Multiple sequence alignment - TraesCS7D01G004600

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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 TraesCS7D01G004600 chr7D 100.000 7776 0 0 1 7776 2360840 2353065 0.000000e+00 14360.0
1 TraesCS7D01G004600 chr7D 95.860 5411 170 20 1684 7044 3634668 3629262 0.000000e+00 8702.0
2 TraesCS7D01G004600 chr7D 92.610 4628 290 26 3182 7776 3786948 3782340 0.000000e+00 6604.0
3 TraesCS7D01G004600 chr7D 91.211 2617 159 34 1696 4299 3905516 3908074 0.000000e+00 3493.0
4 TraesCS7D01G004600 chr7D 85.583 3378 370 69 3182 6486 2609890 2606557 0.000000e+00 3432.0
5 TraesCS7D01G004600 chr7D 93.491 1183 76 1 1684 2866 3788461 3787280 0.000000e+00 1757.0
6 TraesCS7D01G004600 chr7D 91.919 1188 94 2 1691 2877 2567633 2566447 0.000000e+00 1661.0
7 TraesCS7D01G004600 chr7D 92.150 828 41 9 5681 6484 2500874 2500047 0.000000e+00 1147.0
8 TraesCS7D01G004600 chr7D 96.557 639 19 2 7137 7774 3623778 3623142 0.000000e+00 1055.0
9 TraesCS7D01G004600 chr7D 80.412 1261 146 42 365 1551 3641156 3639923 0.000000e+00 867.0
10 TraesCS7D01G004600 chr7D 94.142 478 28 0 5443 5920 3253067 3252590 0.000000e+00 728.0
11 TraesCS7D01G004600 chr7D 88.361 610 39 13 962 1551 3794345 3793748 0.000000e+00 704.0
12 TraesCS7D01G004600 chr7D 85.821 536 60 6 1011 1546 2611968 2611449 8.820000e-154 555.0
13 TraesCS7D01G004600 chr7D 90.594 404 30 6 7365 7763 3426841 3426441 5.340000e-146 529.0
14 TraesCS7D01G004600 chr7D 90.498 221 13 5 7365 7577 3429004 3428784 1.280000e-72 285.0
15 TraesCS7D01G004600 chr7D 92.746 193 11 2 7562 7753 3427174 3426984 7.690000e-70 276.0
16 TraesCS7D01G004600 chr7D 96.364 110 3 1 7037 7145 3624290 3624181 6.200000e-41 180.0
17 TraesCS7D01G004600 chr7D 94.000 100 3 3 1 98 486495928 486495830 1.750000e-31 148.0
18 TraesCS7D01G004600 chr7D 93.939 99 2 3 1 96 35335829 35335732 6.290000e-31 147.0
19 TraesCS7D01G004600 chr7D 94.318 88 3 2 1 87 342595683 342595769 4.900000e-27 134.0
20 TraesCS7D01G004600 chr7D 100.000 37 0 0 3153 3189 2609936 2609900 1.400000e-07 69.4
21 TraesCS7D01G004600 chr7D 96.875 32 1 0 1642 1673 2567707 2567676 4.000000e-03 54.7
22 TraesCS7D01G004600 chr7D 96.875 32 1 0 1642 1673 3905440 3905471 4.000000e-03 54.7
23 TraesCS7D01G004600 chr7A 90.995 3509 259 14 1696 5186 3209458 3205989 0.000000e+00 4676.0
24 TraesCS7D01G004600 chr7A 88.614 3513 335 30 1696 5186 1997949 1994480 0.000000e+00 4211.0
25 TraesCS7D01G004600 chr7A 86.905 3360 348 41 3182 6483 3312676 3316001 0.000000e+00 3683.0
26 TraesCS7D01G004600 chr7A 89.306 1758 120 26 5463 7166 2115265 2113522 0.000000e+00 2143.0
27 TraesCS7D01G004600 chr7A 92.424 1188 85 4 1696 2882 3311130 3312313 0.000000e+00 1690.0
28 TraesCS7D01G004600 chr7A 91.122 1239 95 5 1642 2866 2119074 2117837 0.000000e+00 1664.0
29 TraesCS7D01G004600 chr7A 94.456 938 42 2 1 929 3635988 3635052 0.000000e+00 1435.0
30 TraesCS7D01G004600 chr7A 88.931 1066 78 17 5463 6499 1994239 1993185 0.000000e+00 1279.0
31 TraesCS7D01G004600 chr7A 94.901 608 23 5 7166 7767 2113493 2112888 0.000000e+00 944.0
32 TraesCS7D01G004600 chr7A 91.242 628 45 3 928 1548 3634845 3634221 0.000000e+00 846.0
33 TraesCS7D01G004600 chr7A 88.841 690 37 15 6497 7166 1993106 1992437 0.000000e+00 811.0
34 TraesCS7D01G004600 chr7A 91.225 547 44 2 1002 1548 2002644 2002102 0.000000e+00 741.0
35 TraesCS7D01G004600 chr7A 93.376 468 16 4 7313 7776 1992299 1991843 0.000000e+00 678.0
36 TraesCS7D01G004600 chr7A 89.655 522 45 2 1024 1545 3285291 3285803 0.000000e+00 656.0
37 TraesCS7D01G004600 chr7A 89.815 432 34 4 6620 7042 2112892 2112462 5.310000e-151 545.0
38 TraesCS7D01G004600 chr7A 100.000 30 0 0 1647 1676 85260290 85260261 1.000000e-03 56.5
39 TraesCS7D01G004600 chr7A 96.875 32 1 0 1642 1673 3311052 3311083 4.000000e-03 54.7
40 TraesCS7D01G004600 chr4A 87.168 3881 375 63 3182 6976 740579085 740582928 0.000000e+00 4294.0
41 TraesCS7D01G004600 chr4A 86.799 3674 361 69 3182 6780 741590438 741594062 0.000000e+00 3984.0
42 TraesCS7D01G004600 chr4A 90.380 2027 189 1 3153 5179 740019098 740017078 0.000000e+00 2658.0
43 TraesCS7D01G004600 chr4A 90.758 1991 181 1 3182 5172 739652086 739654073 0.000000e+00 2654.0
44 TraesCS7D01G004600 chr4A 90.658 1991 183 1 3182 5172 742057365 742059352 0.000000e+00 2643.0
45 TraesCS7D01G004600 chr4A 90.457 1991 187 1 3182 5172 739867631 739869618 0.000000e+00 2621.0
46 TraesCS7D01G004600 chr4A 86.357 1979 231 22 3200 5172 740455354 740453409 0.000000e+00 2122.0
47 TraesCS7D01G004600 chr4A 86.941 1922 121 51 5463 7281 741481971 741480077 0.000000e+00 2039.0
48 TraesCS7D01G004600 chr4A 86.962 1672 154 25 5410 7041 740016814 740015167 0.000000e+00 1821.0
49 TraesCS7D01G004600 chr4A 89.872 1254 105 11 1648 2882 739650474 739651724 0.000000e+00 1592.0
50 TraesCS7D01G004600 chr4A 86.407 1258 105 27 5270 6486 740453340 740452108 0.000000e+00 1315.0
51 TraesCS7D01G004600 chr4A 85.848 1279 114 26 5271 6490 740307124 740308394 0.000000e+00 1303.0
52 TraesCS7D01G004600 chr4A 88.399 1043 92 13 5463 6483 740939991 740941026 0.000000e+00 1229.0
53 TraesCS7D01G004600 chr4A 86.515 1053 104 15 5463 6490 739869875 739870914 0.000000e+00 1123.0
54 TraesCS7D01G004600 chr4A 85.948 1039 108 21 5296 6307 741792506 741791479 0.000000e+00 1075.0
55 TraesCS7D01G004600 chr4A 89.020 847 89 4 85 929 740924392 740925236 0.000000e+00 1046.0
56 TraesCS7D01G004600 chr4A 85.668 921 82 21 5271 6148 740350472 740351385 0.000000e+00 924.0
57 TraesCS7D01G004600 chr4A 89.748 634 42 11 928 1542 740926687 740927316 0.000000e+00 789.0
58 TraesCS7D01G004600 chr4A 95.484 465 16 2 7313 7774 741480082 741479620 0.000000e+00 737.0
59 TraesCS7D01G004600 chr4A 90.857 525 45 3 1022 1546 740022760 740022239 0.000000e+00 701.0
60 TraesCS7D01G004600 chr4A 90.720 528 46 2 1019 1546 740268864 740269388 0.000000e+00 701.0
61 TraesCS7D01G004600 chr4A 90.341 528 48 2 1019 1546 740346269 740346793 0.000000e+00 689.0
62 TraesCS7D01G004600 chr4A 90.341 528 45 3 1019 1546 740303017 740303538 0.000000e+00 688.0
63 TraesCS7D01G004600 chr4A 89.831 531 48 2 1019 1546 741588189 741588716 0.000000e+00 676.0
64 TraesCS7D01G004600 chr4A 88.805 527 56 1 1025 1548 739642840 739643366 1.830000e-180 643.0
65 TraesCS7D01G004600 chr4A 88.701 531 54 2 1022 1546 741491248 741490718 1.830000e-180 643.0
66 TraesCS7D01G004600 chr4A 88.258 511 32 10 6295 6780 741785887 741785380 3.130000e-163 586.0
67 TraesCS7D01G004600 chr4A 90.137 365 35 1 1691 2054 740931267 740931631 2.540000e-129 473.0
68 TraesCS7D01G004600 chr4A 85.668 307 29 12 7361 7657 742280429 742280730 7.580000e-80 309.0
69 TraesCS7D01G004600 chr4A 82.096 229 18 10 6935 7160 741785382 741785174 2.880000e-39 174.0
70 TraesCS7D01G004600 chr4A 100.000 30 0 0 1647 1676 47456767 47456738 1.000000e-03 56.5
71 TraesCS7D01G004600 chr2D 80.000 1210 202 24 3185 4374 603139911 603138722 0.000000e+00 857.0
72 TraesCS7D01G004600 chr2D 80.614 521 87 12 177 684 169023518 169024037 2.630000e-104 390.0
73 TraesCS7D01G004600 chr2D 79.385 553 91 20 166 706 641494089 641493548 1.230000e-97 368.0
74 TraesCS7D01G004600 chr4B 78.478 1222 213 32 3187 4374 660134959 660136164 0.000000e+00 754.0
75 TraesCS7D01G004600 chr6B 77.796 1198 224 30 3186 4374 77780938 77782102 0.000000e+00 701.0
76 TraesCS7D01G004600 chr6A 76.853 1201 230 28 3186 4374 45331907 45333071 1.100000e-177 634.0
77 TraesCS7D01G004600 chr6A 100.000 30 0 0 1647 1676 65745423 65745452 1.000000e-03 56.5
78 TraesCS7D01G004600 chr1D 83.613 537 67 9 168 702 247538375 247537858 1.170000e-132 484.0
79 TraesCS7D01G004600 chr1D 81.031 543 97 6 167 706 372522234 372522773 2.010000e-115 427.0
80 TraesCS7D01G004600 chr1D 81.238 517 88 7 166 678 204803868 204803357 7.260000e-110 409.0
81 TraesCS7D01G004600 chr1D 94.792 96 2 3 1 94 307813355 307813449 6.290000e-31 147.0
82 TraesCS7D01G004600 chr1D 92.593 54 4 0 85 138 204804001 204803948 2.330000e-10 78.7
83 TraesCS7D01G004600 chr4D 80.684 497 85 9 166 654 150975385 150975878 7.370000e-100 375.0
84 TraesCS7D01G004600 chr3D 78.623 552 99 17 166 710 85222163 85222702 1.610000e-91 348.0
85 TraesCS7D01G004600 chr3D 95.652 92 3 1 1 91 539682397 539682306 6.290000e-31 147.0
86 TraesCS7D01G004600 chr7B 82.653 196 17 4 1064 1255 708485064 708484882 2.900000e-34 158.0
87 TraesCS7D01G004600 chr5D 93.878 98 3 3 1 96 553688331 553688235 2.260000e-30 145.0
88 TraesCS7D01G004600 chr5B 93.878 98 2 3 1 97 694797021 694797115 2.260000e-30 145.0
89 TraesCS7D01G004600 chr5B 93.878 98 2 3 1 97 695047173 695047267 2.260000e-30 145.0
90 TraesCS7D01G004600 chr2B 100.000 30 0 0 1647 1676 634082842 634082813 1.000000e-03 56.5
91 TraesCS7D01G004600 chr5A 100.000 28 0 0 1648 1675 567961602 567961629 1.400000e-02 52.8


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 TraesCS7D01G004600 chr7D 2353065 2360840 7775 True 14360.000000 14360 100.000000 1 7776 1 chr7D.!!$R1 7775
1 TraesCS7D01G004600 chr7D 3629262 3634668 5406 True 8702.000000 8702 95.860000 1684 7044 1 chr7D.!!$R4 5360
2 TraesCS7D01G004600 chr7D 3782340 3788461 6121 True 4180.500000 6604 93.050500 1684 7776 2 chr7D.!!$R13 6092
3 TraesCS7D01G004600 chr7D 3905440 3908074 2634 False 1773.850000 3493 94.043000 1642 4299 2 chr7D.!!$F2 2657
4 TraesCS7D01G004600 chr7D 2606557 2611968 5411 True 1352.133333 3432 90.468000 1011 6486 3 chr7D.!!$R10 5475
5 TraesCS7D01G004600 chr7D 2500047 2500874 827 True 1147.000000 1147 92.150000 5681 6484 1 chr7D.!!$R2 803
6 TraesCS7D01G004600 chr7D 3639923 3641156 1233 True 867.000000 867 80.412000 365 1551 1 chr7D.!!$R5 1186
7 TraesCS7D01G004600 chr7D 2566447 2567707 1260 True 857.850000 1661 94.397000 1642 2877 2 chr7D.!!$R9 1235
8 TraesCS7D01G004600 chr7D 3793748 3794345 597 True 704.000000 704 88.361000 962 1551 1 chr7D.!!$R6 589
9 TraesCS7D01G004600 chr7D 3623142 3624290 1148 True 617.500000 1055 96.460500 7037 7774 2 chr7D.!!$R12 737
10 TraesCS7D01G004600 chr7D 3426441 3429004 2563 True 363.333333 529 91.279333 7365 7763 3 chr7D.!!$R11 398
11 TraesCS7D01G004600 chr7A 3205989 3209458 3469 True 4676.000000 4676 90.995000 1696 5186 1 chr7A.!!$R2 3490
12 TraesCS7D01G004600 chr7A 3311052 3316001 4949 False 1809.233333 3683 92.068000 1642 6483 3 chr7A.!!$F2 4841
13 TraesCS7D01G004600 chr7A 1991843 1997949 6106 True 1744.750000 4211 89.940500 1696 7776 4 chr7A.!!$R4 6080
14 TraesCS7D01G004600 chr7A 2112462 2119074 6612 True 1324.000000 2143 91.286000 1642 7767 4 chr7A.!!$R5 6125
15 TraesCS7D01G004600 chr7A 3634221 3635988 1767 True 1140.500000 1435 92.849000 1 1548 2 chr7A.!!$R6 1547
16 TraesCS7D01G004600 chr7A 2002102 2002644 542 True 741.000000 741 91.225000 1002 1548 1 chr7A.!!$R1 546
17 TraesCS7D01G004600 chr7A 3285291 3285803 512 False 656.000000 656 89.655000 1024 1545 1 chr7A.!!$F1 521
18 TraesCS7D01G004600 chr4A 740579085 740582928 3843 False 4294.000000 4294 87.168000 3182 6976 1 chr4A.!!$F3 3794
19 TraesCS7D01G004600 chr4A 742057365 742059352 1987 False 2643.000000 2643 90.658000 3182 5172 1 chr4A.!!$F5 1990
20 TraesCS7D01G004600 chr4A 741588189 741594062 5873 False 2330.000000 3984 88.315000 1019 6780 2 chr4A.!!$F12 5761
21 TraesCS7D01G004600 chr4A 739650474 739654073 3599 False 2123.000000 2654 90.315000 1648 5172 2 chr4A.!!$F7 3524
22 TraesCS7D01G004600 chr4A 739867631 739870914 3283 False 1872.000000 2621 88.486000 3182 6490 2 chr4A.!!$F8 3308
23 TraesCS7D01G004600 chr4A 740015167 740022760 7593 True 1726.666667 2658 89.399667 1022 7041 3 chr4A.!!$R4 6019
24 TraesCS7D01G004600 chr4A 740452108 740455354 3246 True 1718.500000 2122 86.382000 3200 6486 2 chr4A.!!$R5 3286
25 TraesCS7D01G004600 chr4A 741479620 741481971 2351 True 1388.000000 2039 91.212500 5463 7774 2 chr4A.!!$R6 2311
26 TraesCS7D01G004600 chr4A 740939991 740941026 1035 False 1229.000000 1229 88.399000 5463 6483 1 chr4A.!!$F4 1020
27 TraesCS7D01G004600 chr4A 741791479 741792506 1027 True 1075.000000 1075 85.948000 5296 6307 1 chr4A.!!$R3 1011
28 TraesCS7D01G004600 chr4A 740303017 740308394 5377 False 995.500000 1303 88.094500 1019 6490 2 chr4A.!!$F9 5471
29 TraesCS7D01G004600 chr4A 740346269 740351385 5116 False 806.500000 924 88.004500 1019 6148 2 chr4A.!!$F10 5129
30 TraesCS7D01G004600 chr4A 740924392 740931631 7239 False 769.333333 1046 89.635000 85 2054 3 chr4A.!!$F11 1969
31 TraesCS7D01G004600 chr4A 740268864 740269388 524 False 701.000000 701 90.720000 1019 1546 1 chr4A.!!$F2 527
32 TraesCS7D01G004600 chr4A 739642840 739643366 526 False 643.000000 643 88.805000 1025 1548 1 chr4A.!!$F1 523
33 TraesCS7D01G004600 chr4A 741490718 741491248 530 True 643.000000 643 88.701000 1022 1546 1 chr4A.!!$R2 524
34 TraesCS7D01G004600 chr4A 741785174 741785887 713 True 380.000000 586 85.177000 6295 7160 2 chr4A.!!$R7 865
35 TraesCS7D01G004600 chr2D 603138722 603139911 1189 True 857.000000 857 80.000000 3185 4374 1 chr2D.!!$R1 1189
36 TraesCS7D01G004600 chr2D 169023518 169024037 519 False 390.000000 390 80.614000 177 684 1 chr2D.!!$F1 507
37 TraesCS7D01G004600 chr2D 641493548 641494089 541 True 368.000000 368 79.385000 166 706 1 chr2D.!!$R2 540
38 TraesCS7D01G004600 chr4B 660134959 660136164 1205 False 754.000000 754 78.478000 3187 4374 1 chr4B.!!$F1 1187
39 TraesCS7D01G004600 chr6B 77780938 77782102 1164 False 701.000000 701 77.796000 3186 4374 1 chr6B.!!$F1 1188
40 TraesCS7D01G004600 chr6A 45331907 45333071 1164 False 634.000000 634 76.853000 3186 4374 1 chr6A.!!$F1 1188
41 TraesCS7D01G004600 chr1D 247537858 247538375 517 True 484.000000 484 83.613000 168 702 1 chr1D.!!$R1 534
42 TraesCS7D01G004600 chr1D 372522234 372522773 539 False 427.000000 427 81.031000 167 706 1 chr1D.!!$F2 539
43 TraesCS7D01G004600 chr1D 204803357 204804001 644 True 243.850000 409 86.915500 85 678 2 chr1D.!!$R2 593
44 TraesCS7D01G004600 chr3D 85222163 85222702 539 False 348.000000 348 78.623000 166 710 1 chr3D.!!$F1 544

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
49 50 0.754957 CACTTGGAGGCCCAACAACA 60.755 55.000 0.00 0.0 46.94 3.33 F
828 936 1.207593 CGCCGTTGAAGAAGCCTTG 59.792 57.895 0.00 0.0 31.62 3.61 F
1548 3195 0.690762 GCCCAAGGTGACACTTCCTA 59.309 55.000 5.39 0.0 33.27 2.94 F
2184 7828 1.672356 CTTTGTGCCCCCTGAGTCG 60.672 63.158 0.00 0.0 0.00 4.18 F
2531 8175 3.452990 TGTTCCGGCCTAGTAATTGATGA 59.547 43.478 0.00 0.0 0.00 2.92 F
2745 8392 5.237127 CCACGACATGCTATCACAATTACAT 59.763 40.000 0.00 0.0 0.00 2.29 F
4519 12142 2.507484 TGGACATGACAGCCTGAAAAG 58.493 47.619 0.00 0.0 0.00 2.27 F
5861 13748 0.321475 TGGCTGATGCGATGAACACA 60.321 50.000 0.00 0.0 40.82 3.72 F
5868 13755 2.677003 GCGATGAACACACCACGGG 61.677 63.158 0.00 0.0 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1529 3173 0.690762 TAGGAAGTGTCACCTTGGGC 59.309 55.000 0.00 0.0 37.68 5.36 R
2163 7801 1.073284 GACTCAGGGGGCACAAAGTTA 59.927 52.381 0.00 0.0 0.00 2.24 R
3389 10853 3.865164 CAGAACCAAAAAGCCTGTCAAAC 59.135 43.478 0.00 0.0 0.00 2.93 R
3555 11019 6.671614 TGACAAACAAGACACTAACGAATT 57.328 33.333 0.00 0.0 0.00 2.17 R
4519 12142 2.676342 CCGTGAGCCACCAGTTTTATAC 59.324 50.000 0.50 0.0 0.00 1.47 R
4604 12227 1.002430 TCAACTCTCTGGACATGGTGC 59.998 52.381 0.00 0.0 0.00 5.01 R
5868 13755 0.868406 CTTGCTGACCCAAACGAGAC 59.132 55.000 0.00 0.0 0.00 3.36 R
6687 14740 1.677576 TGTTTCTGCAGGCACTTTCTG 59.322 47.619 15.13 0.0 34.60 3.02 R
7143 15626 3.932710 GCTAATGTCAGACGGAACATGAA 59.067 43.478 0.00 0.0 0.00 2.57 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
27 28 3.955650 TGCTACTGTCCTACAAACCTC 57.044 47.619 0.00 0.00 0.00 3.85
49 50 0.754957 CACTTGGAGGCCCAACAACA 60.755 55.000 0.00 0.00 46.94 3.33
83 84 5.593095 AGAAGGTTGCGTAGTAGACATCATA 59.407 40.000 0.00 0.00 0.00 2.15
158 220 1.604378 GGACCATGGTGTCTGAGGG 59.396 63.158 25.52 0.00 35.54 4.30
718 811 3.553302 CCGGTTGGTTTAAATGTGGGTTC 60.553 47.826 0.00 0.00 0.00 3.62
730 823 4.893424 ATGTGGGTTCAAATATACACGC 57.107 40.909 0.00 0.00 0.00 5.34
739 832 7.227116 GGGTTCAAATATACACGCTTATGGTTA 59.773 37.037 0.00 0.00 0.00 2.85
806 907 6.934645 TGGATGAACGTGAGAGAAAATTTACT 59.065 34.615 0.00 0.00 0.00 2.24
807 908 7.444183 TGGATGAACGTGAGAGAAAATTTACTT 59.556 33.333 0.00 0.00 0.00 2.24
818 919 4.273969 AGAAAATTTACTTGTCGCCGTTGA 59.726 37.500 0.00 0.00 0.00 3.18
828 936 1.207593 CGCCGTTGAAGAAGCCTTG 59.792 57.895 0.00 0.00 31.62 3.61
1117 2722 1.868251 GCTTCTCTACACGGCGTCG 60.868 63.158 10.85 8.42 43.02 5.12
1458 3075 2.555547 GCCCAAAGTGCAGCGAGTT 61.556 57.895 0.00 0.00 0.00 3.01
1548 3195 0.690762 GCCCAAGGTGACACTTCCTA 59.309 55.000 5.39 0.00 33.27 2.94
1551 3198 2.092914 CCCAAGGTGACACTTCCTATCC 60.093 54.545 5.39 0.00 33.27 2.59
1552 3199 2.571653 CCAAGGTGACACTTCCTATCCA 59.428 50.000 5.39 0.00 33.27 3.41
1554 3201 4.194640 CAAGGTGACACTTCCTATCCATG 58.805 47.826 5.39 0.00 33.27 3.66
1555 3202 3.454858 AGGTGACACTTCCTATCCATGT 58.545 45.455 5.39 0.00 31.66 3.21
1556 3203 4.620723 AGGTGACACTTCCTATCCATGTA 58.379 43.478 5.39 0.00 31.66 2.29
1557 3204 4.406003 AGGTGACACTTCCTATCCATGTAC 59.594 45.833 5.39 0.00 31.66 2.90
1558 3205 4.443034 GGTGACACTTCCTATCCATGTACC 60.443 50.000 5.39 0.00 0.00 3.34
1560 3207 2.102588 ACACTTCCTATCCATGTACCGC 59.897 50.000 0.00 0.00 0.00 5.68
1561 3208 2.365617 CACTTCCTATCCATGTACCGCT 59.634 50.000 0.00 0.00 0.00 5.52
1565 3429 3.418995 TCCTATCCATGTACCGCTAGAC 58.581 50.000 0.00 0.00 0.00 2.59
1590 7161 2.543777 ACTTGCTTAGAGCCGTTTCA 57.456 45.000 0.00 0.00 41.51 2.69
1608 7194 6.348458 CCGTTTCATTTTCTTGATGCTGACTA 60.348 38.462 0.00 0.00 0.00 2.59
1609 7195 6.521133 CGTTTCATTTTCTTGATGCTGACTAC 59.479 38.462 0.00 0.00 0.00 2.73
1610 7196 6.500684 TTCATTTTCTTGATGCTGACTACC 57.499 37.500 0.00 0.00 0.00 3.18
1611 7197 5.559770 TCATTTTCTTGATGCTGACTACCA 58.440 37.500 0.00 0.00 0.00 3.25
1612 7198 5.645067 TCATTTTCTTGATGCTGACTACCAG 59.355 40.000 0.00 0.00 45.67 4.00
1613 7199 4.623932 TTTCTTGATGCTGACTACCAGT 57.376 40.909 0.00 0.00 44.71 4.00
1614 7200 5.738619 TTTCTTGATGCTGACTACCAGTA 57.261 39.130 0.00 0.00 44.71 2.74
1617 7203 4.711846 TCTTGATGCTGACTACCAGTATGT 59.288 41.667 0.00 0.00 46.16 2.29
1620 7206 4.339530 TGATGCTGACTACCAGTATGTCTC 59.660 45.833 0.00 0.00 46.16 3.36
1621 7207 3.697166 TGCTGACTACCAGTATGTCTCA 58.303 45.455 0.00 0.00 44.71 3.27
1623 7209 3.444034 GCTGACTACCAGTATGTCTCACA 59.556 47.826 0.00 0.00 44.71 3.58
1625 7211 4.663334 TGACTACCAGTATGTCTCACACT 58.337 43.478 0.00 0.00 0.00 3.55
1728 7361 7.795047 TGTGTTGGTAGATATGATGAGTGAAT 58.205 34.615 0.00 0.00 0.00 2.57
1832 7465 9.706691 ATACTGGTAGTTATGTATTACATGCAC 57.293 33.333 17.68 13.77 39.53 4.57
1841 7475 3.874543 TGTATTACATGCACCATCCGTTC 59.125 43.478 0.00 0.00 0.00 3.95
1953 7591 3.790437 CTGGGCGCCATGAGACCT 61.790 66.667 30.85 0.00 30.82 3.85
2184 7828 1.672356 CTTTGTGCCCCCTGAGTCG 60.672 63.158 0.00 0.00 0.00 4.18
2198 7842 3.521560 CTGAGTCGCTTGGCTACAAATA 58.478 45.455 0.00 0.00 35.89 1.40
2202 7846 4.122776 AGTCGCTTGGCTACAAATATGAG 58.877 43.478 0.00 0.00 35.89 2.90
2211 7855 5.887598 TGGCTACAAATATGAGCACAAGATT 59.112 36.000 0.00 0.00 37.98 2.40
2531 8175 3.452990 TGTTCCGGCCTAGTAATTGATGA 59.547 43.478 0.00 0.00 0.00 2.92
2745 8392 5.237127 CCACGACATGCTATCACAATTACAT 59.763 40.000 0.00 0.00 0.00 2.29
3389 10853 6.053650 TGATGATCACTCAAGGAAGCTATTG 58.946 40.000 0.00 0.00 34.37 1.90
3555 11019 9.108284 CAGTGGATTTATTGACACACATACATA 57.892 33.333 0.00 0.00 36.35 2.29
4519 12142 2.507484 TGGACATGACAGCCTGAAAAG 58.493 47.619 0.00 0.00 0.00 2.27
4604 12227 5.692613 TGTGGGTTTTGGATAAACTTACG 57.307 39.130 0.00 0.00 0.00 3.18
5205 12880 4.616181 AGCACAGTACAGAAACAACAAC 57.384 40.909 0.00 0.00 0.00 3.32
5750 13625 2.682155 CTGAAAGCTCCTACTGGGAC 57.318 55.000 0.00 0.00 39.58 4.46
5771 13646 1.516603 GCTCGCTGTAGGAACCGAC 60.517 63.158 0.00 0.00 0.00 4.79
5789 13664 1.152567 CCTGCTGGTGTTTGGGGAA 60.153 57.895 0.51 0.00 0.00 3.97
5861 13748 0.321475 TGGCTGATGCGATGAACACA 60.321 50.000 0.00 0.00 40.82 3.72
5868 13755 2.677003 GCGATGAACACACCACGGG 61.677 63.158 0.00 0.00 0.00 5.28
6687 14740 5.486526 AGAGAAGACATGAATGAGTTCCAC 58.513 41.667 0.00 0.00 33.26 4.02
7107 15179 5.562635 TCAACCGAAAATAAGGAAAGGCTA 58.437 37.500 0.00 0.00 0.00 3.93
7379 15904 1.142748 CAACAACCCGGCAAAAGCA 59.857 52.632 0.00 0.00 0.00 3.91
7463 15993 1.470098 AGGCTAGCTGCAAATGTTTCG 59.530 47.619 15.72 0.00 45.15 3.46
7540 16070 1.133025 CGCCCGATCTGCTTCAAATTT 59.867 47.619 3.09 0.00 0.00 1.82
7655 17815 9.252962 CAGAAGAAGAAAATGCATTTAACAACT 57.747 29.630 24.35 18.25 0.00 3.16
7704 18397 7.660112 TGTCTATTGGTTCGTCTTGTAGTTAA 58.340 34.615 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.567615 ACGCAACCTTCTCCTTGTAGAT 59.432 45.455 0.00 0.00 0.00 1.98
83 84 1.689233 TAGTGAAGGATGCGGCCCT 60.689 57.895 0.00 0.00 35.03 5.19
158 220 2.637025 TTGGCGAACGCAAAGAGC 59.363 55.556 20.16 3.06 44.11 4.09
344 416 4.980805 GCCTTGCCGTGACCGACA 62.981 66.667 0.00 0.00 35.63 4.35
674 766 4.505922 GGACAAATTTCATGCAAAACGACA 59.494 37.500 0.00 0.00 0.00 4.35
718 811 9.203421 TCATCTAACCATAAGCGTGTATATTTG 57.797 33.333 0.00 0.00 0.00 2.32
730 823 3.555168 GGAGGCCGTCATCTAACCATAAG 60.555 52.174 0.00 0.00 0.00 1.73
739 832 1.152525 ATACGGGAGGCCGTCATCT 60.153 57.895 0.00 0.00 45.56 2.90
789 890 5.073478 GCGACAAGTAAATTTTCTCTCACG 58.927 41.667 0.00 3.23 0.00 4.35
806 907 1.503818 GGCTTCTTCAACGGCGACAA 61.504 55.000 16.62 1.43 0.00 3.18
807 908 1.959226 GGCTTCTTCAACGGCGACA 60.959 57.895 16.62 0.00 0.00 4.35
1100 2690 1.226323 CCGACGCCGTGTAGAGAAG 60.226 63.158 0.00 0.00 0.00 2.85
1395 3012 2.042831 GCTTGGCAGACGAAGGCAT 61.043 57.895 0.00 0.00 41.43 4.40
1396 3013 2.669569 GCTTGGCAGACGAAGGCA 60.670 61.111 0.00 0.00 40.01 4.75
1529 3173 0.690762 TAGGAAGTGTCACCTTGGGC 59.309 55.000 0.00 0.00 37.68 5.36
1548 3195 2.362397 CAGTGTCTAGCGGTACATGGAT 59.638 50.000 0.00 0.00 0.00 3.41
1551 3198 3.119459 AGTTCAGTGTCTAGCGGTACATG 60.119 47.826 0.00 0.00 0.00 3.21
1552 3199 3.090037 AGTTCAGTGTCTAGCGGTACAT 58.910 45.455 0.00 0.00 0.00 2.29
1554 3201 3.243336 CAAGTTCAGTGTCTAGCGGTAC 58.757 50.000 0.00 0.00 0.00 3.34
1555 3202 2.352421 GCAAGTTCAGTGTCTAGCGGTA 60.352 50.000 0.00 0.00 0.00 4.02
1556 3203 1.605712 GCAAGTTCAGTGTCTAGCGGT 60.606 52.381 0.00 0.00 0.00 5.68
1557 3204 1.071605 GCAAGTTCAGTGTCTAGCGG 58.928 55.000 0.00 0.00 0.00 5.52
1558 3205 2.071688 AGCAAGTTCAGTGTCTAGCG 57.928 50.000 0.00 0.00 0.00 4.26
1560 3207 4.862018 GCTCTAAGCAAGTTCAGTGTCTAG 59.138 45.833 0.00 0.00 41.89 2.43
1561 3208 4.322049 GGCTCTAAGCAAGTTCAGTGTCTA 60.322 45.833 0.86 0.00 44.75 2.59
1565 3429 1.728971 CGGCTCTAAGCAAGTTCAGTG 59.271 52.381 0.86 0.00 44.75 3.66
1608 7194 2.515854 ACGAGTGTGAGACATACTGGT 58.484 47.619 9.50 9.50 38.96 4.00
1623 7209 2.802816 GAGAAAATGAGCACACACGAGT 59.197 45.455 0.00 0.00 0.00 4.18
1625 7211 2.143122 GGAGAAAATGAGCACACACGA 58.857 47.619 0.00 0.00 0.00 4.35
1640 7240 4.326826 ACTCAAAATGAAGCATCGGAGAA 58.673 39.130 0.00 0.00 43.58 2.87
1762 7395 7.936496 TTCTATTCACATAACTGGCATTCAA 57.064 32.000 0.00 0.00 0.00 2.69
1769 7402 8.438513 CGCATCTATTTCTATTCACATAACTGG 58.561 37.037 0.00 0.00 0.00 4.00
2163 7801 1.073284 GACTCAGGGGGCACAAAGTTA 59.927 52.381 0.00 0.00 0.00 2.24
2184 7828 3.378112 TGTGCTCATATTTGTAGCCAAGC 59.622 43.478 0.00 0.00 35.33 4.01
2198 7842 8.043113 TCTTAACATGAGTAATCTTGTGCTCAT 58.957 33.333 11.83 0.00 46.04 2.90
2202 7846 8.125448 GGAATCTTAACATGAGTAATCTTGTGC 58.875 37.037 11.83 0.00 0.00 4.57
2211 7855 6.632672 GCCTCTTGGGAATCTTAACATGAGTA 60.633 42.308 0.00 0.00 34.92 2.59
2531 8175 7.275920 AGAGTTAATAAACTTGCTCATCCGAT 58.724 34.615 0.00 0.00 46.09 4.18
2745 8392 4.722700 GCTTGGGGCTGCTTCCGA 62.723 66.667 0.00 1.09 38.06 4.55
3389 10853 3.865164 CAGAACCAAAAAGCCTGTCAAAC 59.135 43.478 0.00 0.00 0.00 2.93
3555 11019 6.671614 TGACAAACAAGACACTAACGAATT 57.328 33.333 0.00 0.00 0.00 2.17
4519 12142 2.676342 CCGTGAGCCACCAGTTTTATAC 59.324 50.000 0.50 0.00 0.00 1.47
4575 12198 7.847096 AGTTTATCCAAAACCCACATTAATCC 58.153 34.615 0.00 0.00 0.00 3.01
4604 12227 1.002430 TCAACTCTCTGGACATGGTGC 59.998 52.381 0.00 0.00 0.00 5.01
5205 12880 9.482627 GAGTTACTACCTTTTATCATCATCTGG 57.517 37.037 0.00 0.00 0.00 3.86
5594 13454 2.655364 CGCAGGCGGTAGATGTCG 60.655 66.667 5.63 0.00 35.56 4.35
5649 13509 1.798813 CGGAGGATTATTACCGCAAGC 59.201 52.381 0.00 0.00 38.98 4.01
5750 13625 1.226717 GGTTCCTACAGCGAGCGAG 60.227 63.158 0.00 0.00 0.00 5.03
5771 13646 1.152567 TTCCCCAAACACCAGCAGG 60.153 57.895 0.00 0.00 42.21 4.85
5868 13755 0.868406 CTTGCTGACCCAAACGAGAC 59.132 55.000 0.00 0.00 0.00 3.36
5922 13809 6.244654 AGTCATACATCTCTGCAGAGCTATA 58.755 40.000 34.48 21.79 41.80 1.31
6650 14700 9.506018 TCATGTCTTCTCTTTTTGTATCATCAA 57.494 29.630 0.00 0.00 0.00 2.57
6687 14740 1.677576 TGTTTCTGCAGGCACTTTCTG 59.322 47.619 15.13 0.00 34.60 3.02
6717 14770 6.992063 ATTGGAAATAACAGCTAGTGACTG 57.008 37.500 0.00 0.00 41.08 3.51
7107 15179 7.821846 TGCAGTAAAAGAAGGAAAAACATGTTT 59.178 29.630 18.13 18.13 0.00 2.83
7143 15626 3.932710 GCTAATGTCAGACGGAACATGAA 59.067 43.478 0.00 0.00 0.00 2.57
7280 15799 5.261040 ACAATGGAAGAAGAGAAATCCCA 57.739 39.130 0.00 0.00 0.00 4.37
7655 17815 7.179338 ACAAAATGGGGTGTTGTTTATGCTATA 59.821 33.333 0.00 0.00 31.52 1.31
7656 17816 6.013812 ACAAAATGGGGTGTTGTTTATGCTAT 60.014 34.615 0.00 0.00 31.52 2.97
7704 18397 7.293299 TGATTGGAGGATATCAGTTATGAGGTT 59.707 37.037 4.83 0.00 39.29 3.50


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

AutoCloner maintained by Alex Coulton.