Multiple sequence alignment - TraesCS7D01G117100

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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 TraesCS7D01G117100 chr7D 100.000 2605 0 0 1 2605 72215306 72217910 0.000000e+00 4811.0
1 TraesCS7D01G117100 chr7D 86.732 814 71 21 1055 1848 72128493 72129289 0.000000e+00 870.0
2 TraesCS7D01G117100 chr7D 81.690 355 43 15 1727 2065 73116484 73116136 2.550000e-70 276.0
3 TraesCS7D01G117100 chr7D 77.196 535 74 28 1817 2325 71862006 71861494 4.270000e-68 268.0
4 TraesCS7D01G117100 chr7D 78.511 470 54 27 1756 2196 71863439 71862988 5.530000e-67 265.0
5 TraesCS7D01G117100 chr7B 86.640 2253 196 71 1 2187 15017120 15019333 0.000000e+00 2396.0
6 TraesCS7D01G117100 chr7B 85.406 1343 115 35 805 2095 15298113 15299426 0.000000e+00 1319.0
7 TraesCS7D01G117100 chr7B 89.036 757 61 19 1 751 15069610 15070350 0.000000e+00 918.0
8 TraesCS7D01G117100 chr7B 79.195 1192 150 57 1055 2196 14697069 14698212 0.000000e+00 737.0
9 TraesCS7D01G117100 chr7B 77.991 468 57 26 1756 2196 14865211 14864763 4.300000e-63 252.0
10 TraesCS7D01G117100 chr7B 73.488 645 116 37 1984 2604 14863583 14862970 2.650000e-45 193.0
11 TraesCS7D01G117100 chr7B 86.992 123 11 4 1983 2101 286566736 286566615 1.630000e-27 134.0
12 TraesCS7D01G117100 chr7A 86.903 2115 191 49 1 2065 77193848 77195926 0.000000e+00 2292.0
13 TraesCS7D01G117100 chr7A 82.242 1222 143 43 772 1952 77149797 77150985 0.000000e+00 987.0
14 TraesCS7D01G117100 chrUn 86.732 814 71 21 1055 1848 273470864 273470068 0.000000e+00 870.0
15 TraesCS7D01G117100 chrUn 92.437 595 27 7 1055 1632 82565941 82566534 0.000000e+00 833.0
16 TraesCS7D01G117100 chrUn 92.769 567 33 2 1058 1616 84331098 84330532 0.000000e+00 813.0
17 TraesCS7D01G117100 chrUn 81.141 403 42 19 1817 2194 84314671 84314278 2.540000e-75 292.0
18 TraesCS7D01G117100 chrUn 81.100 291 33 9 1817 2090 82602354 82602069 2.030000e-51 213.0
19 TraesCS7D01G117100 chrUn 75.897 390 59 22 1810 2196 82603767 82603410 1.600000e-37 167.0
20 TraesCS7D01G117100 chrUn 74.474 333 63 16 2272 2598 84329861 84329545 9.790000e-25 124.0
21 TraesCS7D01G117100 chr4B 95.455 418 19 0 1055 1472 512335229 512334812 0.000000e+00 667.0
22 TraesCS7D01G117100 chr4D 94.457 433 23 1 1042 1474 415583738 415583307 0.000000e+00 665.0
23 TraesCS7D01G117100 chr3A 70.495 444 117 12 174 611 40998548 40998983 5.980000e-12 82.4


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 TraesCS7D01G117100 chr7D 72215306 72217910 2604 False 4811.0 4811 100.0000 1 2605 1 chr7D.!!$F2 2604
1 TraesCS7D01G117100 chr7D 72128493 72129289 796 False 870.0 870 86.7320 1055 1848 1 chr7D.!!$F1 793
2 TraesCS7D01G117100 chr7D 71861494 71863439 1945 True 266.5 268 77.8535 1756 2325 2 chr7D.!!$R2 569
3 TraesCS7D01G117100 chr7B 15017120 15019333 2213 False 2396.0 2396 86.6400 1 2187 1 chr7B.!!$F2 2186
4 TraesCS7D01G117100 chr7B 15298113 15299426 1313 False 1319.0 1319 85.4060 805 2095 1 chr7B.!!$F4 1290
5 TraesCS7D01G117100 chr7B 15069610 15070350 740 False 918.0 918 89.0360 1 751 1 chr7B.!!$F3 750
6 TraesCS7D01G117100 chr7B 14697069 14698212 1143 False 737.0 737 79.1950 1055 2196 1 chr7B.!!$F1 1141
7 TraesCS7D01G117100 chr7B 14862970 14865211 2241 True 222.5 252 75.7395 1756 2604 2 chr7B.!!$R2 848
8 TraesCS7D01G117100 chr7A 77193848 77195926 2078 False 2292.0 2292 86.9030 1 2065 1 chr7A.!!$F2 2064
9 TraesCS7D01G117100 chr7A 77149797 77150985 1188 False 987.0 987 82.2420 772 1952 1 chr7A.!!$F1 1180
10 TraesCS7D01G117100 chrUn 273470068 273470864 796 True 870.0 870 86.7320 1055 1848 1 chrUn.!!$R2 793
11 TraesCS7D01G117100 chrUn 82565941 82566534 593 False 833.0 833 92.4370 1055 1632 1 chrUn.!!$F1 577
12 TraesCS7D01G117100 chrUn 84329545 84331098 1553 True 468.5 813 83.6215 1058 2598 2 chrUn.!!$R4 1540

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
910 938 0.526211 GATTCCGTCCAAAACCAGGC 59.474 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2482 5497 0.03889 TGGAATCCATGCCACCGAAA 59.961 50.0 0.0 0.0 0.0 3.46 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
27 29 2.299013 CGTCAATCCCCGGATCAATCTA 59.701 50.000 0.73 0.00 33.08 1.98
31 33 4.597075 TCAATCCCCGGATCAATCTATTCA 59.403 41.667 0.73 0.00 33.08 2.57
49 51 5.705397 ATTCAGAGAAAGTCATGATCCCA 57.295 39.130 0.00 0.00 0.00 4.37
88 92 2.368875 AGGTGTCTCAACGTCATTTCCT 59.631 45.455 0.00 0.00 0.00 3.36
92 96 1.067142 TCTCAACGTCATTTCCTCCCG 60.067 52.381 0.00 0.00 0.00 5.14
281 285 7.492020 TTGTCTTTACGTGTAAAGTCAAAGCTA 59.508 33.333 27.25 14.70 46.94 3.32
298 302 3.173965 AGCTATATAGTTGCGGGGTGAT 58.826 45.455 11.38 0.00 33.58 3.06
347 351 5.536161 GGTCATGATACCCTATGTTTTGCAT 59.464 40.000 0.00 0.00 36.25 3.96
415 419 2.280524 CCTTGACGCGGTTGACCA 60.281 61.111 12.47 0.00 35.14 4.02
475 480 1.276622 GTCCCAGAGGCTCTTGGTTA 58.723 55.000 28.24 12.25 31.66 2.85
544 550 0.741326 TGACAGCTCGTAGGCATCTC 59.259 55.000 0.00 0.00 34.17 2.75
589 599 0.533308 GTGTGTGGGTCTTGCGGTTA 60.533 55.000 0.00 0.00 0.00 2.85
652 665 9.801873 AATTATTTTCGTCAGGTTTTCCATATG 57.198 29.630 0.00 0.00 43.73 1.78
657 670 6.730960 TCGTCAGGTTTTCCATATGTTAAC 57.269 37.500 1.24 0.00 43.73 2.01
667 680 9.005777 GTTTTCCATATGTTAACCTGACAACTA 57.994 33.333 2.48 0.00 0.00 2.24
774 789 4.389576 GCCCGCTCAAAGCACACG 62.390 66.667 0.00 0.00 42.58 4.49
796 811 3.373439 GCAAGTGAGAAATGCTACTCCAG 59.627 47.826 0.00 0.00 37.12 3.86
823 838 2.869503 GATCCGTGACCAACCCGCAT 62.870 60.000 0.00 0.00 0.00 4.73
846 861 3.140325 ACACATCTCCAACGTCCATTT 57.860 42.857 0.00 0.00 0.00 2.32
847 862 3.486383 ACACATCTCCAACGTCCATTTT 58.514 40.909 0.00 0.00 0.00 1.82
848 863 4.647611 ACACATCTCCAACGTCCATTTTA 58.352 39.130 0.00 0.00 0.00 1.52
851 867 3.062122 TCTCCAACGTCCATTTTACCC 57.938 47.619 0.00 0.00 0.00 3.69
861 877 2.027007 TCCATTTTACCCGATCCAACGT 60.027 45.455 0.00 0.00 0.00 3.99
907 935 2.235016 CCAAGATTCCGTCCAAAACCA 58.765 47.619 0.00 0.00 0.00 3.67
910 938 0.526211 GATTCCGTCCAAAACCAGGC 59.474 55.000 0.00 0.00 0.00 4.85
938 966 3.127533 GAAATGCTCCAGCCGCGT 61.128 61.111 4.92 0.00 41.18 6.01
961 989 2.550175 CACCCTCCAAAATTTCCCCAT 58.450 47.619 0.00 0.00 0.00 4.00
1036 1064 0.179000 CACCCGATCTCCCAAGAAGG 59.821 60.000 0.00 0.00 34.49 3.46
1050 1078 3.103213 AAGGCACCACCACCACCT 61.103 61.111 0.00 0.00 43.14 4.00
1536 1616 0.586802 GTGTCGGGTGCTTCTGTTTC 59.413 55.000 0.00 0.00 0.00 2.78
1575 1657 5.208121 TGTGTCATCTGGTCCTATGTATCA 58.792 41.667 5.13 2.45 0.00 2.15
1598 1680 3.481028 CGATGCTCGAATGAAATTGCAAG 59.519 43.478 4.94 0.00 43.74 4.01
1603 1685 4.418392 CTCGAATGAAATTGCAAGGGAAG 58.582 43.478 4.94 0.00 36.07 3.46
1640 1730 5.255687 TCTGATGCTAATTTTGCTCTCCAA 58.744 37.500 4.54 0.00 0.00 3.53
1651 1741 0.807496 GCTCTCCAATGCCACTGTTC 59.193 55.000 0.00 0.00 0.00 3.18
1656 1746 1.065491 TCCAATGCCACTGTTCGCTAT 60.065 47.619 0.00 0.00 0.00 2.97
1660 1750 1.075542 TGCCACTGTTCGCTATTTCG 58.924 50.000 0.00 0.00 0.00 3.46
1668 1758 3.840468 TGTTCGCTATTTCGTTGCTCTA 58.160 40.909 0.00 0.00 0.00 2.43
1677 1767 6.201806 GCTATTTCGTTGCTCTATGATTCTGT 59.798 38.462 0.00 0.00 0.00 3.41
1678 1768 6.992063 ATTTCGTTGCTCTATGATTCTGTT 57.008 33.333 0.00 0.00 0.00 3.16
1680 1770 6.887376 TTCGTTGCTCTATGATTCTGTTAC 57.113 37.500 0.00 0.00 0.00 2.50
1692 1783 5.597806 TGATTCTGTTACGTGTTCTTGTCT 58.402 37.500 0.00 0.00 0.00 3.41
1703 1797 4.389992 CGTGTTCTTGTCTCATGTAGCATT 59.610 41.667 0.00 0.00 0.00 3.56
1704 1798 5.576774 CGTGTTCTTGTCTCATGTAGCATTA 59.423 40.000 0.00 0.00 0.00 1.90
1718 1816 7.498570 TCATGTAGCATTATGTTGCAGTGATTA 59.501 33.333 6.04 0.00 45.23 1.75
1719 1817 7.806409 TGTAGCATTATGTTGCAGTGATTAT 57.194 32.000 0.00 0.00 45.23 1.28
1720 1818 8.224389 TGTAGCATTATGTTGCAGTGATTATT 57.776 30.769 0.00 0.00 45.23 1.40
1721 1819 8.685427 TGTAGCATTATGTTGCAGTGATTATTT 58.315 29.630 0.00 0.00 45.23 1.40
1722 1820 7.997107 AGCATTATGTTGCAGTGATTATTTG 57.003 32.000 0.00 0.00 45.23 2.32
1723 1821 7.774134 AGCATTATGTTGCAGTGATTATTTGA 58.226 30.769 0.00 0.00 45.23 2.69
1724 1822 7.703621 AGCATTATGTTGCAGTGATTATTTGAC 59.296 33.333 0.00 0.00 45.23 3.18
1725 1823 7.488792 GCATTATGTTGCAGTGATTATTTGACA 59.511 33.333 0.00 0.00 42.31 3.58
1772 1892 1.734117 GTGATTTTGCTGGCGTGCC 60.734 57.895 3.30 3.30 0.00 5.01
1857 1987 5.136828 TGGTGAACTCATTTTGGCTTTCTA 58.863 37.500 0.00 0.00 0.00 2.10
1859 1989 5.461526 GTGAACTCATTTTGGCTTTCTACC 58.538 41.667 0.00 0.00 0.00 3.18
1905 2042 1.892329 GCTGGGTTGGTTGATGTGGAT 60.892 52.381 0.00 0.00 0.00 3.41
1908 2045 4.085733 CTGGGTTGGTTGATGTGGATTAA 58.914 43.478 0.00 0.00 0.00 1.40
1965 3463 7.836842 TCTGAATTATGTGTTGTCTGCTAGTA 58.163 34.615 0.00 0.00 0.00 1.82
1967 3465 7.611770 TGAATTATGTGTTGTCTGCTAGTACT 58.388 34.615 0.00 0.00 0.00 2.73
2005 3517 9.558396 GATATCTCCATTTCTCAGATCTTGTTT 57.442 33.333 0.00 0.00 0.00 2.83
2006 3518 9.917887 ATATCTCCATTTCTCAGATCTTGTTTT 57.082 29.630 0.00 0.00 0.00 2.43
2008 3520 9.745018 ATCTCCATTTCTCAGATCTTGTTTTAA 57.255 29.630 0.00 0.00 0.00 1.52
2009 3521 9.224267 TCTCCATTTCTCAGATCTTGTTTTAAG 57.776 33.333 0.00 0.00 0.00 1.85
2086 3607 2.223805 GCTGGAGTTTTTCTGGTTGTGG 60.224 50.000 0.00 0.00 0.00 4.17
2095 3616 5.413309 TTTTCTGGTTGTGGTTGTTCATT 57.587 34.783 0.00 0.00 0.00 2.57
2096 3617 4.383850 TTCTGGTTGTGGTTGTTCATTG 57.616 40.909 0.00 0.00 0.00 2.82
2097 3618 3.360867 TCTGGTTGTGGTTGTTCATTGT 58.639 40.909 0.00 0.00 0.00 2.71
2098 3619 3.766591 TCTGGTTGTGGTTGTTCATTGTT 59.233 39.130 0.00 0.00 0.00 2.83
2099 3620 4.111916 CTGGTTGTGGTTGTTCATTGTTC 58.888 43.478 0.00 0.00 0.00 3.18
2104 3625 6.269315 GTTGTGGTTGTTCATTGTTCATGTA 58.731 36.000 0.00 0.00 34.06 2.29
2107 3628 6.922407 TGTGGTTGTTCATTGTTCATGTATTG 59.078 34.615 0.00 0.00 34.06 1.90
2135 5038 8.092068 TGATGATTCTTGTGCATCAGAATTTTT 58.908 29.630 19.15 10.61 42.31 1.94
2140 5043 6.210796 TCTTGTGCATCAGAATTTTTCAGTG 58.789 36.000 0.00 0.00 0.00 3.66
2152 5055 7.115378 CAGAATTTTTCAGTGGACAATTACAGC 59.885 37.037 0.00 0.00 0.00 4.40
2166 5074 7.538678 GGACAATTACAGCAGACTACAATTTTG 59.461 37.037 0.00 0.00 0.00 2.44
2196 5104 4.360951 TCCTTTCAGTACCGTCCATTTT 57.639 40.909 0.00 0.00 0.00 1.82
2197 5105 4.721132 TCCTTTCAGTACCGTCCATTTTT 58.279 39.130 0.00 0.00 0.00 1.94
2246 5154 4.600012 ACAAGTTCACAACATATAGCGC 57.400 40.909 0.00 0.00 0.00 5.92
2247 5155 4.000325 ACAAGTTCACAACATATAGCGCA 59.000 39.130 11.47 0.00 0.00 6.09
2248 5156 4.635765 ACAAGTTCACAACATATAGCGCAT 59.364 37.500 11.47 3.63 0.00 4.73
2249 5157 5.123820 ACAAGTTCACAACATATAGCGCATT 59.876 36.000 11.47 0.00 0.00 3.56
2267 5225 7.658261 AGCGCATTGTAAGAGTATATAACAGA 58.342 34.615 11.47 0.00 0.00 3.41
2270 5228 8.417928 CGCATTGTAAGAGTATATAACAGAACG 58.582 37.037 0.00 0.00 0.00 3.95
2347 5336 8.075574 CAGAAATGTGTAATTTAGTGTCAGCAA 58.924 33.333 0.00 0.00 0.00 3.91
2348 5337 8.796475 AGAAATGTGTAATTTAGTGTCAGCAAT 58.204 29.630 0.00 0.00 0.00 3.56
2351 5340 8.792830 ATGTGTAATTTAGTGTCAGCAATACT 57.207 30.769 0.00 0.00 33.39 2.12
2367 5356 7.810658 CAGCAATACTGTCTCATGTTTTAACT 58.189 34.615 0.00 0.00 41.86 2.24
2368 5357 7.747799 CAGCAATACTGTCTCATGTTTTAACTG 59.252 37.037 0.00 0.00 41.86 3.16
2369 5358 7.023575 GCAATACTGTCTCATGTTTTAACTGG 58.976 38.462 0.00 0.00 0.00 4.00
2370 5359 7.094805 GCAATACTGTCTCATGTTTTAACTGGA 60.095 37.037 0.00 0.00 0.00 3.86
2371 5360 8.783093 CAATACTGTCTCATGTTTTAACTGGAA 58.217 33.333 0.00 0.00 0.00 3.53
2379 5368 6.039616 TCATGTTTTAACTGGAAAGCAACAC 58.960 36.000 0.00 0.00 33.92 3.32
2381 5370 5.406649 TGTTTTAACTGGAAAGCAACACTG 58.593 37.500 0.00 0.00 0.00 3.66
2386 5375 1.876156 CTGGAAAGCAACACTGTCTCC 59.124 52.381 0.00 0.00 32.58 3.71
2389 5378 1.527311 GAAAGCAACACTGTCTCCGAC 59.473 52.381 0.00 0.00 28.89 4.79
2400 5401 0.955905 GTCTCCGACTAGATCAGCCC 59.044 60.000 0.00 0.00 0.00 5.19
2406 5407 1.271934 CGACTAGATCAGCCCATGAGG 59.728 57.143 0.00 0.00 42.53 3.86
2420 5423 4.425577 CCATGAGGGAAAGTTTCGAAAG 57.574 45.455 11.66 0.00 40.01 2.62
2421 5424 4.072131 CCATGAGGGAAAGTTTCGAAAGA 58.928 43.478 11.66 0.00 40.01 2.52
2422 5425 4.518970 CCATGAGGGAAAGTTTCGAAAGAA 59.481 41.667 11.66 0.00 44.49 2.52
2423 5426 5.562890 CCATGAGGGAAAGTTTCGAAAGAAC 60.563 44.000 11.66 0.00 45.44 3.01
2440 5455 5.422214 AAGAACGGAAGGTGAATGAGTAT 57.578 39.130 0.00 0.00 0.00 2.12
2441 5456 4.759782 AGAACGGAAGGTGAATGAGTATG 58.240 43.478 0.00 0.00 0.00 2.39
2443 5458 4.819105 ACGGAAGGTGAATGAGTATGAA 57.181 40.909 0.00 0.00 0.00 2.57
2444 5459 5.359194 ACGGAAGGTGAATGAGTATGAAT 57.641 39.130 0.00 0.00 0.00 2.57
2473 5488 7.166167 TCATCACTGCAGATGCTATGATATTT 58.834 34.615 23.35 0.00 43.94 1.40
2475 5490 7.812690 TCACTGCAGATGCTATGATATTTTT 57.187 32.000 23.35 0.00 42.66 1.94
2492 5507 1.670949 TTTTGCAGCTTTCGGTGGCA 61.671 50.000 0.00 0.00 39.02 4.92
2495 5510 2.879907 CAGCTTTCGGTGGCATGG 59.120 61.111 0.00 0.00 35.06 3.66
2513 5528 0.548031 GGATTCCATCCCAGCTCACA 59.452 55.000 0.00 0.00 43.88 3.58
2522 5537 2.540383 TCCCAGCTCACATAGTTCTGT 58.460 47.619 0.00 0.00 0.00 3.41
2524 5539 2.625737 CCAGCTCACATAGTTCTGTGG 58.374 52.381 4.54 0.00 45.29 4.17
2530 5545 2.832129 TCACATAGTTCTGTGGGTCTCC 59.168 50.000 4.54 0.00 45.29 3.71
2554 5569 1.282570 CCGTCGCACTTGCAATGTT 59.717 52.632 0.00 0.00 42.21 2.71
2575 5590 1.539827 GCCGTTTACAATCTTGCTGGT 59.460 47.619 0.00 0.00 0.00 4.00
2576 5591 2.414161 GCCGTTTACAATCTTGCTGGTC 60.414 50.000 0.00 0.00 0.00 4.02
2585 5602 0.547471 TCTTGCTGGTCCATCTGGGA 60.547 55.000 0.00 0.00 45.89 4.37
2598 5615 5.448654 TCCATCTGGGATAAAATTGTGAGG 58.551 41.667 0.00 0.00 42.15 3.86
2604 5621 5.200483 TGGGATAAAATTGTGAGGTCCATC 58.800 41.667 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 14 3.834813 CTCTGAATAGATTGATCCGGGGA 59.165 47.826 0.00 0.00 31.21 4.81
27 29 5.435291 GTGGGATCATGACTTTCTCTGAAT 58.565 41.667 0.00 0.00 0.00 2.57
31 33 2.419297 GCGTGGGATCATGACTTTCTCT 60.419 50.000 0.00 0.00 31.73 3.10
92 96 1.161563 TTCAAGACGACGCCCCAAAC 61.162 55.000 0.00 0.00 0.00 2.93
276 280 2.969950 TCACCCCGCAACTATATAGCTT 59.030 45.455 9.78 1.30 0.00 3.74
281 285 1.608025 CGCATCACCCCGCAACTATAT 60.608 52.381 0.00 0.00 0.00 0.86
333 337 3.135414 CACGTCATGCAAAACATAGGG 57.865 47.619 0.00 0.00 36.64 3.53
347 351 2.626266 TGTAGGAGAAAGAAGCACGTCA 59.374 45.455 0.00 0.00 0.00 4.35
380 384 2.045242 ACTAGGCGGCTCTGACGA 60.045 61.111 17.67 0.00 35.20 4.20
415 419 3.417101 TGTCGTCCTATGCCAAACAATT 58.583 40.909 0.00 0.00 0.00 2.32
475 480 1.811359 CTAACTTCACCGAGGACGACT 59.189 52.381 0.00 0.00 42.66 4.18
544 550 0.728466 GACGAGAGGAACAACGTCGG 60.728 60.000 0.00 0.00 43.60 4.79
589 599 3.175710 AACCCTGGCCGAAGTGGT 61.176 61.111 0.00 0.00 41.21 4.16
752 765 1.907807 TGCTTTGAGCGGGCCAAAT 60.908 52.632 4.39 0.00 46.26 2.32
774 789 3.338249 TGGAGTAGCATTTCTCACTTGC 58.662 45.455 0.00 0.00 36.63 4.01
812 827 1.816224 GATGTGTTTATGCGGGTTGGT 59.184 47.619 0.00 0.00 0.00 3.67
823 838 3.755112 TGGACGTTGGAGATGTGTTTA 57.245 42.857 0.00 0.00 0.00 2.01
846 861 1.203052 GTGAGACGTTGGATCGGGTAA 59.797 52.381 0.00 0.00 34.94 2.85
847 862 0.813184 GTGAGACGTTGGATCGGGTA 59.187 55.000 0.00 0.00 34.94 3.69
848 863 1.590147 GTGAGACGTTGGATCGGGT 59.410 57.895 0.00 0.00 34.94 5.28
851 867 2.497092 CGCGTGAGACGTTGGATCG 61.497 63.158 0.00 0.00 44.73 3.69
861 877 3.760035 GGGAGGAAGCGCGTGAGA 61.760 66.667 8.43 0.00 0.00 3.27
907 935 0.106519 CATTTCGGGAGGGAATGCCT 60.107 55.000 0.00 0.00 37.23 4.75
910 938 1.312815 GAGCATTTCGGGAGGGAATG 58.687 55.000 0.00 0.00 37.08 2.67
938 966 1.347062 GGAAATTTTGGAGGGTGGCA 58.653 50.000 0.00 0.00 0.00 4.92
961 989 2.046729 AGGTGGATGGGTTAAGTAGGGA 59.953 50.000 0.00 0.00 0.00 4.20
1536 1616 6.541278 AGATGACACATCATATCAACACCAAG 59.459 38.462 13.06 0.00 46.01 3.61
1598 1680 6.227298 TCAGATGATAACTGAACTCTTCCC 57.773 41.667 0.00 0.00 40.70 3.97
1603 1685 8.830201 ATTAGCATCAGATGATAACTGAACTC 57.170 34.615 20.80 0.00 43.03 3.01
1640 1730 1.665679 CGAAATAGCGAACAGTGGCAT 59.334 47.619 0.00 0.00 0.00 4.40
1651 1741 5.403766 AGAATCATAGAGCAACGAAATAGCG 59.596 40.000 0.00 0.00 37.29 4.26
1656 1746 6.034577 CGTAACAGAATCATAGAGCAACGAAA 59.965 38.462 0.00 0.00 0.00 3.46
1660 1750 5.577164 ACACGTAACAGAATCATAGAGCAAC 59.423 40.000 0.00 0.00 0.00 4.17
1668 1758 6.223852 AGACAAGAACACGTAACAGAATCAT 58.776 36.000 0.00 0.00 0.00 2.45
1677 1767 4.921515 GCTACATGAGACAAGAACACGTAA 59.078 41.667 0.00 0.00 0.00 3.18
1678 1768 4.022676 TGCTACATGAGACAAGAACACGTA 60.023 41.667 0.00 0.00 0.00 3.57
1680 1770 3.317150 TGCTACATGAGACAAGAACACG 58.683 45.455 0.00 0.00 0.00 4.49
1692 1783 5.184711 TCACTGCAACATAATGCTACATGA 58.815 37.500 0.00 0.00 46.54 3.07
1703 1797 7.488792 GCATTGTCAAATAATCACTGCAACATA 59.511 33.333 0.00 0.00 37.57 2.29
1704 1798 6.311935 GCATTGTCAAATAATCACTGCAACAT 59.688 34.615 0.00 0.00 37.57 2.71
1815 1945 4.280677 CACCAAATCCCTGTACAAACATGT 59.719 41.667 0.00 0.00 34.37 3.21
1857 1987 0.613292 AGACTCACATCGAGCAGGGT 60.613 55.000 0.00 0.00 46.63 4.34
1859 1989 0.813821 TCAGACTCACATCGAGCAGG 59.186 55.000 0.00 0.00 46.63 4.85
1873 2003 2.689983 CCAACCCAGCCATAATTCAGAC 59.310 50.000 0.00 0.00 0.00 3.51
1905 2042 2.103432 TCGCCACTTCACCTTCAGTTAA 59.897 45.455 0.00 0.00 0.00 2.01
1908 2045 0.249911 GTCGCCACTTCACCTTCAGT 60.250 55.000 0.00 0.00 0.00 3.41
2005 3517 6.237901 ACATAACATCCAAGCACAGACTTAA 58.762 36.000 0.00 0.00 0.00 1.85
2006 3518 5.804639 ACATAACATCCAAGCACAGACTTA 58.195 37.500 0.00 0.00 0.00 2.24
2007 3519 4.655963 ACATAACATCCAAGCACAGACTT 58.344 39.130 0.00 0.00 0.00 3.01
2008 3520 4.292186 ACATAACATCCAAGCACAGACT 57.708 40.909 0.00 0.00 0.00 3.24
2009 3521 5.156355 CAAACATAACATCCAAGCACAGAC 58.844 41.667 0.00 0.00 0.00 3.51
2086 3607 8.969121 TCATCAATACATGAACAATGAACAAC 57.031 30.769 0.00 0.00 42.54 3.32
2095 3616 9.181061 ACAAGAATCATCATCAATACATGAACA 57.819 29.630 0.00 0.00 42.54 3.18
2096 3617 9.447040 CACAAGAATCATCATCAATACATGAAC 57.553 33.333 0.00 0.00 42.54 3.18
2097 3618 8.132995 GCACAAGAATCATCATCAATACATGAA 58.867 33.333 0.00 0.00 42.54 2.57
2098 3619 7.283580 TGCACAAGAATCATCATCAATACATGA 59.716 33.333 0.00 0.00 43.67 3.07
2099 3620 7.422399 TGCACAAGAATCATCATCAATACATG 58.578 34.615 0.00 0.00 0.00 3.21
2104 3625 6.546034 TCTGATGCACAAGAATCATCATCAAT 59.454 34.615 4.84 0.00 43.63 2.57
2107 3628 6.373186 TTCTGATGCACAAGAATCATCATC 57.627 37.500 8.47 0.00 43.63 2.92
2131 5034 5.592282 TCTGCTGTAATTGTCCACTGAAAAA 59.408 36.000 0.00 0.00 0.00 1.94
2135 5038 3.324846 AGTCTGCTGTAATTGTCCACTGA 59.675 43.478 0.00 0.00 0.00 3.41
2140 5043 6.743575 AATTGTAGTCTGCTGTAATTGTCC 57.256 37.500 0.00 0.00 0.00 4.02
2204 5112 9.975218 ACTTGTTAGATTAAATGGATGGTACTT 57.025 29.630 0.00 0.00 0.00 2.24
2205 5113 9.975218 AACTTGTTAGATTAAATGGATGGTACT 57.025 29.630 0.00 0.00 0.00 2.73
2207 5115 9.967451 TGAACTTGTTAGATTAAATGGATGGTA 57.033 29.630 0.00 0.00 0.00 3.25
2208 5116 8.739972 GTGAACTTGTTAGATTAAATGGATGGT 58.260 33.333 0.00 0.00 0.00 3.55
2209 5117 8.739039 TGTGAACTTGTTAGATTAAATGGATGG 58.261 33.333 0.00 0.00 0.00 3.51
2212 5120 9.126151 TGTTGTGAACTTGTTAGATTAAATGGA 57.874 29.630 0.00 0.00 0.00 3.41
2213 5121 9.912634 ATGTTGTGAACTTGTTAGATTAAATGG 57.087 29.630 0.00 0.00 0.00 3.16
2232 5140 6.018751 ACTCTTACAATGCGCTATATGTTGTG 60.019 38.462 9.73 8.25 35.01 3.33
2240 5148 9.574458 CTGTTATATACTCTTACAATGCGCTAT 57.426 33.333 9.73 0.00 0.00 2.97
2244 5152 8.417928 CGTTCTGTTATATACTCTTACAATGCG 58.582 37.037 0.00 0.00 0.00 4.73
2246 5154 9.244799 TGCGTTCTGTTATATACTCTTACAATG 57.755 33.333 0.00 0.00 0.00 2.82
2247 5155 9.245962 GTGCGTTCTGTTATATACTCTTACAAT 57.754 33.333 0.00 0.00 0.00 2.71
2248 5156 8.464404 AGTGCGTTCTGTTATATACTCTTACAA 58.536 33.333 0.00 0.00 0.00 2.41
2249 5157 7.993101 AGTGCGTTCTGTTATATACTCTTACA 58.007 34.615 0.00 0.00 0.00 2.41
2267 5225 7.968405 CAGAAAATAATAGCCTTAAAGTGCGTT 59.032 33.333 0.00 0.00 0.00 4.84
2301 5290 6.220726 TCTGTCAGTTAACAGCTATGCATA 57.779 37.500 8.61 6.20 45.12 3.14
2302 5291 5.089970 TCTGTCAGTTAACAGCTATGCAT 57.910 39.130 8.61 3.79 45.12 3.96
2303 5292 4.535526 TCTGTCAGTTAACAGCTATGCA 57.464 40.909 8.61 0.00 45.12 3.96
2304 5293 5.862924 TTTCTGTCAGTTAACAGCTATGC 57.137 39.130 8.61 0.00 45.12 3.14
2307 5296 6.288294 ACACATTTCTGTCAGTTAACAGCTA 58.712 36.000 8.61 0.00 45.12 3.32
2326 5315 8.792830 AGTATTGCTGACACTAAATTACACAT 57.207 30.769 0.00 0.00 0.00 3.21
2347 5336 8.918202 TTTCCAGTTAAAACATGAGACAGTAT 57.082 30.769 0.00 0.00 0.00 2.12
2348 5337 7.041372 GCTTTCCAGTTAAAACATGAGACAGTA 60.041 37.037 0.00 0.00 0.00 2.74
2351 5340 5.592282 TGCTTTCCAGTTAAAACATGAGACA 59.408 36.000 0.00 0.00 0.00 3.41
2352 5341 6.072112 TGCTTTCCAGTTAAAACATGAGAC 57.928 37.500 0.00 0.00 0.00 3.36
2356 5345 6.019640 CAGTGTTGCTTTCCAGTTAAAACATG 60.020 38.462 0.00 0.00 0.00 3.21
2357 5346 6.042143 CAGTGTTGCTTTCCAGTTAAAACAT 58.958 36.000 0.00 0.00 0.00 2.71
2358 5347 5.047660 ACAGTGTTGCTTTCCAGTTAAAACA 60.048 36.000 0.00 0.00 0.00 2.83
2359 5348 5.407502 ACAGTGTTGCTTTCCAGTTAAAAC 58.592 37.500 0.00 0.00 0.00 2.43
2360 5349 5.417580 AGACAGTGTTGCTTTCCAGTTAAAA 59.582 36.000 0.00 0.00 0.00 1.52
2361 5350 4.947388 AGACAGTGTTGCTTTCCAGTTAAA 59.053 37.500 0.00 0.00 0.00 1.52
2362 5351 4.523083 AGACAGTGTTGCTTTCCAGTTAA 58.477 39.130 0.00 0.00 0.00 2.01
2363 5352 4.127171 GAGACAGTGTTGCTTTCCAGTTA 58.873 43.478 0.00 0.00 0.00 2.24
2364 5353 2.945668 GAGACAGTGTTGCTTTCCAGTT 59.054 45.455 0.00 0.00 0.00 3.16
2365 5354 2.565841 GAGACAGTGTTGCTTTCCAGT 58.434 47.619 0.00 0.00 0.00 4.00
2366 5355 1.876156 GGAGACAGTGTTGCTTTCCAG 59.124 52.381 0.00 0.00 0.00 3.86
2367 5356 1.810031 CGGAGACAGTGTTGCTTTCCA 60.810 52.381 0.00 0.00 0.00 3.53
2368 5357 0.868406 CGGAGACAGTGTTGCTTTCC 59.132 55.000 0.00 0.00 0.00 3.13
2369 5358 1.865865 TCGGAGACAGTGTTGCTTTC 58.134 50.000 0.00 0.00 0.00 2.62
2386 5375 1.271934 CCTCATGGGCTGATCTAGTCG 59.728 57.143 0.00 0.00 32.10 4.18
2400 5401 5.452777 GTTCTTTCGAAACTTTCCCTCATG 58.547 41.667 6.47 0.00 0.00 3.07
2406 5407 4.524749 CTTCCGTTCTTTCGAAACTTTCC 58.475 43.478 6.47 0.00 0.00 3.13
2407 5408 4.034858 ACCTTCCGTTCTTTCGAAACTTTC 59.965 41.667 6.47 0.00 0.00 2.62
2408 5409 3.943381 ACCTTCCGTTCTTTCGAAACTTT 59.057 39.130 6.47 0.00 0.00 2.66
2410 5411 2.870411 CACCTTCCGTTCTTTCGAAACT 59.130 45.455 6.47 0.00 0.00 2.66
2413 5414 2.894763 TCACCTTCCGTTCTTTCGAA 57.105 45.000 0.00 0.00 0.00 3.71
2416 5419 4.065789 ACTCATTCACCTTCCGTTCTTTC 58.934 43.478 0.00 0.00 0.00 2.62
2419 5422 4.466370 TCATACTCATTCACCTTCCGTTCT 59.534 41.667 0.00 0.00 0.00 3.01
2420 5423 4.755411 TCATACTCATTCACCTTCCGTTC 58.245 43.478 0.00 0.00 0.00 3.95
2421 5424 4.819105 TCATACTCATTCACCTTCCGTT 57.181 40.909 0.00 0.00 0.00 4.44
2422 5425 4.819105 TTCATACTCATTCACCTTCCGT 57.181 40.909 0.00 0.00 0.00 4.69
2423 5426 5.235186 GTGATTCATACTCATTCACCTTCCG 59.765 44.000 0.00 0.00 32.47 4.30
2425 5428 7.044181 TGAGTGATTCATACTCATTCACCTTC 58.956 38.462 3.89 0.00 46.92 3.46
2426 5429 6.950842 TGAGTGATTCATACTCATTCACCTT 58.049 36.000 3.89 0.00 46.92 3.50
2427 5430 6.550938 TGAGTGATTCATACTCATTCACCT 57.449 37.500 3.89 0.00 46.92 4.00
2440 5455 3.967332 TCTGCAGTGATGAGTGATTCA 57.033 42.857 14.67 0.00 40.85 2.57
2441 5456 3.002451 GCATCTGCAGTGATGAGTGATTC 59.998 47.826 17.60 0.00 44.71 2.52
2443 5458 2.170817 AGCATCTGCAGTGATGAGTGAT 59.829 45.455 17.60 0.00 44.71 3.06
2444 5459 1.553704 AGCATCTGCAGTGATGAGTGA 59.446 47.619 17.60 0.00 44.71 3.41
2473 5488 1.067250 GCCACCGAAAGCTGCAAAA 59.933 52.632 1.02 0.00 0.00 2.44
2475 5490 1.902918 ATGCCACCGAAAGCTGCAA 60.903 52.632 1.02 0.00 35.30 4.08
2479 5494 0.323725 AATCCATGCCACCGAAAGCT 60.324 50.000 0.00 0.00 0.00 3.74
2482 5497 0.038890 TGGAATCCATGCCACCGAAA 59.961 50.000 0.00 0.00 0.00 3.46
2495 5510 2.653234 ATGTGAGCTGGGATGGAATC 57.347 50.000 0.00 0.00 44.55 2.52
2513 5528 0.824759 GCGGAGACCCACAGAACTAT 59.175 55.000 0.00 0.00 0.00 2.12
2554 5569 1.539388 CCAGCAAGATTGTAAACGGCA 59.461 47.619 0.00 0.00 0.00 5.69
2566 5581 0.547471 TCCCAGATGGACCAGCAAGA 60.547 55.000 13.21 2.31 38.61 3.02
2576 5591 5.203528 ACCTCACAATTTTATCCCAGATGG 58.796 41.667 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.