Multiple sequence alignment - TraesCS1B01G231600

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 TraesCS1B01G231600 chr1B 100.000 5650 0 0 1 5650 416124824 416130473 0.000000e+00 10434.0
1 TraesCS1B01G231600 chr1D 94.409 4579 167 34 940 5476 307459835 307464366 0.000000e+00 6955.0
2 TraesCS1B01G231600 chr1D 85.714 609 67 14 3 607 307458830 307459422 4.810000e-175 625.0
3 TraesCS1B01G231600 chr1D 93.413 334 11 6 600 931 307459451 307459775 8.510000e-133 484.0
4 TraesCS1B01G231600 chr1D 100.000 62 0 0 5464 5525 307464703 307464764 1.290000e-21 115.0
5 TraesCS1B01G231600 chr1A 93.190 4640 194 48 936 5528 386720051 386724615 0.000000e+00 6706.0
6 TraesCS1B01G231600 chr1A 84.934 677 84 11 3 664 386719101 386719774 0.000000e+00 669.0
7 TraesCS1B01G231600 chr1A 91.630 227 8 3 710 931 386719787 386720007 2.560000e-78 303.0
8 TraesCS1B01G231600 chr1A 74.373 359 82 6 176 528 479033764 479033410 1.640000e-30 145.0
9 TraesCS1B01G231600 chr1A 76.168 214 38 10 319 528 549555314 549555518 3.600000e-17 100.0
10 TraesCS1B01G231600 chr1A 82.292 96 5 9 5566 5650 386724614 386724708 7.850000e-09 73.1
11 TraesCS1B01G231600 chr6B 92.879 660 16 5 4782 5433 529654220 529654856 0.000000e+00 929.0
12 TraesCS1B01G231600 chr4D 76.407 462 94 12 96 547 54280501 54280957 9.460000e-58 235.0
13 TraesCS1B01G231600 chr3A 75.276 453 102 8 97 543 158163351 158163799 2.060000e-49 207.0
14 TraesCS1B01G231600 chr7D 76.627 338 59 15 223 552 151014816 151014491 9.740000e-38 169.0
15 TraesCS1B01G231600 chr7D 78.067 269 52 5 191 454 481859557 481859291 4.530000e-36 163.0
16 TraesCS1B01G231600 chr2D 74.693 407 85 13 152 545 645665918 645666319 1.260000e-36 165.0
17 TraesCS1B01G231600 chr3D 73.892 406 94 12 97 494 604656627 604657028 9.800000e-33 152.0


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 TraesCS1B01G231600 chr1B 416124824 416130473 5649 False 10434.000 10434 100.0000 1 5650 1 chr1B.!!$F1 5649
1 TraesCS1B01G231600 chr1D 307458830 307464764 5934 False 2044.750 6955 93.3840 3 5525 4 chr1D.!!$F1 5522
2 TraesCS1B01G231600 chr1A 386719101 386724708 5607 False 1937.775 6706 88.0115 3 5650 4 chr1A.!!$F2 5647
3 TraesCS1B01G231600 chr6B 529654220 529654856 636 False 929.000 929 92.8790 4782 5433 1 chr6B.!!$F1 651

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
935 993 0.035915 AAGAGGAAGAAGAAGCCGCC 60.036 55.000 0.0 0.0 0.00 6.13 F
1851 1970 1.456892 ATCGGAGTATGGCGGGACA 60.457 57.895 0.0 0.0 0.00 4.02 F
2637 2759 0.257039 GGGCTCCACCTGTGAATGAT 59.743 55.000 0.0 0.0 39.10 2.45 F
3115 3248 0.466007 TTCAGCAAAGGCAGCAGTGA 60.466 50.000 0.0 0.0 44.61 3.41 F
4290 4428 0.528684 GATCAAGAAGCGGACCGAGG 60.529 60.000 20.5 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1914 2033 0.112606 TGACCGTGGAGAAGGAGTCT 59.887 55.0 0.0 0.0 40.25 3.24 R
3673 3811 0.962356 ATGTGGTAGTGGCAGCTTGC 60.962 55.0 0.0 0.0 44.08 4.01 R
4290 4428 0.246635 TCCAGCTCCTTTGAGTACGC 59.753 55.0 0.0 0.0 40.95 4.42 R
4637 4775 1.040893 TGACATCCTACCGCACCGAT 61.041 55.0 0.0 0.0 0.00 4.18 R
5535 6098 0.108709 CCATGTCATTGGGCAAACGG 60.109 55.0 0.0 0.0 32.80 4.44 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
60 62 7.445707 AGAGAGGTGGTTTCTTCTGAAAATAAC 59.554 37.037 0.00 0.00 42.94 1.89
111 115 1.071228 GTCCGTTAGGGTTTGTGTCCT 59.929 52.381 0.00 0.00 38.33 3.85
118 122 2.972348 AGGGTTTGTGTCCTACTGAGA 58.028 47.619 0.00 0.00 0.00 3.27
139 143 2.512515 GTGAGGTGATGGCGGCTC 60.513 66.667 11.43 6.00 0.00 4.70
140 144 2.685017 TGAGGTGATGGCGGCTCT 60.685 61.111 11.43 0.00 0.00 4.09
141 145 2.202987 GAGGTGATGGCGGCTCTG 60.203 66.667 11.43 0.00 0.00 3.35
205 209 2.033550 GGTTCGTCTAGCATCGTCAGAT 59.966 50.000 0.00 0.00 37.65 2.90
240 244 4.271816 CTCCGGCGGATCTCGTGG 62.272 72.222 31.23 12.23 41.72 4.94
247 251 1.734137 CGGATCTCGTGGGATTCGT 59.266 57.895 2.13 0.00 39.20 3.85
249 253 1.854227 GGATCTCGTGGGATTCGTTC 58.146 55.000 0.00 0.00 0.00 3.95
250 254 1.136305 GGATCTCGTGGGATTCGTTCA 59.864 52.381 0.00 0.00 0.00 3.18
281 285 1.272490 TCGATGGATACGCTTGGATCC 59.728 52.381 4.20 4.20 41.85 3.36
289 293 1.218047 CGCTTGGATCCGGTCTTCA 59.782 57.895 7.39 0.00 0.00 3.02
293 297 2.680805 GCTTGGATCCGGTCTTCATTCA 60.681 50.000 7.39 0.00 0.00 2.57
295 299 3.475566 TGGATCCGGTCTTCATTCATC 57.524 47.619 7.39 0.00 0.00 2.92
296 300 2.104792 TGGATCCGGTCTTCATTCATCC 59.895 50.000 7.39 3.50 0.00 3.51
303 307 0.824109 TCTTCATTCATCCGCGTCCT 59.176 50.000 4.92 0.00 0.00 3.85
316 321 1.444119 GCGTCCTTGTGTTTGCAGGA 61.444 55.000 0.00 0.00 0.00 3.86
355 361 0.466124 GTTCTCTTCATCGGGGAGGG 59.534 60.000 0.00 0.00 0.00 4.30
361 367 2.438434 CATCGGGGAGGGTGTTGC 60.438 66.667 0.00 0.00 0.00 4.17
373 379 1.202770 GGGTGTTGCTCTGGTGTACTT 60.203 52.381 0.00 0.00 0.00 2.24
392 398 1.218316 GTCTGGGACCTTAGCACGG 59.782 63.158 0.00 0.00 0.00 4.94
417 423 6.034683 GCGATTTTTCGACTGTCTACTACAAT 59.965 38.462 6.21 0.00 34.50 2.71
429 435 5.013287 TGTCTACTACAATAAGGTTTGCCCA 59.987 40.000 0.00 0.00 34.29 5.36
444 460 1.907739 CCCAGCTTCGATGAGGGAA 59.092 57.895 18.72 0.00 42.25 3.97
445 461 0.253044 CCCAGCTTCGATGAGGGAAA 59.747 55.000 18.72 0.00 42.25 3.13
456 472 1.254975 TGAGGGAAAGGCGATGACGA 61.255 55.000 0.00 0.00 42.66 4.20
494 510 9.286946 CAACTCGATCTAGTAAATTTAGTCGTT 57.713 33.333 8.84 0.00 0.00 3.85
502 518 9.177608 TCTAGTAAATTTAGTCGTTGCTAGGTA 57.822 33.333 8.84 0.00 37.83 3.08
505 521 6.963049 AAATTTAGTCGTTGCTAGGTAGTG 57.037 37.500 0.00 0.00 0.00 2.74
528 544 5.644636 TGTACGGACCTGGATGTAATTTTTC 59.355 40.000 0.00 0.00 0.00 2.29
533 549 6.621613 GGACCTGGATGTAATTTTTCACTTC 58.378 40.000 0.00 0.00 0.00 3.01
547 563 7.496529 TTTTTCACTTCTGGTGTTCTCTATG 57.503 36.000 0.00 0.00 45.50 2.23
761 814 1.467342 CGGAAAAGAGGCCCGTTAAAG 59.533 52.381 0.00 0.00 38.55 1.85
763 816 3.151554 GGAAAAGAGGCCCGTTAAAGAA 58.848 45.455 0.00 0.00 0.00 2.52
764 817 3.190744 GGAAAAGAGGCCCGTTAAAGAAG 59.809 47.826 0.00 0.00 0.00 2.85
809 862 9.758651 AATAAAAAGAGCAACGGAAATTAAACT 57.241 25.926 0.00 0.00 0.00 2.66
810 863 9.758651 ATAAAAAGAGCAACGGAAATTAAACTT 57.241 25.926 0.00 0.00 0.00 2.66
926 984 0.608640 GAGTGGGCGAAGAGGAAGAA 59.391 55.000 0.00 0.00 0.00 2.52
931 989 1.364721 GGCGAAGAGGAAGAAGAAGC 58.635 55.000 0.00 0.00 0.00 3.86
932 990 1.364721 GCGAAGAGGAAGAAGAAGCC 58.635 55.000 0.00 0.00 0.00 4.35
934 992 1.364721 GAAGAGGAAGAAGAAGCCGC 58.635 55.000 0.00 0.00 0.00 6.53
935 993 0.035915 AAGAGGAAGAAGAAGCCGCC 60.036 55.000 0.00 0.00 0.00 6.13
937 995 2.820037 GGAAGAAGAAGCCGCCGG 60.820 66.667 0.00 0.00 0.00 6.13
938 996 2.264794 GAAGAAGAAGCCGCCGGA 59.735 61.111 7.68 0.00 0.00 5.14
942 1052 2.047179 AAGAAGCCGCCGGAAGAC 60.047 61.111 7.68 0.00 0.00 3.01
945 1055 4.394712 AAGCCGCCGGAAGACAGG 62.395 66.667 7.68 0.00 34.56 4.00
1746 1865 1.756950 CGGATGGGAGGACGAGGAA 60.757 63.158 0.00 0.00 0.00 3.36
1842 1961 2.920645 CGCGGCCAGATCGGAGTAT 61.921 63.158 2.24 0.00 36.56 2.12
1851 1970 1.456892 ATCGGAGTATGGCGGGACA 60.457 57.895 0.00 0.00 0.00 4.02
1914 2033 1.078356 CGAGAGGTCAGAGGTCGGA 60.078 63.158 0.00 0.00 0.00 4.55
2094 2213 0.751643 ACCGCAACTTCCAGCAACTT 60.752 50.000 0.00 0.00 0.00 2.66
2138 2257 0.395586 TGCGCCCCAGAATGCTATTT 60.396 50.000 4.18 0.00 31.97 1.40
2238 2357 7.396540 TTGGCTTAATCTGATTTCTCCTTTC 57.603 36.000 8.38 0.00 0.00 2.62
2352 2471 2.025981 CACCAATTCACTGGAGATGGGA 60.026 50.000 0.00 0.00 38.96 4.37
2520 2640 4.506758 ACATTGCTCAAATTGGTATTGCC 58.493 39.130 0.00 0.00 37.90 4.52
2637 2759 0.257039 GGGCTCCACCTGTGAATGAT 59.743 55.000 0.00 0.00 39.10 2.45
2645 2767 4.474651 TCCACCTGTGAATGATCCAACTAT 59.525 41.667 0.00 0.00 0.00 2.12
2690 2813 6.983307 TGATGTTTTCGGTCATCAACAAATTT 59.017 30.769 5.54 0.00 44.55 1.82
2706 2829 7.495279 TCAACAAATTTCAAATTCTTCCACCAG 59.505 33.333 0.00 0.00 0.00 4.00
2843 2975 3.960102 AGAGCTCTATCTCTTGGAGGTTG 59.040 47.826 16.50 0.00 40.32 3.77
2866 2998 8.480501 GTTGTAGGATTCTGGTAGGTACAAATA 58.519 37.037 0.00 0.00 32.36 1.40
2914 3047 7.864379 AGACATTGTTTCTGTTTTGCTAGATTG 59.136 33.333 0.00 0.00 0.00 2.67
3077 3210 1.509923 GAACAGCTGGAGCATTGGC 59.490 57.895 19.93 0.00 45.16 4.52
3115 3248 0.466007 TTCAGCAAAGGCAGCAGTGA 60.466 50.000 0.00 0.00 44.61 3.41
3148 3281 4.392921 AGATCTCCTAACCACACATTCG 57.607 45.455 0.00 0.00 0.00 3.34
3422 3555 8.336235 AGTTTGGGATAGAATGTGATTCCTTTA 58.664 33.333 0.00 0.00 40.13 1.85
3448 3581 5.519927 AGTTATTGCACTGCACTTGTTTTTC 59.480 36.000 2.26 0.00 38.71 2.29
3455 3590 4.032104 CACTGCACTTGTTTTTCTTCTTGC 59.968 41.667 0.00 0.00 0.00 4.01
3464 3599 9.630098 ACTTGTTTTTCTTCTTGCATATGTATG 57.370 29.630 4.29 2.40 36.78 2.39
3505 3643 5.354234 ACCCAACTGTTCAGATATTAAAGCG 59.646 40.000 6.83 0.00 0.00 4.68
3512 3650 8.926710 ACTGTTCAGATATTAAAGCGTATATGC 58.073 33.333 9.00 9.00 0.00 3.14
3606 3744 1.771255 CTTGGAATACAGAGGGAGGGG 59.229 57.143 0.00 0.00 0.00 4.79
3667 3805 2.095567 GCTGCAATCACTGATCGTTGTT 60.096 45.455 0.00 0.00 0.00 2.83
3697 3835 0.904649 CTGCCACTACCACATCCTCA 59.095 55.000 0.00 0.00 0.00 3.86
3763 3901 2.348218 CGAGCTTTGTTTCGCGTAAGTT 60.348 45.455 5.77 1.60 41.68 2.66
3950 4088 1.296392 CAACTCCATGGCCGAGTCA 59.704 57.895 6.96 0.00 39.69 3.41
3995 4133 4.193334 CGTGATCTCGAGGCCGCA 62.193 66.667 13.56 3.04 35.37 5.69
4145 4283 1.138459 ACTCATCTCACGCGAGCTG 59.862 57.895 15.93 2.11 39.30 4.24
4190 4328 3.140814 GCATTGGACCGGCTTCCC 61.141 66.667 0.00 0.00 34.33 3.97
4229 4367 2.012673 GCCATCAAGAGCTTCGTGAAT 58.987 47.619 6.06 0.00 38.31 2.57
4262 4400 1.055849 TCTACACCAAGCAGGCAGAA 58.944 50.000 0.00 0.00 43.14 3.02
4290 4428 0.528684 GATCAAGAAGCGGACCGAGG 60.529 60.000 20.50 0.00 0.00 4.63
4337 4475 1.817099 CAACTCGCTGAGGGCCATC 60.817 63.158 11.34 11.34 37.74 3.51
4365 4503 3.876274 AGTACTACCAGTCGTACTCGA 57.124 47.619 8.81 0.00 41.71 4.04
4469 4607 2.680352 ACCGAGATCGCCCAGTGT 60.680 61.111 0.00 0.00 38.18 3.55
4665 4811 2.755208 CGGTAGGATGTCAGACCCCATA 60.755 54.545 10.68 0.00 0.00 2.74
4690 4836 5.240183 AGAACATCATTTTGGTGTGTCTCTG 59.760 40.000 0.00 0.00 41.60 3.35
4988 5148 3.944055 TTACGCTTGCTCTTCTCTCTT 57.056 42.857 0.00 0.00 0.00 2.85
5024 5196 5.830457 TCTATGCTCATGTCTGTAGCTAAGT 59.170 40.000 0.00 0.00 37.16 2.24
5026 5198 5.152623 TGCTCATGTCTGTAGCTAAGTTT 57.847 39.130 0.00 0.00 37.16 2.66
5027 5199 5.551233 TGCTCATGTCTGTAGCTAAGTTTT 58.449 37.500 0.00 0.00 37.16 2.43
5028 5200 5.997746 TGCTCATGTCTGTAGCTAAGTTTTT 59.002 36.000 0.00 0.00 37.16 1.94
5260 5452 0.965363 CCACCGCAGTTAATTGCCCT 60.965 55.000 16.34 0.00 41.01 5.19
5261 5453 0.171007 CACCGCAGTTAATTGCCCTG 59.829 55.000 16.34 8.39 41.01 4.45
5262 5454 1.139520 CCGCAGTTAATTGCCCTGC 59.860 57.895 16.34 10.56 46.25 4.85
5264 5456 3.727419 GCAGTTAATTGCCCTGCTG 57.273 52.632 11.66 0.00 46.23 4.41
5265 5457 0.459063 GCAGTTAATTGCCCTGCTGC 60.459 55.000 11.66 3.37 46.23 5.25
5528 6091 2.042831 GCCAAATGCTGCGTCCTCT 61.043 57.895 0.00 0.00 36.87 3.69
5529 6092 1.589716 GCCAAATGCTGCGTCCTCTT 61.590 55.000 0.00 0.00 36.87 2.85
5530 6093 0.449388 CCAAATGCTGCGTCCTCTTC 59.551 55.000 0.00 0.00 0.00 2.87
5531 6094 0.095935 CAAATGCTGCGTCCTCTTCG 59.904 55.000 0.00 0.00 0.00 3.79
5532 6095 1.021390 AAATGCTGCGTCCTCTTCGG 61.021 55.000 0.00 0.00 0.00 4.30
5533 6096 4.742201 TGCTGCGTCCTCTTCGGC 62.742 66.667 0.00 0.00 0.00 5.54
5534 6097 4.443266 GCTGCGTCCTCTTCGGCT 62.443 66.667 0.00 0.00 0.00 5.52
5535 6098 2.202676 CTGCGTCCTCTTCGGCTC 60.203 66.667 0.00 0.00 0.00 4.70
5536 6099 3.708220 CTGCGTCCTCTTCGGCTCC 62.708 68.421 0.00 0.00 0.00 4.70
5537 6100 4.856607 GCGTCCTCTTCGGCTCCG 62.857 72.222 1.14 1.14 41.35 4.63
5538 6101 3.441290 CGTCCTCTTCGGCTCCGT 61.441 66.667 8.28 0.00 40.74 4.69
5539 6102 2.971452 GTCCTCTTCGGCTCCGTT 59.029 61.111 8.28 0.00 40.74 4.44
5540 6103 1.292541 GTCCTCTTCGGCTCCGTTT 59.707 57.895 8.28 0.00 40.74 3.60
5541 6104 1.014564 GTCCTCTTCGGCTCCGTTTG 61.015 60.000 8.28 0.66 40.74 2.93
5542 6105 2.391389 CCTCTTCGGCTCCGTTTGC 61.391 63.158 8.28 0.00 40.74 3.68
5543 6106 2.358247 TCTTCGGCTCCGTTTGCC 60.358 61.111 8.28 0.00 46.42 4.52
5548 6111 2.573340 GGCTCCGTTTGCCCAATG 59.427 61.111 0.00 0.00 44.32 2.82
5549 6112 1.976474 GGCTCCGTTTGCCCAATGA 60.976 57.895 0.00 0.00 44.32 2.57
5550 6113 1.212751 GCTCCGTTTGCCCAATGAC 59.787 57.895 0.00 0.00 0.00 3.06
5551 6114 1.523154 GCTCCGTTTGCCCAATGACA 61.523 55.000 0.00 0.00 0.00 3.58
5552 6115 1.176527 CTCCGTTTGCCCAATGACAT 58.823 50.000 0.00 0.00 0.00 3.06
5553 6116 0.887247 TCCGTTTGCCCAATGACATG 59.113 50.000 0.00 0.00 0.00 3.21
5554 6117 0.108709 CCGTTTGCCCAATGACATGG 60.109 55.000 0.00 0.00 40.35 3.66
5555 6118 0.737019 CGTTTGCCCAATGACATGGC 60.737 55.000 9.37 9.37 45.56 4.40
5556 6119 0.609662 GTTTGCCCAATGACATGGCT 59.390 50.000 15.66 0.00 45.56 4.75
5557 6120 1.002315 GTTTGCCCAATGACATGGCTT 59.998 47.619 15.66 0.00 45.56 4.35
5558 6121 0.896923 TTGCCCAATGACATGGCTTC 59.103 50.000 15.66 0.00 45.56 3.86
5559 6122 0.251698 TGCCCAATGACATGGCTTCA 60.252 50.000 15.66 0.00 45.56 3.02
5560 6123 1.117150 GCCCAATGACATGGCTTCAT 58.883 50.000 0.00 0.00 42.01 2.57
5561 6124 1.483415 GCCCAATGACATGGCTTCATT 59.517 47.619 0.00 1.92 43.13 2.57
5588 6151 3.726517 CGGCCTGCGTTTCTGTGG 61.727 66.667 0.00 0.00 0.00 4.17
5596 6159 1.450211 CGTTTCTGTGGGTGGGAGT 59.550 57.895 0.00 0.00 0.00 3.85
5601 6164 1.127567 TCTGTGGGTGGGAGTGAAGG 61.128 60.000 0.00 0.00 0.00 3.46
5602 6165 1.385347 TGTGGGTGGGAGTGAAGGT 60.385 57.895 0.00 0.00 0.00 3.50
5604 6167 2.034221 GGGTGGGAGTGAAGGTGC 59.966 66.667 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.678056 ATTTACTCGCTCCAGTTGTGA 57.322 42.857 0.00 0.00 0.00 3.58
1 2 5.168569 TCTTATTTACTCGCTCCAGTTGTG 58.831 41.667 0.00 0.00 0.00 3.33
36 38 6.490381 GGTTATTTTCAGAAGAAACCACCTCT 59.510 38.462 14.25 0.00 43.09 3.69
41 43 6.072175 CCATCGGTTATTTTCAGAAGAAACCA 60.072 38.462 17.22 9.25 43.09 3.67
43 45 7.021790 GTCCATCGGTTATTTTCAGAAGAAAC 58.978 38.462 0.00 0.00 43.09 2.78
50 52 7.553881 ACATTAGTCCATCGGTTATTTTCAG 57.446 36.000 0.00 0.00 0.00 3.02
60 62 4.766375 ACACCTAAACATTAGTCCATCGG 58.234 43.478 0.00 0.00 0.00 4.18
111 115 3.515502 CCATCACCTCACCTTTCTCAGTA 59.484 47.826 0.00 0.00 0.00 2.74
118 122 1.002134 CCGCCATCACCTCACCTTT 60.002 57.895 0.00 0.00 0.00 3.11
139 143 4.452825 AGAGCATCATTCCATCTTCACAG 58.547 43.478 0.00 0.00 37.82 3.66
140 144 4.449131 GAGAGCATCATTCCATCTTCACA 58.551 43.478 0.00 0.00 37.82 3.58
141 145 3.814283 GGAGAGCATCATTCCATCTTCAC 59.186 47.826 0.00 0.00 37.82 3.18
199 203 3.125829 CACAAGTACATGTGCCATCTGAC 59.874 47.826 17.38 0.00 43.67 3.51
209 213 1.337823 GCCGGAGACACAAGTACATGT 60.338 52.381 5.05 2.69 0.00 3.21
210 214 1.359848 GCCGGAGACACAAGTACATG 58.640 55.000 5.05 0.00 0.00 3.21
211 215 0.108804 CGCCGGAGACACAAGTACAT 60.109 55.000 5.05 0.00 0.00 2.29
216 220 1.519455 GATCCGCCGGAGACACAAG 60.519 63.158 13.12 0.00 34.05 3.16
217 221 1.945354 GAGATCCGCCGGAGACACAA 61.945 60.000 13.12 0.00 34.05 3.33
240 244 7.921734 ATCGAAGATAAACGCTGAACGAATCC 61.922 42.308 0.00 0.00 44.37 3.01
247 251 4.118093 TCCATCGAAGATAAACGCTGAA 57.882 40.909 0.00 0.00 45.12 3.02
249 253 4.088638 CGTATCCATCGAAGATAAACGCTG 59.911 45.833 9.41 0.00 45.12 5.18
250 254 4.227538 CGTATCCATCGAAGATAAACGCT 58.772 43.478 9.41 0.00 45.12 5.07
281 285 0.806102 ACGCGGATGAATGAAGACCG 60.806 55.000 12.47 0.00 45.26 4.79
289 293 0.036388 ACACAAGGACGCGGATGAAT 60.036 50.000 12.47 0.00 0.00 2.57
293 297 1.852067 GCAAACACAAGGACGCGGAT 61.852 55.000 12.47 0.00 0.00 4.18
295 299 2.051345 GCAAACACAAGGACGCGG 60.051 61.111 12.47 0.00 0.00 6.46
296 300 1.369209 CTGCAAACACAAGGACGCG 60.369 57.895 3.53 3.53 0.00 6.01
303 307 2.562298 GGATCCAATCCTGCAAACACAA 59.438 45.455 6.95 0.00 46.19 3.33
355 361 2.544267 GACAAGTACACCAGAGCAACAC 59.456 50.000 0.00 0.00 0.00 3.32
361 367 2.028930 GTCCCAGACAAGTACACCAGAG 60.029 54.545 0.00 0.00 32.09 3.35
373 379 1.541310 CCGTGCTAAGGTCCCAGACA 61.541 60.000 0.00 0.00 33.68 3.41
392 398 4.855388 TGTAGTAGACAGTCGAAAAATCGC 59.145 41.667 0.00 0.00 32.86 4.58
417 423 0.398696 TCGAAGCTGGGCAAACCTTA 59.601 50.000 0.00 0.00 41.11 2.69
429 435 0.107459 GCCTTTCCCTCATCGAAGCT 60.107 55.000 0.00 0.00 0.00 3.74
444 460 0.802222 CATGTCGTCGTCATCGCCTT 60.802 55.000 1.83 0.00 36.96 4.35
445 461 1.226688 CATGTCGTCGTCATCGCCT 60.227 57.895 1.83 0.00 36.96 5.52
456 472 0.317160 TCGAGTTGAAGGCATGTCGT 59.683 50.000 0.00 0.00 33.61 4.34
461 477 5.854010 TTACTAGATCGAGTTGAAGGCAT 57.146 39.130 13.99 0.00 0.00 4.40
494 510 1.283029 AGGTCCGTACACTACCTAGCA 59.717 52.381 8.61 0.00 41.86 3.49
502 518 2.519771 TACATCCAGGTCCGTACACT 57.480 50.000 0.00 0.00 0.00 3.55
505 521 5.644636 TGAAAAATTACATCCAGGTCCGTAC 59.355 40.000 0.00 0.00 0.00 3.67
533 549 4.703645 TCGAGAACATAGAGAACACCAG 57.296 45.455 0.00 0.00 0.00 4.00
571 587 6.811170 ACAAATTTACCCATTTCAATACAGCG 59.189 34.615 0.00 0.00 0.00 5.18
578 594 6.393990 CGGATGACAAATTTACCCATTTCAA 58.606 36.000 0.00 0.00 0.00 2.69
657 710 1.132780 GAGAAGCGCGTTACCTCGTC 61.133 60.000 8.43 0.00 0.00 4.20
914 972 1.634702 CGGCTTCTTCTTCCTCTTCG 58.365 55.000 0.00 0.00 0.00 3.79
926 984 3.302347 CTGTCTTCCGGCGGCTTCT 62.302 63.158 23.83 0.00 0.00 2.85
931 989 4.148825 CTCCCTGTCTTCCGGCGG 62.149 72.222 22.51 22.51 0.00 6.13
932 990 3.068691 TCTCCCTGTCTTCCGGCG 61.069 66.667 0.00 0.00 0.00 6.46
934 992 1.040339 CCTCTCTCCCTGTCTTCCGG 61.040 65.000 0.00 0.00 0.00 5.14
935 993 1.040339 CCCTCTCTCCCTGTCTTCCG 61.040 65.000 0.00 0.00 0.00 4.30
937 995 1.687996 CCTCCCTCTCTCCCTGTCTTC 60.688 61.905 0.00 0.00 0.00 2.87
938 996 0.338120 CCTCCCTCTCTCCCTGTCTT 59.662 60.000 0.00 0.00 0.00 3.01
942 1052 1.232792 CCTCCTCCCTCTCTCCCTG 59.767 68.421 0.00 0.00 0.00 4.45
945 1055 2.015726 TCCCCTCCTCCCTCTCTCC 61.016 68.421 0.00 0.00 0.00 3.71
1746 1865 2.866028 GTCGACGCGTAGTGGTCT 59.134 61.111 13.97 0.00 45.78 3.85
1785 1904 2.685380 CCCACCTCGCCTTCCTCT 60.685 66.667 0.00 0.00 0.00 3.69
1914 2033 0.112606 TGACCGTGGAGAAGGAGTCT 59.887 55.000 0.00 0.00 40.25 3.24
2094 2213 6.964741 TTCGTGTAATGGCGATTACTTTTA 57.035 33.333 25.76 8.69 43.10 1.52
2138 2257 6.976934 AAAAATCCTAAAGCACTTGGAGAA 57.023 33.333 0.00 0.00 31.59 2.87
2238 2357 2.959372 TGGTACACCGTCTCTGCG 59.041 61.111 0.00 0.00 39.43 5.18
2352 2471 1.925255 TGGCTCTTCCCTTCCATTGAT 59.075 47.619 0.00 0.00 0.00 2.57
2579 2699 6.458751 GCATGTTCCATCGACAACTAATGAAT 60.459 38.462 0.00 0.00 0.00 2.57
2618 2738 0.257039 ATCATTCACAGGTGGAGCCC 59.743 55.000 0.00 0.00 38.26 5.19
2637 2759 7.618019 AATATCCTCTAGCAACATAGTTGGA 57.382 36.000 11.39 0.28 34.04 3.53
2645 2767 6.268617 ACATCAGCTAATATCCTCTAGCAACA 59.731 38.462 6.86 0.00 42.51 3.33
2840 2972 5.927281 TGTACCTACCAGAATCCTACAAC 57.073 43.478 0.00 0.00 0.00 3.32
2914 3047 3.769844 TCAAATCTAGAGAGGTGTCACCC 59.230 47.826 18.80 10.12 39.75 4.61
3115 3248 6.501805 TGGTTAGGAGATCTAATGGCATGTAT 59.498 38.462 0.00 0.00 39.82 2.29
3148 3281 6.129874 AGCATAAAGGAAGGGAGGAAAATAC 58.870 40.000 0.00 0.00 0.00 1.89
3284 3417 2.007547 GCCTAGGAACTTTCTCGTGCC 61.008 57.143 14.75 0.00 41.75 5.01
3422 3555 4.654091 ACAAGTGCAGTGCAATAACTTT 57.346 36.364 21.67 0.00 41.47 2.66
3464 3599 5.180680 AGTTGGGTTCGATAAACTGTTTAGC 59.819 40.000 16.36 16.36 38.02 3.09
3505 3643 9.734620 TGCAGAAGTTCAAATAAATGCATATAC 57.265 29.630 0.00 0.00 37.50 1.47
3512 3650 5.717119 AGCCTGCAGAAGTTCAAATAAATG 58.283 37.500 17.39 0.00 0.00 2.32
3606 3744 2.138656 CTTGTCCAGCTTGGCACTGC 62.139 60.000 0.00 3.75 37.47 4.40
3667 3805 2.736995 GTGGCAGCTTGCGACGTA 60.737 61.111 7.33 0.00 46.21 3.57
3673 3811 0.962356 ATGTGGTAGTGGCAGCTTGC 60.962 55.000 0.00 0.00 44.08 4.01
3697 3835 4.498520 CGGACGCTGACGATGGCT 62.499 66.667 0.00 0.00 43.93 4.75
3763 3901 1.670791 GTTTCGGAACAAGGGACACA 58.329 50.000 0.38 0.00 35.79 3.72
3950 4088 1.366366 CCTGTGAAGGTCGGACGTT 59.634 57.895 15.24 15.24 0.00 3.99
3995 4133 2.581354 GAGTGCCATGCCGAGACT 59.419 61.111 0.00 0.00 0.00 3.24
4145 4283 1.444553 CTCGTCGCAGAAGGTGGTC 60.445 63.158 0.00 0.00 39.69 4.02
4229 4367 3.774216 TGGTGTAGATGACATGGATGACA 59.226 43.478 0.00 0.00 41.14 3.58
4262 4400 3.703556 TCCGCTTCTTGATCTTCATCTCT 59.296 43.478 0.00 0.00 0.00 3.10
4290 4428 0.246635 TCCAGCTCCTTTGAGTACGC 59.753 55.000 0.00 0.00 40.95 4.42
4337 4475 3.683822 ACGACTGGTAGTACTTCTTCTCG 59.316 47.826 0.00 5.61 0.00 4.04
4469 4607 3.976490 ATCCTCCACCTTCCGGCGA 62.976 63.158 9.30 0.00 0.00 5.54
4637 4775 1.040893 TGACATCCTACCGCACCGAT 61.041 55.000 0.00 0.00 0.00 4.18
4665 4811 5.829924 AGAGACACACCAAAATGATGTTCTT 59.170 36.000 0.00 0.00 0.00 2.52
4690 4836 4.015872 TCAACATACCACCCAAAGAGAC 57.984 45.455 0.00 0.00 0.00 3.36
4988 5148 7.337689 AGACATGAGCATAGATTTTAAGTTGCA 59.662 33.333 0.00 0.00 32.66 4.08
5048 5220 7.545965 TCACTTCAAACAATAGAGCTTAGCTAC 59.454 37.037 6.75 0.89 39.88 3.58
5532 6095 1.212751 GTCATTGGGCAAACGGAGC 59.787 57.895 0.00 0.00 0.00 4.70
5533 6096 1.135315 CATGTCATTGGGCAAACGGAG 60.135 52.381 0.00 0.00 0.00 4.63
5534 6097 0.887247 CATGTCATTGGGCAAACGGA 59.113 50.000 0.00 0.00 0.00 4.69
5535 6098 0.108709 CCATGTCATTGGGCAAACGG 60.109 55.000 0.00 0.00 32.80 4.44
5536 6099 0.737019 GCCATGTCATTGGGCAAACG 60.737 55.000 8.89 0.00 46.92 3.60
5537 6100 3.142124 GCCATGTCATTGGGCAAAC 57.858 52.632 8.89 0.00 46.92 2.93
5541 6104 1.483415 AATGAAGCCATGTCATTGGGC 59.517 47.619 8.74 6.13 42.68 5.36
5545 6108 5.657474 GTGAATCAATGAAGCCATGTCATT 58.343 37.500 4.61 4.61 44.63 2.57
5546 6109 4.201980 CGTGAATCAATGAAGCCATGTCAT 60.202 41.667 0.00 0.00 37.31 3.06
5547 6110 3.127376 CGTGAATCAATGAAGCCATGTCA 59.873 43.478 0.00 0.00 32.36 3.58
5548 6111 3.488047 CCGTGAATCAATGAAGCCATGTC 60.488 47.826 0.00 0.00 32.36 3.06
5549 6112 2.424601 CCGTGAATCAATGAAGCCATGT 59.575 45.455 0.00 0.00 32.36 3.21
5550 6113 2.797087 GCCGTGAATCAATGAAGCCATG 60.797 50.000 0.00 0.00 32.36 3.66
5551 6114 1.406539 GCCGTGAATCAATGAAGCCAT 59.593 47.619 0.00 0.00 33.66 4.40
5552 6115 0.810648 GCCGTGAATCAATGAAGCCA 59.189 50.000 0.00 0.00 0.00 4.75
5553 6116 0.248215 CGCCGTGAATCAATGAAGCC 60.248 55.000 0.00 0.00 0.00 4.35
5554 6117 0.248215 CCGCCGTGAATCAATGAAGC 60.248 55.000 0.00 0.00 0.00 3.86
5555 6118 0.248215 GCCGCCGTGAATCAATGAAG 60.248 55.000 0.00 0.00 0.00 3.02
5556 6119 1.653094 GGCCGCCGTGAATCAATGAA 61.653 55.000 0.00 0.00 0.00 2.57
5557 6120 2.112198 GGCCGCCGTGAATCAATGA 61.112 57.895 0.00 0.00 0.00 2.57
5558 6121 2.114670 AGGCCGCCGTGAATCAATG 61.115 57.895 3.05 0.00 0.00 2.82
5559 6122 2.114670 CAGGCCGCCGTGAATCAAT 61.115 57.895 3.05 0.00 0.00 2.57
5560 6123 2.745884 CAGGCCGCCGTGAATCAA 60.746 61.111 3.05 0.00 0.00 2.57
5580 6143 1.142870 CTTCACTCCCACCCACAGAAA 59.857 52.381 0.00 0.00 0.00 2.52
5588 6151 1.302832 CTGCACCTTCACTCCCACC 60.303 63.158 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.