Multiple sequence alignment - TraesCS5A01G448300

Loading Multiple Alignment...

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 TraesCS5A01G448300 chr5A 100.000 2399 0 0 1 2399 629865525 629867923 0.000000e+00 4431
1 TraesCS5A01G448300 chr5A 92.105 950 57 12 1363 2300 516607171 516608114 0.000000e+00 1323
2 TraesCS5A01G448300 chr5A 95.975 795 31 1 3 796 692979160 692979954 0.000000e+00 1290
3 TraesCS5A01G448300 chr5A 93.523 880 29 3 797 1669 693958185 693959043 0.000000e+00 1284
4 TraesCS5A01G448300 chr5A 93.182 880 32 8 797 1669 692979988 692980846 0.000000e+00 1267
5 TraesCS5A01G448300 chr5A 94.444 612 28 5 1691 2300 692980841 692981448 0.000000e+00 937
6 TraesCS5A01G448300 chr5A 96.970 99 3 0 2300 2398 248691564 248691466 1.480000e-37 167
7 TraesCS5A01G448300 chr5A 96.970 99 3 0 2300 2398 335885199 335885101 1.480000e-37 167
8 TraesCS5A01G448300 chr4A 92.095 1518 80 15 797 2300 574766707 574765216 0.000000e+00 2102
9 TraesCS5A01G448300 chr4A 96.478 795 27 1 3 796 602465199 602464405 0.000000e+00 1312
10 TraesCS5A01G448300 chr4A 95.597 795 34 1 3 796 218050746 218051540 0.000000e+00 1273
11 TraesCS5A01G448300 chr2B 91.470 1524 109 12 797 2304 622029997 622028479 0.000000e+00 2074
12 TraesCS5A01G448300 chr2B 95.696 883 34 4 1425 2304 760346597 760345716 0.000000e+00 1417
13 TraesCS5A01G448300 chr2B 96.604 795 25 2 3 796 435353365 435352572 0.000000e+00 1317
14 TraesCS5A01G448300 chr6A 91.634 1518 90 15 797 2300 394643325 394644819 0.000000e+00 2065
15 TraesCS5A01G448300 chr3A 91.579 1520 83 19 797 2301 224969043 224970532 0.000000e+00 2056
16 TraesCS5A01G448300 chr6B 96.368 881 25 4 1425 2300 101192030 101192908 0.000000e+00 1443
17 TraesCS5A01G448300 chr6B 96.359 879 28 4 1425 2301 423139267 423138391 0.000000e+00 1443
18 TraesCS5A01G448300 chr6B 96.352 795 28 1 3 796 617028522 617029316 0.000000e+00 1306
19 TraesCS5A01G448300 chr6B 95.094 795 38 1 3 796 399208562 399207768 0.000000e+00 1251
20 TraesCS5A01G448300 chr6B 92.449 874 30 6 797 1669 399207734 399206896 0.000000e+00 1216
21 TraesCS5A01G448300 chr6B 92.105 114 8 1 2286 2398 371478417 371478304 2.470000e-35 159
22 TraesCS5A01G448300 chr7A 95.687 881 33 3 1425 2301 14527341 14526462 0.000000e+00 1411
23 TraesCS5A01G448300 chr1B 95.723 795 33 1 3 796 651732063 651731269 0.000000e+00 1279
24 TraesCS5A01G448300 chr1B 95.597 795 32 2 3 796 17134699 17135491 0.000000e+00 1271
25 TraesCS5A01G448300 chr1B 96.016 728 24 5 1576 2300 637283646 637282921 0.000000e+00 1179
26 TraesCS5A01G448300 chr1B 94.575 682 35 2 797 1477 637284330 637283650 0.000000e+00 1053
27 TraesCS5A01G448300 chr5B 95.483 797 32 3 3 796 576501386 576502181 0.000000e+00 1269
28 TraesCS5A01G448300 chr4B 95.374 735 27 6 1576 2307 11347197 11346467 0.000000e+00 1162
29 TraesCS5A01G448300 chr4B 94.838 678 32 3 797 1473 11347880 11347205 0.000000e+00 1055
30 TraesCS5A01G448300 chr4B 96.651 627 19 2 1425 2051 21166283 21166907 0.000000e+00 1040
31 TraesCS5A01G448300 chr4D 96.970 99 3 0 2300 2398 210993584 210993682 1.480000e-37 167
32 TraesCS5A01G448300 chr4D 96.000 100 4 0 2299 2398 252720810 252720711 1.910000e-36 163
33 TraesCS5A01G448300 chr7D 96.040 101 4 0 2299 2399 450514449 450514549 5.310000e-37 165
34 TraesCS5A01G448300 chr1D 96.939 98 3 0 2300 2397 403602477 403602574 5.310000e-37 165
35 TraesCS5A01G448300 chr6D 96.000 100 4 0 2300 2399 187584079 187583980 1.910000e-36 163
36 TraesCS5A01G448300 chr5D 96.000 100 4 0 2300 2399 308369662 308369761 1.910000e-36 163


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 TraesCS5A01G448300 chr5A 629865525 629867923 2398 False 4431.000000 4431 100.000000 1 2399 1 chr5A.!!$F2 2398
1 TraesCS5A01G448300 chr5A 516607171 516608114 943 False 1323.000000 1323 92.105000 1363 2300 1 chr5A.!!$F1 937
2 TraesCS5A01G448300 chr5A 693958185 693959043 858 False 1284.000000 1284 93.523000 797 1669 1 chr5A.!!$F3 872
3 TraesCS5A01G448300 chr5A 692979160 692981448 2288 False 1164.666667 1290 94.533667 3 2300 3 chr5A.!!$F4 2297
4 TraesCS5A01G448300 chr4A 574765216 574766707 1491 True 2102.000000 2102 92.095000 797 2300 1 chr4A.!!$R1 1503
5 TraesCS5A01G448300 chr4A 602464405 602465199 794 True 1312.000000 1312 96.478000 3 796 1 chr4A.!!$R2 793
6 TraesCS5A01G448300 chr4A 218050746 218051540 794 False 1273.000000 1273 95.597000 3 796 1 chr4A.!!$F1 793
7 TraesCS5A01G448300 chr2B 622028479 622029997 1518 True 2074.000000 2074 91.470000 797 2304 1 chr2B.!!$R2 1507
8 TraesCS5A01G448300 chr2B 760345716 760346597 881 True 1417.000000 1417 95.696000 1425 2304 1 chr2B.!!$R3 879
9 TraesCS5A01G448300 chr2B 435352572 435353365 793 True 1317.000000 1317 96.604000 3 796 1 chr2B.!!$R1 793
10 TraesCS5A01G448300 chr6A 394643325 394644819 1494 False 2065.000000 2065 91.634000 797 2300 1 chr6A.!!$F1 1503
11 TraesCS5A01G448300 chr3A 224969043 224970532 1489 False 2056.000000 2056 91.579000 797 2301 1 chr3A.!!$F1 1504
12 TraesCS5A01G448300 chr6B 101192030 101192908 878 False 1443.000000 1443 96.368000 1425 2300 1 chr6B.!!$F1 875
13 TraesCS5A01G448300 chr6B 423138391 423139267 876 True 1443.000000 1443 96.359000 1425 2301 1 chr6B.!!$R2 876
14 TraesCS5A01G448300 chr6B 617028522 617029316 794 False 1306.000000 1306 96.352000 3 796 1 chr6B.!!$F2 793
15 TraesCS5A01G448300 chr6B 399206896 399208562 1666 True 1233.500000 1251 93.771500 3 1669 2 chr6B.!!$R3 1666
16 TraesCS5A01G448300 chr7A 14526462 14527341 879 True 1411.000000 1411 95.687000 1425 2301 1 chr7A.!!$R1 876
17 TraesCS5A01G448300 chr1B 651731269 651732063 794 True 1279.000000 1279 95.723000 3 796 1 chr1B.!!$R1 793
18 TraesCS5A01G448300 chr1B 17134699 17135491 792 False 1271.000000 1271 95.597000 3 796 1 chr1B.!!$F1 793
19 TraesCS5A01G448300 chr1B 637282921 637284330 1409 True 1116.000000 1179 95.295500 797 2300 2 chr1B.!!$R2 1503
20 TraesCS5A01G448300 chr5B 576501386 576502181 795 False 1269.000000 1269 95.483000 3 796 1 chr5B.!!$F1 793
21 TraesCS5A01G448300 chr4B 11346467 11347880 1413 True 1108.500000 1162 95.106000 797 2307 2 chr4B.!!$R1 1510
22 TraesCS5A01G448300 chr4B 21166283 21166907 624 False 1040.000000 1040 96.651000 1425 2051 1 chr4B.!!$F1 626

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
142 145 3.255149 TCGTAAGGGTGAAGAGTTGACTC 59.745 47.826 2.93 2.93 39.87 3.36 F
1144 1190 1.548269 AGTCGAGCTCCAAGAAGAAGG 59.452 52.381 8.47 0.00 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 1330 0.60813 ACAACTGATACTCTGCGGCA 59.392 50.0 1.29 1.29 0.0 5.69 R
2339 2461 0.61326 TGGTGTGGATCCCGAAGAAG 59.387 55.0 9.90 0.00 0.0 2.85 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
98 101 9.829507 ATTGTTTCTTATTGTTCCATTTTGTCA 57.170 25.926 0.00 0.00 0.00 3.58
109 112 8.503458 TGTTCCATTTTGTCATGAACAATTTT 57.497 26.923 0.00 0.00 46.94 1.82
142 145 3.255149 TCGTAAGGGTGAAGAGTTGACTC 59.745 47.826 2.93 2.93 39.87 3.36
143 146 6.099004 TCGTAAGGGTGAAGAGTTGACTCG 62.099 50.000 5.56 0.00 42.70 4.18
373 377 7.972623 TGTTTTGTTATAGTTTGTTTGTCCG 57.027 32.000 0.00 0.00 0.00 4.79
380 384 3.277142 AGTTTGTTTGTCCGAGTCCTT 57.723 42.857 0.00 0.00 0.00 3.36
414 418 8.005192 TGCATTGCATATTCATTTTGGTACTA 57.995 30.769 7.38 0.00 31.71 1.82
593 597 9.553064 GTGGAGAAACTCTGTCATTTCATATAT 57.447 33.333 0.00 0.00 37.30 0.86
700 704 6.748198 CCTGAAACGTACTACATTCTTCTCTC 59.252 42.308 0.00 0.00 0.00 3.20
730 734 5.710099 TGTTCCCATTTAAGCTAAACAGAGG 59.290 40.000 0.00 0.00 0.00 3.69
790 794 6.458232 TTGTTGTGTATGCTTACCTGTTTT 57.542 33.333 7.25 0.00 0.00 2.43
889 930 9.863650 ACTAGTTAATTAGTAGCATGGAGACTA 57.136 33.333 8.76 0.00 33.73 2.59
970 1011 4.761739 AGAACCAACTACAATGACATGTGG 59.238 41.667 1.15 0.00 37.75 4.17
992 1035 7.175990 TGTGGGTACATCTTTCTTTAAATGTCC 59.824 37.037 0.00 0.00 0.00 4.02
1060 1103 3.385755 AGAACCAAAGAATGTTGCTGCTT 59.614 39.130 0.00 0.00 0.00 3.91
1077 1120 4.365723 CTGCTTTTGTTGCTGACATTCTT 58.634 39.130 0.00 0.00 38.26 2.52
1120 1163 4.634199 CACATTCCTTCAAAATGTTGGCT 58.366 39.130 0.00 0.00 43.08 4.75
1144 1190 1.548269 AGTCGAGCTCCAAGAAGAAGG 59.452 52.381 8.47 0.00 0.00 3.46
1272 1318 5.279708 GGTCAAGAAGAAATCAGAGGAGACA 60.280 44.000 0.00 0.00 0.00 3.41
1284 1330 1.005630 GGAGACAGAAGCTGCACGT 60.006 57.895 1.02 0.00 34.37 4.49
1337 1404 3.480133 GGCCACCGATGCTAGGGT 61.480 66.667 0.00 0.00 36.87 4.34
1340 1407 1.819632 CCACCGATGCTAGGGTTGC 60.820 63.158 0.00 0.00 33.23 4.17
1420 1508 1.206578 GACGTGGTTGATGTTGGCG 59.793 57.895 0.00 0.00 0.00 5.69
2305 2427 7.380536 TGACCGTATTTCTTGTAGTGTATGTT 58.619 34.615 0.00 0.00 0.00 2.71
2306 2428 7.329962 TGACCGTATTTCTTGTAGTGTATGTTG 59.670 37.037 0.00 0.00 0.00 3.33
2307 2429 6.592607 ACCGTATTTCTTGTAGTGTATGTTGG 59.407 38.462 0.00 0.00 0.00 3.77
2308 2430 6.456449 CCGTATTTCTTGTAGTGTATGTTGGC 60.456 42.308 0.00 0.00 0.00 4.52
2309 2431 5.545658 ATTTCTTGTAGTGTATGTTGGCG 57.454 39.130 0.00 0.00 0.00 5.69
2310 2432 2.967362 TCTTGTAGTGTATGTTGGCGG 58.033 47.619 0.00 0.00 0.00 6.13
2311 2433 2.563620 TCTTGTAGTGTATGTTGGCGGA 59.436 45.455 0.00 0.00 0.00 5.54
2312 2434 2.665649 TGTAGTGTATGTTGGCGGAG 57.334 50.000 0.00 0.00 0.00 4.63
2313 2435 1.897133 TGTAGTGTATGTTGGCGGAGT 59.103 47.619 0.00 0.00 0.00 3.85
2314 2436 2.094390 TGTAGTGTATGTTGGCGGAGTC 60.094 50.000 0.00 0.00 0.00 3.36
2315 2437 0.973632 AGTGTATGTTGGCGGAGTCA 59.026 50.000 0.00 0.00 45.30 3.41
2322 2444 4.128580 TGGCGGAGTCATCCTCAA 57.871 55.556 0.00 0.00 36.97 3.02
2323 2445 1.900351 TGGCGGAGTCATCCTCAAG 59.100 57.895 0.00 0.00 36.97 3.02
2324 2446 0.614697 TGGCGGAGTCATCCTCAAGA 60.615 55.000 0.00 0.00 36.97 3.02
2325 2447 0.537188 GGCGGAGTCATCCTCAAGAA 59.463 55.000 0.00 0.00 44.22 2.52
2326 2448 1.646189 GCGGAGTCATCCTCAAGAAC 58.354 55.000 0.00 0.00 44.22 3.01
2327 2449 1.205893 GCGGAGTCATCCTCAAGAACT 59.794 52.381 0.00 0.00 44.22 3.01
2328 2450 2.737039 GCGGAGTCATCCTCAAGAACTC 60.737 54.545 0.00 0.00 44.22 3.01
2329 2451 2.757868 CGGAGTCATCCTCAAGAACTCT 59.242 50.000 0.00 0.00 44.22 3.24
2330 2452 3.181491 CGGAGTCATCCTCAAGAACTCTC 60.181 52.174 0.00 0.00 44.22 3.20
2331 2453 4.023291 GGAGTCATCCTCAAGAACTCTCT 58.977 47.826 0.00 0.00 42.94 3.10
2332 2454 5.197451 GGAGTCATCCTCAAGAACTCTCTA 58.803 45.833 0.00 0.00 42.94 2.43
2333 2455 5.299279 GGAGTCATCCTCAAGAACTCTCTAG 59.701 48.000 0.00 0.00 42.94 2.43
2334 2456 5.826643 AGTCATCCTCAAGAACTCTCTAGT 58.173 41.667 0.00 0.00 37.65 2.57
2335 2457 6.377146 GAGTCATCCTCAAGAACTCTCTAGTT 59.623 42.308 0.00 0.00 43.14 2.24
2347 2469 5.890424 ACTCTCTAGTTCTTCTTCTTCGG 57.110 43.478 0.00 0.00 29.00 4.30
2348 2470 4.703093 ACTCTCTAGTTCTTCTTCTTCGGG 59.297 45.833 0.00 0.00 29.00 5.14
2349 2471 4.919793 TCTCTAGTTCTTCTTCTTCGGGA 58.080 43.478 0.00 0.00 0.00 5.14
2350 2472 5.511363 TCTCTAGTTCTTCTTCTTCGGGAT 58.489 41.667 0.00 0.00 0.00 3.85
2351 2473 5.591067 TCTCTAGTTCTTCTTCTTCGGGATC 59.409 44.000 0.00 0.00 0.00 3.36
2352 2474 3.897141 AGTTCTTCTTCTTCGGGATCC 57.103 47.619 1.92 1.92 0.00 3.36
2353 2475 3.173965 AGTTCTTCTTCTTCGGGATCCA 58.826 45.455 15.23 0.00 0.00 3.41
2354 2476 3.055747 AGTTCTTCTTCTTCGGGATCCAC 60.056 47.826 15.23 1.85 0.00 4.02
2355 2477 2.536066 TCTTCTTCTTCGGGATCCACA 58.464 47.619 15.23 0.00 0.00 4.17
2356 2478 2.233922 TCTTCTTCTTCGGGATCCACAC 59.766 50.000 15.23 0.00 0.00 3.82
2357 2479 0.902531 TCTTCTTCGGGATCCACACC 59.097 55.000 15.23 0.00 0.00 4.16
2358 2480 0.613260 CTTCTTCGGGATCCACACCA 59.387 55.000 15.23 0.00 0.00 4.17
2359 2481 1.210478 CTTCTTCGGGATCCACACCAT 59.790 52.381 15.23 0.00 0.00 3.55
2360 2482 0.830648 TCTTCGGGATCCACACCATC 59.169 55.000 15.23 0.00 0.00 3.51
2361 2483 0.833287 CTTCGGGATCCACACCATCT 59.167 55.000 15.23 0.00 0.00 2.90
2362 2484 1.210478 CTTCGGGATCCACACCATCTT 59.790 52.381 15.23 0.00 0.00 2.40
2363 2485 1.285280 TCGGGATCCACACCATCTTT 58.715 50.000 15.23 0.00 0.00 2.52
2364 2486 2.473070 TCGGGATCCACACCATCTTTA 58.527 47.619 15.23 0.00 0.00 1.85
2365 2487 3.045634 TCGGGATCCACACCATCTTTAT 58.954 45.455 15.23 0.00 0.00 1.40
2366 2488 4.228010 TCGGGATCCACACCATCTTTATA 58.772 43.478 15.23 0.00 0.00 0.98
2367 2489 4.283467 TCGGGATCCACACCATCTTTATAG 59.717 45.833 15.23 0.00 0.00 1.31
2368 2490 4.563580 CGGGATCCACACCATCTTTATAGG 60.564 50.000 15.23 0.00 0.00 2.57
2369 2491 4.597507 GGGATCCACACCATCTTTATAGGA 59.402 45.833 15.23 0.00 0.00 2.94
2370 2492 5.073144 GGGATCCACACCATCTTTATAGGAA 59.927 44.000 15.23 0.00 0.00 3.36
2371 2493 6.240292 GGGATCCACACCATCTTTATAGGAAT 60.240 42.308 15.23 0.00 0.00 3.01
2372 2494 6.881602 GGATCCACACCATCTTTATAGGAATC 59.118 42.308 6.95 0.00 0.00 2.52
2373 2495 6.187727 TCCACACCATCTTTATAGGAATCC 57.812 41.667 0.00 0.00 0.00 3.01
2374 2496 4.997395 CCACACCATCTTTATAGGAATCCG 59.003 45.833 0.00 0.00 0.00 4.18
2375 2497 5.454755 CCACACCATCTTTATAGGAATCCGT 60.455 44.000 0.00 0.00 0.00 4.69
2376 2498 5.466728 CACACCATCTTTATAGGAATCCGTG 59.533 44.000 0.00 0.00 0.00 4.94
2377 2499 4.997395 CACCATCTTTATAGGAATCCGTGG 59.003 45.833 0.00 0.00 0.00 4.94
2378 2500 4.905456 ACCATCTTTATAGGAATCCGTGGA 59.095 41.667 0.00 0.00 0.00 4.02
2379 2501 5.012148 ACCATCTTTATAGGAATCCGTGGAG 59.988 44.000 0.00 0.00 0.00 3.86
2380 2502 5.012148 CCATCTTTATAGGAATCCGTGGAGT 59.988 44.000 0.00 0.00 0.00 3.85
2381 2503 6.464465 CCATCTTTATAGGAATCCGTGGAGTT 60.464 42.308 0.00 0.00 0.00 3.01
2382 2504 5.914033 TCTTTATAGGAATCCGTGGAGTTG 58.086 41.667 0.00 0.00 0.00 3.16
2383 2505 5.424252 TCTTTATAGGAATCCGTGGAGTTGT 59.576 40.000 0.00 0.00 0.00 3.32
2384 2506 6.608405 TCTTTATAGGAATCCGTGGAGTTGTA 59.392 38.462 0.00 0.00 0.00 2.41
2385 2507 4.939052 ATAGGAATCCGTGGAGTTGTAG 57.061 45.455 0.00 0.00 0.00 2.74
2386 2508 2.537143 AGGAATCCGTGGAGTTGTAGT 58.463 47.619 0.00 0.00 0.00 2.73
2387 2509 2.496470 AGGAATCCGTGGAGTTGTAGTC 59.504 50.000 0.00 0.00 0.00 2.59
2388 2510 2.527100 GAATCCGTGGAGTTGTAGTCG 58.473 52.381 0.00 0.00 0.00 4.18
2389 2511 1.542492 ATCCGTGGAGTTGTAGTCGT 58.458 50.000 0.00 0.00 0.00 4.34
2390 2512 2.183478 TCCGTGGAGTTGTAGTCGTA 57.817 50.000 0.00 0.00 0.00 3.43
2391 2513 1.806542 TCCGTGGAGTTGTAGTCGTAC 59.193 52.381 0.00 0.00 0.00 3.67
2392 2514 1.808945 CCGTGGAGTTGTAGTCGTACT 59.191 52.381 0.00 0.00 0.00 2.73
2393 2515 2.227388 CCGTGGAGTTGTAGTCGTACTT 59.773 50.000 0.00 0.00 0.00 2.24
2394 2516 3.231965 CGTGGAGTTGTAGTCGTACTTG 58.768 50.000 0.00 0.00 0.00 3.16
2395 2517 3.058708 CGTGGAGTTGTAGTCGTACTTGA 60.059 47.826 0.00 0.00 0.00 3.02
2396 2518 4.379186 CGTGGAGTTGTAGTCGTACTTGAT 60.379 45.833 0.00 0.00 0.00 2.57
2397 2519 4.857588 GTGGAGTTGTAGTCGTACTTGATG 59.142 45.833 0.00 0.00 0.00 3.07
2398 2520 4.521639 TGGAGTTGTAGTCGTACTTGATGT 59.478 41.667 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.795681 GCATGCACATGGGAAATGTACG 60.796 50.000 14.21 0.00 39.16 3.67
1 2 2.428171 AGCATGCACATGGGAAATGTAC 59.572 45.455 21.98 0.00 39.16 2.90
98 101 6.431234 ACGAGCCTCTTTCTAAAATTGTTCAT 59.569 34.615 0.00 0.00 0.00 2.57
109 112 2.758979 CACCCTTACGAGCCTCTTTCTA 59.241 50.000 0.00 0.00 0.00 2.10
371 375 2.293122 TGCAATGAAACAAAGGACTCGG 59.707 45.455 0.00 0.00 0.00 4.63
373 377 4.151157 GCAATGCAATGAAACAAAGGACTC 59.849 41.667 5.79 0.00 0.00 3.36
380 384 7.851387 ATGAATATGCAATGCAATGAAACAA 57.149 28.000 13.45 0.00 43.62 2.83
414 418 3.947196 TGCCTGAATATTGTCGCATTTCT 59.053 39.130 0.00 0.00 0.00 2.52
484 488 8.869897 CATACAACGCTCTCTCTTAATTAACAA 58.130 33.333 0.00 0.00 0.00 2.83
593 597 8.733458 CAAGTCCTAAACATTTCATTCAGATCA 58.267 33.333 0.00 0.00 0.00 2.92
671 675 4.219944 AGAATGTAGTACGTTTCAGGAGCA 59.780 41.667 9.11 0.00 0.00 4.26
760 764 6.717540 AGGTAAGCATACACAACAAACCATTA 59.282 34.615 1.01 0.00 33.45 1.90
898 939 8.012241 GCAAACTACTCAAGAATGTTGACTAAG 58.988 37.037 0.00 0.00 0.00 2.18
946 987 5.937540 CCACATGTCATTGTAGTTGGTTCTA 59.062 40.000 0.00 0.00 0.00 2.10
970 1011 6.677187 GCCGGACATTTAAAGAAAGATGTACC 60.677 42.308 5.05 0.00 33.21 3.34
992 1035 0.883833 AGCTTTTTCCATGTCAGCCG 59.116 50.000 0.00 0.00 0.00 5.52
1060 1103 8.445275 TCTTTAGTAAGAATGTCAGCAACAAA 57.555 30.769 0.00 0.00 37.14 2.83
1077 1120 4.081087 GTGCTGGAGGGACATTCTTTAGTA 60.081 45.833 0.00 0.00 36.25 1.82
1144 1190 2.836262 AGCAGCTGCAGATCTATTGAC 58.164 47.619 38.24 6.24 45.16 3.18
1284 1330 0.608130 ACAACTGATACTCTGCGGCA 59.392 50.000 1.29 1.29 0.00 5.69
1420 1508 4.918810 ACTCAACATCAAAAGTCCCAAC 57.081 40.909 0.00 0.00 0.00 3.77
1678 1778 8.792633 CAGTCAACCAATACAGGAGAATAAAAA 58.207 33.333 0.00 0.00 0.00 1.94
1734 1842 1.202348 GTCCAGCCAATAACCAACAGC 59.798 52.381 0.00 0.00 0.00 4.40
2139 2256 1.337118 TTTTGTCATGGCCACCCTTC 58.663 50.000 8.16 0.00 0.00 3.46
2301 2423 4.963878 GGATGACTCCGCCAACAT 57.036 55.556 0.00 0.00 0.00 2.71
2308 2430 6.148064 TAGAGAGTTCTTGAGGATGACTCCG 61.148 48.000 0.00 0.00 39.54 4.63
2309 2431 4.023291 AGAGAGTTCTTGAGGATGACTCC 58.977 47.826 0.00 0.00 46.01 3.85
2310 2432 5.885912 ACTAGAGAGTTCTTGAGGATGACTC 59.114 44.000 0.00 0.00 39.54 3.36
2311 2433 5.826643 ACTAGAGAGTTCTTGAGGATGACT 58.173 41.667 0.00 0.00 34.79 3.41
2312 2434 6.524101 AACTAGAGAGTTCTTGAGGATGAC 57.476 41.667 0.00 0.00 42.50 3.06
2325 2447 4.703093 CCCGAAGAAGAAGAACTAGAGAGT 59.297 45.833 0.00 0.00 37.59 3.24
2326 2448 4.944930 TCCCGAAGAAGAAGAACTAGAGAG 59.055 45.833 0.00 0.00 0.00 3.20
2327 2449 4.919793 TCCCGAAGAAGAAGAACTAGAGA 58.080 43.478 0.00 0.00 0.00 3.10
2328 2450 5.221165 GGATCCCGAAGAAGAAGAACTAGAG 60.221 48.000 0.00 0.00 0.00 2.43
2329 2451 4.645588 GGATCCCGAAGAAGAAGAACTAGA 59.354 45.833 0.00 0.00 0.00 2.43
2330 2452 4.402793 TGGATCCCGAAGAAGAAGAACTAG 59.597 45.833 9.90 0.00 0.00 2.57
2331 2453 4.159879 GTGGATCCCGAAGAAGAAGAACTA 59.840 45.833 9.90 0.00 0.00 2.24
2332 2454 3.055747 GTGGATCCCGAAGAAGAAGAACT 60.056 47.826 9.90 0.00 0.00 3.01
2333 2455 3.263261 GTGGATCCCGAAGAAGAAGAAC 58.737 50.000 9.90 0.00 0.00 3.01
2334 2456 2.903784 TGTGGATCCCGAAGAAGAAGAA 59.096 45.455 9.90 0.00 0.00 2.52
2335 2457 2.233922 GTGTGGATCCCGAAGAAGAAGA 59.766 50.000 9.90 0.00 0.00 2.87
2336 2458 2.622436 GTGTGGATCCCGAAGAAGAAG 58.378 52.381 9.90 0.00 0.00 2.85
2337 2459 1.278127 GGTGTGGATCCCGAAGAAGAA 59.722 52.381 9.90 0.00 0.00 2.52
2338 2460 0.902531 GGTGTGGATCCCGAAGAAGA 59.097 55.000 9.90 0.00 0.00 2.87
2339 2461 0.613260 TGGTGTGGATCCCGAAGAAG 59.387 55.000 9.90 0.00 0.00 2.85
2340 2462 1.209504 GATGGTGTGGATCCCGAAGAA 59.790 52.381 9.90 0.00 0.00 2.52
2341 2463 0.830648 GATGGTGTGGATCCCGAAGA 59.169 55.000 9.90 0.00 0.00 2.87
2342 2464 0.833287 AGATGGTGTGGATCCCGAAG 59.167 55.000 9.90 0.00 0.00 3.79
2343 2465 1.285280 AAGATGGTGTGGATCCCGAA 58.715 50.000 9.90 0.00 0.00 4.30
2344 2466 1.285280 AAAGATGGTGTGGATCCCGA 58.715 50.000 9.90 0.00 0.00 5.14
2345 2467 3.492102 ATAAAGATGGTGTGGATCCCG 57.508 47.619 9.90 0.00 0.00 5.14
2346 2468 4.597507 TCCTATAAAGATGGTGTGGATCCC 59.402 45.833 9.90 0.85 0.00 3.85
2347 2469 5.825593 TCCTATAAAGATGGTGTGGATCC 57.174 43.478 4.20 4.20 0.00 3.36
2348 2470 6.881602 GGATTCCTATAAAGATGGTGTGGATC 59.118 42.308 0.00 0.00 0.00 3.36
2349 2471 6.520742 CGGATTCCTATAAAGATGGTGTGGAT 60.521 42.308 0.30 0.00 0.00 3.41
2350 2472 5.221641 CGGATTCCTATAAAGATGGTGTGGA 60.222 44.000 0.30 0.00 0.00 4.02
2351 2473 4.997395 CGGATTCCTATAAAGATGGTGTGG 59.003 45.833 0.30 0.00 0.00 4.17
2352 2474 5.466728 CACGGATTCCTATAAAGATGGTGTG 59.533 44.000 0.30 0.00 0.00 3.82
2353 2475 5.454755 CCACGGATTCCTATAAAGATGGTGT 60.455 44.000 0.30 0.00 0.00 4.16
2354 2476 4.997395 CCACGGATTCCTATAAAGATGGTG 59.003 45.833 0.30 0.00 0.00 4.17
2355 2477 4.905456 TCCACGGATTCCTATAAAGATGGT 59.095 41.667 0.30 0.00 0.00 3.55
2356 2478 5.012148 ACTCCACGGATTCCTATAAAGATGG 59.988 44.000 0.30 0.00 0.00 3.51
2357 2479 6.102897 ACTCCACGGATTCCTATAAAGATG 57.897 41.667 0.30 0.00 0.00 2.90
2358 2480 6.099845 ACAACTCCACGGATTCCTATAAAGAT 59.900 38.462 0.30 0.00 0.00 2.40
2359 2481 5.424252 ACAACTCCACGGATTCCTATAAAGA 59.576 40.000 0.30 0.00 0.00 2.52
2360 2482 5.671493 ACAACTCCACGGATTCCTATAAAG 58.329 41.667 0.30 0.00 0.00 1.85
2361 2483 5.687166 ACAACTCCACGGATTCCTATAAA 57.313 39.130 0.30 0.00 0.00 1.40
2362 2484 5.895534 ACTACAACTCCACGGATTCCTATAA 59.104 40.000 0.30 0.00 0.00 0.98
2363 2485 5.452255 ACTACAACTCCACGGATTCCTATA 58.548 41.667 0.30 0.00 0.00 1.31
2364 2486 4.287552 ACTACAACTCCACGGATTCCTAT 58.712 43.478 0.30 0.00 0.00 2.57
2365 2487 3.698040 GACTACAACTCCACGGATTCCTA 59.302 47.826 0.30 0.00 0.00 2.94
2366 2488 2.496470 GACTACAACTCCACGGATTCCT 59.504 50.000 0.30 0.00 0.00 3.36
2367 2489 2.734492 CGACTACAACTCCACGGATTCC 60.734 54.545 0.00 0.00 0.00 3.01
2368 2490 2.094854 ACGACTACAACTCCACGGATTC 60.095 50.000 0.00 0.00 0.00 2.52
2369 2491 1.891150 ACGACTACAACTCCACGGATT 59.109 47.619 0.00 0.00 0.00 3.01
2370 2492 1.542492 ACGACTACAACTCCACGGAT 58.458 50.000 0.00 0.00 0.00 4.18
2371 2493 1.806542 GTACGACTACAACTCCACGGA 59.193 52.381 0.00 0.00 0.00 4.69
2372 2494 1.808945 AGTACGACTACAACTCCACGG 59.191 52.381 0.00 0.00 0.00 4.94
2373 2495 3.058708 TCAAGTACGACTACAACTCCACG 60.059 47.826 0.00 0.00 0.00 4.94
2374 2496 4.494350 TCAAGTACGACTACAACTCCAC 57.506 45.455 0.00 0.00 0.00 4.02
2375 2497 4.521639 ACATCAAGTACGACTACAACTCCA 59.478 41.667 0.00 0.00 0.00 3.86
2376 2498 5.056894 ACATCAAGTACGACTACAACTCC 57.943 43.478 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.