Multiple sequence alignment - TraesCS7A01G021200

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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 TraesCS7A01G021200 chr7A 100.000 4217 0 0 1 4217 8652799 8657015 0.000000e+00 7788.0
1 TraesCS7A01G021200 chr7A 82.385 3338 511 50 909 4217 56204883 56208172 0.000000e+00 2835.0
2 TraesCS7A01G021200 chr7A 81.951 3352 507 65 907 4217 8634296 8637590 0.000000e+00 2748.0
3 TraesCS7A01G021200 chr7A 85.134 1796 241 19 905 2693 8695097 8693321 0.000000e+00 1814.0
4 TraesCS7A01G021200 chr7A 83.555 1502 217 16 2692 4171 3430317 3428824 0.000000e+00 1378.0
5 TraesCS7A01G021200 chr7A 82.687 1548 233 13 2695 4217 8693283 8691746 0.000000e+00 1341.0
6 TraesCS7A01G021200 chr7A 79.968 619 59 38 87 672 8633550 8634136 3.060000e-106 396.0
7 TraesCS7A01G021200 chr7A 96.639 119 3 1 498 616 8653256 8653373 3.330000e-46 196.0
8 TraesCS7A01G021200 chr7A 96.639 119 3 1 458 575 8653296 8653414 3.330000e-46 196.0
9 TraesCS7A01G021200 chr7A 94.937 79 3 1 539 617 8653256 8653333 5.730000e-24 122.0
10 TraesCS7A01G021200 chr7A 94.937 79 3 1 458 535 8653337 8653415 5.730000e-24 122.0
11 TraesCS7A01G021200 chr7D 92.322 3764 208 31 502 4217 7596852 7600582 0.000000e+00 5275.0
12 TraesCS7A01G021200 chr7D 86.298 3233 392 31 964 4164 8177062 8180275 0.000000e+00 3469.0
13 TraesCS7A01G021200 chr7D 86.325 3159 393 25 1077 4217 7606298 7609435 0.000000e+00 3404.0
14 TraesCS7A01G021200 chr7D 84.694 3332 456 38 912 4217 7712562 7715865 0.000000e+00 3278.0
15 TraesCS7A01G021200 chr7D 85.243 3029 406 20 793 3802 7749863 7752869 0.000000e+00 3079.0
16 TraesCS7A01G021200 chr7D 85.802 1796 229 19 905 2693 8256070 8254294 0.000000e+00 1881.0
17 TraesCS7A01G021200 chr7D 86.275 1479 174 11 605 2061 7637396 7638867 0.000000e+00 1580.0
18 TraesCS7A01G021200 chr7D 83.225 1544 237 10 2695 4217 8254256 8252714 0.000000e+00 1397.0
19 TraesCS7A01G021200 chr7D 92.212 321 18 3 220 533 7637021 7637341 8.320000e-122 448.0
20 TraesCS7A01G021200 chr7D 81.099 619 53 35 87 672 8073313 8073900 1.800000e-118 436.0
21 TraesCS7A01G021200 chr7D 77.658 743 92 44 87 788 7711757 7712466 6.610000e-103 385.0
22 TraesCS7A01G021200 chr7D 86.590 261 16 9 87 341 7596514 7596761 1.930000e-68 270.0
23 TraesCS7A01G021200 chr7D 95.210 167 7 1 371 536 7596761 7596927 3.230000e-66 263.0
24 TraesCS7A01G021200 chr7D 80.475 379 27 18 202 533 8084694 8085072 3.260000e-61 246.0
25 TraesCS7A01G021200 chr7D 96.471 85 3 0 549 633 7712169 7712253 1.580000e-29 141.0
26 TraesCS7A01G021200 chr7D 91.753 97 8 0 543 639 7596852 7596948 7.350000e-28 135.0
27 TraesCS7A01G021200 chr7D 81.457 151 23 3 151 296 7749277 7749427 7.410000e-23 119.0
28 TraesCS7A01G021200 chr7D 92.405 79 5 1 539 617 8073724 8073801 1.240000e-20 111.0
29 TraesCS7A01G021200 chr7D 94.737 38 1 1 580 617 8073724 8073760 1.640000e-04 58.4
30 TraesCS7A01G021200 chr4A 84.847 3458 465 36 801 4217 731761386 731757947 0.000000e+00 3428.0
31 TraesCS7A01G021200 chr4A 85.015 3023 395 37 800 3790 731875554 731872558 0.000000e+00 3020.0
32 TraesCS7A01G021200 chr4A 81.082 3346 541 58 909 4217 732354799 732358089 0.000000e+00 2588.0
33 TraesCS7A01G021200 chr4A 85.432 1922 256 18 793 2709 731774481 731772579 0.000000e+00 1977.0
34 TraesCS7A01G021200 chr4A 84.727 1794 258 14 909 2693 731861826 731860040 0.000000e+00 1781.0
35 TraesCS7A01G021200 chr4A 82.460 1545 241 18 2692 4217 732379855 732381388 0.000000e+00 1325.0
36 TraesCS7A01G021200 chr4A 84.089 1081 143 23 2143 3215 732328682 732329741 0.000000e+00 1016.0
37 TraesCS7A01G021200 chr4A 76.957 690 80 38 152 788 731862569 731861906 1.890000e-83 320.0
38 TraesCS7A01G021200 chr4A 94.624 93 5 0 545 637 731862204 731862112 1.220000e-30 145.0
39 TraesCS7A01G021200 chr4A 100.000 49 0 0 1 49 702155633 702155681 1.610000e-14 91.6
40 TraesCS7A01G021200 chr3B 81.988 1549 253 14 2692 4217 741464962 741466507 0.000000e+00 1291.0
41 TraesCS7A01G021200 chrUn 97.959 49 1 0 1 49 330894000 330894048 7.510000e-13 86.1
42 TraesCS7A01G021200 chr1D 96.154 52 2 0 1 52 21861429 21861378 7.510000e-13 86.1
43 TraesCS7A01G021200 chr5D 94.231 52 3 0 1 52 464648360 464648309 3.500000e-11 80.5


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 TraesCS7A01G021200 chr7A 8652799 8657015 4216 False 1684.800000 7788 96.630400 1 4217 5 chr7A.!!$F3 4216
1 TraesCS7A01G021200 chr7A 56204883 56208172 3289 False 2835.000000 2835 82.385000 909 4217 1 chr7A.!!$F1 3308
2 TraesCS7A01G021200 chr7A 8691746 8695097 3351 True 1577.500000 1814 83.910500 905 4217 2 chr7A.!!$R2 3312
3 TraesCS7A01G021200 chr7A 8633550 8637590 4040 False 1572.000000 2748 80.959500 87 4217 2 chr7A.!!$F2 4130
4 TraesCS7A01G021200 chr7A 3428824 3430317 1493 True 1378.000000 1378 83.555000 2692 4171 1 chr7A.!!$R1 1479
5 TraesCS7A01G021200 chr7D 8177062 8180275 3213 False 3469.000000 3469 86.298000 964 4164 1 chr7D.!!$F3 3200
6 TraesCS7A01G021200 chr7D 7606298 7609435 3137 False 3404.000000 3404 86.325000 1077 4217 1 chr7D.!!$F1 3140
7 TraesCS7A01G021200 chr7D 8252714 8256070 3356 True 1639.000000 1881 84.513500 905 4217 2 chr7D.!!$R1 3312
8 TraesCS7A01G021200 chr7D 7749277 7752869 3592 False 1599.000000 3079 83.350000 151 3802 2 chr7D.!!$F7 3651
9 TraesCS7A01G021200 chr7D 7596514 7600582 4068 False 1485.750000 5275 91.468750 87 4217 4 chr7D.!!$F4 4130
10 TraesCS7A01G021200 chr7D 7711757 7715865 4108 False 1268.000000 3278 86.274333 87 4217 3 chr7D.!!$F6 4130
11 TraesCS7A01G021200 chr7D 7637021 7638867 1846 False 1014.000000 1580 89.243500 220 2061 2 chr7D.!!$F5 1841
12 TraesCS7A01G021200 chr7D 8073313 8073900 587 False 201.800000 436 89.413667 87 672 3 chr7D.!!$F8 585
13 TraesCS7A01G021200 chr4A 731757947 731761386 3439 True 3428.000000 3428 84.847000 801 4217 1 chr4A.!!$R1 3416
14 TraesCS7A01G021200 chr4A 731872558 731875554 2996 True 3020.000000 3020 85.015000 800 3790 1 chr4A.!!$R3 2990
15 TraesCS7A01G021200 chr4A 732354799 732358089 3290 False 2588.000000 2588 81.082000 909 4217 1 chr4A.!!$F3 3308
16 TraesCS7A01G021200 chr4A 731772579 731774481 1902 True 1977.000000 1977 85.432000 793 2709 1 chr4A.!!$R2 1916
17 TraesCS7A01G021200 chr4A 732379855 732381388 1533 False 1325.000000 1325 82.460000 2692 4217 1 chr4A.!!$F4 1525
18 TraesCS7A01G021200 chr4A 732328682 732329741 1059 False 1016.000000 1016 84.089000 2143 3215 1 chr4A.!!$F2 1072
19 TraesCS7A01G021200 chr4A 731860040 731862569 2529 True 748.666667 1781 85.436000 152 2693 3 chr4A.!!$R4 2541
20 TraesCS7A01G021200 chr3B 741464962 741466507 1545 False 1291.000000 1291 81.988000 2692 4217 1 chr3B.!!$F1 1525

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
780 1005 0.032540 GCCCTGGACTTGTTTTGCTG 59.967 55.0 0.00 0.0 0.00 4.41 F
1436 1837 0.035915 GGCTTGGAGAGTTCTGTCCC 60.036 60.0 12.41 0.0 31.04 4.46 F
1902 2304 0.462937 TGTGTTCTGTTGGTGGACCG 60.463 55.0 0.00 0.0 39.43 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2564 2978 0.601046 TGCTTTCTGCGGAGTCAGTG 60.601 55.000 3.1 0.0 46.63 3.66 R
2721 3177 3.016736 TGCTCTCAGTGATGTCGATACA 58.983 45.455 0.0 0.0 40.69 2.29 R
3669 4172 1.006832 CCCAACTATTCGCAACTCGG 58.993 55.000 0.0 0.0 39.05 4.63 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
26 27 3.339253 CATCGATATCCTTGATGCCCA 57.661 47.619 0.00 0.00 38.61 5.36
27 28 3.268330 CATCGATATCCTTGATGCCCAG 58.732 50.000 0.00 0.00 38.61 4.45
28 29 1.625315 TCGATATCCTTGATGCCCAGG 59.375 52.381 0.00 0.00 0.00 4.45
29 30 1.831580 GATATCCTTGATGCCCAGGC 58.168 55.000 0.38 0.38 42.35 4.85
30 31 0.407139 ATATCCTTGATGCCCAGGCC 59.593 55.000 6.14 0.00 41.09 5.19
31 32 0.992970 TATCCTTGATGCCCAGGCCA 60.993 55.000 5.01 0.00 41.09 5.36
32 33 2.578586 ATCCTTGATGCCCAGGCCAC 62.579 60.000 5.01 0.71 41.09 5.01
33 34 2.757099 CTTGATGCCCAGGCCACC 60.757 66.667 5.01 0.00 41.09 4.61
34 35 4.380945 TTGATGCCCAGGCCACCC 62.381 66.667 5.01 0.00 41.09 4.61
41 42 4.028490 CCAGGCCACCCACGCTTA 62.028 66.667 5.01 0.00 0.00 3.09
42 43 2.033448 CAGGCCACCCACGCTTAA 59.967 61.111 5.01 0.00 0.00 1.85
43 44 1.602323 CAGGCCACCCACGCTTAAA 60.602 57.895 5.01 0.00 0.00 1.52
44 45 1.303317 AGGCCACCCACGCTTAAAG 60.303 57.895 5.01 0.00 0.00 1.85
45 46 2.340328 GGCCACCCACGCTTAAAGG 61.340 63.158 0.00 0.00 0.00 3.11
46 47 1.602605 GCCACCCACGCTTAAAGGT 60.603 57.895 0.00 0.00 0.00 3.50
48 49 1.579429 CACCCACGCTTAAAGGTGC 59.421 57.895 0.00 0.00 43.02 5.01
49 50 1.602605 ACCCACGCTTAAAGGTGCC 60.603 57.895 1.05 0.00 32.85 5.01
50 51 2.340328 CCCACGCTTAAAGGTGCCC 61.340 63.158 1.05 0.00 32.85 5.36
51 52 1.602323 CCACGCTTAAAGGTGCCCA 60.602 57.895 1.05 0.00 32.85 5.36
52 53 1.579429 CACGCTTAAAGGTGCCCAC 59.421 57.895 0.00 0.00 0.00 4.61
53 54 1.964373 ACGCTTAAAGGTGCCCACG 60.964 57.895 0.00 0.00 0.00 4.94
54 55 1.964373 CGCTTAAAGGTGCCCACGT 60.964 57.895 0.00 0.00 0.00 4.49
55 56 1.512156 CGCTTAAAGGTGCCCACGTT 61.512 55.000 0.90 0.90 40.65 3.99
56 57 0.671796 GCTTAAAGGTGCCCACGTTT 59.328 50.000 19.03 19.03 46.82 3.60
57 58 1.067974 GCTTAAAGGTGCCCACGTTTT 59.932 47.619 19.90 12.30 44.07 2.43
58 59 2.860971 GCTTAAAGGTGCCCACGTTTTC 60.861 50.000 19.90 9.51 44.07 2.29
59 60 0.945813 TAAAGGTGCCCACGTTTTCG 59.054 50.000 19.90 0.00 44.07 3.46
69 70 4.935630 CGTTTTCGTTTGGCCCTC 57.064 55.556 0.00 0.00 38.65 4.30
70 71 1.082366 CGTTTTCGTTTGGCCCTCG 60.082 57.895 0.00 2.18 38.65 4.63
71 72 1.284715 GTTTTCGTTTGGCCCTCGG 59.715 57.895 0.00 0.00 0.00 4.63
72 73 1.148723 TTTTCGTTTGGCCCTCGGA 59.851 52.632 0.00 0.00 0.00 4.55
73 74 0.465824 TTTTCGTTTGGCCCTCGGAA 60.466 50.000 0.00 0.00 0.00 4.30
74 75 0.250989 TTTCGTTTGGCCCTCGGAAT 60.251 50.000 0.00 0.00 0.00 3.01
75 76 0.250989 TTCGTTTGGCCCTCGGAATT 60.251 50.000 0.00 0.00 0.00 2.17
76 77 0.250989 TCGTTTGGCCCTCGGAATTT 60.251 50.000 0.00 0.00 0.00 1.82
77 78 0.601057 CGTTTGGCCCTCGGAATTTT 59.399 50.000 0.00 0.00 0.00 1.82
78 79 1.813786 CGTTTGGCCCTCGGAATTTTA 59.186 47.619 0.00 0.00 0.00 1.52
79 80 2.425668 CGTTTGGCCCTCGGAATTTTAT 59.574 45.455 0.00 0.00 0.00 1.40
80 81 3.119280 CGTTTGGCCCTCGGAATTTTATT 60.119 43.478 0.00 0.00 0.00 1.40
81 82 4.180817 GTTTGGCCCTCGGAATTTTATTG 58.819 43.478 0.00 0.00 0.00 1.90
82 83 2.383855 TGGCCCTCGGAATTTTATTGG 58.616 47.619 0.00 0.00 0.00 3.16
83 84 1.068588 GGCCCTCGGAATTTTATTGGC 59.931 52.381 0.00 0.00 36.92 4.52
84 85 1.754226 GCCCTCGGAATTTTATTGGCA 59.246 47.619 0.00 0.00 37.58 4.92
85 86 2.365293 GCCCTCGGAATTTTATTGGCAT 59.635 45.455 0.00 0.00 37.58 4.40
118 119 4.764823 TGGTTATGCGATCTTTGGTTTTCT 59.235 37.500 0.00 0.00 0.00 2.52
128 129 7.244192 CGATCTTTGGTTTTCTATTTGTCCTC 58.756 38.462 0.00 0.00 0.00 3.71
144 145 1.476891 TCCTCGAGCAGTATCCAACAC 59.523 52.381 6.99 0.00 0.00 3.32
145 146 1.204704 CCTCGAGCAGTATCCAACACA 59.795 52.381 6.99 0.00 0.00 3.72
146 147 2.263077 CTCGAGCAGTATCCAACACAC 58.737 52.381 0.00 0.00 0.00 3.82
147 148 1.616374 TCGAGCAGTATCCAACACACA 59.384 47.619 0.00 0.00 0.00 3.72
148 149 1.726791 CGAGCAGTATCCAACACACAC 59.273 52.381 0.00 0.00 0.00 3.82
149 150 2.766313 GAGCAGTATCCAACACACACA 58.234 47.619 0.00 0.00 0.00 3.72
150 151 2.738846 GAGCAGTATCCAACACACACAG 59.261 50.000 0.00 0.00 0.00 3.66
214 225 2.107041 TTACCAGGTCTGTGTGCCGG 62.107 60.000 0.00 0.00 0.00 6.13
224 237 3.012119 TGTGCCGGGCCTCCAATA 61.012 61.111 17.97 0.00 0.00 1.90
344 382 0.903942 GAAAATGATGCAGGCCCCAA 59.096 50.000 0.00 0.00 0.00 4.12
390 428 5.240891 AGTCATCTGTGATGTTGGTACAAG 58.759 41.667 7.33 0.00 39.45 3.16
558 673 5.462729 CAGTCAATATACAGCTCAGCTCTTG 59.537 44.000 0.00 0.00 36.40 3.02
559 674 4.749099 GTCAATATACAGCTCAGCTCTTGG 59.251 45.833 0.00 0.00 36.40 3.61
561 676 5.306419 TCAATATACAGCTCAGCTCTTGGAT 59.694 40.000 0.00 0.00 36.40 3.41
562 677 5.822132 ATATACAGCTCAGCTCTTGGATT 57.178 39.130 0.00 0.00 36.40 3.01
563 678 2.399916 ACAGCTCAGCTCTTGGATTC 57.600 50.000 0.00 0.00 36.40 2.52
565 680 1.209990 CAGCTCAGCTCTTGGATTCCT 59.790 52.381 0.00 0.00 36.40 3.36
566 681 1.914798 AGCTCAGCTCTTGGATTCCTT 59.085 47.619 0.00 0.00 30.62 3.36
567 682 2.015587 GCTCAGCTCTTGGATTCCTTG 58.984 52.381 3.95 0.00 0.00 3.61
569 684 3.684981 GCTCAGCTCTTGGATTCCTTGAT 60.685 47.826 3.95 0.00 0.00 2.57
572 687 6.257994 TCAGCTCTTGGATTCCTTGATATT 57.742 37.500 3.95 0.00 0.00 1.28
573 688 7.379059 TCAGCTCTTGGATTCCTTGATATTA 57.621 36.000 3.95 0.00 0.00 0.98
574 689 7.982252 TCAGCTCTTGGATTCCTTGATATTAT 58.018 34.615 3.95 0.00 0.00 1.28
575 690 8.443176 TCAGCTCTTGGATTCCTTGATATTATT 58.557 33.333 3.95 0.00 0.00 1.40
577 692 9.956640 AGCTCTTGGATTCCTTGATATTATTAG 57.043 33.333 3.95 0.00 0.00 1.73
578 693 9.732130 GCTCTTGGATTCCTTGATATTATTAGT 57.268 33.333 3.95 0.00 0.00 2.24
596 711 9.868277 ATTATTAGTCAATATACAGCTCAGCTC 57.132 33.333 0.00 0.00 36.40 4.09
641 756 3.914426 TTTGCTTCCATCCTCTCTACC 57.086 47.619 0.00 0.00 0.00 3.18
696 880 3.628982 GGGGGAACGGTGGAACGA 61.629 66.667 0.00 0.00 38.12 3.85
697 881 2.357881 GGGGAACGGTGGAACGAC 60.358 66.667 0.00 0.00 38.12 4.34
698 882 2.357881 GGGAACGGTGGAACGACC 60.358 66.667 0.00 0.00 38.12 4.79
780 1005 0.032540 GCCCTGGACTTGTTTTGCTG 59.967 55.000 0.00 0.00 0.00 4.41
790 1070 5.163612 GGACTTGTTTTGCTGTTCTTCTTCT 60.164 40.000 0.00 0.00 0.00 2.85
798 1078 2.995258 GCTGTTCTTCTTCTGAGAGCTG 59.005 50.000 0.00 0.00 32.44 4.24
834 1162 6.582672 GCTATTGTGGAACTAAGAAACAAAGC 59.417 38.462 0.00 0.00 38.04 3.51
907 1235 7.083062 AGCATAATGATTCCTGACTCCATAA 57.917 36.000 0.00 0.00 0.00 1.90
1021 1418 4.069837 CAGAGTCGCTGCTTCTCG 57.930 61.111 12.60 6.77 37.90 4.04
1110 1507 1.597027 CAAGGACGACCGCCAAACT 60.597 57.895 0.00 0.00 41.83 2.66
1121 1518 2.262915 CCAAACTCTCGAGCGGCT 59.737 61.111 7.81 0.00 0.00 5.52
1185 1582 2.283298 AGCGAGACAAATGGCTATGTG 58.717 47.619 0.00 0.00 31.92 3.21
1263 1660 2.158449 CGATTTCCAATATGAGGCGCTC 59.842 50.000 7.64 3.37 0.00 5.03
1436 1837 0.035915 GGCTTGGAGAGTTCTGTCCC 60.036 60.000 12.41 0.00 31.04 4.46
1485 1886 2.800544 GCAGACGCACTCAAAACTAGAA 59.199 45.455 0.00 0.00 38.36 2.10
1572 1973 1.224592 GGATCAACGGAGGGTGCAT 59.775 57.895 0.00 0.00 0.00 3.96
1902 2304 0.462937 TGTGTTCTGTTGGTGGACCG 60.463 55.000 0.00 0.00 39.43 4.79
1968 2370 1.367346 TAATGCAGACCCTTGGACCA 58.633 50.000 0.00 0.00 0.00 4.02
2010 2412 7.174413 TGAGTGAACAAGATTCATGGGAATTA 58.826 34.615 0.00 0.00 43.69 1.40
2049 2451 3.669251 AGAAACAGTGTAGAGCAGGAC 57.331 47.619 0.00 0.00 0.00 3.85
2305 2716 4.336280 AGCAGTTTTTCCCAAGGACTATC 58.664 43.478 0.00 0.00 0.00 2.08
2317 2728 4.125703 CAAGGACTATCAGATGGACAAGC 58.874 47.826 0.00 0.00 0.00 4.01
2412 2823 8.645110 ACAGGAGAATTCATTTTCAATGAGTTT 58.355 29.630 8.44 3.60 29.87 2.66
2564 2978 4.394300 AGATGAATGTGCAAGTGTAGAAGC 59.606 41.667 0.00 0.00 0.00 3.86
2643 3060 4.460382 GCTGAATTGGAAAAGATGAGTGGA 59.540 41.667 0.00 0.00 0.00 4.02
2721 3177 8.576442 CACAAGGATTTTAAAGAGTTGGTACAT 58.424 33.333 0.00 0.00 39.30 2.29
2795 3255 3.752222 TGCAAGGCCATAAATGCAAAAAG 59.248 39.130 5.01 0.00 45.04 2.27
2937 3397 4.019501 AGAGACATGGCAAGACTGAGAAAT 60.020 41.667 0.00 0.00 0.00 2.17
3203 3663 8.278639 TGAGTTATTTATTATTCTCTTGGGGCA 58.721 33.333 0.00 0.00 0.00 5.36
3478 3981 1.630369 CTTGATGTGGAAGGTGGAGGA 59.370 52.381 0.00 0.00 0.00 3.71
3667 4170 3.434309 CATTCCAGTGATCCCCTTTGTT 58.566 45.455 0.00 0.00 0.00 2.83
3669 4172 3.713826 TCCAGTGATCCCCTTTGTTAC 57.286 47.619 0.00 0.00 0.00 2.50
3823 4326 0.316204 CCCAGCAAAGCCAAAGTGAG 59.684 55.000 0.00 0.00 0.00 3.51
4171 4675 0.767375 TGGCCAAGCTGAAGAGTCTT 59.233 50.000 0.61 4.68 0.00 3.01
4181 4685 6.202516 AGCTGAAGAGTCTTAGTGTGTATC 57.797 41.667 5.09 0.00 0.00 2.24
4195 4699 1.207089 GTGTATCACTGCAGTGGCCTA 59.793 52.381 39.04 26.46 45.65 3.93
4198 4702 1.826385 ATCACTGCAGTGGCCTAAAC 58.174 50.000 39.04 0.00 45.65 2.01
4212 4716 1.075542 CTAAACGCGTTGCCTGATGA 58.924 50.000 27.34 2.86 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.268330 CTGGGCATCAAGGATATCGATG 58.732 50.000 8.54 12.31 39.62 3.84
7 8 2.238144 CCTGGGCATCAAGGATATCGAT 59.762 50.000 2.16 2.16 0.00 3.59
9 10 1.947678 GCCTGGGCATCAAGGATATCG 60.948 57.143 6.75 0.00 41.49 2.92
10 11 1.615384 GGCCTGGGCATCAAGGATATC 60.615 57.143 16.34 0.00 44.11 1.63
11 12 0.407139 GGCCTGGGCATCAAGGATAT 59.593 55.000 16.34 0.00 44.11 1.63
12 13 0.992970 TGGCCTGGGCATCAAGGATA 60.993 55.000 20.19 0.00 44.11 2.59
13 14 2.318966 TGGCCTGGGCATCAAGGAT 61.319 57.895 20.19 0.00 44.11 3.24
14 15 2.940467 TGGCCTGGGCATCAAGGA 60.940 61.111 20.19 0.00 44.11 3.36
15 16 2.757099 GTGGCCTGGGCATCAAGG 60.757 66.667 26.61 0.00 44.11 3.61
16 17 2.757099 GGTGGCCTGGGCATCAAG 60.757 66.667 26.87 0.00 44.11 3.02
17 18 4.380945 GGGTGGCCTGGGCATCAA 62.381 66.667 31.39 4.80 41.19 2.57
24 25 3.561120 TTAAGCGTGGGTGGCCTGG 62.561 63.158 3.32 0.00 0.00 4.45
25 26 1.586154 CTTTAAGCGTGGGTGGCCTG 61.586 60.000 3.32 0.00 0.00 4.85
26 27 1.303317 CTTTAAGCGTGGGTGGCCT 60.303 57.895 3.32 0.00 0.00 5.19
27 28 2.340328 CCTTTAAGCGTGGGTGGCC 61.340 63.158 0.00 0.00 0.00 5.36
28 29 1.602605 ACCTTTAAGCGTGGGTGGC 60.603 57.895 0.00 0.00 0.00 5.01
29 30 1.862602 GCACCTTTAAGCGTGGGTGG 61.863 60.000 17.30 4.04 46.43 4.61
31 32 1.602605 GGCACCTTTAAGCGTGGGT 60.603 57.895 12.84 0.00 0.00 4.51
32 33 3.274067 GGCACCTTTAAGCGTGGG 58.726 61.111 12.84 0.00 0.00 4.61
45 46 0.868177 CCAAACGAAAACGTGGGCAC 60.868 55.000 0.00 0.00 0.00 5.01
46 47 1.433879 CCAAACGAAAACGTGGGCA 59.566 52.632 0.00 0.00 0.00 5.36
47 48 1.947146 GCCAAACGAAAACGTGGGC 60.947 57.895 17.61 17.61 36.50 5.36
48 49 1.299544 GGCCAAACGAAAACGTGGG 60.300 57.895 0.00 0.00 0.00 4.61
49 50 1.299544 GGGCCAAACGAAAACGTGG 60.300 57.895 4.39 0.00 0.00 4.94
50 51 0.317519 GAGGGCCAAACGAAAACGTG 60.318 55.000 6.18 0.00 0.00 4.49
51 52 1.778027 CGAGGGCCAAACGAAAACGT 61.778 55.000 6.18 0.00 0.00 3.99
52 53 1.082366 CGAGGGCCAAACGAAAACG 60.082 57.895 6.18 0.00 0.00 3.60
53 54 1.167781 TCCGAGGGCCAAACGAAAAC 61.168 55.000 6.18 0.00 0.00 2.43
54 55 0.465824 TTCCGAGGGCCAAACGAAAA 60.466 50.000 6.18 4.20 0.00 2.29
55 56 0.250989 ATTCCGAGGGCCAAACGAAA 60.251 50.000 6.18 0.00 0.00 3.46
56 57 0.250989 AATTCCGAGGGCCAAACGAA 60.251 50.000 6.18 1.74 0.00 3.85
57 58 0.250989 AAATTCCGAGGGCCAAACGA 60.251 50.000 6.18 0.00 0.00 3.85
58 59 0.601057 AAAATTCCGAGGGCCAAACG 59.399 50.000 6.18 8.61 0.00 3.60
59 60 4.180817 CAATAAAATTCCGAGGGCCAAAC 58.819 43.478 6.18 0.00 0.00 2.93
60 61 3.196685 CCAATAAAATTCCGAGGGCCAAA 59.803 43.478 6.18 0.00 0.00 3.28
61 62 2.763448 CCAATAAAATTCCGAGGGCCAA 59.237 45.455 6.18 0.00 0.00 4.52
62 63 2.383855 CCAATAAAATTCCGAGGGCCA 58.616 47.619 6.18 0.00 0.00 5.36
63 64 1.068588 GCCAATAAAATTCCGAGGGCC 59.931 52.381 0.00 0.00 34.17 5.80
64 65 1.754226 TGCCAATAAAATTCCGAGGGC 59.246 47.619 0.00 0.00 40.51 5.19
65 66 5.782893 TTATGCCAATAAAATTCCGAGGG 57.217 39.130 0.00 0.00 0.00 4.30
66 67 7.661040 AGAATTATGCCAATAAAATTCCGAGG 58.339 34.615 0.00 0.00 38.51 4.63
67 68 9.533253 AAAGAATTATGCCAATAAAATTCCGAG 57.467 29.630 0.00 0.00 38.51 4.63
68 69 9.528018 GAAAGAATTATGCCAATAAAATTCCGA 57.472 29.630 0.00 0.00 38.51 4.55
69 70 9.533253 AGAAAGAATTATGCCAATAAAATTCCG 57.467 29.630 0.00 0.00 38.51 4.30
83 84 8.092521 AGATCGCATAACCAGAAAGAATTATG 57.907 34.615 0.00 0.00 37.84 1.90
84 85 8.682936 AAGATCGCATAACCAGAAAGAATTAT 57.317 30.769 0.00 0.00 0.00 1.28
85 86 8.397906 CAAAGATCGCATAACCAGAAAGAATTA 58.602 33.333 0.00 0.00 0.00 1.40
118 119 3.958147 TGGATACTGCTCGAGGACAAATA 59.042 43.478 15.58 0.00 37.61 1.40
128 129 1.726791 GTGTGTGTTGGATACTGCTCG 59.273 52.381 0.00 0.00 37.61 5.03
214 225 4.803098 ATGACGTACTATATTGGAGGCC 57.197 45.455 0.00 0.00 0.00 5.19
272 289 2.564771 CTGTGAAGACTGGTTCAGCAA 58.435 47.619 0.00 0.00 37.12 3.91
301 336 2.271800 CGTGCAGATAGGACAAGGAAC 58.728 52.381 0.00 0.00 38.70 3.62
344 382 5.085920 TCCAACCAAATGATGTTCAATCCT 58.914 37.500 0.00 0.00 0.00 3.24
356 394 4.074259 TCACAGATGACTCCAACCAAATG 58.926 43.478 0.00 0.00 0.00 2.32
544 659 1.065564 GGAATCCAAGAGCTGAGCTGT 60.066 52.381 13.71 4.35 39.88 4.40
572 687 8.642935 AGAGCTGAGCTGTATATTGACTAATA 57.357 34.615 13.71 0.00 39.88 0.98
573 688 7.537596 AGAGCTGAGCTGTATATTGACTAAT 57.462 36.000 13.71 0.00 39.88 1.73
574 689 6.968263 AGAGCTGAGCTGTATATTGACTAA 57.032 37.500 13.71 0.00 39.88 2.24
575 690 6.239148 CCAAGAGCTGAGCTGTATATTGACTA 60.239 42.308 13.71 0.00 39.88 2.59
577 692 4.749099 CCAAGAGCTGAGCTGTATATTGAC 59.251 45.833 13.71 0.00 39.88 3.18
578 693 4.651045 TCCAAGAGCTGAGCTGTATATTGA 59.349 41.667 13.71 0.00 39.88 2.57
580 695 5.822132 ATCCAAGAGCTGAGCTGTATATT 57.178 39.130 13.71 0.00 39.88 1.28
581 696 5.279910 GGAATCCAAGAGCTGAGCTGTATAT 60.280 44.000 13.71 0.00 39.88 0.86
582 697 4.039730 GGAATCCAAGAGCTGAGCTGTATA 59.960 45.833 13.71 0.00 39.88 1.47
583 698 3.181456 GGAATCCAAGAGCTGAGCTGTAT 60.181 47.826 13.71 0.00 39.88 2.29
584 699 2.169352 GGAATCCAAGAGCTGAGCTGTA 59.831 50.000 13.71 0.00 39.88 2.74
585 700 1.065564 GGAATCCAAGAGCTGAGCTGT 60.066 52.381 13.71 4.35 39.88 4.40
586 701 1.209990 AGGAATCCAAGAGCTGAGCTG 59.790 52.381 13.71 0.00 39.88 4.24
587 702 1.582389 AGGAATCCAAGAGCTGAGCT 58.418 50.000 6.69 6.69 43.88 4.09
588 703 2.015587 CAAGGAATCCAAGAGCTGAGC 58.984 52.381 0.61 0.00 0.00 4.26
589 704 3.623906 TCAAGGAATCCAAGAGCTGAG 57.376 47.619 0.61 0.00 0.00 3.35
590 705 5.901413 ATATCAAGGAATCCAAGAGCTGA 57.099 39.130 0.61 0.00 0.00 4.26
591 706 8.102047 AGATAATATCAAGGAATCCAAGAGCTG 58.898 37.037 0.61 0.00 0.00 4.24
592 707 8.217188 AGATAATATCAAGGAATCCAAGAGCT 57.783 34.615 0.61 0.00 0.00 4.09
593 708 7.552330 GGAGATAATATCAAGGAATCCAAGAGC 59.448 40.741 0.61 0.00 0.00 4.09
594 709 8.600668 TGGAGATAATATCAAGGAATCCAAGAG 58.399 37.037 0.61 0.00 31.63 2.85
595 710 8.510358 TGGAGATAATATCAAGGAATCCAAGA 57.490 34.615 0.61 0.00 31.63 3.02
596 711 9.750783 AATGGAGATAATATCAAGGAATCCAAG 57.249 33.333 0.61 0.00 37.80 3.61
641 756 1.875963 CACGGCAAGGCTGGTAAAG 59.124 57.895 1.73 0.00 39.57 1.85
679 863 3.628982 TCGTTCCACCGTTCCCCC 61.629 66.667 0.00 0.00 0.00 5.40
680 864 2.357881 GTCGTTCCACCGTTCCCC 60.358 66.667 0.00 0.00 0.00 4.81
681 865 2.357881 GGTCGTTCCACCGTTCCC 60.358 66.667 0.00 0.00 35.97 3.97
682 866 1.666872 CTGGTCGTTCCACCGTTCC 60.667 63.158 0.00 0.00 41.93 3.62
683 867 2.315386 GCTGGTCGTTCCACCGTTC 61.315 63.158 0.00 0.00 41.93 3.95
684 868 2.280592 GCTGGTCGTTCCACCGTT 60.281 61.111 0.00 0.00 41.93 4.44
685 869 3.515316 CTGCTGGTCGTTCCACCGT 62.515 63.158 0.00 0.00 41.93 4.83
686 870 2.149803 TACTGCTGGTCGTTCCACCG 62.150 60.000 0.00 0.00 41.93 4.94
687 871 0.669625 GTACTGCTGGTCGTTCCACC 60.670 60.000 0.00 0.00 41.93 4.61
688 872 0.669625 GGTACTGCTGGTCGTTCCAC 60.670 60.000 0.00 0.00 41.93 4.02
689 873 1.116536 TGGTACTGCTGGTCGTTCCA 61.117 55.000 0.00 2.64 45.01 3.53
690 874 0.249398 ATGGTACTGCTGGTCGTTCC 59.751 55.000 0.00 0.00 0.00 3.62
691 875 1.732259 CAATGGTACTGCTGGTCGTTC 59.268 52.381 0.00 0.00 0.00 3.95
692 876 1.808411 CAATGGTACTGCTGGTCGTT 58.192 50.000 0.00 0.00 0.00 3.85
693 877 0.673644 GCAATGGTACTGCTGGTCGT 60.674 55.000 0.00 0.00 36.84 4.34
694 878 2.089854 GCAATGGTACTGCTGGTCG 58.910 57.895 0.00 0.00 36.84 4.79
700 884 2.162408 GGTGAAAGAGCAATGGTACTGC 59.838 50.000 0.00 0.00 40.24 4.40
729 938 2.039746 ACACCACCGGATTTGATCTTGA 59.960 45.455 9.46 0.00 0.00 3.02
780 1005 5.127693 TGTACAGCTCTCAGAAGAAGAAC 57.872 43.478 0.00 0.00 0.00 3.01
798 1078 5.875359 AGTTCCACAATAGCTTAGCTTGTAC 59.125 40.000 13.44 7.14 40.44 2.90
834 1162 4.142600 CCTCGCAGTCCTCCTTTTATTTTG 60.143 45.833 0.00 0.00 0.00 2.44
907 1235 1.831580 GAACAGCCTTGCAATCCTCT 58.168 50.000 0.00 0.00 0.00 3.69
967 1361 5.063880 GGTCGGAGGAATTATAAACTGCAT 58.936 41.667 0.00 0.00 0.00 3.96
1021 1418 1.566018 GCCACACCACGTAACAGAGC 61.566 60.000 0.00 0.00 0.00 4.09
1110 1507 1.584175 CTAGTAGAAGCCGCTCGAGA 58.416 55.000 18.75 0.00 0.00 4.04
1121 1518 1.890489 TGCACTCAACGGCTAGTAGAA 59.110 47.619 0.00 0.00 0.00 2.10
1185 1582 1.485895 AGCTCCTTCATCCAGCTCTTC 59.514 52.381 0.00 0.00 39.37 2.87
1263 1660 0.443869 CAATCTTTGACTGTCGGCGG 59.556 55.000 7.21 0.00 0.00 6.13
1436 1837 1.690219 ATGTTGCCGCTCCTCCCTAG 61.690 60.000 0.00 0.00 0.00 3.02
1485 1886 4.338795 TCCAAAGATCTGGGTAGTCTCT 57.661 45.455 12.17 0.00 37.06 3.10
1572 1973 1.750018 CCCAATGATCGGCAGCACA 60.750 57.895 0.00 0.00 0.00 4.57
1902 2304 4.445452 TGTCACGACTATTACACTTCCC 57.555 45.455 0.00 0.00 0.00 3.97
1968 2370 4.403752 TCACTCAGACATGCTAGCTTATGT 59.596 41.667 17.91 17.91 40.04 2.29
2010 2412 6.589523 TGTTTCTATATGCTTTTTGCGCAAAT 59.410 30.769 33.94 21.71 46.63 2.32
2305 2716 4.508461 TCAAATTGTGCTTGTCCATCTG 57.492 40.909 0.00 0.00 0.00 2.90
2564 2978 0.601046 TGCTTTCTGCGGAGTCAGTG 60.601 55.000 3.10 0.00 46.63 3.66
2721 3177 3.016736 TGCTCTCAGTGATGTCGATACA 58.983 45.455 0.00 0.00 40.69 2.29
2756 3212 5.824097 GCCTTGCAAATGGAAATTGGATAAT 59.176 36.000 8.85 0.00 0.00 1.28
2795 3255 9.005777 AGTAAGAGAGGTCAAGATATCGTAATC 57.994 37.037 0.00 0.00 0.00 1.75
2937 3397 7.451731 ACCATAAAGATAAAGGTGGATGAGA 57.548 36.000 0.00 0.00 0.00 3.27
3186 3646 9.354673 CTATTTCTTTGCCCCAAGAGAATAATA 57.645 33.333 0.00 0.00 0.00 0.98
3187 3647 8.061304 TCTATTTCTTTGCCCCAAGAGAATAAT 58.939 33.333 0.00 0.00 0.00 1.28
3188 3648 7.410174 TCTATTTCTTTGCCCCAAGAGAATAA 58.590 34.615 0.00 0.00 0.00 1.40
3189 3649 6.969043 TCTATTTCTTTGCCCCAAGAGAATA 58.031 36.000 0.00 0.00 0.00 1.75
3667 4170 2.417651 CCCAACTATTCGCAACTCGGTA 60.418 50.000 0.00 0.00 39.05 4.02
3669 4172 1.006832 CCCAACTATTCGCAACTCGG 58.993 55.000 0.00 0.00 39.05 4.63
3823 4326 3.885901 ACTTCAGTTTTTCAAGAGGCCTC 59.114 43.478 26.22 26.22 0.00 4.70
4181 4685 1.868997 CGTTTAGGCCACTGCAGTG 59.131 57.895 35.15 35.15 45.23 3.66
4195 4699 0.602638 TCTCATCAGGCAACGCGTTT 60.603 50.000 24.21 5.05 46.39 3.60
4198 4702 1.640069 CATCTCATCAGGCAACGCG 59.360 57.895 3.53 3.53 46.39 6.01


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

AutoCloner maintained by Alex Coulton.