Multiple sequence alignment - TraesCS6D01G057600

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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 TraesCS6D01G057600 chr6D 100.000 1714 0 0 1 1714 27419012 27417299 0.000000e+00 3166
1 TraesCS6D01G057600 chr6D 98.625 291 3 1 938 1227 45511483 45511193 4.180000e-142 514
2 TraesCS6D01G057600 chr6D 100.000 237 0 0 1959 2195 27417054 27416818 2.590000e-119 438
3 TraesCS6D01G057600 chr6D 95.238 63 3 0 1377 1439 65298568 65298630 1.390000e-17 100
4 TraesCS6D01G057600 chr6B 93.548 961 35 12 1 937 49982041 49981084 0.000000e+00 1406
5 TraesCS6D01G057600 chr6B 95.400 500 12 2 1226 1714 49981077 49980578 0.000000e+00 785
6 TraesCS6D01G057600 chr6B 96.035 227 7 2 1971 2195 49980491 49980265 3.440000e-98 368
7 TraesCS6D01G057600 chr1A 99.655 290 1 0 935 1224 554456290 554456579 4.150000e-147 531
8 TraesCS6D01G057600 chr1A 99.655 290 1 0 935 1224 554458552 554458841 4.150000e-147 531
9 TraesCS6D01G057600 chr3B 99.310 290 2 0 938 1227 101918957 101918668 1.930000e-145 525
10 TraesCS6D01G057600 chr3B 76.762 525 97 21 1 514 101638249 101638759 9.990000e-69 270
11 TraesCS6D01G057600 chr3B 95.714 70 3 0 1377 1446 830364391 830364322 1.780000e-21 113
12 TraesCS6D01G057600 chr3B 95.714 70 3 0 1377 1446 830653093 830653024 1.780000e-21 113
13 TraesCS6D01G057600 chr2D 99.310 290 2 0 935 1224 9785228 9785517 1.930000e-145 525
14 TraesCS6D01G057600 chr2D 76.199 542 101 23 4 532 601981358 601980832 6.010000e-66 261
15 TraesCS6D01G057600 chr1D 98.966 290 3 0 935 1224 254417150 254417439 8.980000e-144 520
16 TraesCS6D01G057600 chr5D 98.621 290 4 0 938 1227 6180858 6180569 4.180000e-142 514
17 TraesCS6D01G057600 chr5D 98.621 290 4 0 935 1224 503287384 503287673 4.180000e-142 514
18 TraesCS6D01G057600 chr2B 98.621 290 4 0 935 1224 474900427 474900716 4.180000e-142 514
19 TraesCS6D01G057600 chr2B 77.037 540 100 19 4 532 673956595 673956069 2.760000e-74 289
20 TraesCS6D01G057600 chr2B 96.875 64 2 0 1377 1440 155280632 155280569 8.290000e-20 108
21 TraesCS6D01G057600 chr2A 77.372 548 97 20 3 532 765368230 765367692 1.270000e-77 300
22 TraesCS6D01G057600 chr3A 79.714 419 77 6 3 414 705251200 705251617 1.650000e-76 296
23 TraesCS6D01G057600 chr3A 96.875 64 2 0 1377 1440 690954862 690954799 8.290000e-20 108
24 TraesCS6D01G057600 chrUn 77.393 491 92 15 33 513 26570317 26570798 7.720000e-70 274
25 TraesCS6D01G057600 chrUn 76.850 527 96 21 1 514 324145084 324145597 7.720000e-70 274
26 TraesCS6D01G057600 chr5B 76.111 540 107 17 4 532 704217226 704216698 1.670000e-66 263
27 TraesCS6D01G057600 chr5B 95.385 65 3 0 1377 1441 89691238 89691302 1.070000e-18 104
28 TraesCS6D01G057600 chr3D 93.243 74 3 2 1377 1449 193624033 193624105 8.290000e-20 108
29 TraesCS6D01G057600 chr7D 96.825 63 2 0 1377 1439 4584338 4584276 2.980000e-19 106


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 TraesCS6D01G057600 chr6D 27416818 27419012 2194 True 1802 3166 100.000000 1 2195 2 chr6D.!!$R2 2194
1 TraesCS6D01G057600 chr6B 49980265 49982041 1776 True 853 1406 94.994333 1 2195 3 chr6B.!!$R1 2194
2 TraesCS6D01G057600 chr1A 554456290 554458841 2551 False 531 531 99.655000 935 1224 2 chr1A.!!$F1 289
3 TraesCS6D01G057600 chr3B 101638249 101638759 510 False 270 270 76.762000 1 514 1 chr3B.!!$F1 513
4 TraesCS6D01G057600 chr2D 601980832 601981358 526 True 261 261 76.199000 4 532 1 chr2D.!!$R1 528
5 TraesCS6D01G057600 chr2B 673956069 673956595 526 True 289 289 77.037000 4 532 1 chr2B.!!$R2 528
6 TraesCS6D01G057600 chr2A 765367692 765368230 538 True 300 300 77.372000 3 532 1 chr2A.!!$R1 529
7 TraesCS6D01G057600 chrUn 324145084 324145597 513 False 274 274 76.850000 1 514 1 chrUn.!!$F2 513
8 TraesCS6D01G057600 chr5B 704216698 704217226 528 True 263 263 76.111000 4 532 1 chr5B.!!$R1 528

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
540 584 0.107017 ACAGCTACATGGGCATCACC 60.107 55.0 13.84 0.0 37.93 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2129 4392 1.960417 TCACCATGAAAACGCTGACA 58.04 45.0 0.0 0.0 0.0 3.58 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
80 87 3.557577 GCACATAGCAACATGAACACA 57.442 42.857 0.00 0.00 44.79 3.72
99 108 2.224281 ACACACATCAGAACACACCGAT 60.224 45.455 0.00 0.00 0.00 4.18
226 240 1.953686 CCAACCGTTTCTTGACACCAT 59.046 47.619 0.00 0.00 0.00 3.55
385 400 4.065088 TGCCTTCAACAAGATCACAGTAC 58.935 43.478 0.00 0.00 0.00 2.73
396 415 8.547967 ACAAGATCACAGTACAAAAATATCGT 57.452 30.769 0.00 0.00 0.00 3.73
540 584 0.107017 ACAGCTACATGGGCATCACC 60.107 55.000 13.84 0.00 37.93 4.02
577 621 6.647334 TGTTTTCCTTCAAGCAATATGACA 57.353 33.333 0.00 0.00 0.00 3.58
599 643 9.642327 TGACAAATGACAATCAATGGAAAATAG 57.358 29.630 0.00 0.00 0.00 1.73
696 740 1.222115 GCACTTCCACACACTCGTCC 61.222 60.000 0.00 0.00 0.00 4.79
715 759 7.703197 ACTCGTCCGATTTTTGTTTACAAATTT 59.297 29.630 8.70 0.58 44.30 1.82
760 804 8.554490 AAATAGCATAGGAGGACTCTTAGAAA 57.446 34.615 0.00 0.00 0.00 2.52
840 884 7.519002 CCAGTTTCTAAAATCGAAAGTGTAGG 58.481 38.462 15.22 2.03 44.47 3.18
875 919 5.308237 AGGGAATAGAATAGTTCCAAGCGAT 59.692 40.000 6.49 0.00 44.53 4.58
915 960 5.007682 ACCAAATAGTTGTTGCTCGGTTAT 58.992 37.500 1.80 0.00 32.40 1.89
1224 1545 9.113838 CTTTAGTACTCTGTATGCCAAATTGAT 57.886 33.333 0.00 0.00 0.00 2.57
1227 1548 6.886459 AGTACTCTGTATGCCAAATTGATTGT 59.114 34.615 0.00 0.00 37.32 2.71
1228 1549 8.046708 AGTACTCTGTATGCCAAATTGATTGTA 58.953 33.333 0.00 0.00 37.32 2.41
1229 1550 7.701539 ACTCTGTATGCCAAATTGATTGTAA 57.298 32.000 0.00 0.00 37.32 2.41
1231 1552 8.752187 ACTCTGTATGCCAAATTGATTGTAATT 58.248 29.630 0.00 0.00 37.32 1.40
1239 1560 9.716531 TGCCAAATTGATTGTAATTATGTTTGA 57.283 25.926 0.00 0.00 37.32 2.69
1240 1561 9.971744 GCCAAATTGATTGTAATTATGTTTGAC 57.028 29.630 0.00 0.00 37.32 3.18
1302 1623 8.874744 TTGACATTATTATCCATGCAATGTTG 57.125 30.769 0.00 0.00 44.81 3.33
1303 1624 8.009622 TGACATTATTATCCATGCAATGTTGT 57.990 30.769 0.00 0.00 44.81 3.32
1304 1625 8.476447 TGACATTATTATCCATGCAATGTTGTT 58.524 29.630 0.00 0.00 44.81 2.83
1305 1626 9.964303 GACATTATTATCCATGCAATGTTGTTA 57.036 29.630 0.00 0.00 44.81 2.41
1314 1635 8.574251 TCCATGCAATGTTGTTATTAAGTACT 57.426 30.769 0.00 0.00 44.81 2.73
1315 1636 8.673711 TCCATGCAATGTTGTTATTAAGTACTC 58.326 33.333 0.00 0.00 44.81 2.59
1347 1826 8.861033 TTTATTTGCTCTGCATATTAGCTTTG 57.139 30.769 0.00 0.00 38.76 2.77
1350 1829 4.516323 TGCTCTGCATATTAGCTTTGTCA 58.484 39.130 0.00 0.00 37.16 3.58
1352 1831 6.290605 TGCTCTGCATATTAGCTTTGTCATA 58.709 36.000 0.00 0.00 37.16 2.15
1356 1835 8.370493 TCTGCATATTAGCTTTGTCATAAGTC 57.630 34.615 0.00 0.00 34.99 3.01
1358 1837 8.504812 TGCATATTAGCTTTGTCATAAGTCAA 57.495 30.769 0.00 0.00 34.99 3.18
1360 1839 9.604626 GCATATTAGCTTTGTCATAAGTCAATC 57.395 33.333 0.00 0.00 0.00 2.67
1397 2797 9.802039 TTGACTAAATTTTATCTTGGTACCTGT 57.198 29.630 14.36 0.00 0.00 4.00
1412 3018 5.943416 TGGTACCTGTAATCTGAATTTGTGG 59.057 40.000 14.36 0.00 0.00 4.17
1413 3019 5.163652 GGTACCTGTAATCTGAATTTGTGGC 60.164 44.000 4.06 0.00 0.00 5.01
1414 3020 3.763897 ACCTGTAATCTGAATTTGTGGCC 59.236 43.478 0.00 0.00 0.00 5.36
1420 3026 8.995027 TGTAATCTGAATTTGTGGCCTTATAT 57.005 30.769 3.32 0.00 0.00 0.86
1439 3045 8.862091 CTTATATAAGGGAATGGAGGGAGTAT 57.138 38.462 13.82 0.00 0.00 2.12
1440 3046 9.953429 CTTATATAAGGGAATGGAGGGAGTATA 57.047 37.037 13.82 0.00 0.00 1.47
1447 3053 8.805145 AGGGAATGGAGGGAGTATATATTATG 57.195 38.462 0.00 0.00 0.00 1.90
1448 3054 8.362998 AGGGAATGGAGGGAGTATATATTATGT 58.637 37.037 0.00 0.00 0.00 2.29
1453 3716 8.888836 TGGAGGGAGTATATATTATGTCGAAA 57.111 34.615 0.00 0.00 0.00 3.46
1454 3717 9.488762 TGGAGGGAGTATATATTATGTCGAAAT 57.511 33.333 0.00 0.00 0.00 2.17
1455 3718 9.751542 GGAGGGAGTATATATTATGTCGAAATG 57.248 37.037 0.00 0.00 0.00 2.32
1472 3735 9.173021 TGTCGAAATGTATTCAATGGTAAATCT 57.827 29.630 0.00 0.00 0.00 2.40
1480 3743 9.693739 TGTATTCAATGGTAAATCTAATGGTGT 57.306 29.630 0.00 0.00 0.00 4.16
1486 3749 9.874205 CAATGGTAAATCTAATGGTGTTGATTT 57.126 29.630 0.00 0.00 40.69 2.17
1487 3750 9.874205 AATGGTAAATCTAATGGTGTTGATTTG 57.126 29.630 0.00 0.00 38.87 2.32
1488 3751 8.642935 TGGTAAATCTAATGGTGTTGATTTGA 57.357 30.769 0.00 0.00 38.87 2.69
1490 3753 8.519526 GGTAAATCTAATGGTGTTGATTTGACA 58.480 33.333 0.00 0.00 38.87 3.58
1493 3756 8.991243 AATCTAATGGTGTTGATTTGACATTG 57.009 30.769 0.00 0.00 31.71 2.82
1495 3758 7.592938 TCTAATGGTGTTGATTTGACATTGTC 58.407 34.615 9.93 9.93 31.71 3.18
1496 3759 4.221926 TGGTGTTGATTTGACATTGTCG 57.778 40.909 11.97 0.00 34.95 4.35
1498 3761 4.518590 TGGTGTTGATTTGACATTGTCGAT 59.481 37.500 11.97 8.46 34.95 3.59
1499 3762 5.088739 GGTGTTGATTTGACATTGTCGATC 58.911 41.667 18.68 18.68 34.95 3.69
1500 3763 5.106555 GGTGTTGATTTGACATTGTCGATCT 60.107 40.000 22.70 10.27 34.95 2.75
1501 3764 6.373779 GTGTTGATTTGACATTGTCGATCTT 58.626 36.000 22.70 8.55 34.95 2.40
1502 3765 7.360861 GGTGTTGATTTGACATTGTCGATCTTA 60.361 37.037 22.70 13.94 34.95 2.10
1503 3766 8.177663 GTGTTGATTTGACATTGTCGATCTTAT 58.822 33.333 22.70 10.10 34.95 1.73
1504 3767 8.177013 TGTTGATTTGACATTGTCGATCTTATG 58.823 33.333 22.70 0.00 34.95 1.90
1505 3768 6.718388 TGATTTGACATTGTCGATCTTATGC 58.282 36.000 22.70 7.07 34.95 3.14
1506 3769 6.539826 TGATTTGACATTGTCGATCTTATGCT 59.460 34.615 22.70 0.00 34.95 3.79
1507 3770 5.973651 TTGACATTGTCGATCTTATGCTC 57.026 39.130 11.97 0.00 34.95 4.26
1508 3771 5.009854 TGACATTGTCGATCTTATGCTCA 57.990 39.130 11.97 0.00 34.95 4.26
1509 3772 5.418676 TGACATTGTCGATCTTATGCTCAA 58.581 37.500 11.97 0.00 34.95 3.02
1510 3773 5.874261 TGACATTGTCGATCTTATGCTCAAA 59.126 36.000 11.97 0.00 34.95 2.69
1511 3774 6.036408 TGACATTGTCGATCTTATGCTCAAAG 59.964 38.462 11.97 0.00 34.95 2.77
1512 3775 5.877012 ACATTGTCGATCTTATGCTCAAAGT 59.123 36.000 0.00 0.00 0.00 2.66
1513 3776 6.372659 ACATTGTCGATCTTATGCTCAAAGTT 59.627 34.615 0.00 0.00 0.00 2.66
1514 3777 7.549134 ACATTGTCGATCTTATGCTCAAAGTTA 59.451 33.333 0.00 0.00 0.00 2.24
1515 3778 7.899178 TTGTCGATCTTATGCTCAAAGTTAA 57.101 32.000 0.00 0.00 0.00 2.01
1516 3779 7.290857 TGTCGATCTTATGCTCAAAGTTAAC 57.709 36.000 0.00 0.00 0.00 2.01
1517 3780 6.871492 TGTCGATCTTATGCTCAAAGTTAACA 59.129 34.615 8.61 0.00 0.00 2.41
1518 3781 7.386573 TGTCGATCTTATGCTCAAAGTTAACAA 59.613 33.333 8.61 0.00 0.00 2.83
1519 3782 8.227791 GTCGATCTTATGCTCAAAGTTAACAAA 58.772 33.333 8.61 0.00 0.00 2.83
1520 3783 8.443160 TCGATCTTATGCTCAAAGTTAACAAAG 58.557 33.333 8.61 0.69 0.00 2.77
1521 3784 8.230486 CGATCTTATGCTCAAAGTTAACAAAGT 58.770 33.333 8.61 0.00 0.00 2.66
1522 3785 9.899226 GATCTTATGCTCAAAGTTAACAAAGTT 57.101 29.630 8.61 0.00 0.00 2.66
1523 3786 9.899226 ATCTTATGCTCAAAGTTAACAAAGTTC 57.101 29.630 8.61 0.00 0.00 3.01
1524 3787 8.067784 TCTTATGCTCAAAGTTAACAAAGTTCG 58.932 33.333 8.61 0.00 0.00 3.95
1525 3788 5.804692 TGCTCAAAGTTAACAAAGTTCGA 57.195 34.783 8.61 0.00 0.00 3.71
1526 3789 5.565695 TGCTCAAAGTTAACAAAGTTCGAC 58.434 37.500 8.61 0.00 0.00 4.20
1527 3790 5.353123 TGCTCAAAGTTAACAAAGTTCGACT 59.647 36.000 8.61 0.00 0.00 4.18
1528 3791 5.902432 GCTCAAAGTTAACAAAGTTCGACTC 59.098 40.000 8.61 0.00 0.00 3.36
1529 3792 6.456449 GCTCAAAGTTAACAAAGTTCGACTCA 60.456 38.462 8.61 0.00 0.00 3.41
1530 3793 7.367159 TCAAAGTTAACAAAGTTCGACTCAA 57.633 32.000 8.61 0.00 0.00 3.02
1531 3794 7.461107 TCAAAGTTAACAAAGTTCGACTCAAG 58.539 34.615 8.61 0.00 0.00 3.02
1532 3795 7.332430 TCAAAGTTAACAAAGTTCGACTCAAGA 59.668 33.333 8.61 0.00 0.00 3.02
1533 3796 6.585389 AGTTAACAAAGTTCGACTCAAGAC 57.415 37.500 8.61 0.00 0.00 3.01
1534 3797 6.103997 AGTTAACAAAGTTCGACTCAAGACA 58.896 36.000 8.61 0.00 0.00 3.41
1535 3798 6.592607 AGTTAACAAAGTTCGACTCAAGACAA 59.407 34.615 8.61 0.00 0.00 3.18
1536 3799 5.873179 AACAAAGTTCGACTCAAGACAAA 57.127 34.783 0.00 0.00 0.00 2.83
1537 3800 5.470845 ACAAAGTTCGACTCAAGACAAAG 57.529 39.130 0.00 0.00 0.00 2.77
1538 3801 4.935808 ACAAAGTTCGACTCAAGACAAAGT 59.064 37.500 0.00 0.00 0.00 2.66
1539 3802 5.411669 ACAAAGTTCGACTCAAGACAAAGTT 59.588 36.000 0.00 0.00 0.00 2.66
1540 3803 6.592607 ACAAAGTTCGACTCAAGACAAAGTTA 59.407 34.615 0.00 0.00 0.00 2.24
1541 3804 7.118680 ACAAAGTTCGACTCAAGACAAAGTTAA 59.881 33.333 0.00 0.00 0.00 2.01
1542 3805 7.787725 AAGTTCGACTCAAGACAAAGTTAAT 57.212 32.000 0.00 0.00 0.00 1.40
1543 3806 8.882415 AAGTTCGACTCAAGACAAAGTTAATA 57.118 30.769 0.00 0.00 0.00 0.98
1544 3807 9.490379 AAGTTCGACTCAAGACAAAGTTAATAT 57.510 29.630 0.00 0.00 0.00 1.28
1545 3808 8.926710 AGTTCGACTCAAGACAAAGTTAATATG 58.073 33.333 0.00 0.00 0.00 1.78
1546 3809 8.922676 GTTCGACTCAAGACAAAGTTAATATGA 58.077 33.333 0.00 0.00 0.00 2.15
1547 3810 9.483916 TTCGACTCAAGACAAAGTTAATATGAA 57.516 29.630 0.00 0.00 0.00 2.57
1548 3811 9.140286 TCGACTCAAGACAAAGTTAATATGAAG 57.860 33.333 0.00 0.00 0.00 3.02
1549 3812 9.140286 CGACTCAAGACAAAGTTAATATGAAGA 57.860 33.333 0.00 0.00 0.00 2.87
1567 3830 6.790232 TGAAGAATAAATAAAAGCAGGGGG 57.210 37.500 0.00 0.00 0.00 5.40
1568 3831 6.260663 TGAAGAATAAATAAAAGCAGGGGGT 58.739 36.000 0.00 0.00 0.00 4.95
1569 3832 6.379988 TGAAGAATAAATAAAAGCAGGGGGTC 59.620 38.462 0.00 0.00 0.00 4.46
1570 3833 6.092346 AGAATAAATAAAAGCAGGGGGTCT 57.908 37.500 0.00 0.00 0.00 3.85
1571 3834 6.503041 AGAATAAATAAAAGCAGGGGGTCTT 58.497 36.000 0.00 0.00 0.00 3.01
1572 3835 7.648770 AGAATAAATAAAAGCAGGGGGTCTTA 58.351 34.615 0.00 0.00 0.00 2.10
1573 3836 7.780271 AGAATAAATAAAAGCAGGGGGTCTTAG 59.220 37.037 0.00 0.00 0.00 2.18
1574 3837 4.948062 AATAAAAGCAGGGGGTCTTAGT 57.052 40.909 0.00 0.00 0.00 2.24
1575 3838 4.948062 ATAAAAGCAGGGGGTCTTAGTT 57.052 40.909 0.00 0.00 0.00 2.24
1576 3839 6.397217 AATAAAAGCAGGGGGTCTTAGTTA 57.603 37.500 0.00 0.00 0.00 2.24
1577 3840 4.948062 AAAAGCAGGGGGTCTTAGTTAT 57.052 40.909 0.00 0.00 0.00 1.89
1578 3841 7.701257 ATAAAAGCAGGGGGTCTTAGTTATA 57.299 36.000 0.00 0.00 0.00 0.98
1579 3842 6.592207 AAAAGCAGGGGGTCTTAGTTATAT 57.408 37.500 0.00 0.00 0.00 0.86
1580 3843 6.592207 AAAGCAGGGGGTCTTAGTTATATT 57.408 37.500 0.00 0.00 0.00 1.28
1581 3844 5.827326 AGCAGGGGGTCTTAGTTATATTC 57.173 43.478 0.00 0.00 0.00 1.75
1582 3845 4.283722 AGCAGGGGGTCTTAGTTATATTCG 59.716 45.833 0.00 0.00 0.00 3.34
1583 3846 4.040095 GCAGGGGGTCTTAGTTATATTCGT 59.960 45.833 0.00 0.00 0.00 3.85
1584 3847 5.244626 GCAGGGGGTCTTAGTTATATTCGTA 59.755 44.000 0.00 0.00 0.00 3.43
1585 3848 6.070938 GCAGGGGGTCTTAGTTATATTCGTAT 60.071 42.308 0.00 0.00 0.00 3.06
1586 3849 7.545489 CAGGGGGTCTTAGTTATATTCGTATC 58.455 42.308 0.00 0.00 0.00 2.24
1587 3850 6.376581 AGGGGGTCTTAGTTATATTCGTATCG 59.623 42.308 0.00 0.00 0.00 2.92
1588 3851 6.151817 GGGGGTCTTAGTTATATTCGTATCGT 59.848 42.308 0.00 0.00 0.00 3.73
1589 3852 7.309438 GGGGGTCTTAGTTATATTCGTATCGTT 60.309 40.741 0.00 0.00 0.00 3.85
1590 3853 8.730680 GGGGTCTTAGTTATATTCGTATCGTTA 58.269 37.037 0.00 0.00 0.00 3.18
1991 4254 2.621055 GTGAGTGAGTGAGTGAGTGAGT 59.379 50.000 0.00 0.00 0.00 3.41
1992 4255 2.620585 TGAGTGAGTGAGTGAGTGAGTG 59.379 50.000 0.00 0.00 0.00 3.51
1993 4256 2.881513 GAGTGAGTGAGTGAGTGAGTGA 59.118 50.000 0.00 0.00 0.00 3.41
1994 4257 2.884012 AGTGAGTGAGTGAGTGAGTGAG 59.116 50.000 0.00 0.00 0.00 3.51
1995 4258 2.621055 GTGAGTGAGTGAGTGAGTGAGT 59.379 50.000 0.00 0.00 0.00 3.41
1996 4259 2.620585 TGAGTGAGTGAGTGAGTGAGTG 59.379 50.000 0.00 0.00 0.00 3.51
2129 4392 8.539674 GTTGAACTGTTCGCATTAATTTTCTTT 58.460 29.630 15.18 0.00 0.00 2.52
2180 4443 0.605589 GCTAGACGGAGATGGATGGG 59.394 60.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 32 2.082140 TGCAGAGACCGGGTATGTAT 57.918 50.000 6.32 0.00 0.00 2.29
65 67 4.133078 TGATGTGTGTGTTCATGTTGCTA 58.867 39.130 0.00 0.00 0.00 3.49
69 71 4.639755 TGTTCTGATGTGTGTGTTCATGTT 59.360 37.500 0.00 0.00 0.00 2.71
71 73 4.035441 TGTGTTCTGATGTGTGTGTTCATG 59.965 41.667 0.00 0.00 0.00 3.07
72 74 4.035558 GTGTGTTCTGATGTGTGTGTTCAT 59.964 41.667 0.00 0.00 0.00 2.57
73 75 3.373748 GTGTGTTCTGATGTGTGTGTTCA 59.626 43.478 0.00 0.00 0.00 3.18
74 76 3.242739 GGTGTGTTCTGATGTGTGTGTTC 60.243 47.826 0.00 0.00 0.00 3.18
75 77 2.682856 GGTGTGTTCTGATGTGTGTGTT 59.317 45.455 0.00 0.00 0.00 3.32
80 87 2.839486 ATCGGTGTGTTCTGATGTGT 57.161 45.000 0.00 0.00 32.89 3.72
99 108 8.856153 TGGTCTTGTATGACTTTGCTATTTTA 57.144 30.769 0.00 0.00 37.16 1.52
226 240 9.567776 TTAATGTTGAAGAATCTTGTTGTCCTA 57.432 29.630 0.00 0.00 0.00 2.94
313 328 6.215431 TCTTCAGGGTGAAATCCTAGAATTCA 59.785 38.462 8.44 0.00 35.73 2.57
396 415 6.183361 CCTGACTGGGTTATATCTGACAATGA 60.183 42.308 0.00 0.00 0.00 2.57
540 584 4.530875 AGGAAAACAAGGCAGAGGATATG 58.469 43.478 0.00 0.00 0.00 1.78
599 643 5.115773 GCGACGAGAAACATATCAGACATAC 59.884 44.000 0.00 0.00 0.00 2.39
725 769 9.750125 GTCCTCCTATGCTATTTTTAAAAATGG 57.250 33.333 28.45 26.59 38.90 3.16
733 777 8.554490 TCTAAGAGTCCTCCTATGCTATTTTT 57.446 34.615 0.00 0.00 0.00 1.94
738 782 7.839705 TCTTTTTCTAAGAGTCCTCCTATGCTA 59.160 37.037 0.00 0.00 0.00 3.49
760 804 9.331282 GTTAGATGCAGATATAAGTGGTTCTTT 57.669 33.333 0.00 0.00 37.56 2.52
815 859 7.386848 TCCTACACTTTCGATTTTAGAAACTGG 59.613 37.037 0.00 0.00 34.36 4.00
840 884 5.622346 ATTCTATTCCCTCCTTGTGTCTC 57.378 43.478 0.00 0.00 0.00 3.36
848 892 5.072464 GCTTGGAACTATTCTATTCCCTCCT 59.928 44.000 0.73 0.00 43.30 3.69
875 919 1.240256 GGTTCATTGGTTGCACCGTA 58.760 50.000 0.00 0.00 42.58 4.02
892 937 2.858745 ACCGAGCAACAACTATTTGGT 58.141 42.857 0.00 0.00 37.00 3.67
1276 1597 9.483916 CAACATTGCATGGATAATAATGTCAAT 57.516 29.630 2.46 0.00 40.07 2.57
1277 1598 8.476447 ACAACATTGCATGGATAATAATGTCAA 58.524 29.630 2.46 0.00 40.07 3.18
1278 1599 8.009622 ACAACATTGCATGGATAATAATGTCA 57.990 30.769 2.46 0.00 40.07 3.58
1279 1600 8.876275 AACAACATTGCATGGATAATAATGTC 57.124 30.769 2.46 0.00 40.07 3.06
1288 1609 9.189156 AGTACTTAATAACAACATTGCATGGAT 57.811 29.630 0.00 0.00 33.60 3.41
1289 1610 8.574251 AGTACTTAATAACAACATTGCATGGA 57.426 30.769 0.00 0.00 33.60 3.41
1290 1611 8.677300 AGAGTACTTAATAACAACATTGCATGG 58.323 33.333 0.00 0.00 33.60 3.66
1327 1648 4.943093 TGACAAAGCTAATATGCAGAGCAA 59.057 37.500 13.26 0.00 43.62 3.91
1329 1650 5.686159 ATGACAAAGCTAATATGCAGAGC 57.314 39.130 0.00 0.00 36.42 4.09
1330 1651 8.375608 ACTTATGACAAAGCTAATATGCAGAG 57.624 34.615 0.00 0.00 34.99 3.35
1332 1653 8.146479 TGACTTATGACAAAGCTAATATGCAG 57.854 34.615 0.00 0.00 34.99 4.41
1333 1654 8.504812 TTGACTTATGACAAAGCTAATATGCA 57.495 30.769 0.00 0.00 34.99 3.96
1334 1655 9.604626 GATTGACTTATGACAAAGCTAATATGC 57.395 33.333 0.00 0.00 32.36 3.14
1383 2783 9.613428 CAAATTCAGATTACAGGTACCAAGATA 57.387 33.333 15.94 0.00 0.00 1.98
1391 2791 4.947388 GGCCACAAATTCAGATTACAGGTA 59.053 41.667 0.00 0.00 0.00 3.08
1392 2792 3.763897 GGCCACAAATTCAGATTACAGGT 59.236 43.478 0.00 0.00 0.00 4.00
1393 2793 4.019174 AGGCCACAAATTCAGATTACAGG 58.981 43.478 5.01 0.00 0.00 4.00
1394 2794 5.649782 AAGGCCACAAATTCAGATTACAG 57.350 39.130 5.01 0.00 0.00 2.74
1395 2795 8.995027 ATATAAGGCCACAAATTCAGATTACA 57.005 30.769 5.01 0.00 0.00 2.41
1414 3020 8.862091 ATACTCCCTCCATTCCCTTATATAAG 57.138 38.462 14.56 14.56 0.00 1.73
1421 3027 9.230477 CATAATATATACTCCCTCCATTCCCTT 57.770 37.037 0.00 0.00 0.00 3.95
1424 3030 8.361139 CGACATAATATATACTCCCTCCATTCC 58.639 40.741 0.00 0.00 0.00 3.01
1426 3032 9.488762 TTCGACATAATATATACTCCCTCCATT 57.511 33.333 0.00 0.00 0.00 3.16
1427 3033 9.488762 TTTCGACATAATATATACTCCCTCCAT 57.511 33.333 0.00 0.00 0.00 3.41
1428 3034 8.888836 TTTCGACATAATATATACTCCCTCCA 57.111 34.615 0.00 0.00 0.00 3.86
1429 3035 9.751542 CATTTCGACATAATATATACTCCCTCC 57.248 37.037 0.00 0.00 0.00 4.30
1445 3051 9.950680 GATTTACCATTGAATACATTTCGACAT 57.049 29.630 0.00 0.00 0.00 3.06
1446 3052 9.173021 AGATTTACCATTGAATACATTTCGACA 57.827 29.630 0.00 0.00 0.00 4.35
1454 3717 9.693739 ACACCATTAGATTTACCATTGAATACA 57.306 29.630 0.00 0.00 0.00 2.29
1459 3722 8.821686 ATCAACACCATTAGATTTACCATTGA 57.178 30.769 0.00 0.00 0.00 2.57
1461 3724 9.874205 CAAATCAACACCATTAGATTTACCATT 57.126 29.630 0.00 0.00 38.30 3.16
1464 3727 8.519526 TGTCAAATCAACACCATTAGATTTACC 58.480 33.333 0.00 0.00 38.30 2.85
1467 3730 9.426837 CAATGTCAAATCAACACCATTAGATTT 57.573 29.630 0.00 0.00 40.29 2.17
1472 3735 6.205658 TCGACAATGTCAAATCAACACCATTA 59.794 34.615 14.24 0.00 32.09 1.90
1476 3739 4.481930 TCGACAATGTCAAATCAACACC 57.518 40.909 14.24 0.00 32.09 4.16
1480 3743 7.066163 AGCATAAGATCGACAATGTCAAATCAA 59.934 33.333 20.66 12.52 31.20 2.57
1481 3744 6.539826 AGCATAAGATCGACAATGTCAAATCA 59.460 34.615 20.66 7.82 31.20 2.57
1482 3745 6.952743 AGCATAAGATCGACAATGTCAAATC 58.047 36.000 14.24 14.32 32.09 2.17
1486 3749 5.009854 TGAGCATAAGATCGACAATGTCA 57.990 39.130 14.24 1.25 31.29 3.58
1487 3750 5.973651 TTGAGCATAAGATCGACAATGTC 57.026 39.130 2.75 2.75 31.29 3.06
1488 3751 5.877012 ACTTTGAGCATAAGATCGACAATGT 59.123 36.000 0.00 0.00 31.29 2.71
1490 3753 6.992063 AACTTTGAGCATAAGATCGACAAT 57.008 33.333 0.00 0.00 31.29 2.71
1492 3755 6.871492 TGTTAACTTTGAGCATAAGATCGACA 59.129 34.615 7.22 0.00 31.29 4.35
1493 3756 7.290857 TGTTAACTTTGAGCATAAGATCGAC 57.709 36.000 7.22 0.00 31.29 4.20
1495 3758 8.230486 ACTTTGTTAACTTTGAGCATAAGATCG 58.770 33.333 7.22 0.00 31.29 3.69
1496 3759 9.899226 AACTTTGTTAACTTTGAGCATAAGATC 57.101 29.630 7.22 0.00 0.00 2.75
1498 3761 8.067784 CGAACTTTGTTAACTTTGAGCATAAGA 58.932 33.333 7.22 0.00 0.00 2.10
1499 3762 8.067784 TCGAACTTTGTTAACTTTGAGCATAAG 58.932 33.333 7.22 0.00 0.00 1.73
1500 3763 7.853929 GTCGAACTTTGTTAACTTTGAGCATAA 59.146 33.333 7.22 0.00 0.00 1.90
1501 3764 7.225931 AGTCGAACTTTGTTAACTTTGAGCATA 59.774 33.333 7.22 0.00 0.00 3.14
1502 3765 6.038271 AGTCGAACTTTGTTAACTTTGAGCAT 59.962 34.615 7.22 0.00 0.00 3.79
1503 3766 5.353123 AGTCGAACTTTGTTAACTTTGAGCA 59.647 36.000 7.22 0.00 0.00 4.26
1504 3767 5.807344 AGTCGAACTTTGTTAACTTTGAGC 58.193 37.500 7.22 0.00 0.00 4.26
1505 3768 7.000575 TGAGTCGAACTTTGTTAACTTTGAG 57.999 36.000 7.22 2.40 0.00 3.02
1506 3769 6.971527 TGAGTCGAACTTTGTTAACTTTGA 57.028 33.333 7.22 0.00 0.00 2.69
1507 3770 7.425595 GTCTTGAGTCGAACTTTGTTAACTTTG 59.574 37.037 7.22 0.00 0.00 2.77
1508 3771 7.118680 TGTCTTGAGTCGAACTTTGTTAACTTT 59.881 33.333 7.22 0.00 0.00 2.66
1509 3772 6.592607 TGTCTTGAGTCGAACTTTGTTAACTT 59.407 34.615 7.22 0.00 0.00 2.66
1510 3773 6.103997 TGTCTTGAGTCGAACTTTGTTAACT 58.896 36.000 7.22 0.00 0.00 2.24
1511 3774 6.340537 TGTCTTGAGTCGAACTTTGTTAAC 57.659 37.500 0.00 0.00 0.00 2.01
1512 3775 6.971527 TTGTCTTGAGTCGAACTTTGTTAA 57.028 33.333 0.00 0.00 0.00 2.01
1513 3776 6.592607 ACTTTGTCTTGAGTCGAACTTTGTTA 59.407 34.615 0.00 0.00 0.00 2.41
1514 3777 5.411669 ACTTTGTCTTGAGTCGAACTTTGTT 59.588 36.000 0.00 0.00 0.00 2.83
1515 3778 4.935808 ACTTTGTCTTGAGTCGAACTTTGT 59.064 37.500 0.00 0.00 0.00 2.83
1516 3779 5.470845 ACTTTGTCTTGAGTCGAACTTTG 57.529 39.130 0.00 0.00 0.00 2.77
1517 3780 7.605410 TTAACTTTGTCTTGAGTCGAACTTT 57.395 32.000 0.00 0.00 0.00 2.66
1518 3781 7.787725 ATTAACTTTGTCTTGAGTCGAACTT 57.212 32.000 0.00 0.00 0.00 2.66
1519 3782 8.926710 CATATTAACTTTGTCTTGAGTCGAACT 58.073 33.333 0.00 0.00 0.00 3.01
1520 3783 8.922676 TCATATTAACTTTGTCTTGAGTCGAAC 58.077 33.333 0.00 0.00 0.00 3.95
1521 3784 9.483916 TTCATATTAACTTTGTCTTGAGTCGAA 57.516 29.630 0.00 0.00 0.00 3.71
1522 3785 9.140286 CTTCATATTAACTTTGTCTTGAGTCGA 57.860 33.333 0.00 0.00 0.00 4.20
1523 3786 9.140286 TCTTCATATTAACTTTGTCTTGAGTCG 57.860 33.333 0.00 0.00 0.00 4.18
1541 3804 9.093458 CCCCCTGCTTTTATTTATTCTTCATAT 57.907 33.333 0.00 0.00 0.00 1.78
1542 3805 8.065007 ACCCCCTGCTTTTATTTATTCTTCATA 58.935 33.333 0.00 0.00 0.00 2.15
1543 3806 6.902974 ACCCCCTGCTTTTATTTATTCTTCAT 59.097 34.615 0.00 0.00 0.00 2.57
1544 3807 6.260663 ACCCCCTGCTTTTATTTATTCTTCA 58.739 36.000 0.00 0.00 0.00 3.02
1545 3808 6.607600 AGACCCCCTGCTTTTATTTATTCTTC 59.392 38.462 0.00 0.00 0.00 2.87
1546 3809 6.503041 AGACCCCCTGCTTTTATTTATTCTT 58.497 36.000 0.00 0.00 0.00 2.52
1547 3810 6.092346 AGACCCCCTGCTTTTATTTATTCT 57.908 37.500 0.00 0.00 0.00 2.40
1548 3811 6.791867 AAGACCCCCTGCTTTTATTTATTC 57.208 37.500 0.00 0.00 0.00 1.75
1549 3812 7.419203 ACTAAGACCCCCTGCTTTTATTTATT 58.581 34.615 0.00 0.00 0.00 1.40
1550 3813 6.981737 ACTAAGACCCCCTGCTTTTATTTAT 58.018 36.000 0.00 0.00 0.00 1.40
1551 3814 6.397217 ACTAAGACCCCCTGCTTTTATTTA 57.603 37.500 0.00 0.00 0.00 1.40
1552 3815 5.270979 ACTAAGACCCCCTGCTTTTATTT 57.729 39.130 0.00 0.00 0.00 1.40
1553 3816 4.948062 ACTAAGACCCCCTGCTTTTATT 57.052 40.909 0.00 0.00 0.00 1.40
1554 3817 4.948062 AACTAAGACCCCCTGCTTTTAT 57.052 40.909 0.00 0.00 0.00 1.40
1555 3818 7.701257 ATATAACTAAGACCCCCTGCTTTTA 57.299 36.000 0.00 0.00 0.00 1.52
1556 3819 4.948062 ATAACTAAGACCCCCTGCTTTT 57.052 40.909 0.00 0.00 0.00 2.27
1557 3820 6.592207 AATATAACTAAGACCCCCTGCTTT 57.408 37.500 0.00 0.00 0.00 3.51
1558 3821 5.221661 CGAATATAACTAAGACCCCCTGCTT 60.222 44.000 0.00 0.00 0.00 3.91
1559 3822 4.283722 CGAATATAACTAAGACCCCCTGCT 59.716 45.833 0.00 0.00 0.00 4.24
1560 3823 4.040095 ACGAATATAACTAAGACCCCCTGC 59.960 45.833 0.00 0.00 0.00 4.85
1561 3824 5.803237 ACGAATATAACTAAGACCCCCTG 57.197 43.478 0.00 0.00 0.00 4.45
1562 3825 6.376581 CGATACGAATATAACTAAGACCCCCT 59.623 42.308 0.00 0.00 0.00 4.79
1563 3826 6.151817 ACGATACGAATATAACTAAGACCCCC 59.848 42.308 0.00 0.00 0.00 5.40
1564 3827 7.150783 ACGATACGAATATAACTAAGACCCC 57.849 40.000 0.00 0.00 0.00 4.95
1958 4221 4.045104 CACTCACTCACTTAGTCACACAC 58.955 47.826 0.00 0.00 35.76 3.82
1959 4222 3.951680 TCACTCACTCACTTAGTCACACA 59.048 43.478 0.00 0.00 35.76 3.72
1960 4223 4.036971 ACTCACTCACTCACTTAGTCACAC 59.963 45.833 0.00 0.00 35.76 3.82
1961 4224 4.036852 CACTCACTCACTCACTTAGTCACA 59.963 45.833 0.00 0.00 35.76 3.58
2006 4269 8.726988 TGGTTTGTATGCTTTAGAGATTTGTAC 58.273 33.333 0.00 0.00 0.00 2.90
2110 4373 6.143758 GCTGACAAAGAAAATTAATGCGAACA 59.856 34.615 0.00 0.00 0.00 3.18
2129 4392 1.960417 TCACCATGAAAACGCTGACA 58.040 45.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.