Multiple sequence alignment - TraesCS7A01G379400

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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 TraesCS7A01G379400 chr7A 100.000 2273 0 0 1 2273 555424486 555422214 0.000000e+00 4198.0
1 TraesCS7A01G379400 chr7A 91.769 1628 111 4 1 1628 555431602 555429998 0.000000e+00 2242.0
2 TraesCS7A01G379400 chr7A 98.791 579 6 1 1629 2206 555415727 555415149 0.000000e+00 1029.0
3 TraesCS7A01G379400 chr7A 87.117 489 62 1 618 1105 301240712 301240224 9.170000e-154 553.0
4 TraesCS7A01G379400 chr7A 94.737 38 0 2 1346 1382 321409283 321409319 8.770000e-05 58.4
5 TraesCS7A01G379400 chr3A 85.013 1121 133 26 1 1105 276520323 276519222 0.000000e+00 1107.0
6 TraesCS7A01G379400 chr3A 81.323 862 129 26 1 842 362191213 362192062 0.000000e+00 671.0
7 TraesCS7A01G379400 chr3A 81.442 846 126 26 2 831 335307690 335306860 0.000000e+00 664.0
8 TraesCS7A01G379400 chr3A 99.412 170 0 1 1624 1793 438307002 438307170 7.890000e-80 307.0
9 TraesCS7A01G379400 chr3A 98.837 172 1 1 1622 1793 670640614 670640444 2.840000e-79 305.0
10 TraesCS7A01G379400 chr3A 94.000 200 8 4 1595 1790 419314678 419314877 1.320000e-77 300.0
11 TraesCS7A01G379400 chr6A 97.769 493 8 1 1784 2273 387836099 387835607 0.000000e+00 846.0
12 TraesCS7A01G379400 chr6A 97.769 493 8 1 1784 2273 434606616 434607108 0.000000e+00 846.0
13 TraesCS7A01G379400 chr6A 80.739 1137 143 47 1 1096 371814575 371813474 0.000000e+00 817.0
14 TraesCS7A01G379400 chr6A 85.570 596 67 14 1 588 396399441 396400025 6.940000e-170 606.0
15 TraesCS7A01G379400 chr6A 88.344 489 56 1 618 1105 346193993 346194481 9.050000e-164 586.0
16 TraesCS7A01G379400 chr6A 84.564 596 73 14 1 588 396448734 396449318 7.040000e-160 573.0
17 TraesCS7A01G379400 chr6A 88.553 463 50 3 645 1105 371819986 371819525 1.970000e-155 558.0
18 TraesCS7A01G379400 chr6A 87.344 482 60 1 616 1096 346185878 346186359 3.300000e-153 551.0
19 TraesCS7A01G379400 chr6A 81.197 702 111 17 1 697 404812105 404812790 1.540000e-151 545.0
20 TraesCS7A01G379400 chr6A 81.448 663 103 17 23 679 310593443 310594091 2.000000e-145 525.0
21 TraesCS7A01G379400 chr6A 97.191 178 5 0 1616 1793 121991632 121991455 3.670000e-78 302.0
22 TraesCS7A01G379400 chr6A 95.556 45 2 0 1346 1390 346130515 346130471 3.130000e-09 73.1
23 TraesCS7A01G379400 chr6A 94.737 38 0 2 1346 1382 538477094 538477130 8.770000e-05 58.4
24 TraesCS7A01G379400 chr6A 96.970 33 0 1 1346 1377 248626544 248626576 1.000000e-03 54.7
25 TraesCS7A01G379400 chr6A 96.970 33 0 1 1346 1377 538485179 538485211 1.000000e-03 54.7
26 TraesCS7A01G379400 chr5A 97.769 493 8 1 1784 2273 223452021 223452513 0.000000e+00 846.0
27 TraesCS7A01G379400 chr4A 97.769 493 8 2 1784 2273 357489237 357489729 0.000000e+00 846.0
28 TraesCS7A01G379400 chr4A 97.769 493 8 1 1784 2273 493825069 493824577 0.000000e+00 846.0
29 TraesCS7A01G379400 chr4A 87.137 482 61 1 616 1096 153662306 153662787 1.540000e-151 545.0
30 TraesCS7A01G379400 chr4A 85.400 500 57 9 620 1105 153654119 153654616 2.610000e-139 505.0
31 TraesCS7A01G379400 chr4A 93.333 195 10 3 1600 1793 453045724 453045532 3.700000e-73 285.0
32 TraesCS7A01G379400 chr4A 90.909 44 4 0 1336 1379 426437906 426437949 2.440000e-05 60.2
33 TraesCS7A01G379400 chr2A 97.769 493 8 1 1784 2273 429544075 429544567 0.000000e+00 846.0
34 TraesCS7A01G379400 chr2A 97.769 493 8 1 1784 2273 451571518 451571026 0.000000e+00 846.0
35 TraesCS7A01G379400 chr2A 97.769 493 8 3 1784 2273 725115428 725114936 0.000000e+00 846.0
36 TraesCS7A01G379400 chr2A 82.230 861 127 21 1 845 431627710 431626860 0.000000e+00 719.0
37 TraesCS7A01G379400 chr2A 81.765 861 131 22 1 845 431644319 431643469 0.000000e+00 697.0
38 TraesCS7A01G379400 chr2A 95.812 191 6 2 1604 1793 625447180 625446991 7.890000e-80 307.0
39 TraesCS7A01G379400 chr2A 97.191 178 2 3 1616 1793 31359629 31359803 4.750000e-77 298.0
40 TraesCS7A01G379400 chr2A 94.737 38 0 2 1346 1382 362121004 362121040 8.770000e-05 58.4
41 TraesCS7A01G379400 chr2A 94.737 38 0 2 1346 1382 518348609 518348573 8.770000e-05 58.4
42 TraesCS7A01G379400 chr2A 94.737 38 0 2 1346 1382 518858045 518858009 8.770000e-05 58.4
43 TraesCS7A01G379400 chr1A 81.374 859 130 27 1 842 157937066 157936221 0.000000e+00 673.0
44 TraesCS7A01G379400 chr1A 99.405 168 1 0 1623 1790 285329268 285329435 2.840000e-79 305.0
45 TraesCS7A01G379400 chr1A 96.970 33 0 1 1346 1377 125823696 125823664 1.000000e-03 54.7
46 TraesCS7A01G379400 chr3D 83.636 605 79 19 1 598 324711176 324711767 3.300000e-153 551.0
47 TraesCS7A01G379400 chr7D 83.471 605 78 21 1 598 393060432 393061021 5.520000e-151 544.0
48 TraesCS7A01G379400 chr4D 83.471 605 79 20 1 598 103974830 103975420 5.520000e-151 544.0


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 TraesCS7A01G379400 chr7A 555422214 555424486 2272 True 4198 4198 100.000 1 2273 1 chr7A.!!$R3 2272
1 TraesCS7A01G379400 chr7A 555429998 555431602 1604 True 2242 2242 91.769 1 1628 1 chr7A.!!$R4 1627
2 TraesCS7A01G379400 chr7A 555415149 555415727 578 True 1029 1029 98.791 1629 2206 1 chr7A.!!$R2 577
3 TraesCS7A01G379400 chr3A 276519222 276520323 1101 True 1107 1107 85.013 1 1105 1 chr3A.!!$R1 1104
4 TraesCS7A01G379400 chr3A 362191213 362192062 849 False 671 671 81.323 1 842 1 chr3A.!!$F1 841
5 TraesCS7A01G379400 chr3A 335306860 335307690 830 True 664 664 81.442 2 831 1 chr3A.!!$R2 829
6 TraesCS7A01G379400 chr6A 371813474 371814575 1101 True 817 817 80.739 1 1096 1 chr6A.!!$R3 1095
7 TraesCS7A01G379400 chr6A 396399441 396400025 584 False 606 606 85.570 1 588 1 chr6A.!!$F5 587
8 TraesCS7A01G379400 chr6A 396448734 396449318 584 False 573 573 84.564 1 588 1 chr6A.!!$F6 587
9 TraesCS7A01G379400 chr6A 404812105 404812790 685 False 545 545 81.197 1 697 1 chr6A.!!$F7 696
10 TraesCS7A01G379400 chr6A 310593443 310594091 648 False 525 525 81.448 23 679 1 chr6A.!!$F2 656
11 TraesCS7A01G379400 chr2A 431626860 431627710 850 True 719 719 82.230 1 845 1 chr2A.!!$R1 844
12 TraesCS7A01G379400 chr2A 431643469 431644319 850 True 697 697 81.765 1 845 1 chr2A.!!$R2 844
13 TraesCS7A01G379400 chr1A 157936221 157937066 845 True 673 673 81.374 1 842 1 chr1A.!!$R2 841
14 TraesCS7A01G379400 chr3D 324711176 324711767 591 False 551 551 83.636 1 598 1 chr3D.!!$F1 597
15 TraesCS7A01G379400 chr7D 393060432 393061021 589 False 544 544 83.471 1 598 1 chr7D.!!$F1 597
16 TraesCS7A01G379400 chr4D 103974830 103975420 590 False 544 544 83.471 1 598 1 chr4D.!!$F1 597

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
616 667 0.184451 TCGGGAAGCGGTAGAGGTAT 59.816 55.0 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 1906 0.680061 ACCGATTCTTCCTATCCGGC 59.32 55.0 0.0 0.0 0.0 6.13 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
79 81 5.226396 CGGAAATAACAAGCAACAATTCCA 58.774 37.500 0.00 0.00 35.86 3.53
86 88 8.907222 ATAACAAGCAACAATTCCAGAAAATT 57.093 26.923 0.00 0.00 0.00 1.82
91 93 6.218746 AGCAACAATTCCAGAAAATTCTCAC 58.781 36.000 0.00 0.00 34.74 3.51
261 276 0.392998 GGTGCCACGGTGATGAATCT 60.393 55.000 10.28 0.00 0.00 2.40
358 384 0.961019 TGTCAAGCAAGAATGGTGGC 59.039 50.000 0.00 0.00 37.35 5.01
373 399 2.369633 TGGCGTGATCCTGGATGCT 61.370 57.895 15.25 0.00 0.00 3.79
388 414 1.903877 ATGCTGGGTTCCCACGAGAG 61.904 60.000 6.46 0.00 32.02 3.20
394 420 1.321074 GGTTCCCACGAGAGGACGAT 61.321 60.000 0.00 0.00 37.03 3.73
406 443 2.832129 AGAGGACGATAAGGCAACAAGA 59.168 45.455 0.00 0.00 41.41 3.02
455 501 1.331756 GCAAACACGGCCATCTCATAG 59.668 52.381 2.24 0.00 0.00 2.23
490 539 1.667722 CATGGGATCATCGGCTCGA 59.332 57.895 0.00 0.00 41.13 4.04
616 667 0.184451 TCGGGAAGCGGTAGAGGTAT 59.816 55.000 0.00 0.00 0.00 2.73
631 682 2.232941 GAGGTATGGGTCTTCGACAACA 59.767 50.000 0.00 0.00 33.68 3.33
722 804 4.718940 TTCGTAGATGCTTGAGTCATCA 57.281 40.909 13.79 0.00 41.98 3.07
736 818 3.353557 AGTCATCAGTAGCGGTACTTGA 58.646 45.455 23.99 21.69 37.40 3.02
745 827 2.119495 AGCGGTACTTGATGAATCCCT 58.881 47.619 0.00 0.00 0.00 4.20
752 834 3.279434 ACTTGATGAATCCCTAAACGGC 58.721 45.455 0.00 0.00 0.00 5.68
757 839 1.631388 TGAATCCCTAAACGGCCTTGA 59.369 47.619 0.00 0.00 0.00 3.02
788 870 3.007635 GCGTAGAGGTACTTGGCATTTT 58.992 45.455 0.00 0.00 41.55 1.82
919 1005 0.524862 GCAAGACTGGGCATGAACTG 59.475 55.000 0.00 0.00 0.00 3.16
944 1030 2.357034 GCGGCACAAAGACCTCGA 60.357 61.111 0.00 0.00 0.00 4.04
1084 1171 2.825836 CGGCCCTGGCATCACTTC 60.826 66.667 10.86 0.00 44.11 3.01
1148 1235 1.211457 GATCCAGCCACTGAAGACCAT 59.789 52.381 0.00 0.00 32.44 3.55
1178 1265 0.323999 TTCCTGTCCGGATCGAGGAA 60.324 55.000 26.86 26.86 42.70 3.36
1194 1281 0.831711 GGAAAAGCAAAGGAGGCCCA 60.832 55.000 0.00 0.00 33.88 5.36
1197 1284 1.463553 AAAGCAAAGGAGGCCCAACG 61.464 55.000 0.00 0.00 33.88 4.10
1214 1301 3.077556 GAGGAAGGGGCTCGCTGA 61.078 66.667 0.00 0.00 0.00 4.26
1225 1312 1.153667 CTCGCTGACTTGGAGGCTC 60.154 63.158 5.78 5.78 0.00 4.70
1233 1320 2.853542 TTGGAGGCTCTGGTGGCA 60.854 61.111 15.23 0.00 34.73 4.92
1236 1323 4.792804 GAGGCTCTGGTGGCAGGC 62.793 72.222 7.40 0.00 35.42 4.85
1258 1345 2.284699 ACTCCGGAGTGGGGAAGG 60.285 66.667 35.89 8.26 43.10 3.46
1259 1346 3.787001 CTCCGGAGTGGGGAAGGC 61.787 72.222 24.04 0.00 43.10 4.35
1263 1350 4.410400 GGAGTGGGGAAGGCGGTG 62.410 72.222 0.00 0.00 0.00 4.94
1264 1351 4.410400 GAGTGGGGAAGGCGGTGG 62.410 72.222 0.00 0.00 0.00 4.61
1352 1439 3.467226 GGGCGTGAAGGGGATCGA 61.467 66.667 0.00 0.00 0.00 3.59
1383 1470 2.363018 CTGAGGGGGAGCGAGACA 60.363 66.667 0.00 0.00 0.00 3.41
1393 1480 2.113243 GAGCGAGACAAAGGGGTGGT 62.113 60.000 0.00 0.00 0.00 4.16
1394 1481 1.966451 GCGAGACAAAGGGGTGGTG 60.966 63.158 0.00 0.00 0.00 4.17
1395 1482 1.302511 CGAGACAAAGGGGTGGTGG 60.303 63.158 0.00 0.00 0.00 4.61
1396 1483 1.844130 GAGACAAAGGGGTGGTGGT 59.156 57.895 0.00 0.00 0.00 4.16
1399 1486 2.917227 CAAAGGGGTGGTGGTGCC 60.917 66.667 0.00 0.00 37.90 5.01
1408 1495 1.930133 TGGTGGTGCCATGAGGGAT 60.930 57.895 0.00 0.00 43.61 3.85
1466 1553 1.520787 CGGCTAGGGTTTACAGCGG 60.521 63.158 0.00 0.00 36.12 5.52
1524 1611 4.467084 GATGCGTTGGGAGGCCGA 62.467 66.667 0.00 0.00 35.85 5.54
1546 1633 3.203487 ACCCAGTGGAGAGGTAAAACAAA 59.797 43.478 11.95 0.00 34.81 2.83
1624 1711 5.431402 AGAAAGGCAAAAGGAGAGGATAGAT 59.569 40.000 0.00 0.00 0.00 1.98
1834 1922 0.670854 GGCGCCGGATAGGAAGAATC 60.671 60.000 12.58 0.00 45.00 2.52
2093 2181 2.094545 GGTTCCACTTTCACATCCATGC 60.095 50.000 0.00 0.00 0.00 4.06
2198 2286 1.838077 ACCACCTAGGGATAGTTGCAC 59.162 52.381 14.81 0.00 43.89 4.57
2206 2294 5.529060 CCTAGGGATAGTTGCACTTTCAATC 59.471 44.000 0.00 0.00 29.36 2.67
2207 2295 5.184892 AGGGATAGTTGCACTTTCAATCT 57.815 39.130 0.00 0.00 29.36 2.40
2208 2296 5.189180 AGGGATAGTTGCACTTTCAATCTC 58.811 41.667 0.00 0.00 29.36 2.75
2209 2297 4.336713 GGGATAGTTGCACTTTCAATCTCC 59.663 45.833 0.00 0.00 29.36 3.71
2210 2298 4.336713 GGATAGTTGCACTTTCAATCTCCC 59.663 45.833 0.00 0.00 29.36 4.30
2211 2299 2.519013 AGTTGCACTTTCAATCTCCCC 58.481 47.619 0.00 0.00 0.00 4.81
2212 2300 1.546029 GTTGCACTTTCAATCTCCCCC 59.454 52.381 0.00 0.00 0.00 5.40
2213 2301 1.075601 TGCACTTTCAATCTCCCCCT 58.924 50.000 0.00 0.00 0.00 4.79
2214 2302 1.428912 TGCACTTTCAATCTCCCCCTT 59.571 47.619 0.00 0.00 0.00 3.95
2215 2303 2.158325 TGCACTTTCAATCTCCCCCTTT 60.158 45.455 0.00 0.00 0.00 3.11
2216 2304 2.899900 GCACTTTCAATCTCCCCCTTTT 59.100 45.455 0.00 0.00 0.00 2.27
2217 2305 3.324846 GCACTTTCAATCTCCCCCTTTTT 59.675 43.478 0.00 0.00 0.00 1.94
2218 2306 4.800582 GCACTTTCAATCTCCCCCTTTTTG 60.801 45.833 0.00 0.00 0.00 2.44
2219 2307 3.903714 ACTTTCAATCTCCCCCTTTTTGG 59.096 43.478 0.00 0.00 0.00 3.28
2220 2308 3.628832 TTCAATCTCCCCCTTTTTGGT 57.371 42.857 0.00 0.00 0.00 3.67
2221 2309 4.750833 TTCAATCTCCCCCTTTTTGGTA 57.249 40.909 0.00 0.00 0.00 3.25
2222 2310 4.750833 TCAATCTCCCCCTTTTTGGTAA 57.249 40.909 0.00 0.00 0.00 2.85
2223 2311 5.283876 TCAATCTCCCCCTTTTTGGTAAT 57.716 39.130 0.00 0.00 0.00 1.89
2224 2312 5.660533 TCAATCTCCCCCTTTTTGGTAATT 58.339 37.500 0.00 0.00 0.00 1.40
2225 2313 5.483583 TCAATCTCCCCCTTTTTGGTAATTG 59.516 40.000 0.00 0.00 0.00 2.32
2226 2314 4.750833 TCTCCCCCTTTTTGGTAATTGA 57.249 40.909 0.00 0.00 0.00 2.57
2227 2315 5.283876 TCTCCCCCTTTTTGGTAATTGAT 57.716 39.130 0.00 0.00 0.00 2.57
2228 2316 5.022787 TCTCCCCCTTTTTGGTAATTGATG 58.977 41.667 0.00 0.00 0.00 3.07
2229 2317 5.017093 TCCCCCTTTTTGGTAATTGATGA 57.983 39.130 0.00 0.00 0.00 2.92
2230 2318 4.775253 TCCCCCTTTTTGGTAATTGATGAC 59.225 41.667 0.00 0.00 0.00 3.06
2231 2319 4.530161 CCCCCTTTTTGGTAATTGATGACA 59.470 41.667 0.00 0.00 0.00 3.58
2232 2320 5.012561 CCCCCTTTTTGGTAATTGATGACAA 59.987 40.000 0.00 0.00 40.42 3.18
2233 2321 5.931724 CCCCTTTTTGGTAATTGATGACAAC 59.068 40.000 0.00 0.00 38.90 3.32
2234 2322 6.463614 CCCCTTTTTGGTAATTGATGACAACA 60.464 38.462 0.00 0.00 38.90 3.33
2235 2323 7.160726 CCCTTTTTGGTAATTGATGACAACAT 58.839 34.615 0.00 0.00 38.90 2.71
2236 2324 8.310382 CCCTTTTTGGTAATTGATGACAACATA 58.690 33.333 0.00 0.00 38.90 2.29
2237 2325 9.874205 CCTTTTTGGTAATTGATGACAACATAT 57.126 29.630 0.00 0.00 38.90 1.78
2248 2336 8.969260 TTGATGACAACATATAGATCAAAGCT 57.031 30.769 0.00 0.00 36.82 3.74
2249 2337 8.969260 TGATGACAACATATAGATCAAAGCTT 57.031 30.769 0.00 0.00 36.82 3.74
2250 2338 9.399797 TGATGACAACATATAGATCAAAGCTTT 57.600 29.630 5.69 5.69 36.82 3.51
2251 2339 9.661187 GATGACAACATATAGATCAAAGCTTTG 57.339 33.333 29.53 29.53 36.82 2.77
2252 2340 9.399797 ATGACAACATATAGATCAAAGCTTTGA 57.600 29.630 36.74 36.74 41.81 2.69
2267 2355 9.142515 TCAAAGCTTTGACAAATAATAAGCATG 57.857 29.630 32.86 6.76 41.88 4.06
2268 2356 9.142515 CAAAGCTTTGACAAATAATAAGCATGA 57.857 29.630 31.24 0.00 42.68 3.07
2269 2357 9.709495 AAAGCTTTGACAAATAATAAGCATGAA 57.291 25.926 11.80 0.00 42.68 2.57
2270 2358 9.709495 AAGCTTTGACAAATAATAAGCATGAAA 57.291 25.926 0.05 0.00 42.68 2.69
2271 2359 9.880157 AGCTTTGACAAATAATAAGCATGAAAT 57.120 25.926 0.05 0.00 42.68 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
181 191 8.697846 ATGCTCATGTCAACATTTTCATAAAG 57.302 30.769 0.00 0.00 33.61 1.85
261 276 2.620585 TGTTGTCGTGGCATCATTTTCA 59.379 40.909 0.00 0.00 0.00 2.69
313 335 0.881118 CGCCACACTACCTTTTGCAT 59.119 50.000 0.00 0.00 0.00 3.96
358 384 1.227764 CCCAGCATCCAGGATCACG 60.228 63.158 0.00 0.00 0.00 4.35
388 414 3.424433 CGTTTCTTGTTGCCTTATCGTCC 60.424 47.826 0.00 0.00 0.00 4.79
394 420 4.273969 CCTTGTACGTTTCTTGTTGCCTTA 59.726 41.667 0.00 0.00 0.00 2.69
406 443 7.915293 TGTATGAATTGATCCTTGTACGTTT 57.085 32.000 0.00 0.00 0.00 3.60
445 491 3.036075 TGCTTGCGATCTATGAGATGG 57.964 47.619 0.00 0.00 34.53 3.51
455 501 0.940126 ATGGACGAATGCTTGCGATC 59.060 50.000 7.03 0.98 0.00 3.69
490 539 2.997986 CACGCTTCAAAGGTATAACCGT 59.002 45.455 0.00 0.00 44.90 4.83
686 768 5.627499 TCTACGAAAACGTGTACCACTAT 57.373 39.130 5.54 0.00 31.34 2.12
711 793 2.949451 ACCGCTACTGATGACTCAAG 57.051 50.000 0.00 0.00 0.00 3.02
713 795 3.000684 AGTACCGCTACTGATGACTCA 57.999 47.619 0.00 0.00 31.46 3.41
722 804 3.069729 GGGATTCATCAAGTACCGCTACT 59.930 47.826 0.00 0.00 34.38 2.57
736 818 2.241176 TCAAGGCCGTTTAGGGATTCAT 59.759 45.455 0.00 0.00 41.48 2.57
745 827 2.343101 CGAAGATGTCAAGGCCGTTTA 58.657 47.619 0.00 0.00 0.00 2.01
752 834 0.800683 TACGCGCGAAGATGTCAAGG 60.801 55.000 39.36 1.99 0.00 3.61
757 839 1.064296 CCTCTACGCGCGAAGATGT 59.936 57.895 39.36 16.04 0.00 3.06
788 870 1.270625 CCCTCAAGTTCGGCTACACAA 60.271 52.381 0.00 0.00 0.00 3.33
908 994 2.669391 CGCTTCTTTTCAGTTCATGCCC 60.669 50.000 0.00 0.00 0.00 5.36
919 1005 2.385315 GTCTTTGTGCCGCTTCTTTTC 58.615 47.619 0.00 0.00 0.00 2.29
944 1030 1.137594 TCGGACCCCCACCTTTGAAT 61.138 55.000 0.00 0.00 0.00 2.57
1084 1171 0.035630 CCTCTGCTTTCTCCCTGGTG 60.036 60.000 0.00 0.00 0.00 4.17
1118 1205 2.595754 GCTGGATCCGGCCATTCC 60.596 66.667 32.19 6.08 42.15 3.01
1163 1250 0.108329 GCTTTTCCTCGATCCGGACA 60.108 55.000 6.12 0.00 0.00 4.02
1165 1252 0.611200 TTGCTTTTCCTCGATCCGGA 59.389 50.000 6.61 6.61 0.00 5.14
1178 1265 1.463553 CGTTGGGCCTCCTTTGCTTT 61.464 55.000 4.53 0.00 0.00 3.51
1197 1284 3.077556 TCAGCGAGCCCCTTCCTC 61.078 66.667 0.00 0.00 0.00 3.71
1212 1299 1.483595 CCACCAGAGCCTCCAAGTCA 61.484 60.000 0.00 0.00 0.00 3.41
1214 1301 2.900106 GCCACCAGAGCCTCCAAGT 61.900 63.158 0.00 0.00 0.00 3.16
1260 1347 3.414700 CTTCGTCACAGCGCCACC 61.415 66.667 2.29 0.00 0.00 4.61
1261 1348 3.414700 CCTTCGTCACAGCGCCAC 61.415 66.667 2.29 0.00 0.00 5.01
1338 1425 1.739338 CTCCCTCGATCCCCTTCACG 61.739 65.000 0.00 0.00 0.00 4.35
1352 1439 2.042537 TCAGCGCCATCTCTCCCT 60.043 61.111 2.29 0.00 0.00 4.20
1383 1470 3.434179 TGGCACCACCACCCCTTT 61.434 61.111 0.00 0.00 46.36 3.11
1393 1480 1.688884 TCGATCCCTCATGGCACCA 60.689 57.895 0.00 0.00 0.00 4.17
1394 1481 1.070445 CTCGATCCCTCATGGCACC 59.930 63.158 0.00 0.00 0.00 5.01
1395 1482 1.070445 CCTCGATCCCTCATGGCAC 59.930 63.158 0.00 0.00 0.00 5.01
1396 1483 2.142761 CCCTCGATCCCTCATGGCA 61.143 63.158 0.00 0.00 0.00 4.92
1399 1486 1.617850 CTCTTCCCTCGATCCCTCATG 59.382 57.143 0.00 0.00 0.00 3.07
1408 1495 1.763545 TCTCTCGATCTCTTCCCTCGA 59.236 52.381 0.00 0.00 38.95 4.04
1472 1559 4.366684 CAACCTCCCCTGGGCCAC 62.367 72.222 7.39 0.00 34.68 5.01
1524 1611 2.414612 TGTTTTACCTCTCCACTGGGT 58.585 47.619 0.00 0.00 37.16 4.51
1546 1633 2.530151 TCCAGCAGGCCTCCTTGT 60.530 61.111 0.00 0.00 33.74 3.16
1590 1677 5.183140 TCCTTTTGCCTTTCTCTATTTTCGG 59.817 40.000 0.00 0.00 0.00 4.30
1624 1711 7.818997 AGACATACTTTCGATCCTACACATA 57.181 36.000 0.00 0.00 0.00 2.29
1818 1906 0.680061 ACCGATTCTTCCTATCCGGC 59.320 55.000 0.00 0.00 0.00 6.13
1944 2032 4.834406 ACTATCAAGGAGGGATGAGGTA 57.166 45.455 0.00 0.00 0.00 3.08
2018 2106 4.827304 GCTCAAAAGCTCAAGACTCTTT 57.173 40.909 0.00 0.00 45.55 2.52
2093 2181 3.454375 GAAAGCTCAATGATTGGCATGG 58.546 45.455 16.88 1.79 37.28 3.66
2198 2286 3.903714 ACCAAAAAGGGGGAGATTGAAAG 59.096 43.478 0.00 0.00 43.89 2.62
2206 2294 5.022787 TCATCAATTACCAAAAAGGGGGAG 58.977 41.667 0.00 0.00 43.89 4.30
2207 2295 4.775253 GTCATCAATTACCAAAAAGGGGGA 59.225 41.667 0.00 0.00 43.89 4.81
2208 2296 4.530161 TGTCATCAATTACCAAAAAGGGGG 59.470 41.667 0.00 0.00 43.89 5.40
2209 2297 5.736951 TGTCATCAATTACCAAAAAGGGG 57.263 39.130 0.00 0.00 43.89 4.79
2210 2298 6.520272 TGTTGTCATCAATTACCAAAAAGGG 58.480 36.000 0.00 0.00 37.54 3.95
2211 2299 9.874205 ATATGTTGTCATCAATTACCAAAAAGG 57.126 29.630 0.00 0.00 38.51 3.11
2222 2310 9.570468 AGCTTTGATCTATATGTTGTCATCAAT 57.430 29.630 0.00 0.00 35.92 2.57
2223 2311 8.969260 AGCTTTGATCTATATGTTGTCATCAA 57.031 30.769 0.00 0.00 35.70 2.57
2224 2312 8.969260 AAGCTTTGATCTATATGTTGTCATCA 57.031 30.769 0.00 0.00 35.70 3.07
2225 2313 9.661187 CAAAGCTTTGATCTATATGTTGTCATC 57.339 33.333 31.24 0.00 40.55 2.92
2226 2314 9.399797 TCAAAGCTTTGATCTATATGTTGTCAT 57.600 29.630 32.86 0.00 41.88 3.06
2227 2315 8.791327 TCAAAGCTTTGATCTATATGTTGTCA 57.209 30.769 32.86 9.51 41.88 3.58
2241 2329 9.142515 CATGCTTATTATTTGTCAAAGCTTTGA 57.857 29.630 32.86 32.86 44.31 2.69
2242 2330 9.142515 TCATGCTTATTATTTGTCAAAGCTTTG 57.857 29.630 29.53 29.53 42.34 2.77
2243 2331 9.709495 TTCATGCTTATTATTTGTCAAAGCTTT 57.291 25.926 5.69 5.69 42.34 3.51
2244 2332 9.709495 TTTCATGCTTATTATTTGTCAAAGCTT 57.291 25.926 4.03 0.00 42.34 3.74
2245 2333 9.880157 ATTTCATGCTTATTATTTGTCAAAGCT 57.120 25.926 4.03 0.00 42.34 3.74


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

AutoCloner maintained by Alex Coulton.