Multiple sequence alignment - TraesCS6D01G003000

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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 TraesCS6D01G003000 chr6D 100.000 2912 0 0 1 2912 1634743 1637654 0.000000e+00 5378.0
1 TraesCS6D01G003000 chr6D 92.039 1859 100 17 999 2820 1799978 1798131 0.000000e+00 2569.0
2 TraesCS6D01G003000 chr6D 80.928 2134 267 77 465 2491 1850606 1848506 0.000000e+00 1557.0
3 TraesCS6D01G003000 chr6D 84.637 1406 169 26 882 2252 1903537 1902144 0.000000e+00 1356.0
4 TraesCS6D01G003000 chr6D 84.875 1243 145 27 979 2193 1760615 1761842 0.000000e+00 1214.0
5 TraesCS6D01G003000 chr6D 86.957 1012 107 15 1252 2249 1809411 1808411 0.000000e+00 1114.0
6 TraesCS6D01G003000 chr6D 84.130 586 58 12 169 720 1910965 1910381 4.270000e-148 534.0
7 TraesCS6D01G003000 chr6D 88.148 270 23 4 169 430 1851485 1851217 2.180000e-81 313.0
8 TraesCS6D01G003000 chr6D 77.578 446 65 18 2491 2907 1848471 1848032 1.350000e-58 237.0
9 TraesCS6D01G003000 chr6D 81.315 289 47 4 2491 2773 1901918 1901631 8.120000e-56 228.0
10 TraesCS6D01G003000 chr6D 78.804 368 52 17 2559 2907 1762106 1762466 1.050000e-54 224.0
11 TraesCS6D01G003000 chr6D 91.946 149 12 0 572 720 1760141 1760289 2.940000e-50 209.0
12 TraesCS6D01G003000 chr6D 89.474 114 10 2 58 170 1800248 1800136 3.020000e-30 143.0
13 TraesCS6D01G003000 chr6D 93.023 43 3 0 303 345 1851115 1851073 2.420000e-06 63.9
14 TraesCS6D01G003000 chr6D 87.755 49 5 1 2194 2241 1798806 1798758 4.050000e-04 56.5
15 TraesCS6D01G003000 chr6A 94.658 1928 75 12 1013 2912 968782 966855 0.000000e+00 2964.0
16 TraesCS6D01G003000 chr6A 85.875 1246 139 22 973 2193 932237 933470 0.000000e+00 1291.0
17 TraesCS6D01G003000 chr6A 88.571 385 31 8 170 544 931341 931722 3.420000e-124 455.0
18 TraesCS6D01G003000 chr6A 80.480 625 68 23 2194 2773 933426 934041 2.070000e-116 429.0
19 TraesCS6D01G003000 chr6A 77.209 430 57 21 572 969 931780 932200 2.270000e-51 213.0
20 TraesCS6D01G003000 chr6B 84.902 1371 178 19 998 2350 4885291 4883932 0.000000e+00 1358.0
21 TraesCS6D01G003000 chr6B 85.431 1311 165 17 991 2288 4856506 4857803 0.000000e+00 1339.0
22 TraesCS6D01G003000 chr6B 84.589 584 56 19 170 720 4886236 4885654 1.530000e-152 549.0
23 TraesCS6D01G003000 chr6B 85.938 256 32 2 303 558 4855731 4855982 1.330000e-68 270.0
24 TraesCS6D01G003000 chr6B 77.882 425 42 23 574 957 4856025 4856438 1.760000e-52 217.0
25 TraesCS6D01G003000 chr3D 81.078 946 156 17 1019 1955 582909598 582908667 0.000000e+00 734.0
26 TraesCS6D01G003000 chr3D 81.175 919 153 17 1019 1926 582899562 582898653 0.000000e+00 721.0
27 TraesCS6D01G003000 chr3D 80.890 921 153 19 1019 1926 582920745 582919835 0.000000e+00 704.0
28 TraesCS6D01G003000 chr3D 81.872 844 136 14 1019 1853 582922020 582921185 0.000000e+00 695.0
29 TraesCS6D01G003000 chr3B 94.118 51 2 1 803 852 779714447 779714397 3.110000e-10 76.8
30 TraesCS6D01G003000 chr3B 94.118 51 2 1 803 852 779931301 779931251 3.110000e-10 76.8
31 TraesCS6D01G003000 chr3B 94.118 51 2 1 803 852 780133116 780133066 3.110000e-10 76.8


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 TraesCS6D01G003000 chr6D 1634743 1637654 2911 False 5378.000000 5378 100.000000 1 2912 1 chr6D.!!$F1 2911
1 TraesCS6D01G003000 chr6D 1808411 1809411 1000 True 1114.000000 1114 86.957000 1252 2249 1 chr6D.!!$R1 997
2 TraesCS6D01G003000 chr6D 1798131 1800248 2117 True 922.833333 2569 89.756000 58 2820 3 chr6D.!!$R3 2762
3 TraesCS6D01G003000 chr6D 1901631 1903537 1906 True 792.000000 1356 82.976000 882 2773 2 chr6D.!!$R5 1891
4 TraesCS6D01G003000 chr6D 1760141 1762466 2325 False 549.000000 1214 85.208333 572 2907 3 chr6D.!!$F2 2335
5 TraesCS6D01G003000 chr6D 1848032 1851485 3453 True 542.725000 1557 84.919250 169 2907 4 chr6D.!!$R4 2738
6 TraesCS6D01G003000 chr6D 1910381 1910965 584 True 534.000000 534 84.130000 169 720 1 chr6D.!!$R2 551
7 TraesCS6D01G003000 chr6A 966855 968782 1927 True 2964.000000 2964 94.658000 1013 2912 1 chr6A.!!$R1 1899
8 TraesCS6D01G003000 chr6A 931341 934041 2700 False 597.000000 1291 83.033750 170 2773 4 chr6A.!!$F1 2603
9 TraesCS6D01G003000 chr6B 4883932 4886236 2304 True 953.500000 1358 84.745500 170 2350 2 chr6B.!!$R1 2180
10 TraesCS6D01G003000 chr6B 4855731 4857803 2072 False 608.666667 1339 83.083667 303 2288 3 chr6B.!!$F1 1985
11 TraesCS6D01G003000 chr3D 582908667 582909598 931 True 734.000000 734 81.078000 1019 1955 1 chr3D.!!$R2 936
12 TraesCS6D01G003000 chr3D 582898653 582899562 909 True 721.000000 721 81.175000 1019 1926 1 chr3D.!!$R1 907
13 TraesCS6D01G003000 chr3D 582919835 582922020 2185 True 699.500000 704 81.381000 1019 1926 2 chr3D.!!$R3 907

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
50 51 0.106217 AATTGGGCCCCGTCCATTAG 60.106 55.0 22.27 0.0 37.08 1.73 F
979 1686 0.244994 TCTTGCTCCTCTCTTGTCGC 59.755 55.0 0.00 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1272 2070 0.249615 GCATGCAGAGCGTGGAGATA 60.250 55.0 14.21 0.0 44.72 1.98 R
2168 4277 0.454196 AACCAAGAACTTTTGCGCGT 59.546 45.0 8.43 0.0 0.00 6.01 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
44 45 3.620427 AAAAATAAATTGGGCCCCGTC 57.380 42.857 22.27 0.00 0.00 4.79
45 46 1.491668 AAATAAATTGGGCCCCGTCC 58.508 50.000 22.27 0.00 0.00 4.79
46 47 0.336737 AATAAATTGGGCCCCGTCCA 59.663 50.000 22.27 1.37 34.47 4.02
47 48 0.560688 ATAAATTGGGCCCCGTCCAT 59.439 50.000 22.27 4.17 37.08 3.41
48 49 0.336737 TAAATTGGGCCCCGTCCATT 59.663 50.000 22.27 6.87 37.08 3.16
49 50 0.336737 AAATTGGGCCCCGTCCATTA 59.663 50.000 22.27 0.00 37.08 1.90
50 51 0.106217 AATTGGGCCCCGTCCATTAG 60.106 55.000 22.27 0.00 37.08 1.73
51 52 1.286305 ATTGGGCCCCGTCCATTAGT 61.286 55.000 22.27 0.00 37.08 2.24
52 53 1.502527 TTGGGCCCCGTCCATTAGTT 61.503 55.000 22.27 0.00 37.08 2.24
53 54 1.453197 GGGCCCCGTCCATTAGTTG 60.453 63.158 12.23 0.00 0.00 3.16
54 55 2.119029 GGCCCCGTCCATTAGTTGC 61.119 63.158 0.00 0.00 0.00 4.17
55 56 1.377987 GCCCCGTCCATTAGTTGCA 60.378 57.895 0.00 0.00 0.00 4.08
56 57 0.751643 GCCCCGTCCATTAGTTGCAT 60.752 55.000 0.00 0.00 0.00 3.96
63 64 4.635765 CCGTCCATTAGTTGCATATATGGG 59.364 45.833 14.51 4.69 37.07 4.00
82 83 3.886505 TGGGTAAGAACAGCGTTTGAAAT 59.113 39.130 0.00 0.00 0.00 2.17
86 87 5.398416 GGTAAGAACAGCGTTTGAAATGAAC 59.602 40.000 0.48 0.00 0.00 3.18
89 90 4.798387 AGAACAGCGTTTGAAATGAACAAC 59.202 37.500 0.48 0.00 0.00 3.32
91 92 3.857093 ACAGCGTTTGAAATGAACAACAC 59.143 39.130 0.48 0.00 0.00 3.32
145 147 0.800012 CATTAAACCACCGTCCACCG 59.200 55.000 0.00 0.00 0.00 4.94
177 179 1.447838 TCGCCGGATCAAGAAGTGC 60.448 57.895 5.05 0.00 0.00 4.40
239 241 6.321435 GGGAAAGAAACCAAAGGATATACAGG 59.679 42.308 0.00 0.00 0.00 4.00
246 248 5.133221 ACCAAAGGATATACAGGCAATGTC 58.867 41.667 0.00 0.00 42.70 3.06
249 251 3.995199 AGGATATACAGGCAATGTCACG 58.005 45.455 0.00 0.00 42.70 4.35
253 255 3.803082 CAGGCAATGTCACGCGGG 61.803 66.667 12.47 6.51 0.00 6.13
272 274 1.523758 GTTCTTCCATGCCGACAAGT 58.476 50.000 0.00 0.00 0.00 3.16
298 301 2.782341 AGCTGAATTAGGCATCTCCCTT 59.218 45.455 0.00 0.00 36.41 3.95
354 364 3.121944 CGTGTCATGTTCCGAGAAAAGAG 59.878 47.826 0.00 0.00 0.00 2.85
364 374 7.394816 TGTTCCGAGAAAAGAGAAGGAATAAT 58.605 34.615 0.00 0.00 39.55 1.28
500 1086 0.402121 GGGAGTGCAGAAGGGTCTTT 59.598 55.000 0.00 0.00 28.78 2.52
502 1088 0.877743 GAGTGCAGAAGGGTCTTTGC 59.122 55.000 0.00 0.00 28.78 3.68
562 1153 6.713762 TTTTTGCTTGGTCTGATATATGGG 57.286 37.500 0.00 0.00 0.00 4.00
563 1154 5.387113 TTTGCTTGGTCTGATATATGGGT 57.613 39.130 0.00 0.00 0.00 4.51
564 1155 6.508030 TTTGCTTGGTCTGATATATGGGTA 57.492 37.500 0.00 0.00 0.00 3.69
565 1156 6.508030 TTGCTTGGTCTGATATATGGGTAA 57.492 37.500 0.00 0.00 0.00 2.85
566 1157 6.114187 TGCTTGGTCTGATATATGGGTAAG 57.886 41.667 0.00 0.00 0.00 2.34
567 1158 5.013079 TGCTTGGTCTGATATATGGGTAAGG 59.987 44.000 0.00 0.00 0.00 2.69
568 1159 5.013183 GCTTGGTCTGATATATGGGTAAGGT 59.987 44.000 0.00 0.00 0.00 3.50
569 1160 6.465894 GCTTGGTCTGATATATGGGTAAGGTT 60.466 42.308 0.00 0.00 0.00 3.50
570 1161 6.433847 TGGTCTGATATATGGGTAAGGTTG 57.566 41.667 0.00 0.00 0.00 3.77
591 1209 3.193267 TGAATTTTTGGGAGAAGGATGCG 59.807 43.478 0.00 0.00 0.00 4.73
600 1218 2.365617 GGAGAAGGATGCGAAGGATACA 59.634 50.000 0.00 0.00 43.88 2.29
651 1269 7.231925 GGTTTCTTTGGTACCAAATTAAGGAGA 59.768 37.037 34.40 24.63 43.78 3.71
668 1286 4.935578 AGGAGAAATAAAGGTTTGGGAGG 58.064 43.478 0.00 0.00 0.00 4.30
720 1338 6.580788 TGATGTCATCAAATGGTTTGTTTGT 58.419 32.000 13.25 0.00 41.36 2.83
722 1340 7.551974 TGATGTCATCAAATGGTTTGTTTGTTT 59.448 29.630 13.25 0.00 41.36 2.83
729 1385 6.814146 TCAAATGGTTTGTTTGTTTGTAGGTC 59.186 34.615 2.74 0.00 41.36 3.85
733 1389 5.163774 TGGTTTGTTTGTTTGTAGGTCGTAC 60.164 40.000 0.00 0.00 0.00 3.67
744 1400 5.648178 TGTAGGTCGTACAGATTAAGCAA 57.352 39.130 1.23 0.00 36.67 3.91
745 1401 6.216801 TGTAGGTCGTACAGATTAAGCAAT 57.783 37.500 1.23 0.00 36.67 3.56
746 1402 6.636705 TGTAGGTCGTACAGATTAAGCAATT 58.363 36.000 1.23 0.00 36.67 2.32
747 1403 6.755141 TGTAGGTCGTACAGATTAAGCAATTC 59.245 38.462 1.23 0.00 36.67 2.17
748 1404 5.730550 AGGTCGTACAGATTAAGCAATTCA 58.269 37.500 0.00 0.00 0.00 2.57
749 1405 6.349300 AGGTCGTACAGATTAAGCAATTCAT 58.651 36.000 0.00 0.00 0.00 2.57
750 1406 6.823689 AGGTCGTACAGATTAAGCAATTCATT 59.176 34.615 0.00 0.00 0.00 2.57
751 1407 7.985184 AGGTCGTACAGATTAAGCAATTCATTA 59.015 33.333 0.00 0.00 0.00 1.90
752 1408 8.276325 GGTCGTACAGATTAAGCAATTCATTAG 58.724 37.037 0.00 0.00 0.00 1.73
753 1409 7.794349 GTCGTACAGATTAAGCAATTCATTAGC 59.206 37.037 0.00 0.00 0.00 3.09
754 1410 7.494298 TCGTACAGATTAAGCAATTCATTAGCA 59.506 33.333 0.00 0.00 0.00 3.49
755 1411 7.584123 CGTACAGATTAAGCAATTCATTAGCAC 59.416 37.037 0.00 0.00 0.00 4.40
756 1412 7.395190 ACAGATTAAGCAATTCATTAGCACA 57.605 32.000 0.00 0.00 0.00 4.57
757 1413 8.004087 ACAGATTAAGCAATTCATTAGCACAT 57.996 30.769 0.00 0.00 0.00 3.21
758 1414 8.133627 ACAGATTAAGCAATTCATTAGCACATC 58.866 33.333 0.00 0.00 0.00 3.06
759 1415 8.132995 CAGATTAAGCAATTCATTAGCACATCA 58.867 33.333 0.00 0.00 0.00 3.07
760 1416 8.857098 AGATTAAGCAATTCATTAGCACATCAT 58.143 29.630 0.00 0.00 0.00 2.45
795 1451 9.745018 ATATTTAGCAGGATACAATGTATTGCT 57.255 29.630 26.15 26.15 41.38 3.91
801 1481 6.860023 GCAGGATACAATGTATTGCTCATTTC 59.140 38.462 17.94 0.88 41.38 2.17
834 1520 6.899114 AGGATGTAAAACGAACTAAAAGCAG 58.101 36.000 0.00 0.00 0.00 4.24
854 1540 4.679654 GCAGAAAAGGATGTAAAACCAACG 59.320 41.667 0.00 0.00 0.00 4.10
856 1542 5.912955 CAGAAAAGGATGTAAAACCAACGAC 59.087 40.000 0.00 0.00 0.00 4.34
857 1543 5.591067 AGAAAAGGATGTAAAACCAACGACA 59.409 36.000 0.00 0.00 0.00 4.35
859 1545 2.812011 AGGATGTAAAACCAACGACAGC 59.188 45.455 0.00 0.00 0.00 4.40
862 1548 2.634600 TGTAAAACCAACGACAGCAGT 58.365 42.857 0.00 0.00 0.00 4.40
863 1549 3.011119 TGTAAAACCAACGACAGCAGTT 58.989 40.909 0.00 0.00 0.00 3.16
864 1550 3.440872 TGTAAAACCAACGACAGCAGTTT 59.559 39.130 0.00 0.00 32.26 2.66
865 1551 2.844122 AAACCAACGACAGCAGTTTC 57.156 45.000 0.00 0.00 0.00 2.78
866 1552 1.021968 AACCAACGACAGCAGTTTCC 58.978 50.000 0.00 0.00 0.00 3.13
867 1553 0.818040 ACCAACGACAGCAGTTTCCC 60.818 55.000 0.00 0.00 0.00 3.97
868 1554 1.569493 CAACGACAGCAGTTTCCCG 59.431 57.895 0.00 0.00 0.00 5.14
869 1555 2.251642 AACGACAGCAGTTTCCCGC 61.252 57.895 0.00 0.00 0.00 6.13
870 1556 3.423154 CGACAGCAGTTTCCCGCC 61.423 66.667 0.00 0.00 0.00 6.13
871 1557 3.423154 GACAGCAGTTTCCCGCCG 61.423 66.667 0.00 0.00 0.00 6.46
874 1560 4.394712 AGCAGTTTCCCGCCGGAG 62.395 66.667 5.05 0.00 40.10 4.63
906 1611 3.444742 TCTGGCAGCTCATTAAACATTGG 59.555 43.478 10.34 0.00 0.00 3.16
908 1613 2.167075 GGCAGCTCATTAAACATTGGCT 59.833 45.455 0.00 0.00 0.00 4.75
930 1637 4.826274 AGACCAGCAGCTACAAATAAGA 57.174 40.909 0.00 0.00 0.00 2.10
976 1683 1.622811 CCAGTCTTGCTCCTCTCTTGT 59.377 52.381 0.00 0.00 0.00 3.16
977 1684 2.353605 CCAGTCTTGCTCCTCTCTTGTC 60.354 54.545 0.00 0.00 0.00 3.18
978 1685 1.543802 AGTCTTGCTCCTCTCTTGTCG 59.456 52.381 0.00 0.00 0.00 4.35
979 1686 0.244994 TCTTGCTCCTCTCTTGTCGC 59.755 55.000 0.00 0.00 0.00 5.19
981 1688 2.202676 GCTCCTCTCTTGTCGCCG 60.203 66.667 0.00 0.00 0.00 6.46
982 1689 2.701780 GCTCCTCTCTTGTCGCCGA 61.702 63.158 0.00 0.00 0.00 5.54
984 1691 2.182030 CCTCTCTTGTCGCCGACC 59.818 66.667 15.60 0.00 0.00 4.79
985 1692 2.202492 CTCTCTTGTCGCCGACCG 60.202 66.667 15.60 6.04 38.61 4.79
1003 1796 2.187685 CCTGCGGTGCTAGCATGA 59.812 61.111 22.51 4.28 44.26 3.07
1115 1913 2.044946 GGAGCAGGCCCGAAACAT 60.045 61.111 0.00 0.00 0.00 2.71
1213 2011 3.133014 CCATCATCGCGGAGGAGT 58.867 61.111 6.13 0.00 0.00 3.85
1218 2016 1.043116 TCATCGCGGAGGAGTCCAAT 61.043 55.000 12.86 0.00 44.18 3.16
1227 2025 1.201429 AGGAGTCCAATGCCGTCCTT 61.201 55.000 12.86 0.00 33.66 3.36
1238 2036 2.031012 CGTCCTTGAGTGCCTGCA 59.969 61.111 0.00 0.00 0.00 4.41
1250 2048 4.393155 CCTGCACTACCCGCTGCA 62.393 66.667 0.00 0.00 41.13 4.41
1317 2115 1.379443 TGTCTACATCGAGCCGGGT 60.379 57.895 5.45 5.45 0.00 5.28
1323 2121 0.036306 ACATCGAGCCGGGTTTCTTT 59.964 50.000 8.00 0.00 0.00 2.52
1422 2220 4.194640 GCTTGAATGTATTGCTCAGGAGA 58.805 43.478 0.00 0.00 0.00 3.71
1848 3950 2.297701 GAGAGGCTCGTCAAGATCTCT 58.702 52.381 9.22 0.00 40.00 3.10
2006 4108 5.421277 ACCGGATTTGTCGTGTATCATTTA 58.579 37.500 9.46 0.00 0.00 1.40
2168 4277 2.746279 TCCTTCTGCCAAAACCTTGA 57.254 45.000 0.00 0.00 34.14 3.02
2565 4960 2.906389 TGTCAGTGCCTCTGTATCCTTT 59.094 45.455 6.02 0.00 43.97 3.11
2652 5047 2.489329 AGCACCCTTGATTTTCACATCG 59.511 45.455 0.00 0.00 0.00 3.84
2668 5063 4.157840 TCACATCGTGCATACACTACTTCT 59.842 41.667 0.00 0.00 45.10 2.85
2909 5353 1.503542 CAGCAGTGATTGGTTCGCC 59.496 57.895 0.00 0.00 34.69 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.237643 GGACGGGGCCCAATTTATTTTT 59.762 45.455 26.86 0.00 0.00 1.94
25 26 1.834896 GGACGGGGCCCAATTTATTTT 59.165 47.619 26.86 0.00 0.00 1.82
26 27 1.273324 TGGACGGGGCCCAATTTATTT 60.273 47.619 26.86 0.00 0.00 1.40
27 28 0.336737 TGGACGGGGCCCAATTTATT 59.663 50.000 26.86 0.00 0.00 1.40
28 29 0.560688 ATGGACGGGGCCCAATTTAT 59.439 50.000 26.86 9.28 37.22 1.40
29 30 0.336737 AATGGACGGGGCCCAATTTA 59.663 50.000 26.86 6.96 37.22 1.40
30 31 0.336737 TAATGGACGGGGCCCAATTT 59.663 50.000 26.86 10.66 37.22 1.82
31 32 0.106217 CTAATGGACGGGGCCCAATT 60.106 55.000 26.86 17.61 37.22 2.32
32 33 1.286305 ACTAATGGACGGGGCCCAAT 61.286 55.000 26.86 11.18 37.22 3.16
33 34 1.502527 AACTAATGGACGGGGCCCAA 61.503 55.000 26.86 4.88 37.22 4.12
34 35 1.926489 AACTAATGGACGGGGCCCA 60.926 57.895 26.86 1.48 38.19 5.36
35 36 1.453197 CAACTAATGGACGGGGCCC 60.453 63.158 15.76 15.76 0.00 5.80
36 37 2.119029 GCAACTAATGGACGGGGCC 61.119 63.158 0.00 0.00 0.00 5.80
37 38 0.751643 ATGCAACTAATGGACGGGGC 60.752 55.000 0.00 0.00 29.34 5.80
38 39 2.631160 TATGCAACTAATGGACGGGG 57.369 50.000 0.00 0.00 29.34 5.73
39 40 4.635765 CCATATATGCAACTAATGGACGGG 59.364 45.833 7.24 0.00 39.60 5.28
40 41 4.635765 CCCATATATGCAACTAATGGACGG 59.364 45.833 17.57 0.00 39.60 4.79
41 42 5.245531 ACCCATATATGCAACTAATGGACG 58.754 41.667 17.57 8.14 39.60 4.79
42 43 8.100791 TCTTACCCATATATGCAACTAATGGAC 58.899 37.037 17.57 0.00 39.60 4.02
43 44 8.213489 TCTTACCCATATATGCAACTAATGGA 57.787 34.615 17.57 1.82 39.60 3.41
44 45 8.730680 GTTCTTACCCATATATGCAACTAATGG 58.269 37.037 7.24 11.72 37.44 3.16
45 46 9.283768 TGTTCTTACCCATATATGCAACTAATG 57.716 33.333 7.24 0.00 0.00 1.90
46 47 9.507329 CTGTTCTTACCCATATATGCAACTAAT 57.493 33.333 7.24 0.00 0.00 1.73
47 48 7.444183 GCTGTTCTTACCCATATATGCAACTAA 59.556 37.037 7.24 0.00 0.00 2.24
48 49 6.934645 GCTGTTCTTACCCATATATGCAACTA 59.065 38.462 7.24 0.00 0.00 2.24
49 50 5.765182 GCTGTTCTTACCCATATATGCAACT 59.235 40.000 7.24 0.00 0.00 3.16
50 51 5.334105 CGCTGTTCTTACCCATATATGCAAC 60.334 44.000 7.24 3.83 0.00 4.17
51 52 4.754618 CGCTGTTCTTACCCATATATGCAA 59.245 41.667 7.24 0.64 0.00 4.08
52 53 4.202315 ACGCTGTTCTTACCCATATATGCA 60.202 41.667 7.24 0.00 0.00 3.96
53 54 4.315803 ACGCTGTTCTTACCCATATATGC 58.684 43.478 7.24 0.00 0.00 3.14
54 55 6.481976 TCAAACGCTGTTCTTACCCATATATG 59.518 38.462 5.68 5.68 0.00 1.78
55 56 6.588204 TCAAACGCTGTTCTTACCCATATAT 58.412 36.000 0.00 0.00 0.00 0.86
56 57 5.979993 TCAAACGCTGTTCTTACCCATATA 58.020 37.500 0.00 0.00 0.00 0.86
63 64 5.968848 TGTTCATTTCAAACGCTGTTCTTAC 59.031 36.000 0.00 0.00 0.00 2.34
82 83 3.691575 TGGAAGGAAACAGTGTTGTTCA 58.308 40.909 9.79 0.00 46.54 3.18
158 160 1.696832 GCACTTCTTGATCCGGCGAC 61.697 60.000 9.30 0.00 0.00 5.19
159 161 1.447838 GCACTTCTTGATCCGGCGA 60.448 57.895 9.30 0.00 0.00 5.54
160 162 1.298157 TTGCACTTCTTGATCCGGCG 61.298 55.000 0.00 0.00 0.00 6.46
161 163 0.881118 TTTGCACTTCTTGATCCGGC 59.119 50.000 0.00 0.00 0.00 6.13
162 164 1.200020 GGTTTGCACTTCTTGATCCGG 59.800 52.381 0.00 0.00 0.00 5.14
163 165 1.879380 TGGTTTGCACTTCTTGATCCG 59.121 47.619 0.00 0.00 0.00 4.18
164 166 4.320608 TTTGGTTTGCACTTCTTGATCC 57.679 40.909 0.00 0.00 0.00 3.36
165 167 4.507756 GGTTTTGGTTTGCACTTCTTGATC 59.492 41.667 0.00 0.00 0.00 2.92
166 168 4.162131 AGGTTTTGGTTTGCACTTCTTGAT 59.838 37.500 0.00 0.00 0.00 2.57
167 169 3.513515 AGGTTTTGGTTTGCACTTCTTGA 59.486 39.130 0.00 0.00 0.00 3.02
177 179 6.200097 GCACAACAGTTATAGGTTTTGGTTTG 59.800 38.462 0.00 0.00 0.00 2.93
235 237 3.049674 CCGCGTGACATTGCCTGT 61.050 61.111 4.92 0.00 42.15 4.00
239 241 1.852067 AAGAACCCGCGTGACATTGC 61.852 55.000 4.92 0.00 0.00 3.56
246 248 3.039202 GCATGGAAGAACCCGCGTG 62.039 63.158 4.92 0.00 38.00 5.34
249 251 3.508840 CGGCATGGAAGAACCCGC 61.509 66.667 0.00 0.00 38.00 6.13
253 255 1.197721 CACTTGTCGGCATGGAAGAAC 59.802 52.381 7.87 0.00 0.00 3.01
272 274 4.194640 GAGATGCCTAATTCAGCTTGTCA 58.805 43.478 7.39 0.00 29.38 3.58
298 301 0.108520 GTACCGTTTCCGCTCCATGA 60.109 55.000 0.00 0.00 0.00 3.07
342 345 6.096423 TCGATTATTCCTTCTCTTTTCTCGGA 59.904 38.462 0.00 0.00 0.00 4.55
354 364 8.888579 TTTCTATTGTCCTCGATTATTCCTTC 57.111 34.615 0.00 0.00 0.00 3.46
364 374 6.436532 ACTTTACTCCTTTCTATTGTCCTCGA 59.563 38.462 0.00 0.00 0.00 4.04
399 409 3.581101 CACCTCTGATCTCCCCATCTTA 58.419 50.000 0.00 0.00 0.00 2.10
401 411 1.414245 CCACCTCTGATCTCCCCATCT 60.414 57.143 0.00 0.00 0.00 2.90
442 452 5.372343 TTTGGACATGAGCACCTATATGT 57.628 39.130 0.00 0.00 36.54 2.29
456 466 6.604795 CCTCCTCTGTTTCATTATTTGGACAT 59.395 38.462 0.00 0.00 0.00 3.06
545 1131 6.688073 ACCTTACCCATATATCAGACCAAG 57.312 41.667 0.00 0.00 0.00 3.61
547 1133 6.147473 TCAACCTTACCCATATATCAGACCA 58.853 40.000 0.00 0.00 0.00 4.02
548 1139 6.681729 TCAACCTTACCCATATATCAGACC 57.318 41.667 0.00 0.00 0.00 3.85
558 1149 5.158889 TCCCAAAAATTCAACCTTACCCAT 58.841 37.500 0.00 0.00 0.00 4.00
561 1152 6.413783 TTCTCCCAAAAATTCAACCTTACC 57.586 37.500 0.00 0.00 0.00 2.85
562 1153 6.266786 TCCTTCTCCCAAAAATTCAACCTTAC 59.733 38.462 0.00 0.00 0.00 2.34
563 1154 6.377912 TCCTTCTCCCAAAAATTCAACCTTA 58.622 36.000 0.00 0.00 0.00 2.69
564 1155 5.215845 TCCTTCTCCCAAAAATTCAACCTT 58.784 37.500 0.00 0.00 0.00 3.50
565 1156 4.814967 TCCTTCTCCCAAAAATTCAACCT 58.185 39.130 0.00 0.00 0.00 3.50
566 1157 5.482006 CATCCTTCTCCCAAAAATTCAACC 58.518 41.667 0.00 0.00 0.00 3.77
567 1158 4.931601 GCATCCTTCTCCCAAAAATTCAAC 59.068 41.667 0.00 0.00 0.00 3.18
568 1159 4.321899 CGCATCCTTCTCCCAAAAATTCAA 60.322 41.667 0.00 0.00 0.00 2.69
569 1160 3.193267 CGCATCCTTCTCCCAAAAATTCA 59.807 43.478 0.00 0.00 0.00 2.57
570 1161 3.443681 TCGCATCCTTCTCCCAAAAATTC 59.556 43.478 0.00 0.00 0.00 2.17
591 1209 0.249657 CGCCCAGCTCTGTATCCTTC 60.250 60.000 0.00 0.00 0.00 3.46
600 1218 0.905357 ACTTGTTATCGCCCAGCTCT 59.095 50.000 0.00 0.00 0.00 4.09
651 1269 4.202890 ACATCCCCTCCCAAACCTTTATTT 60.203 41.667 0.00 0.00 0.00 1.40
720 1338 6.028146 TGCTTAATCTGTACGACCTACAAA 57.972 37.500 0.00 0.00 34.80 2.83
722 1340 5.648178 TTGCTTAATCTGTACGACCTACA 57.352 39.130 0.00 0.00 34.01 2.74
729 1385 7.584123 GTGCTAATGAATTGCTTAATCTGTACG 59.416 37.037 0.00 0.00 0.00 3.67
733 1389 8.132995 TGATGTGCTAATGAATTGCTTAATCTG 58.867 33.333 0.00 0.00 0.00 2.90
744 1400 3.251729 GGCGTGATGATGTGCTAATGAAT 59.748 43.478 0.00 0.00 0.00 2.57
745 1401 2.613595 GGCGTGATGATGTGCTAATGAA 59.386 45.455 0.00 0.00 0.00 2.57
746 1402 2.212652 GGCGTGATGATGTGCTAATGA 58.787 47.619 0.00 0.00 0.00 2.57
747 1403 1.941975 TGGCGTGATGATGTGCTAATG 59.058 47.619 0.00 0.00 0.00 1.90
748 1404 2.330440 TGGCGTGATGATGTGCTAAT 57.670 45.000 0.00 0.00 0.00 1.73
749 1405 2.330440 ATGGCGTGATGATGTGCTAA 57.670 45.000 0.00 0.00 0.00 3.09
750 1406 3.683365 ATATGGCGTGATGATGTGCTA 57.317 42.857 0.00 0.00 0.00 3.49
751 1407 2.556144 ATATGGCGTGATGATGTGCT 57.444 45.000 0.00 0.00 0.00 4.40
752 1408 4.952262 AATATATGGCGTGATGATGTGC 57.048 40.909 0.00 0.00 0.00 4.57
753 1409 6.092533 TGCTAAATATATGGCGTGATGATGTG 59.907 38.462 0.00 0.00 0.00 3.21
754 1410 6.172630 TGCTAAATATATGGCGTGATGATGT 58.827 36.000 0.00 0.00 0.00 3.06
755 1411 6.238293 CCTGCTAAATATATGGCGTGATGATG 60.238 42.308 0.00 0.00 0.00 3.07
756 1412 5.819379 CCTGCTAAATATATGGCGTGATGAT 59.181 40.000 0.00 0.00 0.00 2.45
757 1413 5.046663 TCCTGCTAAATATATGGCGTGATGA 60.047 40.000 0.00 0.00 0.00 2.92
758 1414 5.178061 TCCTGCTAAATATATGGCGTGATG 58.822 41.667 0.00 0.00 0.00 3.07
759 1415 5.420725 TCCTGCTAAATATATGGCGTGAT 57.579 39.130 0.00 0.00 0.00 3.06
760 1416 4.882842 TCCTGCTAAATATATGGCGTGA 57.117 40.909 0.00 0.00 0.00 4.35
828 1514 6.478512 TGGTTTTACATCCTTTTCTGCTTT 57.521 33.333 0.00 0.00 0.00 3.51
831 1517 4.679654 CGTTGGTTTTACATCCTTTTCTGC 59.320 41.667 0.00 0.00 0.00 4.26
834 1520 5.823353 TGTCGTTGGTTTTACATCCTTTTC 58.177 37.500 0.00 0.00 0.00 2.29
859 1545 4.016706 ACCTCCGGCGGGAAACTG 62.017 66.667 27.98 10.60 43.27 3.16
885 1590 3.777478 CCAATGTTTAATGAGCTGCCAG 58.223 45.455 0.00 0.00 0.00 4.85
891 1596 4.640201 TGGTCTAGCCAATGTTTAATGAGC 59.360 41.667 3.71 0.00 45.94 4.26
908 1613 5.932619 TCTTATTTGTAGCTGCTGGTCTA 57.067 39.130 13.43 0.00 0.00 2.59
928 1635 3.790408 AGAGTCAATGGGGAATGGATTCT 59.210 43.478 0.00 0.00 31.90 2.40
929 1636 4.176120 AGAGTCAATGGGGAATGGATTC 57.824 45.455 0.00 0.00 36.08 2.52
930 1637 4.017222 TGAAGAGTCAATGGGGAATGGATT 60.017 41.667 0.00 0.00 0.00 3.01
987 1694 1.434622 CCTTCATGCTAGCACCGCAG 61.435 60.000 22.07 13.65 41.22 5.18
988 1695 1.450134 CCTTCATGCTAGCACCGCA 60.450 57.895 22.07 3.69 42.25 5.69
993 1786 1.522092 CGACCCCTTCATGCTAGCA 59.478 57.895 21.85 21.85 0.00 3.49
996 1789 2.742116 GGCCGACCCCTTCATGCTA 61.742 63.158 0.00 0.00 0.00 3.49
1003 1796 1.306654 TCATAGTGGCCGACCCCTT 60.307 57.895 0.00 0.00 33.59 3.95
1115 1913 3.819652 ACACCAGCAAGGCCACCA 61.820 61.111 5.01 0.00 43.14 4.17
1201 1999 1.443407 CATTGGACTCCTCCGCGAT 59.557 57.895 8.23 0.00 39.88 4.58
1213 2011 0.321564 CACTCAAGGACGGCATTGGA 60.322 55.000 16.77 1.67 36.51 3.53
1218 2016 3.241530 AGGCACTCAAGGACGGCA 61.242 61.111 0.00 0.00 0.00 5.69
1238 2036 2.436646 GCACATGCAGCGGGTAGT 60.437 61.111 0.00 0.00 41.59 2.73
1272 2070 0.249615 GCATGCAGAGCGTGGAGATA 60.250 55.000 14.21 0.00 44.72 1.98
1317 2115 1.216678 TCCTGGTGGAAGGCAAAGAAA 59.783 47.619 0.00 0.00 39.87 2.52
1323 2121 2.121963 AGGTCCTGGTGGAAGGCA 60.122 61.111 0.00 0.00 45.18 4.75
1422 2220 0.617413 CAACCAGGCCAGTCTCAGAT 59.383 55.000 5.01 0.00 0.00 2.90
1671 3770 6.377712 TGACAAATTGCCAATCATCAGACATA 59.622 34.615 0.00 0.00 0.00 2.29
1848 3950 2.159156 CCAAATCTCACGGTGGTCGATA 60.159 50.000 8.50 0.00 42.43 2.92
2065 4168 5.067805 AGGAGCAACAAACTTTTTCTCGAAT 59.932 36.000 0.00 0.00 0.00 3.34
2168 4277 0.454196 AACCAAGAACTTTTGCGCGT 59.546 45.000 8.43 0.00 0.00 6.01
2333 4676 1.207488 AGAGGGGTGGCTATGTTGCA 61.207 55.000 0.00 0.00 34.04 4.08
2565 4960 3.196685 CCAACAACTTGGGAAAGAAACCA 59.803 43.478 0.00 0.00 43.19 3.67
2685 5080 5.067544 CCCGACAGTAAAAAGTACCCAAAAA 59.932 40.000 0.00 0.00 0.00 1.94
2690 5085 3.407424 ACCCGACAGTAAAAAGTACCC 57.593 47.619 0.00 0.00 0.00 3.69
2691 5086 5.409520 CCTTAACCCGACAGTAAAAAGTACC 59.590 44.000 0.00 0.00 0.00 3.34
2692 5087 5.106948 GCCTTAACCCGACAGTAAAAAGTAC 60.107 44.000 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.