Multiple sequence alignment - TraesCS6D01G231600

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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 TraesCS6D01G231600 chr6D 100.000 4573 0 0 1 4573 325388579 325393151 0.000000e+00 8445.0
1 TraesCS6D01G231600 chr6D 87.790 991 85 20 1621 2603 417474071 417473109 0.000000e+00 1127.0
2 TraesCS6D01G231600 chr6D 87.386 991 89 20 1621 2603 416965090 416964128 0.000000e+00 1105.0
3 TraesCS6D01G231600 chr6D 83.298 952 123 23 2150 3098 415515407 415514489 0.000000e+00 845.0
4 TraesCS6D01G231600 chr6D 84.349 722 63 19 2829 3547 416016237 416015563 0.000000e+00 662.0
5 TraesCS6D01G231600 chr6D 84.349 722 63 19 2829 3547 416123779 416123105 0.000000e+00 662.0
6 TraesCS6D01G231600 chr6D 84.072 722 65 17 2829 3547 417472836 417472162 0.000000e+00 651.0
7 TraesCS6D01G231600 chr6D 84.072 722 64 20 2829 3547 416963855 416963182 0.000000e+00 649.0
8 TraesCS6D01G231600 chr6D 81.646 474 45 25 1621 2090 417480561 417480126 5.630000e-94 355.0
9 TraesCS6D01G231600 chr6D 94.505 182 10 0 2690 2871 417479899 417479718 9.690000e-72 281.0
10 TraesCS6D01G231600 chr6D 81.742 356 42 13 1021 1375 417481430 417481097 4.510000e-70 276.0
11 TraesCS6D01G231600 chr6D 93.407 182 12 0 2690 2871 416016510 416016329 2.100000e-68 270.0
12 TraesCS6D01G231600 chr6D 93.407 182 12 0 2690 2871 416124052 416123871 2.100000e-68 270.0
13 TraesCS6D01G231600 chr6D 93.407 182 12 0 2690 2871 416964128 416963947 2.100000e-68 270.0
14 TraesCS6D01G231600 chr6D 80.618 356 46 13 1021 1375 416018889 416018556 2.110000e-63 254.0
15 TraesCS6D01G231600 chr6D 80.508 354 46 13 1023 1375 416966022 416965691 2.730000e-62 250.0
16 TraesCS6D01G231600 chr6D 76.548 533 71 30 1443 1971 417481098 417480616 4.570000e-60 243.0
17 TraesCS6D01G231600 chr6D 80.000 315 29 12 1660 1971 416018151 416017868 7.760000e-48 202.0
18 TraesCS6D01G231600 chr6D 80.000 315 29 12 1660 1971 416126058 416125775 7.760000e-48 202.0
19 TraesCS6D01G231600 chr6D 80.000 315 29 12 1660 1971 416965428 416965145 7.760000e-48 202.0
20 TraesCS6D01G231600 chr6D 91.549 71 5 1 3158 3228 416016323 416016254 3.770000e-16 97.1
21 TraesCS6D01G231600 chr6D 91.549 71 5 1 3158 3228 416123865 416123796 3.770000e-16 97.1
22 TraesCS6D01G231600 chr6D 91.549 71 5 1 3158 3228 416963941 416963872 3.770000e-16 97.1
23 TraesCS6D01G231600 chr6D 91.549 71 5 1 3158 3228 417472922 417472853 3.770000e-16 97.1
24 TraesCS6D01G231600 chr6A 96.257 2805 84 7 834 3622 463527653 463530452 0.000000e+00 4578.0
25 TraesCS6D01G231600 chr6A 94.675 770 30 8 1 768 463526331 463527091 0.000000e+00 1184.0
26 TraesCS6D01G231600 chr6A 94.286 280 13 2 4291 4570 463531474 463531750 4.230000e-115 425.0
27 TraesCS6D01G231600 chr6A 94.712 208 10 1 3847 4053 463530660 463530867 5.710000e-84 322.0
28 TraesCS6D01G231600 chr6A 93.750 160 10 0 3690 3849 463530452 463530611 1.640000e-59 241.0
29 TraesCS6D01G231600 chr6A 89.933 149 7 6 697 841 463527110 463527254 7.810000e-43 185.0
30 TraesCS6D01G231600 chr6A 100.000 30 0 0 4104 4133 463530790 463530819 6.390000e-04 56.5
31 TraesCS6D01G231600 chr6B 95.260 2806 85 15 1064 3849 497888650 497885873 0.000000e+00 4401.0
32 TraesCS6D01G231600 chr6B 86.456 1078 92 23 1618 2684 629580480 629581514 0.000000e+00 1133.0
33 TraesCS6D01G231600 chr6B 86.364 1078 93 23 1618 2684 628894531 628895565 0.000000e+00 1127.0
34 TraesCS6D01G231600 chr6B 93.667 600 19 8 1 595 497890012 497889427 0.000000e+00 880.0
35 TraesCS6D01G231600 chr6B 93.162 585 32 4 3992 4573 497885715 497885136 0.000000e+00 852.0
36 TraesCS6D01G231600 chr6B 89.206 491 53 0 2381 2871 628893705 628894195 8.410000e-172 614.0
37 TraesCS6D01G231600 chr6B 89.206 491 53 0 2381 2871 629579654 629580144 8.410000e-172 614.0
38 TraesCS6D01G231600 chr6B 82.316 475 48 20 1618 2089 628893258 628893699 3.340000e-101 379.0
39 TraesCS6D01G231600 chr6B 82.316 475 48 20 1618 2089 629579207 629579648 3.340000e-101 379.0
40 TraesCS6D01G231600 chr6B 93.004 243 7 2 816 1048 497888957 497888715 3.390000e-91 346.0
41 TraesCS6D01G231600 chr6B 87.189 281 30 4 3270 3547 628895567 628895844 9.550000e-82 315.0
42 TraesCS6D01G231600 chr6B 86.833 281 31 4 3270 3547 629581516 629581793 4.440000e-80 309.0
43 TraesCS6D01G231600 chr6B 79.494 356 41 16 1021 1375 628892383 628892707 1.660000e-54 224.0
44 TraesCS6D01G231600 chr6B 79.494 356 41 16 1021 1375 629578332 629578656 1.660000e-54 224.0
45 TraesCS6D01G231600 chr6B 95.690 116 4 1 3847 3961 497885826 497885711 7.810000e-43 185.0
46 TraesCS6D01G231600 chr6B 87.742 155 16 2 1820 1971 629578979 629579133 1.310000e-40 178.0
47 TraesCS6D01G231600 chr6B 83.251 203 13 8 3158 3352 628894201 628894390 2.830000e-37 167.0
48 TraesCS6D01G231600 chr6B 83.251 203 13 8 3158 3352 629580150 629580339 2.830000e-37 167.0
49 TraesCS6D01G231600 chr6B 97.059 34 1 0 4071 4104 43088785 43088818 1.780000e-04 58.4
50 TraesCS6D01G231600 chr5B 100.000 34 0 0 4071 4104 433456607 433456640 3.820000e-06 63.9
51 TraesCS6D01G231600 chr5A 100.000 34 0 0 4071 4104 589326455 589326422 3.820000e-06 63.9
52 TraesCS6D01G231600 chr4B 100.000 34 0 0 4071 4104 580964922 580964955 3.820000e-06 63.9
53 TraesCS6D01G231600 chr1D 100.000 32 0 0 4071 4102 460311094 460311063 4.940000e-05 60.2
54 TraesCS6D01G231600 chr3B 100.000 31 0 0 4071 4101 3208751 3208781 1.780000e-04 58.4
55 TraesCS6D01G231600 chr3B 100.000 31 0 0 4071 4101 61873409 61873439 1.780000e-04 58.4
56 TraesCS6D01G231600 chr3A 100.000 28 0 0 4051 4078 645050714 645050687 8.000000e-03 52.8


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 TraesCS6D01G231600 chr6D 325388579 325393151 4572 False 8445.000000 8445 100.000000 1 4573 1 chr6D.!!$F1 4572
1 TraesCS6D01G231600 chr6D 415514489 415515407 918 True 845.000000 845 83.298000 2150 3098 1 chr6D.!!$R1 948
2 TraesCS6D01G231600 chr6D 417472162 417474071 1909 True 625.033333 1127 87.803667 1621 3547 3 chr6D.!!$R5 1926
3 TraesCS6D01G231600 chr6D 416963182 416966022 2840 True 428.850000 1105 86.153667 1023 3547 6 chr6D.!!$R4 2524
4 TraesCS6D01G231600 chr6D 416123105 416126058 2953 True 307.775000 662 87.326250 1660 3547 4 chr6D.!!$R3 1887
5 TraesCS6D01G231600 chr6D 416015563 416018889 3326 True 297.020000 662 85.984600 1021 3547 5 chr6D.!!$R2 2526
6 TraesCS6D01G231600 chr6D 417479718 417481430 1712 True 288.750000 355 83.610250 1021 2871 4 chr6D.!!$R6 1850
7 TraesCS6D01G231600 chr6A 463526331 463531750 5419 False 998.785714 4578 94.801857 1 4570 7 chr6A.!!$F1 4569
8 TraesCS6D01G231600 chr6B 497885136 497890012 4876 True 1332.800000 4401 94.156600 1 4573 5 chr6B.!!$R1 4572
9 TraesCS6D01G231600 chr6B 628892383 628895844 3461 False 471.000000 1127 84.636667 1021 3547 6 chr6B.!!$F2 2526
10 TraesCS6D01G231600 chr6B 629578332 629581793 3461 False 429.142857 1133 85.042571 1021 3547 7 chr6B.!!$F3 2526

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
385 397 1.078823 TGACACTACCCCATGAGAGGT 59.921 52.381 0.0 0.26 40.31 3.85 F
593 610 2.159572 GCAAATGCAGAAATACGTCGGT 60.160 45.455 0.0 0.00 41.59 4.69 F
1619 2549 0.918983 TGGGCTCCATCGATTCCTTT 59.081 50.000 0.0 0.00 0.00 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1581 2368 0.586319 AACACAACTCATGAACCGCG 59.414 50.000 0.0 0.0 0.00 6.46 R
1810 2858 1.091771 GCAGCAAGCCTAGATCGCAA 61.092 55.000 0.0 0.0 37.23 4.85 R
3576 7438 1.466558 GAACTAGCACAAGCAAGAGCC 59.533 52.381 0.0 0.0 45.49 4.70 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
214 226 3.823304 GCTCTTTTGGTCCAGACAGAATT 59.177 43.478 0.00 0.00 0.00 2.17
215 227 4.279420 GCTCTTTTGGTCCAGACAGAATTT 59.721 41.667 0.00 0.00 0.00 1.82
216 228 5.221322 GCTCTTTTGGTCCAGACAGAATTTT 60.221 40.000 0.00 0.00 0.00 1.82
217 229 6.016276 GCTCTTTTGGTCCAGACAGAATTTTA 60.016 38.462 0.00 0.00 0.00 1.52
218 230 7.272037 TCTTTTGGTCCAGACAGAATTTTAC 57.728 36.000 0.00 0.00 0.00 2.01
219 231 5.682943 TTTGGTCCAGACAGAATTTTACG 57.317 39.130 0.00 0.00 0.00 3.18
220 232 4.345859 TGGTCCAGACAGAATTTTACGT 57.654 40.909 0.00 0.00 0.00 3.57
221 233 4.062293 TGGTCCAGACAGAATTTTACGTG 58.938 43.478 0.00 0.00 0.00 4.49
222 234 3.120304 GGTCCAGACAGAATTTTACGTGC 60.120 47.826 0.00 0.00 0.00 5.34
223 235 3.746492 GTCCAGACAGAATTTTACGTGCT 59.254 43.478 0.00 0.00 0.00 4.40
303 315 2.037901 TCATTTTTGGAAGCTGGCACA 58.962 42.857 0.00 0.00 0.00 4.57
328 340 4.019174 CAAGGGCAATTGAGATACCAACT 58.981 43.478 10.34 0.00 31.55 3.16
382 394 1.195115 GCTGACACTACCCCATGAGA 58.805 55.000 0.00 0.00 0.00 3.27
383 395 1.137872 GCTGACACTACCCCATGAGAG 59.862 57.143 0.00 0.00 0.00 3.20
384 396 1.759445 CTGACACTACCCCATGAGAGG 59.241 57.143 0.00 0.00 0.00 3.69
385 397 1.078823 TGACACTACCCCATGAGAGGT 59.921 52.381 0.00 0.26 40.31 3.85
409 421 8.374327 GTTCCTAACCAATATTTATGTACGCT 57.626 34.615 0.00 0.00 0.00 5.07
416 428 9.555727 AACCAATATTTATGTACGCTACAGAAT 57.444 29.630 6.21 8.93 42.77 2.40
557 573 4.383774 CACACTTTGCAATGCAGAAATG 57.616 40.909 8.31 7.97 40.61 2.32
593 610 2.159572 GCAAATGCAGAAATACGTCGGT 60.160 45.455 0.00 0.00 41.59 4.69
595 612 2.380084 ATGCAGAAATACGTCGGTGT 57.620 45.000 0.00 0.00 0.00 4.16
608 625 2.263077 GTCGGTGTCTACTTGATGCAG 58.737 52.381 0.00 0.00 0.00 4.41
615 632 4.058124 TGTCTACTTGATGCAGTGTGTTC 58.942 43.478 0.00 0.00 0.00 3.18
657 674 7.871973 TGGTGATGAATTAATTTGGTTTGTCAG 59.128 33.333 1.43 0.00 0.00 3.51
658 675 8.087750 GGTGATGAATTAATTTGGTTTGTCAGA 58.912 33.333 1.43 0.00 0.00 3.27
703 720 3.244146 TGGAATGTTGATGTTGCCTTTGG 60.244 43.478 0.00 0.00 0.00 3.28
710 727 3.509442 TGATGTTGCCTTTGGATTTCCT 58.491 40.909 0.00 0.00 36.82 3.36
795 901 3.042871 CTGAGCAGCTGTTCTTTCTCT 57.957 47.619 27.78 8.89 0.00 3.10
796 902 2.737783 CTGAGCAGCTGTTCTTTCTCTG 59.262 50.000 27.78 17.35 0.00 3.35
1010 1733 3.880846 CAAGAAGATGGCCGCCGC 61.881 66.667 4.58 0.00 0.00 6.53
1619 2549 0.918983 TGGGCTCCATCGATTCCTTT 59.081 50.000 0.00 0.00 0.00 3.11
1693 2713 1.160137 ATTGCTCACAGGAACGAAGC 58.840 50.000 0.00 0.00 0.00 3.86
1757 2779 7.632861 TCTTGATTGATAGATGTTCCAGGAAA 58.367 34.615 2.45 0.00 0.00 3.13
1822 2870 3.833706 GCACATTTGCGATCTAGGC 57.166 52.632 0.00 0.00 39.50 3.93
1823 2871 1.303309 GCACATTTGCGATCTAGGCT 58.697 50.000 0.00 0.00 39.50 4.58
1894 2946 8.088365 TGGAGTAACATTATCTCAATCATACCG 58.912 37.037 0.00 0.00 0.00 4.02
2026 3489 9.832445 TCTACCCATTTGATCTTTCATAAGTAC 57.168 33.333 0.00 0.00 32.98 2.73
2099 3562 2.338500 ACCAACGAGAGAAGATTTCGC 58.662 47.619 0.00 0.00 37.84 4.70
2220 3683 7.147949 CCTTTCATAGATCAGCCTCACATTTTT 60.148 37.037 0.00 0.00 0.00 1.94
2256 3720 7.595875 TGTCATGTTCAATTAGTTTGCTTGATG 59.404 33.333 0.00 0.00 35.16 3.07
2353 4519 1.846541 GAGCTCGCTCCTCACATAAC 58.153 55.000 7.68 0.00 37.11 1.89
2551 6272 5.479375 AGAACATGCATTTGAGACAATCCTT 59.521 36.000 0.00 0.00 0.00 3.36
2630 6354 2.743664 TCATGATGGTCGTGCTTTTGAG 59.256 45.455 0.00 0.00 33.54 3.02
2845 6570 5.306160 TGTTAGCAGTTAACTAGGGAGTTGT 59.694 40.000 8.04 0.00 45.74 3.32
2930 6786 2.077687 ATGGCTTGGGGAATGATCAC 57.922 50.000 0.00 0.00 0.00 3.06
3079 6937 8.911247 ACTGTCTAGTTTGTTGAAATGAAAAC 57.089 30.769 0.00 0.00 31.66 2.43
3083 6941 7.376072 GTCTAGTTTGTTGAAATGAAAACTCGG 59.624 37.037 3.13 0.08 40.90 4.63
3089 6947 3.420893 TGAAATGAAAACTCGGGCTGAT 58.579 40.909 0.00 0.00 0.00 2.90
3128 6986 7.511959 TCGTGTATAGAGTTCATGAGCTAAT 57.488 36.000 12.49 11.27 0.00 1.73
3191 7049 8.675504 TGTAACTTATCTAGACAGAGCACTTAC 58.324 37.037 7.62 6.20 33.22 2.34
3321 7179 5.779529 ACTTCAGTTCACTGCATTGAATT 57.220 34.783 20.72 14.74 43.46 2.17
3326 7184 6.571605 TCAGTTCACTGCATTGAATTTTTGA 58.428 32.000 20.72 17.56 43.46 2.69
3358 7216 0.250510 TGCACCCGCAGTTTCACATA 60.251 50.000 0.00 0.00 45.36 2.29
3576 7438 2.549754 ACACTTGCTTTTCTGTGATCCG 59.450 45.455 0.00 0.00 34.81 4.18
3613 7475 0.400213 TTCCAGACAAGCCGATTGGT 59.600 50.000 0.00 0.00 43.68 3.67
3668 7530 3.700130 AAACTAACGAAATCGACAGCG 57.300 42.857 10.16 0.00 43.02 5.18
3670 7532 2.248487 ACTAACGAAATCGACAGCGTC 58.752 47.619 10.16 0.00 43.02 5.19
3681 7543 5.950965 ATCGACAGCGTCAAATACTAAAG 57.049 39.130 8.91 0.00 38.98 1.85
3687 7549 6.228258 ACAGCGTCAAATACTAAAGAAAGGA 58.772 36.000 0.00 0.00 0.00 3.36
3723 7585 0.185901 ATGGTGGTTTGCTGTCCTGT 59.814 50.000 0.00 0.00 0.00 4.00
3750 7612 5.945784 TGATGGAAGAAGTTTTAGGTCATGG 59.054 40.000 0.00 0.00 0.00 3.66
3786 7648 7.862372 TCAGCATTTGAACACAGATTCTTAAAC 59.138 33.333 0.00 0.00 31.34 2.01
3824 7686 4.774200 CCCATTGGAGAAGTGGAAAATTCT 59.226 41.667 3.62 0.00 38.46 2.40
3845 7707 2.029739 TGCACTGTTGGCTTGATGATTG 60.030 45.455 0.00 0.00 0.00 2.67
3860 7773 4.525874 TGATGATTGTGGCATTGGTTACAA 59.474 37.500 0.00 0.00 41.59 2.41
3864 7777 1.612950 TGTGGCATTGGTTACAAGCAG 59.387 47.619 0.00 0.00 40.49 4.24
3926 7841 6.187125 TCTGAAATTTATTCTGCAGCTGAC 57.813 37.500 20.43 9.67 0.00 3.51
3996 7911 0.107508 GCCTGCTGCTTCATCAGGTA 60.108 55.000 15.46 0.00 46.01 3.08
4036 7951 2.094675 GGTTGCTCAATATGCCACTGT 58.905 47.619 0.00 0.00 0.00 3.55
4079 8088 9.179909 TCAAAATTCAGTTACCTTTTCAGTACA 57.820 29.630 0.00 0.00 0.00 2.90
4176 8188 9.908152 AAGTTTAGCACATGGAATTACTTTTAC 57.092 29.630 0.00 0.00 0.00 2.01
4182 8194 7.834181 AGCACATGGAATTACTTTTACCTATGT 59.166 33.333 0.00 0.00 0.00 2.29
4183 8195 8.466798 GCACATGGAATTACTTTTACCTATGTT 58.533 33.333 0.00 0.00 0.00 2.71
4213 8308 7.589954 TCAAAAGAATTACTTGCTAGCGAAAAC 59.410 33.333 10.77 0.44 38.98 2.43
4220 8315 3.248602 ACTTGCTAGCGAAAACTCAACAG 59.751 43.478 10.77 0.00 0.00 3.16
4417 8729 0.962855 GCTGAGGTTCTTCAAGGCCC 60.963 60.000 0.00 0.00 0.00 5.80
4471 8783 3.191669 TCGTTATTAGTTGATGTGGCCG 58.808 45.455 0.00 0.00 0.00 6.13
4491 8803 4.430908 CCGGTGATAGTTTTGTCCTAGAC 58.569 47.826 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
221 233 4.278678 AGTATACGAATTTTGCAGCAGC 57.721 40.909 0.00 0.00 42.57 5.25
222 234 5.030295 CCAAGTATACGAATTTTGCAGCAG 58.970 41.667 0.00 0.00 0.00 4.24
223 235 4.697828 TCCAAGTATACGAATTTTGCAGCA 59.302 37.500 0.00 0.00 0.00 4.41
232 244 3.741388 GCACCAGCTCCAAGTATACGAAT 60.741 47.826 0.00 0.00 37.91 3.34
303 315 2.358195 GGTATCTCAATTGCCCTTGGGT 60.358 50.000 7.61 0.00 0.00 4.51
328 340 2.744494 GCCAAAAACACAAATCTGGGCA 60.744 45.455 0.00 0.00 38.71 5.36
384 396 8.374327 AGCGTACATAAATATTGGTTAGGAAC 57.626 34.615 0.00 0.00 0.00 3.62
385 397 9.480053 GTAGCGTACATAAATATTGGTTAGGAA 57.520 33.333 0.00 0.00 0.00 3.36
454 469 2.474359 GCTTCCGTCTGATTCATCATCG 59.526 50.000 7.24 7.24 36.02 3.84
502 518 6.469782 AAACCATTCAACAGTCAAGTCATT 57.530 33.333 0.00 0.00 0.00 2.57
593 610 3.751479 ACACACTGCATCAAGTAGACA 57.249 42.857 0.00 0.00 33.69 3.41
595 612 4.607293 AGAACACACTGCATCAAGTAGA 57.393 40.909 0.00 0.00 33.69 2.59
608 625 3.002246 TCAGATTTGCACGAAGAACACAC 59.998 43.478 0.00 0.00 0.00 3.82
615 632 2.743664 TCACCATCAGATTTGCACGAAG 59.256 45.455 0.00 0.00 0.00 3.79
657 674 2.411904 CAGACTGGCAAGTGAGTCTTC 58.588 52.381 0.00 0.00 45.41 2.87
658 675 1.542108 GCAGACTGGCAAGTGAGTCTT 60.542 52.381 0.00 0.00 45.41 3.01
746 763 1.999648 ATGCAAAGGCTTGTCTCCAA 58.000 45.000 0.00 0.00 41.91 3.53
749 766 2.064014 GCAAATGCAAAGGCTTGTCTC 58.936 47.619 0.00 0.00 41.91 3.36
750 767 2.159327 GCAAATGCAAAGGCTTGTCT 57.841 45.000 0.00 0.00 41.91 3.41
788 894 2.797156 CCTGTTCGTGACACAGAGAAAG 59.203 50.000 6.37 3.68 43.90 2.62
795 901 0.673985 CCTCTCCTGTTCGTGACACA 59.326 55.000 6.37 0.00 33.82 3.72
796 902 0.959553 TCCTCTCCTGTTCGTGACAC 59.040 55.000 0.00 0.00 33.82 3.67
850 1562 4.400961 AAGCGAGGTGGGCTCTGC 62.401 66.667 0.00 0.00 40.53 4.26
1581 2368 0.586319 AACACAACTCATGAACCGCG 59.414 50.000 0.00 0.00 0.00 6.46
1619 2549 3.181451 ACATCTGCTCCAAGACTTGACAA 60.181 43.478 16.99 1.19 0.00 3.18
1693 2713 5.398603 ACAGAATGCTAAGATATCGAGGG 57.601 43.478 9.05 0.00 42.53 4.30
1757 2779 8.980481 AATAATCATTAGGAGTTTCCAATCGT 57.020 30.769 0.00 0.00 39.61 3.73
1805 2853 2.540361 GCAAGCCTAGATCGCAAATGTG 60.540 50.000 0.00 0.00 0.00 3.21
1806 2854 1.672881 GCAAGCCTAGATCGCAAATGT 59.327 47.619 0.00 0.00 0.00 2.71
1807 2855 1.945394 AGCAAGCCTAGATCGCAAATG 59.055 47.619 0.00 0.00 0.00 2.32
1808 2856 1.945394 CAGCAAGCCTAGATCGCAAAT 59.055 47.619 0.00 0.00 0.00 2.32
1809 2857 1.372582 CAGCAAGCCTAGATCGCAAA 58.627 50.000 0.00 0.00 0.00 3.68
1810 2858 1.091771 GCAGCAAGCCTAGATCGCAA 61.092 55.000 0.00 0.00 37.23 4.85
1811 2859 1.522355 GCAGCAAGCCTAGATCGCA 60.522 57.895 0.00 0.00 37.23 5.10
1812 2860 3.328189 GCAGCAAGCCTAGATCGC 58.672 61.111 0.00 0.00 37.23 4.58
1821 2869 3.227810 AGCAGAAATTTAGCAGCAAGC 57.772 42.857 15.12 0.00 46.19 4.01
1822 2870 3.367025 GCAAGCAGAAATTTAGCAGCAAG 59.633 43.478 18.76 8.26 33.62 4.01
1823 2871 3.006110 AGCAAGCAGAAATTTAGCAGCAA 59.994 39.130 22.40 0.00 35.12 3.91
1894 2946 5.215160 GGTCGATCAAATAAATGCACCATC 58.785 41.667 0.00 0.00 0.00 3.51
2220 3683 8.143193 ACTAATTGAACATGACATGCAAGAAAA 58.857 29.630 15.49 2.76 0.00 2.29
2256 3720 3.437049 GGATCCGTTAGCTGCATAATTCC 59.563 47.826 1.02 0.00 0.00 3.01
2353 4519 2.324215 CATGCGCTTCCCATGGTAG 58.676 57.895 11.73 8.83 37.12 3.18
2551 6272 5.000591 TCCAATCACGAGCTGAAACAATAA 58.999 37.500 0.00 0.00 30.60 1.40
2630 6354 2.208431 CAATCCTCGACCTCTGAATGC 58.792 52.381 0.00 0.00 0.00 3.56
2797 6522 7.069085 ACAAATGCATGCTAAGAGGTAATGATT 59.931 33.333 20.33 2.20 0.00 2.57
2812 6537 5.163513 AGTTAACTGCTAACAAATGCATGC 58.836 37.500 11.82 11.82 42.18 4.06
3083 6941 3.179443 TGAGTTGATAACGGATCAGCC 57.821 47.619 11.19 5.78 44.62 4.85
3089 6947 3.861276 ACACGATGAGTTGATAACGGA 57.139 42.857 0.00 0.00 36.23 4.69
3191 7049 5.812642 AGCCTAGTTGATTGAAGTAACATCG 59.187 40.000 0.00 0.00 0.00 3.84
3321 7179 5.642919 GGGTGCAATGCTATCAAATTCAAAA 59.357 36.000 6.82 0.00 0.00 2.44
3326 7184 2.481795 GCGGGTGCAATGCTATCAAATT 60.482 45.455 6.82 0.00 42.15 1.82
3358 7216 4.823442 TCTGCATTCAGTTCAGACACAAAT 59.177 37.500 0.00 0.00 41.10 2.32
3412 7274 1.536766 TCGCCTTTTGCATCTTCACTG 59.463 47.619 0.00 0.00 41.33 3.66
3576 7438 1.466558 GAACTAGCACAAGCAAGAGCC 59.533 52.381 0.00 0.00 45.49 4.70
3613 7475 2.965831 CTGGCACTGGTAGGAGCTTATA 59.034 50.000 0.00 0.00 0.00 0.98
3681 7543 9.877178 CCATTCTATACAGTATATGGTCCTTTC 57.123 37.037 10.91 0.00 0.00 2.62
3687 7549 8.506196 AACCACCATTCTATACAGTATATGGT 57.494 34.615 16.39 16.39 41.34 3.55
3723 7585 6.778821 TGACCTAAAACTTCTTCCATCATCA 58.221 36.000 0.00 0.00 0.00 3.07
3750 7612 3.988379 TCAAATGCTGACCAAGTGTTC 57.012 42.857 0.00 0.00 0.00 3.18
3786 7648 3.198068 CAATGGGGAGACTAATGTCACG 58.802 50.000 0.00 0.00 45.20 4.35
3824 7686 1.913778 ATCATCAAGCCAACAGTGCA 58.086 45.000 0.00 0.00 0.00 4.57
3845 7707 1.613437 ACTGCTTGTAACCAATGCCAC 59.387 47.619 0.00 0.00 0.00 5.01
3996 7911 6.702329 CAACCAGTTTCTTGTCTACTCCTAT 58.298 40.000 0.00 0.00 0.00 2.57
4067 8076 9.965824 ATAACTGAATTTTGTGTACTGAAAAGG 57.034 29.630 0.00 0.00 0.00 3.11
4079 8088 9.878599 CGTACTGAAAAGATAACTGAATTTTGT 57.121 29.630 0.00 0.00 0.00 2.83
4183 8195 8.132362 TCGCTAGCAAGTAATTCTTTTGAAAAA 58.868 29.630 16.45 0.00 42.31 1.94
4213 8308 7.579589 TCAAATTTGTGTCAAAACTGTTGAG 57.420 32.000 17.47 0.00 0.00 3.02
4330 8642 9.804758 AAAACCAAAGTGTTTCGATGTAATAAA 57.195 25.926 0.00 0.00 37.46 1.40
4340 8652 4.617645 TGTTTCGAAAACCAAAGTGTTTCG 59.382 37.500 13.10 10.60 37.46 3.46
4400 8712 0.110486 GTGGGCCTTGAAGAACCTCA 59.890 55.000 4.53 0.00 0.00 3.86
4417 8729 7.044510 CGTTTGATAAAGCATGCTTTCATAGTG 60.045 37.037 40.96 24.83 44.17 2.74
4471 8783 5.046520 AGGTGTCTAGGACAAAACTATCACC 60.047 44.000 1.77 13.78 44.49 4.02


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

AutoCloner maintained by Alex Coulton.