Multiple sequence alignment - TraesCS3B01G281600

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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 TraesCS3B01G281600 chr3B 100.000 3338 0 0 1 3338 452461243 452464580 0.000000e+00 6165.0
1 TraesCS3B01G281600 chr3B 81.040 327 50 9 1732 2054 362054315 362053997 1.990000e-62 250.0
2 TraesCS3B01G281600 chr3B 86.029 136 17 2 2490 2623 226081162 226081297 9.650000e-31 145.0
3 TraesCS3B01G281600 chr3A 91.711 2449 109 40 20 2398 472790084 472792508 0.000000e+00 3312.0
4 TraesCS3B01G281600 chr3A 89.258 391 21 14 2889 3269 472793134 472793513 1.400000e-128 470.0
5 TraesCS3B01G281600 chr3A 98.077 52 1 0 2650 2701 472792621 472792672 1.280000e-14 91.6
6 TraesCS3B01G281600 chr3A 100.000 41 0 0 2395 2435 472792527 472792567 3.570000e-10 76.8
7 TraesCS3B01G281600 chr3D 92.881 1826 62 21 719 2491 354072850 354074660 0.000000e+00 2590.0
8 TraesCS3B01G281600 chr3D 91.261 698 28 15 2657 3338 354074729 354075409 0.000000e+00 920.0
9 TraesCS3B01G281600 chr3D 87.155 724 36 18 1 688 354072162 354072864 0.000000e+00 769.0
10 TraesCS3B01G281600 chr1D 80.058 346 46 14 1722 2044 447550955 447551300 5.570000e-58 235.0
11 TraesCS3B01G281600 chr1A 79.656 349 48 13 1722 2047 543635058 543635406 2.590000e-56 230.0
12 TraesCS3B01G281600 chr1B 78.141 398 56 19 1671 2047 613021405 613021792 1.210000e-54 224.0
13 TraesCS3B01G281600 chr6A 86.131 137 18 1 2487 2622 371331270 371331134 2.680000e-31 147.0
14 TraesCS3B01G281600 chr6A 85.496 131 11 7 2498 2622 45669566 45669438 2.700000e-26 130.0
15 TraesCS3B01G281600 chr5A 82.320 181 19 6 2487 2655 558675485 558675664 9.650000e-31 145.0
16 TraesCS3B01G281600 chr5D 89.474 114 11 1 2498 2610 564987928 564988041 3.470000e-30 143.0
17 TraesCS3B01G281600 chr7A 88.235 119 8 5 2496 2610 14185932 14186048 1.620000e-28 137.0
18 TraesCS3B01G281600 chr7A 100.000 28 0 0 2618 2645 56666736 56666763 6.000000e-03 52.8
19 TraesCS3B01G281600 chr4A 86.885 122 15 1 2497 2617 626035908 626036029 5.810000e-28 135.0
20 TraesCS3B01G281600 chr4A 77.246 167 21 12 2498 2650 661766805 661766968 7.680000e-12 82.4
21 TraesCS3B01G281600 chr2D 85.600 125 17 1 2494 2617 336511130 336511254 2.700000e-26 130.0
22 TraesCS3B01G281600 chr2B 84.783 138 11 7 2497 2627 43380116 43379982 2.700000e-26 130.0


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 TraesCS3B01G281600 chr3B 452461243 452464580 3337 False 6165.000000 6165 100.000000 1 3338 1 chr3B.!!$F2 3337
1 TraesCS3B01G281600 chr3A 472790084 472793513 3429 False 987.600000 3312 94.761500 20 3269 4 chr3A.!!$F1 3249
2 TraesCS3B01G281600 chr3D 354072162 354075409 3247 False 1426.333333 2590 90.432333 1 3338 3 chr3D.!!$F1 3337

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
612 658 0.258774 AATATTTGAGGCCGGCTGGT 59.741 50.0 28.56 11.72 37.67 4.00 F
1293 1382 0.253044 CTGGGATTCTTTGGCTCGGA 59.747 55.0 0.00 0.00 0.00 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 1835 0.537188 CTCCATGTCCGGCTTGTACT 59.463 55.0 0.0 0.0 0.0 2.73 R
2827 3241 0.179059 TTGTGTGAGTGACGGCATGT 60.179 50.0 0.0 0.0 0.0 3.21 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
137 140 1.344438 TGCAAGACACAGGTAGGTCTG 59.656 52.381 0.00 0.00 43.26 3.51
200 203 1.062505 ACATCTTCTCCTCCTCCTCCC 60.063 57.143 0.00 0.00 0.00 4.30
255 259 6.250104 GTCTATGAAGAAATTTGCTTCTTGCG 59.750 38.462 16.41 7.77 43.97 4.85
347 359 0.863144 GTTTCTTGACGGCGTGCTAA 59.137 50.000 21.19 9.09 0.00 3.09
461 489 3.193263 CAGTCATCCGGTTTCATCTCAG 58.807 50.000 0.00 0.00 0.00 3.35
550 590 5.521735 CACACTTAATCAGGCTGCTTAGTAG 59.478 44.000 10.34 8.74 0.00 2.57
552 592 5.521735 CACTTAATCAGGCTGCTTAGTAGTG 59.478 44.000 20.04 20.04 0.00 2.74
566 612 6.148976 TGCTTAGTAGTGAGTAGTACAGTGTG 59.851 42.308 5.88 0.00 35.57 3.82
567 613 6.149142 GCTTAGTAGTGAGTAGTACAGTGTGT 59.851 42.308 5.88 0.00 35.57 3.72
609 655 1.136891 GCAAAATATTTGAGGCCGGCT 59.863 47.619 28.56 12.77 0.00 5.52
612 658 0.258774 AATATTTGAGGCCGGCTGGT 59.741 50.000 28.56 11.72 37.67 4.00
613 659 0.258774 ATATTTGAGGCCGGCTGGTT 59.741 50.000 28.56 9.84 37.67 3.67
614 660 0.679640 TATTTGAGGCCGGCTGGTTG 60.680 55.000 28.56 0.00 37.67 3.77
615 661 2.713531 ATTTGAGGCCGGCTGGTTGT 62.714 55.000 28.56 6.21 37.67 3.32
616 662 2.058125 TTTGAGGCCGGCTGGTTGTA 62.058 55.000 28.56 3.12 37.67 2.41
617 663 2.058125 TTGAGGCCGGCTGGTTGTAA 62.058 55.000 28.56 9.36 37.67 2.41
618 664 1.302993 GAGGCCGGCTGGTTGTAAA 60.303 57.895 28.56 0.00 37.67 2.01
672 728 2.826428 AGTGCATGGCAATACGAGTAG 58.174 47.619 0.00 0.00 41.47 2.57
684 740 6.759827 GGCAATACGAGTAGGATTTTGTAGAA 59.240 38.462 0.00 0.00 28.77 2.10
686 742 8.276325 GCAATACGAGTAGGATTTTGTAGAATG 58.724 37.037 0.00 0.00 28.77 2.67
687 743 8.765219 CAATACGAGTAGGATTTTGTAGAATGG 58.235 37.037 0.00 0.00 28.77 3.16
688 744 5.116882 ACGAGTAGGATTTTGTAGAATGGC 58.883 41.667 0.00 0.00 0.00 4.40
689 745 5.116180 CGAGTAGGATTTTGTAGAATGGCA 58.884 41.667 0.00 0.00 0.00 4.92
690 746 5.006746 CGAGTAGGATTTTGTAGAATGGCAC 59.993 44.000 0.00 0.00 0.00 5.01
691 747 4.876107 AGTAGGATTTTGTAGAATGGCACG 59.124 41.667 0.00 0.00 0.00 5.34
692 748 2.423538 AGGATTTTGTAGAATGGCACGC 59.576 45.455 0.00 0.00 0.00 5.34
693 749 2.163412 GGATTTTGTAGAATGGCACGCA 59.837 45.455 0.00 0.00 0.00 5.24
694 750 3.181487 GGATTTTGTAGAATGGCACGCAT 60.181 43.478 0.00 0.00 0.00 4.73
695 751 2.917701 TTTGTAGAATGGCACGCATG 57.082 45.000 0.00 0.00 0.00 4.06
696 752 1.819928 TTGTAGAATGGCACGCATGT 58.180 45.000 0.00 0.00 0.00 3.21
717 773 6.070951 TGTGTGGTAGTACTATGTAGAGGT 57.929 41.667 5.75 0.00 0.00 3.85
957 1013 5.283953 CGATCGTATTCGTGTCATTCATAGG 59.716 44.000 7.03 0.00 38.33 2.57
958 1014 5.509716 TCGTATTCGTGTCATTCATAGGT 57.490 39.130 0.00 0.00 38.33 3.08
959 1015 6.622833 TCGTATTCGTGTCATTCATAGGTA 57.377 37.500 0.00 0.00 38.33 3.08
960 1016 6.665465 TCGTATTCGTGTCATTCATAGGTAG 58.335 40.000 0.00 0.00 38.33 3.18
961 1017 6.261603 TCGTATTCGTGTCATTCATAGGTAGT 59.738 38.462 0.00 0.00 38.33 2.73
982 1042 3.433513 ACTCTATTTACGGCCGAGAAC 57.566 47.619 35.90 0.00 0.00 3.01
1090 1170 2.264794 GCGATGGTCACCTTCGGT 59.735 61.111 28.12 0.00 46.61 4.69
1123 1203 2.102357 CTGCACGACGACGCCTAT 59.898 61.111 7.30 0.00 43.96 2.57
1140 1220 1.600511 TATCTGCCGCGTCCTGTCAA 61.601 55.000 4.92 0.00 0.00 3.18
1184 1264 3.358076 CTGGACGACGCCTTCCTCC 62.358 68.421 9.24 2.03 32.36 4.30
1243 1323 3.342370 CTCGAGCTACGGTGCTGCA 62.342 63.158 9.10 0.00 44.17 4.41
1293 1382 0.253044 CTGGGATTCTTTGGCTCGGA 59.747 55.000 0.00 0.00 0.00 4.55
1490 1579 1.071699 GGGAGTCCAACAACTACAGCA 59.928 52.381 12.30 0.00 31.13 4.41
1564 1653 4.735132 CCCACCACGACGTCGCAT 62.735 66.667 35.92 19.68 44.43 4.73
1823 1927 4.988716 ACCTCGTCACGGAGCCCA 62.989 66.667 0.00 0.00 32.57 5.36
1876 1980 1.082692 CGTGCGTATCTCGAGCGAT 60.083 57.895 14.00 3.96 42.86 4.58
1951 2055 2.977178 CTGCAGAAGCTCGTCCCT 59.023 61.111 8.42 0.00 42.74 4.20
1954 2058 2.948720 GCAGAAGCTCGTCCCTGGT 61.949 63.158 0.00 0.00 37.91 4.00
2026 2130 1.353091 AGTTCCTCAAGTCCCAGGTC 58.647 55.000 0.00 0.00 0.00 3.85
2231 2344 4.945246 ACTGTTGTAGTACTGTTCAGTGG 58.055 43.478 14.69 7.20 38.04 4.00
2259 2372 7.699391 GTCTATACATGTTGCTGTTTCGTACTA 59.301 37.037 2.30 0.00 0.00 1.82
2261 2374 5.779806 ACATGTTGCTGTTTCGTACTATC 57.220 39.130 0.00 0.00 0.00 2.08
2263 2376 5.348724 ACATGTTGCTGTTTCGTACTATCTG 59.651 40.000 0.00 0.00 0.00 2.90
2270 2383 4.005650 TGTTTCGTACTATCTGAGGTCGT 58.994 43.478 0.00 0.00 0.00 4.34
2271 2384 4.093998 TGTTTCGTACTATCTGAGGTCGTC 59.906 45.833 0.00 0.00 0.00 4.20
2272 2385 2.467838 TCGTACTATCTGAGGTCGTCG 58.532 52.381 0.00 0.00 0.00 5.12
2273 2386 2.159184 TCGTACTATCTGAGGTCGTCGT 60.159 50.000 0.00 0.00 0.00 4.34
2318 2431 7.914346 GTGGTTAAGTAGTGCAGTACTGTATAG 59.086 40.741 30.17 0.00 40.65 1.31
2319 2432 7.830697 TGGTTAAGTAGTGCAGTACTGTATAGA 59.169 37.037 30.17 13.29 40.65 1.98
2320 2433 8.848182 GGTTAAGTAGTGCAGTACTGTATAGAT 58.152 37.037 30.17 17.26 40.65 1.98
2448 2587 6.944290 ACATCATTATGTGTATTGGATGGAGG 59.056 38.462 0.00 0.00 44.79 4.30
2458 2597 5.433051 TGTATTGGATGGAGGAGAAAAGGAT 59.567 40.000 0.00 0.00 0.00 3.24
2464 2603 5.534278 GGATGGAGGAGAAAAGGATGAAATC 59.466 44.000 0.00 0.00 44.55 2.17
2471 2610 9.571816 GAGGAGAAAAGGATGAAATCTATGAAT 57.428 33.333 0.00 0.00 44.71 2.57
2509 2648 8.827177 TTCATTTGTATTCTACTCACTTCGTT 57.173 30.769 0.00 0.00 0.00 3.85
2511 2650 8.922676 TCATTTGTATTCTACTCACTTCGTTTC 58.077 33.333 0.00 0.00 0.00 2.78
2514 2653 9.970395 TTTGTATTCTACTCACTTCGTTTCTAA 57.030 29.630 0.00 0.00 0.00 2.10
2600 2739 7.542025 AGAATGTTGATTTACTCATTTGCTCC 58.458 34.615 0.00 0.00 32.72 4.70
2601 2740 5.295431 TGTTGATTTACTCATTTGCTCCG 57.705 39.130 0.00 0.00 32.72 4.63
2602 2741 4.759693 TGTTGATTTACTCATTTGCTCCGT 59.240 37.500 0.00 0.00 32.72 4.69
2603 2742 5.935206 TGTTGATTTACTCATTTGCTCCGTA 59.065 36.000 0.00 0.00 32.72 4.02
2604 2743 6.597672 TGTTGATTTACTCATTTGCTCCGTAT 59.402 34.615 0.00 0.00 32.72 3.06
2605 2744 6.603237 TGATTTACTCATTTGCTCCGTATG 57.397 37.500 0.00 0.00 0.00 2.39
2606 2745 6.112734 TGATTTACTCATTTGCTCCGTATGT 58.887 36.000 0.00 0.00 0.00 2.29
2607 2746 7.269316 TGATTTACTCATTTGCTCCGTATGTA 58.731 34.615 0.00 0.00 0.00 2.29
2608 2747 7.438160 TGATTTACTCATTTGCTCCGTATGTAG 59.562 37.037 0.00 0.00 0.00 2.74
2609 2748 4.737855 ACTCATTTGCTCCGTATGTAGT 57.262 40.909 0.00 0.00 0.00 2.73
2610 2749 5.086104 ACTCATTTGCTCCGTATGTAGTT 57.914 39.130 0.00 0.00 0.00 2.24
2611 2750 5.109903 ACTCATTTGCTCCGTATGTAGTTC 58.890 41.667 0.00 0.00 0.00 3.01
2612 2751 5.079689 TCATTTGCTCCGTATGTAGTTCA 57.920 39.130 0.00 0.00 0.00 3.18
2613 2752 5.670485 TCATTTGCTCCGTATGTAGTTCAT 58.330 37.500 0.00 0.00 40.25 2.57
2614 2753 6.811954 TCATTTGCTCCGTATGTAGTTCATA 58.188 36.000 0.00 0.00 37.91 2.15
2615 2754 7.441836 TCATTTGCTCCGTATGTAGTTCATAT 58.558 34.615 0.00 0.00 40.54 1.78
2616 2755 7.931407 TCATTTGCTCCGTATGTAGTTCATATT 59.069 33.333 0.00 0.00 40.54 1.28
2617 2756 9.203421 CATTTGCTCCGTATGTAGTTCATATTA 57.797 33.333 0.00 0.00 40.54 0.98
2618 2757 9.772973 ATTTGCTCCGTATGTAGTTCATATTAA 57.227 29.630 0.00 0.00 40.54 1.40
2619 2758 9.602568 TTTGCTCCGTATGTAGTTCATATTAAA 57.397 29.630 0.00 0.00 40.54 1.52
2620 2759 9.602568 TTGCTCCGTATGTAGTTCATATTAAAA 57.397 29.630 0.00 0.00 40.54 1.52
2621 2760 9.772973 TGCTCCGTATGTAGTTCATATTAAAAT 57.227 29.630 0.00 0.00 40.54 1.82
2646 2785 9.860393 ATACTTATATTTAGGGATGGAGGAAGT 57.140 33.333 0.00 0.00 0.00 3.01
2648 2787 9.860393 ACTTATATTTAGGGATGGAGGAAGTAT 57.140 33.333 0.00 0.00 0.00 2.12
2712 2857 3.528597 AAAATCGTAGTGAGAGCCTCC 57.471 47.619 0.00 0.00 0.00 4.30
2724 2869 0.467804 GAGCCTCCCTTCCATGAGTC 59.532 60.000 0.00 0.00 0.00 3.36
2827 3241 1.080637 GTTTGCCGCACATGCATGA 60.081 52.632 32.75 6.55 42.21 3.07
2877 3294 4.260784 GCTAGCATAGGTACAAATGTGTGC 60.261 45.833 10.63 0.00 39.70 4.57
2884 3301 7.308770 GCATAGGTACAAATGTGTGCATCATAT 60.309 37.037 6.44 1.32 41.75 1.78
2886 3303 7.734924 AGGTACAAATGTGTGCATCATATAG 57.265 36.000 6.44 4.54 41.75 1.31
2929 3387 9.628500 AGGAGGTTATTTTAGAATGGTAATGAC 57.372 33.333 0.00 0.00 0.00 3.06
2930 3388 9.628500 GGAGGTTATTTTAGAATGGTAATGACT 57.372 33.333 0.00 0.00 0.00 3.41
2932 3390 9.975218 AGGTTATTTTAGAATGGTAATGACTGT 57.025 29.630 0.00 0.00 0.00 3.55
2995 3453 4.573607 TGATGATTTCTTCCGCTCAATCAG 59.426 41.667 0.00 0.00 38.66 2.90
3080 3542 3.213206 TCATTGGGTACATGGATGAGC 57.787 47.619 0.00 0.00 0.00 4.26
3155 3619 3.502123 ATCTTTTGTTCCAGTTCCGGA 57.498 42.857 0.00 0.00 0.00 5.14
3168 3635 3.065371 CAGTTCCGGAATGATTAACCAGC 59.935 47.826 22.04 2.30 0.00 4.85
3169 3636 3.013921 GTTCCGGAATGATTAACCAGCA 58.986 45.455 22.04 0.00 0.00 4.41
3170 3637 2.917933 TCCGGAATGATTAACCAGCAG 58.082 47.619 0.00 0.00 0.00 4.24
3236 3707 2.087646 GAGTGCAAAAAGGAGCTAGGG 58.912 52.381 0.00 0.00 0.00 3.53
3241 3712 1.636003 CAAAAAGGAGCTAGGGGAGGT 59.364 52.381 0.00 0.00 39.10 3.85
3253 3724 4.264442 GCTAGGGGAGGTGAGGAAGATATA 60.264 50.000 0.00 0.00 0.00 0.86
3298 3771 4.282449 GCTAAGCCTTTTTCCCTACCAAAA 59.718 41.667 0.00 0.00 0.00 2.44
3306 3779 5.753721 TTTTCCCTACCAAAAATGGATGG 57.246 39.130 1.10 3.33 42.60 3.51
3327 3800 4.827835 TGGTCTAGATGCTACACCTATGAC 59.172 45.833 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.688772 CCGGTCTAGCAACCTAGCTA 58.311 55.000 0.00 0.00 44.50 3.32
137 140 5.720371 AGACACTGTGGATAGATAGATGC 57.280 43.478 13.09 0.00 0.00 3.91
200 203 2.821969 ACCAAGCAAGCTACCATGAAAG 59.178 45.455 0.00 0.00 0.00 2.62
255 259 3.844090 GCCTGAGACCTCGAGCCC 61.844 72.222 6.99 0.05 0.00 5.19
461 489 0.178068 TTTGGAGCTCGCCATACCTC 59.822 55.000 7.83 0.00 37.86 3.85
504 532 5.753438 GTGCATGCATTTGCTACTACTAGTA 59.247 40.000 25.64 1.89 43.18 1.82
507 535 4.332543 GTGTGCATGCATTTGCTACTACTA 59.667 41.667 25.64 0.00 43.18 1.82
508 536 3.127548 GTGTGCATGCATTTGCTACTACT 59.872 43.478 25.64 0.00 43.18 2.57
509 537 3.127548 AGTGTGCATGCATTTGCTACTAC 59.872 43.478 25.64 7.17 43.18 2.73
550 590 8.211116 ACTATATGACACACTGTACTACTCAC 57.789 38.462 0.00 0.00 0.00 3.51
552 592 7.716123 AGGACTATATGACACACTGTACTACTC 59.284 40.741 0.00 0.00 0.00 2.59
609 655 9.850198 AAGTAGGTTATTACAAGTTTACAACCA 57.150 29.630 0.00 0.00 37.10 3.67
652 704 2.483714 CCTACTCGTATTGCCATGCACT 60.484 50.000 0.00 0.00 38.71 4.40
672 728 2.163412 TGCGTGCCATTCTACAAAATCC 59.837 45.455 0.00 0.00 0.00 3.01
689 745 3.446161 ACATAGTACTACCACACATGCGT 59.554 43.478 4.31 0.00 0.00 5.24
690 746 4.041740 ACATAGTACTACCACACATGCG 57.958 45.455 4.31 0.00 0.00 4.73
691 747 6.387041 TCTACATAGTACTACCACACATGC 57.613 41.667 4.31 0.00 0.00 4.06
692 748 6.546403 ACCTCTACATAGTACTACCACACATG 59.454 42.308 4.31 1.29 0.00 3.21
693 749 6.546403 CACCTCTACATAGTACTACCACACAT 59.454 42.308 4.31 0.00 0.00 3.21
694 750 5.884232 CACCTCTACATAGTACTACCACACA 59.116 44.000 4.31 0.00 0.00 3.72
695 751 6.118170 TCACCTCTACATAGTACTACCACAC 58.882 44.000 4.31 0.00 0.00 3.82
696 752 6.317663 TCACCTCTACATAGTACTACCACA 57.682 41.667 4.31 0.00 0.00 4.17
697 753 7.720515 AGAATCACCTCTACATAGTACTACCAC 59.279 40.741 4.31 0.00 0.00 4.16
700 756 9.339850 TCAAGAATCACCTCTACATAGTACTAC 57.660 37.037 4.31 0.00 0.00 2.73
701 757 9.562408 CTCAAGAATCACCTCTACATAGTACTA 57.438 37.037 4.77 4.77 0.00 1.82
702 758 8.275758 TCTCAAGAATCACCTCTACATAGTACT 58.724 37.037 0.00 0.00 0.00 2.73
703 759 8.453238 TCTCAAGAATCACCTCTACATAGTAC 57.547 38.462 0.00 0.00 0.00 2.73
704 760 9.647918 AATCTCAAGAATCACCTCTACATAGTA 57.352 33.333 0.00 0.00 0.00 1.82
705 761 8.420222 CAATCTCAAGAATCACCTCTACATAGT 58.580 37.037 0.00 0.00 0.00 2.12
706 762 7.871973 CCAATCTCAAGAATCACCTCTACATAG 59.128 40.741 0.00 0.00 0.00 2.23
717 773 7.093902 ACGACTTACTACCAATCTCAAGAATCA 60.094 37.037 0.00 0.00 0.00 2.57
891 947 2.606587 GCATGGAGTGGAGGGGTGT 61.607 63.158 0.00 0.00 0.00 4.16
892 948 2.273449 GCATGGAGTGGAGGGGTG 59.727 66.667 0.00 0.00 0.00 4.61
893 949 3.017581 GGCATGGAGTGGAGGGGT 61.018 66.667 0.00 0.00 0.00 4.95
957 1013 4.752101 TCTCGGCCGTAAATAGAGTACTAC 59.248 45.833 27.15 0.00 0.00 2.73
958 1014 4.960938 TCTCGGCCGTAAATAGAGTACTA 58.039 43.478 27.15 0.00 0.00 1.82
959 1015 3.813443 TCTCGGCCGTAAATAGAGTACT 58.187 45.455 27.15 0.00 0.00 2.73
960 1016 4.201950 TGTTCTCGGCCGTAAATAGAGTAC 60.202 45.833 27.15 16.67 32.37 2.73
961 1017 3.947196 TGTTCTCGGCCGTAAATAGAGTA 59.053 43.478 27.15 9.67 0.00 2.59
973 1033 2.221055 CGTTAGCATATTGTTCTCGGCC 59.779 50.000 0.00 0.00 0.00 6.13
1123 1203 3.611674 TTGACAGGACGCGGCAGA 61.612 61.111 17.00 0.00 0.00 4.26
1271 1360 1.997928 GAGCCAAAGAATCCCAGCGC 61.998 60.000 0.00 0.00 0.00 5.92
1293 1382 3.741860 ACGAGAACACGTCGACCT 58.258 55.556 10.58 0.00 43.02 3.85
1337 1426 3.506096 CGAGTCGAGCAGGCCGTA 61.506 66.667 6.73 0.00 0.00 4.02
1602 1691 2.202703 CGGGTAGCTTCCGGTTCG 60.203 66.667 17.27 5.95 43.45 3.95
1731 1835 0.537188 CTCCATGTCCGGCTTGTACT 59.463 55.000 0.00 0.00 0.00 2.73
1753 1857 2.046023 TCCTTCACCTGCGCCATG 60.046 61.111 4.18 0.00 0.00 3.66
1839 1943 2.775856 TTTTTGCGCCGTGGCTTGA 61.776 52.632 4.18 0.00 39.32 3.02
1855 1959 1.132199 CGCTCGAGATACGCACGTTT 61.132 55.000 18.75 0.00 42.26 3.60
1951 2055 1.133181 TGTCCATCTTGCTCCCACCA 61.133 55.000 0.00 0.00 0.00 4.17
1954 2058 1.296392 CGTGTCCATCTTGCTCCCA 59.704 57.895 0.00 0.00 0.00 4.37
2231 2344 4.578601 GAAACAGCAACATGTATAGACGC 58.421 43.478 0.00 0.00 31.70 5.19
2259 2372 0.954449 ACACGACGACGACCTCAGAT 60.954 55.000 15.32 0.00 42.66 2.90
2261 2374 1.154450 GACACGACGACGACCTCAG 60.154 63.158 15.32 0.00 42.66 3.35
2263 2376 0.725118 CTTGACACGACGACGACCTC 60.725 60.000 15.32 5.59 42.66 3.85
2270 2383 1.220529 ACGTAGTCTTGACACGACGA 58.779 50.000 22.18 0.00 45.13 4.20
2271 2384 2.490038 GTACGTAGTCTTGACACGACG 58.510 52.381 22.18 19.12 46.92 5.12
2272 2385 2.096713 ACGTACGTAGTCTTGACACGAC 60.097 50.000 21.41 3.95 43.93 4.34
2273 2386 2.096762 CACGTACGTAGTCTTGACACGA 60.097 50.000 22.34 10.50 43.93 4.35
2393 2510 1.794864 CACGGTCTCGATCTCACGT 59.205 57.895 0.00 0.00 40.11 4.49
2574 2713 8.677300 GGAGCAAATGAGTAAATCAACATTCTA 58.323 33.333 0.00 0.00 42.53 2.10
2575 2714 7.542025 GGAGCAAATGAGTAAATCAACATTCT 58.458 34.615 0.00 0.00 42.53 2.40
2576 2715 6.470235 CGGAGCAAATGAGTAAATCAACATTC 59.530 38.462 0.00 0.00 42.53 2.67
2577 2716 6.071952 ACGGAGCAAATGAGTAAATCAACATT 60.072 34.615 0.00 0.00 42.53 2.71
2578 2717 5.415701 ACGGAGCAAATGAGTAAATCAACAT 59.584 36.000 0.00 0.00 42.53 2.71
2579 2718 4.759693 ACGGAGCAAATGAGTAAATCAACA 59.240 37.500 0.00 0.00 42.53 3.33
2580 2719 5.296813 ACGGAGCAAATGAGTAAATCAAC 57.703 39.130 0.00 0.00 42.53 3.18
2581 2720 6.597672 ACATACGGAGCAAATGAGTAAATCAA 59.402 34.615 0.00 0.00 42.53 2.57
2582 2721 6.112734 ACATACGGAGCAAATGAGTAAATCA 58.887 36.000 0.00 0.00 43.70 2.57
2583 2722 6.604735 ACATACGGAGCAAATGAGTAAATC 57.395 37.500 0.00 0.00 0.00 2.17
2584 2723 7.272978 ACTACATACGGAGCAAATGAGTAAAT 58.727 34.615 0.00 0.00 0.00 1.40
2585 2724 6.636705 ACTACATACGGAGCAAATGAGTAAA 58.363 36.000 0.00 0.00 0.00 2.01
2586 2725 6.216801 ACTACATACGGAGCAAATGAGTAA 57.783 37.500 0.00 0.00 0.00 2.24
2587 2726 5.847111 ACTACATACGGAGCAAATGAGTA 57.153 39.130 0.00 0.00 0.00 2.59
2588 2727 4.737855 ACTACATACGGAGCAAATGAGT 57.262 40.909 0.00 0.00 0.00 3.41
2589 2728 5.109210 TGAACTACATACGGAGCAAATGAG 58.891 41.667 0.00 0.00 0.00 2.90
2590 2729 5.079689 TGAACTACATACGGAGCAAATGA 57.920 39.130 0.00 0.00 0.00 2.57
2591 2730 5.991328 ATGAACTACATACGGAGCAAATG 57.009 39.130 0.00 0.00 37.46 2.32
2592 2731 9.772973 TTAATATGAACTACATACGGAGCAAAT 57.227 29.630 0.00 0.00 43.12 2.32
2593 2732 9.602568 TTTAATATGAACTACATACGGAGCAAA 57.397 29.630 0.00 0.00 43.12 3.68
2594 2733 9.602568 TTTTAATATGAACTACATACGGAGCAA 57.397 29.630 0.00 0.00 43.12 3.91
2595 2734 9.772973 ATTTTAATATGAACTACATACGGAGCA 57.227 29.630 0.00 0.00 43.12 4.26
2620 2759 9.860393 ACTTCCTCCATCCCTAAATATAAGTAT 57.140 33.333 0.00 0.00 0.00 2.12
2622 2761 9.860393 ATACTTCCTCCATCCCTAAATATAAGT 57.140 33.333 0.00 0.00 0.00 2.24
2627 2766 9.907819 TTCTAATACTTCCTCCATCCCTAAATA 57.092 33.333 0.00 0.00 0.00 1.40
2628 2767 8.814448 TTCTAATACTTCCTCCATCCCTAAAT 57.186 34.615 0.00 0.00 0.00 1.40
2629 2768 8.814448 ATTCTAATACTTCCTCCATCCCTAAA 57.186 34.615 0.00 0.00 0.00 1.85
2630 2769 8.016652 TGATTCTAATACTTCCTCCATCCCTAA 58.983 37.037 0.00 0.00 0.00 2.69
2631 2770 7.544650 TGATTCTAATACTTCCTCCATCCCTA 58.455 38.462 0.00 0.00 0.00 3.53
2632 2771 6.393897 TGATTCTAATACTTCCTCCATCCCT 58.606 40.000 0.00 0.00 0.00 4.20
2633 2772 6.688073 TGATTCTAATACTTCCTCCATCCC 57.312 41.667 0.00 0.00 0.00 3.85
2634 2773 8.214364 ACTTTGATTCTAATACTTCCTCCATCC 58.786 37.037 0.00 0.00 0.00 3.51
2635 2774 9.050601 CACTTTGATTCTAATACTTCCTCCATC 57.949 37.037 0.00 0.00 0.00 3.51
2636 2775 7.500559 GCACTTTGATTCTAATACTTCCTCCAT 59.499 37.037 0.00 0.00 0.00 3.41
2637 2776 6.823689 GCACTTTGATTCTAATACTTCCTCCA 59.176 38.462 0.00 0.00 0.00 3.86
2638 2777 6.261158 GGCACTTTGATTCTAATACTTCCTCC 59.739 42.308 0.00 0.00 0.00 4.30
2639 2778 7.011857 CAGGCACTTTGATTCTAATACTTCCTC 59.988 40.741 0.00 0.00 34.60 3.71
2640 2779 6.825721 CAGGCACTTTGATTCTAATACTTCCT 59.174 38.462 0.00 0.00 34.60 3.36
2641 2780 6.038714 CCAGGCACTTTGATTCTAATACTTCC 59.961 42.308 0.00 0.00 34.60 3.46
2642 2781 6.038714 CCCAGGCACTTTGATTCTAATACTTC 59.961 42.308 0.00 0.00 34.60 3.01
2643 2782 5.888161 CCCAGGCACTTTGATTCTAATACTT 59.112 40.000 0.00 0.00 34.60 2.24
2644 2783 5.191722 TCCCAGGCACTTTGATTCTAATACT 59.808 40.000 0.00 0.00 34.60 2.12
2645 2784 5.297029 GTCCCAGGCACTTTGATTCTAATAC 59.703 44.000 0.00 0.00 34.60 1.89
2646 2785 5.045213 TGTCCCAGGCACTTTGATTCTAATA 60.045 40.000 0.00 0.00 34.60 0.98
2647 2786 4.263905 TGTCCCAGGCACTTTGATTCTAAT 60.264 41.667 0.00 0.00 34.60 1.73
2648 2787 3.073798 TGTCCCAGGCACTTTGATTCTAA 59.926 43.478 0.00 0.00 34.60 2.10
2712 2857 9.664332 CTATTTTAGGATATGACTCATGGAAGG 57.336 37.037 1.42 0.00 0.00 3.46
2794 3208 2.480759 GGCAAACAGATGATCCATGCAC 60.481 50.000 10.17 0.00 34.14 4.57
2827 3241 0.179059 TTGTGTGAGTGACGGCATGT 60.179 50.000 0.00 0.00 0.00 3.21
2926 3384 8.991243 AAACGCTTTACATATAGTTACAGTCA 57.009 30.769 0.00 0.00 0.00 3.41
2933 3391 9.537192 TGCAGTATAAACGCTTTACATATAGTT 57.463 29.630 0.00 0.00 0.00 2.24
2934 3392 9.706691 ATGCAGTATAAACGCTTTACATATAGT 57.293 29.630 0.00 0.00 0.00 2.12
2935 3393 9.958285 CATGCAGTATAAACGCTTTACATATAG 57.042 33.333 0.00 0.00 0.00 1.31
2936 3394 8.440059 GCATGCAGTATAAACGCTTTACATATA 58.560 33.333 14.21 0.00 0.00 0.86
2937 3395 7.041440 TGCATGCAGTATAAACGCTTTACATAT 60.041 33.333 18.46 0.00 0.00 1.78
2967 3425 3.220110 AGCGGAAGAAATCATCATGCAT 58.780 40.909 0.00 0.00 0.00 3.96
2995 3453 1.750399 ATGTGCAGCAATCGGACCC 60.750 57.895 0.00 0.00 0.00 4.46
3050 3512 7.122048 TCCATGTACCCAATGATTCACATTTA 58.878 34.615 0.00 0.00 45.60 1.40
3080 3542 2.758009 CAAGTTTGCCATGTTTGGGAG 58.242 47.619 0.00 0.00 45.01 4.30
3106 3569 0.392998 GGAGACCGACCAATGCACAT 60.393 55.000 0.00 0.00 0.00 3.21
3107 3570 1.003839 GGAGACCGACCAATGCACA 60.004 57.895 0.00 0.00 0.00 4.57
3155 3619 6.479884 AGAAGAAGACTGCTGGTTAATCATT 58.520 36.000 0.00 0.00 29.45 2.57
3168 3635 3.251972 GGTGCAAAAGGAGAAGAAGACTG 59.748 47.826 0.00 0.00 0.00 3.51
3169 3636 3.481453 GGTGCAAAAGGAGAAGAAGACT 58.519 45.455 0.00 0.00 0.00 3.24
3170 3637 2.554462 GGGTGCAAAAGGAGAAGAAGAC 59.446 50.000 0.00 0.00 0.00 3.01
3236 3707 7.579105 TCTAGCTATATATCTTCCTCACCTCC 58.421 42.308 0.00 0.00 0.00 4.30
3293 3766 4.891756 AGCATCTAGACCATCCATTTTTGG 59.108 41.667 0.00 0.00 39.02 3.28
3298 3771 4.040952 GGTGTAGCATCTAGACCATCCATT 59.959 45.833 13.35 0.00 31.82 3.16
3306 3779 5.074115 AGGTCATAGGTGTAGCATCTAGAC 58.926 45.833 0.00 8.87 30.11 2.59


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

AutoCloner maintained by Alex Coulton.