Multiple sequence alignment - TraesCS2A01G235300

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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 TraesCS2A01G235300 chr2A 100.000 2693 0 0 1 2693 293048856 293051548 0.000000e+00 4974.0
1 TraesCS2A01G235300 chr2A 94.586 1958 55 9 1 1952 35939751 35937839 0.000000e+00 2981.0
2 TraesCS2A01G235300 chr2A 93.343 2043 75 23 1 2034 620728370 620730360 0.000000e+00 2963.0
3 TraesCS2A01G235300 chr2A 93.842 747 35 3 1295 2036 202074603 202075343 0.000000e+00 1114.0
4 TraesCS2A01G235300 chr2A 92.391 276 20 1 2419 2693 481445058 481444783 2.510000e-105 392.0
5 TraesCS2A01G235300 chr2A 82.171 258 38 4 2178 2430 578665649 578665395 5.840000e-52 215.0
6 TraesCS2A01G235300 chr7A 94.288 2066 65 8 1 2037 709855663 709853622 0.000000e+00 3112.0
7 TraesCS2A01G235300 chr7A 95.955 1879 56 9 1 1869 725469880 725471748 0.000000e+00 3031.0
8 TraesCS2A01G235300 chr7A 94.115 2005 70 18 1 1973 564246868 564244880 0.000000e+00 3005.0
9 TraesCS2A01G235300 chr7A 97.250 1309 30 4 1 1304 662137606 662138913 0.000000e+00 2213.0
10 TraesCS2A01G235300 chr7A 93.796 274 17 0 2420 2693 233805768 233806041 1.930000e-111 412.0
11 TraesCS2A01G235300 chr5A 95.935 1919 68 7 1 1914 556779906 556781819 0.000000e+00 3103.0
12 TraesCS2A01G235300 chr5A 92.515 1376 69 16 1 1365 38155421 38156773 0.000000e+00 1940.0
13 TraesCS2A01G235300 chr5A 92.614 1056 43 13 987 2037 401270213 401269188 0.000000e+00 1485.0
14 TraesCS2A01G235300 chr5A 93.130 262 18 0 2432 2693 121081827 121082088 4.210000e-103 385.0
15 TraesCS2A01G235300 chr5A 87.568 185 21 2 2246 2429 568591272 568591089 2.100000e-51 213.0
16 TraesCS2A01G235300 chr4A 94.126 2043 87 11 1 2034 322656468 322658486 0.000000e+00 3077.0
17 TraesCS2A01G235300 chr4A 93.691 745 35 4 1295 2034 612664576 612665313 0.000000e+00 1105.0
18 TraesCS2A01G235300 chr4A 89.902 307 23 5 2037 2337 649025869 649025565 3.250000e-104 388.0
19 TraesCS2A01G235300 chr4A 85.792 183 24 2 2245 2426 331130515 331130696 2.740000e-45 193.0
20 TraesCS2A01G235300 chr6A 93.552 2047 97 15 1 2037 93270619 93268598 0.000000e+00 3016.0
21 TraesCS2A01G235300 chr6A 93.327 2038 86 22 1 2034 616389535 616391526 0.000000e+00 2964.0
22 TraesCS2A01G235300 chr6A 95.570 316 12 1 2030 2343 581486397 581486712 3.090000e-139 505.0
23 TraesCS2A01G235300 chr6A 94.942 257 13 0 2437 2693 581487125 581487381 1.160000e-108 403.0
24 TraesCS2A01G235300 chr2D 91.149 1932 95 38 25 1921 30144091 30142201 0.000000e+00 2551.0
25 TraesCS2A01G235300 chr2D 86.842 114 13 2 2427 2538 284244094 284243981 2.810000e-25 126.0
26 TraesCS2A01G235300 chr5D 88.114 2078 173 38 1 2037 407315312 407317356 0.000000e+00 2401.0
27 TraesCS2A01G235300 chr5D 76.825 315 45 17 2030 2322 510578325 510578633 4.640000e-33 152.0
28 TraesCS2A01G235300 chr5D 96.000 75 3 0 2619 2693 84787558 84787632 3.640000e-24 122.0
29 TraesCS2A01G235300 chr5D 83.810 105 15 2 2439 2543 378339352 378339454 6.140000e-17 99.0
30 TraesCS2A01G235300 chr5D 96.429 56 2 0 2426 2481 317161138 317161193 2.850000e-15 93.5
31 TraesCS2A01G235300 chr5D 84.810 79 8 1 2413 2487 317741276 317741354 2.880000e-10 76.8
32 TraesCS2A01G235300 chr1A 93.302 1284 59 10 546 1827 520127423 520126165 0.000000e+00 1869.0
33 TraesCS2A01G235300 chr1A 94.545 275 15 0 2419 2693 347061683 347061957 2.480000e-115 425.0
34 TraesCS2A01G235300 chr1A 94.545 275 15 0 2419 2693 534669224 534668950 2.480000e-115 425.0
35 TraesCS2A01G235300 chr1A 85.276 163 19 5 2266 2426 294730342 294730501 2.150000e-36 163.0
36 TraesCS2A01G235300 chr2B 90.956 387 31 2 2034 2418 2601458 2601842 3.970000e-143 518.0
37 TraesCS2A01G235300 chr2B 100.000 42 0 0 2652 2693 386316297 386316256 7.990000e-11 78.7
38 TraesCS2A01G235300 chr4B 90.537 391 33 2 2038 2426 419322221 419322609 5.140000e-142 514.0
39 TraesCS2A01G235300 chr4B 89.873 395 36 2 2034 2426 131075503 131075895 3.090000e-139 505.0
40 TraesCS2A01G235300 chr4B 83.217 143 19 3 2426 2568 536477953 536478090 2.810000e-25 126.0
41 TraesCS2A01G235300 chr4B 86.667 90 12 0 2419 2508 324824031 324823942 1.710000e-17 100.0
42 TraesCS2A01G235300 chr4B 94.231 52 3 0 2375 2426 117292823 117292874 2.220000e-11 80.5
43 TraesCS2A01G235300 chr4B 100.000 32 0 0 2395 2426 653716137 653716168 2.900000e-05 60.2
44 TraesCS2A01G235300 chr3A 94.909 275 13 1 2419 2693 336891454 336891727 1.920000e-116 429.0
45 TraesCS2A01G235300 chr3A 89.275 345 29 5 2034 2372 739339169 739339511 2.480000e-115 425.0
46 TraesCS2A01G235300 chr3B 94.182 275 16 0 2419 2693 503717281 503717555 1.150000e-113 420.0
47 TraesCS2A01G235300 chr3B 87.027 185 20 4 2228 2410 389067959 389067777 3.510000e-49 206.0
48 TraesCS2A01G235300 chr3B 84.756 164 19 6 2269 2429 795506829 795506669 2.780000e-35 159.0
49 TraesCS2A01G235300 chr3B 80.488 205 34 6 2228 2429 764853115 764852914 4.640000e-33 152.0
50 TraesCS2A01G235300 chr1B 94.505 273 14 1 2421 2692 380688957 380689229 1.150000e-113 420.0
51 TraesCS2A01G235300 chr1B 86.486 148 17 3 2269 2415 572267679 572267534 2.780000e-35 159.0
52 TraesCS2A01G235300 chr1B 78.049 164 32 4 2268 2429 22121754 22121593 1.710000e-17 100.0
53 TraesCS2A01G235300 chr1B 85.542 83 12 0 2426 2508 303020027 303019945 1.330000e-13 87.9
54 TraesCS2A01G235300 chr1B 85.542 83 9 3 2428 2508 612681407 612681488 1.720000e-12 84.2
55 TraesCS2A01G235300 chr7B 93.841 276 16 1 2419 2693 362413226 362412951 5.360000e-112 414.0
56 TraesCS2A01G235300 chr7B 92.937 269 18 1 2426 2693 454621171 454620903 9.040000e-105 390.0
57 TraesCS2A01G235300 chr6B 86.765 204 23 4 2228 2429 483045292 483045091 9.700000e-55 224.0
58 TraesCS2A01G235300 chr6B 85.455 165 21 2 2266 2429 174657399 174657237 4.610000e-38 169.0
59 TraesCS2A01G235300 chr6D 88.950 181 14 3 2456 2634 201577756 201577932 4.510000e-53 219.0
60 TraesCS2A01G235300 chr6D 88.525 122 12 2 2419 2538 235235099 235234978 2.160000e-31 147.0
61 TraesCS2A01G235300 chr6D 77.570 107 22 2 2321 2426 54660243 54660138 2.240000e-06 63.9
62 TraesCS2A01G235300 chr6D 75.342 146 28 8 2284 2426 232419511 232419651 2.240000e-06 63.9
63 TraesCS2A01G235300 chr6D 94.444 36 2 0 2419 2454 201574971 201575006 3.750000e-04 56.5
64 TraesCS2A01G235300 chr5B 85.802 162 20 3 2269 2429 127187927 127187768 4.610000e-38 169.0
65 TraesCS2A01G235300 chr4D 92.222 90 7 0 2419 2508 201182546 201182635 7.830000e-26 128.0
66 TraesCS2A01G235300 chr4D 89.535 86 9 0 2423 2508 276178455 276178540 2.830000e-20 110.0
67 TraesCS2A01G235300 chr4D 94.030 67 4 0 2419 2485 285351862 285351928 4.740000e-18 102.0
68 TraesCS2A01G235300 chr4D 93.333 60 4 0 2426 2485 166492392 166492333 3.690000e-14 89.8
69 TraesCS2A01G235300 chr4D 85.897 78 11 0 2434 2511 165301708 165301631 1.720000e-12 84.2
70 TraesCS2A01G235300 chr7D 82.500 120 15 5 2423 2539 454524151 454524035 1.710000e-17 100.0
71 TraesCS2A01G235300 chrUn 75.625 160 36 3 2268 2426 117163512 117163669 2.880000e-10 76.8


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 TraesCS2A01G235300 chr2A 293048856 293051548 2692 False 4974 4974 100.000 1 2693 1 chr2A.!!$F2 2692
1 TraesCS2A01G235300 chr2A 35937839 35939751 1912 True 2981 2981 94.586 1 1952 1 chr2A.!!$R1 1951
2 TraesCS2A01G235300 chr2A 620728370 620730360 1990 False 2963 2963 93.343 1 2034 1 chr2A.!!$F3 2033
3 TraesCS2A01G235300 chr2A 202074603 202075343 740 False 1114 1114 93.842 1295 2036 1 chr2A.!!$F1 741
4 TraesCS2A01G235300 chr7A 709853622 709855663 2041 True 3112 3112 94.288 1 2037 1 chr7A.!!$R2 2036
5 TraesCS2A01G235300 chr7A 725469880 725471748 1868 False 3031 3031 95.955 1 1869 1 chr7A.!!$F3 1868
6 TraesCS2A01G235300 chr7A 564244880 564246868 1988 True 3005 3005 94.115 1 1973 1 chr7A.!!$R1 1972
7 TraesCS2A01G235300 chr7A 662137606 662138913 1307 False 2213 2213 97.250 1 1304 1 chr7A.!!$F2 1303
8 TraesCS2A01G235300 chr5A 556779906 556781819 1913 False 3103 3103 95.935 1 1914 1 chr5A.!!$F3 1913
9 TraesCS2A01G235300 chr5A 38155421 38156773 1352 False 1940 1940 92.515 1 1365 1 chr5A.!!$F1 1364
10 TraesCS2A01G235300 chr5A 401269188 401270213 1025 True 1485 1485 92.614 987 2037 1 chr5A.!!$R1 1050
11 TraesCS2A01G235300 chr4A 322656468 322658486 2018 False 3077 3077 94.126 1 2034 1 chr4A.!!$F1 2033
12 TraesCS2A01G235300 chr4A 612664576 612665313 737 False 1105 1105 93.691 1295 2034 1 chr4A.!!$F3 739
13 TraesCS2A01G235300 chr6A 93268598 93270619 2021 True 3016 3016 93.552 1 2037 1 chr6A.!!$R1 2036
14 TraesCS2A01G235300 chr6A 616389535 616391526 1991 False 2964 2964 93.327 1 2034 1 chr6A.!!$F1 2033
15 TraesCS2A01G235300 chr6A 581486397 581487381 984 False 454 505 95.256 2030 2693 2 chr6A.!!$F2 663
16 TraesCS2A01G235300 chr2D 30142201 30144091 1890 True 2551 2551 91.149 25 1921 1 chr2D.!!$R1 1896
17 TraesCS2A01G235300 chr5D 407315312 407317356 2044 False 2401 2401 88.114 1 2037 1 chr5D.!!$F5 2036
18 TraesCS2A01G235300 chr1A 520126165 520127423 1258 True 1869 1869 93.302 546 1827 1 chr1A.!!$R1 1281

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
162 172 2.441410 TGGCTCCAACAATTCGCATTA 58.559 42.857 0.0 0.0 0.00 1.90 F
886 923 2.806608 TACTCGAAGCCAAAACGACT 57.193 45.000 0.0 0.0 32.72 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1234 1274 1.250154 CCCATTGCACGAACCATGGT 61.250 55.0 13.0 13.0 0.00 3.55 R
2183 2434 0.111446 TTCTGCCCGAATGGTTCCAA 59.889 50.0 0.0 0.0 36.04 3.53 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
162 172 2.441410 TGGCTCCAACAATTCGCATTA 58.559 42.857 0.00 0.00 0.00 1.90
358 369 7.624549 TCAAAGTAGAGATGCTTATTGGAACT 58.375 34.615 0.00 0.00 0.00 3.01
782 804 3.011760 GAGCGACAAACGGAAGCGG 62.012 63.158 0.00 0.00 42.83 5.52
886 923 2.806608 TACTCGAAGCCAAAACGACT 57.193 45.000 0.00 0.00 32.72 4.18
1047 1087 3.394836 GAGAGGAGGTTGGCGGCT 61.395 66.667 11.43 0.00 0.00 5.52
1515 1650 1.462616 TCATGGGCGGAATGTCTTTG 58.537 50.000 0.00 0.00 0.00 2.77
1550 1685 2.756760 GCACACATTCCCATGAAGATGT 59.243 45.455 0.00 0.00 34.50 3.06
1649 1784 1.405661 GGAGGCGGAAGAATCGTCTTT 60.406 52.381 0.00 0.00 44.42 2.52
1792 1965 2.821378 TGTGGGCATGAACTTCATCAAG 59.179 45.455 0.00 0.00 34.28 3.02
2124 2375 4.350520 TGCTCCCATGTATTATCCATGACA 59.649 41.667 0.00 0.00 41.78 3.58
2139 2390 3.120923 CCATGACAATGAAAAACGCTTGC 60.121 43.478 0.00 0.00 35.67 4.01
2183 2434 0.753262 GCTGGTACCGATGTCCATCT 59.247 55.000 7.57 0.00 35.72 2.90
2199 2450 0.331278 ATCTTGGAACCATTCGGGCA 59.669 50.000 0.00 0.00 42.05 5.36
2223 2476 1.982395 CGGGTGGTCTGCTGGACTA 60.982 63.158 9.50 2.23 43.97 2.59
2226 2479 2.264124 GTGGTCTGCTGGACTACGA 58.736 57.895 9.95 0.00 44.23 3.43
2265 2518 1.986378 GTGCTGCTGTCTTACACGTAG 59.014 52.381 0.00 0.00 0.00 3.51
2280 2533 1.301165 GTAGCGTGGTCCACCGTTT 60.301 57.895 16.60 7.17 39.43 3.60
2291 2544 5.660463 TGGTCCACCGTTTCCTATAAGAGG 61.660 50.000 0.00 0.00 42.60 3.69
2343 2596 7.880105 AGAAAATGCAAAAGAGGTAAGAGAAG 58.120 34.615 0.00 0.00 0.00 2.85
2344 2597 6.581171 AAATGCAAAAGAGGTAAGAGAAGG 57.419 37.500 0.00 0.00 0.00 3.46
2345 2598 4.021102 TGCAAAAGAGGTAAGAGAAGGG 57.979 45.455 0.00 0.00 0.00 3.95
2347 2600 4.004314 GCAAAAGAGGTAAGAGAAGGGAC 58.996 47.826 0.00 0.00 0.00 4.46
2348 2601 4.580868 CAAAAGAGGTAAGAGAAGGGACC 58.419 47.826 0.00 0.00 0.00 4.46
2349 2602 3.562108 AAGAGGTAAGAGAAGGGACCA 57.438 47.619 0.00 0.00 34.18 4.02
2350 2603 3.108847 AGAGGTAAGAGAAGGGACCAG 57.891 52.381 0.00 0.00 34.18 4.00
2351 2604 2.655407 AGAGGTAAGAGAAGGGACCAGA 59.345 50.000 0.00 0.00 34.18 3.86
2352 2605 3.273618 AGAGGTAAGAGAAGGGACCAGAT 59.726 47.826 0.00 0.00 34.18 2.90
2353 2606 3.639561 GAGGTAAGAGAAGGGACCAGATC 59.360 52.174 0.00 0.00 34.18 2.75
2362 2615 2.620234 GGACCAGATCCCCACATGA 58.380 57.895 0.00 0.00 42.46 3.07
2363 2616 0.918983 GGACCAGATCCCCACATGAA 59.081 55.000 0.00 0.00 42.46 2.57
2364 2617 1.496429 GGACCAGATCCCCACATGAAT 59.504 52.381 0.00 0.00 42.46 2.57
2365 2618 2.579873 GACCAGATCCCCACATGAATG 58.420 52.381 0.00 0.00 0.00 2.67
2366 2619 2.173356 GACCAGATCCCCACATGAATGA 59.827 50.000 0.00 0.00 0.00 2.57
2367 2620 2.174210 ACCAGATCCCCACATGAATGAG 59.826 50.000 0.00 0.00 0.00 2.90
2368 2621 2.228059 CAGATCCCCACATGAATGAGC 58.772 52.381 0.00 0.00 0.00 4.26
2369 2622 1.202734 AGATCCCCACATGAATGAGCG 60.203 52.381 0.00 0.00 0.00 5.03
2370 2623 0.820891 ATCCCCACATGAATGAGCGC 60.821 55.000 0.00 0.00 0.00 5.92
2371 2624 1.452651 CCCCACATGAATGAGCGCT 60.453 57.895 11.27 11.27 0.00 5.92
2372 2625 1.033746 CCCCACATGAATGAGCGCTT 61.034 55.000 13.26 0.00 0.00 4.68
2373 2626 0.813184 CCCACATGAATGAGCGCTTT 59.187 50.000 13.26 1.49 0.00 3.51
2374 2627 1.203052 CCCACATGAATGAGCGCTTTT 59.797 47.619 13.26 9.06 0.00 2.27
2375 2628 2.256174 CCACATGAATGAGCGCTTTTG 58.744 47.619 13.26 1.36 0.00 2.44
2376 2629 2.095110 CCACATGAATGAGCGCTTTTGA 60.095 45.455 13.26 3.15 0.00 2.69
2377 2630 3.428452 CCACATGAATGAGCGCTTTTGAT 60.428 43.478 13.26 5.73 0.00 2.57
2378 2631 4.171005 CACATGAATGAGCGCTTTTGATT 58.829 39.130 13.26 8.00 0.00 2.57
2379 2632 4.031314 CACATGAATGAGCGCTTTTGATTG 59.969 41.667 13.26 9.02 0.00 2.67
2380 2633 2.598589 TGAATGAGCGCTTTTGATTGC 58.401 42.857 13.26 0.00 0.00 3.56
2381 2634 2.030096 TGAATGAGCGCTTTTGATTGCA 60.030 40.909 13.26 1.67 0.00 4.08
2382 2635 2.273370 ATGAGCGCTTTTGATTGCAG 57.727 45.000 13.26 0.00 0.00 4.41
2383 2636 0.387622 TGAGCGCTTTTGATTGCAGC 60.388 50.000 13.26 0.00 0.00 5.25
2384 2637 1.074872 GAGCGCTTTTGATTGCAGCC 61.075 55.000 13.26 0.00 32.38 4.85
2385 2638 2.438954 GCGCTTTTGATTGCAGCCG 61.439 57.895 0.00 0.00 0.00 5.52
2386 2639 2.438954 CGCTTTTGATTGCAGCCGC 61.439 57.895 0.00 0.00 39.24 6.53
2387 2640 2.438954 GCTTTTGATTGCAGCCGCG 61.439 57.895 0.00 0.00 42.97 6.46
2388 2641 2.430582 TTTTGATTGCAGCCGCGC 60.431 55.556 0.00 0.00 42.97 6.86
2389 2642 3.912820 TTTTGATTGCAGCCGCGCC 62.913 57.895 0.00 0.00 42.97 6.53
2396 2649 4.940593 GCAGCCGCGCCAACAAAA 62.941 61.111 0.00 0.00 0.00 2.44
2397 2650 3.029735 CAGCCGCGCCAACAAAAC 61.030 61.111 0.00 0.00 0.00 2.43
2398 2651 3.216292 AGCCGCGCCAACAAAACT 61.216 55.556 0.00 0.00 0.00 2.66
2399 2652 2.279186 GCCGCGCCAACAAAACTT 60.279 55.556 0.00 0.00 0.00 2.66
2400 2653 1.880796 GCCGCGCCAACAAAACTTT 60.881 52.632 0.00 0.00 0.00 2.66
2401 2654 0.595310 GCCGCGCCAACAAAACTTTA 60.595 50.000 0.00 0.00 0.00 1.85
2402 2655 1.933052 GCCGCGCCAACAAAACTTTAT 60.933 47.619 0.00 0.00 0.00 1.40
2403 2656 2.668834 GCCGCGCCAACAAAACTTTATA 60.669 45.455 0.00 0.00 0.00 0.98
2404 2657 3.765026 CCGCGCCAACAAAACTTTATAT 58.235 40.909 0.00 0.00 0.00 0.86
2405 2658 3.789224 CCGCGCCAACAAAACTTTATATC 59.211 43.478 0.00 0.00 0.00 1.63
2406 2659 4.438200 CCGCGCCAACAAAACTTTATATCT 60.438 41.667 0.00 0.00 0.00 1.98
2407 2660 5.092781 CGCGCCAACAAAACTTTATATCTT 58.907 37.500 0.00 0.00 0.00 2.40
2408 2661 5.571357 CGCGCCAACAAAACTTTATATCTTT 59.429 36.000 0.00 0.00 0.00 2.52
2409 2662 6.452350 CGCGCCAACAAAACTTTATATCTTTG 60.452 38.462 0.00 0.00 35.39 2.77
2410 2663 6.669741 GCGCCAACAAAACTTTATATCTTTGC 60.670 38.462 0.00 0.00 33.08 3.68
2411 2664 6.586082 CGCCAACAAAACTTTATATCTTTGCT 59.414 34.615 0.00 0.00 33.08 3.91
2412 2665 7.116233 CGCCAACAAAACTTTATATCTTTGCTT 59.884 33.333 0.00 0.00 33.08 3.91
2413 2666 8.773645 GCCAACAAAACTTTATATCTTTGCTTT 58.226 29.630 0.00 0.00 33.08 3.51
2434 2687 8.802267 TGCTTTTTCCTATATATACATTTGGGC 58.198 33.333 0.00 0.00 0.00 5.36
2435 2688 9.025041 GCTTTTTCCTATATATACATTTGGGCT 57.975 33.333 0.00 0.00 0.00 5.19
2495 3067 4.025015 ACTTGAATTGATGCATTCGAGC 57.975 40.909 12.90 0.00 40.34 5.03
2509 3081 2.273370 TCGAGCGGTTGTACTGATTC 57.727 50.000 1.01 0.00 0.00 2.52
2513 3085 3.326747 GAGCGGTTGTACTGATTCTGTT 58.673 45.455 1.28 0.00 0.00 3.16
2519 3091 7.040686 AGCGGTTGTACTGATTCTGTTATTTTT 60.041 33.333 1.28 0.00 0.00 1.94
2529 3101 8.870160 TGATTCTGTTATTTTTGTTGAACTGG 57.130 30.769 0.00 0.00 0.00 4.00
2598 3170 4.680237 CGTTCAGCCGGCCACTCA 62.680 66.667 26.15 0.00 0.00 3.41
2601 3173 2.818169 TTCAGCCGGCCACTCAAGT 61.818 57.895 26.15 0.00 0.00 3.16
2610 3182 1.442184 CCACTCAAGTCGTCGACCG 60.442 63.158 21.40 13.26 32.18 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 119 6.705381 TCGTTGACATGTATGCATCATCATTA 59.295 34.615 0.19 0.00 31.26 1.90
162 172 3.489355 TGCATGTCATTGGTTTGAGACT 58.511 40.909 0.00 0.00 32.41 3.24
358 369 3.507233 GCATCAAAGTGTTCCTTCATCCA 59.493 43.478 0.00 0.00 31.27 3.41
782 804 8.843262 TCATCATCATCATCCAACTTAATTGTC 58.157 33.333 0.00 0.00 36.47 3.18
834 871 0.615850 GGTGTAGGGCTTCTCTTGCT 59.384 55.000 0.00 0.00 0.00 3.91
886 923 1.547675 GGTCTTTCTTGCACCCATCCA 60.548 52.381 0.00 0.00 0.00 3.41
1047 1087 2.039624 GCCACCCTCCTCTCCTCA 59.960 66.667 0.00 0.00 0.00 3.86
1234 1274 1.250154 CCCATTGCACGAACCATGGT 61.250 55.000 13.00 13.00 0.00 3.55
1515 1650 2.107953 GTGCGAGGAGGCTCATCC 59.892 66.667 22.14 15.30 39.89 3.51
1550 1685 3.507233 GGTGTTGGCAAGATCTTCAATGA 59.493 43.478 4.57 0.00 0.00 2.57
1649 1784 1.380524 GTCCTCGTCCTCATCTTCGA 58.619 55.000 0.00 0.00 0.00 3.71
1961 2211 3.192230 CGCGCATCGGCTGGTTTA 61.192 61.111 8.75 0.00 38.10 2.01
2014 2265 3.442996 GAGCATCTACAACAGGCGT 57.557 52.632 0.00 0.00 0.00 5.68
2124 2375 1.270252 CCCAGGCAAGCGTTTTTCATT 60.270 47.619 0.00 0.00 0.00 2.57
2158 2409 2.687200 ATCGGTACCAGCCCTGCA 60.687 61.111 13.54 0.00 0.00 4.41
2183 2434 0.111446 TTCTGCCCGAATGGTTCCAA 59.889 50.000 0.00 0.00 36.04 3.53
2191 2442 4.489771 CCCGCCTTCTGCCCGAAT 62.490 66.667 0.00 0.00 36.24 3.34
2199 2450 4.021925 GCAGACCACCCGCCTTCT 62.022 66.667 0.00 0.00 0.00 2.85
2265 2518 2.438951 TAGGAAACGGTGGACCACGC 62.439 60.000 18.40 10.36 34.83 5.34
2291 2544 9.929722 TGTTATATGTCGTTTGATGCTTATTTC 57.070 29.630 0.00 0.00 0.00 2.17
2345 2598 2.173356 TCATTCATGTGGGGATCTGGTC 59.827 50.000 0.00 0.00 0.00 4.02
2347 2600 2.860009 CTCATTCATGTGGGGATCTGG 58.140 52.381 0.00 0.00 0.00 3.86
2348 2601 2.228059 GCTCATTCATGTGGGGATCTG 58.772 52.381 0.00 0.00 0.00 2.90
2349 2602 1.202734 CGCTCATTCATGTGGGGATCT 60.203 52.381 0.00 0.00 32.68 2.75
2350 2603 1.233019 CGCTCATTCATGTGGGGATC 58.767 55.000 0.00 0.00 32.68 3.36
2351 2604 0.820891 GCGCTCATTCATGTGGGGAT 60.821 55.000 0.00 0.00 35.57 3.85
2352 2605 1.451927 GCGCTCATTCATGTGGGGA 60.452 57.895 0.00 0.00 35.57 4.81
2353 2606 1.033746 AAGCGCTCATTCATGTGGGG 61.034 55.000 12.06 2.99 35.57 4.96
2354 2607 0.813184 AAAGCGCTCATTCATGTGGG 59.187 50.000 12.06 2.44 37.31 4.61
2355 2608 2.095110 TCAAAAGCGCTCATTCATGTGG 60.095 45.455 12.06 0.00 0.00 4.17
2356 2609 3.206034 TCAAAAGCGCTCATTCATGTG 57.794 42.857 12.06 0.00 0.00 3.21
2357 2610 4.171005 CAATCAAAAGCGCTCATTCATGT 58.829 39.130 12.06 0.00 0.00 3.21
2358 2611 3.000078 GCAATCAAAAGCGCTCATTCATG 60.000 43.478 12.06 8.11 0.00 3.07
2359 2612 3.184541 GCAATCAAAAGCGCTCATTCAT 58.815 40.909 12.06 0.00 0.00 2.57
2360 2613 2.030096 TGCAATCAAAAGCGCTCATTCA 60.030 40.909 12.06 0.00 0.00 2.57
2361 2614 2.597305 CTGCAATCAAAAGCGCTCATTC 59.403 45.455 12.06 0.00 0.00 2.67
2362 2615 2.602878 CTGCAATCAAAAGCGCTCATT 58.397 42.857 12.06 6.46 0.00 2.57
2363 2616 1.734707 GCTGCAATCAAAAGCGCTCAT 60.735 47.619 12.06 0.00 0.00 2.90
2364 2617 0.387622 GCTGCAATCAAAAGCGCTCA 60.388 50.000 12.06 0.00 0.00 4.26
2365 2618 1.074872 GGCTGCAATCAAAAGCGCTC 61.075 55.000 12.06 0.00 37.83 5.03
2366 2619 1.080298 GGCTGCAATCAAAAGCGCT 60.080 52.632 2.64 2.64 37.83 5.92
2367 2620 2.438954 CGGCTGCAATCAAAAGCGC 61.439 57.895 0.00 0.00 37.83 5.92
2368 2621 2.438954 GCGGCTGCAATCAAAAGCG 61.439 57.895 14.08 0.00 42.15 4.68
2369 2622 2.438954 CGCGGCTGCAATCAAAAGC 61.439 57.895 19.50 0.00 42.97 3.51
2370 2623 2.438954 GCGCGGCTGCAATCAAAAG 61.439 57.895 19.50 0.00 42.97 2.27
2371 2624 2.430582 GCGCGGCTGCAATCAAAA 60.431 55.556 19.50 0.00 42.97 2.44
2372 2625 4.418401 GGCGCGGCTGCAATCAAA 62.418 61.111 27.05 0.00 42.97 2.69
2379 2632 4.940593 TTTTGTTGGCGCGGCTGC 62.941 61.111 33.23 24.24 37.91 5.25
2380 2633 2.952291 AAGTTTTGTTGGCGCGGCTG 62.952 55.000 33.23 0.00 0.00 4.85
2381 2634 2.291457 AAAGTTTTGTTGGCGCGGCT 62.291 50.000 33.23 7.69 0.00 5.52
2382 2635 0.595310 TAAAGTTTTGTTGGCGCGGC 60.595 50.000 27.61 27.61 0.00 6.53
2383 2636 2.058913 ATAAAGTTTTGTTGGCGCGG 57.941 45.000 8.83 0.00 0.00 6.46
2384 2637 4.658071 AGATATAAAGTTTTGTTGGCGCG 58.342 39.130 0.00 0.00 0.00 6.86
2385 2638 6.669741 GCAAAGATATAAAGTTTTGTTGGCGC 60.670 38.462 0.00 0.00 34.04 6.53
2386 2639 6.586082 AGCAAAGATATAAAGTTTTGTTGGCG 59.414 34.615 0.00 0.00 34.04 5.69
2387 2640 7.889589 AGCAAAGATATAAAGTTTTGTTGGC 57.110 32.000 0.00 0.00 34.04 4.52
2408 2661 8.802267 GCCCAAATGTATATATAGGAAAAAGCA 58.198 33.333 0.00 0.00 0.00 3.91
2409 2662 9.025041 AGCCCAAATGTATATATAGGAAAAAGC 57.975 33.333 0.00 0.00 0.00 3.51
2421 2674 8.893727 GCGAAATAGAATAGCCCAAATGTATAT 58.106 33.333 0.00 0.00 0.00 0.86
2422 2675 7.064134 CGCGAAATAGAATAGCCCAAATGTATA 59.936 37.037 0.00 0.00 0.00 1.47
2423 2676 6.128282 CGCGAAATAGAATAGCCCAAATGTAT 60.128 38.462 0.00 0.00 0.00 2.29
2424 2677 5.178623 CGCGAAATAGAATAGCCCAAATGTA 59.821 40.000 0.00 0.00 0.00 2.29
2425 2678 4.024048 CGCGAAATAGAATAGCCCAAATGT 60.024 41.667 0.00 0.00 0.00 2.71
2426 2679 4.024048 ACGCGAAATAGAATAGCCCAAATG 60.024 41.667 15.93 0.00 0.00 2.32
2427 2680 4.134563 ACGCGAAATAGAATAGCCCAAAT 58.865 39.130 15.93 0.00 0.00 2.32
2428 2681 3.537580 ACGCGAAATAGAATAGCCCAAA 58.462 40.909 15.93 0.00 0.00 3.28
2429 2682 3.188159 ACGCGAAATAGAATAGCCCAA 57.812 42.857 15.93 0.00 0.00 4.12
2430 2683 2.902705 ACGCGAAATAGAATAGCCCA 57.097 45.000 15.93 0.00 0.00 5.36
2431 2684 4.053295 TGTTACGCGAAATAGAATAGCCC 58.947 43.478 15.93 0.00 0.00 5.19
2432 2685 4.980434 TCTGTTACGCGAAATAGAATAGCC 59.020 41.667 15.93 0.00 0.00 3.93
2433 2686 6.506464 TTCTGTTACGCGAAATAGAATAGC 57.494 37.500 15.93 0.00 33.34 2.97
2466 3038 7.255242 CGAATGCATCAATTCAAGTAGGGTAAT 60.255 37.037 0.00 0.00 36.52 1.89
2481 3053 0.447406 CAACCGCTCGAATGCATCAA 59.553 50.000 0.00 0.00 0.00 2.57
2495 3067 8.073768 ACAAAAATAACAGAATCAGTACAACCG 58.926 33.333 0.00 0.00 0.00 4.44
2509 3081 6.262601 ACGACCAGTTCAACAAAAATAACAG 58.737 36.000 0.00 0.00 0.00 3.16
2513 3085 6.687081 AAGACGACCAGTTCAACAAAAATA 57.313 33.333 0.00 0.00 0.00 1.40
2519 3091 7.789273 TTAATAAAAGACGACCAGTTCAACA 57.211 32.000 0.00 0.00 0.00 3.33
2610 3182 2.437359 ATCGGCCACAAGCAGCTC 60.437 61.111 2.24 0.00 46.50 4.09


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

AutoCloner maintained by Alex Coulton.