Multiple sequence alignment - TraesCS7A01G016600

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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 TraesCS7A01G016600 chr7A 100.000 2315 0 0 1 2315 7246461 7244147 0.000000e+00 4276
1 TraesCS7A01G016600 chr7A 92.005 1676 102 21 649 2315 494280244 494278592 0.000000e+00 2324
2 TraesCS7A01G016600 chr7A 90.849 1672 117 18 649 2315 192970895 192972535 0.000000e+00 2207
3 TraesCS7A01G016600 chr7A 95.815 1123 37 3 1193 2315 232524092 232522980 0.000000e+00 1805
4 TraesCS7A01G016600 chr7A 93.644 236 15 0 1 236 686011597 686011362 1.020000e-93 353
5 TraesCS7A01G016600 chr5A 93.983 1745 71 10 572 2315 670017143 670018854 0.000000e+00 2610
6 TraesCS7A01G016600 chr2D 92.699 1671 94 17 647 2315 71956718 71955074 0.000000e+00 2385
7 TraesCS7A01G016600 chr5B 92.496 1679 95 20 654 2315 695870742 695869078 0.000000e+00 2374
8 TraesCS7A01G016600 chr5B 86.984 315 25 12 1 310 695872256 695871953 7.920000e-90 340
9 TraesCS7A01G016600 chr2A 91.860 1683 94 25 649 2315 759649610 759651265 0.000000e+00 2309
10 TraesCS7A01G016600 chr2A 86.111 288 31 7 1 285 759648932 759649213 3.740000e-78 302
11 TraesCS7A01G016600 chr3D 91.647 1676 112 19 649 2315 591147509 591145853 0.000000e+00 2294
12 TraesCS7A01G016600 chr6A 94.396 1481 66 6 838 2315 549225237 549226703 0.000000e+00 2259
13 TraesCS7A01G016600 chr3B 94.106 1493 73 6 827 2315 822804813 822806294 0.000000e+00 2255
14 TraesCS7A01G016600 chr3B 92.758 1519 87 13 694 2202 827103194 827101689 0.000000e+00 2174
15 TraesCS7A01G016600 chr3B 92.693 1519 88 13 694 2202 827648442 827646937 0.000000e+00 2169
16 TraesCS7A01G016600 chr3B 92.797 236 17 0 1 236 827103896 827103661 2.200000e-90 342
17 TraesCS7A01G016600 chr3B 88.112 286 28 5 1 285 215114174 215113894 3.690000e-88 335
18 TraesCS7A01G016600 chr2B 90.898 1681 119 24 649 2315 456257215 456255555 0.000000e+00 2226
19 TraesCS7A01G016600 chr2B 88.596 342 39 0 1 342 456260284 456259943 1.280000e-112 416
20 TraesCS7A01G016600 chr3A 92.262 1499 107 6 818 2315 435347209 435348699 0.000000e+00 2117
21 TraesCS7A01G016600 chr7D 91.925 1486 104 9 649 2131 616449822 616448350 0.000000e+00 2065
22 TraesCS7A01G016600 chr7D 91.755 1419 93 15 655 2063 241965332 241963928 0.000000e+00 1951
23 TraesCS7A01G016600 chr7D 87.986 283 25 7 1 279 616450466 616450189 2.220000e-85 326
24 TraesCS7A01G016600 chr1B 90.058 342 34 0 1 342 89509098 89509439 5.870000e-121 444
25 TraesCS7A01G016600 chr6D 80.612 392 55 14 2 382 319012808 319012427 1.350000e-72 283


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 TraesCS7A01G016600 chr7A 7244147 7246461 2314 True 4276.0 4276 100.0000 1 2315 1 chr7A.!!$R1 2314
1 TraesCS7A01G016600 chr7A 494278592 494280244 1652 True 2324.0 2324 92.0050 649 2315 1 chr7A.!!$R3 1666
2 TraesCS7A01G016600 chr7A 192970895 192972535 1640 False 2207.0 2207 90.8490 649 2315 1 chr7A.!!$F1 1666
3 TraesCS7A01G016600 chr7A 232522980 232524092 1112 True 1805.0 1805 95.8150 1193 2315 1 chr7A.!!$R2 1122
4 TraesCS7A01G016600 chr5A 670017143 670018854 1711 False 2610.0 2610 93.9830 572 2315 1 chr5A.!!$F1 1743
5 TraesCS7A01G016600 chr2D 71955074 71956718 1644 True 2385.0 2385 92.6990 647 2315 1 chr2D.!!$R1 1668
6 TraesCS7A01G016600 chr5B 695869078 695872256 3178 True 1357.0 2374 89.7400 1 2315 2 chr5B.!!$R1 2314
7 TraesCS7A01G016600 chr2A 759648932 759651265 2333 False 1305.5 2309 88.9855 1 2315 2 chr2A.!!$F1 2314
8 TraesCS7A01G016600 chr3D 591145853 591147509 1656 True 2294.0 2294 91.6470 649 2315 1 chr3D.!!$R1 1666
9 TraesCS7A01G016600 chr6A 549225237 549226703 1466 False 2259.0 2259 94.3960 838 2315 1 chr6A.!!$F1 1477
10 TraesCS7A01G016600 chr3B 822804813 822806294 1481 False 2255.0 2255 94.1060 827 2315 1 chr3B.!!$F1 1488
11 TraesCS7A01G016600 chr3B 827646937 827648442 1505 True 2169.0 2169 92.6930 694 2202 1 chr3B.!!$R2 1508
12 TraesCS7A01G016600 chr3B 827101689 827103896 2207 True 1258.0 2174 92.7775 1 2202 2 chr3B.!!$R3 2201
13 TraesCS7A01G016600 chr2B 456255555 456260284 4729 True 1321.0 2226 89.7470 1 2315 2 chr2B.!!$R1 2314
14 TraesCS7A01G016600 chr3A 435347209 435348699 1490 False 2117.0 2117 92.2620 818 2315 1 chr3A.!!$F1 1497
15 TraesCS7A01G016600 chr7D 241963928 241965332 1404 True 1951.0 1951 91.7550 655 2063 1 chr7D.!!$R1 1408
16 TraesCS7A01G016600 chr7D 616448350 616450466 2116 True 1195.5 2065 89.9555 1 2131 2 chr7D.!!$R2 2130

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
515 3046 0.179103 GTAGGCAATGCATGTTGGGC 60.179 55.0 7.79 3.06 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2186 5721 1.384502 CTCCCCATGGCTCCACCTA 60.385 63.158 6.09 0.0 40.22 3.08 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
39 40 2.879026 CGGATAGATCGGAGTGTGAGAA 59.121 50.000 0.00 0.00 0.00 2.87
40 41 3.504134 CGGATAGATCGGAGTGTGAGAAT 59.496 47.826 0.00 0.00 0.00 2.40
44 45 6.375736 GGATAGATCGGAGTGTGAGAATATCA 59.624 42.308 0.00 0.00 34.79 2.15
70 71 0.810426 TGCGCTCGGTGTTGTACAAA 60.810 50.000 10.51 0.00 0.00 2.83
104 105 0.249699 ACTGCGAACGGATTGTGTCA 60.250 50.000 0.00 0.00 0.00 3.58
242 245 2.031944 GGCGAAGAACCAAGAAACAGAC 60.032 50.000 0.00 0.00 0.00 3.51
342 375 1.154073 GCGTACGAGAAGCTTCGGT 60.154 57.895 21.65 23.45 44.57 4.69
344 377 0.447011 CGTACGAGAAGCTTCGGTCT 59.553 55.000 23.58 7.37 44.57 3.85
354 2827 3.989698 CTTCGGTCTCGTGCGGCAT 62.990 63.158 5.72 0.00 37.69 4.40
365 2890 1.153309 TGCGGCATCAGGTCTCATG 60.153 57.895 0.00 0.00 0.00 3.07
366 2891 1.153289 GCGGCATCAGGTCTCATGT 60.153 57.895 0.00 0.00 0.00 3.21
368 2893 0.812811 CGGCATCAGGTCTCATGTGG 60.813 60.000 0.00 0.00 0.00 4.17
374 2900 3.503363 GGTCTCATGTGGCAGCGC 61.503 66.667 0.00 0.00 0.00 5.92
394 2920 1.370414 CAACGCGTGAAGGCAAAGG 60.370 57.895 14.98 0.00 0.00 3.11
395 2921 3.194272 AACGCGTGAAGGCAAAGGC 62.194 57.895 14.98 0.00 40.13 4.35
396 2922 4.741781 CGCGTGAAGGCAAAGGCG 62.742 66.667 0.00 6.74 42.47 5.52
397 2923 4.404654 GCGTGAAGGCAAAGGCGG 62.405 66.667 0.00 0.00 42.47 6.13
398 2924 3.737172 CGTGAAGGCAAAGGCGGG 61.737 66.667 0.00 0.00 42.47 6.13
403 2929 4.994756 AGGCAAAGGCGGGTTGGG 62.995 66.667 0.00 0.00 42.47 4.12
404 2930 4.986708 GGCAAAGGCGGGTTGGGA 62.987 66.667 0.00 0.00 42.47 4.37
406 2932 2.931068 GCAAAGGCGGGTTGGGAAG 61.931 63.158 1.75 0.00 0.00 3.46
407 2933 2.600470 AAAGGCGGGTTGGGAAGC 60.600 61.111 0.00 0.00 0.00 3.86
410 2936 4.660938 GGCGGGTTGGGAAGCAGT 62.661 66.667 0.00 0.00 0.00 4.40
423 2954 0.392193 AAGCAGTCCAGGCGAGATTG 60.392 55.000 0.00 0.00 36.08 2.67
429 2960 1.069765 CCAGGCGAGATTGGCGTAT 59.930 57.895 0.00 0.00 39.82 3.06
437 2968 2.349580 CGAGATTGGCGTATATGCATGG 59.650 50.000 18.41 0.00 36.28 3.66
438 2969 2.086869 AGATTGGCGTATATGCATGGC 58.913 47.619 18.41 5.34 36.28 4.40
444 2975 1.795768 CGTATATGCATGGCGGTTCT 58.204 50.000 10.16 0.00 0.00 3.01
458 2989 4.580995 TGGCGGTTCTGATTAAACAAAAGA 59.419 37.500 0.00 0.00 0.00 2.52
459 2990 5.067936 TGGCGGTTCTGATTAAACAAAAGAA 59.932 36.000 0.00 0.00 0.00 2.52
461 2992 6.143919 GGCGGTTCTGATTAAACAAAAGAAAG 59.856 38.462 0.00 0.00 0.00 2.62
463 2994 6.143919 CGGTTCTGATTAAACAAAAGAAAGGC 59.856 38.462 0.00 0.00 0.00 4.35
464 2995 7.210174 GGTTCTGATTAAACAAAAGAAAGGCT 58.790 34.615 0.00 0.00 0.00 4.58
465 2996 7.710907 GGTTCTGATTAAACAAAAGAAAGGCTT 59.289 33.333 0.00 0.00 38.88 4.35
466 2997 9.744468 GTTCTGATTAAACAAAAGAAAGGCTTA 57.256 29.630 0.00 0.00 35.24 3.09
467 2998 9.965824 TTCTGATTAAACAAAAGAAAGGCTTAG 57.034 29.630 0.00 0.00 35.24 2.18
468 2999 8.082242 TCTGATTAAACAAAAGAAAGGCTTAGC 58.918 33.333 0.00 0.00 35.24 3.09
469 3000 6.861055 TGATTAAACAAAAGAAAGGCTTAGCG 59.139 34.615 0.00 0.00 35.24 4.26
470 3001 4.649088 AAACAAAAGAAAGGCTTAGCGT 57.351 36.364 0.00 0.00 35.24 5.07
471 3002 4.649088 AACAAAAGAAAGGCTTAGCGTT 57.351 36.364 6.31 6.31 38.30 4.84
472 3003 3.964909 ACAAAAGAAAGGCTTAGCGTTG 58.035 40.909 12.99 6.17 36.74 4.10
473 3004 3.243401 ACAAAAGAAAGGCTTAGCGTTGG 60.243 43.478 12.99 1.04 36.74 3.77
474 3005 0.881796 AAGAAAGGCTTAGCGTTGGC 59.118 50.000 12.99 8.49 36.74 4.52
485 3016 2.978010 CGTTGGCTGGCGGAAGTT 60.978 61.111 0.00 0.00 0.00 2.66
495 3026 1.339610 TGGCGGAAGTTGTTTGGATTG 59.660 47.619 0.00 0.00 0.00 2.67
496 3027 1.336795 GGCGGAAGTTGTTTGGATTGG 60.337 52.381 0.00 0.00 0.00 3.16
500 3031 3.190535 CGGAAGTTGTTTGGATTGGTAGG 59.809 47.826 0.00 0.00 0.00 3.18
501 3032 3.056821 GGAAGTTGTTTGGATTGGTAGGC 60.057 47.826 0.00 0.00 0.00 3.93
503 3034 3.571590 AGTTGTTTGGATTGGTAGGCAA 58.428 40.909 0.00 0.00 0.00 4.52
504 3035 4.159557 AGTTGTTTGGATTGGTAGGCAAT 58.840 39.130 0.00 0.00 0.00 3.56
505 3036 4.021192 AGTTGTTTGGATTGGTAGGCAATG 60.021 41.667 0.00 0.00 0.00 2.82
506 3037 2.233431 TGTTTGGATTGGTAGGCAATGC 59.767 45.455 0.00 0.00 0.00 3.56
507 3038 2.228545 TTGGATTGGTAGGCAATGCA 57.771 45.000 7.79 0.00 38.33 3.96
508 3039 2.457813 TGGATTGGTAGGCAATGCAT 57.542 45.000 7.79 1.39 35.88 3.96
509 3040 2.033372 TGGATTGGTAGGCAATGCATG 58.967 47.619 7.79 0.00 35.88 4.06
511 3042 2.431782 GGATTGGTAGGCAATGCATGTT 59.568 45.455 7.79 0.00 31.89 2.71
512 3043 3.450578 GATTGGTAGGCAATGCATGTTG 58.549 45.455 7.79 0.00 0.00 3.33
513 3044 1.184431 TGGTAGGCAATGCATGTTGG 58.816 50.000 7.79 0.00 0.00 3.77
514 3045 0.461135 GGTAGGCAATGCATGTTGGG 59.539 55.000 7.79 0.00 0.00 4.12
515 3046 0.179103 GTAGGCAATGCATGTTGGGC 60.179 55.000 7.79 3.06 0.00 5.36
516 3047 1.329171 TAGGCAATGCATGTTGGGCC 61.329 55.000 7.79 14.97 41.65 5.80
517 3048 2.125024 GCAATGCATGTTGGGCCC 60.125 61.111 17.59 17.59 0.00 5.80
518 3049 2.957080 GCAATGCATGTTGGGCCCA 61.957 57.895 24.45 24.45 0.00 5.36
519 3050 1.219664 CAATGCATGTTGGGCCCAG 59.780 57.895 26.87 15.03 0.00 4.45
520 3051 1.991167 AATGCATGTTGGGCCCAGG 60.991 57.895 26.87 16.85 0.00 4.45
521 3052 3.988050 ATGCATGTTGGGCCCAGGG 62.988 63.158 26.87 16.48 0.00 4.45
522 3053 4.702274 GCATGTTGGGCCCAGGGT 62.702 66.667 26.87 11.98 0.00 4.34
523 3054 2.120274 CATGTTGGGCCCAGGGTT 59.880 61.111 26.87 8.75 0.00 4.11
524 3055 2.120274 ATGTTGGGCCCAGGGTTG 59.880 61.111 26.87 0.00 0.00 3.77
541 3072 1.399089 GTTGTACAAGGTGTGCACGTT 59.601 47.619 13.13 2.54 42.48 3.99
545 3076 4.898607 AAGGTGTGCACGTTGGAT 57.101 50.000 13.13 0.00 37.92 3.41
547 3078 2.264005 AAGGTGTGCACGTTGGATTA 57.736 45.000 13.13 0.00 37.92 1.75
550 3081 1.810151 GGTGTGCACGTTGGATTACAT 59.190 47.619 13.13 0.00 0.00 2.29
551 3082 2.414029 GGTGTGCACGTTGGATTACATG 60.414 50.000 13.13 0.00 0.00 3.21
552 3083 2.482336 GTGTGCACGTTGGATTACATGA 59.518 45.455 13.13 0.00 0.00 3.07
553 3084 3.058570 GTGTGCACGTTGGATTACATGAA 60.059 43.478 13.13 0.00 0.00 2.57
554 3085 3.565902 TGTGCACGTTGGATTACATGAAA 59.434 39.130 13.13 0.00 0.00 2.69
555 3086 4.036852 TGTGCACGTTGGATTACATGAAAA 59.963 37.500 13.13 0.00 0.00 2.29
556 3087 5.160641 GTGCACGTTGGATTACATGAAAAT 58.839 37.500 0.00 0.00 0.00 1.82
557 3088 6.072452 TGTGCACGTTGGATTACATGAAAATA 60.072 34.615 13.13 0.00 0.00 1.40
558 3089 6.250527 GTGCACGTTGGATTACATGAAAATAC 59.749 38.462 0.00 0.00 0.00 1.89
559 3090 6.072452 TGCACGTTGGATTACATGAAAATACA 60.072 34.615 0.00 2.92 0.00 2.29
560 3091 6.468956 GCACGTTGGATTACATGAAAATACAG 59.531 38.462 0.00 0.00 29.06 2.74
561 3092 7.526608 CACGTTGGATTACATGAAAATACAGT 58.473 34.615 0.00 0.00 29.06 3.55
562 3093 7.481483 CACGTTGGATTACATGAAAATACAGTG 59.519 37.037 0.00 7.54 29.06 3.66
564 3095 8.020819 CGTTGGATTACATGAAAATACAGTGTT 58.979 33.333 0.00 0.00 29.06 3.32
578 3172 1.136252 CAGTGTTACATGAGCGTGCAC 60.136 52.381 6.82 6.82 0.00 4.57
688 4186 4.700365 GAAAACACAGGGCCGCGC 62.700 66.667 0.00 0.00 0.00 6.86
729 4229 3.695606 GGTGACGAGGCTGGCAGA 61.696 66.667 20.86 0.00 0.00 4.26
741 4242 1.241165 CTGGCAGAGCACACAAATCA 58.759 50.000 9.42 0.00 0.00 2.57
755 4257 6.349611 GCACACAAATCAATCTGTAGGTTCAT 60.350 38.462 0.00 0.00 0.00 2.57
756 4258 7.025365 CACACAAATCAATCTGTAGGTTCATG 58.975 38.462 0.00 0.00 0.00 3.07
989 4512 1.674817 CGGCAACAGGTCGGTTAGATT 60.675 52.381 0.00 0.00 42.02 2.40
1039 4562 5.602145 ACCAGGTTTGATTTGGAGAAATTCA 59.398 36.000 0.00 0.00 35.89 2.57
1060 4583 1.301953 GGCACGGGTAACTTCGGTT 60.302 57.895 0.00 0.00 41.52 4.44
1091 4614 5.983540 GACAAGAGTCAAGGATATTCTGGT 58.016 41.667 0.00 0.00 44.34 4.00
1312 4835 5.163754 GCGACCAATAAGCTGTATTTGAAGT 60.164 40.000 0.00 0.00 0.00 3.01
1500 5029 6.266330 TGGTCATTACATTGACACATGGAAAA 59.734 34.615 0.00 0.00 46.32 2.29
1501 5030 6.586082 GGTCATTACATTGACACATGGAAAAC 59.414 38.462 0.00 0.00 46.32 2.43
1502 5031 7.144661 GTCATTACATTGACACATGGAAAACA 58.855 34.615 0.00 0.00 44.38 2.83
1503 5032 7.814107 GTCATTACATTGACACATGGAAAACAT 59.186 33.333 0.00 0.00 44.38 2.71
1662 5194 4.086706 AGAGGCGGAGAAGAAAAAGAAA 57.913 40.909 0.00 0.00 0.00 2.52
1781 5313 2.558795 GTGAGGACTCAGACAGCAGTAA 59.441 50.000 1.56 0.00 40.75 2.24
1869 5401 0.171007 CTTTTCATGCGACGCCCAAT 59.829 50.000 18.69 0.62 0.00 3.16
2043 5576 5.914124 AGGGCTAAGGAGGAATCTAATTTCT 59.086 40.000 0.00 0.00 0.00 2.52
2186 5721 2.162681 GTTGCAAGGGAGCACTATTGT 58.837 47.619 0.00 0.00 45.61 2.71
2237 5772 1.166129 GTAGCAGTGGAGTCTCACGA 58.834 55.000 1.47 0.00 42.10 4.35
2306 5841 1.553704 GACAACCCAAGTCCGGAGTAT 59.446 52.381 13.41 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 1.691127 CGAGCGCATCGTCTTGATAT 58.309 50.000 11.47 0.00 46.62 1.63
40 41 3.164028 CGAGCGCATCGTCTTGATA 57.836 52.632 11.47 0.00 46.62 2.15
91 92 1.282248 CGTCGCTGACACAATCCGTT 61.282 55.000 8.91 0.00 32.09 4.44
204 207 1.806542 CGCCAGCAATCTGTAACTTGT 59.193 47.619 0.00 0.00 38.66 3.16
242 245 1.202087 CGACTGCTCGTCTTCCTAGTG 60.202 57.143 5.43 0.00 40.59 2.74
287 297 2.414994 TCTCTCGGTCCGTACATCTT 57.585 50.000 11.88 0.00 0.00 2.40
342 375 3.356639 GACCTGATGCCGCACGAGA 62.357 63.158 0.00 0.00 0.00 4.04
344 377 3.356639 GAGACCTGATGCCGCACGA 62.357 63.158 0.00 0.00 0.00 4.35
354 2827 1.297689 GCTGCCACATGAGACCTGA 59.702 57.895 0.00 0.00 0.00 3.86
383 2909 2.197324 AACCCGCCTTTGCCTTCA 59.803 55.556 0.00 0.00 0.00 3.02
385 2911 2.917227 CCAACCCGCCTTTGCCTT 60.917 61.111 0.00 0.00 0.00 4.35
387 2913 4.986708 TCCCAACCCGCCTTTGCC 62.987 66.667 0.00 0.00 0.00 4.52
389 2915 2.931068 GCTTCCCAACCCGCCTTTG 61.931 63.158 0.00 0.00 0.00 2.77
394 2920 3.056328 GACTGCTTCCCAACCCGC 61.056 66.667 0.00 0.00 0.00 6.13
395 2921 2.359975 GGACTGCTTCCCAACCCG 60.360 66.667 0.00 0.00 38.70 5.28
396 2922 1.303643 CTGGACTGCTTCCCAACCC 60.304 63.158 2.82 0.00 45.17 4.11
397 2923 1.303643 CCTGGACTGCTTCCCAACC 60.304 63.158 2.82 0.00 45.17 3.77
398 2924 1.973812 GCCTGGACTGCTTCCCAAC 60.974 63.158 0.00 0.00 45.17 3.77
403 2929 0.107945 AATCTCGCCTGGACTGCTTC 60.108 55.000 0.00 0.00 0.00 3.86
404 2930 0.392193 CAATCTCGCCTGGACTGCTT 60.392 55.000 0.00 0.00 0.00 3.91
406 2932 1.817099 CCAATCTCGCCTGGACTGC 60.817 63.158 0.00 0.00 34.35 4.40
407 2933 1.817099 GCCAATCTCGCCTGGACTG 60.817 63.158 0.00 0.00 34.35 3.51
410 2936 1.399744 ATACGCCAATCTCGCCTGGA 61.400 55.000 0.00 0.00 34.35 3.86
412 2938 1.995484 CATATACGCCAATCTCGCCTG 59.005 52.381 0.00 0.00 0.00 4.85
415 2941 1.428448 TGCATATACGCCAATCTCGC 58.572 50.000 0.00 0.00 0.00 5.03
416 2942 2.349580 CCATGCATATACGCCAATCTCG 59.650 50.000 0.00 0.00 0.00 4.04
417 2943 2.096496 GCCATGCATATACGCCAATCTC 59.904 50.000 0.00 0.00 0.00 2.75
423 2954 1.234615 AACCGCCATGCATATACGCC 61.235 55.000 0.00 0.00 0.00 5.68
429 2960 2.346766 AATCAGAACCGCCATGCATA 57.653 45.000 0.00 0.00 0.00 3.14
437 2968 6.143919 CCTTTCTTTTGTTTAATCAGAACCGC 59.856 38.462 0.00 0.00 0.00 5.68
438 2969 6.143919 GCCTTTCTTTTGTTTAATCAGAACCG 59.856 38.462 0.00 0.00 0.00 4.44
444 2975 6.861055 CGCTAAGCCTTTCTTTTGTTTAATCA 59.139 34.615 0.00 0.00 36.25 2.57
458 2989 1.244019 CCAGCCAACGCTAAGCCTTT 61.244 55.000 0.00 0.00 46.25 3.11
459 2990 1.675641 CCAGCCAACGCTAAGCCTT 60.676 57.895 0.00 0.00 46.25 4.35
461 2992 3.815396 GCCAGCCAACGCTAAGCC 61.815 66.667 0.00 0.00 46.25 4.35
463 2994 3.499737 CCGCCAGCCAACGCTAAG 61.500 66.667 0.00 0.00 46.25 2.18
464 2995 3.538785 TTCCGCCAGCCAACGCTAA 62.539 57.895 0.00 0.00 46.25 3.09
465 2996 3.950794 CTTCCGCCAGCCAACGCTA 62.951 63.158 0.00 0.00 46.25 4.26
468 2999 2.978010 AACTTCCGCCAGCCAACG 60.978 61.111 0.00 0.00 0.00 4.10
469 3000 1.734388 AACAACTTCCGCCAGCCAAC 61.734 55.000 0.00 0.00 0.00 3.77
470 3001 1.040339 AAACAACTTCCGCCAGCCAA 61.040 50.000 0.00 0.00 0.00 4.52
471 3002 1.454847 AAACAACTTCCGCCAGCCA 60.455 52.632 0.00 0.00 0.00 4.75
472 3003 1.007387 CAAACAACTTCCGCCAGCC 60.007 57.895 0.00 0.00 0.00 4.85
473 3004 1.007387 CCAAACAACTTCCGCCAGC 60.007 57.895 0.00 0.00 0.00 4.85
474 3005 1.247567 ATCCAAACAACTTCCGCCAG 58.752 50.000 0.00 0.00 0.00 4.85
475 3006 1.339610 CAATCCAAACAACTTCCGCCA 59.660 47.619 0.00 0.00 0.00 5.69
476 3007 1.336795 CCAATCCAAACAACTTCCGCC 60.337 52.381 0.00 0.00 0.00 6.13
477 3008 1.339929 ACCAATCCAAACAACTTCCGC 59.660 47.619 0.00 0.00 0.00 5.54
478 3009 3.190535 CCTACCAATCCAAACAACTTCCG 59.809 47.826 0.00 0.00 0.00 4.30
479 3010 3.056821 GCCTACCAATCCAAACAACTTCC 60.057 47.826 0.00 0.00 0.00 3.46
480 3011 3.572255 TGCCTACCAATCCAAACAACTTC 59.428 43.478 0.00 0.00 0.00 3.01
481 3012 3.571590 TGCCTACCAATCCAAACAACTT 58.428 40.909 0.00 0.00 0.00 2.66
482 3013 3.237268 TGCCTACCAATCCAAACAACT 57.763 42.857 0.00 0.00 0.00 3.16
483 3014 4.244862 CATTGCCTACCAATCCAAACAAC 58.755 43.478 0.00 0.00 42.15 3.32
484 3015 3.306641 GCATTGCCTACCAATCCAAACAA 60.307 43.478 0.00 0.00 42.15 2.83
485 3016 2.233431 GCATTGCCTACCAATCCAAACA 59.767 45.455 0.00 0.00 42.15 2.83
495 3026 0.461135 CCCAACATGCATTGCCTACC 59.539 55.000 6.12 0.00 0.00 3.18
496 3027 0.179103 GCCCAACATGCATTGCCTAC 60.179 55.000 6.12 0.00 0.00 3.18
500 3031 2.125024 GGGCCCAACATGCATTGC 60.125 61.111 19.95 0.46 0.00 3.56
501 3032 1.219664 CTGGGCCCAACATGCATTG 59.780 57.895 28.29 6.72 0.00 2.82
503 3034 2.364579 CCTGGGCCCAACATGCAT 60.365 61.111 28.29 0.00 0.00 3.96
504 3035 4.700448 CCCTGGGCCCAACATGCA 62.700 66.667 28.29 0.00 0.00 3.96
505 3036 4.702274 ACCCTGGGCCCAACATGC 62.702 66.667 28.29 0.00 0.00 4.06
506 3037 2.120274 AACCCTGGGCCCAACATG 59.880 61.111 28.29 14.39 0.00 3.21
507 3038 1.439524 TACAACCCTGGGCCCAACAT 61.440 55.000 28.29 11.04 0.00 2.71
508 3039 2.085562 TACAACCCTGGGCCCAACA 61.086 57.895 28.29 2.15 0.00 3.33
509 3040 1.605451 GTACAACCCTGGGCCCAAC 60.605 63.158 28.29 15.77 0.00 3.77
511 3042 2.075355 CTTGTACAACCCTGGGCCCA 62.075 60.000 26.67 26.67 0.00 5.36
512 3043 1.304134 CTTGTACAACCCTGGGCCC 60.304 63.158 17.59 17.59 0.00 5.80
513 3044 1.304134 CCTTGTACAACCCTGGGCC 60.304 63.158 14.08 0.00 0.00 5.80
514 3045 0.893727 CACCTTGTACAACCCTGGGC 60.894 60.000 14.08 0.00 0.00 5.36
515 3046 0.476771 ACACCTTGTACAACCCTGGG 59.523 55.000 12.28 12.28 0.00 4.45
516 3047 1.604604 CACACCTTGTACAACCCTGG 58.395 55.000 3.59 7.13 0.00 4.45
517 3048 0.951558 GCACACCTTGTACAACCCTG 59.048 55.000 3.59 2.78 0.00 4.45
518 3049 0.548989 TGCACACCTTGTACAACCCT 59.451 50.000 3.59 0.00 0.00 4.34
519 3050 0.666374 GTGCACACCTTGTACAACCC 59.334 55.000 13.17 0.00 40.40 4.11
520 3051 0.306533 CGTGCACACCTTGTACAACC 59.693 55.000 18.64 0.00 40.70 3.77
521 3052 1.011333 ACGTGCACACCTTGTACAAC 58.989 50.000 18.64 0.00 40.70 3.32
522 3053 1.398739 CAACGTGCACACCTTGTACAA 59.601 47.619 18.64 8.28 40.70 2.41
523 3054 1.010580 CAACGTGCACACCTTGTACA 58.989 50.000 18.64 0.00 40.70 2.90
524 3055 0.306533 CCAACGTGCACACCTTGTAC 59.693 55.000 18.64 0.00 37.46 2.90
541 3072 9.508642 TGTAACACTGTATTTTCATGTAATCCA 57.491 29.630 0.00 0.00 0.00 3.41
547 3078 7.530010 GCTCATGTAACACTGTATTTTCATGT 58.470 34.615 14.79 0.00 34.82 3.21
550 3081 5.699001 ACGCTCATGTAACACTGTATTTTCA 59.301 36.000 0.00 0.00 0.00 2.69
551 3082 6.015504 CACGCTCATGTAACACTGTATTTTC 58.984 40.000 0.00 0.00 0.00 2.29
552 3083 5.616866 GCACGCTCATGTAACACTGTATTTT 60.617 40.000 0.00 0.00 0.00 1.82
553 3084 4.142902 GCACGCTCATGTAACACTGTATTT 60.143 41.667 0.00 0.00 0.00 1.40
554 3085 3.370978 GCACGCTCATGTAACACTGTATT 59.629 43.478 0.00 0.00 0.00 1.89
555 3086 2.930040 GCACGCTCATGTAACACTGTAT 59.070 45.455 0.00 0.00 0.00 2.29
556 3087 2.288518 TGCACGCTCATGTAACACTGTA 60.289 45.455 0.00 0.00 0.00 2.74
557 3088 1.148310 GCACGCTCATGTAACACTGT 58.852 50.000 0.00 0.00 0.00 3.55
558 3089 1.136252 GTGCACGCTCATGTAACACTG 60.136 52.381 0.00 0.00 0.00 3.66
559 3090 1.148310 GTGCACGCTCATGTAACACT 58.852 50.000 0.00 0.00 0.00 3.55
560 3091 0.179250 CGTGCACGCTCATGTAACAC 60.179 55.000 28.16 0.00 0.00 3.32
561 3092 0.598942 ACGTGCACGCTCATGTAACA 60.599 50.000 37.35 0.00 44.43 2.41
562 3093 0.511221 AACGTGCACGCTCATGTAAC 59.489 50.000 37.35 0.00 44.43 2.50
564 3095 1.288419 CCAACGTGCACGCTCATGTA 61.288 55.000 37.35 0.00 44.43 2.29
565 3096 2.606961 CCAACGTGCACGCTCATGT 61.607 57.895 37.35 15.76 44.43 3.21
566 3097 2.174107 CCAACGTGCACGCTCATG 59.826 61.111 37.35 27.80 44.43 3.07
578 3172 1.243342 TGATCAGCCTTTGCCCAACG 61.243 55.000 0.00 0.00 38.69 4.10
661 4159 3.243535 GCCCTGTGTTTTCCTTTTCTCAG 60.244 47.826 0.00 0.00 0.00 3.35
688 4186 1.067516 CCTTTTATTGCCGCTGGATGG 59.932 52.381 0.00 0.00 0.00 3.51
689 4187 1.536709 GCCTTTTATTGCCGCTGGATG 60.537 52.381 0.00 0.00 0.00 3.51
729 4229 4.655963 ACCTACAGATTGATTTGTGTGCT 58.344 39.130 0.00 0.00 0.00 4.40
739 4240 7.004086 ACCTTTTTCATGAACCTACAGATTGA 58.996 34.615 7.89 0.00 0.00 2.57
740 4241 7.086376 CACCTTTTTCATGAACCTACAGATTG 58.914 38.462 7.89 0.00 0.00 2.67
741 4242 6.209391 CCACCTTTTTCATGAACCTACAGATT 59.791 38.462 7.89 0.00 0.00 2.40
755 4257 0.106268 TGGCTGCTCCACCTTTTTCA 60.106 50.000 0.00 0.00 40.72 2.69
756 4258 0.600057 CTGGCTGCTCCACCTTTTTC 59.400 55.000 0.00 0.00 40.72 2.29
1039 4562 0.675522 CCGAAGTTACCCGTGCCATT 60.676 55.000 0.00 0.00 0.00 3.16
1060 4583 3.582647 TCCTTGACTCTTGTCTGCCATAA 59.417 43.478 0.00 0.00 43.29 1.90
1091 4614 1.615116 CCTTCAAGATTCCCTGCTGCA 60.615 52.381 0.88 0.88 0.00 4.41
1312 4835 5.590259 GCATCTTCAGCCCATAGAACTTTTA 59.410 40.000 0.00 0.00 0.00 1.52
1500 5029 7.338196 TCATTATTGACGGTTGTATTTCCATGT 59.662 33.333 0.00 0.00 0.00 3.21
1501 5030 7.702386 TCATTATTGACGGTTGTATTTCCATG 58.298 34.615 0.00 0.00 0.00 3.66
1502 5031 7.013274 CCTCATTATTGACGGTTGTATTTCCAT 59.987 37.037 0.00 0.00 0.00 3.41
1503 5032 6.317642 CCTCATTATTGACGGTTGTATTTCCA 59.682 38.462 0.00 0.00 0.00 3.53
1504 5033 6.540914 TCCTCATTATTGACGGTTGTATTTCC 59.459 38.462 0.00 0.00 0.00 3.13
1505 5034 7.548196 TCCTCATTATTGACGGTTGTATTTC 57.452 36.000 0.00 0.00 0.00 2.17
1506 5035 7.610305 ACTTCCTCATTATTGACGGTTGTATTT 59.390 33.333 0.00 0.00 0.00 1.40
1507 5036 7.110155 ACTTCCTCATTATTGACGGTTGTATT 58.890 34.615 0.00 0.00 0.00 1.89
1508 5037 6.650120 ACTTCCTCATTATTGACGGTTGTAT 58.350 36.000 0.00 0.00 0.00 2.29
1509 5038 6.045072 ACTTCCTCATTATTGACGGTTGTA 57.955 37.500 0.00 0.00 0.00 2.41
1554 5083 5.476614 GCATTCTTTTGCTTCCTCAAATCT 58.523 37.500 0.00 0.00 39.57 2.40
1764 5296 3.876274 TCATTACTGCTGTCTGAGTCC 57.124 47.619 0.00 0.00 0.00 3.85
1781 5313 7.042456 GCATGTTTGATACTACGAGAACATCAT 60.042 37.037 0.00 0.00 36.04 2.45
1869 5401 4.401022 TGTACGAAGAGAACCACTCCTTA 58.599 43.478 0.00 0.00 45.96 2.69
2043 5576 4.074259 CACCATCATGAAGAACACCAAGA 58.926 43.478 0.00 0.00 0.00 3.02
2186 5721 1.384502 CTCCCCATGGCTCCACCTA 60.385 63.158 6.09 0.00 40.22 3.08


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

AutoCloner maintained by Alex Coulton.