Multiple sequence alignment - TraesCS6A01G234300

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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 TraesCS6A01G234300 chr6A 100.000 3119 0 0 1 3119 442038951 442035833 0.000000e+00 5760
1 TraesCS6A01G234300 chr6D 90.806 2567 117 46 1 2493 306304909 306302388 0.000000e+00 3323
2 TraesCS6A01G234300 chr6D 91.520 625 27 11 2502 3119 306302337 306301732 0.000000e+00 837
3 TraesCS6A01G234300 chr6B 91.410 1560 69 28 968 2493 473541693 473540165 0.000000e+00 2078
4 TraesCS6A01G234300 chr6B 91.309 909 37 23 3 881 473542794 473541898 0.000000e+00 1203
5 TraesCS6A01G234300 chr6B 88.014 584 40 10 2499 3077 473540117 473539559 0.000000e+00 664
6 TraesCS6A01G234300 chr2A 81.898 453 80 2 1550 2001 617813230 617813681 6.310000e-102 381
7 TraesCS6A01G234300 chr2B 81.236 453 83 2 1550 2001 556676602 556677053 6.360000e-97 364
8 TraesCS6A01G234300 chr2B 80.813 443 81 4 1550 1990 556517600 556518040 8.280000e-91 344
9 TraesCS6A01G234300 chr2B 80.353 453 85 4 1550 2000 556596098 556596548 1.070000e-89 340
10 TraesCS6A01G234300 chr2D 80.995 442 82 2 1550 1990 475985216 475985656 1.780000e-92 350
11 TraesCS6A01G234300 chr2D 80.813 443 81 4 1550 1990 475499558 475499998 8.280000e-91 344
12 TraesCS6A01G234300 chr2D 80.317 442 85 2 1550 1990 475877262 475877702 1.790000e-87 333


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 TraesCS6A01G234300 chr6A 442035833 442038951 3118 True 5760 5760 100.000000 1 3119 1 chr6A.!!$R1 3118
1 TraesCS6A01G234300 chr6D 306301732 306304909 3177 True 2080 3323 91.163000 1 3119 2 chr6D.!!$R1 3118
2 TraesCS6A01G234300 chr6B 473539559 473542794 3235 True 1315 2078 90.244333 3 3077 3 chr6B.!!$R1 3074

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
624 667 0.180878 TCATCCTGCATGCGGATTGA 59.819 50.0 29.44 25.2 39.2 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2360 2577 0.172803 ATGTACGCCGTCAGGAAGAC 59.827 55.0 0.0 0.0 44.02 3.01 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
177 189 1.009829 GCCGAATTCATGACGCTTCT 58.990 50.000 6.22 0.00 0.00 2.85
368 390 3.782443 CTAGGTGTGCCCCCGTCC 61.782 72.222 0.00 0.00 34.57 4.79
398 420 1.573829 TTCAGGCCATCGACGTTTGC 61.574 55.000 5.01 0.00 0.00 3.68
414 436 2.472695 TTGCTGTAGCCTTGTAGGTG 57.527 50.000 0.80 0.00 41.18 4.00
487 509 0.602905 CTGACGGTGTTCCCAGGTTC 60.603 60.000 0.00 0.00 0.00 3.62
490 512 1.959226 CGGTGTTCCCAGGTTCGTG 60.959 63.158 0.00 0.00 0.00 4.35
572 597 0.740737 CCATTTGGCCCAATCTCGTC 59.259 55.000 0.00 0.00 0.00 4.20
576 601 0.400213 TTGGCCCAATCTCGTCAACT 59.600 50.000 0.00 0.00 0.00 3.16
578 603 0.250513 GGCCCAATCTCGTCAACTCT 59.749 55.000 0.00 0.00 0.00 3.24
580 605 1.363744 CCCAATCTCGTCAACTCTGC 58.636 55.000 0.00 0.00 0.00 4.26
585 610 1.550327 TCTCGTCAACTCTGCCAGAT 58.450 50.000 0.00 0.00 0.00 2.90
593 618 1.853963 ACTCTGCCAGATACCGAACT 58.146 50.000 0.00 0.00 0.00 3.01
610 640 1.959042 ACTGGTCGAATGCATCATCC 58.041 50.000 0.00 1.41 0.00 3.51
624 667 0.180878 TCATCCTGCATGCGGATTGA 59.819 50.000 29.44 25.20 39.20 2.57
626 669 0.536687 ATCCTGCATGCGGATTGAGG 60.537 55.000 28.32 19.59 38.05 3.86
627 670 1.452651 CCTGCATGCGGATTGAGGT 60.453 57.895 28.32 0.00 0.00 3.85
633 679 2.358898 GCATGCGGATTGAGGTATGTTT 59.641 45.455 0.00 0.00 0.00 2.83
683 730 2.126031 GAACCGGCTGGACGAGTC 60.126 66.667 21.41 3.43 39.21 3.36
758 805 1.082756 GACACACCGAAAAGCAGCG 60.083 57.895 0.00 0.00 0.00 5.18
814 862 3.681473 CCACCGGGCTCTTTTTCC 58.319 61.111 6.32 0.00 0.00 3.13
860 908 1.279496 TGAGGGGATGAGGACTGTTG 58.721 55.000 0.00 0.00 0.00 3.33
917 965 4.633126 TCGCTCGCGGAATTACTATACTAT 59.367 41.667 6.13 0.00 40.25 2.12
918 966 5.812127 TCGCTCGCGGAATTACTATACTATA 59.188 40.000 6.13 0.00 40.25 1.31
919 967 5.900789 CGCTCGCGGAATTACTATACTATAC 59.099 44.000 6.13 0.00 35.56 1.47
921 969 6.183360 GCTCGCGGAATTACTATACTATACCA 60.183 42.308 6.13 0.00 0.00 3.25
922 970 7.468357 GCTCGCGGAATTACTATACTATACCAT 60.468 40.741 6.13 0.00 0.00 3.55
923 971 8.962884 TCGCGGAATTACTATACTATACCATA 57.037 34.615 6.13 0.00 0.00 2.74
924 972 9.394767 TCGCGGAATTACTATACTATACCATAA 57.605 33.333 6.13 0.00 0.00 1.90
978 1158 1.029681 CCAAGCCGGCCTATAAAACC 58.970 55.000 26.15 0.00 0.00 3.27
1082 1262 3.137459 AGGAGACGGAGCAGAGCG 61.137 66.667 0.00 0.00 0.00 5.03
1084 1264 3.444805 GAGACGGAGCAGAGCGGT 61.445 66.667 0.00 0.00 0.00 5.68
1085 1265 2.992114 AGACGGAGCAGAGCGGTT 60.992 61.111 0.00 0.00 0.00 4.44
1094 1274 0.449388 GCAGAGCGGTTGATTGGAAG 59.551 55.000 0.00 0.00 0.00 3.46
1098 1278 1.131315 GAGCGGTTGATTGGAAGAAGC 59.869 52.381 0.00 0.00 0.00 3.86
1153 1333 2.658321 ATCGGTAGCGATGGAGGGGT 62.658 60.000 27.54 2.87 0.00 4.95
1160 1340 1.141881 CGATGGAGGGGTCAACGAG 59.858 63.158 0.00 0.00 33.27 4.18
1225 1405 0.312416 CATAGAGGAGCCCGACTTCG 59.688 60.000 0.00 0.00 39.44 3.79
1226 1406 0.106619 ATAGAGGAGCCCGACTTCGT 60.107 55.000 0.00 0.00 37.74 3.85
1242 1422 3.403558 GTGGAGGTGGAGGAGGCC 61.404 72.222 0.00 0.00 0.00 5.19
1281 1464 4.396854 GGATTCGTCTCCGGTTCG 57.603 61.111 0.00 5.32 33.95 3.95
1318 1501 2.030958 AACGACGGCGATTCCAACC 61.031 57.895 22.49 0.00 41.64 3.77
1347 1530 4.194720 ACCGATCGCGAGCAGACC 62.195 66.667 25.41 3.48 40.82 3.85
1356 1539 1.739562 CGAGCAGACCAGCCAAGTC 60.740 63.158 0.00 0.00 34.23 3.01
1405 1588 2.812011 GGCATCAAAGAACACGGTAAGT 59.188 45.455 0.00 0.00 0.00 2.24
1521 1732 4.876107 CGTATGCCTTTGGATTGTTAGACT 59.124 41.667 0.00 0.00 0.00 3.24
1522 1733 5.220662 CGTATGCCTTTGGATTGTTAGACTG 60.221 44.000 0.00 0.00 0.00 3.51
1523 1734 4.365514 TGCCTTTGGATTGTTAGACTGA 57.634 40.909 0.00 0.00 0.00 3.41
1528 1739 6.404074 GCCTTTGGATTGTTAGACTGATGAAG 60.404 42.308 0.00 0.00 0.00 3.02
1744 1955 2.586357 GCCGGGATGCTCTTCGTC 60.586 66.667 2.18 0.00 0.00 4.20
1910 2121 1.589993 CAGCGCTACATCGAGGTGG 60.590 63.158 10.99 11.58 0.00 4.61
1961 2172 4.187056 GCTTCGTCAGCTACCACC 57.813 61.111 0.00 0.00 46.27 4.61
2248 2460 2.309136 AAGGAATGGTTTGGTGGGAG 57.691 50.000 0.00 0.00 0.00 4.30
2315 2527 9.943163 GAGCAAGTTTTAGATATCCATTCTTTC 57.057 33.333 0.00 0.00 0.00 2.62
2361 2578 7.928103 AGTACGTATTTGAGATAAGTGATCGT 58.072 34.615 0.00 0.00 39.80 3.73
2362 2579 8.068977 AGTACGTATTTGAGATAAGTGATCGTC 58.931 37.037 0.00 0.00 39.80 4.20
2363 2580 7.028926 ACGTATTTGAGATAAGTGATCGTCT 57.971 36.000 0.00 0.00 39.80 4.18
2364 2581 7.481642 ACGTATTTGAGATAAGTGATCGTCTT 58.518 34.615 7.83 7.83 39.80 3.01
2365 2582 7.644551 ACGTATTTGAGATAAGTGATCGTCTTC 59.355 37.037 6.30 0.00 39.80 2.87
2366 2583 7.113684 CGTATTTGAGATAAGTGATCGTCTTCC 59.886 40.741 6.30 2.10 39.80 3.46
2367 2584 6.531503 TTTGAGATAAGTGATCGTCTTCCT 57.468 37.500 6.30 5.90 39.80 3.36
2368 2585 5.506686 TGAGATAAGTGATCGTCTTCCTG 57.493 43.478 6.30 0.00 39.80 3.86
2369 2586 5.193679 TGAGATAAGTGATCGTCTTCCTGA 58.806 41.667 6.30 0.00 39.80 3.86
2370 2587 5.066634 TGAGATAAGTGATCGTCTTCCTGAC 59.933 44.000 6.30 0.00 39.80 3.51
2377 2594 4.472702 GTCTTCCTGACGGCGTAC 57.527 61.111 14.74 7.58 35.81 3.67
2378 2595 1.582968 GTCTTCCTGACGGCGTACA 59.417 57.895 14.74 12.19 35.81 2.90
2379 2596 0.172803 GTCTTCCTGACGGCGTACAT 59.827 55.000 14.74 0.00 35.81 2.29
2395 2612 4.084013 GCGTACATAACTGGCATTCCATAC 60.084 45.833 0.00 0.00 42.51 2.39
2426 2643 4.095334 TGCAAAATCATTCCGTGATCTCAG 59.905 41.667 0.00 0.00 46.80 3.35
2429 2646 4.743057 AATCATTCCGTGATCTCAGTCA 57.257 40.909 0.00 0.00 46.80 3.41
2430 2647 3.510388 TCATTCCGTGATCTCAGTCAC 57.490 47.619 0.00 0.00 43.90 3.67
2434 2658 6.062095 TCATTCCGTGATCTCAGTCACTATA 58.938 40.000 5.61 0.00 44.89 1.31
2452 2676 7.278646 GTCACTATATGAGATTGTTTGCACTGA 59.721 37.037 0.00 0.00 38.28 3.41
2453 2677 7.493645 TCACTATATGAGATTGTTTGCACTGAG 59.506 37.037 0.00 0.00 31.91 3.35
2459 2688 5.410746 TGAGATTGTTTGCACTGAGATCTTC 59.589 40.000 0.00 0.00 0.00 2.87
2493 2722 5.221783 TGCAGGACAGCAATATCAGTATCAT 60.222 40.000 0.00 0.00 42.46 2.45
2494 2723 6.014327 TGCAGGACAGCAATATCAGTATCATA 60.014 38.462 0.00 0.00 42.46 2.15
2495 2724 7.046652 GCAGGACAGCAATATCAGTATCATAT 58.953 38.462 0.00 0.00 0.00 1.78
2496 2725 8.200120 GCAGGACAGCAATATCAGTATCATATA 58.800 37.037 0.00 0.00 0.00 0.86
2497 2726 9.747293 CAGGACAGCAATATCAGTATCATATAG 57.253 37.037 0.00 0.00 0.00 1.31
2526 2797 2.903784 ACACAGCACCTGTAGTTCCATA 59.096 45.455 0.00 0.00 43.43 2.74
2528 2799 3.684788 CACAGCACCTGTAGTTCCATAAC 59.315 47.826 0.00 0.00 43.43 1.89
2540 2811 8.267620 TGTAGTTCCATAACATTCTGACATTG 57.732 34.615 0.00 0.00 38.12 2.82
2621 2892 4.560128 TCTGAAGAATTCCGACACTGAAG 58.440 43.478 0.65 0.00 46.93 3.02
2747 3018 0.033090 AACGAAGACCCAGTCCGAAC 59.967 55.000 0.00 0.00 32.18 3.95
2788 3059 4.040217 TGCTTTGACAAATAAACAGCCCAT 59.960 37.500 0.05 0.00 0.00 4.00
2876 3147 0.802222 ACAACATCGATCGCTGACCG 60.802 55.000 24.44 13.89 38.61 4.79
2888 3159 1.079819 CTGACCGGCACAATCGACT 60.080 57.895 0.00 0.00 0.00 4.18
2889 3160 0.172578 CTGACCGGCACAATCGACTA 59.827 55.000 0.00 0.00 0.00 2.59
2890 3161 0.604073 TGACCGGCACAATCGACTAA 59.396 50.000 0.00 0.00 0.00 2.24
2980 3251 5.100751 AGCAATCATATTTTACTCGCAGC 57.899 39.130 0.00 0.00 0.00 5.25
3025 3299 2.900546 ACAGATAGGGATGAATCGGTCC 59.099 50.000 0.00 0.00 0.00 4.46
3041 3320 3.133437 TCCGACTGGAGATCCATCC 57.867 57.895 1.15 0.00 46.46 3.51
3050 3329 2.293118 TGGAGATCCATCCCTTGACTCA 60.293 50.000 0.00 0.00 42.01 3.41
3090 3369 0.036732 TCCATGGACCTGCAGTGTTC 59.963 55.000 11.44 9.66 0.00 3.18
3091 3370 0.037303 CCATGGACCTGCAGTGTTCT 59.963 55.000 13.81 0.00 0.00 3.01
3092 3371 1.278985 CCATGGACCTGCAGTGTTCTA 59.721 52.381 13.81 4.39 0.00 2.10
3098 3384 4.081642 TGGACCTGCAGTGTTCTATCTAAC 60.082 45.833 13.81 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 145 3.827898 GCACCGTCCCTCTCCTCG 61.828 72.222 0.00 0.00 0.00 4.63
398 420 3.097614 ACCTACACCTACAAGGCTACAG 58.902 50.000 0.00 0.00 39.63 2.74
414 436 4.429108 GAGATGCAGACAGAAGAACCTAC 58.571 47.826 0.00 0.00 0.00 3.18
477 499 0.834612 ACAGAACACGAACCTGGGAA 59.165 50.000 0.00 0.00 32.52 3.97
480 502 1.268539 GCAAACAGAACACGAACCTGG 60.269 52.381 0.00 0.00 32.52 4.45
487 509 0.522286 TTGCACGCAAACAGAACACG 60.522 50.000 1.07 0.00 32.44 4.49
490 512 2.531998 CGTTTTTGCACGCAAACAGAAC 60.532 45.455 16.37 15.91 44.39 3.01
562 587 1.338105 TGGCAGAGTTGACGAGATTGG 60.338 52.381 0.00 0.00 33.87 3.16
572 597 2.093973 AGTTCGGTATCTGGCAGAGTTG 60.094 50.000 23.24 12.20 0.00 3.16
576 601 0.824109 CCAGTTCGGTATCTGGCAGA 59.176 55.000 21.19 21.19 43.45 4.26
593 618 1.957668 CAGGATGATGCATTCGACCA 58.042 50.000 0.00 0.00 39.69 4.02
610 640 1.534163 CATACCTCAATCCGCATGCAG 59.466 52.381 19.57 6.53 0.00 4.41
624 667 2.854522 GCTCCACGCAAACATACCT 58.145 52.632 0.00 0.00 38.92 3.08
683 730 1.133407 CTCCTCGGAAGAAAGTCTCCG 59.867 57.143 4.14 4.14 46.06 4.63
778 825 1.007580 GCTACCTAACTTTGCGAGGC 58.992 55.000 0.00 0.00 33.28 4.70
814 862 0.598065 AAAAAGTAGGCTTGGCGCTG 59.402 50.000 7.64 0.00 39.13 5.18
860 908 5.751990 GGAATTGTGAATTGAGAATGGATGC 59.248 40.000 0.00 0.00 0.00 3.91
919 967 9.784680 GGTCTACACTATACGAATATGTTATGG 57.215 37.037 0.00 0.00 0.00 2.74
921 969 8.180267 GCGGTCTACACTATACGAATATGTTAT 58.820 37.037 0.00 0.00 0.00 1.89
922 970 7.361201 GGCGGTCTACACTATACGAATATGTTA 60.361 40.741 0.00 0.00 0.00 2.41
923 971 6.376978 GCGGTCTACACTATACGAATATGTT 58.623 40.000 0.00 0.00 0.00 2.71
924 972 5.106396 GGCGGTCTACACTATACGAATATGT 60.106 44.000 0.00 0.00 0.00 2.29
926 974 5.005740 TGGCGGTCTACACTATACGAATAT 58.994 41.667 0.00 0.00 0.00 1.28
982 1162 1.640670 TCCAAATTGAGAAGGGGGAGG 59.359 52.381 0.00 0.00 0.00 4.30
1082 1262 0.179189 CGCGCTTCTTCCAATCAACC 60.179 55.000 5.56 0.00 0.00 3.77
1084 1264 1.078709 CTCGCGCTTCTTCCAATCAA 58.921 50.000 5.56 0.00 0.00 2.57
1085 1265 0.740868 CCTCGCGCTTCTTCCAATCA 60.741 55.000 5.56 0.00 0.00 2.57
1094 1274 1.153349 AAGGAATCCCTCGCGCTTC 60.153 57.895 5.56 0.32 43.48 3.86
1153 1333 2.825532 TCACATGATCCTGACTCGTTGA 59.174 45.455 0.00 0.00 0.00 3.18
1160 1340 3.565764 TCCCAATCACATGATCCTGAC 57.434 47.619 0.00 0.00 32.75 3.51
1225 1405 3.403558 GGCCTCCTCCACCTCCAC 61.404 72.222 0.00 0.00 0.00 4.02
1226 1406 3.273071 ATGGCCTCCTCCACCTCCA 62.273 63.158 3.32 0.00 39.25 3.86
1281 1464 6.077838 GTCGTTGTTGTTGATAGATTGGAAC 58.922 40.000 0.00 0.00 0.00 3.62
1329 1512 2.951745 GTCTGCTCGCGATCGGTG 60.952 66.667 18.30 9.01 36.13 4.94
1347 1530 2.032528 TTCCTGCGGACTTGGCTG 59.967 61.111 0.00 0.00 0.00 4.85
1356 1539 1.078143 CTTTCCCCTCTTCCTGCGG 60.078 63.158 0.00 0.00 0.00 5.69
1424 1607 8.813282 GTTCCGTGTTGAATTAAACAAGAAAAT 58.187 29.630 19.75 0.00 41.52 1.82
1426 1609 6.469595 CGTTCCGTGTTGAATTAAACAAGAAA 59.530 34.615 19.75 6.22 41.52 2.52
1521 1732 2.289444 GGGAACAAGGACGACTTCATCA 60.289 50.000 0.00 0.00 37.29 3.07
1522 1733 2.289444 TGGGAACAAGGACGACTTCATC 60.289 50.000 0.00 0.00 37.29 2.92
1523 1734 1.697432 TGGGAACAAGGACGACTTCAT 59.303 47.619 0.00 0.00 37.29 2.57
1910 2121 2.654912 CGAAGCCGTCGTTGGTGAC 61.655 63.158 0.00 0.00 45.09 3.67
2214 2426 0.606401 TCCTTTCCCAAGCTTGCTCG 60.606 55.000 21.43 10.20 0.00 5.03
2217 2429 1.066645 CCATTCCTTTCCCAAGCTTGC 60.067 52.381 21.43 0.00 0.00 4.01
2271 2483 1.462283 CTCACTGCACTGCACACATAC 59.538 52.381 0.00 0.00 33.79 2.39
2337 2549 8.068977 AGACGATCACTTATCTCAAATACGTAC 58.931 37.037 0.00 0.00 31.87 3.67
2338 2550 8.151141 AGACGATCACTTATCTCAAATACGTA 57.849 34.615 0.00 0.00 31.87 3.57
2339 2551 7.028926 AGACGATCACTTATCTCAAATACGT 57.971 36.000 0.00 0.00 31.87 3.57
2340 2552 7.113684 GGAAGACGATCACTTATCTCAAATACG 59.886 40.741 0.00 0.00 31.87 3.06
2360 2577 0.172803 ATGTACGCCGTCAGGAAGAC 59.827 55.000 0.00 0.00 44.02 3.01
2361 2578 1.753930 TATGTACGCCGTCAGGAAGA 58.246 50.000 0.00 0.00 41.02 2.87
2362 2579 2.159282 AGTTATGTACGCCGTCAGGAAG 60.159 50.000 0.00 0.00 41.02 3.46
2363 2580 1.820519 AGTTATGTACGCCGTCAGGAA 59.179 47.619 0.00 0.00 41.02 3.36
2364 2581 1.133598 CAGTTATGTACGCCGTCAGGA 59.866 52.381 0.00 0.00 41.02 3.86
2365 2582 1.556564 CAGTTATGTACGCCGTCAGG 58.443 55.000 0.00 0.00 41.62 3.86
2366 2583 1.556564 CCAGTTATGTACGCCGTCAG 58.443 55.000 0.00 0.00 0.00 3.51
2367 2584 0.458889 GCCAGTTATGTACGCCGTCA 60.459 55.000 0.00 0.00 0.00 4.35
2368 2585 0.458889 TGCCAGTTATGTACGCCGTC 60.459 55.000 0.00 0.00 0.00 4.79
2369 2586 0.177141 ATGCCAGTTATGTACGCCGT 59.823 50.000 0.00 0.00 0.00 5.68
2370 2587 1.260561 GAATGCCAGTTATGTACGCCG 59.739 52.381 0.00 0.00 0.00 6.46
2371 2588 1.602377 GGAATGCCAGTTATGTACGCC 59.398 52.381 0.00 0.00 0.00 5.68
2372 2589 2.285083 TGGAATGCCAGTTATGTACGC 58.715 47.619 0.00 0.00 39.92 4.42
2395 2612 3.244976 GGAATGATTTTGCAACTGACCG 58.755 45.455 0.00 0.00 0.00 4.79
2426 2643 7.278646 TCAGTGCAAACAATCTCATATAGTGAC 59.721 37.037 0.00 0.00 32.22 3.67
2429 2646 7.559486 TCTCAGTGCAAACAATCTCATATAGT 58.441 34.615 0.00 0.00 0.00 2.12
2430 2647 8.604640 ATCTCAGTGCAAACAATCTCATATAG 57.395 34.615 0.00 0.00 0.00 1.31
2434 2658 5.498393 AGATCTCAGTGCAAACAATCTCAT 58.502 37.500 0.00 0.00 0.00 2.90
2452 2676 1.074405 TGCAGGCCAAGTTGAAGATCT 59.926 47.619 5.01 0.00 0.00 2.75
2453 2677 1.471684 CTGCAGGCCAAGTTGAAGATC 59.528 52.381 5.01 0.00 0.00 2.75
2459 2688 1.521450 CTGTCCTGCAGGCCAAGTTG 61.521 60.000 28.91 7.16 41.42 3.16
2493 2722 6.134055 ACAGGTGCTGTGTAATACTCCTATA 58.866 40.000 0.00 0.00 43.63 1.31
2494 2723 4.962995 ACAGGTGCTGTGTAATACTCCTAT 59.037 41.667 0.00 0.00 43.63 2.57
2495 2724 4.350245 ACAGGTGCTGTGTAATACTCCTA 58.650 43.478 0.00 0.00 43.63 2.94
2496 2725 3.173965 ACAGGTGCTGTGTAATACTCCT 58.826 45.455 0.00 0.00 43.63 3.69
2497 2726 3.611766 ACAGGTGCTGTGTAATACTCC 57.388 47.619 0.00 0.00 43.63 3.85
2526 2797 8.824781 CGATATCTTCTTCAATGTCAGAATGTT 58.175 33.333 0.34 0.00 37.40 2.71
2528 2799 8.585189 TCGATATCTTCTTCAATGTCAGAATG 57.415 34.615 0.34 0.00 37.54 2.67
2540 2811 7.681939 ACAGTATCCTCTCGATATCTTCTTC 57.318 40.000 0.34 0.00 35.87 2.87
2671 2942 1.398390 GATGCGTGGTGGAGATTGTTC 59.602 52.381 0.00 0.00 0.00 3.18
2747 3018 3.285484 AGCAATCCAGCAACCTGATTAG 58.715 45.455 0.00 0.00 41.77 1.73
2788 3059 2.302733 TCTCATGTCTAGTTGGCAAGCA 59.697 45.455 0.00 0.00 32.16 3.91
2814 3085 9.636789 GTATATCCTACCTAATGTTGGGTTTTT 57.363 33.333 6.10 0.00 39.16 1.94
2815 3086 8.783903 TGTATATCCTACCTAATGTTGGGTTTT 58.216 33.333 6.10 0.00 39.16 2.43
2817 3088 7.792736 TCTGTATATCCTACCTAATGTTGGGTT 59.207 37.037 6.10 0.00 39.16 4.11
2818 3089 7.310634 TCTGTATATCCTACCTAATGTTGGGT 58.689 38.462 6.06 6.06 44.79 4.51
2819 3090 7.792364 TCTGTATATCCTACCTAATGTTGGG 57.208 40.000 0.00 0.00 39.94 4.12
2820 3091 9.712305 CTTTCTGTATATCCTACCTAATGTTGG 57.288 37.037 0.00 0.00 40.76 3.77
2862 3133 3.527427 TGCCGGTCAGCGATCGAT 61.527 61.111 21.57 10.64 38.59 3.59
2863 3134 4.492160 GTGCCGGTCAGCGATCGA 62.492 66.667 21.57 0.00 38.59 3.59
2864 3135 4.794439 TGTGCCGGTCAGCGATCG 62.794 66.667 11.69 11.69 35.77 3.69
2876 3147 4.094294 TGCAAGTTATTAGTCGATTGTGCC 59.906 41.667 0.00 0.00 0.00 5.01
2888 3159 8.846211 ACTGAAAGCTTAGTTTGCAAGTTATTA 58.154 29.630 0.00 0.00 37.60 0.98
2889 3160 7.716612 ACTGAAAGCTTAGTTTGCAAGTTATT 58.283 30.769 0.00 0.00 37.60 1.40
2890 3161 7.277174 ACTGAAAGCTTAGTTTGCAAGTTAT 57.723 32.000 0.00 0.00 37.60 1.89
3038 3317 1.615384 GCTTTGGCTGAGTCAAGGGAT 60.615 52.381 10.93 0.00 35.22 3.85
3039 3318 0.250901 GCTTTGGCTGAGTCAAGGGA 60.251 55.000 10.93 0.00 35.22 4.20
3040 3319 1.246737 GGCTTTGGCTGAGTCAAGGG 61.247 60.000 10.93 4.50 38.73 3.95
3041 3320 2.261215 GGCTTTGGCTGAGTCAAGG 58.739 57.895 4.39 4.39 38.73 3.61
3090 3369 3.984633 GCTTCGCAGCTAAGGTTAGATAG 59.015 47.826 8.66 0.00 43.51 2.08
3091 3370 3.550233 CGCTTCGCAGCTAAGGTTAGATA 60.550 47.826 5.33 0.00 44.85 1.98
3092 3371 2.799917 CGCTTCGCAGCTAAGGTTAGAT 60.800 50.000 5.33 0.00 44.85 1.98


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

AutoCloner maintained by Alex Coulton.