTTGTACAAATGTTTA 58.217 33.333 10.51 0.00 0.00 2.01
2812 3654 5.587844 AGCGCATCTATTTTCATCTTCTGTT 59.412 36.000 11.47 0.00 0.00 3.16
2820 3662 6.695429 TCTCTATGAGCGCATCTATTTTCAT 58.305 36.000 11.47 10.00 35.94 2.57
2848 3690 5.934625 ACTAGCACTGTGAATTTAGGTTGAG 59.065 40.000 12.86 0.00 0.00 3.02
3232 4112 3.455910 AGGCAGCTGGAGTATGACAATTA 59.544 43.478 17.12 0.00 0.00 1.40
3338 4218 3.988379 TGATTGTCACAGGCAAAGTTC 57.012 42.857 0.00 0.00 0.00 3.01
3728 6873 5.491982 ACTGTAAGATCACATTTCCCTGAC 58.508 41.667 0.00 0.00 37.43 3.51
3794 6939 0.811281 CAAGAACGGGGATTTCAGGC 59.189 55.000 0.00 0.00 0.00 4.85
3871 7119 3.054728 TGTGGGAGAAACAGAACACAGAA 60.055 43.478 0.00 0.00 34.31 3.02
4094 8012 5.188751 AGCTGAAGCACTAAGGAGTTAAGAT 59.811 40.000 4.90 0.00 45.16 2.40
4407 9577 5.970592 TGGACTGTCACTATGAATCTTCTG 58.029 41.667 10.38 0.00 0.00 3.02
4586 9847 9.232473 GGGATAGTTTTCATATAATGGGAACTC 57.768 37.037 10.15 2.25 37.19 3.01
4601 9862 8.237267 CACAGTACTTTTCATGGGATAGTTTTC 58.763 37.037 0.00 0.00 0.00 2.29
4602 9863 7.309194 GCACAGTACTTTTCATGGGATAGTTTT 60.309 37.037 0.00 0.00 0.00 2.43
4604 9865 5.648092 GCACAGTACTTTTCATGGGATAGTT 59.352 40.000 0.00 0.00 0.00 2.24
4605 9866 5.186198 GCACAGTACTTTTCATGGGATAGT 58.814 41.667 0.00 0.00 0.00 2.12
4606 9867 4.271049 CGCACAGTACTTTTCATGGGATAG 59.729 45.833 0.00 0.00 0.00 2.08
4607 9868 4.188462 CGCACAGTACTTTTCATGGGATA 58.812 43.478 0.00 0.00 0.00 2.59
4611 9872 5.351465 AGATTACGCACAGTACTTTTCATGG 59.649 40.000 0.00 0.00 34.56 3.66
4612 9873 6.408858 AGATTACGCACAGTACTTTTCATG 57.591 37.500 0.00 0.00 34.56 3.07
4613 9874 7.764443 ACATAGATTACGCACAGTACTTTTCAT 59.236 33.333 0.00 0.00 34.56 2.57
4614 9875 7.062956 CACATAGATTACGCACAGTACTTTTCA 59.937 37.037 0.00 0.00 34.56 2.69
4615 9876 7.274904 TCACATAGATTACGCACAGTACTTTTC 59.725 37.037 0.00 0.00 34.56 2.29
4616 9877 7.094631 TCACATAGATTACGCACAGTACTTTT 58.905 34.615 0.00 0.00 34.56 2.27
4620 9881 6.880822 TTTCACATAGATTACGCACAGTAC 57.119 37.500 0.00 0.00 34.56 2.73
4622 9883 6.341316 AGATTTCACATAGATTACGCACAGT 58.659 36.000 0.00 0.00 0.00 3.55
4623 9884 6.834959 AGATTTCACATAGATTACGCACAG 57.165 37.500 0.00 0.00 0.00 3.66
4624 9885 6.593770 ACAAGATTTCACATAGATTACGCACA 59.406 34.615 0.00 0.00 0.00 4.57
4625 9886 7.005062 ACAAGATTTCACATAGATTACGCAC 57.995 36.000 0.00 0.00 0.00 5.34
4628 9924 7.042456 CCTGGACAAGATTTCACATAGATTACG 60.042 40.741 0.00 0.00 0.00 3.18
4629 9925 7.770897 ACCTGGACAAGATTTCACATAGATTAC 59.229 37.037 0.00 0.00 0.00 1.89
4651 9947 6.871844 TCAGAGACTTCATATTCTTCACCTG 58.128 40.000 0.00 0.00 0.00 4.00
4687 10004 4.081198 ACATGAAGAGATTCTCGGAAGCTT 60.081 41.667 0.00 0.00 35.36 3.74
4712 10029 4.091509 GGTGTTATACAAACTCTGTCAGCG 59.908 45.833 0.00 0.00 39.64 5.18
4728 10045 2.867109 AGCTCTTGTGCTGGTGTTAT 57.133 45.000 0.00 0.00 42.33 1.89
4742 10059 5.136105 ACTTTCTCCAACAATTTCAGCTCT 58.864 37.500 0.00 0.00 0.00 4.09
4743 10060 5.444663 ACTTTCTCCAACAATTTCAGCTC 57.555 39.130 0.00 0.00 0.00 4.09
4746 10063 6.039717 TCCTCAACTTTCTCCAACAATTTCAG 59.960 38.462 0.00 0.00 0.00 3.02
4803 10120 0.249676 ACAGTGCTCCTGCTCATGAG 59.750 55.000 18.84 18.84 45.68 2.90
4844 10173 8.942338 AAGAAAATGTTTTCCTTGAACTTACC 57.058 30.769 13.10 0.00 45.84 2.85
4930 10270 4.872691 ACAGATGCAAAGATACTTCGGAAG 59.127 41.667 15.96 15.96 0.00 3.46
4935 10275 8.887717 AGAATAACACAGATGCAAAGATACTTC 58.112 33.333 0.00 0.00 0.00 3.01
4944 10284 9.624697 GAAAATGTTAGAATAACACAGATGCAA 57.375 29.630 4.59 0.00 32.37 4.08
4969 10313 5.087391 TGTTTATACACATAACGCAGGGA 57.913 39.130 0.00 0.00 0.00 4.20
4995 10340 1.514678 CTGCGTACTGCCAGCCAAAA 61.515 55.000 7.13 0.00 45.60 2.44
5030 10375 2.734673 GAGGCAGCAGCGAACTTCG 61.735 63.158 6.82 6.82 43.41 3.79
5037 10382 2.960659 CGATGAGAGGCAGCAGCG 60.961 66.667 0.00 0.00 43.41 5.18
5047 10392 2.690497 GACCATTCTCTCCACGATGAGA 59.310 50.000 8.07 8.07 39.04 3.27
5048 10393 2.223923 GGACCATTCTCTCCACGATGAG 60.224 54.545 0.00 0.00 0.00 2.90
5135 10480 2.144680 GTCGTGTCTAGCGTGCGAC 61.145 63.158 11.10 11.10 43.53 5.19
5215 10560 0.178891 TTGAAGAGGCAGAGGTCCCT 60.179 55.000 0.00 0.00 0.00 4.20
5334 10697 2.597455 CCACAAGTTTTCCACTCCCAT 58.403 47.619 0.00 0.00 32.94 4.00
5430 10804 5.859205 AAAGTTCTGGCAGAAGAAAACAT 57.141 34.783 29.22 9.09 37.90 2.71
5583 11027 4.143284 CGAGAGTCGAAGATCACCGTATAG 60.143 50.000 0.00 0.00 43.74 1.31
5584 11028 3.739810 CGAGAGTCGAAGATCACCGTATA 59.260 47.826 0.00 0.00 43.74 1.47
5598 11042 5.176407 AGTATCTTTCATTCCGAGAGTCG 57.824 43.478 0.00 0.00 40.07 4.18
5599 11043 5.508320 GGGAGTATCTTTCATTCCGAGAGTC 60.508 48.000 0.00 0.00 33.73 3.36
5619 11063 8.646900 AGCTCTTATATTTCTTTACAGAGGGAG 58.353 37.037 0.00 0.00 0.00 4.30
5620 11064 8.554490 AGCTCTTATATTTCTTTACAGAGGGA 57.446 34.615 0.00 0.00 0.00 4.20
5654 11098 7.393841 AGAGCGTTAAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
5655 11099 9.953697 ATAAGAGCGTTAAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
5662 11106 9.988815 ATGAAATATAAGAGCGTTAAGATCACT 57.011 29.630 0.00 0.00 37.82 3.41
5667 11111 8.765219 GCTCAATGAAATATAAGAGCGTTAAGA 58.235 33.333 0.00 0.00 39.04 2.10
5668 11112 8.925788 GCTCAATGAAATATAAGAGCGTTAAG 57.074 34.615 0.00 0.00 39.04 1.85
5674 11118 9.609950 GATTCTTGCTCAATGAAATATAAGAGC 57.390 33.333 0.00 0.00 46.33 4.09
5678 11122 9.740239 GCAAGATTCTTGCTCAATGAAATATAA 57.260 29.630 33.80 0.00 41.87 0.98
5753 11225 8.729756 CAACATCATAGGTTGTTCAAACTGATA 58.270 33.333 12.61 0.00 40.48 2.15
5823 12700 1.047002 AATCCTCTCGATGCTGGAGG 58.953 55.000 10.64 10.64 45.65 4.30
5877 14001 3.795623 TCTTTCGGTGCACTCCTATAC 57.204 47.619 17.98 0.00 0.00 1.47
5908 14032 9.265901 GAACCGTACATGTACTCTAATCTAGTA 57.734 37.037 28.53 0.00 34.04 1.82
5974 14106 4.560128 CTCAATTGGTCGAGAGTTGAGAA 58.440 43.478 18.05 0.00 45.23 2.87
5986 14118 6.373495 TGCATCATCATATAGCTCAATTGGTC 59.627 38.462 5.42 0.00 0.00 4.02
5999 14131 5.538813 ACATTTTCTGCCTGCATCATCATAT 59.461 36.000 0.00 0.00 0.00 1.78
6036 14168 6.241882 AGCTAAAAACCTTTTTGCCCTAAA 57.758 33.333 12.51 0.00 40.33 1.85
6049 14181 6.693315 TTACCTGCATCATAGCTAAAAACC 57.307 37.500 0.00 0.00 34.99 3.27
6050 14182 7.013274 TGGATTACCTGCATCATAGCTAAAAAC 59.987 37.037 0.00 0.00 37.04 2.43
6051 14183 7.013274 GTGGATTACCTGCATCATAGCTAAAAA 59.987 37.037 0.00 0.00 37.04 1.94
6119 14251 5.673130 ATAAGGGAGGTACTAGAGAAGCT 57.327 43.478 0.00 0.00 41.55 3.74
6122 14254 8.674925 TTTGAAATAAGGGAGGTACTAGAGAA 57.325 34.615 0.00 0.00 41.55 2.87
6132 14264 3.119495 CGCCAACTTTGAAATAAGGGAGG 60.119 47.826 0.00 0.00 0.00 4.30
6148 14280 2.223157 GGGTTTTTCTTTTTGCGCCAAC 60.223 45.455 4.18 0.00 0.00 3.77
6149 14281 2.010497 GGGTTTTTCTTTTTGCGCCAA 58.990 42.857 4.18 0.00 0.00 4.52
6154 14286 1.864711 GGAGCGGGTTTTTCTTTTTGC 59.135 47.619 0.00 0.00 0.00 3.68
6202 14335 0.039618 GGAGTTGAAGGGGCCATGAA 59.960 55.000 4.39 0.00 0.00 2.57
6207 14340 2.054453 GCATGGAGTTGAAGGGGCC 61.054 63.158 0.00 0.00 0.00 5.80
6214 14347 2.852449 TGTTTTACGGCATGGAGTTGA 58.148 42.857 0.00 0.00 0.00 3.18
6215 14348 3.634568 TTGTTTTACGGCATGGAGTTG 57.365 42.857 0.00 0.00 0.00 3.16
6236 14369 2.993937 TGAGGTGAAGTGACGGTTTTT 58.006 42.857 0.00 0.00 0.00 1.94
6237 14370 2.702592 TGAGGTGAAGTGACGGTTTT 57.297 45.000 0.00 0.00 0.00 2.43
6238 14371 2.878406 CAATGAGGTGAAGTGACGGTTT 59.122 45.455 0.00 0.00 0.00 3.27
6239 14372 2.494059 CAATGAGGTGAAGTGACGGTT 58.506 47.619 0.00 0.00 0.00 4.44
6240 14373 1.878102 GCAATGAGGTGAAGTGACGGT 60.878 52.381 0.00 0.00 0.00 4.83
6241 14374 0.798776 GCAATGAGGTGAAGTGACGG 59.201 55.000 0.00 0.00 0.00 4.79
6242 14375 0.798776 GGCAATGAGGTGAAGTGACG 59.201 55.000 0.00 0.00 0.00 4.35
6243 14376 0.798776 CGGCAATGAGGTGAAGTGAC 59.201 55.000 0.00 0.00 0.00 3.67
6244 14377 0.396435 ACGGCAATGAGGTGAAGTGA 59.604 50.000 0.00 0.00 0.00 3.41
6260 14393 3.047877 GTGTTCAAGGGGCGACGG 61.048 66.667 0.00 0.00 0.00 4.79
6272 14405 3.165498 GACGACGGCATGGTGTTC 58.835 61.111 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.