Multiple sequence alignment - TraesCS6B01G439700

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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 TraesCS6B01G439700 chr6B 100.000 3629 0 0 1 3629 705157899 705154271 0.000000e+00 6702.0
1 TraesCS6B01G439700 chr6B 88.489 556 58 6 24 575 457428695 457428142 0.000000e+00 667.0
2 TraesCS6B01G439700 chr6D 92.674 2457 83 38 516 2934 462531667 462529270 0.000000e+00 3450.0
3 TraesCS6B01G439700 chr6D 90.058 694 42 17 2935 3628 462527638 462526972 0.000000e+00 874.0
4 TraesCS6B01G439700 chr6A 91.858 2174 97 26 572 2706 609378468 609376336 0.000000e+00 2961.0
5 TraesCS6B01G439700 chr6A 82.507 686 99 12 2963 3629 609342306 609341623 1.880000e-162 582.0
6 TraesCS6B01G439700 chr6A 91.509 212 11 2 2558 2769 609376041 609375837 5.930000e-73 285.0
7 TraesCS6B01G439700 chr6A 89.247 186 18 2 2690 2873 609376321 609376136 7.840000e-57 231.0
8 TraesCS6B01G439700 chr6A 80.347 173 24 9 2963 3130 101857932 101857765 4.920000e-24 122.0
9 TraesCS6B01G439700 chr3B 94.926 473 20 4 105 574 514000267 513999796 0.000000e+00 737.0
10 TraesCS6B01G439700 chr3B 97.183 284 4 4 296 576 811697806 811698088 9.120000e-131 477.0
11 TraesCS6B01G439700 chr3B 85.000 100 15 0 2161 2260 628470771 628470672 6.410000e-18 102.0
12 TraesCS6B01G439700 chr3B 79.452 146 28 2 2958 3102 723611380 723611236 6.410000e-18 102.0
13 TraesCS6B01G439700 chr3B 86.667 60 8 0 1984 2043 797135312 797135253 2.340000e-07 67.6
14 TraesCS6B01G439700 chr3A 84.058 552 70 17 42 583 608488923 608488380 1.930000e-142 516.0
15 TraesCS6B01G439700 chr3A 83.629 507 64 12 24 526 64072341 64071850 3.300000e-125 459.0
16 TraesCS6B01G439700 chr3A 86.000 100 14 0 2161 2260 615715302 615715203 1.380000e-19 108.0
17 TraesCS6B01G439700 chr2B 84.674 522 44 31 73 581 124862430 124861932 4.210000e-134 488.0
18 TraesCS6B01G439700 chr2B 91.798 317 23 3 22 336 557731330 557731645 4.300000e-119 438.0
19 TraesCS6B01G439700 chr2B 80.961 541 76 23 45 572 651985876 651985350 1.570000e-108 403.0
20 TraesCS6B01G439700 chr7A 93.631 314 12 8 262 569 59434102 59434413 2.550000e-126 462.0
21 TraesCS6B01G439700 chr2D 85.523 449 48 11 22 467 158273603 158274037 1.540000e-123 453.0
22 TraesCS6B01G439700 chr2D 80.503 159 28 3 1937 2093 392526099 392526256 6.370000e-23 119.0
23 TraesCS6B01G439700 chrUn 84.778 473 46 17 126 577 11127190 11126723 5.530000e-123 451.0
24 TraesCS6B01G439700 chrUn 92.381 315 24 0 22 336 207007666 207007352 1.990000e-122 449.0
25 TraesCS6B01G439700 chr2A 82.070 541 83 14 11 543 49806217 49806751 1.990000e-122 449.0
26 TraesCS6B01G439700 chr7D 92.138 318 21 4 22 336 432329796 432329480 2.570000e-121 446.0
27 TraesCS6B01G439700 chr5A 82.286 175 28 3 2115 2288 657555149 657554977 8.120000e-32 148.0
28 TraesCS6B01G439700 chr5D 81.595 163 30 0 2126 2288 529542631 529542469 6.320000e-28 135.0
29 TraesCS6B01G439700 chr3D 79.532 171 30 5 2958 3127 546611834 546611668 2.290000e-22 117.0
30 TraesCS6B01G439700 chr3D 84.000 100 16 0 2161 2260 473455875 473455776 2.980000e-16 97.1
31 TraesCS6B01G439700 chr3D 88.333 60 7 0 1984 2043 594157146 594157087 5.030000e-09 73.1
32 TraesCS6B01G439700 chr1D 89.394 66 7 0 1984 2049 53965008 53964943 2.320000e-12 84.2
33 TraesCS6B01G439700 chr1B 89.394 66 7 0 1984 2049 88003172 88003107 2.320000e-12 84.2
34 TraesCS6B01G439700 chr1A 89.394 66 7 0 1984 2049 53455160 53455095 2.320000e-12 84.2
35 TraesCS6B01G439700 chr5B 87.879 66 8 0 1984 2049 527294714 527294779 1.080000e-10 78.7


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 TraesCS6B01G439700 chr6B 705154271 705157899 3628 True 6702 6702 100.000000 1 3629 1 chr6B.!!$R2 3628
1 TraesCS6B01G439700 chr6B 457428142 457428695 553 True 667 667 88.489000 24 575 1 chr6B.!!$R1 551
2 TraesCS6B01G439700 chr6D 462526972 462531667 4695 True 2162 3450 91.366000 516 3628 2 chr6D.!!$R1 3112
3 TraesCS6B01G439700 chr6A 609375837 609378468 2631 True 1159 2961 90.871333 572 2873 3 chr6A.!!$R3 2301
4 TraesCS6B01G439700 chr6A 609341623 609342306 683 True 582 582 82.507000 2963 3629 1 chr6A.!!$R2 666
5 TraesCS6B01G439700 chr3A 608488380 608488923 543 True 516 516 84.058000 42 583 1 chr3A.!!$R2 541
6 TraesCS6B01G439700 chr2B 651985350 651985876 526 True 403 403 80.961000 45 572 1 chr2B.!!$R2 527
7 TraesCS6B01G439700 chr2A 49806217 49806751 534 False 449 449 82.070000 11 543 1 chr2A.!!$F1 532

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
582 587 1.221414 GGCTAGCCTTATGCAGTTCG 58.779 55.0 27.17 0.0 44.83 3.95 F
1329 1372 0.605589 AGAAGAGGTCCAAGCAGACG 59.394 55.0 0.00 0.0 37.66 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1426 0.542333 GGCTGTTAGGGAGAAGGGAC 59.458 60.000 0.0 0.0 0.00 4.46 R
3295 5023 1.278413 GTTCAGGGGTGGAACTAGGAC 59.722 57.143 0.0 0.0 41.05 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
37 38 6.724893 TGCTGTATTAGACTAGCCACAATA 57.275 37.500 0.00 0.00 33.67 1.90
38 39 6.513180 TGCTGTATTAGACTAGCCACAATAC 58.487 40.000 6.61 6.61 33.67 1.89
40 41 7.155328 GCTGTATTAGACTAGCCACAATACAT 58.845 38.462 13.08 0.00 39.82 2.29
121 122 8.989131 AGTGGATAGTAACATAAGTGTGGTAAT 58.011 33.333 0.00 0.00 38.92 1.89
122 123 9.257651 GTGGATAGTAACATAAGTGTGGTAATC 57.742 37.037 0.00 0.00 38.92 1.75
227 229 6.678547 ACTACCTCTCTCCTCATTAACTCAT 58.321 40.000 0.00 0.00 0.00 2.90
269 271 1.728971 GAGTTGGACTCGATGTTGCTG 59.271 52.381 0.00 0.00 35.28 4.41
496 498 6.808321 ATGTTACCACACCTATGACACTAT 57.192 37.500 0.00 0.00 35.03 2.12
498 500 5.955959 TGTTACCACACCTATGACACTATCT 59.044 40.000 0.00 0.00 0.00 1.98
558 563 5.284861 TGTTACTGCTGAAGTTACTTCCA 57.715 39.130 20.69 12.08 38.87 3.53
559 564 5.054477 TGTTACTGCTGAAGTTACTTCCAC 58.946 41.667 20.69 13.54 38.87 4.02
560 565 5.163343 TGTTACTGCTGAAGTTACTTCCACT 60.163 40.000 20.69 5.90 38.87 4.00
561 566 6.041182 TGTTACTGCTGAAGTTACTTCCACTA 59.959 38.462 20.69 3.00 38.87 2.74
562 567 5.746990 ACTGCTGAAGTTACTTCCACTAT 57.253 39.130 20.69 3.05 39.51 2.12
563 568 5.482908 ACTGCTGAAGTTACTTCCACTATG 58.517 41.667 20.69 9.60 39.51 2.23
564 569 4.832248 TGCTGAAGTTACTTCCACTATGG 58.168 43.478 20.69 5.30 39.51 2.74
565 570 3.623510 GCTGAAGTTACTTCCACTATGGC 59.376 47.826 20.69 10.33 39.51 4.40
566 571 4.624125 GCTGAAGTTACTTCCACTATGGCT 60.624 45.833 20.69 0.00 39.51 4.75
567 572 5.395324 GCTGAAGTTACTTCCACTATGGCTA 60.395 44.000 20.69 0.00 39.51 3.93
568 573 6.222038 TGAAGTTACTTCCACTATGGCTAG 57.778 41.667 20.69 0.00 39.51 3.42
569 574 4.674281 AGTTACTTCCACTATGGCTAGC 57.326 45.455 6.04 6.04 37.47 3.42
582 587 1.221414 GGCTAGCCTTATGCAGTTCG 58.779 55.000 27.17 0.00 44.83 3.95
584 589 1.221414 CTAGCCTTATGCAGTTCGCC 58.779 55.000 0.00 0.00 44.83 5.54
610 615 6.796426 TCGAGAGAAATCAAGTCGTATGATT 58.204 36.000 7.09 7.09 46.62 2.57
657 662 4.179579 GGCAAACGGATGGCGAGC 62.180 66.667 0.71 0.00 36.07 5.03
677 682 3.070302 AGCGTGGAAGAATTCTATCCTCC 59.930 47.826 24.65 20.37 46.56 4.30
706 716 3.243401 GGGCATTTATAAAAGGTCGCCTG 60.243 47.826 17.83 6.44 38.37 4.85
740 750 2.033448 TGCATGTGGGTCCCGAAC 59.967 61.111 2.65 0.00 0.00 3.95
810 833 2.595386 GGTGCCGTTTAAATGCTTGAG 58.405 47.619 12.20 0.00 0.00 3.02
835 858 2.552743 GCTGGTTTCTTGGTAGTTGGTC 59.447 50.000 0.00 0.00 0.00 4.02
858 881 3.422796 AGAACTCTTCCACTCTTCGCTA 58.577 45.455 0.00 0.00 0.00 4.26
859 882 3.191791 AGAACTCTTCCACTCTTCGCTAC 59.808 47.826 0.00 0.00 0.00 3.58
879 910 4.323477 TTTGCCCGGTCCAGGTCG 62.323 66.667 0.00 0.00 0.00 4.79
917 949 3.680786 CACTGCGAGTGGGTCCGA 61.681 66.667 8.03 0.00 42.35 4.55
1050 1093 4.120589 CCTTGTCCTCTTCTATAAACCGC 58.879 47.826 0.00 0.00 0.00 5.68
1051 1094 3.431922 TGTCCTCTTCTATAAACCGCG 57.568 47.619 0.00 0.00 0.00 6.46
1092 1135 2.996395 CTGGCTGGAGCTGTGGAT 59.004 61.111 0.00 0.00 41.70 3.41
1284 1327 1.599576 GTTCAGCTCCCTCTCCACC 59.400 63.158 0.00 0.00 0.00 4.61
1327 1370 2.614259 AGAAGAAGAGGTCCAAGCAGA 58.386 47.619 0.00 0.00 0.00 4.26
1328 1371 2.301583 AGAAGAAGAGGTCCAAGCAGAC 59.698 50.000 0.00 0.00 35.95 3.51
1329 1372 0.605589 AGAAGAGGTCCAAGCAGACG 59.394 55.000 0.00 0.00 37.66 4.18
1330 1373 1.004440 AAGAGGTCCAAGCAGACGC 60.004 57.895 0.00 0.00 37.66 5.19
1331 1374 2.435059 GAGGTCCAAGCAGACGCC 60.435 66.667 0.00 0.00 39.83 5.68
1332 1375 4.379243 AGGTCCAAGCAGACGCCG 62.379 66.667 0.00 0.00 39.83 6.46
1333 1376 4.373116 GGTCCAAGCAGACGCCGA 62.373 66.667 0.00 0.00 39.83 5.54
1383 1426 2.746277 AAGCCGCCTTGTAAGCCG 60.746 61.111 0.00 0.00 0.00 5.52
1392 1435 1.405661 CCTTGTAAGCCGTCCCTTCTC 60.406 57.143 0.00 0.00 0.00 2.87
1394 1437 1.262640 TGTAAGCCGTCCCTTCTCCC 61.263 60.000 0.00 0.00 0.00 4.30
1395 1438 0.976590 GTAAGCCGTCCCTTCTCCCT 60.977 60.000 0.00 0.00 0.00 4.20
1396 1439 0.632835 TAAGCCGTCCCTTCTCCCTA 59.367 55.000 0.00 0.00 0.00 3.53
1398 1441 0.976590 AGCCGTCCCTTCTCCCTAAC 60.977 60.000 0.00 0.00 0.00 2.34
1399 1442 1.262640 GCCGTCCCTTCTCCCTAACA 61.263 60.000 0.00 0.00 0.00 2.41
1401 1444 0.175989 CGTCCCTTCTCCCTAACAGC 59.824 60.000 0.00 0.00 0.00 4.40
1405 1448 1.153349 CTTCTCCCTAACAGCCGGC 60.153 63.158 21.89 21.89 0.00 6.13
1423 1466 3.726517 CGGCCGGTCTGCTTGTTG 61.727 66.667 20.10 0.00 0.00 3.33
1424 1467 2.281484 GGCCGGTCTGCTTGTTGA 60.281 61.111 1.90 0.00 0.00 3.18
1425 1468 1.675641 GGCCGGTCTGCTTGTTGAT 60.676 57.895 1.90 0.00 0.00 2.57
1426 1469 1.244019 GGCCGGTCTGCTTGTTGATT 61.244 55.000 1.90 0.00 0.00 2.57
1427 1470 1.448985 GCCGGTCTGCTTGTTGATTA 58.551 50.000 1.90 0.00 0.00 1.75
1428 1471 1.810151 GCCGGTCTGCTTGTTGATTAA 59.190 47.619 1.90 0.00 0.00 1.40
1429 1472 2.414161 GCCGGTCTGCTTGTTGATTAAC 60.414 50.000 1.90 0.00 37.32 2.01
1430 1473 3.074412 CCGGTCTGCTTGTTGATTAACT 58.926 45.455 1.75 0.00 37.68 2.24
1431 1474 4.250464 CCGGTCTGCTTGTTGATTAACTA 58.750 43.478 1.75 0.00 37.68 2.24
1446 1489 0.822164 AACTATCCCCTTCGTCACCG 59.178 55.000 0.00 0.00 0.00 4.94
1455 1498 1.548973 CTTCGTCACCGTGACTGTGC 61.549 60.000 25.37 3.40 44.85 4.57
1458 1501 2.280119 TCACCGTGACTGTGCTGC 60.280 61.111 2.03 0.00 33.71 5.25
1460 1503 2.280389 ACCGTGACTGTGCTGCTG 60.280 61.111 0.00 0.00 0.00 4.41
1464 1507 1.432514 CGTGACTGTGCTGCTGTTAT 58.567 50.000 0.00 0.00 0.00 1.89
1465 1508 1.800586 CGTGACTGTGCTGCTGTTATT 59.199 47.619 0.00 0.00 0.00 1.40
1466 1509 2.224079 CGTGACTGTGCTGCTGTTATTT 59.776 45.455 0.00 0.00 0.00 1.40
1471 1514 4.362279 ACTGTGCTGCTGTTATTTTGTTG 58.638 39.130 0.00 0.00 0.00 3.33
1572 1621 2.647875 CGGAGGAGCCTATCGCAG 59.352 66.667 0.00 0.00 41.38 5.18
1573 1622 1.899054 CGGAGGAGCCTATCGCAGA 60.899 63.158 0.00 0.00 45.75 4.26
1574 1623 1.663173 GGAGGAGCCTATCGCAGAC 59.337 63.158 0.00 0.00 42.51 3.51
1848 1897 0.752009 TCTACGGCTACCTGGAGCAG 60.752 60.000 16.37 14.91 44.76 4.24
2768 2851 6.707161 ACCAAGCGACTGTAATTAAACACTTA 59.293 34.615 0.00 0.00 0.00 2.24
2838 2922 8.289618 TGTGACTTTTCATGATACTTTTGCTAC 58.710 33.333 0.00 0.00 33.11 3.58
2878 2962 7.023575 GCAAGGTTGATTGACTTGTAACATAG 58.976 38.462 0.00 0.00 42.60 2.23
2879 2963 7.308589 GCAAGGTTGATTGACTTGTAACATAGT 60.309 37.037 0.00 0.00 42.60 2.12
2880 2964 9.214957 CAAGGTTGATTGACTTGTAACATAGTA 57.785 33.333 0.00 0.00 37.43 1.82
2911 2995 3.430218 GCTACGATTTGCTATCGCTCAAT 59.570 43.478 17.73 4.98 44.60 2.57
2912 2996 3.867055 ACGATTTGCTATCGCTCAATG 57.133 42.857 17.73 0.00 44.60 2.82
2937 4652 6.417635 GCCAATTTCGTGACATAATGGTATTG 59.582 38.462 0.00 0.00 0.00 1.90
3083 4798 4.657814 TGGATCTTAATCTATTGGCCCC 57.342 45.455 0.00 0.00 32.12 5.80
3152 4877 4.877823 CCAGTCAGCTTATTACATGCTTCA 59.122 41.667 0.00 0.00 35.55 3.02
3228 4956 0.603439 CAACAACCCTGCCAATTGCC 60.603 55.000 0.00 0.00 40.16 4.52
3251 4979 6.183360 GCCTTTTGCAGGGTATAAGAAATCAT 60.183 38.462 4.75 0.00 44.16 2.45
3259 4987 7.687837 GCAGGGTATAAGAAATCATCAGAGTGA 60.688 40.741 0.00 0.00 0.00 3.41
3295 5023 4.567318 GCCCTAAGCATGACCTGG 57.433 61.111 0.00 0.00 42.97 4.45
3335 5069 4.630644 ACTGAAGGATCACATGTTGACT 57.369 40.909 0.00 0.00 36.92 3.41
3385 5119 8.826710 CATCGTTATGTTACTCAATACCATTGT 58.173 33.333 0.00 0.00 0.00 2.71
3487 5249 2.025887 CAGGCAATAGGGAAGGACACTT 60.026 50.000 0.00 0.00 40.34 3.16
3534 5301 9.900710 TGCTAATGTTATTTATTTCGTGTTTGT 57.099 25.926 0.00 0.00 0.00 2.83
3591 5358 9.599322 GACATGTGTTCTAGTCTATTTGTTTTG 57.401 33.333 1.15 0.00 0.00 2.44
3592 5359 8.567948 ACATGTGTTCTAGTCTATTTGTTTTGG 58.432 33.333 0.00 0.00 0.00 3.28
3606 5373 5.476091 TTGTTTTGGGGTTTATCATCCAC 57.524 39.130 0.00 0.00 0.00 4.02
3612 5379 4.599041 TGGGGTTTATCATCCACTTTCTG 58.401 43.478 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 7.040686 AGTCTAATACAGCAAAATTTGTCGGTT 60.041 33.333 7.60 0.40 0.00 4.44
2 3 6.430000 AGTCTAATACAGCAAAATTTGTCGGT 59.570 34.615 7.60 8.82 0.00 4.69
3 4 6.842163 AGTCTAATACAGCAAAATTTGTCGG 58.158 36.000 7.60 3.66 0.00 4.79
4 5 7.636359 GCTAGTCTAATACAGCAAAATTTGTCG 59.364 37.037 7.60 1.69 34.39 4.35
5 6 7.910683 GGCTAGTCTAATACAGCAAAATTTGTC 59.089 37.037 7.60 0.25 35.31 3.18
6 7 7.393234 TGGCTAGTCTAATACAGCAAAATTTGT 59.607 33.333 7.60 0.00 35.31 2.83
8 9 7.393234 TGTGGCTAGTCTAATACAGCAAAATTT 59.607 33.333 0.00 0.00 35.31 1.82
9 10 6.884295 TGTGGCTAGTCTAATACAGCAAAATT 59.116 34.615 0.00 0.00 35.31 1.82
10 11 6.414732 TGTGGCTAGTCTAATACAGCAAAAT 58.585 36.000 0.00 0.00 35.31 1.82
11 12 5.800296 TGTGGCTAGTCTAATACAGCAAAA 58.200 37.500 0.00 0.00 35.31 2.44
12 13 5.414789 TGTGGCTAGTCTAATACAGCAAA 57.585 39.130 0.00 0.00 35.31 3.68
14 15 5.614324 ATTGTGGCTAGTCTAATACAGCA 57.386 39.130 0.00 0.00 35.31 4.41
15 16 6.513180 TGTATTGTGGCTAGTCTAATACAGC 58.487 40.000 22.50 8.01 38.54 4.40
16 17 9.847706 CTATGTATTGTGGCTAGTCTAATACAG 57.152 37.037 26.47 17.68 43.37 2.74
17 18 9.363401 ACTATGTATTGTGGCTAGTCTAATACA 57.637 33.333 25.63 25.63 43.89 2.29
21 22 9.192642 TGTTACTATGTATTGTGGCTAGTCTAA 57.807 33.333 0.00 0.00 0.00 2.10
22 23 8.756486 TGTTACTATGTATTGTGGCTAGTCTA 57.244 34.615 0.00 0.00 0.00 2.59
67 68 9.710818 TGAAGGTAGTAACATAGTCTAGGAATT 57.289 33.333 0.00 0.00 0.00 2.17
142 143 7.880195 GTCCCAATGCAATATGAGTCTATAACT 59.120 37.037 0.00 0.00 42.42 2.24
201 203 7.640313 TGAGTTAATGAGGAGAGAGGTAGTTA 58.360 38.462 0.00 0.00 0.00 2.24
227 229 5.363101 TCAACAAATTTGCTTATGTGGCAA 58.637 33.333 18.12 0.00 46.12 4.52
266 268 1.002544 AGTGGGAGTAACTTCAGCAGC 59.997 52.381 0.00 0.00 0.00 5.25
269 271 2.417719 CACAGTGGGAGTAACTTCAGC 58.582 52.381 0.00 0.00 0.00 4.26
543 547 3.623510 GCCATAGTGGAAGTAACTTCAGC 59.376 47.826 0.00 0.00 40.96 4.26
546 550 5.051153 GCTAGCCATAGTGGAAGTAACTTC 58.949 45.833 2.29 0.00 40.96 3.01
555 560 2.303022 GCATAAGGCTAGCCATAGTGGA 59.697 50.000 34.70 8.79 38.74 4.02
558 563 2.975489 ACTGCATAAGGCTAGCCATAGT 59.025 45.455 34.70 22.94 45.15 2.12
559 564 3.692257 ACTGCATAAGGCTAGCCATAG 57.308 47.619 34.70 22.36 45.15 2.23
560 565 3.554960 CGAACTGCATAAGGCTAGCCATA 60.555 47.826 34.70 27.54 45.15 2.74
561 566 2.808202 CGAACTGCATAAGGCTAGCCAT 60.808 50.000 34.70 26.20 45.15 4.40
562 567 1.473257 CGAACTGCATAAGGCTAGCCA 60.473 52.381 34.70 16.70 45.15 4.75
563 568 1.221414 CGAACTGCATAAGGCTAGCC 58.779 55.000 27.19 27.19 45.15 3.93
564 569 0.583917 GCGAACTGCATAAGGCTAGC 59.416 55.000 6.04 6.04 45.45 3.42
582 587 2.600867 CGACTTGATTTCTCTCGAAGGC 59.399 50.000 0.00 0.00 0.00 4.35
584 589 6.258899 TCATACGACTTGATTTCTCTCGAAG 58.741 40.000 0.00 0.00 0.00 3.79
610 615 8.713971 TCAGCTACCAGGATTCATTTAAGAATA 58.286 33.333 0.00 0.00 38.30 1.75
628 633 1.009829 CGTTTGCCAGATCAGCTACC 58.990 55.000 8.94 0.00 0.00 3.18
657 662 3.643763 CGGAGGATAGAATTCTTCCACG 58.356 50.000 25.56 24.03 40.88 4.94
706 716 1.008538 CAGTTGCCGCAGTGTTTCC 60.009 57.895 0.00 0.00 0.00 3.13
717 727 2.639327 GGACCCACATGCAGTTGCC 61.639 63.158 1.06 0.00 41.18 4.52
740 750 2.672996 CAAGTGGGGCCGGAACAG 60.673 66.667 5.05 0.00 0.00 3.16
792 802 2.346099 GCTCAAGCATTTAAACGGCA 57.654 45.000 14.13 0.00 41.59 5.69
810 833 2.230660 ACTACCAAGAAACCAGCTTGC 58.769 47.619 0.00 0.00 41.00 4.01
818 841 3.986277 TCTCGACCAACTACCAAGAAAC 58.014 45.455 0.00 0.00 0.00 2.78
819 842 4.100498 AGTTCTCGACCAACTACCAAGAAA 59.900 41.667 3.61 0.00 32.08 2.52
820 843 3.640029 AGTTCTCGACCAACTACCAAGAA 59.360 43.478 3.61 0.00 32.08 2.52
835 858 2.857618 CGAAGAGTGGAAGAGTTCTCG 58.142 52.381 0.00 0.00 32.90 4.04
917 949 1.644509 TGTGTCTCTGTATGTGGGCT 58.355 50.000 0.00 0.00 0.00 5.19
1085 1128 2.176273 GCCGCAGCTACATCCACAG 61.176 63.158 0.00 0.00 35.50 3.66
1092 1135 3.625897 ACACAGGCCGCAGCTACA 61.626 61.111 0.00 0.00 39.73 2.74
1100 1143 3.551496 ATGTCCCACACACAGGCCG 62.551 63.158 0.00 0.00 38.04 6.13
1284 1327 2.760385 GAGGTGGGAGACGAGGGG 60.760 72.222 0.00 0.00 0.00 4.79
1383 1426 0.542333 GGCTGTTAGGGAGAAGGGAC 59.458 60.000 0.00 0.00 0.00 4.46
1420 1463 5.522824 GTGACGAAGGGGATAGTTAATCAAC 59.477 44.000 0.00 0.00 36.20 3.18
1422 1465 4.100498 GGTGACGAAGGGGATAGTTAATCA 59.900 45.833 0.00 0.00 36.20 2.57
1423 1466 4.629092 GGTGACGAAGGGGATAGTTAATC 58.371 47.826 0.00 0.00 0.00 1.75
1424 1467 4.684484 GGTGACGAAGGGGATAGTTAAT 57.316 45.455 0.00 0.00 0.00 1.40
1446 1489 3.904136 AAATAACAGCAGCACAGTCAC 57.096 42.857 0.00 0.00 0.00 3.67
1458 1501 3.117832 CGAACGCTGCAACAAAATAACAG 59.882 43.478 0.00 0.00 0.00 3.16
1460 1503 2.403698 CCGAACGCTGCAACAAAATAAC 59.596 45.455 0.00 0.00 0.00 1.89
1464 1507 1.587613 GCCGAACGCTGCAACAAAA 60.588 52.632 0.00 0.00 0.00 2.44
1465 1508 2.025441 GCCGAACGCTGCAACAAA 59.975 55.556 0.00 0.00 0.00 2.83
1554 1603 3.565910 CTGCGATAGGCTCCTCCGC 62.566 68.421 20.95 20.95 43.44 5.54
1572 1621 2.126463 TACTGCTGCTGCGTCGTC 60.126 61.111 11.21 0.00 43.34 4.20
1573 1622 2.430921 GTACTGCTGCTGCGTCGT 60.431 61.111 11.21 10.07 43.34 4.34
1574 1623 3.181967 GGTACTGCTGCTGCGTCG 61.182 66.667 11.21 4.62 43.34 5.12
1983 2032 1.475280 TCGGAGTACATGTGCAGGTAC 59.525 52.381 16.62 16.39 45.72 3.34
2034 2083 1.021390 CGGTGAGCAGGATGTTGGAC 61.021 60.000 0.00 0.00 39.31 4.02
2358 2407 2.284995 GGGTCCAGCACCTCCTCT 60.285 66.667 0.00 0.00 45.95 3.69
2457 2506 3.842923 ATGCTGGGCCTCTCGTCG 61.843 66.667 4.53 0.00 0.00 5.12
2682 2731 3.886549 AGCTATATAGTTCACGTGTCGC 58.113 45.455 16.51 7.03 0.00 5.19
2878 2962 9.530129 GATAGCAAATCGTAGCAATGTTAATAC 57.470 33.333 0.00 0.00 0.00 1.89
2879 2963 8.432359 CGATAGCAAATCGTAGCAATGTTAATA 58.568 33.333 11.98 0.00 36.84 0.98
2880 2964 7.290842 CGATAGCAAATCGTAGCAATGTTAAT 58.709 34.615 11.98 0.00 36.84 1.40
2911 2995 3.761218 ACCATTATGTCACGAAATTGGCA 59.239 39.130 0.00 0.00 35.04 4.92
2912 2996 4.370364 ACCATTATGTCACGAAATTGGC 57.630 40.909 0.00 0.00 0.00 4.52
2993 4708 8.286097 CCAACTACTCTTTCTCTCACAAAATTC 58.714 37.037 0.00 0.00 0.00 2.17
3012 4727 5.119694 CAGCTTTATTCCTCCTCCAACTAC 58.880 45.833 0.00 0.00 0.00 2.73
3152 4877 2.779430 TGGGCAGAGACATCACCATTAT 59.221 45.455 0.00 0.00 0.00 1.28
3228 4956 7.999679 TGATGATTTCTTATACCCTGCAAAAG 58.000 34.615 0.00 0.00 0.00 2.27
3295 5023 1.278413 GTTCAGGGGTGGAACTAGGAC 59.722 57.143 0.00 0.00 41.05 3.85
3335 5069 3.758023 ACAAAATCGACATGCCTTGATGA 59.242 39.130 0.00 0.00 0.00 2.92
3385 5119 5.159273 TGATTGTAGGCAGTCACATGTTA 57.841 39.130 0.00 0.00 36.60 2.41
3386 5120 4.019792 TGATTGTAGGCAGTCACATGTT 57.980 40.909 0.00 0.00 36.60 2.71
3534 5301 5.126699 TGTAACCTTGTGGGACCTAAAAA 57.873 39.130 0.00 0.00 38.76 1.94
3591 5358 4.600062 ACAGAAAGTGGATGATAAACCCC 58.400 43.478 0.00 0.00 0.00 4.95
3592 5359 7.881775 AATACAGAAAGTGGATGATAAACCC 57.118 36.000 0.00 0.00 25.88 4.11


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

AutoCloner maintained by Alex Coulton.