Multiple sequence alignment - TraesCS1B01G076300

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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 TraesCS1B01G076300 chr1B 100.000 6781 0 0 1 6781 59191897 59198677 0.000000e+00 12523.0
1 TraesCS1B01G076300 chr1D 93.471 6877 273 82 1 6780 39293341 39286544 0.000000e+00 10050.0
2 TraesCS1B01G076300 chr1A 93.260 4451 215 45 6 4403 38734509 38730091 0.000000e+00 6479.0
3 TraesCS1B01G076300 chr1A 93.987 2395 86 16 4422 6777 38729997 38727622 0.000000e+00 3572.0
4 TraesCS1B01G076300 chr7D 92.308 91 7 0 1995 2085 614168374 614168284 5.520000e-26 130.0
5 TraesCS1B01G076300 chr7A 92.308 91 7 0 1995 2085 706259399 706259309 5.520000e-26 130.0
6 TraesCS1B01G076300 chr7B 91.209 91 8 0 1995 2085 705967388 705967298 2.570000e-24 124.0
7 TraesCS1B01G076300 chr5B 88.000 75 4 3 3627 3701 532616156 532616087 4.360000e-12 84.2
8 TraesCS1B01G076300 chr5B 86.667 75 5 4 3627 3701 532610873 532610804 2.030000e-10 78.7
9 TraesCS1B01G076300 chr3A 88.000 75 4 3 3627 3701 462635862 462635931 4.360000e-12 84.2
10 TraesCS1B01G076300 chr6A 93.182 44 3 0 936 979 617977586 617977543 1.580000e-06 65.8


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 TraesCS1B01G076300 chr1B 59191897 59198677 6780 False 12523.0 12523 100.0000 1 6781 1 chr1B.!!$F1 6780
1 TraesCS1B01G076300 chr1D 39286544 39293341 6797 True 10050.0 10050 93.4710 1 6780 1 chr1D.!!$R1 6779
2 TraesCS1B01G076300 chr1A 38727622 38734509 6887 True 5025.5 6479 93.6235 6 6777 2 chr1A.!!$R1 6771

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
610 616 0.578683 CAATGCACGAGTATCCGCAG 59.421 55.000 0.0 0.0 42.36 5.18 F
1274 1294 0.250513 GAAGATTGGGACTGAGGCGT 59.749 55.000 0.0 0.0 0.00 5.68 F
2476 2520 0.926155 CGACATGAAGCAGGTGATCG 59.074 55.000 0.0 0.0 0.00 3.69 F
2869 2932 1.003928 TCTGGATGTGATTGTGCTGCT 59.996 47.619 0.0 0.0 0.00 4.24 F
3279 3346 1.268032 GCGATCAAATGCAACGGTAGG 60.268 52.381 0.0 0.0 0.00 3.18 F
4728 4909 1.269448 AGTACGCAGTTTGCCATTTGG 59.731 47.619 0.0 0.0 37.78 3.28 F
5412 5601 1.340889 GCTGCCCAAAGTGAAATGTCA 59.659 47.619 0.0 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 1483 0.387202 CTCCATCGCCGAGATCACTT 59.613 55.000 0.00 0.0 37.52 3.16 R
3024 3090 0.470341 GGAACTCCCTATCCACTGCC 59.530 60.000 0.00 0.0 35.71 4.85 R
3329 3396 0.536006 ACCTTCAGCAGCAACCTCAC 60.536 55.000 0.00 0.0 0.00 3.51 R
4259 4334 0.668401 GCAGCCACACAGGAAAATGC 60.668 55.000 0.00 0.0 41.22 3.56 R
5012 5198 1.070289 CTGCTATGATCTCTGGCTGCA 59.930 52.381 0.50 0.0 0.00 4.41 R
5664 5858 1.601903 TGTACCAGCGCAAGAACAAAG 59.398 47.619 11.47 0.0 43.02 2.77 R
6726 6937 2.232208 CCTTTCAAGTGATTCCCTTGGC 59.768 50.000 8.71 0.0 39.78 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
137 139 2.621055 CTGAGCTAGCTCGTTATCCACT 59.379 50.000 33.55 2.19 45.48 4.00
155 157 6.769134 TCCACTCATCGTCTACTTAATTCA 57.231 37.500 0.00 0.00 0.00 2.57
196 198 7.619698 TCCATCTTCTAAGTGAGGATAAGAACA 59.380 37.037 0.00 0.00 39.14 3.18
217 219 2.035155 ACGGGTTTTGGCTAGCCC 59.965 61.111 30.81 15.05 37.79 5.19
270 272 4.826733 TGGTCCGTTACGATTATAGCCTTA 59.173 41.667 6.24 0.00 0.00 2.69
297 299 7.309805 GGTTAAGTGGGTTCATGCTTTCTAAAT 60.310 37.037 0.00 0.00 0.00 1.40
302 304 4.141869 GGGTTCATGCTTTCTAAATGCCAT 60.142 41.667 0.00 0.00 0.00 4.40
322 324 5.237344 GCCATAGCGACAATTGTCTCTTATT 59.763 40.000 30.15 16.14 40.26 1.40
323 325 6.238484 GCCATAGCGACAATTGTCTCTTATTT 60.238 38.462 30.15 12.95 40.26 1.40
364 366 5.888161 AGCTGAATTGGGTTCGAATAAATCT 59.112 36.000 0.00 0.00 39.80 2.40
493 495 4.701765 GATAAGCAGATGAGCTGGAAAGA 58.298 43.478 0.00 0.00 45.89 2.52
537 539 5.065235 CCTAAAGACCCGGTGAAAAGTAAA 58.935 41.667 0.00 0.00 0.00 2.01
545 547 3.799963 CCGGTGAAAAGTAAACAAAAGGC 59.200 43.478 0.00 0.00 0.00 4.35
562 565 4.440214 CGAATTGCGCAGACAACC 57.560 55.556 11.31 0.00 31.03 3.77
586 589 2.837371 AAACCTCGTCGCTAGCCAGC 62.837 60.000 9.66 0.00 44.90 4.85
610 616 0.578683 CAATGCACGAGTATCCGCAG 59.421 55.000 0.00 0.00 42.36 5.18
718 731 7.285172 CCATAAAAATGTGGTGGTGATCTATCA 59.715 37.037 0.00 0.00 0.00 2.15
723 736 6.560003 ATGTGGTGGTGATCTATCAGTAAA 57.440 37.500 0.00 0.00 37.51 2.01
725 738 6.774673 TGTGGTGGTGATCTATCAGTAAAAA 58.225 36.000 0.00 0.00 37.51 1.94
746 759 6.994421 AAAATAACCACCTGTCCTCAAAAT 57.006 33.333 0.00 0.00 0.00 1.82
885 901 8.655970 CAACAAAAATACCAAATAAAGCTAGGC 58.344 33.333 0.00 0.00 0.00 3.93
994 1010 4.595116 CGACCCCGCTTTCTATATATACG 58.405 47.826 0.00 0.00 0.00 3.06
1022 1038 0.472471 TTTCCACCCTCTCCACACAC 59.528 55.000 0.00 0.00 0.00 3.82
1112 1132 7.043565 CCAAGCTTTTGTTGCATATATCCTTT 58.956 34.615 0.00 0.00 0.00 3.11
1123 1143 8.903820 GTTGCATATATCCTTTACTCCAAAAGT 58.096 33.333 0.00 0.00 42.33 2.66
1125 1145 9.474313 TGCATATATCCTTTACTCCAAAAGTTT 57.526 29.630 0.00 0.00 39.55 2.66
1130 1150 4.577283 TCCTTTACTCCAAAAGTTTCCACG 59.423 41.667 0.00 0.00 39.55 4.94
1170 1190 2.031683 GGATTGGCCGTCGATGTAAAAG 59.968 50.000 3.52 0.00 0.00 2.27
1196 1216 5.977489 TCTTCTTGAATCGTGAGGTTAGA 57.023 39.130 0.00 0.00 32.13 2.10
1255 1275 1.956170 GCGTGTAGGATGCCCATCG 60.956 63.158 2.47 0.00 38.69 3.84
1272 1292 0.537188 TCGAAGATTGGGACTGAGGC 59.463 55.000 0.00 0.00 0.00 4.70
1273 1293 0.807667 CGAAGATTGGGACTGAGGCG 60.808 60.000 0.00 0.00 0.00 5.52
1274 1294 0.250513 GAAGATTGGGACTGAGGCGT 59.749 55.000 0.00 0.00 0.00 5.68
1314 1334 1.565591 CAAAAACGCGTCGGCACTA 59.434 52.632 14.44 0.00 39.92 2.74
1411 1431 4.385748 CGACTCGTGATTGAGATTGTTTGA 59.614 41.667 0.00 0.00 39.35 2.69
1455 1477 5.611796 TCTCGTTGATTGATTGGAAGTTG 57.388 39.130 0.00 0.00 0.00 3.16
1457 1479 4.393834 TCGTTGATTGATTGGAAGTTGGA 58.606 39.130 0.00 0.00 0.00 3.53
1458 1480 4.455533 TCGTTGATTGATTGGAAGTTGGAG 59.544 41.667 0.00 0.00 0.00 3.86
1461 1483 5.503634 TGATTGATTGGAAGTTGGAGAGA 57.496 39.130 0.00 0.00 0.00 3.10
1462 1484 5.879763 TGATTGATTGGAAGTTGGAGAGAA 58.120 37.500 0.00 0.00 0.00 2.87
1726 1748 3.519930 GACGACGAGGAGGAGGCC 61.520 72.222 0.00 0.00 0.00 5.19
1729 1751 2.363147 GACGAGGAGGAGGCCACT 60.363 66.667 5.01 1.49 0.00 4.00
1813 1835 1.303643 CACCCAAGAGCTGTTCCCC 60.304 63.158 0.00 0.00 0.00 4.81
1922 1944 1.126488 GGACATGAGGATCCTGCAGA 58.874 55.000 22.02 1.21 33.75 4.26
2155 2178 8.421249 TTTTCCTCAAATATCACCAACTGATT 57.579 30.769 0.00 0.00 40.38 2.57
2156 2179 7.395190 TTCCTCAAATATCACCAACTGATTG 57.605 36.000 0.00 0.00 40.38 2.67
2196 2219 1.824852 TCTTGCTCCTGTTCATCGCTA 59.175 47.619 0.00 0.00 0.00 4.26
2280 2307 8.755696 TGCAAGGTACAAATTTAATTAAGCAG 57.244 30.769 0.00 0.00 0.00 4.24
2333 2365 4.282703 TGAACTACCTGTACTGAAACCCTC 59.717 45.833 0.60 0.00 0.00 4.30
2476 2520 0.926155 CGACATGAAGCAGGTGATCG 59.074 55.000 0.00 0.00 0.00 3.69
2514 2558 5.009631 CAGTGTTCCTCATCCAACCAAATA 58.990 41.667 0.00 0.00 0.00 1.40
2515 2559 5.124457 CAGTGTTCCTCATCCAACCAAATAG 59.876 44.000 0.00 0.00 0.00 1.73
2576 2620 7.172875 ACTGATGAACTGAAGAAATTCTGACTG 59.827 37.037 0.00 1.59 0.00 3.51
2595 2658 2.687425 CTGTGTGTTGTTTGGTGGATGA 59.313 45.455 0.00 0.00 0.00 2.92
2784 2847 2.243810 TCCCCTTTCCATTTTGAACCG 58.756 47.619 0.00 0.00 0.00 4.44
2790 2853 5.762711 CCCTTTCCATTTTGAACCGATTTTT 59.237 36.000 0.00 0.00 0.00 1.94
2837 2900 5.422666 CACTGAATGCACTTGTGAAGTTA 57.577 39.130 4.79 0.00 40.46 2.24
2869 2932 1.003928 TCTGGATGTGATTGTGCTGCT 59.996 47.619 0.00 0.00 0.00 4.24
2896 2959 7.252708 CCTATCTGATCTGAATCTGAATCTCG 58.747 42.308 6.37 0.00 41.46 4.04
2968 3031 9.515226 AGGAATGTATTTTTAAGCAGTAGTTCA 57.485 29.630 0.00 0.00 0.00 3.18
2980 3043 9.515226 TTAAGCAGTAGTTCATAGGTTGAAAAT 57.485 29.630 0.00 0.00 45.71 1.82
2982 3045 8.494016 AGCAGTAGTTCATAGGTTGAAAATAC 57.506 34.615 0.00 0.00 45.71 1.89
3050 3116 2.500098 TGGATAGGGAGTTCCTCAAACG 59.500 50.000 0.00 0.00 44.06 3.60
3056 3122 2.550208 GGGAGTTCCTCAAACGACATGT 60.550 50.000 0.00 0.00 43.02 3.21
3279 3346 1.268032 GCGATCAAATGCAACGGTAGG 60.268 52.381 0.00 0.00 0.00 3.18
3356 3423 1.946768 TGCTGCTGAAGGTAACAACAC 59.053 47.619 0.00 0.00 41.41 3.32
3360 3427 2.805671 TGCTGAAGGTAACAACACGATG 59.194 45.455 0.00 0.00 41.41 3.84
3365 3432 5.547465 TGAAGGTAACAACACGATGAGAAT 58.453 37.500 0.00 0.00 41.41 2.40
3366 3433 5.995282 TGAAGGTAACAACACGATGAGAATT 59.005 36.000 0.00 0.00 41.41 2.17
3374 3441 6.969366 ACAACACGATGAGAATTTTGATTGA 58.031 32.000 0.00 0.00 0.00 2.57
3375 3442 7.424803 ACAACACGATGAGAATTTTGATTGAA 58.575 30.769 0.00 0.00 0.00 2.69
3408 3483 2.364647 TGTTTGCATCTGTGATTTGGCA 59.635 40.909 0.00 0.00 0.00 4.92
3728 3803 2.799412 GCTAGTGACTGCAGTATGATGC 59.201 50.000 21.73 17.33 46.68 3.91
3738 3813 3.193479 TGCAGTATGATGCCCTATCGTAG 59.807 47.826 1.97 0.00 45.91 3.51
3788 3863 7.561722 TCATAGGAACTTCTACAGCTATTGTCT 59.438 37.037 0.00 0.00 39.79 3.41
3808 3883 6.308675 TGTCTAAATTAAATTTCACCGTCGC 58.691 36.000 0.00 0.00 33.82 5.19
3850 3925 5.818136 ATATTCACCACACAGTAACATGC 57.182 39.130 0.00 0.00 0.00 4.06
3876 3951 2.787473 TTCCTGCCTGACTATGGTTG 57.213 50.000 0.00 0.00 0.00 3.77
4055 4130 1.927487 GCATGGCCAATCATATCCCA 58.073 50.000 10.96 0.00 0.00 4.37
4119 4194 7.360113 AGCTCCTTTCACCTAAAATTTTCAA 57.640 32.000 6.72 0.00 0.00 2.69
4201 4276 3.817084 CTCTGTTTTGCAATCAGGACTGA 59.183 43.478 22.88 4.26 44.59 3.41
4218 4293 4.142071 GGACTGACTGATGCAGACTGATAA 60.142 45.833 6.65 0.00 36.86 1.75
4254 4329 4.977963 TGTTACTGTTGTACTTAGCGTCAC 59.022 41.667 0.00 0.00 0.00 3.67
4259 4334 5.919141 ACTGTTGTACTTAGCGTCACTTAAG 59.081 40.000 0.00 0.00 0.00 1.85
4318 4394 3.206150 CCTGATTTTCATAGTCCACCCG 58.794 50.000 0.00 0.00 0.00 5.28
4323 4399 1.646912 TTCATAGTCCACCCGTTCCA 58.353 50.000 0.00 0.00 0.00 3.53
4400 4476 6.174720 AGTCCTCACAAACTGTCTAATTGA 57.825 37.500 0.00 0.00 0.00 2.57
4403 4479 6.483640 GTCCTCACAAACTGTCTAATTGAGTT 59.516 38.462 0.00 0.00 0.00 3.01
4404 4480 6.706270 TCCTCACAAACTGTCTAATTGAGTTC 59.294 38.462 0.00 0.00 0.00 3.01
4405 4481 6.483307 CCTCACAAACTGTCTAATTGAGTTCA 59.517 38.462 0.00 0.00 0.00 3.18
4406 4482 7.307632 CCTCACAAACTGTCTAATTGAGTTCAG 60.308 40.741 0.00 0.00 35.72 3.02
4411 4495 5.704888 ACTGTCTAATTGAGTTCAGAGTCG 58.295 41.667 0.00 0.00 34.63 4.18
4420 4504 6.378710 TTGAGTTCAGAGTCGTAGGATATG 57.621 41.667 0.00 0.00 0.00 1.78
4481 4632 5.923733 ACATCCTAGAGAGTTGACGATTT 57.076 39.130 0.00 0.00 0.00 2.17
4610 4791 9.698309 TTATTTATAGCGAGAAAAGAGATCTGG 57.302 33.333 0.00 0.00 0.00 3.86
4728 4909 1.269448 AGTACGCAGTTTGCCATTTGG 59.731 47.619 0.00 0.00 37.78 3.28
4737 4918 5.331098 CAGTTTGCCATTTGGTTTGAAAAC 58.669 37.500 0.00 0.00 37.57 2.43
4764 4947 4.980339 ATTGGTTTGCCATTCCTTTTCT 57.020 36.364 0.00 0.00 45.56 2.52
4916 5102 6.867662 AAGCGATAGGAATTAGACCAATTG 57.132 37.500 0.00 0.00 36.96 2.32
4957 5143 6.806388 ACAATCCAATTTCTGCCAATTTTC 57.194 33.333 0.00 0.00 0.00 2.29
4962 5148 6.225318 TCCAATTTCTGCCAATTTTCTTGAG 58.775 36.000 0.00 0.00 0.00 3.02
4980 5166 7.129457 TCTTGAGTTTATCCTACATGAGCAT 57.871 36.000 0.00 0.00 0.00 3.79
5078 5264 1.434513 TTCCAACCTGGGCATGGAGT 61.435 55.000 14.95 0.00 43.69 3.85
5412 5601 1.340889 GCTGCCCAAAGTGAAATGTCA 59.659 47.619 0.00 0.00 0.00 3.58
5454 5648 3.385755 GCAGCATTGGTCCCATAATTCTT 59.614 43.478 0.00 0.00 0.00 2.52
5617 5811 1.909700 TTCTTGGATGTCAGTTGGCC 58.090 50.000 0.00 0.00 0.00 5.36
5664 5858 3.815401 ACCACTGCTGAATTGTACTGTTC 59.185 43.478 0.00 0.00 0.00 3.18
5676 5870 4.530094 TGTACTGTTCTTTGTTCTTGCG 57.470 40.909 0.00 0.00 0.00 4.85
5680 5874 1.065401 TGTTCTTTGTTCTTGCGCTGG 59.935 47.619 9.73 0.68 0.00 4.85
5700 5894 5.235850 TGGTACAAGATTTGGCTCTAACA 57.764 39.130 0.00 0.00 31.92 2.41
6024 6227 5.236911 TGTGCAATTTTCTCCAGCAAAAATC 59.763 36.000 0.00 0.00 34.78 2.17
6178 6382 1.722852 CGGCGTCGATCGAGTCATC 60.723 63.158 20.09 5.25 42.86 2.92
6406 6615 5.375417 TGTGCGAAACAGATGAATTCAAT 57.625 34.783 13.09 1.14 33.78 2.57
6445 6654 4.722361 ACAAGTTTACTTTTGCGGGAAA 57.278 36.364 0.00 0.00 33.11 3.13
6637 6846 7.672983 TTTGAAGCAGACAAGTAGGAAATAG 57.327 36.000 0.00 0.00 0.00 1.73
6663 6872 1.523758 CTGGTTTTGACGAGGAAGGG 58.476 55.000 0.00 0.00 0.00 3.95
6726 6937 1.762708 ATAATGGCACGAAACCCCTG 58.237 50.000 0.00 0.00 0.00 4.45
6763 6975 2.549064 AAGGCAAGGCAAATTTGTCC 57.451 45.000 18.90 18.62 31.90 4.02
6771 6983 2.629617 AGGCAAATTTGTCCCAACAGAG 59.370 45.455 18.90 0.00 36.57 3.35
6780 6992 1.416401 GTCCCAACAGAGACTGGTTCA 59.584 52.381 0.00 0.00 35.51 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.739972 CACTAAACCAAAGGCTAGAATTGTAAT 58.260 33.333 0.00 0.00 0.00 1.89
13 14 3.344515 GACCCACTAAACCAAAGGCTAG 58.655 50.000 0.00 0.00 0.00 3.42
21 22 1.420532 AAGCCCGACCCACTAAACCA 61.421 55.000 0.00 0.00 0.00 3.67
103 105 6.183359 CGAGCTAGCTCAGATCAATTTATTCG 60.183 42.308 36.92 18.73 39.80 3.34
137 139 7.406031 AAGAGGTGAATTAAGTAGACGATGA 57.594 36.000 0.00 0.00 0.00 2.92
155 157 7.264294 AGAAGATGGAAGAACATTAAGAGGT 57.736 36.000 0.00 0.00 0.00 3.85
196 198 1.134189 GGCTAGCCAAAACCCGTCTAT 60.134 52.381 29.33 0.00 35.81 1.98
217 219 2.578495 GCTCATCAGCTTGTCGTTTTG 58.422 47.619 0.00 0.00 43.09 2.44
270 272 3.525800 AAGCATGAACCCACTTAACCT 57.474 42.857 0.00 0.00 0.00 3.50
330 332 2.159198 CCCAATTCAGCTCCCATTTTCG 60.159 50.000 0.00 0.00 0.00 3.46
334 336 2.460669 GAACCCAATTCAGCTCCCATT 58.539 47.619 0.00 0.00 37.27 3.16
339 341 5.560966 TTTATTCGAACCCAATTCAGCTC 57.439 39.130 0.00 0.00 37.12 4.09
364 366 5.415077 GGTGGATAACGAGCTAGCTTAGATA 59.585 44.000 20.42 14.88 0.00 1.98
369 371 1.413077 GGGTGGATAACGAGCTAGCTT 59.587 52.381 20.42 5.57 0.00 3.74
493 495 4.282703 AGGGCTATAATCGTAACGGACAAT 59.717 41.667 0.00 0.00 0.00 2.71
545 547 0.040514 TTGGTTGTCTGCGCAATTCG 60.041 50.000 13.05 0.00 42.12 3.34
586 589 0.227234 GATACTCGTGCATTGCGACG 59.773 55.000 20.27 20.27 35.60 5.12
610 616 4.949856 TGAAAAGAATACAGAGGCATTCCC 59.050 41.667 0.00 0.00 32.61 3.97
652 659 9.479549 TCCTAGGATTTTGCTTGAGAAAATAAT 57.520 29.630 7.62 0.00 34.00 1.28
654 661 8.109634 ACTCCTAGGATTTTGCTTGAGAAAATA 58.890 33.333 13.12 0.00 34.00 1.40
665 672 5.904362 ATTGAACACTCCTAGGATTTTGC 57.096 39.130 13.12 0.00 0.00 3.68
694 701 8.055181 ACTGATAGATCACCACCACATTTTTAT 58.945 33.333 0.00 0.00 32.50 1.40
697 704 5.819991 ACTGATAGATCACCACCACATTTT 58.180 37.500 0.00 0.00 32.50 1.82
723 736 6.994421 ATTTTGAGGACAGGTGGTTATTTT 57.006 33.333 0.00 0.00 0.00 1.82
725 738 6.314917 AGAATTTTGAGGACAGGTGGTTATT 58.685 36.000 0.00 0.00 0.00 1.40
726 739 5.892348 AGAATTTTGAGGACAGGTGGTTAT 58.108 37.500 0.00 0.00 0.00 1.89
727 740 5.319043 AGAATTTTGAGGACAGGTGGTTA 57.681 39.130 0.00 0.00 0.00 2.85
729 742 3.884037 AGAATTTTGAGGACAGGTGGT 57.116 42.857 0.00 0.00 0.00 4.16
731 744 5.772825 TTCAAGAATTTTGAGGACAGGTG 57.227 39.130 4.16 0.00 0.00 4.00
733 746 6.572519 TGTTTTCAAGAATTTTGAGGACAGG 58.427 36.000 11.84 0.00 0.00 4.00
835 848 4.161377 GGGGCAAATTATAAGGAGCAAACA 59.839 41.667 7.74 0.00 0.00 2.83
885 901 7.421530 TTCTTCCTTTTGTTATCTCAAGTCG 57.578 36.000 0.00 0.00 0.00 4.18
994 1010 0.612174 GAGGGTGGAAAAAGAGGCCC 60.612 60.000 0.00 0.00 36.46 5.80
1022 1038 0.688087 AAAGGGCGGAGTAGAGAGGG 60.688 60.000 0.00 0.00 0.00 4.30
1112 1132 5.065474 CAGAAACGTGGAAACTTTTGGAGTA 59.935 40.000 0.00 0.00 37.72 2.59
1123 1143 1.292061 CGGTGTCAGAAACGTGGAAA 58.708 50.000 0.00 0.00 0.00 3.13
1125 1145 0.249155 GACGGTGTCAGAAACGTGGA 60.249 55.000 0.00 0.00 39.95 4.02
1130 1150 2.315386 GGCCGACGGTGTCAGAAAC 61.315 63.158 16.73 0.00 32.09 2.78
1170 1190 4.058817 ACCTCACGATTCAAGAAGAACAC 58.941 43.478 0.00 0.00 39.49 3.32
1196 1216 1.183549 CCTATTCCTACGGCCGCTAT 58.816 55.000 28.58 8.89 0.00 2.97
1255 1275 0.250513 ACGCCTCAGTCCCAATCTTC 59.749 55.000 0.00 0.00 0.00 2.87
1272 1292 2.660552 ATTTATCCGCCGCCGACG 60.661 61.111 0.00 0.00 36.29 5.12
1273 1293 0.598158 TACATTTATCCGCCGCCGAC 60.598 55.000 0.00 0.00 36.29 4.79
1274 1294 0.598158 GTACATTTATCCGCCGCCGA 60.598 55.000 0.00 0.00 36.29 5.54
1299 1319 2.312436 GGTTAGTGCCGACGCGTTT 61.312 57.895 15.53 0.00 38.08 3.60
1314 1334 2.832733 GAGGTACAGGTAGAAGCAGGTT 59.167 50.000 0.00 0.00 0.00 3.50
1386 1406 2.094494 ACAATCTCAATCACGAGTCGCT 60.094 45.455 13.59 0.00 34.46 4.93
1411 1431 8.353684 CGAGAACACCTATAGATGTATCAAACT 58.646 37.037 0.00 0.00 0.00 2.66
1458 1480 1.601663 CCATCGCCGAGATCACTTCTC 60.602 57.143 0.00 0.00 46.36 2.87
1461 1483 0.387202 CTCCATCGCCGAGATCACTT 59.613 55.000 0.00 0.00 37.52 3.16
1462 1484 2.037053 CTCCATCGCCGAGATCACT 58.963 57.895 0.00 0.00 37.52 3.41
1726 1748 3.775654 GGTGGAGGCGAGGGAGTG 61.776 72.222 0.00 0.00 0.00 3.51
1729 1751 4.779733 GGAGGTGGAGGCGAGGGA 62.780 72.222 0.00 0.00 0.00 4.20
1900 1922 1.402896 GCAGGATCCTCATGTCCGGA 61.403 60.000 12.69 0.00 39.54 5.14
2133 2155 6.484288 ACAATCAGTTGGTGATATTTGAGGA 58.516 36.000 0.00 0.00 45.89 3.71
2155 2178 8.868916 GCAAGAAAATTTGTAAGAACTGAAACA 58.131 29.630 0.00 0.00 0.00 2.83
2156 2179 9.087424 AGCAAGAAAATTTGTAAGAACTGAAAC 57.913 29.630 0.00 0.00 0.00 2.78
2280 2307 8.613060 ATGATCACATCACAATTATGTACTCC 57.387 34.615 0.00 0.00 43.01 3.85
2333 2365 3.813800 CACGGTGAAATGACATGACTTG 58.186 45.455 0.74 0.00 0.00 3.16
2576 2620 3.569701 AGATCATCCACCAAACAACACAC 59.430 43.478 0.00 0.00 0.00 3.82
2784 2847 8.761575 TGCCATGAAGTAAGAAATGAAAAATC 57.238 30.769 0.00 0.00 0.00 2.17
2790 2853 6.623486 CAACATGCCATGAAGTAAGAAATGA 58.377 36.000 12.53 0.00 0.00 2.57
2869 2932 6.497606 AGATTCAGATTCAGATCAGATAGGCA 59.502 38.462 0.00 0.00 34.60 4.75
2896 2959 7.509141 TGATCTGATCATGACTCTCTCTTAC 57.491 40.000 16.06 0.00 33.59 2.34
2951 3014 8.911918 TCAACCTATGAACTACTGCTTAAAAA 57.088 30.769 0.00 0.00 34.30 1.94
3022 3088 2.679082 GAACTCCCTATCCACTGCCTA 58.321 52.381 0.00 0.00 0.00 3.93
3023 3089 1.501582 GAACTCCCTATCCACTGCCT 58.498 55.000 0.00 0.00 0.00 4.75
3024 3090 0.470341 GGAACTCCCTATCCACTGCC 59.530 60.000 0.00 0.00 35.71 4.85
3050 3116 1.539827 GTACCTGCACCCAAACATGTC 59.460 52.381 0.00 0.00 0.00 3.06
3056 3122 5.904984 AGATATATGTACCTGCACCCAAA 57.095 39.130 0.00 0.00 0.00 3.28
3279 3346 1.737008 GAAGTTCGTCACGGCCTCC 60.737 63.158 0.00 0.00 0.00 4.30
3329 3396 0.536006 ACCTTCAGCAGCAACCTCAC 60.536 55.000 0.00 0.00 0.00 3.51
3333 3400 1.604604 TGTTACCTTCAGCAGCAACC 58.395 50.000 0.00 0.00 0.00 3.77
3375 3442 9.491675 TCACAGATGCAAACATGAAAAATAAAT 57.508 25.926 0.00 0.00 36.35 1.40
3390 3465 3.747854 TTTGCCAAATCACAGATGCAA 57.252 38.095 0.00 0.00 36.98 4.08
3393 3468 6.619874 GCAGAATTTTTGCCAAATCACAGATG 60.620 38.462 0.54 0.00 35.54 2.90
3400 3475 4.456914 CAACGCAGAATTTTTGCCAAATC 58.543 39.130 6.35 0.00 38.31 2.17
3408 3483 5.183904 AGCTAATCTCCAACGCAGAATTTTT 59.816 36.000 0.00 0.00 0.00 1.94
3623 3698 1.686052 GTGAAATTGGACTGGTTGCCA 59.314 47.619 0.00 0.00 0.00 4.92
3728 3803 5.064834 GGAAAAAGACTTTGCTACGATAGGG 59.935 44.000 0.06 0.00 43.77 3.53
3738 3813 8.403236 TGAAGTAAACTAGGAAAAAGACTTTGC 58.597 33.333 0.06 0.00 0.00 3.68
3788 3863 5.411977 TCAGGCGACGGTGAAATTTAATTTA 59.588 36.000 2.65 0.00 31.47 1.40
3808 3883 3.583882 ATTTGGGCGGTGGGTCAGG 62.584 63.158 0.00 0.00 0.00 3.86
3850 3925 4.878397 CCATAGTCAGGCAGGAAAAGTAAG 59.122 45.833 0.00 0.00 0.00 2.34
3944 4019 2.350192 CCTGCATAACACGCAAACGATA 59.650 45.455 0.00 0.00 43.93 2.92
3948 4023 1.724654 CGACCTGCATAACACGCAAAC 60.725 52.381 0.00 0.00 39.30 2.93
3973 4048 4.554036 GCGACCATCTCAGGGGGC 62.554 72.222 0.00 0.00 0.00 5.80
4055 4130 9.753674 TCACCTCACCTCATTATTTAAAAAGAT 57.246 29.630 0.00 0.00 0.00 2.40
4119 4194 2.581354 GCGTCATCAGAGCCACCT 59.419 61.111 0.00 0.00 0.00 4.00
4201 4276 3.474600 GGCATTATCAGTCTGCATCAGT 58.525 45.455 0.00 0.00 37.64 3.41
4254 4329 3.256631 AGCCACACAGGAAAATGCTTAAG 59.743 43.478 0.00 0.00 41.22 1.85
4259 4334 0.668401 GCAGCCACACAGGAAAATGC 60.668 55.000 0.00 0.00 41.22 3.56
4318 4394 3.246619 GACTCTGAACTCGACATGGAAC 58.753 50.000 0.00 0.00 0.00 3.62
4323 4399 6.758886 GGAATTAATGACTCTGAACTCGACAT 59.241 38.462 0.00 0.00 0.00 3.06
4400 4476 8.377034 ACTATACATATCCTACGACTCTGAACT 58.623 37.037 0.00 0.00 0.00 3.01
4481 4632 8.463930 CAAATTATTGGAGTGGGCTAAATCTA 57.536 34.615 0.00 0.00 32.69 1.98
4713 4894 2.559440 TCAAACCAAATGGCAAACTGC 58.441 42.857 0.00 0.00 44.08 4.40
4751 4932 8.918116 AGAGGATAATTTAAGAAAAGGAATGGC 58.082 33.333 0.00 0.00 0.00 4.40
4764 4947 9.838339 GTTGAGGAATCTGAGAGGATAATTTAA 57.162 33.333 0.00 0.00 0.00 1.52
4916 5102 8.696410 TGGATTGTTCTTTGTTTCTTTTGTAC 57.304 30.769 0.00 0.00 0.00 2.90
4957 5143 6.293298 GCATGCTCATGTAGGATAAACTCAAG 60.293 42.308 11.37 0.00 40.80 3.02
4962 5148 7.496529 TTTAGCATGCTCATGTAGGATAAAC 57.503 36.000 26.57 0.00 40.80 2.01
5012 5198 1.070289 CTGCTATGATCTCTGGCTGCA 59.930 52.381 0.50 0.00 0.00 4.41
5056 5242 1.535204 CCATGCCCAGGTTGGAACAC 61.535 60.000 0.00 0.00 40.96 3.32
5078 5264 2.607750 GGAGGAGGGTGGCTCACA 60.608 66.667 7.49 0.00 35.86 3.58
5358 5547 4.818546 CAGTCATGAATCCAATCCACTACC 59.181 45.833 0.00 0.00 0.00 3.18
5412 5601 2.411904 CAGAGAGCGCAGAAAAGAAGT 58.588 47.619 11.47 0.00 0.00 3.01
5454 5648 4.640647 AGCTGACGTTAGTATCTGACATCA 59.359 41.667 9.29 0.00 0.00 3.07
5471 5665 2.429971 TCAGATGGTGAGATGAGCTGAC 59.570 50.000 0.00 0.00 0.00 3.51
5523 5717 4.515191 GGTACTGCTGAATTTCAGTGACAA 59.485 41.667 23.66 7.21 45.94 3.18
5592 5786 3.160679 ACTGACATCCAAGAAAAGGGG 57.839 47.619 0.00 0.00 0.00 4.79
5664 5858 1.601903 TGTACCAGCGCAAGAACAAAG 59.398 47.619 11.47 0.00 43.02 2.77
5676 5870 2.716217 AGAGCCAAATCTTGTACCAGC 58.284 47.619 0.00 0.00 0.00 4.85
5680 5874 6.457528 GCATCTGTTAGAGCCAAATCTTGTAC 60.458 42.308 0.00 0.00 0.00 2.90
5946 6147 5.255710 TCTAGTGCTTCTGAAGTATCTGC 57.744 43.478 17.97 4.86 0.00 4.26
6178 6382 4.626225 CAAACTTTTGGCCGACCG 57.374 55.556 0.00 0.00 39.70 4.79
6445 6654 6.350949 CCGTTTGGACCAAAGGATTTTGATAT 60.351 38.462 31.72 0.00 41.18 1.63
6637 6846 2.857748 CCTCGTCAAAACCAGCAAAAAC 59.142 45.455 0.00 0.00 0.00 2.43
6663 6872 4.015872 TGGTAAAGTTGATGTGGTCCTC 57.984 45.455 0.00 0.00 0.00 3.71
6726 6937 2.232208 CCTTTCAAGTGATTCCCTTGGC 59.768 50.000 8.71 0.00 39.78 4.52


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

AutoCloner maintained by Alex Coulton.