Multiple sequence alignment - TraesCS6A01G186800

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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 TraesCS6A01G186800 chr6A 100.000 9434 0 0 1 9434 222672333 222681766 0.000000e+00 17422.0
1 TraesCS6A01G186800 chr6A 93.230 1551 96 6 7245 8793 222135368 222136911 0.000000e+00 2274.0
2 TraesCS6A01G186800 chr6A 93.125 1280 83 3 669 1945 222125694 222126971 0.000000e+00 1871.0
3 TraesCS6A01G186800 chr6A 89.624 665 47 8 6607 7252 222128690 222129351 0.000000e+00 826.0
4 TraesCS6A01G186800 chr6A 91.516 554 42 3 1942 2494 222674094 222674643 0.000000e+00 758.0
5 TraesCS6A01G186800 chr6A 89.890 544 48 3 2308 2851 222126785 222127321 0.000000e+00 693.0
6 TraesCS6A01G186800 chr6A 92.471 425 22 6 3260 3676 222127560 222127982 4.880000e-167 599.0
7 TraesCS6A01G186800 chr6A 91.919 297 21 3 6227 6523 222128396 222128689 6.820000e-111 412.0
8 TraesCS6A01G186800 chr6A 92.115 279 22 0 2714 2992 222675190 222675468 2.470000e-105 394.0
9 TraesCS6A01G186800 chr6A 95.726 234 10 0 3989 4222 480579126 480579359 2.490000e-100 377.0
10 TraesCS6A01G186800 chr6A 85.552 353 37 8 100 447 222125166 222125509 3.240000e-94 357.0
11 TraesCS6A01G186800 chr6A 90.909 55 2 1 8820 8874 222136919 222136970 4.730000e-08 71.3
12 TraesCS6A01G186800 chr6D 96.792 3211 75 8 6227 9414 162954158 162957363 0.000000e+00 5334.0
13 TraesCS6A01G186800 chr6D 94.066 2292 76 28 3994 6236 350767077 350769357 0.000000e+00 3424.0
14 TraesCS6A01G186800 chr6D 96.337 1829 60 3 669 2494 162950543 162952367 0.000000e+00 3000.0
15 TraesCS6A01G186800 chr6D 96.353 1508 49 4 1762 3265 162951815 162953320 0.000000e+00 2475.0
16 TraesCS6A01G186800 chr6D 97.693 737 12 4 3260 3994 162953434 162954167 0.000000e+00 1262.0
17 TraesCS6A01G186800 chr6D 94.345 672 32 2 1 671 162949835 162950501 0.000000e+00 1026.0
18 TraesCS6A01G186800 chr6D 91.877 554 40 3 1762 2311 162951998 162952550 0.000000e+00 769.0
19 TraesCS6A01G186800 chr6D 92.115 279 22 0 2858 3136 162952770 162953048 2.470000e-105 394.0
20 TraesCS6A01G186800 chr6D 91.844 282 23 0 2714 2995 162952914 162953195 2.470000e-105 394.0
21 TraesCS6A01G186800 chr5D 94.790 2284 64 16 3994 6236 26276306 26274037 0.000000e+00 3507.0
22 TraesCS6A01G186800 chr5D 95.272 1967 55 11 3991 5932 501490888 501492841 0.000000e+00 3083.0
23 TraesCS6A01G186800 chr5D 88.482 382 29 7 5865 6242 501492808 501493178 1.870000e-121 448.0
24 TraesCS6A01G186800 chr5D 94.000 50 1 1 449 498 461073360 461073407 3.650000e-09 75.0
25 TraesCS6A01G186800 chr5D 97.561 41 1 0 458 498 491432564 491432604 4.730000e-08 71.3
26 TraesCS6A01G186800 chr2D 93.810 2294 70 33 3994 6236 612865483 612867755 0.000000e+00 3384.0
27 TraesCS6A01G186800 chr2D 95.241 1912 43 23 3994 5878 327742918 327741028 0.000000e+00 2983.0
28 TraesCS6A01G186800 chr2D 90.545 1671 139 15 4040 5696 636430849 636429184 0.000000e+00 2193.0
29 TraesCS6A01G186800 chr2D 94.277 332 10 2 5907 6236 327740596 327740272 5.090000e-137 499.0
30 TraesCS6A01G186800 chr2D 94.624 93 5 0 6525 6617 128890639 128890731 2.750000e-30 145.0
31 TraesCS6A01G186800 chr2D 96.552 87 3 0 6524 6610 534925464 534925550 2.750000e-30 145.0
32 TraesCS6A01G186800 chr2D 100.000 38 0 0 461 498 32064114 32064151 4.730000e-08 71.3
33 TraesCS6A01G186800 chr2D 95.000 40 2 0 459 498 46356618 46356579 7.910000e-06 63.9
34 TraesCS6A01G186800 chr2D 94.444 36 2 0 3992 4027 592381025 592381060 1.000000e-03 56.5
35 TraesCS6A01G186800 chr6B 90.832 2476 178 26 6227 8679 299826442 299823993 0.000000e+00 3269.0
36 TraesCS6A01G186800 chr6B 96.716 1827 39 4 6227 8034 299618768 299616944 0.000000e+00 3022.0
37 TraesCS6A01G186800 chr6B 96.002 1826 73 0 669 2494 299622385 299620560 0.000000e+00 2968.0
38 TraesCS6A01G186800 chr6B 96.684 1508 44 4 1762 3265 299621112 299619607 0.000000e+00 2503.0
39 TraesCS6A01G186800 chr6B 93.369 1659 50 20 4276 5914 673822884 673824502 0.000000e+00 2399.0
40 TraesCS6A01G186800 chr6B 95.815 908 20 5 8539 9434 299602335 299601434 0.000000e+00 1450.0
41 TraesCS6A01G186800 chr6B 91.555 1042 62 7 911 1948 299828884 299827865 0.000000e+00 1413.0
42 TraesCS6A01G186800 chr6B 98.234 736 11 2 3260 3994 299619493 299618759 0.000000e+00 1286.0
43 TraesCS6A01G186800 chr6B 93.871 669 32 6 4 671 299623087 299622427 0.000000e+00 1000.0
44 TraesCS6A01G186800 chr6B 96.802 469 13 2 8032 8500 299602799 299602333 0.000000e+00 782.0
45 TraesCS6A01G186800 chr6B 92.058 554 39 3 1762 2311 299620929 299620377 0.000000e+00 774.0
46 TraesCS6A01G186800 chr6B 92.351 536 38 1 1959 2494 299621275 299620743 0.000000e+00 760.0
47 TraesCS6A01G186800 chr6B 86.938 689 39 19 5262 5914 150638993 150639666 0.000000e+00 726.0
48 TraesCS6A01G186800 chr6B 88.603 544 38 5 2308 2851 299828033 299827514 2.870000e-179 640.0
49 TraesCS6A01G186800 chr6B 92.235 425 23 6 3260 3676 299827275 299826853 2.270000e-165 593.0
50 TraesCS6A01G186800 chr6B 91.740 339 17 7 5907 6242 673824528 673824858 2.400000e-125 460.0
51 TraesCS6A01G186800 chr6B 90.798 326 25 3 3670 3994 299826754 299826433 1.880000e-116 431.0
52 TraesCS6A01G186800 chr6B 91.844 282 23 0 2714 2995 299620013 299619732 2.470000e-105 394.0
53 TraesCS6A01G186800 chr6B 86.364 352 39 6 100 447 299838326 299837980 8.940000e-100 375.0
54 TraesCS6A01G186800 chr6B 93.117 247 15 2 669 915 299837713 299837469 2.500000e-95 361.0
55 TraesCS6A01G186800 chr6B 91.255 263 22 1 3002 3264 299827651 299827390 3.240000e-94 357.0
56 TraesCS6A01G186800 chr6B 89.352 216 11 6 8663 8874 299822100 299821893 2.610000e-65 261.0
57 TraesCS6A01G186800 chr6B 95.000 100 5 0 6520 6619 13827521 13827620 3.530000e-34 158.0
58 TraesCS6A01G186800 chr4A 95.219 1778 63 14 4168 5929 447326353 447328124 0.000000e+00 2793.0
59 TraesCS6A01G186800 chr4A 100.000 38 0 0 459 496 164523161 164523124 4.730000e-08 71.3
60 TraesCS6A01G186800 chr2B 95.196 1686 63 8 3986 5656 782024445 782026127 0.000000e+00 2649.0
61 TraesCS6A01G186800 chr2B 100.000 43 0 0 456 498 114408537 114408495 7.850000e-11 80.5
62 TraesCS6A01G186800 chr5B 95.381 1667 58 9 3994 5659 352481632 352479984 0.000000e+00 2634.0
63 TraesCS6A01G186800 chr5B 95.235 1616 60 7 3995 5603 166535849 166534244 0.000000e+00 2542.0
64 TraesCS6A01G186800 chr7D 92.344 1463 101 5 669 2128 388033392 388034846 0.000000e+00 2071.0
65 TraesCS6A01G186800 chr7D 91.362 984 85 0 2125 3108 388034477 388035460 0.000000e+00 1347.0
66 TraesCS6A01G186800 chr7D 87.302 504 47 11 8162 8664 388035463 388035950 2.300000e-155 560.0
67 TraesCS6A01G186800 chr7D 92.115 279 22 0 2858 3136 388035066 388035344 2.470000e-105 394.0
68 TraesCS6A01G186800 chr7D 82.561 453 43 14 1 447 388032847 388033269 5.380000e-97 366.0
69 TraesCS6A01G186800 chr7B 91.456 1463 114 6 669 2128 383511181 383512635 0.000000e+00 1999.0
70 TraesCS6A01G186800 chr7B 89.989 949 94 1 2125 3073 383512266 383513213 0.000000e+00 1225.0
71 TraesCS6A01G186800 chr7B 87.433 939 58 30 5347 6242 531765494 531764573 0.000000e+00 1026.0
72 TraesCS6A01G186800 chr7B 84.932 657 58 17 8013 8665 383514943 383515562 2.240000e-175 627.0
73 TraesCS6A01G186800 chr7B 90.192 469 43 1 2794 3259 383514298 383514766 8.100000e-170 608.0
74 TraesCS6A01G186800 chr7B 80.837 454 51 15 1 447 383510632 383511056 3.290000e-84 324.0
75 TraesCS6A01G186800 chr7B 92.308 91 6 1 3260 3350 383514881 383514970 2.770000e-25 128.0
76 TraesCS6A01G186800 chr7A 90.431 1463 132 3 669 2128 438253593 438255050 0.000000e+00 1919.0
77 TraesCS6A01G186800 chr7A 89.695 1116 95 15 7551 8664 438259934 438261031 0.000000e+00 1406.0
78 TraesCS6A01G186800 chr7A 88.739 888 100 0 2125 3012 438254681 438255568 0.000000e+00 1086.0
79 TraesCS6A01G186800 chr7A 91.304 621 47 2 6881 7501 438259321 438259934 0.000000e+00 841.0
80 TraesCS6A01G186800 chr7A 91.919 396 32 0 2864 3259 438258170 438258565 1.070000e-153 555.0
81 TraesCS6A01G186800 chr7A 90.625 224 17 3 3260 3480 438258661 438258883 2.580000e-75 294.0
82 TraesCS6A01G186800 chr7A 93.893 131 8 0 3544 3674 438259161 438259291 2.080000e-46 198.0
83 TraesCS6A01G186800 chr2A 92.680 929 35 13 5018 5914 501841513 501840586 0.000000e+00 1308.0
84 TraesCS6A01G186800 chr2A 91.818 330 16 7 5907 6236 501840560 501840242 5.200000e-122 449.0
85 TraesCS6A01G186800 chr2A 97.500 40 1 0 459 498 49883566 49883527 1.700000e-07 69.4
86 TraesCS6A01G186800 chr1B 84.686 542 36 30 5730 6236 533854305 533854834 1.830000e-136 497.0
87 TraesCS6A01G186800 chr1D 92.857 336 17 5 5907 6238 24129011 24129343 1.840000e-131 481.0
88 TraesCS6A01G186800 chr4B 93.000 100 4 3 6513 6609 4233616 4233517 9.880000e-30 143.0
89 TraesCS6A01G186800 chr5A 92.857 98 5 2 6514 6610 376465977 376465881 3.550000e-29 141.0
90 TraesCS6A01G186800 chr5A 83.582 67 9 2 5577 5643 387397554 387397618 2.840000e-05 62.1
91 TraesCS6A01G186800 chr3B 89.720 107 10 1 6525 6630 10622597 10622491 1.650000e-27 135.0


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 TraesCS6A01G186800 chr6A 222672333 222681766 9433 False 17422.000000 17422 100.000000 1 9434 1 chr6A.!!$F1 9433
1 TraesCS6A01G186800 chr6A 222135368 222136970 1602 False 1172.650000 2274 92.069500 7245 8874 2 chr6A.!!$F4 1629
2 TraesCS6A01G186800 chr6A 222125166 222129351 4185 False 793.000000 1871 90.430167 100 7252 6 chr6A.!!$F3 7152
3 TraesCS6A01G186800 chr6A 222674094 222675468 1374 False 576.000000 758 91.815500 1942 2992 2 chr6A.!!$F5 1050
4 TraesCS6A01G186800 chr6D 350767077 350769357 2280 False 3424.000000 3424 94.066000 3994 6236 1 chr6D.!!$F1 2242
5 TraesCS6A01G186800 chr6D 162949835 162957363 7528 False 1831.750000 5334 94.669500 1 9414 8 chr6D.!!$F2 9413
6 TraesCS6A01G186800 chr5D 26274037 26276306 2269 True 3507.000000 3507 94.790000 3994 6236 1 chr5D.!!$R1 2242
7 TraesCS6A01G186800 chr5D 501490888 501493178 2290 False 1765.500000 3083 91.877000 3991 6242 2 chr5D.!!$F3 2251
8 TraesCS6A01G186800 chr2D 612865483 612867755 2272 False 3384.000000 3384 93.810000 3994 6236 1 chr2D.!!$F5 2242
9 TraesCS6A01G186800 chr2D 636429184 636430849 1665 True 2193.000000 2193 90.545000 4040 5696 1 chr2D.!!$R2 1656
10 TraesCS6A01G186800 chr2D 327740272 327742918 2646 True 1741.000000 2983 94.759000 3994 6236 2 chr2D.!!$R3 2242
11 TraesCS6A01G186800 chr6B 299616944 299623087 6143 True 1588.375000 3022 94.720000 4 8034 8 chr6B.!!$R2 8030
12 TraesCS6A01G186800 chr6B 673822884 673824858 1974 False 1429.500000 2399 92.554500 4276 6242 2 chr6B.!!$F3 1966
13 TraesCS6A01G186800 chr6B 299601434 299602799 1365 True 1116.000000 1450 96.308500 8032 9434 2 chr6B.!!$R1 1402
14 TraesCS6A01G186800 chr6B 299821893 299828884 6991 True 994.857143 3269 90.661429 911 8874 7 chr6B.!!$R3 7963
15 TraesCS6A01G186800 chr6B 150638993 150639666 673 False 726.000000 726 86.938000 5262 5914 1 chr6B.!!$F2 652
16 TraesCS6A01G186800 chr6B 299837469 299838326 857 True 368.000000 375 89.740500 100 915 2 chr6B.!!$R4 815
17 TraesCS6A01G186800 chr4A 447326353 447328124 1771 False 2793.000000 2793 95.219000 4168 5929 1 chr4A.!!$F1 1761
18 TraesCS6A01G186800 chr2B 782024445 782026127 1682 False 2649.000000 2649 95.196000 3986 5656 1 chr2B.!!$F1 1670
19 TraesCS6A01G186800 chr5B 352479984 352481632 1648 True 2634.000000 2634 95.381000 3994 5659 1 chr5B.!!$R2 1665
20 TraesCS6A01G186800 chr5B 166534244 166535849 1605 True 2542.000000 2542 95.235000 3995 5603 1 chr5B.!!$R1 1608
21 TraesCS6A01G186800 chr7D 388032847 388035950 3103 False 947.600000 2071 89.136800 1 8664 5 chr7D.!!$F1 8663
22 TraesCS6A01G186800 chr7B 531764573 531765494 921 True 1026.000000 1026 87.433000 5347 6242 1 chr7B.!!$R1 895
23 TraesCS6A01G186800 chr7B 383510632 383515562 4930 False 818.500000 1999 88.285667 1 8665 6 chr7B.!!$F1 8664
24 TraesCS6A01G186800 chr7A 438253593 438261031 7438 False 899.857143 1919 90.943714 669 8664 7 chr7A.!!$F1 7995
25 TraesCS6A01G186800 chr2A 501840242 501841513 1271 True 878.500000 1308 92.249000 5018 6236 2 chr2A.!!$R2 1218
26 TraesCS6A01G186800 chr1B 533854305 533854834 529 False 497.000000 497 84.686000 5730 6236 1 chr1B.!!$F1 506

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
983 1173 0.241213 GAAAGCGCCAAAGAAGGACC 59.759 55.000 2.29 0.00 0.00 4.46 F
998 1188 0.951558 GGACCGATTGCAACACAAGT 59.048 50.000 0.00 0.00 42.87 3.16 F
1143 1333 1.302511 CAAACTGGGTACTGCGGCT 60.303 57.895 0.00 0.00 0.00 5.52 F
1457 1647 3.868619 TTTTACTGTAGCAAGGTGGGT 57.131 42.857 0.00 0.00 0.00 4.51 F
3766 9067 3.541632 TCAGACAAAAGGTGAGTCAACC 58.458 45.455 4.04 4.12 40.85 3.77 F
3878 9180 2.664402 AGCATTTGACCACCAGTCTT 57.336 45.000 0.00 0.00 46.46 3.01 F
5272 10591 1.821258 GGATGTACCCACCGGTCTC 59.179 63.158 2.59 0.00 43.29 3.36 F
5525 10857 0.603065 GCAAGTCATCACCAAACCCC 59.397 55.000 0.00 0.00 0.00 4.95 F
7890 13743 0.033504 AAGCTCTCGAACTTTGCCGA 59.966 50.000 0.00 0.00 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3136 7995 2.163454 TGGATTGCCCACCTTCAGT 58.837 52.632 0.00 0.0 40.82 3.41 R
3375 8357 5.613358 TTTTTGCTTCCGATCTCTTCTTC 57.387 39.130 0.00 0.0 0.00 2.87 R
3766 9067 9.236691 GTGTAACAATTTTATGCACATAGGATG 57.763 33.333 0.00 0.0 36.32 3.51 R
3859 9161 2.664402 AAGACTGGTGGTCAAATGCT 57.336 45.000 0.00 0.0 46.72 3.79 R
4892 10203 0.609131 ACCCAAGAAGTCGGCAATGG 60.609 55.000 0.00 0.0 0.00 3.16 R
5525 10857 0.820871 CTCCTTCTCTCGAACCCCTG 59.179 60.000 0.00 0.0 0.00 4.45 R
7549 13394 2.164422 CTGACGTTATCTGGACAGAGCA 59.836 50.000 8.14 0.0 41.33 4.26 R
8044 13897 1.260561 ACGTGCGTTGACAAAGATGAC 59.739 47.619 5.22 0.0 0.00 3.06 R
9324 17098 0.323302 TGCCAGTTATGAAGCGACCA 59.677 50.000 0.00 0.0 0.00 4.02 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
22 23 3.759086 GTCGATCTGATGATGGCTACCTA 59.241 47.826 0.00 0.00 32.19 3.08
29 30 4.717877 TGATGATGGCTACCTATGGTTTG 58.282 43.478 0.00 0.00 37.09 2.93
78 80 3.711059 GAGCTGGGGCCTGATGGTG 62.711 68.421 0.84 0.00 39.73 4.17
106 108 0.466189 GGACCATCGCCATCACCATT 60.466 55.000 0.00 0.00 0.00 3.16
124 126 3.129287 CCATTACATGGCAACTTGGTCTC 59.871 47.826 0.00 0.00 44.70 3.36
384 394 9.152595 GTTTTCTAGGTGTTATTAAGTCTCTGG 57.847 37.037 0.00 0.00 0.00 3.86
392 402 6.201806 GTGTTATTAAGTCTCTGGCATGCTAG 59.798 42.308 24.02 24.02 0.00 3.42
429 442 0.322546 ACATCTTCGGTGGGCTTTCC 60.323 55.000 0.00 0.00 0.00 3.13
498 511 5.834239 ATACTTGTCGTGGTTTTAGTTCG 57.166 39.130 0.00 0.00 0.00 3.95
506 519 3.600011 CGTGGTTTTAGTTCGACGACAAC 60.600 47.826 0.00 0.00 37.83 3.32
522 535 3.124636 CGACAACTATTTTGGAACGGAGG 59.875 47.826 0.00 0.00 0.00 4.30
630 726 6.431234 TCCTAGTTGAGCCAAAAGAAGATTTC 59.569 38.462 0.00 0.00 0.00 2.17
694 879 2.504032 CACCACCACGACCACTGT 59.496 61.111 0.00 0.00 0.00 3.55
870 1059 6.321717 TCCATGCGCTTACTTTATTTCTTTG 58.678 36.000 9.73 0.00 0.00 2.77
898 1088 3.850752 TCTGGTCCTGACTTCTCTCTTT 58.149 45.455 0.00 0.00 0.00 2.52
980 1170 0.242017 CCAGAAAGCGCCAAAGAAGG 59.758 55.000 2.29 0.00 0.00 3.46
983 1173 0.241213 GAAAGCGCCAAAGAAGGACC 59.759 55.000 2.29 0.00 0.00 4.46
998 1188 0.951558 GGACCGATTGCAACACAAGT 59.048 50.000 0.00 0.00 42.87 3.16
1143 1333 1.302511 CAAACTGGGTACTGCGGCT 60.303 57.895 0.00 0.00 0.00 5.52
1293 1483 5.928264 GGCAGCAGTGAAAATTGAACTAAAT 59.072 36.000 0.00 0.00 0.00 1.40
1457 1647 3.868619 TTTTACTGTAGCAAGGTGGGT 57.131 42.857 0.00 0.00 0.00 4.51
1752 1942 4.230502 AGAAGGATAGAAGGGCAATGGAAA 59.769 41.667 0.00 0.00 0.00 3.13
3136 7995 4.448210 AGCTACAGAAGACGTTCCAAAAA 58.552 39.130 0.00 0.00 32.48 1.94
3766 9067 3.541632 TCAGACAAAAGGTGAGTCAACC 58.458 45.455 4.04 4.12 40.85 3.77
3859 9161 7.562088 ACAAGTTAGAAGGAAAACACCCAATTA 59.438 33.333 0.00 0.00 0.00 1.40
3878 9180 2.664402 AGCATTTGACCACCAGTCTT 57.336 45.000 0.00 0.00 46.46 3.01
4735 10046 6.992063 TGATAAGAAGCTTTGTCTCCAATC 57.008 37.500 0.00 0.00 0.00 2.67
4739 10050 4.831107 AGAAGCTTTGTCTCCAATCTCTC 58.169 43.478 0.00 0.00 0.00 3.20
4892 10203 6.495181 TCCTCTTCACTATCATCCATCCTAAC 59.505 42.308 0.00 0.00 0.00 2.34
5045 10360 2.821969 CAGCAATTGCCTCCTACAAACT 59.178 45.455 26.45 0.38 43.38 2.66
5272 10591 1.821258 GGATGTACCCACCGGTCTC 59.179 63.158 2.59 0.00 43.29 3.36
5299 10618 5.356470 GCTTGATCTTGCAATAGAAGTCCTT 59.644 40.000 0.00 0.00 0.00 3.36
5338 10664 3.989167 CGTTTACCTGTTTGATCGGTACA 59.011 43.478 0.00 0.00 33.29 2.90
5525 10857 0.603065 GCAAGTCATCACCAAACCCC 59.397 55.000 0.00 0.00 0.00 4.95
5527 10859 1.888512 CAAGTCATCACCAAACCCCAG 59.111 52.381 0.00 0.00 0.00 4.45
5585 10917 1.839994 TCTTCGAGAAGCCCCATGAAT 59.160 47.619 7.91 0.00 38.28 2.57
5746 11142 1.469335 TTCTTCCTCACCTTCGGCGT 61.469 55.000 6.85 0.00 0.00 5.68
6043 11855 3.542676 AACGACCGGTGGAGTGCA 61.543 61.111 24.54 0.00 0.00 4.57
6304 12128 9.893305 AACATCTTACATTACTGCTTTACAAAC 57.107 29.630 0.00 0.00 0.00 2.93
6306 12130 9.329913 CATCTTACATTACTGCTTTACAAACAC 57.670 33.333 0.00 0.00 0.00 3.32
6400 12224 5.069648 GGGAGATGTGAGATGAGTTATGTGA 59.930 44.000 0.00 0.00 0.00 3.58
6930 12774 5.640732 TGTCTGTTTGTTTCTCTTTCTTGC 58.359 37.500 0.00 0.00 0.00 4.01
7340 13185 2.029828 GCGACTCGATTATGGATCCACT 60.030 50.000 18.99 9.21 0.00 4.00
7454 13299 1.747709 CTCATGCTTGTCTTGGAGGG 58.252 55.000 0.00 0.00 0.00 4.30
7549 13394 1.337260 GGACATGCTGAGAACACGAGT 60.337 52.381 0.00 0.00 0.00 4.18
7776 13629 3.651206 TGTGGCGTCTATTTTCGTAACA 58.349 40.909 0.00 0.00 0.00 2.41
7890 13743 0.033504 AAGCTCTCGAACTTTGCCGA 59.966 50.000 0.00 0.00 0.00 5.54
7983 13836 4.154918 CAGTTCCATGTTAAAGCTGAGGAC 59.845 45.833 0.00 0.00 0.00 3.85
8001 13854 4.372656 AGGACGAAGAGTTGAAGTTTGAG 58.627 43.478 0.00 0.00 0.00 3.02
8328 14184 2.184020 CTGGAGGGATTGGTGTCGCA 62.184 60.000 0.00 0.00 33.85 5.10
8478 14334 4.520874 GTGCACAGATGGCTATCTAGACTA 59.479 45.833 12.76 0.00 41.71 2.59
8479 14335 5.184864 GTGCACAGATGGCTATCTAGACTAT 59.815 44.000 12.76 0.00 41.71 2.12
8480 14336 5.777223 TGCACAGATGGCTATCTAGACTATT 59.223 40.000 12.76 0.00 41.71 1.73
8481 14337 6.268617 TGCACAGATGGCTATCTAGACTATTT 59.731 38.462 12.76 0.00 41.71 1.40
8566 14424 4.204012 TCGTCTTGTGGGATTGAAACTTT 58.796 39.130 0.00 0.00 0.00 2.66
8568 14426 4.976116 CGTCTTGTGGGATTGAAACTTTTC 59.024 41.667 0.00 0.00 37.69 2.29
8738 16505 6.016610 GCACACAGGTTACAGAATCCTTTAAA 60.017 38.462 0.00 0.00 0.00 1.52
8874 16647 7.099764 CACTGAATGAATCTGGTGTTAGTACT 58.900 38.462 0.00 0.00 32.15 2.73
8884 16657 7.744087 TCTGGTGTTAGTACTAGTACGAAAA 57.256 36.000 24.52 18.98 40.80 2.29
8885 16658 7.584987 TCTGGTGTTAGTACTAGTACGAAAAC 58.415 38.462 28.07 28.07 40.80 2.43
8932 16706 2.941415 GCAGGCAATAACTACAGGCACT 60.941 50.000 0.00 0.00 43.88 4.40
9170 16944 2.887151 AGAGATCCAAAACCCTGTGG 57.113 50.000 0.00 0.00 36.13 4.17
9324 17098 3.439513 TTCGGCTGCGCGTGGATAT 62.440 57.895 8.43 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.441217 CCATAGGTAGCCATCATCAGATCG 60.441 50.000 0.00 0.00 30.20 3.69
29 30 7.287005 CCCCCTCCCAAATAAAATAGAGTAAAC 59.713 40.741 0.00 0.00 0.00 2.01
106 108 1.346395 ACGAGACCAAGTTGCCATGTA 59.654 47.619 0.00 0.00 0.00 2.29
356 366 9.930693 AGAGACTTAATAACACCTAGAAAACAG 57.069 33.333 0.00 0.00 0.00 3.16
454 467 5.397142 TTTTAGAACGGAGGGAGTACTTC 57.603 43.478 0.00 0.00 0.00 3.01
498 511 3.742369 TCCGTTCCAAAATAGTTGTCGTC 59.258 43.478 0.00 0.00 0.00 4.20
506 519 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
630 726 6.369615 CCCTTCAGTTTTTGCTTATTGGATTG 59.630 38.462 0.00 0.00 0.00 2.67
980 1170 1.601903 TCACTTGTGTTGCAATCGGTC 59.398 47.619 0.59 0.00 36.36 4.79
983 1173 2.587956 CCATCACTTGTGTTGCAATCG 58.412 47.619 0.59 0.00 36.36 3.34
998 1188 6.724893 TTTCTCGACTATTACATCCCATCA 57.275 37.500 0.00 0.00 0.00 3.07
1143 1333 6.115446 CCTTGTAGAATGTCCAAATAGCTGA 58.885 40.000 0.00 0.00 0.00 4.26
1293 1483 4.323028 CCATCAGTCAGCTTCCAGAACTTA 60.323 45.833 0.00 0.00 0.00 2.24
1419 1609 7.725844 ACAGTAAAATTCACCTCCTTTTCATCT 59.274 33.333 0.00 0.00 0.00 2.90
1457 1647 2.716424 AGTTTCTCCCCATCACCTTCAA 59.284 45.455 0.00 0.00 0.00 2.69
1700 1890 6.549912 TGTCTTCAATCATGAACTTGACTG 57.450 37.500 10.58 7.68 40.59 3.51
1752 1942 4.150359 TGACCTTCCGTTCTTCTACTTCT 58.850 43.478 0.00 0.00 0.00 2.85
3136 7995 2.163454 TGGATTGCCCACCTTCAGT 58.837 52.632 0.00 0.00 40.82 3.41
3375 8357 5.613358 TTTTTGCTTCCGATCTCTTCTTC 57.387 39.130 0.00 0.00 0.00 2.87
3766 9067 9.236691 GTGTAACAATTTTATGCACATAGGATG 57.763 33.333 0.00 0.00 36.32 3.51
3859 9161 2.664402 AAGACTGGTGGTCAAATGCT 57.336 45.000 0.00 0.00 46.72 3.79
4735 10046 2.295885 GGAGGCATTGACAATGGAGAG 58.704 52.381 25.64 4.45 39.31 3.20
4739 10050 1.479323 CAAGGGAGGCATTGACAATGG 59.521 52.381 25.64 10.73 39.31 3.16
4892 10203 0.609131 ACCCAAGAAGTCGGCAATGG 60.609 55.000 0.00 0.00 0.00 3.16
5272 10591 2.564771 TCTATTGCAAGATCAAGCCGG 58.435 47.619 4.94 0.00 0.00 6.13
5299 10618 1.374560 ACGCTATTGGCAACGCATAA 58.625 45.000 19.30 0.00 41.91 1.90
5324 10650 1.346395 AGCACCTGTACCGATCAAACA 59.654 47.619 0.00 0.00 0.00 2.83
5338 10664 1.607467 GGGTTGGATGCAAGCACCT 60.607 57.895 27.00 0.00 34.56 4.00
5525 10857 0.820871 CTCCTTCTCTCGAACCCCTG 59.179 60.000 0.00 0.00 0.00 4.45
5527 10859 1.518302 GCTCCTTCTCTCGAACCCC 59.482 63.158 0.00 0.00 0.00 4.95
5585 10917 4.738998 CCTGCCCCGCCAATGTCA 62.739 66.667 0.00 0.00 0.00 3.58
6043 11855 1.851267 GGAAACCCACCTCCAACCT 59.149 57.895 0.00 0.00 0.00 3.50
6123 11945 4.778232 ACCTAGAACCCCTAAACCCTTAA 58.222 43.478 0.00 0.00 0.00 1.85
6304 12128 9.639601 TTCATATTCTTATCCTATGTAAGCGTG 57.360 33.333 0.00 0.00 0.00 5.34
6306 12130 9.862371 AGTTCATATTCTTATCCTATGTAAGCG 57.138 33.333 0.00 0.00 0.00 4.68
7102 12946 8.552034 GCATCTCAACATAGTAACAGATAAACC 58.448 37.037 0.00 0.00 0.00 3.27
7454 13299 2.417339 TGTGCTCACGAACACTAGTC 57.583 50.000 0.00 0.00 37.68 2.59
7549 13394 2.164422 CTGACGTTATCTGGACAGAGCA 59.836 50.000 8.14 0.00 41.33 4.26
7776 13629 4.768448 TGCAAGAAAGATGAATGGTCACAT 59.232 37.500 0.00 0.00 36.31 3.21
7816 13669 2.174360 GATTTTGGCTGGGAGAAGCTT 58.826 47.619 0.00 0.00 43.06 3.74
7890 13743 6.040166 CCTTCATAGGCTTATTCATGCACTTT 59.960 38.462 0.00 0.00 33.99 2.66
7983 13836 9.322776 CATAATTTCTCAAACTTCAACTCTTCG 57.677 33.333 0.00 0.00 0.00 3.79
8001 13854 9.643693 ATGGTGTCAAAAAGATCACATAATTTC 57.356 29.630 0.00 0.00 33.03 2.17
8044 13897 1.260561 ACGTGCGTTGACAAAGATGAC 59.739 47.619 5.22 0.00 0.00 3.06
8328 14184 0.792640 CACGAGCAACGAAGCTGATT 59.207 50.000 10.83 0.00 46.75 2.57
8412 14268 2.282251 AGGAGGTCAGCGACGTCA 60.282 61.111 22.95 0.00 45.59 4.35
8515 14373 4.217118 ACAATTCAACAGAATGGAGCTGTC 59.783 41.667 0.00 0.00 45.27 3.51
8566 14424 4.641541 TGACATAATACCGGAGAACTCGAA 59.358 41.667 9.46 0.00 0.00 3.71
8568 14426 4.563337 TGACATAATACCGGAGAACTCG 57.437 45.455 9.46 0.00 0.00 4.18
8738 16505 4.406456 TGACCTGCATTATTTGTTCTGGT 58.594 39.130 0.00 0.00 0.00 4.00
8884 16657 7.492352 ACTGAAGCAAGTTAACTTTTATCGT 57.508 32.000 18.25 13.70 33.11 3.73
8885 16658 8.682016 CAAACTGAAGCAAGTTAACTTTTATCG 58.318 33.333 18.25 8.06 39.48 2.92
9324 17098 0.323302 TGCCAGTTATGAAGCGACCA 59.677 50.000 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.