Multiple sequence alignment - TraesCS7A01G558100

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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 TraesCS7A01G558100 chr7A 100.000 5456 0 0 1 5456 730714401 730708946 0.000000e+00 10076.0
1 TraesCS7A01G558100 chr7A 84.459 296 43 1 1 293 730718400 730718105 6.910000e-74 289.0
2 TraesCS7A01G558100 chr7A 88.660 194 14 7 2353 2542 729637997 729638186 4.250000e-56 230.0
3 TraesCS7A01G558100 chr7A 88.947 190 14 6 2356 2542 729612597 729612782 1.530000e-55 228.0
4 TraesCS7A01G558100 chr7A 85.827 127 15 1 2783 2906 730711409 730711283 1.230000e-26 132.0
5 TraesCS7A01G558100 chr7A 85.827 127 15 1 2993 3119 730711619 730711496 1.230000e-26 132.0
6 TraesCS7A01G558100 chr7A 95.455 44 2 0 4143 4186 721201598 721201555 2.730000e-08 71.3
7 TraesCS7A01G558100 chr7A 93.333 45 1 2 4141 4183 41044992 41045036 1.270000e-06 65.8
8 TraesCS7A01G558100 chr7D 90.865 1872 75 34 3171 5005 635398080 635399892 0.000000e+00 2422.0
9 TraesCS7A01G558100 chr7D 95.459 1123 46 3 1475 2595 635396232 635397351 0.000000e+00 1786.0
10 TraesCS7A01G558100 chr7D 93.929 1120 42 7 1476 2595 634893657 634892564 0.000000e+00 1668.0
11 TraesCS7A01G558100 chr7D 96.075 1019 34 5 3171 4186 634891896 634890881 0.000000e+00 1655.0
12 TraesCS7A01G558100 chr7D 85.571 797 56 29 4213 5005 634890766 634890025 0.000000e+00 780.0
13 TraesCS7A01G558100 chr7D 92.966 526 28 5 2653 3173 635397464 635397985 0.000000e+00 758.0
14 TraesCS7A01G558100 chr7D 86.454 657 48 8 1 652 634896526 634895906 0.000000e+00 682.0
15 TraesCS7A01G558100 chr7D 93.103 435 18 6 2596 3026 634892530 634892104 1.290000e-175 627.0
16 TraesCS7A01G558100 chr7D 86.245 458 36 9 1 457 635390329 635390760 6.400000e-129 472.0
17 TraesCS7A01G558100 chr7D 86.863 373 38 3 4999 5361 634889882 634889511 1.830000e-109 407.0
18 TraesCS7A01G558100 chr7D 86.863 373 38 3 4999 5361 635400266 635400637 1.830000e-109 407.0
19 TraesCS7A01G558100 chr7D 93.724 239 9 6 1243 1481 635395972 635396204 2.420000e-93 353.0
20 TraesCS7A01G558100 chr7D 81.935 465 30 18 480 910 635390908 635391352 1.460000e-90 344.0
21 TraesCS7A01G558100 chr7D 90.234 256 14 6 1229 1481 634893930 634893683 1.900000e-84 324.0
22 TraesCS7A01G558100 chr7D 79.550 489 29 32 795 1228 635395368 635395840 3.220000e-72 283.0
23 TraesCS7A01G558100 chr7D 81.892 370 21 20 795 1137 634894524 634894174 2.500000e-68 270.0
24 TraesCS7A01G558100 chr7D 83.278 299 44 5 1 296 634898010 634897715 2.500000e-68 270.0
25 TraesCS7A01G558100 chr7D 92.697 178 9 4 2362 2536 636665207 636665031 2.520000e-63 254.0
26 TraesCS7A01G558100 chr7D 96.460 113 3 1 3061 3173 634892102 634891991 9.330000e-43 185.0
27 TraesCS7A01G558100 chr7D 90.909 110 9 1 2680 2788 550233541 550233650 4.400000e-31 147.0
28 TraesCS7A01G558100 chr7D 93.750 96 4 2 1134 1228 634894142 634894048 5.700000e-30 143.0
29 TraesCS7A01G558100 chr7D 86.614 127 16 1 2993 3119 635397591 635397716 7.370000e-29 139.0
30 TraesCS7A01G558100 chr7D 87.619 105 7 1 903 1007 635393574 635393672 3.450000e-22 117.0
31 TraesCS7A01G558100 chr7D 89.247 93 8 2 5365 5456 634889433 634889342 1.240000e-21 115.0
32 TraesCS7A01G558100 chr7D 89.247 93 8 2 5365 5456 635400715 635400806 1.240000e-21 115.0
33 TraesCS7A01G558100 chr7B 92.931 1160 50 6 1476 2612 741245427 741244277 0.000000e+00 1659.0
34 TraesCS7A01G558100 chr7B 95.400 1000 39 4 3174 4171 741244009 741243015 0.000000e+00 1585.0
35 TraesCS7A01G558100 chr7B 87.560 828 40 20 4213 5005 741242882 741242083 0.000000e+00 900.0
36 TraesCS7A01G558100 chr7B 79.426 1045 118 41 1 1007 741247993 741247008 0.000000e+00 649.0
37 TraesCS7A01G558100 chr7B 87.798 377 31 10 4999 5361 741241939 741241564 1.400000e-115 427.0
38 TraesCS7A01G558100 chr7B 86.327 373 40 3 4999 5361 740916585 740916214 3.960000e-106 396.0
39 TraesCS7A01G558100 chr7B 88.077 260 15 7 1229 1480 741245710 741245459 1.490000e-75 294.0
40 TraesCS7A01G558100 chr7B 88.341 223 26 0 1 223 741250410 741250188 9.010000e-68 268.0
41 TraesCS7A01G558100 chr7B 81.351 370 23 21 795 1137 741246289 741245939 5.420000e-65 259.0
42 TraesCS7A01G558100 chr7B 94.964 139 5 2 3036 3173 741244244 741244107 3.310000e-52 217.0
43 TraesCS7A01G558100 chr7B 92.473 93 7 0 5364 5456 741241487 741241395 3.430000e-27 134.0
44 TraesCS7A01G558100 chr7B 91.753 97 4 4 1134 1228 741245913 741245819 1.230000e-26 132.0
45 TraesCS7A01G558100 chr7B 91.429 70 6 0 5364 5433 740916137 740916068 4.500000e-16 97.1
46 TraesCS7A01G558100 chrUn 82.114 369 25 22 4552 4889 50447813 50448171 1.500000e-70 278.0
47 TraesCS7A01G558100 chr4A 82.065 368 26 21 4552 4889 708069002 708069359 1.500000e-70 278.0
48 TraesCS7A01G558100 chr4A 87.705 122 9 4 4770 4889 708091897 708092014 2.650000e-28 137.0
49 TraesCS7A01G558100 chr5B 91.892 111 7 2 2677 2785 364132776 364132666 2.630000e-33 154.0
50 TraesCS7A01G558100 chr6A 92.523 107 7 1 2680 2785 222555005 222554899 9.470000e-33 152.0
51 TraesCS7A01G558100 chr3D 91.818 110 8 1 2680 2788 463716865 463716974 9.470000e-33 152.0
52 TraesCS7A01G558100 chr3B 92.523 107 7 1 2680 2785 505264572 505264678 9.470000e-33 152.0
53 TraesCS7A01G558100 chr3B 92.523 107 7 1 2680 2785 812340357 812340463 9.470000e-33 152.0
54 TraesCS7A01G558100 chr3B 91.589 107 8 1 2680 2785 41018473 41018579 4.400000e-31 147.0
55 TraesCS7A01G558100 chr2B 97.727 44 1 0 4143 4186 62759661 62759618 5.860000e-10 76.8
56 TraesCS7A01G558100 chr2B 97.561 41 1 0 4146 4186 801055124 801055164 2.730000e-08 71.3
57 TraesCS7A01G558100 chr2D 97.727 44 0 1 4140 4183 192181472 192181514 2.110000e-09 75.0
58 TraesCS7A01G558100 chr5A 93.478 46 3 0 4141 4186 523453218 523453173 9.810000e-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 TraesCS7A01G558100 chr7A 730708946 730714401 5455 True 3446.666667 10076 90.551333 1 5456 3 chr7A.!!$R3 5455
1 TraesCS7A01G558100 chr7D 635390329 635400806 10477 False 654.181818 2422 88.280636 1 5456 11 chr7D.!!$F2 5455
2 TraesCS7A01G558100 chr7D 634889342 634898010 8668 True 593.833333 1668 89.738000 1 5456 12 chr7D.!!$R2 5455
3 TraesCS7A01G558100 chr7B 741241395 741250410 9015 True 593.090909 1659 89.097636 1 5456 11 chr7B.!!$R2 5455
4 TraesCS7A01G558100 chr7B 740916068 740916585 517 True 246.550000 396 88.878000 4999 5433 2 chr7B.!!$R1 434

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
717 3510 0.171455 GTCAGCAGTCCGGTAGTGAG 59.829 60.0 0.0 0.0 0.00 3.51 F
1128 8122 0.036671 CCAACTCCGTGGTAACCTCC 60.037 60.0 0.0 0.0 33.63 4.30 F
1438 8603 0.316841 TCCGTGCCAGAAATTTTGCC 59.683 50.0 0.0 0.0 0.00 4.52 F
2176 9405 0.868406 CACGTCTTGCTTCCTTGACC 59.132 55.0 0.0 0.0 0.00 4.02 F
3550 10945 0.036388 CCTGGCACATCCGTAAGTGT 60.036 55.0 0.0 0.0 38.20 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 8851 0.251922 AACATGCTGTTCTGGGGCAT 60.252 50.0 0.0 0.0 45.91 4.40 R
2131 9360 1.337817 CGTCGCTCACCAAAGACTCG 61.338 60.0 0.0 0.0 0.00 4.18 R
2747 10037 1.504359 TTAGTTGTCGCTCAAACGGG 58.496 50.0 0.0 0.0 37.81 5.28 R
3971 11368 2.031420 GGACGATGCACATGGATGAATG 60.031 50.0 0.0 0.0 0.00 2.67 R
4723 12256 0.108804 GCTGCTGACTACAACGGCTA 60.109 55.0 0.0 0.0 40.19 3.93 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
36 2541 4.778143 GGCTGCGTCCGGGATGTT 62.778 66.667 17.24 0.00 0.00 2.71
39 2544 1.153369 CTGCGTCCGGGATGTTGAT 60.153 57.895 17.24 0.00 0.00 2.57
138 2643 4.289245 CACGTCCCGGTCACCGTT 62.289 66.667 16.87 0.00 46.80 4.44
141 2646 4.309950 GTCCCGGTCACCGTTGCT 62.310 66.667 16.87 0.00 46.80 3.91
144 2649 4.619227 CCGGTCACCGTTGCTGGT 62.619 66.667 16.87 0.00 46.80 4.00
145 2650 2.340809 CGGTCACCGTTGCTGGTA 59.659 61.111 8.54 0.00 41.38 3.25
246 2752 1.529244 GCCTTCCAGTTGCCTGTGT 60.529 57.895 0.00 0.00 36.95 3.72
333 2846 1.134521 TCTGCACAAAACAGAGGACGT 60.135 47.619 0.00 0.00 39.21 4.34
410 2926 8.034058 AGCTCTCAACTGAACATGTAAATAAC 57.966 34.615 0.00 0.00 0.00 1.89
441 2957 3.615592 GCTTGCCTTGCTTGATCAAATGA 60.616 43.478 9.88 0.00 0.00 2.57
452 2968 9.708092 TTGCTTGATCAAATGAAATGAACAATA 57.292 25.926 9.88 0.00 38.41 1.90
536 3178 7.751732 TCTGTATTATGTTGTGCTGAATGAAC 58.248 34.615 0.00 0.00 0.00 3.18
541 3183 7.701539 TTATGTTGTGCTGAATGAACCTTAT 57.298 32.000 0.00 0.00 0.00 1.73
543 3185 6.012658 TGTTGTGCTGAATGAACCTTATTC 57.987 37.500 0.00 0.00 35.59 1.75
553 3195 4.478206 TGAACCTTATTCAGAGCTCAGG 57.522 45.455 17.77 14.86 0.00 3.86
590 3232 7.011669 TGAGATTGTATGCACATGTGTTCTATG 59.988 37.037 26.01 0.01 33.76 2.23
591 3233 7.049754 AGATTGTATGCACATGTGTTCTATGA 58.950 34.615 26.01 8.66 33.76 2.15
643 3290 7.558161 TGTGCTTATGTTAATCTTGATGGAG 57.442 36.000 0.00 0.00 0.00 3.86
688 3481 3.110358 CACTGCACTGTCAAAATGTGTG 58.890 45.455 0.00 0.00 34.52 3.82
689 3482 2.754552 ACTGCACTGTCAAAATGTGTGT 59.245 40.909 0.00 0.00 34.52 3.72
690 3483 3.181497 ACTGCACTGTCAAAATGTGTGTC 60.181 43.478 0.00 0.00 34.52 3.67
691 3484 2.751806 TGCACTGTCAAAATGTGTGTCA 59.248 40.909 0.00 0.00 34.52 3.58
692 3485 3.380954 TGCACTGTCAAAATGTGTGTCAT 59.619 39.130 0.00 0.00 38.57 3.06
693 3486 3.732219 GCACTGTCAAAATGTGTGTCATG 59.268 43.478 0.00 0.00 36.81 3.07
694 3487 4.734402 GCACTGTCAAAATGTGTGTCATGT 60.734 41.667 0.00 0.00 36.81 3.21
717 3510 0.171455 GTCAGCAGTCCGGTAGTGAG 59.829 60.000 0.00 0.00 0.00 3.51
731 3524 1.004080 GTGAGGCAGAGCAGAGCAA 60.004 57.895 0.00 0.00 0.00 3.91
974 6032 1.144057 CGGGCGTCAGGCTCTAAAT 59.856 57.895 0.00 0.00 41.25 1.40
1012 6070 4.969196 CGGCGATGCGGGCATACT 62.969 66.667 0.00 0.00 36.70 2.12
1013 6071 3.044305 GGCGATGCGGGCATACTC 61.044 66.667 6.07 0.00 36.70 2.59
1128 8122 0.036671 CCAACTCCGTGGTAACCTCC 60.037 60.000 0.00 0.00 33.63 4.30
1130 8124 1.196766 AACTCCGTGGTAACCTCCCC 61.197 60.000 0.00 0.00 0.00 4.81
1170 8208 1.927174 CTGGTTAGCTCGTTCCAATCG 59.073 52.381 0.00 0.00 0.00 3.34
1206 8245 3.859414 GCCCGGAGCAGAGCAGAT 61.859 66.667 0.73 0.00 42.97 2.90
1209 8248 1.523258 CCGGAGCAGAGCAGATTGG 60.523 63.158 0.00 0.00 0.00 3.16
1210 8249 2.178890 CGGAGCAGAGCAGATTGGC 61.179 63.158 0.00 0.00 0.00 4.52
1238 8398 0.909610 CTAGTGAGCCTGGGGTTGGA 60.910 60.000 0.00 0.00 0.00 3.53
1240 8400 1.142688 AGTGAGCCTGGGGTTGGATT 61.143 55.000 0.00 0.00 0.00 3.01
1279 8439 7.177392 AGCTATGCTTTTCTTGTTAGGATTTGT 59.823 33.333 0.00 0.00 33.89 2.83
1300 8460 6.471233 TGTCCATTTTTACCATGTGTTTCA 57.529 33.333 0.00 0.00 0.00 2.69
1325 8485 4.699735 TGTAATAACCAGCATGTGAACCTG 59.300 41.667 0.00 0.00 0.00 4.00
1402 8567 7.948137 TCGAAAAATGCTGTGTATTTAAATGC 58.052 30.769 11.05 10.05 28.56 3.56
1403 8568 7.596621 TCGAAAAATGCTGTGTATTTAAATGCA 59.403 29.630 14.12 14.12 28.56 3.96
1438 8603 0.316841 TCCGTGCCAGAAATTTTGCC 59.683 50.000 0.00 0.00 0.00 4.52
1444 8609 2.172293 TGCCAGAAATTTTGCCTTTGGT 59.828 40.909 0.00 0.00 0.00 3.67
1497 8701 9.959749 GTCATTTTGTATTTTTCAAGGTAGACA 57.040 29.630 0.00 0.00 0.00 3.41
1524 8728 3.313690 CATTTACTTTGACCGGCCAAAC 58.686 45.455 12.32 0.00 33.07 2.93
1635 8842 3.360867 ACCGACCAAAAATGGATGCATA 58.639 40.909 0.00 0.00 0.00 3.14
1655 8862 5.509670 GCATATCCTTTAAATGCCCCAGAAC 60.510 44.000 0.17 0.00 40.06 3.01
1686 8910 4.639959 TCTTGTAACAAAACACAACGTCG 58.360 39.130 0.00 0.00 31.61 5.12
1701 8925 1.395608 ACGTCGTGGTTTTGAGTGTTG 59.604 47.619 0.00 0.00 0.00 3.33
1869 9098 5.875359 GGTACAACTCTTCGAAATTCATCCT 59.125 40.000 0.00 0.00 0.00 3.24
1954 9183 1.153823 CGAAGTGGCACGGTCTAGG 60.154 63.158 12.71 0.00 0.00 3.02
2007 9236 3.620488 GCCAGAATGTTATTGAGGTGGA 58.380 45.455 0.00 0.00 0.00 4.02
2131 9360 6.037172 CCTTGATGTACATAGCCAACTTGTAC 59.963 42.308 8.71 5.69 43.74 2.90
2176 9405 0.868406 CACGTCTTGCTTCCTTGACC 59.132 55.000 0.00 0.00 0.00 4.02
2197 9426 3.431766 CCGGATCCCGTGAGAAAACTATT 60.432 47.826 6.06 0.00 46.80 1.73
2272 9504 6.604795 AGTTTCCCAAGAAAGGTATGATGATG 59.395 38.462 0.00 0.00 42.60 3.07
2273 9505 5.974156 TCCCAAGAAAGGTATGATGATGA 57.026 39.130 0.00 0.00 0.00 2.92
2274 9506 6.520021 TCCCAAGAAAGGTATGATGATGAT 57.480 37.500 0.00 0.00 0.00 2.45
2285 9517 8.211030 AGGTATGATGATGATTAGTGAATGGA 57.789 34.615 0.00 0.00 0.00 3.41
2356 9588 3.170717 TCCGAGTCTCCTTTGGTGTTAT 58.829 45.455 0.00 0.00 0.00 1.89
2358 9590 3.306780 CCGAGTCTCCTTTGGTGTTATGT 60.307 47.826 0.00 0.00 0.00 2.29
2359 9591 3.679980 CGAGTCTCCTTTGGTGTTATGTG 59.320 47.826 0.00 0.00 0.00 3.21
2360 9592 4.003648 GAGTCTCCTTTGGTGTTATGTGG 58.996 47.826 0.00 0.00 0.00 4.17
2416 9648 5.392057 GGCTACTTCTAATGCAACAAAGACC 60.392 44.000 0.00 0.00 0.00 3.85
2568 9800 5.474876 CCCTGTATTTCCTTCCTTATGCATC 59.525 44.000 0.19 0.00 0.00 3.91
2590 9822 5.401550 TCTGTTGCTTGTTCACTTTTTCTG 58.598 37.500 0.00 0.00 0.00 3.02
2634 9899 5.705905 ACTTTTGTTATACTCCCTTCAGTGC 59.294 40.000 0.00 0.00 0.00 4.40
2635 9900 5.499004 TTTGTTATACTCCCTTCAGTGCT 57.501 39.130 0.00 0.00 0.00 4.40
2636 9901 6.614694 TTTGTTATACTCCCTTCAGTGCTA 57.385 37.500 0.00 0.00 0.00 3.49
2637 9902 5.593679 TGTTATACTCCCTTCAGTGCTAC 57.406 43.478 0.00 0.00 0.00 3.58
2638 9903 5.269991 TGTTATACTCCCTTCAGTGCTACT 58.730 41.667 0.00 0.00 0.00 2.57
2639 9904 5.360144 TGTTATACTCCCTTCAGTGCTACTC 59.640 44.000 0.00 0.00 0.00 2.59
2671 9958 3.686016 TCAAGCCATTTCTGAGTAACCC 58.314 45.455 0.00 0.00 0.00 4.11
2678 9965 5.944007 GCCATTTCTGAGTAACCCTTTCTTA 59.056 40.000 0.00 0.00 0.00 2.10
2684 9974 7.657023 TCTGAGTAACCCTTTCTTATACTCC 57.343 40.000 8.33 0.00 40.97 3.85
2685 9975 6.610425 TCTGAGTAACCCTTTCTTATACTCCC 59.390 42.308 8.33 0.00 40.97 4.30
2686 9976 6.509386 TGAGTAACCCTTTCTTATACTCCCT 58.491 40.000 8.33 0.00 40.97 4.20
2687 9977 6.610425 TGAGTAACCCTTTCTTATACTCCCTC 59.390 42.308 8.33 0.00 40.97 4.30
2693 9983 5.511545 CCCTTTCTTATACTCCCTCATTCCG 60.512 48.000 0.00 0.00 0.00 4.30
2696 9986 6.896021 TTCTTATACTCCCTCATTCCGTAG 57.104 41.667 0.00 0.00 0.00 3.51
2729 10019 5.277683 GCTGAAACGGATGTATCTAGACGTA 60.278 44.000 0.00 0.00 33.85 3.57
2747 10037 6.496571 AGACGTATTTCAGTGCTAGATACAC 58.503 40.000 0.00 0.00 38.35 2.90
2920 10212 1.917872 TGAATTGGTGGCCCAGTTAC 58.082 50.000 0.00 0.00 40.47 2.50
2988 10283 6.459710 CCCTTCCTTGTTTTGAACTTACAGAC 60.460 42.308 0.00 0.00 0.00 3.51
3028 10323 5.791974 CACTCGAAACAGATACATTGCTTTG 59.208 40.000 0.00 0.00 0.00 2.77
3083 10378 7.069877 TGTAAGTGGTGTGGATAAAGTTACT 57.930 36.000 0.00 0.00 31.10 2.24
3084 10379 8.192743 TGTAAGTGGTGTGGATAAAGTTACTA 57.807 34.615 0.00 0.00 31.10 1.82
3338 10731 6.665248 AGGCAAAAGCTTTATTTATCCTCACT 59.335 34.615 13.10 0.00 0.00 3.41
3539 10934 3.758023 CAGTATTTGACATTCCTGGCACA 59.242 43.478 0.00 0.00 41.21 4.57
3550 10945 0.036388 CCTGGCACATCCGTAAGTGT 60.036 55.000 0.00 0.00 38.20 3.55
3592 10987 2.959516 GGTTGCAGCTAAACCAATTCC 58.040 47.619 20.48 3.61 45.41 3.01
3600 10995 6.154192 TGCAGCTAAACCAATTCCATTATTCA 59.846 34.615 0.00 0.00 0.00 2.57
3711 11106 9.315525 GGTAACTCTTATCTTTTGATACCTGTC 57.684 37.037 0.00 0.00 40.77 3.51
3712 11107 9.871238 GTAACTCTTATCTTTTGATACCTGTCA 57.129 33.333 0.00 0.00 40.77 3.58
3752 11149 3.187227 CCAAATTCACAGTGACTTCTCCG 59.813 47.826 1.52 0.00 0.00 4.63
3814 11211 3.117701 TCATCCACCTTTTCAGTTGGTCA 60.118 43.478 0.00 0.00 30.72 4.02
3971 11368 3.108376 ACATAGTTCTCAGTTCCCTCCC 58.892 50.000 0.00 0.00 0.00 4.30
4069 11466 0.178995 TCCATGCAAGCTGGACACAA 60.179 50.000 3.30 0.00 37.87 3.33
4183 11583 8.147704 TGATCCATATTACTTGTCGCTCAAATA 58.852 33.333 0.00 0.00 35.48 1.40
4206 11664 5.209659 AGACGGAGGGAGTAGTATCAAAAT 58.790 41.667 0.00 0.00 0.00 1.82
4337 11843 6.529125 CACTGTTATTGAATTGTCTTGATGGC 59.471 38.462 0.00 0.00 0.00 4.40
4461 11967 1.573376 AGGCTAGGGATCTGACTGAGT 59.427 52.381 0.00 0.00 0.00 3.41
4492 12012 5.348164 AGTTAAGCAATTTTGTCGCAGTTT 58.652 33.333 0.00 0.00 0.00 2.66
4493 12013 5.231991 AGTTAAGCAATTTTGTCGCAGTTTG 59.768 36.000 0.00 0.00 0.00 2.93
4502 12022 3.332761 TGTCGCAGTTTGATGTTGTTC 57.667 42.857 0.00 0.00 0.00 3.18
4616 12136 5.047519 ACTCTTGCTTCCTTCAATGGAAATG 60.048 40.000 0.00 0.00 44.49 2.32
4643 12163 2.103771 CGATGGATGTGACTCCCTCATT 59.896 50.000 6.97 0.00 34.12 2.57
4730 12263 9.227777 GGAATAAGTGGAATATATTTAGCCGTT 57.772 33.333 0.00 0.00 0.00 4.44
4734 12267 8.603242 AAGTGGAATATATTTAGCCGTTGTAG 57.397 34.615 0.00 0.00 0.00 2.74
4735 12268 7.732996 AGTGGAATATATTTAGCCGTTGTAGT 58.267 34.615 0.00 0.00 0.00 2.73
4736 12269 7.871463 AGTGGAATATATTTAGCCGTTGTAGTC 59.129 37.037 0.00 0.00 0.00 2.59
4737 12270 7.654520 GTGGAATATATTTAGCCGTTGTAGTCA 59.345 37.037 0.00 0.00 0.00 3.41
4738 12271 7.870954 TGGAATATATTTAGCCGTTGTAGTCAG 59.129 37.037 0.00 0.00 0.00 3.51
4754 12287 4.271696 AGTCAGCAGCATACAGTTTACA 57.728 40.909 0.00 0.00 0.00 2.41
4755 12288 4.641396 AGTCAGCAGCATACAGTTTACAA 58.359 39.130 0.00 0.00 0.00 2.41
4838 12377 8.025445 CACTTTCATTCTAAAATTGTCTCCTGG 58.975 37.037 0.00 0.00 0.00 4.45
4839 12378 7.725844 ACTTTCATTCTAAAATTGTCTCCTGGT 59.274 33.333 0.00 0.00 0.00 4.00
4840 12379 7.452880 TTCATTCTAAAATTGTCTCCTGGTG 57.547 36.000 0.00 0.00 0.00 4.17
4841 12380 5.415701 TCATTCTAAAATTGTCTCCTGGTGC 59.584 40.000 0.00 0.00 0.00 5.01
4842 12381 4.365514 TCTAAAATTGTCTCCTGGTGCA 57.634 40.909 0.00 0.00 0.00 4.57
4843 12382 4.326826 TCTAAAATTGTCTCCTGGTGCAG 58.673 43.478 0.00 0.00 0.00 4.41
4844 12383 2.957402 AAATTGTCTCCTGGTGCAGA 57.043 45.000 0.00 0.00 32.44 4.26
4856 12395 5.759059 TCCTGGTGCAGAATCTCATAAAAT 58.241 37.500 0.00 0.00 32.44 1.82
4917 12458 9.878667 TCTTATATTTGAGACCGAATTAACACA 57.121 29.630 0.00 0.00 0.00 3.72
4945 12486 7.113404 CACAAATTGGTCGTCACTTATTTCTTG 59.887 37.037 0.00 0.00 0.00 3.02
4989 12530 7.226523 ACCAAATTAACTTGAAGCCATTTGTTC 59.773 33.333 16.57 0.00 32.19 3.18
5017 12939 1.064240 TGCCATCTCATGCAACTCCAT 60.064 47.619 0.00 0.00 33.87 3.41
5038 12960 2.094494 TGTCAATCTCCTTCAGAGCGTC 60.094 50.000 0.00 0.00 42.90 5.19
5067 12989 1.202521 TCGACAGCTTCAACTTGAGCA 60.203 47.619 12.73 0.00 0.00 4.26
5080 13002 1.774217 TGAGCACCCTCAACCCCTT 60.774 57.895 0.00 0.00 44.79 3.95
5081 13003 1.303643 GAGCACCCTCAACCCCTTG 60.304 63.158 0.00 0.00 38.03 3.61
5116 13038 1.071385 CTCCATCTTTGCCGCCTCTAT 59.929 52.381 0.00 0.00 0.00 1.98
5117 13039 1.490490 TCCATCTTTGCCGCCTCTATT 59.510 47.619 0.00 0.00 0.00 1.73
5122 13044 2.026262 TCTTTGCCGCCTCTATTCCTTT 60.026 45.455 0.00 0.00 0.00 3.11
5166 13088 3.775654 GGGTGAGGAGGCTGTCGG 61.776 72.222 0.00 0.00 0.00 4.79
5345 13280 1.097547 GCTTCTGCATACGCCCATGT 61.098 55.000 0.00 0.00 39.41 3.21
5361 13296 0.395311 ATGTAGGAGCGACTTCCGGA 60.395 55.000 0.00 0.00 42.29 5.14
5362 13297 1.030488 TGTAGGAGCGACTTCCGGAG 61.030 60.000 3.34 1.34 42.29 4.63
5404 13413 1.098869 TTTGCCAACGTTGAGCTCAA 58.901 45.000 29.35 25.16 0.00 3.02
5414 13423 1.615392 GTTGAGCTCAATGCCTGGTTT 59.385 47.619 30.65 0.00 44.23 3.27
5418 13427 1.891150 AGCTCAATGCCTGGTTTCAAG 59.109 47.619 0.00 0.00 44.23 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 2541 1.472480 TCGCACTCGTTGATCTCATCA 59.528 47.619 0.00 0.00 37.55 3.07
39 2544 0.596082 TGTCGCACTCGTTGATCTCA 59.404 50.000 0.00 0.00 36.96 3.27
138 2643 1.907739 GCAGATCCTGGTACCAGCA 59.092 57.895 32.98 22.61 42.35 4.41
141 2646 1.663379 CGTCGCAGATCCTGGTACCA 61.663 60.000 15.39 15.39 40.67 3.25
144 2649 2.782222 GCCGTCGCAGATCCTGGTA 61.782 63.158 0.00 0.00 40.67 3.25
145 2650 4.148825 GCCGTCGCAGATCCTGGT 62.149 66.667 0.00 0.00 40.67 4.00
246 2752 4.558226 ATGCATACACAGAGAGGAACAA 57.442 40.909 0.00 0.00 0.00 2.83
331 2841 1.070309 GTTCTGAAGCAGCAACAGACG 60.070 52.381 17.35 0.00 39.80 4.18
333 2846 2.158914 TCTGTTCTGAAGCAGCAACAGA 60.159 45.455 23.10 23.10 45.01 3.41
441 2957 5.598754 TCCCCAATTCCCTATTGTTCATTT 58.401 37.500 0.00 0.00 41.74 2.32
472 2988 9.071276 CAATGAAGCCATCCAATAAGTATTAGT 57.929 33.333 0.00 0.00 29.83 2.24
490 3131 3.360249 AACTTGACAGTGCAATGAAGC 57.640 42.857 22.73 10.06 31.60 3.86
547 3189 4.268797 TCTCATCATTATCAGCCTGAGC 57.731 45.455 0.00 0.00 40.32 4.26
548 3190 6.231951 ACAATCTCATCATTATCAGCCTGAG 58.768 40.000 0.00 0.00 33.16 3.35
553 3195 7.094933 TGTGCATACAATCTCATCATTATCAGC 60.095 37.037 0.00 0.00 32.88 4.26
590 3232 2.430465 TCTGCTTCACTTTGCTCCATC 58.570 47.619 0.00 0.00 0.00 3.51
591 3233 2.574006 TCTGCTTCACTTTGCTCCAT 57.426 45.000 0.00 0.00 0.00 3.41
643 3290 7.650104 GTGCAAACATCTACTACTTCTAGGATC 59.350 40.741 0.00 0.00 0.00 3.36
717 3510 0.886563 ATTGTTTGCTCTGCTCTGCC 59.113 50.000 0.00 0.00 0.00 4.85
731 3524 3.838317 TGGTGGAGTAGCAGAGTATTGTT 59.162 43.478 0.00 0.00 32.05 2.83
765 3591 3.246112 TGGGTGTGGGGGTCGAAG 61.246 66.667 0.00 0.00 0.00 3.79
840 3666 0.246086 GGATATGCTCGAGCTGGGAG 59.754 60.000 35.27 0.00 42.66 4.30
974 6032 2.295602 GGCCGAAACCCTAGGTGGA 61.296 63.158 8.29 0.00 35.34 4.02
1035 8029 3.441290 CCGTCGCCGAGGAAGACT 61.441 66.667 8.59 0.00 35.63 3.24
1130 8124 1.304282 CATGGGTTCAGTGGAGGGG 59.696 63.158 0.00 0.00 0.00 4.79
1134 8128 1.379916 CAGCCATGGGTTCAGTGGA 59.620 57.895 15.37 0.00 34.94 4.02
1170 8208 0.744281 CAACACTGGGTTTCACCACC 59.256 55.000 0.00 0.00 41.02 4.61
1206 8245 2.289694 GCTCACTAGAGGTTGAAGCCAA 60.290 50.000 0.00 0.00 42.33 4.52
1209 8248 1.552792 AGGCTCACTAGAGGTTGAAGC 59.447 52.381 0.00 0.00 42.33 3.86
1210 8249 2.093764 CCAGGCTCACTAGAGGTTGAAG 60.094 54.545 0.00 0.00 42.33 3.02
1279 8439 7.504403 ACAATGAAACACATGGTAAAAATGGA 58.496 30.769 0.00 0.00 40.94 3.41
1300 8460 5.951747 AGGTTCACATGCTGGTTATTACAAT 59.048 36.000 0.00 0.00 0.00 2.71
1402 8567 4.378046 GCACGGAAACCTTGTACTTATGTG 60.378 45.833 0.00 0.00 0.00 3.21
1403 8568 3.749609 GCACGGAAACCTTGTACTTATGT 59.250 43.478 0.00 0.00 0.00 2.29
1438 8603 2.810032 GCCCCATTCCACAAAACCAAAG 60.810 50.000 0.00 0.00 0.00 2.77
1444 8609 0.112606 TACCGCCCCATTCCACAAAA 59.887 50.000 0.00 0.00 0.00 2.44
1497 8701 2.556622 CCGGTCAAAGTAAATGCCAACT 59.443 45.455 0.00 0.00 0.00 3.16
1524 8728 1.134401 ACACATTCCTACCTCCGCATG 60.134 52.381 0.00 0.00 0.00 4.06
1635 8842 4.026052 CTGTTCTGGGGCATTTAAAGGAT 58.974 43.478 3.61 0.00 0.00 3.24
1642 8849 0.899720 CATGCTGTTCTGGGGCATTT 59.100 50.000 0.00 0.00 43.62 2.32
1644 8851 0.251922 AACATGCTGTTCTGGGGCAT 60.252 50.000 0.00 0.00 45.91 4.40
1655 8862 6.309980 TGTGTTTTGTTACAAGAAACATGCTG 59.690 34.615 15.47 0.00 42.92 4.41
1686 8910 1.741145 ACGGTCAACACTCAAAACCAC 59.259 47.619 0.00 0.00 0.00 4.16
1701 8925 2.866762 CCTAGCAGATAAAGCAACGGTC 59.133 50.000 0.00 0.00 0.00 4.79
1784 9008 0.319900 TGTTCTCAAGAGCCGAGTGC 60.320 55.000 0.00 0.00 41.71 4.40
1869 9098 1.606480 GCAGTAACAGCAGACAGAGCA 60.606 52.381 0.00 0.00 0.00 4.26
1954 9183 3.629398 GGTCAATGATGATGTCCAGGAAC 59.371 47.826 0.00 0.00 38.01 3.62
2007 9236 5.466127 AGAGTCATAGAGAGAGGGTTCTT 57.534 43.478 0.00 0.00 32.53 2.52
2131 9360 1.337817 CGTCGCTCACCAAAGACTCG 61.338 60.000 0.00 0.00 0.00 4.18
2274 9506 9.921637 GACCAAATACAAATTTCCATTCACTAA 57.078 29.630 0.00 0.00 32.87 2.24
2282 9514 3.827625 CGCGACCAAATACAAATTTCCA 58.172 40.909 0.00 0.00 32.87 3.53
2283 9515 2.596862 GCGCGACCAAATACAAATTTCC 59.403 45.455 12.10 0.00 32.87 3.13
2285 9517 2.601804 GGCGCGACCAAATACAAATTT 58.398 42.857 12.10 0.00 38.86 1.82
2356 9588 2.584835 AGCTACAATTTCCTGCCACA 57.415 45.000 0.00 0.00 0.00 4.17
2358 9590 3.084039 CTGAAGCTACAATTTCCTGCCA 58.916 45.455 0.00 0.00 0.00 4.92
2359 9591 2.424956 CCTGAAGCTACAATTTCCTGCC 59.575 50.000 0.00 0.00 0.00 4.85
2360 9592 3.347216 TCCTGAAGCTACAATTTCCTGC 58.653 45.455 0.00 0.00 0.00 4.85
2437 9669 1.587043 GGACCCGCTTTTCTTCCTGC 61.587 60.000 0.00 0.00 0.00 4.85
2568 9800 5.163513 ACAGAAAAAGTGAACAAGCAACAG 58.836 37.500 0.00 0.00 0.00 3.16
2607 9872 8.290325 CACTGAAGGGAGTATAACAAAAGTTTC 58.710 37.037 0.00 0.00 0.00 2.78
2636 9901 9.110382 AGAAATGGCTTGATAATATCTAGGAGT 57.890 33.333 12.29 0.00 33.59 3.85
2637 9902 9.381033 CAGAAATGGCTTGATAATATCTAGGAG 57.619 37.037 12.29 2.78 33.59 3.69
2638 9903 9.104713 TCAGAAATGGCTTGATAATATCTAGGA 57.895 33.333 12.29 0.00 33.59 2.94
2639 9904 9.381033 CTCAGAAATGGCTTGATAATATCTAGG 57.619 37.037 12.29 0.30 33.59 3.02
2671 9958 6.163135 ACGGAATGAGGGAGTATAAGAAAG 57.837 41.667 0.00 0.00 0.00 2.62
2678 9965 5.321934 ACTACTACGGAATGAGGGAGTAT 57.678 43.478 0.00 0.00 0.00 2.12
2684 9974 3.550678 GCGAAAACTACTACGGAATGAGG 59.449 47.826 0.00 0.00 0.00 3.86
2685 9975 4.265556 CAGCGAAAACTACTACGGAATGAG 59.734 45.833 0.00 0.00 0.00 2.90
2686 9976 4.082625 TCAGCGAAAACTACTACGGAATGA 60.083 41.667 0.00 0.00 0.00 2.57
2687 9977 4.171005 TCAGCGAAAACTACTACGGAATG 58.829 43.478 0.00 0.00 0.00 2.67
2693 9983 3.983344 TCCGTTTCAGCGAAAACTACTAC 59.017 43.478 12.95 0.00 37.06 2.73
2696 9986 3.185797 ACATCCGTTTCAGCGAAAACTAC 59.814 43.478 12.95 0.25 37.06 2.73
2729 10019 3.451178 ACGGGTGTATCTAGCACTGAAAT 59.549 43.478 0.00 0.00 37.07 2.17
2747 10037 1.504359 TTAGTTGTCGCTCAAACGGG 58.496 50.000 0.00 0.00 37.81 5.28
2931 10223 5.604565 AGCAGAATTTGGTCAAAGGAAAAG 58.395 37.500 2.55 0.00 33.32 2.27
2988 10283 8.817100 TGTTTCGAGTGCATATTTAATACAGAG 58.183 33.333 0.00 0.00 0.00 3.35
3059 10354 7.069877 AGTAACTTTATCCACACCACTTACA 57.930 36.000 0.00 0.00 0.00 2.41
3103 10398 6.018098 GGAGTCTGTCATTCAAGAATATGCAG 60.018 42.308 0.00 11.09 32.31 4.41
3213 10606 6.353323 TCCTATATTGAAAGCAATCGGACAA 58.647 36.000 0.00 0.00 43.43 3.18
3338 10731 4.885325 GGTACCAAGAGTCAAAGTGGAAAA 59.115 41.667 7.15 0.00 35.04 2.29
3408 10801 6.707440 TCTTTTGAACCTGCACATTTAGAA 57.293 33.333 0.00 0.00 0.00 2.10
3464 10859 9.967346 CGAGGTGAATAGAATTTGTAATCTCTA 57.033 33.333 0.00 0.00 0.00 2.43
3539 10934 9.139734 TCTTAAATCCAGTATACACTTACGGAT 57.860 33.333 5.50 3.84 37.22 4.18
3600 10995 5.222337 ACCTGGACAGAGGAACCAATTAAAT 60.222 40.000 0.00 0.00 36.51 1.40
3711 11106 8.455903 AATTTGGGATATTGTCACTAGTCATG 57.544 34.615 0.00 0.00 0.00 3.07
3712 11107 8.274322 TGAATTTGGGATATTGTCACTAGTCAT 58.726 33.333 0.00 0.00 0.00 3.06
3719 11116 6.150976 TCACTGTGAATTTGGGATATTGTCAC 59.849 38.462 8.27 0.00 0.00 3.67
3726 11123 6.126863 AGAAGTCACTGTGAATTTGGGATA 57.873 37.500 22.35 0.00 34.57 2.59
3752 11149 8.794335 ATCTCATTTAACAAAGTAGAAGGACC 57.206 34.615 0.00 0.00 0.00 4.46
3814 11211 4.141824 GGAAGAGAGCAAGCTATTAGTGGT 60.142 45.833 0.00 0.00 0.00 4.16
3971 11368 2.031420 GGACGATGCACATGGATGAATG 60.031 50.000 0.00 0.00 0.00 2.67
4069 11466 2.526873 AGCGTCCTCCAAGGTGGT 60.527 61.111 7.06 0.00 39.03 4.16
4183 11583 3.947612 TTGATACTACTCCCTCCGTCT 57.052 47.619 0.00 0.00 0.00 4.18
4206 11664 6.150809 TGCAACTAATTACTGCATGATGAACA 59.849 34.615 11.68 0.00 41.01 3.18
4337 11843 4.989797 TGCTTGGCTGAAATACAAAACATG 59.010 37.500 0.00 0.00 0.00 3.21
4461 11967 7.908082 GCGACAAAATTGCTTAACTATGTATCA 59.092 33.333 0.00 0.00 34.45 2.15
4513 12033 2.238521 GAAACAGCATTGAACTCCCCA 58.761 47.619 0.00 0.00 0.00 4.96
4616 12136 4.707448 AGGGAGTCACATCCATCGATATAC 59.293 45.833 0.00 0.00 41.52 1.47
4643 12163 9.899661 ATCATAGTAAGGCACAACAGTTAATAA 57.100 29.630 0.00 0.00 0.00 1.40
4711 12244 7.654520 TGACTACAACGGCTAAATATATTCCAC 59.345 37.037 0.00 0.00 0.00 4.02
4720 12253 3.262420 CTGCTGACTACAACGGCTAAAT 58.738 45.455 0.00 0.00 39.95 1.40
4721 12254 2.683968 CTGCTGACTACAACGGCTAAA 58.316 47.619 0.00 0.00 39.95 1.85
4722 12255 1.671850 GCTGCTGACTACAACGGCTAA 60.672 52.381 0.00 0.00 40.19 3.09
4723 12256 0.108804 GCTGCTGACTACAACGGCTA 60.109 55.000 0.00 0.00 40.19 3.93
4724 12257 1.374758 GCTGCTGACTACAACGGCT 60.375 57.895 0.00 0.00 40.19 5.52
4725 12258 1.021390 ATGCTGCTGACTACAACGGC 61.021 55.000 0.00 0.00 42.66 5.68
4726 12259 1.927174 GTATGCTGCTGACTACAACGG 59.073 52.381 0.00 0.00 0.00 4.44
4727 12260 2.600420 CTGTATGCTGCTGACTACAACG 59.400 50.000 0.00 0.00 0.00 4.10
4730 12263 3.961480 AACTGTATGCTGCTGACTACA 57.039 42.857 0.00 3.41 0.00 2.74
4733 12266 4.271696 TGTAAACTGTATGCTGCTGACT 57.728 40.909 0.00 0.00 0.00 3.41
4734 12267 5.356882 TTTGTAAACTGTATGCTGCTGAC 57.643 39.130 0.00 0.00 0.00 3.51
4735 12268 6.384258 TTTTTGTAAACTGTATGCTGCTGA 57.616 33.333 0.00 0.00 0.00 4.26
4825 12364 2.957402 TCTGCACCAGGAGACAATTT 57.043 45.000 0.00 0.00 37.29 1.82
4834 12373 6.461110 AATTTTATGAGATTCTGCACCAGG 57.539 37.500 0.00 0.00 31.51 4.45
4877 12416 9.123902 CTCAAATATAAGACCAATGGTTCATGA 57.876 33.333 6.30 0.00 35.25 3.07
4878 12417 9.123902 TCTCAAATATAAGACCAATGGTTCATG 57.876 33.333 6.30 0.00 35.25 3.07
4900 12440 3.181464 TGTGGTGTGTTAATTCGGTCTCA 60.181 43.478 0.00 0.00 0.00 3.27
4989 12530 3.473625 TGCATGAGATGGCAAGTGATAG 58.526 45.455 0.00 0.00 37.03 2.08
5017 12939 1.895798 ACGCTCTGAAGGAGATTGACA 59.104 47.619 0.00 0.00 44.45 3.58
5058 12980 0.178990 GGGTTGAGGGTGCTCAAGTT 60.179 55.000 0.00 0.00 43.08 2.66
5062 12984 1.774217 AAGGGGTTGAGGGTGCTCA 60.774 57.895 0.00 0.00 0.00 4.26
5101 13023 1.204146 AGGAATAGAGGCGGCAAAGA 58.796 50.000 13.08 0.00 0.00 2.52
5116 13038 2.507484 CAGATCACCTGCACAAAGGAA 58.493 47.619 0.00 0.00 40.02 3.36
5117 13039 2.189594 CAGATCACCTGCACAAAGGA 57.810 50.000 0.00 0.00 40.02 3.36
5280 13215 2.356382 GAGTGATCATCGAGACGGTTCT 59.644 50.000 0.00 0.00 33.37 3.01
5345 13280 2.119655 GCTCCGGAAGTCGCTCCTA 61.120 63.158 5.23 0.00 37.59 2.94
5361 13296 0.681733 TCAGAAGCTTCAAGGTCGCT 59.318 50.000 27.57 1.82 35.09 4.93
5362 13297 1.462670 CTTCAGAAGCTTCAAGGTCGC 59.537 52.381 27.57 0.00 0.00 5.19
5399 13408 1.067354 CCTTGAAACCAGGCATTGAGC 60.067 52.381 0.00 0.00 44.65 4.26
5404 13413 1.358787 TGGATCCTTGAAACCAGGCAT 59.641 47.619 14.23 0.00 0.00 4.40
5414 13423 3.203710 AGAAGATGGCATTGGATCCTTGA 59.796 43.478 14.23 0.00 0.00 3.02
5418 13427 3.703052 ACAAAGAAGATGGCATTGGATCC 59.297 43.478 4.20 4.20 0.00 3.36


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

AutoCloner maintained by Alex Coulton.