Multiple sequence alignment - TraesCS5B01G184800

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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 TraesCS5B01G184800 chr5B 100.000 5129 0 0 1 5129 335952473 335947345 0.000000e+00 9472
1 TraesCS5B01G184800 chr5A 91.799 2524 111 37 2673 5129 387406904 387404410 0.000000e+00 3426
2 TraesCS5B01G184800 chr5A 92.760 1837 62 17 864 2672 387408734 387406941 0.000000e+00 2590
3 TraesCS5B01G184800 chr5D 93.275 1844 47 22 864 2672 294428129 294426328 0.000000e+00 2647
4 TraesCS5B01G184800 chr5D 93.792 1482 45 14 2841 4276 294425950 294424470 0.000000e+00 2183
5 TraesCS5B01G184800 chr5D 89.894 851 40 20 4274 5115 294424430 294423617 0.000000e+00 1053
6 TraesCS5B01G184800 chr5D 93.678 174 0 2 2673 2835 294426291 294426118 3.070000e-62 250
7 TraesCS5B01G184800 chrUn 89.359 874 83 6 1 867 110693659 110694529 0.000000e+00 1090
8 TraesCS5B01G184800 chr7B 88.850 861 89 4 1 854 143250912 143251772 0.000000e+00 1051
9 TraesCS5B01G184800 chr7A 88.222 866 74 14 4 864 624638518 624639360 0.000000e+00 1009
10 TraesCS5B01G184800 chr7A 85.801 331 38 5 534 862 125914139 125913816 4.920000e-90 342
11 TraesCS5B01G184800 chr6A 89.362 752 73 4 117 863 583133067 583133816 0.000000e+00 939
12 TraesCS5B01G184800 chr6A 93.162 117 8 0 2 118 583132435 583132551 6.830000e-39 172
13 TraesCS5B01G184800 chr6A 77.957 186 30 10 2 184 583132374 583132551 7.020000e-19 106
14 TraesCS5B01G184800 chr2A 89.530 745 70 7 127 865 26882574 26881832 0.000000e+00 937
15 TraesCS5B01G184800 chr1B 86.223 871 99 15 2 863 42019770 42018912 0.000000e+00 924
16 TraesCS5B01G184800 chr1B 94.203 69 4 0 1 69 42020417 42020349 7.020000e-19 106
17 TraesCS5B01G184800 chr4A 84.018 876 101 19 1 867 294299145 294298300 0.000000e+00 806
18 TraesCS5B01G184800 chr7D 85.256 780 74 23 96 866 84325162 84324415 0.000000e+00 765
19 TraesCS5B01G184800 chr7D 86.290 248 26 5 2 242 84325406 84325160 3.940000e-66 263
20 TraesCS5B01G184800 chr2B 87.978 366 37 5 503 866 210710679 210710319 4.750000e-115 425


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 TraesCS5B01G184800 chr5B 335947345 335952473 5128 True 9472.000000 9472 100.00000 1 5129 1 chr5B.!!$R1 5128
1 TraesCS5B01G184800 chr5A 387404410 387408734 4324 True 3008.000000 3426 92.27950 864 5129 2 chr5A.!!$R1 4265
2 TraesCS5B01G184800 chr5D 294423617 294428129 4512 True 1533.250000 2647 92.65975 864 5115 4 chr5D.!!$R1 4251
3 TraesCS5B01G184800 chrUn 110693659 110694529 870 False 1090.000000 1090 89.35900 1 867 1 chrUn.!!$F1 866
4 TraesCS5B01G184800 chr7B 143250912 143251772 860 False 1051.000000 1051 88.85000 1 854 1 chr7B.!!$F1 853
5 TraesCS5B01G184800 chr7A 624638518 624639360 842 False 1009.000000 1009 88.22200 4 864 1 chr7A.!!$F1 860
6 TraesCS5B01G184800 chr6A 583132374 583133816 1442 False 405.666667 939 86.82700 2 863 3 chr6A.!!$F1 861
7 TraesCS5B01G184800 chr2A 26881832 26882574 742 True 937.000000 937 89.53000 127 865 1 chr2A.!!$R1 738
8 TraesCS5B01G184800 chr1B 42018912 42020417 1505 True 515.000000 924 90.21300 1 863 2 chr1B.!!$R1 862
9 TraesCS5B01G184800 chr4A 294298300 294299145 845 True 806.000000 806 84.01800 1 867 1 chr4A.!!$R1 866
10 TraesCS5B01G184800 chr7D 84324415 84325406 991 True 514.000000 765 85.77300 2 866 2 chr7D.!!$R1 864

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
399 1691 1.529948 CCATGGCGGCAGGAATGAT 60.530 57.895 26.15 0.00 0.00 2.45 F
1102 2424 0.251634 CTCAAAGCCCTCCAGTCCTC 59.748 60.000 0.00 0.00 0.00 3.71 F
1601 2928 0.377203 CCGGTAAAAATCGCAGGAGC 59.623 55.000 0.00 0.00 37.42 4.70 F
1613 2940 0.378610 GCAGGAGCGAAACTTATGCC 59.621 55.000 0.00 0.00 35.28 4.40 F
1615 2942 0.618458 AGGAGCGAAACTTATGCCCA 59.382 50.000 0.00 0.00 0.00 5.36 F
1616 2943 0.733150 GGAGCGAAACTTATGCCCAC 59.267 55.000 0.00 0.00 0.00 4.61 F
1617 2944 0.733150 GAGCGAAACTTATGCCCACC 59.267 55.000 0.00 0.00 0.00 4.61 F
3791 5374 0.888285 GGGCAGCTGCACTATGATCC 60.888 60.000 37.63 23.51 42.27 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 2943 0.179018 GATCCCATTCAGTTCCCCGG 60.179 60.000 0.00 0.0 0.00 5.73 R
2584 3948 2.736670 ATACCAAGCCCCACAGAATC 57.263 50.000 0.00 0.0 0.00 2.52 R
3176 4754 3.118629 GGTATGAGATGACCAGTGAAGCA 60.119 47.826 0.00 0.0 35.65 3.91 R
3350 4928 3.137533 ACAGAAGCAAAGAGTGAGAAGC 58.862 45.455 0.00 0.0 0.00 3.86 R
3699 5282 6.350110 GGCAGTTCATATTTAGCACCTGAAAA 60.350 38.462 0.00 0.0 0.00 2.29 R
3835 5418 0.535780 CAGGACACTTGAGCAAGGCA 60.536 55.000 14.14 0.0 42.53 4.75 R
3857 5440 4.883585 TCATTAATCAACCATGCTCCTGTC 59.116 41.667 0.00 0.0 0.00 3.51 R
4636 6309 2.169352 CCCTGCAGATAGTTGTGTAGCT 59.831 50.000 17.39 0.0 29.04 3.32 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
260 1550 2.048877 ACCTTTGTACGGTCGCGG 60.049 61.111 6.13 0.00 0.00 6.46
313 1604 4.084888 CCGGCCGAAACTCGTTGC 62.085 66.667 30.73 0.00 38.40 4.17
323 1614 2.434884 CTCGTTGCATCCAGGCGT 60.435 61.111 0.00 0.00 36.28 5.68
399 1691 1.529948 CCATGGCGGCAGGAATGAT 60.530 57.895 26.15 0.00 0.00 2.45
460 1753 5.654901 AGGAGGAGAAGAAAAAGAAAGGT 57.345 39.130 0.00 0.00 0.00 3.50
461 1754 5.626142 AGGAGGAGAAGAAAAAGAAAGGTC 58.374 41.667 0.00 0.00 0.00 3.85
462 1755 4.452795 GGAGGAGAAGAAAAAGAAAGGTCG 59.547 45.833 0.00 0.00 0.00 4.79
464 1757 3.058155 GGAGAAGAAAAAGAAAGGTCGGC 60.058 47.826 0.00 0.00 0.00 5.54
465 1758 2.548480 AGAAGAAAAAGAAAGGTCGGCG 59.452 45.455 0.00 0.00 0.00 6.46
467 1760 2.143925 AGAAAAAGAAAGGTCGGCGAG 58.856 47.619 11.20 0.00 0.00 5.03
521 1815 2.894126 GTCTCGGATGACCATAGACCAT 59.106 50.000 0.00 0.00 40.23 3.55
527 1821 3.648067 GGATGACCATAGACCATCAAGGA 59.352 47.826 0.00 0.00 38.65 3.36
583 1879 6.486056 TGATAAGCCCATTACCTGTTTGTTA 58.514 36.000 0.00 0.00 0.00 2.41
589 1885 5.641636 GCCCATTACCTGTTTGTTAAAATGG 59.358 40.000 0.00 0.00 40.89 3.16
593 1889 4.762289 ACCTGTTTGTTAAAATGGCCAA 57.238 36.364 10.96 0.00 0.00 4.52
650 1950 2.158127 TCACTTACAGGTGGGTCCCTTA 60.158 50.000 10.00 0.00 37.75 2.69
709 2009 2.765969 CTGACAGGTGGGCCCAAT 59.234 61.111 30.64 16.65 34.66 3.16
786 2087 7.281040 AGTCATTAAGCACATAATTGATGGG 57.719 36.000 0.00 0.00 42.47 4.00
808 2109 2.682155 TTTGTGCCCTGTCCAAAAAC 57.318 45.000 0.00 0.00 0.00 2.43
845 2146 1.697432 CCCTAACTCCAAGTGTGGTGA 59.303 52.381 2.02 0.00 46.11 4.02
952 2261 9.905713 TCTGATATAAGCAAGGTTTGATTTAGT 57.094 29.630 0.00 0.00 40.22 2.24
998 2317 5.479375 ACACTCCTATAAACGAAGACAGGAA 59.521 40.000 0.00 0.00 32.01 3.36
1097 2419 1.606531 CTCCCTCAAAGCCCTCCAG 59.393 63.158 0.00 0.00 0.00 3.86
1098 2420 1.151810 TCCCTCAAAGCCCTCCAGT 60.152 57.895 0.00 0.00 0.00 4.00
1099 2421 1.201429 TCCCTCAAAGCCCTCCAGTC 61.201 60.000 0.00 0.00 0.00 3.51
1100 2422 1.301293 CCTCAAAGCCCTCCAGTCC 59.699 63.158 0.00 0.00 0.00 3.85
1101 2423 1.204113 CCTCAAAGCCCTCCAGTCCT 61.204 60.000 0.00 0.00 0.00 3.85
1102 2424 0.251634 CTCAAAGCCCTCCAGTCCTC 59.748 60.000 0.00 0.00 0.00 3.71
1243 2565 3.265479 CAGATTTCCCCTCCTGTTCTTCT 59.735 47.826 0.00 0.00 0.00 2.85
1260 2582 3.259374 TCTTCTCTTTCTGCTTGATCCGT 59.741 43.478 0.00 0.00 0.00 4.69
1302 2624 1.126846 CGACAAGATTTCTGTGCGACC 59.873 52.381 0.00 0.00 0.00 4.79
1387 2709 2.094390 GGTGTAGATGGCGTCAGTTGTA 60.094 50.000 9.78 0.00 0.00 2.41
1391 2713 2.893637 AGATGGCGTCAGTTGTATGAC 58.106 47.619 9.78 0.00 45.01 3.06
1412 2734 2.679639 CGGGAATGGATTCTTGGTCGAA 60.680 50.000 0.00 0.00 37.00 3.71
1481 2808 6.017440 TCCAAGTTGAGTTATTTGTGTGTAGC 60.017 38.462 3.87 0.00 0.00 3.58
1534 2861 3.431725 GCGCCTTCGTGGAAAGGG 61.432 66.667 0.00 0.00 45.07 3.95
1535 2862 2.345991 CGCCTTCGTGGAAAGGGA 59.654 61.111 4.93 0.00 45.07 4.20
1536 2863 1.078426 CGCCTTCGTGGAAAGGGAT 60.078 57.895 4.93 0.00 45.07 3.85
1537 2864 0.676782 CGCCTTCGTGGAAAGGGATT 60.677 55.000 4.93 0.00 45.07 3.01
1538 2865 1.406341 CGCCTTCGTGGAAAGGGATTA 60.406 52.381 4.93 0.00 45.07 1.75
1539 2866 2.289565 GCCTTCGTGGAAAGGGATTAG 58.710 52.381 4.93 0.00 45.07 1.73
1540 2867 2.093128 GCCTTCGTGGAAAGGGATTAGA 60.093 50.000 4.93 0.00 45.07 2.10
1541 2868 3.798202 CCTTCGTGGAAAGGGATTAGAG 58.202 50.000 0.00 0.00 41.86 2.43
1542 2869 3.197983 CCTTCGTGGAAAGGGATTAGAGT 59.802 47.826 0.00 0.00 41.86 3.24
1543 2870 4.404715 CCTTCGTGGAAAGGGATTAGAGTA 59.595 45.833 0.00 0.00 41.86 2.59
1544 2871 5.452077 CCTTCGTGGAAAGGGATTAGAGTAG 60.452 48.000 0.00 0.00 41.86 2.57
1545 2872 3.958798 TCGTGGAAAGGGATTAGAGTAGG 59.041 47.826 0.00 0.00 0.00 3.18
1593 2920 3.926821 TTGAGTTGGCCGGTAAAAATC 57.073 42.857 1.90 4.88 0.00 2.17
1601 2928 0.377203 CCGGTAAAAATCGCAGGAGC 59.623 55.000 0.00 0.00 37.42 4.70
1612 2939 3.905900 GCAGGAGCGAAACTTATGC 57.094 52.632 0.00 0.00 34.31 3.14
1613 2940 0.378610 GCAGGAGCGAAACTTATGCC 59.621 55.000 0.00 0.00 35.28 4.40
1614 2941 1.017387 CAGGAGCGAAACTTATGCCC 58.983 55.000 0.00 0.00 0.00 5.36
1615 2942 0.618458 AGGAGCGAAACTTATGCCCA 59.382 50.000 0.00 0.00 0.00 5.36
1616 2943 0.733150 GGAGCGAAACTTATGCCCAC 59.267 55.000 0.00 0.00 0.00 4.61
1617 2944 0.733150 GAGCGAAACTTATGCCCACC 59.267 55.000 0.00 0.00 0.00 4.61
1618 2945 1.024579 AGCGAAACTTATGCCCACCG 61.025 55.000 0.00 0.00 0.00 4.94
1619 2946 1.988834 GCGAAACTTATGCCCACCGG 61.989 60.000 0.00 0.00 0.00 5.28
1714 3059 0.915364 AGATGGAGTTGCTTCCCCTC 59.085 55.000 0.97 0.00 36.35 4.30
1760 3105 6.371548 TGCTGAACTGGATTGTGTAACTATTC 59.628 38.462 0.00 0.00 38.04 1.75
1780 3125 1.066858 CAGTGGCGACAGGAGTGTAAT 60.067 52.381 0.00 0.00 44.46 1.89
1782 3127 2.829720 AGTGGCGACAGGAGTGTAATTA 59.170 45.455 0.00 0.00 44.46 1.40
1783 3128 3.119101 AGTGGCGACAGGAGTGTAATTAG 60.119 47.826 0.00 0.00 44.46 1.73
1785 3130 2.167900 GGCGACAGGAGTGTAATTAGGT 59.832 50.000 0.00 0.00 36.88 3.08
1787 3132 3.864003 GCGACAGGAGTGTAATTAGGTTC 59.136 47.826 0.00 0.00 36.88 3.62
1863 3208 6.289064 AGGACACTTTCTGACTTCGTTAATT 58.711 36.000 0.00 0.00 0.00 1.40
1884 3230 9.816787 TTAATTATAGTTTGGTGAAAGGAGGTT 57.183 29.630 0.00 0.00 0.00 3.50
2084 3431 1.019673 GATCCGACAGCATGCACAAT 58.980 50.000 21.98 1.03 42.53 2.71
2170 3517 4.256920 AGTTAGCATAGCAGTCAACAAGG 58.743 43.478 0.00 0.00 0.00 3.61
2247 3594 6.589907 TCTTGAAGGTTTCTGTTTTCTTTTGC 59.410 34.615 0.00 0.00 0.00 3.68
2373 3720 4.216257 GCAAGTTGAATACTGAAAGCTGGA 59.784 41.667 7.16 0.00 37.60 3.86
2390 3737 6.313519 AGCTGGAAACTATACAGGATTTGA 57.686 37.500 0.00 0.00 32.98 2.69
2573 3920 4.452455 CACAAGGACTAGGTTGTGCTAAAG 59.548 45.833 17.01 0.16 45.09 1.85
2584 3948 4.264380 GGTTGTGCTAAAGTGTTTTGAACG 59.736 41.667 0.00 0.00 0.00 3.95
2647 4011 3.751175 ACGTTTGGAACATGATGGTAGTG 59.249 43.478 0.00 0.00 39.30 2.74
3029 4606 7.187480 GCTAGGAAAGACGCCTTAAAATTTAG 58.813 38.462 0.00 0.00 36.96 1.85
3037 4614 8.803397 AGACGCCTTAAAATTTAGAGGTAAAT 57.197 30.769 16.74 5.05 40.04 1.40
3070 4647 6.515272 AATGGGAAGTTGTACAATGATGTC 57.485 37.500 12.26 5.20 41.05 3.06
3079 4657 7.001674 AGTTGTACAATGATGTCCCTGTTAAA 58.998 34.615 12.26 0.00 41.05 1.52
3136 4714 5.414454 ACTGTTTGTCTTTTGTCTTGCACTA 59.586 36.000 0.00 0.00 0.00 2.74
3198 4776 3.118629 TGCTTCACTGGTCATCTCATACC 60.119 47.826 0.00 0.00 36.24 2.73
3350 4928 1.278127 ACTATGGTGGTCGGAAAGGTG 59.722 52.381 0.00 0.00 0.00 4.00
3390 4969 6.944557 TCTGTCGTGTGTCTTTACATAATG 57.055 37.500 0.00 0.00 38.08 1.90
3641 5223 7.219484 TGAAAGAGGTTTGATTTTCCATCTC 57.781 36.000 0.00 0.00 0.00 2.75
3676 5259 4.339247 CCCACTCTTTCAACTGTTGTTCAT 59.661 41.667 19.12 0.63 33.52 2.57
3677 5260 5.530915 CCCACTCTTTCAACTGTTGTTCATA 59.469 40.000 19.12 0.00 33.52 2.15
3791 5374 0.888285 GGGCAGCTGCACTATGATCC 60.888 60.000 37.63 23.51 42.27 3.36
3835 5418 5.627499 TCGCTTCAGATGCTAAAAACAAT 57.373 34.783 6.72 0.00 0.00 2.71
3845 5428 3.069300 TGCTAAAAACAATGCCTTGCTCA 59.931 39.130 1.19 0.00 35.69 4.26
3857 5440 1.233019 CTTGCTCAAGTGTCCTGGTG 58.767 55.000 1.61 0.00 33.87 4.17
4014 5597 1.410153 GCATCCCCTAAATTGGTGCTG 59.590 52.381 0.00 0.00 0.00 4.41
4028 5629 3.334691 TGGTGCTGTTAGAAATCTTCGG 58.665 45.455 0.00 0.00 34.02 4.30
4049 5650 4.868734 CGGTATGGGTTAGAAACTTCAGAC 59.131 45.833 0.00 0.00 0.00 3.51
4111 5712 8.579850 AAGTATGGCAATACATTTCAGAAAGA 57.420 30.769 13.79 0.00 41.09 2.52
4114 5715 9.294030 GTATGGCAATACATTTCAGAAAGAAAG 57.706 33.333 6.35 0.00 38.77 2.62
4201 5824 0.177141 CCATGCATTGCCTCCTTTGG 59.823 55.000 6.12 0.46 0.00 3.28
4241 5866 7.360691 GGAATGTGATGTAGGAAATCATGATCG 60.361 40.741 9.06 0.00 36.49 3.69
4342 6009 3.618351 ACCATGCTACTAGTCGTACTGT 58.382 45.455 0.00 0.00 0.00 3.55
4343 6010 4.015084 ACCATGCTACTAGTCGTACTGTT 58.985 43.478 0.00 0.00 0.00 3.16
4353 6020 1.121378 TCGTACTGTTGTGTTCCCCA 58.879 50.000 0.00 0.00 0.00 4.96
4414 6087 6.258230 TCATGATCTGATGTTGGTTCAAAC 57.742 37.500 0.00 0.00 0.00 2.93
4422 6095 6.931281 TCTGATGTTGGTTCAAACTAAGAGAG 59.069 38.462 0.00 0.00 29.69 3.20
4425 6098 7.939039 TGATGTTGGTTCAAACTAAGAGAGAAT 59.061 33.333 0.00 0.00 29.69 2.40
4436 6109 4.651962 ACTAAGAGAGAATTACAGAGGCCC 59.348 45.833 0.00 0.00 0.00 5.80
4468 6141 2.807967 GCAGCACTGATTATTGGCGATA 59.192 45.455 0.81 0.00 0.00 2.92
4551 6224 7.921787 TCTGAAGAAACGTGCTATTTTTGTTA 58.078 30.769 0.00 0.00 0.00 2.41
4613 6286 2.743195 GCATCGAGCGTTTGAGTCT 58.257 52.632 0.00 0.00 0.00 3.24
4614 6287 1.909376 GCATCGAGCGTTTGAGTCTA 58.091 50.000 0.00 0.00 0.00 2.59
4615 6288 1.584308 GCATCGAGCGTTTGAGTCTAC 59.416 52.381 0.00 0.00 0.00 2.59
4616 6289 2.732597 GCATCGAGCGTTTGAGTCTACT 60.733 50.000 0.00 0.00 0.00 2.57
4617 6290 3.502920 CATCGAGCGTTTGAGTCTACTT 58.497 45.455 0.00 0.00 0.00 2.24
4618 6291 3.198863 TCGAGCGTTTGAGTCTACTTC 57.801 47.619 0.00 0.00 0.00 3.01
4619 6292 2.095364 TCGAGCGTTTGAGTCTACTTCC 60.095 50.000 0.00 0.00 0.00 3.46
4620 6293 2.251893 GAGCGTTTGAGTCTACTTCCG 58.748 52.381 0.00 0.00 0.00 4.30
4621 6294 1.884579 AGCGTTTGAGTCTACTTCCGA 59.115 47.619 0.00 0.00 0.00 4.55
4622 6295 2.095161 AGCGTTTGAGTCTACTTCCGAG 60.095 50.000 0.00 0.00 0.00 4.63
4623 6296 2.351544 GCGTTTGAGTCTACTTCCGAGT 60.352 50.000 0.00 0.00 39.97 4.18
4624 6297 3.120060 GCGTTTGAGTCTACTTCCGAGTA 60.120 47.826 0.00 0.00 37.33 2.59
4625 6298 4.438472 GCGTTTGAGTCTACTTCCGAGTAT 60.438 45.833 0.00 0.00 37.71 2.12
4626 6299 5.264712 CGTTTGAGTCTACTTCCGAGTATC 58.735 45.833 0.00 0.00 37.71 2.24
4627 6300 5.163784 CGTTTGAGTCTACTTCCGAGTATCA 60.164 44.000 0.00 0.00 37.71 2.15
4628 6301 6.458478 CGTTTGAGTCTACTTCCGAGTATCAT 60.458 42.308 0.00 0.00 37.71 2.45
4629 6302 6.378710 TTGAGTCTACTTCCGAGTATCATG 57.621 41.667 0.00 0.00 37.71 3.07
4630 6303 5.437946 TGAGTCTACTTCCGAGTATCATGT 58.562 41.667 0.00 0.00 37.71 3.21
4636 6309 8.350722 GTCTACTTCCGAGTATCATGTTAATGA 58.649 37.037 0.00 0.00 40.90 2.57
4644 6317 6.918022 CGAGTATCATGTTAATGAGCTACACA 59.082 38.462 0.00 0.00 45.88 3.72
4645 6318 7.435192 CGAGTATCATGTTAATGAGCTACACAA 59.565 37.037 0.00 0.00 45.88 3.33
4691 6364 9.299963 CAGTGAACAATTTCTGACAACAAAATA 57.700 29.630 0.00 0.00 32.36 1.40
4774 6448 2.364324 GGTACAATGAGATAGGCACGGA 59.636 50.000 0.00 0.00 0.00 4.69
4775 6449 3.006967 GGTACAATGAGATAGGCACGGAT 59.993 47.826 0.00 0.00 0.00 4.18
4776 6450 3.117491 ACAATGAGATAGGCACGGATG 57.883 47.619 0.00 0.00 0.00 3.51
4778 6452 3.134623 ACAATGAGATAGGCACGGATGAA 59.865 43.478 0.00 0.00 0.00 2.57
4780 6454 4.630644 ATGAGATAGGCACGGATGAATT 57.369 40.909 0.00 0.00 0.00 2.17
4781 6455 4.422073 TGAGATAGGCACGGATGAATTT 57.578 40.909 0.00 0.00 0.00 1.82
4782 6456 4.129380 TGAGATAGGCACGGATGAATTTG 58.871 43.478 0.00 0.00 0.00 2.32
4783 6457 2.880890 AGATAGGCACGGATGAATTTGC 59.119 45.455 0.00 0.00 0.00 3.68
4786 6460 1.895131 AGGCACGGATGAATTTGCTTT 59.105 42.857 0.00 0.00 35.24 3.51
4814 6488 9.082313 ACTGAAAATTCATAAATCAGTTCCAGT 57.918 29.630 1.13 0.00 46.22 4.00
4927 6602 5.154222 GCTAAAGATTTGAAACCTGAACCG 58.846 41.667 0.00 0.00 0.00 4.44
5051 6726 3.941483 CTCAAACCCCATGTACTCATGTC 59.059 47.826 7.30 0.00 46.99 3.06
5112 6787 4.522022 ACCTGAAGATTGAAAAGAAGCAGG 59.478 41.667 0.00 0.00 40.02 4.85
5121 6796 6.767524 TTGAAAAGAAGCAGGTTCTGTTAA 57.232 33.333 16.36 7.88 45.44 2.01
5122 6797 6.131544 TGAAAAGAAGCAGGTTCTGTTAAC 57.868 37.500 16.36 7.25 45.44 2.01
5123 6798 4.813296 AAAGAAGCAGGTTCTGTTAACG 57.187 40.909 15.65 0.00 45.44 3.18
5124 6799 3.470645 AGAAGCAGGTTCTGTTAACGT 57.529 42.857 14.23 0.00 44.41 3.99
5126 6801 3.560068 AGAAGCAGGTTCTGTTAACGTTG 59.440 43.478 14.23 0.00 44.41 4.10
5127 6802 2.914059 AGCAGGTTCTGTTAACGTTGT 58.086 42.857 11.99 0.00 33.43 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 1341 3.322466 CTGGGAGGACTTGGCCGT 61.322 66.667 0.00 0.00 0.00 5.68
243 1415 2.048877 CCGCGACCGTACAAAGGT 60.049 61.111 8.23 0.00 46.16 3.50
313 1604 1.068753 CCTCTGCTACGCCTGGATG 59.931 63.158 0.00 0.00 0.00 3.51
362 1653 0.526662 GATGAACTCGACCTCACCGT 59.473 55.000 0.00 0.00 0.00 4.83
399 1691 4.480115 TCTCTCTCAAACAGGACCAACTA 58.520 43.478 0.00 0.00 0.00 2.24
464 1757 3.847602 CTGCTGGAGCTCCCCTCG 61.848 72.222 29.95 15.95 41.71 4.63
465 1758 4.173924 GCTGCTGGAGCTCCCCTC 62.174 72.222 29.95 18.11 45.21 4.30
515 1809 1.949847 CTCGCCGTCCTTGATGGTCT 61.950 60.000 4.39 0.00 40.59 3.85
615 1915 8.017373 CACCTGTAAGTGACTCATTTGTTTATG 58.983 37.037 0.00 0.00 40.34 1.90
617 1917 6.485313 CCACCTGTAAGTGACTCATTTGTTTA 59.515 38.462 0.00 0.00 40.34 2.01
650 1950 4.202441 GTGGACAATATGCTGAGTTGGAT 58.798 43.478 0.00 0.00 0.00 3.41
786 2087 2.682155 TTTGGACAGGGCACAAAAAC 57.318 45.000 0.00 0.00 31.79 2.43
808 2109 9.543783 GGAGTTAGGGTAACAATTTAGTATCAG 57.456 37.037 0.00 0.00 41.07 2.90
867 2168 8.038944 AGAGTAACTGAAGCCGATAACATAAAA 58.961 33.333 0.00 0.00 0.00 1.52
868 2169 7.553334 AGAGTAACTGAAGCCGATAACATAAA 58.447 34.615 0.00 0.00 0.00 1.40
878 2179 7.137426 ACGTTATAATAGAGTAACTGAAGCCG 58.863 38.462 0.00 0.00 0.00 5.52
899 2200 4.312443 AGAACATCGGATACAACAACGTT 58.688 39.130 0.00 0.00 0.00 3.99
998 2317 7.394144 ACTGTATATCCCCTTTCATAAGCTT 57.606 36.000 3.48 3.48 0.00 3.74
1084 2406 1.544825 CGAGGACTGGAGGGCTTTGA 61.545 60.000 0.00 0.00 0.00 2.69
1243 2565 1.404181 CGGACGGATCAAGCAGAAAGA 60.404 52.381 0.00 0.00 0.00 2.52
1302 2624 0.887933 CCAAGAACCCAATTCCACGG 59.112 55.000 0.00 0.00 38.16 4.94
1387 2709 2.242196 ACCAAGAATCCATTCCCGTCAT 59.758 45.455 0.00 0.00 37.51 3.06
1391 2713 1.134521 TCGACCAAGAATCCATTCCCG 60.135 52.381 0.00 0.00 37.51 5.14
1412 2734 1.228552 AATTCCTGCCAAGCACGGT 60.229 52.632 0.00 0.00 33.79 4.83
1481 2808 1.745653 GCCAAGCCCTTAAGCAACTAG 59.254 52.381 0.00 0.00 34.23 2.57
1534 2861 7.177041 ACTCGACCAATAATCCCTACTCTAATC 59.823 40.741 0.00 0.00 0.00 1.75
1535 2862 7.011382 ACTCGACCAATAATCCCTACTCTAAT 58.989 38.462 0.00 0.00 0.00 1.73
1536 2863 6.371278 ACTCGACCAATAATCCCTACTCTAA 58.629 40.000 0.00 0.00 0.00 2.10
1537 2864 5.950023 ACTCGACCAATAATCCCTACTCTA 58.050 41.667 0.00 0.00 0.00 2.43
1538 2865 4.805744 ACTCGACCAATAATCCCTACTCT 58.194 43.478 0.00 0.00 0.00 3.24
1539 2866 5.163437 ACAACTCGACCAATAATCCCTACTC 60.163 44.000 0.00 0.00 0.00 2.59
1540 2867 4.715297 ACAACTCGACCAATAATCCCTACT 59.285 41.667 0.00 0.00 0.00 2.57
1541 2868 4.809426 CACAACTCGACCAATAATCCCTAC 59.191 45.833 0.00 0.00 0.00 3.18
1542 2869 4.712829 TCACAACTCGACCAATAATCCCTA 59.287 41.667 0.00 0.00 0.00 3.53
1543 2870 3.517901 TCACAACTCGACCAATAATCCCT 59.482 43.478 0.00 0.00 0.00 4.20
1544 2871 3.869065 TCACAACTCGACCAATAATCCC 58.131 45.455 0.00 0.00 0.00 3.85
1545 2872 6.258160 CAAATCACAACTCGACCAATAATCC 58.742 40.000 0.00 0.00 0.00 3.01
1601 2928 1.373590 CCCGGTGGGCATAAGTTTCG 61.374 60.000 0.00 0.00 35.35 3.46
1602 2929 2.489040 CCCGGTGGGCATAAGTTTC 58.511 57.895 0.00 0.00 35.35 2.78
1603 2930 4.755656 CCCGGTGGGCATAAGTTT 57.244 55.556 0.00 0.00 35.35 2.66
1613 2940 1.378514 CCATTCAGTTCCCCGGTGG 60.379 63.158 0.00 0.82 0.00 4.61
1614 2941 1.378514 CCCATTCAGTTCCCCGGTG 60.379 63.158 0.00 0.00 0.00 4.94
1615 2942 0.919289 ATCCCATTCAGTTCCCCGGT 60.919 55.000 0.00 0.00 0.00 5.28
1616 2943 0.179018 GATCCCATTCAGTTCCCCGG 60.179 60.000 0.00 0.00 0.00 5.73
1617 2944 0.546122 TGATCCCATTCAGTTCCCCG 59.454 55.000 0.00 0.00 0.00 5.73
1618 2945 3.319031 AATGATCCCATTCAGTTCCCC 57.681 47.619 0.00 0.00 38.57 4.81
1619 2946 4.026052 ACAAATGATCCCATTCAGTTCCC 58.974 43.478 0.00 0.00 41.84 3.97
1760 3105 0.317160 TTACACTCCTGTCGCCACTG 59.683 55.000 0.00 0.00 0.00 3.66
1799 3144 1.774110 TGCACACAGGGACAACAATT 58.226 45.000 0.00 0.00 0.00 2.32
1863 3208 8.153221 TCATAACCTCCTTTCACCAAACTATA 57.847 34.615 0.00 0.00 0.00 1.31
1884 3230 5.467035 TGTTCACACACTCACTGATCATA 57.533 39.130 0.00 0.00 0.00 2.15
2043 3390 5.639757 TCAAGAAACATTTGTCACACACAG 58.360 37.500 0.00 0.00 35.97 3.66
2084 3431 3.006247 TGCGTCATGTAGCAAAGCATAA 58.994 40.909 13.68 0.00 40.78 1.90
2170 3517 9.090692 AGAATGCAATGAATGTTAAAACTATGC 57.909 29.630 0.00 0.00 0.00 3.14
2373 3720 9.533831 ACAAGGAAATCAAATCCTGTATAGTTT 57.466 29.630 0.00 0.00 46.65 2.66
2411 3758 9.486497 CTGAATACATAGAATGCAACTCTACAT 57.514 33.333 10.24 5.55 0.00 2.29
2412 3759 7.439356 GCTGAATACATAGAATGCAACTCTACA 59.561 37.037 10.24 3.92 0.00 2.74
2573 3920 3.550030 CCCCACAGAATCGTTCAAAACAC 60.550 47.826 1.58 0.00 0.00 3.32
2584 3948 2.736670 ATACCAAGCCCCACAGAATC 57.263 50.000 0.00 0.00 0.00 2.52
2647 4011 6.683974 ATGATGCACAAGGACTTACATAAC 57.316 37.500 0.00 0.00 0.00 1.89
2953 4528 8.791675 CCACAAATATACACATTACATATGGCA 58.208 33.333 7.80 0.00 0.00 4.92
2954 4529 8.792633 ACCACAAATATACACATTACATATGGC 58.207 33.333 7.80 0.00 0.00 4.40
3029 4606 7.095695 TCCCATTCGATGAAAAATTTACCTC 57.904 36.000 0.00 0.00 0.00 3.85
3037 4614 5.782893 ACAACTTCCCATTCGATGAAAAA 57.217 34.783 0.00 0.00 0.00 1.94
3070 4647 7.940850 TCAAAAACTCATCTCTTTTAACAGGG 58.059 34.615 0.00 0.00 0.00 4.45
3079 4657 8.511604 TTTTCACTCTCAAAAACTCATCTCTT 57.488 30.769 0.00 0.00 0.00 2.85
3107 4685 3.509575 AGACAAAAGACAAACAGTGCCAA 59.490 39.130 0.00 0.00 0.00 4.52
3176 4754 3.118629 GGTATGAGATGACCAGTGAAGCA 60.119 47.826 0.00 0.00 35.65 3.91
3198 4776 8.199176 TGCATAAATGAAAAATAAGCCACATG 57.801 30.769 0.00 0.00 0.00 3.21
3350 4928 3.137533 ACAGAAGCAAAGAGTGAGAAGC 58.862 45.455 0.00 0.00 0.00 3.86
3699 5282 6.350110 GGCAGTTCATATTTAGCACCTGAAAA 60.350 38.462 0.00 0.00 0.00 2.29
3835 5418 0.535780 CAGGACACTTGAGCAAGGCA 60.536 55.000 14.14 0.00 42.53 4.75
3857 5440 4.883585 TCATTAATCAACCATGCTCCTGTC 59.116 41.667 0.00 0.00 0.00 3.51
4014 5597 7.495055 TCTAACCCATACCGAAGATTTCTAAC 58.505 38.462 0.00 0.00 0.00 2.34
4028 5629 5.875359 CCAGTCTGAAGTTTCTAACCCATAC 59.125 44.000 0.00 0.00 0.00 2.39
4049 5650 2.490328 ACAAAACATCAACGCACCAG 57.510 45.000 0.00 0.00 0.00 4.00
4201 5824 5.075858 TCACATTCCTCAATTTGCATTCC 57.924 39.130 0.00 0.00 0.00 3.01
4241 5866 0.931005 CTGCCGCCGTAAGATCTTTC 59.069 55.000 14.36 7.71 43.02 2.62
4286 5953 4.401519 CCTTCCAGAACATTTCAGCATCAT 59.598 41.667 0.00 0.00 0.00 2.45
4333 6000 1.202557 TGGGGAACACAACAGTACGAC 60.203 52.381 0.00 0.00 0.00 4.34
4335 6002 1.508632 CTGGGGAACACAACAGTACG 58.491 55.000 0.00 0.00 0.00 3.67
4414 6087 4.651503 TGGGCCTCTGTAATTCTCTCTTAG 59.348 45.833 4.53 0.00 0.00 2.18
4422 6095 2.789409 ACACTGGGCCTCTGTAATTC 57.211 50.000 4.53 0.00 0.00 2.17
4425 6098 2.173782 TGAAAACACTGGGCCTCTGTAA 59.826 45.455 4.53 0.00 0.00 2.41
4468 6141 4.572389 CAGACAAAGATTATAGCGCCACTT 59.428 41.667 2.29 0.00 0.00 3.16
4551 6224 4.044065 TGTTTCTGGATGTCCTACCCATTT 59.956 41.667 0.09 0.00 36.82 2.32
4610 6283 8.350722 TCATTAACATGATACTCGGAAGTAGAC 58.649 37.037 0.00 0.00 41.22 2.59
4611 6284 8.459911 TCATTAACATGATACTCGGAAGTAGA 57.540 34.615 0.00 0.00 41.22 2.59
4612 6285 7.327275 GCTCATTAACATGATACTCGGAAGTAG 59.673 40.741 0.00 0.00 41.22 2.57
4613 6286 7.014326 AGCTCATTAACATGATACTCGGAAGTA 59.986 37.037 0.00 0.00 42.10 2.24
4614 6287 5.986135 GCTCATTAACATGATACTCGGAAGT 59.014 40.000 0.00 0.00 38.81 3.01
4615 6288 6.219473 AGCTCATTAACATGATACTCGGAAG 58.781 40.000 0.00 0.00 38.81 3.46
4616 6289 6.161855 AGCTCATTAACATGATACTCGGAA 57.838 37.500 0.00 0.00 38.81 4.30
4617 6290 5.791336 AGCTCATTAACATGATACTCGGA 57.209 39.130 0.00 0.00 38.81 4.55
4618 6291 6.363626 GTGTAGCTCATTAACATGATACTCGG 59.636 42.308 0.00 0.00 38.81 4.63
4619 6292 6.918022 TGTGTAGCTCATTAACATGATACTCG 59.082 38.462 0.00 0.00 38.81 4.18
4620 6293 8.543774 GTTGTGTAGCTCATTAACATGATACTC 58.456 37.037 0.00 0.00 38.81 2.59
4621 6294 8.260818 AGTTGTGTAGCTCATTAACATGATACT 58.739 33.333 0.00 0.00 38.81 2.12
4622 6295 8.425577 AGTTGTGTAGCTCATTAACATGATAC 57.574 34.615 0.00 0.00 38.81 2.24
4624 6297 9.265901 GATAGTTGTGTAGCTCATTAACATGAT 57.734 33.333 0.00 0.00 38.81 2.45
4625 6298 8.478066 AGATAGTTGTGTAGCTCATTAACATGA 58.522 33.333 0.00 0.00 37.05 3.07
4626 6299 8.546244 CAGATAGTTGTGTAGCTCATTAACATG 58.454 37.037 0.00 0.00 32.39 3.21
4627 6300 7.225538 GCAGATAGTTGTGTAGCTCATTAACAT 59.774 37.037 0.00 0.00 32.39 2.71
4628 6301 6.535150 GCAGATAGTTGTGTAGCTCATTAACA 59.465 38.462 0.00 0.00 32.39 2.41
4629 6302 6.535150 TGCAGATAGTTGTGTAGCTCATTAAC 59.465 38.462 0.00 0.00 0.00 2.01
4630 6303 6.639563 TGCAGATAGTTGTGTAGCTCATTAA 58.360 36.000 0.00 0.00 0.00 1.40
4636 6309 2.169352 CCCTGCAGATAGTTGTGTAGCT 59.831 50.000 17.39 0.00 29.04 3.32
4691 6364 4.655649 TGCAGAATATCACCCTAGATGTGT 59.344 41.667 10.84 3.74 35.25 3.72
5051 6726 2.941064 ACATGATTCACAAGATGGAGCG 59.059 45.455 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.