Multiple sequence alignment - TraesCS1B01G371700

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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 TraesCS1B01G371700 chr1B 100.000 4111 0 0 1 4111 601382329 601386439 0.000000e+00 7592
1 TraesCS1B01G371700 chr1B 92.850 1035 52 12 3081 4111 313229070 313230086 0.000000e+00 1482
2 TraesCS1B01G371700 chr1B 98.810 252 2 1 2840 3091 601402945 601402695 8.110000e-122 448
3 TraesCS1B01G371700 chr1B 93.694 222 13 1 260 480 601382369 601382590 8.520000e-87 331
4 TraesCS1B01G371700 chr1B 93.694 222 13 1 41 262 601382588 601382808 8.520000e-87 331
5 TraesCS1B01G371700 chr1B 98.462 130 2 0 2962 3091 345394333 345394204 3.200000e-56 230
6 TraesCS1B01G371700 chr7A 95.811 2841 87 14 260 3090 91394815 91397633 0.000000e+00 4558
7 TraesCS1B01G371700 chr7A 93.646 1023 48 12 3091 4111 204377654 204376647 0.000000e+00 1513
8 TraesCS1B01G371700 chr7A 93.164 1024 50 13 3091 4111 204367594 204366588 0.000000e+00 1485
9 TraesCS1B01G371700 chr7A 94.077 878 44 5 495 1371 38272753 38273623 0.000000e+00 1327
10 TraesCS1B01G371700 chr7A 95.851 482 20 0 1367 1848 38324661 38325142 0.000000e+00 780
11 TraesCS1B01G371700 chr7A 96.183 262 10 0 1 262 91394775 91395036 2.940000e-116 429
12 TraesCS1B01G371700 chr7A 91.829 257 20 1 3 259 38270459 38270714 1.410000e-94 357
13 TraesCS1B01G371700 chr7A 91.632 239 18 2 265 502 38270502 38270739 3.060000e-86 329
14 TraesCS1B01G371700 chr7A 95.580 181 6 1 1848 2026 38328323 38328503 5.200000e-74 289
15 TraesCS1B01G371700 chr2A 95.925 1767 57 6 462 2220 194553409 194555168 0.000000e+00 2850
16 TraesCS1B01G371700 chr2A 95.923 1766 57 8 462 2220 194858580 194856823 0.000000e+00 2848
17 TraesCS1B01G371700 chr2A 93.087 1027 51 11 3089 4111 244869948 244870958 0.000000e+00 1485
18 TraesCS1B01G371700 chr2A 93.073 1025 51 10 3091 4111 552007016 552006008 0.000000e+00 1482
19 TraesCS1B01G371700 chr2A 96.453 874 30 1 2217 3090 194560618 194561490 0.000000e+00 1441
20 TraesCS1B01G371700 chr2A 97.122 556 15 1 2535 3090 194826919 194826365 0.000000e+00 937
21 TraesCS1B01G371700 chr2A 95.975 323 12 1 2217 2539 194851652 194851331 1.310000e-144 523
22 TraesCS1B01G371700 chr2A 94.922 256 10 3 1 256 194859569 194859317 8.280000e-107 398
23 TraesCS1B01G371700 chr2A 94.915 236 11 1 21 256 194552439 194552673 6.490000e-98 368
24 TraesCS1B01G371700 chr2A 92.558 215 13 3 260 474 194859529 194859318 5.160000e-79 305
25 TraesCS1B01G371700 chr2A 91.628 215 17 1 260 474 194552459 194552672 3.110000e-76 296
26 TraesCS1B01G371700 chr2B 93.780 1029 41 14 3091 4111 121160806 121161819 0.000000e+00 1524
27 TraesCS1B01G371700 chr2B 93.197 1029 47 14 3091 4111 121150299 121151312 0.000000e+00 1491
28 TraesCS1B01G371700 chr2B 97.210 681 19 0 2410 3090 520216931 520216251 0.000000e+00 1153
29 TraesCS1B01G371700 chr4B 93.307 1031 43 16 3091 4111 418109433 418108419 0.000000e+00 1498
30 TraesCS1B01G371700 chr7B 93.053 1022 56 9 3091 4111 492641654 492642661 0.000000e+00 1480
31 TraesCS1B01G371700 chr2D 98.881 447 5 0 2644 3090 648062040 648061594 0.000000e+00 798


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 TraesCS1B01G371700 chr1B 601382329 601386439 4110 False 7592.000000 7592 100.000000 1 4111 1 chr1B.!!$F2 4110
1 TraesCS1B01G371700 chr1B 313229070 313230086 1016 False 1482.000000 1482 92.850000 3081 4111 1 chr1B.!!$F1 1030
2 TraesCS1B01G371700 chr7A 91394775 91397633 2858 False 2493.500000 4558 95.997000 1 3090 2 chr7A.!!$F3 3089
3 TraesCS1B01G371700 chr7A 204376647 204377654 1007 True 1513.000000 1513 93.646000 3091 4111 1 chr7A.!!$R2 1020
4 TraesCS1B01G371700 chr7A 204366588 204367594 1006 True 1485.000000 1485 93.164000 3091 4111 1 chr7A.!!$R1 1020
5 TraesCS1B01G371700 chr7A 38270459 38273623 3164 False 671.000000 1327 92.512667 3 1371 3 chr7A.!!$F1 1368
6 TraesCS1B01G371700 chr7A 38324661 38328503 3842 False 534.500000 780 95.715500 1367 2026 2 chr7A.!!$F2 659
7 TraesCS1B01G371700 chr2A 244869948 244870958 1010 False 1485.000000 1485 93.087000 3089 4111 1 chr2A.!!$F2 1022
8 TraesCS1B01G371700 chr2A 552006008 552007016 1008 True 1482.000000 1482 93.073000 3091 4111 1 chr2A.!!$R3 1020
9 TraesCS1B01G371700 chr2A 194560618 194561490 872 False 1441.000000 1441 96.453000 2217 3090 1 chr2A.!!$F1 873
10 TraesCS1B01G371700 chr2A 194856823 194859569 2746 True 1183.666667 2848 94.467667 1 2220 3 chr2A.!!$R4 2219
11 TraesCS1B01G371700 chr2A 194552439 194555168 2729 False 1171.333333 2850 94.156000 21 2220 3 chr2A.!!$F3 2199
12 TraesCS1B01G371700 chr2A 194826365 194826919 554 True 937.000000 937 97.122000 2535 3090 1 chr2A.!!$R1 555
13 TraesCS1B01G371700 chr2B 121160806 121161819 1013 False 1524.000000 1524 93.780000 3091 4111 1 chr2B.!!$F2 1020
14 TraesCS1B01G371700 chr2B 121150299 121151312 1013 False 1491.000000 1491 93.197000 3091 4111 1 chr2B.!!$F1 1020
15 TraesCS1B01G371700 chr2B 520216251 520216931 680 True 1153.000000 1153 97.210000 2410 3090 1 chr2B.!!$R1 680
16 TraesCS1B01G371700 chr4B 418108419 418109433 1014 True 1498.000000 1498 93.307000 3091 4111 1 chr4B.!!$R1 1020
17 TraesCS1B01G371700 chr7B 492641654 492642661 1007 False 1480.000000 1480 93.053000 3091 4111 1 chr7B.!!$F1 1020

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
460 1211 0.034283 AGTCGTCACTCCCTACCTCC 60.034 60.0 0.00 0.00 0.0 4.30 F
464 1215 0.323178 GTCACTCCCTACCTCCGTCA 60.323 60.0 0.00 0.00 0.0 4.35 F
517 3289 0.324614 TGGCGTCCATCACTTGTGAT 59.675 50.0 10.15 10.15 0.0 3.06 F
1299 4086 0.388520 CAAGCCTCGACGACATCACA 60.389 55.0 0.00 0.00 0.0 3.58 F
2220 8191 0.991355 ATCATAAACTCCCCGCCCCA 60.991 55.0 0.00 0.00 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1433 4221 0.946221 GAAGGTCAGCACGTCACCAG 60.946 60.000 5.54 0.0 31.99 4.00 R
2204 8175 1.064825 CTATGGGGCGGGGAGTTTAT 58.935 55.000 0.00 0.0 0.00 1.40 R
2429 8401 1.286260 GACTCGAGTCCACGTGCTT 59.714 57.895 31.24 0.0 39.07 3.91 R
2648 8620 0.950836 CGTGCACCATCACCTGAAAA 59.049 50.000 12.15 0.0 33.57 2.29 R
3894 9885 0.179205 GAACGCATGAGTGAAGCTGC 60.179 55.000 1.78 0.0 0.00 5.25 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
100 101 2.543238 CGAGCCTATCAGGTTTACCGTC 60.543 54.545 0.00 0.00 42.08 4.79
219 220 1.442184 CTCAGACCAACGTCGACCG 60.442 63.158 10.58 7.90 44.28 4.79
260 1011 3.214123 TCGCCACCGAGGGATACG 61.214 66.667 0.00 0.00 38.82 3.06
261 1012 4.944372 CGCCACCGAGGGATACGC 62.944 72.222 0.00 0.00 38.09 4.42
262 1013 3.537874 GCCACCGAGGGATACGCT 61.538 66.667 0.00 0.00 38.09 5.07
263 1014 2.728817 CCACCGAGGGATACGCTC 59.271 66.667 0.00 0.00 39.57 5.03
268 1019 2.051166 GAGGGATACGCTCGTCGC 60.051 66.667 0.00 0.00 43.23 5.19
277 1028 3.173240 GCTCGTCGCGTCCACTTC 61.173 66.667 5.77 0.00 0.00 3.01
278 1029 2.254350 CTCGTCGCGTCCACTTCA 59.746 61.111 5.77 0.00 0.00 3.02
279 1030 1.154016 CTCGTCGCGTCCACTTCAT 60.154 57.895 5.77 0.00 0.00 2.57
280 1031 1.406219 CTCGTCGCGTCCACTTCATG 61.406 60.000 5.77 0.00 0.00 3.07
288 1039 2.751436 CCACTTCATGGGTGCCGG 60.751 66.667 0.00 0.00 45.95 6.13
289 1040 3.443045 CACTTCATGGGTGCCGGC 61.443 66.667 22.73 22.73 0.00 6.13
309 1060 2.841988 GGAGGGCGAGCCTCTCAT 60.842 66.667 23.88 5.78 36.08 2.90
310 1061 2.420890 GAGGGCGAGCCTCTCATG 59.579 66.667 20.26 0.00 35.16 3.07
311 1062 2.364842 AGGGCGAGCCTCTCATGT 60.365 61.111 14.33 0.00 36.10 3.21
312 1063 1.965754 GAGGGCGAGCCTCTCATGTT 61.966 60.000 20.26 0.00 35.16 2.71
313 1064 1.078143 GGGCGAGCCTCTCATGTTT 60.078 57.895 14.33 0.00 36.10 2.83
314 1065 0.178068 GGGCGAGCCTCTCATGTTTA 59.822 55.000 14.33 0.00 36.10 2.01
315 1066 1.291132 GGCGAGCCTCTCATGTTTAC 58.709 55.000 6.90 0.00 0.00 2.01
316 1067 1.291132 GCGAGCCTCTCATGTTTACC 58.709 55.000 0.00 0.00 0.00 2.85
317 1068 1.560923 CGAGCCTCTCATGTTTACCG 58.439 55.000 0.00 0.00 0.00 4.02
318 1069 1.135083 CGAGCCTCTCATGTTTACCGT 60.135 52.381 0.00 0.00 0.00 4.83
319 1070 2.271800 GAGCCTCTCATGTTTACCGTG 58.728 52.381 0.00 0.00 0.00 4.94
320 1071 1.066143 AGCCTCTCATGTTTACCGTGG 60.066 52.381 0.00 0.00 0.00 4.94
321 1072 1.369625 CCTCTCATGTTTACCGTGGC 58.630 55.000 0.00 0.00 0.00 5.01
322 1073 0.999406 CTCTCATGTTTACCGTGGCG 59.001 55.000 0.00 0.00 0.00 5.69
323 1074 0.319083 TCTCATGTTTACCGTGGCGT 59.681 50.000 0.00 0.00 0.00 5.68
324 1075 0.719465 CTCATGTTTACCGTGGCGTC 59.281 55.000 0.00 0.00 0.00 5.19
325 1076 0.319083 TCATGTTTACCGTGGCGTCT 59.681 50.000 0.00 0.00 0.00 4.18
326 1077 0.442310 CATGTTTACCGTGGCGTCTG 59.558 55.000 0.00 0.00 0.00 3.51
327 1078 0.319083 ATGTTTACCGTGGCGTCTGA 59.681 50.000 0.00 0.00 0.00 3.27
328 1079 0.104487 TGTTTACCGTGGCGTCTGAA 59.896 50.000 0.00 0.00 0.00 3.02
329 1080 0.788391 GTTTACCGTGGCGTCTGAAG 59.212 55.000 0.00 0.00 0.00 3.02
330 1081 0.675083 TTTACCGTGGCGTCTGAAGA 59.325 50.000 0.00 0.00 0.00 2.87
331 1082 0.892755 TTACCGTGGCGTCTGAAGAT 59.107 50.000 0.00 0.00 0.00 2.40
332 1083 1.753930 TACCGTGGCGTCTGAAGATA 58.246 50.000 0.00 0.00 0.00 1.98
333 1084 0.172803 ACCGTGGCGTCTGAAGATAC 59.827 55.000 0.00 0.00 0.00 2.24
334 1085 0.866061 CCGTGGCGTCTGAAGATACG 60.866 60.000 11.01 11.01 41.92 3.06
335 1086 0.866061 CGTGGCGTCTGAAGATACGG 60.866 60.000 10.42 0.00 39.46 4.02
336 1087 0.172803 GTGGCGTCTGAAGATACGGT 59.827 55.000 0.00 0.00 39.46 4.83
337 1088 0.172578 TGGCGTCTGAAGATACGGTG 59.827 55.000 0.00 0.00 39.46 4.94
338 1089 0.454600 GGCGTCTGAAGATACGGTGA 59.545 55.000 0.00 0.00 39.46 4.02
339 1090 1.067212 GGCGTCTGAAGATACGGTGAT 59.933 52.381 0.00 0.00 39.46 3.06
340 1091 2.386249 GCGTCTGAAGATACGGTGATC 58.614 52.381 0.00 0.00 39.46 2.92
341 1092 2.640831 CGTCTGAAGATACGGTGATCG 58.359 52.381 0.00 0.00 45.88 3.69
342 1093 2.287103 CGTCTGAAGATACGGTGATCGA 59.713 50.000 0.00 0.00 42.43 3.59
343 1094 3.619729 GTCTGAAGATACGGTGATCGAC 58.380 50.000 0.00 0.00 42.43 4.20
344 1095 3.312973 GTCTGAAGATACGGTGATCGACT 59.687 47.826 0.00 0.00 42.43 4.18
345 1096 3.312697 TCTGAAGATACGGTGATCGACTG 59.687 47.826 0.00 3.46 42.43 3.51
346 1097 3.014623 TGAAGATACGGTGATCGACTGT 58.985 45.455 12.43 12.43 46.56 3.55
351 1102 2.579207 ACGGTGATCGACTGTAATGG 57.421 50.000 0.00 0.00 42.84 3.16
352 1103 2.097036 ACGGTGATCGACTGTAATGGA 58.903 47.619 0.00 0.00 42.84 3.41
353 1104 2.099263 ACGGTGATCGACTGTAATGGAG 59.901 50.000 0.00 0.00 42.84 3.86
354 1105 2.357952 CGGTGATCGACTGTAATGGAGA 59.642 50.000 0.00 0.00 42.43 3.71
355 1106 3.549019 CGGTGATCGACTGTAATGGAGAG 60.549 52.174 0.00 0.00 42.43 3.20
356 1107 3.243569 GGTGATCGACTGTAATGGAGAGG 60.244 52.174 0.00 0.00 0.00 3.69
357 1108 2.362397 TGATCGACTGTAATGGAGAGGC 59.638 50.000 0.00 0.00 0.00 4.70
358 1109 1.112113 TCGACTGTAATGGAGAGGCC 58.888 55.000 0.00 0.00 37.10 5.19
371 1122 2.679716 AGGCCATTCCTGCACCTC 59.320 61.111 5.01 0.00 45.54 3.85
372 1123 2.233566 AGGCCATTCCTGCACCTCA 61.234 57.895 5.01 0.00 45.54 3.86
373 1124 1.751927 GGCCATTCCTGCACCTCAG 60.752 63.158 0.00 0.00 42.49 3.35
374 1125 2.413142 GCCATTCCTGCACCTCAGC 61.413 63.158 0.00 0.00 41.50 4.26
375 1126 1.751927 CCATTCCTGCACCTCAGCC 60.752 63.158 0.00 0.00 41.50 4.85
376 1127 1.751927 CATTCCTGCACCTCAGCCC 60.752 63.158 0.00 0.00 41.50 5.19
377 1128 3.335356 ATTCCTGCACCTCAGCCCG 62.335 63.158 0.00 0.00 41.50 6.13
426 1177 4.838486 CTCGCCGCGGTCTCAGAC 62.838 72.222 28.70 6.83 0.00 3.51
436 1187 3.089117 GTCTCAGACCAACGTCGAC 57.911 57.895 5.18 5.18 44.28 4.20
437 1188 0.386985 GTCTCAGACCAACGTCGACC 60.387 60.000 10.58 0.00 44.28 4.79
438 1189 0.820482 TCTCAGACCAACGTCGACCA 60.820 55.000 10.58 0.00 44.28 4.02
439 1190 0.663568 CTCAGACCAACGTCGACCAC 60.664 60.000 10.58 0.00 44.28 4.16
451 1202 4.843101 GACCACGAGTCGTCACTC 57.157 61.111 16.86 6.61 45.19 3.51
452 1203 1.209640 GACCACGAGTCGTCACTCC 59.790 63.158 16.86 0.00 45.81 3.85
453 1204 2.197643 GACCACGAGTCGTCACTCCC 62.198 65.000 16.86 0.00 45.81 4.30
454 1205 1.972223 CCACGAGTCGTCACTCCCT 60.972 63.158 16.86 0.00 45.81 4.20
455 1206 0.675837 CCACGAGTCGTCACTCCCTA 60.676 60.000 16.86 0.00 45.81 3.53
456 1207 0.447011 CACGAGTCGTCACTCCCTAC 59.553 60.000 16.86 0.00 45.81 3.18
457 1208 0.676151 ACGAGTCGTCACTCCCTACC 60.676 60.000 13.56 0.00 45.81 3.18
458 1209 0.392729 CGAGTCGTCACTCCCTACCT 60.393 60.000 3.82 0.00 45.81 3.08
459 1210 1.381522 GAGTCGTCACTCCCTACCTC 58.618 60.000 0.00 0.00 43.14 3.85
460 1211 0.034283 AGTCGTCACTCCCTACCTCC 60.034 60.000 0.00 0.00 0.00 4.30
461 1212 1.077930 TCGTCACTCCCTACCTCCG 60.078 63.158 0.00 0.00 0.00 4.63
462 1213 1.378250 CGTCACTCCCTACCTCCGT 60.378 63.158 0.00 0.00 0.00 4.69
463 1214 1.375098 CGTCACTCCCTACCTCCGTC 61.375 65.000 0.00 0.00 0.00 4.79
464 1215 0.323178 GTCACTCCCTACCTCCGTCA 60.323 60.000 0.00 0.00 0.00 4.35
465 1216 0.323178 TCACTCCCTACCTCCGTCAC 60.323 60.000 0.00 0.00 0.00 3.67
466 1217 1.000107 ACTCCCTACCTCCGTCACC 60.000 63.158 0.00 0.00 0.00 4.02
467 1218 1.000019 CTCCCTACCTCCGTCACCA 60.000 63.158 0.00 0.00 0.00 4.17
468 1219 1.304713 TCCCTACCTCCGTCACCAC 60.305 63.158 0.00 0.00 0.00 4.16
469 1220 2.356780 CCCTACCTCCGTCACCACC 61.357 68.421 0.00 0.00 0.00 4.61
470 1221 2.707849 CCTACCTCCGTCACCACCG 61.708 68.421 0.00 0.00 0.00 4.94
471 1222 1.676635 CTACCTCCGTCACCACCGA 60.677 63.158 0.00 0.00 0.00 4.69
472 1223 1.654954 CTACCTCCGTCACCACCGAG 61.655 65.000 0.00 0.00 0.00 4.63
473 1224 3.760035 CCTCCGTCACCACCGAGG 61.760 72.222 0.00 0.00 40.37 4.63
474 1225 2.675423 CTCCGTCACCACCGAGGA 60.675 66.667 0.00 0.00 41.22 3.71
475 1226 2.036731 TCCGTCACCACCGAGGAT 59.963 61.111 0.00 0.00 41.22 3.24
476 1227 0.750546 CTCCGTCACCACCGAGGATA 60.751 60.000 0.00 0.00 41.22 2.59
477 1228 1.033746 TCCGTCACCACCGAGGATAC 61.034 60.000 0.00 0.00 41.22 2.24
503 3275 1.293498 GTCAGAGGTGATGTGGCGT 59.707 57.895 0.00 0.00 34.36 5.68
517 3289 0.324614 TGGCGTCCATCACTTGTGAT 59.675 50.000 10.15 10.15 0.00 3.06
518 3290 1.552792 TGGCGTCCATCACTTGTGATA 59.447 47.619 14.86 0.00 0.00 2.15
519 3291 2.170397 TGGCGTCCATCACTTGTGATAT 59.830 45.455 14.86 0.00 0.00 1.63
520 3292 3.386402 TGGCGTCCATCACTTGTGATATA 59.614 43.478 14.86 4.88 0.00 0.86
586 3361 6.817765 TGATCTTTTCTTAGAAACCGCAAT 57.182 33.333 6.93 0.00 0.00 3.56
652 3427 1.521457 CTCAATCCAGCGCGCCTTA 60.521 57.895 30.33 13.96 0.00 2.69
906 3693 7.475771 TTTATGCATTCTTTTGCTTTCGTTT 57.524 28.000 3.54 0.00 43.18 3.60
919 3706 1.635844 TTCGTTTCTGCGCACGATAT 58.364 45.000 19.51 0.00 44.52 1.63
960 3747 1.176527 CAACGCAGGGATCCAACAAT 58.823 50.000 15.23 0.00 0.00 2.71
1078 3865 1.164411 CCATAACCACGAGCTTGCAA 58.836 50.000 0.00 0.00 0.00 4.08
1299 4086 0.388520 CAAGCCTCGACGACATCACA 60.389 55.000 0.00 0.00 0.00 3.58
1389 4177 2.265739 GAGAGGCGTGTGCATGGA 59.734 61.111 0.00 0.00 45.35 3.41
1433 4221 2.606795 GCCGAGCTGACTATCATCTGTC 60.607 54.545 0.00 0.00 0.00 3.51
1530 4318 4.009675 TGAACAATCACTACCAATCTGCC 58.990 43.478 0.00 0.00 0.00 4.85
1551 4339 3.408634 CCTGTTCGGGTGTGTTATTCTT 58.591 45.455 0.00 0.00 0.00 2.52
1579 4367 6.650390 AGAAGAAAGAGAAGACTCATTCAAGC 59.350 38.462 14.44 6.16 46.63 4.01
1608 4396 6.478512 TTTTCTACCTTTGTTGAAGCCAAT 57.521 33.333 0.00 0.00 37.49 3.16
1631 4419 2.089349 GGAAGACGCTGCAGACGAC 61.089 63.158 28.70 23.70 0.00 4.34
1884 7853 5.347635 CCGAATTGACTTTAATCGTCTCACA 59.652 40.000 6.88 0.00 32.70 3.58
1938 7907 3.009916 GTGGATGGGCTTATCTGATGGAT 59.990 47.826 0.00 0.00 38.38 3.41
2196 8167 8.301002 GGCACACACAAAGAAGGTAAATAAATA 58.699 33.333 0.00 0.00 0.00 1.40
2220 8191 0.991355 ATCATAAACTCCCCGCCCCA 60.991 55.000 0.00 0.00 0.00 4.96
2221 8192 0.991355 TCATAAACTCCCCGCCCCAT 60.991 55.000 0.00 0.00 0.00 4.00
2238 8210 4.085733 CCCCATAGTGGTTCATTGTTTGA 58.914 43.478 0.00 0.00 35.17 2.69
2311 8283 6.217693 AGGTCCTCCATACAAACTTTCCTATT 59.782 38.462 0.00 0.00 35.89 1.73
2340 8312 1.864176 CGTCCAAGGTTTACACGCC 59.136 57.895 0.00 0.00 0.00 5.68
2429 8401 1.666553 GATGGGCGTGTTGTCGTGA 60.667 57.895 0.00 0.00 0.00 4.35
2515 8487 2.355132 CGAGAGCGATACCTACAGTTGT 59.645 50.000 0.00 0.00 40.82 3.32
2604 8576 7.119553 ACCATAAACATTTCCAATCACATTTGC 59.880 33.333 0.00 0.00 0.00 3.68
2620 8592 5.824624 CACATTTGCTCCATCCTTAGTACAT 59.175 40.000 0.00 0.00 0.00 2.29
2642 8614 7.058525 ACATGAGAGATTTGATCCAATTGCTA 58.941 34.615 0.00 0.00 0.00 3.49
2648 8620 4.541250 TTTGATCCAATTGCTATCCCCT 57.459 40.909 13.45 0.00 0.00 4.79
2708 8680 9.753674 ATCCCTAGTCATTACATTTTGAAAAGA 57.246 29.630 0.00 0.00 0.00 2.52
3198 9181 6.127338 ACCTTCCTCTTGAAAACTTCCTTTTG 60.127 38.462 0.00 0.00 31.81 2.44
3199 9182 6.096846 CCTTCCTCTTGAAAACTTCCTTTTGA 59.903 38.462 0.00 0.00 31.81 2.69
3215 9198 6.363882 TCCTTTTGATTTGGCAAGGATTTTT 58.636 32.000 0.00 0.00 39.95 1.94
3267 9252 8.737168 TGAATCTTTTGAAACTTCTTCTCTGA 57.263 30.769 0.00 0.00 0.00 3.27
3271 9256 7.282585 TCTTTTGAAACTTCTTCTCTGATGGA 58.717 34.615 0.00 0.00 0.00 3.41
3272 9257 7.941238 TCTTTTGAAACTTCTTCTCTGATGGAT 59.059 33.333 0.00 0.00 0.00 3.41
3273 9258 8.469309 TTTTGAAACTTCTTCTCTGATGGATT 57.531 30.769 0.00 0.00 0.00 3.01
3274 9259 7.678947 TTGAAACTTCTTCTCTGATGGATTC 57.321 36.000 0.00 0.00 0.00 2.52
3275 9260 6.176183 TGAAACTTCTTCTCTGATGGATTCC 58.824 40.000 0.00 0.00 0.00 3.01
3280 9265 2.109229 TCTCTGATGGATTCCTCCCC 57.891 55.000 3.95 0.00 41.29 4.81
3295 9281 7.092444 GGATTCCTCCCCCTCAAATTTATTTTT 60.092 37.037 0.00 0.00 35.28 1.94
3304 9290 9.958180 CCCCTCAAATTTATTTTTGGAGTTTAT 57.042 29.630 0.00 0.00 37.23 1.40
3359 9347 8.313292 TGAAAACTTGGGATTTTCATATCTTGG 58.687 33.333 8.44 0.00 46.16 3.61
3409 9399 2.668144 TGTGGTAAAACCCCTCCAAG 57.332 50.000 0.00 0.00 37.50 3.61
3527 9517 9.947433 ATCATTTCTGAAAATTTATTTGGAGCA 57.053 25.926 6.95 0.00 32.69 4.26
3607 9597 4.030913 CTCCTGGATAGTCCTTTGTACCA 58.969 47.826 0.00 0.00 37.46 3.25
3629 9619 4.927267 ACAACCCAGAACCATCTTGATA 57.073 40.909 0.00 0.00 32.03 2.15
3787 9777 1.273327 GCCACTCCACCAAAAATCAGG 59.727 52.381 0.00 0.00 0.00 3.86
3788 9778 1.895131 CCACTCCACCAAAAATCAGGG 59.105 52.381 0.00 0.00 0.00 4.45
3894 9885 1.262950 TCAGTGTCATTTTGCGTTCGG 59.737 47.619 0.00 0.00 0.00 4.30
3907 9898 1.016130 CGTTCGGCAGCTTCACTCAT 61.016 55.000 0.00 0.00 0.00 2.90
3926 9917 0.742635 TGCGTTCACAGTGCACTTGA 60.743 50.000 18.94 20.05 32.86 3.02
3990 9981 4.021925 GCGTGGAGCCTTCCTGGT 62.022 66.667 0.00 0.00 44.36 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 0.457337 GACGCGACGGTAAACCTGAT 60.457 55.000 15.93 0.00 0.00 2.90
90 91 0.664166 TTCAGACGCGACGGTAAACC 60.664 55.000 15.93 0.00 0.00 3.27
100 101 0.098200 TCACCGTATCTTCAGACGCG 59.902 55.000 3.53 3.53 37.75 6.01
260 1011 3.173240 GAAGTGGACGCGACGAGC 61.173 66.667 15.93 0.00 43.95 5.03
261 1012 1.154016 ATGAAGTGGACGCGACGAG 60.154 57.895 15.93 0.00 0.00 4.18
262 1013 1.443702 CATGAAGTGGACGCGACGA 60.444 57.895 15.93 0.00 0.00 4.20
263 1014 3.072598 CATGAAGTGGACGCGACG 58.927 61.111 15.93 0.00 0.00 5.12
272 1023 3.443045 GCCGGCACCCATGAAGTG 61.443 66.667 24.80 10.52 38.30 3.16
295 1046 0.178068 TAAACATGAGAGGCTCGCCC 59.822 55.000 15.82 6.71 36.58 6.13
296 1047 1.291132 GTAAACATGAGAGGCTCGCC 58.709 55.000 15.82 9.19 32.35 5.54
297 1048 1.291132 GGTAAACATGAGAGGCTCGC 58.709 55.000 11.63 11.63 32.35 5.03
298 1049 1.135083 ACGGTAAACATGAGAGGCTCG 60.135 52.381 9.22 0.00 32.35 5.03
299 1050 2.271800 CACGGTAAACATGAGAGGCTC 58.728 52.381 6.34 6.34 0.00 4.70
300 1051 1.066143 CCACGGTAAACATGAGAGGCT 60.066 52.381 0.00 0.00 0.00 4.58
301 1052 1.369625 CCACGGTAAACATGAGAGGC 58.630 55.000 0.00 0.00 0.00 4.70
302 1053 1.369625 GCCACGGTAAACATGAGAGG 58.630 55.000 0.00 0.00 0.00 3.69
303 1054 0.999406 CGCCACGGTAAACATGAGAG 59.001 55.000 0.00 0.00 0.00 3.20
304 1055 0.319083 ACGCCACGGTAAACATGAGA 59.681 50.000 0.00 0.00 0.00 3.27
305 1056 0.719465 GACGCCACGGTAAACATGAG 59.281 55.000 0.00 0.00 0.00 2.90
306 1057 0.319083 AGACGCCACGGTAAACATGA 59.681 50.000 0.00 0.00 0.00 3.07
307 1058 0.442310 CAGACGCCACGGTAAACATG 59.558 55.000 0.00 0.00 0.00 3.21
308 1059 0.319083 TCAGACGCCACGGTAAACAT 59.681 50.000 0.00 0.00 0.00 2.71
309 1060 0.104487 TTCAGACGCCACGGTAAACA 59.896 50.000 0.00 0.00 0.00 2.83
310 1061 0.788391 CTTCAGACGCCACGGTAAAC 59.212 55.000 0.00 0.00 0.00 2.01
311 1062 0.675083 TCTTCAGACGCCACGGTAAA 59.325 50.000 0.00 0.00 0.00 2.01
312 1063 0.892755 ATCTTCAGACGCCACGGTAA 59.107 50.000 0.00 0.00 0.00 2.85
313 1064 1.402968 GTATCTTCAGACGCCACGGTA 59.597 52.381 0.00 0.00 0.00 4.02
314 1065 0.172803 GTATCTTCAGACGCCACGGT 59.827 55.000 0.00 0.00 0.00 4.83
315 1066 0.866061 CGTATCTTCAGACGCCACGG 60.866 60.000 0.00 0.00 31.49 4.94
316 1067 0.866061 CCGTATCTTCAGACGCCACG 60.866 60.000 0.00 0.00 37.75 4.94
317 1068 0.172803 ACCGTATCTTCAGACGCCAC 59.827 55.000 0.00 0.00 37.75 5.01
318 1069 0.172578 CACCGTATCTTCAGACGCCA 59.827 55.000 0.00 0.00 37.75 5.69
319 1070 0.454600 TCACCGTATCTTCAGACGCC 59.545 55.000 0.00 0.00 37.75 5.68
320 1071 2.386249 GATCACCGTATCTTCAGACGC 58.614 52.381 0.00 0.00 37.75 5.19
321 1072 2.287103 TCGATCACCGTATCTTCAGACG 59.713 50.000 0.00 0.00 39.75 4.18
322 1073 3.312973 AGTCGATCACCGTATCTTCAGAC 59.687 47.826 0.00 0.00 39.75 3.51
323 1074 3.312697 CAGTCGATCACCGTATCTTCAGA 59.687 47.826 0.00 0.00 39.75 3.27
324 1075 3.065510 ACAGTCGATCACCGTATCTTCAG 59.934 47.826 0.00 0.00 39.75 3.02
325 1076 3.014623 ACAGTCGATCACCGTATCTTCA 58.985 45.455 0.00 0.00 39.75 3.02
326 1077 3.694535 ACAGTCGATCACCGTATCTTC 57.305 47.619 0.00 0.00 39.75 2.87
327 1078 5.507482 CCATTACAGTCGATCACCGTATCTT 60.507 44.000 0.00 0.00 39.75 2.40
328 1079 4.023107 CCATTACAGTCGATCACCGTATCT 60.023 45.833 0.00 0.00 39.75 1.98
329 1080 4.023450 TCCATTACAGTCGATCACCGTATC 60.023 45.833 0.00 0.00 39.75 2.24
330 1081 3.887110 TCCATTACAGTCGATCACCGTAT 59.113 43.478 0.00 0.00 39.75 3.06
331 1082 3.281158 TCCATTACAGTCGATCACCGTA 58.719 45.455 0.00 0.00 39.75 4.02
332 1083 2.097036 TCCATTACAGTCGATCACCGT 58.903 47.619 0.00 0.00 39.75 4.83
333 1084 2.357952 TCTCCATTACAGTCGATCACCG 59.642 50.000 0.00 0.00 40.25 4.94
334 1085 3.243569 CCTCTCCATTACAGTCGATCACC 60.244 52.174 0.00 0.00 0.00 4.02
335 1086 3.797184 GCCTCTCCATTACAGTCGATCAC 60.797 52.174 0.00 0.00 0.00 3.06
336 1087 2.362397 GCCTCTCCATTACAGTCGATCA 59.638 50.000 0.00 0.00 0.00 2.92
337 1088 2.288518 GGCCTCTCCATTACAGTCGATC 60.289 54.545 0.00 0.00 34.01 3.69
338 1089 1.689273 GGCCTCTCCATTACAGTCGAT 59.311 52.381 0.00 0.00 34.01 3.59
339 1090 1.112113 GGCCTCTCCATTACAGTCGA 58.888 55.000 0.00 0.00 34.01 4.20
340 1091 0.824109 TGGCCTCTCCATTACAGTCG 59.176 55.000 3.32 0.00 40.72 4.18
349 1100 1.924939 TGCAGGAATGGCCTCTCCA 60.925 57.895 21.52 1.76 46.97 3.86
350 1101 1.452833 GTGCAGGAATGGCCTCTCC 60.453 63.158 14.14 14.14 46.97 3.71
351 1102 1.452833 GGTGCAGGAATGGCCTCTC 60.453 63.158 3.32 0.00 46.97 3.20
352 1103 1.919600 GAGGTGCAGGAATGGCCTCT 61.920 60.000 3.32 0.00 46.97 3.69
353 1104 1.452833 GAGGTGCAGGAATGGCCTC 60.453 63.158 3.32 1.90 46.97 4.70
355 1106 1.751927 CTGAGGTGCAGGAATGGCC 60.752 63.158 0.00 0.00 41.07 5.36
356 1107 2.413142 GCTGAGGTGCAGGAATGGC 61.413 63.158 0.00 0.00 45.03 4.40
357 1108 1.751927 GGCTGAGGTGCAGGAATGG 60.752 63.158 0.00 0.00 45.03 3.16
358 1109 1.751927 GGGCTGAGGTGCAGGAATG 60.752 63.158 0.00 0.00 45.03 2.67
359 1110 2.679716 GGGCTGAGGTGCAGGAAT 59.320 61.111 0.00 0.00 45.03 3.01
360 1111 4.020617 CGGGCTGAGGTGCAGGAA 62.021 66.667 0.00 0.00 45.03 3.36
409 1160 4.838486 GTCTGAGACCGCGGCGAG 62.838 72.222 28.58 15.85 0.00 5.03
418 1169 0.386985 GGTCGACGTTGGTCTGAGAC 60.387 60.000 9.92 3.47 41.16 3.36
419 1170 0.820482 TGGTCGACGTTGGTCTGAGA 60.820 55.000 9.92 0.00 41.16 3.27
420 1171 0.663568 GTGGTCGACGTTGGTCTGAG 60.664 60.000 9.92 0.00 41.16 3.35
421 1172 1.361271 GTGGTCGACGTTGGTCTGA 59.639 57.895 9.92 0.00 41.16 3.27
422 1173 2.014554 CGTGGTCGACGTTGGTCTG 61.015 63.158 9.92 0.00 43.50 3.51
423 1174 2.333938 CGTGGTCGACGTTGGTCT 59.666 61.111 9.92 0.00 43.50 3.85
434 1185 4.843101 GAGTGACGACTCGTGGTC 57.157 61.111 9.27 1.66 41.37 4.02
441 1192 0.034283 GGAGGTAGGGAGTGACGACT 60.034 60.000 0.00 0.00 33.98 4.18
442 1193 1.375098 CGGAGGTAGGGAGTGACGAC 61.375 65.000 0.00 0.00 0.00 4.34
443 1194 1.077930 CGGAGGTAGGGAGTGACGA 60.078 63.158 0.00 0.00 0.00 4.20
444 1195 1.375098 GACGGAGGTAGGGAGTGACG 61.375 65.000 0.00 0.00 0.00 4.35
445 1196 0.323178 TGACGGAGGTAGGGAGTGAC 60.323 60.000 0.00 0.00 0.00 3.67
446 1197 0.323178 GTGACGGAGGTAGGGAGTGA 60.323 60.000 0.00 0.00 0.00 3.41
447 1198 1.321074 GGTGACGGAGGTAGGGAGTG 61.321 65.000 0.00 0.00 0.00 3.51
448 1199 1.000107 GGTGACGGAGGTAGGGAGT 60.000 63.158 0.00 0.00 0.00 3.85
449 1200 1.000019 TGGTGACGGAGGTAGGGAG 60.000 63.158 0.00 0.00 0.00 4.30
450 1201 1.304713 GTGGTGACGGAGGTAGGGA 60.305 63.158 0.00 0.00 0.00 4.20
451 1202 2.356780 GGTGGTGACGGAGGTAGGG 61.357 68.421 0.00 0.00 0.00 3.53
452 1203 2.707849 CGGTGGTGACGGAGGTAGG 61.708 68.421 0.00 0.00 0.00 3.18
453 1204 1.654954 CTCGGTGGTGACGGAGGTAG 61.655 65.000 0.00 0.00 42.87 3.18
454 1205 1.676635 CTCGGTGGTGACGGAGGTA 60.677 63.158 0.00 0.00 42.87 3.08
455 1206 2.989824 CTCGGTGGTGACGGAGGT 60.990 66.667 0.00 0.00 42.87 3.85
457 1208 0.750546 TATCCTCGGTGGTGACGGAG 60.751 60.000 0.00 0.00 45.02 4.63
458 1209 1.033746 GTATCCTCGGTGGTGACGGA 61.034 60.000 0.00 0.00 37.07 4.69
459 1210 1.436336 GTATCCTCGGTGGTGACGG 59.564 63.158 0.00 0.00 37.07 4.79
460 1211 1.063649 CGTATCCTCGGTGGTGACG 59.936 63.158 9.74 9.74 38.12 4.35
461 1212 1.226888 GCGTATCCTCGGTGGTGAC 60.227 63.158 0.00 0.00 37.07 3.67
462 1213 2.767445 CGCGTATCCTCGGTGGTGA 61.767 63.158 0.00 0.00 37.07 4.02
463 1214 2.278596 CGCGTATCCTCGGTGGTG 60.279 66.667 0.00 0.00 37.07 4.17
464 1215 4.203076 GCGCGTATCCTCGGTGGT 62.203 66.667 8.43 0.00 37.07 4.16
473 1224 4.899687 TCTGACGGCGCGCGTATC 62.900 66.667 32.35 24.54 0.00 2.24
474 1225 4.907034 CTCTGACGGCGCGCGTAT 62.907 66.667 32.35 17.17 0.00 3.06
629 3404 2.486966 GCGCTGGATTGAGTTGGC 59.513 61.111 0.00 0.00 0.00 4.52
906 3693 3.850122 ATAAGCTATATCGTGCGCAGA 57.150 42.857 12.22 11.51 0.00 4.26
919 3706 7.490079 CGTTGGATGTAACACACTAATAAGCTA 59.510 37.037 0.00 0.00 0.00 3.32
960 3747 4.090761 AGCAGATTTTGTGTTCTCCTCA 57.909 40.909 0.00 0.00 0.00 3.86
1078 3865 1.001406 CTTCTTCTCTCCGGCAGTGTT 59.999 52.381 0.00 0.00 0.00 3.32
1299 4086 7.872881 TCTTACTGAATATATCGAGCGTCTTT 58.127 34.615 0.00 0.00 0.00 2.52
1389 4177 4.703897 TCTTCGAGTGACACCAAAGAATT 58.296 39.130 0.84 0.00 0.00 2.17
1433 4221 0.946221 GAAGGTCAGCACGTCACCAG 60.946 60.000 5.54 0.00 31.99 4.00
1530 4318 3.053831 AGAATAACACACCCGAACAGG 57.946 47.619 0.00 0.00 40.63 4.00
1551 4339 8.642935 TGAATGAGTCTTCTCTTTCTTCTCTA 57.357 34.615 17.90 2.51 46.19 2.43
1562 4350 2.275318 CCCGCTTGAATGAGTCTTCTC 58.725 52.381 0.00 0.00 40.79 2.87
1579 4367 3.254657 TCAACAAAGGTAGAAAATGCCCG 59.745 43.478 0.00 0.00 33.23 6.13
1622 4410 1.363807 CCTGTGAGTGTCGTCTGCA 59.636 57.895 0.00 0.00 0.00 4.41
1631 4419 1.806542 GTTGCATGGTACCTGTGAGTG 59.193 52.381 14.36 3.86 0.00 3.51
1884 7853 5.910614 TCATCGACAGTCATCATCTCATTT 58.089 37.500 0.41 0.00 0.00 2.32
1938 7907 1.578897 TGCCAGCAAGTCCATAGGTA 58.421 50.000 0.00 0.00 0.00 3.08
2140 8111 1.364626 CTTCATCCTCACACCGCTGC 61.365 60.000 0.00 0.00 0.00 5.25
2149 8120 4.624843 GCCATCTCAAAGTCTTCATCCTCA 60.625 45.833 0.00 0.00 0.00 3.86
2196 8167 3.222603 GGCGGGGAGTTTATGATGAAAT 58.777 45.455 0.00 0.00 0.00 2.17
2204 8175 1.064825 CTATGGGGCGGGGAGTTTAT 58.935 55.000 0.00 0.00 0.00 1.40
2212 8183 1.994885 ATGAACCACTATGGGGCGGG 61.995 60.000 0.00 0.00 43.37 6.13
2238 8210 6.294731 GGAACCACAAGTCATTAAGCAGATTT 60.295 38.462 0.00 0.00 0.00 2.17
2340 8312 3.565902 GGAGAACAACTTGAACAAGGAGG 59.434 47.826 17.05 9.27 42.53 4.30
2429 8401 1.286260 GACTCGAGTCCACGTGCTT 59.714 57.895 31.24 0.00 39.07 3.91
2604 8576 7.537596 AATCTCTCATGTACTAAGGATGGAG 57.462 40.000 0.00 0.00 0.00 3.86
2620 8592 6.713903 GGATAGCAATTGGATCAAATCTCTCA 59.286 38.462 7.72 0.00 0.00 3.27
2648 8620 0.950836 CGTGCACCATCACCTGAAAA 59.049 50.000 12.15 0.00 33.57 2.29
2708 8680 1.074471 ACGGGCATCCCTACTCCAT 60.074 57.895 0.00 0.00 42.67 3.41
3128 9102 3.871006 CCTCTTTTCAAAACCCACAAAGC 59.129 43.478 0.00 0.00 0.00 3.51
3267 9252 2.000290 TTTGAGGGGGAGGAATCCAT 58.000 50.000 0.61 0.00 0.00 3.41
3271 9256 7.311865 CCAAAAATAAATTTGAGGGGGAGGAAT 60.312 37.037 0.00 0.00 41.73 3.01
3272 9257 6.012945 CCAAAAATAAATTTGAGGGGGAGGAA 60.013 38.462 0.00 0.00 41.73 3.36
3273 9258 5.487131 CCAAAAATAAATTTGAGGGGGAGGA 59.513 40.000 0.00 0.00 41.73 3.71
3274 9259 5.487131 TCCAAAAATAAATTTGAGGGGGAGG 59.513 40.000 0.00 0.00 41.73 4.30
3275 9260 6.213397 ACTCCAAAAATAAATTTGAGGGGGAG 59.787 38.462 17.65 17.65 41.73 4.30
3409 9399 1.081277 ACAAGGAGGAGGGGAGGTC 59.919 63.158 0.00 0.00 0.00 3.85
3517 9507 7.465353 TTGAAAATCACTCATGCTCCAAATA 57.535 32.000 0.00 0.00 0.00 1.40
3527 9517 6.294731 GGGTACTTGCTTTGAAAATCACTCAT 60.295 38.462 0.00 0.00 0.00 2.90
3607 9597 3.593442 TCAAGATGGTTCTGGGTTGTT 57.407 42.857 0.00 0.00 30.72 2.83
3629 9619 7.124147 TGAAAATTTTGAAAAGAGGAGGAGTGT 59.876 33.333 8.47 0.00 0.00 3.55
3787 9777 2.232208 CCTCTGGTGATTTTTCCTTGCC 59.768 50.000 0.00 0.00 0.00 4.52
3788 9778 2.353109 GCCTCTGGTGATTTTTCCTTGC 60.353 50.000 0.00 0.00 0.00 4.01
3894 9885 0.179205 GAACGCATGAGTGAAGCTGC 60.179 55.000 1.78 0.00 0.00 5.25
3907 9898 0.742635 TCAAGTGCACTGTGAACGCA 60.743 50.000 22.49 0.00 0.00 5.24
3926 9917 4.681978 GGGCTGCGAGGAACGTGT 62.682 66.667 0.00 0.00 44.60 4.49
4024 10015 3.774702 GTTCCGACGCCGCAGAAC 61.775 66.667 0.00 0.00 32.74 3.01


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

AutoCloner maintained by Alex Coulton.