Multiple sequence alignment - TraesCS7A01G128100

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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 TraesCS7A01G128100 chr7A 100.000 5178 0 0 1 5178 82157575 82152398 0.000000e+00 9563
1 TraesCS7A01G128100 chr7A 90.984 2174 190 3 2121 4288 80314095 80316268 0.000000e+00 2924
2 TraesCS7A01G128100 chr7A 93.871 930 54 3 1193 2120 643197363 643196435 0.000000e+00 1399
3 TraesCS7A01G128100 chr7A 93.777 932 54 4 1192 2120 449643310 449644240 0.000000e+00 1397
4 TraesCS7A01G128100 chr7A 87.241 627 63 8 1 627 148012586 148011977 0.000000e+00 699
5 TraesCS7A01G128100 chr7A 86.650 397 44 4 785 1179 80313698 80314087 1.030000e-116 431
6 TraesCS7A01G128100 chr7D 93.739 2188 120 4 2120 4300 79360854 79358677 0.000000e+00 3265
7 TraesCS7A01G128100 chr7D 91.217 2186 185 3 2121 4300 76397132 76399316 0.000000e+00 2966
8 TraesCS7A01G128100 chr7D 93.008 1044 68 1 2127 3165 79208192 79207149 0.000000e+00 1519
9 TraesCS7A01G128100 chr7D 92.626 773 31 3 4428 5178 511152824 511152056 0.000000e+00 1088
10 TraesCS7A01G128100 chr7D 92.497 773 32 3 4428 5178 517320075 517320843 0.000000e+00 1083
11 TraesCS7A01G128100 chr7D 92.367 773 33 3 4428 5178 582593997 582593229 0.000000e+00 1077
12 TraesCS7A01G128100 chr7D 94.097 576 29 1 2127 2697 79264926 79264351 0.000000e+00 870
13 TraesCS7A01G128100 chr7D 92.714 398 20 4 785 1180 79265329 79264939 2.710000e-157 566
14 TraesCS7A01G128100 chr7D 91.960 398 23 3 785 1180 79208595 79208205 2.730000e-152 549
15 TraesCS7A01G128100 chr7D 90.274 401 24 8 785 1180 79376380 79375990 1.290000e-140 510
16 TraesCS7A01G128100 chr7D 91.291 333 21 3 850 1180 79299897 79299571 1.020000e-121 448
17 TraesCS7A01G128100 chr7D 85.888 411 49 3 785 1193 76396735 76397138 3.700000e-116 429
18 TraesCS7A01G128100 chr7D 96.053 228 9 0 2127 2354 79299558 79299331 6.330000e-99 372
19 TraesCS7A01G128100 chr7D 96.273 161 6 0 625 785 79265996 79265836 1.110000e-66 265
20 TraesCS7A01G128100 chr7D 93.789 161 4 3 625 785 79300153 79299999 2.410000e-58 237
21 TraesCS7A01G128100 chr7D 94.156 154 9 0 632 785 79376691 79376538 8.670000e-58 235
22 TraesCS7A01G128100 chr7D 93.168 161 5 1 625 785 79265607 79265453 1.120000e-56 231
23 TraesCS7A01G128100 chr7D 92.547 161 6 1 625 785 79208875 79208721 5.220000e-55 226
24 TraesCS7A01G128100 chr3B 91.819 2188 162 4 2125 4300 703922361 703924543 0.000000e+00 3033
25 TraesCS7A01G128100 chr3B 93.985 931 52 4 1192 2120 225448202 225447274 0.000000e+00 1406
26 TraesCS7A01G128100 chr3B 88.676 627 67 2 1 624 812618424 812617799 0.000000e+00 761
27 TraesCS7A01G128100 chr3B 87.520 633 72 6 1 631 802587208 802587835 0.000000e+00 725
28 TraesCS7A01G128100 chr3B 91.785 353 28 1 44 395 736318577 736318225 1.680000e-134 490
29 TraesCS7A01G128100 chr3B 90.058 171 16 1 1010 1180 703922181 703922350 2.430000e-53 220
30 TraesCS7A01G128100 chr7B 92.949 1872 122 6 2120 3985 26654025 26652158 0.000000e+00 2717
31 TraesCS7A01G128100 chr7B 92.045 616 48 1 1 615 611609860 611610475 0.000000e+00 865
32 TraesCS7A01G128100 chr7B 89.614 414 30 7 785 1193 26654423 26654018 9.940000e-142 514
33 TraesCS7A01G128100 chr7B 94.136 324 15 1 3977 4300 26650872 26650553 1.680000e-134 490
34 TraesCS7A01G128100 chr7B 94.156 154 9 0 632 785 26654859 26654706 8.670000e-58 235
35 TraesCS7A01G128100 chr2A 85.242 1965 268 16 2124 4070 52427709 52425749 0.000000e+00 2002
36 TraesCS7A01G128100 chr2A 82.607 2087 340 17 2124 4192 52756837 52758918 0.000000e+00 1821
37 TraesCS7A01G128100 chr2A 97.079 890 16 1 4299 5178 680761783 680760894 0.000000e+00 1491
38 TraesCS7A01G128100 chr2A 93.462 933 55 3 1193 2120 70952383 70951452 0.000000e+00 1380
39 TraesCS7A01G128100 chr2A 81.577 1395 242 11 2127 3508 52540628 52539236 0.000000e+00 1138
40 TraesCS7A01G128100 chr2D 83.704 2025 308 14 2124 4134 51159969 51157953 0.000000e+00 1892
41 TraesCS7A01G128100 chr2D 82.726 2113 343 14 2124 4219 51253468 51255575 0.000000e+00 1860
42 TraesCS7A01G128100 chr2D 89.651 773 28 14 4428 5178 126895232 126894490 0.000000e+00 937
43 TraesCS7A01G128100 chr2B 83.022 2032 315 18 2124 4134 79708899 79706877 0.000000e+00 1814
44 TraesCS7A01G128100 chr2B 95.726 117 3 1 4298 4412 159975036 159974920 2.460000e-43 187
45 TraesCS7A01G128100 chr6D 94.283 927 51 2 1194 2120 51470773 51471697 0.000000e+00 1417
46 TraesCS7A01G128100 chr6D 94.181 928 51 2 1193 2120 226786518 226785594 0.000000e+00 1411
47 TraesCS7A01G128100 chr6D 92.367 773 33 8 4428 5178 67400411 67399643 0.000000e+00 1077
48 TraesCS7A01G128100 chr6D 92.238 773 34 3 4428 5178 103676651 103675883 0.000000e+00 1072
49 TraesCS7A01G128100 chr6D 98.148 108 0 1 4304 4409 348544124 348544231 2.460000e-43 187
50 TraesCS7A01G128100 chr1D 94.073 928 53 1 1193 2120 300834923 300835848 0.000000e+00 1408
51 TraesCS7A01G128100 chr1D 93.496 123 4 3 4292 4412 209986895 209987015 4.120000e-41 180
52 TraesCS7A01G128100 chr6A 94.080 929 49 4 1194 2120 60071461 60070537 0.000000e+00 1406
53 TraesCS7A01G128100 chr6A 96.396 111 2 1 4299 4407 262038846 262038736 1.150000e-41 182
54 TraesCS7A01G128100 chr3D 93.858 928 56 1 1193 2120 110538542 110539468 0.000000e+00 1397
55 TraesCS7A01G128100 chr3D 97.391 115 2 1 4299 4412 178535682 178535796 1.470000e-45 195
56 TraesCS7A01G128100 chr4D 92.497 773 32 3 4428 5178 36472207 36471439 0.000000e+00 1083
57 TraesCS7A01G128100 chr4D 92.497 773 32 3 4428 5178 64578022 64578790 0.000000e+00 1083
58 TraesCS7A01G128100 chr4D 92.497 773 32 3 4428 5178 417870488 417869720 0.000000e+00 1083
59 TraesCS7A01G128100 chr4D 93.910 624 38 0 1 624 150019652 150020275 0.000000e+00 942
60 TraesCS7A01G128100 chr4D 90.096 626 60 2 1 625 236385416 236384792 0.000000e+00 811
61 TraesCS7A01G128100 chr5A 92.671 614 35 4 1 614 605323619 605323016 0.000000e+00 876
62 TraesCS7A01G128100 chr4B 88.027 593 64 6 5 594 301298451 301297863 0.000000e+00 695
63 TraesCS7A01G128100 chr6B 93.204 309 18 3 330 635 37032734 37033042 7.910000e-123 451
64 TraesCS7A01G128100 chr1B 96.552 116 2 1 4299 4412 136011037 136010922 1.900000e-44 191
65 TraesCS7A01G128100 chr5D 95.690 116 3 1 4299 4412 488460064 488459949 8.850000e-43 185
66 TraesCS7A01G128100 chr1A 95.000 120 3 1 4296 4412 12036638 12036757 8.850000e-43 185


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 TraesCS7A01G128100 chr7A 82152398 82157575 5177 True 9563.000000 9563 100.00000 1 5178 1 chr7A.!!$R1 5177
1 TraesCS7A01G128100 chr7A 80313698 80316268 2570 False 1677.500000 2924 88.81700 785 4288 2 chr7A.!!$F2 3503
2 TraesCS7A01G128100 chr7A 643196435 643197363 928 True 1399.000000 1399 93.87100 1193 2120 1 chr7A.!!$R3 927
3 TraesCS7A01G128100 chr7A 449643310 449644240 930 False 1397.000000 1397 93.77700 1192 2120 1 chr7A.!!$F1 928
4 TraesCS7A01G128100 chr7A 148011977 148012586 609 True 699.000000 699 87.24100 1 627 1 chr7A.!!$R2 626
5 TraesCS7A01G128100 chr7D 79358677 79360854 2177 True 3265.000000 3265 93.73900 2120 4300 1 chr7D.!!$R1 2180
6 TraesCS7A01G128100 chr7D 76396735 76399316 2581 False 1697.500000 2966 88.55250 785 4300 2 chr7D.!!$F2 3515
7 TraesCS7A01G128100 chr7D 511152056 511152824 768 True 1088.000000 1088 92.62600 4428 5178 1 chr7D.!!$R2 750
8 TraesCS7A01G128100 chr7D 517320075 517320843 768 False 1083.000000 1083 92.49700 4428 5178 1 chr7D.!!$F1 750
9 TraesCS7A01G128100 chr7D 582593229 582593997 768 True 1077.000000 1077 92.36700 4428 5178 1 chr7D.!!$R3 750
10 TraesCS7A01G128100 chr7D 79207149 79208875 1726 True 764.666667 1519 92.50500 625 3165 3 chr7D.!!$R4 2540
11 TraesCS7A01G128100 chr7D 79264351 79265996 1645 True 483.000000 870 94.06300 625 2697 4 chr7D.!!$R5 2072
12 TraesCS7A01G128100 chr7D 79375990 79376691 701 True 372.500000 510 92.21500 632 1180 2 chr7D.!!$R7 548
13 TraesCS7A01G128100 chr7D 79299331 79300153 822 True 352.333333 448 93.71100 625 2354 3 chr7D.!!$R6 1729
14 TraesCS7A01G128100 chr3B 703922181 703924543 2362 False 1626.500000 3033 90.93850 1010 4300 2 chr3B.!!$F2 3290
15 TraesCS7A01G128100 chr3B 225447274 225448202 928 True 1406.000000 1406 93.98500 1192 2120 1 chr3B.!!$R1 928
16 TraesCS7A01G128100 chr3B 812617799 812618424 625 True 761.000000 761 88.67600 1 624 1 chr3B.!!$R3 623
17 TraesCS7A01G128100 chr3B 802587208 802587835 627 False 725.000000 725 87.52000 1 631 1 chr3B.!!$F1 630
18 TraesCS7A01G128100 chr7B 26650553 26654859 4306 True 989.000000 2717 92.71375 632 4300 4 chr7B.!!$R1 3668
19 TraesCS7A01G128100 chr7B 611609860 611610475 615 False 865.000000 865 92.04500 1 615 1 chr7B.!!$F1 614
20 TraesCS7A01G128100 chr2A 52425749 52427709 1960 True 2002.000000 2002 85.24200 2124 4070 1 chr2A.!!$R1 1946
21 TraesCS7A01G128100 chr2A 52756837 52758918 2081 False 1821.000000 1821 82.60700 2124 4192 1 chr2A.!!$F1 2068
22 TraesCS7A01G128100 chr2A 680760894 680761783 889 True 1491.000000 1491 97.07900 4299 5178 1 chr2A.!!$R4 879
23 TraesCS7A01G128100 chr2A 70951452 70952383 931 True 1380.000000 1380 93.46200 1193 2120 1 chr2A.!!$R3 927
24 TraesCS7A01G128100 chr2A 52539236 52540628 1392 True 1138.000000 1138 81.57700 2127 3508 1 chr2A.!!$R2 1381
25 TraesCS7A01G128100 chr2D 51157953 51159969 2016 True 1892.000000 1892 83.70400 2124 4134 1 chr2D.!!$R1 2010
26 TraesCS7A01G128100 chr2D 51253468 51255575 2107 False 1860.000000 1860 82.72600 2124 4219 1 chr2D.!!$F1 2095
27 TraesCS7A01G128100 chr2D 126894490 126895232 742 True 937.000000 937 89.65100 4428 5178 1 chr2D.!!$R2 750
28 TraesCS7A01G128100 chr2B 79706877 79708899 2022 True 1814.000000 1814 83.02200 2124 4134 1 chr2B.!!$R1 2010
29 TraesCS7A01G128100 chr6D 51470773 51471697 924 False 1417.000000 1417 94.28300 1194 2120 1 chr6D.!!$F1 926
30 TraesCS7A01G128100 chr6D 226785594 226786518 924 True 1411.000000 1411 94.18100 1193 2120 1 chr6D.!!$R3 927
31 TraesCS7A01G128100 chr6D 67399643 67400411 768 True 1077.000000 1077 92.36700 4428 5178 1 chr6D.!!$R1 750
32 TraesCS7A01G128100 chr6D 103675883 103676651 768 True 1072.000000 1072 92.23800 4428 5178 1 chr6D.!!$R2 750
33 TraesCS7A01G128100 chr1D 300834923 300835848 925 False 1408.000000 1408 94.07300 1193 2120 1 chr1D.!!$F2 927
34 TraesCS7A01G128100 chr6A 60070537 60071461 924 True 1406.000000 1406 94.08000 1194 2120 1 chr6A.!!$R1 926
35 TraesCS7A01G128100 chr3D 110538542 110539468 926 False 1397.000000 1397 93.85800 1193 2120 1 chr3D.!!$F1 927
36 TraesCS7A01G128100 chr4D 36471439 36472207 768 True 1083.000000 1083 92.49700 4428 5178 1 chr4D.!!$R1 750
37 TraesCS7A01G128100 chr4D 64578022 64578790 768 False 1083.000000 1083 92.49700 4428 5178 1 chr4D.!!$F1 750
38 TraesCS7A01G128100 chr4D 417869720 417870488 768 True 1083.000000 1083 92.49700 4428 5178 1 chr4D.!!$R3 750
39 TraesCS7A01G128100 chr4D 150019652 150020275 623 False 942.000000 942 93.91000 1 624 1 chr4D.!!$F2 623
40 TraesCS7A01G128100 chr4D 236384792 236385416 624 True 811.000000 811 90.09600 1 625 1 chr4D.!!$R2 624
41 TraesCS7A01G128100 chr5A 605323016 605323619 603 True 876.000000 876 92.67100 1 614 1 chr5A.!!$R1 613
42 TraesCS7A01G128100 chr4B 301297863 301298451 588 True 695.000000 695 88.02700 5 594 1 chr4B.!!$R1 589

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
991 1686 0.317160 CCTTGTGTACCTGTCTGCGA 59.683 55.000 0.0 0.0 0.00 5.10 F
1168 1863 0.967380 CCAGCCACCACCCTTGAATC 60.967 60.000 0.0 0.0 0.00 2.52 F
2164 2870 1.078848 GAGCTCGTTGGCAGGTGAT 60.079 57.895 0.0 0.0 34.17 3.06 F
3159 3899 0.034574 AATCCGCAACATAGTGGGCA 60.035 50.000 0.0 0.0 39.64 5.36 F
3344 4087 0.032403 ACGGCACACAGTTTAGCGTA 59.968 50.000 0.0 0.0 0.00 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2747 0.320697 GCGTAGACTGGTGGAGGTTT 59.679 55.000 0.00 0.00 0.00 3.27 R
2678 3411 0.593128 ACTTGCAATCACGAGCAACC 59.407 50.000 0.00 0.00 44.98 3.77 R
3232 3975 0.600255 AGTCACCTGTACAACGCTGC 60.600 55.000 0.00 0.00 0.00 5.25 R
4143 6184 1.478837 CCGGAGCAGTATCACCTCCTA 60.479 57.143 0.00 0.00 42.34 2.94 R
4332 6377 1.802365 GTATTGTGACGGTGAACCCAC 59.198 52.381 2.84 2.84 42.46 4.61 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
127 138 2.357517 CGCAACTCTTCGTGCCCT 60.358 61.111 0.00 0.00 0.00 5.19
132 143 0.391597 AACTCTTCGTGCCCTTCGAA 59.608 50.000 0.00 0.00 43.41 3.71
228 239 0.653636 GTGACGCAAAGAACGGTCAA 59.346 50.000 1.87 0.00 34.00 3.18
273 284 6.358974 TCACTATCAGGTGATTCACAAGAA 57.641 37.500 18.09 1.59 40.72 2.52
275 286 7.397221 TCACTATCAGGTGATTCACAAGAAAT 58.603 34.615 18.09 6.82 40.72 2.17
362 373 5.651303 TGGTTAGGATATCCAGCTAGCTAA 58.349 41.667 23.81 9.31 35.59 3.09
418 432 1.751927 CCAGCTGCATGTCCTTCCC 60.752 63.158 8.66 0.00 0.00 3.97
475 489 5.163663 GCAACAGCTAGGCAACAATATTGTA 60.164 40.000 21.07 4.76 41.31 2.41
843 1528 6.891908 AGTAGGAATTGAAGCCATTTATGTGT 59.108 34.615 0.00 0.00 0.00 3.72
880 1570 8.993121 CGCTGGATTTATGAATTGACTAATACT 58.007 33.333 0.00 0.00 0.00 2.12
991 1686 0.317160 CCTTGTGTACCTGTCTGCGA 59.683 55.000 0.00 0.00 0.00 5.10
1020 1715 2.736144 TGGCGTCGTTTACAGATCTT 57.264 45.000 0.00 0.00 0.00 2.40
1053 1748 2.560542 TCTCTTGCTCACCACTCTCTTC 59.439 50.000 0.00 0.00 0.00 2.87
1141 1836 4.363138 CTCTGCTTATCGTGCTTACATCA 58.637 43.478 0.00 0.00 0.00 3.07
1168 1863 0.967380 CCAGCCACCACCCTTGAATC 60.967 60.000 0.00 0.00 0.00 2.52
1180 1875 1.373570 CTTGAATCCAGGCGAAGACC 58.626 55.000 0.00 0.00 31.70 3.85
1182 1877 1.521681 GAATCCAGGCGAAGACCCG 60.522 63.158 0.00 0.00 31.70 5.28
1190 1885 4.833811 CGAAGACCCGCATCATCA 57.166 55.556 0.00 0.00 0.00 3.07
1248 1944 1.591594 AGAACGATGCATACGGCCG 60.592 57.895 26.86 26.86 43.89 6.13
1526 2232 1.414158 AGGACCACATACGGATCAGG 58.586 55.000 0.00 0.00 0.00 3.86
1547 2253 3.679824 GCAGTAGCCCGGAATAATACT 57.320 47.619 0.73 0.32 33.58 2.12
1583 2289 8.682710 TGAATAGTTGTTGTTCTGTTAAAAGCT 58.317 29.630 0.00 0.00 0.00 3.74
1614 2320 1.698532 TGCAGTTCCAAATTGCCCATT 59.301 42.857 4.96 0.00 42.75 3.16
1992 2698 6.352016 ACATCTATGTGACTGTGAACTCTT 57.648 37.500 0.00 0.00 40.03 2.85
2004 2710 5.474189 ACTGTGAACTCTTCAGACCTAGTAC 59.526 44.000 0.00 0.00 41.01 2.73
2041 2747 2.067365 TCGGGCTGATGAGCTAACTA 57.933 50.000 3.60 0.00 45.44 2.24
2050 2756 5.086104 TGATGAGCTAACTAAACCTCCAC 57.914 43.478 0.00 0.00 0.00 4.02
2076 2782 1.832883 ACGCACCAAATGAAGCCATA 58.167 45.000 0.00 0.00 31.59 2.74
2164 2870 1.078848 GAGCTCGTTGGCAGGTGAT 60.079 57.895 0.00 0.00 34.17 3.06
2179 2885 4.748892 CAGGTGATTCTATGAAGTCACGT 58.251 43.478 0.00 0.00 41.33 4.49
2383 3089 1.558233 CTGACTACGGGAAGGGAGTT 58.442 55.000 0.00 0.00 0.00 3.01
2444 3150 2.614481 GCTTCCTTCAACGACCATGGTA 60.614 50.000 19.80 0.00 0.00 3.25
2678 3411 5.183713 CCACATTGCCATGTATAAGGTATGG 59.816 44.000 2.64 0.00 42.14 2.74
2816 3550 1.279271 GACCCCATATCTATTGGCGCT 59.721 52.381 7.64 0.00 32.60 5.92
2917 3657 4.643387 ACCCTGGTTGCTCACGGC 62.643 66.667 0.00 0.00 42.22 5.68
2984 3724 1.066716 GGCAATGGCAAGAGCATTGAA 60.067 47.619 14.46 0.00 44.61 2.69
3019 3759 2.486191 CCCAGATAGCGAATCCAAGCTT 60.486 50.000 0.00 0.00 44.15 3.74
3048 3788 2.432874 CACTCTCTCCTCTACTCCGAGA 59.567 54.545 1.33 0.00 32.74 4.04
3083 3823 8.167605 ACTGCAATTACGACTATGATAGTAGT 57.832 34.615 19.57 19.57 44.86 2.73
3159 3899 0.034574 AATCCGCAACATAGTGGGCA 60.035 50.000 0.00 0.00 39.64 5.36
3217 3960 4.413928 TGGCTACACCACCATTGC 57.586 55.556 0.00 0.00 46.36 3.56
3224 3967 0.321298 ACACCACCATTGCTACGGAC 60.321 55.000 0.00 0.00 0.00 4.79
3232 3975 2.930040 CCATTGCTACGGACTACAACTG 59.070 50.000 0.00 0.00 0.00 3.16
3236 3979 1.630148 CTACGGACTACAACTGCAGC 58.370 55.000 15.27 0.00 0.00 5.25
3339 4082 1.859703 CGTACAACGGCACACAGTTTA 59.140 47.619 0.00 0.00 38.08 2.01
3344 4087 0.032403 ACGGCACACAGTTTAGCGTA 59.968 50.000 0.00 0.00 0.00 4.42
3415 4160 0.324275 GCCCCAACATCCTAAAGCCA 60.324 55.000 0.00 0.00 0.00 4.75
3422 4168 4.818546 CCAACATCCTAAAGCCAGACATAG 59.181 45.833 0.00 0.00 0.00 2.23
3447 4193 1.002134 CGGGCCTCAACATCCTTGT 60.002 57.895 0.84 0.00 37.82 3.16
3513 4259 2.712627 TCATATCAGGCACATCCATGGT 59.287 45.455 12.58 0.00 37.29 3.55
3563 4309 3.497405 GCTCATCAAAGGCATCCATCCTA 60.497 47.826 0.00 0.00 32.65 2.94
3608 4354 0.107643 TGCCATCCTGACAACGTCAA 59.892 50.000 0.00 0.00 42.26 3.18
3630 4376 0.746063 ATCATTAACGGTACCGGCGA 59.254 50.000 35.86 23.40 44.69 5.54
3661 4407 0.807667 ACGAGCAGCATAGAAAGGCG 60.808 55.000 0.00 0.00 37.52 5.52
3947 4693 4.309099 GCCAGCAAATTCAACATTCAAGA 58.691 39.130 0.00 0.00 0.00 3.02
3984 6024 3.106407 GTCTCTGACGGTGCGTGC 61.106 66.667 0.00 0.00 41.37 5.34
4082 6123 1.202582 GCAAAGAGCTCTACGTGGAGA 59.797 52.381 30.54 10.50 41.15 3.71
4102 6143 2.501723 GAGAACCTTGAGCTGGGTATCA 59.498 50.000 0.00 0.00 35.09 2.15
4143 6184 2.803670 CGTCGTCGTTGTCGCCAT 60.804 61.111 0.00 0.00 36.96 4.40
4361 6406 2.029290 ACCGTCACAATACGCTTCTTCT 60.029 45.455 0.00 0.00 41.51 2.85
4372 6417 8.391106 ACAATACGCTTCTTCTCATGAATTTAC 58.609 33.333 0.00 0.00 0.00 2.01
4749 6804 0.814457 TGTTTTGCGAGCTGTTGGTT 59.186 45.000 0.00 0.00 0.00 3.67
5002 7131 1.512926 GCTTCAACAAGGAAGAGCGA 58.487 50.000 7.08 0.00 45.66 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.497273 CCATCAATGTGGGGGAGTTTTC 59.503 50.000 0.00 0.00 35.55 2.29
127 138 4.051237 CAGTCATCTGTGTCACTTTCGAA 58.949 43.478 4.27 0.00 36.97 3.71
132 143 1.271054 GGCCAGTCATCTGTGTCACTT 60.271 52.381 0.00 0.00 39.82 3.16
228 239 1.405821 GCTACACATAGACGGAGCTGT 59.594 52.381 0.00 0.00 0.00 4.40
273 284 0.468585 ATCATCCATGGCACGGCATT 60.469 50.000 6.96 0.00 0.00 3.56
275 286 1.526686 GATCATCCATGGCACGGCA 60.527 57.895 6.96 0.00 0.00 5.69
362 373 9.726438 AATACTATTCTGTTGAGCTTTTGTAGT 57.274 29.630 0.00 0.00 0.00 2.73
475 489 1.668237 GTTTGGTTGTTGCCGCAAAAT 59.332 42.857 7.54 0.00 0.00 1.82
642 656 4.863152 GCTGTCAAAAGCACAAAAATGT 57.137 36.364 0.00 0.00 43.01 2.71
802 1486 5.169992 TCCTACTGAATATGGATGGCATG 57.830 43.478 3.81 0.00 0.00 4.06
931 1621 5.603395 TGGAATAGTCAATACCGGGTAATCA 59.397 40.000 11.57 0.00 0.00 2.57
939 1630 4.452455 GGAATGCTGGAATAGTCAATACCG 59.548 45.833 0.00 0.00 0.00 4.02
991 1686 4.751098 TGTAAACGACGCCATTTCTTAAGT 59.249 37.500 1.63 0.00 0.00 2.24
1020 1715 5.989777 GGTGAGCAAGAGAAGTTGTACTAAA 59.010 40.000 0.00 0.00 0.00 1.85
1053 1748 1.693627 AGGATAGTGCGAGTGTAGGG 58.306 55.000 0.00 0.00 0.00 3.53
1111 1806 3.790123 GCACGATAAGCAGAGGATTTTGC 60.790 47.826 0.00 0.00 40.57 3.68
1353 2059 4.514585 TTGCCAGCCGGTTGTGGT 62.515 61.111 17.69 0.00 36.10 4.16
1583 2289 7.118101 GCAATTTGGAACTGCAGAAATGATTTA 59.882 33.333 23.35 0.00 36.09 1.40
1614 2320 1.744522 TGTAGGAGTATGCGCGTTGTA 59.255 47.619 7.78 0.00 0.00 2.41
1974 2680 5.279006 GGTCTGAAGAGTTCACAGTCACATA 60.279 44.000 0.00 0.00 35.46 2.29
1977 2683 3.068873 AGGTCTGAAGAGTTCACAGTCAC 59.931 47.826 0.00 0.00 35.46 3.67
1992 2698 2.490903 GTTGGAAGCGTACTAGGTCTGA 59.509 50.000 0.00 0.00 0.00 3.27
2004 2710 1.136252 CGATCAGTTGTGTTGGAAGCG 60.136 52.381 0.00 0.00 0.00 4.68
2041 2747 0.320697 GCGTAGACTGGTGGAGGTTT 59.679 55.000 0.00 0.00 0.00 3.27
2050 2756 2.093306 TCATTTGGTGCGTAGACTGG 57.907 50.000 0.00 0.00 0.00 4.00
2076 2782 2.267961 GGGCGAACGATGGGAAGT 59.732 61.111 0.00 0.00 0.00 3.01
2164 2870 6.879993 AGTAGAGAAGACGTGACTTCATAGAA 59.120 38.462 16.64 0.00 45.83 2.10
2179 2885 3.118334 CCTCGGTGTAGGAGTAGAGAAGA 60.118 52.174 0.00 0.00 39.15 2.87
2383 3089 0.829990 TGTCAAGCAGCCCGATGATA 59.170 50.000 0.00 0.00 0.00 2.15
2678 3411 0.593128 ACTTGCAATCACGAGCAACC 59.407 50.000 0.00 0.00 44.98 3.77
2816 3550 1.619654 CCTTGGACATGGCACTGAAA 58.380 50.000 0.00 0.00 0.00 2.69
2948 3688 1.153086 GCCGAGATGGATGTTGGCT 60.153 57.895 7.63 0.00 44.87 4.75
2984 3724 2.327325 TCTGGGTAAGTGCTTCTCCT 57.673 50.000 0.00 0.00 0.00 3.69
3048 3788 2.096819 CGTAATTGCAGTACCGCCATTT 59.903 45.455 5.78 0.00 30.59 2.32
3083 3823 5.758296 GCAAACGAGGATCTTACCAATGATA 59.242 40.000 0.00 0.00 0.00 2.15
3088 3828 3.410631 TGCAAACGAGGATCTTACCAA 57.589 42.857 0.00 0.00 0.00 3.67
3217 3960 1.630148 GCTGCAGTTGTAGTCCGTAG 58.370 55.000 16.64 0.00 0.00 3.51
3232 3975 0.600255 AGTCACCTGTACAACGCTGC 60.600 55.000 0.00 0.00 0.00 5.25
3236 3979 1.139989 CTGCAGTCACCTGTACAACG 58.860 55.000 5.25 0.00 41.02 4.10
3415 4160 3.031417 GCCCGGTGCCACTATGTCT 62.031 63.158 0.00 0.00 0.00 3.41
3447 4193 3.354131 GTTTTTGACGGCCAAGCAA 57.646 47.368 2.24 0.00 35.94 3.91
3513 4259 4.359475 CACTGACATGTGGCGTCA 57.641 55.556 1.15 0.00 41.00 4.35
3608 4354 2.282407 GCCGGTACCGTTAATGATGTT 58.718 47.619 31.24 0.00 37.81 2.71
3630 4376 1.674221 GCTGCTCGTCCAAGATTGAGT 60.674 52.381 0.00 0.00 0.00 3.41
4082 6123 2.503356 CTGATACCCAGCTCAAGGTTCT 59.497 50.000 4.99 0.00 37.59 3.01
4143 6184 1.478837 CCGGAGCAGTATCACCTCCTA 60.479 57.143 0.00 0.00 42.34 2.94
4292 6337 9.561069 GCTTTATTATTAGGGAAAGATGAGACA 57.439 33.333 0.00 0.00 31.83 3.41
4332 6377 1.802365 GTATTGTGACGGTGAACCCAC 59.198 52.381 2.84 2.84 42.46 4.61
4361 6406 7.918033 TGAAAAACTGAAAGCGTAAATTCATGA 59.082 29.630 0.00 0.00 37.60 3.07
4872 6979 4.624364 TCCGTGCAGCCACCTGTG 62.624 66.667 0.00 0.00 41.26 3.66
5053 7182 3.069443 GCCACCAACTTTCTTGAATGGAA 59.931 43.478 8.07 0.00 35.16 3.53


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

AutoCloner maintained by Alex Coulton.