Multiple sequence alignment - TraesCS4B01G210300

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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 TraesCS4B01G210300 chr4B 100.000 4140 0 0 1 4140 449013346 449017485 0.000000e+00 7646.0
1 TraesCS4B01G210300 chr4D 91.798 2341 66 39 901 3143 363661535 363663847 0.000000e+00 3144.0
2 TraesCS4B01G210300 chr4D 90.427 867 38 13 4 827 363660649 363661513 0.000000e+00 1099.0
3 TraesCS4B01G210300 chr4D 93.072 332 16 3 3543 3874 363664040 363664364 2.900000e-131 479.0
4 TraesCS4B01G210300 chr4D 93.033 244 11 3 3901 4139 363664361 363664603 6.580000e-93 351.0
5 TraesCS4B01G210300 chr4D 92.754 138 8 1 3136 3271 363663879 363664016 9.080000e-47 198.0
6 TraesCS4B01G210300 chr4A 93.133 1500 42 24 1684 3139 101758557 101757075 0.000000e+00 2143.0
7 TraesCS4B01G210300 chr4A 87.841 1283 73 40 1 1230 101760138 101758886 0.000000e+00 1428.0
8 TraesCS4B01G210300 chr4A 87.888 322 21 6 1371 1677 101758828 101758510 3.040000e-96 363.0
9 TraesCS4B01G210300 chr2B 88.406 207 19 4 3272 3473 693065388 693065594 1.150000e-60 244.0
10 TraesCS4B01G210300 chr2B 89.157 83 8 1 1678 1760 617066138 617066219 7.320000e-18 102.0
11 TraesCS4B01G210300 chrUn 87.204 211 23 4 3272 3478 138271934 138272144 1.920000e-58 237.0
12 TraesCS4B01G210300 chrUn 87.204 211 23 4 3272 3478 138484730 138484940 1.920000e-58 237.0
13 TraesCS4B01G210300 chr1B 85.714 231 26 4 3272 3495 121731949 121731719 1.920000e-58 237.0
14 TraesCS4B01G210300 chr1D 87.081 209 24 3 3272 3477 71764438 71764230 2.490000e-57 233.0
15 TraesCS4B01G210300 chr6A 86.730 211 24 4 3271 3477 542704863 542705073 8.950000e-57 231.0
16 TraesCS4B01G210300 chr6A 86.730 211 24 4 3272 3478 558457705 558457495 8.950000e-57 231.0
17 TraesCS4B01G210300 chr6A 86.730 211 24 4 3272 3478 558461025 558460815 8.950000e-57 231.0
18 TraesCS4B01G210300 chr2A 85.650 223 28 3 3264 3482 6095375 6095597 8.950000e-57 231.0
19 TraesCS4B01G210300 chr3B 87.826 115 14 0 1090 1204 623149141 623149255 7.220000e-28 135.0
20 TraesCS4B01G210300 chr3A 86.179 123 15 2 1090 1212 611701037 611701157 9.340000e-27 132.0
21 TraesCS4B01G210300 chr3D 86.957 115 15 0 1090 1204 469153488 469153602 3.360000e-26 130.0
22 TraesCS4B01G210300 chr3D 89.157 83 8 1 1678 1760 94126282 94126363 7.320000e-18 102.0
23 TraesCS4B01G210300 chr7D 88.372 86 9 1 1678 1763 529901732 529901648 7.320000e-18 102.0
24 TraesCS4B01G210300 chr7D 93.750 48 3 0 1532 1579 6589668 6589715 5.740000e-09 73.1
25 TraesCS4B01G210300 chr7A 91.667 48 4 0 1532 1579 7672337 7672384 2.670000e-07 67.6
26 TraesCS4B01G210300 chr7A 100.000 29 0 0 1853 1881 729645357 729645385 2.000000e-03 54.7


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 TraesCS4B01G210300 chr4B 449013346 449017485 4139 False 7646.000000 7646 100.000000 1 4140 1 chr4B.!!$F1 4139
1 TraesCS4B01G210300 chr4D 363660649 363664603 3954 False 1054.200000 3144 92.216800 4 4139 5 chr4D.!!$F1 4135
2 TraesCS4B01G210300 chr4A 101757075 101760138 3063 True 1311.333333 2143 89.620667 1 3139 3 chr4A.!!$R1 3138
3 TraesCS4B01G210300 chr6A 558457495 558461025 3530 True 231.000000 231 86.730000 3272 3478 2 chr6A.!!$R1 206

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
698 768 0.251341 AAAGGACCATCGGCTGCTTT 60.251 50.0 0.0 0.0 0.0 3.51 F
1301 1412 0.039911 ACTAAGGCACGAGGAGAGGT 59.960 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2184 0.450583 GGTACTCGCTGATCACGTCA 59.549 55.0 14.43 0.0 35.05 4.35 R
3229 3484 0.034337 TGCTCCCGTAACCACAACTC 59.966 55.0 0.00 0.0 0.00 3.01 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
17 18 4.779819 GAGGTACGTACGCACCTG 57.220 61.111 38.24 3.14 45.32 4.00
19 20 2.203972 GAGGTACGTACGCACCTGCA 62.204 60.000 38.24 3.85 45.32 4.41
20 21 1.804326 GGTACGTACGCACCTGCAG 60.804 63.158 26.98 6.78 42.21 4.41
163 194 2.039624 ATGGGTGGCGAGAGAGGT 59.960 61.111 0.00 0.00 0.00 3.85
164 195 1.043116 CATGGGTGGCGAGAGAGGTA 61.043 60.000 0.00 0.00 0.00 3.08
166 197 1.380112 GGGTGGCGAGAGAGGTAGT 60.380 63.158 0.00 0.00 0.00 2.73
183 214 0.834612 AGTGGTTTGGTTCCTCGACA 59.165 50.000 0.00 0.00 0.00 4.35
189 220 2.029964 GGTTCCTCGACACGGCAA 59.970 61.111 0.00 0.00 0.00 4.52
285 316 0.738412 CTTACGTGCGGGGTTAGGTG 60.738 60.000 0.00 0.00 0.00 4.00
291 322 3.327404 CGGGGTTAGGTGGGTGCT 61.327 66.667 0.00 0.00 0.00 4.40
294 325 2.288025 GGGTTAGGTGGGTGCTCGA 61.288 63.158 0.00 0.00 0.00 4.04
344 375 1.066114 CGTCTTTGCTCGTCTCGTCC 61.066 60.000 0.00 0.00 0.00 4.79
542 579 1.156736 AGCAACACGACAGCAATACC 58.843 50.000 0.00 0.00 0.00 2.73
597 639 4.342862 AGGTTGATAGATGGACGGATTG 57.657 45.455 0.00 0.00 0.00 2.67
616 665 1.674322 GGCTTAAAGTGGAGCGGCA 60.674 57.895 1.45 0.00 39.78 5.69
617 666 1.032114 GGCTTAAAGTGGAGCGGCAT 61.032 55.000 1.45 0.00 39.78 4.40
620 669 1.667724 CTTAAAGTGGAGCGGCATCTG 59.332 52.381 1.45 0.00 0.00 2.90
671 741 2.753247 GTCTTCCTCCTCACCCACTAT 58.247 52.381 0.00 0.00 0.00 2.12
672 742 3.687551 CGTCTTCCTCCTCACCCACTATA 60.688 52.174 0.00 0.00 0.00 1.31
691 761 2.710096 ACCACATAAAGGACCATCGG 57.290 50.000 0.00 0.00 0.00 4.18
698 768 0.251341 AAAGGACCATCGGCTGCTTT 60.251 50.000 0.00 0.00 0.00 3.51
700 770 2.115291 GGACCATCGGCTGCTTTCC 61.115 63.158 0.00 0.00 0.00 3.13
827 918 5.445010 CGTTTTGGGCTTTCGTATGTACTAC 60.445 44.000 0.00 0.00 0.00 2.73
828 919 5.410355 TTTGGGCTTTCGTATGTACTACT 57.590 39.130 0.00 0.00 0.00 2.57
829 920 6.528537 TTTGGGCTTTCGTATGTACTACTA 57.471 37.500 0.00 0.00 0.00 1.82
830 921 5.762825 TGGGCTTTCGTATGTACTACTAG 57.237 43.478 0.00 0.00 0.00 2.57
831 922 5.195940 TGGGCTTTCGTATGTACTACTAGT 58.804 41.667 0.00 0.00 0.00 2.57
832 923 5.297776 TGGGCTTTCGTATGTACTACTAGTC 59.702 44.000 0.00 0.00 0.00 2.59
833 924 5.438972 GGCTTTCGTATGTACTACTAGTCG 58.561 45.833 0.00 0.00 0.00 4.18
834 925 5.007136 GGCTTTCGTATGTACTACTAGTCGT 59.993 44.000 0.00 0.95 0.00 4.34
835 926 6.201044 GGCTTTCGTATGTACTACTAGTCGTA 59.799 42.308 0.00 0.00 0.00 3.43
836 927 7.254455 GGCTTTCGTATGTACTACTAGTCGTAA 60.254 40.741 8.70 1.52 0.00 3.18
837 928 7.580882 GCTTTCGTATGTACTACTAGTCGTAAC 59.419 40.741 8.70 3.88 0.00 2.50
838 929 8.474006 TTTCGTATGTACTACTAGTCGTAACA 57.526 34.615 8.70 9.59 0.00 2.41
839 930 8.474006 TTCGTATGTACTACTAGTCGTAACAA 57.526 34.615 8.70 0.00 0.00 2.83
840 931 8.120030 TCGTATGTACTACTAGTCGTAACAAG 57.880 38.462 8.70 0.00 0.00 3.16
841 932 7.973944 TCGTATGTACTACTAGTCGTAACAAGA 59.026 37.037 8.70 8.17 0.00 3.02
842 933 8.265315 CGTATGTACTACTAGTCGTAACAAGAG 58.735 40.741 8.70 0.00 0.00 2.85
843 934 9.092876 GTATGTACTACTAGTCGTAACAAGAGT 57.907 37.037 8.70 2.07 0.00 3.24
849 940 6.512342 ACTAGTCGTAACAAGAGTATGCTT 57.488 37.500 0.00 0.00 0.00 3.91
858 949 8.869897 CGTAACAAGAGTATGCTTCTTGAATTA 58.130 33.333 20.96 12.08 42.29 1.40
875 971 3.887335 TACCCGTGCAAACTCCCGC 62.887 63.158 0.00 0.00 0.00 6.13
880 976 2.203337 TGCAAACTCCCGCTGCTT 60.203 55.556 0.00 0.00 37.00 3.91
882 978 1.968540 GCAAACTCCCGCTGCTTCT 60.969 57.895 0.00 0.00 33.20 2.85
1001 1104 1.152419 TCCGACCCTCTGTGACCAA 60.152 57.895 0.00 0.00 0.00 3.67
1002 1105 0.544357 TCCGACCCTCTGTGACCAAT 60.544 55.000 0.00 0.00 0.00 3.16
1018 1121 4.141779 TGACCAATGAGTCTGGATCAGATG 60.142 45.833 5.46 0.00 42.73 2.90
1019 1122 4.035814 ACCAATGAGTCTGGATCAGATGA 58.964 43.478 5.46 0.00 42.73 2.92
1020 1123 4.101274 ACCAATGAGTCTGGATCAGATGAG 59.899 45.833 5.46 0.00 42.73 2.90
1021 1124 4.344390 CCAATGAGTCTGGATCAGATGAGA 59.656 45.833 0.72 0.00 42.73 3.27
1022 1125 5.012251 CCAATGAGTCTGGATCAGATGAGAT 59.988 44.000 0.72 0.00 42.73 2.75
1074 1185 1.064758 TGCAGTTTCACAGGGTTGAGT 60.065 47.619 0.00 0.00 0.00 3.41
1126 1237 2.124695 GTGGGAGGATTCGGCACC 60.125 66.667 0.00 0.00 0.00 5.01
1212 1323 2.625737 CCTGCATCAGGTCAGTACAAG 58.374 52.381 4.74 0.00 45.82 3.16
1259 1370 8.534333 TCTATATGCTTTAAGTTATTCAGGCG 57.466 34.615 0.00 0.00 0.00 5.52
1278 1389 9.826574 TTCAGGCGAAATAATATTTACTACTGT 57.173 29.630 0.00 0.00 0.00 3.55
1301 1412 0.039911 ACTAAGGCACGAGGAGAGGT 59.960 55.000 0.00 0.00 0.00 3.85
1383 1510 7.827236 CACCTGATTATTTACCTGTGGAGTTTA 59.173 37.037 0.00 0.00 0.00 2.01
1384 1511 7.827729 ACCTGATTATTTACCTGTGGAGTTTAC 59.172 37.037 0.00 0.00 0.00 2.01
1393 1520 5.570320 ACCTGTGGAGTTTACTTATGCAAT 58.430 37.500 0.00 0.00 0.00 3.56
1445 1572 4.747108 GTCCATGTGAATAGATTCCTCACG 59.253 45.833 0.00 0.00 41.94 4.35
1666 1810 0.102120 CACCAGATCGAGGCTCTGAC 59.898 60.000 14.66 3.42 42.22 3.51
1678 1822 2.376518 AGGCTCTGACAGATTTGGGAAA 59.623 45.455 5.42 0.00 0.00 3.13
1733 1900 2.290577 GGCTCTGAAAGATGTGGGAGTT 60.291 50.000 0.00 0.00 45.62 3.01
1748 1915 4.282703 GTGGGAGTTACAGAAGTTGTCCTA 59.717 45.833 0.00 0.00 41.29 2.94
1783 1950 1.952296 GCCAGAGGTAATTGAGCATGG 59.048 52.381 0.00 0.00 37.59 3.66
1840 2007 5.362143 CAGAATCCCAGATCTCACTGTCTTA 59.638 44.000 0.00 0.00 36.30 2.10
1849 2016 4.336889 TCTCACTGTCTTACTTTGGTGG 57.663 45.455 0.00 0.00 0.00 4.61
2017 2184 2.807108 GCCTTTCTTCGTCCTCAACAGT 60.807 50.000 0.00 0.00 0.00 3.55
2109 2276 1.053424 ATGGTCACCAAGGTACGTGT 58.947 50.000 0.00 0.00 36.95 4.49
2128 2303 2.486982 TGTGCCTAGTCACGAGTAGAAC 59.513 50.000 9.98 8.44 39.73 3.01
2190 2369 6.602179 TGAGAAATGTCGCTACTTTGATTTG 58.398 36.000 0.00 0.00 0.00 2.32
2191 2370 5.942872 AGAAATGTCGCTACTTTGATTTGG 58.057 37.500 0.00 0.00 0.00 3.28
2192 2371 5.473504 AGAAATGTCGCTACTTTGATTTGGT 59.526 36.000 0.00 0.00 0.00 3.67
2556 2740 2.031919 CTGGGCAACGTGCTGGTA 59.968 61.111 9.31 0.00 44.28 3.25
2875 3059 1.664302 CCGAGATCGTCATGTGATCGG 60.664 57.143 18.43 16.20 45.44 4.18
2951 3164 6.767524 TTGTTGGTTTATTTGTCTGTCTGT 57.232 33.333 0.00 0.00 0.00 3.41
2952 3165 6.371809 TGTTGGTTTATTTGTCTGTCTGTC 57.628 37.500 0.00 0.00 0.00 3.51
2953 3166 6.119536 TGTTGGTTTATTTGTCTGTCTGTCT 58.880 36.000 0.00 0.00 0.00 3.41
2954 3167 6.038161 TGTTGGTTTATTTGTCTGTCTGTCTG 59.962 38.462 0.00 0.00 0.00 3.51
2970 3183 2.224281 TGTCTGCAAGTGTAACCAGAGG 60.224 50.000 0.00 0.00 34.17 3.69
2976 3189 2.097110 AGTGTAACCAGAGGTGTCCA 57.903 50.000 0.00 0.00 37.80 4.02
2999 3212 3.820467 CCAAACTGCCAAGTGTCTATCAA 59.180 43.478 0.00 0.00 36.51 2.57
3013 3226 7.881142 AGTGTCTATCAAGCTCTATGTATGTC 58.119 38.462 0.00 0.00 0.00 3.06
3114 3328 6.763135 TCAATTTGTAGATAGGTGTCAGATGC 59.237 38.462 0.00 0.00 0.00 3.91
3229 3484 1.337821 GTCGTACTGCGTTCTTCTGG 58.662 55.000 0.00 0.00 42.13 3.86
3234 3489 1.871080 ACTGCGTTCTTCTGGAGTTG 58.129 50.000 0.00 0.00 32.44 3.16
3241 3496 3.493503 CGTTCTTCTGGAGTTGTGGTTAC 59.506 47.826 0.00 0.00 0.00 2.50
3253 3508 1.349688 TGTGGTTACGGGAGCATTTCT 59.650 47.619 0.00 0.00 0.00 2.52
3262 3517 2.094545 CGGGAGCATTTCTTTTTCCAGG 60.095 50.000 0.00 0.00 0.00 4.45
3263 3518 2.899900 GGGAGCATTTCTTTTTCCAGGT 59.100 45.455 0.00 0.00 0.00 4.00
3264 3519 3.324846 GGGAGCATTTCTTTTTCCAGGTT 59.675 43.478 0.00 0.00 0.00 3.50
3265 3520 4.202357 GGGAGCATTTCTTTTTCCAGGTTT 60.202 41.667 0.00 0.00 0.00 3.27
3266 3521 4.751600 GGAGCATTTCTTTTTCCAGGTTTG 59.248 41.667 0.00 0.00 0.00 2.93
3267 3522 4.707105 AGCATTTCTTTTTCCAGGTTTGG 58.293 39.130 0.00 0.00 46.49 3.28
3268 3523 4.164030 AGCATTTCTTTTTCCAGGTTTGGT 59.836 37.500 0.00 0.00 45.26 3.67
3269 3524 5.365314 AGCATTTCTTTTTCCAGGTTTGGTA 59.635 36.000 0.00 0.00 45.26 3.25
3270 3525 6.043127 AGCATTTCTTTTTCCAGGTTTGGTAT 59.957 34.615 0.00 0.00 45.26 2.73
3279 3534 1.211949 CAGGTTTGGTATGGATCCGGT 59.788 52.381 7.39 0.50 0.00 5.28
3283 3538 2.425668 GTTTGGTATGGATCCGGTTTGG 59.574 50.000 7.39 0.00 40.09 3.28
3304 3559 2.040043 CTCCCTCCCCATGCTCCT 60.040 66.667 0.00 0.00 0.00 3.69
3307 3562 0.271927 TCCCTCCCCATGCTCCTATT 59.728 55.000 0.00 0.00 0.00 1.73
3336 3591 2.028476 CCACTTCATCCTACGGTTGTCA 60.028 50.000 0.00 0.00 0.00 3.58
3343 3598 5.556915 TCATCCTACGGTTGTCATTTTTCT 58.443 37.500 0.00 0.00 0.00 2.52
3387 3646 4.844349 CCTCCTGATTTTAAGGGAGTGA 57.156 45.455 0.00 0.00 42.56 3.41
3393 3652 1.354101 TTTTAAGGGAGTGAGGCCGA 58.646 50.000 0.00 0.00 0.00 5.54
3394 3653 0.902531 TTTAAGGGAGTGAGGCCGAG 59.097 55.000 0.00 0.00 0.00 4.63
3395 3654 0.252103 TTAAGGGAGTGAGGCCGAGT 60.252 55.000 0.00 0.00 0.00 4.18
3396 3655 0.252103 TAAGGGAGTGAGGCCGAGTT 60.252 55.000 0.00 0.00 0.00 3.01
3404 3663 4.939439 GGAGTGAGGCCGAGTTTTATTTTA 59.061 41.667 0.00 0.00 0.00 1.52
3407 3666 7.362660 GGAGTGAGGCCGAGTTTTATTTTATTT 60.363 37.037 0.00 0.00 0.00 1.40
3425 3684 8.899427 TTTTATTTCAATCAAATCAAGCCACA 57.101 26.923 0.00 0.00 36.09 4.17
3453 3712 1.059369 GCACAGATAAGCACACGCG 59.941 57.895 3.53 3.53 45.49 6.01
3454 3713 1.351430 GCACAGATAAGCACACGCGA 61.351 55.000 15.93 0.00 45.49 5.87
3455 3714 1.067693 CACAGATAAGCACACGCGAA 58.932 50.000 15.93 0.00 45.49 4.70
3468 3727 2.672996 GCGAAGGGAGCAGGCAAA 60.673 61.111 0.00 0.00 34.19 3.68
3473 3732 0.700564 AAGGGAGCAGGCAAATCTCA 59.299 50.000 0.00 0.00 0.00 3.27
3501 3760 0.863119 GTATACCGTCCACGTCACGC 60.863 60.000 10.46 0.00 35.87 5.34
3518 3777 4.436998 CGGACCGTGGACTCAGCC 62.437 72.222 5.48 0.00 0.00 4.85
3519 3778 3.311110 GGACCGTGGACTCAGCCA 61.311 66.667 0.00 0.00 35.02 4.75
3526 3785 1.524961 TGGACTCAGCCACACGTTT 59.475 52.632 0.00 0.00 31.66 3.60
3527 3786 0.107410 TGGACTCAGCCACACGTTTT 60.107 50.000 0.00 0.00 31.66 2.43
3528 3787 1.021968 GGACTCAGCCACACGTTTTT 58.978 50.000 0.00 0.00 0.00 1.94
3561 3820 1.568025 GACTCGGCCACGTTTTCAC 59.432 57.895 2.24 0.00 41.85 3.18
3671 3930 0.604780 GCAGTCTGTGATGGTGCAGT 60.605 55.000 0.93 0.00 34.18 4.40
3684 3943 1.541233 GGTGCAGTGCAAGTCAGTAGT 60.541 52.381 21.67 0.00 41.47 2.73
3686 3945 2.731976 GTGCAGTGCAAGTCAGTAGTAC 59.268 50.000 21.67 0.00 41.47 2.73
3687 3946 2.364002 TGCAGTGCAAGTCAGTAGTACA 59.636 45.455 17.26 0.00 34.76 2.90
3689 3948 3.997021 GCAGTGCAAGTCAGTAGTACAAT 59.003 43.478 11.09 0.00 0.00 2.71
3690 3949 5.168569 GCAGTGCAAGTCAGTAGTACAATA 58.831 41.667 11.09 0.00 0.00 1.90
3691 3950 5.062308 GCAGTGCAAGTCAGTAGTACAATAC 59.938 44.000 11.09 0.00 0.00 1.89
3728 3987 3.318275 ACACCGATCGTTAGCTGTATGAT 59.682 43.478 15.09 0.29 0.00 2.45
3770 4029 5.258622 CGGAGCATAGAAAAATTCAGAACG 58.741 41.667 0.00 0.00 0.00 3.95
3816 4075 1.779569 ACTTTAACCAGAGTCGCGTG 58.220 50.000 5.77 0.00 0.00 5.34
3818 4077 1.455786 CTTTAACCAGAGTCGCGTGTG 59.544 52.381 5.77 0.00 0.00 3.82
3840 4099 2.107950 TTAGTTTCTGGATGGTGGCG 57.892 50.000 0.00 0.00 0.00 5.69
3852 4111 2.045926 GTGGCGAGGCTTCCATGT 60.046 61.111 11.74 0.00 34.47 3.21
3855 4114 2.268920 GCGAGGCTTCCATGTCCA 59.731 61.111 0.00 0.00 0.00 4.02
3859 4118 1.202463 CGAGGCTTCCATGTCCAGTAG 60.202 57.143 0.00 0.00 0.00 2.57
3871 4130 8.958119 TCCATGTCCAGTAGTATAATTTTGTC 57.042 34.615 0.00 0.00 0.00 3.18
3873 4132 7.228706 CCATGTCCAGTAGTATAATTTTGTCCC 59.771 40.741 0.00 0.00 0.00 4.46
3876 4135 7.037873 TGTCCAGTAGTATAATTTTGTCCCTGT 60.038 37.037 0.00 0.00 0.00 4.00
3878 4137 6.479001 CCAGTAGTATAATTTTGTCCCTGTCG 59.521 42.308 0.00 0.00 0.00 4.35
3884 4143 1.305201 TTTTGTCCCTGTCGAACTGC 58.695 50.000 0.00 0.00 0.00 4.40
3885 4144 0.468226 TTTGTCCCTGTCGAACTGCT 59.532 50.000 0.00 0.00 0.00 4.24
3890 4149 1.001633 TCCCTGTCGAACTGCTAAACC 59.998 52.381 0.00 0.00 0.00 3.27
3892 4151 0.438830 CTGTCGAACTGCTAAACCGC 59.561 55.000 0.00 0.00 0.00 5.68
3898 4157 0.955919 AACTGCTAAACCGCTCCTGC 60.956 55.000 0.00 0.00 0.00 4.85
3899 4158 2.046314 TGCTAAACCGCTCCTGCC 60.046 61.111 0.00 0.00 35.36 4.85
3978 4315 2.031012 CGACAGCAGGGCACTTGA 59.969 61.111 0.00 0.00 0.00 3.02
4015 5015 2.413453 GCTGGATTCAGAAGTTGACGTC 59.587 50.000 9.11 9.11 43.49 4.34
4058 5059 1.361993 CGGGAGAGGAGCAAGATCG 59.638 63.158 0.00 0.00 0.00 3.69
4126 5127 0.519077 GCTTTCAGGGTTGAGCGAAG 59.481 55.000 0.00 0.00 34.15 3.79
4139 5140 1.000955 GAGCGAAGAGGACCTTTCACA 59.999 52.381 0.00 0.00 34.68 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.547292 GAGATCGATCAGCGTGCTGC 61.547 60.000 26.47 3.35 43.31 5.25
19 20 1.009108 CGAGATCGATCAGCGTGCT 60.009 57.895 26.47 4.43 43.02 4.40
20 21 1.265462 GACGAGATCGATCAGCGTGC 61.265 60.000 35.03 25.58 43.02 5.34
163 194 2.040939 TGTCGAGGAACCAAACCACTA 58.959 47.619 0.00 0.00 0.00 2.74
164 195 0.834612 TGTCGAGGAACCAAACCACT 59.165 50.000 0.00 0.00 0.00 4.00
166 197 0.531090 CGTGTCGAGGAACCAAACCA 60.531 55.000 0.00 0.00 0.00 3.67
189 220 1.220206 CGTTGCAGATCTGGCCTCT 59.780 57.895 23.89 0.00 0.00 3.69
231 262 1.064537 AGAGGGGGAGACGAGAAGTAC 60.065 57.143 0.00 0.00 0.00 2.73
344 375 1.001746 CCATGATGAGATGGAGACGGG 59.998 57.143 0.00 0.00 45.24 5.28
542 579 0.456221 ATGTAGTTCTCCGGACGCAG 59.544 55.000 0.00 0.00 0.00 5.18
597 639 2.407428 GCCGCTCCACTTTAAGCCC 61.407 63.158 0.00 0.00 35.00 5.19
616 665 2.130193 TGGAGGAAATAGCCAGCAGAT 58.870 47.619 0.00 0.00 0.00 2.90
617 666 1.210478 GTGGAGGAAATAGCCAGCAGA 59.790 52.381 0.00 0.00 31.18 4.26
620 669 3.102090 GGTGGAGGAAATAGCCAGC 57.898 57.895 0.00 0.00 42.15 4.85
622 671 0.255890 GCAGGTGGAGGAAATAGCCA 59.744 55.000 0.00 0.00 0.00 4.75
623 672 0.255890 TGCAGGTGGAGGAAATAGCC 59.744 55.000 0.00 0.00 0.00 3.93
671 741 2.158871 GCCGATGGTCCTTTATGTGGTA 60.159 50.000 0.00 0.00 0.00 3.25
672 742 1.408266 GCCGATGGTCCTTTATGTGGT 60.408 52.381 0.00 0.00 0.00 4.16
691 761 5.886960 TTTCTCAGATTTAGGAAAGCAGC 57.113 39.130 0.00 0.00 0.00 5.25
698 768 6.062258 ACGGGATTTTTCTCAGATTTAGGA 57.938 37.500 0.00 0.00 0.00 2.94
700 770 6.258947 GGAGACGGGATTTTTCTCAGATTTAG 59.741 42.308 0.00 0.00 38.02 1.85
827 918 6.787225 AGAAGCATACTCTTGTTACGACTAG 58.213 40.000 0.00 0.00 0.00 2.57
828 919 6.754702 AGAAGCATACTCTTGTTACGACTA 57.245 37.500 0.00 0.00 0.00 2.59
829 920 5.646577 AGAAGCATACTCTTGTTACGACT 57.353 39.130 0.00 0.00 0.00 4.18
830 921 5.862323 TCAAGAAGCATACTCTTGTTACGAC 59.138 40.000 11.26 0.00 40.98 4.34
831 922 6.020971 TCAAGAAGCATACTCTTGTTACGA 57.979 37.500 11.26 0.00 40.98 3.43
832 923 6.706055 TTCAAGAAGCATACTCTTGTTACG 57.294 37.500 11.26 0.00 40.98 3.18
833 924 9.974750 GTAATTCAAGAAGCATACTCTTGTTAC 57.025 33.333 11.26 9.89 40.98 2.50
834 925 9.162764 GGTAATTCAAGAAGCATACTCTTGTTA 57.837 33.333 11.26 3.15 40.98 2.41
835 926 7.121315 GGGTAATTCAAGAAGCATACTCTTGTT 59.879 37.037 11.26 3.93 40.98 2.83
836 927 6.599638 GGGTAATTCAAGAAGCATACTCTTGT 59.400 38.462 11.26 0.00 40.98 3.16
837 928 6.238211 CGGGTAATTCAAGAAGCATACTCTTG 60.238 42.308 6.28 6.28 41.39 3.02
838 929 5.817816 CGGGTAATTCAAGAAGCATACTCTT 59.182 40.000 0.00 0.00 0.00 2.85
839 930 5.104900 ACGGGTAATTCAAGAAGCATACTCT 60.105 40.000 0.00 0.00 0.00 3.24
840 931 5.006746 CACGGGTAATTCAAGAAGCATACTC 59.993 44.000 0.00 0.00 0.00 2.59
841 932 4.876107 CACGGGTAATTCAAGAAGCATACT 59.124 41.667 0.00 0.00 0.00 2.12
842 933 4.495844 GCACGGGTAATTCAAGAAGCATAC 60.496 45.833 0.00 0.00 0.00 2.39
843 934 3.625764 GCACGGGTAATTCAAGAAGCATA 59.374 43.478 0.00 0.00 0.00 3.14
844 935 2.423538 GCACGGGTAATTCAAGAAGCAT 59.576 45.455 0.00 0.00 0.00 3.79
849 940 3.482436 AGTTTGCACGGGTAATTCAAGA 58.518 40.909 0.00 0.00 0.00 3.02
1001 1104 5.395611 TGATCTCATCTGATCCAGACTCAT 58.604 41.667 0.00 0.00 43.63 2.90
1002 1105 4.801164 TGATCTCATCTGATCCAGACTCA 58.199 43.478 0.00 2.88 43.63 3.41
1018 1121 7.706179 AGAAGAAGAAACGAATGAGATGATCTC 59.294 37.037 15.36 15.36 43.65 2.75
1019 1122 7.492020 CAGAAGAAGAAACGAATGAGATGATCT 59.508 37.037 0.00 0.00 0.00 2.75
1020 1123 7.277539 ACAGAAGAAGAAACGAATGAGATGATC 59.722 37.037 0.00 0.00 0.00 2.92
1021 1124 7.102346 ACAGAAGAAGAAACGAATGAGATGAT 58.898 34.615 0.00 0.00 0.00 2.45
1022 1125 6.459066 ACAGAAGAAGAAACGAATGAGATGA 58.541 36.000 0.00 0.00 0.00 2.92
1074 1185 0.824109 CATGGTCGCAGTCCTCCTAA 59.176 55.000 0.00 0.00 36.46 2.69
1235 1346 8.534333 TCGCCTGAATAACTTAAAGCATATAG 57.466 34.615 0.00 0.00 0.00 1.31
1236 1347 8.896320 TTCGCCTGAATAACTTAAAGCATATA 57.104 30.769 0.00 0.00 0.00 0.86
1238 1349 7.618502 TTTCGCCTGAATAACTTAAAGCATA 57.381 32.000 0.00 0.00 33.20 3.14
1239 1350 6.509418 TTTCGCCTGAATAACTTAAAGCAT 57.491 33.333 0.00 0.00 33.20 3.79
1240 1351 5.950758 TTTCGCCTGAATAACTTAAAGCA 57.049 34.783 0.00 0.00 33.20 3.91
1277 1388 3.539604 TCTCCTCGTGCCTTAGTAGTAC 58.460 50.000 0.00 0.00 0.00 2.73
1278 1389 3.433314 CCTCTCCTCGTGCCTTAGTAGTA 60.433 52.174 0.00 0.00 0.00 1.82
1279 1390 2.645802 CTCTCCTCGTGCCTTAGTAGT 58.354 52.381 0.00 0.00 0.00 2.73
1280 1391 1.950909 CCTCTCCTCGTGCCTTAGTAG 59.049 57.143 0.00 0.00 0.00 2.57
1281 1392 1.284198 ACCTCTCCTCGTGCCTTAGTA 59.716 52.381 0.00 0.00 0.00 1.82
1282 1393 0.039911 ACCTCTCCTCGTGCCTTAGT 59.960 55.000 0.00 0.00 0.00 2.24
1283 1394 2.054232 TACCTCTCCTCGTGCCTTAG 57.946 55.000 0.00 0.00 0.00 2.18
1284 1395 2.097825 GTTACCTCTCCTCGTGCCTTA 58.902 52.381 0.00 0.00 0.00 2.69
1301 1412 3.323403 CACTGCAATTTCCCCCAAAGTTA 59.677 43.478 0.00 0.00 0.00 2.24
1308 1419 2.056985 TTGCACTGCAATTTCCCCC 58.943 52.632 12.59 0.00 43.99 5.40
1334 1445 9.865321 GGTGACTGAACTACATTATACTGTTTA 57.135 33.333 0.59 0.00 0.00 2.01
1335 1446 8.594550 AGGTGACTGAACTACATTATACTGTTT 58.405 33.333 0.59 0.00 41.13 2.83
1355 1466 5.741011 TCCACAGGTAAATAATCAGGTGAC 58.259 41.667 0.00 0.00 0.00 3.67
1383 1510 3.881688 GACTGATGAGGCATTGCATAAGT 59.118 43.478 11.39 4.16 38.60 2.24
1384 1511 3.252701 GGACTGATGAGGCATTGCATAAG 59.747 47.826 11.39 0.83 0.00 1.73
1393 1520 3.284617 CAAATCATGGACTGATGAGGCA 58.715 45.455 0.00 0.00 44.03 4.75
1445 1572 0.250901 ACAGGTCCATGACTGTTGCC 60.251 55.000 10.58 0.00 32.47 4.52
1678 1822 8.611757 GGTGACAAAAGCATTACAAAAAGAAAT 58.388 29.630 0.00 0.00 0.00 2.17
1733 1900 4.093743 TGATGGCTAGGACAACTTCTGTA 58.906 43.478 0.00 0.00 38.84 2.74
1748 1915 1.565759 TCTGGCTGGTAATTGATGGCT 59.434 47.619 0.00 0.00 0.00 4.75
1840 2007 3.432046 CCTGCAATTTGTTCCACCAAAGT 60.432 43.478 0.00 0.00 37.71 2.66
2017 2184 0.450583 GGTACTCGCTGATCACGTCA 59.549 55.000 14.43 0.00 35.05 4.35
2109 2276 3.069079 AGTTCTACTCGTGACTAGGCA 57.931 47.619 0.00 0.00 0.00 4.75
2128 2303 3.610911 GACACCCATCCTTCAAGGTTAG 58.389 50.000 2.50 0.00 36.53 2.34
2556 2740 3.378331 GATCGTCGCCGTCTCGTGT 62.378 63.158 0.00 0.00 35.01 4.49
2951 3164 2.047061 ACCTCTGGTTACACTTGCAGA 58.953 47.619 0.00 0.00 27.29 4.26
2952 3165 2.146342 CACCTCTGGTTACACTTGCAG 58.854 52.381 0.00 0.00 31.02 4.41
2953 3166 1.488812 ACACCTCTGGTTACACTTGCA 59.511 47.619 0.00 0.00 31.02 4.08
2954 3167 2.143925 GACACCTCTGGTTACACTTGC 58.856 52.381 0.00 0.00 31.02 4.01
2970 3183 0.385390 CTTGGCAGTTTGGTGGACAC 59.615 55.000 0.00 0.00 0.00 3.67
2976 3189 3.181445 TGATAGACACTTGGCAGTTTGGT 60.181 43.478 0.00 0.00 0.00 3.67
2979 3192 3.503748 GCTTGATAGACACTTGGCAGTTT 59.496 43.478 0.00 0.00 0.00 2.66
2999 3212 5.369833 ACACGTCTAGACATACATAGAGCT 58.630 41.667 22.37 0.00 0.00 4.09
3013 3226 3.854286 AAAAACTTGCGACACGTCTAG 57.146 42.857 0.00 0.00 0.00 2.43
3061 3275 3.064408 GGGGCTTAAATTTAACCGAGACG 59.936 47.826 6.54 0.00 0.00 4.18
3114 3328 7.546358 TGTAAAACTGATGCTTTATTCCCATG 58.454 34.615 0.00 0.00 0.00 3.66
3209 3462 0.975544 CAGAAGAACGCAGTACGACG 59.024 55.000 8.73 8.73 45.00 5.12
3211 3464 1.199327 CTCCAGAAGAACGCAGTACGA 59.801 52.381 0.00 0.00 45.00 3.43
3212 3465 1.068472 ACTCCAGAAGAACGCAGTACG 60.068 52.381 0.00 0.00 45.00 3.67
3213 3466 2.726832 ACTCCAGAAGAACGCAGTAC 57.273 50.000 0.00 0.00 45.00 2.73
3214 3467 2.364324 ACAACTCCAGAAGAACGCAGTA 59.636 45.455 0.00 0.00 45.00 2.74
3217 3470 1.581934 CACAACTCCAGAAGAACGCA 58.418 50.000 0.00 0.00 0.00 5.24
3229 3484 0.034337 TGCTCCCGTAACCACAACTC 59.966 55.000 0.00 0.00 0.00 3.01
3234 3489 2.109425 AGAAATGCTCCCGTAACCAC 57.891 50.000 0.00 0.00 0.00 4.16
3241 3496 2.094545 CCTGGAAAAAGAAATGCTCCCG 60.095 50.000 0.00 0.00 0.00 5.14
3253 3508 4.775253 GGATCCATACCAAACCTGGAAAAA 59.225 41.667 6.95 0.00 46.92 1.94
3262 3517 2.425668 CCAAACCGGATCCATACCAAAC 59.574 50.000 9.46 0.00 36.56 2.93
3263 3518 2.729194 CCAAACCGGATCCATACCAAA 58.271 47.619 9.46 0.00 36.56 3.28
3264 3519 1.683629 GCCAAACCGGATCCATACCAA 60.684 52.381 9.46 0.00 36.56 3.67
3265 3520 0.106918 GCCAAACCGGATCCATACCA 60.107 55.000 9.46 0.00 36.56 3.25
3266 3521 0.182775 AGCCAAACCGGATCCATACC 59.817 55.000 9.46 0.00 36.56 2.73
3267 3522 1.308998 CAGCCAAACCGGATCCATAC 58.691 55.000 9.46 0.00 36.56 2.39
3268 3523 0.465460 GCAGCCAAACCGGATCCATA 60.465 55.000 9.46 0.00 36.56 2.74
3269 3524 1.754234 GCAGCCAAACCGGATCCAT 60.754 57.895 9.46 0.00 36.56 3.41
3270 3525 2.361104 GCAGCCAAACCGGATCCA 60.361 61.111 9.46 0.00 36.56 3.41
3279 3534 3.661648 GGGGAGGGAGCAGCCAAA 61.662 66.667 0.00 0.00 38.95 3.28
3283 3538 4.891037 GCATGGGGAGGGAGCAGC 62.891 72.222 0.00 0.00 0.00 5.25
3304 3559 2.158957 GGATGAAGTGGGAGCACGAATA 60.159 50.000 0.00 0.00 0.00 1.75
3307 3562 0.904865 AGGATGAAGTGGGAGCACGA 60.905 55.000 0.00 0.00 0.00 4.35
3368 3627 3.054361 GCCTCACTCCCTTAAAATCAGGA 60.054 47.826 0.00 0.00 32.41 3.86
3383 3642 7.175990 TGAAATAAAATAAAACTCGGCCTCACT 59.824 33.333 0.00 0.00 0.00 3.41
3387 3646 8.527810 TGATTGAAATAAAATAAAACTCGGCCT 58.472 29.630 0.00 0.00 0.00 5.19
3404 3663 6.753279 CGTATGTGGCTTGATTTGATTGAAAT 59.247 34.615 0.00 0.00 36.94 2.17
3407 3666 4.438608 GCGTATGTGGCTTGATTTGATTGA 60.439 41.667 0.00 0.00 0.00 2.57
3425 3684 1.000163 CTTATCTGTGCTCCCGCGTAT 60.000 52.381 4.92 0.00 39.65 3.06
3439 3698 0.460284 CCCTTCGCGTGTGCTTATCT 60.460 55.000 5.77 0.00 39.65 1.98
3443 3702 2.357517 CTCCCTTCGCGTGTGCTT 60.358 61.111 5.77 0.00 39.65 3.91
3453 3712 1.340405 TGAGATTTGCCTGCTCCCTTC 60.340 52.381 0.00 0.00 0.00 3.46
3454 3713 0.700564 TGAGATTTGCCTGCTCCCTT 59.299 50.000 0.00 0.00 0.00 3.95
3455 3714 0.924823 ATGAGATTTGCCTGCTCCCT 59.075 50.000 0.00 0.00 0.00 4.20
3468 3727 3.640029 ACGGTATACCAAACGGATGAGAT 59.360 43.478 21.76 0.00 35.14 2.75
3473 3732 2.109774 TGGACGGTATACCAAACGGAT 58.890 47.619 21.76 0.00 35.14 4.18
3501 3760 4.436998 GGCTGAGTCCACGGTCCG 62.437 72.222 10.48 10.48 0.00 4.79
3509 3768 1.021968 AAAAACGTGTGGCTGAGTCC 58.978 50.000 0.00 0.00 0.00 3.85
3530 3789 2.100087 GGCCGAGTCCTTGTTTCAAAAA 59.900 45.455 0.00 0.00 0.00 1.94
3532 3791 1.314730 GGCCGAGTCCTTGTTTCAAA 58.685 50.000 0.00 0.00 0.00 2.69
3533 3792 0.181587 TGGCCGAGTCCTTGTTTCAA 59.818 50.000 0.00 0.00 0.00 2.69
3534 3793 0.534203 GTGGCCGAGTCCTTGTTTCA 60.534 55.000 0.00 0.00 0.00 2.69
3536 3795 1.597027 CGTGGCCGAGTCCTTGTTT 60.597 57.895 0.00 0.00 35.63 2.83
3538 3797 2.319890 AAACGTGGCCGAGTCCTTGT 62.320 55.000 0.00 0.00 37.88 3.16
3539 3798 1.164041 AAAACGTGGCCGAGTCCTTG 61.164 55.000 0.00 0.00 37.88 3.61
3541 3800 1.301479 GAAAACGTGGCCGAGTCCT 60.301 57.895 0.00 0.00 37.88 3.85
3561 3820 2.518349 AACAACTGGCCACCCACG 60.518 61.111 0.00 0.00 35.79 4.94
3564 3823 3.977244 CGCAACAACTGGCCACCC 61.977 66.667 0.00 0.00 0.00 4.61
3603 3862 7.201857 GCATAAATAAACTTGGGATCAGAAGCT 60.202 37.037 0.00 0.00 0.00 3.74
3686 3945 8.255206 TCGGTGTGCCCTAATTATATAGTATTG 58.745 37.037 0.00 0.00 0.00 1.90
3687 3946 8.370266 TCGGTGTGCCCTAATTATATAGTATT 57.630 34.615 0.00 0.00 0.00 1.89
3689 3948 7.201758 CGATCGGTGTGCCCTAATTATATAGTA 60.202 40.741 7.38 0.00 0.00 1.82
3690 3949 6.405508 CGATCGGTGTGCCCTAATTATATAGT 60.406 42.308 7.38 0.00 0.00 2.12
3691 3950 5.977725 CGATCGGTGTGCCCTAATTATATAG 59.022 44.000 7.38 0.00 0.00 1.31
3770 4029 1.865865 TGAAGAAACAGTCTCGTGCC 58.134 50.000 0.00 0.00 34.56 5.01
3816 4075 3.191371 CCACCATCCAGAAACTAAAGCAC 59.809 47.826 0.00 0.00 0.00 4.40
3818 4077 2.164422 GCCACCATCCAGAAACTAAAGC 59.836 50.000 0.00 0.00 0.00 3.51
3840 4099 1.834263 ACTACTGGACATGGAAGCCTC 59.166 52.381 0.00 0.00 0.00 4.70
3852 4111 7.504926 ACAGGGACAAAATTATACTACTGGA 57.495 36.000 0.00 0.00 0.00 3.86
3855 4114 7.414222 TCGACAGGGACAAAATTATACTACT 57.586 36.000 0.00 0.00 0.00 2.57
3859 4118 6.674760 GCAGTTCGACAGGGACAAAATTATAC 60.675 42.308 0.00 0.00 0.00 1.47
3871 4130 1.439679 GGTTTAGCAGTTCGACAGGG 58.560 55.000 0.00 0.00 0.00 4.45
3873 4132 0.438830 GCGGTTTAGCAGTTCGACAG 59.561 55.000 0.00 0.00 37.05 3.51
3876 4135 0.389426 GGAGCGGTTTAGCAGTTCGA 60.389 55.000 0.00 0.00 40.15 3.71
3878 4137 1.079503 CAGGAGCGGTTTAGCAGTTC 58.920 55.000 0.00 0.00 40.15 3.01
3884 4143 1.153349 GGAGGCAGGAGCGGTTTAG 60.153 63.158 0.00 0.00 43.41 1.85
3885 4144 2.666098 GGGAGGCAGGAGCGGTTTA 61.666 63.158 0.00 0.00 43.41 2.01
3892 4151 4.106925 GCAGGTGGGAGGCAGGAG 62.107 72.222 0.00 0.00 0.00 3.69
3898 4157 0.608035 TTTAAAGCGCAGGTGGGAGG 60.608 55.000 11.47 0.00 39.47 4.30
3899 4158 0.521735 GTTTAAAGCGCAGGTGGGAG 59.478 55.000 11.47 0.00 39.47 4.30
3924 4183 2.232452 ACTTTGTCAGGTCGAGATCCAG 59.768 50.000 0.00 0.00 0.00 3.86
3926 4185 3.320673 AACTTTGTCAGGTCGAGATCC 57.679 47.619 0.00 0.00 0.00 3.36
3969 4306 1.989706 TTTGTTAGGGTCAAGTGCCC 58.010 50.000 3.40 3.40 46.43 5.36
3978 4315 5.653255 ATCCAGCTATCATTTGTTAGGGT 57.347 39.130 0.00 0.00 0.00 4.34
3981 4318 8.442632 TTCTGAATCCAGCTATCATTTGTTAG 57.557 34.615 0.00 0.00 40.20 2.34
4015 5015 2.687297 TCCTGGATGGAATCTCTCAGG 58.313 52.381 0.00 0.00 45.85 3.86
4068 5069 3.255379 GCCTTCCGATCGCACGAC 61.255 66.667 10.32 0.00 35.09 4.34


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

AutoCloner maintained by Alex Coulton.