Multiple sequence alignment - TraesCS6A01G250200

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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 TraesCS6A01G250200 chr6A 100.000 5626 0 0 1 5626 464518006 464512381 0.000000e+00 10390.0
1 TraesCS6A01G250200 chr6A 93.688 301 2 2 5037 5332 587976179 587976467 8.660000e-118 435.0
2 TraesCS6A01G250200 chr6B 94.420 3638 130 27 901 4489 497234835 497238448 0.000000e+00 5526.0
3 TraesCS6A01G250200 chr6B 95.000 160 7 1 4486 4644 497238521 497238680 3.370000e-62 250.0
4 TraesCS6A01G250200 chr6B 94.521 146 5 1 4811 4956 497238713 497238855 7.340000e-54 222.0
5 TraesCS6A01G250200 chr6B 99.153 118 1 0 4695 4812 164883035 164882918 4.420000e-51 213.0
6 TraesCS6A01G250200 chr6B 92.063 126 9 1 815 939 497234710 497234835 5.790000e-40 176.0
7 TraesCS6A01G250200 chr6B 89.815 108 11 0 707 814 222427564 222427457 7.600000e-29 139.0
8 TraesCS6A01G250200 chr6D 98.644 2065 15 5 1643 3694 325729659 325727595 0.000000e+00 3646.0
9 TraesCS6A01G250200 chr6D 93.858 1677 54 20 1 1658 325731420 325729774 0.000000e+00 2481.0
10 TraesCS6A01G250200 chr6D 98.281 931 8 2 3775 4697 325727440 325726510 0.000000e+00 1624.0
11 TraesCS6A01G250200 chr6D 95.238 147 5 1 4811 4957 325726511 325726367 1.220000e-56 231.0
12 TraesCS6A01G250200 chr6D 96.063 127 4 1 4687 4812 394829734 394829860 7.390000e-49 206.0
13 TraesCS6A01G250200 chr6D 84.211 76 12 0 710 785 417518590 417518515 2.170000e-09 75.0
14 TraesCS6A01G250200 chr6D 79.487 117 14 6 708 814 458055125 458055241 2.170000e-09 75.0
15 TraesCS6A01G250200 chr5B 96.540 607 11 3 5029 5626 100352163 100351558 0.000000e+00 996.0
16 TraesCS6A01G250200 chr5B 89.796 147 12 3 1700 1844 524539800 524539655 9.630000e-43 185.0
17 TraesCS6A01G250200 chr5B 90.991 111 10 0 705 815 648850339 648850229 3.510000e-32 150.0
18 TraesCS6A01G250200 chr7B 93.833 600 17 8 5037 5626 220973885 220973296 0.000000e+00 885.0
19 TraesCS6A01G250200 chr7B 96.629 267 3 3 5364 5626 220970353 220970089 6.690000e-119 438.0
20 TraesCS6A01G250200 chr7B 95.420 131 6 0 4692 4822 188974300 188974430 5.710000e-50 209.0
21 TraesCS6A01G250200 chr7B 96.774 124 4 0 4689 4812 535690870 535690747 2.050000e-49 207.0
22 TraesCS6A01G250200 chr7B 92.754 138 2 4 5493 5626 220971744 220971611 5.750000e-45 193.0
23 TraesCS6A01G250200 chr7B 84.564 149 15 4 3574 3722 140938001 140938141 2.110000e-29 141.0
24 TraesCS6A01G250200 chr2A 95.474 464 10 5 5029 5487 214797590 214798047 0.000000e+00 730.0
25 TraesCS6A01G250200 chr2A 83.226 465 59 13 5051 5502 572704917 572704459 5.250000e-110 409.0
26 TraesCS6A01G250200 chr2A 94.631 149 4 4 5482 5626 214798251 214798399 1.580000e-55 228.0
27 TraesCS6A01G250200 chr2A 87.500 160 17 3 1688 1845 709626101 709626259 1.250000e-41 182.0
28 TraesCS6A01G250200 chr2A 82.692 156 21 6 3577 3728 386294501 386294348 3.540000e-27 134.0
29 TraesCS6A01G250200 chr3A 91.152 486 26 13 5021 5495 99257180 99256701 1.320000e-180 643.0
30 TraesCS6A01G250200 chr3A 93.578 327 10 5 5209 5525 686844090 686843765 1.420000e-130 477.0
31 TraesCS6A01G250200 chr3A 97.235 217 1 3 5415 5626 476158236 476158452 4.140000e-96 363.0
32 TraesCS6A01G250200 chr3A 97.541 122 2 1 4696 4817 329189781 329189901 2.050000e-49 207.0
33 TraesCS6A01G250200 chr3A 88.050 159 14 4 1690 1844 509990465 509990308 3.460000e-42 183.0
34 TraesCS6A01G250200 chr3A 89.815 108 11 0 708 815 293412239 293412346 7.600000e-29 139.0
35 TraesCS6A01G250200 chr1A 95.879 364 6 6 5266 5626 402213609 402213966 1.050000e-161 580.0
36 TraesCS6A01G250200 chr1A 86.452 155 14 6 1690 1841 532594833 532594983 4.510000e-36 163.0
37 TraesCS6A01G250200 chr1A 88.785 107 12 0 708 814 13420653 13420759 1.270000e-26 132.0
38 TraesCS6A01G250200 chr1A 92.857 70 5 0 815 884 321292388 321292319 9.970000e-18 102.0
39 TraesCS6A01G250200 chr2D 87.805 451 38 7 5029 5465 542367102 542367549 3.890000e-141 512.0
40 TraesCS6A01G250200 chr2D 88.696 115 12 1 703 817 596246919 596247032 7.600000e-29 139.0
41 TraesCS6A01G250200 chr2D 87.963 108 13 0 707 814 55931527 55931634 1.650000e-25 128.0
42 TraesCS6A01G250200 chr2D 84.545 110 17 0 708 817 615470008 615470117 5.960000e-20 110.0
43 TraesCS6A01G250200 chr2D 84.848 99 7 5 1747 1844 391459929 391459838 6.000000e-15 93.5
44 TraesCS6A01G250200 chr5D 86.071 481 53 8 5029 5502 399990234 399990707 6.500000e-139 505.0
45 TraesCS6A01G250200 chr5D 98.333 120 2 0 4694 4813 47283882 47284001 1.590000e-50 211.0
46 TraesCS6A01G250200 chr5D 87.417 151 11 6 1700 1843 220377553 220377702 3.490000e-37 167.0
47 TraesCS6A01G250200 chr5D 87.417 151 11 6 1700 1843 220380105 220380254 3.490000e-37 167.0
48 TraesCS6A01G250200 chr5D 94.382 89 3 2 3490 3578 122198517 122198431 9.830000e-28 135.0
49 TraesCS6A01G250200 chr5D 92.222 90 5 2 3494 3581 498655369 498655280 5.920000e-25 126.0
50 TraesCS6A01G250200 chr5D 90.909 44 4 0 772 815 423319646 423319603 6.090000e-05 60.2
51 TraesCS6A01G250200 chrUn 86.580 462 46 12 5051 5502 37391958 37391503 3.910000e-136 496.0
52 TraesCS6A01G250200 chr3B 99.153 118 1 0 4696 4813 655032862 655032745 4.420000e-51 213.0
53 TraesCS6A01G250200 chr3B 86.486 148 15 5 1701 1844 210603939 210603793 2.100000e-34 158.0
54 TraesCS6A01G250200 chr1B 96.032 126 4 1 4695 4820 413494706 413494582 2.660000e-48 204.0
55 TraesCS6A01G250200 chr1B 88.288 111 13 0 705 815 624506929 624507039 3.540000e-27 134.0
56 TraesCS6A01G250200 chr2B 94.656 131 6 1 4696 4826 92334458 92334587 9.560000e-48 202.0
57 TraesCS6A01G250200 chr2B 94.186 86 5 0 3493 3578 14834410 14834325 1.270000e-26 132.0
58 TraesCS6A01G250200 chr7D 88.889 153 14 3 1700 1850 385446029 385446180 9.630000e-43 185.0
59 TraesCS6A01G250200 chr7D 86.577 149 17 2 3574 3722 175652475 175652620 1.620000e-35 161.0
60 TraesCS6A01G250200 chr7D 94.318 88 5 0 3493 3580 463263158 463263071 9.830000e-28 135.0
61 TraesCS6A01G250200 chr7D 80.420 143 20 7 3574 3715 71339681 71339816 9.970000e-18 102.0
62 TraesCS6A01G250200 chr7D 77.515 169 30 6 1682 1844 265115440 265115606 1.670000e-15 95.3
63 TraesCS6A01G250200 chr7D 80.247 81 16 0 708 788 442682199 442682119 1.690000e-05 62.1
64 TraesCS6A01G250200 chr4D 87.838 148 14 3 1700 1844 8019089 8019235 2.700000e-38 171.0
65 TraesCS6A01G250200 chr4D 86.331 139 11 6 1711 1846 382332566 382332433 1.630000e-30 145.0
66 TraesCS6A01G250200 chr4D 86.885 122 14 2 1724 1844 69794946 69795066 9.830000e-28 135.0
67 TraesCS6A01G250200 chr4D 81.208 149 22 5 3580 3725 301756453 301756308 1.280000e-21 115.0
68 TraesCS6A01G250200 chr7A 85.906 149 18 3 3574 3722 177333527 177333672 7.550000e-34 156.0
69 TraesCS6A01G250200 chr7A 92.391 92 6 1 3491 3582 40538156 40538246 4.570000e-26 130.0
70 TraesCS6A01G250200 chr4A 85.616 146 17 4 1702 1844 81261797 81261941 3.510000e-32 150.0
71 TraesCS6A01G250200 chr4A 88.889 108 12 0 707 814 729138370 729138477 3.540000e-27 134.0
72 TraesCS6A01G250200 chr4A 92.135 89 6 1 3494 3582 647209389 647209302 2.130000e-24 124.0
73 TraesCS6A01G250200 chr3D 91.667 108 9 0 708 815 66561312 66561419 3.510000e-32 150.0
74 TraesCS6A01G250200 chr3D 90.588 85 7 1 708 791 599162354 599162270 1.660000e-20 111.0
75 TraesCS6A01G250200 chr4B 91.589 107 8 1 708 814 69613116 69613221 4.540000e-31 147.0
76 TraesCS6A01G250200 chr4B 90.741 108 10 0 707 814 281354381 281354274 1.630000e-30 145.0
77 TraesCS6A01G250200 chr4B 84.112 107 17 0 708 814 142542574 142542468 2.770000e-18 104.0
78 TraesCS6A01G250200 chr4B 79.866 149 24 5 3580 3725 376157859 376157714 2.770000e-18 104.0
79 TraesCS6A01G250200 chr5A 89.815 108 11 0 707 814 335592792 335592899 7.600000e-29 139.0
80 TraesCS6A01G250200 chr1D 93.103 87 5 1 3494 3580 78965826 78965911 5.920000e-25 126.0
81 TraesCS6A01G250200 chr1D 81.609 87 5 6 708 785 392130094 392130178 1.690000e-05 62.1


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 TraesCS6A01G250200 chr6A 464512381 464518006 5625 True 10390.000000 10390 100.000000 1 5626 1 chr6A.!!$R1 5625
1 TraesCS6A01G250200 chr6B 497234710 497238855 4145 False 1543.500000 5526 94.001000 815 4956 4 chr6B.!!$F1 4141
2 TraesCS6A01G250200 chr6D 325726367 325731420 5053 True 1995.500000 3646 96.505250 1 4957 4 chr6D.!!$R2 4956
3 TraesCS6A01G250200 chr5B 100351558 100352163 605 True 996.000000 996 96.540000 5029 5626 1 chr5B.!!$R1 597
4 TraesCS6A01G250200 chr7B 220970089 220973885 3796 True 505.333333 885 94.405333 5037 5626 3 chr7B.!!$R2 589
5 TraesCS6A01G250200 chr2A 214797590 214798399 809 False 479.000000 730 95.052500 5029 5626 2 chr2A.!!$F2 597

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
74 75 1.352156 CCCACTTCAGCGTTCGCTAC 61.352 60.0 18.99 0.0 39.76 3.58 F
1281 1368 0.648958 GGGAATTTAACGGCGACTCG 59.351 55.0 16.62 0.0 0.00 4.18 F
2176 2414 2.695147 GCCCATCAGGAATACCCAAAAG 59.305 50.0 0.00 0.0 38.24 2.27 F
3437 3687 0.392060 ATTGAACGTACTTCCCCCGC 60.392 55.0 0.00 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1664 1759 0.878523 TACAGTGGTCTGCACAACGC 60.879 55.0 0.00 0.0 44.77 4.84 R
2915 3155 0.759346 AGTGCTAAATAGAGGGGGCG 59.241 55.0 0.00 0.0 0.00 6.13 R
3759 4009 1.045911 GCTCCCACCACCACCAAAAA 61.046 55.0 0.00 0.0 0.00 1.94 R
4789 5198 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.0 5.23 0.0 44.66 2.24 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
28 29 3.192844 AGCGACATATGTAGGGGATAACG 59.807 47.826 16.45 10.04 0.00 3.18
69 70 2.328099 CCAGCCCACTTCAGCGTTC 61.328 63.158 0.00 0.00 0.00 3.95
74 75 1.352156 CCCACTTCAGCGTTCGCTAC 61.352 60.000 18.99 0.00 39.76 3.58
108 109 7.006210 CGTTTGCTATACTGTTGAATCGTTTTC 59.994 37.037 0.00 0.00 0.00 2.29
112 113 8.564574 TGCTATACTGTTGAATCGTTTTCTTTT 58.435 29.630 0.00 0.00 0.00 2.27
122 123 6.467682 TGAATCGTTTTCTTTTCTCGTTGTTG 59.532 34.615 3.29 0.00 0.00 3.33
165 167 2.166741 TTGTTTCGTTCGTTGCACTG 57.833 45.000 0.00 0.00 0.00 3.66
175 177 1.574428 GTTGCACTGCTACAACGGG 59.426 57.895 10.30 0.00 37.08 5.28
196 198 5.348986 GGGTTTTTCTCCAGTTTTCTTGTC 58.651 41.667 0.00 0.00 0.00 3.18
206 208 4.402474 CCAGTTTTCTTGTCCTGGTCTTTT 59.598 41.667 0.00 0.00 39.70 2.27
272 275 2.093921 CCTTGGTTTTTCGGTTGTGGTT 60.094 45.455 0.00 0.00 0.00 3.67
313 316 7.833285 ATGGTTTACCTTTTTGCTTCTTCTA 57.167 32.000 0.00 0.00 36.82 2.10
411 415 6.136071 CACAGCTAACATGTTTTCAGTACAC 58.864 40.000 17.78 0.00 0.00 2.90
712 717 1.803252 GCCGCTACAAAGAGCTACTCC 60.803 57.143 0.00 0.00 40.51 3.85
717 722 2.327325 ACAAAGAGCTACTCCCTCCA 57.673 50.000 0.00 0.00 0.00 3.86
737 742 5.800296 TCCATTCAGAATTACTCGTCCAAA 58.200 37.500 0.00 0.00 0.00 3.28
800 805 9.782028 CATTCATTTTTGTGACAAGTAATTTCG 57.218 29.630 0.00 0.00 0.00 3.46
801 806 7.922505 TCATTTTTGTGACAAGTAATTTCGG 57.077 32.000 0.00 0.00 0.00 4.30
802 807 7.708051 TCATTTTTGTGACAAGTAATTTCGGA 58.292 30.769 0.00 0.00 0.00 4.55
803 808 7.646130 TCATTTTTGTGACAAGTAATTTCGGAC 59.354 33.333 0.00 0.00 0.00 4.79
804 809 4.718858 TTGTGACAAGTAATTTCGGACG 57.281 40.909 0.00 0.00 0.00 4.79
805 810 3.979948 TGTGACAAGTAATTTCGGACGA 58.020 40.909 0.00 0.00 0.00 4.20
849 860 4.069304 ACAAAGGTTAGCACGCTTATTGA 58.931 39.130 0.00 0.00 0.00 2.57
963 1042 1.463214 TCTGACCCTCCAAAGCCCA 60.463 57.895 0.00 0.00 0.00 5.36
1281 1368 0.648958 GGGAATTTAACGGCGACTCG 59.351 55.000 16.62 0.00 0.00 4.18
1664 1759 9.086336 AGTTGTTTGTGATTGTAATTGAAACAG 57.914 29.630 0.00 0.00 34.37 3.16
1665 1760 7.462109 TGTTTGTGATTGTAATTGAAACAGC 57.538 32.000 0.00 0.00 30.52 4.40
1890 2128 7.016153 AGTTTCACTATGATGTTGGGAACTA 57.984 36.000 0.00 0.00 0.00 2.24
1979 2217 5.305644 CCTCATAGGGCAAGTACTCTACAAT 59.694 44.000 0.00 0.00 0.00 2.71
2164 2402 6.375455 GTGTCATTATTATTAGGCCCATCAGG 59.625 42.308 0.00 0.00 39.47 3.86
2176 2414 2.695147 GCCCATCAGGAATACCCAAAAG 59.305 50.000 0.00 0.00 38.24 2.27
2915 3155 3.068165 ACTTGACAAAAAGTTGCTAGGGC 59.932 43.478 0.00 0.00 37.05 5.19
3168 3408 6.017192 TGGATAGCTACCGATCTATTTCCTT 58.983 40.000 0.00 0.00 0.00 3.36
3437 3687 0.392060 ATTGAACGTACTTCCCCCGC 60.392 55.000 0.00 0.00 0.00 6.13
3696 3946 6.970484 TGAGAAGTTTGAAATAGGACAAAGC 58.030 36.000 0.00 0.00 36.81 3.51
3758 4008 2.869233 AGTTGTGCATGAGCGTTTTT 57.131 40.000 0.00 0.00 46.23 1.94
4134 4458 7.174426 ACTTTTGGTAGTAATCAAACCTACTGC 59.826 37.037 0.00 0.00 33.29 4.40
4547 4956 3.570125 GCTACTCTTTCTTTTGGCAGGTT 59.430 43.478 0.00 0.00 0.00 3.50
4653 5062 8.743085 ATAGAAATTGCTGATGTGTGTTATCT 57.257 30.769 0.00 0.00 0.00 1.98
4683 5092 1.920574 CGCCTATGACAGTGTTCTTCG 59.079 52.381 0.00 0.00 0.00 3.79
4695 5104 5.127845 ACAGTGTTCTTCGTATCATCCATCT 59.872 40.000 0.00 0.00 0.00 2.90
4696 5105 6.321435 ACAGTGTTCTTCGTATCATCCATCTA 59.679 38.462 0.00 0.00 0.00 1.98
4697 5106 6.638873 CAGTGTTCTTCGTATCATCCATCTAC 59.361 42.308 0.00 0.00 0.00 2.59
4698 5107 6.547880 AGTGTTCTTCGTATCATCCATCTACT 59.452 38.462 0.00 0.00 0.00 2.57
4699 5108 6.858993 GTGTTCTTCGTATCATCCATCTACTC 59.141 42.308 0.00 0.00 0.00 2.59
4700 5109 6.016192 TGTTCTTCGTATCATCCATCTACTCC 60.016 42.308 0.00 0.00 0.00 3.85
4701 5110 5.010933 TCTTCGTATCATCCATCTACTCCC 58.989 45.833 0.00 0.00 0.00 4.30
4702 5111 4.659529 TCGTATCATCCATCTACTCCCT 57.340 45.455 0.00 0.00 0.00 4.20
4703 5112 4.590918 TCGTATCATCCATCTACTCCCTC 58.409 47.826 0.00 0.00 0.00 4.30
4704 5113 4.289934 TCGTATCATCCATCTACTCCCTCT 59.710 45.833 0.00 0.00 0.00 3.69
4705 5114 4.397730 CGTATCATCCATCTACTCCCTCTG 59.602 50.000 0.00 0.00 0.00 3.35
4706 5115 3.981516 TCATCCATCTACTCCCTCTGT 57.018 47.619 0.00 0.00 0.00 3.41
4707 5116 3.838565 TCATCCATCTACTCCCTCTGTC 58.161 50.000 0.00 0.00 0.00 3.51
4708 5117 2.757894 TCCATCTACTCCCTCTGTCC 57.242 55.000 0.00 0.00 0.00 4.02
4709 5118 1.133761 TCCATCTACTCCCTCTGTCCG 60.134 57.143 0.00 0.00 0.00 4.79
4710 5119 1.323412 CATCTACTCCCTCTGTCCGG 58.677 60.000 0.00 0.00 0.00 5.14
4711 5120 1.133761 CATCTACTCCCTCTGTCCGGA 60.134 57.143 0.00 0.00 0.00 5.14
4712 5121 0.997363 TCTACTCCCTCTGTCCGGAA 59.003 55.000 5.23 0.00 0.00 4.30
4713 5122 1.356738 TCTACTCCCTCTGTCCGGAAA 59.643 52.381 5.23 0.00 0.00 3.13
4714 5123 2.024273 TCTACTCCCTCTGTCCGGAAAT 60.024 50.000 5.23 0.00 0.00 2.17
4715 5124 2.544844 ACTCCCTCTGTCCGGAAATA 57.455 50.000 5.23 0.00 0.00 1.40
4716 5125 2.108970 ACTCCCTCTGTCCGGAAATAC 58.891 52.381 5.23 0.00 0.00 1.89
4717 5126 2.292323 ACTCCCTCTGTCCGGAAATACT 60.292 50.000 5.23 0.00 0.00 2.12
4718 5127 2.766828 CTCCCTCTGTCCGGAAATACTT 59.233 50.000 5.23 0.00 0.00 2.24
4719 5128 2.500098 TCCCTCTGTCCGGAAATACTTG 59.500 50.000 5.23 0.00 0.00 3.16
4720 5129 2.236395 CCCTCTGTCCGGAAATACTTGT 59.764 50.000 5.23 0.00 0.00 3.16
4721 5130 3.522553 CCTCTGTCCGGAAATACTTGTC 58.477 50.000 5.23 0.00 0.00 3.18
4722 5131 3.056107 CCTCTGTCCGGAAATACTTGTCA 60.056 47.826 5.23 0.00 0.00 3.58
4723 5132 4.383118 CCTCTGTCCGGAAATACTTGTCAT 60.383 45.833 5.23 0.00 0.00 3.06
4724 5133 5.160607 TCTGTCCGGAAATACTTGTCATT 57.839 39.130 5.23 0.00 0.00 2.57
4725 5134 4.935205 TCTGTCCGGAAATACTTGTCATTG 59.065 41.667 5.23 0.00 0.00 2.82
4726 5135 4.900684 TGTCCGGAAATACTTGTCATTGA 58.099 39.130 5.23 0.00 0.00 2.57
4727 5136 5.309638 TGTCCGGAAATACTTGTCATTGAA 58.690 37.500 5.23 0.00 0.00 2.69
4728 5137 5.765677 TGTCCGGAAATACTTGTCATTGAAA 59.234 36.000 5.23 0.00 0.00 2.69
4729 5138 6.432783 TGTCCGGAAATACTTGTCATTGAAAT 59.567 34.615 5.23 0.00 0.00 2.17
4730 5139 6.747280 GTCCGGAAATACTTGTCATTGAAATG 59.253 38.462 5.23 0.00 37.75 2.32
4731 5140 6.035843 CCGGAAATACTTGTCATTGAAATGG 58.964 40.000 0.00 0.00 37.03 3.16
4732 5141 6.127758 CCGGAAATACTTGTCATTGAAATGGA 60.128 38.462 0.00 0.00 37.03 3.41
4733 5142 7.416664 CCGGAAATACTTGTCATTGAAATGGAT 60.417 37.037 0.00 0.00 37.03 3.41
4734 5143 7.433131 CGGAAATACTTGTCATTGAAATGGATG 59.567 37.037 3.31 0.00 37.03 3.51
4735 5144 8.253113 GGAAATACTTGTCATTGAAATGGATGT 58.747 33.333 3.31 2.77 37.03 3.06
4739 5148 9.857656 ATACTTGTCATTGAAATGGATGTATCT 57.142 29.630 3.31 0.00 37.03 1.98
4741 5150 9.334947 ACTTGTCATTGAAATGGATGTATCTAG 57.665 33.333 3.31 0.00 37.03 2.43
4742 5151 9.551734 CTTGTCATTGAAATGGATGTATCTAGA 57.448 33.333 0.00 0.00 37.03 2.43
4744 5153 9.498176 TGTCATTGAAATGGATGTATCTAGATG 57.502 33.333 15.79 0.00 37.03 2.90
4745 5154 9.499479 GTCATTGAAATGGATGTATCTAGATGT 57.501 33.333 15.79 1.25 37.03 3.06
4777 5186 8.717717 AGTTCTAGATACATCCATTTTCATCCA 58.282 33.333 0.00 0.00 0.00 3.41
4778 5187 9.512588 GTTCTAGATACATCCATTTTCATCCAT 57.487 33.333 0.00 0.00 0.00 3.41
4783 5192 9.204337 AGATACATCCATTTTCATCCATTTTGA 57.796 29.630 0.00 0.00 0.00 2.69
4784 5193 9.991906 GATACATCCATTTTCATCCATTTTGAT 57.008 29.630 0.00 0.00 0.00 2.57
4785 5194 9.772973 ATACATCCATTTTCATCCATTTTGATG 57.227 29.630 0.00 0.00 42.84 3.07
4797 5206 8.469200 TCATCCATTTTGATGACAAGTAATTCC 58.531 33.333 0.00 0.00 44.65 3.01
4798 5207 6.851609 TCCATTTTGATGACAAGTAATTCCG 58.148 36.000 0.00 0.00 37.32 4.30
4799 5208 6.035843 CCATTTTGATGACAAGTAATTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
4800 5209 6.127758 CCATTTTGATGACAAGTAATTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
4801 5210 5.873179 TTTGATGACAAGTAATTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
4802 5211 3.517602 TGATGACAAGTAATTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
4803 5212 2.373540 TGACAAGTAATTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
4804 5213 1.894466 TGACAAGTAATTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
4805 5214 2.094390 TGACAAGTAATTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
4806 5215 1.206371 ACAAGTAATTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
4807 5216 0.828677 AAGTAATTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
4808 5217 0.032813 AGTAATTCCGGACGGAGGGA 60.033 55.000 13.64 0.00 46.06 4.20
4809 5218 0.388294 GTAATTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
4826 5235 5.395435 GGAGGGAGTATGTAGTTTCAAGGAC 60.395 48.000 0.00 0.00 0.00 3.85
4935 5344 5.834239 ACGTTGTTGCTACTATGTTGTAC 57.166 39.130 2.20 0.00 0.00 2.90
4957 5366 8.170730 TGTACTGACTCCATGGATATGTAGTAT 58.829 37.037 16.63 0.87 34.10 2.12
4958 5367 9.682465 GTACTGACTCCATGGATATGTAGTATA 57.318 37.037 16.63 0.87 34.10 1.47
5063 5477 4.070552 GCGGGCTTCTGGTCGTCT 62.071 66.667 0.00 0.00 0.00 4.18
5526 6152 8.441312 ACAAAATTTTGCAGATTCAAATGTCT 57.559 26.923 26.94 2.76 41.79 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 1.032080 GCAAACGAAACAACGTAGCG 58.968 50.000 0.00 0.00 45.83 4.26
74 75 5.013861 ACAGTATAGCAAACGAAACAACG 57.986 39.130 0.00 0.00 39.31 4.10
108 109 6.144724 TGGAACAAAAACAACAACGAGAAAAG 59.855 34.615 0.00 0.00 31.92 2.27
112 113 4.477780 GTGGAACAAAAACAACAACGAGA 58.522 39.130 0.00 0.00 44.16 4.04
152 154 0.579630 TTGTAGCAGTGCAACGAACG 59.420 50.000 19.20 0.00 45.86 3.95
165 167 2.223745 TGGAGAAAAACCCGTTGTAGC 58.776 47.619 0.00 0.00 0.00 3.58
174 176 5.127194 AGGACAAGAAAACTGGAGAAAAACC 59.873 40.000 0.00 0.00 0.00 3.27
175 177 6.036470 CAGGACAAGAAAACTGGAGAAAAAC 58.964 40.000 0.00 0.00 0.00 2.43
196 198 6.017523 ACAAACAAACAAAACAAAAGACCAGG 60.018 34.615 0.00 0.00 0.00 4.45
206 208 9.065871 CAAACAAAAGAACAAACAAACAAAACA 57.934 25.926 0.00 0.00 0.00 2.83
247 249 4.048504 CACAACCGAAAAACCAAGGAATC 58.951 43.478 0.00 0.00 0.00 2.52
248 250 3.181470 CCACAACCGAAAAACCAAGGAAT 60.181 43.478 0.00 0.00 0.00 3.01
712 717 4.141937 TGGACGAGTAATTCTGAATGGAGG 60.142 45.833 3.22 0.00 0.00 4.30
795 800 2.173519 TGTACTCCCTTCGTCCGAAAT 58.826 47.619 3.52 0.00 33.34 2.17
796 801 1.619654 TGTACTCCCTTCGTCCGAAA 58.380 50.000 3.52 0.00 33.34 3.46
797 802 1.475280 CATGTACTCCCTTCGTCCGAA 59.525 52.381 1.81 1.81 0.00 4.30
798 803 1.100510 CATGTACTCCCTTCGTCCGA 58.899 55.000 0.00 0.00 0.00 4.55
799 804 0.102481 CCATGTACTCCCTTCGTCCG 59.898 60.000 0.00 0.00 0.00 4.79
800 805 0.179081 GCCATGTACTCCCTTCGTCC 60.179 60.000 0.00 0.00 0.00 4.79
801 806 0.824759 AGCCATGTACTCCCTTCGTC 59.175 55.000 0.00 0.00 0.00 4.20
802 807 1.755380 GTAGCCATGTACTCCCTTCGT 59.245 52.381 0.00 0.00 0.00 3.85
803 808 1.754803 TGTAGCCATGTACTCCCTTCG 59.245 52.381 0.00 0.00 0.00 3.79
804 809 3.031736 TCTGTAGCCATGTACTCCCTTC 58.968 50.000 0.00 0.00 0.00 3.46
805 810 3.116096 TCTGTAGCCATGTACTCCCTT 57.884 47.619 0.00 0.00 0.00 3.95
925 1004 1.757699 AGCAGGTAAATCGAGACCTCC 59.242 52.381 12.31 5.33 44.54 4.30
1281 1368 3.723348 GCGTTGTCCCTGCGAACC 61.723 66.667 0.00 0.00 0.00 3.62
1497 1584 9.950680 CTATGACACCGAATTTGCTTAATTTAT 57.049 29.630 0.00 0.00 36.59 1.40
1664 1759 0.878523 TACAGTGGTCTGCACAACGC 60.879 55.000 0.00 0.00 44.77 4.84
1665 1760 1.577468 TTACAGTGGTCTGCACAACG 58.423 50.000 0.00 0.00 44.77 4.10
1979 2217 6.384224 CAGAATTCAGCATTTTACAGCTTGA 58.616 36.000 8.44 0.00 39.50 3.02
2164 2402 6.084326 TCTTTTGTCAGCTTTTGGGTATTC 57.916 37.500 0.00 0.00 0.00 1.75
2176 2414 4.216257 TCATAAACCTGCTCTTTTGTCAGC 59.784 41.667 0.00 0.00 36.08 4.26
2915 3155 0.759346 AGTGCTAAATAGAGGGGGCG 59.241 55.000 0.00 0.00 0.00 6.13
3168 3408 2.253610 AGAAGACCCCATGTGTCGTAA 58.746 47.619 6.90 0.00 37.80 3.18
3437 3687 9.231297 TCAAGTAGAACTTCCATTAATTTGGAG 57.769 33.333 0.00 0.00 46.22 3.86
3759 4009 1.045911 GCTCCCACCACCACCAAAAA 61.046 55.000 0.00 0.00 0.00 1.94
3760 4010 1.456705 GCTCCCACCACCACCAAAA 60.457 57.895 0.00 0.00 0.00 2.44
3761 4011 2.197324 GCTCCCACCACCACCAAA 59.803 61.111 0.00 0.00 0.00 3.28
3762 4012 3.897122 GGCTCCCACCACCACCAA 61.897 66.667 0.00 0.00 0.00 3.67
3764 4014 2.270874 CTATGGCTCCCACCACCACC 62.271 65.000 0.00 0.00 44.17 4.61
3765 4015 1.224592 CTATGGCTCCCACCACCAC 59.775 63.158 0.00 0.00 44.17 4.16
3766 4016 2.679342 GCTATGGCTCCCACCACCA 61.679 63.158 0.00 0.00 44.17 4.17
3767 4017 2.193248 GCTATGGCTCCCACCACC 59.807 66.667 0.00 0.00 44.17 4.61
4547 4956 1.479323 GGGTGATAAGTGACGCTGGTA 59.521 52.381 0.00 0.00 0.00 3.25
4653 5062 2.294512 CTGTCATAGGCGCATCAGTAGA 59.705 50.000 10.83 0.00 0.00 2.59
4683 5092 5.329399 ACAGAGGGAGTAGATGGATGATAC 58.671 45.833 0.00 0.00 0.00 2.24
4695 5104 2.544844 ATTTCCGGACAGAGGGAGTA 57.455 50.000 1.83 0.00 33.01 2.59
4696 5105 2.108970 GTATTTCCGGACAGAGGGAGT 58.891 52.381 1.83 0.00 33.01 3.85
4697 5106 2.389715 AGTATTTCCGGACAGAGGGAG 58.610 52.381 1.83 0.00 33.01 4.30
4698 5107 2.500098 CAAGTATTTCCGGACAGAGGGA 59.500 50.000 1.83 0.00 0.00 4.20
4699 5108 2.236395 ACAAGTATTTCCGGACAGAGGG 59.764 50.000 1.83 0.00 0.00 4.30
4700 5109 3.056107 TGACAAGTATTTCCGGACAGAGG 60.056 47.826 1.83 0.00 0.00 3.69
4701 5110 4.188247 TGACAAGTATTTCCGGACAGAG 57.812 45.455 1.83 0.00 0.00 3.35
4702 5111 4.819105 ATGACAAGTATTTCCGGACAGA 57.181 40.909 1.83 0.00 0.00 3.41
4703 5112 4.935205 TCAATGACAAGTATTTCCGGACAG 59.065 41.667 1.83 0.00 0.00 3.51
4704 5113 4.900684 TCAATGACAAGTATTTCCGGACA 58.099 39.130 1.83 0.00 0.00 4.02
4705 5114 5.873179 TTCAATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 0.00 4.79
4706 5115 6.127758 CCATTTCAATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 38.70 5.14
4707 5116 6.035843 CCATTTCAATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 38.70 5.14
4708 5117 6.851609 TCCATTTCAATGACAAGTATTTCCG 58.148 36.000 0.81 0.00 38.70 4.30
4709 5118 8.253113 ACATCCATTTCAATGACAAGTATTTCC 58.747 33.333 0.81 0.00 38.70 3.13
4713 5122 9.857656 AGATACATCCATTTCAATGACAAGTAT 57.142 29.630 0.81 4.50 38.70 2.12
4715 5124 9.334947 CTAGATACATCCATTTCAATGACAAGT 57.665 33.333 0.81 0.00 38.70 3.16
4716 5125 9.551734 TCTAGATACATCCATTTCAATGACAAG 57.448 33.333 0.81 0.00 38.70 3.16
4718 5127 9.498176 CATCTAGATACATCCATTTCAATGACA 57.502 33.333 4.54 0.00 38.70 3.58
4719 5128 9.499479 ACATCTAGATACATCCATTTCAATGAC 57.501 33.333 4.54 0.00 38.70 3.06
4751 5160 8.717717 TGGATGAAAATGGATGTATCTAGAACT 58.282 33.333 0.00 0.00 0.00 3.01
4752 5161 8.908786 TGGATGAAAATGGATGTATCTAGAAC 57.091 34.615 0.00 0.00 0.00 3.01
4757 5166 9.204337 TCAAAATGGATGAAAATGGATGTATCT 57.796 29.630 0.00 0.00 0.00 1.98
4758 5167 9.991906 ATCAAAATGGATGAAAATGGATGTATC 57.008 29.630 0.00 0.00 0.00 2.24
4759 5168 9.772973 CATCAAAATGGATGAAAATGGATGTAT 57.227 29.630 0.00 0.00 46.00 2.29
4772 5181 7.433131 CGGAATTACTTGTCATCAAAATGGATG 59.567 37.037 0.00 0.00 44.78 3.51
4773 5182 7.416664 CCGGAATTACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
4774 5183 6.127758 CCGGAATTACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
4775 5184 6.035843 CCGGAATTACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
4776 5185 6.747280 GTCCGGAATTACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
4777 5186 6.403200 CGTCCGGAATTACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
4778 5187 5.106869 CGTCCGGAATTACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
4779 5188 4.390603 CGTCCGGAATTACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
4780 5189 3.930229 CGTCCGGAATTACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
4781 5190 3.517602 CGTCCGGAATTACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
4782 5191 2.864343 CCGTCCGGAATTACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
4783 5192 2.498481 TCCGTCCGGAATTACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
4784 5193 1.894466 TCCGTCCGGAATTACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
4785 5194 2.537401 CTCCGTCCGGAATTACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
4786 5195 1.206371 CCTCCGTCCGGAATTACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
4787 5196 1.472728 CCCTCCGTCCGGAATTACTTG 60.473 57.143 5.23 0.00 44.66 3.16
4788 5197 0.828677 CCCTCCGTCCGGAATTACTT 59.171 55.000 5.23 0.00 44.66 2.24
4789 5198 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.00 44.66 2.24
4790 5199 0.388294 CTCCCTCCGTCCGGAATTAC 59.612 60.000 5.23 0.00 44.66 1.89
4791 5200 0.032813 ACTCCCTCCGTCCGGAATTA 60.033 55.000 5.23 0.00 44.66 1.40
4792 5201 0.032813 TACTCCCTCCGTCCGGAATT 60.033 55.000 5.23 0.00 44.66 2.17
4793 5202 0.187851 ATACTCCCTCCGTCCGGAAT 59.812 55.000 5.23 0.00 44.66 3.01
4794 5203 0.754217 CATACTCCCTCCGTCCGGAA 60.754 60.000 5.23 0.00 44.66 4.30
4795 5204 1.152819 CATACTCCCTCCGTCCGGA 60.153 63.158 0.00 0.00 42.90 5.14
4796 5205 0.179009 TACATACTCCCTCCGTCCGG 60.179 60.000 0.00 0.00 0.00 5.14
4797 5206 1.236628 CTACATACTCCCTCCGTCCG 58.763 60.000 0.00 0.00 0.00 4.79
4798 5207 2.361643 ACTACATACTCCCTCCGTCC 57.638 55.000 0.00 0.00 0.00 4.79
4799 5208 3.698040 TGAAACTACATACTCCCTCCGTC 59.302 47.826 0.00 0.00 0.00 4.79
4800 5209 3.705051 TGAAACTACATACTCCCTCCGT 58.295 45.455 0.00 0.00 0.00 4.69
4801 5210 4.441634 CCTTGAAACTACATACTCCCTCCG 60.442 50.000 0.00 0.00 0.00 4.63
4802 5211 4.715297 TCCTTGAAACTACATACTCCCTCC 59.285 45.833 0.00 0.00 0.00 4.30
4803 5212 5.422650 AGTCCTTGAAACTACATACTCCCTC 59.577 44.000 0.00 0.00 0.00 4.30
4804 5213 5.342866 AGTCCTTGAAACTACATACTCCCT 58.657 41.667 0.00 0.00 0.00 4.20
4805 5214 5.187186 TGAGTCCTTGAAACTACATACTCCC 59.813 44.000 0.00 0.00 32.94 4.30
4806 5215 6.153000 TCTGAGTCCTTGAAACTACATACTCC 59.847 42.308 0.00 0.00 32.94 3.85
4807 5216 7.159322 TCTGAGTCCTTGAAACTACATACTC 57.841 40.000 0.00 0.00 34.18 2.59
4808 5217 7.540474 TTCTGAGTCCTTGAAACTACATACT 57.460 36.000 0.00 0.00 0.00 2.12
4809 5218 6.311690 GCTTCTGAGTCCTTGAAACTACATAC 59.688 42.308 0.00 0.00 0.00 2.39
4826 5235 6.920758 GGAGTAGTACACATTATGCTTCTGAG 59.079 42.308 2.52 0.00 0.00 3.35
5023 5432 9.807649 CCGCTTTATTAGTAGGTAAAGAGTAAA 57.192 33.333 15.74 0.00 39.24 2.01
5024 5433 8.416329 CCCGCTTTATTAGTAGGTAAAGAGTAA 58.584 37.037 15.74 0.00 39.24 2.24
5025 5434 7.470563 GCCCGCTTTATTAGTAGGTAAAGAGTA 60.471 40.741 15.74 0.00 39.24 2.59
5026 5435 6.684865 GCCCGCTTTATTAGTAGGTAAAGAGT 60.685 42.308 15.74 0.00 39.24 3.24
5027 5436 5.695363 GCCCGCTTTATTAGTAGGTAAAGAG 59.305 44.000 15.74 13.27 39.24 2.85


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

AutoCloner maintained by Alex Coulton.