Multiple sequence alignment - TraesCS2B01G278700

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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 TraesCS2B01G278700 chr2B 100.000 7870 0 0 1 7870 384670527 384678396 0.000000e+00 14534.0
1 TraesCS2B01G278700 chr2B 94.624 465 25 0 1 465 238535823 238535359 0.000000e+00 721.0
2 TraesCS2B01G278700 chr2B 87.175 577 42 16 1877 2436 238533916 238533355 1.860000e-175 627.0
3 TraesCS2B01G278700 chr2B 84.708 497 40 10 3 464 651678233 651678728 1.550000e-126 464.0
4 TraesCS2B01G278700 chr2B 89.531 277 23 5 2164 2436 657488704 657488978 5.850000e-91 346.0
5 TraesCS2B01G278700 chr2B 98.276 174 2 1 1505 1677 384671859 384672032 3.570000e-78 303.0
6 TraesCS2B01G278700 chr2B 98.276 174 2 1 1333 1506 384672031 384672203 3.570000e-78 303.0
7 TraesCS2B01G278700 chr2B 84.184 196 12 3 1761 1956 238534134 238533958 1.050000e-38 172.0
8 TraesCS2B01G278700 chr2B 83.673 98 13 2 7458 7554 383562674 383562769 1.090000e-13 89.8
9 TraesCS2B01G278700 chr2A 96.029 5213 128 24 2440 7619 418400792 418395626 0.000000e+00 8407.0
10 TraesCS2B01G278700 chr2A 91.273 275 20 3 2164 2437 441097385 441097114 9.640000e-99 372.0
11 TraesCS2B01G278700 chr2A 90.345 145 12 2 7611 7754 418395231 418395088 1.040000e-43 189.0
12 TraesCS2B01G278700 chr2A 85.714 98 11 2 7458 7554 419198633 419198538 5.030000e-17 100.0
13 TraesCS2B01G278700 chr2D 97.133 4849 102 20 2441 7263 316658443 316653606 0.000000e+00 8150.0
14 TraesCS2B01G278700 chr2D 91.954 261 21 0 7610 7870 316653383 316653123 4.490000e-97 366.0
15 TraesCS2B01G278700 chr2D 91.781 219 14 2 7409 7626 316653610 316653395 1.280000e-77 302.0
16 TraesCS2B01G278700 chr2D 84.536 97 12 2 7458 7553 315865772 315865866 8.410000e-15 93.5
17 TraesCS2B01G278700 chr4B 95.888 1532 37 7 1 1506 77642787 77644318 0.000000e+00 2457.0
18 TraesCS2B01G278700 chr4B 95.368 734 27 7 1707 2436 77644471 77645201 0.000000e+00 1160.0
19 TraesCS2B01G278700 chr4B 88.509 644 43 6 1822 2436 605395965 605396606 0.000000e+00 750.0
20 TraesCS2B01G278700 chr4B 95.484 465 21 0 1 465 605394064 605394528 0.000000e+00 743.0
21 TraesCS2B01G278700 chr4B 97.312 372 9 1 1505 1875 77644145 77644516 1.440000e-176 630.0
22 TraesCS2B01G278700 chr4B 83.333 498 47 5 2 464 524168429 524168925 2.030000e-115 427.0
23 TraesCS2B01G278700 chr4B 78.987 533 61 25 1937 2431 524170350 524170869 4.580000e-82 316.0
24 TraesCS2B01G278700 chr4B 92.929 198 13 1 1760 1957 605395771 605395967 3.590000e-73 287.0
25 TraesCS2B01G278700 chr3D 94.603 982 33 7 542 1506 290139117 290140095 0.000000e+00 1502.0
26 TraesCS2B01G278700 chr3D 95.522 201 6 3 1505 1703 290139921 290140120 1.270000e-82 318.0
27 TraesCS2B01G278700 chr3A 93.666 821 36 9 1 808 168226259 168225442 0.000000e+00 1214.0
28 TraesCS2B01G278700 chr3A 94.262 732 36 5 1707 2436 168224668 168223941 0.000000e+00 1114.0
29 TraesCS2B01G278700 chr3A 92.373 708 34 7 637 1328 382146407 382147110 0.000000e+00 990.0
30 TraesCS2B01G278700 chr3A 94.286 595 16 2 928 1506 168225412 168224820 0.000000e+00 894.0
31 TraesCS2B01G278700 chr3A 94.933 375 17 2 1505 1878 168224993 168224620 3.160000e-163 586.0
32 TraesCS2B01G278700 chr3A 92.893 197 13 1 1505 1700 382147958 382148154 1.290000e-72 285.0
33 TraesCS2B01G278700 chr3A 93.923 181 11 0 1321 1501 382147946 382148126 2.800000e-69 274.0
34 TraesCS2B01G278700 chr3A 100.000 53 0 0 843 895 168225463 168225411 1.810000e-16 99.0
35 TraesCS2B01G278700 chr5D 93.147 715 28 9 811 1506 484657129 484656417 0.000000e+00 1029.0
36 TraesCS2B01G278700 chr5D 95.567 203 8 1 1505 1706 484656590 484656388 2.740000e-84 324.0
37 TraesCS2B01G278700 chr5D 88.298 94 11 0 2764 2857 473363723 473363630 6.450000e-21 113.0
38 TraesCS2B01G278700 chr5D 93.750 48 1 2 7449 7495 520056310 520056356 3.940000e-08 71.3
39 TraesCS2B01G278700 chr3B 96.013 602 20 3 542 1143 382659647 382660244 0.000000e+00 976.0
40 TraesCS2B01G278700 chr3B 92.857 476 23 2 1 465 678782193 678781718 0.000000e+00 680.0
41 TraesCS2B01G278700 chr3B 87.438 605 43 17 1860 2436 678781011 678780412 0.000000e+00 665.0
42 TraesCS2B01G278700 chr3B 93.473 383 8 5 1141 1506 382660582 382660964 3.210000e-153 553.0
43 TraesCS2B01G278700 chr3B 97.015 201 4 1 1505 1703 382660790 382660990 3.520000e-88 337.0
44 TraesCS2B01G278700 chr3B 90.452 199 19 0 1759 1957 678781264 678781066 6.060000e-66 263.0
45 TraesCS2B01G278700 chr6B 93.801 371 20 3 2068 2436 641884587 641884956 8.920000e-154 555.0
46 TraesCS2B01G278700 chr6B 89.928 278 23 3 2164 2439 151876710 151876436 3.490000e-93 353.0
47 TraesCS2B01G278700 chr1A 86.290 496 35 9 2 464 17160579 17161074 7.050000e-140 508.0
48 TraesCS2B01G278700 chr1A 83.333 576 48 22 1897 2436 17162232 17162795 9.180000e-134 488.0
49 TraesCS2B01G278700 chr1A 84.770 499 39 15 1 464 333989266 333989762 4.300000e-127 466.0
50 TraesCS2B01G278700 chr4A 86.089 496 36 9 2 464 483434229 483434724 3.280000e-138 503.0
51 TraesCS2B01G278700 chr4A 80.763 629 58 23 1858 2436 483435855 483436470 4.360000e-117 433.0
52 TraesCS2B01G278700 chr7A 81.429 630 52 28 1858 2436 700902197 700902812 9.310000e-124 455.0
53 TraesCS2B01G278700 chr7A 92.857 84 6 0 6648 6731 367258082 367257999 1.070000e-23 122.0
54 TraesCS2B01G278700 chr7B 78.245 547 65 21 1932 2436 74809541 74810075 1.280000e-77 302.0
55 TraesCS2B01G278700 chr7B 88.259 247 24 5 5759 6002 285460391 285460147 2.780000e-74 291.0
56 TraesCS2B01G278700 chr7B 86.081 273 23 4 6648 6918 285459786 285459527 6.010000e-71 279.0
57 TraesCS2B01G278700 chr1B 77.455 550 70 22 1932 2438 178510202 178510740 6.010000e-71 279.0
58 TraesCS2B01G278700 chr1B 77.866 506 68 20 1932 2409 653853356 653852867 2.800000e-69 274.0
59 TraesCS2B01G278700 chr7D 85.662 272 25 6 6648 6918 303040595 303040853 2.800000e-69 274.0
60 TraesCS2B01G278700 chr5B 88.889 99 10 1 2759 2857 580692691 580692594 3.860000e-23 121.0
61 TraesCS2B01G278700 chr5A 89.474 95 10 0 2763 2857 593178892 593178798 3.860000e-23 121.0
62 TraesCS2B01G278700 chr5A 76.699 206 43 3 83 287 32975007 32975208 8.350000e-20 110.0
63 TraesCS2B01G278700 chr4D 83.051 118 8 6 7448 7554 231216070 231216186 6.500000e-16 97.1
64 TraesCS2B01G278700 chr4D 82.883 111 7 6 7456 7554 175111626 175111736 1.090000e-13 89.8
65 TraesCS2B01G278700 chr6D 93.617 47 3 0 7457 7503 242987580 242987534 3.940000e-08 71.3


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 TraesCS2B01G278700 chr2B 384670527 384678396 7869 False 14534.000000 14534 100.000000 1 7870 1 chr2B.!!$F2 7869
1 TraesCS2B01G278700 chr2B 238533355 238535823 2468 True 506.666667 721 88.661000 1 2436 3 chr2B.!!$R1 2435
2 TraesCS2B01G278700 chr2A 418395088 418400792 5704 True 4298.000000 8407 93.187000 2440 7754 2 chr2A.!!$R3 5314
3 TraesCS2B01G278700 chr2D 316653123 316658443 5320 True 2939.333333 8150 93.622667 2441 7870 3 chr2D.!!$R1 5429
4 TraesCS2B01G278700 chr4B 77642787 77645201 2414 False 1415.666667 2457 96.189333 1 2436 3 chr4B.!!$F1 2435
5 TraesCS2B01G278700 chr4B 605394064 605396606 2542 False 593.333333 750 92.307333 1 2436 3 chr4B.!!$F3 2435
6 TraesCS2B01G278700 chr4B 524168429 524170869 2440 False 371.500000 427 81.160000 2 2431 2 chr4B.!!$F2 2429
7 TraesCS2B01G278700 chr3D 290139117 290140120 1003 False 910.000000 1502 95.062500 542 1703 2 chr3D.!!$F1 1161
8 TraesCS2B01G278700 chr3A 168223941 168226259 2318 True 781.400000 1214 95.429400 1 2436 5 chr3A.!!$R1 2435
9 TraesCS2B01G278700 chr3A 382146407 382148154 1747 False 516.333333 990 93.063000 637 1700 3 chr3A.!!$F1 1063
10 TraesCS2B01G278700 chr5D 484656388 484657129 741 True 676.500000 1029 94.357000 811 1706 2 chr5D.!!$R2 895
11 TraesCS2B01G278700 chr3B 382659647 382660990 1343 False 622.000000 976 95.500333 542 1703 3 chr3B.!!$F1 1161
12 TraesCS2B01G278700 chr3B 678780412 678782193 1781 True 536.000000 680 90.249000 1 2436 3 chr3B.!!$R1 2435
13 TraesCS2B01G278700 chr1A 17160579 17162795 2216 False 498.000000 508 84.811500 2 2436 2 chr1A.!!$F2 2434
14 TraesCS2B01G278700 chr4A 483434229 483436470 2241 False 468.000000 503 83.426000 2 2436 2 chr4A.!!$F1 2434
15 TraesCS2B01G278700 chr7A 700902197 700902812 615 False 455.000000 455 81.429000 1858 2436 1 chr7A.!!$F1 578
16 TraesCS2B01G278700 chr7B 74809541 74810075 534 False 302.000000 302 78.245000 1932 2436 1 chr7B.!!$F1 504
17 TraesCS2B01G278700 chr7B 285459527 285460391 864 True 285.000000 291 87.170000 5759 6918 2 chr7B.!!$R1 1159
18 TraesCS2B01G278700 chr1B 178510202 178510740 538 False 279.000000 279 77.455000 1932 2438 1 chr1B.!!$F1 506

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
27 28 1.660167 CACGTCAGGCATCACATCAT 58.340 50.000 0.00 0.00 0.00 2.45 F
531 1369 2.028476 AGTGCCTGTTAGTGATTACGCA 60.028 45.455 0.00 0.00 0.00 5.24 F
1557 4328 0.033504 TGAAGAACTCTGGCACGTCC 59.966 55.000 0.00 0.00 0.00 4.79 F
1561 4332 0.108756 GAACTCTGGCACGTCCTACC 60.109 60.000 5.77 0.00 35.26 3.18 F
2508 5841 0.250295 TCCCAACACGAGCTCCTTTG 60.250 55.000 8.47 8.71 0.00 2.77 F
2982 6316 1.115467 CGAGGCAGTTCAGGGACTAT 58.885 55.000 0.00 0.00 36.02 2.12 F
3063 6397 1.373748 GTGCCGTGCGGTTAGAGAA 60.374 57.895 12.46 0.00 37.65 2.87 F
4223 7577 1.533711 CCTGCCCCCACAAGGATAG 59.466 63.158 0.00 0.00 38.24 2.08 F
5031 8385 4.142038 ACCATACCAGTCAGTGTTTTTCC 58.858 43.478 0.00 0.00 0.00 3.13 F
5589 8944 7.198390 TCGTACAGTAGTTAATGCTCCATTAC 58.802 38.462 0.00 0.00 36.26 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1501 4230 1.202927 AGCTTTAGTGCAAAGGAGCCA 60.203 47.619 9.08 0.00 43.38 4.75 R
2519 5852 0.535102 CAACTGACAGGTGGGTCCAC 60.535 60.000 13.01 11.47 45.49 4.02 R
3416 6750 1.765904 TGCTGGTGTTGTAGTCCAAGA 59.234 47.619 0.00 0.00 32.51 3.02 R
3547 6881 4.581824 AGCTCAATCAACAAAGTGTGACAT 59.418 37.500 0.00 0.00 0.00 3.06 R
4397 7751 0.560688 TTGCCCCTTCCAACTTTCCT 59.439 50.000 0.00 0.00 0.00 3.36 R
4727 8081 7.649370 AATAGCGAATGTCATAATCTGTCAG 57.351 36.000 0.00 0.00 0.00 3.51 R
5030 8384 1.362224 TGGTCTCCTCAAAAGAGGGG 58.638 55.000 11.34 8.34 44.21 4.79 R
5133 8487 1.526575 AATCCAAAGCCTGCACACGG 61.527 55.000 0.00 0.00 0.00 4.94 R
6285 9719 0.887933 AAAATTAGTGCTGGGTGGCG 59.112 50.000 0.00 0.00 34.52 5.69 R
7280 10728 1.091771 ATTTGACTGCGATCTGGCCG 61.092 55.000 0.00 0.00 0.00 6.13 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
27 28 1.660167 CACGTCAGGCATCACATCAT 58.340 50.000 0.00 0.00 0.00 2.45
95 97 4.813027 TCTACTTGTTCATCAACGGGTAC 58.187 43.478 0.00 0.00 34.95 3.34
270 272 2.682856 GCTTCTTGCATTACCCATTCGA 59.317 45.455 0.00 0.00 42.31 3.71
334 369 7.626487 TGGGAGATGATCAGATGGATATAATGT 59.374 37.037 0.09 0.00 36.00 2.71
524 1362 3.832490 ACATGTAGAGTGCCTGTTAGTGA 59.168 43.478 0.00 0.00 0.00 3.41
529 1367 4.111375 AGAGTGCCTGTTAGTGATTACG 57.889 45.455 0.00 0.00 0.00 3.18
530 1368 2.603560 GAGTGCCTGTTAGTGATTACGC 59.396 50.000 0.00 0.00 0.00 4.42
531 1369 2.028476 AGTGCCTGTTAGTGATTACGCA 60.028 45.455 0.00 0.00 0.00 5.24
532 1370 2.348666 GTGCCTGTTAGTGATTACGCAG 59.651 50.000 0.00 3.98 0.00 5.18
533 1371 2.232696 TGCCTGTTAGTGATTACGCAGA 59.767 45.455 9.99 0.00 32.06 4.26
536 1374 4.682787 CCTGTTAGTGATTACGCAGATCA 58.317 43.478 9.99 0.00 32.06 2.92
539 1377 5.049828 TGTTAGTGATTACGCAGATCATGG 58.950 41.667 0.00 0.00 36.07 3.66
617 1531 6.207810 CCTCTTATTCTACCTCGCTGAACTAT 59.792 42.308 0.00 0.00 0.00 2.12
657 1571 5.491635 ACTGAACTCTGTTCTTTCTTTGC 57.508 39.130 11.06 0.00 0.00 3.68
1228 2551 7.458397 TGAGTCAGTATCCTTAAAATGTTGGT 58.542 34.615 0.00 0.00 0.00 3.67
1507 4236 4.009370 ACTCAGAAGTAGTTTTGGCTCC 57.991 45.455 1.30 0.00 32.59 4.70
1508 4237 3.648545 ACTCAGAAGTAGTTTTGGCTCCT 59.351 43.478 1.30 0.00 32.59 3.69
1509 4238 4.103311 ACTCAGAAGTAGTTTTGGCTCCTT 59.897 41.667 1.30 0.00 32.59 3.36
1510 4239 5.048846 TCAGAAGTAGTTTTGGCTCCTTT 57.951 39.130 1.30 0.00 0.00 3.11
1511 4240 4.821805 TCAGAAGTAGTTTTGGCTCCTTTG 59.178 41.667 1.30 0.00 0.00 2.77
1512 4241 3.570125 AGAAGTAGTTTTGGCTCCTTTGC 59.430 43.478 0.00 0.00 0.00 3.68
1515 4244 1.780503 AGTTTTGGCTCCTTTGCACT 58.219 45.000 0.00 0.00 34.04 4.40
1517 4246 3.295973 AGTTTTGGCTCCTTTGCACTAA 58.704 40.909 0.00 0.00 34.04 2.24
1518 4247 3.704061 AGTTTTGGCTCCTTTGCACTAAA 59.296 39.130 0.00 0.00 34.04 1.85
1519 4248 4.051237 GTTTTGGCTCCTTTGCACTAAAG 58.949 43.478 0.00 0.00 44.35 1.85
1520 4249 1.247567 TGGCTCCTTTGCACTAAAGC 58.752 50.000 0.00 0.00 43.58 3.51
1521 4250 1.202927 TGGCTCCTTTGCACTAAAGCT 60.203 47.619 9.42 0.00 43.58 3.74
1523 4252 2.095008 GGCTCCTTTGCACTAAAGCTTC 60.095 50.000 0.00 0.00 43.58 3.86
1524 4253 2.816672 GCTCCTTTGCACTAAAGCTTCT 59.183 45.455 0.00 0.00 43.58 2.85
1525 4254 3.365767 GCTCCTTTGCACTAAAGCTTCTG 60.366 47.826 0.00 0.00 43.58 3.02
1526 4255 2.554032 TCCTTTGCACTAAAGCTTCTGC 59.446 45.455 14.02 14.02 43.58 4.26
1527 4256 2.294233 CCTTTGCACTAAAGCTTCTGCA 59.706 45.455 17.87 17.87 43.58 4.41
1528 4257 3.057033 CCTTTGCACTAAAGCTTCTGCAT 60.057 43.478 20.84 0.63 43.58 3.96
1529 4258 3.837213 TTGCACTAAAGCTTCTGCATC 57.163 42.857 20.84 3.34 39.32 3.91
1530 4259 2.781923 TGCACTAAAGCTTCTGCATCA 58.218 42.857 17.87 3.54 42.74 3.07
1531 4260 3.148412 TGCACTAAAGCTTCTGCATCAA 58.852 40.909 17.87 1.46 42.74 2.57
1532 4261 3.569277 TGCACTAAAGCTTCTGCATCAAA 59.431 39.130 17.87 1.17 42.74 2.69
1545 4316 7.467557 TTCTGCATCAAATGTTTTGAAGAAC 57.532 32.000 6.75 0.00 31.55 3.01
1546 4317 6.808829 TCTGCATCAAATGTTTTGAAGAACT 58.191 32.000 6.75 0.00 31.55 3.01
1547 4318 6.919662 TCTGCATCAAATGTTTTGAAGAACTC 59.080 34.615 6.75 0.00 31.55 3.01
1548 4319 6.808829 TGCATCAAATGTTTTGAAGAACTCT 58.191 32.000 6.75 0.00 31.55 3.24
1549 4320 6.698329 TGCATCAAATGTTTTGAAGAACTCTG 59.302 34.615 6.75 1.21 31.55 3.35
1550 4321 6.145048 GCATCAAATGTTTTGAAGAACTCTGG 59.855 38.462 6.75 0.00 31.55 3.86
1551 4322 5.591099 TCAAATGTTTTGAAGAACTCTGGC 58.409 37.500 0.37 0.00 0.00 4.85
1552 4323 5.126869 TCAAATGTTTTGAAGAACTCTGGCA 59.873 36.000 0.37 0.00 0.00 4.92
1553 4324 4.574599 ATGTTTTGAAGAACTCTGGCAC 57.425 40.909 0.00 0.00 0.00 5.01
1554 4325 2.354510 TGTTTTGAAGAACTCTGGCACG 59.645 45.455 0.00 0.00 0.00 5.34
1555 4326 2.325583 TTTGAAGAACTCTGGCACGT 57.674 45.000 0.00 0.00 0.00 4.49
1556 4327 1.865865 TTGAAGAACTCTGGCACGTC 58.134 50.000 0.00 0.00 0.00 4.34
1557 4328 0.033504 TGAAGAACTCTGGCACGTCC 59.966 55.000 0.00 0.00 0.00 4.79
1558 4329 0.318762 GAAGAACTCTGGCACGTCCT 59.681 55.000 5.77 0.00 35.26 3.85
1559 4330 1.544691 GAAGAACTCTGGCACGTCCTA 59.455 52.381 5.77 0.00 35.26 2.94
1560 4331 0.889306 AGAACTCTGGCACGTCCTAC 59.111 55.000 5.77 0.00 35.26 3.18
1561 4332 0.108756 GAACTCTGGCACGTCCTACC 60.109 60.000 5.77 0.00 35.26 3.18
1562 4333 0.542232 AACTCTGGCACGTCCTACCT 60.542 55.000 5.77 0.00 35.26 3.08
1563 4334 1.251527 ACTCTGGCACGTCCTACCTG 61.252 60.000 5.77 1.05 35.26 4.00
1564 4335 2.125512 CTGGCACGTCCTACCTGC 60.126 66.667 5.77 0.00 35.26 4.85
1565 4336 2.920384 TGGCACGTCCTACCTGCA 60.920 61.111 5.77 0.00 32.86 4.41
1566 4337 2.345991 GGCACGTCCTACCTGCAA 59.654 61.111 0.00 0.00 32.86 4.08
1570 4341 1.876416 GCACGTCCTACCTGCAAAGAA 60.876 52.381 0.00 0.00 31.79 2.52
1572 4343 3.074412 CACGTCCTACCTGCAAAGAAAT 58.926 45.455 0.00 0.00 0.00 2.17
1599 4370 7.901874 TTCTTTTATTTTTACACGCAGTCAC 57.098 32.000 0.00 0.00 41.61 3.67
1600 4371 7.017498 TCTTTTATTTTTACACGCAGTCACA 57.983 32.000 0.00 0.00 41.61 3.58
1602 4373 8.132362 TCTTTTATTTTTACACGCAGTCACATT 58.868 29.630 0.00 0.00 41.61 2.71
1604 4375 8.635877 TTTATTTTTACACGCAGTCACATTTT 57.364 26.923 0.00 0.00 41.61 1.82
1605 4376 8.635877 TTATTTTTACACGCAGTCACATTTTT 57.364 26.923 0.00 0.00 41.61 1.94
1627 4398 5.585820 TTTGGTTGTGGTTCCTTAAGTTC 57.414 39.130 0.97 0.00 0.00 3.01
1629 4400 5.633655 TGGTTGTGGTTCCTTAAGTTCTA 57.366 39.130 0.97 0.00 0.00 2.10
1631 4402 4.450080 GGTTGTGGTTCCTTAAGTTCTACG 59.550 45.833 0.97 0.00 0.00 3.51
1632 4403 4.261578 TGTGGTTCCTTAAGTTCTACGG 57.738 45.455 0.97 0.00 0.00 4.02
1633 4404 3.642848 TGTGGTTCCTTAAGTTCTACGGT 59.357 43.478 0.97 0.00 0.00 4.83
1634 4405 4.101430 TGTGGTTCCTTAAGTTCTACGGTT 59.899 41.667 0.97 0.00 0.00 4.44
1644 4508 9.428097 CCTTAAGTTCTACGGTTTATAGTTGTT 57.572 33.333 0.97 0.00 0.00 2.83
1648 4512 7.664758 AGTTCTACGGTTTATAGTTGTTCACT 58.335 34.615 0.00 0.00 39.87 3.41
1649 4513 7.597743 AGTTCTACGGTTTATAGTTGTTCACTG 59.402 37.037 0.00 0.00 35.97 3.66
1650 4514 6.392354 TCTACGGTTTATAGTTGTTCACTGG 58.608 40.000 0.00 0.00 35.97 4.00
1651 4515 4.964593 ACGGTTTATAGTTGTTCACTGGT 58.035 39.130 0.00 0.00 35.97 4.00
1652 4516 5.370679 ACGGTTTATAGTTGTTCACTGGTT 58.629 37.500 0.00 0.00 35.97 3.67
1654 4518 6.140110 CGGTTTATAGTTGTTCACTGGTTTG 58.860 40.000 0.00 0.00 35.97 2.93
1655 4519 5.918576 GGTTTATAGTTGTTCACTGGTTTGC 59.081 40.000 0.00 0.00 35.97 3.68
1656 4520 6.238925 GGTTTATAGTTGTTCACTGGTTTGCT 60.239 38.462 0.00 0.00 35.97 3.91
1657 4521 7.040961 GGTTTATAGTTGTTCACTGGTTTGCTA 60.041 37.037 0.00 0.00 35.97 3.49
1660 4524 3.877508 AGTTGTTCACTGGTTTGCTACTC 59.122 43.478 0.00 0.00 32.83 2.59
1661 4525 3.552132 TGTTCACTGGTTTGCTACTCA 57.448 42.857 0.00 0.00 0.00 3.41
1663 4527 3.133901 TGTTCACTGGTTTGCTACTCAGA 59.866 43.478 0.00 0.00 32.58 3.27
1664 4528 4.127171 GTTCACTGGTTTGCTACTCAGAA 58.873 43.478 0.00 0.00 32.58 3.02
1667 4531 4.587262 TCACTGGTTTGCTACTCAGAAGTA 59.413 41.667 0.00 0.00 36.92 2.24
1787 4800 1.346068 TGTGCTGGCAGTGTGTATGTA 59.654 47.619 17.16 0.00 0.00 2.29
1855 5072 4.485163 GGTTCATACCATTGTCTTTGTGC 58.515 43.478 0.00 0.00 44.36 4.57
2225 5554 2.709125 CTTCGACGGTCTGTGGCCAA 62.709 60.000 7.24 0.00 0.00 4.52
2282 5612 3.010027 TGATAAGAATGGGAGGTTGTGCA 59.990 43.478 0.00 0.00 0.00 4.57
2300 5630 3.771160 GGTGCGGGACTCCATCGT 61.771 66.667 0.00 0.00 31.85 3.73
2301 5631 2.420568 GGTGCGGGACTCCATCGTA 61.421 63.158 0.00 0.00 31.85 3.43
2375 5707 3.646637 AGAGGTATCAAAATAGACCGGGG 59.353 47.826 6.32 0.00 37.04 5.73
2438 5771 7.639113 ACTGAGACATTAGGAGTAGAGAAAG 57.361 40.000 0.00 0.00 0.00 2.62
2508 5841 0.250295 TCCCAACACGAGCTCCTTTG 60.250 55.000 8.47 8.71 0.00 2.77
2982 6316 1.115467 CGAGGCAGTTCAGGGACTAT 58.885 55.000 0.00 0.00 36.02 2.12
3030 6364 1.666311 CGTCTTCGGAGGTCTTGTCAC 60.666 57.143 0.00 0.00 0.00 3.67
3063 6397 1.373748 GTGCCGTGCGGTTAGAGAA 60.374 57.895 12.46 0.00 37.65 2.87
3088 6422 1.920574 CGCGTGTTGTAGATTGAGAGG 59.079 52.381 0.00 0.00 0.00 3.69
3416 6750 2.086610 AATTGGGCACTTGAACCTGT 57.913 45.000 0.00 0.00 0.00 4.00
3593 6927 6.562270 GCTGGACTGATTATTTCGTGTTATCG 60.562 42.308 0.00 0.00 0.00 2.92
3703 7037 5.414789 AAACCACATTTACATTAAGGCCC 57.585 39.130 0.00 0.00 0.00 5.80
3753 7087 9.912634 TTCTGTTTCTGTTGAATTGATAATTCC 57.087 29.630 10.72 0.00 45.23 3.01
3787 7121 5.957771 TGAGATAAATAAGGCTCCACTGT 57.042 39.130 0.00 0.00 0.00 3.55
3788 7122 6.313519 TGAGATAAATAAGGCTCCACTGTT 57.686 37.500 0.00 0.00 0.00 3.16
3789 7123 6.115446 TGAGATAAATAAGGCTCCACTGTTG 58.885 40.000 0.00 0.00 0.00 3.33
3790 7124 5.440610 AGATAAATAAGGCTCCACTGTTGG 58.559 41.667 0.00 0.00 45.56 3.77
3805 7154 3.885297 ACTGTTGGAGACCTTGATTTGTG 59.115 43.478 0.00 0.00 0.00 3.33
4048 7401 7.787935 GTCTTGCACGAAAAATATATGTACTCG 59.212 37.037 0.00 5.99 0.00 4.18
4089 7442 4.927267 ACCCCAAAAGTGTCATGAGATA 57.073 40.909 0.00 0.00 0.00 1.98
4096 7449 9.347240 CCCAAAAGTGTCATGAGATATCTTTAT 57.653 33.333 6.70 2.30 0.00 1.40
4151 7504 9.918630 CATCATACAAACAGGAAAAGAAAATCT 57.081 29.630 0.00 0.00 0.00 2.40
4168 7521 5.859205 AAATCTTATGCCTGGAACAATCC 57.141 39.130 0.00 0.00 46.76 3.01
4191 7544 6.434028 TCCAAACTGATTACTTTTAGCATGCT 59.566 34.615 25.99 25.99 0.00 3.79
4223 7577 1.533711 CCTGCCCCCACAAGGATAG 59.466 63.158 0.00 0.00 38.24 2.08
4397 7751 4.223700 AGCAGGATGACTATGAAGTTGTGA 59.776 41.667 0.00 0.00 39.69 3.58
4727 8081 6.480320 AGATTTCAAAGTGCTATATCCGACAC 59.520 38.462 0.00 0.00 0.00 3.67
4750 8104 6.644181 CACTGACAGATTATGACATTCGCTAT 59.356 38.462 10.08 0.00 33.11 2.97
4801 8155 7.723616 TGAATCTTTCCCAAGTTTCTGTTGATA 59.276 33.333 7.11 0.00 38.66 2.15
4946 8300 6.030082 ACTCATTTCCTAGGACCCTTTCTTA 58.970 40.000 12.22 0.00 0.00 2.10
5030 8384 5.519722 CAACCATACCAGTCAGTGTTTTTC 58.480 41.667 0.00 0.00 0.00 2.29
5031 8385 4.142038 ACCATACCAGTCAGTGTTTTTCC 58.858 43.478 0.00 0.00 0.00 3.13
5589 8944 7.198390 TCGTACAGTAGTTAATGCTCCATTAC 58.802 38.462 0.00 0.00 36.26 1.89
6128 9561 8.737168 TGCTCACATGTAATTTCTAGCTTTAT 57.263 30.769 0.00 0.00 0.00 1.40
6285 9719 4.439253 AGCCCTTGTTGGAAGGTATATC 57.561 45.455 0.00 0.00 38.35 1.63
6543 9982 5.503927 AGATTTCCTTGATAAGCTTCTGCA 58.496 37.500 0.00 0.00 42.74 4.41
6544 9983 5.589452 AGATTTCCTTGATAAGCTTCTGCAG 59.411 40.000 7.63 7.63 42.74 4.41
6612 10051 5.750067 GTCTTACTGTTTTCGACTGGTTGTA 59.250 40.000 0.00 0.00 0.00 2.41
6613 10052 6.256321 GTCTTACTGTTTTCGACTGGTTGTAA 59.744 38.462 0.00 0.00 0.00 2.41
6781 10220 6.149633 GTCATGTTTGGAGTTACAATGGTTC 58.850 40.000 0.00 0.00 0.00 3.62
6862 10303 1.583054 GAAAACAGCAGGACTCGTGT 58.417 50.000 0.91 0.00 0.00 4.49
6912 10353 0.950555 TTGAACGAGCAGCGCTTGAT 60.951 50.000 7.50 1.26 42.27 2.57
7176 10618 7.249186 TGCTTTGGATTCAAAATTCTGTTTG 57.751 32.000 0.00 0.00 41.70 2.93
7279 10727 5.360591 TCAAGTCTCTTTCTTCTGTGGTTC 58.639 41.667 0.00 0.00 0.00 3.62
7280 10728 4.344359 AGTCTCTTTCTTCTGTGGTTCC 57.656 45.455 0.00 0.00 0.00 3.62
7289 10737 1.450312 CTGTGGTTCCGGCCAGATC 60.450 63.158 2.24 0.00 39.53 2.75
7302 10750 1.796617 GCCAGATCGCAGTCAAATTGC 60.797 52.381 0.00 0.00 38.18 3.56
7308 10756 1.212751 GCAGTCAAATTGCCGTCCC 59.787 57.895 0.00 0.00 35.54 4.46
7330 10778 2.380365 AGCATCTCCAACTGCTCCA 58.620 52.632 0.00 0.00 45.30 3.86
7345 10793 2.035961 TGCTCCACTATGTCTAATCGCC 59.964 50.000 0.00 0.00 0.00 5.54
7350 10798 3.245284 CCACTATGTCTAATCGCCGTTTG 59.755 47.826 0.00 0.00 0.00 2.93
7439 10887 2.696506 CTCCCGTAAACTGGTCCTTTC 58.303 52.381 0.00 0.00 0.00 2.62
7448 10896 4.576330 AACTGGTCCTTTCCTTCCATAG 57.424 45.455 0.00 0.00 0.00 2.23
7449 10897 3.532102 ACTGGTCCTTTCCTTCCATAGT 58.468 45.455 0.00 0.00 0.00 2.12
7505 10955 4.571176 GCAACTCCACCTTACTGTTATAGC 59.429 45.833 0.00 0.00 0.00 2.97
7557 11008 4.680110 GCGCTAGATATCGCTTTAGAAACA 59.320 41.667 0.00 0.00 46.92 2.83
7558 11009 5.346281 GCGCTAGATATCGCTTTAGAAACAT 59.654 40.000 0.00 0.00 46.92 2.71
7587 11038 5.960202 AGGGCCAAATCTTAAATGAGAACAT 59.040 36.000 6.18 0.00 38.50 2.71
7641 11495 6.514063 AGTCTTGTTACAAACTAGAGGTGAC 58.486 40.000 0.00 0.23 42.38 3.67
7661 11515 7.099120 GGTGACGACCTTTATTTTTAGGACTA 58.901 38.462 0.00 0.00 39.47 2.59
7681 11535 6.155475 ACTATGAGAAGCCTTCACATACTC 57.845 41.667 17.25 2.09 40.60 2.59
7759 11613 7.886446 ACTAGCTAGAAGACTCTAAAAGACAGT 59.114 37.037 27.45 0.00 33.66 3.55
7761 11615 8.276252 AGCTAGAAGACTCTAAAAGACAGTAG 57.724 38.462 0.00 0.00 33.66 2.57
7765 11619 8.570068 AGAAGACTCTAAAAGACAGTAGGTAG 57.430 38.462 0.00 0.00 0.00 3.18
7777 11631 5.246429 AGACAGTAGGTAGGGTTGAGAAAAG 59.754 44.000 0.00 0.00 0.00 2.27
7782 11636 7.501225 CAGTAGGTAGGGTTGAGAAAAGAAAAA 59.499 37.037 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 97 6.700960 TGTTGAAGAATACAATGCAAACTTGG 59.299 34.615 3.73 0.00 0.00 3.61
270 272 1.895131 AGCCAGCGGTCATTTCATTTT 59.105 42.857 0.00 0.00 0.00 1.82
347 382 0.610174 AGTTCGCCATCTCTCTTGCA 59.390 50.000 0.00 0.00 0.00 4.08
453 499 8.443160 TGTTTAGATTAAAGTTCAAGATCTGCG 58.557 33.333 0.00 0.00 0.00 5.18
491 1329 4.002982 CACTCTACATGTGCCTTTTGCTA 58.997 43.478 9.11 0.00 42.00 3.49
516 1354 5.049828 CCATGATCTGCGTAATCACTAACA 58.950 41.667 0.00 0.00 36.04 2.41
524 1362 7.750229 ACAATTTATCCATGATCTGCGTAAT 57.250 32.000 0.00 0.00 0.00 1.89
529 1367 7.358066 CACTGTACAATTTATCCATGATCTGC 58.642 38.462 0.00 0.00 0.00 4.26
530 1368 7.358066 GCACTGTACAATTTATCCATGATCTG 58.642 38.462 0.00 0.00 0.00 2.90
531 1369 6.203530 CGCACTGTACAATTTATCCATGATCT 59.796 38.462 0.00 0.00 0.00 2.75
532 1370 6.017934 ACGCACTGTACAATTTATCCATGATC 60.018 38.462 0.00 0.00 0.00 2.92
533 1371 5.822519 ACGCACTGTACAATTTATCCATGAT 59.177 36.000 0.00 0.00 0.00 2.45
536 1374 6.509418 AAACGCACTGTACAATTTATCCAT 57.491 33.333 0.00 0.00 0.00 3.41
539 1377 9.976255 TGTATAAAACGCACTGTACAATTTATC 57.024 29.630 0.00 0.00 0.00 1.75
657 1571 9.447157 AAGGAGAAAAGATGAGTTCTTATTCAG 57.553 33.333 0.00 0.00 44.09 3.02
1124 2075 6.465439 CCCAATAATAAGGGTTTGGTTCTC 57.535 41.667 0.00 0.00 40.34 2.87
1228 2551 8.625571 TGGGAAAGGGAATTATTAGGTTCTTAA 58.374 33.333 0.00 0.00 0.00 1.85
1339 3509 5.474532 ACATTTGATGCAGAAGCTTTAGTGA 59.525 36.000 0.00 0.00 42.74 3.41
1501 4230 1.202927 AGCTTTAGTGCAAAGGAGCCA 60.203 47.619 9.08 0.00 43.38 4.75
1502 4231 1.539157 AGCTTTAGTGCAAAGGAGCC 58.461 50.000 9.08 0.00 43.38 4.70
1503 4232 2.816672 AGAAGCTTTAGTGCAAAGGAGC 59.183 45.455 0.00 0.00 43.38 4.70
1505 4234 2.554032 GCAGAAGCTTTAGTGCAAAGGA 59.446 45.455 19.11 0.00 43.38 3.36
1506 4235 2.294233 TGCAGAAGCTTTAGTGCAAAGG 59.706 45.455 22.57 0.00 42.79 3.11
1507 4236 3.631145 TGCAGAAGCTTTAGTGCAAAG 57.369 42.857 22.57 0.00 42.79 2.77
1511 4240 3.837213 TTGATGCAGAAGCTTTAGTGC 57.163 42.857 17.84 17.84 42.74 4.40
1512 4241 5.706916 ACATTTGATGCAGAAGCTTTAGTG 58.293 37.500 0.00 0.00 42.74 2.74
1515 4244 7.208777 TCAAAACATTTGATGCAGAAGCTTTA 58.791 30.769 0.00 0.00 42.74 1.85
1517 4246 5.603596 TCAAAACATTTGATGCAGAAGCTT 58.396 33.333 0.00 0.00 42.74 3.74
1518 4247 5.204409 TCAAAACATTTGATGCAGAAGCT 57.796 34.783 1.57 0.00 42.74 3.74
1519 4248 5.693104 TCTTCAAAACATTTGATGCAGAAGC 59.307 36.000 6.38 0.00 42.57 3.86
1520 4249 7.437267 AGTTCTTCAAAACATTTGATGCAGAAG 59.563 33.333 14.21 6.30 28.98 2.85
1521 4250 7.267128 AGTTCTTCAAAACATTTGATGCAGAA 58.733 30.769 11.53 11.53 0.00 3.02
1523 4252 6.921857 AGAGTTCTTCAAAACATTTGATGCAG 59.078 34.615 6.38 2.39 0.00 4.41
1524 4253 6.698329 CAGAGTTCTTCAAAACATTTGATGCA 59.302 34.615 6.38 0.00 0.00 3.96
1525 4254 6.145048 CCAGAGTTCTTCAAAACATTTGATGC 59.855 38.462 6.38 0.00 0.00 3.91
1526 4255 6.145048 GCCAGAGTTCTTCAAAACATTTGATG 59.855 38.462 6.38 8.82 0.00 3.07
1527 4256 6.183360 TGCCAGAGTTCTTCAAAACATTTGAT 60.183 34.615 6.38 0.00 0.00 2.57
1528 4257 5.126869 TGCCAGAGTTCTTCAAAACATTTGA 59.873 36.000 1.57 1.57 0.00 2.69
1529 4258 5.232838 GTGCCAGAGTTCTTCAAAACATTTG 59.767 40.000 0.00 0.00 0.00 2.32
1530 4259 5.351458 GTGCCAGAGTTCTTCAAAACATTT 58.649 37.500 0.00 0.00 0.00 2.32
1531 4260 4.498009 CGTGCCAGAGTTCTTCAAAACATT 60.498 41.667 0.00 0.00 0.00 2.71
1532 4261 3.003689 CGTGCCAGAGTTCTTCAAAACAT 59.996 43.478 0.00 0.00 0.00 2.71
1545 4316 1.513158 CAGGTAGGACGTGCCAGAG 59.487 63.158 2.38 0.00 40.02 3.35
1546 4317 3.694746 CAGGTAGGACGTGCCAGA 58.305 61.111 2.38 0.00 40.02 3.86
1551 4322 2.163818 TTCTTTGCAGGTAGGACGTG 57.836 50.000 0.00 0.00 37.08 4.49
1552 4323 2.922740 TTTCTTTGCAGGTAGGACGT 57.077 45.000 0.00 0.00 0.00 4.34
1553 4324 6.316390 AGAAATATTTCTTTGCAGGTAGGACG 59.684 38.462 22.43 0.00 44.70 4.79
1554 4325 7.631717 AGAAATATTTCTTTGCAGGTAGGAC 57.368 36.000 22.43 0.00 44.70 3.85
1580 4351 8.635877 AAAAATGTGACTGCGTGTAAAAATAA 57.364 26.923 0.00 0.00 0.00 1.40
1604 4375 5.717654 AGAACTTAAGGAACCACAACCAAAA 59.282 36.000 7.53 0.00 0.00 2.44
1605 4376 5.265989 AGAACTTAAGGAACCACAACCAAA 58.734 37.500 7.53 0.00 0.00 3.28
1607 4378 4.513406 AGAACTTAAGGAACCACAACCA 57.487 40.909 7.53 0.00 0.00 3.67
1608 4379 4.450080 CGTAGAACTTAAGGAACCACAACC 59.550 45.833 7.53 0.00 0.00 3.77
1609 4380 4.450080 CCGTAGAACTTAAGGAACCACAAC 59.550 45.833 7.53 0.00 0.00 3.32
1611 4382 3.642848 ACCGTAGAACTTAAGGAACCACA 59.357 43.478 7.53 0.00 0.00 4.17
1612 4383 4.263018 ACCGTAGAACTTAAGGAACCAC 57.737 45.455 7.53 0.00 0.00 4.16
1613 4384 4.961438 AACCGTAGAACTTAAGGAACCA 57.039 40.909 7.53 0.00 0.00 3.67
1614 4385 8.253810 ACTATAAACCGTAGAACTTAAGGAACC 58.746 37.037 7.53 0.00 0.00 3.62
1615 4386 9.645059 AACTATAAACCGTAGAACTTAAGGAAC 57.355 33.333 7.53 0.00 0.00 3.62
1616 4387 9.643693 CAACTATAAACCGTAGAACTTAAGGAA 57.356 33.333 7.53 0.00 0.00 3.36
1617 4388 8.806146 ACAACTATAAACCGTAGAACTTAAGGA 58.194 33.333 7.53 0.00 0.00 3.36
1618 4389 8.992835 ACAACTATAAACCGTAGAACTTAAGG 57.007 34.615 7.53 0.00 0.00 2.69
1620 4391 9.979578 TGAACAACTATAAACCGTAGAACTTAA 57.020 29.630 0.00 0.00 0.00 1.85
1627 4398 6.161381 ACCAGTGAACAACTATAAACCGTAG 58.839 40.000 0.00 0.00 36.83 3.51
1629 4400 4.964593 ACCAGTGAACAACTATAAACCGT 58.035 39.130 0.00 0.00 36.83 4.83
1631 4402 5.918576 GCAAACCAGTGAACAACTATAAACC 59.081 40.000 0.00 0.00 36.83 3.27
1632 4403 6.735130 AGCAAACCAGTGAACAACTATAAAC 58.265 36.000 0.00 0.00 36.83 2.01
1633 4404 6.952773 AGCAAACCAGTGAACAACTATAAA 57.047 33.333 0.00 0.00 36.83 1.40
1634 4405 7.221450 AGTAGCAAACCAGTGAACAACTATAA 58.779 34.615 0.00 0.00 36.83 0.98
1644 4508 3.388024 ACTTCTGAGTAGCAAACCAGTGA 59.612 43.478 0.00 0.00 33.32 3.41
1656 4520 4.755123 GCAAGCCAAAACTACTTCTGAGTA 59.245 41.667 0.00 0.00 37.33 2.59
1657 4521 3.565902 GCAAGCCAAAACTACTTCTGAGT 59.434 43.478 0.00 0.00 39.97 3.41
1660 4524 3.988379 TGCAAGCCAAAACTACTTCTG 57.012 42.857 0.00 0.00 0.00 3.02
1661 4525 4.401925 AGATGCAAGCCAAAACTACTTCT 58.598 39.130 0.00 0.00 0.00 2.85
1663 4527 6.660949 AGAATAGATGCAAGCCAAAACTACTT 59.339 34.615 0.00 0.00 0.00 2.24
1664 4528 6.094603 CAGAATAGATGCAAGCCAAAACTACT 59.905 38.462 0.00 0.00 0.00 2.57
1667 4531 4.768968 ACAGAATAGATGCAAGCCAAAACT 59.231 37.500 0.00 0.00 0.00 2.66
1670 4534 7.122501 TCAATAACAGAATAGATGCAAGCCAAA 59.877 33.333 0.00 0.00 0.00 3.28
1787 4800 7.828508 ACATGATTTCATATACACAGCCATT 57.171 32.000 0.00 0.00 34.26 3.16
2200 5529 3.782046 CCACAGACCGTCGAAGATTAAT 58.218 45.455 0.00 0.00 40.67 1.40
2282 5612 2.849096 TACGATGGAGTCCCGCACCT 62.849 60.000 6.74 0.00 34.29 4.00
2375 5707 3.691118 GGGTTTATTTTCGTCCCACCTAC 59.309 47.826 0.00 0.00 38.15 3.18
2438 5771 3.135994 TCCGAGCTAAGTGTCAAAAACC 58.864 45.455 0.00 0.00 0.00 3.27
2470 5803 0.605319 ACCCAACTGGCACGTGTATG 60.605 55.000 18.38 9.61 37.83 2.39
2477 5810 2.197324 TTGGGACCCAACTGGCAC 59.803 61.111 22.74 0.00 38.75 5.01
2519 5852 0.535102 CAACTGACAGGTGGGTCCAC 60.535 60.000 13.01 11.47 45.49 4.02
2982 6316 2.882927 AGTCGAAGCGCCATTGTATA 57.117 45.000 2.29 0.00 0.00 1.47
3063 6397 2.180159 AATCTACAACACGCGGGCCT 62.180 55.000 9.12 0.00 0.00 5.19
3088 6422 2.048603 GCACATCTGGCAACTCCCC 61.049 63.158 0.00 0.00 37.61 4.81
3416 6750 1.765904 TGCTGGTGTTGTAGTCCAAGA 59.234 47.619 0.00 0.00 32.51 3.02
3547 6881 4.581824 AGCTCAATCAACAAAGTGTGACAT 59.418 37.500 0.00 0.00 0.00 3.06
3645 6979 7.177392 ACAGCTGCTTTGAGATTAAAATTAGGT 59.823 33.333 15.27 0.00 0.00 3.08
3703 7037 5.879223 ACAGGAGTAAATTCTCTTCAGCATG 59.121 40.000 0.00 0.00 35.11 4.06
3753 7087 4.808077 ATTTATCTCATGTTGCTGAGCG 57.192 40.909 0.00 0.00 42.00 5.03
3787 7121 7.004086 ACTAATTCACAAATCAAGGTCTCCAA 58.996 34.615 0.00 0.00 0.00 3.53
3788 7122 6.542821 ACTAATTCACAAATCAAGGTCTCCA 58.457 36.000 0.00 0.00 0.00 3.86
3789 7123 8.738645 ATACTAATTCACAAATCAAGGTCTCC 57.261 34.615 0.00 0.00 0.00 3.71
3866 7215 5.455392 CAATGAGAAGTTACACAAAGGCAG 58.545 41.667 0.00 0.00 0.00 4.85
3867 7216 4.278170 CCAATGAGAAGTTACACAAAGGCA 59.722 41.667 0.00 0.00 0.00 4.75
3965 7318 6.810911 TGCTTCATACTTGAGTTCTATCCTC 58.189 40.000 0.00 0.00 32.27 3.71
4048 7401 9.930693 TTGGGGTATTGTTACATCAAAATAAAC 57.069 29.630 0.00 0.00 0.00 2.01
4118 7471 5.497464 TCCTGTTTGTATGATGGAGAACA 57.503 39.130 0.00 0.00 0.00 3.18
4168 7521 7.430502 GCTAGCATGCTAAAAGTAATCAGTTTG 59.569 37.037 26.71 11.19 0.00 2.93
4397 7751 0.560688 TTGCCCCTTCCAACTTTCCT 59.439 50.000 0.00 0.00 0.00 3.36
4727 8081 7.649370 AATAGCGAATGTCATAATCTGTCAG 57.351 36.000 0.00 0.00 0.00 3.51
4801 8155 8.297470 ACAATCAGTGTTCTTGGCAATATTAT 57.703 30.769 0.00 0.00 37.01 1.28
4946 8300 7.933577 ACTATCACAAATATCATCCACGAACAT 59.066 33.333 0.00 0.00 0.00 2.71
5013 8367 2.781174 AGGGGAAAAACACTGACTGGTA 59.219 45.455 0.00 0.00 0.00 3.25
5030 8384 1.362224 TGGTCTCCTCAAAAGAGGGG 58.638 55.000 11.34 8.34 44.21 4.79
5031 8385 2.639839 TCTTGGTCTCCTCAAAAGAGGG 59.360 50.000 11.34 3.25 42.50 4.30
5133 8487 1.526575 AATCCAAAGCCTGCACACGG 61.527 55.000 0.00 0.00 0.00 4.94
5589 8944 9.180678 GGAAATATTTGGAATATGCAAGTTACG 57.819 33.333 5.17 0.00 0.00 3.18
5810 9166 5.297776 CACCAGTTGAACAAAAGTCTGAGAT 59.702 40.000 0.00 0.00 0.00 2.75
5811 9167 4.635765 CACCAGTTGAACAAAAGTCTGAGA 59.364 41.667 0.00 0.00 0.00 3.27
5812 9168 4.635765 TCACCAGTTGAACAAAAGTCTGAG 59.364 41.667 0.00 0.00 0.00 3.35
5813 9169 4.584874 TCACCAGTTGAACAAAAGTCTGA 58.415 39.130 0.00 0.00 0.00 3.27
5814 9170 4.963276 TCACCAGTTGAACAAAAGTCTG 57.037 40.909 0.00 0.00 0.00 3.51
5815 9171 5.192927 TCATCACCAGTTGAACAAAAGTCT 58.807 37.500 0.00 0.00 37.92 3.24
5816 9172 5.499139 TCATCACCAGTTGAACAAAAGTC 57.501 39.130 0.00 0.00 37.92 3.01
6118 9551 5.826737 ACTACACCGCTAGAATAAAGCTAGA 59.173 40.000 0.00 0.00 38.03 2.43
6128 9561 2.211250 ACAGGACTACACCGCTAGAA 57.789 50.000 0.00 0.00 34.73 2.10
6135 9568 5.818857 TGTTAAGTTCAAACAGGACTACACC 59.181 40.000 0.00 0.00 33.13 4.16
6285 9719 0.887933 AAAATTAGTGCTGGGTGGCG 59.112 50.000 0.00 0.00 34.52 5.69
6543 9982 4.093011 GAGCCTATCCTGGTGATCATACT 58.907 47.826 0.00 0.00 34.76 2.12
6544 9983 3.834813 TGAGCCTATCCTGGTGATCATAC 59.165 47.826 0.00 0.00 34.76 2.39
6781 10220 9.353999 GCATTACACCTTTAAAATTAGAACAGG 57.646 33.333 0.00 0.00 0.00 4.00
6862 10303 8.757997 GCAACAGTCTTGCTATTGCTATTGCA 62.758 42.308 12.47 12.47 43.62 4.08
6912 10353 1.275010 TCACTACAAGGATGCGCTTCA 59.725 47.619 22.93 3.18 0.00 3.02
7122 10564 8.579850 ACCAATGATATTCTTTACAAGCAGAA 57.420 30.769 0.00 0.00 33.55 3.02
7142 10584 8.688747 TTTTGAATCCAAAGCAATTTACCAAT 57.311 26.923 0.00 0.00 42.55 3.16
7176 10618 8.451908 AATAACAAGCTAATAATCCAGTGACC 57.548 34.615 0.00 0.00 0.00 4.02
7261 10709 2.037251 CCGGAACCACAGAAGAAAGAGA 59.963 50.000 0.00 0.00 0.00 3.10
7262 10710 2.417719 CCGGAACCACAGAAGAAAGAG 58.582 52.381 0.00 0.00 0.00 2.85
7279 10727 3.664025 TTGACTGCGATCTGGCCGG 62.664 63.158 4.71 4.71 0.00 6.13
7280 10728 1.091771 ATTTGACTGCGATCTGGCCG 61.092 55.000 0.00 0.00 0.00 6.13
7289 10737 1.154225 GGACGGCAATTTGACTGCG 60.154 57.895 0.00 0.00 40.88 5.18
7302 10750 1.144936 GGAGATGCTCTTGGGACGG 59.855 63.158 0.00 0.00 0.00 4.79
7324 10772 2.035961 GGCGATTAGACATAGTGGAGCA 59.964 50.000 0.00 0.00 0.00 4.26
7330 10778 2.864343 GCAAACGGCGATTAGACATAGT 59.136 45.455 16.62 0.00 0.00 2.12
7345 10793 2.354539 CCCAACTTGCCGCAAACG 60.355 61.111 7.33 0.00 39.67 3.60
7368 10816 2.806818 GGAACCGTTGAAGAGACCTTTC 59.193 50.000 0.00 0.00 31.62 2.62
7374 10822 3.134081 ACTTTCAGGAACCGTTGAAGAGA 59.866 43.478 0.00 0.00 35.01 3.10
7439 10887 7.816995 GCTACTTCATGATCTTACTATGGAAGG 59.183 40.741 0.00 0.00 0.00 3.46
7448 10896 6.109359 ACCTTGTGCTACTTCATGATCTTAC 58.891 40.000 0.00 0.00 0.00 2.34
7449 10897 6.299805 ACCTTGTGCTACTTCATGATCTTA 57.700 37.500 0.00 0.00 0.00 2.10
7505 10955 3.621268 TGAAGTTGTTCCTTCAACACTCG 59.379 43.478 11.22 0.00 45.82 4.18
7557 11008 3.386932 TTAAGATTTGGCCCTGCTCAT 57.613 42.857 0.00 0.00 0.00 2.90
7558 11009 2.897271 TTAAGATTTGGCCCTGCTCA 57.103 45.000 0.00 0.00 0.00 4.26
7587 11038 7.367828 ACCCCACTACCTATTATAGAACTTGA 58.632 38.462 0.03 0.00 0.00 3.02
7641 11495 9.595823 TTCTCATAGTCCTAAAAATAAAGGTCG 57.404 33.333 0.00 0.00 34.30 4.79
7658 11512 5.069781 GGAGTATGTGAAGGCTTCTCATAGT 59.930 44.000 36.24 36.24 45.34 2.12
7661 11515 4.036518 AGGAGTATGTGAAGGCTTCTCAT 58.963 43.478 34.04 34.04 43.78 2.90
7754 11608 5.245526 TCTTTTCTCAACCCTACCTACTGTC 59.754 44.000 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.