Multiple sequence alignment - TraesCS5A01G501700

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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 TraesCS5A01G501700 chr5A 100.000 4067 0 0 1 4067 667065981 667070047 0.000000e+00 7511.0
1 TraesCS5A01G501700 chr5A 97.347 1583 38 1 1560 3138 666874141 666872559 0.000000e+00 2687.0
2 TraesCS5A01G501700 chr5A 84.840 1471 209 11 1596 3056 666825175 666823709 0.000000e+00 1469.0
3 TraesCS5A01G501700 chr5A 78.175 1425 275 30 1624 3036 666751907 666750507 0.000000e+00 876.0
4 TraesCS5A01G501700 chr5A 76.372 893 189 20 1593 2477 666843612 666842734 1.030000e-125 460.0
5 TraesCS5A01G501700 chr5A 88.085 235 22 5 1273 1504 666826046 666825815 1.440000e-69 274.0
6 TraesCS5A01G501700 chr5A 88.496 226 26 0 1280 1505 666844069 666843844 1.440000e-69 274.0
7 TraesCS5A01G501700 chr5A 87.850 214 11 4 1191 1398 666886646 666886442 1.890000e-58 237.0
8 TraesCS5A01G501700 chr5A 93.233 133 5 2 1390 1522 666876505 666876377 4.150000e-45 193.0
9 TraesCS5A01G501700 chr4B 95.811 1695 59 3 1561 3243 621189983 621191677 0.000000e+00 2726.0
10 TraesCS5A01G501700 chr4B 95.624 1668 65 2 1560 3219 621279707 621281374 0.000000e+00 2669.0
11 TraesCS5A01G501700 chr4B 84.348 1495 217 13 1593 3077 620967276 620965789 0.000000e+00 1448.0
12 TraesCS5A01G501700 chr4B 86.446 878 68 17 3217 4062 621281492 621282350 0.000000e+00 915.0
13 TraesCS5A01G501700 chr4B 88.557 769 46 23 776 1530 621189145 621189885 0.000000e+00 894.0
14 TraesCS5A01G501700 chr4B 77.204 1452 305 21 1596 3037 620971141 620969706 0.000000e+00 824.0
15 TraesCS5A01G501700 chr4B 77.166 1454 286 37 1600 3036 620946788 620945364 0.000000e+00 804.0
16 TraesCS5A01G501700 chr4B 97.818 275 6 0 1285 1559 621279396 621279670 3.680000e-130 475.0
17 TraesCS5A01G501700 chr4B 88.743 382 29 6 1 378 621188776 621189147 4.790000e-124 455.0
18 TraesCS5A01G501700 chr4B 83.442 459 45 18 3229 3670 621096365 621095921 8.190000e-107 398.0
19 TraesCS5A01G501700 chr4B 80.841 428 51 20 1097 1504 620968096 620967680 1.420000e-79 307.0
20 TraesCS5A01G501700 chr4B 87.168 226 29 0 1280 1505 620971600 620971375 1.450000e-64 257.0
21 TraesCS5A01G501700 chr4B 81.818 264 27 14 3226 3487 641811445 641811201 6.890000e-48 202.0
22 TraesCS5A01G501700 chr4B 90.909 88 4 4 3277 3363 506639122 506639206 9.240000e-22 115.0
23 TraesCS5A01G501700 chr4D 94.550 1578 71 7 1560 3128 486623250 486621679 0.000000e+00 2423.0
24 TraesCS5A01G501700 chr4D 83.357 1430 206 22 1603 3019 486567219 486565809 0.000000e+00 1293.0
25 TraesCS5A01G501700 chr4D 88.667 803 44 23 754 1530 486624125 486623344 0.000000e+00 935.0
26 TraesCS5A01G501700 chr4D 77.663 1455 280 33 1600 3036 486432429 486433856 0.000000e+00 845.0
27 TraesCS5A01G501700 chr4D 83.102 722 81 16 1 713 486624806 486624117 1.610000e-173 619.0
28 TraesCS5A01G501700 chr6A 79.735 1130 186 31 1933 3036 31369043 31367931 0.000000e+00 778.0
29 TraesCS5A01G501700 chrUn 78.114 1124 215 24 1933 3036 103934273 103933161 0.000000e+00 684.0
30 TraesCS5A01G501700 chr1A 83.709 399 51 10 3281 3670 463454709 463455102 8.310000e-97 364.0
31 TraesCS5A01G501700 chr6B 81.633 294 32 12 3217 3494 26024855 26025142 1.470000e-54 224.0
32 TraesCS5A01G501700 chr6B 81.395 86 15 1 3440 3524 150629718 150629633 7.290000e-08 69.4
33 TraesCS5A01G501700 chr1D 78.830 359 50 19 3318 3673 389598157 389597822 6.840000e-53 219.0
34 TraesCS5A01G501700 chr3D 75.610 369 68 17 3224 3579 393551373 393551732 3.250000e-36 163.0
35 TraesCS5A01G501700 chr2B 78.829 222 40 7 3273 3491 53697704 53697921 4.240000e-30 143.0
36 TraesCS5A01G501700 chr2B 88.000 100 4 7 3281 3374 777302639 777302736 1.190000e-20 111.0
37 TraesCS5A01G501700 chr6D 75.633 316 51 22 3224 3527 458354948 458355249 2.550000e-27 134.0
38 TraesCS5A01G501700 chr6D 100.000 28 0 0 3440 3467 188776385 188776412 7.000000e-03 52.8
39 TraesCS5A01G501700 chr6D 100.000 28 0 0 3440 3467 255765621 255765594 7.000000e-03 52.8
40 TraesCS5A01G501700 chr3A 89.706 68 3 4 3240 3303 11857925 11857858 2.600000e-12 84.2


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 TraesCS5A01G501700 chr5A 667065981 667070047 4066 False 7511.000000 7511 100.00000 1 4067 1 chr5A.!!$F1 4066
1 TraesCS5A01G501700 chr5A 666872559 666876505 3946 True 1440.000000 2687 95.29000 1390 3138 2 chr5A.!!$R5 1748
2 TraesCS5A01G501700 chr5A 666750507 666751907 1400 True 876.000000 876 78.17500 1624 3036 1 chr5A.!!$R1 1412
3 TraesCS5A01G501700 chr5A 666823709 666826046 2337 True 871.500000 1469 86.46250 1273 3056 2 chr5A.!!$R3 1783
4 TraesCS5A01G501700 chr5A 666842734 666844069 1335 True 367.000000 460 82.43400 1280 2477 2 chr5A.!!$R4 1197
5 TraesCS5A01G501700 chr4B 621188776 621191677 2901 False 1358.333333 2726 91.03700 1 3243 3 chr4B.!!$F2 3242
6 TraesCS5A01G501700 chr4B 621279396 621282350 2954 False 1353.000000 2669 93.29600 1285 4062 3 chr4B.!!$F3 2777
7 TraesCS5A01G501700 chr4B 620945364 620946788 1424 True 804.000000 804 77.16600 1600 3036 1 chr4B.!!$R1 1436
8 TraesCS5A01G501700 chr4B 620965789 620971600 5811 True 709.000000 1448 82.39025 1097 3077 4 chr4B.!!$R4 1980
9 TraesCS5A01G501700 chr4D 486621679 486624806 3127 True 1325.666667 2423 88.77300 1 3128 3 chr4D.!!$R2 3127
10 TraesCS5A01G501700 chr4D 486565809 486567219 1410 True 1293.000000 1293 83.35700 1603 3019 1 chr4D.!!$R1 1416
11 TraesCS5A01G501700 chr4D 486432429 486433856 1427 False 845.000000 845 77.66300 1600 3036 1 chr4D.!!$F1 1436
12 TraesCS5A01G501700 chr6A 31367931 31369043 1112 True 778.000000 778 79.73500 1933 3036 1 chr6A.!!$R1 1103
13 TraesCS5A01G501700 chrUn 103933161 103934273 1112 True 684.000000 684 78.11400 1933 3036 1 chrUn.!!$R1 1103

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
53 54 0.038159 GCAGTACCGAAGCTCAGTGT 60.038 55.0 0.0 0.0 0.00 3.55 F
189 193 0.104120 CGGTACATGATTCTGCCCGA 59.896 55.0 0.0 0.0 36.55 5.14 F
517 522 0.458025 GAGAAGTAACCAGGCGACGG 60.458 60.0 0.0 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1229 3641 0.313043 GAAGAAGGACGACGGTGACA 59.687 55.000 0.0 0.0 0.0 3.58 R
1233 3645 0.604780 TCGAGAAGAAGGACGACGGT 60.605 55.000 0.0 0.0 0.0 4.83 R
3067 8313 9.761504 ACATGTCACATCATTTTCAAACAAATA 57.238 25.926 0.0 0.0 0.0 1.40 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
53 54 0.038159 GCAGTACCGAAGCTCAGTGT 60.038 55.000 0.00 0.00 0.00 3.55
58 59 0.464036 ACCGAAGCTCAGTGTGACAA 59.536 50.000 0.00 0.00 0.00 3.18
144 148 1.580059 GTGGGGGAGGTGATGAACTA 58.420 55.000 0.00 0.00 0.00 2.24
189 193 0.104120 CGGTACATGATTCTGCCCGA 59.896 55.000 0.00 0.00 36.55 5.14
215 220 4.848562 ATTGAGCGATATGACCGAACTA 57.151 40.909 0.00 0.00 0.00 2.24
275 280 4.651778 CATGGTGACCTTTGGAGAGTTAA 58.348 43.478 2.11 0.00 0.00 2.01
285 290 4.806342 TTGGAGAGTTAACGAAAGCAAC 57.194 40.909 0.00 0.00 0.00 4.17
336 341 5.890334 TGGTGACTTGAACTTTGATTTGTC 58.110 37.500 0.00 0.00 0.00 3.18
344 349 4.036262 TGAACTTTGATTTGTCTGGAACGG 59.964 41.667 0.00 0.00 0.00 4.44
354 359 1.738099 CTGGAACGGCGAGGTCTTG 60.738 63.158 16.62 1.70 36.61 3.02
359 364 2.892425 CGGCGAGGTCTTGCATCC 60.892 66.667 0.00 0.00 41.74 3.51
417 422 3.565482 AGCTGCATTTTCTCGTCTTCAAA 59.435 39.130 1.02 0.00 0.00 2.69
433 438 8.869897 TCGTCTTCAAACAGTTATGTATTGATC 58.130 33.333 0.00 0.00 39.29 2.92
438 443 6.257849 TCAAACAGTTATGTATTGATCGGCTC 59.742 38.462 0.00 0.00 39.29 4.70
455 460 2.007049 GCTCACAGACATGTTACCCCG 61.007 57.143 0.00 0.00 37.65 5.73
458 463 2.569853 TCACAGACATGTTACCCCGAAT 59.430 45.455 0.00 0.00 37.65 3.34
459 464 3.770388 TCACAGACATGTTACCCCGAATA 59.230 43.478 0.00 0.00 37.65 1.75
478 483 7.878127 CCCGAATATACCAAATCACTATGTTCT 59.122 37.037 0.00 0.00 0.00 3.01
479 484 8.926710 CCGAATATACCAAATCACTATGTTCTC 58.073 37.037 0.00 0.00 0.00 2.87
480 485 9.698309 CGAATATACCAAATCACTATGTTCTCT 57.302 33.333 0.00 0.00 0.00 3.10
517 522 0.458025 GAGAAGTAACCAGGCGACGG 60.458 60.000 0.00 0.00 0.00 4.79
522 527 3.636313 TAACCAGGCGACGGCGAAG 62.636 63.158 18.90 8.08 41.24 3.79
526 531 2.126189 AGGCGACGGCGAAGTAAC 60.126 61.111 18.90 0.00 41.24 2.50
534 539 2.740447 GACGGCGAAGTAACTTTTGGAT 59.260 45.455 16.62 0.00 0.00 3.41
544 549 7.114388 CGAAGTAACTTTTGGATTTTGCTAACC 59.886 37.037 0.00 0.00 0.00 2.85
555 560 1.434555 TTGCTAACCACCGAACATCG 58.565 50.000 0.00 0.00 40.07 3.84
580 585 7.378181 GGATTTTTAAGCAATCCAAGAGAACA 58.622 34.615 17.73 0.00 46.40 3.18
582 587 6.959639 TTTTAAGCAATCCAAGAGAACACT 57.040 33.333 0.00 0.00 0.00 3.55
587 592 5.486526 AGCAATCCAAGAGAACACTCTTAG 58.513 41.667 11.31 5.79 45.56 2.18
590 595 6.648192 CAATCCAAGAGAACACTCTTAGGAT 58.352 40.000 22.48 22.48 45.56 3.24
596 601 5.010933 AGAGAACACTCTTAGGATCGTCAA 58.989 41.667 0.00 0.00 37.70 3.18
609 614 4.588278 GGATCGTCAAATCCGAATCAAAC 58.412 43.478 0.00 0.00 37.93 2.93
612 617 2.166007 GTCAAATCCGAATCAAACGCG 58.834 47.619 3.53 3.53 0.00 6.01
615 620 1.434555 AATCCGAATCAAACGCGTGA 58.565 45.000 14.98 7.32 0.00 4.35
621 626 2.970609 CGAATCAAACGCGTGACAATTT 59.029 40.909 14.98 0.00 0.00 1.82
622 627 3.420576 CGAATCAAACGCGTGACAATTTT 59.579 39.130 14.98 0.00 0.00 1.82
626 631 5.158101 TCAAACGCGTGACAATTTTTCTA 57.842 34.783 14.98 0.00 0.00 2.10
627 632 4.965158 TCAAACGCGTGACAATTTTTCTAC 59.035 37.500 14.98 0.00 0.00 2.59
635 640 5.398122 CGTGACAATTTTTCTACGCAATGTT 59.602 36.000 0.00 0.00 0.00 2.71
636 641 6.075099 CGTGACAATTTTTCTACGCAATGTTT 60.075 34.615 0.00 0.00 0.00 2.83
637 642 7.514435 CGTGACAATTTTTCTACGCAATGTTTT 60.514 33.333 0.00 0.00 0.00 2.43
638 643 7.787480 GTGACAATTTTTCTACGCAATGTTTTC 59.213 33.333 0.00 0.00 0.00 2.29
639 644 7.704472 TGACAATTTTTCTACGCAATGTTTTCT 59.296 29.630 0.00 0.00 0.00 2.52
642 647 4.560136 TTTCTACGCAATGTTTTCTGCA 57.440 36.364 0.00 0.00 38.52 4.41
643 648 4.560136 TTCTACGCAATGTTTTCTGCAA 57.440 36.364 0.00 0.00 38.52 4.08
677 690 3.604130 CGGCAATTGTCGCTTTAGG 57.396 52.632 20.68 0.00 35.94 2.69
695 708 1.385528 GGGCATGGTAAACCCTTACG 58.614 55.000 0.00 0.00 40.75 3.18
697 710 2.618559 GGGCATGGTAAACCCTTACGAA 60.619 50.000 0.00 0.00 40.75 3.85
698 711 2.421073 GGCATGGTAAACCCTTACGAAC 59.579 50.000 0.00 0.00 38.69 3.95
703 716 4.716794 TGGTAAACCCTTACGAACAACAT 58.283 39.130 0.00 0.00 38.69 2.71
706 719 4.823790 AAACCCTTACGAACAACATGAC 57.176 40.909 0.00 0.00 0.00 3.06
707 720 3.478857 ACCCTTACGAACAACATGACA 57.521 42.857 0.00 0.00 0.00 3.58
708 721 3.811083 ACCCTTACGAACAACATGACAA 58.189 40.909 0.00 0.00 0.00 3.18
709 722 4.394729 ACCCTTACGAACAACATGACAAT 58.605 39.130 0.00 0.00 0.00 2.71
710 723 4.825085 ACCCTTACGAACAACATGACAATT 59.175 37.500 0.00 0.00 0.00 2.32
711 724 5.300792 ACCCTTACGAACAACATGACAATTT 59.699 36.000 0.00 0.00 0.00 1.82
712 725 6.183360 ACCCTTACGAACAACATGACAATTTT 60.183 34.615 0.00 0.00 0.00 1.82
741 754 6.741992 TCTATTTTCGCATGTCAATTCTGT 57.258 33.333 0.00 0.00 0.00 3.41
743 756 2.617250 TTCGCATGTCAATTCTGTGC 57.383 45.000 0.00 0.00 0.00 4.57
747 760 1.466360 GCATGTCAATTCTGTGCGTCC 60.466 52.381 0.00 0.00 0.00 4.79
748 761 1.078709 ATGTCAATTCTGTGCGTCCG 58.921 50.000 0.00 0.00 0.00 4.79
749 762 1.132640 GTCAATTCTGTGCGTCCGC 59.867 57.895 4.42 4.42 42.35 5.54
751 764 1.133253 CAATTCTGTGCGTCCGCTG 59.867 57.895 13.31 3.73 42.51 5.18
752 765 2.034879 AATTCTGTGCGTCCGCTGG 61.035 57.895 13.31 3.40 42.51 4.85
757 770 2.746277 GTGCGTCCGCTGGGAAAT 60.746 61.111 13.31 0.00 46.08 2.17
759 772 1.602323 TGCGTCCGCTGGGAAATTT 60.602 52.632 13.31 0.00 46.08 1.82
766 779 4.926832 CGTCCGCTGGGAAATTTTTAAAAT 59.073 37.500 0.55 0.00 46.08 1.82
773 786 6.086785 TGGGAAATTTTTAAAATCCGACGT 57.913 33.333 11.25 0.00 32.03 4.34
774 787 6.151004 TGGGAAATTTTTAAAATCCGACGTC 58.849 36.000 5.18 5.18 32.03 4.34
782 795 5.987777 TTAAAATCCGACGTCAGTTTTGA 57.012 34.783 22.39 16.03 0.00 2.69
791 804 5.263185 CGACGTCAGTTTTGAAACATTTCT 58.737 37.500 17.16 0.00 41.30 2.52
792 805 5.392585 CGACGTCAGTTTTGAAACATTTCTC 59.607 40.000 17.16 0.00 41.30 2.87
797 810 7.913297 CGTCAGTTTTGAAACATTTCTCCTAAA 59.087 33.333 9.08 0.00 41.30 1.85
851 865 2.241259 CGCAAGTAATCCAACAACCG 57.759 50.000 0.00 0.00 0.00 4.44
904 918 1.583556 TATCCAGAGGGCAGCTTGAA 58.416 50.000 0.00 0.00 0.00 2.69
938 953 3.129502 CTGCATCCCACACAGCCG 61.130 66.667 0.00 0.00 0.00 5.52
985 1003 2.298446 ACACCATCACTGTCACTCTCAG 59.702 50.000 0.00 0.00 38.68 3.35
986 1004 2.560105 CACCATCACTGTCACTCTCAGA 59.440 50.000 0.00 0.00 36.81 3.27
987 1005 2.824936 ACCATCACTGTCACTCTCAGAG 59.175 50.000 0.00 0.00 36.81 3.35
988 1006 2.417107 CCATCACTGTCACTCTCAGAGC 60.417 54.545 0.00 0.00 36.81 4.09
989 1007 1.986882 TCACTGTCACTCTCAGAGCA 58.013 50.000 0.00 0.00 36.81 4.26
1039 1064 2.666069 GCGCTGCTCCGTAGACTAATAG 60.666 54.545 0.00 0.00 0.00 1.73
1049 1074 0.603569 AGACTAATAGCCCATCGCCG 59.396 55.000 0.00 0.00 38.78 6.46
1069 1094 2.810887 GCAGCATCGTCAGCGTCA 60.811 61.111 0.00 0.00 39.49 4.35
1131 3540 5.459536 CCACCATTATTCTAATCCCCACCAT 60.460 44.000 0.00 0.00 0.00 3.55
1147 3556 4.072131 CCACCATGGTTATTCTAATCCCG 58.928 47.826 16.84 0.00 31.35 5.14
1148 3557 4.445735 CCACCATGGTTATTCTAATCCCGT 60.446 45.833 16.84 0.00 31.35 5.28
1233 3645 3.691342 CCGTTCGCCTCCCTGTCA 61.691 66.667 0.00 0.00 0.00 3.58
1251 3676 0.454620 CACCGTCGTCCTTCTTCTCG 60.455 60.000 0.00 0.00 0.00 4.04
1258 3683 0.459411 GTCCTTCTTCTCGAGCCTGC 60.459 60.000 7.81 0.00 0.00 4.85
1271 3696 2.677875 CCTGCTTGGAAGGGGTGC 60.678 66.667 0.00 0.00 38.35 5.01
3100 8350 7.687445 TGAAAATGATGTGACATGTCGATTAG 58.313 34.615 20.54 0.00 0.00 1.73
3138 8393 3.211718 TGTTAACTAGCACCCCGTTTT 57.788 42.857 7.22 0.00 0.00 2.43
3163 8418 3.329929 AGACCATGTCGACTAAAACCC 57.670 47.619 17.92 0.36 37.67 4.11
3177 8432 6.649557 CGACTAAAACCCAAGTCATTCTACTT 59.350 38.462 3.65 0.00 41.83 2.24
3243 8618 7.649705 ACACGATAGCTAAATGTCAATAGACTG 59.350 37.037 0.00 0.00 42.71 3.51
3256 8631 8.932945 TGTCAATAGACTGACTTTAGCTATTG 57.067 34.615 0.00 0.00 45.03 1.90
3343 8743 8.246615 ACCCCATTATCTATCTTAGGGTTTAGA 58.753 37.037 0.00 0.00 44.14 2.10
3344 8744 8.763601 CCCCATTATCTATCTTAGGGTTTAGAG 58.236 40.741 0.00 0.00 32.90 2.43
3349 8749 9.589461 TTATCTATCTTAGGGTTTAGAGTGAGG 57.411 37.037 0.00 0.00 0.00 3.86
3385 8787 1.262640 GGTAGGGCTTCACGGGAGAA 61.263 60.000 0.00 0.00 0.00 2.87
3407 8809 2.987355 AAATTGAACGTGGGCGGGGT 62.987 55.000 0.00 0.00 43.45 4.95
3465 8867 4.410400 GTGGTTCAGGGGAGGGCG 62.410 72.222 0.00 0.00 0.00 6.13
3541 8944 1.974343 GCCGGTGGTATGTTTGGCA 60.974 57.895 1.90 0.00 42.03 4.92
3542 8945 1.880186 CCGGTGGTATGTTTGGCAC 59.120 57.895 0.00 0.00 0.00 5.01
3546 8949 1.519408 GTGGTATGTTTGGCACGTCT 58.481 50.000 0.00 0.00 0.00 4.18
3552 8955 4.092968 GGTATGTTTGGCACGTCTAAGAAG 59.907 45.833 0.00 0.00 0.00 2.85
3553 8956 3.462483 TGTTTGGCACGTCTAAGAAGA 57.538 42.857 0.00 0.00 0.00 2.87
3554 8957 3.799366 TGTTTGGCACGTCTAAGAAGAA 58.201 40.909 0.00 0.00 32.16 2.52
3601 9004 4.683781 GCAATCTGCACCGTTTATTTTTCA 59.316 37.500 0.00 0.00 44.26 2.69
3604 9007 5.054390 TCTGCACCGTTTATTTTTCATCC 57.946 39.130 0.00 0.00 0.00 3.51
3605 9008 4.520874 TCTGCACCGTTTATTTTTCATCCA 59.479 37.500 0.00 0.00 0.00 3.41
3606 9009 5.010112 TCTGCACCGTTTATTTTTCATCCAA 59.990 36.000 0.00 0.00 0.00 3.53
3611 9014 4.481463 CGTTTATTTTTCATCCAACGGCT 58.519 39.130 0.00 0.00 34.72 5.52
3616 9019 4.599047 TTTTTCATCCAACGGCTGAAAT 57.401 36.364 11.60 0.00 43.97 2.17
3623 9026 3.153130 TCCAACGGCTGAAATGAAATCA 58.847 40.909 0.00 0.00 0.00 2.57
3685 9088 5.068987 GCCATTCCCTTATTGCACATCTAAA 59.931 40.000 0.00 0.00 0.00 1.85
3792 9198 9.277783 GAATTAGATGTACAATACTTGGAGCAT 57.722 33.333 0.00 0.00 34.12 3.79
3803 9209 8.654997 ACAATACTTGGAGCATATCTAGATGTT 58.345 33.333 15.79 0.00 34.12 2.71
3849 9255 2.036556 AGAAAAATTGTCACGCTGCG 57.963 45.000 21.91 21.91 0.00 5.18
3863 9269 1.136565 CTGCGCGGTTGTATTTGGG 59.863 57.895 8.83 0.00 0.00 4.12
3868 9274 0.679960 GCGGTTGTATTTGGGGAGCT 60.680 55.000 0.00 0.00 0.00 4.09
3871 9277 2.525368 GGTTGTATTTGGGGAGCTGTT 58.475 47.619 0.00 0.00 0.00 3.16
3872 9278 2.897326 GGTTGTATTTGGGGAGCTGTTT 59.103 45.455 0.00 0.00 0.00 2.83
3909 9315 1.302431 TCTGCACCCACCAACGATG 60.302 57.895 0.00 0.00 0.00 3.84
3913 9319 1.644786 GCACCCACCAACGATGCTAC 61.645 60.000 0.00 0.00 33.44 3.58
3921 9327 1.086696 CAACGATGCTACCCCAACTG 58.913 55.000 0.00 0.00 0.00 3.16
3925 9331 0.249398 GATGCTACCCCAACTGACGT 59.751 55.000 0.00 0.00 0.00 4.34
3946 9352 1.572085 CCTTGCAGCTTGTCCTCACG 61.572 60.000 0.00 0.00 0.00 4.35
3971 9377 0.307760 GGTTGAGGTGTTTCGCACTG 59.692 55.000 0.00 0.00 46.86 3.66
4024 9430 0.101579 GAGTAGAGGTTGCTCTCGGC 59.898 60.000 0.00 0.00 38.71 5.54
4037 9443 3.685214 CTCGGCGAACTCCAGGTCG 62.685 68.421 12.13 9.75 0.00 4.79
4046 9452 2.169832 ACTCCAGGTCGTGTTGATTG 57.830 50.000 0.00 0.00 0.00 2.67
4062 9468 2.286872 GATTGTGTCTCTGATGCCTGG 58.713 52.381 0.00 0.00 0.00 4.45
4063 9469 0.325933 TTGTGTCTCTGATGCCTGGG 59.674 55.000 0.00 0.00 0.00 4.45
4064 9470 1.451028 GTGTCTCTGATGCCTGGGC 60.451 63.158 4.43 4.43 42.35 5.36
4065 9471 1.614525 TGTCTCTGATGCCTGGGCT 60.615 57.895 13.05 0.00 42.51 5.19
4066 9472 1.203441 TGTCTCTGATGCCTGGGCTT 61.203 55.000 13.05 6.44 42.51 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 1.289066 CTCGCGAAGGAGGTTGTCA 59.711 57.895 11.33 0.00 0.00 3.58
91 92 2.093658 ACGACAATGCTACCCTAGTTGG 60.094 50.000 0.00 0.00 0.00 3.77
144 148 0.176680 CTATGACACCTTGGCGAGCT 59.823 55.000 0.00 0.00 0.00 4.09
189 193 3.068165 TCGGTCATATCGCTCAATTCTGT 59.932 43.478 0.00 0.00 0.00 3.41
215 220 0.034896 CCGGTGTAAGTGTTGCCTCT 59.965 55.000 0.00 0.00 0.00 3.69
251 256 0.038166 TCTCCAAAGGTCACCATGCC 59.962 55.000 0.00 0.00 0.00 4.40
255 260 3.493699 CGTTAACTCTCCAAAGGTCACCA 60.494 47.826 0.00 0.00 0.00 4.17
275 280 2.388232 GCGGGATCGTTGCTTTCGT 61.388 57.895 0.00 0.00 38.89 3.85
303 308 0.458543 CAAGTCACCAGATCGTCCCG 60.459 60.000 0.00 0.00 0.00 5.14
336 341 1.738099 CAAGACCTCGCCGTTCCAG 60.738 63.158 0.00 0.00 0.00 3.86
344 349 1.372087 CCAAGGATGCAAGACCTCGC 61.372 60.000 10.16 0.00 35.25 5.03
354 359 3.683365 AATTCAAACCACCAAGGATGC 57.317 42.857 0.00 0.00 41.22 3.91
359 364 7.807907 GTGATTACACTAATTCAAACCACCAAG 59.192 37.037 0.00 0.00 42.99 3.61
409 414 8.116753 CCGATCAATACATAACTGTTTGAAGAC 58.883 37.037 0.00 0.00 36.69 3.01
417 422 5.050490 GTGAGCCGATCAATACATAACTGT 58.950 41.667 0.00 0.00 40.43 3.55
433 438 1.359848 GGTAACATGTCTGTGAGCCG 58.640 55.000 0.00 0.00 35.22 5.52
438 443 2.465860 TTCGGGGTAACATGTCTGTG 57.534 50.000 0.00 0.00 35.22 3.66
483 488 6.996879 GGTTACTTCTCTTTTGAACCCTAGTT 59.003 38.462 0.00 0.00 39.54 2.24
486 491 6.465321 CCTGGTTACTTCTCTTTTGAACCCTA 60.465 42.308 0.00 0.00 36.34 3.53
487 492 5.377478 CTGGTTACTTCTCTTTTGAACCCT 58.623 41.667 0.00 0.00 36.34 4.34
488 493 4.519350 CCTGGTTACTTCTCTTTTGAACCC 59.481 45.833 0.00 0.00 36.34 4.11
490 495 4.319549 CGCCTGGTTACTTCTCTTTTGAAC 60.320 45.833 0.00 0.00 0.00 3.18
492 497 3.070446 TCGCCTGGTTACTTCTCTTTTGA 59.930 43.478 0.00 0.00 0.00 2.69
493 498 3.186613 GTCGCCTGGTTACTTCTCTTTTG 59.813 47.826 0.00 0.00 0.00 2.44
495 500 2.609737 CGTCGCCTGGTTACTTCTCTTT 60.610 50.000 0.00 0.00 0.00 2.52
496 501 1.067776 CGTCGCCTGGTTACTTCTCTT 60.068 52.381 0.00 0.00 0.00 2.85
499 504 1.590147 CCGTCGCCTGGTTACTTCT 59.410 57.895 0.00 0.00 0.00 2.85
500 505 2.098831 GCCGTCGCCTGGTTACTTC 61.099 63.158 0.00 0.00 0.00 3.01
502 507 4.430765 CGCCGTCGCCTGGTTACT 62.431 66.667 0.00 0.00 0.00 2.24
503 508 3.919973 TTCGCCGTCGCCTGGTTAC 62.920 63.158 0.00 0.00 35.26 2.50
504 509 3.636313 CTTCGCCGTCGCCTGGTTA 62.636 63.158 0.00 0.00 35.26 2.85
517 522 4.982295 AGCAAAATCCAAAAGTTACTTCGC 59.018 37.500 0.00 0.00 0.00 4.70
522 527 6.422701 GGTGGTTAGCAAAATCCAAAAGTTAC 59.577 38.462 0.00 0.00 0.00 2.50
526 531 3.987220 CGGTGGTTAGCAAAATCCAAAAG 59.013 43.478 0.00 0.00 0.00 2.27
534 539 2.224549 CGATGTTCGGTGGTTAGCAAAA 59.775 45.455 0.00 0.00 36.00 2.44
575 580 5.723672 TTTGACGATCCTAAGAGTGTTCT 57.276 39.130 0.00 0.00 34.29 3.01
580 585 3.952323 TCGGATTTGACGATCCTAAGAGT 59.048 43.478 0.00 0.00 42.84 3.24
582 587 4.994907 TTCGGATTTGACGATCCTAAGA 57.005 40.909 0.00 0.00 42.84 2.10
587 592 4.588278 GTTTGATTCGGATTTGACGATCC 58.412 43.478 0.00 0.00 41.82 3.36
590 595 2.159761 GCGTTTGATTCGGATTTGACGA 60.160 45.455 9.85 0.00 38.78 4.20
596 601 1.127951 GTCACGCGTTTGATTCGGATT 59.872 47.619 10.22 0.00 0.00 3.01
606 611 3.963724 CGTAGAAAAATTGTCACGCGTTT 59.036 39.130 10.22 0.00 0.00 3.60
609 614 1.896193 GCGTAGAAAAATTGTCACGCG 59.104 47.619 3.53 3.53 44.14 6.01
612 617 6.747659 AACATTGCGTAGAAAAATTGTCAC 57.252 33.333 0.00 0.00 0.00 3.67
615 620 7.516627 GCAGAAAACATTGCGTAGAAAAATTGT 60.517 33.333 0.00 0.00 0.00 2.71
621 626 4.560136 TGCAGAAAACATTGCGTAGAAA 57.440 36.364 0.00 0.00 43.13 2.52
622 627 4.560136 TTGCAGAAAACATTGCGTAGAA 57.440 36.364 0.00 0.00 43.13 2.10
626 631 5.482686 AAAAATTGCAGAAAACATTGCGT 57.517 30.435 0.00 0.00 43.13 5.24
655 668 1.231221 AAAGCGACAATTGCCGTGTA 58.769 45.000 15.64 0.00 0.00 2.90
659 672 0.098728 CCCTAAAGCGACAATTGCCG 59.901 55.000 10.02 10.02 0.00 5.69
664 677 1.340991 ACCATGCCCTAAAGCGACAAT 60.341 47.619 0.00 0.00 34.65 2.71
667 680 2.032680 TTACCATGCCCTAAAGCGAC 57.967 50.000 0.00 0.00 34.65 5.19
670 683 1.754803 GGGTTTACCATGCCCTAAAGC 59.245 52.381 0.69 4.41 39.31 3.51
677 690 2.406596 TCGTAAGGGTTTACCATGCC 57.593 50.000 0.69 0.00 43.89 4.40
714 727 9.720667 CAGAATTGACATGCGAAAATAGATAAA 57.279 29.630 0.00 0.00 0.00 1.40
715 728 8.892723 ACAGAATTGACATGCGAAAATAGATAA 58.107 29.630 0.00 0.00 0.00 1.75
716 729 8.337532 CACAGAATTGACATGCGAAAATAGATA 58.662 33.333 0.00 0.00 0.00 1.98
717 730 7.191551 CACAGAATTGACATGCGAAAATAGAT 58.808 34.615 0.00 0.00 0.00 1.98
718 731 6.545508 CACAGAATTGACATGCGAAAATAGA 58.454 36.000 0.00 0.00 0.00 1.98
719 732 5.228635 GCACAGAATTGACATGCGAAAATAG 59.771 40.000 0.00 0.00 0.00 1.73
720 733 5.094812 GCACAGAATTGACATGCGAAAATA 58.905 37.500 0.00 0.00 0.00 1.40
721 734 3.922240 GCACAGAATTGACATGCGAAAAT 59.078 39.130 0.00 0.00 0.00 1.82
723 736 2.932498 GCACAGAATTGACATGCGAAA 58.068 42.857 0.00 0.00 0.00 3.46
724 737 2.617250 GCACAGAATTGACATGCGAA 57.383 45.000 0.00 0.00 0.00 4.70
727 740 1.466360 GGACGCACAGAATTGACATGC 60.466 52.381 0.00 0.00 0.00 4.06
728 741 1.201954 CGGACGCACAGAATTGACATG 60.202 52.381 0.00 0.00 0.00 3.21
730 743 1.565156 GCGGACGCACAGAATTGACA 61.565 55.000 12.31 0.00 41.49 3.58
731 744 1.132640 GCGGACGCACAGAATTGAC 59.867 57.895 12.31 0.00 41.49 3.18
732 745 1.005037 AGCGGACGCACAGAATTGA 60.005 52.632 19.48 0.00 44.88 2.57
733 746 1.133253 CAGCGGACGCACAGAATTG 59.867 57.895 19.48 2.50 44.88 2.32
734 747 2.034879 CCAGCGGACGCACAGAATT 61.035 57.895 19.48 0.00 44.88 2.17
736 749 4.680237 CCCAGCGGACGCACAGAA 62.680 66.667 19.48 0.00 44.88 3.02
738 751 4.680237 TTCCCAGCGGACGCACAG 62.680 66.667 19.48 8.03 44.88 3.66
739 752 3.545124 ATTTCCCAGCGGACGCACA 62.545 57.895 19.48 0.00 44.88 4.57
741 754 1.175983 AAAATTTCCCAGCGGACGCA 61.176 50.000 19.48 0.00 44.88 5.24
743 756 3.562567 TTAAAAATTTCCCAGCGGACG 57.437 42.857 0.00 0.00 38.14 4.79
747 760 5.061684 GTCGGATTTTAAAAATTTCCCAGCG 59.938 40.000 4.44 0.00 0.00 5.18
748 761 5.061684 CGTCGGATTTTAAAAATTTCCCAGC 59.938 40.000 4.44 0.00 0.00 4.85
749 762 6.153756 ACGTCGGATTTTAAAAATTTCCCAG 58.846 36.000 4.44 3.83 0.00 4.45
751 764 6.151004 TGACGTCGGATTTTAAAAATTTCCC 58.849 36.000 11.62 1.52 0.00 3.97
752 765 6.859508 ACTGACGTCGGATTTTAAAAATTTCC 59.140 34.615 30.55 6.84 0.00 3.13
757 770 7.249147 TCAAAACTGACGTCGGATTTTAAAAA 58.751 30.769 30.55 14.29 0.00 1.94
759 772 6.360844 TCAAAACTGACGTCGGATTTTAAA 57.639 33.333 30.55 18.04 0.00 1.52
766 779 2.619147 TGTTTCAAAACTGACGTCGGA 58.381 42.857 30.55 4.90 39.59 4.55
799 812 3.500680 GGAGGTACGCACATCAAGAAAAA 59.499 43.478 2.49 0.00 37.20 1.94
808 821 1.317431 TGCTACGGAGGTACGCACAT 61.317 55.000 0.00 0.00 37.37 3.21
812 825 1.877165 GCTTGCTACGGAGGTACGC 60.877 63.158 0.00 0.00 37.37 4.42
818 831 1.959899 CTTGCGTGCTTGCTACGGAG 61.960 60.000 15.14 0.00 42.57 4.63
851 865 1.284198 CTGATGGGATGGGATGGGATC 59.716 57.143 0.00 0.00 0.00 3.36
904 918 1.610522 GCAGACAACCAACTTGCATCT 59.389 47.619 0.00 0.00 32.41 2.90
939 954 4.457496 AGGATCACGCAGGCCACG 62.457 66.667 15.81 15.81 0.00 4.94
1083 1108 4.385405 AGCTGGCGCTGGACTGAC 62.385 66.667 7.64 0.00 46.86 3.51
1131 3540 2.707257 GGGGACGGGATTAGAATAACCA 59.293 50.000 0.00 0.00 0.00 3.67
1216 3628 3.691342 TGACAGGGAGGCGAACGG 61.691 66.667 0.00 0.00 0.00 4.44
1218 3630 2.047179 GGTGACAGGGAGGCGAAC 60.047 66.667 0.00 0.00 0.00 3.95
1222 3634 4.436998 CGACGGTGACAGGGAGGC 62.437 72.222 0.00 0.00 0.00 4.70
1229 3641 0.313043 GAAGAAGGACGACGGTGACA 59.687 55.000 0.00 0.00 0.00 3.58
1233 3645 0.604780 TCGAGAAGAAGGACGACGGT 60.605 55.000 0.00 0.00 0.00 4.83
1251 3676 2.044551 CCCCTTCCAAGCAGGCTC 60.045 66.667 0.00 0.00 37.29 4.70
1258 3683 2.045926 CTCCGCACCCCTTCCAAG 60.046 66.667 0.00 0.00 0.00 3.61
3067 8313 9.761504 ACATGTCACATCATTTTCAAACAAATA 57.238 25.926 0.00 0.00 0.00 1.40
3100 8350 7.147976 AGTTAACAACTGAATGGCTTCAATTC 58.852 34.615 8.61 0.00 40.78 2.17
3138 8393 6.350445 GGGTTTTAGTCGACATGGTCTTACTA 60.350 42.308 19.50 0.00 31.95 1.82
3177 8432 7.433708 TTTAGAATTTGCTTCAACTCGATCA 57.566 32.000 0.00 0.00 36.24 2.92
3238 8613 5.246203 TGACCACAATAGCTAAAGTCAGTCT 59.754 40.000 18.98 0.00 0.00 3.24
3243 8618 4.563184 CGACTGACCACAATAGCTAAAGTC 59.437 45.833 0.00 1.54 0.00 3.01
3281 8656 2.115427 CCCTTCTCCTTCCTTCTCCTC 58.885 57.143 0.00 0.00 0.00 3.71
3315 8712 8.450780 AAACCCTAAGATAGATAATGGGGTAG 57.549 38.462 0.00 0.00 44.14 3.18
3390 8792 2.127027 TAACCCCGCCCACGTTCAAT 62.127 55.000 0.00 0.00 37.70 2.57
3391 8793 2.734948 CTAACCCCGCCCACGTTCAA 62.735 60.000 0.00 0.00 37.70 2.69
3392 8794 3.240011 TAACCCCGCCCACGTTCA 61.240 61.111 0.00 0.00 37.70 3.18
3393 8795 2.435410 CTAACCCCGCCCACGTTC 60.435 66.667 0.00 0.00 37.70 3.95
3395 8797 3.387947 CTCTAACCCCGCCCACGT 61.388 66.667 0.00 0.00 37.70 4.49
3396 8798 4.157120 CCTCTAACCCCGCCCACG 62.157 72.222 0.00 0.00 39.67 4.94
3397 8799 3.793888 CCCTCTAACCCCGCCCAC 61.794 72.222 0.00 0.00 0.00 4.61
3398 8800 3.341469 ATCCCTCTAACCCCGCCCA 62.341 63.158 0.00 0.00 0.00 5.36
3407 8809 2.447765 CCCCGGCCATCCCTCTAA 60.448 66.667 2.24 0.00 0.00 2.10
3440 8842 4.344865 CCTGAACCACCCCCACCG 62.345 72.222 0.00 0.00 0.00 4.94
3441 8843 3.979497 CCCTGAACCACCCCCACC 61.979 72.222 0.00 0.00 0.00 4.61
3524 8927 1.880186 GTGCCAAACATACCACCGG 59.120 57.895 0.00 0.00 0.00 5.28
3541 8944 6.294286 CCAGACTTCTTCTTCTTCTTAGACGT 60.294 42.308 0.00 0.00 28.96 4.34
3542 8945 6.072397 TCCAGACTTCTTCTTCTTCTTAGACG 60.072 42.308 0.00 0.00 28.96 4.18
3546 8949 9.184523 CTATCTCCAGACTTCTTCTTCTTCTTA 57.815 37.037 0.00 0.00 28.96 2.10
3552 8955 7.639113 TCTTCTATCTCCAGACTTCTTCTTC 57.361 40.000 0.00 0.00 28.96 2.87
3553 8956 7.363793 GCTTCTTCTATCTCCAGACTTCTTCTT 60.364 40.741 0.00 0.00 28.96 2.52
3554 8957 6.096846 GCTTCTTCTATCTCCAGACTTCTTCT 59.903 42.308 0.00 0.00 33.33 2.85
3599 9002 2.488204 TCATTTCAGCCGTTGGATGA 57.512 45.000 0.00 0.00 46.95 2.92
3601 9004 3.763360 TGATTTCATTTCAGCCGTTGGAT 59.237 39.130 0.00 0.00 0.00 3.41
3604 9007 4.383649 CAGTTGATTTCATTTCAGCCGTTG 59.616 41.667 0.00 0.00 0.00 4.10
3605 9008 4.278170 TCAGTTGATTTCATTTCAGCCGTT 59.722 37.500 0.00 0.00 0.00 4.44
3606 9009 3.820467 TCAGTTGATTTCATTTCAGCCGT 59.180 39.130 0.00 0.00 0.00 5.68
3611 9014 4.141287 ACGGGTCAGTTGATTTCATTTCA 58.859 39.130 0.00 0.00 0.00 2.69
3616 9019 4.900684 TGAATACGGGTCAGTTGATTTCA 58.099 39.130 0.00 0.00 0.00 2.69
3623 9026 5.183140 CCTGAAAAATGAATACGGGTCAGTT 59.817 40.000 0.00 0.00 34.96 3.16
3659 9062 2.818921 TGTGCAATAAGGGAATGGCTT 58.181 42.857 0.00 0.00 0.00 4.35
3685 9088 8.908786 TTGTTCTTTCTAGTTTGATGAGTCAT 57.091 30.769 4.98 4.98 33.56 3.06
3770 9173 9.314133 AGATATGCTCCAAGTATTGTACATCTA 57.686 33.333 0.00 0.00 46.99 1.98
3772 9175 9.579768 CTAGATATGCTCCAAGTATTGTACATC 57.420 37.037 0.00 0.00 46.99 3.06
3773 9176 9.314133 TCTAGATATGCTCCAAGTATTGTACAT 57.686 33.333 0.00 0.00 46.99 2.29
3774 9177 8.706322 TCTAGATATGCTCCAAGTATTGTACA 57.294 34.615 0.00 0.00 46.99 2.90
3776 9179 9.314133 ACATCTAGATATGCTCCAAGTATTGTA 57.686 33.333 4.54 0.00 46.99 2.41
3777 9180 8.200024 ACATCTAGATATGCTCCAAGTATTGT 57.800 34.615 4.54 0.00 46.99 2.71
3829 9235 3.181826 CGCAGCGTGACAATTTTTCTA 57.818 42.857 6.65 0.00 0.00 2.10
3849 9255 0.679960 AGCTCCCCAAATACAACCGC 60.680 55.000 0.00 0.00 0.00 5.68
3858 9264 0.260230 TGGTGAAACAGCTCCCCAAA 59.740 50.000 0.00 0.00 39.98 3.28
3868 9274 2.112297 GGCGGAGGTGGTGAAACA 59.888 61.111 0.00 0.00 39.98 2.83
3871 9277 3.948719 GTGGGCGGAGGTGGTGAA 61.949 66.667 0.00 0.00 0.00 3.18
3901 9307 0.035439 AGTTGGGGTAGCATCGTTGG 60.035 55.000 0.00 0.00 0.00 3.77
3909 9315 2.033194 GCACGTCAGTTGGGGTAGC 61.033 63.158 0.00 0.00 0.00 3.58
3913 9319 2.113139 AAGGCACGTCAGTTGGGG 59.887 61.111 0.00 0.00 0.00 4.96
3921 9327 2.253452 CAAGCTGCAAGGCACGTC 59.747 61.111 1.02 0.00 33.79 4.34
3925 9331 1.601759 GAGGACAAGCTGCAAGGCA 60.602 57.895 1.02 0.00 36.92 4.75
3946 9352 2.143925 CGAAACACCTCAACCTCCTTC 58.856 52.381 0.00 0.00 0.00 3.46
3971 9377 1.936547 CCAAAGGCACTATCGAAGCTC 59.063 52.381 0.00 0.00 38.49 4.09
4024 9430 0.031585 TCAACACGACCTGGAGTTCG 59.968 55.000 0.00 1.57 0.00 3.95
4037 9443 3.120060 GGCATCAGAGACACAATCAACAC 60.120 47.826 0.00 0.00 0.00 3.32
4046 9452 1.451028 GCCCAGGCATCAGAGACAC 60.451 63.158 3.12 0.00 41.49 3.67


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

AutoCloner maintained by Alex Coulton.