Multiple sequence alignment - TraesCS3A01G199500

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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 TraesCS3A01G199500 chr3A 100.000 2935 0 0 1 2935 325487828 325490762 0.000000e+00 5421.0
1 TraesCS3A01G199500 chr3A 89.476 2746 229 15 220 2935 325480153 325482868 0.000000e+00 3415.0
2 TraesCS3A01G199500 chr3A 86.294 1233 142 21 1 1222 265533218 265532002 0.000000e+00 1315.0
3 TraesCS3A01G199500 chr3A 90.476 126 10 2 1180 1304 503807548 503807424 6.510000e-37 165.0
4 TraesCS3A01G199500 chr3A 85.859 99 7 6 1276 1373 377110936 377110844 6.690000e-17 99.0
5 TraesCS3A01G199500 chr2A 86.235 1838 199 19 1 1830 483022858 483024649 0.000000e+00 1943.0
6 TraesCS3A01G199500 chr2A 84.670 1833 194 36 1 1817 483030692 483032453 0.000000e+00 1748.0
7 TraesCS3A01G199500 chr2A 78.390 1379 223 57 9 1354 472977869 472979205 0.000000e+00 826.0
8 TraesCS3A01G199500 chr2A 77.431 1378 228 64 9 1354 472955970 472957296 0.000000e+00 745.0
9 TraesCS3A01G199500 chr2A 83.011 465 64 13 2456 2915 351148646 351149100 9.790000e-110 407.0
10 TraesCS3A01G199500 chr2A 92.778 180 11 1 2338 2517 253758359 253758536 2.900000e-65 259.0
11 TraesCS3A01G199500 chr2A 88.889 126 12 2 1180 1304 536242665 536242541 1.410000e-33 154.0
12 TraesCS3A01G199500 chr7A 85.924 1840 202 30 1 1828 393498889 393497095 0.000000e+00 1910.0
13 TraesCS3A01G199500 chr7A 87.997 1208 123 16 1 1201 393491087 393489895 0.000000e+00 1408.0
14 TraesCS3A01G199500 chr7A 85.758 1313 148 24 4 1303 355764003 355762717 0.000000e+00 1352.0
15 TraesCS3A01G199500 chr7A 81.699 153 22 5 1879 2028 347603254 347603403 3.970000e-24 122.0
16 TraesCS3A01G199500 chr3D 86.324 1360 152 21 20 1354 356758085 356759435 0.000000e+00 1450.0
17 TraesCS3A01G199500 chr3D 87.530 1243 130 19 1 1229 356714384 356715615 0.000000e+00 1413.0
18 TraesCS3A01G199500 chr7D 87.520 1234 121 29 15 1237 233882061 233883272 0.000000e+00 1395.0
19 TraesCS3A01G199500 chr4A 79.856 1390 192 57 9 1354 311841412 311842757 0.000000e+00 935.0
20 TraesCS3A01G199500 chr4A 89.552 201 18 2 1154 1354 311834026 311834223 4.860000e-63 252.0
21 TraesCS3A01G199500 chr4A 81.452 124 16 6 1251 1373 231537472 231537589 8.660000e-16 95.3
22 TraesCS3A01G199500 chr4B 89.683 504 42 8 2416 2915 223404473 223404970 4.130000e-178 634.0
23 TraesCS3A01G199500 chr4B 81.985 544 69 22 2389 2920 271231940 271232466 4.490000e-118 435.0
24 TraesCS3A01G199500 chr4B 79.789 569 83 25 2383 2935 345645004 345644452 4.590000e-103 385.0
25 TraesCS3A01G199500 chr4D 82.086 748 106 21 2190 2921 156517343 156518078 5.380000e-172 614.0
26 TraesCS3A01G199500 chr4D 87.342 237 29 1 2190 2425 156682036 156682272 1.340000e-68 270.0
27 TraesCS3A01G199500 chr2D 82.086 748 97 30 2193 2915 572413155 572412420 3.240000e-169 604.0
28 TraesCS3A01G199500 chr2D 82.341 487 67 15 2446 2923 205095172 205094696 3.520000e-109 405.0
29 TraesCS3A01G199500 chr1B 82.109 531 58 29 2407 2920 193236221 193236731 1.260000e-113 420.0
30 TraesCS3A01G199500 chr1B 83.223 453 59 13 2442 2885 89566653 89566209 1.640000e-107 399.0
31 TraesCS3A01G199500 chr6D 81.874 491 69 16 2446 2928 45260855 45261333 2.120000e-106 396.0
32 TraesCS3A01G199500 chr6D 97.059 34 1 0 2131 2164 239408746 239408713 1.140000e-04 58.4
33 TraesCS3A01G199500 chr1A 95.000 180 7 1 2338 2517 127375210 127375033 6.190000e-72 281.0
34 TraesCS3A01G199500 chr3B 86.076 158 18 3 2167 2322 390314974 390314819 1.810000e-37 167.0
35 TraesCS3A01G199500 chr3B 87.407 135 13 4 2168 2301 123808539 123808670 5.070000e-33 152.0
36 TraesCS3A01G199500 chr2B 87.407 135 14 3 2168 2301 776924661 776924529 5.070000e-33 152.0
37 TraesCS3A01G199500 chr2B 85.926 135 16 3 2168 2301 776932473 776932341 1.100000e-29 141.0
38 TraesCS3A01G199500 chr7B 86.667 135 15 3 2168 2301 476998670 476998538 2.360000e-31 147.0
39 TraesCS3A01G199500 chr7B 94.805 77 3 1 1463 1539 561818840 561818765 5.140000e-23 119.0
40 TraesCS3A01G199500 chr5B 97.222 72 2 0 1467 1538 87409041 87408970 3.970000e-24 122.0
41 TraesCS3A01G199500 chr5B 94.667 75 4 0 1464 1538 72748441 72748515 1.850000e-22 117.0
42 TraesCS3A01G199500 chr5B 94.667 75 4 0 1464 1538 203178980 203179054 1.850000e-22 117.0
43 TraesCS3A01G199500 chr5B 94.667 75 4 0 1464 1538 203200091 203200165 1.850000e-22 117.0
44 TraesCS3A01G199500 chr6B 97.101 69 2 0 1470 1538 417899259 417899191 1.850000e-22 117.0


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 TraesCS3A01G199500 chr3A 325487828 325490762 2934 False 5421 5421 100.000 1 2935 1 chr3A.!!$F2 2934
1 TraesCS3A01G199500 chr3A 325480153 325482868 2715 False 3415 3415 89.476 220 2935 1 chr3A.!!$F1 2715
2 TraesCS3A01G199500 chr3A 265532002 265533218 1216 True 1315 1315 86.294 1 1222 1 chr3A.!!$R1 1221
3 TraesCS3A01G199500 chr2A 483022858 483024649 1791 False 1943 1943 86.235 1 1830 1 chr2A.!!$F5 1829
4 TraesCS3A01G199500 chr2A 483030692 483032453 1761 False 1748 1748 84.670 1 1817 1 chr2A.!!$F6 1816
5 TraesCS3A01G199500 chr2A 472977869 472979205 1336 False 826 826 78.390 9 1354 1 chr2A.!!$F4 1345
6 TraesCS3A01G199500 chr2A 472955970 472957296 1326 False 745 745 77.431 9 1354 1 chr2A.!!$F3 1345
7 TraesCS3A01G199500 chr7A 393497095 393498889 1794 True 1910 1910 85.924 1 1828 1 chr7A.!!$R3 1827
8 TraesCS3A01G199500 chr7A 393489895 393491087 1192 True 1408 1408 87.997 1 1201 1 chr7A.!!$R2 1200
9 TraesCS3A01G199500 chr7A 355762717 355764003 1286 True 1352 1352 85.758 4 1303 1 chr7A.!!$R1 1299
10 TraesCS3A01G199500 chr3D 356758085 356759435 1350 False 1450 1450 86.324 20 1354 1 chr3D.!!$F2 1334
11 TraesCS3A01G199500 chr3D 356714384 356715615 1231 False 1413 1413 87.530 1 1229 1 chr3D.!!$F1 1228
12 TraesCS3A01G199500 chr7D 233882061 233883272 1211 False 1395 1395 87.520 15 1237 1 chr7D.!!$F1 1222
13 TraesCS3A01G199500 chr4A 311841412 311842757 1345 False 935 935 79.856 9 1354 1 chr4A.!!$F3 1345
14 TraesCS3A01G199500 chr4B 271231940 271232466 526 False 435 435 81.985 2389 2920 1 chr4B.!!$F2 531
15 TraesCS3A01G199500 chr4B 345644452 345645004 552 True 385 385 79.789 2383 2935 1 chr4B.!!$R1 552
16 TraesCS3A01G199500 chr4D 156517343 156518078 735 False 614 614 82.086 2190 2921 1 chr4D.!!$F1 731
17 TraesCS3A01G199500 chr2D 572412420 572413155 735 True 604 604 82.086 2193 2915 1 chr2D.!!$R2 722
18 TraesCS3A01G199500 chr1B 193236221 193236731 510 False 420 420 82.109 2407 2920 1 chr1B.!!$F1 513

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
312 334 0.109781 GAACACGAACCGGCGTAGTA 60.11 55.0 6.01 0.0 43.59 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2035 2168 0.118346 TTCCCCTCTGCCTCACCTAA 59.882 55.0 0.0 0.0 0.0 2.69 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
128 139 0.251165 TGCTAGGGTGGTGGAAAAGC 60.251 55.000 0.00 0.00 0.00 3.51
138 151 2.910319 TGGTGGAAAAGCTTAGAGGCTA 59.090 45.455 0.00 0.00 42.24 3.93
159 174 3.686227 TTTCATGGCATATTGGGAGGT 57.314 42.857 0.00 0.00 0.00 3.85
222 241 3.315470 TCGAGACGACTAGCATAGCAAAT 59.685 43.478 0.00 0.00 44.39 2.32
247 266 0.247736 AGTGAGATCCAAGGTGACGC 59.752 55.000 0.00 0.00 0.00 5.19
268 287 1.027357 CATCTTGCCTGAAATCCCGG 58.973 55.000 0.00 0.00 0.00 5.73
296 315 3.056465 AGAAGACCGAGTCCATGAAGAAC 60.056 47.826 0.00 0.00 32.18 3.01
312 334 0.109781 GAACACGAACCGGCGTAGTA 60.110 55.000 6.01 0.00 43.59 1.82
440 465 5.589452 TGCACAATCAAGTATGATGCATGTA 59.411 36.000 2.46 0.00 45.60 2.29
453 478 6.502136 TGATGCATGTACGGTTTAATGAAA 57.498 33.333 2.46 0.00 0.00 2.69
565 597 7.549134 CCACATGCAAGTATTTAGTTCACTCTA 59.451 37.037 0.00 0.00 0.00 2.43
659 694 2.093711 GGCAAATTTAAATGAGGCCGGT 60.094 45.455 17.21 0.00 0.00 5.28
694 729 6.983906 ACAATTCTGGAAAATCCCCATATC 57.016 37.500 0.00 0.00 35.03 1.63
824 862 4.426416 TGAGCATGTTATGAAGCATTTGC 58.574 39.130 0.00 0.00 42.49 3.68
909 947 2.130395 CCGATGATCCGACAACTCATG 58.870 52.381 0.00 0.00 30.00 3.07
925 963 2.349590 TCATGAAGATGTCGGTGCAAG 58.650 47.619 0.00 0.00 0.00 4.01
970 1013 1.205417 GCAAAAGATGGTGGGGTGATG 59.795 52.381 0.00 0.00 0.00 3.07
1011 1060 0.939577 GTCGACGCATGGCATACGAT 60.940 55.000 25.68 10.55 32.51 3.73
1043 1093 1.250328 ATGACAACTCGGACACGGTA 58.750 50.000 0.00 0.00 41.39 4.02
1078 1129 5.963176 TCTCATACAACACACATGCATTT 57.037 34.783 0.00 0.00 0.00 2.32
1086 1137 2.098934 ACACACATGCATTTGTTCACGT 59.901 40.909 15.72 8.13 0.00 4.49
1114 1169 3.131046 GTCTCGGGGTTATACCTTCGAAA 59.869 47.826 0.00 0.00 40.79 3.46
1145 1204 2.163010 GGGACAGAACGAGTTCGATGTA 59.837 50.000 8.72 0.00 43.97 2.29
1244 1374 5.937540 TGGTTCATGTTTCATAGATGTTCGT 59.062 36.000 0.00 0.00 0.00 3.85
1265 1395 0.389948 GTCACGGCGAGGAACTTGAT 60.390 55.000 16.62 0.00 44.22 2.57
1278 1408 1.338107 ACTTGATGTCCACGGAGTCA 58.662 50.000 0.00 0.00 41.61 3.41
1370 1500 1.952296 ACACTTGTCGACGAGGTACTT 59.048 47.619 31.38 11.75 41.55 2.24
1443 1573 1.789751 CGGCAGTAGTCGTACGACA 59.210 57.895 40.48 27.10 46.76 4.35
1468 1598 2.187958 TGAACTTGATGGGTCCTCGAT 58.812 47.619 0.00 0.00 0.00 3.59
1483 1613 1.825474 CTCGATGTCCTGGTACTTGGT 59.175 52.381 0.00 0.00 0.00 3.67
1498 1628 1.990160 TTGGTGTCCACTCGGCCTTT 61.990 55.000 0.00 0.00 30.78 3.11
1512 1642 2.156098 GGCCTTTACGGTGATGAAACA 58.844 47.619 0.00 0.00 34.25 2.83
1561 1691 0.911053 AGGGGTTTCGCGGGTTATTA 59.089 50.000 6.13 0.00 0.00 0.98
1576 1706 4.696877 GGGTTATTACTGTACTTGGCGTTT 59.303 41.667 0.00 0.00 0.00 3.60
1605 1735 1.133823 ACTTGGTTGTGCTCATGACCA 60.134 47.619 7.99 7.99 40.23 4.02
1619 1749 3.329542 GACCAAGCTCATGGGCGGA 62.330 63.158 17.43 0.00 45.18 5.54
1624 1754 4.221422 GCTCATGGGCGGACGCTA 62.221 66.667 16.72 6.65 41.60 4.26
1635 1765 1.078426 GGACGCTACATGCCCAAGT 60.078 57.895 0.00 0.00 38.78 3.16
1710 1840 2.203877 TAGTTGGCTCGGGTGGGT 60.204 61.111 0.00 0.00 0.00 4.51
1719 1849 2.184020 CTCGGGTGGGTGCTCATCAA 62.184 60.000 0.00 0.00 0.00 2.57
1759 1892 4.514577 CTCGATGAAGGCGGCGGT 62.515 66.667 9.78 0.00 0.00 5.68
1808 1941 1.381327 CCGAGGTTGGGAGCCTAGA 60.381 63.158 0.00 0.00 36.29 2.43
1822 1955 4.466726 GGAGCCTAGAAGGACTAACAAAGA 59.533 45.833 0.00 0.00 37.67 2.52
1830 1963 5.132144 AGAAGGACTAACAAAGAAGGTCCAA 59.868 40.000 12.06 0.00 46.13 3.53
1881 2014 2.039624 GAGGTGGAGGAGGCAGGA 59.960 66.667 0.00 0.00 0.00 3.86
1883 2016 2.284995 GGTGGAGGAGGCAGGAGT 60.285 66.667 0.00 0.00 0.00 3.85
1915 2048 2.599281 TGAAGGTCGAGGTCGCCA 60.599 61.111 13.06 0.00 37.78 5.69
1917 2050 2.600769 AAGGTCGAGGTCGCCAGT 60.601 61.111 13.06 1.37 37.78 4.00
1926 2059 4.980805 GTCGCCAGTGGGTTCGCA 62.981 66.667 12.15 0.00 36.17 5.10
1943 2076 1.146930 CAGGATGTAGCACGGGCAT 59.853 57.895 14.57 0.00 44.61 4.40
1950 2083 0.461870 GTAGCACGGGCATGACATCA 60.462 55.000 14.57 0.00 44.61 3.07
1952 2085 0.469494 AGCACGGGCATGACATCATA 59.531 50.000 14.57 0.00 44.61 2.15
1963 2096 1.069204 TGACATCATAAGAGAGGCCGC 59.931 52.381 0.00 0.00 0.00 6.53
1964 2097 1.342819 GACATCATAAGAGAGGCCGCT 59.657 52.381 9.51 9.51 0.00 5.52
2004 2137 2.586792 GCGTTGGCTCTCCTGGAT 59.413 61.111 0.00 0.00 35.83 3.41
2017 2150 2.444706 TGGATGAGGAGGAGGCCG 60.445 66.667 0.00 0.00 0.00 6.13
2021 2154 3.317436 ATGAGGAGGAGGCCGTGGA 62.317 63.158 0.00 0.00 0.00 4.02
2032 2165 2.801631 GCCGTGGAGGAGATCAGGG 61.802 68.421 0.00 0.00 45.00 4.45
2035 2168 1.383803 GTGGAGGAGATCAGGGGCT 60.384 63.158 0.00 0.00 0.00 5.19
2036 2169 0.985490 GTGGAGGAGATCAGGGGCTT 60.985 60.000 0.00 0.00 0.00 4.35
2048 2206 1.995626 GGGGCTTAGGTGAGGCAGA 60.996 63.158 0.91 0.00 43.48 4.26
2054 2212 0.118346 TTAGGTGAGGCAGAGGGGAA 59.882 55.000 0.00 0.00 0.00 3.97
2077 2235 3.834799 GGTCACCGGCGGAGGTAG 61.835 72.222 35.78 16.09 43.89 3.18
2126 2284 3.032609 GCGCGACCATGGAGATCG 61.033 66.667 21.47 18.60 38.87 3.69
2133 2291 4.284860 CATGGAGATCGGGCGCGA 62.285 66.667 28.58 28.58 0.00 5.87
2188 2346 3.045601 CGGAGCTGGAGAGAAAAGAAA 57.954 47.619 0.00 0.00 0.00 2.52
2191 2349 4.622695 CGGAGCTGGAGAGAAAAGAAAGAT 60.623 45.833 0.00 0.00 0.00 2.40
2208 2366 0.766288 GATGGGAGGAAGGGAGAGGG 60.766 65.000 0.00 0.00 0.00 4.30
2246 2404 0.633921 AGCTCCTCTCCCTTAGCTCA 59.366 55.000 0.00 0.00 41.35 4.26
2249 2407 2.437651 GCTCCTCTCCCTTAGCTCAATT 59.562 50.000 0.00 0.00 32.18 2.32
2269 2428 4.840005 TGCGGTGTGTGTGGCGAA 62.840 61.111 0.00 0.00 0.00 4.70
2332 2491 2.090719 AGCTAGGGTTAGATAGGCACCA 60.091 50.000 0.00 0.00 31.50 4.17
2333 2492 2.704065 GCTAGGGTTAGATAGGCACCAA 59.296 50.000 0.00 0.00 31.50 3.67
2355 2514 0.255890 TTGGGCCTAGGTGAAGATGC 59.744 55.000 11.31 0.00 0.00 3.91
2360 2519 0.107456 CCTAGGTGAAGATGCGCCAT 59.893 55.000 4.18 0.00 40.91 4.40
2488 2649 4.466015 GGTTGGAGAAAGAATTTGGGCATA 59.534 41.667 0.00 0.00 39.27 3.14
2489 2650 5.129320 GGTTGGAGAAAGAATTTGGGCATAT 59.871 40.000 0.00 0.00 39.27 1.78
2527 2689 4.218200 TGGACTCACAAAATATGCTTGGTG 59.782 41.667 3.56 0.00 0.00 4.17
2528 2690 4.458989 GGACTCACAAAATATGCTTGGTGA 59.541 41.667 0.00 0.00 0.00 4.02
2535 2698 7.652909 TCACAAAATATGCTTGGTGAAAGAAAG 59.347 33.333 0.00 0.00 38.24 2.62
2550 2713 4.756084 AAGAAAGTAGAAGTGTGCATGC 57.244 40.909 11.82 11.82 0.00 4.06
2629 2794 0.044855 AGGTGCTAGGGAGGTCCAAT 59.955 55.000 0.00 0.00 38.24 3.16
2630 2795 0.919710 GGTGCTAGGGAGGTCCAATT 59.080 55.000 0.00 0.00 38.24 2.32
2631 2796 1.408822 GGTGCTAGGGAGGTCCAATTG 60.409 57.143 0.00 0.00 38.24 2.32
2633 2798 1.992557 TGCTAGGGAGGTCCAATTGTT 59.007 47.619 4.43 0.00 38.24 2.83
2674 2839 7.721399 GGAGCCTCAATAAATGGAGAAAGAATA 59.279 37.037 0.00 0.00 32.87 1.75
2676 2842 8.907885 AGCCTCAATAAATGGAGAAAGAATAAC 58.092 33.333 0.00 0.00 32.87 1.89
2677 2843 8.686334 GCCTCAATAAATGGAGAAAGAATAACA 58.314 33.333 0.00 0.00 32.87 2.41
2694 2860 9.579932 AAGAATAACAGAGAAAGTTTGGAGAAT 57.420 29.630 0.00 0.00 0.00 2.40
2833 3014 2.093181 CACCATGTGAATTCCCTCGGTA 60.093 50.000 2.27 0.00 35.23 4.02
2915 3102 3.243737 ATGGCATGATGACATGATGCAAC 60.244 43.478 31.93 20.33 46.11 4.17
2929 3137 2.071688 TGCAACGCAACAAACAAACT 57.928 40.000 0.00 0.00 34.76 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 50 2.166270 GCTAGTTGCAGGTGAGTGC 58.834 57.895 0.00 0.00 44.27 4.40
116 126 1.813178 GCCTCTAAGCTTTTCCACCAC 59.187 52.381 3.20 0.00 0.00 4.16
128 139 7.148120 CCAATATGCCATGAAATAGCCTCTAAG 60.148 40.741 0.00 0.00 26.21 2.18
138 151 4.203342 ACCTCCCAATATGCCATGAAAT 57.797 40.909 0.00 0.00 0.00 2.17
159 174 4.521256 GCTACCCACCACTTGTTTATCAAA 59.479 41.667 0.00 0.00 35.48 2.69
207 225 9.781834 CTCACTACTATATTTGCTATGCTAGTC 57.218 37.037 0.00 0.00 0.00 2.59
222 241 5.763698 CGTCACCTTGGATCTCACTACTATA 59.236 44.000 0.00 0.00 0.00 1.31
247 266 1.945394 CGGGATTTCAGGCAAGATGAG 59.055 52.381 0.00 0.00 0.00 2.90
268 287 2.444421 TGGACTCGGTCTTCTTCCTAC 58.556 52.381 4.41 0.00 32.47 3.18
296 315 0.168788 TTCTACTACGCCGGTTCGTG 59.831 55.000 16.16 9.21 43.21 4.35
312 334 2.271800 GCGATTGTGAGGATTCGTTCT 58.728 47.619 0.00 0.00 34.24 3.01
440 465 4.493547 CATGCCATGTTTCATTAAACCGT 58.506 39.130 0.00 0.00 43.66 4.83
453 478 1.481901 TTTGCCTTGCCATGCCATGT 61.482 50.000 3.63 0.00 0.00 3.21
786 822 6.389622 CATGCTCATGTCAACATTTTCTTG 57.610 37.500 1.84 0.00 33.61 3.02
824 862 2.574322 CTTTCGTTTCGCCATGTTGAG 58.426 47.619 0.00 0.00 0.00 3.02
909 947 1.014044 TCGCTTGCACCGACATCTTC 61.014 55.000 4.66 0.00 0.00 2.87
925 963 4.024387 TGTTTTGTAGATCCACACTTTCGC 60.024 41.667 0.00 0.00 0.00 4.70
1006 1055 1.067060 CATTGCTCGGTCCTCATCGTA 59.933 52.381 0.00 0.00 0.00 3.43
1011 1060 0.684535 TTGTCATTGCTCGGTCCTCA 59.315 50.000 0.00 0.00 0.00 3.86
1043 1093 2.290008 TGTATGAGATGCCCGTGTTTGT 60.290 45.455 0.00 0.00 0.00 2.83
1086 1137 0.747644 TATAACCCCGAGACGACGCA 60.748 55.000 0.00 0.00 0.00 5.24
1114 1169 1.453155 GTTCTGTCCCGAATGCATGT 58.547 50.000 0.00 0.00 0.00 3.21
1145 1204 5.254901 AGAACGTCTACTTCCATCTACACT 58.745 41.667 0.00 0.00 0.00 3.55
1244 1374 2.504274 AAGTTCCTCGCCGTGACCA 61.504 57.895 0.00 0.00 0.00 4.02
1265 1395 0.608130 CCTCAATGACTCCGTGGACA 59.392 55.000 0.00 0.00 0.00 4.02
1278 1408 1.762957 CCACTACCATCGACCCTCAAT 59.237 52.381 0.00 0.00 0.00 2.57
1370 1500 4.443621 TGTTTACCGTTGTCAAGATCACA 58.556 39.130 0.00 0.00 0.00 3.58
1380 1510 4.097286 AGCATCAAGTTTGTTTACCGTTGT 59.903 37.500 0.00 0.00 0.00 3.32
1443 1573 4.039730 CGAGGACCCATCAAGTTCATCTAT 59.960 45.833 0.00 0.00 0.00 1.98
1468 1598 1.053424 GGACACCAAGTACCAGGACA 58.947 55.000 8.10 0.00 0.00 4.02
1498 1628 2.348685 CGCGTTTTGTTTCATCACCGTA 60.349 45.455 0.00 0.00 0.00 4.02
1512 1642 1.264826 GTACCACAACCATCGCGTTTT 59.735 47.619 5.77 0.00 0.00 2.43
1547 1677 4.454728 AGTACAGTAATAACCCGCGAAA 57.545 40.909 8.23 0.00 0.00 3.46
1561 1691 1.305201 CACCAAACGCCAAGTACAGT 58.695 50.000 0.00 0.00 0.00 3.55
1576 1706 0.816018 CACAACCAAGTACCGCACCA 60.816 55.000 0.00 0.00 0.00 4.17
1645 1775 1.071542 TCGTCCCACTCATTTGCTTCA 59.928 47.619 0.00 0.00 0.00 3.02
1652 1782 1.374252 GCACGTCGTCCCACTCATT 60.374 57.895 0.00 0.00 0.00 2.57
1654 1784 4.337060 CGCACGTCGTCCCACTCA 62.337 66.667 0.00 0.00 0.00 3.41
1671 1801 2.635338 GTTGACCGCGTTCCCAAC 59.365 61.111 4.92 9.62 33.24 3.77
1677 1807 1.727022 CTACGTCGTTGACCGCGTT 60.727 57.895 1.78 0.00 43.24 4.84
1693 1823 2.203877 ACCCACCCGAGCCAACTA 60.204 61.111 0.00 0.00 0.00 2.24
1694 1824 3.953775 CACCCACCCGAGCCAACT 61.954 66.667 0.00 0.00 0.00 3.16
1710 1840 2.036571 CGCTGCCTGTTGATGAGCA 61.037 57.895 0.00 0.00 0.00 4.26
1715 1845 2.393768 CGCTTCGCTGCCTGTTGAT 61.394 57.895 0.00 0.00 0.00 2.57
1741 1874 4.514577 CCGCCGCCTTCATCGAGT 62.515 66.667 0.00 0.00 0.00 4.18
1763 1896 2.503375 CGGAGCTTCGCGTACGTT 60.503 61.111 17.90 0.00 41.18 3.99
1805 1938 5.842328 TGGACCTTCTTTGTTAGTCCTTCTA 59.158 40.000 8.78 0.00 45.90 2.10
1808 1941 5.382664 TTGGACCTTCTTTGTTAGTCCTT 57.617 39.130 8.78 0.00 45.90 3.36
1822 1955 1.464722 CACCACCCCATTGGACCTT 59.535 57.895 3.62 0.00 39.24 3.50
1869 2002 4.154347 CGCACTCCTGCCTCCTCC 62.154 72.222 0.00 0.00 40.73 4.30
1888 2021 3.256960 GACCTTCAGGCCACCCCA 61.257 66.667 5.01 0.00 39.32 4.96
1915 2048 0.537188 CTACATCCTGCGAACCCACT 59.463 55.000 0.00 0.00 0.00 4.00
1917 2050 1.220749 GCTACATCCTGCGAACCCA 59.779 57.895 0.00 0.00 0.00 4.51
1926 2059 1.146930 CATGCCCGTGCTACATCCT 59.853 57.895 0.00 0.00 38.71 3.24
1943 2076 1.069204 GCGGCCTCTCTTATGATGTCA 59.931 52.381 0.00 0.00 0.00 3.58
1950 2083 2.825264 GCCAGCGGCCTCTCTTAT 59.175 61.111 0.00 0.00 44.06 1.73
1988 2121 0.179089 CTCATCCAGGAGAGCCAACG 60.179 60.000 0.00 0.00 37.05 4.10
2004 2137 3.965026 CTCCACGGCCTCCTCCTCA 62.965 68.421 0.00 0.00 0.00 3.86
2017 2150 0.985490 AAGCCCCTGATCTCCTCCAC 60.985 60.000 0.00 0.00 0.00 4.02
2021 2154 0.644937 ACCTAAGCCCCTGATCTCCT 59.355 55.000 0.00 0.00 0.00 3.69
2032 2165 1.524482 CCTCTGCCTCACCTAAGCC 59.476 63.158 0.00 0.00 0.00 4.35
2035 2168 0.118346 TTCCCCTCTGCCTCACCTAA 59.882 55.000 0.00 0.00 0.00 2.69
2036 2169 0.617820 GTTCCCCTCTGCCTCACCTA 60.618 60.000 0.00 0.00 0.00 3.08
2048 2206 2.531942 GTGACCCCTGGTTCCCCT 60.532 66.667 0.00 0.00 35.25 4.79
2075 2233 2.194056 CTACTCCCGTCGGCCCTA 59.806 66.667 5.50 0.00 0.00 3.53
2079 2237 4.874977 GCTGCTACTCCCGTCGGC 62.875 72.222 5.50 0.00 0.00 5.54
2081 2239 2.409651 GAGCTGCTACTCCCGTCG 59.590 66.667 0.15 0.00 0.00 5.12
2084 2242 2.196925 ATCCGAGCTGCTACTCCCG 61.197 63.158 0.15 0.79 32.79 5.14
2085 2243 1.365633 CATCCGAGCTGCTACTCCC 59.634 63.158 0.15 0.00 32.79 4.30
2090 2248 2.833121 TCGCCATCCGAGCTGCTA 60.833 61.111 0.15 0.00 41.89 3.49
2112 2270 2.029666 GCCCGATCTCCATGGTCG 59.970 66.667 12.58 13.77 35.29 4.79
2177 2335 5.280934 CCTTCCTCCCATCTTTCTTTTCTCT 60.281 44.000 0.00 0.00 0.00 3.10
2185 2343 2.437651 CTCTCCCTTCCTCCCATCTTTC 59.562 54.545 0.00 0.00 0.00 2.62
2188 2346 0.267356 CCTCTCCCTTCCTCCCATCT 59.733 60.000 0.00 0.00 0.00 2.90
2191 2349 2.787866 CCCTCTCCCTTCCTCCCA 59.212 66.667 0.00 0.00 0.00 4.37
2208 2366 2.969238 CTCACGCCCGATCCATGC 60.969 66.667 0.00 0.00 0.00 4.06
2241 2399 1.301716 ACACCGCACGAATTGAGCT 60.302 52.632 0.00 0.00 31.26 4.09
2246 2404 1.646540 CACACACACCGCACGAATT 59.353 52.632 0.00 0.00 0.00 2.17
2268 2427 2.920912 TCGTTCCCCACCTCGCTT 60.921 61.111 0.00 0.00 0.00 4.68
2269 2428 3.382832 CTCGTTCCCCACCTCGCT 61.383 66.667 0.00 0.00 0.00 4.93
2332 2491 2.062636 TCTTCACCTAGGCCCAACTTT 58.937 47.619 9.30 0.00 0.00 2.66
2333 2492 1.742308 TCTTCACCTAGGCCCAACTT 58.258 50.000 9.30 0.00 0.00 2.66
2360 2519 4.704833 GCTGCAGCCCAACCTCGA 62.705 66.667 28.76 0.00 34.31 4.04
2435 2594 8.133627 TCTTTCTCTCATTTTCTTTCTTTGCTG 58.866 33.333 0.00 0.00 0.00 4.41
2488 2649 4.045334 TGAGTCCAAGAAAATAACCCCCAT 59.955 41.667 0.00 0.00 0.00 4.00
2489 2650 3.399644 TGAGTCCAAGAAAATAACCCCCA 59.600 43.478 0.00 0.00 0.00 4.96
2527 2689 5.149977 GCATGCACACTTCTACTTTCTTTC 58.850 41.667 14.21 0.00 0.00 2.62
2528 2690 4.319766 CGCATGCACACTTCTACTTTCTTT 60.320 41.667 19.57 0.00 0.00 2.52
2535 2698 1.136252 CACACGCATGCACACTTCTAC 60.136 52.381 19.57 0.00 0.00 2.59
2550 2713 4.235360 AGTTCGAAATCTAACCTCACACG 58.765 43.478 0.00 0.00 0.00 4.49
2629 2794 5.476945 GGCTCCTCCTAAATTCTCAAAACAA 59.523 40.000 0.00 0.00 0.00 2.83
2630 2795 5.010282 GGCTCCTCCTAAATTCTCAAAACA 58.990 41.667 0.00 0.00 0.00 2.83
2631 2796 5.257262 AGGCTCCTCCTAAATTCTCAAAAC 58.743 41.667 0.00 0.00 45.41 2.43
2633 2798 6.297243 ATTGAGGCTCCTCCTAAATTCTCAAA 60.297 38.462 12.86 0.00 42.39 2.69
2674 2839 6.830838 AGTTCATTCTCCAAACTTTCTCTGTT 59.169 34.615 0.00 0.00 29.09 3.16
2676 2842 6.874288 AGTTCATTCTCCAAACTTTCTCTG 57.126 37.500 0.00 0.00 29.09 3.35
2677 2843 7.056635 TCAAGTTCATTCTCCAAACTTTCTCT 58.943 34.615 0.00 0.00 40.32 3.10
2694 2860 3.384146 TCATGCCTTTTGCTTCAAGTTCA 59.616 39.130 0.00 0.00 42.00 3.18


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

AutoCloner maintained by Alex Coulton.