Multiple sequence alignment - TraesCS4D01G188700

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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 TraesCS4D01G188700 chr4D 100.000 3101 0 0 1 3101 328186706 328183606 0.000000e+00 5727
1 TraesCS4D01G188700 chr4D 74.091 660 150 18 1424 2075 246517872 246517226 5.130000e-63 252
2 TraesCS4D01G188700 chr4B 94.965 2602 59 27 536 3101 407808966 407806401 0.000000e+00 4013
3 TraesCS4D01G188700 chr4B 73.979 661 149 21 1424 2075 267670065 267670711 2.390000e-61 246
4 TraesCS4D01G188700 chr4A 92.100 2747 71 45 439 3101 142343812 142346496 0.000000e+00 3736
5 TraesCS4D01G188700 chr4A 88.559 236 21 5 206 436 142343428 142343662 6.550000e-72 281
6 TraesCS4D01G188700 chr4A 74.018 662 147 24 1424 2075 239578758 239578112 2.390000e-61 246
7 TraesCS4D01G188700 chr5D 97.988 646 13 0 1045 1690 358593094 358592449 0.000000e+00 1122
8 TraesCS4D01G188700 chr5D 90.674 193 6 3 554 741 358593287 358593102 2.390000e-61 246
9 TraesCS4D01G188700 chr2D 77.239 681 112 33 1423 2071 83859720 83860389 2.940000e-95 359
10 TraesCS4D01G188700 chr2D 75.826 666 127 28 1423 2068 473087689 473087038 1.080000e-79 307
11 TraesCS4D01G188700 chr2A 76.583 679 120 29 1423 2071 84646555 84647224 1.380000e-88 337
12 TraesCS4D01G188700 chr2A 75.262 667 129 27 1423 2068 614523022 614522371 5.060000e-73 285
13 TraesCS4D01G188700 chr2B 76.293 696 119 35 1423 2083 135775808 135776492 2.310000e-86 329
14 TraesCS4D01G188700 chr2B 75.327 689 130 31 1423 2086 552340729 552340056 8.410000e-76 294


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 TraesCS4D01G188700 chr4D 328183606 328186706 3100 True 5727.0 5727 100.0000 1 3101 1 chr4D.!!$R2 3100
1 TraesCS4D01G188700 chr4D 246517226 246517872 646 True 252.0 252 74.0910 1424 2075 1 chr4D.!!$R1 651
2 TraesCS4D01G188700 chr4B 407806401 407808966 2565 True 4013.0 4013 94.9650 536 3101 1 chr4B.!!$R1 2565
3 TraesCS4D01G188700 chr4B 267670065 267670711 646 False 246.0 246 73.9790 1424 2075 1 chr4B.!!$F1 651
4 TraesCS4D01G188700 chr4A 142343428 142346496 3068 False 2008.5 3736 90.3295 206 3101 2 chr4A.!!$F1 2895
5 TraesCS4D01G188700 chr4A 239578112 239578758 646 True 246.0 246 74.0180 1424 2075 1 chr4A.!!$R1 651
6 TraesCS4D01G188700 chr5D 358592449 358593287 838 True 684.0 1122 94.3310 554 1690 2 chr5D.!!$R1 1136
7 TraesCS4D01G188700 chr2D 83859720 83860389 669 False 359.0 359 77.2390 1423 2071 1 chr2D.!!$F1 648
8 TraesCS4D01G188700 chr2D 473087038 473087689 651 True 307.0 307 75.8260 1423 2068 1 chr2D.!!$R1 645
9 TraesCS4D01G188700 chr2A 84646555 84647224 669 False 337.0 337 76.5830 1423 2071 1 chr2A.!!$F1 648
10 TraesCS4D01G188700 chr2A 614522371 614523022 651 True 285.0 285 75.2620 1423 2068 1 chr2A.!!$R1 645
11 TraesCS4D01G188700 chr2B 135775808 135776492 684 False 329.0 329 76.2930 1423 2083 1 chr2B.!!$F1 660
12 TraesCS4D01G188700 chr2B 552340056 552340729 673 True 294.0 294 75.3270 1423 2086 1 chr2B.!!$R1 663

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
135 136 0.040157 AACATGCGATGTGTGTGTGC 60.04 50.0 0.0 0.0 44.07 4.57 F
137 138 0.040246 CATGCGATGTGTGTGTGCAA 60.04 50.0 0.0 0.0 39.26 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1047 1227 2.390599 CGGCGACAAGACCACCATG 61.391 63.158 0.0 0.0 0.00 3.66 R
2318 2525 2.691409 ATATGTGGGACAACAGACCG 57.309 50.000 0.0 0.0 44.16 4.79 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
26 27 8.793592 GGAAAATAAAAAGAGAGTGTACATGGT 58.206 33.333 0.00 0.00 0.00 3.55
27 28 9.612620 GAAAATAAAAAGAGAGTGTACATGGTG 57.387 33.333 0.00 0.00 0.00 4.17
28 29 8.691661 AAATAAAAAGAGAGTGTACATGGTGT 57.308 30.769 0.00 0.00 0.00 4.16
29 30 8.691661 AATAAAAAGAGAGTGTACATGGTGTT 57.308 30.769 0.00 0.00 0.00 3.32
30 31 6.377327 AAAAAGAGAGTGTACATGGTGTTG 57.623 37.500 0.00 0.00 0.00 3.33
31 32 3.685139 AGAGAGTGTACATGGTGTTGG 57.315 47.619 0.00 0.00 0.00 3.77
32 33 2.076863 GAGAGTGTACATGGTGTTGGC 58.923 52.381 0.00 0.00 0.00 4.52
33 34 1.165270 GAGTGTACATGGTGTTGGCC 58.835 55.000 0.00 0.00 0.00 5.36
34 35 0.476338 AGTGTACATGGTGTTGGCCA 59.524 50.000 0.00 0.00 43.48 5.36
35 36 1.133637 AGTGTACATGGTGTTGGCCAA 60.134 47.619 16.05 16.05 42.48 4.52
36 37 1.269448 GTGTACATGGTGTTGGCCAAG 59.731 52.381 21.21 8.67 42.48 3.61
37 38 1.143889 TGTACATGGTGTTGGCCAAGA 59.856 47.619 21.21 16.53 42.48 3.02
38 39 2.224992 TGTACATGGTGTTGGCCAAGAT 60.225 45.455 21.21 4.45 42.48 2.40
39 40 1.549203 ACATGGTGTTGGCCAAGATC 58.451 50.000 21.21 19.88 42.48 2.75
40 41 0.819582 CATGGTGTTGGCCAAGATCC 59.180 55.000 22.29 21.18 42.48 3.36
41 42 0.680921 ATGGTGTTGGCCAAGATCCG 60.681 55.000 22.29 0.00 42.48 4.18
42 43 1.303317 GGTGTTGGCCAAGATCCGT 60.303 57.895 21.21 0.00 0.00 4.69
43 44 1.586154 GGTGTTGGCCAAGATCCGTG 61.586 60.000 21.21 0.00 0.00 4.94
44 45 1.971167 TGTTGGCCAAGATCCGTGC 60.971 57.895 21.21 4.81 0.00 5.34
45 46 1.971167 GTTGGCCAAGATCCGTGCA 60.971 57.895 21.21 0.00 0.00 4.57
46 47 1.228398 TTGGCCAAGATCCGTGCAA 60.228 52.632 16.05 0.00 0.00 4.08
47 48 1.523154 TTGGCCAAGATCCGTGCAAC 61.523 55.000 16.05 0.00 0.00 4.17
60 61 2.281484 GCAACGGCAGGGAAGACA 60.281 61.111 0.00 0.00 40.72 3.41
61 62 1.675641 GCAACGGCAGGGAAGACAT 60.676 57.895 0.00 0.00 40.72 3.06
62 63 1.244019 GCAACGGCAGGGAAGACATT 61.244 55.000 0.00 0.00 40.72 2.71
63 64 0.804989 CAACGGCAGGGAAGACATTC 59.195 55.000 0.00 0.00 34.46 2.67
64 65 0.673644 AACGGCAGGGAAGACATTCG 60.674 55.000 0.00 0.00 36.19 3.34
65 66 2.464459 CGGCAGGGAAGACATTCGC 61.464 63.158 0.00 0.00 46.05 4.70
66 67 2.115291 GGCAGGGAAGACATTCGCC 61.115 63.158 1.90 0.00 46.68 5.54
67 68 2.464459 GCAGGGAAGACATTCGCCG 61.464 63.158 1.90 0.00 46.68 6.46
68 69 1.815421 CAGGGAAGACATTCGCCGG 60.815 63.158 0.00 0.00 46.68 6.13
69 70 2.513897 GGGAAGACATTCGCCGGG 60.514 66.667 2.18 0.00 41.32 5.73
70 71 2.582436 GGAAGACATTCGCCGGGA 59.418 61.111 2.18 0.00 36.19 5.14
71 72 1.146263 GGAAGACATTCGCCGGGAT 59.854 57.895 2.18 0.00 36.19 3.85
72 73 0.463833 GGAAGACATTCGCCGGGATT 60.464 55.000 2.18 0.00 36.19 3.01
73 74 1.202604 GGAAGACATTCGCCGGGATTA 60.203 52.381 2.18 0.00 36.19 1.75
74 75 2.550208 GGAAGACATTCGCCGGGATTAT 60.550 50.000 2.18 0.00 36.19 1.28
75 76 2.457366 AGACATTCGCCGGGATTATC 57.543 50.000 2.18 0.00 0.00 1.75
76 77 1.691976 AGACATTCGCCGGGATTATCA 59.308 47.619 2.18 0.00 0.00 2.15
77 78 1.798813 GACATTCGCCGGGATTATCAC 59.201 52.381 2.18 0.00 0.00 3.06
78 79 1.156736 CATTCGCCGGGATTATCACC 58.843 55.000 2.18 0.00 0.00 4.02
95 96 5.718649 ATCACCGACTGATAACATTTTCG 57.281 39.130 0.00 0.00 37.89 3.46
96 97 4.562082 TCACCGACTGATAACATTTTCGT 58.438 39.130 0.00 0.00 0.00 3.85
97 98 4.992319 TCACCGACTGATAACATTTTCGTT 59.008 37.500 0.00 0.00 0.00 3.85
98 99 5.467399 TCACCGACTGATAACATTTTCGTTT 59.533 36.000 0.00 0.00 0.00 3.60
99 100 6.017770 TCACCGACTGATAACATTTTCGTTTT 60.018 34.615 0.00 0.00 0.00 2.43
100 101 6.635239 CACCGACTGATAACATTTTCGTTTTT 59.365 34.615 0.00 0.00 0.00 1.94
101 102 7.799447 CACCGACTGATAACATTTTCGTTTTTA 59.201 33.333 0.00 0.00 0.00 1.52
102 103 8.344098 ACCGACTGATAACATTTTCGTTTTTAA 58.656 29.630 0.00 0.00 0.00 1.52
103 104 9.171701 CCGACTGATAACATTTTCGTTTTTAAA 57.828 29.630 0.00 0.00 0.00 1.52
133 134 4.560136 TTTTAACATGCGATGTGTGTGT 57.440 36.364 0.00 0.00 44.07 3.72
134 135 3.534524 TTAACATGCGATGTGTGTGTG 57.465 42.857 0.00 0.00 44.07 3.82
135 136 0.040157 AACATGCGATGTGTGTGTGC 60.040 50.000 0.00 0.00 44.07 4.57
136 137 1.165284 ACATGCGATGTGTGTGTGCA 61.165 50.000 0.00 0.00 43.01 4.57
137 138 0.040246 CATGCGATGTGTGTGTGCAA 60.040 50.000 0.00 0.00 39.26 4.08
138 139 0.667453 ATGCGATGTGTGTGTGCAAA 59.333 45.000 0.00 0.00 39.26 3.68
139 140 0.453390 TGCGATGTGTGTGTGCAAAA 59.547 45.000 0.00 0.00 31.69 2.44
140 141 1.135286 TGCGATGTGTGTGTGCAAAAA 60.135 42.857 0.00 0.00 31.69 1.94
187 188 9.956720 AACAAATTCAGTTTTGATAAGTCTCAG 57.043 29.630 4.10 0.00 38.58 3.35
188 189 9.125026 ACAAATTCAGTTTTGATAAGTCTCAGT 57.875 29.630 4.10 0.00 38.58 3.41
189 190 9.956720 CAAATTCAGTTTTGATAAGTCTCAGTT 57.043 29.630 0.00 0.00 38.58 3.16
190 191 9.956720 AAATTCAGTTTTGATAAGTCTCAGTTG 57.043 29.630 0.00 0.00 32.27 3.16
191 192 8.908786 ATTCAGTTTTGATAAGTCTCAGTTGA 57.091 30.769 0.00 0.00 32.27 3.18
192 193 7.715265 TCAGTTTTGATAAGTCTCAGTTGAC 57.285 36.000 0.00 0.00 37.23 3.18
193 194 6.706270 TCAGTTTTGATAAGTCTCAGTTGACC 59.294 38.462 0.00 0.00 37.66 4.02
194 195 5.696724 AGTTTTGATAAGTCTCAGTTGACCG 59.303 40.000 0.00 0.00 37.66 4.79
195 196 5.462530 TTTGATAAGTCTCAGTTGACCGA 57.537 39.130 0.00 0.00 37.66 4.69
196 197 4.703645 TGATAAGTCTCAGTTGACCGAG 57.296 45.455 0.00 0.00 37.66 4.63
197 198 4.332828 TGATAAGTCTCAGTTGACCGAGA 58.667 43.478 0.00 0.00 37.66 4.04
198 199 4.950475 TGATAAGTCTCAGTTGACCGAGAT 59.050 41.667 0.81 0.00 40.27 2.75
199 200 5.419155 TGATAAGTCTCAGTTGACCGAGATT 59.581 40.000 0.81 0.00 40.27 2.40
200 201 4.608948 AAGTCTCAGTTGACCGAGATTT 57.391 40.909 0.81 0.81 40.27 2.17
201 202 4.181309 AGTCTCAGTTGACCGAGATTTC 57.819 45.455 0.81 0.00 40.27 2.17
202 203 2.917971 GTCTCAGTTGACCGAGATTTCG 59.082 50.000 0.00 0.00 46.29 3.46
203 204 2.557056 TCTCAGTTGACCGAGATTTCGT 59.443 45.455 4.82 0.00 45.28 3.85
204 205 3.754850 TCTCAGTTGACCGAGATTTCGTA 59.245 43.478 4.82 0.00 45.28 3.43
225 226 5.745294 CGTATTCCTTTGATTTTGCATGGAG 59.255 40.000 0.00 0.00 0.00 3.86
229 230 7.479352 TTCCTTTGATTTTGCATGGAGATTA 57.521 32.000 0.00 0.00 0.00 1.75
300 302 1.908619 TGCTTGAATGAGACCTAGCCA 59.091 47.619 0.00 0.00 0.00 4.75
304 306 1.555075 TGAATGAGACCTAGCCACACC 59.445 52.381 0.00 0.00 0.00 4.16
325 327 5.584251 CACCCTAACAAATTTGCAAAACAGT 59.416 36.000 17.19 11.52 0.00 3.55
326 328 6.758886 CACCCTAACAAATTTGCAAAACAGTA 59.241 34.615 17.19 4.62 0.00 2.74
336 338 7.698836 ATTTGCAAAACAGTACAGAAATGTC 57.301 32.000 17.19 0.00 0.00 3.06
453 475 3.670629 CTGCCTCCCGTCCTCTCCT 62.671 68.421 0.00 0.00 0.00 3.69
454 476 2.835895 GCCTCCCGTCCTCTCCTC 60.836 72.222 0.00 0.00 0.00 3.71
455 477 3.011885 CCTCCCGTCCTCTCCTCT 58.988 66.667 0.00 0.00 0.00 3.69
457 479 1.641552 CCTCCCGTCCTCTCCTCTCT 61.642 65.000 0.00 0.00 0.00 3.10
459 481 1.152839 CCCGTCCTCTCCTCTCTCC 60.153 68.421 0.00 0.00 0.00 3.71
460 482 1.152839 CCGTCCTCTCCTCTCTCCC 60.153 68.421 0.00 0.00 0.00 4.30
461 483 1.610327 CGTCCTCTCCTCTCTCCCA 59.390 63.158 0.00 0.00 0.00 4.37
462 484 0.750182 CGTCCTCTCCTCTCTCCCAC 60.750 65.000 0.00 0.00 0.00 4.61
463 485 0.750182 GTCCTCTCCTCTCTCCCACG 60.750 65.000 0.00 0.00 0.00 4.94
465 487 2.043852 TCTCCTCTCTCCCACGCC 60.044 66.667 0.00 0.00 0.00 5.68
466 488 3.522731 CTCCTCTCTCCCACGCCG 61.523 72.222 0.00 0.00 0.00 6.46
514 667 0.102481 GGCACGGCGAGAGAGATAAA 59.898 55.000 16.62 0.00 0.00 1.40
543 698 1.660560 CCCCAAAATCAGAGCGCAGG 61.661 60.000 11.47 0.00 0.00 4.85
544 699 1.660560 CCCAAAATCAGAGCGCAGGG 61.661 60.000 11.47 2.29 0.00 4.45
695 869 3.379452 CTCCTATTCTCAACCCCACTCT 58.621 50.000 0.00 0.00 0.00 3.24
696 870 3.375699 TCCTATTCTCAACCCCACTCTC 58.624 50.000 0.00 0.00 0.00 3.20
697 871 2.436173 CCTATTCTCAACCCCACTCTCC 59.564 54.545 0.00 0.00 0.00 3.71
698 872 2.044793 ATTCTCAACCCCACTCTCCA 57.955 50.000 0.00 0.00 0.00 3.86
699 873 1.814429 TTCTCAACCCCACTCTCCAA 58.186 50.000 0.00 0.00 0.00 3.53
700 874 2.044793 TCTCAACCCCACTCTCCAAT 57.955 50.000 0.00 0.00 0.00 3.16
701 875 1.909302 TCTCAACCCCACTCTCCAATC 59.091 52.381 0.00 0.00 0.00 2.67
702 876 1.912043 CTCAACCCCACTCTCCAATCT 59.088 52.381 0.00 0.00 0.00 2.40
2118 2325 4.341502 CCAACCGCCCGCAAACAG 62.342 66.667 0.00 0.00 0.00 3.16
2120 2327 3.284449 AACCGCCCGCAAACAGAC 61.284 61.111 0.00 0.00 0.00 3.51
2121 2328 3.767630 AACCGCCCGCAAACAGACT 62.768 57.895 0.00 0.00 0.00 3.24
2318 2525 3.617263 CCTAGATTGTTCGTGTTGGTAGC 59.383 47.826 0.00 0.00 0.00 3.58
2320 2527 1.127951 GATTGTTCGTGTTGGTAGCGG 59.872 52.381 0.00 0.00 0.00 5.52
2409 2619 1.143620 CTCTACAGAGCTGCAGCCC 59.856 63.158 34.39 24.70 43.38 5.19
2520 2750 4.827284 CGTCTTCCCCTTAAATGGCAATAT 59.173 41.667 0.00 0.00 0.00 1.28
2521 2751 5.048713 CGTCTTCCCCTTAAATGGCAATATC 60.049 44.000 0.00 0.00 0.00 1.63
2522 2752 6.071320 GTCTTCCCCTTAAATGGCAATATCT 58.929 40.000 0.00 0.00 0.00 1.98
2523 2753 6.207614 GTCTTCCCCTTAAATGGCAATATCTC 59.792 42.308 0.00 0.00 0.00 2.75
2524 2754 4.998051 TCCCCTTAAATGGCAATATCTCC 58.002 43.478 0.00 0.00 0.00 3.71
2561 2799 1.423541 TGGTGGCTTGGTCTGTTGTAT 59.576 47.619 0.00 0.00 0.00 2.29
2571 2809 2.744202 GGTCTGTTGTATTGGTGCTCTG 59.256 50.000 0.00 0.00 0.00 3.35
2572 2810 2.160417 GTCTGTTGTATTGGTGCTCTGC 59.840 50.000 0.00 0.00 0.00 4.26
2573 2811 2.153645 CTGTTGTATTGGTGCTCTGCA 58.846 47.619 0.00 0.00 35.60 4.41
2828 3077 1.156736 TTTGAGCTTAAGCACTCGCC 58.843 50.000 28.39 10.73 45.16 5.54
2933 3182 4.570874 GAAGGGAGATGGGCGGGC 62.571 72.222 0.00 0.00 0.00 6.13
3004 3260 2.829458 GAGCTACCGCCCGTCTCT 60.829 66.667 0.00 0.00 36.60 3.10
3005 3261 2.829458 AGCTACCGCCCGTCTCTC 60.829 66.667 0.00 0.00 36.60 3.20
3006 3262 2.829458 GCTACCGCCCGTCTCTCT 60.829 66.667 0.00 0.00 0.00 3.10
3007 3263 2.836793 GCTACCGCCCGTCTCTCTC 61.837 68.421 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.793592 ACCATGTACACTCTCTTTTTATTTTCC 58.206 33.333 0.00 0.00 0.00 3.13
1 2 9.612620 CACCATGTACACTCTCTTTTTATTTTC 57.387 33.333 0.00 0.00 0.00 2.29
2 3 9.131791 ACACCATGTACACTCTCTTTTTATTTT 57.868 29.630 0.00 0.00 0.00 1.82
3 4 8.691661 ACACCATGTACACTCTCTTTTTATTT 57.308 30.769 0.00 0.00 0.00 1.40
4 5 8.567948 CAACACCATGTACACTCTCTTTTTATT 58.432 33.333 0.00 0.00 0.00 1.40
5 6 7.174946 CCAACACCATGTACACTCTCTTTTTAT 59.825 37.037 0.00 0.00 0.00 1.40
6 7 6.485313 CCAACACCATGTACACTCTCTTTTTA 59.515 38.462 0.00 0.00 0.00 1.52
7 8 5.299279 CCAACACCATGTACACTCTCTTTTT 59.701 40.000 0.00 0.00 0.00 1.94
8 9 4.821805 CCAACACCATGTACACTCTCTTTT 59.178 41.667 0.00 0.00 0.00 2.27
9 10 4.389374 CCAACACCATGTACACTCTCTTT 58.611 43.478 0.00 0.00 0.00 2.52
10 11 3.807209 GCCAACACCATGTACACTCTCTT 60.807 47.826 0.00 0.00 0.00 2.85
11 12 2.289694 GCCAACACCATGTACACTCTCT 60.290 50.000 0.00 0.00 0.00 3.10
12 13 2.076863 GCCAACACCATGTACACTCTC 58.923 52.381 0.00 0.00 0.00 3.20
13 14 1.271379 GGCCAACACCATGTACACTCT 60.271 52.381 0.00 0.00 0.00 3.24
14 15 1.165270 GGCCAACACCATGTACACTC 58.835 55.000 0.00 0.00 0.00 3.51
15 16 0.476338 TGGCCAACACCATGTACACT 59.524 50.000 0.61 0.00 33.75 3.55
16 17 1.269448 CTTGGCCAACACCATGTACAC 59.731 52.381 16.05 0.00 40.13 2.90
17 18 1.143889 TCTTGGCCAACACCATGTACA 59.856 47.619 16.05 0.00 40.13 2.90
18 19 1.904287 TCTTGGCCAACACCATGTAC 58.096 50.000 16.05 0.00 40.13 2.90
19 20 2.620367 GGATCTTGGCCAACACCATGTA 60.620 50.000 16.05 0.00 40.13 2.29
20 21 1.549203 GATCTTGGCCAACACCATGT 58.451 50.000 16.05 0.00 40.13 3.21
21 22 0.819582 GGATCTTGGCCAACACCATG 59.180 55.000 16.05 3.61 40.13 3.66
22 23 0.680921 CGGATCTTGGCCAACACCAT 60.681 55.000 16.05 4.04 40.13 3.55
23 24 1.303236 CGGATCTTGGCCAACACCA 60.303 57.895 16.05 0.00 38.16 4.17
24 25 1.303317 ACGGATCTTGGCCAACACC 60.303 57.895 16.05 16.29 0.00 4.16
25 26 1.875963 CACGGATCTTGGCCAACAC 59.124 57.895 16.05 8.62 0.00 3.32
26 27 1.971167 GCACGGATCTTGGCCAACA 60.971 57.895 16.05 4.52 0.00 3.33
27 28 1.523154 TTGCACGGATCTTGGCCAAC 61.523 55.000 16.05 4.84 0.00 3.77
28 29 1.228398 TTGCACGGATCTTGGCCAA 60.228 52.632 19.25 19.25 0.00 4.52
29 30 1.971167 GTTGCACGGATCTTGGCCA 60.971 57.895 0.00 0.00 0.00 5.36
30 31 2.877691 GTTGCACGGATCTTGGCC 59.122 61.111 0.00 0.00 0.00 5.36
31 32 2.480555 CGTTGCACGGATCTTGGC 59.519 61.111 0.00 0.00 38.08 4.52
40 41 3.726517 CTTCCCTGCCGTTGCACG 61.727 66.667 0.00 0.00 44.23 5.34
41 42 2.281484 TCTTCCCTGCCGTTGCAC 60.281 61.111 0.00 0.00 44.23 4.57
43 44 1.244019 AATGTCTTCCCTGCCGTTGC 61.244 55.000 0.00 0.00 38.26 4.17
44 45 0.804989 GAATGTCTTCCCTGCCGTTG 59.195 55.000 0.00 0.00 0.00 4.10
45 46 0.673644 CGAATGTCTTCCCTGCCGTT 60.674 55.000 0.00 0.00 0.00 4.44
46 47 1.079127 CGAATGTCTTCCCTGCCGT 60.079 57.895 0.00 0.00 0.00 5.68
47 48 2.464459 GCGAATGTCTTCCCTGCCG 61.464 63.158 0.00 0.00 0.00 5.69
48 49 2.115291 GGCGAATGTCTTCCCTGCC 61.115 63.158 0.00 0.00 31.22 4.85
49 50 2.464459 CGGCGAATGTCTTCCCTGC 61.464 63.158 0.00 0.00 0.00 4.85
50 51 1.815421 CCGGCGAATGTCTTCCCTG 60.815 63.158 9.30 0.00 0.00 4.45
51 52 2.584608 CCGGCGAATGTCTTCCCT 59.415 61.111 9.30 0.00 0.00 4.20
52 53 2.325393 ATCCCGGCGAATGTCTTCCC 62.325 60.000 9.30 0.00 0.00 3.97
53 54 0.463833 AATCCCGGCGAATGTCTTCC 60.464 55.000 9.30 0.00 0.00 3.46
54 55 2.234300 TAATCCCGGCGAATGTCTTC 57.766 50.000 9.30 0.00 0.00 2.87
55 56 2.104111 TGATAATCCCGGCGAATGTCTT 59.896 45.455 9.30 0.00 0.00 3.01
56 57 1.691976 TGATAATCCCGGCGAATGTCT 59.308 47.619 9.30 0.00 0.00 3.41
57 58 1.798813 GTGATAATCCCGGCGAATGTC 59.201 52.381 9.30 4.91 0.00 3.06
58 59 1.542547 GGTGATAATCCCGGCGAATGT 60.543 52.381 9.30 0.00 0.00 2.71
59 60 1.156736 GGTGATAATCCCGGCGAATG 58.843 55.000 9.30 0.00 0.00 2.67
60 61 0.320421 CGGTGATAATCCCGGCGAAT 60.320 55.000 9.30 0.00 40.54 3.34
61 62 1.068417 CGGTGATAATCCCGGCGAA 59.932 57.895 9.30 0.00 40.54 4.70
62 63 1.829096 TCGGTGATAATCCCGGCGA 60.829 57.895 9.30 0.00 44.32 5.54
63 64 1.663702 GTCGGTGATAATCCCGGCG 60.664 63.158 0.00 0.00 44.32 6.46
64 65 4.355925 GTCGGTGATAATCCCGGC 57.644 61.111 0.00 1.91 44.32 6.13
65 66 1.037493 TCAGTCGGTGATAATCCCGG 58.963 55.000 0.00 0.00 44.32 5.73
72 73 6.334989 ACGAAAATGTTATCAGTCGGTGATA 58.665 36.000 4.76 4.76 44.69 2.15
74 75 4.562082 ACGAAAATGTTATCAGTCGGTGA 58.438 39.130 0.00 0.00 40.38 4.02
75 76 4.921470 ACGAAAATGTTATCAGTCGGTG 57.079 40.909 0.00 0.00 33.57 4.94
76 77 5.934935 AAACGAAAATGTTATCAGTCGGT 57.065 34.783 0.00 0.00 33.57 4.69
77 78 8.716619 TTAAAAACGAAAATGTTATCAGTCGG 57.283 30.769 0.00 0.00 33.57 4.79
111 112 4.737279 CACACACACATCGCATGTTAAAAA 59.263 37.500 0.00 0.00 42.70 1.94
112 113 4.286101 CACACACACATCGCATGTTAAAA 58.714 39.130 0.00 0.00 42.70 1.52
113 114 3.851471 GCACACACACATCGCATGTTAAA 60.851 43.478 0.00 0.00 42.70 1.52
114 115 2.350293 GCACACACACATCGCATGTTAA 60.350 45.455 0.00 0.00 42.70 2.01
115 116 1.196581 GCACACACACATCGCATGTTA 59.803 47.619 0.00 0.00 42.70 2.41
116 117 0.040157 GCACACACACATCGCATGTT 60.040 50.000 0.00 0.00 42.70 2.71
117 118 1.165284 TGCACACACACATCGCATGT 61.165 50.000 0.00 0.00 46.22 3.21
118 119 0.040246 TTGCACACACACATCGCATG 60.040 50.000 0.00 0.00 31.67 4.06
119 120 0.667453 TTTGCACACACACATCGCAT 59.333 45.000 0.00 0.00 31.67 4.73
120 121 0.453390 TTTTGCACACACACATCGCA 59.547 45.000 0.00 0.00 0.00 5.10
121 122 1.554392 TTTTTGCACACACACATCGC 58.446 45.000 0.00 0.00 0.00 4.58
161 162 9.956720 CTGAGACTTATCAAAACTGAATTTGTT 57.043 29.630 9.33 5.56 40.40 2.83
162 163 9.125026 ACTGAGACTTATCAAAACTGAATTTGT 57.875 29.630 9.33 0.00 40.40 2.83
163 164 9.956720 AACTGAGACTTATCAAAACTGAATTTG 57.043 29.630 0.00 4.94 40.78 2.32
164 165 9.956720 CAACTGAGACTTATCAAAACTGAATTT 57.043 29.630 0.00 0.00 0.00 1.82
165 166 9.342308 TCAACTGAGACTTATCAAAACTGAATT 57.658 29.630 0.00 0.00 0.00 2.17
166 167 8.778358 GTCAACTGAGACTTATCAAAACTGAAT 58.222 33.333 0.00 0.00 35.65 2.57
167 168 7.226720 GGTCAACTGAGACTTATCAAAACTGAA 59.773 37.037 0.00 0.00 38.57 3.02
168 169 6.706270 GGTCAACTGAGACTTATCAAAACTGA 59.294 38.462 0.00 0.00 38.57 3.41
169 170 6.346919 CGGTCAACTGAGACTTATCAAAACTG 60.347 42.308 0.00 0.00 38.57 3.16
170 171 5.696724 CGGTCAACTGAGACTTATCAAAACT 59.303 40.000 0.00 0.00 38.57 2.66
171 172 5.694910 TCGGTCAACTGAGACTTATCAAAAC 59.305 40.000 0.00 0.00 38.57 2.43
172 173 5.849510 TCGGTCAACTGAGACTTATCAAAA 58.150 37.500 0.00 0.00 38.57 2.44
173 174 5.462530 TCGGTCAACTGAGACTTATCAAA 57.537 39.130 0.00 0.00 38.57 2.69
194 195 7.754924 TGCAAAATCAAAGGAATACGAAATCTC 59.245 33.333 0.00 0.00 0.00 2.75
195 196 7.601856 TGCAAAATCAAAGGAATACGAAATCT 58.398 30.769 0.00 0.00 0.00 2.40
196 197 7.810766 TGCAAAATCAAAGGAATACGAAATC 57.189 32.000 0.00 0.00 0.00 2.17
197 198 7.278424 CCATGCAAAATCAAAGGAATACGAAAT 59.722 33.333 0.00 0.00 0.00 2.17
198 199 6.589523 CCATGCAAAATCAAAGGAATACGAAA 59.410 34.615 0.00 0.00 0.00 3.46
199 200 6.071672 TCCATGCAAAATCAAAGGAATACGAA 60.072 34.615 0.00 0.00 0.00 3.85
200 201 5.417266 TCCATGCAAAATCAAAGGAATACGA 59.583 36.000 0.00 0.00 0.00 3.43
201 202 5.649557 TCCATGCAAAATCAAAGGAATACG 58.350 37.500 0.00 0.00 0.00 3.06
202 203 6.866480 TCTCCATGCAAAATCAAAGGAATAC 58.134 36.000 0.00 0.00 0.00 1.89
203 204 7.664552 ATCTCCATGCAAAATCAAAGGAATA 57.335 32.000 0.00 0.00 0.00 1.75
204 205 6.555463 ATCTCCATGCAAAATCAAAGGAAT 57.445 33.333 0.00 0.00 0.00 3.01
273 275 6.091986 GCTAGGTCTCATTCAAGCAATATAGC 59.908 42.308 0.00 0.00 0.00 2.97
280 282 1.908619 TGGCTAGGTCTCATTCAAGCA 59.091 47.619 0.00 0.00 0.00 3.91
282 284 3.265791 GTGTGGCTAGGTCTCATTCAAG 58.734 50.000 0.00 0.00 0.00 3.02
287 289 0.043334 AGGGTGTGGCTAGGTCTCAT 59.957 55.000 0.00 0.00 0.00 2.90
300 302 5.491982 TGTTTTGCAAATTTGTTAGGGTGT 58.508 33.333 19.03 0.00 0.00 4.16
304 306 7.704472 TCTGTACTGTTTTGCAAATTTGTTAGG 59.296 33.333 19.03 1.95 0.00 2.69
325 327 6.976636 TGTATTTCATGCGACATTTCTGTA 57.023 33.333 0.00 0.00 35.14 2.74
326 328 5.878332 TGTATTTCATGCGACATTTCTGT 57.122 34.783 0.00 0.00 38.67 3.41
336 338 5.227805 CGAACCAGATTTTGTATTTCATGCG 59.772 40.000 0.00 0.00 0.00 4.73
374 376 5.046950 ACCACTGCTTCCACTTGTTTAAAAA 60.047 36.000 0.00 0.00 0.00 1.94
376 378 4.020543 ACCACTGCTTCCACTTGTTTAAA 58.979 39.130 0.00 0.00 0.00 1.52
378 380 3.290948 ACCACTGCTTCCACTTGTTTA 57.709 42.857 0.00 0.00 0.00 2.01
382 384 4.853924 ATTTTACCACTGCTTCCACTTG 57.146 40.909 0.00 0.00 0.00 3.16
384 386 4.469657 TCAATTTTACCACTGCTTCCACT 58.530 39.130 0.00 0.00 0.00 4.00
385 387 4.798574 CTCAATTTTACCACTGCTTCCAC 58.201 43.478 0.00 0.00 0.00 4.02
386 388 3.255642 GCTCAATTTTACCACTGCTTCCA 59.744 43.478 0.00 0.00 0.00 3.53
387 389 3.255642 TGCTCAATTTTACCACTGCTTCC 59.744 43.478 0.00 0.00 0.00 3.46
389 391 4.935352 TTGCTCAATTTTACCACTGCTT 57.065 36.364 0.00 0.00 0.00 3.91
390 392 4.342092 ACTTTGCTCAATTTTACCACTGCT 59.658 37.500 0.00 0.00 0.00 4.24
392 394 5.830912 TCACTTTGCTCAATTTTACCACTG 58.169 37.500 0.00 0.00 0.00 3.66
459 481 3.589654 TTGAGAAGGAGCGGCGTGG 62.590 63.158 9.37 0.00 0.00 4.94
460 482 1.630244 CTTTGAGAAGGAGCGGCGTG 61.630 60.000 9.37 0.00 0.00 5.34
461 483 1.374758 CTTTGAGAAGGAGCGGCGT 60.375 57.895 9.37 0.00 0.00 5.68
462 484 3.479370 CTTTGAGAAGGAGCGGCG 58.521 61.111 0.51 0.51 0.00 6.46
514 667 0.032515 GATTTTGGGGATTCGGGGGT 60.033 55.000 0.00 0.00 0.00 4.95
695 869 1.134220 GGCGTGGTAATGGAGATTGGA 60.134 52.381 0.00 0.00 0.00 3.53
696 870 1.134098 AGGCGTGGTAATGGAGATTGG 60.134 52.381 0.00 0.00 0.00 3.16
697 871 2.213499 GAGGCGTGGTAATGGAGATTG 58.787 52.381 0.00 0.00 0.00 2.67
698 872 1.202533 CGAGGCGTGGTAATGGAGATT 60.203 52.381 0.00 0.00 0.00 2.40
699 873 0.389391 CGAGGCGTGGTAATGGAGAT 59.611 55.000 0.00 0.00 0.00 2.75
700 874 1.813859 CGAGGCGTGGTAATGGAGA 59.186 57.895 0.00 0.00 0.00 3.71
701 875 1.883084 GCGAGGCGTGGTAATGGAG 60.883 63.158 0.00 0.00 0.00 3.86
702 876 2.185867 GCGAGGCGTGGTAATGGA 59.814 61.111 0.00 0.00 0.00 3.41
1047 1227 2.390599 CGGCGACAAGACCACCATG 61.391 63.158 0.00 0.00 0.00 3.66
2318 2525 2.691409 ATATGTGGGACAACAGACCG 57.309 50.000 0.00 0.00 44.16 4.79
2320 2527 6.325919 TCAAAAATATGTGGGACAACAGAC 57.674 37.500 0.00 0.00 44.16 3.51
2374 2581 9.203421 CTCTGTAGAGTGTAGAGTATGATACAG 57.797 40.741 5.28 0.00 39.13 2.74
2520 2750 0.407528 ACAGCAGAGAGTGAGGGAGA 59.592 55.000 0.00 0.00 0.00 3.71
2521 2751 1.265236 AACAGCAGAGAGTGAGGGAG 58.735 55.000 0.00 0.00 0.00 4.30
2522 2752 1.345741 CAAACAGCAGAGAGTGAGGGA 59.654 52.381 0.00 0.00 0.00 4.20
2523 2753 1.610102 CCAAACAGCAGAGAGTGAGGG 60.610 57.143 0.00 0.00 0.00 4.30
2524 2754 1.071385 ACCAAACAGCAGAGAGTGAGG 59.929 52.381 0.00 0.00 0.00 3.86
2561 2799 1.455402 TTTGCCTGCAGAGCACCAA 60.455 52.632 23.92 16.10 40.69 3.67
2571 2809 3.225069 ATTGCCACCGTTTGCCTGC 62.225 57.895 0.00 0.00 0.00 4.85
2572 2810 1.080569 GATTGCCACCGTTTGCCTG 60.081 57.895 0.00 0.00 0.00 4.85
2573 2811 1.112315 TTGATTGCCACCGTTTGCCT 61.112 50.000 0.00 0.00 0.00 4.75
2789 3038 0.106268 ATGGTTGTTGGTGTCAGCCA 60.106 50.000 0.00 4.22 46.64 4.75
2828 3077 5.416947 TGATGATGAATCTATCGGCAGATG 58.583 41.667 9.82 0.18 35.42 2.90
2971 3220 1.507141 GCTCACAAGTCCCGTGTTGG 61.507 60.000 0.00 0.00 35.79 3.77


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

AutoCloner maintained by Alex Coulton.