Multiple sequence alignment - TraesCS3D01G328200

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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 TraesCS3D01G328200 chr3D 100.000 4343 0 0 1 4343 441140205 441144547 0.000000e+00 8021.0
1 TraesCS3D01G328200 chr3B 92.876 2302 101 21 1 2272 578391721 578393989 0.000000e+00 3284.0
2 TraesCS3D01G328200 chr3B 91.169 1506 100 22 2281 3775 578394103 578395586 0.000000e+00 2013.0
3 TraesCS3D01G328200 chr3B 86.902 397 31 13 3783 4160 578395719 578396113 4.010000e-115 425.0
4 TraesCS3D01G328200 chr3B 91.089 101 9 0 2274 2374 578394021 578394121 2.110000e-28 137.0
5 TraesCS3D01G328200 chr3A 92.940 1643 60 17 1 1615 581266283 581267897 0.000000e+00 2340.0
6 TraesCS3D01G328200 chr3A 91.398 1209 75 20 2663 3869 581269621 581270802 0.000000e+00 1629.0
7 TraesCS3D01G328200 chr3A 91.304 529 35 6 1400 1928 581268173 581268690 0.000000e+00 712.0
8 TraesCS3D01G328200 chr3A 93.084 347 21 3 1927 2272 581268784 581269128 5.010000e-139 505.0
9 TraesCS3D01G328200 chr3A 84.548 343 44 7 2278 2613 581269287 581269627 9.000000e-87 331.0
10 TraesCS3D01G328200 chr3A 79.487 156 29 2 4189 4343 581271225 581271378 1.650000e-19 108.0
11 TraesCS3D01G328200 chr3A 96.774 31 1 0 4125 4155 581271069 581271099 8.000000e-03 52.8
12 TraesCS3D01G328200 chr6A 91.281 367 26 3 1322 1687 594368042 594367681 3.020000e-136 496.0
13 TraesCS3D01G328200 chr6A 94.595 259 14 0 971 1229 594368297 594368039 6.770000e-108 401.0
14 TraesCS3D01G328200 chr6A 89.300 243 25 1 400 641 283493 283735 1.960000e-78 303.0
15 TraesCS3D01G328200 chr1B 87.812 361 20 8 1328 1687 184230339 184230002 6.770000e-108 401.0
16 TraesCS3D01G328200 chr6B 86.066 244 31 3 400 641 3380104 3380346 4.310000e-65 259.0
17 TraesCS3D01G328200 chrUn 91.096 146 12 1 277 422 51455720 51455576 3.430000e-46 196.0
18 TraesCS3D01G328200 chr5A 88.889 144 15 1 277 420 28620104 28620246 4.460000e-40 176.0


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 TraesCS3D01G328200 chr3D 441140205 441144547 4342 False 8021.000000 8021 100.000000 1 4343 1 chr3D.!!$F1 4342
1 TraesCS3D01G328200 chr3B 578391721 578396113 4392 False 1464.750000 3284 90.509000 1 4160 4 chr3B.!!$F1 4159
2 TraesCS3D01G328200 chr3A 581266283 581271378 5095 False 811.114286 2340 89.933571 1 4343 7 chr3A.!!$F1 4342
3 TraesCS3D01G328200 chr6A 594367681 594368297 616 True 448.500000 496 92.938000 971 1687 2 chr6A.!!$R1 716

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
825 826 1.137675 CGTTGGATGGCTCAGATCTCA 59.862 52.381 0.0 0.0 0.0 3.27 F
2365 3142 0.690762 ATGGTCCGGTTGCTACTGTT 59.309 50.000 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2378 3230 1.937223 ACGAAACACAGCGATGAACAA 59.063 42.857 8.12 0.0 0.0 2.83 R
3901 4895 0.470766 TTACGTGGCCCTGTTTCACT 59.529 50.000 0.00 0.0 0.0 3.41 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
124 125 2.776526 TGGCCCAGGAACCACAGT 60.777 61.111 0.00 0.00 0.00 3.55
361 362 2.445654 GGGAGGCAGGAGGAGAGG 60.446 72.222 0.00 0.00 0.00 3.69
403 404 2.032528 TGCGGGCTGTTGAGGAAG 59.967 61.111 0.00 0.00 0.00 3.46
707 708 2.280524 GGTTTTGCGGGTTTGGGC 60.281 61.111 0.00 0.00 0.00 5.36
726 727 4.760220 GGGGGCTGGAGGAAGGGA 62.760 72.222 0.00 0.00 0.00 4.20
727 728 3.412408 GGGGCTGGAGGAAGGGAC 61.412 72.222 0.00 0.00 0.00 4.46
824 825 1.863267 CGTTGGATGGCTCAGATCTC 58.137 55.000 0.00 0.00 0.00 2.75
825 826 1.137675 CGTTGGATGGCTCAGATCTCA 59.862 52.381 0.00 0.00 0.00 3.27
845 846 3.873812 GATCCGGGCCGAATGGGT 61.874 66.667 30.79 6.41 38.44 4.51
923 927 4.373116 GACAGTTCGCCGGCTCCA 62.373 66.667 26.68 4.99 0.00 3.86
926 930 4.514577 AGTTCGCCGGCTCCATCG 62.515 66.667 26.68 7.77 0.00 3.84
1143 1173 2.585153 GCGTCCTTCCCCTTCCTC 59.415 66.667 0.00 0.00 0.00 3.71
1320 1350 2.857744 CGGATGGCTACTCGACCCC 61.858 68.421 0.00 0.00 0.00 4.95
1357 1387 3.322466 CCGGCCTCCCAAGTGAGT 61.322 66.667 0.00 0.00 0.00 3.41
1419 1941 2.793790 CTCTATTGTTAGCTCGCTGCAG 59.206 50.000 10.11 10.11 45.94 4.41
1420 1942 2.427095 TCTATTGTTAGCTCGCTGCAGA 59.573 45.455 20.43 0.00 45.94 4.26
1422 1944 1.432514 TTGTTAGCTCGCTGCAGAAG 58.567 50.000 20.43 14.88 45.94 2.85
1430 1952 0.944386 TCGCTGCAGAAGGTTGTTTC 59.056 50.000 20.43 0.00 0.00 2.78
1455 1977 2.664402 AAGAGTTGGAATGTGGCAGT 57.336 45.000 0.00 0.00 0.00 4.40
1501 2023 6.086785 TGTGTCATCAATTGCAGAAATCAA 57.913 33.333 0.00 0.00 0.00 2.57
1628 2151 1.154672 CGGCATGAACACGTTGTCG 60.155 57.895 0.00 0.00 43.34 4.35
1648 2171 1.574428 GCGTGGCTGTAACACCTTG 59.426 57.895 0.00 0.00 35.46 3.61
1781 2304 2.824041 GCTGGGCATGTACCACGG 60.824 66.667 7.12 1.43 33.63 4.94
1783 2306 3.326578 TGGGCATGTACCACGGCT 61.327 61.111 7.12 0.00 31.83 5.52
1970 2592 5.359576 ACAAGCAACCAATGAACAAGACTTA 59.640 36.000 0.00 0.00 0.00 2.24
2109 2731 1.604147 GCAACATGGGGGTAGCAACC 61.604 60.000 0.00 0.00 45.97 3.77
2211 2834 4.640771 TGGTTCTATCAATAGATGCCCC 57.359 45.455 13.81 7.86 39.02 5.80
2262 2885 3.411446 TGCATCACTACTGTTTTCCCAG 58.589 45.455 0.00 0.00 38.45 4.45
2272 2895 8.027771 CACTACTGTTTTCCCAGTACTTACTAG 58.972 40.741 0.00 0.00 43.71 2.57
2276 3052 8.363390 ACTGTTTTCCCAGTACTTACTAGTTAC 58.637 37.037 0.00 0.00 43.71 2.50
2279 3055 9.847706 GTTTTCCCAGTACTTACTAGTTACTAC 57.152 37.037 0.00 0.00 35.78 2.73
2294 3070 9.007901 ACTAGTTACTACTTACTACTGTGTTGG 57.992 37.037 0.00 0.00 35.78 3.77
2303 3079 4.592485 ACTACTGTGTTGGACTTGAGAG 57.408 45.455 0.00 0.00 0.00 3.20
2304 3080 2.246719 ACTGTGTTGGACTTGAGAGC 57.753 50.000 0.00 0.00 0.00 4.09
2365 3142 0.690762 ATGGTCCGGTTGCTACTGTT 59.309 50.000 0.00 0.00 0.00 3.16
2374 3226 4.439563 CCGGTTGCTACTGTTTTGAACTTT 60.440 41.667 6.38 0.00 0.00 2.66
2378 3230 6.183360 GGTTGCTACTGTTTTGAACTTTAGGT 60.183 38.462 0.00 0.00 0.00 3.08
2396 3248 2.290641 AGGTTGTTCATCGCTGTGTTTC 59.709 45.455 0.00 0.00 0.00 2.78
2438 3290 7.065324 TGTTCAACTTGACTCTAAATTCGTGTT 59.935 33.333 0.00 0.00 0.00 3.32
2497 3354 4.335315 GTCCATGAGTGTCTCTACTCTCTG 59.665 50.000 0.00 5.24 45.70 3.35
2513 3370 5.788450 ACTCTCTGTTGATGGTGTTCTAAG 58.212 41.667 0.00 0.00 0.00 2.18
2542 3399 6.154445 TGTGTAGACGTTGAAAATCTCTACC 58.846 40.000 0.00 0.00 37.11 3.18
2561 3418 2.280628 CCGGTCTTCTACATTTGAGGC 58.719 52.381 0.00 0.00 0.00 4.70
2562 3419 2.354704 CCGGTCTTCTACATTTGAGGCA 60.355 50.000 0.00 0.00 0.00 4.75
2611 3468 5.332743 ACAACATATGGGACCTTGTCATTT 58.667 37.500 7.80 0.00 33.68 2.32
2615 3472 9.130661 CAACATATGGGACCTTGTCATTTTATA 57.869 33.333 7.80 0.00 33.68 0.98
2635 3492 2.622064 AAGCACGTCCAGTTCTCTTT 57.378 45.000 0.00 0.00 0.00 2.52
2660 3517 5.996513 CACCCAAATGAAATTTCAATCACCA 59.003 36.000 23.91 0.35 44.81 4.17
2672 3529 8.816640 AATTTCAATCACCATTCACTTTGTAC 57.183 30.769 0.00 0.00 0.00 2.90
2681 3538 4.460382 CCATTCACTTTGTACCTGCAGAAT 59.540 41.667 17.39 5.38 0.00 2.40
2692 3549 4.590850 ACCTGCAGAATTCCAAGTTTTC 57.409 40.909 17.39 0.00 0.00 2.29
2765 3622 8.628630 TGTAAATACAGAAACATCAATCCACA 57.371 30.769 0.00 0.00 0.00 4.17
2960 3817 2.751259 TGTCTTTCGCTACACGTAGGAT 59.249 45.455 6.36 0.00 44.19 3.24
2974 3831 4.170947 GGATTGATCCAGCCAGGC 57.829 61.111 1.84 1.84 46.38 4.85
3031 3888 3.843422 TGAAACATTTGTCATCTGGGGT 58.157 40.909 0.00 0.00 0.00 4.95
3092 3949 2.837947 TCACTCATCCAGTCCCTGATT 58.162 47.619 0.00 0.00 32.44 2.57
3107 3964 6.271857 AGTCCCTGATTATCACATGCTTCTAT 59.728 38.462 0.00 0.00 0.00 1.98
3112 3969 8.288208 CCTGATTATCACATGCTTCTATTGTTC 58.712 37.037 0.00 0.00 0.00 3.18
3117 3982 7.634671 ATCACATGCTTCTATTGTTCATTGA 57.365 32.000 0.00 0.00 0.00 2.57
3125 3990 9.195411 TGCTTCTATTGTTCATTGATTGTTTTC 57.805 29.630 0.00 0.00 0.00 2.29
3210 4075 1.238439 CTGACGAGGTTGCCATTGTT 58.762 50.000 0.00 0.00 0.00 2.83
3291 4156 4.104086 TCTTGGGATGTCAAGATACACCT 58.896 43.478 3.50 0.00 45.53 4.00
3366 4231 3.653164 TCCACATTGCTCCTATGGTCTA 58.347 45.455 0.00 0.00 0.00 2.59
3417 4284 4.699735 ACAATATGATGTGGCGAAACTGAA 59.300 37.500 0.00 0.00 30.82 3.02
3418 4285 5.182950 ACAATATGATGTGGCGAAACTGAAA 59.817 36.000 0.00 0.00 30.82 2.69
3419 4286 5.895636 ATATGATGTGGCGAAACTGAAAA 57.104 34.783 0.00 0.00 0.00 2.29
3426 4293 4.022416 TGTGGCGAAACTGAAAATAGCATT 60.022 37.500 0.00 0.00 0.00 3.56
3446 4313 4.908601 TTGAGCCTTCAGAATTCACCTA 57.091 40.909 8.44 0.00 34.15 3.08
3569 4437 5.310720 CAAGGGGTTATTCTTGTTACTGC 57.689 43.478 0.00 0.00 36.54 4.40
3614 4483 9.569122 TTGCATATAGTCACTAGTCATGTACTA 57.431 33.333 0.00 0.00 39.80 1.82
3618 4487 9.947433 ATATAGTCACTAGTCATGTACTACTCC 57.053 37.037 0.00 0.00 39.80 3.85
3619 4488 6.316280 AGTCACTAGTCATGTACTACTCCT 57.684 41.667 0.00 0.00 39.80 3.69
3634 4503 8.867097 TGTACTACTCCTTTGTTCAAGTTAGAT 58.133 33.333 0.00 0.00 0.00 1.98
3638 4507 9.706691 CTACTCCTTTGTTCAAGTTAGATACAA 57.293 33.333 0.00 0.00 0.00 2.41
3641 4510 8.974060 TCCTTTGTTCAAGTTAGATACAAACT 57.026 30.769 0.00 0.00 38.82 2.66
3655 4524 5.869888 AGATACAAACTCTACCTTCTTTGCG 59.130 40.000 0.00 0.00 0.00 4.85
3671 4540 4.870426 TCTTTGCGTCAATATTCTCAGGAC 59.130 41.667 0.00 0.00 0.00 3.85
3710 4579 1.433471 CAGCATACGTCTGCCGAGA 59.567 57.895 20.86 0.00 43.33 4.04
3775 4644 4.074259 TGACAAATTGCTGAGCTATGTGT 58.926 39.130 21.59 21.59 42.80 3.72
3776 4645 4.656041 GACAAATTGCTGAGCTATGTGTC 58.344 43.478 27.52 27.52 45.68 3.67
3803 4797 1.739067 ACTAATTTGCAGAGGCCGTC 58.261 50.000 0.00 0.00 40.13 4.79
3816 4810 1.078143 GCCGTCTCATGCCTCCTTT 60.078 57.895 0.00 0.00 0.00 3.11
3859 4853 4.458295 CAGAAATGACCTCTTTGTGCAGAT 59.542 41.667 0.00 0.00 0.00 2.90
3878 4872 5.007332 GCAGATGAATTGCAAAATCATTCCC 59.993 40.000 23.86 15.32 41.17 3.97
3896 4890 7.792032 TCATTCCCGATTCTTCACTATACTTT 58.208 34.615 0.00 0.00 0.00 2.66
3901 4895 9.412460 TCCCGATTCTTCACTATACTTTACTTA 57.588 33.333 0.00 0.00 0.00 2.24
3920 4914 0.470766 AGTGAAACAGGGCCACGTAA 59.529 50.000 6.18 0.00 41.43 3.18
3921 4915 1.134037 AGTGAAACAGGGCCACGTAAA 60.134 47.619 6.18 0.00 41.43 2.01
3945 4939 1.605457 GGACACGTTGATGTGCTCTCA 60.605 52.381 3.34 0.00 43.74 3.27
3980 4986 0.324943 TTGGCTTACACCTCTCTGCC 59.675 55.000 0.00 0.00 40.62 4.85
3981 4987 0.545309 TGGCTTACACCTCTCTGCCT 60.545 55.000 0.00 0.00 40.82 4.75
3982 4988 0.176910 GGCTTACACCTCTCTGCCTC 59.823 60.000 0.00 0.00 37.58 4.70
3983 4989 1.190643 GCTTACACCTCTCTGCCTCT 58.809 55.000 0.00 0.00 0.00 3.69
3984 4990 1.136110 GCTTACACCTCTCTGCCTCTC 59.864 57.143 0.00 0.00 0.00 3.20
3985 4991 1.754226 CTTACACCTCTCTGCCTCTCC 59.246 57.143 0.00 0.00 0.00 3.71
4005 5014 5.190925 TCTCCTCTCTTCTCTACTGTTAGCT 59.809 44.000 0.00 0.00 0.00 3.32
4039 5048 2.248835 CGGCAAGTCGGGTTCGTTT 61.249 57.895 0.00 0.00 37.69 3.60
4125 5147 9.347240 CAAGATGAGTGAGATATTTTAACCCAT 57.653 33.333 0.00 0.00 0.00 4.00
4126 5148 8.915057 AGATGAGTGAGATATTTTAACCCATG 57.085 34.615 0.00 0.00 0.00 3.66
4161 5301 8.738645 ACTTCATCCAAAAAGATACTGATACC 57.261 34.615 0.00 0.00 0.00 2.73
4166 5306 9.956720 CATCCAAAAAGATACTGATACCATTTC 57.043 33.333 0.00 0.00 0.00 2.17
4223 5363 5.317733 TGGTTATTTGATTTTAGGCGTGG 57.682 39.130 0.00 0.00 0.00 4.94
4242 5382 1.564348 GGGGTGCTCCTCAATCCTTTA 59.436 52.381 4.53 0.00 33.58 1.85
4243 5383 2.025321 GGGGTGCTCCTCAATCCTTTAA 60.025 50.000 4.53 0.00 33.58 1.52
4244 5384 3.282885 GGGTGCTCCTCAATCCTTTAAG 58.717 50.000 4.53 0.00 0.00 1.85
4245 5385 3.054361 GGGTGCTCCTCAATCCTTTAAGA 60.054 47.826 4.53 0.00 0.00 2.10
4246 5386 4.567747 GGGTGCTCCTCAATCCTTTAAGAA 60.568 45.833 4.53 0.00 0.00 2.52
4247 5387 5.010282 GGTGCTCCTCAATCCTTTAAGAAA 58.990 41.667 0.00 0.00 0.00 2.52
4248 5388 5.476945 GGTGCTCCTCAATCCTTTAAGAAAA 59.523 40.000 0.00 0.00 0.00 2.29
4249 5389 6.015434 GGTGCTCCTCAATCCTTTAAGAAAAA 60.015 38.462 0.00 0.00 0.00 1.94
4280 5420 4.201881 GGTTTTGTATGTATGAGGCGAACC 60.202 45.833 0.00 0.00 0.00 3.62
4323 5463 8.791675 TGTGAAGAATGCAACACAAATTCTATA 58.208 29.630 0.00 0.00 39.22 1.31
4327 5467 9.461312 AAGAATGCAACACAAATTCTATACCTA 57.539 29.630 0.00 0.00 39.22 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 1.615424 GCAGAGGTACCCCAGGGAA 60.615 63.158 7.25 0.00 38.96 3.97
361 362 3.184683 CTCAAGTCGCTGCCGCTC 61.185 66.667 0.00 0.00 0.00 5.03
680 681 4.362476 GCAAAACCCAGCGGCCAG 62.362 66.667 2.24 0.00 0.00 4.85
707 708 3.415087 CCTTCCTCCAGCCCCCAG 61.415 72.222 0.00 0.00 0.00 4.45
726 727 2.824388 CTTCCCTCCCCCTTCCTCGT 62.824 65.000 0.00 0.00 0.00 4.18
727 728 2.040606 TTCCCTCCCCCTTCCTCG 59.959 66.667 0.00 0.00 0.00 4.63
824 825 4.235762 ATTCGGCCCGGATCCGTG 62.236 66.667 31.22 22.77 46.49 4.94
825 826 4.235762 CATTCGGCCCGGATCCGT 62.236 66.667 31.22 9.45 46.49 4.69
923 927 4.403113 GGAGACTCTACTTTTTCTCCCGAT 59.597 45.833 1.74 0.00 45.91 4.18
935 941 2.829458 GGCGGCGGAGACTCTACT 60.829 66.667 9.78 0.00 0.00 2.57
939 945 4.632458 GATCGGCGGCGGAGACTC 62.632 72.222 31.73 15.75 0.00 3.36
1143 1173 0.753848 GGAGGACGAAGAGGGAGAGG 60.754 65.000 0.00 0.00 0.00 3.69
1419 1941 8.194769 TCCAACTCTTTTATTGAAACAACCTTC 58.805 33.333 0.00 0.00 0.00 3.46
1420 1942 8.073467 TCCAACTCTTTTATTGAAACAACCTT 57.927 30.769 0.00 0.00 0.00 3.50
1422 1944 8.764287 CATTCCAACTCTTTTATTGAAACAACC 58.236 33.333 0.00 0.00 0.00 3.77
1430 1952 5.782047 TGCCACATTCCAACTCTTTTATTG 58.218 37.500 0.00 0.00 0.00 1.90
1501 2023 4.510167 ACAAATATGAACTAGGCAGGCT 57.490 40.909 0.38 0.38 0.00 4.58
1628 2151 4.084888 GGTGTTACAGCCACGCGC 62.085 66.667 5.73 0.00 33.56 6.86
1783 2306 3.192212 TCACACAAACAATGCTGTCAACA 59.808 39.130 0.00 0.00 33.45 3.33
2109 2731 7.273381 CCAACTTGGTTAGCTAAAAATCAATCG 59.727 37.037 7.99 3.61 31.35 3.34
2211 2834 7.176589 AGTCCTCTTGTTTCCTAGTAAGATG 57.823 40.000 0.00 0.00 0.00 2.90
2272 2895 7.880105 AGTCCAACACAGTAGTAAGTAGTAAC 58.120 38.462 0.00 0.00 0.00 2.50
2276 3052 6.978338 TCAAGTCCAACACAGTAGTAAGTAG 58.022 40.000 0.00 0.00 0.00 2.57
2279 3055 6.085555 TCTCAAGTCCAACACAGTAGTAAG 57.914 41.667 0.00 0.00 0.00 2.34
2294 3070 3.243704 ACACTCAACAGAGCTCTCAAGTC 60.244 47.826 14.96 0.00 32.51 3.01
2303 3079 2.744202 CCAACCATACACTCAACAGAGC 59.256 50.000 0.00 0.00 32.51 4.09
2304 3080 4.008074 ACCAACCATACACTCAACAGAG 57.992 45.455 0.00 0.00 35.49 3.35
2374 3226 2.831685 ACACAGCGATGAACAACCTA 57.168 45.000 8.12 0.00 0.00 3.08
2378 3230 1.937223 ACGAAACACAGCGATGAACAA 59.063 42.857 8.12 0.00 0.00 2.83
2463 3320 5.952347 AGACACTCATGGACTACAACATCTA 59.048 40.000 0.00 0.00 0.00 1.98
2497 3354 6.016276 ACACAAATCCTTAGAACACCATCAAC 60.016 38.462 0.00 0.00 0.00 3.18
2513 3370 6.899114 AGATTTTCAACGTCTACACAAATCC 58.101 36.000 0.00 0.00 32.07 3.01
2542 3399 2.972625 TGCCTCAAATGTAGAAGACCG 58.027 47.619 0.00 0.00 0.00 4.79
2561 3418 7.280205 AGACTAGTAATCCGTGCCTAATTTTTG 59.720 37.037 0.00 0.00 0.00 2.44
2562 3419 7.336396 AGACTAGTAATCCGTGCCTAATTTTT 58.664 34.615 0.00 0.00 0.00 1.94
2611 3468 5.401531 AGAGAACTGGACGTGCTTTATAA 57.598 39.130 8.99 0.00 29.01 0.98
2615 3472 2.622064 AAGAGAACTGGACGTGCTTT 57.378 45.000 8.99 0.99 29.01 3.51
2635 3492 6.183361 TGGTGATTGAAATTTCATTTGGGTGA 60.183 34.615 21.10 4.64 37.00 4.02
2660 3517 5.183904 GGAATTCTGCAGGTACAAAGTGAAT 59.816 40.000 15.13 0.00 0.00 2.57
2672 3529 4.861102 AGAAAACTTGGAATTCTGCAGG 57.139 40.909 15.13 0.00 32.42 4.85
2692 3549 6.010219 TCCAGAATAACCCCAAGAAAGAAAG 58.990 40.000 0.00 0.00 0.00 2.62
2793 3650 9.017509 CAGGCAATCACATCCAAGTAAATATAT 57.982 33.333 0.00 0.00 0.00 0.86
2933 3790 2.329379 GTGTAGCGAAAGACAGACCAG 58.671 52.381 0.00 0.00 0.00 4.00
2960 3817 2.424842 AAACCGCCTGGCTGGATCAA 62.425 55.000 28.03 0.00 39.70 2.57
3031 3888 7.050377 TCATTACCCTGAATTTTGTTTTTGCA 58.950 30.769 0.00 0.00 0.00 4.08
3092 3949 8.735692 TCAATGAACAATAGAAGCATGTGATA 57.264 30.769 0.00 0.00 0.00 2.15
3107 3964 5.046529 CACGGGAAAACAATCAATGAACAA 58.953 37.500 0.00 0.00 0.00 2.83
3112 3969 5.058149 TGATCACGGGAAAACAATCAATG 57.942 39.130 0.00 0.00 0.00 2.82
3117 3982 3.888930 ACTGTTGATCACGGGAAAACAAT 59.111 39.130 17.07 7.54 34.92 2.71
3125 3990 5.163754 GGATTTTCTAACTGTTGATCACGGG 60.164 44.000 2.69 0.00 35.83 5.28
3291 4156 9.967451 TCAGTATTTGAACTGTTGGGATTTATA 57.033 29.630 0.00 0.00 45.78 0.98
3366 4231 5.473504 AGTCTTTGAAATATTGCTCACCGTT 59.526 36.000 0.00 0.00 0.00 4.44
3405 4270 4.217334 TCAATGCTATTTTCAGTTTCGCCA 59.783 37.500 0.00 0.00 0.00 5.69
3417 4284 6.379133 TGAATTCTGAAGGCTCAATGCTATTT 59.621 34.615 7.05 0.00 42.39 1.40
3418 4285 5.889853 TGAATTCTGAAGGCTCAATGCTATT 59.110 36.000 7.05 0.00 42.39 1.73
3419 4286 5.298777 GTGAATTCTGAAGGCTCAATGCTAT 59.701 40.000 7.05 0.00 42.39 2.97
3426 4293 3.198635 CCTAGGTGAATTCTGAAGGCTCA 59.801 47.826 7.05 0.00 0.00 4.26
3446 4313 6.963322 AGCATCTACCTTAAAATCTTCACCT 58.037 36.000 0.00 0.00 0.00 4.00
3530 4397 3.862845 CCCTTGTCAACAAAAACGGAAAG 59.137 43.478 0.00 0.00 35.15 2.62
3534 4401 1.478916 ACCCCTTGTCAACAAAAACGG 59.521 47.619 0.00 0.00 35.15 4.44
3536 4403 6.578944 AGAATAACCCCTTGTCAACAAAAAC 58.421 36.000 0.00 0.00 35.15 2.43
3603 4472 6.665992 TGAACAAAGGAGTAGTACATGACT 57.334 37.500 0.00 1.10 42.69 3.41
3614 4483 8.837389 GTTTGTATCTAACTTGAACAAAGGAGT 58.163 33.333 0.00 0.00 39.83 3.85
3617 4486 9.057089 AGAGTTTGTATCTAACTTGAACAAAGG 57.943 33.333 0.00 0.00 39.83 3.11
3634 4503 4.952460 ACGCAAAGAAGGTAGAGTTTGTA 58.048 39.130 0.00 0.00 33.33 2.41
3638 4507 3.746045 TGACGCAAAGAAGGTAGAGTT 57.254 42.857 0.00 0.00 0.00 3.01
3641 4510 6.640518 AGAATATTGACGCAAAGAAGGTAGA 58.359 36.000 0.00 0.00 0.00 2.59
3655 4524 9.780413 GAAAGAAATTGTCCTGAGAATATTGAC 57.220 33.333 0.00 0.00 0.00 3.18
3671 4540 5.798934 GCTGCACATACAGAGAAAGAAATTG 59.201 40.000 0.00 0.00 40.25 2.32
3710 4579 3.007290 TCTGTCAGTTAACAGCTCAGCAT 59.993 43.478 8.61 0.00 45.12 3.79
3775 4644 2.492881 TCTGCAAATTAGTACCCGACGA 59.507 45.455 0.00 0.00 0.00 4.20
3776 4645 2.858344 CTCTGCAAATTAGTACCCGACG 59.142 50.000 0.00 0.00 0.00 5.12
3803 4797 2.033801 CGGCAATAAAAGGAGGCATGAG 59.966 50.000 0.00 0.00 0.00 2.90
3859 4853 4.797800 TCGGGAATGATTTTGCAATTCA 57.202 36.364 13.19 13.19 0.00 2.57
3896 4890 2.289195 CGTGGCCCTGTTTCACTAAGTA 60.289 50.000 0.00 0.00 0.00 2.24
3901 4895 0.470766 TTACGTGGCCCTGTTTCACT 59.529 50.000 0.00 0.00 0.00 3.41
3920 4914 1.593196 CACATCAACGTGTCCTGGTT 58.407 50.000 0.00 0.00 32.00 3.67
3921 4915 0.884704 GCACATCAACGTGTCCTGGT 60.885 55.000 0.00 0.00 39.19 4.00
3945 4939 1.615392 GCCAAATCACAGACCAAGCTT 59.385 47.619 0.00 0.00 0.00 3.74
3980 4986 5.527582 GCTAACAGTAGAGAAGAGAGGAGAG 59.472 48.000 0.00 0.00 0.00 3.20
3981 4987 5.190925 AGCTAACAGTAGAGAAGAGAGGAGA 59.809 44.000 0.00 0.00 0.00 3.71
3982 4988 5.437060 AGCTAACAGTAGAGAAGAGAGGAG 58.563 45.833 0.00 0.00 0.00 3.69
3983 4989 5.444744 AGCTAACAGTAGAGAAGAGAGGA 57.555 43.478 0.00 0.00 0.00 3.71
3984 4990 6.995686 TGATAGCTAACAGTAGAGAAGAGAGG 59.004 42.308 0.00 0.00 0.00 3.69
3985 4991 8.342634 GTTGATAGCTAACAGTAGAGAAGAGAG 58.657 40.741 3.75 0.00 0.00 3.20
4005 5014 3.658757 TGCCGATCGATGATGTTGATA 57.341 42.857 18.66 0.00 30.77 2.15
4039 5048 1.890041 CGCAAGAACCGTGTGGGAA 60.890 57.895 0.00 0.00 39.08 3.97
4125 5147 8.112822 TCTTTTTGGATGAAGTTGTATATCCCA 58.887 33.333 0.00 0.00 38.62 4.37
4126 5148 8.519799 TCTTTTTGGATGAAGTTGTATATCCC 57.480 34.615 0.00 0.00 38.62 3.85
4193 5333 9.569122 GCCTAAAATCAAATAACCATCCTAGTA 57.431 33.333 0.00 0.00 0.00 1.82
4196 5336 7.012894 CACGCCTAAAATCAAATAACCATCCTA 59.987 37.037 0.00 0.00 0.00 2.94
4197 5337 5.891551 ACGCCTAAAATCAAATAACCATCCT 59.108 36.000 0.00 0.00 0.00 3.24
4199 5339 5.977129 CCACGCCTAAAATCAAATAACCATC 59.023 40.000 0.00 0.00 0.00 3.51
4200 5340 5.163457 CCCACGCCTAAAATCAAATAACCAT 60.163 40.000 0.00 0.00 0.00 3.55
4201 5341 4.158764 CCCACGCCTAAAATCAAATAACCA 59.841 41.667 0.00 0.00 0.00 3.67
4202 5342 4.440940 CCCCACGCCTAAAATCAAATAACC 60.441 45.833 0.00 0.00 0.00 2.85
4203 5343 4.158949 ACCCCACGCCTAAAATCAAATAAC 59.841 41.667 0.00 0.00 0.00 1.89
4204 5344 4.158764 CACCCCACGCCTAAAATCAAATAA 59.841 41.667 0.00 0.00 0.00 1.40
4205 5345 3.697045 CACCCCACGCCTAAAATCAAATA 59.303 43.478 0.00 0.00 0.00 1.40
4209 5349 0.963355 GCACCCCACGCCTAAAATCA 60.963 55.000 0.00 0.00 0.00 2.57
4212 5352 1.302993 GAGCACCCCACGCCTAAAA 60.303 57.895 0.00 0.00 0.00 1.52
4218 5358 3.628646 ATTGAGGAGCACCCCACGC 62.629 63.158 0.00 0.00 36.73 5.34
4223 5363 3.054361 TCTTAAAGGATTGAGGAGCACCC 60.054 47.826 0.00 0.00 36.73 4.61
4252 5392 5.220777 CGCCTCATACATACAAAACCGATTT 60.221 40.000 0.00 0.00 0.00 2.17
4253 5393 4.272504 CGCCTCATACATACAAAACCGATT 59.727 41.667 0.00 0.00 0.00 3.34
4254 5394 3.807622 CGCCTCATACATACAAAACCGAT 59.192 43.478 0.00 0.00 0.00 4.18
4255 5395 3.119065 TCGCCTCATACATACAAAACCGA 60.119 43.478 0.00 0.00 0.00 4.69
4256 5396 3.191669 TCGCCTCATACATACAAAACCG 58.808 45.455 0.00 0.00 0.00 4.44
4280 5420 6.602179 TCTTCACACAATTGATTTTCTAGCG 58.398 36.000 13.59 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.