Multiple sequence alignment - TraesCS6A01G156000

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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 TraesCS6A01G156000 chr6A 100.000 5976 0 0 1 5976 144723728 144717753 0.000000e+00 11036
1 TraesCS6A01G156000 chr6D 95.033 6020 191 39 1 5976 116367180 116361225 0.000000e+00 9361
2 TraesCS6A01G156000 chr6B 95.514 3656 106 22 470 4095 206448902 206445275 0.000000e+00 5790
3 TraesCS6A01G156000 chr6B 94.072 1822 58 17 4183 5976 206444969 206443170 0.000000e+00 2721
4 TraesCS6A01G156000 chr6B 98.592 71 1 0 4080 4150 206445037 206444967 6.290000e-25 126
5 TraesCS6A01G156000 chr7D 90.840 262 21 3 3545 3805 45399748 45399489 1.230000e-91 348
6 TraesCS6A01G156000 chr5A 76.224 286 56 9 235 517 355461936 355462212 2.250000e-29 141


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 TraesCS6A01G156000 chr6A 144717753 144723728 5975 True 11036 11036 100.000000 1 5976 1 chr6A.!!$R1 5975
1 TraesCS6A01G156000 chr6D 116361225 116367180 5955 True 9361 9361 95.033000 1 5976 1 chr6D.!!$R1 5975
2 TraesCS6A01G156000 chr6B 206443170 206448902 5732 True 2879 5790 96.059333 470 5976 3 chr6B.!!$R1 5506

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
902 924 0.171455 CCCTCGTCGAAGAACCTGAG 59.829 60.000 1.95 0.0 39.69 3.35 F
1232 1260 1.003355 ACAGGTCCACGAGCAATGG 60.003 57.895 0.00 0.0 38.71 3.16 F
1752 1796 1.332195 GGGGCTCCATTTATGCTTCC 58.668 55.000 0.00 0.0 0.00 3.46 F
1860 1904 2.049627 GATCATTCAGCGGGAGGGCT 62.050 60.000 0.00 0.0 46.13 5.19 F
2020 2064 2.951229 AGTTGTCTGTAGGGTTTGGG 57.049 50.000 0.00 0.0 0.00 4.12 F
3946 3997 2.439156 GTGCAGGGATGAGTGCCC 60.439 66.667 0.00 0.0 46.40 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 1761 0.320050 CCCCATTTTCCACCAAACCG 59.680 55.000 0.00 0.00 0.00 4.44 R
2184 2229 1.098050 AAATGAACAGAGGGCGCATC 58.902 50.000 10.83 6.76 0.00 3.91 R
2707 2754 6.985188 TTTGTGTAGAATGCTCAGGATAAC 57.015 37.500 0.00 0.00 0.00 1.89 R
3776 3826 0.040958 GCTGCTTCACTTTGTCACGG 60.041 55.000 0.00 0.00 0.00 4.94 R
4016 4067 2.480845 GGACATGCGGGTCAACTATAC 58.519 52.381 9.43 0.00 39.59 1.47 R
5582 5912 0.690744 TGAATCCATGGCTCTCCGGA 60.691 55.000 6.96 2.93 34.14 5.14 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
21 22 1.912110 CTTCTGCGAGCGTTACTACAC 59.088 52.381 0.00 0.00 0.00 2.90
28 29 0.458669 AGCGTTACTACACCATCCCG 59.541 55.000 0.00 0.00 0.00 5.14
57 58 1.657751 CGCAGAAAAGCCCCTAAGCC 61.658 60.000 0.00 0.00 0.00 4.35
58 59 0.611896 GCAGAAAAGCCCCTAAGCCA 60.612 55.000 0.00 0.00 0.00 4.75
69 70 1.893801 CCCTAAGCCATAGTAGGTCCG 59.106 57.143 0.00 0.00 35.97 4.79
102 103 3.642755 GTGTCGCTCCACACAAGG 58.357 61.111 5.77 0.00 45.25 3.61
103 104 1.961277 GTGTCGCTCCACACAAGGG 60.961 63.158 5.77 0.00 45.25 3.95
104 105 2.358737 GTCGCTCCACACAAGGGG 60.359 66.667 0.00 0.00 0.00 4.79
105 106 3.636231 TCGCTCCACACAAGGGGG 61.636 66.667 0.00 0.00 0.00 5.40
148 149 2.875080 GCTTTAGTGCGTGGTAACTG 57.125 50.000 0.00 0.00 37.61 3.16
149 150 2.140717 GCTTTAGTGCGTGGTAACTGT 58.859 47.619 0.00 0.00 37.61 3.55
150 151 3.319755 GCTTTAGTGCGTGGTAACTGTA 58.680 45.455 0.00 0.00 37.61 2.74
152 153 3.581024 TTAGTGCGTGGTAACTGTAGG 57.419 47.619 0.00 0.00 37.61 3.18
166 171 6.096564 GGTAACTGTAGGTGTGCTAGAAGTAT 59.903 42.308 0.00 0.00 0.00 2.12
168 173 5.967088 ACTGTAGGTGTGCTAGAAGTATTG 58.033 41.667 0.00 0.00 0.00 1.90
200 205 1.936547 GAGCAGTGCTGGCTACAATAC 59.063 52.381 25.35 0.00 42.78 1.89
205 210 4.740634 GCAGTGCTGGCTACAATACTATCA 60.741 45.833 8.18 0.00 0.00 2.15
212 217 6.731292 TGGCTACAATACTATCAGATGTGT 57.269 37.500 0.00 0.00 0.00 3.72
253 258 5.232414 CGTAAATGGATTCTCTCCTCGAAAC 59.768 44.000 0.00 0.00 45.21 2.78
309 314 9.011407 TGTTTTGTGTACGTGTTTAATTTCATC 57.989 29.630 0.00 0.00 0.00 2.92
319 324 7.148137 ACGTGTTTAATTTCATCCATACCTTCC 60.148 37.037 0.00 0.00 0.00 3.46
327 332 2.241281 TCCATACCTTCCAACTCGGA 57.759 50.000 0.00 0.00 44.40 4.55
329 334 1.553248 CCATACCTTCCAACTCGGACA 59.447 52.381 0.00 0.00 46.36 4.02
333 338 0.320771 CCTTCCAACTCGGACACCTG 60.321 60.000 0.00 0.00 46.36 4.00
345 350 5.217978 TCGGACACCTGTTAAAAGTATGT 57.782 39.130 0.47 0.47 0.00 2.29
346 351 4.992319 TCGGACACCTGTTAAAAGTATGTG 59.008 41.667 4.86 2.61 0.00 3.21
358 363 9.398538 TGTTAAAAGTATGTGTTTCCTACAACT 57.601 29.630 0.00 0.00 38.80 3.16
374 379 7.524065 TCCTACAACTAAAGAAATAAAAGCGC 58.476 34.615 0.00 0.00 0.00 5.92
383 388 4.421058 AGAAATAAAAGCGCCGGAAATTC 58.579 39.130 5.05 2.92 0.00 2.17
384 389 4.157840 AGAAATAAAAGCGCCGGAAATTCT 59.842 37.500 5.05 5.47 0.00 2.40
413 418 6.398918 TCGATCTTTTCCTTACAAAGAGGAG 58.601 40.000 1.93 0.00 43.79 3.69
416 421 4.351111 TCTTTTCCTTACAAAGAGGAGCCT 59.649 41.667 0.00 0.00 43.79 4.58
444 449 4.158394 GTCTTGTGCCACCATTGAATATGT 59.842 41.667 0.00 0.00 0.00 2.29
447 452 5.109500 TGTGCCACCATTGAATATGTCTA 57.891 39.130 0.00 0.00 0.00 2.59
464 469 3.320826 TGTCTACTTAGCTCAAGCACACA 59.679 43.478 4.59 0.00 45.16 3.72
465 470 4.202212 TGTCTACTTAGCTCAAGCACACAA 60.202 41.667 4.59 0.00 45.16 3.33
468 473 4.756084 ACTTAGCTCAAGCACACAATTC 57.244 40.909 4.59 0.00 45.16 2.17
473 478 2.229543 GCTCAAGCACACAATTCATCCA 59.770 45.455 0.00 0.00 41.59 3.41
489 494 8.884726 CAATTCATCCATAAATTGCATTGTCAA 58.115 29.630 0.00 0.00 36.42 3.18
495 500 7.160049 TCCATAAATTGCATTGTCAACAACAT 58.840 30.769 0.00 0.00 38.86 2.71
501 506 6.595772 TTGCATTGTCAACAACATTAAACC 57.404 33.333 0.00 0.00 38.86 3.27
509 514 7.259161 TGTCAACAACATTAAACCCACTTAAC 58.741 34.615 0.00 0.00 31.20 2.01
514 519 5.231702 ACATTAAACCCACTTAACGAGGA 57.768 39.130 0.00 0.00 0.00 3.71
515 520 5.623169 ACATTAAACCCACTTAACGAGGAA 58.377 37.500 0.00 0.00 0.00 3.36
534 539 3.996363 GGAAAATTTGCACTGATTCCACC 59.004 43.478 13.06 4.42 37.02 4.61
549 557 7.775561 ACTGATTCCACCATAAAGAATCTAACC 59.224 37.037 11.87 0.00 44.02 2.85
551 559 7.556275 TGATTCCACCATAAAGAATCTAACCAC 59.444 37.037 11.87 0.00 44.02 4.16
586 594 4.782691 TCAGGAATAACCAACCATCTGAGA 59.217 41.667 0.00 0.00 42.04 3.27
601 609 8.964533 ACCATCTGAGATACACTTAGGAATAT 57.035 34.615 0.00 0.00 33.74 1.28
681 691 8.990163 AAAAAGAGTAAGGAGTACCATTTTGA 57.010 30.769 0.00 0.00 33.97 2.69
683 693 9.588096 AAAAGAGTAAGGAGTACCATTTTGATT 57.412 29.630 0.00 0.00 38.94 2.57
885 907 2.686816 CCACGTGTCGCCATTTCCC 61.687 63.158 15.65 0.00 0.00 3.97
889 911 1.375523 GTGTCGCCATTTCCCTCGT 60.376 57.895 0.00 0.00 0.00 4.18
892 914 2.183300 CGCCATTTCCCTCGTCGA 59.817 61.111 0.00 0.00 0.00 4.20
902 924 0.171455 CCCTCGTCGAAGAACCTGAG 59.829 60.000 1.95 0.00 39.69 3.35
1015 1037 1.518572 CGCATGTGTACCGTCTCCC 60.519 63.158 0.00 0.00 0.00 4.30
1078 1100 4.436998 CCTTCCCGTCGCTCGCTT 62.437 66.667 0.00 0.00 38.35 4.68
1231 1259 2.460330 GACAGGTCCACGAGCAATG 58.540 57.895 0.00 0.00 31.89 2.82
1232 1260 1.003355 ACAGGTCCACGAGCAATGG 60.003 57.895 0.00 0.00 38.71 3.16
1233 1261 2.045926 AGGTCCACGAGCAATGGC 60.046 61.111 0.00 0.00 37.13 4.40
1410 1453 3.373565 GCCCCCTTGCGTTTCTGG 61.374 66.667 0.00 0.00 0.00 3.86
1631 1674 7.337942 AGTGGATCATTCTTGTGATTAGGTTTC 59.662 37.037 0.00 0.00 38.88 2.78
1664 1707 5.277345 GCGCTTATTGTGGATACTAAGTTGG 60.277 44.000 0.00 0.00 37.61 3.77
1677 1720 5.568620 ACTAAGTTGGTTGATGAGGACTT 57.431 39.130 0.00 0.00 0.00 3.01
1699 1742 2.303175 GTTTGTCTGTGCCCCTGTTTA 58.697 47.619 0.00 0.00 0.00 2.01
1714 1758 5.366477 CCCCTGTTTATTTGGGCAATAGATT 59.634 40.000 0.00 0.00 39.61 2.40
1717 1761 7.926018 CCCTGTTTATTTGGGCAATAGATTTAC 59.074 37.037 0.00 0.00 33.88 2.01
1720 1764 7.122948 TGTTTATTTGGGCAATAGATTTACGGT 59.877 33.333 0.00 0.00 0.00 4.83
1752 1796 1.332195 GGGGCTCCATTTATGCTTCC 58.668 55.000 0.00 0.00 0.00 3.46
1860 1904 2.049627 GATCATTCAGCGGGAGGGCT 62.050 60.000 0.00 0.00 46.13 5.19
1924 1968 4.504864 GGCTTTATTTGCCCACCTCTTTTT 60.505 41.667 0.00 0.00 44.32 1.94
2020 2064 2.951229 AGTTGTCTGTAGGGTTTGGG 57.049 50.000 0.00 0.00 0.00 4.12
2062 2106 4.218417 CAGACAACTTTCCCTTTATGGTGG 59.782 45.833 0.00 0.00 0.00 4.61
2119 2163 4.918810 ATGGAGTTTGGTTTCTTGTGTC 57.081 40.909 0.00 0.00 0.00 3.67
2212 2257 5.447818 CGCCCTCTGTTCATTTTGTATTCTC 60.448 44.000 0.00 0.00 0.00 2.87
2407 2454 5.613329 TGCAGCATCTTTTTCCTCAAAATT 58.387 33.333 0.00 0.00 33.73 1.82
2469 2516 3.187700 GCACACAGAGGGTAAACTATCG 58.812 50.000 0.00 0.00 0.00 2.92
2616 2663 6.998673 ACTAGTAATCTTGCTGGACAGTTTTT 59.001 34.615 0.00 0.00 0.00 1.94
2707 2754 6.551736 CGGACTGGTTTTACATTCTTAATGG 58.448 40.000 4.78 0.00 43.21 3.16
3425 3473 9.360093 TGTTAACAGACACCAATTTTTACTTTG 57.640 29.630 3.59 0.00 0.00 2.77
3776 3826 7.780271 AGAGTTAATATGGGATTGAAAACCCTC 59.220 37.037 9.53 0.00 45.74 4.30
3946 3997 2.439156 GTGCAGGGATGAGTGCCC 60.439 66.667 0.00 0.00 46.40 5.36
3968 4019 6.811665 GCCCCATGTTTCTTTACTATTTTGTC 59.188 38.462 0.00 0.00 0.00 3.18
4016 4067 6.096705 TGTTAGCCTTATGACATTTGATTGGG 59.903 38.462 0.00 0.00 0.00 4.12
4038 4089 1.252215 TAGTTGACCCGCATGTCCGA 61.252 55.000 0.00 0.00 34.25 4.55
4069 4120 6.894828 TGGCTAGATTAACGTTTTGAAGTTC 58.105 36.000 5.91 0.00 0.00 3.01
4150 4454 8.585471 ACACATATCATCCTTTTCTTTGATGT 57.415 30.769 0.00 0.00 37.67 3.06
4161 4465 7.340743 TCCTTTTCTTTGATGTGTTTTGGACTA 59.659 33.333 0.00 0.00 0.00 2.59
4236 4540 1.838112 TGGGCAAGTCCATAGCTTTG 58.162 50.000 0.00 0.00 36.21 2.77
4337 4641 4.285003 ACAGTGGTACATGGCTGTTACTTA 59.715 41.667 0.00 0.00 39.64 2.24
4978 5282 4.785341 GCCAAATACGTGAAAGAATAGCGG 60.785 45.833 0.00 0.00 0.00 5.52
4994 5298 7.996385 AGAATAGCGGCACTGTAAAATTTTAT 58.004 30.769 13.54 0.00 0.00 1.40
5077 5382 4.818546 CACCATGTATCTGTCCCTTTGATC 59.181 45.833 0.00 0.00 0.00 2.92
5279 5584 9.757227 TTACACTTGTTTATTTTCCATTCTTGG 57.243 29.630 0.00 0.00 45.15 3.61
5285 5590 7.098477 TGTTTATTTTCCATTCTTGGCATCAG 58.902 34.615 0.00 0.00 43.29 2.90
5306 5611 4.752101 CAGACTCTGAGGTGGTACTTTTTG 59.248 45.833 9.85 0.00 32.44 2.44
5308 5613 4.451900 ACTCTGAGGTGGTACTTTTTGTG 58.548 43.478 9.85 0.00 0.00 3.33
5415 5745 2.432628 CGTGGCGTCTTCACCCTC 60.433 66.667 0.00 0.00 0.00 4.30
5430 5760 3.149981 CACCCTCCCTTGAAGAAAACTC 58.850 50.000 0.00 0.00 0.00 3.01
5441 5771 3.073062 TGAAGAAAACTCTTGGGAGGAGG 59.927 47.826 0.00 0.00 43.46 4.30
5454 5784 1.539157 GAGGAGGCAGAAAACTTGGG 58.461 55.000 0.00 0.00 0.00 4.12
5496 5826 1.813337 GAAGCAAGGAGGCTCGAGC 60.813 63.158 29.38 29.38 45.07 5.03
5657 5987 2.668212 TCGTTTTGCCCCGCAGAG 60.668 61.111 0.00 0.00 40.61 3.35
5665 5995 4.809496 CCCCGCAGAGCAAGGCAT 62.809 66.667 0.00 0.00 0.00 4.40
5667 5997 2.345760 CCCGCAGAGCAAGGCATTT 61.346 57.895 0.00 0.00 0.00 2.32
5672 6002 0.963962 CAGAGCAAGGCATTTGGTGT 59.036 50.000 9.26 3.38 46.90 4.16
5910 6241 4.201679 CCGCCTACGCCGACATGA 62.202 66.667 0.00 0.00 38.22 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.197910 GATGGTGTAGTAACGCTCGC 58.802 55.000 0.00 0.00 36.33 5.03
8 9 1.535437 CGGGATGGTGTAGTAACGCTC 60.535 57.143 0.00 0.00 36.33 5.03
21 22 1.093496 GCGGTTTCCTAACGGGATGG 61.093 60.000 0.00 0.00 44.66 3.51
28 29 2.351447 GGCTTTTCTGCGGTTTCCTAAC 60.351 50.000 0.00 0.00 0.00 2.34
38 39 1.657751 GGCTTAGGGGCTTTTCTGCG 61.658 60.000 0.00 0.00 37.53 5.18
57 58 3.021695 TCCAAGTGTCGGACCTACTATG 58.978 50.000 5.55 5.17 0.00 2.23
58 59 3.288964 CTCCAAGTGTCGGACCTACTAT 58.711 50.000 5.55 0.00 0.00 2.12
137 138 1.425412 CACACCTACAGTTACCACGC 58.575 55.000 0.00 0.00 0.00 5.34
145 146 5.624738 GCAATACTTCTAGCACACCTACAGT 60.625 44.000 0.00 0.00 0.00 3.55
146 147 4.806247 GCAATACTTCTAGCACACCTACAG 59.194 45.833 0.00 0.00 0.00 2.74
147 148 4.466370 AGCAATACTTCTAGCACACCTACA 59.534 41.667 0.00 0.00 0.00 2.74
148 149 5.012328 AGCAATACTTCTAGCACACCTAC 57.988 43.478 0.00 0.00 0.00 3.18
149 150 4.099573 GGAGCAATACTTCTAGCACACCTA 59.900 45.833 0.00 0.00 0.00 3.08
150 151 3.118592 GGAGCAATACTTCTAGCACACCT 60.119 47.826 0.00 0.00 0.00 4.00
152 153 3.118592 AGGGAGCAATACTTCTAGCACAC 60.119 47.826 0.00 0.00 0.00 3.82
183 188 4.948847 TGATAGTATTGTAGCCAGCACTG 58.051 43.478 0.00 0.00 0.00 3.66
184 189 4.895889 TCTGATAGTATTGTAGCCAGCACT 59.104 41.667 0.00 0.00 0.00 4.40
205 210 9.383519 ACGTCTGATTTATGAAAATACACATCT 57.616 29.630 0.00 0.00 35.41 2.90
220 225 8.873215 GAGAGAATCCATTTACGTCTGATTTA 57.127 34.615 0.00 0.00 33.66 1.40
240 245 1.257743 CCACCAGTTTCGAGGAGAGA 58.742 55.000 0.00 0.00 0.00 3.10
253 258 1.895131 CCCACAATTTCTTCCCACCAG 59.105 52.381 0.00 0.00 0.00 4.00
319 324 3.875134 ACTTTTAACAGGTGTCCGAGTTG 59.125 43.478 8.90 0.00 31.45 3.16
327 332 6.831868 AGGAAACACATACTTTTAACAGGTGT 59.168 34.615 0.00 0.00 39.45 4.16
329 334 7.994334 TGTAGGAAACACATACTTTTAACAGGT 59.006 33.333 0.00 0.00 36.81 4.00
358 363 5.373981 TTTCCGGCGCTTTTATTTCTTTA 57.626 34.783 7.64 0.00 0.00 1.85
362 367 4.265320 CAGAATTTCCGGCGCTTTTATTTC 59.735 41.667 7.64 5.00 0.00 2.17
374 379 3.786635 AGATCGAAGACAGAATTTCCGG 58.213 45.455 0.00 0.00 42.51 5.14
383 388 7.385205 TCTTTGTAAGGAAAAGATCGAAGACAG 59.615 37.037 0.00 0.00 38.43 3.51
384 389 7.214381 TCTTTGTAAGGAAAAGATCGAAGACA 58.786 34.615 0.00 0.00 38.43 3.41
413 418 1.302192 TGGCACAAGACGGTTAGGC 60.302 57.895 0.00 0.00 31.92 3.93
416 421 0.398696 ATGGTGGCACAAGACGGTTA 59.601 50.000 20.82 0.00 44.16 2.85
444 449 4.600692 TTGTGTGCTTGAGCTAAGTAGA 57.399 40.909 4.44 0.00 42.66 2.59
447 452 4.136796 TGAATTGTGTGCTTGAGCTAAGT 58.863 39.130 4.44 0.00 42.66 2.24
464 469 8.885722 GTTGACAATGCAATTTATGGATGAATT 58.114 29.630 0.00 0.00 39.46 2.17
465 470 8.041919 TGTTGACAATGCAATTTATGGATGAAT 58.958 29.630 0.00 0.00 39.46 2.57
468 473 7.117956 TGTTGTTGACAATGCAATTTATGGATG 59.882 33.333 0.00 0.00 39.46 3.51
489 494 5.239963 CCTCGTTAAGTGGGTTTAATGTTGT 59.760 40.000 0.00 0.00 33.36 3.32
495 500 7.585579 AATTTTCCTCGTTAAGTGGGTTTAA 57.414 32.000 0.00 0.00 34.38 1.52
500 505 4.234574 GCAAATTTTCCTCGTTAAGTGGG 58.765 43.478 0.00 0.00 34.38 4.61
501 506 4.679654 GTGCAAATTTTCCTCGTTAAGTGG 59.320 41.667 0.00 0.00 34.90 4.00
509 514 4.168760 GGAATCAGTGCAAATTTTCCTCG 58.831 43.478 10.81 0.00 31.90 4.63
514 519 4.686191 TGGTGGAATCAGTGCAAATTTT 57.314 36.364 0.00 0.00 0.00 1.82
515 520 4.895668 ATGGTGGAATCAGTGCAAATTT 57.104 36.364 0.00 0.00 0.00 1.82
534 539 9.994432 GTTTCTCATGTGGTTAGATTCTTTATG 57.006 33.333 0.00 0.00 0.00 1.90
565 573 5.983333 ATCTCAGATGGTTGGTTATTCCT 57.017 39.130 0.00 0.00 37.07 3.36
885 907 0.882474 ACCTCAGGTTCTTCGACGAG 59.118 55.000 0.00 0.00 27.29 4.18
889 911 0.966920 GACCACCTCAGGTTCTTCGA 59.033 55.000 0.00 0.00 43.38 3.71
892 914 1.143073 GTTGGACCACCTCAGGTTCTT 59.857 52.381 0.00 0.00 43.38 2.52
902 924 1.228154 GGTGACTGGTTGGACCACC 60.228 63.158 0.00 0.00 44.79 4.61
1410 1453 0.038166 TGTCAGACCCCAATTCCTGC 59.962 55.000 0.00 0.00 0.00 4.85
1631 1674 0.378257 ACAATAAGCGCATGCCTTCG 59.622 50.000 20.29 14.15 44.31 3.79
1664 1707 4.023707 CAGACAAACCAAGTCCTCATCAAC 60.024 45.833 0.00 0.00 36.68 3.18
1677 1720 1.152777 CAGGGGCACAGACAAACCA 60.153 57.895 0.00 0.00 0.00 3.67
1699 1742 6.337356 CAAACCGTAAATCTATTGCCCAAAT 58.663 36.000 0.00 0.00 0.00 2.32
1714 1758 2.628657 CCCATTTTCCACCAAACCGTAA 59.371 45.455 0.00 0.00 0.00 3.18
1717 1761 0.320050 CCCCATTTTCCACCAAACCG 59.680 55.000 0.00 0.00 0.00 4.44
1720 1764 1.347062 GAGCCCCATTTTCCACCAAA 58.653 50.000 0.00 0.00 0.00 3.28
1752 1796 5.450965 GCTAAATCTTGTCCCCAACATGATG 60.451 44.000 0.00 0.00 46.52 3.07
1881 1925 3.792956 GCCAAATCACACTGCATTATTCG 59.207 43.478 0.00 0.00 0.00 3.34
1924 1968 7.659390 ACATGATGCGAAAAATAAAAGGGAAAA 59.341 29.630 0.00 0.00 0.00 2.29
2020 2064 5.163468 TGTCTGAGAGGAACAATATCAGAGC 60.163 44.000 3.57 1.25 45.09 4.09
2062 2106 4.590850 AAAAGAAGTGGAAGATGCCAAC 57.409 40.909 0.00 0.00 40.20 3.77
2119 2163 2.103263 GGTAGGACTGGCATCTAACAGG 59.897 54.545 0.00 0.00 39.00 4.00
2184 2229 1.098050 AAATGAACAGAGGGCGCATC 58.902 50.000 10.83 6.76 0.00 3.91
2371 2418 7.578310 AAAGATGCTGCATATATGTGAGTTT 57.422 32.000 16.23 0.00 0.00 2.66
2372 2419 7.578310 AAAAGATGCTGCATATATGTGAGTT 57.422 32.000 16.23 0.00 0.00 3.01
2373 2420 7.255381 GGAAAAAGATGCTGCATATATGTGAGT 60.255 37.037 16.23 0.00 0.00 3.41
2407 2454 7.509141 AACATCACATCATGTACAAACTGAA 57.491 32.000 0.00 0.00 35.87 3.02
2469 2516 5.715434 TTCCCCATAAGCTAACACAAAAC 57.285 39.130 0.00 0.00 0.00 2.43
2707 2754 6.985188 TTTGTGTAGAATGCTCAGGATAAC 57.015 37.500 0.00 0.00 0.00 1.89
3284 3332 7.207383 TGATACCTGTGTAGATTCAAATACGG 58.793 38.462 0.00 0.00 0.00 4.02
3419 3467 8.154203 TGATGTTAGTCACAGAAATCCAAAGTA 58.846 33.333 0.00 0.00 39.40 2.24
3425 3473 7.335422 ACAAGATGATGTTAGTCACAGAAATCC 59.665 37.037 0.00 0.00 39.40 3.01
3776 3826 0.040958 GCTGCTTCACTTTGTCACGG 60.041 55.000 0.00 0.00 0.00 4.94
3872 3922 8.893727 ACATTGCCTAGTTACAGTTAATCAATC 58.106 33.333 0.00 0.00 0.00 2.67
3968 4019 8.149973 ACACACAACAAGTAGGTTAATTAGTG 57.850 34.615 0.00 0.00 0.00 2.74
4016 4067 2.480845 GGACATGCGGGTCAACTATAC 58.519 52.381 9.43 0.00 39.59 1.47
4038 4089 7.227910 TCAAAACGTTAATCTAGCCAAGAGTTT 59.772 33.333 0.00 0.00 37.74 2.66
4069 4120 8.661352 ACCAAAAATCCAAAACTACTTTGATG 57.339 30.769 0.00 0.00 46.35 3.07
4150 4454 6.360370 AGAAGTGCTATCTAGTCCAAAACA 57.640 37.500 0.00 0.00 0.00 2.83
4161 4465 9.790344 AAGCATAATTTCATAGAAGTGCTATCT 57.210 29.630 0.00 0.00 40.44 1.98
4236 4540 5.553721 GCTAATGTTTTTAGCTTTGCATGC 58.446 37.500 11.82 11.82 42.91 4.06
4405 4709 9.723447 ATAATACTTACGCATCAGATATCGAAG 57.277 33.333 10.27 10.67 0.00 3.79
4746 5050 4.494199 GCAGCAGTAAACTATTAACAGGCG 60.494 45.833 0.00 0.00 0.00 5.52
4994 5298 4.513692 GCATGCCCGTATTATACTTTGACA 59.486 41.667 6.36 0.00 0.00 3.58
5275 5580 1.554160 ACCTCAGAGTCTGATGCCAAG 59.446 52.381 22.90 10.20 39.92 3.61
5279 5584 0.901124 ACCACCTCAGAGTCTGATGC 59.099 55.000 22.90 0.00 39.92 3.91
5285 5590 4.511826 CACAAAAAGTACCACCTCAGAGTC 59.488 45.833 0.00 0.00 0.00 3.36
5330 5660 7.168219 TGAATCCAACATTTGTAGAGTAAGCT 58.832 34.615 0.00 0.00 0.00 3.74
5367 5697 4.619160 GCAGGGAATCCAAACAACATTCTC 60.619 45.833 0.09 0.00 34.83 2.87
5413 5743 3.823304 CCCAAGAGTTTTCTTCAAGGGAG 59.177 47.826 5.63 0.00 42.65 4.30
5415 5745 3.823304 CTCCCAAGAGTTTTCTTCAAGGG 59.177 47.826 5.31 5.31 41.71 3.95
5430 5760 1.074566 AGTTTTCTGCCTCCTCCCAAG 59.925 52.381 0.00 0.00 0.00 3.61
5441 5771 3.141767 ACTAGGACCCAAGTTTTCTGC 57.858 47.619 0.00 0.00 0.00 4.26
5454 5784 8.603242 TCACAAGAAAACTCATTTACTAGGAC 57.397 34.615 0.00 0.00 0.00 3.85
5496 5826 2.024414 CAGGGATTTAAAAGGGAGCGG 58.976 52.381 0.00 0.00 0.00 5.52
5582 5912 0.690744 TGAATCCATGGCTCTCCGGA 60.691 55.000 6.96 2.93 34.14 5.14
5657 5987 1.952193 AACAACACCAAATGCCTTGC 58.048 45.000 0.00 0.00 33.27 4.01
5665 5995 5.892119 TGGGTTGACTTATAACAACACCAAA 59.108 36.000 15.05 0.00 46.01 3.28
5667 5997 5.050126 TGGGTTGACTTATAACAACACCA 57.950 39.130 15.05 15.89 46.01 4.17
5672 6002 6.366340 TGGTTCTTGGGTTGACTTATAACAA 58.634 36.000 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.