Multiple sequence alignment - TraesCS4A01G083600

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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 TraesCS4A01G083600 chr4A 100.000 5009 0 0 1 5009 87969540 87974548 0.000000e+00 9250.0
1 TraesCS4A01G083600 chr4A 84.820 527 78 2 32 557 648473156 648472631 3.430000e-146 529.0
2 TraesCS4A01G083600 chr4A 97.368 76 2 0 4389 4464 87974003 87973928 4.070000e-26 130.0
3 TraesCS4A01G083600 chr4A 90.361 83 5 2 4387 4467 356552385 356552304 6.860000e-19 106.0
4 TraesCS4A01G083600 chr4D 97.049 4134 80 17 555 4662 377855396 377851279 0.000000e+00 6920.0
5 TraesCS4A01G083600 chr4D 93.088 217 12 2 4793 5009 377851071 377850858 1.050000e-81 315.0
6 TraesCS4A01G083600 chr4D 95.455 66 3 0 4678 4743 377851133 377851068 6.860000e-19 106.0
7 TraesCS4A01G083600 chr4D 87.500 88 4 7 4382 4464 484149204 484149289 1.480000e-15 95.3
8 TraesCS4A01G083600 chr4D 88.462 78 6 2 4392 4467 241799656 241799580 1.920000e-14 91.6
9 TraesCS4A01G083600 chr4D 89.333 75 5 2 4389 4461 241799583 241799656 1.920000e-14 91.6
10 TraesCS4A01G083600 chr4B 96.101 4232 84 22 555 4744 463720391 463716199 0.000000e+00 6826.0
11 TraesCS4A01G083600 chr4B 93.088 217 13 1 4793 5009 463716197 463715983 2.910000e-82 316.0
12 TraesCS4A01G083600 chr4B 90.698 43 4 0 4381 4423 248358241 248358283 1.950000e-04 58.4
13 TraesCS4A01G083600 chr2D 87.026 501 64 1 51 551 372702976 372702477 9.410000e-157 564.0
14 TraesCS4A01G083600 chr2D 85.962 520 70 3 40 558 190599846 190600363 2.040000e-153 553.0
15 TraesCS4A01G083600 chr2D 86.519 497 66 1 1 496 420744809 420745305 3.410000e-151 545.0
16 TraesCS4A01G083600 chr2D 86.022 93 10 1 1696 1788 82376594 82376683 4.130000e-16 97.1
17 TraesCS4A01G083600 chr2D 86.207 58 3 5 4741 4794 27884742 27884798 1.950000e-04 58.4
18 TraesCS4A01G083600 chr7D 85.164 519 76 1 40 558 27179202 27179719 9.550000e-147 531.0
19 TraesCS4A01G083600 chr7D 85.802 486 65 4 48 532 203946599 203947081 3.460000e-141 512.0
20 TraesCS4A01G083600 chr5B 84.820 527 78 2 32 557 508816801 508816276 3.430000e-146 529.0
21 TraesCS4A01G083600 chr5B 84.556 518 80 0 34 551 395736024 395736541 9.620000e-142 514.0
22 TraesCS4A01G083600 chr7B 84.261 521 79 3 40 559 540776484 540777002 5.790000e-139 505.0
23 TraesCS4A01G083600 chr7B 84.507 71 8 3 4736 4803 412773617 412773547 3.240000e-07 67.6
24 TraesCS4A01G083600 chr7B 80.000 95 8 8 4380 4464 427634407 427634314 5.420000e-05 60.2
25 TraesCS4A01G083600 chr7B 92.500 40 2 1 4759 4798 242674986 242674948 7.010000e-04 56.5
26 TraesCS4A01G083600 chr6A 86.667 90 9 1 1696 1785 440809816 440809730 4.130000e-16 97.1
27 TraesCS4A01G083600 chr5A 87.654 81 4 4 4388 4467 622426370 622426295 6.910000e-14 89.8
28 TraesCS4A01G083600 chr5A 84.375 96 6 7 4376 4464 403290643 403290736 8.930000e-13 86.1
29 TraesCS4A01G083600 chr5D 89.231 65 3 2 4403 4467 137975064 137975004 1.500000e-10 78.7
30 TraesCS4A01G083600 chr3B 81.250 96 5 9 4383 4467 55098951 55098858 1.160000e-06 65.8
31 TraesCS4A01G083600 chr3B 100.000 31 0 0 4767 4797 83902626 83902596 1.950000e-04 58.4
32 TraesCS4A01G083600 chr3B 100.000 31 0 0 4767 4797 674419806 674419836 1.950000e-04 58.4
33 TraesCS4A01G083600 chr3B 94.444 36 2 0 4767 4802 530257526 530257561 7.010000e-04 56.5
34 TraesCS4A01G083600 chr7A 80.645 93 5 9 4383 4464 555465431 555465341 5.420000e-05 60.2
35 TraesCS4A01G083600 chr6D 89.583 48 4 1 4380 4427 453351408 453351454 5.420000e-05 60.2
36 TraesCS4A01G083600 chr2B 80.435 92 7 8 4383 4464 774106650 774106560 5.420000e-05 60.2
37 TraesCS4A01G083600 chr2B 97.059 34 1 0 4767 4800 100334120 100334087 1.950000e-04 58.4
38 TraesCS4A01G083600 chr3D 100.000 31 0 0 4767 4797 182607300 182607270 1.950000e-04 58.4
39 TraesCS4A01G083600 chr3D 97.059 34 1 0 4767 4800 512256330 512256363 1.950000e-04 58.4


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 TraesCS4A01G083600 chr4A 87969540 87974548 5008 False 9250 9250 100.000000 1 5009 1 chr4A.!!$F1 5008
1 TraesCS4A01G083600 chr4A 648472631 648473156 525 True 529 529 84.820000 32 557 1 chr4A.!!$R3 525
2 TraesCS4A01G083600 chr4D 377850858 377855396 4538 True 2447 6920 95.197333 555 5009 3 chr4D.!!$R2 4454
3 TraesCS4A01G083600 chr4B 463715983 463720391 4408 True 3571 6826 94.594500 555 5009 2 chr4B.!!$R1 4454
4 TraesCS4A01G083600 chr2D 190599846 190600363 517 False 553 553 85.962000 40 558 1 chr2D.!!$F3 518
5 TraesCS4A01G083600 chr7D 27179202 27179719 517 False 531 531 85.164000 40 558 1 chr7D.!!$F1 518
6 TraesCS4A01G083600 chr5B 508816276 508816801 525 True 529 529 84.820000 32 557 1 chr5B.!!$R1 525
7 TraesCS4A01G083600 chr5B 395736024 395736541 517 False 514 514 84.556000 34 551 1 chr5B.!!$F1 517
8 TraesCS4A01G083600 chr7B 540776484 540777002 518 False 505 505 84.261000 40 559 1 chr7B.!!$F1 519

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
737 740 0.322008 CCAGAAGCAACTCAGACCCC 60.322 60.0 0.00 0.0 0.00 4.95 F
738 741 0.322008 CAGAAGCAACTCAGACCCCC 60.322 60.0 0.00 0.0 0.00 5.40 F
739 742 0.474660 AGAAGCAACTCAGACCCCCT 60.475 55.0 0.00 0.0 0.00 4.79 F
3043 3059 1.358725 TATTCACGCGTCTGCAAGCC 61.359 55.0 9.86 0.0 42.97 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 2167 1.064017 AGCCACCTCTTCAACAACCAA 60.064 47.619 0.00 0.0 0.00 3.67 R
3043 3059 1.236616 TGCAATGCCACAGAGTTCGG 61.237 55.000 1.53 0.0 0.00 4.30 R
3090 3106 1.089481 ATTCATGGCCACGCACGTAG 61.089 55.000 8.16 0.0 0.00 3.51 R
4674 4835 0.041839 CTGTGCACTGAACGTGAAGC 60.042 55.000 19.41 0.0 46.81 3.86 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
27 28 3.913573 CGTCTCGCGGCGGAAATG 61.914 66.667 23.46 9.67 36.85 2.32
28 29 3.564027 GTCTCGCGGCGGAAATGG 61.564 66.667 23.46 6.33 0.00 3.16
37 38 3.550992 CGGAAATGGCGACGACGG 61.551 66.667 9.67 0.00 40.15 4.79
38 39 2.125832 GGAAATGGCGACGACGGA 60.126 61.111 9.67 0.00 40.15 4.69
41 42 2.830704 GAAATGGCGACGACGGAGGT 62.831 60.000 9.67 0.00 40.15 3.85
49 50 4.308458 CGACGGAGGTGGCCACAA 62.308 66.667 35.78 0.00 0.00 3.33
95 96 1.003839 TGAAGAAACGGCAGCGGAT 60.004 52.632 7.02 0.00 0.00 4.18
101 102 0.960364 AAACGGCAGCGGATGAACAT 60.960 50.000 7.02 0.00 0.00 2.71
132 133 2.586245 CCTGAGCAGAATCGGGCA 59.414 61.111 0.00 0.00 38.87 5.36
232 233 2.314256 CGGCTCGATCCGTACTGTA 58.686 57.895 19.25 0.00 44.18 2.74
239 240 3.461061 TCGATCCGTACTGTATCTTCGT 58.539 45.455 0.00 0.00 0.00 3.85
241 242 3.246936 CGATCCGTACTGTATCTTCGTCA 59.753 47.826 0.00 0.00 0.00 4.35
267 268 0.824109 TCCGCGAGAAGGATGACAAT 59.176 50.000 8.23 0.00 31.86 2.71
271 272 2.013563 GCGAGAAGGATGACAATGGCA 61.014 52.381 0.00 0.00 0.00 4.92
351 352 2.158534 TGGTAGTCTGGTGGCATGTTTT 60.159 45.455 0.00 0.00 0.00 2.43
361 362 3.566322 GGTGGCATGTTTTGTGTAGTGTA 59.434 43.478 0.00 0.00 0.00 2.90
362 363 4.320202 GGTGGCATGTTTTGTGTAGTGTAG 60.320 45.833 0.00 0.00 0.00 2.74
394 395 2.805353 GATGCGTGTGCGTCGACT 60.805 61.111 14.70 0.00 46.39 4.18
399 400 1.930816 GCGTGTGCGTCGACTTAGTG 61.931 60.000 14.70 0.00 40.81 2.74
414 415 5.351465 CGACTTAGTGGCATGAGTTTGTATT 59.649 40.000 0.00 0.00 0.00 1.89
421 422 5.577945 GTGGCATGAGTTTGTATTGATTTGG 59.422 40.000 0.00 0.00 0.00 3.28
519 521 1.964373 GCGTCCACGGGTGTTTGAT 60.964 57.895 0.55 0.00 40.23 2.57
532 534 1.967066 TGTTTGATGGGCCGAATTTGT 59.033 42.857 0.00 0.00 0.00 2.83
536 538 2.242926 TGATGGGCCGAATTTGTCAAA 58.757 42.857 0.00 0.00 0.00 2.69
551 553 4.200838 TGTCAAATTCGGCTGTAGATGA 57.799 40.909 0.00 0.00 0.00 2.92
553 555 5.185454 TGTCAAATTCGGCTGTAGATGATT 58.815 37.500 0.00 0.00 0.00 2.57
578 580 2.439156 GGGCCATGTGTCAGCCTC 60.439 66.667 4.39 0.00 46.31 4.70
581 583 1.626356 GGCCATGTGTCAGCCTCCTA 61.626 60.000 0.00 0.00 43.62 2.94
591 593 3.834799 GCCTCCTACACCCGTCGG 61.835 72.222 3.60 3.60 0.00 4.79
737 740 0.322008 CCAGAAGCAACTCAGACCCC 60.322 60.000 0.00 0.00 0.00 4.95
738 741 0.322008 CAGAAGCAACTCAGACCCCC 60.322 60.000 0.00 0.00 0.00 5.40
739 742 0.474660 AGAAGCAACTCAGACCCCCT 60.475 55.000 0.00 0.00 0.00 4.79
833 836 3.670629 CTCGAGCTCCTCCACCCCT 62.671 68.421 8.47 0.00 0.00 4.79
835 838 2.766229 GAGCTCCTCCACCCCTCC 60.766 72.222 0.87 0.00 0.00 4.30
879 883 4.388499 CCCGTACAGTTGCCCGCT 62.388 66.667 0.00 0.00 0.00 5.52
1146 1159 3.448469 GGAGGACGAGGATGAGGAT 57.552 57.895 0.00 0.00 0.00 3.24
1155 1168 2.122768 GAGGATGAGGATGAGGTGGTT 58.877 52.381 0.00 0.00 0.00 3.67
1308 1321 4.176851 GACTCCGTCGACGAGGCC 62.177 72.222 37.65 21.93 43.02 5.19
1623 1639 2.738643 CGTCGACTTGGAGCATAACCAT 60.739 50.000 14.70 0.00 37.26 3.55
1629 1645 3.010584 ACTTGGAGCATAACCATCCTTGT 59.989 43.478 0.00 0.00 37.26 3.16
1635 1651 3.523564 AGCATAACCATCCTTGTACACCT 59.476 43.478 0.00 0.00 0.00 4.00
1657 1673 6.725834 ACCTGATATGGTGAGGTTTTTGAAAT 59.274 34.615 0.00 0.00 36.68 2.17
1721 1737 6.815089 AGATTACTGTTGAGATGGATGAGAC 58.185 40.000 0.00 0.00 0.00 3.36
2151 2167 8.429641 TCCAAAGACAGTAAAGAGAACTATGTT 58.570 33.333 0.00 0.00 0.00 2.71
2271 2287 3.136123 CCAGATGCAAGGCACCGG 61.136 66.667 0.00 0.00 43.04 5.28
2862 2878 3.844211 AGGGCAAGAAGGTTGACTATACA 59.156 43.478 0.00 0.00 0.00 2.29
3043 3059 1.358725 TATTCACGCGTCTGCAAGCC 61.359 55.000 9.86 0.00 42.97 4.35
3090 3106 8.407064 AGAGATTTGAGCATTTTTGATGATCTC 58.593 33.333 5.94 0.00 35.65 2.75
3210 3226 1.004394 GGCAAACTAGTAAGGCCTGGT 59.996 52.381 19.64 0.00 41.39 4.00
3619 3635 2.919859 CACTTCATACACAGCGACAGAG 59.080 50.000 0.00 0.00 0.00 3.35
3753 3769 2.365617 GACGTCCCCTCACATGATACAT 59.634 50.000 3.51 0.00 0.00 2.29
4020 4036 4.345859 TGTGGGGTAGTTTAACTGTCTG 57.654 45.455 8.00 0.00 0.00 3.51
4158 4174 3.955650 TTGTTGGTAGCTCTCCTGTAC 57.044 47.619 8.92 0.00 0.00 2.90
4164 4180 3.451178 TGGTAGCTCTCCTGTACCATTTC 59.549 47.826 8.92 0.00 41.05 2.17
4165 4181 3.181464 GGTAGCTCTCCTGTACCATTTCC 60.181 52.174 0.00 0.00 36.89 3.13
4166 4182 1.840635 AGCTCTCCTGTACCATTTCCC 59.159 52.381 0.00 0.00 0.00 3.97
4219 4242 6.063404 TGAATGGCATTGTTCTCTGCATATA 58.937 36.000 19.07 0.00 40.18 0.86
4220 4243 6.717997 TGAATGGCATTGTTCTCTGCATATAT 59.282 34.615 19.07 0.00 40.18 0.86
4252 4287 4.032960 TCCATCTGGTAATTGCAAGTGT 57.967 40.909 10.14 0.00 36.34 3.55
4360 4395 0.680921 TTGTGCTGGCAGCTTATCCC 60.681 55.000 36.50 18.62 42.97 3.85
4361 4396 1.077501 GTGCTGGCAGCTTATCCCA 60.078 57.895 36.50 14.98 42.97 4.37
4400 4435 8.780003 AGATTAAAGTCTAGTACTCCCTCTGTA 58.220 37.037 0.00 0.00 37.50 2.74
4529 4567 4.574599 CAGTTTAACTGCTTTGGCTCTT 57.425 40.909 12.37 0.00 39.62 2.85
4530 4568 4.936891 CAGTTTAACTGCTTTGGCTCTTT 58.063 39.130 12.37 0.00 39.62 2.52
4531 4569 5.351458 CAGTTTAACTGCTTTGGCTCTTTT 58.649 37.500 12.37 0.00 39.62 2.27
4532 4570 5.812127 CAGTTTAACTGCTTTGGCTCTTTTT 59.188 36.000 12.37 0.00 39.62 1.94
4593 4631 9.659135 TTGGTTGGATATCATGGAAATATTTCT 57.341 29.630 23.85 9.51 37.35 2.52
4594 4632 9.659135 TGGTTGGATATCATGGAAATATTTCTT 57.341 29.630 23.85 11.85 37.35 2.52
4595 4633 9.918630 GGTTGGATATCATGGAAATATTTCTTG 57.081 33.333 23.85 20.57 37.35 3.02
4683 4850 5.652994 AGATAGAGAAGAAGCTTCACGTT 57.347 39.130 27.57 13.77 0.00 3.99
4730 4897 1.334160 TCCCTGTTCTACACGAGCAA 58.666 50.000 0.00 0.00 32.19 3.91
4741 4908 9.811995 TGTTCTACACGAGCAATTAGTTAATAT 57.188 29.630 0.00 0.00 29.28 1.28
4744 4911 9.177304 TCTACACGAGCAATTAGTTAATATTCG 57.823 33.333 0.00 9.24 33.29 3.34
4745 4912 7.766219 ACACGAGCAATTAGTTAATATTCGT 57.234 32.000 0.00 10.07 36.98 3.85
4746 4913 7.838498 ACACGAGCAATTAGTTAATATTCGTC 58.162 34.615 11.73 0.00 35.71 4.20
4747 4914 7.705325 ACACGAGCAATTAGTTAATATTCGTCT 59.295 33.333 11.73 0.00 35.71 4.18
4748 4915 7.998767 CACGAGCAATTAGTTAATATTCGTCTG 59.001 37.037 11.73 3.96 35.71 3.51
4749 4916 7.705325 ACGAGCAATTAGTTAATATTCGTCTGT 59.295 33.333 0.00 0.00 34.27 3.41
4750 4917 9.177304 CGAGCAATTAGTTAATATTCGTCTGTA 57.823 33.333 0.00 0.00 0.00 2.74
4762 4929 8.644318 AATATTCGTCTGTAAAGAAATAGCGT 57.356 30.769 0.00 0.00 0.00 5.07
4763 4930 6.963049 ATTCGTCTGTAAAGAAATAGCGTT 57.037 33.333 0.00 0.00 0.00 4.84
4764 4931 6.774354 TTCGTCTGTAAAGAAATAGCGTTT 57.226 33.333 0.00 0.00 0.00 3.60
4765 4932 7.872163 TTCGTCTGTAAAGAAATAGCGTTTA 57.128 32.000 0.00 0.00 0.00 2.01
4766 4933 7.502177 TCGTCTGTAAAGAAATAGCGTTTAG 57.498 36.000 0.00 0.00 0.00 1.85
4785 4952 8.940924 GCGTTTAGCTTTTATATTTCTTTACGG 58.059 33.333 0.00 0.00 44.04 4.02
4789 4956 7.803279 AGCTTTTATATTTCTTTACGGAGGG 57.197 36.000 0.00 0.00 0.00 4.30
4790 4957 7.571025 AGCTTTTATATTTCTTTACGGAGGGA 58.429 34.615 0.00 0.00 0.00 4.20
4791 4958 7.715686 AGCTTTTATATTTCTTTACGGAGGGAG 59.284 37.037 0.00 0.00 0.00 4.30
4825 4992 2.470362 GCGATGCAGCAGCTGATGT 61.470 57.895 30.78 14.29 42.74 3.06
4826 4993 1.352056 CGATGCAGCAGCTGATGTG 59.648 57.895 30.78 18.32 42.74 3.21
4853 5020 8.570488 CATATTGGCATGCTAACTTTGATCTTA 58.430 33.333 19.51 4.61 0.00 2.10
4915 5082 4.128554 TCGCTTTGTTTGATTCGAACTC 57.871 40.909 16.00 0.12 0.00 3.01
4936 5103 3.630312 TCCCTATAATTGCTTGGAAACGC 59.370 43.478 0.00 0.00 0.00 4.84
4938 5105 2.959507 ATAATTGCTTGGAAACGCCC 57.040 45.000 0.00 0.00 34.97 6.13
4945 5112 1.939381 GCTTGGAAACGCCCCAAAATC 60.939 52.381 5.47 0.00 42.51 2.17
4959 5126 3.824443 CCCAAAATCGTGTTTAAGGAGGT 59.176 43.478 0.00 0.00 0.00 3.85
4960 5127 4.320935 CCCAAAATCGTGTTTAAGGAGGTG 60.321 45.833 0.00 0.00 0.00 4.00
4970 5137 4.885325 TGTTTAAGGAGGTGTTTTGGAGAC 59.115 41.667 0.00 0.00 0.00 3.36
4980 5147 6.784031 AGGTGTTTTGGAGACTTCATCTTAT 58.216 36.000 0.00 0.00 38.00 1.73
4991 5158 9.859427 GGAGACTTCATCTTATAATCATCTCTG 57.141 37.037 0.00 0.00 38.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.913573 CATTTCCGCCGCGAGACG 61.914 66.667 15.93 8.61 43.15 4.18
11 12 3.564027 CCATTTCCGCCGCGAGAC 61.564 66.667 15.93 0.00 0.00 3.36
18 19 3.861263 GTCGTCGCCATTTCCGCC 61.861 66.667 0.00 0.00 0.00 6.13
19 20 4.204891 CGTCGTCGCCATTTCCGC 62.205 66.667 0.00 0.00 0.00 5.54
20 21 3.550992 CCGTCGTCGCCATTTCCG 61.551 66.667 0.00 0.00 35.54 4.30
21 22 2.125832 TCCGTCGTCGCCATTTCC 60.126 61.111 0.00 0.00 35.54 3.13
22 23 2.165301 CCTCCGTCGTCGCCATTTC 61.165 63.158 0.00 0.00 35.54 2.17
23 24 2.125673 CCTCCGTCGTCGCCATTT 60.126 61.111 0.00 0.00 35.54 2.32
24 25 3.379445 ACCTCCGTCGTCGCCATT 61.379 61.111 0.00 0.00 35.54 3.16
25 26 4.129737 CACCTCCGTCGTCGCCAT 62.130 66.667 0.00 0.00 35.54 4.40
30 31 4.736896 GTGGCCACCTCCGTCGTC 62.737 72.222 26.31 0.00 0.00 4.20
37 38 1.303643 CCTCCTTTGTGGCCACCTC 60.304 63.158 32.62 9.38 35.26 3.85
38 39 1.360393 TTCCTCCTTTGTGGCCACCT 61.360 55.000 32.62 0.00 35.26 4.00
41 42 1.228552 GCTTCCTCCTTTGTGGCCA 60.229 57.895 0.00 0.00 35.26 5.36
46 47 0.035056 CGGATGGCTTCCTCCTTTGT 60.035 55.000 16.47 0.00 42.99 2.83
49 50 2.592308 GCGGATGGCTTCCTCCTT 59.408 61.111 16.47 0.00 42.99 3.36
70 71 1.001487 CTGCCGTTTCTTCACAATGCA 60.001 47.619 0.00 0.00 0.00 3.96
95 96 4.695993 TGAGGGCGCGCATGTTCA 62.696 61.111 34.42 24.74 0.00 3.18
116 117 0.809241 GACTGCCCGATTCTGCTCAG 60.809 60.000 0.00 0.00 0.00 3.35
132 133 0.603569 GTCCGGTCATGACACAGACT 59.396 55.000 26.47 0.00 35.18 3.24
200 201 3.889044 GCCGGATCTGCTCGTCGA 61.889 66.667 5.05 0.00 0.00 4.20
232 233 1.134560 GCGGAAGTACCTGACGAAGAT 59.865 52.381 0.00 0.00 36.31 2.40
239 240 0.809385 CTTCTCGCGGAAGTACCTGA 59.191 55.000 21.80 0.00 44.59 3.86
261 262 1.303236 CTTCCCGGTGCCATTGTCA 60.303 57.895 0.00 0.00 0.00 3.58
338 339 2.360483 CACTACACAAAACATGCCACCA 59.640 45.455 0.00 0.00 0.00 4.17
351 352 3.087031 GGCTACTCCACTACACTACACA 58.913 50.000 0.00 0.00 34.01 3.72
361 362 1.076923 ATCGTCCGGCTACTCCACT 60.077 57.895 0.00 0.00 34.01 4.00
362 363 1.065928 CATCGTCCGGCTACTCCAC 59.934 63.158 0.00 0.00 34.01 4.02
394 395 7.701539 AATCAATACAAACTCATGCCACTAA 57.298 32.000 0.00 0.00 0.00 2.24
399 400 5.105392 TCCCAAATCAATACAAACTCATGCC 60.105 40.000 0.00 0.00 0.00 4.40
421 422 9.751542 CATCCGAATACCTCAATTACTATATCC 57.248 37.037 0.00 0.00 0.00 2.59
427 428 5.365605 TCCACATCCGAATACCTCAATTACT 59.634 40.000 0.00 0.00 0.00 2.24
465 466 1.047034 GGGCACTGACCGGGTACTAT 61.047 60.000 6.32 0.00 0.00 2.12
466 467 1.683365 GGGCACTGACCGGGTACTA 60.683 63.158 6.32 0.00 0.00 1.82
519 521 3.311486 GAATTTGACAAATTCGGCCCA 57.689 42.857 28.72 0.00 44.94 5.36
532 534 7.012327 CCTTAAATCATCTACAGCCGAATTTGA 59.988 37.037 0.00 0.00 0.00 2.69
536 538 4.757149 GCCTTAAATCATCTACAGCCGAAT 59.243 41.667 0.00 0.00 0.00 3.34
879 883 0.177141 CGAAATGGCTAGGGTTCGGA 59.823 55.000 5.70 0.00 39.27 4.55
918 922 8.890410 AAAGTATTAACACTAGAGGTACAGGA 57.110 34.615 0.00 0.00 0.00 3.86
973 977 0.105408 CCGAGTATTTACCCACCCCG 59.895 60.000 0.00 0.00 0.00 5.73
1085 1098 2.037121 TCAGCAATCTCGTCTTTGACCA 59.963 45.455 0.00 0.00 0.00 4.02
1146 1159 1.127567 CCTCCTCCACAACCACCTCA 61.128 60.000 0.00 0.00 0.00 3.86
1155 1168 3.992641 TCCTCGCCCTCCTCCACA 61.993 66.667 0.00 0.00 0.00 4.17
1308 1321 3.000322 CGTATGCCTTGTAGAGCGAAAAG 60.000 47.826 0.00 0.00 0.00 2.27
1521 1537 0.034059 CAGTCTTCTCGGCAGTGGTT 59.966 55.000 0.00 0.00 0.00 3.67
1527 1543 1.219124 GCATCCAGTCTTCTCGGCA 59.781 57.895 0.00 0.00 0.00 5.69
1635 1651 6.953520 AGGATTTCAAAAACCTCACCATATCA 59.046 34.615 0.00 0.00 36.57 2.15
1653 1669 2.708325 AGGCATCTCCCTGTAGGATTTC 59.292 50.000 0.00 0.00 46.33 2.17
1657 1673 3.230608 CAGGCATCTCCCTGTAGGA 57.769 57.895 0.00 0.00 45.87 2.94
1674 1690 1.271054 GCCTTCTTCTTGGCTGACTCA 60.271 52.381 0.00 0.00 45.26 3.41
1721 1737 2.029020 TCACTCAATGACTTCTCCACCG 60.029 50.000 0.00 0.00 29.99 4.94
2151 2167 1.064017 AGCCACCTCTTCAACAACCAA 60.064 47.619 0.00 0.00 0.00 3.67
3043 3059 1.236616 TGCAATGCCACAGAGTTCGG 61.237 55.000 1.53 0.00 0.00 4.30
3090 3106 1.089481 ATTCATGGCCACGCACGTAG 61.089 55.000 8.16 0.00 0.00 3.51
3210 3226 0.615331 GATCACCTTGCTGGGTCTGA 59.385 55.000 0.00 0.00 41.11 3.27
3619 3635 5.059833 GGATGTCAGGTTCATATCAACTCC 58.940 45.833 0.00 0.00 0.00 3.85
3753 3769 2.209690 TATCCACTCTCGTGTCACCA 57.790 50.000 0.00 0.00 39.55 4.17
3969 3985 6.895782 TCCACCTCCGATGAAATAAGTATTT 58.104 36.000 0.00 0.00 38.51 1.40
4020 4036 6.363357 CCTTTCTAAACAAATGTTACAGCAGC 59.637 38.462 0.00 0.00 37.25 5.25
4220 4243 9.453572 GCAATTACCAGATGGATATCTATCAAA 57.546 33.333 25.62 15.97 41.71 2.69
4252 4287 1.740380 GCTGCGAAACTAGAGGCATCA 60.740 52.381 0.00 0.00 34.49 3.07
4477 4515 1.270274 TGCGAGTAAGCCACGAAGTTA 59.730 47.619 0.00 0.00 33.80 2.24
4593 4631 4.335315 CCTTCTCAAACAACACAGCTACAA 59.665 41.667 0.00 0.00 0.00 2.41
4594 4632 3.876914 CCTTCTCAAACAACACAGCTACA 59.123 43.478 0.00 0.00 0.00 2.74
4595 4633 3.877508 ACCTTCTCAAACAACACAGCTAC 59.122 43.478 0.00 0.00 0.00 3.58
4596 4634 3.876914 CACCTTCTCAAACAACACAGCTA 59.123 43.478 0.00 0.00 0.00 3.32
4597 4635 2.684881 CACCTTCTCAAACAACACAGCT 59.315 45.455 0.00 0.00 0.00 4.24
4601 4639 1.748493 TGCCACCTTCTCAAACAACAC 59.252 47.619 0.00 0.00 0.00 3.32
4668 4829 2.348966 GCACTGAACGTGAAGCTTCTTC 60.349 50.000 26.09 20.58 46.81 2.87
4669 4830 1.599542 GCACTGAACGTGAAGCTTCTT 59.400 47.619 26.09 13.14 46.81 2.52
4671 4832 0.937304 TGCACTGAACGTGAAGCTTC 59.063 50.000 19.89 19.89 46.81 3.86
4672 4833 0.657840 GTGCACTGAACGTGAAGCTT 59.342 50.000 10.32 0.00 46.81 3.74
4673 4834 0.461870 TGTGCACTGAACGTGAAGCT 60.462 50.000 19.41 0.00 46.81 3.74
4674 4835 0.041839 CTGTGCACTGAACGTGAAGC 60.042 55.000 19.41 0.00 46.81 3.86
4675 4836 0.041839 GCTGTGCACTGAACGTGAAG 60.042 55.000 25.94 9.12 46.81 3.02
4676 4837 0.742635 TGCTGTGCACTGAACGTGAA 60.743 50.000 25.94 0.00 46.81 3.18
4741 4908 6.774354 AAACGCTATTTCTTTACAGACGAA 57.226 33.333 0.00 0.00 0.00 3.85
4759 4926 8.940924 CCGTAAAGAAATATAAAAGCTAAACGC 58.059 33.333 0.00 0.00 39.57 4.84
4763 4930 9.333724 CCCTCCGTAAAGAAATATAAAAGCTAA 57.666 33.333 0.00 0.00 0.00 3.09
4764 4931 8.707449 TCCCTCCGTAAAGAAATATAAAAGCTA 58.293 33.333 0.00 0.00 0.00 3.32
4765 4932 7.571025 TCCCTCCGTAAAGAAATATAAAAGCT 58.429 34.615 0.00 0.00 0.00 3.74
4766 4933 7.498239 ACTCCCTCCGTAAAGAAATATAAAAGC 59.502 37.037 0.00 0.00 0.00 3.51
4767 4934 8.959705 ACTCCCTCCGTAAAGAAATATAAAAG 57.040 34.615 0.00 0.00 0.00 2.27
4771 4938 9.991906 CAAATACTCCCTCCGTAAAGAAATATA 57.008 33.333 0.00 0.00 0.00 0.86
4772 4939 7.444487 GCAAATACTCCCTCCGTAAAGAAATAT 59.556 37.037 0.00 0.00 0.00 1.28
4773 4940 6.764560 GCAAATACTCCCTCCGTAAAGAAATA 59.235 38.462 0.00 0.00 0.00 1.40
4774 4941 5.589050 GCAAATACTCCCTCCGTAAAGAAAT 59.411 40.000 0.00 0.00 0.00 2.17
4775 4942 4.939439 GCAAATACTCCCTCCGTAAAGAAA 59.061 41.667 0.00 0.00 0.00 2.52
4776 4943 4.510571 GCAAATACTCCCTCCGTAAAGAA 58.489 43.478 0.00 0.00 0.00 2.52
4777 4944 3.118519 GGCAAATACTCCCTCCGTAAAGA 60.119 47.826 0.00 0.00 0.00 2.52
4778 4945 3.118371 AGGCAAATACTCCCTCCGTAAAG 60.118 47.826 0.00 0.00 0.00 1.85
4779 4946 2.841881 AGGCAAATACTCCCTCCGTAAA 59.158 45.455 0.00 0.00 0.00 2.01
4780 4947 2.474112 AGGCAAATACTCCCTCCGTAA 58.526 47.619 0.00 0.00 0.00 3.18
4781 4948 2.170012 AGGCAAATACTCCCTCCGTA 57.830 50.000 0.00 0.00 0.00 4.02
4782 4949 1.209747 GAAGGCAAATACTCCCTCCGT 59.790 52.381 0.00 0.00 0.00 4.69
4783 4950 1.486726 AGAAGGCAAATACTCCCTCCG 59.513 52.381 0.00 0.00 0.00 4.63
4784 4951 2.924421 CAGAAGGCAAATACTCCCTCC 58.076 52.381 0.00 0.00 0.00 4.30
4785 4952 2.293170 GCAGAAGGCAAATACTCCCTC 58.707 52.381 0.00 0.00 43.97 4.30
4786 4953 2.426842 GCAGAAGGCAAATACTCCCT 57.573 50.000 0.00 0.00 43.97 4.20
4818 4985 2.672714 CATGCCAATATGCACATCAGC 58.327 47.619 0.00 0.00 45.48 4.26
4915 5082 3.243401 GGCGTTTCCAAGCAATTATAGGG 60.243 47.826 0.00 0.00 34.54 3.53
4936 5103 3.192633 CCTCCTTAAACACGATTTTGGGG 59.807 47.826 0.00 0.00 0.00 4.96
4938 5105 4.277423 ACACCTCCTTAAACACGATTTTGG 59.723 41.667 0.00 0.00 0.00 3.28
4945 5112 3.628487 TCCAAAACACCTCCTTAAACACG 59.372 43.478 0.00 0.00 0.00 4.49
4959 5126 9.958180 TGATTATAAGATGAAGTCTCCAAAACA 57.042 29.630 0.00 0.00 35.67 2.83
4970 5137 7.549842 CAGGCCAGAGATGATTATAAGATGAAG 59.450 40.741 5.01 0.00 0.00 3.02
4980 5147 2.039480 GCATCCAGGCCAGAGATGATTA 59.961 50.000 25.47 0.00 39.84 1.75
4991 5158 2.890371 CAAAGCTGCATCCAGGCC 59.110 61.111 1.02 0.00 39.54 5.19


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

AutoCloner maintained by Alex Coulton.