Multiple sequence alignment - TraesCS6D01G052500

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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 TraesCS6D01G052500 chr6D 100.000 5402 0 0 4003 9404 25009572 25014973 0.000000e+00 9976.0
1 TraesCS6D01G052500 chr6D 95.568 5348 191 28 4055 9383 24609583 24604263 0.000000e+00 8521.0
2 TraesCS6D01G052500 chr6D 100.000 3869 0 0 1 3869 25005570 25009438 0.000000e+00 7145.0
3 TraesCS6D01G052500 chr6D 94.790 3877 179 14 1 3869 24613739 24609878 0.000000e+00 6019.0
4 TraesCS6D01G052500 chr6D 88.810 1269 114 11 8162 9404 25296798 25298064 0.000000e+00 1531.0
5 TraesCS6D01G052500 chr6D 81.263 1852 272 36 4869 6674 25031493 25033315 0.000000e+00 1428.0
6 TraesCS6D01G052500 chr6D 85.372 1128 144 14 2698 3816 25243278 25244393 0.000000e+00 1149.0
7 TraesCS6D01G052500 chr6D 85.232 1097 136 16 2698 3782 25282638 25283720 0.000000e+00 1105.0
8 TraesCS6D01G052500 chr6D 87.487 975 77 10 7215 8168 25295697 25296647 0.000000e+00 1083.0
9 TraesCS6D01G052500 chr6D 84.749 1095 142 15 2699 3782 25233547 25234627 0.000000e+00 1074.0
10 TraesCS6D01G052500 chr6D 78.874 1510 262 42 4869 6351 25249214 25250693 0.000000e+00 968.0
11 TraesCS6D01G052500 chr6D 86.559 863 97 12 4003 4864 25286892 25287736 0.000000e+00 933.0
12 TraesCS6D01G052500 chr6D 86.028 866 105 11 4003 4865 25236045 25236897 0.000000e+00 915.0
13 TraesCS6D01G052500 chr6D 86.166 853 105 10 4003 4852 25279923 25280765 0.000000e+00 909.0
14 TraesCS6D01G052500 chr6D 88.276 435 50 1 6775 7209 25238859 25239292 4.100000e-143 520.0
15 TraesCS6D01G052500 chr6D 84.542 524 74 3 901 1419 25282127 25282648 6.870000e-141 512.0
16 TraesCS6D01G052500 chr6D 84.180 512 78 3 909 1419 25242779 25243288 2.490000e-135 494.0
17 TraesCS6D01G052500 chr6D 82.734 556 87 4 873 1419 25233001 25233556 4.160000e-133 486.0
18 TraesCS6D01G052500 chr6D 80.721 638 103 10 4869 5499 25287786 25288410 6.960000e-131 479.0
19 TraesCS6D01G052500 chr6D 82.396 551 89 5 876 1419 25141476 25142025 3.240000e-129 473.0
20 TraesCS6D01G052500 chr6D 85.511 352 48 2 431 781 25035079 25035428 2.030000e-96 364.0
21 TraesCS6D01G052500 chr6D 84.140 372 55 3 416 785 25281545 25281914 3.400000e-94 357.0
22 TraesCS6D01G052500 chr6D 100.000 155 0 0 9758 9912 24603840 24603686 4.530000e-73 287.0
23 TraesCS6D01G052500 chr6D 100.000 155 0 0 9758 9912 25015327 25015481 4.530000e-73 287.0
24 TraesCS6D01G052500 chr6D 93.000 100 7 0 9758 9857 25298129 25298228 8.020000e-31 147.0
25 TraesCS6D01G052500 chr6B 92.335 3340 192 23 4003 7309 40648970 40652278 0.000000e+00 4691.0
26 TraesCS6D01G052500 chr6B 91.564 3343 220 25 4003 7309 40781207 40784523 0.000000e+00 4554.0
27 TraesCS6D01G052500 chr6B 91.239 2979 193 25 4366 7309 40707540 40710485 0.000000e+00 3993.0
28 TraesCS6D01G052500 chr6B 96.008 2029 80 1 7311 9338 40652538 40654566 0.000000e+00 3297.0
29 TraesCS6D01G052500 chr6B 94.537 2032 82 10 7316 9344 40710742 40712747 0.000000e+00 3110.0
30 TraesCS6D01G052500 chr6B 93.978 2026 86 13 7316 9338 40784782 40786774 0.000000e+00 3033.0
31 TraesCS6D01G052500 chr6B 88.409 2200 189 30 7215 9404 41222980 41225123 0.000000e+00 2590.0
32 TraesCS6D01G052500 chr6B 88.039 1856 188 14 7382 9211 41051031 41052878 0.000000e+00 2167.0
33 TraesCS6D01G052500 chr6B 87.749 1861 193 21 7382 9212 41193597 41195452 0.000000e+00 2141.0
34 TraesCS6D01G052500 chr6B 87.399 1857 204 17 7382 9212 41162769 41164621 0.000000e+00 2106.0
35 TraesCS6D01G052500 chr6B 87.258 1860 204 16 7382 9212 41141494 41143349 0.000000e+00 2091.0
36 TraesCS6D01G052500 chr6B 92.071 1463 87 13 2411 3858 40706009 40707457 0.000000e+00 2032.0
37 TraesCS6D01G052500 chr6B 89.952 1453 99 13 2421 3858 40779373 40780793 0.000000e+00 1831.0
38 TraesCS6D01G052500 chr6B 89.401 1453 96 24 2423 3861 40647170 40648578 0.000000e+00 1777.0
39 TraesCS6D01G052500 chr6B 87.268 1618 105 28 768 2370 40704068 40705599 0.000000e+00 1753.0
40 TraesCS6D01G052500 chr6B 91.179 1247 98 10 1192 2428 40777699 40778943 0.000000e+00 1683.0
41 TraesCS6D01G052500 chr6B 79.093 2248 343 65 4869 7034 40973908 40976110 0.000000e+00 1430.0
42 TraesCS6D01G052500 chr6B 87.621 1244 127 12 7382 8603 41059453 41060691 0.000000e+00 1419.0
43 TraesCS6D01G052500 chr6B 90.133 1054 87 9 1370 2413 40645691 40646737 0.000000e+00 1354.0
44 TraesCS6D01G052500 chr6B 92.664 777 55 2 5 779 40702193 40702969 0.000000e+00 1118.0
45 TraesCS6D01G052500 chr6B 91.995 787 52 5 3 779 40764146 40764931 0.000000e+00 1094.0
46 TraesCS6D01G052500 chr6B 80.560 1394 215 28 5310 6665 41103313 41104688 0.000000e+00 1022.0
47 TraesCS6D01G052500 chr6B 91.516 719 52 4 5 721 40641269 40641980 0.000000e+00 981.0
48 TraesCS6D01G052500 chr6B 79.885 1392 210 35 5310 6665 41022105 41023462 0.000000e+00 955.0
49 TraesCS6D01G052500 chr6B 85.417 864 112 12 4003 4865 41117778 41118628 0.000000e+00 885.0
50 TraesCS6D01G052500 chr6B 78.356 1460 251 39 4869 6309 41197913 41199326 0.000000e+00 885.0
51 TraesCS6D01G052500 chr6B 88.081 688 76 4 8530 9212 41166264 41166950 0.000000e+00 811.0
52 TraesCS6D01G052500 chr6B 87.027 555 65 3 6657 7209 41104706 41105255 3.930000e-173 619.0
53 TraesCS6D01G052500 chr6B 87.382 531 59 4 6681 7209 41049117 41049641 3.960000e-168 603.0
54 TraesCS6D01G052500 chr6B 87.170 530 58 5 6683 7209 41131179 41131701 2.380000e-165 593.0
55 TraesCS6D01G052500 chr6B 85.971 556 70 4 6656 7209 41023479 41024028 1.110000e-163 588.0
56 TraesCS6D01G052500 chr6B 82.732 527 76 9 901 1419 41196770 41197289 1.170000e-123 455.0
57 TraesCS6D01G052500 chr6B 84.140 372 55 3 416 785 41135360 41135729 3.400000e-94 357.0
58 TraesCS6D01G052500 chr6B 83.646 373 55 5 416 785 41144092 41144461 7.370000e-91 346.0
59 TraesCS6D01G052500 chr6B 86.620 284 36 1 416 699 41053620 41053901 7.470000e-81 313.0
60 TraesCS6D01G052500 chr6B 82.432 296 48 2 4869 5161 41047229 41047523 1.280000e-63 255.0
61 TraesCS6D01G052500 chr6B 92.308 156 10 2 9758 9912 41225189 41225343 4.660000e-53 220.0
62 TraesCS6D01G052500 chr6B 92.308 156 7 3 9758 9912 40787100 40787251 6.030000e-52 217.0
63 TraesCS6D01G052500 chr6B 93.333 120 7 1 9794 9912 40712765 40712884 1.020000e-39 176.0
64 TraesCS6D01G052500 chr6B 86.792 53 7 0 2312 2364 40778668 40778720 1.080000e-04 60.2
65 TraesCS6D01G052500 chr6B 86.000 50 7 0 2312 2361 40646477 40646526 5.000000e-03 54.7
66 TraesCS6D01G052500 chr6A 94.614 2451 107 13 4003 6441 23237536 23235099 0.000000e+00 3771.0
67 TraesCS6D01G052500 chr6A 95.002 2101 81 6 7327 9404 23233616 23231517 0.000000e+00 3277.0
68 TraesCS6D01G052500 chr6A 92.199 2269 150 10 1611 3869 23240145 23237894 0.000000e+00 3184.0
69 TraesCS6D01G052500 chr6A 94.175 1528 77 9 1 1519 23241671 23240147 0.000000e+00 2318.0
70 TraesCS6D01G052500 chr6A 80.119 1856 291 43 4869 6674 23176581 23174754 0.000000e+00 1312.0
71 TraesCS6D01G052500 chr6A 94.565 828 40 3 6487 7310 23234749 23233923 0.000000e+00 1275.0
72 TraesCS6D01G052500 chr6A 81.703 552 93 6 876 1419 23073311 23072760 4.220000e-123 453.0
73 TraesCS6D01G052500 chr6A 81.655 278 44 5 2427 2698 445273813 445274089 3.600000e-54 224.0
74 TraesCS6D01G052500 chr6A 97.143 35 1 0 2330 2364 23239593 23239559 1.080000e-04 60.2
75 TraesCS6D01G052500 chrUn 83.967 1104 156 13 2698 3791 71564756 71563664 0.000000e+00 1038.0
76 TraesCS6D01G052500 chrUn 86.199 855 102 13 4003 4852 345346679 345345836 0.000000e+00 911.0
77 TraesCS6D01G052500 chrUn 86.082 855 103 13 4003 4852 71539443 71540286 0.000000e+00 905.0
78 TraesCS6D01G052500 chrUn 82.885 520 81 4 905 1419 341509804 341510320 2.520000e-125 460.0
79 TraesCS6D01G052500 chrUn 83.621 232 34 3 2470 2697 231478956 231478725 2.170000e-51 215.0
80 TraesCS6D01G052500 chrUn 83.404 235 35 3 2467 2697 244854143 244854377 2.170000e-51 215.0
81 TraesCS6D01G052500 chr2B 83.699 1141 139 18 6100 7206 743354973 743356100 0.000000e+00 1033.0
82 TraesCS6D01G052500 chr2B 79.876 323 47 10 1419 1739 8710719 8711025 4.660000e-53 220.0
83 TraesCS6D01G052500 chr4D 81.961 255 41 5 2454 2706 217132131 217131880 2.800000e-50 211.0
84 TraesCS6D01G052500 chr4D 79.333 300 35 10 1418 1717 482937090 482937362 1.700000e-42 185.0
85 TraesCS6D01G052500 chr4D 81.548 168 27 4 1415 1580 294093285 294093120 1.740000e-27 135.0
86 TraesCS6D01G052500 chr2D 78.462 325 55 5 1418 1741 427987650 427987340 2.180000e-46 198.0
87 TraesCS6D01G052500 chr2D 89.333 75 7 1 6100 6173 609309727 609309801 1.060000e-14 93.5
88 TraesCS6D01G052500 chr5A 80.632 253 44 5 2452 2700 42679352 42679603 3.650000e-44 191.0
89 TraesCS6D01G052500 chr1A 78.689 305 39 12 1419 1721 441035204 441034924 7.910000e-41 180.0
90 TraesCS6D01G052500 chr2A 76.471 289 46 12 5790 6077 741101063 741101330 4.830000e-28 137.0
91 TraesCS6D01G052500 chr5B 88.095 84 9 1 1419 1502 75034317 75034235 2.280000e-16 99.0
92 TraesCS6D01G052500 chr1B 82.727 110 17 2 1633 1741 565298663 565298771 8.190000e-16 97.1


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 TraesCS6D01G052500 chr6D 25005570 25015481 9911 False 5802.666667 9976 100.000000 1 9912 3 chr6D.!!$F3 9911
1 TraesCS6D01G052500 chr6D 24603686 24613739 10053 True 4942.333333 8521 96.786000 1 9912 3 chr6D.!!$R1 9911
2 TraesCS6D01G052500 chr6D 25249214 25250693 1479 False 968.000000 968 78.874000 4869 6351 1 chr6D.!!$F2 1482
3 TraesCS6D01G052500 chr6D 25295697 25298228 2531 False 920.333333 1531 89.765667 7215 9857 3 chr6D.!!$F7 2642
4 TraesCS6D01G052500 chr6D 25031493 25035428 3935 False 896.000000 1428 83.387000 431 6674 2 chr6D.!!$F4 6243
5 TraesCS6D01G052500 chr6D 25233001 25244393 11392 False 773.000000 1149 85.223167 873 7209 6 chr6D.!!$F5 6336
6 TraesCS6D01G052500 chr6D 25279923 25288410 8487 False 715.833333 1105 84.560000 416 5499 6 chr6D.!!$F6 5083
7 TraesCS6D01G052500 chr6D 25141476 25142025 549 False 473.000000 473 82.396000 876 1419 1 chr6D.!!$F1 543
8 TraesCS6D01G052500 chr6B 40702193 40712884 10691 False 2030.333333 3993 91.852000 5 9912 6 chr6B.!!$F6 9907
9 TraesCS6D01G052500 chr6B 40641269 40654566 13297 False 2025.783333 4691 90.898833 5 9338 6 chr6B.!!$F5 9333
10 TraesCS6D01G052500 chr6B 40777699 40787251 9552 False 1896.366667 4554 90.962167 1192 9912 6 chr6B.!!$F7 8720
11 TraesCS6D01G052500 chr6B 41162769 41166950 4181 False 1458.500000 2106 87.740000 7382 9212 2 chr6B.!!$F13 1830
12 TraesCS6D01G052500 chr6B 40973908 40976110 2202 False 1430.000000 1430 79.093000 4869 7034 1 chr6B.!!$F2 2165
13 TraesCS6D01G052500 chr6B 41059453 41060691 1238 False 1419.000000 1419 87.621000 7382 8603 1 chr6B.!!$F3 1221
14 TraesCS6D01G052500 chr6B 41222980 41225343 2363 False 1405.000000 2590 90.358500 7215 9912 2 chr6B.!!$F15 2697
15 TraesCS6D01G052500 chr6B 41141494 41144461 2967 False 1218.500000 2091 85.452000 416 9212 2 chr6B.!!$F12 8796
16 TraesCS6D01G052500 chr6B 41193597 41199326 5729 False 1160.333333 2141 82.945667 901 9212 3 chr6B.!!$F14 8311
17 TraesCS6D01G052500 chr6B 40764146 40764931 785 False 1094.000000 1094 91.995000 3 779 1 chr6B.!!$F1 776
18 TraesCS6D01G052500 chr6B 41117778 41118628 850 False 885.000000 885 85.417000 4003 4865 1 chr6B.!!$F4 862
19 TraesCS6D01G052500 chr6B 41047229 41053901 6672 False 834.500000 2167 86.118250 416 9211 4 chr6B.!!$F9 8795
20 TraesCS6D01G052500 chr6B 41103313 41105255 1942 False 820.500000 1022 83.793500 5310 7209 2 chr6B.!!$F10 1899
21 TraesCS6D01G052500 chr6B 41022105 41024028 1923 False 771.500000 955 82.928000 5310 7209 2 chr6B.!!$F8 1899
22 TraesCS6D01G052500 chr6B 41131179 41135729 4550 False 475.000000 593 85.655000 416 7209 2 chr6B.!!$F11 6793
23 TraesCS6D01G052500 chr6A 23231517 23241671 10154 True 2314.200000 3771 94.616333 1 9404 6 chr6A.!!$R3 9403
24 TraesCS6D01G052500 chr6A 23174754 23176581 1827 True 1312.000000 1312 80.119000 4869 6674 1 chr6A.!!$R2 1805
25 TraesCS6D01G052500 chr6A 23072760 23073311 551 True 453.000000 453 81.703000 876 1419 1 chr6A.!!$R1 543
26 TraesCS6D01G052500 chrUn 71563664 71564756 1092 True 1038.000000 1038 83.967000 2698 3791 1 chrUn.!!$R1 1093
27 TraesCS6D01G052500 chrUn 345345836 345346679 843 True 911.000000 911 86.199000 4003 4852 1 chrUn.!!$R3 849
28 TraesCS6D01G052500 chrUn 71539443 71540286 843 False 905.000000 905 86.082000 4003 4852 1 chrUn.!!$F1 849
29 TraesCS6D01G052500 chrUn 341509804 341510320 516 False 460.000000 460 82.885000 905 1419 1 chrUn.!!$F3 514
30 TraesCS6D01G052500 chr2B 743354973 743356100 1127 False 1033.000000 1033 83.699000 6100 7206 1 chr2B.!!$F2 1106

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
754 1968 1.405821 CGCTAATAGGGCGCTATAGCT 59.594 52.381 28.43 17.89 45.83 3.32 F
1770 6344 0.879090 TTAGAGAAGCAGCACGACGA 59.121 50.000 0.00 0.00 0.00 4.20 F
2662 7706 0.249280 CCGGTGTTTTCTGCAAACCC 60.249 55.000 0.00 1.53 43.87 4.11 F
2855 7914 0.831307 ATCGTAGAACTTGAGGCCCC 59.169 55.000 0.00 0.00 43.58 5.80 F
3687 8749 1.028905 TTCCTCGGTGCAAAAACCAG 58.971 50.000 0.00 0.00 40.53 4.00 F
5168 13672 0.383590 ATCAGAGCGAGACGATGGTG 59.616 55.000 0.00 0.00 0.00 4.17 F
5295 13842 0.105194 TCCTTCCAGTGACTCCACCA 60.105 55.000 0.00 0.00 44.22 4.17 F
6633 15576 1.227089 CTCTCGCCGCTAGCAATGT 60.227 57.895 16.45 0.00 44.04 2.71 F
7569 18372 1.192534 CTTCGTCACTCTCAAAACCGC 59.807 52.381 0.00 0.00 0.00 5.68 F
7573 18376 1.795286 GTCACTCTCAAAACCGCTCAG 59.205 52.381 0.00 0.00 0.00 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 6479 0.035343 ATGACTGAGGACGAGGACGA 60.035 55.000 0.00 0.00 42.66 4.20 R
2806 7865 0.105778 GTGGGAGAGAGCACTATGCC 59.894 60.000 9.35 9.35 46.52 4.40 R
4199 12626 1.281899 GAGGATAAGCAGTGACACGC 58.718 55.000 12.53 12.53 0.00 5.34 R
4841 13288 0.255033 AGGGGCCCGTAAAGAATGAC 59.745 55.000 17.40 0.00 0.00 3.06 R
5220 13762 0.409092 ATCATGGAAGGGGTGCACAA 59.591 50.000 20.43 0.00 0.00 3.33 R
6762 15757 0.887387 GTATGTGTGGGGTGTGCGTT 60.887 55.000 0.00 0.00 0.00 4.84 R
6924 15927 2.803956 AGACCATCTCACGTCCTACAA 58.196 47.619 0.00 0.00 0.00 2.41 R
8142 18948 1.350310 ACTGGTGGTTTTCGGTCCCT 61.350 55.000 0.00 0.00 0.00 4.20 R
8761 19760 2.082231 CACAAATGACCAGGAGCAGAG 58.918 52.381 0.00 0.00 0.00 3.35 R
9152 22501 8.723942 ATCACCAATTCTGAAGATACAAGTAC 57.276 34.615 0.00 0.00 0.00 2.73 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
21 22 2.291670 ACGAGACACATAAGGAGAGGGT 60.292 50.000 0.00 0.00 0.00 4.34
62 63 2.035626 ACCCAGCAAATCACGGGG 59.964 61.111 0.00 0.00 43.52 5.73
212 221 3.693572 AGGGAGCCTCCTGGAGCT 61.694 66.667 18.51 17.63 43.55 4.09
234 243 5.820947 GCTAAGTTGGCTAGCAACCTTATAA 59.179 40.000 18.24 0.00 36.86 0.98
268 277 8.526667 TGGCAGGTTGCTATGTATTAATTTTA 57.473 30.769 0.00 0.00 44.28 1.52
294 303 2.031163 GAGTGTGCGGTCTGCCTT 59.969 61.111 0.00 0.00 45.60 4.35
417 426 9.494271 TTGATAGGCTCAAACATATCAGAATAC 57.506 33.333 0.00 0.00 40.92 1.89
419 428 9.494271 GATAGGCTCAAACATATCAGAATACAA 57.506 33.333 0.00 0.00 0.00 2.41
564 1773 8.574251 TGCTAATGTCAACCACAACTTATAAT 57.426 30.769 0.00 0.00 38.97 1.28
567 1777 7.404671 AATGTCAACCACAACTTATAATCCC 57.595 36.000 0.00 0.00 38.97 3.85
667 1879 5.699097 TTTTGGAGCACTAAATACCACAC 57.301 39.130 0.00 0.00 0.00 3.82
683 1895 3.381272 ACCACACACTGTTTCCATCTTTG 59.619 43.478 0.00 0.00 0.00 2.77
715 1928 5.221880 TGATCATGGCTTTTTCAACGAAAG 58.778 37.500 0.00 0.00 37.21 2.62
754 1968 1.405821 CGCTAATAGGGCGCTATAGCT 59.594 52.381 28.43 17.89 45.83 3.32
930 5468 1.511305 CGGCTTCTTCCTCGTGCTA 59.489 57.895 0.00 0.00 0.00 3.49
1234 5792 7.406151 AGGAGAGGTTATTCTTTAGGAATGGAA 59.594 37.037 0.00 0.00 43.68 3.53
1478 6040 2.356382 TGCAGAAAACACCACTTTACGG 59.644 45.455 0.00 0.00 0.00 4.02
1495 6057 6.635239 ACTTTACGGATTTGTGACAAAAATCG 59.365 34.615 20.09 18.67 42.45 3.34
1520 6082 6.699575 TCATTCTTAGCCTAATCTTTTGCC 57.300 37.500 0.00 0.00 0.00 4.52
1568 6142 5.007234 TCGAGCATTTTAACCGTGATTATGG 59.993 40.000 0.00 0.00 39.01 2.74
1576 6150 1.211703 ACCGTGATTATGGCATGTGGA 59.788 47.619 10.98 0.00 36.36 4.02
1693 6267 6.936900 TGAAATTTTAGAGAGACACCCTTCAG 59.063 38.462 0.00 0.00 0.00 3.02
1702 6276 6.214412 AGAGAGACACCCTTCAGTCAATAAAT 59.786 38.462 0.00 0.00 37.23 1.40
1757 6331 1.470979 GCCGAAGCAACCGATTAGAGA 60.471 52.381 0.00 0.00 39.53 3.10
1767 6341 1.202302 CCGATTAGAGAAGCAGCACGA 60.202 52.381 0.00 0.00 0.00 4.35
1770 6344 0.879090 TTAGAGAAGCAGCACGACGA 59.121 50.000 0.00 0.00 0.00 4.20
1921 6496 2.033755 CGTCGTCCTCGTCCTCAGT 61.034 63.158 0.00 0.00 38.33 3.41
1923 6498 0.954449 GTCGTCCTCGTCCTCAGTCA 60.954 60.000 0.00 0.00 38.33 3.41
1941 6516 4.040584 CAGTCATCAGACCATCATCCTCAT 59.959 45.833 0.00 0.00 46.15 2.90
1950 6525 5.026121 GACCATCATCCTCATCCTATGGTA 58.974 45.833 4.86 0.00 45.34 3.25
1953 6528 5.723405 CCATCATCCTCATCCTATGGTAGAA 59.277 44.000 0.00 0.00 31.28 2.10
1972 6550 2.743928 CACCAGAGGAAGCCGCAC 60.744 66.667 0.00 0.00 0.00 5.34
1996 6574 2.346803 GTCTAGCCGCAAAGTTCATCA 58.653 47.619 0.00 0.00 0.00 3.07
2004 6582 2.223203 CGCAAAGTTCATCAGATCCAGC 60.223 50.000 0.00 0.00 0.00 4.85
2040 6618 4.873129 CACCGGATCCAGGACGCG 62.873 72.222 23.89 3.53 0.00 6.01
2063 6641 2.998097 CCACGGTGGATCCATGGT 59.002 61.111 22.77 15.87 43.83 3.55
2099 6677 1.667830 CCATGACCAGCACGTCGTT 60.668 57.895 0.00 0.00 35.40 3.85
2195 6774 1.694169 GGATGGAGAAGGGGAGGCA 60.694 63.158 0.00 0.00 0.00 4.75
2239 6818 4.451150 CCTGCTACGCAAGGCCGA 62.451 66.667 0.00 0.00 46.39 5.54
2515 7559 7.013529 CCTTTAGCGTTGTTTATTGTGTACTC 58.986 38.462 0.00 0.00 0.00 2.59
2529 7573 6.579666 TTGTGTACTCTTACCGACATAAGT 57.420 37.500 0.00 0.00 34.36 2.24
2538 7582 5.716228 TCTTACCGACATAAGTAAAGGGTGA 59.284 40.000 0.00 0.00 34.36 4.02
2546 7590 5.665812 ACATAAGTAAAGGGTGAGCTCCATA 59.334 40.000 12.15 0.00 0.00 2.74
2662 7706 0.249280 CCGGTGTTTTCTGCAAACCC 60.249 55.000 0.00 1.53 43.87 4.11
2739 7783 3.131396 CGTGTATACCATTTGGAGGAGC 58.869 50.000 3.01 0.00 38.94 4.70
2761 7805 3.007398 CCCGCTCCTATTTCTCTTAGCAT 59.993 47.826 0.00 0.00 0.00 3.79
2806 7865 9.778993 CACAATCATTTATTCTTACCACTGAAG 57.221 33.333 0.00 0.00 0.00 3.02
2846 7905 6.293955 CCCACAAACAAATTCATCGTAGAACT 60.294 38.462 0.00 0.00 43.58 3.01
2855 7914 0.831307 ATCGTAGAACTTGAGGCCCC 59.169 55.000 0.00 0.00 43.58 5.80
2977 8037 7.419711 TTCTCTGGGAAGTTGTATAGGTAAG 57.580 40.000 0.00 0.00 0.00 2.34
3254 8314 8.416329 ACCTTGGTTATGCTTTCAAATGATATC 58.584 33.333 0.00 0.00 0.00 1.63
3410 8470 4.890581 TGGTGTTTTGCACTAATGTAGGTT 59.109 37.500 0.00 0.00 46.86 3.50
3455 8515 5.295431 TGTCAATTTCGGCTGATAAAGTG 57.705 39.130 0.00 0.00 33.27 3.16
3470 8530 8.609176 GCTGATAAAGTGATATTTAAACCACGA 58.391 33.333 0.00 3.50 34.93 4.35
3537 8597 3.802948 ACTACATGGCTTCTAGTTCCG 57.197 47.619 0.00 0.00 0.00 4.30
3557 8617 1.283321 GGTCTTCTTTGGAGATGGCCT 59.717 52.381 3.32 0.00 44.39 5.19
3592 8652 5.904080 GCAAGTCGTATTAAAGTGATGATGC 59.096 40.000 0.00 0.00 0.00 3.91
3687 8749 1.028905 TTCCTCGGTGCAAAAACCAG 58.971 50.000 0.00 0.00 40.53 4.00
4040 12463 3.318557 CGAGTCCTAAGCCCTTAGTTAGG 59.681 52.174 12.61 2.26 44.71 2.69
4155 12582 2.025863 GCCCAGTAAGCATGCCTCAAT 61.026 52.381 15.66 0.00 0.00 2.57
4160 12587 4.445453 CAGTAAGCATGCCTCAATACTCA 58.555 43.478 15.66 0.00 0.00 3.41
4241 12668 3.981071 TTTCACCCTCACTGATAGTGG 57.019 47.619 8.91 0.91 45.94 4.00
4309 12736 1.786937 AGAAGATGATCTCGGCCACT 58.213 50.000 2.24 0.00 0.00 4.00
4756 13199 1.064505 CTTGTTGCATGTATCCGCTGG 59.935 52.381 0.00 0.00 0.00 4.85
4852 13299 6.641314 TGAAAGAGTGTCTCGTCATTCTTTAC 59.359 38.462 18.85 15.02 46.49 2.01
5053 13554 1.068474 CATTCCACCTTGTCGTCGTC 58.932 55.000 0.00 0.00 0.00 4.20
5144 13648 3.057548 CAGGGCACAATCGCAGCA 61.058 61.111 0.00 0.00 0.00 4.41
5165 13669 0.996229 GCGATCAGAGCGAGACGATG 60.996 60.000 13.41 0.00 31.74 3.84
5166 13670 0.385348 CGATCAGAGCGAGACGATGG 60.385 60.000 0.46 0.00 31.74 3.51
5167 13671 0.665835 GATCAGAGCGAGACGATGGT 59.334 55.000 0.00 0.00 0.00 3.55
5168 13672 0.383590 ATCAGAGCGAGACGATGGTG 59.616 55.000 0.00 0.00 0.00 4.17
5169 13673 1.875813 CAGAGCGAGACGATGGTGC 60.876 63.158 0.00 0.00 0.00 5.01
5170 13674 2.583593 GAGCGAGACGATGGTGCC 60.584 66.667 0.00 0.00 0.00 5.01
5171 13675 4.148825 AGCGAGACGATGGTGCCC 62.149 66.667 0.00 0.00 0.00 5.36
5173 13677 4.129737 CGAGACGATGGTGCCCGT 62.130 66.667 0.00 0.00 42.17 5.28
5220 13762 2.958543 CATCATCAGCGCGCTCGT 60.959 61.111 34.28 20.33 38.14 4.18
5295 13842 0.105194 TCCTTCCAGTGACTCCACCA 60.105 55.000 0.00 0.00 44.22 4.17
5456 14010 2.280628 GAATCCTTGCCCTACAACGAG 58.719 52.381 0.00 0.00 33.68 4.18
5554 14109 3.085533 CGTGGGACCACAATAAAATGGA 58.914 45.455 20.44 0.00 46.47 3.41
5583 14138 5.195001 ACATCACTTTATGCCAAAAACGT 57.805 34.783 0.00 0.00 0.00 3.99
5781 14340 6.624352 TGTTGGAGATTCTCTGAGTTTTTG 57.376 37.500 13.22 0.00 0.00 2.44
5809 14369 7.166473 GTGTGTTTTTGAAGTAGCTTCTCAATG 59.834 37.037 9.82 0.00 40.73 2.82
5810 14370 6.142958 GTGTTTTTGAAGTAGCTTCTCAATGC 59.857 38.462 9.82 0.00 40.73 3.56
5811 14371 4.668576 TTTGAAGTAGCTTCTCAATGCG 57.331 40.909 9.82 0.00 40.73 4.73
5814 14374 3.433274 TGAAGTAGCTTCTCAATGCGTTG 59.567 43.478 12.66 12.66 40.73 4.10
5815 14375 3.319137 AGTAGCTTCTCAATGCGTTGA 57.681 42.857 19.91 19.91 41.89 3.18
5820 14384 4.479619 AGCTTCTCAATGCGTTGATTTTC 58.520 39.130 21.24 11.30 43.08 2.29
5837 14401 1.748732 TTCCCCCATGGTTCAGTGTA 58.251 50.000 11.73 0.00 34.77 2.90
6093 14665 2.191802 CACTCTAAGACAGCAGCATCG 58.808 52.381 0.00 0.00 0.00 3.84
6475 15110 1.599797 CCACCACCAACGGTTCTCC 60.600 63.158 0.00 0.00 37.07 3.71
6583 15520 3.767673 AGATCCACTAGCGACAAAACCTA 59.232 43.478 0.00 0.00 0.00 3.08
6633 15576 1.227089 CTCTCGCCGCTAGCAATGT 60.227 57.895 16.45 0.00 44.04 2.71
6683 15666 6.069088 ACCATGTTGTCTCTTGGGGATAAATA 60.069 38.462 0.00 0.00 37.08 1.40
6690 15675 8.096621 TGTCTCTTGGGGATAAATATGTAACA 57.903 34.615 0.00 0.00 0.00 2.41
6784 15779 1.241315 GCACACCCCACACATACACC 61.241 60.000 0.00 0.00 0.00 4.16
6808 15811 7.351454 ACCCAACCCAACATATATCCTTACTAA 59.649 37.037 0.00 0.00 0.00 2.24
6842 15845 4.037446 GGTAGAAGTTTGCACCATGTTTCA 59.963 41.667 0.00 0.00 0.00 2.69
6874 15877 8.149973 TGTAACTGTTTTTCTACTCAATCCAC 57.850 34.615 0.00 0.00 0.00 4.02
6924 15927 5.598417 AGGTGTTGAAGCCTTGAAGTTAAAT 59.402 36.000 0.00 0.00 0.00 1.40
6984 15987 9.799106 ATCAATTTTCATAATAGTACAGGGAGG 57.201 33.333 0.00 0.00 0.00 4.30
7058 16065 5.888161 AGAATTTGATAACGAGAGGCCAATT 59.112 36.000 5.01 0.00 0.00 2.32
7060 16067 7.556275 AGAATTTGATAACGAGAGGCCAATTAA 59.444 33.333 5.01 0.00 0.00 1.40
7489 18288 3.502191 TTCAAGATATTGTTTGGCCGC 57.498 42.857 0.00 0.00 0.00 6.53
7569 18372 1.192534 CTTCGTCACTCTCAAAACCGC 59.807 52.381 0.00 0.00 0.00 5.68
7573 18376 1.795286 GTCACTCTCAAAACCGCTCAG 59.205 52.381 0.00 0.00 0.00 3.35
7963 18769 5.663795 AAGCTATTTATGACACTGATGCG 57.336 39.130 0.00 0.00 0.00 4.73
8063 18869 4.570772 CCTGGACACAAGGACATAATAACG 59.429 45.833 0.00 0.00 0.00 3.18
8142 18948 8.385898 AGACTCATTAATCGGTTTTGTTGTAA 57.614 30.769 0.00 0.00 0.00 2.41
8393 19362 3.055819 TCCTCTTTGTGCACCAGTAGATC 60.056 47.826 15.69 0.00 0.00 2.75
8606 19605 2.290960 GGTCAAGGCTTCATTACCCACT 60.291 50.000 0.00 0.00 0.00 4.00
9156 22505 4.734652 CCAACCCGCATTGGTACT 57.265 55.556 7.56 0.00 43.66 2.73
9169 22518 5.580691 CGCATTGGTACTTGTATCTTCAGAA 59.419 40.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 95 2.976356 GCGGTAGTTTCGGAGGGT 59.024 61.111 0.00 0.00 0.00 4.34
234 243 5.658190 ACATAGCAACCTGCCAATTCTAAAT 59.342 36.000 0.00 0.00 46.52 1.40
268 277 3.370978 CAGACCGCACACTCGATAAAATT 59.629 43.478 0.00 0.00 0.00 1.82
416 425 9.195411 CTTATGTATGTTTGTGCTTTTCATTGT 57.805 29.630 0.00 0.00 0.00 2.71
417 426 9.195411 ACTTATGTATGTTTGTGCTTTTCATTG 57.805 29.630 0.00 0.00 0.00 2.82
683 1895 5.831702 AAAAGCCATGATCATCAAGTCTC 57.168 39.130 4.86 0.00 0.00 3.36
715 1928 1.582502 CGAAGAACCGACACGCTATTC 59.417 52.381 0.00 0.00 0.00 1.75
754 1968 0.830444 AGTGTGGGCTCTCCGTGTAA 60.830 55.000 0.00 0.00 38.76 2.41
930 5468 3.714280 GAGGAATAGAAGAAGAGGGGCTT 59.286 47.826 0.00 0.00 40.25 4.35
1234 5792 4.647564 AGAATCAAGTGTCACCAGGATT 57.352 40.909 11.86 11.86 0.00 3.01
1470 6032 6.635239 CGATTTTTGTCACAAATCCGTAAAGT 59.365 34.615 15.55 0.00 37.34 2.66
1478 6040 6.583806 AGAATGAGCGATTTTTGTCACAAATC 59.416 34.615 3.17 12.55 37.30 2.17
1495 6057 6.205071 GCAAAAGATTAGGCTAAGAATGAGC 58.795 40.000 13.15 8.98 44.04 4.26
1531 6100 0.243636 TGCTCGAAGCGACTGATCAA 59.756 50.000 0.00 0.00 46.26 2.57
1537 6111 2.415512 GGTTAAAATGCTCGAAGCGACT 59.584 45.455 0.00 0.00 46.26 4.18
1757 6331 1.568612 CCATTGTCGTCGTGCTGCTT 61.569 55.000 0.00 0.00 0.00 3.91
1770 6344 4.278956 GGCGACGAGAACCATTGT 57.721 55.556 0.00 0.00 0.00 2.71
1895 6469 1.154073 CGAGGACGACGGACCTTTC 60.154 63.158 15.03 5.33 38.48 2.62
1897 6471 2.282040 ACGAGGACGACGGACCTT 60.282 61.111 15.03 0.76 38.48 3.50
1905 6479 0.035343 ATGACTGAGGACGAGGACGA 60.035 55.000 0.00 0.00 42.66 4.20
1921 6496 3.581770 GGATGAGGATGATGGTCTGATGA 59.418 47.826 0.00 0.00 0.00 2.92
1923 6498 3.871810 AGGATGAGGATGATGGTCTGAT 58.128 45.455 0.00 0.00 0.00 2.90
1950 6525 1.831652 CGGCTTCCTCTGGTGGTTCT 61.832 60.000 0.00 0.00 0.00 3.01
1953 6528 4.021925 GCGGCTTCCTCTGGTGGT 62.022 66.667 0.00 0.00 0.00 4.16
1996 6574 1.743321 GCACTAGAGGCGCTGGATCT 61.743 60.000 7.64 8.71 0.00 2.75
2004 6582 0.741221 GACCTTTGGCACTAGAGGCG 60.741 60.000 9.10 0.00 36.77 5.52
2063 6641 4.260355 CGGATCCTAACCGCGCGA 62.260 66.667 34.63 10.92 43.74 5.87
2099 6677 2.915659 ACCTCACCGGCGTCAAGA 60.916 61.111 6.01 0.00 35.61 3.02
2239 6818 1.636519 TCCTCTCTCTCTTTCCCGAGT 59.363 52.381 0.00 0.00 32.83 4.18
2247 6828 1.852965 CTCCTCCCTCCTCTCTCTCTT 59.147 57.143 0.00 0.00 0.00 2.85
2316 6897 0.327591 CTCCCTCTTCTTGCTTGCCT 59.672 55.000 0.00 0.00 0.00 4.75
2515 7559 5.969423 TCACCCTTTACTTATGTCGGTAAG 58.031 41.667 0.00 0.00 37.62 2.34
2529 7573 4.037222 TGACATATGGAGCTCACCCTTTA 58.963 43.478 17.19 0.00 0.00 1.85
2538 7582 7.858498 TGATGATGATTATGACATATGGAGCT 58.142 34.615 7.80 0.00 0.00 4.09
2546 7590 7.450323 TGGCTCATTTGATGATGATTATGACAT 59.550 33.333 0.00 0.00 38.85 3.06
2662 7706 1.750193 AACCACCATATTGGCGTCTG 58.250 50.000 0.00 0.00 42.67 3.51
2739 7783 2.365617 TGCTAAGAGAAATAGGAGCGGG 59.634 50.000 0.00 0.00 32.53 6.13
2806 7865 0.105778 GTGGGAGAGAGCACTATGCC 59.894 60.000 9.35 9.35 46.52 4.40
2855 7914 1.363744 GTGGAGAAGAATCTGTGCGG 58.636 55.000 0.00 0.00 35.54 5.69
2925 7985 2.618241 GTGAGCTGATGTTGTGTTCCAA 59.382 45.455 0.00 0.00 0.00 3.53
2977 8037 5.116180 TGCAGATACTTGTACATGCCTTAC 58.884 41.667 12.91 0.00 32.77 2.34
3039 8099 9.853555 TGTTGTTTAACATCCATGTAAATCATC 57.146 29.630 0.00 0.00 41.66 2.92
3118 8178 3.677700 CGGAGATACGGAACCAATGACAA 60.678 47.826 0.00 0.00 0.00 3.18
3355 8415 5.689835 AGCCAAAACACCAACCATTTTTAT 58.310 33.333 0.00 0.00 0.00 1.40
3462 8522 6.695278 CACAAACTTAATGTTCATCGTGGTTT 59.305 34.615 0.00 0.00 38.03 3.27
3470 8530 7.106439 TGGTTGACACAAACTTAATGTTCAT 57.894 32.000 0.00 0.00 38.03 2.57
3537 8597 1.283321 AGGCCATCTCCAAAGAAGACC 59.717 52.381 5.01 0.00 34.49 3.85
3583 8643 9.846248 ACTAATTGTTCTAAAAAGCATCATCAC 57.154 29.630 0.00 0.00 0.00 3.06
4040 12463 6.455360 TTGGGAAATCAAGTCATAGATTGC 57.545 37.500 0.00 0.00 34.86 3.56
4155 12582 4.783055 GAGGATCTAGACCTGTGTGAGTA 58.217 47.826 15.87 0.00 37.93 2.59
4199 12626 1.281899 GAGGATAAGCAGTGACACGC 58.718 55.000 12.53 12.53 0.00 5.34
4309 12736 3.954200 TCAATGAAAGGTGAGCTATGCA 58.046 40.909 0.00 0.00 0.00 3.96
4420 12851 4.582701 TTGTGGCTAATTGTTCAACCAG 57.417 40.909 0.00 0.00 0.00 4.00
4421 12852 5.772672 ACTATTGTGGCTAATTGTTCAACCA 59.227 36.000 0.00 0.00 0.00 3.67
4756 13199 6.042143 TCAGAAACAAAGAAACAAAGCCATC 58.958 36.000 0.00 0.00 0.00 3.51
4841 13288 0.255033 AGGGGCCCGTAAAGAATGAC 59.745 55.000 17.40 0.00 0.00 3.06
4852 13299 0.473117 TAGGAATAGGAAGGGGCCCG 60.473 60.000 18.95 0.00 0.00 6.13
5053 13554 2.432510 GTGGAGGTCAAGGTGGATAGAG 59.567 54.545 0.00 0.00 0.00 2.43
5144 13648 1.063327 CGTCTCGCTCTGATCGCTT 59.937 57.895 0.00 0.00 0.00 4.68
5220 13762 0.409092 ATCATGGAAGGGGTGCACAA 59.591 50.000 20.43 0.00 0.00 3.33
5295 13842 2.346803 CGGAATCAACAATCCAGTCGT 58.653 47.619 0.00 0.00 35.34 4.34
5554 14109 9.553064 TTTTTGGCATAAAGTGATGTAAAACAT 57.447 25.926 0.00 0.00 42.43 2.71
5583 14138 0.476338 TAGGGCACTTGTTGGAGCAA 59.524 50.000 0.00 0.00 0.00 3.91
5781 14340 5.880341 AGAAGCTACTTCAAAAACACACAC 58.120 37.500 9.80 0.00 42.37 3.82
5809 14369 0.175531 CCATGGGGGAAAATCAACGC 59.824 55.000 2.85 0.00 40.01 4.84
5810 14370 1.555967 ACCATGGGGGAAAATCAACG 58.444 50.000 18.09 0.00 41.15 4.10
5811 14371 2.903135 TGAACCATGGGGGAAAATCAAC 59.097 45.455 18.09 0.00 41.15 3.18
5814 14374 2.497273 CACTGAACCATGGGGGAAAATC 59.503 50.000 18.09 3.23 41.15 2.17
5815 14375 2.158173 ACACTGAACCATGGGGGAAAAT 60.158 45.455 18.09 0.00 41.15 1.82
5820 14384 1.354368 AGTTACACTGAACCATGGGGG 59.646 52.381 18.09 0.85 44.81 5.40
5837 14401 3.492102 TGCTCTTGGTGCTTTCTAGTT 57.508 42.857 0.00 0.00 0.00 2.24
6093 14665 1.965935 AAATTTGTTTGTGGGCTGCC 58.034 45.000 11.05 11.05 0.00 4.85
6583 15520 1.414181 CTCGTGGCTATGGGTGAAGAT 59.586 52.381 0.00 0.00 0.00 2.40
6633 15576 4.409574 TGACACCCAGGTTACAACTAAAGA 59.590 41.667 0.00 0.00 0.00 2.52
6690 15675 9.032624 TGTAGGTTATAGTTAAAGAGCAAGAGT 57.967 33.333 0.00 0.00 0.00 3.24
6762 15757 0.887387 GTATGTGTGGGGTGTGCGTT 60.887 55.000 0.00 0.00 0.00 4.84
6784 15779 8.656806 TCTTAGTAAGGATATATGTTGGGTTGG 58.343 37.037 10.02 0.00 0.00 3.77
6808 15811 5.769662 TGCAAACTTCTACCAATCAACATCT 59.230 36.000 0.00 0.00 0.00 2.90
6874 15877 5.593679 ATGCAAGGAAATGGAGATTTGAG 57.406 39.130 0.00 0.00 31.58 3.02
6924 15927 2.803956 AGACCATCTCACGTCCTACAA 58.196 47.619 0.00 0.00 0.00 2.41
6984 15987 7.568199 AGTACCAATAGAAAATGTATGTGCC 57.432 36.000 0.00 0.00 0.00 5.01
7058 16065 7.040340 TGTTGGAGTTTGACTTGTTTTGACTTA 60.040 33.333 0.00 0.00 0.00 2.24
7060 16067 5.242838 TGTTGGAGTTTGACTTGTTTTGACT 59.757 36.000 0.00 0.00 0.00 3.41
7489 18288 8.025445 CACTCTTCCTTTGATTTCTATGGTTTG 58.975 37.037 0.00 0.00 0.00 2.93
7608 18411 8.812513 TGTCAAATCATAAGAACAAGGATGAT 57.187 30.769 0.00 0.00 40.03 2.45
7963 18769 7.439655 TGTTCACTTTTAACATATTTGCAACCC 59.560 33.333 0.00 0.00 32.07 4.11
8063 18869 5.170748 CAGAAACCATATTTTGCAAGGACC 58.829 41.667 8.55 0.00 0.00 4.46
8142 18948 1.350310 ACTGGTGGTTTTCGGTCCCT 61.350 55.000 0.00 0.00 0.00 4.20
8761 19760 2.082231 CACAAATGACCAGGAGCAGAG 58.918 52.381 0.00 0.00 0.00 3.35
9152 22501 8.723942 ATCACCAATTCTGAAGATACAAGTAC 57.276 34.615 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.