Multiple sequence alignment - TraesCS4D01G122500

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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 TraesCS4D01G122500 chr4D 100.000 5132 0 0 1 5132 106418036 106412905 0.000000e+00 9478
1 TraesCS4D01G122500 chr4A 93.728 4560 118 47 680 5132 469511816 469516314 0.000000e+00 6682
2 TraesCS4D01G122500 chr4A 90.948 696 51 9 3 687 469510997 469511691 0.000000e+00 926
3 TraesCS4D01G122500 chr4B 93.862 3242 121 38 128 3339 149939999 149936806 0.000000e+00 4813
4 TraesCS4D01G122500 chr4B 89.735 1734 63 48 3404 5057 149936769 149935071 0.000000e+00 2109
5 TraesCS4D01G122500 chr4B 89.700 1000 66 10 1 977 149940979 149939994 0.000000e+00 1242
6 TraesCS4D01G122500 chr3B 90.435 230 16 5 3853 4077 422870651 422870879 1.080000e-76 298
7 TraesCS4D01G122500 chr5B 76.480 608 94 25 1325 1904 268431222 268431808 8.410000e-73 285
8 TraesCS4D01G122500 chr5B 91.892 185 15 0 1988 2172 268431926 268432110 5.100000e-65 259
9 TraesCS4D01G122500 chr5B 91.667 168 11 3 1046 1213 268430922 268431086 4.000000e-56 230
10 TraesCS4D01G122500 chr5D 76.144 612 95 26 1325 1904 236664030 236663438 1.820000e-69 274
11 TraesCS4D01G122500 chr5D 92.432 185 14 0 1988 2172 236663316 236663132 1.100000e-66 265
12 TraesCS4D01G122500 chr5D 91.667 168 11 3 1046 1213 236664330 236664166 4.000000e-56 230
13 TraesCS4D01G122500 chr5A 76.144 612 92 32 1325 1904 318755658 318756247 6.550000e-69 272
14 TraesCS4D01G122500 chr5A 92.432 185 14 0 1988 2172 318756379 318756563 1.100000e-66 265
15 TraesCS4D01G122500 chr5A 91.667 168 11 3 1046 1213 318755355 318755519 4.000000e-56 230
16 TraesCS4D01G122500 chr5A 77.177 333 54 10 2237 2555 318756747 318757071 1.900000e-39 174
17 TraesCS4D01G122500 chr6B 88.991 218 20 3 3864 4077 627263269 627263052 3.050000e-67 267


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 TraesCS4D01G122500 chr4D 106412905 106418036 5131 True 9478.000000 9478 100.000000 1 5132 1 chr4D.!!$R1 5131
1 TraesCS4D01G122500 chr4A 469510997 469516314 5317 False 3804.000000 6682 92.338000 3 5132 2 chr4A.!!$F1 5129
2 TraesCS4D01G122500 chr4B 149935071 149940979 5908 True 2721.333333 4813 91.099000 1 5057 3 chr4B.!!$R1 5056
3 TraesCS4D01G122500 chr5B 268430922 268432110 1188 False 258.000000 285 86.679667 1046 2172 3 chr5B.!!$F1 1126
4 TraesCS4D01G122500 chr5D 236663132 236664330 1198 True 256.333333 274 86.747667 1046 2172 3 chr5D.!!$R1 1126
5 TraesCS4D01G122500 chr5A 318755355 318757071 1716 False 235.250000 272 84.355000 1046 2555 4 chr5A.!!$F1 1509

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
356 361 0.320697 AAGGACGTACAGCCTTGACC 59.679 55.000 13.75 0.0 42.67 4.02 F
508 513 1.212688 AGATGGATGCAACCGATGGAA 59.787 47.619 8.65 0.0 30.96 3.53 F
1071 2065 1.218316 CTACGAGGCCACCAAGGTC 59.782 63.158 5.01 0.0 44.66 3.85 F
1569 2617 2.202919 CGGTCGCAGATGATGGCA 60.203 61.111 0.00 0.0 40.67 4.92 F
2860 4129 1.305213 GGGTGGTGATGGCAATGGT 60.305 57.895 0.00 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 2657 1.153269 GCTGCTGTAGGAGGAAGCC 60.153 63.158 2.57 0.0 36.05 4.35 R
2189 3443 1.305633 TGGTGAGGAGAGAGGCAGG 60.306 63.158 0.00 0.0 0.00 4.85 R
2860 4129 0.334335 TGGGACTGCCATTGCCATTA 59.666 50.000 0.00 0.0 36.33 1.90 R
2883 4152 1.059584 TTCCCCAGAGTTGACTGCCA 61.060 55.000 0.00 0.0 36.67 4.92 R
4553 5908 0.749454 CCCTTTGCTATGCTCGGCTT 60.749 55.000 0.00 0.0 0.00 4.35 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
55 59 1.588404 CGACATTGCACTAGCGGTAAG 59.412 52.381 0.00 0.00 46.23 2.34
59 63 2.309528 TTGCACTAGCGGTAAGGATG 57.690 50.000 0.00 0.00 46.23 3.51
64 68 1.480954 ACTAGCGGTAAGGATGTGTGG 59.519 52.381 0.00 0.00 0.00 4.17
74 78 3.404869 AGGATGTGTGGTCCATCTCTA 57.595 47.619 0.00 0.00 38.95 2.43
111 116 4.879545 GGATGTTCTGCGGTAGGAATTTTA 59.120 41.667 0.00 0.00 0.00 1.52
118 123 7.222000 TCTGCGGTAGGAATTTTAAATTTGT 57.778 32.000 4.32 0.00 0.00 2.83
136 141 0.449388 GTAGTCGACACACCCTACCG 59.551 60.000 19.50 0.00 0.00 4.02
137 142 0.324614 TAGTCGACACACCCTACCGA 59.675 55.000 19.50 0.00 0.00 4.69
174 179 4.380531 ACACATTATCATTTCGCTCCGAT 58.619 39.130 0.00 0.00 35.23 4.18
206 211 1.079503 CTTTTCGCTGTAGAGTGGGC 58.920 55.000 0.00 0.00 0.00 5.36
256 261 2.047274 CGATGACCCACCTTGCGT 60.047 61.111 0.00 0.00 0.00 5.24
257 262 2.100631 CGATGACCCACCTTGCGTC 61.101 63.158 0.00 0.00 0.00 5.19
269 274 4.697756 TGCGTCCTCTTTGGCCCG 62.698 66.667 0.00 0.00 35.26 6.13
278 283 3.944250 CTTTGGCCCGCTCCACCAT 62.944 63.158 0.00 0.00 35.50 3.55
281 286 4.195334 GGCCCGCTCCACCATCAT 62.195 66.667 0.00 0.00 0.00 2.45
282 287 2.903855 GCCCGCTCCACCATCATG 60.904 66.667 0.00 0.00 0.00 3.07
290 295 3.244009 CGCTCCACCATCATGTATTCTCT 60.244 47.826 0.00 0.00 0.00 3.10
321 326 1.001181 CAAGTTGGCAATGTTGAGGGG 59.999 52.381 16.26 0.00 0.00 4.79
324 329 2.042979 AGTTGGCAATGTTGAGGGGTAT 59.957 45.455 1.92 0.00 0.00 2.73
334 339 0.824109 TGAGGGGTATTGTCAGCGAG 59.176 55.000 0.00 0.00 0.00 5.03
348 353 0.522180 AGCGAGACAAGGACGTACAG 59.478 55.000 0.00 0.00 0.00 2.74
355 360 3.908737 AAGGACGTACAGCCTTGAC 57.091 52.632 13.75 0.00 42.67 3.18
356 361 0.320697 AAGGACGTACAGCCTTGACC 59.679 55.000 13.75 0.00 42.67 4.02
379 384 1.682087 GGGCTAGAAACATGGGGTCAC 60.682 57.143 0.00 0.00 0.00 3.67
503 508 1.412710 GGAGTAGATGGATGCAACCGA 59.587 52.381 8.65 0.00 0.00 4.69
508 513 1.212688 AGATGGATGCAACCGATGGAA 59.787 47.619 8.65 0.00 30.96 3.53
514 519 2.440247 CAACCGATGGAAGGGGGC 60.440 66.667 0.00 0.00 0.00 5.80
571 579 6.774354 AAAGAAGTAATTACTCGCGTGAAA 57.226 33.333 18.28 3.68 34.99 2.69
603 613 1.951209 TTAGGACATGGAGTGGCAGA 58.049 50.000 0.00 0.00 37.70 4.26
640 1486 5.947228 TTTGACAGCTCATCGAAGAAATT 57.053 34.783 0.00 0.00 43.58 1.82
665 1511 6.370166 TGCATTGATCACACTAATTCGTAACA 59.630 34.615 0.00 0.00 0.00 2.41
674 1520 7.439955 TCACACTAATTCGTAACACATTTGACT 59.560 33.333 0.00 0.00 0.00 3.41
713 1691 4.766404 ACGCAACCTAAATTGAAAGAGG 57.234 40.909 0.00 0.00 35.05 3.69
722 1700 5.191921 CCTAAATTGAAAGAGGGGGAGTACT 59.808 44.000 0.00 0.00 0.00 2.73
736 1715 6.045106 AGGGGGAGTACTAAAATGAAACTCAA 59.955 38.462 0.00 0.00 0.00 3.02
748 1727 5.954296 ATGAAACTCAAGACAACCATCTG 57.046 39.130 0.00 0.00 0.00 2.90
827 1821 4.656100 TGATGGAGGGAAACTGATTTGA 57.344 40.909 0.00 0.00 0.00 2.69
935 1929 1.758906 CCTCCTCGTCTTCCCTCCC 60.759 68.421 0.00 0.00 0.00 4.30
979 1973 3.591835 CGCTCCTCGCTCCCTCTC 61.592 72.222 0.00 0.00 36.13 3.20
980 1974 2.123897 GCTCCTCGCTCCCTCTCT 60.124 66.667 0.00 0.00 35.14 3.10
981 1975 2.193536 GCTCCTCGCTCCCTCTCTC 61.194 68.421 0.00 0.00 35.14 3.20
982 1976 1.528309 CTCCTCGCTCCCTCTCTCC 60.528 68.421 0.00 0.00 0.00 3.71
983 1977 2.520741 CCTCGCTCCCTCTCTCCC 60.521 72.222 0.00 0.00 0.00 4.30
984 1978 2.520741 CTCGCTCCCTCTCTCCCC 60.521 72.222 0.00 0.00 0.00 4.81
1071 2065 1.218316 CTACGAGGCCACCAAGGTC 59.782 63.158 5.01 0.00 44.66 3.85
1569 2617 2.202919 CGGTCGCAGATGATGGCA 60.203 61.111 0.00 0.00 40.67 4.92
1726 2786 4.441495 CCGTCCAGATTACTGATACTTGCA 60.441 45.833 0.00 0.00 46.03 4.08
2237 3491 3.414700 CTCTGTGGGCAACGCGAC 61.415 66.667 15.93 0.00 37.60 5.19
2657 3923 4.803452 TCCAAGGTCCAGTTCTTGAAAAT 58.197 39.130 4.83 0.00 41.94 1.82
2672 3938 9.003112 GTTCTTGAAAATCATTACATGTCGATG 57.997 33.333 0.00 8.69 35.49 3.84
2678 3947 9.559958 GAAAATCATTACATGTCGATGTTTTCT 57.440 29.630 26.38 18.76 40.05 2.52
2860 4129 1.305213 GGGTGGTGATGGCAATGGT 60.305 57.895 0.00 0.00 0.00 3.55
3223 4493 9.102757 CAGTACACATATTATCATATTCAGGCC 57.897 37.037 0.00 0.00 0.00 5.19
3271 4548 4.642445 AAACTTTCAAAAGGTACCACCG 57.358 40.909 15.94 0.00 44.90 4.94
3434 4719 4.093998 CAGTAATTAGTGCAGCAACCTCTG 59.906 45.833 7.36 0.00 37.15 3.35
3528 4823 2.687935 AGACATTGCAAAAAGGTGACGT 59.312 40.909 1.71 0.00 0.00 4.34
3560 4856 2.638480 TGTGGTGCTAATCATAGGCC 57.362 50.000 0.00 0.00 0.00 5.19
3671 5004 0.467804 TTTGCTTCTTTTGTGGGGGC 59.532 50.000 0.00 0.00 0.00 5.80
3672 5005 0.398381 TTGCTTCTTTTGTGGGGGCT 60.398 50.000 0.00 0.00 0.00 5.19
3673 5006 0.827507 TGCTTCTTTTGTGGGGGCTC 60.828 55.000 0.00 0.00 0.00 4.70
3674 5007 0.540597 GCTTCTTTTGTGGGGGCTCT 60.541 55.000 0.00 0.00 0.00 4.09
3675 5008 1.271926 GCTTCTTTTGTGGGGGCTCTA 60.272 52.381 0.00 0.00 0.00 2.43
3676 5009 2.437413 CTTCTTTTGTGGGGGCTCTAC 58.563 52.381 0.00 0.00 0.00 2.59
3678 5011 0.404040 CTTTTGTGGGGGCTCTACCA 59.596 55.000 0.00 0.00 42.05 3.25
3679 5012 1.005924 CTTTTGTGGGGGCTCTACCAT 59.994 52.381 0.00 0.00 42.05 3.55
3680 5013 1.974028 TTTGTGGGGGCTCTACCATA 58.026 50.000 0.00 0.00 42.05 2.74
3681 5014 1.209621 TTGTGGGGGCTCTACCATAC 58.790 55.000 0.00 0.00 42.05 2.39
3682 5015 0.341961 TGTGGGGGCTCTACCATACT 59.658 55.000 0.00 0.00 42.05 2.12
3963 5299 9.474313 AAGTGCCTAGGTGATTATTATTTGAAA 57.526 29.630 11.31 0.00 0.00 2.69
3964 5300 9.474313 AGTGCCTAGGTGATTATTATTTGAAAA 57.526 29.630 11.31 0.00 0.00 2.29
3965 5301 9.516314 GTGCCTAGGTGATTATTATTTGAAAAC 57.484 33.333 11.31 0.00 0.00 2.43
4001 5337 4.038271 TGATTCACTTCCCTTCATGCTT 57.962 40.909 0.00 0.00 0.00 3.91
4006 5342 8.000709 TGATTCACTTCCCTTCATGCTTATATT 58.999 33.333 0.00 0.00 0.00 1.28
4008 5344 8.593945 TTCACTTCCCTTCATGCTTATATTTT 57.406 30.769 0.00 0.00 0.00 1.82
4009 5345 8.225603 TCACTTCCCTTCATGCTTATATTTTC 57.774 34.615 0.00 0.00 0.00 2.29
4070 5414 8.396272 AGAAAATTGTTAACAGCTATGTGAGT 57.604 30.769 8.56 0.00 40.39 3.41
4190 5534 1.071699 TGCTGGGAGTAAGTGTCAACC 59.928 52.381 0.00 0.00 0.00 3.77
4194 5538 1.429463 GGAGTAAGTGTCAACCGCAG 58.571 55.000 0.00 0.00 0.00 5.18
4262 5612 7.226059 AGTAAAATTACCCTCCCTGATGATT 57.774 36.000 0.00 0.00 34.19 2.57
4510 5865 5.630415 AGCAGCATAAAATAGTACCCAGA 57.370 39.130 0.00 0.00 0.00 3.86
4545 5900 9.609346 TTAATTATTACCTAGTTCCTGCAAGAC 57.391 33.333 0.00 0.00 34.07 3.01
4569 5929 1.086696 GTCAAGCCGAGCATAGCAAA 58.913 50.000 0.00 0.00 0.00 3.68
4592 5955 3.564225 GGGAAAGTGTGTGGAAAGTACTG 59.436 47.826 0.00 0.00 0.00 2.74
4593 5956 4.196971 GGAAAGTGTGTGGAAAGTACTGT 58.803 43.478 0.00 0.00 0.00 3.55
4594 5957 5.362263 GGAAAGTGTGTGGAAAGTACTGTA 58.638 41.667 0.00 0.00 0.00 2.74
4595 5958 5.235831 GGAAAGTGTGTGGAAAGTACTGTAC 59.764 44.000 9.93 9.93 0.00 2.90
4596 5959 5.609533 AAGTGTGTGGAAAGTACTGTACT 57.390 39.130 14.53 14.53 41.73 2.73
4659 6025 2.266055 GCTCGGTCAGGTCAAGGG 59.734 66.667 0.00 0.00 0.00 3.95
4780 6168 6.183360 GCCACTTTGTGACTAATGACTATCAC 60.183 42.308 0.00 0.00 41.51 3.06
4782 6170 5.577164 ACTTTGTGACTAATGACTATCACGC 59.423 40.000 0.00 0.00 43.58 5.34
4787 6175 3.393800 ACTAATGACTATCACGCATGCC 58.606 45.455 13.15 0.00 0.00 4.40
4807 6198 3.614870 GCCTTGACATCAAATTGGGTGTC 60.615 47.826 17.98 17.98 40.93 3.67
4814 6205 4.037923 ACATCAAATTGGGTGTCTGTGAAC 59.962 41.667 0.00 0.00 0.00 3.18
4929 6343 1.007238 ACAATCGAGGGAGAGAGGGAA 59.993 52.381 0.00 0.00 0.00 3.97
4930 6344 1.686052 CAATCGAGGGAGAGAGGGAAG 59.314 57.143 0.00 0.00 0.00 3.46
5020 6434 2.871253 GCTGCTTTTGGTGGTGGGG 61.871 63.158 0.00 0.00 0.00 4.96
5114 6533 2.952310 CTGGTCACTCGTCCATCTATCA 59.048 50.000 0.00 0.00 33.01 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.462759 AGTAGAATTGGAGCAGCGCC 60.463 55.000 8.52 8.52 0.00 6.53
40 41 1.553248 ACATCCTTACCGCTAGTGCAA 59.447 47.619 0.00 0.00 39.64 4.08
44 45 1.480954 CCACACATCCTTACCGCTAGT 59.519 52.381 0.00 0.00 0.00 2.57
55 59 3.643320 TGATAGAGATGGACCACACATCC 59.357 47.826 0.00 0.00 44.45 3.51
59 63 2.432146 TGCTGATAGAGATGGACCACAC 59.568 50.000 0.00 0.00 0.00 3.82
64 68 4.527816 AGGAAGATGCTGATAGAGATGGAC 59.472 45.833 0.00 0.00 0.00 4.02
74 78 3.458857 AGAACATCCAGGAAGATGCTGAT 59.541 43.478 0.00 0.00 46.29 2.90
111 116 4.081322 AGGGTGTGTCGACTACAAATTT 57.919 40.909 17.92 4.12 40.63 1.82
118 123 0.324614 TCGGTAGGGTGTGTCGACTA 59.675 55.000 17.92 2.84 0.00 2.59
136 141 0.586802 GTGTCGTTGTTGGGCTCTTC 59.413 55.000 0.00 0.00 0.00 2.87
137 142 0.107410 TGTGTCGTTGTTGGGCTCTT 60.107 50.000 0.00 0.00 0.00 2.85
174 179 3.813166 CAGCGAAAAGAAAGGTCCACTTA 59.187 43.478 0.00 0.00 38.85 2.24
256 261 3.717294 GGAGCGGGCCAAAGAGGA 61.717 66.667 4.39 0.00 41.22 3.71
257 262 4.033776 TGGAGCGGGCCAAAGAGG 62.034 66.667 4.39 0.00 41.84 3.69
269 274 4.348863 AGAGAATACATGATGGTGGAGC 57.651 45.455 0.00 0.00 0.00 4.70
278 283 7.186570 TGTGAAGATCCAAGAGAATACATGA 57.813 36.000 0.00 0.00 0.00 3.07
281 286 7.009179 ACTTGTGAAGATCCAAGAGAATACA 57.991 36.000 14.14 0.00 40.36 2.29
282 287 7.148340 CCAACTTGTGAAGATCCAAGAGAATAC 60.148 40.741 14.14 0.00 40.36 1.89
290 295 2.942804 TGCCAACTTGTGAAGATCCAA 58.057 42.857 0.00 0.00 0.00 3.53
334 339 3.908737 AAGGCTGTACGTCCTTGTC 57.091 52.632 15.22 0.00 40.90 3.18
355 360 0.179045 CCCATGTTTCTAGCCCTCGG 60.179 60.000 0.00 0.00 0.00 4.63
356 361 0.179045 CCCCATGTTTCTAGCCCTCG 60.179 60.000 0.00 0.00 0.00 4.63
379 384 2.491152 GCCACAATGGGTGCATCG 59.509 61.111 0.00 0.00 46.50 3.84
479 484 0.761187 TGCATCCATCTACTCCTGGC 59.239 55.000 0.00 0.00 32.30 4.85
603 613 3.499338 TGTCAAAATTGTCCCTCTGCAT 58.501 40.909 0.00 0.00 0.00 3.96
640 1486 6.370166 TGTTACGAATTAGTGTGATCAATGCA 59.630 34.615 0.00 0.00 0.00 3.96
674 1520 7.927629 AGGTTGCGTATAACTTTTTCCGATATA 59.072 33.333 0.00 0.00 0.00 0.86
713 1691 7.119407 GTCTTGAGTTTCATTTTAGTACTCCCC 59.881 40.741 0.00 0.00 35.51 4.81
722 1700 8.352201 CAGATGGTTGTCTTGAGTTTCATTTTA 58.648 33.333 0.00 0.00 0.00 1.52
736 1715 6.923199 ATTTTGGATTTCAGATGGTTGTCT 57.077 33.333 0.00 0.00 0.00 3.41
748 1727 8.069574 GGTTGTCACATTCAAATTTTGGATTTC 58.930 33.333 9.18 0.00 0.00 2.17
827 1821 1.428869 AGTGCAGTGTCTTCTTCCCT 58.571 50.000 0.00 0.00 0.00 4.20
935 1929 7.260603 GGAATGTGAAAAGATTGGATTACAGG 58.739 38.462 0.00 0.00 0.00 4.00
984 1978 4.862823 GGAGGGGACGAGAGGGGG 62.863 77.778 0.00 0.00 0.00 5.40
1025 2019 2.718731 CGCCGCTAGTCTCTCCAG 59.281 66.667 0.00 0.00 0.00 3.86
1569 2617 3.009714 GAGAAGGGGAAGGCGGGT 61.010 66.667 0.00 0.00 0.00 5.28
1609 2657 1.153269 GCTGCTGTAGGAGGAAGCC 60.153 63.158 2.57 0.00 36.05 4.35
1665 2722 7.132128 AGAAAATGGAAGCTTATGGGGATTAA 58.868 34.615 0.00 0.00 0.00 1.40
1666 2723 6.682537 AGAAAATGGAAGCTTATGGGGATTA 58.317 36.000 0.00 0.00 0.00 1.75
2189 3443 1.305633 TGGTGAGGAGAGAGGCAGG 60.306 63.158 0.00 0.00 0.00 4.85
2860 4129 0.334335 TGGGACTGCCATTGCCATTA 59.666 50.000 0.00 0.00 36.33 1.90
2883 4152 1.059584 TTCCCCAGAGTTGACTGCCA 61.060 55.000 0.00 0.00 36.67 4.92
3232 4502 9.126151 TGAAAGTTTTAGACATACAAACCATGA 57.874 29.630 0.00 0.00 31.83 3.07
3434 4719 8.125448 GCACATATACAGATGAAGAAAAGGAAC 58.875 37.037 0.00 0.00 0.00 3.62
3528 4823 2.041081 AGCACCACAAAAGCCTATACCA 59.959 45.455 0.00 0.00 0.00 3.25
3560 4856 5.239087 GTCCCGTCTAGTACTAATCAAGAGG 59.761 48.000 3.76 4.88 0.00 3.69
3835 5171 1.070445 GCACCAGTGTGAGCTGTCT 59.930 57.895 0.00 0.00 45.76 3.41
3963 5299 5.009010 GTGAATCAACTGGAGTGATGTTGTT 59.991 40.000 0.00 0.00 41.05 2.83
3964 5300 4.516698 GTGAATCAACTGGAGTGATGTTGT 59.483 41.667 0.00 0.00 41.05 3.32
3965 5301 4.758674 AGTGAATCAACTGGAGTGATGTTG 59.241 41.667 0.00 0.00 41.46 3.33
4190 5534 1.150827 TTGAGTCAGTGATTGCTGCG 58.849 50.000 0.00 0.00 36.49 5.18
4194 5538 3.693085 ACCATGATTGAGTCAGTGATTGC 59.307 43.478 0.00 0.00 40.92 3.56
4279 5629 4.457496 ATCACACGAGCCCCTGCG 62.457 66.667 0.00 0.00 44.33 5.18
4510 5865 9.087424 GAACTAGGTAATAATTAAAACGACCGT 57.913 33.333 0.00 0.00 0.00 4.83
4553 5908 0.749454 CCCTTTGCTATGCTCGGCTT 60.749 55.000 0.00 0.00 0.00 4.35
4569 5929 3.458487 AGTACTTTCCACACACTTTCCCT 59.542 43.478 0.00 0.00 0.00 4.20
4592 5955 8.195436 TGCATGATGGTTTCTACTAGTAAGTAC 58.805 37.037 3.76 2.28 37.15 2.73
4593 5956 8.301252 TGCATGATGGTTTCTACTAGTAAGTA 57.699 34.615 3.76 0.00 37.15 2.24
4594 5957 7.182817 TGCATGATGGTTTCTACTAGTAAGT 57.817 36.000 3.76 0.00 39.91 2.24
4595 5958 9.764363 TTATGCATGATGGTTTCTACTAGTAAG 57.236 33.333 10.16 0.00 0.00 2.34
4596 5959 9.542462 GTTATGCATGATGGTTTCTACTAGTAA 57.458 33.333 10.16 0.00 0.00 2.24
4597 5960 8.924303 AGTTATGCATGATGGTTTCTACTAGTA 58.076 33.333 10.16 1.89 0.00 1.82
4598 5961 7.712639 CAGTTATGCATGATGGTTTCTACTAGT 59.287 37.037 10.16 0.00 0.00 2.57
4599 5962 8.081208 CAGTTATGCATGATGGTTTCTACTAG 57.919 38.462 10.16 0.00 0.00 2.57
4659 6025 2.229792 TCCACACAAACAGAGGATTGC 58.770 47.619 0.00 0.00 30.55 3.56
4780 6168 2.572191 ATTTGATGTCAAGGCATGCG 57.428 45.000 12.44 0.00 37.15 4.73
4782 6170 3.055675 ACCCAATTTGATGTCAAGGCATG 60.056 43.478 0.00 0.00 37.15 4.06
4787 6175 4.279169 ACAGACACCCAATTTGATGTCAAG 59.721 41.667 23.95 19.74 43.19 3.02
4807 6198 4.154918 GCAAAGGAGAGGTTATGTTCACAG 59.845 45.833 0.00 0.00 0.00 3.66
4814 6205 7.307632 CGAATGATAAGCAAAGGAGAGGTTATG 60.308 40.741 0.00 0.00 38.22 1.90
4913 6327 1.615814 CCTTCCCTCTCTCCCTCGA 59.384 63.158 0.00 0.00 0.00 4.04
4915 6329 1.074850 CCCCTTCCCTCTCTCCCTC 60.075 68.421 0.00 0.00 0.00 4.30
4916 6330 2.652113 CCCCCTTCCCTCTCTCCCT 61.652 68.421 0.00 0.00 0.00 4.20
4917 6331 2.040359 CCCCCTTCCCTCTCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
5004 6418 2.841988 GCCCCACCACCAAAAGCA 60.842 61.111 0.00 0.00 0.00 3.91
5005 6419 3.625897 GGCCCCACCACCAAAAGC 61.626 66.667 0.00 0.00 38.86 3.51
5006 6420 3.302344 CGGCCCCACCACCAAAAG 61.302 66.667 0.00 0.00 39.03 2.27
5060 6475 1.965643 AGGACACACACGGTAAGCTAA 59.034 47.619 0.00 0.00 0.00 3.09
5095 6514 4.551388 GATTGATAGATGGACGAGTGACC 58.449 47.826 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.