Multiple sequence alignment - TraesCS2D01G175800

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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 TraesCS2D01G175800 chr2D 100.000 4758 0 0 1 4758 119294903 119299660 0.000000e+00 8787.0
1 TraesCS2D01G175800 chr2D 88.889 90 10 0 2604 2693 119297595 119297506 1.400000e-20 111.0
2 TraesCS2D01G175800 chr2B 92.590 1552 69 19 3219 4742 171460080 171461613 0.000000e+00 2187.0
3 TraesCS2D01G175800 chr2B 94.168 823 19 7 2418 3212 171458949 171459770 0.000000e+00 1227.0
4 TraesCS2D01G175800 chr2B 89.516 992 58 18 765 1731 171457172 171458142 0.000000e+00 1214.0
5 TraesCS2D01G175800 chr2B 98.305 649 11 0 1743 2391 171458303 171458951 0.000000e+00 1138.0
6 TraesCS2D01G175800 chr2A 92.702 1425 77 13 1391 2792 121221839 121223259 0.000000e+00 2030.0
7 TraesCS2D01G175800 chr2A 94.842 698 26 4 2789 3482 121223322 121224013 0.000000e+00 1081.0
8 TraesCS2D01G175800 chr2A 94.728 626 22 8 4137 4755 121224812 121225433 0.000000e+00 963.0
9 TraesCS2D01G175800 chr2A 94.737 570 26 4 3481 4048 121224095 121224662 0.000000e+00 883.0
10 TraesCS2D01G175800 chr2A 87.462 662 35 17 742 1358 121221181 121221839 0.000000e+00 719.0
11 TraesCS2D01G175800 chr2A 97.561 41 1 0 4081 4121 121224775 121224815 2.380000e-08 71.3
12 TraesCS2D01G175800 chr2A 93.617 47 2 1 2604 2650 121223157 121223112 8.540000e-08 69.4
13 TraesCS2D01G175800 chr4D 96.904 646 15 5 1 644 24102266 24101624 0.000000e+00 1077.0
14 TraesCS2D01G175800 chr4D 95.455 44 2 0 2623 2666 119751856 119751899 2.380000e-08 71.3
15 TraesCS2D01G175800 chr4D 85.938 64 9 0 2631 2694 119751899 119751836 8.540000e-08 69.4
16 TraesCS2D01G175800 chr7D 99.148 587 5 0 1 587 488055080 488055666 0.000000e+00 1057.0
17 TraesCS2D01G175800 chr7D 98.981 589 5 1 1 589 619216257 619215670 0.000000e+00 1053.0
18 TraesCS2D01G175800 chr7D 98.305 590 9 1 1 589 158943863 158943274 0.000000e+00 1033.0
19 TraesCS2D01G175800 chr7D 97.793 589 13 0 1 589 264956187 264955599 0.000000e+00 1016.0
20 TraesCS2D01G175800 chr7D 97.793 589 12 1 1 589 472892338 472892925 0.000000e+00 1014.0
21 TraesCS2D01G175800 chrUn 98.981 589 6 0 1 589 94055287 94054699 0.000000e+00 1055.0
22 TraesCS2D01G175800 chr3D 98.812 589 7 0 1 589 141368781 141368193 0.000000e+00 1050.0
23 TraesCS2D01G175800 chr3D 98.635 586 8 0 1 586 103817180 103817765 0.000000e+00 1038.0
24 TraesCS2D01G175800 chr5B 94.054 185 10 1 4444 4628 450767418 450767235 3.630000e-71 279.0
25 TraesCS2D01G175800 chr5B 93.578 109 7 0 4622 4730 450767156 450767048 3.810000e-36 163.0
26 TraesCS2D01G175800 chr5A 94.054 185 10 1 4444 4628 478013481 478013298 3.630000e-71 279.0
27 TraesCS2D01G175800 chr5A 91.538 130 8 2 4622 4751 478013116 478012990 4.890000e-40 176.0
28 TraesCS2D01G175800 chr5D 92.973 185 12 1 4444 4628 377482676 377482493 7.850000e-68 268.0
29 TraesCS2D01G175800 chr5D 93.162 117 8 0 4622 4738 377482260 377482144 6.330000e-39 172.0
30 TraesCS2D01G175800 chr7A 89.362 47 5 0 2604 2650 37125299 37125345 5.140000e-05 60.2


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 TraesCS2D01G175800 chr2D 119294903 119299660 4757 False 8787.000000 8787 100.00000 1 4758 1 chr2D.!!$F1 4757
1 TraesCS2D01G175800 chr2B 171457172 171461613 4441 False 1441.500000 2187 93.64475 765 4742 4 chr2B.!!$F1 3977
2 TraesCS2D01G175800 chr2A 121221181 121225433 4252 False 957.883333 2030 93.67200 742 4755 6 chr2A.!!$F1 4013
3 TraesCS2D01G175800 chr4D 24101624 24102266 642 True 1077.000000 1077 96.90400 1 644 1 chr4D.!!$R1 643
4 TraesCS2D01G175800 chr7D 488055080 488055666 586 False 1057.000000 1057 99.14800 1 587 1 chr7D.!!$F2 586
5 TraesCS2D01G175800 chr7D 619215670 619216257 587 True 1053.000000 1053 98.98100 1 589 1 chr7D.!!$R3 588
6 TraesCS2D01G175800 chr7D 158943274 158943863 589 True 1033.000000 1033 98.30500 1 589 1 chr7D.!!$R1 588
7 TraesCS2D01G175800 chr7D 264955599 264956187 588 True 1016.000000 1016 97.79300 1 589 1 chr7D.!!$R2 588
8 TraesCS2D01G175800 chr7D 472892338 472892925 587 False 1014.000000 1014 97.79300 1 589 1 chr7D.!!$F1 588
9 TraesCS2D01G175800 chrUn 94054699 94055287 588 True 1055.000000 1055 98.98100 1 589 1 chrUn.!!$R1 588
10 TraesCS2D01G175800 chr3D 141368193 141368781 588 True 1050.000000 1050 98.81200 1 589 1 chr3D.!!$R1 588
11 TraesCS2D01G175800 chr3D 103817180 103817765 585 False 1038.000000 1038 98.63500 1 586 1 chr3D.!!$F1 585
12 TraesCS2D01G175800 chr5D 377482144 377482676 532 True 220.000000 268 93.06750 4444 4738 2 chr5D.!!$R1 294

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
770 772 0.527817 CTACGATCCGGTCCAAGCAC 60.528 60.0 0.00 0.0 0.00 4.40 F
1415 1467 0.771127 TGGCTGTAGGCTTTGTTCCT 59.229 50.0 6.99 0.0 41.69 3.36 F
2343 2550 2.672961 TGGCTTCCAGTTAGACGATG 57.327 50.0 0.00 0.0 0.00 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1627 1681 3.432186 CGGTGGCATCCTGAAAAGATAGA 60.432 47.826 0.00 0.0 0.00 1.98 R
2498 2706 4.829064 TTCATAAATAAGCATGGCCGTC 57.171 40.909 0.00 0.0 0.00 4.79 R
3953 4640 0.457337 GCAACTTGTAGCTGCATGCC 60.457 55.000 16.68 0.0 44.23 4.40 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
312 313 4.937201 AGTTTTCATTCTTTTTCCGCCT 57.063 36.364 0.00 0.00 0.00 5.52
403 404 1.136329 ACATCAGGTTGAGGCCCAGT 61.136 55.000 0.00 0.00 30.14 4.00
440 441 2.222953 CGGCCTTCGGACTAAATTTTCG 60.223 50.000 0.00 0.00 34.75 3.46
704 706 8.980143 ATATGGGAAAATGTTTTCGTTGTTAG 57.020 30.769 10.98 0.00 45.68 2.34
705 707 6.452494 TGGGAAAATGTTTTCGTTGTTAGA 57.548 33.333 10.98 0.00 45.68 2.10
706 708 7.045126 TGGGAAAATGTTTTCGTTGTTAGAT 57.955 32.000 10.98 0.00 45.68 1.98
707 709 7.142680 TGGGAAAATGTTTTCGTTGTTAGATC 58.857 34.615 10.98 0.00 45.68 2.75
708 710 7.142680 GGGAAAATGTTTTCGTTGTTAGATCA 58.857 34.615 10.98 0.00 45.68 2.92
709 711 7.812669 GGGAAAATGTTTTCGTTGTTAGATCAT 59.187 33.333 10.98 0.00 45.68 2.45
710 712 8.850452 GGAAAATGTTTTCGTTGTTAGATCATC 58.150 33.333 10.98 0.00 45.68 2.92
711 713 9.612620 GAAAATGTTTTCGTTGTTAGATCATCT 57.387 29.630 2.79 0.00 37.42 2.90
712 714 9.965824 AAAATGTTTTCGTTGTTAGATCATCTT 57.034 25.926 0.00 0.00 0.00 2.40
713 715 9.965824 AAATGTTTTCGTTGTTAGATCATCTTT 57.034 25.926 0.00 0.00 0.00 2.52
714 716 9.965824 AATGTTTTCGTTGTTAGATCATCTTTT 57.034 25.926 0.00 0.00 0.00 2.27
715 717 9.965824 ATGTTTTCGTTGTTAGATCATCTTTTT 57.034 25.926 0.00 0.00 0.00 1.94
740 742 2.638480 TTGAATTATCCTCCTGGCCG 57.362 50.000 0.00 0.00 0.00 6.13
764 766 2.728817 CTGGCTACGATCCGGTCC 59.271 66.667 0.00 0.00 0.00 4.46
765 767 2.043752 TGGCTACGATCCGGTCCA 60.044 61.111 0.00 0.00 0.00 4.02
766 768 1.672854 CTGGCTACGATCCGGTCCAA 61.673 60.000 0.00 0.00 0.00 3.53
768 770 1.591863 GCTACGATCCGGTCCAAGC 60.592 63.158 0.00 5.56 0.00 4.01
769 771 1.813859 CTACGATCCGGTCCAAGCA 59.186 57.895 0.00 0.00 0.00 3.91
770 772 0.527817 CTACGATCCGGTCCAAGCAC 60.528 60.000 0.00 0.00 0.00 4.40
771 773 2.274232 TACGATCCGGTCCAAGCACG 62.274 60.000 0.00 0.00 0.00 5.34
809 819 2.203451 CAGGCCATCATCCTGCCC 60.203 66.667 5.01 0.00 46.55 5.36
815 825 1.143813 CCATCATCCTGCCCTACCTT 58.856 55.000 0.00 0.00 0.00 3.50
825 839 1.316969 CCCTACCTTCCTGGGCCTA 59.683 63.158 4.53 0.00 41.11 3.93
850 864 2.436646 CGCAAACCCGAGCCAGAT 60.437 61.111 0.00 0.00 0.00 2.90
874 888 0.830648 ATTAAGTAGAGGCAGCCGCA 59.169 50.000 18.51 0.36 41.24 5.69
910 933 5.333566 AATAACTTCTTCCCCTTTCCACA 57.666 39.130 0.00 0.00 0.00 4.17
1181 1229 2.045561 TTCGGGTTGCAGAAACTTGA 57.954 45.000 0.00 0.00 38.92 3.02
1182 1230 2.270352 TCGGGTTGCAGAAACTTGAT 57.730 45.000 0.00 0.00 38.92 2.57
1183 1231 2.582052 TCGGGTTGCAGAAACTTGATT 58.418 42.857 0.00 0.00 38.92 2.57
1266 1316 3.530398 TTGGGTTTCGAAAGCGCGC 62.530 57.895 28.06 26.66 37.28 6.86
1298 1348 1.138069 TGAGTTCGCACTGGTTCTCAA 59.862 47.619 0.00 0.00 31.22 3.02
1307 1357 4.585879 GCACTGGTTCTCAAGGGTAATAA 58.414 43.478 0.00 0.00 0.00 1.40
1327 1378 1.603802 AGCTCGTGTGTTGTCAATTGG 59.396 47.619 5.42 0.00 0.00 3.16
1336 1387 1.126488 TTGTCAATTGGCAGGGCAAA 58.874 45.000 13.27 0.00 0.00 3.68
1337 1388 1.350071 TGTCAATTGGCAGGGCAAAT 58.650 45.000 9.09 1.02 33.02 2.32
1375 1427 8.893727 AGTTGACTAATATGTGAAATACAAGGC 58.106 33.333 0.00 0.00 43.77 4.35
1415 1467 0.771127 TGGCTGTAGGCTTTGTTCCT 59.229 50.000 6.99 0.00 41.69 3.36
1439 1491 3.509442 TCTGATTTGGAAATTGTGCCCT 58.491 40.909 0.00 0.00 0.00 5.19
1440 1492 3.258872 TCTGATTTGGAAATTGTGCCCTG 59.741 43.478 0.00 0.00 0.00 4.45
1458 1510 3.283751 CCTGGAATTGCGGGTATACAAA 58.716 45.455 16.39 0.00 0.00 2.83
1463 1515 6.702329 TGGAATTGCGGGTATACAAATTTTT 58.298 32.000 5.01 0.00 0.00 1.94
1468 1520 6.837471 TGCGGGTATACAAATTTTTAAGGT 57.163 33.333 5.01 0.00 0.00 3.50
1471 1523 6.127675 GCGGGTATACAAATTTTTAAGGTGGA 60.128 38.462 5.01 0.00 0.00 4.02
1500 1552 8.850454 TGTTTGAGTTAAAAGATTAGTTGCAC 57.150 30.769 0.00 0.00 0.00 4.57
1508 1560 3.354948 AGATTAGTTGCACATGCTCCA 57.645 42.857 5.31 0.00 42.66 3.86
1509 1561 3.894759 AGATTAGTTGCACATGCTCCAT 58.105 40.909 5.31 0.00 42.66 3.41
1545 1598 4.570930 AGCTGTAAGGTCTTGCTTCTAAC 58.429 43.478 0.00 0.00 44.61 2.34
1572 1626 2.730550 AAAATTTCAGCTCGGCCTTG 57.269 45.000 0.00 0.00 0.00 3.61
1591 1645 3.834489 TGCATTTGTGATTTGGTGGTT 57.166 38.095 0.00 0.00 0.00 3.67
1597 1651 6.650390 GCATTTGTGATTTGGTGGTTAAGAAT 59.350 34.615 0.00 0.00 0.00 2.40
1604 1658 9.150348 GTGATTTGGTGGTTAAGAATTTAATGG 57.850 33.333 0.00 0.00 31.81 3.16
1627 1681 6.042781 TGGATTAGTTGGTCAAGTACTCAAGT 59.957 38.462 13.92 1.73 31.41 3.16
1648 1704 3.879892 GTCTATCTTTTCAGGATGCCACC 59.120 47.826 0.00 0.00 34.76 4.61
1760 1966 7.662669 TGTACTTAACTTACTTTGGGGTCAATC 59.337 37.037 0.00 0.00 32.28 2.67
1813 2019 9.838339 CCATTGTACCTATCAGAGTTTATTTCT 57.162 33.333 0.00 0.00 0.00 2.52
2343 2550 2.672961 TGGCTTCCAGTTAGACGATG 57.327 50.000 0.00 0.00 0.00 3.84
2498 2706 1.480954 AGTCGTGTGCCAGGTATAAGG 59.519 52.381 0.00 0.00 0.00 2.69
2684 2909 1.668751 GCAACACTTGTTTCTGGACGA 59.331 47.619 0.00 0.00 35.83 4.20
2686 2911 3.788797 GCAACACTTGTTTCTGGACGAAG 60.789 47.826 0.00 0.00 35.83 3.79
2711 2937 9.939424 AGGGAGTACTTTATATTGAACTACTCT 57.061 33.333 0.00 0.00 32.61 3.24
2720 2946 9.595823 TTTATATTGAACTACTCTGTGCTAACC 57.404 33.333 0.00 0.00 0.00 2.85
2836 3133 1.746615 CACGGGGTCAGCAATCCAG 60.747 63.158 0.00 0.00 0.00 3.86
2837 3134 1.918293 ACGGGGTCAGCAATCCAGA 60.918 57.895 0.00 0.00 0.00 3.86
2942 3239 5.473039 AGTTTGAAGTTTCAATATGCCAGC 58.527 37.500 8.02 0.00 45.65 4.85
3071 3368 9.486857 GAAGTTAATAAGCGTTTCTATTTGTCC 57.513 33.333 0.00 0.00 0.00 4.02
3165 3462 6.432783 CCAGTTGTATGAACAGGGATTGTAAA 59.567 38.462 0.00 0.00 39.73 2.01
3220 3826 6.831664 AGGATGTCCTTGTTAATCACCTAT 57.168 37.500 0.00 0.00 46.09 2.57
3264 3870 6.851609 TGAAACCACATTCTACAATATGTGC 58.148 36.000 9.16 0.00 46.44 4.57
3276 3882 5.034554 ACAATATGTGCTCTGTTTTGTCG 57.965 39.130 0.00 0.00 0.00 4.35
3385 3991 7.330700 GCAAAGGGTAAATGAAATGAAATTCGA 59.669 33.333 0.00 0.00 33.67 3.71
3411 4017 7.174946 ACCTTGTTTGTCAATAGTCCATTACAG 59.825 37.037 0.00 0.00 35.35 2.74
3609 4295 3.920231 CCTGATGGAAGGTGAGATTGA 57.080 47.619 0.00 0.00 34.57 2.57
3612 4298 4.639310 CCTGATGGAAGGTGAGATTGAAAG 59.361 45.833 0.00 0.00 34.57 2.62
3646 4332 0.767375 TCACCTCTCTTTGCTGGCTT 59.233 50.000 0.00 0.00 0.00 4.35
3649 4335 2.941720 CACCTCTCTTTGCTGGCTTATC 59.058 50.000 0.00 0.00 0.00 1.75
3666 4352 4.629200 GCTTATCATGTGCTATAGCCTCAC 59.371 45.833 21.84 13.72 41.18 3.51
3783 4470 5.551233 CTGGTAGACTGTTTGAATGGAAGA 58.449 41.667 0.00 0.00 0.00 2.87
3859 4546 3.837213 ACTGCTGTGACAATGTTATGC 57.163 42.857 0.00 0.00 0.00 3.14
3862 4549 5.188434 ACTGCTGTGACAATGTTATGCTAT 58.812 37.500 0.00 0.00 0.00 2.97
3953 4640 1.342174 AGTTTGCTTGGACCATTGCTG 59.658 47.619 17.34 0.00 0.00 4.41
3980 4667 3.482786 CAGCTACAAGTTGCGAATGAAC 58.517 45.455 1.81 0.00 36.47 3.18
3986 4674 4.072131 ACAAGTTGCGAATGAACACCTAT 58.928 39.130 1.81 0.00 0.00 2.57
3987 4675 4.154195 ACAAGTTGCGAATGAACACCTATC 59.846 41.667 1.81 0.00 0.00 2.08
3996 4684 5.069251 CGAATGAACACCTATCCTAACCTCT 59.931 44.000 0.00 0.00 0.00 3.69
4004 4692 5.648092 CACCTATCCTAACCTCTTTTTGTGG 59.352 44.000 0.00 0.00 35.56 4.17
4006 4694 4.741928 ATCCTAACCTCTTTTTGTGGGT 57.258 40.909 0.00 0.00 33.83 4.51
4025 4713 1.227556 GTGGTGCAGGACGTTCTGT 60.228 57.895 24.56 0.00 37.12 3.41
4051 4739 8.752254 TCGATTATTTAGTGTTCGCATTTCTAG 58.248 33.333 0.00 0.00 0.00 2.43
4063 4751 2.738643 GCATTTCTAGCTCGGTGTAGCA 60.739 50.000 0.00 0.00 45.30 3.49
4077 4768 5.810587 TCGGTGTAGCATTAGAGATTGTTTC 59.189 40.000 0.00 0.00 0.00 2.78
4124 4892 1.833630 CAGAGTGCTAGGGTTGGATCA 59.166 52.381 0.00 0.00 0.00 2.92
4128 4896 0.911769 TGCTAGGGTTGGATCAGTGG 59.088 55.000 0.00 0.00 0.00 4.00
4178 4947 3.250040 GCGCGTCCATTCAAACCTTATAT 59.750 43.478 8.43 0.00 0.00 0.86
4192 4962 9.793259 TCAAACCTTATATGAACTCTCAAAAGT 57.207 29.630 0.00 0.00 34.49 2.66
4342 5114 9.747898 TTTTCCATTTTACAGATCCTTAGCTAA 57.252 29.630 5.94 5.94 0.00 3.09
4371 5144 3.200483 CAGCATCTCGAATGACCAATGA 58.800 45.455 10.52 0.00 0.00 2.57
4416 5189 4.568359 GTCCTTCACAGTATGCAGTATGTG 59.432 45.833 17.40 17.40 42.53 3.21
4578 5351 3.665675 GATCACGTGCTTCGCCCCT 62.666 63.158 11.67 0.00 44.19 4.79
4755 5768 2.665185 ACACGAAGCACCGCCTTC 60.665 61.111 0.00 0.00 38.24 3.46
4756 5769 2.664851 CACGAAGCACCGCCTTCA 60.665 61.111 0.00 0.00 40.94 3.02
4757 5770 2.357517 ACGAAGCACCGCCTTCAG 60.358 61.111 0.00 5.08 40.94 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
679 681 8.798402 TCTAACAACGAAAACATTTTCCCATAT 58.202 29.630 10.70 0.01 42.66 1.78
683 685 7.142680 TGATCTAACAACGAAAACATTTTCCC 58.857 34.615 10.70 0.00 42.66 3.97
684 686 8.742554 ATGATCTAACAACGAAAACATTTTCC 57.257 30.769 10.70 0.00 42.66 3.13
685 687 9.612620 AGATGATCTAACAACGAAAACATTTTC 57.387 29.630 6.97 6.97 42.30 2.29
686 688 9.965824 AAGATGATCTAACAACGAAAACATTTT 57.034 25.926 0.00 0.00 0.00 1.82
718 720 3.699038 CGGCCAGGAGGATAATTCAAAAA 59.301 43.478 2.24 0.00 36.89 1.94
719 721 3.053991 TCGGCCAGGAGGATAATTCAAAA 60.054 43.478 2.24 0.00 36.89 2.44
720 722 2.507886 TCGGCCAGGAGGATAATTCAAA 59.492 45.455 2.24 0.00 36.89 2.69
721 723 2.123589 TCGGCCAGGAGGATAATTCAA 58.876 47.619 2.24 0.00 36.89 2.69
722 724 1.801242 TCGGCCAGGAGGATAATTCA 58.199 50.000 2.24 0.00 36.89 2.57
723 725 3.077359 CAATCGGCCAGGAGGATAATTC 58.923 50.000 2.24 0.00 36.89 2.17
724 726 2.711009 TCAATCGGCCAGGAGGATAATT 59.289 45.455 2.24 0.00 36.89 1.40
725 727 2.304180 CTCAATCGGCCAGGAGGATAAT 59.696 50.000 2.24 0.00 36.89 1.28
726 728 1.694150 CTCAATCGGCCAGGAGGATAA 59.306 52.381 2.24 0.00 36.89 1.75
727 729 1.342074 CTCAATCGGCCAGGAGGATA 58.658 55.000 2.24 0.00 36.89 2.59
728 730 2.049627 GCTCAATCGGCCAGGAGGAT 62.050 60.000 2.24 0.00 36.89 3.24
729 731 2.735772 GCTCAATCGGCCAGGAGGA 61.736 63.158 2.24 0.00 36.89 3.71
730 732 2.203126 GCTCAATCGGCCAGGAGG 60.203 66.667 2.24 0.00 38.23 4.30
731 733 1.523258 CAGCTCAATCGGCCAGGAG 60.523 63.158 2.24 4.49 0.00 3.69
732 734 2.586245 CAGCTCAATCGGCCAGGA 59.414 61.111 2.24 0.00 0.00 3.86
733 735 2.515523 CCAGCTCAATCGGCCAGG 60.516 66.667 2.24 0.00 0.00 4.45
734 736 3.207669 GCCAGCTCAATCGGCCAG 61.208 66.667 2.24 0.00 40.07 4.85
737 739 2.240500 CGTAGCCAGCTCAATCGGC 61.241 63.158 3.84 3.84 46.62 5.54
738 740 0.032678 ATCGTAGCCAGCTCAATCGG 59.967 55.000 0.00 0.00 0.00 4.18
739 741 1.413382 GATCGTAGCCAGCTCAATCG 58.587 55.000 0.00 0.00 0.00 3.34
740 742 1.789506 GGATCGTAGCCAGCTCAATC 58.210 55.000 0.00 0.00 0.00 2.67
764 766 3.793144 GCGCCCTCTTCGTGCTTG 61.793 66.667 0.00 0.00 33.91 4.01
765 767 3.825160 TTGCGCCCTCTTCGTGCTT 62.825 57.895 4.18 0.00 37.62 3.91
766 768 3.825160 TTTGCGCCCTCTTCGTGCT 62.825 57.895 4.18 0.00 37.62 4.40
768 770 1.082104 GTTTTGCGCCCTCTTCGTG 60.082 57.895 4.18 0.00 0.00 4.35
769 771 2.258726 GGTTTTGCGCCCTCTTCGT 61.259 57.895 4.18 0.00 0.00 3.85
770 772 2.561373 GGTTTTGCGCCCTCTTCG 59.439 61.111 4.18 0.00 0.00 3.79
771 773 2.561373 CGGTTTTGCGCCCTCTTC 59.439 61.111 4.18 0.00 0.00 2.87
809 819 1.123928 CTGTAGGCCCAGGAAGGTAG 58.876 60.000 0.00 0.00 34.66 3.18
815 825 2.285368 CCCACTGTAGGCCCAGGA 60.285 66.667 12.93 0.00 36.75 3.86
850 864 1.687123 GCTGCCTCTACTTAATCGGGA 59.313 52.381 0.00 0.00 0.00 5.14
874 888 7.201983 GGAAGAAGTTATTAAGGGAGTACCGAT 60.202 40.741 0.00 0.00 46.96 4.18
876 890 6.279123 GGAAGAAGTTATTAAGGGAGTACCG 58.721 44.000 0.00 0.00 46.96 4.02
883 906 5.892119 GGAAAGGGGAAGAAGTTATTAAGGG 59.108 44.000 0.00 0.00 0.00 3.95
910 933 1.964373 GTGGGTGTTCGCCGACAAT 60.964 57.895 11.53 0.00 37.23 2.71
1181 1229 4.761975 AGCGCCAAATCAATCATCAAAAT 58.238 34.783 2.29 0.00 0.00 1.82
1182 1230 4.175516 GAGCGCCAAATCAATCATCAAAA 58.824 39.130 2.29 0.00 0.00 2.44
1183 1231 3.429272 GGAGCGCCAAATCAATCATCAAA 60.429 43.478 2.29 0.00 0.00 2.69
1221 1271 1.048724 TACCCAGGGCCTGATTCTCG 61.049 60.000 34.84 16.26 32.44 4.04
1266 1316 0.994995 CGAACTCAGAATCAGCACCG 59.005 55.000 0.00 0.00 0.00 4.94
1277 1327 1.269778 TGAGAACCAGTGCGAACTCAG 60.270 52.381 0.00 0.00 32.04 3.35
1298 1348 3.007614 ACAACACACGAGCTTATTACCCT 59.992 43.478 0.00 0.00 0.00 4.34
1307 1357 1.603802 CCAATTGACAACACACGAGCT 59.396 47.619 7.12 0.00 0.00 4.09
1327 1378 3.465871 TGAAGACAAAAATTTGCCCTGC 58.534 40.909 5.82 3.53 41.79 4.85
1359 1410 3.433031 CGGAGGGCCTTGTATTTCACATA 60.433 47.826 7.89 0.00 36.90 2.29
1388 1440 1.147153 GCCTACAGCCATGTCCTCC 59.853 63.158 0.00 0.00 41.01 4.30
1390 1442 0.995024 AAAGCCTACAGCCATGTCCT 59.005 50.000 0.00 0.00 45.47 3.85
1398 1450 2.185004 TGAGGAACAAAGCCTACAGC 57.815 50.000 0.00 0.00 44.25 4.40
1415 1467 4.081531 GGGCACAATTTCCAAATCAGATGA 60.082 41.667 0.00 0.00 0.00 2.92
1439 1491 5.923733 AAATTTGTATACCCGCAATTCCA 57.076 34.783 0.00 0.00 0.00 3.53
1440 1492 8.705048 TTAAAAATTTGTATACCCGCAATTCC 57.295 30.769 0.00 0.00 0.00 3.01
1458 1510 9.679661 AACTCAAACATTTTCCACCTTAAAAAT 57.320 25.926 0.00 0.00 35.91 1.82
1463 1515 9.810545 CTTTTAACTCAAACATTTTCCACCTTA 57.189 29.630 0.00 0.00 0.00 2.69
1498 1550 3.441222 TGCTAACTTCAATGGAGCATGTG 59.559 43.478 0.00 0.00 38.20 3.21
1499 1551 3.689347 TGCTAACTTCAATGGAGCATGT 58.311 40.909 0.00 0.00 38.20 3.21
1500 1552 3.066342 CCTGCTAACTTCAATGGAGCATG 59.934 47.826 0.00 0.00 41.98 4.06
1545 1598 4.734695 GCCGAGCTGAAATTTTTATCCCAG 60.735 45.833 0.00 0.00 0.00 4.45
1572 1626 5.537188 TCTTAACCACCAAATCACAAATGC 58.463 37.500 0.00 0.00 0.00 3.56
1597 1651 9.444600 GAGTACTTGACCAACTAATCCATTAAA 57.555 33.333 0.00 0.00 0.00 1.52
1604 1658 7.379750 AGACTTGAGTACTTGACCAACTAATC 58.620 38.462 0.00 0.00 0.00 1.75
1627 1681 3.432186 CGGTGGCATCCTGAAAAGATAGA 60.432 47.826 0.00 0.00 0.00 1.98
1731 1788 7.833183 TGACCCCAAAGTAAGTTAAGTACAAAA 59.167 33.333 0.00 0.00 0.00 2.44
1734 1791 6.497624 TGACCCCAAAGTAAGTTAAGTACA 57.502 37.500 0.00 0.00 0.00 2.90
1741 1798 5.701224 TCAAGATTGACCCCAAAGTAAGTT 58.299 37.500 0.00 0.00 35.67 2.66
1760 1966 9.263538 CATGAGAAGAGAAATAGAAGGATCAAG 57.736 37.037 0.00 0.00 0.00 3.02
2211 2418 4.433186 TGCTACAAAAATCAATGGGTCG 57.567 40.909 0.00 0.00 0.00 4.79
2498 2706 4.829064 TTCATAAATAAGCATGGCCGTC 57.171 40.909 0.00 0.00 0.00 4.79
2561 2769 7.610692 ACATCAGAATGTCAATCTTCTCATTGT 59.389 33.333 0.00 0.00 42.59 2.71
2711 2937 5.948758 TGTTGGATATTCATTGGTTAGCACA 59.051 36.000 0.00 0.00 0.00 4.57
2720 2946 8.774890 TTTCCAACAATGTTGGATATTCATTG 57.225 30.769 38.59 14.99 46.85 2.82
2836 3133 7.417612 ACAATGAAAACACATCAGTAACTGTC 58.582 34.615 0.00 0.00 32.61 3.51
2837 3134 7.333528 ACAATGAAAACACATCAGTAACTGT 57.666 32.000 0.00 0.00 32.61 3.55
2942 3239 5.771469 TGCACATAAGAACATTTCCTTGTG 58.229 37.500 0.00 0.00 37.36 3.33
3071 3368 6.808008 ACAATGACTAAACCAGATTCAGTG 57.192 37.500 0.00 0.00 38.06 3.66
3219 3825 5.538877 TCAGAGAAAGGGGTAGAACCATAT 58.461 41.667 0.00 0.00 41.02 1.78
3220 3826 4.955335 TCAGAGAAAGGGGTAGAACCATA 58.045 43.478 0.00 0.00 41.02 2.74
3385 3991 7.001674 TGTAATGGACTATTGACAAACAAGGT 58.998 34.615 0.00 0.00 42.02 3.50
3458 4064 5.028549 AGAAATGAGTCAAGCGATGGTAT 57.971 39.130 0.00 0.00 0.00 2.73
3608 4294 4.498241 GTGATGATTGGCTTTTCCCTTTC 58.502 43.478 0.00 0.00 0.00 2.62
3609 4295 3.261643 GGTGATGATTGGCTTTTCCCTTT 59.738 43.478 0.00 0.00 0.00 3.11
3612 4298 2.428530 GAGGTGATGATTGGCTTTTCCC 59.571 50.000 0.00 0.00 0.00 3.97
3646 4332 6.425210 AAAGTGAGGCTATAGCACATGATA 57.575 37.500 25.53 2.45 44.36 2.15
3649 4335 6.051717 AGTAAAAGTGAGGCTATAGCACATG 58.948 40.000 25.53 0.00 44.36 3.21
3783 4470 1.134946 GGTTTTGTTGCAGCACAGAGT 59.865 47.619 1.37 0.00 0.00 3.24
3859 4546 3.179443 AGCCCACACATGTTACGATAG 57.821 47.619 0.00 0.00 46.19 2.08
3862 4549 2.235155 ACATAGCCCACACATGTTACGA 59.765 45.455 0.00 0.00 28.56 3.43
3953 4640 0.457337 GCAACTTGTAGCTGCATGCC 60.457 55.000 16.68 0.00 44.23 4.40
3980 4667 5.648092 CCACAAAAAGAGGTTAGGATAGGTG 59.352 44.000 0.00 0.00 0.00 4.00
3986 4674 3.203487 ACACCCACAAAAAGAGGTTAGGA 59.797 43.478 0.00 0.00 0.00 2.94
3987 4675 3.317993 CACACCCACAAAAAGAGGTTAGG 59.682 47.826 0.00 0.00 0.00 2.69
3996 4684 0.534412 CTGCACCACACCCACAAAAA 59.466 50.000 0.00 0.00 0.00 1.94
4004 4692 2.203153 AACGTCCTGCACCACACC 60.203 61.111 0.00 0.00 0.00 4.16
4006 4694 1.227527 CAGAACGTCCTGCACCACA 60.228 57.895 0.00 0.00 0.00 4.17
4025 4713 7.534085 AGAAATGCGAACACTAAATAATCGA 57.466 32.000 0.00 0.00 35.65 3.59
4051 4739 3.651803 ATCTCTAATGCTACACCGAGC 57.348 47.619 0.00 0.00 43.16 5.03
4063 4751 9.953697 GTCATCTACTACGAAACAATCTCTAAT 57.046 33.333 0.00 0.00 0.00 1.73
4077 4768 9.388346 GTTGATCTATTCAAGTCATCTACTACG 57.612 37.037 0.00 0.00 44.89 3.51
4124 4892 3.031013 CTGTTCCCAAAAACTTCCCACT 58.969 45.455 0.00 0.00 0.00 4.00
4128 4896 8.581578 TGTATTTATCTGTTCCCAAAAACTTCC 58.418 33.333 0.00 0.00 0.00 3.46
4308 5078 8.966868 GGATCTGTAAAATGGAAAATTGGAGTA 58.033 33.333 0.00 0.00 0.00 2.59
4310 5080 8.071177 AGGATCTGTAAAATGGAAAATTGGAG 57.929 34.615 0.00 0.00 0.00 3.86
4342 5114 5.509840 GGTCATTCGAGATGCTGGTAGTAAT 60.510 44.000 3.57 0.00 0.00 1.89
4430 5203 1.664017 CTCTGATGAGGGATGCGCG 60.664 63.158 0.00 0.00 36.70 6.86
4435 5208 0.758310 TCGCTGCTCTGATGAGGGAT 60.758 55.000 0.00 0.00 40.53 3.85
4438 5211 1.227205 GGTCGCTGCTCTGATGAGG 60.227 63.158 0.00 0.00 40.53 3.86
4722 5733 2.689471 TCGTGTGTGTGTGTAGGTAGTT 59.311 45.455 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.