Multiple sequence alignment - TraesCS6D01G288800

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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 TraesCS6D01G288800 chr6D 100.000 4069 0 0 1 4069 399221707 399217639 0.000000e+00 7515.0
1 TraesCS6D01G288800 chr6D 75.721 902 195 24 1969 2861 56552223 56553109 8.080000e-117 431.0
2 TraesCS6D01G288800 chr6D 88.235 85 8 2 3585 3669 342464573 342464491 2.590000e-17 100.0
3 TraesCS6D01G288800 chr6A 92.267 3789 162 48 357 4069 545321390 545317657 0.000000e+00 5252.0
4 TraesCS6D01G288800 chr6A 75.664 904 192 26 1969 2861 71066981 71067867 3.760000e-115 425.0
5 TraesCS6D01G288800 chr6B 91.257 3340 127 61 796 4068 597558790 597555549 0.000000e+00 4397.0
6 TraesCS6D01G288800 chr6B 88.406 345 28 7 425 758 597559134 597558791 4.900000e-109 405.0
7 TraesCS6D01G288800 chr6B 74.834 902 203 24 1969 2861 127040030 127040916 1.770000e-103 387.0
8 TraesCS6D01G288800 chr6B 88.104 269 18 8 4 262 597559503 597559239 1.420000e-79 307.0
9 TraesCS6D01G288800 chr6B 91.860 86 6 1 357 441 597559228 597559143 7.140000e-23 119.0
10 TraesCS6D01G288800 chr7D 83.102 1154 172 16 1726 2861 198501231 198502379 0.000000e+00 1029.0
11 TraesCS6D01G288800 chr7D 84.524 84 13 0 3586 3669 634043545 634043462 2.610000e-12 84.2
12 TraesCS6D01G288800 chr7A 82.738 1147 177 15 1733 2861 207547417 207548560 0.000000e+00 1002.0
13 TraesCS6D01G288800 chr7A 94.505 91 5 0 262 352 184126739 184126829 1.520000e-29 141.0
14 TraesCS6D01G288800 chr7A 94.253 87 5 0 262 348 83936191 83936105 2.550000e-27 134.0
15 TraesCS6D01G288800 chr7B 82.134 1153 185 15 1733 2867 162924203 162923054 0.000000e+00 968.0
16 TraesCS6D01G288800 chr4D 89.744 117 7 5 253 364 28237904 28237788 1.180000e-30 145.0
17 TraesCS6D01G288800 chr2B 94.624 93 5 0 258 350 691994786 691994694 1.180000e-30 145.0
18 TraesCS6D01G288800 chr2B 92.079 101 7 1 258 358 159893124 159893223 1.520000e-29 141.0
19 TraesCS6D01G288800 chr4B 92.157 102 7 1 257 358 91298309 91298409 4.240000e-30 143.0
20 TraesCS6D01G288800 chr5A 92.079 101 7 1 256 356 519884773 519884872 1.520000e-29 141.0
21 TraesCS6D01G288800 chr3B 88.596 114 7 5 252 360 728584194 728584306 2.550000e-27 134.0
22 TraesCS6D01G288800 chr2A 89.524 105 10 1 262 365 615288758 615288862 9.180000e-27 132.0
23 TraesCS6D01G288800 chr2A 84.444 90 10 3 3584 3673 510302630 510302715 7.250000e-13 86.1
24 TraesCS6D01G288800 chr5D 94.203 69 4 0 3601 3669 356839632 356839700 5.560000e-19 106.0
25 TraesCS6D01G288800 chr5D 87.342 79 7 3 3595 3671 349372389 349372466 2.010000e-13 87.9
26 TraesCS6D01G288800 chr1B 85.556 90 10 3 3575 3662 252971693 252971781 1.560000e-14 91.6
27 TraesCS6D01G288800 chr1D 83.871 93 12 3 3571 3662 182032541 182032631 7.250000e-13 86.1
28 TraesCS6D01G288800 chr1D 72.100 319 66 23 2510 2818 15049043 15048738 1.570000e-09 75.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G288800 chr6D 399217639 399221707 4068 True 7515 7515 100.00000 1 4069 1 chr6D.!!$R2 4068
1 TraesCS6D01G288800 chr6D 56552223 56553109 886 False 431 431 75.72100 1969 2861 1 chr6D.!!$F1 892
2 TraesCS6D01G288800 chr6A 545317657 545321390 3733 True 5252 5252 92.26700 357 4069 1 chr6A.!!$R1 3712
3 TraesCS6D01G288800 chr6A 71066981 71067867 886 False 425 425 75.66400 1969 2861 1 chr6A.!!$F1 892
4 TraesCS6D01G288800 chr6B 597555549 597559503 3954 True 1307 4397 89.90675 4 4068 4 chr6B.!!$R1 4064
5 TraesCS6D01G288800 chr6B 127040030 127040916 886 False 387 387 74.83400 1969 2861 1 chr6B.!!$F1 892
6 TraesCS6D01G288800 chr7D 198501231 198502379 1148 False 1029 1029 83.10200 1726 2861 1 chr7D.!!$F1 1135
7 TraesCS6D01G288800 chr7A 207547417 207548560 1143 False 1002 1002 82.73800 1733 2861 1 chr7A.!!$F2 1128
8 TraesCS6D01G288800 chr7B 162923054 162924203 1149 True 968 968 82.13400 1733 2867 1 chr7B.!!$R1 1134

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
614 662 0.793250 GCCTCGAAGTGAGCAAACTC 59.207 55.0 0.0 0.0 43.82 3.01 F
1374 1475 0.250081 GGAGGTCGCCCATCAAGATC 60.250 60.0 0.0 0.0 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 1598 1.201414 CAAATTTCCTGCCGTACCACC 59.799 52.381 0.00 0.00 0.0 4.61 R
3230 3369 0.741915 GATGAGAGACCGGACTCCAC 59.258 60.000 26.94 21.31 37.6 4.02 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
26 27 9.699410 TTGGGTATTCTAGATGTTGATGAATTT 57.301 29.630 0.00 0.00 0.00 1.82
60 61 4.773013 AGGTCAAAGGTCGTAAAGTTTGA 58.227 39.130 0.00 0.00 36.74 2.69
107 109 6.704056 ATATTTTAGGACTGGGGAGTATGG 57.296 41.667 0.00 0.00 0.00 2.74
117 119 6.295916 GGACTGGGGAGTATGGTATTAGATTG 60.296 46.154 0.00 0.00 0.00 2.67
157 162 4.319766 CCATTGTGATGGCGCTATCTTTAC 60.320 45.833 30.29 21.61 45.96 2.01
159 164 2.434336 TGTGATGGCGCTATCTTTACCT 59.566 45.455 30.29 0.00 0.00 3.08
171 176 6.929606 CGCTATCTTTACCTATAAACTTGGCT 59.070 38.462 0.00 0.00 0.00 4.75
192 197 7.394816 TGGCTAGAGTTTATAAAGCTTGACTT 58.605 34.615 0.00 0.00 41.70 3.01
210 215 6.539649 TGACTTAGAACAACACTAACATGC 57.460 37.500 0.00 0.00 0.00 4.06
262 272 8.573035 TCGATAGTGCGCATATCCATAATAATA 58.427 33.333 15.91 0.00 37.40 0.98
263 273 8.639428 CGATAGTGCGCATATCCATAATAATAC 58.361 37.037 15.91 0.00 0.00 1.89
264 274 9.698309 GATAGTGCGCATATCCATAATAATACT 57.302 33.333 15.91 1.85 0.00 2.12
266 276 6.986817 AGTGCGCATATCCATAATAATACTCC 59.013 38.462 15.91 0.00 0.00 3.85
267 277 6.202954 GTGCGCATATCCATAATAATACTCCC 59.797 42.308 15.91 0.00 0.00 4.30
269 279 6.647067 GCGCATATCCATAATAATACTCCCTC 59.353 42.308 0.30 0.00 0.00 4.30
271 281 7.155328 GCATATCCATAATAATACTCCCTCCG 58.845 42.308 0.00 0.00 0.00 4.63
272 282 7.202011 GCATATCCATAATAATACTCCCTCCGT 60.202 40.741 0.00 0.00 0.00 4.69
273 283 8.705594 CATATCCATAATAATACTCCCTCCGTT 58.294 37.037 0.00 0.00 0.00 4.44
274 284 6.600882 TCCATAATAATACTCCCTCCGTTC 57.399 41.667 0.00 0.00 0.00 3.95
275 285 5.482878 TCCATAATAATACTCCCTCCGTTCC 59.517 44.000 0.00 0.00 0.00 3.62
276 286 5.247564 CCATAATAATACTCCCTCCGTTCCA 59.752 44.000 0.00 0.00 0.00 3.53
277 287 6.239772 CCATAATAATACTCCCTCCGTTCCAA 60.240 42.308 0.00 0.00 0.00 3.53
278 288 5.703730 AATAATACTCCCTCCGTTCCAAA 57.296 39.130 0.00 0.00 0.00 3.28
279 289 5.703730 ATAATACTCCCTCCGTTCCAAAA 57.296 39.130 0.00 0.00 0.00 2.44
280 290 4.586306 AATACTCCCTCCGTTCCAAAAT 57.414 40.909 0.00 0.00 0.00 1.82
281 291 5.703730 AATACTCCCTCCGTTCCAAAATA 57.296 39.130 0.00 0.00 0.00 1.40
282 292 5.703730 ATACTCCCTCCGTTCCAAAATAA 57.296 39.130 0.00 0.00 0.00 1.40
283 293 3.951663 ACTCCCTCCGTTCCAAAATAAG 58.048 45.455 0.00 0.00 0.00 1.73
284 294 3.329814 ACTCCCTCCGTTCCAAAATAAGT 59.670 43.478 0.00 0.00 0.00 2.24
285 295 3.681593 TCCCTCCGTTCCAAAATAAGTG 58.318 45.455 0.00 0.00 0.00 3.16
286 296 3.328343 TCCCTCCGTTCCAAAATAAGTGA 59.672 43.478 0.00 0.00 0.00 3.41
287 297 3.439129 CCCTCCGTTCCAAAATAAGTGAC 59.561 47.826 0.00 0.00 0.00 3.67
288 298 4.324267 CCTCCGTTCCAAAATAAGTGACT 58.676 43.478 0.00 0.00 0.00 3.41
289 299 4.392138 CCTCCGTTCCAAAATAAGTGACTC 59.608 45.833 0.00 0.00 0.00 3.36
290 300 4.963373 TCCGTTCCAAAATAAGTGACTCA 58.037 39.130 0.00 0.00 0.00 3.41
291 301 5.369833 TCCGTTCCAAAATAAGTGACTCAA 58.630 37.500 0.00 0.00 0.00 3.02
292 302 5.237779 TCCGTTCCAAAATAAGTGACTCAAC 59.762 40.000 0.00 0.00 0.00 3.18
293 303 5.238650 CCGTTCCAAAATAAGTGACTCAACT 59.761 40.000 0.00 0.00 0.00 3.16
294 304 6.238648 CCGTTCCAAAATAAGTGACTCAACTT 60.239 38.462 0.00 0.00 42.89 2.66
295 305 7.193595 CGTTCCAAAATAAGTGACTCAACTTT 58.806 34.615 0.00 0.00 40.77 2.66
296 306 7.165812 CGTTCCAAAATAAGTGACTCAACTTTG 59.834 37.037 0.00 0.00 40.77 2.77
297 307 7.639113 TCCAAAATAAGTGACTCAACTTTGT 57.361 32.000 0.00 0.00 40.77 2.83
298 308 8.740123 TCCAAAATAAGTGACTCAACTTTGTA 57.260 30.769 0.00 0.00 40.77 2.41
299 309 8.617809 TCCAAAATAAGTGACTCAACTTTGTAC 58.382 33.333 0.00 0.00 40.77 2.90
300 310 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
307 317 9.880157 AAGTGACTCAACTTTGTACTAAAGTTA 57.120 29.630 23.56 15.88 45.57 2.24
308 318 9.530633 AGTGACTCAACTTTGTACTAAAGTTAG 57.469 33.333 23.56 21.61 45.57 2.34
309 319 9.310716 GTGACTCAACTTTGTACTAAAGTTAGT 57.689 33.333 23.56 23.28 45.57 2.24
324 334 9.310716 ACTAAAGTTAGTACAAAGTTGAGTCAC 57.689 33.333 1.81 0.00 41.92 3.67
325 335 9.530633 CTAAAGTTAGTACAAAGTTGAGTCACT 57.469 33.333 0.00 0.00 0.00 3.41
326 336 8.788325 AAAGTTAGTACAAAGTTGAGTCACTT 57.212 30.769 0.00 0.00 38.74 3.16
327 337 9.880157 AAAGTTAGTACAAAGTTGAGTCACTTA 57.120 29.630 0.00 0.00 35.87 2.24
333 343 9.391006 AGTACAAAGTTGAGTCACTTATTTTGA 57.609 29.630 14.62 1.37 35.87 2.69
334 344 9.651718 GTACAAAGTTGAGTCACTTATTTTGAG 57.348 33.333 14.62 0.00 35.87 3.02
335 345 8.506168 ACAAAGTTGAGTCACTTATTTTGAGA 57.494 30.769 14.62 0.00 35.87 3.27
336 346 8.398665 ACAAAGTTGAGTCACTTATTTTGAGAC 58.601 33.333 14.62 0.00 35.87 3.36
337 347 8.397906 CAAAGTTGAGTCACTTATTTTGAGACA 58.602 33.333 5.72 0.00 35.87 3.41
338 348 7.721286 AGTTGAGTCACTTATTTTGAGACAG 57.279 36.000 0.00 0.00 0.00 3.51
339 349 7.500992 AGTTGAGTCACTTATTTTGAGACAGA 58.499 34.615 0.00 0.00 0.00 3.41
340 350 7.655328 AGTTGAGTCACTTATTTTGAGACAGAG 59.345 37.037 0.00 0.00 0.00 3.35
341 351 6.459066 TGAGTCACTTATTTTGAGACAGAGG 58.541 40.000 0.00 0.00 0.00 3.69
342 352 5.799213 AGTCACTTATTTTGAGACAGAGGG 58.201 41.667 0.00 0.00 0.00 4.30
343 353 5.544176 AGTCACTTATTTTGAGACAGAGGGA 59.456 40.000 0.00 0.00 0.00 4.20
344 354 6.043243 AGTCACTTATTTTGAGACAGAGGGAA 59.957 38.462 0.00 0.00 0.00 3.97
345 355 6.881602 GTCACTTATTTTGAGACAGAGGGAAT 59.118 38.462 0.00 0.00 0.00 3.01
346 356 8.041323 GTCACTTATTTTGAGACAGAGGGAATA 58.959 37.037 0.00 0.00 0.00 1.75
347 357 8.772250 TCACTTATTTTGAGACAGAGGGAATAT 58.228 33.333 0.00 0.00 0.00 1.28
435 445 1.812235 TGCTGTTGATTCGACTGCAT 58.188 45.000 26.04 0.00 44.00 3.96
516 552 8.492673 TTTGCAGTTACTTGGTAGATAATCTG 57.507 34.615 0.00 0.00 0.00 2.90
609 657 2.351244 ATCCGCCTCGAAGTGAGCA 61.351 57.895 0.00 0.00 43.82 4.26
613 661 0.946221 CGCCTCGAAGTGAGCAAACT 60.946 55.000 0.00 0.00 43.82 2.66
614 662 0.793250 GCCTCGAAGTGAGCAAACTC 59.207 55.000 0.00 0.00 43.82 3.01
615 663 1.433534 CCTCGAAGTGAGCAAACTCC 58.566 55.000 0.00 0.00 43.82 3.85
616 664 1.270305 CCTCGAAGTGAGCAAACTCCA 60.270 52.381 0.00 0.00 43.82 3.86
617 665 1.795286 CTCGAAGTGAGCAAACTCCAC 59.205 52.381 0.00 0.00 42.74 4.02
618 666 1.138069 TCGAAGTGAGCAAACTCCACA 59.862 47.619 0.00 0.00 42.74 4.17
683 734 2.833582 GGAGATCGACGGAGCCCA 60.834 66.667 0.00 0.00 0.00 5.36
706 757 4.794439 TGATCACTGACGGCGGCG 62.794 66.667 31.06 31.06 0.00 6.46
743 798 2.031012 CTGTGCTGCCGGAGTCAA 59.969 61.111 5.05 0.00 0.00 3.18
1044 1112 1.675720 GCACCCAGAGAGAGAGGAGC 61.676 65.000 0.00 0.00 0.00 4.70
1249 1343 2.132740 TTGATTCTTGTGCGTTTGGC 57.867 45.000 0.00 0.00 43.96 4.52
1328 1429 2.359230 AAAGCAGAGGAGCGGCAC 60.359 61.111 1.45 0.00 40.40 5.01
1370 1471 3.739922 ATGGAGGTCGCCCATCAA 58.260 55.556 0.00 0.00 40.16 2.57
1371 1472 1.528824 ATGGAGGTCGCCCATCAAG 59.471 57.895 0.00 0.00 40.16 3.02
1372 1473 0.982852 ATGGAGGTCGCCCATCAAGA 60.983 55.000 0.00 0.00 40.16 3.02
1373 1474 0.982852 TGGAGGTCGCCCATCAAGAT 60.983 55.000 0.00 0.00 0.00 2.40
1374 1475 0.250081 GGAGGTCGCCCATCAAGATC 60.250 60.000 0.00 0.00 0.00 2.75
1378 1479 1.134401 GGTCGCCCATCAAGATCAAGA 60.134 52.381 0.00 0.00 0.00 3.02
1382 1483 3.387699 TCGCCCATCAAGATCAAGATGTA 59.612 43.478 19.68 6.06 39.92 2.29
1385 1486 5.128919 GCCCATCAAGATCAAGATGTAGTT 58.871 41.667 19.68 0.00 39.92 2.24
1386 1487 5.591877 GCCCATCAAGATCAAGATGTAGTTT 59.408 40.000 19.68 0.00 39.92 2.66
1387 1488 6.096001 GCCCATCAAGATCAAGATGTAGTTTT 59.904 38.462 19.68 0.00 39.92 2.43
1397 1498 6.161381 TCAAGATGTAGTTTTAACTCCGGAC 58.839 40.000 0.00 0.00 40.37 4.79
1401 1502 5.534207 TGTAGTTTTAACTCCGGACTCAA 57.466 39.130 0.00 0.00 40.37 3.02
1483 1598 1.188863 CCATTTCCTTTGGGAGCTGG 58.811 55.000 0.00 0.00 43.29 4.85
1484 1599 1.188863 CATTTCCTTTGGGAGCTGGG 58.811 55.000 0.00 0.00 43.29 4.45
1487 1602 2.036256 CCTTTGGGAGCTGGGTGG 59.964 66.667 0.00 0.00 33.58 4.61
1557 1672 2.943033 GGTATCGAATGGAGTTTGTGGG 59.057 50.000 0.00 0.00 0.00 4.61
1626 1744 1.290732 AGGAGGAGGAGGAGGAAGAAG 59.709 57.143 0.00 0.00 0.00 2.85
3097 3236 0.831711 TAGCGGCTATCCCTGCATCA 60.832 55.000 5.42 0.00 36.16 3.07
3197 3336 4.583489 GGATTACATACTCCTTCGGTGAGA 59.417 45.833 4.19 0.00 33.95 3.27
3201 3340 5.422214 ACATACTCCTTCGGTGAGAAAAT 57.578 39.130 4.19 0.00 38.57 1.82
3230 3369 2.442236 AATGCATAAGGGTGGACAGG 57.558 50.000 0.00 0.00 0.00 4.00
3258 3397 3.133003 TCCGGTCTCTCATCCATTTCTTC 59.867 47.826 0.00 0.00 0.00 2.87
3266 3405 6.660949 TCTCTCATCCATTTCTTCCCTTTTTC 59.339 38.462 0.00 0.00 0.00 2.29
3281 3420 4.103943 CCCTTTTTCCCCCTTTCAAAATGA 59.896 41.667 0.00 0.00 0.00 2.57
3294 3433 7.013559 CCCTTTCAAAATGAAGGCAAAAGATTT 59.986 33.333 0.00 0.00 37.70 2.17
3298 3437 9.558396 TTCAAAATGAAGGCAAAAGATTTACAT 57.442 25.926 0.00 0.00 31.83 2.29
3304 3443 7.028962 TGAAGGCAAAAGATTTACATCATTCG 58.971 34.615 0.00 0.00 0.00 3.34
3305 3444 6.757897 AGGCAAAAGATTTACATCATTCGA 57.242 33.333 0.00 0.00 0.00 3.71
3319 3460 9.737427 TTACATCATTCGATTTAAGAGAGAGTC 57.263 33.333 0.00 0.00 0.00 3.36
3450 3611 2.464189 GTAGCACACGTCGTTGCG 59.536 61.111 19.53 3.86 37.94 4.85
3475 3636 7.592533 CGTCAATTTTAATCTTGCATAGGATGG 59.407 37.037 0.00 0.00 0.00 3.51
3482 3643 2.705658 TCTTGCATAGGATGGTGGTAGG 59.294 50.000 0.00 0.00 0.00 3.18
3505 3667 4.734402 GCATTGTCAAAACAGCTGAAGACA 60.734 41.667 23.35 22.34 36.57 3.41
3564 3726 1.152777 CACAGGTGAAGGTGCCCAA 60.153 57.895 0.00 0.00 0.00 4.12
3574 3736 1.610379 GGTGCCCAATGCCTTTCCT 60.610 57.895 0.00 0.00 40.16 3.36
3578 3740 0.615827 GCCCAATGCCTTTCCTCCTT 60.616 55.000 0.00 0.00 0.00 3.36
3591 3754 4.937201 TTCCTCCTTCTTTCTTTTTGCC 57.063 40.909 0.00 0.00 0.00 4.52
3598 3761 6.106003 TCCTTCTTTCTTTTTGCCAGAAAAC 58.894 36.000 0.00 0.00 39.28 2.43
3639 3802 6.040278 TCAAACATCATGGCAGTACAAAGAAA 59.960 34.615 0.00 0.00 0.00 2.52
3665 3828 8.588290 ACAAGAAGCAATATAAATTACACCCA 57.412 30.769 0.00 0.00 0.00 4.51
3675 3838 3.781079 AATTACACCCATGTTCATGCG 57.219 42.857 7.21 2.06 40.48 4.73
3684 3847 3.674753 CCCATGTTCATGCGTTTCTTTTC 59.325 43.478 7.21 0.00 0.00 2.29
3697 3860 4.097286 CGTTTCTTTTCCCTCCTTTCACAA 59.903 41.667 0.00 0.00 0.00 3.33
3699 3862 6.582636 GTTTCTTTTCCCTCCTTTCACAAAT 58.417 36.000 0.00 0.00 0.00 2.32
3700 3863 6.806668 TTCTTTTCCCTCCTTTCACAAATT 57.193 33.333 0.00 0.00 0.00 1.82
3729 3898 8.256356 TCCCAAGGAAGAATTGTTAATTTCAA 57.744 30.769 0.00 0.00 0.00 2.69
3745 3914 2.693797 TCAACTACACGACGGTCTTC 57.306 50.000 6.57 0.00 0.00 2.87
3746 3915 1.069703 TCAACTACACGACGGTCTTCG 60.070 52.381 6.57 0.00 44.87 3.79
3748 3917 1.513586 CTACACGACGGTCTTCGGC 60.514 63.158 6.57 0.00 43.58 5.54
3779 3948 2.436115 GGCTACGACCACTTGGGC 60.436 66.667 0.00 0.00 42.05 5.36
3868 4037 3.426309 ATGCTGATGCTTCCCCGGG 62.426 63.158 15.80 15.80 40.48 5.73
3942 4124 1.485066 CTTGACTGCCCCGGTTAGTAT 59.515 52.381 0.00 0.00 0.00 2.12
3956 4138 7.667219 CCCCGGTTAGTATTAGTAACTGAGATA 59.333 40.741 23.28 0.00 40.94 1.98
3957 4139 9.240734 CCCGGTTAGTATTAGTAACTGAGATAT 57.759 37.037 23.28 0.00 40.94 1.63
3959 4141 9.970243 CGGTTAGTATTAGTAACTGAGATATCG 57.030 37.037 19.27 9.74 40.94 2.92
3960 4142 9.771915 GGTTAGTATTAGTAACTGAGATATCGC 57.228 37.037 17.01 0.00 35.05 4.58
3961 4143 9.771915 GTTAGTATTAGTAACTGAGATATCGCC 57.228 37.037 12.30 0.00 32.62 5.54
3962 4144 7.074507 AGTATTAGTAACTGAGATATCGCCG 57.925 40.000 3.86 0.03 0.00 6.46
3963 4145 6.877855 AGTATTAGTAACTGAGATATCGCCGA 59.122 38.462 3.86 0.00 0.00 5.54
4017 4201 2.877582 ACGTTACGTGATCGGCGC 60.878 61.111 10.39 0.00 39.18 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.699410 AAATTCATCAACATCTAGAATACCCAA 57.301 29.630 0.00 0.00 0.00 4.12
1 2 9.699410 AAAATTCATCAACATCTAGAATACCCA 57.301 29.630 0.00 0.00 0.00 4.51
26 27 8.302515 ACGACCTTTGACCTATAAGATAGAAA 57.697 34.615 0.00 0.00 0.00 2.52
38 39 4.573607 GTCAAACTTTACGACCTTTGACCT 59.426 41.667 9.86 0.00 43.35 3.85
78 79 8.171337 ACTCCCCAGTCCTAAAATATACTTTT 57.829 34.615 0.00 0.00 0.00 2.27
82 83 7.237055 ACCATACTCCCCAGTCCTAAAATATAC 59.763 40.741 0.00 0.00 33.62 1.47
88 89 3.502051 ACCATACTCCCCAGTCCTAAA 57.498 47.619 0.00 0.00 33.62 1.85
137 139 3.118408 AGGTAAAGATAGCGCCATCACAA 60.118 43.478 18.05 0.00 34.69 3.33
138 140 2.434336 AGGTAAAGATAGCGCCATCACA 59.566 45.455 18.05 0.00 34.69 3.58
147 152 9.425577 CTAGCCAAGTTTATAGGTAAAGATAGC 57.574 37.037 0.00 0.00 30.76 2.97
185 190 7.041780 AGCATGTTAGTGTTGTTCTAAGTCAAG 60.042 37.037 0.00 0.00 0.00 3.02
192 197 6.052360 TGTTGAGCATGTTAGTGTTGTTCTA 58.948 36.000 0.00 0.00 0.00 2.10
200 205 6.129009 GCTTTCAAATGTTGAGCATGTTAGTG 60.129 38.462 0.00 0.00 41.38 2.74
210 215 3.904136 ACTCCGCTTTCAAATGTTGAG 57.096 42.857 0.00 0.00 41.38 3.02
262 272 3.329814 ACTTATTTTGGAACGGAGGGAGT 59.670 43.478 0.00 0.00 0.00 3.85
263 273 3.689649 CACTTATTTTGGAACGGAGGGAG 59.310 47.826 0.00 0.00 0.00 4.30
264 274 3.328343 TCACTTATTTTGGAACGGAGGGA 59.672 43.478 0.00 0.00 0.00 4.20
266 276 4.324267 AGTCACTTATTTTGGAACGGAGG 58.676 43.478 0.00 0.00 0.00 4.30
267 277 4.994852 TGAGTCACTTATTTTGGAACGGAG 59.005 41.667 0.00 0.00 0.00 4.63
269 279 5.238650 AGTTGAGTCACTTATTTTGGAACGG 59.761 40.000 0.00 0.00 0.00 4.44
271 281 7.973944 ACAAAGTTGAGTCACTTATTTTGGAAC 59.026 33.333 12.94 0.00 35.87 3.62
272 282 8.062065 ACAAAGTTGAGTCACTTATTTTGGAA 57.938 30.769 12.94 0.00 35.87 3.53
273 283 7.639113 ACAAAGTTGAGTCACTTATTTTGGA 57.361 32.000 12.94 0.00 35.87 3.53
274 284 8.621286 AGTACAAAGTTGAGTCACTTATTTTGG 58.379 33.333 12.94 0.78 35.87 3.28
280 290 9.880157 AACTTTAGTACAAAGTTGAGTCACTTA 57.120 29.630 23.48 0.00 45.58 2.24
281 291 8.788325 AACTTTAGTACAAAGTTGAGTCACTT 57.212 30.769 23.48 0.00 45.58 3.16
282 292 9.530633 CTAACTTTAGTACAAAGTTGAGTCACT 57.469 33.333 27.85 13.98 46.41 3.41
283 293 9.310716 ACTAACTTTAGTACAAAGTTGAGTCAC 57.689 33.333 27.85 0.00 46.41 3.67
298 308 9.310716 GTGACTCAACTTTGTACTAACTTTAGT 57.689 33.333 6.85 6.85 45.39 2.24
299 309 9.530633 AGTGACTCAACTTTGTACTAACTTTAG 57.469 33.333 0.00 0.00 36.82 1.85
300 310 9.880157 AAGTGACTCAACTTTGTACTAACTTTA 57.120 29.630 0.00 0.00 37.05 1.85
301 311 8.788325 AAGTGACTCAACTTTGTACTAACTTT 57.212 30.769 0.00 0.00 37.05 2.66
307 317 9.391006 TCAAAATAAGTGACTCAACTTTGTACT 57.609 29.630 0.00 0.00 40.77 2.73
308 318 9.651718 CTCAAAATAAGTGACTCAACTTTGTAC 57.348 33.333 0.00 0.00 40.77 2.90
309 319 9.607988 TCTCAAAATAAGTGACTCAACTTTGTA 57.392 29.630 0.00 0.00 40.77 2.41
310 320 8.398665 GTCTCAAAATAAGTGACTCAACTTTGT 58.601 33.333 0.00 0.00 40.77 2.83
311 321 8.397906 TGTCTCAAAATAAGTGACTCAACTTTG 58.602 33.333 0.00 0.00 40.77 2.77
312 322 8.506168 TGTCTCAAAATAAGTGACTCAACTTT 57.494 30.769 0.00 0.00 40.77 2.66
313 323 7.987458 TCTGTCTCAAAATAAGTGACTCAACTT 59.013 33.333 0.00 0.00 42.89 2.66
314 324 7.500992 TCTGTCTCAAAATAAGTGACTCAACT 58.499 34.615 0.00 0.00 32.38 3.16
315 325 7.095439 CCTCTGTCTCAAAATAAGTGACTCAAC 60.095 40.741 0.00 0.00 32.38 3.18
316 326 6.931281 CCTCTGTCTCAAAATAAGTGACTCAA 59.069 38.462 0.00 0.00 32.38 3.02
317 327 6.459066 CCTCTGTCTCAAAATAAGTGACTCA 58.541 40.000 0.00 0.00 32.38 3.41
318 328 5.872070 CCCTCTGTCTCAAAATAAGTGACTC 59.128 44.000 0.00 0.00 32.38 3.36
319 329 5.544176 TCCCTCTGTCTCAAAATAAGTGACT 59.456 40.000 0.00 0.00 32.38 3.41
320 330 5.794894 TCCCTCTGTCTCAAAATAAGTGAC 58.205 41.667 0.00 0.00 0.00 3.67
321 331 6.433847 TTCCCTCTGTCTCAAAATAAGTGA 57.566 37.500 0.00 0.00 0.00 3.41
322 332 8.970859 ATATTCCCTCTGTCTCAAAATAAGTG 57.029 34.615 0.00 0.00 0.00 3.16
331 341 9.547279 TGCTTATTATATATTCCCTCTGTCTCA 57.453 33.333 0.00 0.00 0.00 3.27
335 345 9.401058 GCATTGCTTATTATATATTCCCTCTGT 57.599 33.333 0.16 0.00 0.00 3.41
336 346 9.399797 TGCATTGCTTATTATATATTCCCTCTG 57.600 33.333 10.49 0.00 0.00 3.35
337 347 9.979897 TTGCATTGCTTATTATATATTCCCTCT 57.020 29.630 10.49 0.00 0.00 3.69
346 356 9.726232 CGCTATCAATTGCATTGCTTATTATAT 57.274 29.630 10.49 8.86 40.05 0.86
347 357 7.697710 GCGCTATCAATTGCATTGCTTATTATA 59.302 33.333 10.49 2.54 40.05 0.98
348 358 6.529125 GCGCTATCAATTGCATTGCTTATTAT 59.471 34.615 10.49 1.50 40.05 1.28
349 359 5.858049 GCGCTATCAATTGCATTGCTTATTA 59.142 36.000 10.49 0.00 40.05 0.98
350 360 4.682860 GCGCTATCAATTGCATTGCTTATT 59.317 37.500 10.49 6.93 40.05 1.40
351 361 4.022589 AGCGCTATCAATTGCATTGCTTAT 60.023 37.500 8.99 0.74 40.05 1.73
352 362 3.316029 AGCGCTATCAATTGCATTGCTTA 59.684 39.130 8.99 0.00 40.05 3.09
353 363 2.100252 AGCGCTATCAATTGCATTGCTT 59.900 40.909 8.99 0.00 40.05 3.91
354 364 1.679680 AGCGCTATCAATTGCATTGCT 59.320 42.857 8.99 11.74 40.05 3.91
355 365 1.784856 CAGCGCTATCAATTGCATTGC 59.215 47.619 10.99 0.46 40.05 3.56
371 381 3.127548 AGGCAGTTGAATCAATTACAGCG 59.872 43.478 0.00 0.00 0.00 5.18
373 383 9.643693 AAATTAAGGCAGTTGAATCAATTACAG 57.356 29.630 0.00 0.00 0.00 2.74
448 483 1.163554 CTGAAGCAAGCACTTCCCTC 58.836 55.000 10.50 0.00 44.50 4.30
450 485 1.583477 GCTGAAGCAAGCACTTCCC 59.417 57.895 10.50 0.90 44.50 3.97
538 574 6.600032 TCCAAGTTTACTGTTGAAAAGTGCTA 59.400 34.615 0.00 0.00 0.00 3.49
609 657 0.597637 CGCTGTCGTCTGTGGAGTTT 60.598 55.000 0.00 0.00 0.00 2.66
613 661 2.643272 GTCGCTGTCGTCTGTGGA 59.357 61.111 0.90 0.00 36.96 4.02
614 662 2.801162 CGTCGCTGTCGTCTGTGG 60.801 66.667 0.90 0.00 36.96 4.17
615 663 2.801162 CCGTCGCTGTCGTCTGTG 60.801 66.667 0.00 0.00 36.96 3.66
616 664 4.702081 GCCGTCGCTGTCGTCTGT 62.702 66.667 0.00 0.00 36.96 3.41
665 713 2.833582 GGGCTCCGTCGATCTCCA 60.834 66.667 0.00 0.00 0.00 3.86
683 734 1.608717 GCCGTCAGTGATCAGTCCCT 61.609 60.000 0.00 0.00 0.00 4.20
728 783 0.598065 AAAATTGACTCCGGCAGCAC 59.402 50.000 0.00 0.00 0.00 4.40
743 798 1.272704 GCAGGGGAGACTTGGGAAAAT 60.273 52.381 0.00 0.00 0.00 1.82
835 891 2.386660 GCGGACAGAGACAAGCTGC 61.387 63.158 0.00 0.00 36.86 5.25
836 892 2.091112 CGCGGACAGAGACAAGCTG 61.091 63.158 0.00 0.00 39.26 4.24
837 893 2.259818 CGCGGACAGAGACAAGCT 59.740 61.111 0.00 0.00 0.00 3.74
1044 1112 2.036475 CTCTCTCTCTCTCTCCCTCTCG 59.964 59.091 0.00 0.00 0.00 4.04
1213 1291 1.272490 TCAATCACCACGAGTCTGTCC 59.728 52.381 0.00 0.00 0.00 4.02
1214 1292 2.724977 TCAATCACCACGAGTCTGTC 57.275 50.000 0.00 0.00 0.00 3.51
1215 1293 3.259374 AGAATCAATCACCACGAGTCTGT 59.741 43.478 0.00 0.00 33.21 3.41
1216 1294 3.854666 AGAATCAATCACCACGAGTCTG 58.145 45.455 0.00 0.00 33.21 3.51
1217 1295 4.248859 CAAGAATCAATCACCACGAGTCT 58.751 43.478 0.00 0.00 35.76 3.24
1218 1296 3.997021 ACAAGAATCAATCACCACGAGTC 59.003 43.478 0.00 0.00 0.00 3.36
1219 1297 3.748048 CACAAGAATCAATCACCACGAGT 59.252 43.478 0.00 0.00 0.00 4.18
1220 1298 3.425359 GCACAAGAATCAATCACCACGAG 60.425 47.826 0.00 0.00 0.00 4.18
1221 1299 2.483877 GCACAAGAATCAATCACCACGA 59.516 45.455 0.00 0.00 0.00 4.35
1222 1300 2.725759 CGCACAAGAATCAATCACCACG 60.726 50.000 0.00 0.00 0.00 4.94
1223 1301 2.226437 ACGCACAAGAATCAATCACCAC 59.774 45.455 0.00 0.00 0.00 4.16
1224 1302 2.503331 ACGCACAAGAATCAATCACCA 58.497 42.857 0.00 0.00 0.00 4.17
1249 1343 5.131809 AGAAAGATAACCCCCTCATTCAGAG 59.868 44.000 0.00 0.00 44.31 3.35
1328 1429 0.882042 CGCTTCCCTTGATCATCCCG 60.882 60.000 0.00 0.00 0.00 5.14
1336 1437 1.339055 CCATCTTGACGCTTCCCTTGA 60.339 52.381 0.00 0.00 0.00 3.02
1368 1469 8.383619 CGGAGTTAAAACTACATCTTGATCTTG 58.616 37.037 5.93 0.00 39.97 3.02
1369 1470 7.549488 CCGGAGTTAAAACTACATCTTGATCTT 59.451 37.037 0.00 0.00 39.97 2.40
1370 1471 7.042335 CCGGAGTTAAAACTACATCTTGATCT 58.958 38.462 0.00 0.00 39.97 2.75
1371 1472 7.010275 GTCCGGAGTTAAAACTACATCTTGATC 59.990 40.741 3.06 0.00 39.97 2.92
1372 1473 6.817140 GTCCGGAGTTAAAACTACATCTTGAT 59.183 38.462 3.06 0.00 39.97 2.57
1373 1474 6.014840 AGTCCGGAGTTAAAACTACATCTTGA 60.015 38.462 3.06 0.00 39.97 3.02
1374 1475 6.164176 AGTCCGGAGTTAAAACTACATCTTG 58.836 40.000 3.06 0.00 39.97 3.02
1378 1479 5.733620 TGAGTCCGGAGTTAAAACTACAT 57.266 39.130 14.37 0.00 39.97 2.29
1382 1483 4.377897 CAGTTGAGTCCGGAGTTAAAACT 58.622 43.478 17.34 19.74 43.16 2.66
1385 1486 2.701951 ACCAGTTGAGTCCGGAGTTAAA 59.298 45.455 17.34 10.63 0.00 1.52
1386 1487 2.322658 ACCAGTTGAGTCCGGAGTTAA 58.677 47.619 14.37 13.20 0.00 2.01
1387 1488 2.005370 ACCAGTTGAGTCCGGAGTTA 57.995 50.000 14.37 6.43 0.00 2.24
1401 1502 0.690762 AAGGGTCGCAACATACCAGT 59.309 50.000 0.00 0.00 37.51 4.00
1468 1580 1.460255 CACCCAGCTCCCAAAGGAA 59.540 57.895 0.00 0.00 43.40 3.36
1472 1584 1.765074 GTACCACCCAGCTCCCAAA 59.235 57.895 0.00 0.00 0.00 3.28
1475 1587 3.782443 CCGTACCACCCAGCTCCC 61.782 72.222 0.00 0.00 0.00 4.30
1483 1598 1.201414 CAAATTTCCTGCCGTACCACC 59.799 52.381 0.00 0.00 0.00 4.61
1484 1599 2.156098 TCAAATTTCCTGCCGTACCAC 58.844 47.619 0.00 0.00 0.00 4.16
1487 1602 4.412207 GAACATCAAATTTCCTGCCGTAC 58.588 43.478 0.00 0.00 0.00 3.67
2735 2868 3.147595 TGGATGGAGAGCGGGTCG 61.148 66.667 0.96 0.00 0.00 4.79
3230 3369 0.741915 GATGAGAGACCGGACTCCAC 59.258 60.000 26.94 21.31 37.60 4.02
3258 3397 4.103943 TCATTTTGAAAGGGGGAAAAAGGG 59.896 41.667 0.00 0.00 0.00 3.95
3266 3405 1.977129 TGCCTTCATTTTGAAAGGGGG 59.023 47.619 3.53 0.00 35.73 5.40
3281 3420 7.156876 TCGAATGATGTAAATCTTTTGCCTT 57.843 32.000 4.50 0.00 0.00 4.35
3294 3433 8.903820 TGACTCTCTCTTAAATCGAATGATGTA 58.096 33.333 0.00 0.00 34.24 2.29
3298 3437 9.737427 GTTATGACTCTCTCTTAAATCGAATGA 57.263 33.333 0.00 0.00 0.00 2.57
3341 3487 6.320164 TGTTTGTTAGCTCTGGTTGTTACAAT 59.680 34.615 0.00 0.00 0.00 2.71
3344 3490 5.744666 TGTTTGTTAGCTCTGGTTGTTAC 57.255 39.130 0.00 0.00 0.00 2.50
3450 3611 8.416329 ACCATCCTATGCAAGATTAAAATTGAC 58.584 33.333 0.00 0.95 0.00 3.18
3475 3636 3.857010 GCTGTTTTGACAATGCCTACCAC 60.857 47.826 0.00 0.00 0.00 4.16
3482 3643 3.732721 GTCTTCAGCTGTTTTGACAATGC 59.267 43.478 14.67 0.00 0.00 3.56
3534 3696 4.338118 CCTTCACCTGTGCTTTTTCACTTA 59.662 41.667 0.00 0.00 37.81 2.24
3538 3700 2.426738 CACCTTCACCTGTGCTTTTTCA 59.573 45.455 0.00 0.00 0.00 2.69
3564 3726 4.394797 AAGAAAGAAGGAGGAAAGGCAT 57.605 40.909 0.00 0.00 0.00 4.40
3574 3736 5.930837 TTTCTGGCAAAAAGAAAGAAGGA 57.069 34.783 0.00 0.00 38.43 3.36
3578 3740 5.675684 AGGTTTTCTGGCAAAAAGAAAGA 57.324 34.783 7.51 0.00 42.82 2.52
3639 3802 9.030452 TGGGTGTAATTTATATTGCTTCTTGTT 57.970 29.630 0.00 0.00 0.00 2.83
3665 3828 3.573967 AGGGAAAAGAAACGCATGAACAT 59.426 39.130 0.00 0.00 0.00 2.71
3675 3838 5.592104 TTGTGAAAGGAGGGAAAAGAAAC 57.408 39.130 0.00 0.00 0.00 2.78
3684 3847 2.162408 GAGCGAATTTGTGAAAGGAGGG 59.838 50.000 0.00 0.00 0.00 4.30
3697 3860 2.879103 TTCTTCCTTGGGAGCGAATT 57.121 45.000 0.00 0.00 31.21 2.17
3699 3862 2.224769 ACAATTCTTCCTTGGGAGCGAA 60.225 45.455 0.00 0.00 31.21 4.70
3700 3863 1.351017 ACAATTCTTCCTTGGGAGCGA 59.649 47.619 0.00 0.00 31.21 4.93
3729 3898 1.871772 CCGAAGACCGTCGTGTAGT 59.128 57.895 4.83 0.00 39.43 2.73
3748 3917 2.598787 TAGCCAAAGACCCCCACGG 61.599 63.158 0.00 0.00 37.81 4.94
3750 3919 1.376812 CGTAGCCAAAGACCCCCAC 60.377 63.158 0.00 0.00 0.00 4.61
3751 3920 1.536907 TCGTAGCCAAAGACCCCCA 60.537 57.895 0.00 0.00 0.00 4.96
3752 3921 1.078637 GTCGTAGCCAAAGACCCCC 60.079 63.158 0.00 0.00 31.12 5.40
3779 3948 1.268032 GCGCGTTGGACTGGAATAATG 60.268 52.381 8.43 0.00 0.00 1.90
3833 4002 7.277098 GCATCAGCATGTCAATTTAATCTTTGT 59.723 33.333 0.00 0.00 41.58 2.83
3868 4037 5.030936 GGCTTGCTTTTCGATCACTATTTC 58.969 41.667 0.00 0.00 0.00 2.17
3942 4124 4.084171 CGTCGGCGATATCTCAGTTACTAA 60.084 45.833 14.79 0.00 41.33 2.24
3957 4139 4.170062 GTGGATCGTCGTCGGCGA 62.170 66.667 25.43 25.43 45.79 5.54
3958 4140 4.175489 AGTGGATCGTCGTCGGCG 62.175 66.667 14.12 14.12 37.69 6.46
3959 4141 2.579787 CAGTGGATCGTCGTCGGC 60.580 66.667 1.55 0.00 37.69 5.54
3960 4142 2.102357 CCAGTGGATCGTCGTCGG 59.898 66.667 1.68 0.00 37.69 4.79
3961 4143 2.579787 GCCAGTGGATCGTCGTCG 60.580 66.667 15.20 0.00 38.55 5.12
3962 4144 1.805945 GTGCCAGTGGATCGTCGTC 60.806 63.158 15.20 0.00 0.00 4.20
3963 4145 2.261671 GTGCCAGTGGATCGTCGT 59.738 61.111 15.20 0.00 0.00 4.34
4017 4201 2.651703 CGTACGCAATTTTGACTTGCTG 59.348 45.455 0.52 3.29 45.32 4.41


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

AutoCloner maintained by Alex Coulton.