Multiple sequence alignment - TraesCS4D01G069100

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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 TraesCS4D01G069100 chr4D 100.000 5059 0 0 1 5059 44547072 44542014 0.000000e+00 9343.0
1 TraesCS4D01G069100 chr4D 96.187 577 16 4 4486 5059 92719070 92718497 0.000000e+00 939.0
2 TraesCS4D01G069100 chr4D 93.275 461 28 3 1942 2399 44529284 44528824 0.000000e+00 676.0
3 TraesCS4D01G069100 chr4D 88.710 372 19 10 1586 1942 44543073 44542710 2.800000e-117 433.0
4 TraesCS4D01G069100 chr4D 88.710 372 19 10 4000 4363 44545487 44545131 2.800000e-117 433.0
5 TraesCS4D01G069100 chr4A 88.453 2217 155 53 1 2162 555439320 555441490 0.000000e+00 2582.0
6 TraesCS4D01G069100 chr4A 90.591 372 21 5 4000 4365 555440896 555441259 9.850000e-132 481.0
7 TraesCS4D01G069100 chr4A 92.913 127 7 2 4360 4485 467669245 467669370 3.110000e-42 183.0
8 TraesCS4D01G069100 chr4A 100.000 42 0 0 4444 4485 467669411 467669452 1.510000e-10 78.7
9 TraesCS4D01G069100 chr4B 89.559 1906 123 49 200 2058 64613001 64611125 0.000000e+00 2348.0
10 TraesCS4D01G069100 chr4B 82.724 1505 175 48 2463 3928 412111267 412112725 0.000000e+00 1260.0
11 TraesCS4D01G069100 chr4B 91.530 366 20 3 4000 4363 64611592 64611236 1.270000e-135 494.0
12 TraesCS4D01G069100 chr4B 95.973 149 6 0 2239 2387 64610874 64610726 5.060000e-60 243.0
13 TraesCS4D01G069100 chr4B 90.099 101 10 0 2140 2240 64611019 64610919 1.140000e-26 132.0
14 TraesCS4D01G069100 chr6D 88.557 1407 119 20 2536 3927 418532208 418533587 0.000000e+00 1668.0
15 TraesCS4D01G069100 chr6D 95.502 578 22 2 4485 5059 381399452 381398876 0.000000e+00 920.0
16 TraesCS4D01G069100 chr6D 94.118 34 2 0 3943 3976 13565647 13565614 9.000000e-03 52.8
17 TraesCS4D01G069100 chr5D 87.112 1482 147 25 2483 3928 337142344 337143817 0.000000e+00 1639.0
18 TraesCS4D01G069100 chr5D 96.068 585 15 6 4478 5059 538093792 538093213 0.000000e+00 946.0
19 TraesCS4D01G069100 chr5D 100.000 30 0 0 3974 4003 22401382 22401353 7.080000e-04 56.5
20 TraesCS4D01G069100 chr5D 96.875 32 1 0 3946 3977 546838930 546838961 3.000000e-03 54.7
21 TraesCS4D01G069100 chr2D 86.188 1477 178 14 2476 3928 543809648 543811122 0.000000e+00 1574.0
22 TraesCS4D01G069100 chr2D 85.637 1476 188 12 2476 3928 543757913 543759387 0.000000e+00 1530.0
23 TraesCS4D01G069100 chr2D 84.564 1490 173 33 2482 3926 446241374 446239897 0.000000e+00 1424.0
24 TraesCS4D01G069100 chr2D 84.630 1054 98 26 2476 3492 113511401 113512427 0.000000e+00 990.0
25 TraesCS4D01G069100 chr2D 97.391 575 13 2 4486 5059 307852469 307851896 0.000000e+00 977.0
26 TraesCS4D01G069100 chr2D 95.841 577 17 5 4486 5059 427937200 427937772 0.000000e+00 926.0
27 TraesCS4D01G069100 chr2A 86.145 1494 143 30 2474 3928 115142379 115143847 0.000000e+00 1554.0
28 TraesCS4D01G069100 chr2A 94.444 36 2 0 3942 3977 115712638 115712603 7.080000e-04 56.5
29 TraesCS4D01G069100 chr3A 84.916 1485 164 24 2463 3928 352492796 352494239 0.000000e+00 1447.0
30 TraesCS4D01G069100 chr3A 97.143 35 0 1 3972 4006 67912148 67912115 1.970000e-04 58.4
31 TraesCS4D01G069100 chrUn 84.867 1467 155 31 2482 3927 39801005 39799585 0.000000e+00 1417.0
32 TraesCS4D01G069100 chrUn 84.867 1467 155 31 2482 3927 300441781 300440361 0.000000e+00 1417.0
33 TraesCS4D01G069100 chrUn 92.473 93 4 3 4394 4485 28694195 28694285 4.110000e-26 130.0
34 TraesCS4D01G069100 chrUn 100.000 29 0 0 3942 3970 71332921 71332949 3.000000e-03 54.7
35 TraesCS4D01G069100 chr2B 87.743 1134 124 7 2808 3927 450372428 450373560 0.000000e+00 1310.0
36 TraesCS4D01G069100 chr2B 83.974 312 41 4 2467 2776 450372128 450372432 1.780000e-74 291.0
37 TraesCS4D01G069100 chr2B 97.059 34 0 1 3974 4007 321689874 321689906 7.080000e-04 56.5
38 TraesCS4D01G069100 chr7D 87.202 1008 115 8 2928 3922 479136723 479135717 0.000000e+00 1134.0
39 TraesCS4D01G069100 chr7D 96.341 574 17 2 4486 5056 5002076 5002648 0.000000e+00 941.0
40 TraesCS4D01G069100 chr5A 84.276 1132 169 4 2803 3927 237459850 237458721 0.000000e+00 1096.0
41 TraesCS4D01G069100 chr5A 100.000 30 0 0 3974 4003 15866793 15866764 7.080000e-04 56.5
42 TraesCS4D01G069100 chr5A 100.000 30 0 0 3974 4003 469109890 469109919 7.080000e-04 56.5
43 TraesCS4D01G069100 chr3D 87.356 957 99 8 2479 3419 516967184 516968134 0.000000e+00 1077.0
44 TraesCS4D01G069100 chr3D 85.697 818 82 20 2463 3276 271484597 271485383 0.000000e+00 830.0
45 TraesCS4D01G069100 chr3D 92.857 126 7 2 4361 4485 190251537 190251413 1.120000e-41 182.0
46 TraesCS4D01G069100 chr3D 100.000 29 0 0 3945 3973 613757086 613757114 3.000000e-03 54.7
47 TraesCS4D01G069100 chr1D 96.886 578 13 3 4486 5059 30934137 30933561 0.000000e+00 963.0
48 TraesCS4D01G069100 chr1D 96.713 578 14 4 4486 5059 488630148 488629572 0.000000e+00 957.0
49 TraesCS4D01G069100 chr1D 96.207 580 17 3 4483 5059 25817258 25817835 0.000000e+00 944.0
50 TraesCS4D01G069100 chr1D 100.000 30 0 0 3948 3977 308266794 308266823 7.080000e-04 56.5
51 TraesCS4D01G069100 chr3B 87.389 563 64 2 3373 3928 676218807 676219369 1.540000e-179 640.0
52 TraesCS4D01G069100 chr6A 84.553 369 37 9 2509 2877 560830201 560830549 1.040000e-91 348.0
53 TraesCS4D01G069100 chr6A 97.059 34 0 1 3974 4007 573510845 573510877 7.080000e-04 56.5
54 TraesCS4D01G069100 chr1A 92.857 126 7 2 4361 4485 67733560 67733684 1.120000e-41 182.0
55 TraesCS4D01G069100 chr1B 90.476 126 10 2 4361 4485 670289503 670289627 1.130000e-36 165.0
56 TraesCS4D01G069100 chr7B 94.737 38 2 0 4361 4398 64508665 64508702 5.470000e-05 60.2
57 TraesCS4D01G069100 chr7B 96.970 33 0 1 3974 4006 267241255 267241286 3.000000e-03 54.7
58 TraesCS4D01G069100 chr7B 100.000 29 0 0 3942 3970 576429488 576429516 3.000000e-03 54.7
59 TraesCS4D01G069100 chr5B 97.059 34 1 0 3974 4007 370194739 370194772 1.970000e-04 58.4
60 TraesCS4D01G069100 chr5B 97.059 34 1 0 3974 4007 370239599 370239632 1.970000e-04 58.4
61 TraesCS4D01G069100 chr5B 96.875 32 1 0 3946 3977 328244202 328244233 3.000000e-03 54.7
62 TraesCS4D01G069100 chr6B 96.875 32 1 0 3946 3977 481696505 481696474 3.000000e-03 54.7


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 TraesCS4D01G069100 chr4D 44542014 44547072 5058 True 9343.00 9343 100.00000 1 5059 1 chr4D.!!$R2 5058
1 TraesCS4D01G069100 chr4D 92718497 92719070 573 True 939.00 939 96.18700 4486 5059 1 chr4D.!!$R3 573
2 TraesCS4D01G069100 chr4D 44542710 44545487 2777 True 433.00 433 88.71000 1586 4363 2 chr4D.!!$R4 2777
3 TraesCS4D01G069100 chr4A 555439320 555441490 2170 False 1531.50 2582 89.52200 1 4365 2 chr4A.!!$F2 4364
4 TraesCS4D01G069100 chr4B 412111267 412112725 1458 False 1260.00 1260 82.72400 2463 3928 1 chr4B.!!$F1 1465
5 TraesCS4D01G069100 chr4B 64610726 64613001 2275 True 804.25 2348 91.79025 200 4363 4 chr4B.!!$R1 4163
6 TraesCS4D01G069100 chr6D 418532208 418533587 1379 False 1668.00 1668 88.55700 2536 3927 1 chr6D.!!$F1 1391
7 TraesCS4D01G069100 chr6D 381398876 381399452 576 True 920.00 920 95.50200 4485 5059 1 chr6D.!!$R2 574
8 TraesCS4D01G069100 chr5D 337142344 337143817 1473 False 1639.00 1639 87.11200 2483 3928 1 chr5D.!!$F1 1445
9 TraesCS4D01G069100 chr5D 538093213 538093792 579 True 946.00 946 96.06800 4478 5059 1 chr5D.!!$R2 581
10 TraesCS4D01G069100 chr2D 543809648 543811122 1474 False 1574.00 1574 86.18800 2476 3928 1 chr2D.!!$F4 1452
11 TraesCS4D01G069100 chr2D 543757913 543759387 1474 False 1530.00 1530 85.63700 2476 3928 1 chr2D.!!$F3 1452
12 TraesCS4D01G069100 chr2D 446239897 446241374 1477 True 1424.00 1424 84.56400 2482 3926 1 chr2D.!!$R2 1444
13 TraesCS4D01G069100 chr2D 113511401 113512427 1026 False 990.00 990 84.63000 2476 3492 1 chr2D.!!$F1 1016
14 TraesCS4D01G069100 chr2D 307851896 307852469 573 True 977.00 977 97.39100 4486 5059 1 chr2D.!!$R1 573
15 TraesCS4D01G069100 chr2D 427937200 427937772 572 False 926.00 926 95.84100 4486 5059 1 chr2D.!!$F2 573
16 TraesCS4D01G069100 chr2A 115142379 115143847 1468 False 1554.00 1554 86.14500 2474 3928 1 chr2A.!!$F1 1454
17 TraesCS4D01G069100 chr3A 352492796 352494239 1443 False 1447.00 1447 84.91600 2463 3928 1 chr3A.!!$F1 1465
18 TraesCS4D01G069100 chrUn 39799585 39801005 1420 True 1417.00 1417 84.86700 2482 3927 1 chrUn.!!$R1 1445
19 TraesCS4D01G069100 chrUn 300440361 300441781 1420 True 1417.00 1417 84.86700 2482 3927 1 chrUn.!!$R2 1445
20 TraesCS4D01G069100 chr2B 450372128 450373560 1432 False 800.50 1310 85.85850 2467 3927 2 chr2B.!!$F2 1460
21 TraesCS4D01G069100 chr7D 479135717 479136723 1006 True 1134.00 1134 87.20200 2928 3922 1 chr7D.!!$R1 994
22 TraesCS4D01G069100 chr7D 5002076 5002648 572 False 941.00 941 96.34100 4486 5056 1 chr7D.!!$F1 570
23 TraesCS4D01G069100 chr5A 237458721 237459850 1129 True 1096.00 1096 84.27600 2803 3927 1 chr5A.!!$R2 1124
24 TraesCS4D01G069100 chr3D 516967184 516968134 950 False 1077.00 1077 87.35600 2479 3419 1 chr3D.!!$F2 940
25 TraesCS4D01G069100 chr3D 271484597 271485383 786 False 830.00 830 85.69700 2463 3276 1 chr3D.!!$F1 813
26 TraesCS4D01G069100 chr1D 30933561 30934137 576 True 963.00 963 96.88600 4486 5059 1 chr1D.!!$R1 573
27 TraesCS4D01G069100 chr1D 488629572 488630148 576 True 957.00 957 96.71300 4486 5059 1 chr1D.!!$R2 573
28 TraesCS4D01G069100 chr1D 25817258 25817835 577 False 944.00 944 96.20700 4483 5059 1 chr1D.!!$F1 576
29 TraesCS4D01G069100 chr3B 676218807 676219369 562 False 640.00 640 87.38900 3373 3928 1 chr3B.!!$F1 555

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
200 201 0.039035 TAGCTTTGGATGGCCGGTTT 59.961 50.0 1.9 0.0 36.79 3.27 F
204 205 0.178975 TTTGGATGGCCGGTTTCTGT 60.179 50.0 1.9 0.0 36.79 3.41 F
1555 1602 0.465460 ACGGGCGAACATGGCAATAT 60.465 50.0 0.0 0.0 35.84 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1526 1557 0.383860 GTTCGCCCGTTTCAAGTTCG 60.384 55.000 0.00 0.00 0.00 3.95 R
1565 1612 2.353579 ACGTGGCAGCGTTATTATTTCC 59.646 45.455 8.87 0.00 43.04 3.13 R
4366 4772 4.431131 CCAGATGGCGCCCCAACT 62.431 66.667 26.77 14.69 46.14 3.16 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
65 66 9.855021 CCGATTTAAATGAAAAGTATCAGGTTT 57.145 29.630 5.17 0.00 31.76 3.27
109 110 5.794894 AGTATGAATGAATATCACCCGGTC 58.205 41.667 0.00 0.00 0.00 4.79
177 178 6.925610 TTCGAAATGAAACTGGATAGATGG 57.074 37.500 0.00 0.00 32.37 3.51
178 179 5.368145 TCGAAATGAAACTGGATAGATGGG 58.632 41.667 0.00 0.00 0.00 4.00
179 180 4.516698 CGAAATGAAACTGGATAGATGGGG 59.483 45.833 0.00 0.00 0.00 4.96
188 189 4.288105 ACTGGATAGATGGGGATAGCTTTG 59.712 45.833 0.00 0.00 0.00 2.77
189 190 3.588842 TGGATAGATGGGGATAGCTTTGG 59.411 47.826 0.00 0.00 0.00 3.28
198 199 0.179018 GATAGCTTTGGATGGCCGGT 60.179 55.000 1.90 0.00 36.79 5.28
200 201 0.039035 TAGCTTTGGATGGCCGGTTT 59.961 50.000 1.90 0.00 36.79 3.27
201 202 1.215382 GCTTTGGATGGCCGGTTTC 59.785 57.895 1.90 0.00 36.79 2.78
203 204 0.527565 CTTTGGATGGCCGGTTTCTG 59.472 55.000 1.90 0.00 36.79 3.02
204 205 0.178975 TTTGGATGGCCGGTTTCTGT 60.179 50.000 1.90 0.00 36.79 3.41
211 212 1.549620 TGGCCGGTTTCTGTATTCGTA 59.450 47.619 1.90 0.00 0.00 3.43
213 214 2.542595 GGCCGGTTTCTGTATTCGTATG 59.457 50.000 1.90 0.00 0.00 2.39
218 219 3.861113 GGTTTCTGTATTCGTATGCGTGA 59.139 43.478 2.37 0.00 39.49 4.35
226 227 0.800631 TCGTATGCGTGAACTCGTCT 59.199 50.000 2.37 0.00 39.49 4.18
230 231 1.251527 ATGCGTGAACTCGTCTCCCT 61.252 55.000 0.00 0.00 0.00 4.20
246 247 5.440610 GTCTCCCTGTTTGTGAATGGATAT 58.559 41.667 0.00 0.00 0.00 1.63
250 251 3.638160 CCTGTTTGTGAATGGATATGGGG 59.362 47.826 0.00 0.00 0.00 4.96
300 303 1.166531 ACTTCCGCTTGGTTGCAGAC 61.167 55.000 0.00 0.00 0.00 3.51
303 306 1.893808 CCGCTTGGTTGCAGACTGT 60.894 57.895 3.99 0.00 0.00 3.55
312 315 5.276461 TGGTTGCAGACTGTAGTATATGG 57.724 43.478 3.99 0.00 0.00 2.74
313 316 4.058817 GGTTGCAGACTGTAGTATATGGC 58.941 47.826 3.99 0.00 0.00 4.40
321 324 5.129485 AGACTGTAGTATATGGCAAGCTGTT 59.871 40.000 0.00 0.00 0.00 3.16
382 385 5.105797 GCATGTCACATTCCAGATGGTTTTA 60.106 40.000 0.00 0.00 36.34 1.52
437 440 3.320626 ACTTCGCCGTAGTTAAAACTCC 58.679 45.455 0.00 0.00 40.37 3.85
502 505 4.412796 TGGTGATCTGTCCATTCTCATC 57.587 45.455 0.00 0.00 0.00 2.92
505 508 4.141756 GGTGATCTGTCCATTCTCATCACT 60.142 45.833 9.15 0.00 37.77 3.41
512 515 6.652481 TCTGTCCATTCTCATCACTCTTTTTC 59.348 38.462 0.00 0.00 0.00 2.29
551 557 2.601367 GTGCCCCACTGCCACATT 60.601 61.111 0.00 0.00 0.00 2.71
553 559 4.073200 GCCCCACTGCCACATTGC 62.073 66.667 0.00 0.00 0.00 3.56
653 659 4.456806 GGCACGACTGTCCAAAGT 57.543 55.556 1.55 0.00 0.00 2.66
722 728 2.073816 CGTCCGGTCAAAACAAGCTAT 58.926 47.619 0.00 0.00 0.00 2.97
730 736 4.327680 GTCAAAACAAGCTATCCTCACCT 58.672 43.478 0.00 0.00 0.00 4.00
734 740 1.209019 ACAAGCTATCCTCACCTGCAG 59.791 52.381 6.78 6.78 0.00 4.41
858 869 1.301087 TAACGCAACCTGACGGTGG 60.301 57.895 0.00 0.00 44.73 4.61
889 900 2.444351 GTCGCTGCATGATTTAAGTGC 58.556 47.619 0.00 0.00 39.26 4.40
941 952 1.599542 GCACTTGATCTTATCGGTGGC 59.400 52.381 11.80 0.00 36.67 5.01
945 956 3.704566 ACTTGATCTTATCGGTGGCAGTA 59.295 43.478 0.00 0.00 0.00 2.74
1114 1126 2.484264 GCCATCAACACAGGTACAGTTC 59.516 50.000 0.00 0.00 0.00 3.01
1115 1127 2.736721 CCATCAACACAGGTACAGTTCG 59.263 50.000 0.00 0.00 0.00 3.95
1152 1164 1.612199 GGTACCGACATGGCCTGAAAA 60.612 52.381 3.32 0.00 43.94 2.29
1196 1220 1.338020 GCACCAGTGGTTTTCAGAAGG 59.662 52.381 13.62 0.00 31.02 3.46
1214 1238 5.649395 CAGAAGGAGATTTGATGCTTAACCA 59.351 40.000 0.00 0.00 0.00 3.67
1490 1521 1.011019 CGACTGGTACGCTAGCTCG 60.011 63.158 13.93 9.47 0.00 5.03
1500 1531 2.495084 ACGCTAGCTCGTGATCTATCA 58.505 47.619 13.93 0.00 41.62 2.15
1501 1532 3.078097 ACGCTAGCTCGTGATCTATCAT 58.922 45.455 13.93 0.00 41.62 2.45
1502 1533 3.126171 ACGCTAGCTCGTGATCTATCATC 59.874 47.826 13.93 0.00 41.62 2.92
1503 1534 3.126000 CGCTAGCTCGTGATCTATCATCA 59.874 47.826 13.93 0.00 39.30 3.07
1507 1538 5.918426 AGCTCGTGATCTATCATCATCAT 57.082 39.130 0.00 0.00 39.30 2.45
1508 1539 5.893687 AGCTCGTGATCTATCATCATCATC 58.106 41.667 0.00 0.00 39.30 2.92
1541 1588 1.084289 ATAGCGAACTTGAAACGGGC 58.916 50.000 0.00 0.00 0.00 6.13
1553 1600 1.531739 AAACGGGCGAACATGGCAAT 61.532 50.000 0.00 0.00 35.84 3.56
1554 1601 0.678366 AACGGGCGAACATGGCAATA 60.678 50.000 0.00 0.00 35.84 1.90
1555 1602 0.465460 ACGGGCGAACATGGCAATAT 60.465 50.000 0.00 0.00 35.84 1.28
1556 1603 0.667993 CGGGCGAACATGGCAATATT 59.332 50.000 0.00 0.00 35.84 1.28
1558 1605 2.292016 CGGGCGAACATGGCAATATTTA 59.708 45.455 0.00 0.00 35.84 1.40
1560 1607 4.048504 GGGCGAACATGGCAATATTTAAC 58.951 43.478 0.00 0.00 35.84 2.01
1562 1609 4.502645 GGCGAACATGGCAATATTTAACAC 59.497 41.667 0.00 0.00 0.00 3.32
1565 1612 5.743398 CGAACATGGCAATATTTAACACCAG 59.257 40.000 0.00 0.00 0.00 4.00
4363 4769 5.068234 TCTCGATGTTTAACCACCTACTG 57.932 43.478 0.00 0.00 0.00 2.74
4365 4771 2.676342 CGATGTTTAACCACCTACTGGC 59.324 50.000 0.00 0.00 45.32 4.85
4366 4772 3.681593 GATGTTTAACCACCTACTGGCA 58.318 45.455 0.00 0.00 45.32 4.92
4367 4773 3.134574 TGTTTAACCACCTACTGGCAG 57.865 47.619 14.16 14.16 45.32 4.85
4368 4774 2.440253 TGTTTAACCACCTACTGGCAGT 59.560 45.455 25.34 25.34 45.32 4.40
4369 4775 3.117813 TGTTTAACCACCTACTGGCAGTT 60.118 43.478 27.24 8.30 45.32 3.16
4370 4776 2.851263 TAACCACCTACTGGCAGTTG 57.149 50.000 27.24 23.25 45.32 3.16
4371 4777 0.110486 AACCACCTACTGGCAGTTGG 59.890 55.000 35.94 35.94 45.32 3.77
4372 4778 1.002134 CCACCTACTGGCAGTTGGG 60.002 63.158 38.49 32.47 43.89 4.12
4373 4779 1.002134 CACCTACTGGCAGTTGGGG 60.002 63.158 38.49 34.98 43.89 4.96
4374 4780 2.044946 CCTACTGGCAGTTGGGGC 60.045 66.667 32.22 0.00 37.44 5.80
4375 4781 2.436646 CTACTGGCAGTTGGGGCG 60.437 66.667 27.24 4.09 35.84 6.13
4376 4782 4.715523 TACTGGCAGTTGGGGCGC 62.716 66.667 27.24 0.00 35.84 6.53
4382 4788 3.136123 CAGTTGGGGCGCCATCTG 61.136 66.667 33.64 33.64 33.23 2.90
4383 4789 4.431131 AGTTGGGGCGCCATCTGG 62.431 66.667 30.85 0.00 38.53 3.86
4384 4790 4.740822 GTTGGGGCGCCATCTGGT 62.741 66.667 30.85 0.00 37.57 4.00
4402 4808 4.760047 GGCGCCGCTTGAGAGGAA 62.760 66.667 12.58 0.00 37.14 3.36
4403 4809 3.191539 GCGCCGCTTGAGAGGAAG 61.192 66.667 0.00 0.00 37.14 3.46
4404 4810 3.191539 CGCCGCTTGAGAGGAAGC 61.192 66.667 4.87 0.00 44.21 3.86
4405 4811 2.267324 GCCGCTTGAGAGGAAGCT 59.733 61.111 4.87 0.00 45.26 3.74
4406 4812 1.376553 GCCGCTTGAGAGGAAGCTT 60.377 57.895 0.00 0.00 45.26 3.74
4407 4813 1.642952 GCCGCTTGAGAGGAAGCTTG 61.643 60.000 2.10 0.00 45.26 4.01
4408 4814 1.023513 CCGCTTGAGAGGAAGCTTGG 61.024 60.000 2.10 0.00 45.26 3.61
4409 4815 1.642952 CGCTTGAGAGGAAGCTTGGC 61.643 60.000 2.10 0.00 45.26 4.52
4410 4816 1.642952 GCTTGAGAGGAAGCTTGGCG 61.643 60.000 2.10 0.00 44.26 5.69
4411 4817 1.003355 TTGAGAGGAAGCTTGGCGG 60.003 57.895 2.10 0.00 0.00 6.13
4412 4818 1.768684 TTGAGAGGAAGCTTGGCGGT 61.769 55.000 2.10 0.00 0.00 5.68
4413 4819 1.743252 GAGAGGAAGCTTGGCGGTG 60.743 63.158 2.10 0.00 0.00 4.94
4414 4820 2.032681 GAGGAAGCTTGGCGGTGT 59.967 61.111 2.10 0.00 0.00 4.16
4415 4821 2.032681 AGGAAGCTTGGCGGTGTC 59.967 61.111 2.10 0.00 0.00 3.67
4416 4822 2.281484 GGAAGCTTGGCGGTGTCA 60.281 61.111 2.10 0.00 0.00 3.58
4417 4823 2.328099 GGAAGCTTGGCGGTGTCAG 61.328 63.158 2.10 0.00 0.00 3.51
4418 4824 2.281761 AAGCTTGGCGGTGTCAGG 60.282 61.111 0.00 0.00 0.00 3.86
4419 4825 3.120086 AAGCTTGGCGGTGTCAGGT 62.120 57.895 0.00 0.00 0.00 4.00
4420 4826 3.357079 GCTTGGCGGTGTCAGGTG 61.357 66.667 0.00 0.00 0.00 4.00
4421 4827 2.425592 CTTGGCGGTGTCAGGTGA 59.574 61.111 0.00 0.00 0.00 4.02
4422 4828 1.669115 CTTGGCGGTGTCAGGTGAG 60.669 63.158 0.00 0.00 0.00 3.51
4423 4829 2.099652 CTTGGCGGTGTCAGGTGAGA 62.100 60.000 0.00 0.00 0.00 3.27
4424 4830 2.099652 TTGGCGGTGTCAGGTGAGAG 62.100 60.000 0.00 0.00 0.00 3.20
4425 4831 2.262915 GCGGTGTCAGGTGAGAGG 59.737 66.667 0.00 0.00 0.00 3.69
4426 4832 2.262915 CGGTGTCAGGTGAGAGGC 59.737 66.667 0.00 0.00 0.00 4.70
4427 4833 2.279069 CGGTGTCAGGTGAGAGGCT 61.279 63.158 0.00 0.00 0.00 4.58
4428 4834 1.594310 GGTGTCAGGTGAGAGGCTC 59.406 63.158 6.34 6.34 0.00 4.70
4429 4835 1.594310 GTGTCAGGTGAGAGGCTCC 59.406 63.158 11.71 3.35 0.00 4.70
4430 4836 1.610673 TGTCAGGTGAGAGGCTCCC 60.611 63.158 11.71 5.46 0.00 4.30
4431 4837 1.305718 GTCAGGTGAGAGGCTCCCT 60.306 63.158 11.71 7.99 33.57 4.20
4432 4838 0.907230 GTCAGGTGAGAGGCTCCCTT 60.907 60.000 11.71 0.00 31.88 3.95
4433 4839 0.178891 TCAGGTGAGAGGCTCCCTTT 60.179 55.000 11.71 0.00 31.88 3.11
4434 4840 0.251634 CAGGTGAGAGGCTCCCTTTC 59.748 60.000 11.71 2.45 35.59 2.62
4435 4841 0.178891 AGGTGAGAGGCTCCCTTTCA 60.179 55.000 11.71 5.42 41.53 2.69
4437 4843 3.483352 TGAGAGGCTCCCTTTCACT 57.517 52.632 11.71 0.00 39.39 3.41
4438 4844 1.734655 TGAGAGGCTCCCTTTCACTT 58.265 50.000 11.71 0.00 39.39 3.16
4439 4845 2.057922 TGAGAGGCTCCCTTTCACTTT 58.942 47.619 11.71 0.00 39.39 2.66
4440 4846 2.039084 TGAGAGGCTCCCTTTCACTTTC 59.961 50.000 11.71 0.00 39.39 2.62
4441 4847 1.352687 AGAGGCTCCCTTTCACTTTCC 59.647 52.381 11.71 0.00 31.76 3.13
4442 4848 1.352687 GAGGCTCCCTTTCACTTTCCT 59.647 52.381 2.15 0.00 31.76 3.36
4443 4849 1.783365 AGGCTCCCTTTCACTTTCCTT 59.217 47.619 0.00 0.00 0.00 3.36
4444 4850 2.177888 AGGCTCCCTTTCACTTTCCTTT 59.822 45.455 0.00 0.00 0.00 3.11
4445 4851 2.965831 GGCTCCCTTTCACTTTCCTTTT 59.034 45.455 0.00 0.00 0.00 2.27
4446 4852 3.388024 GGCTCCCTTTCACTTTCCTTTTT 59.612 43.478 0.00 0.00 0.00 1.94
4471 4877 9.674068 TTTAAACTATGTAGTGGTATTGCATCA 57.326 29.630 0.00 0.00 36.50 3.07
4472 4878 9.845740 TTAAACTATGTAGTGGTATTGCATCAT 57.154 29.630 0.00 0.00 36.50 2.45
4474 4880 9.494271 AAACTATGTAGTGGTATTGCATCATAG 57.506 33.333 0.00 0.00 39.22 2.23
4475 4881 7.615403 ACTATGTAGTGGTATTGCATCATAGG 58.385 38.462 0.00 0.00 38.30 2.57
4476 4882 4.641396 TGTAGTGGTATTGCATCATAGGC 58.359 43.478 0.00 0.00 0.00 3.93
4477 4883 3.862877 AGTGGTATTGCATCATAGGCA 57.137 42.857 0.00 0.00 40.00 4.75
4478 4884 4.377762 AGTGGTATTGCATCATAGGCAT 57.622 40.909 0.00 0.00 41.58 4.40
4479 4885 5.503634 AGTGGTATTGCATCATAGGCATA 57.496 39.130 0.00 0.00 41.58 3.14
4480 4886 6.070951 AGTGGTATTGCATCATAGGCATAT 57.929 37.500 0.00 0.00 41.58 1.78
4481 4887 6.487828 AGTGGTATTGCATCATAGGCATATT 58.512 36.000 0.00 0.00 41.58 1.28
4482 4888 7.632861 AGTGGTATTGCATCATAGGCATATTA 58.367 34.615 0.00 0.00 41.58 0.98
4483 4889 8.108999 AGTGGTATTGCATCATAGGCATATTAA 58.891 33.333 0.00 0.00 41.58 1.40
4682 5091 4.643387 GCGGCCTGTGGTTGGTCT 62.643 66.667 0.00 0.00 0.00 3.85
4854 5263 3.521126 CCTTCCTCCATTCTTCTTCTCCA 59.479 47.826 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 103 2.224670 TGCAAACTCAAATAGACCGGGT 60.225 45.455 6.32 0.00 0.00 5.28
103 104 2.432444 TGCAAACTCAAATAGACCGGG 58.568 47.619 6.32 0.00 0.00 5.73
153 154 6.488006 CCCATCTATCCAGTTTCATTTCGAAT 59.512 38.462 0.00 0.00 32.32 3.34
156 157 4.516698 CCCCATCTATCCAGTTTCATTTCG 59.483 45.833 0.00 0.00 0.00 3.46
163 164 4.507342 AGCTATCCCCATCTATCCAGTTT 58.493 43.478 0.00 0.00 0.00 2.66
167 168 3.588842 CCAAAGCTATCCCCATCTATCCA 59.411 47.826 0.00 0.00 0.00 3.41
177 178 0.890996 CGGCCATCCAAAGCTATCCC 60.891 60.000 2.24 0.00 0.00 3.85
178 179 0.890996 CCGGCCATCCAAAGCTATCC 60.891 60.000 2.24 0.00 0.00 2.59
179 180 0.179018 ACCGGCCATCCAAAGCTATC 60.179 55.000 0.00 0.00 0.00 2.08
188 189 1.947456 GAATACAGAAACCGGCCATCC 59.053 52.381 0.00 0.00 0.00 3.51
189 190 1.597663 CGAATACAGAAACCGGCCATC 59.402 52.381 0.00 0.00 0.00 3.51
198 199 5.165676 AGTTCACGCATACGAATACAGAAA 58.834 37.500 0.00 0.00 43.93 2.52
200 201 4.348656 GAGTTCACGCATACGAATACAGA 58.651 43.478 0.00 0.00 43.93 3.41
201 202 3.177838 CGAGTTCACGCATACGAATACAG 59.822 47.826 0.00 0.00 43.93 2.74
203 204 3.103738 ACGAGTTCACGCATACGAATAC 58.896 45.455 0.00 0.00 43.93 1.89
204 205 3.064408 AGACGAGTTCACGCATACGAATA 59.936 43.478 0.00 0.00 43.93 1.75
211 212 1.215647 GGGAGACGAGTTCACGCAT 59.784 57.895 0.00 0.00 36.70 4.73
213 214 1.444553 CAGGGAGACGAGTTCACGC 60.445 63.158 0.00 0.00 36.70 5.34
218 219 1.760613 TCACAAACAGGGAGACGAGTT 59.239 47.619 0.00 0.00 0.00 3.01
226 227 4.535781 CCATATCCATTCACAAACAGGGA 58.464 43.478 0.00 0.00 0.00 4.20
230 231 3.641046 CCCCCATATCCATTCACAAACA 58.359 45.455 0.00 0.00 0.00 2.83
250 251 1.401800 CGGTGACCGTAAAATTTGCCC 60.402 52.381 17.28 0.00 42.73 5.36
274 275 0.674895 ACCAAGCGGAAGTGCATCTC 60.675 55.000 0.00 0.00 37.31 2.75
300 303 6.516718 AGTAACAGCTTGCCATATACTACAG 58.483 40.000 0.00 0.00 0.00 2.74
303 306 9.542462 CTAAAAGTAACAGCTTGCCATATACTA 57.458 33.333 0.00 0.00 0.00 1.82
312 315 5.179555 AGTGTAGCTAAAAGTAACAGCTTGC 59.820 40.000 0.00 0.00 42.95 4.01
313 316 6.787085 AGTGTAGCTAAAAGTAACAGCTTG 57.213 37.500 0.00 0.00 42.95 4.01
382 385 4.154195 GCACCGATCTTGTGTCTTTGTATT 59.846 41.667 12.20 0.00 36.11 1.89
437 440 5.817988 TCGTACAAAAGACTATGAGATCCG 58.182 41.667 0.00 0.00 0.00 4.18
502 505 9.057089 AGCGGGAAATATATTAGAAAAAGAGTG 57.943 33.333 0.00 0.00 0.00 3.51
537 543 3.751246 CGCAATGTGGCAGTGGGG 61.751 66.667 5.87 0.00 38.40 4.96
551 557 3.932580 CTGACTTACGGGCAGCGCA 62.933 63.158 11.47 0.00 44.93 6.09
594 600 0.107017 CCCCACTGCTCGATTGGATT 60.107 55.000 4.51 0.00 31.39 3.01
653 659 2.028125 GATTGGATGACGAGCCCGGA 62.028 60.000 0.73 0.00 40.78 5.14
722 728 3.703556 CTCTAGAAATCTGCAGGTGAGGA 59.296 47.826 15.13 1.34 0.00 3.71
730 736 1.134699 CGTGGCCTCTAGAAATCTGCA 60.135 52.381 3.32 0.00 0.00 4.41
734 740 2.993539 GGCGTGGCCTCTAGAAATC 58.006 57.895 3.32 0.00 46.69 2.17
899 910 1.218316 GGCCGACTGAGTTAGGTGG 59.782 63.158 9.26 0.00 0.00 4.61
941 952 3.235195 GTGTCACTCGCTTGTAGTACTG 58.765 50.000 5.39 0.00 0.00 2.74
945 956 2.100916 ACTTGTGTCACTCGCTTGTAGT 59.899 45.455 4.27 0.00 0.00 2.73
1114 1126 3.687572 ACCTCTGTGCTAACGTATACG 57.312 47.619 23.24 23.24 46.33 3.06
1115 1127 4.553547 CGGTACCTCTGTGCTAACGTATAC 60.554 50.000 10.90 0.00 0.00 1.47
1152 1164 6.586844 GCTAGTTCTTACGTTCTTCTCAACAT 59.413 38.462 0.00 0.00 0.00 2.71
1196 1220 5.431765 TCCTCTGGTTAAGCATCAAATCTC 58.568 41.667 7.98 0.00 0.00 2.75
1214 1238 7.056635 CACACAATAAACCCAATAGATCCTCT 58.943 38.462 0.00 0.00 0.00 3.69
1522 1553 1.084289 GCCCGTTTCAAGTTCGCTAT 58.916 50.000 0.00 0.00 0.00 2.97
1524 1555 2.604174 CGCCCGTTTCAAGTTCGCT 61.604 57.895 0.00 0.00 0.00 4.93
1525 1556 2.108344 TTCGCCCGTTTCAAGTTCGC 62.108 55.000 0.00 0.00 0.00 4.70
1526 1557 0.383860 GTTCGCCCGTTTCAAGTTCG 60.384 55.000 0.00 0.00 0.00 3.95
1541 1588 5.645624 TGGTGTTAAATATTGCCATGTTCG 58.354 37.500 0.00 0.00 0.00 3.95
1553 1600 9.398538 AGCGTTATTATTTCCTGGTGTTAAATA 57.601 29.630 0.00 0.00 0.00 1.40
1554 1601 8.188139 CAGCGTTATTATTTCCTGGTGTTAAAT 58.812 33.333 0.00 0.00 0.00 1.40
1555 1602 7.531716 CAGCGTTATTATTTCCTGGTGTTAAA 58.468 34.615 0.00 0.00 0.00 1.52
1556 1603 6.403855 GCAGCGTTATTATTTCCTGGTGTTAA 60.404 38.462 0.00 0.00 0.00 2.01
1558 1605 4.142469 GCAGCGTTATTATTTCCTGGTGTT 60.142 41.667 0.00 0.00 0.00 3.32
1560 1607 3.243068 GGCAGCGTTATTATTTCCTGGTG 60.243 47.826 0.00 0.00 0.00 4.17
1562 1609 2.948979 TGGCAGCGTTATTATTTCCTGG 59.051 45.455 0.00 0.00 0.00 4.45
1565 1612 2.353579 ACGTGGCAGCGTTATTATTTCC 59.646 45.455 8.87 0.00 43.04 3.13
4366 4772 4.431131 CCAGATGGCGCCCCAACT 62.431 66.667 26.77 14.69 46.14 3.16
4367 4773 4.740822 ACCAGATGGCGCCCCAAC 62.741 66.667 26.77 12.48 46.14 3.77
4368 4774 4.738998 CACCAGATGGCGCCCCAA 62.739 66.667 26.77 5.45 46.14 4.12
4385 4791 4.760047 TTCCTCTCAAGCGGCGCC 62.760 66.667 30.40 19.07 0.00 6.53
4386 4792 3.191539 CTTCCTCTCAAGCGGCGC 61.192 66.667 26.86 26.86 0.00 6.53
4387 4793 3.191539 GCTTCCTCTCAAGCGGCG 61.192 66.667 0.51 0.51 39.55 6.46
4392 4798 1.023513 CCGCCAAGCTTCCTCTCAAG 61.024 60.000 0.00 0.00 0.00 3.02
4393 4799 1.003355 CCGCCAAGCTTCCTCTCAA 60.003 57.895 0.00 0.00 0.00 3.02
4394 4800 2.217038 ACCGCCAAGCTTCCTCTCA 61.217 57.895 0.00 0.00 0.00 3.27
4395 4801 1.743252 CACCGCCAAGCTTCCTCTC 60.743 63.158 0.00 0.00 0.00 3.20
4396 4802 2.348998 CACCGCCAAGCTTCCTCT 59.651 61.111 0.00 0.00 0.00 3.69
4397 4803 2.032681 ACACCGCCAAGCTTCCTC 59.967 61.111 0.00 0.00 0.00 3.71
4398 4804 2.032681 GACACCGCCAAGCTTCCT 59.967 61.111 0.00 0.00 0.00 3.36
4399 4805 2.281484 TGACACCGCCAAGCTTCC 60.281 61.111 0.00 0.00 0.00 3.46
4400 4806 2.328099 CCTGACACCGCCAAGCTTC 61.328 63.158 0.00 0.00 0.00 3.86
4401 4807 2.281761 CCTGACACCGCCAAGCTT 60.282 61.111 0.00 0.00 0.00 3.74
4402 4808 3.560251 ACCTGACACCGCCAAGCT 61.560 61.111 0.00 0.00 0.00 3.74
4403 4809 3.357079 CACCTGACACCGCCAAGC 61.357 66.667 0.00 0.00 0.00 4.01
4404 4810 1.669115 CTCACCTGACACCGCCAAG 60.669 63.158 0.00 0.00 0.00 3.61
4405 4811 2.099652 CTCTCACCTGACACCGCCAA 62.100 60.000 0.00 0.00 0.00 4.52
4406 4812 2.523168 TCTCACCTGACACCGCCA 60.523 61.111 0.00 0.00 0.00 5.69
4407 4813 2.262915 CTCTCACCTGACACCGCC 59.737 66.667 0.00 0.00 0.00 6.13
4408 4814 2.262915 CCTCTCACCTGACACCGC 59.737 66.667 0.00 0.00 0.00 5.68
4409 4815 2.219325 GAGCCTCTCACCTGACACCG 62.219 65.000 0.00 0.00 0.00 4.94
4410 4816 1.594310 GAGCCTCTCACCTGACACC 59.406 63.158 0.00 0.00 0.00 4.16
4411 4817 1.594310 GGAGCCTCTCACCTGACAC 59.406 63.158 0.00 0.00 31.08 3.67
4412 4818 1.610673 GGGAGCCTCTCACCTGACA 60.611 63.158 0.00 0.00 31.08 3.58
4413 4819 0.907230 AAGGGAGCCTCTCACCTGAC 60.907 60.000 0.00 0.00 33.78 3.51
4414 4820 0.178891 AAAGGGAGCCTCTCACCTGA 60.179 55.000 0.00 0.00 33.78 3.86
4415 4821 0.251634 GAAAGGGAGCCTCTCACCTG 59.748 60.000 0.00 0.00 33.78 4.00
4416 4822 0.178891 TGAAAGGGAGCCTCTCACCT 60.179 55.000 0.00 0.00 33.78 4.00
4417 4823 0.035915 GTGAAAGGGAGCCTCTCACC 60.036 60.000 0.00 0.00 33.78 4.02
4418 4824 0.980423 AGTGAAAGGGAGCCTCTCAC 59.020 55.000 0.00 0.00 33.42 3.51
4419 4825 1.734655 AAGTGAAAGGGAGCCTCTCA 58.265 50.000 0.00 0.00 30.89 3.27
4420 4826 2.616765 GGAAAGTGAAAGGGAGCCTCTC 60.617 54.545 0.00 0.00 30.89 3.20
4421 4827 1.352687 GGAAAGTGAAAGGGAGCCTCT 59.647 52.381 0.00 0.00 30.89 3.69
4422 4828 1.352687 AGGAAAGTGAAAGGGAGCCTC 59.647 52.381 0.00 0.00 30.89 4.70
4423 4829 1.450360 AGGAAAGTGAAAGGGAGCCT 58.550 50.000 0.00 0.00 33.87 4.58
4424 4830 2.294449 AAGGAAAGTGAAAGGGAGCC 57.706 50.000 0.00 0.00 0.00 4.70
4425 4831 4.672587 AAAAAGGAAAGTGAAAGGGAGC 57.327 40.909 0.00 0.00 0.00 4.70
4445 4851 9.674068 TGATGCAATACCACTACATAGTTTAAA 57.326 29.630 0.00 0.00 33.46 1.52
4446 4852 9.845740 ATGATGCAATACCACTACATAGTTTAA 57.154 29.630 0.00 0.00 33.46 1.52
4448 4854 9.494271 CTATGATGCAATACCACTACATAGTTT 57.506 33.333 0.00 0.00 34.48 2.66
4449 4855 8.097038 CCTATGATGCAATACCACTACATAGTT 58.903 37.037 0.00 0.00 36.19 2.24
4450 4856 7.615403 CCTATGATGCAATACCACTACATAGT 58.385 38.462 0.00 0.00 36.19 2.12
4451 4857 6.536582 GCCTATGATGCAATACCACTACATAG 59.463 42.308 0.00 0.00 37.06 2.23
4452 4858 6.013812 TGCCTATGATGCAATACCACTACATA 60.014 38.462 0.00 0.00 35.40 2.29
4453 4859 5.221904 TGCCTATGATGCAATACCACTACAT 60.222 40.000 0.00 0.00 35.40 2.29
4454 4860 4.102367 TGCCTATGATGCAATACCACTACA 59.898 41.667 0.00 0.00 35.40 2.74
4455 4861 4.641396 TGCCTATGATGCAATACCACTAC 58.359 43.478 0.00 0.00 35.40 2.73
4456 4862 4.972751 TGCCTATGATGCAATACCACTA 57.027 40.909 0.00 0.00 35.40 2.74
4457 4863 3.862877 TGCCTATGATGCAATACCACT 57.137 42.857 0.00 0.00 35.40 4.00
4458 4864 6.764308 AATATGCCTATGATGCAATACCAC 57.236 37.500 0.00 0.00 42.92 4.16
4459 4865 7.557358 CCTTAATATGCCTATGATGCAATACCA 59.443 37.037 0.00 0.00 42.92 3.25
4460 4866 7.469181 GCCTTAATATGCCTATGATGCAATACC 60.469 40.741 0.00 0.00 42.92 2.73
4461 4867 7.284034 AGCCTTAATATGCCTATGATGCAATAC 59.716 37.037 0.00 0.00 42.92 1.89
4462 4868 7.348815 AGCCTTAATATGCCTATGATGCAATA 58.651 34.615 0.00 0.00 42.92 1.90
4463 4869 6.192773 AGCCTTAATATGCCTATGATGCAAT 58.807 36.000 0.00 0.00 42.92 3.56
4464 4870 5.573219 AGCCTTAATATGCCTATGATGCAA 58.427 37.500 0.00 0.00 42.92 4.08
4465 4871 5.183530 AGCCTTAATATGCCTATGATGCA 57.816 39.130 0.00 0.00 43.97 3.96
4466 4872 7.814264 ATTAGCCTTAATATGCCTATGATGC 57.186 36.000 0.00 0.00 0.00 3.91
4807 5216 3.714280 AGGAAGGAAAGAGAGGATAAGGC 59.286 47.826 0.00 0.00 0.00 4.35
4854 5263 6.360618 AGGAAGAACACAGAAGAAATGAACT 58.639 36.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.