Multiple sequence alignment - TraesCS3B01G572300

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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 TraesCS3B01G572300 chr3B 100.000 2225 0 0 1 2225 803227292 803229516 0.000000e+00 4109.0
1 TraesCS3B01G572300 chr3B 93.229 827 49 7 1305 2127 802707053 802706230 0.000000e+00 1210.0
2 TraesCS3B01G572300 chr3B 92.561 820 50 9 193 1005 802714071 802713256 0.000000e+00 1166.0
3 TraesCS3B01G572300 chr3B 86.786 280 26 6 1899 2176 786619098 786619368 3.590000e-78 302.0
4 TraesCS3B01G572300 chr3B 85.971 278 31 4 1899 2176 103746753 103747022 7.770000e-75 291.0
5 TraesCS3B01G572300 chr3B 78.606 416 80 7 272 683 62880244 62879834 1.310000e-67 267.0
6 TraesCS3B01G572300 chr3B 93.296 179 12 0 1 179 802715545 802715367 4.710000e-67 265.0
7 TraesCS3B01G572300 chr3B 100.000 36 0 0 2187 2222 508729063 508729098 1.430000e-07 67.6
8 TraesCS3B01G572300 chr1D 85.822 1065 110 25 698 1749 122842503 122841467 0.000000e+00 1092.0
9 TraesCS3B01G572300 chr1D 88.467 685 68 10 4 683 122843349 122842671 0.000000e+00 817.0
10 TraesCS3B01G572300 chr1D 83.082 331 45 9 1423 1749 318381480 318381803 7.770000e-75 291.0
11 TraesCS3B01G572300 chr4B 85.714 1064 116 16 698 1748 320322093 320323133 0.000000e+00 1090.0
12 TraesCS3B01G572300 chr4B 86.978 599 69 7 75 668 320066427 320067021 0.000000e+00 665.0
13 TraesCS3B01G572300 chr4B 84.912 285 32 8 1894 2176 95881281 95881006 6.050000e-71 278.0
14 TraesCS3B01G572300 chr5D 85.495 979 102 23 799 1749 535527125 535526159 0.000000e+00 985.0
15 TraesCS3B01G572300 chr5D 85.211 284 32 8 1470 1749 520124179 520124456 1.300000e-72 283.0
16 TraesCS3B01G572300 chr1B 84.654 997 111 25 698 1678 187186354 187187324 0.000000e+00 955.0
17 TraesCS3B01G572300 chr1B 84.964 685 72 17 1 683 187185531 187186186 0.000000e+00 665.0
18 TraesCS3B01G572300 chr1B 97.297 37 0 1 2187 2223 373590314 373590349 6.630000e-06 62.1
19 TraesCS3B01G572300 chr1A 88.029 685 77 5 1 683 134968836 134968155 0.000000e+00 806.0
20 TraesCS3B01G572300 chr2B 80.019 1076 170 37 706 1763 212061417 212060369 0.000000e+00 754.0
21 TraesCS3B01G572300 chr2B 78.195 1064 189 30 698 1749 213955769 213956801 6.700000e-180 640.0
22 TraesCS3B01G572300 chr2B 77.327 666 115 28 21 683 212096802 212096170 5.840000e-96 361.0
23 TraesCS3B01G572300 chr2B 100.000 37 0 0 2189 2225 559573529 559573493 3.960000e-08 69.4
24 TraesCS3B01G572300 chr2D 85.690 587 51 17 1114 1690 493877739 493878302 2.460000e-164 588.0
25 TraesCS3B01G572300 chr2D 80.082 733 115 28 741 1460 154959561 154958847 1.180000e-142 516.0
26 TraesCS3B01G572300 chr2D 79.487 585 98 17 103 683 154960306 154959740 1.600000e-106 396.0
27 TraesCS3B01G572300 chr2D 82.979 282 41 6 1470 1749 564706513 564706237 4.740000e-62 248.0
28 TraesCS3B01G572300 chr7A 80.290 690 121 13 1 683 450568951 450568270 7.090000e-140 507.0
29 TraesCS3B01G572300 chr6A 89.196 398 40 3 1 397 146354612 146354217 5.520000e-136 494.0
30 TraesCS3B01G572300 chrUn 81.416 565 90 12 698 1259 75467931 75468483 4.360000e-122 448.0
31 TraesCS3B01G572300 chr3D 81.603 549 85 12 686 1229 166289993 166290530 7.290000e-120 440.0
32 TraesCS3B01G572300 chr3D 86.268 284 29 7 1895 2176 40988900 40988625 1.290000e-77 300.0
33 TraesCS3B01G572300 chr7D 88.087 277 25 5 1899 2175 44670294 44670026 2.760000e-84 322.0
34 TraesCS3B01G572300 chr7D 80.383 418 69 8 272 683 54566257 54565847 2.780000e-79 305.0
35 TraesCS3B01G572300 chr4D 86.765 272 24 7 1907 2176 401067362 401067101 2.160000e-75 292.0
36 TraesCS3B01G572300 chr5B 80.387 413 55 18 1348 1755 564973892 564973501 7.770000e-75 291.0
37 TraesCS3B01G572300 chr5B 97.436 39 0 1 2187 2225 534482956 534482993 5.130000e-07 65.8
38 TraesCS3B01G572300 chr5B 97.297 37 0 1 2187 2223 408570767 408570732 6.630000e-06 62.1
39 TraesCS3B01G572300 chr5B 97.297 37 0 1 2187 2223 472858650 472858685 6.630000e-06 62.1
40 TraesCS3B01G572300 chr2A 85.915 284 26 6 1899 2176 99128682 99128957 7.770000e-75 291.0
41 TraesCS3B01G572300 chr2A 100.000 35 0 0 2191 2225 101533964 101533998 5.130000e-07 65.8
42 TraesCS3B01G572300 chr6B 85.409 281 31 6 1899 2177 368464570 368464842 1.300000e-72 283.0
43 TraesCS3B01G572300 chr6B 97.368 38 0 1 2186 2223 602557401 602557365 1.840000e-06 63.9
44 TraesCS3B01G572300 chr6D 82.371 329 44 10 1429 1755 397345641 397345325 7.830000e-70 274.0
45 TraesCS3B01G572300 chr5A 100.000 35 0 0 2191 2225 530003675 530003709 5.130000e-07 65.8


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 TraesCS3B01G572300 chr3B 803227292 803229516 2224 False 4109.0 4109 100.0000 1 2225 1 chr3B.!!$F4 2224
1 TraesCS3B01G572300 chr3B 802706230 802707053 823 True 1210.0 1210 93.2290 1305 2127 1 chr3B.!!$R2 822
2 TraesCS3B01G572300 chr3B 802713256 802715545 2289 True 715.5 1166 92.9285 1 1005 2 chr3B.!!$R3 1004
3 TraesCS3B01G572300 chr1D 122841467 122843349 1882 True 954.5 1092 87.1445 4 1749 2 chr1D.!!$R1 1745
4 TraesCS3B01G572300 chr4B 320322093 320323133 1040 False 1090.0 1090 85.7140 698 1748 1 chr4B.!!$F2 1050
5 TraesCS3B01G572300 chr4B 320066427 320067021 594 False 665.0 665 86.9780 75 668 1 chr4B.!!$F1 593
6 TraesCS3B01G572300 chr5D 535526159 535527125 966 True 985.0 985 85.4950 799 1749 1 chr5D.!!$R1 950
7 TraesCS3B01G572300 chr1B 187185531 187187324 1793 False 810.0 955 84.8090 1 1678 2 chr1B.!!$F2 1677
8 TraesCS3B01G572300 chr1A 134968155 134968836 681 True 806.0 806 88.0290 1 683 1 chr1A.!!$R1 682
9 TraesCS3B01G572300 chr2B 212060369 212061417 1048 True 754.0 754 80.0190 706 1763 1 chr2B.!!$R1 1057
10 TraesCS3B01G572300 chr2B 213955769 213956801 1032 False 640.0 640 78.1950 698 1749 1 chr2B.!!$F1 1051
11 TraesCS3B01G572300 chr2B 212096170 212096802 632 True 361.0 361 77.3270 21 683 1 chr2B.!!$R2 662
12 TraesCS3B01G572300 chr2D 493877739 493878302 563 False 588.0 588 85.6900 1114 1690 1 chr2D.!!$F1 576
13 TraesCS3B01G572300 chr2D 154958847 154960306 1459 True 456.0 516 79.7845 103 1460 2 chr2D.!!$R2 1357
14 TraesCS3B01G572300 chr7A 450568270 450568951 681 True 507.0 507 80.2900 1 683 1 chr7A.!!$R1 682
15 TraesCS3B01G572300 chrUn 75467931 75468483 552 False 448.0 448 81.4160 698 1259 1 chrUn.!!$F1 561
16 TraesCS3B01G572300 chr3D 166289993 166290530 537 False 440.0 440 81.6030 686 1229 1 chr3D.!!$F1 543

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
779 2240 0.901827 ATCTGTGTGTATGGTGCGGA 59.098 50.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 3380 0.540597 GCCCTGGGAACTTGAAGCTT 60.541 55.0 19.27 0.0 0.0 3.74 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
101 102 8.831550 GGATGAAGCTAACTTAATTAAGTCTGG 58.168 37.037 26.87 20.03 45.17 3.86
111 112 7.506114 ACTTAATTAAGTCTGGTCAAGTCACA 58.494 34.615 22.49 0.00 42.52 3.58
179 180 5.192927 TGTTGAATACCTTCTTAGGCATGG 58.807 41.667 0.00 0.00 46.22 3.66
223 1513 3.698040 AGGTGATGATGGTCTCATTTTGC 59.302 43.478 0.00 0.00 44.83 3.68
241 1531 1.480545 TGCGCAGTACCTATGTGATGT 59.519 47.619 5.66 0.00 0.00 3.06
322 1612 5.219633 GTTATGTTGGTCGCTTGTTGATTT 58.780 37.500 0.00 0.00 0.00 2.17
359 1651 3.008375 AGCATAGTTGACAGTGATGGTGT 59.992 43.478 0.00 0.00 0.00 4.16
462 1758 8.388484 ACCATTTATTGATCAAGCATACTCTC 57.612 34.615 14.54 0.00 0.00 3.20
469 1765 5.181009 TGATCAAGCATACTCTCTTTGTGG 58.819 41.667 0.00 0.00 0.00 4.17
507 1809 3.888323 TCTTTGTAGCAACATGGCTGAAA 59.112 39.130 6.71 5.24 45.44 2.69
540 1842 1.927174 CTGCAAGGAGGAATTACGTCG 59.073 52.381 0.00 0.00 34.64 5.12
543 1845 2.343101 CAAGGAGGAATTACGTCGCAA 58.657 47.619 0.00 0.00 34.64 4.85
546 1848 1.405121 GGAGGAATTACGTCGCAAGGT 60.405 52.381 0.00 0.00 34.64 3.50
549 1851 4.261741 GGAGGAATTACGTCGCAAGGTATA 60.262 45.833 0.00 0.00 34.64 1.47
588 1890 5.335897 GCATTTCTTGAGGTGCTTGTTCATA 60.336 40.000 0.00 0.00 34.85 2.15
762 2223 6.183360 TGGGGCAACAACTATACTCTTCTATC 60.183 42.308 0.00 0.00 39.74 2.08
779 2240 0.901827 ATCTGTGTGTATGGTGCGGA 59.098 50.000 0.00 0.00 0.00 5.54
789 2250 3.692101 TGTATGGTGCGGACAAATAAAGG 59.308 43.478 9.96 0.00 0.00 3.11
795 2256 3.673338 GTGCGGACAAATAAAGGAAAAGC 59.327 43.478 0.63 0.00 0.00 3.51
839 2300 5.774630 AGACTAAAGTAGTGAAGCACTGAC 58.225 41.667 10.15 5.11 45.01 3.51
843 2304 6.992715 ACTAAAGTAGTGAAGCACTGACATTT 59.007 34.615 10.15 7.88 45.01 2.32
879 2341 9.546909 CATATATTCAAAAGATCATACAACGGC 57.453 33.333 0.00 0.00 0.00 5.68
929 2391 3.629398 GGTGCATATCCAGAAGAACCAAG 59.371 47.826 0.00 0.00 0.00 3.61
942 2404 3.931578 AGAACCAAGTGAAATCTCTCCG 58.068 45.455 0.00 0.00 0.00 4.63
963 2425 1.203287 GAAATGCCACCAAAGAGAGCC 59.797 52.381 0.00 0.00 0.00 4.70
1005 2467 3.129813 TGTGCATGATTGGAGAAATGAGC 59.870 43.478 0.00 0.00 0.00 4.26
1006 2468 3.380637 GTGCATGATTGGAGAAATGAGCT 59.619 43.478 0.00 0.00 0.00 4.09
1023 2485 7.928307 AATGAGCTCTACTTTTAAAGATGCA 57.072 32.000 16.19 0.00 0.00 3.96
1047 2509 0.613777 AGACAACCGATCCACTTCCC 59.386 55.000 0.00 0.00 0.00 3.97
1048 2510 0.392595 GACAACCGATCCACTTCCCC 60.393 60.000 0.00 0.00 0.00 4.81
1063 2525 1.450312 CCCCTGCGAAAGGCTACTG 60.450 63.158 0.00 0.00 45.89 2.74
1074 2536 2.173126 AGGCTACTGCTCCTTCTGAT 57.827 50.000 0.00 0.00 39.59 2.90
1080 2542 5.336372 GGCTACTGCTCCTTCTGATATACTG 60.336 48.000 0.00 0.00 39.59 2.74
1099 2561 4.655963 ACTGGTTGCACTTCAGTTGATAT 58.344 39.130 9.24 0.00 38.44 1.63
1102 2564 5.069318 TGGTTGCACTTCAGTTGATATCAA 58.931 37.500 14.23 14.23 0.00 2.57
1177 2639 3.361940 GCGTTTGTTTGAAGCTCTAATGC 59.638 43.478 0.00 0.00 0.00 3.56
1189 2651 3.054139 AGCTCTAATGCAGTTTCCCATGA 60.054 43.478 0.00 0.00 34.99 3.07
1191 2653 4.201990 GCTCTAATGCAGTTTCCCATGAAG 60.202 45.833 0.00 0.00 0.00 3.02
1211 2673 0.034670 ATGAGGAAGACTTGGCTGCC 60.035 55.000 12.87 12.87 33.35 4.85
1225 2688 0.248289 GCTGCCATTGTTGCCTTGAT 59.752 50.000 0.00 0.00 0.00 2.57
1262 2726 7.346751 TGCTTTCCTTTAAGTCTTGTTGAAT 57.653 32.000 0.00 0.00 0.00 2.57
1311 2777 3.598019 ACATTTGGAACCATGTCATGC 57.402 42.857 7.35 0.00 0.00 4.06
1332 2798 6.791887 TGCTGAACTTGAACTTATCTGAAG 57.208 37.500 0.00 0.00 0.00 3.02
1343 2809 9.554395 TTGAACTTATCTGAAGTATTGTGTTGA 57.446 29.630 0.00 0.00 0.00 3.18
1365 2852 6.572519 TGATAAATTTGGAACTATGCCTTGC 58.427 36.000 0.00 0.00 0.00 4.01
1369 2856 2.584835 TGGAACTATGCCTTGCTGTT 57.415 45.000 0.00 0.00 0.00 3.16
1656 3170 3.312146 GCCAATTCAACAAACACCCAAAG 59.688 43.478 0.00 0.00 0.00 2.77
1714 3228 4.580167 TGAGTGAATTGGAACTGAAACCAG 59.420 41.667 0.00 0.00 37.48 4.00
1743 3257 5.361285 ACATAGAGGACTCCAATACAGACAC 59.639 44.000 0.00 0.00 0.00 3.67
1745 3259 2.832129 GAGGACTCCAATACAGACACCA 59.168 50.000 0.00 0.00 0.00 4.17
1748 3262 3.751698 GGACTCCAATACAGACACCAAAC 59.248 47.826 0.00 0.00 0.00 2.93
1749 3263 3.399330 ACTCCAATACAGACACCAAACG 58.601 45.455 0.00 0.00 0.00 3.60
1766 3281 1.460504 ACGTAGCGGATGAGAACTCA 58.539 50.000 6.98 6.98 44.59 3.41
1790 3305 5.271598 TCATTAATTTCAGGGCATGGACTT 58.728 37.500 0.00 0.00 0.00 3.01
1863 3379 0.666274 TTCGTACTCTTGCAGCACCG 60.666 55.000 0.00 0.00 0.00 4.94
1864 3380 1.080772 CGTACTCTTGCAGCACCGA 60.081 57.895 0.00 0.00 0.00 4.69
1883 3399 0.540597 AAGCTTCAAGTTCCCAGGGC 60.541 55.000 0.00 0.00 0.00 5.19
1884 3400 2.335712 GCTTCAAGTTCCCAGGGCG 61.336 63.158 0.00 0.00 0.00 6.13
1885 3401 1.073199 CTTCAAGTTCCCAGGGCGT 59.927 57.895 0.00 0.00 0.00 5.68
1887 3403 0.536460 TTCAAGTTCCCAGGGCGTTC 60.536 55.000 0.00 0.00 0.00 3.95
1888 3404 1.228124 CAAGTTCCCAGGGCGTTCA 60.228 57.895 0.00 0.00 0.00 3.18
1904 3420 3.859386 GCGTTCAAAATATTTGAGGCTGG 59.141 43.478 16.78 5.60 31.42 4.85
1948 3464 7.282585 AGCTACTATCATGCACTTGGAAATAA 58.717 34.615 0.00 0.00 0.00 1.40
1956 3472 5.330455 TGCACTTGGAAATAACAAACACA 57.670 34.783 0.00 0.00 0.00 3.72
1984 3500 3.696548 GTGGCAGGGAATTAAAGAAGAGG 59.303 47.826 0.00 0.00 0.00 3.69
1995 3511 6.816616 ATTAAAGAAGAGGGAGGGTTAGAG 57.183 41.667 0.00 0.00 0.00 2.43
1998 3514 4.969136 AGAAGAGGGAGGGTTAGAGTAA 57.031 45.455 0.00 0.00 0.00 2.24
2009 3525 6.489700 GGAGGGTTAGAGTAACATAGGTAGAC 59.510 46.154 0.00 0.00 40.39 2.59
2010 3526 6.978261 AGGGTTAGAGTAACATAGGTAGACA 58.022 40.000 0.00 0.00 40.39 3.41
2051 3567 3.835378 TGCTACTTTGTGTCATGCATG 57.165 42.857 21.07 21.07 0.00 4.06
2052 3568 2.488937 TGCTACTTTGTGTCATGCATGG 59.511 45.455 25.97 10.76 0.00 3.66
2162 3678 9.355916 TGCATGATACTAGTATATGATACTCCC 57.644 37.037 22.89 9.00 0.00 4.30
2163 3679 8.798402 GCATGATACTAGTATATGATACTCCCC 58.202 40.741 22.89 8.64 0.00 4.81
2164 3680 9.303116 CATGATACTAGTATATGATACTCCCCC 57.697 40.741 15.42 0.00 0.00 5.40
2165 3681 8.415392 TGATACTAGTATATGATACTCCCCCA 57.585 38.462 15.42 2.16 0.00 4.96
2166 3682 8.280084 TGATACTAGTATATGATACTCCCCCAC 58.720 40.741 15.42 0.00 0.00 4.61
2167 3683 6.738205 ACTAGTATATGATACTCCCCCACT 57.262 41.667 0.00 0.00 0.00 4.00
2168 3684 7.842260 ACTAGTATATGATACTCCCCCACTA 57.158 40.000 0.00 0.00 0.00 2.74
2169 3685 8.422163 ACTAGTATATGATACTCCCCCACTAT 57.578 38.462 0.00 0.00 0.00 2.12
2170 3686 8.282982 ACTAGTATATGATACTCCCCCACTATG 58.717 40.741 0.00 0.00 0.00 2.23
2171 3687 7.298678 AGTATATGATACTCCCCCACTATGA 57.701 40.000 0.00 0.00 0.00 2.15
2172 3688 7.358263 AGTATATGATACTCCCCCACTATGAG 58.642 42.308 0.00 0.00 0.00 2.90
2173 3689 3.993658 TGATACTCCCCCACTATGAGT 57.006 47.619 0.00 0.00 41.88 3.41
2174 3690 5.616975 ATGATACTCCCCCACTATGAGTA 57.383 43.478 0.00 0.00 43.54 2.59
2175 3691 4.999310 TGATACTCCCCCACTATGAGTAG 58.001 47.826 0.00 0.00 42.89 2.57
2176 3692 4.419200 TGATACTCCCCCACTATGAGTAGT 59.581 45.833 0.00 0.00 42.89 2.73
2177 3693 3.778622 ACTCCCCCACTATGAGTAGTT 57.221 47.619 0.00 0.00 39.12 2.24
2178 3694 3.644335 ACTCCCCCACTATGAGTAGTTC 58.356 50.000 0.00 0.00 39.12 3.01
2179 3695 2.623889 CTCCCCCACTATGAGTAGTTCG 59.376 54.545 0.00 0.00 39.12 3.95
2180 3696 2.242965 TCCCCCACTATGAGTAGTTCGA 59.757 50.000 0.00 0.00 39.12 3.71
2181 3697 3.117246 TCCCCCACTATGAGTAGTTCGAT 60.117 47.826 0.00 0.00 39.12 3.59
2182 3698 4.105217 TCCCCCACTATGAGTAGTTCGATA 59.895 45.833 0.00 0.00 39.12 2.92
2183 3699 5.017490 CCCCCACTATGAGTAGTTCGATAT 58.983 45.833 0.00 0.00 39.12 1.63
2184 3700 6.012245 TCCCCCACTATGAGTAGTTCGATATA 60.012 42.308 0.00 0.00 39.12 0.86
2185 3701 6.095160 CCCCCACTATGAGTAGTTCGATATAC 59.905 46.154 0.00 0.00 39.12 1.47
2186 3702 6.657966 CCCCACTATGAGTAGTTCGATATACA 59.342 42.308 9.45 0.00 39.12 2.29
2187 3703 7.339721 CCCCACTATGAGTAGTTCGATATACAT 59.660 40.741 9.45 0.00 39.12 2.29
2188 3704 8.184848 CCCACTATGAGTAGTTCGATATACATG 58.815 40.741 9.45 0.00 39.12 3.21
2189 3705 8.947115 CCACTATGAGTAGTTCGATATACATGA 58.053 37.037 0.00 0.00 39.12 3.07
2199 3715 8.508883 AGTTCGATATACATGATACTACCTCC 57.491 38.462 0.00 0.00 0.00 4.30
2200 3716 8.107729 AGTTCGATATACATGATACTACCTCCA 58.892 37.037 0.00 0.00 0.00 3.86
2201 3717 8.904834 GTTCGATATACATGATACTACCTCCAT 58.095 37.037 0.00 0.00 0.00 3.41
2202 3718 8.678593 TCGATATACATGATACTACCTCCATC 57.321 38.462 0.00 0.00 0.00 3.51
2203 3719 8.495260 TCGATATACATGATACTACCTCCATCT 58.505 37.037 0.00 0.00 0.00 2.90
2204 3720 9.780186 CGATATACATGATACTACCTCCATCTA 57.220 37.037 0.00 0.00 0.00 1.98
2218 3734 6.678568 CCTCCATCTAGGTGAATAAGTCAT 57.321 41.667 3.99 0.00 38.90 3.06
2219 3735 7.072263 CCTCCATCTAGGTGAATAAGTCATT 57.928 40.000 3.99 0.00 38.90 2.57
2220 3736 7.158021 CCTCCATCTAGGTGAATAAGTCATTC 58.842 42.308 3.99 0.00 38.90 2.67
2221 3737 7.202038 CCTCCATCTAGGTGAATAAGTCATTCA 60.202 40.741 3.99 0.00 42.69 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 9.282247 GTCAACTTCTTGTAGCAATAAATCATG 57.718 33.333 0.00 0.00 0.00 3.07
101 102 5.695851 AGTCCATTCATTTGTGACTTGAC 57.304 39.130 0.00 0.00 32.61 3.18
179 180 6.829811 ACCTAGTTACTCCATCTCTAGTTCAC 59.170 42.308 0.00 0.00 0.00 3.18
223 1513 2.866156 CCAACATCACATAGGTACTGCG 59.134 50.000 0.00 0.00 41.52 5.18
241 1531 5.995282 CAGGTACTACACAAAATGAGACCAA 59.005 40.000 0.00 0.00 36.02 3.67
359 1651 4.097135 CCATGTACAAAGGAACACACAACA 59.903 41.667 11.27 0.00 0.00 3.33
462 1758 5.816449 AAAGAAAAATTGCACCCACAAAG 57.184 34.783 0.00 0.00 32.27 2.77
469 1765 7.125755 GCTACAAAGAAAAGAAAAATTGCACC 58.874 34.615 0.00 0.00 0.00 5.01
540 1842 6.441274 CAATGTCCATGTCATTATACCTTGC 58.559 40.000 11.30 0.00 34.34 4.01
543 1845 5.693961 TGCAATGTCCATGTCATTATACCT 58.306 37.500 11.30 0.00 34.34 3.08
546 1848 8.467963 AGAAATGCAATGTCCATGTCATTATA 57.532 30.769 11.30 6.11 34.34 0.98
549 1851 5.670792 AGAAATGCAATGTCCATGTCATT 57.329 34.783 0.00 7.31 36.16 2.57
588 1890 2.673775 TGGTCACCCATGTTGTGATT 57.326 45.000 15.77 0.00 43.98 2.57
762 2223 0.320334 TGTCCGCACCATACACACAG 60.320 55.000 0.00 0.00 0.00 3.66
779 2240 5.303333 TCCCTTTCGCTTTTCCTTTATTTGT 59.697 36.000 0.00 0.00 0.00 2.83
789 2250 5.819825 AGAATGTATCCCTTTCGCTTTTC 57.180 39.130 0.00 0.00 33.57 2.29
795 2256 7.042335 AGTCTTGTAAGAATGTATCCCTTTCG 58.958 38.462 0.00 0.00 36.68 3.46
879 2341 1.002134 ACCCATCTTGGCACCTTCG 60.002 57.895 0.00 0.00 35.79 3.79
929 2391 2.356069 GGCATTTCCGGAGAGATTTCAC 59.644 50.000 3.34 0.00 0.00 3.18
942 2404 1.203287 GCTCTCTTTGGTGGCATTTCC 59.797 52.381 0.00 0.00 0.00 3.13
963 2425 0.390603 TAATGGCCTCACGTGTTCGG 60.391 55.000 16.51 15.07 41.85 4.30
1005 2467 9.766277 GTCTTCAATGCATCTTTAAAAGTAGAG 57.234 33.333 0.00 0.00 0.00 2.43
1006 2468 9.283768 TGTCTTCAATGCATCTTTAAAAGTAGA 57.716 29.630 0.00 0.00 0.00 2.59
1023 2485 3.703001 AGTGGATCGGTTGTCTTCAAT 57.297 42.857 0.00 0.00 35.92 2.57
1048 2510 1.086634 GGAGCAGTAGCCTTTCGCAG 61.087 60.000 0.00 0.00 43.56 5.18
1063 2525 4.061596 GCAACCAGTATATCAGAAGGAGC 58.938 47.826 0.00 0.00 0.00 4.70
1074 2536 5.222079 TCAACTGAAGTGCAACCAGTATA 57.778 39.130 14.66 6.11 38.19 1.47
1080 2542 5.627499 TTGATATCAACTGAAGTGCAACC 57.373 39.130 14.23 0.00 37.80 3.77
1099 2561 3.295093 TGTCCACTTCTGCCAAATTTGA 58.705 40.909 19.86 0.00 0.00 2.69
1102 2564 3.233507 ACATGTCCACTTCTGCCAAATT 58.766 40.909 0.00 0.00 0.00 1.82
1177 2639 4.226427 TCCTCATCTTCATGGGAAACTG 57.774 45.455 0.00 0.00 31.02 3.16
1189 2651 2.617532 GCAGCCAAGTCTTCCTCATCTT 60.618 50.000 0.00 0.00 0.00 2.40
1191 2653 1.377536 GCAGCCAAGTCTTCCTCATC 58.622 55.000 0.00 0.00 0.00 2.92
1211 2673 3.132160 TGCAAACATCAAGGCAACAATG 58.868 40.909 0.00 0.00 41.41 2.82
1249 2713 8.697507 AGATAGGTTCAAATTCAACAAGACTT 57.302 30.769 3.38 0.00 0.00 3.01
1250 2714 9.442047 CTAGATAGGTTCAAATTCAACAAGACT 57.558 33.333 3.38 0.00 0.00 3.24
1343 2809 6.155049 ACAGCAAGGCATAGTTCCAAATTTAT 59.845 34.615 0.00 0.00 0.00 1.40
1365 2852 4.654091 AGGTGTTCCAATTTCACAACAG 57.346 40.909 0.00 0.00 35.89 3.16
1369 2856 8.919145 AGTTTAAATAGGTGTTCCAATTTCACA 58.081 29.630 0.00 0.00 35.89 3.58
1656 3170 6.189677 TGGACATGAATACGAATTTGGTTC 57.810 37.500 0.00 2.40 0.00 3.62
1714 3228 6.640518 TGTATTGGAGTCCTCTATGTTGAAC 58.359 40.000 11.33 0.00 0.00 3.18
1720 3234 5.221342 GGTGTCTGTATTGGAGTCCTCTATG 60.221 48.000 11.33 0.00 0.00 2.23
1743 3257 1.659098 GTTCTCATCCGCTACGTTTGG 59.341 52.381 0.00 0.00 0.00 3.28
1745 3259 2.230508 TGAGTTCTCATCCGCTACGTTT 59.769 45.455 0.00 0.00 0.00 3.60
1748 3262 2.033424 TGATGAGTTCTCATCCGCTACG 59.967 50.000 28.57 0.00 44.24 3.51
1749 3263 3.717400 TGATGAGTTCTCATCCGCTAC 57.283 47.619 28.57 12.59 44.24 3.58
1766 3281 5.461327 AGTCCATGCCCTGAAATTAATGAT 58.539 37.500 0.00 0.00 0.00 2.45
1778 3293 2.629017 AATTTGGAAGTCCATGCCCT 57.371 45.000 0.00 0.00 46.97 5.19
1835 3351 5.196341 TGCAAGAGTACGAAGAAAGAAGA 57.804 39.130 0.00 0.00 0.00 2.87
1842 3358 1.336887 GGTGCTGCAAGAGTACGAAGA 60.337 52.381 2.77 0.00 38.15 2.87
1846 3362 0.666274 TTCGGTGCTGCAAGAGTACG 60.666 55.000 2.77 2.95 38.15 3.67
1863 3379 1.539157 CCCTGGGAACTTGAAGCTTC 58.461 55.000 19.89 19.89 0.00 3.86
1864 3380 0.540597 GCCCTGGGAACTTGAAGCTT 60.541 55.000 19.27 0.00 0.00 3.74
1883 3399 3.859386 GCCAGCCTCAAATATTTTGAACG 59.141 43.478 0.00 0.00 0.00 3.95
1884 3400 4.183865 GGCCAGCCTCAAATATTTTGAAC 58.816 43.478 0.00 0.78 0.00 3.18
1885 3401 3.837146 TGGCCAGCCTCAAATATTTTGAA 59.163 39.130 0.00 0.00 36.94 2.69
1887 3403 3.891422 TGGCCAGCCTCAAATATTTTG 57.109 42.857 0.00 0.00 36.94 2.44
1888 3404 5.069516 CACTATGGCCAGCCTCAAATATTTT 59.930 40.000 13.05 0.00 36.94 1.82
1904 3420 3.325135 AGCTAAGATACCACCACTATGGC 59.675 47.826 0.00 0.00 44.33 4.40
1956 3472 5.826643 TCTTTAATTCCCTGCCACATAAGT 58.173 37.500 0.00 0.00 0.00 2.24
1969 3485 4.864483 ACCCTCCCTCTTCTTTAATTCC 57.136 45.455 0.00 0.00 0.00 3.01
1984 3500 6.489700 GTCTACCTATGTTACTCTAACCCTCC 59.510 46.154 0.00 0.00 37.88 4.30
1995 3511 6.624352 TGATACGGTGTCTACCTATGTTAC 57.376 41.667 6.45 0.00 45.22 2.50
1998 3514 9.524496 TTAATATGATACGGTGTCTACCTATGT 57.476 33.333 6.45 0.00 45.22 2.29
2028 3544 5.009310 CCATGCATGACACAAAGTAGCATAT 59.991 40.000 28.31 0.00 39.67 1.78
2036 3552 2.442212 TTGCCATGCATGACACAAAG 57.558 45.000 28.31 10.23 38.76 2.77
2136 3652 9.355916 GGGAGTATCATATACTAGTATCATGCA 57.644 37.037 18.68 1.71 36.25 3.96
2137 3653 8.798402 GGGGAGTATCATATACTAGTATCATGC 58.202 40.741 18.68 12.34 36.25 4.06
2138 3654 9.303116 GGGGGAGTATCATATACTAGTATCATG 57.697 40.741 18.68 17.93 36.25 3.07
2139 3655 9.026170 TGGGGGAGTATCATATACTAGTATCAT 57.974 37.037 18.68 11.67 36.25 2.45
2140 3656 8.280084 GTGGGGGAGTATCATATACTAGTATCA 58.720 40.741 18.68 5.25 36.25 2.15
2141 3657 8.504409 AGTGGGGGAGTATCATATACTAGTATC 58.496 40.741 18.68 3.97 36.25 2.24
2142 3658 8.422163 AGTGGGGGAGTATCATATACTAGTAT 57.578 38.462 19.07 19.07 36.25 2.12
2143 3659 7.842260 AGTGGGGGAGTATCATATACTAGTA 57.158 40.000 4.77 4.77 36.25 1.82
2144 3660 6.738205 AGTGGGGGAGTATCATATACTAGT 57.262 41.667 0.00 0.00 36.25 2.57
2145 3661 8.503573 TCATAGTGGGGGAGTATCATATACTAG 58.496 40.741 0.00 0.00 36.25 2.57
2146 3662 8.415392 TCATAGTGGGGGAGTATCATATACTA 57.585 38.462 0.00 0.00 36.25 1.82
2147 3663 7.035764 ACTCATAGTGGGGGAGTATCATATACT 60.036 40.741 0.00 0.00 39.95 2.12
2148 3664 7.126733 ACTCATAGTGGGGGAGTATCATATAC 58.873 42.308 0.00 0.00 39.95 1.47
2149 3665 7.298678 ACTCATAGTGGGGGAGTATCATATA 57.701 40.000 0.00 0.00 39.95 0.86
2150 3666 6.172350 ACTCATAGTGGGGGAGTATCATAT 57.828 41.667 0.00 0.00 39.95 1.78
2151 3667 5.616975 ACTCATAGTGGGGGAGTATCATA 57.383 43.478 0.00 0.00 39.95 2.15
2152 3668 4.493819 ACTCATAGTGGGGGAGTATCAT 57.506 45.455 0.00 0.00 39.95 2.45
2153 3669 3.993658 ACTCATAGTGGGGGAGTATCA 57.006 47.619 0.00 0.00 39.95 2.15
2154 3670 5.000570 ACTACTCATAGTGGGGGAGTATC 57.999 47.826 0.00 0.00 41.72 2.24
2155 3671 5.395611 GAACTACTCATAGTGGGGGAGTAT 58.604 45.833 0.00 0.00 41.00 2.12
2156 3672 4.688045 CGAACTACTCATAGTGGGGGAGTA 60.688 50.000 0.00 0.00 41.00 2.59
2157 3673 3.644335 GAACTACTCATAGTGGGGGAGT 58.356 50.000 0.00 0.00 41.00 3.85
2158 3674 2.623889 CGAACTACTCATAGTGGGGGAG 59.376 54.545 0.00 0.00 41.00 4.30
2159 3675 2.242965 TCGAACTACTCATAGTGGGGGA 59.757 50.000 0.00 0.00 41.00 4.81
2160 3676 2.662866 TCGAACTACTCATAGTGGGGG 58.337 52.381 0.00 0.00 41.00 5.40
2161 3677 6.657966 TGTATATCGAACTACTCATAGTGGGG 59.342 42.308 8.63 0.00 41.00 4.96
2162 3678 7.683437 TGTATATCGAACTACTCATAGTGGG 57.317 40.000 8.63 0.00 41.00 4.61
2163 3679 8.947115 TCATGTATATCGAACTACTCATAGTGG 58.053 37.037 8.63 0.00 41.00 4.00
2173 3689 9.610705 GGAGGTAGTATCATGTATATCGAACTA 57.389 37.037 0.00 0.00 0.00 2.24
2174 3690 8.107729 TGGAGGTAGTATCATGTATATCGAACT 58.892 37.037 0.00 0.00 0.00 3.01
2175 3691 8.277490 TGGAGGTAGTATCATGTATATCGAAC 57.723 38.462 0.00 0.00 0.00 3.95
2176 3692 9.121658 GATGGAGGTAGTATCATGTATATCGAA 57.878 37.037 0.00 0.00 0.00 3.71
2177 3693 8.495260 AGATGGAGGTAGTATCATGTATATCGA 58.505 37.037 0.00 0.00 0.00 3.59
2178 3694 8.684386 AGATGGAGGTAGTATCATGTATATCG 57.316 38.462 0.00 0.00 0.00 2.92
2195 3711 6.678568 ATGACTTATTCACCTAGATGGAGG 57.321 41.667 0.00 0.00 42.89 4.30


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

AutoCloner maintained by Alex Coulton.