Multiple sequence alignment - TraesCS7D01G496600

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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 TraesCS7D01G496600 chr7D 100.000 2795 0 0 1 2795 603501079 603498285 0.000000e+00 5162.0
1 TraesCS7D01G496600 chr7D 88.691 955 56 8 1771 2691 603646801 603647737 0.000000e+00 1118.0
2 TraesCS7D01G496600 chr7D 93.155 336 23 0 1387 1722 603646474 603646809 6.950000e-136 494.0
3 TraesCS7D01G496600 chr7D 88.921 343 16 8 971 1296 603605390 603605727 1.210000e-108 403.0
4 TraesCS7D01G496600 chr7D 85.000 280 20 6 1 263 263969257 263968983 5.940000e-67 265.0
5 TraesCS7D01G496600 chr7D 88.636 220 14 6 384 603 263968765 263968557 9.930000e-65 257.0
6 TraesCS7D01G496600 chr7D 94.444 54 3 0 254 307 263968963 263968910 1.780000e-12 84.2
7 TraesCS7D01G496600 chr7A 94.671 1032 42 6 893 1917 696200727 696199702 0.000000e+00 1589.0
8 TraesCS7D01G496600 chr7A 90.415 1158 87 15 783 1920 696251242 696252395 0.000000e+00 1502.0
9 TraesCS7D01G496600 chr7A 93.694 111 6 1 2242 2351 696252396 696252506 6.190000e-37 165.0
10 TraesCS7D01G496600 chr7A 88.372 129 15 0 2360 2488 696253684 696253812 3.730000e-34 156.0
11 TraesCS7D01G496600 chr7A 91.379 58 3 2 786 842 696200796 696200740 8.300000e-11 78.7
12 TraesCS7D01G496600 chr7A 96.970 33 1 0 2659 2691 696071241 696071209 3.890000e-04 56.5
13 TraesCS7D01G496600 chr7B 88.287 794 74 14 1033 1824 684616015 684615239 0.000000e+00 933.0
14 TraesCS7D01G496600 chr7B 94.600 537 28 1 1385 1920 685378944 685379480 0.000000e+00 830.0
15 TraesCS7D01G496600 chr7B 86.146 794 71 20 1033 1824 684643909 684643153 0.000000e+00 821.0
16 TraesCS7D01G496600 chr7B 93.893 393 16 5 946 1331 685378552 685378943 1.120000e-163 586.0
17 TraesCS7D01G496600 chr7B 86.085 424 54 5 2242 2662 685379481 685379902 4.250000e-123 451.0
18 TraesCS7D01G496600 chr7B 90.446 314 12 5 603 906 685378251 685378556 5.610000e-107 398.0
19 TraesCS7D01G496600 chr7B 86.777 242 32 0 2000 2241 748589375 748589616 1.280000e-68 270.0
20 TraesCS7D01G496600 chr7B 84.351 262 20 13 3 263 74587523 74587764 1.290000e-58 237.0
21 TraesCS7D01G496600 chr7B 96.396 111 4 0 254 364 74587784 74587894 1.710000e-42 183.0
22 TraesCS7D01G496600 chr7B 93.814 97 4 2 1825 1920 684596124 684596029 8.070000e-31 145.0
23 TraesCS7D01G496600 chr7B 93.103 87 6 0 373 459 74596753 74596839 8.130000e-26 128.0
24 TraesCS7D01G496600 chr7B 94.118 51 2 1 2719 2769 60047472 60047521 2.990000e-10 76.8
25 TraesCS7D01G496600 chr7B 100.000 28 0 0 2664 2691 685381220 685381247 5.000000e-03 52.8
26 TraesCS7D01G496600 chrUn 86.524 794 68 20 1033 1824 202524067 202523311 0.000000e+00 837.0
27 TraesCS7D01G496600 chrUn 86.146 794 71 20 1033 1824 224017047 224016291 0.000000e+00 821.0
28 TraesCS7D01G496600 chrUn 86.146 794 71 20 1033 1824 399485431 399486187 0.000000e+00 821.0
29 TraesCS7D01G496600 chrUn 86.020 794 72 20 1033 1824 197869352 197868596 0.000000e+00 815.0
30 TraesCS7D01G496600 chr4D 90.503 358 24 4 1 357 165590900 165591248 5.450000e-127 464.0
31 TraesCS7D01G496600 chr4D 85.209 311 42 2 1932 2241 431025918 431025611 1.620000e-82 316.0
32 TraesCS7D01G496600 chr4D 91.189 227 20 0 378 604 165592394 165592620 2.700000e-80 309.0
33 TraesCS7D01G496600 chr4D 78.846 208 43 1 2454 2660 485603994 485604201 3.750000e-29 139.0
34 TraesCS7D01G496600 chr4D 100.000 35 0 0 2761 2795 108900093 108900059 6.460000e-07 65.8
35 TraesCS7D01G496600 chr4D 94.737 38 1 1 2757 2794 473828937 473828901 1.080000e-04 58.4
36 TraesCS7D01G496600 chr1D 87.948 307 35 1 1932 2238 401659328 401659632 7.360000e-96 361.0
37 TraesCS7D01G496600 chr1D 88.843 242 27 0 2000 2241 10592527 10592768 5.850000e-77 298.0
38 TraesCS7D01G496600 chr5B 87.087 333 23 5 254 574 507689220 507689544 2.650000e-95 359.0
39 TraesCS7D01G496600 chr5B 100.000 34 0 0 2761 2794 65248995 65249028 2.320000e-06 63.9
40 TraesCS7D01G496600 chr5B 97.143 35 0 1 2761 2794 144857635 144857669 1.080000e-04 58.4
41 TraesCS7D01G496600 chr2D 90.123 243 23 1 2000 2241 32759082 32759324 5.810000e-82 315.0
42 TraesCS7D01G496600 chr2D 85.000 280 20 6 1 263 55390359 55390633 5.940000e-67 265.0
43 TraesCS7D01G496600 chr2D 88.128 219 15 6 384 602 55390854 55391061 1.660000e-62 250.0
44 TraesCS7D01G496600 chr2D 81.250 288 50 3 1958 2245 638451349 638451632 2.170000e-56 230.0
45 TraesCS7D01G496600 chr2B 90.083 242 23 1 2000 2241 507194270 507194030 2.090000e-81 313.0
46 TraesCS7D01G496600 chr5D 89.030 237 16 4 366 602 550967823 550967597 4.560000e-73 285.0
47 TraesCS7D01G496600 chr5D 93.860 114 7 0 254 367 550981900 550981787 3.700000e-39 172.0
48 TraesCS7D01G496600 chr6D 85.357 280 19 6 1 263 473512228 473511954 1.280000e-68 270.0
49 TraesCS7D01G496600 chr6D 88.584 219 14 6 384 602 473511733 473511526 3.570000e-64 255.0
50 TraesCS7D01G496600 chr6D 82.822 163 27 1 2499 2660 3225362 3225200 8.070000e-31 145.0
51 TraesCS7D01G496600 chr6D 94.444 54 3 0 254 307 473511935 473511882 1.780000e-12 84.2
52 TraesCS7D01G496600 chr1B 83.557 298 27 12 1932 2207 453321566 453321863 2.760000e-65 259.0
53 TraesCS7D01G496600 chr1B 97.143 35 0 1 2761 2795 82301358 82301325 1.080000e-04 58.4
54 TraesCS7D01G496600 chr1B 97.143 35 0 1 2762 2795 269897750 269897784 1.080000e-04 58.4
55 TraesCS7D01G496600 chr3D 79.327 208 42 1 2454 2660 30686511 30686718 8.070000e-31 145.0
56 TraesCS7D01G496600 chr1A 82.317 164 28 1 2498 2660 11179968 11179805 1.040000e-29 141.0
57 TraesCS7D01G496600 chr1A 82.317 164 28 1 2498 2660 268390351 268390514 1.040000e-29 141.0
58 TraesCS7D01G496600 chr6A 84.173 139 21 1 2523 2660 5110774 5110912 1.750000e-27 134.0
59 TraesCS7D01G496600 chr3A 82.734 139 22 2 2524 2660 77915171 77915309 3.780000e-24 122.0
60 TraesCS7D01G496600 chr3A 92.683 41 3 0 2755 2795 302227203 302227243 3.010000e-05 60.2
61 TraesCS7D01G496600 chr4A 88.000 75 9 0 528 602 696093359 696093433 3.830000e-14 89.8
62 TraesCS7D01G496600 chr4A 94.737 38 1 1 2758 2794 107889206 107889169 1.080000e-04 58.4
63 TraesCS7D01G496600 chr4B 97.143 35 1 0 2761 2795 122469681 122469647 3.010000e-05 60.2


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 TraesCS7D01G496600 chr7D 603498285 603501079 2794 True 5162.000000 5162 100.000000 1 2795 1 chr7D.!!$R1 2794
1 TraesCS7D01G496600 chr7D 603646474 603647737 1263 False 806.000000 1118 90.923000 1387 2691 2 chr7D.!!$F2 1304
2 TraesCS7D01G496600 chr7D 263968557 263969257 700 True 202.066667 265 89.360000 1 603 3 chr7D.!!$R2 602
3 TraesCS7D01G496600 chr7A 696199702 696200796 1094 True 833.850000 1589 93.025000 786 1917 2 chr7A.!!$R2 1131
4 TraesCS7D01G496600 chr7A 696251242 696253812 2570 False 607.666667 1502 90.827000 783 2488 3 chr7A.!!$F1 1705
5 TraesCS7D01G496600 chr7B 684615239 684616015 776 True 933.000000 933 88.287000 1033 1824 1 chr7B.!!$R2 791
6 TraesCS7D01G496600 chr7B 684643153 684643909 756 True 821.000000 821 86.146000 1033 1824 1 chr7B.!!$R3 791
7 TraesCS7D01G496600 chr7B 685378251 685381247 2996 False 463.560000 830 93.004800 603 2691 5 chr7B.!!$F5 2088
8 TraesCS7D01G496600 chrUn 202523311 202524067 756 True 837.000000 837 86.524000 1033 1824 1 chrUn.!!$R2 791
9 TraesCS7D01G496600 chrUn 224016291 224017047 756 True 821.000000 821 86.146000 1033 1824 1 chrUn.!!$R3 791
10 TraesCS7D01G496600 chrUn 399485431 399486187 756 False 821.000000 821 86.146000 1033 1824 1 chrUn.!!$F1 791
11 TraesCS7D01G496600 chrUn 197868596 197869352 756 True 815.000000 815 86.020000 1033 1824 1 chrUn.!!$R1 791
12 TraesCS7D01G496600 chr4D 165590900 165592620 1720 False 386.500000 464 90.846000 1 604 2 chr4D.!!$F2 603
13 TraesCS7D01G496600 chr2D 55390359 55391061 702 False 257.500000 265 86.564000 1 602 2 chr2D.!!$F3 601
14 TraesCS7D01G496600 chr6D 473511526 473512228 702 True 203.066667 270 89.461667 1 602 3 chr6D.!!$R2 601

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
739 1999 0.593008 TCGTGAGTCGTGAACCAACG 60.593 55.0 0.0 0.0 44.92 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2704 6515 0.035176 TTGTACGCAGGGGGTTGTAC 59.965 55.0 0.0 0.0 38.1 2.9 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
22 23 4.568152 AAAGCGCAATTTTCTGTGTAGT 57.432 36.364 11.47 0.00 0.00 2.73
65 66 7.390440 TCATTATTCTGTTTAAGGTGACACCAG 59.610 37.037 26.30 13.52 41.95 4.00
77 78 7.568199 AAGGTGACACCAGCATAATTATTAC 57.432 36.000 26.30 0.00 41.95 1.89
131 132 6.999871 TCCATGATTAGTGTGCATGAATGTAT 59.000 34.615 0.00 0.00 41.35 2.29
144 146 9.655769 GTGCATGAATGTATATAACTGAAACAG 57.344 33.333 0.00 0.00 37.52 3.16
283 329 6.085555 TGTACTACACTGGTTTTCTCTGAG 57.914 41.667 0.00 0.00 0.00 3.35
359 446 1.138883 CTGACAGCCATGCATGTGC 59.861 57.895 24.58 24.41 42.50 4.57
445 1695 4.009675 GGAAGAAGTGTATGGATGTGCAA 58.990 43.478 0.00 0.00 0.00 4.08
463 1713 1.659098 CAAGCCATCGTTCGGAGTTAC 59.341 52.381 0.00 0.00 0.00 2.50
465 1715 1.143969 GCCATCGTTCGGAGTTACGG 61.144 60.000 1.37 0.00 37.28 4.02
485 1735 2.434331 CAGGCCCAGGTTTCCGAA 59.566 61.111 0.00 0.00 0.00 4.30
534 1784 2.514824 GGGCAGGCTCAATCGACC 60.515 66.667 0.00 0.00 0.00 4.79
559 1809 4.345859 ACAAATTTGGGTCAGTCGACTA 57.654 40.909 19.57 0.19 42.21 2.59
561 1811 5.313712 ACAAATTTGGGTCAGTCGACTAAT 58.686 37.500 19.57 10.41 42.21 1.73
586 1836 8.830201 TCCAAATTATGTTTTCAGTTGATTGG 57.170 30.769 0.00 0.00 34.17 3.16
606 1856 0.759436 CCTGTAGCCGGTCCCATACT 60.759 60.000 1.90 0.00 0.00 2.12
611 1861 1.520787 GCCGGTCCCATACTTGACG 60.521 63.158 1.90 0.00 32.19 4.35
619 1869 1.472728 CCCATACTTGACGCACCCTAC 60.473 57.143 0.00 0.00 0.00 3.18
635 1886 7.386848 ACGCACCCTACAAAATATATATGTGAC 59.613 37.037 12.18 3.46 0.00 3.67
668 1919 5.575606 CAGAACAACAAAAGATGGATGATGC 59.424 40.000 0.00 0.00 0.00 3.91
674 1925 4.202121 ACAAAAGATGGATGATGCTGCATC 60.202 41.667 30.56 30.56 42.44 3.91
699 1950 4.921470 ACCGACATGAAACGAAATACAG 57.079 40.909 0.00 0.00 0.00 2.74
734 1994 3.843985 GGCTCGTGAGTCGTGAAC 58.156 61.111 0.00 0.00 40.80 3.18
736 1996 1.007734 GCTCGTGAGTCGTGAACCA 60.008 57.895 0.00 0.00 40.80 3.67
737 1997 0.596600 GCTCGTGAGTCGTGAACCAA 60.597 55.000 0.00 0.00 40.80 3.67
738 1998 1.129326 CTCGTGAGTCGTGAACCAAC 58.871 55.000 0.00 0.00 40.80 3.77
739 1999 0.593008 TCGTGAGTCGTGAACCAACG 60.593 55.000 0.00 0.00 44.92 4.10
872 2134 5.251700 CCAGGCTATTTACTCCAGGGAATAT 59.748 44.000 0.00 0.00 0.00 1.28
918 2180 5.473504 TCTGCCAACTACTGAAAAGAAATCC 59.526 40.000 0.00 0.00 0.00 3.01
922 2184 5.385617 CAACTACTGAAAAGAAATCCAGCG 58.614 41.667 0.00 0.00 0.00 5.18
927 2189 3.655486 TGAAAAGAAATCCAGCGTACGA 58.345 40.909 21.65 0.00 0.00 3.43
931 2193 1.137086 AGAAATCCAGCGTACGATGCT 59.863 47.619 27.15 15.51 42.06 3.79
967 2232 3.380320 ACAACCAAACAGCCTAACAGAAC 59.620 43.478 0.00 0.00 0.00 3.01
1115 2384 2.089349 GCTTCACCGCTGTCGAGAC 61.089 63.158 0.00 0.00 38.10 3.36
1406 2691 1.001181 GGTGGAGCAGGTAACGTACAA 59.999 52.381 0.00 0.00 46.39 2.41
1434 2719 0.907704 TGTGGCAGTTCGAGGGGTAT 60.908 55.000 0.00 0.00 0.00 2.73
1561 2846 3.681855 CTCGTGTACTACAACGATGAGG 58.318 50.000 6.62 0.00 33.65 3.86
1593 2878 0.957395 ACGACCACATCTACGACCGT 60.957 55.000 0.00 0.00 0.00 4.83
1879 3166 2.276732 TGGCAAGTGGAAGGAAAGAG 57.723 50.000 0.00 0.00 0.00 2.85
2024 3348 3.047718 GCATGTCGTCCCTCGTCGA 62.048 63.158 0.00 0.00 40.80 4.20
2025 3349 1.728069 CATGTCGTCCCTCGTCGAT 59.272 57.895 0.00 0.00 40.80 3.59
2039 3363 4.383052 CCTCGTCGATTGTAGCACATTATC 59.617 45.833 0.00 0.00 0.00 1.75
2082 3406 5.531659 TCCTTTGACGGTTGTAGCATTTTTA 59.468 36.000 0.00 0.00 0.00 1.52
2084 3408 6.526674 CCTTTGACGGTTGTAGCATTTTTATC 59.473 38.462 0.00 0.00 0.00 1.75
2103 3427 6.584185 TTATCAGAGCGGTTGTAGCATATA 57.416 37.500 0.00 0.00 37.01 0.86
2117 3441 7.806409 TGTAGCATATATTGTCATTGCTTGT 57.194 32.000 0.65 0.00 43.08 3.16
2118 3442 8.900983 TGTAGCATATATTGTCATTGCTTGTA 57.099 30.769 0.65 0.00 43.08 2.41
2122 3446 8.993121 AGCATATATTGTCATTGCTTGTAGTAC 58.007 33.333 0.00 0.00 40.58 2.73
2131 3455 2.773487 TGCTTGTAGTACCGTTGCAAT 58.227 42.857 0.59 0.00 0.00 3.56
2157 3481 2.268076 ACCACCGTTTGCAGCATCC 61.268 57.895 0.00 0.00 0.00 3.51
2193 3517 0.878523 GCACCACAACTACGCTGACA 60.879 55.000 0.00 0.00 0.00 3.58
2205 3529 0.169009 CGCTGACATCACTCGACTGA 59.831 55.000 0.00 0.00 0.00 3.41
2213 3537 1.880271 TCACTCGACTGAGACTTCGT 58.120 50.000 0.00 0.00 45.57 3.85
2214 3538 2.219458 TCACTCGACTGAGACTTCGTT 58.781 47.619 0.00 0.00 45.57 3.85
2215 3539 3.396560 TCACTCGACTGAGACTTCGTTA 58.603 45.455 0.00 0.00 45.57 3.18
2216 3540 3.811497 TCACTCGACTGAGACTTCGTTAA 59.189 43.478 0.00 0.00 45.57 2.01
2217 3541 4.083961 TCACTCGACTGAGACTTCGTTAAG 60.084 45.833 0.00 0.00 45.57 1.85
2228 3552 3.050619 ACTTCGTTAAGTCTCAGTTGCG 58.949 45.455 0.00 0.00 42.42 4.85
2232 3556 2.405357 CGTTAAGTCTCAGTTGCGTGAG 59.595 50.000 4.54 4.54 44.71 3.51
2276 3601 7.910584 TCTATCTGCCTGAGATATTAATGCAA 58.089 34.615 0.00 0.00 41.90 4.08
2314 3639 4.599720 TCCATGATTACAAATCACCCCA 57.400 40.909 4.54 0.00 0.00 4.96
2383 4877 9.419297 CATCTCAAATCATTCTCAAATGTTTGT 57.581 29.630 16.50 5.22 42.46 2.83
2395 4889 5.224188 TCAAATGTTTGTGGATGTGTCCGA 61.224 41.667 5.48 0.00 40.94 4.55
2652 5147 2.284405 GGTCGGACCTTCCTCCCA 60.284 66.667 19.92 0.00 34.73 4.37
2662 5157 1.563410 CCTTCCTCCCAGCTTCTGAAT 59.437 52.381 0.00 0.00 32.44 2.57
2697 6508 9.822185 ATATTGCATAATTTTTCAAAGAGTCCC 57.178 29.630 0.00 0.00 0.00 4.46
2698 6509 5.708948 TGCATAATTTTTCAAAGAGTCCCG 58.291 37.500 0.00 0.00 0.00 5.14
2699 6510 4.562789 GCATAATTTTTCAAAGAGTCCCGC 59.437 41.667 0.00 0.00 0.00 6.13
2700 6511 5.622233 GCATAATTTTTCAAAGAGTCCCGCT 60.622 40.000 0.00 0.00 0.00 5.52
2701 6512 4.937201 AATTTTTCAAAGAGTCCCGCTT 57.063 36.364 0.00 0.00 0.00 4.68
2702 6513 3.982576 TTTTTCAAAGAGTCCCGCTTC 57.017 42.857 0.00 0.00 0.00 3.86
2703 6514 1.508632 TTTCAAAGAGTCCCGCTTCG 58.491 50.000 0.00 0.00 0.00 3.79
2705 6516 1.004918 CAAAGAGTCCCGCTTCGGT 60.005 57.895 4.47 0.00 46.80 4.69
2706 6517 0.245539 CAAAGAGTCCCGCTTCGGTA 59.754 55.000 4.47 0.00 46.80 4.02
2707 6518 0.245813 AAAGAGTCCCGCTTCGGTAC 59.754 55.000 4.47 0.00 46.80 3.34
2708 6519 0.896940 AAGAGTCCCGCTTCGGTACA 60.897 55.000 3.93 0.00 46.80 2.90
2709 6520 0.896940 AGAGTCCCGCTTCGGTACAA 60.897 55.000 3.93 0.00 46.80 2.41
2710 6521 0.735287 GAGTCCCGCTTCGGTACAAC 60.735 60.000 3.93 0.00 46.80 3.32
2711 6522 1.739196 GTCCCGCTTCGGTACAACC 60.739 63.158 4.47 0.00 46.80 3.77
2712 6523 2.435410 CCCGCTTCGGTACAACCC 60.435 66.667 4.47 0.00 46.80 4.11
2713 6524 2.435410 CCGCTTCGGTACAACCCC 60.435 66.667 0.00 0.00 42.73 4.95
2714 6525 2.435410 CGCTTCGGTACAACCCCC 60.435 66.667 0.00 0.00 33.75 5.40
2715 6526 2.951101 CGCTTCGGTACAACCCCCT 61.951 63.158 0.00 0.00 33.75 4.79
2716 6527 1.376812 GCTTCGGTACAACCCCCTG 60.377 63.158 0.00 0.00 33.75 4.45
2717 6528 1.376812 CTTCGGTACAACCCCCTGC 60.377 63.158 0.00 0.00 33.75 4.85
2718 6529 3.242897 TTCGGTACAACCCCCTGCG 62.243 63.158 0.00 0.00 33.75 5.18
2719 6530 4.011517 CGGTACAACCCCCTGCGT 62.012 66.667 0.00 0.00 33.75 5.24
2720 6531 2.648143 CGGTACAACCCCCTGCGTA 61.648 63.158 0.00 0.00 33.75 4.42
2721 6532 1.078918 GGTACAACCCCCTGCGTAC 60.079 63.158 0.00 0.00 34.74 3.67
2722 6533 1.672898 GTACAACCCCCTGCGTACA 59.327 57.895 0.00 0.00 35.41 2.90
2723 6534 0.035176 GTACAACCCCCTGCGTACAA 59.965 55.000 0.00 0.00 35.41 2.41
2724 6535 0.035176 TACAACCCCCTGCGTACAAC 59.965 55.000 0.00 0.00 0.00 3.32
2725 6536 1.969589 CAACCCCCTGCGTACAACC 60.970 63.158 0.00 0.00 0.00 3.77
2726 6537 3.200329 AACCCCCTGCGTACAACCC 62.200 63.158 0.00 0.00 0.00 4.11
2727 6538 4.419921 CCCCCTGCGTACAACCCC 62.420 72.222 0.00 0.00 0.00 4.95
2728 6539 4.419921 CCCCTGCGTACAACCCCC 62.420 72.222 0.00 0.00 0.00 5.40
2746 6557 3.408634 CCCCCTGCAATACGTATAAAGG 58.591 50.000 8.83 14.71 0.00 3.11
2747 6558 3.408634 CCCCTGCAATACGTATAAAGGG 58.591 50.000 27.86 27.86 42.21 3.95
2748 6559 3.408634 CCCTGCAATACGTATAAAGGGG 58.591 50.000 27.47 22.32 39.42 4.79
2749 6560 3.181448 CCCTGCAATACGTATAAAGGGGT 60.181 47.826 27.47 5.36 39.42 4.95
2750 6561 4.040706 CCCTGCAATACGTATAAAGGGGTA 59.959 45.833 27.47 8.88 39.42 3.69
2751 6562 5.455040 CCCTGCAATACGTATAAAGGGGTAA 60.455 44.000 27.47 0.00 39.42 2.85
2752 6563 6.235664 CCTGCAATACGTATAAAGGGGTAAT 58.764 40.000 8.83 0.00 0.00 1.89
2753 6564 7.388437 CCTGCAATACGTATAAAGGGGTAATA 58.612 38.462 8.83 0.00 0.00 0.98
2754 6565 8.044908 CCTGCAATACGTATAAAGGGGTAATAT 58.955 37.037 8.83 0.00 0.00 1.28
2755 6566 8.780846 TGCAATACGTATAAAGGGGTAATATG 57.219 34.615 8.83 0.00 0.00 1.78
2756 6567 7.825270 TGCAATACGTATAAAGGGGTAATATGG 59.175 37.037 8.83 0.00 0.00 2.74
2757 6568 8.042515 GCAATACGTATAAAGGGGTAATATGGA 58.957 37.037 8.83 0.00 0.00 3.41
2758 6569 9.374838 CAATACGTATAAAGGGGTAATATGGAC 57.625 37.037 8.83 0.00 0.00 4.02
2759 6570 6.364568 ACGTATAAAGGGGTAATATGGACC 57.635 41.667 0.00 0.00 36.12 4.46
2760 6571 6.086775 ACGTATAAAGGGGTAATATGGACCT 58.913 40.000 6.94 0.00 37.13 3.85
2761 6572 6.559921 ACGTATAAAGGGGTAATATGGACCTT 59.440 38.462 6.94 0.00 43.01 3.50
2763 6574 7.605309 CGTATAAAGGGGTAATATGGACCTTTC 59.395 40.741 9.97 0.00 45.63 2.62
2764 6575 5.806955 AAAGGGGTAATATGGACCTTTCA 57.193 39.130 0.00 0.00 45.63 2.69
2765 6576 4.790718 AGGGGTAATATGGACCTTTCAC 57.209 45.455 6.94 0.00 37.13 3.18
2766 6577 4.116113 AGGGGTAATATGGACCTTTCACA 58.884 43.478 6.94 0.00 37.13 3.58
2767 6578 4.542525 AGGGGTAATATGGACCTTTCACAA 59.457 41.667 6.94 0.00 37.13 3.33
2768 6579 5.195756 AGGGGTAATATGGACCTTTCACAAT 59.804 40.000 6.94 0.00 37.13 2.71
2769 6580 5.535030 GGGGTAATATGGACCTTTCACAATC 59.465 44.000 6.94 0.00 37.13 2.67
2770 6581 6.365520 GGGTAATATGGACCTTTCACAATCT 58.634 40.000 6.94 0.00 37.13 2.40
2771 6582 6.486993 GGGTAATATGGACCTTTCACAATCTC 59.513 42.308 6.94 0.00 37.13 2.75
2772 6583 7.283329 GGTAATATGGACCTTTCACAATCTCT 58.717 38.462 0.00 0.00 33.86 3.10
2773 6584 8.429641 GGTAATATGGACCTTTCACAATCTCTA 58.570 37.037 0.00 0.00 33.86 2.43
2774 6585 9.262358 GTAATATGGACCTTTCACAATCTCTAC 57.738 37.037 0.00 0.00 0.00 2.59
2775 6586 7.682787 ATATGGACCTTTCACAATCTCTACT 57.317 36.000 0.00 0.00 0.00 2.57
2776 6587 5.407407 TGGACCTTTCACAATCTCTACTC 57.593 43.478 0.00 0.00 0.00 2.59
2777 6588 4.223032 TGGACCTTTCACAATCTCTACTCC 59.777 45.833 0.00 0.00 0.00 3.85
2778 6589 4.468153 GGACCTTTCACAATCTCTACTCCT 59.532 45.833 0.00 0.00 0.00 3.69
2779 6590 5.657302 GGACCTTTCACAATCTCTACTCCTA 59.343 44.000 0.00 0.00 0.00 2.94
2780 6591 6.154706 GGACCTTTCACAATCTCTACTCCTAA 59.845 42.308 0.00 0.00 0.00 2.69
2781 6592 7.147637 GGACCTTTCACAATCTCTACTCCTAAT 60.148 40.741 0.00 0.00 0.00 1.73
2782 6593 7.560368 ACCTTTCACAATCTCTACTCCTAATG 58.440 38.462 0.00 0.00 0.00 1.90
2783 6594 6.989169 CCTTTCACAATCTCTACTCCTAATGG 59.011 42.308 0.00 0.00 0.00 3.16
2784 6595 7.147655 CCTTTCACAATCTCTACTCCTAATGGA 60.148 40.741 0.00 0.00 40.69 3.41
2794 6605 2.787473 TCCTAATGGAGCAGTTGGTG 57.213 50.000 0.00 0.00 37.46 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 7.744087 ATCTGCACATAAACTACACAGAAAA 57.256 32.000 0.00 0.00 36.38 2.29
47 48 2.571212 TGCTGGTGTCACCTTAAACAG 58.429 47.619 22.56 11.44 39.58 3.16
77 78 2.482721 AGTCGTCCGTTGCCTAAAATTG 59.517 45.455 0.00 0.00 0.00 2.32
166 168 5.245751 ACATGCCCAAACTACATGAATTTGA 59.754 36.000 17.06 4.20 43.04 2.69
174 176 2.875296 ACACACATGCCCAAACTACAT 58.125 42.857 0.00 0.00 0.00 2.29
251 297 9.273016 GAAAACCAGTGTAGTACATGCATATAT 57.727 33.333 6.21 0.00 0.00 0.86
252 298 8.482943 AGAAAACCAGTGTAGTACATGCATATA 58.517 33.333 6.21 0.00 0.00 0.86
283 329 6.455113 CCAACAAGCAATGTACACGTATAGTC 60.455 42.308 0.00 0.00 42.99 2.59
359 446 2.220824 CACATACACACGTGTTGTCAGG 59.779 50.000 20.79 9.31 41.83 3.86
445 1695 0.179145 CGTAACTCCGAACGATGGCT 60.179 55.000 0.00 0.00 41.55 4.75
465 1715 2.991540 GGAAACCTGGGCCTGTGC 60.992 66.667 4.53 0.00 0.00 4.57
485 1735 4.183101 CACTTGCACCACACTTTTCATTT 58.817 39.130 0.00 0.00 0.00 2.32
534 1784 3.002862 TCGACTGACCCAAATTTGTTTCG 59.997 43.478 16.73 13.37 0.00 3.46
561 1811 7.387397 GCCAATCAACTGAAAACATAATTTGGA 59.613 33.333 0.00 0.00 0.00 3.53
586 1836 2.138179 TATGGGACCGGCTACAGGC 61.138 63.158 0.00 0.00 40.90 4.85
606 1856 7.934665 ACATATATATTTTGTAGGGTGCGTCAA 59.065 33.333 0.00 0.00 0.00 3.18
611 1861 7.386848 ACGTCACATATATATTTTGTAGGGTGC 59.613 37.037 0.00 0.00 0.00 5.01
635 1886 9.277565 CCATCTTTTGTTGTTCTGATATTTACG 57.722 33.333 0.00 0.00 0.00 3.18
652 1903 3.793797 TGCAGCATCATCCATCTTTTG 57.206 42.857 0.00 0.00 0.00 2.44
662 1913 1.273327 TCGGTATCGATGCAGCATCAT 59.727 47.619 30.49 23.73 40.54 2.45
674 1925 4.772046 ATTTCGTTTCATGTCGGTATCG 57.228 40.909 0.00 0.00 37.82 2.92
730 1990 2.623878 TAGGCTTGTTCGTTGGTTCA 57.376 45.000 0.00 0.00 0.00 3.18
731 1991 3.974871 TTTAGGCTTGTTCGTTGGTTC 57.025 42.857 0.00 0.00 0.00 3.62
732 1992 4.583073 AGATTTTAGGCTTGTTCGTTGGTT 59.417 37.500 0.00 0.00 0.00 3.67
734 1994 4.766404 AGATTTTAGGCTTGTTCGTTGG 57.234 40.909 0.00 0.00 0.00 3.77
736 1996 5.300792 TCCAAAGATTTTAGGCTTGTTCGTT 59.699 36.000 0.00 0.00 0.00 3.85
737 1997 4.825085 TCCAAAGATTTTAGGCTTGTTCGT 59.175 37.500 0.00 0.00 0.00 3.85
738 1998 5.371115 TCCAAAGATTTTAGGCTTGTTCG 57.629 39.130 0.00 0.00 0.00 3.95
739 1999 6.591448 CCAATCCAAAGATTTTAGGCTTGTTC 59.409 38.462 0.00 0.00 40.89 3.18
740 2000 6.466812 CCAATCCAAAGATTTTAGGCTTGTT 58.533 36.000 0.00 0.00 40.89 2.83
741 2001 5.046376 CCCAATCCAAAGATTTTAGGCTTGT 60.046 40.000 0.00 0.00 40.89 3.16
742 2002 5.422145 CCCAATCCAAAGATTTTAGGCTTG 58.578 41.667 0.00 0.00 40.89 4.01
743 2003 4.080919 GCCCAATCCAAAGATTTTAGGCTT 60.081 41.667 0.00 0.00 42.31 4.35
918 2180 8.169910 GGATATATATAGTAGCATCGTACGCTG 58.830 40.741 14.50 14.50 40.73 5.18
931 2193 9.938280 GCTGTTTGGTTGTGGATATATATAGTA 57.062 33.333 0.00 0.00 0.00 1.82
1107 2376 1.970114 GTCCTCCGTGGTCTCGACA 60.970 63.158 0.00 0.00 37.07 4.35
1192 2461 4.778143 GACCCAGAACCGCCGCAT 62.778 66.667 0.00 0.00 0.00 4.73
1467 2752 1.672356 GCCGAACACCTGCATCACT 60.672 57.895 0.00 0.00 0.00 3.41
1561 2846 2.737376 GTCGTCGACCACCTTGGC 60.737 66.667 14.60 0.00 42.67 4.52
1593 2878 0.817634 CCACGTTGAGCCTGAACCAA 60.818 55.000 0.00 0.00 0.00 3.67
1879 3166 6.494893 TGCCTCATCACACTAATACAAAAC 57.505 37.500 0.00 0.00 0.00 2.43
1998 3301 2.476051 GACGACATGCTGCAACCG 59.524 61.111 6.36 12.81 0.00 4.44
2024 3348 4.141711 ACCGGTGAGATAATGTGCTACAAT 60.142 41.667 6.12 0.00 0.00 2.71
2025 3349 3.196901 ACCGGTGAGATAATGTGCTACAA 59.803 43.478 6.12 0.00 0.00 2.41
2039 3363 2.100631 GGATGTTGCGACCGGTGAG 61.101 63.158 14.63 7.14 0.00 3.51
2082 3406 5.667539 ATATATGCTACAACCGCTCTGAT 57.332 39.130 0.00 0.00 0.00 2.90
2084 3408 4.991056 ACAATATATGCTACAACCGCTCTG 59.009 41.667 0.00 0.00 0.00 3.35
2103 3427 4.575885 ACGGTACTACAAGCAATGACAAT 58.424 39.130 0.00 0.00 0.00 2.71
2117 3441 6.430308 TGGTGAAAAATATTGCAACGGTACTA 59.570 34.615 0.00 0.00 34.13 1.82
2118 3442 5.241949 TGGTGAAAAATATTGCAACGGTACT 59.758 36.000 0.00 0.00 34.13 2.73
2122 3446 3.677596 GGTGGTGAAAAATATTGCAACGG 59.322 43.478 0.00 0.00 34.13 4.44
2131 3455 3.797184 GCTGCAAACGGTGGTGAAAAATA 60.797 43.478 0.00 0.00 0.00 1.40
2193 3517 2.428491 ACGAAGTCTCAGTCGAGTGAT 58.572 47.619 22.72 8.58 29.74 3.06
2213 3537 3.728076 ACTCACGCAACTGAGACTTAA 57.272 42.857 7.68 0.00 40.28 1.85
2214 3538 3.318275 AGAACTCACGCAACTGAGACTTA 59.682 43.478 7.68 0.00 40.28 2.24
2215 3539 2.101582 AGAACTCACGCAACTGAGACTT 59.898 45.455 7.68 0.00 40.28 3.01
2216 3540 1.683917 AGAACTCACGCAACTGAGACT 59.316 47.619 7.68 4.28 40.28 3.24
2217 3541 2.141535 AGAACTCACGCAACTGAGAC 57.858 50.000 7.68 2.37 40.28 3.36
2218 3542 3.058155 GTCTAGAACTCACGCAACTGAGA 60.058 47.826 7.68 0.00 40.28 3.27
2219 3543 3.057876 AGTCTAGAACTCACGCAACTGAG 60.058 47.826 0.00 0.00 43.06 3.35
2220 3544 2.885266 AGTCTAGAACTCACGCAACTGA 59.115 45.455 0.00 0.00 30.02 3.41
2221 3545 3.290308 AGTCTAGAACTCACGCAACTG 57.710 47.619 0.00 0.00 30.02 3.16
2222 3546 3.819337 TGTAGTCTAGAACTCACGCAACT 59.181 43.478 0.00 0.00 39.55 3.16
2223 3547 4.156664 TGTAGTCTAGAACTCACGCAAC 57.843 45.455 0.00 0.00 39.55 4.17
2224 3548 6.095021 ACATATGTAGTCTAGAACTCACGCAA 59.905 38.462 6.56 0.00 39.55 4.85
2225 3549 5.589050 ACATATGTAGTCTAGAACTCACGCA 59.411 40.000 6.56 0.00 39.55 5.24
2226 3550 6.017770 AGACATATGTAGTCTAGAACTCACGC 60.018 42.308 8.71 0.00 44.10 5.34
2227 3551 7.439955 AGAGACATATGTAGTCTAGAACTCACG 59.560 40.741 15.51 0.00 45.79 4.35
2228 3552 8.671384 AGAGACATATGTAGTCTAGAACTCAC 57.329 38.462 15.51 0.00 45.79 3.51
2276 3601 3.834489 TGGATGTGCCACAACATTTTT 57.166 38.095 0.00 0.00 43.33 1.94
2314 3639 4.039357 CGACGCACTGGACCGACT 62.039 66.667 0.00 0.00 0.00 4.18
2351 3676 4.080919 TGAGAATGATTTGAGATGACCGGT 60.081 41.667 6.92 6.92 0.00 5.28
2383 4877 1.555967 TCACTGATCGGACACATCCA 58.444 50.000 9.00 0.00 46.67 3.41
2395 4889 4.097551 TCTCTCATCTCCGATCACTGAT 57.902 45.455 0.00 0.00 0.00 2.90
2520 5015 3.224324 CCTTAGCCCTCGCCGCTA 61.224 66.667 0.00 0.00 37.79 4.26
2572 5067 1.198759 ACCAGCACTACCCACCGATT 61.199 55.000 0.00 0.00 0.00 3.34
2581 5076 2.742372 CCACGCCACCAGCACTAC 60.742 66.667 0.00 0.00 44.04 2.73
2582 5077 4.697756 GCCACGCCACCAGCACTA 62.698 66.667 0.00 0.00 44.04 2.74
2641 5136 0.178891 TCAGAAGCTGGGAGGAAGGT 60.179 55.000 0.00 0.00 31.51 3.50
2697 6508 2.435410 GGGGGTTGTACCGAAGCG 60.435 66.667 0.00 0.00 39.83 4.68
2698 6509 1.376812 CAGGGGGTTGTACCGAAGC 60.377 63.158 0.00 0.00 39.83 3.86
2699 6510 1.376812 GCAGGGGGTTGTACCGAAG 60.377 63.158 0.00 0.00 39.83 3.79
2700 6511 2.751688 GCAGGGGGTTGTACCGAA 59.248 61.111 0.00 0.00 39.83 4.30
2701 6512 3.697747 CGCAGGGGGTTGTACCGA 61.698 66.667 0.00 0.00 39.83 4.69
2702 6513 2.648143 TACGCAGGGGGTTGTACCG 61.648 63.158 0.00 0.00 39.83 4.02
2703 6514 1.078918 GTACGCAGGGGGTTGTACC 60.079 63.158 0.00 0.00 37.60 3.34
2704 6515 0.035176 TTGTACGCAGGGGGTTGTAC 59.965 55.000 0.00 0.00 38.10 2.90
2705 6516 0.035176 GTTGTACGCAGGGGGTTGTA 59.965 55.000 0.00 0.00 0.00 2.41
2706 6517 1.228033 GTTGTACGCAGGGGGTTGT 60.228 57.895 0.00 0.00 0.00 3.32
2707 6518 1.969589 GGTTGTACGCAGGGGGTTG 60.970 63.158 0.00 0.00 0.00 3.77
2708 6519 2.433004 GGTTGTACGCAGGGGGTT 59.567 61.111 0.00 0.00 0.00 4.11
2709 6520 3.643554 GGGTTGTACGCAGGGGGT 61.644 66.667 0.00 0.00 0.00 4.95
2710 6521 4.419921 GGGGTTGTACGCAGGGGG 62.420 72.222 0.00 0.00 32.03 5.40
2711 6522 4.419921 GGGGGTTGTACGCAGGGG 62.420 72.222 0.00 0.00 32.03 4.79
2725 6536 3.408634 CCTTTATACGTATTGCAGGGGG 58.591 50.000 14.33 3.66 0.00 5.40
2726 6537 3.408634 CCCTTTATACGTATTGCAGGGG 58.591 50.000 25.48 19.30 36.57 4.79
2727 6538 3.181448 ACCCCTTTATACGTATTGCAGGG 60.181 47.826 25.88 25.88 39.51 4.45
2728 6539 4.081322 ACCCCTTTATACGTATTGCAGG 57.919 45.455 14.33 15.15 0.00 4.85
2729 6540 8.879759 CATATTACCCCTTTATACGTATTGCAG 58.120 37.037 14.33 7.29 0.00 4.41
2730 6541 7.825270 CCATATTACCCCTTTATACGTATTGCA 59.175 37.037 14.33 0.00 0.00 4.08
2731 6542 8.042515 TCCATATTACCCCTTTATACGTATTGC 58.957 37.037 14.33 0.00 0.00 3.56
2732 6543 9.374838 GTCCATATTACCCCTTTATACGTATTG 57.625 37.037 14.33 4.82 0.00 1.90
2733 6544 8.542926 GGTCCATATTACCCCTTTATACGTATT 58.457 37.037 14.33 0.00 0.00 1.89
2734 6545 7.902941 AGGTCCATATTACCCCTTTATACGTAT 59.097 37.037 13.54 13.54 37.77 3.06
2735 6546 7.248237 AGGTCCATATTACCCCTTTATACGTA 58.752 38.462 0.00 0.00 37.77 3.57
2736 6547 6.086775 AGGTCCATATTACCCCTTTATACGT 58.913 40.000 0.00 0.00 37.77 3.57
2737 6548 6.616237 AGGTCCATATTACCCCTTTATACG 57.384 41.667 0.00 0.00 37.77 3.06
2738 6549 8.442374 TGAAAGGTCCATATTACCCCTTTATAC 58.558 37.037 0.00 0.00 43.63 1.47
2739 6550 8.442374 GTGAAAGGTCCATATTACCCCTTTATA 58.558 37.037 0.00 0.00 43.63 0.98
2740 6551 7.091720 TGTGAAAGGTCCATATTACCCCTTTAT 60.092 37.037 0.00 0.00 43.63 1.40
2741 6552 6.217900 TGTGAAAGGTCCATATTACCCCTTTA 59.782 38.462 0.00 0.00 43.63 1.85
2742 6553 5.015817 TGTGAAAGGTCCATATTACCCCTTT 59.984 40.000 0.00 0.00 45.63 3.11
2743 6554 4.542525 TGTGAAAGGTCCATATTACCCCTT 59.457 41.667 0.00 0.00 37.77 3.95
2744 6555 4.116113 TGTGAAAGGTCCATATTACCCCT 58.884 43.478 0.00 0.00 37.77 4.79
2745 6556 4.513406 TGTGAAAGGTCCATATTACCCC 57.487 45.455 0.00 0.00 37.77 4.95
2746 6557 6.365520 AGATTGTGAAAGGTCCATATTACCC 58.634 40.000 0.00 0.00 37.77 3.69
2747 6558 7.283329 AGAGATTGTGAAAGGTCCATATTACC 58.717 38.462 0.00 0.00 37.27 2.85
2748 6559 9.262358 GTAGAGATTGTGAAAGGTCCATATTAC 57.738 37.037 0.00 0.00 0.00 1.89
2749 6560 9.213777 AGTAGAGATTGTGAAAGGTCCATATTA 57.786 33.333 0.00 0.00 0.00 0.98
2750 6561 8.095452 AGTAGAGATTGTGAAAGGTCCATATT 57.905 34.615 0.00 0.00 0.00 1.28
2751 6562 7.202047 GGAGTAGAGATTGTGAAAGGTCCATAT 60.202 40.741 0.00 0.00 0.00 1.78
2752 6563 6.098409 GGAGTAGAGATTGTGAAAGGTCCATA 59.902 42.308 0.00 0.00 0.00 2.74
2753 6564 5.104735 GGAGTAGAGATTGTGAAAGGTCCAT 60.105 44.000 0.00 0.00 0.00 3.41
2754 6565 4.223032 GGAGTAGAGATTGTGAAAGGTCCA 59.777 45.833 0.00 0.00 0.00 4.02
2755 6566 4.468153 AGGAGTAGAGATTGTGAAAGGTCC 59.532 45.833 0.00 0.00 0.00 4.46
2756 6567 5.669164 AGGAGTAGAGATTGTGAAAGGTC 57.331 43.478 0.00 0.00 0.00 3.85
2757 6568 7.365117 CCATTAGGAGTAGAGATTGTGAAAGGT 60.365 40.741 0.00 0.00 36.89 3.50
2758 6569 6.989169 CCATTAGGAGTAGAGATTGTGAAAGG 59.011 42.308 0.00 0.00 36.89 3.11
2759 6570 7.786030 TCCATTAGGAGTAGAGATTGTGAAAG 58.214 38.462 0.00 0.00 39.61 2.62
2760 6571 7.733773 TCCATTAGGAGTAGAGATTGTGAAA 57.266 36.000 0.00 0.00 39.61 2.69
2775 6586 2.787473 CACCAACTGCTCCATTAGGA 57.213 50.000 0.00 0.00 43.21 2.94


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

AutoCloner maintained by Alex Coulton.