Multiple sequence alignment - TraesCS6D01G358300

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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 TraesCS6D01G358300 chr6D 100.000 3283 0 0 1 3283 451170051 451166769 0.000000e+00 6063.0
1 TraesCS6D01G358300 chr6D 84.103 390 48 9 1994 2381 49618102 49618479 6.690000e-97 364.0
2 TraesCS6D01G358300 chr6B 89.397 1924 130 30 825 2703 685340883 685338989 0.000000e+00 2355.0
3 TraesCS6D01G358300 chr6B 88.053 837 55 21 1 793 58307609 58308444 0.000000e+00 950.0
4 TraesCS6D01G358300 chr6B 91.736 484 27 6 2806 3283 685338538 685338062 0.000000e+00 660.0
5 TraesCS6D01G358300 chr6B 90.769 65 6 0 1875 1939 250665410 250665346 1.620000e-13 87.9
6 TraesCS6D01G358300 chr6A 86.193 1521 101 54 1226 2703 596901566 596900112 0.000000e+00 1544.0
7 TraesCS6D01G358300 chr6A 95.060 587 19 5 2702 3283 596900068 596899487 0.000000e+00 915.0
8 TraesCS6D01G358300 chr7D 94.349 814 22 7 1 793 123213867 123214677 0.000000e+00 1227.0
9 TraesCS6D01G358300 chr7D 82.368 397 58 9 1994 2388 18030612 18030998 5.250000e-88 335.0
10 TraesCS6D01G358300 chr7D 97.006 167 5 0 626 792 123214677 123214843 6.940000e-72 281.0
11 TraesCS6D01G358300 chr7D 81.364 220 20 5 1875 2073 552330426 552330207 3.390000e-35 159.0
12 TraesCS6D01G358300 chr7D 90.083 121 8 2 1 120 83325309 83325426 1.580000e-33 154.0
13 TraesCS6D01G358300 chr7D 80.930 215 20 6 1875 2068 72833778 72833564 2.040000e-32 150.0
14 TraesCS6D01G358300 chr3D 92.241 812 19 10 2 793 21378961 21378174 0.000000e+00 1110.0
15 TraesCS6D01G358300 chr3D 89.367 837 44 16 2 794 460259972 460260807 0.000000e+00 1011.0
16 TraesCS6D01G358300 chr3D 86.409 699 63 14 1 670 346819747 346820442 0.000000e+00 736.0
17 TraesCS6D01G358300 chr3D 84.606 799 54 28 2 754 164524991 164524216 0.000000e+00 730.0
18 TraesCS6D01G358300 chr3D 82.243 214 17 5 1875 2067 506924564 506924777 7.290000e-37 165.0
19 TraesCS6D01G358300 chr7A 88.717 842 39 13 1 792 78081572 78082407 0.000000e+00 977.0
20 TraesCS6D01G358300 chr7A 83.077 325 46 6 2065 2388 724638158 724638474 1.490000e-73 287.0
21 TraesCS6D01G358300 chr2A 88.743 835 45 11 1 792 712979645 712978817 0.000000e+00 976.0
22 TraesCS6D01G358300 chr2A 79.902 204 36 4 2296 2496 399423610 399423409 9.490000e-31 145.0
23 TraesCS6D01G358300 chr2A 80.874 183 32 2 2296 2477 397874637 397874817 1.230000e-29 141.0
24 TraesCS6D01G358300 chr7B 88.186 838 52 18 1 792 217787311 217786475 0.000000e+00 955.0
25 TraesCS6D01G358300 chr2B 88.144 835 54 20 1 791 695894655 695893822 0.000000e+00 952.0
26 TraesCS6D01G358300 chr2B 88.144 835 53 21 1 791 695931357 695930525 0.000000e+00 952.0
27 TraesCS6D01G358300 chr2B 87.665 835 56 22 1 791 695967358 695966527 0.000000e+00 928.0
28 TraesCS6D01G358300 chr2B 83.805 389 52 6 1994 2381 38902500 38902122 3.110000e-95 359.0
29 TraesCS6D01G358300 chr1B 87.618 638 38 19 1 612 39669645 39670267 0.000000e+00 702.0
30 TraesCS6D01G358300 chr1B 82.462 325 48 7 2065 2388 127646655 127646971 3.230000e-70 276.0
31 TraesCS6D01G358300 chr1B 92.742 124 7 1 1 122 389319877 389320000 9.360000e-41 178.0
32 TraesCS6D01G358300 chr1B 79.808 208 33 7 2295 2496 478104783 478104579 3.410000e-30 143.0
33 TraesCS6D01G358300 chr3B 83.812 383 51 7 1994 2375 557795600 557795972 1.450000e-93 353.0
34 TraesCS6D01G358300 chr5B 82.872 397 56 6 1994 2388 496304521 496304135 2.420000e-91 346.0
35 TraesCS6D01G358300 chr5D 82.353 221 17 6 1875 2073 31262431 31262211 4.360000e-39 172.0
36 TraesCS6D01G358300 chr5D 81.860 215 18 5 1875 2068 356536561 356536347 9.430000e-36 161.0
37 TraesCS6D01G358300 chr5D 79.227 207 36 5 2295 2496 47937166 47937370 1.590000e-28 137.0
38 TraesCS6D01G358300 chr1D 82.326 215 17 5 1875 2068 299570855 299571069 2.030000e-37 167.0
39 TraesCS6D01G358300 chr2D 79.612 206 35 5 2296 2496 346050801 346051004 1.230000e-29 141.0
40 TraesCS6D01G358300 chr4D 79.024 205 36 5 2296 2495 486496313 486496111 2.060000e-27 134.0
41 TraesCS6D01G358300 chr4D 78.431 204 39 4 2296 2496 80235230 80235029 9.560000e-26 128.0


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 TraesCS6D01G358300 chr6D 451166769 451170051 3282 True 6063.0 6063 100.0000 1 3283 1 chr6D.!!$R1 3282
1 TraesCS6D01G358300 chr6B 685338062 685340883 2821 True 1507.5 2355 90.5665 825 3283 2 chr6B.!!$R2 2458
2 TraesCS6D01G358300 chr6B 58307609 58308444 835 False 950.0 950 88.0530 1 793 1 chr6B.!!$F1 792
3 TraesCS6D01G358300 chr6A 596899487 596901566 2079 True 1229.5 1544 90.6265 1226 3283 2 chr6A.!!$R1 2057
4 TraesCS6D01G358300 chr7D 123213867 123214843 976 False 754.0 1227 95.6775 1 793 2 chr7D.!!$F3 792
5 TraesCS6D01G358300 chr3D 21378174 21378961 787 True 1110.0 1110 92.2410 2 793 1 chr3D.!!$R1 791
6 TraesCS6D01G358300 chr3D 460259972 460260807 835 False 1011.0 1011 89.3670 2 794 1 chr3D.!!$F2 792
7 TraesCS6D01G358300 chr3D 346819747 346820442 695 False 736.0 736 86.4090 1 670 1 chr3D.!!$F1 669
8 TraesCS6D01G358300 chr3D 164524216 164524991 775 True 730.0 730 84.6060 2 754 1 chr3D.!!$R2 752
9 TraesCS6D01G358300 chr7A 78081572 78082407 835 False 977.0 977 88.7170 1 792 1 chr7A.!!$F1 791
10 TraesCS6D01G358300 chr2A 712978817 712979645 828 True 976.0 976 88.7430 1 792 1 chr2A.!!$R2 791
11 TraesCS6D01G358300 chr7B 217786475 217787311 836 True 955.0 955 88.1860 1 792 1 chr7B.!!$R1 791
12 TraesCS6D01G358300 chr2B 695893822 695894655 833 True 952.0 952 88.1440 1 791 1 chr2B.!!$R2 790
13 TraesCS6D01G358300 chr2B 695930525 695931357 832 True 952.0 952 88.1440 1 791 1 chr2B.!!$R3 790
14 TraesCS6D01G358300 chr2B 695966527 695967358 831 True 928.0 928 87.6650 1 791 1 chr2B.!!$R4 790
15 TraesCS6D01G358300 chr1B 39669645 39670267 622 False 702.0 702 87.6180 1 612 1 chr1B.!!$F1 611

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
943 1061 0.321298 GTAAACAGGAGCTTGCCGGA 60.321 55.0 5.05 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2646 2824 1.133199 AGGTGGATTGGCAGGTTCAAA 60.133 47.619 0.0 0.0 0.0 2.69 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
376 423 4.754322 AGCAAATTTTGAAACACCGAACT 58.246 34.783 13.26 0.00 0.00 3.01
638 715 1.109920 TGGCTAGACTCGCATCTCCC 61.110 60.000 0.00 0.00 0.00 4.30
794 873 0.605589 GGCGAATAGGGAATTCCGGG 60.606 60.000 18.30 4.81 40.91 5.73
795 874 0.395312 GCGAATAGGGAATTCCGGGA 59.605 55.000 18.30 6.25 40.91 5.14
796 875 1.003233 GCGAATAGGGAATTCCGGGAT 59.997 52.381 18.30 8.32 40.91 3.85
797 876 2.935676 GCGAATAGGGAATTCCGGGATC 60.936 54.545 18.30 12.44 40.91 3.36
798 877 2.567615 CGAATAGGGAATTCCGGGATCT 59.432 50.000 18.30 11.38 40.91 2.75
799 878 3.368531 CGAATAGGGAATTCCGGGATCTC 60.369 52.174 18.30 8.71 40.91 2.75
800 879 2.025636 TAGGGAATTCCGGGATCTCC 57.974 55.000 18.30 13.94 41.52 3.71
809 888 3.035727 GGGATCTCCGCTCGAGTC 58.964 66.667 15.13 5.54 39.84 3.36
810 889 1.824329 GGGATCTCCGCTCGAGTCA 60.824 63.158 15.13 0.00 39.84 3.41
811 890 1.357334 GGATCTCCGCTCGAGTCAC 59.643 63.158 15.13 0.00 39.84 3.67
812 891 1.357334 GATCTCCGCTCGAGTCACC 59.643 63.158 15.13 0.00 39.84 4.02
813 892 2.065906 GATCTCCGCTCGAGTCACCC 62.066 65.000 15.13 0.00 39.84 4.61
814 893 2.559922 ATCTCCGCTCGAGTCACCCT 62.560 60.000 15.13 0.00 39.84 4.34
815 894 1.451567 CTCCGCTCGAGTCACCCTA 60.452 63.158 15.13 0.00 33.51 3.53
817 896 2.409651 CGCTCGAGTCACCCTAGC 59.590 66.667 15.13 0.00 0.00 3.42
818 897 2.407428 CGCTCGAGTCACCCTAGCA 61.407 63.158 15.13 0.00 32.69 3.49
819 898 1.435515 GCTCGAGTCACCCTAGCAG 59.564 63.158 15.13 0.00 33.38 4.24
938 1056 1.795768 TGCGAGTAAACAGGAGCTTG 58.204 50.000 0.00 0.00 0.00 4.01
939 1057 0.444260 GCGAGTAAACAGGAGCTTGC 59.556 55.000 0.00 0.00 0.00 4.01
941 1059 1.079503 GAGTAAACAGGAGCTTGCCG 58.920 55.000 0.00 0.00 0.00 5.69
943 1061 0.321298 GTAAACAGGAGCTTGCCGGA 60.321 55.000 5.05 0.00 0.00 5.14
944 1062 0.398696 TAAACAGGAGCTTGCCGGAA 59.601 50.000 5.05 0.00 0.00 4.30
945 1063 0.890996 AAACAGGAGCTTGCCGGAAG 60.891 55.000 5.05 7.51 34.41 3.46
995 1113 1.381327 ATCGGCGAGGAAGGAGGAA 60.381 57.895 17.22 0.00 0.00 3.36
1000 1121 1.115467 GCGAGGAAGGAGGAAGATGA 58.885 55.000 0.00 0.00 0.00 2.92
1001 1122 1.691434 GCGAGGAAGGAGGAAGATGAT 59.309 52.381 0.00 0.00 0.00 2.45
1006 1127 2.371510 GGAAGGAGGAAGATGATGGGAG 59.628 54.545 0.00 0.00 0.00 4.30
1009 1130 2.021639 AGGAGGAAGATGATGGGAGGAA 60.022 50.000 0.00 0.00 0.00 3.36
1011 1132 3.312890 GAGGAAGATGATGGGAGGAAGA 58.687 50.000 0.00 0.00 0.00 2.87
1022 1143 0.761323 GGAGGAAGAGGGGGAGTAGC 60.761 65.000 0.00 0.00 0.00 3.58
1023 1144 0.032017 GAGGAAGAGGGGGAGTAGCA 60.032 60.000 0.00 0.00 0.00 3.49
1029 1150 3.081409 GGGGGAGTAGCAAGCGGA 61.081 66.667 0.00 0.00 0.00 5.54
1211 1338 1.541368 CCTTCCCCTCTTCCCCACA 60.541 63.158 0.00 0.00 0.00 4.17
1213 1340 0.548510 CTTCCCCTCTTCCCCACATC 59.451 60.000 0.00 0.00 0.00 3.06
1214 1341 0.178846 TTCCCCTCTTCCCCACATCA 60.179 55.000 0.00 0.00 0.00 3.07
1215 1342 0.046242 TCCCCTCTTCCCCACATCAT 59.954 55.000 0.00 0.00 0.00 2.45
1217 1344 1.133668 CCCCTCTTCCCCACATCATTC 60.134 57.143 0.00 0.00 0.00 2.67
1218 1345 1.849039 CCCTCTTCCCCACATCATTCT 59.151 52.381 0.00 0.00 0.00 2.40
1219 1346 2.422519 CCCTCTTCCCCACATCATTCTG 60.423 54.545 0.00 0.00 0.00 3.02
1220 1347 2.295885 CTCTTCCCCACATCATTCTGC 58.704 52.381 0.00 0.00 0.00 4.26
1243 1375 1.529309 GGATCCTCAGGCCTGTTCC 59.471 63.158 31.58 25.84 0.00 3.62
1261 1393 1.820906 CACGGGTGGATCATGGCTG 60.821 63.158 0.00 0.00 0.00 4.85
1268 1400 1.058428 TGGATCATGGCTGGGAGGAG 61.058 60.000 0.00 0.00 0.00 3.69
1269 1401 1.759881 GATCATGGCTGGGAGGAGG 59.240 63.158 0.00 0.00 0.00 4.30
1271 1403 0.767446 ATCATGGCTGGGAGGAGGAG 60.767 60.000 0.00 0.00 0.00 3.69
1272 1404 1.383664 CATGGCTGGGAGGAGGAGA 60.384 63.158 0.00 0.00 0.00 3.71
1274 1406 2.766229 GGCTGGGAGGAGGAGACC 60.766 72.222 0.00 0.00 0.00 3.85
1285 1417 2.506065 AGGAGACCCTCGAATTCGG 58.494 57.895 26.47 16.85 38.86 4.30
1286 1418 1.043673 AGGAGACCCTCGAATTCGGG 61.044 60.000 26.47 23.86 46.26 5.14
1305 1437 0.179124 GGCACCTCGCTTCTGTAGAG 60.179 60.000 0.00 0.00 41.91 2.43
1314 1446 2.428890 CGCTTCTGTAGAGTGGATTCCT 59.571 50.000 3.95 0.00 0.00 3.36
1316 1448 4.098044 CGCTTCTGTAGAGTGGATTCCTAA 59.902 45.833 3.95 0.00 0.00 2.69
1318 1450 5.452636 GCTTCTGTAGAGTGGATTCCTAAGG 60.453 48.000 3.95 0.00 0.00 2.69
1331 1463 5.765677 GGATTCCTAAGGGCAAATCTTAGTC 59.234 44.000 9.20 2.44 41.04 2.59
1333 1465 3.134081 TCCTAAGGGCAAATCTTAGTCGG 59.866 47.826 9.20 0.00 41.04 4.79
1334 1466 2.420058 AAGGGCAAATCTTAGTCGGG 57.580 50.000 0.00 0.00 0.00 5.14
1335 1467 1.286248 AGGGCAAATCTTAGTCGGGT 58.714 50.000 0.00 0.00 0.00 5.28
1336 1468 1.633945 AGGGCAAATCTTAGTCGGGTT 59.366 47.619 0.00 0.00 0.00 4.11
1338 1470 2.014857 GGCAAATCTTAGTCGGGTTCC 58.985 52.381 0.00 0.00 0.00 3.62
1339 1471 2.617021 GGCAAATCTTAGTCGGGTTCCA 60.617 50.000 0.00 0.00 0.00 3.53
1340 1472 2.678336 GCAAATCTTAGTCGGGTTCCAG 59.322 50.000 0.00 0.00 0.00 3.86
1341 1473 2.678336 CAAATCTTAGTCGGGTTCCAGC 59.322 50.000 0.00 0.00 0.00 4.85
1360 1492 1.755179 CCGAGTCCTGGCATTTCATT 58.245 50.000 0.00 0.00 0.00 2.57
1365 1497 2.827921 AGTCCTGGCATTTCATTTCACC 59.172 45.455 0.00 0.00 0.00 4.02
1399 1531 7.606456 TGTAAGAAACAATGGATCCAGACTTAC 59.394 37.037 26.42 26.42 37.51 2.34
1402 1534 7.177878 AGAAACAATGGATCCAGACTTACATT 58.822 34.615 21.33 3.74 0.00 2.71
1407 1541 4.454678 TGGATCCAGACTTACATTGCATC 58.545 43.478 11.44 0.00 0.00 3.91
1460 1594 0.979709 CCTGCTCCCAGTCCAGATGA 60.980 60.000 0.00 0.00 37.38 2.92
1480 1614 2.996249 TCTGAGAATTAGCTGGCTGG 57.004 50.000 5.25 0.00 0.00 4.85
1489 1623 1.289160 TAGCTGGCTGGTCAAGGATT 58.711 50.000 5.25 0.00 0.00 3.01
1490 1624 0.034670 AGCTGGCTGGTCAAGGATTC 60.035 55.000 0.00 0.00 0.00 2.52
1491 1625 0.322816 GCTGGCTGGTCAAGGATTCA 60.323 55.000 0.00 0.00 0.00 2.57
1492 1626 1.887956 GCTGGCTGGTCAAGGATTCAA 60.888 52.381 0.00 0.00 0.00 2.69
1532 1668 3.843893 ATTGGGGCATTATTTCCTTGC 57.156 42.857 0.00 0.00 35.64 4.01
1534 1670 2.387757 TGGGGCATTATTTCCTTGCTC 58.612 47.619 0.00 0.00 36.10 4.26
1542 1678 6.417930 GGCATTATTTCCTTGCTCGTTTATTC 59.582 38.462 0.00 0.00 36.62 1.75
1549 1685 3.334691 CTTGCTCGTTTATTCCCACTGA 58.665 45.455 0.00 0.00 0.00 3.41
1551 1687 3.950397 TGCTCGTTTATTCCCACTGAAT 58.050 40.909 0.00 0.00 45.64 2.57
1555 1691 6.704493 TGCTCGTTTATTCCCACTGAATATAC 59.296 38.462 0.00 0.00 43.66 1.47
1560 1696 7.848491 GTTTATTCCCACTGAATATACGTGTC 58.152 38.462 0.00 0.00 43.66 3.67
1576 1713 0.678950 TGTCTGCCATTGTCGTCTCA 59.321 50.000 0.00 0.00 0.00 3.27
1580 1717 1.462283 CTGCCATTGTCGTCTCAAGTG 59.538 52.381 0.00 0.00 0.00 3.16
1633 1773 4.836125 TGCTTAAGCTATATTTGCCTGC 57.164 40.909 26.90 0.00 42.66 4.85
1666 1814 9.360514 CAGAACATTGTTGATTTTGATTTTTCG 57.639 29.630 6.80 0.00 0.00 3.46
1686 1834 1.134965 GCATAGCGGTTGTCTGTCTCT 60.135 52.381 0.00 0.00 0.00 3.10
1762 1914 5.911421 TCGTGTTATCTTGATGTTTTGTCG 58.089 37.500 0.00 0.00 0.00 4.35
1788 1940 1.099689 TGGCTAAGCGGTTTATTGGC 58.900 50.000 4.64 7.02 32.66 4.52
1941 2095 5.130311 ACTTTTAAAGGTTGGTTCCATTGCT 59.870 36.000 9.64 0.00 0.00 3.91
1942 2096 5.622346 TTTAAAGGTTGGTTCCATTGCTT 57.378 34.783 0.00 0.00 0.00 3.91
1966 2143 4.212214 GCATTCTCCCATGATTTACGTCTC 59.788 45.833 0.00 0.00 0.00 3.36
1974 2151 3.079960 TGATTTACGTCTCCGATGCTC 57.920 47.619 0.00 0.00 37.88 4.26
2084 2261 6.642131 GCAAATTTCAGTGCATTTTCTCACTA 59.358 34.615 0.00 0.00 41.19 2.74
2182 2359 2.749076 TGTACATGCCTTGCTTAAGCTG 59.251 45.455 26.90 17.84 42.66 4.24
2189 2366 2.208431 CCTTGCTTAAGCTGATCTCCG 58.792 52.381 26.90 7.29 42.66 4.63
2493 2671 3.119849 GCATAAGTGTGTTTTCGGCTCAT 60.120 43.478 0.00 0.00 0.00 2.90
2568 2746 1.003116 GCAGCTGTACATATGCAGTGC 60.003 52.381 21.35 8.58 40.46 4.40
2593 2771 7.308830 GCAGTGATGGTTATATCCAATTCCTTC 60.309 40.741 6.62 0.22 41.09 3.46
2646 2824 5.385198 TGGCTGTAGACATTCCTTTTCTTT 58.615 37.500 0.00 0.00 0.00 2.52
2669 2847 0.038744 AACCTGCCAATCCACCTGAG 59.961 55.000 0.00 0.00 0.00 3.35
2722 3162 1.675801 CAGAGGCCTGTCTTGCTCA 59.324 57.895 12.00 0.00 35.70 4.26
2739 3179 2.891112 CTCATCTTGTCTCTGACCAGC 58.109 52.381 0.00 0.00 0.00 4.85
2831 3319 7.437793 CAACAGTTGCCAAATCCAAAATATT 57.562 32.000 0.00 0.00 0.00 1.28
2969 3509 1.842052 ATGCATCATGCTTGTGACCA 58.158 45.000 11.84 0.00 45.31 4.02
3038 3578 0.392998 AAGAACACTATGCCAGGCGG 60.393 55.000 7.03 1.93 0.00 6.13
3155 3700 3.281727 TCAGCACTTCAAGAACCAACT 57.718 42.857 0.00 0.00 0.00 3.16
3168 3713 6.940298 TCAAGAACCAACTTTACAAGATAGGG 59.060 38.462 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
376 423 9.956720 ACAAAATTTGTTTGTGTTTCAAAATGA 57.043 22.222 5.41 0.00 45.84 2.57
567 626 9.225682 TCCTATTATATGTTCCCTTCTTTCACT 57.774 33.333 0.00 0.00 0.00 3.41
638 715 0.396811 ACCTCAAACCTCCCACTTCG 59.603 55.000 0.00 0.00 0.00 3.79
794 873 1.357334 GGTGACTCGAGCGGAGATC 59.643 63.158 13.61 1.54 46.23 2.75
795 874 2.122167 GGGTGACTCGAGCGGAGAT 61.122 63.158 13.61 0.00 46.23 2.75
796 875 1.907222 TAGGGTGACTCGAGCGGAGA 61.907 60.000 13.61 0.00 46.23 3.71
798 877 1.451567 CTAGGGTGACTCGAGCGGA 60.452 63.158 13.61 0.00 0.00 5.54
799 878 3.111939 CTAGGGTGACTCGAGCGG 58.888 66.667 13.61 0.00 0.00 5.52
800 879 2.329678 CTGCTAGGGTGACTCGAGCG 62.330 65.000 13.61 4.31 35.88 5.03
801 880 1.435515 CTGCTAGGGTGACTCGAGC 59.564 63.158 13.61 10.81 0.00 5.03
802 881 2.111162 CCTGCTAGGGTGACTCGAG 58.889 63.158 11.84 11.84 0.00 4.04
803 882 4.338815 CCTGCTAGGGTGACTCGA 57.661 61.111 0.00 0.00 0.00 4.04
917 1035 2.086054 AGCTCCTGTTTACTCGCAAG 57.914 50.000 0.00 0.00 0.00 4.01
918 1036 2.143122 CAAGCTCCTGTTTACTCGCAA 58.857 47.619 0.00 0.00 0.00 4.85
919 1037 1.795768 CAAGCTCCTGTTTACTCGCA 58.204 50.000 0.00 0.00 0.00 5.10
954 1072 3.966543 CTCCACACCCCACACCCC 61.967 72.222 0.00 0.00 0.00 4.95
955 1073 3.966543 CCTCCACACCCCACACCC 61.967 72.222 0.00 0.00 0.00 4.61
956 1074 3.966543 CCCTCCACACCCCACACC 61.967 72.222 0.00 0.00 0.00 4.16
957 1075 4.660938 GCCCTCCACACCCCACAC 62.661 72.222 0.00 0.00 0.00 3.82
995 1113 1.415716 CCCCTCTTCCTCCCATCATCT 60.416 57.143 0.00 0.00 0.00 2.90
1000 1121 1.319799 CTCCCCCTCTTCCTCCCAT 59.680 63.158 0.00 0.00 0.00 4.00
1001 1122 0.858598 TACTCCCCCTCTTCCTCCCA 60.859 60.000 0.00 0.00 0.00 4.37
1006 1127 0.833949 CTTGCTACTCCCCCTCTTCC 59.166 60.000 0.00 0.00 0.00 3.46
1009 1130 2.060980 CGCTTGCTACTCCCCCTCT 61.061 63.158 0.00 0.00 0.00 3.69
1011 1132 3.083997 CCGCTTGCTACTCCCCCT 61.084 66.667 0.00 0.00 0.00 4.79
1022 1143 3.474570 CCCCTCCTCCTCCGCTTG 61.475 72.222 0.00 0.00 0.00 4.01
1023 1144 4.806339 CCCCCTCCTCCTCCGCTT 62.806 72.222 0.00 0.00 0.00 4.68
1191 1312 3.421386 GGGGAAGAGGGGAAGGGC 61.421 72.222 0.00 0.00 0.00 5.19
1211 1338 0.034059 GGATCCGTCGGCAGAATGAT 59.966 55.000 6.34 0.00 39.69 2.45
1213 1340 0.598680 GAGGATCCGTCGGCAGAATG 60.599 60.000 6.34 0.00 40.87 2.67
1214 1341 1.043116 TGAGGATCCGTCGGCAGAAT 61.043 55.000 6.34 0.00 0.00 2.40
1215 1342 1.667154 CTGAGGATCCGTCGGCAGAA 61.667 60.000 6.34 0.00 31.61 3.02
1217 1344 2.415010 CTGAGGATCCGTCGGCAG 59.585 66.667 6.34 3.81 0.00 4.85
1218 1345 3.147595 CCTGAGGATCCGTCGGCA 61.148 66.667 6.34 0.00 0.00 5.69
1219 1346 4.593864 GCCTGAGGATCCGTCGGC 62.594 72.222 20.40 20.40 0.00 5.54
1220 1347 3.917760 GGCCTGAGGATCCGTCGG 61.918 72.222 0.65 4.39 0.00 4.79
1243 1375 1.820906 CAGCCATGATCCACCCGTG 60.821 63.158 0.00 0.00 0.00 4.94
1268 1400 1.442148 CCCGAATTCGAGGGTCTCC 59.558 63.158 28.76 0.00 42.67 3.71
1269 1401 1.442148 CCCCGAATTCGAGGGTCTC 59.558 63.158 30.87 0.00 46.17 3.36
1271 1403 2.203029 GCCCCGAATTCGAGGGTC 60.203 66.667 34.95 27.78 46.17 4.46
1272 1404 3.006728 TGCCCCGAATTCGAGGGT 61.007 61.111 34.95 0.00 46.17 4.34
1274 1406 2.513897 GGTGCCCCGAATTCGAGG 60.514 66.667 28.76 25.74 43.02 4.63
1276 1408 2.582436 GAGGTGCCCCGAATTCGA 59.418 61.111 28.76 6.12 43.02 3.71
1277 1409 2.890474 CGAGGTGCCCCGAATTCG 60.890 66.667 20.92 20.92 39.44 3.34
1278 1410 3.202706 GCGAGGTGCCCCGAATTC 61.203 66.667 0.00 0.00 37.76 2.17
1287 1419 0.528470 ACTCTACAGAAGCGAGGTGC 59.472 55.000 0.00 0.00 46.98 5.01
1288 1420 1.135257 CCACTCTACAGAAGCGAGGTG 60.135 57.143 0.00 0.00 0.00 4.00
1289 1421 1.178276 CCACTCTACAGAAGCGAGGT 58.822 55.000 0.00 0.00 0.00 3.85
1290 1422 1.464734 TCCACTCTACAGAAGCGAGG 58.535 55.000 0.00 0.00 0.00 4.63
1291 1423 3.490078 GGAATCCACTCTACAGAAGCGAG 60.490 52.174 0.00 0.00 0.00 5.03
1292 1424 2.427453 GGAATCCACTCTACAGAAGCGA 59.573 50.000 0.00 0.00 0.00 4.93
1293 1425 2.428890 AGGAATCCACTCTACAGAAGCG 59.571 50.000 0.61 0.00 0.00 4.68
1294 1426 5.452636 CCTTAGGAATCCACTCTACAGAAGC 60.453 48.000 0.61 0.00 0.00 3.86
1295 1427 5.069781 CCCTTAGGAATCCACTCTACAGAAG 59.930 48.000 0.61 0.00 33.47 2.85
1296 1428 4.962995 CCCTTAGGAATCCACTCTACAGAA 59.037 45.833 0.61 0.00 33.47 3.02
1305 1437 3.903467 AGATTTGCCCTTAGGAATCCAC 58.097 45.455 0.61 0.00 30.12 4.02
1314 1446 2.841881 ACCCGACTAAGATTTGCCCTTA 59.158 45.455 0.00 0.00 0.00 2.69
1316 1448 1.286248 ACCCGACTAAGATTTGCCCT 58.714 50.000 0.00 0.00 0.00 5.19
1318 1450 2.014857 GGAACCCGACTAAGATTTGCC 58.985 52.381 0.00 0.00 0.00 4.52
1331 1463 4.452733 GGACTCGGCTGGAACCCG 62.453 72.222 0.00 0.00 46.88 5.28
1333 1465 2.266055 CAGGACTCGGCTGGAACC 59.734 66.667 0.00 0.00 0.00 3.62
1334 1466 2.266055 CCAGGACTCGGCTGGAAC 59.734 66.667 0.00 0.00 40.50 3.62
1335 1467 3.706373 GCCAGGACTCGGCTGGAA 61.706 66.667 0.00 0.00 46.56 3.53
1341 1473 1.755179 AATGAAATGCCAGGACTCGG 58.245 50.000 0.00 0.00 0.00 4.63
1344 1476 2.827921 GGTGAAATGAAATGCCAGGACT 59.172 45.455 0.00 0.00 0.00 3.85
1345 1477 2.562298 TGGTGAAATGAAATGCCAGGAC 59.438 45.455 0.00 0.00 0.00 3.85
1351 1483 4.950434 CCCAAATGGTGAAATGAAATGC 57.050 40.909 0.00 0.00 0.00 3.56
1365 1497 6.095432 TCCATTGTTTCTTACACCCAAATG 57.905 37.500 0.00 0.00 36.21 2.32
1383 1515 4.858850 TGCAATGTAAGTCTGGATCCATT 58.141 39.130 16.63 9.70 0.00 3.16
1407 1541 7.432350 AGAAACTAGAAAAAGTGAGCATCTG 57.568 36.000 0.00 0.00 34.92 2.90
1447 1581 2.675583 TCTCAGATCATCTGGACTGGG 58.324 52.381 14.96 0.00 44.39 4.45
1460 1594 2.776536 ACCAGCCAGCTAATTCTCAGAT 59.223 45.455 0.00 0.00 0.00 2.90
1476 1610 4.381292 CCTTGAATTGAATCCTTGACCAGC 60.381 45.833 0.00 0.00 0.00 4.85
1480 1614 4.344104 TCCCCTTGAATTGAATCCTTGAC 58.656 43.478 0.00 0.00 0.00 3.18
1489 1623 4.996793 TCATCAAACTCCCCTTGAATTGA 58.003 39.130 0.00 0.00 36.43 2.57
1490 1624 5.726980 TTCATCAAACTCCCCTTGAATTG 57.273 39.130 0.00 0.00 36.43 2.32
1491 1625 6.296030 CCAATTCATCAAACTCCCCTTGAATT 60.296 38.462 0.00 0.00 41.80 2.17
1492 1626 5.188359 CCAATTCATCAAACTCCCCTTGAAT 59.812 40.000 0.00 0.00 36.43 2.57
1542 1678 3.123804 GCAGACACGTATATTCAGTGGG 58.876 50.000 0.00 1.86 39.95 4.61
1549 1685 3.802139 CGACAATGGCAGACACGTATATT 59.198 43.478 0.00 0.00 0.00 1.28
1551 1687 2.164827 ACGACAATGGCAGACACGTATA 59.835 45.455 9.90 0.00 0.00 1.47
1555 1691 0.667487 AGACGACAATGGCAGACACG 60.667 55.000 0.00 0.00 0.00 4.49
1560 1696 1.462283 CACTTGAGACGACAATGGCAG 59.538 52.381 0.00 0.00 0.00 4.85
1576 1713 2.363038 TCTTGCTGAAAAGCATGCACTT 59.637 40.909 21.98 12.35 44.94 3.16
1580 1717 4.449743 TCAAAATCTTGCTGAAAAGCATGC 59.550 37.500 10.51 10.51 44.94 4.06
1633 1773 8.298854 TCAAAATCAACAATGTTCTGTATGGAG 58.701 33.333 0.00 0.00 0.00 3.86
1666 1814 1.134965 AGAGACAGACAACCGCTATGC 60.135 52.381 0.00 0.00 0.00 3.14
1679 1827 6.566197 AGCTTAAAATTTGACCAGAGACAG 57.434 37.500 0.00 0.00 0.00 3.51
1686 1834 4.698304 CGGACCTAGCTTAAAATTTGACCA 59.302 41.667 0.00 0.00 0.00 4.02
1736 1888 6.133392 ACAAAACATCAAGATAACACGAACG 58.867 36.000 0.00 0.00 0.00 3.95
1762 1914 2.592861 CCGCTTAGCCATGCCTCC 60.593 66.667 0.00 0.00 0.00 4.30
1788 1940 4.796038 AAGATGACCCAGCAAAAGAATG 57.204 40.909 0.00 0.00 0.00 2.67
1941 2095 4.269183 ACGTAAATCATGGGAGAATGCAA 58.731 39.130 0.00 0.00 0.00 4.08
1942 2096 3.876914 GACGTAAATCATGGGAGAATGCA 59.123 43.478 0.00 0.00 0.00 3.96
1966 2143 1.202734 AGATTGTCCCATGAGCATCGG 60.203 52.381 0.00 0.00 38.61 4.18
1974 2151 7.339212 TGACCTACAAATAAAGATTGTCCCATG 59.661 37.037 0.00 0.00 41.11 3.66
1989 2166 4.348168 ACAGTGAGGTCTTGACCTACAAAT 59.652 41.667 20.86 7.79 40.86 2.32
2084 2261 9.614792 GGATACACAAAACTAAGGTTCTGATAT 57.385 33.333 0.00 0.00 34.14 1.63
2101 2278 5.049060 CGGTCAAATGAAACAGGATACACAA 60.049 40.000 0.00 0.00 41.41 3.33
2182 2359 2.081425 ATCCTGCAGCGACGGAGATC 62.081 60.000 8.66 0.00 0.00 2.75
2189 2366 2.515926 TCTCATTATCCTGCAGCGAC 57.484 50.000 8.66 0.00 0.00 5.19
2514 2692 4.280677 TCCCAAATCCAGCACAAAACTTAG 59.719 41.667 0.00 0.00 0.00 2.18
2568 2746 7.095060 CGAAGGAATTGGATATAACCATCACTG 60.095 40.741 2.09 0.00 39.82 3.66
2619 2797 4.851639 AAGGAATGTCTACAGCCAAGAT 57.148 40.909 7.33 0.00 0.00 2.40
2630 2808 7.267857 CAGGTTCAAAAAGAAAAGGAATGTCT 58.732 34.615 0.00 0.00 38.13 3.41
2646 2824 1.133199 AGGTGGATTGGCAGGTTCAAA 60.133 47.619 0.00 0.00 0.00 2.69
2685 2863 5.516339 CCTCTGTTTAATATGCCGCTTTTTG 59.484 40.000 0.00 0.00 0.00 2.44
2690 2868 2.222027 GCCTCTGTTTAATATGCCGCT 58.778 47.619 0.00 0.00 0.00 5.52
2722 3162 3.317711 CGATAGCTGGTCAGAGACAAGAT 59.682 47.826 5.75 1.71 35.75 2.40
2739 3179 6.312426 ACTTGAAGAGAATTTCACAGCGATAG 59.688 38.462 0.00 0.00 36.84 2.08
2831 3319 8.375506 AGAAGTGAATAGGTTTATGACAACTGA 58.624 33.333 0.00 0.00 0.00 3.41
2960 3500 5.359009 AGGATTAGCATTGAATGGTCACAAG 59.641 40.000 13.67 0.00 41.83 3.16
2969 3509 4.789807 ACTGAGCAGGATTAGCATTGAAT 58.210 39.130 2.20 0.00 0.00 2.57
3038 3578 2.602257 AAAAGGTTGCTTGGTTGAGC 57.398 45.000 0.00 0.00 43.00 4.26
3155 3700 6.553953 TGATGTGCTACCCTATCTTGTAAA 57.446 37.500 0.00 0.00 0.00 2.01
3168 3713 3.441163 CAACCATGCATTGATGTGCTAC 58.559 45.455 4.52 0.00 45.27 3.58
3189 3734 0.664761 TTCAGCTTTGAGCAGTGTGC 59.335 50.000 2.47 0.00 45.56 4.57


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

AutoCloner maintained by Alex Coulton.