Multiple sequence alignment - TraesCS2D01G396600

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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 TraesCS2D01G396600 chr2D 100.000 4443 0 0 1 4443 507828735 507824293 0.000000e+00 8205.0
1 TraesCS2D01G396600 chr2B 93.743 3740 131 27 1 3687 596653101 596649412 0.000000e+00 5515.0
2 TraesCS2D01G396600 chr2B 95.844 818 18 10 3627 4443 596649430 596648628 0.000000e+00 1308.0
3 TraesCS2D01G396600 chr2A 96.833 1989 55 6 1272 3257 652332166 652330183 0.000000e+00 3317.0
4 TraesCS2D01G396600 chr2A 92.371 1219 63 10 1 1217 652333459 652332269 0.000000e+00 1709.0
5 TraesCS2D01G396600 chr2A 90.871 712 21 18 3734 4443 652329283 652328614 0.000000e+00 915.0
6 TraesCS2D01G396600 chr2A 94.038 369 20 1 3253 3619 652329872 652329504 3.880000e-155 558.0
7 TraesCS2D01G396600 chr2A 81.897 116 15 2 3618 3733 652329414 652329305 4.730000e-15 93.5
8 TraesCS2D01G396600 chr6D 83.127 646 101 7 1331 1972 338933007 338933648 2.300000e-162 582.0
9 TraesCS2D01G396600 chr6D 82.149 577 96 7 2611 3182 338934204 338934778 5.170000e-134 488.0
10 TraesCS2D01G396600 chr6D 80.590 407 69 9 2118 2519 338933805 338934206 5.580000e-79 305.0
11 TraesCS2D01G396600 chr6B 83.127 646 101 7 1331 1972 481397777 481397136 2.300000e-162 582.0
12 TraesCS2D01G396600 chr6B 82.007 578 95 9 2611 3182 481396584 481396010 2.400000e-132 483.0
13 TraesCS2D01G396600 chr6B 81.773 406 66 8 2118 2519 481396983 481396582 2.560000e-87 333.0
14 TraesCS2D01G396600 chr6A 82.764 644 107 4 1331 1972 479635716 479636357 4.990000e-159 571.0
15 TraesCS2D01G396600 chr6A 82.872 578 90 7 2611 3182 479636911 479637485 1.100000e-140 510.0
16 TraesCS2D01G396600 chr6A 80.590 407 69 9 2118 2519 479636512 479636913 5.580000e-79 305.0
17 TraesCS2D01G396600 chr4D 80.407 541 93 12 1370 1902 500851787 500851252 2.490000e-107 399.0
18 TraesCS2D01G396600 chr4B 79.298 541 99 12 1370 1902 644828267 644827732 2.530000e-97 366.0
19 TraesCS2D01G396600 chr4B 74.407 590 119 25 2611 3181 644827051 644826475 1.610000e-54 224.0
20 TraesCS2D01G396600 chr1B 78.216 583 115 12 2611 3187 350398094 350397518 3.270000e-96 363.0
21 TraesCS2D01G396600 chr1D 77.797 581 121 8 2611 3187 261735503 261736079 7.070000e-93 351.0
22 TraesCS2D01G396600 chr1A 77.586 580 124 6 2611 3187 338589537 338588961 3.290000e-91 346.0
23 TraesCS2D01G396600 chr7A 79.528 127 17 7 2123 2242 10985262 10985138 1.020000e-11 82.4
24 TraesCS2D01G396600 chr7D 92.453 53 2 2 2191 2242 11611740 11611689 1.710000e-09 75.0
25 TraesCS2D01G396600 chr4A 88.679 53 4 2 2191 2242 726326244 726326295 3.710000e-06 63.9


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 TraesCS2D01G396600 chr2D 507824293 507828735 4442 True 8205.000000 8205 100.000000 1 4443 1 chr2D.!!$R1 4442
1 TraesCS2D01G396600 chr2B 596648628 596653101 4473 True 3411.500000 5515 94.793500 1 4443 2 chr2B.!!$R1 4442
2 TraesCS2D01G396600 chr2A 652328614 652333459 4845 True 1318.500000 3317 91.202000 1 4443 5 chr2A.!!$R1 4442
3 TraesCS2D01G396600 chr6D 338933007 338934778 1771 False 458.333333 582 81.955333 1331 3182 3 chr6D.!!$F1 1851
4 TraesCS2D01G396600 chr6B 481396010 481397777 1767 True 466.000000 582 82.302333 1331 3182 3 chr6B.!!$R1 1851
5 TraesCS2D01G396600 chr6A 479635716 479637485 1769 False 462.000000 571 82.075333 1331 3182 3 chr6A.!!$F1 1851
6 TraesCS2D01G396600 chr4D 500851252 500851787 535 True 399.000000 399 80.407000 1370 1902 1 chr4D.!!$R1 532
7 TraesCS2D01G396600 chr4B 644826475 644828267 1792 True 295.000000 366 76.852500 1370 3181 2 chr4B.!!$R1 1811
8 TraesCS2D01G396600 chr1B 350397518 350398094 576 True 363.000000 363 78.216000 2611 3187 1 chr1B.!!$R1 576
9 TraesCS2D01G396600 chr1D 261735503 261736079 576 False 351.000000 351 77.797000 2611 3187 1 chr1D.!!$F1 576
10 TraesCS2D01G396600 chr1A 338588961 338589537 576 True 346.000000 346 77.586000 2611 3187 1 chr1A.!!$R1 576

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
451 457 0.179258 GAAAAAGGCGTCGTAGTGCG 60.179 55.0 0.00 0.0 43.01 5.34 F
1112 1172 0.550914 AAGAACCAAGCTCCACCACA 59.449 50.0 0.00 0.0 0.00 4.17 F
2599 2738 0.330604 ACTGTGATCCCAGCTTGCAT 59.669 50.0 4.97 0.0 35.83 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1254 1354 0.247460 TGCAAGATGGACACGGAGAG 59.753 55.000 0.00 0.0 0.00 3.20 R
2607 2746 1.073722 CCAGCTGCCCAGTCTGAAA 59.926 57.895 8.66 0.0 35.83 2.69 R
4302 4967 0.752743 ACAAGCAAGCAAGCAGTCCA 60.753 50.000 3.19 0.0 36.85 4.02 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
60 61 2.032634 GCTTTCGCGGGTCATGTCA 61.033 57.895 6.13 0.00 0.00 3.58
237 238 1.443702 CGTCTCCATCGTCGCAACA 60.444 57.895 0.00 0.00 0.00 3.33
328 329 2.242043 CAGGCAGTGAAAATGGTTCCT 58.758 47.619 0.00 0.00 28.90 3.36
451 457 0.179258 GAAAAAGGCGTCGTAGTGCG 60.179 55.000 0.00 0.00 43.01 5.34
457 463 1.866496 GCGTCGTAGTGCGGTAGTG 60.866 63.158 0.00 0.00 41.72 2.74
466 472 2.173020 TGCGGTAGTGCATGCATCG 61.173 57.895 25.64 23.46 40.62 3.84
608 625 9.841295 TTTAAAGTGACAAGGTATTTCTGTACT 57.159 29.630 0.00 0.00 0.00 2.73
609 626 7.964604 AAAGTGACAAGGTATTTCTGTACTC 57.035 36.000 0.00 0.00 0.00 2.59
610 627 6.038997 AGTGACAAGGTATTTCTGTACTCC 57.961 41.667 0.00 0.00 0.00 3.85
611 628 5.780793 AGTGACAAGGTATTTCTGTACTCCT 59.219 40.000 0.00 0.00 0.00 3.69
812 847 4.803426 CTCACCCGCTGACTCGCC 62.803 72.222 0.00 0.00 0.00 5.54
1077 1137 1.136828 TAAAGGGCGCATGGTATCCT 58.863 50.000 10.83 0.45 0.00 3.24
1083 1143 2.046938 CGCATGGTATCCTACGGGT 58.953 57.895 0.00 0.00 0.00 5.28
1112 1172 0.550914 AAGAACCAAGCTCCACCACA 59.449 50.000 0.00 0.00 0.00 4.17
1254 1354 1.880027 CCACAAGGTGACTGGTTTAGC 59.120 52.381 0.00 0.00 44.30 3.09
1269 1369 2.145397 TTAGCTCTCCGTGTCCATCT 57.855 50.000 0.00 0.00 0.00 2.90
1276 1376 2.499693 TCTCCGTGTCCATCTTGCATTA 59.500 45.455 0.00 0.00 0.00 1.90
1291 1399 4.383850 TGCATTATGCCATTGTGTTACC 57.616 40.909 15.06 0.00 44.23 2.85
1311 1419 1.063027 CGATTGATGAGCGTGTGCATT 59.937 47.619 0.00 0.00 46.23 3.56
1313 1421 1.521580 TTGATGAGCGTGTGCATTGA 58.478 45.000 0.00 0.00 46.23 2.57
1314 1422 1.741528 TGATGAGCGTGTGCATTGAT 58.258 45.000 0.00 0.00 46.23 2.57
1315 1423 1.399089 TGATGAGCGTGTGCATTGATG 59.601 47.619 0.00 0.00 46.23 3.07
1316 1424 1.399440 GATGAGCGTGTGCATTGATGT 59.601 47.619 0.00 0.00 46.23 3.06
1329 1437 5.005203 GTGCATTGATGTCGTGAAACAAAAA 59.995 36.000 0.00 0.00 35.74 1.94
2091 2220 4.368808 CGTCACCCGCGCTTGTTG 62.369 66.667 5.56 0.00 0.00 3.33
2206 2335 1.601663 CGCAACGAGATCATCCTCTCC 60.602 57.143 0.00 0.00 38.78 3.71
2528 2664 1.002430 TCTCTCCACAGGTACGTACGT 59.998 52.381 25.98 25.98 0.00 3.57
2529 2665 2.233676 TCTCTCCACAGGTACGTACGTA 59.766 50.000 23.60 23.60 0.00 3.57
2530 2666 3.118629 TCTCTCCACAGGTACGTACGTAT 60.119 47.826 29.05 13.24 32.82 3.06
2538 2674 3.660813 CAGGTACGTACGTATACATTGCG 59.339 47.826 29.05 9.94 32.82 4.85
2562 2700 2.163412 TGACACTGACAACTTGCCAAAC 59.837 45.455 0.00 0.00 0.00 2.93
2591 2730 2.224523 GGAACAGAACACTGTGATCCCA 60.225 50.000 15.86 0.00 43.00 4.37
2598 2737 0.607217 CACTGTGATCCCAGCTTGCA 60.607 55.000 4.97 0.00 35.83 4.08
2599 2738 0.330604 ACTGTGATCCCAGCTTGCAT 59.669 50.000 4.97 0.00 35.83 3.96
2600 2739 0.738975 CTGTGATCCCAGCTTGCATG 59.261 55.000 0.00 0.00 0.00 4.06
2607 2746 0.963962 CCCAGCTTGCATGTTGTTCT 59.036 50.000 13.99 0.00 0.00 3.01
2783 2941 2.429930 CTGCGGAACCTCAACCCA 59.570 61.111 0.00 0.00 0.00 4.51
3329 3816 3.436243 AGGTCGGATCCTATCAATCTCC 58.564 50.000 10.75 0.00 35.87 3.71
3340 3827 6.448202 TCCTATCAATCTCCCTTTCTCTCTT 58.552 40.000 0.00 0.00 0.00 2.85
3341 3828 7.596407 TCCTATCAATCTCCCTTTCTCTCTTA 58.404 38.462 0.00 0.00 0.00 2.10
3342 3829 8.068110 TCCTATCAATCTCCCTTTCTCTCTTAA 58.932 37.037 0.00 0.00 0.00 1.85
3442 3932 7.569599 AGGATTAAGGAGGAGAAAACTGTAA 57.430 36.000 0.00 0.00 0.00 2.41
3499 4010 6.808212 GCATTTGTTATTGCAGTATGTGAACT 59.192 34.615 0.00 0.00 39.31 3.01
3500 4011 7.967854 GCATTTGTTATTGCAGTATGTGAACTA 59.032 33.333 0.00 0.00 39.31 2.24
3503 4014 9.838975 TTTGTTATTGCAGTATGTGAACTATTG 57.161 29.630 0.00 0.00 39.31 1.90
3504 4015 8.560355 TGTTATTGCAGTATGTGAACTATTGT 57.440 30.769 0.00 0.00 39.31 2.71
3505 4016 8.664798 TGTTATTGCAGTATGTGAACTATTGTC 58.335 33.333 0.00 0.00 39.31 3.18
3506 4017 8.664798 GTTATTGCAGTATGTGAACTATTGTCA 58.335 33.333 0.00 0.00 39.31 3.58
3507 4018 6.480524 TTGCAGTATGTGAACTATTGTCAC 57.519 37.500 0.00 0.00 39.31 3.67
3508 4019 4.625311 TGCAGTATGTGAACTATTGTCACG 59.375 41.667 0.57 0.00 39.31 4.35
3509 4020 4.032900 GCAGTATGTGAACTATTGTCACGG 59.967 45.833 0.57 0.00 39.31 4.94
3510 4021 5.407502 CAGTATGTGAACTATTGTCACGGA 58.592 41.667 0.57 0.00 37.20 4.69
3511 4022 5.288712 CAGTATGTGAACTATTGTCACGGAC 59.711 44.000 0.57 0.00 37.20 4.79
3512 4023 4.537135 ATGTGAACTATTGTCACGGACT 57.463 40.909 5.77 0.00 37.20 3.85
3513 4024 5.654603 ATGTGAACTATTGTCACGGACTA 57.345 39.130 5.77 0.00 37.20 2.59
3514 4025 5.055642 TGTGAACTATTGTCACGGACTAG 57.944 43.478 5.77 0.00 37.20 2.57
3515 4026 4.763279 TGTGAACTATTGTCACGGACTAGA 59.237 41.667 0.00 0.00 37.20 2.43
3516 4027 5.242171 TGTGAACTATTGTCACGGACTAGAA 59.758 40.000 0.00 0.00 37.20 2.10
3517 4028 6.071560 TGTGAACTATTGTCACGGACTAGAAT 60.072 38.462 0.00 1.30 37.20 2.40
3518 4029 6.812160 GTGAACTATTGTCACGGACTAGAATT 59.188 38.462 0.00 0.00 33.15 2.17
3519 4030 7.009357 GTGAACTATTGTCACGGACTAGAATTC 59.991 40.741 0.00 0.00 33.15 2.17
3572 4083 1.127701 GCGTGTTCGTTTGTACCGTA 58.872 50.000 0.00 0.00 39.49 4.02
3581 4092 4.366586 TCGTTTGTACCGTAATCAACACA 58.633 39.130 0.00 0.00 0.00 3.72
3635 4237 8.638685 ATTTGTGTTTGAGAAGAAATCTTGTG 57.361 30.769 0.00 0.00 38.96 3.33
3641 4243 5.936686 TGAGAAGAAATCTTGTGCAGAAG 57.063 39.130 17.19 17.19 38.96 2.85
3642 4244 5.371526 TGAGAAGAAATCTTGTGCAGAAGT 58.628 37.500 21.71 7.99 38.96 3.01
3674 4318 7.497925 ACTGACTTACTTTTGGTCAAATCTC 57.502 36.000 0.00 0.00 39.11 2.75
4018 4683 6.230472 AGAAGAAGAAGAAGAAGAAGAAGGC 58.770 40.000 0.00 0.00 0.00 4.35
4020 4685 3.712016 AGAAGAAGAAGAAGAAGGCCC 57.288 47.619 0.00 0.00 0.00 5.80
4021 4686 2.027653 AGAAGAAGAAGAAGAAGGCCCG 60.028 50.000 0.00 0.00 0.00 6.13
4023 4688 1.978580 AGAAGAAGAAGAAGGCCCGAA 59.021 47.619 0.00 0.00 0.00 4.30
4024 4689 2.027653 AGAAGAAGAAGAAGGCCCGAAG 60.028 50.000 0.00 0.00 0.00 3.79
4025 4690 0.035915 AGAAGAAGAAGGCCCGAAGC 60.036 55.000 0.00 0.00 42.60 3.86
4026 4691 0.035915 GAAGAAGAAGGCCCGAAGCT 60.036 55.000 0.00 0.00 43.05 3.74
4027 4692 0.035915 AAGAAGAAGGCCCGAAGCTC 60.036 55.000 0.00 0.00 43.05 4.09
4063 4728 8.462811 TCAAGATTCAGTAGTGAGATGTCTAAC 58.537 37.037 0.00 0.00 32.98 2.34
4191 4856 3.074538 AGCTTAAGGTTCAGGGATTGTGT 59.925 43.478 0.12 0.00 0.00 3.72
4233 4898 1.528129 GCCTTCAGCTACACTGCTTT 58.472 50.000 0.00 0.00 46.76 3.51
4240 4905 1.082690 GCTACACTGCTTTCAGCCTC 58.917 55.000 0.00 0.00 44.10 4.70
4241 4906 1.338579 GCTACACTGCTTTCAGCCTCT 60.339 52.381 0.00 0.00 44.10 3.69
4242 4907 2.615869 CTACACTGCTTTCAGCCTCTC 58.384 52.381 0.00 0.00 44.10 3.20
4243 4908 0.761187 ACACTGCTTTCAGCCTCTCA 59.239 50.000 0.00 0.00 44.10 3.27
4246 4911 1.270732 ACTGCTTTCAGCCTCTCACTG 60.271 52.381 0.00 0.00 44.10 3.66
4302 4967 8.868522 TGGTCTTTGATCTCTGTAAATTGATT 57.131 30.769 0.00 0.00 0.00 2.57
4306 4971 8.950210 TCTTTGATCTCTGTAAATTGATTGGAC 58.050 33.333 0.00 0.00 0.00 4.02
4390 5059 3.032017 TGTTGCTCACTGCTACTCTTC 57.968 47.619 0.00 0.00 45.30 2.87
4391 5060 2.630098 TGTTGCTCACTGCTACTCTTCT 59.370 45.455 0.00 0.00 45.30 2.85
4415 5084 3.570912 AGAAAAAGGGAAGAACACGGA 57.429 42.857 0.00 0.00 0.00 4.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.488937 TGCATTTGATCGTGAGCAATGT 59.511 40.909 0.93 0.00 36.53 2.71
60 61 3.893763 CCTCGCGACAGCCTCGAT 61.894 66.667 3.71 0.00 46.14 3.59
144 145 3.781307 TAGCCCGCTGCGGTGATT 61.781 61.111 35.82 21.19 46.80 2.57
153 154 3.155167 GTGCCTAGGTAGCCCGCT 61.155 66.667 11.31 0.00 35.12 5.52
237 238 3.009473 AGAGGGTGTTGTATGTGCAGAAT 59.991 43.478 0.00 0.00 0.00 2.40
280 281 7.659390 ACATTCTTCAGAGAGTAGAAAAGGTTG 59.341 37.037 0.00 0.00 37.22 3.77
347 349 5.488341 ACAAATATCGCCACTACTTGAACT 58.512 37.500 0.00 0.00 0.00 3.01
411 417 2.760634 TACATGGACGTGCAACAGAT 57.239 45.000 15.51 0.00 35.74 2.90
451 457 1.328680 CTGTTCGATGCATGCACTACC 59.671 52.381 25.37 11.56 0.00 3.18
510 517 4.968181 CACTAAATGCATCTGAATTCGCAG 59.032 41.667 0.00 0.56 37.88 5.18
602 619 4.646945 TCAGGATTGCTTAGAGGAGTACAG 59.353 45.833 0.00 0.00 0.00 2.74
603 620 4.610333 TCAGGATTGCTTAGAGGAGTACA 58.390 43.478 0.00 0.00 0.00 2.90
604 621 4.038642 CCTCAGGATTGCTTAGAGGAGTAC 59.961 50.000 5.85 0.00 46.89 2.73
605 622 4.219115 CCTCAGGATTGCTTAGAGGAGTA 58.781 47.826 5.85 0.00 46.89 2.59
606 623 3.037549 CCTCAGGATTGCTTAGAGGAGT 58.962 50.000 5.85 0.00 46.89 3.85
607 624 2.224257 GCCTCAGGATTGCTTAGAGGAG 60.224 54.545 13.67 0.32 46.89 3.69
608 625 1.765314 GCCTCAGGATTGCTTAGAGGA 59.235 52.381 13.67 0.00 46.89 3.71
609 626 1.767681 AGCCTCAGGATTGCTTAGAGG 59.232 52.381 0.00 7.08 46.71 3.69
610 627 3.557228 AAGCCTCAGGATTGCTTAGAG 57.443 47.619 0.00 0.00 43.14 2.43
611 628 5.435686 TTAAAGCCTCAGGATTGCTTAGA 57.564 39.130 0.00 0.00 44.11 2.10
662 697 3.609644 CGCGTGGAGTTAGATCATCTACC 60.610 52.174 0.00 0.00 0.00 3.18
1077 1137 1.121378 TCTTGTGTGACCAACCCGTA 58.879 50.000 0.00 0.00 0.00 4.02
1083 1143 1.748493 GCTTGGTTCTTGTGTGACCAA 59.252 47.619 6.96 6.96 38.04 3.67
1112 1172 0.972883 GAGGTTGGACTGAGAGTGCT 59.027 55.000 0.00 0.00 37.46 4.40
1254 1354 0.247460 TGCAAGATGGACACGGAGAG 59.753 55.000 0.00 0.00 0.00 3.20
1276 1376 3.351740 TCAATCGGTAACACAATGGCAT 58.648 40.909 0.00 0.00 0.00 4.40
1291 1399 0.654160 ATGCACACGCTCATCAATCG 59.346 50.000 0.00 0.00 39.64 3.34
1311 1419 4.101942 GCTGTTTTTGTTTCACGACATCA 58.898 39.130 0.00 0.00 0.00 3.07
1313 1421 3.105203 CGCTGTTTTTGTTTCACGACAT 58.895 40.909 0.00 0.00 0.00 3.06
1314 1422 2.510874 CGCTGTTTTTGTTTCACGACA 58.489 42.857 0.00 0.00 0.00 4.35
1315 1423 1.251762 GCGCTGTTTTTGTTTCACGAC 59.748 47.619 0.00 0.00 0.00 4.34
1316 1424 1.540407 GCGCTGTTTTTGTTTCACGA 58.460 45.000 0.00 0.00 0.00 4.35
1499 1607 3.319198 TTCTCCACCCGCTGGTCC 61.319 66.667 0.00 0.00 45.57 4.46
1829 1937 2.048597 GTGCCGTCGATGTGGTCA 60.049 61.111 3.52 0.04 0.00 4.02
2528 2664 4.082463 TGTCAGTGTCACTCGCAATGTATA 60.082 41.667 1.37 0.00 34.13 1.47
2529 2665 3.254060 GTCAGTGTCACTCGCAATGTAT 58.746 45.455 1.37 0.00 34.13 2.29
2530 2666 2.035321 TGTCAGTGTCACTCGCAATGTA 59.965 45.455 1.37 0.00 34.13 2.29
2538 2674 1.599542 GGCAAGTTGTCAGTGTCACTC 59.400 52.381 1.37 0.00 0.00 3.51
2562 2700 1.202533 AGTGTTCTGTTCCACTGACCG 60.203 52.381 0.00 0.00 40.30 4.79
2591 2730 3.633525 TCTGAAAGAACAACATGCAAGCT 59.366 39.130 0.00 0.00 42.31 3.74
2607 2746 1.073722 CCAGCTGCCCAGTCTGAAA 59.926 57.895 8.66 0.00 35.83 2.69
3240 3410 3.824443 GGACCTTGGCTAAAAAGTGCTAA 59.176 43.478 0.00 0.00 0.00 3.09
3364 3854 5.041015 ACCCCCATATACCTGTCAAGTTAA 58.959 41.667 0.00 0.00 0.00 2.01
3482 3972 7.010091 CGTGACAATAGTTCACATACTGCAATA 59.990 37.037 3.58 0.00 34.33 1.90
3484 3974 5.120053 CGTGACAATAGTTCACATACTGCAA 59.880 40.000 3.58 0.00 34.33 4.08
3499 4010 7.279981 CCAATTGAATTCTAGTCCGTGACAATA 59.720 37.037 7.12 0.00 34.60 1.90
3500 4011 6.094048 CCAATTGAATTCTAGTCCGTGACAAT 59.906 38.462 7.12 0.00 34.60 2.71
3501 4012 5.411361 CCAATTGAATTCTAGTCCGTGACAA 59.589 40.000 7.12 0.00 34.60 3.18
3502 4013 4.935205 CCAATTGAATTCTAGTCCGTGACA 59.065 41.667 7.12 0.00 34.60 3.58
3503 4014 5.175859 TCCAATTGAATTCTAGTCCGTGAC 58.824 41.667 7.12 0.00 0.00 3.67
3504 4015 5.414789 TCCAATTGAATTCTAGTCCGTGA 57.585 39.130 7.12 0.00 0.00 4.35
3505 4016 6.316140 TCATTCCAATTGAATTCTAGTCCGTG 59.684 38.462 7.12 0.00 41.85 4.94
3506 4017 6.414732 TCATTCCAATTGAATTCTAGTCCGT 58.585 36.000 7.12 0.00 41.85 4.69
3507 4018 6.540189 ACTCATTCCAATTGAATTCTAGTCCG 59.460 38.462 7.12 0.00 41.85 4.79
3508 4019 7.872113 ACTCATTCCAATTGAATTCTAGTCC 57.128 36.000 7.12 0.00 41.85 3.85
3509 4020 7.699812 GCAACTCATTCCAATTGAATTCTAGTC 59.300 37.037 7.12 0.00 41.85 2.59
3510 4021 7.542025 GCAACTCATTCCAATTGAATTCTAGT 58.458 34.615 7.12 0.00 41.85 2.57
3511 4022 6.690098 CGCAACTCATTCCAATTGAATTCTAG 59.310 38.462 7.12 0.00 41.85 2.43
3512 4023 6.554419 CGCAACTCATTCCAATTGAATTCTA 58.446 36.000 7.12 0.00 41.85 2.10
3513 4024 5.404946 CGCAACTCATTCCAATTGAATTCT 58.595 37.500 7.12 0.00 41.85 2.40
3514 4025 4.032104 GCGCAACTCATTCCAATTGAATTC 59.968 41.667 7.12 0.00 41.85 2.17
3515 4026 3.928375 GCGCAACTCATTCCAATTGAATT 59.072 39.130 7.12 0.00 41.85 2.17
3516 4027 3.514645 GCGCAACTCATTCCAATTGAAT 58.485 40.909 7.12 2.31 44.67 2.57
3517 4028 2.668001 CGCGCAACTCATTCCAATTGAA 60.668 45.455 8.75 0.00 37.38 2.69
3518 4029 1.135717 CGCGCAACTCATTCCAATTGA 60.136 47.619 8.75 0.00 0.00 2.57
3519 4030 1.261989 CGCGCAACTCATTCCAATTG 58.738 50.000 8.75 0.00 0.00 2.32
3581 4092 9.981114 AATTTTTCTTCGGACAATACAGATTTT 57.019 25.926 0.00 0.00 0.00 1.82
3620 4222 5.238214 ACACTTCTGCACAAGATTTCTTCTC 59.762 40.000 8.85 0.00 33.93 2.87
3635 4237 3.134458 AGTCAGTAGCAAACACTTCTGC 58.866 45.455 0.00 0.00 35.65 4.26
3641 4243 6.183360 ACCAAAAGTAAGTCAGTAGCAAACAC 60.183 38.462 0.00 0.00 0.00 3.32
3642 4244 5.883673 ACCAAAAGTAAGTCAGTAGCAAACA 59.116 36.000 0.00 0.00 0.00 2.83
4018 4683 2.275318 GATTGTTCAGAGAGCTTCGGG 58.725 52.381 0.00 0.00 0.00 5.14
4020 4685 4.240888 TCTTGATTGTTCAGAGAGCTTCG 58.759 43.478 0.00 0.00 32.27 3.79
4021 4686 6.370994 TGAATCTTGATTGTTCAGAGAGCTTC 59.629 38.462 0.09 0.00 32.27 3.86
4023 4688 5.802465 TGAATCTTGATTGTTCAGAGAGCT 58.198 37.500 0.09 0.00 32.27 4.09
4063 4728 2.704572 CCCTGAAACTGGACTGCTTAG 58.295 52.381 0.00 0.00 0.00 2.18
4191 4856 3.422303 GCTGTCAACGCCGATGCA 61.422 61.111 0.00 0.00 37.32 3.96
4233 4898 0.829182 TGCAGTCAGTGAGAGGCTGA 60.829 55.000 11.57 0.00 40.28 4.26
4246 4911 3.349006 CGGTGCCACACTGCAGTC 61.349 66.667 18.64 6.33 43.02 3.51
4302 4967 0.752743 ACAAGCAAGCAAGCAGTCCA 60.753 50.000 3.19 0.00 36.85 4.02
4306 4971 1.484356 GAACACAAGCAAGCAAGCAG 58.516 50.000 3.19 0.00 36.85 4.24
4390 5059 5.277828 CCGTGTTCTTCCCTTTTTCTTACAG 60.278 44.000 0.00 0.00 0.00 2.74
4391 5060 4.577283 CCGTGTTCTTCCCTTTTTCTTACA 59.423 41.667 0.00 0.00 0.00 2.41
4415 5084 3.790437 CACCTCCCGGCTGATGCT 61.790 66.667 0.00 0.00 39.59 3.79


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

AutoCloner maintained by Alex Coulton.