Multiple sequence alignment - TraesCS7D01G470400

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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 TraesCS7D01G470400 chr7D 100.000 2902 0 0 1 2902 583548058 583550959 0.000000e+00 5360.0
1 TraesCS7D01G470400 chr7D 84.666 1989 249 28 241 2195 634650392 634652358 0.000000e+00 1932.0
2 TraesCS7D01G470400 chr7D 83.403 1434 187 35 512 1924 634751433 634750030 0.000000e+00 1282.0
3 TraesCS7D01G470400 chr7D 82.201 736 76 29 2198 2902 634652399 634653110 1.500000e-162 582.0
4 TraesCS7D01G470400 chr7D 81.567 651 78 22 2278 2902 634661023 634661657 1.550000e-137 499.0
5 TraesCS7D01G470400 chr7A 94.731 1746 74 9 395 2124 675021797 675023540 0.000000e+00 2699.0
6 TraesCS7D01G470400 chr7A 86.543 1724 199 20 477 2185 731571434 731569729 0.000000e+00 1868.0
7 TraesCS7D01G470400 chr7A 83.825 1626 210 28 512 2091 731000689 731002307 0.000000e+00 1496.0
8 TraesCS7D01G470400 chr7A 82.872 1518 216 29 575 2072 731743631 731742138 0.000000e+00 1323.0
9 TraesCS7D01G470400 chr7A 95.471 817 29 6 2088 2902 675026234 675027044 0.000000e+00 1297.0
10 TraesCS7D01G470400 chr7A 93.252 741 46 4 2161 2900 675023548 675024285 0.000000e+00 1088.0
11 TraesCS7D01G470400 chr7A 82.398 1301 180 27 1049 2325 730881877 730883152 0.000000e+00 1088.0
12 TraesCS7D01G470400 chr7A 80.383 1096 176 24 895 1985 731774520 731773459 0.000000e+00 797.0
13 TraesCS7D01G470400 chr7A 88.123 522 57 4 512 1029 730881201 730881721 1.480000e-172 616.0
14 TraesCS7D01G470400 chr7A 85.523 449 43 14 2313 2753 731505616 731505182 1.590000e-122 449.0
15 TraesCS7D01G470400 chr7A 80.092 653 77 34 2278 2902 731012487 731013114 1.230000e-118 436.0
16 TraesCS7D01G470400 chr7A 80.230 521 64 29 2398 2902 730883158 730883655 3.560000e-94 355.0
17 TraesCS7D01G470400 chr7A 83.086 337 36 9 30 347 675021319 675021653 1.320000e-73 287.0
18 TraesCS7D01G470400 chr7A 81.034 232 33 6 1961 2185 731505416 731505189 1.070000e-39 174.0
19 TraesCS7D01G470400 chr7A 79.535 215 32 7 1977 2185 730883283 730883491 3.010000e-30 143.0
20 TraesCS7D01G470400 chr7B 90.667 1350 112 9 923 2265 651134870 651136212 0.000000e+00 1783.0
21 TraesCS7D01G470400 chr7B 86.839 1588 186 13 484 2055 741625006 741623426 0.000000e+00 1753.0
22 TraesCS7D01G470400 chr7B 83.438 1274 170 22 1079 2337 741482663 741483910 0.000000e+00 1146.0
23 TraesCS7D01G470400 chr7B 84.813 1014 137 14 1051 2055 741541900 741542905 0.000000e+00 1003.0
24 TraesCS7D01G470400 chr7B 83.425 730 70 27 269 963 741541196 741541909 5.280000e-177 630.0
25 TraesCS7D01G470400 chr7B 93.976 415 21 4 2474 2887 651142241 651142652 2.460000e-175 625.0
26 TraesCS7D01G470400 chr7B 84.937 478 56 11 2278 2750 741542903 741543369 1.220000e-128 470.0
27 TraesCS7D01G470400 chr7B 92.233 206 15 1 2270 2475 651141923 651142127 1.020000e-74 291.0
28 TraesCS7D01G470400 chr7B 83.333 180 24 5 2294 2469 741666964 741666787 8.320000e-36 161.0
29 TraesCS7D01G470400 chr7B 78.899 218 34 7 1974 2185 741484002 741484213 1.400000e-28 137.0
30 TraesCS7D01G470400 chr4B 84.277 1590 211 22 481 2055 625072774 625074339 0.000000e+00 1515.0
31 TraesCS7D01G470400 chr4B 86.207 87 11 1 2523 2609 625074254 625074339 3.080000e-15 93.5


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 TraesCS7D01G470400 chr7D 583548058 583550959 2901 False 5360.00 5360 100.000000 1 2902 1 chr7D.!!$F1 2901
1 TraesCS7D01G470400 chr7D 634750030 634751433 1403 True 1282.00 1282 83.403000 512 1924 1 chr7D.!!$R1 1412
2 TraesCS7D01G470400 chr7D 634650392 634653110 2718 False 1257.00 1932 83.433500 241 2902 2 chr7D.!!$F3 2661
3 TraesCS7D01G470400 chr7D 634661023 634661657 634 False 499.00 499 81.567000 2278 2902 1 chr7D.!!$F2 624
4 TraesCS7D01G470400 chr7A 731569729 731571434 1705 True 1868.00 1868 86.543000 477 2185 1 chr7A.!!$R1 1708
5 TraesCS7D01G470400 chr7A 731000689 731002307 1618 False 1496.00 1496 83.825000 512 2091 1 chr7A.!!$F1 1579
6 TraesCS7D01G470400 chr7A 675021319 675027044 5725 False 1342.75 2699 91.635000 30 2902 4 chr7A.!!$F3 2872
7 TraesCS7D01G470400 chr7A 731742138 731743631 1493 True 1323.00 1323 82.872000 575 2072 1 chr7A.!!$R2 1497
8 TraesCS7D01G470400 chr7A 731773459 731774520 1061 True 797.00 797 80.383000 895 1985 1 chr7A.!!$R3 1090
9 TraesCS7D01G470400 chr7A 730881201 730883655 2454 False 550.50 1088 82.571500 512 2902 4 chr7A.!!$F4 2390
10 TraesCS7D01G470400 chr7A 731012487 731013114 627 False 436.00 436 80.092000 2278 2902 1 chr7A.!!$F2 624
11 TraesCS7D01G470400 chr7B 651134870 651136212 1342 False 1783.00 1783 90.667000 923 2265 1 chr7B.!!$F1 1342
12 TraesCS7D01G470400 chr7B 741623426 741625006 1580 True 1753.00 1753 86.839000 484 2055 1 chr7B.!!$R1 1571
13 TraesCS7D01G470400 chr7B 741541196 741543369 2173 False 701.00 1003 84.391667 269 2750 3 chr7B.!!$F4 2481
14 TraesCS7D01G470400 chr7B 741482663 741484213 1550 False 641.50 1146 81.168500 1079 2337 2 chr7B.!!$F3 1258
15 TraesCS7D01G470400 chr7B 651141923 651142652 729 False 458.00 625 93.104500 2270 2887 2 chr7B.!!$F2 617
16 TraesCS7D01G470400 chr4B 625072774 625074339 1565 False 804.25 1515 85.242000 481 2609 2 chr4B.!!$F1 2128

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
24 25 0.108585 ACAAGAGGATGCCACGTTGT 59.891 50.0 0.00 0.00 0.0 3.32 F
468 616 0.173029 TTCGCTAAATGGCCGTACGA 59.827 50.0 18.76 2.83 0.0 3.43 F
469 617 0.526096 TCGCTAAATGGCCGTACGAC 60.526 55.0 18.76 4.45 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 2060 0.108138 AGAACAAGAATCCCTCCGCG 60.108 55.0 0.0 0.0 0.00 6.46 R
1831 2194 0.872388 ACGTTTGCGATTGAGGAACC 59.128 50.0 0.0 0.0 42.00 3.62 R
2162 5860 2.307934 AGCGAGAGAGCCATTTTCTC 57.692 50.0 0.0 0.0 41.08 2.87 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
17 18 4.232310 GAGCCACAAGAGGATGCC 57.768 61.111 0.00 0.00 0.00 4.40
18 19 1.300963 GAGCCACAAGAGGATGCCA 59.699 57.895 0.00 0.00 0.00 4.92
19 20 1.001641 AGCCACAAGAGGATGCCAC 60.002 57.895 0.00 0.00 0.00 5.01
20 21 2.401766 GCCACAAGAGGATGCCACG 61.402 63.158 0.00 0.00 0.00 4.94
21 22 1.003355 CCACAAGAGGATGCCACGT 60.003 57.895 0.00 0.00 0.00 4.49
22 23 0.606401 CCACAAGAGGATGCCACGTT 60.606 55.000 0.00 0.00 0.00 3.99
23 24 0.518636 CACAAGAGGATGCCACGTTG 59.481 55.000 0.00 0.00 0.00 4.10
24 25 0.108585 ACAAGAGGATGCCACGTTGT 59.891 50.000 0.00 0.00 0.00 3.32
25 26 0.518636 CAAGAGGATGCCACGTTGTG 59.481 55.000 0.00 0.00 0.00 3.33
26 27 1.237285 AAGAGGATGCCACGTTGTGC 61.237 55.000 0.00 0.00 31.34 4.57
27 28 1.965930 GAGGATGCCACGTTGTGCA 60.966 57.895 6.63 6.63 31.34 4.57
28 29 1.915614 GAGGATGCCACGTTGTGCAG 61.916 60.000 9.66 0.00 31.34 4.41
55 56 3.015145 GCCAAGCCTCCCCCACTA 61.015 66.667 0.00 0.00 0.00 2.74
56 57 2.386935 GCCAAGCCTCCCCCACTAT 61.387 63.158 0.00 0.00 0.00 2.12
57 58 1.060163 GCCAAGCCTCCCCCACTATA 61.060 60.000 0.00 0.00 0.00 1.31
58 59 1.747444 CCAAGCCTCCCCCACTATAT 58.253 55.000 0.00 0.00 0.00 0.86
59 60 1.352352 CCAAGCCTCCCCCACTATATG 59.648 57.143 0.00 0.00 0.00 1.78
60 61 1.068121 AAGCCTCCCCCACTATATGC 58.932 55.000 0.00 0.00 0.00 3.14
68 73 3.181389 TCCCCCACTATATGCCTTATGGA 60.181 47.826 0.00 0.00 34.57 3.41
87 92 1.051556 AAAAGGAAAAAGCCCCGCCA 61.052 50.000 0.00 0.00 0.00 5.69
89 94 4.050934 GGAAAAAGCCCCGCCACG 62.051 66.667 0.00 0.00 0.00 4.94
102 107 2.433145 CCACGCTGTCGACTGCAT 60.433 61.111 36.11 25.65 40.28 3.96
103 108 2.733671 CCACGCTGTCGACTGCATG 61.734 63.158 36.11 32.75 40.28 4.06
116 121 1.001020 TGCATGTTCTTGGCCCGAT 60.001 52.632 0.00 0.00 0.00 4.18
119 124 0.680921 CATGTTCTTGGCCCGATGGT 60.681 55.000 0.00 0.00 0.00 3.55
129 134 1.220749 CCCGATGGTGTCATTCGGT 59.779 57.895 16.09 0.00 39.81 4.69
162 177 2.121963 AGGGGGTGAGCAGTGGAA 60.122 61.111 0.00 0.00 0.00 3.53
165 180 2.431683 GGGTGAGCAGTGGAAGCA 59.568 61.111 0.00 0.00 0.00 3.91
168 183 1.571460 GTGAGCAGTGGAAGCAACG 59.429 57.895 0.00 0.00 0.00 4.10
180 195 4.868171 GTGGAAGCAACGTCACAATATAGA 59.132 41.667 0.00 0.00 0.00 1.98
186 201 4.868171 GCAACGTCACAATATAGAGTTCCA 59.132 41.667 0.00 0.00 0.00 3.53
195 210 5.428457 ACAATATAGAGTTCCACCCATGTCA 59.572 40.000 0.00 0.00 0.00 3.58
196 211 5.815233 ATATAGAGTTCCACCCATGTCAG 57.185 43.478 0.00 0.00 0.00 3.51
197 212 2.030027 AGAGTTCCACCCATGTCAGA 57.970 50.000 0.00 0.00 0.00 3.27
205 221 5.191727 TCCACCCATGTCAGAATGTTTAT 57.808 39.130 0.00 0.00 37.40 1.40
237 253 8.491605 TTTAAATTTTACAACCTTTACGAGCG 57.508 30.769 0.00 0.00 0.00 5.03
242 260 2.401351 ACAACCTTTACGAGCGAGAAC 58.599 47.619 0.00 0.00 0.00 3.01
256 274 2.349886 GCGAGAACTATGTGGCTTCAAG 59.650 50.000 0.00 0.00 0.00 3.02
277 295 8.020861 TCAAGCTGCAATTTACATTTCAAATC 57.979 30.769 1.02 0.00 0.00 2.17
335 353 9.113838 AGCTGGAGATTTTAGTGTGTAAATATG 57.886 33.333 0.00 0.00 0.00 1.78
381 399 8.506168 TGTAAAAAGGAAGCGAGAATTATGAT 57.494 30.769 0.00 0.00 0.00 2.45
390 408 8.386606 GGAAGCGAGAATTATGATGCTTTATAG 58.613 37.037 5.57 0.00 42.23 1.31
422 548 9.396938 CAATTTCATTTAAAATGTTTTGAGGGC 57.603 29.630 0.00 0.00 0.00 5.19
439 577 2.827921 AGGGCTACAATTTTCCAAGCTG 59.172 45.455 0.00 0.00 33.67 4.24
442 580 4.380550 GGGCTACAATTTTCCAAGCTGTAC 60.381 45.833 0.00 0.00 33.67 2.90
447 595 1.519408 TTTTCCAAGCTGTACGAGGC 58.481 50.000 0.00 0.00 0.00 4.70
463 611 2.022762 GCGTTCGCTAAATGGCCG 59.977 61.111 9.99 0.00 0.00 6.13
464 612 2.746803 GCGTTCGCTAAATGGCCGT 61.747 57.895 9.99 0.00 0.00 5.68
465 613 1.422950 GCGTTCGCTAAATGGCCGTA 61.423 55.000 9.99 0.00 0.00 4.02
466 614 0.299597 CGTTCGCTAAATGGCCGTAC 59.700 55.000 0.00 0.00 0.00 3.67
467 615 0.299597 GTTCGCTAAATGGCCGTACG 59.700 55.000 8.69 8.69 0.00 3.67
468 616 0.173029 TTCGCTAAATGGCCGTACGA 59.827 50.000 18.76 2.83 0.00 3.43
469 617 0.526096 TCGCTAAATGGCCGTACGAC 60.526 55.000 18.76 4.45 0.00 4.34
470 618 0.526954 CGCTAAATGGCCGTACGACT 60.527 55.000 18.76 0.00 0.00 4.18
472 620 1.202382 GCTAAATGGCCGTACGACTCT 60.202 52.381 18.76 0.00 0.00 3.24
506 659 1.591059 CTCTTCGCTCCCAGCATCG 60.591 63.158 0.00 0.00 42.58 3.84
869 1032 5.415389 GTCGTTTCTTCTTCCTCCTACTACT 59.585 44.000 0.00 0.00 0.00 2.57
1123 1442 2.516888 CCGTCTGTGACCCCCTGTT 61.517 63.158 0.00 0.00 0.00 3.16
1125 1444 1.472662 CGTCTGTGACCCCCTGTTCT 61.473 60.000 0.00 0.00 0.00 3.01
1240 1559 2.911143 CGACAATGGGGAGGAGGG 59.089 66.667 0.00 0.00 0.00 4.30
1277 1596 7.173907 GTGATATGCATAGCAAAATACCAGACT 59.826 37.037 25.18 0.00 43.62 3.24
1312 1631 1.342174 TGTCTTCCCGTCCACAACTAC 59.658 52.381 0.00 0.00 0.00 2.73
1379 1717 5.749109 CCATATGTCCTCTTTTGACTACGTC 59.251 44.000 1.24 0.00 33.83 4.34
1380 1718 6.405953 CCATATGTCCTCTTTTGACTACGTCT 60.406 42.308 1.24 0.00 33.15 4.18
1493 1831 1.553248 CTCACCGGTTACCATCAGGAA 59.447 52.381 2.97 0.00 38.69 3.36
1712 2060 1.535204 CCATTTCCACAGTGGGTGCC 61.535 60.000 20.14 0.00 46.50 5.01
1755 2103 0.912486 AGGCGCTCCAGAAGGTATTT 59.088 50.000 7.64 0.00 35.89 1.40
1781 2144 6.668541 ATTGAGAATGTGGATTGTTACTCG 57.331 37.500 0.00 0.00 0.00 4.18
1787 2150 4.545208 TGTGGATTGTTACTCGATGGAA 57.455 40.909 0.00 0.00 0.00 3.53
1831 2194 1.478510 AGTCTGTACAAGGATGGAGCG 59.521 52.381 0.00 0.00 0.00 5.03
1914 2277 6.213600 ACCAACTATCTGATCAACTGGTAAGT 59.786 38.462 10.27 0.00 38.71 2.24
2056 3024 6.949352 AGATGTAGCTAATTGATGGTTTGG 57.051 37.500 0.00 0.00 0.00 3.28
2063 3031 4.082026 GCTAATTGATGGTTTGGTTCTGCT 60.082 41.667 0.00 0.00 0.00 4.24
2179 5877 4.647424 AGTAGAGAAAATGGCTCTCTCG 57.353 45.455 7.22 0.00 45.24 4.04
2268 5966 4.975502 TGATGATGTTCAAAACAAGAACGC 59.024 37.500 0.00 0.00 46.34 4.84
2286 5984 1.798223 CGCTGCACAACTTGTAAGCTA 59.202 47.619 19.25 3.37 37.20 3.32
2361 6065 8.391106 CAGATGTTAAGGTCTGCTATTTTGTAC 58.609 37.037 4.59 0.00 35.87 2.90
2437 6145 6.991938 TGAATAAATAGCTTGTGTGCCTTTT 58.008 32.000 0.00 0.00 0.00 2.27
2496 6321 3.839490 AGGAAATTCCCATTGCATCAACA 59.161 39.130 8.66 0.00 37.19 3.33
2589 6887 4.896482 ACCTTGTCCAACTAGCTAGGATAG 59.104 45.833 24.35 13.38 43.09 2.08
2768 7096 4.444720 GCATCGTTAGTCATACTTAGCACC 59.555 45.833 0.00 0.00 0.00 5.01
2805 7133 4.973396 TCATTCAATTCAACAGCGATGTC 58.027 39.130 6.84 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.028868 GTGGCATCCTCTTGTGGCTC 61.029 60.000 0.00 0.00 41.07 4.70
1 2 1.001641 GTGGCATCCTCTTGTGGCT 60.002 57.895 0.00 0.00 41.07 4.75
2 3 2.401766 CGTGGCATCCTCTTGTGGC 61.402 63.158 0.00 0.00 40.89 5.01
3 4 0.606401 AACGTGGCATCCTCTTGTGG 60.606 55.000 0.00 0.00 0.00 4.17
4 5 0.518636 CAACGTGGCATCCTCTTGTG 59.481 55.000 0.00 0.00 0.00 3.33
5 6 0.108585 ACAACGTGGCATCCTCTTGT 59.891 50.000 0.00 0.00 0.00 3.16
6 7 0.518636 CACAACGTGGCATCCTCTTG 59.481 55.000 0.00 0.00 0.00 3.02
7 8 1.237285 GCACAACGTGGCATCCTCTT 61.237 55.000 0.00 0.00 33.64 2.85
8 9 1.672356 GCACAACGTGGCATCCTCT 60.672 57.895 0.00 0.00 33.64 3.69
9 10 1.915614 CTGCACAACGTGGCATCCTC 61.916 60.000 9.80 0.00 39.65 3.71
10 11 1.968017 CTGCACAACGTGGCATCCT 60.968 57.895 9.80 0.00 39.65 3.24
11 12 2.562912 CTGCACAACGTGGCATCC 59.437 61.111 9.80 0.00 39.65 3.51
12 13 2.562912 CCTGCACAACGTGGCATC 59.437 61.111 9.80 0.00 39.65 3.91
13 14 3.673484 GCCTGCACAACGTGGCAT 61.673 61.111 7.48 0.00 44.34 4.40
15 16 3.423162 TTTGCCTGCACAACGTGGC 62.423 57.895 5.48 5.48 45.10 5.01
16 17 1.299316 CTTTGCCTGCACAACGTGG 60.299 57.895 0.00 0.00 33.64 4.94
17 18 1.299316 CCTTTGCCTGCACAACGTG 60.299 57.895 0.00 0.00 36.51 4.49
18 19 2.489275 CCCTTTGCCTGCACAACGT 61.489 57.895 0.00 0.00 0.00 3.99
19 20 2.336088 CCCTTTGCCTGCACAACG 59.664 61.111 0.00 0.00 0.00 4.10
20 21 2.736531 CCCCTTTGCCTGCACAAC 59.263 61.111 0.00 0.00 0.00 3.32
21 22 2.523902 CCCCCTTTGCCTGCACAA 60.524 61.111 0.00 0.00 0.00 3.33
41 42 1.068121 GCATATAGTGGGGGAGGCTT 58.932 55.000 0.00 0.00 0.00 4.35
54 55 8.421002 GCTTTTTCCTTTTCCATAAGGCATATA 58.579 33.333 0.00 0.00 43.62 0.86
55 56 7.275183 GCTTTTTCCTTTTCCATAAGGCATAT 58.725 34.615 0.00 0.00 43.62 1.78
56 57 6.351796 GGCTTTTTCCTTTTCCATAAGGCATA 60.352 38.462 0.00 0.00 43.62 3.14
57 58 5.491070 GCTTTTTCCTTTTCCATAAGGCAT 58.509 37.500 0.00 0.00 43.62 4.40
58 59 4.262851 GGCTTTTTCCTTTTCCATAAGGCA 60.263 41.667 0.00 0.00 43.62 4.75
59 60 4.253685 GGCTTTTTCCTTTTCCATAAGGC 58.746 43.478 0.00 0.00 43.62 4.35
60 61 4.323485 GGGGCTTTTTCCTTTTCCATAAGG 60.323 45.833 0.00 0.00 45.01 2.69
68 73 1.051556 TGGCGGGGCTTTTTCCTTTT 61.052 50.000 0.00 0.00 0.00 2.27
87 92 1.284982 GAACATGCAGTCGACAGCGT 61.285 55.000 25.14 22.95 38.98 5.07
89 94 1.136141 CAAGAACATGCAGTCGACAGC 60.136 52.381 24.38 24.38 0.00 4.40
99 104 1.434696 CATCGGGCCAAGAACATGC 59.565 57.895 4.39 0.00 0.00 4.06
102 107 1.303236 CACCATCGGGCCAAGAACA 60.303 57.895 4.39 0.00 37.90 3.18
103 108 1.303317 ACACCATCGGGCCAAGAAC 60.303 57.895 4.39 0.00 37.90 3.01
129 134 3.733960 CTGGTCGTCGGCTCGTCA 61.734 66.667 0.00 0.00 0.00 4.35
140 145 4.087892 CTGCTCACCCCCTGGTCG 62.088 72.222 0.00 0.00 45.57 4.79
155 170 1.013596 TTGTGACGTTGCTTCCACTG 58.986 50.000 4.70 0.00 0.00 3.66
162 177 5.109903 GGAACTCTATATTGTGACGTTGCT 58.890 41.667 0.00 0.00 0.00 3.91
165 180 5.416947 GGTGGAACTCTATATTGTGACGTT 58.583 41.667 0.00 0.00 36.74 3.99
168 183 5.353394 TGGGTGGAACTCTATATTGTGAC 57.647 43.478 0.00 0.00 38.97 3.67
180 195 2.376518 ACATTCTGACATGGGTGGAACT 59.623 45.455 0.00 0.00 36.74 3.01
186 201 8.415950 TTTTACATAAACATTCTGACATGGGT 57.584 30.769 0.00 0.00 0.00 4.51
222 238 2.035576 AGTTCTCGCTCGTAAAGGTTGT 59.964 45.455 0.00 0.00 0.00 3.32
229 245 2.479049 GCCACATAGTTCTCGCTCGTAA 60.479 50.000 0.00 0.00 0.00 3.18
232 248 0.101399 AGCCACATAGTTCTCGCTCG 59.899 55.000 0.00 0.00 0.00 5.03
234 250 1.550524 TGAAGCCACATAGTTCTCGCT 59.449 47.619 0.00 0.00 0.00 4.93
235 251 2.010145 TGAAGCCACATAGTTCTCGC 57.990 50.000 0.00 0.00 0.00 5.03
236 252 2.349886 GCTTGAAGCCACATAGTTCTCG 59.650 50.000 5.74 0.00 34.48 4.04
237 253 3.373439 CAGCTTGAAGCCACATAGTTCTC 59.627 47.826 14.45 0.00 43.77 2.87
242 260 1.456296 TGCAGCTTGAAGCCACATAG 58.544 50.000 14.45 0.00 43.77 2.23
256 274 7.355332 ACAGATTTGAAATGTAAATTGCAGC 57.645 32.000 0.00 0.00 0.00 5.25
367 385 9.360093 GTACTATAAAGCATCATAATTCTCGCT 57.640 33.333 0.00 0.00 0.00 4.93
419 545 2.562738 ACAGCTTGGAAAATTGTAGCCC 59.437 45.455 0.00 0.00 32.36 5.19
421 547 4.153475 TCGTACAGCTTGGAAAATTGTAGC 59.847 41.667 0.00 0.00 29.07 3.58
422 548 5.163854 CCTCGTACAGCTTGGAAAATTGTAG 60.164 44.000 0.00 0.00 29.07 2.74
447 595 0.299597 GTACGGCCATTTAGCGAACG 59.700 55.000 2.24 0.00 0.00 3.95
463 611 0.452585 GAGTGGGCTGAGAGTCGTAC 59.547 60.000 0.00 0.00 0.00 3.67
464 612 0.037734 TGAGTGGGCTGAGAGTCGTA 59.962 55.000 0.00 0.00 0.00 3.43
465 613 1.228583 TGAGTGGGCTGAGAGTCGT 60.229 57.895 0.00 0.00 0.00 4.34
466 614 1.214062 GTGAGTGGGCTGAGAGTCG 59.786 63.158 0.00 0.00 0.00 4.18
467 615 0.530288 GAGTGAGTGGGCTGAGAGTC 59.470 60.000 0.00 0.00 0.00 3.36
468 616 0.178950 TGAGTGAGTGGGCTGAGAGT 60.179 55.000 0.00 0.00 0.00 3.24
469 617 0.246086 GTGAGTGAGTGGGCTGAGAG 59.754 60.000 0.00 0.00 0.00 3.20
470 618 0.178950 AGTGAGTGAGTGGGCTGAGA 60.179 55.000 0.00 0.00 0.00 3.27
472 620 0.178950 AGAGTGAGTGAGTGGGCTGA 60.179 55.000 0.00 0.00 0.00 4.26
506 659 0.533085 GATCGAGGGTTAGGGCTTGC 60.533 60.000 0.00 0.00 0.00 4.01
984 1158 2.159366 CGTCATCTTCGGAGTAGCAACT 60.159 50.000 0.00 0.00 39.21 3.16
1240 1559 3.281727 TGCATATCACCTTGAAGGGTC 57.718 47.619 16.78 0.00 40.58 4.46
1277 1596 4.505039 GGGAAGACAAAGAGGACAAGCTTA 60.505 45.833 0.00 0.00 0.00 3.09
1312 1631 1.775039 CTCGGCCATACACCATTGCG 61.775 60.000 2.24 0.00 0.00 4.85
1379 1717 1.517257 CCAGTAGAAGCGACCGCAG 60.517 63.158 16.97 0.00 44.88 5.18
1380 1718 1.974875 TCCAGTAGAAGCGACCGCA 60.975 57.895 16.97 0.00 44.88 5.69
1447 1785 2.367241 TCGACAGTGGAAAACCTCATGA 59.633 45.455 0.00 0.00 0.00 3.07
1493 1831 0.901124 GGTGGTGCAGATCTCTGAGT 59.099 55.000 11.34 0.00 46.59 3.41
1712 2060 0.108138 AGAACAAGAATCCCTCCGCG 60.108 55.000 0.00 0.00 0.00 6.46
1715 2063 3.721087 TGGAAGAACAAGAATCCCTCC 57.279 47.619 0.00 0.00 0.00 4.30
1755 2103 9.476202 CGAGTAACAATCCACATTCTCAATATA 57.524 33.333 0.00 0.00 0.00 0.86
1787 2150 9.574516 ACTTTGGTAATTTCATAAGTCTTGACT 57.425 29.630 0.00 0.00 0.00 3.41
1831 2194 0.872388 ACGTTTGCGATTGAGGAACC 59.128 50.000 0.00 0.00 42.00 3.62
2056 3024 6.697019 ACAATTGTTAAACATGTGAGCAGAAC 59.303 34.615 4.92 0.00 0.00 3.01
2063 3031 6.036470 TCGCAAACAATTGTTAAACATGTGA 58.964 32.000 23.53 23.13 38.85 3.58
2125 5823 8.267894 TGGAGCAATAAGAACTAGCTTTCTAAT 58.732 33.333 1.10 0.00 34.60 1.73
2126 5824 7.620880 TGGAGCAATAAGAACTAGCTTTCTAA 58.379 34.615 1.10 0.00 34.60 2.10
2127 5825 7.182817 TGGAGCAATAAGAACTAGCTTTCTA 57.817 36.000 1.10 0.00 34.60 2.10
2128 5826 6.054860 TGGAGCAATAAGAACTAGCTTTCT 57.945 37.500 0.00 0.00 37.44 2.52
2162 5860 2.307934 AGCGAGAGAGCCATTTTCTC 57.692 50.000 0.00 0.00 41.08 2.87
2225 5923 5.169992 TCATTCAGTTGGATGAGTGATGT 57.830 39.130 0.00 0.00 39.97 3.06
2268 5966 5.362556 ACATTAGCTTACAAGTTGTGCAG 57.637 39.130 18.90 14.40 0.00 4.41
2286 5984 8.626526 ACGGTAAACAAAGAATACTCAAACATT 58.373 29.630 0.00 0.00 0.00 2.71
2361 6065 2.622942 TGCAGTTTGGAAGCAAGGTTAG 59.377 45.455 0.00 0.00 34.97 2.34
2437 6145 9.884636 TTGCAGAGTACAATATAGCTTAAGAAA 57.115 29.630 6.67 0.00 0.00 2.52
2496 6321 6.336842 AGTAGAAATTTGAAGCAACTGCAT 57.663 33.333 4.22 0.00 45.16 3.96
2589 6887 4.086457 ACCAAACCATGAATTGACTACCC 58.914 43.478 10.82 0.00 0.00 3.69
2805 7133 7.818930 ACTGGTTATGCAACATTCTTATTTTGG 59.181 33.333 0.00 0.00 36.29 3.28
2847 7176 7.044798 GCTCATAAATACAAGACTCAAGGACT 58.955 38.462 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.