Multiple sequence alignment - TraesCS2B01G534100

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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 TraesCS2B01G534100 chr2B 100.000 2594 0 0 1 2594 730525798 730528391 0.000000e+00 4791.0
1 TraesCS2B01G534100 chr2B 82.888 187 24 6 2386 2567 133160403 133160586 7.430000e-36 161.0
2 TraesCS2B01G534100 chr3A 87.422 1916 166 34 1 1885 688613403 688611532 0.000000e+00 2134.0
3 TraesCS2B01G534100 chr3A 89.653 1324 93 9 52 1331 70485318 70483995 0.000000e+00 1646.0
4 TraesCS2B01G534100 chr3A 91.992 512 36 2 849 1355 264036417 264036928 0.000000e+00 713.0
5 TraesCS2B01G534100 chr3A 81.853 259 35 8 1389 1643 70483984 70483734 9.410000e-50 207.0
6 TraesCS2B01G534100 chr4A 86.227 1924 172 31 1 1885 44781622 44783491 0.000000e+00 1999.0
7 TraesCS2B01G534100 chr4A 90.711 1378 86 23 1 1355 44650148 44651506 0.000000e+00 1797.0
8 TraesCS2B01G534100 chr4A 89.383 989 63 23 1 966 44646319 44645350 0.000000e+00 1206.0
9 TraesCS2B01G534100 chr4A 91.456 316 22 4 2251 2562 691801733 691802047 1.840000e-116 429.0
10 TraesCS2B01G534100 chr4A 85.090 389 44 8 1831 2209 691801350 691801734 4.050000e-103 385.0
11 TraesCS2B01G534100 chr6A 91.667 1380 88 9 1 1353 85351451 85352830 0.000000e+00 1886.0
12 TraesCS2B01G534100 chr1D 91.098 1393 86 8 1 1355 456809857 456811249 0.000000e+00 1851.0
13 TraesCS2B01G534100 chr1D 92.500 80 6 0 1397 1476 456811251 456811330 5.870000e-22 115.0
14 TraesCS2B01G534100 chr7B 89.971 1396 99 17 1 1355 471226752 471225357 0.000000e+00 1764.0
15 TraesCS2B01G534100 chr6B 90.132 1368 105 14 1 1357 708191263 708192611 0.000000e+00 1751.0
16 TraesCS2B01G534100 chr3D 92.774 858 52 4 1 849 50895076 50895932 0.000000e+00 1232.0
17 TraesCS2B01G534100 chr3D 93.542 511 28 3 849 1355 50895962 50896471 0.000000e+00 756.0
18 TraesCS2B01G534100 chr3D 82.626 495 70 14 1399 1885 50896473 50896959 8.580000e-115 424.0
19 TraesCS2B01G534100 chr6D 83.234 501 68 13 1393 1885 28691715 28691223 1.830000e-121 446.0
20 TraesCS2B01G534100 chr6D 97.143 35 1 0 1480 1514 229383805 229383839 2.790000e-05 60.2
21 TraesCS2B01G534100 chr1B 90.123 324 28 3 2251 2571 86570380 86570058 3.990000e-113 418.0
22 TraesCS2B01G534100 chr1B 85.233 386 43 7 1835 2209 86570761 86570379 4.050000e-103 385.0
23 TraesCS2B01G534100 chr1B 78.571 84 18 0 1431 1514 89439994 89439911 3.610000e-04 56.5
24 TraesCS2B01G534100 chr5B 85.492 386 41 8 1835 2209 173008522 173008141 3.130000e-104 388.0
25 TraesCS2B01G534100 chr5B 87.440 207 21 5 2251 2453 173008142 173007937 1.550000e-57 233.0
26 TraesCS2B01G534100 chr5B 83.889 180 25 3 2395 2571 473875608 473875786 4.440000e-38 169.0
27 TraesCS2B01G534100 chr3B 85.195 385 44 7 1835 2209 289898643 289899024 1.460000e-102 383.0
28 TraesCS2B01G534100 chr3B 89.706 204 19 2 2251 2453 289899023 289899225 2.560000e-65 259.0
29 TraesCS2B01G534100 chr3B 88.235 204 22 2 2251 2453 291046501 291046703 2.580000e-60 243.0
30 TraesCS2B01G534100 chr3B 78.824 85 16 2 1431 1514 312165357 312165274 3.610000e-04 56.5
31 TraesCS2B01G534100 chr3B 78.571 84 18 0 1431 1514 795970706 795970789 3.610000e-04 56.5
32 TraesCS2B01G534100 chr2D 83.914 373 48 6 2187 2555 41219916 41219552 1.910000e-91 346.0
33 TraesCS2B01G534100 chr1A 82.540 189 26 5 2386 2570 365417943 365418128 2.670000e-35 159.0
34 TraesCS2B01G534100 chr7D 80.861 209 31 8 2371 2575 623865484 623865687 3.460000e-34 156.0
35 TraesCS2B01G534100 chr4B 81.407 199 29 7 2374 2568 546050776 546050582 3.460000e-34 156.0
36 TraesCS2B01G534100 chr4D 81.000 200 29 8 2380 2575 187471958 187471764 1.610000e-32 150.0


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 TraesCS2B01G534100 chr2B 730525798 730528391 2593 False 4791.0 4791 100.000000 1 2594 1 chr2B.!!$F2 2593
1 TraesCS2B01G534100 chr3A 688611532 688613403 1871 True 2134.0 2134 87.422000 1 1885 1 chr3A.!!$R1 1884
2 TraesCS2B01G534100 chr3A 70483734 70485318 1584 True 926.5 1646 85.753000 52 1643 2 chr3A.!!$R2 1591
3 TraesCS2B01G534100 chr3A 264036417 264036928 511 False 713.0 713 91.992000 849 1355 1 chr3A.!!$F1 506
4 TraesCS2B01G534100 chr4A 44781622 44783491 1869 False 1999.0 1999 86.227000 1 1885 1 chr4A.!!$F2 1884
5 TraesCS2B01G534100 chr4A 44650148 44651506 1358 False 1797.0 1797 90.711000 1 1355 1 chr4A.!!$F1 1354
6 TraesCS2B01G534100 chr4A 44645350 44646319 969 True 1206.0 1206 89.383000 1 966 1 chr4A.!!$R1 965
7 TraesCS2B01G534100 chr4A 691801350 691802047 697 False 407.0 429 88.273000 1831 2562 2 chr4A.!!$F3 731
8 TraesCS2B01G534100 chr6A 85351451 85352830 1379 False 1886.0 1886 91.667000 1 1353 1 chr6A.!!$F1 1352
9 TraesCS2B01G534100 chr1D 456809857 456811330 1473 False 983.0 1851 91.799000 1 1476 2 chr1D.!!$F1 1475
10 TraesCS2B01G534100 chr7B 471225357 471226752 1395 True 1764.0 1764 89.971000 1 1355 1 chr7B.!!$R1 1354
11 TraesCS2B01G534100 chr6B 708191263 708192611 1348 False 1751.0 1751 90.132000 1 1357 1 chr6B.!!$F1 1356
12 TraesCS2B01G534100 chr3D 50895076 50896959 1883 False 804.0 1232 89.647333 1 1885 3 chr3D.!!$F1 1884
13 TraesCS2B01G534100 chr1B 86570058 86570761 703 True 401.5 418 87.678000 1835 2571 2 chr1B.!!$R2 736
14 TraesCS2B01G534100 chr5B 173007937 173008522 585 True 310.5 388 86.466000 1835 2453 2 chr5B.!!$R1 618
15 TraesCS2B01G534100 chr3B 289898643 289899225 582 False 321.0 383 87.450500 1835 2453 2 chr3B.!!$F3 618

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
750 763 1.583556 TGCTAGGATGTGTGGGTCAT 58.416 50.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1907 0.250513 AGCCATTCCGTCCTGAACTC 59.749 55.0 0.0 0.0 0.0 3.01 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
31 32 2.166870 TGATCCACCAAGATGCATTTGC 59.833 45.455 0.00 0.00 42.50 3.68
101 104 9.209175 CTCTGTAATTGTTAGCTAACTCACTTT 57.791 33.333 31.14 20.09 37.12 2.66
122 125 7.444183 CACTTTCTTGACACACTAGGGAAATAA 59.556 37.037 0.00 0.00 0.00 1.40
172 175 2.123589 TCCGGGATTTCTTGCTCCATA 58.876 47.619 0.00 0.00 32.90 2.74
216 219 7.996644 ACTTAAAAGAGTGGGTATCAAGTCAAA 59.003 33.333 0.00 0.00 0.00 2.69
262 265 8.768397 AGAGTTGTATAACTTATGTCATTCCCA 58.232 33.333 6.31 0.00 46.79 4.37
308 312 4.141733 ACATTTGGGTTGTGGAAGAAAAGG 60.142 41.667 0.00 0.00 0.00 3.11
309 313 2.838637 TGGGTTGTGGAAGAAAAGGT 57.161 45.000 0.00 0.00 0.00 3.50
317 321 2.959030 GTGGAAGAAAAGGTGGCTTTCT 59.041 45.455 0.00 0.00 43.38 2.52
329 333 3.547413 GGTGGCTTTCTTACGTTGTCAAC 60.547 47.826 5.58 5.58 0.00 3.18
399 408 9.154847 GCTAAGATGCAAACTAAATGGAAAATT 57.845 29.630 0.00 0.00 0.00 1.82
476 485 4.098914 ACACAACTTTGCAAGGGATAGA 57.901 40.909 13.65 0.00 0.00 1.98
482 491 2.113860 TTGCAAGGGATAGACAGCAC 57.886 50.000 0.00 0.00 0.00 4.40
497 506 3.084039 ACAGCACGTGATGGATGATTTT 58.916 40.909 34.31 10.94 35.42 1.82
544 553 6.744175 AATAGCCTCTTCTGAAGATGATCA 57.256 37.500 21.88 0.00 36.82 2.92
549 558 6.015180 AGCCTCTTCTGAAGATGATCATCTAC 60.015 42.308 33.10 11.32 46.75 2.59
603 612 2.624838 AGCACTTCATGGACCAACTTTG 59.375 45.455 0.00 0.00 0.00 2.77
680 689 2.234908 AGAGTTGGAGTAGGATGTGTGC 59.765 50.000 0.00 0.00 0.00 4.57
750 763 1.583556 TGCTAGGATGTGTGGGTCAT 58.416 50.000 0.00 0.00 0.00 3.06
770 783 3.138884 TCACTGCATGGACTTTGCTTA 57.861 42.857 0.00 0.00 40.77 3.09
811 824 3.979101 ATGGTGCCTTTTGGGTATTTG 57.021 42.857 0.00 0.00 40.82 2.32
819 832 4.382577 GCCTTTTGGGTATTTGGTACATGG 60.383 45.833 0.00 0.00 38.14 3.66
821 834 2.445682 TGGGTATTTGGTACATGGCC 57.554 50.000 0.00 0.00 39.30 5.36
834 847 6.068010 TGGTACATGGCCCATATTAAGAAAG 58.932 40.000 0.00 0.00 0.00 2.62
875 939 8.015658 GTGTGTGATATTACCTTGTTGTCTTTC 58.984 37.037 0.00 0.00 0.00 2.62
877 941 9.431887 GTGTGATATTACCTTGTTGTCTTTCTA 57.568 33.333 0.00 0.00 0.00 2.10
921 985 9.559958 CTTATGTTGTCTTTGTGTTTGGATATC 57.440 33.333 0.00 0.00 0.00 1.63
949 1016 3.763897 GCATTTTCTTGTAGGACCATGGT 59.236 43.478 19.89 19.89 0.00 3.55
975 1044 4.416516 AGGAGGTGGAAAAATTTGGTAGG 58.583 43.478 0.00 0.00 0.00 3.18
981 1050 8.679344 AGGTGGAAAAATTTGGTAGGAATTAT 57.321 30.769 0.00 0.00 0.00 1.28
1009 1078 5.359009 ACATGGACAGATGAAATGGACATTC 59.641 40.000 0.00 0.00 0.00 2.67
1106 1182 4.875536 CAGTGCTGTTATAGGTAATGTGCA 59.124 41.667 0.00 0.00 0.00 4.57
1145 1221 5.362143 TGACCATCACAAAGGAAAACATCAA 59.638 36.000 0.00 0.00 0.00 2.57
1265 1341 6.595326 TCAATTGATAGTGAAGATGTGTGGAC 59.405 38.462 3.38 0.00 0.00 4.02
1295 1371 5.945155 TGTTGCGGTAAGAAATTTATCCAC 58.055 37.500 0.00 0.00 0.00 4.02
1357 1433 7.869800 ACATTTGTTTGACAATTCTCTCTCTC 58.130 34.615 0.00 0.00 38.00 3.20
1358 1434 7.718753 ACATTTGTTTGACAATTCTCTCTCTCT 59.281 33.333 0.00 0.00 38.00 3.10
1359 1435 7.721286 TTTGTTTGACAATTCTCTCTCTCTC 57.279 36.000 0.00 0.00 38.00 3.20
1360 1436 6.662865 TGTTTGACAATTCTCTCTCTCTCT 57.337 37.500 0.00 0.00 0.00 3.10
1361 1437 6.686630 TGTTTGACAATTCTCTCTCTCTCTC 58.313 40.000 0.00 0.00 0.00 3.20
1362 1438 6.493115 TGTTTGACAATTCTCTCTCTCTCTCT 59.507 38.462 0.00 0.00 0.00 3.10
1363 1439 6.757897 TTGACAATTCTCTCTCTCTCTCTC 57.242 41.667 0.00 0.00 0.00 3.20
1364 1440 6.065976 TGACAATTCTCTCTCTCTCTCTCT 57.934 41.667 0.00 0.00 0.00 3.10
1365 1441 6.115446 TGACAATTCTCTCTCTCTCTCTCTC 58.885 44.000 0.00 0.00 0.00 3.20
1366 1442 6.070021 TGACAATTCTCTCTCTCTCTCTCTCT 60.070 42.308 0.00 0.00 0.00 3.10
1367 1443 6.352516 ACAATTCTCTCTCTCTCTCTCTCTC 58.647 44.000 0.00 0.00 0.00 3.20
1368 1444 6.157645 ACAATTCTCTCTCTCTCTCTCTCTCT 59.842 42.308 0.00 0.00 0.00 3.10
1369 1445 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
1370 1446 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
1371 1447 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1372 1448 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1373 1449 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1374 1450 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1375 1451 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1376 1452 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1377 1453 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
1378 1454 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1379 1455 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
1380 1456 4.614475 TCTCTCTCTCTCTCTCTCTCTGT 58.386 47.826 0.00 0.00 0.00 3.41
1381 1457 4.403752 TCTCTCTCTCTCTCTCTCTCTGTG 59.596 50.000 0.00 0.00 0.00 3.66
1382 1458 4.096681 TCTCTCTCTCTCTCTCTCTGTGT 58.903 47.826 0.00 0.00 0.00 3.72
1383 1459 4.081476 TCTCTCTCTCTCTCTCTCTGTGTG 60.081 50.000 0.00 0.00 0.00 3.82
1384 1460 3.582647 TCTCTCTCTCTCTCTCTGTGTGT 59.417 47.826 0.00 0.00 0.00 3.72
1385 1461 3.673902 TCTCTCTCTCTCTCTGTGTGTG 58.326 50.000 0.00 0.00 0.00 3.82
1386 1462 3.072330 TCTCTCTCTCTCTCTGTGTGTGT 59.928 47.826 0.00 0.00 0.00 3.72
1387 1463 3.145286 TCTCTCTCTCTCTGTGTGTGTG 58.855 50.000 0.00 0.00 0.00 3.82
1422 1510 1.238439 GTGTGTGTGTGCAGGCTAAT 58.762 50.000 0.00 0.00 0.00 1.73
1429 1517 4.824537 TGTGTGTGCAGGCTAATAAGAAAA 59.175 37.500 0.00 0.00 0.00 2.29
1434 1522 6.038714 GTGTGCAGGCTAATAAGAAAATAGCT 59.961 38.462 0.00 0.00 41.35 3.32
1465 1553 7.287696 ACAAGAACAAGGTCATTAAGAATTGGT 59.712 33.333 0.00 0.00 32.30 3.67
1482 1570 3.769739 TGGTATGCTATCACCACCATC 57.230 47.619 0.00 0.00 39.91 3.51
1500 1588 5.008415 CACCATCTACTCAAAAGATCATGCC 59.992 44.000 0.00 0.00 31.22 4.40
1514 1602 1.203038 TCATGCCAATGGTGAAGGTGT 60.203 47.619 0.00 0.00 34.30 4.16
1515 1603 1.203052 CATGCCAATGGTGAAGGTGTC 59.797 52.381 0.00 0.00 0.00 3.67
1524 1612 0.512952 GTGAAGGTGTCGTCACATGC 59.487 55.000 14.58 6.80 46.65 4.06
1527 1615 0.944311 AAGGTGTCGTCACATGCGTC 60.944 55.000 14.58 0.00 45.45 5.19
1532 1620 0.091344 GTCGTCACATGCGTCGAAAG 59.909 55.000 4.69 0.00 34.23 2.62
1534 1622 0.091344 CGTCACATGCGTCGAAAGTC 59.909 55.000 0.00 0.00 0.00 3.01
1539 1627 1.526887 ACATGCGTCGAAAGTCTTGTG 59.473 47.619 0.00 0.00 0.00 3.33
1540 1628 0.512952 ATGCGTCGAAAGTCTTGTGC 59.487 50.000 0.00 0.00 0.00 4.57
1541 1629 1.204312 GCGTCGAAAGTCTTGTGCC 59.796 57.895 0.00 0.00 0.00 5.01
1544 1632 1.583054 GTCGAAAGTCTTGTGCCACT 58.417 50.000 0.00 0.00 0.00 4.00
1546 1634 2.731976 GTCGAAAGTCTTGTGCCACTAG 59.268 50.000 0.00 0.00 0.00 2.57
1547 1635 2.364324 TCGAAAGTCTTGTGCCACTAGT 59.636 45.455 6.20 0.00 0.00 2.57
1549 1637 3.059597 CGAAAGTCTTGTGCCACTAGTTG 60.060 47.826 6.20 0.00 0.00 3.16
1551 1639 1.140852 AGTCTTGTGCCACTAGTTGCA 59.859 47.619 17.13 17.13 34.54 4.08
1553 1641 0.877071 CTTGTGCCACTAGTTGCAGG 59.123 55.000 21.06 11.00 38.34 4.85
1555 1643 0.035317 TGTGCCACTAGTTGCAGGAG 59.965 55.000 21.06 0.00 38.34 3.69
1576 1664 3.063485 GCAACTGAAGACTCTCCTGAAC 58.937 50.000 0.00 0.00 0.00 3.18
1577 1665 3.658709 CAACTGAAGACTCTCCTGAACC 58.341 50.000 0.00 0.00 0.00 3.62
1578 1666 2.252714 ACTGAAGACTCTCCTGAACCC 58.747 52.381 0.00 0.00 0.00 4.11
1583 1671 0.325272 GACTCTCCTGAACCCCCAAC 59.675 60.000 0.00 0.00 0.00 3.77
1614 1702 2.213499 CAAACCGGTGATGCTATCCTC 58.787 52.381 8.52 0.00 0.00 3.71
1638 1726 3.498661 GCCTACTTGGGGATATGAAAGGG 60.499 52.174 0.00 0.00 36.00 3.95
1644 1732 4.453480 TGGGGATATGAAAGGGTCATTC 57.547 45.455 0.00 0.00 45.13 2.67
1654 1742 2.653234 AGGGTCATTCCATGATGCTC 57.347 50.000 0.00 0.00 42.04 4.26
1668 1756 4.341366 TGATGCTCTGAAGTCACTTGAA 57.659 40.909 0.00 0.00 0.00 2.69
1678 1766 6.325545 TCTGAAGTCACTTGAACCTTTACCTA 59.674 38.462 0.00 0.00 0.00 3.08
1680 1768 8.197592 TGAAGTCACTTGAACCTTTACCTATA 57.802 34.615 0.00 0.00 0.00 1.31
1686 1774 5.191124 ACTTGAACCTTTACCTATACCCCAG 59.809 44.000 0.00 0.00 0.00 4.45
1687 1775 4.962839 TGAACCTTTACCTATACCCCAGA 58.037 43.478 0.00 0.00 0.00 3.86
1698 1786 2.953093 TACCCCAGATTACACCTCCA 57.047 50.000 0.00 0.00 0.00 3.86
1711 1799 2.108952 ACACCTCCAGCTGAAATCCTTT 59.891 45.455 17.39 0.00 0.00 3.11
1758 1846 1.491670 CTCGTGGAGACATATTGCGG 58.508 55.000 0.00 0.00 46.14 5.69
1767 1855 4.262463 GGAGACATATTGCGGTCTTATGGA 60.262 45.833 0.00 0.00 44.03 3.41
1771 1859 4.275936 ACATATTGCGGTCTTATGGAAAGC 59.724 41.667 0.00 0.00 0.00 3.51
1773 1861 2.024176 TGCGGTCTTATGGAAAGCTC 57.976 50.000 0.00 0.00 32.38 4.09
1782 1870 6.408662 GGTCTTATGGAAAGCTCATCCTTAGT 60.409 42.308 16.91 6.03 37.85 2.24
1786 1874 5.441718 TGGAAAGCTCATCCTTAGTGAAT 57.558 39.130 16.91 0.00 37.85 2.57
1788 1876 5.189180 GGAAAGCTCATCCTTAGTGAATGT 58.811 41.667 10.52 0.00 33.98 2.71
1793 1881 6.006449 AGCTCATCCTTAGTGAATGTTTGTT 58.994 36.000 0.00 0.00 0.00 2.83
1800 1888 5.010012 CCTTAGTGAATGTTTGTTCCAAGCT 59.990 40.000 0.00 0.00 0.00 3.74
1801 1889 6.461509 CCTTAGTGAATGTTTGTTCCAAGCTT 60.462 38.462 0.00 0.00 0.00 3.74
1803 1891 5.111293 AGTGAATGTTTGTTCCAAGCTTTG 58.889 37.500 0.00 0.00 0.00 2.77
1804 1892 5.105392 AGTGAATGTTTGTTCCAAGCTTTGA 60.105 36.000 0.00 0.00 0.00 2.69
1806 1894 5.754406 TGAATGTTTGTTCCAAGCTTTGATG 59.246 36.000 0.00 0.00 0.00 3.07
1829 1917 3.425162 ACTTCCAATGGAGTTCAGGAC 57.575 47.619 0.86 0.00 31.21 3.85
1837 1925 0.744771 GGAGTTCAGGACGGAATGGC 60.745 60.000 0.00 0.00 0.00 4.40
1840 1928 1.377202 TTCAGGACGGAATGGCTGC 60.377 57.895 0.00 0.00 0.00 5.25
1845 1933 0.106708 GGACGGAATGGCTGCTGATA 59.893 55.000 0.00 0.00 0.00 2.15
1852 1940 4.615223 CGGAATGGCTGCTGATATTGAATG 60.615 45.833 0.00 0.00 0.00 2.67
1857 1945 6.474140 TGGCTGCTGATATTGAATGAAAAT 57.526 33.333 0.00 0.00 0.00 1.82
1860 1948 7.922278 TGGCTGCTGATATTGAATGAAAATAAC 59.078 33.333 0.00 0.00 0.00 1.89
1861 1949 7.922278 GGCTGCTGATATTGAATGAAAATAACA 59.078 33.333 0.00 0.00 0.00 2.41
1888 1976 8.557864 GCTCTTGATGGATATTATGTATGCATC 58.442 37.037 18.91 18.91 46.34 3.91
1894 1982 7.562454 TGGATATTATGTATGCATCATGCTG 57.438 36.000 11.84 0.00 45.31 4.41
1917 2005 8.066595 GCTGCTTATAATCTGATTTAGTGTGTG 58.933 37.037 8.38 0.00 0.00 3.82
1939 2027 6.312918 TGTGTCAGACTTCTAAACTTGTTGTC 59.687 38.462 1.31 0.00 0.00 3.18
1942 2030 7.147794 TGTCAGACTTCTAAACTTGTTGTCCTA 60.148 37.037 1.31 0.00 0.00 2.94
1943 2031 7.709613 GTCAGACTTCTAAACTTGTTGTCCTAA 59.290 37.037 0.00 0.00 0.00 2.69
1944 2032 8.262227 TCAGACTTCTAAACTTGTTGTCCTAAA 58.738 33.333 0.00 0.00 0.00 1.85
1950 2038 7.992008 TCTAAACTTGTTGTCCTAAAACTTGG 58.008 34.615 0.00 0.00 0.00 3.61
1955 2043 5.195001 TGTTGTCCTAAAACTTGGAATGC 57.805 39.130 0.00 0.00 33.72 3.56
1956 2044 4.892934 TGTTGTCCTAAAACTTGGAATGCT 59.107 37.500 0.00 0.00 33.72 3.79
1964 2052 1.831580 ACTTGGAATGCTGCCTCTTC 58.168 50.000 0.00 0.00 0.00 2.87
1969 2057 0.450983 GAATGCTGCCTCTTCTGTGC 59.549 55.000 0.00 0.00 0.00 4.57
2012 2100 5.189180 GTTGCCATCCTTATGAGACTTCTT 58.811 41.667 0.00 0.00 34.84 2.52
2014 2102 6.166984 TGCCATCCTTATGAGACTTCTTAG 57.833 41.667 0.00 0.00 34.84 2.18
2076 2168 7.149973 TGCTATTGTTACGTACATCTATTCCC 58.850 38.462 0.00 0.00 36.44 3.97
2082 2175 8.795842 TGTTACGTACATCTATTCCCATTTTT 57.204 30.769 0.00 0.00 0.00 1.94
2126 2222 8.806429 ATGTTGTGAAGTTCACCATAATATGA 57.194 30.769 28.67 7.99 46.40 2.15
2136 2232 9.342308 AGTTCACCATAATATGATACTGTTTGG 57.658 33.333 1.10 0.00 0.00 3.28
2208 2306 8.892723 TGTCAAGTCCATAATAATTTACTGCTG 58.107 33.333 0.00 0.00 0.00 4.41
2209 2307 9.109393 GTCAAGTCCATAATAATTTACTGCTGA 57.891 33.333 0.00 0.00 0.00 4.26
2210 2308 9.679661 TCAAGTCCATAATAATTTACTGCTGAA 57.320 29.630 0.00 0.00 0.00 3.02
2211 2309 9.941664 CAAGTCCATAATAATTTACTGCTGAAG 57.058 33.333 0.00 0.00 0.00 3.02
2212 2310 9.686683 AAGTCCATAATAATTTACTGCTGAAGT 57.313 29.630 0.00 0.00 43.40 3.01
2218 2316 9.899661 ATAATAATTTACTGCTGAAGTACACCA 57.100 29.630 0.00 0.00 41.21 4.17
2219 2317 5.941948 AATTTACTGCTGAAGTACACCAC 57.058 39.130 0.00 0.00 41.21 4.16
2220 2318 4.409718 TTTACTGCTGAAGTACACCACA 57.590 40.909 0.00 0.00 41.21 4.17
2221 2319 4.409718 TTACTGCTGAAGTACACCACAA 57.590 40.909 0.00 0.00 41.21 3.33
2222 2320 2.838736 ACTGCTGAAGTACACCACAAG 58.161 47.619 0.00 0.00 37.36 3.16
2223 2321 1.532868 CTGCTGAAGTACACCACAAGC 59.467 52.381 0.00 0.00 33.37 4.01
2224 2322 1.140852 TGCTGAAGTACACCACAAGCT 59.859 47.619 0.00 0.00 33.71 3.74
2225 2323 2.222027 GCTGAAGTACACCACAAGCTT 58.778 47.619 0.00 0.00 31.31 3.74
2226 2324 2.618709 GCTGAAGTACACCACAAGCTTT 59.381 45.455 0.00 0.00 31.31 3.51
2227 2325 3.304057 GCTGAAGTACACCACAAGCTTTC 60.304 47.826 0.00 0.00 31.31 2.62
2228 2326 4.130118 CTGAAGTACACCACAAGCTTTCT 58.870 43.478 0.00 0.00 0.00 2.52
2229 2327 4.523083 TGAAGTACACCACAAGCTTTCTT 58.477 39.130 0.00 0.00 0.00 2.52
2230 2328 4.574828 TGAAGTACACCACAAGCTTTCTTC 59.425 41.667 0.00 2.55 0.00 2.87
2231 2329 4.150897 AGTACACCACAAGCTTTCTTCA 57.849 40.909 0.00 0.00 0.00 3.02
2232 2330 4.718961 AGTACACCACAAGCTTTCTTCAT 58.281 39.130 0.00 0.00 0.00 2.57
2233 2331 3.996150 ACACCACAAGCTTTCTTCATG 57.004 42.857 0.00 0.00 0.00 3.07
2234 2332 3.290710 ACACCACAAGCTTTCTTCATGT 58.709 40.909 0.00 0.00 0.00 3.21
2235 2333 3.701040 ACACCACAAGCTTTCTTCATGTT 59.299 39.130 0.00 0.00 0.00 2.71
2236 2334 4.887071 ACACCACAAGCTTTCTTCATGTTA 59.113 37.500 0.00 0.00 0.00 2.41
2237 2335 5.536161 ACACCACAAGCTTTCTTCATGTTAT 59.464 36.000 0.00 0.00 0.00 1.89
2238 2336 6.040842 ACACCACAAGCTTTCTTCATGTTATT 59.959 34.615 0.00 0.00 0.00 1.40
2239 2337 6.925165 CACCACAAGCTTTCTTCATGTTATTT 59.075 34.615 0.00 0.00 0.00 1.40
2240 2338 6.925165 ACCACAAGCTTTCTTCATGTTATTTG 59.075 34.615 0.00 0.00 0.00 2.32
2241 2339 6.366877 CCACAAGCTTTCTTCATGTTATTTGG 59.633 38.462 0.00 0.00 0.00 3.28
2242 2340 7.147312 CACAAGCTTTCTTCATGTTATTTGGA 58.853 34.615 0.00 0.00 0.00 3.53
2243 2341 7.115378 CACAAGCTTTCTTCATGTTATTTGGAC 59.885 37.037 0.00 0.00 0.00 4.02
2244 2342 6.899393 AGCTTTCTTCATGTTATTTGGACA 57.101 33.333 0.00 0.00 0.00 4.02
2245 2343 7.288810 AGCTTTCTTCATGTTATTTGGACAA 57.711 32.000 0.00 0.00 0.00 3.18
2246 2344 7.373493 AGCTTTCTTCATGTTATTTGGACAAG 58.627 34.615 0.00 0.00 0.00 3.16
2247 2345 7.231317 AGCTTTCTTCATGTTATTTGGACAAGA 59.769 33.333 0.00 0.00 0.00 3.02
2248 2346 8.031277 GCTTTCTTCATGTTATTTGGACAAGAT 58.969 33.333 0.00 0.00 0.00 2.40
2249 2347 9.350357 CTTTCTTCATGTTATTTGGACAAGATG 57.650 33.333 0.00 0.00 0.00 2.90
2250 2348 8.408043 TTCTTCATGTTATTTGGACAAGATGT 57.592 30.769 0.00 0.00 29.93 3.06
2254 2352 4.148079 TGTTATTTGGACAAGATGTGGCA 58.852 39.130 0.00 0.00 36.72 4.92
2267 2365 4.202441 AGATGTGGCATGTACCATCTTTC 58.798 43.478 10.72 3.17 40.77 2.62
2269 2367 3.760738 TGTGGCATGTACCATCTTTCAA 58.239 40.909 0.00 0.00 43.01 2.69
2270 2368 4.343231 TGTGGCATGTACCATCTTTCAAT 58.657 39.130 0.00 0.00 43.01 2.57
2435 2537 5.360714 TGATTTGGCATTGTTCCTTCCTATC 59.639 40.000 0.00 0.00 0.00 2.08
2461 2563 2.355756 CCAAGAGCCCAATACATGAACG 59.644 50.000 0.00 0.00 0.00 3.95
2462 2564 2.332063 AGAGCCCAATACATGAACGG 57.668 50.000 0.00 0.00 0.00 4.44
2471 2573 0.869068 TACATGAACGGCCAAACACG 59.131 50.000 2.24 0.00 0.00 4.49
2562 2666 4.019174 GTCCTCAATGTCCATCCAAACAT 58.981 43.478 0.00 0.00 37.71 2.71
2568 2672 3.897141 TGTCCATCCAAACATAGCGTA 57.103 42.857 0.00 0.00 0.00 4.42
2571 2675 4.081365 TGTCCATCCAAACATAGCGTAAGA 60.081 41.667 0.00 0.00 43.02 2.10
2572 2676 4.270325 GTCCATCCAAACATAGCGTAAGAC 59.730 45.833 0.00 0.00 43.02 3.01
2573 2677 4.081365 TCCATCCAAACATAGCGTAAGACA 60.081 41.667 0.00 0.00 43.02 3.41
2574 2678 4.634004 CCATCCAAACATAGCGTAAGACAA 59.366 41.667 0.00 0.00 43.02 3.18
2575 2679 5.123186 CCATCCAAACATAGCGTAAGACAAA 59.877 40.000 0.00 0.00 43.02 2.83
2576 2680 6.348950 CCATCCAAACATAGCGTAAGACAAAA 60.349 38.462 0.00 0.00 43.02 2.44
2577 2681 5.992729 TCCAAACATAGCGTAAGACAAAAC 58.007 37.500 0.00 0.00 43.02 2.43
2578 2682 5.761234 TCCAAACATAGCGTAAGACAAAACT 59.239 36.000 0.00 0.00 43.02 2.66
2579 2683 6.073440 TCCAAACATAGCGTAAGACAAAACTC 60.073 38.462 0.00 0.00 43.02 3.01
2580 2684 6.293190 CCAAACATAGCGTAAGACAAAACTCA 60.293 38.462 0.00 0.00 43.02 3.41
2581 2685 7.298122 CAAACATAGCGTAAGACAAAACTCAT 58.702 34.615 0.00 0.00 43.02 2.90
2582 2686 6.648725 ACATAGCGTAAGACAAAACTCATC 57.351 37.500 0.00 0.00 43.02 2.92
2583 2687 6.163476 ACATAGCGTAAGACAAAACTCATCA 58.837 36.000 0.00 0.00 43.02 3.07
2584 2688 6.818644 ACATAGCGTAAGACAAAACTCATCAT 59.181 34.615 0.00 0.00 43.02 2.45
2585 2689 5.536554 AGCGTAAGACAAAACTCATCATG 57.463 39.130 0.00 0.00 43.02 3.07
2586 2690 4.997395 AGCGTAAGACAAAACTCATCATGT 59.003 37.500 0.00 0.00 43.02 3.21
2587 2691 5.120830 AGCGTAAGACAAAACTCATCATGTC 59.879 40.000 0.00 0.00 41.88 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 0.896923 GGCAAATGCATCTTGGTGGA 59.103 50.000 17.53 0.00 44.36 4.02
142 145 0.970427 AAATCCCGGACCATTGGTGC 60.970 55.000 14.44 15.75 40.73 5.01
172 175 2.920524 AGTGATACCGAGTCGATCTGT 58.079 47.619 15.64 5.72 0.00 3.41
216 219 2.452600 TTGGGAGTTTGGAGCTGTTT 57.547 45.000 0.00 0.00 0.00 2.83
251 254 5.513233 ACATTTCTAGCTTGGGAATGACAT 58.487 37.500 20.35 3.19 0.00 3.06
252 255 4.922206 ACATTTCTAGCTTGGGAATGACA 58.078 39.130 20.35 0.14 0.00 3.58
262 265 6.151312 TGTTCTCTCGACTACATTTCTAGCTT 59.849 38.462 0.00 0.00 0.00 3.74
308 312 3.547413 GGTTGACAACGTAAGAAAGCCAC 60.547 47.826 12.07 0.00 43.62 5.01
309 313 2.614983 GGTTGACAACGTAAGAAAGCCA 59.385 45.455 12.07 0.00 43.62 4.75
476 485 2.408271 AATCATCCATCACGTGCTGT 57.592 45.000 17.38 0.00 0.00 4.40
497 506 4.018506 TCATTATCCACTTCCTCCAGCAAA 60.019 41.667 0.00 0.00 0.00 3.68
549 558 8.668510 ACACTCCTAATTAAGTTAGCATCATG 57.331 34.615 0.00 0.00 38.78 3.07
603 612 4.862902 TGTCATTAGATAGCTGCTCTCC 57.137 45.455 4.91 0.00 0.00 3.71
615 624 7.851228 AGGTACTCATCAAACATGTCATTAGA 58.149 34.615 0.00 0.00 0.00 2.10
680 689 6.565234 AGAGAACACCATTATCTAGTTGACG 58.435 40.000 0.00 0.00 0.00 4.35
750 763 1.985473 AAGCAAAGTCCATGCAGTGA 58.015 45.000 0.00 0.00 46.22 3.41
811 824 6.068670 ACTTTCTTAATATGGGCCATGTACC 58.931 40.000 29.14 0.00 0.00 3.34
845 871 8.856153 ACAACAAGGTAATATCACACACATAA 57.144 30.769 0.00 0.00 0.00 1.90
847 911 7.168219 AGACAACAAGGTAATATCACACACAT 58.832 34.615 0.00 0.00 0.00 3.21
921 985 4.418392 GTCCTACAAGAAAATGCATGCAG 58.582 43.478 26.69 12.73 0.00 4.41
949 1016 4.719273 ACCAAATTTTTCCACCTCCTTCAA 59.281 37.500 0.00 0.00 0.00 2.69
975 1044 8.442632 TTTCATCTGTCCATGTGAGATAATTC 57.557 34.615 0.00 0.00 0.00 2.17
981 1050 4.225717 TCCATTTCATCTGTCCATGTGAGA 59.774 41.667 0.00 0.00 0.00 3.27
1009 1078 1.645710 ACAAGGACCTCCAGTAGTGG 58.354 55.000 10.66 10.66 46.63 4.00
1106 1182 3.144657 TGGTCACATTGCACTTCTCAT 57.855 42.857 0.00 0.00 0.00 2.90
1201 1277 2.785357 TCCCACCCAAATCCACTTTT 57.215 45.000 0.00 0.00 0.00 2.27
1357 1433 4.648762 ACAGAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
1358 1434 4.403752 CACAGAGAGAGAGAGAGAGAGAGA 59.596 50.000 0.00 0.00 0.00 3.10
1359 1435 4.161189 ACACAGAGAGAGAGAGAGAGAGAG 59.839 50.000 0.00 0.00 0.00 3.20
1360 1436 4.081476 CACACAGAGAGAGAGAGAGAGAGA 60.081 50.000 0.00 0.00 0.00 3.10
1361 1437 4.186926 CACACAGAGAGAGAGAGAGAGAG 58.813 52.174 0.00 0.00 0.00 3.20
1362 1438 3.582647 ACACACAGAGAGAGAGAGAGAGA 59.417 47.826 0.00 0.00 0.00 3.10
1363 1439 3.686241 CACACACAGAGAGAGAGAGAGAG 59.314 52.174 0.00 0.00 0.00 3.20
1364 1440 3.072330 ACACACACAGAGAGAGAGAGAGA 59.928 47.826 0.00 0.00 0.00 3.10
1365 1441 3.189080 CACACACACAGAGAGAGAGAGAG 59.811 52.174 0.00 0.00 0.00 3.20
1366 1442 3.145286 CACACACACAGAGAGAGAGAGA 58.855 50.000 0.00 0.00 0.00 3.10
1367 1443 2.884012 ACACACACACAGAGAGAGAGAG 59.116 50.000 0.00 0.00 0.00 3.20
1368 1444 2.620585 CACACACACACAGAGAGAGAGA 59.379 50.000 0.00 0.00 0.00 3.10
1369 1445 2.360483 ACACACACACACAGAGAGAGAG 59.640 50.000 0.00 0.00 0.00 3.20
1370 1446 2.099756 CACACACACACACAGAGAGAGA 59.900 50.000 0.00 0.00 0.00 3.10
1371 1447 2.159184 ACACACACACACACAGAGAGAG 60.159 50.000 0.00 0.00 0.00 3.20
1372 1448 1.824852 ACACACACACACACAGAGAGA 59.175 47.619 0.00 0.00 0.00 3.10
1373 1449 1.929169 CACACACACACACACAGAGAG 59.071 52.381 0.00 0.00 0.00 3.20
1374 1450 1.275010 ACACACACACACACACAGAGA 59.725 47.619 0.00 0.00 0.00 3.10
1375 1451 1.394572 CACACACACACACACACAGAG 59.605 52.381 0.00 0.00 0.00 3.35
1376 1452 1.270571 ACACACACACACACACACAGA 60.271 47.619 0.00 0.00 0.00 3.41
1377 1453 1.136000 CACACACACACACACACACAG 60.136 52.381 0.00 0.00 0.00 3.66
1378 1454 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1379 1455 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1380 1456 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1381 1457 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1382 1458 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1383 1459 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1384 1460 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1385 1461 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1386 1462 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1387 1463 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1429 1517 7.817418 TGACCTTGTTCTTGTAAAAAGCTAT 57.183 32.000 0.00 0.00 0.00 2.97
1465 1553 5.393866 TGAGTAGATGGTGGTGATAGCATA 58.606 41.667 0.00 0.00 38.76 3.14
1482 1570 5.359009 ACCATTGGCATGATCTTTTGAGTAG 59.641 40.000 1.54 0.00 31.07 2.57
1500 1588 1.531149 GTGACGACACCTTCACCATTG 59.469 52.381 6.77 0.00 40.74 2.82
1514 1602 0.318360 ACTTTCGACGCATGTGACGA 60.318 50.000 25.61 25.61 0.00 4.20
1515 1603 0.091344 GACTTTCGACGCATGTGACG 59.909 55.000 22.10 22.10 0.00 4.35
1522 1610 1.495584 GGCACAAGACTTTCGACGCA 61.496 55.000 0.00 0.00 0.00 5.24
1524 1612 0.232303 GTGGCACAAGACTTTCGACG 59.768 55.000 13.86 0.00 44.16 5.12
1527 1615 2.755650 ACTAGTGGCACAAGACTTTCG 58.244 47.619 21.41 0.00 44.16 3.46
1532 1620 1.532868 CTGCAACTAGTGGCACAAGAC 59.467 52.381 21.38 4.49 44.16 3.01
1534 1622 0.877071 CCTGCAACTAGTGGCACAAG 59.123 55.000 21.38 11.61 44.16 3.16
1539 1627 3.896479 GCTCCTGCAACTAGTGGC 58.104 61.111 15.84 15.84 39.41 5.01
1549 1637 1.001860 AGAGTCTTCAGTTGCTCCTGC 59.998 52.381 0.00 0.00 40.20 4.85
1551 1639 1.899142 GGAGAGTCTTCAGTTGCTCCT 59.101 52.381 0.00 0.00 39.01 3.69
1553 1641 2.560542 TCAGGAGAGTCTTCAGTTGCTC 59.439 50.000 0.06 0.00 0.00 4.26
1555 1643 3.063485 GTTCAGGAGAGTCTTCAGTTGC 58.937 50.000 0.06 0.00 0.00 4.17
1557 1645 2.635427 GGGTTCAGGAGAGTCTTCAGTT 59.365 50.000 0.06 0.00 0.00 3.16
1559 1647 1.552792 GGGGTTCAGGAGAGTCTTCAG 59.447 57.143 0.06 0.00 0.00 3.02
1565 1653 0.401395 TGTTGGGGGTTCAGGAGAGT 60.401 55.000 0.00 0.00 0.00 3.24
1599 1687 0.320247 GGCAGAGGATAGCATCACCG 60.320 60.000 0.00 0.00 0.00 4.94
1608 1696 1.578703 TCCCCAAGTAGGCAGAGGATA 59.421 52.381 0.00 0.00 35.39 2.59
1614 1702 4.392940 CTTTCATATCCCCAAGTAGGCAG 58.607 47.826 0.00 0.00 35.39 4.85
1644 1732 3.263489 AGTGACTTCAGAGCATCATGG 57.737 47.619 0.00 0.00 37.82 3.66
1654 1742 5.368989 AGGTAAAGGTTCAAGTGACTTCAG 58.631 41.667 0.00 0.00 0.00 3.02
1668 1756 6.328410 GTGTAATCTGGGGTATAGGTAAAGGT 59.672 42.308 0.00 0.00 0.00 3.50
1678 1766 3.318313 CTGGAGGTGTAATCTGGGGTAT 58.682 50.000 0.00 0.00 0.00 2.73
1680 1768 1.584724 CTGGAGGTGTAATCTGGGGT 58.415 55.000 0.00 0.00 0.00 4.95
1687 1775 3.525199 AGGATTTCAGCTGGAGGTGTAAT 59.475 43.478 15.13 9.60 43.04 1.89
1711 1799 7.470935 AATCATGGATCATTTCAAGTGTTGA 57.529 32.000 0.00 0.00 38.04 3.18
1730 1818 1.278985 TGTCTCCACGAGCCAAATCAT 59.721 47.619 0.00 0.00 0.00 2.45
1746 1834 4.955811 TCCATAAGACCGCAATATGTCT 57.044 40.909 0.00 0.00 43.47 3.41
1758 1846 6.481644 CACTAAGGATGAGCTTTCCATAAGAC 59.518 42.308 16.47 0.00 35.59 3.01
1767 1855 6.491403 ACAAACATTCACTAAGGATGAGCTTT 59.509 34.615 0.00 0.00 0.00 3.51
1771 1859 6.430925 TGGAACAAACATTCACTAAGGATGAG 59.569 38.462 0.00 0.00 31.92 2.90
1773 1861 6.573664 TGGAACAAACATTCACTAAGGATG 57.426 37.500 0.00 0.00 31.92 3.51
1793 1881 3.157087 GGAAGTTCCATCAAAGCTTGGA 58.843 45.455 17.44 5.87 40.24 3.53
1806 1894 3.084786 CCTGAACTCCATTGGAAGTTCC 58.915 50.000 27.19 15.50 38.18 3.62
1809 1897 2.289694 CGTCCTGAACTCCATTGGAAGT 60.290 50.000 6.88 4.58 0.00 3.01
1815 1903 2.356125 CCATTCCGTCCTGAACTCCATT 60.356 50.000 0.00 0.00 0.00 3.16
1819 1907 0.250513 AGCCATTCCGTCCTGAACTC 59.749 55.000 0.00 0.00 0.00 3.01
1821 1909 1.648467 GCAGCCATTCCGTCCTGAAC 61.648 60.000 0.00 0.00 0.00 3.18
1829 1917 2.497138 TCAATATCAGCAGCCATTCCG 58.503 47.619 0.00 0.00 0.00 4.30
1845 1933 9.582431 CATCAAGAGCTGTTATTTTCATTCAAT 57.418 29.630 0.00 0.00 0.00 2.57
1860 1948 7.551617 TGCATACATAATATCCATCAAGAGCTG 59.448 37.037 0.00 0.00 0.00 4.24
1861 1949 7.627311 TGCATACATAATATCCATCAAGAGCT 58.373 34.615 0.00 0.00 0.00 4.09
1888 1976 8.781196 ACACTAAATCAGATTATAAGCAGCATG 58.219 33.333 3.17 0.00 40.87 4.06
1889 1977 8.781196 CACACTAAATCAGATTATAAGCAGCAT 58.219 33.333 3.17 0.00 0.00 3.79
1894 1982 9.098355 TGACACACACTAAATCAGATTATAAGC 57.902 33.333 0.00 0.00 0.00 3.09
1917 2005 6.049790 AGGACAACAAGTTTAGAAGTCTGAC 58.950 40.000 0.00 0.00 0.00 3.51
1939 2027 2.827921 AGGCAGCATTCCAAGTTTTAGG 59.172 45.455 0.00 0.00 0.00 2.69
1942 2030 2.601905 AGAGGCAGCATTCCAAGTTTT 58.398 42.857 0.00 0.00 0.00 2.43
1943 2031 2.299326 AGAGGCAGCATTCCAAGTTT 57.701 45.000 0.00 0.00 0.00 2.66
1944 2032 2.165998 GAAGAGGCAGCATTCCAAGTT 58.834 47.619 0.00 0.00 0.00 2.66
1950 2038 0.450983 GCACAGAAGAGGCAGCATTC 59.549 55.000 0.00 0.00 0.00 2.67
1955 2043 1.155042 GTCTTGCACAGAAGAGGCAG 58.845 55.000 0.00 0.00 38.97 4.85
1956 2044 0.761187 AGTCTTGCACAGAAGAGGCA 59.239 50.000 0.00 0.00 32.53 4.75
1964 2052 8.292448 ACAACAAATTATAGAAGTCTTGCACAG 58.708 33.333 0.00 0.00 0.00 3.66
1969 2057 8.452989 GGCAACAACAAATTATAGAAGTCTTG 57.547 34.615 0.00 0.00 0.00 3.02
2055 2147 8.974060 AAATGGGAATAGATGTACGTAACAAT 57.026 30.769 0.00 0.00 42.70 2.71
2056 2148 8.795842 AAAATGGGAATAGATGTACGTAACAA 57.204 30.769 0.00 0.00 42.70 2.83
2063 2155 9.705290 AAAACACAAAAATGGGAATAGATGTAC 57.295 29.630 0.00 0.00 0.00 2.90
2093 2186 5.273944 GTGAACTTCACAACATCAACTTCC 58.726 41.667 15.77 0.00 46.22 3.46
2126 2222 9.211485 GTTGTATGTAACAGTACCAAACAGTAT 57.789 33.333 0.00 0.00 39.87 2.12
2129 2225 6.708949 AGGTTGTATGTAACAGTACCAAACAG 59.291 38.462 0.00 0.00 40.23 3.16
2208 2306 4.574828 TGAAGAAAGCTTGTGGTGTACTTC 59.425 41.667 0.00 6.39 33.61 3.01
2209 2307 4.523083 TGAAGAAAGCTTGTGGTGTACTT 58.477 39.130 0.00 0.00 33.61 2.24
2210 2308 4.150897 TGAAGAAAGCTTGTGGTGTACT 57.849 40.909 0.00 0.00 33.61 2.73
2211 2309 4.275936 ACATGAAGAAAGCTTGTGGTGTAC 59.724 41.667 0.00 0.00 33.61 2.90
2212 2310 4.460263 ACATGAAGAAAGCTTGTGGTGTA 58.540 39.130 0.00 0.00 33.61 2.90
2213 2311 3.290710 ACATGAAGAAAGCTTGTGGTGT 58.709 40.909 0.00 0.00 33.61 4.16
2214 2312 3.996150 ACATGAAGAAAGCTTGTGGTG 57.004 42.857 0.00 0.00 33.61 4.17
2215 2313 6.655078 AATAACATGAAGAAAGCTTGTGGT 57.345 33.333 0.00 0.00 33.61 4.16
2216 2314 6.366877 CCAAATAACATGAAGAAAGCTTGTGG 59.633 38.462 0.00 0.00 33.61 4.17
2217 2315 7.115378 GTCCAAATAACATGAAGAAAGCTTGTG 59.885 37.037 0.00 0.00 33.61 3.33
2218 2316 7.147976 GTCCAAATAACATGAAGAAAGCTTGT 58.852 34.615 0.00 0.00 33.61 3.16
2219 2317 7.147312 TGTCCAAATAACATGAAGAAAGCTTG 58.853 34.615 0.00 0.00 33.61 4.01
2220 2318 7.288810 TGTCCAAATAACATGAAGAAAGCTT 57.711 32.000 0.00 0.00 36.96 3.74
2221 2319 6.899393 TGTCCAAATAACATGAAGAAAGCT 57.101 33.333 0.00 0.00 0.00 3.74
2222 2320 7.370383 TCTTGTCCAAATAACATGAAGAAAGC 58.630 34.615 0.00 0.00 30.53 3.51
2223 2321 9.350357 CATCTTGTCCAAATAACATGAAGAAAG 57.650 33.333 0.00 0.00 35.32 2.62
2224 2322 8.859090 ACATCTTGTCCAAATAACATGAAGAAA 58.141 29.630 0.00 0.00 35.32 2.52
2225 2323 8.298854 CACATCTTGTCCAAATAACATGAAGAA 58.701 33.333 0.00 0.00 35.32 2.52
2226 2324 7.094248 CCACATCTTGTCCAAATAACATGAAGA 60.094 37.037 0.00 0.00 35.32 2.87
2227 2325 7.031372 CCACATCTTGTCCAAATAACATGAAG 58.969 38.462 0.00 0.00 35.32 3.02
2228 2326 6.572119 GCCACATCTTGTCCAAATAACATGAA 60.572 38.462 0.00 0.00 35.32 2.57
2229 2327 5.105797 GCCACATCTTGTCCAAATAACATGA 60.106 40.000 0.00 0.00 35.89 3.07
2230 2328 5.104374 GCCACATCTTGTCCAAATAACATG 58.896 41.667 0.00 0.00 0.00 3.21
2231 2329 4.771577 TGCCACATCTTGTCCAAATAACAT 59.228 37.500 0.00 0.00 0.00 2.71
2232 2330 4.148079 TGCCACATCTTGTCCAAATAACA 58.852 39.130 0.00 0.00 0.00 2.41
2233 2331 4.782019 TGCCACATCTTGTCCAAATAAC 57.218 40.909 0.00 0.00 0.00 1.89
2234 2332 4.771577 ACATGCCACATCTTGTCCAAATAA 59.228 37.500 0.00 0.00 0.00 1.40
2235 2333 4.343231 ACATGCCACATCTTGTCCAAATA 58.657 39.130 0.00 0.00 0.00 1.40
2236 2334 3.167485 ACATGCCACATCTTGTCCAAAT 58.833 40.909 0.00 0.00 0.00 2.32
2237 2335 2.596346 ACATGCCACATCTTGTCCAAA 58.404 42.857 0.00 0.00 0.00 3.28
2238 2336 2.291209 ACATGCCACATCTTGTCCAA 57.709 45.000 0.00 0.00 0.00 3.53
2239 2337 2.617788 GGTACATGCCACATCTTGTCCA 60.618 50.000 0.00 0.00 0.00 4.02
2240 2338 2.017049 GGTACATGCCACATCTTGTCC 58.983 52.381 0.00 0.00 0.00 4.02
2241 2339 2.710377 TGGTACATGCCACATCTTGTC 58.290 47.619 0.00 0.00 32.81 3.18
2242 2340 2.877097 TGGTACATGCCACATCTTGT 57.123 45.000 0.00 0.00 32.81 3.16
2243 2341 3.548770 AGATGGTACATGCCACATCTTG 58.451 45.455 16.44 0.00 45.57 3.02
2244 2342 3.939740 AGATGGTACATGCCACATCTT 57.060 42.857 16.44 5.88 45.57 2.40
2298 2398 9.524106 ACACATGCATATATTTGAAAGTTGATG 57.476 29.630 0.00 0.00 0.00 3.07
2435 2537 4.646040 TCATGTATTGGGCTCTTGGAATTG 59.354 41.667 0.00 0.00 0.00 2.32
2461 2563 1.285641 CCACACATCGTGTTTGGCC 59.714 57.895 0.00 0.00 45.08 5.36
2462 2564 4.942090 CCACACATCGTGTTTGGC 57.058 55.556 9.37 0.00 45.08 4.52
2471 2573 1.814394 TGAGCTTCAATGCCACACATC 59.186 47.619 0.00 0.00 38.34 3.06
2562 2666 6.163476 ACATGATGAGTTTTGTCTTACGCTA 58.837 36.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.