Multiple sequence alignment - TraesCS1B01G120000

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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 TraesCS1B01G120000 chr1B 100.000 2926 0 0 1 2926 142133752 142130827 0.000000e+00 5404.0
1 TraesCS1B01G120000 chr1B 86.538 416 30 14 5 410 142038271 142038670 4.480000e-118 435.0
2 TraesCS1B01G120000 chr1B 81.331 541 26 33 5 521 141845762 141846251 1.280000e-98 370.0
3 TraesCS1B01G120000 chr1B 86.916 107 13 1 573 679 141846345 141846450 5.120000e-23 119.0
4 TraesCS1B01G120000 chr1B 93.750 48 3 0 999 1046 142103366 142103413 4.040000e-09 73.1
5 TraesCS1B01G120000 chr1A 92.948 1418 63 14 690 2100 84795289 84793902 0.000000e+00 2030.0
6 TraesCS1B01G120000 chr1A 86.441 590 53 9 2151 2738 84793823 84793259 3.200000e-174 621.0
7 TraesCS1B01G120000 chr1A 82.474 679 34 21 5 639 84795920 84795283 1.550000e-142 516.0
8 TraesCS1B01G120000 chr1A 86.187 514 26 6 5 511 85005804 85005329 5.590000e-142 514.0
9 TraesCS1B01G120000 chr1A 86.683 413 29 10 5 412 84621721 84622112 4.480000e-118 435.0
10 TraesCS1B01G120000 chr1A 86.441 413 30 10 5 412 84484524 84484915 2.080000e-116 429.0
11 TraesCS1B01G120000 chr1A 94.697 132 7 0 2795 2926 84793250 84793119 3.820000e-49 206.0
12 TraesCS1B01G120000 chr1A 93.750 48 2 1 804 851 84485526 84485572 1.450000e-08 71.3
13 TraesCS1B01G120000 chr1A 93.750 48 2 1 804 851 84622727 84622773 1.450000e-08 71.3
14 TraesCS1B01G120000 chr1D 92.968 1351 45 20 690 2037 88242987 88241684 0.000000e+00 1923.0
15 TraesCS1B01G120000 chr1D 88.279 674 46 18 5 653 88281808 88281143 0.000000e+00 776.0
16 TraesCS1B01G120000 chr1D 92.529 522 27 5 5 521 88243656 88243142 0.000000e+00 737.0
17 TraesCS1B01G120000 chr1D 91.284 436 28 6 2328 2753 88226531 88226096 1.170000e-163 586.0
18 TraesCS1B01G120000 chr1D 87.409 413 26 11 5 412 87904436 87904827 4.450000e-123 451.0
19 TraesCS1B01G120000 chr1D 87.409 413 26 11 5 412 88215219 88215610 4.450000e-123 451.0
20 TraesCS1B01G120000 chr1D 78.414 227 37 10 464 687 87905029 87905246 1.410000e-28 137.0
21 TraesCS1B01G120000 chr1D 98.113 53 1 0 1088 1140 88216367 88216419 3.100000e-15 93.5
22 TraesCS1B01G120000 chr1D 97.500 40 1 0 1000 1039 88216304 88216343 5.230000e-08 69.4
23 TraesCS1B01G120000 chr1D 89.286 56 5 1 2205 2260 88226629 88226575 5.230000e-08 69.4
24 TraesCS1B01G120000 chr4D 87.794 1147 54 21 690 1834 464796552 464795490 0.000000e+00 1264.0
25 TraesCS1B01G120000 chr4D 84.780 841 84 23 2112 2922 464795315 464794489 0.000000e+00 804.0
26 TraesCS1B01G120000 chr4D 91.103 517 36 6 5 521 464797213 464796707 0.000000e+00 691.0
27 TraesCS1B01G120000 chr4D 83.794 253 10 21 1860 2104 464795494 464795265 8.220000e-51 211.0
28 TraesCS1B01G120000 chr4D 96.875 64 1 1 577 640 464796607 464796545 3.990000e-19 106.0
29 TraesCS1B01G120000 chr3B 86.441 413 30 11 5 412 535704829 535704438 2.080000e-116 429.0
30 TraesCS1B01G120000 chr3B 77.632 228 31 11 464 687 535704246 535704035 1.420000e-23 121.0


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 TraesCS1B01G120000 chr1B 142130827 142133752 2925 True 5404.000000 5404 100.000000 1 2926 1 chr1B.!!$R1 2925
1 TraesCS1B01G120000 chr1B 141845762 141846450 688 False 244.500000 370 84.123500 5 679 2 chr1B.!!$F3 674
2 TraesCS1B01G120000 chr1A 84793119 84795920 2801 True 843.250000 2030 89.140000 5 2926 4 chr1A.!!$R2 2921
3 TraesCS1B01G120000 chr1A 84621721 84622773 1052 False 253.150000 435 90.216500 5 851 2 chr1A.!!$F2 846
4 TraesCS1B01G120000 chr1A 84484524 84485572 1048 False 250.150000 429 90.095500 5 851 2 chr1A.!!$F1 846
5 TraesCS1B01G120000 chr1D 88241684 88243656 1972 True 1330.000000 1923 92.748500 5 2037 2 chr1D.!!$R3 2032
6 TraesCS1B01G120000 chr1D 88281143 88281808 665 True 776.000000 776 88.279000 5 653 1 chr1D.!!$R1 648
7 TraesCS1B01G120000 chr1D 88226096 88226629 533 True 327.700000 586 90.285000 2205 2753 2 chr1D.!!$R2 548
8 TraesCS1B01G120000 chr1D 87904436 87905246 810 False 294.000000 451 82.911500 5 687 2 chr1D.!!$F1 682
9 TraesCS1B01G120000 chr1D 88215219 88216419 1200 False 204.633333 451 94.340667 5 1140 3 chr1D.!!$F2 1135
10 TraesCS1B01G120000 chr4D 464794489 464797213 2724 True 615.200000 1264 88.869200 5 2922 5 chr4D.!!$R1 2917
11 TraesCS1B01G120000 chr3B 535704035 535704829 794 True 275.000000 429 82.036500 5 687 2 chr3B.!!$R1 682

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
526 876 0.107945 AGCTTCTGAATCTGTCGGGC 60.108 55.0 0.0 0.0 32.9 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2132 2579 0.683973 ACATGCATTTTTCCCGCCAA 59.316 45.0 0.0 0.0 0.0 4.52 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
152 153 2.203280 CCAGCACCGGTGGTTCAA 60.203 61.111 35.55 0.00 45.06 2.69
168 169 1.172180 TCAACAAGCCCAAAGGAGCG 61.172 55.000 0.00 0.00 33.47 5.03
263 267 5.231991 GGTTAATTATTTCATTGCAGTGCCG 59.768 40.000 13.72 0.88 0.00 5.69
365 377 1.964223 TCCTCGCCATGTAATCCTCTC 59.036 52.381 0.00 0.00 0.00 3.20
412 453 6.832900 TGTAGCATGGAAATTACATGATGGAA 59.167 34.615 21.50 3.25 46.60 3.53
413 454 6.152932 AGCATGGAAATTACATGATGGAAC 57.847 37.500 21.50 3.02 46.60 3.62
414 455 5.895534 AGCATGGAAATTACATGATGGAACT 59.104 36.000 21.50 5.28 46.60 3.01
415 456 7.062322 AGCATGGAAATTACATGATGGAACTA 58.938 34.615 21.50 0.00 46.60 2.24
416 457 7.560991 AGCATGGAAATTACATGATGGAACTAA 59.439 33.333 21.50 0.00 46.60 2.24
417 458 8.196771 GCATGGAAATTACATGATGGAACTAAA 58.803 33.333 21.50 0.00 46.60 1.85
461 811 3.758554 GTCTGAATCTGCTAAAGGCCAAA 59.241 43.478 5.01 0.00 40.92 3.28
490 840 6.656902 TGAATCTGGTTGAGCTTTCTATGAT 58.343 36.000 0.00 0.00 0.00 2.45
495 845 3.557595 GGTTGAGCTTTCTATGATCGGTG 59.442 47.826 0.00 0.00 0.00 4.94
521 871 4.815533 TCTGCTAAGCTTCTGAATCTGT 57.184 40.909 0.00 0.00 0.00 3.41
523 873 3.515630 TGCTAAGCTTCTGAATCTGTCG 58.484 45.455 0.00 0.00 0.00 4.35
525 875 2.393271 AAGCTTCTGAATCTGTCGGG 57.607 50.000 0.00 0.00 32.90 5.14
526 876 0.107945 AGCTTCTGAATCTGTCGGGC 60.108 55.000 0.00 0.00 32.90 6.13
527 877 0.107945 GCTTCTGAATCTGTCGGGCT 60.108 55.000 0.00 0.00 32.90 5.19
550 921 6.371548 GCTAAATACAGATGTGAAGTCCAACA 59.628 38.462 0.00 0.00 0.00 3.33
552 923 6.560253 AATACAGATGTGAAGTCCAACAAC 57.440 37.500 0.00 0.00 0.00 3.32
569 940 5.006552 CCAACAACGAAAAACAAATGCTGAT 59.993 36.000 0.00 0.00 0.00 2.90
629 1023 2.034432 ACGCACATGAAATCTGCACAAA 59.966 40.909 0.00 0.00 0.00 2.83
656 1051 8.352942 AGTAAACAGGCAATCAAGTTTTTCTAG 58.647 33.333 0.00 0.00 35.90 2.43
659 1054 7.346751 ACAGGCAATCAAGTTTTTCTAGAAA 57.653 32.000 13.99 13.99 0.00 2.52
671 1066 9.626045 AAGTTTTTCTAGAAACAACAAAGACTG 57.374 29.630 26.81 0.00 40.98 3.51
693 1088 6.071952 ACTGAAATTCTTTGATGTGCGGTAAT 60.072 34.615 0.00 0.00 0.00 1.89
734 1130 8.668510 AAAGATGGCACTAACAGATAATACAG 57.331 34.615 0.00 0.00 0.00 2.74
738 1160 6.573434 TGGCACTAACAGATAATACAGTGAG 58.427 40.000 0.00 0.00 36.37 3.51
766 1190 5.278315 GGGAACATCCGCATAAAAATCCTAC 60.278 44.000 0.00 0.00 37.43 3.18
1062 1500 2.363172 GGCTCTCCCAGGTGACTCC 61.363 68.421 0.00 0.00 40.21 3.85
1063 1501 1.610673 GCTCTCCCAGGTGACTCCA 60.611 63.158 0.00 0.00 40.21 3.86
1065 1503 0.252012 CTCTCCCAGGTGACTCCACT 60.252 60.000 0.00 0.00 42.77 4.00
1066 1504 0.251832 TCTCCCAGGTGACTCCACTC 60.252 60.000 0.00 0.00 42.77 3.51
1067 1505 0.542938 CTCCCAGGTGACTCCACTCA 60.543 60.000 0.00 0.00 42.77 3.41
1068 1506 0.117140 TCCCAGGTGACTCCACTCAT 59.883 55.000 0.00 0.00 42.77 2.90
1069 1507 0.539051 CCCAGGTGACTCCACTCATC 59.461 60.000 0.00 0.00 42.77 2.92
1070 1508 1.269958 CCAGGTGACTCCACTCATCA 58.730 55.000 0.00 0.00 42.77 3.07
1071 1509 1.066573 CCAGGTGACTCCACTCATCAC 60.067 57.143 0.00 0.00 42.77 3.06
1072 1510 1.898472 CAGGTGACTCCACTCATCACT 59.102 52.381 3.83 0.00 42.00 3.41
1073 1511 2.094286 CAGGTGACTCCACTCATCACTC 60.094 54.545 3.83 0.00 42.00 3.51
1074 1512 1.895798 GGTGACTCCACTCATCACTCA 59.104 52.381 3.83 0.00 42.00 3.41
1075 1513 2.499289 GGTGACTCCACTCATCACTCAT 59.501 50.000 3.83 0.00 42.00 2.90
1076 1514 3.430098 GGTGACTCCACTCATCACTCATC 60.430 52.174 3.83 0.00 42.00 2.92
1077 1515 3.194329 GTGACTCCACTCATCACTCATCA 59.806 47.826 0.00 0.00 39.72 3.07
1078 1516 3.446516 TGACTCCACTCATCACTCATCAG 59.553 47.826 0.00 0.00 0.00 2.90
1079 1517 3.439154 ACTCCACTCATCACTCATCAGT 58.561 45.455 0.00 0.00 0.00 3.41
1080 1518 8.983097 GTGACTCCACTCATCACTCATCAGTG 62.983 50.000 0.00 0.00 44.11 3.66
1132 1570 1.025113 TAGCTACTCGACTGCTGCGT 61.025 55.000 11.01 0.00 37.62 5.24
1135 1573 0.710567 CTACTCGACTGCTGCGTTTG 59.289 55.000 0.00 0.00 0.00 2.93
1138 1576 1.891060 CTCGACTGCTGCGTTTGGAC 61.891 60.000 0.00 0.00 0.00 4.02
1921 2359 3.391665 GAGATCGTGTGGCCCAGGG 62.392 68.421 0.00 0.00 0.00 4.45
1967 2410 9.073368 GGACTGTGCTACGTATGTATTTATATG 57.927 37.037 0.00 0.00 0.00 1.78
2138 2585 9.959749 AAAAATAATACATGTACTATTTGGCGG 57.040 29.630 25.09 0.00 30.71 6.13
2139 2586 7.681939 AATAATACATGTACTATTTGGCGGG 57.318 36.000 12.62 0.00 0.00 6.13
2140 2587 4.967084 ATACATGTACTATTTGGCGGGA 57.033 40.909 7.96 0.00 0.00 5.14
2146 2593 5.317733 TGTACTATTTGGCGGGAAAAATG 57.682 39.130 0.00 0.00 0.00 2.32
2177 2682 0.175760 TAGAGGCTAAGGTGCGCTTG 59.824 55.000 9.73 0.00 0.00 4.01
2191 2696 3.793144 CTTGGCCGCGCTGTTCTC 61.793 66.667 5.56 0.00 0.00 2.87
2199 2724 2.536365 CCGCGCTGTTCTCTATTTGTA 58.464 47.619 5.56 0.00 0.00 2.41
2249 2774 5.346822 GGTTGTCATTGCAGTTGATGATTTC 59.653 40.000 2.29 0.00 35.01 2.17
2250 2775 4.725359 TGTCATTGCAGTTGATGATTTCG 58.275 39.130 2.29 0.00 35.01 3.46
2268 2793 5.975693 TTTCGGGTTTGATTTTATCTGCT 57.024 34.783 0.00 0.00 0.00 4.24
2286 2811 2.358898 TGCTTTGCCTTGAGTTGTCTTC 59.641 45.455 0.00 0.00 0.00 2.87
2293 2818 3.627577 GCCTTGAGTTGTCTTCTTTGACA 59.372 43.478 0.00 0.00 44.17 3.58
2323 2848 4.292977 GCTAGGCGCTTATTTTCATTGT 57.707 40.909 7.64 0.00 35.14 2.71
2559 3094 5.710513 TCTTGACTTGACCAAATCAATGG 57.289 39.130 7.02 0.00 46.37 3.16
2582 3117 5.106673 GGAGGATTCAGTTAAACAAGTTCCG 60.107 44.000 0.00 0.00 0.00 4.30
2601 3136 5.080969 TCCGTTCATTTTAGTGTCCCTAG 57.919 43.478 0.00 0.00 0.00 3.02
2638 3173 9.970395 CTCAATGTTAATTGCCATAATGTGTAT 57.030 29.630 0.00 0.00 42.55 2.29
2757 3292 8.668510 TGCACCTAAATCATAAGAATCTCTTC 57.331 34.615 0.00 0.00 37.89 2.87
2763 3298 3.706698 TCATAAGAATCTCTTCGTGCGG 58.293 45.455 0.00 0.00 37.89 5.69
2769 3304 2.309528 ATCTCTTCGTGCGGCAATTA 57.690 45.000 3.23 0.00 0.00 1.40
2774 3309 0.320858 TTCGTGCGGCAATTACCTGA 60.321 50.000 3.23 0.00 0.00 3.86
2781 3316 3.118408 TGCGGCAATTACCTGAGACTATT 60.118 43.478 0.00 0.00 0.00 1.73
2793 3328 4.099573 CCTGAGACTATTACCACAACGGAT 59.900 45.833 0.00 0.00 38.63 4.18
2802 3337 1.602237 CACAACGGATAGGGGCACT 59.398 57.895 0.00 0.00 0.00 4.40
2824 3359 5.712917 ACTAAAAGAAATACCGGCATTCCAA 59.287 36.000 0.00 0.00 0.00 3.53
2826 3361 4.918810 AAGAAATACCGGCATTCCAATC 57.081 40.909 0.00 0.00 0.00 2.67
2923 3461 0.182775 AAACTTCCTTGAGCACGGGT 59.817 50.000 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.889044 GCGATCTGGTCTCGGCGA 61.889 66.667 10.14 10.14 36.65 5.54
1 2 3.417275 AAGCGATCTGGTCTCGGCG 62.417 63.158 0.00 0.00 36.65 6.46
2 3 1.590259 GAAGCGATCTGGTCTCGGC 60.590 63.158 0.00 0.00 36.65 5.54
3 4 1.002251 GTAGAAGCGATCTGGTCTCGG 60.002 57.143 5.44 0.00 39.30 4.63
136 137 1.380403 TTGTTGAACCACCGGTGCTG 61.380 55.000 29.75 18.80 35.34 4.41
152 153 2.282462 CCGCTCCTTTGGGCTTGT 60.282 61.111 0.00 0.00 0.00 3.16
168 169 2.116125 ACAAAGCCAGGGTGCTCC 59.884 61.111 0.00 0.00 41.80 4.70
263 267 6.814146 AGTAATTAAGCTAACTCAGTGTCAGC 59.186 38.462 0.00 0.00 0.00 4.26
298 302 7.438459 CCCTGCAACTAATTACAGACATACTAC 59.562 40.741 3.10 0.00 31.62 2.73
299 303 7.497595 CCCTGCAACTAATTACAGACATACTA 58.502 38.462 3.10 0.00 31.62 1.82
300 304 6.349300 CCCTGCAACTAATTACAGACATACT 58.651 40.000 3.10 0.00 31.62 2.12
301 305 5.007724 GCCCTGCAACTAATTACAGACATAC 59.992 44.000 3.10 0.00 31.62 2.39
302 306 5.123227 GCCCTGCAACTAATTACAGACATA 58.877 41.667 3.10 0.00 31.62 2.29
303 307 3.947834 GCCCTGCAACTAATTACAGACAT 59.052 43.478 3.10 0.00 31.62 3.06
304 308 3.343617 GCCCTGCAACTAATTACAGACA 58.656 45.455 3.10 0.00 31.62 3.41
305 309 2.683362 GGCCCTGCAACTAATTACAGAC 59.317 50.000 0.00 0.00 31.62 3.51
306 310 2.356741 GGGCCCTGCAACTAATTACAGA 60.357 50.000 17.04 0.00 31.62 3.41
365 377 6.849502 ACAGTAACTGAATCATTGATTGCTG 58.150 36.000 16.41 13.35 31.89 4.41
412 453 3.547746 TCGTTCAAACTTGGCCTTTAGT 58.452 40.909 3.32 1.66 0.00 2.24
413 454 4.201970 TGTTCGTTCAAACTTGGCCTTTAG 60.202 41.667 3.32 0.94 0.00 1.85
414 455 3.695060 TGTTCGTTCAAACTTGGCCTTTA 59.305 39.130 3.32 0.00 0.00 1.85
415 456 2.494073 TGTTCGTTCAAACTTGGCCTTT 59.506 40.909 3.32 0.00 0.00 3.11
416 457 2.096248 TGTTCGTTCAAACTTGGCCTT 58.904 42.857 3.32 0.00 0.00 4.35
417 458 1.757682 TGTTCGTTCAAACTTGGCCT 58.242 45.000 3.32 0.00 0.00 5.19
461 811 6.008960 AGAAAGCTCAACCAGATTCAGAAAT 58.991 36.000 0.00 0.00 27.49 2.17
490 840 1.550524 AGCTTAGCAGATTCACACCGA 59.449 47.619 7.07 0.00 0.00 4.69
495 845 5.816777 AGATTCAGAAGCTTAGCAGATTCAC 59.183 40.000 7.07 0.00 46.28 3.18
521 871 4.161565 ACTTCACATCTGTATTTAGCCCGA 59.838 41.667 0.00 0.00 0.00 5.14
523 873 4.816925 GGACTTCACATCTGTATTTAGCCC 59.183 45.833 0.00 0.00 0.00 5.19
525 875 6.371548 TGTTGGACTTCACATCTGTATTTAGC 59.628 38.462 0.00 0.00 0.00 3.09
526 876 7.905604 TGTTGGACTTCACATCTGTATTTAG 57.094 36.000 0.00 0.00 0.00 1.85
527 877 7.095397 CGTTGTTGGACTTCACATCTGTATTTA 60.095 37.037 0.00 0.00 0.00 1.40
550 921 6.042143 AGACAATCAGCATTTGTTTTTCGTT 58.958 32.000 1.26 0.00 37.43 3.85
552 923 5.686841 TGAGACAATCAGCATTTGTTTTTCG 59.313 36.000 1.26 0.00 37.43 3.46
569 940 4.623932 ATCCAAGTTGCTAGTGAGACAA 57.376 40.909 0.00 0.00 0.00 3.18
629 1023 7.555965 AGAAAAACTTGATTGCCTGTTTACTT 58.444 30.769 0.00 0.00 33.07 2.24
671 1066 7.693952 TCTATTACCGCACATCAAAGAATTTC 58.306 34.615 0.00 0.00 35.03 2.17
734 1130 1.087501 GCGGATGTTCCCTTTCTCAC 58.912 55.000 0.00 0.00 31.13 3.51
738 1160 4.712122 TTTTATGCGGATGTTCCCTTTC 57.288 40.909 0.00 0.00 31.13 2.62
766 1190 2.985282 TGCTGGGCCAAGAAAGCG 60.985 61.111 12.85 0.00 38.53 4.68
1070 1508 2.216046 CAAGCACACACACTGATGAGT 58.784 47.619 0.00 0.00 0.00 3.41
1071 1509 2.032290 CACAAGCACACACACTGATGAG 60.032 50.000 0.00 0.00 0.00 2.90
1072 1510 1.941975 CACAAGCACACACACTGATGA 59.058 47.619 0.00 0.00 0.00 2.92
1073 1511 1.941975 TCACAAGCACACACACTGATG 59.058 47.619 0.00 0.00 0.00 3.07
1074 1512 2.330440 TCACAAGCACACACACTGAT 57.670 45.000 0.00 0.00 0.00 2.90
1075 1513 2.106477 TTCACAAGCACACACACTGA 57.894 45.000 0.00 0.00 0.00 3.41
1076 1514 2.917701 TTTCACAAGCACACACACTG 57.082 45.000 0.00 0.00 0.00 3.66
1077 1515 2.754552 ACATTTCACAAGCACACACACT 59.245 40.909 0.00 0.00 0.00 3.55
1078 1516 2.853594 CACATTTCACAAGCACACACAC 59.146 45.455 0.00 0.00 0.00 3.82
1079 1517 2.751806 TCACATTTCACAAGCACACACA 59.248 40.909 0.00 0.00 0.00 3.72
1080 1518 3.419264 TCACATTTCACAAGCACACAC 57.581 42.857 0.00 0.00 0.00 3.82
1081 1519 3.631227 TCATCACATTTCACAAGCACACA 59.369 39.130 0.00 0.00 0.00 3.72
1132 1570 4.097741 CACATGTTCAGTCCAAAGTCCAAA 59.902 41.667 0.00 0.00 0.00 3.28
1135 1573 2.030805 GCACATGTTCAGTCCAAAGTCC 60.031 50.000 0.00 0.00 0.00 3.85
1138 1576 2.606308 GCTGCACATGTTCAGTCCAAAG 60.606 50.000 23.55 1.36 33.09 2.77
1220 1658 4.804806 GGGAACGGGCACTTGTTA 57.195 55.556 0.00 0.00 0.00 2.41
1904 2342 3.402681 CCCTGGGCCACACGATCT 61.403 66.667 0.00 0.00 0.00 2.75
1921 2359 3.368571 GGCTGCCCACTGCTCAAC 61.369 66.667 7.66 0.00 42.00 3.18
1979 2422 8.426489 ACACCTCATGTATAAAATACATACGGT 58.574 33.333 17.81 17.81 40.88 4.83
1997 2441 8.296713 GTCAACACAAAATATTACACACCTCAT 58.703 33.333 0.00 0.00 0.00 2.90
2000 2444 7.575414 TGTCAACACAAAATATTACACACCT 57.425 32.000 0.00 0.00 0.00 4.00
2084 2531 9.344772 TGCGGGAAAATAGTACATGTATTATTT 57.655 29.630 27.71 27.71 38.64 1.40
2085 2532 8.911918 TGCGGGAAAATAGTACATGTATTATT 57.088 30.769 21.60 21.60 31.85 1.40
2086 2533 8.911918 TTGCGGGAAAATAGTACATGTATTAT 57.088 30.769 13.54 13.54 0.00 1.28
2087 2534 8.734218 TTTGCGGGAAAATAGTACATGTATTA 57.266 30.769 9.18 9.74 0.00 0.98
2088 2535 7.633193 TTTGCGGGAAAATAGTACATGTATT 57.367 32.000 9.18 7.53 0.00 1.89
2130 2577 2.290197 ACATGCATTTTTCCCGCCAAAT 60.290 40.909 0.00 0.00 0.00 2.32
2131 2578 1.071385 ACATGCATTTTTCCCGCCAAA 59.929 42.857 0.00 0.00 0.00 3.28
2132 2579 0.683973 ACATGCATTTTTCCCGCCAA 59.316 45.000 0.00 0.00 0.00 4.52
2134 2581 1.476488 AGTACATGCATTTTTCCCGCC 59.524 47.619 0.00 0.00 0.00 6.13
2135 2582 2.939460 AGTACATGCATTTTTCCCGC 57.061 45.000 0.00 0.00 0.00 6.13
2136 2583 7.925993 TCTAAATAGTACATGCATTTTTCCCG 58.074 34.615 0.00 0.00 0.00 5.14
2137 2584 8.352942 CCTCTAAATAGTACATGCATTTTTCCC 58.647 37.037 0.00 0.00 0.00 3.97
2138 2585 7.862873 GCCTCTAAATAGTACATGCATTTTTCC 59.137 37.037 0.00 0.00 0.00 3.13
2139 2586 8.624776 AGCCTCTAAATAGTACATGCATTTTTC 58.375 33.333 0.00 0.00 0.00 2.29
2140 2587 8.525290 AGCCTCTAAATAGTACATGCATTTTT 57.475 30.769 0.00 0.00 0.00 1.94
2146 2593 6.647067 CACCTTAGCCTCTAAATAGTACATGC 59.353 42.308 0.00 0.00 0.00 4.06
2177 2682 1.090052 AAATAGAGAACAGCGCGGCC 61.090 55.000 8.83 0.00 0.00 6.13
2199 2724 8.519799 TGTCAAAGAAAACAAGAGTTAATCCT 57.480 30.769 0.00 0.00 36.84 3.24
2249 2774 4.327087 GCAAAGCAGATAAAATCAAACCCG 59.673 41.667 0.00 0.00 0.00 5.28
2250 2775 4.631377 GGCAAAGCAGATAAAATCAAACCC 59.369 41.667 0.00 0.00 0.00 4.11
2268 2793 4.704540 TCAAAGAAGACAACTCAAGGCAAA 59.295 37.500 0.00 0.00 0.00 3.68
2472 2998 6.741992 TCATCTCCAACAACATCATAACAC 57.258 37.500 0.00 0.00 0.00 3.32
2477 3012 8.529424 ACAAATATCATCTCCAACAACATCAT 57.471 30.769 0.00 0.00 0.00 2.45
2553 3088 7.004086 ACTTGTTTAACTGAATCCTCCATTGA 58.996 34.615 0.00 0.00 0.00 2.57
2559 3094 5.469084 ACGGAACTTGTTTAACTGAATCCTC 59.531 40.000 0.00 0.00 0.00 3.71
2582 3117 6.935208 ACTTGACTAGGGACACTAAAATGAAC 59.065 38.462 0.00 0.00 0.00 3.18
2601 3136 7.009540 GGCAATTAACATTGAGCATAACTTGAC 59.990 37.037 0.00 0.00 42.35 3.18
2757 3292 0.739462 TCTCAGGTAATTGCCGCACG 60.739 55.000 6.95 0.00 0.00 5.34
2763 3298 6.346096 TGTGGTAATAGTCTCAGGTAATTGC 58.654 40.000 0.00 0.00 0.00 3.56
2769 3304 3.194968 CCGTTGTGGTAATAGTCTCAGGT 59.805 47.826 0.00 0.00 0.00 4.00
2774 3309 4.587684 CCCTATCCGTTGTGGTAATAGTCT 59.412 45.833 0.00 0.00 39.52 3.24
2781 3316 0.618107 TGCCCCTATCCGTTGTGGTA 60.618 55.000 0.00 0.00 39.52 3.25
2793 3328 4.384427 CCGGTATTTCTTTTAGTGCCCCTA 60.384 45.833 0.00 0.00 0.00 3.53
2802 3337 6.459024 CGATTGGAATGCCGGTATTTCTTTTA 60.459 38.462 22.39 7.66 36.79 1.52
2824 3359 6.039493 ACAGGTTTCAGAGTTACGATATCGAT 59.961 38.462 30.75 16.96 43.02 3.59
2826 3361 5.455849 CACAGGTTTCAGAGTTACGATATCG 59.544 44.000 23.18 23.18 46.33 2.92


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

AutoCloner maintained by Alex Coulton.