Multiple sequence alignment - TraesCS4D01G009400

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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 TraesCS4D01G009400 chr4D 100.000 4251 0 0 1 4251 4458014 4462264 0.000000e+00 7851
1 TraesCS4D01G009400 chr4D 84.225 1870 228 39 1654 3469 4418054 4419910 0.000000e+00 1757
2 TraesCS4D01G009400 chr4D 89.808 1040 86 9 525 1546 4416666 4417703 0.000000e+00 1315
3 TraesCS4D01G009400 chr4D 84.538 498 69 5 3488 3983 4419899 4420390 1.780000e-133 486
4 TraesCS4D01G009400 chr4A 91.660 2566 193 17 1636 4185 598814698 598812138 0.000000e+00 3533
5 TraesCS4D01G009400 chr4A 88.394 1594 130 29 5 1561 599126790 599125215 0.000000e+00 1868
6 TraesCS4D01G009400 chr4A 88.180 1599 133 26 1 1561 599159756 599158176 0.000000e+00 1855
7 TraesCS4D01G009400 chr4A 88.028 1587 148 17 1 1561 599085578 599084008 0.000000e+00 1840
8 TraesCS4D01G009400 chr4A 88.035 1588 147 16 1 1561 599180681 599179110 0.000000e+00 1840
9 TraesCS4D01G009400 chr4A 87.972 1588 148 16 1 1561 599103302 599101731 0.000000e+00 1834
10 TraesCS4D01G009400 chr4A 87.909 1588 149 16 1 1561 599224108 599222537 0.000000e+00 1829
11 TraesCS4D01G009400 chr4A 87.846 1588 146 18 1 1561 599147518 599145951 0.000000e+00 1820
12 TraesCS4D01G009400 chr4A 83.039 1869 245 34 1654 3469 598909404 598907555 0.000000e+00 1629
13 TraesCS4D01G009400 chr4A 82.061 1873 223 38 1654 3468 599101390 599099573 0.000000e+00 1493
14 TraesCS4D01G009400 chr4A 83.653 1670 187 35 1836 3469 599246791 599245172 0.000000e+00 1493
15 TraesCS4D01G009400 chr4A 83.533 1670 189 35 1836 3469 599157712 599156093 0.000000e+00 1482
16 TraesCS4D01G009400 chr4A 81.901 1873 226 38 1654 3468 599222196 599220379 0.000000e+00 1476
17 TraesCS4D01G009400 chr4A 83.463 1669 191 35 1836 3469 599124753 599123135 0.000000e+00 1474
18 TraesCS4D01G009400 chr4A 84.755 551 60 12 1019 1561 599155656 599155122 8.090000e-147 531
19 TraesCS4D01G009400 chr4A 86.123 454 59 4 3488 3939 598957933 598957482 1.780000e-133 486
20 TraesCS4D01G009400 chr4A 86.353 447 57 4 3488 3932 599123146 599122702 6.390000e-133 484
21 TraesCS4D01G009400 chr4A 88.550 131 14 1 1505 1634 598815050 598814920 1.580000e-34 158
22 TraesCS4D01G009400 chr4B 83.591 2395 276 55 1654 3983 7264124 7266466 0.000000e+00 2137
23 TraesCS4D01G009400 chr4B 83.563 2397 276 51 1654 3983 7218507 7220852 0.000000e+00 2135
24 TraesCS4D01G009400 chr4B 91.667 1452 108 8 1638 3080 7376815 7378262 0.000000e+00 1999
25 TraesCS4D01G009400 chr4B 84.813 1870 222 28 1654 3469 7354520 7356381 0.000000e+00 1823
26 TraesCS4D01G009400 chr4B 84.427 1875 216 32 1654 3469 7171548 7173405 0.000000e+00 1775
27 TraesCS4D01G009400 chr4B 84.320 1875 218 31 1654 3469 7309614 7311471 0.000000e+00 1764
28 TraesCS4D01G009400 chr4B 90.359 1141 101 8 3114 4248 7378267 7379404 0.000000e+00 1489
29 TraesCS4D01G009400 chr4B 87.051 919 87 17 662 1558 7308357 7309265 0.000000e+00 1009
30 TraesCS4D01G009400 chr4B 87.900 876 79 13 705 1558 7170329 7171199 0.000000e+00 1005
31 TraesCS4D01G009400 chr4B 87.671 876 81 13 705 1558 7217288 7218158 0.000000e+00 994
32 TraesCS4D01G009400 chr4B 87.443 876 83 13 705 1558 7262904 7263774 0.000000e+00 983
33 TraesCS4D01G009400 chr4B 86.120 915 88 21 662 1558 7353292 7354185 0.000000e+00 950
34 TraesCS4D01G009400 chr4B 86.427 501 60 6 3488 3983 7173394 7173891 3.740000e-150 542
35 TraesCS4D01G009400 chr4B 86.228 501 61 6 3488 3983 7311460 7311957 1.740000e-148 536
36 TraesCS4D01G009400 chrUn 89.224 1225 100 9 1 1207 216652989 216651779 0.000000e+00 1502
37 TraesCS4D01G009400 chrUn 83.593 1670 188 35 1836 3469 216674910 216673291 0.000000e+00 1487
38 TraesCS4D01G009400 chrUn 90.592 946 71 9 1 934 385953353 385952414 0.000000e+00 1238
39 TraesCS4D01G009400 chrUn 86.123 454 50 5 1120 1561 216675825 216675373 1.070000e-130 477
40 TraesCS4D01G009400 chr6A 83.611 1202 145 19 1654 2808 593026082 593024886 0.000000e+00 1081
41 TraesCS4D01G009400 chr6D 91.093 247 21 1 4006 4251 84938566 84938812 2.450000e-87 333


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 TraesCS4D01G009400 chr4D 4458014 4462264 4250 False 7851.000000 7851 100.000000 1 4251 1 chr4D.!!$F1 4250
1 TraesCS4D01G009400 chr4D 4416666 4420390 3724 False 1186.000000 1757 86.190333 525 3983 3 chr4D.!!$F2 3458
2 TraesCS4D01G009400 chr4A 598812138 598815050 2912 True 1845.500000 3533 90.105000 1505 4185 2 chr4A.!!$R7 2680
3 TraesCS4D01G009400 chr4A 599084008 599085578 1570 True 1840.000000 1840 88.028000 1 1561 1 chr4A.!!$R3 1560
4 TraesCS4D01G009400 chr4A 599179110 599180681 1571 True 1840.000000 1840 88.035000 1 1561 1 chr4A.!!$R5 1560
5 TraesCS4D01G009400 chr4A 599145951 599147518 1567 True 1820.000000 1820 87.846000 1 1561 1 chr4A.!!$R4 1560
6 TraesCS4D01G009400 chr4A 599099573 599103302 3729 True 1663.500000 1834 85.016500 1 3468 2 chr4A.!!$R8 3467
7 TraesCS4D01G009400 chr4A 599220379 599224108 3729 True 1652.500000 1829 84.905000 1 3468 2 chr4A.!!$R11 3467
8 TraesCS4D01G009400 chr4A 598907555 598909404 1849 True 1629.000000 1629 83.039000 1654 3469 1 chr4A.!!$R1 1815
9 TraesCS4D01G009400 chr4A 599245172 599246791 1619 True 1493.000000 1493 83.653000 1836 3469 1 chr4A.!!$R6 1633
10 TraesCS4D01G009400 chr4A 599155122 599159756 4634 True 1289.333333 1855 85.489333 1 3469 3 chr4A.!!$R10 3468
11 TraesCS4D01G009400 chr4A 599122702 599126790 4088 True 1275.333333 1868 86.070000 5 3932 3 chr4A.!!$R9 3927
12 TraesCS4D01G009400 chr4B 7376815 7379404 2589 False 1744.000000 1999 91.013000 1638 4248 2 chr4B.!!$F6 2610
13 TraesCS4D01G009400 chr4B 7217288 7220852 3564 False 1564.500000 2135 85.617000 705 3983 2 chr4B.!!$F2 3278
14 TraesCS4D01G009400 chr4B 7262904 7266466 3562 False 1560.000000 2137 85.517000 705 3983 2 chr4B.!!$F3 3278
15 TraesCS4D01G009400 chr4B 7353292 7356381 3089 False 1386.500000 1823 85.466500 662 3469 2 chr4B.!!$F5 2807
16 TraesCS4D01G009400 chr4B 7170329 7173891 3562 False 1107.333333 1775 86.251333 705 3983 3 chr4B.!!$F1 3278
17 TraesCS4D01G009400 chr4B 7308357 7311957 3600 False 1103.000000 1764 85.866333 662 3983 3 chr4B.!!$F4 3321
18 TraesCS4D01G009400 chrUn 216651779 216652989 1210 True 1502.000000 1502 89.224000 1 1207 1 chrUn.!!$R1 1206
19 TraesCS4D01G009400 chrUn 385952414 385953353 939 True 1238.000000 1238 90.592000 1 934 1 chrUn.!!$R2 933
20 TraesCS4D01G009400 chrUn 216673291 216675825 2534 True 982.000000 1487 84.858000 1120 3469 2 chrUn.!!$R3 2349
21 TraesCS4D01G009400 chr6A 593024886 593026082 1196 True 1081.000000 1081 83.611000 1654 2808 1 chr6A.!!$R1 1154

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
538 542 0.323629 TGACTGGGCGTAAAGGGAAG 59.676 55.0 0.00 0.0 0.00 3.46 F
1041 1079 0.179048 TCCAGCTGAACGCCCATATG 60.179 55.0 17.39 0.0 40.39 1.78 F
1596 1675 0.447801 CTTGCATTGTCGTGTAGCCC 59.552 55.0 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 2312 0.248458 CCAAATAACGCCCATGACGC 60.248 55.000 7.85 1.74 0.00 5.19 R
2905 3334 1.204312 GTGCTCCAAAACGAGACGC 59.796 57.895 0.00 0.00 30.97 5.19 R
3358 3850 0.873721 TTAAGTTTTACGCGCACCCC 59.126 50.000 5.73 0.00 0.00 4.95 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
34 36 3.844211 ACCCCATAGCTAAAGTTGTCTCA 59.156 43.478 0.00 0.00 0.00 3.27
36 38 4.323485 CCCCATAGCTAAAGTTGTCTCACA 60.323 45.833 0.00 0.00 0.00 3.58
118 120 9.277783 CTGGAATTAATCGGAATAGTTGAGAAT 57.722 33.333 0.00 0.00 0.00 2.40
125 129 8.438676 AATCGGAATAGTTGAGAATAAAGTGG 57.561 34.615 0.00 0.00 0.00 4.00
126 130 6.942976 TCGGAATAGTTGAGAATAAAGTGGT 58.057 36.000 0.00 0.00 0.00 4.16
131 135 8.918202 AATAGTTGAGAATAAAGTGGTGAACA 57.082 30.769 0.00 0.00 0.00 3.18
156 160 0.663153 GTAATGCGTGGGAATCTGCC 59.337 55.000 0.00 0.00 0.00 4.85
186 190 0.735471 GGCCGAATCCTGAAGAAAGC 59.265 55.000 0.00 0.00 0.00 3.51
193 197 4.453819 CGAATCCTGAAGAAAGCTCAAAGT 59.546 41.667 0.00 0.00 0.00 2.66
205 209 2.295349 AGCTCAAAGTGCTGTTTGATGG 59.705 45.455 12.58 5.72 43.72 3.51
276 280 3.507233 TGATGCTTAGCTGGTCTTTTTGG 59.493 43.478 5.60 0.00 0.00 3.28
286 290 4.400567 GCTGGTCTTTTTGGATGATTAGCT 59.599 41.667 0.00 0.00 0.00 3.32
291 295 6.183360 GGTCTTTTTGGATGATTAGCTACACC 60.183 42.308 0.00 0.00 0.00 4.16
294 298 2.673258 TGGATGATTAGCTACACCGGA 58.327 47.619 9.46 0.00 0.00 5.14
395 399 1.423395 GCGTGAGTGAAGAAGGTCAG 58.577 55.000 0.00 0.00 0.00 3.51
400 404 2.224137 TGAGTGAAGAAGGTCAGTGCTG 60.224 50.000 0.00 0.00 31.14 4.41
409 413 3.146104 AGGTCAGTGCTGCTTGTAAAT 57.854 42.857 0.00 0.00 0.00 1.40
417 421 5.641209 CAGTGCTGCTTGTAAATCTCTTACT 59.359 40.000 0.00 0.00 0.00 2.24
434 438 0.380733 ACTTCGAGTGCGCGATCATA 59.619 50.000 12.10 0.00 40.35 2.15
438 442 0.920664 CGAGTGCGCGATCATAACAA 59.079 50.000 12.10 0.00 0.00 2.83
440 444 2.033747 CGAGTGCGCGATCATAACAAAT 60.034 45.455 12.10 0.00 0.00 2.32
443 447 3.246226 AGTGCGCGATCATAACAAATCTC 59.754 43.478 12.10 0.00 0.00 2.75
476 480 2.674220 GGCTAACTCCCTGCCAGCT 61.674 63.158 0.00 0.00 45.46 4.24
491 495 3.558411 GCTGCCGCGCTAAGACAG 61.558 66.667 5.56 6.73 0.00 3.51
536 540 0.988832 AATGACTGGGCGTAAAGGGA 59.011 50.000 0.00 0.00 0.00 4.20
538 542 0.323629 TGACTGGGCGTAAAGGGAAG 59.676 55.000 0.00 0.00 0.00 3.46
663 668 7.850935 TGGTCTTCTATTCGTCCCTATAAAT 57.149 36.000 0.00 0.00 0.00 1.40
727 740 2.609459 AGTTGAAACAGACGCTCACTTG 59.391 45.455 0.00 0.00 0.00 3.16
764 781 4.666253 AACCGGTGGCTGCATGCT 62.666 61.111 20.33 0.00 42.39 3.79
779 802 2.581409 GCTTGCATGCATCGCACC 60.581 61.111 27.65 11.85 43.04 5.01
997 1035 2.352032 CGGACCTCTCCTCGCCTTT 61.352 63.158 0.00 0.00 33.79 3.11
1041 1079 0.179048 TCCAGCTGAACGCCCATATG 60.179 55.000 17.39 0.00 40.39 1.78
1071 1109 2.120718 ACCGAGGTGAGGCTCCTT 59.879 61.111 12.86 0.00 35.20 3.36
1098 1136 1.611977 CCTCTAGTCGTGTGGTTGTGA 59.388 52.381 0.00 0.00 0.00 3.58
1194 1256 2.504244 CGAGGACACGTTCGAGGC 60.504 66.667 1.14 0.00 39.06 4.70
1241 1303 3.074369 TCGCCCGCCTCTTCATCA 61.074 61.111 0.00 0.00 0.00 3.07
1243 1305 1.524621 CGCCCGCCTCTTCATCAAT 60.525 57.895 0.00 0.00 0.00 2.57
1251 1313 2.483714 GCCTCTTCATCAATGACGCCTA 60.484 50.000 0.00 0.00 36.36 3.93
1259 1321 1.002792 TCAATGACGCCTACGAGATCG 60.003 52.381 0.00 0.00 43.93 3.69
1308 1374 1.519751 CCCACGCCCTCTATCTCTCG 61.520 65.000 0.00 0.00 0.00 4.04
1314 1380 1.533625 CCCTCTATCTCTCGCTCTGG 58.466 60.000 0.00 0.00 0.00 3.86
1319 1385 1.798223 CTATCTCTCGCTCTGGTCTCG 59.202 57.143 0.00 0.00 0.00 4.04
1323 1389 2.750637 TCGCTCTGGTCTCGGTCC 60.751 66.667 0.00 0.00 0.00 4.46
1324 1390 2.752238 CGCTCTGGTCTCGGTCCT 60.752 66.667 0.00 0.00 0.00 3.85
1331 1398 2.413142 GGTCTCGGTCCTGGGTACG 61.413 68.421 0.00 0.00 0.00 3.67
1355 1426 5.396213 GGACTCATCTTAACTGCTCTGGAAT 60.396 44.000 0.00 0.00 0.00 3.01
1357 1428 6.479884 ACTCATCTTAACTGCTCTGGAATTT 58.520 36.000 0.00 0.00 0.00 1.82
1366 1437 1.101331 CTCTGGAATTTGCAGGGAGC 58.899 55.000 12.09 0.00 38.76 4.70
1404 1475 2.583441 CGAGGTGGAAGCCCTGACA 61.583 63.158 0.00 0.00 32.25 3.58
1448 1519 3.527253 TCCAGGTGGTGACCATCATAAAT 59.473 43.478 18.48 0.00 45.98 1.40
1456 1527 6.378280 GTGGTGACCATCATAAATCCTTTCTT 59.622 38.462 7.94 0.00 35.28 2.52
1458 1529 7.454380 TGGTGACCATCATAAATCCTTTCTTTT 59.546 33.333 0.00 0.00 0.00 2.27
1459 1530 8.966868 GGTGACCATCATAAATCCTTTCTTTTA 58.033 33.333 0.00 0.00 0.00 1.52
1474 1545 7.176690 TCCTTTCTTTTATTTCCACCTGCTTAG 59.823 37.037 0.00 0.00 0.00 2.18
1483 1554 9.921637 TTATTTCCACCTGCTTAGTTTTAAATG 57.078 29.630 0.00 0.00 0.00 2.32
1501 1576 3.726291 ATGTATGTTTATTTGCCCGCC 57.274 42.857 0.00 0.00 0.00 6.13
1517 1592 1.587876 GCCGCATCGATGTCGTGTA 60.588 57.895 27.86 0.00 40.80 2.90
1565 1644 7.656948 TGGGCAACAGATTCTATTTTTCAAAAG 59.343 33.333 0.00 0.00 39.74 2.27
1583 1662 6.050432 TCAAAAGAAAAGATGTTGCTTGCAT 58.950 32.000 0.00 0.00 0.00 3.96
1588 1667 2.624316 AGATGTTGCTTGCATTGTCG 57.376 45.000 0.00 0.00 0.00 4.35
1596 1675 0.447801 CTTGCATTGTCGTGTAGCCC 59.552 55.000 0.00 0.00 0.00 5.19
1635 1714 6.183359 CGAGTTTAGTCGTGTTTCCTGTAATC 60.183 42.308 0.00 0.00 35.14 1.75
1637 1716 3.655276 AGTCGTGTTTCCTGTAATCGT 57.345 42.857 0.00 0.00 0.00 3.73
1638 1717 3.986277 AGTCGTGTTTCCTGTAATCGTT 58.014 40.909 0.00 0.00 0.00 3.85
1639 1718 3.739300 AGTCGTGTTTCCTGTAATCGTTG 59.261 43.478 0.00 0.00 0.00 4.10
1641 1720 3.491639 TCGTGTTTCCTGTAATCGTTGTG 59.508 43.478 0.00 0.00 0.00 3.33
1642 1721 3.246699 CGTGTTTCCTGTAATCGTTGTGT 59.753 43.478 0.00 0.00 0.00 3.72
1643 1722 4.260456 CGTGTTTCCTGTAATCGTTGTGTT 60.260 41.667 0.00 0.00 0.00 3.32
1648 2002 0.869068 TGTAATCGTTGTGTTGGCCG 59.131 50.000 0.00 0.00 0.00 6.13
1700 2055 3.438781 TCTCATGTAACGGAATTGTTGGC 59.561 43.478 0.00 0.00 33.32 4.52
1851 2224 5.551233 TGGCTGGTATTAATGATCTGCTAC 58.449 41.667 0.00 0.00 0.00 3.58
1914 2289 7.379529 CACCTGAATGTTGTTGTTTCTATTCAC 59.620 37.037 0.00 0.00 32.83 3.18
1937 2312 4.293648 TCAGACGGCGGGTGTGTG 62.294 66.667 13.24 0.00 40.62 3.82
1981 2356 6.598753 TGTCGTATAGCCAAAATTAGAAGC 57.401 37.500 0.00 0.00 0.00 3.86
1982 2357 6.346096 TGTCGTATAGCCAAAATTAGAAGCT 58.654 36.000 0.00 0.00 37.58 3.74
2004 2379 8.220755 AGCTGTGAATTTAGTTGTGTTTTCTA 57.779 30.769 0.00 0.00 0.00 2.10
2017 2392 9.683069 AGTTGTGTTTTCTATAGCAGAATTTTG 57.317 29.630 0.00 0.00 42.88 2.44
2025 2400 9.920946 TTTCTATAGCAGAATTTTGGGTATTCT 57.079 29.630 0.00 0.00 42.88 2.40
2050 2427 4.079253 ACAATGTTAGTCCGGCAAGAAAT 58.921 39.130 0.00 0.00 0.00 2.17
2233 2626 6.899892 AAGTTCCTAATTTCCTGATCCTCT 57.100 37.500 0.00 0.00 0.00 3.69
2295 2693 2.032376 TCGCCTGCATGCACTTCA 59.968 55.556 18.46 0.00 0.00 3.02
2415 2816 2.113860 TGTAAACCTGCCAGCTCATC 57.886 50.000 0.00 0.00 0.00 2.92
2419 2820 0.694771 AACCTGCCAGCTCATCTTGA 59.305 50.000 0.00 0.00 0.00 3.02
2434 2835 6.183360 GCTCATCTTGACTTTTAGGTCGTTAC 60.183 42.308 0.00 0.00 38.91 2.50
2499 2903 2.975410 TGCTTTTCACTTCATCTGCG 57.025 45.000 0.00 0.00 0.00 5.18
2525 2929 6.651086 TCACATTGTTGATATTACCCGGTTA 58.349 36.000 0.00 0.00 0.00 2.85
2659 3079 8.773033 AAATATAGGGCATTTCATCTCAGTTT 57.227 30.769 0.00 0.00 0.00 2.66
2830 3254 7.685481 TGGATTTGATACCAACTTCTCACTAA 58.315 34.615 0.00 0.00 32.93 2.24
2909 3338 6.848451 TGGTTAATCTTATTCTTTTGGCGTC 58.152 36.000 0.00 0.00 0.00 5.19
2911 3340 7.148306 TGGTTAATCTTATTCTTTTGGCGTCTC 60.148 37.037 0.00 0.00 0.00 3.36
2959 3388 2.665519 CGGAAAGTCTCATTTTGCCGTG 60.666 50.000 0.00 0.00 33.35 4.94
2989 3419 9.183368 TGGTTATGCTATAATTTTGTCATCACA 57.817 29.630 0.00 0.00 0.00 3.58
3014 3446 4.804597 TGGTAGATGTACATGGTAGCTCT 58.195 43.478 14.43 5.59 0.00 4.09
3159 3623 9.905713 TGTGCCATAGACTTATCTTAATCTTTT 57.094 29.630 0.00 0.00 36.29 2.27
3317 3808 1.340889 GCATTGTGGTGTCCATGTGTT 59.659 47.619 0.00 0.00 35.28 3.32
3339 3831 0.097674 CAAGGATGGAGCGCTTTTCG 59.902 55.000 13.26 0.00 42.12 3.46
3352 3844 1.542547 GCTTTTCGAAGGGTGTCTGGA 60.543 52.381 0.00 0.00 0.00 3.86
3357 3849 2.168496 TCGAAGGGTGTCTGGAACTAG 58.832 52.381 0.00 0.00 0.00 2.57
3358 3850 1.204941 CGAAGGGTGTCTGGAACTAGG 59.795 57.143 0.00 0.00 0.00 3.02
3416 3930 2.014857 GAACTTTGGGCTCGTAATCCC 58.985 52.381 0.00 0.00 42.93 3.85
3436 3950 3.242936 CCCGTGAACGAAAATTGTTGTCT 60.243 43.478 4.03 0.00 43.02 3.41
3457 3971 4.940654 TCTTGTGTTGATGTCAGTTTGTCA 59.059 37.500 0.00 0.00 0.00 3.58
3505 4019 8.783660 AGGAATCAAGTCCATATTCTAGTGTA 57.216 34.615 0.00 0.00 40.48 2.90
3587 4101 6.681729 TGGTCCTCTAGTGACTATGTTTTT 57.318 37.500 12.64 0.00 33.22 1.94
3643 4157 5.007682 AGTCTTGTTGTTGGTTGTTGTACT 58.992 37.500 0.00 0.00 0.00 2.73
3720 4234 2.032528 TTCAGCGTGGCCCTCTTG 59.967 61.111 0.00 0.00 0.00 3.02
3743 4260 0.246635 GAGTACCACAGCACCACGAT 59.753 55.000 0.00 0.00 0.00 3.73
3782 4300 3.878778 CAAAACAGAGGGGATAGTCTGG 58.121 50.000 4.49 0.00 43.89 3.86
3810 4328 2.735151 TCTCGAGGGATCACAAAGCTA 58.265 47.619 13.56 0.00 0.00 3.32
3865 4384 0.238817 TTCGGTATGTTTGCGTTGGC 59.761 50.000 0.00 0.00 40.52 4.52
3896 4415 3.118038 TCTGGGCTAATTAAGTCGCCAAT 60.118 43.478 18.64 0.00 44.23 3.16
3909 4428 4.718961 AGTCGCCAATTTATAGCTCCAAT 58.281 39.130 0.00 0.00 0.00 3.16
3987 4506 0.608856 ATCACGAACTGGGCATTGCA 60.609 50.000 11.39 0.00 0.00 4.08
4024 4543 0.478072 TGGCAATGGTGGTTCAGACT 59.522 50.000 0.00 0.00 0.00 3.24
4042 4561 0.995024 CTTGGTTGATCCTGGGGACT 59.005 55.000 0.00 0.00 32.98 3.85
4058 4577 3.165071 GGGACTGGTTGTTTGATTGGAT 58.835 45.455 0.00 0.00 0.00 3.41
4060 4579 4.040339 GGGACTGGTTGTTTGATTGGATTT 59.960 41.667 0.00 0.00 0.00 2.17
4065 4584 7.734942 ACTGGTTGTTTGATTGGATTTACATT 58.265 30.769 0.00 0.00 0.00 2.71
4102 4621 4.771114 AGTGCAATAGTAGCAATACCCA 57.229 40.909 0.00 0.00 44.64 4.51
4205 4724 6.327154 AGTTCAGTTGTTTTTACCCTTTTCG 58.673 36.000 0.00 0.00 0.00 3.46
4209 4728 6.263617 TCAGTTGTTTTTACCCTTTTCGCTAT 59.736 34.615 0.00 0.00 0.00 2.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 36 3.005791 GCCCTGTAGTTTTGAAGCAATGT 59.994 43.478 0.00 0.00 0.00 2.71
36 38 2.228822 CGCCCTGTAGTTTTGAAGCAAT 59.771 45.455 0.00 0.00 0.00 3.56
118 120 3.120321 ACGCATCTGTTCACCACTTTA 57.880 42.857 0.00 0.00 0.00 1.85
125 129 2.077155 CGCATTACGCATCTGTTCAC 57.923 50.000 0.00 0.00 42.60 3.18
186 190 2.608752 GCCCATCAAACAGCACTTTGAG 60.609 50.000 12.67 6.72 42.13 3.02
193 197 2.277591 GCAGGCCCATCAAACAGCA 61.278 57.895 0.00 0.00 0.00 4.41
205 209 4.581077 ACTAACTAATACTACGCAGGCC 57.419 45.455 0.00 0.00 0.00 5.19
276 280 4.051922 CAGTTCCGGTGTAGCTAATCATC 58.948 47.826 0.00 0.00 0.00 2.92
286 290 1.611977 CTGTGTCTCAGTTCCGGTGTA 59.388 52.381 0.00 0.00 39.17 2.90
291 295 1.374758 GGGCTGTGTCTCAGTTCCG 60.375 63.158 3.97 0.00 45.23 4.30
294 298 1.837051 TCCGGGCTGTGTCTCAGTT 60.837 57.895 0.00 0.00 45.23 3.16
332 336 1.006998 CCCATTGTCCAAGATTCCCCA 59.993 52.381 0.00 0.00 0.00 4.96
395 399 6.487689 AAGTAAGAGATTTACAAGCAGCAC 57.512 37.500 0.00 0.00 0.00 4.40
400 404 6.454450 GCACTCGAAGTAAGAGATTTACAAGC 60.454 42.308 0.00 0.00 38.97 4.01
409 413 0.179197 CGCGCACTCGAAGTAAGAGA 60.179 55.000 8.75 0.00 38.97 3.10
417 421 1.197055 GTTATGATCGCGCACTCGAA 58.803 50.000 8.75 0.00 42.15 3.71
434 438 3.339141 GGCTTCTTCCTCGAGATTTGTT 58.661 45.455 15.71 0.00 0.00 2.83
438 442 0.833949 GGGGCTTCTTCCTCGAGATT 59.166 55.000 15.71 0.00 0.00 2.40
440 444 4.035843 GGGGCTTCTTCCTCGAGA 57.964 61.111 15.71 0.00 0.00 4.04
508 512 1.200020 CGCCCAGTCATTCCAAAGAAC 59.800 52.381 0.00 0.00 33.97 3.01
509 513 1.202879 ACGCCCAGTCATTCCAAAGAA 60.203 47.619 0.00 0.00 36.15 2.52
536 540 1.520666 CCGATTCACCGCCTACCTT 59.479 57.895 0.00 0.00 0.00 3.50
538 542 2.108362 CCCGATTCACCGCCTACC 59.892 66.667 0.00 0.00 0.00 3.18
580 584 1.270550 AGAGCATTCCGCCACTTTTTG 59.729 47.619 0.00 0.00 44.04 2.44
727 740 0.041312 GTGTGTCCACGTGTTCATGC 60.041 55.000 15.65 6.53 0.00 4.06
764 781 2.675772 TGGGTGCGATGCATGCAA 60.676 55.556 26.68 4.80 45.23 4.08
802 825 1.539496 CGGGCGCCATTAGTTAGCTTA 60.539 52.381 30.85 0.00 0.00 3.09
1067 1105 0.935194 GACTAGAGGGGAGGGAAGGA 59.065 60.000 0.00 0.00 0.00 3.36
1071 1109 1.212934 ACACGACTAGAGGGGAGGGA 61.213 60.000 0.00 0.00 0.00 4.20
1115 1153 0.250295 TCAAAGGCCAAGTCAGTCGG 60.250 55.000 5.01 0.00 0.00 4.79
1158 1220 1.151921 TCCACCACACCCTGGATCA 60.152 57.895 0.00 0.00 43.95 2.92
1226 1288 0.464373 TCATTGATGAAGAGGCGGGC 60.464 55.000 0.00 0.00 33.08 6.13
1241 1303 3.847621 CGATCTCGTAGGCGTCATT 57.152 52.632 0.00 0.00 39.49 2.57
1308 1374 2.716017 CCAGGACCGAGACCAGAGC 61.716 68.421 0.00 0.00 0.00 4.09
1314 1380 2.413142 CCGTACCCAGGACCGAGAC 61.413 68.421 0.00 0.00 0.00 3.36
1323 1389 3.700038 AGTTAAGATGAGTCCGTACCCAG 59.300 47.826 0.00 0.00 0.00 4.45
1324 1390 3.446161 CAGTTAAGATGAGTCCGTACCCA 59.554 47.826 0.00 0.00 0.00 4.51
1331 1398 3.449018 TCCAGAGCAGTTAAGATGAGTCC 59.551 47.826 0.00 0.00 0.00 3.85
1448 1519 5.393866 AGCAGGTGGAAATAAAAGAAAGGA 58.606 37.500 0.00 0.00 0.00 3.36
1458 1529 9.084533 ACATTTAAAACTAAGCAGGTGGAAATA 57.915 29.630 0.00 0.00 0.00 1.40
1459 1530 7.962441 ACATTTAAAACTAAGCAGGTGGAAAT 58.038 30.769 0.00 0.00 0.00 2.17
1460 1531 7.354751 ACATTTAAAACTAAGCAGGTGGAAA 57.645 32.000 0.00 0.00 0.00 3.13
1474 1545 7.900864 GCGGGCAAATAAACATACATTTAAAAC 59.099 33.333 0.00 0.00 0.00 2.43
1481 1552 2.034053 CGGCGGGCAAATAAACATACAT 59.966 45.455 0.00 0.00 0.00 2.29
1483 1554 1.862411 GCGGCGGGCAAATAAACATAC 60.862 52.381 9.78 0.00 42.87 2.39
1501 1576 3.569304 AAATTACACGACATCGATGCG 57.431 42.857 28.34 28.34 43.02 4.73
1517 1592 9.780186 GCCCAGTATACTAAACAGATCTAAATT 57.220 33.333 4.74 0.00 0.00 1.82
1533 1611 8.451908 AAAATAGAATCTGTTGCCCAGTATAC 57.548 34.615 0.00 0.00 42.19 1.47
1558 1636 5.873712 TGCAAGCAACATCTTTTCTTTTGAA 59.126 32.000 0.00 0.00 36.52 2.69
1565 1644 4.143473 CGACAATGCAAGCAACATCTTTTC 60.143 41.667 0.00 0.00 0.00 2.29
1569 1648 1.881973 ACGACAATGCAAGCAACATCT 59.118 42.857 0.00 0.00 0.00 2.90
1570 1649 1.980844 CACGACAATGCAAGCAACATC 59.019 47.619 0.00 0.00 0.00 3.06
1583 1662 5.419788 TCTTCTAATTAGGGCTACACGACAA 59.580 40.000 12.54 0.00 0.00 3.18
1588 1667 6.746120 TCGATTCTTCTAATTAGGGCTACAC 58.254 40.000 12.54 0.00 0.00 2.90
1596 1675 9.719279 ACGACTAAACTCGATTCTTCTAATTAG 57.281 33.333 6.11 6.11 37.11 1.73
1635 1714 1.392168 CTATGTACGGCCAACACAACG 59.608 52.381 9.97 0.00 0.00 4.10
1637 1716 3.007074 TCTTCTATGTACGGCCAACACAA 59.993 43.478 9.97 3.71 0.00 3.33
1638 1717 2.563620 TCTTCTATGTACGGCCAACACA 59.436 45.455 9.97 6.78 0.00 3.72
1639 1718 3.187700 CTCTTCTATGTACGGCCAACAC 58.812 50.000 9.97 0.81 0.00 3.32
1641 1720 2.159085 AGCTCTTCTATGTACGGCCAAC 60.159 50.000 2.24 0.00 0.00 3.77
1642 1721 2.108168 AGCTCTTCTATGTACGGCCAA 58.892 47.619 2.24 0.00 0.00 4.52
1643 1722 1.409064 CAGCTCTTCTATGTACGGCCA 59.591 52.381 2.24 0.00 0.00 5.36
1648 2002 7.763356 TGACTAAACTCAGCTCTTCTATGTAC 58.237 38.462 0.00 0.00 0.00 2.90
1719 2074 2.637872 TGCCCTCACCAAGCTATATACC 59.362 50.000 0.00 0.00 0.00 2.73
1720 2075 4.065789 GTTGCCCTCACCAAGCTATATAC 58.934 47.826 0.00 0.00 0.00 1.47
1808 2166 6.372659 CAGCCATACTTTGTTCATTGTCTACT 59.627 38.462 0.00 0.00 0.00 2.57
1811 2169 4.460382 CCAGCCATACTTTGTTCATTGTCT 59.540 41.667 0.00 0.00 0.00 3.41
1851 2224 3.990092 TGGCCATTAGCGTTATGTAGAG 58.010 45.455 0.00 0.00 45.17 2.43
1881 2256 4.709397 ACAACAACATTCAGGTGGAGAAAA 59.291 37.500 0.00 0.00 40.07 2.29
1914 2289 2.815211 CCCGCCGTCTGACACATG 60.815 66.667 8.73 0.00 0.00 3.21
1937 2312 0.248458 CCAAATAACGCCCATGACGC 60.248 55.000 7.85 1.74 0.00 5.19
2004 2379 7.615365 TGTCAAGAATACCCAAAATTCTGCTAT 59.385 33.333 0.00 0.00 41.68 2.97
2017 2392 5.293569 CGGACTAACATTGTCAAGAATACCC 59.706 44.000 6.21 0.00 36.26 3.69
2025 2400 2.552599 TGCCGGACTAACATTGTCAA 57.447 45.000 5.05 0.00 36.26 3.18
2161 2543 8.853126 CAATAATATTCTCAAGGAGCCATTTCA 58.147 33.333 0.00 0.00 0.00 2.69
2434 2835 8.539770 AATGTTAGATTGATATGAGCCGTAAG 57.460 34.615 0.00 0.00 0.00 2.34
2477 2880 4.232221 CGCAGATGAAGTGAAAAGCAAAT 58.768 39.130 0.00 0.00 0.00 2.32
2499 2903 5.355910 ACCGGGTAATATCAACAATGTGAAC 59.644 40.000 6.32 0.00 0.00 3.18
2659 3079 6.017440 CGGTCAAATTCTGAAGAGGTTAACAA 60.017 38.462 8.10 0.00 35.22 2.83
2886 3315 7.085052 AGACGCCAAAAGAATAAGATTAACC 57.915 36.000 0.00 0.00 0.00 2.85
2905 3334 1.204312 GTGCTCCAAAACGAGACGC 59.796 57.895 0.00 0.00 30.97 5.19
2909 3338 4.272504 TCAAACTAAGTGCTCCAAAACGAG 59.727 41.667 0.00 0.00 0.00 4.18
2911 3340 4.527564 CTCAAACTAAGTGCTCCAAAACG 58.472 43.478 0.00 0.00 0.00 3.60
2989 3419 6.327626 AGAGCTACCATGTACATCTACCAAAT 59.672 38.462 5.07 0.00 0.00 2.32
3020 3453 3.244596 GCTGGGAAACAAGTTCTACCTCT 60.245 47.826 0.00 0.00 36.40 3.69
3021 3454 3.075148 GCTGGGAAACAAGTTCTACCTC 58.925 50.000 0.00 0.00 36.40 3.85
3022 3455 2.711547 AGCTGGGAAACAAGTTCTACCT 59.288 45.455 0.00 0.00 36.40 3.08
3025 3458 7.833285 AATTTAAGCTGGGAAACAAGTTCTA 57.167 32.000 0.00 0.00 36.40 2.10
3026 3459 6.731292 AATTTAAGCTGGGAAACAAGTTCT 57.269 33.333 0.00 0.00 36.40 3.01
3027 3460 8.520835 CTTAATTTAAGCTGGGAAACAAGTTC 57.479 34.615 3.33 0.00 35.28 3.01
3058 3494 9.126151 TGGTCAGTTTCTTATTTGTACATTTGA 57.874 29.630 0.00 0.00 0.00 2.69
3065 3501 8.514330 ACAAGTTGGTCAGTTTCTTATTTGTA 57.486 30.769 7.96 0.00 0.00 2.41
3080 3516 3.146066 TCAACCATGCTACAAGTTGGTC 58.854 45.455 7.96 0.00 41.53 4.02
3081 3517 3.222173 TCAACCATGCTACAAGTTGGT 57.778 42.857 7.96 0.00 44.20 3.67
3098 3534 9.208022 CTCAAGTCACATAGTTTCACTAATCAA 57.792 33.333 0.00 0.00 33.89 2.57
3112 3548 5.585844 CACATAATGGTGCTCAAGTCACATA 59.414 40.000 6.82 0.00 36.22 2.29
3162 3626 9.668497 GTCAATTATTAAGACAAGTACCTTCCT 57.332 33.333 0.00 0.00 32.68 3.36
3163 3627 9.668497 AGTCAATTATTAAGACAAGTACCTTCC 57.332 33.333 0.00 0.00 34.80 3.46
3189 3680 8.071967 CGAGCTGCATCAAAAGATGAATAATAA 58.928 33.333 9.49 0.00 42.54 1.40
3328 3819 1.228657 ACACCCTTCGAAAAGCGCTC 61.229 55.000 12.06 0.00 40.61 5.03
3339 3831 1.555533 CCCTAGTTCCAGACACCCTTC 59.444 57.143 0.00 0.00 0.00 3.46
3352 3844 1.829523 TTTACGCGCACCCCCTAGTT 61.830 55.000 5.73 0.00 0.00 2.24
3357 3849 0.954938 TAAGTTTTACGCGCACCCCC 60.955 55.000 5.73 0.00 0.00 5.40
3358 3850 0.873721 TTAAGTTTTACGCGCACCCC 59.126 50.000 5.73 0.00 0.00 4.95
3394 3908 2.617021 GGATTACGAGCCCAAAGTTCCA 60.617 50.000 0.00 0.00 0.00 3.53
3416 3930 4.791163 ACAAGACAACAATTTTCGTTCACG 59.209 37.500 0.00 0.00 41.45 4.35
3436 3950 5.182950 ACTTGACAAACTGACATCAACACAA 59.817 36.000 0.00 0.00 0.00 3.33
3457 3971 8.331740 TCCTCTCAGAAAAATGAATATGGACTT 58.668 33.333 0.00 0.00 0.00 3.01
3505 4019 2.398554 GCGGCAACACATCCACGAT 61.399 57.895 0.00 0.00 0.00 3.73
3561 4075 4.673968 ACATAGTCACTAGAGGACCAACA 58.326 43.478 13.27 1.46 35.89 3.33
3618 4132 5.208463 ACAACAACCAACAACAAGACTTT 57.792 34.783 0.00 0.00 0.00 2.66
3643 4157 0.175760 GGCGATTGGCTACACTCTCA 59.824 55.000 0.00 0.00 42.94 3.27
3720 4234 2.685100 GTGGTGCTGTGGTACTCTTAC 58.315 52.381 0.00 0.00 0.00 2.34
3733 4247 1.517832 GGCTACTGATCGTGGTGCT 59.482 57.895 1.23 0.00 0.00 4.40
3743 4260 2.279073 CCCTCCTCCGGCTACTGA 59.721 66.667 0.00 0.00 0.00 3.41
3782 4300 1.152226 ATCCCTCGAGATGACCCCC 60.152 63.158 15.71 0.00 0.00 5.40
3790 4308 1.561643 AGCTTTGTGATCCCTCGAGA 58.438 50.000 15.71 0.00 0.00 4.04
3791 4309 3.648009 GATAGCTTTGTGATCCCTCGAG 58.352 50.000 5.13 5.13 0.00 4.04
3810 4328 2.203070 GCTGCCCCACGAATCGAT 60.203 61.111 10.55 0.00 0.00 3.59
3844 4363 1.533731 CCAACGCAAACATACCGAAGT 59.466 47.619 0.00 0.00 0.00 3.01
3848 4367 1.576920 TGCCAACGCAAACATACCG 59.423 52.632 0.00 0.00 43.74 4.02
3865 4384 5.411669 ACTTAATTAGCCCAGACTTTTCGTG 59.588 40.000 0.00 0.00 0.00 4.35
3896 4415 8.165397 TCCATCAATCATCATTGGAGCTATAAA 58.835 33.333 0.00 0.00 40.08 1.40
3909 4428 8.267183 AGTAGTATGTTGTTCCATCAATCATCA 58.733 33.333 0.00 0.00 0.00 3.07
3987 4506 2.558359 GCCAGGAGCAGTAACAACAATT 59.442 45.455 0.00 0.00 42.97 2.32
4010 4529 2.174639 TCAACCAAGTCTGAACCACCAT 59.825 45.455 0.00 0.00 0.00 3.55
4024 4543 0.698238 CAGTCCCCAGGATCAACCAA 59.302 55.000 0.00 0.00 42.04 3.67
4042 4561 6.933521 CCAATGTAAATCCAATCAAACAACCA 59.066 34.615 0.00 0.00 0.00 3.67
4060 4579 8.650490 TGCACTTGATAGAGATAATCCAATGTA 58.350 33.333 0.00 0.00 0.00 2.29
4065 4584 8.874156 ACTATTGCACTTGATAGAGATAATCCA 58.126 33.333 9.59 0.00 31.75 3.41
4205 4724 8.893727 ACAGAAAACCATGTATTTCACTATAGC 58.106 33.333 17.64 0.00 37.87 2.97


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

AutoCloner maintained by Alex Coulton.