Multiple sequence alignment - TraesCS2A01G328100

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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 TraesCS2A01G328100 chr2A 100.000 3476 0 0 1 3476 559671205 559667730 0.000000e+00 6420.0
1 TraesCS2A01G328100 chr2A 84.665 313 36 8 151 456 559833462 559833155 5.640000e-78 302.0
2 TraesCS2A01G328100 chr2A 78.486 502 66 29 2559 3041 738801192 738800714 1.220000e-74 291.0
3 TraesCS2A01G328100 chr2A 83.601 311 40 7 151 456 559776594 559776290 7.350000e-72 281.0
4 TraesCS2A01G328100 chr2A 78.487 423 65 19 1152 1564 560679746 560679340 1.600000e-63 254.0
5 TraesCS2A01G328100 chr2A 77.017 409 65 19 1147 1536 595225904 595226302 1.260000e-49 207.0
6 TraesCS2A01G328100 chr2A 83.838 99 8 4 3 100 559703494 559703403 1.720000e-13 87.9
7 TraesCS2A01G328100 chr2B 90.418 2557 146 38 283 2786 504772640 504775150 0.000000e+00 3273.0
8 TraesCS2A01G328100 chr2B 89.856 2573 150 52 283 2810 512355975 512353469 0.000000e+00 3203.0
9 TraesCS2A01G328100 chr2B 91.751 691 49 4 2790 3476 512352079 512351393 0.000000e+00 953.0
10 TraesCS2A01G328100 chr2B 88.750 640 57 8 2837 3476 504775150 504775774 0.000000e+00 769.0
11 TraesCS2A01G328100 chr2B 89.912 228 11 7 1 217 504772118 504772344 2.040000e-72 283.0
12 TraesCS2A01G328100 chr2B 89.140 221 12 6 8 217 512356489 512356270 7.400000e-67 265.0
13 TraesCS2A01G328100 chr2B 86.842 152 17 2 251 401 504755551 504755700 2.150000e-37 167.0
14 TraesCS2A01G328100 chr2B 82.119 151 20 1 251 401 512363549 512363406 4.710000e-24 122.0
15 TraesCS2A01G328100 chr2D 92.929 1584 65 18 972 2554 427951587 427953124 0.000000e+00 2261.0
16 TraesCS2A01G328100 chr2D 89.951 607 26 16 365 956 427949553 427950139 0.000000e+00 750.0
17 TraesCS2A01G328100 chr2D 88.781 517 27 5 2552 3041 427953147 427953659 3.840000e-169 604.0
18 TraesCS2A01G328100 chr2D 92.736 413 26 2 3065 3476 427953767 427954176 8.310000e-166 593.0
19 TraesCS2A01G328100 chr2D 94.954 218 10 1 1 217 427949209 427949426 1.190000e-89 340.0
20 TraesCS2A01G328100 chr2D 90.598 234 19 1 223 456 427911595 427911825 1.210000e-79 307.0
21 TraesCS2A01G328100 chr2D 77.506 409 63 20 1147 1536 455518582 455518184 5.840000e-53 219.0
22 TraesCS2A01G328100 chr2D 88.356 146 17 0 256 401 427934771 427934916 3.570000e-40 176.0
23 TraesCS2A01G328100 chr2D 86.986 146 19 0 256 401 427917277 427917422 7.720000e-37 165.0
24 TraesCS2A01G328100 chr2D 91.139 79 7 0 2870 2948 196724150 196724072 1.320000e-19 108.0
25 TraesCS2A01G328100 chr2D 86.869 99 6 3 2 100 427785719 427785810 1.710000e-18 104.0
26 TraesCS2A01G328100 chr2D 88.372 86 2 2 218 295 427949467 427949552 2.860000e-16 97.1
27 TraesCS2A01G328100 chr5A 79.630 594 75 25 2559 3140 113586667 113587226 5.440000e-103 385.0
28 TraesCS2A01G328100 chr6A 83.092 414 45 14 2734 3140 79406937 79407332 1.530000e-93 353.0


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 TraesCS2A01G328100 chr2A 559667730 559671205 3475 True 6420.000000 6420 100.000000 1 3476 1 chr2A.!!$R1 3475
1 TraesCS2A01G328100 chr2B 512351393 512356489 5096 True 1473.666667 3203 90.249000 8 3476 3 chr2B.!!$R2 3468
2 TraesCS2A01G328100 chr2B 504772118 504775774 3656 False 1441.666667 3273 89.693333 1 3476 3 chr2B.!!$F2 3475
3 TraesCS2A01G328100 chr2D 427949209 427954176 4967 False 774.183333 2261 91.287167 1 3476 6 chr2D.!!$F5 3475
4 TraesCS2A01G328100 chr5A 113586667 113587226 559 False 385.000000 385 79.630000 2559 3140 1 chr5A.!!$F1 581

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
861 1154 0.110486 TGGACTTGGCCTTGGAGAAC 59.89 55.0 3.32 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2824 4665 1.538047 GCACCATCTGCCTTGAAGAA 58.462 50.0 0.0 0.0 40.42 2.52 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
95 98 6.339730 CAATTGCATTTGCCAAGGAGTAATA 58.660 36.000 8.29 0.00 41.18 0.98
129 132 7.601856 TCAACAAATAATTAGTGCCTTTCTGG 58.398 34.615 0.00 0.00 39.35 3.86
179 184 4.142337 TGCACATTCACCTTGCATAATGAG 60.142 41.667 11.04 6.39 41.29 2.90
208 231 6.756542 ACAAAATTTCAGAAAACTGCCAGTAC 59.243 34.615 0.00 0.00 0.00 2.73
253 316 9.982651 CTGTTTAGAGATTATAATTTCCGAGGA 57.017 33.333 11.38 0.00 0.00 3.71
259 322 7.880195 AGAGATTATAATTTCCGAGGATTGGTG 59.120 37.037 11.38 0.00 41.84 4.17
297 558 4.439057 TCACCTAATCATAGTGCGGAAAC 58.561 43.478 0.00 0.00 0.00 2.78
306 567 5.597806 TCATAGTGCGGAAACTTGTATAGG 58.402 41.667 0.00 0.00 0.00 2.57
310 571 3.749609 GTGCGGAAACTTGTATAGGTGTT 59.250 43.478 0.00 0.00 0.00 3.32
312 573 5.409214 GTGCGGAAACTTGTATAGGTGTTAA 59.591 40.000 0.00 0.00 0.00 2.01
319 580 9.135843 GAAACTTGTATAGGTGTTAAAATTGGC 57.864 33.333 0.00 0.00 0.00 4.52
538 800 5.385617 CGAGCATTTAGTTTCCACTTTCTG 58.614 41.667 0.00 0.00 34.06 3.02
542 804 7.875971 AGCATTTAGTTTCCACTTTCTGTTAG 58.124 34.615 0.00 0.00 34.06 2.34
575 855 5.335191 GCAGATCATGACGAGGAAAGTTTTT 60.335 40.000 0.00 0.00 0.00 1.94
684 966 6.961360 TGTATCTGTGACTTACCATCCTAG 57.039 41.667 0.00 0.00 0.00 3.02
688 970 4.705507 TCTGTGACTTACCATCCTAGTGTC 59.294 45.833 0.00 0.00 0.00 3.67
756 1046 4.727507 ATCTACCACTGCTGTTACAGAG 57.272 45.455 17.40 12.47 40.25 3.35
765 1055 1.404851 GCTGTTACAGAGAGTCCCAGC 60.405 57.143 17.40 0.00 42.82 4.85
766 1056 1.895798 CTGTTACAGAGAGTCCCAGCA 59.104 52.381 6.50 0.00 32.44 4.41
767 1057 1.895798 TGTTACAGAGAGTCCCAGCAG 59.104 52.381 0.00 0.00 0.00 4.24
780 1070 1.605992 CAGCAGGAGGCCAGAATCA 59.394 57.895 5.01 0.00 46.50 2.57
785 1075 2.158696 GCAGGAGGCCAGAATCAACTAT 60.159 50.000 5.01 0.00 36.11 2.12
810 1100 7.881775 TCCCAGGATTTTTAGAAGCTTATTC 57.118 36.000 0.00 0.00 0.00 1.75
811 1101 7.410174 TCCCAGGATTTTTAGAAGCTTATTCA 58.590 34.615 0.00 0.00 0.00 2.57
812 1102 7.339466 TCCCAGGATTTTTAGAAGCTTATTCAC 59.661 37.037 0.00 0.00 0.00 3.18
813 1103 7.340487 CCCAGGATTTTTAGAAGCTTATTCACT 59.660 37.037 0.00 0.00 0.00 3.41
814 1104 8.743714 CCAGGATTTTTAGAAGCTTATTCACTT 58.256 33.333 0.00 0.00 0.00 3.16
817 1107 9.278734 GGATTTTTAGAAGCTTATTCACTTTCG 57.721 33.333 0.00 0.00 0.00 3.46
820 1110 9.825972 TTTTTAGAAGCTTATTCACTTTCGATG 57.174 29.630 0.00 0.00 0.00 3.84
821 1111 7.539712 TTAGAAGCTTATTCACTTTCGATGG 57.460 36.000 0.00 0.00 0.00 3.51
822 1112 5.734720 AGAAGCTTATTCACTTTCGATGGA 58.265 37.500 0.00 0.00 0.00 3.41
823 1113 5.582665 AGAAGCTTATTCACTTTCGATGGAC 59.417 40.000 0.00 0.00 0.00 4.02
825 1115 5.245531 AGCTTATTCACTTTCGATGGACAA 58.754 37.500 0.00 0.00 0.00 3.18
832 1122 5.551233 TCACTTTCGATGGACAAAATCTCT 58.449 37.500 0.00 0.00 0.00 3.10
841 1131 5.988310 TGGACAAAATCTCTGATTTGCAT 57.012 34.783 6.34 0.00 39.55 3.96
843 1133 6.160684 TGGACAAAATCTCTGATTTGCATTG 58.839 36.000 6.34 4.29 39.55 2.82
845 1135 6.349243 ACAAAATCTCTGATTTGCATTGGA 57.651 33.333 6.34 0.00 39.55 3.53
846 1136 6.161381 ACAAAATCTCTGATTTGCATTGGAC 58.839 36.000 6.34 0.00 39.55 4.02
847 1137 6.014840 ACAAAATCTCTGATTTGCATTGGACT 60.015 34.615 6.34 0.00 39.55 3.85
849 1142 5.578005 ATCTCTGATTTGCATTGGACTTG 57.422 39.130 0.00 0.00 0.00 3.16
851 1144 2.231964 TCTGATTTGCATTGGACTTGGC 59.768 45.455 0.00 0.00 0.00 4.52
855 1148 0.680618 TTGCATTGGACTTGGCCTTG 59.319 50.000 3.32 0.00 0.00 3.61
856 1149 1.186917 TGCATTGGACTTGGCCTTGG 61.187 55.000 3.32 0.00 0.00 3.61
857 1150 0.899717 GCATTGGACTTGGCCTTGGA 60.900 55.000 3.32 0.00 0.00 3.53
858 1151 1.180029 CATTGGACTTGGCCTTGGAG 58.820 55.000 3.32 0.00 0.00 3.86
859 1152 1.075601 ATTGGACTTGGCCTTGGAGA 58.924 50.000 3.32 0.00 0.00 3.71
860 1153 0.850100 TTGGACTTGGCCTTGGAGAA 59.150 50.000 3.32 0.00 0.00 2.87
861 1154 0.110486 TGGACTTGGCCTTGGAGAAC 59.890 55.000 3.32 0.00 0.00 3.01
862 1155 0.110486 GGACTTGGCCTTGGAGAACA 59.890 55.000 3.32 0.00 0.00 3.18
863 1156 1.239347 GACTTGGCCTTGGAGAACAC 58.761 55.000 3.32 0.00 0.00 3.32
864 1157 0.535102 ACTTGGCCTTGGAGAACACG 60.535 55.000 3.32 0.00 0.00 4.49
865 1158 1.228124 TTGGCCTTGGAGAACACGG 60.228 57.895 3.32 0.00 41.27 4.94
916 1209 5.448632 CGATCGTGCCACTATATATACAGCA 60.449 44.000 7.03 3.55 0.00 4.41
922 1218 4.630069 GCCACTATATATACAGCAAACCCG 59.370 45.833 0.00 0.00 0.00 5.28
956 1256 0.324460 TCGAACTCCTCTTCCCTCCC 60.324 60.000 0.00 0.00 0.00 4.30
964 1264 1.465188 TCTTCCCTCCCAAGCCCAA 60.465 57.895 0.00 0.00 0.00 4.12
965 1265 1.304464 CTTCCCTCCCAAGCCCAAC 60.304 63.158 0.00 0.00 0.00 3.77
966 1266 2.080336 CTTCCCTCCCAAGCCCAACA 62.080 60.000 0.00 0.00 0.00 3.33
967 1267 2.036256 CCCTCCCAAGCCCAACAG 59.964 66.667 0.00 0.00 0.00 3.16
968 1268 2.036256 CCTCCCAAGCCCAACAGG 59.964 66.667 0.00 0.00 39.47 4.00
969 1269 2.538141 CCTCCCAAGCCCAACAGGA 61.538 63.158 0.00 0.00 38.24 3.86
970 1270 1.001641 CTCCCAAGCCCAACAGGAG 60.002 63.158 0.00 0.00 38.24 3.69
987 2730 2.476499 GCTCTTCGCTTCGCAACC 59.524 61.111 0.00 0.00 35.14 3.77
988 2731 3.028366 GCTCTTCGCTTCGCAACCC 62.028 63.158 0.00 0.00 35.14 4.11
989 2732 2.358247 TCTTCGCTTCGCAACCCC 60.358 61.111 0.00 0.00 0.00 4.95
1644 3387 2.920912 TTCGTCAAGGCCCGAGGT 60.921 61.111 0.00 0.00 34.16 3.85
1657 3400 4.373116 GAGGTGGCGCTCAACCGA 62.373 66.667 7.64 0.00 32.21 4.69
1779 3522 4.537433 GCGGCGCCTCTGATCCTT 62.537 66.667 26.68 0.00 0.00 3.36
1781 3524 2.899339 GGCGCCTCTGATCCTTGC 60.899 66.667 22.15 0.00 0.00 4.01
1782 3525 2.124983 GCGCCTCTGATCCTTGCA 60.125 61.111 0.00 0.00 0.00 4.08
1783 3526 2.467826 GCGCCTCTGATCCTTGCAC 61.468 63.158 0.00 0.00 0.00 4.57
1784 3527 1.817099 CGCCTCTGATCCTTGCACC 60.817 63.158 0.00 0.00 0.00 5.01
1785 3528 1.817099 GCCTCTGATCCTTGCACCG 60.817 63.158 0.00 0.00 0.00 4.94
1786 3529 1.817099 CCTCTGATCCTTGCACCGC 60.817 63.158 0.00 0.00 0.00 5.68
1787 3530 1.817099 CTCTGATCCTTGCACCGCC 60.817 63.158 0.00 0.00 0.00 6.13
1788 3531 2.249413 CTCTGATCCTTGCACCGCCT 62.249 60.000 0.00 0.00 0.00 5.52
1789 3532 2.046023 TGATCCTTGCACCGCCTG 60.046 61.111 0.00 0.00 0.00 4.85
1830 3573 1.009108 CAACCGCAACGACAATGCA 60.009 52.632 0.00 0.00 44.01 3.96
1986 3729 1.299976 GGAGGGCGTGGACATCTTT 59.700 57.895 0.00 0.00 0.00 2.52
2361 4104 2.847234 AAGCCGGTGGTCACTCCA 60.847 61.111 1.90 0.00 45.01 3.86
2428 4201 0.249657 GGGCGCTGGATCTAGTTCAG 60.250 60.000 7.64 0.00 0.00 3.02
2429 4202 0.747255 GGCGCTGGATCTAGTTCAGA 59.253 55.000 7.64 0.00 37.79 3.27
2476 4249 6.951256 TCGACATTGATCTGAACAACTAAG 57.049 37.500 2.28 0.00 0.00 2.18
2480 4253 2.346803 TGATCTGAACAACTAAGCGCC 58.653 47.619 2.29 0.00 0.00 6.53
2585 4395 2.427410 GCAGCCAGCAAACGTTCG 60.427 61.111 0.00 0.00 44.79 3.95
2587 4397 3.660111 AGCCAGCAAACGTTCGCC 61.660 61.111 7.78 0.00 0.00 5.54
2591 4401 1.370414 CAGCAAACGTTCGCCAAGG 60.370 57.895 7.78 0.00 0.00 3.61
2606 4416 2.807967 GCCAAGGTTTTGATTTGCCTTC 59.192 45.455 0.00 0.00 39.11 3.46
2625 4441 1.818060 TCCATGGATTTTCGTTGGCAG 59.182 47.619 11.44 0.00 0.00 4.85
2633 4449 0.318869 TTTCGTTGGCAGCTGCATTG 60.319 50.000 37.63 23.84 44.36 2.82
2647 4463 2.156917 TGCATTGCTCTCTGAAAGTGG 58.843 47.619 10.49 0.00 33.76 4.00
2661 4479 6.411376 TCTGAAAGTGGAGAAACTTGTACAA 58.589 36.000 8.28 8.28 40.28 2.41
2785 4626 6.579145 GCAATTGGCAAGAACAGATGAACTG 61.579 44.000 7.72 0.00 46.44 3.16
2799 4640 7.308782 CAGATGAACTGTTATGTTTACTCCC 57.691 40.000 0.00 0.00 41.30 4.30
2800 4641 6.878923 CAGATGAACTGTTATGTTTACTCCCA 59.121 38.462 0.00 0.00 41.30 4.37
2801 4642 7.065085 CAGATGAACTGTTATGTTTACTCCCAG 59.935 40.741 0.00 0.00 41.30 4.45
2802 4643 6.428083 TGAACTGTTATGTTTACTCCCAGA 57.572 37.500 0.00 0.00 0.00 3.86
2803 4644 7.016153 TGAACTGTTATGTTTACTCCCAGAT 57.984 36.000 0.00 0.00 0.00 2.90
2804 4645 8.141298 TGAACTGTTATGTTTACTCCCAGATA 57.859 34.615 0.00 0.00 0.00 1.98
2805 4646 8.258007 TGAACTGTTATGTTTACTCCCAGATAG 58.742 37.037 0.00 0.00 0.00 2.08
2806 4647 6.583562 ACTGTTATGTTTACTCCCAGATAGC 58.416 40.000 0.00 0.00 0.00 2.97
2807 4648 6.384305 ACTGTTATGTTTACTCCCAGATAGCT 59.616 38.462 0.00 0.00 0.00 3.32
2808 4649 6.582636 TGTTATGTTTACTCCCAGATAGCTG 58.417 40.000 0.00 0.00 41.93 4.24
2809 4650 6.156256 TGTTATGTTTACTCCCAGATAGCTGT 59.844 38.462 7.31 0.00 40.63 4.40
2810 4651 7.343574 TGTTATGTTTACTCCCAGATAGCTGTA 59.656 37.037 7.31 0.00 40.63 2.74
2811 4652 6.808321 ATGTTTACTCCCAGATAGCTGTAA 57.192 37.500 7.31 0.00 40.63 2.41
2812 4653 6.222038 TGTTTACTCCCAGATAGCTGTAAG 57.778 41.667 7.31 6.30 40.63 2.34
2813 4654 5.955959 TGTTTACTCCCAGATAGCTGTAAGA 59.044 40.000 7.31 0.07 40.63 2.10
2814 4655 6.127423 TGTTTACTCCCAGATAGCTGTAAGAC 60.127 42.308 7.31 0.00 40.63 3.01
2815 4656 3.982516 ACTCCCAGATAGCTGTAAGACA 58.017 45.455 7.31 0.00 40.63 3.41
2816 4657 4.551671 ACTCCCAGATAGCTGTAAGACAT 58.448 43.478 7.31 0.00 40.63 3.06
2817 4658 4.586841 ACTCCCAGATAGCTGTAAGACATC 59.413 45.833 7.31 0.00 40.63 3.06
2818 4659 4.809193 TCCCAGATAGCTGTAAGACATCT 58.191 43.478 7.31 0.00 40.63 2.90
2819 4660 5.211973 TCCCAGATAGCTGTAAGACATCTT 58.788 41.667 7.31 0.00 40.63 2.40
2820 4661 6.373759 TCCCAGATAGCTGTAAGACATCTTA 58.626 40.000 7.31 0.00 40.63 2.10
2821 4662 7.013220 TCCCAGATAGCTGTAAGACATCTTAT 58.987 38.462 7.31 0.00 40.20 1.73
2822 4663 7.177568 TCCCAGATAGCTGTAAGACATCTTATC 59.822 40.741 7.31 0.00 40.20 1.75
2823 4664 7.178274 CCCAGATAGCTGTAAGACATCTTATCT 59.822 40.741 7.31 1.48 40.20 1.98
2824 4665 8.584157 CCAGATAGCTGTAAGACATCTTATCTT 58.416 37.037 7.31 0.00 40.20 2.40
2825 4666 9.979578 CAGATAGCTGTAAGACATCTTATCTTT 57.020 33.333 0.00 0.00 40.20 2.52
2829 4670 8.940768 AGCTGTAAGACATCTTATCTTTCTTC 57.059 34.615 4.70 0.00 40.20 2.87
2830 4671 8.535335 AGCTGTAAGACATCTTATCTTTCTTCA 58.465 33.333 4.70 0.00 40.20 3.02
2831 4672 9.155975 GCTGTAAGACATCTTATCTTTCTTCAA 57.844 33.333 4.70 0.00 40.20 2.69
2833 4674 9.658799 TGTAAGACATCTTATCTTTCTTCAAGG 57.341 33.333 4.70 0.00 40.20 3.61
2834 4675 7.622893 AAGACATCTTATCTTTCTTCAAGGC 57.377 36.000 0.00 0.00 32.32 4.35
2835 4676 6.715280 AGACATCTTATCTTTCTTCAAGGCA 58.285 36.000 0.00 0.00 32.64 4.75
2875 6178 2.161609 GCAAGCAAGTACGTAGCCATTT 59.838 45.455 0.00 0.00 0.00 2.32
2888 6191 7.715265 ACGTAGCCATTTATACTGAAATGAG 57.285 36.000 9.82 2.92 45.70 2.90
2948 6251 5.069119 TCAGTGTGACTGTACATTCAGAAGT 59.931 40.000 15.52 7.95 46.03 3.01
2950 6253 6.584184 CAGTGTGACTGTACATTCAGAAGTAG 59.416 42.308 15.52 3.08 41.19 2.57
2978 6281 8.668510 ATGTGATTGATTATACACAGAGAACC 57.331 34.615 0.00 0.00 44.39 3.62
3030 6334 6.931840 ACTCCTAGAGAAAAACATGAACTGAC 59.068 38.462 0.00 0.00 33.32 3.51
3184 6590 8.877808 TCATCTGTTCTAACACTGCATAATAG 57.122 34.615 0.00 0.00 34.70 1.73
3189 6595 8.703604 TGTTCTAACACTGCATAATAGACTTC 57.296 34.615 0.00 0.00 33.17 3.01
3191 6597 9.319143 GTTCTAACACTGCATAATAGACTTCAT 57.681 33.333 0.00 0.00 0.00 2.57
3198 6604 8.269424 CACTGCATAATAGACTTCATAAACGAC 58.731 37.037 0.00 0.00 0.00 4.34
3207 6613 2.953466 TCATAAACGACTCCCTTCCG 57.047 50.000 0.00 0.00 0.00 4.30
3287 6693 1.338200 CGTCAAAGAAGTCCCAGAGGG 60.338 57.143 0.00 0.00 46.11 4.30
3364 6770 2.879103 GGGATTCAAGACCCTTGACA 57.121 50.000 8.72 2.53 42.56 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
253 316 7.425606 GTGATTACAACTTTTCTGTCACCAAT 58.574 34.615 0.00 0.00 0.00 3.16
259 322 8.999431 TGATTAGGTGATTACAACTTTTCTGTC 58.001 33.333 0.00 0.00 41.81 3.51
297 558 7.826690 AGTGCCAATTTTAACACCTATACAAG 58.173 34.615 0.00 0.00 33.46 3.16
306 567 4.600692 AAGGGAGTGCCAATTTTAACAC 57.399 40.909 2.50 0.00 35.15 3.32
310 571 7.309770 ACAAAATAAGGGAGTGCCAATTTTA 57.690 32.000 19.48 4.93 33.99 1.52
312 573 5.823861 ACAAAATAAGGGAGTGCCAATTT 57.176 34.783 2.50 5.85 35.15 1.82
319 580 5.634859 GTGCATTGAACAAAATAAGGGAGTG 59.365 40.000 0.00 0.00 0.00 3.51
538 800 6.088749 CGTCATGATCTGCTGCTATTACTAAC 59.911 42.308 0.00 0.00 0.00 2.34
542 804 4.550422 TCGTCATGATCTGCTGCTATTAC 58.450 43.478 0.00 0.00 0.00 1.89
575 855 0.653636 GCCTCGTTTCGAACACACAA 59.346 50.000 0.00 0.00 34.74 3.33
608 890 1.457346 AGCAAGTTATCTGTGCTGCC 58.543 50.000 0.00 0.00 46.58 4.85
684 966 5.006649 GCATTTTCCTCCAACAAAAAGACAC 59.993 40.000 0.00 0.00 0.00 3.67
688 970 5.118286 ACAGCATTTTCCTCCAACAAAAAG 58.882 37.500 0.00 0.00 0.00 2.27
756 1046 3.791586 GGCCTCCTGCTGGGACTC 61.792 72.222 10.07 0.00 39.58 3.36
765 1055 3.853355 ATAGTTGATTCTGGCCTCCTG 57.147 47.619 3.32 0.00 0.00 3.86
766 1056 3.137360 GGAATAGTTGATTCTGGCCTCCT 59.863 47.826 3.32 0.00 43.20 3.69
767 1057 3.481453 GGAATAGTTGATTCTGGCCTCC 58.519 50.000 3.32 0.00 43.20 4.30
780 1070 7.414266 AGCTTCTAAAAATCCTGGGAATAGTT 58.586 34.615 0.00 0.00 0.00 2.24
785 1075 7.893302 TGAATAAGCTTCTAAAAATCCTGGGAA 59.107 33.333 0.00 0.00 0.00 3.97
810 1100 5.409520 TCAGAGATTTTGTCCATCGAAAGTG 59.590 40.000 0.00 0.00 33.52 3.16
811 1101 5.551233 TCAGAGATTTTGTCCATCGAAAGT 58.449 37.500 0.00 0.00 33.52 2.66
812 1102 6.674694 ATCAGAGATTTTGTCCATCGAAAG 57.325 37.500 0.00 0.00 33.52 2.62
813 1103 7.307694 CAAATCAGAGATTTTGTCCATCGAAA 58.692 34.615 2.42 0.00 34.39 3.46
814 1104 6.623549 GCAAATCAGAGATTTTGTCCATCGAA 60.624 38.462 2.42 0.00 35.69 3.71
815 1105 5.163723 GCAAATCAGAGATTTTGTCCATCGA 60.164 40.000 2.42 0.00 35.69 3.59
816 1106 5.032863 GCAAATCAGAGATTTTGTCCATCG 58.967 41.667 2.42 0.00 35.69 3.84
817 1107 5.957798 TGCAAATCAGAGATTTTGTCCATC 58.042 37.500 2.42 0.00 35.69 3.51
818 1108 5.988310 TGCAAATCAGAGATTTTGTCCAT 57.012 34.783 2.42 0.00 35.69 3.41
819 1109 5.988310 ATGCAAATCAGAGATTTTGTCCA 57.012 34.783 2.42 0.15 35.69 4.02
820 1110 5.579511 CCAATGCAAATCAGAGATTTTGTCC 59.420 40.000 2.42 0.00 35.69 4.02
821 1111 6.309737 GTCCAATGCAAATCAGAGATTTTGTC 59.690 38.462 2.42 0.00 35.69 3.18
822 1112 6.014840 AGTCCAATGCAAATCAGAGATTTTGT 60.015 34.615 2.42 0.00 35.69 2.83
823 1113 6.395629 AGTCCAATGCAAATCAGAGATTTTG 58.604 36.000 2.42 0.00 36.21 2.44
825 1115 6.395629 CAAGTCCAATGCAAATCAGAGATTT 58.604 36.000 0.00 0.00 0.00 2.17
832 1122 1.275856 GGCCAAGTCCAATGCAAATCA 59.724 47.619 0.00 0.00 0.00 2.57
841 1131 0.850100 TTCTCCAAGGCCAAGTCCAA 59.150 50.000 5.01 0.00 0.00 3.53
843 1133 0.110486 TGTTCTCCAAGGCCAAGTCC 59.890 55.000 5.01 0.00 0.00 3.85
845 1135 0.535102 CGTGTTCTCCAAGGCCAAGT 60.535 55.000 5.01 0.00 0.00 3.16
846 1136 1.237285 CCGTGTTCTCCAAGGCCAAG 61.237 60.000 5.01 0.00 35.86 3.61
847 1137 1.228124 CCGTGTTCTCCAAGGCCAA 60.228 57.895 5.01 0.00 35.86 4.52
851 1144 2.742372 CCGCCGTGTTCTCCAAGG 60.742 66.667 0.00 0.00 44.69 3.61
855 1148 1.737008 GTTCTCCGCCGTGTTCTCC 60.737 63.158 0.00 0.00 0.00 3.71
856 1149 1.006571 TGTTCTCCGCCGTGTTCTC 60.007 57.895 0.00 0.00 0.00 2.87
857 1150 1.300697 GTGTTCTCCGCCGTGTTCT 60.301 57.895 0.00 0.00 0.00 3.01
858 1151 2.315386 GGTGTTCTCCGCCGTGTTC 61.315 63.158 0.00 0.00 33.11 3.18
859 1152 2.280592 GGTGTTCTCCGCCGTGTT 60.281 61.111 0.00 0.00 33.11 3.32
864 1157 3.050275 GCAGTGGTGTTCTCCGCC 61.050 66.667 0.00 0.00 44.53 6.13
865 1158 1.598130 AAGCAGTGGTGTTCTCCGC 60.598 57.895 0.00 0.00 38.17 5.54
866 1159 1.845809 GCAAGCAGTGGTGTTCTCCG 61.846 60.000 0.00 0.00 0.00 4.63
916 1209 0.774908 TCATGGGAGGTTTCGGGTTT 59.225 50.000 0.00 0.00 0.00 3.27
922 1218 2.028020 AGTTCGAGTCATGGGAGGTTTC 60.028 50.000 0.00 0.00 0.00 2.78
956 1256 0.251077 AAGAGCTCCTGTTGGGCTTG 60.251 55.000 10.93 0.00 39.07 4.01
987 2730 3.907130 GCCATGGGGATGGAGGGG 61.907 72.222 15.13 0.00 44.39 4.79
988 2731 4.275508 CGCCATGGGGATGGAGGG 62.276 72.222 23.98 0.00 44.39 4.30
989 2732 3.170672 TCGCCATGGGGATGGAGG 61.171 66.667 26.54 0.00 44.39 4.30
1036 2779 2.743928 CCTGAACACCGCTCCTGC 60.744 66.667 0.00 0.00 0.00 4.85
1309 3052 1.507174 GCTCGTACAGCTTCTCGGT 59.493 57.895 9.26 0.00 45.83 4.69
1319 3062 0.970937 CTCCCCCTTGAGCTCGTACA 60.971 60.000 9.64 0.00 0.00 2.90
1644 3387 1.153647 CAGTATCGGTTGAGCGCCA 60.154 57.895 2.29 0.00 0.00 5.69
1652 3395 1.740296 GCACACGGCAGTATCGGTT 60.740 57.895 0.00 0.00 43.97 4.44
1765 3508 2.124983 TGCAAGGATCAGAGGCGC 60.125 61.111 0.00 0.00 0.00 6.53
1771 3514 2.110967 CAGGCGGTGCAAGGATCAG 61.111 63.158 0.00 0.00 0.00 2.90
1772 3515 2.046023 CAGGCGGTGCAAGGATCA 60.046 61.111 0.00 0.00 0.00 2.92
1785 3528 4.329545 TCGTTGGAGTGGGCAGGC 62.330 66.667 0.00 0.00 0.00 4.85
1786 3529 2.046892 CTCGTTGGAGTGGGCAGG 60.047 66.667 0.00 0.00 35.48 4.85
1787 3530 2.046892 CCTCGTTGGAGTGGGCAG 60.047 66.667 0.00 0.00 38.70 4.85
1788 3531 2.525629 TCCTCGTTGGAGTGGGCA 60.526 61.111 0.00 0.00 40.56 5.36
1923 3666 3.987404 GCGATCTTGCCAGTGGTT 58.013 55.556 11.74 0.00 0.00 3.67
2020 3763 2.360475 GTCCTGCTTCCTGTGGCC 60.360 66.667 0.00 0.00 0.00 5.36
2205 3948 4.988598 CACGTCACCTTGCCGCCT 62.989 66.667 0.00 0.00 0.00 5.52
2376 4131 4.779966 TCCGCCTCGCTCGAGAGT 62.780 66.667 18.75 0.00 44.53 3.24
2378 4133 3.971109 TTCTCCGCCTCGCTCGAGA 62.971 63.158 18.75 0.00 44.53 4.04
2415 4188 3.646736 TCCGAGTCTGAACTAGATCCA 57.353 47.619 0.00 0.00 37.83 3.41
2428 4201 4.899239 CCTGGGCGCATCCGAGTC 62.899 72.222 10.83 0.00 38.86 3.36
2495 4269 2.229062 TCAAACGAGACCTCTGCTACAG 59.771 50.000 0.00 0.00 0.00 2.74
2585 4395 2.549064 AGGCAAATCAAAACCTTGGC 57.451 45.000 0.00 0.00 43.78 4.52
2587 4397 4.070630 TGGAAGGCAAATCAAAACCTTG 57.929 40.909 0.00 0.00 42.54 3.61
2591 4401 4.270245 TCCATGGAAGGCAAATCAAAAC 57.730 40.909 13.46 0.00 0.00 2.43
2606 4416 1.736696 GCTGCCAACGAAAATCCATGG 60.737 52.381 4.97 4.97 0.00 3.66
2625 4441 1.811359 ACTTTCAGAGAGCAATGCAGC 59.189 47.619 8.35 0.00 0.00 5.25
2633 4449 4.001618 AGTTTCTCCACTTTCAGAGAGC 57.998 45.455 0.00 0.00 40.13 4.09
2661 4479 4.020128 GGAACATTCCTACCAACTCTCACT 60.020 45.833 3.24 0.00 44.11 3.41
2785 4626 6.583562 ACAGCTATCTGGGAGTAAACATAAC 58.416 40.000 0.00 0.00 44.54 1.89
2786 4627 6.808321 ACAGCTATCTGGGAGTAAACATAA 57.192 37.500 0.00 0.00 44.54 1.90
2787 4628 7.783119 TCTTACAGCTATCTGGGAGTAAACATA 59.217 37.037 0.00 0.00 44.54 2.29
2788 4629 6.611642 TCTTACAGCTATCTGGGAGTAAACAT 59.388 38.462 0.00 0.00 44.54 2.71
2789 4630 5.955959 TCTTACAGCTATCTGGGAGTAAACA 59.044 40.000 0.00 0.00 44.54 2.83
2790 4631 6.127423 TGTCTTACAGCTATCTGGGAGTAAAC 60.127 42.308 0.00 0.00 44.54 2.01
2791 4632 5.955959 TGTCTTACAGCTATCTGGGAGTAAA 59.044 40.000 0.00 0.00 44.54 2.01
2792 4633 5.516044 TGTCTTACAGCTATCTGGGAGTAA 58.484 41.667 0.00 0.00 44.54 2.24
2793 4634 5.125367 TGTCTTACAGCTATCTGGGAGTA 57.875 43.478 0.00 0.00 44.54 2.59
2794 4635 3.982516 TGTCTTACAGCTATCTGGGAGT 58.017 45.455 0.00 0.00 44.54 3.85
2795 4636 4.832266 AGATGTCTTACAGCTATCTGGGAG 59.168 45.833 0.00 0.00 43.87 4.30
2796 4637 4.809193 AGATGTCTTACAGCTATCTGGGA 58.191 43.478 0.00 0.00 43.87 4.37
2797 4638 5.543507 AAGATGTCTTACAGCTATCTGGG 57.456 43.478 0.00 0.00 45.10 4.45
2798 4639 8.121305 AGATAAGATGTCTTACAGCTATCTGG 57.879 38.462 4.70 0.00 45.10 3.86
2799 4640 9.979578 AAAGATAAGATGTCTTACAGCTATCTG 57.020 33.333 4.70 0.00 45.10 2.90
2805 4646 8.709386 TGAAGAAAGATAAGATGTCTTACAGC 57.291 34.615 4.70 0.00 40.81 4.40
2807 4648 9.658799 CCTTGAAGAAAGATAAGATGTCTTACA 57.341 33.333 4.70 0.00 38.24 2.41
2808 4649 8.608317 GCCTTGAAGAAAGATAAGATGTCTTAC 58.392 37.037 4.70 0.87 38.24 2.34
2809 4650 8.321353 TGCCTTGAAGAAAGATAAGATGTCTTA 58.679 33.333 5.05 5.05 38.24 2.10
2810 4651 7.170965 TGCCTTGAAGAAAGATAAGATGTCTT 58.829 34.615 0.00 0.45 38.24 3.01
2811 4652 6.715280 TGCCTTGAAGAAAGATAAGATGTCT 58.285 36.000 0.00 0.00 38.24 3.41
2812 4653 6.820656 TCTGCCTTGAAGAAAGATAAGATGTC 59.179 38.462 0.00 0.00 38.24 3.06
2813 4654 6.715280 TCTGCCTTGAAGAAAGATAAGATGT 58.285 36.000 0.00 0.00 38.24 3.06
2814 4655 7.255173 CCATCTGCCTTGAAGAAAGATAAGATG 60.255 40.741 8.59 0.00 41.15 2.90
2815 4656 6.771749 CCATCTGCCTTGAAGAAAGATAAGAT 59.228 38.462 8.59 0.00 38.24 2.40
2816 4657 6.118170 CCATCTGCCTTGAAGAAAGATAAGA 58.882 40.000 8.59 0.00 38.24 2.10
2817 4658 5.884792 ACCATCTGCCTTGAAGAAAGATAAG 59.115 40.000 8.59 6.87 38.24 1.73
2818 4659 5.649395 CACCATCTGCCTTGAAGAAAGATAA 59.351 40.000 8.59 0.00 38.24 1.75
2819 4660 5.188434 CACCATCTGCCTTGAAGAAAGATA 58.812 41.667 8.59 0.00 38.24 1.98
2820 4661 4.015084 CACCATCTGCCTTGAAGAAAGAT 58.985 43.478 0.00 0.00 38.24 2.40
2821 4662 3.415212 CACCATCTGCCTTGAAGAAAGA 58.585 45.455 0.00 0.00 38.24 2.52
2822 4663 2.094854 GCACCATCTGCCTTGAAGAAAG 60.095 50.000 0.00 0.00 40.42 2.62
2823 4664 1.888512 GCACCATCTGCCTTGAAGAAA 59.111 47.619 0.00 0.00 40.42 2.52
2824 4665 1.538047 GCACCATCTGCCTTGAAGAA 58.462 50.000 0.00 0.00 40.42 2.52
2825 4666 3.254629 GCACCATCTGCCTTGAAGA 57.745 52.632 0.00 0.00 40.42 2.87
2833 4674 2.223340 CGAAAATGTAGGCACCATCTGC 60.223 50.000 0.00 0.00 46.31 4.26
2834 4675 2.223340 GCGAAAATGTAGGCACCATCTG 60.223 50.000 0.00 0.00 0.00 2.90
2835 4676 2.017049 GCGAAAATGTAGGCACCATCT 58.983 47.619 0.00 0.00 0.00 2.90
2941 6244 8.969260 ATAATCAATCACATTGCTACTTCTGA 57.031 30.769 0.00 0.00 40.05 3.27
2948 6251 9.264719 CTCTGTGTATAATCAATCACATTGCTA 57.735 33.333 0.00 0.00 39.51 3.49
2950 6253 8.146479 TCTCTGTGTATAATCAATCACATTGC 57.854 34.615 0.00 0.00 39.51 3.56
2978 6281 6.846325 ACTTGTTAGTTTTTCCTTCGAGAG 57.154 37.500 0.00 0.00 0.00 3.20
3030 6334 2.037136 CCTCCAGGCTGCAACTTCG 61.037 63.158 9.56 0.00 0.00 3.79
3035 6339 2.671070 GCTACCTCCAGGCTGCAA 59.329 61.111 9.56 0.00 39.32 4.08
3036 6340 3.402681 GGCTACCTCCAGGCTGCA 61.403 66.667 9.56 0.00 38.10 4.41
3037 6341 4.182433 GGGCTACCTCCAGGCTGC 62.182 72.222 9.56 0.00 40.78 5.25
3038 6342 2.366167 AGGGCTACCTCCAGGCTG 60.366 66.667 7.75 7.75 46.95 4.85
3080 6483 8.730948 TGAGTTACTAGTACCATTATCTACCCT 58.269 37.037 0.91 0.00 0.00 4.34
3184 6590 4.182339 GGAAGGGAGTCGTTTATGAAGTC 58.818 47.826 0.00 0.00 0.00 3.01
3189 6595 2.094390 TGTCGGAAGGGAGTCGTTTATG 60.094 50.000 0.00 0.00 0.00 1.90
3191 6597 1.619654 TGTCGGAAGGGAGTCGTTTA 58.380 50.000 0.00 0.00 0.00 2.01
3195 6601 1.141881 CCATGTCGGAAGGGAGTCG 59.858 63.158 0.00 0.00 36.56 4.18
3198 6604 1.987807 ATGGCCATGTCGGAAGGGAG 61.988 60.000 20.04 0.00 36.56 4.30
3207 6613 2.620115 CAGGATGTTGTATGGCCATGTC 59.380 50.000 29.04 20.14 0.00 3.06
3287 6693 2.704572 AGCAGAAAGTGACTATGGTGC 58.295 47.619 0.00 0.00 0.00 5.01
3364 6770 6.530120 TGACAGGACAACATACATAACACTT 58.470 36.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.