Multiple sequence alignment - TraesCS7A01G437100

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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 TraesCS7A01G437100 chr7A 100.000 5015 0 0 1 5015 631979132 631974118 0.000000e+00 9262.0
1 TraesCS7A01G437100 chr7D 95.956 4377 101 20 676 5015 548205557 548201220 0.000000e+00 7033.0
2 TraesCS7A01G437100 chr7D 93.810 420 26 0 1 420 548207624 548207205 2.550000e-177 632.0
3 TraesCS7A01G437100 chr7D 92.513 187 10 3 411 597 548206063 548205881 1.070000e-66 265.0
4 TraesCS7A01G437100 chr7B 96.604 3416 86 8 707 4100 591391431 591388024 0.000000e+00 5638.0
5 TraesCS7A01G437100 chr7B 95.873 848 34 1 4168 5015 591388031 591387185 0.000000e+00 1371.0
6 TraesCS7A01G437100 chr7B 94.316 475 25 2 1 474 591453135 591452662 0.000000e+00 726.0
7 TraesCS7A01G437100 chr7B 85.938 64 4 3 4122 4180 508189441 508189378 4.190000e-06 63.9
8 TraesCS7A01G437100 chr4B 88.754 2054 229 2 1994 4046 636982762 636980710 0.000000e+00 2512.0
9 TraesCS7A01G437100 chr4B 88.456 2053 235 2 1994 4046 636971522 636969472 0.000000e+00 2477.0
10 TraesCS7A01G437100 chr4B 86.524 653 85 2 1238 1887 636985426 636984774 0.000000e+00 715.0
11 TraesCS7A01G437100 chr4B 77.778 558 82 19 4456 5005 636980381 636979858 6.310000e-79 305.0
12 TraesCS7A01G437100 chr1A 84.324 185 15 3 1097 1281 558091734 558091904 8.630000e-38 169.0
13 TraesCS7A01G437100 chrUn 87.500 64 4 2 4122 4181 16235130 16235193 2.500000e-08 71.3
14 TraesCS7A01G437100 chr3B 86.567 67 4 3 4122 4183 616774451 616774385 9.010000e-08 69.4
15 TraesCS7A01G437100 chr3B 86.885 61 3 4 4122 4177 289705443 289705503 4.190000e-06 63.9
16 TraesCS7A01G437100 chr3B 84.848 66 3 6 4122 4181 119469050 119469114 5.420000e-05 60.2
17 TraesCS7A01G437100 chr2D 85.714 70 4 2 4122 4185 95416598 95416529 9.010000e-08 69.4
18 TraesCS7A01G437100 chr1D 93.617 47 2 1 4138 4184 261260713 261260758 9.010000e-08 69.4
19 TraesCS7A01G437100 chr5D 82.500 80 6 4 4098 4177 527624309 527624380 4.190000e-06 63.9


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 TraesCS7A01G437100 chr7A 631974118 631979132 5014 True 9262.000000 9262 100.0000 1 5015 1 chr7A.!!$R1 5014
1 TraesCS7A01G437100 chr7D 548201220 548207624 6404 True 2643.333333 7033 94.0930 1 5015 3 chr7D.!!$R1 5014
2 TraesCS7A01G437100 chr7B 591387185 591391431 4246 True 3504.500000 5638 96.2385 707 5015 2 chr7B.!!$R3 4308
3 TraesCS7A01G437100 chr4B 636969472 636971522 2050 True 2477.000000 2477 88.4560 1994 4046 1 chr4B.!!$R1 2052
4 TraesCS7A01G437100 chr4B 636979858 636985426 5568 True 1177.333333 2512 84.3520 1238 5005 3 chr4B.!!$R2 3767

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
632 1780 0.179086 AAACCAAGTTTTGCCAGGCG 60.179 50.000 7.03 0.00 31.10 5.52 F
652 1800 1.180456 CCAAACTGGGTGCAGATGCA 61.180 55.000 2.75 2.75 40.66 3.96 F
739 2136 1.487850 GGAATTTTTGGCTGGGGGCA 61.488 55.000 0.00 0.00 46.41 5.36 F
1926 5160 1.694696 CTATGTAAGGAGGGCAGGGTC 59.305 57.143 0.00 0.00 0.00 4.46 F
2503 5842 1.847818 CGATGATTGCCAGCCAAATG 58.152 50.000 0.00 0.00 36.92 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 5134 1.122019 CCCTCCTTACATAGGCCGCT 61.122 60.000 0.00 0.00 44.37 5.52 R
2013 5352 1.354031 TGCATCCTTCCTGCCTTACAA 59.646 47.619 0.00 0.00 38.89 2.41 R
2722 6061 1.897398 GCACCAGTTAAGACGGCGTG 61.897 60.000 21.19 1.98 0.00 5.34 R
2883 6222 1.212688 CACCCCTCACCAATCATGCTA 59.787 52.381 0.00 0.00 0.00 3.49 R
4154 7543 0.324091 GTACTCCCTCCGTCCCAGAA 60.324 60.000 0.00 0.00 0.00 3.02 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
57 58 3.181471 GGAACGACACTCATGATCTGGAT 60.181 47.826 0.00 0.00 0.00 3.41
67 68 1.349627 GATCTGGATGCACGCAACG 59.650 57.895 0.00 0.00 0.00 4.10
79 80 4.021925 GCAACGACCAGGGGAGCT 62.022 66.667 0.00 0.00 0.00 4.09
217 218 0.244721 GGAAGTGGAATGGCTTGTGC 59.755 55.000 0.00 0.00 38.76 4.57
238 239 1.300963 GACCATGAGAAGCCAGCCA 59.699 57.895 0.00 0.00 0.00 4.75
257 258 1.916651 CACAGCTCTCGAATTCGACAG 59.083 52.381 25.96 24.74 44.22 3.51
262 263 1.133216 CTCTCGAATTCGACAGAGGCA 59.867 52.381 27.21 9.49 44.22 4.75
289 290 2.450479 ATAGCGCGCTGGTTATCCCC 62.450 60.000 41.85 3.53 0.00 4.81
352 353 2.746269 CTGTTGTGTTCCATGGCAAAG 58.254 47.619 6.96 2.92 0.00 2.77
355 356 1.619654 TGTGTTCCATGGCAAAGAGG 58.380 50.000 6.96 0.00 0.00 3.69
385 386 1.913262 TGCCCTCGCCTCTTCAGAA 60.913 57.895 0.00 0.00 0.00 3.02
387 388 1.893919 GCCCTCGCCTCTTCAGAAGT 61.894 60.000 10.09 0.00 0.00 3.01
391 392 0.241213 TCGCCTCTTCAGAAGTGTCG 59.759 55.000 10.09 9.46 0.00 4.35
395 396 2.924454 GCCTCTTCAGAAGTGTCGTCTG 60.924 54.545 10.09 6.40 43.28 3.51
397 398 3.560503 CTCTTCAGAAGTGTCGTCTGTC 58.439 50.000 10.09 0.00 42.63 3.51
420 421 2.195922 GACGGCATTTGATTCCATTGC 58.804 47.619 0.00 0.00 33.54 3.56
421 422 1.134729 ACGGCATTTGATTCCATTGCC 60.135 47.619 11.67 11.67 43.22 4.52
422 423 1.807377 CGGCATTTGATTCCATTGCCC 60.807 52.381 14.57 2.47 43.49 5.36
425 426 2.940410 GCATTTGATTCCATTGCCCAAG 59.060 45.455 0.00 0.00 0.00 3.61
426 427 3.537580 CATTTGATTCCATTGCCCAAGG 58.462 45.455 0.00 0.00 0.00 3.61
428 429 2.852714 TGATTCCATTGCCCAAGGAT 57.147 45.000 0.00 0.00 0.00 3.24
429 430 3.969466 TGATTCCATTGCCCAAGGATA 57.031 42.857 0.00 0.00 0.00 2.59
430 431 3.565307 TGATTCCATTGCCCAAGGATAC 58.435 45.455 0.00 0.00 0.00 2.24
431 432 2.452600 TTCCATTGCCCAAGGATACC 57.547 50.000 0.00 0.00 37.17 2.73
432 433 1.607225 TCCATTGCCCAAGGATACCT 58.393 50.000 0.00 0.00 33.87 3.08
433 434 1.215173 TCCATTGCCCAAGGATACCTG 59.785 52.381 0.00 0.00 32.13 4.00
434 435 1.696063 CATTGCCCAAGGATACCTGG 58.304 55.000 0.00 0.00 32.13 4.45
459 1607 6.094048 GCAGAAGCAATGTGGACTTATTAGAA 59.906 38.462 0.00 0.00 41.58 2.10
486 1634 8.647796 CATCAGTGGAGTACAGGGTTTATATTA 58.352 37.037 0.00 0.00 0.00 0.98
496 1644 8.953313 GTACAGGGTTTATATTAATATGGTGGC 58.047 37.037 16.72 4.25 0.00 5.01
526 1674 9.349713 CCTATACTAGAGAGTCTCTTGTGATTT 57.650 37.037 33.79 22.20 43.78 2.17
567 1715 4.640771 TCTGATAAACCTGCAAACCTCT 57.359 40.909 0.00 0.00 0.00 3.69
579 1727 6.115446 CCTGCAAACCTCTATAATCTGTGAA 58.885 40.000 0.00 0.00 0.00 3.18
594 1742 7.617041 AATCTGTGAAGAATTGGTTACTAGC 57.383 36.000 0.00 0.00 0.00 3.42
597 1745 6.595326 TCTGTGAAGAATTGGTTACTAGCATG 59.405 38.462 0.00 0.00 0.00 4.06
599 1747 5.648092 GTGAAGAATTGGTTACTAGCATGGT 59.352 40.000 1.62 1.62 0.00 3.55
617 1765 6.142139 GCATGGTTGCTTAAAAATGAAAACC 58.858 36.000 0.00 0.00 45.77 3.27
618 1766 6.238593 GCATGGTTGCTTAAAAATGAAAACCA 60.239 34.615 6.81 6.81 46.82 3.67
620 1768 7.313951 TGGTTGCTTAAAAATGAAAACCAAG 57.686 32.000 2.03 0.00 41.81 3.61
621 1769 6.881602 TGGTTGCTTAAAAATGAAAACCAAGT 59.118 30.769 2.03 0.00 41.81 3.16
624 1772 9.619316 GTTGCTTAAAAATGAAAACCAAGTTTT 57.381 25.926 5.19 5.19 46.51 2.43
625 1773 9.617975 TTGCTTAAAAATGAAAACCAAGTTTTG 57.382 25.926 10.00 0.00 44.33 2.44
626 1774 7.752686 TGCTTAAAAATGAAAACCAAGTTTTGC 59.247 29.630 10.00 5.06 44.33 3.68
627 1775 7.219917 GCTTAAAAATGAAAACCAAGTTTTGCC 59.780 33.333 10.00 0.00 44.33 4.52
628 1776 6.581171 AAAAATGAAAACCAAGTTTTGCCA 57.419 29.167 10.00 3.95 44.33 4.92
629 1777 5.816449 AAATGAAAACCAAGTTTTGCCAG 57.184 34.783 10.00 0.00 44.33 4.85
630 1778 3.258971 TGAAAACCAAGTTTTGCCAGG 57.741 42.857 10.00 0.00 44.33 4.45
632 1780 0.179086 AAACCAAGTTTTGCCAGGCG 60.179 50.000 7.03 0.00 31.10 5.52
634 1782 2.356194 CAAGTTTTGCCAGGCGCC 60.356 61.111 21.89 21.89 36.24 6.53
635 1783 2.837291 AAGTTTTGCCAGGCGCCA 60.837 55.556 31.54 4.11 36.24 5.69
637 1785 1.965754 AAGTTTTGCCAGGCGCCAAA 61.966 50.000 31.54 17.65 36.24 3.28
638 1786 2.107953 TTTTGCCAGGCGCCAAAC 59.892 55.556 31.54 17.53 36.24 2.93
639 1787 2.430610 TTTTGCCAGGCGCCAAACT 61.431 52.632 31.54 4.11 36.24 2.66
640 1788 2.641439 TTTTGCCAGGCGCCAAACTG 62.641 55.000 31.54 18.24 36.24 3.16
644 1792 3.673484 CAGGCGCCAAACTGGGTG 61.673 66.667 31.54 11.85 38.19 4.61
649 1797 1.973281 CGCCAAACTGGGTGCAGAT 60.973 57.895 0.00 0.00 38.19 2.90
650 1798 1.588082 GCCAAACTGGGTGCAGATG 59.412 57.895 0.00 0.00 38.19 2.90
651 1799 1.588082 CCAAACTGGGTGCAGATGC 59.412 57.895 0.00 0.00 36.18 3.91
652 1800 1.180456 CCAAACTGGGTGCAGATGCA 61.180 55.000 2.75 2.75 40.66 3.96
670 1818 5.879223 AGATGCATCTGCCACTTATTATAGC 59.121 40.000 28.21 0.00 41.18 2.97
739 2136 1.487850 GGAATTTTTGGCTGGGGGCA 61.488 55.000 0.00 0.00 46.41 5.36
882 2291 5.991606 GTGGATTGGGGAAAAAGAAAGAAAG 59.008 40.000 0.00 0.00 0.00 2.62
883 2292 5.902431 TGGATTGGGGAAAAAGAAAGAAAGA 59.098 36.000 0.00 0.00 0.00 2.52
884 2293 6.385467 TGGATTGGGGAAAAAGAAAGAAAGAA 59.615 34.615 0.00 0.00 0.00 2.52
885 2294 7.092668 TGGATTGGGGAAAAAGAAAGAAAGAAA 60.093 33.333 0.00 0.00 0.00 2.52
1705 3139 4.028490 TGCTGGGTTACTGCCGGG 62.028 66.667 2.18 0.00 42.74 5.73
1719 3153 4.776322 CGGGCGGGCAACATCAGA 62.776 66.667 3.27 0.00 39.74 3.27
1836 3270 1.809684 GTGTAAGGGAGGCACTTGTC 58.190 55.000 0.00 0.00 41.55 3.18
1900 5134 4.996758 CACACACATACAAGTTCCTGATCA 59.003 41.667 0.00 0.00 0.00 2.92
1926 5160 1.694696 CTATGTAAGGAGGGCAGGGTC 59.305 57.143 0.00 0.00 0.00 4.46
1977 5211 3.322466 CGGGGAGGTGTTGCTCCT 61.322 66.667 0.00 0.00 39.58 3.69
1986 5220 4.404715 GGAGGTGTTGCTCCTAGTGTTATA 59.595 45.833 0.00 0.00 36.84 0.98
2013 5352 8.486210 ACATATAATGCAATGATCGTAGGGTAT 58.514 33.333 3.15 0.00 0.00 2.73
2342 5681 5.816955 AGCCTCATTAAGAAGGATAGGTC 57.183 43.478 9.55 0.00 0.00 3.85
2503 5842 1.847818 CGATGATTGCCAGCCAAATG 58.152 50.000 0.00 0.00 36.92 2.32
2722 6061 2.936498 CTGACACCCGATGACCAATTAC 59.064 50.000 0.00 0.00 0.00 1.89
2883 6222 1.344953 TTGCCGCCACCCTCATAGAT 61.345 55.000 0.00 0.00 0.00 1.98
2901 6240 2.374504 AGATAGCATGATTGGTGAGGGG 59.625 50.000 0.00 0.00 34.79 4.79
3090 6429 6.889301 CATGACCATGCTAAAAGGATGTAT 57.111 37.500 7.51 0.00 41.74 2.29
3341 6680 2.229675 TGTGAGCCAGATTATGCGAG 57.770 50.000 0.00 0.00 0.00 5.03
3568 6907 7.218228 TGTGTTCTTTTTGATCATATGTGCT 57.782 32.000 1.90 0.00 0.00 4.40
4065 7454 6.645415 ACATTTAGTCTGTAACTTTCAGTCCG 59.355 38.462 0.00 0.00 39.55 4.79
4109 7498 3.801620 GGAGTCCTCCGTCCCAAA 58.198 61.111 0.41 0.00 40.36 3.28
4110 7499 2.297937 GGAGTCCTCCGTCCCAAAT 58.702 57.895 0.41 0.00 40.36 2.32
4111 7500 0.618981 GGAGTCCTCCGTCCCAAATT 59.381 55.000 0.41 0.00 40.36 1.82
4112 7501 1.835531 GGAGTCCTCCGTCCCAAATTA 59.164 52.381 0.41 0.00 40.36 1.40
4113 7502 2.158943 GGAGTCCTCCGTCCCAAATTAG 60.159 54.545 0.41 0.00 40.36 1.73
4114 7503 1.838077 AGTCCTCCGTCCCAAATTAGG 59.162 52.381 0.00 0.00 0.00 2.69
4115 7504 1.558294 GTCCTCCGTCCCAAATTAGGT 59.442 52.381 0.00 0.00 0.00 3.08
4116 7505 1.557832 TCCTCCGTCCCAAATTAGGTG 59.442 52.381 0.00 0.00 0.00 4.00
4117 7506 1.280998 CCTCCGTCCCAAATTAGGTGT 59.719 52.381 0.00 0.00 0.00 4.16
4118 7507 2.629051 CTCCGTCCCAAATTAGGTGTC 58.371 52.381 0.00 0.00 0.00 3.67
4119 7508 2.236395 CTCCGTCCCAAATTAGGTGTCT 59.764 50.000 0.00 0.00 0.00 3.41
4120 7509 2.640826 TCCGTCCCAAATTAGGTGTCTT 59.359 45.455 0.00 0.00 0.00 3.01
4121 7510 3.839490 TCCGTCCCAAATTAGGTGTCTTA 59.161 43.478 0.00 0.00 0.00 2.10
4122 7511 4.286549 TCCGTCCCAAATTAGGTGTCTTAA 59.713 41.667 0.00 0.00 0.00 1.85
4123 7512 4.393990 CCGTCCCAAATTAGGTGTCTTAAC 59.606 45.833 0.00 0.00 0.00 2.01
4124 7513 5.243207 CGTCCCAAATTAGGTGTCTTAACT 58.757 41.667 0.00 0.00 0.00 2.24
4125 7514 5.704053 CGTCCCAAATTAGGTGTCTTAACTT 59.296 40.000 0.00 0.00 0.00 2.66
4126 7515 6.206048 CGTCCCAAATTAGGTGTCTTAACTTT 59.794 38.462 0.00 0.00 0.00 2.66
4127 7516 7.368059 GTCCCAAATTAGGTGTCTTAACTTTG 58.632 38.462 0.00 0.00 0.00 2.77
4128 7517 7.013942 GTCCCAAATTAGGTGTCTTAACTTTGT 59.986 37.037 0.00 0.00 0.00 2.83
4129 7518 8.219178 TCCCAAATTAGGTGTCTTAACTTTGTA 58.781 33.333 0.00 0.00 0.00 2.41
4130 7519 8.294577 CCCAAATTAGGTGTCTTAACTTTGTAC 58.705 37.037 0.00 0.00 0.00 2.90
4131 7520 9.063615 CCAAATTAGGTGTCTTAACTTTGTACT 57.936 33.333 0.00 0.00 0.00 2.73
4159 7548 9.503399 ACTTTAAGGTTAAGACACTTATTCTGG 57.497 33.333 0.00 0.00 0.00 3.86
4160 7549 8.857694 TTTAAGGTTAAGACACTTATTCTGGG 57.142 34.615 0.00 0.00 0.00 4.45
4161 7550 6.697641 AAGGTTAAGACACTTATTCTGGGA 57.302 37.500 0.00 0.00 0.00 4.37
4162 7551 6.051179 AGGTTAAGACACTTATTCTGGGAC 57.949 41.667 0.00 0.00 0.00 4.46
4163 7552 4.868734 GGTTAAGACACTTATTCTGGGACG 59.131 45.833 0.00 0.00 0.00 4.79
4164 7553 3.611766 AAGACACTTATTCTGGGACGG 57.388 47.619 0.00 0.00 0.00 4.79
4165 7554 2.816411 AGACACTTATTCTGGGACGGA 58.184 47.619 0.00 0.00 45.11 4.69
4290 7781 7.669427 TGAAAATCTTGCCTACAAATTGTCAT 58.331 30.769 0.22 0.00 34.74 3.06
4364 7855 5.368145 TGTCACATGGCTCTATATGGTTTC 58.632 41.667 0.00 0.00 0.00 2.78
4645 8137 1.906994 TTGCATGCAGTACCGCGTTC 61.907 55.000 21.50 0.00 33.35 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 1.809271 GCGTGCATCCAGATCATGAGT 60.809 52.381 0.09 0.00 0.00 3.41
67 68 1.904990 GAAGTGGAGCTCCCCTGGTC 61.905 65.000 29.95 15.20 34.29 4.02
79 80 0.611062 ATCCTCGTCGTGGAAGTGGA 60.611 55.000 19.11 5.16 37.87 4.02
88 89 0.461516 TCTACGCTGATCCTCGTCGT 60.462 55.000 11.78 6.39 39.79 4.34
217 218 1.153289 CTGGCTTCTCATGGTCCGG 60.153 63.158 0.00 0.00 0.00 5.14
257 258 0.871057 GCGCTATTTCCAGATGCCTC 59.129 55.000 0.00 0.00 0.00 4.70
262 263 0.882042 CCAGCGCGCTATTTCCAGAT 60.882 55.000 36.02 4.43 0.00 2.90
271 272 2.420043 GGGATAACCAGCGCGCTA 59.580 61.111 36.02 19.81 39.85 4.26
367 368 1.892819 CTTCTGAAGAGGCGAGGGCA 61.893 60.000 12.01 0.00 42.47 5.36
368 369 1.153469 CTTCTGAAGAGGCGAGGGC 60.153 63.158 12.01 0.00 38.90 5.19
391 392 2.143122 TCAAATGCCGTCAAGACAGAC 58.857 47.619 0.72 0.00 35.19 3.51
395 396 2.487762 TGGAATCAAATGCCGTCAAGAC 59.512 45.455 0.00 0.00 0.00 3.01
397 398 3.788333 ATGGAATCAAATGCCGTCAAG 57.212 42.857 0.00 0.00 0.00 3.02
405 406 3.198200 TCCTTGGGCAATGGAATCAAATG 59.802 43.478 0.00 0.00 0.00 2.32
408 409 2.619697 TCCTTGGGCAATGGAATCAA 57.380 45.000 0.00 0.00 0.00 2.57
420 421 0.918983 TTCTGCCAGGTATCCTTGGG 59.081 55.000 0.00 0.00 0.00 4.12
421 422 1.748591 GCTTCTGCCAGGTATCCTTGG 60.749 57.143 0.00 0.00 0.00 3.61
422 423 1.065199 TGCTTCTGCCAGGTATCCTTG 60.065 52.381 0.00 0.00 38.71 3.61
425 426 1.952296 CATTGCTTCTGCCAGGTATCC 59.048 52.381 0.00 0.00 38.71 2.59
426 427 2.357009 CACATTGCTTCTGCCAGGTATC 59.643 50.000 0.00 0.00 38.71 2.24
428 429 1.614051 CCACATTGCTTCTGCCAGGTA 60.614 52.381 0.00 0.00 38.71 3.08
429 430 0.896940 CCACATTGCTTCTGCCAGGT 60.897 55.000 0.00 0.00 38.71 4.00
430 431 0.609957 TCCACATTGCTTCTGCCAGG 60.610 55.000 0.00 0.00 38.71 4.45
431 432 0.524862 GTCCACATTGCTTCTGCCAG 59.475 55.000 0.00 0.00 38.71 4.85
432 433 0.111061 AGTCCACATTGCTTCTGCCA 59.889 50.000 0.00 0.00 38.71 4.92
433 434 1.251251 AAGTCCACATTGCTTCTGCC 58.749 50.000 0.00 0.00 38.71 4.85
434 435 4.708726 AATAAGTCCACATTGCTTCTGC 57.291 40.909 0.00 0.00 40.20 4.26
459 1607 2.327325 ACCCTGTACTCCACTGATGT 57.673 50.000 0.00 0.00 0.00 3.06
496 1644 8.402472 CACAAGAGACTCTCTAGTATAGGTTTG 58.598 40.741 9.08 2.80 40.28 2.93
554 1702 5.189736 TCACAGATTATAGAGGTTTGCAGGT 59.810 40.000 0.00 0.00 0.00 4.00
594 1742 7.256756 TGGTTTTCATTTTTAAGCAACCATG 57.743 32.000 0.00 0.00 37.79 3.66
597 1745 7.315247 ACTTGGTTTTCATTTTTAAGCAACC 57.685 32.000 0.00 0.00 35.20 3.77
599 1747 9.617975 CAAAACTTGGTTTTCATTTTTAAGCAA 57.382 25.926 5.55 0.00 42.78 3.91
602 1750 8.239998 TGGCAAAACTTGGTTTTCATTTTTAAG 58.760 29.630 5.55 0.00 42.78 1.85
603 1751 8.110860 TGGCAAAACTTGGTTTTCATTTTTAA 57.889 26.923 5.55 0.00 42.78 1.52
604 1752 7.148171 CCTGGCAAAACTTGGTTTTCATTTTTA 60.148 33.333 5.55 0.00 42.78 1.52
609 1757 3.807553 CCTGGCAAAACTTGGTTTTCAT 58.192 40.909 5.55 0.00 42.78 2.57
611 1759 1.939934 GCCTGGCAAAACTTGGTTTTC 59.060 47.619 15.17 2.53 42.78 2.29
616 1764 2.356194 GCGCCTGGCAAAACTTGG 60.356 61.111 20.29 0.12 42.87 3.61
617 1765 2.356194 GGCGCCTGGCAAAACTTG 60.356 61.111 22.15 0.93 46.16 3.16
626 1774 4.974721 ACCCAGTTTGGCGCCTGG 62.975 66.667 29.70 25.58 46.43 4.45
627 1775 3.673484 CACCCAGTTTGGCGCCTG 61.673 66.667 29.70 17.50 35.79 4.85
630 1778 4.347453 CTGCACCCAGTTTGGCGC 62.347 66.667 0.00 0.00 35.79 6.53
632 1780 1.588082 CATCTGCACCCAGTTTGGC 59.412 57.895 0.00 0.00 40.09 4.52
646 1794 5.879223 GCTATAATAAGTGGCAGATGCATCT 59.121 40.000 23.75 23.75 44.36 2.90
647 1795 5.645067 TGCTATAATAAGTGGCAGATGCATC 59.355 40.000 19.37 19.37 44.36 3.91
649 1797 4.971939 TGCTATAATAAGTGGCAGATGCA 58.028 39.130 7.19 0.00 44.36 3.96
655 1803 4.756642 GTGCATCTGCTATAATAAGTGGCA 59.243 41.667 3.53 0.00 42.66 4.92
656 1804 4.143030 CGTGCATCTGCTATAATAAGTGGC 60.143 45.833 3.53 0.00 42.66 5.01
657 1805 4.389992 CCGTGCATCTGCTATAATAAGTGG 59.610 45.833 3.53 0.00 42.66 4.00
658 1806 4.143030 GCCGTGCATCTGCTATAATAAGTG 60.143 45.833 3.53 0.00 42.66 3.16
660 1808 3.061295 CGCCGTGCATCTGCTATAATAAG 59.939 47.826 3.53 0.00 42.66 1.73
661 1809 2.993220 CGCCGTGCATCTGCTATAATAA 59.007 45.455 3.53 0.00 42.66 1.40
663 1811 1.432514 CGCCGTGCATCTGCTATAAT 58.567 50.000 3.53 0.00 42.66 1.28
665 1813 1.006220 CCGCCGTGCATCTGCTATA 60.006 57.895 3.53 0.00 42.66 1.31
770 2168 3.869272 GCTGATCTGCGCCGTTGG 61.869 66.667 4.18 0.00 0.00 3.77
803 2201 4.101448 AGGCCCCGCTTACTGCAG 62.101 66.667 13.48 13.48 43.06 4.41
851 2253 0.698238 TTCCCCAATCCACTCTGGTG 59.302 55.000 0.00 0.00 39.03 4.17
882 2291 1.441016 CGTGCTTCGCTGGCTTTTC 60.441 57.895 0.00 0.00 0.00 2.29
883 2292 2.639286 CGTGCTTCGCTGGCTTTT 59.361 55.556 0.00 0.00 0.00 2.27
884 2293 3.357079 CCGTGCTTCGCTGGCTTT 61.357 61.111 0.00 0.00 38.35 3.51
1346 2777 1.272781 GAACATGGAGAAGACGAGCG 58.727 55.000 0.00 0.00 0.00 5.03
1491 2922 1.874019 CTCCGTCATGTCGAAGCGG 60.874 63.158 14.01 9.04 43.32 5.52
1705 3139 3.499737 CCGTCTGATGTTGCCCGC 61.500 66.667 0.00 0.00 0.00 6.13
1714 3148 3.790437 CCAGCAGGCCCGTCTGAT 61.790 66.667 15.65 0.00 36.93 2.90
1836 3270 3.194116 CACCCCTCATCATCAAAAACAGG 59.806 47.826 0.00 0.00 0.00 4.00
1900 5134 1.122019 CCCTCCTTACATAGGCCGCT 61.122 60.000 0.00 0.00 44.37 5.52
1929 5163 2.034879 AAGCAACATCCTGGCGTCG 61.035 57.895 0.00 0.00 0.00 5.12
1986 5220 7.168219 ACCCTACGATCATTGCATTATATGTT 58.832 34.615 0.00 0.00 0.00 2.71
2013 5352 1.354031 TGCATCCTTCCTGCCTTACAA 59.646 47.619 0.00 0.00 38.89 2.41
2088 5427 2.093306 TCAAAGTGCCGTATGTCCAG 57.907 50.000 0.00 0.00 0.00 3.86
2342 5681 2.222027 ACAACTCCTTCGCCTCTTTTG 58.778 47.619 0.00 0.00 0.00 2.44
2503 5842 2.497675 TCAGAGAGTTGTAGGTCCATGC 59.502 50.000 0.00 0.00 0.00 4.06
2722 6061 1.897398 GCACCAGTTAAGACGGCGTG 61.897 60.000 21.19 1.98 0.00 5.34
2883 6222 1.212688 CACCCCTCACCAATCATGCTA 59.787 52.381 0.00 0.00 0.00 3.49
2901 6240 1.459592 GTGTACGAATCTGGTGTGCAC 59.540 52.381 10.75 10.75 40.88 4.57
3568 6907 8.096621 TCTTCATTGGGTGGTATATCTTTACA 57.903 34.615 0.00 0.00 0.00 2.41
3724 7063 6.292923 TCTCAAATTCTCCCTCGTTACAAAA 58.707 36.000 0.00 0.00 0.00 2.44
4065 7454 4.759693 TGATTTGTGTGGACACTTACCATC 59.240 41.667 11.09 6.12 46.55 3.51
4097 7486 1.280998 ACACCTAATTTGGGACGGAGG 59.719 52.381 10.77 0.00 0.00 4.30
4098 7487 2.236395 AGACACCTAATTTGGGACGGAG 59.764 50.000 10.77 0.00 0.00 4.63
4099 7488 2.262637 AGACACCTAATTTGGGACGGA 58.737 47.619 10.77 0.00 0.00 4.69
4100 7489 2.781681 AGACACCTAATTTGGGACGG 57.218 50.000 10.77 0.14 0.00 4.79
4101 7490 5.243207 AGTTAAGACACCTAATTTGGGACG 58.757 41.667 10.77 1.39 0.00 4.79
4102 7491 7.013942 ACAAAGTTAAGACACCTAATTTGGGAC 59.986 37.037 10.77 1.77 32.19 4.46
4103 7492 7.064229 ACAAAGTTAAGACACCTAATTTGGGA 58.936 34.615 10.77 0.00 32.19 4.37
4104 7493 7.284919 ACAAAGTTAAGACACCTAATTTGGG 57.715 36.000 10.77 0.00 32.19 4.12
4105 7494 9.063615 AGTACAAAGTTAAGACACCTAATTTGG 57.936 33.333 4.22 4.22 32.19 3.28
4133 7522 9.503399 CCAGAATAAGTGTCTTAACCTTAAAGT 57.497 33.333 0.00 0.00 0.00 2.66
4134 7523 8.947115 CCCAGAATAAGTGTCTTAACCTTAAAG 58.053 37.037 0.00 0.00 0.00 1.85
4135 7524 8.662255 TCCCAGAATAAGTGTCTTAACCTTAAA 58.338 33.333 0.00 0.00 0.00 1.52
4136 7525 8.098912 GTCCCAGAATAAGTGTCTTAACCTTAA 58.901 37.037 0.00 0.00 0.00 1.85
4137 7526 7.578189 CGTCCCAGAATAAGTGTCTTAACCTTA 60.578 40.741 0.00 0.00 0.00 2.69
4138 7527 6.473758 GTCCCAGAATAAGTGTCTTAACCTT 58.526 40.000 0.00 0.00 0.00 3.50
4139 7528 5.337330 CGTCCCAGAATAAGTGTCTTAACCT 60.337 44.000 0.00 0.00 0.00 3.50
4140 7529 4.868734 CGTCCCAGAATAAGTGTCTTAACC 59.131 45.833 0.00 0.00 0.00 2.85
4141 7530 4.868734 CCGTCCCAGAATAAGTGTCTTAAC 59.131 45.833 0.00 0.00 0.00 2.01
4142 7531 4.773674 TCCGTCCCAGAATAAGTGTCTTAA 59.226 41.667 0.00 0.00 0.00 1.85
4143 7532 4.346730 TCCGTCCCAGAATAAGTGTCTTA 58.653 43.478 0.00 0.00 0.00 2.10
4144 7533 3.170717 TCCGTCCCAGAATAAGTGTCTT 58.829 45.455 0.00 0.00 0.00 3.01
4145 7534 2.761208 CTCCGTCCCAGAATAAGTGTCT 59.239 50.000 0.00 0.00 0.00 3.41
4146 7535 2.159085 CCTCCGTCCCAGAATAAGTGTC 60.159 54.545 0.00 0.00 0.00 3.67
4147 7536 1.831736 CCTCCGTCCCAGAATAAGTGT 59.168 52.381 0.00 0.00 0.00 3.55
4148 7537 1.139058 CCCTCCGTCCCAGAATAAGTG 59.861 57.143 0.00 0.00 0.00 3.16
4149 7538 1.007963 TCCCTCCGTCCCAGAATAAGT 59.992 52.381 0.00 0.00 0.00 2.24
4150 7539 1.689273 CTCCCTCCGTCCCAGAATAAG 59.311 57.143 0.00 0.00 0.00 1.73
4151 7540 1.007963 ACTCCCTCCGTCCCAGAATAA 59.992 52.381 0.00 0.00 0.00 1.40
4152 7541 0.635009 ACTCCCTCCGTCCCAGAATA 59.365 55.000 0.00 0.00 0.00 1.75
4153 7542 0.635009 TACTCCCTCCGTCCCAGAAT 59.365 55.000 0.00 0.00 0.00 2.40
4154 7543 0.324091 GTACTCCCTCCGTCCCAGAA 60.324 60.000 0.00 0.00 0.00 3.02
4155 7544 1.212934 AGTACTCCCTCCGTCCCAGA 61.213 60.000 0.00 0.00 0.00 3.86
4156 7545 0.549950 TAGTACTCCCTCCGTCCCAG 59.450 60.000 0.00 0.00 0.00 4.45
4157 7546 1.229131 ATAGTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
4158 7547 3.735720 ATATAGTACTCCCTCCGTCCC 57.264 52.381 0.00 0.00 0.00 4.46
4159 7548 8.993404 ATAAATATATAGTACTCCCTCCGTCC 57.007 38.462 0.00 0.00 0.00 4.79
4160 7549 9.065798 GGATAAATATATAGTACTCCCTCCGTC 57.934 40.741 0.00 0.00 0.00 4.79
4161 7550 8.563502 TGGATAAATATATAGTACTCCCTCCGT 58.436 37.037 0.00 0.00 0.00 4.69
4162 7551 8.991783 TGGATAAATATATAGTACTCCCTCCG 57.008 38.462 0.00 0.00 0.00 4.63
4290 7781 9.906660 GATACAGGTTATGATTTGAAAACAACA 57.093 29.630 0.00 0.00 0.00 3.33
4364 7855 1.396301 GTGGAGCTTTCAGCAGATTCG 59.604 52.381 0.00 0.00 45.56 3.34
4578 8070 2.885135 ATTGCACATGTCTTCCTGGA 57.115 45.000 0.00 0.00 0.00 3.86
4636 8128 2.086094 TCAGTCATGTAGAACGCGGTA 58.914 47.619 12.47 0.00 0.00 4.02
4645 8137 5.042593 GCTCATCTCAAGTCAGTCATGTAG 58.957 45.833 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.