Multiple sequence alignment - TraesCS1D01G233900

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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 TraesCS1D01G233900 chr1D 100.000 2956 0 0 1 2956 322261437 322264392 0.000000e+00 5459.0
1 TraesCS1D01G233900 chr1D 89.610 77 5 2 1374 1447 322165243 322165319 8.720000e-16 95.3
2 TraesCS1D01G233900 chr1A 91.418 1340 38 33 586 1874 406142490 406143803 0.000000e+00 1766.0
3 TraesCS1D01G233900 chr1A 89.756 615 57 4 2341 2950 406144581 406145194 0.000000e+00 782.0
4 TraesCS1D01G233900 chr1A 84.582 467 38 14 1882 2341 406144116 406144555 1.630000e-117 433.0
5 TraesCS1D01G233900 chr1A 88.696 345 22 10 240 583 406142209 406142537 3.550000e-109 405.0
6 TraesCS1D01G233900 chr1A 83.264 239 15 16 1 215 406141973 406142210 2.320000e-46 196.0
7 TraesCS1D01G233900 chr1A 93.939 66 4 0 1382 1447 405869121 405869186 1.870000e-17 100.0
8 TraesCS1D01G233900 chr1B 88.472 1414 100 30 968 2341 435042588 435043978 0.000000e+00 1650.0
9 TraesCS1D01G233900 chr1B 89.744 585 55 5 2341 2923 435044005 435044586 0.000000e+00 743.0
10 TraesCS1D01G233900 chr1B 89.157 415 26 6 161 573 435041744 435042141 1.580000e-137 499.0
11 TraesCS1D01G233900 chr1B 89.610 77 5 3 1374 1447 434835515 434835591 8.720000e-16 95.3


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 TraesCS1D01G233900 chr1D 322261437 322264392 2955 False 5459.0 5459 100.000000 1 2956 1 chr1D.!!$F2 2955
1 TraesCS1D01G233900 chr1A 406141973 406145194 3221 False 716.4 1766 87.543200 1 2950 5 chr1A.!!$F2 2949
2 TraesCS1D01G233900 chr1B 435041744 435044586 2842 False 964.0 1650 89.124333 161 2923 3 chr1B.!!$F2 2762

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
261 287 0.039035 GGTCAGGGCCCAACACATAA 59.961 55.000 27.56 0.0 0.00 1.90 F
1848 2132 1.147824 AGCTCCATATGCTTGCGCT 59.852 52.632 9.73 0.0 37.52 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 2503 0.327924 TCCATGTACCTGTGGGCTTG 59.672 55.0 8.61 0.0 36.15 4.01 R
2863 3499 0.251297 CCACCAAGGAGACCAATGCA 60.251 55.0 0.00 0.0 41.22 3.96 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
28 34 2.208431 CCTCAATCTCAATGAGTCGCC 58.792 52.381 10.36 0.00 42.19 5.54
31 37 1.148157 AATCTCAATGAGTCGCCGCG 61.148 55.000 10.36 6.39 0.00 6.46
35 41 4.373116 AATGAGTCGCCGCGGTGT 62.373 61.111 35.52 20.12 0.00 4.16
36 42 4.796231 ATGAGTCGCCGCGGTGTC 62.796 66.667 35.52 30.34 0.00 3.67
52 58 3.741344 CGGTGTCTGGTTCTTAAACAGAG 59.259 47.826 7.62 0.00 37.10 3.35
56 62 4.100963 TGTCTGGTTCTTAAACAGAGAGCA 59.899 41.667 7.62 0.75 37.10 4.26
93 100 3.961480 GCCCTTGGCCATAATTAATCC 57.039 47.619 6.09 0.00 44.06 3.01
95 102 3.006859 GCCCTTGGCCATAATTAATCCAC 59.993 47.826 6.09 0.00 44.06 4.02
96 103 4.482990 CCCTTGGCCATAATTAATCCACT 58.517 43.478 6.09 0.00 0.00 4.00
97 104 5.640147 CCCTTGGCCATAATTAATCCACTA 58.360 41.667 6.09 0.00 0.00 2.74
98 105 5.711976 CCCTTGGCCATAATTAATCCACTAG 59.288 44.000 6.09 0.00 0.00 2.57
99 106 5.711976 CCTTGGCCATAATTAATCCACTAGG 59.288 44.000 6.09 0.07 0.00 3.02
100 107 5.922960 TGGCCATAATTAATCCACTAGGT 57.077 39.130 0.00 0.00 35.89 3.08
101 108 6.274322 TGGCCATAATTAATCCACTAGGTT 57.726 37.500 0.00 0.00 35.89 3.50
102 109 7.395525 TGGCCATAATTAATCCACTAGGTTA 57.604 36.000 0.00 0.00 35.89 2.85
103 110 7.228590 TGGCCATAATTAATCCACTAGGTTAC 58.771 38.462 0.00 0.00 35.89 2.50
105 112 7.888546 GGCCATAATTAATCCACTAGGTTACAT 59.111 37.037 0.00 0.00 35.89 2.29
122 139 5.357596 GGTTACATTAGAGAACTCGAGGAGT 59.642 44.000 18.41 0.71 45.64 3.85
223 248 3.134081 GTCCTCGTCCCTCCATTATTTCA 59.866 47.826 0.00 0.00 0.00 2.69
230 255 5.126779 GTCCCTCCATTATTTCAGGAAGAC 58.873 45.833 0.00 0.00 31.62 3.01
232 257 4.464947 CCTCCATTATTTCAGGAAGACCC 58.535 47.826 0.00 0.00 36.73 4.46
256 282 3.579302 CCTGGTCAGGGCCCAACA 61.579 66.667 27.56 12.86 44.87 3.33
257 283 2.282462 CTGGTCAGGGCCCAACAC 60.282 66.667 27.56 16.88 0.00 3.32
258 284 3.099841 TGGTCAGGGCCCAACACA 61.100 61.111 27.56 17.52 0.00 3.72
259 285 2.430704 CTGGTCAGGGCCCAACACAT 62.431 60.000 27.56 0.00 0.00 3.21
260 286 1.136961 TGGTCAGGGCCCAACACATA 61.137 55.000 27.56 7.18 0.00 2.29
261 287 0.039035 GGTCAGGGCCCAACACATAA 59.961 55.000 27.56 0.00 0.00 1.90
262 288 1.549037 GGTCAGGGCCCAACACATAAA 60.549 52.381 27.56 0.00 0.00 1.40
263 289 1.818674 GTCAGGGCCCAACACATAAAG 59.181 52.381 27.56 0.00 0.00 1.85
264 290 1.427368 TCAGGGCCCAACACATAAAGT 59.573 47.619 27.56 0.00 0.00 2.66
265 291 2.158385 TCAGGGCCCAACACATAAAGTT 60.158 45.455 27.56 0.00 0.00 2.66
266 292 2.632512 CAGGGCCCAACACATAAAGTTT 59.367 45.455 27.56 0.00 0.00 2.66
267 293 3.070878 CAGGGCCCAACACATAAAGTTTT 59.929 43.478 27.56 0.00 0.00 2.43
268 294 4.282195 CAGGGCCCAACACATAAAGTTTTA 59.718 41.667 27.56 0.00 0.00 1.52
309 335 4.202141 CCACGGTTACTCGGTATCCATAAA 60.202 45.833 10.08 0.00 30.62 1.40
352 378 6.547141 TGGATCGAATTTTTCATTGCCTAGAT 59.453 34.615 0.00 0.00 0.00 1.98
353 379 7.719193 TGGATCGAATTTTTCATTGCCTAGATA 59.281 33.333 0.00 0.00 0.00 1.98
354 380 8.017946 GGATCGAATTTTTCATTGCCTAGATAC 58.982 37.037 0.00 0.00 0.00 2.24
355 381 8.682936 ATCGAATTTTTCATTGCCTAGATACT 57.317 30.769 0.00 0.00 0.00 2.12
356 382 9.778741 ATCGAATTTTTCATTGCCTAGATACTA 57.221 29.630 0.00 0.00 0.00 1.82
357 383 9.261180 TCGAATTTTTCATTGCCTAGATACTAG 57.739 33.333 0.00 0.00 0.00 2.57
375 401 4.487019 ACTAGAGTAGAAAACTTGCGCTC 58.513 43.478 9.73 0.00 39.07 5.03
442 468 6.128661 CGTTTTCTCTTCGTCCATGATTTGTA 60.129 38.462 0.00 0.00 0.00 2.41
492 518 1.730121 CGTGGCAGTGCAATGAATCAC 60.730 52.381 20.00 19.20 0.00 3.06
583 609 4.625742 GCGTAGTATTGAAGACAGAAGCAA 59.374 41.667 0.00 0.00 0.00 3.91
584 610 5.292101 GCGTAGTATTGAAGACAGAAGCAAT 59.708 40.000 0.00 0.00 35.38 3.56
585 611 6.700020 CGTAGTATTGAAGACAGAAGCAATG 58.300 40.000 0.00 0.00 33.45 2.82
586 612 6.531594 CGTAGTATTGAAGACAGAAGCAATGA 59.468 38.462 0.00 0.00 33.45 2.57
587 613 7.223582 CGTAGTATTGAAGACAGAAGCAATGAT 59.776 37.037 0.00 0.00 33.45 2.45
588 614 7.551035 AGTATTGAAGACAGAAGCAATGATC 57.449 36.000 0.00 0.00 33.45 2.92
589 615 4.934075 TTGAAGACAGAAGCAATGATCG 57.066 40.909 0.00 0.00 0.00 3.69
590 616 2.674852 TGAAGACAGAAGCAATGATCGC 59.325 45.455 0.00 0.00 0.00 4.58
591 617 2.391616 AGACAGAAGCAATGATCGCA 57.608 45.000 0.00 0.00 0.00 5.10
592 618 2.703416 AGACAGAAGCAATGATCGCAA 58.297 42.857 0.00 0.00 0.00 4.85
593 619 3.276857 AGACAGAAGCAATGATCGCAAT 58.723 40.909 0.00 0.00 0.00 3.56
594 620 3.311871 AGACAGAAGCAATGATCGCAATC 59.688 43.478 0.00 0.00 0.00 2.67
595 621 3.276857 ACAGAAGCAATGATCGCAATCT 58.723 40.909 0.00 0.00 32.75 2.40
596 622 4.445453 ACAGAAGCAATGATCGCAATCTA 58.555 39.130 0.00 0.00 32.75 1.98
597 623 4.877823 ACAGAAGCAATGATCGCAATCTAA 59.122 37.500 0.00 0.00 32.75 2.10
598 624 5.203370 CAGAAGCAATGATCGCAATCTAAC 58.797 41.667 0.00 0.00 32.75 2.34
599 625 4.877823 AGAAGCAATGATCGCAATCTAACA 59.122 37.500 0.00 0.00 32.75 2.41
600 626 5.530171 AGAAGCAATGATCGCAATCTAACAT 59.470 36.000 0.00 0.00 32.75 2.71
601 627 6.707608 AGAAGCAATGATCGCAATCTAACATA 59.292 34.615 0.00 0.00 32.75 2.29
602 628 6.866010 AGCAATGATCGCAATCTAACATAA 57.134 33.333 0.00 0.00 32.75 1.90
603 629 7.263100 AGCAATGATCGCAATCTAACATAAA 57.737 32.000 0.00 0.00 32.75 1.40
604 630 7.879070 AGCAATGATCGCAATCTAACATAAAT 58.121 30.769 0.00 0.00 32.75 1.40
605 631 7.806487 AGCAATGATCGCAATCTAACATAAATG 59.194 33.333 0.00 0.00 32.75 2.32
606 632 7.410087 GCAATGATCGCAATCTAACATAAATGC 60.410 37.037 0.00 0.00 32.75 3.56
607 633 6.000891 TGATCGCAATCTAACATAAATGCC 57.999 37.500 0.00 0.00 32.75 4.40
608 634 5.530543 TGATCGCAATCTAACATAAATGCCA 59.469 36.000 0.00 0.00 32.75 4.92
609 635 5.168526 TCGCAATCTAACATAAATGCCAC 57.831 39.130 0.00 0.00 0.00 5.01
610 636 3.968096 CGCAATCTAACATAAATGCCACG 59.032 43.478 0.00 0.00 0.00 4.94
611 637 3.730715 GCAATCTAACATAAATGCCACGC 59.269 43.478 0.00 0.00 0.00 5.34
612 638 4.733230 GCAATCTAACATAAATGCCACGCA 60.733 41.667 0.00 0.00 44.86 5.24
613 639 5.339177 CAATCTAACATAAATGCCACGCAA 58.661 37.500 0.00 0.00 43.62 4.85
614 640 5.772825 ATCTAACATAAATGCCACGCAAT 57.227 34.783 0.00 0.00 43.62 3.56
615 641 5.168526 TCTAACATAAATGCCACGCAATC 57.831 39.130 0.00 0.00 43.62 2.67
616 642 4.881273 TCTAACATAAATGCCACGCAATCT 59.119 37.500 0.00 0.00 43.62 2.40
617 643 6.052360 TCTAACATAAATGCCACGCAATCTA 58.948 36.000 0.00 0.00 43.62 1.98
618 644 5.574891 AACATAAATGCCACGCAATCTAA 57.425 34.783 0.00 0.00 43.62 2.10
619 645 4.920376 ACATAAATGCCACGCAATCTAAC 58.080 39.130 0.00 0.00 43.62 2.34
620 646 4.397730 ACATAAATGCCACGCAATCTAACA 59.602 37.500 0.00 0.00 43.62 2.41
621 647 5.067674 ACATAAATGCCACGCAATCTAACAT 59.932 36.000 0.00 0.00 43.62 2.71
622 648 6.262049 ACATAAATGCCACGCAATCTAACATA 59.738 34.615 0.00 0.00 43.62 2.29
623 649 5.574891 AAATGCCACGCAATCTAACATAA 57.425 34.783 0.00 0.00 43.62 1.90
624 650 4.818534 ATGCCACGCAATCTAACATAAG 57.181 40.909 0.00 0.00 43.62 1.73
716 937 3.596310 TGCAGCATAAAATGTGCACAT 57.404 38.095 26.61 26.61 44.87 3.21
758 979 4.914312 TGCACATTTTAGCACGTACTAC 57.086 40.909 0.00 0.00 35.51 2.73
849 1076 7.452562 ACATAATTTTGAATGATTATGCCCCC 58.547 34.615 15.69 0.00 44.38 5.40
994 1235 6.767524 ACCGGCATTTAGACATAATCAAAA 57.232 33.333 0.00 0.00 0.00 2.44
1120 1365 2.422597 AGCCATATCTCGTCTCTCTCG 58.577 52.381 0.00 0.00 0.00 4.04
1464 1741 2.184322 GCATGAACGAGAGCGGGA 59.816 61.111 0.00 0.00 43.17 5.14
1718 2001 4.773117 GGAGTCGTCACGCCGTCC 62.773 72.222 0.00 0.00 32.15 4.79
1719 2002 4.773117 GAGTCGTCACGCCGTCCC 62.773 72.222 0.00 0.00 0.00 4.46
1749 2032 4.382147 GGAAAGTTTGACTCTCTATCGCCT 60.382 45.833 0.00 0.00 0.00 5.52
1838 2122 1.480954 GTCACGGAGGAAAGCTCCATA 59.519 52.381 0.00 0.00 45.24 2.74
1839 2123 2.103263 GTCACGGAGGAAAGCTCCATAT 59.897 50.000 0.00 0.00 45.24 1.78
1848 2132 1.147824 AGCTCCATATGCTTGCGCT 59.852 52.632 9.73 0.00 37.52 5.92
1935 2525 0.840288 AGCCCACAGGTACATGGACA 60.840 55.000 10.99 0.00 38.93 4.02
2072 2669 3.619038 GCAATGCCGCTAGAGGTTATATC 59.381 47.826 14.51 0.00 0.00 1.63
2085 2682 5.364157 AGAGGTTATATCTGCGGTCTTTCTT 59.636 40.000 0.00 0.00 0.00 2.52
2111 2708 6.147821 CACTGGATCAGAGTGTAATTCGTTTT 59.852 38.462 13.51 0.00 36.79 2.43
2151 2753 1.511850 TGAATATCATGGCTTCGGCG 58.488 50.000 0.00 0.00 42.91 6.46
2153 2755 1.728971 GAATATCATGGCTTCGGCGAG 59.271 52.381 10.46 5.82 42.91 5.03
2166 2768 2.227194 TCGGCGAGTTAGATGCTATGA 58.773 47.619 4.99 0.00 0.00 2.15
2175 2777 7.244192 CGAGTTAGATGCTATGATGATACGAA 58.756 38.462 0.00 0.00 0.00 3.85
2213 2815 3.854437 TCTCTGATCCTATGGCATCTGT 58.146 45.455 1.65 0.00 0.00 3.41
2233 2835 7.275697 TCTGTGCAATTTTTGTATTTATGCG 57.724 32.000 0.00 0.00 35.18 4.73
2260 2862 4.170468 TCCAAACTCTCTGAAGGCTTTT 57.830 40.909 0.00 0.00 0.00 2.27
2262 2864 4.140536 CCAAACTCTCTGAAGGCTTTTCT 58.859 43.478 0.00 0.00 0.00 2.52
2304 2908 1.694696 GGGCCGTTGGATCTAAGATCT 59.305 52.381 0.00 0.00 0.00 2.75
2347 2978 1.135527 TCTATGGTGCGGGAAGTAACG 59.864 52.381 0.00 0.00 0.00 3.18
2394 3025 1.470098 ACAGCATCTCCAAACGCAATC 59.530 47.619 0.00 0.00 0.00 2.67
2406 3037 0.816018 ACGCAATCACCAAACGGACA 60.816 50.000 0.00 0.00 0.00 4.02
2419 3050 2.511900 GGACACCCCAAACGTCCA 59.488 61.111 2.98 0.00 46.98 4.02
2452 3083 3.508840 GCGAAGGCCATCCAACCG 61.509 66.667 5.01 0.00 33.74 4.44
2459 3090 1.202952 AGGCCATCCAACCGTGTTTTA 60.203 47.619 5.01 0.00 33.74 1.52
2460 3091 1.068125 GGCCATCCAACCGTGTTTTAC 60.068 52.381 0.00 0.00 0.00 2.01
2499 3131 8.713737 TCAAATGATGAAAACACAAATTGTGA 57.286 26.923 30.09 9.82 42.23 3.58
2643 3278 0.750850 GCGGGCAGTGACCTATTAGA 59.249 55.000 14.67 0.00 0.00 2.10
2673 3308 2.436646 GGCCACATGGACCGTCAG 60.437 66.667 0.87 0.00 37.19 3.51
2708 3344 0.311790 CATTGTTGCTGTTGACGCCT 59.688 50.000 0.00 0.00 0.00 5.52
2709 3345 1.535028 CATTGTTGCTGTTGACGCCTA 59.465 47.619 0.00 0.00 0.00 3.93
2719 3355 1.549243 TTGACGCCTAGGATGCCACA 61.549 55.000 14.75 3.06 0.00 4.17
2722 3358 2.735772 CGCCTAGGATGCCACAGGT 61.736 63.158 14.75 0.00 32.61 4.00
2726 3362 0.249489 CTAGGATGCCACAGGTACGC 60.249 60.000 0.00 0.00 0.00 4.42
2727 3363 0.973496 TAGGATGCCACAGGTACGCA 60.973 55.000 0.00 0.00 36.84 5.24
2762 3398 0.250640 CCAGCCTCTGTGTTGCTTCT 60.251 55.000 0.00 0.00 31.77 2.85
2765 3401 0.601311 GCCTCTGTGTTGCTTCTCGT 60.601 55.000 0.00 0.00 0.00 4.18
2844 3480 2.415010 CGAGGAGGAGGACGCATG 59.585 66.667 0.00 0.00 0.00 4.06
2936 3572 1.378124 CCCCTCGTCGGAGAGAACTC 61.378 65.000 9.16 0.00 43.27 3.01
2942 3578 0.612453 GTCGGAGAGAACTCAGGGGT 60.612 60.000 4.64 0.00 44.22 4.95
2950 3586 4.701437 ACTCAGGGGTGGGGCCAT 62.701 66.667 4.39 0.00 39.65 4.40
2951 3587 3.350163 CTCAGGGGTGGGGCCATT 61.350 66.667 4.39 0.00 39.65 3.16
2952 3588 3.667217 CTCAGGGGTGGGGCCATTG 62.667 68.421 4.39 0.00 39.65 2.82
2953 3589 4.783501 CAGGGGTGGGGCCATTGG 62.784 72.222 4.39 0.00 39.65 3.16
2955 3591 3.766096 GGGGTGGGGCCATTGGAT 61.766 66.667 6.95 0.00 39.65 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.148157 CGCGGCGACTCATTGAGATT 61.148 55.000 19.16 0.00 33.32 2.40
14 15 2.202610 CGCGGCGACTCATTGAGA 60.203 61.111 19.16 0.00 33.32 3.27
15 16 3.257561 CCGCGGCGACTCATTGAG 61.258 66.667 25.92 12.17 35.52 3.02
16 17 4.063967 ACCGCGGCGACTCATTGA 62.064 61.111 28.58 0.00 0.00 2.57
18 19 4.373116 ACACCGCGGCGACTCATT 62.373 61.111 28.58 0.00 0.00 2.57
28 34 1.193874 GTTTAAGAACCAGACACCGCG 59.806 52.381 0.00 0.00 0.00 6.46
31 37 4.957296 TCTCTGTTTAAGAACCAGACACC 58.043 43.478 0.00 0.00 33.37 4.16
35 41 4.345257 AGTGCTCTCTGTTTAAGAACCAGA 59.655 41.667 0.00 0.00 33.37 3.86
36 42 4.636249 AGTGCTCTCTGTTTAAGAACCAG 58.364 43.478 0.00 0.00 33.37 4.00
56 62 1.361668 GGCATCGCACGTCATCAAGT 61.362 55.000 0.00 0.00 0.00 3.16
92 99 6.318144 TCGAGTTCTCTAATGTAACCTAGTGG 59.682 42.308 0.00 0.00 39.83 4.00
93 100 7.317842 TCGAGTTCTCTAATGTAACCTAGTG 57.682 40.000 0.00 0.00 0.00 2.74
95 102 6.766944 TCCTCGAGTTCTCTAATGTAACCTAG 59.233 42.308 12.31 0.00 0.00 3.02
96 103 6.656902 TCCTCGAGTTCTCTAATGTAACCTA 58.343 40.000 12.31 0.00 0.00 3.08
97 104 5.507637 TCCTCGAGTTCTCTAATGTAACCT 58.492 41.667 12.31 0.00 0.00 3.50
98 105 5.357596 ACTCCTCGAGTTCTCTAATGTAACC 59.642 44.000 12.31 0.00 40.28 2.85
99 106 6.439675 ACTCCTCGAGTTCTCTAATGTAAC 57.560 41.667 12.31 0.00 40.28 2.50
100 107 7.337167 AGTACTCCTCGAGTTCTCTAATGTAA 58.663 38.462 12.31 0.00 40.28 2.41
101 108 6.887013 AGTACTCCTCGAGTTCTCTAATGTA 58.113 40.000 12.31 0.00 40.28 2.29
102 109 5.747342 AGTACTCCTCGAGTTCTCTAATGT 58.253 41.667 12.31 0.00 40.28 2.71
103 110 6.987992 ACTAGTACTCCTCGAGTTCTCTAATG 59.012 42.308 12.31 0.00 40.28 1.90
105 112 6.339730 CACTAGTACTCCTCGAGTTCTCTAA 58.660 44.000 12.31 0.00 40.28 2.10
149 174 9.048446 GCACCGTCCTATACTATTATTCAAAAA 57.952 33.333 0.00 0.00 0.00 1.94
223 248 1.791230 AGGTAGCCTGGGTCTTCCT 59.209 57.895 0.00 6.53 36.20 3.36
244 270 1.427368 ACTTTATGTGTTGGGCCCTGA 59.573 47.619 25.70 9.11 0.00 3.86
255 281 9.997482 AGTGTAACACTGTTAAAACTTTATGTG 57.003 29.630 3.10 0.00 43.63 3.21
260 286 9.401873 GTCAAAGTGTAACACTGTTAAAACTTT 57.598 29.630 23.35 23.35 44.62 2.66
261 287 8.024865 GGTCAAAGTGTAACACTGTTAAAACTT 58.975 33.333 17.74 17.74 44.62 2.66
262 288 7.175293 TGGTCAAAGTGTAACACTGTTAAAACT 59.825 33.333 3.10 7.70 44.62 2.66
263 289 7.271868 GTGGTCAAAGTGTAACACTGTTAAAAC 59.728 37.037 3.10 5.74 44.62 2.43
264 290 7.306953 GTGGTCAAAGTGTAACACTGTTAAAA 58.693 34.615 3.10 0.00 44.62 1.52
265 291 6.402334 CGTGGTCAAAGTGTAACACTGTTAAA 60.402 38.462 3.10 0.00 44.62 1.52
266 292 5.063691 CGTGGTCAAAGTGTAACACTGTTAA 59.936 40.000 3.10 0.00 44.62 2.01
267 293 4.567558 CGTGGTCAAAGTGTAACACTGTTA 59.432 41.667 0.00 0.00 44.62 2.41
268 294 3.372822 CGTGGTCAAAGTGTAACACTGTT 59.627 43.478 0.00 0.00 44.62 3.16
309 335 0.465705 CACTGTGGTGTCTGACAGGT 59.534 55.000 11.41 3.02 43.33 4.00
352 378 5.415077 AGAGCGCAAGTTTTCTACTCTAGTA 59.585 40.000 11.47 0.00 35.54 1.82
353 379 4.218852 AGAGCGCAAGTTTTCTACTCTAGT 59.781 41.667 11.47 0.00 35.54 2.57
354 380 4.560819 CAGAGCGCAAGTTTTCTACTCTAG 59.439 45.833 11.47 0.00 35.54 2.43
355 381 4.486090 CAGAGCGCAAGTTTTCTACTCTA 58.514 43.478 11.47 0.00 35.54 2.43
356 382 3.321497 CAGAGCGCAAGTTTTCTACTCT 58.679 45.455 11.47 0.00 35.54 3.24
357 383 2.159774 GCAGAGCGCAAGTTTTCTACTC 60.160 50.000 11.47 0.00 41.79 2.59
375 401 0.599728 GGAATAGAGCAGAGCCGCAG 60.600 60.000 0.00 0.00 0.00 5.18
414 440 2.163818 TGGACGAAGAGAAAACGCAT 57.836 45.000 0.00 0.00 0.00 4.73
442 468 1.609208 AAAGCATCAGCAACGTCCTT 58.391 45.000 0.00 0.00 45.49 3.36
476 502 3.430895 CCTTTTGTGATTCATTGCACTGC 59.569 43.478 0.00 0.00 36.05 4.40
492 518 3.837213 ATGATGCACTTCGACCTTTTG 57.163 42.857 0.00 0.00 0.00 2.44
517 543 4.800471 GCGATCTTAAAATTGAAGCCTTGG 59.200 41.667 0.00 0.00 0.00 3.61
583 609 6.207221 TGGCATTTATGTTAGATTGCGATCAT 59.793 34.615 16.42 4.10 34.60 2.45
584 610 5.530543 TGGCATTTATGTTAGATTGCGATCA 59.469 36.000 16.42 0.00 34.60 2.92
585 611 5.853282 GTGGCATTTATGTTAGATTGCGATC 59.147 40.000 5.74 5.74 0.00 3.69
586 612 5.560760 CGTGGCATTTATGTTAGATTGCGAT 60.561 40.000 0.00 0.00 0.00 4.58
587 613 4.260579 CGTGGCATTTATGTTAGATTGCGA 60.261 41.667 0.00 0.00 0.00 5.10
588 614 3.968096 CGTGGCATTTATGTTAGATTGCG 59.032 43.478 0.00 0.00 0.00 4.85
589 615 3.730715 GCGTGGCATTTATGTTAGATTGC 59.269 43.478 0.00 0.00 0.00 3.56
590 616 4.919206 TGCGTGGCATTTATGTTAGATTG 58.081 39.130 0.00 0.00 31.71 2.67
591 617 5.574891 TTGCGTGGCATTTATGTTAGATT 57.425 34.783 0.00 0.00 38.76 2.40
592 618 5.532406 AGATTGCGTGGCATTTATGTTAGAT 59.468 36.000 0.00 0.00 38.76 1.98
593 619 4.881273 AGATTGCGTGGCATTTATGTTAGA 59.119 37.500 0.00 0.00 38.76 2.10
594 620 5.173774 AGATTGCGTGGCATTTATGTTAG 57.826 39.130 0.00 0.00 38.76 2.34
595 621 6.094186 TGTTAGATTGCGTGGCATTTATGTTA 59.906 34.615 0.00 0.00 38.76 2.41
596 622 5.105957 TGTTAGATTGCGTGGCATTTATGTT 60.106 36.000 0.00 0.00 38.76 2.71
597 623 4.397730 TGTTAGATTGCGTGGCATTTATGT 59.602 37.500 0.00 0.00 38.76 2.29
598 624 4.919206 TGTTAGATTGCGTGGCATTTATG 58.081 39.130 0.00 0.00 38.76 1.90
599 625 5.772825 ATGTTAGATTGCGTGGCATTTAT 57.227 34.783 0.00 0.00 38.76 1.40
600 626 6.238621 CCTTATGTTAGATTGCGTGGCATTTA 60.239 38.462 0.00 0.00 38.76 1.40
601 627 5.450412 CCTTATGTTAGATTGCGTGGCATTT 60.450 40.000 0.00 0.00 38.76 2.32
602 628 4.036734 CCTTATGTTAGATTGCGTGGCATT 59.963 41.667 0.00 0.00 38.76 3.56
603 629 3.565482 CCTTATGTTAGATTGCGTGGCAT 59.435 43.478 0.00 0.00 38.76 4.40
604 630 2.942376 CCTTATGTTAGATTGCGTGGCA 59.058 45.455 0.00 0.00 36.47 4.92
605 631 2.943033 ACCTTATGTTAGATTGCGTGGC 59.057 45.455 0.00 0.00 0.00 5.01
606 632 5.560966 AAACCTTATGTTAGATTGCGTGG 57.439 39.130 0.00 0.00 35.67 4.94
607 633 5.163893 ACGAAACCTTATGTTAGATTGCGTG 60.164 40.000 0.00 0.00 35.67 5.34
608 634 4.933400 ACGAAACCTTATGTTAGATTGCGT 59.067 37.500 0.00 0.00 35.67 5.24
609 635 5.464965 ACGAAACCTTATGTTAGATTGCG 57.535 39.130 0.00 0.00 35.67 4.85
610 636 7.971455 AGTAACGAAACCTTATGTTAGATTGC 58.029 34.615 0.00 0.00 35.67 3.56
611 637 9.146984 TGAGTAACGAAACCTTATGTTAGATTG 57.853 33.333 0.00 0.00 35.67 2.67
612 638 9.367444 CTGAGTAACGAAACCTTATGTTAGATT 57.633 33.333 0.00 0.00 35.67 2.40
613 639 8.529476 ACTGAGTAACGAAACCTTATGTTAGAT 58.471 33.333 0.00 0.00 35.67 1.98
614 640 7.889469 ACTGAGTAACGAAACCTTATGTTAGA 58.111 34.615 0.00 0.00 35.67 2.10
615 641 8.530269 AACTGAGTAACGAAACCTTATGTTAG 57.470 34.615 0.00 0.00 35.67 2.34
616 642 7.326789 CGAACTGAGTAACGAAACCTTATGTTA 59.673 37.037 6.31 0.00 35.67 2.41
617 643 6.145048 CGAACTGAGTAACGAAACCTTATGTT 59.855 38.462 6.31 0.00 39.43 2.71
618 644 5.632347 CGAACTGAGTAACGAAACCTTATGT 59.368 40.000 6.31 0.00 0.00 2.29
619 645 5.860182 TCGAACTGAGTAACGAAACCTTATG 59.140 40.000 11.18 0.00 0.00 1.90
620 646 6.017400 TCGAACTGAGTAACGAAACCTTAT 57.983 37.500 11.18 0.00 0.00 1.73
621 647 5.437289 TCGAACTGAGTAACGAAACCTTA 57.563 39.130 11.18 0.00 0.00 2.69
622 648 4.311816 TCGAACTGAGTAACGAAACCTT 57.688 40.909 11.18 0.00 0.00 3.50
623 649 3.996150 TCGAACTGAGTAACGAAACCT 57.004 42.857 11.18 0.00 0.00 3.50
624 650 6.882458 ATTATCGAACTGAGTAACGAAACC 57.118 37.500 15.92 0.00 38.22 3.27
757 978 7.933215 TGACACACATATACTGTACTGTAGT 57.067 36.000 16.42 8.16 35.91 2.73
758 979 8.076781 GGATGACACACATATACTGTACTGTAG 58.923 40.741 16.42 7.26 39.56 2.74
774 995 2.416547 CAGACAATTCGGGATGACACAC 59.583 50.000 0.00 0.00 0.00 3.82
776 997 2.673368 GTCAGACAATTCGGGATGACAC 59.327 50.000 0.00 0.00 37.56 3.67
866 1093 3.030291 TCTTTTTGCGGGGCATAATCAT 58.970 40.909 0.00 0.00 38.76 2.45
867 1094 2.451490 TCTTTTTGCGGGGCATAATCA 58.549 42.857 0.00 0.00 38.76 2.57
1018 1263 4.553429 CCGTGATTCGTGCTAAAAATTGTC 59.447 41.667 0.00 0.00 37.94 3.18
1107 1352 1.546923 AGTGAGACGAGAGAGACGAGA 59.453 52.381 0.00 0.00 34.70 4.04
1120 1365 4.311606 GGAAAGAAACAGAGGAGTGAGAC 58.688 47.826 0.00 0.00 0.00 3.36
1351 1628 3.744719 TAGCGCTCGTCGTTGCCT 61.745 61.111 16.34 0.00 41.07 4.75
1547 1824 4.697756 CTGAACGCCGGCCTCCAA 62.698 66.667 23.46 1.63 0.00 3.53
1637 1914 3.628646 CTTGGTCTCCTTGCCCGGG 62.629 68.421 19.09 19.09 0.00 5.73
1718 2001 3.326297 AGAGTCAAACTTTCCTCTCTGGG 59.674 47.826 0.00 0.00 36.20 4.45
1719 2002 4.565022 GAGAGTCAAACTTTCCTCTCTGG 58.435 47.826 14.94 0.00 44.15 3.86
1743 2026 0.747255 AGTATCAGCGACAAGGCGAT 59.253 50.000 0.00 0.00 38.18 4.58
1749 2032 0.740868 GCAGCCAGTATCAGCGACAA 60.741 55.000 0.00 0.00 0.00 3.18
1807 2091 4.712425 CCGTGACCCACCGACGAC 62.712 72.222 0.00 0.00 35.05 4.34
1808 2092 4.953010 TCCGTGACCCACCGACGA 62.953 66.667 0.00 0.00 35.05 4.20
1843 2127 1.077858 TGGACATGGCATAAGCGCA 60.078 52.632 11.47 0.00 43.41 6.09
1848 2132 3.079131 GTCGCTGGACATGGCATAA 57.921 52.632 0.00 0.00 42.91 1.90
1914 2503 0.327924 TCCATGTACCTGTGGGCTTG 59.672 55.000 8.61 0.00 36.15 4.01
1935 2525 1.234615 CCGGGAAGAAACGCACATGT 61.235 55.000 0.00 0.00 0.00 3.21
2072 2669 1.151668 CCAGTGAAGAAAGACCGCAG 58.848 55.000 0.00 0.00 0.00 5.18
2085 2682 4.462834 ACGAATTACACTCTGATCCAGTGA 59.537 41.667 22.59 7.16 43.54 3.41
2111 2708 1.159285 ACGATTCGTCAGGTACACGA 58.841 50.000 5.75 3.05 44.36 4.35
2151 2753 8.240682 AGTTCGTATCATCATAGCATCTAACTC 58.759 37.037 0.00 0.00 0.00 3.01
2153 2755 8.749841 AAGTTCGTATCATCATAGCATCTAAC 57.250 34.615 0.00 0.00 0.00 2.34
2166 2768 3.934068 ACCGTCCAAAAGTTCGTATCAT 58.066 40.909 0.00 0.00 0.00 2.45
2175 2777 2.372172 AGAGATCCAACCGTCCAAAAGT 59.628 45.455 0.00 0.00 0.00 2.66
2226 2828 7.389330 TCAGAGAGTTTGGAAATTACGCATAAA 59.611 33.333 0.00 0.00 0.00 1.40
2233 2835 5.707764 AGCCTTCAGAGAGTTTGGAAATTAC 59.292 40.000 0.00 0.00 0.00 1.89
2273 2875 3.622060 AACGGCCCCCAGAATGTCG 62.622 63.158 0.00 0.00 0.00 4.35
2285 2889 3.056465 CCTAGATCTTAGATCCAACGGCC 60.056 52.174 17.61 0.00 0.00 6.13
2347 2978 1.718757 GGTGCCACTTGCGATGATCC 61.719 60.000 0.00 0.00 45.60 3.36
2394 3025 1.038130 TTTGGGGTGTCCGTTTGGTG 61.038 55.000 0.00 0.00 38.76 4.17
2406 3037 3.162858 TCCGTGGACGTTTGGGGT 61.163 61.111 0.00 0.00 37.74 4.95
2419 3050 1.141881 CGCTTGGCTAGATGTCCGT 59.858 57.895 0.00 0.00 0.00 4.69
2452 3083 9.628746 TTTGAAAGTAGGAAAGTTGTAAAACAC 57.371 29.630 0.00 0.00 0.00 3.32
2459 3090 8.463930 TCATCATTTGAAAGTAGGAAAGTTGT 57.536 30.769 0.00 0.00 0.00 3.32
2460 3091 9.748708 TTTCATCATTTGAAAGTAGGAAAGTTG 57.251 29.630 0.00 0.00 46.80 3.16
2690 3326 1.806542 CTAGGCGTCAACAGCAACAAT 59.193 47.619 0.00 0.00 36.08 2.71
2708 3344 0.973496 TGCGTACCTGTGGCATCCTA 60.973 55.000 0.00 0.00 0.00 2.94
2709 3345 2.290287 TGCGTACCTGTGGCATCCT 61.290 57.895 0.00 0.00 0.00 3.24
2727 3363 4.057428 GGAGCCTGACGCGTGAGT 62.057 66.667 23.91 6.76 44.76 3.41
2807 3443 2.751913 CGGCGTCTAGTCAGAGCGT 61.752 63.158 0.00 0.00 31.86 5.07
2842 3478 2.124983 AACTGCGGATCAGCGCAT 60.125 55.556 17.48 3.52 46.76 4.73
2844 3480 4.527157 GCAACTGCGGATCAGCGC 62.527 66.667 13.25 11.10 46.76 5.92
2856 3492 1.237285 GGAGACCAATGCACGCAACT 61.237 55.000 0.00 0.00 0.00 3.16
2863 3499 0.251297 CCACCAAGGAGACCAATGCA 60.251 55.000 0.00 0.00 41.22 3.96
2868 3504 0.764890 CAAGACCACCAAGGAGACCA 59.235 55.000 0.00 0.00 41.22 4.02
2936 3572 4.783501 CCAATGGCCCCACCCCTG 62.784 72.222 0.00 0.00 37.83 4.45


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

AutoCloner maintained by Alex Coulton.