Multiple sequence alignment - TraesCS7B01G075100

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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 TraesCS7B01G075100 chr7B 100.000 2360 0 0 1 2360 84527264 84529623 0.000000e+00 4359.0
1 TraesCS7B01G075100 chr7B 88.482 191 19 1 1385 1575 84566418 84566605 6.560000e-56 228.0
2 TraesCS7B01G075100 chr7B 87.603 121 14 1 1383 1503 725395584 725395465 3.160000e-29 139.0
3 TraesCS7B01G075100 chr7B 78.295 258 20 8 1498 1719 716530206 716530463 1.470000e-27 134.0
4 TraesCS7B01G075100 chr7B 93.478 46 3 0 1718 1763 625400954 625400909 4.210000e-08 69.4
5 TraesCS7B01G075100 chr3D 97.977 1384 27 1 1 1383 69660428 69661811 0.000000e+00 2399.0
6 TraesCS7B01G075100 chr3D 91.225 604 48 4 1757 2360 462839184 462839782 0.000000e+00 817.0
7 TraesCS7B01G075100 chr3D 91.015 601 52 2 1760 2360 147469764 147470362 0.000000e+00 809.0
8 TraesCS7B01G075100 chr3D 80.709 254 26 7 1493 1723 128873600 128873853 2.410000e-40 176.0
9 TraesCS7B01G075100 chr6A 97.543 1384 30 2 1 1383 502339291 502340671 0.000000e+00 2364.0
10 TraesCS7B01G075100 chr6A 97.178 1311 36 1 74 1383 532870195 532871505 0.000000e+00 2215.0
11 TraesCS7B01G075100 chr6A 97.647 170 4 0 1207 1376 599196907 599197076 2.290000e-75 292.0
12 TraesCS7B01G075100 chr6A 92.000 50 2 2 1713 1760 68989722 68989771 4.210000e-08 69.4
13 TraesCS7B01G075100 chr2B 98.068 1346 23 2 41 1383 717931261 717929916 0.000000e+00 2338.0
14 TraesCS7B01G075100 chr2B 91.348 601 52 0 1760 2360 622655892 622655292 0.000000e+00 822.0
15 TraesCS7B01G075100 chr2B 97.222 36 1 0 1718 1753 780044842 780044807 7.040000e-06 62.1
16 TraesCS7B01G075100 chr3A 96.893 1384 41 2 1 1383 681100868 681099486 0.000000e+00 2316.0
17 TraesCS7B01G075100 chr3A 89.381 113 9 1 1474 1583 59953628 59953740 3.160000e-29 139.0
18 TraesCS7B01G075100 chr4A 96.171 1384 52 1 1 1383 107232285 107230902 0.000000e+00 2261.0
19 TraesCS7B01G075100 chr4A 93.069 101 7 0 1383 1483 510447113 510447213 5.260000e-32 148.0
20 TraesCS7B01G075100 chr2A 95.743 1386 50 5 1 1384 148651646 148653024 0.000000e+00 2224.0
21 TraesCS7B01G075100 chr2A 79.585 289 21 12 1471 1722 146796930 146796643 3.120000e-39 172.0
22 TraesCS7B01G075100 chr2A 79.348 276 23 16 1480 1721 93459035 93459310 1.880000e-36 163.0
23 TraesCS7B01G075100 chr2A 94.059 101 6 0 1383 1483 93459283 93459183 1.130000e-33 154.0
24 TraesCS7B01G075100 chr6B 95.448 1384 62 1 1 1383 695056652 695058035 0.000000e+00 2206.0
25 TraesCS7B01G075100 chr6B 92.193 602 47 0 1759 2360 349469309 349469910 0.000000e+00 852.0
26 TraesCS7B01G075100 chr5B 95.231 1384 64 2 1 1383 633276926 633278308 0.000000e+00 2189.0
27 TraesCS7B01G075100 chr5B 78.947 418 40 19 1385 1760 532841370 532841781 8.430000e-60 241.0
28 TraesCS7B01G075100 chr5B 87.069 116 10 5 1472 1584 665738624 665738511 2.460000e-25 126.0
29 TraesCS7B01G075100 chr7D 92.869 603 42 1 1759 2360 208652581 208651979 0.000000e+00 874.0
30 TraesCS7B01G075100 chr7D 93.069 101 7 0 1383 1483 282878137 282878237 5.260000e-32 148.0
31 TraesCS7B01G075100 chr6D 92.000 600 48 0 1761 2360 20125823 20126422 0.000000e+00 843.0
32 TraesCS7B01G075100 chr6D 91.089 606 50 1 1759 2360 467999701 467999096 0.000000e+00 817.0
33 TraesCS7B01G075100 chr6D 91.589 107 7 2 1480 1584 80060759 80060865 1.890000e-31 147.0
34 TraesCS7B01G075100 chr2D 91.240 605 52 1 1757 2360 12910812 12910208 0.000000e+00 822.0
35 TraesCS7B01G075100 chr3B 90.492 610 54 4 1753 2360 9861199 9861806 0.000000e+00 802.0
36 TraesCS7B01G075100 chr3B 79.851 268 18 14 1488 1719 576172320 576172053 1.880000e-36 163.0
37 TraesCS7B01G075100 chr3B 94.737 95 5 0 1 95 21802306 21802212 5.260000e-32 148.0
38 TraesCS7B01G075100 chr5A 79.630 270 26 14 1480 1722 341259981 341260248 1.450000e-37 167.0
39 TraesCS7B01G075100 chr5A 79.496 278 21 14 1480 1721 480277262 480277539 5.220000e-37 165.0
40 TraesCS7B01G075100 chr5A 82.400 125 14 4 1607 1724 509906332 509906455 4.150000e-18 102.0
41 TraesCS7B01G075100 chr4B 93.069 101 7 0 1383 1483 545236816 545236716 5.260000e-32 148.0
42 TraesCS7B01G075100 chr4D 93.000 100 7 0 1384 1483 419446026 419446125 1.890000e-31 147.0
43 TraesCS7B01G075100 chr4D 92.079 101 8 0 1383 1483 437030198 437030298 2.440000e-30 143.0
44 TraesCS7B01G075100 chr4D 95.349 43 2 0 1718 1760 480518335 480518377 4.210000e-08 69.4
45 TraesCS7B01G075100 chr1B 78.058 278 25 11 1480 1721 184768823 184768546 2.440000e-30 143.0
46 TraesCS7B01G075100 chr1B 76.384 271 28 15 1488 1722 583752332 583752062 1.920000e-21 113.0
47 TraesCS7B01G075100 chr1B 76.000 275 30 16 1488 1726 662013811 662013537 2.480000e-20 110.0
48 TraesCS7B01G075100 chr1B 75.277 271 31 18 1488 1722 613732144 613731874 1.930000e-16 97.1
49 TraesCS7B01G075100 chr1D 92.157 102 5 1 1488 1586 268943634 268943735 8.790000e-30 141.0
50 TraesCS7B01G075100 chr7A 79.221 231 21 10 1479 1682 702982001 702982231 4.090000e-28 135.0
51 TraesCS7B01G075100 chr1A 92.000 50 2 2 1713 1760 510910615 510910664 4.210000e-08 69.4


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 TraesCS7B01G075100 chr7B 84527264 84529623 2359 False 4359 4359 100.000 1 2360 1 chr7B.!!$F1 2359
1 TraesCS7B01G075100 chr3D 69660428 69661811 1383 False 2399 2399 97.977 1 1383 1 chr3D.!!$F1 1382
2 TraesCS7B01G075100 chr3D 462839184 462839782 598 False 817 817 91.225 1757 2360 1 chr3D.!!$F4 603
3 TraesCS7B01G075100 chr3D 147469764 147470362 598 False 809 809 91.015 1760 2360 1 chr3D.!!$F3 600
4 TraesCS7B01G075100 chr6A 502339291 502340671 1380 False 2364 2364 97.543 1 1383 1 chr6A.!!$F2 1382
5 TraesCS7B01G075100 chr6A 532870195 532871505 1310 False 2215 2215 97.178 74 1383 1 chr6A.!!$F3 1309
6 TraesCS7B01G075100 chr2B 717929916 717931261 1345 True 2338 2338 98.068 41 1383 1 chr2B.!!$R2 1342
7 TraesCS7B01G075100 chr2B 622655292 622655892 600 True 822 822 91.348 1760 2360 1 chr2B.!!$R1 600
8 TraesCS7B01G075100 chr3A 681099486 681100868 1382 True 2316 2316 96.893 1 1383 1 chr3A.!!$R1 1382
9 TraesCS7B01G075100 chr4A 107230902 107232285 1383 True 2261 2261 96.171 1 1383 1 chr4A.!!$R1 1382
10 TraesCS7B01G075100 chr2A 148651646 148653024 1378 False 2224 2224 95.743 1 1384 1 chr2A.!!$F2 1383
11 TraesCS7B01G075100 chr6B 695056652 695058035 1383 False 2206 2206 95.448 1 1383 1 chr6B.!!$F2 1382
12 TraesCS7B01G075100 chr6B 349469309 349469910 601 False 852 852 92.193 1759 2360 1 chr6B.!!$F1 601
13 TraesCS7B01G075100 chr5B 633276926 633278308 1382 False 2189 2189 95.231 1 1383 1 chr5B.!!$F2 1382
14 TraesCS7B01G075100 chr7D 208651979 208652581 602 True 874 874 92.869 1759 2360 1 chr7D.!!$R1 601
15 TraesCS7B01G075100 chr6D 20125823 20126422 599 False 843 843 92.000 1761 2360 1 chr6D.!!$F1 599
16 TraesCS7B01G075100 chr6D 467999096 467999701 605 True 817 817 91.089 1759 2360 1 chr6D.!!$R1 601
17 TraesCS7B01G075100 chr2D 12910208 12910812 604 True 822 822 91.240 1757 2360 1 chr2D.!!$R1 603
18 TraesCS7B01G075100 chr3B 9861199 9861806 607 False 802 802 90.492 1753 2360 1 chr3B.!!$F1 607

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
680 681 3.068024 GTGCCTTCCAGAACAACAAATCA 59.932 43.478 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2249 2256 0.240945 CGGTGTTTCATCTTGCCCAC 59.759 55.0 0.0 0.0 0.0 4.61 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
29 30 4.098960 TCAGACGTGGGTATATTTGGAGAC 59.901 45.833 0.00 0.00 0.00 3.36
437 438 9.029243 CAAAGATAAAAATATTTATGTGGCGCA 57.971 29.630 10.83 1.92 40.87 6.09
680 681 3.068024 GTGCCTTCCAGAACAACAAATCA 59.932 43.478 0.00 0.00 0.00 2.57
750 751 4.667573 TGGTATTTGTGGTATGAAAGGCA 58.332 39.130 0.00 0.00 0.00 4.75
919 920 3.750639 TTAAATGTTGACGCGGGATTC 57.249 42.857 12.47 0.00 0.00 2.52
1259 1261 4.157840 TCGAGTAGCTCATGAACTAGCAAA 59.842 41.667 6.08 0.00 41.32 3.68
1397 1399 2.981400 AAAAAGGAATGCCACGTACG 57.019 45.000 15.01 15.01 36.29 3.67
1398 1400 2.172851 AAAAGGAATGCCACGTACGA 57.827 45.000 24.41 0.00 36.29 3.43
1399 1401 2.396590 AAAGGAATGCCACGTACGAT 57.603 45.000 24.41 1.09 36.29 3.73
1400 1402 3.530265 AAAGGAATGCCACGTACGATA 57.470 42.857 24.41 5.13 36.29 2.92
1401 1403 3.530265 AAGGAATGCCACGTACGATAA 57.470 42.857 24.41 4.68 36.29 1.75
1402 1404 3.530265 AGGAATGCCACGTACGATAAA 57.470 42.857 24.41 5.08 36.29 1.40
1403 1405 4.067972 AGGAATGCCACGTACGATAAAT 57.932 40.909 24.41 7.33 36.29 1.40
1404 1406 3.807622 AGGAATGCCACGTACGATAAATG 59.192 43.478 24.41 9.15 36.29 2.32
1405 1407 3.805422 GGAATGCCACGTACGATAAATGA 59.195 43.478 24.41 0.00 0.00 2.57
1406 1408 4.451096 GGAATGCCACGTACGATAAATGAT 59.549 41.667 24.41 0.48 0.00 2.45
1407 1409 5.636121 GGAATGCCACGTACGATAAATGATA 59.364 40.000 24.41 2.15 0.00 2.15
1408 1410 6.146510 GGAATGCCACGTACGATAAATGATAA 59.853 38.462 24.41 0.00 0.00 1.75
1409 1411 6.706055 ATGCCACGTACGATAAATGATAAG 57.294 37.500 24.41 0.00 0.00 1.73
1410 1412 4.986034 TGCCACGTACGATAAATGATAAGG 59.014 41.667 24.41 6.72 0.00 2.69
1411 1413 4.986659 GCCACGTACGATAAATGATAAGGT 59.013 41.667 24.41 0.00 0.00 3.50
1412 1414 5.107607 GCCACGTACGATAAATGATAAGGTG 60.108 44.000 24.41 3.97 0.00 4.00
1413 1415 5.404366 CCACGTACGATAAATGATAAGGTGG 59.596 44.000 24.41 9.79 34.75 4.61
1414 1416 6.210796 CACGTACGATAAATGATAAGGTGGA 58.789 40.000 24.41 0.00 0.00 4.02
1415 1417 6.362551 CACGTACGATAAATGATAAGGTGGAG 59.637 42.308 24.41 0.00 0.00 3.86
1416 1418 5.862323 CGTACGATAAATGATAAGGTGGAGG 59.138 44.000 10.44 0.00 0.00 4.30
1417 1419 6.294342 CGTACGATAAATGATAAGGTGGAGGA 60.294 42.308 10.44 0.00 0.00 3.71
1418 1420 6.102897 ACGATAAATGATAAGGTGGAGGAG 57.897 41.667 0.00 0.00 0.00 3.69
1419 1421 5.839063 ACGATAAATGATAAGGTGGAGGAGA 59.161 40.000 0.00 0.00 0.00 3.71
1420 1422 6.015010 ACGATAAATGATAAGGTGGAGGAGAG 60.015 42.308 0.00 0.00 0.00 3.20
1421 1423 6.209589 CGATAAATGATAAGGTGGAGGAGAGA 59.790 42.308 0.00 0.00 0.00 3.10
1422 1424 5.885449 AAATGATAAGGTGGAGGAGAGAG 57.115 43.478 0.00 0.00 0.00 3.20
1423 1425 4.823364 ATGATAAGGTGGAGGAGAGAGA 57.177 45.455 0.00 0.00 0.00 3.10
1424 1426 4.609866 TGATAAGGTGGAGGAGAGAGAA 57.390 45.455 0.00 0.00 0.00 2.87
1425 1427 4.947883 TGATAAGGTGGAGGAGAGAGAAA 58.052 43.478 0.00 0.00 0.00 2.52
1426 1428 5.533112 TGATAAGGTGGAGGAGAGAGAAAT 58.467 41.667 0.00 0.00 0.00 2.17
1427 1429 5.600484 TGATAAGGTGGAGGAGAGAGAAATC 59.400 44.000 0.00 0.00 0.00 2.17
1428 1430 3.774842 AGGTGGAGGAGAGAGAAATCT 57.225 47.619 0.00 0.00 0.00 2.40
1429 1431 4.073425 AGGTGGAGGAGAGAGAAATCTT 57.927 45.455 0.00 0.00 0.00 2.40
1430 1432 4.030216 AGGTGGAGGAGAGAGAAATCTTC 58.970 47.826 0.00 0.00 0.00 2.87
1431 1433 3.772025 GGTGGAGGAGAGAGAAATCTTCA 59.228 47.826 0.00 0.00 0.00 3.02
1432 1434 4.141959 GGTGGAGGAGAGAGAAATCTTCAG 60.142 50.000 0.00 0.00 0.00 3.02
1433 1435 4.709397 GTGGAGGAGAGAGAAATCTTCAGA 59.291 45.833 0.00 0.00 0.00 3.27
1434 1436 5.186797 GTGGAGGAGAGAGAAATCTTCAGAA 59.813 44.000 0.00 0.00 0.00 3.02
1435 1437 5.782331 TGGAGGAGAGAGAAATCTTCAGAAA 59.218 40.000 0.00 0.00 0.00 2.52
1436 1438 6.270927 TGGAGGAGAGAGAAATCTTCAGAAAA 59.729 38.462 0.00 0.00 0.00 2.29
1437 1439 6.818142 GGAGGAGAGAGAAATCTTCAGAAAAG 59.182 42.308 0.00 0.00 0.00 2.27
1438 1440 6.710278 AGGAGAGAGAAATCTTCAGAAAAGG 58.290 40.000 0.00 0.00 0.00 3.11
1439 1441 5.353956 GGAGAGAGAAATCTTCAGAAAAGGC 59.646 44.000 0.00 0.00 0.00 4.35
1440 1442 6.125589 AGAGAGAAATCTTCAGAAAAGGCT 57.874 37.500 0.00 0.00 0.00 4.58
1441 1443 6.541907 AGAGAGAAATCTTCAGAAAAGGCTT 58.458 36.000 0.00 0.00 0.00 4.35
1442 1444 6.430616 AGAGAGAAATCTTCAGAAAAGGCTTG 59.569 38.462 0.00 0.00 0.00 4.01
1443 1445 6.067350 AGAGAAATCTTCAGAAAAGGCTTGT 58.933 36.000 0.00 0.00 0.00 3.16
1444 1446 6.206438 AGAGAAATCTTCAGAAAAGGCTTGTC 59.794 38.462 9.51 9.51 0.00 3.18
1445 1447 6.067350 AGAAATCTTCAGAAAAGGCTTGTCT 58.933 36.000 14.33 14.33 0.00 3.41
1446 1448 6.548993 AGAAATCTTCAGAAAAGGCTTGTCTT 59.451 34.615 17.39 1.11 0.00 3.01
1447 1449 5.956068 ATCTTCAGAAAAGGCTTGTCTTC 57.044 39.130 17.39 9.45 0.00 2.87
1448 1450 5.041191 TCTTCAGAAAAGGCTTGTCTTCT 57.959 39.130 17.39 11.62 0.00 2.85
1449 1451 5.059833 TCTTCAGAAAAGGCTTGTCTTCTC 58.940 41.667 17.39 0.08 0.00 2.87
1450 1452 4.696479 TCAGAAAAGGCTTGTCTTCTCT 57.304 40.909 17.39 2.33 0.00 3.10
1451 1453 5.041191 TCAGAAAAGGCTTGTCTTCTCTT 57.959 39.130 17.39 0.00 0.00 2.85
1452 1454 6.174720 TCAGAAAAGGCTTGTCTTCTCTTA 57.825 37.500 17.39 0.75 0.00 2.10
1453 1455 6.773638 TCAGAAAAGGCTTGTCTTCTCTTAT 58.226 36.000 17.39 0.00 0.00 1.73
1454 1456 7.227156 TCAGAAAAGGCTTGTCTTCTCTTATT 58.773 34.615 17.39 0.00 0.00 1.40
1455 1457 7.721399 TCAGAAAAGGCTTGTCTTCTCTTATTT 59.279 33.333 17.39 0.00 0.00 1.40
1456 1458 9.003658 CAGAAAAGGCTTGTCTTCTCTTATTTA 57.996 33.333 17.39 0.00 0.00 1.40
1457 1459 9.574516 AGAAAAGGCTTGTCTTCTCTTATTTAA 57.425 29.630 14.33 0.00 0.00 1.52
1458 1460 9.833182 GAAAAGGCTTGTCTTCTCTTATTTAAG 57.167 33.333 10.26 0.00 34.65 1.85
1459 1461 9.574516 AAAAGGCTTGTCTTCTCTTATTTAAGA 57.425 29.630 0.00 0.44 39.82 2.10
1497 1499 9.990868 ATAATCTCTTAGGGTTTGTAAAATGGT 57.009 29.630 0.00 0.00 0.00 3.55
1498 1500 8.721133 AATCTCTTAGGGTTTGTAAAATGGTT 57.279 30.769 0.00 0.00 0.00 3.67
1499 1501 7.519032 TCTCTTAGGGTTTGTAAAATGGTTG 57.481 36.000 0.00 0.00 0.00 3.77
1500 1502 7.291566 TCTCTTAGGGTTTGTAAAATGGTTGA 58.708 34.615 0.00 0.00 0.00 3.18
1501 1503 7.947890 TCTCTTAGGGTTTGTAAAATGGTTGAT 59.052 33.333 0.00 0.00 0.00 2.57
1502 1504 9.238368 CTCTTAGGGTTTGTAAAATGGTTGATA 57.762 33.333 0.00 0.00 0.00 2.15
1503 1505 9.589461 TCTTAGGGTTTGTAAAATGGTTGATAA 57.411 29.630 0.00 0.00 0.00 1.75
1504 1506 9.855021 CTTAGGGTTTGTAAAATGGTTGATAAG 57.145 33.333 0.00 0.00 0.00 1.73
1505 1507 9.589461 TTAGGGTTTGTAAAATGGTTGATAAGA 57.411 29.630 0.00 0.00 0.00 2.10
1506 1508 8.664669 AGGGTTTGTAAAATGGTTGATAAGAT 57.335 30.769 0.00 0.00 0.00 2.40
1507 1509 9.762381 AGGGTTTGTAAAATGGTTGATAAGATA 57.238 29.630 0.00 0.00 0.00 1.98
1542 1544 9.719355 TTAAGTCTTGCATGTAATTTAGAGACA 57.281 29.630 11.88 0.00 35.83 3.41
1543 1545 8.621532 AAGTCTTGCATGTAATTTAGAGACAA 57.378 30.769 11.88 0.00 35.83 3.18
1544 1546 8.621532 AGTCTTGCATGTAATTTAGAGACAAA 57.378 30.769 11.88 0.00 35.83 2.83
1545 1547 9.066892 AGTCTTGCATGTAATTTAGAGACAAAA 57.933 29.630 11.88 0.00 35.83 2.44
1546 1548 9.677567 GTCTTGCATGTAATTTAGAGACAAAAA 57.322 29.630 0.00 0.00 34.09 1.94
1568 1570 6.949352 AAAACATGTCTATGATGGGTCATC 57.051 37.500 0.00 1.28 43.87 2.92
1569 1571 5.901413 AACATGTCTATGATGGGTCATCT 57.099 39.130 0.00 0.00 43.87 2.90
1570 1572 5.480642 ACATGTCTATGATGGGTCATCTC 57.519 43.478 9.00 0.00 43.87 2.75
1571 1573 5.153675 ACATGTCTATGATGGGTCATCTCT 58.846 41.667 9.00 0.72 43.87 3.10
1572 1574 5.605908 ACATGTCTATGATGGGTCATCTCTT 59.394 40.000 9.00 0.00 43.87 2.85
1573 1575 6.784473 ACATGTCTATGATGGGTCATCTCTTA 59.216 38.462 9.00 0.00 43.87 2.10
1574 1576 6.907853 TGTCTATGATGGGTCATCTCTTAG 57.092 41.667 9.00 7.64 43.87 2.18
1575 1577 5.244851 TGTCTATGATGGGTCATCTCTTAGC 59.755 44.000 9.00 0.00 43.87 3.09
1576 1578 4.774726 TCTATGATGGGTCATCTCTTAGCC 59.225 45.833 9.00 0.00 43.87 3.93
1577 1579 3.051940 TGATGGGTCATCTCTTAGCCT 57.948 47.619 9.00 0.00 41.06 4.58
1578 1580 3.387962 TGATGGGTCATCTCTTAGCCTT 58.612 45.455 9.00 0.00 41.06 4.35
1579 1581 4.556697 TGATGGGTCATCTCTTAGCCTTA 58.443 43.478 9.00 0.00 41.06 2.69
1580 1582 5.158141 TGATGGGTCATCTCTTAGCCTTAT 58.842 41.667 9.00 0.00 41.06 1.73
1581 1583 5.247110 TGATGGGTCATCTCTTAGCCTTATC 59.753 44.000 9.00 0.00 41.06 1.75
1582 1584 4.820775 TGGGTCATCTCTTAGCCTTATCT 58.179 43.478 0.00 0.00 34.30 1.98
1583 1585 5.219739 TGGGTCATCTCTTAGCCTTATCTT 58.780 41.667 0.00 0.00 34.30 2.40
1584 1586 5.667626 TGGGTCATCTCTTAGCCTTATCTTT 59.332 40.000 0.00 0.00 34.30 2.52
1585 1587 6.844388 TGGGTCATCTCTTAGCCTTATCTTTA 59.156 38.462 0.00 0.00 34.30 1.85
1586 1588 7.514127 TGGGTCATCTCTTAGCCTTATCTTTAT 59.486 37.037 0.00 0.00 34.30 1.40
1587 1589 8.379331 GGGTCATCTCTTAGCCTTATCTTTATT 58.621 37.037 0.00 0.00 0.00 1.40
1593 1595 9.128404 TCTCTTAGCCTTATCTTTATTACGACA 57.872 33.333 0.00 0.00 0.00 4.35
1594 1596 9.915629 CTCTTAGCCTTATCTTTATTACGACAT 57.084 33.333 0.00 0.00 0.00 3.06
1595 1597 9.692749 TCTTAGCCTTATCTTTATTACGACATG 57.307 33.333 0.00 0.00 0.00 3.21
1596 1598 8.827177 TTAGCCTTATCTTTATTACGACATGG 57.173 34.615 0.00 0.00 0.00 3.66
1597 1599 6.827727 AGCCTTATCTTTATTACGACATGGT 58.172 36.000 0.00 0.00 0.00 3.55
1598 1600 6.706270 AGCCTTATCTTTATTACGACATGGTG 59.294 38.462 0.00 0.00 0.00 4.17
1599 1601 6.704493 GCCTTATCTTTATTACGACATGGTGA 59.296 38.462 0.00 0.00 0.00 4.02
1600 1602 7.095607 GCCTTATCTTTATTACGACATGGTGAG 60.096 40.741 0.00 0.00 0.00 3.51
1601 1603 8.141909 CCTTATCTTTATTACGACATGGTGAGA 58.858 37.037 0.00 0.00 0.00 3.27
1602 1604 8.867112 TTATCTTTATTACGACATGGTGAGAC 57.133 34.615 0.00 0.00 0.00 3.36
1603 1605 6.275494 TCTTTATTACGACATGGTGAGACA 57.725 37.500 0.00 0.00 0.00 3.41
1604 1606 6.873997 TCTTTATTACGACATGGTGAGACAT 58.126 36.000 0.00 0.00 0.00 3.06
1605 1607 6.978659 TCTTTATTACGACATGGTGAGACATC 59.021 38.462 0.00 0.00 0.00 3.06
1606 1608 6.465439 TTATTACGACATGGTGAGACATCT 57.535 37.500 0.00 0.00 0.00 2.90
1607 1609 7.576861 TTATTACGACATGGTGAGACATCTA 57.423 36.000 0.00 0.00 0.00 1.98
1608 1610 5.907866 TTACGACATGGTGAGACATCTAA 57.092 39.130 0.00 0.00 0.00 2.10
1609 1611 4.377839 ACGACATGGTGAGACATCTAAG 57.622 45.455 0.00 0.00 0.00 2.18
1610 1612 4.017126 ACGACATGGTGAGACATCTAAGA 58.983 43.478 0.00 0.00 0.00 2.10
1611 1613 4.097135 ACGACATGGTGAGACATCTAAGAG 59.903 45.833 0.00 0.00 0.00 2.85
1612 1614 4.336713 CGACATGGTGAGACATCTAAGAGA 59.663 45.833 0.00 0.00 0.00 3.10
1613 1615 5.009510 CGACATGGTGAGACATCTAAGAGAT 59.990 44.000 0.00 0.00 34.74 2.75
1614 1616 6.403866 ACATGGTGAGACATCTAAGAGATC 57.596 41.667 0.00 0.00 31.32 2.75
1615 1617 5.896106 ACATGGTGAGACATCTAAGAGATCA 59.104 40.000 0.00 0.00 31.32 2.92
1616 1618 6.554228 ACATGGTGAGACATCTAAGAGATCAT 59.446 38.462 0.00 0.00 31.32 2.45
1617 1619 6.647334 TGGTGAGACATCTAAGAGATCATC 57.353 41.667 0.00 0.00 31.32 2.92
1618 1620 6.372104 TGGTGAGACATCTAAGAGATCATCT 58.628 40.000 0.00 0.00 41.27 2.90
1619 1621 6.489700 TGGTGAGACATCTAAGAGATCATCTC 59.510 42.308 6.55 6.55 43.70 2.75
1662 1664 8.831715 AGAAAAGACAAGATTTCTCTCTTCTC 57.168 34.615 0.00 0.00 40.87 2.87
1663 1665 7.877612 AGAAAAGACAAGATTTCTCTCTTCTCC 59.122 37.037 0.00 0.00 40.87 3.71
1664 1666 6.678568 AAGACAAGATTTCTCTCTTCTCCA 57.321 37.500 0.00 0.00 33.18 3.86
1665 1667 6.036577 AGACAAGATTTCTCTCTTCTCCAC 57.963 41.667 0.00 0.00 33.18 4.02
1666 1668 5.046663 AGACAAGATTTCTCTCTTCTCCACC 60.047 44.000 0.00 0.00 33.18 4.61
1667 1669 4.843516 ACAAGATTTCTCTCTTCTCCACCT 59.156 41.667 0.00 0.00 33.18 4.00
1668 1670 5.046663 ACAAGATTTCTCTCTTCTCCACCTC 60.047 44.000 0.00 0.00 33.18 3.85
1669 1671 3.699038 AGATTTCTCTCTTCTCCACCTCG 59.301 47.826 0.00 0.00 0.00 4.63
1670 1672 2.588464 TTCTCTCTTCTCCACCTCGT 57.412 50.000 0.00 0.00 0.00 4.18
1671 1673 2.116827 TCTCTCTTCTCCACCTCGTC 57.883 55.000 0.00 0.00 0.00 4.20
1672 1674 1.351350 TCTCTCTTCTCCACCTCGTCA 59.649 52.381 0.00 0.00 0.00 4.35
1673 1675 2.025793 TCTCTCTTCTCCACCTCGTCAT 60.026 50.000 0.00 0.00 0.00 3.06
1674 1676 2.757868 CTCTCTTCTCCACCTCGTCATT 59.242 50.000 0.00 0.00 0.00 2.57
1675 1677 3.165875 TCTCTTCTCCACCTCGTCATTT 58.834 45.455 0.00 0.00 0.00 2.32
1676 1678 4.341487 TCTCTTCTCCACCTCGTCATTTA 58.659 43.478 0.00 0.00 0.00 1.40
1677 1679 4.956700 TCTCTTCTCCACCTCGTCATTTAT 59.043 41.667 0.00 0.00 0.00 1.40
1678 1680 5.422331 TCTCTTCTCCACCTCGTCATTTATT 59.578 40.000 0.00 0.00 0.00 1.40
1679 1681 5.661458 TCTTCTCCACCTCGTCATTTATTC 58.339 41.667 0.00 0.00 0.00 1.75
1680 1682 5.422331 TCTTCTCCACCTCGTCATTTATTCT 59.578 40.000 0.00 0.00 0.00 2.40
1681 1683 6.605995 TCTTCTCCACCTCGTCATTTATTCTA 59.394 38.462 0.00 0.00 0.00 2.10
1682 1684 6.978674 TCTCCACCTCGTCATTTATTCTAT 57.021 37.500 0.00 0.00 0.00 1.98
1683 1685 8.473358 TTCTCCACCTCGTCATTTATTCTATA 57.527 34.615 0.00 0.00 0.00 1.31
1684 1686 8.651589 TCTCCACCTCGTCATTTATTCTATAT 57.348 34.615 0.00 0.00 0.00 0.86
1685 1687 8.523658 TCTCCACCTCGTCATTTATTCTATATG 58.476 37.037 0.00 0.00 0.00 1.78
1686 1688 7.611770 TCCACCTCGTCATTTATTCTATATGG 58.388 38.462 0.00 0.00 0.00 2.74
1687 1689 6.313905 CCACCTCGTCATTTATTCTATATGGC 59.686 42.308 0.00 0.00 0.00 4.40
1688 1690 6.873605 CACCTCGTCATTTATTCTATATGGCA 59.126 38.462 0.00 0.00 0.00 4.92
1689 1691 7.550551 CACCTCGTCATTTATTCTATATGGCAT 59.449 37.037 4.88 4.88 0.00 4.40
1690 1692 8.103305 ACCTCGTCATTTATTCTATATGGCATT 58.897 33.333 4.78 0.00 0.00 3.56
1691 1693 8.607459 CCTCGTCATTTATTCTATATGGCATTC 58.393 37.037 4.78 0.00 0.00 2.67
1692 1694 8.492673 TCGTCATTTATTCTATATGGCATTCC 57.507 34.615 4.78 0.00 0.00 3.01
1693 1695 8.321353 TCGTCATTTATTCTATATGGCATTCCT 58.679 33.333 4.78 0.00 0.00 3.36
1694 1696 9.599866 CGTCATTTATTCTATATGGCATTCCTA 57.400 33.333 4.78 0.00 0.00 2.94
1704 1706 9.959721 TCTATATGGCATTCCTAAGATAAAACC 57.040 33.333 4.78 0.00 0.00 3.27
1705 1707 9.739276 CTATATGGCATTCCTAAGATAAAACCA 57.261 33.333 4.78 0.00 0.00 3.67
1707 1709 7.919385 ATGGCATTCCTAAGATAAAACCATT 57.081 32.000 0.00 0.00 30.15 3.16
1708 1710 7.111247 TGGCATTCCTAAGATAAAACCATTG 57.889 36.000 0.00 0.00 0.00 2.82
1709 1711 6.667414 TGGCATTCCTAAGATAAAACCATTGT 59.333 34.615 0.00 0.00 0.00 2.71
1710 1712 7.836685 TGGCATTCCTAAGATAAAACCATTGTA 59.163 33.333 0.00 0.00 0.00 2.41
1711 1713 8.691797 GGCATTCCTAAGATAAAACCATTGTAA 58.308 33.333 0.00 0.00 0.00 2.41
1722 1724 9.516314 GATAAAACCATTGTAAATGTCCTTAGC 57.484 33.333 0.00 0.00 0.00 3.09
1723 1725 6.909550 AAACCATTGTAAATGTCCTTAGCA 57.090 33.333 0.00 0.00 0.00 3.49
1724 1726 5.897377 ACCATTGTAAATGTCCTTAGCAC 57.103 39.130 0.00 0.00 0.00 4.40
1725 1727 5.321102 ACCATTGTAAATGTCCTTAGCACA 58.679 37.500 0.00 0.00 0.00 4.57
1726 1728 5.772672 ACCATTGTAAATGTCCTTAGCACAA 59.227 36.000 0.00 0.00 0.00 3.33
1727 1729 6.437162 ACCATTGTAAATGTCCTTAGCACAAT 59.563 34.615 0.00 0.00 35.99 2.71
1728 1730 7.613801 ACCATTGTAAATGTCCTTAGCACAATA 59.386 33.333 0.00 0.00 34.36 1.90
1729 1731 8.632679 CCATTGTAAATGTCCTTAGCACAATAT 58.367 33.333 0.00 0.00 34.36 1.28
1730 1732 9.454585 CATTGTAAATGTCCTTAGCACAATATG 57.545 33.333 0.00 0.00 34.36 1.78
1731 1733 8.574251 TTGTAAATGTCCTTAGCACAATATGT 57.426 30.769 0.00 0.00 0.00 2.29
1732 1734 8.208718 TGTAAATGTCCTTAGCACAATATGTC 57.791 34.615 0.00 0.00 0.00 3.06
1733 1735 8.046708 TGTAAATGTCCTTAGCACAATATGTCT 58.953 33.333 0.00 0.00 0.00 3.41
1734 1736 7.559590 AAATGTCCTTAGCACAATATGTCTC 57.440 36.000 0.00 0.00 0.00 3.36
1735 1737 4.682787 TGTCCTTAGCACAATATGTCTCG 58.317 43.478 0.00 0.00 0.00 4.04
1736 1738 3.491267 GTCCTTAGCACAATATGTCTCGC 59.509 47.826 0.00 0.00 0.00 5.03
1737 1739 2.802816 CCTTAGCACAATATGTCTCGCC 59.197 50.000 0.00 0.00 0.00 5.54
1738 1740 3.457234 CTTAGCACAATATGTCTCGCCA 58.543 45.455 0.00 0.00 0.00 5.69
1739 1741 2.627515 AGCACAATATGTCTCGCCAT 57.372 45.000 0.00 0.00 0.00 4.40
1740 1742 3.751479 AGCACAATATGTCTCGCCATA 57.249 42.857 0.00 0.00 0.00 2.74
1741 1743 4.277515 AGCACAATATGTCTCGCCATAT 57.722 40.909 0.00 0.00 39.20 1.78
1742 1744 4.645535 AGCACAATATGTCTCGCCATATT 58.354 39.130 8.22 8.22 44.78 1.28
1743 1745 5.065914 AGCACAATATGTCTCGCCATATTT 58.934 37.500 10.29 3.54 42.54 1.40
1744 1746 5.532406 AGCACAATATGTCTCGCCATATTTT 59.468 36.000 10.29 4.57 42.54 1.82
1745 1747 6.039717 AGCACAATATGTCTCGCCATATTTTT 59.960 34.615 10.29 2.13 42.54 1.94
1746 1748 7.228507 AGCACAATATGTCTCGCCATATTTTTA 59.771 33.333 10.29 0.00 42.54 1.52
1747 1749 7.535258 GCACAATATGTCTCGCCATATTTTTAG 59.465 37.037 10.29 4.94 42.54 1.85
1748 1750 8.017373 CACAATATGTCTCGCCATATTTTTAGG 58.983 37.037 10.29 0.00 42.54 2.69
1749 1751 7.936847 ACAATATGTCTCGCCATATTTTTAGGA 59.063 33.333 10.29 0.00 42.54 2.94
1750 1752 8.783093 CAATATGTCTCGCCATATTTTTAGGAA 58.217 33.333 10.29 0.00 42.54 3.36
1751 1753 9.520515 AATATGTCTCGCCATATTTTTAGGAAT 57.479 29.630 8.22 0.00 42.54 3.01
1754 1756 8.547967 TGTCTCGCCATATTTTTAGGAATATC 57.452 34.615 0.00 0.00 31.52 1.63
1755 1757 8.375506 TGTCTCGCCATATTTTTAGGAATATCT 58.624 33.333 0.00 0.00 31.52 1.98
1791 1793 4.677151 AGGAAGACCCCCGGCCTT 62.677 66.667 0.00 0.00 36.73 4.35
1858 1860 6.147164 CACACGACCTTACAAAGTCATACAAT 59.853 38.462 0.00 0.00 0.00 2.71
2063 2070 0.464036 CAGGACGCTTGCTGGGTATA 59.536 55.000 3.59 0.00 42.14 1.47
2100 2107 2.358957 CTGCGACCAATCCATCTTCAA 58.641 47.619 0.00 0.00 0.00 2.69
2127 2134 3.784701 ACTACTGCATCTACCTTGTCG 57.215 47.619 0.00 0.00 0.00 4.35
2156 2163 2.202743 CGCCGACGTCACCATGAT 60.203 61.111 17.16 0.00 33.53 2.45
2166 2173 0.986527 TCACCATGATGCCAGACAGT 59.013 50.000 0.00 0.00 0.00 3.55
2195 2202 1.938657 CTGCGTGAGTCCATCTCCGT 61.939 60.000 0.00 0.00 42.12 4.69
2249 2256 1.940294 GCCGAGATCTGCCATCATCAG 60.940 57.143 0.00 0.00 0.00 2.90
2283 2290 2.344203 ACCGCTCCTCCTCTTGTCG 61.344 63.158 0.00 0.00 0.00 4.35
2294 2301 0.250295 CTCTTGTCGCCTCCAACCAA 60.250 55.000 0.00 0.00 0.00 3.67
2310 2317 2.175202 ACCAACACTTGCTCCAAAACA 58.825 42.857 0.00 0.00 0.00 2.83
2341 2348 0.826672 AGGGAGAACGACACCGAAGT 60.827 55.000 0.00 0.00 39.50 3.01
2354 2361 1.275291 ACCGAAGTCACCATCATCGTT 59.725 47.619 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 5.183713 TGCTAATTTTCTCACCATCACCAAG 59.816 40.000 0.00 0.00 0.00 3.61
122 123 8.746052 TCAATGAGGTCAGAAACTTTAGAAAA 57.254 30.769 0.00 0.00 0.00 2.29
311 312 4.637091 CCCAAATTGAAATTCCCATTCTGC 59.363 41.667 0.00 0.00 0.00 4.26
437 438 0.461961 GGAATAGCACTCTGGAGCGT 59.538 55.000 0.00 0.00 34.32 5.07
487 488 4.866486 GCTGGGCAACTCAGATTTATTTTG 59.134 41.667 0.00 0.00 37.13 2.44
572 573 1.198713 AGACCGAGCATCTTCCACAT 58.801 50.000 0.00 0.00 0.00 3.21
680 681 1.040339 TTCGGCAAGCCCAACACTTT 61.040 50.000 5.34 0.00 0.00 2.66
750 751 7.257722 AGTTTCTTCGTCATGTGTCAATTTTT 58.742 30.769 0.00 0.00 0.00 1.94
857 858 4.305989 GTTTCAACCAAGCATCTGAACA 57.694 40.909 0.00 0.00 0.00 3.18
919 920 1.539341 CTGCGAGTGTGTCACTATCG 58.461 55.000 19.64 19.64 45.44 2.92
1259 1261 4.771054 TCGGAGAAGAAAACCTAGCTAACT 59.229 41.667 0.00 0.00 0.00 2.24
1384 1386 5.591643 ATCATTTATCGTACGTGGCATTC 57.408 39.130 16.05 0.00 0.00 2.67
1385 1387 6.147164 CCTTATCATTTATCGTACGTGGCATT 59.853 38.462 16.05 0.00 0.00 3.56
1386 1388 5.637810 CCTTATCATTTATCGTACGTGGCAT 59.362 40.000 16.05 3.69 0.00 4.40
1387 1389 4.986034 CCTTATCATTTATCGTACGTGGCA 59.014 41.667 16.05 0.00 0.00 4.92
1388 1390 4.986659 ACCTTATCATTTATCGTACGTGGC 59.013 41.667 16.05 0.00 0.00 5.01
1389 1391 5.404366 CCACCTTATCATTTATCGTACGTGG 59.596 44.000 16.05 6.28 0.00 4.94
1390 1392 6.210796 TCCACCTTATCATTTATCGTACGTG 58.789 40.000 16.05 5.79 0.00 4.49
1391 1393 6.395426 TCCACCTTATCATTTATCGTACGT 57.605 37.500 16.05 5.39 0.00 3.57
1392 1394 5.862323 CCTCCACCTTATCATTTATCGTACG 59.138 44.000 9.53 9.53 0.00 3.67
1393 1395 6.989659 TCCTCCACCTTATCATTTATCGTAC 58.010 40.000 0.00 0.00 0.00 3.67
1394 1396 7.008332 TCTCCTCCACCTTATCATTTATCGTA 58.992 38.462 0.00 0.00 0.00 3.43
1395 1397 5.839063 TCTCCTCCACCTTATCATTTATCGT 59.161 40.000 0.00 0.00 0.00 3.73
1396 1398 6.209589 TCTCTCCTCCACCTTATCATTTATCG 59.790 42.308 0.00 0.00 0.00 2.92
1397 1399 7.453126 TCTCTCTCCTCCACCTTATCATTTATC 59.547 40.741 0.00 0.00 0.00 1.75
1398 1400 7.309091 TCTCTCTCCTCCACCTTATCATTTAT 58.691 38.462 0.00 0.00 0.00 1.40
1399 1401 6.683537 TCTCTCTCCTCCACCTTATCATTTA 58.316 40.000 0.00 0.00 0.00 1.40
1400 1402 5.533112 TCTCTCTCCTCCACCTTATCATTT 58.467 41.667 0.00 0.00 0.00 2.32
1401 1403 5.149584 TCTCTCTCCTCCACCTTATCATT 57.850 43.478 0.00 0.00 0.00 2.57
1402 1404 4.823364 TCTCTCTCCTCCACCTTATCAT 57.177 45.455 0.00 0.00 0.00 2.45
1403 1405 4.609866 TTCTCTCTCCTCCACCTTATCA 57.390 45.455 0.00 0.00 0.00 2.15
1404 1406 5.838521 AGATTTCTCTCTCCTCCACCTTATC 59.161 44.000 0.00 0.00 0.00 1.75
1405 1407 5.787327 AGATTTCTCTCTCCTCCACCTTAT 58.213 41.667 0.00 0.00 0.00 1.73
1406 1408 5.213868 AGATTTCTCTCTCCTCCACCTTA 57.786 43.478 0.00 0.00 0.00 2.69
1407 1409 4.073425 AGATTTCTCTCTCCTCCACCTT 57.927 45.455 0.00 0.00 0.00 3.50
1408 1410 3.774842 AGATTTCTCTCTCCTCCACCT 57.225 47.619 0.00 0.00 0.00 4.00
1409 1411 3.772025 TGAAGATTTCTCTCTCCTCCACC 59.228 47.826 0.00 0.00 0.00 4.61
1410 1412 4.709397 TCTGAAGATTTCTCTCTCCTCCAC 59.291 45.833 0.00 0.00 0.00 4.02
1411 1413 4.940483 TCTGAAGATTTCTCTCTCCTCCA 58.060 43.478 0.00 0.00 0.00 3.86
1412 1414 5.930837 TTCTGAAGATTTCTCTCTCCTCC 57.069 43.478 0.00 0.00 0.00 4.30
1413 1415 6.818142 CCTTTTCTGAAGATTTCTCTCTCCTC 59.182 42.308 0.00 0.00 0.00 3.71
1414 1416 6.710278 CCTTTTCTGAAGATTTCTCTCTCCT 58.290 40.000 0.00 0.00 0.00 3.69
1415 1417 5.353956 GCCTTTTCTGAAGATTTCTCTCTCC 59.646 44.000 0.00 0.00 0.00 3.71
1416 1418 6.172630 AGCCTTTTCTGAAGATTTCTCTCTC 58.827 40.000 0.00 0.00 0.00 3.20
1417 1419 6.125589 AGCCTTTTCTGAAGATTTCTCTCT 57.874 37.500 0.00 0.00 0.00 3.10
1418 1420 6.206438 ACAAGCCTTTTCTGAAGATTTCTCTC 59.794 38.462 0.00 0.00 0.00 3.20
1419 1421 6.067350 ACAAGCCTTTTCTGAAGATTTCTCT 58.933 36.000 0.00 0.00 0.00 3.10
1420 1422 6.206438 AGACAAGCCTTTTCTGAAGATTTCTC 59.794 38.462 0.00 0.00 0.00 2.87
1421 1423 6.067350 AGACAAGCCTTTTCTGAAGATTTCT 58.933 36.000 0.00 0.00 0.00 2.52
1422 1424 6.324561 AGACAAGCCTTTTCTGAAGATTTC 57.675 37.500 0.00 0.00 0.00 2.17
1423 1425 6.548993 AGAAGACAAGCCTTTTCTGAAGATTT 59.451 34.615 0.00 0.00 0.00 2.17
1424 1426 6.067350 AGAAGACAAGCCTTTTCTGAAGATT 58.933 36.000 0.00 0.00 0.00 2.40
1425 1427 5.629125 AGAAGACAAGCCTTTTCTGAAGAT 58.371 37.500 0.00 0.00 0.00 2.40
1426 1428 5.041191 AGAAGACAAGCCTTTTCTGAAGA 57.959 39.130 0.00 0.00 0.00 2.87
1427 1429 5.062528 AGAGAAGACAAGCCTTTTCTGAAG 58.937 41.667 0.00 0.00 36.59 3.02
1428 1430 5.041191 AGAGAAGACAAGCCTTTTCTGAA 57.959 39.130 0.00 0.00 36.59 3.02
1429 1431 4.696479 AGAGAAGACAAGCCTTTTCTGA 57.304 40.909 0.00 0.00 36.59 3.27
1430 1432 7.446001 AATAAGAGAAGACAAGCCTTTTCTG 57.554 36.000 0.00 0.00 37.58 3.02
1431 1433 9.574516 TTAAATAAGAGAAGACAAGCCTTTTCT 57.425 29.630 0.00 0.00 38.69 2.52
1432 1434 9.833182 CTTAAATAAGAGAAGACAAGCCTTTTC 57.167 33.333 0.00 0.00 35.33 2.29
1433 1435 9.574516 TCTTAAATAAGAGAAGACAAGCCTTTT 57.425 29.630 0.00 0.00 37.40 2.27
1471 1473 9.990868 ACCATTTTACAAACCCTAAGAGATTAT 57.009 29.630 0.00 0.00 0.00 1.28
1472 1474 9.816787 AACCATTTTACAAACCCTAAGAGATTA 57.183 29.630 0.00 0.00 0.00 1.75
1473 1475 8.585018 CAACCATTTTACAAACCCTAAGAGATT 58.415 33.333 0.00 0.00 0.00 2.40
1474 1476 7.947890 TCAACCATTTTACAAACCCTAAGAGAT 59.052 33.333 0.00 0.00 0.00 2.75
1475 1477 7.291566 TCAACCATTTTACAAACCCTAAGAGA 58.708 34.615 0.00 0.00 0.00 3.10
1476 1478 7.519032 TCAACCATTTTACAAACCCTAAGAG 57.481 36.000 0.00 0.00 0.00 2.85
1477 1479 9.589461 TTATCAACCATTTTACAAACCCTAAGA 57.411 29.630 0.00 0.00 0.00 2.10
1478 1480 9.855021 CTTATCAACCATTTTACAAACCCTAAG 57.145 33.333 0.00 0.00 0.00 2.18
1479 1481 9.589461 TCTTATCAACCATTTTACAAACCCTAA 57.411 29.630 0.00 0.00 0.00 2.69
1480 1482 9.762381 ATCTTATCAACCATTTTACAAACCCTA 57.238 29.630 0.00 0.00 0.00 3.53
1481 1483 8.664669 ATCTTATCAACCATTTTACAAACCCT 57.335 30.769 0.00 0.00 0.00 4.34
1516 1518 9.719355 TGTCTCTAAATTACATGCAAGACTTAA 57.281 29.630 0.00 0.00 34.44 1.85
1517 1519 9.719355 TTGTCTCTAAATTACATGCAAGACTTA 57.281 29.630 0.00 0.00 34.44 2.24
1518 1520 8.621532 TTGTCTCTAAATTACATGCAAGACTT 57.378 30.769 0.00 0.00 34.44 3.01
1519 1521 8.621532 TTTGTCTCTAAATTACATGCAAGACT 57.378 30.769 0.00 0.00 34.44 3.24
1520 1522 9.677567 TTTTTGTCTCTAAATTACATGCAAGAC 57.322 29.630 0.00 0.00 34.04 3.01
1544 1546 7.121382 AGATGACCCATCATAGACATGTTTTT 58.879 34.615 0.00 0.00 46.01 1.94
1545 1547 6.666678 AGATGACCCATCATAGACATGTTTT 58.333 36.000 0.00 0.00 46.01 2.43
1546 1548 6.100859 AGAGATGACCCATCATAGACATGTTT 59.899 38.462 0.00 0.00 46.01 2.83
1547 1549 5.605908 AGAGATGACCCATCATAGACATGTT 59.394 40.000 0.00 0.00 46.01 2.71
1548 1550 5.153675 AGAGATGACCCATCATAGACATGT 58.846 41.667 0.00 0.00 46.01 3.21
1549 1551 5.741962 AGAGATGACCCATCATAGACATG 57.258 43.478 9.30 0.00 46.01 3.21
1550 1552 6.070881 GCTAAGAGATGACCCATCATAGACAT 60.071 42.308 9.30 0.00 46.01 3.06
1551 1553 5.244851 GCTAAGAGATGACCCATCATAGACA 59.755 44.000 9.30 0.00 46.01 3.41
1552 1554 5.337169 GGCTAAGAGATGACCCATCATAGAC 60.337 48.000 9.30 6.99 46.01 2.59
1553 1555 4.774726 GGCTAAGAGATGACCCATCATAGA 59.225 45.833 9.30 0.00 46.01 1.98
1554 1556 4.776837 AGGCTAAGAGATGACCCATCATAG 59.223 45.833 9.30 8.92 46.01 2.23
1555 1557 4.756564 AGGCTAAGAGATGACCCATCATA 58.243 43.478 9.30 0.23 46.01 2.15
1557 1559 3.051940 AGGCTAAGAGATGACCCATCA 57.948 47.619 9.30 0.00 42.72 3.07
1558 1560 5.483583 AGATAAGGCTAAGAGATGACCCATC 59.516 44.000 0.00 0.00 40.80 3.51
1559 1561 5.410602 AGATAAGGCTAAGAGATGACCCAT 58.589 41.667 0.00 0.00 0.00 4.00
1560 1562 4.820775 AGATAAGGCTAAGAGATGACCCA 58.179 43.478 0.00 0.00 0.00 4.51
1561 1563 5.816955 AAGATAAGGCTAAGAGATGACCC 57.183 43.478 0.00 0.00 0.00 4.46
1567 1569 9.128404 TGTCGTAATAAAGATAAGGCTAAGAGA 57.872 33.333 0.00 0.00 0.00 3.10
1568 1570 9.915629 ATGTCGTAATAAAGATAAGGCTAAGAG 57.084 33.333 0.00 0.00 0.00 2.85
1569 1571 9.692749 CATGTCGTAATAAAGATAAGGCTAAGA 57.307 33.333 0.00 0.00 0.00 2.10
1570 1572 8.926710 CCATGTCGTAATAAAGATAAGGCTAAG 58.073 37.037 0.00 0.00 0.00 2.18
1571 1573 8.426489 ACCATGTCGTAATAAAGATAAGGCTAA 58.574 33.333 0.00 0.00 0.00 3.09
1572 1574 7.870954 CACCATGTCGTAATAAAGATAAGGCTA 59.129 37.037 0.00 0.00 0.00 3.93
1573 1575 6.706270 CACCATGTCGTAATAAAGATAAGGCT 59.294 38.462 0.00 0.00 0.00 4.58
1574 1576 6.704493 TCACCATGTCGTAATAAAGATAAGGC 59.296 38.462 0.00 0.00 0.00 4.35
1575 1577 8.141909 TCTCACCATGTCGTAATAAAGATAAGG 58.858 37.037 0.00 0.00 0.00 2.69
1576 1578 8.969267 GTCTCACCATGTCGTAATAAAGATAAG 58.031 37.037 0.00 0.00 0.00 1.73
1577 1579 8.471609 TGTCTCACCATGTCGTAATAAAGATAA 58.528 33.333 0.00 0.00 0.00 1.75
1578 1580 8.002984 TGTCTCACCATGTCGTAATAAAGATA 57.997 34.615 0.00 0.00 0.00 1.98
1579 1581 6.873997 TGTCTCACCATGTCGTAATAAAGAT 58.126 36.000 0.00 0.00 0.00 2.40
1580 1582 6.275494 TGTCTCACCATGTCGTAATAAAGA 57.725 37.500 0.00 0.00 0.00 2.52
1581 1583 6.980978 AGATGTCTCACCATGTCGTAATAAAG 59.019 38.462 0.00 0.00 0.00 1.85
1582 1584 6.873997 AGATGTCTCACCATGTCGTAATAAA 58.126 36.000 0.00 0.00 0.00 1.40
1583 1585 6.465439 AGATGTCTCACCATGTCGTAATAA 57.535 37.500 0.00 0.00 0.00 1.40
1584 1586 7.501225 TCTTAGATGTCTCACCATGTCGTAATA 59.499 37.037 0.00 0.00 0.00 0.98
1585 1587 6.321435 TCTTAGATGTCTCACCATGTCGTAAT 59.679 38.462 0.00 0.00 0.00 1.89
1586 1588 5.650703 TCTTAGATGTCTCACCATGTCGTAA 59.349 40.000 0.00 0.00 0.00 3.18
1587 1589 5.190677 TCTTAGATGTCTCACCATGTCGTA 58.809 41.667 0.00 0.00 0.00 3.43
1588 1590 4.017126 TCTTAGATGTCTCACCATGTCGT 58.983 43.478 0.00 0.00 0.00 4.34
1589 1591 4.336713 TCTCTTAGATGTCTCACCATGTCG 59.663 45.833 0.00 0.00 0.00 4.35
1590 1592 5.843673 TCTCTTAGATGTCTCACCATGTC 57.156 43.478 0.00 0.00 0.00 3.06
1591 1593 5.896106 TGATCTCTTAGATGTCTCACCATGT 59.104 40.000 0.00 0.00 34.53 3.21
1592 1594 6.402456 TGATCTCTTAGATGTCTCACCATG 57.598 41.667 0.00 0.00 34.53 3.66
1593 1595 7.011994 AGATGATCTCTTAGATGTCTCACCAT 58.988 38.462 0.00 0.00 34.53 3.55
1594 1596 6.372104 AGATGATCTCTTAGATGTCTCACCA 58.628 40.000 0.00 0.00 34.53 4.17
1595 1597 6.899393 AGATGATCTCTTAGATGTCTCACC 57.101 41.667 0.00 0.00 34.53 4.02
1638 1640 7.659390 TGGAGAAGAGAGAAATCTTGTCTTTTC 59.341 37.037 11.80 13.29 44.75 2.29
1639 1641 7.443879 GTGGAGAAGAGAGAAATCTTGTCTTTT 59.556 37.037 11.80 5.39 44.75 2.27
1640 1642 6.934083 GTGGAGAAGAGAGAAATCTTGTCTTT 59.066 38.462 11.80 0.00 44.75 2.52
1641 1643 6.463360 GTGGAGAAGAGAGAAATCTTGTCTT 58.537 40.000 11.80 8.10 44.75 3.01
1642 1644 5.046663 GGTGGAGAAGAGAGAAATCTTGTCT 60.047 44.000 11.80 1.92 44.75 3.41
1643 1645 5.046663 AGGTGGAGAAGAGAGAAATCTTGTC 60.047 44.000 5.34 5.34 44.68 3.18
1644 1646 4.843516 AGGTGGAGAAGAGAGAAATCTTGT 59.156 41.667 0.00 0.00 39.63 3.16
1645 1647 5.418676 GAGGTGGAGAAGAGAGAAATCTTG 58.581 45.833 0.00 0.00 39.63 3.02
1646 1648 4.159506 CGAGGTGGAGAAGAGAGAAATCTT 59.840 45.833 0.00 0.00 42.23 2.40
1647 1649 3.699038 CGAGGTGGAGAAGAGAGAAATCT 59.301 47.826 0.00 0.00 0.00 2.40
1648 1650 3.445805 ACGAGGTGGAGAAGAGAGAAATC 59.554 47.826 0.00 0.00 0.00 2.17
1649 1651 3.436243 ACGAGGTGGAGAAGAGAGAAAT 58.564 45.455 0.00 0.00 0.00 2.17
1650 1652 2.820787 GACGAGGTGGAGAAGAGAGAAA 59.179 50.000 0.00 0.00 0.00 2.52
1651 1653 2.224793 TGACGAGGTGGAGAAGAGAGAA 60.225 50.000 0.00 0.00 0.00 2.87
1652 1654 1.351350 TGACGAGGTGGAGAAGAGAGA 59.649 52.381 0.00 0.00 0.00 3.10
1653 1655 1.827681 TGACGAGGTGGAGAAGAGAG 58.172 55.000 0.00 0.00 0.00 3.20
1654 1656 2.516227 ATGACGAGGTGGAGAAGAGA 57.484 50.000 0.00 0.00 0.00 3.10
1655 1657 3.601443 AAATGACGAGGTGGAGAAGAG 57.399 47.619 0.00 0.00 0.00 2.85
1656 1658 5.422331 AGAATAAATGACGAGGTGGAGAAGA 59.578 40.000 0.00 0.00 0.00 2.87
1657 1659 5.665459 AGAATAAATGACGAGGTGGAGAAG 58.335 41.667 0.00 0.00 0.00 2.85
1658 1660 5.677319 AGAATAAATGACGAGGTGGAGAA 57.323 39.130 0.00 0.00 0.00 2.87
1659 1661 6.978674 ATAGAATAAATGACGAGGTGGAGA 57.021 37.500 0.00 0.00 0.00 3.71
1660 1662 7.761704 CCATATAGAATAAATGACGAGGTGGAG 59.238 40.741 0.00 0.00 0.00 3.86
1661 1663 7.611770 CCATATAGAATAAATGACGAGGTGGA 58.388 38.462 0.00 0.00 0.00 4.02
1662 1664 6.313905 GCCATATAGAATAAATGACGAGGTGG 59.686 42.308 0.00 0.00 0.00 4.61
1663 1665 6.873605 TGCCATATAGAATAAATGACGAGGTG 59.126 38.462 0.00 0.00 0.00 4.00
1664 1666 7.004555 TGCCATATAGAATAAATGACGAGGT 57.995 36.000 0.00 0.00 0.00 3.85
1665 1667 8.498054 AATGCCATATAGAATAAATGACGAGG 57.502 34.615 0.00 0.00 0.00 4.63
1666 1668 8.607459 GGAATGCCATATAGAATAAATGACGAG 58.393 37.037 0.00 0.00 0.00 4.18
1667 1669 8.321353 AGGAATGCCATATAGAATAAATGACGA 58.679 33.333 0.00 0.00 36.29 4.20
1668 1670 8.498054 AGGAATGCCATATAGAATAAATGACG 57.502 34.615 0.00 0.00 36.29 4.35
1678 1680 9.959721 GGTTTTATCTTAGGAATGCCATATAGA 57.040 33.333 0.00 0.00 36.29 1.98
1679 1681 9.739276 TGGTTTTATCTTAGGAATGCCATATAG 57.261 33.333 0.00 0.00 36.29 1.31
1681 1683 9.605951 AATGGTTTTATCTTAGGAATGCCATAT 57.394 29.630 0.00 0.00 36.29 1.78
1682 1684 8.859090 CAATGGTTTTATCTTAGGAATGCCATA 58.141 33.333 0.00 0.00 36.29 2.74
1683 1685 7.345392 ACAATGGTTTTATCTTAGGAATGCCAT 59.655 33.333 0.00 0.00 36.29 4.40
1684 1686 6.667414 ACAATGGTTTTATCTTAGGAATGCCA 59.333 34.615 0.00 0.00 36.29 4.92
1685 1687 7.112452 ACAATGGTTTTATCTTAGGAATGCC 57.888 36.000 0.00 0.00 0.00 4.40
1696 1698 9.516314 GCTAAGGACATTTACAATGGTTTTATC 57.484 33.333 1.72 0.00 0.00 1.75
1697 1699 9.030452 TGCTAAGGACATTTACAATGGTTTTAT 57.970 29.630 1.72 0.00 0.00 1.40
1698 1700 8.301002 GTGCTAAGGACATTTACAATGGTTTTA 58.699 33.333 1.72 0.00 0.00 1.52
1699 1701 7.151976 GTGCTAAGGACATTTACAATGGTTTT 58.848 34.615 1.72 0.00 0.00 2.43
1700 1702 6.266558 TGTGCTAAGGACATTTACAATGGTTT 59.733 34.615 1.72 0.00 0.00 3.27
1701 1703 5.772672 TGTGCTAAGGACATTTACAATGGTT 59.227 36.000 1.72 0.00 0.00 3.67
1702 1704 5.321102 TGTGCTAAGGACATTTACAATGGT 58.679 37.500 1.72 0.00 0.00 3.55
1703 1705 5.895636 TGTGCTAAGGACATTTACAATGG 57.104 39.130 1.72 0.00 0.00 3.16
1704 1706 9.454585 CATATTGTGCTAAGGACATTTACAATG 57.545 33.333 14.55 0.00 37.69 2.82
1705 1707 9.189156 ACATATTGTGCTAAGGACATTTACAAT 57.811 29.630 0.00 0.00 39.65 2.71
1706 1708 8.574251 ACATATTGTGCTAAGGACATTTACAA 57.426 30.769 0.00 0.00 0.00 2.41
1707 1709 8.046708 AGACATATTGTGCTAAGGACATTTACA 58.953 33.333 0.00 0.00 0.00 2.41
1708 1710 8.438676 AGACATATTGTGCTAAGGACATTTAC 57.561 34.615 0.00 0.00 0.00 2.01
1709 1711 7.438160 CGAGACATATTGTGCTAAGGACATTTA 59.562 37.037 0.00 0.00 0.00 1.40
1710 1712 6.258727 CGAGACATATTGTGCTAAGGACATTT 59.741 38.462 0.00 0.00 0.00 2.32
1711 1713 5.755375 CGAGACATATTGTGCTAAGGACATT 59.245 40.000 0.00 0.00 0.00 2.71
1712 1714 5.292765 CGAGACATATTGTGCTAAGGACAT 58.707 41.667 0.00 0.00 0.00 3.06
1713 1715 4.682787 CGAGACATATTGTGCTAAGGACA 58.317 43.478 0.00 0.00 0.00 4.02
1714 1716 3.491267 GCGAGACATATTGTGCTAAGGAC 59.509 47.826 0.00 0.00 0.00 3.85
1715 1717 3.492656 GGCGAGACATATTGTGCTAAGGA 60.493 47.826 0.00 0.00 0.00 3.36
1716 1718 2.802816 GGCGAGACATATTGTGCTAAGG 59.197 50.000 0.00 0.00 0.00 2.69
1717 1719 3.457234 TGGCGAGACATATTGTGCTAAG 58.543 45.455 0.00 0.00 0.00 2.18
1718 1720 3.535280 TGGCGAGACATATTGTGCTAA 57.465 42.857 0.00 0.00 0.00 3.09
1719 1721 3.751479 ATGGCGAGACATATTGTGCTA 57.249 42.857 0.00 0.00 0.00 3.49
1720 1722 2.627515 ATGGCGAGACATATTGTGCT 57.372 45.000 0.00 0.00 0.00 4.40
1728 1730 9.167311 GATATTCCTAAAAATATGGCGAGACAT 57.833 33.333 0.00 0.00 33.10 3.06
1729 1731 8.375506 AGATATTCCTAAAAATATGGCGAGACA 58.624 33.333 0.00 0.00 33.10 3.41
1730 1732 8.779354 AGATATTCCTAAAAATATGGCGAGAC 57.221 34.615 0.00 0.00 33.10 3.36
1732 1734 9.877178 ACTAGATATTCCTAAAAATATGGCGAG 57.123 33.333 0.00 0.00 33.10 5.03
1831 1833 4.652421 TGACTTTGTAAGGTCGTGTGTA 57.348 40.909 3.01 0.00 35.45 2.90
1837 1839 9.577110 TTACTATTGTATGACTTTGTAAGGTCG 57.423 33.333 3.01 0.00 35.45 4.79
1867 1869 3.128349 TGTTGCTTAGACGGTGACTTTC 58.872 45.455 0.00 0.00 0.00 2.62
1872 1874 2.299013 ACAGATGTTGCTTAGACGGTGA 59.701 45.455 0.00 0.00 0.00 4.02
2052 2059 1.153046 GCGGCCTTATACCCAGCAA 60.153 57.895 0.00 0.00 0.00 3.91
2084 2091 5.712152 ACAACTTTGAAGATGGATTGGTC 57.288 39.130 6.06 0.00 33.60 4.02
2100 2107 6.014499 ACAAGGTAGATGCAGTAGTACAACTT 60.014 38.462 2.52 0.00 0.00 2.66
2147 2154 0.986527 ACTGTCTGGCATCATGGTGA 59.013 50.000 11.02 0.00 0.00 4.02
2156 2163 1.758440 GAGGGTGACACTGTCTGGCA 61.758 60.000 10.54 0.00 34.41 4.92
2249 2256 0.240945 CGGTGTTTCATCTTGCCCAC 59.759 55.000 0.00 0.00 0.00 4.61
2283 2290 1.109323 AGCAAGTGTTGGTTGGAGGC 61.109 55.000 0.00 0.00 38.40 4.70
2294 2301 2.483538 GGCATTGTTTTGGAGCAAGTGT 60.484 45.455 0.00 0.00 29.23 3.55


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

AutoCloner maintained by Alex Coulton.