Multiple sequence alignment - TraesCS6D01G324900

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 TraesCS6D01G324900 chr6D 100.000 4482 0 0 1 4482 431270984 431266503 0.000000e+00 8277.0
1 TraesCS6D01G324900 chr6D 88.426 1080 95 17 999 2052 431210627 431209552 0.000000e+00 1275.0
2 TraesCS6D01G324900 chr6D 88.134 1045 99 14 2714 3753 431209204 431208180 0.000000e+00 1219.0
3 TraesCS6D01G324900 chr6D 84.615 364 40 10 3820 4179 431208155 431207804 9.230000e-92 348.0
4 TraesCS6D01G324900 chr6D 86.486 222 26 4 2442 2661 431209424 431209205 1.610000e-59 241.0
5 TraesCS6D01G324900 chr6D 91.358 81 5 2 4403 4482 431204840 431204761 4.740000e-20 110.0
6 TraesCS6D01G324900 chr6A 93.783 2075 70 10 2442 4482 578038416 578036367 0.000000e+00 3062.0
7 TraesCS6D01G324900 chr6A 93.168 1288 70 11 896 2170 578039697 578038415 0.000000e+00 1875.0
8 TraesCS6D01G324900 chr6A 86.840 1155 116 23 999 2123 577881593 577880445 0.000000e+00 1258.0
9 TraesCS6D01G324900 chr6A 85.599 1118 116 21 2442 3543 577880379 577879291 0.000000e+00 1131.0
10 TraesCS6D01G324900 chr6B 92.079 2083 101 24 2442 4482 650923738 650921678 0.000000e+00 2874.0
11 TraesCS6D01G324900 chr6B 92.366 1192 79 6 943 2134 650924961 650923782 0.000000e+00 1687.0
12 TraesCS6D01G324900 chr6B 88.056 1080 99 17 999 2052 650805515 650804440 0.000000e+00 1253.0
13 TraesCS6D01G324900 chr6B 88.987 1017 100 10 2743 3753 650804064 650803054 0.000000e+00 1247.0
14 TraesCS6D01G324900 chr4D 98.884 896 9 1 1 895 399423581 399424476 0.000000e+00 1598.0
15 TraesCS6D01G324900 chr1D 98.547 895 13 0 1 895 60309795 60310689 0.000000e+00 1581.0
16 TraesCS6D01G324900 chr1D 98.094 892 17 0 4 895 403523469 403522578 0.000000e+00 1554.0
17 TraesCS6D01G324900 chr7D 98.434 894 13 1 1 894 47479704 47480596 0.000000e+00 1572.0
18 TraesCS6D01G324900 chr3D 98.425 889 13 1 4 892 516887754 516886867 0.000000e+00 1563.0
19 TraesCS6D01G324900 chr5D 97.989 895 17 1 1 895 495220195 495221088 0.000000e+00 1552.0
20 TraesCS6D01G324900 chr2D 97.770 897 19 1 1 896 517044533 517045429 0.000000e+00 1544.0
21 TraesCS6D01G324900 chr2D 98.083 887 17 0 1 887 620266997 620267883 0.000000e+00 1544.0
22 TraesCS6D01G324900 chr2D 97.865 890 19 0 4 893 606523498 606522609 0.000000e+00 1539.0
23 TraesCS6D01G324900 chr2A 91.429 175 15 0 1195 1369 474320092 474319918 1.610000e-59 241.0
24 TraesCS6D01G324900 chrUn 97.619 42 1 0 1487 1528 40196085 40196126 6.220000e-09 73.1


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 TraesCS6D01G324900 chr6D 431266503 431270984 4481 True 8277.0 8277 100.0000 1 4482 1 chr6D.!!$R1 4481
1 TraesCS6D01G324900 chr6D 431204761 431210627 5866 True 638.6 1275 87.8038 999 4482 5 chr6D.!!$R2 3483
2 TraesCS6D01G324900 chr6A 578036367 578039697 3330 True 2468.5 3062 93.4755 896 4482 2 chr6A.!!$R2 3586
3 TraesCS6D01G324900 chr6A 577879291 577881593 2302 True 1194.5 1258 86.2195 999 3543 2 chr6A.!!$R1 2544
4 TraesCS6D01G324900 chr6B 650921678 650924961 3283 True 2280.5 2874 92.2225 943 4482 2 chr6B.!!$R2 3539
5 TraesCS6D01G324900 chr6B 650803054 650805515 2461 True 1250.0 1253 88.5215 999 3753 2 chr6B.!!$R1 2754
6 TraesCS6D01G324900 chr4D 399423581 399424476 895 False 1598.0 1598 98.8840 1 895 1 chr4D.!!$F1 894
7 TraesCS6D01G324900 chr1D 60309795 60310689 894 False 1581.0 1581 98.5470 1 895 1 chr1D.!!$F1 894
8 TraesCS6D01G324900 chr1D 403522578 403523469 891 True 1554.0 1554 98.0940 4 895 1 chr1D.!!$R1 891
9 TraesCS6D01G324900 chr7D 47479704 47480596 892 False 1572.0 1572 98.4340 1 894 1 chr7D.!!$F1 893
10 TraesCS6D01G324900 chr3D 516886867 516887754 887 True 1563.0 1563 98.4250 4 892 1 chr3D.!!$R1 888
11 TraesCS6D01G324900 chr5D 495220195 495221088 893 False 1552.0 1552 97.9890 1 895 1 chr5D.!!$F1 894
12 TraesCS6D01G324900 chr2D 517044533 517045429 896 False 1544.0 1544 97.7700 1 896 1 chr2D.!!$F1 895
13 TraesCS6D01G324900 chr2D 620266997 620267883 886 False 1544.0 1544 98.0830 1 887 1 chr2D.!!$F2 886
14 TraesCS6D01G324900 chr2D 606522609 606523498 889 True 1539.0 1539 97.8650 4 893 1 chr2D.!!$R1 889

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
608 609 0.611340 GGTACTGGGAGACACGTCCT 60.611 60.000 0.00 0.0 36.75 3.85 F
1323 1334 2.032681 GAGGCCTCCGTGCAGTTT 59.967 61.111 23.19 0.0 0.00 2.66 F
2333 2397 0.606604 GGAGCTCCTTTCACGTACCA 59.393 55.000 26.25 0.0 0.00 3.25 F
2492 2557 0.832626 ACCATCACAGCATCATCCGA 59.167 50.000 0.00 0.0 0.00 4.55 F
3120 3211 1.512926 CGAACTGACCCAAACCAGAG 58.487 55.000 0.00 0.0 34.65 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 2072 0.442310 GTAGCACGTACGTACCGACA 59.558 55.000 22.34 0.37 0.00 4.35 R
3103 3194 0.550914 TGCTCTGGTTTGGGTCAGTT 59.449 50.000 0.00 0.00 33.13 3.16 R
3159 3250 0.817654 CGTGCCACCTAGATCTGACA 59.182 55.000 5.18 0.00 0.00 3.58 R
3359 3450 2.032681 GTGCACTCCACCCCACTC 59.967 66.667 10.32 0.00 38.55 3.51 R
4381 7216 4.075682 TGAGTTGGACAAACAAACTCACA 58.924 39.130 13.58 0.00 41.61 3.58 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
608 609 0.611340 GGTACTGGGAGACACGTCCT 60.611 60.000 0.00 0.00 36.75 3.85
647 648 2.055042 CCCTCACCCTCCTCGTCTG 61.055 68.421 0.00 0.00 0.00 3.51
918 919 3.610911 GCCTAGGTAGCAGAACAACATT 58.389 45.455 11.31 0.00 0.00 2.71
972 974 6.850752 AATGTCACTATAAAAACCCTTGGG 57.149 37.500 3.77 3.77 0.00 4.12
994 996 3.934962 TGCCTGTACGCTGCACCA 61.935 61.111 0.00 0.00 0.00 4.17
1165 1176 4.452733 CGACGGCCTCCAGGGTTC 62.453 72.222 0.00 0.00 37.43 3.62
1176 1187 4.699522 AGGGTTCTCGGCGGCAAC 62.700 66.667 10.53 10.16 0.00 4.17
1307 1318 3.327404 GGCCAAGGACCCCTTCGA 61.327 66.667 0.00 0.00 42.67 3.71
1323 1334 2.032681 GAGGCCTCCGTGCAGTTT 59.967 61.111 23.19 0.00 0.00 2.66
1653 1664 2.281761 CACGCCAAGCTCAAGGGT 60.282 61.111 0.00 0.00 0.00 4.34
2069 2101 2.949678 CGTGCTACGGTGCTAGCG 60.950 66.667 10.77 0.00 41.93 4.26
2126 2163 3.898482 AGGACCACTGCTACAAAAAGTT 58.102 40.909 0.00 0.00 0.00 2.66
2130 2167 5.277828 GGACCACTGCTACAAAAAGTTACAG 60.278 44.000 0.00 0.00 37.73 2.74
2134 2171 7.717875 ACCACTGCTACAAAAAGTTACAGATAA 59.282 33.333 0.00 0.00 36.19 1.75
2158 2219 2.285827 TGGTTGCAACGTTTTCTTGG 57.714 45.000 22.67 0.00 0.00 3.61
2165 2229 1.880027 CAACGTTTTCTTGGCCTAGCT 59.120 47.619 9.60 0.00 0.00 3.32
2166 2230 3.071479 CAACGTTTTCTTGGCCTAGCTA 58.929 45.455 9.60 0.00 0.00 3.32
2167 2231 2.696506 ACGTTTTCTTGGCCTAGCTAC 58.303 47.619 9.60 6.27 0.00 3.58
2168 2232 2.302157 ACGTTTTCTTGGCCTAGCTACT 59.698 45.455 9.60 0.00 0.00 2.57
2169 2233 3.512724 ACGTTTTCTTGGCCTAGCTACTA 59.487 43.478 9.60 0.00 0.00 1.82
2170 2234 3.864003 CGTTTTCTTGGCCTAGCTACTAC 59.136 47.826 9.60 2.68 0.00 2.73
2171 2235 4.381718 CGTTTTCTTGGCCTAGCTACTACT 60.382 45.833 9.60 0.00 0.00 2.57
2172 2236 5.163581 CGTTTTCTTGGCCTAGCTACTACTA 60.164 44.000 9.60 0.00 0.00 1.82
2173 2237 5.848833 TTTCTTGGCCTAGCTACTACTAC 57.151 43.478 9.60 0.00 0.00 2.73
2174 2238 4.792513 TCTTGGCCTAGCTACTACTACT 57.207 45.455 9.60 0.00 0.00 2.57
2175 2239 5.901413 TCTTGGCCTAGCTACTACTACTA 57.099 43.478 9.60 0.00 0.00 1.82
2176 2240 6.451292 TCTTGGCCTAGCTACTACTACTAT 57.549 41.667 9.60 0.00 0.00 2.12
2177 2241 7.565190 TCTTGGCCTAGCTACTACTACTATA 57.435 40.000 9.60 0.00 0.00 1.31
2178 2242 8.160434 TCTTGGCCTAGCTACTACTACTATAT 57.840 38.462 9.60 0.00 0.00 0.86
2179 2243 9.276791 TCTTGGCCTAGCTACTACTACTATATA 57.723 37.037 9.60 0.00 0.00 0.86
2263 2327 9.558396 TTTTTGAAACTGCCTTTGATCATTATT 57.442 25.926 0.00 0.00 0.00 1.40
2266 2330 9.859427 TTGAAACTGCCTTTGATCATTATTAAG 57.141 29.630 0.00 0.00 0.00 1.85
2267 2331 9.241919 TGAAACTGCCTTTGATCATTATTAAGA 57.758 29.630 0.00 0.00 0.00 2.10
2332 2396 0.896226 AGGAGCTCCTTTCACGTACC 59.104 55.000 30.40 0.00 46.09 3.34
2333 2397 0.606604 GGAGCTCCTTTCACGTACCA 59.393 55.000 26.25 0.00 0.00 3.25
2334 2398 1.001633 GGAGCTCCTTTCACGTACCAA 59.998 52.381 26.25 0.00 0.00 3.67
2335 2399 2.354805 GGAGCTCCTTTCACGTACCAAT 60.355 50.000 26.25 0.00 0.00 3.16
2336 2400 3.335579 GAGCTCCTTTCACGTACCAATT 58.664 45.455 0.87 0.00 0.00 2.32
2337 2401 3.751518 AGCTCCTTTCACGTACCAATTT 58.248 40.909 0.00 0.00 0.00 1.82
2338 2402 3.502211 AGCTCCTTTCACGTACCAATTTG 59.498 43.478 0.00 0.00 0.00 2.32
2339 2403 3.500680 GCTCCTTTCACGTACCAATTTGA 59.499 43.478 0.00 0.00 0.00 2.69
2340 2404 4.156008 GCTCCTTTCACGTACCAATTTGAT 59.844 41.667 0.00 0.00 0.00 2.57
2341 2405 5.621197 TCCTTTCACGTACCAATTTGATG 57.379 39.130 0.00 0.00 0.00 3.07
2342 2406 4.457603 TCCTTTCACGTACCAATTTGATGG 59.542 41.667 0.00 0.00 46.38 3.51
2359 2423 9.533253 AATTTGATGGTATGCTTTATAACTTGC 57.467 29.630 0.00 0.00 29.93 4.01
2360 2424 7.637631 TTGATGGTATGCTTTATAACTTGCA 57.362 32.000 8.72 8.72 39.83 4.08
2361 2425 7.822161 TGATGGTATGCTTTATAACTTGCAT 57.178 32.000 17.94 17.94 46.22 3.96
2362 2426 7.650890 TGATGGTATGCTTTATAACTTGCATG 58.349 34.615 20.77 0.00 44.52 4.06
2363 2427 7.285172 TGATGGTATGCTTTATAACTTGCATGT 59.715 33.333 20.77 0.00 44.52 3.21
2364 2428 7.026631 TGGTATGCTTTATAACTTGCATGTC 57.973 36.000 20.77 15.58 44.52 3.06
2365 2429 6.601217 TGGTATGCTTTATAACTTGCATGTCA 59.399 34.615 20.77 16.82 44.52 3.58
2366 2430 7.285172 TGGTATGCTTTATAACTTGCATGTCAT 59.715 33.333 20.77 0.00 44.52 3.06
2367 2431 8.783093 GGTATGCTTTATAACTTGCATGTCATA 58.217 33.333 20.77 0.00 44.52 2.15
2398 2462 9.793259 ATTGATTTAATATGTGGTCCGATTAGT 57.207 29.630 0.00 0.00 0.00 2.24
2399 2463 8.827177 TGATTTAATATGTGGTCCGATTAGTC 57.173 34.615 0.00 0.00 0.00 2.59
2400 2464 8.647796 TGATTTAATATGTGGTCCGATTAGTCT 58.352 33.333 0.00 0.00 0.00 3.24
2401 2465 9.141400 GATTTAATATGTGGTCCGATTAGTCTC 57.859 37.037 0.00 0.00 0.00 3.36
2402 2466 7.591421 TTAATATGTGGTCCGATTAGTCTCA 57.409 36.000 0.00 0.00 0.00 3.27
2403 2467 5.713792 ATATGTGGTCCGATTAGTCTCAG 57.286 43.478 0.00 0.00 0.00 3.35
2404 2468 3.081710 TGTGGTCCGATTAGTCTCAGA 57.918 47.619 0.00 0.00 0.00 3.27
2405 2469 3.427573 TGTGGTCCGATTAGTCTCAGAA 58.572 45.455 0.00 0.00 0.00 3.02
2406 2470 3.830178 TGTGGTCCGATTAGTCTCAGAAA 59.170 43.478 0.00 0.00 0.00 2.52
2407 2471 4.282449 TGTGGTCCGATTAGTCTCAGAAAA 59.718 41.667 0.00 0.00 0.00 2.29
2408 2472 4.626172 GTGGTCCGATTAGTCTCAGAAAAC 59.374 45.833 0.00 0.00 0.00 2.43
2409 2473 4.282449 TGGTCCGATTAGTCTCAGAAAACA 59.718 41.667 0.00 0.00 0.00 2.83
2410 2474 4.626172 GGTCCGATTAGTCTCAGAAAACAC 59.374 45.833 0.00 0.00 0.00 3.32
2411 2475 5.227908 GTCCGATTAGTCTCAGAAAACACA 58.772 41.667 0.00 0.00 0.00 3.72
2412 2476 5.869888 GTCCGATTAGTCTCAGAAAACACAT 59.130 40.000 0.00 0.00 0.00 3.21
2413 2477 6.369065 GTCCGATTAGTCTCAGAAAACACATT 59.631 38.462 0.00 0.00 0.00 2.71
2414 2478 7.544566 GTCCGATTAGTCTCAGAAAACACATTA 59.455 37.037 0.00 0.00 0.00 1.90
2415 2479 7.759886 TCCGATTAGTCTCAGAAAACACATTAG 59.240 37.037 0.00 0.00 0.00 1.73
2416 2480 7.759886 CCGATTAGTCTCAGAAAACACATTAGA 59.240 37.037 0.00 0.00 0.00 2.10
2417 2481 9.307121 CGATTAGTCTCAGAAAACACATTAGAT 57.693 33.333 0.00 0.00 0.00 1.98
2419 2483 8.689251 TTAGTCTCAGAAAACACATTAGATCG 57.311 34.615 0.00 0.00 0.00 3.69
2420 2484 6.692486 AGTCTCAGAAAACACATTAGATCGT 58.308 36.000 0.00 0.00 0.00 3.73
2421 2485 7.827701 AGTCTCAGAAAACACATTAGATCGTA 58.172 34.615 0.00 0.00 0.00 3.43
2422 2486 8.470805 AGTCTCAGAAAACACATTAGATCGTAT 58.529 33.333 0.00 0.00 0.00 3.06
2423 2487 9.731819 GTCTCAGAAAACACATTAGATCGTATA 57.268 33.333 0.00 0.00 0.00 1.47
2451 2515 5.537300 TGATAGAGGGAGTATGTTCTTGC 57.463 43.478 0.00 0.00 0.00 4.01
2491 2556 2.410939 CTACCATCACAGCATCATCCG 58.589 52.381 0.00 0.00 0.00 4.18
2492 2557 0.832626 ACCATCACAGCATCATCCGA 59.167 50.000 0.00 0.00 0.00 4.55
2516 2583 4.275689 GCAAAAGCTAAAGCCCAAAAATGT 59.724 37.500 0.00 0.00 43.38 2.71
2648 2732 4.991056 CACCACTTTATATCCACCATCTCG 59.009 45.833 0.00 0.00 0.00 4.04
2689 2779 7.826252 CACTATCAACAGATCCTATTTATGGGG 59.174 40.741 0.00 0.00 0.00 4.96
2735 2825 3.023119 TGTTTCACTTGCCAATGTCACT 58.977 40.909 0.00 0.00 0.00 3.41
2736 2826 3.066621 TGTTTCACTTGCCAATGTCACTC 59.933 43.478 0.00 0.00 0.00 3.51
2737 2827 2.636647 TCACTTGCCAATGTCACTCA 57.363 45.000 0.00 0.00 0.00 3.41
2738 2828 2.221169 TCACTTGCCAATGTCACTCAC 58.779 47.619 0.00 0.00 0.00 3.51
2739 2829 1.948834 CACTTGCCAATGTCACTCACA 59.051 47.619 0.00 0.00 40.18 3.58
2741 2831 2.555325 ACTTGCCAATGTCACTCACATG 59.445 45.455 0.00 0.00 45.77 3.21
2857 2948 1.518352 CATCATCAACGACGCCGGA 60.518 57.895 5.05 0.00 40.78 5.14
3120 3211 1.512926 CGAACTGACCCAAACCAGAG 58.487 55.000 0.00 0.00 34.65 3.35
3166 3257 3.774959 GATCGCCGCCGTGTCAGAT 62.775 63.158 0.00 0.00 35.54 2.90
3516 3610 2.697751 GGAGTCTGTGGTCTGCTGATAT 59.302 50.000 0.00 0.00 0.00 1.63
3638 3734 5.689383 TGACTTTCCAAGCTATTGTTGTC 57.311 39.130 0.00 0.00 34.39 3.18
3651 3747 0.322322 TGTTGTCCATGTCCCGTACC 59.678 55.000 0.00 0.00 0.00 3.34
3779 3875 4.069304 CCTTTGTCCCGAATTACTTGTCA 58.931 43.478 0.00 0.00 0.00 3.58
3781 3877 2.679450 TGTCCCGAATTACTTGTCACG 58.321 47.619 0.00 0.00 0.00 4.35
3888 3996 5.335661 CCTCAACACCTTACAAATAACTGCC 60.336 44.000 0.00 0.00 0.00 4.85
4061 4171 0.455464 GGGCAAATGCGTAACCGAAC 60.455 55.000 0.00 0.00 43.26 3.95
4077 4187 3.572255 ACCGAACACCTGCAATAACAATT 59.428 39.130 0.00 0.00 0.00 2.32
4381 7216 6.614906 TGGATTATGTGCCAAAATCCCTAAAT 59.385 34.615 10.06 0.00 45.37 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
608 609 1.228245 GCCAAGGCACTCCTGTTGA 60.228 57.895 6.14 0.00 43.40 3.18
647 648 2.019984 GTTCATTCCAGATGGTCCAGC 58.980 52.381 0.00 0.00 36.34 4.85
737 738 2.229792 CAGCTGTAACCCAAAGCTTGA 58.770 47.619 5.25 0.00 44.79 3.02
918 919 0.537143 CTGTTGTAGCCTGGTTGCCA 60.537 55.000 0.00 0.00 0.00 4.92
972 974 2.787249 CAGCGTACAGGCACATGC 59.213 61.111 0.00 0.00 41.14 4.06
980 982 0.447801 GGATTTGGTGCAGCGTACAG 59.552 55.000 11.91 0.00 0.00 2.74
994 996 1.512926 GACGATAGGCGCATGGATTT 58.487 50.000 10.83 0.00 46.04 2.17
1120 1128 2.105128 CTCTCCCGCGGTAGCAAG 59.895 66.667 26.12 8.32 45.49 4.01
1126 1134 3.883744 CTTGTTGCTCTCCCGCGGT 62.884 63.158 26.12 0.00 0.00 5.68
1131 1139 0.603569 TCGTCTCTTGTTGCTCTCCC 59.396 55.000 0.00 0.00 0.00 4.30
1176 1187 2.202146 GACGAGACGACCGTGACG 60.202 66.667 0.00 0.00 40.67 4.35
1307 1318 2.281761 CAAACTGCACGGAGGCCT 60.282 61.111 3.86 3.86 0.00 5.19
1714 1746 1.374758 GGAGCTTCCTGTCGTGGTG 60.375 63.158 0.00 0.00 32.53 4.17
1879 1911 1.478510 CACGTAGATCACCTTCCTGCT 59.521 52.381 0.00 0.00 0.00 4.24
2040 2072 0.442310 GTAGCACGTACGTACCGACA 59.558 55.000 22.34 0.37 0.00 4.35
2069 2101 3.617669 GGCATGCACATCAAATACGTAC 58.382 45.455 21.36 0.00 0.00 3.67
2126 2163 6.740110 ACGTTGCAACCAAATTTTATCTGTA 58.260 32.000 23.42 0.00 31.68 2.74
2130 2167 7.626446 AGAAAACGTTGCAACCAAATTTTATC 58.374 30.769 23.42 13.01 34.34 1.75
2134 2171 5.391416 CCAAGAAAACGTTGCAACCAAATTT 60.391 36.000 23.42 17.42 31.68 1.82
2237 2301 9.558396 AATAATGATCAAAGGCAGTTTCAAAAA 57.442 25.926 0.00 0.00 0.00 1.94
2240 2304 9.859427 CTTAATAATGATCAAAGGCAGTTTCAA 57.141 29.630 0.00 0.00 0.00 2.69
2241 2305 9.241919 TCTTAATAATGATCAAAGGCAGTTTCA 57.758 29.630 0.00 0.00 0.00 2.69
2314 2378 0.606604 TGGTACGTGAAAGGAGCTCC 59.393 55.000 26.22 26.22 0.00 4.70
2315 2379 2.450609 TTGGTACGTGAAAGGAGCTC 57.549 50.000 4.71 4.71 0.00 4.09
2316 2380 3.418684 AATTGGTACGTGAAAGGAGCT 57.581 42.857 0.00 0.00 0.00 4.09
2317 2381 3.500680 TCAAATTGGTACGTGAAAGGAGC 59.499 43.478 0.00 0.00 0.00 4.70
2318 2382 5.391950 CCATCAAATTGGTACGTGAAAGGAG 60.392 44.000 0.00 0.00 31.74 3.69
2319 2383 4.457603 CCATCAAATTGGTACGTGAAAGGA 59.542 41.667 0.00 0.00 31.74 3.36
2320 2384 4.732784 CCATCAAATTGGTACGTGAAAGG 58.267 43.478 0.00 0.00 31.74 3.11
2333 2397 9.533253 GCAAGTTATAAAGCATACCATCAAATT 57.467 29.630 0.00 0.00 0.00 1.82
2334 2398 8.694540 TGCAAGTTATAAAGCATACCATCAAAT 58.305 29.630 4.84 0.00 31.05 2.32
2335 2399 8.060931 TGCAAGTTATAAAGCATACCATCAAA 57.939 30.769 4.84 0.00 31.05 2.69
2336 2400 7.637631 TGCAAGTTATAAAGCATACCATCAA 57.362 32.000 4.84 0.00 31.05 2.57
2337 2401 7.285172 ACATGCAAGTTATAAAGCATACCATCA 59.715 33.333 16.35 0.00 45.14 3.07
2338 2402 7.651808 ACATGCAAGTTATAAAGCATACCATC 58.348 34.615 16.35 0.00 45.14 3.51
2339 2403 7.285172 TGACATGCAAGTTATAAAGCATACCAT 59.715 33.333 16.35 7.09 45.14 3.55
2340 2404 6.601217 TGACATGCAAGTTATAAAGCATACCA 59.399 34.615 16.35 14.31 45.14 3.25
2341 2405 7.026631 TGACATGCAAGTTATAAAGCATACC 57.973 36.000 16.35 12.71 45.14 2.73
2372 2436 9.793259 ACTAATCGGACCACATATTAAATCAAT 57.207 29.630 0.00 0.00 0.00 2.57
2373 2437 9.268268 GACTAATCGGACCACATATTAAATCAA 57.732 33.333 0.00 0.00 0.00 2.57
2374 2438 8.647796 AGACTAATCGGACCACATATTAAATCA 58.352 33.333 0.00 0.00 0.00 2.57
2375 2439 9.141400 GAGACTAATCGGACCACATATTAAATC 57.859 37.037 0.00 0.00 0.00 2.17
2376 2440 8.647796 TGAGACTAATCGGACCACATATTAAAT 58.352 33.333 0.00 0.00 0.00 1.40
2377 2441 8.014070 TGAGACTAATCGGACCACATATTAAA 57.986 34.615 0.00 0.00 0.00 1.52
2378 2442 7.504574 TCTGAGACTAATCGGACCACATATTAA 59.495 37.037 0.00 0.00 29.46 1.40
2379 2443 7.002276 TCTGAGACTAATCGGACCACATATTA 58.998 38.462 0.00 0.00 29.46 0.98
2380 2444 5.833667 TCTGAGACTAATCGGACCACATATT 59.166 40.000 0.00 0.00 29.46 1.28
2381 2445 5.386060 TCTGAGACTAATCGGACCACATAT 58.614 41.667 0.00 0.00 29.46 1.78
2382 2446 4.788679 TCTGAGACTAATCGGACCACATA 58.211 43.478 0.00 0.00 29.46 2.29
2383 2447 3.632333 TCTGAGACTAATCGGACCACAT 58.368 45.455 0.00 0.00 29.46 3.21
2384 2448 3.081710 TCTGAGACTAATCGGACCACA 57.918 47.619 0.00 0.00 29.46 4.17
2385 2449 4.451629 TTTCTGAGACTAATCGGACCAC 57.548 45.455 0.00 0.00 34.30 4.16
2386 2450 4.282449 TGTTTTCTGAGACTAATCGGACCA 59.718 41.667 0.00 0.00 34.30 4.02
2387 2451 4.626172 GTGTTTTCTGAGACTAATCGGACC 59.374 45.833 0.00 0.00 34.30 4.46
2388 2452 5.227908 TGTGTTTTCTGAGACTAATCGGAC 58.772 41.667 0.00 0.00 34.30 4.79
2389 2453 5.462530 TGTGTTTTCTGAGACTAATCGGA 57.537 39.130 0.00 0.00 32.68 4.55
2390 2454 6.727824 AATGTGTTTTCTGAGACTAATCGG 57.272 37.500 0.00 0.00 0.00 4.18
2391 2455 8.689251 TCTAATGTGTTTTCTGAGACTAATCG 57.311 34.615 0.00 0.00 0.00 3.34
2393 2457 9.307121 CGATCTAATGTGTTTTCTGAGACTAAT 57.693 33.333 0.00 0.00 0.00 1.73
2394 2458 8.304596 ACGATCTAATGTGTTTTCTGAGACTAA 58.695 33.333 0.00 0.00 0.00 2.24
2395 2459 7.827701 ACGATCTAATGTGTTTTCTGAGACTA 58.172 34.615 0.00 0.00 0.00 2.59
2396 2460 6.692486 ACGATCTAATGTGTTTTCTGAGACT 58.308 36.000 0.00 0.00 0.00 3.24
2397 2461 6.952935 ACGATCTAATGTGTTTTCTGAGAC 57.047 37.500 0.00 0.00 0.00 3.36
2425 2489 8.317679 GCAAGAACATACTCCCTCTATCAATAT 58.682 37.037 0.00 0.00 0.00 1.28
2426 2490 7.290014 TGCAAGAACATACTCCCTCTATCAATA 59.710 37.037 0.00 0.00 0.00 1.90
2427 2491 6.100279 TGCAAGAACATACTCCCTCTATCAAT 59.900 38.462 0.00 0.00 0.00 2.57
2428 2492 5.425217 TGCAAGAACATACTCCCTCTATCAA 59.575 40.000 0.00 0.00 0.00 2.57
2429 2493 4.962362 TGCAAGAACATACTCCCTCTATCA 59.038 41.667 0.00 0.00 0.00 2.15
2430 2494 5.303078 TCTGCAAGAACATACTCCCTCTATC 59.697 44.000 0.00 0.00 42.31 2.08
2431 2495 5.211973 TCTGCAAGAACATACTCCCTCTAT 58.788 41.667 0.00 0.00 42.31 1.98
2432 2496 4.610333 TCTGCAAGAACATACTCCCTCTA 58.390 43.478 0.00 0.00 42.31 2.43
2433 2497 3.445008 TCTGCAAGAACATACTCCCTCT 58.555 45.455 0.00 0.00 42.31 3.69
2434 2498 3.895232 TCTGCAAGAACATACTCCCTC 57.105 47.619 0.00 0.00 42.31 4.30
2463 2527 4.937201 TGCTGTGATGGTAGGTATGTAG 57.063 45.455 0.00 0.00 0.00 2.74
2467 2531 4.019860 GGATGATGCTGTGATGGTAGGTAT 60.020 45.833 0.00 0.00 0.00 2.73
2516 2583 0.904865 ACTGTAGTGGCCAGCTGCTA 60.905 55.000 5.11 0.00 40.92 3.49
2672 2762 4.041691 ACGGTTCCCCATAAATAGGATCTG 59.958 45.833 0.00 0.00 33.66 2.90
2682 2772 3.443145 ACATTTGACGGTTCCCCATAA 57.557 42.857 0.00 0.00 0.00 1.90
2689 2779 4.547587 CGCTATCGTTACATTTGACGGTTC 60.548 45.833 0.00 0.00 39.59 3.62
2702 2792 4.032445 GCAAGTGAAACATCGCTATCGTTA 59.968 41.667 0.00 0.00 41.43 3.18
2735 2825 4.082625 GGAAAAGATGCATGTGACATGTGA 60.083 41.667 24.73 13.50 0.00 3.58
2736 2826 4.171005 GGAAAAGATGCATGTGACATGTG 58.829 43.478 24.73 4.60 0.00 3.21
2737 2827 3.119743 CGGAAAAGATGCATGTGACATGT 60.120 43.478 24.73 7.88 0.00 3.21
2738 2828 3.431856 CGGAAAAGATGCATGTGACATG 58.568 45.455 20.66 20.66 0.00 3.21
2739 2829 2.424601 CCGGAAAAGATGCATGTGACAT 59.575 45.455 2.46 0.00 0.00 3.06
2740 2830 1.811965 CCGGAAAAGATGCATGTGACA 59.188 47.619 2.46 0.00 0.00 3.58
2741 2831 1.812571 ACCGGAAAAGATGCATGTGAC 59.187 47.619 9.46 0.00 0.00 3.67
2782 2873 3.737172 GCCATGCACACACGACCC 61.737 66.667 0.00 0.00 0.00 4.46
3025 3116 1.202758 TCGCAGTTTTGGATGACCACT 60.203 47.619 0.00 0.00 46.80 4.00
3103 3194 0.550914 TGCTCTGGTTTGGGTCAGTT 59.449 50.000 0.00 0.00 33.13 3.16
3120 3211 2.592861 GGATGGAGATGCCGGTGC 60.593 66.667 1.90 0.00 40.66 5.01
3159 3250 0.817654 CGTGCCACCTAGATCTGACA 59.182 55.000 5.18 0.00 0.00 3.58
3163 3254 1.115467 CCTTCGTGCCACCTAGATCT 58.885 55.000 0.00 0.00 0.00 2.75
3166 3257 0.830444 ACACCTTCGTGCCACCTAGA 60.830 55.000 0.00 0.00 44.40 2.43
3359 3450 2.032681 GTGCACTCCACCCCACTC 59.967 66.667 10.32 0.00 38.55 3.51
3516 3610 5.705441 GTGATCTGGTTCCATGTTTCAAGTA 59.295 40.000 0.00 0.00 0.00 2.24
3651 3747 6.771188 ATAACAAGCCTCGATAAGATTTCG 57.229 37.500 0.00 0.00 37.94 3.46
3718 3814 5.476254 TGATTGTTGGTTACATTCAGCATCA 59.524 36.000 0.00 0.00 40.41 3.07
3779 3875 8.750298 CATACTCCCATTACTATCTATTTCCGT 58.250 37.037 0.00 0.00 0.00 4.69
3888 3996 3.504906 ACTGATGAACTGATTGTGCAAGG 59.495 43.478 0.00 0.00 37.83 3.61
4061 4171 7.370383 ACTTCTAACAATTGTTATTGCAGGTG 58.630 34.615 26.87 15.01 44.05 4.00
4187 6896 7.700234 TGTGTGCAAATTTGAACTACACTTTAG 59.300 33.333 26.12 0.00 37.62 1.85
4248 6961 8.263940 TCAAGTTAACTTTCTGGGATAATTCG 57.736 34.615 18.25 2.56 33.11 3.34
4381 7216 4.075682 TGAGTTGGACAAACAAACTCACA 58.924 39.130 13.58 0.00 41.61 3.58


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

AutoCloner maintained by Alex Coulton.