Multiple sequence alignment - TraesCS5A01G207800

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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 TraesCS5A01G207800 chr5A 100.000 2968 0 0 1 2968 419869531 419872498 0.000000e+00 5481.0
1 TraesCS5A01G207800 chr5A 77.446 838 116 37 1131 1921 422029702 422028891 1.630000e-117 433.0
2 TraesCS5A01G207800 chr5B 89.439 1818 126 28 1183 2949 375416657 375418459 0.000000e+00 2233.0
3 TraesCS5A01G207800 chr5B 89.160 1190 71 32 45 1191 375415397 375416571 0.000000e+00 1430.0
4 TraesCS5A01G207800 chr5B 76.550 1258 188 65 803 1979 375744355 375743124 9.160000e-165 590.0
5 TraesCS5A01G207800 chr5B 80.157 383 59 8 2598 2968 701206374 701206751 1.360000e-68 270.0
6 TraesCS5A01G207800 chr1D 76.821 1428 236 46 773 2164 230219662 230218294 0.000000e+00 715.0
7 TraesCS5A01G207800 chr1D 80.606 495 76 8 2418 2894 357220080 357220572 6.050000e-97 364.0
8 TraesCS5A01G207800 chr1D 80.444 496 76 8 2418 2894 357216552 357217045 2.810000e-95 359.0
9 TraesCS5A01G207800 chr1D 80.444 496 76 8 2418 2894 357218315 357218808 2.810000e-95 359.0
10 TraesCS5A01G207800 chr2D 79.391 558 89 18 2418 2960 498236230 498235684 1.300000e-98 370.0
11 TraesCS5A01G207800 chr6B 80.779 385 61 11 2576 2953 182354460 182354838 3.740000e-74 289.0
12 TraesCS5A01G207800 chr6B 76.611 419 58 14 2418 2798 717143949 717144365 8.390000e-46 195.0
13 TraesCS5A01G207800 chr4A 80.206 389 60 9 2590 2966 621263463 621263846 2.910000e-70 276.0
14 TraesCS5A01G207800 chr5D 76.527 524 85 18 2464 2968 357511596 357511092 4.910000e-63 252.0
15 TraesCS5A01G207800 chr7D 77.934 426 76 11 2554 2968 84181629 84181211 1.770000e-62 250.0
16 TraesCS5A01G207800 chr6A 79.019 367 72 5 2589 2952 199986632 199986268 2.280000e-61 246.0
17 TraesCS5A01G207800 chr6A 76.250 480 94 15 2507 2968 450106593 450106116 1.380000e-58 237.0
18 TraesCS5A01G207800 chr6A 76.064 376 47 19 2355 2693 617551641 617551272 3.960000e-34 156.0
19 TraesCS5A01G207800 chr3B 76.265 514 89 25 2473 2964 102973700 102974202 2.960000e-60 243.0
20 TraesCS5A01G207800 chr7B 78.701 385 65 10 2429 2797 613478570 613478187 1.060000e-59 241.0
21 TraesCS5A01G207800 chr6D 76.904 394 53 12 2442 2798 472430885 472431277 3.910000e-44 189.0
22 TraesCS5A01G207800 chr6D 74.783 230 37 16 83 294 434165717 434165943 1.900000e-12 84.2


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 TraesCS5A01G207800 chr5A 419869531 419872498 2967 False 5481.000000 5481 100.0000 1 2968 1 chr5A.!!$F1 2967
1 TraesCS5A01G207800 chr5A 422028891 422029702 811 True 433.000000 433 77.4460 1131 1921 1 chr5A.!!$R1 790
2 TraesCS5A01G207800 chr5B 375415397 375418459 3062 False 1831.500000 2233 89.2995 45 2949 2 chr5B.!!$F2 2904
3 TraesCS5A01G207800 chr5B 375743124 375744355 1231 True 590.000000 590 76.5500 803 1979 1 chr5B.!!$R1 1176
4 TraesCS5A01G207800 chr1D 230218294 230219662 1368 True 715.000000 715 76.8210 773 2164 1 chr1D.!!$R1 1391
5 TraesCS5A01G207800 chr1D 357216552 357220572 4020 False 360.666667 364 80.4980 2418 2894 3 chr1D.!!$F1 476
6 TraesCS5A01G207800 chr2D 498235684 498236230 546 True 370.000000 370 79.3910 2418 2960 1 chr2D.!!$R1 542
7 TraesCS5A01G207800 chr5D 357511092 357511596 504 True 252.000000 252 76.5270 2464 2968 1 chr5D.!!$R1 504
8 TraesCS5A01G207800 chr3B 102973700 102974202 502 False 243.000000 243 76.2650 2473 2964 1 chr3B.!!$F1 491

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
390 429 0.101759 CCATTCTGGCGGCTGATTTG 59.898 55.0 18.99 17.64 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2224 2504 0.166814 GCTAGCCACGCTTCAACAAG 59.833 55.0 2.29 0.0 40.44 3.16 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
36 37 7.130303 AGTTTTGAGGTCTACTTTTATTCGC 57.870 36.000 0.00 0.00 0.00 4.70
37 38 6.708949 AGTTTTGAGGTCTACTTTTATTCGCA 59.291 34.615 0.00 0.00 0.00 5.10
38 39 7.227910 AGTTTTGAGGTCTACTTTTATTCGCAA 59.772 33.333 0.00 0.00 0.00 4.85
39 40 7.499321 TTTGAGGTCTACTTTTATTCGCAAA 57.501 32.000 0.00 0.00 0.00 3.68
40 41 7.499321 TTGAGGTCTACTTTTATTCGCAAAA 57.501 32.000 0.00 0.00 0.00 2.44
41 42 7.499321 TGAGGTCTACTTTTATTCGCAAAAA 57.501 32.000 0.00 0.00 0.00 1.94
238 244 5.335827 TGTTTAACATTTTTCCAATGCGC 57.664 34.783 0.00 0.00 0.00 6.09
242 248 2.261345 ACATTTTTCCAATGCGCGATG 58.739 42.857 12.10 4.97 0.00 3.84
243 249 2.094803 ACATTTTTCCAATGCGCGATGA 60.095 40.909 12.10 0.00 0.00 2.92
244 250 2.713895 TTTTTCCAATGCGCGATGAA 57.286 40.000 12.10 5.69 0.00 2.57
254 260 2.323959 TGCGCGATGAAACATTTTTCC 58.676 42.857 12.10 0.00 40.55 3.13
364 403 5.944599 TGTAAAATGTAAAATGTCCCCGCTA 59.055 36.000 0.00 0.00 0.00 4.26
390 429 0.101759 CCATTCTGGCGGCTGATTTG 59.898 55.000 18.99 17.64 0.00 2.32
391 430 1.097232 CATTCTGGCGGCTGATTTGA 58.903 50.000 18.99 4.95 0.00 2.69
392 431 1.098050 ATTCTGGCGGCTGATTTGAC 58.902 50.000 18.99 0.00 0.00 3.18
393 432 1.298157 TTCTGGCGGCTGATTTGACG 61.298 55.000 18.99 0.00 42.16 4.35
397 436 2.697425 CGGCTGATTTGACGCGAG 59.303 61.111 15.93 0.00 0.00 5.03
398 437 2.802667 CGGCTGATTTGACGCGAGG 61.803 63.158 15.93 0.00 0.00 4.63
399 438 2.401195 GCTGATTTGACGCGAGGC 59.599 61.111 15.93 1.62 42.12 4.70
400 439 2.103042 GCTGATTTGACGCGAGGCT 61.103 57.895 15.93 0.00 42.42 4.58
401 440 0.806102 GCTGATTTGACGCGAGGCTA 60.806 55.000 15.93 0.00 42.42 3.93
402 441 0.924090 CTGATTTGACGCGAGGCTAC 59.076 55.000 15.93 0.17 42.42 3.58
403 442 0.800683 TGATTTGACGCGAGGCTACG 60.801 55.000 15.93 7.77 42.42 3.51
495 534 1.765314 CTCCATTCTCCTTCCGTCCAT 59.235 52.381 0.00 0.00 0.00 3.41
647 686 3.393800 CGGATGAAATTCGCAGGATACT 58.606 45.455 0.00 0.00 43.63 2.12
689 728 4.696479 ACCCAGGTATTGATCAGATCAC 57.304 45.455 13.01 1.87 39.39 3.06
710 749 1.307097 GTTGCCATCTCTCTCCATGC 58.693 55.000 0.00 0.00 0.00 4.06
745 790 5.126779 GGATACTTCTCCCTCCATGTTTTC 58.873 45.833 0.00 0.00 0.00 2.29
824 869 2.533266 TTGGCCAGATATCTTCGAGC 57.467 50.000 5.11 4.02 0.00 5.03
865 910 2.739932 GCTACTGCCACAAGACATCGAT 60.740 50.000 0.00 0.00 0.00 3.59
878 923 3.130516 AGACATCGATTGCTCGGACTTTA 59.869 43.478 0.00 0.00 45.10 1.85
879 924 4.051922 GACATCGATTGCTCGGACTTTAT 58.948 43.478 0.00 0.00 45.10 1.40
916 961 1.001268 GAGTATCTGAGGCGCAATCGA 60.001 52.381 10.83 9.03 38.10 3.59
923 971 1.776034 GAGGCGCAATCGAATGGACC 61.776 60.000 10.83 0.00 38.10 4.46
1005 1065 2.027385 GGAGGATGTTCCCAAATGCTC 58.973 52.381 0.00 0.00 39.70 4.26
1012 1079 2.440247 CCCAAATGCTCCCCGGAC 60.440 66.667 0.73 0.00 0.00 4.79
1148 1233 0.462581 GATGGAGCGGCAGTTCATGA 60.463 55.000 1.45 0.00 0.00 3.07
1149 1234 0.035152 ATGGAGCGGCAGTTCATGAA 60.035 50.000 3.38 3.38 0.00 2.57
1228 1407 2.586792 GCCAGTCGCCTCATCCTT 59.413 61.111 0.00 0.00 0.00 3.36
1231 1410 0.824109 CCAGTCGCCTCATCCTTGTA 59.176 55.000 0.00 0.00 0.00 2.41
1235 1414 0.325296 TCGCCTCATCCTTGTAGGGT 60.325 55.000 0.00 0.00 35.59 4.34
1285 1466 6.403049 CAACTTGGTGGTATGTACTATGTGA 58.597 40.000 0.00 0.00 0.00 3.58
1295 1476 8.033038 TGGTATGTACTATGTGAGAAACTGTTC 58.967 37.037 0.00 0.00 0.00 3.18
1305 1503 4.859798 GTGAGAAACTGTTCTACCATCTCG 59.140 45.833 11.10 0.00 44.42 4.04
1761 1988 6.942005 TGTTGAATTCTACAGGGCATATATGG 59.058 38.462 17.14 0.35 0.00 2.74
1768 1995 8.673456 TTCTACAGGGCATATATGGTATACAA 57.327 34.615 14.51 0.00 0.00 2.41
1809 2071 9.432982 TCATATTACCCTTTTAGGCATTTCATT 57.567 29.630 0.00 0.00 32.73 2.57
1815 2082 7.161404 ACCCTTTTAGGCATTTCATTTTCTTC 58.839 34.615 0.00 0.00 32.73 2.87
1816 2083 7.016563 ACCCTTTTAGGCATTTCATTTTCTTCT 59.983 33.333 0.00 0.00 32.73 2.85
1817 2084 7.879677 CCCTTTTAGGCATTTCATTTTCTTCTT 59.120 33.333 0.00 0.00 32.73 2.52
1820 2087 8.606040 TTTAGGCATTTCATTTTCTTCTTTGG 57.394 30.769 0.00 0.00 0.00 3.28
1821 2088 6.178607 AGGCATTTCATTTTCTTCTTTGGT 57.821 33.333 0.00 0.00 0.00 3.67
2021 2289 0.861837 CTGTTTCTCGCGCAGAACTT 59.138 50.000 17.92 0.00 41.13 2.66
2131 2408 0.033503 TGGACAGCTCATCCGGTAGA 60.034 55.000 0.00 0.00 39.30 2.59
2152 2432 7.864882 GGTAGACGTAGATTAGTATTTCCAACC 59.135 40.741 0.00 0.00 0.00 3.77
2156 2436 7.844009 ACGTAGATTAGTATTTCCAACCTGAA 58.156 34.615 0.00 0.00 0.00 3.02
2204 2484 7.765307 TGATTAGATTTTTCAGGAGTTGCATC 58.235 34.615 0.00 0.00 0.00 3.91
2205 2485 7.394077 TGATTAGATTTTTCAGGAGTTGCATCA 59.606 33.333 0.00 0.00 0.00 3.07
2210 2490 9.412460 AGATTTTTCAGGAGTTGCATCATATAA 57.588 29.630 0.00 0.00 0.00 0.98
2217 2497 4.042187 GGAGTTGCATCATATAAGGAGGGT 59.958 45.833 0.00 0.00 0.00 4.34
2224 2504 6.166982 GCATCATATAAGGAGGGTACTTGTC 58.833 44.000 0.00 0.00 0.00 3.18
2255 2540 0.630673 TGGCTAGCATCCCCATTTGT 59.369 50.000 18.24 0.00 0.00 2.83
2256 2541 1.006998 TGGCTAGCATCCCCATTTGTT 59.993 47.619 18.24 0.00 0.00 2.83
2323 2608 2.416547 GCAGCGTATTCTGATGTGTTGT 59.583 45.455 0.00 0.00 36.19 3.32
2352 2637 6.014647 AGTAGTACTTACAACTCCCACATGA 58.985 40.000 0.00 0.00 34.56 3.07
2353 2638 5.407407 AGTACTTACAACTCCCACATGAG 57.593 43.478 0.00 0.00 38.37 2.90
2355 2640 4.543590 ACTTACAACTCCCACATGAGAG 57.456 45.455 0.00 5.16 36.22 3.20
2360 2645 1.576577 ACTCCCACATGAGAGCATCA 58.423 50.000 0.00 0.00 43.70 3.07
2370 2656 2.353323 TGAGAGCATCAACAGCATGAC 58.647 47.619 0.00 0.00 37.19 3.06
2391 2677 5.046304 TGACTAGGAAATTCAGACCCTCAAG 60.046 44.000 0.00 0.00 0.00 3.02
2393 2679 2.376518 AGGAAATTCAGACCCTCAAGCA 59.623 45.455 0.00 0.00 0.00 3.91
2401 2687 4.722700 CCCTCAAGCACCCACGGG 62.723 72.222 0.00 0.00 42.03 5.28
2403 2689 4.641645 CTCAAGCACCCACGGGCA 62.642 66.667 0.69 0.00 39.32 5.36
2404 2690 4.947147 TCAAGCACCCACGGGCAC 62.947 66.667 0.69 0.00 39.32 5.01
2450 2740 0.107831 TGTTAGCTTTCCACAGCCGT 59.892 50.000 0.00 0.00 41.12 5.68
2479 2778 5.265989 TCATATCCAAAACCCTAAACCCAC 58.734 41.667 0.00 0.00 0.00 4.61
2508 2811 7.149973 ACGCTATGTATAAACACGATAACCAT 58.850 34.615 0.00 0.00 38.78 3.55
2509 2812 7.115805 ACGCTATGTATAAACACGATAACCATG 59.884 37.037 0.00 0.00 38.78 3.66
2510 2813 7.115805 CGCTATGTATAAACACGATAACCATGT 59.884 37.037 0.00 0.00 38.78 3.21
2565 2884 2.320781 AGGACCATAGTTCATCGGAGG 58.679 52.381 0.00 0.00 0.00 4.30
2566 2885 2.091278 AGGACCATAGTTCATCGGAGGA 60.091 50.000 0.00 0.00 0.00 3.71
2569 2888 2.695666 ACCATAGTTCATCGGAGGACAG 59.304 50.000 0.00 0.00 0.00 3.51
2572 2891 0.247736 AGTTCATCGGAGGACAGTGC 59.752 55.000 0.00 0.00 0.00 4.40
2573 2892 0.037326 GTTCATCGGAGGACAGTGCA 60.037 55.000 0.00 0.00 0.00 4.57
2574 2893 0.904649 TTCATCGGAGGACAGTGCAT 59.095 50.000 0.00 0.00 0.00 3.96
2591 2924 7.636326 ACAGTGCATTACTACAAACAACTTAC 58.364 34.615 0.00 0.00 37.60 2.34
2616 2960 2.312424 AAATAAAACGGGGAAGGGCA 57.688 45.000 0.00 0.00 0.00 5.36
2617 2961 2.312424 AATAAAACGGGGAAGGGCAA 57.688 45.000 0.00 0.00 0.00 4.52
2624 2968 1.532604 CGGGGAAGGGCAAAGGAAAC 61.533 60.000 0.00 0.00 0.00 2.78
2626 2970 1.532604 GGGAAGGGCAAAGGAAACCG 61.533 60.000 0.00 0.00 0.00 4.44
2641 2985 3.508840 CCGCCATTTCCTCACCGC 61.509 66.667 0.00 0.00 0.00 5.68
2642 2986 2.436646 CGCCATTTCCTCACCGCT 60.437 61.111 0.00 0.00 0.00 5.52
2674 3018 4.409218 GTCGTCGGCGTGGCTGTA 62.409 66.667 10.18 0.00 39.49 2.74
2688 4795 0.691078 GCTGTACCCCTCCTCCATGA 60.691 60.000 0.00 0.00 0.00 3.07
2749 4857 2.276116 GGAGCCGTCTGTCAGGTCA 61.276 63.158 0.00 0.00 0.00 4.02
2786 4894 3.878667 GCCCCAAGATCCTCCGGG 61.879 72.222 0.00 0.00 38.52 5.73
2812 4920 2.124983 TCCTGCTCCTTCGCATGC 60.125 61.111 7.91 7.91 39.52 4.06
2837 4945 1.606313 GCCTTTGCCTTGGCCACTA 60.606 57.895 3.88 0.00 43.11 2.74
2957 6502 2.203788 AGCGGAGGAGGACCAACA 60.204 61.111 0.00 0.00 38.94 3.33
2960 6505 2.663196 GGAGGAGGACCAACACGG 59.337 66.667 0.00 0.00 42.50 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.715088 GCGAATAAAAGTAGACCTCAAAACTTA 58.285 33.333 0.00 0.00 32.09 2.24
11 12 7.227910 TGCGAATAAAAGTAGACCTCAAAACTT 59.772 33.333 0.00 0.00 33.72 2.66
12 13 6.708949 TGCGAATAAAAGTAGACCTCAAAACT 59.291 34.615 0.00 0.00 0.00 2.66
13 14 6.894828 TGCGAATAAAAGTAGACCTCAAAAC 58.105 36.000 0.00 0.00 0.00 2.43
14 15 7.499321 TTGCGAATAAAAGTAGACCTCAAAA 57.501 32.000 0.00 0.00 0.00 2.44
15 16 7.499321 TTTGCGAATAAAAGTAGACCTCAAA 57.501 32.000 0.00 0.00 0.00 2.69
16 17 7.499321 TTTTGCGAATAAAAGTAGACCTCAA 57.501 32.000 0.00 0.00 0.00 3.02
17 18 7.499321 TTTTTGCGAATAAAAGTAGACCTCA 57.501 32.000 0.00 0.00 31.80 3.86
210 216 9.757859 GCATTGGAAAAATGTTAAACATGTATG 57.242 29.630 0.00 0.00 37.97 2.39
231 237 3.976468 AAAATGTTTCATCGCGCATTG 57.024 38.095 8.75 3.89 32.64 2.82
238 244 8.800972 CATACAGAATGGAAAAATGTTTCATCG 58.199 33.333 10.53 5.12 44.29 3.84
347 363 1.407712 GCCTAGCGGGGACATTTTACA 60.408 52.381 2.20 0.00 35.12 2.41
348 364 1.306148 GCCTAGCGGGGACATTTTAC 58.694 55.000 2.20 0.00 35.12 2.01
349 365 0.181824 GGCCTAGCGGGGACATTTTA 59.818 55.000 0.00 0.00 33.76 1.52
350 366 1.076995 GGCCTAGCGGGGACATTTT 60.077 57.895 0.00 0.00 33.76 1.82
351 367 2.595655 GGCCTAGCGGGGACATTT 59.404 61.111 0.00 0.00 33.76 2.32
352 368 3.861797 CGGCCTAGCGGGGACATT 61.862 66.667 0.00 0.00 32.93 2.71
386 425 4.088421 CGTAGCCTCGCGTCAAAT 57.912 55.556 5.77 0.00 0.00 2.32
403 442 0.940047 GATACGGGCGCAAGAGTAGC 60.940 60.000 10.83 6.52 43.02 3.58
404 443 0.669077 AGATACGGGCGCAAGAGTAG 59.331 55.000 10.83 0.00 43.02 2.57
405 444 0.666913 GAGATACGGGCGCAAGAGTA 59.333 55.000 10.83 7.86 43.02 2.59
406 445 1.437986 GAGATACGGGCGCAAGAGT 59.562 57.895 10.83 5.58 43.02 3.24
407 446 1.300233 GGAGATACGGGCGCAAGAG 60.300 63.158 10.83 0.00 43.02 2.85
408 447 2.792947 GGGAGATACGGGCGCAAGA 61.793 63.158 10.83 0.00 43.02 3.02
409 448 2.280186 GGGAGATACGGGCGCAAG 60.280 66.667 10.83 4.46 43.44 4.01
410 449 4.215742 CGGGAGATACGGGCGCAA 62.216 66.667 10.83 0.00 0.00 4.85
495 534 4.037222 TGATGGATCTAGGGTTTACTGCA 58.963 43.478 0.00 0.00 0.00 4.41
572 611 6.716934 TGTATATTCTCTCGGCTTCTTCTT 57.283 37.500 0.00 0.00 0.00 2.52
647 686 0.247460 CAGGACAATCTGTCTCGGCA 59.753 55.000 6.74 0.00 46.19 5.69
680 719 1.487976 AGATGGCAACGGTGATCTGAT 59.512 47.619 3.55 0.00 42.51 2.90
689 728 0.467384 ATGGAGAGAGATGGCAACGG 59.533 55.000 0.00 0.00 42.51 4.44
716 755 3.245984 TGGAGGGAGAAGTATCCTTGACA 60.246 47.826 0.00 0.00 39.50 3.58
717 756 3.375699 TGGAGGGAGAAGTATCCTTGAC 58.624 50.000 0.00 0.00 39.50 3.18
824 869 1.078426 GATCCCAACCCCACACTCG 60.078 63.158 0.00 0.00 0.00 4.18
865 910 7.175990 AGGTAATCAAAAATAAAGTCCGAGCAA 59.824 33.333 0.00 0.00 0.00 3.91
967 1021 4.280019 ACCGGTGGTGGGGCTTTC 62.280 66.667 6.12 0.00 32.98 2.62
1021 1088 2.282040 GCAGCAACAGTGAGGGCT 60.282 61.111 0.00 0.00 36.99 5.19
1148 1233 1.003233 GGGTCGATTCTTCCACACCTT 59.997 52.381 0.00 0.00 0.00 3.50
1149 1234 0.613777 GGGTCGATTCTTCCACACCT 59.386 55.000 0.00 0.00 0.00 4.00
1228 1407 4.223032 GGTTCAGAGAATTCTCACCCTACA 59.777 45.833 31.79 9.97 45.21 2.74
1231 1410 3.262915 CAGGTTCAGAGAATTCTCACCCT 59.737 47.826 31.79 25.47 45.21 4.34
1235 1414 2.354103 CGGCAGGTTCAGAGAATTCTCA 60.354 50.000 31.79 13.89 45.21 3.27
1263 1442 5.955959 TCTCACATAGTACATACCACCAAGT 59.044 40.000 0.00 0.00 0.00 3.16
1285 1466 4.767928 AGACGAGATGGTAGAACAGTTTCT 59.232 41.667 0.00 0.00 44.70 2.52
1295 1476 6.565234 ACAAGAAATACAGACGAGATGGTAG 58.435 40.000 0.00 0.00 0.00 3.18
1305 1503 8.704234 CACAGAGTTTAGACAAGAAATACAGAC 58.296 37.037 0.00 0.00 0.00 3.51
1388 1590 2.178273 GCTTTAGCCCCGCGTTTG 59.822 61.111 4.92 0.00 34.31 2.93
1537 1746 6.130569 AGATCGAATACTAGAAGTTCAGGGT 58.869 40.000 5.50 3.45 0.00 4.34
1538 1747 6.642707 AGATCGAATACTAGAAGTTCAGGG 57.357 41.667 5.50 0.00 0.00 4.45
1539 1748 8.812329 CAAAAGATCGAATACTAGAAGTTCAGG 58.188 37.037 5.50 0.00 0.00 3.86
1540 1749 9.360093 ACAAAAGATCGAATACTAGAAGTTCAG 57.640 33.333 5.50 3.46 0.00 3.02
1552 1773 4.574892 TGGTCAGCACAAAAGATCGAATA 58.425 39.130 0.00 0.00 0.00 1.75
1652 1879 3.880490 TCTTCGAGAGTAGGATCTGAAGC 59.120 47.826 0.00 0.00 36.04 3.86
1704 1931 2.095567 CAGAAGATCAAAGGTGGCAACG 60.096 50.000 0.00 0.00 42.51 4.10
1778 2006 7.633018 TGCCTAAAAGGGTAATATGAGATCT 57.367 36.000 0.00 0.00 35.37 2.75
1809 2071 6.746745 AACTACGTTTGACCAAAGAAGAAA 57.253 33.333 0.00 0.00 0.00 2.52
1815 2082 6.731164 ACCAATTAACTACGTTTGACCAAAG 58.269 36.000 0.00 0.00 0.00 2.77
1816 2083 6.318144 TGACCAATTAACTACGTTTGACCAAA 59.682 34.615 0.00 0.00 0.00 3.28
1817 2084 5.821470 TGACCAATTAACTACGTTTGACCAA 59.179 36.000 0.00 0.00 0.00 3.67
1819 2086 5.927954 TGACCAATTAACTACGTTTGACC 57.072 39.130 0.00 0.00 0.00 4.02
1820 2087 9.485591 CATATTGACCAATTAACTACGTTTGAC 57.514 33.333 0.00 0.00 32.50 3.18
1821 2088 9.438228 TCATATTGACCAATTAACTACGTTTGA 57.562 29.630 0.00 0.00 32.50 2.69
2131 2408 7.414222 TCAGGTTGGAAATACTAATCTACGT 57.586 36.000 0.00 0.00 29.41 3.57
2183 2463 8.985315 ATATGATGCAACTCCTGAAAAATCTA 57.015 30.769 0.00 0.00 0.00 1.98
2204 2484 7.125792 ACAAGACAAGTACCCTCCTTATATG 57.874 40.000 0.00 0.00 0.00 1.78
2205 2485 7.402071 TCAACAAGACAAGTACCCTCCTTATAT 59.598 37.037 0.00 0.00 0.00 0.86
2210 2490 3.314693 TCAACAAGACAAGTACCCTCCT 58.685 45.455 0.00 0.00 0.00 3.69
2217 2497 2.869801 CCACGCTTCAACAAGACAAGTA 59.130 45.455 0.00 0.00 0.00 2.24
2224 2504 0.166814 GCTAGCCACGCTTCAACAAG 59.833 55.000 2.29 0.00 40.44 3.16
2255 2540 7.701539 ATGAATATTGTTGTGAGCTACCAAA 57.298 32.000 0.00 0.00 0.00 3.28
2256 2541 7.826744 TGTATGAATATTGTTGTGAGCTACCAA 59.173 33.333 0.00 0.00 0.00 3.67
2323 2608 8.108999 TGTGGGAGTTGTAAGTACTACTACATA 58.891 37.037 14.56 8.91 41.34 2.29
2339 2624 2.286872 GATGCTCTCATGTGGGAGTTG 58.713 52.381 11.29 0.00 36.30 3.16
2342 2627 2.286872 GTTGATGCTCTCATGTGGGAG 58.713 52.381 5.52 5.52 32.72 4.30
2352 2637 2.783609 AGTCATGCTGTTGATGCTCT 57.216 45.000 0.00 0.00 0.00 4.09
2353 2638 2.871022 CCTAGTCATGCTGTTGATGCTC 59.129 50.000 0.00 0.00 0.00 4.26
2355 2640 2.910199 TCCTAGTCATGCTGTTGATGC 58.090 47.619 0.00 0.00 0.00 3.91
2360 2645 5.645497 GTCTGAATTTCCTAGTCATGCTGTT 59.355 40.000 0.00 0.00 29.25 3.16
2370 2656 4.195416 GCTTGAGGGTCTGAATTTCCTAG 58.805 47.826 0.00 0.00 0.00 3.02
2403 2689 4.681978 GACCTTGCCTGCGGACGT 62.682 66.667 0.00 0.00 0.00 4.34
2404 2690 4.680237 TGACCTTGCCTGCGGACG 62.680 66.667 0.00 0.00 0.00 4.79
2405 2691 3.050275 GTGACCTTGCCTGCGGAC 61.050 66.667 0.00 0.00 0.00 4.79
2406 2692 4.680237 CGTGACCTTGCCTGCGGA 62.680 66.667 0.00 0.00 0.00 5.54
2450 2740 3.197983 AGGGTTTTGGATATGAGGGACA 58.802 45.455 0.00 0.00 0.00 4.02
2479 2778 3.241091 TCGTGTTTATACATAGCGTTGCG 59.759 43.478 0.00 0.00 36.50 4.85
2508 2811 8.756486 ATGAAATGATGATCCAATGAACTACA 57.244 30.769 0.00 0.00 0.00 2.74
2509 2812 8.013947 CGATGAAATGATGATCCAATGAACTAC 58.986 37.037 0.00 0.00 0.00 2.73
2510 2813 7.308169 GCGATGAAATGATGATCCAATGAACTA 60.308 37.037 0.00 0.00 0.00 2.24
2565 2884 6.300354 AGTTGTTTGTAGTAATGCACTGTC 57.700 37.500 0.00 0.00 38.24 3.51
2566 2885 6.693315 AAGTTGTTTGTAGTAATGCACTGT 57.307 33.333 0.00 0.00 38.24 3.55
2569 2888 7.911205 TGTTGTAAGTTGTTTGTAGTAATGCAC 59.089 33.333 0.00 0.00 0.00 4.57
2591 2924 5.656480 CCCTTCCCCGTTTTATTTATGTTG 58.344 41.667 0.00 0.00 0.00 3.33
2624 2968 3.508840 GCGGTGAGGAAATGGCGG 61.509 66.667 0.00 0.00 0.00 6.13
2626 2970 2.115291 GGAGCGGTGAGGAAATGGC 61.115 63.158 0.00 0.00 0.00 4.40
2674 3018 2.003548 GCCTTCATGGAGGAGGGGT 61.004 63.158 25.42 0.00 39.25 4.95
2714 4822 2.279120 CATCTCCAGCTCCGACGC 60.279 66.667 0.00 0.00 0.00 5.19
2749 4857 0.990374 AAGCATGCTCCAAGGAGTCT 59.010 50.000 22.93 0.00 43.70 3.24
2834 4942 3.857157 TGAAGCAAACAAGGAGGTAGT 57.143 42.857 0.00 0.00 0.00 2.73
2837 4945 1.615392 GCATGAAGCAAACAAGGAGGT 59.385 47.619 0.00 0.00 44.79 3.85


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

AutoCloner maintained by Alex Coulton.