Multiple sequence alignment - TraesCS5A01G173700

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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 TraesCS5A01G173700 chr5A 100.000 3743 0 0 1 3743 367079365 367083107 0.000000e+00 6913.0
1 TraesCS5A01G173700 chr5A 84.211 475 64 6 2202 2671 356538511 356538979 5.700000e-123 451.0
2 TraesCS5A01G173700 chr5A 87.685 203 18 3 1801 1996 356538302 356538504 2.910000e-56 230.0
3 TraesCS5A01G173700 chr5B 90.654 1744 98 27 715 2410 315895689 315897415 0.000000e+00 2257.0
4 TraesCS5A01G173700 chr5B 90.842 404 32 5 287 686 315895210 315895612 1.530000e-148 536.0
5 TraesCS5A01G173700 chr5B 95.975 323 12 1 2450 2771 315897734 315898056 1.190000e-144 523.0
6 TraesCS5A01G173700 chr5D 92.688 1354 68 17 1438 2766 277722351 277723698 0.000000e+00 1923.0
7 TraesCS5A01G173700 chr5D 90.890 977 73 6 2778 3741 499262380 499263353 0.000000e+00 1297.0
8 TraesCS5A01G173700 chr5D 93.658 883 29 16 746 1606 277720774 277721651 0.000000e+00 1295.0
9 TraesCS5A01G173700 chr5D 88.644 590 42 14 113 688 277719799 277720377 0.000000e+00 695.0
10 TraesCS5A01G173700 chr5D 81.250 688 118 11 3062 3743 562056118 562055436 2.540000e-151 545.0
11 TraesCS5A01G173700 chr5D 94.886 176 2 2 1274 1448 277722143 277722312 6.160000e-68 268.0
12 TraesCS5A01G173700 chr6A 90.808 903 70 2 2788 3677 126462711 126461809 0.000000e+00 1195.0
13 TraesCS5A01G173700 chr2A 88.889 990 80 11 2771 3743 311163359 311164335 0.000000e+00 1192.0
14 TraesCS5A01G173700 chr2A 87.800 500 55 6 2787 3282 20005122 20005619 6.970000e-162 580.0
15 TraesCS5A01G173700 chr1A 92.939 609 43 0 3135 3743 50807381 50806773 0.000000e+00 887.0
16 TraesCS5A01G173700 chr1A 89.422 709 63 3 2978 3674 423989633 423990341 0.000000e+00 883.0
17 TraesCS5A01G173700 chr2B 83.493 939 139 5 2776 3698 728230448 728231386 0.000000e+00 861.0
18 TraesCS5A01G173700 chr2B 93.694 111 7 0 1 111 158305656 158305766 2.310000e-37 167.0
19 TraesCS5A01G173700 chr3D 82.661 992 148 18 2770 3743 461316159 461317144 0.000000e+00 857.0
20 TraesCS5A01G173700 chr3D 86.578 529 51 9 2769 3282 598482401 598482924 1.950000e-157 566.0
21 TraesCS5A01G173700 chr3D 100.000 31 0 0 113 143 603306671 603306701 1.450000e-04 58.4
22 TraesCS5A01G173700 chr6D 86.207 783 88 8 2763 3530 445039446 445040223 0.000000e+00 830.0
23 TraesCS5A01G173700 chr4D 81.947 986 154 17 2777 3743 311199194 311200174 0.000000e+00 813.0
24 TraesCS5A01G173700 chr4D 87.048 525 46 9 2774 3282 328539998 328539480 1.170000e-159 573.0
25 TraesCS5A01G173700 chr4A 85.271 774 95 8 2772 3530 672201321 672200552 0.000000e+00 780.0
26 TraesCS5A01G173700 chr4A 84.632 475 62 6 2202 2671 92378121 92377653 2.630000e-126 462.0
27 TraesCS5A01G173700 chr4A 87.685 203 18 2 1801 1996 92378329 92378127 2.910000e-56 230.0
28 TraesCS5A01G173700 chr2D 86.998 523 48 9 2778 3282 178766755 178767275 4.190000e-159 571.0
29 TraesCS5A01G173700 chr2D 91.089 101 9 0 1 101 561317211 561317111 1.810000e-28 137.0
30 TraesCS5A01G173700 chr2D 90.698 43 3 1 401 442 427609833 427609875 5.220000e-04 56.5
31 TraesCS5A01G173700 chr7D 85.902 532 54 9 2769 3282 28406197 28406725 7.070000e-152 547.0
32 TraesCS5A01G173700 chr7D 86.304 460 45 9 2753 3197 524535746 524535290 5.620000e-133 484.0
33 TraesCS5A01G173700 chr3B 85.263 475 59 8 2201 2671 126844295 126844762 2.620000e-131 479.0
34 TraesCS5A01G173700 chr3B 84.421 475 64 6 2201 2671 430592945 430593413 3.410000e-125 459.0
35 TraesCS5A01G173700 chr3B 86.634 202 20 2 1801 1995 78137857 78138058 2.260000e-52 217.0
36 TraesCS5A01G173700 chr3B 84.932 219 22 4 1786 1995 430592722 430592938 1.050000e-50 211.0
37 TraesCS5A01G173700 chr4B 85.053 475 61 6 2201 2671 192127988 192127520 3.380000e-130 475.0
38 TraesCS5A01G173700 chr4B 86.634 202 19 3 1801 1995 192128195 192127995 2.260000e-52 217.0
39 TraesCS5A01G173700 chr3A 85.084 476 58 10 2201 2671 152282602 152283069 1.220000e-129 473.0
40 TraesCS5A01G173700 chr3A 87.065 201 19 3 1801 1994 152282394 152282594 1.750000e-53 220.0
41 TraesCS5A01G173700 chr6B 87.047 193 18 2 1810 1995 700780767 700780575 1.050000e-50 211.0
42 TraesCS5A01G173700 chr6B 90.090 111 11 0 1 111 326967115 326967005 1.080000e-30 145.0


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 TraesCS5A01G173700 chr5A 367079365 367083107 3742 False 6913.000000 6913 100.000000 1 3743 1 chr5A.!!$F1 3742
1 TraesCS5A01G173700 chr5A 356538302 356538979 677 False 340.500000 451 85.948000 1801 2671 2 chr5A.!!$F2 870
2 TraesCS5A01G173700 chr5B 315895210 315898056 2846 False 1105.333333 2257 92.490333 287 2771 3 chr5B.!!$F1 2484
3 TraesCS5A01G173700 chr5D 499262380 499263353 973 False 1297.000000 1297 90.890000 2778 3741 1 chr5D.!!$F1 963
4 TraesCS5A01G173700 chr5D 277719799 277723698 3899 False 1045.250000 1923 92.469000 113 2766 4 chr5D.!!$F2 2653
5 TraesCS5A01G173700 chr5D 562055436 562056118 682 True 545.000000 545 81.250000 3062 3743 1 chr5D.!!$R1 681
6 TraesCS5A01G173700 chr6A 126461809 126462711 902 True 1195.000000 1195 90.808000 2788 3677 1 chr6A.!!$R1 889
7 TraesCS5A01G173700 chr2A 311163359 311164335 976 False 1192.000000 1192 88.889000 2771 3743 1 chr2A.!!$F2 972
8 TraesCS5A01G173700 chr1A 50806773 50807381 608 True 887.000000 887 92.939000 3135 3743 1 chr1A.!!$R1 608
9 TraesCS5A01G173700 chr1A 423989633 423990341 708 False 883.000000 883 89.422000 2978 3674 1 chr1A.!!$F1 696
10 TraesCS5A01G173700 chr2B 728230448 728231386 938 False 861.000000 861 83.493000 2776 3698 1 chr2B.!!$F2 922
11 TraesCS5A01G173700 chr3D 461316159 461317144 985 False 857.000000 857 82.661000 2770 3743 1 chr3D.!!$F1 973
12 TraesCS5A01G173700 chr3D 598482401 598482924 523 False 566.000000 566 86.578000 2769 3282 1 chr3D.!!$F2 513
13 TraesCS5A01G173700 chr6D 445039446 445040223 777 False 830.000000 830 86.207000 2763 3530 1 chr6D.!!$F1 767
14 TraesCS5A01G173700 chr4D 311199194 311200174 980 False 813.000000 813 81.947000 2777 3743 1 chr4D.!!$F1 966
15 TraesCS5A01G173700 chr4D 328539480 328539998 518 True 573.000000 573 87.048000 2774 3282 1 chr4D.!!$R1 508
16 TraesCS5A01G173700 chr4A 672200552 672201321 769 True 780.000000 780 85.271000 2772 3530 1 chr4A.!!$R1 758
17 TraesCS5A01G173700 chr4A 92377653 92378329 676 True 346.000000 462 86.158500 1801 2671 2 chr4A.!!$R2 870
18 TraesCS5A01G173700 chr2D 178766755 178767275 520 False 571.000000 571 86.998000 2778 3282 1 chr2D.!!$F1 504
19 TraesCS5A01G173700 chr7D 28406197 28406725 528 False 547.000000 547 85.902000 2769 3282 1 chr7D.!!$F1 513
20 TraesCS5A01G173700 chr3B 430592722 430593413 691 False 335.000000 459 84.676500 1786 2671 2 chr3B.!!$F3 885
21 TraesCS5A01G173700 chr4B 192127520 192128195 675 True 346.000000 475 85.843500 1801 2671 2 chr4B.!!$R1 870
22 TraesCS5A01G173700 chr3A 152282394 152283069 675 False 346.500000 473 86.074500 1801 2671 2 chr3A.!!$F1 870

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
95 96 0.097499 ATCGTGCATGCACAATCGTG 59.903 50.0 40.95 27.28 46.47 4.35 F
160 161 0.247460 TGACCAGCCTCATGACTTCG 59.753 55.0 0.00 0.00 0.00 3.79 F
841 1218 0.840288 ATATGCTATCGTGGGCCCCA 60.840 55.0 22.27 8.44 0.00 4.96 F
1696 2965 0.548031 CCCCTTCATCAGGCTGCTAA 59.452 55.0 10.34 2.81 42.29 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1131 1516 0.518636 CTCTGCACCACACGGATTTG 59.481 55.000 0.0 0.00 35.59 2.32 R
1539 2807 1.207329 GTGAAGGACAGGCCGTAGAAT 59.793 52.381 0.0 0.00 43.43 2.40 R
2257 3572 0.179124 GCCGACTCGAAGATCTGCTT 60.179 55.000 0.0 0.00 40.25 3.91 R
3415 5034 0.737715 CCGAGGAGAAGTTCAAGGCG 60.738 60.000 5.5 3.71 0.00 5.52 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
19 20 1.900237 GCACGATGGACAAAAGCATC 58.100 50.000 0.00 0.00 0.00 3.91
20 21 1.468054 GCACGATGGACAAAAGCATCC 60.468 52.381 0.00 0.00 35.37 3.51
26 27 2.886913 TGGACAAAAGCATCCATTGGA 58.113 42.857 8.08 8.08 40.17 3.53
27 28 3.443052 TGGACAAAAGCATCCATTGGAT 58.557 40.909 12.62 12.62 44.21 3.41
28 29 3.839490 TGGACAAAAGCATCCATTGGATT 59.161 39.130 15.75 0.00 39.79 3.01
29 30 4.186159 GGACAAAAGCATCCATTGGATTG 58.814 43.478 15.75 13.79 39.79 2.67
30 31 4.322953 GGACAAAAGCATCCATTGGATTGT 60.323 41.667 15.75 16.74 39.79 2.71
31 32 5.105392 GGACAAAAGCATCCATTGGATTGTA 60.105 40.000 15.75 0.00 39.79 2.41
32 33 6.407299 GGACAAAAGCATCCATTGGATTGTAT 60.407 38.462 15.75 0.63 39.79 2.29
33 34 6.949715 ACAAAAGCATCCATTGGATTGTATT 58.050 32.000 15.75 6.59 39.79 1.89
34 35 6.819649 ACAAAAGCATCCATTGGATTGTATTG 59.180 34.615 15.75 18.21 39.79 1.90
35 36 6.549433 AAAGCATCCATTGGATTGTATTGT 57.451 33.333 15.75 0.00 39.79 2.71
36 37 5.779529 AGCATCCATTGGATTGTATTGTC 57.220 39.130 15.75 2.55 39.79 3.18
37 38 5.452255 AGCATCCATTGGATTGTATTGTCT 58.548 37.500 15.75 4.59 39.79 3.41
38 39 5.895534 AGCATCCATTGGATTGTATTGTCTT 59.104 36.000 15.75 0.00 39.79 3.01
39 40 5.981315 GCATCCATTGGATTGTATTGTCTTG 59.019 40.000 15.75 3.04 39.79 3.02
40 41 5.581126 TCCATTGGATTGTATTGTCTTGC 57.419 39.130 0.00 0.00 0.00 4.01
41 42 5.015515 TCCATTGGATTGTATTGTCTTGCA 58.984 37.500 0.00 0.00 0.00 4.08
42 43 5.479724 TCCATTGGATTGTATTGTCTTGCAA 59.520 36.000 0.00 0.00 41.89 4.08
43 44 6.014755 TCCATTGGATTGTATTGTCTTGCAAA 60.015 34.615 0.00 0.00 40.91 3.68
44 45 6.819649 CCATTGGATTGTATTGTCTTGCAAAT 59.180 34.615 0.00 0.00 40.91 2.32
45 46 7.010738 CCATTGGATTGTATTGTCTTGCAAATC 59.989 37.037 0.00 0.00 40.91 2.17
46 47 6.839124 TGGATTGTATTGTCTTGCAAATCT 57.161 33.333 0.00 0.00 40.91 2.40
47 48 6.623486 TGGATTGTATTGTCTTGCAAATCTG 58.377 36.000 0.00 0.00 40.91 2.90
63 64 6.403333 CAAATCTGCATTGTTCAAGGAATG 57.597 37.500 1.37 0.00 33.46 2.67
69 70 4.100707 CATTGTTCAAGGAATGCATCGT 57.899 40.909 0.00 0.00 0.00 3.73
70 71 3.829886 TTGTTCAAGGAATGCATCGTC 57.170 42.857 0.00 0.00 0.00 4.20
71 72 2.083774 TGTTCAAGGAATGCATCGTCC 58.916 47.619 9.11 9.11 0.00 4.79
72 73 2.083774 GTTCAAGGAATGCATCGTCCA 58.916 47.619 17.74 0.00 36.28 4.02
73 74 2.487762 GTTCAAGGAATGCATCGTCCAA 59.512 45.455 17.74 3.06 36.28 3.53
74 75 2.789213 TCAAGGAATGCATCGTCCAAA 58.211 42.857 17.74 2.20 36.28 3.28
75 76 3.153130 TCAAGGAATGCATCGTCCAAAA 58.847 40.909 17.74 1.89 36.28 2.44
76 77 3.571828 TCAAGGAATGCATCGTCCAAAAA 59.428 39.130 17.74 0.35 36.28 1.94
77 78 4.220382 TCAAGGAATGCATCGTCCAAAAAT 59.780 37.500 17.74 0.00 36.28 1.82
78 79 4.376340 AGGAATGCATCGTCCAAAAATC 57.624 40.909 17.74 0.22 36.28 2.17
79 80 3.108144 GGAATGCATCGTCCAAAAATCG 58.892 45.455 11.83 0.00 33.79 3.34
80 81 3.427503 GGAATGCATCGTCCAAAAATCGT 60.428 43.478 11.83 0.00 33.79 3.73
81 82 2.610219 TGCATCGTCCAAAAATCGTG 57.390 45.000 0.00 0.00 0.00 4.35
82 83 1.259316 GCATCGTCCAAAAATCGTGC 58.741 50.000 0.00 0.00 0.00 5.34
83 84 1.400888 GCATCGTCCAAAAATCGTGCA 60.401 47.619 0.00 0.00 34.54 4.57
84 85 2.731968 GCATCGTCCAAAAATCGTGCAT 60.732 45.455 0.00 0.00 34.54 3.96
85 86 2.610219 TCGTCCAAAAATCGTGCATG 57.390 45.000 0.00 0.00 0.00 4.06
86 87 0.984109 CGTCCAAAAATCGTGCATGC 59.016 50.000 11.82 11.82 0.00 4.06
87 88 1.665448 CGTCCAAAAATCGTGCATGCA 60.665 47.619 18.46 18.46 0.00 3.96
88 89 1.720852 GTCCAAAAATCGTGCATGCAC 59.279 47.619 35.76 35.76 43.01 4.57
89 90 1.339291 TCCAAAAATCGTGCATGCACA 59.661 42.857 40.95 30.30 46.47 4.57
90 91 2.133553 CCAAAAATCGTGCATGCACAA 58.866 42.857 40.95 30.50 46.47 3.33
91 92 2.737783 CCAAAAATCGTGCATGCACAAT 59.262 40.909 40.95 31.28 46.47 2.71
92 93 3.181528 CCAAAAATCGTGCATGCACAATC 60.182 43.478 40.95 21.42 46.47 2.67
93 94 1.898938 AAATCGTGCATGCACAATCG 58.101 45.000 40.95 30.34 46.47 3.34
94 95 0.804364 AATCGTGCATGCACAATCGT 59.196 45.000 40.95 23.03 46.47 3.73
95 96 0.097499 ATCGTGCATGCACAATCGTG 59.903 50.000 40.95 27.28 46.47 4.35
96 97 1.207339 CGTGCATGCACAATCGTGT 59.793 52.632 40.95 0.00 46.47 4.49
110 111 5.152097 ACAATCGTGTGTAGAGTAGTTTCG 58.848 41.667 0.00 0.00 36.31 3.46
111 112 3.818961 TCGTGTGTAGAGTAGTTTCGG 57.181 47.619 0.00 0.00 0.00 4.30
124 125 7.479150 AGAGTAGTTTCGGTTATGTTACTAGC 58.521 38.462 0.00 0.00 0.00 3.42
128 129 9.741647 GTAGTTTCGGTTATGTTACTAGCTAAT 57.258 33.333 0.00 0.00 0.00 1.73
135 136 9.962783 CGGTTATGTTACTAGCTAATTTACTCT 57.037 33.333 0.00 0.00 0.00 3.24
145 146 8.852135 ACTAGCTAATTTACTCTCACTATGACC 58.148 37.037 0.00 0.00 0.00 4.02
160 161 0.247460 TGACCAGCCTCATGACTTCG 59.753 55.000 0.00 0.00 0.00 3.79
179 180 7.095397 TGACTTCGTGACATTAAAAGTACATGG 60.095 37.037 0.00 0.00 30.68 3.66
180 181 6.932400 ACTTCGTGACATTAAAAGTACATGGA 59.068 34.615 0.00 0.00 0.00 3.41
241 242 4.895668 TTTTTACACCGATGTACTCCCT 57.104 40.909 0.00 0.00 41.12 4.20
243 244 3.377253 TTACACCGATGTACTCCCTCT 57.623 47.619 0.00 0.00 41.12 3.69
278 282 7.151308 TGTAAGTCAGCAACATTTATTTTGGG 58.849 34.615 0.00 0.00 0.00 4.12
283 287 3.056179 AGCAACATTTATTTTGGGACGGG 60.056 43.478 0.00 0.00 0.00 5.28
285 289 3.178412 ACATTTATTTTGGGACGGGGT 57.822 42.857 0.00 0.00 0.00 4.95
288 292 2.423446 TTATTTTGGGACGGGGTAGC 57.577 50.000 0.00 0.00 0.00 3.58
480 496 9.322773 TCGGACAGAGGTAATAGTATAATATCG 57.677 37.037 0.00 0.00 0.00 2.92
481 497 8.068977 CGGACAGAGGTAATAGTATAATATCGC 58.931 40.741 0.00 0.00 0.00 4.58
482 498 9.122779 GGACAGAGGTAATAGTATAATATCGCT 57.877 37.037 0.00 0.00 0.00 4.93
587 604 8.200792 ACCATCTTTTTGTATGCAACTAAAACA 58.799 29.630 13.06 7.57 37.71 2.83
594 611 6.307031 TGTATGCAACTAAAACAACGACAT 57.693 33.333 0.00 0.00 0.00 3.06
620 638 7.947782 AATTTTGGATAGGAGGAGTACCATA 57.052 36.000 0.00 0.00 38.94 2.74
672 692 5.393902 CAAAGTTTGCTTTCATTCACCAC 57.606 39.130 1.96 0.00 42.54 4.16
673 693 4.734398 AAGTTTGCTTTCATTCACCACA 57.266 36.364 0.00 0.00 0.00 4.17
674 694 4.942761 AGTTTGCTTTCATTCACCACAT 57.057 36.364 0.00 0.00 0.00 3.21
675 695 6.403866 AAGTTTGCTTTCATTCACCACATA 57.596 33.333 0.00 0.00 0.00 2.29
676 696 6.594788 AGTTTGCTTTCATTCACCACATAT 57.405 33.333 0.00 0.00 0.00 1.78
677 697 7.701539 AGTTTGCTTTCATTCACCACATATA 57.298 32.000 0.00 0.00 0.00 0.86
678 698 7.765307 AGTTTGCTTTCATTCACCACATATAG 58.235 34.615 0.00 0.00 0.00 1.31
679 699 5.756195 TGCTTTCATTCACCACATATAGC 57.244 39.130 0.00 0.00 0.00 2.97
682 702 6.377996 TGCTTTCATTCACCACATATAGCTTT 59.622 34.615 0.00 0.00 0.00 3.51
841 1218 0.840288 ATATGCTATCGTGGGCCCCA 60.840 55.000 22.27 8.44 0.00 4.96
950 1329 1.276138 CATTTGCCTCCCCCAAAGAAC 59.724 52.381 0.00 0.00 35.84 3.01
982 1361 8.525290 TCTTTCTTCTCCAAGAGAACAAAAAT 57.475 30.769 2.94 0.00 42.78 1.82
999 1378 9.958285 GAACAAAAATTTCTGAAACAAAGAGAC 57.042 29.630 4.73 0.00 0.00 3.36
1084 1463 1.589716 GGTGAGCCAAGATGCGCTTT 61.590 55.000 9.73 0.00 34.84 3.51
1120 1505 2.682856 TCCATTGTTAATCTGGCTTCGC 59.317 45.455 0.00 0.00 0.00 4.70
1131 1516 2.394563 GGCTTCGCTCTGAGCAACC 61.395 63.158 27.46 18.22 42.58 3.77
1184 1569 2.203126 GAGGCTCAGGAATGGCGG 60.203 66.667 10.25 0.00 0.00 6.13
1223 1608 2.664081 GGCTGTCCCTGAGGAGGTG 61.664 68.421 0.00 0.00 45.21 4.00
1224 1609 2.664081 GCTGTCCCTGAGGAGGTGG 61.664 68.421 0.00 0.00 45.21 4.61
1225 1610 1.229336 CTGTCCCTGAGGAGGTGGT 60.229 63.158 0.00 0.00 45.21 4.16
1445 2712 3.831911 AGAGCTTGCTTACACTCTCTCTT 59.168 43.478 0.00 0.00 34.42 2.85
1539 2807 1.669760 CAACAACTTCGCCGGCCTA 60.670 57.895 23.46 6.42 0.00 3.93
1696 2965 0.548031 CCCCTTCATCAGGCTGCTAA 59.452 55.000 10.34 2.81 42.29 3.09
1764 3069 9.419737 CAAATTTTCTTTTTGTAATTCACCGTG 57.580 29.630 0.00 0.00 31.05 4.94
1979 3293 4.614946 AGAGTGTTTTGCAATTCTTCTGC 58.385 39.130 0.00 0.00 40.35 4.26
1997 3311 5.710513 TCTGCTTTGTGCTGTAATGAATT 57.289 34.783 0.00 0.00 43.37 2.17
2008 3323 6.032775 GTGCTGTAATGAATTGTCATGTTTCG 59.967 38.462 0.00 0.00 44.02 3.46
2142 3457 3.637694 AGACCGAGCTAACTTTCCCTATC 59.362 47.826 0.00 0.00 0.00 2.08
2207 3522 4.504097 TCAGCTCATGATCGTCGTTTTATG 59.496 41.667 0.00 0.00 31.12 1.90
2257 3572 2.120940 TGTTCCCGGACCAGGCTA 59.879 61.111 0.73 0.00 0.00 3.93
2310 3625 0.249657 GATCAGGATCGCCGCTCTTT 60.250 55.000 0.00 0.00 39.96 2.52
2322 3637 3.188492 GCCGCTCTTTTAGTTACTCTCC 58.812 50.000 0.00 0.00 0.00 3.71
2423 3858 8.662781 ATCGATGCTACTGATTTAAGCTTAAA 57.337 30.769 28.78 28.78 37.16 1.52
2424 3859 7.906160 TCGATGCTACTGATTTAAGCTTAAAC 58.094 34.615 29.11 22.38 35.65 2.01
2439 3874 3.239712 GCTTAAACGCACAAACAACAGTC 59.760 43.478 0.00 0.00 0.00 3.51
2448 4045 0.106519 AAACAACAGTCCCTGCTGCT 60.107 50.000 0.00 0.00 39.96 4.24
2482 4080 7.582719 AGGCCAGTTGTTATAAAATCTGGATA 58.417 34.615 27.04 0.00 43.28 2.59
2681 4281 6.928348 TTTTCTCACATACACCCTCTTCTA 57.072 37.500 0.00 0.00 0.00 2.10
2682 4282 5.916661 TTCTCACATACACCCTCTTCTAC 57.083 43.478 0.00 0.00 0.00 2.59
2690 4290 6.379133 ACATACACCCTCTTCTACGTCAATTA 59.621 38.462 0.00 0.00 0.00 1.40
2824 4425 2.163509 GGCCTCTGCATCTAGACGATA 58.836 52.381 0.00 0.00 40.13 2.92
2968 4573 3.527665 AGTCTGGGCCTAATACCAAACAT 59.472 43.478 4.53 0.00 36.09 2.71
2997 4602 4.884164 GCAGCCAAACCTAACATCTAAGAT 59.116 41.667 0.00 0.00 0.00 2.40
3011 4616 4.823364 TCTAAGATCTGAGGTCCCATCT 57.177 45.455 7.28 0.00 0.00 2.90
3075 4692 1.613928 TCAACCGGGTATGAGGCCA 60.614 57.895 6.32 0.00 0.00 5.36
3104 4721 3.028850 CACCTGCCATCAATCCATCTTT 58.971 45.455 0.00 0.00 0.00 2.52
3118 4735 8.475639 TCAATCCATCTTTAGAGTTGTACTACC 58.524 37.037 3.72 0.00 0.00 3.18
3244 4863 4.615815 GCCATGCCGCCGAGATCT 62.616 66.667 0.00 0.00 0.00 2.75
3306 4925 2.455960 ATCCGTCCACTGGTCCCTCA 62.456 60.000 0.00 0.00 0.00 3.86
3377 4996 1.067416 GCACCGCCGTCATCTGATA 59.933 57.895 0.00 0.00 0.00 2.15
3380 4999 2.417379 GCACCGCCGTCATCTGATATAT 60.417 50.000 0.00 0.00 0.00 0.86
3415 5034 1.742768 CCCGAGGTAGCAGATGGTC 59.257 63.158 0.00 0.00 0.00 4.02
3525 5145 0.397187 TTTTCACCCGGATCCGTTCA 59.603 50.000 31.22 10.58 37.81 3.18
3532 5152 1.082117 CCGGATCCGTTCAAAGGTCG 61.082 60.000 31.22 9.25 37.81 4.79
3559 5179 3.443045 CATCTTGTGCACGGGCCC 61.443 66.667 13.57 13.57 40.13 5.80
3699 5322 4.473520 CAGATCTGCCGGCCCGTT 62.474 66.667 26.77 10.18 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.468054 GGATGCTTTTGTCCATCGTGC 60.468 52.381 0.00 0.00 38.93 5.34
1 2 1.811965 TGGATGCTTTTGTCCATCGTG 59.188 47.619 0.00 0.00 39.51 4.35
7 8 4.186159 CAATCCAATGGATGCTTTTGTCC 58.814 43.478 16.52 0.00 42.27 4.02
10 11 6.819649 ACAATACAATCCAATGGATGCTTTTG 59.180 34.615 16.52 17.83 42.27 2.44
11 12 6.949715 ACAATACAATCCAATGGATGCTTTT 58.050 32.000 16.52 5.37 42.27 2.27
12 13 6.381994 AGACAATACAATCCAATGGATGCTTT 59.618 34.615 16.52 5.01 42.27 3.51
13 14 5.895534 AGACAATACAATCCAATGGATGCTT 59.104 36.000 16.52 5.70 42.27 3.91
14 15 5.452255 AGACAATACAATCCAATGGATGCT 58.548 37.500 16.52 6.37 42.27 3.79
15 16 5.779529 AGACAATACAATCCAATGGATGC 57.220 39.130 16.52 0.73 42.27 3.91
16 17 5.981315 GCAAGACAATACAATCCAATGGATG 59.019 40.000 16.52 12.13 42.27 3.51
17 18 5.657745 TGCAAGACAATACAATCCAATGGAT 59.342 36.000 9.36 9.36 45.46 3.41
18 19 5.015515 TGCAAGACAATACAATCCAATGGA 58.984 37.500 3.67 3.67 35.55 3.41
19 20 5.327616 TGCAAGACAATACAATCCAATGG 57.672 39.130 0.00 0.00 0.00 3.16
20 21 7.762615 AGATTTGCAAGACAATACAATCCAATG 59.237 33.333 0.00 0.00 38.31 2.82
21 22 7.762615 CAGATTTGCAAGACAATACAATCCAAT 59.237 33.333 0.00 0.00 38.31 3.16
22 23 7.092079 CAGATTTGCAAGACAATACAATCCAA 58.908 34.615 0.00 0.00 38.31 3.53
23 24 6.623486 CAGATTTGCAAGACAATACAATCCA 58.377 36.000 0.00 0.00 38.31 3.41
40 41 6.403333 CATTCCTTGAACAATGCAGATTTG 57.597 37.500 0.00 0.00 0.00 2.32
48 49 4.100529 GACGATGCATTCCTTGAACAATG 58.899 43.478 0.00 0.00 33.77 2.82
49 50 3.129287 GGACGATGCATTCCTTGAACAAT 59.871 43.478 9.78 0.00 0.00 2.71
50 51 2.487762 GGACGATGCATTCCTTGAACAA 59.512 45.455 9.78 0.00 0.00 2.83
51 52 2.083774 GGACGATGCATTCCTTGAACA 58.916 47.619 9.78 0.00 0.00 3.18
52 53 2.083774 TGGACGATGCATTCCTTGAAC 58.916 47.619 16.58 0.00 32.55 3.18
53 54 2.488204 TGGACGATGCATTCCTTGAA 57.512 45.000 16.58 0.00 32.55 2.69
54 55 2.488204 TTGGACGATGCATTCCTTGA 57.512 45.000 16.58 2.80 32.55 3.02
55 56 3.574284 TTTTGGACGATGCATTCCTTG 57.426 42.857 16.58 1.55 32.55 3.61
56 57 4.675146 CGATTTTTGGACGATGCATTCCTT 60.675 41.667 16.58 0.00 32.55 3.36
57 58 3.181497 CGATTTTTGGACGATGCATTCCT 60.181 43.478 16.58 0.00 32.55 3.36
58 59 3.108144 CGATTTTTGGACGATGCATTCC 58.892 45.455 10.08 10.08 0.00 3.01
59 60 3.543494 CACGATTTTTGGACGATGCATTC 59.457 43.478 0.00 0.00 0.00 2.67
60 61 3.500982 CACGATTTTTGGACGATGCATT 58.499 40.909 0.00 0.00 0.00 3.56
61 62 2.731968 GCACGATTTTTGGACGATGCAT 60.732 45.455 0.00 0.00 35.74 3.96
62 63 1.400888 GCACGATTTTTGGACGATGCA 60.401 47.619 0.00 0.00 35.74 3.96
63 64 1.259316 GCACGATTTTTGGACGATGC 58.741 50.000 0.00 0.00 0.00 3.91
64 65 2.610219 TGCACGATTTTTGGACGATG 57.390 45.000 0.00 0.00 0.00 3.84
65 66 2.731968 GCATGCACGATTTTTGGACGAT 60.732 45.455 14.21 0.00 0.00 3.73
66 67 1.400888 GCATGCACGATTTTTGGACGA 60.401 47.619 14.21 0.00 0.00 4.20
67 68 0.984109 GCATGCACGATTTTTGGACG 59.016 50.000 14.21 0.00 0.00 4.79
68 69 1.720852 GTGCATGCACGATTTTTGGAC 59.279 47.619 33.20 7.91 37.19 4.02
69 70 2.063156 GTGCATGCACGATTTTTGGA 57.937 45.000 33.20 0.00 37.19 3.53
70 71 2.737783 ATTGTGCATGCACGATTTTTGG 59.262 40.909 37.30 0.00 45.82 3.28
87 88 5.152097 CGAAACTACTCTACACACGATTGT 58.848 41.667 0.00 0.00 35.84 2.71
88 89 4.557690 CCGAAACTACTCTACACACGATTG 59.442 45.833 0.00 0.00 0.00 2.67
89 90 4.217118 ACCGAAACTACTCTACACACGATT 59.783 41.667 0.00 0.00 0.00 3.34
90 91 3.755378 ACCGAAACTACTCTACACACGAT 59.245 43.478 0.00 0.00 0.00 3.73
91 92 3.141398 ACCGAAACTACTCTACACACGA 58.859 45.455 0.00 0.00 0.00 4.35
92 93 3.549299 ACCGAAACTACTCTACACACG 57.451 47.619 0.00 0.00 0.00 4.49
93 94 6.385033 ACATAACCGAAACTACTCTACACAC 58.615 40.000 0.00 0.00 0.00 3.82
94 95 6.579666 ACATAACCGAAACTACTCTACACA 57.420 37.500 0.00 0.00 0.00 3.72
95 96 8.239998 AGTAACATAACCGAAACTACTCTACAC 58.760 37.037 0.00 0.00 0.00 2.90
96 97 8.340618 AGTAACATAACCGAAACTACTCTACA 57.659 34.615 0.00 0.00 0.00 2.74
97 98 9.928236 CTAGTAACATAACCGAAACTACTCTAC 57.072 37.037 0.00 0.00 0.00 2.59
98 99 8.616076 GCTAGTAACATAACCGAAACTACTCTA 58.384 37.037 0.00 0.00 0.00 2.43
99 100 7.338957 AGCTAGTAACATAACCGAAACTACTCT 59.661 37.037 0.00 0.00 0.00 3.24
100 101 7.479150 AGCTAGTAACATAACCGAAACTACTC 58.521 38.462 0.00 0.00 0.00 2.59
101 102 7.401955 AGCTAGTAACATAACCGAAACTACT 57.598 36.000 0.00 0.00 0.00 2.57
102 103 9.741647 ATTAGCTAGTAACATAACCGAAACTAC 57.258 33.333 0.00 0.00 0.00 2.73
104 105 9.662947 AAATTAGCTAGTAACATAACCGAAACT 57.337 29.630 0.00 0.00 0.00 2.66
108 109 9.956720 GAGTAAATTAGCTAGTAACATAACCGA 57.043 33.333 0.00 0.00 0.00 4.69
109 110 9.962783 AGAGTAAATTAGCTAGTAACATAACCG 57.037 33.333 0.00 0.00 0.00 4.44
124 125 6.926272 GGCTGGTCATAGTGAGAGTAAATTAG 59.074 42.308 0.00 0.00 0.00 1.73
128 129 4.353777 AGGCTGGTCATAGTGAGAGTAAA 58.646 43.478 0.00 0.00 0.00 2.01
135 136 2.432146 GTCATGAGGCTGGTCATAGTGA 59.568 50.000 0.00 0.00 35.30 3.41
138 139 3.726607 GAAGTCATGAGGCTGGTCATAG 58.273 50.000 0.00 0.00 35.30 2.23
145 146 1.337167 TGTCACGAAGTCATGAGGCTG 60.337 52.381 0.00 0.00 41.61 4.85
198 199 8.789881 AAAATGTCACAATGAAATGCATTTTG 57.210 26.923 24.81 20.44 44.68 2.44
220 221 4.529377 AGAGGGAGTACATCGGTGTAAAAA 59.471 41.667 10.76 0.00 42.18 1.94
241 242 5.666462 TGCTGACTTACAACTTTGTACAGA 58.334 37.500 16.60 0.00 42.84 3.41
243 244 5.644206 TGTTGCTGACTTACAACTTTGTACA 59.356 36.000 1.18 0.00 45.07 2.90
278 282 1.687123 AGTGATGTATGCTACCCCGTC 59.313 52.381 0.00 0.00 0.00 4.79
481 497 6.221659 TCTGCTCTTTGTCATGCTCATATAG 58.778 40.000 0.00 0.00 0.00 1.31
482 498 6.165700 TCTGCTCTTTGTCATGCTCATATA 57.834 37.500 0.00 0.00 0.00 0.86
483 499 5.032327 TCTGCTCTTTGTCATGCTCATAT 57.968 39.130 0.00 0.00 0.00 1.78
484 500 4.476628 TCTGCTCTTTGTCATGCTCATA 57.523 40.909 0.00 0.00 0.00 2.15
572 589 8.716619 TTAATGTCGTTGTTTTAGTTGCATAC 57.283 30.769 0.00 0.00 0.00 2.39
587 604 7.343357 TCCTCCTATCCAAAATTAATGTCGTT 58.657 34.615 0.00 0.00 0.00 3.85
594 611 7.758820 TGGTACTCCTCCTATCCAAAATTAA 57.241 36.000 0.00 0.00 34.23 1.40
606 623 7.149202 TGCATAAAAATATGGTACTCCTCCT 57.851 36.000 0.00 0.00 34.23 3.69
682 702 5.399113 AGCAGGATTTGTAACCCCTAAAAA 58.601 37.500 0.00 0.00 0.00 1.94
685 705 4.384868 GCTAGCAGGATTTGTAACCCCTAA 60.385 45.833 10.63 0.00 0.00 2.69
687 707 2.092375 GCTAGCAGGATTTGTAACCCCT 60.092 50.000 10.63 0.00 0.00 4.79
688 708 2.092375 AGCTAGCAGGATTTGTAACCCC 60.092 50.000 18.83 0.00 0.00 4.95
689 709 3.283259 AGCTAGCAGGATTTGTAACCC 57.717 47.619 18.83 0.00 0.00 4.11
690 710 5.644977 AAAAGCTAGCAGGATTTGTAACC 57.355 39.130 18.83 0.00 0.00 2.85
717 795 5.774690 AGCAGGATTTGTATCACCTCAAAAA 59.225 36.000 0.00 0.00 37.16 1.94
718 796 5.324409 AGCAGGATTTGTATCACCTCAAAA 58.676 37.500 0.00 0.00 37.16 2.44
719 797 4.922206 AGCAGGATTTGTATCACCTCAAA 58.078 39.130 0.00 0.00 37.82 2.69
720 798 4.574674 AGCAGGATTTGTATCACCTCAA 57.425 40.909 0.00 0.00 32.09 3.02
721 799 4.443457 GCTAGCAGGATTTGTATCACCTCA 60.443 45.833 10.63 0.00 32.09 3.86
722 800 4.061596 GCTAGCAGGATTTGTATCACCTC 58.938 47.826 10.63 0.00 32.09 3.85
723 801 3.713764 AGCTAGCAGGATTTGTATCACCT 59.286 43.478 18.83 0.00 32.09 4.00
724 802 4.078639 AGCTAGCAGGATTTGTATCACC 57.921 45.455 18.83 0.00 32.09 4.02
725 803 6.201806 CACTTAGCTAGCAGGATTTGTATCAC 59.798 42.308 18.83 0.00 32.09 3.06
726 804 6.127054 ACACTTAGCTAGCAGGATTTGTATCA 60.127 38.462 18.83 0.00 32.09 2.15
727 805 6.284459 ACACTTAGCTAGCAGGATTTGTATC 58.716 40.000 18.83 0.00 0.00 2.24
728 806 6.240549 ACACTTAGCTAGCAGGATTTGTAT 57.759 37.500 18.83 0.00 0.00 2.29
729 807 5.677319 ACACTTAGCTAGCAGGATTTGTA 57.323 39.130 18.83 0.00 0.00 2.41
841 1218 4.809007 GCTGGAGAGGGAGAGTTTTCATTT 60.809 45.833 0.00 0.00 0.00 2.32
950 1329 4.666512 TCTTGGAGAAGAAAGAAATGGGG 58.333 43.478 0.00 0.00 35.14 4.96
982 1361 4.188462 TGCTCGTCTCTTTGTTTCAGAAA 58.812 39.130 0.00 0.00 0.00 2.52
999 1378 3.434641 TGCTTCTTGATTTTCTCTGCTCG 59.565 43.478 0.00 0.00 0.00 5.03
1084 1463 2.000290 ATGGAGAAAATGGAGGGGGA 58.000 50.000 0.00 0.00 0.00 4.81
1120 1505 1.466167 CACGGATTTGGTTGCTCAGAG 59.534 52.381 0.00 0.00 0.00 3.35
1131 1516 0.518636 CTCTGCACCACACGGATTTG 59.481 55.000 0.00 0.00 35.59 2.32
1145 1530 1.808133 CGGCTATCCAAGAACCTCTGC 60.808 57.143 0.00 0.00 0.00 4.26
1206 1591 2.664081 CCACCTCCTCAGGGACAGC 61.664 68.421 0.00 0.00 45.53 4.40
1434 2651 6.060788 AGAAAAATGCAAGAAGAGAGAGTGT 58.939 36.000 0.00 0.00 0.00 3.55
1436 2653 6.769822 TGAAGAAAAATGCAAGAAGAGAGAGT 59.230 34.615 0.00 0.00 0.00 3.24
1445 2712 7.986320 TGAATTTCCTTGAAGAAAAATGCAAGA 59.014 29.630 9.74 0.00 39.97 3.02
1539 2807 1.207329 GTGAAGGACAGGCCGTAGAAT 59.793 52.381 0.00 0.00 43.43 2.40
1764 3069 2.498644 AAGGGCCAAGTTAGCTTCTC 57.501 50.000 6.18 0.00 31.49 2.87
1979 3293 6.864685 ACATGACAATTCATTACAGCACAAAG 59.135 34.615 0.00 0.00 40.79 2.77
2008 3323 3.302968 CGGTCTCGAACGTTCCTAC 57.697 57.895 22.07 16.19 36.64 3.18
2257 3572 0.179124 GCCGACTCGAAGATCTGCTT 60.179 55.000 0.00 0.00 40.25 3.91
2322 3637 6.258230 TGCCAGTGAAAAATATGAACTCAG 57.742 37.500 0.00 0.00 0.00 3.35
2330 3645 5.765510 TCCATACCTGCCAGTGAAAAATAT 58.234 37.500 0.00 0.00 0.00 1.28
2331 3646 5.186256 TCCATACCTGCCAGTGAAAAATA 57.814 39.130 0.00 0.00 0.00 1.40
2393 3711 7.710907 AGCTTAAATCAGTAGCATCGATTGTAA 59.289 33.333 0.00 0.00 37.37 2.41
2394 3712 7.210174 AGCTTAAATCAGTAGCATCGATTGTA 58.790 34.615 0.00 0.00 37.37 2.41
2400 3718 6.841286 CGTTTAAGCTTAAATCAGTAGCATCG 59.159 38.462 29.16 20.44 37.37 3.84
2423 3858 0.393808 AGGGACTGTTGTTTGTGCGT 60.394 50.000 0.00 0.00 37.18 5.24
2424 3859 2.404083 AGGGACTGTTGTTTGTGCG 58.596 52.632 0.00 0.00 37.18 5.34
2439 3874 2.548920 GCCTACATACTAAGCAGCAGGG 60.549 54.545 0.00 0.00 0.00 4.45
2494 4092 6.662414 TGAAACAAACAACACACAAAAACA 57.338 29.167 0.00 0.00 0.00 2.83
2681 4281 9.706691 ATTTATGGATCGAACTATAATTGACGT 57.293 29.630 11.34 0.00 0.00 4.34
2690 4290 7.425606 GCCACAAAATTTATGGATCGAACTAT 58.574 34.615 20.51 0.00 35.33 2.12
2779 4380 6.294731 CGGGAGTCTTCCTCATTTTCAAAAAT 60.295 38.462 0.00 0.00 43.49 1.82
2790 4391 2.683933 GGCCGGGAGTCTTCCTCA 60.684 66.667 2.18 0.00 43.49 3.86
2824 4425 6.284891 ACAATTAATAAAGTGGCTGCATGT 57.715 33.333 0.50 0.00 35.01 3.21
2968 4573 0.978151 TTAGGTTTGGCTGCGAGGTA 59.022 50.000 0.00 0.00 0.00 3.08
3011 4616 1.835267 ATACCCGGCATGCGTCCTA 60.835 57.895 12.44 0.00 0.00 2.94
3104 4721 4.818546 GGTAGATGCGGTAGTACAACTCTA 59.181 45.833 2.06 0.70 0.00 2.43
3118 4735 1.421410 GACCGTGCAAGGTAGATGCG 61.421 60.000 24.86 2.12 46.09 4.73
3244 4863 1.550072 TCTCACTCATTGATGTCGGCA 59.450 47.619 0.00 0.00 32.17 5.69
3249 4868 3.193263 GCGTCATCTCACTCATTGATGT 58.807 45.455 0.00 0.00 38.78 3.06
3306 4925 0.838608 TTGGAGGTGTACACGGGTTT 59.161 50.000 19.41 2.92 0.00 3.27
3399 5018 1.299468 GCGACCATCTGCTACCTCG 60.299 63.158 0.00 0.00 0.00 4.63
3415 5034 0.737715 CCGAGGAGAAGTTCAAGGCG 60.738 60.000 5.50 3.71 0.00 5.52
3525 5145 2.026822 AGATGCTTGATGGACGACCTTT 60.027 45.455 5.33 0.00 37.04 3.11
3658 5281 4.840005 GGCTACAGGAGGGCGTGC 62.840 72.222 0.00 0.00 33.32 5.34


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

AutoCloner maintained by Alex Coulton.