Multiple sequence alignment - TraesCS4D01G083300

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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 TraesCS4D01G083300 chr4D 100.000 3161 0 0 1 3161 57078374 57075214 0.000000e+00 5838
1 TraesCS4D01G083300 chr4D 89.720 107 7 1 398 500 444524049 444523943 1.980000e-27 134
2 TraesCS4D01G083300 chr4B 94.993 2696 89 18 497 3161 85704177 85701497 0.000000e+00 4189
3 TraesCS4D01G083300 chr4B 93.580 405 19 3 1 400 85704575 85704173 5.840000e-167 597
4 TraesCS4D01G083300 chr4A 94.914 2143 80 17 338 2477 539752682 539754798 0.000000e+00 3326
5 TraesCS4D01G083300 chr4A 97.935 339 6 1 1 339 539752240 539752577 1.260000e-163 586
6 TraesCS4D01G083300 chr3A 92.233 103 8 0 398 500 406731 406629 2.540000e-31 147
7 TraesCS4D01G083300 chr2B 91.262 103 7 2 398 500 173468312 173468212 4.250000e-29 139
8 TraesCS4D01G083300 chr2B 87.850 107 5 4 398 500 657077573 657077675 5.540000e-23 119
9 TraesCS4D01G083300 chr2B 87.037 108 8 4 393 500 551551630 551551529 1.990000e-22 117
10 TraesCS4D01G083300 chr3B 87.069 116 9 4 393 508 111669788 111669679 3.310000e-25 126
11 TraesCS4D01G083300 chr5B 88.462 104 10 2 398 500 21548829 21548727 1.190000e-24 124
12 TraesCS4D01G083300 chr1D 90.625 96 5 2 405 500 27695746 27695655 1.190000e-24 124
13 TraesCS4D01G083300 chr6B 86.486 111 12 2 391 501 219773387 219773494 5.540000e-23 119


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 TraesCS4D01G083300 chr4D 57075214 57078374 3160 True 5838 5838 100.0000 1 3161 1 chr4D.!!$R1 3160
1 TraesCS4D01G083300 chr4B 85701497 85704575 3078 True 2393 4189 94.2865 1 3161 2 chr4B.!!$R1 3160
2 TraesCS4D01G083300 chr4A 539752240 539754798 2558 False 1956 3326 96.4245 1 2477 2 chr4A.!!$F1 2476

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
407 519 0.178903 ACAGCCAAGTACTCCCTCCA 60.179 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2218 2331 0.916086 ACACTGGTGACAACAAGGGA 59.084 50.0 7.78 0.0 42.06 4.2 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
393 505 5.529791 TGACTCTTATCGCTAATAACAGCC 58.470 41.667 0.00 0.00 38.37 4.85
401 513 4.679662 TCGCTAATAACAGCCAAGTACTC 58.320 43.478 0.00 0.00 38.37 2.59
407 519 0.178903 ACAGCCAAGTACTCCCTCCA 60.179 55.000 0.00 0.00 0.00 3.86
439 551 3.629398 GCTTGTCCCTCAAATGGATGTAG 59.371 47.826 0.00 0.00 35.48 2.74
440 552 4.848357 CTTGTCCCTCAAATGGATGTAGT 58.152 43.478 0.00 0.00 35.48 2.73
441 553 4.220693 TGTCCCTCAAATGGATGTAGTG 57.779 45.455 0.00 0.00 33.65 2.74
442 554 2.945668 GTCCCTCAAATGGATGTAGTGC 59.054 50.000 0.00 0.00 33.65 4.40
443 555 2.846206 TCCCTCAAATGGATGTAGTGCT 59.154 45.455 0.00 0.00 0.00 4.40
444 556 4.037222 TCCCTCAAATGGATGTAGTGCTA 58.963 43.478 0.00 0.00 0.00 3.49
445 557 4.101585 TCCCTCAAATGGATGTAGTGCTAG 59.898 45.833 0.00 0.00 0.00 3.42
446 558 4.101585 CCCTCAAATGGATGTAGTGCTAGA 59.898 45.833 0.00 0.00 0.00 2.43
447 559 5.221803 CCCTCAAATGGATGTAGTGCTAGAT 60.222 44.000 0.00 0.00 0.00 1.98
449 561 6.870965 CCTCAAATGGATGTAGTGCTAGATAC 59.129 42.308 0.00 0.00 0.00 2.24
450 562 7.360113 TCAAATGGATGTAGTGCTAGATACA 57.640 36.000 4.10 4.10 34.64 2.29
451 563 7.966812 TCAAATGGATGTAGTGCTAGATACAT 58.033 34.615 12.75 12.75 40.77 2.29
458 570 8.249327 GATGTAGTGCTAGATACATCCATTTG 57.751 38.462 21.21 0.00 46.59 2.32
459 571 7.360113 TGTAGTGCTAGATACATCCATTTGA 57.640 36.000 0.00 0.00 0.00 2.69
460 572 7.436933 TGTAGTGCTAGATACATCCATTTGAG 58.563 38.462 0.00 0.00 0.00 3.02
461 573 5.862845 AGTGCTAGATACATCCATTTGAGG 58.137 41.667 0.00 0.00 0.00 3.86
462 574 4.999950 GTGCTAGATACATCCATTTGAGGG 59.000 45.833 0.00 0.00 0.00 4.30
463 575 4.907269 TGCTAGATACATCCATTTGAGGGA 59.093 41.667 0.00 0.00 39.14 4.20
464 576 5.549228 TGCTAGATACATCCATTTGAGGGAT 59.451 40.000 0.00 0.00 45.98 3.85
465 577 6.730507 TGCTAGATACATCCATTTGAGGGATA 59.269 38.462 0.00 0.00 43.24 2.59
466 578 7.237471 TGCTAGATACATCCATTTGAGGGATAA 59.763 37.037 0.00 0.00 43.24 1.75
467 579 7.768120 GCTAGATACATCCATTTGAGGGATAAG 59.232 40.741 0.00 0.00 43.24 1.73
468 580 6.479884 AGATACATCCATTTGAGGGATAAGC 58.520 40.000 0.00 0.00 43.24 3.09
469 581 4.803329 ACATCCATTTGAGGGATAAGCT 57.197 40.909 0.00 0.00 43.24 3.74
470 582 5.134725 ACATCCATTTGAGGGATAAGCTT 57.865 39.130 3.48 3.48 43.24 3.74
489 601 1.314730 TGGGACAAGCTTTTTCGGAC 58.685 50.000 0.00 0.00 31.92 4.79
566 678 8.147704 CCCTTCTGTACAAAACATTTTTGGTAT 58.852 33.333 14.24 0.00 34.29 2.73
867 980 7.349065 TGTGGATCATCTATTGGCTATGGATAT 59.651 37.037 7.39 3.26 33.15 1.63
984 1097 6.045072 TCAGACGGTACTCAATAATTGGTT 57.955 37.500 0.00 0.00 0.00 3.67
1103 1216 3.476552 AGCTTGAAAGTGAATCGGACAA 58.523 40.909 0.00 0.00 0.00 3.18
1122 1235 4.616953 ACAAGAATGCTTTTGGGTTAACG 58.383 39.130 0.00 0.00 30.14 3.18
1416 1529 7.798071 TCGGATGTCCTAATTTGGTTATAGTT 58.202 34.615 5.81 0.00 0.00 2.24
1514 1627 2.729028 AACCTTGGTTACTGCACAGT 57.271 45.000 8.57 8.57 45.02 3.55
1515 1628 2.729028 ACCTTGGTTACTGCACAGTT 57.271 45.000 8.86 0.00 42.54 3.16
1572 1685 1.135915 TGCCGAAACATTTGTGCACTT 59.864 42.857 19.41 1.94 0.00 3.16
1962 2075 4.821805 AGAATTCTTCATGTGAACCGTTGT 59.178 37.500 0.88 0.00 0.00 3.32
1984 2097 2.030457 CGAAACATATGCGACCAAGGAC 59.970 50.000 1.58 0.00 0.00 3.85
2041 2154 3.007940 GGTCCTGCATATACATGGCTGTA 59.992 47.826 0.00 0.45 41.92 2.74
2127 2240 0.038166 ACGAAGCCATGTCCATTGGT 59.962 50.000 1.86 0.00 0.00 3.67
2130 2243 0.680921 AAGCCATGTCCATTGGTCCG 60.681 55.000 1.86 0.00 0.00 4.79
2218 2331 2.363306 TGACTTGAACAAGGTGCCAT 57.637 45.000 17.05 0.00 42.53 4.40
2255 2369 5.339177 CAGTGTGTTTGTCATTACAGCAAA 58.661 37.500 0.00 0.00 36.83 3.68
2256 2370 5.456497 CAGTGTGTTTGTCATTACAGCAAAG 59.544 40.000 0.00 0.00 36.83 2.77
2257 2371 5.125417 AGTGTGTTTGTCATTACAGCAAAGT 59.875 36.000 0.00 0.00 36.83 2.66
2321 2435 5.562635 TCCGGTTCATACTTATTTGGTTGT 58.437 37.500 0.00 0.00 0.00 3.32
2324 2438 6.090129 CGGTTCATACTTATTTGGTTGTTGG 58.910 40.000 0.00 0.00 0.00 3.77
2415 2529 0.813184 ATTTGCATGTTCCCGCTCTG 59.187 50.000 0.00 0.00 0.00 3.35
2453 2567 9.793252 GTAAAGTGCTGTCATGAAATTTGATAT 57.207 29.630 0.00 0.00 0.00 1.63
2455 2569 8.697846 AAGTGCTGTCATGAAATTTGATATTG 57.302 30.769 0.00 0.00 0.00 1.90
2457 2571 7.037438 GTGCTGTCATGAAATTTGATATTGGT 58.963 34.615 0.00 0.00 0.00 3.67
2496 2610 9.612620 CTTATTTAGTCATTTCGAAAGCACTTT 57.387 29.630 22.70 13.94 35.14 2.66
2528 2643 3.815401 GTGATTCATAACCATTCCCCGAG 59.185 47.826 0.00 0.00 0.00 4.63
2530 2645 3.838244 TTCATAACCATTCCCCGAGAG 57.162 47.619 0.00 0.00 0.00 3.20
2532 2647 0.393077 ATAACCATTCCCCGAGAGCG 59.607 55.000 0.00 0.00 37.24 5.03
2558 2674 6.963796 AGCTTGACTTCAGTTTCTACAAATG 58.036 36.000 0.00 0.00 0.00 2.32
2559 2675 5.626955 GCTTGACTTCAGTTTCTACAAATGC 59.373 40.000 0.00 0.00 0.00 3.56
2561 2677 7.307989 GCTTGACTTCAGTTTCTACAAATGCTA 60.308 37.037 0.00 0.00 0.00 3.49
2562 2678 8.621532 TTGACTTCAGTTTCTACAAATGCTAT 57.378 30.769 0.00 0.00 0.00 2.97
2580 2697 6.817765 TGCTATAAGAACCAAAAAGTCCTG 57.182 37.500 0.00 0.00 0.00 3.86
2589 2706 4.398319 ACCAAAAAGTCCTGACCAGTATG 58.602 43.478 0.00 0.00 0.00 2.39
2591 2708 5.222130 ACCAAAAAGTCCTGACCAGTATGAT 60.222 40.000 0.00 0.00 39.69 2.45
2630 2749 6.309357 TCTTGGTAAGAGTTGTGTAGGTCTA 58.691 40.000 0.00 0.00 32.71 2.59
2652 2771 4.647611 ACACCAAATTGGAACTACGATCA 58.352 39.130 20.25 0.00 40.96 2.92
2669 2788 8.904834 ACTACGATCAGTCAAATAGTAATCACT 58.095 33.333 0.00 0.00 38.91 3.41
2716 2837 3.002791 ACATGAAACTGCCACATACTCG 58.997 45.455 0.00 0.00 0.00 4.18
2724 2845 3.760151 ACTGCCACATACTCGTACACTTA 59.240 43.478 0.00 0.00 0.00 2.24
2725 2846 4.219070 ACTGCCACATACTCGTACACTTAA 59.781 41.667 0.00 0.00 0.00 1.85
2726 2847 5.136816 TGCCACATACTCGTACACTTAAA 57.863 39.130 0.00 0.00 0.00 1.52
2727 2848 5.539979 TGCCACATACTCGTACACTTAAAA 58.460 37.500 0.00 0.00 0.00 1.52
2728 2849 5.636121 TGCCACATACTCGTACACTTAAAAG 59.364 40.000 0.00 0.00 0.00 2.27
2729 2850 5.445540 GCCACATACTCGTACACTTAAAAGC 60.446 44.000 0.00 0.00 0.00 3.51
2730 2851 5.636121 CCACATACTCGTACACTTAAAAGCA 59.364 40.000 0.00 0.00 0.00 3.91
2731 2852 6.312918 CCACATACTCGTACACTTAAAAGCAT 59.687 38.462 0.00 0.00 0.00 3.79
2732 2853 7.173419 CACATACTCGTACACTTAAAAGCATG 58.827 38.462 0.00 0.00 0.00 4.06
2733 2854 7.062956 CACATACTCGTACACTTAAAAGCATGA 59.937 37.037 0.00 0.00 0.00 3.07
2735 2856 6.408858 ACTCGTACACTTAAAAGCATGATG 57.591 37.500 0.00 0.00 0.00 3.07
2736 2857 5.351465 ACTCGTACACTTAAAAGCATGATGG 59.649 40.000 0.00 0.00 0.00 3.51
2737 2858 4.094294 TCGTACACTTAAAAGCATGATGGC 59.906 41.667 0.00 0.00 0.00 4.40
2783 2904 3.327757 TGCTTGTACACTCAGGATCCTTT 59.672 43.478 13.00 0.00 0.00 3.11
2784 2905 3.935828 GCTTGTACACTCAGGATCCTTTC 59.064 47.826 13.00 0.00 0.00 2.62
2830 2951 4.568072 ACTGCCACAATTCACTGGTATA 57.432 40.909 0.00 0.00 0.00 1.47
2831 2952 4.261801 ACTGCCACAATTCACTGGTATAC 58.738 43.478 0.00 0.00 0.00 1.47
2832 2953 4.019321 ACTGCCACAATTCACTGGTATACT 60.019 41.667 2.25 0.00 0.00 2.12
2833 2954 5.188948 ACTGCCACAATTCACTGGTATACTA 59.811 40.000 2.25 0.00 0.00 1.82
2834 2955 5.670485 TGCCACAATTCACTGGTATACTAG 58.330 41.667 14.21 14.21 0.00 2.57
2955 3099 7.831753 GCTCAACAGCTATATAGTTCCAGATA 58.168 38.462 11.38 0.00 43.09 1.98
2959 3103 6.256819 ACAGCTATATAGTTCCAGATAGCCA 58.743 40.000 11.38 0.00 45.17 4.75
3013 3157 4.183865 TGGCAACAGTTTAGATCAGATCG 58.816 43.478 4.67 0.00 46.17 3.69
3032 3176 2.404789 CGCCACGCTAAAGCCATG 59.595 61.111 0.00 0.00 37.91 3.66
3034 3178 1.439353 CGCCACGCTAAAGCCATGAT 61.439 55.000 0.00 0.00 37.91 2.45
3035 3179 0.029834 GCCACGCTAAAGCCATGATG 59.970 55.000 0.00 0.00 37.91 3.07
3058 3202 3.563808 TGTCATGAGTAAAACACCTGTGC 59.436 43.478 0.00 0.00 0.00 4.57
3089 3233 0.034059 CGGCATCACCCTGACCTATC 59.966 60.000 0.00 0.00 33.26 2.08
3124 3268 1.334243 CTACTACCCGAAGAAGCTCCG 59.666 57.143 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
393 505 1.776662 TCGGATGGAGGGAGTACTTG 58.223 55.000 0.00 0.00 0.00 3.16
401 513 1.474077 CAAGCTTTTTCGGATGGAGGG 59.526 52.381 0.00 0.00 0.00 4.30
407 519 2.224769 TGAGGGACAAGCTTTTTCGGAT 60.225 45.455 0.00 0.00 0.00 4.18
439 551 4.999950 CCCTCAAATGGATGTATCTAGCAC 59.000 45.833 0.00 0.00 0.00 4.40
440 552 4.907269 TCCCTCAAATGGATGTATCTAGCA 59.093 41.667 0.00 0.00 0.00 3.49
441 553 5.489792 TCCCTCAAATGGATGTATCTAGC 57.510 43.478 0.00 0.00 0.00 3.42
442 554 7.768120 GCTTATCCCTCAAATGGATGTATCTAG 59.232 40.741 2.10 0.00 42.57 2.43
443 555 7.459125 AGCTTATCCCTCAAATGGATGTATCTA 59.541 37.037 2.10 0.00 42.57 1.98
444 556 6.274200 AGCTTATCCCTCAAATGGATGTATCT 59.726 38.462 2.10 0.00 42.57 1.98
445 557 6.479884 AGCTTATCCCTCAAATGGATGTATC 58.520 40.000 2.10 0.00 42.57 2.24
446 558 6.460103 AGCTTATCCCTCAAATGGATGTAT 57.540 37.500 2.10 0.00 42.57 2.29
447 559 5.912149 AGCTTATCCCTCAAATGGATGTA 57.088 39.130 2.10 0.00 42.57 2.29
449 561 4.280174 CCAAGCTTATCCCTCAAATGGATG 59.720 45.833 0.00 0.00 42.57 3.51
450 562 4.477249 CCAAGCTTATCCCTCAAATGGAT 58.523 43.478 0.00 0.00 44.71 3.41
451 563 3.373001 CCCAAGCTTATCCCTCAAATGGA 60.373 47.826 0.00 0.00 36.05 3.41
452 564 2.961062 CCCAAGCTTATCCCTCAAATGG 59.039 50.000 0.00 0.00 0.00 3.16
453 565 3.633986 GTCCCAAGCTTATCCCTCAAATG 59.366 47.826 0.00 0.00 0.00 2.32
454 566 3.269381 TGTCCCAAGCTTATCCCTCAAAT 59.731 43.478 0.00 0.00 0.00 2.32
455 567 2.647299 TGTCCCAAGCTTATCCCTCAAA 59.353 45.455 0.00 0.00 0.00 2.69
456 568 2.274542 TGTCCCAAGCTTATCCCTCAA 58.725 47.619 0.00 0.00 0.00 3.02
457 569 1.965414 TGTCCCAAGCTTATCCCTCA 58.035 50.000 0.00 0.00 0.00 3.86
458 570 2.924421 CTTGTCCCAAGCTTATCCCTC 58.076 52.381 0.00 0.00 0.00 4.30
459 571 1.064389 GCTTGTCCCAAGCTTATCCCT 60.064 52.381 18.97 0.00 40.01 4.20
460 572 1.393603 GCTTGTCCCAAGCTTATCCC 58.606 55.000 18.97 0.00 40.01 3.85
467 579 1.602920 CCGAAAAAGCTTGTCCCAAGC 60.603 52.381 18.69 18.69 43.31 4.01
468 580 1.953686 TCCGAAAAAGCTTGTCCCAAG 59.046 47.619 0.00 0.00 0.00 3.61
469 581 1.679153 GTCCGAAAAAGCTTGTCCCAA 59.321 47.619 0.00 0.00 0.00 4.12
470 582 1.314730 GTCCGAAAAAGCTTGTCCCA 58.685 50.000 0.00 0.00 0.00 4.37
489 601 0.970937 TCAAGCTGGTACTCCCTCCG 60.971 60.000 0.00 0.00 0.00 4.63
529 641 1.879575 ACAGAAGGGGCATAGTAGCA 58.120 50.000 0.00 0.00 35.83 3.49
566 678 9.418045 CAGAAAAAGAAAGGAAAAACAGTACAA 57.582 29.630 0.00 0.00 0.00 2.41
572 684 7.102346 TCATGCAGAAAAAGAAAGGAAAAACA 58.898 30.769 0.00 0.00 0.00 2.83
1103 1216 3.634910 ACACGTTAACCCAAAAGCATTCT 59.365 39.130 0.00 0.00 0.00 2.40
1122 1235 5.237779 TCGAACCTTGAACCAATTCTTACAC 59.762 40.000 0.00 0.00 35.69 2.90
1196 1309 3.759581 CACTGGGCATGCTCCTTATATT 58.240 45.455 16.70 0.00 0.00 1.28
1200 1313 1.077501 GCACTGGGCATGCTCCTTA 60.078 57.895 16.70 0.00 43.97 2.69
1299 1412 5.163141 TGTTCCAGAAACTCCCACTTCATAA 60.163 40.000 0.00 0.00 38.76 1.90
1416 1529 6.596106 TGATATTTAAGCAGCGGTAAAGTTCA 59.404 34.615 9.39 10.50 0.00 3.18
1514 1627 8.018537 TGAACTAATCCCTCGATCTGAAATAA 57.981 34.615 0.00 0.00 0.00 1.40
1515 1628 7.597288 TGAACTAATCCCTCGATCTGAAATA 57.403 36.000 0.00 0.00 0.00 1.40
1962 2075 2.093921 TCCTTGGTCGCATATGTTTCGA 60.094 45.455 4.29 2.16 0.00 3.71
1984 2097 1.447489 CGTCCTTGAGAGCCTGCAG 60.447 63.158 6.78 6.78 0.00 4.41
2041 2154 5.069516 CCAGGCCATTATTTGTAATCTTGCT 59.930 40.000 5.01 0.00 0.00 3.91
2218 2331 0.916086 ACACTGGTGACAACAAGGGA 59.084 50.000 7.78 0.00 42.06 4.20
2321 2435 3.568007 GTCTGCAACATCCTTTACACCAA 59.432 43.478 0.00 0.00 0.00 3.67
2324 2438 6.314784 GTTATGTCTGCAACATCCTTTACAC 58.685 40.000 14.94 3.23 45.78 2.90
2415 2529 2.102420 AGCACTTTACAGCCAAAAACCC 59.898 45.455 0.00 0.00 0.00 4.11
2485 2599 8.728088 ATCACATTAAACTTAAAGTGCTTTCG 57.272 30.769 11.05 0.00 40.32 3.46
2513 2628 0.393077 CGCTCTCGGGGAATGGTTAT 59.607 55.000 0.00 0.00 0.00 1.89
2558 2674 6.127980 GGTCAGGACTTTTTGGTTCTTATAGC 60.128 42.308 0.00 0.00 0.00 2.97
2559 2675 6.940298 TGGTCAGGACTTTTTGGTTCTTATAG 59.060 38.462 0.00 0.00 0.00 1.31
2561 2677 5.701224 TGGTCAGGACTTTTTGGTTCTTAT 58.299 37.500 0.00 0.00 0.00 1.73
2562 2678 5.118729 TGGTCAGGACTTTTTGGTTCTTA 57.881 39.130 0.00 0.00 0.00 2.10
2607 2724 5.470047 AGACCTACACAACTCTTACCAAG 57.530 43.478 0.00 0.00 0.00 3.61
2608 2725 5.834742 TGTAGACCTACACAACTCTTACCAA 59.165 40.000 5.82 0.00 40.77 3.67
2610 2727 5.972107 TGTAGACCTACACAACTCTTACC 57.028 43.478 5.82 0.00 40.77 2.85
2630 2749 4.647611 TGATCGTAGTTCCAATTTGGTGT 58.352 39.130 14.98 4.13 39.03 4.16
2652 2771 9.256228 TGGAGTTAGAGTGATTACTATTTGACT 57.744 33.333 0.00 0.00 37.25 3.41
2669 2788 3.578282 TGTTGCTGATCTGTGGAGTTAGA 59.422 43.478 1.27 0.00 0.00 2.10
2716 2837 5.567138 AGCCATCATGCTTTTAAGTGTAC 57.433 39.130 0.00 0.00 38.85 2.90
2727 2848 4.529897 TGAAGTTATCAAGCCATCATGCT 58.470 39.130 0.00 0.00 45.43 3.79
2728 2849 4.577693 TCTGAAGTTATCAAGCCATCATGC 59.422 41.667 0.00 0.00 37.67 4.06
2729 2850 6.688637 TTCTGAAGTTATCAAGCCATCATG 57.311 37.500 0.00 0.00 37.67 3.07
2730 2851 7.893124 ATTTCTGAAGTTATCAAGCCATCAT 57.107 32.000 0.00 0.00 37.67 2.45
2731 2852 8.806429 TTATTTCTGAAGTTATCAAGCCATCA 57.194 30.769 0.00 0.00 37.67 3.07
2763 2884 4.508662 GGAAAGGATCCTGAGTGTACAAG 58.491 47.826 17.02 0.00 45.56 3.16
2776 2897 4.021104 CACTTCAAAAAGGGGGAAAGGATC 60.021 45.833 0.00 0.00 36.78 3.36
2783 2904 1.342474 TGCACACTTCAAAAAGGGGGA 60.342 47.619 0.00 0.00 42.36 4.81
2784 2905 1.118838 TGCACACTTCAAAAAGGGGG 58.881 50.000 0.00 0.00 42.67 5.40
2823 2944 4.082895 GCGGATGTACCACTAGTATACCAG 60.083 50.000 11.92 0.00 38.90 4.00
2830 2951 3.688694 TTTTGCGGATGTACCACTAGT 57.311 42.857 0.00 0.00 38.90 2.57
2831 2952 6.260050 ACATATTTTTGCGGATGTACCACTAG 59.740 38.462 0.00 0.00 38.90 2.57
2832 2953 6.116806 ACATATTTTTGCGGATGTACCACTA 58.883 36.000 0.00 0.00 38.90 2.74
2833 2954 4.947388 ACATATTTTTGCGGATGTACCACT 59.053 37.500 0.00 0.00 38.90 4.00
2834 2955 5.243426 ACATATTTTTGCGGATGTACCAC 57.757 39.130 0.00 0.00 38.90 4.16
2862 2984 5.133941 TGCCTGTGGTAGTTTTATTTCACA 58.866 37.500 0.00 0.00 34.54 3.58
2940 3084 6.936279 GCTGTTGGCTATCTGGAACTATATA 58.064 40.000 0.00 0.00 38.06 0.86
2942 3086 5.215252 GCTGTTGGCTATCTGGAACTATA 57.785 43.478 0.00 0.00 38.06 1.31
2959 3103 6.318648 TCAACAATGTTTCTACTCAAGCTGTT 59.681 34.615 0.00 0.00 0.00 3.16
2973 3117 2.158827 GCCAAGGGGTTCAACAATGTTT 60.159 45.455 0.00 0.00 36.17 2.83
2998 3142 1.269831 GGCGCCGATCTGATCTAAACT 60.270 52.381 12.58 0.00 0.00 2.66
3032 3176 5.470098 ACAGGTGTTTTACTCATGACACATC 59.530 40.000 13.25 3.41 43.06 3.06
3034 3178 4.574421 CACAGGTGTTTTACTCATGACACA 59.426 41.667 13.25 0.61 43.06 3.72
3035 3179 4.554723 GCACAGGTGTTTTACTCATGACAC 60.555 45.833 4.88 4.88 41.14 3.67
3058 3202 1.517694 GATGCCGCATGGTGCAAAG 60.518 57.895 11.49 0.00 45.36 2.77
3089 3233 5.391736 CGGGTAGTAGCTTTATATCTGGTCG 60.392 48.000 0.00 0.00 0.00 4.79
3124 3268 1.098050 GAGATGTTCCATGTGCCACC 58.902 55.000 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.