Multiple sequence alignment - TraesCS4A01G120600

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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 TraesCS4A01G120600 chr4A 100.000 2393 0 0 1 2393 148756720 148759112 0.000000e+00 4420.0
1 TraesCS4A01G120600 chr4A 94.444 198 7 4 635 830 11366009 11366204 3.870000e-78 302.0
2 TraesCS4A01G120600 chr4A 91.981 212 15 2 630 840 381476999 381476789 1.800000e-76 296.0
3 TraesCS4A01G120600 chr4D 92.190 1562 80 19 839 2393 323355128 323353602 0.000000e+00 2170.0
4 TraesCS4A01G120600 chr4D 93.109 653 31 11 1 647 323355769 323355125 0.000000e+00 944.0
5 TraesCS4A01G120600 chr4B 94.656 917 42 3 843 1758 403624969 403624059 0.000000e+00 1415.0
6 TraesCS4A01G120600 chr4B 91.988 649 35 13 1 644 403625607 403624971 0.000000e+00 894.0
7 TraesCS4A01G120600 chr4B 91.556 450 30 4 1952 2393 403623804 403623355 4.370000e-172 614.0
8 TraesCS4A01G120600 chr4B 89.444 180 6 8 1792 1968 403624063 403623894 5.180000e-52 215.0
9 TraesCS4A01G120600 chr4B 82.160 213 28 6 86 291 44311533 44311324 8.790000e-40 174.0
10 TraesCS4A01G120600 chr4B 91.935 62 5 0 378 439 618339877 618339816 1.180000e-13 87.9
11 TraesCS4A01G120600 chr6A 96.216 185 6 1 646 830 180309156 180309339 3.870000e-78 302.0
12 TraesCS4A01G120600 chr6A 93.000 100 4 3 1661 1757 18580781 18580880 2.480000e-30 143.0
13 TraesCS4A01G120600 chr6A 92.157 102 4 4 1658 1758 520853853 520853755 8.920000e-30 141.0
14 TraesCS4A01G120600 chr2A 94.416 197 9 2 644 839 196518152 196517957 3.870000e-78 302.0
15 TraesCS4A01G120600 chr2A 80.769 260 38 11 1150 1405 15270128 15270379 2.430000e-45 193.0
16 TraesCS4A01G120600 chr3A 94.792 192 8 2 648 838 56664110 56664300 5.000000e-77 298.0
17 TraesCS4A01G120600 chr3A 91.388 209 16 2 634 841 434835110 434834903 3.890000e-73 285.0
18 TraesCS4A01G120600 chr3A 94.624 93 4 1 1667 1759 25368086 25367995 2.480000e-30 143.0
19 TraesCS4A01G120600 chr5A 93.909 197 11 1 639 835 656052155 656052350 1.800000e-76 296.0
20 TraesCS4A01G120600 chr5A 89.024 82 8 1 88 168 19486562 19486481 1.510000e-17 100.0
21 TraesCS4A01G120600 chr1A 92.683 205 14 1 638 841 309178222 309178426 6.470000e-76 294.0
22 TraesCS4A01G120600 chr1A 92.157 204 14 2 638 841 397087438 397087639 1.080000e-73 287.0
23 TraesCS4A01G120600 chr1A 74.351 308 49 19 75 363 94109031 94109327 1.170000e-18 104.0
24 TraesCS4A01G120600 chr2D 80.385 260 39 12 1150 1405 13228795 13229046 1.130000e-43 187.0
25 TraesCS4A01G120600 chr2D 88.034 117 7 7 1669 1779 617538277 617538392 5.370000e-27 132.0
26 TraesCS4A01G120600 chr2D 77.778 126 24 4 85 207 72349248 72349124 9.170000e-10 75.0
27 TraesCS4A01G120600 chr2B 80.876 251 36 11 1159 1405 23878254 23878496 1.130000e-43 187.0
28 TraesCS4A01G120600 chr6B 95.604 91 2 2 1658 1747 32295641 32295730 6.890000e-31 145.0
29 TraesCS4A01G120600 chr6D 93.684 95 2 4 1654 1747 17998717 17998808 3.210000e-29 139.0
30 TraesCS4A01G120600 chr6D 78.824 85 14 3 86 168 386057130 386057212 1.000000e-03 54.7
31 TraesCS4A01G120600 chr3B 90.566 106 5 4 1670 1774 5587343 5587444 4.150000e-28 135.0
32 TraesCS4A01G120600 chr1B 78.199 211 37 4 86 288 584313902 584314111 2.500000e-25 126.0
33 TraesCS4A01G120600 chr5D 84.553 123 15 4 86 207 56917259 56917378 4.180000e-23 119.0
34 TraesCS4A01G120600 chr7B 83.529 85 10 4 438 520 635941889 635941807 2.550000e-10 76.8
35 TraesCS4A01G120600 chr7A 84.375 64 10 0 376 439 176725786 176725849 1.990000e-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 TraesCS4A01G120600 chr4A 148756720 148759112 2392 False 4420.0 4420 100.0000 1 2393 1 chr4A.!!$F2 2392
1 TraesCS4A01G120600 chr4D 323353602 323355769 2167 True 1557.0 2170 92.6495 1 2393 2 chr4D.!!$R1 2392
2 TraesCS4A01G120600 chr4B 403623355 403625607 2252 True 784.5 1415 91.9110 1 2393 4 chr4B.!!$R3 2392

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
835 843 0.462047 GCCCTAGACACACCCGATTG 60.462 60.0 0.0 0.0 0.0 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2269 2393 0.035439 ACCCTGCATTACTTGGACGG 60.035 55.0 0.0 0.0 0.0 4.79 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
168 169 1.403679 TGTGGAAGTCGTGGCAAAAAG 59.596 47.619 0.00 0.00 0.00 2.27
170 171 2.098443 GTGGAAGTCGTGGCAAAAAGAA 59.902 45.455 0.00 0.00 0.00 2.52
171 172 2.357637 TGGAAGTCGTGGCAAAAAGAAG 59.642 45.455 0.00 0.00 0.00 2.85
283 286 7.148356 TGCAAGCACACAAAATATTTGTCAAAA 60.148 29.630 0.39 0.00 0.00 2.44
353 358 1.549203 TCAAGGGGCATTTTGAGCTC 58.451 50.000 6.82 6.82 0.00 4.09
369 374 3.319405 TGAGCTCGGGATCAGAATAGAAC 59.681 47.826 0.00 0.00 32.54 3.01
443 448 8.834465 ACATGATGAGAGATATTGTGCTTAAAC 58.166 33.333 0.00 0.00 0.00 2.01
460 465 5.855395 GCTTAAACAAGAGAAGACAAGCATG 59.145 40.000 0.00 0.00 37.63 4.06
461 466 3.911661 AACAAGAGAAGACAAGCATGC 57.088 42.857 10.51 10.51 0.00 4.06
462 467 2.157738 ACAAGAGAAGACAAGCATGCC 58.842 47.619 15.66 0.00 0.00 4.40
482 488 5.308825 TGCCTTTTCGATTTCTCTCTTCTT 58.691 37.500 0.00 0.00 0.00 2.52
547 555 4.134563 AGCAATTTATACAGGCCCTTACG 58.865 43.478 0.00 0.00 0.00 3.18
548 556 4.131596 GCAATTTATACAGGCCCTTACGA 58.868 43.478 0.00 0.00 0.00 3.43
622 630 3.626670 CCTGTAACAAACCCGTAACAACA 59.373 43.478 0.00 0.00 0.00 3.33
650 658 8.794553 CGTAGGTCTAGGATTATTGATAACAGT 58.205 37.037 0.00 0.00 0.00 3.55
655 663 9.937175 GTCTAGGATTATTGATAACAGTTTTGC 57.063 33.333 0.00 0.00 0.00 3.68
656 664 9.905713 TCTAGGATTATTGATAACAGTTTTGCT 57.094 29.630 0.00 0.00 0.00 3.91
687 695 7.651808 ACATCTAAATGTGCCATAAGTATTGC 58.348 34.615 0.00 0.00 44.51 3.56
688 696 7.285172 ACATCTAAATGTGCCATAAGTATTGCA 59.715 33.333 0.00 0.00 44.51 4.08
696 704 6.866010 TGCCATAAGTATTGCACATCTAAG 57.134 37.500 0.00 0.00 30.49 2.18
697 705 6.356556 TGCCATAAGTATTGCACATCTAAGT 58.643 36.000 0.00 0.00 30.49 2.24
698 706 6.483307 TGCCATAAGTATTGCACATCTAAGTC 59.517 38.462 0.00 0.00 30.49 3.01
699 707 6.483307 GCCATAAGTATTGCACATCTAAGTCA 59.517 38.462 0.00 0.00 0.00 3.41
700 708 7.173907 GCCATAAGTATTGCACATCTAAGTCAT 59.826 37.037 0.00 0.00 0.00 3.06
701 709 9.710900 CCATAAGTATTGCACATCTAAGTCATA 57.289 33.333 0.00 0.00 0.00 2.15
705 713 8.824159 AGTATTGCACATCTAAGTCATATGTC 57.176 34.615 1.90 0.00 31.60 3.06
706 714 8.424133 AGTATTGCACATCTAAGTCATATGTCA 58.576 33.333 1.90 0.00 31.60 3.58
707 715 9.212641 GTATTGCACATCTAAGTCATATGTCAT 57.787 33.333 1.90 0.00 31.60 3.06
708 716 8.687292 ATTGCACATCTAAGTCATATGTCATT 57.313 30.769 1.90 0.00 31.60 2.57
709 717 7.486802 TGCACATCTAAGTCATATGTCATTG 57.513 36.000 1.90 0.00 31.60 2.82
710 718 7.274447 TGCACATCTAAGTCATATGTCATTGA 58.726 34.615 1.90 0.00 31.60 2.57
711 719 7.935210 TGCACATCTAAGTCATATGTCATTGAT 59.065 33.333 1.90 0.00 31.60 2.57
712 720 8.781196 GCACATCTAAGTCATATGTCATTGATT 58.219 33.333 1.90 0.00 31.60 2.57
781 789 8.801715 TTTTCTTTTATGCTTGATTCACTCAC 57.198 30.769 0.00 0.00 32.17 3.51
782 790 7.750229 TTCTTTTATGCTTGATTCACTCACT 57.250 32.000 0.00 0.00 32.17 3.41
783 791 7.750229 TCTTTTATGCTTGATTCACTCACTT 57.250 32.000 0.00 0.00 32.17 3.16
784 792 8.846943 TCTTTTATGCTTGATTCACTCACTTA 57.153 30.769 0.00 0.00 32.17 2.24
785 793 8.939929 TCTTTTATGCTTGATTCACTCACTTAG 58.060 33.333 0.00 0.00 32.17 2.18
786 794 8.846943 TTTTATGCTTGATTCACTCACTTAGA 57.153 30.769 0.00 0.00 32.17 2.10
787 795 9.453572 TTTTATGCTTGATTCACTCACTTAGAT 57.546 29.630 0.00 0.00 32.17 1.98
788 796 6.922247 ATGCTTGATTCACTCACTTAGATG 57.078 37.500 0.00 0.00 32.17 2.90
789 797 5.798132 TGCTTGATTCACTCACTTAGATGT 58.202 37.500 0.00 0.00 32.17 3.06
790 798 5.640783 TGCTTGATTCACTCACTTAGATGTG 59.359 40.000 0.00 0.00 39.15 3.21
791 799 5.447010 GCTTGATTCACTCACTTAGATGTGC 60.447 44.000 0.00 0.00 37.81 4.57
792 800 5.151297 TGATTCACTCACTTAGATGTGCA 57.849 39.130 0.00 0.00 37.81 4.57
793 801 5.550290 TGATTCACTCACTTAGATGTGCAA 58.450 37.500 0.00 0.00 37.81 4.08
794 802 6.175471 TGATTCACTCACTTAGATGTGCAAT 58.825 36.000 0.00 0.00 37.81 3.56
795 803 7.330262 TGATTCACTCACTTAGATGTGCAATA 58.670 34.615 0.00 0.00 37.81 1.90
796 804 7.823799 TGATTCACTCACTTAGATGTGCAATAA 59.176 33.333 0.00 0.00 37.81 1.40
797 805 6.968131 TCACTCACTTAGATGTGCAATAAC 57.032 37.500 0.00 0.00 37.81 1.89
798 806 6.701340 TCACTCACTTAGATGTGCAATAACT 58.299 36.000 0.00 0.00 37.81 2.24
799 807 7.836842 TCACTCACTTAGATGTGCAATAACTA 58.163 34.615 0.00 0.00 37.81 2.24
800 808 8.311109 TCACTCACTTAGATGTGCAATAACTAA 58.689 33.333 0.00 0.00 37.81 2.24
801 809 8.935844 CACTCACTTAGATGTGCAATAACTAAA 58.064 33.333 0.00 0.00 37.81 1.85
802 810 9.155975 ACTCACTTAGATGTGCAATAACTAAAG 57.844 33.333 0.00 0.00 37.81 1.85
803 811 7.974675 TCACTTAGATGTGCAATAACTAAAGC 58.025 34.615 0.00 0.00 37.81 3.51
804 812 7.606073 TCACTTAGATGTGCAATAACTAAAGCA 59.394 33.333 0.00 0.00 37.81 3.91
805 813 8.400947 CACTTAGATGTGCAATAACTAAAGCAT 58.599 33.333 0.00 0.00 39.43 3.79
806 814 9.613428 ACTTAGATGTGCAATAACTAAAGCATA 57.387 29.630 0.00 0.00 39.43 3.14
824 832 5.004922 GCATATCTAGATGTGCCCTAGAC 57.995 47.826 32.93 12.44 46.14 2.59
825 833 4.464244 GCATATCTAGATGTGCCCTAGACA 59.536 45.833 32.93 4.75 46.14 3.41
826 834 5.623368 GCATATCTAGATGTGCCCTAGACAC 60.623 48.000 32.93 11.25 46.14 3.67
830 838 3.478780 TGTGCCCTAGACACACCC 58.521 61.111 12.81 0.00 42.88 4.61
831 839 2.264794 GTGCCCTAGACACACCCG 59.735 66.667 10.07 0.00 37.96 5.28
832 840 2.118732 TGCCCTAGACACACCCGA 59.881 61.111 0.00 0.00 0.00 5.14
833 841 1.305802 TGCCCTAGACACACCCGAT 60.306 57.895 0.00 0.00 0.00 4.18
834 842 0.907704 TGCCCTAGACACACCCGATT 60.908 55.000 0.00 0.00 0.00 3.34
835 843 0.462047 GCCCTAGACACACCCGATTG 60.462 60.000 0.00 0.00 0.00 2.67
836 844 1.191535 CCCTAGACACACCCGATTGA 58.808 55.000 0.00 0.00 0.00 2.57
837 845 1.762957 CCCTAGACACACCCGATTGAT 59.237 52.381 0.00 0.00 0.00 2.57
838 846 2.963101 CCCTAGACACACCCGATTGATA 59.037 50.000 0.00 0.00 0.00 2.15
839 847 3.386726 CCCTAGACACACCCGATTGATAA 59.613 47.826 0.00 0.00 0.00 1.75
840 848 4.141801 CCCTAGACACACCCGATTGATAAA 60.142 45.833 0.00 0.00 0.00 1.40
841 849 5.454755 CCCTAGACACACCCGATTGATAAAT 60.455 44.000 0.00 0.00 0.00 1.40
865 873 5.762179 TCTTCTAGAAAGGAAATCTGCCA 57.238 39.130 6.63 0.00 0.00 4.92
938 946 4.712122 CCACATAAAAATGGCGTAACCT 57.288 40.909 0.00 0.00 40.22 3.50
978 988 3.073946 CCAAAACCTTCTCTTCCACCCTA 59.926 47.826 0.00 0.00 0.00 3.53
993 1003 0.673644 CCCTACTGCGAACCAAGTGG 60.674 60.000 0.00 0.00 42.17 4.00
1285 1295 1.986757 GAGGTGGAGGAGCTCAGCA 60.987 63.158 17.19 0.00 46.77 4.41
1432 1442 2.751436 GCTTCTGCCATTGCCGGA 60.751 61.111 5.05 0.00 36.33 5.14
1469 1479 1.427020 CTTCTGGCTTAGCTTGCGC 59.573 57.895 0.00 0.00 0.00 6.09
1522 1533 5.918608 TGGTTTGTTGCTTTATTTGGCTTA 58.081 33.333 0.00 0.00 0.00 3.09
1630 1644 0.745845 CAAGGCAAGCTGCGAGGTAT 60.746 55.000 0.00 0.00 46.21 2.73
1640 1654 2.670414 GCTGCGAGGTATCATGCTAATC 59.330 50.000 0.00 0.00 0.00 1.75
1644 1658 4.202253 TGCGAGGTATCATGCTAATCAAGT 60.202 41.667 0.00 0.00 0.00 3.16
1645 1659 5.010617 TGCGAGGTATCATGCTAATCAAGTA 59.989 40.000 0.00 0.00 0.00 2.24
1646 1660 5.926542 GCGAGGTATCATGCTAATCAAGTAA 59.073 40.000 0.00 0.00 0.00 2.24
1647 1661 6.090088 GCGAGGTATCATGCTAATCAAGTAAG 59.910 42.308 0.00 0.00 0.00 2.34
1656 1670 9.453572 TCATGCTAATCAAGTAAGACTTCAATT 57.546 29.630 0.00 0.00 36.03 2.32
1762 1776 9.426837 CTGATATTTTTCCTTCATTTTTGCAGA 57.573 29.630 0.00 0.00 0.00 4.26
1763 1777 9.947433 TGATATTTTTCCTTCATTTTTGCAGAT 57.053 25.926 0.00 0.00 0.00 2.90
1824 1838 5.221283 CCGTTTTTCCCCTTTGCTTTTACTA 60.221 40.000 0.00 0.00 0.00 1.82
1825 1839 5.918576 CGTTTTTCCCCTTTGCTTTTACTAG 59.081 40.000 0.00 0.00 0.00 2.57
1826 1840 6.460537 CGTTTTTCCCCTTTGCTTTTACTAGT 60.461 38.462 0.00 0.00 0.00 2.57
1827 1841 7.270047 GTTTTTCCCCTTTGCTTTTACTAGTT 58.730 34.615 0.00 0.00 0.00 2.24
1828 1842 6.644248 TTTCCCCTTTGCTTTTACTAGTTC 57.356 37.500 0.00 0.00 0.00 3.01
1829 1843 5.578157 TCCCCTTTGCTTTTACTAGTTCT 57.422 39.130 0.00 0.00 0.00 3.01
1853 1870 2.847901 CAGCATGCTCTTTCAGAAACG 58.152 47.619 19.68 0.00 0.00 3.60
1868 1885 6.479972 TCAGAAACGATGTAGGGTCATATT 57.520 37.500 0.00 0.00 0.00 1.28
1899 1916 3.275617 ACTTAGCAACTGGTTGTGACA 57.724 42.857 13.85 0.00 42.31 3.58
2003 2126 6.833416 AGAAGCCAGCATAAAAATACATACCA 59.167 34.615 0.00 0.00 0.00 3.25
2024 2147 5.121142 ACCAACAAAAACATCTATACCGACG 59.879 40.000 0.00 0.00 0.00 5.12
2101 2224 2.484742 ACCGTCCAAGTAATTCCACC 57.515 50.000 0.00 0.00 0.00 4.61
2105 2228 1.467342 GTCCAAGTAATTCCACCGTGC 59.533 52.381 0.00 0.00 0.00 5.34
2107 2230 1.468520 CCAAGTAATTCCACCGTGCTG 59.531 52.381 0.00 0.00 0.00 4.41
2120 2243 1.308998 CGTGCTGACCAAAGAAACCT 58.691 50.000 0.00 0.00 0.00 3.50
2207 2330 1.877443 AGGTTATTGCACGGTGTTCAC 59.123 47.619 10.24 0.45 0.00 3.18
2226 2349 5.560722 TCACCAGAGAAACCAAGATACAA 57.439 39.130 0.00 0.00 0.00 2.41
2269 2393 1.883084 CCCACTGCGGCGTCTATTC 60.883 63.158 9.37 0.00 0.00 1.75
2285 2409 4.508124 GTCTATTCCGTCCAAGTAATGCAG 59.492 45.833 0.00 0.00 0.00 4.41
2318 2449 0.961857 TGTAGTCGCCGCTTAGGACA 60.962 55.000 0.00 0.00 45.00 4.02
2347 2478 4.598036 ACTCATGTCCCAGAATCCAATT 57.402 40.909 0.00 0.00 0.00 2.32
2355 2486 3.102204 CCCAGAATCCAATTTCCAGCTT 58.898 45.455 0.00 0.00 0.00 3.74
2356 2487 4.017591 TCCCAGAATCCAATTTCCAGCTTA 60.018 41.667 0.00 0.00 0.00 3.09
2362 2493 2.825532 TCCAATTTCCAGCTTAAGCACC 59.174 45.455 28.39 0.05 45.16 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.247185 CAAATTCTTGGCCCGCATGT 59.753 50.000 0.00 0.00 0.00 3.21
84 85 6.777526 TTTGTCAAAGTTCACCACAAAAAG 57.222 33.333 0.00 0.00 34.76 2.27
89 90 5.398603 AACATTTGTCAAAGTTCACCACA 57.601 34.783 4.03 0.00 0.00 4.17
90 91 6.147000 ACAAAACATTTGTCAAAGTTCACCAC 59.853 34.615 4.03 0.00 0.00 4.16
144 145 2.552599 TGCCACGACTTCCACAAATA 57.447 45.000 0.00 0.00 0.00 1.40
151 152 2.357952 ACTTCTTTTTGCCACGACTTCC 59.642 45.455 0.00 0.00 0.00 3.46
152 153 3.692791 ACTTCTTTTTGCCACGACTTC 57.307 42.857 0.00 0.00 0.00 3.01
168 169 7.597386 ACTAGAATTTTTGGAGCATCAACTTC 58.403 34.615 0.00 0.00 36.25 3.01
170 171 7.530426 AACTAGAATTTTTGGAGCATCAACT 57.470 32.000 0.00 0.00 36.25 3.16
171 172 8.490355 CAAAACTAGAATTTTTGGAGCATCAAC 58.510 33.333 0.00 0.00 39.34 3.18
258 261 5.903764 TGACAAATATTTTGTGTGCTTGC 57.096 34.783 10.13 0.00 31.96 4.01
337 341 1.379044 CCGAGCTCAAAATGCCCCT 60.379 57.895 15.40 0.00 0.00 4.79
340 344 0.665298 GATCCCGAGCTCAAAATGCC 59.335 55.000 15.40 0.00 0.00 4.40
353 358 4.446371 AGCAAAGTTCTATTCTGATCCCG 58.554 43.478 0.00 0.00 0.00 5.14
369 374 8.900983 AAGATAAGGCTAAGAGATAAGCAAAG 57.099 34.615 0.00 0.00 40.61 2.77
422 427 9.107177 CTCTTGTTTAAGCACAATATCTCTCAT 57.893 33.333 0.00 0.00 36.08 2.90
424 429 8.709386 TCTCTTGTTTAAGCACAATATCTCTC 57.291 34.615 0.00 0.00 36.08 3.20
427 432 8.940952 GTCTTCTCTTGTTTAAGCACAATATCT 58.059 33.333 0.00 0.00 36.08 1.98
443 448 2.434428 AGGCATGCTTGTCTTCTCTTG 58.566 47.619 18.92 0.00 32.61 3.02
460 465 5.409826 TGAAGAAGAGAGAAATCGAAAAGGC 59.590 40.000 0.00 0.00 0.00 4.35
461 466 7.548780 AGATGAAGAAGAGAGAAATCGAAAAGG 59.451 37.037 0.00 0.00 0.00 3.11
462 467 8.477984 AGATGAAGAAGAGAGAAATCGAAAAG 57.522 34.615 0.00 0.00 0.00 2.27
482 488 9.625747 TGCCACATAAGATAAATGTTAAGATGA 57.374 29.630 0.00 0.00 35.39 2.92
520 526 5.377478 AGGGCCTGTATAAATTGCTAAGAC 58.623 41.667 4.50 0.00 0.00 3.01
547 555 3.858247 ACCGAAAATGCTACACCTACTC 58.142 45.455 0.00 0.00 0.00 2.59
548 556 3.975168 ACCGAAAATGCTACACCTACT 57.025 42.857 0.00 0.00 0.00 2.57
622 630 7.727186 TGTTATCAATAATCCTAGACCTACGGT 59.273 37.037 0.00 0.00 39.44 4.83
673 681 6.356556 ACTTAGATGTGCAATACTTATGGCA 58.643 36.000 0.00 0.00 40.19 4.92
674 682 6.483307 TGACTTAGATGTGCAATACTTATGGC 59.517 38.462 0.00 0.00 33.16 4.40
675 683 8.613060 ATGACTTAGATGTGCAATACTTATGG 57.387 34.615 0.00 0.00 0.00 2.74
679 687 9.265901 GACATATGACTTAGATGTGCAATACTT 57.734 33.333 10.38 0.00 41.09 2.24
680 688 8.424133 TGACATATGACTTAGATGTGCAATACT 58.576 33.333 10.38 0.00 41.09 2.12
681 689 8.593492 TGACATATGACTTAGATGTGCAATAC 57.407 34.615 10.38 0.00 41.09 1.89
682 690 9.783081 AATGACATATGACTTAGATGTGCAATA 57.217 29.630 10.38 0.00 41.09 1.90
683 691 8.565416 CAATGACATATGACTTAGATGTGCAAT 58.435 33.333 10.38 0.00 41.09 3.56
684 692 7.769970 TCAATGACATATGACTTAGATGTGCAA 59.230 33.333 10.38 0.00 41.09 4.08
685 693 7.274447 TCAATGACATATGACTTAGATGTGCA 58.726 34.615 10.38 0.00 41.09 4.57
686 694 7.719778 TCAATGACATATGACTTAGATGTGC 57.280 36.000 10.38 0.00 41.09 4.57
755 763 9.248291 GTGAGTGAATCAAGCATAAAAGAAAAA 57.752 29.630 0.00 0.00 40.43 1.94
756 764 8.632679 AGTGAGTGAATCAAGCATAAAAGAAAA 58.367 29.630 0.00 0.00 40.43 2.29
757 765 8.169977 AGTGAGTGAATCAAGCATAAAAGAAA 57.830 30.769 0.00 0.00 40.43 2.52
758 766 7.750229 AGTGAGTGAATCAAGCATAAAAGAA 57.250 32.000 0.00 0.00 40.43 2.52
759 767 7.750229 AAGTGAGTGAATCAAGCATAAAAGA 57.250 32.000 0.00 0.00 40.43 2.52
760 768 8.939929 TCTAAGTGAGTGAATCAAGCATAAAAG 58.060 33.333 0.00 0.00 40.43 2.27
761 769 8.846943 TCTAAGTGAGTGAATCAAGCATAAAA 57.153 30.769 0.00 0.00 40.43 1.52
762 770 8.886719 CATCTAAGTGAGTGAATCAAGCATAAA 58.113 33.333 0.00 0.00 40.43 1.40
763 771 8.043113 ACATCTAAGTGAGTGAATCAAGCATAA 58.957 33.333 0.00 0.00 40.43 1.90
764 772 7.493645 CACATCTAAGTGAGTGAATCAAGCATA 59.506 37.037 0.00 0.00 42.05 3.14
765 773 6.315642 CACATCTAAGTGAGTGAATCAAGCAT 59.684 38.462 0.00 0.00 42.05 3.79
766 774 5.640783 CACATCTAAGTGAGTGAATCAAGCA 59.359 40.000 0.00 0.00 42.05 3.91
767 775 5.447010 GCACATCTAAGTGAGTGAATCAAGC 60.447 44.000 0.00 0.00 42.05 4.01
768 776 5.640783 TGCACATCTAAGTGAGTGAATCAAG 59.359 40.000 0.00 0.00 42.05 3.02
769 777 5.550290 TGCACATCTAAGTGAGTGAATCAA 58.450 37.500 0.00 0.00 42.05 2.57
770 778 5.151297 TGCACATCTAAGTGAGTGAATCA 57.849 39.130 0.00 0.00 42.05 2.57
771 779 6.674694 ATTGCACATCTAAGTGAGTGAATC 57.325 37.500 0.00 0.00 42.05 2.52
772 780 7.826252 AGTTATTGCACATCTAAGTGAGTGAAT 59.174 33.333 0.00 0.00 42.05 2.57
773 781 7.161404 AGTTATTGCACATCTAAGTGAGTGAA 58.839 34.615 0.00 0.00 42.05 3.18
774 782 6.701340 AGTTATTGCACATCTAAGTGAGTGA 58.299 36.000 0.00 0.00 42.05 3.41
775 783 6.974932 AGTTATTGCACATCTAAGTGAGTG 57.025 37.500 0.00 0.00 42.05 3.51
776 784 9.155975 CTTTAGTTATTGCACATCTAAGTGAGT 57.844 33.333 0.00 0.00 42.05 3.41
777 785 8.119226 GCTTTAGTTATTGCACATCTAAGTGAG 58.881 37.037 0.00 0.00 42.05 3.51
778 786 7.606073 TGCTTTAGTTATTGCACATCTAAGTGA 59.394 33.333 0.00 0.00 42.05 3.41
779 787 7.751732 TGCTTTAGTTATTGCACATCTAAGTG 58.248 34.615 0.00 0.00 42.37 3.16
780 788 7.921786 TGCTTTAGTTATTGCACATCTAAGT 57.078 32.000 0.00 0.00 0.00 2.24
784 792 8.915057 AGATATGCTTTAGTTATTGCACATCT 57.085 30.769 2.31 2.31 42.53 2.90
792 800 9.442047 GGCACATCTAGATATGCTTTAGTTATT 57.558 33.333 29.70 0.00 40.81 1.40
793 801 8.043710 GGGCACATCTAGATATGCTTTAGTTAT 58.956 37.037 29.70 0.00 40.81 1.89
794 802 7.235606 AGGGCACATCTAGATATGCTTTAGTTA 59.764 37.037 29.70 0.00 40.81 2.24
795 803 6.043706 AGGGCACATCTAGATATGCTTTAGTT 59.956 38.462 29.70 10.86 40.81 2.24
796 804 5.545723 AGGGCACATCTAGATATGCTTTAGT 59.454 40.000 29.70 11.62 40.81 2.24
797 805 6.047511 AGGGCACATCTAGATATGCTTTAG 57.952 41.667 29.70 8.18 40.81 1.85
798 806 6.954102 TCTAGGGCACATCTAGATATGCTTTA 59.046 38.462 29.70 21.31 40.81 1.85
799 807 4.989875 AGGGCACATCTAGATATGCTTT 57.010 40.909 29.70 18.03 40.81 3.51
800 808 5.186797 GTCTAGGGCACATCTAGATATGCTT 59.813 44.000 29.70 21.62 43.25 3.91
801 809 4.709397 GTCTAGGGCACATCTAGATATGCT 59.291 45.833 29.70 17.06 43.25 3.79
802 810 4.464244 TGTCTAGGGCACATCTAGATATGC 59.536 45.833 24.83 24.83 43.25 3.14
803 811 5.478332 TGTGTCTAGGGCACATCTAGATATG 59.522 44.000 6.64 6.64 43.25 1.78
804 812 5.478679 GTGTGTCTAGGGCACATCTAGATAT 59.521 44.000 18.92 0.00 46.66 1.63
805 813 4.827835 GTGTGTCTAGGGCACATCTAGATA 59.172 45.833 18.92 0.00 46.66 1.98
806 814 3.639094 GTGTGTCTAGGGCACATCTAGAT 59.361 47.826 18.92 0.00 46.66 1.98
807 815 3.024547 GTGTGTCTAGGGCACATCTAGA 58.975 50.000 18.92 0.00 46.66 2.43
808 816 2.101582 GGTGTGTCTAGGGCACATCTAG 59.898 54.545 18.92 0.00 46.66 2.43
809 817 2.108168 GGTGTGTCTAGGGCACATCTA 58.892 52.381 18.92 0.21 46.66 1.98
810 818 0.905357 GGTGTGTCTAGGGCACATCT 59.095 55.000 18.92 0.00 46.66 2.90
811 819 0.107654 GGGTGTGTCTAGGGCACATC 60.108 60.000 18.92 18.25 46.66 3.06
812 820 1.899437 CGGGTGTGTCTAGGGCACAT 61.899 60.000 18.92 0.00 46.66 3.21
813 821 2.579657 CGGGTGTGTCTAGGGCACA 61.580 63.158 14.22 14.22 43.60 4.57
814 822 1.614241 ATCGGGTGTGTCTAGGGCAC 61.614 60.000 10.20 10.20 37.37 5.01
815 823 0.907704 AATCGGGTGTGTCTAGGGCA 60.908 55.000 0.00 0.00 0.00 5.36
816 824 0.462047 CAATCGGGTGTGTCTAGGGC 60.462 60.000 0.00 0.00 0.00 5.19
817 825 1.191535 TCAATCGGGTGTGTCTAGGG 58.808 55.000 0.00 0.00 0.00 3.53
818 826 4.665833 TTATCAATCGGGTGTGTCTAGG 57.334 45.455 0.00 0.00 0.00 3.02
819 827 8.307483 AGATATTTATCAATCGGGTGTGTCTAG 58.693 37.037 0.74 0.00 35.17 2.43
820 828 8.190326 AGATATTTATCAATCGGGTGTGTCTA 57.810 34.615 0.74 0.00 35.17 2.59
821 829 7.067496 AGATATTTATCAATCGGGTGTGTCT 57.933 36.000 0.74 0.00 35.17 3.41
822 830 7.657761 AGAAGATATTTATCAATCGGGTGTGTC 59.342 37.037 0.74 0.00 35.17 3.67
823 831 7.509546 AGAAGATATTTATCAATCGGGTGTGT 58.490 34.615 0.74 0.00 35.17 3.72
824 832 7.969536 AGAAGATATTTATCAATCGGGTGTG 57.030 36.000 0.74 0.00 35.17 3.82
825 833 9.090103 TCTAGAAGATATTTATCAATCGGGTGT 57.910 33.333 0.00 0.00 35.17 4.16
826 834 9.929180 TTCTAGAAGATATTTATCAATCGGGTG 57.071 33.333 0.00 0.00 35.17 4.61
838 846 9.348476 GGCAGATTTCCTTTCTAGAAGATATTT 57.652 33.333 5.12 0.00 0.00 1.40
839 847 8.497745 TGGCAGATTTCCTTTCTAGAAGATATT 58.502 33.333 5.12 0.00 0.00 1.28
840 848 8.038862 TGGCAGATTTCCTTTCTAGAAGATAT 57.961 34.615 5.12 1.81 0.00 1.63
841 849 7.437713 TGGCAGATTTCCTTTCTAGAAGATA 57.562 36.000 5.12 0.00 0.00 1.98
853 861 0.700564 TCAGCCTTGGCAGATTTCCT 59.299 50.000 14.54 0.00 0.00 3.36
865 873 1.609061 CCGTTGTGACAGATCAGCCTT 60.609 52.381 0.00 0.00 34.75 4.35
900 908 1.035923 TGGCTCTCTGCTCCTTATCG 58.964 55.000 0.00 0.00 42.39 2.92
935 943 2.599757 GGGGTCTGGCCGTTTAGGT 61.600 63.158 0.00 0.00 43.70 3.08
938 946 1.073548 GTTGGGGTCTGGCCGTTTA 59.926 57.895 0.00 0.00 38.44 2.01
978 988 0.535102 CTTCCCACTTGGTTCGCAGT 60.535 55.000 0.00 0.00 34.77 4.40
993 1003 2.042639 ATGGTGGCCATGGCTTCC 60.043 61.111 34.70 31.94 43.39 3.46
1415 1425 2.751436 TCCGGCAATGGCAGAAGC 60.751 61.111 7.75 0.00 43.71 3.86
1432 1442 0.249073 GCTACCGCTCATGATGACGT 60.249 55.000 13.41 0.00 0.00 4.34
1469 1479 1.140161 CCAAGATGCCAATGTGCCG 59.860 57.895 0.00 0.00 0.00 5.69
1630 1644 9.453572 AATTGAAGTCTTACTTGATTAGCATGA 57.546 29.630 0.00 0.00 38.80 3.07
1656 1670 5.817296 GCCACTCTGATTTGTGTATGATGTA 59.183 40.000 0.00 0.00 32.76 2.29
1657 1671 4.637534 GCCACTCTGATTTGTGTATGATGT 59.362 41.667 0.00 0.00 32.76 3.06
1661 1675 2.223112 GCGCCACTCTGATTTGTGTATG 60.223 50.000 0.00 0.00 32.76 2.39
1662 1676 2.009774 GCGCCACTCTGATTTGTGTAT 58.990 47.619 0.00 0.00 32.76 2.29
1663 1677 1.270571 TGCGCCACTCTGATTTGTGTA 60.271 47.619 4.18 0.00 32.76 2.90
1791 1805 6.038382 GCAAAGGGGAAAAACGGATTTAAAAA 59.962 34.615 0.00 0.00 0.00 1.94
1796 1810 2.703536 AGCAAAGGGGAAAAACGGATTT 59.296 40.909 0.00 0.00 0.00 2.17
1801 1815 4.689071 AGTAAAAGCAAAGGGGAAAAACG 58.311 39.130 0.00 0.00 0.00 3.60
1853 1870 6.150318 CAGTACGTCAATATGACCCTACATC 58.850 44.000 0.00 0.00 44.20 3.06
1868 1885 4.320714 CCAGTTGCTAAGTACAGTACGTCA 60.321 45.833 2.04 0.00 0.00 4.35
1899 1916 5.543507 TGTTGCCATGTGAAAACCTAAAT 57.456 34.783 0.00 0.00 0.00 1.40
2003 2126 5.121142 CACCGTCGGTATAGATGTTTTTGTT 59.879 40.000 18.38 0.00 32.11 2.83
2024 2147 1.856265 CTGAAAACCTCGGCTGCACC 61.856 60.000 0.50 0.00 0.00 5.01
2101 2224 1.308998 AGGTTTCTTTGGTCAGCACG 58.691 50.000 0.00 0.00 0.00 5.34
2105 2228 5.577164 CACGTATCTAGGTTTCTTTGGTCAG 59.423 44.000 0.00 0.00 0.00 3.51
2107 2230 5.717119 TCACGTATCTAGGTTTCTTTGGTC 58.283 41.667 0.00 0.00 0.00 4.02
2207 2330 4.019321 TCCCTTGTATCTTGGTTTCTCTGG 60.019 45.833 0.00 0.00 0.00 3.86
2226 2349 5.324409 TCAGCATTTTACTGTCATTTCCCT 58.676 37.500 0.00 0.00 36.50 4.20
2262 2386 4.439057 TGCATTACTTGGACGGAATAGAC 58.561 43.478 0.00 0.00 0.00 2.59
2269 2393 0.035439 ACCCTGCATTACTTGGACGG 60.035 55.000 0.00 0.00 0.00 4.79
2285 2409 0.321298 ACTACATCGTGCCAACACCC 60.321 55.000 0.00 0.00 44.40 4.61
2318 2449 3.784178 TCTGGGACATGAGTTCTTCTCT 58.216 45.455 0.00 0.00 43.13 3.10
2347 2478 0.398696 TTCGGGTGCTTAAGCTGGAA 59.601 50.000 26.90 19.68 42.66 3.53
2355 2486 1.073284 AGGCTTTTCTTCGGGTGCTTA 59.927 47.619 0.00 0.00 0.00 3.09
2356 2487 0.178990 AGGCTTTTCTTCGGGTGCTT 60.179 50.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.