Multiple sequence alignment - TraesCS7D01G495800

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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 TraesCS7D01G495800 chr7D 100.000 4064 0 0 1 4064 602773152 602769089 0.000000e+00 7505
1 TraesCS7D01G495800 chr7D 86.100 1223 140 22 1879 3085 602722603 602721395 0.000000e+00 1290
2 TraesCS7D01G495800 chr7D 78.747 814 135 19 994 1776 602751501 602750695 1.010000e-140 510
3 TraesCS7D01G495800 chr7D 77.432 771 143 20 1035 1776 602673521 602672753 8.070000e-117 431
4 TraesCS7D01G495800 chr7D 75.912 822 142 30 1001 1776 602664450 602663639 1.780000e-98 370
5 TraesCS7D01G495800 chr7A 89.358 3289 259 47 13 3279 694423362 694420143 0.000000e+00 4050
6 TraesCS7D01G495800 chr7A 85.939 1209 140 20 1882 3074 694357232 694356038 0.000000e+00 1264
7 TraesCS7D01G495800 chr7A 84.746 649 96 2 1686 2331 669397103 669396455 0.000000e+00 647
8 TraesCS7D01G495800 chr7A 77.025 827 142 28 987 1774 694196437 694197254 8.070000e-117 431
9 TraesCS7D01G495800 chr7A 77.065 811 146 25 1001 1776 694331903 694331098 8.070000e-117 431
10 TraesCS7D01G495800 chr7A 76.989 817 148 23 994 1776 694375882 694375072 8.070000e-117 431
11 TraesCS7D01G495800 chr7A 77.447 705 119 17 996 1681 669398103 669397420 6.370000e-103 385
12 TraesCS7D01G495800 chr7A 84.069 408 56 8 1901 2305 694117351 694117752 6.370000e-103 385
13 TraesCS7D01G495800 chr7A 84.655 391 44 13 2 380 8335517 8335903 3.840000e-100 375
14 TraesCS7D01G495800 chr7A 75.524 764 146 21 1047 1776 694358142 694357386 1.810000e-88 337
15 TraesCS7D01G495800 chr7A 76.709 395 57 15 987 1347 694135994 694136387 1.930000e-43 187
16 TraesCS7D01G495800 chr7B 93.928 2355 125 13 827 3172 683419907 683417562 0.000000e+00 3541
17 TraesCS7D01G495800 chr7B 93.571 1260 80 1 1861 3119 683325164 683323905 0.000000e+00 1877
18 TraesCS7D01G495800 chr7B 85.575 1331 184 6 1632 2958 640353877 640355203 0.000000e+00 1387
19 TraesCS7D01G495800 chr7B 78.796 2193 369 58 1001 3128 683169245 683167084 0.000000e+00 1386
20 TraesCS7D01G495800 chr7B 85.055 1278 156 22 1828 3085 683230580 683229318 0.000000e+00 1269
21 TraesCS7D01G495800 chr7B 84.155 1319 170 25 1820 3112 683106653 683107958 0.000000e+00 1242
22 TraesCS7D01G495800 chr7B 82.348 1286 190 20 1836 3094 682843095 682844370 0.000000e+00 1083
23 TraesCS7D01G495800 chr7B 90.931 419 35 3 1 419 683437203 683436788 9.860000e-156 560
24 TraesCS7D01G495800 chr7B 88.279 401 39 8 1472 1871 683326261 683325868 1.320000e-129 473
25 TraesCS7D01G495800 chr7B 77.503 809 151 16 994 1776 683243790 683242987 1.330000e-124 457
26 TraesCS7D01G495800 chr7B 85.480 427 36 8 417 819 683420378 683419954 4.860000e-114 422
27 TraesCS7D01G495800 chr7B 75.216 811 166 18 994 1773 682842184 682842990 6.460000e-93 351
28 TraesCS7D01G495800 chr7B 89.362 282 25 5 3293 3571 656422390 656422111 2.320000e-92 350
29 TraesCS7D01G495800 chr7B 86.316 190 24 2 3116 3304 683316710 683316522 5.320000e-49 206
30 TraesCS7D01G495800 chrUn 84.671 2218 286 34 909 3087 92685862 92683660 0.000000e+00 2163
31 TraesCS7D01G495800 chrUn 84.671 2218 286 34 909 3087 291005364 291003162 0.000000e+00 2163
32 TraesCS7D01G495800 chr2D 97.801 773 17 0 3292 4064 523013076 523012304 0.000000e+00 1334
33 TraesCS7D01G495800 chr2D 94.088 592 28 2 3293 3884 1944952 1944368 0.000000e+00 893
34 TraesCS7D01G495800 chr2D 84.000 375 50 7 1 371 12918636 12919004 6.460000e-93 351
35 TraesCS7D01G495800 chr2D 93.893 131 8 0 3932 4062 1944181 1944051 8.910000e-47 198
36 TraesCS7D01G495800 chr6A 91.538 520 37 1 3545 4064 575175771 575175259 0.000000e+00 710
37 TraesCS7D01G495800 chr6A 90.595 521 44 5 3545 4064 18853304 18852788 0.000000e+00 686
38 TraesCS7D01G495800 chr6A 92.355 327 25 0 3293 3619 575176075 575175749 2.210000e-127 466
39 TraesCS7D01G495800 chr6A 87.409 413 40 4 3569 3981 94268912 94268512 7.960000e-127 464
40 TraesCS7D01G495800 chr6A 87.869 305 33 2 3308 3608 94269217 94268913 5.000000e-94 355
41 TraesCS7D01G495800 chr1B 85.545 422 53 3 3554 3975 456842292 456842705 6.240000e-118 435
42 TraesCS7D01G495800 chr1B 90.462 325 27 3 3293 3615 456841978 456842300 3.750000e-115 425
43 TraesCS7D01G495800 chr4B 76.521 822 152 20 990 1774 28536571 28537388 1.050000e-110 411
44 TraesCS7D01G495800 chr2B 85.526 380 49 6 1 377 373994211 373994587 3.810000e-105 392
45 TraesCS7D01G495800 chr2B 85.792 366 50 2 13 377 776035815 776036179 1.770000e-103 387
46 TraesCS7D01G495800 chr2B 87.829 304 33 4 3293 3594 699046789 699046488 1.800000e-93 353
47 TraesCS7D01G495800 chr3B 89.180 305 28 5 3293 3594 44291283 44291585 3.840000e-100 375
48 TraesCS7D01G495800 chr6B 83.763 388 48 10 1 377 132305725 132306108 1.800000e-93 353
49 TraesCS7D01G495800 chr5B 87.829 304 33 4 3293 3594 458927446 458927145 1.800000e-93 353
50 TraesCS7D01G495800 chr1D 83.377 379 56 6 1 375 35572709 35573084 1.080000e-90 344
51 TraesCS7D01G495800 chr5D 83.333 378 56 7 1 375 339664911 339664538 3.890000e-90 342
52 TraesCS7D01G495800 chr5A 83.073 384 57 7 1 379 113613352 113613732 3.890000e-90 342


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 TraesCS7D01G495800 chr7D 602769089 602773152 4063 True 7505.0 7505 100.0000 1 4064 1 chr7D.!!$R5 4063
1 TraesCS7D01G495800 chr7D 602721395 602722603 1208 True 1290.0 1290 86.1000 1879 3085 1 chr7D.!!$R3 1206
2 TraesCS7D01G495800 chr7D 602750695 602751501 806 True 510.0 510 78.7470 994 1776 1 chr7D.!!$R4 782
3 TraesCS7D01G495800 chr7D 602672753 602673521 768 True 431.0 431 77.4320 1035 1776 1 chr7D.!!$R2 741
4 TraesCS7D01G495800 chr7D 602663639 602664450 811 True 370.0 370 75.9120 1001 1776 1 chr7D.!!$R1 775
5 TraesCS7D01G495800 chr7A 694420143 694423362 3219 True 4050.0 4050 89.3580 13 3279 1 chr7A.!!$R3 3266
6 TraesCS7D01G495800 chr7A 694356038 694358142 2104 True 800.5 1264 80.7315 1047 3074 2 chr7A.!!$R5 2027
7 TraesCS7D01G495800 chr7A 669396455 669398103 1648 True 516.0 647 81.0965 996 2331 2 chr7A.!!$R4 1335
8 TraesCS7D01G495800 chr7A 694196437 694197254 817 False 431.0 431 77.0250 987 1774 1 chr7A.!!$F4 787
9 TraesCS7D01G495800 chr7A 694331098 694331903 805 True 431.0 431 77.0650 1001 1776 1 chr7A.!!$R1 775
10 TraesCS7D01G495800 chr7A 694375072 694375882 810 True 431.0 431 76.9890 994 1776 1 chr7A.!!$R2 782
11 TraesCS7D01G495800 chr7B 683417562 683420378 2816 True 1981.5 3541 89.7040 417 3172 2 chr7B.!!$R8 2755
12 TraesCS7D01G495800 chr7B 640353877 640355203 1326 False 1387.0 1387 85.5750 1632 2958 1 chr7B.!!$F1 1326
13 TraesCS7D01G495800 chr7B 683167084 683169245 2161 True 1386.0 1386 78.7960 1001 3128 1 chr7B.!!$R2 2127
14 TraesCS7D01G495800 chr7B 683229318 683230580 1262 True 1269.0 1269 85.0550 1828 3085 1 chr7B.!!$R3 1257
15 TraesCS7D01G495800 chr7B 683106653 683107958 1305 False 1242.0 1242 84.1550 1820 3112 1 chr7B.!!$F2 1292
16 TraesCS7D01G495800 chr7B 683323905 683326261 2356 True 1175.0 1877 90.9250 1472 3119 2 chr7B.!!$R7 1647
17 TraesCS7D01G495800 chr7B 682842184 682844370 2186 False 717.0 1083 78.7820 994 3094 2 chr7B.!!$F3 2100
18 TraesCS7D01G495800 chr7B 683242987 683243790 803 True 457.0 457 77.5030 994 1776 1 chr7B.!!$R4 782
19 TraesCS7D01G495800 chrUn 92683660 92685862 2202 True 2163.0 2163 84.6710 909 3087 1 chrUn.!!$R1 2178
20 TraesCS7D01G495800 chrUn 291003162 291005364 2202 True 2163.0 2163 84.6710 909 3087 1 chrUn.!!$R2 2178
21 TraesCS7D01G495800 chr2D 523012304 523013076 772 True 1334.0 1334 97.8010 3292 4064 1 chr2D.!!$R1 772
22 TraesCS7D01G495800 chr2D 1944051 1944952 901 True 545.5 893 93.9905 3293 4062 2 chr2D.!!$R2 769
23 TraesCS7D01G495800 chr6A 18852788 18853304 516 True 686.0 686 90.5950 3545 4064 1 chr6A.!!$R1 519
24 TraesCS7D01G495800 chr6A 575175259 575176075 816 True 588.0 710 91.9465 3293 4064 2 chr6A.!!$R3 771
25 TraesCS7D01G495800 chr6A 94268512 94269217 705 True 409.5 464 87.6390 3308 3981 2 chr6A.!!$R2 673
26 TraesCS7D01G495800 chr1B 456841978 456842705 727 False 430.0 435 88.0035 3293 3975 2 chr1B.!!$F1 682
27 TraesCS7D01G495800 chr4B 28536571 28537388 817 False 411.0 411 76.5210 990 1774 1 chr4B.!!$F1 784

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
825 867 0.248661 CGATCTGCTTCGTCGTGGAT 60.249 55.0 0.00 0.0 34.46 3.41 F
835 901 0.318445 CGTCGTGGATACCGATTCCC 60.318 60.0 0.00 0.0 40.47 3.97 F
1475 1620 0.464452 AACTCCTACTATGGCGGCAC 59.536 55.0 16.34 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1777 2282 0.408309 TTCCTGGTCGGAAGAGGAGA 59.592 55.0 6.41 0.0 46.8 3.71 R
2079 3316 0.670546 CGGTGGCTACAGTTGTGAGG 60.671 60.0 1.52 0.0 0.0 3.86 R
3145 4413 0.891904 TTAGCCGCAACTTTCCCCAC 60.892 55.0 0.00 0.0 0.0 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
32 33 4.703093 TCCAAAGAAAACTTCGTGGAAACT 59.297 37.500 10.60 0.00 42.20 2.66
45 46 6.687081 TCGTGGAAACTATGTTTGAAAGTT 57.313 33.333 0.10 0.00 35.01 2.66
46 47 7.090953 TCGTGGAAACTATGTTTGAAAGTTT 57.909 32.000 0.10 0.00 44.05 2.66
101 102 8.585471 AAAAGGATGATGTTCTATTGTCATGT 57.415 30.769 0.00 0.00 31.86 3.21
102 103 7.563888 AAGGATGATGTTCTATTGTCATGTG 57.436 36.000 0.00 0.00 31.86 3.21
120 121 9.645059 TGTCATGTGAAATTTCAAGTAAAAACA 57.355 25.926 22.07 13.29 39.21 2.83
121 122 9.900264 GTCATGTGAAATTTCAAGTAAAAACAC 57.100 29.630 22.07 7.32 39.21 3.32
122 123 9.645059 TCATGTGAAATTTCAAGTAAAAACACA 57.355 25.926 22.07 12.47 39.83 3.72
145 146 0.249868 CGGGGATGCGAGCTATGAAA 60.250 55.000 0.00 0.00 0.00 2.69
147 148 1.876156 GGGGATGCGAGCTATGAAAAG 59.124 52.381 0.00 0.00 0.00 2.27
163 165 7.201496 GCTATGAAAAGGACAAATTCAGCAATG 60.201 37.037 0.00 0.00 36.59 2.82
170 172 7.472334 AGGACAAATTCAGCAATGAATAGTT 57.528 32.000 4.04 0.00 37.52 2.24
172 174 8.462016 AGGACAAATTCAGCAATGAATAGTTAC 58.538 33.333 4.04 4.79 37.52 2.50
181 183 8.959548 TCAGCAATGAATAGTTACATCAATGTT 58.040 29.630 0.20 0.00 41.97 2.71
183 185 8.408601 AGCAATGAATAGTTACATCAATGTTCC 58.591 33.333 0.20 0.00 41.97 3.62
199 201 6.883756 TCAATGTTCCACACTATTCAATGCTA 59.116 34.615 0.00 0.00 0.00 3.49
220 222 9.987272 ATGCTAATTTTATCTTTTTCATAGCCC 57.013 29.630 0.00 0.00 33.96 5.19
239 241 2.422127 CCCACATCCCGTAACATGTTTC 59.578 50.000 17.78 10.94 30.48 2.78
245 247 4.822036 TCCCGTAACATGTTTCAACTTG 57.178 40.909 17.78 3.26 39.26 3.16
246 248 4.452825 TCCCGTAACATGTTTCAACTTGA 58.547 39.130 17.78 5.47 37.47 3.02
258 260 6.783162 TGTTTCAACTTGAAATTTTGCATGG 58.217 32.000 17.84 0.00 46.55 3.66
276 278 3.737559 TGGCAATAGAACATCACCCTT 57.262 42.857 0.00 0.00 0.00 3.95
285 287 8.960591 CAATAGAACATCACCCTTTTAACATCT 58.039 33.333 0.00 0.00 0.00 2.90
286 288 9.533831 AATAGAACATCACCCTTTTAACATCTT 57.466 29.630 0.00 0.00 0.00 2.40
287 289 7.839680 AGAACATCACCCTTTTAACATCTTT 57.160 32.000 0.00 0.00 0.00 2.52
288 290 8.250143 AGAACATCACCCTTTTAACATCTTTT 57.750 30.769 0.00 0.00 0.00 2.27
289 291 8.704668 AGAACATCACCCTTTTAACATCTTTTT 58.295 29.630 0.00 0.00 0.00 1.94
329 332 9.650539 TCAAAACTTCAAAACATCATTTTCTCA 57.349 25.926 0.00 0.00 0.00 3.27
337 340 9.044150 TCAAAACATCATTTTCTCATGGTTTTC 57.956 29.630 0.00 0.00 35.66 2.29
341 344 7.898918 ACATCATTTTCTCATGGTTTTCATCA 58.101 30.769 0.00 0.00 32.92 3.07
342 345 8.033038 ACATCATTTTCTCATGGTTTTCATCAG 58.967 33.333 0.00 0.00 32.92 2.90
343 346 6.392354 TCATTTTCTCATGGTTTTCATCAGC 58.608 36.000 0.00 0.00 32.92 4.26
350 353 5.957798 TCATGGTTTTCATCAGCTTTCATC 58.042 37.500 0.00 0.00 32.92 2.92
358 361 5.885230 TCATCAGCTTTCATCGAATGTTT 57.115 34.783 0.00 0.00 0.00 2.83
365 368 4.088496 GCTTTCATCGAATGTTTGTTTCCG 59.912 41.667 0.00 0.00 0.00 4.30
368 371 6.489127 TTCATCGAATGTTTGTTTCCGTAT 57.511 33.333 0.00 0.00 0.00 3.06
369 372 5.863898 TCATCGAATGTTTGTTTCCGTATG 58.136 37.500 0.00 0.00 0.00 2.39
385 388 7.948034 TTCCGTATGATATTTTTCCTGGTTT 57.052 32.000 0.00 0.00 0.00 3.27
387 390 6.320164 TCCGTATGATATTTTTCCTGGTTTGG 59.680 38.462 0.00 0.00 0.00 3.28
389 392 4.448537 TGATATTTTTCCTGGTTTGGCG 57.551 40.909 0.00 0.00 0.00 5.69
396 399 2.260869 CCTGGTTTGGCGTGTCAGG 61.261 63.158 0.00 0.00 38.96 3.86
399 402 2.904866 GTTTGGCGTGTCAGGGCA 60.905 61.111 16.88 16.88 36.75 5.36
411 414 0.824109 TCAGGGCACGAAGTATGAGG 59.176 55.000 0.00 0.00 41.61 3.86
439 442 1.289066 CTCTCAACTCGGCGAACCA 59.711 57.895 12.13 0.00 34.57 3.67
580 599 3.119096 GAAACTCCGGCGAGGTGC 61.119 66.667 9.30 0.00 40.77 5.01
628 649 3.118454 CACAACGGCCGCGAGAAT 61.118 61.111 28.58 0.00 0.00 2.40
629 650 2.813908 ACAACGGCCGCGAGAATC 60.814 61.111 28.58 0.00 0.00 2.52
727 755 2.953466 TCGTCCTGTGTAGCCATTAC 57.047 50.000 0.00 0.00 0.00 1.89
825 867 0.248661 CGATCTGCTTCGTCGTGGAT 60.249 55.000 0.00 0.00 34.46 3.41
829 871 0.866061 CTGCTTCGTCGTGGATACCG 60.866 60.000 0.00 0.00 0.00 4.02
835 901 0.318445 CGTCGTGGATACCGATTCCC 60.318 60.000 0.00 0.00 40.47 3.97
943 1009 4.040095 ACGAGCTATACAATTTCCCCCTAC 59.960 45.833 0.00 0.00 0.00 3.18
964 1033 6.984474 CCTACTTTTATAATGCTCGAGGTTCA 59.016 38.462 15.58 3.93 0.00 3.18
1040 1124 2.670148 CCACCACCCTAGTCCTGGC 61.670 68.421 0.00 0.00 0.00 4.85
1088 1172 3.452786 CTGGGCCTTCTCGCTCGA 61.453 66.667 4.53 0.00 28.91 4.04
1180 1280 3.184683 CAAGGCTCGAGCTGACGC 61.185 66.667 34.46 18.89 41.70 5.19
1475 1620 0.464452 AACTCCTACTATGGCGGCAC 59.536 55.000 16.34 0.00 0.00 5.01
1477 1622 2.029073 CCTACTATGGCGGCACCG 59.971 66.667 16.34 11.07 43.94 4.94
1509 1654 0.522626 TCGGCATCGACGTAAACTCA 59.477 50.000 0.00 0.00 40.88 3.41
1523 1668 5.118990 CGTAAACTCAATGATCTCCATGGT 58.881 41.667 12.58 0.00 35.24 3.55
1525 1670 2.928334 ACTCAATGATCTCCATGGTGC 58.072 47.619 12.58 0.00 35.24 5.01
1526 1671 2.240414 ACTCAATGATCTCCATGGTGCA 59.760 45.455 12.58 4.08 35.24 4.57
1539 1684 2.512745 GTGCACACGGACACCACA 60.513 61.111 13.17 0.00 32.83 4.17
1546 1691 2.970324 CGGACACCACAACCACGG 60.970 66.667 0.00 0.00 0.00 4.94
1777 2282 5.426509 TCATGGTCATTCAGTTCCACTCTAT 59.573 40.000 0.00 0.00 32.60 1.98
2079 3316 1.482748 TTTACCGGGGTCACCTCACC 61.483 60.000 6.32 0.00 36.97 4.02
2086 3323 2.142220 GGTCACCTCACCCTCACAA 58.858 57.895 0.00 0.00 0.00 3.33
2090 3327 0.469917 CACCTCACCCTCACAACTGT 59.530 55.000 0.00 0.00 0.00 3.55
2305 3558 3.513119 AGACAAGCATCTCTACAGCAAGA 59.487 43.478 0.00 0.00 0.00 3.02
2312 3565 5.709164 AGCATCTCTACAGCAAGAACAAATT 59.291 36.000 0.00 0.00 0.00 1.82
2325 3581 3.057315 AGAACAAATTTCTCACATGGCCG 60.057 43.478 0.00 0.00 0.00 6.13
2344 3600 2.101415 CCGCAGAGGTACAAGATCATCA 59.899 50.000 0.00 0.00 34.51 3.07
2868 4124 2.333417 GCAGTCCGACGAGGTGAGA 61.333 63.158 0.00 0.00 41.99 3.27
3131 4399 2.527497 ACATCCACCATGCATTGACAA 58.473 42.857 4.52 0.00 35.65 3.18
3145 4413 9.108449 CATGCATTGACAACAACAATTATTTTG 57.892 29.630 0.00 0.00 38.90 2.44
3149 4417 7.545362 TTGACAACAACAATTATTTTGTGGG 57.455 32.000 10.06 7.32 36.08 4.61
3150 4418 6.051717 TGACAACAACAATTATTTTGTGGGG 58.948 36.000 10.06 5.79 36.08 4.96
3179 4447 0.324943 GCTAAACCTGAGAGCACCCA 59.675 55.000 0.00 0.00 36.20 4.51
3180 4448 1.065126 GCTAAACCTGAGAGCACCCAT 60.065 52.381 0.00 0.00 36.20 4.00
3194 4463 2.224793 GCACCCATCCCCTTATCTAACC 60.225 54.545 0.00 0.00 0.00 2.85
3208 4477 6.980397 CCTTATCTAACCATTCATTTTGTGCC 59.020 38.462 0.00 0.00 0.00 5.01
3212 4481 2.238521 ACCATTCATTTTGTGCCTCGT 58.761 42.857 0.00 0.00 0.00 4.18
3213 4482 2.030007 ACCATTCATTTTGTGCCTCGTG 60.030 45.455 0.00 0.00 0.00 4.35
3217 4486 3.057969 TCATTTTGTGCCTCGTGATCT 57.942 42.857 0.00 0.00 0.00 2.75
3222 4491 1.374631 GTGCCTCGTGATCTGTGCA 60.375 57.895 0.00 0.00 0.00 4.57
3231 4500 5.523552 CCTCGTGATCTGTGCATAAACATTA 59.476 40.000 0.00 0.00 0.00 1.90
3270 4540 9.880157 CCTCAAATGAAAGAATATTTGGACAAT 57.120 29.630 0.00 0.00 41.98 2.71
3279 4549 8.421249 AAGAATATTTGGACAATCTTTGTGGA 57.579 30.769 0.00 0.00 45.52 4.02
3280 4550 8.599624 AGAATATTTGGACAATCTTTGTGGAT 57.400 30.769 0.00 0.00 45.52 3.41
3281 4551 8.689972 AGAATATTTGGACAATCTTTGTGGATC 58.310 33.333 0.00 0.00 45.52 3.36
3282 4552 7.959658 ATATTTGGACAATCTTTGTGGATCA 57.040 32.000 0.00 0.00 45.52 2.92
3283 4553 5.710513 TTTGGACAATCTTTGTGGATCAG 57.289 39.130 0.00 0.00 45.52 2.90
3284 4554 3.689347 TGGACAATCTTTGTGGATCAGG 58.311 45.455 0.00 0.00 45.52 3.86
3285 4555 3.019564 GGACAATCTTTGTGGATCAGGG 58.980 50.000 0.00 0.00 45.52 4.45
3286 4556 3.308402 GGACAATCTTTGTGGATCAGGGA 60.308 47.826 0.00 0.00 45.52 4.20
3287 4557 4.335416 GACAATCTTTGTGGATCAGGGAA 58.665 43.478 0.00 0.00 45.52 3.97
3288 4558 4.739793 ACAATCTTTGTGGATCAGGGAAA 58.260 39.130 0.00 0.00 43.48 3.13
3289 4559 4.524328 ACAATCTTTGTGGATCAGGGAAAC 59.476 41.667 0.00 0.00 43.48 2.78
3290 4560 3.874383 TCTTTGTGGATCAGGGAAACA 57.126 42.857 0.00 0.00 0.00 2.83
3352 4623 3.459145 TGCAGAAAACACTACGCTACAA 58.541 40.909 0.00 0.00 0.00 2.41
3928 5300 0.040351 AGCAGTCAGAGGGCAGTCTA 59.960 55.000 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.017440 TCCACGAAGTTTTCTTTGGATGTTAG 60.017 38.462 0.00 0.00 41.61 2.34
4 5 5.823570 TCCACGAAGTTTTCTTTGGATGTTA 59.176 36.000 0.00 0.00 41.61 2.41
5 6 4.642885 TCCACGAAGTTTTCTTTGGATGTT 59.357 37.500 0.00 0.00 41.61 2.71
6 7 4.204012 TCCACGAAGTTTTCTTTGGATGT 58.796 39.130 0.00 0.00 41.61 3.06
7 8 4.829064 TCCACGAAGTTTTCTTTGGATG 57.171 40.909 0.00 0.00 41.61 3.51
8 9 5.359860 AGTTTCCACGAAGTTTTCTTTGGAT 59.640 36.000 8.82 0.00 42.70 3.41
9 10 4.703093 AGTTTCCACGAAGTTTTCTTTGGA 59.297 37.500 0.00 5.42 41.61 3.53
10 11 4.993905 AGTTTCCACGAAGTTTTCTTTGG 58.006 39.130 0.00 0.00 41.61 3.28
11 12 7.193595 ACATAGTTTCCACGAAGTTTTCTTTG 58.806 34.615 0.00 0.00 41.61 2.77
12 13 7.329588 ACATAGTTTCCACGAAGTTTTCTTT 57.670 32.000 0.00 0.00 41.61 2.52
13 14 6.937436 ACATAGTTTCCACGAAGTTTTCTT 57.063 33.333 0.00 0.00 41.61 2.52
14 15 6.937436 AACATAGTTTCCACGAAGTTTTCT 57.063 33.333 0.00 0.00 41.61 2.52
15 16 7.190871 TCAAACATAGTTTCCACGAAGTTTTC 58.809 34.615 0.00 0.00 41.61 2.29
16 17 7.090953 TCAAACATAGTTTCCACGAAGTTTT 57.909 32.000 0.00 0.00 41.61 2.43
17 18 6.687081 TCAAACATAGTTTCCACGAAGTTT 57.313 33.333 0.00 0.00 41.61 2.66
23 24 7.376530 GAAACTTTCAAACATAGTTTCCACG 57.623 36.000 13.29 0.00 46.01 4.94
78 79 7.341030 TCACATGACAATAGAACATCATCCTT 58.659 34.615 0.00 0.00 29.25 3.36
84 85 9.844790 TGAAATTTCACATGACAATAGAACATC 57.155 29.630 16.91 0.00 31.01 3.06
115 116 1.470890 CGCATCCCCGTAATGTGTTTT 59.529 47.619 0.00 0.00 31.51 2.43
117 118 0.250793 TCGCATCCCCGTAATGTGTT 59.749 50.000 0.00 0.00 36.31 3.32
119 120 1.498865 GCTCGCATCCCCGTAATGTG 61.499 60.000 0.00 0.00 36.25 3.21
120 121 1.227556 GCTCGCATCCCCGTAATGT 60.228 57.895 0.00 0.00 0.00 2.71
121 122 0.317160 TAGCTCGCATCCCCGTAATG 59.683 55.000 0.00 0.00 0.00 1.90
122 123 1.066858 CATAGCTCGCATCCCCGTAAT 60.067 52.381 0.00 0.00 0.00 1.89
123 124 0.317160 CATAGCTCGCATCCCCGTAA 59.683 55.000 0.00 0.00 0.00 3.18
124 125 0.538746 TCATAGCTCGCATCCCCGTA 60.539 55.000 0.00 0.00 0.00 4.02
125 126 1.399744 TTCATAGCTCGCATCCCCGT 61.400 55.000 0.00 0.00 0.00 5.28
126 127 0.249868 TTTCATAGCTCGCATCCCCG 60.250 55.000 0.00 0.00 0.00 5.73
127 128 1.876156 CTTTTCATAGCTCGCATCCCC 59.124 52.381 0.00 0.00 0.00 4.81
128 129 1.876156 CCTTTTCATAGCTCGCATCCC 59.124 52.381 0.00 0.00 0.00 3.85
199 201 9.822185 GATGTGGGCTATGAAAAAGATAAAATT 57.178 29.630 0.00 0.00 0.00 1.82
209 211 1.283613 ACGGGATGTGGGCTATGAAAA 59.716 47.619 0.00 0.00 0.00 2.29
220 222 4.215399 AGTTGAAACATGTTACGGGATGTG 59.785 41.667 12.39 0.00 33.03 3.21
239 241 4.815040 TGCCATGCAAAATTTCAAGTTG 57.185 36.364 0.00 0.00 34.76 3.16
258 260 6.919721 TGTTAAAAGGGTGATGTTCTATTGC 58.080 36.000 0.00 0.00 0.00 3.56
264 266 8.887036 AAAAAGATGTTAAAAGGGTGATGTTC 57.113 30.769 0.00 0.00 0.00 3.18
329 332 4.701651 TCGATGAAAGCTGATGAAAACCAT 59.298 37.500 0.00 0.00 38.43 3.55
337 340 5.396484 ACAAACATTCGATGAAAGCTGATG 58.604 37.500 0.00 0.00 0.00 3.07
341 344 5.222631 GGAAACAAACATTCGATGAAAGCT 58.777 37.500 0.00 0.00 0.00 3.74
342 345 4.088496 CGGAAACAAACATTCGATGAAAGC 59.912 41.667 0.00 0.00 0.00 3.51
343 346 5.212194 ACGGAAACAAACATTCGATGAAAG 58.788 37.500 0.00 0.00 0.00 2.62
350 353 8.835467 AAATATCATACGGAAACAAACATTCG 57.165 30.769 0.00 0.00 0.00 3.34
358 361 6.887545 ACCAGGAAAAATATCATACGGAAACA 59.112 34.615 0.00 0.00 0.00 2.83
365 368 5.977129 CGCCAAACCAGGAAAAATATCATAC 59.023 40.000 0.00 0.00 0.00 2.39
368 371 3.829601 ACGCCAAACCAGGAAAAATATCA 59.170 39.130 0.00 0.00 0.00 2.15
369 372 4.173256 CACGCCAAACCAGGAAAAATATC 58.827 43.478 0.00 0.00 0.00 1.63
389 392 1.067142 TCATACTTCGTGCCCTGACAC 60.067 52.381 0.00 0.00 37.19 3.67
396 399 2.688958 AGACTACCTCATACTTCGTGCC 59.311 50.000 0.00 0.00 0.00 5.01
411 414 3.671164 GCCGAGTTGAGAGTTGAGACTAC 60.671 52.174 0.00 0.00 35.88 2.73
426 429 2.660552 CACGTGGTTCGCCGAGTT 60.661 61.111 7.95 0.00 44.19 3.01
586 605 0.676782 AAGGATGTTAGCGTGGCCAC 60.677 55.000 26.78 26.78 0.00 5.01
600 619 0.321653 GCCGTTGTGGAGTCAAGGAT 60.322 55.000 0.00 0.00 42.00 3.24
628 649 2.151202 GCGAAAATGACTTCACTGGGA 58.849 47.619 0.00 0.00 0.00 4.37
629 650 1.200020 GGCGAAAATGACTTCACTGGG 59.800 52.381 0.00 0.00 0.00 4.45
727 755 0.455410 CTCCGACTGAGCTCTCCAAG 59.545 60.000 16.19 6.25 33.47 3.61
825 867 1.548081 TGAACGTCAGGGAATCGGTA 58.452 50.000 0.00 0.00 0.00 4.02
829 871 3.492829 GGACCTATGAACGTCAGGGAATC 60.493 52.174 9.45 0.00 33.48 2.52
835 901 2.093973 AGCTTGGACCTATGAACGTCAG 60.094 50.000 0.00 0.00 0.00 3.51
943 1009 6.892691 GGATGAACCTCGAGCATTATAAAAG 58.107 40.000 6.99 0.00 35.41 2.27
964 1033 1.726853 GTACAGTGCTTGCGAAGGAT 58.273 50.000 0.00 0.00 0.00 3.24
1087 1171 2.694213 GGAGAAGTTGAGGCTGAAGTC 58.306 52.381 0.00 0.00 0.00 3.01
1088 1172 1.001406 CGGAGAAGTTGAGGCTGAAGT 59.999 52.381 0.00 0.00 0.00 3.01
1180 1280 1.447489 CGCTGCTCAGGAGGTTCTG 60.447 63.158 0.00 0.00 36.17 3.02
1451 1596 1.404391 CGCCATAGTAGGAGTTGTCGT 59.596 52.381 0.00 0.00 0.00 4.34
1475 1620 2.398554 CCGACATGGTTCTTGCCGG 61.399 63.158 0.00 0.00 33.84 6.13
1477 1622 1.315257 ATGCCGACATGGTTCTTGCC 61.315 55.000 0.00 0.00 41.21 4.52
1503 1648 3.698040 GCACCATGGAGATCATTGAGTTT 59.302 43.478 21.47 0.00 32.92 2.66
1509 1654 2.372264 GTGTGCACCATGGAGATCATT 58.628 47.619 21.47 0.00 32.92 2.57
1523 1668 2.109739 GTTGTGGTGTCCGTGTGCA 61.110 57.895 0.00 0.00 0.00 4.57
1525 1670 1.450491 TGGTTGTGGTGTCCGTGTG 60.450 57.895 0.00 0.00 0.00 3.82
1526 1671 1.450669 GTGGTTGTGGTGTCCGTGT 60.451 57.895 0.00 0.00 0.00 4.49
1539 1684 2.193536 GTTCTTGCCTGCCGTGGTT 61.194 57.895 0.00 0.00 0.00 3.67
1546 1691 1.569479 GACGTGAGGTTCTTGCCTGC 61.569 60.000 0.00 0.00 39.34 4.85
1777 2282 0.408309 TTCCTGGTCGGAAGAGGAGA 59.592 55.000 6.41 0.00 46.80 3.71
1810 2333 4.730966 ACGGATGACAGGATCACTACTAT 58.269 43.478 0.00 0.00 41.24 2.12
2079 3316 0.670546 CGGTGGCTACAGTTGTGAGG 60.671 60.000 1.52 0.00 0.00 3.86
2086 3323 4.065281 GCGGTCGGTGGCTACAGT 62.065 66.667 1.52 0.00 0.00 3.55
2141 3393 4.033776 CCTTTCTCCCCTGCGCCA 62.034 66.667 4.18 0.00 0.00 5.69
2305 3558 2.610232 GCGGCCATGTGAGAAATTTGTT 60.610 45.455 2.24 0.00 0.00 2.83
2312 3565 1.078918 CTCTGCGGCCATGTGAGAA 60.079 57.895 2.24 0.00 0.00 2.87
2325 3581 3.986572 CGATGATGATCTTGTACCTCTGC 59.013 47.826 0.00 0.00 0.00 4.26
2436 3692 1.371337 GCTTGGTGCTCATCGATGCA 61.371 55.000 20.81 13.34 38.95 3.96
2437 3693 1.354506 GCTTGGTGCTCATCGATGC 59.645 57.895 20.81 10.65 38.95 3.91
2943 4199 2.475666 GCTGGAGCTGTCAATGGAC 58.524 57.895 0.00 0.00 44.57 4.02
3107 4375 3.696051 GTCAATGCATGGTGGATGTAACT 59.304 43.478 0.00 0.00 34.14 2.24
3131 4399 6.894682 ACTTTCCCCACAAAATAATTGTTGT 58.105 32.000 0.00 0.00 38.49 3.32
3145 4413 0.891904 TTAGCCGCAACTTTCCCCAC 60.892 55.000 0.00 0.00 0.00 4.61
3149 4417 1.068541 CAGGTTTAGCCGCAACTTTCC 60.069 52.381 0.00 0.00 43.70 3.13
3150 4418 1.877443 TCAGGTTTAGCCGCAACTTTC 59.123 47.619 0.00 0.00 43.70 2.62
3179 4447 8.067488 ACAAAATGAATGGTTAGATAAGGGGAT 58.933 33.333 0.00 0.00 0.00 3.85
3180 4448 7.341769 CACAAAATGAATGGTTAGATAAGGGGA 59.658 37.037 0.00 0.00 0.00 4.81
3194 4463 3.557577 TCACGAGGCACAAAATGAATG 57.442 42.857 0.00 0.00 0.00 2.67
3208 4477 5.475273 AATGTTTATGCACAGATCACGAG 57.525 39.130 0.00 0.00 0.00 4.18
3212 4481 8.565896 AAAGAGTAATGTTTATGCACAGATCA 57.434 30.769 0.00 0.00 0.00 2.92
3213 4482 9.846248 AAAAAGAGTAATGTTTATGCACAGATC 57.154 29.630 0.00 0.00 0.00 2.75
3241 4510 8.531146 GTCCAAATATTCTTTCATTTGAGGGAA 58.469 33.333 8.26 0.00 42.25 3.97
3242 4511 7.673504 TGTCCAAATATTCTTTCATTTGAGGGA 59.326 33.333 8.26 0.00 42.25 4.20
3252 4522 9.143631 CCACAAAGATTGTCCAAATATTCTTTC 57.856 33.333 4.26 0.00 43.23 2.62
3254 4524 8.421249 TCCACAAAGATTGTCCAAATATTCTT 57.579 30.769 0.00 0.00 43.23 2.52
3259 4529 6.377996 CCTGATCCACAAAGATTGTCCAAATA 59.622 38.462 0.00 0.00 43.23 1.40
3270 4540 3.874383 TGTTTCCCTGATCCACAAAGA 57.126 42.857 0.00 0.00 0.00 2.52
3271 4541 4.081406 TCATGTTTCCCTGATCCACAAAG 58.919 43.478 0.00 0.00 0.00 2.77
3276 4546 5.512942 TTTACTCATGTTTCCCTGATCCA 57.487 39.130 0.00 0.00 0.00 3.41
3279 4549 7.888021 TGTGTAATTTACTCATGTTTCCCTGAT 59.112 33.333 7.99 0.00 0.00 2.90
3280 4550 7.227873 TGTGTAATTTACTCATGTTTCCCTGA 58.772 34.615 7.99 0.00 0.00 3.86
3281 4551 7.447374 TGTGTAATTTACTCATGTTTCCCTG 57.553 36.000 7.99 0.00 0.00 4.45
3282 4552 8.472007 TTTGTGTAATTTACTCATGTTTCCCT 57.528 30.769 11.03 0.00 32.90 4.20
3283 4553 8.974408 GTTTTGTGTAATTTACTCATGTTTCCC 58.026 33.333 11.03 0.00 32.90 3.97
3284 4554 8.974408 GGTTTTGTGTAATTTACTCATGTTTCC 58.026 33.333 11.03 7.26 32.90 3.13
3285 4555 9.522804 TGGTTTTGTGTAATTTACTCATGTTTC 57.477 29.630 11.03 3.73 32.90 2.78
3286 4556 9.308318 GTGGTTTTGTGTAATTTACTCATGTTT 57.692 29.630 11.03 0.00 32.90 2.83
3287 4557 7.923878 GGTGGTTTTGTGTAATTTACTCATGTT 59.076 33.333 11.03 0.00 32.90 2.71
3288 4558 7.068839 TGGTGGTTTTGTGTAATTTACTCATGT 59.931 33.333 11.03 0.00 32.90 3.21
3289 4559 7.381139 GTGGTGGTTTTGTGTAATTTACTCATG 59.619 37.037 11.03 0.00 32.90 3.07
3290 4560 7.286775 AGTGGTGGTTTTGTGTAATTTACTCAT 59.713 33.333 11.03 0.00 32.90 2.90
3301 4571 3.056179 CCTTCAAAGTGGTGGTTTTGTGT 60.056 43.478 0.00 0.00 36.09 3.72
3360 4631 3.926616 CCGTAGAGGTGATGTTTTCTGT 58.073 45.455 0.00 0.00 34.51 3.41
3480 4755 2.607187 CTCATCTAACGCTGTTTCGGT 58.393 47.619 0.00 0.00 0.00 4.69
3893 5265 0.032017 TGCTCTCCCCTCCCTCTAAC 60.032 60.000 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.