Multiple sequence alignment - TraesCS2A01G204900

Loading Multiple Alignment...

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 TraesCS2A01G204900 chr2A 100.000 3584 0 0 1 3584 182312129 182308546 0.000000e+00 6619.0
1 TraesCS2A01G204900 chr2D 94.167 3103 103 21 2 3049 168233704 168236783 0.000000e+00 4656.0
2 TraesCS2A01G204900 chr2D 86.558 491 37 13 3048 3530 168237807 168238276 6.860000e-142 514.0
3 TraesCS2A01G204900 chr2D 80.516 349 53 13 3232 3571 237982427 237982769 1.650000e-63 254.0
4 TraesCS2A01G204900 chr2D 86.458 96 12 1 28 122 546414381 546414476 1.760000e-18 104.0
5 TraesCS2A01G204900 chr2D 93.878 49 2 1 30 78 637030847 637030800 4.960000e-09 73.1
6 TraesCS2A01G204900 chr2B 94.157 2704 75 33 249 2919 229995039 229992386 0.000000e+00 4041.0
7 TraesCS2A01G204900 chr2B 98.492 199 3 0 2912 3110 229991985 229991787 5.690000e-93 351.0
8 TraesCS2A01G204900 chr2B 87.432 183 18 3 3391 3571 377238603 377238782 4.690000e-49 206.0
9 TraesCS2A01G204900 chr2B 91.525 118 7 3 3109 3223 229991630 229991513 3.700000e-35 159.0
10 TraesCS2A01G204900 chr2B 83.673 147 15 3 2 148 230024223 230024086 2.900000e-26 130.0
11 TraesCS2A01G204900 chr4A 89.545 1540 122 23 1000 2522 613667356 613668873 0.000000e+00 1916.0
12 TraesCS2A01G204900 chr5D 90.385 1352 104 19 1191 2526 556154727 556153386 0.000000e+00 1753.0
13 TraesCS2A01G204900 chr7B 81.138 334 41 13 3238 3571 247178470 247178159 7.680000e-62 248.0
14 TraesCS2A01G204900 chr7B 88.398 181 20 1 3391 3571 314567518 314567697 2.170000e-52 217.0
15 TraesCS2A01G204900 chr7B 86.740 181 24 0 3391 3571 314350635 314350815 6.070000e-48 202.0
16 TraesCS2A01G204900 chr7B 83.333 84 6 7 64 143 61862455 61862376 1.790000e-08 71.3
17 TraesCS2A01G204900 chr7B 79.439 107 16 6 44 145 634521323 634521428 1.790000e-08 71.3
18 TraesCS2A01G204900 chr5B 88.830 188 18 3 3391 3576 293580400 293580214 1.000000e-55 228.0
19 TraesCS2A01G204900 chr5B 88.764 178 18 2 3400 3576 293610840 293610664 2.170000e-52 217.0
20 TraesCS2A01G204900 chr3A 88.770 187 19 2 3391 3576 174130620 174130435 1.000000e-55 228.0
21 TraesCS2A01G204900 chr5A 87.850 107 12 1 31 137 473361645 473361750 1.350000e-24 124.0
22 TraesCS2A01G204900 chr7A 84.091 132 15 6 17 145 463674687 463674559 4.860000e-24 122.0
23 TraesCS2A01G204900 chr3B 86.667 105 11 2 26 128 665489507 665489610 2.920000e-21 113.0
24 TraesCS2A01G204900 chr3B 87.097 93 11 1 36 128 630871629 630871538 1.760000e-18 104.0


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 TraesCS2A01G204900 chr2A 182308546 182312129 3583 True 6619 6619 100.000000 1 3584 1 chr2A.!!$R1 3583
1 TraesCS2A01G204900 chr2D 168233704 168238276 4572 False 2585 4656 90.362500 2 3530 2 chr2D.!!$F3 3528
2 TraesCS2A01G204900 chr2B 229991513 229995039 3526 True 1517 4041 94.724667 249 3223 3 chr2B.!!$R2 2974
3 TraesCS2A01G204900 chr4A 613667356 613668873 1517 False 1916 1916 89.545000 1000 2522 1 chr4A.!!$F1 1522
4 TraesCS2A01G204900 chr5D 556153386 556154727 1341 True 1753 1753 90.385000 1191 2526 1 chr5D.!!$R1 1335

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
602 621 0.109504 CTAGCTAATCGCCGAGCTCC 60.110 60.0 8.47 0.0 46.08 4.7 F
681 700 0.652592 GAGCGCCGTAGTACGTAGAA 59.347 55.0 20.60 0.0 40.58 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2055 2123 0.173708 CGCTCAGGTAGAGGTTGGAC 59.826 60.0 0.00 0.0 44.86 4.02 R
2677 2752 0.580104 GTTCTCACGTGTTGGGTTCG 59.420 55.0 16.51 0.0 0.00 3.95 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
46 47 3.316588 TGATTGCTAGATCTCAGTCGACC 59.683 47.826 13.01 0.00 0.00 4.79
73 74 5.844004 ACTTAACGAAGTCTCAGTCAATGT 58.156 37.500 0.00 0.00 45.00 2.71
96 97 9.645059 ATGTTATATTCGTGAGATCTTATGTGG 57.355 33.333 6.61 0.00 41.60 4.17
110 111 6.479972 TCTTATGTGGAGATCCGTGTAAAT 57.520 37.500 0.00 0.00 39.43 1.40
121 122 9.556030 GGAGATCCGTGTAAATTTTTCTTTTAG 57.444 33.333 0.00 0.00 0.00 1.85
161 162 3.826236 TGTTCTACTCTTTCCGTCTCG 57.174 47.619 0.00 0.00 0.00 4.04
163 164 3.058432 TGTTCTACTCTTTCCGTCTCGTG 60.058 47.826 0.00 0.00 0.00 4.35
201 202 4.390909 GCTAGTGTGGTGTTATAAACGCTT 59.609 41.667 6.44 0.00 41.52 4.68
207 208 9.169592 AGTGTGGTGTTATAAACGCTTTTATAT 57.830 29.630 14.16 0.00 39.08 0.86
208 209 9.777575 GTGTGGTGTTATAAACGCTTTTATATT 57.222 29.630 14.16 0.00 39.08 1.28
283 287 6.146347 GGTAACTGAAACAGTCAAGAGACATC 59.854 42.308 4.88 0.00 44.62 3.06
315 319 6.531503 TTCCAAAACCAAGTAAACACATGA 57.468 33.333 0.00 0.00 0.00 3.07
320 324 3.219281 ACCAAGTAAACACATGACACCC 58.781 45.455 0.00 0.00 0.00 4.61
333 337 4.162320 ACATGACACCCTAGAAGTACCATG 59.838 45.833 0.00 16.31 34.78 3.66
357 369 2.523015 CCATGCGAGATTTTTGTGAGC 58.477 47.619 0.00 0.00 0.00 4.26
364 376 1.551883 AGATTTTTGTGAGCATGGCCC 59.448 47.619 0.00 0.00 0.00 5.80
409 421 0.183731 CCATCCTGGAAAGGGTAGCC 59.816 60.000 1.60 1.60 40.96 3.93
416 428 3.181450 CCTGGAAAGGGTAGCCAAGATAG 60.181 52.174 14.62 5.72 0.00 2.08
418 430 4.627015 TGGAAAGGGTAGCCAAGATAGTA 58.373 43.478 14.62 0.00 0.00 1.82
419 431 4.407945 TGGAAAGGGTAGCCAAGATAGTAC 59.592 45.833 14.62 0.00 0.00 2.73
602 621 0.109504 CTAGCTAATCGCCGAGCTCC 60.110 60.000 8.47 0.00 46.08 4.70
618 637 1.009829 CTCCTACGCAAGAACATGCC 58.990 55.000 0.00 0.00 43.47 4.40
680 699 1.154205 GGAGCGCCGTAGTACGTAGA 61.154 60.000 20.60 0.00 40.58 2.59
681 700 0.652592 GAGCGCCGTAGTACGTAGAA 59.347 55.000 20.60 0.00 40.58 2.10
684 703 1.332728 GCGCCGTAGTACGTAGAAGAG 60.333 57.143 20.60 8.34 40.58 2.85
685 704 1.929836 CGCCGTAGTACGTAGAAGAGT 59.070 52.381 20.60 0.00 40.58 3.24
687 706 2.031437 GCCGTAGTACGTAGAAGAGTGG 59.969 54.545 20.60 3.28 40.58 4.00
688 707 2.611292 CCGTAGTACGTAGAAGAGTGGG 59.389 54.545 20.60 0.00 40.58 4.61
690 709 3.686726 CGTAGTACGTAGAAGAGTGGGTT 59.313 47.826 14.62 0.00 36.74 4.11
691 710 4.870426 CGTAGTACGTAGAAGAGTGGGTTA 59.130 45.833 14.62 0.00 36.74 2.85
694 713 2.174360 ACGTAGAAGAGTGGGTTACCC 58.826 52.381 14.66 14.66 45.71 3.69
696 715 3.010584 ACGTAGAAGAGTGGGTTACCCTA 59.989 47.826 22.29 5.21 45.70 3.53
714 741 2.357154 CCTAATACCCCTATGCATGGCC 60.357 54.545 10.16 0.00 0.00 5.36
754 781 4.083431 CCTCGGGTCATCAAGTATACTACG 60.083 50.000 5.65 0.72 0.00 3.51
803 831 0.911769 TGGATCTCACATGTGTCCCC 59.088 55.000 24.63 19.79 0.00 4.81
844 872 4.933064 GCAGCTCGTCGATCCCCG 62.933 72.222 0.00 0.00 40.25 5.73
936 974 0.765510 AAATACCCCCGCTCTCATCC 59.234 55.000 0.00 0.00 0.00 3.51
1003 1056 1.098712 ACACCAAACCGTGCGAATGT 61.099 50.000 0.00 0.00 37.25 2.71
1052 1105 2.791868 GCCACAAAACAAGGCCGGT 61.792 57.895 1.90 0.00 42.58 5.28
1101 1154 3.943479 GACGTACATGGGCGCCACA 62.943 63.158 30.85 23.70 35.80 4.17
1129 1182 3.394836 AGCTCCTCAAGGCCGTCC 61.395 66.667 0.00 0.00 34.44 4.79
1320 1382 2.567049 GTGGTCTCGGAGTGGTCG 59.433 66.667 4.69 0.00 0.00 4.79
1404 1466 4.821589 GGCGGCTTCCTCCTCACG 62.822 72.222 0.00 0.00 0.00 4.35
1569 1631 4.666532 GTTGGCACGTGCACGCTC 62.667 66.667 38.60 27.41 44.43 5.03
2055 2123 4.636435 AACGTCGGCAACCTGGGG 62.636 66.667 0.00 0.00 0.00 4.96
2154 2222 3.371097 GATCAACCGCCGGAGCTCA 62.371 63.158 11.71 0.00 36.60 4.26
2586 2658 3.581024 AACAGCGACCTCGTGTAATTA 57.419 42.857 0.00 0.00 42.22 1.40
2622 2697 6.676213 GCGGGTTGATGTACAAAGTTAATACC 60.676 42.308 0.00 0.00 40.36 2.73
2623 2698 6.372103 CGGGTTGATGTACAAAGTTAATACCA 59.628 38.462 0.00 0.00 40.36 3.25
2624 2699 7.066525 CGGGTTGATGTACAAAGTTAATACCAT 59.933 37.037 0.00 0.00 40.36 3.55
2625 2700 8.188139 GGGTTGATGTACAAAGTTAATACCATG 58.812 37.037 0.00 0.00 40.36 3.66
2651 2726 5.083122 TGCTCCCATTCCAATCAAGTAAAA 58.917 37.500 0.00 0.00 0.00 1.52
2652 2727 5.047377 TGCTCCCATTCCAATCAAGTAAAAC 60.047 40.000 0.00 0.00 0.00 2.43
2677 2752 1.369091 CCAGGTCGCAGCACATTACC 61.369 60.000 0.00 0.00 0.00 2.85
2770 2859 1.081376 GTCGTCCGAGTCACTGGTG 60.081 63.158 0.00 0.00 0.00 4.17
2771 2860 1.228033 TCGTCCGAGTCACTGGTGA 60.228 57.895 0.00 0.00 37.24 4.02
2816 2905 7.615365 AGATGAGAGATCGGAGCTTATTCTAAT 59.385 37.037 0.00 0.00 0.00 1.73
2935 3434 0.248336 TGTCTACTTATGTCGGCGCG 60.248 55.000 0.00 0.00 0.00 6.86
3191 4878 7.050377 AGGAAATGTTAATGATGAGACGTCAT 58.950 34.615 19.50 3.51 46.75 3.06
3244 4937 0.030092 TTGGGGATAGCTGGTAGGCT 60.030 55.000 0.00 0.00 45.29 4.58
3248 4941 1.277557 GGGATAGCTGGTAGGCTCATG 59.722 57.143 0.00 0.00 42.97 3.07
3251 4944 3.306641 GGATAGCTGGTAGGCTCATGAAG 60.307 52.174 0.00 0.00 42.97 3.02
3252 4945 1.871418 AGCTGGTAGGCTCATGAAGA 58.129 50.000 0.00 0.00 38.24 2.87
3276 4969 5.088739 GTCAAAATATCACAAAGCACGAGG 58.911 41.667 0.00 0.00 0.00 4.63
3286 4979 0.108585 AAGCACGAGGTCCACACATT 59.891 50.000 0.00 0.00 0.00 2.71
3289 4982 1.067142 GCACGAGGTCCACACATTAGA 60.067 52.381 0.00 0.00 0.00 2.10
3302 4995 5.760253 CCACACATTAGATGGGTTCAGATAC 59.240 44.000 0.00 0.00 46.78 2.24
3306 4999 8.055181 ACACATTAGATGGGTTCAGATACATTT 58.945 33.333 0.00 0.00 46.78 2.32
3316 5009 8.663167 TGGGTTCAGATACATTTCATATCAGAT 58.337 33.333 0.00 0.00 32.37 2.90
3368 5061 2.945456 ACTAGGACGATGTCTATGCCA 58.055 47.619 0.00 0.00 32.47 4.92
3378 5071 1.200519 GTCTATGCCACCACTACCCA 58.799 55.000 0.00 0.00 0.00 4.51
3397 5090 1.683385 CAGGTGATCATCTACTCGGCA 59.317 52.381 8.51 0.00 0.00 5.69
3441 5134 1.845809 GACCAACAGTCAGCAAGGCG 61.846 60.000 0.00 0.00 45.55 5.52
3476 5169 9.775854 ATCATCTTCATAGTGAAGGTTTCATAG 57.224 33.333 16.99 0.99 44.88 2.23
3519 5212 9.368674 CATTGATGCTCCATTTTGTAACATAAA 57.631 29.630 0.00 0.00 0.00 1.40
3530 5223 7.519032 TTTTGTAACATAAAAGGTGAGAGGG 57.481 36.000 0.00 0.00 0.00 4.30
3531 5224 5.836024 TGTAACATAAAAGGTGAGAGGGT 57.164 39.130 0.00 0.00 0.00 4.34
3532 5225 5.556915 TGTAACATAAAAGGTGAGAGGGTG 58.443 41.667 0.00 0.00 0.00 4.61
3533 5226 3.721087 ACATAAAAGGTGAGAGGGTGG 57.279 47.619 0.00 0.00 0.00 4.61
3534 5227 2.290960 ACATAAAAGGTGAGAGGGTGGC 60.291 50.000 0.00 0.00 0.00 5.01
3535 5228 0.323629 TAAAAGGTGAGAGGGTGGCG 59.676 55.000 0.00 0.00 0.00 5.69
3536 5229 1.705997 AAAAGGTGAGAGGGTGGCGT 61.706 55.000 0.00 0.00 0.00 5.68
3537 5230 0.834687 AAAGGTGAGAGGGTGGCGTA 60.835 55.000 0.00 0.00 0.00 4.42
3538 5231 1.542187 AAGGTGAGAGGGTGGCGTAC 61.542 60.000 0.00 0.00 0.00 3.67
3539 5232 1.982938 GGTGAGAGGGTGGCGTACT 60.983 63.158 0.00 0.00 0.00 2.73
3540 5233 1.511768 GTGAGAGGGTGGCGTACTC 59.488 63.158 0.00 0.00 0.00 2.59
3541 5234 0.966370 GTGAGAGGGTGGCGTACTCT 60.966 60.000 4.61 4.61 44.88 3.24
3542 5235 0.622136 TGAGAGGGTGGCGTACTCTA 59.378 55.000 4.90 0.00 41.28 2.43
3543 5236 1.214673 TGAGAGGGTGGCGTACTCTAT 59.785 52.381 4.90 0.00 41.28 1.98
3544 5237 2.440627 TGAGAGGGTGGCGTACTCTATA 59.559 50.000 4.90 0.00 41.28 1.31
3545 5238 3.074094 TGAGAGGGTGGCGTACTCTATAT 59.926 47.826 4.90 0.00 41.28 0.86
3546 5239 4.287845 TGAGAGGGTGGCGTACTCTATATA 59.712 45.833 4.90 0.00 41.28 0.86
3547 5240 5.221986 TGAGAGGGTGGCGTACTCTATATAA 60.222 44.000 4.90 0.00 41.28 0.98
3548 5241 5.254901 AGAGGGTGGCGTACTCTATATAAG 58.745 45.833 3.27 0.00 41.28 1.73
3549 5242 3.762823 AGGGTGGCGTACTCTATATAAGC 59.237 47.826 0.00 0.00 38.72 3.09
3550 5243 3.119209 GGGTGGCGTACTCTATATAAGCC 60.119 52.174 2.49 2.49 44.61 4.35
3553 5246 4.107363 GGCGTACTCTATATAAGCCACC 57.893 50.000 4.40 0.00 44.02 4.61
3554 5247 3.119209 GGCGTACTCTATATAAGCCACCC 60.119 52.174 4.40 0.00 44.02 4.61
3555 5248 3.119209 GCGTACTCTATATAAGCCACCCC 60.119 52.174 0.00 0.00 0.00 4.95
3556 5249 3.446516 CGTACTCTATATAAGCCACCCCC 59.553 52.174 0.00 0.00 0.00 5.40
3557 5250 3.945283 ACTCTATATAAGCCACCCCCT 57.055 47.619 0.00 0.00 0.00 4.79
3558 5251 5.574326 CGTACTCTATATAAGCCACCCCCTA 60.574 48.000 0.00 0.00 0.00 3.53
3559 5252 4.685807 ACTCTATATAAGCCACCCCCTAC 58.314 47.826 0.00 0.00 0.00 3.18
3560 5253 4.031611 CTCTATATAAGCCACCCCCTACC 58.968 52.174 0.00 0.00 0.00 3.18
3561 5254 2.827528 ATATAAGCCACCCCCTACCA 57.172 50.000 0.00 0.00 0.00 3.25
3562 5255 1.810455 TATAAGCCACCCCCTACCAC 58.190 55.000 0.00 0.00 0.00 4.16
3563 5256 0.253441 ATAAGCCACCCCCTACCACA 60.253 55.000 0.00 0.00 0.00 4.17
3564 5257 0.253441 TAAGCCACCCCCTACCACAT 60.253 55.000 0.00 0.00 0.00 3.21
3565 5258 0.253441 AAGCCACCCCCTACCACATA 60.253 55.000 0.00 0.00 0.00 2.29
3566 5259 0.694444 AGCCACCCCCTACCACATAG 60.694 60.000 0.00 0.00 0.00 2.23
3567 5260 1.837090 CCACCCCCTACCACATAGC 59.163 63.158 0.00 0.00 0.00 2.97
3568 5261 0.694444 CCACCCCCTACCACATAGCT 60.694 60.000 0.00 0.00 0.00 3.32
3569 5262 0.759346 CACCCCCTACCACATAGCTC 59.241 60.000 0.00 0.00 0.00 4.09
3570 5263 0.759436 ACCCCCTACCACATAGCTCG 60.759 60.000 0.00 0.00 0.00 5.03
3571 5264 1.472662 CCCCCTACCACATAGCTCGG 61.473 65.000 0.00 0.00 0.00 4.63
3572 5265 1.472662 CCCCTACCACATAGCTCGGG 61.473 65.000 0.00 0.00 0.00 5.14
3573 5266 1.472662 CCCTACCACATAGCTCGGGG 61.473 65.000 2.76 2.76 0.00 5.73
3574 5267 1.472662 CCTACCACATAGCTCGGGGG 61.473 65.000 9.09 6.78 0.00 5.40
3575 5268 2.100879 CTACCACATAGCTCGGGGGC 62.101 65.000 9.09 0.00 0.00 5.80
3576 5269 4.256180 CCACATAGCTCGGGGGCC 62.256 72.222 0.00 0.00 0.00 5.80
3577 5270 3.479203 CACATAGCTCGGGGGCCA 61.479 66.667 4.39 0.00 0.00 5.36
3578 5271 2.448542 ACATAGCTCGGGGGCCAT 60.449 61.111 4.39 0.00 0.00 4.40
3579 5272 2.033141 CATAGCTCGGGGGCCATG 59.967 66.667 4.39 0.00 0.00 3.66
3580 5273 3.252284 ATAGCTCGGGGGCCATGG 61.252 66.667 7.63 7.63 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.088739 CGAACTAAAACTGCATCCAATGTC 58.911 41.667 0.00 0.00 0.00 3.06
19 20 4.677584 ACTGAGATCTAGCAATCACGAAC 58.322 43.478 0.00 0.00 0.00 3.95
22 23 3.002759 TCGACTGAGATCTAGCAATCACG 59.997 47.826 0.00 0.00 0.00 4.35
56 57 7.432545 ACGAATATAACATTGACTGAGACTTCG 59.567 37.037 0.00 0.00 36.33 3.79
72 73 9.347934 CTCCACATAAGATCTCACGAATATAAC 57.652 37.037 0.00 0.00 0.00 1.89
73 74 9.297037 TCTCCACATAAGATCTCACGAATATAA 57.703 33.333 0.00 0.00 0.00 0.98
92 93 6.001460 AGAAAAATTTACACGGATCTCCACA 58.999 36.000 0.00 0.00 35.14 4.17
93 94 6.496338 AGAAAAATTTACACGGATCTCCAC 57.504 37.500 0.00 0.00 35.14 4.02
152 153 0.806868 AACGCTATCACGAGACGGAA 59.193 50.000 0.00 0.00 36.70 4.30
177 178 3.241868 GCGTTTATAACACCACACTAGCG 60.242 47.826 0.00 0.00 0.00 4.26
207 208 7.929785 AGTTGATTGAGACTTAACGAAACCTAA 59.070 33.333 0.00 0.00 0.00 2.69
208 209 7.384115 CAGTTGATTGAGACTTAACGAAACCTA 59.616 37.037 0.00 0.00 0.00 3.08
209 210 6.202954 CAGTTGATTGAGACTTAACGAAACCT 59.797 38.462 0.00 0.00 0.00 3.50
212 213 7.207383 TCTCAGTTGATTGAGACTTAACGAAA 58.793 34.615 2.49 0.00 46.42 3.46
283 287 2.791383 TGGTTTTGGAATGTTCAGCG 57.209 45.000 0.00 0.00 0.00 5.18
315 319 3.105283 GGTCATGGTACTTCTAGGGTGT 58.895 50.000 0.00 0.00 0.00 4.16
320 324 4.342862 CATGGGGTCATGGTACTTCTAG 57.657 50.000 0.00 0.00 45.19 2.43
333 337 1.818674 ACAAAAATCTCGCATGGGGTC 59.181 47.619 10.21 0.00 0.00 4.46
364 376 7.012421 GTGCTAATCAAGGTACCCAAATCTTAG 59.988 40.741 8.74 9.68 0.00 2.18
602 621 1.258982 GATCGGCATGTTCTTGCGTAG 59.741 52.381 0.00 0.87 43.71 3.51
688 707 5.497474 CATGCATAGGGGTATTAGGGTAAC 58.503 45.833 0.00 0.00 0.00 2.50
690 709 4.108570 CCATGCATAGGGGTATTAGGGTA 58.891 47.826 0.00 0.00 0.00 3.69
691 710 2.919602 CCATGCATAGGGGTATTAGGGT 59.080 50.000 0.00 0.00 0.00 4.34
694 713 2.357154 GGGCCATGCATAGGGGTATTAG 60.357 54.545 4.39 0.00 0.00 1.73
696 715 0.409484 GGGCCATGCATAGGGGTATT 59.591 55.000 4.39 0.00 0.00 1.89
754 781 2.062636 TGTTAGAATATGGGAGGGGGC 58.937 52.381 0.00 0.00 0.00 5.80
844 872 0.772926 CGCACAAGATCGATCGCTAC 59.227 55.000 19.33 8.73 0.00 3.58
936 974 1.002868 CTGGCTGTGTGGGGAGAAG 60.003 63.158 0.00 0.00 0.00 2.85
988 1026 0.865111 TCAGACATTCGCACGGTTTG 59.135 50.000 0.00 0.00 0.00 2.93
989 1027 0.865769 GTCAGACATTCGCACGGTTT 59.134 50.000 0.00 0.00 0.00 3.27
1052 1105 4.847516 CGATCGACGGCGCCTTGA 62.848 66.667 26.68 20.01 38.46 3.02
1569 1631 2.752238 AGCTCCGTGGAGAGGACG 60.752 66.667 19.98 0.00 44.53 4.79
1833 1895 2.892334 GCTGTTGCCGTTGAGCGAA 61.892 57.895 0.00 0.00 44.77 4.70
2055 2123 0.173708 CGCTCAGGTAGAGGTTGGAC 59.826 60.000 0.00 0.00 44.86 4.02
2586 2658 3.634910 ACATCAACCCGCAGTTTAGTTTT 59.365 39.130 0.00 0.00 36.18 2.43
2622 2697 1.116308 TTGGAATGGGAGCATGCATG 58.884 50.000 22.70 22.70 0.00 4.06
2623 2698 1.968493 GATTGGAATGGGAGCATGCAT 59.032 47.619 21.98 4.75 0.00 3.96
2624 2699 1.342175 TGATTGGAATGGGAGCATGCA 60.342 47.619 21.98 0.00 0.00 3.96
2625 2700 1.405872 TGATTGGAATGGGAGCATGC 58.594 50.000 10.51 10.51 0.00 4.06
2677 2752 0.580104 GTTCTCACGTGTTGGGTTCG 59.420 55.000 16.51 0.00 0.00 3.95
2729 2812 9.950680 CGACCAGCTGTTTTATAATAATTGAAT 57.049 29.630 13.81 0.00 0.00 2.57
2774 2863 5.311265 TCTCATCTAATCATTGGCATCACC 58.689 41.667 0.00 0.00 39.84 4.02
2775 2864 6.228995 TCTCTCATCTAATCATTGGCATCAC 58.771 40.000 0.00 0.00 0.00 3.06
2776 2865 6.429521 TCTCTCATCTAATCATTGGCATCA 57.570 37.500 0.00 0.00 0.00 3.07
2816 2905 2.097036 CCAAGCAGATTCCATGCAGAA 58.903 47.619 0.00 0.00 46.31 3.02
2935 3434 2.482721 ACACGGCTATGTGCTTTTACAC 59.517 45.455 4.56 0.00 43.74 2.90
3191 4878 4.422073 TGCTCAAGAAAAACCTCTGAGA 57.578 40.909 6.17 0.00 0.00 3.27
3234 4921 1.484240 ACTCTTCATGAGCCTACCAGC 59.516 52.381 0.00 0.00 46.41 4.85
3235 4922 2.762887 TGACTCTTCATGAGCCTACCAG 59.237 50.000 0.00 0.00 46.41 4.00
3236 4923 2.820178 TGACTCTTCATGAGCCTACCA 58.180 47.619 0.00 0.00 46.41 3.25
3244 4937 8.239314 GCTTTGTGATATTTTGACTCTTCATGA 58.761 33.333 0.00 0.00 0.00 3.07
3248 4941 6.521133 CGTGCTTTGTGATATTTTGACTCTTC 59.479 38.462 0.00 0.00 0.00 2.87
3251 4944 5.927030 TCGTGCTTTGTGATATTTTGACTC 58.073 37.500 0.00 0.00 0.00 3.36
3252 4945 5.106555 CCTCGTGCTTTGTGATATTTTGACT 60.107 40.000 0.00 0.00 0.00 3.41
3255 4948 5.046910 ACCTCGTGCTTTGTGATATTTTG 57.953 39.130 0.00 0.00 0.00 2.44
3261 4954 0.396435 TGGACCTCGTGCTTTGTGAT 59.604 50.000 0.00 0.00 0.00 3.06
3262 4955 0.531974 GTGGACCTCGTGCTTTGTGA 60.532 55.000 0.00 0.00 0.00 3.58
3263 4956 0.813610 TGTGGACCTCGTGCTTTGTG 60.814 55.000 0.00 0.00 0.00 3.33
3264 4957 0.814010 GTGTGGACCTCGTGCTTTGT 60.814 55.000 0.00 0.00 0.00 2.83
3265 4958 0.813610 TGTGTGGACCTCGTGCTTTG 60.814 55.000 0.00 0.00 0.00 2.77
3276 4969 3.941483 CTGAACCCATCTAATGTGTGGAC 59.059 47.826 0.00 0.00 34.94 4.02
3289 4982 8.663167 TCTGATATGAAATGTATCTGAACCCAT 58.337 33.333 0.00 0.00 35.17 4.00
3330 5023 4.275443 CCTAGTAGACGGATAGTGTTGTCC 59.725 50.000 0.00 0.00 31.75 4.02
3331 5024 5.007528 GTCCTAGTAGACGGATAGTGTTGTC 59.992 48.000 0.00 0.00 0.00 3.18
3332 5025 4.880696 GTCCTAGTAGACGGATAGTGTTGT 59.119 45.833 0.00 0.00 0.00 3.32
3333 5026 5.421212 GTCCTAGTAGACGGATAGTGTTG 57.579 47.826 0.00 0.00 0.00 3.33
3351 5044 0.753262 GGTGGCATAGACATCGTCCT 59.247 55.000 0.00 0.00 32.18 3.85
3368 5061 2.119495 GATGATCACCTGGGTAGTGGT 58.881 52.381 0.00 0.00 35.87 4.16
3378 5071 1.959985 CTGCCGAGTAGATGATCACCT 59.040 52.381 0.00 0.00 0.00 4.00
3397 5090 3.732169 CGCACGTCTGAATGAGTCATACT 60.732 47.826 5.94 0.00 35.07 2.12
3408 5101 0.103390 TTGGTCTTCGCACGTCTGAA 59.897 50.000 0.00 0.00 0.00 3.02
3409 5102 0.596600 GTTGGTCTTCGCACGTCTGA 60.597 55.000 0.00 0.00 0.00 3.27
3411 5104 0.597637 CTGTTGGTCTTCGCACGTCT 60.598 55.000 0.00 0.00 0.00 4.18
3476 5169 4.081406 TCAATGCCATAATATCAGCCCAC 58.919 43.478 0.00 0.00 0.00 4.61
3519 5212 1.229082 TACGCCACCCTCTCACCTT 60.229 57.895 0.00 0.00 0.00 3.50
3530 5223 4.778534 TGGCTTATATAGAGTACGCCAC 57.221 45.455 0.00 0.00 40.32 5.01
3531 5224 3.508793 GGTGGCTTATATAGAGTACGCCA 59.491 47.826 0.00 0.00 42.17 5.69
3532 5225 3.119209 GGGTGGCTTATATAGAGTACGCC 60.119 52.174 0.00 0.00 37.09 5.68
3533 5226 3.119209 GGGGTGGCTTATATAGAGTACGC 60.119 52.174 0.00 0.00 0.00 4.42
3534 5227 3.446516 GGGGGTGGCTTATATAGAGTACG 59.553 52.174 0.00 0.00 0.00 3.67
3535 5228 4.685807 AGGGGGTGGCTTATATAGAGTAC 58.314 47.826 0.00 0.00 0.00 2.73
3536 5229 5.281927 GGTAGGGGGTGGCTTATATAGAGTA 60.282 48.000 0.00 0.00 0.00 2.59
3537 5230 3.945283 AGGGGGTGGCTTATATAGAGT 57.055 47.619 0.00 0.00 0.00 3.24
3538 5231 4.031611 GGTAGGGGGTGGCTTATATAGAG 58.968 52.174 0.00 0.00 0.00 2.43
3539 5232 3.406845 TGGTAGGGGGTGGCTTATATAGA 59.593 47.826 0.00 0.00 0.00 1.98
3540 5233 3.518303 GTGGTAGGGGGTGGCTTATATAG 59.482 52.174 0.00 0.00 0.00 1.31
3541 5234 3.116277 TGTGGTAGGGGGTGGCTTATATA 60.116 47.826 0.00 0.00 0.00 0.86
3542 5235 2.345560 GTGGTAGGGGGTGGCTTATAT 58.654 52.381 0.00 0.00 0.00 0.86
3543 5236 1.009799 TGTGGTAGGGGGTGGCTTATA 59.990 52.381 0.00 0.00 0.00 0.98
3544 5237 0.253441 TGTGGTAGGGGGTGGCTTAT 60.253 55.000 0.00 0.00 0.00 1.73
3545 5238 0.253441 ATGTGGTAGGGGGTGGCTTA 60.253 55.000 0.00 0.00 0.00 3.09
3546 5239 0.253441 TATGTGGTAGGGGGTGGCTT 60.253 55.000 0.00 0.00 0.00 4.35
3547 5240 0.694444 CTATGTGGTAGGGGGTGGCT 60.694 60.000 0.00 0.00 0.00 4.75
3548 5241 1.837090 CTATGTGGTAGGGGGTGGC 59.163 63.158 0.00 0.00 0.00 5.01
3549 5242 0.694444 AGCTATGTGGTAGGGGGTGG 60.694 60.000 0.00 0.00 0.00 4.61
3550 5243 0.759346 GAGCTATGTGGTAGGGGGTG 59.241 60.000 0.00 0.00 0.00 4.61
3551 5244 0.759436 CGAGCTATGTGGTAGGGGGT 60.759 60.000 0.00 0.00 0.00 4.95
3552 5245 1.472662 CCGAGCTATGTGGTAGGGGG 61.473 65.000 0.00 0.00 35.68 5.40
3553 5246 2.050269 CCGAGCTATGTGGTAGGGG 58.950 63.158 0.00 0.00 35.68 4.79
3555 5248 1.472662 CCCCCGAGCTATGTGGTAGG 61.473 65.000 0.00 0.00 38.43 3.18
3556 5249 2.050269 CCCCCGAGCTATGTGGTAG 58.950 63.158 0.00 0.00 0.00 3.18
3557 5250 2.138179 GCCCCCGAGCTATGTGGTA 61.138 63.158 0.00 0.00 0.00 3.25
3558 5251 3.480133 GCCCCCGAGCTATGTGGT 61.480 66.667 0.00 0.00 0.00 4.16
3559 5252 4.256180 GGCCCCCGAGCTATGTGG 62.256 72.222 0.00 0.00 0.00 4.17
3560 5253 2.822637 ATGGCCCCCGAGCTATGTG 61.823 63.158 0.00 0.00 32.04 3.21
3561 5254 2.448542 ATGGCCCCCGAGCTATGT 60.449 61.111 0.00 0.00 32.04 2.29
3562 5255 2.033141 CATGGCCCCCGAGCTATG 59.967 66.667 0.00 4.54 43.92 2.23
3563 5256 3.252284 CCATGGCCCCCGAGCTAT 61.252 66.667 0.00 0.00 33.73 2.97


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

AutoCloner maintained by Alex Coulton.