Multiple sequence alignment - TraesCS1D01G285200

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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 TraesCS1D01G285200 chr1D 100.000 3418 0 0 798 4215 383317005 383313588 0.000000e+00 6312.0
1 TraesCS1D01G285200 chr1D 100.000 345 0 0 1 345 383317802 383317458 4.600000e-179 638.0
2 TraesCS1D01G285200 chr1B 92.670 3465 150 36 801 4214 513542282 513538871 0.000000e+00 4896.0
3 TraesCS1D01G285200 chr1B 92.222 360 5 12 1 345 513542613 513542262 4.900000e-134 488.0
4 TraesCS1D01G285200 chr1B 97.222 36 1 0 2715 2750 527452367 527452402 1.270000e-05 62.1
5 TraesCS1D01G285200 chr1A 93.257 1839 71 17 1771 3587 483028413 483026606 0.000000e+00 2660.0
6 TraesCS1D01G285200 chr1A 92.111 976 55 14 801 1773 483029641 483028685 0.000000e+00 1356.0
7 TraesCS1D01G285200 chr1A 93.262 282 16 3 3937 4215 483025650 483025369 3.030000e-111 412.0
8 TraesCS1D01G285200 chr1A 88.286 350 20 11 1 345 483029986 483029653 2.360000e-107 399.0
9 TraesCS1D01G285200 chr3B 81.893 243 33 11 2820 3056 612101910 612102147 1.200000e-45 195.0
10 TraesCS1D01G285200 chr3B 78.623 276 33 16 2438 2693 612101076 612101345 4.360000e-35 159.0
11 TraesCS1D01G285200 chr3B 90.426 94 7 1 982 1075 612098431 612098522 5.720000e-24 122.0
12 TraesCS1D01G285200 chr3B 100.000 36 0 0 2715 2750 171174248 171174213 2.720000e-07 67.6
13 TraesCS1D01G285200 chr3A 81.481 243 34 11 2820 3056 603811296 603811533 5.560000e-44 189.0
14 TraesCS1D01G285200 chr3A 79.926 269 37 14 2438 2693 603810664 603810928 9.310000e-42 182.0
15 TraesCS1D01G285200 chr3A 91.011 89 6 1 987 1075 603807978 603808064 7.400000e-23 119.0
16 TraesCS1D01G285200 chr3D 81.224 245 32 13 2820 3056 461311198 461311436 7.200000e-43 185.0
17 TraesCS1D01G285200 chr3D 79.021 286 34 15 2428 2693 461310302 461310581 5.600000e-39 172.0
18 TraesCS1D01G285200 chr3D 90.217 92 6 2 985 1075 461307923 461308012 2.660000e-22 117.0
19 TraesCS1D01G285200 chr3D 85.841 113 8 6 994 1105 599592635 599592740 3.440000e-21 113.0
20 TraesCS1D01G285200 chr5D 90.323 93 5 3 994 1086 524586647 524586735 7.400000e-23 119.0
21 TraesCS1D01G285200 chr5B 90.323 93 5 2 994 1086 659169297 659169385 7.400000e-23 119.0
22 TraesCS1D01G285200 chr5A 90.323 93 5 2 994 1086 650834309 650834397 7.400000e-23 119.0
23 TraesCS1D01G285200 chr7D 100.000 37 0 0 2714 2750 431251675 431251639 7.560000e-08 69.4
24 TraesCS1D01G285200 chr6D 100.000 36 0 0 2715 2750 361526336 361526301 2.720000e-07 67.6
25 TraesCS1D01G285200 chr4D 94.872 39 1 1 2714 2751 73469871 73469909 4.550000e-05 60.2
26 TraesCS1D01G285200 chr4D 94.872 39 1 1 2714 2751 73576528 73576566 4.550000e-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 TraesCS1D01G285200 chr1D 383313588 383317802 4214 True 3475.00 6312 100.000 1 4215 2 chr1D.!!$R1 4214
1 TraesCS1D01G285200 chr1B 513538871 513542613 3742 True 2692.00 4896 92.446 1 4214 2 chr1B.!!$R1 4213
2 TraesCS1D01G285200 chr1A 483025369 483029986 4617 True 1206.75 2660 91.729 1 4215 4 chr1A.!!$R1 4214

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
969 1016 0.186630 GGTAGGAGGAGGAGGAGGAC 59.813 65.0 0.00 0.00 0.00 3.85 F
1257 1309 0.677731 CTTCCATTTGGAGCGCCAGA 60.678 55.0 9.79 5.55 46.91 3.86 F
2714 3052 0.477597 TGTCCACAAATCCCCTCCCT 60.478 55.0 0.00 0.00 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2267 2602 1.594331 GGAAACGTTCTTGACCAGCT 58.406 50.0 0.0 0.0 0.00 4.24 R
2911 3250 1.931635 AGACTCCTCTCCACTGGAAC 58.068 55.0 0.0 0.0 31.23 3.62 R
3579 3931 0.889306 AGTGAGCGAGACCAACTACC 59.111 55.0 0.0 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
36 37 2.126307 CACAGGTCAGCGTCTCCG 60.126 66.667 0.00 0.00 37.07 4.63
909 956 1.098712 TGACGCTCGTTTTGGCCTTT 61.099 50.000 3.32 0.00 0.00 3.11
911 958 1.371635 CGCTCGTTTTGGCCTTTGG 60.372 57.895 3.32 0.00 0.00 3.28
969 1016 0.186630 GGTAGGAGGAGGAGGAGGAC 59.813 65.000 0.00 0.00 0.00 3.85
1098 1149 4.105388 CCCCCGCTAGATCTCTCC 57.895 66.667 0.00 0.00 0.00 3.71
1172 1224 1.377987 GGCAGGATTTGGGCGTGTA 60.378 57.895 0.00 0.00 0.00 2.90
1198 1250 1.005630 CGGATCTCGCAGGGATTCC 60.006 63.158 0.00 0.00 0.00 3.01
1210 1262 3.312697 GCAGGGATTCCTCATTTACGTTC 59.687 47.826 2.01 0.00 42.67 3.95
1211 1263 3.877508 CAGGGATTCCTCATTTACGTTCC 59.122 47.826 2.01 0.00 42.67 3.62
1257 1309 0.677731 CTTCCATTTGGAGCGCCAGA 60.678 55.000 9.79 5.55 46.91 3.86
1337 1389 3.869187 TGCGTACAAGCATCCGTG 58.131 55.556 0.00 0.00 42.92 4.94
1414 1466 1.571919 AATCGGGAGAATTTCGAGCG 58.428 50.000 0.00 0.00 45.37 5.03
1507 1559 0.967380 GTGGTTGGAGGAGCATTGGG 60.967 60.000 0.00 0.00 0.00 4.12
1534 1586 2.408271 CAGCTTCTGGAATGGTGCTA 57.592 50.000 0.00 0.00 0.00 3.49
1545 1597 3.388024 GGAATGGTGCTATCACACTCCTA 59.612 47.826 0.00 0.00 44.87 2.94
1556 1608 3.774734 TCACACTCCTAGCTTGGTAGAA 58.225 45.455 14.12 0.00 0.00 2.10
1617 1669 4.334759 CAGGCTTGACTTTATCATCTGTGG 59.665 45.833 0.00 0.00 37.11 4.17
1641 1693 6.016108 GGTTGTTTGTATAGTTTACAAGGCCA 60.016 38.462 5.01 3.52 38.47 5.36
1642 1694 6.563222 TGTTTGTATAGTTTACAAGGCCAC 57.437 37.500 5.01 0.00 38.47 5.01
1645 1697 4.581868 TGTATAGTTTACAAGGCCACACC 58.418 43.478 5.01 0.00 39.61 4.16
1657 1709 2.738521 CACACCGAGAACAGGCCG 60.739 66.667 0.00 0.00 0.00 6.13
1692 1744 1.242076 TTCTTTTGCTGCTCCTGCTC 58.758 50.000 0.00 0.00 40.48 4.26
1743 1795 7.771183 AGCTTGAAATATAAATTGCTTCGGAA 58.229 30.769 0.00 0.00 0.00 4.30
1858 2188 9.527157 TTGATAAAGATAGAGATAGAGGGAGTG 57.473 37.037 0.00 0.00 0.00 3.51
2184 2518 6.349363 CCTTTGTTGCCCTACACTAATTCTTC 60.349 42.308 0.00 0.00 0.00 2.87
2329 2664 5.360714 TGAATAAGGATTGTTCCAATCTGCC 59.639 40.000 14.60 2.03 44.39 4.85
2490 2825 2.159881 GCTTGTTTATGACGTCACCGAC 60.160 50.000 22.71 18.50 37.88 4.79
2702 3040 4.595781 AGAGTAAAAGGGTATGTGTCCACA 59.404 41.667 2.09 2.09 46.44 4.17
2714 3052 0.477597 TGTCCACAAATCCCCTCCCT 60.478 55.000 0.00 0.00 0.00 4.20
2715 3053 1.203505 TGTCCACAAATCCCCTCCCTA 60.204 52.381 0.00 0.00 0.00 3.53
2716 3054 1.490910 GTCCACAAATCCCCTCCCTAG 59.509 57.143 0.00 0.00 0.00 3.02
2718 3056 2.319747 TCCACAAATCCCCTCCCTAGTA 59.680 50.000 0.00 0.00 0.00 1.82
2719 3057 2.438392 CCACAAATCCCCTCCCTAGTAC 59.562 54.545 0.00 0.00 0.00 2.73
2720 3058 3.112263 CACAAATCCCCTCCCTAGTACA 58.888 50.000 0.00 0.00 0.00 2.90
2721 3059 3.521937 CACAAATCCCCTCCCTAGTACAA 59.478 47.826 0.00 0.00 0.00 2.41
2722 3060 4.018779 CACAAATCCCCTCCCTAGTACAAA 60.019 45.833 0.00 0.00 0.00 2.83
2726 3064 3.178865 TCCCCTCCCTAGTACAAAGTTG 58.821 50.000 0.00 0.00 0.00 3.16
2740 3078 4.850680 ACAAAGTTGTACCAAGGTTGAGA 58.149 39.130 0.00 0.00 40.16 3.27
2741 3079 4.638865 ACAAAGTTGTACCAAGGTTGAGAC 59.361 41.667 0.00 0.00 40.16 3.36
2743 3081 3.805207 AGTTGTACCAAGGTTGAGACAC 58.195 45.455 0.00 0.00 0.00 3.67
2744 3082 3.454812 AGTTGTACCAAGGTTGAGACACT 59.545 43.478 0.00 0.00 0.00 3.55
3145 3497 1.211703 TCCACTTTGCAGGACAAGACA 59.788 47.619 2.92 0.00 40.06 3.41
3266 3618 6.616947 TGTTTATTTGACATCATTCGGTTCC 58.383 36.000 0.00 0.00 0.00 3.62
3267 3619 6.432783 TGTTTATTTGACATCATTCGGTTCCT 59.567 34.615 0.00 0.00 0.00 3.36
3268 3620 4.970662 ATTTGACATCATTCGGTTCCTG 57.029 40.909 0.00 0.00 0.00 3.86
3512 3864 2.726066 GCTGTTTCTTTCCGAGCAATCG 60.726 50.000 0.00 0.00 0.00 3.34
3557 3909 0.533531 TGCTGTGGTGTGAGCTCTTG 60.534 55.000 16.19 0.00 36.11 3.02
3579 3931 4.392754 TGTGCTGTTCTTGCATGTATACAG 59.607 41.667 11.91 18.55 42.69 2.74
3611 3963 2.806244 TCGCTCACTTTTTGTAGCCTTC 59.194 45.455 0.00 0.00 0.00 3.46
3647 4203 3.312421 ACAATCAACGGTGTTCTGTCTTG 59.688 43.478 0.00 0.00 32.07 3.02
3659 4215 6.094061 GTGTTCTGTCTTGTCTCATACTACC 58.906 44.000 0.00 0.00 0.00 3.18
3662 4218 6.456795 TCTGTCTTGTCTCATACTACCATG 57.543 41.667 0.00 0.00 0.00 3.66
3670 4226 6.573434 TGTCTCATACTACCATGTGTTGATC 58.427 40.000 0.00 0.00 0.00 2.92
3676 4232 5.946942 ACTACCATGTGTTGATCTCTCAT 57.053 39.130 0.00 0.00 0.00 2.90
3683 4239 6.872547 CCATGTGTTGATCTCTCATATGGTAG 59.127 42.308 20.81 1.02 42.08 3.18
3700 4378 5.628797 TGGTAGATTGCATATTGGTCTGA 57.371 39.130 0.00 0.00 0.00 3.27
3775 4559 5.359576 ACCAACACTGAGAATAAAAAGCACA 59.640 36.000 0.00 0.00 0.00 4.57
3778 4562 4.153986 CACTGAGAATAAAAAGCACAGCG 58.846 43.478 0.00 0.00 0.00 5.18
3790 4574 2.494059 AGCACAGCGTAACAAAGACAT 58.506 42.857 0.00 0.00 0.00 3.06
3798 4582 5.848036 CAGCGTAACAAAGACATCAGAAAAG 59.152 40.000 0.00 0.00 0.00 2.27
3799 4583 5.527582 AGCGTAACAAAGACATCAGAAAAGT 59.472 36.000 0.00 0.00 0.00 2.66
3800 4584 6.704493 AGCGTAACAAAGACATCAGAAAAGTA 59.296 34.615 0.00 0.00 0.00 2.24
3801 4585 7.225931 AGCGTAACAAAGACATCAGAAAAGTAA 59.774 33.333 0.00 0.00 0.00 2.24
3802 4586 7.320560 GCGTAACAAAGACATCAGAAAAGTAAC 59.679 37.037 0.00 0.00 0.00 2.50
3803 4587 8.548721 CGTAACAAAGACATCAGAAAAGTAACT 58.451 33.333 0.00 0.00 0.00 2.24
3804 4588 9.651718 GTAACAAAGACATCAGAAAAGTAACTG 57.348 33.333 0.00 0.00 35.72 3.16
3805 4589 6.729187 ACAAAGACATCAGAAAAGTAACTGC 58.271 36.000 0.00 0.00 34.57 4.40
3806 4590 6.318648 ACAAAGACATCAGAAAAGTAACTGCA 59.681 34.615 0.00 0.00 34.57 4.41
3807 4591 6.942532 AAGACATCAGAAAAGTAACTGCAA 57.057 33.333 0.00 0.00 34.57 4.08
3808 4592 7.516198 AAGACATCAGAAAAGTAACTGCAAT 57.484 32.000 0.00 0.00 34.57 3.56
3809 4593 7.138692 AGACATCAGAAAAGTAACTGCAATC 57.861 36.000 0.00 0.00 34.57 2.67
3810 4594 6.712095 AGACATCAGAAAAGTAACTGCAATCA 59.288 34.615 0.00 0.00 34.57 2.57
3811 4595 6.672147 ACATCAGAAAAGTAACTGCAATCAC 58.328 36.000 0.00 0.00 34.57 3.06
3812 4596 5.342806 TCAGAAAAGTAACTGCAATCACG 57.657 39.130 0.00 0.00 34.57 4.35
3813 4597 4.814234 TCAGAAAAGTAACTGCAATCACGT 59.186 37.500 0.00 0.00 34.57 4.49
3814 4598 4.905866 CAGAAAAGTAACTGCAATCACGTG 59.094 41.667 9.94 9.94 0.00 4.49
3815 4599 4.814234 AGAAAAGTAACTGCAATCACGTGA 59.186 37.500 22.48 22.48 0.00 4.35
3816 4600 5.470098 AGAAAAGTAACTGCAATCACGTGAT 59.530 36.000 25.18 25.18 36.07 3.06
3817 4601 5.689383 AAAGTAACTGCAATCACGTGATT 57.311 34.783 32.82 32.82 44.93 2.57
3818 4602 5.689383 AAGTAACTGCAATCACGTGATTT 57.311 34.783 35.15 24.44 42.41 2.17
3819 4603 5.034554 AGTAACTGCAATCACGTGATTTG 57.965 39.130 35.15 28.84 42.41 2.32
3820 4604 4.754618 AGTAACTGCAATCACGTGATTTGA 59.245 37.500 35.15 24.21 42.41 2.69
3821 4605 4.566545 AACTGCAATCACGTGATTTGAA 57.433 36.364 35.15 24.31 42.41 2.69
3822 4606 4.566545 ACTGCAATCACGTGATTTGAAA 57.433 36.364 35.15 21.20 42.41 2.69
3823 4607 5.125100 ACTGCAATCACGTGATTTGAAAT 57.875 34.783 35.15 19.65 42.41 2.17
3824 4608 5.531634 ACTGCAATCACGTGATTTGAAATT 58.468 33.333 35.15 15.79 42.41 1.82
3825 4609 5.984926 ACTGCAATCACGTGATTTGAAATTT 59.015 32.000 35.15 15.07 42.41 1.82
3835 4757 6.586082 ACGTGATTTGAAATTTGTAGGCATTC 59.414 34.615 0.00 0.00 0.00 2.67
3868 4790 8.352942 GGAATTGAAATATTTAGGTGCAGTAGG 58.647 37.037 0.00 0.00 0.00 3.18
3920 4843 7.642071 AATTCAGATTTTGTTGAAACATCGG 57.358 32.000 0.00 0.00 38.95 4.18
3952 4941 3.210857 TGTAGCGTTCCTGCACTTC 57.789 52.632 0.00 0.00 37.31 3.01
3958 4947 3.345808 TTCCTGCACTTCGCGCAC 61.346 61.111 8.75 0.00 46.97 5.34
3999 4988 1.333636 AAGTCCAGGCAGATCTCGGG 61.334 60.000 0.00 0.00 0.00 5.14
4006 4995 2.887568 CAGATCTCGGGCGTGCAC 60.888 66.667 6.82 6.82 0.00 4.57
4007 4996 3.071206 AGATCTCGGGCGTGCACT 61.071 61.111 16.19 0.00 0.00 4.40
4009 4998 3.069980 GATCTCGGGCGTGCACTCT 62.070 63.158 16.19 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 113 2.659610 GAAGACAGTGCTCCCGCT 59.340 61.111 0.00 0.00 36.97 5.52
110 114 2.435059 GGAAGACAGTGCTCCCGC 60.435 66.667 0.00 0.00 0.00 6.13
111 115 0.036010 ATTGGAAGACAGTGCTCCCG 60.036 55.000 4.51 0.00 0.00 5.14
112 116 1.680249 GGATTGGAAGACAGTGCTCCC 60.680 57.143 4.51 0.00 0.00 4.30
861 908 0.757935 AATAATGGCTGGCTGGCTGG 60.758 55.000 18.27 0.85 42.34 4.85
862 909 0.672342 GAATAATGGCTGGCTGGCTG 59.328 55.000 18.27 2.91 42.34 4.85
863 910 0.468771 GGAATAATGGCTGGCTGGCT 60.469 55.000 18.27 2.43 42.34 4.75
969 1016 3.213402 GCCTCCTCCTCGTCCTCG 61.213 72.222 0.00 0.00 38.55 4.63
1156 1208 1.369625 GTCTACACGCCCAAATCCTG 58.630 55.000 0.00 0.00 0.00 3.86
1169 1221 0.738975 CGAGATCCGCTTGGTCTACA 59.261 55.000 0.00 0.00 0.00 2.74
1198 1250 1.006832 CGCAGGGGAACGTAAATGAG 58.993 55.000 0.00 0.00 0.00 2.90
1210 1262 3.264897 CGAATTCGCTCGCAGGGG 61.265 66.667 15.93 0.00 31.04 4.79
1211 1263 2.509336 ACGAATTCGCTCGCAGGG 60.509 61.111 27.03 0.00 42.69 4.45
1337 1389 2.019984 CACCTCATCCTAAAGCAAGCC 58.980 52.381 0.00 0.00 0.00 4.35
1341 1393 1.908619 TGAGCACCTCATCCTAAAGCA 59.091 47.619 0.00 0.00 35.39 3.91
1367 1419 3.879295 TCAGAAACTAATGCATGCTAGCC 59.121 43.478 20.33 6.41 0.00 3.93
1368 1420 5.450171 CATCAGAAACTAATGCATGCTAGC 58.550 41.667 20.33 8.10 0.00 3.42
1414 1466 1.052617 GCAACCTATCCCCTCTCCTC 58.947 60.000 0.00 0.00 0.00 3.71
1534 1586 3.982516 TCTACCAAGCTAGGAGTGTGAT 58.017 45.455 0.00 0.00 0.00 3.06
1545 1597 9.853177 AAGTATTAATGCTTATTCTACCAAGCT 57.147 29.630 16.13 0.00 45.89 3.74
1617 1669 6.859508 GTGGCCTTGTAAACTATACAAACAAC 59.140 38.462 3.32 0.00 37.04 3.32
1641 1693 4.681978 GCGGCCTGTTCTCGGTGT 62.682 66.667 0.00 0.00 0.00 4.16
1642 1694 4.680237 TGCGGCCTGTTCTCGGTG 62.680 66.667 0.00 0.00 0.00 4.94
1645 1697 1.970917 GATTGTGCGGCCTGTTCTCG 61.971 60.000 0.00 0.00 0.00 4.04
1657 1709 6.245724 GCAAAAGAATGCTAAATGATTGTGC 58.754 36.000 0.00 0.00 43.06 4.57
1732 1784 3.820467 TCTTTGACATGTTCCGAAGCAAT 59.180 39.130 0.00 0.00 0.00 3.56
1735 1787 3.751621 CATCTTTGACATGTTCCGAAGC 58.248 45.455 0.00 0.00 0.00 3.86
1743 1795 3.446442 AAGGAGGCATCTTTGACATGT 57.554 42.857 0.00 0.00 30.96 3.21
2184 2518 7.582435 AGTCAATACTACACGAACAAATGAG 57.418 36.000 0.00 0.00 32.84 2.90
2267 2602 1.594331 GGAAACGTTCTTGACCAGCT 58.406 50.000 0.00 0.00 0.00 4.24
2329 2664 7.324375 CACAATAACTTCACAGCAAACAGTATG 59.676 37.037 0.00 0.00 46.00 2.39
2490 2825 3.608506 CGGTACTGTTGAAAGATGACTCG 59.391 47.826 0.00 0.00 0.00 4.18
2702 3040 4.445564 ACTTTGTACTAGGGAGGGGATTT 58.554 43.478 0.00 0.00 0.00 2.17
2726 3064 6.708949 TCAAATAAGTGTCTCAACCTTGGTAC 59.291 38.462 0.00 0.00 0.00 3.34
2729 3067 5.765182 AGTCAAATAAGTGTCTCAACCTTGG 59.235 40.000 0.00 0.00 0.00 3.61
2730 3068 6.867662 AGTCAAATAAGTGTCTCAACCTTG 57.132 37.500 0.00 0.00 0.00 3.61
2732 3070 6.702329 CCTAGTCAAATAAGTGTCTCAACCT 58.298 40.000 0.00 0.00 0.00 3.50
2733 3071 5.351740 GCCTAGTCAAATAAGTGTCTCAACC 59.648 44.000 0.00 0.00 0.00 3.77
2734 3072 5.351740 GGCCTAGTCAAATAAGTGTCTCAAC 59.648 44.000 0.00 0.00 0.00 3.18
2735 3073 5.248477 AGGCCTAGTCAAATAAGTGTCTCAA 59.752 40.000 1.29 0.00 0.00 3.02
2737 3075 5.346181 AGGCCTAGTCAAATAAGTGTCTC 57.654 43.478 1.29 0.00 0.00 3.36
2738 3076 5.763876 AAGGCCTAGTCAAATAAGTGTCT 57.236 39.130 5.16 0.00 0.00 3.41
2739 3077 6.641474 AGTAAGGCCTAGTCAAATAAGTGTC 58.359 40.000 5.16 0.00 0.00 3.67
2740 3078 6.622427 AGTAAGGCCTAGTCAAATAAGTGT 57.378 37.500 5.16 0.00 0.00 3.55
2741 3079 7.390718 ACAAAGTAAGGCCTAGTCAAATAAGTG 59.609 37.037 5.16 0.00 0.00 3.16
2743 3081 7.923414 ACAAAGTAAGGCCTAGTCAAATAAG 57.077 36.000 5.16 0.00 0.00 1.73
2744 3082 9.969001 AATACAAAGTAAGGCCTAGTCAAATAA 57.031 29.630 5.16 0.00 0.00 1.40
2911 3250 1.931635 AGACTCCTCTCCACTGGAAC 58.068 55.000 0.00 0.00 31.23 3.62
2912 3251 2.704190 AAGACTCCTCTCCACTGGAA 57.296 50.000 0.00 0.00 31.23 3.53
2913 3252 2.110899 AGAAAGACTCCTCTCCACTGGA 59.889 50.000 0.00 0.00 0.00 3.86
2914 3253 2.534990 AGAAAGACTCCTCTCCACTGG 58.465 52.381 0.00 0.00 0.00 4.00
2915 3254 5.930837 ATTAGAAAGACTCCTCTCCACTG 57.069 43.478 0.00 0.00 0.00 3.66
2916 3255 6.498651 TGAAATTAGAAAGACTCCTCTCCACT 59.501 38.462 0.00 0.00 0.00 4.00
3081 3433 2.670148 AAGATGGTGGAGACCCGGC 61.670 63.158 0.00 0.00 42.34 6.13
3145 3497 5.105595 GCCTTCTGCCTTGTTAATCTTGATT 60.106 40.000 1.35 1.35 0.00 2.57
3266 3618 1.516161 TAACAGACAAGCAGCAGCAG 58.484 50.000 3.17 0.00 45.49 4.24
3267 3619 2.189594 ATAACAGACAAGCAGCAGCA 57.810 45.000 3.17 0.00 45.49 4.41
3268 3620 2.611292 CCTATAACAGACAAGCAGCAGC 59.389 50.000 0.00 0.00 42.56 5.25
3512 3864 7.706159 TCACAACAAGTTATTCCATGCATATC 58.294 34.615 0.00 0.00 0.00 1.63
3557 3909 4.201851 CCTGTATACATGCAAGAACAGCAC 60.202 45.833 5.91 0.00 45.95 4.40
3579 3931 0.889306 AGTGAGCGAGACCAACTACC 59.111 55.000 0.00 0.00 0.00 3.18
3611 3963 5.626543 CCGTTGATTGTTGTTCAGAATTCAG 59.373 40.000 8.44 0.00 0.00 3.02
3647 4203 6.810911 AGATCAACACATGGTAGTATGAGAC 58.189 40.000 0.00 0.77 0.00 3.36
3659 4215 7.664758 TCTACCATATGAGAGATCAACACATG 58.335 38.462 3.65 0.00 0.00 3.21
3662 4218 7.117523 GCAATCTACCATATGAGAGATCAACAC 59.882 40.741 15.61 5.15 0.00 3.32
3670 4226 8.045507 ACCAATATGCAATCTACCATATGAGAG 58.954 37.037 3.65 0.80 35.45 3.20
3676 4232 7.315066 TCAGACCAATATGCAATCTACCATA 57.685 36.000 0.00 0.00 0.00 2.74
3683 4239 4.517832 TGCAGATCAGACCAATATGCAATC 59.482 41.667 3.18 0.00 45.41 2.67
3700 4378 4.392940 AGTGCTCACTTTAAGTTGCAGAT 58.607 39.130 18.25 10.45 38.83 2.90
3775 4559 5.527582 ACTTTTCTGATGTCTTTGTTACGCT 59.472 36.000 0.00 0.00 0.00 5.07
3778 4562 9.651718 CAGTTACTTTTCTGATGTCTTTGTTAC 57.348 33.333 0.00 0.00 34.02 2.50
3790 4574 4.814234 ACGTGATTGCAGTTACTTTTCTGA 59.186 37.500 2.71 0.00 34.02 3.27
3798 4582 5.029650 TCAAATCACGTGATTGCAGTTAC 57.970 39.130 37.07 0.00 43.41 2.50
3799 4583 5.681337 TTCAAATCACGTGATTGCAGTTA 57.319 34.783 37.07 19.80 43.41 2.24
3800 4584 4.566545 TTCAAATCACGTGATTGCAGTT 57.433 36.364 37.07 22.28 43.41 3.16
3801 4585 4.566545 TTTCAAATCACGTGATTGCAGT 57.433 36.364 37.07 22.62 43.41 4.40
3802 4586 6.074195 ACAAATTTCAAATCACGTGATTGCAG 60.074 34.615 37.07 28.91 43.41 4.41
3803 4587 5.752472 ACAAATTTCAAATCACGTGATTGCA 59.248 32.000 37.07 25.66 43.41 4.08
3804 4588 6.214205 ACAAATTTCAAATCACGTGATTGC 57.786 33.333 37.07 0.00 43.41 3.56
3805 4589 7.410728 GCCTACAAATTTCAAATCACGTGATTG 60.411 37.037 37.07 29.27 43.41 2.67
3806 4590 6.586082 GCCTACAAATTTCAAATCACGTGATT 59.414 34.615 32.82 32.82 45.91 2.57
3807 4591 6.092748 GCCTACAAATTTCAAATCACGTGAT 58.907 36.000 25.18 25.18 36.07 3.06
3808 4592 5.009110 TGCCTACAAATTTCAAATCACGTGA 59.991 36.000 22.48 22.48 0.00 4.35
3809 4593 5.218885 TGCCTACAAATTTCAAATCACGTG 58.781 37.500 9.94 9.94 0.00 4.49
3810 4594 5.446143 TGCCTACAAATTTCAAATCACGT 57.554 34.783 0.00 0.00 0.00 4.49
3811 4595 6.237279 CGAATGCCTACAAATTTCAAATCACG 60.237 38.462 0.00 0.00 0.00 4.35
3812 4596 6.034898 CCGAATGCCTACAAATTTCAAATCAC 59.965 38.462 0.00 0.00 0.00 3.06
3813 4597 6.071672 TCCGAATGCCTACAAATTTCAAATCA 60.072 34.615 0.00 0.00 0.00 2.57
3814 4598 6.329496 TCCGAATGCCTACAAATTTCAAATC 58.671 36.000 0.00 0.00 0.00 2.17
3815 4599 6.279513 TCCGAATGCCTACAAATTTCAAAT 57.720 33.333 0.00 0.00 0.00 2.32
3816 4600 5.713792 TCCGAATGCCTACAAATTTCAAA 57.286 34.783 0.00 0.00 0.00 2.69
3817 4601 5.713792 TTCCGAATGCCTACAAATTTCAA 57.286 34.783 0.00 0.00 0.00 2.69
3818 4602 5.913137 ATTCCGAATGCCTACAAATTTCA 57.087 34.783 0.00 0.00 0.00 2.69
3819 4603 5.519927 CCAATTCCGAATGCCTACAAATTTC 59.480 40.000 0.00 0.00 0.00 2.17
3820 4604 5.186797 TCCAATTCCGAATGCCTACAAATTT 59.813 36.000 0.00 0.00 0.00 1.82
3821 4605 4.709397 TCCAATTCCGAATGCCTACAAATT 59.291 37.500 0.00 0.00 0.00 1.82
3822 4606 4.277476 TCCAATTCCGAATGCCTACAAAT 58.723 39.130 0.00 0.00 0.00 2.32
3823 4607 3.691575 TCCAATTCCGAATGCCTACAAA 58.308 40.909 0.00 0.00 0.00 2.83
3824 4608 3.358111 TCCAATTCCGAATGCCTACAA 57.642 42.857 0.00 0.00 0.00 2.41
3825 4609 3.358111 TTCCAATTCCGAATGCCTACA 57.642 42.857 0.00 0.00 0.00 2.74
3835 4757 9.248291 CACCTAAATATTTCAATTCCAATTCCG 57.752 33.333 3.39 0.00 0.00 4.30
3919 4842 6.691388 GGAACGCTACACATAAATCAAATTCC 59.309 38.462 0.00 0.00 0.00 3.01
3920 4843 7.429340 CAGGAACGCTACACATAAATCAAATTC 59.571 37.037 0.00 0.00 0.00 2.17
3979 4968 1.403814 CCGAGATCTGCCTGGACTTA 58.596 55.000 0.00 0.00 0.00 2.24
4009 4998 4.819761 GATGACGGCGCTGGAGCA 62.820 66.667 22.44 15.65 42.21 4.26
4084 5079 4.704833 ATGAAGCGGCACCGTGCT 62.705 61.111 22.41 2.90 44.28 4.40


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

AutoCloner maintained by Alex Coulton.