Multiple sequence alignment - TraesCS1D01G128700

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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 TraesCS1D01G128700 chr1D 100.000 3152 0 0 1 3152 141901091 141897940 0.000000e+00 5821.0
1 TraesCS1D01G128700 chr1D 90.215 419 40 1 1 418 383180329 383180747 2.140000e-151 545.0
2 TraesCS1D01G128700 chr1D 89.226 297 21 2 2193 2479 84806250 84806545 8.310000e-96 361.0
3 TraesCS1D01G128700 chr1D 84.821 336 41 7 2784 3114 338746917 338746587 2.340000e-86 329.0
4 TraesCS1D01G128700 chr1D 79.801 302 49 10 2777 3075 114212199 114212491 3.190000e-50 209.0
5 TraesCS1D01G128700 chr1D 91.406 128 6 5 2380 2504 141898600 141898475 1.500000e-38 171.0
6 TraesCS1D01G128700 chr1D 91.406 128 6 5 2492 2617 141898712 141898588 1.500000e-38 171.0
7 TraesCS1D01G128700 chr1B 96.265 2142 59 10 1 2134 196063327 196061199 0.000000e+00 3493.0
8 TraesCS1D01G128700 chr1B 89.232 938 51 20 2237 3151 196060815 196059905 0.000000e+00 1127.0
9 TraesCS1D01G128700 chr1B 73.994 323 58 20 2198 2505 457047808 457048119 1.200000e-19 108.0
10 TraesCS1D01G128700 chr1A 94.379 1281 47 3 539 1817 148744347 148745604 0.000000e+00 1943.0
11 TraesCS1D01G128700 chr1A 94.415 376 17 2 1822 2196 148745692 148746064 2.730000e-160 575.0
12 TraesCS1D01G128700 chr1A 91.211 421 34 3 1 418 557890220 557890640 1.270000e-158 569.0
13 TraesCS1D01G128700 chr1A 82.548 361 46 10 2781 3132 148746067 148746419 5.110000e-78 302.0
14 TraesCS1D01G128700 chr5B 90.931 419 37 1 1 418 361013591 361014009 2.120000e-156 562.0
15 TraesCS1D01G128700 chr5B 84.387 269 37 4 2492 2758 490235699 490235434 3.120000e-65 259.0
16 TraesCS1D01G128700 chr5B 79.359 281 44 6 2884 3150 44769357 44769077 5.370000e-43 185.0
17 TraesCS1D01G128700 chr5B 85.185 81 10 2 2198 2277 331553101 331553022 7.250000e-12 82.4
18 TraesCS1D01G128700 chr5B 84.146 82 11 2 2197 2277 315527500 315527420 9.370000e-11 78.7
19 TraesCS1D01G128700 chr7D 89.796 441 40 3 1 438 168500932 168500494 7.630000e-156 560.0
20 TraesCS1D01G128700 chr7D 91.418 268 21 2 2492 2758 58994807 58994541 1.790000e-97 366.0
21 TraesCS1D01G128700 chr7D 87.037 270 31 4 2492 2760 165487302 165487036 5.110000e-78 302.0
22 TraesCS1D01G128700 chr7D 85.714 126 12 6 2361 2485 85204664 85204544 9.180000e-26 128.0
23 TraesCS1D01G128700 chr2D 90.499 421 33 4 1 419 194805948 194806363 1.650000e-152 549.0
24 TraesCS1D01G128700 chr2D 85.556 270 20 5 2492 2758 645179526 645179273 6.700000e-67 265.0
25 TraesCS1D01G128700 chr2D 79.225 284 34 11 2237 2498 84744997 84744717 1.160000e-39 174.0
26 TraesCS1D01G128700 chr4B 89.425 435 44 2 1 434 592196194 592195761 5.940000e-152 547.0
27 TraesCS1D01G128700 chr4B 95.556 45 2 0 473 517 23827272 23827228 4.360000e-09 73.1
28 TraesCS1D01G128700 chr2A 90.338 414 38 2 1 413 431081792 431082204 2.770000e-150 542.0
29 TraesCS1D01G128700 chr2A 89.041 438 36 5 1 435 5385464 5385892 1.660000e-147 532.0
30 TraesCS1D01G128700 chr2A 77.551 343 38 19 2197 2504 74956528 74956866 1.500000e-38 171.0
31 TraesCS1D01G128700 chr3D 89.952 418 36 4 1 418 467734996 467734585 4.630000e-148 534.0
32 TraesCS1D01G128700 chr3D 86.562 320 21 6 2200 2504 36573083 36572771 1.810000e-87 333.0
33 TraesCS1D01G128700 chr3D 89.952 209 19 1 2549 2757 461374510 461374304 5.180000e-68 268.0
34 TraesCS1D01G128700 chr4A 89.179 268 26 3 2492 2758 676494598 676494333 6.520000e-87 331.0
35 TraesCS1D01G128700 chr4A 85.124 242 28 6 2841 3075 518857216 518856976 1.130000e-59 241.0
36 TraesCS1D01G128700 chr7A 88.433 268 26 5 2492 2758 38207203 38206940 5.070000e-83 318.0
37 TraesCS1D01G128700 chr7B 91.204 216 17 2 2542 2757 691041414 691041627 3.070000e-75 292.0
38 TraesCS1D01G128700 chrUn 83.007 306 22 6 2194 2469 93046571 93046266 1.880000e-62 250.0
39 TraesCS1D01G128700 chrUn 88.298 94 9 2 2492 2584 93046355 93046263 9.240000e-21 111.0
40 TraesCS1D01G128700 chr3B 93.130 131 8 1 2361 2491 41348943 41349072 1.150000e-44 191.0
41 TraesCS1D01G128700 chr3B 88.321 137 13 1 2193 2329 41336172 41336305 9.050000e-36 161.0
42 TraesCS1D01G128700 chr2B 86.875 160 18 3 2917 3075 449838608 449838451 3.230000e-40 176.0
43 TraesCS1D01G128700 chr5D 76.667 240 38 15 2198 2426 405678302 405678070 1.990000e-22 117.0
44 TraesCS1D01G128700 chr5D 89.855 69 7 0 2965 3033 300127164 300127232 4.330000e-14 89.8
45 TraesCS1D01G128700 chr5D 80.000 105 15 6 2197 2298 175658743 175658844 4.360000e-09 73.1
46 TraesCS1D01G128700 chr4D 74.224 322 60 17 2198 2504 484995915 484996228 2.570000e-21 113.0
47 TraesCS1D01G128700 chr5A 92.593 54 4 0 2197 2250 208352580 208352633 9.370000e-11 78.7


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 TraesCS1D01G128700 chr1D 141897940 141901091 3151 True 2054.333333 5821 94.270667 1 3152 3 chr1D.!!$R2 3151
1 TraesCS1D01G128700 chr1B 196059905 196063327 3422 True 2310.000000 3493 92.748500 1 3151 2 chr1B.!!$R1 3150
2 TraesCS1D01G128700 chr1A 148744347 148746419 2072 False 940.000000 1943 90.447333 539 3132 3 chr1A.!!$F2 2593

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
522 524 0.033781 TCCGTTTGGGATCGTTCGTT 59.966 50.0 0.0 0.0 40.94 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2257 2662 0.026285 GCCGTTGGATTTCGATCGTG 59.974 55.0 15.94 0.0 0.0 4.35 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
31 32 0.325933 TGGGAGGTGATGACTGCTTG 59.674 55.000 0.00 0.00 0.00 4.01
43 44 0.800631 ACTGCTTGTGTGATCATGCG 59.199 50.000 0.00 0.00 40.02 4.73
267 268 8.865001 GCAATCAGTAGATCTATCGGTTTAATC 58.135 37.037 5.57 0.00 31.90 1.75
292 293 6.162079 TCTTTTCATGTGCACAAACTTTGAA 58.838 32.000 25.72 23.84 0.00 2.69
294 295 7.978414 TCTTTTCATGTGCACAAACTTTGAATA 59.022 29.630 25.44 20.94 0.00 1.75
295 296 7.697352 TTTCATGTGCACAAACTTTGAATAG 57.303 32.000 25.44 6.90 0.00 1.73
296 297 6.389830 TCATGTGCACAAACTTTGAATAGT 57.610 33.333 25.72 0.00 0.00 2.12
297 298 6.804677 TCATGTGCACAAACTTTGAATAGTT 58.195 32.000 25.72 0.00 39.97 2.24
298 299 7.264221 TCATGTGCACAAACTTTGAATAGTTT 58.736 30.769 25.72 0.00 46.42 2.66
299 300 7.763528 TCATGTGCACAAACTTTGAATAGTTTT 59.236 29.630 25.72 0.00 43.85 2.43
300 301 7.288317 TGTGCACAAACTTTGAATAGTTTTG 57.712 32.000 19.28 0.00 43.85 2.44
301 302 6.870965 TGTGCACAAACTTTGAATAGTTTTGT 59.129 30.769 19.28 0.00 43.85 2.83
302 303 8.029522 TGTGCACAAACTTTGAATAGTTTTGTA 58.970 29.630 19.28 0.00 43.85 2.41
419 420 9.906660 TGCTTAATTTTATTGTACTTGACCTTG 57.093 29.630 0.00 0.00 0.00 3.61
420 421 9.353999 GCTTAATTTTATTGTACTTGACCTTGG 57.646 33.333 0.00 0.00 0.00 3.61
421 422 9.855021 CTTAATTTTATTGTACTTGACCTTGGG 57.145 33.333 0.00 0.00 0.00 4.12
422 423 6.850752 ATTTTATTGTACTTGACCTTGGGG 57.149 37.500 0.00 0.00 38.88 4.96
434 435 0.250901 CCTTGGGGCGGATAAGATGG 60.251 60.000 0.00 0.00 0.00 3.51
451 452 1.523032 GGAACATAAGTCCGGGCGG 60.523 63.158 0.00 0.00 0.00 6.13
479 481 6.742264 ACGGTTTTATTATCGCTTTAAAACGG 59.258 34.615 10.82 16.64 42.54 4.44
482 484 7.750014 GGTTTTATTATCGCTTTAAAACGGACA 59.250 33.333 10.82 0.00 42.54 4.02
521 523 1.667151 TCCGTTTGGGATCGTTCGT 59.333 52.632 0.00 0.00 40.94 3.85
522 524 0.033781 TCCGTTTGGGATCGTTCGTT 59.966 50.000 0.00 0.00 40.94 3.85
523 525 0.165079 CCGTTTGGGATCGTTCGTTG 59.835 55.000 0.00 0.00 38.47 4.10
524 526 0.165079 CGTTTGGGATCGTTCGTTGG 59.835 55.000 0.00 0.00 0.00 3.77
525 527 1.232119 GTTTGGGATCGTTCGTTGGT 58.768 50.000 0.00 0.00 0.00 3.67
526 528 1.069500 GTTTGGGATCGTTCGTTGGTG 60.069 52.381 0.00 0.00 0.00 4.17
527 529 0.107081 TTGGGATCGTTCGTTGGTGT 59.893 50.000 0.00 0.00 0.00 4.16
528 530 0.107081 TGGGATCGTTCGTTGGTGTT 59.893 50.000 0.00 0.00 0.00 3.32
529 531 0.515564 GGGATCGTTCGTTGGTGTTG 59.484 55.000 0.00 0.00 0.00 3.33
530 532 0.515564 GGATCGTTCGTTGGTGTTGG 59.484 55.000 0.00 0.00 0.00 3.77
532 534 1.512156 ATCGTTCGTTGGTGTTGGGC 61.512 55.000 0.00 0.00 0.00 5.36
534 536 1.720694 CGTTCGTTGGTGTTGGGCTT 61.721 55.000 0.00 0.00 0.00 4.35
535 537 1.310904 GTTCGTTGGTGTTGGGCTTA 58.689 50.000 0.00 0.00 0.00 3.09
537 539 2.279935 TCGTTGGTGTTGGGCTTATT 57.720 45.000 0.00 0.00 0.00 1.40
1203 1212 4.099170 CCGCTTCGTCGTCGTCCT 62.099 66.667 1.33 0.00 38.33 3.85
1265 1274 2.432628 GACCTTGACCGGCACTCG 60.433 66.667 0.00 0.00 38.88 4.18
1596 1605 1.593209 GTGTTCCACCGCGTCTCAA 60.593 57.895 4.92 0.00 0.00 3.02
2072 2166 5.644644 GAATCCATTGAACTCCATGTTGTC 58.355 41.667 0.00 0.00 39.30 3.18
2175 2580 3.620821 CGGCAAGGAAACAAAACACAAAT 59.379 39.130 0.00 0.00 0.00 2.32
2176 2581 4.493872 CGGCAAGGAAACAAAACACAAATG 60.494 41.667 0.00 0.00 0.00 2.32
2177 2582 4.341935 GCAAGGAAACAAAACACAAATGC 58.658 39.130 0.00 0.00 0.00 3.56
2183 2588 2.553086 ACAAAACACAAATGCTGCTGG 58.447 42.857 0.00 0.00 0.00 4.85
2199 2604 1.276138 GCTGGCTAAAAGCAAATGGGT 59.724 47.619 0.78 0.00 44.75 4.51
2207 2612 1.839424 AAGCAAATGGGTGAGGCTAC 58.161 50.000 0.00 0.00 33.80 3.58
2208 2613 0.698238 AGCAAATGGGTGAGGCTACA 59.302 50.000 0.00 0.00 32.09 2.74
2209 2614 0.811281 GCAAATGGGTGAGGCTACAC 59.189 55.000 8.11 8.11 39.70 2.90
2210 2615 1.086696 CAAATGGGTGAGGCTACACG 58.913 55.000 9.81 0.00 41.12 4.49
2211 2616 0.690762 AAATGGGTGAGGCTACACGT 59.309 50.000 9.81 0.00 41.12 4.49
2212 2617 0.249398 AATGGGTGAGGCTACACGTC 59.751 55.000 9.81 6.58 41.12 4.34
2213 2618 0.902984 ATGGGTGAGGCTACACGTCA 60.903 55.000 9.81 10.49 40.76 4.35
2214 2619 1.215647 GGGTGAGGCTACACGTCAG 59.784 63.158 9.81 0.00 43.50 3.51
2215 2620 1.533469 GGGTGAGGCTACACGTCAGT 61.533 60.000 9.81 0.00 43.50 3.41
2216 2621 0.317479 GGTGAGGCTACACGTCAGTT 59.683 55.000 9.81 0.00 43.50 3.16
2217 2622 1.419374 GTGAGGCTACACGTCAGTTG 58.581 55.000 0.00 0.00 43.50 3.16
2218 2623 1.000607 GTGAGGCTACACGTCAGTTGA 60.001 52.381 0.00 0.00 43.50 3.18
2219 2624 1.000607 TGAGGCTACACGTCAGTTGAC 60.001 52.381 2.16 2.16 38.23 3.18
2220 2625 1.269998 GAGGCTACACGTCAGTTGACT 59.730 52.381 10.27 0.00 42.66 3.41
2221 2626 1.000163 AGGCTACACGTCAGTTGACTG 60.000 52.381 10.27 4.77 42.66 3.51
2257 2662 2.971261 GGTCAGTCGATTTTTCAAACGC 59.029 45.455 0.00 0.00 0.00 4.84
2270 2675 1.392168 TCAAACGCACGATCGAAATCC 59.608 47.619 24.34 3.79 0.00 3.01
2277 2682 1.272715 CGATCGAAATCCAACGGCG 59.727 57.895 10.26 4.80 0.00 6.46
2298 2703 2.458620 CCCGACCTTTCTTCTACCTCT 58.541 52.381 0.00 0.00 0.00 3.69
2315 2720 7.514721 TCTACCTCTATCTCTTCTTCTTCTCC 58.485 42.308 0.00 0.00 0.00 3.71
2447 2871 1.610038 CCCGCCCTCGTTTAAGTTTTT 59.390 47.619 0.00 0.00 0.00 1.94
2525 2949 4.770874 GTTTAGCCGCTGCCCCGA 62.771 66.667 2.16 0.00 38.69 5.14
2540 2965 1.182385 CCCGACCATCTCTCTAGGCC 61.182 65.000 0.00 0.00 0.00 5.19
2645 3070 5.713807 CCCTAAGTTAGATACTGGGGTAGT 58.286 45.833 11.66 0.00 41.80 2.73
2651 3076 1.504221 AGATACTGGGGTAGTCCTCCC 59.496 57.143 0.00 0.00 43.90 4.30
2682 3107 3.117552 TCCTTCTCCTTCCTTACCTCC 57.882 52.381 0.00 0.00 0.00 4.30
2703 3128 1.965754 GCTCACTCCGGCCATCTCTT 61.966 60.000 2.24 0.00 0.00 2.85
2761 3186 7.217070 CGATTGACATTTAGCTAAACTGAAAGC 59.783 37.037 20.85 17.47 37.60 3.51
2821 3246 4.351874 TGCCATAATAGCCTACACTTCC 57.648 45.455 0.00 0.00 0.00 3.46
2880 3313 7.692460 AAACATCTGCATCTAGTTTGATTGA 57.308 32.000 6.07 0.00 31.81 2.57
2882 3315 5.587844 ACATCTGCATCTAGTTTGATTGACC 59.412 40.000 0.00 0.00 0.00 4.02
2948 3381 0.671796 GGTTGGCCGCTTGTTTAAGT 59.328 50.000 0.00 0.00 36.27 2.24
2983 3416 3.834489 TGGTGTTTGGTTTCATGCAAT 57.166 38.095 0.00 0.00 0.00 3.56
2988 3421 5.508825 GGTGTTTGGTTTCATGCAATGTCTA 60.509 40.000 0.00 0.00 46.80 2.59
3033 3466 1.064003 TGGTGAGGTTACCAGCACAT 58.936 50.000 22.30 0.00 45.46 3.21
3050 3483 2.866156 CACATATGGGCGTGTAGAACAG 59.134 50.000 7.80 0.00 0.00 3.16
3081 3514 4.516698 ACACACAAAAGATAGCAAGGAGTG 59.483 41.667 0.00 0.00 0.00 3.51
3107 3540 8.040716 AGCAATTTAACATACTACCACACTTC 57.959 34.615 0.00 0.00 0.00 3.01
3108 3541 7.120726 AGCAATTTAACATACTACCACACTTCC 59.879 37.037 0.00 0.00 0.00 3.46
3151 3584 7.545362 AGCAAGCAGTTCTAAACATAGTATG 57.455 36.000 8.66 8.66 0.00 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.802960 CACACAAGCAGTCATCACCTC 59.197 52.381 0.00 0.00 0.00 3.85
53 54 3.194861 GCCATTACGCTCATACTCAACA 58.805 45.455 0.00 0.00 0.00 3.33
54 55 3.194861 TGCCATTACGCTCATACTCAAC 58.805 45.455 0.00 0.00 0.00 3.18
57 58 1.795286 GCTGCCATTACGCTCATACTC 59.205 52.381 0.00 0.00 0.00 2.59
60 61 2.037641 AGATGCTGCCATTACGCTCATA 59.962 45.455 0.00 0.00 0.00 2.15
267 268 5.806502 TCAAAGTTTGTGCACATGAAAAGAG 59.193 36.000 22.39 7.30 0.00 2.85
273 274 6.389830 ACTATTCAAAGTTTGTGCACATGA 57.610 33.333 22.39 17.85 0.00 3.07
351 352 9.264782 GATCAAACACAAAAACATGTTCAAAAG 57.735 29.630 12.39 5.25 38.08 2.27
406 407 1.373435 CGCCCCAAGGTCAAGTACA 59.627 57.895 0.00 0.00 34.57 2.90
419 420 0.472471 TGTTCCATCTTATCCGCCCC 59.528 55.000 0.00 0.00 0.00 5.80
420 421 2.568623 ATGTTCCATCTTATCCGCCC 57.431 50.000 0.00 0.00 0.00 6.13
421 422 4.642429 ACTTATGTTCCATCTTATCCGCC 58.358 43.478 0.00 0.00 0.00 6.13
422 423 4.691216 GGACTTATGTTCCATCTTATCCGC 59.309 45.833 0.00 0.00 0.00 5.54
434 435 1.518774 TCCGCCCGGACTTATGTTC 59.481 57.895 0.73 0.00 39.76 3.18
449 450 5.834239 AAGCGATAATAAAACCGTATCCG 57.166 39.130 0.00 0.00 0.00 4.18
453 454 7.902403 CCGTTTTAAAGCGATAATAAAACCGTA 59.098 33.333 23.70 0.00 42.39 4.02
461 462 9.493206 GATTTTGTCCGTTTTAAAGCGATAATA 57.507 29.630 23.70 11.55 34.38 0.98
465 466 5.158494 GGATTTTGTCCGTTTTAAAGCGAT 58.842 37.500 23.70 9.46 37.23 4.58
466 467 4.538917 GGATTTTGTCCGTTTTAAAGCGA 58.461 39.130 23.70 8.84 37.23 4.93
510 512 0.515564 CAACACCAACGAACGATCCC 59.484 55.000 0.14 0.00 0.00 3.85
511 513 0.515564 CCAACACCAACGAACGATCC 59.484 55.000 0.14 0.00 0.00 3.36
513 515 1.512156 GCCCAACACCAACGAACGAT 61.512 55.000 0.14 0.00 0.00 3.73
515 517 1.720694 AAGCCCAACACCAACGAACG 61.721 55.000 0.00 0.00 0.00 3.95
516 518 1.310904 TAAGCCCAACACCAACGAAC 58.689 50.000 0.00 0.00 0.00 3.95
521 523 1.540267 CGGAATAAGCCCAACACCAA 58.460 50.000 0.00 0.00 0.00 3.67
522 524 0.322997 CCGGAATAAGCCCAACACCA 60.323 55.000 0.00 0.00 0.00 4.17
523 525 0.034863 TCCGGAATAAGCCCAACACC 60.035 55.000 0.00 0.00 0.00 4.16
524 526 1.828979 TTCCGGAATAAGCCCAACAC 58.171 50.000 14.35 0.00 0.00 3.32
525 527 2.818751 ATTCCGGAATAAGCCCAACA 57.181 45.000 28.25 0.00 0.00 3.33
526 528 4.023193 CACATATTCCGGAATAAGCCCAAC 60.023 45.833 34.40 0.00 36.90 3.77
527 529 4.141287 CACATATTCCGGAATAAGCCCAA 58.859 43.478 34.40 17.10 36.90 4.12
528 530 3.497763 CCACATATTCCGGAATAAGCCCA 60.498 47.826 34.40 17.79 36.90 5.36
529 531 3.081804 CCACATATTCCGGAATAAGCCC 58.918 50.000 34.40 0.00 36.90 5.19
530 532 4.015872 TCCACATATTCCGGAATAAGCC 57.984 45.455 34.40 0.00 36.90 4.35
532 534 4.330074 GCGATCCACATATTCCGGAATAAG 59.670 45.833 34.40 31.57 36.90 1.73
534 536 3.259625 TGCGATCCACATATTCCGGAATA 59.740 43.478 33.28 33.28 37.64 1.75
535 537 2.038426 TGCGATCCACATATTCCGGAAT 59.962 45.455 31.30 31.30 31.18 3.01
537 539 1.044611 TGCGATCCACATATTCCGGA 58.955 50.000 0.00 0.00 0.00 5.14
905 914 0.099968 GCCGCAGATCTACACGTACA 59.900 55.000 0.00 0.00 0.00 2.90
1203 1212 1.407936 GAGCTGCTGGATAGAGGTGA 58.592 55.000 7.01 0.00 0.00 4.02
1265 1274 1.208293 GAGGATGTGGAGGACAAGGAC 59.792 57.143 0.00 0.00 38.36 3.85
1771 1780 2.279741 GCAAACCATGCGAGATACTGA 58.720 47.619 0.00 0.00 46.87 3.41
2072 2166 2.202932 CCCTTCCACAGCCGATCG 60.203 66.667 8.51 8.51 0.00 3.69
2183 2588 2.675032 GCCTCACCCATTTGCTTTTAGC 60.675 50.000 0.00 0.00 42.82 3.09
2199 2604 1.000607 GTCAACTGACGTGTAGCCTCA 60.001 52.381 0.00 0.00 35.12 3.86
2225 2630 9.458374 GAAAAATCGACTGACCTGATTTAAAAA 57.542 29.630 0.00 0.00 40.42 1.94
2226 2631 8.625651 TGAAAAATCGACTGACCTGATTTAAAA 58.374 29.630 0.00 0.00 40.42 1.52
2227 2632 8.160521 TGAAAAATCGACTGACCTGATTTAAA 57.839 30.769 0.00 0.00 40.42 1.52
2228 2633 7.737972 TGAAAAATCGACTGACCTGATTTAA 57.262 32.000 0.00 0.00 40.42 1.52
2229 2634 7.737972 TTGAAAAATCGACTGACCTGATTTA 57.262 32.000 0.00 0.00 40.42 1.40
2230 2635 6.633500 TTGAAAAATCGACTGACCTGATTT 57.367 33.333 0.00 0.00 42.44 2.17
2231 2636 6.438763 GTTTGAAAAATCGACTGACCTGATT 58.561 36.000 0.00 0.00 33.94 2.57
2232 2637 5.334105 CGTTTGAAAAATCGACTGACCTGAT 60.334 40.000 0.00 0.00 0.00 2.90
2233 2638 4.025229 CGTTTGAAAAATCGACTGACCTGA 60.025 41.667 0.00 0.00 0.00 3.86
2234 2639 4.211389 CGTTTGAAAAATCGACTGACCTG 58.789 43.478 0.00 0.00 0.00 4.00
2235 2640 3.303791 GCGTTTGAAAAATCGACTGACCT 60.304 43.478 0.00 0.00 0.00 3.85
2257 2662 0.026285 GCCGTTGGATTTCGATCGTG 59.974 55.000 15.94 0.00 0.00 4.35
2277 2682 0.903236 AGGTAGAAGAAAGGTCGGGC 59.097 55.000 0.00 0.00 0.00 6.13
2282 2687 7.648770 AGAAGAGATAGAGGTAGAAGAAAGGT 58.351 38.462 0.00 0.00 0.00 3.50
2298 2703 3.634448 CGGCTGGAGAAGAAGAAGAGATA 59.366 47.826 0.00 0.00 0.00 1.98
2327 2744 3.195698 GATGGTCGCAGGCGGTTC 61.196 66.667 14.24 5.04 40.25 3.62
2413 2837 3.631046 CGGGCCTAGAGGGATGGC 61.631 72.222 0.84 0.00 45.42 4.40
2447 2871 2.357034 GTGCACTTCGCCGGAGAA 60.357 61.111 19.99 19.99 41.33 2.87
2448 2872 4.373116 GGTGCACTTCGCCGGAGA 62.373 66.667 17.98 3.81 41.33 3.71
2498 2922 2.435410 GGCTAAACCGTCGGTGGG 60.435 66.667 19.67 12.01 35.34 4.61
2520 2944 1.182385 GCCTAGAGAGATGGTCGGGG 61.182 65.000 0.00 0.00 0.00 5.73
2524 2948 1.811645 GCGGGCCTAGAGAGATGGTC 61.812 65.000 0.84 0.00 0.00 4.02
2525 2949 1.834822 GCGGGCCTAGAGAGATGGT 60.835 63.158 0.84 0.00 0.00 3.55
2563 2988 3.041940 GGTGGTGCACTTCGTCGG 61.042 66.667 17.98 0.00 34.40 4.79
2610 3035 1.073098 ACTTAGGGTTCAAGGTGGGG 58.927 55.000 0.00 0.00 0.00 4.96
2617 3042 5.427481 CCCCAGTATCTAACTTAGGGTTCAA 59.573 44.000 0.00 0.00 41.56 2.69
2651 3076 3.724914 GAGAAGGAAGGGGCTCGCG 62.725 68.421 0.00 0.00 0.00 5.87
2660 3085 3.452990 GGAGGTAAGGAAGGAGAAGGAAG 59.547 52.174 0.00 0.00 0.00 3.46
2693 3118 1.468914 GTCGGTTTTCAAGAGATGGCC 59.531 52.381 0.00 0.00 0.00 5.36
2703 3128 4.202377 TGAAATAGGGTCAGTCGGTTTTCA 60.202 41.667 0.00 0.00 31.50 2.69
2748 3173 9.840427 TTCTTATGTATTTGCTTTCAGTTTAGC 57.160 29.630 0.00 0.00 37.89 3.09
2761 3186 8.073768 AGAACCAAACACGTTCTTATGTATTTG 58.926 33.333 0.00 0.00 46.01 2.32
2805 3230 5.454187 CCGGATTTGGAAGTGTAGGCTATTA 60.454 44.000 0.00 0.00 0.00 0.98
2880 3313 1.962100 GTAGGCTAGAAGGTATGCGGT 59.038 52.381 0.00 0.00 0.00 5.68
2882 3315 3.381949 GTTGTAGGCTAGAAGGTATGCG 58.618 50.000 4.08 0.00 0.00 4.73
2948 3381 3.883830 ACACCATGCTTTGTGTTTTCA 57.116 38.095 3.86 0.00 42.82 2.69
2983 3416 5.929992 CGAAAAGGTTACCAGACAATAGACA 59.070 40.000 3.51 0.00 0.00 3.41
2988 3421 2.817844 GCCGAAAAGGTTACCAGACAAT 59.182 45.455 3.51 0.00 43.70 2.71
3033 3466 0.177141 GGCTGTTCTACACGCCCATA 59.823 55.000 8.27 0.00 36.82 2.74
3050 3483 3.733443 ATCTTTTGTGTGTCTTTGGGC 57.267 42.857 0.00 0.00 0.00 5.36
3081 3514 7.611213 AGTGTGGTAGTATGTTAAATTGCTC 57.389 36.000 0.00 0.00 0.00 4.26
3107 3540 7.649306 GCTTGCTATGGTTTAGAATTATGTTGG 59.351 37.037 0.00 0.00 0.00 3.77
3108 3541 8.190122 TGCTTGCTATGGTTTAGAATTATGTTG 58.810 33.333 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.