Multiple sequence alignment - TraesCS6A01G080100

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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 TraesCS6A01G080100 chr6A 100.000 5273 0 0 1 5273 49106598 49101326 0.000000e+00 9738.0
1 TraesCS6A01G080100 chr6B 95.208 4111 163 14 524 4615 88321071 88316976 0.000000e+00 6469.0
2 TraesCS6A01G080100 chr6B 93.535 495 23 6 4782 5273 88316737 88316249 0.000000e+00 728.0
3 TraesCS6A01G080100 chr6B 86.198 384 25 15 56 436 88321468 88321110 1.780000e-104 390.0
4 TraesCS6A01G080100 chr6B 83.571 140 10 9 612 738 88320851 88320712 9.280000e-23 119.0
5 TraesCS6A01G080100 chr6B 100.000 30 0 0 464 493 88321115 88321086 7.380000e-04 56.5
6 TraesCS6A01G080100 chr6D 97.513 3016 62 5 1640 4650 37673345 37670338 0.000000e+00 5142.0
7 TraesCS6A01G080100 chr6D 94.025 1021 44 11 612 1617 37674351 37673333 0.000000e+00 1531.0
8 TraesCS6A01G080100 chr6D 92.517 882 33 11 32 892 37675069 37674200 0.000000e+00 1232.0
9 TraesCS6A01G080100 chr6D 76.752 1441 282 43 1666 3073 58043702 58045122 0.000000e+00 756.0
10 TraesCS6A01G080100 chr6D 95.031 161 2 4 5113 5273 37670033 37669879 1.130000e-61 248.0
11 TraesCS6A01G080100 chr6D 91.852 135 8 2 739 870 37674494 37674360 9.020000e-43 185.0
12 TraesCS6A01G080100 chr6D 82.836 134 10 7 618 738 37674206 37674073 2.010000e-19 108.0
13 TraesCS6A01G080100 chr6D 90.141 71 4 3 4650 4719 460864549 460864481 7.270000e-14 89.8
14 TraesCS6A01G080100 chr5D 79.817 1863 329 32 1879 3709 371807011 371805164 0.000000e+00 1314.0
15 TraesCS6A01G080100 chr5D 85.211 142 21 0 1705 1846 371830104 371829963 4.260000e-31 147.0
16 TraesCS6A01G080100 chr5D 97.059 34 1 0 1 34 561918922 561918889 2.050000e-04 58.4
17 TraesCS6A01G080100 chr1D 75.200 2121 454 61 986 3073 431518320 431520401 0.000000e+00 937.0
18 TraesCS6A01G080100 chr1D 88.636 88 5 1 4620 4702 459929446 459929533 9.340000e-18 102.0
19 TraesCS6A01G080100 chr1B 75.292 2056 443 52 986 3013 582688639 582690657 0.000000e+00 922.0
20 TraesCS6A01G080100 chr7A 74.966 2181 438 78 939 3065 679877456 679875330 0.000000e+00 904.0
21 TraesCS6A01G080100 chr7A 100.000 29 0 0 3 31 111886795 111886823 3.000000e-03 54.7
22 TraesCS6A01G080100 chr2D 78.409 1408 248 48 1697 3073 637340688 637339306 0.000000e+00 865.0
23 TraesCS6A01G080100 chr2D 74.585 2050 437 65 1022 3035 637381176 637379175 0.000000e+00 822.0
24 TraesCS6A01G080100 chr2D 74.240 2073 444 71 1022 3055 637021490 637019469 0.000000e+00 787.0
25 TraesCS6A01G080100 chr2D 76.157 1405 281 42 1662 3035 636794847 636793466 0.000000e+00 689.0
26 TraesCS6A01G080100 chr2D 72.010 418 103 14 3811 4221 637378237 637377827 1.550000e-20 111.0
27 TraesCS6A01G080100 chr4A 74.546 2094 455 56 996 3053 618121152 618123203 0.000000e+00 843.0
28 TraesCS6A01G080100 chr4A 81.065 169 24 6 1695 1856 618172197 618172364 1.540000e-25 128.0
29 TraesCS6A01G080100 chr7B 74.222 2153 454 74 953 3068 660240276 660238188 0.000000e+00 808.0
30 TraesCS6A01G080100 chr7B 74.240 559 120 21 2497 3047 746114949 746114407 4.140000e-51 213.0
31 TraesCS6A01G080100 chr7B 73.651 482 107 17 2572 3047 746120726 746120259 9.080000e-38 169.0
32 TraesCS6A01G080100 chr7B 82.353 204 25 9 1662 1855 746156734 746156532 3.270000e-37 167.0
33 TraesCS6A01G080100 chr7B 100.000 31 0 0 1 31 23605029 23605059 2.050000e-04 58.4
34 TraesCS6A01G080100 chr7D 74.439 1917 415 58 1145 3021 588023325 588021444 0.000000e+00 756.0
35 TraesCS6A01G080100 chr7D 95.000 60 3 0 4647 4706 623531878 623531937 1.560000e-15 95.3
36 TraesCS6A01G080100 chr7D 100.000 33 0 0 4620 4652 180070572 180070540 1.590000e-05 62.1
37 TraesCS6A01G080100 chr2A 76.000 1400 285 43 1685 3055 762891600 762892977 0.000000e+00 676.0
38 TraesCS6A01G080100 chr2A 76.190 546 107 18 1019 1548 762759240 762759778 3.130000e-67 267.0
39 TraesCS6A01G080100 chr2A 74.780 567 128 12 986 1546 762883986 762884543 1.900000e-59 241.0
40 TraesCS6A01G080100 chr2A 73.684 418 96 14 3811 4221 762751760 762752170 3.290000e-32 150.0
41 TraesCS6A01G080100 chr2A 72.249 418 102 12 3811 4221 762950426 762950836 3.340000e-22 117.0
42 TraesCS6A01G080100 chr2A 77.157 197 39 6 4028 4221 762894060 762894253 5.580000e-20 110.0
43 TraesCS6A01G080100 chr2A 77.717 184 35 6 4027 4207 762689198 762689378 2.010000e-19 108.0
44 TraesCS6A01G080100 chr2A 97.222 36 1 0 1 36 25123964 25123929 1.590000e-05 62.1
45 TraesCS6A01G080100 chr2B 75.713 1437 294 47 1659 3063 794427895 794426482 0.000000e+00 669.0
46 TraesCS6A01G080100 chr2B 74.802 1262 270 33 1793 3039 794484987 794486215 4.680000e-145 525.0
47 TraesCS6A01G080100 chr2B 98.182 55 1 0 4650 4704 491564581 491564527 4.350000e-16 97.1
48 TraesCS6A01G080100 chr2B 100.000 32 0 0 4619 4650 134906991 134907022 5.700000e-05 60.2
49 TraesCS6A01G080100 chr2B 88.462 52 3 3 4620 4670 144435967 144435918 5.700000e-05 60.2
50 TraesCS6A01G080100 chr5B 75.616 1259 253 45 1697 2922 691581912 691583149 4.580000e-160 575.0
51 TraesCS6A01G080100 chr5B 75.604 414 78 16 1131 1540 691504419 691504813 3.240000e-42 183.0
52 TraesCS6A01G080100 chr5B 90.588 85 3 4 4620 4702 331013050 331013131 2.010000e-19 108.0
53 TraesCS6A01G080100 chr3D 72.366 579 128 23 2509 3077 613403333 613402777 2.540000e-33 154.0
54 TraesCS6A01G080100 chrUn 72.414 406 94 16 3811 4207 234397490 234397886 4.320000e-21 113.0
55 TraesCS6A01G080100 chrUn 72.414 406 94 16 3811 4207 283153510 283153906 4.320000e-21 113.0
56 TraesCS6A01G080100 chrUn 72.527 364 86 13 3811 4167 312593957 312593601 7.220000e-19 106.0
57 TraesCS6A01G080100 chr1A 98.387 62 1 0 4652 4713 449855571 449855632 5.580000e-20 110.0
58 TraesCS6A01G080100 chr1A 90.909 77 3 2 4621 4697 491646534 491646606 3.360000e-17 100.0
59 TraesCS6A01G080100 chr3A 89.655 87 5 2 4620 4702 686615486 686615572 2.010000e-19 108.0
60 TraesCS6A01G080100 chr3A 100.000 31 0 0 1 31 693630727 693630757 2.050000e-04 58.4
61 TraesCS6A01G080100 chr3A 97.059 34 1 0 1 34 704498701 704498668 2.050000e-04 58.4
62 TraesCS6A01G080100 chr4B 93.651 63 2 2 4640 4702 112187611 112187671 5.620000e-15 93.5
63 TraesCS6A01G080100 chr3B 100.000 33 0 0 4618 4650 266534551 266534519 1.590000e-05 62.1


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 TraesCS6A01G080100 chr6A 49101326 49106598 5272 True 9738.000000 9738 100.000000 1 5273 1 chr6A.!!$R1 5272
1 TraesCS6A01G080100 chr6B 88316249 88321468 5219 True 1552.500000 6469 91.702400 56 5273 5 chr6B.!!$R1 5217
2 TraesCS6A01G080100 chr6D 37669879 37675069 5190 True 1407.666667 5142 92.295667 32 5273 6 chr6D.!!$R2 5241
3 TraesCS6A01G080100 chr6D 58043702 58045122 1420 False 756.000000 756 76.752000 1666 3073 1 chr6D.!!$F1 1407
4 TraesCS6A01G080100 chr5D 371805164 371807011 1847 True 1314.000000 1314 79.817000 1879 3709 1 chr5D.!!$R1 1830
5 TraesCS6A01G080100 chr1D 431518320 431520401 2081 False 937.000000 937 75.200000 986 3073 1 chr1D.!!$F1 2087
6 TraesCS6A01G080100 chr1B 582688639 582690657 2018 False 922.000000 922 75.292000 986 3013 1 chr1B.!!$F1 2027
7 TraesCS6A01G080100 chr7A 679875330 679877456 2126 True 904.000000 904 74.966000 939 3065 1 chr7A.!!$R1 2126
8 TraesCS6A01G080100 chr2D 637339306 637340688 1382 True 865.000000 865 78.409000 1697 3073 1 chr2D.!!$R3 1376
9 TraesCS6A01G080100 chr2D 637019469 637021490 2021 True 787.000000 787 74.240000 1022 3055 1 chr2D.!!$R2 2033
10 TraesCS6A01G080100 chr2D 636793466 636794847 1381 True 689.000000 689 76.157000 1662 3035 1 chr2D.!!$R1 1373
11 TraesCS6A01G080100 chr2D 637377827 637381176 3349 True 466.500000 822 73.297500 1022 4221 2 chr2D.!!$R4 3199
12 TraesCS6A01G080100 chr4A 618121152 618123203 2051 False 843.000000 843 74.546000 996 3053 1 chr4A.!!$F1 2057
13 TraesCS6A01G080100 chr7B 660238188 660240276 2088 True 808.000000 808 74.222000 953 3068 1 chr7B.!!$R1 2115
14 TraesCS6A01G080100 chr7B 746114407 746114949 542 True 213.000000 213 74.240000 2497 3047 1 chr7B.!!$R2 550
15 TraesCS6A01G080100 chr7D 588021444 588023325 1881 True 756.000000 756 74.439000 1145 3021 1 chr7D.!!$R2 1876
16 TraesCS6A01G080100 chr2A 762891600 762894253 2653 False 393.000000 676 76.578500 1685 4221 2 chr2A.!!$F6 2536
17 TraesCS6A01G080100 chr2A 762759240 762759778 538 False 267.000000 267 76.190000 1019 1548 1 chr2A.!!$F3 529
18 TraesCS6A01G080100 chr2A 762883986 762884543 557 False 241.000000 241 74.780000 986 1546 1 chr2A.!!$F4 560
19 TraesCS6A01G080100 chr2B 794426482 794427895 1413 True 669.000000 669 75.713000 1659 3063 1 chr2B.!!$R3 1404
20 TraesCS6A01G080100 chr2B 794484987 794486215 1228 False 525.000000 525 74.802000 1793 3039 1 chr2B.!!$F2 1246
21 TraesCS6A01G080100 chr5B 691581912 691583149 1237 False 575.000000 575 75.616000 1697 2922 1 chr5B.!!$F3 1225

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
499 508 0.036010 CACGAAGGATGTCTTGGGCT 60.036 55.000 0.00 0.00 35.80 5.19 F
500 509 0.250513 ACGAAGGATGTCTTGGGCTC 59.749 55.000 0.00 0.00 35.80 4.70 F
501 510 0.539051 CGAAGGATGTCTTGGGCTCT 59.461 55.000 0.00 0.00 35.50 4.09 F
504 513 0.622665 AGGATGTCTTGGGCTCTTGG 59.377 55.000 0.00 0.00 0.00 3.61 F
516 525 1.745489 CTCTTGGCCAGCCGGTAAC 60.745 63.158 5.11 0.00 39.42 2.50 F
3109 3455 1.751351 ACTGCGATGCACTAGAAGCTA 59.249 47.619 11.93 1.64 33.79 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2178 0.321564 TTCAAGGCATCGTCCCACAG 60.322 55.000 0.00 0.0 0.00 3.66 R
2948 3216 5.709631 TGCAAATTATAGAGGCAACAGAACA 59.290 36.000 0.00 0.0 41.41 3.18 R
3021 3289 5.028549 TCCTCAAGCTGATCAACTTATCC 57.971 43.478 10.93 0.0 0.00 2.59 R
3195 3562 3.506398 ACCATTGGGAGGTTGTAAAAGG 58.494 45.455 7.78 0.0 35.33 3.11 R
3533 3975 0.108424 CCTCTTGAGTGAAGGAGCCG 60.108 60.000 0.00 0.0 31.85 5.52 R
4484 4935 0.030773 GCGATCCACAGATACAGCGA 59.969 55.000 0.00 0.0 30.90 4.93 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
23 24 4.900154 CAGAGCTCCTGTCGGTTC 57.100 61.111 10.93 0.00 38.10 3.62
24 25 1.153939 CAGAGCTCCTGTCGGTTCG 60.154 63.158 10.93 0.00 38.10 3.95
25 26 2.182030 GAGCTCCTGTCGGTTCGG 59.818 66.667 0.87 0.00 0.00 4.30
26 27 3.358076 GAGCTCCTGTCGGTTCGGG 62.358 68.421 0.87 0.00 35.33 5.14
27 28 3.692406 GCTCCTGTCGGTTCGGGT 61.692 66.667 0.00 0.00 35.51 5.28
28 29 2.572284 CTCCTGTCGGTTCGGGTC 59.428 66.667 0.00 0.00 35.51 4.46
29 30 2.203523 TCCTGTCGGTTCGGGTCA 60.204 61.111 0.00 0.00 35.51 4.02
30 31 1.812686 CTCCTGTCGGTTCGGGTCAA 61.813 60.000 0.00 0.00 35.51 3.18
47 48 5.822519 CGGGTCAATAATCCTCAATTTCTCA 59.177 40.000 0.00 0.00 0.00 3.27
49 50 7.521099 CGGGTCAATAATCCTCAATTTCTCATG 60.521 40.741 0.00 0.00 0.00 3.07
50 51 7.144000 GGTCAATAATCCTCAATTTCTCATGC 58.856 38.462 0.00 0.00 0.00 4.06
51 52 7.201848 GGTCAATAATCCTCAATTTCTCATGCA 60.202 37.037 0.00 0.00 0.00 3.96
52 53 8.358148 GTCAATAATCCTCAATTTCTCATGCAT 58.642 33.333 0.00 0.00 0.00 3.96
53 54 9.577222 TCAATAATCCTCAATTTCTCATGCATA 57.423 29.630 0.00 0.00 0.00 3.14
95 100 6.590068 TCCTCATCTCTCAGATCCAAAATTC 58.410 40.000 0.00 0.00 31.32 2.17
229 237 0.397254 AGGAGTGGTGATACGAGGGG 60.397 60.000 0.00 0.00 0.00 4.79
245 253 3.498121 CGAGGGGTAGATACTAGAGGCAA 60.498 52.174 0.00 0.00 0.00 4.52
304 312 2.159170 GGCGAGCTTAGAGTGAAGACAT 60.159 50.000 0.00 0.00 0.00 3.06
385 393 2.824041 CCCGGCTTGGTTGATCCG 60.824 66.667 0.00 0.00 41.41 4.18
497 506 0.321564 TGCACGAAGGATGTCTTGGG 60.322 55.000 0.00 0.00 35.80 4.12
498 507 1.648467 GCACGAAGGATGTCTTGGGC 61.648 60.000 0.00 0.00 35.80 5.36
499 508 0.036010 CACGAAGGATGTCTTGGGCT 60.036 55.000 0.00 0.00 35.80 5.19
500 509 0.250513 ACGAAGGATGTCTTGGGCTC 59.749 55.000 0.00 0.00 35.80 4.70
501 510 0.539051 CGAAGGATGTCTTGGGCTCT 59.461 55.000 0.00 0.00 35.50 4.09
502 511 1.065854 CGAAGGATGTCTTGGGCTCTT 60.066 52.381 0.00 0.00 35.50 2.85
503 512 2.363683 GAAGGATGTCTTGGGCTCTTG 58.636 52.381 0.00 0.00 35.50 3.02
504 513 0.622665 AGGATGTCTTGGGCTCTTGG 59.377 55.000 0.00 0.00 0.00 3.61
516 525 1.745489 CTCTTGGCCAGCCGGTAAC 60.745 63.158 5.11 0.00 39.42 2.50
708 734 7.552687 TGTGATTTGTCATAATCCAGTTAGGTC 59.447 37.037 0.00 0.00 39.02 3.85
752 782 5.817816 AGTATTAGTGCTGTTATGAGGTTGC 59.182 40.000 0.00 0.00 0.00 4.17
815 845 8.760103 TCACATTACATTCAATTGTGATTTGG 57.240 30.769 5.13 0.00 32.48 3.28
830 860 5.697178 TGTGATTTGGCATTCTTGTGATTTG 59.303 36.000 0.00 0.00 0.00 2.32
860 1030 4.654262 TCCAGTTAGGTCCATACATTCTCC 59.346 45.833 0.00 0.00 39.02 3.71
874 1044 7.012704 CCATACATTCTCCCATACAAAGAACTG 59.987 40.741 0.00 0.00 32.22 3.16
1381 1564 6.521133 CGATTTCTTTAACTGTGTCATTCAGC 59.479 38.462 0.00 0.00 36.50 4.26
1519 1705 8.527810 CAGAGACTAGTTCTTTTCCTATTGAGT 58.472 37.037 0.00 0.00 33.22 3.41
1561 1747 7.439655 GTGATCAGGAGTTAAATCAGGTGATAC 59.560 40.741 12.06 8.76 33.73 2.24
1600 1789 7.589958 AGAGAAGATGATAGTACCACGAAAT 57.410 36.000 0.00 0.00 0.00 2.17
1613 1802 3.634448 ACCACGAAATCACATTCCAAACA 59.366 39.130 0.00 0.00 0.00 2.83
1787 2010 5.594926 ACAAGTGAAGCCTCATTTCAAAAG 58.405 37.500 0.00 0.00 36.41 2.27
1928 2154 6.403866 TCATAAAACTGTGTGCCAGAAAAT 57.596 33.333 0.00 0.00 44.49 1.82
1951 2178 7.976135 ATGCTACTTATTGTCCTTGATGATC 57.024 36.000 0.00 0.00 0.00 2.92
2034 2261 3.463048 AATGTGAGGAAGGGAAGCATT 57.537 42.857 0.00 0.00 0.00 3.56
2277 2507 2.609459 GCTAAGGATGAACCGTCACATG 59.391 50.000 0.00 0.00 44.74 3.21
2701 2951 7.728148 TCGTCATCTATCAGTACTCTCTAACT 58.272 38.462 0.00 0.00 0.00 2.24
3021 3289 7.162082 AGATAGAAAGTTTACCCAGTGACTTG 58.838 38.462 0.00 0.00 33.02 3.16
3109 3455 1.751351 ACTGCGATGCACTAGAAGCTA 59.249 47.619 11.93 1.64 33.79 3.32
3195 3562 3.706055 TGGGACAGAAGCACTTCAC 57.294 52.632 12.65 4.01 41.84 3.18
3785 4233 6.038271 GGCATTACATCGTTCTTGTTCCTTAT 59.962 38.462 0.00 0.00 0.00 1.73
3967 4415 4.704540 TGGAGATTTATGATTGCCAACGTT 59.295 37.500 0.00 0.00 0.00 3.99
4072 4520 1.152368 AGCTGCCTGCAAAACCTCT 59.848 52.632 0.00 0.00 45.94 3.69
4314 4762 4.328536 GAGACTAGCTAAGATCCCATCGA 58.671 47.826 0.00 0.00 0.00 3.59
4334 4782 4.802039 TCGATTTTCAAGTCTATGGTACGC 59.198 41.667 0.00 0.00 0.00 4.42
4350 4801 4.987285 TGGTACGCGTGTTTAATTTACAGA 59.013 37.500 24.59 0.00 0.00 3.41
4386 4837 9.649167 TCTTACTAGTTAACCTGCAGATTTTAC 57.351 33.333 17.39 11.65 0.00 2.01
4453 4904 4.937201 ACGTATCTATGTCATGCAGGAA 57.063 40.909 0.92 0.00 0.00 3.36
4476 4927 4.511617 TTTGTTGTTGTTGCACTGAGAA 57.488 36.364 0.00 0.00 0.00 2.87
4478 4929 4.291540 TGTTGTTGTTGCACTGAGAATC 57.708 40.909 0.00 0.00 0.00 2.52
4479 4930 3.947196 TGTTGTTGTTGCACTGAGAATCT 59.053 39.130 0.00 0.00 34.92 2.40
4480 4931 4.201940 TGTTGTTGTTGCACTGAGAATCTG 60.202 41.667 0.00 0.00 40.23 2.90
4481 4932 3.807553 TGTTGTTGCACTGAGAATCTGA 58.192 40.909 0.00 0.00 37.51 3.27
4482 4933 3.811497 TGTTGTTGCACTGAGAATCTGAG 59.189 43.478 0.00 0.00 37.51 3.35
4484 4935 4.548451 TGTTGCACTGAGAATCTGAGAT 57.452 40.909 3.22 0.00 37.51 2.75
4485 4936 4.502016 TGTTGCACTGAGAATCTGAGATC 58.498 43.478 3.22 0.00 37.51 2.75
4486 4937 3.433513 TGCACTGAGAATCTGAGATCG 57.566 47.619 3.22 0.00 37.51 3.69
4487 4938 2.126467 GCACTGAGAATCTGAGATCGC 58.874 52.381 3.22 0.00 37.51 4.58
4491 4942 4.036144 CACTGAGAATCTGAGATCGCTGTA 59.964 45.833 3.22 0.00 37.51 2.74
4493 4944 5.048782 ACTGAGAATCTGAGATCGCTGTATC 60.049 44.000 3.22 1.35 37.51 2.24
4620 5071 5.504994 GCAACATTTGTTAACGGAGACTTGA 60.505 40.000 0.26 0.00 36.32 3.02
4665 5128 8.902540 TCACTCATTTAGTCACTTGTTGTAAT 57.097 30.769 0.00 0.00 35.76 1.89
4666 5129 8.988934 TCACTCATTTAGTCACTTGTTGTAATC 58.011 33.333 0.00 0.00 35.76 1.75
4667 5130 8.993121 CACTCATTTAGTCACTTGTTGTAATCT 58.007 33.333 0.00 0.00 35.76 2.40
4668 5131 9.209175 ACTCATTTAGTCACTTGTTGTAATCTC 57.791 33.333 0.00 0.00 30.33 2.75
4669 5132 9.429359 CTCATTTAGTCACTTGTTGTAATCTCT 57.571 33.333 0.00 0.00 0.00 3.10
4676 5139 9.832445 AGTCACTTGTTGTAATCTCTAAAAAGA 57.168 29.630 0.00 0.00 0.00 2.52
4677 5140 9.865484 GTCACTTGTTGTAATCTCTAAAAAGAC 57.135 33.333 0.00 0.00 0.00 3.01
4697 5160 6.253946 AGACTTATATTTGGGAACAGAGGG 57.746 41.667 0.00 0.00 44.54 4.30
4698 5161 5.970640 AGACTTATATTTGGGAACAGAGGGA 59.029 40.000 0.00 0.00 44.54 4.20
4731 5302 6.053632 TGGATTGCTTCTTTGATACTCTGA 57.946 37.500 0.00 0.00 0.00 3.27
4738 5309 6.975197 TGCTTCTTTGATACTCTGATCTTACG 59.025 38.462 0.00 0.00 0.00 3.18
4747 5318 4.079970 ACTCTGATCTTACGTTCCTGTGA 58.920 43.478 0.00 0.00 0.00 3.58
4748 5319 4.082679 ACTCTGATCTTACGTTCCTGTGAC 60.083 45.833 0.00 0.00 0.00 3.67
4749 5320 3.824443 TCTGATCTTACGTTCCTGTGACA 59.176 43.478 0.00 0.00 0.00 3.58
4750 5321 4.082733 TCTGATCTTACGTTCCTGTGACAG 60.083 45.833 5.42 5.42 0.00 3.51
4796 5367 1.609783 GACTGGACCAATCCCCTGG 59.390 63.158 0.00 0.00 45.59 4.45
4830 5428 9.554053 AGATTATTACTCACTAGATATTGGGCT 57.446 33.333 0.00 0.00 0.00 5.19
4836 5434 6.821388 ACTCACTAGATATTGGGCTAAGTTG 58.179 40.000 0.00 0.00 0.00 3.16
4848 5446 1.802365 GCTAAGTTGTTACACACCGGG 59.198 52.381 6.32 0.00 0.00 5.73
4850 5448 0.107116 AAGTTGTTACACACCGGGCA 60.107 50.000 6.32 0.00 0.00 5.36
4853 5451 0.739561 TTGTTACACACCGGGCAAAC 59.260 50.000 6.32 3.42 0.00 2.93
4888 5486 8.420222 TGTAAATTTGAAGAAAAGATTGCAGGA 58.580 29.630 0.00 0.00 0.00 3.86
4938 5536 6.249035 TCGGAAGGAACATGTACAATTTTC 57.751 37.500 0.00 2.83 0.00 2.29
4963 5561 9.253832 TCTATGGAAGCATGAAAATTCCTTTAA 57.746 29.630 15.86 2.27 42.50 1.52
5066 5664 6.012745 AGAAAAATGTTCATCCACCTTAGCT 58.987 36.000 0.00 0.00 0.00 3.32
5099 5698 4.275936 CACGTGGATCCCAAGAAATATTCC 59.724 45.833 9.90 0.00 36.54 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.344203 CCGAACCGACAGGAGCTCT 61.344 63.158 14.64 0.00 41.02 4.09
8 9 2.182030 CCGAACCGACAGGAGCTC 59.818 66.667 4.71 4.71 41.02 4.09
10 11 3.644399 GACCCGAACCGACAGGAGC 62.644 68.421 0.00 0.00 41.02 4.70
15 16 2.419021 GGATTATTGACCCGAACCGACA 60.419 50.000 0.00 0.00 0.00 4.35
16 17 2.159000 AGGATTATTGACCCGAACCGAC 60.159 50.000 0.00 0.00 0.00 4.79
18 19 2.159014 TGAGGATTATTGACCCGAACCG 60.159 50.000 0.00 0.00 0.00 4.44
19 20 3.553828 TGAGGATTATTGACCCGAACC 57.446 47.619 0.00 0.00 0.00 3.62
20 21 6.318900 AGAAATTGAGGATTATTGACCCGAAC 59.681 38.462 0.00 0.00 0.00 3.95
23 24 5.822519 TGAGAAATTGAGGATTATTGACCCG 59.177 40.000 0.00 0.00 0.00 5.28
24 25 7.655490 CATGAGAAATTGAGGATTATTGACCC 58.345 38.462 0.00 0.00 0.00 4.46
25 26 7.144000 GCATGAGAAATTGAGGATTATTGACC 58.856 38.462 0.00 0.00 0.00 4.02
26 27 7.709947 TGCATGAGAAATTGAGGATTATTGAC 58.290 34.615 0.00 0.00 0.00 3.18
27 28 7.885009 TGCATGAGAAATTGAGGATTATTGA 57.115 32.000 0.00 0.00 0.00 2.57
79 84 3.669939 GGGGGAATTTTGGATCTGAGA 57.330 47.619 0.00 0.00 0.00 3.27
229 237 3.816523 AGCTCGTTGCCTCTAGTATCTAC 59.183 47.826 0.00 0.00 44.23 2.59
245 253 0.601311 GGTCAAGCAACAGAGCTCGT 60.601 55.000 8.37 6.73 45.89 4.18
304 312 3.742327 CGAGAGCCAATGCCTAATCTCAA 60.742 47.826 0.00 0.00 35.76 3.02
385 393 0.459759 GCGGCTGTACCAACTAGGAC 60.460 60.000 0.00 0.00 41.22 3.85
497 506 3.622060 TTACCGGCTGGCCAAGAGC 62.622 63.158 12.89 6.95 39.70 4.09
498 507 1.745489 GTTACCGGCTGGCCAAGAG 60.745 63.158 12.89 0.00 39.70 2.85
499 508 0.905809 TAGTTACCGGCTGGCCAAGA 60.906 55.000 12.89 0.00 39.70 3.02
500 509 0.035820 TTAGTTACCGGCTGGCCAAG 60.036 55.000 12.89 1.85 39.70 3.61
501 510 0.321830 GTTAGTTACCGGCTGGCCAA 60.322 55.000 12.89 2.83 39.70 4.52
502 511 1.297364 GTTAGTTACCGGCTGGCCA 59.703 57.895 12.89 4.71 39.70 5.36
503 512 1.450848 GGTTAGTTACCGGCTGGCC 60.451 63.158 12.89 0.00 39.70 5.36
504 513 4.213666 GGTTAGTTACCGGCTGGC 57.786 61.111 12.89 0.00 39.70 4.85
516 525 3.126831 CTCGCCTAATCAGCTTGGTTAG 58.873 50.000 8.43 8.43 40.00 2.34
668 678 5.933790 ACAAATCACAATTGAATGCAATGC 58.066 33.333 13.59 0.00 43.71 3.56
673 683 8.545420 GGATTATGACAAATCACAATTGAATGC 58.455 33.333 13.59 0.00 31.95 3.56
815 845 5.739161 GGATTACGACAAATCACAAGAATGC 59.261 40.000 0.00 0.00 37.56 3.56
830 860 4.667519 ATGGACCTAACTGGATTACGAC 57.332 45.455 0.00 0.00 39.71 4.34
860 1030 8.356657 TGAAATTAACACCAGTTCTTTGTATGG 58.643 33.333 0.00 0.00 39.15 2.74
1381 1564 3.108144 CCTTCACTTTGTTGAAACTGCG 58.892 45.455 0.00 0.00 35.07 5.18
1519 1705 4.013050 TGATCACGGCCAAACATTATTGA 58.987 39.130 2.24 0.00 31.84 2.57
1561 1747 8.484641 TCATCTTCTCTTACAACTAGCAATTG 57.515 34.615 0.00 0.00 0.00 2.32
1600 1789 5.551305 TCTCTCTTCTGTTTGGAATGTGA 57.449 39.130 0.00 0.00 0.00 3.58
1613 1802 3.583806 CTTGTGCGACATTCTCTCTTCT 58.416 45.455 0.00 0.00 0.00 2.85
1693 1901 4.813027 ACTATTGGCAAAACAGCAAGATG 58.187 39.130 3.01 0.00 35.83 2.90
1787 2010 3.569701 TGAGACAGAAAGCCAAATTGTCC 59.430 43.478 0.00 0.00 39.08 4.02
1928 2154 6.988580 CAGATCATCAAGGACAATAAGTAGCA 59.011 38.462 0.00 0.00 0.00 3.49
1951 2178 0.321564 TTCAAGGCATCGTCCCACAG 60.322 55.000 0.00 0.00 0.00 3.66
2948 3216 5.709631 TGCAAATTATAGAGGCAACAGAACA 59.290 36.000 0.00 0.00 41.41 3.18
3021 3289 5.028549 TCCTCAAGCTGATCAACTTATCC 57.971 43.478 10.93 0.00 0.00 2.59
3195 3562 3.506398 ACCATTGGGAGGTTGTAAAAGG 58.494 45.455 7.78 0.00 35.33 3.11
3533 3975 0.108424 CCTCTTGAGTGAAGGAGCCG 60.108 60.000 0.00 0.00 31.85 5.52
3967 4415 2.206900 TCCCCTCTGCCAGTCCAA 59.793 61.111 0.00 0.00 0.00 3.53
4072 4520 1.371267 CCAGCGAAACGAGTGACGA 60.371 57.895 0.00 0.00 45.77 4.20
4242 4690 0.405198 TCATCTTTGGGCAGCCAGAA 59.595 50.000 15.19 6.15 0.00 3.02
4314 4762 4.328983 CACGCGTACCATAGACTTGAAAAT 59.671 41.667 13.44 0.00 0.00 1.82
4386 4837 3.440173 ACGAGTGGCAGAAAACATATTGG 59.560 43.478 0.00 0.00 0.00 3.16
4453 4904 5.070770 TCTCAGTGCAACAACAACAAAAT 57.929 34.783 0.00 0.00 41.43 1.82
4476 4927 3.255395 CCACAGATACAGCGATCTCAGAT 59.745 47.826 0.00 0.00 33.75 2.90
4478 4929 2.620585 TCCACAGATACAGCGATCTCAG 59.379 50.000 0.00 0.00 33.75 3.35
4479 4930 2.654863 TCCACAGATACAGCGATCTCA 58.345 47.619 0.00 0.00 33.75 3.27
4480 4931 3.669290 CGATCCACAGATACAGCGATCTC 60.669 52.174 0.00 0.00 33.75 2.75
4481 4932 2.227626 CGATCCACAGATACAGCGATCT 59.772 50.000 0.00 0.00 36.58 2.75
4482 4933 2.590073 CGATCCACAGATACAGCGATC 58.410 52.381 0.00 0.00 30.90 3.69
4484 4935 0.030773 GCGATCCACAGATACAGCGA 59.969 55.000 0.00 0.00 30.90 4.93
4485 4936 0.031314 AGCGATCCACAGATACAGCG 59.969 55.000 0.00 0.00 34.54 5.18
4486 4937 1.863454 CAAGCGATCCACAGATACAGC 59.137 52.381 0.00 0.00 30.90 4.40
4487 4938 1.863454 GCAAGCGATCCACAGATACAG 59.137 52.381 0.00 0.00 30.90 2.74
4491 4942 0.035152 TTGGCAAGCGATCCACAGAT 60.035 50.000 0.00 0.00 34.57 2.90
4493 4944 0.109597 GTTTGGCAAGCGATCCACAG 60.110 55.000 0.00 0.00 30.97 3.66
4670 5133 9.025041 CCTCTGTTCCCAAATATAAGTCTTTTT 57.975 33.333 0.00 0.00 0.00 1.94
4672 5135 7.036863 TCCCTCTGTTCCCAAATATAAGTCTTT 60.037 37.037 0.00 0.00 0.00 2.52
4673 5136 6.447084 TCCCTCTGTTCCCAAATATAAGTCTT 59.553 38.462 0.00 0.00 0.00 3.01
4676 5139 5.731678 ACTCCCTCTGTTCCCAAATATAAGT 59.268 40.000 0.00 0.00 0.00 2.24
4677 5140 6.253946 ACTCCCTCTGTTCCCAAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
4679 5142 7.947782 ATTACTCCCTCTGTTCCCAAATATA 57.052 36.000 0.00 0.00 0.00 0.86
4680 5143 6.848562 ATTACTCCCTCTGTTCCCAAATAT 57.151 37.500 0.00 0.00 0.00 1.28
4681 5144 6.011981 ACAATTACTCCCTCTGTTCCCAAATA 60.012 38.462 0.00 0.00 0.00 1.40
4682 5145 5.222337 ACAATTACTCCCTCTGTTCCCAAAT 60.222 40.000 0.00 0.00 0.00 2.32
4683 5146 4.105697 ACAATTACTCCCTCTGTTCCCAAA 59.894 41.667 0.00 0.00 0.00 3.28
4684 5147 3.655777 ACAATTACTCCCTCTGTTCCCAA 59.344 43.478 0.00 0.00 0.00 4.12
4685 5148 3.256704 ACAATTACTCCCTCTGTTCCCA 58.743 45.455 0.00 0.00 0.00 4.37
4687 5150 4.459337 CCAAACAATTACTCCCTCTGTTCC 59.541 45.833 0.00 0.00 30.16 3.62
4689 5152 5.319043 TCCAAACAATTACTCCCTCTGTT 57.681 39.130 0.00 0.00 0.00 3.16
4693 5156 4.706962 AGCAATCCAAACAATTACTCCCTC 59.293 41.667 0.00 0.00 0.00 4.30
4697 5160 7.867403 TCAAAGAAGCAATCCAAACAATTACTC 59.133 33.333 0.00 0.00 0.00 2.59
4698 5161 7.725251 TCAAAGAAGCAATCCAAACAATTACT 58.275 30.769 0.00 0.00 0.00 2.24
4747 5318 5.601313 TCGCCTAGAATTATAAGGTTCCTGT 59.399 40.000 0.00 0.00 32.67 4.00
4748 5319 6.097915 TCGCCTAGAATTATAAGGTTCCTG 57.902 41.667 0.00 0.00 32.67 3.86
4749 5320 6.741801 GCTTCGCCTAGAATTATAAGGTTCCT 60.742 42.308 0.00 0.00 38.34 3.36
4750 5321 5.408909 GCTTCGCCTAGAATTATAAGGTTCC 59.591 44.000 0.00 0.00 38.34 3.62
4751 5322 6.224584 AGCTTCGCCTAGAATTATAAGGTTC 58.775 40.000 0.00 0.00 38.34 3.62
4752 5323 6.176014 AGCTTCGCCTAGAATTATAAGGTT 57.824 37.500 0.00 0.00 38.34 3.50
4753 5324 5.810080 AGCTTCGCCTAGAATTATAAGGT 57.190 39.130 0.00 0.00 38.34 3.50
4754 5325 6.153000 TCCTAGCTTCGCCTAGAATTATAAGG 59.847 42.308 0.00 0.00 37.57 2.69
4755 5326 7.030768 GTCCTAGCTTCGCCTAGAATTATAAG 58.969 42.308 0.00 0.00 37.57 1.73
4756 5327 6.720288 AGTCCTAGCTTCGCCTAGAATTATAA 59.280 38.462 0.00 0.00 37.57 0.98
4796 5367 8.179509 TCTAGTGAGTAATAATCTAGCCCAAC 57.820 38.462 0.00 0.00 0.00 3.77
4836 5434 1.655885 GGTTTGCCCGGTGTGTAAC 59.344 57.895 0.00 0.00 37.35 2.50
4848 5446 5.994668 TCAAATTTACATTCTTGGGGTTTGC 59.005 36.000 0.00 0.00 0.00 3.68
4850 5448 8.028652 TCTTCAAATTTACATTCTTGGGGTTT 57.971 30.769 0.00 0.00 0.00 3.27
4853 5451 8.900983 TTTTCTTCAAATTTACATTCTTGGGG 57.099 30.769 0.00 0.00 0.00 4.96
4927 5525 7.936496 TCATGCTTCCATAGAAAATTGTACA 57.064 32.000 0.00 0.00 0.00 2.90
4928 5526 9.638239 TTTTCATGCTTCCATAGAAAATTGTAC 57.362 29.630 0.00 0.00 35.73 2.90
4938 5536 9.525409 CTTAAAGGAATTTTCATGCTTCCATAG 57.475 33.333 14.53 6.08 40.77 2.23
4963 5561 5.474876 ACATGAAAGAAAAATCGCTCTTCCT 59.525 36.000 0.00 0.00 30.57 3.36
5020 5618 5.033326 TGTGATGATGTGATGAACAAACG 57.967 39.130 0.00 0.00 43.61 3.60
5142 5742 4.657814 ACAGTTTCCATGACTGGGTAAT 57.342 40.909 15.27 0.00 46.77 1.89
5144 5744 3.392947 TGAACAGTTTCCATGACTGGGTA 59.607 43.478 15.27 1.32 46.77 3.69
5145 5745 2.174639 TGAACAGTTTCCATGACTGGGT 59.825 45.455 15.27 5.04 46.77 4.51
5147 5747 3.480470 AGTGAACAGTTTCCATGACTGG 58.520 45.455 15.27 0.00 46.77 4.00
5149 5749 6.773638 AGATAAGTGAACAGTTTCCATGACT 58.226 36.000 0.00 0.00 0.00 3.41
5150 5750 6.092807 GGAGATAAGTGAACAGTTTCCATGAC 59.907 42.308 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.