Multiple sequence alignment - TraesCS6B01G273000

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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 TraesCS6B01G273000 chr6B 100.000 2805 0 0 1 2805 492496175 492493371 0.000000e+00 5180.0
1 TraesCS6B01G273000 chr6B 96.286 350 12 1 361 710 492504354 492504006 8.720000e-160 573.0
2 TraesCS6B01G273000 chr6B 100.000 147 0 0 708 854 492504501 492504355 3.560000e-69 272.0
3 TraesCS6B01G273000 chr6D 90.752 1276 72 23 708 1964 328631557 328630309 0.000000e+00 1661.0
4 TraesCS6B01G273000 chr6D 87.418 763 66 17 2049 2805 328615150 328614412 0.000000e+00 850.0
5 TraesCS6B01G273000 chr6D 93.939 99 5 1 2573 2670 389141712 389141614 6.260000e-32 148.0
6 TraesCS6B01G273000 chr6D 90.265 113 9 2 2573 2683 439506478 439506366 2.250000e-31 147.0
7 TraesCS6B01G273000 chr6D 95.556 90 4 0 1961 2050 328629807 328629718 8.100000e-31 145.0
8 TraesCS6B01G273000 chr6A 88.343 1201 90 22 963 2132 467490268 467489087 0.000000e+00 1397.0
9 TraesCS6B01G273000 chr6A 89.407 236 14 5 708 941 467490484 467490258 1.270000e-73 287.0
10 TraesCS6B01G273000 chr6A 86.574 216 22 4 2364 2575 467488664 467488452 6.040000e-57 231.0
11 TraesCS6B01G273000 chr6A 92.727 110 7 1 2573 2681 532902361 532902252 1.040000e-34 158.0
12 TraesCS6B01G273000 chr5B 91.311 702 59 2 1 701 20701629 20702329 0.000000e+00 957.0
13 TraesCS6B01G273000 chr5B 100.000 29 0 0 2448 2476 281174157 281174129 1.000000e-03 54.7
14 TraesCS6B01G273000 chr7D 91.964 112 7 2 2560 2669 180531483 180531372 3.740000e-34 156.0
15 TraesCS6B01G273000 chr7D 96.875 32 0 1 2445 2476 409170296 409170326 5.000000e-03 52.8
16 TraesCS6B01G273000 chr3A 96.774 93 3 0 2568 2660 739275014 739275106 3.740000e-34 156.0
17 TraesCS6B01G273000 chr3D 94.000 100 5 1 2570 2668 79532550 79532649 1.740000e-32 150.0
18 TraesCS6B01G273000 chr3B 92.381 105 6 2 2572 2675 417054915 417055018 6.260000e-32 148.0
19 TraesCS6B01G273000 chr3B 89.362 47 3 2 2448 2494 556644701 556644745 1.090000e-04 58.4
20 TraesCS6B01G273000 chr2D 90.991 111 8 2 2564 2673 9906443 9906334 6.260000e-32 148.0
21 TraesCS6B01G273000 chr4B 89.381 113 10 2 2573 2684 28229261 28229372 1.050000e-29 141.0
22 TraesCS6B01G273000 chr7A 93.182 44 1 2 2451 2494 602498093 602498134 2.330000e-06 63.9
23 TraesCS6B01G273000 chr1A 91.304 46 2 1 2449 2494 495674806 495674849 8.390000e-06 62.1
24 TraesCS6B01G273000 chr1A 100.000 28 0 0 2449 2476 570270262 570270235 5.000000e-03 52.8
25 TraesCS6B01G273000 chr4D 100.000 29 0 0 2448 2476 77263543 77263571 1.000000e-03 54.7


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 TraesCS6B01G273000 chr6B 492493371 492496175 2804 True 5180.000000 5180 100.000 1 2805 1 chr6B.!!$R1 2804
1 TraesCS6B01G273000 chr6D 328629718 328631557 1839 True 903.000000 1661 93.154 708 2050 2 chr6D.!!$R4 1342
2 TraesCS6B01G273000 chr6D 328614412 328615150 738 True 850.000000 850 87.418 2049 2805 1 chr6D.!!$R1 756
3 TraesCS6B01G273000 chr6A 467488452 467490484 2032 True 638.333333 1397 88.108 708 2575 3 chr6A.!!$R2 1867
4 TraesCS6B01G273000 chr5B 20701629 20702329 700 False 957.000000 957 91.311 1 701 1 chr5B.!!$F1 700

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
944 947 0.10212 CTCCAAGCTCCGCAGTAGAG 59.898 60.0 0.0 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2759 3527 0.251634 TATGTGCATTCGTCCTGGCA 59.748 50.0 0.0 0.0 0.0 4.92 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
39 40 3.705051 ACCAAGAGATGTGCAAATCCAT 58.295 40.909 13.50 0.00 0.00 3.41
54 55 1.819928 TCCATCCGGTGTTTCATGTG 58.180 50.000 0.00 0.00 0.00 3.21
78 79 2.029649 CCAGCTGAAGAAACACATTGGG 60.030 50.000 17.39 0.00 0.00 4.12
79 80 2.029649 CAGCTGAAGAAACACATTGGGG 60.030 50.000 8.42 0.00 0.00 4.96
84 85 4.144297 TGAAGAAACACATTGGGGAGAAG 58.856 43.478 0.00 0.00 0.00 2.85
85 86 3.884037 AGAAACACATTGGGGAGAAGT 57.116 42.857 0.00 0.00 0.00 3.01
163 164 4.020128 GTCCAGAAGAAGTATTGGAGGTGT 60.020 45.833 0.00 0.00 40.20 4.16
175 176 1.172812 GGAGGTGTGCCAAGTTCCAC 61.173 60.000 0.00 0.00 37.19 4.02
234 235 1.451449 TAAACCTGCCCCCTGAAGAA 58.549 50.000 0.00 0.00 0.00 2.52
240 241 1.228552 GCCCCCTGAAGAAGCAACA 60.229 57.895 0.00 0.00 0.00 3.33
249 250 4.015084 CTGAAGAAGCAACATGGGAAGAT 58.985 43.478 0.00 0.00 0.00 2.40
276 277 7.362401 GCTGACTTCATCAAATACACATTTCCT 60.362 37.037 0.00 0.00 36.69 3.36
279 280 8.048534 ACTTCATCAAATACACATTTCCTGAG 57.951 34.615 0.00 0.00 31.82 3.35
300 301 4.304939 AGTTTTTCAGTACCACTACTCGC 58.695 43.478 0.00 0.00 30.03 5.03
303 304 1.582937 CAGTACCACTACTCGCGCG 60.583 63.158 26.76 26.76 30.03 6.86
318 319 4.704833 GCGTGGAGGGAAGCAGCA 62.705 66.667 0.00 0.00 0.00 4.41
323 324 1.379576 GGAGGGAAGCAGCAGCAAT 60.380 57.895 3.17 0.00 45.49 3.56
324 325 1.664321 GGAGGGAAGCAGCAGCAATG 61.664 60.000 3.17 0.00 45.49 2.82
350 351 0.309922 GGACACGTCGACACTCAAGA 59.690 55.000 17.16 0.00 0.00 3.02
351 352 1.268896 GGACACGTCGACACTCAAGAA 60.269 52.381 17.16 0.00 0.00 2.52
374 375 2.497675 GGAGCAATGTCAGGACTACAGA 59.502 50.000 0.65 0.00 0.00 3.41
386 387 0.531200 ACTACAGAGCAGGGCGTTAC 59.469 55.000 0.00 0.00 0.00 2.50
388 389 1.204941 CTACAGAGCAGGGCGTTACTT 59.795 52.381 0.00 0.00 0.00 2.24
399 400 3.577415 AGGGCGTTACTTCTTCAGTTAGT 59.423 43.478 0.00 0.00 36.88 2.24
407 408 7.148950 CGTTACTTCTTCAGTTAGTTGTAGCTG 60.149 40.741 0.00 0.00 38.51 4.24
411 412 5.297547 TCTTCAGTTAGTTGTAGCTGGTTG 58.702 41.667 0.00 0.00 37.90 3.77
419 420 3.134804 AGTTGTAGCTGGTTGTGAGAGTT 59.865 43.478 0.00 0.00 0.00 3.01
426 427 3.746492 GCTGGTTGTGAGAGTTAACGATT 59.254 43.478 0.00 0.00 0.00 3.34
431 432 6.154445 GGTTGTGAGAGTTAACGATTCAGTA 58.846 40.000 0.00 0.00 0.00 2.74
432 433 6.308282 GGTTGTGAGAGTTAACGATTCAGTAG 59.692 42.308 0.00 0.00 0.00 2.57
436 437 7.120726 TGTGAGAGTTAACGATTCAGTAGATGA 59.879 37.037 0.00 0.00 35.62 2.92
451 452 1.264557 AGATGAACGGTAGAGATCGCG 59.735 52.381 0.00 0.00 29.81 5.87
468 469 2.025418 CGCCTCACGTTACCGCTTT 61.025 57.895 0.00 0.00 37.70 3.51
488 489 1.448893 TCGTAGGCCGTTGGATTGC 60.449 57.895 0.00 0.00 37.94 3.56
498 499 1.880221 CGTTGGATTGCCACTGTACCA 60.880 52.381 0.00 0.00 45.94 3.25
504 505 3.701040 GGATTGCCACTGTACCATTTCAT 59.299 43.478 0.00 0.00 0.00 2.57
506 507 4.782019 TTGCCACTGTACCATTTCATTC 57.218 40.909 0.00 0.00 0.00 2.67
552 553 0.463833 GGGACCGCTTTCCACCTATG 60.464 60.000 3.12 0.00 37.40 2.23
577 579 4.601794 CTGGGTTGTGGCTGGCCA 62.602 66.667 10.55 10.55 45.02 5.36
593 595 4.015084 CTGGCCAAGACATTGAATCTTCT 58.985 43.478 7.01 0.00 38.83 2.85
625 627 5.767665 TGCTGTGAAGGCTAAGAAAACATAA 59.232 36.000 0.00 0.00 0.00 1.90
630 632 7.014230 TGTGAAGGCTAAGAAAACATAAAGCTT 59.986 33.333 0.00 0.00 0.00 3.74
647 649 9.337396 CATAAAGCTTAATACATACACTCCCAA 57.663 33.333 0.00 0.00 0.00 4.12
671 673 1.203125 TGGGCGATTTTCCCCTTTCTT 60.203 47.619 0.00 0.00 43.24 2.52
672 674 1.476891 GGGCGATTTTCCCCTTTCTTC 59.523 52.381 0.00 0.00 38.30 2.87
682 684 2.644798 TCCCCTTTCTTCTTCCCTCAAG 59.355 50.000 0.00 0.00 0.00 3.02
690 692 3.077695 TCTTCTTCCCTCAAGTCCCTAGT 59.922 47.826 0.00 0.00 33.27 2.57
691 693 3.562108 TCTTCCCTCAAGTCCCTAGTT 57.438 47.619 0.00 0.00 33.27 2.24
701 703 2.448453 AGTCCCTAGTTCGTGAAGAGG 58.552 52.381 4.25 4.25 0.00 3.69
702 704 2.041350 AGTCCCTAGTTCGTGAAGAGGA 59.959 50.000 10.65 0.59 30.01 3.71
703 705 2.424246 GTCCCTAGTTCGTGAAGAGGAG 59.576 54.545 10.65 3.70 30.01 3.69
704 706 2.041350 TCCCTAGTTCGTGAAGAGGAGT 59.959 50.000 10.65 0.00 30.01 3.85
705 707 3.265221 TCCCTAGTTCGTGAAGAGGAGTA 59.735 47.826 10.65 0.00 30.01 2.59
706 708 4.079901 TCCCTAGTTCGTGAAGAGGAGTAT 60.080 45.833 10.65 0.00 30.01 2.12
741 743 1.926426 CTCCACTCCATCCCCCAACC 61.926 65.000 0.00 0.00 0.00 3.77
759 762 4.379394 CCAACCGAAATATTCCCGCATATG 60.379 45.833 0.00 0.00 0.00 1.78
782 785 4.256180 GGGATCCCGCATCGCCTT 62.256 66.667 17.02 0.00 38.31 4.35
877 880 4.155733 CGCCATGCCACCGTCCTA 62.156 66.667 0.00 0.00 0.00 2.94
894 897 3.277211 TACGTCAGCCCACTCGCAC 62.277 63.158 0.00 0.00 0.00 5.34
914 917 0.316689 CGGATCGCCATTTAAACGCC 60.317 55.000 0.00 0.00 0.00 5.68
915 918 0.316689 GGATCGCCATTTAAACGCCG 60.317 55.000 0.00 0.00 0.00 6.46
916 919 0.928451 GATCGCCATTTAAACGCCGC 60.928 55.000 0.00 0.00 0.00 6.53
917 920 1.649390 ATCGCCATTTAAACGCCGCA 61.649 50.000 0.00 0.00 0.00 5.69
919 922 1.803922 GCCATTTAAACGCCGCACC 60.804 57.895 0.00 0.00 0.00 5.01
920 923 1.880186 CCATTTAAACGCCGCACCT 59.120 52.632 0.00 0.00 0.00 4.00
922 925 1.336424 CCATTTAAACGCCGCACCTTT 60.336 47.619 0.00 0.00 0.00 3.11
935 938 0.600057 CACCTTTTGCTCCAAGCTCC 59.400 55.000 0.11 0.00 42.97 4.70
936 939 0.890996 ACCTTTTGCTCCAAGCTCCG 60.891 55.000 0.11 0.00 42.97 4.63
937 940 1.211190 CTTTTGCTCCAAGCTCCGC 59.789 57.895 0.11 0.00 42.97 5.54
938 941 1.518056 CTTTTGCTCCAAGCTCCGCA 61.518 55.000 0.11 0.00 42.97 5.69
939 942 1.518056 TTTTGCTCCAAGCTCCGCAG 61.518 55.000 0.11 0.00 42.97 5.18
940 943 2.680974 TTTGCTCCAAGCTCCGCAGT 62.681 55.000 0.11 0.00 42.97 4.40
941 944 1.826340 TTGCTCCAAGCTCCGCAGTA 61.826 55.000 0.11 0.00 42.97 2.74
942 945 1.520342 GCTCCAAGCTCCGCAGTAG 60.520 63.158 0.00 0.00 38.45 2.57
943 946 1.949847 GCTCCAAGCTCCGCAGTAGA 61.950 60.000 0.00 0.00 38.45 2.59
944 947 0.102120 CTCCAAGCTCCGCAGTAGAG 59.898 60.000 0.00 0.00 0.00 2.43
945 948 0.612174 TCCAAGCTCCGCAGTAGAGT 60.612 55.000 0.00 0.00 0.00 3.24
946 949 0.247736 CCAAGCTCCGCAGTAGAGTT 59.752 55.000 0.00 0.00 0.00 3.01
947 950 1.634702 CAAGCTCCGCAGTAGAGTTC 58.365 55.000 0.00 0.00 0.00 3.01
948 951 1.203523 CAAGCTCCGCAGTAGAGTTCT 59.796 52.381 0.00 0.00 0.00 3.01
949 952 1.099689 AGCTCCGCAGTAGAGTTCTC 58.900 55.000 0.00 0.00 0.00 2.87
950 953 0.811915 GCTCCGCAGTAGAGTTCTCA 59.188 55.000 2.64 0.00 0.00 3.27
951 954 1.202582 GCTCCGCAGTAGAGTTCTCAA 59.797 52.381 2.64 0.00 0.00 3.02
952 955 2.352814 GCTCCGCAGTAGAGTTCTCAAA 60.353 50.000 2.64 0.00 0.00 2.69
953 956 3.861131 GCTCCGCAGTAGAGTTCTCAAAA 60.861 47.826 2.64 0.00 0.00 2.44
954 957 4.307432 CTCCGCAGTAGAGTTCTCAAAAA 58.693 43.478 2.64 0.00 0.00 1.94
1081 1101 2.819154 CGATCACCGTGCATGGCA 60.819 61.111 25.30 12.30 35.60 4.92
1089 1109 2.177531 GTGCATGGCAGCGACAAG 59.822 61.111 0.00 0.00 40.08 3.16
1091 1111 2.747460 GCATGGCAGCGACAAGGA 60.747 61.111 0.00 0.00 0.00 3.36
1120 1140 3.872728 TCGTCAGGATCGTCGGCG 61.873 66.667 1.15 1.15 39.92 6.46
1142 1162 4.439968 GAGTACTTCCCCGGTAAGATTTG 58.560 47.826 18.00 0.00 0.00 2.32
1147 1167 3.918294 TCCCCGGTAAGATTTGGTTAG 57.082 47.619 0.00 0.00 0.00 2.34
1155 1182 5.454187 CGGTAAGATTTGGTTAGCCCATAGA 60.454 44.000 0.00 0.00 44.74 1.98
1169 1196 1.133761 CCATAGAGGTCTGGTCTCGGA 60.134 57.143 0.00 0.00 36.45 4.55
1180 1207 2.160205 TGGTCTCGGATCGGATATGTC 58.840 52.381 3.13 0.00 0.00 3.06
1192 1219 1.014352 GATATGTCCGCGCAAAAGGT 58.986 50.000 8.75 0.00 0.00 3.50
1193 1220 1.400494 GATATGTCCGCGCAAAAGGTT 59.600 47.619 8.75 0.00 0.00 3.50
1217 1244 1.153862 CAGGTCTCTGTCTCTGCGC 60.154 63.158 0.00 0.00 36.30 6.09
1506 1533 0.537188 CTTCAGCTCCGGGTATGTGT 59.463 55.000 0.00 0.00 0.00 3.72
1509 1536 2.513897 GCTCCGGGTATGTGTGGC 60.514 66.667 0.00 0.00 0.00 5.01
1576 1605 5.309323 TGTCCGCTGAAATTAAATCTTGG 57.691 39.130 0.00 0.00 0.00 3.61
1579 1608 5.123979 GTCCGCTGAAATTAAATCTTGGACT 59.876 40.000 15.26 0.00 39.18 3.85
1669 1698 2.283966 CTGGAGGTCCCGGAGTGT 60.284 66.667 0.73 0.00 44.44 3.55
1729 1758 1.008767 GGACTACGGAATCGAGGCG 60.009 63.158 0.00 0.00 40.11 5.52
1867 1914 5.539955 AGGCCTCTTGATGTTTGTTTGTAAT 59.460 36.000 0.00 0.00 0.00 1.89
1868 1915 5.863935 GGCCTCTTGATGTTTGTTTGTAATC 59.136 40.000 0.00 0.00 0.00 1.75
1870 1917 6.583806 GCCTCTTGATGTTTGTTTGTAATCTG 59.416 38.462 0.00 0.00 0.00 2.90
1872 1919 8.783093 CCTCTTGATGTTTGTTTGTAATCTGTA 58.217 33.333 0.00 0.00 0.00 2.74
1984 2543 3.184986 GCGTTGTACACCTAAAACACGAT 59.815 43.478 14.68 0.00 0.00 3.73
2064 2623 2.895404 ACGTTAGAGGTTAGAGCCAACA 59.105 45.455 0.00 0.00 0.00 3.33
2104 2663 0.945813 TGCTTTTACCAAACGGACCG 59.054 50.000 13.61 13.61 0.00 4.79
2194 2880 7.824779 AGACAGAAGATGTAAAAGGTTGGTATC 59.175 37.037 0.00 0.00 44.17 2.24
2333 3095 4.500545 CGTTATCAGCAGCAGGATAAGTCT 60.501 45.833 15.93 0.00 36.84 3.24
2358 3120 0.625316 AATGTGCCCTGCATACCAGA 59.375 50.000 0.00 0.00 44.64 3.86
2418 3180 4.338682 CCAGTAGCGGAGTTGAACTACTAT 59.661 45.833 5.94 0.00 42.56 2.12
2422 3184 3.890147 AGCGGAGTTGAACTACTATAGGG 59.110 47.826 5.94 0.00 0.00 3.53
2460 3222 5.163405 TGAGCAAATGTATGTACTCCCTCTC 60.163 44.000 0.00 0.00 0.00 3.20
2477 3239 9.590828 ACTCCCTCTCTAAACTAATATAAGACC 57.409 37.037 0.00 0.00 0.00 3.85
2529 3295 0.694771 ACAGATCATGTGGCACAGGT 59.305 50.000 28.77 17.63 41.91 4.00
2538 3304 1.303236 TGGCACAGGTGTACATGGC 60.303 57.895 12.46 12.46 38.08 4.40
2542 3308 2.213499 GCACAGGTGTACATGGCTATC 58.787 52.381 0.00 0.00 30.95 2.08
2547 3313 4.080356 ACAGGTGTACATGGCTATCAACAT 60.080 41.667 0.00 0.00 30.95 2.71
2585 3351 6.787170 TGTATGTATAATACTCCCTCCGTCT 58.213 40.000 0.00 0.00 0.00 4.18
2593 3359 6.555463 AATACTCCCTCCGTCTCAAAATAA 57.445 37.500 0.00 0.00 0.00 1.40
2594 3360 4.473477 ACTCCCTCCGTCTCAAAATAAG 57.527 45.455 0.00 0.00 0.00 1.73
2595 3361 3.838903 ACTCCCTCCGTCTCAAAATAAGT 59.161 43.478 0.00 0.00 0.00 2.24
2599 3365 4.322801 CCCTCCGTCTCAAAATAAGTGACT 60.323 45.833 0.00 0.00 0.00 3.41
2600 3366 4.865365 CCTCCGTCTCAAAATAAGTGACTC 59.135 45.833 0.00 0.00 0.00 3.36
2601 3367 5.462530 TCCGTCTCAAAATAAGTGACTCA 57.537 39.130 0.00 0.00 0.00 3.41
2602 3368 5.849510 TCCGTCTCAAAATAAGTGACTCAA 58.150 37.500 0.00 0.00 0.00 3.02
2603 3369 5.694910 TCCGTCTCAAAATAAGTGACTCAAC 59.305 40.000 0.00 0.00 0.00 3.18
2604 3370 5.696724 CCGTCTCAAAATAAGTGACTCAACT 59.303 40.000 0.00 0.00 0.00 3.16
2606 3372 7.254795 CCGTCTCAAAATAAGTGACTCAACTTT 60.255 37.037 0.00 0.00 40.77 2.66
2607 3373 7.584123 CGTCTCAAAATAAGTGACTCAACTTTG 59.416 37.037 0.00 0.00 40.77 2.77
2618 3384 9.555727 AAGTGACTCAACTTTGTATTAGCTTTA 57.444 29.630 0.00 0.00 37.05 1.85
2619 3385 9.209175 AGTGACTCAACTTTGTATTAGCTTTAG 57.791 33.333 0.00 0.00 0.00 1.85
2620 3386 8.989980 GTGACTCAACTTTGTATTAGCTTTAGT 58.010 33.333 0.00 0.00 0.00 2.24
2623 3389 9.991906 ACTCAACTTTGTATTAGCTTTAGTACA 57.008 29.630 0.00 0.00 0.00 2.90
2644 3410 9.189723 AGTACAAAATTAGTACAAAGTCGAGTC 57.810 33.333 18.07 0.00 43.24 3.36
2645 3411 8.971321 GTACAAAATTAGTACAAAGTCGAGTCA 58.029 33.333 13.38 0.00 41.08 3.41
2646 3412 7.848491 ACAAAATTAGTACAAAGTCGAGTCAC 58.152 34.615 0.00 0.00 0.00 3.67
2648 3414 8.548721 CAAAATTAGTACAAAGTCGAGTCACTT 58.451 33.333 0.00 3.11 38.30 3.16
2649 3415 9.754382 AAAATTAGTACAAAGTCGAGTCACTTA 57.246 29.630 0.00 0.00 35.45 2.24
2650 3416 9.924650 AAATTAGTACAAAGTCGAGTCACTTAT 57.075 29.630 0.00 0.00 35.45 1.73
2651 3417 9.924650 AATTAGTACAAAGTCGAGTCACTTATT 57.075 29.630 0.00 0.00 35.45 1.40
2652 3418 9.924650 ATTAGTACAAAGTCGAGTCACTTATTT 57.075 29.630 0.00 1.15 35.45 1.40
2653 3419 9.754382 TTAGTACAAAGTCGAGTCACTTATTTT 57.246 29.630 0.00 0.00 35.45 1.82
2655 3421 6.300354 ACAAAGTCGAGTCACTTATTTTGG 57.700 37.500 11.39 0.00 35.45 3.28
2656 3422 5.238650 ACAAAGTCGAGTCACTTATTTTGGG 59.761 40.000 11.39 0.00 35.45 4.12
2657 3423 4.884668 AGTCGAGTCACTTATTTTGGGA 57.115 40.909 0.00 0.00 0.00 4.37
2658 3424 4.566987 AGTCGAGTCACTTATTTTGGGAC 58.433 43.478 0.00 0.00 0.00 4.46
2662 3428 4.566987 GAGTCACTTATTTTGGGACGAGT 58.433 43.478 0.00 0.00 33.84 4.18
2687 3453 5.523369 AGTACTTCAAAGTGAGCAAATTGC 58.477 37.500 10.41 10.41 41.00 3.56
2714 3480 6.578020 TTTGTCGAGTAACAGTAAACACAG 57.422 37.500 0.00 0.00 0.00 3.66
2722 3490 9.953825 CGAGTAACAGTAAACACAGAAATTATC 57.046 33.333 0.00 0.00 0.00 1.75
2724 3492 8.932791 AGTAACAGTAAACACAGAAATTATCCG 58.067 33.333 0.00 0.00 0.00 4.18
2733 3501 3.885297 ACAGAAATTATCCGAGCAATGGG 59.115 43.478 0.00 0.00 0.00 4.00
2750 3518 5.533903 GCAATGGGTATGAGTCTGAATCAAT 59.466 40.000 12.12 3.99 0.00 2.57
2751 3519 6.040166 GCAATGGGTATGAGTCTGAATCAATT 59.960 38.462 12.12 4.25 0.00 2.32
2752 3520 7.417116 GCAATGGGTATGAGTCTGAATCAATTT 60.417 37.037 12.12 0.00 0.00 1.82
2753 3521 7.578310 ATGGGTATGAGTCTGAATCAATTTG 57.422 36.000 12.12 0.00 0.00 2.32
2754 3522 5.887598 TGGGTATGAGTCTGAATCAATTTGG 59.112 40.000 12.12 0.00 0.00 3.28
2755 3523 6.122277 GGGTATGAGTCTGAATCAATTTGGA 58.878 40.000 12.12 0.00 0.00 3.53
2756 3524 6.261826 GGGTATGAGTCTGAATCAATTTGGAG 59.738 42.308 12.12 0.00 0.00 3.86
2757 3525 5.831702 ATGAGTCTGAATCAATTTGGAGC 57.168 39.130 12.12 0.00 0.00 4.70
2758 3526 4.914983 TGAGTCTGAATCAATTTGGAGCT 58.085 39.130 5.19 0.00 0.00 4.09
2759 3527 5.319453 TGAGTCTGAATCAATTTGGAGCTT 58.681 37.500 5.19 0.00 0.00 3.74
2764 3532 3.056393 TGAATCAATTTGGAGCTTGCCAG 60.056 43.478 0.00 0.00 39.52 4.85
2781 3549 3.138304 GCCAGGACGAATGCACATAATA 58.862 45.455 0.00 0.00 0.00 0.98
2786 3554 6.818142 CCAGGACGAATGCACATAATATGATA 59.182 38.462 7.33 0.00 0.00 2.15
2791 3559 9.877137 GACGAATGCACATAATATGATAACAAA 57.123 29.630 7.33 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.264253 TGGATTTGCACATCTCTTGGTAG 58.736 43.478 12.39 0.00 0.00 3.18
39 40 0.605319 GGCTCACATGAAACACCGGA 60.605 55.000 9.46 0.00 0.00 5.14
54 55 1.597742 TGTGTTTCTTCAGCTGGCTC 58.402 50.000 15.13 0.00 0.00 4.70
78 79 3.375699 TGGGTCAGGAATAGACTTCTCC 58.624 50.000 0.00 0.00 36.29 3.71
79 80 5.179533 GTTTGGGTCAGGAATAGACTTCTC 58.820 45.833 0.00 0.00 36.29 2.87
84 85 4.383880 GGTAGGTTTGGGTCAGGAATAGAC 60.384 50.000 0.00 0.00 35.29 2.59
85 86 3.778629 GGTAGGTTTGGGTCAGGAATAGA 59.221 47.826 0.00 0.00 0.00 1.98
163 164 0.179234 TTCTGTCGTGGAACTTGGCA 59.821 50.000 0.00 0.00 31.75 4.92
171 172 2.492088 CACTGGTAGATTCTGTCGTGGA 59.508 50.000 0.00 0.00 0.00 4.02
175 176 3.442625 TGTACCACTGGTAGATTCTGTCG 59.557 47.826 8.29 0.00 39.02 4.35
234 235 1.005097 TCAGCATCTTCCCATGTTGCT 59.995 47.619 0.00 0.00 44.05 3.91
240 241 3.201487 TGATGAAGTCAGCATCTTCCCAT 59.799 43.478 0.00 0.00 42.00 4.00
249 250 6.822667 AATGTGTATTTGATGAAGTCAGCA 57.177 33.333 0.00 0.00 40.88 4.41
276 277 5.526115 CGAGTAGTGGTACTGAAAAACTCA 58.474 41.667 8.63 0.00 39.78 3.41
279 280 3.120782 CGCGAGTAGTGGTACTGAAAAAC 59.879 47.826 0.00 0.00 39.78 2.43
288 289 2.481919 CACGCGCGAGTAGTGGTA 59.518 61.111 39.36 0.00 37.90 3.25
303 304 2.749441 GCTGCTGCTTCCCTCCAC 60.749 66.667 8.53 0.00 36.03 4.02
307 308 2.348888 GCATTGCTGCTGCTTCCCT 61.349 57.895 17.00 0.00 45.32 4.20
318 319 1.672356 GTGTCCTCACGGCATTGCT 60.672 57.895 8.82 0.00 34.79 3.91
350 351 1.366319 AGTCCTGACATTGCTCCCTT 58.634 50.000 0.00 0.00 0.00 3.95
351 352 1.834263 GTAGTCCTGACATTGCTCCCT 59.166 52.381 0.00 0.00 0.00 4.20
374 375 0.685097 TGAAGAAGTAACGCCCTGCT 59.315 50.000 0.00 0.00 0.00 4.24
386 387 5.542779 ACCAGCTACAACTAACTGAAGAAG 58.457 41.667 0.00 0.00 31.67 2.85
388 389 5.163343 ACAACCAGCTACAACTAACTGAAGA 60.163 40.000 0.00 0.00 31.67 2.87
399 400 3.838244 AACTCTCACAACCAGCTACAA 57.162 42.857 0.00 0.00 0.00 2.41
407 408 4.989168 ACTGAATCGTTAACTCTCACAACC 59.011 41.667 3.71 0.00 0.00 3.77
411 412 7.473366 TCATCTACTGAATCGTTAACTCTCAC 58.527 38.462 3.71 0.00 0.00 3.51
419 420 5.571784 ACCGTTCATCTACTGAATCGTTA 57.428 39.130 0.00 0.00 45.36 3.18
426 427 4.750598 CGATCTCTACCGTTCATCTACTGA 59.249 45.833 0.00 0.00 0.00 3.41
431 432 1.264557 CGCGATCTCTACCGTTCATCT 59.735 52.381 0.00 0.00 0.00 2.90
432 433 1.676057 CGCGATCTCTACCGTTCATC 58.324 55.000 0.00 0.00 0.00 2.92
436 437 2.061182 GAGGCGCGATCTCTACCGTT 62.061 60.000 12.10 0.00 0.00 4.44
442 443 1.374343 TAACGTGAGGCGCGATCTCT 61.374 55.000 23.50 10.47 46.11 3.10
443 444 1.063649 TAACGTGAGGCGCGATCTC 59.936 57.895 12.10 16.55 46.11 2.75
458 459 0.717784 GCCTACGACAAAGCGGTAAC 59.282 55.000 0.00 0.00 35.12 2.50
498 499 9.659830 GTGAAAAGTAACAGTAACGAATGAAAT 57.340 29.630 0.00 0.00 0.00 2.17
504 505 4.507388 CGGGTGAAAAGTAACAGTAACGAA 59.493 41.667 0.00 0.00 0.00 3.85
506 507 3.803778 ACGGGTGAAAAGTAACAGTAACG 59.196 43.478 0.00 0.00 0.00 3.18
537 538 1.668419 CCTTCATAGGTGGAAAGCGG 58.332 55.000 0.00 0.00 36.74 5.52
552 553 2.270986 CCACAACCCAGCTGCCTTC 61.271 63.158 8.66 0.00 0.00 3.46
577 579 8.411683 GCAATTCCATAGAAGATTCAATGTCTT 58.588 33.333 0.00 0.00 38.57 3.01
578 580 7.778853 AGCAATTCCATAGAAGATTCAATGTCT 59.221 33.333 0.00 0.00 34.86 3.41
593 595 3.370840 AGCCTTCACAGCAATTCCATA 57.629 42.857 0.00 0.00 0.00 2.74
625 627 8.275040 AGATTTGGGAGTGTATGTATTAAGCTT 58.725 33.333 3.48 3.48 0.00 3.74
671 673 3.442076 GAACTAGGGACTTGAGGGAAGA 58.558 50.000 0.00 0.00 41.75 2.87
672 674 2.166664 CGAACTAGGGACTTGAGGGAAG 59.833 54.545 0.00 0.00 41.75 3.46
682 684 2.424246 CTCCTCTTCACGAACTAGGGAC 59.576 54.545 0.00 0.00 0.00 4.46
690 692 1.134367 CGCCATACTCCTCTTCACGAA 59.866 52.381 0.00 0.00 0.00 3.85
691 693 0.738975 CGCCATACTCCTCTTCACGA 59.261 55.000 0.00 0.00 0.00 4.35
721 723 2.308722 TTGGGGGATGGAGTGGAGC 61.309 63.158 0.00 0.00 0.00 4.70
877 880 4.664677 GTGCGAGTGGGCTGACGT 62.665 66.667 0.00 0.00 0.00 4.34
894 897 0.316689 GCGTTTAAATGGCGATCCGG 60.317 55.000 9.42 0.00 34.14 5.14
916 919 0.600057 GGAGCTTGGAGCAAAAGGTG 59.400 55.000 2.47 0.00 45.56 4.00
917 920 0.890996 CGGAGCTTGGAGCAAAAGGT 60.891 55.000 2.47 0.00 45.56 3.50
932 935 3.577649 TTTGAGAACTCTACTGCGGAG 57.422 47.619 0.85 0.85 36.92 4.63
933 936 4.330944 TTTTTGAGAACTCTACTGCGGA 57.669 40.909 0.00 0.00 0.00 5.54
953 956 5.737349 GCCTAACTGCAGAGCTTTTCTTTTT 60.737 40.000 23.35 1.57 32.41 1.94
954 957 4.261783 GCCTAACTGCAGAGCTTTTCTTTT 60.262 41.667 23.35 2.14 32.41 2.27
955 958 3.254411 GCCTAACTGCAGAGCTTTTCTTT 59.746 43.478 23.35 2.95 32.41 2.52
956 959 2.816672 GCCTAACTGCAGAGCTTTTCTT 59.183 45.455 23.35 3.76 32.41 2.52
957 960 2.431454 GCCTAACTGCAGAGCTTTTCT 58.569 47.619 23.35 0.00 36.25 2.52
958 961 1.129437 CGCCTAACTGCAGAGCTTTTC 59.871 52.381 23.35 2.08 0.00 2.29
959 962 1.160137 CGCCTAACTGCAGAGCTTTT 58.840 50.000 23.35 6.20 0.00 2.27
960 963 1.301677 GCGCCTAACTGCAGAGCTTT 61.302 55.000 23.35 6.63 0.00 3.51
961 964 1.743252 GCGCCTAACTGCAGAGCTT 60.743 57.895 23.35 7.04 0.00 3.74
1077 1097 4.020617 CCCTCCTTGTCGCTGCCA 62.021 66.667 0.00 0.00 0.00 4.92
1120 1140 4.439968 CAAATCTTACCGGGGAAGTACTC 58.560 47.826 18.45 0.00 0.00 2.59
1147 1167 1.044611 GAGACCAGACCTCTATGGGC 58.955 60.000 0.00 0.00 45.77 5.36
1155 1182 1.454111 CCGATCCGAGACCAGACCT 60.454 63.158 0.00 0.00 0.00 3.85
1180 1207 0.110373 GTCAGTAACCTTTTGCGCGG 60.110 55.000 8.83 0.00 0.00 6.46
1301 1328 2.908940 ACGACCACGAACTCCCGT 60.909 61.111 0.00 0.00 44.43 5.28
1316 1343 0.802222 CGAGGGAGTGCATGTACACG 60.802 60.000 16.62 9.28 45.45 4.49
1379 1406 4.436998 GGCAGGCACTCGTACGCT 62.437 66.667 11.24 0.00 34.60 5.07
1576 1605 2.433868 TCTCGTACAACCTGCAAGTC 57.566 50.000 0.00 0.00 0.00 3.01
1579 1608 1.070134 AGCTTCTCGTACAACCTGCAA 59.930 47.619 0.00 0.00 0.00 4.08
1795 1824 4.096003 GGTGCCCGCTAGGAGCAA 62.096 66.667 0.00 0.00 42.58 3.91
1837 1884 3.439857 AACATCAAGAGGCCTGCTAAA 57.560 42.857 12.00 0.00 0.00 1.85
1984 2543 2.187100 TCAGCACCCACAGACATGATA 58.813 47.619 0.00 0.00 0.00 2.15
2038 2597 3.695556 GGCTCTAACCTCTAACGTCTCTT 59.304 47.826 0.00 0.00 0.00 2.85
2064 2623 7.961326 AGCATAATATGTTTTCCAGTTTCCT 57.039 32.000 1.92 0.00 0.00 3.36
2124 2683 5.156804 TCAAAGAACAAACTCTCTTTCGC 57.843 39.130 0.00 0.00 39.34 4.70
2333 3095 2.512692 ATGCAGGGCACATTCTGTTA 57.487 45.000 0.00 0.00 43.04 2.41
2346 3108 2.034124 CCCCAATTTCTGGTATGCAGG 58.966 52.381 0.00 0.00 44.76 4.85
2358 3120 0.856982 TGGTGTCCTGACCCCAATTT 59.143 50.000 0.00 0.00 35.91 1.82
2388 3150 0.834687 ACTCCGCTACTGGTTCCCAA 60.835 55.000 0.00 0.00 30.80 4.12
2418 3180 4.020928 TGCTCACTTTGTCGTATTTCCCTA 60.021 41.667 0.00 0.00 0.00 3.53
2422 3184 6.142817 ACATTTGCTCACTTTGTCGTATTTC 58.857 36.000 0.00 0.00 0.00 2.17
2476 3238 4.455606 CTGCCTTAGTGATCTAAAAGGGG 58.544 47.826 16.99 4.01 35.98 4.79
2477 3239 4.455606 CCTGCCTTAGTGATCTAAAAGGG 58.544 47.826 16.99 5.26 35.98 3.95
2494 3256 2.198304 CTGTTGGTACTCCCCCTGCC 62.198 65.000 0.00 0.00 0.00 4.85
2529 3295 9.845740 AACTTATTATGTTGATAGCCATGTACA 57.154 29.630 0.00 0.00 0.00 2.90
2575 3341 3.835978 TCACTTATTTTGAGACGGAGGGA 59.164 43.478 0.00 0.00 0.00 4.20
2593 3359 9.209175 CTAAAGCTAATACAAAGTTGAGTCACT 57.791 33.333 0.00 0.00 0.00 3.41
2594 3360 8.989980 ACTAAAGCTAATACAAAGTTGAGTCAC 58.010 33.333 0.00 0.00 0.00 3.67
2618 3384 9.189723 GACTCGACTTTGTACTAATTTTGTACT 57.810 33.333 17.79 2.73 40.44 2.73
2619 3385 8.971321 TGACTCGACTTTGTACTAATTTTGTAC 58.029 33.333 12.39 12.39 40.27 2.90
2620 3386 8.971321 GTGACTCGACTTTGTACTAATTTTGTA 58.029 33.333 0.00 0.00 0.00 2.41
2623 3389 8.658499 AAGTGACTCGACTTTGTACTAATTTT 57.342 30.769 0.00 0.00 31.92 1.82
2625 3391 9.924650 AATAAGTGACTCGACTTTGTACTAATT 57.075 29.630 0.00 0.00 37.38 1.40
2626 3392 9.924650 AAATAAGTGACTCGACTTTGTACTAAT 57.075 29.630 0.00 0.00 37.38 1.73
2627 3393 9.754382 AAAATAAGTGACTCGACTTTGTACTAA 57.246 29.630 0.00 0.00 37.38 2.24
2629 3395 7.170998 CCAAAATAAGTGACTCGACTTTGTACT 59.829 37.037 0.00 0.00 37.38 2.73
2630 3396 7.288672 CCAAAATAAGTGACTCGACTTTGTAC 58.711 38.462 0.00 0.00 37.38 2.90
2631 3397 6.425721 CCCAAAATAAGTGACTCGACTTTGTA 59.574 38.462 0.00 0.00 37.38 2.41
2633 3399 5.468746 TCCCAAAATAAGTGACTCGACTTTG 59.531 40.000 0.00 0.00 37.38 2.77
2636 3402 4.566987 GTCCCAAAATAAGTGACTCGACT 58.433 43.478 0.00 0.00 0.00 4.18
2638 3404 3.256383 TCGTCCCAAAATAAGTGACTCGA 59.744 43.478 0.00 0.00 0.00 4.04
2640 3406 4.389077 CACTCGTCCCAAAATAAGTGACTC 59.611 45.833 0.00 0.00 36.99 3.36
2641 3407 4.039973 TCACTCGTCCCAAAATAAGTGACT 59.960 41.667 0.00 0.00 38.47 3.41
2642 3408 4.312443 TCACTCGTCCCAAAATAAGTGAC 58.688 43.478 0.00 0.00 38.47 3.67
2643 3409 4.039973 ACTCACTCGTCCCAAAATAAGTGA 59.960 41.667 0.00 0.00 40.42 3.41
2644 3410 4.315803 ACTCACTCGTCCCAAAATAAGTG 58.684 43.478 0.00 0.00 36.36 3.16
2645 3411 4.618920 ACTCACTCGTCCCAAAATAAGT 57.381 40.909 0.00 0.00 0.00 2.24
2646 3412 5.721232 AGTACTCACTCGTCCCAAAATAAG 58.279 41.667 0.00 0.00 0.00 1.73
2648 3414 5.244402 TGAAGTACTCACTCGTCCCAAAATA 59.756 40.000 0.00 0.00 32.29 1.40
2649 3415 4.039973 TGAAGTACTCACTCGTCCCAAAAT 59.960 41.667 0.00 0.00 32.29 1.82
2650 3416 3.385433 TGAAGTACTCACTCGTCCCAAAA 59.615 43.478 0.00 0.00 32.29 2.44
2651 3417 2.960384 TGAAGTACTCACTCGTCCCAAA 59.040 45.455 0.00 0.00 32.29 3.28
2652 3418 2.589720 TGAAGTACTCACTCGTCCCAA 58.410 47.619 0.00 0.00 32.29 4.12
2653 3419 2.281539 TGAAGTACTCACTCGTCCCA 57.718 50.000 0.00 0.00 32.29 4.37
2655 3421 3.982058 CACTTTGAAGTACTCACTCGTCC 59.018 47.826 0.00 0.00 37.08 4.79
2656 3422 4.856664 TCACTTTGAAGTACTCACTCGTC 58.143 43.478 0.00 0.00 37.08 4.20
2657 3423 4.793353 GCTCACTTTGAAGTACTCACTCGT 60.793 45.833 0.00 0.00 37.08 4.18
2658 3424 3.670991 GCTCACTTTGAAGTACTCACTCG 59.329 47.826 0.00 0.00 37.08 4.18
2662 3428 6.728200 CAATTTGCTCACTTTGAAGTACTCA 58.272 36.000 0.00 0.00 37.08 3.41
2687 3453 6.844279 GTGTTTACTGTTACTCGACAAATGTG 59.156 38.462 0.00 0.00 0.00 3.21
2714 3480 5.705441 TCATACCCATTGCTCGGATAATTTC 59.295 40.000 0.00 0.00 0.00 2.17
2722 3490 1.414181 AGACTCATACCCATTGCTCGG 59.586 52.381 0.00 0.00 0.00 4.63
2724 3492 3.827008 TCAGACTCATACCCATTGCTC 57.173 47.619 0.00 0.00 0.00 4.26
2733 3501 6.541641 AGCTCCAAATTGATTCAGACTCATAC 59.458 38.462 0.00 0.00 0.00 2.39
2750 3518 1.600636 CGTCCTGGCAAGCTCCAAA 60.601 57.895 0.00 0.00 35.36 3.28
2751 3519 2.032528 CGTCCTGGCAAGCTCCAA 59.967 61.111 0.00 0.00 35.36 3.53
2752 3520 1.841302 ATTCGTCCTGGCAAGCTCCA 61.841 55.000 0.00 0.00 34.42 3.86
2753 3521 1.078143 ATTCGTCCTGGCAAGCTCC 60.078 57.895 0.00 0.00 0.00 4.70
2754 3522 1.986575 GCATTCGTCCTGGCAAGCTC 61.987 60.000 0.00 0.00 0.00 4.09
2755 3523 2.042831 GCATTCGTCCTGGCAAGCT 61.043 57.895 0.00 0.00 0.00 3.74
2756 3524 2.334946 TGCATTCGTCCTGGCAAGC 61.335 57.895 0.00 0.00 32.54 4.01
2757 3525 1.236616 TGTGCATTCGTCCTGGCAAG 61.237 55.000 0.00 0.00 38.10 4.01
2758 3526 0.608856 ATGTGCATTCGTCCTGGCAA 60.609 50.000 0.00 0.00 38.10 4.52
2759 3527 0.251634 TATGTGCATTCGTCCTGGCA 59.748 50.000 0.00 0.00 0.00 4.92
2764 3532 8.028540 TGTTATCATATTATGTGCATTCGTCC 57.971 34.615 3.67 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.