Multiple sequence alignment - TraesCS5B01G517800

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 TraesCS5B01G517800 chr5B 100.000 3148 0 0 1 3148 681052745 681049598 0.000000e+00 5814.0
1 TraesCS5B01G517800 chr5B 94.941 850 36 4 1 843 93179036 93179885 0.000000e+00 1325.0
2 TraesCS5B01G517800 chr5B 94.235 850 42 4 1 843 97533047 97532198 0.000000e+00 1291.0
3 TraesCS5B01G517800 chr5B 79.603 554 93 13 1216 1755 690548987 690548440 2.290000e-101 379.0
4 TraesCS5B01G517800 chr5B 80.577 381 52 13 1756 2122 690548402 690548030 1.110000e-69 274.0
5 TraesCS5B01G517800 chr1B 92.263 1564 91 6 844 2383 660430497 660432054 0.000000e+00 2191.0
6 TraesCS5B01G517800 chr1B 95.529 850 31 4 1 843 480626882 480626033 0.000000e+00 1352.0
7 TraesCS5B01G517800 chr1B 94.817 849 37 4 2 843 312548503 312549351 0.000000e+00 1317.0
8 TraesCS5B01G517800 chr1B 95.926 270 10 1 2515 2784 660432050 660432318 1.340000e-118 436.0
9 TraesCS5B01G517800 chr1B 94.958 238 11 1 2912 3148 660432322 660432559 3.830000e-99 372.0
10 TraesCS5B01G517800 chr1B 86.897 145 13 4 1617 1755 512175839 512175695 1.170000e-34 158.0
11 TraesCS5B01G517800 chr6B 94.150 1436 66 12 1728 3148 1585314 1583882 0.000000e+00 2170.0
12 TraesCS5B01G517800 chr6B 87.713 822 86 9 2212 3020 356571710 356570891 0.000000e+00 944.0
13 TraesCS5B01G517800 chr6B 84.541 621 45 19 1617 2207 356572785 356572186 4.560000e-158 568.0
14 TraesCS5B01G517800 chr6B 90.130 385 29 6 1303 1685 1585677 1585300 2.820000e-135 492.0
15 TraesCS5B01G517800 chr6B 80.851 188 29 7 844 1029 18279921 18279739 1.180000e-29 141.0
16 TraesCS5B01G517800 chr6B 77.698 139 19 2 1629 1755 647588903 647589041 1.210000e-09 75.0
17 TraesCS5B01G517800 chr6B 84.507 71 11 0 1632 1702 647932858 647932788 1.570000e-08 71.3
18 TraesCS5B01G517800 chr6B 85.938 64 9 0 1637 1700 647707974 647708037 5.630000e-08 69.4
19 TraesCS5B01G517800 chr3B 94.438 863 38 7 1 856 128832593 128831734 0.000000e+00 1319.0
20 TraesCS5B01G517800 chr3B 94.340 848 41 5 3 843 436599596 436600443 0.000000e+00 1293.0
21 TraesCS5B01G517800 chr3B 88.029 827 83 9 2206 3018 778635810 778636634 0.000000e+00 965.0
22 TraesCS5B01G517800 chr3B 75.506 494 60 32 1617 2074 556082065 556081597 5.360000e-43 185.0
23 TraesCS5B01G517800 chr3B 76.471 442 44 27 1617 2018 768763799 768764220 5.360000e-43 185.0
24 TraesCS5B01G517800 chr7B 94.471 850 40 2 1 843 491338801 491339650 0.000000e+00 1303.0
25 TraesCS5B01G517800 chr7B 94.229 849 42 4 2 843 168777624 168776776 0.000000e+00 1290.0
26 TraesCS5B01G517800 chr4B 94.438 845 43 2 3 843 473162883 473163727 0.000000e+00 1297.0
27 TraesCS5B01G517800 chr4B 87.863 758 77 8 2206 2950 601870601 601871356 0.000000e+00 876.0
28 TraesCS5B01G517800 chr4B 87.591 548 53 9 2212 2746 581142316 581141771 3.450000e-174 621.0
29 TraesCS5B01G517800 chr4B 84.416 616 50 17 1617 2207 581143368 581142774 5.890000e-157 564.0
30 TraesCS5B01G517800 chr4B 83.062 614 60 12 1618 2207 601869539 601870132 4.650000e-143 518.0
31 TraesCS5B01G517800 chr4B 88.636 264 28 2 2758 3019 40741012 40740749 1.410000e-83 320.0
32 TraesCS5B01G517800 chr4B 77.206 136 19 3 1632 1755 438607083 438606948 5.630000e-08 69.4
33 TraesCS5B01G517800 chr2D 88.193 830 81 10 2206 3021 647501377 647502203 0.000000e+00 974.0
34 TraesCS5B01G517800 chr2D 84.390 615 52 19 1617 2207 647500313 647500907 5.890000e-157 564.0
35 TraesCS5B01G517800 chr2B 87.831 830 83 10 2206 3020 795607255 795608081 0.000000e+00 957.0
36 TraesCS5B01G517800 chr2B 84.124 611 55 17 1617 2207 797851993 797851405 1.280000e-153 553.0
37 TraesCS5B01G517800 chr2B 84.228 615 45 21 1617 2207 795606200 795606786 4.590000e-153 551.0
38 TraesCS5B01G517800 chr2B 83.252 615 59 14 1617 2207 144972117 144972711 2.780000e-145 525.0
39 TraesCS5B01G517800 chr2B 91.031 223 20 0 2798 3020 797850954 797850732 5.100000e-78 302.0
40 TraesCS5B01G517800 chr5A 87.772 826 86 8 2206 3018 580102955 580103778 0.000000e+00 952.0
41 TraesCS5B01G517800 chr5A 86.598 194 19 6 844 1030 566341705 566341512 1.140000e-49 207.0
42 TraesCS5B01G517800 chr3A 91.400 593 39 4 1626 2207 183837334 183836743 0.000000e+00 802.0
43 TraesCS5B01G517800 chr3A 85.714 196 21 6 842 1030 708963338 708963143 1.910000e-47 200.0
44 TraesCS5B01G517800 chr2A 87.869 643 63 8 2206 2835 21291517 21292157 0.000000e+00 741.0
45 TraesCS5B01G517800 chr2A 87.869 643 63 8 2206 2835 21316003 21316643 0.000000e+00 741.0
46 TraesCS5B01G517800 chr2A 87.869 643 63 8 2206 2835 21323667 21324307 0.000000e+00 741.0
47 TraesCS5B01G517800 chr2A 81.667 300 22 12 1925 2207 21322911 21323194 5.290000e-53 219.0
48 TraesCS5B01G517800 chr6D 78.313 498 57 31 1617 2074 201271544 201272030 1.110000e-69 274.0
49 TraesCS5B01G517800 chr6D 85.052 194 22 6 844 1030 32353103 32352910 1.150000e-44 191.0
50 TraesCS5B01G517800 chr6D 78.151 119 14 2 1649 1755 429666550 429666668 7.290000e-07 65.8
51 TraesCS5B01G517800 chr5D 78.000 500 52 30 1617 2074 17693875 17693392 8.660000e-66 261.0
52 TraesCS5B01G517800 chr6A 78.149 389 63 18 840 1213 23170713 23170332 8.780000e-56 228.0
53 TraesCS5B01G517800 chr6A 85.052 194 22 6 844 1030 43721862 43721669 1.150000e-44 191.0
54 TraesCS5B01G517800 chr6A 77.941 136 18 6 1632 1755 575143310 575143175 1.210000e-09 75.0
55 TraesCS5B01G517800 chr6A 88.462 52 6 0 1629 1680 574911647 574911698 2.620000e-06 63.9
56 TraesCS5B01G517800 chr6A 84.375 64 10 0 1637 1700 574935312 574935375 2.620000e-06 63.9
57 TraesCS5B01G517800 chr4A 78.385 384 56 18 1756 2122 741988355 741988728 1.140000e-54 224.0
58 TraesCS5B01G517800 chr4A 77.941 136 18 3 1632 1755 109787659 109787794 1.210000e-09 75.0
59 TraesCS5B01G517800 chr7A 77.494 391 63 19 840 1213 154041557 154041175 8.850000e-51 211.0
60 TraesCS5B01G517800 chr1D 83.908 174 25 3 844 1015 489692328 489692500 2.510000e-36 163.0
61 TraesCS5B01G517800 chr1D 85.517 145 15 4 1617 1755 382237649 382237505 2.530000e-31 147.0
62 TraesCS5B01G517800 chr1A 86.897 145 13 4 1617 1755 482338987 482338843 1.170000e-34 158.0
63 TraesCS5B01G517800 chr4D 83.582 67 11 0 1632 1698 354890688 354890622 2.620000e-06 63.9


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 TraesCS5B01G517800 chr5B 681049598 681052745 3147 True 5814.000000 5814 100.000000 1 3148 1 chr5B.!!$R2 3147
1 TraesCS5B01G517800 chr5B 93179036 93179885 849 False 1325.000000 1325 94.941000 1 843 1 chr5B.!!$F1 842
2 TraesCS5B01G517800 chr5B 97532198 97533047 849 True 1291.000000 1291 94.235000 1 843 1 chr5B.!!$R1 842
3 TraesCS5B01G517800 chr5B 690548030 690548987 957 True 326.500000 379 80.090000 1216 2122 2 chr5B.!!$R3 906
4 TraesCS5B01G517800 chr1B 480626033 480626882 849 True 1352.000000 1352 95.529000 1 843 1 chr1B.!!$R1 842
5 TraesCS5B01G517800 chr1B 312548503 312549351 848 False 1317.000000 1317 94.817000 2 843 1 chr1B.!!$F1 841
6 TraesCS5B01G517800 chr1B 660430497 660432559 2062 False 999.666667 2191 94.382333 844 3148 3 chr1B.!!$F2 2304
7 TraesCS5B01G517800 chr6B 1583882 1585677 1795 True 1331.000000 2170 92.140000 1303 3148 2 chr6B.!!$R3 1845
8 TraesCS5B01G517800 chr6B 356570891 356572785 1894 True 756.000000 944 86.127000 1617 3020 2 chr6B.!!$R4 1403
9 TraesCS5B01G517800 chr3B 128831734 128832593 859 True 1319.000000 1319 94.438000 1 856 1 chr3B.!!$R1 855
10 TraesCS5B01G517800 chr3B 436599596 436600443 847 False 1293.000000 1293 94.340000 3 843 1 chr3B.!!$F1 840
11 TraesCS5B01G517800 chr3B 778635810 778636634 824 False 965.000000 965 88.029000 2206 3018 1 chr3B.!!$F3 812
12 TraesCS5B01G517800 chr7B 491338801 491339650 849 False 1303.000000 1303 94.471000 1 843 1 chr7B.!!$F1 842
13 TraesCS5B01G517800 chr7B 168776776 168777624 848 True 1290.000000 1290 94.229000 2 843 1 chr7B.!!$R1 841
14 TraesCS5B01G517800 chr4B 473162883 473163727 844 False 1297.000000 1297 94.438000 3 843 1 chr4B.!!$F1 840
15 TraesCS5B01G517800 chr4B 601869539 601871356 1817 False 697.000000 876 85.462500 1618 2950 2 chr4B.!!$F2 1332
16 TraesCS5B01G517800 chr4B 581141771 581143368 1597 True 592.500000 621 86.003500 1617 2746 2 chr4B.!!$R3 1129
17 TraesCS5B01G517800 chr2D 647500313 647502203 1890 False 769.000000 974 86.291500 1617 3021 2 chr2D.!!$F1 1404
18 TraesCS5B01G517800 chr2B 795606200 795608081 1881 False 754.000000 957 86.029500 1617 3020 2 chr2B.!!$F2 1403
19 TraesCS5B01G517800 chr2B 144972117 144972711 594 False 525.000000 525 83.252000 1617 2207 1 chr2B.!!$F1 590
20 TraesCS5B01G517800 chr2B 797850732 797851993 1261 True 427.500000 553 87.577500 1617 3020 2 chr2B.!!$R1 1403
21 TraesCS5B01G517800 chr5A 580102955 580103778 823 False 952.000000 952 87.772000 2206 3018 1 chr5A.!!$F1 812
22 TraesCS5B01G517800 chr3A 183836743 183837334 591 True 802.000000 802 91.400000 1626 2207 1 chr3A.!!$R1 581
23 TraesCS5B01G517800 chr2A 21291517 21292157 640 False 741.000000 741 87.869000 2206 2835 1 chr2A.!!$F1 629
24 TraesCS5B01G517800 chr2A 21316003 21316643 640 False 741.000000 741 87.869000 2206 2835 1 chr2A.!!$F2 629
25 TraesCS5B01G517800 chr2A 21322911 21324307 1396 False 480.000000 741 84.768000 1925 2835 2 chr2A.!!$F3 910

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
926 934 1.090052 GCTTAGTACAGCCCCGCAAG 61.090 60.0 0.0 0.0 33.21 4.01 F
1155 1175 0.181350 CCCTCATTCCTTCCTTCCGG 59.819 60.0 0.0 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 1910 2.301870 TGGGAATAGAACAACGACTGCT 59.698 45.455 0.0 0.0 0.0 4.24 R
2970 3605 3.237268 AGCCAACCTACAAATCACCAA 57.763 42.857 0.0 0.0 0.0 3.67 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
52 53 4.761739 ACATCATTAACGCCAAGGATATGG 59.238 41.667 0.00 0.00 43.70 2.74
92 93 1.805428 AAGGTTTCGCATGCCCACAC 61.805 55.000 13.15 3.76 0.00 3.82
141 142 8.624776 CCAACCTTTAGAGGATTTAGCAATTAG 58.375 37.037 6.26 0.00 46.74 1.73
494 495 3.431626 GGTCATGTGATCGGTACATCCAA 60.432 47.826 0.00 0.00 36.67 3.53
533 534 3.585077 TTCCTCCTGCCATATATCCCT 57.415 47.619 0.00 0.00 0.00 4.20
566 567 5.163713 GCCATAAGACCAAAGTGTCTCATTC 60.164 44.000 0.00 0.00 44.68 2.67
674 681 8.012241 GTGATTCATTAGAGTGAGTTTGACAAC 58.988 37.037 0.00 0.00 0.00 3.32
913 921 1.267121 ACTGTCATGGACGGCTTAGT 58.733 50.000 5.15 0.00 42.17 2.24
926 934 1.090052 GCTTAGTACAGCCCCGCAAG 61.090 60.000 0.00 0.00 33.21 4.01
955 963 2.668632 CCACTCAAGCCCGCCTAA 59.331 61.111 0.00 0.00 0.00 2.69
973 981 3.128242 CCTAACCGCTCCGTGTATATAGG 59.872 52.174 0.00 0.00 0.00 2.57
994 1002 2.435069 GGCTAACCCTAAACTCTCCTCC 59.565 54.545 0.00 0.00 0.00 4.30
1040 1060 4.173924 GCAGCCAGAGCCCCTCTC 62.174 72.222 0.00 0.00 38.99 3.20
1061 1081 2.358737 CCACCACGCCACTCCTTC 60.359 66.667 0.00 0.00 0.00 3.46
1064 1084 1.229082 ACCACGCCACTCCTTCCTA 60.229 57.895 0.00 0.00 0.00 2.94
1069 1089 1.142097 GCCACTCCTTCCTAGCGTC 59.858 63.158 0.00 0.00 0.00 5.19
1126 1146 0.537188 CGTAGCACACCCTCATCCTT 59.463 55.000 0.00 0.00 0.00 3.36
1140 1160 2.956077 ATCCTTCCCTCGCTCCCCTC 62.956 65.000 0.00 0.00 0.00 4.30
1145 1165 2.812619 CCCTCGCTCCCCTCATTCC 61.813 68.421 0.00 0.00 0.00 3.01
1150 1170 1.341156 CGCTCCCCTCATTCCTTCCT 61.341 60.000 0.00 0.00 0.00 3.36
1153 1173 1.492599 CTCCCCTCATTCCTTCCTTCC 59.507 57.143 0.00 0.00 0.00 3.46
1155 1175 0.181350 CCCTCATTCCTTCCTTCCGG 59.819 60.000 0.00 0.00 0.00 5.14
1173 1193 2.496070 CCGGTTAGATTCACCAGTCTCA 59.504 50.000 0.00 0.00 33.36 3.27
1174 1194 3.133003 CCGGTTAGATTCACCAGTCTCAT 59.867 47.826 0.00 0.00 33.36 2.90
1178 1198 1.759445 AGATTCACCAGTCTCATCCCG 59.241 52.381 0.00 0.00 0.00 5.14
1190 1210 1.045350 TCATCCCGCAGAGCTAGCTT 61.045 55.000 20.42 6.14 0.00 3.74
1198 1218 0.997932 CAGAGCTAGCTTGCAAGACG 59.002 55.000 30.39 16.68 34.99 4.18
1287 1307 4.467084 GCTCCGCCGATTGGGTCA 62.467 66.667 0.00 0.00 38.44 4.02
1298 1318 2.552155 CGATTGGGTCAAGGAAAGGACA 60.552 50.000 0.00 0.00 35.74 4.02
1359 1379 3.079478 TCTGCAGAGCCAGCGGAT 61.079 61.111 13.74 0.00 42.13 4.18
1469 1489 2.507102 CGCGACTGCTCCGACAAT 60.507 61.111 0.00 0.00 39.65 2.71
1470 1490 2.094659 CGCGACTGCTCCGACAATT 61.095 57.895 0.00 0.00 39.65 2.32
1550 1570 1.596934 CACCACACTAGGGCACGAT 59.403 57.895 0.00 0.00 0.00 3.73
1566 1586 0.314935 CGATTTTGGCAGCCAACACT 59.685 50.000 27.40 13.87 43.82 3.55
1584 1604 2.515991 GGCGCCCAAATCGGATCA 60.516 61.111 18.11 0.00 36.56 2.92
1587 1607 1.376609 GCGCCCAAATCGGATCAACT 61.377 55.000 0.00 0.00 36.56 3.16
2037 2145 9.907576 GTTGTCAAATTAGATACTTCAGAATCG 57.092 33.333 0.00 0.00 0.00 3.34
2038 2146 8.648557 TGTCAAATTAGATACTTCAGAATCGG 57.351 34.615 0.00 0.00 0.00 4.18
2039 2147 8.258007 TGTCAAATTAGATACTTCAGAATCGGT 58.742 33.333 0.00 0.00 0.00 4.69
2042 2150 7.484035 AATTAGATACTTCAGAATCGGTTGC 57.516 36.000 0.00 0.00 0.00 4.17
2044 2152 5.091261 AGATACTTCAGAATCGGTTGCTT 57.909 39.130 0.00 0.00 0.00 3.91
2086 2211 9.071276 GCTTCCTTAGGATTGAAATAATGATGA 57.929 33.333 0.12 0.00 0.00 2.92
2138 2269 0.038744 AGCATAGTTTGGCAGCACCT 59.961 50.000 0.00 0.00 40.22 4.00
2253 2869 1.282930 GCGAGGCGACGAGTTCTTTT 61.283 55.000 0.00 0.00 35.09 2.27
2621 3253 1.176527 CAAATGTCGTGCCCTCCAAT 58.823 50.000 0.00 0.00 0.00 3.16
2670 3303 9.880157 AGAAACTACACTTCAAAACTAACAGTA 57.120 29.630 0.00 0.00 0.00 2.74
2852 3487 4.751767 TTTGGCTTGTGGAATTTCAAGT 57.248 36.364 15.24 0.00 41.83 3.16
2967 3602 6.919721 TGTTACTTAGAATTTTGGCATGGTC 58.080 36.000 0.00 0.00 0.00 4.02
2970 3605 5.086621 ACTTAGAATTTTGGCATGGTCCTT 58.913 37.500 0.00 0.00 0.00 3.36
3023 3659 4.199310 TCCATGGCTTGTAGCTACAATTC 58.801 43.478 33.45 27.04 44.34 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 7.658261 ACCTTGACAAGCTTATTAAAGGAAAC 58.342 34.615 24.89 0.00 36.91 2.78
92 93 5.812642 GGTTATGGCATAGATGATTAGGTCG 59.187 44.000 7.35 0.00 0.00 4.79
141 142 1.454201 GGCTCAACCTAGAACTTGCC 58.546 55.000 0.00 0.00 34.51 4.52
188 189 6.264067 GTCTTTACCGGTATACATAGAGGTGT 59.736 42.308 16.67 0.00 36.13 4.16
275 276 6.318900 TCAGTATCTAGACTTGCTGATTTCGA 59.681 38.462 9.34 0.00 0.00 3.71
419 420 2.080286 AATGACGACCCTCGAAAGTG 57.920 50.000 0.00 0.00 43.74 3.16
494 495 6.347061 AGGAAAGGAATGGGTTCTTGATAT 57.653 37.500 0.00 0.00 34.68 1.63
533 534 5.774690 ACTTTGGTCTTATGGCAAATCTTCA 59.225 36.000 0.00 0.00 0.00 3.02
566 567 7.119407 GGATGATGATAGTGACTTTGATGATGG 59.881 40.741 0.00 0.00 0.00 3.51
674 681 8.946085 AGCTACTAGAATTCATAGAGAAGATCG 58.054 37.037 8.44 0.00 40.15 3.69
870 878 6.595772 TTTGAAAATGTCACCAAAAATCCG 57.404 33.333 0.00 0.00 35.39 4.18
955 963 1.542492 CCCTATATACACGGAGCGGT 58.458 55.000 0.00 0.00 0.00 5.68
973 981 2.435069 GGAGGAGAGTTTAGGGTTAGCC 59.565 54.545 0.00 0.00 0.00 3.93
985 993 3.351885 AGGGGCGAGGAGGAGAGT 61.352 66.667 0.00 0.00 0.00 3.24
987 995 4.144727 GGAGGGGCGAGGAGGAGA 62.145 72.222 0.00 0.00 0.00 3.71
1006 1014 4.896829 CGCCGCTAGGGAGGAGGA 62.897 72.222 8.65 0.00 38.47 3.71
1040 1060 2.357517 GAGTGGCGTGGTGGACAG 60.358 66.667 0.00 0.00 0.00 3.51
1042 1062 3.178540 AAGGAGTGGCGTGGTGGAC 62.179 63.158 0.00 0.00 0.00 4.02
1061 1081 2.354773 GAATCGGGCGACGCTAGG 60.355 66.667 20.77 9.26 43.86 3.02
1082 1102 2.658593 CATAGGCGCCGGAAGTCG 60.659 66.667 23.20 0.00 38.88 4.18
1116 1136 1.753368 GAGCGAGGGAAGGATGAGGG 61.753 65.000 0.00 0.00 0.00 4.30
1126 1146 1.762460 GAATGAGGGGAGCGAGGGA 60.762 63.158 0.00 0.00 0.00 4.20
1150 1170 3.170717 AGACTGGTGAATCTAACCGGAA 58.829 45.455 9.46 0.00 45.52 4.30
1153 1173 3.868757 TGAGACTGGTGAATCTAACCG 57.131 47.619 0.00 0.00 40.86 4.44
1155 1175 4.698575 GGGATGAGACTGGTGAATCTAAC 58.301 47.826 0.00 0.00 0.00 2.34
1173 1193 1.445095 CAAGCTAGCTCTGCGGGAT 59.555 57.895 19.65 0.00 35.28 3.85
1174 1194 2.895680 CAAGCTAGCTCTGCGGGA 59.104 61.111 19.65 0.00 35.28 5.14
1178 1198 0.726256 GTCTTGCAAGCTAGCTCTGC 59.274 55.000 29.43 29.43 34.99 4.26
1198 1218 0.035739 TGTTTCCTAGCCACGGGAAC 59.964 55.000 0.00 1.68 40.76 3.62
1213 1233 2.887152 GGAGTTGCTTGTCTGGATGTTT 59.113 45.455 0.00 0.00 0.00 2.83
1287 1307 2.490902 GGTGGGTTGATGTCCTTTCCTT 60.491 50.000 0.00 0.00 0.00 3.36
1298 1318 2.034066 CAGGTGCGGTGGGTTGAT 59.966 61.111 0.00 0.00 0.00 2.57
1358 1378 0.395862 AGTGACCTCGACGGATCCAT 60.396 55.000 13.41 0.00 36.31 3.41
1359 1379 1.001269 AGTGACCTCGACGGATCCA 60.001 57.895 13.41 0.00 36.31 3.41
1388 1408 0.253327 GCGGGGAGGACAAGAAGATT 59.747 55.000 0.00 0.00 0.00 2.40
1469 1489 2.357034 GCACCTCGCGTCTTCCAA 60.357 61.111 5.77 0.00 0.00 3.53
1540 1560 1.312371 GCTGCCAAAATCGTGCCCTA 61.312 55.000 0.00 0.00 0.00 3.53
1550 1570 1.821936 CCAGTGTTGGCTGCCAAAA 59.178 52.632 33.75 27.24 45.73 2.44
1566 1586 2.515991 GATCCGATTTGGGCGCCA 60.516 61.111 30.85 12.04 38.76 5.69
1584 1604 2.113139 CCACGCCTGGGTTCAGTT 59.887 61.111 0.00 0.00 39.31 3.16
1607 1627 0.629596 ATCTCCTCCTCACACCCGTA 59.370 55.000 0.00 0.00 0.00 4.02
1809 1892 4.180057 CTGCTCGCACTAGAAGAAATTCT 58.820 43.478 0.00 0.00 35.17 2.40
1827 1910 2.301870 TGGGAATAGAACAACGACTGCT 59.698 45.455 0.00 0.00 0.00 4.24
2036 2144 3.254657 TCCCAACTTAAATCAAGCAACCG 59.745 43.478 0.00 0.00 37.83 4.44
2037 2145 4.864704 TCCCAACTTAAATCAAGCAACC 57.135 40.909 0.00 0.00 37.83 3.77
2038 2146 4.627035 GCATCCCAACTTAAATCAAGCAAC 59.373 41.667 0.00 0.00 37.83 4.17
2039 2147 4.527816 AGCATCCCAACTTAAATCAAGCAA 59.472 37.500 0.00 0.00 37.83 3.91
2042 2150 5.654497 GGAAGCATCCCAACTTAAATCAAG 58.346 41.667 0.00 0.00 40.10 3.02
2086 2211 5.822519 TCTGAAACAGCAGAATGTAACACTT 59.177 36.000 0.00 0.00 41.65 3.16
2159 2299 6.723977 TCCTTGCCCACAGATTTAAAAACTAT 59.276 34.615 0.00 0.00 0.00 2.12
2172 2312 4.019174 ACTTGAATATTCCTTGCCCACAG 58.981 43.478 12.90 0.00 0.00 3.66
2207 2823 7.133891 ACGTCCAAAGTTGATAAAATGAGAG 57.866 36.000 0.00 0.00 0.00 3.20
2253 2869 6.938596 GGGCCTCTTTTTACTAAACTGAACTA 59.061 38.462 0.84 0.00 0.00 2.24
2412 3042 7.037438 ACTGTGATTGGATGCAATGTATTTTC 58.963 34.615 17.95 2.35 0.00 2.29
2453 3083 5.644977 ATCGATAGCGTAATTCTGATCCA 57.355 39.130 0.00 0.00 38.98 3.41
2486 3118 7.538678 GCACTGAAACTAATGTTCAATTCGATT 59.461 33.333 0.00 0.00 34.96 3.34
2487 3119 7.023575 GCACTGAAACTAATGTTCAATTCGAT 58.976 34.615 0.00 0.00 34.96 3.59
2670 3303 8.969260 TTGTGTATCAGATCAAGCTATCAATT 57.031 30.769 0.00 0.00 0.00 2.32
2852 3487 6.839124 ATTATCAGTGGAACAAGCATTCAA 57.161 33.333 0.00 0.00 44.16 2.69
2967 3602 3.306019 GCCAACCTACAAATCACCAAAGG 60.306 47.826 0.00 0.00 0.00 3.11
2970 3605 3.237268 AGCCAACCTACAAATCACCAA 57.763 42.857 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.