Multiple sequence alignment - TraesCS7A01G505900

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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 TraesCS7A01G505900 chr7A 100.000 1408 0 0 866 2273 693809985 693808578 0.000000e+00 2601.0
1 TraesCS7A01G505900 chr7A 100.000 545 0 0 1 545 693810850 693810306 0.000000e+00 1007.0
2 TraesCS7A01G505900 chr7A 84.514 833 94 21 1461 2267 693641351 693640528 0.000000e+00 791.0
3 TraesCS7A01G505900 chr7A 83.215 423 57 10 1590 2005 118101384 118100969 2.130000e-100 375.0
4 TraesCS7A01G505900 chr7A 97.222 36 0 1 2232 2267 696859145 696859111 2.440000e-05 60.2
5 TraesCS7A01G505900 chr7A 96.970 33 1 0 2235 2267 518751758 518751790 3.150000e-04 56.5
6 TraesCS7A01G505900 chr1D 96.147 545 21 0 1 545 485494965 485494421 0.000000e+00 891.0
7 TraesCS7A01G505900 chr1D 94.064 438 26 0 866 1303 485494399 485493962 0.000000e+00 665.0
8 TraesCS7A01G505900 chr1D 87.593 540 64 3 1 539 64752192 64751655 6.890000e-175 623.0
9 TraesCS7A01G505900 chr7B 90.826 545 50 0 1 545 48255270 48254726 0.000000e+00 730.0
10 TraesCS7A01G505900 chr7B 82.681 664 78 14 1461 2118 681681760 681681128 2.550000e-154 555.0
11 TraesCS7A01G505900 chr7B 87.330 442 55 1 866 1307 48254703 48254263 2.610000e-139 505.0
12 TraesCS7A01G505900 chr7B 88.396 293 24 5 1461 1744 681522065 681521774 6.010000e-91 344.0
13 TraesCS7A01G505900 chr7B 88.571 280 16 7 1855 2130 681521733 681521466 2.180000e-85 326.0
14 TraesCS7A01G505900 chr4B 90.459 545 52 0 1 545 115548687 115548143 0.000000e+00 719.0
15 TraesCS7A01G505900 chr4B 87.162 444 56 1 866 1308 660146982 660146539 9.370000e-139 503.0
16 TraesCS7A01G505900 chr4B 89.614 337 35 0 1 337 660150168 660149832 1.610000e-116 429.0
17 TraesCS7A01G505900 chr4B 89.952 209 21 0 337 545 660147213 660147005 1.030000e-68 270.0
18 TraesCS7A01G505900 chr5D 87.156 545 70 0 1 545 305814305 305814849 8.920000e-174 619.0
19 TraesCS7A01G505900 chr5A 89.269 438 46 1 866 1303 376539407 376539843 4.270000e-152 547.0
20 TraesCS7A01G505900 chr5A 89.744 351 36 0 187 537 376538768 376539118 1.240000e-122 449.0
21 TraesCS7A01G505900 chr6D 88.435 441 47 4 866 1303 449846105 449845666 1.550000e-146 529.0
22 TraesCS7A01G505900 chr6D 88.858 359 40 0 187 545 449846493 449846135 2.070000e-120 442.0
23 TraesCS7A01G505900 chr6D 80.040 501 85 12 1481 1972 140082504 140082010 7.720000e-95 357.0
24 TraesCS7A01G505900 chr6B 88.128 438 50 1 866 1303 53593359 53593794 9.310000e-144 520.0
25 TraesCS7A01G505900 chr6B 79.353 402 77 5 1577 1972 240038038 240037637 6.180000e-71 278.0
26 TraesCS7A01G505900 chr6B 91.304 46 3 1 2223 2267 592941110 592941065 6.780000e-06 62.1
27 TraesCS7A01G505900 chr5B 87.727 440 54 0 866 1305 604577857 604578296 4.330000e-142 514.0
28 TraesCS7A01G505900 chr7D 81.897 580 73 9 1695 2267 602026336 602025782 5.720000e-126 460.0
29 TraesCS7A01G505900 chr3A 79.819 441 82 6 867 1304 82344297 82344733 4.710000e-82 315.0
30 TraesCS7A01G505900 chr3D 90.909 55 2 2 2214 2267 519176974 519177026 1.130000e-08 71.3
31 TraesCS7A01G505900 chr3D 92.157 51 1 3 2219 2267 422554408 422554457 4.050000e-08 69.4
32 TraesCS7A01G505900 chr6A 88.136 59 4 3 2212 2267 156456665 156456607 1.460000e-07 67.6
33 TraesCS7A01G505900 chr3B 89.286 56 2 3 2214 2267 110739673 110739726 1.460000e-07 67.6
34 TraesCS7A01G505900 chr3B 97.059 34 1 0 2234 2267 821221631 821221664 8.770000e-05 58.4


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 TraesCS7A01G505900 chr7A 693808578 693810850 2272 True 1804.000000 2601 100.000000 1 2273 2 chr7A.!!$R4 2272
1 TraesCS7A01G505900 chr7A 693640528 693641351 823 True 791.000000 791 84.514000 1461 2267 1 chr7A.!!$R2 806
2 TraesCS7A01G505900 chr1D 485493962 485494965 1003 True 778.000000 891 95.105500 1 1303 2 chr1D.!!$R2 1302
3 TraesCS7A01G505900 chr1D 64751655 64752192 537 True 623.000000 623 87.593000 1 539 1 chr1D.!!$R1 538
4 TraesCS7A01G505900 chr7B 48254263 48255270 1007 True 617.500000 730 89.078000 1 1307 2 chr7B.!!$R2 1306
5 TraesCS7A01G505900 chr7B 681681128 681681760 632 True 555.000000 555 82.681000 1461 2118 1 chr7B.!!$R1 657
6 TraesCS7A01G505900 chr7B 681521466 681522065 599 True 335.000000 344 88.483500 1461 2130 2 chr7B.!!$R3 669
7 TraesCS7A01G505900 chr4B 115548143 115548687 544 True 719.000000 719 90.459000 1 545 1 chr4B.!!$R1 544
8 TraesCS7A01G505900 chr4B 660146539 660150168 3629 True 400.666667 503 88.909333 1 1308 3 chr4B.!!$R2 1307
9 TraesCS7A01G505900 chr5D 305814305 305814849 544 False 619.000000 619 87.156000 1 545 1 chr5D.!!$F1 544
10 TraesCS7A01G505900 chr5A 376538768 376539843 1075 False 498.000000 547 89.506500 187 1303 2 chr5A.!!$F1 1116
11 TraesCS7A01G505900 chr6D 449845666 449846493 827 True 485.500000 529 88.646500 187 1303 2 chr6D.!!$R2 1116
12 TraesCS7A01G505900 chr7D 602025782 602026336 554 True 460.000000 460 81.897000 1695 2267 1 chr7D.!!$R1 572

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
261 262 0.460311 CCGGCTACCAAATCTCTCGT 59.54 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1359 3980 0.041684 AAGGCCCCCAAGATTCAAGG 59.958 55.0 0.0 0.0 0.0 3.61 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
118 119 1.684450 TGAGTACACGCTCAAGAACCA 59.316 47.619 0.00 0.00 41.93 3.67
248 249 1.475034 GCATGGTTTGATCTCCGGCTA 60.475 52.381 0.00 0.00 0.00 3.93
261 262 0.460311 CCGGCTACCAAATCTCTCGT 59.540 55.000 0.00 0.00 0.00 4.18
306 307 3.758023 CACATGTAGCCCACAATTCTCAA 59.242 43.478 0.00 0.00 41.55 3.02
307 308 3.758554 ACATGTAGCCCACAATTCTCAAC 59.241 43.478 0.00 0.00 41.55 3.18
320 321 2.408271 TCTCAACTGATGACCATGCC 57.592 50.000 0.00 0.00 33.47 4.40
335 2955 5.822519 TGACCATGCCAAGATTACAACTATC 59.177 40.000 0.00 0.00 0.00 2.08
364 2984 6.730507 TGGTCTATATGGCATTCTAGGAATCA 59.269 38.462 4.78 0.00 0.00 2.57
377 2997 4.903649 TCTAGGAATCAGATCAAGCATGGA 59.096 41.667 0.00 0.00 0.00 3.41
920 3540 3.018149 GCAAACCGTTTGATGGGGTATA 58.982 45.455 24.99 0.00 43.26 1.47
950 3570 4.943705 TCTTATCATTGAGGCTTTGTCACC 59.056 41.667 0.00 0.00 0.00 4.02
1013 3633 4.976864 CATGTGATCATGGAGGTGGATTA 58.023 43.478 0.00 0.00 45.30 1.75
1026 3646 4.631234 AGGTGGATTATCTGGAGTTGGTA 58.369 43.478 0.00 0.00 0.00 3.25
1044 3664 2.354805 GGTAATGCTCTGGGAAACTCGT 60.355 50.000 0.00 0.00 0.00 4.18
1055 3675 3.181459 TGGGAAACTCGTCACAATTCTCA 60.181 43.478 0.00 0.00 0.00 3.27
1077 3697 6.899089 TCATTCTATTGTGGCTCCAATCTTA 58.101 36.000 6.30 0.00 36.48 2.10
1237 3857 1.277557 CTAGCTTCCTTGTGACCAGCT 59.722 52.381 0.00 0.00 43.33 4.24
1275 3896 6.264067 GTCCAAGGAATGCTCTTGCTTAATAT 59.736 38.462 6.15 0.00 40.00 1.28
1339 3960 6.753107 TTAGGATTTGCAAGTAAGGTTAGC 57.247 37.500 0.00 0.00 0.00 3.09
1340 3961 4.017126 AGGATTTGCAAGTAAGGTTAGCC 58.983 43.478 0.00 0.00 0.00 3.93
1341 3962 3.181500 GGATTTGCAAGTAAGGTTAGCCG 60.181 47.826 0.00 0.00 40.50 5.52
1342 3963 1.816074 TTGCAAGTAAGGTTAGCCGG 58.184 50.000 0.00 0.00 40.50 6.13
1343 3964 0.675522 TGCAAGTAAGGTTAGCCGGC 60.676 55.000 21.89 21.89 40.50 6.13
1344 3965 1.374343 GCAAGTAAGGTTAGCCGGCC 61.374 60.000 26.15 7.93 40.50 6.13
1345 3966 0.252197 CAAGTAAGGTTAGCCGGCCT 59.748 55.000 26.15 10.49 40.50 5.19
1346 3967 0.989602 AAGTAAGGTTAGCCGGCCTT 59.010 50.000 26.15 21.19 45.95 4.35
1347 3968 0.540454 AGTAAGGTTAGCCGGCCTTC 59.460 55.000 26.15 13.45 43.40 3.46
1348 3969 0.463295 GTAAGGTTAGCCGGCCTTCC 60.463 60.000 26.15 22.07 43.40 3.46
1349 3970 0.910566 TAAGGTTAGCCGGCCTTCCA 60.911 55.000 26.15 5.08 43.40 3.53
1350 3971 1.571773 AAGGTTAGCCGGCCTTCCAT 61.572 55.000 26.15 13.02 40.81 3.41
1351 3972 1.076995 GGTTAGCCGGCCTTCCATT 60.077 57.895 26.15 4.77 0.00 3.16
1352 3973 0.683179 GGTTAGCCGGCCTTCCATTT 60.683 55.000 26.15 3.86 0.00 2.32
1353 3974 0.455815 GTTAGCCGGCCTTCCATTTG 59.544 55.000 26.15 0.00 0.00 2.32
1354 3975 1.319614 TTAGCCGGCCTTCCATTTGC 61.320 55.000 26.15 0.00 0.00 3.68
1355 3976 4.147449 GCCGGCCTTCCATTTGCC 62.147 66.667 18.11 0.00 41.85 4.52
1358 3979 2.885113 GGCCTTCCATTTGCCGTC 59.115 61.111 0.00 0.00 35.08 4.79
1359 3980 2.710902 GGCCTTCCATTTGCCGTCC 61.711 63.158 0.00 0.00 35.08 4.79
1360 3981 2.710902 GCCTTCCATTTGCCGTCCC 61.711 63.158 0.00 0.00 0.00 4.46
1361 3982 1.000896 CCTTCCATTTGCCGTCCCT 60.001 57.895 0.00 0.00 0.00 4.20
1362 3983 0.611896 CCTTCCATTTGCCGTCCCTT 60.612 55.000 0.00 0.00 0.00 3.95
1363 3984 0.527565 CTTCCATTTGCCGTCCCTTG 59.472 55.000 0.00 0.00 0.00 3.61
1364 3985 0.111446 TTCCATTTGCCGTCCCTTGA 59.889 50.000 0.00 0.00 0.00 3.02
1365 3986 0.111446 TCCATTTGCCGTCCCTTGAA 59.889 50.000 0.00 0.00 0.00 2.69
1366 3987 1.185315 CCATTTGCCGTCCCTTGAAT 58.815 50.000 0.00 0.00 0.00 2.57
1367 3988 1.134946 CCATTTGCCGTCCCTTGAATC 59.865 52.381 0.00 0.00 0.00 2.52
1368 3989 2.094675 CATTTGCCGTCCCTTGAATCT 58.905 47.619 0.00 0.00 0.00 2.40
1369 3990 2.286365 TTTGCCGTCCCTTGAATCTT 57.714 45.000 0.00 0.00 0.00 2.40
1370 3991 1.533625 TTGCCGTCCCTTGAATCTTG 58.466 50.000 0.00 0.00 0.00 3.02
1371 3992 0.322456 TGCCGTCCCTTGAATCTTGG 60.322 55.000 0.00 0.00 0.00 3.61
1372 3993 1.032114 GCCGTCCCTTGAATCTTGGG 61.032 60.000 5.09 5.09 42.20 4.12
1373 3994 0.394352 CCGTCCCTTGAATCTTGGGG 60.394 60.000 10.25 5.61 41.22 4.96
1374 3995 0.394352 CGTCCCTTGAATCTTGGGGG 60.394 60.000 10.25 0.00 41.22 5.40
1375 3996 0.684479 GTCCCTTGAATCTTGGGGGC 60.684 60.000 10.25 3.61 41.22 5.80
1376 3997 1.381735 CCCTTGAATCTTGGGGGCC 60.382 63.158 0.00 0.00 37.37 5.80
1377 3998 1.699752 CCTTGAATCTTGGGGGCCT 59.300 57.895 0.84 0.00 0.00 5.19
1378 3999 0.041684 CCTTGAATCTTGGGGGCCTT 59.958 55.000 0.84 0.00 0.00 4.35
1379 4000 1.188863 CTTGAATCTTGGGGGCCTTG 58.811 55.000 0.84 0.00 0.00 3.61
1380 4001 0.904394 TTGAATCTTGGGGGCCTTGC 60.904 55.000 0.84 0.00 0.00 4.01
1391 4012 4.699522 GCCTTGCCGTTCGGGACT 62.700 66.667 13.16 0.00 38.47 3.85
1392 4013 2.032071 CCTTGCCGTTCGGGACTT 59.968 61.111 13.16 0.00 38.47 3.01
1393 4014 2.033194 CCTTGCCGTTCGGGACTTC 61.033 63.158 13.16 0.00 38.47 3.01
1394 4015 2.031465 TTGCCGTTCGGGACTTCC 59.969 61.111 13.16 0.00 38.47 3.46
1421 4042 4.758251 CTGCGTGTGCCCGATGGA 62.758 66.667 0.00 0.00 41.78 3.41
1422 4043 4.094646 TGCGTGTGCCCGATGGAT 62.095 61.111 0.00 0.00 41.78 3.41
1423 4044 2.824041 GCGTGTGCCCGATGGATT 60.824 61.111 0.00 0.00 33.98 3.01
1424 4045 2.406616 GCGTGTGCCCGATGGATTT 61.407 57.895 0.00 0.00 33.98 2.17
1425 4046 1.092921 GCGTGTGCCCGATGGATTTA 61.093 55.000 0.00 0.00 33.98 1.40
1426 4047 0.937304 CGTGTGCCCGATGGATTTAG 59.063 55.000 0.00 0.00 0.00 1.85
1427 4048 0.663153 GTGTGCCCGATGGATTTAGC 59.337 55.000 0.00 0.00 0.00 3.09
1428 4049 0.546122 TGTGCCCGATGGATTTAGCT 59.454 50.000 0.00 0.00 0.00 3.32
1429 4050 1.064758 TGTGCCCGATGGATTTAGCTT 60.065 47.619 0.00 0.00 0.00 3.74
1430 4051 1.604278 GTGCCCGATGGATTTAGCTTC 59.396 52.381 0.00 0.00 0.00 3.86
1431 4052 1.211703 TGCCCGATGGATTTAGCTTCA 59.788 47.619 0.00 0.00 0.00 3.02
1432 4053 2.297701 GCCCGATGGATTTAGCTTCAA 58.702 47.619 0.00 0.00 0.00 2.69
1433 4054 2.033424 GCCCGATGGATTTAGCTTCAAC 59.967 50.000 0.00 0.00 0.00 3.18
1434 4055 2.287915 CCCGATGGATTTAGCTTCAACG 59.712 50.000 0.00 0.00 0.00 4.10
1435 4056 2.286418 CCGATGGATTTAGCTTCAACGC 60.286 50.000 0.00 0.00 0.00 4.84
1436 4057 2.351418 CGATGGATTTAGCTTCAACGCA 59.649 45.455 0.00 0.00 0.00 5.24
1437 4058 3.685058 GATGGATTTAGCTTCAACGCAC 58.315 45.455 0.00 0.00 0.00 5.34
1438 4059 1.810151 TGGATTTAGCTTCAACGCACC 59.190 47.619 0.00 0.00 0.00 5.01
1439 4060 1.202031 GGATTTAGCTTCAACGCACCG 60.202 52.381 0.00 0.00 0.00 4.94
1440 4061 1.730064 GATTTAGCTTCAACGCACCGA 59.270 47.619 0.00 0.00 0.00 4.69
1441 4062 0.863144 TTTAGCTTCAACGCACCGAC 59.137 50.000 0.00 0.00 0.00 4.79
1442 4063 0.947180 TTAGCTTCAACGCACCGACC 60.947 55.000 0.00 0.00 0.00 4.79
1443 4064 2.775032 TAGCTTCAACGCACCGACCC 62.775 60.000 0.00 0.00 0.00 4.46
1444 4065 2.280524 CTTCAACGCACCGACCCA 60.281 61.111 0.00 0.00 0.00 4.51
1445 4066 1.890041 CTTCAACGCACCGACCCAA 60.890 57.895 0.00 0.00 0.00 4.12
1446 4067 1.440938 CTTCAACGCACCGACCCAAA 61.441 55.000 0.00 0.00 0.00 3.28
1447 4068 1.716826 TTCAACGCACCGACCCAAAC 61.717 55.000 0.00 0.00 0.00 2.93
1448 4069 2.903350 AACGCACCGACCCAAACC 60.903 61.111 0.00 0.00 0.00 3.27
1451 4072 3.351416 GCACCGACCCAAACCGTC 61.351 66.667 0.00 0.00 0.00 4.79
1452 4073 2.667199 CACCGACCCAAACCGTCC 60.667 66.667 0.00 0.00 0.00 4.79
1453 4074 3.944945 ACCGACCCAAACCGTCCC 61.945 66.667 0.00 0.00 0.00 4.46
1454 4075 3.633116 CCGACCCAAACCGTCCCT 61.633 66.667 0.00 0.00 0.00 4.20
1455 4076 2.358247 CGACCCAAACCGTCCCTG 60.358 66.667 0.00 0.00 0.00 4.45
1456 4077 2.033602 GACCCAAACCGTCCCTGG 59.966 66.667 0.00 0.00 0.00 4.45
1457 4078 2.448931 ACCCAAACCGTCCCTGGA 60.449 61.111 0.00 0.00 31.38 3.86
1458 4079 2.059345 GACCCAAACCGTCCCTGGAA 62.059 60.000 0.00 0.00 31.38 3.53
1459 4080 1.151908 CCCAAACCGTCCCTGGAAA 59.848 57.895 0.00 0.00 31.38 3.13
1465 4086 1.350310 ACCGTCCCTGGAAACTTGGT 61.350 55.000 0.00 0.00 0.00 3.67
1468 4089 1.476110 CGTCCCTGGAAACTTGGTTCA 60.476 52.381 0.00 0.00 0.00 3.18
1472 4093 2.365293 CCCTGGAAACTTGGTTCAAAGG 59.635 50.000 10.59 10.59 34.74 3.11
1556 4179 1.412710 ACATACCATACTCCCTGCACG 59.587 52.381 0.00 0.00 0.00 5.34
1588 4211 5.755861 GCTTGTCTATCATTGGACTAGTTCC 59.244 44.000 0.00 1.65 46.13 3.62
1671 4301 1.999648 TGGCAGCTCACTTGGAAAAT 58.000 45.000 0.00 0.00 0.00 1.82
1677 4307 4.019174 CAGCTCACTTGGAAAATATGGGT 58.981 43.478 0.00 0.00 0.00 4.51
1686 4316 3.011144 TGGAAAATATGGGTGCCTCTTCA 59.989 43.478 0.00 0.00 0.00 3.02
1688 4318 4.651045 GGAAAATATGGGTGCCTCTTCATT 59.349 41.667 0.00 0.00 0.00 2.57
1731 4361 2.768527 CCTCCCAAGAGTGATGCTAGAA 59.231 50.000 0.00 0.00 38.58 2.10
1744 4374 5.645497 GTGATGCTAGAACATGGAAAGACTT 59.355 40.000 0.00 0.00 0.00 3.01
1746 4376 5.227569 TGCTAGAACATGGAAAGACTTGA 57.772 39.130 0.00 0.00 0.00 3.02
1782 4412 2.140792 ACGCGGATAGATGCCCCTT 61.141 57.895 12.47 0.00 0.00 3.95
1785 4415 0.179018 GCGGATAGATGCCCCTTTGT 60.179 55.000 0.00 0.00 0.00 2.83
1798 4431 1.476110 CCCTTTGTGACCAAGAACCGA 60.476 52.381 0.00 0.00 0.00 4.69
1807 4494 3.190874 GACCAAGAACCGAAGAGCATAG 58.809 50.000 0.00 0.00 0.00 2.23
1822 4509 3.378512 AGCATAGATCACCTCTTGGTCA 58.621 45.455 0.00 0.00 46.60 4.02
1899 4592 3.182263 CCACCCCACCCCAACTCA 61.182 66.667 0.00 0.00 0.00 3.41
1907 4600 2.391130 ACCCCAACTCACCCTTGCA 61.391 57.895 0.00 0.00 0.00 4.08
1912 4605 1.073897 AACTCACCCTTGCAGGAGC 59.926 57.895 0.00 0.00 37.67 4.70
1931 4624 1.486726 GCAGTGGCAAGATACCCTAGT 59.513 52.381 0.00 0.00 40.72 2.57
2025 4722 1.800713 GAAGCGTCTTCGACCGACC 60.801 63.158 8.09 2.78 39.71 4.79
2046 4743 1.279271 AGAACCCTCCTTGACCAATCG 59.721 52.381 0.00 0.00 0.00 3.34
2048 4745 1.815421 CCCTCCTTGACCAATCGCG 60.815 63.158 0.00 0.00 0.00 5.87
2049 4746 2.464459 CCTCCTTGACCAATCGCGC 61.464 63.158 0.00 0.00 0.00 6.86
2050 4747 2.435938 TCCTTGACCAATCGCGCC 60.436 61.111 0.00 0.00 0.00 6.53
2051 4748 2.436646 CCTTGACCAATCGCGCCT 60.437 61.111 0.00 0.00 0.00 5.52
2053 4750 1.429148 CCTTGACCAATCGCGCCTAC 61.429 60.000 0.00 0.00 0.00 3.18
2054 4751 0.739462 CTTGACCAATCGCGCCTACA 60.739 55.000 0.00 0.00 0.00 2.74
2056 4753 0.529773 TGACCAATCGCGCCTACATC 60.530 55.000 0.00 0.00 0.00 3.06
2057 4754 0.249489 GACCAATCGCGCCTACATCT 60.249 55.000 0.00 0.00 0.00 2.90
2058 4755 0.249489 ACCAATCGCGCCTACATCTC 60.249 55.000 0.00 0.00 0.00 2.75
2059 4756 0.249447 CCAATCGCGCCTACATCTCA 60.249 55.000 0.00 0.00 0.00 3.27
2060 4757 1.606480 CCAATCGCGCCTACATCTCAT 60.606 52.381 0.00 0.00 0.00 2.90
2061 4758 1.458445 CAATCGCGCCTACATCTCATG 59.542 52.381 0.00 0.00 0.00 3.07
2132 4829 7.550906 GCTTGGCCAACATAATTACCAAATAAA 59.449 33.333 16.05 0.00 36.78 1.40
2158 4855 3.579534 TGTGGTAGTTTGCAACCCTAA 57.420 42.857 0.00 0.00 34.69 2.69
2165 4862 0.189822 TTTGCAACCCTAAGGCCCTT 59.810 50.000 0.00 0.00 36.11 3.95
2169 4866 0.107654 CAACCCTAAGGCCCTTCTCG 60.108 60.000 0.00 0.00 36.11 4.04
2180 4891 2.131067 CCTTCTCGCCCCTCTCTCC 61.131 68.421 0.00 0.00 0.00 3.71
2188 4899 4.465446 CCCTCTCTCCCGGCCTCA 62.465 72.222 0.00 0.00 0.00 3.86
2189 4900 2.123077 CCTCTCTCCCGGCCTCAT 60.123 66.667 0.00 0.00 0.00 2.90
2192 4903 1.743321 CTCTCTCCCGGCCTCATGTC 61.743 65.000 0.00 0.00 0.00 3.06
2207 4918 2.027285 TCATGTCGTGTGTTGGATCCAT 60.027 45.455 17.06 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 4.527038 TCGAAGTACTCTCCACCAGAAAAT 59.473 41.667 0.00 0.00 0.00 1.82
94 95 4.142447 GGTTCTTGAGCGTGTACTCATCTA 60.142 45.833 0.00 0.00 45.75 1.98
118 119 3.260475 TGCTAACGTCTGCAATATGGT 57.740 42.857 12.09 0.00 36.15 3.55
248 249 1.067776 GTCACCGACGAGAGATTTGGT 60.068 52.381 0.00 0.00 0.00 3.67
306 307 3.377253 AATCTTGGCATGGTCATCAGT 57.623 42.857 0.00 0.00 0.00 3.41
307 308 4.201657 TGTAATCTTGGCATGGTCATCAG 58.798 43.478 0.00 0.00 0.00 2.90
320 321 9.770097 ATAGACCACATGATAGTTGTAATCTTG 57.230 33.333 0.00 0.00 35.63 3.02
335 2955 6.070596 TCCTAGAATGCCATATAGACCACATG 60.071 42.308 0.00 0.00 0.00 3.21
364 2984 2.971330 CCTACCTCTCCATGCTTGATCT 59.029 50.000 0.22 0.00 0.00 2.75
874 3494 0.938008 GCACCTAGGAACGCATTAGC 59.062 55.000 17.98 1.33 37.42 3.09
950 3570 0.739813 AAATCGAACTCCTTCCCGCG 60.740 55.000 0.00 0.00 0.00 6.46
1013 3633 3.118112 CCAGAGCATTACCAACTCCAGAT 60.118 47.826 0.00 0.00 0.00 2.90
1026 3646 1.347707 TGACGAGTTTCCCAGAGCATT 59.652 47.619 0.00 0.00 0.00 3.56
1055 3675 9.512588 CTAATAAGATTGGAGCCACAATAGAAT 57.487 33.333 3.70 0.00 40.92 2.40
1197 3817 1.544691 GGAGTCTTGTCGAGCCAACTA 59.455 52.381 0.00 0.00 0.00 2.24
1237 3857 3.831323 TCCTTGGACAATCAGCAAGAAA 58.169 40.909 0.00 0.00 0.00 2.52
1275 3896 0.179073 GCGGGCAAATCAGAGAGCTA 60.179 55.000 0.00 0.00 0.00 3.32
1313 3934 8.085909 GCTAACCTTACTTGCAAATCCTAAAAA 58.914 33.333 0.00 0.00 0.00 1.94
1314 3935 7.309560 GGCTAACCTTACTTGCAAATCCTAAAA 60.310 37.037 0.00 0.00 0.00 1.52
1315 3936 6.152154 GGCTAACCTTACTTGCAAATCCTAAA 59.848 38.462 0.00 0.00 0.00 1.85
1316 3937 5.650703 GGCTAACCTTACTTGCAAATCCTAA 59.349 40.000 0.00 0.00 0.00 2.69
1317 3938 5.190677 GGCTAACCTTACTTGCAAATCCTA 58.809 41.667 0.00 0.00 0.00 2.94
1318 3939 4.017126 GGCTAACCTTACTTGCAAATCCT 58.983 43.478 0.00 0.00 0.00 3.24
1319 3940 3.181500 CGGCTAACCTTACTTGCAAATCC 60.181 47.826 0.00 0.00 0.00 3.01
1320 3941 3.181500 CCGGCTAACCTTACTTGCAAATC 60.181 47.826 0.00 0.00 0.00 2.17
1321 3942 2.752903 CCGGCTAACCTTACTTGCAAAT 59.247 45.455 0.00 0.00 0.00 2.32
1322 3943 2.156098 CCGGCTAACCTTACTTGCAAA 58.844 47.619 0.00 0.00 0.00 3.68
1323 3944 1.816074 CCGGCTAACCTTACTTGCAA 58.184 50.000 0.00 0.00 0.00 4.08
1324 3945 0.675522 GCCGGCTAACCTTACTTGCA 60.676 55.000 22.15 0.00 0.00 4.08
1325 3946 1.374343 GGCCGGCTAACCTTACTTGC 61.374 60.000 28.56 0.00 0.00 4.01
1326 3947 0.252197 AGGCCGGCTAACCTTACTTG 59.748 55.000 28.56 0.00 29.74 3.16
1327 3948 0.989602 AAGGCCGGCTAACCTTACTT 59.010 50.000 28.56 15.38 44.52 2.24
1328 3949 0.540454 GAAGGCCGGCTAACCTTACT 59.460 55.000 28.56 9.32 46.33 2.24
1329 3950 0.463295 GGAAGGCCGGCTAACCTTAC 60.463 60.000 28.56 17.86 46.33 2.34
1330 3951 0.910566 TGGAAGGCCGGCTAACCTTA 60.911 55.000 28.56 9.08 46.33 2.69
1332 3953 1.571773 AATGGAAGGCCGGCTAACCT 61.572 55.000 28.56 12.32 38.14 3.50
1333 3954 0.683179 AAATGGAAGGCCGGCTAACC 60.683 55.000 28.56 24.72 36.79 2.85
1334 3955 0.455815 CAAATGGAAGGCCGGCTAAC 59.544 55.000 28.56 16.80 36.79 2.34
1335 3956 1.319614 GCAAATGGAAGGCCGGCTAA 61.320 55.000 28.56 7.99 36.79 3.09
1336 3957 1.752694 GCAAATGGAAGGCCGGCTA 60.753 57.895 28.56 8.37 36.79 3.93
1337 3958 3.070576 GCAAATGGAAGGCCGGCT 61.071 61.111 28.56 7.30 36.79 5.52
1338 3959 4.147449 GGCAAATGGAAGGCCGGC 62.147 66.667 21.18 21.18 38.04 6.13
1341 3962 2.710902 GGACGGCAAATGGAAGGCC 61.711 63.158 0.00 0.00 44.27 5.19
1342 3963 2.710902 GGGACGGCAAATGGAAGGC 61.711 63.158 0.00 0.00 0.00 4.35
1343 3964 0.611896 AAGGGACGGCAAATGGAAGG 60.612 55.000 0.00 0.00 0.00 3.46
1344 3965 0.527565 CAAGGGACGGCAAATGGAAG 59.472 55.000 0.00 0.00 0.00 3.46
1345 3966 0.111446 TCAAGGGACGGCAAATGGAA 59.889 50.000 0.00 0.00 0.00 3.53
1346 3967 0.111446 TTCAAGGGACGGCAAATGGA 59.889 50.000 0.00 0.00 0.00 3.41
1347 3968 1.134946 GATTCAAGGGACGGCAAATGG 59.865 52.381 0.00 0.00 0.00 3.16
1348 3969 2.094675 AGATTCAAGGGACGGCAAATG 58.905 47.619 0.00 0.00 0.00 2.32
1349 3970 2.493278 CAAGATTCAAGGGACGGCAAAT 59.507 45.455 0.00 0.00 0.00 2.32
1350 3971 1.885887 CAAGATTCAAGGGACGGCAAA 59.114 47.619 0.00 0.00 0.00 3.68
1351 3972 1.533625 CAAGATTCAAGGGACGGCAA 58.466 50.000 0.00 0.00 0.00 4.52
1352 3973 0.322456 CCAAGATTCAAGGGACGGCA 60.322 55.000 0.00 0.00 0.00 5.69
1353 3974 1.032114 CCCAAGATTCAAGGGACGGC 61.032 60.000 7.48 0.00 45.80 5.68
1354 3975 0.394352 CCCCAAGATTCAAGGGACGG 60.394 60.000 13.39 0.00 45.80 4.79
1355 3976 0.394352 CCCCCAAGATTCAAGGGACG 60.394 60.000 13.39 1.95 45.80 4.79
1356 3977 0.684479 GCCCCCAAGATTCAAGGGAC 60.684 60.000 13.39 3.73 45.80 4.46
1357 3978 1.697297 GCCCCCAAGATTCAAGGGA 59.303 57.895 13.39 0.00 45.80 4.20
1358 3979 1.381735 GGCCCCCAAGATTCAAGGG 60.382 63.158 0.00 6.49 42.44 3.95
1359 3980 0.041684 AAGGCCCCCAAGATTCAAGG 59.958 55.000 0.00 0.00 0.00 3.61
1360 3981 1.188863 CAAGGCCCCCAAGATTCAAG 58.811 55.000 0.00 0.00 0.00 3.02
1361 3982 0.904394 GCAAGGCCCCCAAGATTCAA 60.904 55.000 0.00 0.00 0.00 2.69
1362 3983 1.305213 GCAAGGCCCCCAAGATTCA 60.305 57.895 0.00 0.00 0.00 2.57
1363 3984 2.060383 GGCAAGGCCCCCAAGATTC 61.060 63.158 0.00 0.00 44.06 2.52
1364 3985 2.039462 GGCAAGGCCCCCAAGATT 59.961 61.111 0.00 0.00 44.06 2.40
1374 3995 4.699522 AGTCCCGAACGGCAAGGC 62.700 66.667 7.80 0.00 0.00 4.35
1375 3996 2.032071 AAGTCCCGAACGGCAAGG 59.968 61.111 7.80 0.00 0.00 3.61
1376 3997 2.033194 GGAAGTCCCGAACGGCAAG 61.033 63.158 7.80 0.00 0.00 4.01
1377 3998 2.031465 GGAAGTCCCGAACGGCAA 59.969 61.111 7.80 0.00 0.00 4.52
1404 4025 4.758251 TCCATCGGGCACACGCAG 62.758 66.667 0.00 0.00 41.24 5.18
1405 4026 3.620419 AATCCATCGGGCACACGCA 62.620 57.895 0.00 0.00 41.24 5.24
1406 4027 1.092921 TAAATCCATCGGGCACACGC 61.093 55.000 0.00 0.00 37.44 5.34
1407 4028 0.937304 CTAAATCCATCGGGCACACG 59.063 55.000 0.00 0.00 0.00 4.49
1408 4029 0.663153 GCTAAATCCATCGGGCACAC 59.337 55.000 0.00 0.00 0.00 3.82
1409 4030 0.546122 AGCTAAATCCATCGGGCACA 59.454 50.000 0.00 0.00 0.00 4.57
1410 4031 1.604278 GAAGCTAAATCCATCGGGCAC 59.396 52.381 0.00 0.00 0.00 5.01
1411 4032 1.211703 TGAAGCTAAATCCATCGGGCA 59.788 47.619 0.00 0.00 0.00 5.36
1412 4033 1.967319 TGAAGCTAAATCCATCGGGC 58.033 50.000 0.00 0.00 0.00 6.13
1413 4034 2.287915 CGTTGAAGCTAAATCCATCGGG 59.712 50.000 0.00 0.00 0.00 5.14
1414 4035 2.286418 GCGTTGAAGCTAAATCCATCGG 60.286 50.000 0.00 0.00 0.00 4.18
1415 4036 2.351418 TGCGTTGAAGCTAAATCCATCG 59.649 45.455 0.00 0.00 38.13 3.84
1416 4037 3.487544 GGTGCGTTGAAGCTAAATCCATC 60.488 47.826 0.00 0.00 38.13 3.51
1417 4038 2.423538 GGTGCGTTGAAGCTAAATCCAT 59.576 45.455 0.00 0.00 38.13 3.41
1418 4039 1.810151 GGTGCGTTGAAGCTAAATCCA 59.190 47.619 0.00 0.00 38.13 3.41
1419 4040 1.202031 CGGTGCGTTGAAGCTAAATCC 60.202 52.381 0.00 0.00 38.13 3.01
1420 4041 1.730064 TCGGTGCGTTGAAGCTAAATC 59.270 47.619 0.00 0.00 38.13 2.17
1421 4042 1.463444 GTCGGTGCGTTGAAGCTAAAT 59.537 47.619 0.00 0.00 38.13 1.40
1422 4043 0.863144 GTCGGTGCGTTGAAGCTAAA 59.137 50.000 0.00 0.00 38.13 1.85
1423 4044 0.947180 GGTCGGTGCGTTGAAGCTAA 60.947 55.000 0.00 0.00 38.13 3.09
1424 4045 1.373748 GGTCGGTGCGTTGAAGCTA 60.374 57.895 0.00 0.00 38.13 3.32
1425 4046 2.665185 GGTCGGTGCGTTGAAGCT 60.665 61.111 0.00 0.00 38.13 3.74
1426 4047 3.723348 GGGTCGGTGCGTTGAAGC 61.723 66.667 0.00 0.00 37.71 3.86
1427 4048 1.440938 TTTGGGTCGGTGCGTTGAAG 61.441 55.000 0.00 0.00 0.00 3.02
1428 4049 1.451567 TTTGGGTCGGTGCGTTGAA 60.452 52.632 0.00 0.00 0.00 2.69
1429 4050 2.181521 GTTTGGGTCGGTGCGTTGA 61.182 57.895 0.00 0.00 0.00 3.18
1430 4051 2.330041 GTTTGGGTCGGTGCGTTG 59.670 61.111 0.00 0.00 0.00 4.10
1431 4052 2.903350 GGTTTGGGTCGGTGCGTT 60.903 61.111 0.00 0.00 0.00 4.84
1434 4055 3.351416 GACGGTTTGGGTCGGTGC 61.351 66.667 0.00 0.00 0.00 5.01
1435 4056 2.667199 GGACGGTTTGGGTCGGTG 60.667 66.667 0.00 0.00 35.24 4.94
1436 4057 3.944945 GGGACGGTTTGGGTCGGT 61.945 66.667 0.00 0.00 35.24 4.69
1437 4058 3.633116 AGGGACGGTTTGGGTCGG 61.633 66.667 0.00 0.00 35.24 4.79
1438 4059 2.358247 CAGGGACGGTTTGGGTCG 60.358 66.667 0.00 0.00 35.24 4.79
1439 4060 2.033602 CCAGGGACGGTTTGGGTC 59.966 66.667 0.00 0.00 0.00 4.46
1440 4061 1.647334 TTTCCAGGGACGGTTTGGGT 61.647 55.000 7.22 0.00 32.76 4.51
1441 4062 1.151908 TTTCCAGGGACGGTTTGGG 59.848 57.895 7.22 0.00 32.76 4.12
1442 4063 0.179001 AGTTTCCAGGGACGGTTTGG 60.179 55.000 0.00 2.06 0.00 3.28
1443 4064 1.336755 CAAGTTTCCAGGGACGGTTTG 59.663 52.381 0.00 0.00 0.00 2.93
1444 4065 1.687563 CAAGTTTCCAGGGACGGTTT 58.312 50.000 0.00 0.00 0.00 3.27
1445 4066 0.179001 CCAAGTTTCCAGGGACGGTT 60.179 55.000 0.00 0.00 0.00 4.44
1446 4067 1.350310 ACCAAGTTTCCAGGGACGGT 61.350 55.000 0.00 0.00 0.00 4.83
1447 4068 0.179001 AACCAAGTTTCCAGGGACGG 60.179 55.000 0.00 0.00 0.00 4.79
1448 4069 1.235724 GAACCAAGTTTCCAGGGACG 58.764 55.000 0.00 0.00 0.00 4.79
1449 4070 2.358322 TGAACCAAGTTTCCAGGGAC 57.642 50.000 0.00 0.00 0.00 4.46
1450 4071 3.295973 CTTTGAACCAAGTTTCCAGGGA 58.704 45.455 0.00 0.00 0.00 4.20
1451 4072 2.365293 CCTTTGAACCAAGTTTCCAGGG 59.635 50.000 0.00 0.00 0.00 4.45
1452 4073 2.224042 GCCTTTGAACCAAGTTTCCAGG 60.224 50.000 0.00 0.00 31.89 4.45
1453 4074 2.430332 TGCCTTTGAACCAAGTTTCCAG 59.570 45.455 0.00 0.00 0.00 3.86
1454 4075 2.461695 TGCCTTTGAACCAAGTTTCCA 58.538 42.857 0.00 0.00 0.00 3.53
1455 4076 3.554960 GGATGCCTTTGAACCAAGTTTCC 60.555 47.826 0.00 0.00 0.00 3.13
1456 4077 3.069443 TGGATGCCTTTGAACCAAGTTTC 59.931 43.478 0.00 0.00 0.00 2.78
1457 4078 3.037549 TGGATGCCTTTGAACCAAGTTT 58.962 40.909 0.00 0.00 0.00 2.66
1458 4079 2.365293 GTGGATGCCTTTGAACCAAGTT 59.635 45.455 0.00 0.00 32.32 2.66
1459 4080 1.963515 GTGGATGCCTTTGAACCAAGT 59.036 47.619 0.00 0.00 32.32 3.16
1465 4086 1.523154 GCACCGTGGATGCCTTTGAA 61.523 55.000 0.00 0.00 37.08 2.69
1496 4117 1.470805 CGATGTACTGAACCATGGCGA 60.471 52.381 13.04 0.00 0.00 5.54
1588 4211 0.176680 AGGCAGCAATGTAGACTCCG 59.823 55.000 0.00 0.00 0.00 4.63
1671 4301 6.073447 TCTTAAAATGAAGAGGCACCCATA 57.927 37.500 0.00 0.00 31.72 2.74
1677 4307 7.613022 ACATGAAGATCTTAAAATGAAGAGGCA 59.387 33.333 22.63 8.87 38.80 4.75
1686 4316 5.163478 GCCAGCCACATGAAGATCTTAAAAT 60.163 40.000 8.25 0.00 0.00 1.82
1688 4318 3.696051 GCCAGCCACATGAAGATCTTAAA 59.304 43.478 8.25 0.00 0.00 1.52
1731 4361 2.158623 TGGCACTCAAGTCTTTCCATGT 60.159 45.455 0.00 0.00 0.00 3.21
1744 4374 1.271840 GGGGTAGACCATGGCACTCA 61.272 60.000 13.04 0.00 42.91 3.41
1746 4376 1.229820 TGGGGTAGACCATGGCACT 60.230 57.895 13.04 14.20 42.91 4.40
1782 4412 2.833794 CTCTTCGGTTCTTGGTCACAA 58.166 47.619 0.00 0.00 34.87 3.33
1785 4415 0.756294 TGCTCTTCGGTTCTTGGTCA 59.244 50.000 0.00 0.00 0.00 4.02
1798 4431 4.686191 CCAAGAGGTGATCTATGCTCTT 57.314 45.455 0.00 0.00 37.23 2.85
1849 4539 3.058160 GCACCATGCGAGCACCTT 61.058 61.111 0.00 0.00 31.71 3.50
1907 4600 0.543749 GGTATCTTGCCACTGCTCCT 59.456 55.000 0.00 0.00 38.71 3.69
1912 4605 2.766263 TGACTAGGGTATCTTGCCACTG 59.234 50.000 0.00 0.00 0.00 3.66
1913 4606 3.116096 TGACTAGGGTATCTTGCCACT 57.884 47.619 0.00 0.00 0.00 4.00
2025 4722 2.716217 GATTGGTCAAGGAGGGTTCTG 58.284 52.381 0.00 0.00 0.00 3.02
2046 4743 0.795085 GATGCATGAGATGTAGGCGC 59.205 55.000 2.46 0.00 0.00 6.53
2048 4745 2.812591 CCTTGATGCATGAGATGTAGGC 59.187 50.000 2.46 0.00 0.00 3.93
2049 4746 4.063689 GTCCTTGATGCATGAGATGTAGG 58.936 47.826 2.46 0.00 0.00 3.18
2050 4747 3.739810 CGTCCTTGATGCATGAGATGTAG 59.260 47.826 2.46 0.00 0.00 2.74
2051 4748 3.384467 TCGTCCTTGATGCATGAGATGTA 59.616 43.478 2.46 0.00 0.00 2.29
2053 4750 2.830104 TCGTCCTTGATGCATGAGATG 58.170 47.619 2.46 0.78 0.00 2.90
2054 4751 3.464907 CTTCGTCCTTGATGCATGAGAT 58.535 45.455 2.46 0.00 0.00 2.75
2056 4753 1.329906 GCTTCGTCCTTGATGCATGAG 59.670 52.381 2.46 1.29 38.51 2.90
2057 4754 1.065926 AGCTTCGTCCTTGATGCATGA 60.066 47.619 2.46 0.00 40.43 3.07
2058 4755 1.329906 GAGCTTCGTCCTTGATGCATG 59.670 52.381 2.46 0.00 40.43 4.06
2059 4756 1.661341 GAGCTTCGTCCTTGATGCAT 58.339 50.000 0.00 0.00 40.43 3.96
2060 4757 0.737367 CGAGCTTCGTCCTTGATGCA 60.737 55.000 0.00 0.00 40.43 3.96
2061 4758 2.002127 CGAGCTTCGTCCTTGATGC 58.998 57.895 0.00 0.00 38.82 3.91
2150 4847 0.107654 CGAGAAGGGCCTTAGGGTTG 60.108 60.000 20.97 4.58 34.45 3.77
2165 4862 4.507916 CGGGAGAGAGGGGCGAGA 62.508 72.222 0.00 0.00 0.00 4.04
2180 4891 2.815211 CACACGACATGAGGCCGG 60.815 66.667 0.00 0.00 0.00 6.13
2187 4898 1.807139 TGGATCCAACACACGACATG 58.193 50.000 13.46 0.00 0.00 3.21
2188 4899 2.787473 ATGGATCCAACACACGACAT 57.213 45.000 20.67 0.00 0.00 3.06
2189 4900 2.565391 ACTATGGATCCAACACACGACA 59.435 45.455 20.67 0.00 0.00 4.35
2192 4903 2.168521 AGGACTATGGATCCAACACACG 59.831 50.000 20.67 6.17 38.86 4.49


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

AutoCloner maintained by Alex Coulton.