Multiple sequence alignment - TraesCS1D01G161400

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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 TraesCS1D01G161400 chr1D 100.000 4818 0 0 1 4818 228305655 228300838 0.000000e+00 8898.0
1 TraesCS1D01G161400 chr1D 96.395 2968 78 9 1362 4315 208820534 208823486 0.000000e+00 4861.0
2 TraesCS1D01G161400 chr1D 97.534 365 8 1 999 1363 208820107 208820470 1.470000e-174 623.0
3 TraesCS1D01G161400 chr1D 86.964 560 36 8 1 560 208817615 208818137 3.210000e-166 595.0
4 TraesCS1D01G161400 chr1D 96.286 350 9 2 4312 4658 208823542 208823890 5.410000e-159 571.0
5 TraesCS1D01G161400 chr1D 89.895 287 19 6 555 837 208818056 208818336 1.270000e-95 361.0
6 TraesCS1D01G161400 chr1D 83.862 347 32 10 4474 4818 208823806 208824130 4.680000e-80 309.0
7 TraesCS1D01G161400 chr1D 94.805 154 2 2 858 1010 208818322 208818470 8.060000e-58 235.0
8 TraesCS1D01G161400 chr1D 94.872 39 2 0 4183 4221 8798008 8798046 1.450000e-05 62.1
9 TraesCS1D01G161400 chr1B 95.587 3444 93 16 858 4287 327845402 327842004 0.000000e+00 5463.0
10 TraesCS1D01G161400 chr1B 92.110 507 38 1 4312 4818 327841926 327841422 0.000000e+00 713.0
11 TraesCS1D01G161400 chr1B 88.372 258 18 2 1 258 327900592 327900347 2.820000e-77 300.0
12 TraesCS1D01G161400 chr1A 94.325 1674 62 10 2569 4236 296213719 296212073 0.000000e+00 2534.0
13 TraesCS1D01G161400 chr1A 94.190 1222 49 7 1362 2569 296215013 296213800 0.000000e+00 1844.0
14 TraesCS1D01G161400 chr1A 95.652 506 21 1 858 1363 296215554 296215050 0.000000e+00 811.0
15 TraesCS1D01G161400 chr1A 86.372 521 45 11 4312 4818 296211957 296211449 3.280000e-151 545.0
16 TraesCS1D01G161400 chr1A 83.096 562 54 19 1 560 296216300 296215778 1.570000e-129 473.0
17 TraesCS1D01G161400 chr1A 90.580 138 6 6 705 837 296215675 296215540 4.960000e-40 176.0
18 TraesCS1D01G161400 chr5A 91.503 153 11 2 4642 4793 526384593 526384744 4.890000e-50 209.0
19 TraesCS1D01G161400 chr4A 89.333 150 12 4 4647 4794 577540911 577541058 8.230000e-43 185.0
20 TraesCS1D01G161400 chr4A 88.387 155 9 8 4642 4792 622182311 622182162 1.380000e-40 178.0
21 TraesCS1D01G161400 chr3D 88.816 152 15 2 4642 4792 25130106 25130256 8.230000e-43 185.0
22 TraesCS1D01G161400 chr3D 87.742 155 17 2 4642 4795 23088333 23088180 3.830000e-41 180.0
23 TraesCS1D01G161400 chr3D 92.500 40 1 2 4187 4225 445342978 445342940 6.740000e-04 56.5
24 TraesCS1D01G161400 chr5B 94.872 117 6 0 4642 4758 498822155 498822271 2.960000e-42 183.0
25 TraesCS1D01G161400 chr4D 89.333 150 11 5 4646 4793 25493064 25492918 2.960000e-42 183.0
26 TraesCS1D01G161400 chr7A 86.667 60 2 3 4158 4213 54191243 54191300 1.450000e-05 62.1
27 TraesCS1D01G161400 chr7A 83.871 62 7 3 4153 4214 616747174 616747232 6.740000e-04 56.5
28 TraesCS1D01G161400 chr2B 100.000 31 0 0 4186 4216 137261988 137261958 1.870000e-04 58.4
29 TraesCS1D01G161400 chr3B 92.500 40 1 1 4176 4215 360090838 360090875 6.740000e-04 56.5
30 TraesCS1D01G161400 chr6B 85.000 60 2 4 4153 4212 49827855 49827907 2.000000e-03 54.7


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 TraesCS1D01G161400 chr1D 228300838 228305655 4817 True 8898.000000 8898 100.000000 1 4818 1 chr1D.!!$R1 4817
1 TraesCS1D01G161400 chr1D 208817615 208824130 6515 False 1079.285714 4861 92.248714 1 4818 7 chr1D.!!$F2 4817
2 TraesCS1D01G161400 chr1B 327841422 327845402 3980 True 3088.000000 5463 93.848500 858 4818 2 chr1B.!!$R2 3960
3 TraesCS1D01G161400 chr1A 296211449 296216300 4851 True 1063.833333 2534 90.702500 1 4818 6 chr1A.!!$R1 4817

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
577 580 0.963962 ACTGGCATTCCTTGTGCTTG 59.036 50.0 0.00 0.0 42.16 4.01 F
910 952 1.187567 AGCGGGCCAAGCTGAAAAAT 61.188 50.0 22.01 0.0 44.22 1.82 F
1896 3663 0.679640 TTGACGGCATGGGATGTTCC 60.680 55.0 0.00 0.0 35.23 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1562 3318 1.529226 TACCACTGCAAATTCCCACG 58.471 50.000 0.0 0.0 0.0 4.94 R
2781 4644 1.594862 GCTCATCACAACTGCGGATAC 59.405 52.381 0.0 0.0 0.0 2.24 R
4181 6051 6.187682 CCTCCATCCCAAAATAAGTGTAGTT 58.812 40.000 0.0 0.0 0.0 2.24 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
44 46 2.679837 CCTGGAACCAAACTCGATGATG 59.320 50.000 0.00 0.00 0.00 3.07
53 55 4.440525 CCAAACTCGATGATGGGGATTTTG 60.441 45.833 3.28 0.00 33.03 2.44
112 115 6.587608 GCTTAGCTTTGATAATGTTTTGTGCT 59.412 34.615 0.00 0.00 0.00 4.40
113 116 7.411157 GCTTAGCTTTGATAATGTTTTGTGCTG 60.411 37.037 0.00 0.00 0.00 4.41
114 117 5.846203 AGCTTTGATAATGTTTTGTGCTGT 58.154 33.333 0.00 0.00 0.00 4.40
115 118 6.282930 AGCTTTGATAATGTTTTGTGCTGTT 58.717 32.000 0.00 0.00 0.00 3.16
116 119 6.762661 AGCTTTGATAATGTTTTGTGCTGTTT 59.237 30.769 0.00 0.00 0.00 2.83
117 120 7.280652 AGCTTTGATAATGTTTTGTGCTGTTTT 59.719 29.630 0.00 0.00 0.00 2.43
118 121 7.373966 GCTTTGATAATGTTTTGTGCTGTTTTG 59.626 33.333 0.00 0.00 0.00 2.44
119 122 7.840342 TTGATAATGTTTTGTGCTGTTTTGT 57.160 28.000 0.00 0.00 0.00 2.83
120 123 7.231705 TGATAATGTTTTGTGCTGTTTTGTG 57.768 32.000 0.00 0.00 0.00 3.33
121 124 7.038048 TGATAATGTTTTGTGCTGTTTTGTGA 58.962 30.769 0.00 0.00 0.00 3.58
189 192 4.453480 GGAACCATTTCATCCCATCCTA 57.547 45.455 0.00 0.00 32.80 2.94
321 324 3.704061 GCTCTCCATAGGAACTCTTGAGT 59.296 47.826 0.00 0.00 41.75 3.41
322 325 4.161377 GCTCTCCATAGGAACTCTTGAGTT 59.839 45.833 14.94 14.94 41.75 3.01
323 326 5.337975 GCTCTCCATAGGAACTCTTGAGTTT 60.338 44.000 15.94 5.43 41.75 2.66
324 327 6.042638 TCTCCATAGGAACTCTTGAGTTTG 57.957 41.667 15.94 10.55 41.75 2.93
325 328 5.780282 TCTCCATAGGAACTCTTGAGTTTGA 59.220 40.000 15.94 6.47 41.75 2.69
326 329 6.270000 TCTCCATAGGAACTCTTGAGTTTGAA 59.730 38.462 15.94 6.35 41.75 2.69
327 330 6.231211 TCCATAGGAACTCTTGAGTTTGAAC 58.769 40.000 15.94 8.31 41.75 3.18
328 331 6.043243 TCCATAGGAACTCTTGAGTTTGAACT 59.957 38.462 15.94 13.62 40.66 3.01
329 332 7.234782 TCCATAGGAACTCTTGAGTTTGAACTA 59.765 37.037 15.94 14.91 38.78 2.24
330 333 7.547370 CCATAGGAACTCTTGAGTTTGAACTAG 59.453 40.741 15.94 0.00 38.78 2.57
337 340 6.010294 TCTTGAGTTTGAACTAGTCGTAGG 57.990 41.667 0.00 0.00 39.88 3.18
346 349 5.311265 TGAACTAGTCGTAGGAACTCTTGA 58.689 41.667 0.00 0.00 41.75 3.02
350 353 5.769162 ACTAGTCGTAGGAACTCTTGAGTTT 59.231 40.000 15.94 5.43 41.75 2.66
427 430 3.694072 CCTGTTTATTTTCCTCGCATGGA 59.306 43.478 0.00 0.00 0.00 3.41
453 456 4.546829 AGAACGTAAAGTTGGGCTATCA 57.453 40.909 0.00 0.00 44.35 2.15
492 495 7.615757 ACTTTATTAGTTTTAAGCTGGCATCCT 59.384 33.333 0.00 0.00 31.29 3.24
495 498 7.954666 ATTAGTTTTAAGCTGGCATCCTTTA 57.045 32.000 5.96 0.00 0.00 1.85
547 550 5.652744 AACTGTTGTGTCGTCTTCAATAC 57.347 39.130 0.00 0.00 0.00 1.89
548 551 4.689071 ACTGTTGTGTCGTCTTCAATACA 58.311 39.130 0.00 0.00 0.00 2.29
549 552 4.506654 ACTGTTGTGTCGTCTTCAATACAC 59.493 41.667 0.00 0.00 42.00 2.90
550 553 4.689071 TGTTGTGTCGTCTTCAATACACT 58.311 39.130 0.00 0.00 42.12 3.55
551 554 5.113383 TGTTGTGTCGTCTTCAATACACTT 58.887 37.500 0.00 0.00 42.12 3.16
552 555 5.583061 TGTTGTGTCGTCTTCAATACACTTT 59.417 36.000 0.00 0.00 42.12 2.66
553 556 6.757478 TGTTGTGTCGTCTTCAATACACTTTA 59.243 34.615 0.00 0.00 42.12 1.85
554 557 7.439955 TGTTGTGTCGTCTTCAATACACTTTAT 59.560 33.333 0.00 0.00 42.12 1.40
555 558 7.576750 TGTGTCGTCTTCAATACACTTTATC 57.423 36.000 0.00 0.00 42.12 1.75
556 559 7.149307 TGTGTCGTCTTCAATACACTTTATCA 58.851 34.615 0.00 0.00 42.12 2.15
557 560 7.654116 TGTGTCGTCTTCAATACACTTTATCAA 59.346 33.333 0.00 0.00 42.12 2.57
558 561 8.492748 GTGTCGTCTTCAATACACTTTATCAAA 58.507 33.333 0.00 0.00 39.27 2.69
559 562 8.492748 TGTCGTCTTCAATACACTTTATCAAAC 58.507 33.333 0.00 0.00 0.00 2.93
560 563 8.709646 GTCGTCTTCAATACACTTTATCAAACT 58.290 33.333 0.00 0.00 0.00 2.66
561 564 8.708742 TCGTCTTCAATACACTTTATCAAACTG 58.291 33.333 0.00 0.00 0.00 3.16
562 565 7.957484 CGTCTTCAATACACTTTATCAAACTGG 59.043 37.037 0.00 0.00 0.00 4.00
563 566 7.750903 GTCTTCAATACACTTTATCAAACTGGC 59.249 37.037 0.00 0.00 0.00 4.85
564 567 7.446931 TCTTCAATACACTTTATCAAACTGGCA 59.553 33.333 0.00 0.00 0.00 4.92
565 568 7.701539 TCAATACACTTTATCAAACTGGCAT 57.298 32.000 0.00 0.00 0.00 4.40
566 569 8.121305 TCAATACACTTTATCAAACTGGCATT 57.879 30.769 0.00 0.00 0.00 3.56
567 570 8.243426 TCAATACACTTTATCAAACTGGCATTC 58.757 33.333 0.00 0.00 0.00 2.67
568 571 5.391312 ACACTTTATCAAACTGGCATTCC 57.609 39.130 0.00 0.00 0.00 3.01
569 572 5.079643 ACACTTTATCAAACTGGCATTCCT 58.920 37.500 0.00 0.00 0.00 3.36
570 573 5.539955 ACACTTTATCAAACTGGCATTCCTT 59.460 36.000 0.00 0.00 0.00 3.36
571 574 5.865552 CACTTTATCAAACTGGCATTCCTTG 59.134 40.000 0.00 0.00 0.00 3.61
572 575 5.539955 ACTTTATCAAACTGGCATTCCTTGT 59.460 36.000 0.00 0.00 0.00 3.16
573 576 3.947910 ATCAAACTGGCATTCCTTGTG 57.052 42.857 0.00 0.00 0.00 3.33
574 577 1.340889 TCAAACTGGCATTCCTTGTGC 59.659 47.619 0.00 0.00 41.78 4.57
575 578 1.342174 CAAACTGGCATTCCTTGTGCT 59.658 47.619 0.00 0.00 42.16 4.40
576 579 1.708341 AACTGGCATTCCTTGTGCTT 58.292 45.000 0.00 0.00 42.16 3.91
577 580 0.963962 ACTGGCATTCCTTGTGCTTG 59.036 50.000 0.00 0.00 42.16 4.01
578 581 0.963962 CTGGCATTCCTTGTGCTTGT 59.036 50.000 0.00 0.00 42.16 3.16
579 582 1.342174 CTGGCATTCCTTGTGCTTGTT 59.658 47.619 0.00 0.00 42.16 2.83
580 583 1.761784 TGGCATTCCTTGTGCTTGTTT 59.238 42.857 0.00 0.00 42.16 2.83
581 584 2.170187 TGGCATTCCTTGTGCTTGTTTT 59.830 40.909 0.00 0.00 42.16 2.43
582 585 3.205338 GGCATTCCTTGTGCTTGTTTTT 58.795 40.909 0.00 0.00 42.16 1.94
615 618 5.622770 AACAAAAACTGTTGTCTCGTCTT 57.377 34.783 0.00 0.00 46.80 3.01
616 619 5.217895 ACAAAAACTGTTGTCTCGTCTTC 57.782 39.130 0.00 0.00 37.10 2.87
617 620 4.693566 ACAAAAACTGTTGTCTCGTCTTCA 59.306 37.500 0.00 0.00 37.10 3.02
618 621 5.180492 ACAAAAACTGTTGTCTCGTCTTCAA 59.820 36.000 0.00 0.00 37.10 2.69
619 622 6.128007 ACAAAAACTGTTGTCTCGTCTTCAAT 60.128 34.615 0.00 0.00 37.10 2.57
620 623 7.065324 ACAAAAACTGTTGTCTCGTCTTCAATA 59.935 33.333 0.00 0.00 37.10 1.90
667 670 4.081972 AGCACATCTTCTCACGTTGATAGT 60.082 41.667 0.00 0.00 0.00 2.12
684 687 7.043258 CGTTGATAGTACGCCACATTGTAAATA 60.043 37.037 0.00 0.00 31.73 1.40
732 768 4.615815 GGATCCATCTGCGCCGCT 62.616 66.667 11.67 0.00 0.00 5.52
837 875 2.808543 ACTCTTTGTTGGCATCGAGTTC 59.191 45.455 0.00 0.00 33.58 3.01
838 876 3.070018 CTCTTTGTTGGCATCGAGTTCT 58.930 45.455 0.00 0.00 0.00 3.01
839 877 3.476552 TCTTTGTTGGCATCGAGTTCTT 58.523 40.909 0.00 0.00 0.00 2.52
841 879 4.338118 TCTTTGTTGGCATCGAGTTCTTTT 59.662 37.500 0.00 0.00 0.00 2.27
842 880 4.647424 TTGTTGGCATCGAGTTCTTTTT 57.353 36.364 0.00 0.00 0.00 1.94
873 911 4.323417 AGACAATGTTGGCATCGAGTTAA 58.677 39.130 0.86 0.00 39.18 2.01
877 915 3.394674 TGTTGGCATCGAGTTAACTCA 57.605 42.857 29.95 19.33 43.00 3.41
880 918 5.109210 TGTTGGCATCGAGTTAACTCATAG 58.891 41.667 29.95 20.32 43.00 2.23
910 952 1.187567 AGCGGGCCAAGCTGAAAAAT 61.188 50.000 22.01 0.00 44.22 1.82
1176 2867 2.492090 GTCATCGCAGACCTCGCT 59.508 61.111 0.00 0.00 42.51 4.93
1664 3420 3.317711 TGTGGTACATTTGTTTGCCAGAG 59.682 43.478 0.00 0.00 44.52 3.35
1672 3428 5.070847 ACATTTGTTTGCCAGAGAAAGGATT 59.929 36.000 0.00 0.00 0.00 3.01
1694 3450 8.813282 GGATTTAGGTTGTTTTGTTTAAGTGTG 58.187 33.333 0.00 0.00 0.00 3.82
1703 3459 6.608002 TGTTTTGTTTAAGTGTGGAATAGGGT 59.392 34.615 0.00 0.00 0.00 4.34
1723 3479 1.648116 AGGCCTACGGTCCAGTTTTA 58.352 50.000 1.29 0.00 0.00 1.52
1759 3515 5.811399 TGGAAGCAGTAATCGTATTTTGG 57.189 39.130 0.00 0.00 0.00 3.28
1773 3529 6.636705 TCGTATTTTGGTCTGCTACACTATT 58.363 36.000 0.00 0.00 0.00 1.73
1896 3663 0.679640 TTGACGGCATGGGATGTTCC 60.680 55.000 0.00 0.00 35.23 3.62
1937 3704 2.594592 GGCGTGGTTGGTGCTCTT 60.595 61.111 0.00 0.00 0.00 2.85
2017 3784 1.732405 GCATAAGCAAGCGAAACCACC 60.732 52.381 0.00 0.00 41.58 4.61
2057 3824 4.758773 TCACAATCATCTAGGCATGTCA 57.241 40.909 0.00 0.00 0.00 3.58
2185 3952 7.335673 TGCTATTTTCCATAGTTGAATCGTTCA 59.664 33.333 0.00 0.00 38.04 3.18
2283 4063 5.473504 TGTAAGCATTCTCCTGAACTTTTCC 59.526 40.000 0.00 0.00 34.71 3.13
2326 4107 4.689812 TCTCACCTTCGTAGTATATCGAGC 59.310 45.833 0.00 0.00 37.38 5.03
2335 4116 5.923114 TCGTAGTATATCGAGCGACTTACTT 59.077 40.000 16.58 6.59 31.71 2.24
2417 4198 7.395190 TGAAATAAGCTTGCTATGTGACATT 57.605 32.000 9.86 0.00 0.00 2.71
2501 4282 8.647226 GCATGTATTTTCAATTTTGTGGTAGTC 58.353 33.333 0.00 0.00 0.00 2.59
2592 4454 9.587772 CTAGTTGTTACTGTTAGCATCAATAGT 57.412 33.333 0.00 0.00 35.78 2.12
2617 4479 8.879759 GTTGCTAACATTAGTTAAGCAGTGATA 58.120 33.333 0.00 0.00 41.17 2.15
2636 4498 9.035607 CAGTGATATACATTGTTCTGTACCTTC 57.964 37.037 0.00 0.00 34.59 3.46
2652 4514 7.618117 TCTGTACCTTCCATGAGATAGTAAACA 59.382 37.037 0.00 0.00 0.00 2.83
2732 4595 9.226606 TGCTTACTAATTACTGCTATGTTGTTT 57.773 29.630 0.00 0.00 0.00 2.83
2737 4600 8.936864 ACTAATTACTGCTATGTTGTTTGACTC 58.063 33.333 0.00 0.00 0.00 3.36
4170 6039 4.431416 ACACCCACAAATAAGTGTCTCA 57.569 40.909 0.00 0.00 39.14 3.27
4287 6157 9.649024 CGCAATTTCTTGTTAAAATGTCATTTT 57.351 25.926 23.40 23.40 38.93 1.82
4747 6804 4.269123 TCGTTCCAATTTTATCGGATGTCG 59.731 41.667 0.00 0.00 40.90 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 46 4.062293 GTTTTAACAGTGCCAAAATCCCC 58.938 43.478 5.93 0.00 0.00 4.81
53 55 0.240145 GCGGGAGTTTTAACAGTGCC 59.760 55.000 0.00 0.00 0.00 5.01
112 115 4.791411 GCGACCAAGCTAAATCACAAAACA 60.791 41.667 0.00 0.00 0.00 2.83
113 116 3.668656 GCGACCAAGCTAAATCACAAAAC 59.331 43.478 0.00 0.00 0.00 2.43
114 117 3.896122 GCGACCAAGCTAAATCACAAAA 58.104 40.909 0.00 0.00 0.00 2.44
115 118 3.552604 GCGACCAAGCTAAATCACAAA 57.447 42.857 0.00 0.00 0.00 2.83
161 164 2.171870 GGATGAAATGGTTCCCTCGGTA 59.828 50.000 0.00 0.00 32.28 4.02
213 216 2.615869 GGCGCCATTGCTGAAAAATAA 58.384 42.857 24.80 0.00 34.43 1.40
232 235 3.205733 AGTCCTTCCTACTCCTTAGAGGG 59.794 52.174 0.00 0.00 45.11 4.30
321 324 6.263842 TCAAGAGTTCCTACGACTAGTTCAAA 59.736 38.462 0.00 0.00 0.00 2.69
322 325 5.766670 TCAAGAGTTCCTACGACTAGTTCAA 59.233 40.000 0.00 0.00 0.00 2.69
323 326 5.311265 TCAAGAGTTCCTACGACTAGTTCA 58.689 41.667 0.00 0.00 0.00 3.18
324 327 5.412286 ACTCAAGAGTTCCTACGACTAGTTC 59.588 44.000 0.00 0.00 38.83 3.01
325 328 5.315348 ACTCAAGAGTTCCTACGACTAGTT 58.685 41.667 0.00 0.00 38.83 2.24
326 329 4.909001 ACTCAAGAGTTCCTACGACTAGT 58.091 43.478 0.00 0.00 38.83 2.57
346 349 4.771054 ACTATGGTCCGACTAGTTCAAACT 59.229 41.667 0.00 0.46 42.91 2.66
350 353 3.959293 TCACTATGGTCCGACTAGTTCA 58.041 45.455 0.00 0.00 0.00 3.18
427 430 4.648651 AGCCCAACTTTACGTTCTTACAT 58.351 39.130 0.00 0.00 32.27 2.29
453 456 2.814280 ATAAAGTGCGCGTAGGCTAT 57.186 45.000 8.43 0.00 36.88 2.97
463 466 5.511729 GCCAGCTTAAAACTAATAAAGTGCG 59.488 40.000 0.00 0.00 38.88 5.34
547 550 5.649782 AGGAATGCCAGTTTGATAAAGTG 57.350 39.130 0.00 2.85 40.66 3.16
548 551 5.539955 ACAAGGAATGCCAGTTTGATAAAGT 59.460 36.000 0.00 0.00 36.29 2.66
549 552 5.865552 CACAAGGAATGCCAGTTTGATAAAG 59.134 40.000 0.00 0.00 36.29 1.85
550 553 5.782047 CACAAGGAATGCCAGTTTGATAAA 58.218 37.500 0.00 0.00 36.29 1.40
551 554 4.321899 GCACAAGGAATGCCAGTTTGATAA 60.322 41.667 0.00 0.00 37.08 1.75
552 555 3.193267 GCACAAGGAATGCCAGTTTGATA 59.807 43.478 0.00 0.00 37.08 2.15
553 556 2.028748 GCACAAGGAATGCCAGTTTGAT 60.029 45.455 0.00 0.00 37.08 2.57
554 557 1.340889 GCACAAGGAATGCCAGTTTGA 59.659 47.619 0.00 0.00 37.08 2.69
555 558 1.342174 AGCACAAGGAATGCCAGTTTG 59.658 47.619 0.00 0.00 44.53 2.93
556 559 1.708341 AGCACAAGGAATGCCAGTTT 58.292 45.000 0.00 0.00 44.53 2.66
557 560 1.342174 CAAGCACAAGGAATGCCAGTT 59.658 47.619 0.00 0.00 44.53 3.16
558 561 0.963962 CAAGCACAAGGAATGCCAGT 59.036 50.000 0.00 0.00 44.53 4.00
559 562 0.963962 ACAAGCACAAGGAATGCCAG 59.036 50.000 0.00 0.00 44.53 4.85
560 563 1.412079 AACAAGCACAAGGAATGCCA 58.588 45.000 0.00 0.00 44.53 4.92
561 564 2.531522 AAACAAGCACAAGGAATGCC 57.468 45.000 0.00 0.00 44.53 4.40
594 597 4.693566 TGAAGACGAGACAACAGTTTTTGT 59.306 37.500 0.00 0.00 42.55 2.83
595 598 5.216566 TGAAGACGAGACAACAGTTTTTG 57.783 39.130 0.00 0.00 0.00 2.44
596 599 5.873179 TTGAAGACGAGACAACAGTTTTT 57.127 34.783 0.00 0.00 0.00 1.94
597 600 6.537301 TGTATTGAAGACGAGACAACAGTTTT 59.463 34.615 0.00 0.00 30.00 2.43
598 601 6.018994 GTGTATTGAAGACGAGACAACAGTTT 60.019 38.462 0.00 0.00 34.09 2.66
599 602 5.462398 GTGTATTGAAGACGAGACAACAGTT 59.538 40.000 0.00 0.00 34.09 3.16
600 603 4.982916 GTGTATTGAAGACGAGACAACAGT 59.017 41.667 0.00 0.00 34.09 3.55
601 604 5.223382 AGTGTATTGAAGACGAGACAACAG 58.777 41.667 0.00 0.00 34.09 3.16
602 605 5.196341 AGTGTATTGAAGACGAGACAACA 57.804 39.130 0.00 0.00 34.09 3.33
603 606 6.526566 AAAGTGTATTGAAGACGAGACAAC 57.473 37.500 0.00 0.00 34.09 3.32
604 607 8.085909 TGATAAAGTGTATTGAAGACGAGACAA 58.914 33.333 0.00 0.00 34.09 3.18
605 608 7.599171 TGATAAAGTGTATTGAAGACGAGACA 58.401 34.615 0.00 0.00 30.38 3.41
606 609 8.462143 TTGATAAAGTGTATTGAAGACGAGAC 57.538 34.615 0.00 0.00 0.00 3.36
607 610 8.922676 GTTTGATAAAGTGTATTGAAGACGAGA 58.077 33.333 0.00 0.00 0.00 4.04
608 611 8.169268 GGTTTGATAAAGTGTATTGAAGACGAG 58.831 37.037 0.00 0.00 0.00 4.18
609 612 7.148705 CGGTTTGATAAAGTGTATTGAAGACGA 60.149 37.037 0.00 0.00 0.00 4.20
610 613 6.953743 CGGTTTGATAAAGTGTATTGAAGACG 59.046 38.462 0.00 0.00 0.00 4.18
611 614 7.094933 ACCGGTTTGATAAAGTGTATTGAAGAC 60.095 37.037 0.00 0.00 0.00 3.01
612 615 6.938030 ACCGGTTTGATAAAGTGTATTGAAGA 59.062 34.615 0.00 0.00 0.00 2.87
613 616 7.141100 ACCGGTTTGATAAAGTGTATTGAAG 57.859 36.000 0.00 0.00 0.00 3.02
614 617 7.513371 AACCGGTTTGATAAAGTGTATTGAA 57.487 32.000 15.86 0.00 0.00 2.69
615 618 7.513371 AAACCGGTTTGATAAAGTGTATTGA 57.487 32.000 31.17 0.00 0.00 2.57
667 670 9.347934 CAAAATTCTTATTTACAATGTGGCGTA 57.652 29.630 0.00 0.00 32.85 4.42
684 687 6.830838 TGTAAAATGCAAACCCCAAAATTCTT 59.169 30.769 0.00 0.00 0.00 2.52
732 768 4.675976 TTTCTTTGGTGAAGTCCTCGTA 57.324 40.909 0.00 0.00 36.70 3.43
812 850 4.097892 ACTCGATGCCAACAAAGAGTTTTT 59.902 37.500 0.00 0.00 41.09 1.94
845 883 4.037327 TCGATGCCAACATTGTCTCAAAAA 59.963 37.500 0.00 0.00 38.62 1.94
846 884 3.567585 TCGATGCCAACATTGTCTCAAAA 59.432 39.130 0.00 0.00 38.62 2.44
847 885 3.145286 TCGATGCCAACATTGTCTCAAA 58.855 40.909 0.00 0.00 38.62 2.69
848 886 2.743664 CTCGATGCCAACATTGTCTCAA 59.256 45.455 0.00 0.00 38.62 3.02
849 887 2.289631 ACTCGATGCCAACATTGTCTCA 60.290 45.455 0.00 0.00 38.62 3.27
850 888 2.350522 ACTCGATGCCAACATTGTCTC 58.649 47.619 0.00 0.00 38.62 3.36
851 889 2.479566 ACTCGATGCCAACATTGTCT 57.520 45.000 0.00 0.00 38.62 3.41
852 890 4.154195 AGTTAACTCGATGCCAACATTGTC 59.846 41.667 1.12 0.00 38.62 3.18
853 891 4.072131 AGTTAACTCGATGCCAACATTGT 58.928 39.130 1.12 0.00 38.62 2.71
854 892 4.154015 TGAGTTAACTCGATGCCAACATTG 59.846 41.667 26.35 0.00 45.72 2.82
855 893 4.323417 TGAGTTAACTCGATGCCAACATT 58.677 39.130 26.35 0.00 45.72 2.71
856 894 3.937814 TGAGTTAACTCGATGCCAACAT 58.062 40.909 26.35 0.00 45.72 2.71
864 902 9.121658 TGAACATACTCTATGAGTTAACTCGAT 57.878 33.333 26.35 21.80 45.72 3.59
873 911 4.202161 CCCGCTTGAACATACTCTATGAGT 60.202 45.833 5.53 5.53 45.54 3.41
877 915 2.224305 GGCCCGCTTGAACATACTCTAT 60.224 50.000 0.00 0.00 0.00 1.98
880 918 0.392461 TGGCCCGCTTGAACATACTC 60.392 55.000 0.00 0.00 0.00 2.59
910 952 4.087892 GCCCAGGAGCAGCTTCGA 62.088 66.667 0.00 0.00 0.00 3.71
979 1021 4.553330 TCGCTAGGGTTTCTCAATTTCT 57.447 40.909 6.70 0.00 0.00 2.52
1128 2819 1.738099 GCAAGCGACAGTCACCGAT 60.738 57.895 0.41 0.00 0.00 4.18
1562 3318 1.529226 TACCACTGCAAATTCCCACG 58.471 50.000 0.00 0.00 0.00 4.94
1672 3428 7.463961 TCCACACTTAAACAAAACAACCTAA 57.536 32.000 0.00 0.00 0.00 2.69
1723 3479 4.768968 ACTGCTTCCATTCAATACAGCTTT 59.231 37.500 0.00 0.00 0.00 3.51
1759 3515 3.887621 TCCACCAATAGTGTAGCAGAC 57.112 47.619 0.00 0.00 45.74 3.51
1896 3663 7.011857 GCCAGGAACTCTGAATAAAGTGAATAG 59.988 40.741 0.00 0.00 46.18 1.73
1937 3704 7.012044 GCCGGAATACTTTCAGCTTAAGAAATA 59.988 37.037 5.05 2.55 34.75 1.40
2017 3784 4.799428 TGTGAAATGTATTGCATGCAATCG 59.201 37.500 41.17 0.00 44.50 3.34
2057 3824 3.773119 AGTTTAGGGACATACGACATGGT 59.227 43.478 0.00 0.00 0.00 3.55
2185 3952 5.928264 GCAAGGAATCTGCACAAAGTTAATT 59.072 36.000 0.00 0.00 0.00 1.40
2283 4063 7.148069 GGTGAGAATGGGATAAAACCAAGTTAG 60.148 40.741 0.00 0.00 42.17 2.34
2326 4107 9.914131 TTATCCTATCATGAATCAAGTAAGTCG 57.086 33.333 0.00 0.00 0.00 4.18
2417 4198 7.987458 CCTTAAGCTCAATCAGTGGATACTTAA 59.013 37.037 0.00 0.00 34.07 1.85
2501 4282 6.338937 GTGAAGGTTACTATAGTTCCACTGG 58.661 44.000 21.08 0.00 0.00 4.00
2592 4454 7.921786 ATCACTGCTTAACTAATGTTAGCAA 57.078 32.000 0.00 0.00 39.63 3.91
2617 4479 6.957631 TCATGGAAGGTACAGAACAATGTAT 58.042 36.000 0.00 0.00 37.93 2.29
2636 4498 7.765307 ACAATTGCTTGTTTACTATCTCATGG 58.235 34.615 5.05 0.00 43.05 3.66
2652 4514 2.560981 CGGGGGAAAACTACAATTGCTT 59.439 45.455 5.05 0.00 0.00 3.91
2732 4595 4.038763 ACATGTCTAAGACCAAACGAGTCA 59.961 41.667 0.00 0.00 36.68 3.41
2737 4600 5.862924 AATGACATGTCTAAGACCAAACG 57.137 39.130 25.55 0.00 0.00 3.60
2778 4641 3.669536 TCATCACAACTGCGGATACAAA 58.330 40.909 0.00 0.00 0.00 2.83
2781 4644 1.594862 GCTCATCACAACTGCGGATAC 59.405 52.381 0.00 0.00 0.00 2.24
4181 6051 6.187682 CCTCCATCCCAAAATAAGTGTAGTT 58.812 40.000 0.00 0.00 0.00 2.24
4287 6157 5.484290 CCTTTAGGGAACTCCTTTCTCTACA 59.516 44.000 0.00 0.00 45.52 2.74
4291 6161 4.912317 ACCTTTAGGGAACTCCTTTCTC 57.088 45.455 0.10 0.00 45.47 2.87
4292 6162 6.089502 TCTTACCTTTAGGGAACTCCTTTCT 58.910 40.000 0.10 0.00 45.47 2.52
4333 6276 5.928264 GCCACTATTCTTTTCTGTTTTGCAT 59.072 36.000 0.00 0.00 0.00 3.96
4675 6732 2.587956 CAAGGATGACACGCACAAATG 58.412 47.619 0.00 0.00 0.00 2.32
4701 6758 4.052159 ACAGAGAAGATTAGCATGGTCG 57.948 45.455 0.00 0.00 0.00 4.79
4703 6760 5.303078 ACGATACAGAGAAGATTAGCATGGT 59.697 40.000 1.62 1.62 0.00 3.55
4747 6804 1.515304 GCACTCTCGTCTCTTCGGC 60.515 63.158 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.