Multiple sequence alignment - TraesCS2D01G225600

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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 TraesCS2D01G225600 chr2D 100.000 2579 0 0 1 2579 193337496 193340074 0.000000e+00 4763
1 TraesCS2D01G225600 chr2D 87.712 236 24 5 451 684 37219735 37219503 1.180000e-68 270
2 TraesCS2D01G225600 chr2B 89.730 2444 160 43 1 2401 249457038 249459433 0.000000e+00 3038
3 TraesCS2D01G225600 chr2B 80.115 523 82 16 174 676 363772369 363772889 1.130000e-98 370
4 TraesCS2D01G225600 chr2A 87.688 1933 142 45 681 2547 207487487 207489389 0.000000e+00 2163
5 TraesCS2D01G225600 chr2A 82.353 629 83 11 61 662 765574507 765573880 2.940000e-144 521
6 TraesCS2D01G225600 chr5D 82.226 647 81 21 58 675 318867302 318867943 6.320000e-146 527
7 TraesCS2D01G225600 chr5D 76.292 658 100 31 63 678 548674560 548675203 1.500000e-77 300
8 TraesCS2D01G225600 chr1D 82.059 641 85 15 50 662 306222257 306222895 1.060000e-143 520
9 TraesCS2D01G225600 chr3D 82.222 630 85 13 59 662 601003827 601004455 3.800000e-143 518
10 TraesCS2D01G225600 chr3D 78.947 646 103 18 62 677 463682144 463681502 2.390000e-110 409
11 TraesCS2D01G225600 chr4B 82.229 619 82 16 61 653 64076372 64076988 2.290000e-140 508
12 TraesCS2D01G225600 chr1A 81.567 651 89 16 61 684 572682271 572681625 2.290000e-140 508
13 TraesCS2D01G225600 chr3A 80.960 646 94 13 61 678 111881168 111880524 3.860000e-133 484
14 TraesCS2D01G225600 chr7A 80.186 646 99 14 45 663 287892204 287892847 8.410000e-125 457
15 TraesCS2D01G225600 chr7A 87.288 236 29 1 445 680 6799483 6799717 4.230000e-68 268
16 TraesCS2D01G225600 chr7B 79.231 650 92 27 64 681 608187067 608187705 1.850000e-111 412
17 TraesCS2D01G225600 chr1B 79.623 584 85 22 131 684 352332517 352331938 3.110000e-104 388
18 TraesCS2D01G225600 chr7D 88.312 231 25 2 445 675 127762243 127762471 2.530000e-70 276


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 TraesCS2D01G225600 chr2D 193337496 193340074 2578 False 4763 4763 100.000 1 2579 1 chr2D.!!$F1 2578
1 TraesCS2D01G225600 chr2B 249457038 249459433 2395 False 3038 3038 89.730 1 2401 1 chr2B.!!$F1 2400
2 TraesCS2D01G225600 chr2B 363772369 363772889 520 False 370 370 80.115 174 676 1 chr2B.!!$F2 502
3 TraesCS2D01G225600 chr2A 207487487 207489389 1902 False 2163 2163 87.688 681 2547 1 chr2A.!!$F1 1866
4 TraesCS2D01G225600 chr2A 765573880 765574507 627 True 521 521 82.353 61 662 1 chr2A.!!$R1 601
5 TraesCS2D01G225600 chr5D 318867302 318867943 641 False 527 527 82.226 58 675 1 chr5D.!!$F1 617
6 TraesCS2D01G225600 chr5D 548674560 548675203 643 False 300 300 76.292 63 678 1 chr5D.!!$F2 615
7 TraesCS2D01G225600 chr1D 306222257 306222895 638 False 520 520 82.059 50 662 1 chr1D.!!$F1 612
8 TraesCS2D01G225600 chr3D 601003827 601004455 628 False 518 518 82.222 59 662 1 chr3D.!!$F1 603
9 TraesCS2D01G225600 chr3D 463681502 463682144 642 True 409 409 78.947 62 677 1 chr3D.!!$R1 615
10 TraesCS2D01G225600 chr4B 64076372 64076988 616 False 508 508 82.229 61 653 1 chr4B.!!$F1 592
11 TraesCS2D01G225600 chr1A 572681625 572682271 646 True 508 508 81.567 61 684 1 chr1A.!!$R1 623
12 TraesCS2D01G225600 chr3A 111880524 111881168 644 True 484 484 80.960 61 678 1 chr3A.!!$R1 617
13 TraesCS2D01G225600 chr7A 287892204 287892847 643 False 457 457 80.186 45 663 1 chr7A.!!$F2 618
14 TraesCS2D01G225600 chr7B 608187067 608187705 638 False 412 412 79.231 64 681 1 chr7B.!!$F1 617
15 TraesCS2D01G225600 chr1B 352331938 352332517 579 True 388 388 79.623 131 684 1 chr1B.!!$R1 553

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
931 990 1.032794 AGATCCTAATCGACGCAGCA 58.967 50.0 0.0 0.0 36.97 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2527 2687 0.036388 ATACGACAAGTGCCCTGTGG 60.036 55.0 0.0 0.0 0.0 4.17 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
25 26 5.863397 GCATTTCGGTGATCAAATCAAAAGA 59.137 36.000 0.00 0.00 41.69 2.52
28 29 7.692908 TTTCGGTGATCAAATCAAAAGAAAC 57.307 32.000 0.00 0.00 41.69 2.78
153 157 3.327404 CCTTAGGGCCACGGTGGT 61.327 66.667 26.86 11.22 40.46 4.16
210 217 4.638421 TCTGTTTCAATTGTTCCTTCACGT 59.362 37.500 5.13 0.00 0.00 4.49
243 250 4.082463 GGTTTGTGTGTTGTTCAGGAAGAA 60.082 41.667 0.00 0.00 0.00 2.52
252 259 2.218603 GTTCAGGAAGAAAAGACGGCA 58.781 47.619 0.00 0.00 38.13 5.69
300 309 3.631046 CTCGCCTAGCCCCATCCC 61.631 72.222 0.00 0.00 0.00 3.85
304 313 2.529744 GCCTAGCCCCATCCCGATT 61.530 63.158 0.00 0.00 0.00 3.34
318 327 3.562182 TCCCGATTGTGAGTCTAGCATA 58.438 45.455 0.00 0.00 0.00 3.14
443 489 7.242322 TCCTTCTGATCTACGCTATCTACTA 57.758 40.000 0.00 0.00 0.00 1.82
495 541 5.391736 CGACTTTCCGACTGTCTACTACAAT 60.392 44.000 6.21 0.00 37.74 2.71
635 681 5.227908 CCTAGTGTTCGTTGTACTGTCATT 58.772 41.667 0.00 0.00 0.00 2.57
670 716 7.764443 TGAATAGATCGGAAGTTTCTCGAAAAT 59.236 33.333 8.67 0.00 34.99 1.82
723 769 3.625313 GCTCTCCTTCAGTTTTAGGCATC 59.375 47.826 0.00 0.00 0.00 3.91
930 989 1.413382 CAGATCCTAATCGACGCAGC 58.587 55.000 0.00 0.00 36.97 5.25
931 990 1.032794 AGATCCTAATCGACGCAGCA 58.967 50.000 0.00 0.00 36.97 4.41
968 1027 2.685850 ACAGGCCATACCGAAAGTAC 57.314 50.000 5.01 0.00 46.52 2.73
1078 1137 1.463018 ATCCTGGGCATCCTCTCCC 60.463 63.158 0.00 0.00 42.93 4.30
1168 1227 2.685380 ACTTCAGCCTCCTCCCGG 60.685 66.667 0.00 0.00 0.00 5.73
1357 1416 4.608774 TGACGGAGGTGGACGGGT 62.609 66.667 0.00 0.00 0.00 5.28
1476 1535 2.551270 GCGTTTGAGGTGAGCGTG 59.449 61.111 0.00 0.00 0.00 5.34
1585 1685 2.444351 GACGTAATTACTAGCGTGCGT 58.556 47.619 13.56 3.84 37.71 5.24
1587 1687 1.442087 CGTAATTACTAGCGTGCGTCG 59.558 52.381 13.56 0.00 43.12 5.12
1626 1730 3.803778 CCTCTTGTGCCACAATTTGTTTC 59.196 43.478 11.26 0.00 37.48 2.78
1627 1731 3.791245 TCTTGTGCCACAATTTGTTTCC 58.209 40.909 11.26 0.00 37.48 3.13
1628 1732 3.450457 TCTTGTGCCACAATTTGTTTCCT 59.550 39.130 11.26 0.00 37.48 3.36
1629 1733 3.902881 TGTGCCACAATTTGTTTCCTT 57.097 38.095 0.00 0.00 0.00 3.36
1679 1787 0.390735 ACTATGGACGTTCCGGTTGC 60.391 55.000 0.00 0.00 40.17 4.17
1691 1799 0.813184 CCGGTTGCGAGTTCCTACTA 59.187 55.000 0.00 0.00 33.84 1.82
1736 1844 5.825593 TTCCAAATGACTCTACCAGTTCT 57.174 39.130 0.00 0.00 34.41 3.01
1757 1871 3.140814 GGCGGGCCCATGAACTTC 61.141 66.667 24.92 0.00 0.00 3.01
1828 1944 9.484326 CATAATTTCAATACGACGATTCAAACA 57.516 29.630 0.00 0.00 0.00 2.83
1830 1946 8.964420 AATTTCAATACGACGATTCAAACATT 57.036 26.923 0.00 0.00 0.00 2.71
1925 2041 5.905913 AGCATTAAGAGGTTAGGGTATCTGT 59.094 40.000 0.00 0.00 0.00 3.41
1935 2051 2.648059 AGGGTATCTGTAACGCGTACT 58.352 47.619 14.46 0.00 35.15 2.73
1945 2061 1.280206 AACGCGTACTCTCAAACCGC 61.280 55.000 14.46 0.00 40.87 5.68
2009 2129 2.303311 TGATGTCCCGTATTTGTCCACA 59.697 45.455 0.00 0.00 0.00 4.17
2012 2132 2.569853 TGTCCCGTATTTGTCCACAGAT 59.430 45.455 0.00 0.00 0.00 2.90
2021 2141 1.183030 TGTCCACAGATCGGTTCGGT 61.183 55.000 0.00 0.00 32.53 4.69
2032 2152 2.299521 TCGGTTCGGTTGTCCATTTTT 58.700 42.857 0.00 0.00 0.00 1.94
2035 2155 2.288579 GGTTCGGTTGTCCATTTTTCCC 60.289 50.000 0.00 0.00 0.00 3.97
2042 2172 3.311486 TGTCCATTTTTCCCGCAAATC 57.689 42.857 0.00 0.00 0.00 2.17
2043 2173 2.630098 TGTCCATTTTTCCCGCAAATCA 59.370 40.909 0.00 0.00 0.00 2.57
2070 2200 3.063084 GCGAGAGTCCGGACACCT 61.063 66.667 35.00 28.95 0.00 4.00
2072 2202 1.674651 CGAGAGTCCGGACACCTGA 60.675 63.158 35.00 0.00 0.00 3.86
2116 2246 1.606313 CCACCCAAAACCGAGGCAT 60.606 57.895 0.00 0.00 0.00 4.40
2135 2265 1.862049 TAGCCTGCCCATTTGGAGCA 61.862 55.000 10.87 10.87 38.46 4.26
2143 2282 3.148412 GCCCATTTGGAGCAATTTTTGT 58.852 40.909 0.00 0.00 37.39 2.83
2149 2288 6.016943 CCATTTGGAGCAATTTTTGTGACAAT 60.017 34.615 0.00 0.00 37.39 2.71
2176 2323 1.551452 CTTTCTCCACCCTCTCGACT 58.449 55.000 0.00 0.00 0.00 4.18
2177 2324 2.620886 CCTTTCTCCACCCTCTCGACTA 60.621 54.545 0.00 0.00 0.00 2.59
2187 2334 3.085533 CCCTCTCGACTATACCATCCTG 58.914 54.545 0.00 0.00 0.00 3.86
2188 2335 3.498841 CCCTCTCGACTATACCATCCTGT 60.499 52.174 0.00 0.00 0.00 4.00
2198 2345 1.722034 ACCATCCTGTCGCTATCCAT 58.278 50.000 0.00 0.00 0.00 3.41
2250 2397 0.733150 GGACCCATACGAAAAGCTGC 59.267 55.000 0.00 0.00 0.00 5.25
2291 2438 1.645710 ATCCGAAGAAGGTGGTCACT 58.354 50.000 0.93 0.00 0.00 3.41
2314 2461 3.614150 CGGAAGATCAACTCGGAGACAAA 60.614 47.826 12.86 0.00 0.00 2.83
2326 2473 2.985847 GACAAAGGCAAGCCCGCT 60.986 61.111 7.62 0.00 39.21 5.52
2335 2482 2.036256 AAGCCCGCTGCCTCAAAT 59.964 55.556 0.00 0.00 42.71 2.32
2357 2504 4.056125 GGCAAAGGACAAGGCGGC 62.056 66.667 0.00 0.00 0.00 6.53
2378 2525 2.343101 CGACATAAAGAAGGGCAACGA 58.657 47.619 0.00 0.00 37.60 3.85
2415 2562 3.672503 GGATGGGGTGCAGGGGTT 61.673 66.667 0.00 0.00 0.00 4.11
2469 2629 2.577059 CGTCCTAGCCGGAGCAAA 59.423 61.111 5.05 0.00 44.20 3.68
2479 2639 1.302832 CGGAGCAAAACCAGCCTCT 60.303 57.895 0.00 0.00 0.00 3.69
2487 2647 2.996621 CAAAACCAGCCTCTCTACTTCG 59.003 50.000 0.00 0.00 0.00 3.79
2490 2650 0.378962 CCAGCCTCTCTACTTCGACG 59.621 60.000 0.00 0.00 0.00 5.12
2504 2664 2.434359 GACGCCGCCAAGTAGCTT 60.434 61.111 0.00 0.00 0.00 3.74
2506 2666 4.166011 CGCCGCCAAGTAGCTTGC 62.166 66.667 0.00 0.00 39.85 4.01
2508 2668 3.134127 CCGCCAAGTAGCTTGCCC 61.134 66.667 0.00 0.00 39.85 5.36
2509 2669 3.499737 CGCCAAGTAGCTTGCCCG 61.500 66.667 0.00 4.99 39.85 6.13
2547 2707 1.359848 CACAGGGCACTTGTCGTATC 58.640 55.000 0.00 0.00 0.00 2.24
2548 2708 0.249398 ACAGGGCACTTGTCGTATCC 59.751 55.000 0.00 0.00 0.00 2.59
2549 2709 0.249120 CAGGGCACTTGTCGTATCCA 59.751 55.000 0.00 0.00 0.00 3.41
2550 2710 0.537188 AGGGCACTTGTCGTATCCAG 59.463 55.000 0.00 0.00 0.00 3.86
2551 2711 0.535335 GGGCACTTGTCGTATCCAGA 59.465 55.000 0.00 0.00 0.00 3.86
2552 2712 1.641577 GGCACTTGTCGTATCCAGAC 58.358 55.000 0.00 0.00 38.98 3.51
2553 2713 1.269166 GCACTTGTCGTATCCAGACG 58.731 55.000 0.00 0.00 44.29 4.18
2559 2719 3.091318 TCGTATCCAGACGAGTCCC 57.909 57.895 0.00 0.00 46.43 4.46
2560 2720 0.253894 TCGTATCCAGACGAGTCCCA 59.746 55.000 0.00 0.00 46.43 4.37
2561 2721 0.381089 CGTATCCAGACGAGTCCCAC 59.619 60.000 0.00 0.00 45.82 4.61
2562 2722 1.471119 GTATCCAGACGAGTCCCACA 58.529 55.000 0.00 0.00 0.00 4.17
2563 2723 1.822990 GTATCCAGACGAGTCCCACAA 59.177 52.381 0.00 0.00 0.00 3.33
2564 2724 1.348064 ATCCAGACGAGTCCCACAAA 58.652 50.000 0.00 0.00 0.00 2.83
2565 2725 1.124780 TCCAGACGAGTCCCACAAAA 58.875 50.000 0.00 0.00 0.00 2.44
2566 2726 1.487142 TCCAGACGAGTCCCACAAAAA 59.513 47.619 0.00 0.00 0.00 1.94
2567 2727 2.105821 TCCAGACGAGTCCCACAAAAAT 59.894 45.455 0.00 0.00 0.00 1.82
2568 2728 3.325425 TCCAGACGAGTCCCACAAAAATA 59.675 43.478 0.00 0.00 0.00 1.40
2569 2729 4.019681 TCCAGACGAGTCCCACAAAAATAT 60.020 41.667 0.00 0.00 0.00 1.28
2570 2730 5.188163 TCCAGACGAGTCCCACAAAAATATA 59.812 40.000 0.00 0.00 0.00 0.86
2571 2731 6.055588 CCAGACGAGTCCCACAAAAATATAT 58.944 40.000 0.00 0.00 0.00 0.86
2572 2732 6.202954 CCAGACGAGTCCCACAAAAATATATC 59.797 42.308 0.00 0.00 0.00 1.63
2573 2733 6.761242 CAGACGAGTCCCACAAAAATATATCA 59.239 38.462 0.00 0.00 0.00 2.15
2574 2734 7.442364 CAGACGAGTCCCACAAAAATATATCAT 59.558 37.037 0.00 0.00 0.00 2.45
2575 2735 8.647796 AGACGAGTCCCACAAAAATATATCATA 58.352 33.333 0.00 0.00 0.00 2.15
2576 2736 9.436957 GACGAGTCCCACAAAAATATATCATAT 57.563 33.333 0.00 0.00 0.00 1.78
2577 2737 9.436957 ACGAGTCCCACAAAAATATATCATATC 57.563 33.333 0.00 0.00 0.00 1.63
2578 2738 9.658799 CGAGTCCCACAAAAATATATCATATCT 57.341 33.333 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.967890 ATTGGTTTCTTTTGATTTGATCACC 57.032 32.000 0.00 0.00 39.39 4.02
9 10 8.829612 ACAATTGGTTTCTTTTGATTTGATCAC 58.170 29.630 10.83 0.00 39.39 3.06
12 13 9.048446 CAGACAATTGGTTTCTTTTGATTTGAT 57.952 29.630 10.83 0.00 0.00 2.57
25 26 6.989759 GGTTATTTTGGTCAGACAATTGGTTT 59.010 34.615 10.83 0.00 0.00 3.27
28 29 6.095432 TGGTTATTTTGGTCAGACAATTGG 57.905 37.500 10.83 0.00 0.00 3.16
112 116 2.163815 ACCGAAAACGAGACAGATCGAT 59.836 45.455 0.00 0.00 45.56 3.59
147 151 1.436336 GAGATCCACCGTACCACCG 59.564 63.158 0.00 0.00 0.00 4.94
153 157 2.836360 GGGCCGAGATCCACCGTA 60.836 66.667 0.00 0.00 0.00 4.02
210 217 5.855045 ACAACACACAAACCCTAACAAAAA 58.145 33.333 0.00 0.00 0.00 1.94
252 259 2.739996 CCATCTTCAGGGAGCCGCT 61.740 63.158 0.00 0.00 0.00 5.52
300 309 4.618912 CCGATTATGCTAGACTCACAATCG 59.381 45.833 12.52 12.52 41.59 3.34
304 313 3.068165 CCACCGATTATGCTAGACTCACA 59.932 47.826 0.00 0.00 0.00 3.58
318 327 1.993391 ATCCACCCGTCCACCGATT 60.993 57.895 0.00 0.00 39.56 3.34
443 489 1.652947 AGACCCCATAAGACCAACGT 58.347 50.000 0.00 0.00 0.00 3.99
495 541 0.108520 CCGAAGCTGGGCTAAACGTA 60.109 55.000 0.00 0.00 38.25 3.57
556 602 4.038036 CGACGACTACACGCACTC 57.962 61.111 0.00 0.00 36.70 3.51
635 681 6.878317 ACTTCCGATCTATTCATCTTCAACA 58.122 36.000 0.00 0.00 0.00 3.33
930 989 3.734463 TGTATGTGTACCTGGTTGTGTG 58.266 45.455 3.84 0.00 0.00 3.82
931 990 3.244422 CCTGTATGTGTACCTGGTTGTGT 60.244 47.826 3.84 0.00 0.00 3.72
1142 1201 2.182030 GGCTGAAGTCCTCGACGG 59.818 66.667 0.00 0.00 37.67 4.79
1357 1416 2.347490 GCTCTCGGCCACCTTGAA 59.653 61.111 2.24 0.00 34.27 2.69
1476 1535 2.049433 CACACCACCTCGACGGTC 60.049 66.667 0.00 0.00 44.93 4.79
1585 1685 1.272490 GGATGGATGGATTACGAGCGA 59.728 52.381 0.00 0.00 0.00 4.93
1587 1687 2.564947 AGAGGATGGATGGATTACGAGC 59.435 50.000 0.00 0.00 0.00 5.03
1679 1787 5.973651 TGTACGTATGTAGTAGGAACTCG 57.026 43.478 0.00 0.00 41.75 4.18
1691 1799 5.324784 TCAGCTTCAGAATGTACGTATGT 57.675 39.130 0.00 0.00 37.40 2.29
1736 1844 3.012119 TTCATGGGCCCGCCACTA 61.012 61.111 19.37 0.00 37.98 2.74
1757 1871 2.047844 CGTGGGACTCCAGTGCTG 60.048 66.667 0.00 0.00 45.05 4.41
1925 2041 1.967762 CGGTTTGAGAGTACGCGTTA 58.032 50.000 20.78 0.00 0.00 3.18
1935 2051 0.675083 TGGTTACGAGCGGTTTGAGA 59.325 50.000 0.00 0.00 0.00 3.27
1945 2061 0.533491 TTGGTCCGGATGGTTACGAG 59.467 55.000 7.81 0.00 36.30 4.18
2009 2129 0.902531 ATGGACAACCGAACCGATCT 59.097 50.000 0.00 0.00 39.42 2.75
2012 2132 1.970092 AAAATGGACAACCGAACCGA 58.030 45.000 0.00 0.00 39.42 4.69
2021 2141 3.070159 TGATTTGCGGGAAAAATGGACAA 59.930 39.130 0.00 0.00 0.00 3.18
2032 2152 4.440829 GCCCCCTGATTTGCGGGA 62.441 66.667 0.00 0.00 46.81 5.14
2035 2155 1.216178 CAAAGCCCCCTGATTTGCG 59.784 57.895 0.00 0.00 0.00 4.85
2042 2172 2.437359 CTCTCGCAAAGCCCCCTG 60.437 66.667 0.00 0.00 0.00 4.45
2043 2173 2.930562 ACTCTCGCAAAGCCCCCT 60.931 61.111 0.00 0.00 0.00 4.79
2070 2200 2.826128 GGTGTCAGAGTCCTATGTGTCA 59.174 50.000 0.00 0.00 0.00 3.58
2072 2202 2.180276 GGGTGTCAGAGTCCTATGTGT 58.820 52.381 0.00 0.00 0.00 3.72
2116 2246 1.076777 GCTCCAAATGGGCAGGCTA 60.077 57.895 0.00 0.00 36.21 3.93
2121 2251 3.147629 CAAAAATTGCTCCAAATGGGCA 58.852 40.909 10.37 10.37 38.82 5.36
2135 2265 5.397360 AGGGAGGAGATTGTCACAAAAATT 58.603 37.500 0.00 0.00 0.00 1.82
2143 2282 2.840651 GGAGAAAGGGAGGAGATTGTCA 59.159 50.000 0.00 0.00 0.00 3.58
2149 2288 0.252742 GGGTGGAGAAAGGGAGGAGA 60.253 60.000 0.00 0.00 0.00 3.71
2176 2323 4.042271 TGGATAGCGACAGGATGGTATA 57.958 45.455 0.00 0.00 43.62 1.47
2177 2324 2.889512 TGGATAGCGACAGGATGGTAT 58.110 47.619 0.00 0.00 43.62 2.73
2187 2334 4.413087 CGAGTATTGGTATGGATAGCGAC 58.587 47.826 0.00 0.00 33.65 5.19
2188 2335 3.119602 GCGAGTATTGGTATGGATAGCGA 60.120 47.826 0.00 0.00 33.65 4.93
2198 2345 2.896168 CGAAAAGGGCGAGTATTGGTA 58.104 47.619 0.00 0.00 0.00 3.25
2223 2370 2.510906 GTATGGGTCCATGCGGCT 59.489 61.111 12.42 0.00 37.82 5.52
2250 2397 0.609406 TCCACCTCTGTCGTCTCCAG 60.609 60.000 0.00 0.00 0.00 3.86
2277 2424 1.344763 CTTCCGAGTGACCACCTTCTT 59.655 52.381 0.00 0.00 0.00 2.52
2291 2438 1.743958 GTCTCCGAGTTGATCTTCCGA 59.256 52.381 0.00 0.00 0.00 4.55
2335 2482 0.889186 GCCTTGTCCTTTGCCTTCGA 60.889 55.000 0.00 0.00 0.00 3.71
2357 2504 1.396996 CGTTGCCCTTCTTTATGTCGG 59.603 52.381 0.00 0.00 0.00 4.79
2362 2509 2.489938 TGCTCGTTGCCCTTCTTTAT 57.510 45.000 1.30 0.00 42.00 1.40
2421 2568 3.155167 CGACCCTGTCCTAGGCCC 61.155 72.222 2.96 0.00 45.89 5.80
2422 2569 3.851128 GCGACCCTGTCCTAGGCC 61.851 72.222 2.96 0.00 45.89 5.19
2453 2601 1.025113 GGTTTTGCTCCGGCTAGGAC 61.025 60.000 0.00 0.00 45.98 3.85
2469 2629 1.819903 GTCGAAGTAGAGAGGCTGGTT 59.180 52.381 0.00 0.00 0.00 3.67
2479 2639 2.537792 CTTGGCGGCGTCGAAGTAGA 62.538 60.000 16.53 0.00 39.00 2.59
2487 2647 2.434359 AAGCTACTTGGCGGCGTC 60.434 61.111 3.62 3.62 37.29 5.19
2527 2687 0.036388 ATACGACAAGTGCCCTGTGG 60.036 55.000 0.00 0.00 0.00 4.17
2529 2689 0.249398 GGATACGACAAGTGCCCTGT 59.751 55.000 0.00 0.00 0.00 4.00
2530 2690 0.249120 TGGATACGACAAGTGCCCTG 59.751 55.000 0.00 0.00 42.51 4.45
2531 2691 0.537188 CTGGATACGACAAGTGCCCT 59.463 55.000 0.00 0.00 42.51 5.19
2532 2692 0.535335 TCTGGATACGACAAGTGCCC 59.465 55.000 0.00 0.00 42.51 5.36
2539 2699 1.376543 GGACTCGTCTGGATACGACA 58.623 55.000 0.00 0.00 46.29 4.35
2547 2707 1.961793 TTTTTGTGGGACTCGTCTGG 58.038 50.000 0.00 0.00 0.00 3.86
2548 2708 6.761242 TGATATATTTTTGTGGGACTCGTCTG 59.239 38.462 0.00 0.00 0.00 3.51
2549 2709 6.884832 TGATATATTTTTGTGGGACTCGTCT 58.115 36.000 0.00 0.00 0.00 4.18
2550 2710 7.730364 ATGATATATTTTTGTGGGACTCGTC 57.270 36.000 0.00 0.00 0.00 4.20
2551 2711 9.436957 GATATGATATATTTTTGTGGGACTCGT 57.563 33.333 0.00 0.00 0.00 4.18
2552 2712 9.658799 AGATATGATATATTTTTGTGGGACTCG 57.341 33.333 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.