Multiple sequence alignment - TraesCS1B01G002700

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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 TraesCS1B01G002700 chr1B 100.000 4970 0 0 1 4970 1830429 1825460 0.000000e+00 9178.0
1 TraesCS1B01G002700 chr1B 97.454 3496 59 11 459 3941 3143539 3147017 0.000000e+00 5936.0
2 TraesCS1B01G002700 chr1B 95.562 1014 19 2 3973 4970 3147006 3148009 0.000000e+00 1600.0
3 TraesCS1B01G002700 chr1B 72.056 2913 699 86 1097 3947 683584382 683581523 0.000000e+00 763.0
4 TraesCS1B01G002700 chr2D 96.384 3180 80 15 922 4085 43670953 43674113 0.000000e+00 5203.0
5 TraesCS1B01G002700 chr2D 90.486 494 11 10 406 891 43670491 43670956 1.970000e-173 619.0
6 TraesCS1B01G002700 chr2D 96.377 276 5 1 4319 4594 43674119 43674389 2.730000e-122 449.0
7 TraesCS1B01G002700 chr2D 92.182 307 19 2 54 356 43666269 43666574 3.550000e-116 429.0
8 TraesCS1B01G002700 chr2D 96.639 238 8 0 4733 4970 43688629 43688866 3.610000e-106 396.0
9 TraesCS1B01G002700 chr2D 100.000 31 0 0 379 409 43666981 43667011 1.930000e-04 58.4
10 TraesCS1B01G002700 chrUn 95.786 3180 88 10 922 4085 260346430 260343281 0.000000e+00 5088.0
11 TraesCS1B01G002700 chrUn 97.071 239 7 0 4359 4597 260343247 260343009 2.150000e-108 403.0
12 TraesCS1B01G002700 chrUn 96.639 238 8 0 4733 4970 260342500 260342263 3.610000e-106 396.0
13 TraesCS1B01G002700 chrUn 94.024 251 7 3 641 891 260346669 260346427 1.690000e-99 374.0
14 TraesCS1B01G002700 chrUn 100.000 33 0 0 4319 4351 260343275 260343243 1.490000e-05 62.1
15 TraesCS1B01G002700 chr5D 74.223 2929 649 74 1097 3972 434473721 434476596 0.000000e+00 1129.0
16 TraesCS1B01G002700 chr5B 73.568 2898 663 81 1097 3956 527248979 527251811 0.000000e+00 1013.0
17 TraesCS1B01G002700 chr1D 72.510 2892 708 73 1097 3947 491640239 491637394 0.000000e+00 856.0
18 TraesCS1B01G002700 chr1D 82.584 178 28 2 1097 1271 491667029 491666852 2.400000e-33 154.0
19 TraesCS1B01G002700 chr4B 94.977 219 8 3 4099 4316 491117442 491117226 1.710000e-89 340.0
20 TraesCS1B01G002700 chr4B 91.855 221 15 3 4099 4318 491098588 491098370 6.250000e-79 305.0
21 TraesCS1B01G002700 chr3B 87.442 215 23 4 4105 4318 794782786 794782997 1.380000e-60 244.0
22 TraesCS1B01G002700 chr3B 87.678 211 22 4 4109 4318 794808504 794808711 4.970000e-60 243.0
23 TraesCS1B01G002700 chr3B 85.981 214 24 6 4109 4319 794763881 794764091 1.800000e-54 224.0
24 TraesCS1B01G002700 chr1A 70.968 496 124 16 1742 2223 589454573 589454084 3.170000e-17 100.0


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 TraesCS1B01G002700 chr1B 1825460 1830429 4969 True 9178.00 9178 100.0000 1 4970 1 chr1B.!!$R1 4969
1 TraesCS1B01G002700 chr1B 3143539 3148009 4470 False 3768.00 5936 96.5080 459 4970 2 chr1B.!!$F1 4511
2 TraesCS1B01G002700 chr1B 683581523 683584382 2859 True 763.00 763 72.0560 1097 3947 1 chr1B.!!$R2 2850
3 TraesCS1B01G002700 chr2D 43666269 43674389 8120 False 1351.68 5203 95.0858 54 4594 5 chr2D.!!$F2 4540
4 TraesCS1B01G002700 chrUn 260342263 260346669 4406 True 1264.62 5088 96.7040 641 4970 5 chrUn.!!$R1 4329
5 TraesCS1B01G002700 chr5D 434473721 434476596 2875 False 1129.00 1129 74.2230 1097 3972 1 chr5D.!!$F1 2875
6 TraesCS1B01G002700 chr5B 527248979 527251811 2832 False 1013.00 1013 73.5680 1097 3956 1 chr5B.!!$F1 2859
7 TraesCS1B01G002700 chr1D 491637394 491640239 2845 True 856.00 856 72.5100 1097 3947 1 chr1D.!!$R1 2850

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
810 4692 0.249322 ACAAGTCGTGGTCTCGTTGG 60.249 55.000 0.00 0.0 0.00 3.77 F
915 4806 1.337118 GATCCCCAGCTACTCTCCAG 58.663 60.000 0.00 0.0 0.00 3.86 F
2336 6270 1.586154 GGTTTGGCAGTCATCGTGGG 61.586 60.000 0.00 0.0 0.00 4.61 F
2848 6782 1.946768 CCGACTGTGGCAGAAAAGAAA 59.053 47.619 2.91 0.0 35.18 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2336 6270 1.295746 GGAGGTTCCCAGTCCGAAC 59.704 63.158 0.00 0.00 39.12 3.95 R
2848 6782 1.203758 TGTGTTATGCCATCGTCTCGT 59.796 47.619 0.00 0.00 0.00 4.18 R
3546 7486 1.264288 GATAAGCCCAGCGGAATTTCG 59.736 52.381 0.39 0.39 0.00 3.46 R
4698 8668 0.326238 AAGGAATAGGAGGACGGCCA 60.326 55.000 11.69 0.00 36.29 5.36 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 3.753294 ATCGGTGGGCTATAGACTTTG 57.247 47.619 5.35 0.00 0.00 2.77
22 23 2.463752 TCGGTGGGCTATAGACTTTGT 58.536 47.619 5.35 0.00 0.00 2.83
23 24 3.634504 TCGGTGGGCTATAGACTTTGTA 58.365 45.455 5.35 0.00 0.00 2.41
24 25 4.025360 TCGGTGGGCTATAGACTTTGTAA 58.975 43.478 5.35 0.00 0.00 2.41
25 26 4.467082 TCGGTGGGCTATAGACTTTGTAAA 59.533 41.667 5.35 0.00 0.00 2.01
26 27 5.129815 TCGGTGGGCTATAGACTTTGTAAAT 59.870 40.000 5.35 0.00 0.00 1.40
27 28 5.236478 CGGTGGGCTATAGACTTTGTAAATG 59.764 44.000 5.35 0.00 0.00 2.32
28 29 5.531287 GGTGGGCTATAGACTTTGTAAATGG 59.469 44.000 5.35 0.00 0.00 3.16
29 30 5.008712 GTGGGCTATAGACTTTGTAAATGGC 59.991 44.000 5.35 0.00 0.00 4.40
30 31 4.519350 GGGCTATAGACTTTGTAAATGGCC 59.481 45.833 5.35 0.00 41.86 5.36
31 32 4.213482 GGCTATAGACTTTGTAAATGGCCG 59.787 45.833 3.21 0.00 35.00 6.13
32 33 5.054477 GCTATAGACTTTGTAAATGGCCGA 58.946 41.667 3.21 0.00 26.97 5.54
33 34 5.526111 GCTATAGACTTTGTAAATGGCCGAA 59.474 40.000 3.21 0.00 26.97 4.30
34 35 6.037830 GCTATAGACTTTGTAAATGGCCGAAA 59.962 38.462 3.21 0.00 26.97 3.46
35 36 6.827586 ATAGACTTTGTAAATGGCCGAAAA 57.172 33.333 0.00 0.00 26.97 2.29
36 37 5.523438 AGACTTTGTAAATGGCCGAAAAA 57.477 34.783 0.00 0.00 26.97 1.94
37 38 5.528870 AGACTTTGTAAATGGCCGAAAAAG 58.471 37.500 0.00 3.16 26.97 2.27
38 39 5.068591 AGACTTTGTAAATGGCCGAAAAAGT 59.931 36.000 12.45 12.45 38.66 2.66
39 40 5.047188 ACTTTGTAAATGGCCGAAAAAGTG 58.953 37.500 12.02 0.00 35.63 3.16
40 41 4.920640 TTGTAAATGGCCGAAAAAGTGA 57.079 36.364 0.00 0.00 0.00 3.41
41 42 4.920640 TGTAAATGGCCGAAAAAGTGAA 57.079 36.364 0.00 0.00 0.00 3.18
42 43 5.263968 TGTAAATGGCCGAAAAAGTGAAA 57.736 34.783 0.00 0.00 0.00 2.69
43 44 5.044558 TGTAAATGGCCGAAAAAGTGAAAC 58.955 37.500 0.00 0.00 0.00 2.78
70 71 3.140814 GGGCGCAAATCCTCACCC 61.141 66.667 10.83 0.00 0.00 4.61
71 72 2.361104 GGCGCAAATCCTCACCCA 60.361 61.111 10.83 0.00 0.00 4.51
72 73 2.700773 GGCGCAAATCCTCACCCAC 61.701 63.158 10.83 0.00 0.00 4.61
75 76 0.390603 CGCAAATCCTCACCCACGTA 60.391 55.000 0.00 0.00 0.00 3.57
101 102 2.746277 GTTACCCACCAGCTGGCG 60.746 66.667 33.06 23.76 39.01 5.69
122 123 1.185315 CTGCTGGTGGGTAAATTGGG 58.815 55.000 0.00 0.00 0.00 4.12
128 129 2.090719 TGGTGGGTAAATTGGGTTGGAA 60.091 45.455 0.00 0.00 0.00 3.53
156 157 1.601663 CGATCTCAAGATGGCTCGGAC 60.602 57.143 0.00 0.00 34.37 4.79
167 168 1.064458 GCTCGGACGAGGTTAGCTC 59.936 63.158 21.57 0.72 42.19 4.09
175 176 0.381089 CGAGGTTAGCTCGGTACCAG 59.619 60.000 23.84 9.65 40.27 4.00
177 178 1.143401 GGTTAGCTCGGTACCAGGC 59.857 63.158 13.54 14.81 32.12 4.85
197 198 2.820330 CAAAACAATGGGTCAAGCGTT 58.180 42.857 0.00 0.00 0.00 4.84
295 300 8.548877 ACAAGGTTATTACATGGTTCAGATACT 58.451 33.333 0.00 0.00 0.00 2.12
346 351 1.806542 ACTGTTCGGTGCACAATGATC 59.193 47.619 20.43 12.18 0.00 2.92
347 352 0.795698 TGTTCGGTGCACAATGATCG 59.204 50.000 20.43 11.84 0.00 3.69
351 356 2.689646 TCGGTGCACAATGATCGTAAA 58.310 42.857 20.43 0.00 0.00 2.01
356 361 5.390040 CGGTGCACAATGATCGTAAAAACTA 60.390 40.000 20.43 0.00 0.00 2.24
357 362 5.793457 GGTGCACAATGATCGTAAAAACTAC 59.207 40.000 20.43 0.00 0.00 2.73
358 363 5.793457 GTGCACAATGATCGTAAAAACTACC 59.207 40.000 13.17 0.00 0.00 3.18
359 364 5.106475 TGCACAATGATCGTAAAAACTACCC 60.106 40.000 0.00 0.00 0.00 3.69
360 365 5.556470 CACAATGATCGTAAAAACTACCCG 58.444 41.667 0.00 0.00 0.00 5.28
363 368 6.596497 ACAATGATCGTAAAAACTACCCGAAT 59.404 34.615 0.00 0.00 0.00 3.34
365 370 5.969423 TGATCGTAAAAACTACCCGAATCT 58.031 37.500 0.00 0.00 0.00 2.40
366 371 6.038356 TGATCGTAAAAACTACCCGAATCTC 58.962 40.000 0.00 0.00 0.00 2.75
368 373 6.029346 TCGTAAAAACTACCCGAATCTCTT 57.971 37.500 0.00 0.00 0.00 2.85
369 374 5.865552 TCGTAAAAACTACCCGAATCTCTTG 59.134 40.000 0.00 0.00 0.00 3.02
370 375 5.636543 CGTAAAAACTACCCGAATCTCTTGT 59.363 40.000 0.00 0.00 0.00 3.16
371 376 6.808212 CGTAAAAACTACCCGAATCTCTTGTA 59.192 38.462 0.00 0.00 0.00 2.41
372 377 7.329226 CGTAAAAACTACCCGAATCTCTTGTAA 59.671 37.037 0.00 0.00 0.00 2.41
373 378 7.430992 AAAAACTACCCGAATCTCTTGTAAC 57.569 36.000 0.00 0.00 0.00 2.50
375 380 5.326200 ACTACCCGAATCTCTTGTAACAG 57.674 43.478 0.00 0.00 0.00 3.16
377 382 4.618920 ACCCGAATCTCTTGTAACAGTT 57.381 40.909 0.00 0.00 0.00 3.16
429 4301 0.723414 CAGGTAGCACTGCGACATTG 59.277 55.000 15.17 9.35 35.94 2.82
431 4303 0.443869 GGTAGCACTGCGACATTGTG 59.556 55.000 15.17 0.00 35.94 3.33
432 4304 1.148310 GTAGCACTGCGACATTGTGT 58.852 50.000 9.20 0.00 34.45 3.72
557 4432 7.662897 TCGTACATCCAGTATATAAATGCACA 58.337 34.615 0.00 0.00 34.67 4.57
559 4434 7.383843 CGTACATCCAGTATATAAATGCACACA 59.616 37.037 0.00 0.00 34.67 3.72
560 4435 7.734924 ACATCCAGTATATAAATGCACACAG 57.265 36.000 0.00 0.00 0.00 3.66
580 4459 4.238514 CAGAGCCTGAGTTACTTGTACAC 58.761 47.826 0.00 0.00 32.44 2.90
732 4614 4.040936 AGAAGAGACAACAGAGGCTCTA 57.959 45.455 18.26 0.00 36.76 2.43
771 4653 9.756571 ATATCCATACTCTATTTCCTAACGACT 57.243 33.333 0.00 0.00 0.00 4.18
773 4655 8.388484 TCCATACTCTATTTCCTAACGACTAC 57.612 38.462 0.00 0.00 0.00 2.73
774 4656 8.216423 TCCATACTCTATTTCCTAACGACTACT 58.784 37.037 0.00 0.00 0.00 2.57
775 4657 8.291032 CCATACTCTATTTCCTAACGACTACTG 58.709 40.741 0.00 0.00 0.00 2.74
810 4692 0.249322 ACAAGTCGTGGTCTCGTTGG 60.249 55.000 0.00 0.00 0.00 3.77
860 4742 3.200593 GGCAGACGCTGAGCATGG 61.201 66.667 4.88 0.00 38.60 3.66
915 4806 1.337118 GATCCCCAGCTACTCTCCAG 58.663 60.000 0.00 0.00 0.00 3.86
1188 5104 3.842923 CTCCTCGGCTCGTGGCAT 61.843 66.667 11.75 0.00 44.01 4.40
1971 5905 2.074547 TACCGGCGACTCTGAAAAAG 57.925 50.000 9.30 0.00 0.00 2.27
1980 5914 4.552184 GCGACTCTGAAAAAGGTGTGTAAC 60.552 45.833 0.00 0.00 37.35 2.50
2259 6193 9.787435 TTTAACAAACTTACTGGTGTGATATCT 57.213 29.630 3.98 0.00 0.00 1.98
2293 6227 8.623310 TTTTTCTGGTCTGACGAATTTAAAAC 57.377 30.769 1.07 0.00 0.00 2.43
2336 6270 1.586154 GGTTTGGCAGTCATCGTGGG 61.586 60.000 0.00 0.00 0.00 4.61
2848 6782 1.946768 CCGACTGTGGCAGAAAAGAAA 59.053 47.619 2.91 0.00 35.18 2.52
4104 8053 5.519566 TCGTTGTTAAACATACACGTTCTGT 59.480 36.000 0.00 0.00 35.94 3.41
4109 8058 7.201835 TGTTAAACATACACGTTCTGTACTCA 58.798 34.615 0.00 0.00 38.22 3.41
4202 8151 5.712917 ACCGATTGTATCTCTTCTCTATCCC 59.287 44.000 0.00 0.00 0.00 3.85
4300 8249 2.188829 TCGCCCTCGGTATGGTACG 61.189 63.158 0.00 0.00 36.13 3.67
4350 8315 4.448537 AGTTTGCTTGTTGTGCTTGTTA 57.551 36.364 0.00 0.00 0.00 2.41
4351 8316 4.173256 AGTTTGCTTGTTGTGCTTGTTAC 58.827 39.130 0.00 0.00 0.00 2.50
4352 8317 3.857549 TTGCTTGTTGTGCTTGTTACA 57.142 38.095 0.00 0.00 0.00 2.41
4353 8318 3.419264 TGCTTGTTGTGCTTGTTACAG 57.581 42.857 0.00 0.00 0.00 2.74
4354 8319 2.752354 TGCTTGTTGTGCTTGTTACAGT 59.248 40.909 0.00 0.00 0.00 3.55
4529 8499 4.014406 GTCCCCTTGAATAAATTCCACGT 58.986 43.478 0.41 0.00 35.97 4.49
4540 8510 0.904865 ATTCCACGTGGCCTCTCTCA 60.905 55.000 30.25 7.02 34.44 3.27
4692 8662 2.824041 CGTGGCATACAGGTGGGC 60.824 66.667 0.00 0.00 0.00 5.36
4693 8663 2.677228 GTGGCATACAGGTGGGCT 59.323 61.111 0.00 0.00 0.00 5.19
4694 8664 1.750399 GTGGCATACAGGTGGGCTG 60.750 63.158 0.00 0.00 0.00 4.85
4695 8665 2.830370 GGCATACAGGTGGGCTGC 60.830 66.667 0.00 0.00 0.00 5.25
4696 8666 3.204827 GCATACAGGTGGGCTGCG 61.205 66.667 0.00 0.00 0.00 5.18
4697 8667 2.514592 CATACAGGTGGGCTGCGG 60.515 66.667 0.00 0.00 0.00 5.69
4698 8668 3.009115 ATACAGGTGGGCTGCGGT 61.009 61.111 0.00 0.00 0.00 5.68
4731 8701 2.579410 TTCCTTAACAAGTCAGGGGC 57.421 50.000 0.00 0.00 0.00 5.80
4822 9165 8.797438 AGCTATGAATTATCTCGACACATCTTA 58.203 33.333 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.454812 ACAAAGTCTATAGCCCACCGATT 59.545 43.478 0.00 0.00 0.00 3.34
1 2 3.039011 ACAAAGTCTATAGCCCACCGAT 58.961 45.455 0.00 0.00 0.00 4.18
2 3 2.463752 ACAAAGTCTATAGCCCACCGA 58.536 47.619 0.00 0.00 0.00 4.69
3 4 2.981859 ACAAAGTCTATAGCCCACCG 57.018 50.000 0.00 0.00 0.00 4.94
4 5 5.531287 CCATTTACAAAGTCTATAGCCCACC 59.469 44.000 0.00 0.00 0.00 4.61
5 6 5.008712 GCCATTTACAAAGTCTATAGCCCAC 59.991 44.000 0.00 0.00 0.00 4.61
6 7 5.130350 GCCATTTACAAAGTCTATAGCCCA 58.870 41.667 0.00 0.00 0.00 5.36
7 8 4.519350 GGCCATTTACAAAGTCTATAGCCC 59.481 45.833 0.00 0.00 0.00 5.19
8 9 4.213482 CGGCCATTTACAAAGTCTATAGCC 59.787 45.833 2.24 0.00 0.00 3.93
9 10 5.054477 TCGGCCATTTACAAAGTCTATAGC 58.946 41.667 2.24 0.00 0.00 2.97
10 11 7.548196 TTTCGGCCATTTACAAAGTCTATAG 57.452 36.000 2.24 0.00 0.00 1.31
11 12 7.925043 TTTTCGGCCATTTACAAAGTCTATA 57.075 32.000 2.24 0.00 0.00 1.31
12 13 6.827586 TTTTCGGCCATTTACAAAGTCTAT 57.172 33.333 2.24 0.00 0.00 1.98
13 14 6.263617 ACTTTTTCGGCCATTTACAAAGTCTA 59.736 34.615 2.24 0.00 29.06 2.59
14 15 5.068591 ACTTTTTCGGCCATTTACAAAGTCT 59.931 36.000 2.24 0.00 29.06 3.24
15 16 5.174943 CACTTTTTCGGCCATTTACAAAGTC 59.825 40.000 2.24 0.00 32.07 3.01
16 17 5.047188 CACTTTTTCGGCCATTTACAAAGT 58.953 37.500 2.24 5.17 34.16 2.66
17 18 5.285651 TCACTTTTTCGGCCATTTACAAAG 58.714 37.500 2.24 4.52 0.00 2.77
18 19 5.263968 TCACTTTTTCGGCCATTTACAAA 57.736 34.783 2.24 0.00 0.00 2.83
19 20 4.920640 TCACTTTTTCGGCCATTTACAA 57.079 36.364 2.24 0.00 0.00 2.41
20 21 4.920640 TTCACTTTTTCGGCCATTTACA 57.079 36.364 2.24 0.00 0.00 2.41
21 22 5.286438 AGTTTCACTTTTTCGGCCATTTAC 58.714 37.500 2.24 0.00 0.00 2.01
22 23 5.523438 AGTTTCACTTTTTCGGCCATTTA 57.477 34.783 2.24 0.00 0.00 1.40
23 24 4.400529 AGTTTCACTTTTTCGGCCATTT 57.599 36.364 2.24 0.00 0.00 2.32
24 25 4.400529 AAGTTTCACTTTTTCGGCCATT 57.599 36.364 2.24 0.00 34.11 3.16
25 26 4.119136 CAAAGTTTCACTTTTTCGGCCAT 58.881 39.130 2.24 0.00 45.38 4.40
26 27 3.193691 TCAAAGTTTCACTTTTTCGGCCA 59.806 39.130 2.24 0.00 45.38 5.36
27 28 3.776340 TCAAAGTTTCACTTTTTCGGCC 58.224 40.909 0.00 0.00 45.38 6.13
28 29 5.771602 TTTCAAAGTTTCACTTTTTCGGC 57.228 34.783 0.00 0.00 45.38 5.54
29 30 6.238076 CCCATTTCAAAGTTTCACTTTTTCGG 60.238 38.462 0.00 0.00 45.38 4.30
30 31 6.238076 CCCCATTTCAAAGTTTCACTTTTTCG 60.238 38.462 0.00 0.00 45.38 3.46
31 32 6.458206 GCCCCATTTCAAAGTTTCACTTTTTC 60.458 38.462 0.00 0.00 45.38 2.29
32 33 5.356751 GCCCCATTTCAAAGTTTCACTTTTT 59.643 36.000 0.00 0.00 45.38 1.94
33 34 4.881273 GCCCCATTTCAAAGTTTCACTTTT 59.119 37.500 0.00 0.00 45.38 2.27
35 36 3.492482 CGCCCCATTTCAAAGTTTCACTT 60.492 43.478 0.00 0.00 40.80 3.16
36 37 2.035832 CGCCCCATTTCAAAGTTTCACT 59.964 45.455 0.00 0.00 0.00 3.41
37 38 2.403259 CGCCCCATTTCAAAGTTTCAC 58.597 47.619 0.00 0.00 0.00 3.18
38 39 1.270041 GCGCCCCATTTCAAAGTTTCA 60.270 47.619 0.00 0.00 0.00 2.69
39 40 1.270041 TGCGCCCCATTTCAAAGTTTC 60.270 47.619 4.18 0.00 0.00 2.78
40 41 0.755686 TGCGCCCCATTTCAAAGTTT 59.244 45.000 4.18 0.00 0.00 2.66
41 42 0.755686 TTGCGCCCCATTTCAAAGTT 59.244 45.000 4.18 0.00 0.00 2.66
42 43 0.755686 TTTGCGCCCCATTTCAAAGT 59.244 45.000 4.18 0.00 0.00 2.66
43 44 2.001872 GATTTGCGCCCCATTTCAAAG 58.998 47.619 4.18 0.00 32.78 2.77
44 45 1.338579 GGATTTGCGCCCCATTTCAAA 60.339 47.619 4.18 0.00 33.64 2.69
45 46 0.248843 GGATTTGCGCCCCATTTCAA 59.751 50.000 4.18 0.00 0.00 2.69
46 47 0.614415 AGGATTTGCGCCCCATTTCA 60.614 50.000 4.18 0.00 0.00 2.69
47 48 0.103026 GAGGATTTGCGCCCCATTTC 59.897 55.000 4.18 0.00 0.00 2.17
48 49 0.614415 TGAGGATTTGCGCCCCATTT 60.614 50.000 4.18 0.00 0.00 2.32
49 50 1.000233 TGAGGATTTGCGCCCCATT 60.000 52.632 4.18 0.00 0.00 3.16
50 51 1.754234 GTGAGGATTTGCGCCCCAT 60.754 57.895 4.18 0.00 0.00 4.00
51 52 2.361104 GTGAGGATTTGCGCCCCA 60.361 61.111 4.18 0.00 0.00 4.96
52 53 3.140814 GGTGAGGATTTGCGCCCC 61.141 66.667 4.18 0.34 0.00 5.80
98 99 2.741486 TTTACCCACCAGCAGTCGCC 62.741 60.000 0.00 0.00 39.83 5.54
101 102 1.818674 CCAATTTACCCACCAGCAGTC 59.181 52.381 0.00 0.00 0.00 3.51
122 123 6.565234 TCTTGAGATCGAATCTACTTCCAAC 58.435 40.000 0.00 0.00 40.38 3.77
128 129 4.832266 AGCCATCTTGAGATCGAATCTACT 59.168 41.667 0.00 0.00 40.38 2.57
167 168 1.067915 CCATTGTTTTGCCTGGTACCG 60.068 52.381 7.57 1.95 0.00 4.02
169 170 1.967779 ACCCATTGTTTTGCCTGGTAC 59.032 47.619 0.00 0.00 0.00 3.34
175 176 1.511850 GCTTGACCCATTGTTTTGCC 58.488 50.000 0.00 0.00 0.00 4.52
177 178 2.507339 ACGCTTGACCCATTGTTTTG 57.493 45.000 0.00 0.00 0.00 2.44
295 300 9.729281 ATAAAACTGATTCGGGTAGTTCTTTAA 57.271 29.630 0.00 0.00 33.82 1.52
300 305 6.592607 TGTGATAAAACTGATTCGGGTAGTTC 59.407 38.462 0.00 0.00 33.82 3.01
332 337 3.463533 TTTTACGATCATTGTGCACCG 57.536 42.857 15.69 11.84 0.00 4.94
346 351 5.636543 ACAAGAGATTCGGGTAGTTTTTACG 59.363 40.000 0.00 0.00 0.00 3.18
347 352 8.438513 GTTACAAGAGATTCGGGTAGTTTTTAC 58.561 37.037 0.00 0.00 0.00 2.01
351 356 6.105397 TGTTACAAGAGATTCGGGTAGTTT 57.895 37.500 0.00 0.00 0.00 2.66
356 361 4.618920 AACTGTTACAAGAGATTCGGGT 57.381 40.909 0.00 0.00 0.00 5.28
357 362 5.006746 GCATAACTGTTACAAGAGATTCGGG 59.993 44.000 1.73 0.00 0.00 5.14
358 363 5.812642 AGCATAACTGTTACAAGAGATTCGG 59.187 40.000 1.73 0.00 0.00 4.30
359 364 6.019479 GGAGCATAACTGTTACAAGAGATTCG 60.019 42.308 1.73 0.00 0.00 3.34
360 365 6.818644 TGGAGCATAACTGTTACAAGAGATTC 59.181 38.462 1.73 0.00 0.00 2.52
363 368 5.738619 TGGAGCATAACTGTTACAAGAGA 57.261 39.130 1.73 0.00 0.00 3.10
365 370 7.446931 TCAATTTGGAGCATAACTGTTACAAGA 59.553 33.333 1.73 0.00 37.66 3.02
366 371 7.538678 GTCAATTTGGAGCATAACTGTTACAAG 59.461 37.037 1.73 0.00 37.66 3.16
368 373 6.714810 AGTCAATTTGGAGCATAACTGTTACA 59.285 34.615 1.73 0.00 0.00 2.41
369 374 7.145932 AGTCAATTTGGAGCATAACTGTTAC 57.854 36.000 1.73 0.00 0.00 2.50
370 375 7.592938 CAAGTCAATTTGGAGCATAACTGTTA 58.407 34.615 2.26 2.26 0.00 2.41
371 376 6.449698 CAAGTCAATTTGGAGCATAACTGTT 58.550 36.000 0.00 0.00 0.00 3.16
372 377 6.017400 CAAGTCAATTTGGAGCATAACTGT 57.983 37.500 0.00 0.00 0.00 3.55
424 4296 4.501071 GGTATCGTACCTGAACACAATGT 58.499 43.478 6.87 0.00 45.52 2.71
512 4387 2.309528 TGACCTGGATGATTACACGC 57.690 50.000 0.00 0.00 0.00 5.34
557 4432 3.895656 TGTACAAGTAACTCAGGCTCTGT 59.104 43.478 0.00 0.00 32.61 3.41
559 4434 3.057456 CGTGTACAAGTAACTCAGGCTCT 60.057 47.826 0.00 0.00 0.00 4.09
560 4435 3.243336 CGTGTACAAGTAACTCAGGCTC 58.757 50.000 0.00 0.00 0.00 4.70
580 4459 3.125316 GCTGTTTGATCTTTACTGGGACG 59.875 47.826 0.00 0.00 0.00 4.79
732 4614 2.799126 TGGATATGGACGGCAAAAGT 57.201 45.000 0.00 0.00 0.00 2.66
849 4731 2.887568 GTCGTCCCATGCTCAGCG 60.888 66.667 0.00 0.00 0.00 5.18
1088 5004 1.856265 GCAGCTCCCGTTTCCACTTG 61.856 60.000 0.00 0.00 0.00 3.16
1137 5053 0.611618 TTGTGATGGCGGCCTTGAAT 60.612 50.000 21.46 4.74 0.00 2.57
1186 5102 1.450848 AGCAGTCGTGGCCATGATG 60.451 57.895 29.86 25.58 0.00 3.07
1187 5103 1.450848 CAGCAGTCGTGGCCATGAT 60.451 57.895 29.86 16.08 0.00 2.45
1188 5104 2.046988 CAGCAGTCGTGGCCATGA 60.047 61.111 24.15 24.15 0.00 3.07
1971 5905 7.285858 AGGTCTAGATATCTCAAGTTACACACC 59.714 40.741 8.95 4.85 0.00 4.16
1980 5914 6.708502 TCACTTCGAGGTCTAGATATCTCAAG 59.291 42.308 8.95 2.07 0.00 3.02
2259 6193 5.248640 GTCAGACCAGAAAAATGATCCTCA 58.751 41.667 0.00 0.00 0.00 3.86
2272 6206 6.928979 TTGTTTTAAATTCGTCAGACCAGA 57.071 33.333 0.00 0.00 0.00 3.86
2336 6270 1.295746 GGAGGTTCCCAGTCCGAAC 59.704 63.158 0.00 0.00 39.12 3.95
2848 6782 1.203758 TGTGTTATGCCATCGTCTCGT 59.796 47.619 0.00 0.00 0.00 4.18
3546 7486 1.264288 GATAAGCCCAGCGGAATTTCG 59.736 52.381 0.39 0.39 0.00 3.46
4104 8053 8.725256 AGTACAACCTATAATCTCCTCTGAGTA 58.275 37.037 3.66 0.00 39.75 2.59
4109 8058 6.487331 CACGAGTACAACCTATAATCTCCTCT 59.513 42.308 0.00 0.00 0.00 3.69
4225 8174 4.185394 TGGTATATGCGTACAGGTTGTTG 58.815 43.478 0.00 0.00 0.00 3.33
4350 8315 4.261801 GTTGGCACCATAACATCTACTGT 58.738 43.478 0.00 0.00 40.84 3.55
4351 8316 3.627577 GGTTGGCACCATAACATCTACTG 59.372 47.826 0.00 0.00 43.61 2.74
4352 8317 3.886123 GGTTGGCACCATAACATCTACT 58.114 45.455 0.00 0.00 43.61 2.57
4540 8510 4.075963 TGGTAAAGCGTTGTAACCTCTT 57.924 40.909 4.74 0.00 0.00 2.85
4657 8627 0.537143 CGCCCCTAATTATGCTGCCA 60.537 55.000 0.00 0.00 0.00 4.92
4696 8666 1.446366 GAATAGGAGGACGGCCACC 59.554 63.158 17.39 17.39 44.52 4.61
4697 8667 1.049289 AGGAATAGGAGGACGGCCAC 61.049 60.000 11.69 1.47 36.29 5.01
4698 8668 0.326238 AAGGAATAGGAGGACGGCCA 60.326 55.000 11.69 0.00 36.29 5.36
4700 8670 2.433239 TGTTAAGGAATAGGAGGACGGC 59.567 50.000 0.00 0.00 0.00 5.68
4731 8701 2.412870 TCTGAAGTATTGTGTGCCACG 58.587 47.619 0.00 0.00 37.14 4.94
4822 9165 5.543507 TGGTCATATTTTGGTGCTTTTGT 57.456 34.783 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.