Multiple sequence alignment - TraesCS7A01G204800

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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 TraesCS7A01G204800 chr7A 100.000 3280 0 0 1 3280 166989783 166986504 0.000000e+00 6058.0
1 TraesCS7A01G204800 chr7A 93.694 111 5 1 2343 2453 166987398 166987290 7.280000e-37 165.0
2 TraesCS7A01G204800 chr7A 93.694 111 5 1 2386 2494 166987441 166987331 7.280000e-37 165.0
3 TraesCS7A01G204800 chr7A 89.706 68 5 1 2343 2410 166987355 166987290 5.830000e-13 86.1
4 TraesCS7A01G204800 chr7A 89.706 68 5 1 2429 2494 166987441 166987374 5.830000e-13 86.1
5 TraesCS7A01G204800 chr7D 93.921 2188 66 17 459 2637 165155000 165152871 0.000000e+00 3241.0
6 TraesCS7A01G204800 chr7D 85.629 334 24 10 2699 3011 165152863 165152533 2.440000e-86 329.0
7 TraesCS7A01G204800 chr7D 84.281 299 41 3 1 297 165155458 165155164 1.490000e-73 287.0
8 TraesCS7A01G204800 chr7D 87.006 177 9 11 3101 3275 165152361 165152197 1.550000e-43 187.0
9 TraesCS7A01G204800 chr7D 84.298 121 10 6 305 416 165155116 165154996 3.460000e-20 110.0
10 TraesCS7A01G204800 chr7B 96.131 1835 52 14 623 2445 128446785 128444958 0.000000e+00 2977.0
11 TraesCS7A01G204800 chr7B 87.040 625 43 13 2397 3005 128445047 128444445 0.000000e+00 671.0
12 TraesCS7A01G204800 chr7B 86.580 231 20 5 3051 3280 128444300 128444080 9.090000e-61 244.0
13 TraesCS7A01G204800 chr7B 80.537 298 33 6 1 297 128447326 128447053 4.290000e-49 206.0
14 TraesCS7A01G204800 chr7B 88.350 103 9 2 459 560 128446895 128446795 1.600000e-23 121.0
15 TraesCS7A01G204800 chr5B 89.352 432 45 1 1644 2075 254501350 254501780 2.880000e-150 542.0
16 TraesCS7A01G204800 chr1A 91.960 199 16 0 1644 1842 277625470 277625272 2.490000e-71 279.0
17 TraesCS7A01G204800 chr1A 92.147 191 15 0 1646 1836 277622954 277622764 1.500000e-68 270.0
18 TraesCS7A01G204800 chr1A 91.623 191 16 0 1646 1836 277617006 277616816 6.980000e-67 265.0
19 TraesCS7A01G204800 chr1A 91.623 191 16 0 1646 1836 277618988 277618798 6.980000e-67 265.0
20 TraesCS7A01G204800 chr1A 91.623 191 16 0 1646 1836 277620971 277620781 6.980000e-67 265.0
21 TraesCS7A01G204800 chr1A 91.623 191 16 0 1646 1836 277625015 277624825 6.980000e-67 265.0
22 TraesCS7A01G204800 chr4A 92.381 105 8 0 1811 1915 494075107 494075211 2.040000e-32 150.0
23 TraesCS7A01G204800 chr5A 82.759 87 15 0 1042 1128 663763415 663763501 9.760000e-11 78.7


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 TraesCS7A01G204800 chr7A 166986504 166989783 3279 True 1312.040000 6058 93.3600 1 3280 5 chr7A.!!$R1 3279
1 TraesCS7A01G204800 chr7D 165152197 165155458 3261 True 830.800000 3241 87.0270 1 3275 5 chr7D.!!$R1 3274
2 TraesCS7A01G204800 chr7B 128444080 128447326 3246 True 843.800000 2977 87.7276 1 3280 5 chr7B.!!$R1 3279
3 TraesCS7A01G204800 chr1A 277616816 277625470 8654 True 268.166667 279 91.7665 1644 1842 6 chr1A.!!$R1 198

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
269 271 0.185901 ATTATGCGCTTGGGACCCAT 59.814 50.0 15.83 0.0 31.53 4.0 F
584 636 0.251073 TAACTTAACAGGCGAGCCCC 59.749 55.0 10.95 0.0 36.58 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1241 1302 1.512310 CTCGTCGTTGGAGAGCGTC 60.512 63.158 0.00 0.0 33.27 5.19 R
2549 10689 0.399949 TCGGGCCATAGAGGATTGGT 60.400 55.000 4.39 0.0 41.22 3.67 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
68 70 3.390639 TGGTGGAATCAGTGCCAATTTTT 59.609 39.130 0.00 0.00 35.63 1.94
71 73 2.743664 GGAATCAGTGCCAATTTTTGCC 59.256 45.455 0.00 0.00 0.00 4.52
108 110 2.972625 TGCTTTACTGACCATCGAAGG 58.027 47.619 4.85 4.85 0.00 3.46
111 113 4.020928 TGCTTTACTGACCATCGAAGGTTA 60.021 41.667 14.49 9.06 43.38 2.85
118 120 3.322541 TGACCATCGAAGGTTACTGTTCA 59.677 43.478 14.49 2.37 43.38 3.18
162 164 2.353889 GCGGAGTTAGTAGATGACGACA 59.646 50.000 0.00 0.00 0.00 4.35
169 171 2.085320 AGTAGATGACGACAGCGAACT 58.915 47.619 7.95 7.95 41.64 3.01
222 224 2.387309 CGATTGAGCGCTGGAACAT 58.613 52.632 18.48 0.00 38.20 2.71
226 228 3.512516 GAGCGCTGGAACATGCCC 61.513 66.667 18.48 0.00 39.91 5.36
229 231 3.197790 CGCTGGAACATGCCCTCG 61.198 66.667 6.33 6.10 38.20 4.63
252 254 3.510531 AGAGCTGCATCCATGATGATT 57.489 42.857 8.21 0.00 42.09 2.57
253 255 4.635699 AGAGCTGCATCCATGATGATTA 57.364 40.909 8.21 0.00 42.09 1.75
269 271 0.185901 ATTATGCGCTTGGGACCCAT 59.814 50.000 15.83 0.00 31.53 4.00
336 378 6.180472 ACACTACCTTTTGATGTATGGAAGG 58.820 40.000 0.00 0.00 41.98 3.46
340 382 2.051334 TTTGATGTATGGAAGGGGCG 57.949 50.000 0.00 0.00 0.00 6.13
345 387 1.764854 GTATGGAAGGGGCGAGGGA 60.765 63.158 0.00 0.00 0.00 4.20
346 388 1.003704 TATGGAAGGGGCGAGGGAA 59.996 57.895 0.00 0.00 0.00 3.97
347 389 1.054406 TATGGAAGGGGCGAGGGAAG 61.054 60.000 0.00 0.00 0.00 3.46
349 391 3.009714 GAAGGGGCGAGGGAAGGT 61.010 66.667 0.00 0.00 0.00 3.50
381 429 4.758251 TGCGGATGGTGAGCGTGG 62.758 66.667 0.00 0.00 0.00 4.94
403 454 2.289756 GGAAGAAGACACAAGGAGGGAC 60.290 54.545 0.00 0.00 0.00 4.46
438 489 2.928036 AAAAATTGAGGGAGGGGGAG 57.072 50.000 0.00 0.00 0.00 4.30
439 490 1.010795 AAAATTGAGGGAGGGGGAGG 58.989 55.000 0.00 0.00 0.00 4.30
440 491 0.926220 AAATTGAGGGAGGGGGAGGG 60.926 60.000 0.00 0.00 0.00 4.30
441 492 2.883316 AATTGAGGGAGGGGGAGGGG 62.883 65.000 0.00 0.00 0.00 4.79
443 494 4.179599 GAGGGAGGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
468 519 1.063266 GGAGGGGCAATCCAATGGTTA 60.063 52.381 0.00 0.00 36.79 2.85
473 524 1.816224 GGCAATCCAATGGTTACACGT 59.184 47.619 0.00 0.00 0.00 4.49
477 528 3.695830 ATCCAATGGTTACACGTGACT 57.304 42.857 25.01 2.62 0.00 3.41
532 584 1.167851 CGCTGCCATTCTTCCTTTGA 58.832 50.000 0.00 0.00 0.00 2.69
536 588 2.163815 CTGCCATTCTTCCTTTGAGCTG 59.836 50.000 0.00 0.00 0.00 4.24
537 589 2.224843 TGCCATTCTTCCTTTGAGCTGA 60.225 45.455 0.00 0.00 0.00 4.26
570 622 3.747388 CGGGCCACATCATACCATAACTT 60.747 47.826 4.39 0.00 0.00 2.66
571 623 4.504165 CGGGCCACATCATACCATAACTTA 60.504 45.833 4.39 0.00 0.00 2.24
572 624 5.381757 GGGCCACATCATACCATAACTTAA 58.618 41.667 4.39 0.00 0.00 1.85
573 625 5.240844 GGGCCACATCATACCATAACTTAAC 59.759 44.000 4.39 0.00 0.00 2.01
574 626 5.825679 GGCCACATCATACCATAACTTAACA 59.174 40.000 0.00 0.00 0.00 2.41
575 627 6.017109 GGCCACATCATACCATAACTTAACAG 60.017 42.308 0.00 0.00 0.00 3.16
576 628 6.017109 GCCACATCATACCATAACTTAACAGG 60.017 42.308 0.00 0.00 0.00 4.00
577 629 6.017109 CCACATCATACCATAACTTAACAGGC 60.017 42.308 0.00 0.00 0.00 4.85
578 630 5.758296 ACATCATACCATAACTTAACAGGCG 59.242 40.000 0.00 0.00 0.00 5.52
579 631 5.601583 TCATACCATAACTTAACAGGCGA 57.398 39.130 0.00 0.00 0.00 5.54
580 632 5.597806 TCATACCATAACTTAACAGGCGAG 58.402 41.667 0.00 0.00 0.00 5.03
581 633 2.629051 ACCATAACTTAACAGGCGAGC 58.371 47.619 0.00 0.00 0.00 5.03
582 634 1.940613 CCATAACTTAACAGGCGAGCC 59.059 52.381 5.89 5.89 0.00 4.70
583 635 1.940613 CATAACTTAACAGGCGAGCCC 59.059 52.381 10.95 0.00 36.58 5.19
584 636 0.251073 TAACTTAACAGGCGAGCCCC 59.749 55.000 10.95 0.00 36.58 5.80
585 637 2.124695 CTTAACAGGCGAGCCCCC 60.125 66.667 10.95 0.00 36.58 5.40
586 638 2.609610 TTAACAGGCGAGCCCCCT 60.610 61.111 10.95 0.00 36.58 4.79
587 639 1.306312 TTAACAGGCGAGCCCCCTA 60.306 57.895 10.95 0.00 36.58 3.53
588 640 0.910566 TTAACAGGCGAGCCCCCTAA 60.911 55.000 10.95 3.19 36.58 2.69
589 641 0.910566 TAACAGGCGAGCCCCCTAAA 60.911 55.000 10.95 0.00 36.58 1.85
590 642 1.785353 AACAGGCGAGCCCCCTAAAA 61.785 55.000 10.95 0.00 36.58 1.52
591 643 1.001393 CAGGCGAGCCCCCTAAAAA 60.001 57.895 10.95 0.00 36.58 1.94
656 712 2.159226 CCCAGTCACGAGATACTTCCAC 60.159 54.545 0.00 0.00 0.00 4.02
657 713 2.478031 CCAGTCACGAGATACTTCCACG 60.478 54.545 0.00 0.00 0.00 4.94
721 777 5.977489 ACCTAGCTTCCCAAAATAAACAC 57.023 39.130 0.00 0.00 0.00 3.32
894 951 1.077429 AGGAGCCGCCAAATCCTTC 60.077 57.895 0.00 0.00 40.65 3.46
942 999 1.070289 CACCCTATAAACCTCCTCCGC 59.930 57.143 0.00 0.00 0.00 5.54
983 1040 3.484806 ACAACCACCGCCAGTCCA 61.485 61.111 0.00 0.00 0.00 4.02
1004 1062 2.568546 TCTCCCAAATCCCTAGCAGA 57.431 50.000 0.00 0.00 0.00 4.26
1766 1827 1.934956 CCGCGTCTTCGAGATCGTG 60.935 63.158 4.92 10.25 39.07 4.35
2086 10226 0.033920 TTCTGATCGGCCCGATGATG 59.966 55.000 25.80 12.87 47.00 3.07
2309 10449 0.610232 ATCTTGTGCTGCCCCTGTTC 60.610 55.000 0.00 0.00 0.00 3.18
2327 10467 3.265791 GTTCGAGGAATTGTCTCTGCAT 58.734 45.455 0.00 0.00 0.00 3.96
2330 10470 4.433615 TCGAGGAATTGTCTCTGCATAAC 58.566 43.478 0.00 0.00 0.00 1.89
2345 10485 1.666209 ATAACCATGCCAACCTGCGC 61.666 55.000 0.00 0.00 0.00 6.09
2363 10503 3.039588 GCAGGGCGTTCGACGAAA 61.040 61.111 12.67 0.00 46.05 3.46
2364 10504 2.851104 CAGGGCGTTCGACGAAAC 59.149 61.111 12.67 7.57 46.05 2.78
2370 10510 4.038373 GTTCGACGAAACGCGCGT 62.038 61.111 32.73 32.73 46.04 6.01
2371 10511 4.037148 TTCGACGAAACGCGCGTG 62.037 61.111 38.44 26.26 46.04 5.34
2407 10547 2.851104 CAGGGCGTTCGACGAAAC 59.149 61.111 12.67 7.57 46.05 2.78
2450 10590 2.851104 CAGGGCGTTCGACGAAAC 59.149 61.111 12.67 7.57 46.05 2.78
2557 10697 4.473520 CGCAGCGGGACCAATCCT 62.474 66.667 7.00 0.00 45.46 3.24
2560 10700 1.686325 GCAGCGGGACCAATCCTCTA 61.686 60.000 0.00 0.00 45.46 2.43
2677 10819 4.106029 TCGCAGACTTGGAGTACAATAC 57.894 45.455 0.00 0.00 38.65 1.89
2678 10820 3.762288 TCGCAGACTTGGAGTACAATACT 59.238 43.478 0.00 0.00 42.86 2.12
2679 10821 3.859961 CGCAGACTTGGAGTACAATACTG 59.140 47.826 13.87 13.87 39.59 2.74
2680 10822 4.618460 CGCAGACTTGGAGTACAATACTGT 60.618 45.833 17.29 1.48 40.69 3.55
2681 10823 5.392703 CGCAGACTTGGAGTACAATACTGTA 60.393 44.000 17.29 0.00 40.69 2.74
2682 10824 6.574350 GCAGACTTGGAGTACAATACTGTAT 58.426 40.000 17.29 0.00 40.16 2.29
2683 10825 6.697892 GCAGACTTGGAGTACAATACTGTATC 59.302 42.308 17.29 4.08 40.16 2.24
2684 10826 6.913132 CAGACTTGGAGTACAATACTGTATCG 59.087 42.308 11.31 0.00 40.16 2.92
2685 10827 6.039493 AGACTTGGAGTACAATACTGTATCGG 59.961 42.308 0.00 0.00 40.16 4.18
2686 10828 4.579454 TGGAGTACAATACTGTATCGGC 57.421 45.455 0.00 0.00 40.16 5.54
2687 10829 3.319972 TGGAGTACAATACTGTATCGGCC 59.680 47.826 0.00 0.00 40.16 6.13
2688 10830 3.573110 GGAGTACAATACTGTATCGGCCT 59.427 47.826 0.00 0.00 40.16 5.19
2689 10831 4.763793 GGAGTACAATACTGTATCGGCCTA 59.236 45.833 0.00 0.00 40.16 3.93
2690 10832 5.335504 GGAGTACAATACTGTATCGGCCTAC 60.336 48.000 0.00 0.00 40.16 3.18
2691 10833 5.135383 AGTACAATACTGTATCGGCCTACA 58.865 41.667 0.00 2.52 40.16 2.74
2692 10834 5.595542 AGTACAATACTGTATCGGCCTACAA 59.404 40.000 0.00 0.00 40.16 2.41
2693 10835 5.546621 ACAATACTGTATCGGCCTACAAT 57.453 39.130 0.00 0.00 32.54 2.71
2694 10836 6.659745 ACAATACTGTATCGGCCTACAATA 57.340 37.500 0.00 0.00 32.54 1.90
2695 10837 6.453092 ACAATACTGTATCGGCCTACAATAC 58.547 40.000 0.00 4.46 32.54 1.89
2799 10946 2.097825 CCCAAAAGCAAGATCCTCTGG 58.902 52.381 0.00 0.00 0.00 3.86
2822 10969 2.631062 CGTGATATGGGCTGGGTAGTAA 59.369 50.000 0.00 0.00 0.00 2.24
2824 10971 2.637872 TGATATGGGCTGGGTAGTAAGC 59.362 50.000 0.00 0.00 38.76 3.09
2825 10972 2.184088 TATGGGCTGGGTAGTAAGCA 57.816 50.000 0.00 0.00 41.36 3.91
2826 10973 0.839946 ATGGGCTGGGTAGTAAGCAG 59.160 55.000 0.00 0.00 41.36 4.24
2836 10988 4.019174 GGGTAGTAAGCAGTACTGTACCA 58.981 47.826 27.74 12.45 43.24 3.25
2877 11042 2.540515 CGTGACAACTGACTGACAAGT 58.459 47.619 0.00 0.00 40.21 3.16
2878 11043 2.282555 CGTGACAACTGACTGACAAGTG 59.717 50.000 0.00 0.00 36.52 3.16
2880 11045 3.307242 GTGACAACTGACTGACAAGTGAC 59.693 47.826 0.00 0.00 36.52 3.67
2881 11046 3.056179 TGACAACTGACTGACAAGTGACA 60.056 43.478 0.00 0.00 36.52 3.58
2882 11047 3.932710 GACAACTGACTGACAAGTGACAA 59.067 43.478 0.00 0.00 36.52 3.18
2902 11071 1.154225 CGATCGGGCACTTTGTTGC 60.154 57.895 7.38 0.00 42.18 4.17
2928 11097 0.902516 GGCACAAAAGTGGCCCCATA 60.903 55.000 10.64 0.00 43.08 2.74
2965 11134 2.050351 AGCACGTCGACGGTGAAG 60.050 61.111 37.89 23.09 44.95 3.02
2971 11140 1.799121 GTCGACGGTGAAGCGTACC 60.799 63.158 7.62 0.00 34.81 3.34
3012 11181 1.569493 CAAACTGCCTGTTCCGTCG 59.431 57.895 0.00 0.00 38.03 5.12
3015 11184 0.670546 AACTGCCTGTTCCGTCGATG 60.671 55.000 0.00 0.00 32.63 3.84
3016 11185 1.811266 CTGCCTGTTCCGTCGATGG 60.811 63.158 18.13 18.13 0.00 3.51
3019 11188 1.945354 GCCTGTTCCGTCGATGGAGA 61.945 60.000 24.84 15.27 39.72 3.71
3048 11302 3.276091 CGCGCACACCAGACCAAA 61.276 61.111 8.75 0.00 0.00 3.28
3049 11303 2.331451 GCGCACACCAGACCAAAC 59.669 61.111 0.30 0.00 0.00 2.93
3087 11381 1.081774 CCAAAATGGTTTCGCGCGA 60.082 52.632 31.40 31.40 31.35 5.87
3088 11382 0.455972 CCAAAATGGTTTCGCGCGAT 60.456 50.000 35.21 16.17 31.35 4.58
3089 11383 0.907171 CAAAATGGTTTCGCGCGATC 59.093 50.000 35.21 27.07 0.00 3.69
3090 11384 0.520412 AAAATGGTTTCGCGCGATCG 60.520 50.000 35.21 11.69 39.07 3.69
3091 11385 1.355796 AAATGGTTTCGCGCGATCGA 61.356 50.000 35.21 25.06 38.10 3.59
3092 11386 1.355796 AATGGTTTCGCGCGATCGAA 61.356 50.000 35.21 22.47 45.40 3.71
3137 11431 3.373565 CCCTGCCCTGCGAAAACC 61.374 66.667 0.00 0.00 0.00 3.27
3144 11438 1.457009 CCCTGCGAAAACCGGGAAAA 61.457 55.000 6.32 0.00 39.08 2.29
3145 11439 0.386113 CCTGCGAAAACCGGGAAAAA 59.614 50.000 6.32 0.00 39.04 1.94
3172 11466 1.100510 ATCTGTTCGGCGTAGTGCTA 58.899 50.000 6.85 0.00 45.43 3.49
3188 11482 2.548480 GTGCTACAACACTTTCTGGACC 59.452 50.000 0.00 0.00 37.58 4.46
3190 11484 3.118038 TGCTACAACACTTTCTGGACCTT 60.118 43.478 0.00 0.00 0.00 3.50
3199 11493 9.810545 CAACACTTTCTGGACCTTTTATTTTTA 57.189 29.630 0.00 0.00 0.00 1.52
3206 11500 9.699703 TTCTGGACCTTTTATTTTTATTTTCCG 57.300 29.630 0.00 0.00 0.00 4.30
3215 11509 7.941431 TTATTTTTATTTTCCGGGCTAGACA 57.059 32.000 0.00 0.00 0.00 3.41
3220 11514 4.983671 ATTTTCCGGGCTAGACATTTTC 57.016 40.909 0.00 0.00 0.00 2.29
3228 11522 4.621747 CGGGCTAGACATTTTCTCTTGAGT 60.622 45.833 0.00 0.00 35.55 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 62 2.470983 ATGGTTCCGGCAAAAATTGG 57.529 45.000 0.00 0.00 0.00 3.16
85 87 4.215399 CCTTCGATGGTCAGTAAAGCAAAA 59.785 41.667 9.17 0.00 0.00 2.44
86 88 3.751175 CCTTCGATGGTCAGTAAAGCAAA 59.249 43.478 9.17 0.00 0.00 3.68
89 91 2.973945 ACCTTCGATGGTCAGTAAAGC 58.026 47.619 16.84 0.00 34.86 3.51
90 92 5.577164 CAGTAACCTTCGATGGTCAGTAAAG 59.423 44.000 22.05 6.62 39.83 1.85
91 93 5.011329 ACAGTAACCTTCGATGGTCAGTAAA 59.989 40.000 22.05 3.18 39.83 2.01
92 94 4.525487 ACAGTAACCTTCGATGGTCAGTAA 59.475 41.667 22.05 4.76 39.83 2.24
93 95 4.084287 ACAGTAACCTTCGATGGTCAGTA 58.916 43.478 22.05 9.46 39.83 2.74
105 107 7.054124 TGAAGAACTCAATGAACAGTAACCTT 58.946 34.615 0.00 0.00 0.00 3.50
139 141 1.948145 CGTCATCTACTAACTCCGCCT 59.052 52.381 0.00 0.00 0.00 5.52
145 147 3.268330 TCGCTGTCGTCATCTACTAACT 58.732 45.455 0.00 0.00 36.96 2.24
162 164 4.379243 CACCCGCTCCAGTTCGCT 62.379 66.667 0.00 0.00 0.00 4.93
175 177 4.500116 GCCTCTCTCGCGTCACCC 62.500 72.222 5.77 0.00 0.00 4.61
176 178 3.444805 AGCCTCTCTCGCGTCACC 61.445 66.667 5.77 0.00 0.00 4.02
208 210 2.747460 GGCATGTTCCAGCGCTCA 60.747 61.111 7.13 1.98 0.00 4.26
226 228 2.133553 CATGGATGCAGCTCTAACGAG 58.866 52.381 0.22 0.00 40.35 4.18
229 231 3.736720 TCATCATGGATGCAGCTCTAAC 58.263 45.455 0.22 0.00 39.63 2.34
252 254 0.396435 CTATGGGTCCCAAGCGCATA 59.604 55.000 16.55 0.04 39.62 3.14
253 255 1.149174 CTATGGGTCCCAAGCGCAT 59.851 57.895 16.55 0.00 41.38 4.73
340 382 2.610859 TGCTCCCCACCTTCCCTC 60.611 66.667 0.00 0.00 0.00 4.30
345 387 2.856000 AGCACTGCTCCCCACCTT 60.856 61.111 0.00 0.00 30.62 3.50
381 429 1.003696 CCCTCCTTGTGTCTTCTTCCC 59.996 57.143 0.00 0.00 0.00 3.97
419 470 1.362584 CCTCCCCCTCCCTCAATTTTT 59.637 52.381 0.00 0.00 0.00 1.94
420 471 1.010795 CCTCCCCCTCCCTCAATTTT 58.989 55.000 0.00 0.00 0.00 1.82
421 472 0.926220 CCCTCCCCCTCCCTCAATTT 60.926 60.000 0.00 0.00 0.00 1.82
422 473 1.309102 CCCTCCCCCTCCCTCAATT 60.309 63.158 0.00 0.00 0.00 2.32
423 474 2.378522 CCCTCCCCCTCCCTCAAT 59.621 66.667 0.00 0.00 0.00 2.57
424 475 4.038804 CCCCTCCCCCTCCCTCAA 62.039 72.222 0.00 0.00 0.00 3.02
426 477 4.179599 CTCCCCTCCCCCTCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
445 496 2.715125 ATTGGATTGCCCCTCCCCC 61.715 63.158 0.00 0.00 31.32 5.40
446 497 1.458209 CATTGGATTGCCCCTCCCC 60.458 63.158 0.00 0.00 31.32 4.81
447 498 1.458209 CCATTGGATTGCCCCTCCC 60.458 63.158 0.00 0.00 31.32 4.30
448 499 0.325577 AACCATTGGATTGCCCCTCC 60.326 55.000 10.37 0.00 0.00 4.30
449 500 2.031870 GTAACCATTGGATTGCCCCTC 58.968 52.381 10.37 0.00 0.00 4.30
450 501 1.360852 TGTAACCATTGGATTGCCCCT 59.639 47.619 10.37 0.00 0.00 4.79
451 502 1.480545 GTGTAACCATTGGATTGCCCC 59.519 52.381 10.37 0.00 0.00 5.80
452 503 1.134175 CGTGTAACCATTGGATTGCCC 59.866 52.381 10.37 0.00 0.00 5.36
453 504 1.816224 ACGTGTAACCATTGGATTGCC 59.184 47.619 10.37 0.00 0.00 4.52
454 505 2.486203 TCACGTGTAACCATTGGATTGC 59.514 45.455 16.51 4.63 0.00 3.56
455 506 3.751175 AGTCACGTGTAACCATTGGATTG 59.249 43.478 16.51 0.00 0.00 2.67
456 507 3.751175 CAGTCACGTGTAACCATTGGATT 59.249 43.478 16.51 2.87 0.00 3.01
457 508 3.007506 TCAGTCACGTGTAACCATTGGAT 59.992 43.478 16.51 0.00 0.00 3.41
468 519 1.292223 CCCCGATTCAGTCACGTGT 59.708 57.895 16.51 0.00 0.00 4.49
473 524 2.989639 CAGCCCCCGATTCAGTCA 59.010 61.111 0.00 0.00 0.00 3.41
520 572 5.010415 CCTGTTTTCAGCTCAAAGGAAGAAT 59.990 40.000 0.00 0.00 45.76 2.40
526 578 1.000171 GGCCTGTTTTCAGCTCAAAGG 60.000 52.381 0.00 0.00 45.76 3.11
532 584 2.282462 CGGGGCCTGTTTTCAGCT 60.282 61.111 3.48 0.00 45.76 4.24
570 622 0.910566 TTTAGGGGGCTCGCCTGTTA 60.911 55.000 17.43 4.19 46.39 2.41
571 623 1.785353 TTTTAGGGGGCTCGCCTGTT 61.785 55.000 17.43 0.00 46.39 3.16
572 624 1.785353 TTTTTAGGGGGCTCGCCTGT 61.785 55.000 17.43 0.00 46.39 4.00
573 625 1.001393 TTTTTAGGGGGCTCGCCTG 60.001 57.895 17.43 0.00 46.39 4.85
589 641 4.156008 AGTTGACTCGCTTGTTCAGTTTTT 59.844 37.500 0.00 0.00 0.00 1.94
590 642 3.689649 AGTTGACTCGCTTGTTCAGTTTT 59.310 39.130 0.00 0.00 0.00 2.43
591 643 3.270877 AGTTGACTCGCTTGTTCAGTTT 58.729 40.909 0.00 0.00 0.00 2.66
592 644 2.906354 AGTTGACTCGCTTGTTCAGTT 58.094 42.857 0.00 0.00 0.00 3.16
593 645 2.604046 AGTTGACTCGCTTGTTCAGT 57.396 45.000 0.00 0.00 0.00 3.41
594 646 3.369147 CCATAGTTGACTCGCTTGTTCAG 59.631 47.826 0.00 0.00 0.00 3.02
595 647 3.325870 CCATAGTTGACTCGCTTGTTCA 58.674 45.455 0.00 0.00 0.00 3.18
656 712 3.069729 TGTTTTGGTAAAAATGGGGGTCG 59.930 43.478 0.00 0.00 37.59 4.79
657 713 4.382291 GTGTTTTGGTAAAAATGGGGGTC 58.618 43.478 0.00 0.00 37.59 4.46
721 777 4.012895 GTGCGGTTGCTCACGTGG 62.013 66.667 17.00 7.71 43.34 4.94
894 951 2.952310 GGAGGGAAGATTTCGAATTGGG 59.048 50.000 0.00 0.00 0.00 4.12
950 1007 2.037208 GTGGTGTGGGGGAATGGG 59.963 66.667 0.00 0.00 0.00 4.00
983 1040 3.397527 TCTGCTAGGGATTTGGGAGATT 58.602 45.455 0.00 0.00 0.00 2.40
1004 1062 1.282157 CCTCGAGGTGGGAAGGATTTT 59.718 52.381 24.04 0.00 0.00 1.82
1034 1092 4.438562 TTCGGAATTCGGCGGCGA 62.439 61.111 31.46 31.46 39.77 5.54
1241 1302 1.512310 CTCGTCGTTGGAGAGCGTC 60.512 63.158 0.00 0.00 33.27 5.19
2086 10226 6.314896 GCTATTGGTAATGGAGACTGCATATC 59.685 42.308 10.15 6.36 0.00 1.63
2148 10288 3.814283 CGCTACAACTACTAGGACTAGGG 59.186 52.174 10.81 5.87 37.49 3.53
2150 10290 4.272991 CACCGCTACAACTACTAGGACTAG 59.727 50.000 4.86 4.86 39.04 2.57
2221 10361 4.558226 ACATCACCAATAAGAGACAGCA 57.442 40.909 0.00 0.00 0.00 4.41
2309 10449 3.557595 GGTTATGCAGAGACAATTCCTCG 59.442 47.826 0.00 0.00 35.88 4.63
2327 10467 2.339556 GCGCAGGTTGGCATGGTTA 61.340 57.895 0.30 0.00 0.00 2.85
2348 10488 2.732094 CGTTTCGTCGAACGCCCT 60.732 61.111 7.29 0.00 44.70 5.19
2353 10493 4.038373 ACGCGCGTTTCGTCGAAC 62.038 61.111 32.73 2.56 39.61 3.95
2354 10494 4.037148 CACGCGCGTTTCGTCGAA 62.037 61.111 35.90 2.90 38.19 3.71
2390 10530 2.851104 GTTTCGTCGAACGCCCTG 59.149 61.111 7.29 0.00 42.21 4.45
2476 10616 1.136774 GGCATTTCTTCGAACGCCC 59.863 57.895 0.00 0.00 33.31 6.13
2549 10689 0.399949 TCGGGCCATAGAGGATTGGT 60.400 55.000 4.39 0.00 41.22 3.67
2550 10690 0.987294 ATCGGGCCATAGAGGATTGG 59.013 55.000 4.39 0.00 41.22 3.16
2552 10692 1.271597 GCAATCGGGCCATAGAGGATT 60.272 52.381 4.39 0.00 41.22 3.01
2554 10694 1.754745 GCAATCGGGCCATAGAGGA 59.245 57.895 4.39 0.00 41.22 3.71
2555 10695 1.669115 CGCAATCGGGCCATAGAGG 60.669 63.158 4.39 0.00 41.84 3.69
2579 10721 1.150827 CAAGCAAGCATCACGTCTGA 58.849 50.000 0.00 0.00 0.00 3.27
2593 10735 1.382420 AAAACAGTGGGGCCAAGCA 60.382 52.632 4.39 0.00 0.00 3.91
2677 10819 3.572682 TCTGGTATTGTAGGCCGATACAG 59.427 47.826 17.42 10.93 40.80 2.74
2678 10820 3.568443 TCTGGTATTGTAGGCCGATACA 58.432 45.455 17.42 11.01 40.80 2.29
2679 10821 3.825014 TCTCTGGTATTGTAGGCCGATAC 59.175 47.826 0.00 5.15 39.02 2.24
2680 10822 3.825014 GTCTCTGGTATTGTAGGCCGATA 59.175 47.826 0.00 0.00 0.00 2.92
2681 10823 2.628657 GTCTCTGGTATTGTAGGCCGAT 59.371 50.000 0.00 0.00 0.00 4.18
2682 10824 2.029623 GTCTCTGGTATTGTAGGCCGA 58.970 52.381 0.00 0.00 0.00 5.54
2683 10825 1.269102 CGTCTCTGGTATTGTAGGCCG 60.269 57.143 0.00 0.00 0.00 6.13
2684 10826 1.538419 GCGTCTCTGGTATTGTAGGCC 60.538 57.143 0.00 0.00 0.00 5.19
2685 10827 1.409427 AGCGTCTCTGGTATTGTAGGC 59.591 52.381 0.00 0.00 0.00 3.93
2686 10828 3.448686 CAAGCGTCTCTGGTATTGTAGG 58.551 50.000 0.00 0.00 0.00 3.18
2687 10829 3.130516 TCCAAGCGTCTCTGGTATTGTAG 59.869 47.826 0.00 0.00 0.00 2.74
2688 10830 3.093814 TCCAAGCGTCTCTGGTATTGTA 58.906 45.455 0.00 0.00 0.00 2.41
2689 10831 1.899814 TCCAAGCGTCTCTGGTATTGT 59.100 47.619 0.00 0.00 0.00 2.71
2690 10832 2.672961 TCCAAGCGTCTCTGGTATTG 57.327 50.000 0.00 0.00 0.00 1.90
2691 10833 3.914426 AATCCAAGCGTCTCTGGTATT 57.086 42.857 0.00 0.00 0.00 1.89
2692 10834 3.914426 AAATCCAAGCGTCTCTGGTAT 57.086 42.857 0.00 0.00 0.00 2.73
2693 10835 5.353394 AATAAATCCAAGCGTCTCTGGTA 57.647 39.130 0.00 0.00 0.00 3.25
2694 10836 3.914426 ATAAATCCAAGCGTCTCTGGT 57.086 42.857 0.00 0.00 0.00 4.00
2695 10837 4.201950 CCAAATAAATCCAAGCGTCTCTGG 60.202 45.833 0.00 0.00 0.00 3.86
2799 10946 1.000955 CTACCCAGCCCATATCACGTC 59.999 57.143 0.00 0.00 0.00 4.34
2864 11029 2.555199 GCTTGTCACTTGTCAGTCAGT 58.445 47.619 0.00 0.00 0.00 3.41
2877 11042 2.434185 GTGCCCGATCGCTTGTCA 60.434 61.111 10.32 0.00 0.00 3.58
2878 11043 1.298859 AAAGTGCCCGATCGCTTGTC 61.299 55.000 10.32 0.00 36.95 3.18
2880 11045 1.135315 CAAAGTGCCCGATCGCTTG 59.865 57.895 10.32 1.09 36.95 4.01
2881 11046 0.889186 AACAAAGTGCCCGATCGCTT 60.889 50.000 10.32 4.66 38.32 4.68
2882 11047 1.302511 AACAAAGTGCCCGATCGCT 60.303 52.632 10.32 0.00 0.00 4.93
2902 11071 1.205064 CACTTTTGTGCCTCGCTCG 59.795 57.895 0.00 0.00 44.07 5.03
2924 11093 1.289109 CGGCCGCCGTAGAAATATGG 61.289 60.000 24.08 0.00 42.73 2.74
2948 11117 2.050351 CTTCACCGTCGACGTGCT 60.050 61.111 33.49 14.92 37.74 4.40
2949 11118 3.764049 GCTTCACCGTCGACGTGC 61.764 66.667 33.49 23.80 37.74 5.34
2971 11140 2.096442 TTGCAGATGAGTCGCAGCG 61.096 57.895 9.06 9.06 38.13 5.18
2981 11150 1.664016 GCAGTTTGGACGTTGCAGATG 60.664 52.381 2.87 0.00 36.59 2.90
3012 11181 1.000731 CGGCTGATTCTCCTCTCCATC 59.999 57.143 0.00 0.00 0.00 3.51
3015 11184 1.068921 GCGGCTGATTCTCCTCTCC 59.931 63.158 0.00 0.00 0.00 3.71
3016 11185 1.299773 CGCGGCTGATTCTCCTCTC 60.300 63.158 0.00 0.00 0.00 3.20
3019 11188 3.774528 TGCGCGGCTGATTCTCCT 61.775 61.111 8.83 0.00 0.00 3.69
3119 11413 3.373565 GTTTTCGCAGGGCAGGGG 61.374 66.667 0.00 0.00 0.00 4.79
3137 11431 1.131883 CAGATGCTCTGCTTTTTCCCG 59.868 52.381 1.08 0.00 37.72 5.14
3172 11466 7.418337 AAATAAAAGGTCCAGAAAGTGTTGT 57.582 32.000 0.00 0.00 0.00 3.32
3188 11482 9.297586 GTCTAGCCCGGAAAATAAAAATAAAAG 57.702 33.333 0.73 0.00 0.00 2.27
3190 11484 8.350852 TGTCTAGCCCGGAAAATAAAAATAAA 57.649 30.769 0.73 0.00 0.00 1.40
3199 11493 4.600062 AGAAAATGTCTAGCCCGGAAAAT 58.400 39.130 0.73 0.00 33.56 1.82
3205 11499 3.861840 TCAAGAGAAAATGTCTAGCCCG 58.138 45.455 0.00 0.00 36.41 6.13
3206 11500 4.633565 CACTCAAGAGAAAATGTCTAGCCC 59.366 45.833 3.73 0.00 36.41 5.19
3215 11509 2.646798 AGCCCTCCACTCAAGAGAAAAT 59.353 45.455 3.73 0.00 32.86 1.82
3220 11514 0.463620 GCTAGCCCTCCACTCAAGAG 59.536 60.000 2.29 0.00 0.00 2.85
3228 11522 1.357420 TGAAAAATGGCTAGCCCTCCA 59.643 47.619 30.81 12.95 36.70 3.86


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

AutoCloner maintained by Alex Coulton.