Multiple sequence alignment - TraesCS5D01G070700

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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 TraesCS5D01G070700 chr5D 100.000 4382 0 0 1 4382 68692663 68697044 0.000000e+00 8093
1 TraesCS5D01G070700 chr5D 96.364 110 4 0 4225 4334 365693411 365693302 9.680000e-42 182
2 TraesCS5D01G070700 chr5B 96.158 4060 119 22 229 4272 74632807 74636845 0.000000e+00 6599
3 TraesCS5D01G070700 chr5B 90.308 227 15 2 1 220 74619740 74619966 1.540000e-74 291
4 TraesCS5D01G070700 chr5B 96.296 108 4 0 4225 4332 617823476 617823369 1.250000e-40 178
5 TraesCS5D01G070700 chr5A 93.532 4159 171 41 102 4199 59595679 59599800 0.000000e+00 6100
6 TraesCS5D01G070700 chr5A 90.000 120 8 1 1 116 59595516 59595635 7.590000e-33 152
7 TraesCS5D01G070700 chr7B 97.222 108 3 0 4226 4333 683101573 683101466 2.690000e-42 183
8 TraesCS5D01G070700 chr4B 95.575 113 5 0 4223 4335 87405227 87405115 9.680000e-42 182
9 TraesCS5D01G070700 chr7A 95.536 112 5 0 4222 4333 35772704 35772593 3.480000e-41 180
10 TraesCS5D01G070700 chr3D 95.536 112 4 1 4222 4332 44007326 44007437 1.250000e-40 178
11 TraesCS5D01G070700 chr3D 95.495 111 5 0 4223 4333 536331029 536331139 1.250000e-40 178
12 TraesCS5D01G070700 chr7D 92.562 121 8 1 4216 4335 617094140 617094260 5.830000e-39 172
13 TraesCS5D01G070700 chr2B 94.595 111 6 0 4223 4333 663123540 663123650 5.830000e-39 172
14 TraesCS5D01G070700 chr4A 84.049 163 22 4 1047 1207 556537589 556537749 2.110000e-33 154


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 TraesCS5D01G070700 chr5D 68692663 68697044 4381 False 8093 8093 100.000 1 4382 1 chr5D.!!$F1 4381
1 TraesCS5D01G070700 chr5B 74632807 74636845 4038 False 6599 6599 96.158 229 4272 1 chr5B.!!$F2 4043
2 TraesCS5D01G070700 chr5A 59595516 59599800 4284 False 3126 6100 91.766 1 4199 2 chr5A.!!$F1 4198

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
441 504 0.806241 CCCGTACCCAACATTTTCGG 59.194 55.000 0.00 0.0 36.85 4.30 F
1007 1078 0.790814 GCAAGAACGAGAAGAACGGG 59.209 55.000 0.00 0.0 34.93 5.28 F
1430 1501 1.805539 CGACGCAGCCTCGATTTGA 60.806 57.895 7.96 0.0 32.65 2.69 F
2997 3091 0.253327 CTTCCTTCCCCCAGCTACAC 59.747 60.000 0.00 0.0 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 1802 0.320683 CACATTCAGTGGGTCGCTCA 60.321 55.000 0.00 0.0 44.69 4.26 R
2908 2994 1.677052 GCTCCTACTTTCGAGATCCGT 59.323 52.381 3.97 0.0 39.75 4.69 R
3132 3227 1.906574 GAACCCCACCTGTCACTATCA 59.093 52.381 0.00 0.0 0.00 2.15 R
3911 4024 0.036732 TTTTGTCCATCTCAGCGCCT 59.963 50.000 2.29 0.0 0.00 5.52 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
80 81 5.501897 GCTTGCATCTTTATTCAAAGCATGC 60.502 40.000 10.51 10.51 44.64 4.06
87 92 6.165577 TCTTTATTCAAAGCATGCCTTTTCC 58.834 36.000 15.66 0.00 41.75 3.13
135 197 4.873827 TGAAGCAGTCAAACTACGTCTTTT 59.126 37.500 0.00 0.00 31.51 2.27
145 207 8.333186 GTCAAACTACGTCTTTTGTATTCAACT 58.667 33.333 17.00 0.00 34.81 3.16
208 271 3.880047 AATCTCATCGAACCACGGTAA 57.120 42.857 0.00 0.00 42.82 2.85
214 277 1.880271 TCGAACCACGGTAATTTGCA 58.120 45.000 0.00 0.00 42.82 4.08
385 448 1.446907 CAGCCAAAGCAACGATCTCT 58.553 50.000 0.00 0.00 43.56 3.10
396 459 1.874019 CGATCTCTGCCGTCCGTTG 60.874 63.158 0.00 0.00 0.00 4.10
398 461 3.989698 ATCTCTGCCGTCCGTTGCG 62.990 63.158 0.00 0.00 0.00 4.85
416 479 1.592669 GCCATCGACGTCCCAGATG 60.593 63.158 19.24 19.24 40.86 2.90
441 504 0.806241 CCCGTACCCAACATTTTCGG 59.194 55.000 0.00 0.00 36.85 4.30
702 771 2.671963 GGTGCTTTCCCGGGACAC 60.672 66.667 26.87 26.92 0.00 3.67
703 772 2.112297 GTGCTTTCCCGGGACACA 59.888 61.111 28.88 22.05 0.00 3.72
706 775 2.700773 GCTTTCCCGGGACACATGC 61.701 63.158 26.87 18.94 0.00 4.06
838 907 2.285368 ATGGCTTCCCGAGTCCCA 60.285 61.111 0.00 0.00 0.00 4.37
875 944 2.096318 GCGACGAAAATTCCAAACCGTA 60.096 45.455 0.00 0.00 0.00 4.02
901 970 8.877601 ATGAGCATTTCACGGAGATCTATCTCA 61.878 40.741 19.02 0.58 45.61 3.27
939 1010 2.109128 TCCTTCTCTCAGGTCAGTGAGT 59.891 50.000 0.00 0.00 43.89 3.41
986 1057 5.066593 CCAAGACTGTAAAAGGAAGAGCTT 58.933 41.667 0.00 0.00 0.00 3.74
1003 1074 3.206150 AGCTTTGCAAGAACGAGAAGAA 58.794 40.909 0.00 0.00 0.00 2.52
1004 1075 3.002759 AGCTTTGCAAGAACGAGAAGAAC 59.997 43.478 0.00 0.00 0.00 3.01
1007 1078 0.790814 GCAAGAACGAGAAGAACGGG 59.209 55.000 0.00 0.00 34.93 5.28
1009 1080 2.480845 CAAGAACGAGAAGAACGGGTT 58.519 47.619 0.00 0.00 34.93 4.11
1010 1081 3.645884 CAAGAACGAGAAGAACGGGTTA 58.354 45.455 0.00 0.00 34.93 2.85
1011 1082 4.243270 CAAGAACGAGAAGAACGGGTTAT 58.757 43.478 0.00 0.00 34.93 1.89
1012 1083 5.404946 CAAGAACGAGAAGAACGGGTTATA 58.595 41.667 0.00 0.00 34.93 0.98
1430 1501 1.805539 CGACGCAGCCTCGATTTGA 60.806 57.895 7.96 0.00 32.65 2.69
1471 1542 2.520458 CACCAGTTTGGCCCTCCA 59.480 61.111 0.00 0.00 42.67 3.86
1947 2018 6.346096 CAGGAAATTACGGATTAAGAGGTCA 58.654 40.000 0.00 0.00 0.00 4.02
2013 2084 3.476552 GGATGAATACTCATGGCGGAAA 58.523 45.455 0.00 0.00 42.60 3.13
2016 2087 5.882557 GGATGAATACTCATGGCGGAAATAT 59.117 40.000 0.00 0.00 42.60 1.28
2065 2136 6.595772 CTCATCCGAGGTATGAAAGAAAAG 57.404 41.667 0.00 0.00 35.44 2.27
2070 2141 7.996098 TCCGAGGTATGAAAGAAAAGAAAAT 57.004 32.000 0.00 0.00 0.00 1.82
2139 2212 8.592105 ACATTGGTCAAAATAACACTTGAATG 57.408 30.769 0.00 0.00 33.52 2.67
2524 2609 4.528076 TTAATGCCTGCCCTTAATGGTA 57.472 40.909 0.00 0.00 0.00 3.25
2626 2711 5.241949 TCTTGTCTCCACAGAAGACTAACTC 59.758 44.000 5.03 0.00 32.71 3.01
2917 3003 1.956297 ACTAGGTCTCACGGATCTCG 58.044 55.000 0.00 0.00 45.88 4.04
2997 3091 0.253327 CTTCCTTCCCCCAGCTACAC 59.747 60.000 0.00 0.00 0.00 2.90
3132 3227 3.382546 GGAAGAACATGCATATGCTGGTT 59.617 43.478 26.62 26.62 42.66 3.67
3433 3531 3.884037 AGGAGGACCATGTGTTTTCTT 57.116 42.857 0.00 0.00 38.94 2.52
3434 3532 4.184649 AGGAGGACCATGTGTTTTCTTT 57.815 40.909 0.00 0.00 38.94 2.52
3449 3547 8.212312 TGTGTTTTCTTTACAGGTGTAATAGGA 58.788 33.333 3.46 1.34 39.89 2.94
3450 3548 9.059260 GTGTTTTCTTTACAGGTGTAATAGGAA 57.941 33.333 3.46 6.44 39.89 3.36
3451 3549 9.280174 TGTTTTCTTTACAGGTGTAATAGGAAG 57.720 33.333 3.46 0.00 39.89 3.46
3452 3550 8.727910 GTTTTCTTTACAGGTGTAATAGGAAGG 58.272 37.037 3.46 0.00 39.89 3.46
3550 3648 3.758554 GAGTTTTGTGCTATCATGGGTGT 59.241 43.478 0.00 0.00 0.00 4.16
3587 3687 5.362143 TCTCTCTCTGGTCTGGACAATAATG 59.638 44.000 3.10 0.00 0.00 1.90
3674 3777 8.575454 GTTTCTGTTATAAAAATGTAAGCGCAG 58.425 33.333 11.47 0.00 0.00 5.18
3684 3787 1.375908 TAAGCGCAGTTGCTCAGGG 60.376 57.895 11.47 0.00 46.60 4.45
3711 3823 8.701908 AATTCAAGATGAACTATGCCATACAT 57.298 30.769 0.00 0.00 39.45 2.29
3721 3833 9.800433 TGAACTATGCCATACATTAATGTTTTG 57.200 29.630 25.31 20.83 41.97 2.44
3911 4024 5.360429 TGGTACGTGCTGTATTATTGAGGTA 59.640 40.000 3.01 0.00 35.02 3.08
3914 4027 3.741344 CGTGCTGTATTATTGAGGTAGGC 59.259 47.826 0.00 0.00 0.00 3.93
3971 4084 5.714333 TGGTTTATTGCATGGTCAACTACAT 59.286 36.000 0.00 0.00 0.00 2.29
4007 4120 6.173339 ACAAACAACTATCCATGAGTACAGG 58.827 40.000 0.00 0.00 0.00 4.00
4045 4158 5.198207 GGAGAAGATCTAGCTAGTATCCCC 58.802 50.000 20.10 10.60 0.00 4.81
4091 4218 7.856145 AGAAGATCTCGTAGCATTTCATTTT 57.144 32.000 0.00 0.00 0.00 1.82
4092 4219 8.273780 AGAAGATCTCGTAGCATTTCATTTTT 57.726 30.769 0.00 0.00 0.00 1.94
4093 4220 8.180267 AGAAGATCTCGTAGCATTTCATTTTTG 58.820 33.333 0.00 0.00 0.00 2.44
4094 4221 7.383102 AGATCTCGTAGCATTTCATTTTTGT 57.617 32.000 0.00 0.00 0.00 2.83
4095 4222 8.492673 AGATCTCGTAGCATTTCATTTTTGTA 57.507 30.769 0.00 0.00 0.00 2.41
4249 4377 6.812879 ACTCCCTCCGTTTGTTTTTATAAG 57.187 37.500 0.00 0.00 0.00 1.73
4251 4379 7.173032 ACTCCCTCCGTTTGTTTTTATAAGAT 58.827 34.615 0.00 0.00 0.00 2.40
4272 4400 2.122564 GTTTCAGACAGCTTGCTTTGC 58.877 47.619 0.00 0.00 0.00 3.68
4273 4401 1.391577 TTCAGACAGCTTGCTTTGCA 58.608 45.000 0.00 0.00 36.47 4.08
4274 4402 0.664761 TCAGACAGCTTGCTTTGCAC 59.335 50.000 0.00 0.00 38.71 4.57
4275 4403 0.666913 CAGACAGCTTGCTTTGCACT 59.333 50.000 0.00 0.00 38.71 4.40
4276 4404 0.666913 AGACAGCTTGCTTTGCACTG 59.333 50.000 8.10 8.10 38.71 3.66
4277 4405 0.383231 GACAGCTTGCTTTGCACTGT 59.617 50.000 13.19 13.19 44.56 3.55
4278 4406 0.819582 ACAGCTTGCTTTGCACTGTT 59.180 45.000 9.13 0.00 41.04 3.16
4279 4407 1.205417 ACAGCTTGCTTTGCACTGTTT 59.795 42.857 9.13 0.00 41.04 2.83
4280 4408 2.273557 CAGCTTGCTTTGCACTGTTTT 58.726 42.857 0.00 0.00 38.71 2.43
4281 4409 2.029970 CAGCTTGCTTTGCACTGTTTTG 59.970 45.455 0.00 0.00 38.71 2.44
4282 4410 2.094078 AGCTTGCTTTGCACTGTTTTGA 60.094 40.909 0.00 0.00 38.71 2.69
4283 4411 2.672381 GCTTGCTTTGCACTGTTTTGAA 59.328 40.909 0.00 0.00 38.71 2.69
4284 4412 3.484065 GCTTGCTTTGCACTGTTTTGAAC 60.484 43.478 0.00 0.00 38.71 3.18
4285 4413 3.309961 TGCTTTGCACTGTTTTGAACA 57.690 38.095 0.00 0.00 35.00 3.18
4298 4426 6.942886 TGTTTTGAACAGTGTTTGAATGTC 57.057 33.333 10.45 0.00 36.25 3.06
4299 4427 6.686630 TGTTTTGAACAGTGTTTGAATGTCT 58.313 32.000 10.45 0.00 36.25 3.41
4300 4428 7.821652 TGTTTTGAACAGTGTTTGAATGTCTA 58.178 30.769 10.45 0.00 36.25 2.59
4301 4429 8.300286 TGTTTTGAACAGTGTTTGAATGTCTAA 58.700 29.630 10.45 0.00 36.25 2.10
4302 4430 9.134734 GTTTTGAACAGTGTTTGAATGTCTAAA 57.865 29.630 10.45 2.56 0.00 1.85
4303 4431 9.698309 TTTTGAACAGTGTTTGAATGTCTAAAA 57.302 25.926 10.45 3.40 0.00 1.52
4304 4432 8.682128 TTGAACAGTGTTTGAATGTCTAAAAC 57.318 30.769 10.45 0.00 34.97 2.43
4305 4433 6.964370 TGAACAGTGTTTGAATGTCTAAAACG 59.036 34.615 10.45 0.00 36.75 3.60
4306 4434 6.431198 ACAGTGTTTGAATGTCTAAAACGT 57.569 33.333 0.00 0.00 36.75 3.99
4307 4435 6.483687 ACAGTGTTTGAATGTCTAAAACGTC 58.516 36.000 0.00 0.00 36.75 4.34
4308 4436 6.315393 ACAGTGTTTGAATGTCTAAAACGTCT 59.685 34.615 0.00 0.00 36.75 4.18
4309 4437 7.148306 ACAGTGTTTGAATGTCTAAAACGTCTT 60.148 33.333 0.00 0.00 36.75 3.01
4310 4438 8.332464 CAGTGTTTGAATGTCTAAAACGTCTTA 58.668 33.333 0.00 0.00 36.75 2.10
4311 4439 9.052759 AGTGTTTGAATGTCTAAAACGTCTTAT 57.947 29.630 0.00 0.00 36.75 1.73
4326 4454 9.893305 AAAACGTCTTATAAAAATGAACAGAGG 57.107 29.630 0.00 0.00 0.00 3.69
4327 4455 8.617290 AACGTCTTATAAAAATGAACAGAGGT 57.383 30.769 0.00 0.00 31.12 3.85
4328 4456 9.715121 AACGTCTTATAAAAATGAACAGAGGTA 57.285 29.630 0.00 0.00 30.04 3.08
4329 4457 9.367444 ACGTCTTATAAAAATGAACAGAGGTAG 57.633 33.333 0.00 0.00 0.00 3.18
4330 4458 9.367444 CGTCTTATAAAAATGAACAGAGGTAGT 57.633 33.333 0.00 0.00 0.00 2.73
4338 4466 7.973048 AAATGAACAGAGGTAGTACATAGGA 57.027 36.000 2.06 0.00 0.00 2.94
4339 4467 6.963083 ATGAACAGAGGTAGTACATAGGAC 57.037 41.667 2.06 0.00 0.00 3.85
4340 4468 5.198965 TGAACAGAGGTAGTACATAGGACC 58.801 45.833 2.06 0.00 0.00 4.46
4341 4469 4.181799 ACAGAGGTAGTACATAGGACCC 57.818 50.000 2.06 0.00 31.93 4.46
4342 4470 3.117208 ACAGAGGTAGTACATAGGACCCC 60.117 52.174 2.06 0.00 31.93 4.95
4343 4471 3.117246 CAGAGGTAGTACATAGGACCCCA 60.117 52.174 2.06 0.00 31.93 4.96
4344 4472 3.534747 AGAGGTAGTACATAGGACCCCAA 59.465 47.826 2.06 0.00 31.93 4.12
4345 4473 3.640498 GAGGTAGTACATAGGACCCCAAC 59.360 52.174 2.06 0.00 31.93 3.77
4346 4474 3.013188 AGGTAGTACATAGGACCCCAACA 59.987 47.826 2.06 0.00 31.93 3.33
4347 4475 3.387050 GGTAGTACATAGGACCCCAACAG 59.613 52.174 2.06 0.00 0.00 3.16
4348 4476 1.838077 AGTACATAGGACCCCAACAGC 59.162 52.381 0.00 0.00 0.00 4.40
4349 4477 1.134189 GTACATAGGACCCCAACAGCC 60.134 57.143 0.00 0.00 0.00 4.85
4350 4478 0.844661 ACATAGGACCCCAACAGCCA 60.845 55.000 0.00 0.00 0.00 4.75
4351 4479 0.107017 CATAGGACCCCAACAGCCAG 60.107 60.000 0.00 0.00 0.00 4.85
4352 4480 0.253160 ATAGGACCCCAACAGCCAGA 60.253 55.000 0.00 0.00 0.00 3.86
4353 4481 0.909610 TAGGACCCCAACAGCCAGAG 60.910 60.000 0.00 0.00 0.00 3.35
4354 4482 2.529744 GGACCCCAACAGCCAGAGT 61.530 63.158 0.00 0.00 0.00 3.24
4355 4483 1.198759 GGACCCCAACAGCCAGAGTA 61.199 60.000 0.00 0.00 0.00 2.59
4356 4484 0.912486 GACCCCAACAGCCAGAGTAT 59.088 55.000 0.00 0.00 0.00 2.12
4357 4485 0.620556 ACCCCAACAGCCAGAGTATG 59.379 55.000 0.00 0.00 0.00 2.39
4358 4486 0.620556 CCCCAACAGCCAGAGTATGT 59.379 55.000 0.00 0.00 0.00 2.29
4359 4487 1.004745 CCCCAACAGCCAGAGTATGTT 59.995 52.381 0.00 0.00 37.64 2.71
4360 4488 2.359900 CCCAACAGCCAGAGTATGTTC 58.640 52.381 0.00 0.00 35.04 3.18
4361 4489 2.002586 CCAACAGCCAGAGTATGTTCG 58.997 52.381 0.00 0.00 35.04 3.95
4362 4490 1.394917 CAACAGCCAGAGTATGTTCGC 59.605 52.381 0.00 0.00 35.04 4.70
4363 4491 0.898320 ACAGCCAGAGTATGTTCGCT 59.102 50.000 0.00 0.00 0.00 4.93
4364 4492 1.284657 CAGCCAGAGTATGTTCGCTG 58.715 55.000 1.01 1.01 36.04 5.18
4365 4493 0.898320 AGCCAGAGTATGTTCGCTGT 59.102 50.000 0.00 0.00 34.35 4.40
4366 4494 1.002366 GCCAGAGTATGTTCGCTGTG 58.998 55.000 0.00 0.00 34.35 3.66
4367 4495 1.404181 GCCAGAGTATGTTCGCTGTGA 60.404 52.381 0.00 0.00 34.35 3.58
4368 4496 2.930887 GCCAGAGTATGTTCGCTGTGAA 60.931 50.000 0.00 0.00 34.35 3.18
4369 4497 2.926200 CCAGAGTATGTTCGCTGTGAAG 59.074 50.000 3.49 0.00 37.23 3.02
4370 4498 3.367395 CCAGAGTATGTTCGCTGTGAAGA 60.367 47.826 3.49 3.31 37.23 2.87
4371 4499 3.856521 CAGAGTATGTTCGCTGTGAAGAG 59.143 47.826 3.49 0.00 37.23 2.85
4372 4500 3.508012 AGAGTATGTTCGCTGTGAAGAGT 59.492 43.478 3.49 0.00 37.23 3.24
4373 4501 3.579709 AGTATGTTCGCTGTGAAGAGTG 58.420 45.455 3.49 0.00 37.23 3.51
4374 4502 2.820059 ATGTTCGCTGTGAAGAGTGA 57.180 45.000 3.49 0.00 37.23 3.41
4375 4503 1.852942 TGTTCGCTGTGAAGAGTGAC 58.147 50.000 3.49 0.00 37.23 3.67
4376 4504 1.136110 TGTTCGCTGTGAAGAGTGACA 59.864 47.619 3.49 0.00 37.23 3.58
4377 4505 2.224042 TGTTCGCTGTGAAGAGTGACAT 60.224 45.455 3.49 0.00 37.23 3.06
4378 4506 2.802816 GTTCGCTGTGAAGAGTGACATT 59.197 45.455 3.49 0.00 37.23 2.71
4379 4507 3.111853 TCGCTGTGAAGAGTGACATTT 57.888 42.857 0.00 0.00 0.00 2.32
4380 4508 2.802247 TCGCTGTGAAGAGTGACATTTG 59.198 45.455 0.00 0.00 0.00 2.32
4381 4509 2.663879 CGCTGTGAAGAGTGACATTTGC 60.664 50.000 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.933723 CAGAAAATCATCAAAAATACCCTTTCT 57.066 29.630 0.00 0.00 31.40 2.52
35 36 4.081309 AGCTAATAACTTTGTCCGGCTACA 60.081 41.667 0.00 0.00 0.00 2.74
38 39 3.629142 AGCTAATAACTTTGTCCGGCT 57.371 42.857 0.00 0.00 0.00 5.52
108 113 5.344207 ACGTAGTTTGACTGCTTCAATTC 57.656 39.130 2.65 1.06 43.99 2.17
117 122 8.332464 TTGAATACAAAAGACGTAGTTTGACTG 58.668 33.333 23.20 9.73 37.98 3.51
118 123 8.333186 GTTGAATACAAAAGACGTAGTTTGACT 58.667 33.333 23.20 11.27 38.35 3.41
214 277 8.121305 TGGAATAAATAAATGTGACTGCTTGT 57.879 30.769 0.00 0.00 0.00 3.16
368 431 0.179179 GCAGAGATCGTTGCTTTGGC 60.179 55.000 14.74 0.00 37.35 4.52
398 461 1.592669 CATCTGGGACGTCGATGGC 60.593 63.158 18.70 5.58 32.84 4.40
416 479 2.739671 GTTGGGTACGGGTCGTGC 60.740 66.667 3.03 1.53 41.39 5.34
441 504 1.295746 GGGAGTTCGAGGGTGGAAC 59.704 63.158 0.00 0.00 43.15 3.62
745 814 0.602638 GATTCATGGCGCGGGTATGA 60.603 55.000 8.83 14.34 0.00 2.15
748 817 2.110213 GGATTCATGGCGCGGGTA 59.890 61.111 8.83 0.00 0.00 3.69
838 907 3.927142 TCGTCGCAAAACACCAAATTTTT 59.073 34.783 0.00 0.00 0.00 1.94
875 944 3.834489 AGATCTCCGTGAAATGCTCAT 57.166 42.857 0.00 0.00 36.14 2.90
901 970 8.602472 AGAGAAGGAAGATACAAATCAGTACT 57.398 34.615 0.00 0.00 34.28 2.73
939 1010 1.450025 CAGCTCAGATTCTTGCAGCA 58.550 50.000 10.29 0.00 32.17 4.41
986 1057 1.864711 CCGTTCTTCTCGTTCTTGCAA 59.135 47.619 0.00 0.00 0.00 4.08
1413 1484 0.579156 GATCAAATCGAGGCTGCGTC 59.421 55.000 12.07 12.07 0.00 5.19
1525 1596 1.379642 GCTGCTGCTGGAATGGGTAC 61.380 60.000 8.53 0.00 36.03 3.34
1726 1797 2.919856 AGTGGGTCGCTCACAGCT 60.920 61.111 11.54 0.00 39.60 4.24
1731 1802 0.320683 CACATTCAGTGGGTCGCTCA 60.321 55.000 0.00 0.00 44.69 4.26
1856 1927 5.888161 ACCCTTATAAAAGAATCACAGCAGG 59.112 40.000 0.00 0.00 34.37 4.85
1947 2018 2.100749 GCTAATGGCGGGCACTTTAATT 59.899 45.455 6.33 0.00 0.00 1.40
2524 2609 7.229506 GCTTTCATGGTATAGCTACATTTTCCT 59.770 37.037 0.00 0.00 0.00 3.36
2832 2918 1.819632 GGCCTCGCGTTCATGGATT 60.820 57.895 5.77 0.00 0.00 3.01
2908 2994 1.677052 GCTCCTACTTTCGAGATCCGT 59.323 52.381 3.97 0.00 39.75 4.69
2917 3003 5.243426 TGTTGTTTGTTGCTCCTACTTTC 57.757 39.130 0.00 0.00 0.00 2.62
2997 3091 2.736682 CGCCGAAACCCTAACAGCG 61.737 63.158 0.00 0.00 35.82 5.18
3132 3227 1.906574 GAACCCCACCTGTCACTATCA 59.093 52.381 0.00 0.00 0.00 2.15
3433 3531 7.391620 CAACTTCCTTCCTATTACACCTGTAA 58.608 38.462 0.43 0.43 43.71 2.41
3434 3532 6.575649 GCAACTTCCTTCCTATTACACCTGTA 60.576 42.308 0.00 0.00 0.00 2.74
3449 3547 4.464008 TGAGAAATCACAGCAACTTCCTT 58.536 39.130 0.00 0.00 0.00 3.36
3450 3548 4.070716 CTGAGAAATCACAGCAACTTCCT 58.929 43.478 0.00 0.00 0.00 3.36
3451 3549 3.817647 ACTGAGAAATCACAGCAACTTCC 59.182 43.478 7.63 0.00 37.97 3.46
3452 3550 4.512944 TGACTGAGAAATCACAGCAACTTC 59.487 41.667 7.63 0.00 37.97 3.01
3622 3722 1.628846 TCTTGGGGAAGAACTGGCTAC 59.371 52.381 0.00 0.00 0.00 3.58
3647 3750 7.539366 TGCGCTTACATTTTTATAACAGAAACC 59.461 33.333 9.73 0.00 0.00 3.27
3674 3777 4.460382 TCATCTTGAATTTCCCTGAGCAAC 59.540 41.667 0.00 0.00 0.00 4.17
3684 3787 8.623903 TGTATGGCATAGTTCATCTTGAATTTC 58.376 33.333 7.61 0.00 38.79 2.17
3711 3823 4.211125 TGGGAGCACTGACAAAACATTAA 58.789 39.130 0.00 0.00 0.00 1.40
3721 3833 3.010420 GTTAGGATTTGGGAGCACTGAC 58.990 50.000 0.00 0.00 0.00 3.51
3824 3936 5.538813 CCACCAGATACTGCTAATACCTACA 59.461 44.000 0.00 0.00 0.00 2.74
3825 3937 5.567025 GCCACCAGATACTGCTAATACCTAC 60.567 48.000 0.00 0.00 0.00 3.18
3888 4001 4.690122 ACCTCAATAATACAGCACGTACC 58.310 43.478 0.00 0.00 31.27 3.34
3894 4007 3.802329 GCGCCTACCTCAATAATACAGCA 60.802 47.826 0.00 0.00 0.00 4.41
3895 4008 2.737252 GCGCCTACCTCAATAATACAGC 59.263 50.000 0.00 0.00 0.00 4.40
3911 4024 0.036732 TTTTGTCCATCTCAGCGCCT 59.963 50.000 2.29 0.00 0.00 5.52
3914 4027 2.733227 GCCATTTTTGTCCATCTCAGCG 60.733 50.000 0.00 0.00 0.00 5.18
3971 4084 7.103641 GGATAGTTGTTTGTAGACCATCTCAA 58.896 38.462 0.00 0.00 0.00 3.02
4067 4180 7.856145 AAAATGAAATGCTACGAGATCTTCT 57.144 32.000 0.00 0.00 0.00 2.85
4094 4221 9.308318 GCTTGAAGAAATGTTTGTTTACCTTTA 57.692 29.630 0.00 0.00 0.00 1.85
4095 4222 7.821846 TGCTTGAAGAAATGTTTGTTTACCTTT 59.178 29.630 0.00 0.00 0.00 3.11
4229 4357 7.153217 ACATCTTATAAAAACAAACGGAGGG 57.847 36.000 0.00 0.00 0.00 4.30
4249 4377 3.911661 AAGCAAGCTGTCTGAAACATC 57.088 42.857 0.00 0.00 37.23 3.06
4251 4379 2.480073 GCAAAGCAAGCTGTCTGAAACA 60.480 45.455 0.00 0.00 36.18 2.83
4275 4403 6.686630 AGACATTCAAACACTGTTCAAAACA 58.313 32.000 0.00 0.00 39.52 2.83
4276 4404 8.682128 TTAGACATTCAAACACTGTTCAAAAC 57.318 30.769 0.00 0.00 0.00 2.43
4277 4405 9.698309 TTTTAGACATTCAAACACTGTTCAAAA 57.302 25.926 0.00 0.00 0.00 2.44
4278 4406 9.134734 GTTTTAGACATTCAAACACTGTTCAAA 57.865 29.630 0.00 0.00 31.81 2.69
4279 4407 7.483375 CGTTTTAGACATTCAAACACTGTTCAA 59.517 33.333 0.00 0.00 31.81 2.69
4280 4408 6.964370 CGTTTTAGACATTCAAACACTGTTCA 59.036 34.615 0.00 0.00 31.81 3.18
4281 4409 6.964934 ACGTTTTAGACATTCAAACACTGTTC 59.035 34.615 0.00 0.00 31.81 3.18
4282 4410 6.848451 ACGTTTTAGACATTCAAACACTGTT 58.152 32.000 0.00 0.00 31.81 3.16
4283 4411 6.315393 AGACGTTTTAGACATTCAAACACTGT 59.685 34.615 0.00 0.00 31.81 3.55
4284 4412 6.715464 AGACGTTTTAGACATTCAAACACTG 58.285 36.000 0.00 0.00 31.81 3.66
4285 4413 6.920569 AGACGTTTTAGACATTCAAACACT 57.079 33.333 0.00 0.00 31.81 3.55
4300 4428 9.893305 CCTCTGTTCATTTTTATAAGACGTTTT 57.107 29.630 0.00 0.00 0.00 2.43
4301 4429 9.063615 ACCTCTGTTCATTTTTATAAGACGTTT 57.936 29.630 0.00 0.00 0.00 3.60
4302 4430 8.617290 ACCTCTGTTCATTTTTATAAGACGTT 57.383 30.769 0.00 0.00 0.00 3.99
4303 4431 9.367444 CTACCTCTGTTCATTTTTATAAGACGT 57.633 33.333 0.00 0.00 0.00 4.34
4304 4432 9.367444 ACTACCTCTGTTCATTTTTATAAGACG 57.633 33.333 0.00 0.00 0.00 4.18
4312 4440 8.822805 TCCTATGTACTACCTCTGTTCATTTTT 58.177 33.333 0.00 0.00 30.30 1.94
4313 4441 8.258708 GTCCTATGTACTACCTCTGTTCATTTT 58.741 37.037 0.00 0.00 30.30 1.82
4314 4442 7.147707 GGTCCTATGTACTACCTCTGTTCATTT 60.148 40.741 0.00 0.00 30.30 2.32
4315 4443 6.324254 GGTCCTATGTACTACCTCTGTTCATT 59.676 42.308 0.00 0.00 30.30 2.57
4316 4444 5.834204 GGTCCTATGTACTACCTCTGTTCAT 59.166 44.000 0.00 0.00 31.97 2.57
4317 4445 5.198965 GGTCCTATGTACTACCTCTGTTCA 58.801 45.833 0.00 0.00 0.00 3.18
4318 4446 4.583907 GGGTCCTATGTACTACCTCTGTTC 59.416 50.000 0.00 0.00 32.38 3.18
4319 4447 4.544683 GGGTCCTATGTACTACCTCTGTT 58.455 47.826 0.00 0.00 32.38 3.16
4320 4448 3.117208 GGGGTCCTATGTACTACCTCTGT 60.117 52.174 0.00 0.00 32.38 3.41
4321 4449 3.117246 TGGGGTCCTATGTACTACCTCTG 60.117 52.174 0.00 0.00 33.38 3.35
4322 4450 3.136896 TGGGGTCCTATGTACTACCTCT 58.863 50.000 0.00 0.00 33.38 3.69
4323 4451 3.607490 TGGGGTCCTATGTACTACCTC 57.393 52.381 0.00 0.00 32.78 3.85
4324 4452 3.013188 TGTTGGGGTCCTATGTACTACCT 59.987 47.826 0.00 0.00 32.38 3.08
4325 4453 3.377573 TGTTGGGGTCCTATGTACTACC 58.622 50.000 0.00 0.00 0.00 3.18
4326 4454 3.181468 GCTGTTGGGGTCCTATGTACTAC 60.181 52.174 0.00 0.00 0.00 2.73
4327 4455 3.036091 GCTGTTGGGGTCCTATGTACTA 58.964 50.000 0.00 0.00 0.00 1.82
4328 4456 1.838077 GCTGTTGGGGTCCTATGTACT 59.162 52.381 0.00 0.00 0.00 2.73
4329 4457 1.134189 GGCTGTTGGGGTCCTATGTAC 60.134 57.143 0.00 0.00 0.00 2.90
4330 4458 1.209621 GGCTGTTGGGGTCCTATGTA 58.790 55.000 0.00 0.00 0.00 2.29
4331 4459 0.844661 TGGCTGTTGGGGTCCTATGT 60.845 55.000 0.00 0.00 0.00 2.29
4332 4460 0.107017 CTGGCTGTTGGGGTCCTATG 60.107 60.000 0.00 0.00 0.00 2.23
4333 4461 0.253160 TCTGGCTGTTGGGGTCCTAT 60.253 55.000 0.00 0.00 0.00 2.57
4334 4462 0.909610 CTCTGGCTGTTGGGGTCCTA 60.910 60.000 0.00 0.00 0.00 2.94
4335 4463 2.121963 TCTGGCTGTTGGGGTCCT 60.122 61.111 0.00 0.00 0.00 3.85
4336 4464 1.198759 TACTCTGGCTGTTGGGGTCC 61.199 60.000 0.00 0.00 0.00 4.46
4337 4465 0.912486 ATACTCTGGCTGTTGGGGTC 59.088 55.000 0.00 0.00 0.00 4.46
4338 4466 0.620556 CATACTCTGGCTGTTGGGGT 59.379 55.000 0.00 0.00 0.00 4.95
4339 4467 0.620556 ACATACTCTGGCTGTTGGGG 59.379 55.000 0.00 0.00 0.00 4.96
4340 4468 2.359900 GAACATACTCTGGCTGTTGGG 58.640 52.381 0.00 0.00 33.46 4.12
4341 4469 2.002586 CGAACATACTCTGGCTGTTGG 58.997 52.381 0.00 0.00 33.46 3.77
4342 4470 1.394917 GCGAACATACTCTGGCTGTTG 59.605 52.381 0.00 0.00 33.46 3.33
4343 4471 1.276421 AGCGAACATACTCTGGCTGTT 59.724 47.619 0.00 0.00 35.89 3.16
4344 4472 0.898320 AGCGAACATACTCTGGCTGT 59.102 50.000 0.00 0.00 0.00 4.40
4345 4473 1.284657 CAGCGAACATACTCTGGCTG 58.715 55.000 0.00 0.00 41.42 4.85
4346 4474 0.898320 ACAGCGAACATACTCTGGCT 59.102 50.000 0.00 0.00 0.00 4.75
4347 4475 1.002366 CACAGCGAACATACTCTGGC 58.998 55.000 0.00 0.00 0.00 4.85
4348 4476 2.654749 TCACAGCGAACATACTCTGG 57.345 50.000 0.00 0.00 0.00 3.86
4349 4477 3.838120 TCTTCACAGCGAACATACTCTG 58.162 45.455 0.00 0.00 0.00 3.35
4350 4478 3.508012 ACTCTTCACAGCGAACATACTCT 59.492 43.478 0.00 0.00 0.00 3.24
4351 4479 3.610242 CACTCTTCACAGCGAACATACTC 59.390 47.826 0.00 0.00 0.00 2.59
4352 4480 3.255888 TCACTCTTCACAGCGAACATACT 59.744 43.478 0.00 0.00 0.00 2.12
4353 4481 3.365220 GTCACTCTTCACAGCGAACATAC 59.635 47.826 0.00 0.00 0.00 2.39
4354 4482 3.005367 TGTCACTCTTCACAGCGAACATA 59.995 43.478 0.00 0.00 0.00 2.29
4355 4483 2.224042 TGTCACTCTTCACAGCGAACAT 60.224 45.455 0.00 0.00 0.00 2.71
4356 4484 1.136110 TGTCACTCTTCACAGCGAACA 59.864 47.619 0.00 0.00 0.00 3.18
4357 4485 1.852942 TGTCACTCTTCACAGCGAAC 58.147 50.000 0.00 0.00 0.00 3.95
4358 4486 2.820059 ATGTCACTCTTCACAGCGAA 57.180 45.000 0.00 0.00 0.00 4.70
4359 4487 2.802247 CAAATGTCACTCTTCACAGCGA 59.198 45.455 0.00 0.00 0.00 4.93
4360 4488 2.663879 GCAAATGTCACTCTTCACAGCG 60.664 50.000 0.00 0.00 0.00 5.18
4361 4489 2.926165 GCAAATGTCACTCTTCACAGC 58.074 47.619 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.