Multiple sequence alignment - TraesCS1D01G442800

Loading Multiple Alignment...

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 TraesCS1D01G442800 chr1D 100.000 3766 0 0 1 3766 486927372 486923607 0.000000e+00 6955.0
1 TraesCS1D01G442800 chr1D 100.000 29 0 0 3267 3295 486924178 486924150 2.000000e-03 54.7
2 TraesCS1D01G442800 chr1B 95.037 3103 41 20 1 3047 678117251 678114206 0.000000e+00 4772.0
3 TraesCS1D01G442800 chr1B 99.611 257 1 0 3335 3591 678114112 678113856 1.580000e-128 470.0
4 TraesCS1D01G442800 chr1B 98.901 91 1 0 3143 3233 678114205 678114115 3.010000e-36 163.0
5 TraesCS1D01G442800 chr1B 100.000 72 0 0 3695 3766 678113688 678113617 2.360000e-27 134.0
6 TraesCS1D01G442800 chr1B 100.000 29 0 0 3267 3295 678114153 678114125 2.000000e-03 54.7
7 TraesCS1D01G442800 chr1B 100.000 29 0 0 3304 3332 678114205 678114177 2.000000e-03 54.7
8 TraesCS1D01G442800 chr7D 86.786 1506 138 35 1763 3227 66516499 66515014 0.000000e+00 1622.0
9 TraesCS1D01G442800 chr7D 85.768 794 69 18 813 1586 66538829 66538060 0.000000e+00 800.0
10 TraesCS1D01G442800 chr7D 90.636 566 42 3 985 1550 68801659 68802213 0.000000e+00 741.0
11 TraesCS1D01G442800 chr7D 89.474 589 51 3 962 1550 66517144 66516567 0.000000e+00 734.0
12 TraesCS1D01G442800 chr7D 88.702 593 43 14 2419 2991 68802957 68803545 0.000000e+00 702.0
13 TraesCS1D01G442800 chr7D 88.649 555 47 12 1763 2305 68802281 68802831 0.000000e+00 662.0
14 TraesCS1D01G442800 chr7D 82.951 698 81 9 4 699 231389917 231389256 2.500000e-166 595.0
15 TraesCS1D01G442800 chr7D 89.731 409 40 2 1106 1513 68918930 68919337 4.310000e-144 521.0
16 TraesCS1D01G442800 chr7D 85.830 494 52 10 1741 2233 68919464 68919940 3.360000e-140 508.0
17 TraesCS1D01G442800 chr7D 95.302 298 13 1 3461 3758 68803937 68804233 4.400000e-129 472.0
18 TraesCS1D01G442800 chr7D 95.122 205 9 1 3554 3758 66514905 66514702 4.690000e-84 322.0
19 TraesCS1D01G442800 chr7D 91.518 224 15 2 3478 3701 68922219 68922438 4.730000e-79 305.0
20 TraesCS1D01G442800 chr7D 85.621 306 22 4 810 1115 68917470 68917753 6.110000e-78 302.0
21 TraesCS1D01G442800 chr7D 76.829 574 53 37 2685 3209 68911256 68911798 2.250000e-62 250.0
22 TraesCS1D01G442800 chr7D 95.918 147 6 0 3336 3482 68803862 68804008 4.860000e-59 239.0
23 TraesCS1D01G442800 chr7D 88.462 182 10 4 3057 3227 68803677 68803858 3.810000e-50 209.0
24 TraesCS1D01G442800 chr7D 83.929 224 26 3 2984 3207 68804759 68804972 4.930000e-49 206.0
25 TraesCS1D01G442800 chr7D 99.065 107 1 0 3336 3442 66515010 66514904 3.840000e-45 193.0
26 TraesCS1D01G442800 chr7D 82.470 251 12 11 699 921 66517396 66517150 1.380000e-44 191.0
27 TraesCS1D01G442800 chr7D 95.192 104 4 1 810 912 68801529 68801632 3.010000e-36 163.0
28 TraesCS1D01G442800 chr7D 93.458 107 3 2 819 921 68901795 68901901 5.040000e-34 156.0
29 TraesCS1D01G442800 chr7D 94.318 88 5 0 2984 3071 68803571 68803658 6.560000e-28 135.0
30 TraesCS1D01G442800 chr7D 87.324 71 8 1 695 765 68801342 68801411 3.120000e-11 80.5
31 TraesCS1D01G442800 chr7D 100.000 31 0 0 3032 3062 68911699 68911729 1.460000e-04 58.4
32 TraesCS1D01G442800 chr7B 87.195 1148 98 28 2117 3227 10209758 10210893 0.000000e+00 1260.0
33 TraesCS1D01G442800 chr7B 84.226 1382 119 56 961 2312 10208450 10209762 0.000000e+00 1253.0
34 TraesCS1D01G442800 chr7B 84.233 1148 93 31 2125 3227 9812736 9813840 0.000000e+00 1037.0
35 TraesCS1D01G442800 chr7B 92.373 708 44 3 816 1523 9811314 9812011 0.000000e+00 1000.0
36 TraesCS1D01G442800 chr7B 87.424 827 65 21 699 1504 10101763 10102571 0.000000e+00 915.0
37 TraesCS1D01G442800 chr7B 86.909 634 59 12 1763 2385 10102677 10103297 0.000000e+00 689.0
38 TraesCS1D01G442800 chr7B 85.738 603 52 17 1734 2334 9812151 9812721 1.160000e-169 606.0
39 TraesCS1D01G442800 chr7B 92.435 423 19 4 3335 3757 9813843 9814252 3.240000e-165 592.0
40 TraesCS1D01G442800 chr7B 81.223 703 97 18 1 699 444121384 444122055 5.540000e-148 534.0
41 TraesCS1D01G442800 chr7B 89.548 354 23 4 3336 3688 10210897 10211237 1.610000e-118 436.0
42 TraesCS1D01G442800 chr7B 93.796 274 16 1 3478 3751 10104120 10104392 9.740000e-111 411.0
43 TraesCS1D01G442800 chr7B 76.102 590 97 25 820 1381 592418980 592418407 6.200000e-68 268.0
44 TraesCS1D01G442800 chr7B 83.088 272 30 9 2125 2381 10104102 10104372 2.260000e-57 233.0
45 TraesCS1D01G442800 chr7B 81.731 208 10 10 731 912 10208234 10208439 8.430000e-32 148.0
46 TraesCS1D01G442800 chr7B 78.571 182 32 5 1 181 524812959 524812784 3.070000e-21 113.0
47 TraesCS1D01G442800 chr7B 93.750 64 4 0 3164 3227 10103956 10104019 3.100000e-16 97.1
48 TraesCS1D01G442800 chr7B 100.000 31 0 0 1525 1555 9812032 9812062 1.460000e-04 58.4
49 TraesCS1D01G442800 chr7B 100.000 29 0 0 3267 3295 9813808 9813836 2.000000e-03 54.7
50 TraesCS1D01G442800 chr7B 100.000 28 0 0 1747 1774 10640110 10640137 7.000000e-03 52.8
51 TraesCS1D01G442800 chr7A 84.122 1310 114 35 1724 2986 74601951 74603213 0.000000e+00 1181.0
52 TraesCS1D01G442800 chr7A 89.510 715 40 12 813 1523 71134893 71134210 0.000000e+00 872.0
53 TraesCS1D01G442800 chr7A 87.158 732 66 14 959 1666 74601202 74601929 0.000000e+00 806.0
54 TraesCS1D01G442800 chr7A 84.078 873 82 18 1734 2600 71134125 71133304 0.000000e+00 789.0
55 TraesCS1D01G442800 chr7A 84.500 600 71 9 104 699 100178315 100178896 1.170000e-159 573.0
56 TraesCS1D01G442800 chr7A 93.280 372 23 2 3388 3758 74603668 74604038 7.110000e-152 547.0
57 TraesCS1D01G442800 chr7A 82.975 511 41 22 2625 3125 71121120 71120646 1.620000e-113 420.0
58 TraesCS1D01G442800 chr7A 90.909 242 16 4 3478 3719 71120485 71120250 1.690000e-83 320.0
59 TraesCS1D01G442800 chr7A 85.167 209 10 4 3030 3227 74603435 74603633 1.070000e-45 195.0
60 TraesCS1D01G442800 chr7A 86.986 146 13 5 3336 3476 71120581 71120437 3.890000e-35 159.0
61 TraesCS1D01G442800 chr7A 94.231 104 5 1 818 921 74592348 74592450 1.400000e-34 158.0
62 TraesCS1D01G442800 chr7A 71.614 694 142 35 1 688 561995345 561994701 5.070000e-29 139.0
63 TraesCS1D01G442800 chr7A 87.500 120 5 6 3030 3149 74603294 74603403 3.050000e-26 130.0
64 TraesCS1D01G442800 chr7A 85.496 131 11 6 820 943 74856766 74856895 3.050000e-26 130.0
65 TraesCS1D01G442800 chr7A 85.039 127 14 4 822 946 70247846 70247723 1.420000e-24 124.0
66 TraesCS1D01G442800 chr7A 85.965 114 9 3 3659 3766 70781395 70781283 8.550000e-22 115.0
67 TraesCS1D01G442800 chr7A 96.552 58 2 0 3170 3227 71120642 71120585 3.100000e-16 97.1
68 TraesCS1D01G442800 chr7A 97.059 34 1 0 3336 3369 74603637 74603670 1.460000e-04 58.4
69 TraesCS1D01G442800 chrUn 83.261 693 90 11 1 688 211918141 211918812 6.910000e-172 614.0
70 TraesCS1D01G442800 chrUn 84.392 378 54 5 1 376 434862411 434862037 2.140000e-97 366.0
71 TraesCS1D01G442800 chr6B 83.261 693 90 11 1 688 714411936 714411265 6.910000e-172 614.0
72 TraesCS1D01G442800 chr6B 76.937 568 110 16 1 562 63735813 63736365 1.700000e-78 303.0
73 TraesCS1D01G442800 chr2B 82.203 708 101 11 1 702 795984944 795984256 1.510000e-163 586.0
74 TraesCS1D01G442800 chr2D 84.743 544 63 7 152 691 2040697 2040170 9.270000e-146 527.0
75 TraesCS1D01G442800 chr6D 84.598 435 46 8 270 702 65646720 65646305 2.710000e-111 412.0
76 TraesCS1D01G442800 chr6D 85.043 234 31 4 1 231 65646950 65646718 6.290000e-58 235.0
77 TraesCS1D01G442800 chr5B 85.472 413 39 11 288 699 220583606 220583214 9.740000e-111 411.0
78 TraesCS1D01G442800 chr5B 91.892 74 6 0 622 695 665897422 665897495 1.850000e-18 104.0
79 TraesCS1D01G442800 chr4B 87.252 353 40 4 2141 2492 258794756 258794408 7.580000e-107 398.0
80 TraesCS1D01G442800 chr3A 91.403 221 15 2 3411 3628 694350572 694350791 2.200000e-77 300.0
81 TraesCS1D01G442800 chr3D 89.630 135 12 2 565 699 564375477 564375609 1.800000e-38 171.0


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 TraesCS1D01G442800 chr1D 486923607 486927372 3765 True 3504.850000 6955 100.000000 1 3766 2 chr1D.!!$R1 3765
1 TraesCS1D01G442800 chr1B 678113617 678117251 3634 True 941.400000 4772 98.924833 1 3766 6 chr1B.!!$R1 3765
2 TraesCS1D01G442800 chr7D 66538060 66538829 769 True 800.000000 800 85.768000 813 1586 1 chr7D.!!$R1 773
3 TraesCS1D01G442800 chr7D 66514702 66517396 2694 True 612.400000 1622 90.583400 699 3758 5 chr7D.!!$R3 3059
4 TraesCS1D01G442800 chr7D 231389256 231389917 661 True 595.000000 595 82.951000 4 699 1 chr7D.!!$R2 695
5 TraesCS1D01G442800 chr7D 68917470 68922438 4968 False 409.000000 521 88.175000 810 3701 4 chr7D.!!$F4 2891
6 TraesCS1D01G442800 chr7D 68801342 68804972 3630 False 360.950000 741 90.843200 695 3758 10 chr7D.!!$F2 3063
7 TraesCS1D01G442800 chr7B 10208234 10211237 3003 False 774.250000 1260 85.675000 731 3688 4 chr7B.!!$F5 2957
8 TraesCS1D01G442800 chr7B 9811314 9814252 2938 False 558.016667 1037 92.463167 816 3757 6 chr7B.!!$F3 2941
9 TraesCS1D01G442800 chr7B 444121384 444122055 671 False 534.000000 534 81.223000 1 699 1 chr7B.!!$F2 698
10 TraesCS1D01G442800 chr7B 10101763 10104392 2629 False 469.020000 915 88.993400 699 3751 5 chr7B.!!$F4 3052
11 TraesCS1D01G442800 chr7B 592418407 592418980 573 True 268.000000 268 76.102000 820 1381 1 chr7B.!!$R2 561
12 TraesCS1D01G442800 chr7A 71133304 71134893 1589 True 830.500000 872 86.794000 813 2600 2 chr7A.!!$R5 1787
13 TraesCS1D01G442800 chr7A 100178315 100178896 581 False 573.000000 573 84.500000 104 699 1 chr7A.!!$F3 595
14 TraesCS1D01G442800 chr7A 74601202 74604038 2836 False 486.233333 1181 89.047667 959 3758 6 chr7A.!!$F4 2799
15 TraesCS1D01G442800 chr7A 71120250 71121120 870 True 249.025000 420 89.355500 2625 3719 4 chr7A.!!$R4 1094
16 TraesCS1D01G442800 chrUn 211918141 211918812 671 False 614.000000 614 83.261000 1 688 1 chrUn.!!$F1 687
17 TraesCS1D01G442800 chr6B 714411265 714411936 671 True 614.000000 614 83.261000 1 688 1 chr6B.!!$R1 687
18 TraesCS1D01G442800 chr6B 63735813 63736365 552 False 303.000000 303 76.937000 1 562 1 chr6B.!!$F1 561
19 TraesCS1D01G442800 chr2B 795984256 795984944 688 True 586.000000 586 82.203000 1 702 1 chr2B.!!$R1 701
20 TraesCS1D01G442800 chr2D 2040170 2040697 527 True 527.000000 527 84.743000 152 691 1 chr2D.!!$R1 539
21 TraesCS1D01G442800 chr6D 65646305 65646950 645 True 323.500000 412 84.820500 1 702 2 chr6D.!!$R1 701

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
194 195 0.719465 CAACGATGGCACCTACGAAC 59.281 55.000 11.53 0.0 0.00 3.95 F
1578 2962 2.186826 GGATTCAACCGCGGGGATG 61.187 63.158 31.76 23.8 37.44 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 3186 2.124277 TACGAAGCAGAGGCAGAGTA 57.876 50.0 0.00 0.00 44.61 2.59 R
3318 6607 0.107508 ATACAACAGCGCTGGCATCT 60.108 50.0 38.27 17.02 43.41 2.90 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
35 36 1.338674 CCTGGTGTCATCGTGGCTTTA 60.339 52.381 0.00 0.00 0.00 1.85
194 195 0.719465 CAACGATGGCACCTACGAAC 59.281 55.000 11.53 0.00 0.00 3.95
940 1096 3.767268 ATCCCCGCCTCTCCTCCA 61.767 66.667 0.00 0.00 0.00 3.86
1578 2962 2.186826 GGATTCAACCGCGGGGATG 61.187 63.158 31.76 23.80 37.44 3.51
1723 3186 4.348486 TGAGGAAGATTCAGAGCAGTACT 58.652 43.478 0.00 0.00 0.00 2.73
1725 3188 5.358442 TGAGGAAGATTCAGAGCAGTACTAC 59.642 44.000 0.00 0.00 0.00 2.73
1726 3189 5.515106 AGGAAGATTCAGAGCAGTACTACT 58.485 41.667 0.00 0.00 0.00 2.57
1727 3190 5.592688 AGGAAGATTCAGAGCAGTACTACTC 59.407 44.000 14.37 14.37 0.00 2.59
1728 3191 5.592688 GGAAGATTCAGAGCAGTACTACTCT 59.407 44.000 18.37 18.37 44.06 3.24
2093 3567 1.213537 CGCCATTGCCAACTTCCTG 59.786 57.895 0.00 0.00 0.00 3.86
2412 5413 5.690865 ACAGACAAGTCAGTTTTCCCATTA 58.309 37.500 2.72 0.00 0.00 1.90
2639 5692 6.726230 CATGAGCTGTCTTCATTAATTCTGG 58.274 40.000 0.00 0.00 0.00 3.86
3138 6416 0.109132 CTTCAGCATTTGAACCGCCC 60.109 55.000 0.00 0.00 40.82 6.13
3155 6444 0.321346 CCCAGTGCATTTGTTTCCCC 59.679 55.000 0.00 0.00 0.00 4.81
3233 6522 5.163447 TGCAAGATATGTACTGGTAGTGGTC 60.163 44.000 0.00 0.00 0.00 4.02
3234 6523 5.069251 GCAAGATATGTACTGGTAGTGGTCT 59.931 44.000 0.00 0.00 0.00 3.85
3235 6524 6.407074 GCAAGATATGTACTGGTAGTGGTCTT 60.407 42.308 0.00 0.00 0.00 3.01
3236 6525 7.556844 CAAGATATGTACTGGTAGTGGTCTTT 58.443 38.462 0.00 0.00 0.00 2.52
3237 6526 7.735326 AGATATGTACTGGTAGTGGTCTTTT 57.265 36.000 0.00 0.00 0.00 2.27
3238 6527 7.556844 AGATATGTACTGGTAGTGGTCTTTTG 58.443 38.462 0.00 0.00 0.00 2.44
3239 6528 4.345859 TGTACTGGTAGTGGTCTTTTGG 57.654 45.455 0.00 0.00 0.00 3.28
3240 6529 2.951229 ACTGGTAGTGGTCTTTTGGG 57.049 50.000 0.00 0.00 0.00 4.12
3241 6530 2.414612 ACTGGTAGTGGTCTTTTGGGA 58.585 47.619 0.00 0.00 0.00 4.37
3242 6531 2.986728 ACTGGTAGTGGTCTTTTGGGAT 59.013 45.455 0.00 0.00 0.00 3.85
3243 6532 3.397955 ACTGGTAGTGGTCTTTTGGGATT 59.602 43.478 0.00 0.00 0.00 3.01
3244 6533 4.600111 ACTGGTAGTGGTCTTTTGGGATTA 59.400 41.667 0.00 0.00 0.00 1.75
3245 6534 5.253096 ACTGGTAGTGGTCTTTTGGGATTAT 59.747 40.000 0.00 0.00 0.00 1.28
3246 6535 6.147437 TGGTAGTGGTCTTTTGGGATTATT 57.853 37.500 0.00 0.00 0.00 1.40
3247 6536 6.557568 TGGTAGTGGTCTTTTGGGATTATTT 58.442 36.000 0.00 0.00 0.00 1.40
3248 6537 6.435904 TGGTAGTGGTCTTTTGGGATTATTTG 59.564 38.462 0.00 0.00 0.00 2.32
3249 6538 5.405935 AGTGGTCTTTTGGGATTATTTGC 57.594 39.130 0.00 0.00 0.00 3.68
3250 6539 5.086621 AGTGGTCTTTTGGGATTATTTGCT 58.913 37.500 0.00 0.00 0.00 3.91
3251 6540 5.047092 AGTGGTCTTTTGGGATTATTTGCTG 60.047 40.000 0.00 0.00 0.00 4.41
3252 6541 4.837860 TGGTCTTTTGGGATTATTTGCTGT 59.162 37.500 0.00 0.00 0.00 4.40
3253 6542 5.306678 TGGTCTTTTGGGATTATTTGCTGTT 59.693 36.000 0.00 0.00 0.00 3.16
3254 6543 5.639082 GGTCTTTTGGGATTATTTGCTGTTG 59.361 40.000 0.00 0.00 0.00 3.33
3255 6544 6.223120 GTCTTTTGGGATTATTTGCTGTTGT 58.777 36.000 0.00 0.00 0.00 3.32
3256 6545 7.375053 GTCTTTTGGGATTATTTGCTGTTGTA 58.625 34.615 0.00 0.00 0.00 2.41
3257 6546 8.034804 GTCTTTTGGGATTATTTGCTGTTGTAT 58.965 33.333 0.00 0.00 0.00 2.29
3258 6547 8.592809 TCTTTTGGGATTATTTGCTGTTGTATT 58.407 29.630 0.00 0.00 0.00 1.89
3259 6548 9.868277 CTTTTGGGATTATTTGCTGTTGTATTA 57.132 29.630 0.00 0.00 0.00 0.98
3263 6552 9.814899 TGGGATTATTTGCTGTTGTATTATTTG 57.185 29.630 0.00 0.00 0.00 2.32
3264 6553 8.764287 GGGATTATTTGCTGTTGTATTATTTGC 58.236 33.333 0.00 0.00 0.00 3.68
3265 6554 9.533253 GGATTATTTGCTGTTGTATTATTTGCT 57.467 29.630 0.00 0.00 0.00 3.91
3267 6556 6.651755 ATTTGCTGTTGTATTATTTGCTGC 57.348 33.333 0.00 0.00 0.00 5.25
3268 6557 4.780275 TGCTGTTGTATTATTTGCTGCA 57.220 36.364 0.00 0.00 0.00 4.41
3269 6558 4.735985 TGCTGTTGTATTATTTGCTGCAG 58.264 39.130 10.11 10.11 0.00 4.41
3270 6559 4.458642 TGCTGTTGTATTATTTGCTGCAGA 59.541 37.500 20.43 0.00 0.00 4.26
3271 6560 5.048154 TGCTGTTGTATTATTTGCTGCAGAA 60.048 36.000 20.43 2.96 0.00 3.02
3272 6561 5.863397 GCTGTTGTATTATTTGCTGCAGAAA 59.137 36.000 20.43 11.53 0.00 2.52
3273 6562 6.365789 GCTGTTGTATTATTTGCTGCAGAAAA 59.634 34.615 22.17 22.17 0.00 2.29
3274 6563 7.063780 GCTGTTGTATTATTTGCTGCAGAAAAT 59.936 33.333 30.80 30.80 37.13 1.82
3275 6564 8.242085 TGTTGTATTATTTGCTGCAGAAAATG 57.758 30.769 34.03 3.42 34.32 2.32
3276 6565 8.087136 TGTTGTATTATTTGCTGCAGAAAATGA 58.913 29.630 34.03 28.64 34.32 2.57
3277 6566 8.924691 GTTGTATTATTTGCTGCAGAAAATGAA 58.075 29.630 34.03 24.67 34.32 2.57
3278 6567 9.656040 TTGTATTATTTGCTGCAGAAAATGAAT 57.344 25.926 34.03 27.85 34.32 2.57
3279 6568 9.656040 TGTATTATTTGCTGCAGAAAATGAATT 57.344 25.926 34.03 19.05 34.32 2.17
3282 6571 9.834628 ATTATTTGCTGCAGAAAATGAATTTTG 57.165 25.926 34.03 0.00 39.86 2.44
3283 6572 4.735662 TGCTGCAGAAAATGAATTTTGC 57.264 36.364 20.43 5.77 39.86 3.68
3284 6573 4.127907 TGCTGCAGAAAATGAATTTTGCA 58.872 34.783 20.43 12.28 39.86 4.08
3285 6574 4.575236 TGCTGCAGAAAATGAATTTTGCAA 59.425 33.333 20.43 0.00 40.79 4.08
3286 6575 5.144359 GCTGCAGAAAATGAATTTTGCAAG 58.856 37.500 20.43 9.90 40.79 4.01
3287 6576 5.049954 GCTGCAGAAAATGAATTTTGCAAGA 60.050 36.000 20.43 0.00 40.79 3.02
3288 6577 6.348213 GCTGCAGAAAATGAATTTTGCAAGAT 60.348 34.615 20.43 0.00 40.79 2.40
3289 6578 7.148540 GCTGCAGAAAATGAATTTTGCAAGATA 60.149 33.333 20.43 0.00 40.79 1.98
3290 6579 8.780846 TGCAGAAAATGAATTTTGCAAGATAT 57.219 26.923 11.02 0.00 39.64 1.63
3291 6580 8.661257 TGCAGAAAATGAATTTTGCAAGATATG 58.339 29.630 11.02 0.00 39.64 1.78
3292 6581 8.662141 GCAGAAAATGAATTTTGCAAGATATGT 58.338 29.630 2.45 0.00 39.86 2.29
3296 6585 8.633075 AAATGAATTTTGCAAGATATGTACCG 57.367 30.769 2.45 0.00 0.00 4.02
3297 6586 5.577835 TGAATTTTGCAAGATATGTACCGC 58.422 37.500 2.45 0.00 0.00 5.68
3298 6587 4.568152 ATTTTGCAAGATATGTACCGCC 57.432 40.909 0.00 0.00 0.00 6.13
3299 6588 2.700722 TTGCAAGATATGTACCGCCA 57.299 45.000 0.00 0.00 0.00 5.69
3300 6589 2.700722 TGCAAGATATGTACCGCCAA 57.299 45.000 0.00 0.00 0.00 4.52
3301 6590 2.560504 TGCAAGATATGTACCGCCAAG 58.439 47.619 0.00 0.00 0.00 3.61
3302 6591 2.093181 TGCAAGATATGTACCGCCAAGT 60.093 45.455 0.00 0.00 0.00 3.16
3303 6592 2.287915 GCAAGATATGTACCGCCAAGTG 59.712 50.000 0.00 0.00 0.00 3.16
3304 6593 2.240493 AGATATGTACCGCCAAGTGC 57.760 50.000 0.00 0.00 0.00 4.40
3305 6594 1.484653 AGATATGTACCGCCAAGTGCA 59.515 47.619 0.00 0.00 41.33 4.57
3306 6595 2.104792 AGATATGTACCGCCAAGTGCAT 59.895 45.455 0.00 5.37 44.07 3.96
3307 6596 2.411628 TATGTACCGCCAAGTGCATT 57.588 45.000 5.35 0.00 39.68 3.56
3308 6597 1.544724 ATGTACCGCCAAGTGCATTT 58.455 45.000 0.00 0.00 39.68 2.32
3309 6598 0.595588 TGTACCGCCAAGTGCATTTG 59.404 50.000 14.58 14.58 41.33 2.32
3310 6599 0.596082 GTACCGCCAAGTGCATTTGT 59.404 50.000 19.19 4.83 41.33 2.83
3311 6600 1.000717 GTACCGCCAAGTGCATTTGTT 60.001 47.619 19.19 4.89 41.33 2.83
3312 6601 0.463620 ACCGCCAAGTGCATTTGTTT 59.536 45.000 19.19 0.00 41.33 2.83
3313 6602 1.139163 CCGCCAAGTGCATTTGTTTC 58.861 50.000 19.19 8.21 41.33 2.78
3314 6603 1.139163 CGCCAAGTGCATTTGTTTCC 58.861 50.000 19.19 5.43 41.33 3.13
3315 6604 1.511850 GCCAAGTGCATTTGTTTCCC 58.488 50.000 19.19 0.82 40.77 3.97
3316 6605 1.070601 GCCAAGTGCATTTGTTTCCCT 59.929 47.619 19.19 0.00 40.77 4.20
3317 6606 2.485302 GCCAAGTGCATTTGTTTCCCTT 60.485 45.455 19.19 0.00 40.77 3.95
3318 6607 3.244044 GCCAAGTGCATTTGTTTCCCTTA 60.244 43.478 19.19 0.00 40.77 2.69
3319 6608 4.559153 CCAAGTGCATTTGTTTCCCTTAG 58.441 43.478 19.19 0.00 0.00 2.18
3320 6609 4.280677 CCAAGTGCATTTGTTTCCCTTAGA 59.719 41.667 19.19 0.00 0.00 2.10
3321 6610 5.047092 CCAAGTGCATTTGTTTCCCTTAGAT 60.047 40.000 19.19 0.00 0.00 1.98
3322 6611 5.649782 AGTGCATTTGTTTCCCTTAGATG 57.350 39.130 0.00 0.00 0.00 2.90
3323 6612 4.082026 AGTGCATTTGTTTCCCTTAGATGC 60.082 41.667 0.00 0.00 38.97 3.91
3324 6613 3.195396 TGCATTTGTTTCCCTTAGATGCC 59.805 43.478 0.00 0.00 38.03 4.40
3325 6614 3.195396 GCATTTGTTTCCCTTAGATGCCA 59.805 43.478 0.00 0.00 34.03 4.92
3326 6615 4.678840 GCATTTGTTTCCCTTAGATGCCAG 60.679 45.833 0.00 0.00 34.03 4.85
3327 6616 2.128771 TGTTTCCCTTAGATGCCAGC 57.871 50.000 0.00 0.00 0.00 4.85
3328 6617 1.017387 GTTTCCCTTAGATGCCAGCG 58.983 55.000 0.00 0.00 0.00 5.18
3329 6618 0.748005 TTTCCCTTAGATGCCAGCGC 60.748 55.000 0.00 0.00 0.00 5.92
3330 6619 1.626356 TTCCCTTAGATGCCAGCGCT 61.626 55.000 2.64 2.64 35.36 5.92
3331 6620 1.890979 CCCTTAGATGCCAGCGCTG 60.891 63.158 30.52 30.52 35.36 5.18
3332 6621 1.153289 CCTTAGATGCCAGCGCTGT 60.153 57.895 33.75 17.78 35.36 4.40
3333 6622 0.745845 CCTTAGATGCCAGCGCTGTT 60.746 55.000 33.75 19.33 35.36 3.16
3675 7171 5.016173 TGTTGGGGGAGAAAATCATTACTG 58.984 41.667 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
194 195 1.437986 CCCCTAGAGGAAAGCGACG 59.562 63.158 0.00 0.00 38.24 5.12
318 329 2.732016 CGAGGGTCCACAACGACA 59.268 61.111 0.00 0.00 34.24 4.35
723 756 0.744414 ATTCCTCAACACATCCGCGG 60.744 55.000 22.12 22.12 0.00 6.46
940 1096 1.677637 GAGAGAAACCGAGCGGGGAT 61.678 60.000 14.07 0.00 41.60 3.85
1723 3186 2.124277 TACGAAGCAGAGGCAGAGTA 57.876 50.000 0.00 0.00 44.61 2.59
1725 3188 2.593346 AATACGAAGCAGAGGCAGAG 57.407 50.000 0.00 0.00 44.61 3.35
1726 3189 2.233676 TCAAATACGAAGCAGAGGCAGA 59.766 45.455 0.00 0.00 44.61 4.26
1727 3190 2.621338 TCAAATACGAAGCAGAGGCAG 58.379 47.619 0.00 0.00 44.61 4.85
1728 3191 2.760634 TCAAATACGAAGCAGAGGCA 57.239 45.000 0.00 0.00 44.61 4.75
1729 3192 2.289002 CCATCAAATACGAAGCAGAGGC 59.711 50.000 0.00 0.00 41.61 4.70
1730 3193 3.535561 ACCATCAAATACGAAGCAGAGG 58.464 45.455 0.00 0.00 0.00 3.69
2026 3499 3.280920 GATGATGTCGAGGGTCTGC 57.719 57.895 0.00 0.00 0.00 4.26
2093 3567 3.631145 TCTTCAGTCAATGCAGCAAAC 57.369 42.857 0.00 0.00 0.00 2.93
2412 5413 3.838317 TCTACAGGTGACAAATAGTGCCT 59.162 43.478 0.00 0.00 33.85 4.75
2510 5548 7.048629 TGGTTCACATGTTGTTCACATAATT 57.951 32.000 0.00 0.00 45.06 1.40
2511 5549 6.647334 TGGTTCACATGTTGTTCACATAAT 57.353 33.333 0.00 0.00 45.06 1.28
2516 5554 5.809562 TGAATTTGGTTCACATGTTGTTCAC 59.190 36.000 0.00 0.00 41.79 3.18
3138 6416 3.420893 TCTAGGGGAAACAAATGCACTG 58.579 45.455 0.00 0.00 0.00 3.66
3233 6522 8.776376 AATACAACAGCAAATAATCCCAAAAG 57.224 30.769 0.00 0.00 0.00 2.27
3237 6526 9.814899 CAAATAATACAACAGCAAATAATCCCA 57.185 29.630 0.00 0.00 0.00 4.37
3238 6527 8.764287 GCAAATAATACAACAGCAAATAATCCC 58.236 33.333 0.00 0.00 0.00 3.85
3239 6528 9.533253 AGCAAATAATACAACAGCAAATAATCC 57.467 29.630 0.00 0.00 0.00 3.01
3241 6530 8.819974 GCAGCAAATAATACAACAGCAAATAAT 58.180 29.630 0.00 0.00 0.00 1.28
3242 6531 7.816513 TGCAGCAAATAATACAACAGCAAATAA 59.183 29.630 0.00 0.00 0.00 1.40
3243 6532 7.318893 TGCAGCAAATAATACAACAGCAAATA 58.681 30.769 0.00 0.00 0.00 1.40
3244 6533 6.164876 TGCAGCAAATAATACAACAGCAAAT 58.835 32.000 0.00 0.00 0.00 2.32
3245 6534 5.536260 TGCAGCAAATAATACAACAGCAAA 58.464 33.333 0.00 0.00 0.00 3.68
3246 6535 5.048154 TCTGCAGCAAATAATACAACAGCAA 60.048 36.000 9.47 0.00 0.00 3.91
3247 6536 4.458642 TCTGCAGCAAATAATACAACAGCA 59.541 37.500 9.47 0.00 0.00 4.41
3248 6537 4.985413 TCTGCAGCAAATAATACAACAGC 58.015 39.130 9.47 0.00 0.00 4.40
3249 6538 7.872163 TTTTCTGCAGCAAATAATACAACAG 57.128 32.000 9.47 0.00 0.00 3.16
3250 6539 8.087136 TCATTTTCTGCAGCAAATAATACAACA 58.913 29.630 21.40 0.00 0.00 3.33
3251 6540 8.464770 TCATTTTCTGCAGCAAATAATACAAC 57.535 30.769 21.40 0.00 0.00 3.32
3252 6541 9.656040 ATTCATTTTCTGCAGCAAATAATACAA 57.344 25.926 21.40 11.13 0.00 2.41
3253 6542 9.656040 AATTCATTTTCTGCAGCAAATAATACA 57.344 25.926 21.40 6.93 0.00 2.29
3256 6545 9.834628 CAAAATTCATTTTCTGCAGCAAATAAT 57.165 25.926 21.40 17.21 37.86 1.28
3257 6546 7.804129 GCAAAATTCATTTTCTGCAGCAAATAA 59.196 29.630 21.40 16.05 37.86 1.40
3258 6547 7.041303 TGCAAAATTCATTTTCTGCAGCAAATA 60.041 29.630 21.40 9.84 37.86 1.40
3259 6548 6.146898 GCAAAATTCATTTTCTGCAGCAAAT 58.853 32.000 17.17 17.17 37.86 2.32
3260 6549 5.066117 TGCAAAATTCATTTTCTGCAGCAAA 59.934 32.000 13.90 13.90 37.86 3.68
3261 6550 4.575236 TGCAAAATTCATTTTCTGCAGCAA 59.425 33.333 9.47 0.30 37.86 3.91
3262 6551 4.127907 TGCAAAATTCATTTTCTGCAGCA 58.872 34.783 9.47 0.00 37.86 4.41
3263 6552 4.735662 TGCAAAATTCATTTTCTGCAGC 57.264 36.364 9.47 3.50 37.86 5.25
3264 6553 6.533819 TCTTGCAAAATTCATTTTCTGCAG 57.466 33.333 7.63 7.63 39.81 4.41
3265 6554 8.661257 CATATCTTGCAAAATTCATTTTCTGCA 58.339 29.630 0.00 7.31 37.86 4.41
3266 6555 8.662141 ACATATCTTGCAAAATTCATTTTCTGC 58.338 29.630 0.00 3.06 37.86 4.26
3270 6559 9.086336 CGGTACATATCTTGCAAAATTCATTTT 57.914 29.630 0.00 0.00 40.37 1.82
3271 6560 7.222611 GCGGTACATATCTTGCAAAATTCATTT 59.777 33.333 0.00 0.00 0.00 2.32
3272 6561 6.697019 GCGGTACATATCTTGCAAAATTCATT 59.303 34.615 0.00 0.00 0.00 2.57
3273 6562 6.208644 GCGGTACATATCTTGCAAAATTCAT 58.791 36.000 0.00 0.00 0.00 2.57
3274 6563 5.449862 GGCGGTACATATCTTGCAAAATTCA 60.450 40.000 0.00 0.00 0.00 2.57
3275 6564 4.976116 GGCGGTACATATCTTGCAAAATTC 59.024 41.667 0.00 0.00 0.00 2.17
3276 6565 4.400884 TGGCGGTACATATCTTGCAAAATT 59.599 37.500 0.00 0.00 0.00 1.82
3277 6566 3.951037 TGGCGGTACATATCTTGCAAAAT 59.049 39.130 0.00 0.00 0.00 1.82
3278 6567 3.348119 TGGCGGTACATATCTTGCAAAA 58.652 40.909 0.00 0.00 0.00 2.44
3279 6568 2.992593 TGGCGGTACATATCTTGCAAA 58.007 42.857 0.00 0.00 0.00 3.68
3280 6569 2.700722 TGGCGGTACATATCTTGCAA 57.299 45.000 0.00 0.00 0.00 4.08
3281 6570 2.093181 ACTTGGCGGTACATATCTTGCA 60.093 45.455 0.00 0.00 0.00 4.08
3282 6571 2.287915 CACTTGGCGGTACATATCTTGC 59.712 50.000 0.00 0.00 0.00 4.01
3283 6572 2.287915 GCACTTGGCGGTACATATCTTG 59.712 50.000 0.00 0.00 0.00 3.02
3284 6573 2.561569 GCACTTGGCGGTACATATCTT 58.438 47.619 0.00 0.00 0.00 2.40
3285 6574 2.240493 GCACTTGGCGGTACATATCT 57.760 50.000 0.00 0.00 0.00 1.98
3296 6585 1.070601 AGGGAAACAAATGCACTTGGC 59.929 47.619 13.13 1.19 45.13 4.52
3297 6586 3.473923 AAGGGAAACAAATGCACTTGG 57.526 42.857 13.13 0.00 0.00 3.61
3298 6587 5.452078 TCTAAGGGAAACAAATGCACTTG 57.548 39.130 6.30 6.30 0.00 3.16
3299 6588 5.567423 GCATCTAAGGGAAACAAATGCACTT 60.567 40.000 0.00 0.00 38.27 3.16
3300 6589 4.082026 GCATCTAAGGGAAACAAATGCACT 60.082 41.667 0.00 0.00 38.27 4.40
3301 6590 4.176271 GCATCTAAGGGAAACAAATGCAC 58.824 43.478 0.00 0.00 38.27 4.57
3302 6591 3.195396 GGCATCTAAGGGAAACAAATGCA 59.805 43.478 6.74 0.00 39.72 3.96
3303 6592 3.195396 TGGCATCTAAGGGAAACAAATGC 59.805 43.478 0.00 0.00 37.80 3.56
3304 6593 4.678840 GCTGGCATCTAAGGGAAACAAATG 60.679 45.833 0.00 0.00 0.00 2.32
3305 6594 3.448660 GCTGGCATCTAAGGGAAACAAAT 59.551 43.478 0.00 0.00 0.00 2.32
3306 6595 2.825532 GCTGGCATCTAAGGGAAACAAA 59.174 45.455 0.00 0.00 0.00 2.83
3307 6596 2.446435 GCTGGCATCTAAGGGAAACAA 58.554 47.619 0.00 0.00 0.00 2.83
3308 6597 1.678728 CGCTGGCATCTAAGGGAAACA 60.679 52.381 0.00 0.00 0.00 2.83
3309 6598 1.017387 CGCTGGCATCTAAGGGAAAC 58.983 55.000 0.00 0.00 0.00 2.78
3310 6599 0.748005 GCGCTGGCATCTAAGGGAAA 60.748 55.000 0.00 0.00 39.62 3.13
3311 6600 1.153168 GCGCTGGCATCTAAGGGAA 60.153 57.895 0.00 0.00 39.62 3.97
3312 6601 2.066393 AGCGCTGGCATCTAAGGGA 61.066 57.895 10.39 0.00 43.41 4.20
3313 6602 1.890979 CAGCGCTGGCATCTAAGGG 60.891 63.158 29.88 0.00 43.41 3.95
3314 6603 0.745845 AACAGCGCTGGCATCTAAGG 60.746 55.000 38.27 12.35 43.41 2.69
3315 6604 0.376152 CAACAGCGCTGGCATCTAAG 59.624 55.000 38.27 13.12 43.41 2.18
3316 6605 0.321564 ACAACAGCGCTGGCATCTAA 60.322 50.000 38.27 0.00 43.41 2.10
3317 6606 0.534873 TACAACAGCGCTGGCATCTA 59.465 50.000 38.27 18.10 43.41 1.98
3318 6607 0.107508 ATACAACAGCGCTGGCATCT 60.108 50.000 38.27 17.02 43.41 2.90
3319 6608 0.734889 AATACAACAGCGCTGGCATC 59.265 50.000 38.27 0.00 43.41 3.91
3320 6609 2.036958 TAATACAACAGCGCTGGCAT 57.963 45.000 38.27 25.04 43.41 4.40
3321 6610 2.036958 ATAATACAACAGCGCTGGCA 57.963 45.000 38.27 21.35 43.41 4.92
3322 6611 3.108144 CAAATAATACAACAGCGCTGGC 58.892 45.455 38.27 0.00 40.37 4.85
3323 6612 3.108144 GCAAATAATACAACAGCGCTGG 58.892 45.455 38.27 24.96 34.19 4.85
3324 6613 3.787634 CAGCAAATAATACAACAGCGCTG 59.212 43.478 34.89 34.89 38.46 5.18
3325 6614 3.731867 GCAGCAAATAATACAACAGCGCT 60.732 43.478 2.64 2.64 0.00 5.92
3326 6615 2.531508 GCAGCAAATAATACAACAGCGC 59.468 45.455 0.00 0.00 0.00 5.92
3327 6616 3.757184 TGCAGCAAATAATACAACAGCG 58.243 40.909 0.00 0.00 0.00 5.18
3328 6617 5.806502 TCAATGCAGCAAATAATACAACAGC 59.193 36.000 0.00 0.00 0.00 4.40
3329 6618 6.807720 TGTCAATGCAGCAAATAATACAACAG 59.192 34.615 0.00 0.00 0.00 3.16
3330 6619 6.685657 TGTCAATGCAGCAAATAATACAACA 58.314 32.000 0.00 0.00 0.00 3.33
3331 6620 7.488792 TCATGTCAATGCAGCAAATAATACAAC 59.511 33.333 0.00 0.00 33.47 3.32
3332 6621 7.545489 TCATGTCAATGCAGCAAATAATACAA 58.455 30.769 0.00 0.00 33.47 2.41
3333 6622 7.098074 TCATGTCAATGCAGCAAATAATACA 57.902 32.000 0.00 0.00 33.47 2.29
3675 7171 7.907214 AGGTTTAGTGTGAATATGTGACTTC 57.093 36.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.