Multiple sequence alignment - TraesCS4A01G140400

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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 TraesCS4A01G140400 chr4A 100.000 4589 0 0 1 4589 215954945 215959533 0.000000e+00 8475
1 TraesCS4A01G140400 chr4A 96.926 553 9 3 11 555 216007454 216008006 0.000000e+00 920
2 TraesCS4A01G140400 chr7A 95.921 4045 138 10 554 4589 57795926 57791900 0.000000e+00 6530
3 TraesCS4A01G140400 chr7A 95.518 2811 115 8 1784 4587 732248969 732246163 0.000000e+00 4482
4 TraesCS4A01G140400 chr7A 94.765 1108 56 2 678 1783 732295900 732294793 0.000000e+00 1724
5 TraesCS4A01G140400 chr4B 96.041 3663 136 8 555 4213 63769435 63773092 0.000000e+00 5952
6 TraesCS4A01G140400 chr4B 90.102 293 9 9 158 450 361984294 361984022 3.370000e-96 363
7 TraesCS4A01G140400 chr4B 90.000 250 9 5 158 407 361996968 361996735 4.460000e-80 309
8 TraesCS4A01G140400 chr4B 88.125 160 11 3 1 160 361999333 361999182 2.820000e-42 183
9 TraesCS4A01G140400 chr5B 95.545 3636 151 6 581 4213 537887373 537883746 0.000000e+00 5806
10 TraesCS4A01G140400 chr5B 95.853 2170 83 6 556 2720 545611739 545609572 0.000000e+00 3502
11 TraesCS4A01G140400 chr3A 97.056 2955 74 9 1637 4586 689009220 689012166 0.000000e+00 4963
12 TraesCS4A01G140400 chr3A 95.404 2981 129 6 1613 4589 113916272 113913296 0.000000e+00 4739
13 TraesCS4A01G140400 chr3A 96.528 144 5 0 4446 4589 113913115 113912972 5.930000e-59 239
14 TraesCS4A01G140400 chr3A 94.444 144 8 0 4446 4589 709934119 709933976 5.980000e-54 222
15 TraesCS4A01G140400 chr3A 93.793 145 8 1 4446 4589 37074619 37074763 2.780000e-52 217
16 TraesCS4A01G140400 chrUn 95.607 2982 120 8 1613 4587 241092453 241089476 0.000000e+00 4771
17 TraesCS4A01G140400 chrUn 95.372 2982 126 9 1613 4587 83847802 83844826 0.000000e+00 4732
18 TraesCS4A01G140400 chrUn 94.856 1108 55 2 678 1783 83848568 83847461 0.000000e+00 1729
19 TraesCS4A01G140400 chrUn 94.856 1108 55 2 678 1783 281117757 281118864 0.000000e+00 1729
20 TraesCS4A01G140400 chrUn 94.675 1108 57 2 678 1783 387009198 387010305 0.000000e+00 1718
21 TraesCS4A01G140400 chrUn 94.495 1108 59 2 678 1783 241093219 241092112 0.000000e+00 1707
22 TraesCS4A01G140400 chr3B 95.922 2722 105 5 1495 4213 31615742 31618460 0.000000e+00 4407
23 TraesCS4A01G140400 chr4D 89.767 430 24 7 126 555 294092273 294091864 2.430000e-147 532
24 TraesCS4A01G140400 chr5A 97.163 141 4 0 4446 4586 17491982 17492122 5.930000e-59 239
25 TraesCS4A01G140400 chr5A 96.454 141 4 1 4446 4586 17491661 17491800 9.930000e-57 231


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 TraesCS4A01G140400 chr4A 215954945 215959533 4588 False 8475.0 8475 100.0000 1 4589 1 chr4A.!!$F1 4588
1 TraesCS4A01G140400 chr4A 216007454 216008006 552 False 920.0 920 96.9260 11 555 1 chr4A.!!$F2 544
2 TraesCS4A01G140400 chr7A 57791900 57795926 4026 True 6530.0 6530 95.9210 554 4589 1 chr7A.!!$R1 4035
3 TraesCS4A01G140400 chr7A 732246163 732248969 2806 True 4482.0 4482 95.5180 1784 4587 1 chr7A.!!$R2 2803
4 TraesCS4A01G140400 chr7A 732294793 732295900 1107 True 1724.0 1724 94.7650 678 1783 1 chr7A.!!$R3 1105
5 TraesCS4A01G140400 chr4B 63769435 63773092 3657 False 5952.0 5952 96.0410 555 4213 1 chr4B.!!$F1 3658
6 TraesCS4A01G140400 chr4B 361996735 361999333 2598 True 246.0 309 89.0625 1 407 2 chr4B.!!$R2 406
7 TraesCS4A01G140400 chr5B 537883746 537887373 3627 True 5806.0 5806 95.5450 581 4213 1 chr5B.!!$R1 3632
8 TraesCS4A01G140400 chr5B 545609572 545611739 2167 True 3502.0 3502 95.8530 556 2720 1 chr5B.!!$R2 2164
9 TraesCS4A01G140400 chr3A 689009220 689012166 2946 False 4963.0 4963 97.0560 1637 4586 1 chr3A.!!$F2 2949
10 TraesCS4A01G140400 chr3A 113912972 113916272 3300 True 2489.0 4739 95.9660 1613 4589 2 chr3A.!!$R2 2976
11 TraesCS4A01G140400 chrUn 241089476 241093219 3743 True 3239.0 4771 95.0510 678 4587 2 chrUn.!!$R2 3909
12 TraesCS4A01G140400 chrUn 83844826 83848568 3742 True 3230.5 4732 95.1140 678 4587 2 chrUn.!!$R1 3909
13 TraesCS4A01G140400 chrUn 281117757 281118864 1107 False 1729.0 1729 94.8560 678 1783 1 chrUn.!!$F1 1105
14 TraesCS4A01G140400 chrUn 387009198 387010305 1107 False 1718.0 1718 94.6750 678 1783 1 chrUn.!!$F2 1105
15 TraesCS4A01G140400 chr3B 31615742 31618460 2718 False 4407.0 4407 95.9220 1495 4213 1 chr3B.!!$F1 2718

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
621 2851 0.321671 CACAAGGACGGTCCAGATGT 59.678 55.000 27.87 23.71 39.61 3.06 F
1081 3313 0.525668 GACCGTGACAGATAGCGTGG 60.526 60.000 0.00 0.00 0.00 4.94 F
1329 3576 0.544833 TCCGTTGCTAGTTACCCCCA 60.545 55.000 0.00 0.00 0.00 4.96 F
1391 3638 1.000521 TTGCTGCATCCCCTTCTGG 60.001 57.895 1.84 0.00 0.00 3.86 F
2867 6153 4.662468 TTGCATTGCCTGTCAAAAACTA 57.338 36.364 6.12 0.00 38.34 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1460 3707 5.767670 AGCCTAACTACTTGATCTACTGGA 58.232 41.667 0.00 0.00 0.00 3.86 R
3030 6316 4.006319 GCATAATGATGGGAAGCTCCTAC 58.994 47.826 0.00 0.00 36.57 3.18 R
3040 6326 6.819649 ACAAGTTGATTTTGCATAATGATGGG 59.180 34.615 10.54 0.00 33.26 4.00 R
3387 6673 0.267658 TAGCAGATCCTTGGGCCCTA 59.732 55.000 25.70 15.88 0.00 3.53 R
3998 7284 0.109781 GCATGTTACACAAGGCCACG 60.110 55.000 5.01 0.00 0.00 4.94 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
103 105 6.357367 ACTGCTCCTTTGATCGGTTAATATT 58.643 36.000 0.00 0.00 0.00 1.28
196 2413 1.668151 GACACGTGTCCTTGCTCCC 60.668 63.158 33.62 9.82 39.07 4.30
197 2414 2.377628 GACACGTGTCCTTGCTCCCA 62.378 60.000 33.62 0.00 39.07 4.37
198 2415 1.003355 CACGTGTCCTTGCTCCCAT 60.003 57.895 7.58 0.00 0.00 4.00
199 2416 0.606401 CACGTGTCCTTGCTCCCATT 60.606 55.000 7.58 0.00 0.00 3.16
200 2417 0.981183 ACGTGTCCTTGCTCCCATTA 59.019 50.000 0.00 0.00 0.00 1.90
210 2432 3.916359 TGCTCCCATTACATTAACCGA 57.084 42.857 0.00 0.00 0.00 4.69
454 2676 9.702494 ATACGTTTCTACTGCTTTACTTACTTT 57.298 29.630 0.00 0.00 0.00 2.66
456 2678 9.189723 ACGTTTCTACTGCTTTACTTACTTTAG 57.810 33.333 0.00 0.00 0.00 1.85
520 2748 3.991773 CTCCTCTCGATCTAGTACTTCCG 59.008 52.174 0.00 0.08 0.00 4.30
529 2757 5.404968 CGATCTAGTACTTCCGTCTACGAAT 59.595 44.000 0.00 0.00 43.02 3.34
565 2793 1.961277 CCGGACAGCGTTTCTGCTT 60.961 57.895 0.00 0.00 44.46 3.91
573 2801 1.941812 CGTTTCTGCTTCGGTGCTT 59.058 52.632 2.64 0.00 0.00 3.91
588 2818 3.170362 CTTCCCCTGGGCTGAACA 58.830 61.111 7.39 0.00 34.68 3.18
621 2851 0.321671 CACAAGGACGGTCCAGATGT 59.678 55.000 27.87 23.71 39.61 3.06
636 2866 0.739462 GATGTGTCGATGGCGGTTCA 60.739 55.000 0.00 0.00 38.28 3.18
778 3008 3.283684 CTGGCGGTTGCGTTTCCA 61.284 61.111 0.00 0.00 44.10 3.53
819 3051 2.944349 GTGTTCGTGGGTAGTTTCCAAA 59.056 45.455 0.00 0.00 35.86 3.28
888 3120 2.550175 CCACCCCATTTCCTCCAAATT 58.450 47.619 0.00 0.00 31.79 1.82
1012 3244 2.906458 CTCGGATGGAGCAAGGCT 59.094 61.111 0.00 0.00 43.88 4.58
1081 3313 0.525668 GACCGTGACAGATAGCGTGG 60.526 60.000 0.00 0.00 0.00 4.94
1329 3576 0.544833 TCCGTTGCTAGTTACCCCCA 60.545 55.000 0.00 0.00 0.00 4.96
1391 3638 1.000521 TTGCTGCATCCCCTTCTGG 60.001 57.895 1.84 0.00 0.00 3.86
1451 3698 9.743057 AATGAATGTTAAGTTTCGATTTTGTGA 57.257 25.926 0.00 0.00 0.00 3.58
1452 3699 9.912634 ATGAATGTTAAGTTTCGATTTTGTGAT 57.087 25.926 0.00 0.00 0.00 3.06
1453 3700 9.743057 TGAATGTTAAGTTTCGATTTTGTGATT 57.257 25.926 0.00 0.00 0.00 2.57
1454 3701 9.993881 GAATGTTAAGTTTCGATTTTGTGATTG 57.006 29.630 0.00 0.00 0.00 2.67
1455 3702 9.743057 AATGTTAAGTTTCGATTTTGTGATTGA 57.257 25.926 0.00 0.00 0.00 2.57
1456 3703 9.743057 ATGTTAAGTTTCGATTTTGTGATTGAA 57.257 25.926 0.00 0.00 0.00 2.69
1457 3704 9.743057 TGTTAAGTTTCGATTTTGTGATTGAAT 57.257 25.926 0.00 0.00 31.29 2.57
1459 3706 9.958234 TTAAGTTTCGATTTTGTGATTGAATCA 57.042 25.926 3.29 3.29 36.84 2.57
1461 3708 8.679288 AGTTTCGATTTTGTGATTGAATCATC 57.321 30.769 11.46 3.58 42.04 2.92
1462 3709 7.756722 AGTTTCGATTTTGTGATTGAATCATCC 59.243 33.333 11.46 0.00 42.04 3.51
1463 3710 6.756299 TCGATTTTGTGATTGAATCATCCA 57.244 33.333 11.46 2.79 42.04 3.41
1464 3711 6.788243 TCGATTTTGTGATTGAATCATCCAG 58.212 36.000 11.46 0.79 42.04 3.86
1465 3712 6.375174 TCGATTTTGTGATTGAATCATCCAGT 59.625 34.615 11.46 0.00 42.04 4.00
1466 3713 7.552330 TCGATTTTGTGATTGAATCATCCAGTA 59.448 33.333 11.46 0.00 42.04 2.74
1467 3714 7.854422 CGATTTTGTGATTGAATCATCCAGTAG 59.146 37.037 11.46 0.00 42.04 2.57
1468 3715 8.812513 ATTTTGTGATTGAATCATCCAGTAGA 57.187 30.769 11.46 0.00 42.04 2.59
1469 3716 8.812513 TTTTGTGATTGAATCATCCAGTAGAT 57.187 30.769 11.46 0.00 42.04 1.98
1470 3717 8.442632 TTTGTGATTGAATCATCCAGTAGATC 57.557 34.615 11.46 0.00 42.04 2.75
1471 3718 7.128234 TGTGATTGAATCATCCAGTAGATCA 57.872 36.000 11.46 0.00 42.04 2.92
1472 3719 7.567458 TGTGATTGAATCATCCAGTAGATCAA 58.433 34.615 11.46 0.00 42.04 2.57
1473 3720 7.713942 TGTGATTGAATCATCCAGTAGATCAAG 59.286 37.037 11.46 0.00 42.04 3.02
1474 3721 7.714377 GTGATTGAATCATCCAGTAGATCAAGT 59.286 37.037 11.46 0.00 42.04 3.16
1475 3722 8.927411 TGATTGAATCATCCAGTAGATCAAGTA 58.073 33.333 3.29 0.00 33.59 2.24
1476 3723 9.421806 GATTGAATCATCCAGTAGATCAAGTAG 57.578 37.037 0.00 0.00 30.59 2.57
1477 3724 7.904558 TGAATCATCCAGTAGATCAAGTAGT 57.095 36.000 0.00 0.00 30.59 2.73
1478 3725 8.311395 TGAATCATCCAGTAGATCAAGTAGTT 57.689 34.615 0.00 0.00 30.59 2.24
1479 3726 9.421399 TGAATCATCCAGTAGATCAAGTAGTTA 57.579 33.333 0.00 0.00 30.59 2.24
1480 3727 9.906660 GAATCATCCAGTAGATCAAGTAGTTAG 57.093 37.037 0.00 0.00 30.59 2.34
1481 3728 7.825331 TCATCCAGTAGATCAAGTAGTTAGG 57.175 40.000 0.00 0.00 30.59 2.69
1482 3729 6.265649 TCATCCAGTAGATCAAGTAGTTAGGC 59.734 42.308 0.00 0.00 30.59 3.93
1483 3730 5.767670 TCCAGTAGATCAAGTAGTTAGGCT 58.232 41.667 0.00 0.00 0.00 4.58
1484 3731 6.195700 TCCAGTAGATCAAGTAGTTAGGCTT 58.804 40.000 0.00 0.00 0.00 4.35
1485 3732 6.668283 TCCAGTAGATCAAGTAGTTAGGCTTT 59.332 38.462 0.00 0.00 0.00 3.51
1486 3733 7.180408 TCCAGTAGATCAAGTAGTTAGGCTTTT 59.820 37.037 0.00 0.00 0.00 2.27
1487 3734 7.824779 CCAGTAGATCAAGTAGTTAGGCTTTTT 59.175 37.037 0.00 0.00 0.00 1.94
1539 3787 6.889177 TGTATTGGATTCAATTAGAGGCACAA 59.111 34.615 4.09 0.00 42.90 3.33
1641 3889 5.536161 TGTGATCGAATCATCCAGTAGATCA 59.464 40.000 0.00 1.65 42.04 2.92
1642 3890 6.040842 TGTGATCGAATCATCCAGTAGATCAA 59.959 38.462 6.78 0.00 42.74 2.57
1643 3891 6.585702 GTGATCGAATCATCCAGTAGATCAAG 59.414 42.308 6.78 0.00 42.74 3.02
1644 3892 6.266330 TGATCGAATCATCCAGTAGATCAAGT 59.734 38.462 0.00 0.00 39.67 3.16
1645 3893 7.448469 TGATCGAATCATCCAGTAGATCAAGTA 59.552 37.037 0.00 0.00 39.67 2.24
1646 3894 7.208225 TCGAATCATCCAGTAGATCAAGTAG 57.792 40.000 0.00 0.00 30.59 2.57
1647 3895 6.773200 TCGAATCATCCAGTAGATCAAGTAGT 59.227 38.462 0.00 0.00 30.59 2.73
1648 3896 7.285629 TCGAATCATCCAGTAGATCAAGTAGTT 59.714 37.037 0.00 0.00 30.59 2.24
1649 3897 8.568794 CGAATCATCCAGTAGATCAAGTAGTTA 58.431 37.037 0.00 0.00 30.59 2.24
1650 3898 9.906660 GAATCATCCAGTAGATCAAGTAGTTAG 57.093 37.037 0.00 0.00 30.59 2.34
1651 3899 7.825331 TCATCCAGTAGATCAAGTAGTTAGG 57.175 40.000 0.00 0.00 30.59 2.69
1652 3900 7.583625 TCATCCAGTAGATCAAGTAGTTAGGA 58.416 38.462 0.00 0.00 30.59 2.94
1653 3901 8.228206 TCATCCAGTAGATCAAGTAGTTAGGAT 58.772 37.037 0.00 0.00 30.59 3.24
1654 3902 8.865090 CATCCAGTAGATCAAGTAGTTAGGATT 58.135 37.037 0.00 0.00 30.59 3.01
1655 3903 8.840200 TCCAGTAGATCAAGTAGTTAGGATTT 57.160 34.615 0.00 0.00 0.00 2.17
1656 3904 9.268282 TCCAGTAGATCAAGTAGTTAGGATTTT 57.732 33.333 0.00 0.00 0.00 1.82
1657 3905 9.892130 CCAGTAGATCAAGTAGTTAGGATTTTT 57.108 33.333 0.00 0.00 0.00 1.94
1679 3927 8.713708 TTTTTAATGAGATGTTAAGTTGGGGA 57.286 30.769 0.00 0.00 0.00 4.81
1680 3928 8.893563 TTTTAATGAGATGTTAAGTTGGGGAT 57.106 30.769 0.00 0.00 0.00 3.85
1681 3929 8.893563 TTTAATGAGATGTTAAGTTGGGGATT 57.106 30.769 0.00 0.00 0.00 3.01
1682 3930 8.893563 TTAATGAGATGTTAAGTTGGGGATTT 57.106 30.769 0.00 0.00 0.00 2.17
1683 3931 7.797121 AATGAGATGTTAAGTTGGGGATTTT 57.203 32.000 0.00 0.00 0.00 1.82
1684 3932 7.797121 ATGAGATGTTAAGTTGGGGATTTTT 57.203 32.000 0.00 0.00 0.00 1.94
1709 3957 9.679661 TTTGTATTAGATTCAATTAGAGGCACA 57.320 29.630 0.00 0.00 0.00 4.57
1710 3958 9.679661 TTGTATTAGATTCAATTAGAGGCACAA 57.320 29.630 0.00 0.00 0.00 3.33
1711 3959 9.679661 TGTATTAGATTCAATTAGAGGCACAAA 57.320 29.630 0.00 0.00 0.00 2.83
1716 3964 8.757982 AGATTCAATTAGAGGCACAAATATGT 57.242 30.769 0.00 0.00 41.61 2.29
1717 3965 9.193806 AGATTCAATTAGAGGCACAAATATGTT 57.806 29.630 0.00 0.00 37.82 2.71
1718 3966 9.241317 GATTCAATTAGAGGCACAAATATGTTG 57.759 33.333 0.00 0.00 37.82 3.33
1719 3967 7.701539 TCAATTAGAGGCACAAATATGTTGT 57.298 32.000 0.00 0.00 37.82 3.32
1720 3968 8.800370 TCAATTAGAGGCACAAATATGTTGTA 57.200 30.769 3.86 0.00 37.82 2.41
1721 3969 9.407380 TCAATTAGAGGCACAAATATGTTGTAT 57.593 29.630 3.86 0.00 37.82 2.29
1722 3970 9.669353 CAATTAGAGGCACAAATATGTTGTATC 57.331 33.333 3.86 3.91 37.82 2.24
1723 3971 9.632638 AATTAGAGGCACAAATATGTTGTATCT 57.367 29.630 3.86 8.77 37.82 1.98
1724 3972 6.932356 AGAGGCACAAATATGTTGTATCTG 57.068 37.500 3.86 0.00 37.82 2.90
1725 3973 6.418101 AGAGGCACAAATATGTTGTATCTGT 58.582 36.000 3.86 2.18 37.82 3.41
1726 3974 6.317140 AGAGGCACAAATATGTTGTATCTGTG 59.683 38.462 0.95 0.95 37.82 3.66
1727 3975 6.179756 AGGCACAAATATGTTGTATCTGTGA 58.820 36.000 7.81 0.00 37.82 3.58
1728 3976 6.830324 AGGCACAAATATGTTGTATCTGTGAT 59.170 34.615 7.81 0.00 37.82 3.06
1729 3977 7.340232 AGGCACAAATATGTTGTATCTGTGATT 59.660 33.333 7.81 0.00 37.82 2.57
1730 3978 7.433131 GGCACAAATATGTTGTATCTGTGATTG 59.567 37.037 7.81 0.00 37.82 2.67
1731 3979 8.183536 GCACAAATATGTTGTATCTGTGATTGA 58.816 33.333 7.81 0.00 37.82 2.57
1760 4008 7.455641 CATCCAGTAGATGTACTAGTTAGGG 57.544 44.000 0.00 0.00 46.32 3.53
1761 4009 6.587560 TCCAGTAGATGTACTAGTTAGGGT 57.412 41.667 0.00 0.00 37.40 4.34
1762 4010 6.978261 TCCAGTAGATGTACTAGTTAGGGTT 58.022 40.000 0.00 0.00 37.40 4.11
1763 4011 7.416731 TCCAGTAGATGTACTAGTTAGGGTTT 58.583 38.462 0.00 0.00 37.40 3.27
1764 4012 7.559170 TCCAGTAGATGTACTAGTTAGGGTTTC 59.441 40.741 0.00 0.00 37.40 2.78
1765 4013 7.560626 CCAGTAGATGTACTAGTTAGGGTTTCT 59.439 40.741 0.00 0.00 37.40 2.52
1766 4014 8.968969 CAGTAGATGTACTAGTTAGGGTTTCTT 58.031 37.037 0.00 0.00 37.40 2.52
2092 5372 9.905713 TTTTGTACTAGATTCAATTAGAGCCAT 57.094 29.630 0.00 0.00 0.00 4.40
2783 6069 8.939929 TGAGAACTGCTCTGAACTAAATATTTG 58.060 33.333 11.05 3.88 44.27 2.32
2867 6153 4.662468 TTGCATTGCCTGTCAAAAACTA 57.338 36.364 6.12 0.00 38.34 2.24
3040 6326 8.808092 AGTGTATGAAATATAGGTAGGAGCTTC 58.192 37.037 0.00 0.00 0.00 3.86
3266 6552 6.968131 TGTGCATTGACTTAGTGTTAGATC 57.032 37.500 0.00 0.00 0.00 2.75
3387 6673 3.180507 AGAGAAGGAGGTGCTGAAGATT 58.819 45.455 0.00 0.00 0.00 2.40
3521 6807 0.035881 CGGGCTACATCCATCAGCAT 59.964 55.000 0.00 0.00 37.02 3.79
3568 6854 0.768221 TTCTGCCCTCCACAAGGTCT 60.768 55.000 0.00 0.00 44.56 3.85
3965 7251 2.360350 CTGCGGCCATGTGGAACT 60.360 61.111 2.24 0.00 38.04 3.01
3967 7253 0.676466 CTGCGGCCATGTGGAACTTA 60.676 55.000 2.24 0.00 38.04 2.24
3970 7256 1.406341 GCGGCCATGTGGAACTTACTA 60.406 52.381 2.24 0.00 38.04 1.82
3998 7284 4.734398 TGGTGCAATAAATTCCCATGTC 57.266 40.909 0.00 0.00 0.00 3.06
4010 7296 1.600636 CCATGTCGTGGCCTTGTGT 60.601 57.895 3.32 0.00 42.12 3.72
4139 7426 8.156820 TGACATCTTTCCTTCATTTGAGTAAGA 58.843 33.333 0.00 0.00 0.00 2.10
4180 7467 8.408043 TCCACCATATGATCAAATATTCCAAC 57.592 34.615 3.65 0.00 0.00 3.77
4383 7677 1.776662 TATAGTGGCTCCGTGAAGCT 58.223 50.000 2.32 0.00 42.13 3.74
4395 7689 1.129251 CGTGAAGCTGCATGTTTCGAT 59.871 47.619 5.65 0.00 38.50 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 105 2.093128 GGAGGACGCTTCCCATTTTCTA 60.093 50.000 5.45 0.00 44.10 2.10
210 2432 2.359169 ACGGCCTGGTCGACATGAT 61.359 57.895 29.43 0.00 33.65 2.45
281 2503 1.002857 ACTGGGAGGCCTATGCTTTT 58.997 50.000 4.42 0.00 37.74 2.27
334 2556 5.748630 AGGAATTCGTTTGCTTTTGTCTTTC 59.251 36.000 0.00 0.00 30.85 2.62
454 2676 2.174107 CGTCGTCGTCGGTTGCTA 59.826 61.111 3.90 0.00 37.69 3.49
456 2678 3.456039 GTCGTCGTCGTCGGTTGC 61.456 66.667 11.74 0.00 38.33 4.17
520 2748 4.233789 GCCATCTCATCTCATTCGTAGAC 58.766 47.826 0.00 0.00 34.32 2.59
529 2757 0.543277 GGTGTGGCCATCTCATCTCA 59.457 55.000 9.72 0.00 37.17 3.27
573 2801 3.636231 CGTGTTCAGCCCAGGGGA 61.636 66.667 7.91 0.00 37.50 4.81
588 2818 2.021457 CCTTGTGTTTTTCCCACTCGT 58.979 47.619 0.00 0.00 33.92 4.18
621 2851 1.206132 AGTTATGAACCGCCATCGACA 59.794 47.619 0.00 0.00 38.10 4.35
636 2866 1.692519 GACCATCGTGCCCCTAGTTAT 59.307 52.381 0.00 0.00 0.00 1.89
724 2954 3.900446 GCCCGGCGTACAATAGTAT 57.100 52.632 6.01 0.00 31.84 2.12
819 3051 6.126739 CCTCCTCTTATACTAGGTGGCTTTTT 60.127 42.308 7.42 0.00 39.11 1.94
827 3059 4.447470 CGTTCCCCTCCTCTTATACTAGGT 60.447 50.000 0.00 0.00 34.30 3.08
888 3120 2.955246 AGGAGGGAGAGGGAGGCA 60.955 66.667 0.00 0.00 0.00 4.75
967 3199 1.206849 CAAGCAGGAGAAGAGAGGGAC 59.793 57.143 0.00 0.00 0.00 4.46
1036 3268 1.110442 CCCGTCTTCTGCAGATCTCT 58.890 55.000 19.04 0.00 32.60 3.10
1069 3301 0.033011 AGGGTCTCCACGCTATCTGT 60.033 55.000 0.00 0.00 43.81 3.41
1106 3338 2.446848 GGGGATGCAGCAGCTCCTA 61.447 63.158 23.20 0.00 42.74 2.94
1151 3383 2.045047 ACCTTCTTCTCCTCCAGATCCA 59.955 50.000 0.00 0.00 0.00 3.41
1329 3576 7.002276 ACTAACACCCAAAACTACTGCTTAAT 58.998 34.615 0.00 0.00 0.00 1.40
1426 3673 9.912634 ATCACAAAATCGAAACTTAACATTCAT 57.087 25.926 0.00 0.00 0.00 2.57
1431 3678 9.743057 ATTCAATCACAAAATCGAAACTTAACA 57.257 25.926 0.00 0.00 0.00 2.41
1440 3687 6.375174 ACTGGATGATTCAATCACAAAATCGA 59.625 34.615 0.98 0.00 43.01 3.59
1441 3688 6.558009 ACTGGATGATTCAATCACAAAATCG 58.442 36.000 0.98 0.00 43.01 3.34
1442 3689 8.896744 TCTACTGGATGATTCAATCACAAAATC 58.103 33.333 0.98 0.00 43.01 2.17
1443 3690 8.812513 TCTACTGGATGATTCAATCACAAAAT 57.187 30.769 0.98 0.00 43.01 1.82
1444 3691 8.812513 ATCTACTGGATGATTCAATCACAAAA 57.187 30.769 0.98 0.00 43.01 2.44
1445 3692 8.048514 TGATCTACTGGATGATTCAATCACAAA 58.951 33.333 0.98 0.00 43.01 2.83
1446 3693 7.567458 TGATCTACTGGATGATTCAATCACAA 58.433 34.615 0.98 0.00 43.01 3.33
1447 3694 7.128234 TGATCTACTGGATGATTCAATCACA 57.872 36.000 0.98 0.00 43.01 3.58
1448 3695 7.714377 ACTTGATCTACTGGATGATTCAATCAC 59.286 37.037 0.98 0.00 43.01 3.06
1449 3696 7.799081 ACTTGATCTACTGGATGATTCAATCA 58.201 34.615 1.59 1.59 44.55 2.57
1450 3697 9.421806 CTACTTGATCTACTGGATGATTCAATC 57.578 37.037 0.00 0.00 34.33 2.67
1451 3698 8.932610 ACTACTTGATCTACTGGATGATTCAAT 58.067 33.333 0.00 0.00 34.33 2.57
1452 3699 8.311395 ACTACTTGATCTACTGGATGATTCAA 57.689 34.615 0.00 0.00 34.33 2.69
1453 3700 7.904558 ACTACTTGATCTACTGGATGATTCA 57.095 36.000 0.00 0.00 34.33 2.57
1454 3701 9.906660 CTAACTACTTGATCTACTGGATGATTC 57.093 37.037 0.00 0.00 34.33 2.52
1455 3702 8.865090 CCTAACTACTTGATCTACTGGATGATT 58.135 37.037 0.00 0.00 34.33 2.57
1456 3703 7.039363 GCCTAACTACTTGATCTACTGGATGAT 60.039 40.741 0.00 0.00 34.33 2.45
1457 3704 6.265649 GCCTAACTACTTGATCTACTGGATGA 59.734 42.308 0.00 0.00 34.33 2.92
1458 3705 6.266558 AGCCTAACTACTTGATCTACTGGATG 59.733 42.308 0.00 0.00 34.33 3.51
1459 3706 6.377912 AGCCTAACTACTTGATCTACTGGAT 58.622 40.000 0.00 0.00 37.37 3.41
1460 3707 5.767670 AGCCTAACTACTTGATCTACTGGA 58.232 41.667 0.00 0.00 0.00 3.86
1461 3708 6.472686 AAGCCTAACTACTTGATCTACTGG 57.527 41.667 0.00 0.00 0.00 4.00
1462 3709 8.779354 AAAAAGCCTAACTACTTGATCTACTG 57.221 34.615 0.00 0.00 0.00 2.74
1517 3765 6.855763 TTTGTGCCTCTAATTGAATCCAAT 57.144 33.333 0.00 0.00 44.38 3.16
1534 3782 8.183536 TCAATCACAGATACAACATATTTGTGC 58.816 33.333 10.99 5.88 38.88 4.57
1568 3816 7.560626 AGAAACCCTAACTAGTACATCTACTGG 59.439 40.741 0.00 0.00 37.46 4.00
1616 3864 5.852282 TCTACTGGATGATTCGATCACAA 57.148 39.130 0.00 0.00 43.01 3.33
1654 3902 8.713708 TCCCCAACTTAACATCTCATTAAAAA 57.286 30.769 0.00 0.00 0.00 1.94
1655 3903 8.893563 ATCCCCAACTTAACATCTCATTAAAA 57.106 30.769 0.00 0.00 0.00 1.52
1656 3904 8.893563 AATCCCCAACTTAACATCTCATTAAA 57.106 30.769 0.00 0.00 0.00 1.52
1657 3905 8.893563 AAATCCCCAACTTAACATCTCATTAA 57.106 30.769 0.00 0.00 0.00 1.40
1658 3906 8.893563 AAAATCCCCAACTTAACATCTCATTA 57.106 30.769 0.00 0.00 0.00 1.90
1659 3907 7.797121 AAAATCCCCAACTTAACATCTCATT 57.203 32.000 0.00 0.00 0.00 2.57
1660 3908 7.797121 AAAAATCCCCAACTTAACATCTCAT 57.203 32.000 0.00 0.00 0.00 2.90
1683 3931 9.679661 TGTGCCTCTAATTGAATCTAATACAAA 57.320 29.630 0.00 0.00 0.00 2.83
1684 3932 9.679661 TTGTGCCTCTAATTGAATCTAATACAA 57.320 29.630 0.00 0.00 0.00 2.41
1685 3933 9.679661 TTTGTGCCTCTAATTGAATCTAATACA 57.320 29.630 0.00 0.00 0.00 2.29
1690 3938 9.851686 ACATATTTGTGCCTCTAATTGAATCTA 57.148 29.630 0.00 0.00 33.85 1.98
1691 3939 8.757982 ACATATTTGTGCCTCTAATTGAATCT 57.242 30.769 0.00 0.00 33.85 2.40
1692 3940 9.241317 CAACATATTTGTGCCTCTAATTGAATC 57.759 33.333 0.00 0.00 35.83 2.52
1693 3941 8.752187 ACAACATATTTGTGCCTCTAATTGAAT 58.248 29.630 0.00 0.00 35.83 2.57
1694 3942 8.121305 ACAACATATTTGTGCCTCTAATTGAA 57.879 30.769 0.00 0.00 35.83 2.69
1695 3943 7.701539 ACAACATATTTGTGCCTCTAATTGA 57.298 32.000 0.00 0.00 35.83 2.57
1696 3944 9.669353 GATACAACATATTTGTGCCTCTAATTG 57.331 33.333 11.29 0.00 35.83 2.32
1697 3945 9.632638 AGATACAACATATTTGTGCCTCTAATT 57.367 29.630 11.29 0.00 35.83 1.40
1698 3946 9.060347 CAGATACAACATATTTGTGCCTCTAAT 57.940 33.333 11.29 0.00 35.83 1.73
1699 3947 8.046708 ACAGATACAACATATTTGTGCCTCTAA 58.953 33.333 11.29 0.00 35.83 2.10
1700 3948 7.495606 CACAGATACAACATATTTGTGCCTCTA 59.504 37.037 11.29 0.00 34.68 2.43
1701 3949 6.317140 CACAGATACAACATATTTGTGCCTCT 59.683 38.462 11.29 8.62 34.68 3.69
1702 3950 6.316140 TCACAGATACAACATATTTGTGCCTC 59.684 38.462 10.99 7.21 38.88 4.70
1703 3951 6.179756 TCACAGATACAACATATTTGTGCCT 58.820 36.000 10.99 6.99 38.88 4.75
1704 3952 6.435430 TCACAGATACAACATATTTGTGCC 57.565 37.500 10.99 5.50 38.88 5.01
1705 3953 8.183536 TCAATCACAGATACAACATATTTGTGC 58.816 33.333 10.99 5.88 38.88 4.57
1737 3985 7.164233 ACCCTAACTAGTACATCTACTGGAT 57.836 40.000 0.00 0.00 35.51 3.41
1738 3986 6.587560 ACCCTAACTAGTACATCTACTGGA 57.412 41.667 0.00 0.00 35.51 3.86
1739 3987 7.560626 AGAAACCCTAACTAGTACATCTACTGG 59.439 40.741 0.00 0.00 37.46 4.00
1740 3988 8.522542 AGAAACCCTAACTAGTACATCTACTG 57.477 38.462 0.00 0.00 34.79 2.74
1770 4018 9.942850 TCAATCACAGAATCAACTAAACATCTA 57.057 29.630 0.00 0.00 0.00 1.98
1771 4019 8.853077 TCAATCACAGAATCAACTAAACATCT 57.147 30.769 0.00 0.00 0.00 2.90
1772 4020 9.334693 GTTCAATCACAGAATCAACTAAACATC 57.665 33.333 0.00 0.00 0.00 3.06
1773 4021 8.849168 TGTTCAATCACAGAATCAACTAAACAT 58.151 29.630 0.00 0.00 0.00 2.71
1774 4022 8.219546 TGTTCAATCACAGAATCAACTAAACA 57.780 30.769 0.00 0.00 0.00 2.83
1775 4023 9.683069 AATGTTCAATCACAGAATCAACTAAAC 57.317 29.630 0.00 0.00 0.00 2.01
1776 4024 9.681692 CAATGTTCAATCACAGAATCAACTAAA 57.318 29.630 0.00 0.00 0.00 1.85
1777 4025 8.849168 ACAATGTTCAATCACAGAATCAACTAA 58.151 29.630 0.00 0.00 0.00 2.24
1778 4026 8.291740 CACAATGTTCAATCACAGAATCAACTA 58.708 33.333 0.00 0.00 0.00 2.24
1779 4027 7.143340 CACAATGTTCAATCACAGAATCAACT 58.857 34.615 0.00 0.00 0.00 3.16
1780 4028 6.919662 ACACAATGTTCAATCACAGAATCAAC 59.080 34.615 0.00 0.00 0.00 3.18
1781 4029 7.041635 ACACAATGTTCAATCACAGAATCAA 57.958 32.000 0.00 0.00 0.00 2.57
1782 4030 6.638096 ACACAATGTTCAATCACAGAATCA 57.362 33.333 0.00 0.00 0.00 2.57
2464 5745 8.846943 AAATGAATCCAATACAAAAGAAACCC 57.153 30.769 0.00 0.00 0.00 4.11
2713 5999 7.337942 AGAATAAGTGAAATGGTGAAGCCTAAG 59.662 37.037 0.00 0.00 38.35 2.18
2854 6140 7.993183 ACCCATGATATAGTAGTTTTTGACAGG 59.007 37.037 0.00 0.00 0.00 4.00
3030 6316 4.006319 GCATAATGATGGGAAGCTCCTAC 58.994 47.826 0.00 0.00 36.57 3.18
3040 6326 6.819649 ACAAGTTGATTTTGCATAATGATGGG 59.180 34.615 10.54 0.00 33.26 4.00
3300 6586 8.962884 ATTGATACTGCACACATTAATGACTA 57.037 30.769 22.16 3.07 0.00 2.59
3387 6673 0.267658 TAGCAGATCCTTGGGCCCTA 59.732 55.000 25.70 15.88 0.00 3.53
3488 6774 1.153086 GCCCGACAATGCTCCATCT 60.153 57.895 0.00 0.00 0.00 2.90
3521 6807 3.776969 AGCCCTGATCTTGTAGTCATGAA 59.223 43.478 0.00 0.00 32.81 2.57
3568 6854 4.974645 ACTACATGTCAGGGTTTCTCAA 57.025 40.909 0.00 0.00 0.00 3.02
3998 7284 0.109781 GCATGTTACACAAGGCCACG 60.110 55.000 5.01 0.00 0.00 4.94
4010 7296 2.092484 TGCTTATGGGCAGAGCATGTTA 60.092 45.455 0.00 0.00 41.15 2.41
4180 7467 6.446781 AATGAAGGAATATGTGCTCAGTTG 57.553 37.500 0.00 0.00 0.00 3.16
4383 7677 0.747644 ATGCCGGATCGAAACATGCA 60.748 50.000 5.05 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.