Multiple sequence alignment - TraesCS2D01G235400

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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 TraesCS2D01G235400 chr2D 100.000 2483 0 0 1 2483 220967971 220970453 0.000000e+00 4586
1 TraesCS2D01G235400 chr2D 90.373 322 25 5 1458 1773 373896537 373896858 3.820000e-113 418
2 TraesCS2D01G235400 chr2B 95.887 1799 60 4 654 2438 291608719 291610517 0.000000e+00 2900
3 TraesCS2D01G235400 chr2B 92.743 689 28 4 1 668 291602635 291603322 0.000000e+00 976
4 TraesCS2D01G235400 chr2A 92.797 708 29 9 1 687 240468586 240469292 0.000000e+00 1005
5 TraesCS2D01G235400 chr7A 91.875 320 21 4 1458 1772 503428825 503428506 2.270000e-120 442
6 TraesCS2D01G235400 chr7B 91.250 320 22 6 1458 1772 446166208 446166526 4.910000e-117 431
7 TraesCS2D01G235400 chr4D 90.909 319 24 5 1458 1772 304305052 304304735 8.210000e-115 424
8 TraesCS2D01G235400 chr1A 90.030 331 28 4 1456 1781 208893884 208894214 8.210000e-115 424
9 TraesCS2D01G235400 chr7D 90.625 320 24 5 1458 1772 428731822 428732140 1.060000e-113 420
10 TraesCS2D01G235400 chr1B 89.458 332 29 5 1456 1781 231648816 231648485 4.940000e-112 414
11 TraesCS2D01G235400 chr1D 89.426 331 30 4 1456 1781 150941770 150941440 1.780000e-111 412


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 TraesCS2D01G235400 chr2D 220967971 220970453 2482 False 4586 4586 100.000 1 2483 1 chr2D.!!$F1 2482
1 TraesCS2D01G235400 chr2B 291608719 291610517 1798 False 2900 2900 95.887 654 2438 1 chr2B.!!$F2 1784
2 TraesCS2D01G235400 chr2B 291602635 291603322 687 False 976 976 92.743 1 668 1 chr2B.!!$F1 667
3 TraesCS2D01G235400 chr2A 240468586 240469292 706 False 1005 1005 92.797 1 687 1 chr2A.!!$F1 686

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
577 599 0.033894 GGGTCTCTCTCTTCCGAGGT 60.034 60.0 0.0 0.0 37.86 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2453 2488 0.112606 TCCTCGGTCTCTGTTGAGGT 59.887 55.0 6.98 0.0 46.48 3.85 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
154 155 4.269183 CAACCCATGGACTAAGTAATGCA 58.731 43.478 15.22 0.00 0.00 3.96
165 166 4.813235 TAATGCAGCACCCGCCCC 62.813 66.667 0.00 0.00 39.83 5.80
193 194 3.624410 CCATCATGAATGAAGCTGAACGA 59.376 43.478 0.00 0.00 40.69 3.85
373 390 4.196626 TCCGTTTCGTCAGTTATTGGAT 57.803 40.909 0.00 0.00 0.00 3.41
437 454 5.354234 CAGTTTCACCTGTTGTCACTAGTTT 59.646 40.000 0.00 0.00 0.00 2.66
438 455 6.537301 CAGTTTCACCTGTTGTCACTAGTTTA 59.463 38.462 0.00 0.00 0.00 2.01
439 456 6.537660 AGTTTCACCTGTTGTCACTAGTTTAC 59.462 38.462 0.00 0.00 0.00 2.01
440 457 4.952460 TCACCTGTTGTCACTAGTTTACC 58.048 43.478 0.00 0.00 0.00 2.85
441 458 3.739300 CACCTGTTGTCACTAGTTTACCG 59.261 47.826 0.00 0.00 0.00 4.02
444 461 5.068987 ACCTGTTGTCACTAGTTTACCGTAA 59.931 40.000 0.00 0.00 0.00 3.18
452 474 6.476706 GTCACTAGTTTACCGTAACACTTGTT 59.523 38.462 0.00 0.00 41.73 2.83
458 480 6.476706 AGTTTACCGTAACACTTGTTGAGTAC 59.523 38.462 4.82 0.00 38.90 2.73
464 486 3.679824 ACACTTGTTGAGTACCTAGCC 57.320 47.619 0.00 0.00 36.65 3.93
522 544 8.457261 GTTAGCCATTCATTGATCATTATCCTC 58.543 37.037 0.00 0.00 0.00 3.71
523 545 6.791371 AGCCATTCATTGATCATTATCCTCT 58.209 36.000 0.00 0.00 0.00 3.69
577 599 0.033894 GGGTCTCTCTCTTCCGAGGT 60.034 60.000 0.00 0.00 37.86 3.85
627 649 7.040478 TCGTTTTCCATTTCTCATGATTTCACT 60.040 33.333 0.00 0.00 0.00 3.41
641 663 8.939929 TCATGATTTCACTGATCTGAGTAAAAC 58.060 33.333 6.60 3.82 0.00 2.43
758 780 4.821589 CTCCCTTCTCGCGGTGGC 62.822 72.222 6.13 0.00 0.00 5.01
774 796 2.322081 GGCGGCGTTTCTGTTGCTA 61.322 57.895 9.37 0.00 0.00 3.49
782 804 1.135689 GTTTCTGTTGCTATGGTGGCG 60.136 52.381 0.00 0.00 0.00 5.69
806 828 1.278637 GCGGCGGTGATTTATTCGG 59.721 57.895 9.78 0.00 0.00 4.30
944 966 2.125633 GGCTCCGTCGGGTTTCTC 60.126 66.667 12.29 0.00 33.83 2.87
988 1010 3.571828 CCTCTTCGGCTCATCTAAGATCA 59.428 47.826 0.00 0.00 0.00 2.92
993 1015 4.461198 TCGGCTCATCTAAGATCAGTACA 58.539 43.478 0.00 0.00 0.00 2.90
994 1016 4.517075 TCGGCTCATCTAAGATCAGTACAG 59.483 45.833 0.00 0.00 0.00 2.74
997 1019 4.560513 GCTCATCTAAGATCAGTACAGGGC 60.561 50.000 0.00 0.00 0.00 5.19
1053 1075 3.795639 CAGAGTTGTATGCAGAGATCACG 59.204 47.826 0.00 0.00 0.00 4.35
1073 1095 5.030295 CACGGATAATCATCAAGCAACAAC 58.970 41.667 0.00 0.00 32.32 3.32
1074 1096 4.699735 ACGGATAATCATCAAGCAACAACA 59.300 37.500 0.00 0.00 32.32 3.33
1083 1105 2.293122 TCAAGCAACAACAAAGATCCGG 59.707 45.455 0.00 0.00 0.00 5.14
1123 1145 5.907207 TCAAGACAGATGTTGGAGCTATAC 58.093 41.667 0.00 0.00 30.04 1.47
1127 1149 5.068460 AGACAGATGTTGGAGCTATACAGAC 59.932 44.000 0.00 0.00 0.00 3.51
1183 1205 0.169009 GCAATCCGCAGTTCAAGACC 59.831 55.000 0.00 0.00 41.79 3.85
1252 1274 2.034104 TGAACCATCAGATCAGCTGC 57.966 50.000 9.47 0.00 44.52 5.25
1276 1298 3.081804 GGATCCCAAACACAACCTGTAG 58.918 50.000 0.00 0.00 30.51 2.74
1278 1300 3.655615 TCCCAAACACAACCTGTAGTT 57.344 42.857 0.00 0.00 40.16 2.24
1297 1319 1.527034 TCAACCATCAGCTGAGCAAC 58.473 50.000 22.96 0.00 0.00 4.17
1315 1337 2.514205 ACAGCAACAACAAATGCCTC 57.486 45.000 0.00 0.00 43.57 4.70
1316 1338 1.069049 ACAGCAACAACAAATGCCTCC 59.931 47.619 0.00 0.00 43.57 4.30
1336 1358 5.246981 TCCAGTGAATCAAAGGACTGAAT 57.753 39.130 0.00 0.00 38.49 2.57
1394 1416 5.484715 CACTTGGCAAATTGGATTTCTGAT 58.515 37.500 0.00 0.00 0.00 2.90
1485 1507 1.912731 TGTAAGTGGATTGCCTAGCCA 59.087 47.619 0.00 0.00 34.31 4.75
1489 1511 2.659428 AGTGGATTGCCTAGCCATTTC 58.341 47.619 0.00 0.00 33.66 2.17
1496 1518 1.565759 TGCCTAGCCATTTCCATCAGT 59.434 47.619 0.00 0.00 0.00 3.41
1499 1521 3.889815 CCTAGCCATTTCCATCAGTTCA 58.110 45.455 0.00 0.00 0.00 3.18
1516 1538 3.942748 AGTTCAGACTTTTGGTTGCGTTA 59.057 39.130 0.00 0.00 29.87 3.18
1561 1583 3.307762 GGTATCAGAGCCAGGTTTTGAGT 60.308 47.826 2.84 0.00 0.00 3.41
1562 1584 2.260844 TCAGAGCCAGGTTTTGAGTG 57.739 50.000 0.00 0.00 0.00 3.51
1577 1599 0.877743 GAGTGCAAGTCCTGGCTTTC 59.122 55.000 0.00 0.00 0.00 2.62
1656 1678 4.586841 AGCCATACCTCTGAGACTATTCAC 59.413 45.833 6.17 0.00 0.00 3.18
1669 1691 3.660865 ACTATTCACGTGTTGACTTCCC 58.339 45.455 16.51 0.00 32.26 3.97
1679 1701 2.028484 GACTTCCCGCGTCACACA 59.972 61.111 4.92 0.00 0.00 3.72
1683 1705 1.354337 CTTCCCGCGTCACACATGAG 61.354 60.000 4.92 0.00 34.75 2.90
1694 1716 1.149101 ACACATGAGAGGGGGTGTTT 58.851 50.000 0.00 0.00 41.36 2.83
1729 1752 3.893813 GGATTGCTTAGCCCTTTCATCAT 59.106 43.478 0.29 0.00 0.00 2.45
1730 1753 5.072741 GGATTGCTTAGCCCTTTCATCATA 58.927 41.667 0.29 0.00 0.00 2.15
1736 1759 3.409026 AGCCCTTTCATCATATCGGAC 57.591 47.619 0.00 0.00 0.00 4.79
1839 1862 6.362283 GGACACAGTTTTTAATTTCCATCACG 59.638 38.462 0.00 0.00 0.00 4.35
1860 1883 5.183140 CACGAAAGGACCTTGTATGGATTTT 59.817 40.000 7.72 0.00 0.00 1.82
1864 1887 5.117406 AGGACCTTGTATGGATTTTCCTC 57.883 43.478 0.00 0.00 37.46 3.71
1944 1967 1.210478 GGCTGGCACTCCTGAAGAATA 59.790 52.381 0.00 0.00 33.56 1.75
1997 2020 2.133742 CTTTGTGGGGCAAGCAGACG 62.134 60.000 0.00 0.00 38.47 4.18
2001 2024 3.357079 GGGGCAAGCAGACGTGTG 61.357 66.667 8.61 8.61 0.00 3.82
2057 2080 5.841810 TCACATGGGAAAAATTCTGTGAAC 58.158 37.500 0.00 0.00 38.57 3.18
2120 2143 9.950680 AACTGACTGTTAATTTATGTGAAACAG 57.049 29.630 11.63 11.63 44.21 3.16
2165 2190 0.723981 GCCGCATCTGAAACTGACTC 59.276 55.000 0.00 0.00 0.00 3.36
2294 2329 3.054802 CCTCTCAGGCCAGTCAGTTTAAT 60.055 47.826 5.01 0.00 0.00 1.40
2300 2335 5.183140 TCAGGCCAGTCAGTTTAATTAAAGC 59.817 40.000 10.92 8.80 0.00 3.51
2358 2393 4.444733 CCCCCAAAGAAAATTGTTTCAGCT 60.445 41.667 2.35 0.00 44.82 4.24
2392 2427 5.652452 AGTAAACCAGCTTGAAACAACTTCT 59.348 36.000 0.00 0.00 34.86 2.85
2447 2482 1.729586 AGGCAACCTGAACTCCTACA 58.270 50.000 0.00 0.00 29.57 2.74
2448 2483 1.625818 AGGCAACCTGAACTCCTACAG 59.374 52.381 0.00 0.00 29.57 2.74
2449 2484 1.348036 GGCAACCTGAACTCCTACAGT 59.652 52.381 0.00 0.00 36.64 3.55
2450 2485 2.565834 GGCAACCTGAACTCCTACAGTA 59.434 50.000 0.00 0.00 32.30 2.74
2451 2486 3.007614 GGCAACCTGAACTCCTACAGTAA 59.992 47.826 0.00 0.00 32.30 2.24
2452 2487 4.323562 GGCAACCTGAACTCCTACAGTAAT 60.324 45.833 0.00 0.00 32.30 1.89
2453 2488 5.105064 GGCAACCTGAACTCCTACAGTAATA 60.105 44.000 0.00 0.00 32.30 0.98
2454 2489 5.811100 GCAACCTGAACTCCTACAGTAATAC 59.189 44.000 0.00 0.00 32.30 1.89
2455 2490 6.338937 CAACCTGAACTCCTACAGTAATACC 58.661 44.000 0.00 0.00 32.30 2.73
2456 2491 5.840081 ACCTGAACTCCTACAGTAATACCT 58.160 41.667 0.00 0.00 32.30 3.08
2457 2492 5.892686 ACCTGAACTCCTACAGTAATACCTC 59.107 44.000 0.00 0.00 32.30 3.85
2458 2493 5.892119 CCTGAACTCCTACAGTAATACCTCA 59.108 44.000 0.00 0.00 32.30 3.86
2459 2494 6.380274 CCTGAACTCCTACAGTAATACCTCAA 59.620 42.308 0.00 0.00 32.30 3.02
2460 2495 7.166691 TGAACTCCTACAGTAATACCTCAAC 57.833 40.000 0.00 0.00 32.30 3.18
2461 2496 6.722590 TGAACTCCTACAGTAATACCTCAACA 59.277 38.462 0.00 0.00 32.30 3.33
2462 2497 6.777213 ACTCCTACAGTAATACCTCAACAG 57.223 41.667 0.00 0.00 31.37 3.16
2463 2498 6.491383 ACTCCTACAGTAATACCTCAACAGA 58.509 40.000 0.00 0.00 31.37 3.41
2464 2499 6.603997 ACTCCTACAGTAATACCTCAACAGAG 59.396 42.308 0.00 0.00 31.37 3.35
2465 2500 6.728411 TCCTACAGTAATACCTCAACAGAGA 58.272 40.000 0.00 0.00 0.00 3.10
2466 2501 6.602406 TCCTACAGTAATACCTCAACAGAGAC 59.398 42.308 0.00 0.00 0.00 3.36
2467 2502 5.662674 ACAGTAATACCTCAACAGAGACC 57.337 43.478 0.00 0.00 0.00 3.85
2468 2503 4.158025 ACAGTAATACCTCAACAGAGACCG 59.842 45.833 0.00 0.00 0.00 4.79
2469 2504 4.398358 CAGTAATACCTCAACAGAGACCGA 59.602 45.833 0.00 0.00 0.00 4.69
2470 2505 4.641094 AGTAATACCTCAACAGAGACCGAG 59.359 45.833 0.00 0.00 0.00 4.63
2472 2507 0.112606 ACCTCAACAGAGACCGAGGA 59.887 55.000 11.12 0.00 46.71 3.71
2473 2508 1.257743 CCTCAACAGAGACCGAGGAA 58.742 55.000 0.00 0.00 46.71 3.36
2474 2509 1.618837 CCTCAACAGAGACCGAGGAAA 59.381 52.381 0.00 0.00 46.71 3.13
2475 2510 2.610727 CCTCAACAGAGACCGAGGAAAC 60.611 54.545 0.00 0.00 46.71 2.78
2476 2511 4.874459 CCTCAACAGAGACCGAGGAAACT 61.874 52.174 0.00 0.00 46.71 2.66
2477 2512 2.698797 TCAACAGAGACCGAGGAAACTT 59.301 45.455 0.00 0.00 44.43 2.66
2478 2513 2.802816 CAACAGAGACCGAGGAAACTTG 59.197 50.000 0.00 0.00 44.43 3.16
2479 2514 2.317040 ACAGAGACCGAGGAAACTTGA 58.683 47.619 0.00 0.00 45.46 3.02
2480 2515 2.698797 ACAGAGACCGAGGAAACTTGAA 59.301 45.455 0.00 0.00 45.46 2.69
2481 2516 3.243907 ACAGAGACCGAGGAAACTTGAAG 60.244 47.826 0.00 0.00 45.46 3.02
2482 2517 2.966516 AGAGACCGAGGAAACTTGAAGT 59.033 45.455 0.00 0.00 45.46 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 166 3.132289 AGCTTCATTCATGATGGCTTTGG 59.868 43.478 0.00 0.00 40.61 3.28
373 390 1.811558 GCCTTGCGATCATCTTGGCTA 60.812 52.381 0.00 0.00 36.32 3.93
437 454 4.584325 AGGTACTCAACAAGTGTTACGGTA 59.416 41.667 0.00 0.00 39.11 4.02
438 455 3.385755 AGGTACTCAACAAGTGTTACGGT 59.614 43.478 0.00 0.00 39.11 4.83
439 456 3.986277 AGGTACTCAACAAGTGTTACGG 58.014 45.455 0.00 0.00 39.11 4.02
440 457 4.620184 GCTAGGTACTCAACAAGTGTTACG 59.380 45.833 0.00 0.00 41.75 3.18
441 458 4.928020 GGCTAGGTACTCAACAAGTGTTAC 59.072 45.833 0.00 0.00 41.75 2.50
444 461 2.302157 GGGCTAGGTACTCAACAAGTGT 59.698 50.000 0.00 0.00 41.75 3.55
452 474 0.041238 ACTGCTGGGCTAGGTACTCA 59.959 55.000 0.00 0.00 41.75 3.41
458 480 3.429547 CGCTTATATACTGCTGGGCTAGG 60.430 52.174 0.00 0.00 0.00 3.02
464 486 2.612972 CCCCACGCTTATATACTGCTGG 60.613 54.545 12.90 12.90 0.00 4.85
577 599 7.333423 CGAAAGTGAAATTGTATCTAGGGTTCA 59.667 37.037 0.00 0.00 0.00 3.18
627 649 5.627735 GCAGATCCCTGTTTTACTCAGATCA 60.628 44.000 0.00 0.00 42.35 2.92
641 663 2.734755 TACCATTTGGCAGATCCCTG 57.265 50.000 0.00 0.00 43.22 4.45
758 780 0.096976 CCATAGCAACAGAAACGCCG 59.903 55.000 0.00 0.00 0.00 6.46
793 815 4.693566 TGTTCTGTGTCCGAATAAATCACC 59.306 41.667 0.00 0.00 0.00 4.02
800 822 1.403647 CGCCTGTTCTGTGTCCGAATA 60.404 52.381 0.00 0.00 0.00 1.75
806 828 2.031163 AGCCGCCTGTTCTGTGTC 59.969 61.111 0.00 0.00 0.00 3.67
853 875 5.013599 AGGATAGAGCATGGGATTTTACCTC 59.986 44.000 0.00 0.00 0.00 3.85
929 951 1.154073 GTCGAGAAACCCGACGGAG 60.154 63.158 17.49 8.21 45.23 4.63
944 966 6.091437 AGGAATTTTACACTAGAACTCGTCG 58.909 40.000 0.00 0.00 0.00 5.12
988 1010 1.191535 TGCTTCATACGCCCTGTACT 58.808 50.000 0.00 0.00 35.44 2.73
993 1015 0.745845 CAGCTTGCTTCATACGCCCT 60.746 55.000 0.00 0.00 0.00 5.19
994 1016 1.723870 CAGCTTGCTTCATACGCCC 59.276 57.895 0.00 0.00 0.00 6.13
997 1019 1.083806 TCCGCAGCTTGCTTCATACG 61.084 55.000 6.58 0.00 42.25 3.06
1053 1075 7.315142 TCTTTGTTGTTGCTTGATGATTATCC 58.685 34.615 0.00 0.00 32.09 2.59
1073 1095 4.720649 TCTAACTCAGACCGGATCTTTG 57.279 45.455 9.46 5.13 34.41 2.77
1074 1096 7.419711 TTTATCTAACTCAGACCGGATCTTT 57.580 36.000 9.46 1.76 34.41 2.52
1083 1105 9.862371 TCTGTCTTGATTTTATCTAACTCAGAC 57.138 33.333 0.00 0.00 35.62 3.51
1123 1145 5.102313 TGTGAGATATACTTGTTGCGTCTG 58.898 41.667 0.00 0.00 0.00 3.51
1127 1149 5.807520 ACTTCTGTGAGATATACTTGTTGCG 59.192 40.000 0.00 0.00 0.00 4.85
1183 1205 5.048921 ACATGATCTGCAGTTGTTGAGAAAG 60.049 40.000 14.67 0.00 0.00 2.62
1252 1274 1.203050 AGGTTGTGTTTGGGATCCTGG 60.203 52.381 12.58 0.00 0.00 4.45
1276 1298 1.527034 TGCTCAGCTGATGGTTGAAC 58.473 50.000 18.63 0.46 34.86 3.18
1278 1300 1.202794 TGTTGCTCAGCTGATGGTTGA 60.203 47.619 18.63 0.00 34.14 3.18
1297 1319 1.068895 TGGAGGCATTTGTTGTTGCTG 59.931 47.619 0.00 0.00 38.88 4.41
1303 1325 3.256383 TGATTCACTGGAGGCATTTGTTG 59.744 43.478 0.00 0.00 0.00 3.33
1315 1337 5.251764 AGATTCAGTCCTTTGATTCACTGG 58.748 41.667 0.00 0.90 37.46 4.00
1316 1338 6.171921 AGAGATTCAGTCCTTTGATTCACTG 58.828 40.000 0.00 0.00 38.09 3.66
1336 1358 7.555965 TCATTGGATAATTTCTGACGAAGAGA 58.444 34.615 0.00 0.00 35.91 3.10
1485 1507 5.835280 ACCAAAAGTCTGAACTGATGGAAAT 59.165 36.000 13.68 0.00 41.39 2.17
1489 1511 4.794003 GCAACCAAAAGTCTGAACTGATGG 60.794 45.833 7.83 7.83 43.11 3.51
1496 1518 3.242936 GCTAACGCAACCAAAAGTCTGAA 60.243 43.478 0.00 0.00 35.78 3.02
1499 1521 2.572290 AGCTAACGCAACCAAAAGTCT 58.428 42.857 0.00 0.00 39.10 3.24
1516 1538 3.942829 TGTTAAGCTTCATGCACTAGCT 58.057 40.909 0.00 11.98 46.63 3.32
1561 1583 4.063529 CGAAAGCCAGGACTTGCA 57.936 55.556 0.00 0.00 0.00 4.08
1656 1678 2.654912 GACGCGGGAAGTCAACACG 61.655 63.158 12.47 0.00 38.42 4.49
1669 1691 1.807165 CCCTCTCATGTGTGACGCG 60.807 63.158 3.53 3.53 0.00 6.01
1679 1701 2.986728 ACACTTAAACACCCCCTCTCAT 59.013 45.455 0.00 0.00 0.00 2.90
1683 1705 3.775261 TGTACACTTAAACACCCCCTC 57.225 47.619 0.00 0.00 0.00 4.30
1694 1716 5.584649 GCTAAGCAATCCACATGTACACTTA 59.415 40.000 0.00 0.00 0.00 2.24
1729 1752 2.172851 ACGCAACCAAAAGTCCGATA 57.827 45.000 0.00 0.00 0.00 2.92
1730 1753 1.001815 CAACGCAACCAAAAGTCCGAT 60.002 47.619 0.00 0.00 0.00 4.18
1736 1759 1.336755 ACTAGCCAACGCAACCAAAAG 59.663 47.619 0.00 0.00 37.52 2.27
1839 1862 5.952347 AGGAAAATCCATACAAGGTCCTTTC 59.048 40.000 0.00 0.00 39.61 2.62
1860 1883 1.137594 ATCCCCCACCAAAACGAGGA 61.138 55.000 0.00 0.00 0.00 3.71
1864 1887 2.028876 GGATTATCCCCCACCAAAACG 58.971 52.381 0.00 0.00 0.00 3.60
1997 2020 1.298859 CCTGAACGCCTAAGCCACAC 61.299 60.000 0.00 0.00 34.57 3.82
2001 2024 2.824489 GGCCTGAACGCCTAAGCC 60.824 66.667 0.00 0.00 46.10 4.35
2057 2080 9.775854 AGATCCTGAATAACTATGAATCACTTG 57.224 33.333 0.00 0.00 0.00 3.16
2120 2143 4.453478 TGTGAGAAATTGACATCAGCAGTC 59.547 41.667 0.00 0.00 36.55 3.51
2165 2190 4.082625 TGCCATTACATCTTCAAACAGCAG 60.083 41.667 0.00 0.00 0.00 4.24
2294 2329 4.462483 CCCTTGCTAACCAATGAGCTTTAA 59.538 41.667 0.00 0.00 39.54 1.52
2300 2335 3.071874 TGTCCCTTGCTAACCAATGAG 57.928 47.619 0.00 0.00 31.91 2.90
2331 2366 4.639078 AACAATTTTCTTTGGGGGATGG 57.361 40.909 0.00 0.00 0.00 3.51
2374 2409 7.084486 GGTTTATAGAAGTTGTTTCAAGCTGG 58.916 38.462 0.00 0.00 38.31 4.85
2392 2427 3.073678 CAGTGTGCTGTGCTGGTTTATA 58.926 45.455 0.00 0.00 37.92 0.98
2434 2469 5.892119 TGAGGTATTACTGTAGGAGTTCAGG 59.108 44.000 0.00 0.00 35.96 3.86
2436 2471 6.722590 TGTTGAGGTATTACTGTAGGAGTTCA 59.277 38.462 0.00 0.00 35.96 3.18
2437 2472 7.122353 TCTGTTGAGGTATTACTGTAGGAGTTC 59.878 40.741 0.00 0.00 35.96 3.01
2438 2473 6.952358 TCTGTTGAGGTATTACTGTAGGAGTT 59.048 38.462 0.00 0.00 35.96 3.01
2439 2474 6.491383 TCTGTTGAGGTATTACTGTAGGAGT 58.509 40.000 0.00 0.00 38.88 3.85
2440 2475 6.829298 TCTCTGTTGAGGTATTACTGTAGGAG 59.171 42.308 0.00 0.00 40.58 3.69
2441 2476 6.602406 GTCTCTGTTGAGGTATTACTGTAGGA 59.398 42.308 0.00 0.00 40.58 2.94
2442 2477 6.183360 GGTCTCTGTTGAGGTATTACTGTAGG 60.183 46.154 0.00 0.00 40.58 3.18
2443 2478 6.458478 CGGTCTCTGTTGAGGTATTACTGTAG 60.458 46.154 0.00 0.00 40.58 2.74
2444 2479 5.356190 CGGTCTCTGTTGAGGTATTACTGTA 59.644 44.000 0.00 0.00 40.58 2.74
2445 2480 4.158025 CGGTCTCTGTTGAGGTATTACTGT 59.842 45.833 0.00 0.00 40.58 3.55
2446 2481 4.398358 TCGGTCTCTGTTGAGGTATTACTG 59.602 45.833 0.00 0.00 40.58 2.74
2447 2482 4.597004 TCGGTCTCTGTTGAGGTATTACT 58.403 43.478 0.00 0.00 40.58 2.24
2448 2483 4.202030 CCTCGGTCTCTGTTGAGGTATTAC 60.202 50.000 0.00 0.00 42.45 1.89
2449 2484 3.952323 CCTCGGTCTCTGTTGAGGTATTA 59.048 47.826 0.00 0.00 42.45 0.98
2450 2485 2.761208 CCTCGGTCTCTGTTGAGGTATT 59.239 50.000 0.00 0.00 42.45 1.89
2451 2486 2.025226 TCCTCGGTCTCTGTTGAGGTAT 60.025 50.000 6.98 0.00 46.48 2.73
2452 2487 1.353358 TCCTCGGTCTCTGTTGAGGTA 59.647 52.381 6.98 0.00 46.48 3.08
2453 2488 0.112606 TCCTCGGTCTCTGTTGAGGT 59.887 55.000 6.98 0.00 46.48 3.85
2455 2490 2.297597 AGTTTCCTCGGTCTCTGTTGAG 59.702 50.000 0.00 0.00 41.51 3.02
2456 2491 2.317040 AGTTTCCTCGGTCTCTGTTGA 58.683 47.619 0.00 0.00 0.00 3.18
2457 2492 2.802816 CAAGTTTCCTCGGTCTCTGTTG 59.197 50.000 0.00 0.00 0.00 3.33
2458 2493 2.698797 TCAAGTTTCCTCGGTCTCTGTT 59.301 45.455 0.00 0.00 0.00 3.16
2459 2494 2.317040 TCAAGTTTCCTCGGTCTCTGT 58.683 47.619 0.00 0.00 0.00 3.41
2460 2495 3.243907 ACTTCAAGTTTCCTCGGTCTCTG 60.244 47.826 0.00 0.00 0.00 3.35
2461 2496 2.966516 ACTTCAAGTTTCCTCGGTCTCT 59.033 45.455 0.00 0.00 0.00 3.10
2462 2497 3.388345 ACTTCAAGTTTCCTCGGTCTC 57.612 47.619 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.