Multiple sequence alignment - TraesCS5D01G372900

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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 TraesCS5D01G372900 chr5D 100.000 4729 0 0 335 5063 446479832 446475104 0.000000e+00 8733.0
1 TraesCS5D01G372900 chr5D 87.262 1994 192 26 2131 4109 446502003 446500057 0.000000e+00 2218.0
2 TraesCS5D01G372900 chr5D 79.791 287 32 17 1197 1463 543129204 543129484 8.660000e-43 185.0
3 TraesCS5D01G372900 chr5D 100.000 73 0 0 1 73 446480166 446480094 8.840000e-28 135.0
4 TraesCS5D01G372900 chr7D 86.706 2362 164 71 890 3190 142193267 142195539 0.000000e+00 2484.0
5 TraesCS5D01G372900 chr7D 85.044 916 117 13 3134 4038 142195537 142196443 0.000000e+00 915.0
6 TraesCS5D01G372900 chr5A 95.918 1078 28 8 2119 3188 564177639 564176570 0.000000e+00 1733.0
7 TraesCS5D01G372900 chr5A 94.636 783 22 13 4261 5028 466717484 466718261 0.000000e+00 1195.0
8 TraesCS5D01G372900 chr5A 87.859 906 46 15 796 1662 564179117 564178237 0.000000e+00 1005.0
9 TraesCS5D01G372900 chr5A 88.959 788 73 7 1988 2774 564242601 564241827 0.000000e+00 961.0
10 TraesCS5D01G372900 chr5A 92.842 461 18 5 1660 2120 564178166 564177721 0.000000e+00 654.0
11 TraesCS5D01G372900 chr5A 89.871 464 43 1 3538 4001 564176268 564175809 1.210000e-165 593.0
12 TraesCS5D01G372900 chr5A 85.159 566 66 9 3134 3695 564241469 564240918 9.520000e-157 564.0
13 TraesCS5D01G372900 chr5A 91.316 380 27 2 2814 3190 564241816 564241440 9.720000e-142 514.0
14 TraesCS5D01G372900 chr5A 97.351 302 5 1 3136 3434 564176568 564176267 1.260000e-140 510.0
15 TraesCS5D01G372900 chr5A 86.859 312 36 1 338 644 564179855 564179544 1.350000e-90 344.0
16 TraesCS5D01G372900 chr5A 81.230 309 49 8 3733 4038 564240912 564240610 1.820000e-59 241.0
17 TraesCS5D01G372900 chr5A 84.783 184 13 4 1069 1237 564243786 564243603 2.420000e-38 171.0
18 TraesCS5D01G372900 chr5A 100.000 46 0 0 1 46 564179959 564179914 9.030000e-13 86.1
19 TraesCS5D01G372900 chr5A 100.000 34 0 0 5030 5063 466718536 466718569 4.230000e-06 63.9
20 TraesCS5D01G372900 chr3D 97.037 810 7 2 4271 5063 141483571 141482762 0.000000e+00 1347.0
21 TraesCS5D01G372900 chr3D 96.675 812 10 8 4267 5063 32169978 32169169 0.000000e+00 1334.0
22 TraesCS5D01G372900 chr3D 90.000 70 4 1 1188 1254 33323535 33323604 2.510000e-13 87.9
23 TraesCS5D01G372900 chr7A 94.452 775 25 11 4270 5028 450326337 450327109 0.000000e+00 1177.0
24 TraesCS5D01G372900 chr7A 80.993 1047 144 26 3250 4268 608992029 608991010 0.000000e+00 780.0
25 TraesCS5D01G372900 chr7A 84.615 416 57 6 2010 2422 608993130 608992719 1.700000e-109 407.0
26 TraesCS5D01G372900 chr7A 81.818 176 9 10 1110 1282 608994072 608993917 5.320000e-25 126.0
27 TraesCS5D01G372900 chr7A 87.037 54 6 1 4245 4298 617429588 617429640 5.470000e-05 60.2
28 TraesCS5D01G372900 chr5B 93.074 823 25 14 3469 4270 544400039 544399228 0.000000e+00 1175.0
29 TraesCS5D01G372900 chr5B 93.562 730 41 5 2080 2806 544402389 544401663 0.000000e+00 1083.0
30 TraesCS5D01G372900 chr5B 88.388 887 77 14 2247 3113 544377482 544376602 0.000000e+00 1044.0
31 TraesCS5D01G372900 chr5B 93.516 694 35 4 2790 3476 544401642 544400952 0.000000e+00 1024.0
32 TraesCS5D01G372900 chr5B 84.450 418 37 13 1100 1491 544402850 544402435 2.210000e-103 387.0
33 TraesCS5D01G372900 chr5B 82.609 230 16 15 842 1066 544403148 544402938 1.120000e-41 182.0
34 TraesCS5D01G372900 chr5B 77.451 306 53 11 2438 2735 676113630 676113333 8.720000e-38 169.0
35 TraesCS5D01G372900 chr2D 93.684 760 35 10 4273 5025 261958880 261959633 0.000000e+00 1125.0
36 TraesCS5D01G372900 chr2D 93.846 585 32 4 4372 4953 632808393 632807810 0.000000e+00 878.0
37 TraesCS5D01G372900 chr2D 100.000 34 0 0 5030 5063 261959851 261959884 4.230000e-06 63.9
38 TraesCS5D01G372900 chr4B 95.286 700 28 5 4261 4959 240136041 240135346 0.000000e+00 1105.0
39 TraesCS5D01G372900 chr3A 92.418 765 44 8 4271 5025 209136967 209137727 0.000000e+00 1079.0
40 TraesCS5D01G372900 chr3A 97.059 34 1 0 5030 5063 209137878 209137911 1.970000e-04 58.4
41 TraesCS5D01G372900 chr4A 77.008 2079 332 91 2034 4021 636641692 636643715 0.000000e+00 1057.0
42 TraesCS5D01G372900 chr4A 78.158 1140 162 42 3184 4269 637164098 637162992 0.000000e+00 645.0
43 TraesCS5D01G372900 chr4A 85.757 337 29 13 2032 2355 637165331 637165001 6.280000e-89 339.0
44 TraesCS5D01G372900 chr4A 94.000 50 3 0 1204 1253 202490561 202490610 5.440000e-10 76.8
45 TraesCS5D01G372900 chr6D 91.085 774 38 12 4269 5027 381369692 381370449 0.000000e+00 1018.0
46 TraesCS5D01G372900 chr6D 100.000 34 0 0 5030 5063 381370717 381370750 4.230000e-06 63.9
47 TraesCS5D01G372900 chr1B 92.918 706 29 10 4321 5009 633707143 633707844 0.000000e+00 1007.0
48 TraesCS5D01G372900 chr1B 82.270 141 20 5 2088 2226 623451548 623451411 3.200000e-22 117.0
49 TraesCS5D01G372900 chr1B 100.000 34 0 0 5030 5063 633753590 633753623 4.230000e-06 63.9
50 TraesCS5D01G372900 chr7B 71.445 865 191 32 2277 3100 675188928 675189777 1.450000e-40 178.0
51 TraesCS5D01G372900 chr7B 71.648 455 106 14 2150 2589 675212374 675212820 2.490000e-18 104.0
52 TraesCS5D01G372900 chr4D 81.383 188 25 9 1288 1473 42796934 42796755 1.470000e-30 145.0
53 TraesCS5D01G372900 chr2A 97.500 40 1 0 4262 4301 277174653 277174692 9.100000e-08 69.4


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 TraesCS5D01G372900 chr5D 446475104 446480166 5062 True 4434.000000 8733 100.000000 1 5063 2 chr5D.!!$R2 5062
1 TraesCS5D01G372900 chr5D 446500057 446502003 1946 True 2218.000000 2218 87.262000 2131 4109 1 chr5D.!!$R1 1978
2 TraesCS5D01G372900 chr7D 142193267 142196443 3176 False 1699.500000 2484 85.875000 890 4038 2 chr7D.!!$F1 3148
3 TraesCS5D01G372900 chr5A 564175809 564179959 4150 True 703.585714 1733 92.957143 1 4001 7 chr5A.!!$R1 4000
4 TraesCS5D01G372900 chr5A 466717484 466718569 1085 False 629.450000 1195 97.318000 4261 5063 2 chr5A.!!$F1 802
5 TraesCS5D01G372900 chr5A 564240610 564243786 3176 True 490.200000 961 86.289400 1069 4038 5 chr5A.!!$R2 2969
6 TraesCS5D01G372900 chr3D 141482762 141483571 809 True 1347.000000 1347 97.037000 4271 5063 1 chr3D.!!$R2 792
7 TraesCS5D01G372900 chr3D 32169169 32169978 809 True 1334.000000 1334 96.675000 4267 5063 1 chr3D.!!$R1 796
8 TraesCS5D01G372900 chr7A 450326337 450327109 772 False 1177.000000 1177 94.452000 4270 5028 1 chr7A.!!$F1 758
9 TraesCS5D01G372900 chr7A 608991010 608994072 3062 True 437.666667 780 82.475333 1110 4268 3 chr7A.!!$R1 3158
10 TraesCS5D01G372900 chr5B 544376602 544377482 880 True 1044.000000 1044 88.388000 2247 3113 1 chr5B.!!$R1 866
11 TraesCS5D01G372900 chr5B 544399228 544403148 3920 True 770.200000 1175 89.442200 842 4270 5 chr5B.!!$R3 3428
12 TraesCS5D01G372900 chr2D 632807810 632808393 583 True 878.000000 878 93.846000 4372 4953 1 chr2D.!!$R1 581
13 TraesCS5D01G372900 chr2D 261958880 261959884 1004 False 594.450000 1125 96.842000 4273 5063 2 chr2D.!!$F1 790
14 TraesCS5D01G372900 chr4B 240135346 240136041 695 True 1105.000000 1105 95.286000 4261 4959 1 chr4B.!!$R1 698
15 TraesCS5D01G372900 chr3A 209136967 209137911 944 False 568.700000 1079 94.738500 4271 5063 2 chr3A.!!$F1 792
16 TraesCS5D01G372900 chr4A 636641692 636643715 2023 False 1057.000000 1057 77.008000 2034 4021 1 chr4A.!!$F2 1987
17 TraesCS5D01G372900 chr4A 637162992 637165331 2339 True 492.000000 645 81.957500 2032 4269 2 chr4A.!!$R1 2237
18 TraesCS5D01G372900 chr6D 381369692 381370750 1058 False 540.950000 1018 95.542500 4269 5063 2 chr6D.!!$F1 794
19 TraesCS5D01G372900 chr1B 633707143 633707844 701 False 1007.000000 1007 92.918000 4321 5009 1 chr1B.!!$F1 688

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
785 1121 0.039165 GCAAAGCAAAAGACGGAGGG 60.039 55.0 0.00 0.0 0.00 4.30 F
805 1141 0.047176 AGAGAGGGAGAGAGGGAGGA 59.953 60.0 0.00 0.0 0.00 3.71 F
806 1142 0.478507 GAGAGGGAGAGAGGGAGGAG 59.521 65.0 0.00 0.0 0.00 3.69 F
2106 3215 0.947244 GTGAAACTCAGTGCCCACAG 59.053 55.0 0.82 0.0 0.00 3.66 F
2966 4299 0.462047 CGTACTCCAATCTGGGTGGC 60.462 60.0 0.00 0.0 38.32 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2709 3979 1.156736 ACTTACAACATGGCAGTCGC 58.843 50.000 0.00 0.0 37.44 5.19 R
2775 4054 7.991084 AGACAGAATCTTGATCAACATGAAA 57.009 32.000 3.38 0.0 36.51 2.69 R
2825 4143 3.450817 AGTGGTATGTACTGCAGCATGTA 59.549 43.478 15.27 0.0 39.31 2.29 R
3599 6008 1.002430 TCTGAACTCACCAGATGTGCC 59.998 52.381 0.00 0.0 45.03 5.01 R
4196 6654 2.609427 TAATCAGCAGCAGCACTAGG 57.391 50.000 3.17 0.0 45.49 3.02 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
43 44 4.135153 CGACACCAGAGGGCGGAG 62.135 72.222 0.00 0.00 37.90 4.63
44 45 3.775654 GACACCAGAGGGCGGAGG 61.776 72.222 0.00 0.00 37.90 4.30
380 381 3.825611 GAACGCCATTGCCGCCAT 61.826 61.111 0.00 0.00 0.00 4.40
408 409 3.012722 TCGGGGGAGCCGGAAATT 61.013 61.111 5.05 0.00 0.00 1.82
433 434 1.378514 GGAGGGCTGGATTTTGCGA 60.379 57.895 0.00 0.00 0.00 5.10
434 435 1.657751 GGAGGGCTGGATTTTGCGAC 61.658 60.000 0.00 0.00 0.00 5.19
436 437 2.485122 GGCTGGATTTTGCGACGG 59.515 61.111 0.00 0.00 0.00 4.79
438 439 1.425428 GCTGGATTTTGCGACGGAG 59.575 57.895 0.00 0.00 0.00 4.63
442 443 0.657840 GGATTTTGCGACGGAGATGG 59.342 55.000 0.00 0.00 0.00 3.51
447 448 3.032609 GCGACGGAGATGGATGCG 61.033 66.667 0.00 0.00 40.19 4.73
448 449 2.721859 CGACGGAGATGGATGCGA 59.278 61.111 0.00 0.00 37.47 5.10
449 450 1.371022 CGACGGAGATGGATGCGAG 60.371 63.158 0.00 0.00 37.47 5.03
477 478 7.383156 TGACGGATAGGAACCCTAAAATTAT 57.617 36.000 0.00 0.00 39.77 1.28
479 480 7.071447 TGACGGATAGGAACCCTAAAATTATCA 59.929 37.037 0.00 0.00 39.77 2.15
480 481 7.985589 ACGGATAGGAACCCTAAAATTATCAT 58.014 34.615 0.00 0.00 39.77 2.45
483 484 7.148239 GGATAGGAACCCTAAAATTATCATGCG 60.148 40.741 0.00 0.00 39.77 4.73
486 487 3.561143 ACCCTAAAATTATCATGCGCCA 58.439 40.909 4.18 0.00 0.00 5.69
502 503 1.476891 CGCCAGCATATATACCGGAGT 59.523 52.381 9.46 0.00 0.00 3.85
504 505 2.893637 CCAGCATATATACCGGAGTGC 58.106 52.381 9.46 8.85 0.00 4.40
556 557 1.823899 GGCCGGGCCTCATTTGTAG 60.824 63.158 30.86 0.00 46.69 2.74
565 566 3.069729 GGCCTCATTTGTAGGATCTACGT 59.930 47.826 0.00 0.00 36.08 3.57
569 570 2.973694 TTTGTAGGATCTACGTGGGC 57.026 50.000 0.00 0.00 0.00 5.36
621 627 3.814577 ACGCAGTTCGCAGAGTTAT 57.185 47.368 0.00 0.00 37.78 1.89
623 629 2.798680 ACGCAGTTCGCAGAGTTATAG 58.201 47.619 0.00 0.00 37.78 1.31
644 650 2.364970 GTGGATGTGCTAGAGATGCTCT 59.635 50.000 0.00 2.22 43.83 4.09
645 651 3.036819 TGGATGTGCTAGAGATGCTCTT 58.963 45.455 1.88 0.00 41.50 2.85
646 652 4.038522 GTGGATGTGCTAGAGATGCTCTTA 59.961 45.833 1.88 0.00 41.50 2.10
648 654 4.321899 GGATGTGCTAGAGATGCTCTTAGG 60.322 50.000 1.88 0.00 41.50 2.69
649 655 3.903467 TGTGCTAGAGATGCTCTTAGGA 58.097 45.455 1.88 0.00 41.50 2.94
650 656 4.281657 TGTGCTAGAGATGCTCTTAGGAA 58.718 43.478 1.88 0.00 41.50 3.36
651 657 4.098654 TGTGCTAGAGATGCTCTTAGGAAC 59.901 45.833 1.88 0.43 41.50 3.62
652 658 3.639094 TGCTAGAGATGCTCTTAGGAACC 59.361 47.826 1.88 0.00 41.50 3.62
654 660 4.500716 GCTAGAGATGCTCTTAGGAACCAC 60.501 50.000 1.88 0.00 41.50 4.16
655 661 2.769095 AGAGATGCTCTTAGGAACCACC 59.231 50.000 0.00 0.00 37.60 4.61
695 1031 1.472878 TCACGCATCTCTACCTGTGTC 59.527 52.381 0.00 0.00 34.04 3.67
697 1033 1.474478 ACGCATCTCTACCTGTGTCTG 59.526 52.381 0.00 0.00 30.64 3.51
698 1034 1.474478 CGCATCTCTACCTGTGTCTGT 59.526 52.381 0.00 0.00 0.00 3.41
699 1035 2.733542 CGCATCTCTACCTGTGTCTGTG 60.734 54.545 0.00 0.00 0.00 3.66
700 1036 2.232452 GCATCTCTACCTGTGTCTGTGT 59.768 50.000 0.00 0.00 0.00 3.72
701 1037 3.842820 CATCTCTACCTGTGTCTGTGTG 58.157 50.000 0.00 0.00 0.00 3.82
702 1038 2.945456 TCTCTACCTGTGTCTGTGTGT 58.055 47.619 0.00 0.00 0.00 3.72
703 1039 2.623416 TCTCTACCTGTGTCTGTGTGTG 59.377 50.000 0.00 0.00 0.00 3.82
704 1040 1.068588 TCTACCTGTGTCTGTGTGTGC 59.931 52.381 0.00 0.00 0.00 4.57
705 1041 1.069204 CTACCTGTGTCTGTGTGTGCT 59.931 52.381 0.00 0.00 0.00 4.40
706 1042 0.462581 ACCTGTGTCTGTGTGTGCTG 60.463 55.000 0.00 0.00 0.00 4.41
707 1043 1.645455 CTGTGTCTGTGTGTGCTGC 59.355 57.895 0.00 0.00 0.00 5.25
708 1044 1.078567 TGTGTCTGTGTGTGCTGCA 60.079 52.632 0.00 0.00 0.00 4.41
709 1045 0.464193 TGTGTCTGTGTGTGCTGCAT 60.464 50.000 5.27 0.00 0.00 3.96
718 1054 1.811965 TGTGTGCTGCATTGTATCCAC 59.188 47.619 5.27 7.96 0.00 4.02
728 1064 4.021456 TGCATTGTATCCACCTATCTACCG 60.021 45.833 0.00 0.00 0.00 4.02
749 1085 3.247648 CGCGGTAGGTCAAATAATTGAGG 59.752 47.826 0.00 0.00 45.88 3.86
750 1086 4.448210 GCGGTAGGTCAAATAATTGAGGA 58.552 43.478 0.00 0.00 45.88 3.71
751 1087 4.511826 GCGGTAGGTCAAATAATTGAGGAG 59.488 45.833 0.00 0.00 45.88 3.69
752 1088 4.511826 CGGTAGGTCAAATAATTGAGGAGC 59.488 45.833 0.00 0.00 45.88 4.70
753 1089 4.822350 GGTAGGTCAAATAATTGAGGAGCC 59.178 45.833 0.00 0.00 45.88 4.70
754 1090 4.870021 AGGTCAAATAATTGAGGAGCCT 57.130 40.909 0.00 0.00 45.88 4.58
755 1091 4.786425 AGGTCAAATAATTGAGGAGCCTC 58.214 43.478 9.61 9.61 45.88 4.70
756 1092 3.885901 GGTCAAATAATTGAGGAGCCTCC 59.114 47.826 13.69 1.26 45.88 4.30
757 1093 3.885901 GTCAAATAATTGAGGAGCCTCCC 59.114 47.826 7.26 0.00 45.88 4.30
758 1094 3.527253 TCAAATAATTGAGGAGCCTCCCA 59.473 43.478 7.26 2.22 40.59 4.37
759 1095 4.017591 TCAAATAATTGAGGAGCCTCCCAA 60.018 41.667 7.26 11.76 40.59 4.12
760 1096 4.821532 AATAATTGAGGAGCCTCCCAAT 57.178 40.909 16.96 16.96 42.09 3.16
761 1097 2.744352 AATTGAGGAGCCTCCCAATC 57.256 50.000 20.71 9.10 42.09 2.67
762 1098 0.849417 ATTGAGGAGCCTCCCAATCC 59.151 55.000 16.96 1.19 42.09 3.01
763 1099 1.281925 TTGAGGAGCCTCCCAATCCC 61.282 60.000 7.26 0.00 42.09 3.85
764 1100 1.694169 GAGGAGCCTCCCAATCCCA 60.694 63.158 7.26 0.00 37.19 4.37
765 1101 1.230281 AGGAGCCTCCCAATCCCAA 60.230 57.895 7.26 0.00 37.19 4.12
766 1102 1.228510 GGAGCCTCCCAATCCCAAG 59.771 63.158 0.00 0.00 0.00 3.61
767 1103 1.454663 GAGCCTCCCAATCCCAAGC 60.455 63.158 0.00 0.00 0.00 4.01
768 1104 2.215451 GAGCCTCCCAATCCCAAGCA 62.215 60.000 0.00 0.00 0.00 3.91
769 1105 1.305213 GCCTCCCAATCCCAAGCAA 60.305 57.895 0.00 0.00 0.00 3.91
770 1106 0.904394 GCCTCCCAATCCCAAGCAAA 60.904 55.000 0.00 0.00 0.00 3.68
771 1107 1.188863 CCTCCCAATCCCAAGCAAAG 58.811 55.000 0.00 0.00 0.00 2.77
772 1108 0.533951 CTCCCAATCCCAAGCAAAGC 59.466 55.000 0.00 0.00 0.00 3.51
773 1109 0.178938 TCCCAATCCCAAGCAAAGCA 60.179 50.000 0.00 0.00 0.00 3.91
774 1110 0.686224 CCCAATCCCAAGCAAAGCAA 59.314 50.000 0.00 0.00 0.00 3.91
775 1111 1.072015 CCCAATCCCAAGCAAAGCAAA 59.928 47.619 0.00 0.00 0.00 3.68
776 1112 2.486907 CCCAATCCCAAGCAAAGCAAAA 60.487 45.455 0.00 0.00 0.00 2.44
777 1113 2.809696 CCAATCCCAAGCAAAGCAAAAG 59.190 45.455 0.00 0.00 0.00 2.27
778 1114 3.494749 CCAATCCCAAGCAAAGCAAAAGA 60.495 43.478 0.00 0.00 0.00 2.52
779 1115 2.888834 TCCCAAGCAAAGCAAAAGAC 57.111 45.000 0.00 0.00 0.00 3.01
780 1116 1.066908 TCCCAAGCAAAGCAAAAGACG 59.933 47.619 0.00 0.00 0.00 4.18
781 1117 1.490621 CCAAGCAAAGCAAAAGACGG 58.509 50.000 0.00 0.00 0.00 4.79
782 1118 1.066908 CCAAGCAAAGCAAAAGACGGA 59.933 47.619 0.00 0.00 0.00 4.69
783 1119 2.388121 CAAGCAAAGCAAAAGACGGAG 58.612 47.619 0.00 0.00 0.00 4.63
784 1120 0.954452 AGCAAAGCAAAAGACGGAGG 59.046 50.000 0.00 0.00 0.00 4.30
785 1121 0.039165 GCAAAGCAAAAGACGGAGGG 60.039 55.000 0.00 0.00 0.00 4.30
786 1122 1.604604 CAAAGCAAAAGACGGAGGGA 58.395 50.000 0.00 0.00 0.00 4.20
787 1123 1.537202 CAAAGCAAAAGACGGAGGGAG 59.463 52.381 0.00 0.00 0.00 4.30
788 1124 1.056660 AAGCAAAAGACGGAGGGAGA 58.943 50.000 0.00 0.00 0.00 3.71
789 1125 0.610687 AGCAAAAGACGGAGGGAGAG 59.389 55.000 0.00 0.00 0.00 3.20
790 1126 0.608640 GCAAAAGACGGAGGGAGAGA 59.391 55.000 0.00 0.00 0.00 3.10
791 1127 1.404851 GCAAAAGACGGAGGGAGAGAG 60.405 57.143 0.00 0.00 0.00 3.20
792 1128 1.205893 CAAAAGACGGAGGGAGAGAGG 59.794 57.143 0.00 0.00 0.00 3.69
793 1129 0.324830 AAAGACGGAGGGAGAGAGGG 60.325 60.000 0.00 0.00 0.00 4.30
794 1130 1.215679 AAGACGGAGGGAGAGAGGGA 61.216 60.000 0.00 0.00 0.00 4.20
795 1131 1.152839 GACGGAGGGAGAGAGGGAG 60.153 68.421 0.00 0.00 0.00 4.30
796 1132 1.619975 ACGGAGGGAGAGAGGGAGA 60.620 63.158 0.00 0.00 0.00 3.71
797 1133 1.150536 CGGAGGGAGAGAGGGAGAG 59.849 68.421 0.00 0.00 0.00 3.20
798 1134 1.349542 CGGAGGGAGAGAGGGAGAGA 61.350 65.000 0.00 0.00 0.00 3.10
799 1135 0.478507 GGAGGGAGAGAGGGAGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
800 1136 0.478507 GAGGGAGAGAGGGAGAGAGG 59.521 65.000 0.00 0.00 0.00 3.69
805 1141 0.047176 AGAGAGGGAGAGAGGGAGGA 59.953 60.000 0.00 0.00 0.00 3.71
806 1142 0.478507 GAGAGGGAGAGAGGGAGGAG 59.521 65.000 0.00 0.00 0.00 3.69
808 1144 2.018086 AGGGAGAGAGGGAGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
811 1147 1.075600 GAGAGAGGGAGGAGGGGTG 60.076 68.421 0.00 0.00 0.00 4.61
854 1190 1.500396 CGGCCGCAGTTTACCTTTC 59.500 57.895 14.67 0.00 0.00 2.62
866 1202 1.559065 TACCTTTCGGGCTTGGGAGG 61.559 60.000 0.00 0.00 39.10 4.30
867 1203 2.044946 CTTTCGGGCTTGGGAGGG 60.045 66.667 0.00 0.00 0.00 4.30
868 1204 2.530661 TTTCGGGCTTGGGAGGGA 60.531 61.111 0.00 0.00 0.00 4.20
869 1205 2.543067 CTTTCGGGCTTGGGAGGGAG 62.543 65.000 0.00 0.00 0.00 4.30
872 1208 3.803162 GGGCTTGGGAGGGAGCTC 61.803 72.222 4.71 4.71 38.89 4.09
873 1209 4.168291 GGCTTGGGAGGGAGCTCG 62.168 72.222 7.83 0.00 38.89 5.03
1463 2295 8.175925 TGTTTCACAACATATGGATGAAGAAA 57.824 30.769 15.29 17.70 38.03 2.52
1493 2325 5.010933 CAGGAGGAAGAACACTCTGTACTA 58.989 45.833 0.00 0.00 34.22 1.82
1495 2327 5.011586 GGAGGAAGAACACTCTGTACTACT 58.988 45.833 0.00 0.00 34.22 2.57
1607 2505 5.234972 GGGTGCTCAAAATTTCACTGAAAAG 59.765 40.000 8.28 2.62 35.11 2.27
1616 2514 9.853921 CAAAATTTCACTGAAAAGAATGCTTAC 57.146 29.630 8.28 0.00 35.11 2.34
1618 2516 8.807667 AATTTCACTGAAAAGAATGCTTACTG 57.192 30.769 8.28 0.00 35.11 2.74
1621 2519 6.291377 TCACTGAAAAGAATGCTTACTGTCT 58.709 36.000 0.00 0.00 32.98 3.41
1655 2557 2.536066 TGTGTGCCTGTAGTAGATGGT 58.464 47.619 0.00 0.00 0.00 3.55
1744 2721 3.565902 AGAGGAAGCAGCAAAACAACTAC 59.434 43.478 0.00 0.00 0.00 2.73
1745 2722 3.555966 AGGAAGCAGCAAAACAACTACT 58.444 40.909 0.00 0.00 0.00 2.57
1746 2723 3.565902 AGGAAGCAGCAAAACAACTACTC 59.434 43.478 0.00 0.00 0.00 2.59
1747 2724 3.315191 GGAAGCAGCAAAACAACTACTCA 59.685 43.478 0.00 0.00 0.00 3.41
1884 2975 2.103094 ACACTGCCGATGCACTACATAT 59.897 45.455 0.00 0.00 44.23 1.78
2029 3132 4.625311 AGTCTTTGCTTTGTTTGTTTTCCG 59.375 37.500 0.00 0.00 0.00 4.30
2062 3165 4.106029 AGTGCATGCAATCTGAATTGTC 57.894 40.909 24.58 5.09 43.54 3.18
2106 3215 0.947244 GTGAAACTCAGTGCCCACAG 59.053 55.000 0.82 0.00 0.00 3.66
2117 3226 1.598130 GCCCACAGACGCTGAAACT 60.598 57.895 12.77 0.00 35.18 2.66
2709 3979 1.659601 CGAGAGCAATGTCAGCTTGAG 59.340 52.381 0.00 0.00 43.58 3.02
2811 4127 6.990349 TCAAGATTCTGTCTTTTAAACCTCGT 59.010 34.615 0.00 0.00 44.80 4.18
2966 4299 0.462047 CGTACTCCAATCTGGGTGGC 60.462 60.000 0.00 0.00 38.32 5.01
3181 4551 5.540337 TGAACTTACTGACCTGAGTTCTGAT 59.460 40.000 14.02 0.00 45.05 2.90
3680 6090 7.388437 TCTCATCCAAAATTAAGCTTGCAAAT 58.612 30.769 9.86 0.00 0.00 2.32
3732 6142 1.415659 CGGCCTGAGAGAGATTGGATT 59.584 52.381 0.00 0.00 0.00 3.01
3871 6281 2.413351 GGAGTAGCGCGCTGATGA 59.587 61.111 41.85 21.34 0.00 2.92
4078 6501 3.467803 AGTTAGTGGTCTCTTTGTGTGC 58.532 45.455 0.00 0.00 0.00 4.57
4096 6521 1.554617 TGCGGTCTCAAGAATGATGGA 59.445 47.619 0.00 0.00 34.37 3.41
4168 6609 6.127591 ACCTGCAAGTCTCTAGTGTGTAATAG 60.128 42.308 0.00 0.00 0.00 1.73
4169 6610 6.208988 TGCAAGTCTCTAGTGTGTAATAGG 57.791 41.667 0.00 0.00 0.00 2.57
4196 6654 1.351017 TGAATCCTTGACCCACCTGTC 59.649 52.381 0.00 0.00 35.77 3.51
4532 6996 5.500234 TCTTTAATGCACTATTCCAGCTGT 58.500 37.500 13.81 0.00 0.00 4.40
4783 7249 1.335233 CGCTTCTGCATGCAAGTTTGA 60.335 47.619 22.88 12.21 39.64 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 4.173924 GCTGCTCCCTCTGCCCTC 62.174 72.222 0.00 0.00 0.00 4.30
45 46 4.828925 GACGGCTGCTCCCTCTGC 62.829 72.222 0.00 0.00 0.00 4.26
46 47 4.504916 CGACGGCTGCTCCCTCTG 62.505 72.222 0.00 0.00 0.00 3.35
394 395 2.043953 AGCAATTTCCGGCTCCCC 60.044 61.111 0.00 0.00 34.76 4.81
395 396 3.068729 GCAGCAATTTCCGGCTCCC 62.069 63.158 0.00 0.00 38.56 4.30
403 404 3.200522 CCCTCCGGCAGCAATTTC 58.799 61.111 0.00 0.00 0.00 2.17
433 434 1.043116 TTCCTCGCATCCATCTCCGT 61.043 55.000 0.00 0.00 0.00 4.69
434 435 0.319728 ATTCCTCGCATCCATCTCCG 59.680 55.000 0.00 0.00 0.00 4.63
436 437 2.411904 GTCATTCCTCGCATCCATCTC 58.588 52.381 0.00 0.00 0.00 2.75
438 439 1.143305 CGTCATTCCTCGCATCCATC 58.857 55.000 0.00 0.00 0.00 3.51
442 443 2.600731 CTATCCGTCATTCCTCGCATC 58.399 52.381 0.00 0.00 0.00 3.91
447 448 2.037381 GGGTTCCTATCCGTCATTCCTC 59.963 54.545 0.00 0.00 0.00 3.71
448 449 2.047830 GGGTTCCTATCCGTCATTCCT 58.952 52.381 0.00 0.00 0.00 3.36
449 450 2.047830 AGGGTTCCTATCCGTCATTCC 58.952 52.381 0.00 0.00 28.47 3.01
483 484 2.893637 CACTCCGGTATATATGCTGGC 58.106 52.381 20.74 0.00 38.63 4.85
515 516 3.819902 TGTAAATGTTTTACGGGTGGTCC 59.180 43.478 5.86 0.00 0.00 4.46
524 525 2.416296 GCCCGGCCTGTAAATGTTTTAC 60.416 50.000 0.00 3.72 0.00 2.01
554 555 2.170012 AAAGGCCCACGTAGATCCTA 57.830 50.000 0.00 0.00 0.00 2.94
556 557 2.124277 AAAAAGGCCCACGTAGATCC 57.876 50.000 0.00 0.00 0.00 3.36
584 590 3.306703 GCGTTTTTCCGGACATTATACGA 59.693 43.478 1.83 0.00 0.00 3.43
595 601 1.724581 GCGAACTGCGTTTTTCCGG 60.725 57.895 0.00 0.00 43.41 5.14
611 617 2.797156 GCACATCCACTATAACTCTGCG 59.203 50.000 0.00 0.00 0.00 5.18
621 627 3.570540 AGCATCTCTAGCACATCCACTA 58.429 45.455 0.00 0.00 0.00 2.74
623 629 2.753296 GAGCATCTCTAGCACATCCAC 58.247 52.381 0.00 0.00 0.00 4.02
652 658 3.982372 ATGCTCGCGTACCGTGGTG 62.982 63.158 5.77 0.00 37.97 4.17
654 660 2.954868 GATGCTCGCGTACCGTGG 60.955 66.667 5.77 0.00 37.97 4.94
655 661 2.202557 TGATGCTCGCGTACCGTG 60.203 61.111 5.77 3.36 38.82 4.94
664 1000 1.485838 GATGCGTGAGGTGATGCTCG 61.486 60.000 0.00 0.00 0.00 5.03
667 1003 0.179089 AGAGATGCGTGAGGTGATGC 60.179 55.000 0.00 0.00 0.00 3.91
672 1008 1.107114 CAGGTAGAGATGCGTGAGGT 58.893 55.000 0.00 0.00 0.00 3.85
695 1031 2.159476 GGATACAATGCAGCACACACAG 60.159 50.000 0.00 0.00 0.00 3.66
697 1033 2.549633 GGATACAATGCAGCACACAC 57.450 50.000 0.00 0.00 0.00 3.82
728 1064 4.448210 TCCTCAATTATTTGACCTACCGC 58.552 43.478 0.00 0.00 36.94 5.68
749 1085 1.454663 GCTTGGGATTGGGAGGCTC 60.455 63.158 5.78 5.78 0.00 4.70
750 1086 1.803453 TTGCTTGGGATTGGGAGGCT 61.803 55.000 0.00 0.00 0.00 4.58
751 1087 0.904394 TTTGCTTGGGATTGGGAGGC 60.904 55.000 0.00 0.00 0.00 4.70
752 1088 1.188863 CTTTGCTTGGGATTGGGAGG 58.811 55.000 0.00 0.00 0.00 4.30
753 1089 0.533951 GCTTTGCTTGGGATTGGGAG 59.466 55.000 0.00 0.00 0.00 4.30
754 1090 0.178938 TGCTTTGCTTGGGATTGGGA 60.179 50.000 0.00 0.00 0.00 4.37
755 1091 0.686224 TTGCTTTGCTTGGGATTGGG 59.314 50.000 0.00 0.00 0.00 4.12
756 1092 2.547299 TTTGCTTTGCTTGGGATTGG 57.453 45.000 0.00 0.00 0.00 3.16
757 1093 3.495753 GTCTTTTGCTTTGCTTGGGATTG 59.504 43.478 0.00 0.00 0.00 2.67
758 1094 3.732212 GTCTTTTGCTTTGCTTGGGATT 58.268 40.909 0.00 0.00 0.00 3.01
759 1095 2.288395 CGTCTTTTGCTTTGCTTGGGAT 60.288 45.455 0.00 0.00 0.00 3.85
760 1096 1.066908 CGTCTTTTGCTTTGCTTGGGA 59.933 47.619 0.00 0.00 0.00 4.37
761 1097 1.490621 CGTCTTTTGCTTTGCTTGGG 58.509 50.000 0.00 0.00 0.00 4.12
762 1098 1.066908 TCCGTCTTTTGCTTTGCTTGG 59.933 47.619 0.00 0.00 0.00 3.61
763 1099 2.388121 CTCCGTCTTTTGCTTTGCTTG 58.612 47.619 0.00 0.00 0.00 4.01
764 1100 1.338020 CCTCCGTCTTTTGCTTTGCTT 59.662 47.619 0.00 0.00 0.00 3.91
765 1101 0.954452 CCTCCGTCTTTTGCTTTGCT 59.046 50.000 0.00 0.00 0.00 3.91
766 1102 0.039165 CCCTCCGTCTTTTGCTTTGC 60.039 55.000 0.00 0.00 0.00 3.68
767 1103 1.537202 CTCCCTCCGTCTTTTGCTTTG 59.463 52.381 0.00 0.00 0.00 2.77
768 1104 1.420138 TCTCCCTCCGTCTTTTGCTTT 59.580 47.619 0.00 0.00 0.00 3.51
769 1105 1.002544 CTCTCCCTCCGTCTTTTGCTT 59.997 52.381 0.00 0.00 0.00 3.91
770 1106 0.610687 CTCTCCCTCCGTCTTTTGCT 59.389 55.000 0.00 0.00 0.00 3.91
771 1107 0.608640 TCTCTCCCTCCGTCTTTTGC 59.391 55.000 0.00 0.00 0.00 3.68
772 1108 1.205893 CCTCTCTCCCTCCGTCTTTTG 59.794 57.143 0.00 0.00 0.00 2.44
773 1109 1.562783 CCTCTCTCCCTCCGTCTTTT 58.437 55.000 0.00 0.00 0.00 2.27
774 1110 0.324830 CCCTCTCTCCCTCCGTCTTT 60.325 60.000 0.00 0.00 0.00 2.52
775 1111 1.215679 TCCCTCTCTCCCTCCGTCTT 61.216 60.000 0.00 0.00 0.00 3.01
776 1112 1.619975 TCCCTCTCTCCCTCCGTCT 60.620 63.158 0.00 0.00 0.00 4.18
777 1113 1.152839 CTCCCTCTCTCCCTCCGTC 60.153 68.421 0.00 0.00 0.00 4.79
778 1114 1.619975 TCTCCCTCTCTCCCTCCGT 60.620 63.158 0.00 0.00 0.00 4.69
779 1115 1.150536 CTCTCCCTCTCTCCCTCCG 59.849 68.421 0.00 0.00 0.00 4.63
780 1116 0.478507 CTCTCTCCCTCTCTCCCTCC 59.521 65.000 0.00 0.00 0.00 4.30
781 1117 0.478507 CCTCTCTCCCTCTCTCCCTC 59.521 65.000 0.00 0.00 0.00 4.30
782 1118 0.998945 CCCTCTCTCCCTCTCTCCCT 60.999 65.000 0.00 0.00 0.00 4.20
783 1119 0.996762 TCCCTCTCTCCCTCTCTCCC 60.997 65.000 0.00 0.00 0.00 4.30
784 1120 0.478507 CTCCCTCTCTCCCTCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
785 1121 0.478507 CCTCCCTCTCTCCCTCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
786 1122 0.047176 TCCTCCCTCTCTCCCTCTCT 59.953 60.000 0.00 0.00 0.00 3.10
787 1123 0.478507 CTCCTCCCTCTCTCCCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
788 1124 0.998945 CCTCCTCCCTCTCTCCCTCT 60.999 65.000 0.00 0.00 0.00 3.69
789 1125 1.541672 CCTCCTCCCTCTCTCCCTC 59.458 68.421 0.00 0.00 0.00 4.30
790 1126 2.018086 CCCTCCTCCCTCTCTCCCT 61.018 68.421 0.00 0.00 0.00 4.20
791 1127 2.612251 CCCTCCTCCCTCTCTCCC 59.388 72.222 0.00 0.00 0.00 4.30
792 1128 2.329399 ACCCCTCCTCCCTCTCTCC 61.329 68.421 0.00 0.00 0.00 3.71
793 1129 1.075600 CACCCCTCCTCCCTCTCTC 60.076 68.421 0.00 0.00 0.00 3.20
794 1130 1.547755 TCACCCCTCCTCCCTCTCT 60.548 63.158 0.00 0.00 0.00 3.10
795 1131 1.382009 GTCACCCCTCCTCCCTCTC 60.382 68.421 0.00 0.00 0.00 3.20
796 1132 2.781406 GTCACCCCTCCTCCCTCT 59.219 66.667 0.00 0.00 0.00 3.69
797 1133 2.760385 CGTCACCCCTCCTCCCTC 60.760 72.222 0.00 0.00 0.00 4.30
837 1173 1.500396 CGAAAGGTAAACTGCGGCC 59.500 57.895 0.00 0.00 0.00 6.13
1157 1561 1.979155 CCTCCACTCCTCGCAGTCA 60.979 63.158 0.00 0.00 0.00 3.41
1454 2280 4.080863 TCCTCCTGCTACCTTTTCTTCATC 60.081 45.833 0.00 0.00 0.00 2.92
1463 2295 2.303311 GTGTTCTTCCTCCTGCTACCTT 59.697 50.000 0.00 0.00 0.00 3.50
1607 2505 6.976636 AGCTAAGAAAGACAGTAAGCATTC 57.023 37.500 0.00 0.00 0.00 2.67
1616 2514 6.619446 GCACACAACATAGCTAAGAAAGACAG 60.619 42.308 2.38 0.00 0.00 3.51
1618 2516 5.390991 GGCACACAACATAGCTAAGAAAGAC 60.391 44.000 2.38 0.00 0.00 3.01
1621 2519 4.455533 CAGGCACACAACATAGCTAAGAAA 59.544 41.667 2.38 0.00 0.00 2.52
1655 2557 8.887036 AGCAATTCAATTCTATCGTGTATACA 57.113 30.769 0.08 0.08 0.00 2.29
1666 2641 8.593945 AAATACCCTGAAGCAATTCAATTCTA 57.406 30.769 0.00 0.00 0.00 2.10
2106 3215 6.500041 AGAGTCAGATATAAGTTTCAGCGTC 58.500 40.000 0.00 0.00 0.00 5.19
2709 3979 1.156736 ACTTACAACATGGCAGTCGC 58.843 50.000 0.00 0.00 37.44 5.19
2775 4054 7.991084 AGACAGAATCTTGATCAACATGAAA 57.009 32.000 3.38 0.00 36.51 2.69
2825 4143 3.450817 AGTGGTATGTACTGCAGCATGTA 59.549 43.478 15.27 0.00 39.31 2.29
2826 4144 2.237143 AGTGGTATGTACTGCAGCATGT 59.763 45.455 15.27 0.00 39.31 3.21
2827 4145 2.610833 CAGTGGTATGTACTGCAGCATG 59.389 50.000 15.27 0.00 39.09 4.06
2828 4146 2.501316 TCAGTGGTATGTACTGCAGCAT 59.499 45.455 15.27 12.70 43.97 3.79
2830 4148 2.093973 ACTCAGTGGTATGTACTGCAGC 60.094 50.000 15.27 0.00 43.97 5.25
2831 4149 3.445450 AGACTCAGTGGTATGTACTGCAG 59.555 47.826 13.48 13.48 43.97 4.41
2966 4299 3.438087 CACTGAGAAGCCACAAACCTATG 59.562 47.826 0.00 0.00 0.00 2.23
3181 4551 5.073144 AGTGTCTTTTCCCAGGACTTCATAA 59.927 40.000 0.00 0.00 0.00 1.90
3599 6008 1.002430 TCTGAACTCACCAGATGTGCC 59.998 52.381 0.00 0.00 45.03 5.01
3732 6142 1.296392 CCCGTCAGTCAAGATGGCA 59.704 57.895 0.00 0.00 42.25 4.92
3871 6281 6.515531 CGCCTCACATTATTATTTTGCTGGAT 60.516 38.462 0.00 0.00 0.00 3.41
4078 6501 5.824904 AAAATCCATCATTCTTGAGACCG 57.175 39.130 0.00 0.00 34.73 4.79
4096 6521 5.815581 TCCATACACCAGCTGAGTTAAAAT 58.184 37.500 17.39 1.06 0.00 1.82
4168 6609 2.820197 GGGTCAAGGATTCAGTGTTTCC 59.180 50.000 6.12 6.12 0.00 3.13
4169 6610 3.253432 GTGGGTCAAGGATTCAGTGTTTC 59.747 47.826 0.00 0.00 0.00 2.78
4196 6654 2.609427 TAATCAGCAGCAGCACTAGG 57.391 50.000 3.17 0.00 45.49 3.02
4574 7039 6.977213 AGTTGTACGGTTGCAATTTAAATCT 58.023 32.000 0.59 0.00 29.30 2.40
4783 7249 9.330063 ACTGATAAACAACACATCATAATCGAT 57.670 29.630 0.00 0.00 0.00 3.59


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

AutoCloner maintained by Alex Coulton.