Multiple sequence alignment - TraesCS7A01G212700

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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 TraesCS7A01G212700 chr7A 100.000 2576 0 0 1 2576 176276942 176279517 0.000000e+00 4758
1 TraesCS7A01G212700 chr7A 94.763 993 40 9 1583 2572 670563403 670564386 0.000000e+00 1535
2 TraesCS7A01G212700 chr7A 83.824 612 65 18 177 760 692282712 692282107 3.750000e-153 551
3 TraesCS7A01G212700 chr7A 80.891 696 81 32 100 760 731025109 731025787 3.830000e-138 501
4 TraesCS7A01G212700 chr7A 78.510 698 96 31 107 760 34453792 34453105 2.390000e-110 409
5 TraesCS7A01G212700 chr7A 83.500 400 49 15 125 515 68169807 68170198 8.770000e-95 357
6 TraesCS7A01G212700 chr7A 76.091 527 114 10 1016 1539 7817274 7817791 5.470000e-67 265
7 TraesCS7A01G212700 chr7A 87.671 219 17 4 1581 1798 670565546 670565337 1.980000e-61 246
8 TraesCS7A01G212700 chr7A 85.590 229 25 4 1579 1806 671505221 671505442 1.540000e-57 233
9 TraesCS7A01G212700 chr3A 95.156 991 37 5 1582 2571 693452536 693453516 0.000000e+00 1554
10 TraesCS7A01G212700 chr3A 87.783 221 18 5 1579 1798 693454691 693454479 1.530000e-62 250
11 TraesCS7A01G212700 chr2D 94.595 999 31 6 1582 2572 643636235 643637218 0.000000e+00 1524
12 TraesCS7A01G212700 chr2D 88.712 753 43 17 1842 2572 486955849 486956581 0.000000e+00 881
13 TraesCS7A01G212700 chr2D 88.837 215 16 3 1585 1798 643638420 643638213 9.150000e-65 257
14 TraesCS7A01G212700 chr5D 94.254 992 32 9 1582 2572 365089043 365088076 0.000000e+00 1493
15 TraesCS7A01G212700 chr5D 82.726 631 57 29 172 760 334945267 334944647 4.920000e-142 514
16 TraesCS7A01G212700 chr5D 75.000 512 121 6 1016 1525 553910517 553911023 1.990000e-56 230
17 TraesCS7A01G212700 chrUn 96.608 737 14 4 1847 2572 116831392 116830656 0.000000e+00 1212
18 TraesCS7A01G212700 chr7D 93.000 800 52 1 772 1571 174295793 174296588 0.000000e+00 1164
19 TraesCS7A01G212700 chr7D 88.788 330 29 4 440 761 613059338 613059667 5.160000e-107 398
20 TraesCS7A01G212700 chr7D 84.987 393 46 9 380 760 613099967 613100358 1.120000e-103 387
21 TraesCS7A01G212700 chr7D 87.879 330 31 5 440 761 562029119 562028791 1.870000e-101 379
22 TraesCS7A01G212700 chr7D 83.251 406 52 15 125 521 64336034 64336432 2.440000e-95 359
23 TraesCS7A01G212700 chr7B 92.393 815 53 4 760 1571 138755158 138755966 0.000000e+00 1153
24 TraesCS7A01G212700 chr2B 88.512 766 45 17 1842 2572 571531832 571532589 0.000000e+00 887
25 TraesCS7A01G212700 chr2B 87.658 316 32 7 125 436 278815606 278815294 6.780000e-96 361
26 TraesCS7A01G212700 chr2A 87.863 758 58 12 1842 2572 631967708 631968458 0.000000e+00 859
27 TraesCS7A01G212700 chr2A 83.359 655 76 20 126 760 532514688 532514047 2.220000e-160 575
28 TraesCS7A01G212700 chr2A 79.265 680 85 39 124 760 71689177 71689843 8.520000e-115 424
29 TraesCS7A01G212700 chr2A 89.118 340 24 2 427 761 532519570 532519239 6.630000e-111 411
30 TraesCS7A01G212700 chr4A 85.878 609 54 19 177 760 616795842 616795241 1.010000e-173 619
31 TraesCS7A01G212700 chr4A 84.906 265 29 11 172 432 321941366 321941623 9.150000e-65 257
32 TraesCS7A01G212700 chr4A 85.652 230 21 8 1580 1806 546579963 546579743 5.540000e-57 231
33 TraesCS7A01G212700 chr6D 83.200 625 65 27 172 764 126422542 126423158 1.050000e-148 536
34 TraesCS7A01G212700 chr6D 87.887 355 28 10 427 771 227385962 227386311 1.110000e-108 403
35 TraesCS7A01G212700 chr6D 76.817 289 60 7 1241 1525 470104292 470104007 3.430000e-34 156
36 TraesCS7A01G212700 chr5A 88.663 344 31 4 425 761 458286845 458287187 1.840000e-111 412
37 TraesCS7A01G212700 chr4B 89.456 294 31 0 1245 1538 602296971 602296678 3.130000e-99 372
38 TraesCS7A01G212700 chr4B 76.281 527 116 7 999 1522 2205413 2205933 3.270000e-69 272
39 TraesCS7A01G212700 chr4B 76.091 527 117 7 999 1522 2234822 2235342 1.520000e-67 267
40 TraesCS7A01G212700 chr3B 90.254 236 14 3 2147 2374 32280279 32280513 1.500000e-77 300
41 TraesCS7A01G212700 chr3B 90.955 199 15 3 2376 2572 32282052 32282249 5.470000e-67 265
42 TraesCS7A01G212700 chr3B 87.783 221 19 3 1582 1801 32282496 32282283 4.260000e-63 252
43 TraesCS7A01G212700 chr5B 76.321 549 115 14 998 1537 543282511 543281969 1.950000e-71 279
44 TraesCS7A01G212700 chr5B 75.915 519 110 9 1000 1516 543272458 543271953 4.260000e-63 252
45 TraesCS7A01G212700 chr6A 83.832 167 27 0 1251 1417 614967574 614967408 2.650000e-35 159


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 TraesCS7A01G212700 chr7A 176276942 176279517 2575 False 4758.0 4758 100.0000 1 2576 1 chr7A.!!$F3 2575
1 TraesCS7A01G212700 chr7A 670563403 670564386 983 False 1535.0 1535 94.7630 1583 2572 1 chr7A.!!$F4 989
2 TraesCS7A01G212700 chr7A 692282107 692282712 605 True 551.0 551 83.8240 177 760 1 chr7A.!!$R3 583
3 TraesCS7A01G212700 chr7A 731025109 731025787 678 False 501.0 501 80.8910 100 760 1 chr7A.!!$F6 660
4 TraesCS7A01G212700 chr7A 34453105 34453792 687 True 409.0 409 78.5100 107 760 1 chr7A.!!$R1 653
5 TraesCS7A01G212700 chr7A 7817274 7817791 517 False 265.0 265 76.0910 1016 1539 1 chr7A.!!$F1 523
6 TraesCS7A01G212700 chr3A 693452536 693453516 980 False 1554.0 1554 95.1560 1582 2571 1 chr3A.!!$F1 989
7 TraesCS7A01G212700 chr2D 643636235 643637218 983 False 1524.0 1524 94.5950 1582 2572 1 chr2D.!!$F2 990
8 TraesCS7A01G212700 chr2D 486955849 486956581 732 False 881.0 881 88.7120 1842 2572 1 chr2D.!!$F1 730
9 TraesCS7A01G212700 chr5D 365088076 365089043 967 True 1493.0 1493 94.2540 1582 2572 1 chr5D.!!$R2 990
10 TraesCS7A01G212700 chr5D 334944647 334945267 620 True 514.0 514 82.7260 172 760 1 chr5D.!!$R1 588
11 TraesCS7A01G212700 chr5D 553910517 553911023 506 False 230.0 230 75.0000 1016 1525 1 chr5D.!!$F1 509
12 TraesCS7A01G212700 chrUn 116830656 116831392 736 True 1212.0 1212 96.6080 1847 2572 1 chrUn.!!$R1 725
13 TraesCS7A01G212700 chr7D 174295793 174296588 795 False 1164.0 1164 93.0000 772 1571 1 chr7D.!!$F2 799
14 TraesCS7A01G212700 chr7B 138755158 138755966 808 False 1153.0 1153 92.3930 760 1571 1 chr7B.!!$F1 811
15 TraesCS7A01G212700 chr2B 571531832 571532589 757 False 887.0 887 88.5120 1842 2572 1 chr2B.!!$F1 730
16 TraesCS7A01G212700 chr2A 631967708 631968458 750 False 859.0 859 87.8630 1842 2572 1 chr2A.!!$F2 730
17 TraesCS7A01G212700 chr2A 532514047 532514688 641 True 575.0 575 83.3590 126 760 1 chr2A.!!$R1 634
18 TraesCS7A01G212700 chr2A 71689177 71689843 666 False 424.0 424 79.2650 124 760 1 chr2A.!!$F1 636
19 TraesCS7A01G212700 chr4A 616795241 616795842 601 True 619.0 619 85.8780 177 760 1 chr4A.!!$R2 583
20 TraesCS7A01G212700 chr6D 126422542 126423158 616 False 536.0 536 83.2000 172 764 1 chr6D.!!$F1 592
21 TraesCS7A01G212700 chr4B 2205413 2205933 520 False 272.0 272 76.2810 999 1522 1 chr4B.!!$F1 523
22 TraesCS7A01G212700 chr4B 2234822 2235342 520 False 267.0 267 76.0910 999 1522 1 chr4B.!!$F2 523
23 TraesCS7A01G212700 chr3B 32280279 32282249 1970 False 282.5 300 90.6045 2147 2572 2 chr3B.!!$F1 425
24 TraesCS7A01G212700 chr5B 543281969 543282511 542 True 279.0 279 76.3210 998 1537 1 chr5B.!!$R2 539
25 TraesCS7A01G212700 chr5B 543271953 543272458 505 True 252.0 252 75.9150 1000 1516 1 chr5B.!!$R1 516

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
27 28 0.034574 TGCCGGCTGGTTCATATGTT 60.035 50.0 29.7 0.0 37.67 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 2032 0.397187 TTTTGATCCGACCGGGTTCA 59.603 50.0 6.32 9.32 41.68 3.18 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 4.415150 ATGGACTGTGCCGGCTGG 62.415 66.667 29.70 19.05 38.77 4.85
19 20 4.643387 GGACTGTGCCGGCTGGTT 62.643 66.667 29.70 9.66 37.67 3.67
20 21 3.050275 GACTGTGCCGGCTGGTTC 61.050 66.667 29.70 15.06 37.67 3.62
21 22 3.825160 GACTGTGCCGGCTGGTTCA 62.825 63.158 29.70 16.63 37.67 3.18
22 23 2.360350 CTGTGCCGGCTGGTTCAT 60.360 61.111 29.70 0.00 37.67 2.57
23 24 1.078497 CTGTGCCGGCTGGTTCATA 60.078 57.895 29.70 0.07 37.67 2.15
24 25 0.464373 CTGTGCCGGCTGGTTCATAT 60.464 55.000 29.70 0.00 37.67 1.78
25 26 0.747644 TGTGCCGGCTGGTTCATATG 60.748 55.000 29.70 0.00 37.67 1.78
26 27 0.748005 GTGCCGGCTGGTTCATATGT 60.748 55.000 29.70 0.00 37.67 2.29
27 28 0.034574 TGCCGGCTGGTTCATATGTT 60.035 50.000 29.70 0.00 37.67 2.71
28 29 1.102978 GCCGGCTGGTTCATATGTTT 58.897 50.000 22.15 0.00 37.67 2.83
29 30 1.065551 GCCGGCTGGTTCATATGTTTC 59.934 52.381 22.15 0.00 37.67 2.78
30 31 2.643551 CCGGCTGGTTCATATGTTTCT 58.356 47.619 2.29 0.00 0.00 2.52
31 32 3.016736 CCGGCTGGTTCATATGTTTCTT 58.983 45.455 2.29 0.00 0.00 2.52
32 33 3.443681 CCGGCTGGTTCATATGTTTCTTT 59.556 43.478 2.29 0.00 0.00 2.52
33 34 4.438744 CCGGCTGGTTCATATGTTTCTTTC 60.439 45.833 2.29 0.00 0.00 2.62
34 35 4.662145 GGCTGGTTCATATGTTTCTTTCG 58.338 43.478 1.90 0.00 0.00 3.46
35 36 4.394920 GGCTGGTTCATATGTTTCTTTCGA 59.605 41.667 1.90 0.00 0.00 3.71
36 37 5.106317 GGCTGGTTCATATGTTTCTTTCGAA 60.106 40.000 1.90 0.00 0.00 3.71
37 38 6.378582 GCTGGTTCATATGTTTCTTTCGAAA 58.621 36.000 10.71 10.71 36.82 3.46
38 39 6.861055 GCTGGTTCATATGTTTCTTTCGAAAA 59.139 34.615 12.41 0.00 40.57 2.29
39 40 7.061094 GCTGGTTCATATGTTTCTTTCGAAAAG 59.939 37.037 12.41 6.54 40.57 2.27
40 41 7.367285 TGGTTCATATGTTTCTTTCGAAAAGG 58.633 34.615 12.41 1.25 40.57 3.11
41 42 7.229707 TGGTTCATATGTTTCTTTCGAAAAGGA 59.770 33.333 12.41 3.86 40.57 3.36
42 43 8.079809 GGTTCATATGTTTCTTTCGAAAAGGAA 58.920 33.333 12.41 9.98 40.57 3.36
43 44 9.118236 GTTCATATGTTTCTTTCGAAAAGGAAG 57.882 33.333 12.41 0.00 40.57 3.46
44 45 8.615878 TCATATGTTTCTTTCGAAAAGGAAGA 57.384 30.769 12.41 2.04 40.57 2.87
45 46 9.231297 TCATATGTTTCTTTCGAAAAGGAAGAT 57.769 29.630 12.41 12.39 40.57 2.40
49 50 8.215926 TGTTTCTTTCGAAAAGGAAGATAACA 57.784 30.769 12.41 13.47 40.57 2.41
50 51 8.846211 TGTTTCTTTCGAAAAGGAAGATAACAT 58.154 29.630 12.41 0.00 40.57 2.71
51 52 9.331106 GTTTCTTTCGAAAAGGAAGATAACATC 57.669 33.333 12.41 0.00 40.57 3.06
52 53 7.611213 TCTTTCGAAAAGGAAGATAACATCC 57.389 36.000 12.41 0.00 34.50 3.51
53 54 6.598064 TCTTTCGAAAAGGAAGATAACATCCC 59.402 38.462 12.41 0.00 34.80 3.85
54 55 4.777463 TCGAAAAGGAAGATAACATCCCC 58.223 43.478 0.00 0.00 34.80 4.81
55 56 3.560068 CGAAAAGGAAGATAACATCCCCG 59.440 47.826 0.00 0.00 34.80 5.73
56 57 4.682320 CGAAAAGGAAGATAACATCCCCGA 60.682 45.833 0.00 0.00 34.80 5.14
57 58 3.840124 AAGGAAGATAACATCCCCGAC 57.160 47.619 0.00 0.00 34.80 4.79
58 59 3.047695 AGGAAGATAACATCCCCGACT 57.952 47.619 0.00 0.00 34.80 4.18
59 60 2.700897 AGGAAGATAACATCCCCGACTG 59.299 50.000 0.00 0.00 34.80 3.51
60 61 2.224305 GGAAGATAACATCCCCGACTGG 60.224 54.545 0.00 0.00 0.00 4.00
61 62 2.176247 AGATAACATCCCCGACTGGT 57.824 50.000 0.00 0.00 0.00 4.00
62 63 2.478292 AGATAACATCCCCGACTGGTT 58.522 47.619 0.00 0.00 0.00 3.67
63 64 2.434702 AGATAACATCCCCGACTGGTTC 59.565 50.000 0.00 0.00 0.00 3.62
64 65 0.906775 TAACATCCCCGACTGGTTCC 59.093 55.000 0.00 0.00 0.00 3.62
65 66 0.840722 AACATCCCCGACTGGTTCCT 60.841 55.000 0.00 0.00 0.00 3.36
66 67 0.042131 ACATCCCCGACTGGTTCCTA 59.958 55.000 0.00 0.00 0.00 2.94
67 68 1.344087 ACATCCCCGACTGGTTCCTAT 60.344 52.381 0.00 0.00 0.00 2.57
68 69 2.090943 ACATCCCCGACTGGTTCCTATA 60.091 50.000 0.00 0.00 0.00 1.31
69 70 2.376695 TCCCCGACTGGTTCCTATAG 57.623 55.000 0.00 0.00 0.00 1.31
70 71 1.133262 TCCCCGACTGGTTCCTATAGG 60.133 57.143 13.07 13.07 0.00 2.57
71 72 1.133262 CCCCGACTGGTTCCTATAGGA 60.133 57.143 18.00 18.00 43.73 2.94
91 92 6.274157 AGGAATATACTGATAGACCTTGCG 57.726 41.667 0.00 0.00 0.00 4.85
92 93 5.186021 AGGAATATACTGATAGACCTTGCGG 59.814 44.000 0.00 0.00 0.00 5.69
93 94 5.185249 GGAATATACTGATAGACCTTGCGGA 59.815 44.000 0.00 0.00 0.00 5.54
94 95 6.127310 GGAATATACTGATAGACCTTGCGGAT 60.127 42.308 0.00 0.00 0.00 4.18
95 96 4.792521 ATACTGATAGACCTTGCGGATC 57.207 45.455 0.00 0.00 0.00 3.36
96 97 1.338337 ACTGATAGACCTTGCGGATCG 59.662 52.381 0.00 0.00 0.00 3.69
97 98 1.609072 CTGATAGACCTTGCGGATCGA 59.391 52.381 0.00 0.00 0.00 3.59
98 99 1.609072 TGATAGACCTTGCGGATCGAG 59.391 52.381 0.00 0.00 0.00 4.04
101 102 1.227002 GACCTTGCGGATCGAGTCC 60.227 63.158 0.00 0.00 44.10 3.85
123 124 2.182030 CTGCTCCCCTTCGACGAC 59.818 66.667 0.00 0.00 0.00 4.34
171 172 0.320073 TGACACGTTTCCCTTAGCGG 60.320 55.000 0.00 0.00 0.00 5.52
216 218 1.602888 CTGCTGTGCTCTTTGCCCT 60.603 57.895 0.00 0.00 42.00 5.19
218 220 2.633509 GCTGTGCTCTTTGCCCTGG 61.634 63.158 0.00 0.00 42.00 4.45
239 242 0.977395 CGGGGTGGAGTTCTTCTTCT 59.023 55.000 0.00 0.00 0.00 2.85
286 291 1.716826 GAGATCGAGAGGAACGGCGT 61.717 60.000 6.77 6.77 0.00 5.68
311 317 3.115892 CGGCGGCGCTACTTTTCA 61.116 61.111 32.30 0.00 0.00 2.69
462 512 5.620205 CGGATCGAGTAGGTCAGATAATTGG 60.620 48.000 0.00 0.00 0.00 3.16
546 633 1.228769 AGAGTAGTGGTGGCGGTGA 60.229 57.895 0.00 0.00 0.00 4.02
595 683 1.941403 CGGTAGGGGACTAGGTGGGA 61.941 65.000 0.00 0.00 45.49 4.37
628 721 4.421479 CGAACCTCGTGAGCCGCT 62.421 66.667 0.00 0.00 34.72 5.52
630 723 3.575351 GAACCTCGTGAGCCGCTGT 62.575 63.158 0.00 0.00 36.19 4.40
654 747 5.135362 TCCCCCACCTTTTTATATAGTGCAT 59.865 40.000 0.00 0.00 0.00 3.96
725 818 1.764854 GATCTAAGGGCCCGGTGGA 60.765 63.158 18.44 16.61 0.00 4.02
784 877 8.595533 CATATACATGTATAACAAGATGGCGAC 58.404 37.037 25.41 0.00 32.39 5.19
804 897 4.201812 CGACTAGCTAGCTAGATGCAGATC 60.202 50.000 43.93 30.86 46.56 2.75
808 901 5.581126 AGCTAGCTAGATGCAGATCATAC 57.419 43.478 25.15 1.59 45.94 2.39
812 905 7.395772 AGCTAGCTAGATGCAGATCATACTTAA 59.604 37.037 25.15 0.00 45.94 1.85
813 906 8.031864 GCTAGCTAGATGCAGATCATACTTAAA 58.968 37.037 25.15 0.00 45.94 1.52
846 939 3.858238 GCAACTTCGTCGAGCTACTTAAT 59.142 43.478 0.00 0.00 0.00 1.40
886 979 1.884075 TTCAGCCGGACAGCATACGT 61.884 55.000 5.05 0.00 34.23 3.57
887 980 1.447838 CAGCCGGACAGCATACGTT 60.448 57.895 5.05 0.00 34.23 3.99
892 985 2.546778 CCGGACAGCATACGTTAACAT 58.453 47.619 6.39 0.00 0.00 2.71
893 986 2.933906 CCGGACAGCATACGTTAACATT 59.066 45.455 6.39 0.00 0.00 2.71
955 1051 5.953571 AGAGATTAAGGGGTGAGTTTTGTT 58.046 37.500 0.00 0.00 0.00 2.83
960 1056 3.884037 AGGGGTGAGTTTTGTTCAGAT 57.116 42.857 0.00 0.00 0.00 2.90
1013 1109 0.532573 TTGCAGATGGGTCTCTCGAC 59.467 55.000 0.00 0.00 39.49 4.20
1147 1243 4.384208 CCTCCTTCCGACTTTTGATATGGT 60.384 45.833 0.00 0.00 0.00 3.55
1206 1302 2.746277 GCCGCCCTGTTCAATCGT 60.746 61.111 0.00 0.00 0.00 3.73
1540 1645 0.109735 CAGCGCTTCTGACACTACGA 60.110 55.000 7.50 0.00 45.72 3.43
1542 1647 0.386858 GCGCTTCTGACACTACGACA 60.387 55.000 0.00 0.00 0.00 4.35
1545 1650 2.739292 GCTTCTGACACTACGACACAA 58.261 47.619 0.00 0.00 0.00 3.33
1552 1657 2.735134 GACACTACGACACAAATGGACC 59.265 50.000 0.00 0.00 0.00 4.46
1571 1676 1.069765 ATGAGGAATACAGCCGCGG 59.930 57.895 24.05 24.05 0.00 6.46
1572 1677 1.686325 ATGAGGAATACAGCCGCGGT 61.686 55.000 28.70 9.89 0.00 5.68
1573 1678 1.153429 GAGGAATACAGCCGCGGTT 60.153 57.895 28.70 20.13 0.00 4.44
1574 1679 0.103572 GAGGAATACAGCCGCGGTTA 59.896 55.000 28.70 15.99 0.00 2.85
1575 1680 0.538118 AGGAATACAGCCGCGGTTAA 59.462 50.000 28.70 13.07 0.00 2.01
1576 1681 1.065998 AGGAATACAGCCGCGGTTAAA 60.066 47.619 28.70 12.66 0.00 1.52
1577 1682 1.329599 GGAATACAGCCGCGGTTAAAG 59.670 52.381 28.70 11.91 0.00 1.85
1578 1683 2.273557 GAATACAGCCGCGGTTAAAGA 58.726 47.619 28.70 8.07 0.00 2.52
1579 1684 2.389962 ATACAGCCGCGGTTAAAGAA 57.610 45.000 28.70 6.55 0.00 2.52
1580 1685 2.166821 TACAGCCGCGGTTAAAGAAA 57.833 45.000 28.70 1.35 0.00 2.52
1595 1700 6.444633 GTTAAAGAAAGAGGTAAAAGCACCC 58.555 40.000 0.00 0.00 39.62 4.61
1596 1701 4.455070 AAGAAAGAGGTAAAAGCACCCT 57.545 40.909 0.00 0.00 39.62 4.34
1732 1837 1.815817 TAGCTCGACAAGTGGCAGCA 61.816 55.000 10.05 0.00 32.21 4.41
1753 1858 1.376812 GTGGTTGGACCGGTCATCC 60.377 63.158 34.40 28.97 42.58 3.51
1759 1864 4.832608 GACCGGTCATCCCCGCAC 62.833 72.222 29.75 0.00 46.71 5.34
1816 1921 3.706600 ACCCGCAGTATAACCTTTTCA 57.293 42.857 0.00 0.00 0.00 2.69
1938 2043 1.803334 TCAAAGATTGAACCCGGTCG 58.197 50.000 0.00 0.00 36.59 4.79
2172 2305 2.621338 TCACTCACTTGATGAATCGGC 58.379 47.619 0.00 0.00 36.69 5.54
2174 2307 3.447229 TCACTCACTTGATGAATCGGCTA 59.553 43.478 0.00 0.00 36.69 3.93
2295 2442 7.607991 GGATCAAGGAGAAAAATCAGACAAGTA 59.392 37.037 0.00 0.00 0.00 2.24
2336 2491 8.557592 TTGGTACTCCTACAGTCGTATATATG 57.442 38.462 0.00 0.00 36.43 1.78
2543 4261 2.224209 ACTCGAAAACTCCATTGACCGT 60.224 45.455 0.00 0.00 0.00 4.83
2572 4291 7.606073 AGAAAGAATCCTTAAAAGAGAGACAGC 59.394 37.037 0.00 0.00 31.15 4.40
2573 4292 6.365970 AGAATCCTTAAAAGAGAGACAGCA 57.634 37.500 0.00 0.00 0.00 4.41
2574 4293 6.169800 AGAATCCTTAAAAGAGAGACAGCAC 58.830 40.000 0.00 0.00 0.00 4.40
2575 4294 3.914312 TCCTTAAAAGAGAGACAGCACG 58.086 45.455 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.836999 TATGAACCAGCCGGCACAGT 61.837 55.000 31.54 19.77 34.57 3.55
5 6 0.464373 ATATGAACCAGCCGGCACAG 60.464 55.000 31.54 19.03 34.57 3.66
7 8 0.748005 ACATATGAACCAGCCGGCAC 60.748 55.000 31.54 14.36 34.57 5.01
8 9 0.034574 AACATATGAACCAGCCGGCA 60.035 50.000 31.54 6.82 34.57 5.69
9 10 1.065551 GAAACATATGAACCAGCCGGC 59.934 52.381 21.89 21.89 34.57 6.13
10 11 2.643551 AGAAACATATGAACCAGCCGG 58.356 47.619 10.38 0.00 38.77 6.13
11 12 4.662145 GAAAGAAACATATGAACCAGCCG 58.338 43.478 10.38 0.00 0.00 5.52
12 13 4.394920 TCGAAAGAAACATATGAACCAGCC 59.605 41.667 10.38 0.00 37.03 4.85
13 14 5.545658 TCGAAAGAAACATATGAACCAGC 57.454 39.130 10.38 0.00 37.03 4.85
27 28 7.120726 GGGATGTTATCTTCCTTTTCGAAAGAA 59.879 37.037 10.98 10.95 41.23 2.52
28 29 6.598064 GGGATGTTATCTTCCTTTTCGAAAGA 59.402 38.462 10.98 4.80 37.82 2.52
29 30 6.183360 GGGGATGTTATCTTCCTTTTCGAAAG 60.183 42.308 10.98 5.63 37.82 2.62
30 31 5.650703 GGGGATGTTATCTTCCTTTTCGAAA 59.349 40.000 6.47 6.47 37.82 3.46
31 32 5.190677 GGGGATGTTATCTTCCTTTTCGAA 58.809 41.667 0.00 0.00 37.82 3.71
32 33 4.682320 CGGGGATGTTATCTTCCTTTTCGA 60.682 45.833 5.87 0.00 37.82 3.71
33 34 3.560068 CGGGGATGTTATCTTCCTTTTCG 59.440 47.826 5.87 3.03 37.82 3.46
34 35 4.575236 GTCGGGGATGTTATCTTCCTTTTC 59.425 45.833 5.87 0.00 37.82 2.29
35 36 4.227527 AGTCGGGGATGTTATCTTCCTTTT 59.772 41.667 5.87 0.00 37.82 2.27
36 37 3.780850 AGTCGGGGATGTTATCTTCCTTT 59.219 43.478 5.87 0.00 37.82 3.11
37 38 3.134804 CAGTCGGGGATGTTATCTTCCTT 59.865 47.826 5.87 0.00 37.82 3.36
38 39 2.700897 CAGTCGGGGATGTTATCTTCCT 59.299 50.000 5.87 0.00 37.82 3.36
39 40 2.224305 CCAGTCGGGGATGTTATCTTCC 60.224 54.545 0.00 0.00 37.22 3.46
40 41 2.434702 ACCAGTCGGGGATGTTATCTTC 59.565 50.000 0.00 0.00 42.91 2.87
41 42 2.478292 ACCAGTCGGGGATGTTATCTT 58.522 47.619 0.00 0.00 42.91 2.40
42 43 2.176247 ACCAGTCGGGGATGTTATCT 57.824 50.000 0.00 0.00 42.91 1.98
43 44 2.484947 GGAACCAGTCGGGGATGTTATC 60.485 54.545 0.00 0.00 42.91 1.75
44 45 1.489230 GGAACCAGTCGGGGATGTTAT 59.511 52.381 0.00 0.00 42.91 1.89
45 46 0.906775 GGAACCAGTCGGGGATGTTA 59.093 55.000 0.00 0.00 42.91 2.41
46 47 0.840722 AGGAACCAGTCGGGGATGTT 60.841 55.000 0.00 0.00 42.91 2.71
47 48 0.042131 TAGGAACCAGTCGGGGATGT 59.958 55.000 0.00 0.00 42.91 3.06
48 49 1.424638 ATAGGAACCAGTCGGGGATG 58.575 55.000 0.00 0.00 42.91 3.51
49 50 2.492940 CCTATAGGAACCAGTCGGGGAT 60.493 54.545 14.11 0.00 38.17 3.85
50 51 1.133262 CCTATAGGAACCAGTCGGGGA 60.133 57.143 14.11 0.00 38.17 4.81
51 52 1.133262 TCCTATAGGAACCAGTCGGGG 60.133 57.143 19.59 0.00 42.18 5.73
52 53 2.376695 TCCTATAGGAACCAGTCGGG 57.623 55.000 19.59 0.00 42.18 5.14
65 66 9.121658 CGCAAGGTCTATCAGTATATTCCTATA 57.878 37.037 0.00 0.00 0.00 1.31
66 67 8.001881 CGCAAGGTCTATCAGTATATTCCTAT 57.998 38.462 0.00 0.00 0.00 2.57
67 68 7.392494 CGCAAGGTCTATCAGTATATTCCTA 57.608 40.000 0.00 0.00 0.00 2.94
68 69 6.274157 CGCAAGGTCTATCAGTATATTCCT 57.726 41.667 0.00 0.00 0.00 3.36
96 97 2.730524 GGGGAGCAGAGCAGGACTC 61.731 68.421 0.00 0.00 46.66 3.36
97 98 2.686835 GGGGAGCAGAGCAGGACT 60.687 66.667 0.00 0.00 0.00 3.85
98 99 2.250741 GAAGGGGAGCAGAGCAGGAC 62.251 65.000 0.00 0.00 0.00 3.85
101 102 2.186384 CGAAGGGGAGCAGAGCAG 59.814 66.667 0.00 0.00 0.00 4.24
129 130 2.747855 GAAGGGGAGGCAACAGCG 60.748 66.667 0.00 0.00 41.41 5.18
156 157 0.672711 GCTTCCGCTAAGGGAAACGT 60.673 55.000 0.00 0.00 45.08 3.99
216 218 1.460689 AAGAACTCCACCCCGACCA 60.461 57.895 0.00 0.00 0.00 4.02
218 220 0.685660 AAGAAGAACTCCACCCCGAC 59.314 55.000 0.00 0.00 0.00 4.79
265 269 1.649815 CCGTTCCTCTCGATCTCGG 59.350 63.158 0.00 0.00 40.29 4.63
311 317 7.293828 ACAGAGAAAAGAGGGAAAAGAAATCT 58.706 34.615 0.00 0.00 0.00 2.40
371 407 6.539649 TCGGTACAAAGAAAAACAGAGATG 57.460 37.500 0.00 0.00 0.00 2.90
462 512 2.744202 CACAAGCAGAAGGTATGACCAC 59.256 50.000 0.00 0.00 41.95 4.16
546 633 1.672356 GTGCAGTGCTGACGGGAAT 60.672 57.895 17.60 0.00 0.00 3.01
586 673 1.362717 CGCCGTACATCCCACCTAG 59.637 63.158 0.00 0.00 0.00 3.02
628 721 5.632902 GCACTATATAAAAAGGTGGGGGACA 60.633 44.000 0.00 0.00 0.00 4.02
630 723 4.479056 TGCACTATATAAAAAGGTGGGGGA 59.521 41.667 0.00 0.00 0.00 4.81
640 733 6.061441 CCCCTGTCACATGCACTATATAAAA 58.939 40.000 0.00 0.00 0.00 1.52
693 786 2.632987 TAGATCCACGTCCTGATCGA 57.367 50.000 11.50 0.00 41.76 3.59
705 798 2.070039 CACCGGGCCCTTAGATCCA 61.070 63.158 22.43 0.00 0.00 3.41
767 860 4.872664 AGCTAGTCGCCATCTTGTTATAC 58.127 43.478 0.00 0.00 40.39 1.47
770 863 3.243434 GCTAGCTAGTCGCCATCTTGTTA 60.243 47.826 21.62 0.00 40.39 2.41
780 873 1.537638 TGCATCTAGCTAGCTAGTCGC 59.462 52.381 38.27 36.76 44.59 5.19
784 877 5.840243 ATGATCTGCATCTAGCTAGCTAG 57.160 43.478 36.20 36.20 45.38 3.42
804 897 6.972328 AGTTGCCGTGCATTAATTTAAGTATG 59.028 34.615 0.00 0.00 38.76 2.39
808 901 5.003402 CGAAGTTGCCGTGCATTAATTTAAG 59.997 40.000 0.00 0.00 38.76 1.85
812 905 2.227865 ACGAAGTTGCCGTGCATTAATT 59.772 40.909 0.00 0.00 37.78 1.40
813 906 1.810151 ACGAAGTTGCCGTGCATTAAT 59.190 42.857 0.00 0.00 37.78 1.40
814 907 1.231221 ACGAAGTTGCCGTGCATTAA 58.769 45.000 0.00 0.00 37.78 1.40
815 908 2.921374 ACGAAGTTGCCGTGCATTA 58.079 47.368 0.00 0.00 37.78 1.90
846 939 8.400947 GCTGAATTTCTTATGCTGATCACTTTA 58.599 33.333 0.00 0.00 0.00 1.85
867 960 1.153647 CGTATGCTGTCCGGCTGAA 60.154 57.895 0.00 0.00 0.00 3.02
886 979 6.825944 TGGTTAGCAGTAATGCAATGTTAA 57.174 33.333 18.53 3.87 37.25 2.01
887 980 6.376864 ACATGGTTAGCAGTAATGCAATGTTA 59.623 34.615 18.53 0.00 37.25 2.41
892 985 3.119531 GCACATGGTTAGCAGTAATGCAA 60.120 43.478 18.53 6.91 37.25 4.08
893 986 2.423185 GCACATGGTTAGCAGTAATGCA 59.577 45.455 18.53 0.33 37.25 3.96
955 1051 4.081254 CCTCTCACTCAATGGTCAATCTGA 60.081 45.833 0.00 0.00 0.00 3.27
960 1056 1.980765 AGCCTCTCACTCAATGGTCAA 59.019 47.619 0.00 0.00 0.00 3.18
1013 1109 2.751436 CCCACCAATCCACAGCGG 60.751 66.667 0.00 0.00 0.00 5.52
1147 1243 2.607038 CGTCGCTGCCTATGTATGCTAA 60.607 50.000 0.00 0.00 0.00 3.09
1206 1302 2.159382 GAATTTTCCGGCTTCCTGTGA 58.841 47.619 0.00 0.00 0.00 3.58
1540 1645 3.524095 TTCCTCATGGTCCATTTGTGT 57.476 42.857 0.00 0.00 34.23 3.72
1542 1647 5.191727 TGTATTCCTCATGGTCCATTTGT 57.808 39.130 0.00 0.00 34.23 2.83
1545 1650 3.435601 GGCTGTATTCCTCATGGTCCATT 60.436 47.826 0.00 0.00 34.23 3.16
1552 1657 1.224069 CCGCGGCTGTATTCCTCATG 61.224 60.000 14.67 0.00 0.00 3.07
1571 1676 6.264744 AGGGTGCTTTTACCTCTTTCTTTAAC 59.735 38.462 0.00 0.00 40.66 2.01
1572 1677 6.370453 AGGGTGCTTTTACCTCTTTCTTTAA 58.630 36.000 0.00 0.00 40.66 1.52
1573 1678 5.948842 AGGGTGCTTTTACCTCTTTCTTTA 58.051 37.500 0.00 0.00 40.66 1.85
1574 1679 4.804597 AGGGTGCTTTTACCTCTTTCTTT 58.195 39.130 0.00 0.00 40.66 2.52
1575 1680 4.455070 AGGGTGCTTTTACCTCTTTCTT 57.545 40.909 0.00 0.00 40.66 2.52
1576 1681 4.019231 CCTAGGGTGCTTTTACCTCTTTCT 60.019 45.833 0.00 0.00 40.66 2.52
1577 1682 4.262617 CCTAGGGTGCTTTTACCTCTTTC 58.737 47.826 0.00 0.00 40.66 2.62
1578 1683 3.656264 ACCTAGGGTGCTTTTACCTCTTT 59.344 43.478 14.81 0.00 40.66 2.52
1579 1684 3.257578 ACCTAGGGTGCTTTTACCTCTT 58.742 45.455 14.81 0.00 40.66 2.85
1580 1685 2.917205 ACCTAGGGTGCTTTTACCTCT 58.083 47.619 14.81 0.00 40.66 3.69
1595 1700 5.854010 TCTGTGCAAGTTAGGATACCTAG 57.146 43.478 0.00 0.00 37.42 3.02
1596 1701 6.156256 ACATTCTGTGCAAGTTAGGATACCTA 59.844 38.462 0.00 0.00 34.61 3.08
1630 1735 9.961265 GCACTTTGTAAATTTAGGACTAAAACT 57.039 29.630 8.43 2.46 38.38 2.66
1631 1736 9.738832 TGCACTTTGTAAATTTAGGACTAAAAC 57.261 29.630 8.43 4.00 38.38 2.43
1661 1766 3.003394 CTGCAAGTTGGGGTATGATGA 57.997 47.619 4.75 0.00 0.00 2.92
1732 1837 1.423794 ATGACCGGTCCAACCACCTT 61.424 55.000 31.19 0.00 38.47 3.50
1757 1862 5.500825 GCAAGGTGTTATTTGCAAAAAGTG 58.499 37.500 17.19 7.17 46.72 3.16
1758 1863 5.733226 GCAAGGTGTTATTTGCAAAAAGT 57.267 34.783 17.19 2.12 46.72 2.66
1777 1882 5.175859 CGGGTTAATTAGAGAAGACTGCAA 58.824 41.667 0.00 0.00 0.00 4.08
1816 1921 1.692042 CACCTCCATGCTCCCTCCT 60.692 63.158 0.00 0.00 0.00 3.69
1927 2032 0.397187 TTTTGATCCGACCGGGTTCA 59.603 50.000 6.32 9.32 41.68 3.18
1938 2043 8.514594 TCTATTTCTCAACACACATTTTGATCC 58.485 33.333 0.00 0.00 31.41 3.36
2172 2305 3.192422 CAGAGAGTTCCCTCGGCATATAG 59.808 52.174 0.00 0.00 42.86 1.31
2174 2307 1.967066 CAGAGAGTTCCCTCGGCATAT 59.033 52.381 0.00 0.00 42.86 1.78
2265 2412 4.651778 TGATTTTTCTCCTTGATCCGTGT 58.348 39.130 0.00 0.00 0.00 4.49
2295 2442 1.671901 CCAAACGGCCAACAGGTTGT 61.672 55.000 2.24 0.00 38.85 3.32
2336 2491 2.674796 ATCAGTTCTGTAGGTTCCGC 57.325 50.000 0.00 0.00 0.00 5.54
2543 4261 8.097662 GTCTCTCTTTTAAGGATTCTTTCTGGA 58.902 37.037 0.00 0.00 34.59 3.86


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

AutoCloner maintained by Alex Coulton.