Multiple sequence alignment - TraesCS1A01G336800

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 TraesCS1A01G336800 chr1A 100.000 2505 0 0 1 2505 525042143 525039639 0.000000e+00 4626
1 TraesCS1A01G336800 chr1A 95.756 2262 84 4 1 2260 488623168 488620917 0.000000e+00 3635
2 TraesCS1A01G336800 chr1A 96.294 1403 51 1 1 1402 590651522 590652924 0.000000e+00 2302
3 TraesCS1A01G336800 chr1A 94.798 865 36 1 1396 2260 590671440 590672295 0.000000e+00 1339
4 TraesCS1A01G336800 chr1A 97.656 256 5 1 2250 2505 292578491 292578237 2.960000e-119 438
5 TraesCS1A01G336800 chr1A 95.911 269 6 4 2240 2505 466601431 466601165 4.950000e-117 431
6 TraesCS1A01G336800 chr1A 94.565 276 13 2 2232 2505 471341409 471341684 2.300000e-115 425
7 TraesCS1A01G336800 chr7A 95.489 2261 89 6 1 2260 92422393 92424641 0.000000e+00 3598
8 TraesCS1A01G336800 chr7A 80.139 861 159 10 1 853 726502112 726501256 1.260000e-177 632
9 TraesCS1A01G336800 chr3A 93.725 2263 121 8 1 2260 732976655 732974411 0.000000e+00 3373
10 TraesCS1A01G336800 chr3A 97.656 256 6 0 2250 2505 99605556 99605301 8.220000e-120 440
11 TraesCS1A01G336800 chr5A 95.821 1723 61 3 347 2068 41388046 41389758 0.000000e+00 2772
12 TraesCS1A01G336800 chr5A 94.757 801 31 2 1268 2068 41391129 41391918 0.000000e+00 1236
13 TraesCS1A01G336800 chr5A 99.194 248 2 0 2258 2505 653893836 653894083 4.920000e-122 448
14 TraesCS1A01G336800 chr5A 97.647 255 6 0 2251 2505 473388724 473388470 2.960000e-119 438
15 TraesCS1A01G336800 chr5A 92.105 190 14 1 2072 2260 41389965 41390154 1.480000e-67 267
16 TraesCS1A01G336800 chr2A 89.554 1704 146 15 1 1677 88740737 88739039 0.000000e+00 2132
17 TraesCS1A01G336800 chr2A 82.759 580 77 15 1664 2230 88732329 88731760 1.730000e-136 496
18 TraesCS1A01G336800 chr2A 99.190 247 2 0 2259 2505 776459751 776459505 1.770000e-121 446
19 TraesCS1A01G336800 chr6B 92.116 1484 86 13 586 2062 351230068 351228609 0.000000e+00 2063
20 TraesCS1A01G336800 chr6B 96.095 589 22 1 1 588 351230961 351230373 0.000000e+00 959
21 TraesCS1A01G336800 chr6B 85.549 346 43 3 1922 2260 351228806 351228461 3.060000e-94 355
22 TraesCS1A01G336800 chr4A 94.331 1323 60 6 1 1323 723795472 723794165 0.000000e+00 2013
23 TraesCS1A01G336800 chr4A 97.656 256 6 0 2250 2505 606130815 606130560 8.220000e-120 440
24 TraesCS1A01G336800 chr2B 95.769 709 29 1 1 708 748163517 748164225 0.000000e+00 1142
25 TraesCS1A01G336800 chr2B 96.935 261 4 3 2248 2505 563331245 563331504 3.830000e-118 435
26 TraesCS1A01G336800 chr4B 92.281 583 36 5 1455 2031 562692280 562691701 0.000000e+00 819
27 TraesCS1A01G336800 chr4B 85.061 328 39 4 1943 2260 562691897 562691570 2.400000e-85 326
28 TraesCS1A01G336800 chr5D 84.070 747 90 14 1531 2260 228504036 228504770 0.000000e+00 693


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 TraesCS1A01G336800 chr1A 525039639 525042143 2504 True 4626.000000 4626 100.000000 1 2505 1 chr1A.!!$R4 2504
1 TraesCS1A01G336800 chr1A 488620917 488623168 2251 True 3635.000000 3635 95.756000 1 2260 1 chr1A.!!$R3 2259
2 TraesCS1A01G336800 chr1A 590651522 590652924 1402 False 2302.000000 2302 96.294000 1 1402 1 chr1A.!!$F2 1401
3 TraesCS1A01G336800 chr1A 590671440 590672295 855 False 1339.000000 1339 94.798000 1396 2260 1 chr1A.!!$F3 864
4 TraesCS1A01G336800 chr7A 92422393 92424641 2248 False 3598.000000 3598 95.489000 1 2260 1 chr7A.!!$F1 2259
5 TraesCS1A01G336800 chr7A 726501256 726502112 856 True 632.000000 632 80.139000 1 853 1 chr7A.!!$R1 852
6 TraesCS1A01G336800 chr3A 732974411 732976655 2244 True 3373.000000 3373 93.725000 1 2260 1 chr3A.!!$R2 2259
7 TraesCS1A01G336800 chr5A 41388046 41391918 3872 False 1425.000000 2772 94.227667 347 2260 3 chr5A.!!$F2 1913
8 TraesCS1A01G336800 chr2A 88739039 88740737 1698 True 2132.000000 2132 89.554000 1 1677 1 chr2A.!!$R2 1676
9 TraesCS1A01G336800 chr2A 88731760 88732329 569 True 496.000000 496 82.759000 1664 2230 1 chr2A.!!$R1 566
10 TraesCS1A01G336800 chr6B 351228461 351230961 2500 True 1125.666667 2063 91.253333 1 2260 3 chr6B.!!$R1 2259
11 TraesCS1A01G336800 chr4A 723794165 723795472 1307 True 2013.000000 2013 94.331000 1 1323 1 chr4A.!!$R2 1322
12 TraesCS1A01G336800 chr2B 748163517 748164225 708 False 1142.000000 1142 95.769000 1 708 1 chr2B.!!$F2 707
13 TraesCS1A01G336800 chr4B 562691570 562692280 710 True 572.500000 819 88.671000 1455 2260 2 chr4B.!!$R1 805
14 TraesCS1A01G336800 chr5D 228504036 228504770 734 False 693.000000 693 84.070000 1531 2260 1 chr5D.!!$F1 729

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
445 450 1.340248 GACAGTGACACCGAGGAGAAA 59.66 52.381 0.84 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1877 2237 1.771255 GGAGCTGGGTGTCCTATCATT 59.229 52.381 0.0 0.0 0.0 2.57 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
59 60 6.047511 AGATGCTTGACAAGTATGAACTCT 57.952 37.500 21.60 11.14 33.79 3.24
82 83 1.820519 GACAATGCATGGCTCCAAAGA 59.179 47.619 0.00 0.00 32.61 2.52
89 90 5.266733 TGCATGGCTCCAAAGATTATTTC 57.733 39.130 0.00 0.00 0.00 2.17
133 134 5.760253 CCTAGTGTATGGCAGGAATACTTTG 59.240 44.000 0.00 0.00 32.70 2.77
148 149 2.923121 ACTTTGTCTGCACACATGAGT 58.077 42.857 0.00 1.05 29.76 3.41
247 249 3.499048 TGAGCATTTCGAACGTCTAGTC 58.501 45.455 0.00 0.00 0.00 2.59
248 250 3.057806 TGAGCATTTCGAACGTCTAGTCA 60.058 43.478 0.00 0.00 0.00 3.41
335 340 6.253946 AGGCAGAAAGCTATATGTTAAGGT 57.746 37.500 0.00 0.00 44.79 3.50
406 411 3.922910 AGTGCTTCGGACCTTAAACTAC 58.077 45.455 0.00 0.00 0.00 2.73
445 450 1.340248 GACAGTGACACCGAGGAGAAA 59.660 52.381 0.84 0.00 0.00 2.52
663 976 9.638239 GATGCAAAAGTTTTGGATATAACAAGA 57.362 29.630 28.55 0.00 30.51 3.02
761 1074 4.426112 TGCTCGAGCCGCAGAGTG 62.426 66.667 33.23 0.00 41.18 3.51
794 1107 9.219603 GTCATACTTAATGGCTGCTAATTATGA 57.780 33.333 18.76 15.59 37.22 2.15
806 1119 9.061435 GGCTGCTAATTATGAAGAGAAATTAGT 57.939 33.333 12.90 0.00 41.79 2.24
916 1235 9.577110 TTTATGCTCTCATCAAGCTTAAATTTG 57.423 29.630 0.00 0.00 41.01 2.32
963 1282 6.090898 ACTCAAACAATATCACGACTACAAGC 59.909 38.462 0.00 0.00 0.00 4.01
989 1308 3.356529 ACAAAATGAGAGGCCTACCAG 57.643 47.619 4.42 0.00 39.06 4.00
1139 1460 2.851263 TTACAGTTGCAGACCCGAAT 57.149 45.000 0.00 0.00 0.00 3.34
1228 1549 2.698797 AGAAGACTGTTCGAGGGTCAAA 59.301 45.455 13.92 0.00 32.98 2.69
1253 1574 3.485463 CCCGTTGATATGGGTGTGTAT 57.515 47.619 0.00 0.00 44.49 2.29
1349 1670 7.368198 AGTTCAAAACAAAATAAGGGGCTTA 57.632 32.000 0.00 0.00 0.00 3.09
1407 1728 4.803098 TTCAAGGAGCAAGTAGACCTAC 57.197 45.455 0.00 0.00 36.35 3.18
1442 1795 7.785033 AGAGAAAGCAAAATCAAAGAGGAAAA 58.215 30.769 0.00 0.00 0.00 2.29
1443 1796 7.924947 AGAGAAAGCAAAATCAAAGAGGAAAAG 59.075 33.333 0.00 0.00 0.00 2.27
1444 1797 6.988580 AGAAAGCAAAATCAAAGAGGAAAAGG 59.011 34.615 0.00 0.00 0.00 3.11
1445 1798 6.484364 AAGCAAAATCAAAGAGGAAAAGGA 57.516 33.333 0.00 0.00 0.00 3.36
1446 1799 6.484364 AGCAAAATCAAAGAGGAAAAGGAA 57.516 33.333 0.00 0.00 0.00 3.36
1447 1800 6.888105 AGCAAAATCAAAGAGGAAAAGGAAA 58.112 32.000 0.00 0.00 0.00 3.13
1448 1801 6.763135 AGCAAAATCAAAGAGGAAAAGGAAAC 59.237 34.615 0.00 0.00 0.00 2.78
1484 1837 3.895232 ATCCTGTAGCACTACAACCTG 57.105 47.619 11.42 0.78 44.47 4.00
1677 2030 3.084039 CAAGACCAAAGATTGCCAGCTA 58.916 45.455 0.00 0.00 0.00 3.32
1690 2043 3.327626 TGCCAGCTAAATTGCAACATTG 58.672 40.909 0.00 0.00 34.99 2.82
1863 2223 2.158842 GCTCTGGATGCCTCACTATTGT 60.159 50.000 0.00 0.00 0.00 2.71
1877 2237 4.763279 TCACTATTGTCGTCTCTTGGTACA 59.237 41.667 0.00 0.00 0.00 2.90
2009 2369 1.250328 CTCCAAATGCCTCACTGCAA 58.750 50.000 0.00 0.00 45.84 4.08
2041 2401 0.984230 ACGATGACAGGACACCCAAT 59.016 50.000 0.00 0.00 33.88 3.16
2043 2403 2.224769 ACGATGACAGGACACCCAATTT 60.225 45.455 0.00 0.00 33.88 1.82
2053 2464 3.769300 GGACACCCAATTTAGAATGCCTT 59.231 43.478 0.00 0.00 0.00 4.35
2068 2682 0.326927 GCCTTACTACAGCACCCCAA 59.673 55.000 0.00 0.00 0.00 4.12
2191 2805 3.684788 ACTTAATCTGCCATCGTTGTCAC 59.315 43.478 0.00 0.00 0.00 3.67
2260 2884 3.455910 CTGGATTTATGGGGAGTCTGTGA 59.544 47.826 0.00 0.00 0.00 3.58
2262 2886 4.080356 TGGATTTATGGGGAGTCTGTGAAG 60.080 45.833 0.00 0.00 0.00 3.02
2263 2887 4.455606 GATTTATGGGGAGTCTGTGAAGG 58.544 47.826 0.00 0.00 0.00 3.46
2264 2888 2.940514 TATGGGGAGTCTGTGAAGGA 57.059 50.000 0.00 0.00 0.00 3.36
2265 2889 2.044793 ATGGGGAGTCTGTGAAGGAA 57.955 50.000 0.00 0.00 0.00 3.36
2266 2890 1.814429 TGGGGAGTCTGTGAAGGAAA 58.186 50.000 0.00 0.00 0.00 3.13
2267 2891 2.348472 TGGGGAGTCTGTGAAGGAAAT 58.652 47.619 0.00 0.00 0.00 2.17
2268 2892 3.526899 TGGGGAGTCTGTGAAGGAAATA 58.473 45.455 0.00 0.00 0.00 1.40
2269 2893 4.111577 TGGGGAGTCTGTGAAGGAAATAT 58.888 43.478 0.00 0.00 0.00 1.28
2271 2895 3.879892 GGGAGTCTGTGAAGGAAATATGC 59.120 47.826 0.00 0.00 0.00 3.14
2272 2896 3.879892 GGAGTCTGTGAAGGAAATATGCC 59.120 47.826 0.00 0.00 0.00 4.40
2273 2897 3.879892 GAGTCTGTGAAGGAAATATGCCC 59.120 47.826 0.00 0.00 0.00 5.36
2274 2898 3.525199 AGTCTGTGAAGGAAATATGCCCT 59.475 43.478 0.00 0.00 0.00 5.19
2275 2899 4.721776 AGTCTGTGAAGGAAATATGCCCTA 59.278 41.667 0.00 0.00 31.36 3.53
2276 2900 5.059833 GTCTGTGAAGGAAATATGCCCTAG 58.940 45.833 0.00 0.00 31.36 3.02
2277 2901 4.968719 TCTGTGAAGGAAATATGCCCTAGA 59.031 41.667 0.00 0.00 31.36 2.43
2278 2902 5.070981 TCTGTGAAGGAAATATGCCCTAGAG 59.929 44.000 0.00 0.00 31.36 2.43
2279 2903 4.103153 TGTGAAGGAAATATGCCCTAGAGG 59.897 45.833 0.00 0.00 39.47 3.69
2357 3012 9.679661 TCATGCTAGAATTGTATTAACCAGAAA 57.320 29.630 0.00 0.00 0.00 2.52
2360 3015 9.461312 TGCTAGAATTGTATTAACCAGAAACAT 57.539 29.630 0.00 0.00 0.00 2.71
2375 3030 8.579850 ACCAGAAACATAATACATGTGTGAAT 57.420 30.769 9.11 0.00 31.80 2.57
2376 3031 9.679661 ACCAGAAACATAATACATGTGTGAATA 57.320 29.630 9.11 0.00 31.80 1.75
2393 3048 9.586435 TGTGTGAATACATAGACAAATAGAGTG 57.414 33.333 0.00 0.00 39.39 3.51
2394 3049 9.587772 GTGTGAATACATAGACAAATAGAGTGT 57.412 33.333 0.00 0.00 39.39 3.55
2395 3050 9.803315 TGTGAATACATAGACAAATAGAGTGTC 57.197 33.333 0.00 0.00 44.75 3.67
2396 3051 9.803315 GTGAATACATAGACAAATAGAGTGTCA 57.197 33.333 7.26 0.00 46.44 3.58
2401 3056 8.582657 ACATAGACAAATAGAGTGTCACTAGT 57.417 34.615 5.21 0.00 46.44 2.57
2402 3057 9.682465 ACATAGACAAATAGAGTGTCACTAGTA 57.318 33.333 5.21 1.21 46.44 1.82
2406 3061 6.574350 ACAAATAGAGTGTCACTAGTATGCC 58.426 40.000 5.21 0.00 0.00 4.40
2407 3062 6.381420 ACAAATAGAGTGTCACTAGTATGCCT 59.619 38.462 5.21 0.00 0.00 4.75
2408 3063 6.642707 AATAGAGTGTCACTAGTATGCCTC 57.357 41.667 5.21 0.00 0.00 4.70
2409 3064 4.243793 AGAGTGTCACTAGTATGCCTCT 57.756 45.455 5.21 1.89 0.00 3.69
2412 3067 5.104277 AGAGTGTCACTAGTATGCCTCTACT 60.104 44.000 5.21 0.00 36.04 2.57
2413 3068 5.511363 AGTGTCACTAGTATGCCTCTACTT 58.489 41.667 2.87 0.00 33.96 2.24
2414 3069 5.358442 AGTGTCACTAGTATGCCTCTACTTG 59.642 44.000 2.87 0.00 33.96 3.16
2416 3071 5.357314 TGTCACTAGTATGCCTCTACTTGAC 59.643 44.000 0.00 11.98 38.64 3.18
2421 3076 4.798882 AGTATGCCTCTACTTGACTAGCT 58.201 43.478 0.00 0.00 0.00 3.32
2422 3077 4.825085 AGTATGCCTCTACTTGACTAGCTC 59.175 45.833 0.00 0.00 0.00 4.09
2423 3078 2.017782 TGCCTCTACTTGACTAGCTCG 58.982 52.381 0.00 0.00 0.00 5.03
2425 3080 2.424246 GCCTCTACTTGACTAGCTCGTT 59.576 50.000 0.00 0.00 0.00 3.85
2426 3081 3.626670 GCCTCTACTTGACTAGCTCGTTA 59.373 47.826 0.00 0.00 0.00 3.18
2427 3082 4.096081 GCCTCTACTTGACTAGCTCGTTAA 59.904 45.833 0.00 0.00 0.00 2.01
2431 3086 7.387119 TCTACTTGACTAGCTCGTTAATCAA 57.613 36.000 0.00 0.00 0.00 2.57
2433 3088 6.952935 ACTTGACTAGCTCGTTAATCAAAG 57.047 37.500 0.00 0.00 0.00 2.77
2436 3091 7.276658 ACTTGACTAGCTCGTTAATCAAAGATG 59.723 37.037 0.00 0.00 0.00 2.90
2437 3092 6.042777 TGACTAGCTCGTTAATCAAAGATGG 58.957 40.000 0.00 0.00 0.00 3.51
2438 3093 5.978814 ACTAGCTCGTTAATCAAAGATGGT 58.021 37.500 0.00 0.00 0.00 3.55
2439 3094 6.407202 ACTAGCTCGTTAATCAAAGATGGTT 58.593 36.000 0.00 0.00 33.49 3.67
2441 3096 8.204836 ACTAGCTCGTTAATCAAAGATGGTTAT 58.795 33.333 0.00 0.00 32.32 1.89
2442 3097 7.251704 AGCTCGTTAATCAAAGATGGTTATG 57.748 36.000 0.00 0.00 32.32 1.90
2443 3098 6.823689 AGCTCGTTAATCAAAGATGGTTATGT 59.176 34.615 0.00 0.00 32.32 2.29
2444 3099 7.336931 AGCTCGTTAATCAAAGATGGTTATGTT 59.663 33.333 0.00 0.00 32.32 2.71
2445 3100 7.968405 GCTCGTTAATCAAAGATGGTTATGTTT 59.032 33.333 0.00 0.00 32.32 2.83
2446 3101 9.490663 CTCGTTAATCAAAGATGGTTATGTTTC 57.509 33.333 0.00 0.00 32.32 2.78
2448 3103 8.458843 CGTTAATCAAAGATGGTTATGTTTCCT 58.541 33.333 0.00 0.00 32.32 3.36
2452 3107 7.696992 TCAAAGATGGTTATGTTTCCTAACC 57.303 36.000 5.49 5.49 45.53 2.85
2458 3113 5.830000 GGTTATGTTTCCTAACCATGGAC 57.170 43.478 21.47 4.44 44.95 4.02
2459 3114 5.258051 GGTTATGTTTCCTAACCATGGACA 58.742 41.667 21.47 10.90 44.95 4.02
2460 3115 5.712917 GGTTATGTTTCCTAACCATGGACAA 59.287 40.000 21.47 1.70 44.95 3.18
2463 3118 5.055265 TGTTTCCTAACCATGGACAAAGA 57.945 39.130 21.47 5.44 33.15 2.52
2464 3119 5.070001 TGTTTCCTAACCATGGACAAAGAG 58.930 41.667 21.47 5.61 33.15 2.85
2465 3120 4.993705 TTCCTAACCATGGACAAAGAGT 57.006 40.909 21.47 0.00 32.65 3.24
2467 3122 4.651778 TCCTAACCATGGACAAAGAGTTG 58.348 43.478 21.47 0.00 40.84 3.16
2483 3138 9.965824 ACAAAGAGTTGTTATTTGATTAACAGG 57.034 29.630 4.08 0.00 46.01 4.00
2489 3144 9.295825 AGTTGTTATTTGATTAACAGGATCACA 57.704 29.630 0.00 0.00 41.65 3.58
2499 3154 9.112725 TGATTAACAGGATCACATCATTAGTTG 57.887 33.333 0.00 0.00 0.00 3.16
2500 3155 9.330063 GATTAACAGGATCACATCATTAGTTGA 57.670 33.333 0.00 0.00 39.12 3.18
2501 3156 9.685276 ATTAACAGGATCACATCATTAGTTGAA 57.315 29.630 0.00 0.00 38.03 2.69
2502 3157 9.685276 TTAACAGGATCACATCATTAGTTGAAT 57.315 29.630 0.00 0.00 38.03 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 5.064452 CCAGAGTTCATACTTGTCAAGCATC 59.936 44.000 12.66 1.29 33.84 3.91
59 60 1.380246 GGAGCCATGCATTGTCCCA 60.380 57.895 0.00 0.00 0.00 4.37
82 83 6.126968 CCCAATGCTCCCTTTTCTGAAATAAT 60.127 38.462 3.31 0.00 0.00 1.28
89 90 0.533951 GCCCAATGCTCCCTTTTCTG 59.466 55.000 0.00 0.00 36.87 3.02
133 134 3.512680 GGTACTACTCATGTGTGCAGAC 58.487 50.000 7.12 7.12 0.00 3.51
148 149 3.649023 TGCTTTCACTCCTTTGGGTACTA 59.351 43.478 0.00 0.00 0.00 1.82
247 249 8.327941 TCACCTCTTCAAATCTTTTATCTGTG 57.672 34.615 0.00 0.00 0.00 3.66
248 250 8.378565 TCTCACCTCTTCAAATCTTTTATCTGT 58.621 33.333 0.00 0.00 0.00 3.41
335 340 7.289084 TGGTGGAGTATATGTAGTTGATGCTTA 59.711 37.037 0.00 0.00 0.00 3.09
406 411 5.582269 ACTGTCATCACAAAGGAATGTATCG 59.418 40.000 0.00 0.00 29.82 2.92
689 1002 3.813529 AGCGTTTTGTCAGTATTGCTC 57.186 42.857 0.00 0.00 0.00 4.26
761 1074 5.007136 GCAGCCATTAAGTATGACTCTTCAC 59.993 44.000 0.00 0.00 36.26 3.18
777 1090 7.886629 TTTCTCTTCATAATTAGCAGCCATT 57.113 32.000 0.00 0.00 0.00 3.16
794 1107 7.896496 TCTCCACCTCTTCTACTAATTTCTCTT 59.104 37.037 0.00 0.00 0.00 2.85
806 1119 7.792364 TTTAGACATTTCTCCACCTCTTCTA 57.208 36.000 0.00 0.00 32.75 2.10
935 1254 8.047413 TGTAGTCGTGATATTGTTTGAGTCTA 57.953 34.615 0.00 0.00 0.00 2.59
963 1282 3.683802 AGGCCTCTCATTTTGTTCTGAG 58.316 45.455 0.00 0.00 40.20 3.35
989 1308 2.247358 TGACCTTCATTCCTTTTGGCC 58.753 47.619 0.00 0.00 40.12 5.36
1349 1670 6.303839 TCAACTTGATACCTTTTGGCTTAGT 58.696 36.000 0.00 0.00 45.59 2.24
1442 1795 9.508721 AGGATTATCTACTTTCCTAAGTTTCCT 57.491 33.333 0.00 0.00 41.85 3.36
1443 1796 9.549078 CAGGATTATCTACTTTCCTAAGTTTCC 57.451 37.037 0.00 0.00 41.85 3.13
1447 1800 8.862085 GCTACAGGATTATCTACTTTCCTAAGT 58.138 37.037 0.00 0.00 46.18 2.24
1448 1801 8.861086 TGCTACAGGATTATCTACTTTCCTAAG 58.139 37.037 0.00 0.00 36.45 2.18
1449 1802 8.639761 GTGCTACAGGATTATCTACTTTCCTAA 58.360 37.037 0.00 0.00 36.45 2.69
1450 1803 8.005388 AGTGCTACAGGATTATCTACTTTCCTA 58.995 37.037 0.00 0.00 36.45 2.94
1553 1906 5.989477 TGACCCTATAAAACATGGTGAGAG 58.011 41.667 0.00 0.00 0.00 3.20
1863 2223 5.067413 GTCCTATCATTGTACCAAGAGACGA 59.933 44.000 0.00 0.00 0.00 4.20
1877 2237 1.771255 GGAGCTGGGTGTCCTATCATT 59.229 52.381 0.00 0.00 0.00 2.57
2041 2401 5.183228 GGTGCTGTAGTAAGGCATTCTAAA 58.817 41.667 0.00 0.00 38.27 1.85
2043 2403 3.134081 GGGTGCTGTAGTAAGGCATTCTA 59.866 47.826 0.00 0.00 38.27 2.10
2068 2682 4.502415 TGGGTGTCCTATCATCATACCAT 58.498 43.478 0.00 0.00 0.00 3.55
2125 2739 6.966534 AGACTTGATTTTGACCTGTCATTT 57.033 33.333 0.03 0.00 39.64 2.32
2330 2954 9.679661 TTCTGGTTAATACAATTCTAGCATGAA 57.320 29.630 0.00 0.00 0.00 2.57
2331 2955 9.679661 TTTCTGGTTAATACAATTCTAGCATGA 57.320 29.630 0.00 0.00 0.00 3.07
2332 2956 9.722056 GTTTCTGGTTAATACAATTCTAGCATG 57.278 33.333 0.00 0.00 0.00 4.06
2334 2958 8.856153 TGTTTCTGGTTAATACAATTCTAGCA 57.144 30.769 0.00 0.00 0.00 3.49
2348 2972 9.508642 TTCACACATGTATTATGTTTCTGGTTA 57.491 29.630 0.00 0.00 0.00 2.85
2349 2973 7.994425 TCACACATGTATTATGTTTCTGGTT 57.006 32.000 0.00 0.00 0.00 3.67
2370 3025 9.803315 TGACACTCTATTTGTCTATGTATTCAC 57.197 33.333 4.27 0.00 43.30 3.18
2371 3026 9.803315 GTGACACTCTATTTGTCTATGTATTCA 57.197 33.333 0.00 0.00 43.30 2.57
2375 3030 9.682465 ACTAGTGACACTCTATTTGTCTATGTA 57.318 33.333 12.39 0.00 43.30 2.29
2376 3031 8.582657 ACTAGTGACACTCTATTTGTCTATGT 57.417 34.615 12.39 0.00 43.30 2.29
2382 3037 6.381420 AGGCATACTAGTGACACTCTATTTGT 59.619 38.462 12.39 5.61 0.00 2.83
2383 3038 6.810911 AGGCATACTAGTGACACTCTATTTG 58.189 40.000 12.39 6.28 0.00 2.32
2384 3039 6.836527 AGAGGCATACTAGTGACACTCTATTT 59.163 38.462 12.39 0.00 32.75 1.40
2385 3040 6.369629 AGAGGCATACTAGTGACACTCTATT 58.630 40.000 12.39 0.00 32.75 1.73
2386 3041 5.947663 AGAGGCATACTAGTGACACTCTAT 58.052 41.667 12.39 5.69 32.75 1.98
2388 3043 4.243793 AGAGGCATACTAGTGACACTCT 57.756 45.455 12.39 10.40 0.00 3.24
2389 3044 5.127491 AGTAGAGGCATACTAGTGACACTC 58.873 45.833 12.39 8.31 34.21 3.51
2391 3046 5.357314 TCAAGTAGAGGCATACTAGTGACAC 59.643 44.000 5.39 0.00 34.90 3.67
2392 3047 5.357314 GTCAAGTAGAGGCATACTAGTGACA 59.643 44.000 19.41 0.00 40.28 3.58
2393 3048 5.591067 AGTCAAGTAGAGGCATACTAGTGAC 59.409 44.000 17.97 17.97 40.57 3.67
2394 3049 5.756918 AGTCAAGTAGAGGCATACTAGTGA 58.243 41.667 5.39 2.59 34.90 3.41
2395 3050 6.293735 GCTAGTCAAGTAGAGGCATACTAGTG 60.294 46.154 5.39 0.00 38.02 2.74
2396 3051 5.766174 GCTAGTCAAGTAGAGGCATACTAGT 59.234 44.000 0.00 0.00 38.02 2.57
2398 3053 5.942961 AGCTAGTCAAGTAGAGGCATACTA 58.057 41.667 3.23 0.00 34.90 1.82
2400 3055 4.319911 CGAGCTAGTCAAGTAGAGGCATAC 60.320 50.000 0.00 0.00 0.00 2.39
2401 3056 3.815962 CGAGCTAGTCAAGTAGAGGCATA 59.184 47.826 0.00 0.00 0.00 3.14
2402 3057 2.621055 CGAGCTAGTCAAGTAGAGGCAT 59.379 50.000 0.00 0.00 0.00 4.40
2403 3058 2.017782 CGAGCTAGTCAAGTAGAGGCA 58.982 52.381 0.00 0.00 0.00 4.75
2404 3059 2.018515 ACGAGCTAGTCAAGTAGAGGC 58.981 52.381 0.00 0.00 0.00 4.70
2406 3061 7.017498 TGATTAACGAGCTAGTCAAGTAGAG 57.983 40.000 0.00 0.00 0.00 2.43
2407 3062 6.997239 TGATTAACGAGCTAGTCAAGTAGA 57.003 37.500 0.00 0.00 0.00 2.59
2408 3063 7.968956 TCTTTGATTAACGAGCTAGTCAAGTAG 59.031 37.037 0.00 0.00 31.56 2.57
2409 3064 7.823665 TCTTTGATTAACGAGCTAGTCAAGTA 58.176 34.615 0.00 0.00 31.56 2.24
2412 3067 6.535150 CCATCTTTGATTAACGAGCTAGTCAA 59.465 38.462 0.00 0.00 0.00 3.18
2413 3068 6.042777 CCATCTTTGATTAACGAGCTAGTCA 58.957 40.000 0.00 0.00 0.00 3.41
2414 3069 6.043411 ACCATCTTTGATTAACGAGCTAGTC 58.957 40.000 0.00 0.00 0.00 2.59
2416 3071 6.910536 AACCATCTTTGATTAACGAGCTAG 57.089 37.500 0.00 0.00 0.00 3.42
2421 3076 8.455682 GGAAACATAACCATCTTTGATTAACGA 58.544 33.333 0.00 0.00 0.00 3.85
2422 3077 8.458843 AGGAAACATAACCATCTTTGATTAACG 58.541 33.333 0.00 0.00 0.00 3.18
2437 3092 6.827586 TTGTCCATGGTTAGGAAACATAAC 57.172 37.500 12.58 0.00 36.80 1.89
2438 3093 7.235079 TCTTTGTCCATGGTTAGGAAACATAA 58.765 34.615 12.58 3.91 36.80 1.90
2439 3094 6.785076 TCTTTGTCCATGGTTAGGAAACATA 58.215 36.000 12.58 1.27 36.80 2.29
2441 3096 5.055265 TCTTTGTCCATGGTTAGGAAACA 57.945 39.130 12.58 3.66 36.80 2.83
2442 3097 5.070685 ACTCTTTGTCCATGGTTAGGAAAC 58.929 41.667 12.58 0.61 36.80 2.78
2443 3098 5.319043 ACTCTTTGTCCATGGTTAGGAAA 57.681 39.130 12.58 4.26 36.80 3.13
2444 3099 4.993705 ACTCTTTGTCCATGGTTAGGAA 57.006 40.909 12.58 0.56 36.80 3.36
2445 3100 4.104102 ACAACTCTTTGTCCATGGTTAGGA 59.896 41.667 12.58 3.65 42.67 2.94
2446 3101 4.398319 ACAACTCTTTGTCCATGGTTAGG 58.602 43.478 12.58 0.00 42.67 2.69
2448 3103 8.356657 CAAATAACAACTCTTTGTCCATGGTTA 58.643 33.333 12.58 0.00 45.69 2.85
2449 3104 6.976934 AATAACAACTCTTTGTCCATGGTT 57.023 33.333 12.58 0.00 45.69 3.67
2450 3105 6.549364 TCAAATAACAACTCTTTGTCCATGGT 59.451 34.615 12.58 0.00 45.69 3.55
2454 3109 9.959749 GTTAATCAAATAACAACTCTTTGTCCA 57.040 29.630 0.00 0.00 45.69 4.02
2455 3110 9.959749 TGTTAATCAAATAACAACTCTTTGTCC 57.040 29.630 0.00 0.00 45.69 4.02
2463 3118 9.295825 TGTGATCCTGTTAATCAAATAACAACT 57.704 29.630 2.04 0.00 43.21 3.16
2471 3126 9.685276 ACTAATGATGTGATCCTGTTAATCAAA 57.315 29.630 0.00 0.00 35.04 2.69
2472 3127 9.685276 AACTAATGATGTGATCCTGTTAATCAA 57.315 29.630 0.00 0.00 35.04 2.57
2473 3128 9.112725 CAACTAATGATGTGATCCTGTTAATCA 57.887 33.333 0.00 0.00 0.00 2.57
2474 3129 9.330063 TCAACTAATGATGTGATCCTGTTAATC 57.670 33.333 0.00 0.00 31.50 1.75
2475 3130 9.685276 TTCAACTAATGATGTGATCCTGTTAAT 57.315 29.630 0.00 0.00 38.03 1.40
2477 3132 9.112725 CATTCAACTAATGATGTGATCCTGTTA 57.887 33.333 0.00 0.00 46.81 2.41
2478 3133 7.993101 CATTCAACTAATGATGTGATCCTGTT 58.007 34.615 0.00 0.00 46.81 3.16
2479 3134 7.563888 CATTCAACTAATGATGTGATCCTGT 57.436 36.000 0.00 0.00 46.81 4.00


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

AutoCloner maintained by Alex Coulton.