Multiple sequence alignment - TraesCS6A01G076500

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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 TraesCS6A01G076500 chr6A 100.000 3295 0 0 1 3295 46763417 46760123 0.000000e+00 6085.0
1 TraesCS6A01G076500 chr6A 92.799 1347 83 4 1488 2831 46872473 46871138 0.000000e+00 1938.0
2 TraesCS6A01G076500 chr6A 82.297 836 98 28 1807 2612 46782991 46782176 0.000000e+00 678.0
3 TraesCS6A01G076500 chr6A 98.876 356 4 0 2891 3246 46871142 46870787 1.290000e-178 636.0
4 TraesCS6A01G076500 chr6A 88.973 526 42 6 977 1495 46873149 46872633 1.290000e-178 636.0
5 TraesCS6A01G076500 chr6A 88.110 328 31 4 599 918 46874479 46874152 1.860000e-102 383.0
6 TraesCS6A01G076500 chr6A 96.667 60 1 1 3237 3295 46870715 46870656 7.520000e-17 99.0
7 TraesCS6A01G076500 chr6A 97.368 38 1 0 868 905 46762486 46762449 7.630000e-07 65.8
8 TraesCS6A01G076500 chr6A 97.368 38 1 0 932 969 46762550 46762513 7.630000e-07 65.8
9 TraesCS6A01G076500 chr6B 91.485 1421 101 9 1369 2775 80776062 80774648 0.000000e+00 1936.0
10 TraesCS6A01G076500 chr6B 81.718 2177 263 69 599 2722 80841109 80839015 0.000000e+00 1690.0
11 TraesCS6A01G076500 chr6B 80.306 1437 192 52 348 1737 80236206 80234814 0.000000e+00 1002.0
12 TraesCS6A01G076500 chr6B 90.483 746 64 7 599 1343 80781204 80780465 0.000000e+00 977.0
13 TraesCS6A01G076500 chr6B 92.958 426 28 2 2821 3246 80774565 80774142 1.300000e-173 619.0
14 TraesCS6A01G076500 chr6B 81.445 706 92 17 1807 2500 80821758 80821080 2.890000e-150 542.0
15 TraesCS6A01G076500 chr6B 79.793 772 110 28 976 1737 80740945 80740210 1.360000e-143 520.0
16 TraesCS6A01G076500 chr6B 79.534 772 112 28 976 1737 80733989 80733254 2.930000e-140 508.0
17 TraesCS6A01G076500 chr6B 79.534 772 112 28 976 1737 80737467 80736732 2.930000e-140 508.0
18 TraesCS6A01G076500 chr6B 95.370 216 9 1 2986 3201 80838583 80838369 3.150000e-90 342.0
19 TraesCS6A01G076500 chr6B 87.823 271 27 4 1 271 80236851 80236587 2.470000e-81 313.0
20 TraesCS6A01G076500 chr6B 87.500 184 21 2 1 184 80823616 80823435 9.260000e-51 211.0
21 TraesCS6A01G076500 chr6B 89.091 165 18 0 9 173 80741966 80741802 4.310000e-49 206.0
22 TraesCS6A01G076500 chr6B 91.667 108 9 0 3140 3247 80735691 80735584 2.050000e-32 150.0
23 TraesCS6A01G076500 chr6B 91.667 108 9 0 3140 3247 80739169 80739062 2.050000e-32 150.0
24 TraesCS6A01G076500 chr6B 87.273 110 13 1 3142 3250 80233840 80233731 1.240000e-24 124.0
25 TraesCS6A01G076500 chr6B 100.000 32 0 0 2790 2821 80774648 80774617 3.550000e-05 60.2
26 TraesCS6A01G076500 chrUn 82.135 2183 278 58 599 2722 27017424 27015295 0.000000e+00 1768.0
27 TraesCS6A01G076500 chrUn 82.209 1720 210 45 1047 2722 27158888 27160555 0.000000e+00 1393.0
28 TraesCS6A01G076500 chrUn 82.222 1170 155 38 599 1737 27273327 27274474 0.000000e+00 959.0
29 TraesCS6A01G076500 chrUn 80.991 989 152 25 597 1563 27165079 27166053 0.000000e+00 752.0
30 TraesCS6A01G076500 chrUn 83.911 808 90 21 1807 2591 27268711 27269501 0.000000e+00 736.0
31 TraesCS6A01G076500 chrUn 82.603 707 85 11 1807 2502 27183625 27184304 1.020000e-164 590.0
32 TraesCS6A01G076500 chrUn 95.019 261 12 1 2986 3246 27160985 27161244 3.060000e-110 409.0
33 TraesCS6A01G076500 chrUn 84.932 292 38 5 599 887 27267510 27267798 1.160000e-74 291.0
34 TraesCS6A01G076500 chrUn 77.339 481 88 16 1393 1864 62699990 62700458 7.010000e-67 265.0
35 TraesCS6A01G076500 chrUn 91.071 168 15 0 1 168 27266836 27267003 9.200000e-56 228.0
36 TraesCS6A01G076500 chrUn 88.043 184 21 1 1 184 27164451 27164633 1.990000e-52 217.0
37 TraesCS6A01G076500 chrUn 87.500 184 20 3 1 184 27163368 27163548 3.330000e-50 209.0
38 TraesCS6A01G076500 chrUn 89.091 110 11 1 3142 3250 27269635 27269744 5.740000e-28 135.0
39 TraesCS6A01G076500 chrUn 87.156 109 13 1 3142 3250 27275551 27275658 4.470000e-24 122.0
40 TraesCS6A01G076500 chrUn 84.211 114 16 2 2993 3106 27184910 27185021 3.480000e-20 110.0
41 TraesCS6A01G076500 chr1B 78.431 765 129 30 597 1350 477410521 477409782 1.790000e-127 466.0
42 TraesCS6A01G076500 chr6D 75.410 915 165 36 1393 2280 5818983 5818102 3.990000e-104 388.0


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 TraesCS6A01G076500 chr6A 46760123 46763417 3294 True 2072.200000 6085 98.245333 1 3295 3 chr6A.!!$R2 3294
1 TraesCS6A01G076500 chr6A 46870656 46874479 3823 True 738.400000 1938 93.085000 599 3295 5 chr6A.!!$R3 2696
2 TraesCS6A01G076500 chr6A 46782176 46782991 815 True 678.000000 678 82.297000 1807 2612 1 chr6A.!!$R1 805
3 TraesCS6A01G076500 chr6B 80838369 80841109 2740 True 1016.000000 1690 88.544000 599 3201 2 chr6B.!!$R6 2602
4 TraesCS6A01G076500 chr6B 80780465 80781204 739 True 977.000000 977 90.483000 599 1343 1 chr6B.!!$R1 744
5 TraesCS6A01G076500 chr6B 80774142 80776062 1920 True 871.733333 1936 94.814333 1369 3246 3 chr6B.!!$R4 1877
6 TraesCS6A01G076500 chr6B 80233731 80236851 3120 True 479.666667 1002 85.134000 1 3250 3 chr6B.!!$R2 3249
7 TraesCS6A01G076500 chr6B 80821080 80823616 2536 True 376.500000 542 84.472500 1 2500 2 chr6B.!!$R5 2499
8 TraesCS6A01G076500 chr6B 80733254 80741966 8712 True 340.333333 520 85.214333 9 3247 6 chr6B.!!$R3 3238
9 TraesCS6A01G076500 chrUn 27015295 27017424 2129 True 1768.000000 1768 82.135000 599 2722 1 chrUn.!!$R1 2123
10 TraesCS6A01G076500 chrUn 27158888 27166053 7165 False 596.000000 1393 86.752400 1 3246 5 chrUn.!!$F2 3245
11 TraesCS6A01G076500 chrUn 27266836 27275658 8822 False 411.833333 959 86.397167 1 3250 6 chrUn.!!$F4 3249
12 TraesCS6A01G076500 chrUn 27183625 27185021 1396 False 350.000000 590 83.407000 1807 3106 2 chrUn.!!$F3 1299
13 TraesCS6A01G076500 chr1B 477409782 477410521 739 True 466.000000 466 78.431000 597 1350 1 chr1B.!!$R1 753
14 TraesCS6A01G076500 chr6D 5818102 5818983 881 True 388.000000 388 75.410000 1393 2280 1 chr6D.!!$R1 887

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
371 769 0.036952 CAGGACCACATCGAACAGCT 60.037 55.0 0.00 0.00 0.0 4.24 F
372 770 0.036952 AGGACCACATCGAACAGCTG 60.037 55.0 13.48 13.48 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 11998 0.033504 CGTCCGTCCTTCCATATGGG 59.966 60.000 21.78 6.47 35.41 4.00 R
2333 12309 2.046314 AACTTGATCGCCCCGGTG 60.046 61.111 0.00 0.00 0.00 4.94 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
132 134 4.350245 TCTAGGGTAAGCTTGCTTAGTGA 58.650 43.478 14.47 4.50 0.00 3.41
139 141 3.064900 AGCTTGCTTAGTGAAGAAGGG 57.935 47.619 0.00 0.00 34.25 3.95
218 309 6.369615 TGCTTAAGAGGTTTGTATTTCGGTAC 59.630 38.462 6.67 0.00 0.00 3.34
233 324 5.801531 TTCGGTACTAGCCACATAATCAT 57.198 39.130 0.00 0.00 0.00 2.45
254 348 8.725405 ATCATGTATTACCATAACACGTGAAA 57.275 30.769 25.01 9.96 38.31 2.69
255 349 8.192068 TCATGTATTACCATAACACGTGAAAG 57.808 34.615 25.01 8.73 33.44 2.62
258 352 6.591062 TGTATTACCATAACACGTGAAAGGTC 59.409 38.462 25.01 11.83 28.88 3.85
276 625 4.798882 AGGTCCCAAATATATTTCGCCAA 58.201 39.130 7.76 0.00 0.00 4.52
277 626 5.393866 AGGTCCCAAATATATTTCGCCAAT 58.606 37.500 7.76 0.00 0.00 3.16
278 627 6.548321 AGGTCCCAAATATATTTCGCCAATA 58.452 36.000 7.76 0.00 0.00 1.90
279 628 7.007723 AGGTCCCAAATATATTTCGCCAATAA 58.992 34.615 7.76 0.00 30.78 1.40
281 630 8.311109 GGTCCCAAATATATTTCGCCAATAAAT 58.689 33.333 7.76 0.00 30.78 1.40
282 631 9.705290 GTCCCAAATATATTTCGCCAATAAATT 57.295 29.630 7.76 0.00 30.78 1.82
306 677 4.939052 TTAGGGAAATTTCGCCAACAAA 57.061 36.364 26.39 13.41 40.63 2.83
321 692 3.299162 CAACAAATGTCACGACCACATG 58.701 45.455 0.00 0.00 34.59 3.21
371 769 0.036952 CAGGACCACATCGAACAGCT 60.037 55.000 0.00 0.00 0.00 4.24
372 770 0.036952 AGGACCACATCGAACAGCTG 60.037 55.000 13.48 13.48 0.00 4.24
376 774 1.012086 CCACATCGAACAGCTGATGG 58.988 55.000 23.35 10.63 44.90 3.51
385 783 1.644509 ACAGCTGATGGTACTGGACA 58.355 50.000 23.35 0.00 35.70 4.02
417 869 2.864114 GCTGCATTTCTCTCAGCCA 58.136 52.632 0.00 0.00 45.34 4.75
430 882 6.073327 TCTCTCAGCCAATGTATAAGTACG 57.927 41.667 0.00 0.00 33.36 3.67
431 883 5.009710 TCTCTCAGCCAATGTATAAGTACGG 59.990 44.000 0.00 0.00 33.36 4.02
432 884 4.891168 TCTCAGCCAATGTATAAGTACGGA 59.109 41.667 0.00 0.00 33.36 4.69
456 909 0.324738 TGAGGCAGTAGGTGGAGAGG 60.325 60.000 0.00 0.00 0.00 3.69
460 913 2.247635 AGGCAGTAGGTGGAGAGGAATA 59.752 50.000 0.00 0.00 0.00 1.75
461 914 3.116551 AGGCAGTAGGTGGAGAGGAATAT 60.117 47.826 0.00 0.00 0.00 1.28
468 943 4.484912 AGGTGGAGAGGAATATGAGGTAC 58.515 47.826 0.00 0.00 0.00 3.34
484 959 6.516739 TGAGGTACTATGAACTGTCTTCAG 57.483 41.667 0.00 0.00 41.55 3.02
488 963 7.607250 AGGTACTATGAACTGTCTTCAGAAAG 58.393 38.462 2.17 0.00 39.92 2.62
491 966 6.459923 ACTATGAACTGTCTTCAGAAAGTCC 58.540 40.000 0.00 0.00 41.57 3.85
492 967 4.073293 TGAACTGTCTTCAGAAAGTCCC 57.927 45.455 0.00 0.00 41.57 4.46
496 971 5.825593 ACTGTCTTCAGAAAGTCCCAATA 57.174 39.130 2.17 0.00 38.16 1.90
512 987 4.788075 TCCCAATACCAAATCCTCTCTTCA 59.212 41.667 0.00 0.00 0.00 3.02
546 1021 1.699930 GCCCCCAATTCCTCCCCTA 60.700 63.158 0.00 0.00 0.00 3.53
549 1024 1.866269 CCCCCAATTCCTCCCCTAAAT 59.134 52.381 0.00 0.00 0.00 1.40
577 1064 5.145528 GATCTGGATCCATCGACGACGAA 62.146 52.174 16.63 0.00 40.59 3.85
578 1065 6.557649 GATCTGGATCCATCGACGACGAAA 62.558 50.000 16.63 3.55 40.59 3.46
585 1072 3.317608 TCGACGACGAAACATAGCC 57.682 52.632 7.68 0.00 45.74 3.93
586 1073 0.806868 TCGACGACGAAACATAGCCT 59.193 50.000 7.68 0.00 45.74 4.58
588 1075 1.189403 GACGACGAAACATAGCCTCG 58.811 55.000 0.00 0.00 38.53 4.63
589 1076 0.801067 ACGACGAAACATAGCCTCGC 60.801 55.000 0.00 0.00 36.03 5.03
591 1078 0.645868 GACGAAACATAGCCTCGCAC 59.354 55.000 0.00 0.00 36.03 5.34
592 1079 1.076533 ACGAAACATAGCCTCGCACG 61.077 55.000 0.00 0.00 36.03 5.34
593 1080 1.752501 CGAAACATAGCCTCGCACGG 61.753 60.000 0.00 0.00 0.00 4.94
594 1081 0.459585 GAAACATAGCCTCGCACGGA 60.460 55.000 0.00 0.00 0.00 4.69
595 1082 0.178068 AAACATAGCCTCGCACGGAT 59.822 50.000 0.00 0.00 0.00 4.18
603 1125 0.390340 CCTCGCACGGATATGATGGG 60.390 60.000 0.00 0.00 0.00 4.00
671 1193 4.057428 GTCTCCTGCCGCACGTCT 62.057 66.667 0.00 0.00 0.00 4.18
744 1274 4.645921 GCGCGGCAACCTGCTTTT 62.646 61.111 8.83 0.00 44.28 2.27
850 1386 1.485066 GACGGAGGGCTCAATTTCCTA 59.515 52.381 0.00 0.00 0.00 2.94
943 2464 4.429212 CCACGCGATCACGGACCA 62.429 66.667 15.93 0.00 40.15 4.02
944 2465 3.179265 CACGCGATCACGGACCAC 61.179 66.667 15.93 0.00 40.15 4.16
946 2467 2.880879 CGCGATCACGGACCACTG 60.881 66.667 0.00 0.00 40.15 3.66
947 2468 3.188786 GCGATCACGGACCACTGC 61.189 66.667 0.00 0.00 40.15 4.40
948 2469 2.880879 CGATCACGGACCACTGCG 60.881 66.667 0.00 0.00 37.24 5.18
949 2470 2.571757 GATCACGGACCACTGCGA 59.428 61.111 0.00 0.00 34.80 5.10
950 2471 1.805945 GATCACGGACCACTGCGAC 60.806 63.158 0.00 0.00 34.80 5.19
951 2472 3.626680 ATCACGGACCACTGCGACG 62.627 63.158 0.00 0.00 34.80 5.12
956 2477 2.338984 GACCACTGCGACGGTCTT 59.661 61.111 6.57 0.00 46.83 3.01
958 2479 2.143594 GACCACTGCGACGGTCTTCT 62.144 60.000 6.57 0.00 46.83 2.85
959 2480 1.734477 CCACTGCGACGGTCTTCTG 60.734 63.158 6.57 4.89 0.00 3.02
961 2482 2.259818 CTGCGACGGTCTTCTGCT 59.740 61.111 6.57 0.00 0.00 4.24
962 2483 1.373497 CTGCGACGGTCTTCTGCTT 60.373 57.895 6.57 0.00 0.00 3.91
963 2484 0.946221 CTGCGACGGTCTTCTGCTTT 60.946 55.000 6.57 0.00 0.00 3.51
966 2487 0.946221 CGACGGTCTTCTGCTTTGCT 60.946 55.000 6.57 0.00 0.00 3.91
968 2489 1.208614 CGGTCTTCTGCTTTGCTGC 59.791 57.895 0.00 0.00 0.00 5.25
969 2490 1.233285 CGGTCTTCTGCTTTGCTGCT 61.233 55.000 0.00 0.00 0.00 4.24
970 2491 0.957362 GGTCTTCTGCTTTGCTGCTT 59.043 50.000 0.00 0.00 0.00 3.91
971 2492 1.068679 GGTCTTCTGCTTTGCTGCTTC 60.069 52.381 0.00 0.00 0.00 3.86
984 2506 0.038526 CTGCTTCTGCTTTGCCCAAG 60.039 55.000 0.00 0.00 40.48 3.61
1056 2578 4.552365 CCCACCATCTCGCCGCAT 62.552 66.667 0.00 0.00 0.00 4.73
1125 2659 2.025727 GGCGAATCCGACGACGAT 59.974 61.111 9.28 0.00 42.66 3.73
1166 2710 2.109181 GCCTCCAGCGTCATACCC 59.891 66.667 0.00 0.00 0.00 3.69
1182 2726 1.371467 ACCCCATCCATGTGTTCTCA 58.629 50.000 0.00 0.00 0.00 3.27
1250 2794 1.597302 CTGCAGGGATCATCGCCAG 60.597 63.158 5.57 0.00 0.00 4.85
1362 2924 2.595238 ACCAGGTATTCTAGTAGCCCG 58.405 52.381 0.00 0.00 0.00 6.13
1366 2928 4.079970 CAGGTATTCTAGTAGCCCGATCA 58.920 47.826 0.00 0.00 0.00 2.92
1415 2991 7.946207 AGTATATACCACTGTGATTCACTCAG 58.054 38.462 17.26 10.00 43.24 3.35
1420 2996 2.810274 CACTGTGATTCACTCAGGTTGG 59.190 50.000 17.26 1.69 42.31 3.77
1468 3049 2.653726 TGTGTGCAGAATGTCCTTGTT 58.346 42.857 0.00 0.00 39.31 2.83
1543 3328 0.255890 CCCAAACACCATCTCGGGAT 59.744 55.000 0.00 0.00 40.22 3.85
1546 3331 3.435026 CCCAAACACCATCTCGGGATATT 60.435 47.826 0.00 0.00 40.22 1.28
1640 3461 2.513753 TGCGGTCAAACAGATTGGATT 58.486 42.857 0.00 0.00 39.62 3.01
1678 3499 6.656693 ACCTGTCTTAAGATCTTTGAACATGG 59.343 38.462 14.36 17.00 0.00 3.66
1726 3547 9.778993 CAAACAATGGATCTTACAAGATGTTAG 57.221 33.333 9.16 0.00 45.39 2.34
1872 3693 3.058914 CGTCGTTGAAAAGGCTGAAGAAT 60.059 43.478 0.00 0.00 0.00 2.40
1879 11825 7.852945 CGTTGAAAAGGCTGAAGAATATGATAC 59.147 37.037 0.00 0.00 0.00 2.24
1945 11892 5.047021 AGGTCGTCTTCTTGATTTCATCAGA 60.047 40.000 0.00 0.00 40.94 3.27
1957 11904 8.812513 TTGATTTCATCAGAGATAACAACCAT 57.187 30.769 0.00 0.00 40.94 3.55
2009 11956 2.561478 TTCAGTACTTGGGCAGTTCC 57.439 50.000 0.00 0.00 36.88 3.62
2039 11998 2.418884 GCTAGAAGCTTACACTGACCCC 60.419 54.545 0.00 0.00 38.45 4.95
2148 12110 8.806429 TGAAGATGAGAAGCTATATAGGAGAG 57.194 38.462 11.72 0.00 0.00 3.20
2322 12298 0.038618 CGTCACCGACATCAAGTCCA 60.039 55.000 0.00 0.00 44.66 4.02
2323 12299 1.604438 CGTCACCGACATCAAGTCCAA 60.604 52.381 0.00 0.00 44.66 3.53
2324 12300 2.069273 GTCACCGACATCAAGTCCAAG 58.931 52.381 0.00 0.00 44.66 3.61
2325 12301 1.001974 TCACCGACATCAAGTCCAAGG 59.998 52.381 0.00 0.00 44.66 3.61
2326 12302 1.056660 ACCGACATCAAGTCCAAGGT 58.943 50.000 0.00 0.00 44.66 3.50
2327 12303 1.270839 ACCGACATCAAGTCCAAGGTG 60.271 52.381 0.00 0.00 44.66 4.00
2328 12304 1.001974 CCGACATCAAGTCCAAGGTGA 59.998 52.381 0.00 0.00 44.66 4.02
2329 12305 2.355108 CCGACATCAAGTCCAAGGTGAT 60.355 50.000 0.00 0.00 44.66 3.06
2330 12306 3.338249 CGACATCAAGTCCAAGGTGATT 58.662 45.455 0.00 0.00 44.66 2.57
2331 12307 3.753272 CGACATCAAGTCCAAGGTGATTT 59.247 43.478 0.00 0.00 44.66 2.17
2332 12308 4.378770 CGACATCAAGTCCAAGGTGATTTG 60.379 45.833 0.00 0.00 44.66 2.32
2333 12309 3.256631 ACATCAAGTCCAAGGTGATTTGC 59.743 43.478 0.00 0.00 33.43 3.68
2334 12310 2.942804 TCAAGTCCAAGGTGATTTGCA 58.057 42.857 0.00 0.00 33.43 4.08
2335 12311 2.622942 TCAAGTCCAAGGTGATTTGCAC 59.377 45.455 0.00 0.00 46.98 4.57
2351 12327 2.046314 ACCGGGGCGATCAAGTTG 60.046 61.111 6.32 0.00 0.00 3.16
2352 12328 2.046314 CCGGGGCGATCAAGTTGT 60.046 61.111 2.11 0.00 0.00 3.32
2455 12444 8.216423 AGATGAGTAGGTATTTGCAAATCAGAT 58.784 33.333 27.28 14.44 0.00 2.90
2851 13391 1.534595 CCATATTTGGCGCTGCAGTTC 60.535 52.381 16.64 7.19 35.85 3.01
2852 13392 1.132834 CATATTTGGCGCTGCAGTTCA 59.867 47.619 16.64 8.54 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 4.922206 ACTTATGATGCAAGTTCCTTCCA 58.078 39.130 0.00 0.00 32.28 3.53
90 92 8.915036 CCCTAGAAGCTAGTTTCACTATTAAGA 58.085 37.037 19.87 0.00 29.08 2.10
111 113 4.737855 TCACTAAGCAAGCTTACCCTAG 57.262 45.455 10.29 5.36 37.47 3.02
132 134 3.806949 TGCCATACAAGTTCCCTTCTT 57.193 42.857 0.00 0.00 0.00 2.52
139 141 6.293135 GCTAAGCTAGATTGCCATACAAGTTC 60.293 42.308 2.82 0.00 42.87 3.01
233 324 6.465948 ACCTTTCACGTGTTATGGTAATACA 58.534 36.000 16.51 0.00 0.00 2.29
254 348 4.447138 TGGCGAAATATATTTGGGACCT 57.553 40.909 15.39 0.00 0.00 3.85
255 349 5.722021 ATTGGCGAAATATATTTGGGACC 57.278 39.130 15.39 11.45 0.00 4.46
282 631 5.277857 TGTTGGCGAAATTTCCCTAAAAA 57.722 34.783 19.93 8.64 0.00 1.94
283 632 4.939052 TGTTGGCGAAATTTCCCTAAAA 57.061 36.364 19.93 7.29 0.00 1.52
306 677 0.674581 CAGGCATGTGGTCGTGACAT 60.675 55.000 2.00 0.00 40.82 3.06
371 769 1.548719 CTTCGGTGTCCAGTACCATCA 59.451 52.381 0.00 0.00 38.11 3.07
372 770 1.739371 GCTTCGGTGTCCAGTACCATC 60.739 57.143 0.00 0.00 38.11 3.51
376 774 1.079336 GGGCTTCGGTGTCCAGTAC 60.079 63.158 0.00 0.00 0.00 2.73
404 856 7.653713 CGTACTTATACATTGGCTGAGAGAAAT 59.346 37.037 0.00 0.00 0.00 2.17
417 869 5.535406 CCTCACTCCTCCGTACTTATACATT 59.465 44.000 0.00 0.00 0.00 2.71
430 882 0.324830 ACCTACTGCCTCACTCCTCC 60.325 60.000 0.00 0.00 0.00 4.30
431 883 0.820871 CACCTACTGCCTCACTCCTC 59.179 60.000 0.00 0.00 0.00 3.71
432 884 0.616111 CCACCTACTGCCTCACTCCT 60.616 60.000 0.00 0.00 0.00 3.69
456 909 9.685828 GAAGACAGTTCATAGTACCTCATATTC 57.314 37.037 0.00 0.00 0.00 1.75
460 913 6.892456 TCTGAAGACAGTTCATAGTACCTCAT 59.108 38.462 0.00 0.00 43.81 2.90
461 914 6.246163 TCTGAAGACAGTTCATAGTACCTCA 58.754 40.000 0.00 0.00 43.81 3.86
468 943 5.872070 GGGACTTTCTGAAGACAGTTCATAG 59.128 44.000 7.12 0.00 43.81 2.23
484 959 5.510430 AGAGGATTTGGTATTGGGACTTTC 58.490 41.667 0.00 0.00 0.00 2.62
488 963 4.779993 AGAGAGGATTTGGTATTGGGAC 57.220 45.455 0.00 0.00 0.00 4.46
491 966 6.599445 AGATGAAGAGAGGATTTGGTATTGG 58.401 40.000 0.00 0.00 0.00 3.16
492 967 9.434420 GATAGATGAAGAGAGGATTTGGTATTG 57.566 37.037 0.00 0.00 0.00 1.90
496 971 7.688918 AAGATAGATGAAGAGAGGATTTGGT 57.311 36.000 0.00 0.00 0.00 3.67
512 987 1.783365 GGGGCCAGGGAAAAGATAGAT 59.217 52.381 4.39 0.00 0.00 1.98
546 1021 6.152661 GTCGATGGATCCAGATCTAGAGATTT 59.847 42.308 21.33 0.00 37.92 2.17
549 1024 4.584874 GTCGATGGATCCAGATCTAGAGA 58.415 47.826 21.33 7.28 37.92 3.10
577 1064 1.037493 TATCCGTGCGAGGCTATGTT 58.963 50.000 0.00 0.00 0.00 2.71
578 1065 1.067565 CATATCCGTGCGAGGCTATGT 60.068 52.381 10.97 0.00 36.28 2.29
579 1066 1.202348 TCATATCCGTGCGAGGCTATG 59.798 52.381 12.30 12.30 40.11 2.23
580 1067 1.545841 TCATATCCGTGCGAGGCTAT 58.454 50.000 0.00 0.00 0.00 2.97
581 1068 1.202348 CATCATATCCGTGCGAGGCTA 59.798 52.381 0.00 0.00 0.00 3.93
585 1072 0.603065 TCCCATCATATCCGTGCGAG 59.397 55.000 0.00 0.00 0.00 5.03
586 1073 1.204704 GATCCCATCATATCCGTGCGA 59.795 52.381 0.00 0.00 0.00 5.10
588 1075 1.645034 CGATCCCATCATATCCGTGC 58.355 55.000 0.00 0.00 0.00 5.34
589 1076 1.824852 TCCGATCCCATCATATCCGTG 59.175 52.381 0.00 0.00 0.00 4.94
591 1078 1.202463 GCTCCGATCCCATCATATCCG 60.202 57.143 0.00 0.00 0.00 4.18
592 1079 1.139853 GGCTCCGATCCCATCATATCC 59.860 57.143 0.00 0.00 0.00 2.59
593 1080 1.202463 CGGCTCCGATCCCATCATATC 60.202 57.143 1.35 0.00 42.83 1.63
594 1081 0.826715 CGGCTCCGATCCCATCATAT 59.173 55.000 1.35 0.00 42.83 1.78
595 1082 1.257750 CCGGCTCCGATCCCATCATA 61.258 60.000 10.28 0.00 42.83 2.15
869 1435 2.261671 GTCGCAGTGGTCCGTGAT 59.738 61.111 0.00 0.00 0.00 3.06
889 1455 0.955428 ATTCGCGGCAAAGCAGAAGA 60.955 50.000 6.13 0.00 34.89 2.87
932 2453 1.805945 GTCGCAGTGGTCCGTGATC 60.806 63.158 0.00 0.00 0.00 2.92
933 2454 2.261671 GTCGCAGTGGTCCGTGAT 59.738 61.111 0.00 0.00 0.00 3.06
934 2455 4.337060 CGTCGCAGTGGTCCGTGA 62.337 66.667 0.00 0.00 0.00 4.35
940 2461 2.201022 AGAAGACCGTCGCAGTGGT 61.201 57.895 0.00 0.00 39.73 4.16
941 2462 1.734477 CAGAAGACCGTCGCAGTGG 60.734 63.158 0.00 0.00 0.00 4.00
942 2463 2.375766 GCAGAAGACCGTCGCAGTG 61.376 63.158 0.00 0.00 0.00 3.66
943 2464 2.049063 GCAGAAGACCGTCGCAGT 60.049 61.111 0.00 0.00 0.00 4.40
944 2465 0.946221 AAAGCAGAAGACCGTCGCAG 60.946 55.000 0.00 0.00 0.00 5.18
946 2467 1.493311 CAAAGCAGAAGACCGTCGC 59.507 57.895 0.00 0.00 0.00 5.19
947 2468 0.946221 AGCAAAGCAGAAGACCGTCG 60.946 55.000 0.00 0.00 0.00 5.12
948 2469 0.514691 CAGCAAAGCAGAAGACCGTC 59.485 55.000 0.00 0.00 0.00 4.79
949 2470 1.510480 GCAGCAAAGCAGAAGACCGT 61.510 55.000 0.00 0.00 0.00 4.83
950 2471 1.208614 GCAGCAAAGCAGAAGACCG 59.791 57.895 0.00 0.00 0.00 4.79
951 2472 0.957362 AAGCAGCAAAGCAGAAGACC 59.043 50.000 0.00 0.00 36.85 3.85
952 2473 1.878734 AGAAGCAGCAAAGCAGAAGAC 59.121 47.619 0.00 0.00 36.85 3.01
953 2474 1.878088 CAGAAGCAGCAAAGCAGAAGA 59.122 47.619 0.00 0.00 36.85 2.87
955 2476 0.313043 GCAGAAGCAGCAAAGCAGAA 59.687 50.000 0.00 0.00 41.58 3.02
956 2477 0.536687 AGCAGAAGCAGCAAAGCAGA 60.537 50.000 0.00 0.00 45.49 4.26
958 2479 0.748450 AAAGCAGAAGCAGCAAAGCA 59.252 45.000 0.00 0.00 45.49 3.91
959 2480 1.137513 CAAAGCAGAAGCAGCAAAGC 58.862 50.000 0.00 0.00 45.49 3.51
961 2482 0.249573 GGCAAAGCAGAAGCAGCAAA 60.250 50.000 0.00 0.00 45.49 3.68
962 2483 1.364901 GGCAAAGCAGAAGCAGCAA 59.635 52.632 0.00 0.00 45.49 3.91
963 2484 2.567497 GGGCAAAGCAGAAGCAGCA 61.567 57.895 0.00 0.00 45.49 4.41
966 2487 2.043625 CTTGGGCAAAGCAGAAGCA 58.956 52.632 0.00 0.00 45.49 3.91
1042 2564 1.227556 GGTAATGCGGCGAGATGGT 60.228 57.895 12.98 0.00 0.00 3.55
1045 2567 1.069765 CCTGGTAATGCGGCGAGAT 59.930 57.895 12.98 0.00 0.00 2.75
1056 2578 3.263425 GTGGGATCAGAAAGACCTGGTAA 59.737 47.826 0.00 0.00 34.99 2.85
1166 2710 2.216046 CCGATGAGAACACATGGATGG 58.784 52.381 0.00 0.00 0.00 3.51
1182 2726 1.439228 CCATCGCTGAGTCACCGAT 59.561 57.895 15.93 15.93 41.85 4.18
1250 2794 5.357878 TCATACCAAGAATTCCACTTCATGC 59.642 40.000 0.65 0.00 0.00 4.06
1362 2924 9.869844 CGTATTTGTTAAAGGAGAATGATGATC 57.130 33.333 0.00 0.00 0.00 2.92
1366 2928 8.047310 ACTCCGTATTTGTTAAAGGAGAATGAT 58.953 33.333 15.23 0.00 45.88 2.45
1543 3328 3.181469 GCAATACACCCCTCTCGACAATA 60.181 47.826 0.00 0.00 0.00 1.90
1546 3331 0.535335 GCAATACACCCCTCTCGACA 59.465 55.000 0.00 0.00 0.00 4.35
1666 3487 4.910195 AGCATAGTCACCATGTTCAAAGA 58.090 39.130 0.00 0.00 0.00 2.52
1678 3499 2.744202 CCCAGTTGTTGAGCATAGTCAC 59.256 50.000 0.00 0.00 0.00 3.67
1726 3547 1.063764 CAGAGGTCGACTTACGGTAGC 59.936 57.143 16.46 0.00 42.82 3.58
1945 11892 5.468658 AGGCTAGTCCTATGGTTGTTATCT 58.531 41.667 4.13 0.00 45.41 1.98
2009 11956 2.706339 AAGCTTCTAGCCATGGACAG 57.294 50.000 18.40 11.42 43.77 3.51
2039 11998 0.033504 CGTCCGTCCTTCCATATGGG 59.966 60.000 21.78 6.47 35.41 4.00
2148 12110 4.646572 AGTTGAGATTCCTGTTCCAACTC 58.353 43.478 0.00 0.00 39.72 3.01
2325 12301 4.114997 CGCCCCGGTGCAAATCAC 62.115 66.667 10.26 0.00 44.90 3.06
2326 12302 3.636929 ATCGCCCCGGTGCAAATCA 62.637 57.895 10.26 0.00 0.00 2.57
2327 12303 2.828549 ATCGCCCCGGTGCAAATC 60.829 61.111 10.26 0.00 0.00 2.17
2328 12304 2.828549 GATCGCCCCGGTGCAAAT 60.829 61.111 10.26 1.07 0.00 2.32
2329 12305 3.851897 TTGATCGCCCCGGTGCAAA 62.852 57.895 10.26 0.00 0.00 3.68
2330 12306 4.337177 TTGATCGCCCCGGTGCAA 62.337 61.111 10.26 0.00 0.00 4.08
2331 12307 4.776322 CTTGATCGCCCCGGTGCA 62.776 66.667 10.26 0.00 0.00 4.57
2332 12308 4.778143 ACTTGATCGCCCCGGTGC 62.778 66.667 0.00 0.00 0.00 5.01
2333 12309 2.046314 AACTTGATCGCCCCGGTG 60.046 61.111 0.00 0.00 0.00 4.94
2334 12310 2.046314 CAACTTGATCGCCCCGGT 60.046 61.111 0.00 0.00 0.00 5.28
2335 12311 2.046314 ACAACTTGATCGCCCCGG 60.046 61.111 0.00 0.00 0.00 5.73
2455 12444 1.142870 AGCTGGCGATAATTAGGGCAA 59.857 47.619 13.99 3.13 35.72 4.52
2567 12588 3.450578 TCACAAAGTCACGGTCTTACAC 58.549 45.455 0.00 0.00 0.00 2.90
2834 13374 1.132834 CATGAACTGCAGCGCCAAATA 59.867 47.619 15.27 0.00 0.00 1.40
2846 13386 7.825681 TGTATTACAAAACATCCCATGAACTG 58.174 34.615 0.00 0.00 0.00 3.16
2876 13416 8.582657 AAATCACTTCTACTACTGAGAGCTAA 57.417 34.615 0.00 0.00 0.00 3.09
2963 16610 8.448615 CCTAGTAAATGTAGCTTACACCAAAAC 58.551 37.037 0.00 0.00 42.23 2.43


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

AutoCloner maintained by Alex Coulton.