Multiple sequence alignment - TraesCS4D01G244100

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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 TraesCS4D01G244100 chr4D 100.000 7638 0 0 1 7638 408802339 408794702 0.000000e+00 14105
1 TraesCS4D01G244100 chr4D 92.441 635 47 1 3215 3848 82039945 82039311 0.000000e+00 905
2 TraesCS4D01G244100 chr4D 93.878 245 5 1 6302 6536 408801007 408800763 2.030000e-95 361
3 TraesCS4D01G244100 chr3D 89.519 5219 472 48 1333 6538 30435915 30430759 0.000000e+00 6538
4 TraesCS4D01G244100 chr3D 86.745 5183 611 63 1333 6482 111883224 111878085 0.000000e+00 5696
5 TraesCS4D01G244100 chr1B 88.900 5108 501 47 1333 6413 1869197 1874265 0.000000e+00 6231
6 TraesCS4D01G244100 chr1B 87.086 2780 298 34 1333 4069 643496867 643499628 0.000000e+00 3088
7 TraesCS4D01G244100 chr1B 86.549 2773 336 32 3729 6482 6143649 6146403 0.000000e+00 3020
8 TraesCS4D01G244100 chr6D 95.173 3128 129 10 1332 4458 158455316 158458422 0.000000e+00 4920
9 TraesCS4D01G244100 chr6D 95.577 1741 62 4 4806 6536 158458417 158460152 0.000000e+00 2774
10 TraesCS4D01G244100 chr6D 96.735 245 8 0 1333 1577 158459908 158460152 7.130000e-110 409
11 TraesCS4D01G244100 chr2D 86.608 4092 459 55 2446 6507 459110779 459106747 0.000000e+00 4438
12 TraesCS4D01G244100 chr2D 91.654 635 52 1 3215 3848 621146064 621146698 0.000000e+00 878
13 TraesCS4D01G244100 chr5D 82.672 4963 752 78 1569 6464 500639692 500634771 0.000000e+00 4301
14 TraesCS4D01G244100 chr5D 91.811 635 51 1 3215 3848 449474010 449474644 0.000000e+00 883
15 TraesCS4D01G244100 chr2B 82.311 4941 787 57 1569 6464 161386833 161391731 0.000000e+00 4202
16 TraesCS4D01G244100 chr5A 81.173 5200 840 92 1333 6464 442289335 442284207 0.000000e+00 4050
17 TraesCS4D01G244100 chr7A 80.530 4525 792 67 1332 5826 38341108 38345573 0.000000e+00 3393
18 TraesCS4D01G244100 chr4A 83.120 3596 547 41 2823 6399 578564610 578568164 0.000000e+00 3223
19 TraesCS4D01G244100 chr4A 96.293 1106 24 3 6537 7638 80170526 80169434 0.000000e+00 1799
20 TraesCS4D01G244100 chr4A 89.674 1075 60 26 296 1332 80171583 80170522 0.000000e+00 1323
21 TraesCS4D01G244100 chr4A 87.540 313 20 10 2 303 80171906 80171602 2.040000e-90 344
22 TraesCS4D01G244100 chrUn 87.086 2780 298 34 1333 4069 34554797 34557558 0.000000e+00 3088
23 TraesCS4D01G244100 chrUn 87.086 2780 298 34 1333 4069 205171193 205173954 0.000000e+00 3088
24 TraesCS4D01G244100 chrUn 89.284 2165 216 13 1333 3487 117078691 117076533 0.000000e+00 2699
25 TraesCS4D01G244100 chrUn 90.462 1688 147 7 3669 5354 117067537 117065862 0.000000e+00 2213
26 TraesCS4D01G244100 chrUn 88.000 250 19 10 1333 1577 34568889 34569132 1.250000e-72 285
27 TraesCS4D01G244100 chr5B 87.086 2780 298 34 1333 4069 647481992 647479231 0.000000e+00 3088
28 TraesCS4D01G244100 chr4B 87.086 2780 298 34 1333 4069 657639981 657637220 0.000000e+00 3088
29 TraesCS4D01G244100 chr4B 90.639 1378 68 24 1 1332 507243584 507244946 0.000000e+00 1773
30 TraesCS4D01G244100 chr4B 91.214 1104 66 7 6537 7638 507244942 507246016 0.000000e+00 1472
31 TraesCS4D01G244100 chr7D 92.283 635 47 2 3215 3848 421097997 421098630 0.000000e+00 900
32 TraesCS4D01G244100 chr7D 91.811 635 51 1 3215 3848 520305271 520304637 0.000000e+00 883
33 TraesCS4D01G244100 chr1D 92.283 635 48 1 3215 3848 92156229 92156863 0.000000e+00 900
34 TraesCS4D01G244100 chr1D 92.283 635 48 1 3215 3848 397268827 397269461 0.000000e+00 900
35 TraesCS4D01G244100 chr1D 91.969 635 50 1 3215 3848 467777543 467778177 0.000000e+00 889


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 TraesCS4D01G244100 chr4D 408794702 408802339 7637 True 7233.000000 14105 96.939000 1 7638 2 chr4D.!!$R2 7637
1 TraesCS4D01G244100 chr4D 82039311 82039945 634 True 905.000000 905 92.441000 3215 3848 1 chr4D.!!$R1 633
2 TraesCS4D01G244100 chr3D 30430759 30435915 5156 True 6538.000000 6538 89.519000 1333 6538 1 chr3D.!!$R1 5205
3 TraesCS4D01G244100 chr3D 111878085 111883224 5139 True 5696.000000 5696 86.745000 1333 6482 1 chr3D.!!$R2 5149
4 TraesCS4D01G244100 chr1B 1869197 1874265 5068 False 6231.000000 6231 88.900000 1333 6413 1 chr1B.!!$F1 5080
5 TraesCS4D01G244100 chr1B 643496867 643499628 2761 False 3088.000000 3088 87.086000 1333 4069 1 chr1B.!!$F3 2736
6 TraesCS4D01G244100 chr1B 6143649 6146403 2754 False 3020.000000 3020 86.549000 3729 6482 1 chr1B.!!$F2 2753
7 TraesCS4D01G244100 chr6D 158455316 158460152 4836 False 2701.000000 4920 95.828333 1332 6536 3 chr6D.!!$F1 5204
8 TraesCS4D01G244100 chr2D 459106747 459110779 4032 True 4438.000000 4438 86.608000 2446 6507 1 chr2D.!!$R1 4061
9 TraesCS4D01G244100 chr2D 621146064 621146698 634 False 878.000000 878 91.654000 3215 3848 1 chr2D.!!$F1 633
10 TraesCS4D01G244100 chr5D 500634771 500639692 4921 True 4301.000000 4301 82.672000 1569 6464 1 chr5D.!!$R1 4895
11 TraesCS4D01G244100 chr5D 449474010 449474644 634 False 883.000000 883 91.811000 3215 3848 1 chr5D.!!$F1 633
12 TraesCS4D01G244100 chr2B 161386833 161391731 4898 False 4202.000000 4202 82.311000 1569 6464 1 chr2B.!!$F1 4895
13 TraesCS4D01G244100 chr5A 442284207 442289335 5128 True 4050.000000 4050 81.173000 1333 6464 1 chr5A.!!$R1 5131
14 TraesCS4D01G244100 chr7A 38341108 38345573 4465 False 3393.000000 3393 80.530000 1332 5826 1 chr7A.!!$F1 4494
15 TraesCS4D01G244100 chr4A 578564610 578568164 3554 False 3223.000000 3223 83.120000 2823 6399 1 chr4A.!!$F1 3576
16 TraesCS4D01G244100 chr4A 80169434 80171906 2472 True 1155.333333 1799 91.169000 2 7638 3 chr4A.!!$R1 7636
17 TraesCS4D01G244100 chrUn 34554797 34557558 2761 False 3088.000000 3088 87.086000 1333 4069 1 chrUn.!!$F1 2736
18 TraesCS4D01G244100 chrUn 205171193 205173954 2761 False 3088.000000 3088 87.086000 1333 4069 1 chrUn.!!$F3 2736
19 TraesCS4D01G244100 chrUn 117076533 117078691 2158 True 2699.000000 2699 89.284000 1333 3487 1 chrUn.!!$R2 2154
20 TraesCS4D01G244100 chrUn 117065862 117067537 1675 True 2213.000000 2213 90.462000 3669 5354 1 chrUn.!!$R1 1685
21 TraesCS4D01G244100 chr5B 647479231 647481992 2761 True 3088.000000 3088 87.086000 1333 4069 1 chr5B.!!$R1 2736
22 TraesCS4D01G244100 chr4B 657637220 657639981 2761 True 3088.000000 3088 87.086000 1333 4069 1 chr4B.!!$R1 2736
23 TraesCS4D01G244100 chr4B 507243584 507246016 2432 False 1622.500000 1773 90.926500 1 7638 2 chr4B.!!$F1 7637
24 TraesCS4D01G244100 chr7D 421097997 421098630 633 False 900.000000 900 92.283000 3215 3848 1 chr7D.!!$F1 633
25 TraesCS4D01G244100 chr7D 520304637 520305271 634 True 883.000000 883 91.811000 3215 3848 1 chr7D.!!$R1 633
26 TraesCS4D01G244100 chr1D 92156229 92156863 634 False 900.000000 900 92.283000 3215 3848 1 chr1D.!!$F1 633
27 TraesCS4D01G244100 chr1D 397268827 397269461 634 False 900.000000 900 92.283000 3215 3848 1 chr1D.!!$F2 633
28 TraesCS4D01G244100 chr1D 467777543 467778177 634 False 889.000000 889 91.969000 3215 3848 1 chr1D.!!$F3 633

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
350 397 0.314935 CAATTTGGTGCGCTCCAAGT 59.685 50.000 34.51 30.98 46.27 3.16 F
780 856 0.538057 CAGTGGCCTGCTTTTCCTGA 60.538 55.000 3.32 0.00 0.00 3.86 F
1234 1325 1.004560 TCAGCTCAAACTCTGGCCG 60.005 57.895 0.00 0.00 0.00 6.13 F
1330 1421 1.135575 GCCAAGAGCGAAAACCTGATG 60.136 52.381 0.00 0.00 0.00 3.07 F
3254 3409 1.591863 GCCGCAGAAGATCCCGTAC 60.592 63.158 0.00 0.00 0.00 3.67 F
4092 4309 1.136828 TTACACCCCTCTGTTGTGCT 58.863 50.000 0.00 0.00 33.30 4.40 F
5257 5480 0.246635 GGCACCACTGTCGACATACT 59.753 55.000 20.40 1.39 0.00 2.12 F
5402 5625 0.182061 ATCTGGCATCGAGGTGCATT 59.818 50.000 12.73 0.00 46.81 3.56 F
5408 5631 1.742761 CATCGAGGTGCATTTGGACT 58.257 50.000 2.19 0.00 36.56 3.85 F
6054 6290 2.494918 CGCCGACGATTCCTTCCT 59.505 61.111 0.00 0.00 43.93 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1321 1412 0.035317 TCTCGCACAGCATCAGGTTT 59.965 50.000 0.00 0.00 0.00 3.27 R
1987 2123 2.280524 TCAACTGGTGGGTTCGCG 60.281 61.111 0.00 0.00 0.00 5.87 R
2128 2264 2.283298 ACTGTTCACTTGACAGCTGTG 58.717 47.619 27.27 12.98 35.08 3.66 R
3315 3476 0.618968 AGAAGATCAGGACCGCCCTT 60.619 55.000 0.00 0.00 44.85 3.95 R
4139 4356 2.601905 ACCTACGTCCCTACAACAAGT 58.398 47.619 0.00 0.00 0.00 3.16 R
5283 5506 0.318955 AATTTGTTGCTGCTGCGGAC 60.319 50.000 13.72 12.15 43.34 4.79 R
6617 6899 0.253020 TACTCCACCTTCCCCTTCCC 60.253 60.000 0.00 0.00 0.00 3.97 R
6620 6902 0.914902 GCCTACTCCACCTTCCCCTT 60.915 60.000 0.00 0.00 0.00 3.95 R
6621 6903 1.307084 GCCTACTCCACCTTCCCCT 60.307 63.158 0.00 0.00 0.00 4.79 R
7016 7298 1.815003 GGCTCTCTGGTGACAAAATGG 59.185 52.381 0.00 0.00 42.06 3.16 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
49 50 8.851960 AAAAATAAGAAGAGAAAAACGTGGTC 57.148 30.769 0.00 0.00 0.00 4.02
77 78 0.388520 GCAATTTTCACGGTCCTGCC 60.389 55.000 0.00 0.00 0.00 4.85
169 179 2.376695 TCTACGGCCTAGCTGGTAAT 57.623 50.000 0.00 0.00 39.57 1.89
333 380 4.994852 CCAATTCGACCAGTCTAGTTTCAA 59.005 41.667 0.00 0.00 0.00 2.69
350 397 0.314935 CAATTTGGTGCGCTCCAAGT 59.685 50.000 34.51 30.98 46.27 3.16
375 422 1.021202 AGTCGATCGAAGGCTCTGAG 58.979 55.000 21.31 0.00 0.00 3.35
469 520 9.451002 TTTGGTATTTAATCGTTGGAATACAGA 57.549 29.630 12.69 0.00 36.93 3.41
471 522 9.621629 TGGTATTTAATCGTTGGAATACAGAAT 57.378 29.630 12.69 0.00 36.93 2.40
479 530 4.324402 CGTTGGAATACAGAATTTGCAAGC 59.676 41.667 0.00 0.00 0.00 4.01
497 548 7.969387 TGCAAGCAGAATATAATTTTCGTTC 57.031 32.000 0.00 0.00 0.00 3.95
537 591 1.277557 TGGGCAAAACAAGCACAGTTT 59.722 42.857 0.00 0.00 41.18 2.66
585 661 2.024414 CCCAAAATCTAGGCTTTCCCG 58.976 52.381 0.00 0.00 39.21 5.14
599 675 4.316645 GCTTTCCCGAGAAGTAGAAAAGT 58.683 43.478 0.00 0.00 32.35 2.66
600 676 5.476614 GCTTTCCCGAGAAGTAGAAAAGTA 58.523 41.667 0.00 0.00 32.35 2.24
601 677 5.348179 GCTTTCCCGAGAAGTAGAAAAGTAC 59.652 44.000 0.00 0.00 32.35 2.73
641 717 3.947910 AACTCACAATGCTGGATTTGG 57.052 42.857 0.00 0.00 0.00 3.28
712 788 3.501445 GGCTGGCAGATGAGATGTATTTC 59.499 47.826 20.86 0.00 0.00 2.17
722 798 9.993454 CAGATGAGATGTATTTCCTTGATTAGA 57.007 33.333 0.00 0.00 0.00 2.10
780 856 0.538057 CAGTGGCCTGCTTTTCCTGA 60.538 55.000 3.32 0.00 0.00 3.86
786 862 2.127251 GCCTGCTTTTCCTGAAAAACG 58.873 47.619 6.53 0.00 39.49 3.60
787 863 2.127251 CCTGCTTTTCCTGAAAAACGC 58.873 47.619 6.53 7.76 39.49 4.84
788 864 2.481104 CCTGCTTTTCCTGAAAAACGCA 60.481 45.455 14.62 14.62 39.49 5.24
789 865 3.186119 CTGCTTTTCCTGAAAAACGCAA 58.814 40.909 15.61 5.40 38.89 4.85
791 867 3.186909 GCTTTTCCTGAAAAACGCAACT 58.813 40.909 6.53 0.00 39.49 3.16
793 869 4.441087 GCTTTTCCTGAAAAACGCAACTAG 59.559 41.667 6.53 0.00 39.49 2.57
794 870 3.619233 TTCCTGAAAAACGCAACTAGC 57.381 42.857 0.00 0.00 40.87 3.42
836 921 2.519771 ATAGGGTACGGGATATGCGA 57.480 50.000 0.00 0.00 0.00 5.10
922 1012 7.538327 AGATCATATCTGTCCTAGTATCCCT 57.462 40.000 0.00 0.00 38.44 4.20
926 1016 2.950781 TCTGTCCTAGTATCCCTGCAG 58.049 52.381 6.78 6.78 0.00 4.41
927 1017 2.245028 TCTGTCCTAGTATCCCTGCAGT 59.755 50.000 13.81 0.00 0.00 4.40
928 1018 3.034635 CTGTCCTAGTATCCCTGCAGTT 58.965 50.000 13.81 0.00 0.00 3.16
929 1019 4.079385 TCTGTCCTAGTATCCCTGCAGTTA 60.079 45.833 13.81 0.00 0.00 2.24
930 1020 4.215908 TGTCCTAGTATCCCTGCAGTTAG 58.784 47.826 13.81 0.78 0.00 2.34
1025 1115 7.458409 TGTCTGGAGTAATAACTAAGTTCGT 57.542 36.000 0.00 0.00 35.56 3.85
1051 1141 2.615447 ACATCGATGTTCATGTGGATGC 59.385 45.455 25.18 0.00 37.90 3.91
1056 1146 2.120909 GTTCATGTGGATGCCCCCG 61.121 63.158 0.00 0.00 0.00 5.73
1088 1178 3.522759 TGTATGGGTTCTACCACCAGAA 58.477 45.455 0.00 0.00 44.72 3.02
1106 1196 4.273235 CCAGAATTTTCCAGGTTTGTTTGC 59.727 41.667 0.00 0.00 0.00 3.68
1123 1213 6.214191 TGTTTGCTGTTCCTTTCATGTTAA 57.786 33.333 0.00 0.00 0.00 2.01
1221 1312 2.264455 AGTCACCTTTCATCCTCAGCT 58.736 47.619 0.00 0.00 0.00 4.24
1234 1325 1.004560 TCAGCTCAAACTCTGGCCG 60.005 57.895 0.00 0.00 0.00 6.13
1328 1419 2.629002 GCCAAGAGCGAAAACCTGA 58.371 52.632 0.00 0.00 0.00 3.86
1329 1420 1.168714 GCCAAGAGCGAAAACCTGAT 58.831 50.000 0.00 0.00 0.00 2.90
1330 1421 1.135575 GCCAAGAGCGAAAACCTGATG 60.136 52.381 0.00 0.00 0.00 3.07
1421 1519 4.621991 AGACCTGATACGCATACAATGTC 58.378 43.478 0.00 0.00 0.00 3.06
1464 1594 6.551601 TGGAGGAGAAGAAATACAGGAGATAC 59.448 42.308 0.00 0.00 0.00 2.24
1928 2063 2.724977 TTCTGCCTCTGTACTTGACG 57.275 50.000 0.00 0.00 0.00 4.35
2042 2178 1.661463 TCCTGCCCAATCAGAGTCTT 58.339 50.000 0.00 0.00 36.19 3.01
2118 2254 7.433708 TCAATGTGTTTTTGACGTATCTGAT 57.566 32.000 0.00 0.00 0.00 2.90
2209 2345 2.180946 ATGAGATGTCAGGCCTGGTA 57.819 50.000 32.23 21.16 35.66 3.25
2290 2426 4.654262 TCCAAGAGTGTTCCTTCTGTAAGT 59.346 41.667 0.00 0.00 33.76 2.24
2355 2491 4.141344 ACAACCTTGTAGACCAGCCTTTTA 60.141 41.667 0.00 0.00 40.16 1.52
2491 2627 1.883926 CCCAAGTCCTTTAACAACCCG 59.116 52.381 0.00 0.00 0.00 5.28
2787 2925 2.734606 CACCATGAAGAAACGCGTTCTA 59.265 45.455 26.77 10.27 46.36 2.10
2965 3103 9.481340 CGATCAATAGTTCCATCAGATTTTCTA 57.519 33.333 0.00 0.00 0.00 2.10
2993 3134 2.486982 CTGAACTCCCACTTGCAATCAG 59.513 50.000 0.00 3.69 0.00 2.90
3171 3314 7.781056 AGCCCATACTTGGTTATATTTTTGTG 58.219 34.615 0.00 0.00 41.91 3.33
3254 3409 1.591863 GCCGCAGAAGATCCCGTAC 60.592 63.158 0.00 0.00 0.00 3.67
3315 3476 2.582436 GCCTACAGCAGCCGGTTA 59.418 61.111 1.90 0.00 42.97 2.85
3459 3642 1.725557 GCTGTCTCGACATCCGCCTA 61.726 60.000 0.00 0.00 41.01 3.93
3565 3748 1.452651 CAGTGATTGATGCGGGCCT 60.453 57.895 0.84 0.00 0.00 5.19
4033 4250 3.966218 GGTTTCATCAAAAACGACGTCTG 59.034 43.478 14.70 9.79 39.52 3.51
4045 4262 3.139850 ACGACGTCTGGTGAGATATAGG 58.860 50.000 14.70 0.00 0.00 2.57
4092 4309 1.136828 TTACACCCCTCTGTTGTGCT 58.863 50.000 0.00 0.00 33.30 4.40
4139 4356 7.945863 TGCTTAGAGCGAAACATTAGTTTGCA 61.946 38.462 13.63 0.00 46.26 4.08
4340 4557 2.040278 TGGAGGCATGTGCTAAAAGAGT 59.960 45.455 4.84 0.00 41.70 3.24
4511 4732 8.621532 ACAGCAATGATTTTAGAGTCAAACTA 57.378 30.769 0.00 0.00 0.00 2.24
4539 4760 5.777802 TCAACAAGTGCTTGAAAGTTTTGA 58.222 33.333 17.62 12.32 42.93 2.69
4562 4783 4.404507 ACACTTGAAAAACATCGGATCG 57.595 40.909 0.00 0.00 0.00 3.69
4707 4928 4.082136 GGTTTGGTAGAGACACTAGTGGAG 60.082 50.000 26.12 2.30 34.19 3.86
4857 5080 0.248743 TAATCGATCGTGCCACCGTC 60.249 55.000 15.94 0.00 0.00 4.79
4972 5195 2.160721 AGGATTCTCCTCGTTGCCTA 57.839 50.000 0.00 0.00 45.66 3.93
5040 5263 8.627403 ACATTATTGTCAAGAGCAATTCTATGG 58.373 33.333 0.00 0.00 37.65 2.74
5257 5480 0.246635 GGCACCACTGTCGACATACT 59.753 55.000 20.40 1.39 0.00 2.12
5283 5506 1.006102 GTCGATCCCATAGGCACCG 60.006 63.158 0.00 0.00 0.00 4.94
5300 5523 2.721231 GTCCGCAGCAGCAACAAA 59.279 55.556 0.82 0.00 42.27 2.83
5364 5587 2.743928 CAGCAGTCCTTGGCCGTC 60.744 66.667 0.00 0.00 0.00 4.79
5402 5625 0.182061 ATCTGGCATCGAGGTGCATT 59.818 50.000 12.73 0.00 46.81 3.56
5408 5631 1.742761 CATCGAGGTGCATTTGGACT 58.257 50.000 2.19 0.00 36.56 3.85
5495 5731 4.265056 GTTGCCACCGTGTCCCCT 62.265 66.667 0.00 0.00 0.00 4.79
5509 5745 2.747855 CCCTGCCGGAGTTCTTGC 60.748 66.667 5.05 0.00 0.00 4.01
6054 6290 2.494918 CGCCGACGATTCCTTCCT 59.505 61.111 0.00 0.00 43.93 3.36
6390 6649 4.621991 AGACCTGATACGCATACAATGTC 58.378 43.478 0.00 0.00 0.00 3.06
6515 6797 8.287439 ACAAGAGAATATCTCCTATATGACCG 57.713 38.462 3.82 0.00 44.42 4.79
6610 6892 5.485620 TCTCAAGTGAGTGATGATTCCAAG 58.514 41.667 8.14 0.00 42.60 3.61
6622 6904 4.268757 TCCAAGGGGAAGGGGAAG 57.731 61.111 0.00 0.00 41.32 3.46
6785 7067 9.343539 GAAGTATGAAGCCAGAACCTAATATTT 57.656 33.333 0.00 0.00 0.00 1.40
6985 7267 8.698210 TGATTATCATTGGAAGGGAAAGATTTG 58.302 33.333 0.00 0.00 0.00 2.32
7016 7298 5.989168 ACTTGCTTTTAATTTGCCTTGTACC 59.011 36.000 0.00 0.00 0.00 3.34
7228 7512 7.812669 ACTTTTCATTTTCACGAAGTTTTCACT 59.187 29.630 0.00 0.00 41.61 3.41
7238 7522 3.243068 CGAAGTTTTCACTCCTTTGGTGG 60.243 47.826 0.00 0.00 35.61 4.61
7254 7538 6.652900 CCTTTGGTGGAACAAAAAGAAAGAAA 59.347 34.615 0.00 0.00 39.72 2.52
7390 7678 4.649674 GTCATAAGGGACAGTGATGGACTA 59.350 45.833 0.00 0.00 37.73 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 6.110707 ACAAGACCACGTTTTTCTCTTCTTA 58.889 36.000 0.00 0.00 0.00 2.10
34 35 6.725246 CAAATACAAGACCACGTTTTTCTCT 58.275 36.000 0.00 0.00 0.00 3.10
35 36 5.398416 GCAAATACAAGACCACGTTTTTCTC 59.602 40.000 0.00 0.00 0.00 2.87
36 37 5.163602 TGCAAATACAAGACCACGTTTTTCT 60.164 36.000 0.00 0.00 0.00 2.52
49 50 5.118510 GGACCGTGAAAATTGCAAATACAAG 59.881 40.000 1.71 4.45 31.96 3.16
169 179 4.746309 GGCATGGGAGCAGGTGCA 62.746 66.667 4.48 0.00 45.16 4.57
303 350 2.169769 GACTGGTCGAATTGGGTCCATA 59.830 50.000 0.00 0.00 0.00 2.74
305 352 0.323629 GACTGGTCGAATTGGGTCCA 59.676 55.000 0.00 5.55 0.00 4.02
350 397 5.298527 TCAGAGCCTTCGATCGACTATTAAA 59.701 40.000 19.26 0.00 0.00 1.52
375 422 5.998363 CCCATCAAATACCTAAGTAGAAGCC 59.002 44.000 0.00 0.00 0.00 4.35
465 514 9.880157 AAATTATATTCTGCTTGCAAATTCTGT 57.120 25.926 0.00 0.00 0.00 3.41
469 520 9.369904 ACGAAAATTATATTCTGCTTGCAAATT 57.630 25.926 0.00 0.00 0.00 1.82
471 522 8.755696 AACGAAAATTATATTCTGCTTGCAAA 57.244 26.923 0.00 0.00 0.00 3.68
493 544 7.218773 CCATCAACTGCTAATTTGTTATGAACG 59.781 37.037 0.00 0.00 0.00 3.95
497 548 5.750067 GCCCATCAACTGCTAATTTGTTATG 59.250 40.000 0.00 0.00 0.00 1.90
506 557 2.961741 TGTTTTGCCCATCAACTGCTAA 59.038 40.909 0.00 0.00 33.73 3.09
537 591 1.228245 GCTGGGCAAGTGAGGTTCA 60.228 57.895 0.00 0.00 0.00 3.18
582 658 7.330900 TCATAGTACTTTTCTACTTCTCGGG 57.669 40.000 0.00 0.00 0.00 5.14
617 693 6.038356 CCAAATCCAGCATTGTGAGTTAATC 58.962 40.000 0.00 0.00 0.00 1.75
641 717 2.159000 CCCATACCTCACGGTTTCTACC 60.159 54.545 0.00 0.00 42.13 3.18
683 759 2.239402 TCTCATCTGCCAGCCAACATTA 59.761 45.455 0.00 0.00 0.00 1.90
712 788 5.885230 TGTGCTCAACATTCTAATCAAGG 57.115 39.130 0.00 0.00 32.36 3.61
722 798 4.852134 TGCAGTTATTGTGCTCAACATT 57.148 36.364 2.82 0.00 41.78 2.71
786 862 0.734942 TTGCCGTCTACGCTAGTTGC 60.735 55.000 0.00 0.00 38.18 4.17
787 863 1.705256 TTTGCCGTCTACGCTAGTTG 58.295 50.000 0.00 0.00 38.18 3.16
788 864 2.443887 TTTTGCCGTCTACGCTAGTT 57.556 45.000 0.00 0.00 38.18 2.24
789 865 2.667473 ATTTTGCCGTCTACGCTAGT 57.333 45.000 0.00 0.00 38.18 2.57
791 867 2.861935 GCTAATTTTGCCGTCTACGCTA 59.138 45.455 0.00 0.00 38.18 4.26
793 869 1.395608 TGCTAATTTTGCCGTCTACGC 59.604 47.619 0.00 0.00 38.18 4.42
794 870 2.671396 AGTGCTAATTTTGCCGTCTACG 59.329 45.455 0.43 0.00 39.44 3.51
796 872 6.704493 CCTATTAGTGCTAATTTTGCCGTCTA 59.296 38.462 9.40 0.00 37.07 2.59
797 873 5.527582 CCTATTAGTGCTAATTTTGCCGTCT 59.472 40.000 9.40 0.48 37.07 4.18
836 921 3.216292 GGGGTGCAAGCAACACGT 61.216 61.111 12.66 0.00 38.98 4.49
922 1012 4.471904 ACATACAGCTAAGCTAACTGCA 57.528 40.909 9.74 0.00 45.94 4.41
926 1016 8.475331 TGAGTTTAACATACAGCTAAGCTAAC 57.525 34.615 0.00 0.00 36.40 2.34
927 1017 9.098355 CATGAGTTTAACATACAGCTAAGCTAA 57.902 33.333 0.00 0.00 36.40 3.09
928 1018 7.710907 CCATGAGTTTAACATACAGCTAAGCTA 59.289 37.037 0.00 0.00 36.40 3.32
929 1019 6.540189 CCATGAGTTTAACATACAGCTAAGCT 59.460 38.462 0.00 0.00 40.77 3.74
930 1020 6.316390 ACCATGAGTTTAACATACAGCTAAGC 59.684 38.462 0.00 0.00 0.00 3.09
1025 1115 5.241662 TCCACATGAACATCGATGTAACAA 58.758 37.500 30.16 16.36 40.80 2.83
1051 1141 2.060050 TACATAATTGCAACCGGGGG 57.940 50.000 6.32 0.00 0.00 5.40
1056 1146 5.852282 AGAACCCATACATAATTGCAACC 57.148 39.130 0.00 0.00 0.00 3.77
1088 1178 4.486125 ACAGCAAACAAACCTGGAAAAT 57.514 36.364 0.00 0.00 0.00 1.82
1106 1196 8.103948 AGAACATCTTAACATGAAAGGAACAG 57.896 34.615 0.00 0.00 0.00 3.16
1221 1312 2.429930 CCACCGGCCAGAGTTTGA 59.570 61.111 0.00 0.00 0.00 2.69
1234 1325 0.251341 ATGACAGCAAGGAACCCACC 60.251 55.000 0.00 0.00 0.00 4.61
1289 1380 2.496817 GAGCCTCCTTCATCGCGT 59.503 61.111 5.77 0.00 0.00 6.01
1319 1410 0.874390 TCGCACAGCATCAGGTTTTC 59.126 50.000 0.00 0.00 0.00 2.29
1321 1412 0.035317 TCTCGCACAGCATCAGGTTT 59.965 50.000 0.00 0.00 0.00 3.27
1328 1419 2.786539 TTTCCGCTCTCGCACAGCAT 62.787 55.000 0.00 0.00 36.61 3.79
1329 1420 3.513768 TTTCCGCTCTCGCACAGCA 62.514 57.895 0.00 0.00 36.61 4.41
1330 1421 2.738521 TTTCCGCTCTCGCACAGC 60.739 61.111 0.00 0.00 35.30 4.40
1421 1519 4.572389 CCTCCAAGATTGTAATCTCCAACG 59.428 45.833 7.52 0.00 44.67 4.10
1869 2004 4.797800 GCTACAGCAGAGATCATATGGA 57.202 45.455 2.13 0.00 41.59 3.41
1987 2123 2.280524 TCAACTGGTGGGTTCGCG 60.281 61.111 0.00 0.00 0.00 5.87
2042 2178 5.184096 CCTCTACTCTTGTCAGTGCTTTCTA 59.816 44.000 0.00 0.00 0.00 2.10
2118 2254 5.176774 CACTTGACAGCTGTGAAACGTATAA 59.823 40.000 27.27 0.00 42.39 0.98
2128 2264 2.283298 ACTGTTCACTTGACAGCTGTG 58.717 47.619 27.27 12.98 35.08 3.66
2129 2265 2.698855 ACTGTTCACTTGACAGCTGT 57.301 45.000 21.88 21.88 35.08 4.40
2209 2345 4.440880 GAGCATTGCAGTATCTCACTCTT 58.559 43.478 11.91 0.00 34.26 2.85
2355 2491 3.508845 AGTATGCAACTGACCTGGTTT 57.491 42.857 0.00 0.00 36.93 3.27
2491 2627 2.606725 CTCGTCTGATGAAGCAATCACC 59.393 50.000 0.66 0.00 41.93 4.02
2787 2925 6.662755 TGGAGTTTGAGGCAATTAGATGTAT 58.337 36.000 0.00 0.00 0.00 2.29
2965 3103 5.324409 TGCAAGTGGGAGTTCAGAATTAAT 58.676 37.500 0.00 0.00 0.00 1.40
2978 3116 2.375174 ACCTTACTGATTGCAAGTGGGA 59.625 45.455 4.94 0.00 0.00 4.37
3171 3314 7.903145 ACAAGGGGTAATTCAACCTTTAAATC 58.097 34.615 5.10 0.00 41.17 2.17
3302 3463 2.351276 CCCTTAACCGGCTGCTGT 59.649 61.111 0.00 0.00 0.00 4.40
3315 3476 0.618968 AGAAGATCAGGACCGCCCTT 60.619 55.000 0.00 0.00 44.85 3.95
3513 3696 2.679342 CCCGAGAATGGCCAGGGAA 61.679 63.158 20.15 0.00 44.70 3.97
3548 3731 1.452651 CAGGCCCGCATCAATCACT 60.453 57.895 0.00 0.00 0.00 3.41
3797 4014 5.180271 ACAGTGAAAACGGTGAAGAAACTA 58.820 37.500 0.00 0.00 0.00 2.24
4033 4250 1.272769 GGGTCGTGCCTATATCTCACC 59.727 57.143 0.00 0.00 37.43 4.02
4081 4298 6.154203 TCTTGGATATAGAGCACAACAGAG 57.846 41.667 0.00 0.00 0.00 3.35
4083 4300 7.615582 TTTTCTTGGATATAGAGCACAACAG 57.384 36.000 0.00 0.00 0.00 3.16
4092 4309 7.031226 GCAATGTGCTTTTCTTGGATATAGA 57.969 36.000 0.00 0.00 40.96 1.98
4139 4356 2.601905 ACCTACGTCCCTACAACAAGT 58.398 47.619 0.00 0.00 0.00 3.16
4511 4732 3.840890 TTCAAGCACTTGTTGAACGTT 57.159 38.095 0.00 0.00 38.66 3.99
4539 4760 5.212194 CGATCCGATGTTTTTCAAGTGTTT 58.788 37.500 0.00 0.00 0.00 2.83
4857 5080 4.095610 GGTGTTGTCAAACTTTCGTCAAG 58.904 43.478 0.00 0.00 37.19 3.02
5005 5228 6.128282 GCTCTTGACAATAATGTTTTCCTCGA 60.128 38.462 0.00 0.00 40.74 4.04
5040 5263 4.024472 GCCAACAAAAGTCTTCTCTCTGTC 60.024 45.833 0.00 0.00 0.00 3.51
5257 5480 2.963101 CCTATGGGATCGACACCAACTA 59.037 50.000 13.27 2.93 40.73 2.24
5283 5506 0.318955 AATTTGTTGCTGCTGCGGAC 60.319 50.000 13.72 12.15 43.34 4.79
5300 5523 6.593382 CGACTCCTCTCAAGATGAAGAAAAAT 59.407 38.462 0.00 0.00 0.00 1.82
5391 5614 1.522668 CAAGTCCAAATGCACCTCGA 58.477 50.000 0.00 0.00 0.00 4.04
5402 5625 0.397941 CTCCACCAGAGCAAGTCCAA 59.602 55.000 0.00 0.00 35.31 3.53
5431 5654 1.057275 TACACCAGCAACAGGGGTCA 61.057 55.000 0.00 0.00 38.83 4.02
5495 5731 4.344865 GGGGCAAGAACTCCGGCA 62.345 66.667 0.00 0.00 0.00 5.69
6054 6290 2.166459 CTCGTCAGCAAGGATAAGGACA 59.834 50.000 0.00 0.00 0.00 4.02
6330 6574 1.603171 ATGCAACATGTCGCCCACA 60.603 52.632 6.26 0.00 40.18 4.17
6340 6584 4.937620 CGCCTCCTATATAACATGCAACAT 59.062 41.667 0.00 0.00 0.00 2.71
6390 6649 4.572389 CCTCCAAGATTGTAATCTCCAACG 59.428 45.833 7.52 0.00 44.67 4.10
6515 6797 8.620416 TGCATCTGTTAAACATACAATGTATCC 58.380 33.333 2.41 0.00 44.07 2.59
6567 6849 5.163163 TGAGAAGATGCTGGCTGGTTAATAT 60.163 40.000 0.00 0.00 0.00 1.28
6610 6892 2.204401 TTCCCCTTCCCCTTCCCC 60.204 66.667 0.00 0.00 0.00 4.81
6617 6899 0.253020 TACTCCACCTTCCCCTTCCC 60.253 60.000 0.00 0.00 0.00 3.97
6618 6900 1.205055 CTACTCCACCTTCCCCTTCC 58.795 60.000 0.00 0.00 0.00 3.46
6619 6901 1.205055 CCTACTCCACCTTCCCCTTC 58.795 60.000 0.00 0.00 0.00 3.46
6620 6902 0.914902 GCCTACTCCACCTTCCCCTT 60.915 60.000 0.00 0.00 0.00 3.95
6621 6903 1.307084 GCCTACTCCACCTTCCCCT 60.307 63.158 0.00 0.00 0.00 4.79
6622 6904 1.615424 TGCCTACTCCACCTTCCCC 60.615 63.158 0.00 0.00 0.00 4.81
6785 7067 4.201647 GCTAGCGCAAAGTTAAACATACGA 60.202 41.667 11.47 0.00 35.78 3.43
6917 7199 3.071479 GCCAGTCACCGAAAGAATACAA 58.929 45.455 0.00 0.00 0.00 2.41
6985 7267 6.923508 AGGCAAATTAAAAGCAAGTACAAGAC 59.076 34.615 0.00 0.00 0.00 3.01
7016 7298 1.815003 GGCTCTCTGGTGACAAAATGG 59.185 52.381 0.00 0.00 42.06 3.16
7153 7437 4.572389 AGCGAGCATAGGAAACATGTAAAG 59.428 41.667 0.00 0.00 0.00 1.85
7228 7512 5.482175 TCTTTCTTTTTGTTCCACCAAAGGA 59.518 36.000 0.00 0.00 35.85 3.36
7390 7678 9.713684 TCCATCCCTTTATTCATGTAAAAGATT 57.286 29.630 14.54 2.24 33.05 2.40


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

AutoCloner maintained by Alex Coulton.