Multiple sequence alignment - TraesCS7D01G168700

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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 TraesCS7D01G168700 chr7D 100.000 5402 0 0 1 5402 119570016 119564615 0.000000e+00 9976.0
1 TraesCS7D01G168700 chr7D 92.133 572 39 4 4835 5402 636717740 636717171 0.000000e+00 802.0
2 TraesCS7D01G168700 chr7D 91.071 56 5 0 3967 4022 249429163 249429218 5.800000e-10 76.8
3 TraesCS7D01G168700 chr7A 93.731 4259 126 56 325 4508 124071498 124067306 0.000000e+00 6255.0
4 TraesCS7D01G168700 chr7A 92.091 569 38 4 4840 5402 634327315 634327882 0.000000e+00 795.0
5 TraesCS7D01G168700 chr7A 96.417 307 7 2 4500 4802 124067181 124066875 2.250000e-138 503.0
6 TraesCS7D01G168700 chr7A 93.827 324 13 2 17 336 124072131 124071811 1.050000e-131 481.0
7 TraesCS7D01G168700 chr7B 92.575 3111 131 41 1 3049 80663662 80660590 0.000000e+00 4373.0
8 TraesCS7D01G168700 chr7B 94.371 1812 55 30 3028 4822 80660587 80658806 0.000000e+00 2737.0
9 TraesCS7D01G168700 chr7B 91.986 574 40 3 4832 5402 541951320 541951890 0.000000e+00 800.0
10 TraesCS7D01G168700 chr1D 92.240 567 39 2 4839 5402 213373780 213374344 0.000000e+00 798.0
11 TraesCS7D01G168700 chr1D 83.065 124 19 2 1249 1371 278109820 278109698 1.590000e-20 111.0
12 TraesCS7D01G168700 chr1D 91.071 56 5 0 3967 4022 453205151 453205206 5.800000e-10 76.8
13 TraesCS7D01G168700 chr6D 91.769 571 43 2 4835 5402 460866404 460865835 0.000000e+00 791.0
14 TraesCS7D01G168700 chr6D 78.013 473 84 15 2486 2951 413271006 413270547 4.120000e-71 279.0
15 TraesCS7D01G168700 chr3D 91.769 571 43 2 4835 5402 489528357 489527788 0.000000e+00 791.0
16 TraesCS7D01G168700 chr6B 91.638 574 42 3 4832 5402 65133992 65134562 0.000000e+00 789.0
17 TraesCS7D01G168700 chr6B 77.311 476 91 15 2485 2951 623082732 623082265 1.150000e-66 265.0
18 TraesCS7D01G168700 chr6B 86.702 188 18 6 1501 1683 623083790 623083605 9.170000e-48 202.0
19 TraesCS7D01G168700 chr3B 91.887 567 41 3 4839 5402 519864668 519864104 0.000000e+00 787.0
20 TraesCS7D01G168700 chr4D 91.419 571 45 2 4835 5402 346203687 346204256 0.000000e+00 780.0
21 TraesCS7D01G168700 chr6A 77.637 474 91 15 2486 2951 558787239 558786773 1.920000e-69 274.0
22 TraesCS7D01G168700 chr6A 87.234 188 17 6 1501 1683 558788302 558788117 1.970000e-49 207.0
23 TraesCS7D01G168700 chr1A 77.972 286 20 19 22 284 16097332 16097597 7.300000e-29 139.0
24 TraesCS7D01G168700 chr1A 83.871 124 18 2 1249 1371 350400269 350400147 3.420000e-22 117.0
25 TraesCS7D01G168700 chr1B 83.871 124 18 2 1249 1371 377969155 377969033 3.420000e-22 117.0
26 TraesCS7D01G168700 chr1B 91.228 57 5 0 50 106 21358226 21358170 1.610000e-10 78.7
27 TraesCS7D01G168700 chr2A 78.462 130 25 3 1249 1377 654907886 654908013 1.250000e-11 82.4
28 TraesCS7D01G168700 chr2D 91.071 56 5 0 3967 4022 523630157 523630212 5.800000e-10 76.8


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 TraesCS7D01G168700 chr7D 119564615 119570016 5401 True 9976.0 9976 100.000000 1 5402 1 chr7D.!!$R1 5401
1 TraesCS7D01G168700 chr7D 636717171 636717740 569 True 802.0 802 92.133000 4835 5402 1 chr7D.!!$R2 567
2 TraesCS7D01G168700 chr7A 124066875 124072131 5256 True 2413.0 6255 94.658333 17 4802 3 chr7A.!!$R1 4785
3 TraesCS7D01G168700 chr7A 634327315 634327882 567 False 795.0 795 92.091000 4840 5402 1 chr7A.!!$F1 562
4 TraesCS7D01G168700 chr7B 80658806 80663662 4856 True 3555.0 4373 93.473000 1 4822 2 chr7B.!!$R1 4821
5 TraesCS7D01G168700 chr7B 541951320 541951890 570 False 800.0 800 91.986000 4832 5402 1 chr7B.!!$F1 570
6 TraesCS7D01G168700 chr1D 213373780 213374344 564 False 798.0 798 92.240000 4839 5402 1 chr1D.!!$F1 563
7 TraesCS7D01G168700 chr6D 460865835 460866404 569 True 791.0 791 91.769000 4835 5402 1 chr6D.!!$R2 567
8 TraesCS7D01G168700 chr3D 489527788 489528357 569 True 791.0 791 91.769000 4835 5402 1 chr3D.!!$R1 567
9 TraesCS7D01G168700 chr6B 65133992 65134562 570 False 789.0 789 91.638000 4832 5402 1 chr6B.!!$F1 570
10 TraesCS7D01G168700 chr6B 623082265 623083790 1525 True 233.5 265 82.006500 1501 2951 2 chr6B.!!$R1 1450
11 TraesCS7D01G168700 chr3B 519864104 519864668 564 True 787.0 787 91.887000 4839 5402 1 chr3B.!!$R1 563
12 TraesCS7D01G168700 chr4D 346203687 346204256 569 False 780.0 780 91.419000 4835 5402 1 chr4D.!!$F1 567
13 TraesCS7D01G168700 chr6A 558786773 558788302 1529 True 240.5 274 82.435500 1501 2951 2 chr6A.!!$R1 1450

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
936 1323 0.907230 AGTGCCAAGGTCTCTCTCCC 60.907 60.000 0.0 0.0 0.0 4.30 F
1080 1467 2.328099 GCAGAACCAGAACCAGCGG 61.328 63.158 0.0 0.0 0.0 5.52 F
2224 2765 1.592223 GACCCGGTGAGTCTTCCAG 59.408 63.158 0.0 0.0 0.0 3.86 F
3668 4283 0.102663 TGCGTTAATGGCGTCCGATA 59.897 50.000 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2224 2765 0.179054 GAACGGTTAGAGGGGATGGC 60.179 60.0 0.00 0.0 0.00 4.40 R
2235 2776 0.737019 GGCAATCGGTCGAACGGTTA 60.737 55.0 22.71 2.4 34.48 2.85 R
3677 4297 0.602562 CAGGGCCTGCGATTCAAAAA 59.397 50.0 22.68 0.0 0.00 1.94 R
5245 6024 0.038892 TCTGGGTTCGTAGTTCGTGC 60.039 55.0 0.00 0.0 40.80 5.34 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
191 198 7.012989 CCAAAGTTAATACTAGCCATACCAACC 59.987 40.741 0.00 0.00 33.17 3.77
320 327 1.955778 TCCAAATGCCACAAGTGTCAG 59.044 47.619 0.00 0.00 0.00 3.51
336 343 2.171237 TGTCAGGTATCATCCAGGCTTG 59.829 50.000 0.00 0.00 0.00 4.01
338 345 1.143813 AGGTATCATCCAGGCTTGGG 58.856 55.000 15.86 0.00 45.10 4.12
339 346 1.140312 GGTATCATCCAGGCTTGGGA 58.860 55.000 15.86 5.61 45.10 4.37
367 698 1.216178 GGTTTGCGCTACTACGGGA 59.784 57.895 9.73 0.00 0.00 5.14
581 922 2.288666 CCGCACCGGTTACTACTAGTA 58.711 52.381 2.97 1.89 42.73 1.82
582 923 2.032178 CCGCACCGGTTACTACTAGTAC 59.968 54.545 2.97 0.00 42.73 2.73
583 924 2.032178 CGCACCGGTTACTACTAGTACC 59.968 54.545 2.97 0.08 28.93 3.34
650 1002 0.935194 AGGATAGGGACGAAGGGAGT 59.065 55.000 0.00 0.00 0.00 3.85
653 1005 1.957877 GATAGGGACGAAGGGAGTGAG 59.042 57.143 0.00 0.00 0.00 3.51
655 1007 2.359967 GGGACGAAGGGAGTGAGGG 61.360 68.421 0.00 0.00 0.00 4.30
656 1008 1.305046 GGACGAAGGGAGTGAGGGA 60.305 63.158 0.00 0.00 0.00 4.20
657 1009 1.324005 GGACGAAGGGAGTGAGGGAG 61.324 65.000 0.00 0.00 0.00 4.30
660 1033 1.392534 GAAGGGAGTGAGGGAGGGA 59.607 63.158 0.00 0.00 0.00 4.20
665 1038 1.075600 GAGTGAGGGAGGGAGGAGG 60.076 68.421 0.00 0.00 0.00 4.30
672 1045 2.015726 GGAGGGAGGAGGGAGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
673 1046 1.541672 GAGGGAGGAGGGAGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
675 1048 2.520741 GGAGGAGGGAGAGGAGCG 60.521 72.222 0.00 0.00 0.00 5.03
676 1049 2.277404 GAGGAGGGAGAGGAGCGT 59.723 66.667 0.00 0.00 0.00 5.07
726 1108 1.211709 CCAATCGGCCGTTTCAACC 59.788 57.895 27.15 0.00 0.00 3.77
936 1323 0.907230 AGTGCCAAGGTCTCTCTCCC 60.907 60.000 0.00 0.00 0.00 4.30
1054 1441 3.982241 GCAACCAGCACCAGCACC 61.982 66.667 0.00 0.00 45.49 5.01
1055 1442 2.519063 CAACCAGCACCAGCACCA 60.519 61.111 0.00 0.00 45.49 4.17
1056 1443 2.519302 AACCAGCACCAGCACCAC 60.519 61.111 0.00 0.00 45.49 4.16
1080 1467 2.328099 GCAGAACCAGAACCAGCGG 61.328 63.158 0.00 0.00 0.00 5.52
1183 1583 3.501950 CCTTAATTCTCGCCTTGTTTGC 58.498 45.455 0.00 0.00 0.00 3.68
1333 1737 4.292178 CTCGAGGCCCGCCAGATC 62.292 72.222 8.74 0.00 38.92 2.75
1403 1809 3.266510 TCCATGGACTCGAATCTTTGG 57.733 47.619 11.44 8.66 0.00 3.28
1410 1816 2.416893 GACTCGAATCTTTGGTTGCTCC 59.583 50.000 0.00 0.00 0.00 4.70
1421 1827 2.851195 TGGTTGCTCCAAGTTTCTCTC 58.149 47.619 0.00 0.00 44.12 3.20
1433 1855 7.569240 TCCAAGTTTCTCTCTTTTTCTTCTCT 58.431 34.615 0.00 0.00 0.00 3.10
2224 2765 1.592223 GACCCGGTGAGTCTTCCAG 59.408 63.158 0.00 0.00 0.00 3.86
2235 2776 0.985490 GTCTTCCAGCCATCCCCTCT 60.985 60.000 0.00 0.00 0.00 3.69
3025 3609 2.171003 CCCTTAAACCCCAAGCAAGAG 58.829 52.381 0.00 0.00 0.00 2.85
3049 3658 6.412362 AGCGTTTTTGTTGTTTTGTTTTGTTC 59.588 30.769 0.00 0.00 0.00 3.18
3051 3660 7.583040 GCGTTTTTGTTGTTTTGTTTTGTTCTA 59.417 29.630 0.00 0.00 0.00 2.10
3052 3661 9.422196 CGTTTTTGTTGTTTTGTTTTGTTCTAA 57.578 25.926 0.00 0.00 0.00 2.10
3066 3675 8.739039 TGTTTTGTTCTAATCTAACCATGATGG 58.261 33.333 10.53 10.53 45.02 3.51
3389 3998 1.554042 CCTACGTTCACGCACCACAC 61.554 60.000 0.00 0.00 44.43 3.82
3405 4014 2.798283 CCACACTACACTGTTACGGTTG 59.202 50.000 0.00 0.00 0.00 3.77
3406 4015 3.450578 CACACTACACTGTTACGGTTGT 58.549 45.455 0.00 0.00 0.00 3.32
3407 4016 3.866910 CACACTACACTGTTACGGTTGTT 59.133 43.478 0.00 0.00 0.00 2.83
3408 4017 5.042593 CACACTACACTGTTACGGTTGTTA 58.957 41.667 0.00 0.00 0.00 2.41
3409 4018 5.693104 CACACTACACTGTTACGGTTGTTAT 59.307 40.000 0.00 0.00 0.00 1.89
3410 4019 5.922544 ACACTACACTGTTACGGTTGTTATC 59.077 40.000 0.00 0.00 0.00 1.75
3411 4020 5.921976 CACTACACTGTTACGGTTGTTATCA 59.078 40.000 0.00 0.00 0.00 2.15
3471 4085 1.215382 CCATGTCTCTCGCCGTTGA 59.785 57.895 0.00 0.00 0.00 3.18
3612 4227 1.004277 GAGGCGATAATGCTCCGTCG 61.004 60.000 0.00 0.00 37.17 5.12
3664 4279 2.353579 AGTATTTGCGTTAATGGCGTCC 59.646 45.455 0.00 0.00 0.00 4.79
3668 4283 0.102663 TGCGTTAATGGCGTCCGATA 59.897 50.000 0.00 0.00 0.00 2.92
3677 4297 1.153628 GCGTCCGATACTGGCAACT 60.154 57.895 0.00 0.00 37.61 3.16
3786 4406 2.440599 GGGTGCTCCATGGTGGTT 59.559 61.111 12.58 0.00 39.03 3.67
4126 4746 2.683867 TCCGAGCTAAGCTAGAGTGTTC 59.316 50.000 0.00 0.00 39.88 3.18
4163 4784 2.036475 CGAGGGAGAGAGAGAGAGAGAG 59.964 59.091 0.00 0.00 0.00 3.20
4285 4908 3.445687 CGTCCGTCCGTCCATCCA 61.446 66.667 0.00 0.00 0.00 3.41
4286 4909 2.782222 CGTCCGTCCGTCCATCCAT 61.782 63.158 0.00 0.00 0.00 3.41
4287 4910 1.067582 GTCCGTCCGTCCATCCATC 59.932 63.158 0.00 0.00 0.00 3.51
4288 4911 2.131709 TCCGTCCGTCCATCCATCC 61.132 63.158 0.00 0.00 0.00 3.51
4289 4912 2.431454 CCGTCCGTCCATCCATCCA 61.431 63.158 0.00 0.00 0.00 3.41
4290 4913 1.520192 CGTCCGTCCATCCATCCAA 59.480 57.895 0.00 0.00 0.00 3.53
4291 4914 0.106708 CGTCCGTCCATCCATCCAAT 59.893 55.000 0.00 0.00 0.00 3.16
4292 4915 1.873903 CGTCCGTCCATCCATCCAATC 60.874 57.143 0.00 0.00 0.00 2.67
4293 4916 0.764890 TCCGTCCATCCATCCAATCC 59.235 55.000 0.00 0.00 0.00 3.01
4302 4925 0.885879 CCATCCAATCCATCCATGCG 59.114 55.000 0.00 0.00 0.00 4.73
4309 4932 1.634865 ATCCATCCATGCGTCCACCA 61.635 55.000 0.00 0.00 0.00 4.17
4331 4954 1.551430 CACACCATCCCATTGCATGTT 59.449 47.619 0.00 0.00 0.00 2.71
4392 5016 9.616156 TTTCCATTAGCGTAATTTTACAGGATA 57.384 29.630 1.76 0.00 33.28 2.59
4413 5037 8.053355 AGGATATTTCCCACCTTAAACTAGTTG 58.947 37.037 9.34 0.00 43.76 3.16
4450 5079 1.335415 CGTCAGGTCAGTCAGTCAGTG 60.335 57.143 0.00 0.00 0.00 3.66
4517 5280 0.613260 TGATAGGCGCCTTTGACAGT 59.387 50.000 37.74 10.55 0.00 3.55
4593 5359 2.672996 AGCACCGCCACCATTGTC 60.673 61.111 0.00 0.00 0.00 3.18
4624 5395 0.523072 CCTATGTGTTGGTGCTGTGC 59.477 55.000 0.00 0.00 0.00 4.57
4822 5595 2.282462 CACCCCCGCTTGCTTTCT 60.282 61.111 0.00 0.00 0.00 2.52
4823 5596 1.903404 CACCCCCGCTTGCTTTCTT 60.903 57.895 0.00 0.00 0.00 2.52
4824 5597 1.152546 ACCCCCGCTTGCTTTCTTT 60.153 52.632 0.00 0.00 0.00 2.52
4825 5598 1.179174 ACCCCCGCTTGCTTTCTTTC 61.179 55.000 0.00 0.00 0.00 2.62
4826 5599 0.895559 CCCCCGCTTGCTTTCTTTCT 60.896 55.000 0.00 0.00 0.00 2.52
4827 5600 0.961753 CCCCGCTTGCTTTCTTTCTT 59.038 50.000 0.00 0.00 0.00 2.52
4828 5601 1.341209 CCCCGCTTGCTTTCTTTCTTT 59.659 47.619 0.00 0.00 0.00 2.52
4829 5602 2.224042 CCCCGCTTGCTTTCTTTCTTTT 60.224 45.455 0.00 0.00 0.00 2.27
4830 5603 3.457234 CCCGCTTGCTTTCTTTCTTTTT 58.543 40.909 0.00 0.00 0.00 1.94
4831 5604 3.490896 CCCGCTTGCTTTCTTTCTTTTTC 59.509 43.478 0.00 0.00 0.00 2.29
4832 5605 4.111916 CCGCTTGCTTTCTTTCTTTTTCA 58.888 39.130 0.00 0.00 0.00 2.69
4833 5606 4.746611 CCGCTTGCTTTCTTTCTTTTTCAT 59.253 37.500 0.00 0.00 0.00 2.57
4837 5610 5.971895 TGCTTTCTTTCTTTTTCATGTGC 57.028 34.783 0.00 0.00 0.00 4.57
4902 5678 3.243068 CCGACCTGACAAAACTGAAAAGG 60.243 47.826 0.00 0.00 0.00 3.11
4917 5693 1.523758 AAAGGCAACAGAACGCTAGG 58.476 50.000 0.00 0.00 41.41 3.02
4929 5705 0.817634 ACGCTAGGCTTTGCACACAA 60.818 50.000 11.63 0.00 0.00 3.33
4960 5736 8.428852 ACCAGCCAAGAAGTAAAAATTACAAAT 58.571 29.630 3.37 0.00 0.00 2.32
5169 5948 4.263572 CAGACCGGGGCAACACCA 62.264 66.667 6.32 0.00 42.05 4.17
5242 6021 3.655777 TGGAGAAGGAAACCATACCTGTT 59.344 43.478 0.00 0.00 36.56 3.16
5245 6024 4.407365 AGAAGGAAACCATACCTGTTTGG 58.593 43.478 5.37 5.37 36.13 3.28
5253 6032 2.151202 CATACCTGTTTGGCACGAACT 58.849 47.619 3.92 0.00 40.22 3.01
5282 6061 3.906218 CCAGATCCACCATCTTCCAGATA 59.094 47.826 0.00 0.00 40.20 1.98
5315 6094 1.640069 CACAATCTGCATCCGCTCG 59.360 57.895 0.00 0.00 39.64 5.03
5361 6141 1.285641 CGTTGGAGCAAACGCCATT 59.714 52.632 6.44 0.00 45.96 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 7.947890 ACCAGGTTTCAGAAATTACAATCCTTA 59.052 33.333 0.00 0.00 0.00 2.69
191 198 5.298527 ACATGTTGATCTAATGACCATGCTG 59.701 40.000 0.00 0.00 0.00 4.41
285 292 2.495155 TTGGACCTGATGATGGTGTG 57.505 50.000 0.00 0.00 38.03 3.82
320 327 1.072965 CTCCCAAGCCTGGATGATACC 59.927 57.143 1.80 0.00 46.92 2.73
336 343 1.685820 CAAACCACTCCCTCCTCCC 59.314 63.158 0.00 0.00 0.00 4.30
338 345 1.376037 CGCAAACCACTCCCTCCTC 60.376 63.158 0.00 0.00 0.00 3.71
339 346 2.750350 CGCAAACCACTCCCTCCT 59.250 61.111 0.00 0.00 0.00 3.69
367 698 1.377994 CTTTGCTGTCAGCCCTCCT 59.622 57.895 21.99 0.00 41.51 3.69
650 1002 2.204624 TCCCTCCTCCCTCCCTCA 60.205 66.667 0.00 0.00 0.00 3.86
653 1005 2.612251 CTCTCCCTCCTCCCTCCC 59.388 72.222 0.00 0.00 0.00 4.30
655 1007 1.541672 CTCCTCTCCCTCCTCCCTC 59.458 68.421 0.00 0.00 0.00 4.30
656 1008 2.710826 GCTCCTCTCCCTCCTCCCT 61.711 68.421 0.00 0.00 0.00 4.20
657 1009 2.123033 GCTCCTCTCCCTCCTCCC 60.123 72.222 0.00 0.00 0.00 4.30
660 1033 2.277404 GACGCTCCTCTCCCTCCT 59.723 66.667 0.00 0.00 0.00 3.69
665 1038 3.844090 GGCTGGACGCTCCTCTCC 61.844 72.222 5.77 0.00 37.46 3.71
709 1091 1.211709 GGGTTGAAACGGCCGATTG 59.788 57.895 35.90 1.98 0.00 2.67
726 1108 0.453793 TATGCCGATTTTTGCACCGG 59.546 50.000 0.00 0.00 40.88 5.28
936 1323 2.069430 GCAGGAGGAGGAAGGAGGG 61.069 68.421 0.00 0.00 0.00 4.30
1053 1440 1.970114 CTGGTTCTGCTGCTGGTGG 60.970 63.158 6.69 0.00 0.00 4.61
1054 1441 0.535780 TTCTGGTTCTGCTGCTGGTG 60.536 55.000 6.69 0.00 0.00 4.17
1055 1442 0.536006 GTTCTGGTTCTGCTGCTGGT 60.536 55.000 6.69 0.00 0.00 4.00
1056 1443 1.239968 GGTTCTGGTTCTGCTGCTGG 61.240 60.000 6.69 0.00 0.00 4.85
1080 1467 4.285149 CGATGGTAGCGCTTGCGC 62.285 66.667 29.21 29.21 45.69 6.09
1183 1583 1.070577 CGGCGGCAAGAATTAAGATCG 60.071 52.381 10.53 0.00 0.00 3.69
1403 1809 5.506686 AAAAGAGAGAAACTTGGAGCAAC 57.493 39.130 0.00 0.00 0.00 4.17
1419 1825 8.477256 AGACCAGATCATAGAGAAGAAAAAGAG 58.523 37.037 0.00 0.00 0.00 2.85
1421 1827 8.881743 CAAGACCAGATCATAGAGAAGAAAAAG 58.118 37.037 0.00 0.00 0.00 2.27
1433 1855 7.337689 CAGGAAACAATTCAAGACCAGATCATA 59.662 37.037 0.00 0.00 37.29 2.15
1830 2368 3.497884 GAACTGCTGGTGGTGCCCT 62.498 63.158 0.00 0.00 36.04 5.19
2224 2765 0.179054 GAACGGTTAGAGGGGATGGC 60.179 60.000 0.00 0.00 0.00 4.40
2235 2776 0.737019 GGCAATCGGTCGAACGGTTA 60.737 55.000 22.71 2.40 34.48 2.85
3025 3609 6.412362 AGAACAAAACAAAACAACAAAAACGC 59.588 30.769 0.00 0.00 0.00 4.84
3066 3675 2.032894 CGTCACTGTCAACAACATCCAC 60.033 50.000 0.00 0.00 37.23 4.02
3389 3998 6.154445 AGTGATAACAACCGTAACAGTGTAG 58.846 40.000 0.00 0.00 0.00 2.74
3405 4014 5.385617 ACTACGTACGTGACAAGTGATAAC 58.614 41.667 30.25 0.00 0.00 1.89
3406 4015 5.611796 ACTACGTACGTGACAAGTGATAA 57.388 39.130 30.25 5.04 0.00 1.75
3407 4016 5.063438 GGTACTACGTACGTGACAAGTGATA 59.937 44.000 30.25 8.36 39.64 2.15
3408 4017 4.142816 GGTACTACGTACGTGACAAGTGAT 60.143 45.833 30.25 6.92 39.64 3.06
3409 4018 3.186409 GGTACTACGTACGTGACAAGTGA 59.814 47.826 30.25 7.12 39.64 3.41
3410 4019 3.482786 GGTACTACGTACGTGACAAGTG 58.517 50.000 30.25 12.99 39.64 3.16
3411 4020 2.157668 CGGTACTACGTACGTGACAAGT 59.842 50.000 30.25 25.23 39.64 3.16
3459 4073 1.086067 ATGCACATCAACGGCGAGAG 61.086 55.000 16.62 2.29 0.00 3.20
3471 4085 2.042259 CGTCCCACTGCATGCACAT 61.042 57.895 18.46 4.89 0.00 3.21
3612 4227 3.933955 TGTTAATGCAGCAATTCAATGGC 59.066 39.130 0.00 0.00 0.00 4.40
3664 4279 4.788100 CGATTCAAAAAGTTGCCAGTATCG 59.212 41.667 0.00 0.00 34.50 2.92
3668 4283 2.100584 TGCGATTCAAAAAGTTGCCAGT 59.899 40.909 0.00 0.00 34.50 4.00
3677 4297 0.602562 CAGGGCCTGCGATTCAAAAA 59.397 50.000 22.68 0.00 0.00 1.94
3709 4329 4.748144 CTGGCCACCTTGGGGAGC 62.748 72.222 0.00 0.00 38.19 4.70
3735 4355 2.436292 CTCTCCTGCAGCACCAGC 60.436 66.667 8.66 0.00 42.56 4.85
4126 4746 1.202087 CCTCGTCAGAAGCACTAGACG 60.202 57.143 18.86 18.86 43.83 4.18
4163 4784 1.588667 CAACGCACCAACCAACTGC 60.589 57.895 0.00 0.00 0.00 4.40
4200 4821 2.195567 GCAGCAACAGCAGGTGGAA 61.196 57.895 4.26 0.00 35.17 3.53
4285 4908 1.546323 GGACGCATGGATGGATTGGAT 60.546 52.381 0.00 0.00 0.00 3.41
4286 4909 0.179020 GGACGCATGGATGGATTGGA 60.179 55.000 0.00 0.00 0.00 3.53
4287 4910 0.466007 TGGACGCATGGATGGATTGG 60.466 55.000 0.00 0.00 0.00 3.16
4288 4911 0.664761 GTGGACGCATGGATGGATTG 59.335 55.000 0.00 0.00 0.00 2.67
4289 4912 0.466189 GGTGGACGCATGGATGGATT 60.466 55.000 0.00 0.00 0.00 3.01
4290 4913 1.149174 GGTGGACGCATGGATGGAT 59.851 57.895 0.00 0.00 0.00 3.41
4291 4914 1.634865 ATGGTGGACGCATGGATGGA 61.635 55.000 0.00 0.00 0.00 3.41
4292 4915 1.152902 ATGGTGGACGCATGGATGG 60.153 57.895 0.00 0.00 0.00 3.51
4293 4916 0.464193 TGATGGTGGACGCATGGATG 60.464 55.000 0.00 0.00 0.00 3.51
4302 4925 0.394352 GGGATGGTGTGATGGTGGAC 60.394 60.000 0.00 0.00 0.00 4.02
4309 4932 2.036387 CATGCAATGGGATGGTGTGAT 58.964 47.619 0.00 0.00 41.79 3.06
4331 4954 1.001487 TGACGAACGAACGAAGCCTAA 60.001 47.619 11.97 0.00 37.03 2.69
4392 5016 6.152831 GCATCAACTAGTTTAAGGTGGGAAAT 59.847 38.462 5.07 0.00 34.79 2.17
4450 5079 3.407698 TCTGACTCTGACTGACTCACTC 58.592 50.000 0.00 0.00 0.00 3.51
4517 5280 2.956333 TGGTTCGTTCTTGACTCTCTCA 59.044 45.455 0.00 0.00 0.00 3.27
4593 5359 4.160252 CCAACACATAGGAGGAAAAATGGG 59.840 45.833 0.00 0.00 0.00 4.00
4624 5395 3.705638 CTCTGCCGCACACACACG 61.706 66.667 0.00 0.00 0.00 4.49
4806 5577 1.152546 AAAGAAAGCAAGCGGGGGT 60.153 52.632 0.00 0.00 0.00 4.95
4824 5597 9.187996 TGATATAAATGAGGCACATGAAAAAGA 57.812 29.630 0.00 0.00 39.39 2.52
4825 5598 9.976511 ATGATATAAATGAGGCACATGAAAAAG 57.023 29.630 0.00 0.00 39.39 2.27
4829 5602 9.234827 CCTTATGATATAAATGAGGCACATGAA 57.765 33.333 0.00 0.00 39.39 2.57
4830 5603 8.605065 TCCTTATGATATAAATGAGGCACATGA 58.395 33.333 0.00 0.00 39.39 3.07
4831 5604 8.797350 TCCTTATGATATAAATGAGGCACATG 57.203 34.615 0.00 0.00 39.39 3.21
4832 5605 9.624373 GATCCTTATGATATAAATGAGGCACAT 57.376 33.333 0.00 0.00 35.66 3.21
4833 5606 8.605065 TGATCCTTATGATATAAATGAGGCACA 58.395 33.333 4.55 0.00 32.24 4.57
4862 5638 2.689471 TCGGTATGTACGTGGCTTGTAT 59.311 45.455 0.00 0.00 0.00 2.29
4902 5678 0.875059 AAAGCCTAGCGTTCTGTTGC 59.125 50.000 0.00 0.00 0.00 4.17
4917 5693 2.072298 TGGTGTTTTTGTGTGCAAAGC 58.928 42.857 0.00 0.00 44.32 3.51
4929 5705 5.669164 TTTTACTTCTTGGCTGGTGTTTT 57.331 34.783 0.00 0.00 0.00 2.43
4960 5736 6.849085 AGCTCAGAAGATTCTTCAGTCTTA 57.151 37.500 24.51 4.06 34.97 2.10
4975 5751 1.865865 GGACGTTGTCAAGCTCAGAA 58.134 50.000 0.00 0.00 33.68 3.02
5019 5798 1.808411 TTTCTCCTTTGGTAGCTGCG 58.192 50.000 0.00 0.00 0.00 5.18
5025 5804 4.627284 TCCGTCATTTTCTCCTTTGGTA 57.373 40.909 0.00 0.00 0.00 3.25
5126 5905 2.672996 AACGGCAATGGCTTCGCT 60.673 55.556 5.02 0.00 40.87 4.93
5169 5948 2.431942 GTTCGATGGCGTGTCCGT 60.432 61.111 0.00 0.00 38.98 4.69
5225 6004 2.897326 GCCAAACAGGTATGGTTTCCTT 59.103 45.455 0.00 0.00 32.64 3.36
5242 6021 0.600782 GGGTTCGTAGTTCGTGCCAA 60.601 55.000 6.95 0.00 40.80 4.52
5245 6024 0.038892 TCTGGGTTCGTAGTTCGTGC 60.039 55.000 0.00 0.00 40.80 5.34
5253 6032 1.760613 GATGGTGGATCTGGGTTCGTA 59.239 52.381 0.00 0.00 0.00 3.43
5282 6061 2.094757 TTGTGGTCTGCATCGACGGT 62.095 55.000 0.00 0.00 34.75 4.83
5361 6141 4.695993 TCGTGCTCCGCCATTGCA 62.696 61.111 0.00 0.00 37.32 4.08
5375 6155 1.480954 GTGGTGGATATGTGTCCTCGT 59.519 52.381 0.00 0.00 39.12 4.18


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

AutoCloner maintained by Alex Coulton.