Multiple sequence alignment - TraesCS3A01G266500

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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 TraesCS3A01G266500 chr3A 100.000 5737 0 0 1 5737 491187279 491181543 0.000000e+00 10595.0
1 TraesCS3A01G266500 chr3B 92.227 4001 171 38 12 3944 481623550 481619622 0.000000e+00 5537.0
2 TraesCS3A01G266500 chr3B 88.919 740 49 7 4415 5124 481619088 481618352 0.000000e+00 881.0
3 TraesCS3A01G266500 chr3B 88.930 542 42 10 3937 4471 481619513 481618983 0.000000e+00 652.0
4 TraesCS3A01G266500 chr3B 87.912 546 54 10 5195 5737 41618186 41618722 2.920000e-177 632.0
5 TraesCS3A01G266500 chr3B 97.500 80 2 0 2584 2663 481620932 481620853 2.790000e-28 137.0
6 TraesCS3A01G266500 chr3D 95.090 2933 102 21 1 2915 370113593 370110685 0.000000e+00 4580.0
7 TraesCS3A01G266500 chr3D 93.127 1484 55 12 3076 4518 370110582 370109105 0.000000e+00 2132.0
8 TraesCS3A01G266500 chr3D 89.693 815 45 10 4423 5206 370109151 370108345 0.000000e+00 1003.0
9 TraesCS3A01G266500 chr3D 88.806 536 50 8 5206 5737 540258373 540257844 0.000000e+00 649.0
10 TraesCS3A01G266500 chr3D 98.750 80 1 0 2584 2663 370110938 370110859 5.990000e-30 143.0
11 TraesCS3A01G266500 chr3D 88.764 89 1 3 2910 2989 370110669 370110581 3.660000e-17 100.0
12 TraesCS3A01G266500 chr5A 91.445 526 39 5 5213 5737 413194481 413195001 0.000000e+00 717.0
13 TraesCS3A01G266500 chr5A 86.207 58 6 2 3563 3620 706787758 706787703 1.730000e-05 62.1
14 TraesCS3A01G266500 chr7B 89.354 526 49 7 5213 5737 44786948 44786429 0.000000e+00 654.0
15 TraesCS3A01G266500 chr7B 83.721 86 7 1 3524 3609 588500562 588500640 2.220000e-09 75.0
16 TraesCS3A01G266500 chr6B 88.108 555 54 10 5185 5737 160920563 160920019 0.000000e+00 649.0
17 TraesCS3A01G266500 chr1D 88.910 532 50 8 5208 5737 58824303 58824827 0.000000e+00 647.0
18 TraesCS3A01G266500 chr2B 88.519 540 51 9 5202 5737 686054384 686053852 1.350000e-180 643.0
19 TraesCS3A01G266500 chr2B 88.235 85 9 1 4261 4345 442520237 442520154 3.660000e-17 100.0
20 TraesCS3A01G266500 chr1B 88.454 537 51 10 5205 5737 432799368 432799897 6.270000e-179 638.0
21 TraesCS3A01G266500 chr1B 88.029 543 55 9 5198 5737 351236457 351236992 8.110000e-178 634.0
22 TraesCS3A01G266500 chr1B 87.500 56 6 1 3561 3616 610165094 610165040 4.800000e-06 63.9
23 TraesCS3A01G266500 chr5B 77.122 271 48 12 4077 4345 328374009 328373751 1.670000e-30 145.0
24 TraesCS3A01G266500 chr2A 78.541 233 35 13 4112 4341 504339077 504339297 7.750000e-29 139.0
25 TraesCS3A01G266500 chr2A 100.000 30 0 0 3525 3554 712059998 712060027 8.030000e-04 56.5
26 TraesCS3A01G266500 chr2D 77.447 235 36 16 4112 4342 372929901 372929680 2.170000e-24 124.0
27 TraesCS3A01G266500 chr2D 90.667 75 6 1 5126 5200 532566071 532566144 1.320000e-16 99.0
28 TraesCS3A01G266500 chr2D 90.667 75 6 1 5126 5200 532628674 532628747 1.320000e-16 99.0
29 TraesCS3A01G266500 chr2D 100.000 30 0 0 3525 3554 572800085 572800114 8.030000e-04 56.5
30 TraesCS3A01G266500 chr5D 75.277 271 41 14 4077 4345 289080797 289080551 7.860000e-19 106.0
31 TraesCS3A01G266500 chrUn 90.667 75 6 1 5126 5200 271274238 271274311 1.320000e-16 99.0
32 TraesCS3A01G266500 chrUn 90.667 75 6 1 5126 5200 349126947 349126874 1.320000e-16 99.0
33 TraesCS3A01G266500 chrUn 90.667 75 6 1 5126 5200 370910527 370910454 1.320000e-16 99.0
34 TraesCS3A01G266500 chrUn 90.667 75 6 1 5126 5200 396077637 396077710 1.320000e-16 99.0
35 TraesCS3A01G266500 chrUn 90.667 75 6 1 5126 5200 419073173 419073246 1.320000e-16 99.0
36 TraesCS3A01G266500 chrUn 89.333 75 7 1 5126 5200 183923740 183923667 6.120000e-15 93.5
37 TraesCS3A01G266500 chr7D 78.750 160 25 6 4175 4334 175652467 175652617 1.320000e-16 99.0
38 TraesCS3A01G266500 chr7D 92.857 42 3 0 3566 3607 165882647 165882688 1.730000e-05 62.1
39 TraesCS3A01G266500 chr7A 75.893 224 37 14 4119 4334 177333455 177333669 1.320000e-16 99.0
40 TraesCS3A01G266500 chr7A 93.478 46 2 1 3514 3559 625535776 625535732 3.710000e-07 67.6
41 TraesCS3A01G266500 chr6D 85.185 81 10 2 3526 3605 346074021 346073942 1.320000e-11 82.4
42 TraesCS3A01G266500 chr6D 94.444 36 2 0 3524 3559 218453869 218453904 8.030000e-04 56.5


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 TraesCS3A01G266500 chr3A 491181543 491187279 5736 True 10595.00 10595 100.0000 1 5737 1 chr3A.!!$R1 5736
1 TraesCS3A01G266500 chr3B 481618352 481623550 5198 True 1801.75 5537 91.8940 12 5124 4 chr3B.!!$R1 5112
2 TraesCS3A01G266500 chr3B 41618186 41618722 536 False 632.00 632 87.9120 5195 5737 1 chr3B.!!$F1 542
3 TraesCS3A01G266500 chr3D 370108345 370113593 5248 True 1591.60 4580 93.0848 1 5206 5 chr3D.!!$R2 5205
4 TraesCS3A01G266500 chr3D 540257844 540258373 529 True 649.00 649 88.8060 5206 5737 1 chr3D.!!$R1 531
5 TraesCS3A01G266500 chr5A 413194481 413195001 520 False 717.00 717 91.4450 5213 5737 1 chr5A.!!$F1 524
6 TraesCS3A01G266500 chr7B 44786429 44786948 519 True 654.00 654 89.3540 5213 5737 1 chr7B.!!$R1 524
7 TraesCS3A01G266500 chr6B 160920019 160920563 544 True 649.00 649 88.1080 5185 5737 1 chr6B.!!$R1 552
8 TraesCS3A01G266500 chr1D 58824303 58824827 524 False 647.00 647 88.9100 5208 5737 1 chr1D.!!$F1 529
9 TraesCS3A01G266500 chr2B 686053852 686054384 532 True 643.00 643 88.5190 5202 5737 1 chr2B.!!$R2 535
10 TraesCS3A01G266500 chr1B 432799368 432799897 529 False 638.00 638 88.4540 5205 5737 1 chr1B.!!$F2 532
11 TraesCS3A01G266500 chr1B 351236457 351236992 535 False 634.00 634 88.0290 5198 5737 1 chr1B.!!$F1 539

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
891 910 0.031721 CGGACGGCCTGAGTTATACC 59.968 60.0 5.33 0.0 0.00 2.73 F
940 971 0.715987 AGCCCCCTCTTTCTCTCTCT 59.284 55.0 0.00 0.0 0.00 3.10 F
1704 1735 2.754552 TGTGGTGTATACCCGACTGTAC 59.245 50.0 6.15 0.0 46.96 2.90 F
3022 3114 0.674895 GGCAGCTGAATTCTCGTGGT 60.675 55.0 20.43 0.0 0.00 4.16 F
3697 3817 0.995024 CCCTGGGAGTCTTTGGTGAT 59.005 55.0 7.01 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1879 1912 0.907486 TCCTTGGCATCCAGACTCAG 59.093 55.000 0.00 0.00 33.81 3.35 R
2194 2227 3.403038 AGAATAACACACACAGTCCAGC 58.597 45.455 0.00 0.00 0.00 4.85 R
3311 3403 1.065272 TCTGCACCAGCTGATTATGCA 60.065 47.619 24.04 24.04 42.77 3.96 R
4569 4868 1.189752 GTCCATGAGTCTGGAGCTCA 58.810 55.000 17.19 0.61 45.87 4.26 R
5598 5932 0.327924 TGATGGTGGGAAGCGATGTT 59.672 50.000 0.00 0.00 0.00 2.71 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
54 55 0.243636 ATTGTTACCGCAAAGCAGCC 59.756 50.000 0.00 0.00 31.63 4.85
64 65 2.289002 CGCAAAGCAGCCCTAGATTAAG 59.711 50.000 0.00 0.00 0.00 1.85
168 172 2.700897 CAACCTATCGGGGAATGACTCT 59.299 50.000 0.00 0.00 40.03 3.24
183 187 2.433145 TCTACGCCGACGACGACT 60.433 61.111 11.37 0.00 43.93 4.18
345 352 4.703703 GGGATCCCGAAGCTATGC 57.296 61.111 17.02 0.00 0.00 3.14
483 495 1.442526 GAGGAGTCGCGGACGGAATA 61.443 60.000 6.13 0.00 40.63 1.75
576 589 3.740397 CGCCTGTCGGTCGGTGTA 61.740 66.667 0.00 0.00 33.78 2.90
646 659 1.076192 GAGAGGCCGGGGAAGTAGA 60.076 63.158 2.18 0.00 0.00 2.59
656 669 0.179142 GGGAAGTAGACCGAGAACGC 60.179 60.000 0.00 0.00 38.29 4.84
814 833 4.641645 TGCTTGTGGGCAGACCGG 62.642 66.667 0.00 0.00 44.64 5.28
887 906 0.395311 AGATCGGACGGCCTGAGTTA 60.395 55.000 5.33 0.00 0.00 2.24
889 908 1.884579 GATCGGACGGCCTGAGTTATA 59.115 52.381 5.33 0.00 0.00 0.98
890 909 1.027357 TCGGACGGCCTGAGTTATAC 58.973 55.000 5.33 0.00 0.00 1.47
891 910 0.031721 CGGACGGCCTGAGTTATACC 59.968 60.000 5.33 0.00 0.00 2.73
892 911 1.117150 GGACGGCCTGAGTTATACCA 58.883 55.000 0.00 0.00 0.00 3.25
909 931 1.233019 CCAATCCTAGGCGCTTCATG 58.767 55.000 7.64 0.00 0.00 3.07
910 932 1.475751 CCAATCCTAGGCGCTTCATGT 60.476 52.381 7.64 0.00 0.00 3.21
911 933 1.869767 CAATCCTAGGCGCTTCATGTC 59.130 52.381 7.64 0.00 0.00 3.06
912 943 1.123077 ATCCTAGGCGCTTCATGTCA 58.877 50.000 7.64 0.00 0.00 3.58
930 961 2.306219 GTCAAAAAGTCTAGCCCCCTCT 59.694 50.000 0.00 0.00 0.00 3.69
933 964 3.722908 AAAAGTCTAGCCCCCTCTTTC 57.277 47.619 0.00 0.00 0.00 2.62
934 965 2.651642 AAGTCTAGCCCCCTCTTTCT 57.348 50.000 0.00 0.00 0.00 2.52
935 966 2.168458 AGTCTAGCCCCCTCTTTCTC 57.832 55.000 0.00 0.00 0.00 2.87
936 967 1.649100 AGTCTAGCCCCCTCTTTCTCT 59.351 52.381 0.00 0.00 0.00 3.10
937 968 2.036387 GTCTAGCCCCCTCTTTCTCTC 58.964 57.143 0.00 0.00 0.00 3.20
938 969 1.933765 TCTAGCCCCCTCTTTCTCTCT 59.066 52.381 0.00 0.00 0.00 3.10
939 970 2.091555 TCTAGCCCCCTCTTTCTCTCTC 60.092 54.545 0.00 0.00 0.00 3.20
940 971 0.715987 AGCCCCCTCTTTCTCTCTCT 59.284 55.000 0.00 0.00 0.00 3.10
1665 1696 6.259550 AGCTTAAAATTTGGTGAGTGCTAG 57.740 37.500 0.00 0.00 0.00 3.42
1677 1708 4.024809 GGTGAGTGCTAGAACAACAACTTC 60.025 45.833 3.00 0.00 0.00 3.01
1704 1735 2.754552 TGTGGTGTATACCCGACTGTAC 59.245 50.000 6.15 0.00 46.96 2.90
1845 1878 6.959639 TTGATTTTGTTGAGAAGTTAGCCT 57.040 33.333 0.00 0.00 0.00 4.58
1879 1912 5.640189 TCTAGTAGCTTGTCTGGTACAAC 57.360 43.478 0.00 0.00 43.22 3.32
1914 1947 3.261897 CCAAGGATAAGTCTGGACTGTGT 59.738 47.826 3.88 0.00 41.58 3.72
1992 2025 3.906720 ATACGGTGGTGCTCTATGTTT 57.093 42.857 0.00 0.00 0.00 2.83
2194 2227 7.783090 ATCAAGCATGTTATACTGAAGAGTG 57.217 36.000 0.00 0.00 33.21 3.51
2218 2251 5.063944 GCTGGACTGTGTGTGTTATTCTATG 59.936 44.000 0.00 0.00 0.00 2.23
2522 2560 9.579932 GGAATCCATGGAAGTAAAGATTAGATT 57.420 33.333 20.67 2.53 0.00 2.40
2675 2713 3.823281 ATCAGATGCTCCTGAGAACAG 57.177 47.619 12.70 0.00 45.27 3.16
2678 2716 3.326006 TCAGATGCTCCTGAGAACAGTTT 59.674 43.478 0.00 0.00 42.05 2.66
2702 2740 7.822161 TTGAAAATGGAACTTCTGAGAATGA 57.178 32.000 0.00 0.00 0.00 2.57
2714 2752 5.528043 TCTGAGAATGATAAGAGTGCTCC 57.472 43.478 0.00 0.00 0.00 4.70
2940 3020 6.876789 TCACCACAGTTACATAATAACACTGG 59.123 38.462 0.00 9.55 39.39 4.00
2956 3036 1.915489 ACTGGGCCAGACATGTTGATA 59.085 47.619 38.99 0.00 35.18 2.15
2957 3037 2.092753 ACTGGGCCAGACATGTTGATAG 60.093 50.000 38.99 9.87 35.18 2.08
2958 3038 1.212688 TGGGCCAGACATGTTGATAGG 59.787 52.381 0.00 0.00 0.00 2.57
3019 3111 2.100584 CTCTAGGCAGCTGAATTCTCGT 59.899 50.000 20.43 2.36 0.00 4.18
3022 3114 0.674895 GGCAGCTGAATTCTCGTGGT 60.675 55.000 20.43 0.00 0.00 4.16
3040 3132 5.924254 TCGTGGTAATTCAGTAACTTGACAG 59.076 40.000 0.00 0.00 0.00 3.51
3126 3218 3.563808 TCACAATGACAGCACAAGTTACC 59.436 43.478 0.00 0.00 0.00 2.85
3373 3468 6.414732 TGTACTCAACCTGCATAATTAGCTT 58.585 36.000 0.00 0.00 0.00 3.74
3421 3517 3.197766 TGGATCCACCTGTGATAACAGTC 59.802 47.826 11.44 0.00 39.86 3.51
3538 3658 1.688772 TTCTTACTCCCTCCGATCCG 58.311 55.000 0.00 0.00 0.00 4.18
3570 3690 3.560896 TCGCTGGTTTACAAAGTTGTACC 59.439 43.478 3.38 6.33 42.84 3.34
3583 3703 1.263217 GTTGTACCAAACCAGCGACAG 59.737 52.381 0.00 0.00 0.00 3.51
3595 3715 5.036117 ACCAGCGACAGTTAATATGGATT 57.964 39.130 0.00 0.00 0.00 3.01
3697 3817 0.995024 CCCTGGGAGTCTTTGGTGAT 59.005 55.000 7.01 0.00 0.00 3.06
3701 3821 3.274288 CTGGGAGTCTTTGGTGATAAGC 58.726 50.000 0.00 0.00 0.00 3.09
3714 3834 3.494048 GGTGATAAGCTGGGTCATCTCTG 60.494 52.174 0.00 0.00 0.00 3.35
3771 3894 8.539770 AGCAATAATATGTCTTTCTACCATCG 57.460 34.615 0.00 0.00 0.00 3.84
3961 4203 2.760650 TCTCGTATCCTTCATGCTGTGT 59.239 45.455 0.00 0.00 0.00 3.72
4063 4307 5.012046 TCTGAGCTCTTTGTTCTAATGTCCA 59.988 40.000 16.19 0.00 0.00 4.02
4130 4375 6.946583 TCTAGCTTGTCCTAGTCAAACTTCTA 59.053 38.462 0.00 3.15 36.89 2.10
4184 4429 5.197451 ACTAACATCTCACCAACACCAAAA 58.803 37.500 0.00 0.00 0.00 2.44
4186 4431 5.612725 AACATCTCACCAACACCAAAATT 57.387 34.783 0.00 0.00 0.00 1.82
4188 4433 4.405358 ACATCTCACCAACACCAAAATTGT 59.595 37.500 0.00 0.00 0.00 2.71
4226 4475 9.685276 ATTCATCATAGAACACATTTCCTTACA 57.315 29.630 0.00 0.00 0.00 2.41
4372 4621 9.294030 GTAAAATCTATTTGCCATCTTCTGTTG 57.706 33.333 0.00 0.00 0.00 3.33
4427 4678 2.726760 CACACTTCGCTGTAGAACTCAC 59.273 50.000 0.00 0.00 0.00 3.51
4475 4726 5.128335 TCTCTGACATATCATGTTGCACTCT 59.872 40.000 0.00 0.00 45.03 3.24
4519 4818 6.291648 AGTGTCTCTGACATATCATGTTGT 57.708 37.500 3.65 0.00 44.63 3.32
4543 4842 6.358974 TCATAAACTCTGTTGTCATCCAGA 57.641 37.500 3.49 3.49 36.35 3.86
4544 4843 6.950842 TCATAAACTCTGTTGTCATCCAGAT 58.049 36.000 3.85 0.00 37.11 2.90
4680 4979 1.881973 CTACCAAAGAAGCTGCTTGCA 59.118 47.619 21.25 0.00 45.94 4.08
4686 4985 1.113788 AGAAGCTGCTTGCAAAACCA 58.886 45.000 21.25 0.00 45.94 3.67
4763 5062 7.908193 AAACAAATTACGATGTCAAGTTCAC 57.092 32.000 0.00 0.00 0.00 3.18
4802 5101 8.725148 ACTTGTTGTAATGTGATCAGAAATCTC 58.275 33.333 0.00 0.00 0.00 2.75
4808 5107 2.159043 TGTGATCAGAAATCTCTCGCCC 60.159 50.000 0.00 0.00 0.00 6.13
4858 5157 5.756347 TGTATGTATTATGTCGTTCCTTGCC 59.244 40.000 0.00 0.00 0.00 4.52
4898 5197 0.839946 ATTATCGCTGGAGGTGCCTT 59.160 50.000 0.00 0.00 37.63 4.35
4914 5213 1.447838 CTTGGCCTCGAGCGCTAAA 60.448 57.895 11.50 15.05 45.17 1.85
4935 5234 8.129211 GCTAAAGTTTGTACATTCACATATCCC 58.871 37.037 0.00 0.00 0.00 3.85
4958 5257 5.123820 CCGAGGCTGAATTTTCTTGTAATCA 59.876 40.000 0.00 0.00 0.00 2.57
4969 5268 3.937814 TCTTGTAATCACTGACGCCATT 58.062 40.909 0.00 0.00 0.00 3.16
4985 5292 6.479990 TGACGCCATTATCAGAACTTAATCTG 59.520 38.462 0.36 0.36 46.62 2.90
4987 5294 5.334414 CGCCATTATCAGAACTTAATCTGCC 60.334 44.000 1.79 0.00 45.21 4.85
5013 5320 7.496920 CCAAAGACATAATACAAGATGAGCTGA 59.503 37.037 0.00 0.00 0.00 4.26
5072 5401 5.052481 TCCTTTAGACGCAATGAGATGATG 58.948 41.667 0.00 0.00 0.00 3.07
5080 5409 2.288213 GCAATGAGATGATGCACCATGG 60.288 50.000 11.19 11.19 39.81 3.66
5106 5435 3.059461 GCTGTGTGATTTTGGTTGCAATG 60.059 43.478 0.59 0.00 0.00 2.82
5321 5654 3.335711 GGCCAAGCCCACTCCTAT 58.664 61.111 0.00 0.00 44.06 2.57
5322 5655 2.539983 GGCCAAGCCCACTCCTATA 58.460 57.895 0.00 0.00 44.06 1.31
5323 5656 0.398318 GGCCAAGCCCACTCCTATAG 59.602 60.000 0.00 0.00 44.06 1.31
5399 5732 1.668751 GTCAGACAACGCAACTCCAAA 59.331 47.619 0.00 0.00 0.00 3.28
5499 5833 0.902984 TCATCGTACACCACAGGCCT 60.903 55.000 0.00 0.00 0.00 5.19
5592 5926 0.741574 CTACCGCAACCATTACCGCA 60.742 55.000 0.00 0.00 0.00 5.69
5598 5932 0.529833 CAACCATTACCGCATTGCCA 59.470 50.000 2.41 0.00 0.00 4.92
5606 5940 2.486504 CGCATTGCCAACATCGCT 59.513 55.556 2.41 0.00 0.00 4.93
5626 5960 1.077501 CCCACCATCATCGTTGCCT 60.078 57.895 0.00 0.00 0.00 4.75
5654 5988 2.086869 CTGGTCGCCACAATGATTCTT 58.913 47.619 0.00 0.00 0.00 2.52
5714 6048 2.642129 CGCAATCAAACGGCACCA 59.358 55.556 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 6.870965 AGCGATTGCATAAGTCTTAATCTAGG 59.129 38.462 7.90 0.00 46.23 3.02
64 65 2.221981 GCCTGTAGCGATTGCATAAGTC 59.778 50.000 7.90 0.00 46.23 3.01
168 172 2.802667 GCTAGTCGTCGTCGGCGTA 61.803 63.158 19.81 4.22 46.96 4.42
333 340 0.599991 TGCATACGCATAGCTTCGGG 60.600 55.000 0.00 0.00 45.36 5.14
483 495 1.227853 GTGCGGTTGAAGTCACCCT 60.228 57.895 0.00 0.00 0.00 4.34
576 589 2.569134 GAGAGAAGACGCCGCTGT 59.431 61.111 0.00 0.00 0.00 4.40
679 692 2.826287 TCTCTGCTCCTCTCCGCG 60.826 66.667 0.00 0.00 0.00 6.46
789 808 0.968405 TGCCCACAAGCAAAGGAATC 59.032 50.000 0.00 0.00 40.56 2.52
814 833 0.179067 TCCCCGATTATTCCACACGC 60.179 55.000 0.00 0.00 0.00 5.34
880 899 4.810790 CGCCTAGGATTGGTATAACTCAG 58.189 47.826 14.75 0.00 0.00 3.35
887 906 2.047061 TGAAGCGCCTAGGATTGGTAT 58.953 47.619 14.75 0.00 0.00 2.73
889 908 0.839946 ATGAAGCGCCTAGGATTGGT 59.160 50.000 14.75 3.77 0.00 3.67
890 909 1.233019 CATGAAGCGCCTAGGATTGG 58.767 55.000 14.75 0.00 0.00 3.16
891 910 1.869767 GACATGAAGCGCCTAGGATTG 59.130 52.381 14.75 1.92 0.00 2.67
892 911 1.486310 TGACATGAAGCGCCTAGGATT 59.514 47.619 14.75 3.19 0.00 3.01
909 931 2.306219 AGAGGGGGCTAGACTTTTTGAC 59.694 50.000 0.00 0.00 0.00 3.18
910 932 2.632537 AGAGGGGGCTAGACTTTTTGA 58.367 47.619 0.00 0.00 0.00 2.69
911 933 3.441500 AAGAGGGGGCTAGACTTTTTG 57.558 47.619 0.00 0.00 0.00 2.44
912 943 3.658216 AGAAAGAGGGGGCTAGACTTTTT 59.342 43.478 0.00 0.00 32.20 1.94
930 961 6.659242 GGAAAAGAGAGAGAGAGAGAGAGAAA 59.341 42.308 0.00 0.00 0.00 2.52
933 964 4.884164 GGGAAAAGAGAGAGAGAGAGAGAG 59.116 50.000 0.00 0.00 0.00 3.20
934 965 4.325030 GGGGAAAAGAGAGAGAGAGAGAGA 60.325 50.000 0.00 0.00 0.00 3.10
935 966 3.954258 GGGGAAAAGAGAGAGAGAGAGAG 59.046 52.174 0.00 0.00 0.00 3.20
936 967 3.596046 AGGGGAAAAGAGAGAGAGAGAGA 59.404 47.826 0.00 0.00 0.00 3.10
937 968 3.981212 AGGGGAAAAGAGAGAGAGAGAG 58.019 50.000 0.00 0.00 0.00 3.20
938 969 4.349365 GAAGGGGAAAAGAGAGAGAGAGA 58.651 47.826 0.00 0.00 0.00 3.10
939 970 3.450817 GGAAGGGGAAAAGAGAGAGAGAG 59.549 52.174 0.00 0.00 0.00 3.20
940 971 3.445987 GGAAGGGGAAAAGAGAGAGAGA 58.554 50.000 0.00 0.00 0.00 3.10
1172 1203 3.148279 GTGACGAGGCGGAGGGAT 61.148 66.667 0.00 0.00 0.00 3.85
1535 1566 1.560923 CATCCTTGCGGTACTTCTCG 58.439 55.000 0.00 0.00 0.00 4.04
1628 1659 0.999406 TAAGCTTCTTCGCATCACGC 59.001 50.000 0.00 0.00 43.23 5.34
1637 1668 6.144563 GCACTCACCAAATTTTAAGCTTCTTC 59.855 38.462 0.00 0.00 0.00 2.87
1804 1837 9.748708 CAAAATCAAACACTAAAATTCCAGAGA 57.251 29.630 0.00 0.00 0.00 3.10
1879 1912 0.907486 TCCTTGGCATCCAGACTCAG 59.093 55.000 0.00 0.00 33.81 3.35
1971 2004 4.403113 TCAAACATAGAGCACCACCGTATA 59.597 41.667 0.00 0.00 0.00 1.47
2194 2227 3.403038 AGAATAACACACACAGTCCAGC 58.597 45.455 0.00 0.00 0.00 4.85
2522 2560 3.772572 TCCCGACTCAAAATCACATCCTA 59.227 43.478 0.00 0.00 0.00 2.94
2675 2713 8.758715 CATTCTCAGAAGTTCCATTTTCAAAAC 58.241 33.333 0.00 0.00 0.00 2.43
2678 2716 7.822161 TCATTCTCAGAAGTTCCATTTTCAA 57.178 32.000 0.00 0.00 0.00 2.69
2702 2740 5.976458 CTTCTTCTGAAGGAGCACTCTTAT 58.024 41.667 16.83 0.00 44.33 1.73
2814 2852 7.688372 ACTTGTTATTTACATCAGCAGATTCG 58.312 34.615 0.00 0.00 36.44 3.34
2940 3020 2.486191 CCTCCTATCAACATGTCTGGCC 60.486 54.545 0.00 0.00 0.00 5.36
2956 3036 6.875972 ATGACAAAATCACTACTACCTCCT 57.124 37.500 0.00 0.00 41.24 3.69
2957 3037 9.614792 ATTTATGACAAAATCACTACTACCTCC 57.385 33.333 0.00 0.00 41.24 4.30
3019 3111 8.426489 ACTTACTGTCAAGTTACTGAATTACCA 58.574 33.333 0.00 0.00 35.16 3.25
3040 3132 4.451629 TTGGTACTAGCAGCTGACTTAC 57.548 45.455 20.43 13.25 0.00 2.34
3087 3179 8.755941 GTCATTGTGATAGTATGACATGTGTAC 58.244 37.037 1.15 6.48 44.67 2.90
3310 3402 1.954382 CTGCACCAGCTGATTATGCAT 59.046 47.619 25.08 3.79 44.73 3.96
3311 3403 1.065272 TCTGCACCAGCTGATTATGCA 60.065 47.619 24.04 24.04 42.77 3.96
3312 3404 1.671979 TCTGCACCAGCTGATTATGC 58.328 50.000 17.39 18.57 42.77 3.14
3313 3405 2.033049 GCTTCTGCACCAGCTGATTATG 59.967 50.000 17.39 8.99 46.18 1.90
3314 3406 2.092538 AGCTTCTGCACCAGCTGATTAT 60.093 45.455 17.39 0.00 44.98 1.28
3315 3407 1.280133 AGCTTCTGCACCAGCTGATTA 59.720 47.619 17.39 0.00 44.98 1.75
3356 3451 6.414732 TCTACACAAGCTAATTATGCAGGTT 58.585 36.000 0.00 0.00 32.93 3.50
3373 3468 6.295249 TGAATGACAATGGAAGTTCTACACA 58.705 36.000 2.25 0.00 0.00 3.72
3538 3658 8.019094 ACTTTGTAAACCAGCGACAATTAATAC 58.981 33.333 0.00 0.00 33.33 1.89
3570 3690 4.634004 TCCATATTAACTGTCGCTGGTTTG 59.366 41.667 0.00 0.00 0.00 2.93
3583 3703 7.317722 AGTACTCCCTCCAATCCATATTAAC 57.682 40.000 0.00 0.00 0.00 2.01
3595 3715 6.296259 GGTCAAAATTTCTAGTACTCCCTCCA 60.296 42.308 0.00 0.00 0.00 3.86
3697 3817 2.906389 ACAACAGAGATGACCCAGCTTA 59.094 45.455 0.00 0.00 26.98 3.09
3701 3821 4.691175 CATAGACAACAGAGATGACCCAG 58.309 47.826 0.00 0.00 0.00 4.45
3961 4203 3.658346 ATAGAGGGCAGGGGTGGCA 62.658 63.158 1.10 0.00 35.93 4.92
4063 4307 4.223032 CAGAGGGTGTACTGAACATAAGGT 59.777 45.833 0.00 0.00 41.10 3.50
4163 4408 6.097554 ACAATTTTGGTGTTGGTGAGATGTTA 59.902 34.615 0.00 0.00 0.00 2.41
4224 4473 9.304731 GTGCAACATCAATCAAACATATAATGT 57.695 29.630 0.00 0.00 40.84 2.71
4225 4474 9.303537 TGTGCAACATCAATCAAACATATAATG 57.696 29.630 0.00 0.00 45.67 1.90
4258 4507 7.994425 TTGACCAAGTCTATAGAAAAATGCA 57.006 32.000 3.40 0.00 33.15 3.96
4321 4570 8.778059 ACATACTCCCTCTGTTCCAAATTATTA 58.222 33.333 0.00 0.00 0.00 0.98
4499 4750 7.783090 ATGAACAACATGATATGTCAGAGAC 57.217 36.000 0.00 0.00 44.07 3.36
4519 4818 6.768483 TCTGGATGACAACAGAGTTTATGAA 58.232 36.000 8.63 0.00 38.71 2.57
4543 4842 4.778213 TTAGCTTCTCCATGCCAAGTAT 57.222 40.909 0.00 0.00 0.00 2.12
4544 4843 4.517285 CTTTAGCTTCTCCATGCCAAGTA 58.483 43.478 0.00 0.00 0.00 2.24
4569 4868 1.189752 GTCCATGAGTCTGGAGCTCA 58.810 55.000 17.19 0.61 45.87 4.26
4686 4985 2.977808 TCTCACTTCCCTCCAGAGTTT 58.022 47.619 0.00 0.00 0.00 2.66
4763 5062 9.431887 ACATTACAACAAGTACAGTATTACAGG 57.568 33.333 0.00 0.00 30.91 4.00
4802 5101 2.826777 ATTTCCAGTGCCAGGGCGAG 62.827 60.000 5.74 0.00 45.51 5.03
4808 5107 6.352516 AGATCTAGTTAATTTCCAGTGCCAG 58.647 40.000 0.00 0.00 0.00 4.85
4898 5197 2.167398 AACTTTAGCGCTCGAGGCCA 62.167 55.000 16.34 2.11 37.74 5.36
4905 5204 5.080068 GTGAATGTACAAACTTTAGCGCTC 58.920 41.667 16.34 0.00 0.00 5.03
4914 5213 5.984725 TCGGGATATGTGAATGTACAAACT 58.015 37.500 0.00 0.00 33.69 2.66
4935 5234 6.024049 GTGATTACAAGAAAATTCAGCCTCG 58.976 40.000 0.00 0.00 0.00 4.63
4958 5257 3.895232 AGTTCTGATAATGGCGTCAGT 57.105 42.857 0.00 0.00 41.92 3.41
4969 5268 6.823689 GTCTTTGGGCAGATTAAGTTCTGATA 59.176 38.462 9.76 0.00 44.88 2.15
4985 5292 6.514048 GCTCATCTTGTATTATGTCTTTGGGC 60.514 42.308 0.00 0.00 0.00 5.36
4987 5294 7.496920 TCAGCTCATCTTGTATTATGTCTTTGG 59.503 37.037 0.00 0.00 0.00 3.28
5013 5320 5.339008 TCACAACAATAGATAGGAAGCGT 57.661 39.130 0.00 0.00 0.00 5.07
5080 5409 3.184986 GCAACCAAAATCACACAGCAATC 59.815 43.478 0.00 0.00 0.00 2.67
5206 5535 6.597262 CAACCTTTGCCTTCGTTTAAAAAT 57.403 33.333 0.00 0.00 0.00 1.82
5319 5652 6.438108 TGCCCTGTGTTGTTTAGTCTACTATA 59.562 38.462 0.00 0.00 0.00 1.31
5320 5653 5.247564 TGCCCTGTGTTGTTTAGTCTACTAT 59.752 40.000 0.00 0.00 0.00 2.12
5321 5654 4.589798 TGCCCTGTGTTGTTTAGTCTACTA 59.410 41.667 0.00 0.00 0.00 1.82
5322 5655 3.389983 TGCCCTGTGTTGTTTAGTCTACT 59.610 43.478 0.00 0.00 0.00 2.57
5323 5656 3.735591 TGCCCTGTGTTGTTTAGTCTAC 58.264 45.455 0.00 0.00 0.00 2.59
5377 5710 1.684450 TGGAGTTGCGTTGTCTGACTA 59.316 47.619 9.51 0.00 0.00 2.59
5380 5713 2.031258 TTTGGAGTTGCGTTGTCTGA 57.969 45.000 0.00 0.00 0.00 3.27
5399 5732 5.477291 TGTTCTTCTAAGTTCTCCGTCAGAT 59.523 40.000 0.00 0.00 0.00 2.90
5469 5802 1.153568 TACGATGACTGGCTGCAGC 60.154 57.895 30.88 30.88 41.14 5.25
5592 5926 0.611618 TGGGAAGCGATGTTGGCAAT 60.612 50.000 1.92 0.00 0.00 3.56
5598 5932 0.327924 TGATGGTGGGAAGCGATGTT 59.672 50.000 0.00 0.00 0.00 2.71
5606 5940 0.679640 GGCAACGATGATGGTGGGAA 60.680 55.000 0.00 0.00 0.00 3.97
5626 5960 2.117423 TGGCGACCAGACTCCTGA 59.883 61.111 0.00 0.00 43.02 3.86
5671 6005 2.264794 GACGGAGCGGTGGATGTT 59.735 61.111 0.00 0.00 0.00 2.71
5693 6027 2.257302 TGCCGTTTGATTGCGCTGA 61.257 52.632 9.73 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.