Multiple sequence alignment - TraesCS7B01G234800

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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 TraesCS7B01G234800 chr7B 100.000 2249 0 0 1 2249 438990265 438992513 0.000000e+00 4154
1 TraesCS7B01G234800 chr7A 87.380 1355 104 25 14 1349 511053784 511055090 0.000000e+00 1493
2 TraesCS7B01G234800 chr7A 84.549 233 20 6 1454 1684 511055093 511055311 1.350000e-52 217
3 TraesCS7B01G234800 chr7A 93.827 81 5 0 2035 2115 511055615 511055695 3.030000e-24 122
4 TraesCS7B01G234800 chr7D 93.914 953 50 5 736 1685 422109650 422108703 0.000000e+00 1432
5 TraesCS7B01G234800 chr7D 90.019 521 33 7 183 685 422110175 422109656 0.000000e+00 656
6 TraesCS7B01G234800 chr7D 89.249 493 35 12 1766 2249 422108704 422108221 3.200000e-168 601
7 TraesCS7B01G234800 chr7D 97.674 43 1 0 2128 2170 422108312 422108270 8.610000e-10 75
8 TraesCS7B01G234800 chr2D 93.548 93 4 2 1683 1773 565156920 565156828 1.080000e-28 137
9 TraesCS7B01G234800 chr3B 93.333 90 4 2 1680 1767 9287114 9287025 5.040000e-27 132
10 TraesCS7B01G234800 chr3B 93.182 88 5 1 1681 1767 138269216 138269303 6.520000e-26 128
11 TraesCS7B01G234800 chr3B 88.350 103 9 3 1675 1775 70285844 70285945 1.090000e-23 121
12 TraesCS7B01G234800 chr4B 91.398 93 7 1 1677 1768 507357681 507357773 2.340000e-25 126
13 TraesCS7B01G234800 chr3D 91.398 93 7 1 1680 1771 172830828 172830736 2.340000e-25 126
14 TraesCS7B01G234800 chr1D 91.398 93 7 1 1680 1771 473932927 473933019 2.340000e-25 126
15 TraesCS7B01G234800 chr1D 89.796 98 8 2 1684 1779 451135473 451135376 8.430000e-25 124
16 TraesCS7B01G234800 chr5D 89.796 98 9 1 1675 1771 383747175 383747272 8.430000e-25 124


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 TraesCS7B01G234800 chr7B 438990265 438992513 2248 False 4154.000000 4154 100.000000 1 2249 1 chr7B.!!$F1 2248
1 TraesCS7B01G234800 chr7A 511053784 511055695 1911 False 610.666667 1493 88.585333 14 2115 3 chr7A.!!$F1 2101
2 TraesCS7B01G234800 chr7D 422108221 422110175 1954 True 691.000000 1432 92.714000 183 2249 4 chr7D.!!$R1 2066

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
697 722 0.467474 TGGTGAGTGTGAGAGGACGT 60.467 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2197 2359 0.108472 GCATTTTGGCCTTCAGCTCC 60.108 55.0 3.32 0.0 43.05 4.7 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
25 26 4.952957 TCCTCTGATCAGTAGAAAGGACAG 59.047 45.833 20.74 9.16 0.00 3.51
31 32 2.037251 TCAGTAGAAAGGACAGGCACAC 59.963 50.000 0.00 0.00 0.00 3.82
33 34 2.706190 AGTAGAAAGGACAGGCACACTT 59.294 45.455 0.00 0.00 0.00 3.16
44 45 1.168714 GGCACACTTCATGAACCTCC 58.831 55.000 3.38 0.00 0.00 4.30
45 46 1.545428 GGCACACTTCATGAACCTCCA 60.545 52.381 3.38 0.00 0.00 3.86
46 47 2.440409 GCACACTTCATGAACCTCCAT 58.560 47.619 3.38 0.00 0.00 3.41
51 52 4.163078 ACACTTCATGAACCTCCATCCTAG 59.837 45.833 3.38 0.00 0.00 3.02
56 57 7.348274 ACTTCATGAACCTCCATCCTAGAAATA 59.652 37.037 3.38 0.00 0.00 1.40
61 62 3.648545 ACCTCCATCCTAGAAATACCAGC 59.351 47.826 0.00 0.00 0.00 4.85
73 74 6.365970 AGAAATACCAGCTCTATACATGGG 57.634 41.667 0.00 0.00 37.13 4.00
79 80 1.893801 AGCTCTATACATGGGGTACGC 59.106 52.381 0.29 0.29 43.69 4.42
96 97 2.880879 CGCGCACGCACTCACTAT 60.881 61.111 16.04 0.00 42.06 2.12
102 103 1.536284 GCACGCACTCACTATCCCTAC 60.536 57.143 0.00 0.00 0.00 3.18
108 109 2.887783 CACTCACTATCCCTACGAGCAT 59.112 50.000 0.00 0.00 0.00 3.79
112 113 5.180810 TCACTATCCCTACGAGCATATCT 57.819 43.478 0.00 0.00 0.00 1.98
117 118 4.100279 TCCCTACGAGCATATCTGAGAA 57.900 45.455 0.00 0.00 0.00 2.87
119 120 4.893524 TCCCTACGAGCATATCTGAGAAAA 59.106 41.667 0.00 0.00 0.00 2.29
123 124 4.384056 ACGAGCATATCTGAGAAAATGGG 58.616 43.478 9.36 0.00 0.00 4.00
125 126 3.494332 AGCATATCTGAGAAAATGGGCC 58.506 45.455 0.00 0.00 0.00 5.80
126 127 2.227388 GCATATCTGAGAAAATGGGCCG 59.773 50.000 0.00 0.00 0.00 6.13
128 129 0.753111 ATCTGAGAAAATGGGCCGGC 60.753 55.000 21.18 21.18 0.00 6.13
139 140 2.811514 GGGCCGGCAGATCATGAGA 61.812 63.158 30.85 0.00 0.00 3.27
144 145 2.028658 GCCGGCAGATCATGAGAATCTA 60.029 50.000 24.80 0.00 34.92 1.98
148 149 5.392919 CCGGCAGATCATGAGAATCTACTAG 60.393 48.000 0.09 0.00 34.92 2.57
160 161 8.932434 TGAGAATCTACTAGAGATGCACTTAT 57.068 34.615 0.00 0.00 44.68 1.73
161 162 9.360901 TGAGAATCTACTAGAGATGCACTTATT 57.639 33.333 0.00 0.00 44.68 1.40
170 171 7.785506 ACTAGAGATGCACTTATTAGTTACCCT 59.214 37.037 0.00 0.00 30.26 4.34
172 173 7.501844 AGAGATGCACTTATTAGTTACCCTTC 58.498 38.462 0.00 0.00 30.26 3.46
175 176 6.528537 TGCACTTATTAGTTACCCTTCGTA 57.471 37.500 0.00 0.00 30.26 3.43
181 182 8.193438 ACTTATTAGTTACCCTTCGTATGTGTC 58.807 37.037 0.00 0.00 0.00 3.67
201 208 2.655407 TCCCTCTAGGTCTTCACTTCCT 59.345 50.000 0.00 0.00 36.75 3.36
264 277 7.439108 AGAGGAACTAATGCCTAGTGTAAAT 57.561 36.000 0.00 0.00 41.55 1.40
268 281 6.598064 GGAACTAATGCCTAGTGTAAATGTGT 59.402 38.462 0.00 0.00 40.14 3.72
282 295 3.585748 AATGTGTCGACACTTGAAACG 57.414 42.857 39.62 0.00 46.55 3.60
400 413 4.406943 GCGATGACTTGAAAAAGGATGTC 58.593 43.478 0.00 0.00 0.00 3.06
447 462 3.229293 TGAAAGGAACATGCATGTGGAA 58.771 40.909 31.98 11.54 41.61 3.53
452 467 2.624838 GGAACATGCATGTGGAATAGGG 59.375 50.000 31.98 2.26 41.61 3.53
458 473 2.244510 TGCATGTGGAATAGGGTGGATT 59.755 45.455 0.00 0.00 0.00 3.01
509 524 9.154847 CTTGATCATGTGTTGAGTTGACTTATA 57.845 33.333 0.00 0.00 37.89 0.98
519 534 5.109210 TGAGTTGACTTATACCGCATCAAG 58.891 41.667 0.00 0.00 30.25 3.02
533 552 5.885912 ACCGCATCAAGTATTAAGTTCCAAT 59.114 36.000 0.00 0.00 0.00 3.16
539 558 8.830580 CATCAAGTATTAAGTTCCAATGACGAT 58.169 33.333 0.00 0.00 0.00 3.73
618 643 6.491062 TCATATCATGCCAAAATACCCAGAAG 59.509 38.462 0.00 0.00 0.00 2.85
644 669 6.430925 CACACTTCAAAGGAAAGATGGATACA 59.569 38.462 0.00 0.00 41.90 2.29
690 715 2.034104 CCATGGATGGTGAGTGTGAG 57.966 55.000 5.56 0.00 43.05 3.51
691 716 1.556451 CCATGGATGGTGAGTGTGAGA 59.444 52.381 5.56 0.00 43.05 3.27
692 717 2.419713 CCATGGATGGTGAGTGTGAGAG 60.420 54.545 5.56 0.00 43.05 3.20
693 718 1.269958 TGGATGGTGAGTGTGAGAGG 58.730 55.000 0.00 0.00 0.00 3.69
694 719 1.203174 TGGATGGTGAGTGTGAGAGGA 60.203 52.381 0.00 0.00 0.00 3.71
695 720 1.205893 GGATGGTGAGTGTGAGAGGAC 59.794 57.143 0.00 0.00 0.00 3.85
696 721 0.891373 ATGGTGAGTGTGAGAGGACG 59.109 55.000 0.00 0.00 0.00 4.79
697 722 0.467474 TGGTGAGTGTGAGAGGACGT 60.467 55.000 0.00 0.00 0.00 4.34
712 737 1.261354 GGACGTACGTGTTGGAAAACC 59.739 52.381 28.16 13.39 0.00 3.27
716 741 3.129871 CGTACGTGTTGGAAAACCCTAA 58.870 45.455 7.22 0.00 35.38 2.69
756 786 1.280206 GCCGAAAGCTCACGTACGTT 61.280 55.000 20.23 2.27 38.99 3.99
764 794 1.892468 CTCACGTACGTTGGCTAGAC 58.108 55.000 20.23 0.00 0.00 2.59
829 859 0.471617 GTGGCAGCTGATCCCACTAT 59.528 55.000 26.01 0.00 44.32 2.12
833 863 2.354259 GCAGCTGATCCCACTATATGC 58.646 52.381 20.43 0.00 0.00 3.14
837 867 5.114780 CAGCTGATCCCACTATATGCATAC 58.885 45.833 8.42 0.00 0.00 2.39
847 877 6.712095 CCCACTATATGCATACACAATTCAGT 59.288 38.462 8.99 0.24 0.00 3.41
856 886 1.511850 CACAATTCAGTGTCGGCAGA 58.488 50.000 0.00 0.00 34.83 4.26
896 928 4.035208 GGCTTATAAATGCACGTACAAGCT 59.965 41.667 16.74 0.00 37.78 3.74
927 959 4.377897 CAGCTCATCATCACTGCAGATTA 58.622 43.478 23.35 5.21 0.00 1.75
932 964 5.114081 TCATCATCACTGCAGATTACACAG 58.886 41.667 23.35 3.91 37.45 3.66
988 1021 3.311486 AGTGAGCAAAGCTAGACAGAC 57.689 47.619 0.00 0.00 39.88 3.51
1024 1057 0.095935 GCTAGTGATGTGCTTGTGCG 59.904 55.000 0.00 0.00 43.34 5.34
1033 1066 0.867746 GTGCTTGTGCGTCTTCATCA 59.132 50.000 0.00 0.00 43.34 3.07
1045 1078 3.420249 CGTCTTCATCATTCTCGTCATCG 59.580 47.826 0.00 0.00 38.55 3.84
1319 1356 4.806330 TGTCAACATTTCTCTACTCGACC 58.194 43.478 0.00 0.00 0.00 4.79
1357 1394 0.108585 ACAACGGTGAATGCTGGTCT 59.891 50.000 7.88 0.00 0.00 3.85
1366 1403 4.125703 GTGAATGCTGGTCTGGAGATTAG 58.874 47.826 0.00 0.00 0.00 1.73
1424 1463 3.015293 GATGTCCTGCGTGTGTGCG 62.015 63.158 0.00 0.00 37.81 5.34
1511 1550 4.651778 TGAGTTTAAGTCCCTGGTCAATG 58.348 43.478 0.00 0.00 0.00 2.82
1526 1565 3.674753 GGTCAATGATGCAAGTTTTTCGG 59.325 43.478 0.00 0.00 0.00 4.30
1533 1572 1.285578 GCAAGTTTTTCGGCTGCAAA 58.714 45.000 0.50 0.00 0.00 3.68
1550 1591 7.862372 CGGCTGCAAATTTCTTATATGTATTGT 59.138 33.333 0.50 0.00 0.00 2.71
1600 1641 7.928167 CACACATACCATAATGAGTGAGTGTAT 59.072 37.037 8.20 0.00 45.62 2.29
1673 1714 8.281212 TGTCTTGATTTCCTAATTTAGGCTTC 57.719 34.615 16.38 12.66 45.82 3.86
1689 1730 8.667076 TTTAGGCTTCGTTATTATTTACTCCC 57.333 34.615 0.00 0.00 0.00 4.30
1690 1731 6.496144 AGGCTTCGTTATTATTTACTCCCT 57.504 37.500 0.00 0.00 0.00 4.20
1691 1732 6.522946 AGGCTTCGTTATTATTTACTCCCTC 58.477 40.000 0.00 0.00 0.00 4.30
1692 1733 5.699915 GGCTTCGTTATTATTTACTCCCTCC 59.300 44.000 0.00 0.00 0.00 4.30
1693 1734 5.404667 GCTTCGTTATTATTTACTCCCTCCG 59.595 44.000 0.00 0.00 0.00 4.63
1694 1735 6.469782 TTCGTTATTATTTACTCCCTCCGT 57.530 37.500 0.00 0.00 0.00 4.69
1695 1736 6.469782 TCGTTATTATTTACTCCCTCCGTT 57.530 37.500 0.00 0.00 0.00 4.44
1696 1737 6.507023 TCGTTATTATTTACTCCCTCCGTTC 58.493 40.000 0.00 0.00 0.00 3.95
1697 1738 5.693555 CGTTATTATTTACTCCCTCCGTTCC 59.306 44.000 0.00 0.00 0.00 3.62
1698 1739 6.585416 GTTATTATTTACTCCCTCCGTTCCA 58.415 40.000 0.00 0.00 0.00 3.53
1699 1740 5.906772 ATTATTTACTCCCTCCGTTCCAT 57.093 39.130 0.00 0.00 0.00 3.41
1700 1741 8.370182 GTTATTATTTACTCCCTCCGTTCCATA 58.630 37.037 0.00 0.00 0.00 2.74
1701 1742 6.811634 TTATTTACTCCCTCCGTTCCATAA 57.188 37.500 0.00 0.00 0.00 1.90
1702 1743 5.906772 ATTTACTCCCTCCGTTCCATAAT 57.093 39.130 0.00 0.00 0.00 1.28
1703 1744 8.495160 TTATTTACTCCCTCCGTTCCATAATA 57.505 34.615 0.00 0.00 0.00 0.98
1704 1745 7.569599 ATTTACTCCCTCCGTTCCATAATAT 57.430 36.000 0.00 0.00 0.00 1.28
1705 1746 8.674925 ATTTACTCCCTCCGTTCCATAATATA 57.325 34.615 0.00 0.00 0.00 0.86
1706 1747 8.495160 TTTACTCCCTCCGTTCCATAATATAA 57.505 34.615 0.00 0.00 0.00 0.98
1707 1748 6.607004 ACTCCCTCCGTTCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
1708 1749 6.320518 ACTCCCTCCGTTCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
1709 1750 6.785963 ACTCCCTCCGTTCCATAATATAAGAA 59.214 38.462 0.00 0.00 0.00 2.52
1710 1751 7.291651 ACTCCCTCCGTTCCATAATATAAGAAA 59.708 37.037 0.00 0.00 0.00 2.52
1711 1752 7.676947 TCCCTCCGTTCCATAATATAAGAAAG 58.323 38.462 0.00 0.00 0.00 2.62
1712 1753 7.291651 TCCCTCCGTTCCATAATATAAGAAAGT 59.708 37.037 0.00 0.00 0.00 2.66
1713 1754 7.937394 CCCTCCGTTCCATAATATAAGAAAGTT 59.063 37.037 0.00 0.00 0.00 2.66
1714 1755 9.338622 CCTCCGTTCCATAATATAAGAAAGTTT 57.661 33.333 0.00 0.00 0.00 2.66
1743 1784 9.918630 AACACTACACTATGTAAATAACGTTCT 57.081 29.630 2.82 0.00 31.67 3.01
1744 1785 9.918630 ACACTACACTATGTAAATAACGTTCTT 57.081 29.630 2.82 0.00 31.67 2.52
1778 1819 4.225942 ACAGAGGGAGTATTTGCAATCTCA 59.774 41.667 20.35 0.92 0.00 3.27
1850 1892 7.201539 GCATTTTATAGCATTCAACATGCAACA 60.202 33.333 9.39 0.00 46.77 3.33
2116 2244 9.890629 TGCATATCTTAATGAAGTCAAAGTAGT 57.109 29.630 0.00 0.00 34.03 2.73
2158 2320 7.770366 AAGGACCGTTGAATTAATTTAAGGT 57.230 32.000 18.41 18.33 0.00 3.50
2176 2338 9.868160 ATTTAAGGTATGATAAAGGAAAGGAGG 57.132 33.333 0.00 0.00 0.00 4.30
2177 2339 5.311844 AGGTATGATAAAGGAAAGGAGGC 57.688 43.478 0.00 0.00 0.00 4.70
2178 2340 4.104897 AGGTATGATAAAGGAAAGGAGGCC 59.895 45.833 0.00 0.00 0.00 5.19
2179 2341 2.710096 TGATAAAGGAAAGGAGGCCG 57.290 50.000 0.00 0.00 0.00 6.13
2180 2342 1.913419 TGATAAAGGAAAGGAGGCCGT 59.087 47.619 0.00 0.00 0.00 5.68
2181 2343 2.289565 GATAAAGGAAAGGAGGCCGTG 58.710 52.381 0.00 0.00 0.00 4.94
2182 2344 0.322187 TAAAGGAAAGGAGGCCGTGC 60.322 55.000 0.00 0.00 0.00 5.34
2183 2345 2.069165 AAAGGAAAGGAGGCCGTGCT 62.069 55.000 0.00 0.00 0.00 4.40
2184 2346 2.034221 GGAAAGGAGGCCGTGCTT 59.966 61.111 0.00 0.00 38.77 3.91
2185 2347 2.041115 GGAAAGGAGGCCGTGCTTC 61.041 63.158 8.88 5.94 35.37 3.86
2186 2348 1.302511 GAAAGGAGGCCGTGCTTCA 60.303 57.895 8.88 0.00 35.37 3.02
2187 2349 0.889186 GAAAGGAGGCCGTGCTTCAA 60.889 55.000 8.88 0.00 35.37 2.69
2188 2350 0.467290 AAAGGAGGCCGTGCTTCAAA 60.467 50.000 8.88 0.00 35.37 2.69
2189 2351 0.467290 AAGGAGGCCGTGCTTCAAAA 60.467 50.000 0.00 0.00 36.34 2.44
2190 2352 0.467290 AGGAGGCCGTGCTTCAAAAA 60.467 50.000 0.00 0.00 36.34 1.94
2220 2382 1.799544 CTGAAGGCCAAAATGCAACC 58.200 50.000 5.01 0.00 0.00 3.77
2230 2392 3.740321 CCAAAATGCAACCACACATACAC 59.260 43.478 0.00 0.00 0.00 2.90
2238 2400 7.511959 TGCAACCACACATACACTAATTAAA 57.488 32.000 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.960811 TGTCCTTTCTACTGATCAGAGGATT 59.039 40.000 29.27 8.86 32.67 3.01
1 2 5.523588 TGTCCTTTCTACTGATCAGAGGAT 58.476 41.667 29.27 9.25 36.13 3.24
2 3 4.935578 TGTCCTTTCTACTGATCAGAGGA 58.064 43.478 29.27 24.38 0.00 3.71
3 4 4.099266 CCTGTCCTTTCTACTGATCAGAGG 59.901 50.000 29.27 22.60 0.00 3.69
4 5 4.441356 GCCTGTCCTTTCTACTGATCAGAG 60.441 50.000 29.27 19.86 0.00 3.35
5 6 3.449018 GCCTGTCCTTTCTACTGATCAGA 59.551 47.826 29.27 11.66 0.00 3.27
6 7 3.196469 TGCCTGTCCTTTCTACTGATCAG 59.804 47.826 21.37 21.37 0.00 2.90
7 8 3.055819 GTGCCTGTCCTTTCTACTGATCA 60.056 47.826 0.00 0.00 0.00 2.92
8 9 3.055819 TGTGCCTGTCCTTTCTACTGATC 60.056 47.826 0.00 0.00 0.00 2.92
9 10 2.906389 TGTGCCTGTCCTTTCTACTGAT 59.094 45.455 0.00 0.00 0.00 2.90
10 11 2.037251 GTGTGCCTGTCCTTTCTACTGA 59.963 50.000 0.00 0.00 0.00 3.41
11 12 2.037772 AGTGTGCCTGTCCTTTCTACTG 59.962 50.000 0.00 0.00 0.00 2.74
12 13 2.330216 AGTGTGCCTGTCCTTTCTACT 58.670 47.619 0.00 0.00 0.00 2.57
25 26 1.168714 GGAGGTTCATGAAGTGTGCC 58.831 55.000 8.80 6.15 0.00 5.01
31 32 5.620738 TTCTAGGATGGAGGTTCATGAAG 57.379 43.478 8.80 0.00 0.00 3.02
33 34 6.043243 GGTATTTCTAGGATGGAGGTTCATGA 59.957 42.308 0.00 0.00 0.00 3.07
44 45 8.354711 TGTATAGAGCTGGTATTTCTAGGATG 57.645 38.462 0.00 0.00 0.00 3.51
45 46 8.976353 CATGTATAGAGCTGGTATTTCTAGGAT 58.024 37.037 0.00 0.00 0.00 3.24
46 47 7.397476 CCATGTATAGAGCTGGTATTTCTAGGA 59.603 40.741 0.00 0.00 0.00 2.94
51 52 5.013183 ACCCCATGTATAGAGCTGGTATTTC 59.987 44.000 0.00 0.00 0.00 2.17
56 57 2.496679 ACCCCATGTATAGAGCTGGT 57.503 50.000 0.00 0.00 0.00 4.00
61 62 1.402456 GCGCGTACCCCATGTATAGAG 60.402 57.143 8.43 0.00 0.00 2.43
79 80 2.849966 GATAGTGAGTGCGTGCGCG 61.850 63.158 16.86 16.86 45.51 6.86
82 83 0.744874 TAGGGATAGTGAGTGCGTGC 59.255 55.000 0.00 0.00 0.00 5.34
91 92 4.944317 TCAGATATGCTCGTAGGGATAGTG 59.056 45.833 0.00 0.00 0.00 2.74
92 93 5.045505 TCTCAGATATGCTCGTAGGGATAGT 60.046 44.000 0.00 0.00 0.00 2.12
96 97 3.790089 TCTCAGATATGCTCGTAGGGA 57.210 47.619 0.00 0.00 0.00 4.20
102 103 3.188048 GCCCATTTTCTCAGATATGCTCG 59.812 47.826 0.00 0.00 0.00 5.03
108 109 1.476833 GCCGGCCCATTTTCTCAGATA 60.477 52.381 18.11 0.00 0.00 1.98
112 113 1.678635 CTGCCGGCCCATTTTCTCA 60.679 57.895 26.77 0.00 0.00 3.27
117 118 1.111116 CATGATCTGCCGGCCCATTT 61.111 55.000 26.77 3.75 0.00 2.32
119 120 2.114625 CATGATCTGCCGGCCCAT 59.885 61.111 26.77 16.12 0.00 4.00
123 124 1.155042 GATTCTCATGATCTGCCGGC 58.845 55.000 22.73 22.73 0.00 6.13
125 126 4.517952 AGTAGATTCTCATGATCTGCCG 57.482 45.455 7.45 0.00 0.00 5.69
126 127 6.658816 TCTCTAGTAGATTCTCATGATCTGCC 59.341 42.308 7.45 0.00 0.00 4.85
128 129 8.186163 GCATCTCTAGTAGATTCTCATGATCTG 58.814 40.741 7.45 0.00 42.62 2.90
144 145 7.785506 AGGGTAACTAATAAGTGCATCTCTAGT 59.214 37.037 0.00 0.00 35.62 2.57
148 149 6.421202 CGAAGGGTAACTAATAAGTGCATCTC 59.579 42.308 0.00 0.00 35.62 2.75
160 161 4.160252 GGGACACATACGAAGGGTAACTAA 59.840 45.833 0.00 0.00 34.09 2.24
161 162 3.701040 GGGACACATACGAAGGGTAACTA 59.299 47.826 0.00 0.00 34.09 2.24
162 163 2.498885 GGGACACATACGAAGGGTAACT 59.501 50.000 0.00 0.00 34.09 2.24
166 167 1.192428 GAGGGACACATACGAAGGGT 58.808 55.000 0.00 0.00 0.00 4.34
170 171 3.053842 AGACCTAGAGGGACACATACGAA 60.054 47.826 0.00 0.00 40.27 3.85
172 173 2.933573 AGACCTAGAGGGACACATACG 58.066 52.381 0.00 0.00 40.27 3.06
175 176 3.100671 GTGAAGACCTAGAGGGACACAT 58.899 50.000 0.00 0.00 40.27 3.21
181 182 3.108847 AGGAAGTGAAGACCTAGAGGG 57.891 52.381 0.00 0.00 40.27 4.30
201 208 6.992715 GCTTAATATAGAGAAGGACAAGGCAA 59.007 38.462 0.00 0.00 0.00 4.52
245 258 6.312918 CGACACATTTACACTAGGCATTAGTT 59.687 38.462 0.00 0.00 40.68 2.24
268 281 0.865111 CCATGCGTTTCAAGTGTCGA 59.135 50.000 0.00 0.00 0.00 4.20
282 295 1.127397 CGCGTATGTCATCATCCATGC 59.873 52.381 0.00 0.00 35.70 4.06
356 369 4.028383 CGCATTGCAAACCTTAATCTACG 58.972 43.478 1.71 0.00 0.00 3.51
400 413 5.880341 TCATCCGATATAATACAGTCAGCG 58.120 41.667 0.00 0.00 0.00 5.18
447 462 2.713167 CACATCCAGGAATCCACCCTAT 59.287 50.000 0.61 0.00 31.64 2.57
452 467 5.249393 AGGATATACACATCCAGGAATCCAC 59.751 44.000 14.22 0.00 46.04 4.02
458 473 5.467738 AGACAAGGATATACACATCCAGGA 58.532 41.667 5.02 0.00 46.04 3.86
509 524 4.839121 TGGAACTTAATACTTGATGCGGT 58.161 39.130 0.00 0.00 0.00 5.68
539 558 4.951254 TGTTGACTTCACGATGGAGTTTA 58.049 39.130 0.00 0.00 0.00 2.01
618 643 3.569701 TCCATCTTTCCTTTGAAGTGTGC 59.430 43.478 0.00 0.00 0.00 4.57
644 669 5.048224 CCATCTCATCCGTTACCTTACGTAT 60.048 44.000 0.00 0.00 39.81 3.06
657 682 0.321387 CCATGGCTCCATCTCATCCG 60.321 60.000 0.00 0.00 33.90 4.18
685 710 1.002142 CAACACGTACGTCCTCTCACA 60.002 52.381 19.94 0.00 0.00 3.58
687 712 0.594602 CCAACACGTACGTCCTCTCA 59.405 55.000 19.94 0.00 0.00 3.27
688 713 0.877071 TCCAACACGTACGTCCTCTC 59.123 55.000 19.94 0.00 0.00 3.20
689 714 1.321474 TTCCAACACGTACGTCCTCT 58.679 50.000 19.94 0.00 0.00 3.69
690 715 2.138596 TTTCCAACACGTACGTCCTC 57.861 50.000 19.94 0.00 0.00 3.71
691 716 2.204237 GTTTTCCAACACGTACGTCCT 58.796 47.619 19.94 5.34 32.54 3.85
692 717 1.261354 GGTTTTCCAACACGTACGTCC 59.739 52.381 19.94 9.61 40.31 4.79
693 718 1.261354 GGGTTTTCCAACACGTACGTC 59.739 52.381 19.94 3.52 42.91 4.34
694 719 1.134431 AGGGTTTTCCAACACGTACGT 60.134 47.619 16.72 16.72 41.74 3.57
695 720 1.585297 AGGGTTTTCCAACACGTACG 58.415 50.000 15.01 15.01 41.74 3.67
696 721 4.129380 ACTTAGGGTTTTCCAACACGTAC 58.871 43.478 0.00 0.00 41.74 3.67
697 722 4.420522 ACTTAGGGTTTTCCAACACGTA 57.579 40.909 0.00 0.00 41.74 3.57
741 771 0.249741 AGCCAACGTACGTGAGCTTT 60.250 50.000 29.55 15.89 34.85 3.51
764 794 9.449550 TTTAGAGACATTGCAAAAATATATGCG 57.550 29.630 1.71 0.00 45.47 4.73
837 867 1.511850 TCTGCCGACACTGAATTGTG 58.488 50.000 0.00 0.00 43.07 3.33
864 896 2.375110 CATTTATAAGCCAAGCGTGCG 58.625 47.619 0.00 0.00 0.00 5.34
896 928 1.139654 GATGATGAGCTGCACCCTACA 59.860 52.381 1.02 0.00 0.00 2.74
927 959 1.546029 TCGAGCTGCTTGATACTGTGT 59.454 47.619 15.54 0.00 0.00 3.72
932 964 1.483424 GCGGTCGAGCTGCTTGATAC 61.483 60.000 21.74 16.24 45.76 2.24
966 999 4.322049 GGTCTGTCTAGCTTTGCTCACTTA 60.322 45.833 0.00 0.00 40.44 2.24
988 1021 4.993584 CACTAGCTTCATGGCTAATACAGG 59.006 45.833 0.00 0.00 43.11 4.00
1024 1057 3.181377 GCGATGACGAGAATGATGAAGAC 59.819 47.826 0.00 0.00 42.66 3.01
1033 1066 0.029567 GACGAGGCGATGACGAGAAT 59.970 55.000 0.00 0.00 42.66 2.40
1319 1356 5.581085 CGTTGTTAGGAATCTAGTTTGGGAG 59.419 44.000 0.00 0.00 0.00 4.30
1366 1403 7.880713 ACAAAAATAGGGAGAGAGAAAGAGAAC 59.119 37.037 0.00 0.00 0.00 3.01
1411 1450 4.969196 ACTCCGCACACACGCAGG 62.969 66.667 0.00 0.00 0.00 4.85
1424 1463 5.421374 AGGTGTATAGTGGTTAAGACACTCC 59.579 44.000 14.18 10.04 45.50 3.85
1511 1550 1.063031 GCAGCCGAAAAACTTGCATC 58.937 50.000 0.00 0.00 0.00 3.91
1526 1565 8.895845 CGACAATACATATAAGAAATTTGCAGC 58.104 33.333 0.00 0.00 0.00 5.25
1533 1572 6.868864 AGAGCGCGACAATACATATAAGAAAT 59.131 34.615 12.10 0.00 0.00 2.17
1550 1591 3.302434 CGTTTACAAGATAAAGAGCGCGA 59.698 43.478 12.10 0.00 0.00 5.87
1600 1641 7.574607 AGGGAACTCTTCTCTTGTCTTTTTAA 58.425 34.615 0.00 0.00 37.10 1.52
1669 1710 5.404667 CGGAGGGAGTAAATAATAACGAAGC 59.595 44.000 0.00 0.00 0.00 3.86
1673 1714 5.693555 GGAACGGAGGGAGTAAATAATAACG 59.306 44.000 0.00 0.00 0.00 3.18
1683 1724 7.472741 TCTTATATTATGGAACGGAGGGAGTA 58.527 38.462 0.00 0.00 0.00 2.59
1684 1725 6.320518 TCTTATATTATGGAACGGAGGGAGT 58.679 40.000 0.00 0.00 0.00 3.85
1685 1726 6.852420 TCTTATATTATGGAACGGAGGGAG 57.148 41.667 0.00 0.00 0.00 4.30
1686 1727 7.291651 ACTTTCTTATATTATGGAACGGAGGGA 59.708 37.037 0.00 0.00 0.00 4.20
1687 1728 7.450903 ACTTTCTTATATTATGGAACGGAGGG 58.549 38.462 0.00 0.00 0.00 4.30
1688 1729 8.904099 AACTTTCTTATATTATGGAACGGAGG 57.096 34.615 0.00 0.00 0.00 4.30
1717 1758 9.918630 AGAACGTTATTTACATAGTGTAGTGTT 57.081 29.630 0.00 0.00 33.92 3.32
1718 1759 9.918630 AAGAACGTTATTTACATAGTGTAGTGT 57.081 29.630 0.00 0.00 33.92 3.55
1735 1776 8.582437 CCTCTGTCCCATAATATAAGAACGTTA 58.418 37.037 0.00 0.00 0.00 3.18
1736 1777 7.442656 CCTCTGTCCCATAATATAAGAACGTT 58.557 38.462 0.00 0.00 0.00 3.99
1737 1778 6.014499 CCCTCTGTCCCATAATATAAGAACGT 60.014 42.308 0.00 0.00 0.00 3.99
1738 1779 6.210784 TCCCTCTGTCCCATAATATAAGAACG 59.789 42.308 0.00 0.00 0.00 3.95
1739 1780 7.235812 ACTCCCTCTGTCCCATAATATAAGAAC 59.764 40.741 0.00 0.00 0.00 3.01
1740 1781 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
1741 1782 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
1742 1783 8.846423 ATACTCCCTCTGTCCCATAATATAAG 57.154 38.462 0.00 0.00 0.00 1.73
1743 1784 9.629649 AAATACTCCCTCTGTCCCATAATATAA 57.370 33.333 0.00 0.00 0.00 0.98
1744 1785 9.046846 CAAATACTCCCTCTGTCCCATAATATA 57.953 37.037 0.00 0.00 0.00 0.86
1745 1786 7.529560 GCAAATACTCCCTCTGTCCCATAATAT 60.530 40.741 0.00 0.00 0.00 1.28
1746 1787 6.239887 GCAAATACTCCCTCTGTCCCATAATA 60.240 42.308 0.00 0.00 0.00 0.98
1747 1788 5.456763 GCAAATACTCCCTCTGTCCCATAAT 60.457 44.000 0.00 0.00 0.00 1.28
1748 1789 4.141482 GCAAATACTCCCTCTGTCCCATAA 60.141 45.833 0.00 0.00 0.00 1.90
1749 1790 3.391296 GCAAATACTCCCTCTGTCCCATA 59.609 47.826 0.00 0.00 0.00 2.74
1750 1791 2.173569 GCAAATACTCCCTCTGTCCCAT 59.826 50.000 0.00 0.00 0.00 4.00
1751 1792 1.559682 GCAAATACTCCCTCTGTCCCA 59.440 52.381 0.00 0.00 0.00 4.37
1752 1793 1.559682 TGCAAATACTCCCTCTGTCCC 59.440 52.381 0.00 0.00 0.00 4.46
1753 1794 3.350219 TTGCAAATACTCCCTCTGTCC 57.650 47.619 0.00 0.00 0.00 4.02
1754 1795 4.775236 AGATTGCAAATACTCCCTCTGTC 58.225 43.478 1.71 0.00 0.00 3.51
1755 1796 4.225942 TGAGATTGCAAATACTCCCTCTGT 59.774 41.667 20.65 0.00 0.00 3.41
1756 1797 4.774124 TGAGATTGCAAATACTCCCTCTG 58.226 43.478 20.65 0.00 0.00 3.35
1757 1798 5.643421 ATGAGATTGCAAATACTCCCTCT 57.357 39.130 20.65 10.67 0.00 3.69
1758 1799 5.824624 TGAATGAGATTGCAAATACTCCCTC 59.175 40.000 20.65 17.61 0.00 4.30
1759 1800 5.759059 TGAATGAGATTGCAAATACTCCCT 58.241 37.500 20.65 12.32 0.00 4.20
1760 1801 5.009410 CCTGAATGAGATTGCAAATACTCCC 59.991 44.000 20.65 13.79 0.00 4.30
1761 1802 5.591877 ACCTGAATGAGATTGCAAATACTCC 59.408 40.000 20.65 11.36 0.00 3.85
1762 1803 6.690194 ACCTGAATGAGATTGCAAATACTC 57.310 37.500 18.31 18.31 0.00 2.59
1763 1804 7.994911 TCATACCTGAATGAGATTGCAAATACT 59.005 33.333 1.71 3.36 32.18 2.12
1764 1805 8.158169 TCATACCTGAATGAGATTGCAAATAC 57.842 34.615 1.71 0.00 32.18 1.89
1778 1819 5.772672 AGTCTCGCTAAGATCATACCTGAAT 59.227 40.000 0.00 0.00 36.11 2.57
1901 2006 6.882610 TGAAAAGTGCTTCATGATGTAACT 57.117 33.333 10.05 10.62 30.31 2.24
1945 2073 8.623030 TGATACTGGTTAAACAAAACTAACACC 58.377 33.333 0.00 0.00 30.97 4.16
2059 2187 5.007724 GTGGTCCAATATCCATTTCGACTTC 59.992 44.000 0.00 0.00 36.09 3.01
2115 2243 7.689400 CGGTCCTTTTTCGTTAACACAATATAC 59.311 37.037 6.39 0.00 0.00 1.47
2116 2244 7.387397 ACGGTCCTTTTTCGTTAACACAATATA 59.613 33.333 6.39 0.00 32.95 0.86
2158 2320 3.714798 ACGGCCTCCTTTCCTTTATCATA 59.285 43.478 0.00 0.00 0.00 2.15
2170 2332 0.467290 TTTTGAAGCACGGCCTCCTT 60.467 50.000 0.00 0.00 0.00 3.36
2171 2333 0.467290 TTTTTGAAGCACGGCCTCCT 60.467 50.000 0.00 0.00 0.00 3.69
2172 2334 2.037871 TTTTTGAAGCACGGCCTCC 58.962 52.632 0.00 0.00 0.00 4.30
2192 2354 2.086610 TTGGCCTTCAGCTCCTTTTT 57.913 45.000 3.32 0.00 43.05 1.94
2193 2355 2.086610 TTTGGCCTTCAGCTCCTTTT 57.913 45.000 3.32 0.00 43.05 2.27
2194 2356 2.086610 TTTTGGCCTTCAGCTCCTTT 57.913 45.000 3.32 0.00 43.05 3.11
2195 2357 1.897802 CATTTTGGCCTTCAGCTCCTT 59.102 47.619 3.32 0.00 43.05 3.36
2196 2358 1.553706 CATTTTGGCCTTCAGCTCCT 58.446 50.000 3.32 0.00 43.05 3.69
2197 2359 0.108472 GCATTTTGGCCTTCAGCTCC 60.108 55.000 3.32 0.00 43.05 4.70
2198 2360 0.604578 TGCATTTTGGCCTTCAGCTC 59.395 50.000 3.32 0.00 43.05 4.09
2199 2361 1.050204 TTGCATTTTGGCCTTCAGCT 58.950 45.000 3.32 0.00 43.05 4.24


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

AutoCloner maintained by Alex Coulton.