Multiple sequence alignment - TraesCS3D01G327700

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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 TraesCS3D01G327700 chr3D 100.000 4248 0 0 1 4248 439837620 439841867 0.000000e+00 7845
1 TraesCS3D01G327700 chr3B 93.531 3339 86 49 405 3662 576656804 576660093 0.000000e+00 4850
2 TraesCS3D01G327700 chr3B 83.521 443 52 13 3499 3935 576660086 576660513 1.110000e-105 394
3 TraesCS3D01G327700 chr3B 93.678 174 11 0 4075 4248 576662368 576662541 1.170000e-65 261
4 TraesCS3D01G327700 chr3B 85.276 163 21 3 242 404 20157722 20157881 9.450000e-37 165
5 TraesCS3D01G327700 chr3A 91.081 3375 128 65 405 3723 579552273 579555530 0.000000e+00 4405
6 TraesCS3D01G327700 chr3A 91.084 415 31 6 1 413 579551812 579552222 1.330000e-154 556
7 TraesCS3D01G327700 chr1A 87.568 555 65 4 1096 1648 500343382 500342830 1.290000e-179 640
8 TraesCS3D01G327700 chr1A 77.160 648 121 23 2009 2643 500342679 500342046 6.760000e-93 351
9 TraesCS3D01G327700 chr1A 95.035 141 6 1 2725 2864 500341973 500341833 1.990000e-53 220
10 TraesCS3D01G327700 chr1A 90.210 143 14 0 1773 1915 500342826 500342684 2.020000e-43 187
11 TraesCS3D01G327700 chr1B 87.547 530 64 2 1126 1654 544726918 544726390 2.810000e-171 612
12 TraesCS3D01G327700 chr1B 76.198 647 123 26 2009 2642 544726245 544725617 3.190000e-81 313
13 TraesCS3D01G327700 chr1B 94.815 135 7 0 2730 2864 544725534 544725400 1.200000e-50 211
14 TraesCS3D01G327700 chr1B 88.966 145 15 1 1772 1915 544726394 544726250 1.210000e-40 178
15 TraesCS3D01G327700 chr4A 87.146 529 68 0 1126 1654 466926025 466926553 6.080000e-168 601
16 TraesCS3D01G327700 chr1D 87.405 524 64 2 1126 1648 404970811 404970289 6.080000e-168 601
17 TraesCS3D01G327700 chr1D 77.573 651 107 32 2009 2643 404970138 404969511 1.450000e-94 357
18 TraesCS3D01G327700 chr1D 94.326 141 7 1 2725 2864 404969438 404969298 9.250000e-52 215
19 TraesCS3D01G327700 chr1D 90.909 143 13 0 1773 1915 404970285 404970143 4.330000e-45 193
20 TraesCS3D01G327700 chr4B 86.792 530 68 2 1126 1654 171028540 171028012 1.320000e-164 590
21 TraesCS3D01G327700 chr4B 85.417 144 21 0 1772 1915 171028015 171027872 2.650000e-32 150
22 TraesCS3D01G327700 chr4D 86.578 529 71 0 1126 1654 109911952 109911424 6.120000e-163 584
23 TraesCS3D01G327700 chr4D 84.722 144 22 0 1772 1915 109911427 109911284 1.230000e-30 145
24 TraesCS3D01G327700 chr5B 82.298 531 90 4 1126 1654 259538264 259538792 1.390000e-124 457
25 TraesCS3D01G327700 chr5B 82.069 145 16 7 264 405 302843320 302843457 9.650000e-22 115
26 TraesCS3D01G327700 chr6B 84.946 186 17 4 219 404 394693782 394693956 1.210000e-40 178
27 TraesCS3D01G327700 chr6B 82.353 170 26 4 219 387 625364891 625365057 1.230000e-30 145
28 TraesCS3D01G327700 chr5D 83.871 186 25 4 219 404 339760313 339760493 5.650000e-39 172
29 TraesCS3D01G327700 chr5D 80.690 145 19 6 264 405 267821596 267821734 2.090000e-18 104
30 TraesCS3D01G327700 chr7D 81.609 174 24 6 242 414 511661213 511661379 2.060000e-28 137
31 TraesCS3D01G327700 chrUn 81.879 149 21 4 256 404 18059952 18060094 2.070000e-23 121


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 TraesCS3D01G327700 chr3D 439837620 439841867 4247 False 7845.0 7845 100.000000 1 4248 1 chr3D.!!$F1 4247
1 TraesCS3D01G327700 chr3B 576656804 576662541 5737 False 1835.0 4850 90.243333 405 4248 3 chr3B.!!$F2 3843
2 TraesCS3D01G327700 chr3A 579551812 579555530 3718 False 2480.5 4405 91.082500 1 3723 2 chr3A.!!$F1 3722
3 TraesCS3D01G327700 chr1A 500341833 500343382 1549 True 349.5 640 87.493250 1096 2864 4 chr1A.!!$R1 1768
4 TraesCS3D01G327700 chr1B 544725400 544726918 1518 True 328.5 612 86.881500 1126 2864 4 chr1B.!!$R1 1738
5 TraesCS3D01G327700 chr4A 466926025 466926553 528 False 601.0 601 87.146000 1126 1654 1 chr4A.!!$F1 528
6 TraesCS3D01G327700 chr1D 404969298 404970811 1513 True 341.5 601 87.553250 1126 2864 4 chr1D.!!$R1 1738
7 TraesCS3D01G327700 chr4B 171027872 171028540 668 True 370.0 590 86.104500 1126 1915 2 chr4B.!!$R1 789
8 TraesCS3D01G327700 chr4D 109911284 109911952 668 True 364.5 584 85.650000 1126 1915 2 chr4D.!!$R1 789
9 TraesCS3D01G327700 chr5B 259538264 259538792 528 False 457.0 457 82.298000 1126 1654 1 chr5B.!!$F1 528

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
193 194 0.179018 GTCAGCCACTGTCCCAAACT 60.179 55.000 0.00 0.00 32.61 2.66 F
613 682 1.003355 ATCGGAGGTGCACAACAGG 60.003 57.895 20.43 7.66 0.00 4.00 F
1197 1294 1.511305 CAGCATCTACACCGTCGGT 59.489 57.895 12.23 12.23 35.62 4.69 F
2438 2593 1.956477 GTGCACAACTGAACCTCCATT 59.044 47.619 13.17 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 2078 3.371591 TGCGTTTCGTTTAGACTGTTTGT 59.628 39.13 0.00 0.00 0.00 2.83 R
2456 2629 0.030235 CGATGACCTGCATGCAATGG 59.970 55.00 22.88 21.93 46.86 3.16 R
2458 2631 1.731433 GGCGATGACCTGCATGCAAT 61.731 55.00 22.88 12.30 37.34 3.56 R
4091 6225 0.040781 CTTTGGGTTGTTACACGCGG 60.041 55.00 12.47 1.27 32.29 6.46 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
26 27 9.124807 GTAATTTTCTATGTGTGCACCTTTAAC 57.875 33.333 15.69 5.80 0.00 2.01
193 194 0.179018 GTCAGCCACTGTCCCAAACT 60.179 55.000 0.00 0.00 32.61 2.66
201 202 3.315191 CCACTGTCCCAAACTAAACACAG 59.685 47.826 0.00 0.00 37.78 3.66
210 211 5.591067 CCCAAACTAAACACAGTACTTTCCA 59.409 40.000 0.00 0.00 0.00 3.53
211 212 6.264518 CCCAAACTAAACACAGTACTTTCCAT 59.735 38.462 0.00 0.00 0.00 3.41
225 226 7.975616 CAGTACTTTCCATAAACCCAAATGATG 59.024 37.037 0.00 0.00 0.00 3.07
237 238 2.802816 CCAAATGATGAGTAGCTACCGC 59.197 50.000 20.31 13.15 0.00 5.68
295 296 4.343231 TGGCAATTCTTATGAAGCAAGGA 58.657 39.130 0.00 0.00 35.44 3.36
317 318 5.295787 GGATGACAAGTTAGTTGACACACAA 59.704 40.000 6.80 0.00 42.42 3.33
318 319 6.183360 GGATGACAAGTTAGTTGACACACAAA 60.183 38.462 6.80 0.00 42.42 2.83
319 320 5.933790 TGACAAGTTAGTTGACACACAAAC 58.066 37.500 6.80 0.00 40.36 2.93
320 321 4.965062 ACAAGTTAGTTGACACACAAACG 58.035 39.130 6.80 0.00 40.36 3.60
321 322 4.453136 ACAAGTTAGTTGACACACAAACGT 59.547 37.500 6.80 0.00 40.36 3.99
322 323 4.852609 AGTTAGTTGACACACAAACGTC 57.147 40.909 0.00 0.00 40.36 4.34
362 363 2.250939 CCGAAGCACGAAGTTGCCA 61.251 57.895 4.96 0.00 41.61 4.92
366 367 1.601759 AGCACGAAGTTGCCATGCT 60.602 52.632 0.00 0.00 41.61 3.79
367 368 1.154150 GCACGAAGTTGCCATGCTC 60.154 57.895 0.00 0.00 41.61 4.26
369 370 1.301716 ACGAAGTTGCCATGCTCGT 60.302 52.632 0.00 0.00 37.78 4.18
404 405 2.342910 TCCTCGCGTCACTAAACTTC 57.657 50.000 5.77 0.00 0.00 3.01
405 406 1.884579 TCCTCGCGTCACTAAACTTCT 59.115 47.619 5.77 0.00 0.00 2.85
407 408 2.662156 CCTCGCGTCACTAAACTTCTTC 59.338 50.000 5.77 0.00 0.00 2.87
554 616 1.573108 AGGGGTTGAGATCGTGTCAT 58.427 50.000 0.00 0.00 0.00 3.06
613 682 1.003355 ATCGGAGGTGCACAACAGG 60.003 57.895 20.43 7.66 0.00 4.00
839 936 2.948979 CAGGCTACAACAAACACAAGGA 59.051 45.455 0.00 0.00 0.00 3.36
840 937 3.003689 CAGGCTACAACAAACACAAGGAG 59.996 47.826 0.00 0.00 0.00 3.69
1197 1294 1.511305 CAGCATCTACACCGTCGGT 59.489 57.895 12.23 12.23 35.62 4.69
1987 2110 7.117236 AGTCTAAACGAAACGCATCAATTAAGA 59.883 33.333 0.00 0.00 0.00 2.10
2197 2341 6.765036 TCTTTGCCTTTTTATCATTGTTTGCA 59.235 30.769 0.00 0.00 0.00 4.08
2205 2349 7.551035 TTTTATCATTGTTTGCAAGCAGTTT 57.449 28.000 15.79 6.23 38.10 2.66
2210 2354 7.551035 TCATTGTTTGCAAGCAGTTTTATTT 57.449 28.000 15.79 0.00 38.10 1.40
2219 2363 7.812648 TGCAAGCAGTTTTATTTACGTATTCT 58.187 30.769 0.00 0.00 0.00 2.40
2221 2365 7.218204 GCAAGCAGTTTTATTTACGTATTCTGG 59.782 37.037 0.00 0.00 0.00 3.86
2225 2369 9.783256 GCAGTTTTATTTACGTATTCTGGATTT 57.217 29.630 0.00 0.00 0.00 2.17
2438 2593 1.956477 GTGCACAACTGAACCTCCATT 59.044 47.619 13.17 0.00 0.00 3.16
2443 2598 4.557496 GCACAACTGAACCTCCATTTTCTC 60.557 45.833 0.00 0.00 0.00 2.87
2456 2629 4.695455 TCCATTTTCTCAACTGAACGGATC 59.305 41.667 0.00 0.00 0.00 3.36
2458 2631 3.762407 TTTCTCAACTGAACGGATCCA 57.238 42.857 13.41 0.00 0.00 3.41
2459 2632 3.981071 TTCTCAACTGAACGGATCCAT 57.019 42.857 13.41 0.00 0.00 3.41
2460 2633 3.981071 TCTCAACTGAACGGATCCATT 57.019 42.857 13.41 1.38 0.00 3.16
2461 2634 3.599343 TCTCAACTGAACGGATCCATTG 58.401 45.455 13.41 6.10 0.00 2.82
2462 2635 2.083774 TCAACTGAACGGATCCATTGC 58.916 47.619 13.41 0.00 0.00 3.56
2643 2816 1.137872 AGCTCATGGAAGCCGTAAGAG 59.862 52.381 2.91 0.00 43.56 2.85
2694 2893 6.040166 CCGCTTAATTACTACTCTAGGTCCAA 59.960 42.308 0.00 0.00 0.00 3.53
2935 3138 2.087646 GAACTCACTCATTCTTGGCCC 58.912 52.381 0.00 0.00 0.00 5.80
3374 3586 4.025229 TGAGCTCGTGTACATTTTTCACAC 60.025 41.667 9.64 0.00 39.32 3.82
3533 3763 7.339466 AGTTGAGTAAGTTGGACATTTTTGAGT 59.661 33.333 0.00 0.00 0.00 3.41
3537 3767 5.520376 AAGTTGGACATTTTTGAGTCTGG 57.480 39.130 0.00 0.00 35.18 3.86
3596 3826 6.309737 GGTATGTAACTTGAGTGAAGTAACGG 59.690 42.308 0.00 0.00 44.68 4.44
3615 3845 2.726633 GGGTGTGTTTTTGATGTGTCG 58.273 47.619 0.00 0.00 0.00 4.35
3621 3851 0.237235 TTTTTGATGTGTCGCTCGCC 59.763 50.000 0.00 0.00 0.00 5.54
3640 3876 0.654683 CTGCAAACTCTATGGCTCGC 59.345 55.000 0.00 0.00 0.00 5.03
3649 3885 1.148157 CTATGGCTCGCGGAACAGTG 61.148 60.000 6.13 0.00 0.00 3.66
3655 3891 1.891060 CTCGCGGAACAGTGTGAAGC 61.891 60.000 6.13 1.58 0.00 3.86
3679 4068 3.703001 ACAACTGTATAAGCAGGCAGT 57.297 42.857 0.00 0.00 43.13 4.40
3683 4072 5.411669 ACAACTGTATAAGCAGGCAGTTTAC 59.588 40.000 6.11 0.00 46.18 2.01
3685 4074 5.420409 ACTGTATAAGCAGGCAGTTTACTC 58.580 41.667 0.00 0.00 38.86 2.59
3686 4075 4.430007 TGTATAAGCAGGCAGTTTACTCG 58.570 43.478 0.00 0.00 0.00 4.18
3698 4087 4.330074 GCAGTTTACTCGCATGTAGAACAT 59.670 41.667 4.46 0.00 39.91 2.71
3729 4119 3.574284 TCAAAATCAATGGCCTGAACG 57.426 42.857 3.32 0.00 0.00 3.95
3735 4125 1.448540 AATGGCCTGAACGAGCTCG 60.449 57.895 33.45 33.45 46.33 5.03
3746 4136 4.838486 GAGCTCGGCTCGTCGGTG 62.838 72.222 9.63 0.00 45.85 4.94
3749 4139 4.498520 CTCGGCTCGTCGGTGCAT 62.499 66.667 11.85 0.00 34.40 3.96
3750 4140 3.120979 CTCGGCTCGTCGGTGCATA 62.121 63.158 11.85 0.92 34.40 3.14
3753 4143 2.494918 GCTCGTCGGTGCATACCT 59.505 61.111 0.00 0.00 45.22 3.08
3754 4144 1.589196 GCTCGTCGGTGCATACCTC 60.589 63.158 0.00 0.00 45.22 3.85
3755 4145 2.005960 GCTCGTCGGTGCATACCTCT 62.006 60.000 0.00 0.00 45.22 3.69
3756 4146 0.029567 CTCGTCGGTGCATACCTCTC 59.970 60.000 0.00 0.00 45.22 3.20
3757 4147 0.393944 TCGTCGGTGCATACCTCTCT 60.394 55.000 0.00 0.00 45.22 3.10
3758 4148 0.248661 CGTCGGTGCATACCTCTCTG 60.249 60.000 0.00 0.00 45.22 3.35
3759 4149 0.818296 GTCGGTGCATACCTCTCTGT 59.182 55.000 0.00 0.00 45.22 3.41
3780 4170 2.250237 GCTCTGCTATTCTGCGGGC 61.250 63.158 0.00 0.00 39.62 6.13
3782 4172 2.969238 CTGCTATTCTGCGGGCCG 60.969 66.667 24.35 24.35 35.80 6.13
3783 4173 3.445518 CTGCTATTCTGCGGGCCGA 62.446 63.158 33.44 14.18 35.80 5.54
3784 4174 2.031163 GCTATTCTGCGGGCCGAT 59.969 61.111 33.44 16.99 0.00 4.18
3785 4175 2.029844 GCTATTCTGCGGGCCGATC 61.030 63.158 33.44 14.10 0.00 3.69
3818 4208 4.416738 GGGACACCTGAGCTGCCC 62.417 72.222 0.00 0.00 0.00 5.36
3830 4220 1.674962 GAGCTGCCCATCACAAAGATC 59.325 52.381 0.00 0.00 33.72 2.75
3840 4230 1.895798 TCACAAAGATCGAGCTCCACT 59.104 47.619 2.43 2.07 0.00 4.00
3855 4245 2.362503 ACTCGAGACCCGCCATCA 60.363 61.111 21.68 0.00 38.37 3.07
3856 4246 1.982395 ACTCGAGACCCGCCATCAA 60.982 57.895 21.68 0.00 38.37 2.57
3885 4275 1.760192 AGAATTGGACATGCTGGAGC 58.240 50.000 0.00 0.00 42.50 4.70
3906 4296 1.270305 GCCTAGCTCACGCCAATCATA 60.270 52.381 0.00 0.00 36.60 2.15
3940 4357 1.128188 AACACAGGAGAGGGTGGGTC 61.128 60.000 0.00 0.00 39.31 4.46
3946 4363 0.396695 GGAGAGGGTGGGTCGTCATA 60.397 60.000 0.00 0.00 0.00 2.15
3951 4368 0.249322 GGGTGGGTCGTCATACATCG 60.249 60.000 0.00 0.00 0.00 3.84
3971 4388 3.960755 TCGAGAGAAAAGGCTCATGGATA 59.039 43.478 0.00 0.00 37.37 2.59
3972 4389 4.054671 CGAGAGAAAAGGCTCATGGATAC 58.945 47.826 0.00 0.00 37.37 2.24
3975 4392 6.461648 CGAGAGAAAAGGCTCATGGATACTTA 60.462 42.308 0.00 0.00 37.37 2.24
3976 4393 6.825610 AGAGAAAAGGCTCATGGATACTTAG 58.174 40.000 0.00 0.00 37.37 2.18
3977 4394 6.613271 AGAGAAAAGGCTCATGGATACTTAGA 59.387 38.462 0.00 0.00 37.37 2.10
3978 4395 7.126421 AGAGAAAAGGCTCATGGATACTTAGAA 59.874 37.037 0.00 0.00 37.37 2.10
3979 4396 7.633789 AGAAAAGGCTCATGGATACTTAGAAA 58.366 34.615 0.00 0.00 37.61 2.52
3980 4397 8.109634 AGAAAAGGCTCATGGATACTTAGAAAA 58.890 33.333 0.00 0.00 37.61 2.29
3982 4399 6.814954 AGGCTCATGGATACTTAGAAAAGA 57.185 37.500 0.00 0.00 36.50 2.52
3985 4402 7.772757 AGGCTCATGGATACTTAGAAAAGAAAG 59.227 37.037 0.00 0.00 36.50 2.62
3986 4403 7.770897 GGCTCATGGATACTTAGAAAAGAAAGA 59.229 37.037 0.00 0.00 36.50 2.52
4045 6179 5.105392 ACAAAGTTTCTCAAAAGTGATGGCA 60.105 36.000 0.00 0.00 31.85 4.92
4046 6180 5.796424 AAGTTTCTCAAAAGTGATGGCAT 57.204 34.783 0.00 0.00 31.85 4.40
4047 6181 5.796424 AGTTTCTCAAAAGTGATGGCATT 57.204 34.783 0.00 0.00 31.85 3.56
4048 6182 5.535333 AGTTTCTCAAAAGTGATGGCATTG 58.465 37.500 0.00 0.00 31.85 2.82
4049 6183 5.302568 AGTTTCTCAAAAGTGATGGCATTGA 59.697 36.000 0.00 0.00 31.85 2.57
4050 6184 5.787953 TTCTCAAAAGTGATGGCATTGAA 57.212 34.783 0.00 0.00 31.85 2.69
4051 6185 5.787953 TCTCAAAAGTGATGGCATTGAAA 57.212 34.783 0.00 0.00 31.85 2.69
4052 6186 5.531634 TCTCAAAAGTGATGGCATTGAAAC 58.468 37.500 0.00 0.00 31.85 2.78
4053 6187 5.302568 TCTCAAAAGTGATGGCATTGAAACT 59.697 36.000 0.00 0.84 31.85 2.66
4054 6188 5.291178 TCAAAAGTGATGGCATTGAAACTG 58.709 37.500 0.00 0.00 0.00 3.16
4055 6189 3.308438 AAGTGATGGCATTGAAACTGC 57.692 42.857 0.00 0.00 38.93 4.40
4091 6225 3.234386 GTCGCATTGAAACTGCCTTAAC 58.766 45.455 0.00 0.00 36.24 2.01
4104 6238 1.398832 GCCTTAACCGCGTGTAACAAC 60.399 52.381 4.92 0.00 35.74 3.32
4146 6280 6.264067 GCTCCAAGGATCTATTTGCTATTTGT 59.736 38.462 0.00 0.00 0.00 2.83
4225 6359 5.743872 GTCAACTTTGTGTCAATCCAAACTC 59.256 40.000 0.00 0.00 0.00 3.01
4227 6361 5.505173 ACTTTGTGTCAATCCAAACTCAG 57.495 39.130 0.00 0.00 0.00 3.35
4229 6363 5.418840 ACTTTGTGTCAATCCAAACTCAGTT 59.581 36.000 0.00 0.00 0.00 3.16
4242 6376 5.105756 CCAAACTCAGTTTCTTGGTCACTTT 60.106 40.000 0.00 0.00 33.10 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
193 194 7.288560 TGGGTTTATGGAAAGTACTGTGTTTA 58.711 34.615 0.00 0.00 0.00 2.01
201 202 8.062065 TCATCATTTGGGTTTATGGAAAGTAC 57.938 34.615 0.00 0.00 0.00 2.73
210 211 6.998673 GGTAGCTACTCATCATTTGGGTTTAT 59.001 38.462 22.74 0.00 40.45 1.40
211 212 6.354130 GGTAGCTACTCATCATTTGGGTTTA 58.646 40.000 22.74 0.00 40.45 2.01
237 238 0.459899 TGCCATGTGCTCGTACCTAG 59.540 55.000 7.54 0.00 42.00 3.02
238 239 0.899019 TTGCCATGTGCTCGTACCTA 59.101 50.000 7.54 0.00 42.00 3.08
244 245 0.447406 TTCGATTTGCCATGTGCTCG 59.553 50.000 7.54 8.26 42.00 5.03
271 272 6.128486 TCCTTGCTTCATAAGAATTGCCATA 58.872 36.000 0.00 0.00 32.31 2.74
272 273 4.957954 TCCTTGCTTCATAAGAATTGCCAT 59.042 37.500 0.00 0.00 32.31 4.40
273 274 4.343231 TCCTTGCTTCATAAGAATTGCCA 58.657 39.130 0.00 0.00 32.31 4.92
274 275 4.989279 TCCTTGCTTCATAAGAATTGCC 57.011 40.909 0.00 0.00 32.31 4.52
275 276 5.975939 GTCATCCTTGCTTCATAAGAATTGC 59.024 40.000 0.00 0.00 32.31 3.56
283 284 6.711277 ACTAACTTGTCATCCTTGCTTCATA 58.289 36.000 0.00 0.00 0.00 2.15
295 296 6.551736 GTTTGTGTGTCAACTAACTTGTCAT 58.448 36.000 0.00 0.00 35.61 3.06
345 346 0.453282 CATGGCAACTTCGTGCTTCG 60.453 55.000 0.00 0.00 44.31 3.79
352 353 1.291184 TGACGAGCATGGCAACTTCG 61.291 55.000 13.81 13.81 37.61 3.79
389 390 2.049228 ACGAAGAAGTTTAGTGACGCG 58.951 47.619 3.53 3.53 0.00 6.01
554 616 2.203139 CCCACTGGTTGCACACGA 60.203 61.111 0.00 0.00 0.00 4.35
613 682 4.260538 CGCTCTTTTCTGGCTAATGATCAC 60.261 45.833 0.00 0.00 0.00 3.06
673 743 1.283029 AGCTGGCTAGGAAAATGCAGA 59.717 47.619 0.00 0.00 0.00 4.26
675 745 2.220653 AAGCTGGCTAGGAAAATGCA 57.779 45.000 0.00 0.00 0.00 3.96
1677 1782 6.590292 AGAAGAAGAAGAAAAATGCATGCATG 59.410 34.615 32.79 22.70 36.68 4.06
1678 1783 6.698380 AGAAGAAGAAGAAAAATGCATGCAT 58.302 32.000 27.46 27.46 38.46 3.96
1679 1784 6.092955 AGAAGAAGAAGAAAAATGCATGCA 57.907 33.333 25.04 25.04 0.00 3.96
1680 1785 7.359849 GGAAAGAAGAAGAAGAAAAATGCATGC 60.360 37.037 11.82 11.82 0.00 4.06
1681 1786 7.871463 AGGAAAGAAGAAGAAGAAAAATGCATG 59.129 33.333 0.00 0.00 0.00 4.06
1682 1787 7.871463 CAGGAAAGAAGAAGAAGAAAAATGCAT 59.129 33.333 0.00 0.00 0.00 3.96
1944 2067 6.956102 TTAGACTGTTTGTTATTAGGGGGA 57.044 37.500 0.00 0.00 0.00 4.81
1954 2077 4.142859 TGCGTTTCGTTTAGACTGTTTGTT 60.143 37.500 0.00 0.00 0.00 2.83
1955 2078 3.371591 TGCGTTTCGTTTAGACTGTTTGT 59.628 39.130 0.00 0.00 0.00 2.83
1956 2079 3.930618 TGCGTTTCGTTTAGACTGTTTG 58.069 40.909 0.00 0.00 0.00 2.93
1957 2080 4.271533 TGATGCGTTTCGTTTAGACTGTTT 59.728 37.500 0.00 0.00 0.00 2.83
2197 2341 8.556213 TCCAGAATACGTAAATAAAACTGCTT 57.444 30.769 0.00 0.00 0.00 3.91
2221 2365 7.754027 GCAACAGCATATCATTGGATCTAAATC 59.246 37.037 0.00 0.00 34.89 2.17
2225 2369 5.872963 AGCAACAGCATATCATTGGATCTA 58.127 37.500 0.00 0.00 34.89 1.98
2226 2370 4.726583 AGCAACAGCATATCATTGGATCT 58.273 39.130 0.00 0.00 34.89 2.75
2438 2593 3.762407 TGGATCCGTTCAGTTGAGAAA 57.238 42.857 7.39 0.00 0.00 2.52
2443 2598 1.811965 TGCAATGGATCCGTTCAGTTG 59.188 47.619 16.68 7.21 0.00 3.16
2456 2629 0.030235 CGATGACCTGCATGCAATGG 59.970 55.000 22.88 21.93 46.86 3.16
2458 2631 1.731433 GGCGATGACCTGCATGCAAT 61.731 55.000 22.88 12.30 37.34 3.56
2459 2632 2.409055 GGCGATGACCTGCATGCAA 61.409 57.895 22.88 7.10 37.34 4.08
2460 2633 2.825387 GGCGATGACCTGCATGCA 60.825 61.111 21.29 21.29 37.34 3.96
2461 2634 3.945434 CGGCGATGACCTGCATGC 61.945 66.667 11.82 11.82 37.34 4.06
2462 2635 3.274586 CCGGCGATGACCTGCATG 61.275 66.667 9.30 0.00 37.34 4.06
2872 3075 3.668447 TGAGGAGAGAATGTGAACTTGC 58.332 45.455 0.00 0.00 0.00 4.01
3103 3310 4.698651 ATTTGGCCAACGCACGCG 62.699 61.111 20.35 10.36 46.03 6.01
3374 3586 2.009774 CATTTGCTACTCGACCCCTTG 58.990 52.381 0.00 0.00 0.00 3.61
3533 3763 2.070783 GAAACCGCGTACAAATCCAGA 58.929 47.619 4.92 0.00 0.00 3.86
3537 3767 1.465187 GCCTGAAACCGCGTACAAATC 60.465 52.381 4.92 0.00 0.00 2.17
3567 3797 3.845178 TCACTCAAGTTACATACCTGCG 58.155 45.455 0.00 0.00 0.00 5.18
3596 3826 2.116366 GCGACACATCAAAAACACACC 58.884 47.619 0.00 0.00 0.00 4.16
3615 3845 0.654683 CATAGAGTTTGCAGGCGAGC 59.345 55.000 0.00 0.00 0.00 5.03
3621 3851 0.654683 GCGAGCCATAGAGTTTGCAG 59.345 55.000 0.00 0.00 0.00 4.41
3640 3876 1.792949 GTACTGCTTCACACTGTTCCG 59.207 52.381 0.00 0.00 0.00 4.30
3668 4057 1.001520 TGCGAGTAAACTGCCTGCTTA 59.998 47.619 0.00 0.00 0.00 3.09
3698 4087 4.380761 CCATTGATTTTGATCCTGCGTTCA 60.381 41.667 0.00 0.00 0.00 3.18
3702 4092 2.466846 GCCATTGATTTTGATCCTGCG 58.533 47.619 0.00 0.00 0.00 5.18
3707 4097 4.107622 CGTTCAGGCCATTGATTTTGATC 58.892 43.478 5.01 0.00 0.00 2.92
3735 4125 2.585247 GGTATGCACCGACGAGCC 60.585 66.667 0.00 0.00 34.36 4.70
3747 4137 2.223782 GCAGAGCAGACAGAGAGGTATG 60.224 54.545 0.00 0.00 33.28 2.39
3748 4138 2.031120 GCAGAGCAGACAGAGAGGTAT 58.969 52.381 0.00 0.00 0.00 2.73
3749 4139 1.005332 AGCAGAGCAGACAGAGAGGTA 59.995 52.381 0.00 0.00 0.00 3.08
3750 4140 0.251742 AGCAGAGCAGACAGAGAGGT 60.252 55.000 0.00 0.00 0.00 3.85
3753 4143 3.380954 CAGAATAGCAGAGCAGACAGAGA 59.619 47.826 0.00 0.00 0.00 3.10
3754 4144 3.708890 CAGAATAGCAGAGCAGACAGAG 58.291 50.000 0.00 0.00 0.00 3.35
3755 4145 2.159128 GCAGAATAGCAGAGCAGACAGA 60.159 50.000 0.00 0.00 0.00 3.41
3756 4146 2.203401 GCAGAATAGCAGAGCAGACAG 58.797 52.381 0.00 0.00 0.00 3.51
3757 4147 1.470458 CGCAGAATAGCAGAGCAGACA 60.470 52.381 0.00 0.00 0.00 3.41
3758 4148 1.207390 CGCAGAATAGCAGAGCAGAC 58.793 55.000 0.00 0.00 0.00 3.51
3759 4149 0.103755 CCGCAGAATAGCAGAGCAGA 59.896 55.000 0.00 0.00 0.00 4.26
3793 4183 3.011517 CAGGTGTCCCCTCCCCAG 61.012 72.222 0.00 0.00 43.86 4.45
3812 4202 0.379669 CGATCTTTGTGATGGGCAGC 59.620 55.000 0.00 0.00 35.14 5.25
3818 4208 2.606725 GTGGAGCTCGATCTTTGTGATG 59.393 50.000 7.83 0.00 35.14 3.07
3840 4230 2.577059 GTTGATGGCGGGTCTCGA 59.423 61.111 0.00 0.00 42.43 4.04
3855 4245 5.337491 GCATGTCCAATTCTTTACCATGGTT 60.337 40.000 25.38 7.42 32.90 3.67
3856 4246 4.160252 GCATGTCCAATTCTTTACCATGGT 59.840 41.667 23.55 23.55 32.90 3.55
3863 4253 3.696051 GCTCCAGCATGTCCAATTCTTTA 59.304 43.478 0.00 0.00 41.59 1.85
3906 4296 6.601613 TCTCCTGTGTTGTTTTTCACTACAAT 59.398 34.615 0.00 0.00 41.92 2.71
3940 4357 3.487574 GCCTTTTCTCTCGATGTATGACG 59.512 47.826 0.00 0.00 0.00 4.35
3946 4363 3.529533 CATGAGCCTTTTCTCTCGATGT 58.470 45.455 0.00 0.00 34.29 3.06
3951 4368 5.289083 AGTATCCATGAGCCTTTTCTCTC 57.711 43.478 0.00 0.00 34.29 3.20
3971 4388 8.739972 TGTGCTTCTTTTCTTTCTTTTCTAAGT 58.260 29.630 0.00 0.00 32.98 2.24
3972 4389 9.573133 TTGTGCTTCTTTTCTTTCTTTTCTAAG 57.427 29.630 0.00 0.00 0.00 2.18
3975 4392 8.253113 TCATTGTGCTTCTTTTCTTTCTTTTCT 58.747 29.630 0.00 0.00 0.00 2.52
3976 4393 8.411318 TCATTGTGCTTCTTTTCTTTCTTTTC 57.589 30.769 0.00 0.00 0.00 2.29
3977 4394 8.953368 ATCATTGTGCTTCTTTTCTTTCTTTT 57.047 26.923 0.00 0.00 0.00 2.27
3978 4395 8.823818 CAATCATTGTGCTTCTTTTCTTTCTTT 58.176 29.630 0.00 0.00 0.00 2.52
3979 4396 7.983484 ACAATCATTGTGCTTCTTTTCTTTCTT 59.017 29.630 0.98 0.00 43.48 2.52
3980 4397 7.495055 ACAATCATTGTGCTTCTTTTCTTTCT 58.505 30.769 0.98 0.00 43.48 2.52
3982 4399 9.252962 CTAACAATCATTGTGCTTCTTTTCTTT 57.747 29.630 3.07 0.00 44.59 2.52
3985 4402 8.976986 ATCTAACAATCATTGTGCTTCTTTTC 57.023 30.769 3.07 0.00 44.59 2.29
3986 4403 8.579006 TGATCTAACAATCATTGTGCTTCTTTT 58.421 29.630 3.07 0.00 44.59 2.27
3989 4406 7.175467 TGTTGATCTAACAATCATTGTGCTTCT 59.825 33.333 3.07 0.00 45.86 2.85
3991 4408 7.218228 TGTTGATCTAACAATCATTGTGCTT 57.782 32.000 3.07 0.00 45.86 3.91
3992 4409 6.822667 TGTTGATCTAACAATCATTGTGCT 57.177 33.333 3.07 0.00 45.86 4.40
4021 6155 5.105392 TGCCATCACTTTTGAGAAACTTTGT 60.105 36.000 0.00 0.00 34.35 2.83
4022 6156 5.350633 TGCCATCACTTTTGAGAAACTTTG 58.649 37.500 0.00 0.00 34.35 2.77
4030 6164 5.404366 CAGTTTCAATGCCATCACTTTTGAG 59.596 40.000 0.00 0.00 34.35 3.02
4067 6201 1.154225 GCAGTTTCAATGCGACCCG 60.154 57.895 0.00 0.00 33.31 5.28
4068 6202 1.212751 GGCAGTTTCAATGCGACCC 59.787 57.895 0.00 0.00 44.80 4.46
4069 6203 0.598065 AAGGCAGTTTCAATGCGACC 59.402 50.000 0.00 0.00 44.80 4.79
4070 6204 3.234386 GTTAAGGCAGTTTCAATGCGAC 58.766 45.455 0.00 0.00 44.80 5.19
4071 6205 2.227865 GGTTAAGGCAGTTTCAATGCGA 59.772 45.455 0.00 0.00 44.80 5.10
4072 6206 2.595386 GGTTAAGGCAGTTTCAATGCG 58.405 47.619 0.00 0.00 44.80 4.73
4073 6207 2.595386 CGGTTAAGGCAGTTTCAATGC 58.405 47.619 0.00 0.00 43.09 3.56
4091 6225 0.040781 CTTTGGGTTGTTACACGCGG 60.041 55.000 12.47 1.27 32.29 6.46
4123 6257 9.866655 ATTACAAATAGCAAATAGATCCTTGGA 57.133 29.630 0.00 0.00 0.00 3.53
4225 6359 5.818136 TTCTGAAAGTGACCAAGAAACTG 57.182 39.130 0.00 0.00 33.76 3.16


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

AutoCloner maintained by Alex Coulton.