Multiple sequence alignment - TraesCS4B01G255400

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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 TraesCS4B01G255400 chr4B 100.000 4075 0 0 1 4075 520243140 520239066 0.000000e+00 7526.0
1 TraesCS4B01G255400 chr4B 89.595 346 31 1 1 341 56981689 56982034 6.260000e-118 435.0
2 TraesCS4B01G255400 chr4B 82.195 483 61 12 1 472 23679495 23679963 3.820000e-105 392.0
3 TraesCS4B01G255400 chr4B 88.312 77 9 0 3999 4075 520230743 520230667 4.340000e-15 93.5
4 TraesCS4B01G255400 chr4D 93.621 2477 94 23 738 3194 423947836 423945404 0.000000e+00 3640.0
5 TraesCS4B01G255400 chr4D 95.255 548 25 1 3528 4075 423908690 423908144 0.000000e+00 867.0
6 TraesCS4B01G255400 chr4D 95.035 141 6 1 3389 3528 423944709 423944569 1.910000e-53 220.0
7 TraesCS4B01G255400 chr4D 96.040 101 4 0 3291 3391 423945266 423945166 9.060000e-37 165.0
8 TraesCS4B01G255400 chr4D 98.077 52 1 0 3200 3251 423945315 423945264 1.560000e-14 91.6
9 TraesCS4B01G255400 chr4D 91.304 46 4 0 4009 4054 423881695 423881650 3.400000e-06 63.9
10 TraesCS4B01G255400 chr4A 95.469 1523 51 10 1838 3357 40282864 40284371 0.000000e+00 2414.0
11 TraesCS4B01G255400 chr4A 87.108 1117 81 30 738 1834 40281665 40282738 0.000000e+00 1206.0
12 TraesCS4B01G255400 chr4A 95.010 521 25 1 3555 4075 40435105 40435624 0.000000e+00 817.0
13 TraesCS4B01G255400 chr4A 95.699 93 4 0 3470 3562 40285473 40285565 2.540000e-32 150.0
14 TraesCS4B01G255400 chr6D 91.185 692 37 3 4 676 462176693 462176007 0.000000e+00 918.0
15 TraesCS4B01G255400 chr2D 89.322 693 49 8 4 674 622249661 622248972 0.000000e+00 846.0
16 TraesCS4B01G255400 chr5D 89.099 688 54 5 7 674 436784175 436783489 0.000000e+00 835.0
17 TraesCS4B01G255400 chr5D 89.552 402 27 8 287 674 471831288 471830888 2.830000e-136 496.0
18 TraesCS4B01G255400 chr5D 88.308 402 32 3 287 674 471619858 471619458 6.170000e-128 468.0
19 TraesCS4B01G255400 chr5D 88.308 402 32 3 287 674 471695280 471694880 6.170000e-128 468.0
20 TraesCS4B01G255400 chr5D 88.308 402 32 3 287 674 471771650 471771250 6.170000e-128 468.0
21 TraesCS4B01G255400 chr5D 86.550 342 41 1 5 341 53764966 53764625 4.970000e-99 372.0
22 TraesCS4B01G255400 chr3D 84.490 677 83 5 17 674 512695182 512695855 0.000000e+00 649.0
23 TraesCS4B01G255400 chrUn 88.032 493 38 4 208 680 28920642 28920151 7.650000e-157 564.0
24 TraesCS4B01G255400 chr5A 80.379 581 63 23 113 674 644016683 644017231 1.060000e-105 394.0
25 TraesCS4B01G255400 chr3A 84.887 397 52 7 284 679 747396503 747396892 1.060000e-105 394.0
26 TraesCS4B01G255400 chr2B 82.195 483 61 17 4 472 410163474 410163003 3.820000e-105 392.0
27 TraesCS4B01G255400 chr1D 85.443 316 37 3 34 341 296972694 296973008 1.830000e-83 320.0
28 TraesCS4B01G255400 chr1A 90.741 54 2 3 3507 3558 68456878 68456826 7.310000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G255400 chr4B 520239066 520243140 4074 True 7526.000000 7526 100.000000 1 4075 1 chr4B.!!$R2 4074
1 TraesCS4B01G255400 chr4D 423944569 423947836 3267 True 1029.150000 3640 95.693250 738 3528 4 chr4D.!!$R3 2790
2 TraesCS4B01G255400 chr4D 423908144 423908690 546 True 867.000000 867 95.255000 3528 4075 1 chr4D.!!$R2 547
3 TraesCS4B01G255400 chr4A 40281665 40285565 3900 False 1256.666667 2414 92.758667 738 3562 3 chr4A.!!$F2 2824
4 TraesCS4B01G255400 chr4A 40435105 40435624 519 False 817.000000 817 95.010000 3555 4075 1 chr4A.!!$F1 520
5 TraesCS4B01G255400 chr6D 462176007 462176693 686 True 918.000000 918 91.185000 4 676 1 chr6D.!!$R1 672
6 TraesCS4B01G255400 chr2D 622248972 622249661 689 True 846.000000 846 89.322000 4 674 1 chr2D.!!$R1 670
7 TraesCS4B01G255400 chr5D 436783489 436784175 686 True 835.000000 835 89.099000 7 674 1 chr5D.!!$R2 667
8 TraesCS4B01G255400 chr3D 512695182 512695855 673 False 649.000000 649 84.490000 17 674 1 chr3D.!!$F1 657
9 TraesCS4B01G255400 chr5A 644016683 644017231 548 False 394.000000 394 80.379000 113 674 1 chr5A.!!$F1 561

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
687 711 0.107703 TTTGCCTATGCTCGTCCCTG 60.108 55.0 0.00 0.0 38.71 4.45 F
711 735 0.317160 TGACCATCACTGACACGTCC 59.683 55.0 0.00 0.0 0.00 4.79 F
727 751 0.318699 GTCCTTTGCCTGCGGTTTTC 60.319 55.0 0.00 0.0 0.00 2.29 F
1565 1624 0.469070 CAGCCTGGCTTGATAGCTCT 59.531 55.0 20.79 0.0 46.90 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 1735 0.548510 CCTGGTCCCCTCAGAAATCC 59.451 60.000 0.00 0.0 34.36 3.01 R
1727 1789 1.472480 GCCAACATTCCAAGCGTACAT 59.528 47.619 0.00 0.0 0.00 2.29 R
1758 1820 1.963747 GCGTTGGCAACTTACACATC 58.036 50.000 26.26 0.0 39.62 3.06 R
3279 3550 0.339859 AGCTGGGTCCCACTCATAGA 59.660 55.000 6.47 0.0 0.00 1.98 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
110 112 6.561737 TTTGTGAAACTTGCCGTGATATTA 57.438 33.333 0.00 0.00 38.04 0.98
299 306 1.493022 TGCAAAACACAGGACCCTACT 59.507 47.619 0.00 0.00 0.00 2.57
344 351 4.028490 CAACCTACCGCCAGCCCA 62.028 66.667 0.00 0.00 0.00 5.36
395 418 4.751060 TCGTCACAGAAACTTTACACTGT 58.249 39.130 0.00 0.00 43.05 3.55
495 518 2.831685 ACTTATCCACGTCAGCACAA 57.168 45.000 0.00 0.00 0.00 3.33
567 590 1.691801 GGTAGCCTGCCTAACCCTACT 60.692 57.143 0.00 0.00 31.47 2.57
619 643 7.277760 GGGTCAAATCCCGAAAATATTTCAAAG 59.722 37.037 0.10 0.00 37.93 2.77
634 658 2.832838 TCAAAGCAGGGTCAGATCCTA 58.167 47.619 0.32 0.00 32.49 2.94
635 659 2.501723 TCAAAGCAGGGTCAGATCCTAC 59.498 50.000 0.32 0.00 32.49 3.18
676 700 5.694458 GGTCAAAACACGAAATTTTGCCTAT 59.306 36.000 5.27 0.00 43.62 2.57
677 701 6.346518 GGTCAAAACACGAAATTTTGCCTATG 60.347 38.462 5.27 0.00 43.62 2.23
678 702 5.176590 TCAAAACACGAAATTTTGCCTATGC 59.823 36.000 5.27 0.00 43.62 3.14
679 703 4.519540 AACACGAAATTTTGCCTATGCT 57.480 36.364 5.27 0.00 38.71 3.79
680 704 4.096732 ACACGAAATTTTGCCTATGCTC 57.903 40.909 5.27 0.00 38.71 4.26
681 705 3.100817 CACGAAATTTTGCCTATGCTCG 58.899 45.455 5.27 0.00 38.71 5.03
682 706 2.747446 ACGAAATTTTGCCTATGCTCGT 59.253 40.909 5.27 0.00 38.71 4.18
683 707 3.181510 ACGAAATTTTGCCTATGCTCGTC 60.182 43.478 5.27 0.00 38.71 4.20
684 708 3.695816 GAAATTTTGCCTATGCTCGTCC 58.304 45.455 0.00 0.00 38.71 4.79
685 709 1.680338 ATTTTGCCTATGCTCGTCCC 58.320 50.000 0.00 0.00 38.71 4.46
686 710 0.618458 TTTTGCCTATGCTCGTCCCT 59.382 50.000 0.00 0.00 38.71 4.20
687 711 0.107703 TTTGCCTATGCTCGTCCCTG 60.108 55.000 0.00 0.00 38.71 4.45
688 712 0.975556 TTGCCTATGCTCGTCCCTGA 60.976 55.000 0.00 0.00 38.71 3.86
689 713 0.760567 TGCCTATGCTCGTCCCTGAT 60.761 55.000 0.00 0.00 38.71 2.90
690 714 1.257743 GCCTATGCTCGTCCCTGATA 58.742 55.000 0.00 0.00 33.53 2.15
691 715 1.067495 GCCTATGCTCGTCCCTGATAC 60.067 57.143 0.00 0.00 33.53 2.24
692 716 2.520069 CCTATGCTCGTCCCTGATACT 58.480 52.381 0.00 0.00 0.00 2.12
693 717 2.230025 CCTATGCTCGTCCCTGATACTG 59.770 54.545 0.00 0.00 0.00 2.74
694 718 2.073252 ATGCTCGTCCCTGATACTGA 57.927 50.000 0.00 0.00 0.00 3.41
695 719 1.103803 TGCTCGTCCCTGATACTGAC 58.896 55.000 0.00 0.00 0.00 3.51
696 720 0.386113 GCTCGTCCCTGATACTGACC 59.614 60.000 0.00 0.00 0.00 4.02
697 721 1.763968 CTCGTCCCTGATACTGACCA 58.236 55.000 0.00 0.00 0.00 4.02
698 722 2.311463 CTCGTCCCTGATACTGACCAT 58.689 52.381 0.00 0.00 0.00 3.55
699 723 2.294791 CTCGTCCCTGATACTGACCATC 59.705 54.545 0.00 0.00 0.00 3.51
700 724 2.031870 CGTCCCTGATACTGACCATCA 58.968 52.381 0.00 0.00 0.00 3.07
701 725 2.223829 CGTCCCTGATACTGACCATCAC 60.224 54.545 0.00 0.00 0.00 3.06
702 726 3.034635 GTCCCTGATACTGACCATCACT 58.965 50.000 0.00 0.00 0.00 3.41
703 727 3.033909 TCCCTGATACTGACCATCACTG 58.966 50.000 0.00 0.00 0.00 3.66
704 728 3.033909 CCCTGATACTGACCATCACTGA 58.966 50.000 0.00 0.00 0.00 3.41
705 729 3.181471 CCCTGATACTGACCATCACTGAC 60.181 52.174 0.00 0.00 0.00 3.51
706 730 3.448660 CCTGATACTGACCATCACTGACA 59.551 47.826 0.00 0.00 0.00 3.58
707 731 4.428209 CTGATACTGACCATCACTGACAC 58.572 47.826 0.00 0.00 0.00 3.67
708 732 3.119495 TGATACTGACCATCACTGACACG 60.119 47.826 0.00 0.00 0.00 4.49
709 733 1.040646 ACTGACCATCACTGACACGT 58.959 50.000 0.00 0.00 0.00 4.49
710 734 1.000163 ACTGACCATCACTGACACGTC 60.000 52.381 0.00 0.00 0.00 4.34
711 735 0.317160 TGACCATCACTGACACGTCC 59.683 55.000 0.00 0.00 0.00 4.79
712 736 0.603569 GACCATCACTGACACGTCCT 59.396 55.000 0.00 0.00 0.00 3.85
713 737 1.000955 GACCATCACTGACACGTCCTT 59.999 52.381 0.00 0.00 0.00 3.36
714 738 1.416401 ACCATCACTGACACGTCCTTT 59.584 47.619 0.00 0.00 0.00 3.11
715 739 1.800586 CCATCACTGACACGTCCTTTG 59.199 52.381 0.00 0.00 0.00 2.77
716 740 1.195448 CATCACTGACACGTCCTTTGC 59.805 52.381 0.00 0.00 0.00 3.68
717 741 0.531974 TCACTGACACGTCCTTTGCC 60.532 55.000 0.00 0.00 0.00 4.52
718 742 0.532862 CACTGACACGTCCTTTGCCT 60.533 55.000 0.00 0.00 0.00 4.75
719 743 0.532862 ACTGACACGTCCTTTGCCTG 60.533 55.000 0.00 0.00 0.00 4.85
720 744 1.845809 CTGACACGTCCTTTGCCTGC 61.846 60.000 0.00 0.00 0.00 4.85
721 745 2.954753 GACACGTCCTTTGCCTGCG 61.955 63.158 0.00 0.00 0.00 5.18
722 746 3.726517 CACGTCCTTTGCCTGCGG 61.727 66.667 0.00 0.00 0.00 5.69
723 747 4.250305 ACGTCCTTTGCCTGCGGT 62.250 61.111 0.00 0.00 0.00 5.68
724 748 2.978010 CGTCCTTTGCCTGCGGTT 60.978 61.111 0.00 0.00 0.00 4.44
725 749 2.551912 CGTCCTTTGCCTGCGGTTT 61.552 57.895 0.00 0.00 0.00 3.27
726 750 1.739667 GTCCTTTGCCTGCGGTTTT 59.260 52.632 0.00 0.00 0.00 2.43
727 751 0.318699 GTCCTTTGCCTGCGGTTTTC 60.319 55.000 0.00 0.00 0.00 2.29
728 752 1.006220 CCTTTGCCTGCGGTTTTCC 60.006 57.895 0.00 0.00 0.00 3.13
741 765 1.837947 TTTTCCGTCTCCCCGACCA 60.838 57.895 0.00 0.00 39.56 4.02
774 804 2.768527 AGCAAATCTAGCTAGGCAGTGA 59.231 45.455 20.58 0.50 41.32 3.41
1060 1103 2.668550 GACGAGCGCCAACCCTTT 60.669 61.111 2.29 0.00 0.00 3.11
1109 1160 4.944372 GCGCCTGATCCGTACGGG 62.944 72.222 32.80 17.93 36.91 5.28
1113 1164 4.944372 CTGATCCGTACGGGCGCC 62.944 72.222 32.80 21.18 34.94 6.53
1383 1441 0.680280 TCCTACACGGTGAGAGCCTC 60.680 60.000 16.29 0.00 0.00 4.70
1384 1442 1.668101 CCTACACGGTGAGAGCCTCC 61.668 65.000 16.29 0.00 0.00 4.30
1385 1443 0.681564 CTACACGGTGAGAGCCTCCT 60.682 60.000 16.29 0.00 0.00 3.69
1386 1444 0.965866 TACACGGTGAGAGCCTCCTG 60.966 60.000 16.29 0.80 0.00 3.86
1387 1445 3.386237 ACGGTGAGAGCCTCCTGC 61.386 66.667 0.00 0.00 41.71 4.85
1399 1457 4.465446 TCCTGCTCCTCCTCCCCG 62.465 72.222 0.00 0.00 0.00 5.73
1449 1507 2.695359 GTGGTTGGTTAGATCGAAGCA 58.305 47.619 15.27 15.27 35.11 3.91
1454 1512 4.394920 GGTTGGTTAGATCGAAGCATTTCA 59.605 41.667 19.04 3.91 36.74 2.69
1565 1624 0.469070 CAGCCTGGCTTGATAGCTCT 59.531 55.000 20.79 0.00 46.90 4.09
1638 1697 8.065407 CGTTCTTGTAATTTTTGTGCTGTAGTA 58.935 33.333 0.00 0.00 0.00 1.82
1639 1698 9.382244 GTTCTTGTAATTTTTGTGCTGTAGTAG 57.618 33.333 0.00 0.00 0.00 2.57
1640 1699 8.671384 TCTTGTAATTTTTGTGCTGTAGTAGT 57.329 30.769 0.00 0.00 0.00 2.73
1641 1700 9.116067 TCTTGTAATTTTTGTGCTGTAGTAGTT 57.884 29.630 0.00 0.00 0.00 2.24
1644 1703 9.767228 TGTAATTTTTGTGCTGTAGTAGTTAGA 57.233 29.630 0.00 0.00 0.00 2.10
1673 1735 8.031864 AGAAACGATATGGATAGCTCATAAGTG 58.968 37.037 0.00 0.00 31.80 3.16
1714 1776 6.202954 CAGGGTTATTAATTAGAGTTCCTGCG 59.797 42.308 10.93 0.00 32.90 5.18
1715 1777 5.469084 GGGTTATTAATTAGAGTTCCTGCGG 59.531 44.000 0.00 0.00 0.00 5.69
1727 1789 5.710099 AGAGTTCCTGCGGAATTAATTTTGA 59.290 36.000 12.13 0.00 44.04 2.69
1734 1796 5.031578 TGCGGAATTAATTTTGATGTACGC 58.968 37.500 1.43 2.98 42.10 4.42
1758 1820 4.269183 TGGAATGTTGGCTACACAATAGG 58.731 43.478 3.38 0.00 40.19 2.57
1761 1823 5.009010 GGAATGTTGGCTACACAATAGGATG 59.991 44.000 3.38 0.00 40.19 3.51
1774 1836 5.182950 CACAATAGGATGTGTAAGTTGCCAA 59.817 40.000 0.00 0.00 44.46 4.52
1797 1859 3.494626 CGCAGAAGTTAAAGCAAGTCAGA 59.505 43.478 0.00 0.00 0.00 3.27
1828 1890 6.293462 GCTGAGAAACGAAACCAGACTAAATT 60.293 38.462 0.00 0.00 0.00 1.82
1857 2041 6.689178 ATAAGTTAAACAAAGCATTGCACG 57.311 33.333 11.91 0.91 40.34 5.34
1894 2079 4.379339 TTGAGCAAACCAAAAGGTACAC 57.621 40.909 0.00 0.00 0.00 2.90
2082 2268 2.919229 GTCTTCTTGCCATTTTGATGCG 59.081 45.455 0.00 0.00 0.00 4.73
2101 2287 5.682943 TGCGCTAACTTCAGTTTATTGTT 57.317 34.783 9.73 0.00 39.31 2.83
2104 2290 6.975772 TGCGCTAACTTCAGTTTATTGTTTTT 59.024 30.769 9.73 0.00 39.31 1.94
2136 2322 0.546122 TTGAGTGGCAGTGTTCCTGT 59.454 50.000 0.00 0.00 43.55 4.00
2409 2597 2.425312 CAGGCACGTGTTCTAGAGAGAT 59.575 50.000 18.38 0.00 0.00 2.75
2552 2740 2.121948 TGGCCTAGCTCATCATCTGTT 58.878 47.619 3.32 0.00 0.00 3.16
2566 2754 2.203195 TGTTCAGCCAAGCAGCGT 60.203 55.556 0.00 0.00 38.01 5.07
2581 2769 0.888619 AGCGTGTCGGATGAAGAGAA 59.111 50.000 0.00 0.00 0.00 2.87
2672 2860 5.703592 TCTTCGGCTACAGATAGAGATCTTC 59.296 44.000 0.00 0.00 40.68 2.87
2738 2926 5.902681 TCGATTTGTCTCGATGGTTTCTAT 58.097 37.500 0.00 0.00 42.38 1.98
2769 2957 1.816679 CTGATAAGGCTGCGCTGCA 60.817 57.895 35.16 19.29 36.92 4.41
2920 3108 3.072622 GGGGGTATGACCTTATGACTTCC 59.927 52.174 0.00 0.00 38.64 3.46
3092 3280 8.930760 GTTTTATGCATATCTGAGGTATCTGTC 58.069 37.037 7.36 0.00 0.00 3.51
3227 3498 0.798776 GTGTGAATTCGAGTGCCCTG 59.201 55.000 0.04 0.00 0.00 4.45
3248 3519 5.220931 CCTGTTTCTCCAAAACTCTTCTGTG 60.221 44.000 2.73 0.00 0.00 3.66
3249 3520 5.496556 TGTTTCTCCAAAACTCTTCTGTGA 58.503 37.500 2.73 0.00 0.00 3.58
3250 3521 5.354234 TGTTTCTCCAAAACTCTTCTGTGAC 59.646 40.000 2.73 0.00 0.00 3.67
3251 3522 5.359194 TTCTCCAAAACTCTTCTGTGACT 57.641 39.130 0.00 0.00 0.00 3.41
3252 3523 4.697514 TCTCCAAAACTCTTCTGTGACTG 58.302 43.478 0.00 0.00 0.00 3.51
3253 3524 3.808728 TCCAAAACTCTTCTGTGACTGG 58.191 45.455 0.00 0.00 0.00 4.00
3254 3525 3.454447 TCCAAAACTCTTCTGTGACTGGA 59.546 43.478 0.00 0.00 0.00 3.86
3255 3526 3.812053 CCAAAACTCTTCTGTGACTGGAG 59.188 47.826 0.00 0.00 0.00 3.86
3256 3527 4.446371 CAAAACTCTTCTGTGACTGGAGT 58.554 43.478 0.00 0.00 38.66 3.85
3257 3528 4.762289 AAACTCTTCTGTGACTGGAGTT 57.238 40.909 7.81 7.81 45.39 3.01
3258 3529 4.762289 AACTCTTCTGTGACTGGAGTTT 57.238 40.909 7.81 0.00 42.29 2.66
3259 3530 4.329462 ACTCTTCTGTGACTGGAGTTTC 57.671 45.455 0.00 0.00 34.13 2.78
3260 3531 3.070302 ACTCTTCTGTGACTGGAGTTTCC 59.930 47.826 0.00 0.00 34.13 3.13
3261 3532 2.368875 TCTTCTGTGACTGGAGTTTCCC 59.631 50.000 0.00 0.00 35.03 3.97
3262 3533 1.801242 TCTGTGACTGGAGTTTCCCA 58.199 50.000 0.00 0.00 35.03 4.37
3263 3534 2.338809 TCTGTGACTGGAGTTTCCCAT 58.661 47.619 0.00 0.00 35.03 4.00
3264 3535 2.711009 TCTGTGACTGGAGTTTCCCATT 59.289 45.455 0.00 0.00 35.03 3.16
3265 3536 3.138283 TCTGTGACTGGAGTTTCCCATTT 59.862 43.478 0.00 0.00 35.03 2.32
3266 3537 3.891366 CTGTGACTGGAGTTTCCCATTTT 59.109 43.478 0.00 0.00 35.03 1.82
3267 3538 4.285863 TGTGACTGGAGTTTCCCATTTTT 58.714 39.130 0.00 0.00 35.03 1.94
3287 3558 3.788227 TTTGGTGGCAACTCTATGAGT 57.212 42.857 3.27 0.00 45.64 3.41
3288 3559 2.768253 TGGTGGCAACTCTATGAGTG 57.232 50.000 3.27 0.00 42.59 3.51
3289 3560 1.278985 TGGTGGCAACTCTATGAGTGG 59.721 52.381 3.27 0.00 42.59 4.00
3327 3638 2.511659 CATGCTGTGAAGGGGGATATG 58.488 52.381 0.00 0.00 0.00 1.78
3539 4921 1.969256 GCAGAACATTACGCAACAACG 59.031 47.619 0.00 0.00 39.50 4.10
3639 5021 0.752658 GGCATTTTCATAGGGCCACC 59.247 55.000 6.18 0.00 44.01 4.61
3661 5043 2.353573 GGCGGAGGGGCAAAAGTA 59.646 61.111 0.00 0.00 41.77 2.24
3841 5223 2.166254 CCAGTTTCCACAAGCACAAAGT 59.834 45.455 0.00 0.00 0.00 2.66
3997 5380 5.009610 CCCAAGATACCAAATGATAAACGGG 59.990 44.000 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 8.905850 TCACAAAATATGACAGCAATATCACAT 58.094 29.630 0.00 0.00 0.00 3.21
110 112 8.981647 GCTTGTTTTCAAATTCAATATGACAGT 58.018 29.630 0.00 0.00 39.47 3.55
190 192 0.908180 AGGCTGCTTAACCCTACCGT 60.908 55.000 0.00 0.00 0.00 4.83
233 235 1.153168 CCCTGGCGGTAGGTTCATG 60.153 63.158 0.00 0.00 36.02 3.07
234 236 1.615424 ACCCTGGCGGTAGGTTCAT 60.615 57.895 0.00 0.00 45.97 2.57
254 256 4.630505 TGTAAAGTTTCTGTAACGTGCACA 59.369 37.500 18.64 0.00 41.78 4.57
395 418 1.074244 GTAGGGTGTGGCAGGGTTTTA 59.926 52.381 0.00 0.00 0.00 1.52
556 579 1.123928 CCTCTGGCAGTAGGGTTAGG 58.876 60.000 15.27 8.08 0.00 2.69
609 633 5.103771 AGGATCTGACCCTGCTTTGAAATAT 60.104 40.000 0.00 0.00 31.66 1.28
611 635 3.011032 AGGATCTGACCCTGCTTTGAAAT 59.989 43.478 0.00 0.00 31.66 2.17
619 643 3.209410 CAATTGTAGGATCTGACCCTGC 58.791 50.000 0.00 0.00 37.00 4.85
634 658 4.810345 TGACCCTTTTCCCTAACAATTGT 58.190 39.130 4.92 4.92 0.00 2.71
635 659 5.799827 TTGACCCTTTTCCCTAACAATTG 57.200 39.130 3.24 3.24 0.00 2.32
676 700 1.103803 GTCAGTATCAGGGACGAGCA 58.896 55.000 0.00 0.00 0.00 4.26
677 701 0.386113 GGTCAGTATCAGGGACGAGC 59.614 60.000 0.00 0.00 32.39 5.03
678 702 1.763968 TGGTCAGTATCAGGGACGAG 58.236 55.000 0.00 0.00 32.39 4.18
679 703 2.307768 GATGGTCAGTATCAGGGACGA 58.692 52.381 0.00 0.00 32.39 4.20
680 704 2.031870 TGATGGTCAGTATCAGGGACG 58.968 52.381 0.00 0.00 31.35 4.79
681 705 3.034635 AGTGATGGTCAGTATCAGGGAC 58.965 50.000 0.00 0.00 35.39 4.46
682 706 3.033909 CAGTGATGGTCAGTATCAGGGA 58.966 50.000 0.00 0.00 35.39 4.20
683 707 3.033909 TCAGTGATGGTCAGTATCAGGG 58.966 50.000 0.00 0.00 35.39 4.45
684 708 3.448660 TGTCAGTGATGGTCAGTATCAGG 59.551 47.826 0.00 0.00 35.39 3.86
685 709 4.428209 GTGTCAGTGATGGTCAGTATCAG 58.572 47.826 0.00 0.00 35.39 2.90
686 710 3.119495 CGTGTCAGTGATGGTCAGTATCA 60.119 47.826 0.00 0.00 32.44 2.15
687 711 3.119459 ACGTGTCAGTGATGGTCAGTATC 60.119 47.826 0.00 0.00 0.00 2.24
688 712 2.826128 ACGTGTCAGTGATGGTCAGTAT 59.174 45.455 0.00 0.00 0.00 2.12
689 713 2.228103 GACGTGTCAGTGATGGTCAGTA 59.772 50.000 13.23 0.00 0.00 2.74
690 714 1.000163 GACGTGTCAGTGATGGTCAGT 60.000 52.381 13.23 2.61 0.00 3.41
691 715 1.670087 GGACGTGTCAGTGATGGTCAG 60.670 57.143 17.46 2.85 0.00 3.51
692 716 0.317160 GGACGTGTCAGTGATGGTCA 59.683 55.000 17.46 1.30 0.00 4.02
693 717 0.603569 AGGACGTGTCAGTGATGGTC 59.396 55.000 0.00 4.46 0.00 4.02
694 718 1.048601 AAGGACGTGTCAGTGATGGT 58.951 50.000 0.00 0.00 0.00 3.55
695 719 1.800586 CAAAGGACGTGTCAGTGATGG 59.199 52.381 0.00 0.00 0.00 3.51
696 720 1.195448 GCAAAGGACGTGTCAGTGATG 59.805 52.381 0.00 0.00 0.00 3.07
697 721 1.512926 GCAAAGGACGTGTCAGTGAT 58.487 50.000 0.00 0.00 0.00 3.06
698 722 0.531974 GGCAAAGGACGTGTCAGTGA 60.532 55.000 0.00 0.00 0.00 3.41
699 723 0.532862 AGGCAAAGGACGTGTCAGTG 60.533 55.000 0.00 0.00 0.00 3.66
700 724 0.532862 CAGGCAAAGGACGTGTCAGT 60.533 55.000 0.00 0.00 0.00 3.41
701 725 1.845809 GCAGGCAAAGGACGTGTCAG 61.846 60.000 0.00 0.00 0.00 3.51
702 726 1.891919 GCAGGCAAAGGACGTGTCA 60.892 57.895 0.00 0.00 0.00 3.58
703 727 2.946762 GCAGGCAAAGGACGTGTC 59.053 61.111 0.00 0.00 0.00 3.67
704 728 2.972505 CGCAGGCAAAGGACGTGT 60.973 61.111 0.00 0.00 0.00 4.49
705 729 3.726517 CCGCAGGCAAAGGACGTG 61.727 66.667 0.00 0.00 46.14 4.49
717 741 2.033194 GGGAGACGGAAAACCGCAG 61.033 63.158 8.59 0.00 36.58 5.18
718 742 2.031465 GGGAGACGGAAAACCGCA 59.969 61.111 8.59 0.00 36.58 5.69
719 743 2.745100 GGGGAGACGGAAAACCGC 60.745 66.667 8.59 2.30 36.58 5.68
720 744 2.433664 CGGGGAGACGGAAAACCG 60.434 66.667 7.12 7.12 39.31 4.44
721 745 1.375140 GTCGGGGAGACGGAAAACC 60.375 63.158 0.00 0.00 40.43 3.27
722 746 4.273811 GTCGGGGAGACGGAAAAC 57.726 61.111 0.00 0.00 40.43 2.43
730 754 1.532316 AAGTCGTTGGTCGGGGAGA 60.532 57.895 0.00 0.00 40.32 3.71
731 755 1.374252 CAAGTCGTTGGTCGGGGAG 60.374 63.158 0.00 0.00 40.32 4.30
732 756 2.738480 CAAGTCGTTGGTCGGGGA 59.262 61.111 0.00 0.00 40.32 4.81
741 765 1.956477 AGATTTGCTTGCCAAGTCGTT 59.044 42.857 6.28 0.00 42.91 3.85
943 976 3.126528 CGTGGGACGGGATAGGAC 58.873 66.667 0.00 0.00 38.08 3.85
1115 1166 3.866582 CTGCCGGATCCCCACCTC 61.867 72.222 5.05 0.00 0.00 3.85
1454 1512 6.126409 TCACAAATTTTACAGGACAAGACCT 58.874 36.000 0.00 0.00 41.43 3.85
1565 1624 3.476552 GAATGATCGCTACCCATTTCCA 58.523 45.455 0.00 0.00 31.40 3.53
1602 1661 2.862674 TACAAGAACGCGGGCCCATC 62.863 60.000 24.92 14.03 0.00 3.51
1615 1674 8.671384 ACTACTACAGCACAAAAATTACAAGA 57.329 30.769 0.00 0.00 0.00 3.02
1638 1697 8.732531 GCTATCCATATCGTTTCTAGTCTAACT 58.267 37.037 0.00 0.00 0.00 2.24
1639 1698 8.732531 AGCTATCCATATCGTTTCTAGTCTAAC 58.267 37.037 0.00 0.00 0.00 2.34
1640 1699 8.865420 AGCTATCCATATCGTTTCTAGTCTAA 57.135 34.615 0.00 0.00 0.00 2.10
1641 1700 8.101419 TGAGCTATCCATATCGTTTCTAGTCTA 58.899 37.037 0.00 0.00 0.00 2.59
1642 1701 6.943146 TGAGCTATCCATATCGTTTCTAGTCT 59.057 38.462 0.00 0.00 0.00 3.24
1643 1702 7.147143 TGAGCTATCCATATCGTTTCTAGTC 57.853 40.000 0.00 0.00 0.00 2.59
1644 1703 7.710676 ATGAGCTATCCATATCGTTTCTAGT 57.289 36.000 0.00 0.00 0.00 2.57
1645 1704 9.729023 CTTATGAGCTATCCATATCGTTTCTAG 57.271 37.037 0.00 0.00 0.00 2.43
1673 1735 0.548510 CCTGGTCCCCTCAGAAATCC 59.451 60.000 0.00 0.00 34.36 3.01
1714 1776 7.254852 TCCAAGCGTACATCAAAATTAATTCC 58.745 34.615 0.10 0.00 0.00 3.01
1715 1777 8.682128 TTCCAAGCGTACATCAAAATTAATTC 57.318 30.769 0.10 0.00 0.00 2.17
1727 1789 1.472480 GCCAACATTCCAAGCGTACAT 59.528 47.619 0.00 0.00 0.00 2.29
1734 1796 4.789012 ATTGTGTAGCCAACATTCCAAG 57.211 40.909 0.00 0.00 41.10 3.61
1758 1820 1.963747 GCGTTGGCAACTTACACATC 58.036 50.000 26.26 0.00 39.62 3.06
1774 1836 3.202906 TGACTTGCTTTAACTTCTGCGT 58.797 40.909 0.00 0.00 0.00 5.24
1779 1841 6.606768 CCTGAATCTGACTTGCTTTAACTTC 58.393 40.000 0.00 0.00 0.00 3.01
1797 1859 2.814336 GGTTTCGTTTCTCAGCCTGAAT 59.186 45.455 0.00 0.00 0.00 2.57
1834 1896 6.212955 ACGTGCAATGCTTTGTTTAACTTAT 58.787 32.000 6.82 0.00 35.17 1.73
1836 1898 4.429108 ACGTGCAATGCTTTGTTTAACTT 58.571 34.783 6.82 0.26 35.17 2.66
2003 2189 9.920133 GCTGAAGTTTCATCTATACATATCTCA 57.080 33.333 0.00 0.00 36.46 3.27
2013 2199 8.079211 TGGTACTAAGCTGAAGTTTCATCTAT 57.921 34.615 7.25 0.00 32.94 1.98
2101 2287 8.862325 TGCCACTCAATTAGAAGATAAGAAAA 57.138 30.769 0.00 0.00 0.00 2.29
2104 2290 7.044181 CACTGCCACTCAATTAGAAGATAAGA 58.956 38.462 0.00 0.00 0.00 2.10
2136 2322 3.967326 TCTTCTCTCTTTGTGGAACCAGA 59.033 43.478 0.00 0.00 34.36 3.86
2409 2597 4.709886 TGATCCGATAGAAACACCTCTCAA 59.290 41.667 0.00 0.00 39.76 3.02
2552 2740 2.666190 GACACGCTGCTTGGCTGA 60.666 61.111 11.00 0.00 0.00 4.26
2566 2754 2.897326 TCCAAGTTCTCTTCATCCGACA 59.103 45.455 0.00 0.00 0.00 4.35
2581 2769 3.328931 ACTGATGGATGTGTTCTCCAAGT 59.671 43.478 0.00 0.00 45.57 3.16
2672 2860 4.245660 TGTTGTCATCTTTCTTAGCCTCG 58.754 43.478 0.00 0.00 0.00 4.63
2738 2926 1.671328 CTTATCAGCTCGTCTCCGTCA 59.329 52.381 0.00 0.00 35.01 4.35
2769 2957 0.674534 GTCGAGTGGAACCTGTGTCT 59.325 55.000 0.00 0.00 37.80 3.41
2920 3108 8.656849 GTGGATTACAACAACACATCTTACTAG 58.343 37.037 0.00 0.00 32.58 2.57
3092 3280 6.137794 AGGTACATAACATCTCTCGACAAG 57.862 41.667 0.00 0.00 0.00 3.16
3196 3384 8.048436 CACTCGAATTCACACGTAAATGTATAC 58.952 37.037 6.22 0.00 0.00 1.47
3197 3385 7.253850 GCACTCGAATTCACACGTAAATGTATA 60.254 37.037 6.22 0.00 0.00 1.47
3198 3386 6.455113 GCACTCGAATTCACACGTAAATGTAT 60.455 38.462 6.22 0.00 0.00 2.29
3227 3498 5.586643 AGTCACAGAAGAGTTTTGGAGAAAC 59.413 40.000 0.00 0.00 0.00 2.78
3265 3536 4.278170 CACTCATAGAGTTGCCACCAAAAA 59.722 41.667 0.00 0.00 41.37 1.94
3266 3537 3.820467 CACTCATAGAGTTGCCACCAAAA 59.180 43.478 0.00 0.00 41.37 2.44
3267 3538 3.411446 CACTCATAGAGTTGCCACCAAA 58.589 45.455 0.00 0.00 41.37 3.28
3268 3539 2.290260 CCACTCATAGAGTTGCCACCAA 60.290 50.000 0.00 0.00 41.37 3.67
3269 3540 1.278985 CCACTCATAGAGTTGCCACCA 59.721 52.381 0.00 0.00 41.37 4.17
3270 3541 1.407437 CCCACTCATAGAGTTGCCACC 60.407 57.143 0.00 0.00 41.37 4.61
3271 3542 1.555075 TCCCACTCATAGAGTTGCCAC 59.445 52.381 0.00 0.00 41.37 5.01
3272 3543 1.555075 GTCCCACTCATAGAGTTGCCA 59.445 52.381 0.00 0.00 41.37 4.92
3273 3544 1.134371 GGTCCCACTCATAGAGTTGCC 60.134 57.143 0.00 0.00 41.37 4.52
3274 3545 1.134371 GGGTCCCACTCATAGAGTTGC 60.134 57.143 1.78 0.00 41.37 4.17
3275 3546 2.169352 CTGGGTCCCACTCATAGAGTTG 59.831 54.545 6.47 0.00 41.37 3.16
3276 3547 2.472029 CTGGGTCCCACTCATAGAGTT 58.528 52.381 6.47 0.00 41.37 3.01
3277 3548 1.967274 GCTGGGTCCCACTCATAGAGT 60.967 57.143 6.47 0.00 44.44 3.24
3278 3549 0.755686 GCTGGGTCCCACTCATAGAG 59.244 60.000 6.47 0.00 35.52 2.43
3279 3550 0.339859 AGCTGGGTCCCACTCATAGA 59.660 55.000 6.47 0.00 0.00 1.98
3280 3551 0.467384 CAGCTGGGTCCCACTCATAG 59.533 60.000 6.47 0.00 0.00 2.23
3281 3552 0.982852 CCAGCTGGGTCCCACTCATA 60.983 60.000 26.14 0.00 0.00 2.15
3282 3553 2.304056 CCAGCTGGGTCCCACTCAT 61.304 63.158 26.14 0.00 0.00 2.90
3283 3554 2.930019 CCAGCTGGGTCCCACTCA 60.930 66.667 26.14 0.00 0.00 3.41
3284 3555 4.416738 GCCAGCTGGGTCCCACTC 62.417 72.222 33.46 10.92 39.65 3.51
3286 3557 4.729918 CTGCCAGCTGGGTCCCAC 62.730 72.222 33.46 16.33 39.65 4.61
3288 3559 4.729918 CACTGCCAGCTGGGTCCC 62.730 72.222 33.46 17.46 39.65 4.46
3289 3560 4.729918 CCACTGCCAGCTGGGTCC 62.730 72.222 33.46 17.84 39.65 4.46
3327 3638 5.293560 GGTGGCTATTCAGATACAGAAGAC 58.706 45.833 0.00 0.00 0.00 3.01
3375 4297 0.534203 TTTTTCCACGAAGCTCGGCT 60.534 50.000 9.75 0.00 45.59 5.52
3395 4776 3.012518 GTTATGCATGTTGAGGTGAGCT 58.987 45.455 10.16 0.00 0.00 4.09
3539 4921 5.255710 ACACACTAGATGATACTCTGCAC 57.744 43.478 0.00 0.00 0.00 4.57
3639 5021 3.615509 TTTGCCCCTCCGCCGTTAG 62.616 63.158 0.00 0.00 0.00 2.34
3661 5043 7.525158 TTATCCCTATCTTTTGGAACTCCTT 57.475 36.000 0.00 0.00 36.82 3.36
3717 5099 4.556697 AGGTTTATGAATCCAAATCCCCC 58.443 43.478 0.00 0.00 0.00 5.40
3718 5100 5.163311 CCAAGGTTTATGAATCCAAATCCCC 60.163 44.000 0.00 0.00 0.00 4.81
3765 5147 8.353684 ACGGTTGAAATATTACAATGTGAACAA 58.646 29.630 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.