Multiple sequence alignment - TraesCS4D01G295700

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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 TraesCS4D01G295700 chr4D 100.000 5302 0 0 1 5302 465564885 465559584 0.000000e+00 9792
1 TraesCS4D01G295700 chr4D 78.391 1069 115 57 3952 4968 465415339 465414335 5.920000e-164 588
2 TraesCS4D01G295700 chr4B 96.433 2271 66 12 2355 4621 582360770 582358511 0.000000e+00 3731
3 TraesCS4D01G295700 chr4B 94.767 707 32 5 1180 1884 582362242 582361539 0.000000e+00 1096
4 TraesCS4D01G295700 chr4B 88.504 635 39 14 558 1160 582363048 582362416 0.000000e+00 737
5 TraesCS4D01G295700 chr4B 94.068 472 24 2 1885 2356 582361487 582361020 0.000000e+00 713
6 TraesCS4D01G295700 chr4B 89.305 561 38 9 1 539 582367080 582366520 0.000000e+00 684
7 TraesCS4D01G295700 chr4B 88.026 309 18 8 4673 4965 582358521 582358216 1.090000e-91 348
8 TraesCS4D01G295700 chr4B 95.484 155 7 0 5148 5302 582357633 582357479 1.140000e-61 248
9 TraesCS4D01G295700 chr4B 89.062 192 18 1 4964 5152 582357867 582357676 8.880000e-58 235
10 TraesCS4D01G295700 chr4B 84.211 152 11 4 3918 4056 582161240 582161089 9.260000e-28 135
11 TraesCS4D01G295700 chr4A 89.236 2852 213 43 1879 4695 4868479 4871271 0.000000e+00 3480
12 TraesCS4D01G295700 chr4A 87.522 1162 106 31 749 1886 4867247 4868393 0.000000e+00 1306
13 TraesCS4D01G295700 chr4A 87.034 563 38 15 230 763 4866422 4866978 2.110000e-168 603
14 TraesCS4D01G295700 chr4A 85.328 259 18 6 4724 4965 4871268 4871523 3.170000e-62 250
15 TraesCS4D01G295700 chr4A 91.150 113 7 1 5149 5258 4872211 4872323 3.310000e-32 150
16 TraesCS4D01G295700 chr5A 87.892 2552 219 58 2050 4554 540276829 540274321 0.000000e+00 2918
17 TraesCS4D01G295700 chr5A 87.677 495 59 2 1351 1844 540277791 540277298 4.610000e-160 575
18 TraesCS4D01G295700 chr5A 92.241 116 8 1 992 1107 540279187 540279073 4.250000e-36 163
19 TraesCS4D01G295700 chr5A 88.889 135 8 3 1834 1961 540277273 540277139 5.500000e-35 159
20 TraesCS4D01G295700 chr5B 88.603 2448 213 46 2050 4465 515400649 515398236 0.000000e+00 2915
21 TraesCS4D01G295700 chr5B 84.343 677 86 13 1182 1844 515401785 515401115 0.000000e+00 645
22 TraesCS4D01G295700 chr5B 92.188 128 10 0 1834 1961 515401090 515400963 1.170000e-41 182
23 TraesCS4D01G295700 chr5D 88.089 2485 215 50 2119 4554 425996907 425994455 0.000000e+00 2874
24 TraesCS4D01G295700 chr5D 83.636 605 74 15 1174 1760 425997972 425997375 3.610000e-151 545
25 TraesCS4D01G295700 chr5D 92.241 116 9 0 992 1107 425998275 425998160 1.180000e-36 165


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 TraesCS4D01G295700 chr4D 465559584 465564885 5301 True 9792.000000 9792 100.000000 1 5302 1 chr4D.!!$R2 5301
1 TraesCS4D01G295700 chr4D 465414335 465415339 1004 True 588.000000 588 78.391000 3952 4968 1 chr4D.!!$R1 1016
2 TraesCS4D01G295700 chr4B 582357479 582367080 9601 True 974.000000 3731 91.956125 1 5302 8 chr4B.!!$R2 5301
3 TraesCS4D01G295700 chr4A 4866422 4872323 5901 False 1157.800000 3480 88.054000 230 5258 5 chr4A.!!$F1 5028
4 TraesCS4D01G295700 chr5A 540274321 540279187 4866 True 953.750000 2918 89.174750 992 4554 4 chr5A.!!$R1 3562
5 TraesCS4D01G295700 chr5B 515398236 515401785 3549 True 1247.333333 2915 88.378000 1182 4465 3 chr5B.!!$R1 3283
6 TraesCS4D01G295700 chr5D 425994455 425998275 3820 True 1194.666667 2874 87.988667 992 4554 3 chr5D.!!$R1 3562

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
337 351 0.321564 CAGCCACCGGAATGTTCTCA 60.322 55.000 9.46 0.0 0.00 3.27 F
842 4627 0.765510 GGGACCAACAGTTCAGGACT 59.234 55.000 0.00 0.0 39.89 3.85 F
1092 4894 0.965866 TGCAGTACCACTCCCTCTCG 60.966 60.000 0.00 0.0 0.00 4.04 F
1151 4959 1.794222 CGTCTGTTTTGGCCGGATC 59.206 57.895 5.05 0.0 0.00 3.36 F
2363 8381 2.033927 TCGCTTATCTGCTAGACTGCTG 59.966 50.000 0.00 0.0 0.00 4.41 F
2761 8786 0.385390 GTTGTTCTGCAGGTTGGGTG 59.615 55.000 15.13 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 6372 0.620556 GGGGATCACTTCCTGCTCAA 59.379 55.00 0.00 0.0 44.75 3.02 R
2541 8560 0.240678 TGCGCACAACAGCCTTAATG 59.759 50.00 5.66 0.0 0.00 1.90 R
2583 8608 4.925068 ACTGTTGCTCTGAAAATTGTGAC 58.075 39.13 0.00 0.0 0.00 3.67 R
2584 8609 5.357878 AGAACTGTTGCTCTGAAAATTGTGA 59.642 36.00 0.00 0.0 0.00 3.58 R
3425 9463 0.878523 CGGAAGGCAACACGTCTCAA 60.879 55.00 0.00 0.0 41.41 3.02 R
4424 10505 0.035915 GCCCTCTCCTCAACCTCAAC 60.036 60.00 0.00 0.0 0.00 3.18 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
40 41 1.880819 GCTCCACAAACTGGCCATGG 61.881 60.000 15.14 15.14 40.39 3.66
46 47 1.184431 CAAACTGGCCATGGCATACA 58.816 50.000 36.56 24.12 44.11 2.29
81 83 5.664294 ATCAGTTCAATAATGGCAGCAAA 57.336 34.783 0.00 0.00 0.00 3.68
97 102 2.027837 AGCAAAATCATGTTTGGGGCTC 60.028 45.455 9.95 0.00 38.64 4.70
120 125 8.493547 GCTCCTTTCATTTTGAATTCTTTTCTG 58.506 33.333 7.05 0.00 36.11 3.02
121 126 8.369218 TCCTTTCATTTTGAATTCTTTTCTGC 57.631 30.769 7.05 0.00 36.11 4.26
129 134 6.774354 TTGAATTCTTTTCTGCATTTGCTC 57.226 33.333 7.05 0.00 42.66 4.26
217 222 4.272489 TGGACAAATCCTCCAATCACATC 58.728 43.478 0.00 0.00 46.43 3.06
251 261 9.372369 ACAAGTACTCAAGAAGTAAGCAATATC 57.628 33.333 0.00 0.00 42.11 1.63
269 279 6.094603 GCAATATCCAAGAACACTGACTCAAT 59.905 38.462 0.00 0.00 0.00 2.57
270 280 7.678218 GCAATATCCAAGAACACTGACTCAATC 60.678 40.741 0.00 0.00 0.00 2.67
320 334 5.050644 TGACACATTTTGCTGCTTATCAG 57.949 39.130 0.00 0.00 45.62 2.90
337 351 0.321564 CAGCCACCGGAATGTTCTCA 60.322 55.000 9.46 0.00 0.00 3.27
348 362 4.332819 CGGAATGTTCTCAAGGATGGTTAC 59.667 45.833 0.00 0.00 0.00 2.50
380 394 5.011329 ACTGCAAGATTCATCACCATTGTTT 59.989 36.000 0.00 0.00 37.43 2.83
437 467 8.892723 TGCAGAAATACATTCCACATAGTTTAG 58.107 33.333 0.00 0.00 38.94 1.85
462 494 8.527810 AGAACTATCTGTAATCTAAGGCATAGC 58.472 37.037 0.00 0.00 33.59 2.97
472 504 1.978454 AAGGCATAGCTGGAGAATGC 58.022 50.000 9.49 9.49 44.16 3.56
484 516 3.976339 AGAATGCCGATTCTCCTCG 57.024 52.632 0.00 0.00 44.30 4.63
531 563 1.834188 CGCTAACTTTTGGGGGATGT 58.166 50.000 0.00 0.00 0.00 3.06
587 4073 6.196538 GTGCAGAAAATAGCTTTAATAACGCC 59.803 38.462 0.00 0.00 0.00 5.68
592 4078 4.699925 ATAGCTTTAATAACGCCAGGGA 57.300 40.909 0.00 0.00 0.00 4.20
767 4552 0.881118 CGTGGTGGAATGTTTCAGGG 59.119 55.000 0.00 0.00 0.00 4.45
811 4596 1.586154 GCAACTGGACCCGTCAATGG 61.586 60.000 0.00 0.00 0.00 3.16
826 4611 3.889525 ATGGCCCTGACAGGTGGGA 62.890 63.158 20.24 1.69 46.15 4.37
830 4615 2.153401 CCCTGACAGGTGGGACCAA 61.153 63.158 20.24 0.00 46.15 3.67
842 4627 0.765510 GGGACCAACAGTTCAGGACT 59.234 55.000 0.00 0.00 39.89 3.85
843 4628 1.143073 GGGACCAACAGTTCAGGACTT 59.857 52.381 0.00 0.00 36.10 3.01
966 4759 4.537433 CACCTAGCGCTGCCCCTC 62.537 72.222 22.90 0.00 0.00 4.30
989 4791 1.705186 CCTCACTCTGGGGGAAAAAGA 59.295 52.381 0.00 0.00 33.20 2.52
1092 4894 0.965866 TGCAGTACCACTCCCTCTCG 60.966 60.000 0.00 0.00 0.00 4.04
1151 4959 1.794222 CGTCTGTTTTGGCCGGATC 59.206 57.895 5.05 0.00 0.00 3.36
1419 6363 7.014711 TGTTGAGATCTGACCTTGTATCCTATC 59.985 40.741 0.00 0.00 0.00 2.08
1428 6372 7.306013 TGACCTTGTATCCTATCCTATGTCTT 58.694 38.462 0.00 0.00 0.00 3.01
1479 6423 6.466038 CCCTGAGAGAGAATCCATCAATTCAT 60.466 42.308 0.00 0.00 37.98 2.57
1507 6451 5.290885 CACGAGATGGTATTGATCGTTTGAA 59.709 40.000 0.00 0.00 43.51 2.69
1508 6452 5.520288 ACGAGATGGTATTGATCGTTTGAAG 59.480 40.000 0.00 0.00 43.51 3.02
1513 6457 9.396022 AGATGGTATTGATCGTTTGAAGTATTT 57.604 29.630 0.00 0.00 0.00 1.40
1554 6503 9.578576 TCTCTTACTACAGTTAACTTCCAAGTA 57.421 33.333 5.07 8.39 38.57 2.24
1718 6669 5.818136 TCAGGTAAAATTACATGCAGCTC 57.182 39.130 11.89 0.00 43.08 4.09
1792 6747 7.272084 CACTAGCATTGTCAGCAAATTTAGTTC 59.728 37.037 0.00 0.00 38.21 3.01
1829 6785 7.962964 TTCAACAATCTAGAATTCGTTGTCT 57.037 32.000 18.53 8.45 36.14 3.41
1835 6791 8.692710 ACAATCTAGAATTCGTTGTCTACCATA 58.307 33.333 0.00 0.00 0.00 2.74
1920 7060 7.040961 TCGTGCTATGCTATATGTACAGTAACA 60.041 37.037 0.33 0.00 0.00 2.41
1968 7373 7.439157 TGGCAATGCTGATTGTAGTATATTC 57.561 36.000 4.82 0.00 41.09 1.75
1995 7400 3.975168 TTGCTTACTCTGACCCTTACC 57.025 47.619 0.00 0.00 0.00 2.85
2022 7427 7.038659 AGTTACAGAATATGCTTCAGTCTCAC 58.961 38.462 0.00 0.00 0.00 3.51
2048 7454 6.424207 CCCGTTAAGATTTAATCACCTAGAGC 59.576 42.308 7.74 0.00 0.00 4.09
2343 8110 3.203487 TGGTAACCCCTCCAACCATATTC 59.797 47.826 0.00 0.00 37.09 1.75
2363 8381 2.033927 TCGCTTATCTGCTAGACTGCTG 59.966 50.000 0.00 0.00 0.00 4.41
2419 8437 9.185680 AGTGTTGTTTTCTTGTATTCTAGGTTT 57.814 29.630 0.00 0.00 0.00 3.27
2434 8452 3.297134 AGGTTTGAGAAGCACTTTGGA 57.703 42.857 0.00 0.00 35.74 3.53
2437 8455 2.325583 TTGAGAAGCACTTTGGACGT 57.674 45.000 0.00 0.00 0.00 4.34
2583 8608 7.293745 GCATGCTGCAGTTTATACTAACATAG 58.706 38.462 16.64 3.01 44.26 2.23
2584 8609 7.041780 GCATGCTGCAGTTTATACTAACATAGT 60.042 37.037 16.64 0.00 44.26 2.12
2761 8786 0.385390 GTTGTTCTGCAGGTTGGGTG 59.615 55.000 15.13 0.00 0.00 4.61
3519 9559 8.008586 AGCCACTTGCCAAAAGAATTTTATACC 61.009 37.037 0.00 0.00 44.13 2.73
3643 9685 7.659652 ACTCACAACATCTTCTTACTTAAGC 57.340 36.000 1.29 0.00 33.40 3.09
4180 10244 1.479323 CAAATGGTCAGCAGAATGGGG 59.521 52.381 0.00 0.00 35.86 4.96
4304 10369 6.239008 GCAATTTGCAGGTCATAGGCTAAATA 60.239 38.462 16.35 0.00 44.26 1.40
4312 10378 7.547370 GCAGGTCATAGGCTAAATACTCAATAG 59.453 40.741 0.00 0.00 0.00 1.73
4378 10444 6.114089 CCTGAATATCTGCTGATTCCATAGG 58.886 44.000 11.65 9.50 34.32 2.57
4422 10503 6.850752 TGAGTGACCAGATGTACATTAGAA 57.149 37.500 10.30 0.00 0.00 2.10
4423 10504 6.867550 TGAGTGACCAGATGTACATTAGAAG 58.132 40.000 10.30 0.70 0.00 2.85
4424 10505 6.127338 TGAGTGACCAGATGTACATTAGAAGG 60.127 42.308 10.30 10.01 0.00 3.46
4425 10506 5.721960 AGTGACCAGATGTACATTAGAAGGT 59.278 40.000 10.30 12.92 0.00 3.50
4426 10507 6.213600 AGTGACCAGATGTACATTAGAAGGTT 59.786 38.462 10.30 0.00 0.00 3.50
4427 10508 6.313905 GTGACCAGATGTACATTAGAAGGTTG 59.686 42.308 10.30 0.00 0.00 3.77
4591 10693 5.437060 ACTACCTAAATGCCCAGTTACATG 58.563 41.667 0.00 0.00 0.00 3.21
4732 10838 0.461548 CGCCCTGCTAGTTCAGATCA 59.538 55.000 0.00 0.00 36.19 2.92
4838 10959 5.293814 CACTCTGAATCTGTTGTGATCCATC 59.706 44.000 9.02 0.00 0.00 3.51
4847 10968 3.274288 GTTGTGATCCATCTGTTCCCTC 58.726 50.000 0.00 0.00 0.00 4.30
4855 10976 0.613777 ATCTGTTCCCTCGTTCACCC 59.386 55.000 0.00 0.00 0.00 4.61
4894 11015 2.026014 GGCAATTGCGCCGTATGG 59.974 61.111 23.48 0.00 43.52 2.74
4895 11016 2.770589 GGCAATTGCGCCGTATGGT 61.771 57.895 23.48 0.00 43.52 3.55
4911 11032 0.175760 TGGTGGTAGCTCTTGATCGC 59.824 55.000 0.00 0.00 0.00 4.58
4918 11039 2.279784 CTCTTGATCGCGGCCTCC 60.280 66.667 6.13 0.00 0.00 4.30
4919 11040 3.074369 TCTTGATCGCGGCCTCCA 61.074 61.111 6.13 0.00 0.00 3.86
4921 11042 2.125147 TTGATCGCGGCCTCCAAG 60.125 61.111 6.13 0.00 0.00 3.61
4922 11043 2.859273 CTTGATCGCGGCCTCCAAGT 62.859 60.000 6.13 0.00 32.06 3.16
4923 11044 2.586357 GATCGCGGCCTCCAAGTC 60.586 66.667 6.13 0.00 0.00 3.01
4983 11469 2.835317 TACCCCGAACGTCCCGATCA 62.835 60.000 11.21 0.00 0.00 2.92
4998 11484 3.974835 ATCAACAGCATCGCCGCCA 62.975 57.895 0.00 0.00 0.00 5.69
5026 11512 4.681978 GTGGCGGTGGAGCTCGTT 62.682 66.667 7.83 0.00 37.29 3.85
5076 11562 0.459489 TGCAAAGTGTGGGTTTCAGC 59.541 50.000 0.00 0.00 0.00 4.26
5104 11594 1.066143 TGATGAAGGCGAAGAGGGAAC 60.066 52.381 0.00 0.00 0.00 3.62
5105 11595 0.984230 ATGAAGGCGAAGAGGGAACA 59.016 50.000 0.00 0.00 0.00 3.18
5106 11596 0.984230 TGAAGGCGAAGAGGGAACAT 59.016 50.000 0.00 0.00 0.00 2.71
5111 11601 1.604278 GGCGAAGAGGGAACATATTGC 59.396 52.381 0.00 0.00 0.00 3.56
5133 11623 3.304391 CGGTTTCAGGTTGGTGTTACATG 60.304 47.826 0.00 0.00 0.00 3.21
5138 11635 3.084039 CAGGTTGGTGTTACATGCTGAT 58.916 45.455 0.00 0.00 0.00 2.90
5196 11866 0.947244 CTGCGCTGAACTCTGGTTTT 59.053 50.000 9.73 0.00 35.58 2.43
5269 11942 1.529244 AGCAGCACAAGGACCCAAC 60.529 57.895 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 5.099484 TGATTCAAGCGATCAATGTATGC 57.901 39.130 0.00 0.00 0.00 3.14
77 79 2.349590 GAGCCCCAAACATGATTTTGC 58.650 47.619 0.00 0.00 35.48 3.68
81 83 2.629017 AAGGAGCCCCAAACATGATT 57.371 45.000 0.00 0.00 33.88 2.57
97 102 8.145316 TGCAGAAAAGAATTCAAAATGAAAGG 57.855 30.769 8.44 0.00 40.12 3.11
269 279 5.755375 GTGTGTTTCTCTTCTTGATGTCTGA 59.245 40.000 0.00 0.00 0.00 3.27
270 280 5.049818 GGTGTGTTTCTCTTCTTGATGTCTG 60.050 44.000 0.00 0.00 0.00 3.51
320 334 0.804989 CTTGAGAACATTCCGGTGGC 59.195 55.000 0.00 0.00 0.00 5.01
337 351 2.026262 AGTGCGAATGGTAACCATCCTT 60.026 45.455 0.00 0.00 44.40 3.36
348 362 1.469703 TGAATCTTGCAGTGCGAATGG 59.530 47.619 11.20 0.00 0.00 3.16
380 394 4.338795 AGAGGAGGACAAGGACATAGAA 57.661 45.455 0.00 0.00 0.00 2.10
437 467 8.527810 AGCTATGCCTTAGATTACAGATAGTTC 58.472 37.037 0.00 0.00 0.00 3.01
472 504 0.390860 ATTCCTGCGAGGAGAATCGG 59.609 55.000 5.26 0.00 46.73 4.18
479 511 1.220749 CCCGAAATTCCTGCGAGGA 59.779 57.895 1.25 1.25 44.10 3.71
482 514 0.463654 CATCCCCGAAATTCCTGCGA 60.464 55.000 0.00 0.00 0.00 5.10
484 516 1.109323 CCCATCCCCGAAATTCCTGC 61.109 60.000 0.00 0.00 0.00 4.85
587 4073 2.045045 TGAGCCCGCAATTCCCTG 60.045 61.111 0.00 0.00 0.00 4.45
811 4596 4.035102 GGTCCCACCTGTCAGGGC 62.035 72.222 23.06 7.35 45.07 5.19
826 4611 3.947834 CTGAAAAGTCCTGAACTGTTGGT 59.052 43.478 0.00 0.00 35.45 3.67
830 4615 2.576615 GGCTGAAAAGTCCTGAACTGT 58.423 47.619 0.00 0.00 38.58 3.55
842 4627 2.036604 GGGATCCAAAAACGGCTGAAAA 59.963 45.455 15.23 0.00 0.00 2.29
843 4628 1.616374 GGGATCCAAAAACGGCTGAAA 59.384 47.619 15.23 0.00 0.00 2.69
937 4730 4.682334 TAGGTGTGGACGGCGGGA 62.682 66.667 13.24 0.00 0.00 5.14
939 4732 4.814294 GCTAGGTGTGGACGGCGG 62.814 72.222 13.24 0.00 0.00 6.13
971 4764 3.559171 CGAATCTTTTTCCCCCAGAGTGA 60.559 47.826 0.00 0.00 0.00 3.41
973 4766 2.642807 TCGAATCTTTTTCCCCCAGAGT 59.357 45.455 0.00 0.00 0.00 3.24
1151 4959 7.251704 ACACAAAATCCTATGCTCTAATTCG 57.748 36.000 0.00 0.00 0.00 3.34
1419 6363 3.937706 CACTTCCTGCTCAAAGACATAGG 59.062 47.826 0.00 0.00 0.00 2.57
1428 6372 0.620556 GGGGATCACTTCCTGCTCAA 59.379 55.000 0.00 0.00 44.75 3.02
1455 6399 5.926663 TGAATTGATGGATTCTCTCTCAGG 58.073 41.667 0.00 0.00 37.04 3.86
1479 6423 6.812879 ACGATCAATACCATCTCGTGTATA 57.187 37.500 0.00 0.00 40.68 1.47
1549 6498 8.886719 TGCACTGATTTCTGAAGATAATACTTG 58.113 33.333 0.00 0.00 0.00 3.16
1554 6503 7.934855 AACTGCACTGATTTCTGAAGATAAT 57.065 32.000 0.00 0.00 0.00 1.28
1718 6669 7.558161 TCTGAACCACATATGCAAATAAGAG 57.442 36.000 1.58 0.00 0.00 2.85
1771 6726 7.412137 AAAGAACTAAATTTGCTGACAATGC 57.588 32.000 0.00 0.00 35.21 3.56
1803 6759 8.446273 AGACAACGAATTCTAGATTGTTGAATG 58.554 33.333 24.15 7.26 39.11 2.67
1896 7031 8.988064 ATGTTACTGTACATATAGCATAGCAC 57.012 34.615 12.23 0.00 36.99 4.40
1920 7060 9.874205 CCAAAATGAGAATGGTGTAAACAATAT 57.126 29.630 0.00 0.00 0.00 1.28
1968 7373 4.520492 AGGGTCAGAGTAAGCAATTTTGTG 59.480 41.667 0.00 0.00 0.00 3.33
1995 7400 8.409371 TGAGACTGAAGCATATTCTGTAACTAG 58.591 37.037 0.89 0.00 32.04 2.57
2022 7427 6.823497 TCTAGGTGATTAAATCTTAACGGGG 58.177 40.000 0.00 0.00 0.00 5.73
2095 7502 8.145312 GTGAAACGCGATAACTAAATTTTTGAC 58.855 33.333 15.93 0.00 0.00 3.18
2096 7503 7.856398 TGTGAAACGCGATAACTAAATTTTTGA 59.144 29.630 15.93 0.00 42.39 2.69
2097 7504 7.987486 TGTGAAACGCGATAACTAAATTTTTG 58.013 30.769 15.93 0.00 42.39 2.44
2098 7505 7.858879 ACTGTGAAACGCGATAACTAAATTTTT 59.141 29.630 15.93 0.00 42.39 1.94
2320 8087 1.462426 ATGGTTGGAGGGGTTACCAA 58.538 50.000 2.98 0.00 43.35 3.67
2343 8110 2.392821 CAGCAGTCTAGCAGATAAGCG 58.607 52.381 0.00 0.00 40.15 4.68
2363 8381 5.036117 ACACATGACCAATAGGATACACC 57.964 43.478 0.00 0.00 38.69 4.16
2397 8415 9.621629 TCTCAAACCTAGAATACAAGAAAACAA 57.378 29.630 0.00 0.00 0.00 2.83
2405 8423 6.769512 AGTGCTTCTCAAACCTAGAATACAA 58.230 36.000 0.00 0.00 32.72 2.41
2419 8437 3.325870 CATACGTCCAAAGTGCTTCTCA 58.674 45.455 0.00 0.00 0.00 3.27
2434 8452 4.540153 GCACCATCAGCCATACGT 57.460 55.556 0.00 0.00 0.00 3.57
2538 8557 1.535028 CGCACAACAGCCTTAATGACA 59.465 47.619 0.00 0.00 0.00 3.58
2539 8558 1.729149 GCGCACAACAGCCTTAATGAC 60.729 52.381 0.30 0.00 0.00 3.06
2540 8559 0.521291 GCGCACAACAGCCTTAATGA 59.479 50.000 0.30 0.00 0.00 2.57
2541 8560 0.240678 TGCGCACAACAGCCTTAATG 59.759 50.000 5.66 0.00 0.00 1.90
2543 8562 0.240678 CATGCGCACAACAGCCTTAA 59.759 50.000 14.90 0.00 0.00 1.85
2583 8608 4.925068 ACTGTTGCTCTGAAAATTGTGAC 58.075 39.130 0.00 0.00 0.00 3.67
2584 8609 5.357878 AGAACTGTTGCTCTGAAAATTGTGA 59.642 36.000 0.00 0.00 0.00 3.58
3425 9463 0.878523 CGGAAGGCAACACGTCTCAA 60.879 55.000 0.00 0.00 41.41 3.02
4180 10244 4.518970 TCACCAAAGGAAGTGCATTAGTTC 59.481 41.667 0.00 0.00 37.89 3.01
4304 10369 9.486497 CACATCTGATTAGCATTACTATTGAGT 57.514 33.333 0.00 0.00 39.92 3.41
4312 10378 9.109393 TCCTTTTACACATCTGATTAGCATTAC 57.891 33.333 0.00 0.00 0.00 1.89
4317 10383 6.543831 ACCATCCTTTTACACATCTGATTAGC 59.456 38.462 0.00 0.00 0.00 3.09
4422 10503 1.650528 CCTCTCCTCAACCTCAACCT 58.349 55.000 0.00 0.00 0.00 3.50
4423 10504 0.615850 CCCTCTCCTCAACCTCAACC 59.384 60.000 0.00 0.00 0.00 3.77
4424 10505 0.035915 GCCCTCTCCTCAACCTCAAC 60.036 60.000 0.00 0.00 0.00 3.18
4425 10506 0.473694 TGCCCTCTCCTCAACCTCAA 60.474 55.000 0.00 0.00 0.00 3.02
4426 10507 0.252881 ATGCCCTCTCCTCAACCTCA 60.253 55.000 0.00 0.00 0.00 3.86
4427 10508 0.179936 CATGCCCTCTCCTCAACCTC 59.820 60.000 0.00 0.00 0.00 3.85
4512 10608 2.612221 CGGTAGGTTCTGTCAAAGACCC 60.612 54.545 0.00 0.00 37.76 4.46
4720 10826 6.377780 CAGATATCGTGGTGATCTGAACTAG 58.622 44.000 5.37 0.00 46.31 2.57
4721 10827 5.241728 CCAGATATCGTGGTGATCTGAACTA 59.758 44.000 11.70 0.00 46.31 2.24
4732 10838 0.753262 GTGCCTCCAGATATCGTGGT 59.247 55.000 16.20 0.00 36.37 4.16
4838 10959 1.374252 CGGGTGAACGAGGGAACAG 60.374 63.158 0.00 0.00 35.47 3.16
4891 11012 1.202580 GCGATCAAGAGCTACCACCAT 60.203 52.381 0.00 0.00 0.00 3.55
4892 11013 0.175760 GCGATCAAGAGCTACCACCA 59.824 55.000 0.00 0.00 0.00 4.17
4893 11014 0.872021 CGCGATCAAGAGCTACCACC 60.872 60.000 0.00 0.00 0.00 4.61
4894 11015 0.872021 CCGCGATCAAGAGCTACCAC 60.872 60.000 8.23 0.00 0.00 4.16
4895 11016 1.437573 CCGCGATCAAGAGCTACCA 59.562 57.895 8.23 0.00 0.00 3.25
4918 11039 0.108804 ACATACCCAGCGACGACTTG 60.109 55.000 0.00 0.00 0.00 3.16
4919 11040 0.172803 GACATACCCAGCGACGACTT 59.827 55.000 0.00 0.00 0.00 3.01
4921 11042 1.585521 CGACATACCCAGCGACGAC 60.586 63.158 0.00 0.00 0.00 4.34
4922 11043 1.588824 AACGACATACCCAGCGACGA 61.589 55.000 0.00 0.00 0.00 4.20
4923 11044 0.099259 TAACGACATACCCAGCGACG 59.901 55.000 0.00 0.00 0.00 5.12
5026 11512 2.670229 GCTGATACTGAACGTTCCGACA 60.670 50.000 24.78 17.91 0.00 4.35
5076 11562 2.084610 TCGCCTTCATCACAAGTGAG 57.915 50.000 8.99 1.93 43.61 3.51
5104 11594 2.491693 ACCAACCTGAAACCGCAATATG 59.508 45.455 0.00 0.00 0.00 1.78
5105 11595 2.491693 CACCAACCTGAAACCGCAATAT 59.508 45.455 0.00 0.00 0.00 1.28
5106 11596 1.883275 CACCAACCTGAAACCGCAATA 59.117 47.619 0.00 0.00 0.00 1.90
5111 11601 2.290464 TGTAACACCAACCTGAAACCG 58.710 47.619 0.00 0.00 0.00 4.44
5133 11623 4.156556 TCATGGCAGTTTCAACTTATCAGC 59.843 41.667 0.00 0.00 37.08 4.26
5269 11942 0.811281 GGACGCTGATTTCCTTTGGG 59.189 55.000 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.