Multiple sequence alignment - TraesCS7A01G348800

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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 TraesCS7A01G348800 chr7A 100.000 2651 0 0 1 2651 511544512 511547162 0.000000e+00 4896
1 TraesCS7A01G348800 chr7B 90.983 1730 100 24 735 2446 437725706 437724015 0.000000e+00 2279
2 TraesCS7A01G348800 chr7B 84.672 137 13 4 2462 2597 437723964 437723835 2.140000e-26 130
3 TraesCS7A01G348800 chr7D 93.096 1434 74 10 595 2007 421447794 421446365 0.000000e+00 2076
4 TraesCS7A01G348800 chr7D 95.361 582 26 1 1 582 616450508 616451088 0.000000e+00 924
5 TraesCS7A01G348800 chr3B 96.220 582 22 0 1 582 827103938 827104519 0.000000e+00 953
6 TraesCS7A01G348800 chr3B 96.220 582 22 0 1 582 827649186 827649767 0.000000e+00 953
7 TraesCS7A01G348800 chr3B 95.385 585 24 2 1 583 822804051 822803468 0.000000e+00 928
8 TraesCS7A01G348800 chr3B 95.385 585 22 3 1 582 763008249 763008831 0.000000e+00 926
9 TraesCS7A01G348800 chr3B 95.214 585 26 1 1 583 215114216 215114800 0.000000e+00 924
10 TraesCS7A01G348800 chr3A 96.048 582 23 0 1 582 534371545 534370964 0.000000e+00 948
11 TraesCS7A01G348800 chr5A 95.556 585 24 1 1 583 708852086 708851502 0.000000e+00 935
12 TraesCS7A01G348800 chr5D 95.556 585 23 2 1 583 159652923 159653506 0.000000e+00 933


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 TraesCS7A01G348800 chr7A 511544512 511547162 2650 False 4896.0 4896 100.0000 1 2651 1 chr7A.!!$F1 2650
1 TraesCS7A01G348800 chr7B 437723835 437725706 1871 True 1204.5 2279 87.8275 735 2597 2 chr7B.!!$R1 1862
2 TraesCS7A01G348800 chr7D 421446365 421447794 1429 True 2076.0 2076 93.0960 595 2007 1 chr7D.!!$R1 1412
3 TraesCS7A01G348800 chr7D 616450508 616451088 580 False 924.0 924 95.3610 1 582 1 chr7D.!!$F1 581
4 TraesCS7A01G348800 chr3B 827103938 827104519 581 False 953.0 953 96.2200 1 582 1 chr3B.!!$F3 581
5 TraesCS7A01G348800 chr3B 827649186 827649767 581 False 953.0 953 96.2200 1 582 1 chr3B.!!$F4 581
6 TraesCS7A01G348800 chr3B 822803468 822804051 583 True 928.0 928 95.3850 1 583 1 chr3B.!!$R1 582
7 TraesCS7A01G348800 chr3B 763008249 763008831 582 False 926.0 926 95.3850 1 582 1 chr3B.!!$F2 581
8 TraesCS7A01G348800 chr3B 215114216 215114800 584 False 924.0 924 95.2140 1 583 1 chr3B.!!$F1 582
9 TraesCS7A01G348800 chr3A 534370964 534371545 581 True 948.0 948 96.0480 1 582 1 chr3A.!!$R1 581
10 TraesCS7A01G348800 chr5A 708851502 708852086 584 True 935.0 935 95.5560 1 583 1 chr5A.!!$R1 582
11 TraesCS7A01G348800 chr5D 159652923 159653506 583 False 933.0 933 95.5560 1 583 1 chr5D.!!$F1 582

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
189 190 0.039074 CGAGCATGATCCTCGTACCC 60.039 60.0 5.18 0.0 45.17 3.69 F
615 619 0.990374 AAGCCTGTCTGAAGCATCCT 59.010 50.0 0.00 0.0 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1327 1353 0.959372 TCCACGGAGTCGGAGAAGAC 60.959 60.0 4.48 0.0 41.61 3.01 R
2466 2543 1.282248 CGGTCAACCTGTACACAGCG 61.282 60.0 3.75 0.8 42.47 5.18 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
78 79 1.673009 GCCCATCGAACGGTCCAAA 60.673 57.895 0.00 0.00 0.00 3.28
144 145 2.629656 GCCATGCTCAACCTTGCGT 61.630 57.895 0.00 0.00 0.00 5.24
149 150 1.317613 TGCTCAACCTTGCGTCAATT 58.682 45.000 0.00 0.00 0.00 2.32
153 154 2.489329 CTCAACCTTGCGTCAATTGGAT 59.511 45.455 5.42 0.00 0.00 3.41
189 190 0.039074 CGAGCATGATCCTCGTACCC 60.039 60.000 5.18 0.00 45.17 3.69
469 471 2.369532 GTGGTGCCCCTCCGTATATAAA 59.630 50.000 0.00 0.00 0.00 1.40
504 506 2.526432 AGTGTCCGACTCCTACACAAT 58.474 47.619 7.49 0.00 44.68 2.71
510 512 3.949754 TCCGACTCCTACACAATTCGTAT 59.050 43.478 0.00 0.00 0.00 3.06
585 589 8.987599 AATATTCGACACAAATATAACAAGCG 57.012 30.769 0.00 0.00 30.86 4.68
586 590 5.849357 TTCGACACAAATATAACAAGCGT 57.151 34.783 0.00 0.00 0.00 5.07
587 591 5.198116 TCGACACAAATATAACAAGCGTG 57.802 39.130 0.00 0.00 0.00 5.34
588 592 4.924462 TCGACACAAATATAACAAGCGTGA 59.076 37.500 6.65 0.00 0.00 4.35
589 593 5.405873 TCGACACAAATATAACAAGCGTGAA 59.594 36.000 6.65 0.00 0.00 3.18
590 594 5.503376 CGACACAAATATAACAAGCGTGAAC 59.497 40.000 6.65 0.00 0.00 3.18
591 595 6.307031 ACACAAATATAACAAGCGTGAACA 57.693 33.333 6.65 0.00 0.00 3.18
592 596 6.908825 ACACAAATATAACAAGCGTGAACAT 58.091 32.000 6.65 0.00 0.00 2.71
593 597 7.367285 ACACAAATATAACAAGCGTGAACATT 58.633 30.769 6.65 0.00 0.00 2.71
597 601 8.910666 CAAATATAACAAGCGTGAACATTTGAA 58.089 29.630 6.65 0.00 34.39 2.69
601 605 1.609208 AGCGTGAACATTTGAAGCCT 58.391 45.000 0.00 0.00 0.00 4.58
615 619 0.990374 AAGCCTGTCTGAAGCATCCT 59.010 50.000 0.00 0.00 0.00 3.24
619 623 2.630158 CCTGTCTGAAGCATCCTTCTG 58.370 52.381 0.00 0.00 46.13 3.02
631 635 6.264841 AGCATCCTTCTGAGTTGAAATTTC 57.735 37.500 11.41 11.41 0.00 2.17
632 636 5.091431 GCATCCTTCTGAGTTGAAATTTCG 58.909 41.667 13.34 0.00 0.00 3.46
634 638 6.128282 GCATCCTTCTGAGTTGAAATTTCGTA 60.128 38.462 13.34 1.45 0.00 3.43
636 640 7.979444 TCCTTCTGAGTTGAAATTTCGTAAT 57.021 32.000 13.34 3.48 0.00 1.89
642 646 5.121142 TGAGTTGAAATTTCGTAATCGGACC 59.879 40.000 13.34 0.00 37.69 4.46
697 716 1.373497 CGTCCCTCACACAGCTCAC 60.373 63.158 0.00 0.00 0.00 3.51
944 970 2.696526 TGTCTACTTCAGTCCCCACT 57.303 50.000 0.00 0.00 0.00 4.00
982 1008 3.025978 GCAATCCCATCAGTCCATCAAA 58.974 45.455 0.00 0.00 0.00 2.69
991 1017 3.678289 TCAGTCCATCAAACACCATCTG 58.322 45.455 0.00 0.00 0.00 2.90
1018 1044 2.606213 TGGAGATCACCGCCACCA 60.606 61.111 4.63 0.00 39.94 4.17
1042 1068 3.838271 GCGGGGAGATCGACAGCA 61.838 66.667 0.00 0.00 0.00 4.41
1134 1160 2.360852 GGCAGCTCATGTGGCAGT 60.361 61.111 13.76 0.00 40.16 4.40
1160 1186 2.684843 CCAGCTCCAAGTTCAGCGC 61.685 63.158 0.00 0.00 40.84 5.92
1226 1252 1.545706 AAGAAGCTGGAGGTCGACCC 61.546 60.000 30.82 21.02 36.42 4.46
1327 1353 4.659172 TCGCAAACAGCCTGGGGG 62.659 66.667 0.00 0.00 41.38 5.40
1500 1526 2.760385 AGCCTCGAGTACCTGCCC 60.760 66.667 12.31 0.00 0.00 5.36
1562 1588 5.668471 TGACATAAGGAAGATGAAGAGCAG 58.332 41.667 0.00 0.00 0.00 4.24
1620 1646 0.171455 AGAATGCGGTCTCACTCGTC 59.829 55.000 0.00 0.00 0.00 4.20
1635 1661 1.298713 CGTCGGAGGCATCTTCTCG 60.299 63.158 0.00 0.00 32.34 4.04
1662 1688 1.450312 CAGGTGATCGGAGGCAACC 60.450 63.158 0.00 0.00 37.17 3.77
1681 1707 6.351749 GCAACCGTATTTTGTTTTGTTCATC 58.648 36.000 0.00 0.00 0.00 2.92
1717 1743 2.859165 TGAGGAGTGTCCATTTGTCC 57.141 50.000 0.00 0.00 39.61 4.02
1718 1744 2.338809 TGAGGAGTGTCCATTTGTCCT 58.661 47.619 0.00 0.00 39.61 3.85
1829 1856 2.777114 TCCATTCTCATCGGATTTGGGA 59.223 45.455 0.00 0.00 0.00 4.37
1888 1924 9.934190 CCAAATAGGACTTTTGATTTTGTTTTG 57.066 29.630 0.00 0.00 41.22 2.44
1950 1986 5.779771 TGGAATTTCAATTACTCCTTGCCTT 59.220 36.000 0.00 0.00 30.33 4.35
2019 2055 6.981762 CAGAGAACTTCTGCATATCTTTGT 57.018 37.500 0.00 0.00 46.30 2.83
2071 2108 9.661563 TTTGTATGTATGGTAAAAGTCTACAGG 57.338 33.333 0.00 0.00 0.00 4.00
2078 2115 4.906664 TGGTAAAAGTCTACAGGGTTACCA 59.093 41.667 2.98 8.62 45.00 3.25
2098 2135 5.402630 ACCAAACCATTCCTTACCAGAAAT 58.597 37.500 0.00 0.00 0.00 2.17
2102 2139 5.269554 ACCATTCCTTACCAGAAATTCCA 57.730 39.130 0.00 0.00 0.00 3.53
2111 2148 9.847224 TCCTTACCAGAAATTCCAGATAATAAC 57.153 33.333 0.00 0.00 0.00 1.89
2160 2197 9.112789 CATGTTGAGCAATGAAATTTCAATTTG 57.887 29.630 23.91 22.82 41.13 2.32
2164 2201 3.535288 GCAATGAAATTTCAATTTGCGCG 59.465 39.130 29.56 0.00 40.88 6.86
2170 2207 5.060323 TGAAATTTCAATTTGCGCGTATCAC 59.940 36.000 18.45 0.00 38.64 3.06
2173 2210 3.755965 TCAATTTGCGCGTATCACAAT 57.244 38.095 8.43 0.00 0.00 2.71
2191 2228 4.338964 CACAATCATAATGCTTACCCTGCA 59.661 41.667 0.00 0.00 44.95 4.41
2264 2303 2.614212 CGCGAGCGTTATGTGTTATTG 58.386 47.619 0.00 0.00 34.35 1.90
2286 2325 1.064803 CAGTACGTTGCAGGCAAACAA 59.935 47.619 8.47 0.00 37.70 2.83
2298 2337 4.261572 GCAGGCAAACAACAGTAATTCAGA 60.262 41.667 0.00 0.00 0.00 3.27
2333 2372 2.620242 CCAAAATTGGGCAGCATGTAC 58.380 47.619 4.18 0.00 44.70 2.90
2337 2376 2.220653 ATTGGGCAGCATGTACACTT 57.779 45.000 0.00 0.00 39.31 3.16
2361 2401 1.478654 GGTGAAGGAGAAAGTTGCCCA 60.479 52.381 0.00 0.00 0.00 5.36
2382 2422 5.864474 CCCAAGCTAGCTTATTGTATACTCG 59.136 44.000 28.87 12.15 34.50 4.18
2392 2432 6.016443 GCTTATTGTATACTCGTAGGTGGTCT 60.016 42.308 4.17 0.00 0.00 3.85
2405 2447 5.337330 CGTAGGTGGTCTAGGACAGAAAAAT 60.337 44.000 0.14 0.00 36.28 1.82
2426 2468 5.947228 ATAATAACTGATGAACATGGCCG 57.053 39.130 0.00 0.00 0.00 6.13
2439 2481 0.777446 ATGGCCGGGGCTTATTGTAT 59.223 50.000 22.12 1.65 41.60 2.29
2446 2488 2.798283 CGGGGCTTATTGTATACACACG 59.202 50.000 4.68 1.94 33.30 4.49
2447 2489 3.491276 CGGGGCTTATTGTATACACACGA 60.491 47.826 4.68 0.00 33.30 4.35
2448 2490 4.638304 GGGGCTTATTGTATACACACGAT 58.362 43.478 4.68 0.00 33.30 3.73
2450 2492 6.225318 GGGGCTTATTGTATACACACGATAA 58.775 40.000 4.68 6.34 34.83 1.75
2451 2493 6.367969 GGGGCTTATTGTATACACACGATAAG 59.632 42.308 20.91 20.91 46.64 1.73
2452 2494 6.367969 GGGCTTATTGTATACACACGATAAGG 59.632 42.308 23.80 13.35 45.32 2.69
2454 2496 7.654520 GGCTTATTGTATACACACGATAAGGAA 59.345 37.037 23.80 3.53 45.32 3.36
2455 2497 9.037737 GCTTATTGTATACACACGATAAGGAAA 57.962 33.333 23.80 3.38 45.32 3.13
2485 2563 1.282248 CGCTGTGTACAGGTTGACCG 61.282 60.000 13.41 4.05 43.94 4.79
2505 2583 2.549754 CGCCATTGATAAGGTCCATGTC 59.450 50.000 0.00 0.00 30.05 3.06
2509 2587 5.142639 CCATTGATAAGGTCCATGTCCATT 58.857 41.667 6.89 0.00 30.05 3.16
2515 2593 7.581814 TGATAAGGTCCATGTCCATTGATTTA 58.418 34.615 6.89 0.00 0.00 1.40
2517 2595 6.530019 AAGGTCCATGTCCATTGATTTAAC 57.470 37.500 6.89 0.00 0.00 2.01
2521 2599 6.601613 GGTCCATGTCCATTGATTTAACTGTA 59.398 38.462 0.00 0.00 0.00 2.74
2528 2606 7.442969 TGTCCATTGATTTAACTGTAAAGACGT 59.557 33.333 0.00 0.00 32.76 4.34
2534 2612 7.654568 TGATTTAACTGTAAAGACGTGAGAGA 58.345 34.615 0.00 0.00 32.76 3.10
2535 2613 7.808381 TGATTTAACTGTAAAGACGTGAGAGAG 59.192 37.037 0.00 0.00 32.76 3.20
2537 2615 5.769484 AACTGTAAAGACGTGAGAGAGAA 57.231 39.130 0.00 0.00 0.00 2.87
2538 2616 5.769484 ACTGTAAAGACGTGAGAGAGAAA 57.231 39.130 0.00 0.00 0.00 2.52
2539 2617 6.334102 ACTGTAAAGACGTGAGAGAGAAAT 57.666 37.500 0.00 0.00 0.00 2.17
2568 2646 6.152661 TGGAATCATTTGTAAGGTTGACCATC 59.847 38.462 2.56 0.00 38.89 3.51
2569 2647 5.818136 ATCATTTGTAAGGTTGACCATCG 57.182 39.130 2.56 0.00 38.89 3.84
2570 2648 4.647611 TCATTTGTAAGGTTGACCATCGT 58.352 39.130 2.56 0.00 38.89 3.73
2571 2649 4.693566 TCATTTGTAAGGTTGACCATCGTC 59.306 41.667 2.56 0.00 38.89 4.20
2594 2672 7.475840 GTCATGGTCAACCTTTCAATAAGATC 58.524 38.462 0.10 0.00 36.82 2.75
2597 2675 9.347240 CATGGTCAACCTTTCAATAAGATCTAT 57.653 33.333 0.00 0.00 36.82 1.98
2598 2676 9.927081 ATGGTCAACCTTTCAATAAGATCTATT 57.073 29.630 0.00 0.00 36.82 1.73
2599 2677 9.753674 TGGTCAACCTTTCAATAAGATCTATTT 57.246 29.630 0.00 0.00 36.82 1.40
2620 2698 9.740239 CTATTTGACTTTCATGACATATTTGGG 57.260 33.333 0.00 0.00 0.00 4.12
2621 2699 5.581126 TGACTTTCATGACATATTTGGGC 57.419 39.130 0.00 0.00 0.00 5.36
2622 2700 5.015515 TGACTTTCATGACATATTTGGGCA 58.984 37.500 0.00 0.00 0.00 5.36
2623 2701 5.479724 TGACTTTCATGACATATTTGGGCAA 59.520 36.000 0.00 0.00 0.00 4.52
2624 2702 6.014755 TGACTTTCATGACATATTTGGGCAAA 60.015 34.615 0.00 0.00 34.46 3.68
2625 2703 6.400568 ACTTTCATGACATATTTGGGCAAAG 58.599 36.000 0.00 0.00 33.32 2.77
2626 2704 4.389890 TCATGACATATTTGGGCAAAGC 57.610 40.909 0.00 0.00 33.32 3.51
2638 2716 3.296516 GCAAAGCCATCGAAACTCG 57.703 52.632 0.00 0.00 42.10 4.18
2639 2717 0.794605 GCAAAGCCATCGAAACTCGC 60.795 55.000 0.00 0.00 40.21 5.03
2640 2718 0.179189 CAAAGCCATCGAAACTCGCC 60.179 55.000 0.00 0.00 40.21 5.54
2641 2719 0.605319 AAAGCCATCGAAACTCGCCA 60.605 50.000 0.00 0.00 40.21 5.69
2642 2720 0.605319 AAGCCATCGAAACTCGCCAA 60.605 50.000 0.00 0.00 40.21 4.52
2643 2721 0.605319 AGCCATCGAAACTCGCCAAA 60.605 50.000 0.00 0.00 40.21 3.28
2644 2722 0.451783 GCCATCGAAACTCGCCAAAT 59.548 50.000 0.00 0.00 40.21 2.32
2645 2723 1.135402 GCCATCGAAACTCGCCAAATT 60.135 47.619 0.00 0.00 40.21 1.82
2646 2724 2.785679 CCATCGAAACTCGCCAAATTC 58.214 47.619 0.00 0.00 40.21 2.17
2647 2725 2.430956 CATCGAAACTCGCCAAATTCG 58.569 47.619 0.00 0.00 44.34 3.34
2648 2726 1.504359 TCGAAACTCGCCAAATTCGT 58.496 45.000 6.65 0.00 43.64 3.85
2649 2727 1.458064 TCGAAACTCGCCAAATTCGTC 59.542 47.619 6.65 0.00 43.64 4.20
2650 2728 1.782023 CGAAACTCGCCAAATTCGTCG 60.782 52.381 0.00 0.00 39.67 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 2.526873 ACACTTCGGGCAGGAGGT 60.527 61.111 0.00 0.00 0.00 3.85
235 236 7.960738 GCATTAGCGTTTTATTCTAACAAGTGA 59.039 33.333 0.00 0.00 0.00 3.41
469 471 2.772515 GGACACTTGTATCCTAGGCCTT 59.227 50.000 12.58 0.00 31.75 4.35
504 506 6.699366 TGTAATTGGTGTGGTTAGATACGAA 58.301 36.000 0.00 0.00 0.00 3.85
510 512 5.163184 TGGAGTTGTAATTGGTGTGGTTAGA 60.163 40.000 0.00 0.00 0.00 2.10
583 587 1.001378 ACAGGCTTCAAATGTTCACGC 60.001 47.619 0.00 0.00 0.00 5.34
584 588 2.549754 AGACAGGCTTCAAATGTTCACG 59.450 45.455 0.00 0.00 0.00 4.35
585 589 3.565482 TCAGACAGGCTTCAAATGTTCAC 59.435 43.478 0.00 0.00 0.00 3.18
586 590 3.819368 TCAGACAGGCTTCAAATGTTCA 58.181 40.909 0.00 0.00 0.00 3.18
587 591 4.791974 CTTCAGACAGGCTTCAAATGTTC 58.208 43.478 0.00 0.00 0.00 3.18
588 592 3.005155 GCTTCAGACAGGCTTCAAATGTT 59.995 43.478 0.00 0.00 0.00 2.71
589 593 2.555757 GCTTCAGACAGGCTTCAAATGT 59.444 45.455 0.00 0.00 0.00 2.71
590 594 2.555325 TGCTTCAGACAGGCTTCAAATG 59.445 45.455 0.00 0.00 0.00 2.32
591 595 2.867624 TGCTTCAGACAGGCTTCAAAT 58.132 42.857 0.00 0.00 0.00 2.32
592 596 2.346766 TGCTTCAGACAGGCTTCAAA 57.653 45.000 0.00 0.00 0.00 2.69
593 597 2.430465 GATGCTTCAGACAGGCTTCAA 58.570 47.619 0.00 0.00 32.70 2.69
597 601 0.990374 AAGGATGCTTCAGACAGGCT 59.010 50.000 0.00 0.00 0.00 4.58
601 605 2.902486 ACTCAGAAGGATGCTTCAGACA 59.098 45.455 26.36 8.07 35.91 3.41
615 619 6.647481 TCCGATTACGAAATTTCAACTCAGAA 59.353 34.615 17.99 1.87 42.66 3.02
619 623 5.121142 TGGTCCGATTACGAAATTTCAACTC 59.879 40.000 17.99 8.05 42.66 3.01
623 627 4.334203 CCATGGTCCGATTACGAAATTTCA 59.666 41.667 17.99 0.00 42.66 2.69
631 635 4.043168 GGCCATGGTCCGATTACG 57.957 61.111 14.67 0.00 39.43 3.18
642 646 4.175337 ATGGGTCGTCCGGCCATG 62.175 66.667 12.92 0.00 42.75 3.66
681 696 0.760567 ACTGTGAGCTGTGTGAGGGA 60.761 55.000 0.00 0.00 0.00 4.20
944 970 2.203470 TGCATGGCAAGAATGTGAGA 57.797 45.000 0.00 0.00 34.76 3.27
982 1008 3.359033 CCATGAATGGTTCAGATGGTGT 58.641 45.455 0.82 0.00 43.98 4.16
1023 1049 4.271816 CTGTCGATCTCCCCGCGG 62.272 72.222 21.04 21.04 0.00 6.46
1028 1054 2.501610 GGGTGCTGTCGATCTCCC 59.498 66.667 0.00 0.00 0.00 4.30
1115 1141 4.334118 TGCCACATGAGCTGCCGT 62.334 61.111 0.00 0.00 0.00 5.68
1116 1142 2.857575 TACTGCCACATGAGCTGCCG 62.858 60.000 15.42 5.32 32.91 5.69
1117 1143 1.078214 TACTGCCACATGAGCTGCC 60.078 57.895 15.42 0.00 32.91 4.85
1125 1151 1.524621 GGATGCGCTACTGCCACAT 60.525 57.895 9.73 0.00 35.86 3.21
1126 1152 2.125147 GGATGCGCTACTGCCACA 60.125 61.111 9.73 0.00 35.36 4.17
1327 1353 0.959372 TCCACGGAGTCGGAGAAGAC 60.959 60.000 4.48 0.00 41.61 3.01
1461 1487 2.444895 ATCCACTCCTCGGCCCTC 60.445 66.667 0.00 0.00 0.00 4.30
1562 1588 2.035066 TGCTTCTTCTTGGCTTTCTTGC 59.965 45.455 0.00 0.00 0.00 4.01
1620 1646 1.299773 GCTCGAGAAGATGCCTCCG 60.300 63.158 18.75 0.00 0.00 4.63
1635 1661 1.364626 CCGATCACCTGCACTTGCTC 61.365 60.000 2.33 0.00 42.66 4.26
1662 1688 5.797909 TGCGATGAACAAAACAAAATACG 57.202 34.783 0.00 0.00 0.00 3.06
1665 1691 6.764094 GCATATGCGATGAACAAAACAAAAT 58.236 32.000 12.82 0.00 0.00 1.82
1717 1743 3.544684 TGCAGCTTATGAACCACCATAG 58.455 45.455 0.00 0.00 31.42 2.23
1718 1744 3.643199 TGCAGCTTATGAACCACCATA 57.357 42.857 0.00 0.00 0.00 2.74
1847 1874 4.227527 CCTATTTGGAAGGTAAGGTCCTGT 59.772 45.833 0.00 0.00 37.93 4.00
1849 1876 4.706616 TCCTATTTGGAAGGTAAGGTCCT 58.293 43.478 0.00 0.00 42.94 3.85
1888 1924 4.560427 GCTAACAGAAAGCAAGCATTAAGC 59.440 41.667 0.00 0.00 40.88 3.09
1950 1986 3.198068 GCATGCGAATAGAAGTCCAAGA 58.802 45.455 0.00 0.00 0.00 3.02
2025 2061 7.660030 ACAAAAGAATGTATGATAAAGGGGG 57.340 36.000 0.00 0.00 0.00 5.40
2078 2115 6.081356 TGGAATTTCTGGTAAGGAATGGTTT 58.919 36.000 0.00 0.00 31.48 3.27
2098 2135 9.679661 TTTAGCATTGAGTGTTATTATCTGGAA 57.320 29.630 0.00 0.00 0.00 3.53
2140 2177 4.784550 GCGCAAATTGAAATTTCATTGCTC 59.215 37.500 34.42 29.18 44.71 4.26
2142 2179 3.535288 CGCGCAAATTGAAATTTCATTGC 59.465 39.130 31.52 31.52 44.03 3.56
2160 2197 3.120546 AGCATTATGATTGTGATACGCGC 60.121 43.478 5.73 0.00 0.00 6.86
2164 2201 7.573843 GCAGGGTAAGCATTATGATTGTGATAC 60.574 40.741 5.92 0.00 30.46 2.24
2170 2207 5.508489 CCTTGCAGGGTAAGCATTATGATTG 60.508 44.000 6.72 0.00 42.33 2.67
2173 2210 3.554934 CCTTGCAGGGTAAGCATTATGA 58.445 45.455 6.72 0.00 42.33 2.15
2244 2283 2.596575 CCAATAACACATAACGCTCGCG 60.597 50.000 10.06 10.06 46.03 5.87
2259 2298 2.080693 CCTGCAACGTACTGCCAATAA 58.919 47.619 9.62 0.00 41.90 1.40
2264 2303 1.791103 TTTGCCTGCAACGTACTGCC 61.791 55.000 9.62 0.00 41.90 4.85
2286 2325 7.177216 TGGATTGCTTTCATTCTGAATTACTGT 59.823 33.333 0.00 0.00 36.11 3.55
2298 2337 5.474189 CCAATTTTGGTGGATTGCTTTCATT 59.526 36.000 0.95 0.00 43.43 2.57
2333 2372 4.392940 ACTTTCTCCTTCACCATCAAGTG 58.607 43.478 0.00 0.00 39.20 3.16
2337 2376 3.149196 GCAACTTTCTCCTTCACCATCA 58.851 45.455 0.00 0.00 0.00 3.07
2361 2401 7.447853 ACCTACGAGTATACAATAAGCTAGCTT 59.552 37.037 31.38 31.38 39.83 3.74
2382 2422 5.479124 TTTTTCTGTCCTAGACCACCTAC 57.521 43.478 0.00 0.00 34.43 3.18
2405 2447 4.133820 CCGGCCATGTTCATCAGTTATTA 58.866 43.478 2.24 0.00 0.00 0.98
2426 2468 4.062677 TCGTGTGTATACAATAAGCCCC 57.937 45.455 7.25 0.00 38.82 5.80
2454 2496 7.878036 ACCTGTACACAGCGTTTATTATTTTT 58.122 30.769 3.75 0.00 42.47 1.94
2455 2497 7.443259 ACCTGTACACAGCGTTTATTATTTT 57.557 32.000 3.75 0.00 42.47 1.82
2457 2499 6.651643 TCAACCTGTACACAGCGTTTATTATT 59.348 34.615 3.75 0.00 42.47 1.40
2458 2500 6.091713 GTCAACCTGTACACAGCGTTTATTAT 59.908 38.462 3.75 0.00 42.47 1.28
2460 2502 4.212636 GTCAACCTGTACACAGCGTTTATT 59.787 41.667 3.75 0.00 42.47 1.40
2466 2543 1.282248 CGGTCAACCTGTACACAGCG 61.282 60.000 3.75 0.80 42.47 5.18
2475 2552 2.036958 TATCAATGGCGGTCAACCTG 57.963 50.000 0.00 0.00 0.00 4.00
2485 2563 2.887152 GGACATGGACCTTATCAATGGC 59.113 50.000 0.00 0.00 45.44 4.40
2505 2583 7.802738 TCACGTCTTTACAGTTAAATCAATGG 58.197 34.615 0.00 0.00 0.00 3.16
2509 2587 7.654568 TCTCTCACGTCTTTACAGTTAAATCA 58.345 34.615 0.00 0.00 0.00 2.57
2515 2593 5.769484 TTCTCTCTCACGTCTTTACAGTT 57.231 39.130 0.00 0.00 0.00 3.16
2517 2595 6.642950 ACAATTTCTCTCTCACGTCTTTACAG 59.357 38.462 0.00 0.00 0.00 2.74
2521 2599 5.237344 CCAACAATTTCTCTCTCACGTCTTT 59.763 40.000 0.00 0.00 0.00 2.52
2528 2606 8.301720 CAAATGATTCCAACAATTTCTCTCTCA 58.698 33.333 0.00 0.00 0.00 3.27
2534 2612 8.650490 ACCTTACAAATGATTCCAACAATTTCT 58.350 29.630 0.00 0.00 0.00 2.52
2535 2613 8.831715 ACCTTACAAATGATTCCAACAATTTC 57.168 30.769 0.00 0.00 0.00 2.17
2537 2615 8.428063 TCAACCTTACAAATGATTCCAACAATT 58.572 29.630 0.00 0.00 0.00 2.32
2538 2616 7.872483 GTCAACCTTACAAATGATTCCAACAAT 59.128 33.333 0.00 0.00 0.00 2.71
2539 2617 7.206687 GTCAACCTTACAAATGATTCCAACAA 58.793 34.615 0.00 0.00 0.00 2.83
2568 2646 5.411361 TCTTATTGAAAGGTTGACCATGACG 59.589 40.000 2.56 0.00 38.89 4.35
2569 2647 6.817765 TCTTATTGAAAGGTTGACCATGAC 57.182 37.500 2.56 0.00 38.89 3.06
2570 2648 7.405292 AGATCTTATTGAAAGGTTGACCATGA 58.595 34.615 2.56 0.00 38.89 3.07
2571 2649 7.636150 AGATCTTATTGAAAGGTTGACCATG 57.364 36.000 2.56 0.00 38.89 3.66
2572 2650 9.927081 AATAGATCTTATTGAAAGGTTGACCAT 57.073 29.630 0.00 0.00 38.89 3.55
2573 2651 9.753674 AAATAGATCTTATTGAAAGGTTGACCA 57.246 29.630 0.00 0.00 38.89 4.02
2594 2672 9.740239 CCCAAATATGTCATGAAAGTCAAATAG 57.260 33.333 0.00 0.00 0.00 1.73
2597 2675 6.014755 TGCCCAAATATGTCATGAAAGTCAAA 60.015 34.615 0.00 0.00 0.00 2.69
2598 2676 5.479724 TGCCCAAATATGTCATGAAAGTCAA 59.520 36.000 0.00 0.00 0.00 3.18
2599 2677 5.015515 TGCCCAAATATGTCATGAAAGTCA 58.984 37.500 0.00 0.00 0.00 3.41
2600 2678 5.581126 TGCCCAAATATGTCATGAAAGTC 57.419 39.130 0.00 0.00 0.00 3.01
2601 2679 5.999205 TTGCCCAAATATGTCATGAAAGT 57.001 34.783 0.00 0.00 0.00 2.66
2602 2680 5.292589 GCTTTGCCCAAATATGTCATGAAAG 59.707 40.000 0.00 0.00 0.00 2.62
2603 2681 5.177326 GCTTTGCCCAAATATGTCATGAAA 58.823 37.500 0.00 0.00 0.00 2.69
2604 2682 4.382901 GGCTTTGCCCAAATATGTCATGAA 60.383 41.667 0.00 0.00 44.06 2.57
2605 2683 3.132646 GGCTTTGCCCAAATATGTCATGA 59.867 43.478 0.00 0.00 44.06 3.07
2606 2684 3.460103 GGCTTTGCCCAAATATGTCATG 58.540 45.455 0.00 0.00 44.06 3.07
2607 2685 3.825143 GGCTTTGCCCAAATATGTCAT 57.175 42.857 0.00 0.00 44.06 3.06
2618 2696 3.452681 CGAGTTTCGATGGCTTTGCCC 62.453 57.143 6.10 0.00 45.50 5.36
2619 2697 0.179189 CGAGTTTCGATGGCTTTGCC 60.179 55.000 1.01 1.01 45.99 4.52
2620 2698 0.794605 GCGAGTTTCGATGGCTTTGC 60.795 55.000 2.20 0.00 43.74 3.68
2621 2699 0.179189 GGCGAGTTTCGATGGCTTTG 60.179 55.000 2.20 0.00 43.74 2.77
2622 2700 0.605319 TGGCGAGTTTCGATGGCTTT 60.605 50.000 2.20 0.00 43.74 3.51
2623 2701 0.605319 TTGGCGAGTTTCGATGGCTT 60.605 50.000 2.20 0.00 43.74 4.35
2624 2702 0.605319 TTTGGCGAGTTTCGATGGCT 60.605 50.000 2.20 0.00 43.74 4.75
2625 2703 0.451783 ATTTGGCGAGTTTCGATGGC 59.548 50.000 2.20 0.00 43.74 4.40
2626 2704 2.785679 GAATTTGGCGAGTTTCGATGG 58.214 47.619 2.20 0.00 43.74 3.51
2627 2705 2.159707 ACGAATTTGGCGAGTTTCGATG 60.160 45.455 21.52 1.99 43.74 3.84
2628 2706 2.073816 ACGAATTTGGCGAGTTTCGAT 58.926 42.857 21.52 8.85 43.74 3.59
2629 2707 1.458064 GACGAATTTGGCGAGTTTCGA 59.542 47.619 21.52 0.00 43.74 3.71
2630 2708 1.782023 CGACGAATTTGGCGAGTTTCG 60.782 52.381 16.40 16.01 44.73 3.46
2631 2709 1.865725 CGACGAATTTGGCGAGTTTC 58.134 50.000 16.40 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.