Multiple sequence alignment - TraesCS4A01G034600

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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 TraesCS4A01G034600 chr4A 100.000 2512 0 0 1 2512 26546100 26548611 0.000000e+00 4639.0
1 TraesCS4A01G034600 chrUn 95.541 785 31 2 1731 2512 63574480 63575263 0.000000e+00 1253.0
2 TraesCS4A01G034600 chrUn 95.300 617 25 2 1899 2512 334462992 334462377 0.000000e+00 976.0
3 TraesCS4A01G034600 chrUn 81.667 240 17 10 1020 1235 324121911 324121675 9.240000e-40 174.0
4 TraesCS4A01G034600 chrUn 81.667 240 17 10 1020 1235 353962982 353962746 9.240000e-40 174.0
5 TraesCS4A01G034600 chrUn 98.765 81 1 0 2215 2295 334460717 334460637 7.240000e-31 145.0
6 TraesCS4A01G034600 chrUn 91.935 62 5 0 1068 1129 316546041 316545980 1.240000e-13 87.9
7 TraesCS4A01G034600 chrUn 86.154 65 6 2 1483 1545 324121238 324121175 1.610000e-07 67.6
8 TraesCS4A01G034600 chrUn 86.154 65 6 2 1483 1545 353962309 353962246 1.610000e-07 67.6
9 TraesCS4A01G034600 chr3A 94.139 819 43 3 1697 2512 132162175 132162991 0.000000e+00 1242.0
10 TraesCS4A01G034600 chr3A 95.982 224 8 1 2290 2512 342073850 342074073 1.840000e-96 363.0
11 TraesCS4A01G034600 chr3A 97.561 82 2 0 2215 2296 734111980 734112061 9.370000e-30 141.0
12 TraesCS4A01G034600 chr3A 95.455 88 3 1 2215 2302 205711906 205711820 3.370000e-29 139.0
13 TraesCS4A01G034600 chr7A 93.738 527 23 5 1697 2218 501589938 501590459 0.000000e+00 782.0
14 TraesCS4A01G034600 chr7A 95.556 225 8 2 2290 2512 562182309 562182085 2.380000e-95 359.0
15 TraesCS4A01G034600 chr7A 98.765 81 1 0 2215 2295 635545778 635545698 7.240000e-31 145.0
16 TraesCS4A01G034600 chr6A 93.585 530 25 4 1694 2218 592441286 592441811 0.000000e+00 782.0
17 TraesCS4A01G034600 chr6A 98.765 81 1 0 2215 2295 9472916 9472996 7.240000e-31 145.0
18 TraesCS4A01G034600 chr3B 93.110 537 26 5 1687 2218 690453682 690454212 0.000000e+00 776.0
19 TraesCS4A01G034600 chr2B 93.548 527 25 3 1697 2218 25978217 25978739 0.000000e+00 776.0
20 TraesCS4A01G034600 chr2B 93.359 527 26 4 1697 2218 77776263 77776785 0.000000e+00 771.0
21 TraesCS4A01G034600 chr2A 93.548 527 25 3 1697 2218 736030617 736031139 0.000000e+00 776.0
22 TraesCS4A01G034600 chr2A 96.429 224 7 1 2290 2512 565072101 565072324 3.950000e-98 368.0
23 TraesCS4A01G034600 chr2A 95.279 233 10 1 2281 2512 734075937 734076169 3.950000e-98 368.0
24 TraesCS4A01G034600 chr2A 95.982 224 8 1 2290 2512 154810129 154809906 1.840000e-96 363.0
25 TraesCS4A01G034600 chr1B 93.384 529 24 5 1695 2218 377260597 377261119 0.000000e+00 773.0
26 TraesCS4A01G034600 chr4D 90.515 369 24 3 1 358 441076931 441076563 6.290000e-131 477.0
27 TraesCS4A01G034600 chr4D 83.594 384 24 21 405 762 441076473 441076103 8.670000e-85 324.0
28 TraesCS4A01G034600 chr4D 100.000 28 0 0 368 395 441076522 441076495 5.000000e-03 52.8
29 TraesCS4A01G034600 chr4B 89.459 351 26 5 13 358 546819182 546818838 1.380000e-117 433.0
30 TraesCS4A01G034600 chr4B 82.495 497 27 17 1231 1696 546733505 546733038 5.070000e-102 381.0
31 TraesCS4A01G034600 chr4B 83.566 286 14 18 535 800 546734397 546734125 1.160000e-58 237.0
32 TraesCS4A01G034600 chr4B 79.625 373 16 26 809 1133 546734015 546733655 1.960000e-51 213.0
33 TraesCS4A01G034600 chr4B 84.043 94 5 4 595 686 546818675 546818590 5.760000e-12 82.4
34 TraesCS4A01G034600 chr1A 96.429 224 7 1 2290 2512 319423613 319423390 3.950000e-98 368.0
35 TraesCS4A01G034600 chr5D 85.479 365 35 11 1231 1582 35326605 35326246 5.110000e-97 364.0
36 TraesCS4A01G034600 chr5D 92.126 127 8 2 1010 1136 35326882 35326758 7.140000e-41 178.0
37 TraesCS4A01G034600 chr5D 93.805 113 5 2 1021 1133 35534188 35534298 4.300000e-38 169.0
38 TraesCS4A01G034600 chr5A 81.579 456 37 12 1020 1434 23938711 23938262 1.440000e-87 333.0
39 TraesCS4A01G034600 chr5A 80.315 254 19 14 905 1133 24176977 24177224 2.000000e-36 163.0
40 TraesCS4A01G034600 chr2D 98.795 83 1 0 2215 2297 166810226 166810308 5.600000e-32 148.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G034600 chr4A 26546100 26548611 2511 False 4639.0 4639 100.000000 1 2512 1 chr4A.!!$F1 2511
1 TraesCS4A01G034600 chrUn 63574480 63575263 783 False 1253.0 1253 95.541000 1731 2512 1 chrUn.!!$F1 781
2 TraesCS4A01G034600 chrUn 334460637 334462992 2355 True 560.5 976 97.032500 1899 2512 2 chrUn.!!$R3 613
3 TraesCS4A01G034600 chr3A 132162175 132162991 816 False 1242.0 1242 94.139000 1697 2512 1 chr3A.!!$F1 815
4 TraesCS4A01G034600 chr7A 501589938 501590459 521 False 782.0 782 93.738000 1697 2218 1 chr7A.!!$F1 521
5 TraesCS4A01G034600 chr6A 592441286 592441811 525 False 782.0 782 93.585000 1694 2218 1 chr6A.!!$F2 524
6 TraesCS4A01G034600 chr3B 690453682 690454212 530 False 776.0 776 93.110000 1687 2218 1 chr3B.!!$F1 531
7 TraesCS4A01G034600 chr2B 25978217 25978739 522 False 776.0 776 93.548000 1697 2218 1 chr2B.!!$F1 521
8 TraesCS4A01G034600 chr2B 77776263 77776785 522 False 771.0 771 93.359000 1697 2218 1 chr2B.!!$F2 521
9 TraesCS4A01G034600 chr2A 736030617 736031139 522 False 776.0 776 93.548000 1697 2218 1 chr2A.!!$F3 521
10 TraesCS4A01G034600 chr1B 377260597 377261119 522 False 773.0 773 93.384000 1695 2218 1 chr1B.!!$F1 523
11 TraesCS4A01G034600 chr4D 441076103 441076931 828 True 284.6 477 91.369667 1 762 3 chr4D.!!$R1 761
12 TraesCS4A01G034600 chr4B 546733038 546734397 1359 True 277.0 381 81.895333 535 1696 3 chr4B.!!$R1 1161
13 TraesCS4A01G034600 chr4B 546818590 546819182 592 True 257.7 433 86.751000 13 686 2 chr4B.!!$R2 673
14 TraesCS4A01G034600 chr5D 35326246 35326882 636 True 271.0 364 88.802500 1010 1582 2 chr5D.!!$R1 572

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
711 800 0.035458 GTATGGCCGGGGAGATTCTG 59.965 60.0 2.18 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1592 1955 1.745653 GTTGCTGCCTAGGAAATGGTC 59.254 52.381 14.75 0.0 35.94 4.02 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
17 18 3.352512 AAGCTTTGGTGGGTGGGA 58.647 55.556 0.00 0.00 0.00 4.37
32 33 5.010012 GTGGGTGGGATGCTTAAAGATTATG 59.990 44.000 0.00 0.00 0.00 1.90
76 77 1.264749 CCCTGATCTTGTCCCCGACA 61.265 60.000 0.00 0.00 41.09 4.35
79 80 1.153628 GATCTTGTCCCCGACACCG 60.154 63.158 0.00 0.00 42.60 4.94
82 83 3.934391 CTTGTCCCCGACACCGAGC 62.934 68.421 0.00 0.00 42.60 5.03
187 188 1.360393 ACCTCACCCCTTTCCTGCAA 61.360 55.000 0.00 0.00 0.00 4.08
207 215 2.030562 CCACCCGTTCGTCAGCTT 59.969 61.111 0.00 0.00 0.00 3.74
245 257 0.038526 GAGAGCCGAACGGAACAAGA 60.039 55.000 17.63 0.00 37.50 3.02
251 263 0.589708 CGAACGGAACAAGAAACCCC 59.410 55.000 0.00 0.00 0.00 4.95
263 275 2.529632 AGAAACCCCAATCAAGAAGGC 58.470 47.619 0.00 0.00 0.00 4.35
282 294 2.421424 GGCTCTTGAATTACCTGTGCAG 59.579 50.000 0.00 0.00 0.00 4.41
350 362 2.835431 CCTCGACGCCCTCCATCT 60.835 66.667 0.00 0.00 0.00 2.90
358 370 1.760875 GCCCTCCATCTACCGTGGA 60.761 63.158 0.00 0.00 43.26 4.02
363 375 2.526888 TCCATCTACCGTGGAGACTT 57.473 50.000 0.00 0.00 40.72 3.01
395 438 4.045636 GCTAGAGCAAGAAGAAGAGAGG 57.954 50.000 0.00 0.00 41.59 3.69
398 441 3.723325 AGAGCAAGAAGAAGAGAGGGAT 58.277 45.455 0.00 0.00 0.00 3.85
399 442 3.706086 AGAGCAAGAAGAAGAGAGGGATC 59.294 47.826 0.00 0.00 0.00 3.36
400 443 2.771372 AGCAAGAAGAAGAGAGGGATCC 59.229 50.000 1.92 1.92 0.00 3.36
401 444 2.482839 GCAAGAAGAAGAGAGGGATCCG 60.483 54.545 5.45 0.00 0.00 4.18
403 446 1.289530 AGAAGAAGAGAGGGATCCGGT 59.710 52.381 5.45 0.00 0.00 5.28
429 484 1.349026 TGGAAGAACCAGGAGCTTCAG 59.651 52.381 20.38 0.00 44.64 3.02
444 499 4.878439 AGCTTCAGTGTGTGACGTATTTA 58.122 39.130 0.00 0.00 33.71 1.40
445 500 5.479306 AGCTTCAGTGTGTGACGTATTTAT 58.521 37.500 0.00 0.00 33.71 1.40
446 501 6.627243 AGCTTCAGTGTGTGACGTATTTATA 58.373 36.000 0.00 0.00 33.71 0.98
447 502 7.094631 AGCTTCAGTGTGTGACGTATTTATAA 58.905 34.615 0.00 0.00 33.71 0.98
448 503 7.764443 AGCTTCAGTGTGTGACGTATTTATAAT 59.236 33.333 0.00 0.00 33.71 1.28
449 504 8.388103 GCTTCAGTGTGTGACGTATTTATAATT 58.612 33.333 0.00 0.00 33.71 1.40
494 567 4.918201 CTGGAAGGCCGGCCGATC 62.918 72.222 38.88 35.91 41.95 3.69
502 575 4.271816 CCGGCCGATCGAGGTGAG 62.272 72.222 30.73 0.44 0.00 3.51
575 652 3.628032 GGATGACCGGATTCTTTCTTTCC 59.372 47.826 9.46 1.43 0.00 3.13
687 773 1.299562 GGCTCTCACGTCGTCAGAGA 61.300 60.000 27.85 19.85 36.52 3.10
688 774 0.730265 GCTCTCACGTCGTCAGAGAT 59.270 55.000 27.85 0.00 37.73 2.75
711 800 0.035458 GTATGGCCGGGGAGATTCTG 59.965 60.000 2.18 0.00 0.00 3.02
712 801 0.399949 TATGGCCGGGGAGATTCTGT 60.400 55.000 2.18 0.00 0.00 3.41
713 802 1.700042 ATGGCCGGGGAGATTCTGTC 61.700 60.000 2.18 0.00 0.00 3.51
714 803 2.107141 GCCGGGGAGATTCTGTCG 59.893 66.667 2.18 0.00 0.00 4.35
715 804 2.107141 CCGGGGAGATTCTGTCGC 59.893 66.667 0.00 0.00 0.00 5.19
717 806 1.218047 CGGGGAGATTCTGTCGCAA 59.782 57.895 0.00 0.00 0.00 4.85
718 807 0.391130 CGGGGAGATTCTGTCGCAAA 60.391 55.000 0.00 0.00 0.00 3.68
765 866 1.509644 CTGCGAATGCCTGTGTGTGT 61.510 55.000 0.00 0.00 41.78 3.72
766 867 0.250081 TGCGAATGCCTGTGTGTGTA 60.250 50.000 0.00 0.00 41.78 2.90
771 872 4.678622 CGAATGCCTGTGTGTGTATAGTA 58.321 43.478 0.00 0.00 0.00 1.82
777 878 3.119602 CCTGTGTGTGTATAGTAGCGTGT 60.120 47.826 0.00 0.00 0.00 4.49
781 882 3.063045 TGTGTGTATAGTAGCGTGTCTCG 59.937 47.826 0.00 0.00 43.12 4.04
804 905 3.820689 TCGCAAGATTTGTTGTACATGC 58.179 40.909 0.00 0.00 45.01 4.06
805 906 3.251972 TCGCAAGATTTGTTGTACATGCA 59.748 39.130 12.73 5.76 45.01 3.96
806 907 3.361644 CGCAAGATTTGTTGTACATGCAC 59.638 43.478 12.73 2.46 43.02 4.57
835 1040 0.771127 TGCCTAGCTGGTTTCCTTGT 59.229 50.000 0.00 0.00 38.35 3.16
851 1056 7.148590 GGTTTCCTTGTGCAATTCATTATTGAC 60.149 37.037 0.00 0.00 45.35 3.18
852 1057 6.839124 TCCTTGTGCAATTCATTATTGACT 57.161 33.333 0.00 0.00 45.35 3.41
853 1058 7.936496 TCCTTGTGCAATTCATTATTGACTA 57.064 32.000 0.00 0.00 45.35 2.59
854 1059 7.988737 TCCTTGTGCAATTCATTATTGACTAG 58.011 34.615 0.00 0.00 45.35 2.57
880 1085 1.897802 CCAATCTGCAGGCTCCTTTTT 59.102 47.619 15.13 0.00 0.00 1.94
881 1086 2.094338 CCAATCTGCAGGCTCCTTTTTC 60.094 50.000 15.13 0.00 0.00 2.29
882 1087 2.824341 CAATCTGCAGGCTCCTTTTTCT 59.176 45.455 15.13 0.00 0.00 2.52
883 1088 2.664402 TCTGCAGGCTCCTTTTTCTT 57.336 45.000 15.13 0.00 0.00 2.52
884 1089 2.949447 TCTGCAGGCTCCTTTTTCTTT 58.051 42.857 15.13 0.00 0.00 2.52
885 1090 3.299503 TCTGCAGGCTCCTTTTTCTTTT 58.700 40.909 15.13 0.00 0.00 2.27
896 1101 4.469586 TCCTTTTTCTTTTCCTGGCAAAGT 59.530 37.500 16.56 0.00 33.61 2.66
907 1141 2.556622 CCTGGCAAAGTTACACGGAATT 59.443 45.455 0.00 0.00 0.00 2.17
915 1149 6.453396 GCAAAGTTACACGGAATTACGACTAG 60.453 42.308 18.96 7.26 37.61 2.57
919 1153 0.590732 ACGGAATTACGACTAGCGCG 60.591 55.000 18.96 0.00 46.04 6.86
941 1175 4.673320 CGTTTATTTGGATTTGGACCGGAC 60.673 45.833 9.46 0.00 0.00 4.79
945 1179 3.275617 TTGGATTTGGACCGGACTATG 57.724 47.619 9.46 0.00 0.00 2.23
952 1186 2.759355 TGGACCGGACTATGGAATTCT 58.241 47.619 9.46 0.00 0.00 2.40
968 1202 6.480763 TGGAATTCTTTGGCAGTGAGTATAA 58.519 36.000 5.23 0.00 0.00 0.98
969 1203 7.118723 TGGAATTCTTTGGCAGTGAGTATAAT 58.881 34.615 5.23 0.00 0.00 1.28
970 1204 8.271458 TGGAATTCTTTGGCAGTGAGTATAATA 58.729 33.333 5.23 0.00 0.00 0.98
971 1205 9.289782 GGAATTCTTTGGCAGTGAGTATAATAT 57.710 33.333 5.23 0.00 0.00 1.28
1001 1257 4.442893 GGTCTGATTTGATATCCACCGTGA 60.443 45.833 0.00 0.00 0.00 4.35
1002 1258 4.508124 GTCTGATTTGATATCCACCGTGAC 59.492 45.833 0.00 0.00 0.00 3.67
1003 1259 4.161377 TCTGATTTGATATCCACCGTGACA 59.839 41.667 0.00 0.00 0.00 3.58
1004 1260 4.441792 TGATTTGATATCCACCGTGACAG 58.558 43.478 0.00 0.00 0.00 3.51
1007 1263 2.184533 TGATATCCACCGTGACAGGTT 58.815 47.619 0.00 0.00 43.00 3.50
1008 1264 2.093711 TGATATCCACCGTGACAGGTTG 60.094 50.000 0.00 0.00 43.00 3.77
1010 1266 1.344065 ATCCACCGTGACAGGTTGTA 58.656 50.000 0.00 0.00 43.00 2.41
1011 1267 1.344065 TCCACCGTGACAGGTTGTAT 58.656 50.000 0.00 0.00 43.00 2.29
1012 1268 1.695242 TCCACCGTGACAGGTTGTATT 59.305 47.619 0.00 0.00 43.00 1.89
1013 1269 1.804151 CCACCGTGACAGGTTGTATTG 59.196 52.381 0.00 0.00 43.00 1.90
1014 1270 1.196808 CACCGTGACAGGTTGTATTGC 59.803 52.381 0.00 0.00 43.00 3.56
1015 1271 0.802494 CCGTGACAGGTTGTATTGCC 59.198 55.000 0.00 0.00 0.00 4.52
1016 1272 1.518325 CGTGACAGGTTGTATTGCCA 58.482 50.000 0.00 0.00 0.00 4.92
1017 1273 1.464608 CGTGACAGGTTGTATTGCCAG 59.535 52.381 0.00 0.00 0.00 4.85
1018 1274 1.812571 GTGACAGGTTGTATTGCCAGG 59.187 52.381 0.00 0.00 0.00 4.45
1066 1322 4.081185 TGCTCATCGGCGCCTTCA 62.081 61.111 26.68 8.65 34.52 3.02
1150 1433 1.372251 CAGCAGAGCGTTGTCGACT 60.372 57.895 17.92 0.00 39.71 4.18
1274 1593 1.664151 GTCGGTTAAAGAAGATGGCCG 59.336 52.381 0.00 0.00 39.13 6.13
1473 1801 0.827368 GCTACAGCTAGAGCAGGGTT 59.173 55.000 12.92 0.00 45.16 4.11
1474 1802 1.472376 GCTACAGCTAGAGCAGGGTTG 60.472 57.143 12.92 1.92 45.16 3.77
1510 1850 5.088739 GGTCGAATGAATCACACATTTGTC 58.911 41.667 0.00 0.00 39.08 3.18
1590 1953 0.464036 ACAAACTGCCTCTCGTGTCA 59.536 50.000 0.00 0.00 0.00 3.58
1592 1955 0.034059 AAACTGCCTCTCGTGTCAGG 59.966 55.000 0.00 0.00 0.00 3.86
1622 1985 3.070734 CCTAGGCAGCAACAGATCATAGT 59.929 47.826 0.00 0.00 0.00 2.12
1639 2002 4.738252 TCATAGTGTAGCTAATTCGCGTTG 59.262 41.667 5.77 0.00 32.72 4.10
1643 2006 3.800506 GTGTAGCTAATTCGCGTTGGTAT 59.199 43.478 5.77 0.00 34.40 2.73
1658 2021 5.335504 GCGTTGGTATATGTCTCCTACTACC 60.336 48.000 0.00 0.00 0.00 3.18
1659 2022 5.766670 CGTTGGTATATGTCTCCTACTACCA 59.233 44.000 0.00 0.00 37.44 3.25
1666 2029 2.380932 TGTCTCCTACTACCAACTCCCA 59.619 50.000 0.00 0.00 0.00 4.37
1677 2040 4.724279 ACCAACTCCCACTGTTTCTAAT 57.276 40.909 0.00 0.00 0.00 1.73
1678 2041 5.836024 ACCAACTCCCACTGTTTCTAATA 57.164 39.130 0.00 0.00 0.00 0.98
1679 2042 6.388619 ACCAACTCCCACTGTTTCTAATAT 57.611 37.500 0.00 0.00 0.00 1.28
1680 2043 7.504926 ACCAACTCCCACTGTTTCTAATATA 57.495 36.000 0.00 0.00 0.00 0.86
1681 2044 8.102484 ACCAACTCCCACTGTTTCTAATATAT 57.898 34.615 0.00 0.00 0.00 0.86
1682 2045 8.211629 ACCAACTCCCACTGTTTCTAATATATC 58.788 37.037 0.00 0.00 0.00 1.63
1683 2046 8.432805 CCAACTCCCACTGTTTCTAATATATCT 58.567 37.037 0.00 0.00 0.00 1.98
1684 2047 9.838339 CAACTCCCACTGTTTCTAATATATCTT 57.162 33.333 0.00 0.00 0.00 2.40
1752 2115 3.243941 TGGACTAATAAGTGTGCACGTGT 60.244 43.478 18.38 1.55 35.56 4.49
1759 2122 1.948104 AGTGTGCACGTGTAACACAT 58.052 45.000 36.13 25.84 45.28 3.21
1762 2125 2.010497 TGTGCACGTGTAACACATGTT 58.990 42.857 19.40 2.32 45.33 2.71
1933 2296 0.179001 AAGACCACCCACTTTTCCCG 60.179 55.000 0.00 0.00 0.00 5.14
1988 2351 8.873186 TTCATCATAATTCTCCATATGCACAT 57.127 30.769 0.00 0.00 31.11 3.21
2149 2523 6.462347 GGTTTGTTGAAAAGAGGAAGCCATTA 60.462 38.462 0.00 0.00 0.00 1.90
2151 2525 6.916360 TGTTGAAAAGAGGAAGCCATTATT 57.084 33.333 0.00 0.00 0.00 1.40
2270 2644 4.513318 GGGTGCACTTAGAGAAGATAATGC 59.487 45.833 17.98 0.00 36.45 3.56
2391 2765 1.000506 TCGTCACCTCTACCAAAGTGC 59.999 52.381 0.00 0.00 0.00 4.40
2479 2853 7.285172 CCATGACCACAAAATATCCTACATTCA 59.715 37.037 0.00 0.00 0.00 2.57
2503 2877 8.458843 TCATCATCATCATAATCAACATGCATC 58.541 33.333 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.821388 ACGAGAGGTCATAATCTTTAAGCAT 58.179 36.000 0.00 0.00 0.00 3.79
46 47 1.422531 AGATCAGGGAGCACCATCTC 58.577 55.000 1.58 0.00 43.89 2.75
187 188 2.420043 CTGACGAACGGGTGGTGT 59.580 61.111 0.00 0.00 0.00 4.16
226 238 0.038526 TCTTGTTCCGTTCGGCTCTC 60.039 55.000 6.35 0.00 0.00 3.20
229 241 0.942252 GTTTCTTGTTCCGTTCGGCT 59.058 50.000 6.35 0.00 0.00 5.52
237 249 3.895041 TCTTGATTGGGGTTTCTTGTTCC 59.105 43.478 0.00 0.00 0.00 3.62
245 257 2.110721 AGAGCCTTCTTGATTGGGGTTT 59.889 45.455 0.00 0.00 0.00 3.27
263 275 2.421424 GGCTGCACAGGTAATTCAAGAG 59.579 50.000 0.50 0.00 0.00 2.85
268 280 0.323360 TGGGGCTGCACAGGTAATTC 60.323 55.000 3.46 0.00 0.00 2.17
350 362 4.008330 CTCTTCACTAAGTCTCCACGGTA 58.992 47.826 0.00 0.00 34.13 4.02
358 370 4.398044 GCTCTAGCACTCTTCACTAAGTCT 59.602 45.833 0.00 0.00 41.59 3.24
360 372 4.712122 GCTCTAGCACTCTTCACTAAGT 57.288 45.455 0.00 0.00 41.59 2.24
395 438 1.762957 TCTTCCATCAGAACCGGATCC 59.237 52.381 9.46 0.00 0.00 3.36
398 441 2.762535 GTTCTTCCATCAGAACCGGA 57.237 50.000 9.46 0.00 44.84 5.14
403 446 2.026822 GCTCCTGGTTCTTCCATCAGAA 60.027 50.000 0.00 0.00 46.12 3.02
444 499 6.432162 CCAGTCCATGCTGCTGTTATAATTAT 59.568 38.462 2.97 2.97 35.28 1.28
445 500 5.764686 CCAGTCCATGCTGCTGTTATAATTA 59.235 40.000 0.00 0.00 35.28 1.40
446 501 4.581824 CCAGTCCATGCTGCTGTTATAATT 59.418 41.667 0.00 0.00 35.28 1.40
447 502 4.139786 CCAGTCCATGCTGCTGTTATAAT 58.860 43.478 0.00 0.00 35.28 1.28
448 503 3.199727 TCCAGTCCATGCTGCTGTTATAA 59.800 43.478 0.00 0.00 35.28 0.98
449 504 2.771372 TCCAGTCCATGCTGCTGTTATA 59.229 45.455 0.00 0.00 35.28 0.98
485 558 4.271816 CTCACCTCGATCGGCCGG 62.272 72.222 27.83 15.31 0.00 6.13
494 567 1.339610 GATGATCACCTCCTCACCTCG 59.660 57.143 0.00 0.00 0.00 4.63
500 573 4.588106 TGAAGATGAGATGATCACCTCCTC 59.412 45.833 14.81 13.90 41.91 3.71
501 574 4.344679 GTGAAGATGAGATGATCACCTCCT 59.655 45.833 14.81 4.41 41.91 3.69
502 575 4.630111 GTGAAGATGAGATGATCACCTCC 58.370 47.826 14.81 0.00 41.91 4.30
600 681 2.135933 GTGGACCAAAGTCAGAGTTCG 58.864 52.381 0.00 0.00 45.48 3.95
637 718 2.034879 CATGCCTGGACGTGGTCAC 61.035 63.158 0.00 0.00 33.68 3.67
638 719 1.188871 TACATGCCTGGACGTGGTCA 61.189 55.000 0.00 0.00 33.68 4.02
639 720 0.739813 GTACATGCCTGGACGTGGTC 60.740 60.000 0.00 0.00 0.00 4.02
640 721 1.192146 AGTACATGCCTGGACGTGGT 61.192 55.000 0.00 0.00 41.49 4.16
687 773 1.229529 CTCCCCGGCCATACCCTAT 60.230 63.158 2.24 0.00 33.26 2.57
688 774 1.746929 ATCTCCCCGGCCATACCCTA 61.747 60.000 2.24 0.00 33.26 3.53
711 800 4.359706 ACAATCTTGAAACCTTTTGCGAC 58.640 39.130 0.00 0.00 0.00 5.19
712 801 4.647424 ACAATCTTGAAACCTTTTGCGA 57.353 36.364 0.00 0.00 0.00 5.10
713 802 4.566360 ACAACAATCTTGAAACCTTTTGCG 59.434 37.500 0.00 0.00 0.00 4.85
714 803 5.727515 GCACAACAATCTTGAAACCTTTTGC 60.728 40.000 0.00 0.00 0.00 3.68
715 804 5.581874 AGCACAACAATCTTGAAACCTTTTG 59.418 36.000 0.00 0.00 0.00 2.44
717 806 5.111293 CAGCACAACAATCTTGAAACCTTT 58.889 37.500 0.00 0.00 0.00 3.11
718 807 4.685924 CAGCACAACAATCTTGAAACCTT 58.314 39.130 0.00 0.00 0.00 3.50
765 866 2.130395 CGACCGAGACACGCTACTATA 58.870 52.381 0.00 0.00 41.07 1.31
766 867 0.935898 CGACCGAGACACGCTACTAT 59.064 55.000 0.00 0.00 41.07 2.12
777 878 1.798223 CAACAAATCTTGCGACCGAGA 59.202 47.619 0.00 0.00 35.96 4.04
781 882 3.889196 TGTACAACAAATCTTGCGACC 57.111 42.857 0.00 0.00 0.00 4.79
789 890 4.455533 TCCTCTGTGCATGTACAACAAATC 59.544 41.667 17.61 0.00 0.00 2.17
793 894 3.483808 TTCCTCTGTGCATGTACAACA 57.516 42.857 17.61 6.58 0.00 3.33
800 901 0.524862 GGCAGTTTCCTCTGTGCATG 59.475 55.000 0.00 0.00 37.68 4.06
801 902 0.403271 AGGCAGTTTCCTCTGTGCAT 59.597 50.000 0.00 0.00 37.68 3.96
802 903 1.002430 CTAGGCAGTTTCCTCTGTGCA 59.998 52.381 0.00 0.00 37.68 4.57
803 904 1.731720 CTAGGCAGTTTCCTCTGTGC 58.268 55.000 0.00 0.00 37.66 4.57
804 905 1.277557 AGCTAGGCAGTTTCCTCTGTG 59.722 52.381 0.00 0.00 37.66 3.66
805 906 1.277557 CAGCTAGGCAGTTTCCTCTGT 59.722 52.381 0.00 0.00 37.66 3.41
806 907 1.406614 CCAGCTAGGCAGTTTCCTCTG 60.407 57.143 0.00 0.00 37.66 3.35
851 1056 2.547642 GCCTGCAGATTGGTCTAGCTAG 60.548 54.545 17.39 15.01 32.92 3.42
852 1057 1.414181 GCCTGCAGATTGGTCTAGCTA 59.586 52.381 17.39 0.00 32.92 3.32
853 1058 0.179936 GCCTGCAGATTGGTCTAGCT 59.820 55.000 17.39 0.00 32.92 3.32
854 1059 0.179936 AGCCTGCAGATTGGTCTAGC 59.820 55.000 17.39 6.49 32.09 3.42
880 1085 3.314080 CGTGTAACTTTGCCAGGAAAAGA 59.686 43.478 25.24 2.00 37.91 2.52
881 1086 3.550030 CCGTGTAACTTTGCCAGGAAAAG 60.550 47.826 17.73 17.73 39.92 2.27
882 1087 2.359531 CCGTGTAACTTTGCCAGGAAAA 59.640 45.455 0.00 0.00 31.75 2.29
883 1088 1.950909 CCGTGTAACTTTGCCAGGAAA 59.049 47.619 0.00 0.00 31.75 3.13
884 1089 1.141254 TCCGTGTAACTTTGCCAGGAA 59.859 47.619 0.00 0.00 31.75 3.36
885 1090 0.759959 TCCGTGTAACTTTGCCAGGA 59.240 50.000 0.00 0.00 31.75 3.86
896 1101 3.683989 CGCTAGTCGTAATTCCGTGTAA 58.316 45.455 0.00 0.00 0.00 2.41
907 1141 2.853594 CCAAATAAACGCGCTAGTCGTA 59.146 45.455 5.73 0.00 39.48 3.43
915 1149 2.596862 GTCCAAATCCAAATAAACGCGC 59.403 45.455 5.73 0.00 0.00 6.86
919 1153 4.461431 AGTCCGGTCCAAATCCAAATAAAC 59.539 41.667 0.00 0.00 0.00 2.01
941 1175 4.946157 ACTCACTGCCAAAGAATTCCATAG 59.054 41.667 0.65 0.00 0.00 2.23
945 1179 7.573968 ATTATACTCACTGCCAAAGAATTCC 57.426 36.000 0.65 0.00 0.00 3.01
970 1204 9.896645 GTGGATATCAAATCAGACCACATATAT 57.103 33.333 4.83 0.00 43.59 0.86
971 1205 8.321353 GGTGGATATCAAATCAGACCACATATA 58.679 37.037 0.00 0.00 45.20 0.86
972 1206 7.170965 GGTGGATATCAAATCAGACCACATAT 58.829 38.462 0.00 0.00 45.20 1.78
973 1207 6.533730 GGTGGATATCAAATCAGACCACATA 58.466 40.000 0.00 0.00 45.20 2.29
974 1208 5.380043 GGTGGATATCAAATCAGACCACAT 58.620 41.667 0.00 0.00 45.20 3.21
975 1209 4.683129 CGGTGGATATCAAATCAGACCACA 60.683 45.833 0.00 0.00 45.20 4.17
988 1244 2.093658 ACAACCTGTCACGGTGGATATC 60.094 50.000 8.50 0.00 37.36 1.63
994 1250 1.196808 GCAATACAACCTGTCACGGTG 59.803 52.381 0.56 0.56 37.36 4.94
1001 1257 0.112218 TGCCTGGCAATACAACCTGT 59.888 50.000 21.08 0.00 34.76 4.00
1002 1258 0.813184 CTGCCTGGCAATACAACCTG 59.187 55.000 23.51 3.48 38.41 4.00
1003 1259 0.967380 GCTGCCTGGCAATACAACCT 60.967 55.000 23.51 0.00 38.41 3.50
1004 1260 1.512694 GCTGCCTGGCAATACAACC 59.487 57.895 23.51 1.61 38.41 3.77
1007 1263 1.745115 GTCGCTGCCTGGCAATACA 60.745 57.895 23.51 3.98 38.41 2.29
1008 1264 2.472909 GGTCGCTGCCTGGCAATAC 61.473 63.158 23.51 18.82 38.41 1.89
1010 1266 4.349503 TGGTCGCTGCCTGGCAAT 62.350 61.111 23.51 0.00 38.41 3.56
1014 1270 4.415150 ATGGTGGTCGCTGCCTGG 62.415 66.667 0.00 0.00 0.00 4.45
1015 1271 3.129502 CATGGTGGTCGCTGCCTG 61.130 66.667 0.00 0.00 0.00 4.85
1082 1338 3.141488 CGGTGGAGAGGGAGACGG 61.141 72.222 0.00 0.00 0.00 4.79
1136 1419 0.110147 CTCGAAGTCGACAACGCTCT 60.110 55.000 19.50 0.00 44.22 4.09
1209 1501 1.710013 CAGCCGACGAATACACTGTT 58.290 50.000 0.00 0.00 0.00 3.16
1252 1571 2.344025 GCCATCTTCTTTAACCGACGT 58.656 47.619 0.00 0.00 0.00 4.34
1260 1579 1.153249 CGCCCGGCCATCTTCTTTA 60.153 57.895 2.24 0.00 0.00 1.85
1261 1580 2.438434 CGCCCGGCCATCTTCTTT 60.438 61.111 2.24 0.00 0.00 2.52
1454 1782 0.827368 AACCCTGCTCTAGCTGTAGC 59.173 55.000 13.60 13.60 42.66 3.58
1455 1783 1.472376 GCAACCCTGCTCTAGCTGTAG 60.472 57.143 0.00 0.00 45.74 2.74
1456 1784 0.537188 GCAACCCTGCTCTAGCTGTA 59.463 55.000 0.00 0.00 45.74 2.74
1457 1785 1.298014 GCAACCCTGCTCTAGCTGT 59.702 57.895 0.00 0.00 45.74 4.40
1458 1786 4.215349 GCAACCCTGCTCTAGCTG 57.785 61.111 0.00 2.66 45.74 4.24
1474 1802 1.017177 TTCGACCCATGCGTGTTAGC 61.017 55.000 4.96 0.00 37.71 3.09
1475 1803 1.327460 CATTCGACCCATGCGTGTTAG 59.673 52.381 4.96 0.00 0.00 2.34
1476 1804 1.066787 TCATTCGACCCATGCGTGTTA 60.067 47.619 4.96 0.00 0.00 2.41
1479 1807 1.003545 GATTCATTCGACCCATGCGTG 60.004 52.381 0.00 0.00 0.00 5.34
1592 1955 1.745653 GTTGCTGCCTAGGAAATGGTC 59.254 52.381 14.75 0.00 35.94 4.02
1622 1985 2.373540 ACCAACGCGAATTAGCTACA 57.626 45.000 15.93 0.00 34.40 2.74
1639 2002 6.433716 GGAGTTGGTAGTAGGAGACATATACC 59.566 46.154 0.00 0.00 35.45 2.73
1643 2006 4.231195 TGGGAGTTGGTAGTAGGAGACATA 59.769 45.833 0.00 0.00 0.00 2.29
1658 2021 9.838339 AAGATATATTAGAAACAGTGGGAGTTG 57.162 33.333 0.00 0.00 0.00 3.16
1685 2048 9.635520 GTGCACACTTACTAGTATCTCTAAAAA 57.364 33.333 13.17 0.00 31.96 1.94
1686 2049 7.966753 CGTGCACACTTACTAGTATCTCTAAAA 59.033 37.037 18.64 0.00 31.96 1.52
1687 2050 7.120285 ACGTGCACACTTACTAGTATCTCTAAA 59.880 37.037 18.64 0.00 31.96 1.85
1688 2051 6.596888 ACGTGCACACTTACTAGTATCTCTAA 59.403 38.462 18.64 0.00 31.96 2.10
1689 2052 6.036844 CACGTGCACACTTACTAGTATCTCTA 59.963 42.308 18.64 0.00 31.96 2.43
1690 2053 4.942483 ACGTGCACACTTACTAGTATCTCT 59.058 41.667 18.64 0.00 31.96 3.10
1691 2054 5.029014 CACGTGCACACTTACTAGTATCTC 58.971 45.833 18.64 0.00 31.96 2.75
1692 2055 4.674623 GCACGTGCACACTTACTAGTATCT 60.675 45.833 34.52 0.00 41.59 1.98
1829 2192 9.838339 AGGGAATAAGAGATTGTGTACTTTATG 57.162 33.333 0.00 0.00 0.00 1.90
2043 2410 4.701171 TGGAGTTTGTTACTGAAACGGTTT 59.299 37.500 5.68 5.68 41.30 3.27
2098 2472 5.205056 AGAGGTCTCTTCCTACTATTGTGG 58.795 45.833 0.00 0.00 36.31 4.17
2151 2525 9.554395 CAAGACATCTCTACACTTCTCTATCTA 57.446 37.037 0.00 0.00 0.00 1.98
2303 2677 7.654923 TCTTGAATCATGATCCTTATGACTTCG 59.345 37.037 9.06 0.00 37.38 3.79
2391 2765 7.535599 CACTCTACATTACATACTATGCACGAG 59.464 40.741 0.00 0.00 0.00 4.18
2479 2853 8.581253 AGATGCATGTTGATTATGATGATGAT 57.419 30.769 2.46 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.