Multiple sequence alignment - TraesCS1A01G115900

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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 TraesCS1A01G115900 chr1A 100.000 3032 0 0 1 3032 121131160 121128129 0.000000e+00 5600.0
1 TraesCS1A01G115900 chr1A 96.078 102 4 0 2380 2481 487800097 487799996 1.870000e-37 167.0
2 TraesCS1A01G115900 chr1B 93.219 1342 28 15 1088 2377 173122688 173121358 0.000000e+00 1916.0
3 TraesCS1A01G115900 chr1B 93.595 687 19 4 405 1090 173123390 173122728 0.000000e+00 1002.0
4 TraesCS1A01G115900 chr1B 96.119 438 16 1 2475 2912 173121357 173120921 0.000000e+00 713.0
5 TraesCS1A01G115900 chr1B 96.145 415 13 3 1 414 173123877 173123465 0.000000e+00 675.0
6 TraesCS1A01G115900 chr1B 95.041 121 6 0 2912 3032 173118918 173118798 1.110000e-44 191.0
7 TraesCS1A01G115900 chr4D 93.232 1049 31 15 1088 2112 123141390 123140358 0.000000e+00 1507.0
8 TraesCS1A01G115900 chr4D 93.306 986 50 10 1 983 123142500 123141528 0.000000e+00 1441.0
9 TraesCS1A01G115900 chr4D 94.432 431 23 1 2475 2905 123101542 123101113 0.000000e+00 662.0
10 TraesCS1A01G115900 chr4D 91.011 267 11 3 2124 2377 123101809 123101543 6.220000e-92 348.0
11 TraesCS1A01G115900 chr4D 96.732 153 5 0 2133 2285 123101974 123101822 3.880000e-64 255.0
12 TraesCS1A01G115900 chr4D 97.122 139 4 0 2894 3032 123100547 123100409 5.050000e-58 235.0
13 TraesCS1A01G115900 chr4B 90.783 1085 42 16 1088 2136 187727148 187726086 0.000000e+00 1397.0
14 TraesCS1A01G115900 chr4B 91.433 642 37 11 351 983 187727921 187727289 0.000000e+00 865.0
15 TraesCS1A01G115900 chr4B 88.693 566 39 10 2475 3032 187724501 187723953 0.000000e+00 667.0
16 TraesCS1A01G115900 chr4B 94.634 205 9 1 1 203 187728361 187728157 1.750000e-82 316.0
17 TraesCS1A01G115900 chr4B 82.960 223 26 3 2145 2358 187726029 187725810 1.110000e-44 191.0
18 TraesCS1A01G115900 chr4B 92.920 113 8 0 2380 2492 294107600 294107712 6.720000e-37 165.0
19 TraesCS1A01G115900 chr4B 93.333 105 4 2 217 321 187728108 187728007 5.240000e-33 152.0
20 TraesCS1A01G115900 chr4B 98.305 59 0 1 310 368 187727992 187727935 5.350000e-18 102.0
21 TraesCS1A01G115900 chr4A 91.952 994 45 18 1 983 446612874 446613843 0.000000e+00 1360.0
22 TraesCS1A01G115900 chr4A 88.337 1046 50 23 1088 2089 446613975 446614992 0.000000e+00 1190.0
23 TraesCS1A01G115900 chr4A 91.257 549 18 4 2484 3032 446615331 446615849 0.000000e+00 721.0
24 TraesCS1A01G115900 chr4A 89.490 314 18 3 2077 2375 446615018 446615331 1.710000e-102 383.0
25 TraesCS1A01G115900 chr4A 97.059 102 3 0 2380 2481 567877987 567878088 4.020000e-39 172.0
26 TraesCS1A01G115900 chr2A 97.059 102 3 0 2380 2481 523882662 523882763 4.020000e-39 172.0
27 TraesCS1A01G115900 chr3B 94.595 111 5 1 2380 2489 45520776 45520886 1.450000e-38 171.0
28 TraesCS1A01G115900 chr3B 92.982 114 7 1 2380 2493 636270277 636270389 6.720000e-37 165.0
29 TraesCS1A01G115900 chr3A 96.154 104 4 0 2380 2483 677775296 677775399 1.450000e-38 171.0
30 TraesCS1A01G115900 chr7B 96.078 102 4 0 2380 2481 690381796 690381695 1.870000e-37 167.0
31 TraesCS1A01G115900 chr5A 93.636 110 7 0 2380 2489 569174347 569174456 6.720000e-37 165.0
32 TraesCS1A01G115900 chr5A 100.000 28 0 0 1027 1054 78965550 78965523 5.000000e-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 TraesCS1A01G115900 chr1A 121128129 121131160 3031 True 5600.000000 5600 100.000000 1 3032 1 chr1A.!!$R1 3031
1 TraesCS1A01G115900 chr1B 173118798 173123877 5079 True 899.400000 1916 94.823800 1 3032 5 chr1B.!!$R1 3031
2 TraesCS1A01G115900 chr4D 123140358 123142500 2142 True 1474.000000 1507 93.269000 1 2112 2 chr4D.!!$R2 2111
3 TraesCS1A01G115900 chr4D 123100409 123101974 1565 True 375.000000 662 94.824250 2124 3032 4 chr4D.!!$R1 908
4 TraesCS1A01G115900 chr4B 187723953 187728361 4408 True 527.142857 1397 91.448714 1 3032 7 chr4B.!!$R1 3031
5 TraesCS1A01G115900 chr4A 446612874 446615849 2975 False 913.500000 1360 90.259000 1 3032 4 chr4A.!!$F2 3031

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
996 1207 0.036671 ACCGCAGTAAGCCAGTAACC 60.037 55.0 0.0 0.0 41.38 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2332 2943 0.319555 TTTGCGTGAGACGAAGGGAG 60.32 55.0 0.0 0.0 46.05 4.3 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
32 33 1.508632 TTTTGACGTGCAGGACTAGC 58.491 50.000 14.38 0.00 0.00 3.42
479 659 9.654663 AGAAAGTACTTATGTTCACCATACTTC 57.345 33.333 8.92 0.00 35.75 3.01
606 788 6.293027 CCGCAAAAGAAATTTTGAGAAGCAAT 60.293 34.615 15.60 0.00 41.94 3.56
627 810 2.174360 GAAGAAGGCCCATTTCTTGCT 58.826 47.619 19.99 0.14 43.07 3.91
636 819 2.232941 CCCATTTCTTGCTGTCTTGCAT 59.767 45.455 0.00 0.00 42.96 3.96
684 867 5.752955 TCATGCCTTTTTCTTTTCTTTTCGG 59.247 36.000 0.00 0.00 0.00 4.30
783 971 7.173047 GCATTATTCCTTTTGACACAAACCATT 59.827 33.333 0.00 0.00 0.00 3.16
896 1088 5.357257 CGTGCTGAACTATTATTAGTGGGT 58.643 41.667 0.00 0.00 38.69 4.51
915 1107 8.893563 AGTGGGTTTGGATATTTTCTTATTCA 57.106 30.769 0.00 0.00 0.00 2.57
983 1194 2.094762 AACTTAACCAGCTACCGCAG 57.905 50.000 0.00 0.00 39.10 5.18
984 1195 0.974383 ACTTAACCAGCTACCGCAGT 59.026 50.000 0.00 0.00 39.10 4.40
985 1196 2.173519 ACTTAACCAGCTACCGCAGTA 58.826 47.619 0.00 0.00 39.10 2.74
986 1197 2.564062 ACTTAACCAGCTACCGCAGTAA 59.436 45.455 0.00 0.00 39.10 2.24
987 1198 2.953466 TAACCAGCTACCGCAGTAAG 57.047 50.000 0.00 0.00 39.10 2.34
988 1199 0.391263 AACCAGCTACCGCAGTAAGC 60.391 55.000 0.00 0.00 39.10 3.09
989 1200 1.521681 CCAGCTACCGCAGTAAGCC 60.522 63.158 0.00 0.00 41.38 4.35
990 1201 1.218047 CAGCTACCGCAGTAAGCCA 59.782 57.895 0.00 0.00 41.38 4.75
991 1202 0.807667 CAGCTACCGCAGTAAGCCAG 60.808 60.000 0.00 0.00 41.38 4.85
992 1203 1.218316 GCTACCGCAGTAAGCCAGT 59.782 57.895 0.00 0.00 41.38 4.00
993 1204 0.458669 GCTACCGCAGTAAGCCAGTA 59.541 55.000 0.00 0.00 41.38 2.74
994 1205 1.134907 GCTACCGCAGTAAGCCAGTAA 60.135 52.381 0.00 0.00 41.38 2.24
995 1206 2.537401 CTACCGCAGTAAGCCAGTAAC 58.463 52.381 0.00 0.00 41.38 2.50
996 1207 0.036671 ACCGCAGTAAGCCAGTAACC 60.037 55.000 0.00 0.00 41.38 2.85
997 1208 0.249398 CCGCAGTAAGCCAGTAACCT 59.751 55.000 0.00 0.00 41.38 3.50
998 1209 1.479323 CCGCAGTAAGCCAGTAACCTA 59.521 52.381 0.00 0.00 41.38 3.08
999 1210 2.093869 CCGCAGTAAGCCAGTAACCTAA 60.094 50.000 0.00 0.00 41.38 2.69
1143 1411 1.226491 GGCGTACGTGTAGCATCGT 60.226 57.895 17.90 0.00 42.82 3.73
1144 1412 1.469126 GGCGTACGTGTAGCATCGTG 61.469 60.000 17.90 0.00 40.50 4.35
1145 1413 1.908089 CGTACGTGTAGCATCGTGC 59.092 57.895 7.22 2.28 45.46 5.34
1171 1439 0.794229 CACGCAACGGCAGCTTATTG 60.794 55.000 0.00 0.00 41.24 1.90
1208 1476 2.431057 CCTCCTCTTGTACGCTACCAAT 59.569 50.000 0.00 0.00 0.00 3.16
1275 1545 6.608405 AGGCTATCCATTCAATTCAATTGTGA 59.392 34.615 9.98 0.00 36.86 3.58
1801 2116 3.735181 GTGAATAACGAGCGTCCCT 57.265 52.632 0.00 0.00 0.00 4.20
1802 2117 1.557651 GTGAATAACGAGCGTCCCTC 58.442 55.000 0.00 0.00 37.22 4.30
1909 2227 2.286950 CCTTGTGTGTATGTGTGTGCAC 60.287 50.000 10.75 10.75 45.44 4.57
2046 2377 1.331756 CGGCGCATCTTCAGCTATTTT 59.668 47.619 10.83 0.00 0.00 1.82
2130 2502 9.056005 CCACCTATAAAATGAAGATTTCGATCA 57.944 33.333 0.00 0.00 30.02 2.92
2249 2850 3.435186 GTTTCTGGGCAGCGCTCC 61.435 66.667 7.13 12.42 0.00 4.70
2377 4277 4.631813 AGGACACATTTGCTAGTTCGATTC 59.368 41.667 0.00 0.00 0.00 2.52
2379 4279 5.065218 GGACACATTTGCTAGTTCGATTCAT 59.935 40.000 0.00 0.00 0.00 2.57
2380 4280 6.111768 ACACATTTGCTAGTTCGATTCATC 57.888 37.500 0.00 0.00 0.00 2.92
2381 4281 5.877012 ACACATTTGCTAGTTCGATTCATCT 59.123 36.000 0.00 0.00 0.00 2.90
2382 4282 6.372659 ACACATTTGCTAGTTCGATTCATCTT 59.627 34.615 0.00 0.00 0.00 2.40
2383 4283 6.685828 CACATTTGCTAGTTCGATTCATCTTG 59.314 38.462 0.00 0.00 0.00 3.02
2384 4284 5.801350 TTTGCTAGTTCGATTCATCTTGG 57.199 39.130 0.00 0.00 0.00 3.61
2385 4285 4.736126 TGCTAGTTCGATTCATCTTGGA 57.264 40.909 0.00 0.00 0.00 3.53
2386 4286 5.282055 TGCTAGTTCGATTCATCTTGGAT 57.718 39.130 0.00 0.00 0.00 3.41
2387 4287 5.674525 TGCTAGTTCGATTCATCTTGGATT 58.325 37.500 0.00 0.00 0.00 3.01
2388 4288 6.115446 TGCTAGTTCGATTCATCTTGGATTT 58.885 36.000 0.00 0.00 0.00 2.17
2389 4289 6.037500 TGCTAGTTCGATTCATCTTGGATTTG 59.962 38.462 0.00 0.00 0.00 2.32
2390 4290 6.037610 GCTAGTTCGATTCATCTTGGATTTGT 59.962 38.462 0.00 0.00 0.00 2.83
2391 4291 6.428385 AGTTCGATTCATCTTGGATTTGTC 57.572 37.500 0.00 0.00 0.00 3.18
2392 4292 6.176183 AGTTCGATTCATCTTGGATTTGTCT 58.824 36.000 0.00 0.00 0.00 3.41
2393 4293 7.331026 AGTTCGATTCATCTTGGATTTGTCTA 58.669 34.615 0.00 0.00 0.00 2.59
2394 4294 7.989741 AGTTCGATTCATCTTGGATTTGTCTAT 59.010 33.333 0.00 0.00 0.00 1.98
2395 4295 9.261180 GTTCGATTCATCTTGGATTTGTCTATA 57.739 33.333 0.00 0.00 0.00 1.31
2403 4303 9.610705 CATCTTGGATTTGTCTATATATGGAGG 57.389 37.037 0.00 0.00 0.00 4.30
2404 4304 8.742125 TCTTGGATTTGTCTATATATGGAGGT 57.258 34.615 0.00 0.00 0.00 3.85
2405 4305 9.837681 TCTTGGATTTGTCTATATATGGAGGTA 57.162 33.333 0.00 0.00 0.00 3.08
2412 4312 9.990868 TTTGTCTATATATGGAGGTATCTAGCA 57.009 33.333 0.00 0.00 0.00 3.49
2413 4313 8.982091 TGTCTATATATGGAGGTATCTAGCAC 57.018 38.462 0.00 0.00 0.00 4.40
2414 4314 8.782927 TGTCTATATATGGAGGTATCTAGCACT 58.217 37.037 0.00 0.00 0.00 4.40
2421 4321 7.618019 ATGGAGGTATCTAGCACTAAAATGA 57.382 36.000 0.00 0.00 0.00 2.57
2422 4322 7.055667 TGGAGGTATCTAGCACTAAAATGAG 57.944 40.000 0.00 0.00 0.00 2.90
2423 4323 6.611642 TGGAGGTATCTAGCACTAAAATGAGT 59.388 38.462 0.00 0.00 0.00 3.41
2424 4324 7.149307 GGAGGTATCTAGCACTAAAATGAGTC 58.851 42.308 0.00 0.00 0.00 3.36
2425 4325 7.014808 GGAGGTATCTAGCACTAAAATGAGTCT 59.985 40.741 0.00 0.00 0.00 3.24
2426 4326 8.998277 AGGTATCTAGCACTAAAATGAGTCTA 57.002 34.615 0.00 0.00 0.00 2.59
2427 4327 9.073475 AGGTATCTAGCACTAAAATGAGTCTAG 57.927 37.037 0.00 0.00 33.29 2.43
2428 4328 9.069082 GGTATCTAGCACTAAAATGAGTCTAGA 57.931 37.037 11.59 11.59 38.76 2.43
2432 4332 9.628500 TCTAGCACTAAAATGAGTCTAGATACA 57.372 33.333 0.00 0.00 34.65 2.29
2435 4335 8.364142 AGCACTAAAATGAGTCTAGATACATCC 58.636 37.037 12.66 0.00 0.00 3.51
2436 4336 7.327275 GCACTAAAATGAGTCTAGATACATCCG 59.673 40.741 12.66 6.68 0.00 4.18
2437 4337 8.353684 CACTAAAATGAGTCTAGATACATCCGT 58.646 37.037 12.66 7.10 0.00 4.69
2438 4338 9.570468 ACTAAAATGAGTCTAGATACATCCGTA 57.430 33.333 12.66 6.93 0.00 4.02
2452 4352 7.776618 ATACATCCGTATCTAGACAAATCCA 57.223 36.000 0.00 0.00 32.66 3.41
2453 4353 6.479972 ACATCCGTATCTAGACAAATCCAA 57.520 37.500 0.00 0.00 0.00 3.53
2454 4354 6.516718 ACATCCGTATCTAGACAAATCCAAG 58.483 40.000 0.00 0.00 0.00 3.61
2455 4355 6.323996 ACATCCGTATCTAGACAAATCCAAGA 59.676 38.462 0.00 0.00 0.00 3.02
2456 4356 6.145338 TCCGTATCTAGACAAATCCAAGAC 57.855 41.667 0.00 0.00 0.00 3.01
2457 4357 5.655090 TCCGTATCTAGACAAATCCAAGACA 59.345 40.000 0.00 0.00 0.00 3.41
2458 4358 6.153851 TCCGTATCTAGACAAATCCAAGACAA 59.846 38.462 0.00 0.00 0.00 3.18
2459 4359 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
2460 4360 7.036220 CGTATCTAGACAAATCCAAGACAAGT 58.964 38.462 0.00 0.00 0.00 3.16
2461 4361 8.188799 CGTATCTAGACAAATCCAAGACAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
2462 4362 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
2464 4364 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
2465 4365 9.793259 TCTAGACAAATCCAAGACAAGTAATTT 57.207 29.630 0.00 0.00 0.00 1.82
2468 4368 9.793259 AGACAAATCCAAGACAAGTAATTTAGA 57.207 29.630 0.00 0.00 0.00 2.10
2471 4371 9.329913 CAAATCCAAGACAAGTAATTTAGAACG 57.670 33.333 0.00 0.00 0.00 3.95
2472 4372 7.611213 ATCCAAGACAAGTAATTTAGAACGG 57.389 36.000 0.00 0.00 0.00 4.44
2473 4373 6.761312 TCCAAGACAAGTAATTTAGAACGGA 58.239 36.000 0.00 0.00 0.00 4.69
2474 4374 6.872020 TCCAAGACAAGTAATTTAGAACGGAG 59.128 38.462 0.00 0.00 0.00 4.63
2475 4375 6.872020 CCAAGACAAGTAATTTAGAACGGAGA 59.128 38.462 0.00 0.00 0.00 3.71
2476 4376 7.063544 CCAAGACAAGTAATTTAGAACGGAGAG 59.936 40.741 0.00 0.00 0.00 3.20
2477 4377 7.463961 AGACAAGTAATTTAGAACGGAGAGA 57.536 36.000 0.00 0.00 0.00 3.10
2549 4449 6.839124 ACTTTTCCATCTCATGCAAATACA 57.161 33.333 0.00 0.00 0.00 2.29
2641 4543 8.967664 AAATCGTGCTATAGGTAAACCAAATA 57.032 30.769 1.04 0.00 38.89 1.40
2827 4735 5.462034 TTCACAAATTTTGGCGACTTTTG 57.538 34.783 13.42 6.91 34.34 2.44
3013 6926 9.606631 GGGTTTATGGAATTTGCATTTGTTATA 57.393 29.630 8.77 0.00 29.08 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 9.303116 AGATTATGTCACATCCTTAGGTACTAG 57.697 37.037 0.00 0.00 44.25 2.57
316 356 5.759763 GCAATTGTTTTCTCCACTCCAATTT 59.240 36.000 7.40 0.00 32.00 1.82
479 659 9.696917 AGTGCAACATTTCTATTTCTTTTAAGG 57.303 29.630 0.00 0.00 41.43 2.69
606 788 1.895131 GCAAGAAATGGGCCTTCTTCA 59.105 47.619 15.69 0.00 40.37 3.02
627 810 7.692460 ATATGACTTTCTCAAATGCAAGACA 57.308 32.000 0.00 0.00 30.60 3.41
664 847 4.689071 TCCCGAAAAGAAAAGAAAAAGGC 58.311 39.130 0.00 0.00 0.00 4.35
665 848 6.569780 TCTTCCCGAAAAGAAAAGAAAAAGG 58.430 36.000 0.00 0.00 32.42 3.11
666 849 9.181805 GTATCTTCCCGAAAAGAAAAGAAAAAG 57.818 33.333 3.97 0.00 38.69 2.27
783 971 3.069586 ACTGTTCCTTGATGAAGACGTGA 59.930 43.478 0.00 0.00 0.00 4.35
870 1062 4.211374 CACTAATAATAGTTCAGCACGCCC 59.789 45.833 0.00 0.00 40.44 6.13
908 1100 8.592105 TGGTTGCTTTCTGAAAAATGAATAAG 57.408 30.769 4.18 0.00 0.00 1.73
915 1107 6.877236 TCTTTCTGGTTGCTTTCTGAAAAAT 58.123 32.000 4.18 0.00 32.98 1.82
983 1194 6.872628 AAAGTGTTTAGGTTACTGGCTTAC 57.127 37.500 0.00 0.00 0.00 2.34
984 1195 7.885009 AAAAAGTGTTTAGGTTACTGGCTTA 57.115 32.000 0.00 0.00 0.00 3.09
985 1196 6.785337 AAAAAGTGTTTAGGTTACTGGCTT 57.215 33.333 0.00 0.00 0.00 4.35
986 1197 7.722285 TGATAAAAAGTGTTTAGGTTACTGGCT 59.278 33.333 0.00 0.00 0.00 4.75
987 1198 7.806487 GTGATAAAAAGTGTTTAGGTTACTGGC 59.194 37.037 0.00 0.00 0.00 4.85
988 1199 9.063615 AGTGATAAAAAGTGTTTAGGTTACTGG 57.936 33.333 0.00 0.00 0.00 4.00
994 1205 9.841295 TCTTGTAGTGATAAAAAGTGTTTAGGT 57.159 29.630 0.00 0.00 0.00 3.08
1143 1411 4.249020 CGTTGCGTGGCAGTTGCA 62.249 61.111 6.43 5.02 44.36 4.08
1144 1412 4.980903 CCGTTGCGTGGCAGTTGC 62.981 66.667 0.00 0.00 40.61 4.17
1171 1439 1.324383 GAGGCCACTCTAGTCTAGCC 58.676 60.000 5.01 0.64 40.68 3.93
1208 1476 1.346395 AGCCGAATGGTGTACACAAGA 59.654 47.619 26.51 10.82 37.67 3.02
1275 1545 2.967887 TGGTGTCGAGGATGATGATGAT 59.032 45.455 0.00 0.00 0.00 2.45
1419 1689 6.896021 AGGAGAAGCATCCATTAATGATTG 57.104 37.500 17.23 13.66 42.26 2.67
1421 1691 5.243283 GCAAGGAGAAGCATCCATTAATGAT 59.757 40.000 17.23 5.88 42.26 2.45
1561 1860 2.044946 ATCTTCCTGCAACGGGCC 60.045 61.111 0.00 0.00 43.89 5.80
1799 2114 2.553602 CTCGACTCCATCAGATCAGAGG 59.446 54.545 10.49 0.00 0.00 3.69
1800 2115 2.030893 GCTCGACTCCATCAGATCAGAG 60.031 54.545 0.00 5.68 0.00 3.35
1801 2116 1.952990 GCTCGACTCCATCAGATCAGA 59.047 52.381 0.00 0.00 0.00 3.27
1802 2117 1.680207 TGCTCGACTCCATCAGATCAG 59.320 52.381 0.00 0.00 0.00 2.90
1909 2227 2.422597 TGAAGCAATTACAGGGACACG 58.577 47.619 0.00 0.00 0.00 4.49
2046 2377 7.664318 TCGCTGTATACTTCATGTTAGAGGATA 59.336 37.037 4.17 0.00 0.00 2.59
2113 2485 8.030692 TGCAATTCTTGATCGAAATCTTCATTT 58.969 29.630 0.00 0.00 34.70 2.32
2130 2502 2.032030 CGTTCTGACGGTTGCAATTCTT 60.032 45.455 0.59 0.00 45.32 2.52
2332 2943 0.319555 TTTGCGTGAGACGAAGGGAG 60.320 55.000 0.00 0.00 46.05 4.30
2355 2966 4.391830 TGAATCGAACTAGCAAATGTGTCC 59.608 41.667 0.00 0.00 0.00 4.02
2377 4277 9.610705 CCTCCATATATAGACAAATCCAAGATG 57.389 37.037 0.00 0.00 0.00 2.90
2379 4279 8.742125 ACCTCCATATATAGACAAATCCAAGA 57.258 34.615 0.00 0.00 0.00 3.02
2386 4286 9.990868 TGCTAGATACCTCCATATATAGACAAA 57.009 33.333 0.00 0.00 30.91 2.83
2387 4287 9.409918 GTGCTAGATACCTCCATATATAGACAA 57.590 37.037 0.00 0.00 30.91 3.18
2388 4288 8.782927 AGTGCTAGATACCTCCATATATAGACA 58.217 37.037 0.00 0.00 30.91 3.41
2395 4295 9.326489 TCATTTTAGTGCTAGATACCTCCATAT 57.674 33.333 0.00 0.00 0.00 1.78
2396 4296 8.721133 TCATTTTAGTGCTAGATACCTCCATA 57.279 34.615 0.00 0.00 0.00 2.74
2397 4297 7.291182 ACTCATTTTAGTGCTAGATACCTCCAT 59.709 37.037 0.00 0.00 0.00 3.41
2398 4298 6.611642 ACTCATTTTAGTGCTAGATACCTCCA 59.388 38.462 0.00 0.00 0.00 3.86
2399 4299 7.014808 AGACTCATTTTAGTGCTAGATACCTCC 59.985 40.741 0.00 0.00 0.00 4.30
2400 4300 7.947282 AGACTCATTTTAGTGCTAGATACCTC 58.053 38.462 0.00 0.00 0.00 3.85
2401 4301 7.906199 AGACTCATTTTAGTGCTAGATACCT 57.094 36.000 0.00 0.00 0.00 3.08
2402 4302 9.069082 TCTAGACTCATTTTAGTGCTAGATACC 57.931 37.037 0.00 0.00 34.69 2.73
2406 4306 9.628500 TGTATCTAGACTCATTTTAGTGCTAGA 57.372 33.333 0.00 0.00 38.76 2.43
2409 4309 8.364142 GGATGTATCTAGACTCATTTTAGTGCT 58.636 37.037 11.25 0.00 0.00 4.40
2410 4310 7.327275 CGGATGTATCTAGACTCATTTTAGTGC 59.673 40.741 11.25 0.00 0.00 4.40
2411 4311 8.353684 ACGGATGTATCTAGACTCATTTTAGTG 58.646 37.037 11.25 3.85 0.00 2.74
2412 4312 8.466617 ACGGATGTATCTAGACTCATTTTAGT 57.533 34.615 11.25 7.70 0.00 2.24
2428 4328 7.776618 TGGATTTGTCTAGATACGGATGTAT 57.223 36.000 0.00 0.00 43.97 2.29
2429 4329 7.504574 TCTTGGATTTGTCTAGATACGGATGTA 59.495 37.037 0.00 0.00 34.45 2.29
2430 4330 6.323996 TCTTGGATTTGTCTAGATACGGATGT 59.676 38.462 0.00 0.00 0.00 3.06
2431 4331 6.642950 GTCTTGGATTTGTCTAGATACGGATG 59.357 42.308 0.00 0.00 0.00 3.51
2432 4332 6.323996 TGTCTTGGATTTGTCTAGATACGGAT 59.676 38.462 0.00 0.00 0.00 4.18
2433 4333 5.655090 TGTCTTGGATTTGTCTAGATACGGA 59.345 40.000 0.00 0.00 0.00 4.69
2434 4334 5.902681 TGTCTTGGATTTGTCTAGATACGG 58.097 41.667 0.00 0.00 0.00 4.02
2435 4335 7.036220 ACTTGTCTTGGATTTGTCTAGATACG 58.964 38.462 0.00 0.00 0.00 3.06
2436 4336 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
2438 4338 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
2439 4339 9.793259 AAATTACTTGTCTTGGATTTGTCTAGA 57.207 29.630 0.00 0.00 0.00 2.43
2442 4342 9.793259 TCTAAATTACTTGTCTTGGATTTGTCT 57.207 29.630 0.00 0.00 0.00 3.41
2445 4345 9.329913 CGTTCTAAATTACTTGTCTTGGATTTG 57.670 33.333 0.00 0.00 0.00 2.32
2446 4346 8.512138 CCGTTCTAAATTACTTGTCTTGGATTT 58.488 33.333 0.00 0.00 0.00 2.17
2447 4347 7.881232 TCCGTTCTAAATTACTTGTCTTGGATT 59.119 33.333 0.00 0.00 0.00 3.01
2448 4348 7.391620 TCCGTTCTAAATTACTTGTCTTGGAT 58.608 34.615 0.00 0.00 0.00 3.41
2449 4349 6.761312 TCCGTTCTAAATTACTTGTCTTGGA 58.239 36.000 0.00 0.00 0.00 3.53
2450 4350 6.872020 TCTCCGTTCTAAATTACTTGTCTTGG 59.128 38.462 0.00 0.00 0.00 3.61
2451 4351 7.813148 TCTCTCCGTTCTAAATTACTTGTCTTG 59.187 37.037 0.00 0.00 0.00 3.02
2452 4352 7.893658 TCTCTCCGTTCTAAATTACTTGTCTT 58.106 34.615 0.00 0.00 0.00 3.01
2453 4353 7.177041 ACTCTCTCCGTTCTAAATTACTTGTCT 59.823 37.037 0.00 0.00 0.00 3.41
2454 4354 7.314393 ACTCTCTCCGTTCTAAATTACTTGTC 58.686 38.462 0.00 0.00 0.00 3.18
2455 4355 7.229581 ACTCTCTCCGTTCTAAATTACTTGT 57.770 36.000 0.00 0.00 0.00 3.16
2456 4356 7.701501 GGTACTCTCTCCGTTCTAAATTACTTG 59.298 40.741 0.00 0.00 0.00 3.16
2457 4357 7.395489 TGGTACTCTCTCCGTTCTAAATTACTT 59.605 37.037 0.00 0.00 0.00 2.24
2458 4358 6.888632 TGGTACTCTCTCCGTTCTAAATTACT 59.111 38.462 0.00 0.00 0.00 2.24
2459 4359 7.093322 TGGTACTCTCTCCGTTCTAAATTAC 57.907 40.000 0.00 0.00 0.00 1.89
2460 4360 7.707624 TTGGTACTCTCTCCGTTCTAAATTA 57.292 36.000 0.00 0.00 0.00 1.40
2461 4361 6.600882 TTGGTACTCTCTCCGTTCTAAATT 57.399 37.500 0.00 0.00 0.00 1.82
2462 4362 6.793505 ATTGGTACTCTCTCCGTTCTAAAT 57.206 37.500 0.00 0.00 0.00 1.40
2463 4363 6.600882 AATTGGTACTCTCTCCGTTCTAAA 57.399 37.500 0.00 0.00 0.00 1.85
2464 4364 7.395489 ACTTAATTGGTACTCTCTCCGTTCTAA 59.605 37.037 0.00 0.00 0.00 2.10
2465 4365 6.888632 ACTTAATTGGTACTCTCTCCGTTCTA 59.111 38.462 0.00 0.00 0.00 2.10
2466 4366 5.715753 ACTTAATTGGTACTCTCTCCGTTCT 59.284 40.000 0.00 0.00 0.00 3.01
2467 4367 5.805994 CACTTAATTGGTACTCTCTCCGTTC 59.194 44.000 0.00 0.00 0.00 3.95
2468 4368 5.479375 TCACTTAATTGGTACTCTCTCCGTT 59.521 40.000 0.00 0.00 0.00 4.44
2469 4369 5.014858 TCACTTAATTGGTACTCTCTCCGT 58.985 41.667 0.00 0.00 0.00 4.69
2470 4370 5.578005 TCACTTAATTGGTACTCTCTCCG 57.422 43.478 0.00 0.00 0.00 4.63
2471 4371 6.284459 CCATCACTTAATTGGTACTCTCTCC 58.716 44.000 0.00 0.00 0.00 3.71
2472 4372 5.755861 GCCATCACTTAATTGGTACTCTCTC 59.244 44.000 0.00 0.00 32.90 3.20
2473 4373 5.189736 TGCCATCACTTAATTGGTACTCTCT 59.810 40.000 0.00 0.00 32.90 3.10
2474 4374 5.294552 GTGCCATCACTTAATTGGTACTCTC 59.705 44.000 2.68 0.00 41.31 3.20
2475 4375 5.186198 GTGCCATCACTTAATTGGTACTCT 58.814 41.667 2.68 0.00 41.31 3.24
2476 4376 4.335594 GGTGCCATCACTTAATTGGTACTC 59.664 45.833 8.86 0.00 43.26 2.59
2477 4377 4.270008 GGTGCCATCACTTAATTGGTACT 58.730 43.478 8.86 0.00 43.26 2.73
2588 4490 7.552458 AAAACTGACCAAAATTCATGTTTCC 57.448 32.000 0.00 0.00 30.63 3.13
2641 4543 2.225117 ACCACTTGCTTAGAAATGCCCT 60.225 45.455 0.00 0.00 0.00 5.19
2688 4590 5.222130 CCCCATTTTGGTCTACCTATAGCAT 60.222 44.000 0.02 0.00 35.17 3.79


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

AutoCloner maintained by Alex Coulton.