Multiple sequence alignment - TraesCS3D01G458500

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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 TraesCS3D01G458500 chr3D 100.000 4490 0 0 1 4490 563858566 563863055 0.000000e+00 8292
1 TraesCS3D01G458500 chr3D 92.593 108 6 1 2495 2600 563860850 563860957 2.160000e-33 154
2 TraesCS3D01G458500 chr2A 96.663 3746 82 18 755 4490 7919070 7922782 0.000000e+00 6185
3 TraesCS3D01G458500 chr2A 82.918 1686 191 54 838 2485 8182756 8181130 0.000000e+00 1428
4 TraesCS3D01G458500 chr2A 91.681 577 45 2 185 758 7915901 7916477 0.000000e+00 797
5 TraesCS3D01G458500 chr2A 81.686 617 73 20 3251 3844 8180854 8180255 1.130000e-130 477
6 TraesCS3D01G458500 chr2A 82.318 509 64 17 2755 3254 8369577 8369086 6.950000e-113 418
7 TraesCS3D01G458500 chr2A 90.909 231 17 4 3026 3253 8181051 8180822 1.570000e-79 307
8 TraesCS3D01G458500 chr2A 84.132 334 23 13 2784 3098 8046685 8047007 3.400000e-76 296
9 TraesCS3D01G458500 chr2A 94.022 184 11 0 1 184 7857980 7858163 3.420000e-71 279
10 TraesCS3D01G458500 chr2A 80.556 360 48 17 1153 1498 8370810 8370459 1.600000e-64 257
11 TraesCS3D01G458500 chr2A 83.721 258 18 14 2755 3005 7808188 7808428 5.850000e-54 222
12 TraesCS3D01G458500 chr2A 79.496 278 42 11 454 722 197806283 197806012 2.760000e-42 183
13 TraesCS3D01G458500 chr2A 76.166 386 61 19 2069 2435 7796620 7796247 1.660000e-39 174
14 TraesCS3D01G458500 chr2A 94.444 108 4 1 2495 2600 8181333 8181226 9.990000e-37 165
15 TraesCS3D01G458500 chr7A 86.443 1372 145 24 1256 2600 466508137 466509494 0.000000e+00 1465
16 TraesCS3D01G458500 chr7A 83.123 397 26 20 2883 3253 466509686 466510067 1.560000e-84 324
17 TraesCS3D01G458500 chr7A 80.000 475 61 18 1963 2425 466492000 466492452 2.020000e-83 320
18 TraesCS3D01G458500 chr7A 80.392 408 48 16 3251 3650 466510035 466510418 9.510000e-72 281
19 TraesCS3D01G458500 chr7A 91.753 194 12 1 2763 2956 466509499 466509688 2.660000e-67 267
20 TraesCS3D01G458500 chr7A 89.573 211 17 3 2279 2486 466509383 466509591 3.440000e-66 263
21 TraesCS3D01G458500 chr7A 75.737 577 77 34 775 1327 466507556 466508093 9.710000e-57 231
22 TraesCS3D01G458500 chr7A 93.578 109 5 1 2495 2601 466509178 466509286 1.290000e-35 161
23 TraesCS3D01G458500 chr2B 85.381 1286 139 27 1135 2392 70882008 70880744 0.000000e+00 1288
24 TraesCS3D01G458500 chr2B 82.952 786 93 27 2748 3515 12076257 12075495 0.000000e+00 671
25 TraesCS3D01G458500 chr2B 82.353 510 62 19 2755 3254 12025631 12025140 6.950000e-113 418
26 TraesCS3D01G458500 chr2B 78.317 618 99 21 1883 2482 12026137 12025537 2.550000e-97 366
27 TraesCS3D01G458500 chr2B 77.761 670 100 32 846 1498 12027150 12026513 2.550000e-97 366
28 TraesCS3D01G458500 chr2B 84.131 397 43 12 2763 3147 70880446 70880058 2.550000e-97 366
29 TraesCS3D01G458500 chr2B 90.187 214 16 3 2279 2489 70880562 70880351 1.590000e-69 274
30 TraesCS3D01G458500 chr2B 84.674 261 27 6 2755 3009 11985947 11986200 9.640000e-62 248
31 TraesCS3D01G458500 chr2B 88.649 185 17 2 1 184 302100699 302100880 5.850000e-54 222
32 TraesCS3D01G458500 chr2B 84.793 217 24 6 2389 2600 70880663 70880451 4.550000e-50 209
33 TraesCS3D01G458500 chr2B 78.006 341 60 12 369 700 463863908 463864242 2.740000e-47 200
34 TraesCS3D01G458500 chr2B 84.286 210 18 10 846 1041 12077811 12077603 1.650000e-44 191
35 TraesCS3D01G458500 chr2B 92.126 127 6 3 2495 2619 70880851 70880727 4.620000e-40 176
36 TraesCS3D01G458500 chr2B 81.212 165 24 5 499 662 767963683 767963525 4.720000e-25 126
37 TraesCS3D01G458500 chr2B 93.506 77 2 3 836 912 70882806 70882733 1.320000e-20 111
38 TraesCS3D01G458500 chr2D 89.664 803 68 7 1809 2600 8928474 8929272 0.000000e+00 1009
39 TraesCS3D01G458500 chr2D 76.969 1689 285 72 846 2485 8888810 8890443 0.000000e+00 869
40 TraesCS3D01G458500 chr2D 77.644 1078 145 56 762 1817 8920019 8921022 6.520000e-158 568
41 TraesCS3D01G458500 chr2D 85.010 507 50 18 2763 3253 8929277 8929773 4.040000e-135 492
42 TraesCS3D01G458500 chr2D 82.840 507 63 15 2755 3254 8717550 8718039 2.480000e-117 433
43 TraesCS3D01G458500 chr2D 87.637 364 33 4 368 723 131195253 131194894 3.230000e-111 412
44 TraesCS3D01G458500 chr2D 79.248 612 103 12 1884 2486 8717052 8717648 5.410000e-109 405
45 TraesCS3D01G458500 chr2D 83.527 431 50 14 2755 3175 8890345 8890764 2.530000e-102 383
46 TraesCS3D01G458500 chr2D 77.033 701 98 39 810 1495 8715963 8716615 1.200000e-90 344
47 TraesCS3D01G458500 chr2D 89.450 218 17 4 2279 2492 8929161 8929376 2.060000e-68 270
48 TraesCS3D01G458500 chr2D 93.902 164 8 2 2596 2757 134301650 134301487 3.470000e-61 246
49 TraesCS3D01G458500 chr2D 91.954 174 11 2 2585 2756 560153876 560154048 1.610000e-59 241
50 TraesCS3D01G458500 chr2D 94.444 108 4 1 2495 2600 8928956 8929063 9.990000e-37 165
51 TraesCS3D01G458500 chr2D 92.941 85 6 0 3629 3713 8930265 8930349 1.700000e-24 124
52 TraesCS3D01G458500 chr5D 87.912 364 35 2 368 723 417664037 417663675 1.930000e-113 420
53 TraesCS3D01G458500 chr5D 94.410 161 9 0 2596 2756 150835465 150835305 9.640000e-62 248
54 TraesCS3D01G458500 chr4B 93.989 183 10 1 1 182 96445139 96444957 4.420000e-70 276
55 TraesCS3D01G458500 chr4B 93.514 185 11 1 1 184 29878497 29878681 1.590000e-69 274
56 TraesCS3D01G458500 chr4B 93.373 166 9 1 2596 2759 606916762 606916927 1.250000e-60 244
57 TraesCS3D01G458500 chr4B 88.947 190 18 2 185 371 29880375 29880564 9.710000e-57 231
58 TraesCS3D01G458500 chr6D 94.479 163 9 0 2597 2759 178849199 178849361 7.460000e-63 252
59 TraesCS3D01G458500 chr5A 94.479 163 7 1 2597 2757 653299601 653299439 2.680000e-62 250
60 TraesCS3D01G458500 chr5A 93.902 164 8 1 2595 2756 320214242 320214405 3.470000e-61 246
61 TraesCS3D01G458500 chr1B 92.982 171 10 1 2597 2765 436689151 436688981 9.640000e-62 248
62 TraesCS3D01G458500 chr1B 88.298 188 20 1 185 370 29782063 29781876 1.630000e-54 224
63 TraesCS3D01G458500 chr7D 78.738 301 50 5 406 698 48356117 48355823 5.930000e-44 189
64 TraesCS3D01G458500 chr1D 80.571 175 28 4 488 661 260614289 260614458 3.650000e-26 130
65 TraesCS3D01G458500 chr3A 77.083 240 42 7 433 663 169843831 169843596 4.720000e-25 126


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 TraesCS3D01G458500 chr3D 563858566 563863055 4489 False 4223.000000 8292 96.296500 1 4490 2 chr3D.!!$F1 4489
1 TraesCS3D01G458500 chr2A 7915901 7922782 6881 False 3491.000000 6185 94.172000 185 4490 2 chr2A.!!$F4 4305
2 TraesCS3D01G458500 chr2A 8180255 8182756 2501 True 594.250000 1428 87.489250 838 3844 4 chr2A.!!$R3 3006
3 TraesCS3D01G458500 chr2A 8369086 8370810 1724 True 337.500000 418 81.437000 1153 3254 2 chr2A.!!$R4 2101
4 TraesCS3D01G458500 chr7A 466507556 466510418 2862 False 427.428571 1465 85.799857 775 3650 7 chr7A.!!$F2 2875
5 TraesCS3D01G458500 chr2B 12075495 12077811 2316 True 431.000000 671 83.619000 846 3515 2 chr2B.!!$R3 2669
6 TraesCS3D01G458500 chr2B 70880058 70882806 2748 True 404.000000 1288 88.354000 836 3147 6 chr2B.!!$R4 2311
7 TraesCS3D01G458500 chr2B 12025140 12027150 2010 True 383.333333 418 79.477000 846 3254 3 chr2B.!!$R2 2408
8 TraesCS3D01G458500 chr2D 8888810 8890764 1954 False 626.000000 869 80.248000 846 3175 2 chr2D.!!$F4 2329
9 TraesCS3D01G458500 chr2D 8920019 8921022 1003 False 568.000000 568 77.644000 762 1817 1 chr2D.!!$F1 1055
10 TraesCS3D01G458500 chr2D 8928474 8930349 1875 False 412.000000 1009 90.301800 1809 3713 5 chr2D.!!$F5 1904
11 TraesCS3D01G458500 chr2D 8715963 8718039 2076 False 394.000000 433 79.707000 810 3254 3 chr2D.!!$F3 2444
12 TraesCS3D01G458500 chr4B 29878497 29880564 2067 False 252.500000 274 91.230500 1 371 2 chr4B.!!$F2 370

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
787 5081 0.029035 CTGGTCGATCTAACGGTCCG 59.971 60.000 10.48 10.48 33.48 4.79 F
790 5084 1.012841 GTCGATCTAACGGTCCGAGT 58.987 55.000 20.51 7.91 0.00 4.18 F
912 5244 1.274767 ACCCAATCCTAACCCTAGCCA 60.275 52.381 0.00 0.00 0.00 4.75 F
1776 6935 1.445942 CGATTATCCACACGGCCCT 59.554 57.895 0.00 0.00 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 7020 0.729140 GCCAGTCCAAATGTTTCGCG 60.729 55.000 0.0 0.0 0.00 5.87 R
2087 7252 1.602165 CGACACGAAGCAAGTACTGGT 60.602 52.381 0.0 0.0 37.35 4.00 R
2220 7395 3.560636 ACTATGATTGGTGGTGGTAGC 57.439 47.619 0.0 0.0 0.00 3.58 R
3521 9486 1.094785 ACAACTGATAATGGTGCGGC 58.905 50.000 0.0 0.0 0.00 6.53 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
19 20 1.432514 CAAGCAGCGCTCAAGAAGTA 58.567 50.000 7.13 0.00 38.25 2.24
24 25 2.677199 CAGCGCTCAAGAAGTAGAACA 58.323 47.619 7.13 0.00 0.00 3.18
31 32 6.508721 GCGCTCAAGAAGTAGAACACATAATC 60.509 42.308 0.00 0.00 0.00 1.75
46 47 7.928307 ACACATAATCAACATATATGGGAGC 57.072 36.000 16.96 0.00 34.72 4.70
86 87 7.781324 ATAAACAAGGACAAGTCATCCATTT 57.219 32.000 2.29 0.59 38.86 2.32
113 114 3.994317 AGCAAAAATATAAGGCCCTGGT 58.006 40.909 0.00 0.00 0.00 4.00
118 119 6.239036 GCAAAAATATAAGGCCCTGGTAGAAG 60.239 42.308 0.00 0.00 0.00 2.85
162 164 2.035632 CATTAGTCGGAAGGCCTCTCT 58.964 52.381 5.23 2.99 35.23 3.10
177 179 4.576873 GGCCTCTCTTCAAAATACTTAGGC 59.423 45.833 0.00 0.00 44.94 3.93
195 1890 3.444029 AGGCCTTCCATTGTAAATTGCT 58.556 40.909 0.00 0.00 33.74 3.91
231 1926 0.958382 GGTGGCACATGGTTTAGCGA 60.958 55.000 20.82 0.00 44.52 4.93
254 1949 4.390909 ACTTTCGGTGCTAGGTTAAATTCG 59.609 41.667 0.00 0.00 0.00 3.34
258 1953 3.430651 CGGTGCTAGGTTAAATTCGGGTA 60.431 47.826 0.00 0.00 0.00 3.69
273 1968 0.105408 GGGTACGTGTGTCACTTGGT 59.895 55.000 4.27 2.35 31.34 3.67
362 2057 2.163412 GGAATGCAAGCGTGTTCCATTA 59.837 45.455 14.44 0.00 39.86 1.90
363 2058 3.366883 GGAATGCAAGCGTGTTCCATTAA 60.367 43.478 14.44 0.00 39.86 1.40
391 2088 1.680249 CCAAGAACTAGGGAGGCAAGC 60.680 57.143 0.00 0.00 0.00 4.01
417 2114 5.692613 ACTAGTACGGCATCTAACATCTC 57.307 43.478 0.00 0.00 0.00 2.75
442 2139 1.135402 GCTAAACATTGGGGACGCTTG 60.135 52.381 0.00 0.00 0.00 4.01
479 2176 2.789409 CCTTGAAGAAGGGGAACGAT 57.211 50.000 0.00 0.00 44.76 3.73
482 2179 2.762535 TGAAGAAGGGGAACGATGTC 57.237 50.000 0.00 0.00 0.00 3.06
492 2189 3.371097 AACGATGTCGCCGCCATCT 62.371 57.895 6.56 0.00 44.43 2.90
493 2190 3.333189 CGATGTCGCCGCCATCTG 61.333 66.667 6.56 0.00 37.22 2.90
506 2203 1.858091 CCATCTGATCCGAAGAACCG 58.142 55.000 0.00 0.00 0.00 4.44
514 2211 2.181021 CGAAGAACCGGACCCGAG 59.819 66.667 9.46 2.86 42.83 4.63
536 2233 3.127030 GGTTTCCCTCGTTGCTTGAATAG 59.873 47.826 0.00 0.00 0.00 1.73
543 2240 1.544724 GTTGCTTGAATAGGGGCACA 58.455 50.000 0.00 0.00 34.30 4.57
549 2246 4.141181 TGCTTGAATAGGGGCACAGATAAT 60.141 41.667 0.00 0.00 0.00 1.28
641 2338 1.379044 AGCAGGGATTTCGCCTTGG 60.379 57.895 0.00 0.00 35.70 3.61
651 2348 2.511600 CGCCTTGGCCTAAGTCCG 60.512 66.667 3.32 7.43 34.45 4.79
658 2355 0.178068 TGGCCTAAGTCCGAGCAATC 59.822 55.000 3.32 0.00 0.00 2.67
677 2374 0.388907 CCCATTTGTCGGCAAAGCAG 60.389 55.000 21.05 12.51 46.30 4.24
682 2379 2.704725 TTGTCGGCAAAGCAGAATTC 57.295 45.000 0.00 0.00 34.22 2.17
683 2380 0.516877 TGTCGGCAAAGCAGAATTCG 59.483 50.000 0.00 0.00 34.22 3.34
684 2381 0.794605 GTCGGCAAAGCAGAATTCGC 60.795 55.000 12.44 12.44 34.22 4.70
709 2406 0.326264 ATGAAGTCAGGCCACTGGTC 59.674 55.000 5.01 0.00 44.99 4.02
712 2409 0.109342 AAGTCAGGCCACTGGTCAAG 59.891 55.000 5.01 0.00 44.99 3.02
744 2442 4.021719 CCCATTGCATTTCCATCATAGGAC 60.022 45.833 0.00 0.00 37.42 3.85
746 2444 5.069383 CCATTGCATTTCCATCATAGGACAA 59.931 40.000 0.00 0.00 37.42 3.18
748 2446 4.598022 TGCATTTCCATCATAGGACAACA 58.402 39.130 0.00 0.00 37.42 3.33
787 5081 0.029035 CTGGTCGATCTAACGGTCCG 59.971 60.000 10.48 10.48 33.48 4.79
790 5084 1.012841 GTCGATCTAACGGTCCGAGT 58.987 55.000 20.51 7.91 0.00 4.18
791 5085 1.399791 GTCGATCTAACGGTCCGAGTT 59.600 52.381 20.51 5.20 35.75 3.01
795 5089 3.064545 CGATCTAACGGTCCGAGTTAGTT 59.935 47.826 20.51 11.12 46.59 2.24
831 5126 2.281761 CGGTTTCCCTGCTGCTGT 60.282 61.111 0.00 0.00 0.00 4.40
898 5218 1.566298 GCTGTCCTCCTCCACCCAAT 61.566 60.000 0.00 0.00 0.00 3.16
912 5244 1.274767 ACCCAATCCTAACCCTAGCCA 60.275 52.381 0.00 0.00 0.00 4.75
986 5773 3.715315 ACCAAACCCTAATCCCTAGCTAC 59.285 47.826 0.00 0.00 0.00 3.58
1082 5970 2.897350 CGAAGGGCCAATCCGCTC 60.897 66.667 6.18 0.00 34.94 5.03
1345 6375 4.096003 GCTACAGCTTGCCGGGGA 62.096 66.667 2.18 0.00 38.21 4.81
1776 6935 1.445942 CGATTATCCACACGGCCCT 59.554 57.895 0.00 0.00 0.00 5.19
1861 7020 1.862602 ATTTGTTGAACGCGAGCCCC 61.863 55.000 15.93 0.00 0.00 5.80
1910 7069 1.810606 CTGTCGCCTGACCACTCAGT 61.811 60.000 0.00 0.00 44.86 3.41
2087 7252 2.606308 GCCGTCGACTAGTGTTCAAAGA 60.606 50.000 14.70 0.00 0.00 2.52
2220 7395 2.579201 CAGGAGCACCCGGTACTG 59.421 66.667 0.00 0.00 44.85 2.74
2454 7644 6.908870 TCAACAGTAGATGTGTGATATTGC 57.091 37.500 0.00 0.00 43.00 3.56
2463 7653 7.059202 AGATGTGTGATATTGCTACTCATCA 57.941 36.000 16.17 0.00 42.89 3.07
2606 7802 2.912956 AGTTTGCTTCATACTCCCTCCA 59.087 45.455 0.00 0.00 0.00 3.86
2836 8242 0.939419 TTGATGCTCATCGGCAATCG 59.061 50.000 5.51 0.00 45.68 3.34
3521 9486 5.524646 GCAACATATCATGTGGAAATTTGGG 59.475 40.000 0.00 0.00 44.07 4.12
3597 9562 9.947669 AATGTCGTCATTATCAAGTAGTAGTAC 57.052 33.333 6.08 0.00 41.76 2.73
3683 9826 5.175673 GCTTCTTTTGGATTGTAACTTGCAC 59.824 40.000 0.00 0.00 0.00 4.57
3718 9861 6.061022 TCTTGCATGAATCCTACTGGTTTA 57.939 37.500 0.00 0.00 34.23 2.01
3910 10056 7.011389 GGCATTGGCTTTTCTTGGTTATATTTC 59.989 37.037 2.42 0.00 40.87 2.17
4226 10372 3.389983 GGAGGCCCCAAAAACTTTTTAGT 59.610 43.478 0.00 0.00 34.14 2.24
4261 10408 0.035458 CCCTATCTTCCATGGTCGGC 59.965 60.000 12.58 0.00 0.00 5.54
4308 10455 4.131088 GCGGGGGTCGTGAGTCTC 62.131 72.222 0.00 0.00 41.72 3.36
4352 10500 4.243008 GGAGCTAGGCGGGGAAGC 62.243 72.222 0.00 0.00 36.48 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.730705 CTCCCATATATGTTGATTATGTGTTCT 57.269 33.333 11.73 0.00 0.00 3.01
24 25 6.600822 GCAGCTCCCATATATGTTGATTATGT 59.399 38.462 11.73 0.00 0.00 2.29
31 32 2.998670 CGAGCAGCTCCCATATATGTTG 59.001 50.000 17.16 2.94 0.00 3.33
46 47 5.811399 TGTTTATTATTTGTCCCGAGCAG 57.189 39.130 0.00 0.00 0.00 4.24
86 87 7.327214 CAGGGCCTTATATTTTTGCTAAACAA 58.673 34.615 1.32 0.00 36.13 2.83
109 110 5.584251 GCTCTTCATTTCTTCCTTCTACCAG 59.416 44.000 0.00 0.00 0.00 4.00
113 114 6.212388 AGACTGCTCTTCATTTCTTCCTTCTA 59.788 38.462 0.00 0.00 0.00 2.10
118 119 6.428159 TGTTTAGACTGCTCTTCATTTCTTCC 59.572 38.462 0.00 0.00 0.00 3.46
162 164 6.723977 ACAATGGAAGGCCTAAGTATTTTGAA 59.276 34.615 5.16 0.00 34.31 2.69
177 179 4.635765 TCGAGAGCAATTTACAATGGAAGG 59.364 41.667 0.00 0.00 0.00 3.46
195 1890 2.749076 CCACCAAATTTCATGCTCGAGA 59.251 45.455 18.75 1.31 0.00 4.04
206 1901 3.574354 AAACCATGTGCCACCAAATTT 57.426 38.095 0.00 0.00 0.00 1.82
231 1926 4.390909 CGAATTTAACCTAGCACCGAAAGT 59.609 41.667 0.00 0.00 0.00 2.66
254 1949 0.105408 ACCAAGTGACACACGTACCC 59.895 55.000 8.59 0.00 39.64 3.69
258 1953 1.651987 CTCAACCAAGTGACACACGT 58.348 50.000 8.59 0.00 39.64 4.49
273 1968 1.661463 AACTCTGGGAGATGCCTCAA 58.339 50.000 1.31 0.00 41.20 3.02
383 2080 1.798079 CGTACTAGTTCGGCTTGCCTC 60.798 57.143 13.52 0.80 0.00 4.70
404 2101 7.530010 TGTTTAGCTTTTGAGATGTTAGATGC 58.470 34.615 0.00 0.00 0.00 3.91
417 2114 3.574614 CGTCCCCAATGTTTAGCTTTTG 58.425 45.455 0.00 0.00 0.00 2.44
442 2139 1.226773 GCGCCATCATGTTTGCTCC 60.227 57.895 0.00 0.00 0.00 4.70
478 2175 1.301244 GATCAGATGGCGGCGACAT 60.301 57.895 31.16 31.16 31.76 3.06
479 2176 2.106938 GATCAGATGGCGGCGACA 59.893 61.111 21.84 21.84 0.00 4.35
482 2179 3.790334 TTCGGATCAGATGGCGGCG 62.790 63.158 0.51 0.51 0.00 6.46
523 2220 0.451783 GTGCCCCTATTCAAGCAACG 59.548 55.000 0.00 0.00 36.91 4.10
530 2227 3.498481 GCCATTATCTGTGCCCCTATTCA 60.498 47.826 0.00 0.00 0.00 2.57
536 2233 0.178953 ATGGCCATTATCTGTGCCCC 60.179 55.000 14.09 0.00 39.27 5.80
543 2240 1.321474 CGTTGCCATGGCCATTATCT 58.679 50.000 33.44 0.00 41.09 1.98
566 2263 2.483013 CGAGTGTTGTGTCCCTTCTTGA 60.483 50.000 0.00 0.00 0.00 3.02
573 2270 2.022129 CTCGCGAGTGTTGTGTCCC 61.022 63.158 27.79 0.00 0.00 4.46
641 2338 0.533085 GGGATTGCTCGGACTTAGGC 60.533 60.000 0.00 0.00 0.00 3.93
651 2348 0.101219 GCCGACAAATGGGATTGCTC 59.899 55.000 0.00 0.00 33.52 4.26
658 2355 0.388907 CTGCTTTGCCGACAAATGGG 60.389 55.000 0.00 0.00 44.54 4.00
682 2379 1.416813 GCCTGACTTCATCGTCTGCG 61.417 60.000 0.00 0.00 39.92 5.18
683 2380 1.086634 GGCCTGACTTCATCGTCTGC 61.087 60.000 0.00 0.00 35.00 4.26
684 2381 0.247460 TGGCCTGACTTCATCGTCTG 59.753 55.000 3.32 0.00 35.00 3.51
724 2422 5.657745 TGTTGTCCTATGATGGAAATGCAAT 59.342 36.000 0.00 0.00 37.93 3.56
778 5072 1.818674 GGGAACTAACTCGGACCGTTA 59.181 52.381 14.79 5.29 0.00 3.18
787 5081 4.202430 TGAAGGGAAAGTGGGAACTAACTC 60.202 45.833 0.00 0.00 0.00 3.01
790 5084 3.495453 CGTGAAGGGAAAGTGGGAACTAA 60.495 47.826 0.00 0.00 0.00 2.24
791 5085 2.038033 CGTGAAGGGAAAGTGGGAACTA 59.962 50.000 0.00 0.00 0.00 2.24
795 5089 1.072505 GCGTGAAGGGAAAGTGGGA 59.927 57.895 0.00 0.00 0.00 4.37
831 5126 2.858768 AGGAGAAGGGGGATTTGCAATA 59.141 45.455 0.00 0.00 0.00 1.90
898 5218 2.062177 GGCGTGGCTAGGGTTAGGA 61.062 63.158 0.00 0.00 0.00 2.94
929 5262 4.008933 GGGATCGAGGATGGCGGG 62.009 72.222 0.00 0.00 0.00 6.13
1093 5987 3.791245 CTGATCTTCTTGCTGGTAGTCC 58.209 50.000 0.00 0.00 0.00 3.85
1094 5988 3.194062 GCTGATCTTCTTGCTGGTAGTC 58.806 50.000 0.00 0.00 0.00 2.59
1095 5989 2.093235 GGCTGATCTTCTTGCTGGTAGT 60.093 50.000 0.00 0.00 0.00 2.73
1124 6018 2.213499 CTGCGTCACTCAACTTTTCCT 58.787 47.619 0.00 0.00 0.00 3.36
1127 6021 1.593006 CGACTGCGTCACTCAACTTTT 59.407 47.619 8.91 0.00 32.09 2.27
1536 6575 3.234630 TTTGGCGGACGACTCCCAG 62.235 63.158 0.00 0.00 31.93 4.45
1776 6935 2.048222 CGGAACTCCTCAGCGCAA 60.048 61.111 11.47 0.00 0.00 4.85
1861 7020 0.729140 GCCAGTCCAAATGTTTCGCG 60.729 55.000 0.00 0.00 0.00 5.87
2087 7252 1.602165 CGACACGAAGCAAGTACTGGT 60.602 52.381 0.00 0.00 37.35 4.00
2220 7395 3.560636 ACTATGATTGGTGGTGGTAGC 57.439 47.619 0.00 0.00 0.00 3.58
2454 7644 6.766429 TCCCAGAATCATGAATGATGAGTAG 58.234 40.000 6.56 0.00 46.22 2.57
2980 8898 2.026262 ACGGGGTGAAGCTAATGACAAT 60.026 45.455 0.00 0.00 0.00 2.71
3192 9130 3.629855 TGTTGAAACGACCATTGTGTCAT 59.370 39.130 0.00 0.00 33.74 3.06
3307 9246 3.864540 GCTGAGTACATATGCGGCCATAA 60.865 47.826 2.24 0.00 37.47 1.90
3430 9390 3.333313 AGATTCCATCTCTCTCTGGCT 57.667 47.619 0.00 0.00 33.42 4.75
3521 9486 1.094785 ACAACTGATAATGGTGCGGC 58.905 50.000 0.00 0.00 0.00 6.53
3591 9556 6.470278 ACCCAACATCCAGTTTAAGTACTAC 58.530 40.000 0.00 0.00 38.74 2.73
3597 9562 6.038271 GCATACTACCCAACATCCAGTTTAAG 59.962 42.308 0.00 0.00 38.74 1.85
3683 9826 4.508461 TCATGCAAGAAAATGACACTGG 57.492 40.909 0.00 0.00 0.00 4.00
3891 10037 9.346725 CACAGAAGAAATATAACCAAGAAAAGC 57.653 33.333 0.00 0.00 0.00 3.51
3910 10056 0.395311 ATCCAGCCATGCCACAGAAG 60.395 55.000 0.00 0.00 0.00 2.85
4180 10326 4.079443 AGGGTTGCAGTATCTCTCTAGTCT 60.079 45.833 0.00 0.00 0.00 3.24
4190 10336 0.464554 GCCTCCAGGGTTGCAGTATC 60.465 60.000 0.00 0.00 37.43 2.24
4233 10380 2.044450 AAGATAGGGGCAGGGGCA 59.956 61.111 0.00 0.00 43.71 5.36
4293 10440 4.131088 GCGAGACTCACGACCCCC 62.131 72.222 2.82 0.00 0.00 5.40
4352 10500 2.659897 GCCAGCACCTCTATCGCG 60.660 66.667 0.00 0.00 0.00 5.87
4377 10525 3.570212 GCCACCAGGGTGTCCACT 61.570 66.667 16.74 0.00 44.02 4.00


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

AutoCloner maintained by Alex Coulton.