Multiple sequence alignment - TraesCS2D01G480900

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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 TraesCS2D01G480900 chr2D 100.000 3924 0 0 1 3924 584247668 584251591 0.000000e+00 7247.0
1 TraesCS2D01G480900 chr2D 80.618 712 103 19 905 1610 545746960 545747642 5.810000e-143 518.0
2 TraesCS2D01G480900 chr2D 96.512 86 3 0 3831 3916 99134716 99134631 4.090000e-30 143.0
3 TraesCS2D01G480900 chr2D 88.298 94 8 2 3017 3109 545763500 545763591 4.150000e-20 110.0
4 TraesCS2D01G480900 chr2B 97.539 1869 41 3 1131 2999 703614195 703616058 0.000000e+00 3192.0
5 TraesCS2D01G480900 chr2B 96.667 840 21 5 2993 3827 703616177 703617014 0.000000e+00 1389.0
6 TraesCS2D01G480900 chr2B 95.784 593 25 0 1 593 733043706 733043114 0.000000e+00 957.0
7 TraesCS2D01G480900 chr2B 92.857 140 3 3 962 1095 703613753 703613891 3.090000e-46 196.0
8 TraesCS2D01G480900 chr2B 80.919 283 20 18 3541 3823 703617837 703618085 4.000000e-45 193.0
9 TraesCS2D01G480900 chr2B 97.403 77 2 0 840 916 703613503 703613579 8.850000e-27 132.0
10 TraesCS2D01G480900 chr2B 97.183 71 2 0 651 721 703613125 703613195 1.920000e-23 121.0
11 TraesCS2D01G480900 chr2B 97.015 67 1 1 599 665 703613047 703613112 1.150000e-20 111.0
12 TraesCS2D01G480900 chr4D 96.796 593 18 1 1 592 40620070 40619478 0.000000e+00 989.0
13 TraesCS2D01G480900 chr4D 91.709 591 46 3 1 590 337934489 337933901 0.000000e+00 817.0
14 TraesCS2D01G480900 chr4D 91.089 101 8 1 3819 3919 256559530 256559431 6.840000e-28 135.0
15 TraesCS2D01G480900 chr4D 85.593 118 13 3 3803 3916 426786227 426786344 1.920000e-23 121.0
16 TraesCS2D01G480900 chr2A 96.627 593 19 1 1 592 712964006 712964598 0.000000e+00 983.0
17 TraesCS2D01G480900 chr2A 95.025 201 9 1 3619 3818 718336649 718336849 8.180000e-82 315.0
18 TraesCS2D01G480900 chr2A 93.333 90 6 0 3830 3919 522494957 522494868 2.460000e-27 134.0
19 TraesCS2D01G480900 chr2A 89.189 74 4 1 3533 3602 718336506 718336579 5.400000e-14 89.8
20 TraesCS2D01G480900 chr7D 96.108 591 23 0 1 591 9041921 9042511 0.000000e+00 965.0
21 TraesCS2D01G480900 chr7D 94.444 90 5 0 3827 3916 83666086 83666175 5.290000e-29 139.0
22 TraesCS2D01G480900 chr5D 96.102 590 23 0 1 590 198230765 198230176 0.000000e+00 963.0
23 TraesCS2D01G480900 chr6A 95.798 595 24 1 1 594 13606022 13606616 0.000000e+00 959.0
24 TraesCS2D01G480900 chr6A 95.791 594 23 2 1 592 473741376 473741969 0.000000e+00 957.0
25 TraesCS2D01G480900 chr6A 96.552 87 3 0 3831 3917 447873602 447873688 1.140000e-30 145.0
26 TraesCS2D01G480900 chr6A 96.429 84 3 0 3830 3913 594956105 594956188 5.290000e-29 139.0
27 TraesCS2D01G480900 chr7A 95.771 402 16 1 192 592 727996669 727997070 0.000000e+00 647.0
28 TraesCS2D01G480900 chr6D 94.624 93 3 1 3823 3915 471303224 471303314 4.090000e-30 143.0
29 TraesCS2D01G480900 chr6D 93.478 46 3 0 3541 3586 17886929 17886974 7.040000e-08 69.4
30 TraesCS2D01G480900 chr1B 92.473 93 7 0 3824 3916 606634232 606634324 2.460000e-27 134.0
31 TraesCS2D01G480900 chr6B 82.796 93 7 8 3506 3595 31779604 31779690 1.510000e-09 75.0
32 TraesCS2D01G480900 chr6B 90.909 55 5 0 3541 3595 32018547 32018601 1.510000e-09 75.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G480900 chr2D 584247668 584251591 3923 False 7247 7247 100.000000 1 3924 1 chr2D.!!$F3 3923
1 TraesCS2D01G480900 chr2D 545746960 545747642 682 False 518 518 80.618000 905 1610 1 chr2D.!!$F1 705
2 TraesCS2D01G480900 chr2B 733043114 733043706 592 True 957 957 95.784000 1 593 1 chr2B.!!$R1 592
3 TraesCS2D01G480900 chr2B 703613047 703618085 5038 False 762 3192 94.226143 599 3827 7 chr2B.!!$F1 3228
4 TraesCS2D01G480900 chr4D 40619478 40620070 592 True 989 989 96.796000 1 592 1 chr4D.!!$R1 591
5 TraesCS2D01G480900 chr4D 337933901 337934489 588 True 817 817 91.709000 1 590 1 chr4D.!!$R3 589
6 TraesCS2D01G480900 chr2A 712964006 712964598 592 False 983 983 96.627000 1 592 1 chr2A.!!$F1 591
7 TraesCS2D01G480900 chr7D 9041921 9042511 590 False 965 965 96.108000 1 591 1 chr7D.!!$F1 590
8 TraesCS2D01G480900 chr5D 198230176 198230765 589 True 963 963 96.102000 1 590 1 chr5D.!!$R1 589
9 TraesCS2D01G480900 chr6A 13606022 13606616 594 False 959 959 95.798000 1 594 1 chr6A.!!$F1 593
10 TraesCS2D01G480900 chr6A 473741376 473741969 593 False 957 957 95.791000 1 592 1 chr6A.!!$F3 591

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
739 768 0.029834 CAGGTTATGAATGGCTGCGC 59.970 55.000 0.00 0.0 0.00 6.09 F
893 1185 0.171455 CACCGGGAAGACGAAGAGAG 59.829 60.000 6.32 0.0 35.47 3.20 F
939 1231 1.140134 TCCCCTCCCCTGTTCTTTGG 61.140 60.000 0.00 0.0 0.00 3.28 F
2490 3183 1.417890 CTAGGGAGGGCATGTACAAGG 59.582 57.143 0.00 0.0 0.00 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2714 3407 0.468226 TTACCCCGACAGGATCATGC 59.532 55.000 7.4 0.0 41.02 4.06 R
2871 3564 3.620427 ACGTTGCACCATATACTCCAA 57.380 42.857 0.0 0.0 0.00 3.53 R
2906 3599 3.840124 AGATCATCCGGGACCTTTTAC 57.160 47.619 0.0 0.0 0.00 2.01 R
3902 5799 0.395311 CCGCAGGTACTCCCTCTGTA 60.395 60.000 0.0 0.0 43.86 2.74 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
160 162 3.705579 ACTGCAGCTATTCTCAGAGACAT 59.294 43.478 15.27 0.37 0.00 3.06
178 180 7.123247 CAGAGACATCAGGGGAAATTTTATTGT 59.877 37.037 0.00 0.00 0.00 2.71
185 187 4.467438 AGGGGAAATTTTATTGTGGCTCAG 59.533 41.667 0.00 0.00 0.00 3.35
247 249 1.977056 GCAATGGCCATGAGAGATGA 58.023 50.000 21.63 0.00 0.00 2.92
354 356 2.846206 ACAAGATGGTGGGATGAAGCTA 59.154 45.455 0.00 0.00 0.00 3.32
357 359 2.846206 AGATGGTGGGATGAAGCTACAA 59.154 45.455 0.00 0.00 0.00 2.41
464 466 3.061831 CGCATGTGCTAGCTAATCATAGC 59.938 47.826 17.23 16.55 45.83 2.97
512 514 1.221021 GGACGAGCCTCCCGATTTT 59.779 57.895 0.00 0.00 0.00 1.82
665 694 8.482128 TGTAATATAAGGAAAATGCAAAAGGGG 58.518 33.333 0.00 0.00 0.00 4.79
728 757 0.394352 GTGAGCCCACCCAGGTTATG 60.394 60.000 0.00 0.00 37.33 1.90
729 758 0.548926 TGAGCCCACCCAGGTTATGA 60.549 55.000 0.00 0.00 34.66 2.15
730 759 0.623723 GAGCCCACCCAGGTTATGAA 59.376 55.000 0.00 0.00 34.66 2.57
732 761 1.063717 AGCCCACCCAGGTTATGAATG 60.064 52.381 0.00 0.00 34.66 2.67
733 762 2.028996 GCCCACCCAGGTTATGAATGG 61.029 57.143 0.00 0.00 34.88 3.16
734 763 1.402787 CCACCCAGGTTATGAATGGC 58.597 55.000 0.00 0.00 32.46 4.40
735 764 1.063717 CCACCCAGGTTATGAATGGCT 60.064 52.381 0.00 0.00 32.46 4.75
737 766 1.035139 CCCAGGTTATGAATGGCTGC 58.965 55.000 0.00 0.00 32.46 5.25
739 768 0.029834 CAGGTTATGAATGGCTGCGC 59.970 55.000 0.00 0.00 0.00 6.09
765 1057 0.898326 CCTTACAAAGGCACCCCCAC 60.898 60.000 0.00 0.00 42.78 4.61
766 1058 0.898326 CTTACAAAGGCACCCCCACC 60.898 60.000 0.00 0.00 35.39 4.61
767 1059 2.374781 TTACAAAGGCACCCCCACCC 62.375 60.000 0.00 0.00 35.39 4.61
778 1070 4.016706 CCCACCCGACTCCACCAC 62.017 72.222 0.00 0.00 0.00 4.16
779 1071 4.016706 CCACCCGACTCCACCACC 62.017 72.222 0.00 0.00 0.00 4.61
780 1072 2.923035 CACCCGACTCCACCACCT 60.923 66.667 0.00 0.00 0.00 4.00
781 1073 1.608336 CACCCGACTCCACCACCTA 60.608 63.158 0.00 0.00 0.00 3.08
782 1074 1.305046 ACCCGACTCCACCACCTAG 60.305 63.158 0.00 0.00 0.00 3.02
783 1075 2.058595 CCCGACTCCACCACCTAGG 61.059 68.421 7.41 7.41 45.67 3.02
784 1076 1.000019 CCGACTCCACCACCTAGGA 60.000 63.158 17.98 0.00 41.22 2.94
785 1077 0.613853 CCGACTCCACCACCTAGGAA 60.614 60.000 17.98 0.00 41.22 3.36
786 1078 1.263356 CGACTCCACCACCTAGGAAA 58.737 55.000 17.98 0.00 41.22 3.13
787 1079 1.621814 CGACTCCACCACCTAGGAAAA 59.378 52.381 17.98 0.00 41.22 2.29
788 1080 2.612221 CGACTCCACCACCTAGGAAAAC 60.612 54.545 17.98 0.00 41.22 2.43
789 1081 1.703513 ACTCCACCACCTAGGAAAACC 59.296 52.381 17.98 0.00 41.22 3.27
790 1082 1.985895 CTCCACCACCTAGGAAAACCT 59.014 52.381 17.98 0.00 41.22 3.50
791 1083 3.178865 CTCCACCACCTAGGAAAACCTA 58.821 50.000 17.98 0.00 41.22 3.08
792 1084 3.585732 CTCCACCACCTAGGAAAACCTAA 59.414 47.826 17.98 0.00 41.22 2.69
793 1085 3.982052 TCCACCACCTAGGAAAACCTAAA 59.018 43.478 17.98 0.00 41.22 1.85
794 1086 4.077108 CCACCACCTAGGAAAACCTAAAC 58.923 47.826 17.98 0.00 41.22 2.01
795 1087 4.077108 CACCACCTAGGAAAACCTAAACC 58.923 47.826 17.98 0.00 41.22 3.27
796 1088 3.074985 ACCACCTAGGAAAACCTAAACCC 59.925 47.826 17.98 0.00 41.22 4.11
797 1089 3.332783 CCACCTAGGAAAACCTAAACCCT 59.667 47.826 17.98 0.00 41.22 4.34
798 1090 4.537288 CCACCTAGGAAAACCTAAACCCTA 59.463 45.833 17.98 0.00 41.22 3.53
799 1091 5.338953 CCACCTAGGAAAACCTAAACCCTAG 60.339 48.000 17.98 0.00 43.67 3.02
800 1092 5.486419 CACCTAGGAAAACCTAAACCCTAGA 59.514 44.000 17.98 0.00 45.73 2.43
801 1093 6.158169 CACCTAGGAAAACCTAAACCCTAGAT 59.842 42.308 17.98 0.00 45.73 1.98
802 1094 6.386342 ACCTAGGAAAACCTAAACCCTAGATC 59.614 42.308 17.98 0.00 45.73 2.75
803 1095 5.712084 AGGAAAACCTAAACCCTAGATCC 57.288 43.478 0.00 0.00 0.00 3.36
804 1096 4.477581 AGGAAAACCTAAACCCTAGATCCC 59.522 45.833 0.00 0.00 0.00 3.85
805 1097 4.228895 GGAAAACCTAAACCCTAGATCCCA 59.771 45.833 0.00 0.00 0.00 4.37
806 1098 4.857130 AAACCTAAACCCTAGATCCCAC 57.143 45.455 0.00 0.00 0.00 4.61
807 1099 3.797671 ACCTAAACCCTAGATCCCACT 57.202 47.619 0.00 0.00 0.00 4.00
808 1100 3.385115 ACCTAAACCCTAGATCCCACTG 58.615 50.000 0.00 0.00 0.00 3.66
809 1101 2.104963 CCTAAACCCTAGATCCCACTGC 59.895 54.545 0.00 0.00 0.00 4.40
810 1102 0.919710 AAACCCTAGATCCCACTGCC 59.080 55.000 0.00 0.00 0.00 4.85
811 1103 1.338136 AACCCTAGATCCCACTGCCG 61.338 60.000 0.00 0.00 0.00 5.69
812 1104 2.423446 CCTAGATCCCACTGCCGC 59.577 66.667 0.00 0.00 0.00 6.53
813 1105 2.423446 CTAGATCCCACTGCCGCC 59.577 66.667 0.00 0.00 0.00 6.13
814 1106 3.506059 CTAGATCCCACTGCCGCCG 62.506 68.421 0.00 0.00 0.00 6.46
834 1126 3.365265 GCCCTCCCTGCACGTTTG 61.365 66.667 0.00 0.00 0.00 2.93
893 1185 0.171455 CACCGGGAAGACGAAGAGAG 59.829 60.000 6.32 0.00 35.47 3.20
903 1195 5.758784 GGAAGACGAAGAGAGGAAAAGAAAA 59.241 40.000 0.00 0.00 0.00 2.29
919 1211 7.418597 GGAAAAGAAAACCCAGGTATGTTTCTT 60.419 37.037 16.65 16.65 33.76 2.52
920 1212 7.432148 AAAGAAAACCCAGGTATGTTTCTTT 57.568 32.000 22.93 22.93 33.76 2.52
924 1216 2.042569 ACCCAGGTATGTTTCTTTCCCC 59.957 50.000 0.00 0.00 0.00 4.81
939 1231 1.140134 TCCCCTCCCCTGTTCTTTGG 61.140 60.000 0.00 0.00 0.00 3.28
944 1236 2.666317 CTCCCCTGTTCTTTGGTTTGT 58.334 47.619 0.00 0.00 0.00 2.83
945 1237 3.031013 CTCCCCTGTTCTTTGGTTTGTT 58.969 45.455 0.00 0.00 0.00 2.83
946 1238 3.445987 TCCCCTGTTCTTTGGTTTGTTT 58.554 40.909 0.00 0.00 0.00 2.83
947 1239 4.611367 TCCCCTGTTCTTTGGTTTGTTTA 58.389 39.130 0.00 0.00 0.00 2.01
949 1241 5.663556 TCCCCTGTTCTTTGGTTTGTTTATT 59.336 36.000 0.00 0.00 0.00 1.40
950 1242 6.157123 TCCCCTGTTCTTTGGTTTGTTTATTT 59.843 34.615 0.00 0.00 0.00 1.40
1025 1445 1.753073 CCAAATGGAAGTGGATCAGCC 59.247 52.381 0.00 0.00 37.03 4.85
1087 1513 4.309933 CTTTGCATCCAAGTTTTTCCTCC 58.690 43.478 0.00 0.00 31.52 4.30
1092 1518 4.561530 GCATCCAAGTTTTTCCTCCTTTCC 60.562 45.833 0.00 0.00 0.00 3.13
1094 1520 4.878968 TCCAAGTTTTTCCTCCTTTCCTT 58.121 39.130 0.00 0.00 0.00 3.36
1098 1524 6.538742 CCAAGTTTTTCCTCCTTTCCTTTTTC 59.461 38.462 0.00 0.00 0.00 2.29
1099 1525 6.235231 AGTTTTTCCTCCTTTCCTTTTTCC 57.765 37.500 0.00 0.00 0.00 3.13
1100 1526 5.130477 AGTTTTTCCTCCTTTCCTTTTTCCC 59.870 40.000 0.00 0.00 0.00 3.97
1101 1527 2.992847 TCCTCCTTTCCTTTTTCCCC 57.007 50.000 0.00 0.00 0.00 4.81
1102 1528 1.431633 TCCTCCTTTCCTTTTTCCCCC 59.568 52.381 0.00 0.00 0.00 5.40
1119 1545 3.493767 CCCCCTCAACCTAATAAGCTC 57.506 52.381 0.00 0.00 0.00 4.09
1129 1555 2.982488 CCTAATAAGCTCATCCCCACCT 59.018 50.000 0.00 0.00 0.00 4.00
1168 1861 6.089954 GCAGCAAAGTGAGAAACAAATATTCC 59.910 38.462 0.00 0.00 0.00 3.01
1177 1870 7.800380 GTGAGAAACAAATATTCCATAGATGCG 59.200 37.037 0.00 0.00 0.00 4.73
1181 1874 6.545504 ACAAATATTCCATAGATGCGTGAC 57.454 37.500 0.00 0.00 0.00 3.67
1183 1876 6.203530 ACAAATATTCCATAGATGCGTGACAG 59.796 38.462 0.00 0.00 0.00 3.51
1205 1898 4.691216 AGATAAAACCAGAGACTTTCGTGC 59.309 41.667 0.00 0.00 0.00 5.34
1339 2032 3.215151 GGGAATCCGGAAGAAGGATTTC 58.785 50.000 9.01 4.76 42.62 2.17
1484 2177 4.081642 TGTCGCCTATAATAGGGAGATTGC 60.082 45.833 0.00 0.00 46.32 3.56
1917 2610 2.693069 CACTTGAGGTTCTGCTAGTGG 58.307 52.381 0.00 0.00 31.69 4.00
2009 2702 8.353423 AGGAATTTGAATTTGTATGTAGCACT 57.647 30.769 0.00 0.00 0.00 4.40
2012 2705 9.624697 GAATTTGAATTTGTATGTAGCACTTGA 57.375 29.630 0.00 0.00 0.00 3.02
2113 2806 8.918202 TTAATCATGGTAGGGATTTGTATGAC 57.082 34.615 0.00 0.00 35.49 3.06
2159 2852 5.808042 AAACATGACAGTAGATGATGTGC 57.192 39.130 0.00 0.00 0.00 4.57
2160 2853 4.476628 ACATGACAGTAGATGATGTGCA 57.523 40.909 0.00 0.00 0.00 4.57
2206 2899 4.031418 TGGCGACATGATGCAAATTAAG 57.969 40.909 14.15 0.00 33.40 1.85
2235 2928 4.094887 CCATGTTCGTGTAAGGAATCTTGG 59.905 45.833 0.00 0.00 43.20 3.61
2236 2929 4.345859 TGTTCGTGTAAGGAATCTTGGT 57.654 40.909 0.00 0.00 43.20 3.67
2237 2930 4.062293 TGTTCGTGTAAGGAATCTTGGTG 58.938 43.478 0.00 0.00 43.20 4.17
2280 2973 3.953612 GGTTTGGCAGACATGATATTCCA 59.046 43.478 10.57 0.00 0.00 3.53
2288 2981 7.175467 TGGCAGACATGATATTCCACAATATTC 59.825 37.037 0.00 0.00 35.63 1.75
2320 3013 6.294176 GCTGGACAAATGATGTTGAACTAAGT 60.294 38.462 0.00 0.00 44.12 2.24
2460 3153 4.842948 TCCTCAATCATCCATTCCTAGGAG 59.157 45.833 12.26 0.83 38.83 3.69
2461 3154 4.019501 CCTCAATCATCCATTCCTAGGAGG 60.020 50.000 12.26 11.16 38.83 4.30
2490 3183 1.417890 CTAGGGAGGGCATGTACAAGG 59.582 57.143 0.00 0.00 0.00 3.61
2646 3339 6.538945 TTCAGAAAATTAATAAGTGGGCCC 57.461 37.500 17.59 17.59 0.00 5.80
2648 3341 6.019748 TCAGAAAATTAATAAGTGGGCCCAA 58.980 36.000 30.64 12.75 0.00 4.12
2714 3407 2.231478 AGCCGTATCCCATTATCACGAG 59.769 50.000 0.00 0.00 34.66 4.18
2871 3564 4.957327 GGATCTTCTACCTGGACTACTTGT 59.043 45.833 0.00 0.00 0.00 3.16
2898 3591 6.293244 GGAGTATATGGTGCAACGTTTAATCC 60.293 42.308 20.22 20.22 38.12 3.01
2906 3599 3.231160 GCAACGTTTAATCCGGACTTTG 58.769 45.455 6.12 5.65 0.00 2.77
2944 3637 2.595009 CTACCTGGCCTTCCTTCGCC 62.595 65.000 3.32 0.00 45.92 5.54
2957 3650 1.822990 CCTTCGCCTAACTGGAGTGTA 59.177 52.381 0.00 0.00 38.35 2.90
3109 3927 1.583404 GTTGTGTGCTTGCTTTGTTCG 59.417 47.619 0.00 0.00 0.00 3.95
3193 4013 1.375326 GCTCCTCCCCACGTTTCTT 59.625 57.895 0.00 0.00 0.00 2.52
3194 4014 0.955919 GCTCCTCCCCACGTTTCTTG 60.956 60.000 0.00 0.00 0.00 3.02
3233 4053 1.412343 CCTTCTTCCTCTAGCTCTGGC 59.588 57.143 0.00 0.00 39.06 4.85
3287 4107 0.038310 CCCTTCTCCTTTGGTGGACC 59.962 60.000 0.00 0.00 31.94 4.46
3323 4143 0.810648 GGATCAATCAACGCTGGCAA 59.189 50.000 0.00 0.00 0.00 4.52
3345 4165 1.289066 CGTGAGCCAAGAACGGAGA 59.711 57.895 0.00 0.00 33.77 3.71
3493 4313 0.322726 TCACCAGTGCACCCATGATG 60.323 55.000 14.63 2.46 0.00 3.07
3587 4409 6.180472 ACTAGGTGCTTATAACAATTGCAGT 58.820 36.000 5.05 0.00 34.15 4.40
3619 4441 4.345547 TCACAAGTGACAACCCACTACATA 59.654 41.667 0.00 0.00 45.82 2.29
3669 4492 4.593206 ACCACAAGGACAAGATTAGACTGA 59.407 41.667 0.00 0.00 38.69 3.41
3679 4502 7.604164 GGACAAGATTAGACTGACAAGATGAAA 59.396 37.037 0.00 0.00 0.00 2.69
3696 4519 0.889186 AAACCGACAGCCATGGACAC 60.889 55.000 18.40 0.00 0.00 3.67
3725 4548 2.360475 GCTTCCTTTGGCCGAGCT 60.360 61.111 0.00 0.00 0.00 4.09
3805 5702 1.317613 TCAGGCGCAATGTCAGTTTT 58.682 45.000 10.83 0.00 0.00 2.43
3807 5704 2.225491 TCAGGCGCAATGTCAGTTTTAC 59.775 45.455 10.83 0.00 0.00 2.01
3819 5716 6.164408 TGTCAGTTTTACGATACATGCAAG 57.836 37.500 0.00 0.00 0.00 4.01
3820 5717 5.929415 TGTCAGTTTTACGATACATGCAAGA 59.071 36.000 0.00 0.00 0.00 3.02
3821 5718 6.593770 TGTCAGTTTTACGATACATGCAAGAT 59.406 34.615 0.00 0.00 0.00 2.40
3822 5719 6.901887 GTCAGTTTTACGATACATGCAAGATG 59.098 38.462 0.00 0.00 0.00 2.90
3823 5720 6.593770 TCAGTTTTACGATACATGCAAGATGT 59.406 34.615 0.00 0.00 36.13 3.06
3824 5721 6.684131 CAGTTTTACGATACATGCAAGATGTG 59.316 38.462 1.64 0.00 33.76 3.21
3825 5722 6.371548 AGTTTTACGATACATGCAAGATGTGT 59.628 34.615 1.64 0.00 33.76 3.72
3826 5723 7.547722 AGTTTTACGATACATGCAAGATGTGTA 59.452 33.333 1.64 0.73 33.76 2.90
3827 5724 8.335356 GTTTTACGATACATGCAAGATGTGTAT 58.665 33.333 9.16 9.16 40.64 2.29
3828 5725 8.432110 TTTACGATACATGCAAGATGTGTATT 57.568 30.769 10.43 0.69 38.71 1.89
3829 5726 6.291067 ACGATACATGCAAGATGTGTATTG 57.709 37.500 17.50 17.50 42.18 1.90
3830 5727 5.817296 ACGATACATGCAAGATGTGTATTGT 59.183 36.000 18.47 18.47 43.51 2.71
3831 5728 6.983890 ACGATACATGCAAGATGTGTATTGTA 59.016 34.615 21.08 9.40 45.11 2.41
3832 5729 7.042725 ACGATACATGCAAGATGTGTATTGTAC 60.043 37.037 21.08 6.27 45.11 2.90
3833 5730 7.169813 CGATACATGCAAGATGTGTATTGTACT 59.830 37.037 10.43 0.00 38.71 2.73
3834 5731 6.668541 ACATGCAAGATGTGTATTGTACTC 57.331 37.500 0.00 0.00 28.71 2.59
3835 5732 5.586243 ACATGCAAGATGTGTATTGTACTCC 59.414 40.000 0.00 0.00 28.71 3.85
3836 5733 4.513442 TGCAAGATGTGTATTGTACTCCC 58.487 43.478 0.00 0.00 0.00 4.30
3837 5734 4.225042 TGCAAGATGTGTATTGTACTCCCT 59.775 41.667 0.00 0.00 0.00 4.20
3838 5735 5.186198 GCAAGATGTGTATTGTACTCCCTT 58.814 41.667 0.00 0.00 0.00 3.95
3839 5736 5.294552 GCAAGATGTGTATTGTACTCCCTTC 59.705 44.000 0.00 0.00 0.00 3.46
3840 5737 5.263968 AGATGTGTATTGTACTCCCTTCG 57.736 43.478 0.00 0.00 0.00 3.79
3841 5738 4.710375 AGATGTGTATTGTACTCCCTTCGT 59.290 41.667 0.00 0.00 0.00 3.85
3842 5739 5.889853 AGATGTGTATTGTACTCCCTTCGTA 59.110 40.000 0.00 0.00 0.00 3.43
3843 5740 5.981088 TGTGTATTGTACTCCCTTCGTAA 57.019 39.130 0.00 0.00 0.00 3.18
3844 5741 6.343716 TGTGTATTGTACTCCCTTCGTAAA 57.656 37.500 0.00 0.00 0.00 2.01
3845 5742 6.158598 TGTGTATTGTACTCCCTTCGTAAAC 58.841 40.000 0.00 0.00 0.00 2.01
3846 5743 6.015180 TGTGTATTGTACTCCCTTCGTAAACT 60.015 38.462 0.00 0.00 0.00 2.66
3847 5744 7.176515 TGTGTATTGTACTCCCTTCGTAAACTA 59.823 37.037 0.00 0.00 0.00 2.24
3848 5745 8.028938 GTGTATTGTACTCCCTTCGTAAACTAA 58.971 37.037 0.00 0.00 0.00 2.24
3849 5746 8.752187 TGTATTGTACTCCCTTCGTAAACTAAT 58.248 33.333 0.00 0.00 0.00 1.73
3857 5754 8.358895 ACTCCCTTCGTAAACTAATATAAGAGC 58.641 37.037 0.00 0.00 0.00 4.09
3858 5755 8.241497 TCCCTTCGTAAACTAATATAAGAGCA 57.759 34.615 0.00 0.00 0.00 4.26
3859 5756 8.867097 TCCCTTCGTAAACTAATATAAGAGCAT 58.133 33.333 0.00 0.00 0.00 3.79
3860 5757 9.490379 CCCTTCGTAAACTAATATAAGAGCATT 57.510 33.333 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 162 4.424842 AGCCACAATAAAATTTCCCCTGA 58.575 39.130 0.00 0.00 0.00 3.86
178 180 3.306917 CAATGAATTTGCACTGAGCCA 57.693 42.857 0.00 0.00 44.83 4.75
247 249 7.514721 TCCAAGGGAATTAGCGAATAGTAATT 58.485 34.615 0.00 0.00 32.65 1.40
512 514 1.974957 TCCACGAGTTCCCTCATCAAA 59.025 47.619 0.00 0.00 37.59 2.69
542 544 8.580720 TGGCTAGCTTTATTGAATTAAAACACA 58.419 29.630 15.72 0.00 0.00 3.72
652 681 4.875536 GCGATTATTTCCCCTTTTGCATTT 59.124 37.500 0.00 0.00 0.00 2.32
665 694 1.388547 TGGGCCTGTGCGATTATTTC 58.611 50.000 4.53 0.00 38.85 2.17
750 1042 4.233558 GGGTGGGGGTGCCTTTGT 62.234 66.667 0.00 0.00 0.00 2.83
765 1057 2.058595 CCTAGGTGGTGGAGTCGGG 61.059 68.421 0.00 0.00 0.00 5.14
766 1058 0.613853 TTCCTAGGTGGTGGAGTCGG 60.614 60.000 9.08 0.00 37.07 4.79
767 1059 1.263356 TTTCCTAGGTGGTGGAGTCG 58.737 55.000 9.08 0.00 37.07 4.18
768 1060 2.290134 GGTTTTCCTAGGTGGTGGAGTC 60.290 54.545 9.08 0.00 37.07 3.36
769 1061 1.703513 GGTTTTCCTAGGTGGTGGAGT 59.296 52.381 9.08 0.00 37.07 3.85
770 1062 2.491675 GGTTTTCCTAGGTGGTGGAG 57.508 55.000 9.08 0.00 37.07 3.86
782 1074 4.228895 TGGGATCTAGGGTTTAGGTTTTCC 59.771 45.833 0.00 0.00 41.05 3.13
783 1075 5.045066 AGTGGGATCTAGGGTTTAGGTTTTC 60.045 44.000 0.00 0.00 0.00 2.29
784 1076 4.856182 AGTGGGATCTAGGGTTTAGGTTTT 59.144 41.667 0.00 0.00 0.00 2.43
785 1077 4.227527 CAGTGGGATCTAGGGTTTAGGTTT 59.772 45.833 0.00 0.00 0.00 3.27
786 1078 3.780850 CAGTGGGATCTAGGGTTTAGGTT 59.219 47.826 0.00 0.00 0.00 3.50
787 1079 3.385115 CAGTGGGATCTAGGGTTTAGGT 58.615 50.000 0.00 0.00 0.00 3.08
788 1080 2.104963 GCAGTGGGATCTAGGGTTTAGG 59.895 54.545 0.00 0.00 0.00 2.69
789 1081 2.104963 GGCAGTGGGATCTAGGGTTTAG 59.895 54.545 0.00 0.00 0.00 1.85
790 1082 2.124411 GGCAGTGGGATCTAGGGTTTA 58.876 52.381 0.00 0.00 0.00 2.01
791 1083 0.919710 GGCAGTGGGATCTAGGGTTT 59.080 55.000 0.00 0.00 0.00 3.27
792 1084 1.338136 CGGCAGTGGGATCTAGGGTT 61.338 60.000 0.00 0.00 0.00 4.11
793 1085 1.762460 CGGCAGTGGGATCTAGGGT 60.762 63.158 0.00 0.00 0.00 4.34
794 1086 3.142393 CGGCAGTGGGATCTAGGG 58.858 66.667 0.00 0.00 0.00 3.53
795 1087 2.423446 GCGGCAGTGGGATCTAGG 59.577 66.667 0.00 0.00 0.00 3.02
796 1088 2.423446 GGCGGCAGTGGGATCTAG 59.577 66.667 3.07 0.00 0.00 2.43
797 1089 3.536917 CGGCGGCAGTGGGATCTA 61.537 66.667 10.53 0.00 0.00 1.98
817 1109 3.365265 CAAACGTGCAGGGAGGGC 61.365 66.667 11.67 0.00 0.00 5.19
827 1119 4.389576 GCAGCCCGAGCAAACGTG 62.390 66.667 0.00 0.00 43.56 4.49
828 1120 4.626081 AGCAGCCCGAGCAAACGT 62.626 61.111 0.00 0.00 43.56 3.99
829 1121 3.793144 GAGCAGCCCGAGCAAACG 61.793 66.667 0.00 0.00 43.56 3.60
830 1122 3.435186 GGAGCAGCCCGAGCAAAC 61.435 66.667 0.00 0.00 43.56 2.93
893 1185 5.801531 AACATACCTGGGTTTTCTTTTCC 57.198 39.130 0.00 0.00 0.00 3.13
903 1195 2.042569 GGGGAAAGAAACATACCTGGGT 59.957 50.000 0.00 0.00 0.00 4.51
919 1211 0.777446 CAAAGAACAGGGGAGGGGAA 59.223 55.000 0.00 0.00 0.00 3.97
920 1212 1.140134 CCAAAGAACAGGGGAGGGGA 61.140 60.000 0.00 0.00 0.00 4.81
924 1216 2.666317 ACAAACCAAAGAACAGGGGAG 58.334 47.619 0.00 0.00 0.00 4.30
946 1238 9.360093 ACACATGAGAAACGAAAAACAAAAATA 57.640 25.926 0.00 0.00 0.00 1.40
947 1239 8.250538 ACACATGAGAAACGAAAAACAAAAAT 57.749 26.923 0.00 0.00 0.00 1.82
949 1241 8.918961 ATACACATGAGAAACGAAAAACAAAA 57.081 26.923 0.00 0.00 0.00 2.44
950 1242 8.918961 AATACACATGAGAAACGAAAAACAAA 57.081 26.923 0.00 0.00 0.00 2.83
958 1250 7.490962 ACAAAGAAATACACATGAGAAACGA 57.509 32.000 0.00 0.00 0.00 3.85
1025 1445 6.403200 GCTTATACTTACATGGTGTGGTTGTG 60.403 42.308 0.00 0.00 0.00 3.33
1029 1449 5.188948 TCTGCTTATACTTACATGGTGTGGT 59.811 40.000 0.00 0.00 0.00 4.16
1099 1525 2.777692 TGAGCTTATTAGGTTGAGGGGG 59.222 50.000 0.00 0.00 30.79 5.40
1100 1526 4.505742 GGATGAGCTTATTAGGTTGAGGGG 60.506 50.000 0.00 0.00 30.79 4.79
1101 1527 4.505742 GGGATGAGCTTATTAGGTTGAGGG 60.506 50.000 0.00 0.00 30.79 4.30
1102 1528 4.505742 GGGGATGAGCTTATTAGGTTGAGG 60.506 50.000 0.00 0.00 30.79 3.86
1111 1537 2.208872 ACAGGTGGGGATGAGCTTATT 58.791 47.619 0.00 0.00 0.00 1.40
1119 1545 1.628340 TGTACAGAACAGGTGGGGATG 59.372 52.381 0.00 0.00 33.01 3.51
1129 1555 4.097741 ACTTTGCTGCAATTGTACAGAACA 59.902 37.500 16.77 4.07 35.90 3.18
1168 1861 5.523552 TGGTTTTATCTGTCACGCATCTATG 59.476 40.000 0.00 0.00 0.00 2.23
1177 1870 6.128795 CGAAAGTCTCTGGTTTTATCTGTCAC 60.129 42.308 0.00 0.00 0.00 3.67
1205 1898 8.983724 GCTGAATAAGAGTACCATAGCTTTTAG 58.016 37.037 0.00 0.00 0.00 1.85
1339 2032 5.179045 AGTTTCTGCACTTCTGTTGAATG 57.821 39.130 0.00 0.00 0.00 2.67
1484 2177 4.075763 GCATAAGCTGTCACAGTTCTTG 57.924 45.455 6.68 3.22 37.91 3.02
1823 2516 9.423061 AGCACAATTTAGGTAAATTTTCATCAC 57.577 29.630 5.18 0.00 42.26 3.06
2113 2806 4.030913 TGTCCCATAACCTCTCAAGTAGG 58.969 47.826 0.00 0.00 40.20 3.18
2159 2852 5.046591 TGAGACCATAAGTTCCACTAAGGTG 60.047 44.000 0.00 0.00 42.65 4.00
2160 2853 5.091552 TGAGACCATAAGTTCCACTAAGGT 58.908 41.667 0.00 0.00 39.02 3.50
2206 2899 1.670811 CTTACACGAACATGGGATGGC 59.329 52.381 0.00 0.00 33.60 4.40
2235 2928 1.889573 GAAGGCCGCCTAGCATCAC 60.890 63.158 13.73 0.00 31.13 3.06
2236 2929 2.505982 GAAGGCCGCCTAGCATCA 59.494 61.111 13.73 0.00 31.13 3.07
2237 2930 2.663188 CGAAGGCCGCCTAGCATC 60.663 66.667 13.73 5.50 31.13 3.91
2280 2973 3.270877 GTCCAGCGGTTCAGAATATTGT 58.729 45.455 0.00 0.00 0.00 2.71
2288 2981 1.522668 TCATTTGTCCAGCGGTTCAG 58.477 50.000 0.00 0.00 0.00 3.02
2320 3013 9.396022 GTATTAAGGAGGAATTGATGAAAGTGA 57.604 33.333 0.00 0.00 0.00 3.41
2460 3153 3.541713 CTCCCTAGCACCGGAGCC 61.542 72.222 20.91 2.64 39.36 4.70
2461 3154 3.541713 CCTCCCTAGCACCGGAGC 61.542 72.222 16.88 16.88 43.78 4.70
2619 3312 9.448438 GGCCCACTTATTAATTTTCTGAAAAAT 57.552 29.630 18.43 13.23 44.97 1.82
2631 3324 2.306847 CGCTTGGGCCCACTTATTAAT 58.693 47.619 28.70 0.00 34.44 1.40
2632 3325 1.004979 ACGCTTGGGCCCACTTATTAA 59.995 47.619 28.70 7.00 34.44 1.40
2633 3326 0.621609 ACGCTTGGGCCCACTTATTA 59.378 50.000 28.70 7.92 34.44 0.98
2646 3339 3.559238 AGTATTTGGCTCAAACGCTTG 57.441 42.857 2.96 0.00 36.13 4.01
2648 3341 2.228822 CCAAGTATTTGGCTCAAACGCT 59.771 45.455 3.81 2.60 46.84 5.07
2714 3407 0.468226 TTACCCCGACAGGATCATGC 59.532 55.000 7.40 0.00 41.02 4.06
2791 3484 4.039852 ACACAAAACACACAAAAAGGGTCT 59.960 37.500 0.00 0.00 0.00 3.85
2871 3564 3.620427 ACGTTGCACCATATACTCCAA 57.380 42.857 0.00 0.00 0.00 3.53
2906 3599 3.840124 AGATCATCCGGGACCTTTTAC 57.160 47.619 0.00 0.00 0.00 2.01
2944 3637 2.236146 TGGCACCATACACTCCAGTTAG 59.764 50.000 0.00 0.00 0.00 2.34
3233 4053 1.077787 TAGGACCTGGCATTTGGCG 60.078 57.895 3.53 0.00 46.16 5.69
3345 4165 3.433740 GGAGAAAACCAACCTGTGTCTCT 60.434 47.826 0.00 0.00 33.69 3.10
3493 4313 3.155750 CCCTGGATGGCCTAGCTC 58.844 66.667 3.32 0.00 34.31 4.09
3587 4409 3.885724 TGTCACTTGTGACTTGTCAGA 57.114 42.857 27.23 8.96 39.41 3.27
3619 4441 6.849085 TTTGGTAAAATGGCATAGTGATGT 57.151 33.333 0.00 0.00 35.30 3.06
3669 4492 1.202758 TGGCTGTCGGTTTCATCTTGT 60.203 47.619 0.00 0.00 0.00 3.16
3679 4502 2.347490 GTGTCCATGGCTGTCGGT 59.653 61.111 6.96 0.00 0.00 4.69
3696 4519 0.811616 AAGGAAGCTGCTAATCGCCG 60.812 55.000 0.90 0.00 38.05 6.46
3748 4571 3.245948 CTGTGTGTTCAGGCGCTGC 62.246 63.158 7.64 0.00 0.00 5.25
3790 5687 2.587612 TCGTAAAACTGACATTGCGC 57.412 45.000 0.00 0.00 35.13 6.09
3805 5702 6.983890 ACAATACACATCTTGCATGTATCGTA 59.016 34.615 9.69 1.47 38.33 3.43
3807 5704 6.291067 ACAATACACATCTTGCATGTATCG 57.709 37.500 9.69 2.81 38.33 2.92
3819 5716 5.007385 ACGAAGGGAGTACAATACACATC 57.993 43.478 0.00 0.00 0.00 3.06
3820 5717 6.534475 TTACGAAGGGAGTACAATACACAT 57.466 37.500 0.00 0.00 0.00 3.21
3821 5718 5.981088 TTACGAAGGGAGTACAATACACA 57.019 39.130 0.00 0.00 0.00 3.72
3822 5719 6.393171 AGTTTACGAAGGGAGTACAATACAC 58.607 40.000 0.00 0.00 0.00 2.90
3823 5720 6.594788 AGTTTACGAAGGGAGTACAATACA 57.405 37.500 0.00 0.00 0.00 2.29
3831 5728 8.358895 GCTCTTATATTAGTTTACGAAGGGAGT 58.641 37.037 0.00 0.00 0.00 3.85
3832 5729 8.358148 TGCTCTTATATTAGTTTACGAAGGGAG 58.642 37.037 0.00 0.00 0.00 4.30
3833 5730 8.241497 TGCTCTTATATTAGTTTACGAAGGGA 57.759 34.615 0.00 0.00 0.00 4.20
3834 5731 9.490379 AATGCTCTTATATTAGTTTACGAAGGG 57.510 33.333 0.00 0.00 0.00 3.95
3892 5789 9.584008 CAGGTACTCCCTCTGTAAACTAATATA 57.416 37.037 0.00 0.00 43.86 0.86
3893 5790 7.015389 GCAGGTACTCCCTCTGTAAACTAATAT 59.985 40.741 0.00 0.00 43.86 1.28
3894 5791 6.323225 GCAGGTACTCCCTCTGTAAACTAATA 59.677 42.308 0.00 0.00 43.86 0.98
3895 5792 5.128991 GCAGGTACTCCCTCTGTAAACTAAT 59.871 44.000 0.00 0.00 43.86 1.73
3896 5793 4.465305 GCAGGTACTCCCTCTGTAAACTAA 59.535 45.833 0.00 0.00 43.86 2.24
3897 5794 4.021916 GCAGGTACTCCCTCTGTAAACTA 58.978 47.826 0.00 0.00 43.86 2.24
3898 5795 2.832733 GCAGGTACTCCCTCTGTAAACT 59.167 50.000 0.00 0.00 43.86 2.66
3899 5796 2.416972 CGCAGGTACTCCCTCTGTAAAC 60.417 54.545 0.00 0.00 43.86 2.01
3900 5797 1.822990 CGCAGGTACTCCCTCTGTAAA 59.177 52.381 0.00 0.00 43.86 2.01
3901 5798 1.471119 CGCAGGTACTCCCTCTGTAA 58.529 55.000 0.00 0.00 43.86 2.41
3902 5799 0.395311 CCGCAGGTACTCCCTCTGTA 60.395 60.000 0.00 0.00 43.86 2.74
3903 5800 1.682684 CCGCAGGTACTCCCTCTGT 60.683 63.158 0.00 0.00 43.86 3.41
3904 5801 3.211288 CCGCAGGTACTCCCTCTG 58.789 66.667 0.00 0.00 43.86 3.35


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

AutoCloner maintained by Alex Coulton.