Multiple sequence alignment - TraesCS2D01G067500

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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 TraesCS2D01G067500 chr2D 100.000 5211 0 0 1 5211 28095639 28090429 0.000000e+00 9624.0
1 TraesCS2D01G067500 chr2D 84.748 2898 378 40 1388 4263 27957294 27960149 0.000000e+00 2844.0
2 TraesCS2D01G067500 chr2D 82.847 3154 441 65 1388 4502 28001271 27998179 0.000000e+00 2736.0
3 TraesCS2D01G067500 chr2D 85.785 1421 142 39 2 1398 27955848 27957232 0.000000e+00 1450.0
4 TraesCS2D01G067500 chr2D 81.786 571 54 25 4 562 28002685 28002153 2.880000e-117 433.0
5 TraesCS2D01G067500 chr2D 84.840 343 38 9 4829 5167 28085557 28085225 3.010000e-87 333.0
6 TraesCS2D01G067500 chr2D 84.120 233 29 2 4590 4819 28085831 28085604 8.790000e-53 219.0
7 TraesCS2D01G067500 chr2B 83.493 3126 422 65 1388 4479 44754243 44751178 0.000000e+00 2828.0
8 TraesCS2D01G067500 chr2B 86.717 2251 267 22 1388 3633 45542869 45545092 0.000000e+00 2471.0
9 TraesCS2D01G067500 chr2B 83.810 2551 339 44 1388 3915 45032634 45030135 0.000000e+00 2355.0
10 TraesCS2D01G067500 chr2B 92.991 1498 100 4 2975 4472 45692137 45693629 0.000000e+00 2180.0
11 TraesCS2D01G067500 chr2B 92.867 1500 86 11 1498 2982 45689269 45690762 0.000000e+00 2158.0
12 TraesCS2D01G067500 chr2B 87.510 1273 96 39 232 1472 45688029 45689270 0.000000e+00 1411.0
13 TraesCS2D01G067500 chr2B 84.497 1361 146 44 75 1400 45137748 45136418 0.000000e+00 1284.0
14 TraesCS2D01G067500 chr2B 92.568 767 48 4 638 1398 45033459 45032696 0.000000e+00 1092.0
15 TraesCS2D01G067500 chr2B 78.222 1226 157 54 217 1396 44755468 44754307 0.000000e+00 684.0
16 TraesCS2D01G067500 chr2B 76.954 1241 234 36 3052 4263 45134688 45133471 0.000000e+00 660.0
17 TraesCS2D01G067500 chr2B 75.717 1186 235 32 3120 4269 45536554 45537722 3.550000e-151 545.0
18 TraesCS2D01G067500 chr2B 75.758 1122 222 35 3052 4147 45668285 45669382 2.150000e-143 520.0
19 TraesCS2D01G067500 chr2B 88.889 315 26 6 4899 5209 44901804 44902113 3.810000e-101 379.0
20 TraesCS2D01G067500 chr2B 82.127 442 77 2 956 1396 45542365 45542805 1.370000e-100 377.0
21 TraesCS2D01G067500 chr2B 80.769 442 68 6 3830 4267 45038302 45037874 3.890000e-86 329.0
22 TraesCS2D01G067500 chr2B 87.778 270 27 4 1 264 45540693 45540962 1.410000e-80 311.0
23 TraesCS2D01G067500 chr2B 87.552 241 22 5 4596 4830 44901448 44901686 6.650000e-69 272.0
24 TraesCS2D01G067500 chr2B 85.660 265 28 4 5 265 105097499 105097757 2.390000e-68 270.0
25 TraesCS2D01G067500 chr2B 84.528 265 31 4 5 265 105083641 105083899 2.410000e-63 254.0
26 TraesCS2D01G067500 chr2B 85.714 231 23 5 4 229 44761919 44761694 8.720000e-58 235.0
27 TraesCS2D01G067500 chr2B 75.513 633 73 42 4 613 45034751 45034178 8.720000e-58 235.0
28 TraesCS2D01G067500 chr2B 93.077 130 9 0 473 602 45033597 45033468 1.920000e-44 191.0
29 TraesCS2D01G067500 chr2B 95.413 109 5 0 4469 4577 45693754 45693862 1.930000e-39 174.0
30 TraesCS2D01G067500 chr2B 97.727 44 1 0 5168 5211 45694406 45694449 5.600000e-10 76.8
31 TraesCS2D01G067500 chr2B 95.000 40 2 0 272 311 105097780 105097819 4.360000e-06 63.9
32 TraesCS2D01G067500 chr2A 83.529 2902 405 37 1388 4265 30164423 30161571 0.000000e+00 2643.0
33 TraesCS2D01G067500 chr2A 95.884 1555 59 4 2771 4325 30201816 30200267 0.000000e+00 2512.0
34 TraesCS2D01G067500 chr2A 95.122 1394 63 2 1301 2694 30203201 30201813 0.000000e+00 2193.0
35 TraesCS2D01G067500 chr2A 86.271 1668 221 7 1391 3053 30301462 30303126 0.000000e+00 1805.0
36 TraesCS2D01G067500 chr2A 85.174 1349 156 27 75 1407 30165796 30164476 0.000000e+00 1343.0
37 TraesCS2D01G067500 chr2A 85.414 1330 83 50 1 1303 30213470 30212225 0.000000e+00 1279.0
38 TraesCS2D01G067500 chr2A 81.187 1297 159 47 114 1396 30188868 30187643 0.000000e+00 965.0
39 TraesCS2D01G067500 chr2A 87.781 401 31 5 4829 5211 30199819 30199419 2.210000e-123 453.0
40 TraesCS2D01G067500 chr2A 85.714 343 35 9 4829 5167 30277764 30277432 2.990000e-92 350.0
41 TraesCS2D01G067500 chr2A 81.279 438 65 6 3834 4267 30185029 30184605 6.460000e-89 339.0
42 TraesCS2D01G067500 chr2A 92.827 237 7 7 4595 4830 30200082 30199855 8.360000e-88 335.0
43 TraesCS2D01G067500 chr2A 82.734 278 29 6 4 274 22273529 22273794 4.060000e-56 230.0
44 TraesCS2D01G067500 chr2A 83.794 253 22 5 78 311 22435251 22435503 6.790000e-54 222.0
45 TraesCS2D01G067500 chr2A 82.661 248 31 4 4590 4830 30278042 30277800 5.290000e-50 209.0
46 TraesCS2D01G067500 chr1A 86.691 278 25 4 4 274 242073066 242072794 1.100000e-76 298.0
47 TraesCS2D01G067500 chr1A 83.333 330 31 9 4 314 240954348 240954024 3.070000e-72 283.0


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 TraesCS2D01G067500 chr2D 28090429 28095639 5210 True 9624.00 9624 100.00000 1 5211 1 chr2D.!!$R1 5210
1 TraesCS2D01G067500 chr2D 27955848 27960149 4301 False 2147.00 2844 85.26650 2 4263 2 chr2D.!!$F1 4261
2 TraesCS2D01G067500 chr2D 27998179 28002685 4506 True 1584.50 2736 82.31650 4 4502 2 chr2D.!!$R2 4498
3 TraesCS2D01G067500 chr2D 28085225 28085831 606 True 276.00 333 84.48000 4590 5167 2 chr2D.!!$R3 577
4 TraesCS2D01G067500 chr2B 44751178 44755468 4290 True 1756.00 2828 80.85750 217 4479 2 chr2B.!!$R2 4262
5 TraesCS2D01G067500 chr2B 45688029 45694449 6420 False 1199.96 2180 93.30160 232 5211 5 chr2B.!!$F5 4979
6 TraesCS2D01G067500 chr2B 45133471 45137748 4277 True 972.00 1284 80.72550 75 4263 2 chr2B.!!$R4 4188
7 TraesCS2D01G067500 chr2B 45536554 45545092 8538 False 926.00 2471 83.08475 1 4269 4 chr2B.!!$F4 4268
8 TraesCS2D01G067500 chr2B 45030135 45038302 8167 True 840.40 2355 85.14740 4 4267 5 chr2B.!!$R3 4263
9 TraesCS2D01G067500 chr2B 45668285 45669382 1097 False 520.00 520 75.75800 3052 4147 1 chr2B.!!$F1 1095
10 TraesCS2D01G067500 chr2B 44901448 44902113 665 False 325.50 379 88.22050 4596 5209 2 chr2B.!!$F3 613
11 TraesCS2D01G067500 chr2A 30161571 30165796 4225 True 1993.00 2643 84.35150 75 4265 2 chr2A.!!$R2 4190
12 TraesCS2D01G067500 chr2A 30301462 30303126 1664 False 1805.00 1805 86.27100 1391 3053 1 chr2A.!!$F3 1662
13 TraesCS2D01G067500 chr2A 30199419 30203201 3782 True 1373.25 2512 92.90350 1301 5211 4 chr2A.!!$R4 3910
14 TraesCS2D01G067500 chr2A 30212225 30213470 1245 True 1279.00 1279 85.41400 1 1303 1 chr2A.!!$R1 1302
15 TraesCS2D01G067500 chr2A 30184605 30188868 4263 True 652.00 965 81.23300 114 4267 2 chr2A.!!$R3 4153
16 TraesCS2D01G067500 chr2A 30277432 30278042 610 True 279.50 350 84.18750 4590 5167 2 chr2A.!!$R5 577

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
388 4606 0.254747 CATCCCACGTTACCCCATGT 59.745 55.000 0.0 0.0 0.00 3.21 F
390 4608 0.772384 TCCCACGTTACCCCATGTTT 59.228 50.000 0.0 0.0 0.00 2.83 F
2220 8514 1.268352 TCAAACCAAATTTCGGGCTCG 59.732 47.619 0.0 0.0 37.82 5.03 F
3865 11741 1.303309 GAATGGGTTGCCAGATCTCG 58.697 55.000 0.0 0.0 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 8120 1.544724 GTCCAACAAGGGCATTGCTA 58.455 50.000 12.40 0.0 43.39 3.49 R
2449 8743 1.270907 AGTCCCTTGCACTGACCTAG 58.729 55.000 5.97 0.0 0.00 3.02 R
4036 11914 1.569493 CACTTCTTCGCACCGTTGG 59.431 57.895 0.00 0.0 0.00 3.77 R
4948 13359 1.153756 CCAAGAACAAGGGCAGGGT 59.846 57.895 0.00 0.0 0.00 4.34 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
138 4303 1.585895 GCCTAGGGTTTCTCCTTCCT 58.414 55.000 11.72 0.00 38.30 3.36
172 4347 0.319469 GCTAGCTGGATTCGCTCTCC 60.319 60.000 7.70 0.00 38.86 3.71
177 4352 1.615124 TGGATTCGCTCTCCCCCAA 60.615 57.895 0.00 0.00 31.32 4.12
237 4423 4.116926 CCATTTCCTTGGCAGGCA 57.883 55.556 0.00 0.00 40.58 4.75
319 4532 6.267014 AGCTAGATTCCCAATTTTCCATGATG 59.733 38.462 0.00 0.00 0.00 3.07
323 4536 7.506114 AGATTCCCAATTTTCCATGATGAATG 58.494 34.615 0.00 0.00 35.89 2.67
324 4537 6.623979 TTCCCAATTTTCCATGATGAATGT 57.376 33.333 0.00 0.00 34.11 2.71
325 4538 7.730672 TTCCCAATTTTCCATGATGAATGTA 57.269 32.000 0.00 0.00 34.11 2.29
326 4539 7.730672 TCCCAATTTTCCATGATGAATGTAA 57.269 32.000 0.00 0.00 34.11 2.41
327 4540 8.143673 TCCCAATTTTCCATGATGAATGTAAA 57.856 30.769 0.00 0.00 34.11 2.01
328 4541 8.770322 TCCCAATTTTCCATGATGAATGTAAAT 58.230 29.630 0.00 0.00 33.45 1.40
332 4545 9.962809 AATTTTCCATGATGAATGTAAATTGGT 57.037 25.926 0.00 0.00 37.29 3.67
350 4563 7.435068 AATTGGTTGCGATATGGTTATCTAC 57.565 36.000 0.00 0.00 33.39 2.59
374 4590 3.618150 CGAAATTTGCATTGTTCCATCCC 59.382 43.478 0.00 0.00 0.00 3.85
387 4605 0.465460 CCATCCCACGTTACCCCATG 60.465 60.000 0.00 0.00 0.00 3.66
388 4606 0.254747 CATCCCACGTTACCCCATGT 59.745 55.000 0.00 0.00 0.00 3.21
389 4607 0.996583 ATCCCACGTTACCCCATGTT 59.003 50.000 0.00 0.00 0.00 2.71
390 4608 0.772384 TCCCACGTTACCCCATGTTT 59.228 50.000 0.00 0.00 0.00 2.83
393 4611 2.552591 CCCACGTTACCCCATGTTTGTA 60.553 50.000 0.00 0.00 0.00 2.41
394 4612 3.147629 CCACGTTACCCCATGTTTGTAA 58.852 45.455 0.00 0.00 0.00 2.41
396 4614 4.218852 CCACGTTACCCCATGTTTGTAAAT 59.781 41.667 0.00 0.00 0.00 1.40
397 4615 5.279056 CCACGTTACCCCATGTTTGTAAATT 60.279 40.000 0.00 0.00 0.00 1.82
398 4616 5.631512 CACGTTACCCCATGTTTGTAAATTG 59.368 40.000 0.00 0.00 0.00 2.32
400 4618 3.694043 ACCCCATGTTTGTAAATTGGC 57.306 42.857 0.00 0.00 0.00 4.52
401 4619 2.028567 ACCCCATGTTTGTAAATTGGCG 60.029 45.455 0.00 0.00 0.00 5.69
402 4620 2.615869 CCCATGTTTGTAAATTGGCGG 58.384 47.619 0.00 0.00 0.00 6.13
403 4621 1.999024 CCATGTTTGTAAATTGGCGGC 59.001 47.619 0.00 0.00 0.00 6.53
404 4622 2.353605 CCATGTTTGTAAATTGGCGGCT 60.354 45.455 11.43 0.00 0.00 5.52
405 4623 2.430546 TGTTTGTAAATTGGCGGCTG 57.569 45.000 11.43 0.00 0.00 4.85
468 4691 7.879677 TGAATCAGTTTGCTCTCTGAAGAAATA 59.120 33.333 8.71 0.00 42.67 1.40
504 4732 5.305902 TGAGTGGTTCAGGTCTGTTTATGTA 59.694 40.000 0.00 0.00 0.00 2.29
716 5670 8.908903 TCTTCCAGTTTTTATTTTGCTTACTGA 58.091 29.630 0.00 0.00 34.87 3.41
811 6951 4.464597 ACTTTTCTTTACCCTTGCAACACA 59.535 37.500 0.00 0.00 0.00 3.72
928 7097 2.679837 GGCATCCACATTCTACACACAG 59.320 50.000 0.00 0.00 0.00 3.66
931 7100 3.678056 TCCACATTCTACACACAGGAC 57.322 47.619 0.00 0.00 0.00 3.85
1476 7736 8.630917 AGCACACTTATACTGTCTCGTAATAAT 58.369 33.333 0.00 0.00 0.00 1.28
1730 7990 7.973048 TTCCAGAAACTATAGGTCACACTAT 57.027 36.000 4.43 0.00 37.44 2.12
1827 8120 6.827586 TCACTCAAAAACTTTAGTGTTGGT 57.172 33.333 0.00 2.90 40.18 3.67
2220 8514 1.268352 TCAAACCAAATTTCGGGCTCG 59.732 47.619 0.00 0.00 37.82 5.03
2731 9094 4.819105 TCTCACAATGACTTATCCGGTT 57.181 40.909 0.00 0.00 0.00 4.44
2732 9095 5.925506 TCTCACAATGACTTATCCGGTTA 57.074 39.130 0.00 0.00 0.00 2.85
2740 9103 3.962063 TGACTTATCCGGTTATGTGCCTA 59.038 43.478 14.05 0.00 0.00 3.93
2741 9104 4.591498 TGACTTATCCGGTTATGTGCCTAT 59.409 41.667 14.05 0.00 0.00 2.57
2813 9176 5.222547 ACAACTTGGAAGGGGAAATTCCTAT 60.223 40.000 12.28 0.00 45.45 2.57
2882 9245 3.385115 AGGGACTATGTTCGAATTCCCT 58.615 45.455 20.23 20.23 46.92 4.20
2939 9314 4.597079 TCTTCAGCAACTAAAACAAAGCG 58.403 39.130 0.00 0.00 0.00 4.68
3019 10776 6.953101 TGTTTCCTAGTATTGTCATGGCTTA 58.047 36.000 0.00 0.00 0.00 3.09
3036 10793 4.263905 TGGCTTATGTTCACTCTTTGGGAT 60.264 41.667 0.00 0.00 0.00 3.85
3046 10803 4.077982 TCACTCTTTGGGATAGAGGGGTAT 60.078 45.833 0.00 0.00 42.28 2.73
3048 10805 5.844516 CACTCTTTGGGATAGAGGGGTATTA 59.155 44.000 0.00 0.00 42.73 0.98
3059 10816 8.661345 GGATAGAGGGGTATTATTCACTCTTTT 58.339 37.037 0.25 0.00 36.73 2.27
3088 10872 4.805219 AGCGGTTTTATCATTTTCACCAC 58.195 39.130 0.00 0.00 0.00 4.16
3654 11469 7.315890 AGCCAAGCAACATTCTTTTAGATTAC 58.684 34.615 0.00 0.00 0.00 1.89
3865 11741 1.303309 GAATGGGTTGCCAGATCTCG 58.697 55.000 0.00 0.00 0.00 4.04
3995 11873 3.330405 TGAATCCATGTTCCCAGACAGAA 59.670 43.478 0.00 0.00 32.19 3.02
4036 11914 2.029020 TCATATGGCGCATGAGGAGTAC 60.029 50.000 10.83 0.00 0.00 2.73
4054 11952 1.157870 ACCAACGGTGCGAAGAAGTG 61.158 55.000 0.00 0.00 32.98 3.16
4055 11953 1.569493 CAACGGTGCGAAGAAGTGG 59.431 57.895 0.00 0.00 0.00 4.00
4056 11954 0.878523 CAACGGTGCGAAGAAGTGGA 60.879 55.000 0.00 0.00 0.00 4.02
4057 11955 0.878961 AACGGTGCGAAGAAGTGGAC 60.879 55.000 0.00 0.00 0.00 4.02
4058 11956 2.372690 CGGTGCGAAGAAGTGGACG 61.373 63.158 0.00 0.00 0.00 4.79
4061 11959 3.479269 GCGAAGAAGTGGACGCGG 61.479 66.667 12.47 0.00 41.49 6.46
4062 11960 2.257371 CGAAGAAGTGGACGCGGA 59.743 61.111 12.47 0.00 0.00 5.54
4063 11961 1.372499 CGAAGAAGTGGACGCGGAA 60.372 57.895 12.47 0.00 0.00 4.30
4064 11962 1.344942 CGAAGAAGTGGACGCGGAAG 61.345 60.000 12.47 0.00 0.00 3.46
4218 12119 6.457851 ACGTCGTGATGATTGATGAATATG 57.542 37.500 0.00 0.00 0.00 1.78
4332 12239 5.632959 TGACGAAACTAAAACAAACTGTGG 58.367 37.500 0.00 0.00 0.00 4.17
4353 12260 4.715792 TGGGGACAAATATGTGATTTGCAT 59.284 37.500 0.00 0.00 40.74 3.96
4358 12265 7.981225 GGGACAAATATGTGATTTGCATTTAGT 59.019 33.333 0.00 0.00 40.74 2.24
4410 12317 7.283625 ACCATGCTTTGTTGTAGATTTGTTA 57.716 32.000 0.00 0.00 0.00 2.41
4514 12551 8.755018 CATAAAGGTGTTTTTGAATGAACTGAC 58.245 33.333 0.00 0.00 28.84 3.51
4515 12552 6.530019 AAGGTGTTTTTGAATGAACTGACT 57.470 33.333 0.00 0.00 0.00 3.41
4522 12559 7.541783 TGTTTTTGAATGAACTGACTTGTTGAG 59.458 33.333 0.00 0.00 0.00 3.02
4577 12614 0.403271 ACACCTCTTTGCAGCCTGAT 59.597 50.000 0.00 0.00 0.00 2.90
4578 12615 0.809385 CACCTCTTTGCAGCCTGATG 59.191 55.000 0.00 0.00 0.00 3.07
4579 12616 0.323178 ACCTCTTTGCAGCCTGATGG 60.323 55.000 0.00 0.00 0.00 3.51
4582 12619 0.034767 TCTTTGCAGCCTGATGGAGG 60.035 55.000 0.00 0.00 46.13 4.30
4583 12620 0.034767 CTTTGCAGCCTGATGGAGGA 60.035 55.000 0.00 0.00 46.33 3.71
4584 12621 0.405198 TTTGCAGCCTGATGGAGGAA 59.595 50.000 0.00 0.00 46.33 3.36
4585 12622 0.405198 TTGCAGCCTGATGGAGGAAA 59.595 50.000 0.00 0.00 46.33 3.13
4586 12623 0.322816 TGCAGCCTGATGGAGGAAAC 60.323 55.000 0.00 0.00 46.33 2.78
4587 12624 0.034670 GCAGCCTGATGGAGGAAACT 60.035 55.000 0.00 0.00 46.33 2.66
4693 13049 5.048713 GGTTGTTTTGCAGCTATACAGAGTT 60.049 40.000 0.00 0.00 0.00 3.01
4698 13054 4.808414 TGCAGCTATACAGAGTTCAGTT 57.192 40.909 0.00 0.00 0.00 3.16
4701 13057 5.171476 GCAGCTATACAGAGTTCAGTTCAA 58.829 41.667 0.00 0.00 0.00 2.69
5033 13447 9.813080 CTTCTTGCTAAGTGTTTACATTAGTTC 57.187 33.333 10.73 0.00 0.00 3.01
5071 13485 4.197750 GACAGAATGCATGTCTGAATCCT 58.802 43.478 29.49 16.25 44.44 3.24
5072 13486 3.945921 ACAGAATGCATGTCTGAATCCTG 59.054 43.478 29.49 16.21 44.44 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 4275 2.313051 GAAACCCTAGGCGAGGCTCC 62.313 65.000 9.32 1.49 45.17 4.70
319 4532 6.503524 ACCATATCGCAACCAATTTACATTC 58.496 36.000 0.00 0.00 0.00 2.67
323 4536 7.871853 AGATAACCATATCGCAACCAATTTAC 58.128 34.615 0.00 0.00 42.35 2.01
324 4537 8.995220 GTAGATAACCATATCGCAACCAATTTA 58.005 33.333 0.00 0.00 42.35 1.40
325 4538 6.959639 AGATAACCATATCGCAACCAATTT 57.040 33.333 0.00 0.00 42.35 1.82
326 4539 7.435068 GTAGATAACCATATCGCAACCAATT 57.565 36.000 0.00 0.00 42.35 2.32
350 4563 3.037431 TGGAACAATGCAAATTTCGGG 57.963 42.857 0.00 0.00 31.92 5.14
374 4590 4.832590 TTTACAAACATGGGGTAACGTG 57.167 40.909 0.00 0.00 37.60 4.49
387 4605 2.432206 ACAGCCGCCAATTTACAAAC 57.568 45.000 0.00 0.00 0.00 2.93
388 4606 2.095668 CGTACAGCCGCCAATTTACAAA 60.096 45.455 0.00 0.00 0.00 2.83
389 4607 1.465387 CGTACAGCCGCCAATTTACAA 59.535 47.619 0.00 0.00 0.00 2.41
390 4608 1.080298 CGTACAGCCGCCAATTTACA 58.920 50.000 0.00 0.00 0.00 2.41
393 4611 0.802494 CTTCGTACAGCCGCCAATTT 59.198 50.000 0.00 0.00 0.00 1.82
394 4612 1.644786 GCTTCGTACAGCCGCCAATT 61.645 55.000 0.00 0.00 33.21 2.32
396 4614 2.740826 GCTTCGTACAGCCGCCAA 60.741 61.111 0.00 0.00 33.21 4.52
397 4615 3.309436 ATGCTTCGTACAGCCGCCA 62.309 57.895 2.98 0.00 39.25 5.69
398 4616 2.511600 ATGCTTCGTACAGCCGCC 60.512 61.111 2.98 0.00 39.25 6.13
400 4618 0.796312 AAACATGCTTCGTACAGCCG 59.204 50.000 2.98 0.00 39.25 5.52
401 4619 1.535462 ACAAACATGCTTCGTACAGCC 59.465 47.619 2.98 0.00 39.25 4.85
402 4620 2.574322 CACAAACATGCTTCGTACAGC 58.426 47.619 0.00 0.00 40.55 4.40
403 4621 2.032117 TGCACAAACATGCTTCGTACAG 60.032 45.455 0.00 0.00 46.28 2.74
404 4622 1.943340 TGCACAAACATGCTTCGTACA 59.057 42.857 0.00 0.00 46.28 2.90
405 4623 2.679355 TGCACAAACATGCTTCGTAC 57.321 45.000 0.00 0.00 46.28 3.67
504 4732 0.904649 TGGTGGCATCGACTCAGAAT 59.095 50.000 0.00 0.00 0.00 2.40
621 5562 2.171448 GTCCTGGCTCATACCTGATTGT 59.829 50.000 0.00 0.00 0.00 2.71
625 5566 2.245028 ACTAGTCCTGGCTCATACCTGA 59.755 50.000 0.00 0.00 0.00 3.86
716 5670 4.046286 TGGATTGTGGCCAGTAGAATTT 57.954 40.909 5.11 0.00 0.00 1.82
811 6951 2.586792 GGCTGTCTCGCCCTGAAT 59.413 61.111 0.00 0.00 44.41 2.57
931 7100 0.991920 TTAGGTTGGAGCTTGGGAGG 59.008 55.000 0.00 0.00 0.00 4.30
1730 7990 7.732996 ACTTAGGTCAAGCTCAAGTAGTTTTA 58.267 34.615 0.00 0.00 37.83 1.52
1827 8120 1.544724 GTCCAACAAGGGCATTGCTA 58.455 50.000 12.40 0.00 43.39 3.49
2449 8743 1.270907 AGTCCCTTGCACTGACCTAG 58.729 55.000 5.97 0.00 0.00 3.02
2731 9094 6.507485 AGGTCCCCAAATAATATAGGCACATA 59.493 38.462 0.00 0.00 0.00 2.29
2732 9095 5.315914 AGGTCCCCAAATAATATAGGCACAT 59.684 40.000 0.00 0.00 0.00 3.21
2740 9103 6.335580 AGCTTAGGAAGGTCCCCAAATAATAT 59.664 38.462 0.00 0.00 37.19 1.28
2741 9104 5.674958 AGCTTAGGAAGGTCCCCAAATAATA 59.325 40.000 0.00 0.00 37.19 0.98
2813 9176 5.509498 CAGAATTCCCAAAGATCCCACTTA 58.491 41.667 0.65 0.00 0.00 2.24
2868 9231 1.561542 AGCCTCAGGGAATTCGAACAT 59.438 47.619 0.00 0.00 33.58 2.71
2882 9245 4.088634 ACAAATTGGAAATGCTAGCCTCA 58.911 39.130 13.29 0.40 0.00 3.86
2939 9314 3.915575 CCAGCAAGGACAGATGGC 58.084 61.111 0.00 0.00 41.22 4.40
3019 10776 4.164988 CCCTCTATCCCAAAGAGTGAACAT 59.835 45.833 0.00 0.00 39.09 2.71
3036 10793 8.618240 TCAAAAGAGTGAATAATACCCCTCTA 57.382 34.615 0.00 0.00 0.00 2.43
3046 10803 6.262273 ACCGCTTTCTTCAAAAGAGTGAATAA 59.738 34.615 1.85 0.00 39.03 1.40
3048 10805 4.580580 ACCGCTTTCTTCAAAAGAGTGAAT 59.419 37.500 1.85 0.00 39.03 2.57
3059 10816 7.381139 GTGAAAATGATAAAACCGCTTTCTTCA 59.619 33.333 0.00 0.00 0.00 3.02
3088 10872 2.819608 ACATCTTGGACAAAACATCCGG 59.180 45.455 0.00 0.00 39.30 5.14
3654 11469 2.155732 GCCAATACGTGCAGTCATATCG 59.844 50.000 0.00 0.00 0.00 2.92
3865 11741 3.235200 ACTATAGACATCACCTCCTGCC 58.765 50.000 6.78 0.00 0.00 4.85
3995 11873 6.938698 ATGAGGATCTAGAATCTCTGCAAT 57.061 37.500 19.73 8.07 34.92 3.56
4036 11914 1.569493 CACTTCTTCGCACCGTTGG 59.431 57.895 0.00 0.00 0.00 3.77
4054 11952 2.203070 ATCCATGCTTCCGCGTCC 60.203 61.111 4.92 0.00 39.65 4.79
4055 11953 3.017323 CATCCATGCTTCCGCGTC 58.983 61.111 4.92 0.00 39.65 5.19
4060 11958 9.401239 ACAATATATTGCTGCATCCATGCTTCC 62.401 40.741 22.66 2.23 46.21 3.46
4061 11959 6.571731 ACAATATATTGCTGCATCCATGCTTC 60.572 38.462 22.66 5.15 46.21 3.86
4062 11960 5.245301 ACAATATATTGCTGCATCCATGCTT 59.755 36.000 22.66 0.00 46.21 3.91
4063 11961 4.770531 ACAATATATTGCTGCATCCATGCT 59.229 37.500 22.66 0.00 46.21 3.79
4064 11962 5.068234 ACAATATATTGCTGCATCCATGC 57.932 39.130 22.66 4.48 46.23 4.06
4065 11963 5.393787 GGGACAATATATTGCTGCATCCATG 60.394 44.000 22.66 7.69 41.38 3.66
4077 11975 2.884639 GCAACCAGCGGGACAATATATT 59.115 45.455 10.86 0.00 38.05 1.28
4218 12119 3.858247 AGTACGCCCTAACAGAATTGAC 58.142 45.455 0.00 0.00 0.00 3.18
4332 12239 7.981225 ACTAAATGCAAATCACATATTTGTCCC 59.019 33.333 11.03 0.00 40.19 4.46
4353 12260 7.093068 TGCTTCCAGTATCCAACTATGACTAAA 60.093 37.037 0.00 0.00 35.76 1.85
4358 12265 5.366477 TGATGCTTCCAGTATCCAACTATGA 59.634 40.000 0.00 0.00 36.64 2.15
4425 12332 7.114106 CACAATGCACACACGTCAATATAAAAA 59.886 33.333 0.00 0.00 0.00 1.94
4426 12333 6.580416 CACAATGCACACACGTCAATATAAAA 59.420 34.615 0.00 0.00 0.00 1.52
4438 12347 4.805192 ACAAGAATTTCACAATGCACACAC 59.195 37.500 0.00 0.00 0.00 3.82
4579 12616 2.446341 CGCTTCACGGAGTTTCCTC 58.554 57.895 0.00 0.00 41.61 3.71
4670 13026 5.613358 ACTCTGTATAGCTGCAAAACAAC 57.387 39.130 1.02 0.00 0.00 3.32
4693 13049 3.476552 GGTTGAGACCATGTTGAACTGA 58.523 45.455 0.00 0.00 45.77 3.41
4946 13357 1.534729 CAAGAACAAGGGCAGGGTAC 58.465 55.000 0.00 0.00 0.00 3.34
4948 13359 1.153756 CCAAGAACAAGGGCAGGGT 59.846 57.895 0.00 0.00 0.00 4.34
5033 13447 2.493675 TCTGTCTTCCATCTCTTGACCG 59.506 50.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.