Multiple sequence alignment - TraesCS7D01G108300

Loading Multiple Alignment...

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 TraesCS7D01G108300 chr7D 100.000 2294 0 0 1 2294 64892828 64895121 0.000000e+00 4237
1 TraesCS7D01G108300 chr7D 81.429 840 121 12 1486 2294 412968200 412967365 0.000000e+00 654
2 TraesCS7D01G108300 chr7D 86.581 313 27 11 985 1294 64912471 64912771 4.720000e-87 331
3 TraesCS7D01G108300 chr7D 76.625 646 76 59 699 1295 65390151 65390770 1.040000e-73 287
4 TraesCS7D01G108300 chr7D 75.831 451 62 25 856 1302 64950224 64950631 3.890000e-43 185
5 TraesCS7D01G108300 chr7B 86.364 924 66 24 576 1466 6754961 6755857 0.000000e+00 953
6 TraesCS7D01G108300 chr7B 88.403 595 24 20 1 583 6754358 6754919 0.000000e+00 675
7 TraesCS7D01G108300 chr7B 78.851 818 149 17 1486 2292 745914810 745915614 4.340000e-147 531
8 TraesCS7D01G108300 chr7B 76.852 648 73 59 699 1295 6796667 6797288 6.200000e-76 294
9 TraesCS7D01G108300 chr7B 79.150 494 52 29 829 1295 6921477 6921008 6.200000e-76 294
10 TraesCS7D01G108300 chr7A 85.749 828 61 24 576 1376 69224716 69225513 0.000000e+00 822
11 TraesCS7D01G108300 chr7A 89.711 554 25 18 40 583 69224139 69224670 0.000000e+00 678
12 TraesCS7D01G108300 chr7A 78.261 782 82 55 744 1465 69363755 69364508 2.720000e-114 422
13 TraesCS7D01G108300 chr7A 78.078 593 64 48 742 1295 69526639 69527204 4.760000e-82 315
14 TraesCS7D01G108300 chr4B 84.793 822 109 10 1486 2294 265216065 265215247 0.000000e+00 811
15 TraesCS7D01G108300 chr4B 81.971 832 123 15 1486 2294 265211199 265210372 0.000000e+00 680
16 TraesCS7D01G108300 chr4B 83.538 571 67 22 1742 2293 412715096 412714534 2.030000e-140 508
17 TraesCS7D01G108300 chr3D 82.005 828 123 19 1486 2293 287914742 287915563 0.000000e+00 680
18 TraesCS7D01G108300 chr3D 85.857 502 62 9 1486 1983 402859871 402860367 2.020000e-145 525
19 TraesCS7D01G108300 chr6B 90.780 423 31 3 1879 2294 717882145 717882566 1.990000e-155 558
20 TraesCS7D01G108300 chr6B 78.788 825 152 17 1486 2291 381363422 381362602 1.210000e-147 532
21 TraesCS7D01G108300 chr6B 84.294 503 69 10 1486 1983 6301627 6302124 1.230000e-132 483
22 TraesCS7D01G108300 chr2B 78.597 827 154 16 1484 2292 641688993 641688172 2.020000e-145 525
23 TraesCS7D01G108300 chr2B 78.022 728 149 8 1486 2204 641684564 641683839 4.500000e-122 448
24 TraesCS7D01G108300 chr2D 90.076 393 36 3 1486 1876 242154977 242155368 7.310000e-140 507
25 TraesCS7D01G108300 chr1B 89.567 393 37 4 1486 1876 43186381 43186771 1.580000e-136 496


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 TraesCS7D01G108300 chr7D 64892828 64895121 2293 False 4237.0 4237 100.0000 1 2294 1 chr7D.!!$F1 2293
1 TraesCS7D01G108300 chr7D 412967365 412968200 835 True 654.0 654 81.4290 1486 2294 1 chr7D.!!$R1 808
2 TraesCS7D01G108300 chr7D 65390151 65390770 619 False 287.0 287 76.6250 699 1295 1 chr7D.!!$F4 596
3 TraesCS7D01G108300 chr7B 6754358 6755857 1499 False 814.0 953 87.3835 1 1466 2 chr7B.!!$F3 1465
4 TraesCS7D01G108300 chr7B 745914810 745915614 804 False 531.0 531 78.8510 1486 2292 1 chr7B.!!$F2 806
5 TraesCS7D01G108300 chr7B 6796667 6797288 621 False 294.0 294 76.8520 699 1295 1 chr7B.!!$F1 596
6 TraesCS7D01G108300 chr7A 69224139 69225513 1374 False 750.0 822 87.7300 40 1376 2 chr7A.!!$F3 1336
7 TraesCS7D01G108300 chr7A 69363755 69364508 753 False 422.0 422 78.2610 744 1465 1 chr7A.!!$F1 721
8 TraesCS7D01G108300 chr7A 69526639 69527204 565 False 315.0 315 78.0780 742 1295 1 chr7A.!!$F2 553
9 TraesCS7D01G108300 chr4B 265215247 265216065 818 True 811.0 811 84.7930 1486 2294 1 chr4B.!!$R2 808
10 TraesCS7D01G108300 chr4B 265210372 265211199 827 True 680.0 680 81.9710 1486 2294 1 chr4B.!!$R1 808
11 TraesCS7D01G108300 chr4B 412714534 412715096 562 True 508.0 508 83.5380 1742 2293 1 chr4B.!!$R3 551
12 TraesCS7D01G108300 chr3D 287914742 287915563 821 False 680.0 680 82.0050 1486 2293 1 chr3D.!!$F1 807
13 TraesCS7D01G108300 chr6B 381362602 381363422 820 True 532.0 532 78.7880 1486 2291 1 chr6B.!!$R1 805
14 TraesCS7D01G108300 chr2B 641683839 641688993 5154 True 486.5 525 78.3095 1484 2292 2 chr2B.!!$R1 808

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
289 291 0.618458 GGACACAACCTCCATGCCTA 59.382 55.0 0.0 0.0 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 2003 0.106708 GACAGGGCTGCATTCCGATA 59.893 55.0 0.5 0.0 0.0 2.92 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
125 127 3.265479 AGACGTACTAGGGTGGTTACTCT 59.735 47.826 0.00 0.00 41.57 3.24
135 137 3.197333 GGGTGGTTACTCTCCTTTAGGAC 59.803 52.174 0.00 0.00 39.78 3.85
141 143 3.035055 ACTCTCCTTTAGGACTAGCCC 57.965 52.381 0.00 0.00 39.78 5.19
142 144 2.321719 CTCTCCTTTAGGACTAGCCCC 58.678 57.143 0.00 0.00 39.78 5.80
143 145 1.938069 TCTCCTTTAGGACTAGCCCCT 59.062 52.381 9.03 9.03 39.78 4.79
144 146 3.136896 TCTCCTTTAGGACTAGCCCCTA 58.863 50.000 7.26 7.26 39.78 3.53
145 147 3.140519 TCTCCTTTAGGACTAGCCCCTAG 59.859 52.174 10.35 3.98 39.78 3.02
146 148 3.136896 TCCTTTAGGACTAGCCCCTAGA 58.863 50.000 10.35 6.70 39.78 2.43
147 149 3.117208 TCCTTTAGGACTAGCCCCTAGAC 60.117 52.174 10.35 0.38 39.78 2.59
148 150 2.653234 TTAGGACTAGCCCCTAGACG 57.347 55.000 10.35 0.00 37.55 4.18
155 157 2.228925 CTAGCCCCTAGACGTACTTCC 58.771 57.143 0.00 0.00 36.26 3.46
166 168 5.148651 AGACGTACTTCCTTTAGCAATGT 57.851 39.130 0.00 0.00 0.00 2.71
168 170 4.000988 ACGTACTTCCTTTAGCAATGTGG 58.999 43.478 0.00 0.00 0.00 4.17
264 266 3.626930 GGTGGAGTTATAAATGGGTGCA 58.373 45.455 0.00 0.00 0.00 4.57
283 285 1.537814 ATACGCGGACACAACCTCCA 61.538 55.000 12.47 0.00 0.00 3.86
285 287 2.390599 CGCGGACACAACCTCCATG 61.391 63.158 0.00 0.00 0.00 3.66
286 288 2.690778 GCGGACACAACCTCCATGC 61.691 63.158 0.00 0.00 0.00 4.06
287 289 2.040544 CGGACACAACCTCCATGCC 61.041 63.158 0.00 0.00 0.00 4.40
288 290 1.380302 GGACACAACCTCCATGCCT 59.620 57.895 0.00 0.00 0.00 4.75
289 291 0.618458 GGACACAACCTCCATGCCTA 59.382 55.000 0.00 0.00 0.00 3.93
374 384 4.222145 ACGAGGAAATGCTACTCCACTTAA 59.778 41.667 0.00 0.00 33.83 1.85
397 407 4.461081 AGAAGCGGTGAGAGATATGTATCC 59.539 45.833 0.00 0.00 33.17 2.59
398 408 3.093057 AGCGGTGAGAGATATGTATCCC 58.907 50.000 0.00 0.00 33.17 3.85
402 412 4.035792 CGGTGAGAGATATGTATCCCGATC 59.964 50.000 14.89 0.00 35.76 3.69
403 413 4.035792 GGTGAGAGATATGTATCCCGATCG 59.964 50.000 8.51 8.51 33.17 3.69
404 414 4.876679 GTGAGAGATATGTATCCCGATCGA 59.123 45.833 18.66 0.00 33.17 3.59
405 415 5.529430 GTGAGAGATATGTATCCCGATCGAT 59.471 44.000 18.66 5.53 33.17 3.59
406 416 5.529060 TGAGAGATATGTATCCCGATCGATG 59.471 44.000 18.66 7.52 33.17 3.84
407 417 5.685728 AGAGATATGTATCCCGATCGATGA 58.314 41.667 18.66 13.17 33.17 2.92
424 434 1.741770 GAAAGATCACGGCGGCTGT 60.742 57.895 13.24 9.04 0.00 4.40
467 478 3.554934 GATCAAAGATACCATGCCCACA 58.445 45.455 0.00 0.00 0.00 4.17
470 481 2.684881 CAAAGATACCATGCCCACAGAC 59.315 50.000 0.00 0.00 0.00 3.51
473 484 3.384168 AGATACCATGCCCACAGACTTA 58.616 45.455 0.00 0.00 0.00 2.24
514 528 6.077838 GTCATACAACGGTTTTCAACTCATC 58.922 40.000 0.00 0.00 0.00 2.92
515 529 5.760743 TCATACAACGGTTTTCAACTCATCA 59.239 36.000 0.00 0.00 0.00 3.07
516 530 6.429692 TCATACAACGGTTTTCAACTCATCAT 59.570 34.615 0.00 0.00 0.00 2.45
517 531 4.858935 ACAACGGTTTTCAACTCATCATG 58.141 39.130 0.00 0.00 0.00 3.07
571 587 3.502211 GGTCCAACGAACAAATCAGTCAT 59.498 43.478 0.00 0.00 0.00 3.06
622 691 5.070047 AGAGAAAGGTCTTTTTCTACGTCCA 59.930 40.000 12.83 0.00 45.00 4.02
662 738 0.975135 CAACATGGCATGGGTTTGGA 59.025 50.000 29.49 0.00 33.60 3.53
663 739 0.975887 AACATGGCATGGGTTTGGAC 59.024 50.000 29.49 0.00 33.60 4.02
664 740 0.904394 ACATGGCATGGGTTTGGACC 60.904 55.000 29.49 0.00 45.75 4.46
806 893 3.559657 GAGTGCGACACAGGCGACT 62.560 63.158 11.58 0.00 46.44 4.18
832 926 0.881118 ATCGCAATGCTTGGTTCGTT 59.119 45.000 2.94 0.00 0.00 3.85
887 995 0.874607 ATAAATCACCTCGGCGTCGC 60.875 55.000 9.22 9.22 36.13 5.19
926 1044 1.982395 CCACCACCGCCAGTCTAGA 60.982 63.158 0.00 0.00 0.00 2.43
937 1055 1.377463 AGTCTAGAGCGCACGAGGT 60.377 57.895 11.47 0.00 0.00 3.85
941 1059 1.715862 CTAGAGCGCACGAGGTAGCA 61.716 60.000 11.47 0.00 0.00 3.49
946 1064 1.080772 CGCACGAGGTAGCAACAGA 60.081 57.895 0.00 0.00 0.00 3.41
968 1107 1.279496 ACAGAGCCTAGCATTCCACA 58.721 50.000 0.00 0.00 0.00 4.17
969 1108 1.209019 ACAGAGCCTAGCATTCCACAG 59.791 52.381 0.00 0.00 0.00 3.66
982 1128 2.838386 TCCACAGCGTACGAATCTAC 57.162 50.000 21.65 0.00 0.00 2.59
990 1136 4.392445 CAGCGTACGAATCTACCTAGCTAT 59.608 45.833 21.65 0.00 0.00 2.97
991 1137 5.579904 CAGCGTACGAATCTACCTAGCTATA 59.420 44.000 21.65 0.00 0.00 1.31
993 1139 5.220567 GCGTACGAATCTACCTAGCTATACC 60.221 48.000 21.65 0.00 0.00 2.73
994 1140 5.005203 CGTACGAATCTACCTAGCTATACCG 59.995 48.000 10.44 0.00 0.00 4.02
1073 1247 4.694233 CCTGCTGCTGCTGTCCGT 62.694 66.667 17.00 0.00 40.48 4.69
1074 1248 3.117171 CTGCTGCTGCTGTCCGTC 61.117 66.667 17.00 0.00 40.48 4.79
1119 1293 3.034635 CCTCCTGCAGGTAATAGTGTCT 58.965 50.000 31.58 0.00 37.53 3.41
1337 1529 5.697633 TGTAAAGTTGTCGGTTAAGGATGAC 59.302 40.000 0.00 0.00 0.00 3.06
1388 1584 5.593679 CCTCGACTTCTAGGGAATGTTAA 57.406 43.478 0.00 0.00 0.00 2.01
1398 1594 9.720769 CTTCTAGGGAATGTTAAGTTACTCAAA 57.279 33.333 0.00 0.00 0.00 2.69
1420 1617 3.788434 ATGAGTTTTGTAGTTCGTGCG 57.212 42.857 0.00 0.00 0.00 5.34
1422 1619 2.931325 TGAGTTTTGTAGTTCGTGCGTT 59.069 40.909 0.00 0.00 0.00 4.84
1451 1648 6.358762 GCATGCAAAAACAAATAAAGCGTAA 58.641 32.000 14.21 0.00 0.00 3.18
1452 1649 7.014702 GCATGCAAAAACAAATAAAGCGTAAT 58.985 30.769 14.21 0.00 0.00 1.89
1514 1712 3.328505 CCAGATTTTGGCATGGTCAAAC 58.671 45.455 0.00 0.00 36.85 2.93
1517 1715 3.387374 AGATTTTGGCATGGTCAAACACA 59.613 39.130 0.00 0.00 36.85 3.72
1539 1737 5.716228 ACACAATTAAGATGGCCTCAAATGA 59.284 36.000 3.32 0.00 0.00 2.57
1546 1744 5.397142 AGATGGCCTCAAATGAAAAAGTC 57.603 39.130 3.32 0.00 0.00 3.01
1554 1752 5.693555 CCTCAAATGAAAAAGTCCTCAAAGC 59.306 40.000 0.00 0.00 0.00 3.51
1565 1763 3.070302 AGTCCTCAAAGCGAGAAAGTTCT 59.930 43.478 0.00 0.00 45.45 3.01
1581 1779 8.077836 AGAAAGTTCTGTATCGTCAAAAGAAG 57.922 34.615 0.00 0.00 35.89 2.85
1599 1798 9.264719 CAAAAGAAGAAACTTTGATATTTGGCT 57.735 29.630 0.00 0.00 39.57 4.75
1625 1824 3.761218 GCCATCCGATCTCATCTCTAAGA 59.239 47.826 0.00 0.00 0.00 2.10
1674 1873 7.989826 AGATTTTGTATTCAGAACACTATGCC 58.010 34.615 0.00 0.00 0.00 4.40
1697 1896 1.963464 GATTACGCCCCCAAGACGGA 61.963 60.000 0.00 0.00 36.56 4.69
1698 1897 1.342672 ATTACGCCCCCAAGACGGAT 61.343 55.000 0.00 0.00 36.56 4.18
1701 1900 2.513897 GCCCCCAAGACGGATTCG 60.514 66.667 0.00 0.00 43.02 3.34
1737 1936 8.260270 TGATCTACACAAATTGTCTTCATCTG 57.740 34.615 0.00 0.00 39.91 2.90
1783 1985 2.938956 ATCATCCCAATCCGAGTTCC 57.061 50.000 0.00 0.00 0.00 3.62
1791 1993 2.398498 CAATCCGAGTTCCTATGCGAG 58.602 52.381 0.00 0.00 0.00 5.03
1793 1995 1.758936 TCCGAGTTCCTATGCGAGAA 58.241 50.000 0.00 0.00 0.00 2.87
1801 2003 4.586841 AGTTCCTATGCGAGAATTAGAGCT 59.413 41.667 0.00 0.00 0.00 4.09
1822 2024 2.110967 CGGAATGCAGCCCTGTCAG 61.111 63.158 0.00 0.00 0.00 3.51
1833 2035 0.830648 CCCTGTCAGGAGGCGAAATA 59.169 55.000 21.23 0.00 37.67 1.40
1835 2037 2.632996 CCCTGTCAGGAGGCGAAATATA 59.367 50.000 21.23 0.00 37.67 0.86
1838 2040 2.698274 TGTCAGGAGGCGAAATATAGCA 59.302 45.455 0.00 0.00 34.54 3.49
1852 2054 2.284798 ATAGCACGCTCCACCAGACG 62.285 60.000 0.00 0.00 0.00 4.18
1868 2091 0.464036 GACGCCATGTCTGATGGGTA 59.536 55.000 0.00 0.00 44.58 3.69
1895 2118 1.334384 TGATTCGGCCCGGAAGATGA 61.334 55.000 0.73 0.00 0.00 2.92
1975 2198 3.438183 AGCTTTTGGGCTCATCTTCATT 58.562 40.909 0.00 0.00 38.24 2.57
2068 2293 7.149307 GGTTAATTTTGGAAAGATTTGGACGA 58.851 34.615 0.00 0.00 0.00 4.20
2122 2360 6.324254 GTCCATCCGCCTCTTATATACCTAAT 59.676 42.308 0.00 0.00 0.00 1.73
2163 2403 5.645624 ACAACACACAATCGAACAAATCAA 58.354 33.333 0.00 0.00 0.00 2.57
2198 2467 9.720769 TTACCCTAGTTTTACATCTCTTCTTTG 57.279 33.333 0.00 0.00 0.00 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.203394 GACCCGGCCATGCATGAT 60.203 61.111 28.31 5.80 0.00 2.45
125 127 3.117208 GTCTAGGGGCTAGTCCTAAAGGA 60.117 52.174 14.34 5.67 36.54 3.36
135 137 2.158638 AGGAAGTACGTCTAGGGGCTAG 60.159 54.545 8.73 0.00 35.57 3.42
141 143 4.978083 TGCTAAAGGAAGTACGTCTAGG 57.022 45.455 8.73 0.00 0.00 3.02
142 144 6.253727 CACATTGCTAAAGGAAGTACGTCTAG 59.746 42.308 8.73 4.36 0.00 2.43
143 145 6.097356 CACATTGCTAAAGGAAGTACGTCTA 58.903 40.000 8.73 0.00 0.00 2.59
144 146 4.929808 CACATTGCTAAAGGAAGTACGTCT 59.070 41.667 8.73 0.00 0.00 4.18
145 147 4.092968 CCACATTGCTAAAGGAAGTACGTC 59.907 45.833 0.00 0.00 0.00 4.34
146 148 4.000988 CCACATTGCTAAAGGAAGTACGT 58.999 43.478 0.00 0.00 0.00 3.57
147 149 4.250464 TCCACATTGCTAAAGGAAGTACG 58.750 43.478 0.00 0.00 0.00 3.67
148 150 5.705905 AGTTCCACATTGCTAAAGGAAGTAC 59.294 40.000 0.00 0.00 39.55 2.73
155 157 8.099364 TCTTTAAGAGTTCCACATTGCTAAAG 57.901 34.615 0.00 0.00 0.00 1.85
166 168 3.554337 GCACCGTCTCTTTAAGAGTTCCA 60.554 47.826 19.87 0.00 42.83 3.53
168 170 3.915536 AGCACCGTCTCTTTAAGAGTTC 58.084 45.455 19.87 13.57 42.83 3.01
181 183 4.459089 GGCAGGAGGAGCACCGTC 62.459 72.222 0.00 0.00 41.83 4.79
264 266 1.217244 GGAGGTTGTGTCCGCGTAT 59.783 57.895 4.92 0.00 0.00 3.06
283 285 5.105064 ACCATTAACGTACTTGTCTAGGCAT 60.105 40.000 0.00 0.00 0.00 4.40
285 287 4.565564 CACCATTAACGTACTTGTCTAGGC 59.434 45.833 0.00 0.00 0.00 3.93
286 288 4.565564 GCACCATTAACGTACTTGTCTAGG 59.434 45.833 0.00 0.00 0.00 3.02
287 289 4.264614 CGCACCATTAACGTACTTGTCTAG 59.735 45.833 0.00 0.00 0.00 2.43
288 290 4.168014 CGCACCATTAACGTACTTGTCTA 58.832 43.478 0.00 0.00 0.00 2.59
289 291 2.991190 CGCACCATTAACGTACTTGTCT 59.009 45.455 0.00 0.00 0.00 3.41
374 384 4.461081 GGATACATATCTCTCACCGCTTCT 59.539 45.833 0.00 0.00 33.28 2.85
397 407 2.054363 CCGTGATCTTTCATCGATCGG 58.946 52.381 16.41 0.00 40.05 4.18
398 408 1.453524 GCCGTGATCTTTCATCGATCG 59.546 52.381 9.36 9.36 40.05 3.69
402 412 1.927210 CCGCCGTGATCTTTCATCG 59.073 57.895 0.00 0.00 33.56 3.84
403 413 0.811616 AGCCGCCGTGATCTTTCATC 60.812 55.000 0.00 0.00 33.56 2.92
404 414 1.091771 CAGCCGCCGTGATCTTTCAT 61.092 55.000 0.00 0.00 33.56 2.57
405 415 1.741401 CAGCCGCCGTGATCTTTCA 60.741 57.895 0.00 0.00 0.00 2.69
406 416 1.298859 AACAGCCGCCGTGATCTTTC 61.299 55.000 0.00 0.00 0.00 2.62
407 417 1.302511 AACAGCCGCCGTGATCTTT 60.303 52.632 0.00 0.00 0.00 2.52
424 434 3.673956 ATCACCCCGCGCGAATCAA 62.674 57.895 34.63 14.18 0.00 2.57
467 478 4.607293 TGTTGACATGACAGCTAAGTCT 57.393 40.909 12.51 0.00 39.27 3.24
514 528 2.327568 GGTCCATTCGTTGTTTGCATG 58.672 47.619 0.00 0.00 0.00 4.06
515 529 1.068610 CGGTCCATTCGTTGTTTGCAT 60.069 47.619 0.00 0.00 0.00 3.96
516 530 0.309302 CGGTCCATTCGTTGTTTGCA 59.691 50.000 0.00 0.00 0.00 4.08
517 531 0.589223 TCGGTCCATTCGTTGTTTGC 59.411 50.000 0.00 0.00 0.00 3.68
571 587 0.250234 CCTCCAGATCGGTGCTGAAA 59.750 55.000 0.00 0.00 35.39 2.69
806 893 0.527113 CAAGCATTGCGATGGTGGAA 59.473 50.000 19.14 0.00 42.86 3.53
887 995 0.457337 GAGTTGGGTACGTACCTGCG 60.457 60.000 36.70 0.00 45.72 5.18
892 1000 1.337167 GGTGGTGAGTTGGGTACGTAC 60.337 57.143 17.56 17.56 0.00 3.67
926 1044 2.432628 GTTGCTACCTCGTGCGCT 60.433 61.111 9.73 0.00 0.00 5.92
937 1055 2.808919 AGGCTCTGTAGTCTGTTGCTA 58.191 47.619 0.00 0.00 35.94 3.49
941 1059 2.808919 TGCTAGGCTCTGTAGTCTGTT 58.191 47.619 0.00 0.00 38.43 3.16
946 1064 2.432510 GTGGAATGCTAGGCTCTGTAGT 59.567 50.000 0.00 0.00 0.00 2.73
968 1107 2.848691 AGCTAGGTAGATTCGTACGCT 58.151 47.619 11.24 4.66 0.00 5.07
969 1108 4.943142 ATAGCTAGGTAGATTCGTACGC 57.057 45.455 11.24 0.00 0.00 4.42
982 1128 3.067461 GCCATGAGATCGGTATAGCTAGG 59.933 52.174 0.00 0.00 0.00 3.02
990 1136 0.753848 TGGACGCCATGAGATCGGTA 60.754 55.000 0.00 0.00 0.00 4.02
991 1137 2.021068 CTGGACGCCATGAGATCGGT 62.021 60.000 0.00 0.00 30.82 4.69
993 1139 1.953138 GCTGGACGCCATGAGATCG 60.953 63.158 0.00 0.00 30.82 3.69
994 1140 0.599728 GAGCTGGACGCCATGAGATC 60.600 60.000 0.00 0.00 40.39 2.75
1117 1291 4.161295 CATTCTCCGGCCGCCAGA 62.161 66.667 22.85 20.17 0.00 3.86
1231 1417 2.279517 CTCGGAGTACGGCATGGC 60.280 66.667 9.69 9.69 44.45 4.40
1232 1418 1.065928 GACTCGGAGTACGGCATGG 59.934 63.158 11.27 0.00 44.45 3.66
1233 1419 1.298413 CGACTCGGAGTACGGCATG 60.298 63.158 11.27 0.00 44.45 4.06
1398 1594 4.034742 ACGCACGAACTACAAAACTCATTT 59.965 37.500 0.00 0.00 0.00 2.32
1406 1603 1.592590 CGCAAACGCACGAACTACAAA 60.593 47.619 0.00 0.00 0.00 2.83
1426 1623 4.150343 CGCTTTATTTGTTTTTGCATGCC 58.850 39.130 16.68 0.00 0.00 4.40
1430 1627 9.411801 TGATATTACGCTTTATTTGTTTTTGCA 57.588 25.926 0.00 0.00 0.00 4.08
1435 1632 8.194104 TGGCATGATATTACGCTTTATTTGTTT 58.806 29.630 0.00 0.00 0.00 2.83
1466 1664 7.070571 TGTCAACAGTATGATGTCACCCATATA 59.929 37.037 0.00 0.00 40.13 0.86
1467 1665 6.126796 TGTCAACAGTATGATGTCACCCATAT 60.127 38.462 0.00 0.00 40.13 1.78
1468 1666 5.188751 TGTCAACAGTATGATGTCACCCATA 59.811 40.000 0.00 0.00 40.13 2.74
1469 1667 4.019411 TGTCAACAGTATGATGTCACCCAT 60.019 41.667 0.00 0.00 40.13 4.00
1470 1668 3.326297 TGTCAACAGTATGATGTCACCCA 59.674 43.478 0.00 0.00 40.13 4.51
1471 1669 3.684788 GTGTCAACAGTATGATGTCACCC 59.315 47.826 6.27 0.00 46.27 4.61
1472 1670 4.928661 GTGTCAACAGTATGATGTCACC 57.071 45.455 6.27 0.00 46.27 4.02
1474 1672 4.283212 TCTGGTGTCAACAGTATGATGTCA 59.717 41.667 17.43 0.00 40.13 3.58
1475 1673 4.820897 TCTGGTGTCAACAGTATGATGTC 58.179 43.478 17.43 0.00 40.13 3.06
1476 1674 4.890158 TCTGGTGTCAACAGTATGATGT 57.110 40.909 17.43 0.00 40.13 3.06
1477 1675 6.748333 AAATCTGGTGTCAACAGTATGATG 57.252 37.500 17.43 0.00 40.64 3.07
1478 1676 6.151648 CCAAAATCTGGTGTCAACAGTATGAT 59.848 38.462 17.43 1.22 40.78 2.45
1479 1677 5.473162 CCAAAATCTGGTGTCAACAGTATGA 59.527 40.000 17.43 0.00 40.78 2.15
1480 1678 5.702865 CCAAAATCTGGTGTCAACAGTATG 58.297 41.667 17.43 11.52 40.78 2.39
1481 1679 5.964958 CCAAAATCTGGTGTCAACAGTAT 57.035 39.130 17.43 7.29 40.78 2.12
1514 1712 5.389859 TTTGAGGCCATCTTAATTGTGTG 57.610 39.130 5.01 0.00 0.00 3.82
1517 1715 6.855763 TTCATTTGAGGCCATCTTAATTGT 57.144 33.333 5.01 0.00 0.00 2.71
1539 1737 4.640647 ACTTTCTCGCTTTGAGGACTTTTT 59.359 37.500 0.00 0.00 45.32 1.94
1546 1744 3.134458 ACAGAACTTTCTCGCTTTGAGG 58.866 45.455 0.00 0.00 45.32 3.86
1554 1752 6.362551 TCTTTTGACGATACAGAACTTTCTCG 59.637 38.462 0.00 0.00 34.74 4.04
1565 1763 8.203937 TCAAAGTTTCTTCTTTTGACGATACA 57.796 30.769 0.00 0.00 35.77 2.29
1599 1798 5.122707 AGAGATGAGATCGGATGGCTATA 57.877 43.478 0.00 0.00 0.00 1.31
1625 1824 4.331717 CAGTACTTCAAACACAACTTCGGT 59.668 41.667 0.00 0.00 0.00 4.69
1674 1873 2.124901 TTGGGGGCGTAATCAGCG 60.125 61.111 0.00 0.00 35.00 5.18
1697 1896 7.272244 TGTGTAGATCATTGTTCCATACGAAT 58.728 34.615 0.00 0.00 31.67 3.34
1698 1897 6.635755 TGTGTAGATCATTGTTCCATACGAA 58.364 36.000 0.00 0.00 0.00 3.85
1701 1900 9.507280 CAATTTGTGTAGATCATTGTTCCATAC 57.493 33.333 0.00 0.00 0.00 2.39
1709 1908 9.499585 GATGAAGACAATTTGTGTAGATCATTG 57.500 33.333 6.80 0.00 41.96 2.82
1712 1911 7.335171 CCAGATGAAGACAATTTGTGTAGATCA 59.665 37.037 6.80 4.52 41.96 2.92
1713 1912 7.335422 ACCAGATGAAGACAATTTGTGTAGATC 59.665 37.037 6.80 7.98 41.96 2.75
1714 1913 7.170965 ACCAGATGAAGACAATTTGTGTAGAT 58.829 34.615 6.80 0.00 41.96 1.98
1721 1920 5.385617 GTTCGACCAGATGAAGACAATTTG 58.614 41.667 0.00 0.00 0.00 2.32
1722 1921 4.152402 CGTTCGACCAGATGAAGACAATTT 59.848 41.667 0.00 0.00 0.00 1.82
1783 1985 5.065346 TCCGATAGCTCTAATTCTCGCATAG 59.935 44.000 0.00 0.00 0.00 2.23
1791 1993 4.092675 GCTGCATTCCGATAGCTCTAATTC 59.907 45.833 0.00 0.00 33.53 2.17
1793 1995 3.594134 GCTGCATTCCGATAGCTCTAAT 58.406 45.455 0.00 0.00 33.53 1.73
1801 2003 0.106708 GACAGGGCTGCATTCCGATA 59.893 55.000 0.50 0.00 0.00 2.92
1822 2024 0.790814 GCGTGCTATATTTCGCCTCC 59.209 55.000 0.00 0.00 42.33 4.30
1828 2030 2.802816 CTGGTGGAGCGTGCTATATTTC 59.197 50.000 0.00 0.00 0.00 2.17
1833 2035 1.517832 GTCTGGTGGAGCGTGCTAT 59.482 57.895 0.00 0.00 0.00 2.97
1835 2037 4.363990 CGTCTGGTGGAGCGTGCT 62.364 66.667 0.00 0.00 0.00 4.40
1842 2044 2.662596 GACATGGCGTCTGGTGGA 59.337 61.111 0.00 0.00 41.81 4.02
1852 2054 0.882042 CGCTACCCATCAGACATGGC 60.882 60.000 0.00 0.00 37.85 4.40
1854 2056 1.217585 CGCGCTACCCATCAGACATG 61.218 60.000 5.56 0.00 0.00 3.21
1887 2110 6.237861 CGTTTTTCTATTCGAGGTCATCTTCC 60.238 42.308 0.00 0.00 0.00 3.46
1895 2118 5.524646 TGTTGAACGTTTTTCTATTCGAGGT 59.475 36.000 0.46 0.00 0.00 3.85
1922 2145 2.028287 TCGACGAGACGAACAACTTC 57.972 50.000 0.00 0.00 39.34 3.01
1975 2198 0.824109 CATAGGCCACAAGACCTCGA 59.176 55.000 5.01 0.00 37.50 4.04
2068 2293 5.701290 CGTACAAGAAAAGGACTCCAAATCT 59.299 40.000 0.00 0.00 0.00 2.40
2122 2360 2.884980 TTCAATCGGCCGTCACCCA 61.885 57.895 27.15 4.32 0.00 4.51
2190 2456 6.019801 CGAAGAACGAGAAAGAACAAAGAAGA 60.020 38.462 0.00 0.00 45.77 2.87
2198 2467 3.485013 ACGAACGAAGAACGAGAAAGAAC 59.515 43.478 0.14 0.00 45.77 3.01


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

AutoCloner maintained by Alex Coulton.