Multiple sequence alignment - TraesCS7A01G023700

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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 TraesCS7A01G023700 chr7A 100.000 3248 0 0 1 3248 9381016 9384263 0.000000e+00 5999.0
1 TraesCS7A01G023700 chr7A 77.987 1272 215 33 998 2228 9486675 9487922 0.000000e+00 737.0
2 TraesCS7A01G023700 chr7A 76.953 1306 231 44 1018 2287 114414385 114413114 0.000000e+00 680.0
3 TraesCS7A01G023700 chr7A 76.074 1350 253 40 998 2298 10092034 10090706 9.830000e-180 640.0
4 TraesCS7A01G023700 chr7A 82.913 714 94 21 28 728 9679643 9678945 4.600000e-173 617.0
5 TraesCS7A01G023700 chr7A 76.085 1313 237 43 1018 2287 114688753 114687475 5.960000e-172 614.0
6 TraesCS7A01G023700 chr7A 82.639 288 34 13 452 728 9676629 9676347 1.160000e-59 241.0
7 TraesCS7A01G023700 chr7A 76.792 293 44 12 2347 2634 10271072 10271345 3.380000e-30 143.0
8 TraesCS7A01G023700 chr7D 92.694 1533 63 7 794 2287 8818639 8820161 0.000000e+00 2165.0
9 TraesCS7A01G023700 chr7D 78.901 1237 195 42 1031 2228 10087843 10086634 0.000000e+00 778.0
10 TraesCS7A01G023700 chr7D 78.054 1326 219 46 998 2287 109144722 109143433 0.000000e+00 771.0
11 TraesCS7A01G023700 chr7D 77.424 1351 225 44 999 2298 10963662 10962341 0.000000e+00 732.0
12 TraesCS7A01G023700 chr7D 76.026 1560 250 57 791 2298 10465830 10464343 0.000000e+00 695.0
13 TraesCS7A01G023700 chr7D 75.758 1320 238 44 1032 2298 1520512 1519222 1.000000e-164 590.0
14 TraesCS7A01G023700 chr7D 95.294 340 9 2 2295 2634 8820250 8820582 1.720000e-147 532.0
15 TraesCS7A01G023700 chr7D 85.586 444 62 2 170 612 8816969 8817411 6.350000e-127 464.0
16 TraesCS7A01G023700 chr7D 87.151 358 34 4 2697 3053 8820719 8821065 2.350000e-106 396.0
17 TraesCS7A01G023700 chr7D 79.116 498 88 12 28 516 10466838 10466348 2.420000e-86 329.0
18 TraesCS7A01G023700 chr7D 90.395 177 13 3 3039 3212 8821122 8821297 2.520000e-56 230.0
19 TraesCS7A01G023700 chr4A 90.069 1601 107 26 728 2298 729818963 729820541 0.000000e+00 2028.0
20 TraesCS7A01G023700 chr4A 93.027 1219 69 5 1096 2298 728443463 728442245 0.000000e+00 1766.0
21 TraesCS7A01G023700 chr4A 87.795 1524 132 21 794 2287 729157102 729158601 0.000000e+00 1735.0
22 TraesCS7A01G023700 chr4A 92.707 905 56 2 809 1710 729677564 729678461 0.000000e+00 1297.0
23 TraesCS7A01G023700 chr4A 77.751 1681 267 71 1012 2616 729426121 729424472 0.000000e+00 933.0
24 TraesCS7A01G023700 chr4A 86.786 840 60 28 2295 3109 728442170 728441357 0.000000e+00 889.0
25 TraesCS7A01G023700 chr4A 92.243 593 33 4 1708 2287 729678543 729679135 0.000000e+00 828.0
26 TraesCS7A01G023700 chr4A 78.108 1311 225 35 998 2262 730322761 730324055 0.000000e+00 774.0
27 TraesCS7A01G023700 chr4A 77.554 1341 219 43 997 2298 729880854 729882151 0.000000e+00 734.0
28 TraesCS7A01G023700 chr4A 77.685 1322 215 56 1028 2298 730388767 730390059 0.000000e+00 734.0
29 TraesCS7A01G023700 chr4A 78.058 1112 175 30 799 1860 729925353 729926445 3.530000e-179 638.0
30 TraesCS7A01G023700 chr4A 76.439 1303 221 48 1027 2276 743634605 743635874 7.650000e-176 627.0
31 TraesCS7A01G023700 chr4A 91.860 430 33 2 2793 3220 730002106 730001677 1.670000e-167 599.0
32 TraesCS7A01G023700 chr4A 80.027 731 108 21 5 716 729924517 729925228 1.040000e-139 507.0
33 TraesCS7A01G023700 chr4A 92.941 340 17 2 2295 2634 729679224 729679556 3.770000e-134 488.0
34 TraesCS7A01G023700 chr4A 91.176 340 21 4 2295 2634 729158690 729159020 1.370000e-123 453.0
35 TraesCS7A01G023700 chr4A 83.640 489 73 7 6 491 729659480 729659964 1.370000e-123 453.0
36 TraesCS7A01G023700 chr4A 81.888 519 82 4 86 602 730005665 730005157 8.330000e-116 427.0
37 TraesCS7A01G023700 chr4A 78.298 705 122 18 984 1665 727123012 727123708 3.000000e-115 425.0
38 TraesCS7A01G023700 chr4A 79.871 621 85 18 44 648 730062257 730061661 5.010000e-113 418.0
39 TraesCS7A01G023700 chr4A 81.288 497 55 14 790 1256 728662500 728662012 5.120000e-98 368.0
40 TraesCS7A01G023700 chr4A 95.890 219 8 1 3030 3248 728441485 728441268 1.430000e-93 353.0
41 TraesCS7A01G023700 chr4A 84.366 339 35 2 801 1122 730061515 730061178 1.880000e-82 316.0
42 TraesCS7A01G023700 chr4A 81.449 345 53 7 2296 2638 728569680 728569345 4.130000e-69 272.0
43 TraesCS7A01G023700 chr4A 87.129 101 6 5 588 686 730005027 730004932 1.230000e-19 108.0
44 TraesCS7A01G023700 chr4A 94.231 52 3 0 3197 3248 730001676 730001625 2.690000e-11 80.5
45 TraesCS7A01G023700 chr4A 91.525 59 3 2 790 848 730004768 730004712 2.690000e-11 80.5
46 TraesCS7A01G023700 chr4A 91.837 49 3 1 2776 2824 728568048 728568001 2.090000e-07 67.6
47 TraesCS7A01G023700 chr4B 78.228 1580 231 59 803 2298 654201713 654203263 0.000000e+00 907.0
48 TraesCS7A01G023700 chr4B 89.550 555 40 9 2697 3248 654203827 654204366 0.000000e+00 688.0
49 TraesCS7A01G023700 chr4B 91.401 314 22 3 2322 2634 654203339 654203648 3.000000e-115 425.0
50 TraesCS7A01G023700 chr4B 86.792 106 11 3 3056 3159 654204132 654204236 7.360000e-22 115.0
51 TraesCS7A01G023700 chr4D 84.957 585 47 22 2687 3248 507350366 507349800 3.660000e-154 555.0
52 TraesCS7A01G023700 chr4D 90.446 314 25 3 2322 2634 507350844 507350535 3.020000e-110 409.0
53 TraesCS7A01G023700 chr5A 90.816 392 30 3 2697 3087 691822880 691823266 1.340000e-143 520.0
54 TraesCS7A01G023700 chr5A 90.764 314 24 3 2322 2634 691822379 691822688 6.480000e-112 414.0


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 TraesCS7A01G023700 chr7A 9381016 9384263 3247 False 5999.000000 5999 100.000000 1 3248 1 chr7A.!!$F1 3247
1 TraesCS7A01G023700 chr7A 9486675 9487922 1247 False 737.000000 737 77.987000 998 2228 1 chr7A.!!$F2 1230
2 TraesCS7A01G023700 chr7A 114413114 114414385 1271 True 680.000000 680 76.953000 1018 2287 1 chr7A.!!$R2 1269
3 TraesCS7A01G023700 chr7A 10090706 10092034 1328 True 640.000000 640 76.074000 998 2298 1 chr7A.!!$R1 1300
4 TraesCS7A01G023700 chr7A 114687475 114688753 1278 True 614.000000 614 76.085000 1018 2287 1 chr7A.!!$R3 1269
5 TraesCS7A01G023700 chr7A 9676347 9679643 3296 True 429.000000 617 82.776000 28 728 2 chr7A.!!$R4 700
6 TraesCS7A01G023700 chr7D 10086634 10087843 1209 True 778.000000 778 78.901000 1031 2228 1 chr7D.!!$R2 1197
7 TraesCS7A01G023700 chr7D 109143433 109144722 1289 True 771.000000 771 78.054000 998 2287 1 chr7D.!!$R4 1289
8 TraesCS7A01G023700 chr7D 8816969 8821297 4328 False 757.400000 2165 90.224000 170 3212 5 chr7D.!!$F1 3042
9 TraesCS7A01G023700 chr7D 10962341 10963662 1321 True 732.000000 732 77.424000 999 2298 1 chr7D.!!$R3 1299
10 TraesCS7A01G023700 chr7D 1519222 1520512 1290 True 590.000000 590 75.758000 1032 2298 1 chr7D.!!$R1 1266
11 TraesCS7A01G023700 chr7D 10464343 10466838 2495 True 512.000000 695 77.571000 28 2298 2 chr7D.!!$R5 2270
12 TraesCS7A01G023700 chr4A 729818963 729820541 1578 False 2028.000000 2028 90.069000 728 2298 1 chr4A.!!$F3 1570
13 TraesCS7A01G023700 chr4A 729157102 729159020 1918 False 1094.000000 1735 89.485500 794 2634 2 chr4A.!!$F8 1840
14 TraesCS7A01G023700 chr4A 728441268 728443463 2195 True 1002.666667 1766 91.901000 1096 3248 3 chr4A.!!$R3 2152
15 TraesCS7A01G023700 chr4A 729424472 729426121 1649 True 933.000000 933 77.751000 1012 2616 1 chr4A.!!$R2 1604
16 TraesCS7A01G023700 chr4A 729677564 729679556 1992 False 871.000000 1297 92.630333 809 2634 3 chr4A.!!$F9 1825
17 TraesCS7A01G023700 chr4A 730322761 730324055 1294 False 774.000000 774 78.108000 998 2262 1 chr4A.!!$F5 1264
18 TraesCS7A01G023700 chr4A 729880854 729882151 1297 False 734.000000 734 77.554000 997 2298 1 chr4A.!!$F4 1301
19 TraesCS7A01G023700 chr4A 730388767 730390059 1292 False 734.000000 734 77.685000 1028 2298 1 chr4A.!!$F6 1270
20 TraesCS7A01G023700 chr4A 743634605 743635874 1269 False 627.000000 627 76.439000 1027 2276 1 chr4A.!!$F7 1249
21 TraesCS7A01G023700 chr4A 729924517 729926445 1928 False 572.500000 638 79.042500 5 1860 2 chr4A.!!$F10 1855
22 TraesCS7A01G023700 chr4A 727123012 727123708 696 False 425.000000 425 78.298000 984 1665 1 chr4A.!!$F1 681
23 TraesCS7A01G023700 chr4A 730061178 730062257 1079 True 367.000000 418 82.118500 44 1122 2 chr4A.!!$R6 1078
24 TraesCS7A01G023700 chr4A 730001625 730005665 4040 True 259.000000 599 89.326600 86 3248 5 chr4A.!!$R5 3162
25 TraesCS7A01G023700 chr4B 654201713 654204366 2653 False 533.750000 907 86.492750 803 3248 4 chr4B.!!$F1 2445
26 TraesCS7A01G023700 chr4D 507349800 507350844 1044 True 482.000000 555 87.701500 2322 3248 2 chr4D.!!$R1 926
27 TraesCS7A01G023700 chr5A 691822379 691823266 887 False 467.000000 520 90.790000 2322 3087 2 chr5A.!!$F1 765

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
373 389 0.317799 TTGCTGAAATGCGTGCCATT 59.682 45.0 0.0 0.00 45.9 3.16 F
1813 3978 0.179108 GCAGTACGGCCGAAGATCTT 60.179 55.0 35.9 7.95 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 5836 0.250338 ACGGTTCTTGGAGGAAGCAC 60.250 55.0 7.1 0.0 41.91 4.40 R
2735 6843 0.608640 AGCCGACTCAAACAGGGTAG 59.391 55.0 0.0 0.0 32.10 3.18 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
80 87 4.212716 ACAGGTTTAGGGAAGGTTCAAAC 58.787 43.478 0.00 0.00 0.00 2.93
96 103 4.263452 ACCCGGTGGTGGAAAAAC 57.737 55.556 0.00 0.00 45.58 2.43
99 106 2.557372 CCGGTGGTGGAAAAACCCG 61.557 63.158 0.00 0.00 39.70 5.28
113 120 1.939980 AACCCGTCTAGAGAAGGCTT 58.060 50.000 0.00 0.00 41.47 4.35
128 142 2.038975 CTTGGACGAGGAGGGGGA 59.961 66.667 0.00 0.00 0.00 4.81
147 161 2.424379 GGAAGGTTTGGAGAAGGTGGTT 60.424 50.000 0.00 0.00 0.00 3.67
225 240 1.548719 CGACATCACACCCACCTCTTA 59.451 52.381 0.00 0.00 0.00 2.10
263 278 4.006319 GAGCACTTCTGCCTCTTAAATGT 58.994 43.478 0.00 0.00 45.53 2.71
269 284 4.640771 TCTGCCTCTTAAATGTTGGAGT 57.359 40.909 0.00 0.00 0.00 3.85
373 389 0.317799 TTGCTGAAATGCGTGCCATT 59.682 45.000 0.00 0.00 45.90 3.16
385 401 1.386533 GTGCCATTCTGGAGTCCATG 58.613 55.000 13.56 8.36 40.96 3.66
417 433 2.418356 GGTGTCGACGAACCACCA 59.582 61.111 24.94 6.85 46.33 4.17
456 472 1.674221 CCAAGAGCCGAAGAAGACCTG 60.674 57.143 0.00 0.00 0.00 4.00
470 486 1.073444 AGACCTGTGTAGACGAGGACA 59.927 52.381 13.13 0.00 0.00 4.02
471 487 1.199558 GACCTGTGTAGACGAGGACAC 59.800 57.143 13.13 10.23 45.06 3.67
548 769 3.935024 CGATCCCCTCGGACAAGA 58.065 61.111 0.00 0.00 42.48 3.02
666 1893 5.689068 AGTTGTAGTTGTAGCTCGTTTGTAC 59.311 40.000 0.00 0.00 0.00 2.90
669 1896 6.605849 TGTAGTTGTAGCTCGTTTGTACTAG 58.394 40.000 0.00 0.00 0.00 2.57
671 1898 6.081872 AGTTGTAGCTCGTTTGTACTAGTT 57.918 37.500 0.00 0.00 0.00 2.24
672 1899 6.148264 AGTTGTAGCTCGTTTGTACTAGTTC 58.852 40.000 0.00 0.00 0.00 3.01
673 1900 5.954296 TGTAGCTCGTTTGTACTAGTTCT 57.046 39.130 0.00 0.00 0.00 3.01
676 1903 8.722480 TGTAGCTCGTTTGTACTAGTTCTATA 57.278 34.615 0.00 0.00 0.00 1.31
677 1904 8.824781 TGTAGCTCGTTTGTACTAGTTCTATAG 58.175 37.037 0.00 0.00 0.00 1.31
678 1905 7.261829 AGCTCGTTTGTACTAGTTCTATAGG 57.738 40.000 0.00 0.00 0.00 2.57
679 1906 5.914074 GCTCGTTTGTACTAGTTCTATAGGC 59.086 44.000 0.00 0.00 0.00 3.93
680 1907 6.459298 GCTCGTTTGTACTAGTTCTATAGGCA 60.459 42.308 0.00 0.00 0.00 4.75
681 1908 7.578310 TCGTTTGTACTAGTTCTATAGGCAT 57.422 36.000 0.00 0.00 0.00 4.40
683 1910 7.919091 TCGTTTGTACTAGTTCTATAGGCATTG 59.081 37.037 0.00 0.00 0.00 2.82
685 1912 9.379791 GTTTGTACTAGTTCTATAGGCATTGTT 57.620 33.333 0.00 0.00 0.00 2.83
686 1913 9.953565 TTTGTACTAGTTCTATAGGCATTGTTT 57.046 29.630 0.00 0.00 0.00 2.83
687 1914 8.942338 TGTACTAGTTCTATAGGCATTGTTTG 57.058 34.615 0.00 0.00 0.00 2.93
747 2080 2.175931 TCCAACTGGACTGGGCTTTTTA 59.824 45.455 0.00 0.00 39.78 1.52
751 2084 5.454613 CCAACTGGACTGGGCTTTTTATTTT 60.455 40.000 0.00 0.00 37.39 1.82
781 2140 1.882623 CGGCTGGAGAAGAAAAGCTTT 59.117 47.619 5.69 5.69 36.83 3.51
782 2141 2.095516 CGGCTGGAGAAGAAAAGCTTTC 60.096 50.000 13.10 6.36 36.83 2.62
783 2142 3.153130 GGCTGGAGAAGAAAAGCTTTCT 58.847 45.455 13.10 4.98 36.83 2.52
784 2143 3.571828 GGCTGGAGAAGAAAAGCTTTCTT 59.428 43.478 13.10 16.22 41.08 2.52
786 2145 4.276926 GCTGGAGAAGAAAAGCTTTCTTGA 59.723 41.667 21.09 4.11 38.73 3.02
787 2146 5.562501 GCTGGAGAAGAAAAGCTTTCTTGAG 60.563 44.000 21.09 11.90 38.73 3.02
920 2303 1.415672 GGAAGAGGTCACCACCACCA 61.416 60.000 0.00 0.00 46.68 4.17
938 2451 4.080863 CCACCAGCTACTACCTGATTTTCT 60.081 45.833 0.00 0.00 32.03 2.52
1152 2780 0.909610 TCAGATCCCTCCACCGCTTT 60.910 55.000 0.00 0.00 0.00 3.51
1212 2840 1.231958 CCGCCAACCGCAAGAAGTTA 61.232 55.000 0.00 0.00 43.02 2.24
1291 2938 3.680786 CCAGTGTCTCGGGCGACA 61.681 66.667 0.00 0.00 41.33 4.35
1467 3498 2.153401 CACTGGGAGGTGGGTGGAA 61.153 63.158 0.00 0.00 33.95 3.53
1477 3513 2.612746 GGGTGGAACTGCCCCCTA 60.613 66.667 0.00 0.00 41.50 3.53
1531 3585 6.058833 TGTACCACAAGTCTTGCTTTTGATA 58.941 36.000 12.66 0.00 37.12 2.15
1552 3606 1.407299 CGGCAGTCTCATCCCATTTCA 60.407 52.381 0.00 0.00 0.00 2.69
1635 3689 2.725312 GCGGACAGGAGCATGGAGA 61.725 63.158 0.00 0.00 0.00 3.71
1762 3927 2.034879 GTGCTGATGGTGGTGGACG 61.035 63.158 0.00 0.00 0.00 4.79
1813 3978 0.179108 GCAGTACGGCCGAAGATCTT 60.179 55.000 35.90 7.95 0.00 2.40
2007 4908 2.127651 TTGGGGAGAAGTACAGGGTT 57.872 50.000 0.00 0.00 0.00 4.11
2200 5824 2.436173 AGATGGGCAGTAGCTTTACCTC 59.564 50.000 0.00 0.00 41.70 3.85
2201 5825 1.651737 TGGGCAGTAGCTTTACCTCA 58.348 50.000 0.00 0.00 41.70 3.86
2202 5826 1.982226 TGGGCAGTAGCTTTACCTCAA 59.018 47.619 0.00 0.00 41.70 3.02
2203 5827 2.027192 TGGGCAGTAGCTTTACCTCAAG 60.027 50.000 0.00 0.00 41.70 3.02
2209 5833 1.502190 GCTTTACCTCAAGCCACGC 59.498 57.895 0.00 0.00 43.03 5.34
2212 5836 0.605319 TTTACCTCAAGCCACGCCAG 60.605 55.000 0.00 0.00 0.00 4.85
2265 5903 3.734597 GCTGAACAATTTGTCTGTGCACA 60.735 43.478 20.37 20.37 29.01 4.57
2289 5927 2.691526 GGAATCTGCTTCAATCATGCCA 59.308 45.455 0.00 0.00 35.41 4.92
2321 6042 5.009610 TCCAAAGAACAATGTTACTCTTGGC 59.990 40.000 16.62 0.00 0.00 4.52
2323 6044 4.373156 AGAACAATGTTACTCTTGGCCT 57.627 40.909 3.32 0.00 0.00 5.19
2324 6045 4.074970 AGAACAATGTTACTCTTGGCCTG 58.925 43.478 3.32 0.00 0.00 4.85
2325 6046 3.508845 ACAATGTTACTCTTGGCCTGT 57.491 42.857 3.32 0.05 0.00 4.00
2326 6047 3.832527 ACAATGTTACTCTTGGCCTGTT 58.167 40.909 3.32 0.00 0.00 3.16
2330 6051 2.360801 TGTTACTCTTGGCCTGTTTTGC 59.639 45.455 3.32 0.00 0.00 3.68
2367 6088 2.884012 TGTTGTTCTGGGCATGTGTTAG 59.116 45.455 0.00 0.00 0.00 2.34
2368 6089 2.884639 GTTGTTCTGGGCATGTGTTAGT 59.115 45.455 0.00 0.00 0.00 2.24
2369 6090 2.778299 TGTTCTGGGCATGTGTTAGTC 58.222 47.619 0.00 0.00 0.00 2.59
2733 6841 0.102844 TTGCTTTGGCTGTGTTGCTC 59.897 50.000 0.00 0.00 39.59 4.26
2734 6842 1.370900 GCTTTGGCTGTGTTGCTCG 60.371 57.895 0.00 0.00 35.22 5.03
2735 6843 1.370900 CTTTGGCTGTGTTGCTCGC 60.371 57.895 0.00 0.00 0.00 5.03
2736 6844 1.789078 CTTTGGCTGTGTTGCTCGCT 61.789 55.000 0.00 0.00 0.00 4.93
2755 6863 1.002087 CTACCCTGTTTGAGTCGGCTT 59.998 52.381 0.00 0.00 0.00 4.35
2824 6937 8.576442 TGATTCTTGAATGTTCTTTTTAGGACC 58.424 33.333 0.09 0.00 0.00 4.46
2833 6946 5.077564 GTTCTTTTTAGGACCCTGGAATGT 58.922 41.667 0.00 0.00 0.00 2.71
2945 7067 8.752005 AGCAGTTTTATATTCATAAAGAGCCA 57.248 30.769 0.00 0.00 37.78 4.75
2965 7087 1.985159 AGCCACCCATTTGTCAGTCTA 59.015 47.619 0.00 0.00 0.00 2.59
2990 7112 3.207669 GCCGCAATGAGCAGAGGG 61.208 66.667 0.00 0.00 46.13 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 5.337554 ACCTGTTTTTCGTGTTTCTTTAGC 58.662 37.500 0.00 0.00 0.00 3.09
42 43 7.969508 CCTAAACCTGTTTTTCGTGTTTCTTTA 59.030 33.333 0.00 0.00 34.23 1.85
46 53 5.038683 CCCTAAACCTGTTTTTCGTGTTTC 58.961 41.667 0.00 0.00 34.23 2.78
52 59 3.887110 ACCTTCCCTAAACCTGTTTTTCG 59.113 43.478 0.00 0.00 34.23 3.46
80 87 2.204461 GGGTTTTTCCACCACCGGG 61.204 63.158 6.32 0.00 38.79 5.73
96 103 0.461961 CCAAGCCTTCTCTAGACGGG 59.538 60.000 4.83 0.27 34.37 5.28
99 106 2.093106 TCGTCCAAGCCTTCTCTAGAC 58.907 52.381 0.00 0.00 0.00 2.59
113 120 2.038975 CTTCCCCCTCCTCGTCCA 59.961 66.667 0.00 0.00 0.00 4.02
128 142 4.407365 CATAACCACCTTCTCCAAACCTT 58.593 43.478 0.00 0.00 0.00 3.50
147 161 1.985662 AACTGGGTCGACCGCCATA 60.986 57.895 27.68 10.67 44.64 2.74
174 188 0.182061 ATGCTGTCGCCATCTCCAAT 59.818 50.000 0.00 0.00 34.43 3.16
225 240 1.983224 CTCCCACACGTCCTCCATT 59.017 57.895 0.00 0.00 0.00 3.16
258 273 2.038557 ACGAGGTGCTACTCCAACATTT 59.961 45.455 0.00 0.00 33.93 2.32
263 278 1.541310 CCCACGAGGTGCTACTCCAA 61.541 60.000 0.00 0.00 33.93 3.53
269 284 2.363795 CTCCCCCACGAGGTGCTA 60.364 66.667 0.00 0.00 31.34 3.49
385 401 3.083997 ACCACCCGCTCATCCTCC 61.084 66.667 0.00 0.00 0.00 4.30
417 433 4.849813 TGGTCATGAATGAAGATCCTGT 57.150 40.909 0.00 0.00 38.75 4.00
456 472 0.454620 CTGCGTGTCCTCGTCTACAC 60.455 60.000 0.00 0.00 42.04 2.90
679 1906 9.950680 AACCTTCGATATTATAAGCAAACAATG 57.049 29.630 0.00 0.00 0.00 2.82
717 1953 0.759346 GTCCAGTTGGAGGTGTGACT 59.241 55.000 0.00 0.00 46.49 3.41
718 1954 0.759346 AGTCCAGTTGGAGGTGTGAC 59.241 55.000 0.00 0.00 46.49 3.67
720 2053 0.250467 CCAGTCCAGTTGGAGGTGTG 60.250 60.000 0.00 0.00 46.49 3.82
781 2140 0.251386 AGACAGGAGGACGCTCAAGA 60.251 55.000 0.00 0.00 0.00 3.02
782 2141 0.108898 CAGACAGGAGGACGCTCAAG 60.109 60.000 0.00 0.00 0.00 3.02
783 2142 0.827925 ACAGACAGGAGGACGCTCAA 60.828 55.000 0.00 0.00 0.00 3.02
784 2143 1.228583 ACAGACAGGAGGACGCTCA 60.229 57.895 0.00 0.00 0.00 4.26
786 2145 1.528292 GACACAGACAGGAGGACGCT 61.528 60.000 0.00 0.00 0.00 5.07
787 2146 1.080434 GACACAGACAGGAGGACGC 60.080 63.158 0.00 0.00 0.00 5.19
789 2148 1.080434 GCGACACAGACAGGAGGAC 60.080 63.158 0.00 0.00 0.00 3.85
888 2271 1.949847 CTCTTCCTCGCCGTGGTGAT 61.950 60.000 4.98 0.00 33.90 3.06
920 2303 4.944317 GCCAAAGAAAATCAGGTAGTAGCT 59.056 41.667 0.00 0.00 0.00 3.32
938 2451 2.091541 GGAATCACGAATCAGGCCAAA 58.908 47.619 5.01 0.00 0.00 3.28
1531 3585 0.620556 AAATGGGATGAGACTGCCGT 59.379 50.000 0.00 0.00 0.00 5.68
1552 3606 3.309954 GTCTGCTCAAAGTGAAGAACGTT 59.690 43.478 0.00 0.00 0.00 3.99
1635 3689 3.136641 ACCATCCTACCACTCCTGAAT 57.863 47.619 0.00 0.00 0.00 2.57
1762 3927 4.410400 CCACACTTCCCCCTCCGC 62.410 72.222 0.00 0.00 0.00 5.54
2007 4908 4.080751 TCACAATCTGGATGAATCTCAGCA 60.081 41.667 0.00 0.00 33.81 4.41
2208 5832 0.250901 TTCTTGGAGGAAGCACTGGC 60.251 55.000 0.00 0.00 41.61 4.85
2209 5833 1.528129 GTTCTTGGAGGAAGCACTGG 58.472 55.000 0.00 0.00 0.00 4.00
2212 5836 0.250338 ACGGTTCTTGGAGGAAGCAC 60.250 55.000 7.10 0.00 41.91 4.40
2265 5903 4.202223 GGCATGATTGAAGCAGATTCCAAT 60.202 41.667 0.00 0.00 37.08 3.16
2289 5927 8.695456 AGTAACATTGTTCTTTGGAAATTCAGT 58.305 29.630 5.07 0.00 32.81 3.41
2321 6042 1.740025 GTGCTAGCTAGGCAAAACAGG 59.260 52.381 22.10 0.00 41.54 4.00
2323 6044 2.426522 CAGTGCTAGCTAGGCAAAACA 58.573 47.619 22.10 7.58 41.54 2.83
2324 6045 1.740025 CCAGTGCTAGCTAGGCAAAAC 59.260 52.381 22.10 2.69 41.54 2.43
2325 6046 1.351017 ACCAGTGCTAGCTAGGCAAAA 59.649 47.619 22.10 0.00 41.54 2.44
2326 6047 0.984230 ACCAGTGCTAGCTAGGCAAA 59.016 50.000 22.10 0.00 41.54 3.68
2330 6051 2.289694 ACAACAACCAGTGCTAGCTAGG 60.290 50.000 22.10 16.46 0.00 3.02
2331 6052 3.045601 ACAACAACCAGTGCTAGCTAG 57.954 47.619 16.84 16.84 0.00 3.42
2334 6055 2.031682 CAGAACAACAACCAGTGCTAGC 60.032 50.000 8.10 8.10 0.00 3.42
2367 6088 3.689649 AGAATTTAGCCACATGGAACGAC 59.310 43.478 0.87 0.00 37.39 4.34
2368 6089 3.950397 AGAATTTAGCCACATGGAACGA 58.050 40.909 0.87 0.00 37.39 3.85
2369 6090 4.876107 AGTAGAATTTAGCCACATGGAACG 59.124 41.667 0.87 0.00 37.39 3.95
2444 6173 4.044336 CAGGTTCACAATCTGCAACAAA 57.956 40.909 0.00 0.00 0.00 2.83
2691 6767 9.448438 GCAATCAACCACACCAAGATATATATA 57.552 33.333 0.00 0.00 0.00 0.86
2692 6768 8.166061 AGCAATCAACCACACCAAGATATATAT 58.834 33.333 0.00 0.00 0.00 0.86
2698 6806 2.880443 AGCAATCAACCACACCAAGAT 58.120 42.857 0.00 0.00 0.00 2.40
2733 6841 0.736325 CCGACTCAAACAGGGTAGCG 60.736 60.000 0.00 0.00 0.00 4.26
2734 6842 1.019805 GCCGACTCAAACAGGGTAGC 61.020 60.000 0.00 0.00 0.00 3.58
2735 6843 0.608640 AGCCGACTCAAACAGGGTAG 59.391 55.000 0.00 0.00 32.10 3.18
2736 6844 1.053424 AAGCCGACTCAAACAGGGTA 58.947 50.000 0.00 0.00 33.69 3.69
2755 6863 2.634600 ACACAGAAACAACGCTGGTTA 58.365 42.857 0.00 0.00 30.55 2.85
2833 6946 7.190335 TCGGAGGTTTTCTAGGAATAAATGA 57.810 36.000 0.00 0.00 0.00 2.57
2945 7067 0.773644 AGACTGACAAATGGGTGGCT 59.226 50.000 0.00 0.00 0.00 4.75
2965 7087 1.270199 TGCTCATTGCGGCAAATGTTT 60.270 42.857 20.48 0.00 46.63 2.83


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

AutoCloner maintained by Alex Coulton.