Multiple sequence alignment - TraesCS4A01G189700

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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 TraesCS4A01G189700 chr4A 100.000 3122 0 0 1 3122 468602186 468605307 0.000000e+00 5766.0
1 TraesCS4A01G189700 chr4A 81.685 273 41 5 1064 1330 724782635 724782904 5.240000e-53 219.0
2 TraesCS4A01G189700 chr4B 90.037 2961 136 59 1 2888 168983829 168986703 0.000000e+00 3687.0
3 TraesCS4A01G189700 chr4B 89.216 204 14 5 2922 3122 168987341 168987539 6.690000e-62 248.0
4 TraesCS4A01G189700 chr4D 93.490 2212 76 17 578 2768 107711221 107709057 0.000000e+00 3225.0
5 TraesCS4A01G189700 chr4D 91.781 292 16 6 2838 3122 107701003 107700713 1.740000e-107 399.0
6 TraesCS4A01G189700 chr4D 80.812 271 47 3 1064 1330 506607108 506606839 1.130000e-49 207.0
7 TraesCS4A01G189700 chr4D 97.059 102 3 0 2751 2852 107709044 107708943 4.140000e-39 172.0
8 TraesCS4A01G189700 chr5D 83.871 527 61 16 1065 1579 238557791 238557277 6.060000e-132 481.0
9 TraesCS4A01G189700 chr5D 91.057 123 11 0 1065 1187 342713137 342713015 1.930000e-37 167.0
10 TraesCS4A01G189700 chr5D 92.308 91 5 2 1444 1533 342712637 342712548 9.090000e-26 128.0
11 TraesCS4A01G189700 chr5B 83.523 528 60 20 1065 1579 266501407 266501920 4.710000e-128 468.0
12 TraesCS4A01G189700 chr5B 91.209 91 6 2 1444 1533 402751166 402751077 4.230000e-24 122.0
13 TraesCS4A01G189700 chr5A 83.495 515 62 15 1065 1566 316085021 316085525 2.840000e-125 459.0
14 TraesCS4A01G189700 chr5A 90.244 123 12 0 1065 1187 443742801 443742679 8.960000e-36 161.0
15 TraesCS4A01G189700 chr7A 81.250 272 44 5 1064 1330 12429647 12429378 2.440000e-51 213.0
16 TraesCS4A01G189700 chr7D 80.147 272 47 5 1064 1330 13029512 13029243 2.460000e-46 196.0
17 TraesCS4A01G189700 chr2B 77.725 211 35 7 594 803 144558654 144558853 5.470000e-23 119.0
18 TraesCS4A01G189700 chr2B 84.946 93 9 5 1441 1530 158146717 158146807 4.290000e-14 89.8
19 TraesCS4A01G189700 chr2D 84.946 93 9 5 1441 1530 108313429 108313519 4.290000e-14 89.8


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 TraesCS4A01G189700 chr4A 468602186 468605307 3121 False 5766.0 5766 100.0000 1 3122 1 chr4A.!!$F1 3121
1 TraesCS4A01G189700 chr4B 168983829 168987539 3710 False 1967.5 3687 89.6265 1 3122 2 chr4B.!!$F1 3121
2 TraesCS4A01G189700 chr4D 107708943 107711221 2278 True 1698.5 3225 95.2745 578 2852 2 chr4D.!!$R3 2274
3 TraesCS4A01G189700 chr5D 238557277 238557791 514 True 481.0 481 83.8710 1065 1579 1 chr5D.!!$R1 514
4 TraesCS4A01G189700 chr5B 266501407 266501920 513 False 468.0 468 83.5230 1065 1579 1 chr5B.!!$F1 514
5 TraesCS4A01G189700 chr5A 316085021 316085525 504 False 459.0 459 83.4950 1065 1566 1 chr5A.!!$F1 501

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
668 674 0.034476 GATGAGCCATCTGCCATCGA 59.966 55.0 7.65 0.0 42.71 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2509 2623 0.17895 TGGTCAGAGTGCTCTCCAGT 60.179 55.0 12.06 0.0 41.26 4.0 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
19 20 0.306533 CACCACAAGGAACCGAAACG 59.693 55.000 0.00 0.00 38.69 3.60
21 22 1.138661 ACCACAAGGAACCGAAACGTA 59.861 47.619 0.00 0.00 38.69 3.57
27 28 3.183793 AGGAACCGAAACGTAAAGTGT 57.816 42.857 0.00 0.00 0.00 3.55
28 29 3.534554 AGGAACCGAAACGTAAAGTGTT 58.465 40.909 0.00 0.00 0.00 3.32
29 30 3.310501 AGGAACCGAAACGTAAAGTGTTG 59.689 43.478 0.00 0.00 0.00 3.33
43 44 8.881743 ACGTAAAGTGTTGTGTATGTTTTCTAA 58.118 29.630 0.00 0.00 0.00 2.10
101 102 9.959749 TCAAGTGAATAGTTTGGTTTTATTGAC 57.040 29.630 0.00 0.00 0.00 3.18
139 140 6.992063 AGTCAGATACACCAAAATAAGCAG 57.008 37.500 0.00 0.00 0.00 4.24
195 198 9.717892 AAAGTTAAATCAAGTTTCTTCGAAGTC 57.282 29.630 23.85 15.21 35.27 3.01
196 199 8.433421 AGTTAAATCAAGTTTCTTCGAAGTCA 57.567 30.769 23.85 10.09 0.00 3.41
199 202 4.131649 TCAAGTTTCTTCGAAGTCACCA 57.868 40.909 23.85 2.04 0.00 4.17
206 209 5.568685 TTCTTCGAAGTCACCATCTCTAG 57.431 43.478 23.85 0.00 0.00 2.43
213 216 5.564848 CGAAGTCACCATCTCTAGTTTCACA 60.565 44.000 0.00 0.00 0.00 3.58
234 237 7.406553 TCACATTTTGTAACTCGAGTTTTCTG 58.593 34.615 33.82 22.55 39.31 3.02
250 253 7.254556 CGAGTTTTCTGCATGCTCAATAATCTA 60.255 37.037 20.33 0.00 0.00 1.98
293 299 6.204882 AGCACTCTAAACTACAAAATGTGGTC 59.795 38.462 0.00 0.00 41.34 4.02
317 323 1.089920 CACCTCTCGATGCCAAAAGG 58.910 55.000 0.00 0.00 0.00 3.11
323 329 2.182537 GATGCCAAAAGGCCTGCG 59.817 61.111 5.69 0.00 0.00 5.18
324 330 2.283101 ATGCCAAAAGGCCTGCGA 60.283 55.556 5.69 0.00 0.00 5.10
325 331 2.275547 GATGCCAAAAGGCCTGCGAG 62.276 60.000 5.69 0.00 0.00 5.03
326 332 3.752339 GCCAAAAGGCCTGCGAGG 61.752 66.667 5.69 7.82 38.80 4.63
327 333 3.064324 CCAAAAGGCCTGCGAGGG 61.064 66.667 5.69 0.00 35.37 4.30
342 348 1.821216 GAGGGCAAGGAAAATCGACA 58.179 50.000 0.00 0.00 0.00 4.35
373 379 2.407428 GCCAGCGGCTAGGGTTTTC 61.407 63.158 16.60 0.89 46.69 2.29
378 384 1.359459 GCGGCTAGGGTTTTCTGTCG 61.359 60.000 0.00 0.00 0.00 4.35
440 446 6.071278 AGCCGCCACTGGTTTTATTTTATTTA 60.071 34.615 0.00 0.00 0.00 1.40
441 447 6.759356 GCCGCCACTGGTTTTATTTTATTTAT 59.241 34.615 0.00 0.00 0.00 1.40
442 448 7.279090 GCCGCCACTGGTTTTATTTTATTTATT 59.721 33.333 0.00 0.00 0.00 1.40
443 449 9.157104 CCGCCACTGGTTTTATTTTATTTATTT 57.843 29.630 0.00 0.00 0.00 1.40
516 522 5.546621 ACTGGTAGTTTTGCTGTCTTCTA 57.453 39.130 0.00 0.00 0.00 2.10
530 536 6.708949 TGCTGTCTTCTATACGAAAAAGGTTT 59.291 34.615 0.00 0.00 0.00 3.27
531 537 7.874016 TGCTGTCTTCTATACGAAAAAGGTTTA 59.126 33.333 0.00 0.00 0.00 2.01
541 547 5.838529 ACGAAAAAGGTTTAAGAATGGTGG 58.161 37.500 0.00 0.00 0.00 4.61
546 552 6.800072 AAAGGTTTAAGAATGGTGGTTTCA 57.200 33.333 0.00 0.00 0.00 2.69
610 616 0.589729 GGCTATGCGTGATTTGTGCG 60.590 55.000 0.00 0.00 0.00 5.34
624 630 1.160989 TGTGCGTGTTATTGCGGAAT 58.839 45.000 7.49 7.49 0.00 3.01
668 674 0.034476 GATGAGCCATCTGCCATCGA 59.966 55.000 7.65 0.00 42.71 3.59
723 729 7.174253 CCTTTAAATTTCACACAGTAGGCAGTA 59.826 37.037 0.00 0.00 0.00 2.74
724 730 5.941948 AAATTTCACACAGTAGGCAGTAC 57.058 39.130 0.00 0.00 0.00 2.73
725 731 4.617253 ATTTCACACAGTAGGCAGTACA 57.383 40.909 0.00 0.00 33.55 2.90
726 732 3.380479 TTCACACAGTAGGCAGTACAC 57.620 47.619 0.00 0.00 33.55 2.90
727 733 1.616865 TCACACAGTAGGCAGTACACC 59.383 52.381 0.00 0.00 33.55 4.16
728 734 1.618837 CACACAGTAGGCAGTACACCT 59.381 52.381 11.74 11.74 41.57 4.00
729 735 1.893801 ACACAGTAGGCAGTACACCTC 59.106 52.381 10.50 4.16 38.81 3.85
730 736 1.135373 CACAGTAGGCAGTACACCTCG 60.135 57.143 10.50 4.58 38.81 4.63
731 737 0.456221 CAGTAGGCAGTACACCTCGG 59.544 60.000 10.50 1.82 38.81 4.63
732 738 0.039326 AGTAGGCAGTACACCTCGGT 59.961 55.000 10.50 0.00 38.81 4.69
762 768 2.389715 GCTATATGGCTATCCCGTCCT 58.610 52.381 3.42 0.00 35.87 3.85
773 779 0.117742 TCCCGTCCTCCCTTTAAGGT 59.882 55.000 10.40 0.00 35.29 3.50
981 997 4.113354 GCTCCTTGCTATATATACGCACC 58.887 47.826 13.22 2.12 38.95 5.01
1031 1047 4.954092 AAAGACGAGATCAAATCAAGCC 57.046 40.909 0.00 0.00 0.00 4.35
1250 1280 1.534476 TGGACCAACTACCTCCGCA 60.534 57.895 0.00 0.00 0.00 5.69
1333 1363 1.068741 CTCCTCGGCAACAGGTATACC 59.931 57.143 14.54 14.54 36.57 2.73
1349 1379 6.481434 GGTATACCTACCACTGATCAACTT 57.519 41.667 15.09 0.00 45.88 2.66
1350 1380 6.514063 GGTATACCTACCACTGATCAACTTC 58.486 44.000 15.09 0.00 45.88 3.01
1351 1381 6.097839 GGTATACCTACCACTGATCAACTTCA 59.902 42.308 15.09 0.00 45.88 3.02
1352 1382 6.814954 ATACCTACCACTGATCAACTTCAT 57.185 37.500 0.00 0.00 0.00 2.57
1353 1383 7.914427 ATACCTACCACTGATCAACTTCATA 57.086 36.000 0.00 0.00 0.00 2.15
1354 1384 6.814954 ACCTACCACTGATCAACTTCATAT 57.185 37.500 0.00 0.00 0.00 1.78
1355 1385 6.821388 ACCTACCACTGATCAACTTCATATC 58.179 40.000 0.00 0.00 0.00 1.63
1370 1410 8.418662 CAACTTCATATCATCAAATCAATGGGT 58.581 33.333 0.00 0.00 0.00 4.51
1417 1502 3.381045 TGGCGATCGATTTAGCTAACAG 58.619 45.455 21.57 0.71 0.00 3.16
1552 1647 3.455469 GCAAGCCATGGGAGCCAC 61.455 66.667 15.13 0.00 35.80 5.01
1553 1648 2.357836 CAAGCCATGGGAGCCACT 59.642 61.111 15.13 0.00 35.80 4.00
1598 1693 4.030452 GGCACAGCAGGCGACAAC 62.030 66.667 0.00 0.00 0.00 3.32
1619 1714 2.184167 CGACCACCACAACCACCAC 61.184 63.158 0.00 0.00 0.00 4.16
1672 1767 0.958382 GGCCAGGCGTACATGAACAA 60.958 55.000 5.00 0.00 0.00 2.83
1694 1789 2.959071 GTCTCGCAGCTGATCGCC 60.959 66.667 20.43 0.00 40.39 5.54
1985 2080 0.795085 AGTACGACGACGAGACCAAG 59.205 55.000 15.32 0.00 42.66 3.61
1987 2082 1.229975 TACGACGACGAGACCAAGCA 61.230 55.000 15.32 0.00 42.66 3.91
1988 2083 1.797933 CGACGACGAGACCAAGCAG 60.798 63.158 0.00 0.00 42.66 4.24
1989 2084 1.579932 GACGACGAGACCAAGCAGA 59.420 57.895 0.00 0.00 0.00 4.26
2015 2110 2.821366 CATCAGGCGCCACTGTCC 60.821 66.667 31.54 0.00 39.48 4.02
2031 2126 1.096416 GTCCTCGATCGAGAAGTGGT 58.904 55.000 39.64 0.00 44.53 4.16
2036 2131 2.917971 CTCGATCGAGAAGTGGTTGTTC 59.082 50.000 36.13 0.00 44.53 3.18
2051 2146 4.508128 TTCGATGAGGCCGCGGAC 62.508 66.667 33.48 30.81 0.00 4.79
2127 2222 5.793457 CGCTGGGAAAGTAAATTAAGAAACG 59.207 40.000 0.00 0.00 0.00 3.60
2233 2338 7.389232 TCTACCTATGCATCCATGTTTGATAG 58.611 38.462 0.19 0.00 32.85 2.08
2234 2339 5.945310 ACCTATGCATCCATGTTTGATAGT 58.055 37.500 0.19 0.00 32.85 2.12
2235 2340 7.078249 ACCTATGCATCCATGTTTGATAGTA 57.922 36.000 0.19 0.00 32.85 1.82
2251 2356 7.827819 TTGATAGTACACACAAGTAATGAGC 57.172 36.000 0.00 0.00 0.00 4.26
2306 2418 0.232046 CGCATTACGCATACGCATGT 59.768 50.000 0.00 0.00 45.53 3.21
2319 2431 1.019278 CGCATGTACGCACCTCCTTT 61.019 55.000 0.00 0.00 0.00 3.11
2320 2432 0.447801 GCATGTACGCACCTCCTTTG 59.552 55.000 0.00 0.00 0.00 2.77
2321 2433 1.808411 CATGTACGCACCTCCTTTGT 58.192 50.000 0.00 0.00 0.00 2.83
2322 2434 2.933492 GCATGTACGCACCTCCTTTGTA 60.933 50.000 0.00 0.00 0.00 2.41
2323 2435 2.443887 TGTACGCACCTCCTTTGTAC 57.556 50.000 0.00 0.00 36.74 2.90
2324 2436 1.687660 TGTACGCACCTCCTTTGTACA 59.312 47.619 0.00 0.00 42.05 2.90
2341 2453 0.462789 ACACTGAAACGTCGAAGGGT 59.537 50.000 0.00 0.00 0.00 4.34
2370 2482 1.941325 CGACAGGGATTTAGCAGGAC 58.059 55.000 0.00 0.00 0.00 3.85
2442 2554 8.401709 GTTATCTATGCTCAAAAAGGGAAGAAG 58.598 37.037 0.00 0.00 0.00 2.85
2455 2567 2.502295 GGAAGAAGAGGCCTGCATATG 58.498 52.381 12.00 0.00 0.00 1.78
2459 2571 3.285484 AGAAGAGGCCTGCATATGTTTG 58.715 45.455 12.00 0.00 0.00 2.93
2480 2592 4.269183 TGTGTCACTTGACCTTGAACAAT 58.731 39.130 6.91 0.00 44.15 2.71
2482 2595 5.883115 TGTGTCACTTGACCTTGAACAATTA 59.117 36.000 6.91 0.00 44.15 1.40
2488 2601 5.998363 ACTTGACCTTGAACAATTAGTCTCC 59.002 40.000 0.00 0.00 0.00 3.71
2526 2640 1.472480 GAGACTGGAGAGCACTCTGAC 59.528 57.143 11.09 5.37 40.61 3.51
2539 2653 5.564550 AGCACTCTGACCATGTTATTTCTT 58.435 37.500 0.00 0.00 0.00 2.52
2597 2711 2.167487 TGGGTGCTTGTTTTGTTCTTCC 59.833 45.455 0.00 0.00 0.00 3.46
2601 2715 1.753956 CTTGTTTTGTTCTTCCCGCG 58.246 50.000 0.00 0.00 0.00 6.46
2610 2724 0.536460 TTCTTCCCGCGGAAAAGCTT 60.536 50.000 30.73 0.00 41.54 3.74
2634 2748 5.304778 TGCAGAGAAATGTGCAAACTACTA 58.695 37.500 0.00 0.00 46.53 1.82
2636 2750 5.409826 GCAGAGAAATGTGCAAACTACTACT 59.590 40.000 0.00 0.00 39.62 2.57
2637 2751 6.401581 GCAGAGAAATGTGCAAACTACTACTC 60.402 42.308 0.00 0.00 39.62 2.59
2640 2754 4.634012 AATGTGCAAACTACTACTCCCA 57.366 40.909 0.00 0.00 0.00 4.37
2641 2755 3.396260 TGTGCAAACTACTACTCCCAC 57.604 47.619 0.00 0.00 0.00 4.61
2642 2756 2.701423 TGTGCAAACTACTACTCCCACA 59.299 45.455 0.00 0.00 0.00 4.17
2643 2757 3.244078 TGTGCAAACTACTACTCCCACAG 60.244 47.826 0.00 0.00 0.00 3.66
2708 2853 6.988580 TGTACAAAATTTCACATTTGATGGCA 59.011 30.769 0.00 0.00 38.50 4.92
2715 2860 2.027653 TCACATTTGATGGCACCTACGA 60.028 45.455 0.00 0.00 33.60 3.43
2778 2953 9.341899 CTTGTTAGTGTTATAGGTCAAAATTGC 57.658 33.333 0.00 0.00 0.00 3.56
2844 3025 7.594015 GGAAATGCTTAGTAATTGCATGATCAG 59.406 37.037 9.64 0.00 45.29 2.90
2888 3069 1.540797 CCGTTACACGTCCCCTTTGAA 60.541 52.381 0.00 0.00 40.58 2.69
2889 3070 1.528161 CGTTACACGTCCCCTTTGAAC 59.472 52.381 0.00 0.00 36.74 3.18
2890 3071 1.875514 GTTACACGTCCCCTTTGAACC 59.124 52.381 0.00 0.00 0.00 3.62
2891 3072 0.397564 TACACGTCCCCTTTGAACCC 59.602 55.000 0.00 0.00 0.00 4.11
2892 3073 1.602605 CACGTCCCCTTTGAACCCC 60.603 63.158 0.00 0.00 0.00 4.95
2893 3074 2.035155 CGTCCCCTTTGAACCCCC 59.965 66.667 0.00 0.00 0.00 5.40
2913 3094 5.723295 CCCCCAGTGTAAATTCAATTTCTG 58.277 41.667 0.00 1.14 33.82 3.02
2914 3095 5.170748 CCCCAGTGTAAATTCAATTTCTGC 58.829 41.667 0.00 0.00 33.82 4.26
2915 3096 5.279406 CCCCAGTGTAAATTCAATTTCTGCA 60.279 40.000 0.00 0.00 33.82 4.41
2916 3097 6.222389 CCCAGTGTAAATTCAATTTCTGCAA 58.778 36.000 0.00 0.00 33.82 4.08
2917 3098 6.705381 CCCAGTGTAAATTCAATTTCTGCAAA 59.295 34.615 0.00 0.00 33.82 3.68
2918 3099 7.307337 CCCAGTGTAAATTCAATTTCTGCAAAC 60.307 37.037 0.00 0.00 33.82 2.93
2919 3100 7.439056 CCAGTGTAAATTCAATTTCTGCAAACT 59.561 33.333 0.00 0.00 33.82 2.66
2920 3101 8.482429 CAGTGTAAATTCAATTTCTGCAAACTC 58.518 33.333 0.00 0.00 33.82 3.01
2933 3718 4.081697 TCTGCAAACTCCGATGTAGATTCA 60.082 41.667 0.00 0.00 34.08 2.57
2945 3730 5.752472 CGATGTAGATTCAGAGCTGACAAAT 59.248 40.000 0.00 0.00 39.66 2.32
2947 3732 7.436376 CGATGTAGATTCAGAGCTGACAAATTA 59.564 37.037 0.00 0.00 39.66 1.40
2948 3733 8.659925 ATGTAGATTCAGAGCTGACAAATTAG 57.340 34.615 0.00 0.00 39.66 1.73
2949 3734 7.615403 TGTAGATTCAGAGCTGACAAATTAGT 58.385 34.615 0.00 0.00 39.66 2.24
2950 3735 8.097038 TGTAGATTCAGAGCTGACAAATTAGTT 58.903 33.333 0.00 0.00 39.66 2.24
2951 3736 7.608308 AGATTCAGAGCTGACAAATTAGTTC 57.392 36.000 0.00 0.00 39.66 3.01
3002 3790 1.618447 AATTACCCCCGGCCTCTGT 60.618 57.895 0.00 0.00 0.00 3.41
3028 3816 1.593006 GCGATACGAAACACCATCTGG 59.407 52.381 0.00 0.00 42.17 3.86
3035 3823 4.843728 ACGAAACACCATCTGGATGTAAT 58.156 39.130 2.55 0.00 37.11 1.89
3039 3827 6.128035 CGAAACACCATCTGGATGTAATTCAA 60.128 38.462 2.55 0.00 37.11 2.69
3047 3835 8.857098 CCATCTGGATGTAATTCAAATTCATCT 58.143 33.333 17.52 5.57 37.11 2.90
3114 3902 9.826574 TGGTATATTACTGTGTTTAACTCATCC 57.173 33.333 0.22 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.958112 AAACATACACAACACTTTACGTTTC 57.042 32.000 0.00 0.00 0.00 2.78
17 18 7.311364 AGAAAACATACACAACACTTTACGT 57.689 32.000 0.00 0.00 0.00 3.57
176 179 5.123227 TGGTGACTTCGAAGAAACTTGATT 58.877 37.500 31.08 5.46 45.90 2.57
183 186 4.873746 AGAGATGGTGACTTCGAAGAAA 57.126 40.909 31.08 15.44 45.90 2.52
184 187 5.010933 ACTAGAGATGGTGACTTCGAAGAA 58.989 41.667 31.08 15.80 45.90 2.52
185 188 4.590918 ACTAGAGATGGTGACTTCGAAGA 58.409 43.478 31.08 9.12 39.38 2.87
186 189 4.974368 ACTAGAGATGGTGACTTCGAAG 57.026 45.455 23.43 23.43 39.38 3.79
187 190 5.243060 TGAAACTAGAGATGGTGACTTCGAA 59.757 40.000 0.00 0.00 39.38 3.71
188 191 4.765339 TGAAACTAGAGATGGTGACTTCGA 59.235 41.667 0.00 0.00 39.38 3.71
189 192 4.859798 GTGAAACTAGAGATGGTGACTTCG 59.140 45.833 0.00 0.00 39.38 3.79
190 193 5.784177 TGTGAAACTAGAGATGGTGACTTC 58.216 41.667 0.00 0.00 38.04 3.01
191 194 5.808366 TGTGAAACTAGAGATGGTGACTT 57.192 39.130 0.00 0.00 38.04 3.01
192 195 6.365970 AATGTGAAACTAGAGATGGTGACT 57.634 37.500 0.00 0.00 38.04 3.41
193 196 7.041098 ACAAAATGTGAAACTAGAGATGGTGAC 60.041 37.037 0.00 0.00 38.04 3.67
194 197 6.998074 ACAAAATGTGAAACTAGAGATGGTGA 59.002 34.615 0.00 0.00 38.04 4.02
195 198 7.206981 ACAAAATGTGAAACTAGAGATGGTG 57.793 36.000 0.00 0.00 38.04 4.17
196 199 8.784043 GTTACAAAATGTGAAACTAGAGATGGT 58.216 33.333 0.00 0.00 38.04 3.55
199 202 8.926710 CGAGTTACAAAATGTGAAACTAGAGAT 58.073 33.333 0.00 0.00 31.45 2.75
206 209 7.964545 AAACTCGAGTTACAAAATGTGAAAC 57.035 32.000 29.91 0.00 37.25 2.78
213 216 6.371809 TGCAGAAAACTCGAGTTACAAAAT 57.628 33.333 29.91 11.56 37.25 1.82
293 299 2.801631 GGCATCGAGAGGTGGAGGG 61.802 68.421 0.00 0.00 44.18 4.30
323 329 1.740025 CTGTCGATTTTCCTTGCCCTC 59.260 52.381 0.00 0.00 0.00 4.30
324 330 1.614317 CCTGTCGATTTTCCTTGCCCT 60.614 52.381 0.00 0.00 0.00 5.19
325 331 0.811281 CCTGTCGATTTTCCTTGCCC 59.189 55.000 0.00 0.00 0.00 5.36
326 332 1.821216 TCCTGTCGATTTTCCTTGCC 58.179 50.000 0.00 0.00 0.00 4.52
327 333 3.181496 GGATTCCTGTCGATTTTCCTTGC 60.181 47.826 0.00 0.00 0.00 4.01
328 334 4.265073 AGGATTCCTGTCGATTTTCCTTG 58.735 43.478 3.86 0.00 29.57 3.61
329 335 4.576330 AGGATTCCTGTCGATTTTCCTT 57.424 40.909 3.86 0.00 29.57 3.36
330 336 5.604650 AGATAGGATTCCTGTCGATTTTCCT 59.395 40.000 20.05 1.72 44.77 3.36
331 337 5.698545 CAGATAGGATTCCTGTCGATTTTCC 59.301 44.000 20.05 0.00 44.77 3.13
332 338 5.178438 GCAGATAGGATTCCTGTCGATTTTC 59.822 44.000 20.05 6.79 44.77 2.29
333 339 5.059833 GCAGATAGGATTCCTGTCGATTTT 58.940 41.667 20.05 3.62 44.77 1.82
334 340 4.503991 GGCAGATAGGATTCCTGTCGATTT 60.504 45.833 20.05 3.95 44.77 2.17
342 348 0.683973 CGCTGGCAGATAGGATTCCT 59.316 55.000 20.86 10.72 37.71 3.36
364 370 1.336517 CGTGCTCGACAGAAAACCCTA 60.337 52.381 1.00 0.00 39.71 3.53
378 384 1.733399 GACCAGGTCGTTCGTGCTC 60.733 63.158 3.05 0.00 0.00 4.26
486 492 8.100791 AGACAGCAAAACTACCAGTTATATCAA 58.899 33.333 0.00 0.00 37.47 2.57
493 499 4.781934 AGAAGACAGCAAAACTACCAGTT 58.218 39.130 0.00 0.00 40.80 3.16
496 502 6.071784 TCGTATAGAAGACAGCAAAACTACCA 60.072 38.462 0.00 0.00 0.00 3.25
506 512 6.723131 AACCTTTTTCGTATAGAAGACAGC 57.277 37.500 0.00 0.00 40.40 4.40
516 522 7.231925 ACCACCATTCTTAAACCTTTTTCGTAT 59.768 33.333 0.00 0.00 0.00 3.06
610 616 3.551485 GGCATTTCATTCCGCAATAACAC 59.449 43.478 0.00 0.00 0.00 3.32
624 630 3.065786 GCTTGATTCATCGAGGCATTTCA 59.934 43.478 6.24 0.00 38.49 2.69
723 729 0.898789 CCAGAGGTGTACCGAGGTGT 60.899 60.000 4.80 0.00 42.08 4.16
724 730 1.890894 CCAGAGGTGTACCGAGGTG 59.109 63.158 4.80 0.00 42.08 4.00
725 731 1.982938 GCCAGAGGTGTACCGAGGT 60.983 63.158 0.00 0.00 42.08 3.85
726 732 0.395311 TAGCCAGAGGTGTACCGAGG 60.395 60.000 0.00 0.80 42.08 4.63
727 733 1.693627 ATAGCCAGAGGTGTACCGAG 58.306 55.000 0.00 0.00 42.08 4.63
728 734 3.154710 CATATAGCCAGAGGTGTACCGA 58.845 50.000 0.00 0.00 42.08 4.69
729 735 2.231478 CCATATAGCCAGAGGTGTACCG 59.769 54.545 0.00 0.00 42.08 4.02
730 736 2.028020 GCCATATAGCCAGAGGTGTACC 60.028 54.545 0.00 0.00 0.00 3.34
731 737 2.900546 AGCCATATAGCCAGAGGTGTAC 59.099 50.000 0.00 0.00 0.00 2.90
732 738 3.260269 AGCCATATAGCCAGAGGTGTA 57.740 47.619 0.00 0.00 0.00 2.90
762 768 1.068943 TGGCCCACACCTTAAAGGGA 61.069 55.000 0.00 0.00 44.30 4.20
773 779 3.716195 CGATCCACCTGGCCCACA 61.716 66.667 0.00 0.00 34.44 4.17
981 997 1.153597 TGCACTGTCTCAAGCGTGTG 61.154 55.000 0.00 0.00 0.00 3.82
1031 1047 0.106469 TCACTCTCTCTGGATCCCCG 60.106 60.000 9.90 0.00 34.29 5.73
1333 1363 8.146412 TGATGATATGAAGTTGATCAGTGGTAG 58.854 37.037 0.00 0.00 33.29 3.18
1345 1375 8.418662 CACCCATTGATTTGATGATATGAAGTT 58.581 33.333 0.00 0.00 0.00 2.66
1347 1377 7.375834 CCACCCATTGATTTGATGATATGAAG 58.624 38.462 0.00 0.00 0.00 3.02
1348 1378 6.239373 GCCACCCATTGATTTGATGATATGAA 60.239 38.462 0.00 0.00 0.00 2.57
1349 1379 5.244402 GCCACCCATTGATTTGATGATATGA 59.756 40.000 0.00 0.00 0.00 2.15
1350 1380 5.245301 AGCCACCCATTGATTTGATGATATG 59.755 40.000 0.00 0.00 0.00 1.78
1351 1381 5.245301 CAGCCACCCATTGATTTGATGATAT 59.755 40.000 0.00 0.00 0.00 1.63
1352 1382 4.585581 CAGCCACCCATTGATTTGATGATA 59.414 41.667 0.00 0.00 0.00 2.15
1353 1383 3.386726 CAGCCACCCATTGATTTGATGAT 59.613 43.478 0.00 0.00 0.00 2.45
1354 1384 2.761767 CAGCCACCCATTGATTTGATGA 59.238 45.455 0.00 0.00 0.00 2.92
1355 1385 2.159014 CCAGCCACCCATTGATTTGATG 60.159 50.000 0.00 0.00 0.00 3.07
1417 1502 5.382618 ACATTCAAAGCAAGAGATGGAAC 57.617 39.130 0.00 0.00 0.00 3.62
1460 1555 4.509737 GTCCTCCGCGGCAGGTAC 62.510 72.222 30.31 24.43 32.20 3.34
1598 1693 1.164041 GGTGGTTGTGGTGGTCGAAG 61.164 60.000 0.00 0.00 0.00 3.79
1619 1714 2.187946 GCCCTGGAGACCATGTCG 59.812 66.667 0.00 0.00 37.67 4.35
1672 1767 1.381056 ATCAGCTGCGAGACCTCCT 60.381 57.895 9.47 0.00 0.00 3.69
1735 1830 1.451567 TAGGACGACGAGGAGCAGG 60.452 63.158 0.00 0.00 0.00 4.85
1985 2080 1.429825 CTGATGCTGCTGCTTCTGC 59.570 57.895 24.98 7.19 41.96 4.26
1987 2082 1.749638 GCCTGATGCTGCTGCTTCT 60.750 57.895 24.98 8.78 41.96 2.85
1988 2083 2.799371 GCCTGATGCTGCTGCTTC 59.201 61.111 20.27 20.27 41.84 3.86
1989 2084 3.132139 CGCCTGATGCTGCTGCTT 61.132 61.111 17.00 10.47 40.48 3.91
2015 2110 2.638556 ACAACCACTTCTCGATCGAG 57.361 50.000 34.20 34.20 43.21 4.04
2031 2126 2.813474 CGCGGCCTCATCGAACAA 60.813 61.111 0.00 0.00 0.00 2.83
2051 2146 1.326213 ACTCATCGGACAGCTCCAGG 61.326 60.000 0.00 0.00 36.12 4.45
2103 2198 5.793457 CGTTTCTTAATTTACTTTCCCAGCG 59.207 40.000 0.00 0.00 0.00 5.18
2147 2249 2.474266 CAGTATGTTTGCGCGCGT 59.526 55.556 32.35 13.04 0.00 6.01
2233 2338 4.378459 GCTTGGCTCATTACTTGTGTGTAC 60.378 45.833 0.00 0.00 0.00 2.90
2234 2339 3.751175 GCTTGGCTCATTACTTGTGTGTA 59.249 43.478 0.00 0.00 0.00 2.90
2235 2340 2.554032 GCTTGGCTCATTACTTGTGTGT 59.446 45.455 0.00 0.00 0.00 3.72
2251 2356 3.193479 GGAAATTACCAACTGAGGCTTGG 59.807 47.826 1.36 1.36 43.49 3.61
2306 2418 1.965643 AGTGTACAAAGGAGGTGCGTA 59.034 47.619 0.00 0.00 0.00 4.42
2319 2431 2.544277 CCCTTCGACGTTTCAGTGTACA 60.544 50.000 0.00 0.00 0.00 2.90
2320 2432 2.056577 CCCTTCGACGTTTCAGTGTAC 58.943 52.381 0.00 0.00 0.00 2.90
2321 2433 1.682854 ACCCTTCGACGTTTCAGTGTA 59.317 47.619 0.00 0.00 0.00 2.90
2322 2434 0.462789 ACCCTTCGACGTTTCAGTGT 59.537 50.000 0.00 0.00 0.00 3.55
2323 2435 2.427232 TACCCTTCGACGTTTCAGTG 57.573 50.000 0.00 0.00 0.00 3.66
2324 2436 2.624838 TCTTACCCTTCGACGTTTCAGT 59.375 45.455 0.00 0.00 0.00 3.41
2341 2453 2.145397 ATCCCTGTCGCTGTCTCTTA 57.855 50.000 0.00 0.00 0.00 2.10
2370 2482 1.073964 CAGATGACACAGTTCGCCAG 58.926 55.000 0.00 0.00 0.00 4.85
2442 2554 2.094675 ACACAAACATATGCAGGCCTC 58.905 47.619 0.00 0.00 0.00 4.70
2455 2567 4.083003 TGTTCAAGGTCAAGTGACACAAAC 60.083 41.667 13.21 10.95 46.47 2.93
2459 2571 4.900635 ATTGTTCAAGGTCAAGTGACAC 57.099 40.909 13.21 0.00 46.47 3.67
2509 2623 0.178950 TGGTCAGAGTGCTCTCCAGT 60.179 55.000 12.06 0.00 41.26 4.00
2539 2653 7.509141 TCTGCTTCTTGTGATTGATAAAACA 57.491 32.000 0.00 0.00 0.00 2.83
2597 2711 1.730547 CTGCAAAGCTTTTCCGCGG 60.731 57.895 22.12 22.12 34.40 6.46
2601 2715 4.446719 CACATTTCTCTGCAAAGCTTTTCC 59.553 41.667 9.53 4.29 0.00 3.13
2636 2750 7.630082 AGTTGCTTAATTATTACTCTGTGGGA 58.370 34.615 0.00 0.00 0.00 4.37
2637 2751 7.865706 AGTTGCTTAATTATTACTCTGTGGG 57.134 36.000 0.00 0.00 0.00 4.61
2641 2755 9.922305 GCTTGTAGTTGCTTAATTATTACTCTG 57.078 33.333 0.00 0.00 0.00 3.35
2642 2756 9.892130 AGCTTGTAGTTGCTTAATTATTACTCT 57.108 29.630 0.00 0.00 35.86 3.24
2671 2816 9.406828 GTGAAATTTTGTACAATCTTCTAACCC 57.593 33.333 9.56 0.00 0.00 4.11
2672 2817 9.959749 TGTGAAATTTTGTACAATCTTCTAACC 57.040 29.630 9.56 4.21 0.00 2.85
2708 2853 1.971357 CTGATGGCCCTATTCGTAGGT 59.029 52.381 0.00 0.00 35.45 3.08
2778 2953 1.599667 CCGTGTAGTACTGCCTATGCG 60.600 57.143 5.39 4.15 41.78 4.73
2817 2998 6.772360 TCATGCAATTACTAAGCATTTCCA 57.228 33.333 0.00 0.00 45.98 3.53
2844 3025 4.388499 ACGTGACGGCCCATGTCC 62.388 66.667 10.66 0.00 35.46 4.02
2890 3071 5.723295 CAGAAATTGAATTTACACTGGGGG 58.277 41.667 2.71 0.00 31.47 5.40
2891 3072 5.170748 GCAGAAATTGAATTTACACTGGGG 58.829 41.667 15.30 0.00 31.47 4.96
2892 3073 5.782047 TGCAGAAATTGAATTTACACTGGG 58.218 37.500 15.30 0.00 31.47 4.45
2893 3074 7.439056 AGTTTGCAGAAATTGAATTTACACTGG 59.561 33.333 15.30 3.26 31.47 4.00
2894 3075 8.356533 AGTTTGCAGAAATTGAATTTACACTG 57.643 30.769 2.71 8.06 31.47 3.66
2895 3076 7.653311 GGAGTTTGCAGAAATTGAATTTACACT 59.347 33.333 2.71 0.00 31.47 3.55
2896 3077 7.358352 CGGAGTTTGCAGAAATTGAATTTACAC 60.358 37.037 2.71 0.00 31.47 2.90
2897 3078 6.640499 CGGAGTTTGCAGAAATTGAATTTACA 59.360 34.615 2.71 0.27 31.47 2.41
2898 3079 6.861055 TCGGAGTTTGCAGAAATTGAATTTAC 59.139 34.615 2.71 0.00 31.47 2.01
2899 3080 6.976088 TCGGAGTTTGCAGAAATTGAATTTA 58.024 32.000 2.71 0.00 31.47 1.40
2900 3081 5.841810 TCGGAGTTTGCAGAAATTGAATTT 58.158 33.333 2.27 2.27 34.64 1.82
2901 3082 5.452078 TCGGAGTTTGCAGAAATTGAATT 57.548 34.783 0.00 0.00 0.00 2.17
2902 3083 5.047802 ACATCGGAGTTTGCAGAAATTGAAT 60.048 36.000 0.00 0.00 0.00 2.57
2903 3084 4.278170 ACATCGGAGTTTGCAGAAATTGAA 59.722 37.500 0.00 0.00 0.00 2.69
2904 3085 3.820467 ACATCGGAGTTTGCAGAAATTGA 59.180 39.130 0.00 0.00 0.00 2.57
2905 3086 4.164822 ACATCGGAGTTTGCAGAAATTG 57.835 40.909 0.00 0.00 0.00 2.32
2906 3087 5.245531 TCTACATCGGAGTTTGCAGAAATT 58.754 37.500 0.00 0.00 0.00 1.82
2907 3088 4.832248 TCTACATCGGAGTTTGCAGAAAT 58.168 39.130 0.00 0.00 0.00 2.17
2908 3089 4.265904 TCTACATCGGAGTTTGCAGAAA 57.734 40.909 0.00 0.00 0.00 2.52
2909 3090 3.953712 TCTACATCGGAGTTTGCAGAA 57.046 42.857 0.00 0.00 0.00 3.02
2910 3091 4.081697 TGAATCTACATCGGAGTTTGCAGA 60.082 41.667 0.00 0.00 0.00 4.26
2911 3092 4.183865 TGAATCTACATCGGAGTTTGCAG 58.816 43.478 0.00 0.00 0.00 4.41
2912 3093 4.081697 TCTGAATCTACATCGGAGTTTGCA 60.082 41.667 0.00 0.00 0.00 4.08
2913 3094 4.433615 TCTGAATCTACATCGGAGTTTGC 58.566 43.478 0.00 0.00 0.00 3.68
2919 3100 3.316588 GTCAGCTCTGAATCTACATCGGA 59.683 47.826 0.54 0.00 41.85 4.55
2920 3101 3.067320 TGTCAGCTCTGAATCTACATCGG 59.933 47.826 0.54 0.00 41.85 4.18
2933 3718 6.631016 TCGTATGAACTAATTTGTCAGCTCT 58.369 36.000 0.00 0.00 0.00 4.09
2975 3763 2.092267 GCCGGGGGTAATTCTCCTTTTA 60.092 50.000 2.18 0.00 36.78 1.52
2984 3772 0.326808 TACAGAGGCCGGGGGTAATT 60.327 55.000 2.18 0.00 0.00 1.40
3002 3790 4.112716 TGGTGTTTCGTATCGCTTGATA 57.887 40.909 0.00 0.00 33.40 2.15
3039 3827 9.745018 TTTCCTGACTTTTGAGATAGATGAATT 57.255 29.630 0.00 0.00 0.00 2.17
3079 3867 8.506168 AACACAGTAATATACCAACAAGATGG 57.494 34.615 0.00 0.00 46.38 3.51
3097 3885 3.821033 GGCTTGGATGAGTTAAACACAGT 59.179 43.478 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.