Multiple sequence alignment - TraesCS2D01G308000

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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 TraesCS2D01G308000 chr2D 100.000 3993 0 0 1 3993 394801555 394797563 0.000000e+00 7374
1 TraesCS2D01G308000 chr2A 90.487 4110 167 86 1 3993 532868798 532864796 0.000000e+00 5217
2 TraesCS2D01G308000 chr2B 91.033 3736 157 64 337 3993 467873630 467869994 0.000000e+00 4879
3 TraesCS2D01G308000 chr2B 95.415 349 12 2 1 346 467874010 467873663 1.620000e-153 553


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 TraesCS2D01G308000 chr2D 394797563 394801555 3992 True 7374 7374 100.000 1 3993 1 chr2D.!!$R1 3992
1 TraesCS2D01G308000 chr2A 532864796 532868798 4002 True 5217 5217 90.487 1 3993 1 chr2A.!!$R1 3992
2 TraesCS2D01G308000 chr2B 467869994 467874010 4016 True 2716 4879 93.224 1 3993 2 chr2B.!!$R1 3992

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
157 164 0.040958 CACTCAAGCAGCGGAAACAC 60.041 55.0 0.00 0.0 0.00 3.32 F
1330 1499 0.041090 TCCTTTCCTTCCCCATTGCC 59.959 55.0 0.00 0.0 0.00 4.52 F
1977 2212 0.109153 AAGGTGCACATCTCACTGCA 59.891 50.0 20.43 0.0 41.13 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1351 1520 0.107410 TTCAGAGCAAACGTGGTGGT 60.107 50.000 4.04 4.04 35.0 4.16 R
2495 2736 1.069823 AGGTATCAGCTGCAGGATTCG 59.930 52.381 17.12 0.00 0.0 3.34 R
3685 3930 1.381928 TAGCAGTAGGAAGACGGGCG 61.382 60.000 0.00 0.00 32.1 6.13 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
41 42 8.043113 TCCACTTGCTATATATTTAGCTGGATG 58.957 37.037 20.86 15.23 44.03 3.51
68 70 0.457337 GGCGAGCAAAGCAAAGATGG 60.457 55.000 0.00 0.00 36.08 3.51
97 101 9.671279 TGTCTTATCTGGTTATGCATATATTGG 57.329 33.333 7.36 0.00 0.00 3.16
150 157 4.099170 GCCAGCACTCAAGCAGCG 62.099 66.667 0.00 0.00 36.85 5.18
157 164 0.040958 CACTCAAGCAGCGGAAACAC 60.041 55.000 0.00 0.00 0.00 3.32
257 284 0.173255 CGCCATAAAACAAGCCAGGG 59.827 55.000 0.00 0.00 0.00 4.45
373 444 2.993220 GCGGGTCAAATGGTTTTCAATC 59.007 45.455 0.00 0.00 0.00 2.67
398 478 1.735571 ACGAACATAATCACCAACGCC 59.264 47.619 0.00 0.00 0.00 5.68
435 515 8.902540 AATTGTTTTACTAGCCGATGATATGA 57.097 30.769 0.00 0.00 0.00 2.15
436 516 8.902540 ATTGTTTTACTAGCCGATGATATGAA 57.097 30.769 0.00 0.00 0.00 2.57
437 517 8.902540 TTGTTTTACTAGCCGATGATATGAAT 57.097 30.769 0.00 0.00 0.00 2.57
438 518 8.534333 TGTTTTACTAGCCGATGATATGAATC 57.466 34.615 0.00 0.00 0.00 2.52
530 628 1.673337 GAACGGACCGGGGAAAAGG 60.673 63.158 20.00 0.00 0.00 3.11
531 629 3.200329 AACGGACCGGGGAAAAGGG 62.200 63.158 20.00 0.00 0.00 3.95
532 630 3.324108 CGGACCGGGGAAAAGGGA 61.324 66.667 6.32 0.00 0.00 4.20
533 631 2.897762 CGGACCGGGGAAAAGGGAA 61.898 63.158 6.32 0.00 0.00 3.97
534 632 1.461589 GGACCGGGGAAAAGGGAAA 59.538 57.895 6.32 0.00 0.00 3.13
535 633 0.611062 GGACCGGGGAAAAGGGAAAG 60.611 60.000 6.32 0.00 0.00 2.62
536 634 0.611062 GACCGGGGAAAAGGGAAAGG 60.611 60.000 6.32 0.00 0.00 3.11
537 635 1.304962 CCGGGGAAAAGGGAAAGGG 60.305 63.158 0.00 0.00 0.00 3.95
538 636 1.771646 CGGGGAAAAGGGAAAGGGA 59.228 57.895 0.00 0.00 0.00 4.20
539 637 0.113580 CGGGGAAAAGGGAAAGGGAA 59.886 55.000 0.00 0.00 0.00 3.97
540 638 1.481615 CGGGGAAAAGGGAAAGGGAAA 60.482 52.381 0.00 0.00 0.00 3.13
541 639 1.975680 GGGGAAAAGGGAAAGGGAAAC 59.024 52.381 0.00 0.00 0.00 2.78
736 854 0.043334 CCCCCTGAAGAAGAGGAGGA 59.957 60.000 0.00 0.00 31.48 3.71
741 859 2.024464 CCTGAAGAAGAGGAGGAGAGGA 60.024 54.545 0.00 0.00 31.48 3.71
742 860 3.290710 CTGAAGAAGAGGAGGAGAGGAG 58.709 54.545 0.00 0.00 0.00 3.69
743 861 2.922955 TGAAGAAGAGGAGGAGAGGAGA 59.077 50.000 0.00 0.00 0.00 3.71
744 862 3.053693 TGAAGAAGAGGAGGAGAGGAGAG 60.054 52.174 0.00 0.00 0.00 3.20
745 863 1.852965 AGAAGAGGAGGAGAGGAGAGG 59.147 57.143 0.00 0.00 0.00 3.69
799 917 1.202177 CGGGTCCTCAAATCAAATGCG 60.202 52.381 0.00 0.00 0.00 4.73
1137 1288 1.160870 TCAGCTCCCTTCCCTTCCA 59.839 57.895 0.00 0.00 0.00 3.53
1139 1290 0.106819 CAGCTCCCTTCCCTTCCATG 60.107 60.000 0.00 0.00 0.00 3.66
1142 1293 1.230281 TCCCTTCCCTTCCATGCCT 60.230 57.895 0.00 0.00 0.00 4.75
1143 1294 1.228510 CCCTTCCCTTCCATGCCTC 59.771 63.158 0.00 0.00 0.00 4.70
1144 1295 1.284841 CCCTTCCCTTCCATGCCTCT 61.285 60.000 0.00 0.00 0.00 3.69
1145 1296 0.182299 CCTTCCCTTCCATGCCTCTC 59.818 60.000 0.00 0.00 0.00 3.20
1146 1297 1.211456 CTTCCCTTCCATGCCTCTCT 58.789 55.000 0.00 0.00 0.00 3.10
1147 1298 1.563410 CTTCCCTTCCATGCCTCTCTT 59.437 52.381 0.00 0.00 0.00 2.85
1149 1300 2.845659 TCCCTTCCATGCCTCTCTTTA 58.154 47.619 0.00 0.00 0.00 1.85
1151 1302 2.774234 CCCTTCCATGCCTCTCTTTAGA 59.226 50.000 0.00 0.00 0.00 2.10
1163 1326 7.628234 TGCCTCTCTTTAGATTGAATTCTCTT 58.372 34.615 7.05 0.00 0.00 2.85
1164 1327 7.768120 TGCCTCTCTTTAGATTGAATTCTCTTC 59.232 37.037 7.05 1.28 0.00 2.87
1165 1328 7.768120 GCCTCTCTTTAGATTGAATTCTCTTCA 59.232 37.037 7.05 0.00 0.00 3.02
1166 1329 9.664332 CCTCTCTTTAGATTGAATTCTCTTCAA 57.336 33.333 7.05 3.15 41.91 2.69
1171 1334 5.848833 AGATTGAATTCTCTTCAATGGCC 57.151 39.130 15.70 0.00 45.88 5.36
1174 1337 1.066152 GAATTCTCTTCAATGGCCGCC 59.934 52.381 1.04 1.04 0.00 6.13
1275 1444 4.991056 TGTGTGCAAACTGAAGATAGAGAC 59.009 41.667 8.83 0.00 0.00 3.36
1310 1479 5.163804 CGTCATCGTCCCATGTTTTTAATCA 60.164 40.000 0.00 0.00 0.00 2.57
1330 1499 0.041090 TCCTTTCCTTCCCCATTGCC 59.959 55.000 0.00 0.00 0.00 4.52
1332 1501 1.948721 CTTTCCTTCCCCATTGCCGC 61.949 60.000 0.00 0.00 0.00 6.53
1333 1502 4.794648 TCCTTCCCCATTGCCGCG 62.795 66.667 0.00 0.00 0.00 6.46
1341 1510 4.101790 CATTGCCGCGGCGTTTCT 62.102 61.111 41.73 22.79 45.51 2.52
1342 1511 4.101790 ATTGCCGCGGCGTTTCTG 62.102 61.111 41.73 8.11 45.51 3.02
1347 1516 3.414700 CGCGGCGTTTCTGAGCTT 61.415 61.111 15.36 0.00 0.00 3.74
1348 1517 2.946762 GCGGCGTTTCTGAGCTTT 59.053 55.556 9.37 0.00 0.00 3.51
1349 1518 1.282875 GCGGCGTTTCTGAGCTTTT 59.717 52.632 9.37 0.00 0.00 2.27
1350 1519 0.317854 GCGGCGTTTCTGAGCTTTTT 60.318 50.000 9.37 0.00 0.00 1.94
1351 1520 1.069500 GCGGCGTTTCTGAGCTTTTTA 60.069 47.619 9.37 0.00 0.00 1.52
1352 1521 2.571206 CGGCGTTTCTGAGCTTTTTAC 58.429 47.619 0.00 0.00 0.00 2.01
1353 1522 2.664698 CGGCGTTTCTGAGCTTTTTACC 60.665 50.000 0.00 0.00 0.00 2.85
1354 1523 2.292292 GGCGTTTCTGAGCTTTTTACCA 59.708 45.455 0.00 0.00 0.00 3.25
1369 1564 0.753867 TACCACCACGTTTGCTCTGA 59.246 50.000 0.00 0.00 0.00 3.27
1382 1577 8.230486 CACGTTTGCTCTGAACTAAAATCTTAT 58.770 33.333 0.00 0.00 0.00 1.73
1383 1578 8.784043 ACGTTTGCTCTGAACTAAAATCTTATT 58.216 29.630 0.00 0.00 0.00 1.40
1389 1584 9.162764 GCTCTGAACTAAAATCTTATTACCACA 57.837 33.333 0.00 0.00 0.00 4.17
1499 1709 0.249489 ATCGCCTCGCATTCAGTACC 60.249 55.000 0.00 0.00 0.00 3.34
1500 1710 1.153647 CGCCTCGCATTCAGTACCA 60.154 57.895 0.00 0.00 0.00 3.25
1512 1722 4.558226 TTCAGTACCACAGAGCAATCAT 57.442 40.909 0.00 0.00 0.00 2.45
1526 1736 3.061322 GCAATCATCAACTGCAAAGCAA 58.939 40.909 0.00 0.00 38.41 3.91
1553 1763 9.995957 GACTTGCTTCTCCTCTTATTTAATTTC 57.004 33.333 0.00 0.00 0.00 2.17
1554 1764 8.669243 ACTTGCTTCTCCTCTTATTTAATTTCG 58.331 33.333 0.00 0.00 0.00 3.46
1559 1769 6.601332 TCTCCTCTTATTTAATTTCGCCCAT 58.399 36.000 0.00 0.00 0.00 4.00
1686 1917 1.002087 GGAGGACGAGAGCCAGAAAAA 59.998 52.381 0.00 0.00 0.00 1.94
1844 2076 6.670077 GCAGGGTAATAATAATCTGCTAGC 57.330 41.667 8.10 8.10 42.77 3.42
1933 2168 0.910338 ACTGCATGCCTGAGATGACT 59.090 50.000 16.68 0.00 0.00 3.41
1974 2209 2.617276 CCATCAAGGTGCACATCTCACT 60.617 50.000 20.43 1.74 34.97 3.41
1975 2210 2.174363 TCAAGGTGCACATCTCACTG 57.826 50.000 20.43 6.48 34.97 3.66
1976 2211 0.520404 CAAGGTGCACATCTCACTGC 59.480 55.000 20.43 0.00 34.97 4.40
1977 2212 0.109153 AAGGTGCACATCTCACTGCA 59.891 50.000 20.43 0.00 41.13 4.41
1985 2220 2.940410 CACATCTCACTGCATGCATACA 59.060 45.455 22.97 6.63 0.00 2.29
1987 2222 4.753107 CACATCTCACTGCATGCATACATA 59.247 41.667 22.97 7.74 33.67 2.29
1990 2225 3.389002 TCTCACTGCATGCATACATACCT 59.611 43.478 22.97 0.00 33.67 3.08
1993 2228 5.240121 TCACTGCATGCATACATACCTATG 58.760 41.667 22.97 7.24 39.55 2.23
1999 2234 6.772233 TGCATGCATACATACCTATGTTTTCT 59.228 34.615 18.46 0.00 43.99 2.52
2001 2236 7.805071 GCATGCATACATACCTATGTTTTCTTC 59.195 37.037 14.21 0.00 43.99 2.87
2012 2247 5.634859 CCTATGTTTTCTTCCACATTTGTGC 59.365 40.000 5.15 0.00 44.34 4.57
2017 2252 2.653726 TCTTCCACATTTGTGCTGTGT 58.346 42.857 5.15 0.00 44.34 3.72
2018 2253 2.618241 TCTTCCACATTTGTGCTGTGTC 59.382 45.455 5.15 0.00 44.34 3.67
2019 2254 2.049888 TCCACATTTGTGCTGTGTCA 57.950 45.000 5.15 0.00 44.34 3.58
2020 2255 1.948834 TCCACATTTGTGCTGTGTCAG 59.051 47.619 5.15 0.00 44.34 3.51
2021 2256 1.677576 CCACATTTGTGCTGTGTCAGT 59.322 47.619 5.15 0.00 44.34 3.41
2022 2257 2.287188 CCACATTTGTGCTGTGTCAGTC 60.287 50.000 5.15 0.00 44.34 3.51
2023 2258 2.355444 CACATTTGTGCTGTGTCAGTCA 59.645 45.455 0.00 0.00 39.30 3.41
2024 2259 3.004002 CACATTTGTGCTGTGTCAGTCAT 59.996 43.478 0.00 0.00 39.30 3.06
2025 2260 3.633525 ACATTTGTGCTGTGTCAGTCATT 59.366 39.130 0.00 0.00 33.43 2.57
2026 2261 4.821260 ACATTTGTGCTGTGTCAGTCATTA 59.179 37.500 0.00 0.00 33.43 1.90
2027 2262 5.474532 ACATTTGTGCTGTGTCAGTCATTAT 59.525 36.000 0.00 0.00 33.43 1.28
2028 2263 6.016024 ACATTTGTGCTGTGTCAGTCATTATT 60.016 34.615 0.00 0.00 33.43 1.40
2029 2264 5.611796 TTGTGCTGTGTCAGTCATTATTC 57.388 39.130 0.00 0.00 33.43 1.75
2030 2265 4.898320 TGTGCTGTGTCAGTCATTATTCT 58.102 39.130 0.00 0.00 33.43 2.40
2031 2266 4.692155 TGTGCTGTGTCAGTCATTATTCTG 59.308 41.667 0.00 0.00 33.43 3.02
2032 2267 4.093998 GTGCTGTGTCAGTCATTATTCTGG 59.906 45.833 0.00 0.00 33.43 3.86
2033 2268 3.064545 GCTGTGTCAGTCATTATTCTGGC 59.935 47.826 0.00 0.00 36.90 4.85
2034 2269 4.511527 CTGTGTCAGTCATTATTCTGGCT 58.488 43.478 0.00 0.00 37.23 4.75
2036 2271 3.624861 GTGTCAGTCATTATTCTGGCTGG 59.375 47.826 5.91 0.00 46.50 4.85
2037 2272 3.264193 TGTCAGTCATTATTCTGGCTGGT 59.736 43.478 5.91 0.00 46.50 4.00
2042 2277 5.525378 CAGTCATTATTCTGGCTGGTAGAAC 59.475 44.000 0.00 0.00 43.57 3.01
2064 2299 2.726821 TGTCCAATGCTCCCAGAATTC 58.273 47.619 0.00 0.00 0.00 2.17
2082 2317 9.135189 CCAGAATTCCATTACTAATTTCCATGA 57.865 33.333 0.65 0.00 0.00 3.07
2180 2415 1.813513 CAGGTGAGCCTCGATTTTGT 58.186 50.000 0.00 0.00 44.97 2.83
2295 2530 1.475751 GGCAGACAGTACATCATGGGG 60.476 57.143 0.00 0.00 0.00 4.96
2527 2768 3.827302 AGCTGATACCTGATAGTAACCGG 59.173 47.826 0.00 0.00 0.00 5.28
2583 2824 3.261580 TGGTGCTGAAGATTACATCGTG 58.738 45.455 0.00 0.00 0.00 4.35
2673 2914 0.883814 GCAGCACTGTGAGCAAGAGT 60.884 55.000 12.86 0.00 0.00 3.24
2697 2938 0.108615 ACCACATAGCTGCTGTCGAC 60.109 55.000 13.43 9.11 0.00 4.20
3341 3582 0.861837 CGACTGCTCACCTGTTTCAC 59.138 55.000 0.00 0.00 0.00 3.18
3487 3729 3.371965 ACCGTCCATGTATTGTACTCCT 58.628 45.455 0.00 0.00 0.00 3.69
3526 3768 2.299867 TCATGCAGTAGTTCAGACAGCA 59.700 45.455 0.00 0.00 34.78 4.41
3571 3814 5.428457 TGCTTTCAGATGGGACCTTCTATTA 59.572 40.000 6.45 0.00 0.00 0.98
3637 3881 8.519799 AATAATAATGTACAAAGGTGGGTGAG 57.480 34.615 0.00 0.00 0.00 3.51
3674 3919 5.263599 TGAAATCACAATATTGCCTCCTGT 58.736 37.500 15.48 0.00 0.00 4.00
3675 3920 5.357878 TGAAATCACAATATTGCCTCCTGTC 59.642 40.000 15.48 5.50 0.00 3.51
3685 3930 1.070445 CCTCCTGTCGCATGGGATC 59.930 63.158 16.24 10.06 0.00 3.36
3726 3971 5.199424 ACGTCTGTTGTATTTATCGTTGC 57.801 39.130 0.00 0.00 0.00 4.17
3880 4125 6.470877 TCAACGCAAACAAGAAAACATTAGTC 59.529 34.615 0.00 0.00 0.00 2.59
3958 4204 6.683974 TCTAATAAAATGAAGGAGCAGCAC 57.316 37.500 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.669569 TTTGCTCGCCCTGTCTGC 60.670 61.111 0.00 0.00 0.00 4.26
150 157 6.795098 TGCGGATTATGTATATGTGTTTCC 57.205 37.500 0.00 0.00 0.00 3.13
157 164 6.475402 TGCGTATCTTGCGGATTATGTATATG 59.525 38.462 0.00 0.00 35.98 1.78
373 444 4.391358 GTTGGTGATTATGTTCGTTCGTG 58.609 43.478 0.00 0.00 0.00 4.35
422 502 6.427242 GCATCATATGATTCATATCATCGGCT 59.573 38.462 15.74 0.00 46.19 5.52
435 515 2.031769 CCACGCGTTGCATCATATGATT 60.032 45.455 15.74 0.00 31.21 2.57
436 516 1.532437 CCACGCGTTGCATCATATGAT 59.468 47.619 10.22 12.62 34.56 2.45
437 517 0.936600 CCACGCGTTGCATCATATGA 59.063 50.000 10.22 8.10 0.00 2.15
438 518 0.658244 GCCACGCGTTGCATCATATG 60.658 55.000 28.17 4.74 0.00 1.78
530 628 2.557056 CCTTTTCTCCGTTTCCCTTTCC 59.443 50.000 0.00 0.00 0.00 3.13
531 629 2.557056 CCCTTTTCTCCGTTTCCCTTTC 59.443 50.000 0.00 0.00 0.00 2.62
532 630 2.594131 CCCTTTTCTCCGTTTCCCTTT 58.406 47.619 0.00 0.00 0.00 3.11
533 631 1.203013 CCCCTTTTCTCCGTTTCCCTT 60.203 52.381 0.00 0.00 0.00 3.95
534 632 0.404426 CCCCTTTTCTCCGTTTCCCT 59.596 55.000 0.00 0.00 0.00 4.20
535 633 0.402887 TCCCCTTTTCTCCGTTTCCC 59.597 55.000 0.00 0.00 0.00 3.97
536 634 1.613520 CCTCCCCTTTTCTCCGTTTCC 60.614 57.143 0.00 0.00 0.00 3.13
537 635 1.613520 CCCTCCCCTTTTCTCCGTTTC 60.614 57.143 0.00 0.00 0.00 2.78
538 636 0.404426 CCCTCCCCTTTTCTCCGTTT 59.596 55.000 0.00 0.00 0.00 3.60
539 637 1.498176 CCCCTCCCCTTTTCTCCGTT 61.498 60.000 0.00 0.00 0.00 4.44
540 638 1.923909 CCCCTCCCCTTTTCTCCGT 60.924 63.158 0.00 0.00 0.00 4.69
541 639 1.615424 TCCCCTCCCCTTTTCTCCG 60.615 63.158 0.00 0.00 0.00 4.63
677 779 2.042435 AGAGAGGGAAGAGGCGGG 60.042 66.667 0.00 0.00 0.00 6.13
678 780 1.076339 AGAGAGAGGGAAGAGGCGG 60.076 63.158 0.00 0.00 0.00 6.13
680 782 1.215423 AGAGAGAGAGAGGGAAGAGGC 59.785 57.143 0.00 0.00 0.00 4.70
688 790 1.101049 GCGTGGGAGAGAGAGAGAGG 61.101 65.000 0.00 0.00 0.00 3.69
736 854 2.710826 GGCTCCTCCCCTCTCCTCT 61.711 68.421 0.00 0.00 0.00 3.69
741 859 0.399806 GATGAAGGCTCCTCCCCTCT 60.400 60.000 0.00 0.00 34.51 3.69
742 860 0.692419 TGATGAAGGCTCCTCCCCTC 60.692 60.000 0.00 0.00 34.51 4.30
743 861 0.985490 GTGATGAAGGCTCCTCCCCT 60.985 60.000 0.00 0.00 34.51 4.79
744 862 0.985490 AGTGATGAAGGCTCCTCCCC 60.985 60.000 0.00 0.00 34.51 4.81
745 863 0.179936 CAGTGATGAAGGCTCCTCCC 59.820 60.000 0.00 0.00 34.51 4.30
785 903 3.062639 AGAGTACGCGCATTTGATTTGAG 59.937 43.478 5.73 0.00 0.00 3.02
799 917 1.385756 GGAGGTGGGAGAGAGTACGC 61.386 65.000 0.00 0.00 0.00 4.42
904 1037 6.743788 AGTGGTAAGAAAGATACTAGAGGGT 58.256 40.000 0.00 0.00 0.00 4.34
1023 1174 3.991051 ACCAGCACCCTCGTCACG 61.991 66.667 0.00 0.00 0.00 4.35
1039 1190 4.065281 CGGGGAGTCGTCCACCAC 62.065 72.222 0.00 0.00 44.63 4.16
1137 1288 7.804147 AGAGAATTCAATCTAAAGAGAGGCAT 58.196 34.615 8.44 0.00 34.35 4.40
1139 1290 7.768120 TGAAGAGAATTCAATCTAAAGAGAGGC 59.232 37.037 8.44 0.00 34.35 4.70
1144 1295 8.680903 GCCATTGAAGAGAATTCAATCTAAAGA 58.319 33.333 8.44 0.00 44.60 2.52
1145 1296 7.919621 GGCCATTGAAGAGAATTCAATCTAAAG 59.080 37.037 8.44 2.88 44.60 1.85
1146 1297 7.415541 CGGCCATTGAAGAGAATTCAATCTAAA 60.416 37.037 8.44 2.43 44.60 1.85
1147 1298 6.038603 CGGCCATTGAAGAGAATTCAATCTAA 59.961 38.462 8.44 0.00 44.60 2.10
1149 1300 4.337555 CGGCCATTGAAGAGAATTCAATCT 59.662 41.667 8.44 0.00 44.60 2.40
1151 1302 3.181483 GCGGCCATTGAAGAGAATTCAAT 60.181 43.478 8.44 9.45 46.59 2.57
1163 1326 1.247419 AATTGAACGGCGGCCATTGA 61.247 50.000 20.71 0.00 0.00 2.57
1164 1327 0.389687 AAATTGAACGGCGGCCATTG 60.390 50.000 20.71 5.25 0.00 2.82
1165 1328 0.320050 AAAATTGAACGGCGGCCATT 59.680 45.000 20.71 10.68 0.00 3.16
1166 1329 0.108851 GAAAATTGAACGGCGGCCAT 60.109 50.000 20.71 6.96 0.00 4.40
1167 1330 1.287503 GAAAATTGAACGGCGGCCA 59.712 52.632 20.71 5.50 0.00 5.36
1168 1331 1.445410 GGAAAATTGAACGGCGGCC 60.445 57.895 13.24 9.54 0.00 6.13
1171 1334 1.729149 GCAGAGGAAAATTGAACGGCG 60.729 52.381 4.80 4.80 0.00 6.46
1174 1337 1.729149 GCGGCAGAGGAAAATTGAACG 60.729 52.381 0.00 0.00 0.00 3.95
1265 1434 6.655425 TGACGATCGATTATGGTCTCTATCTT 59.345 38.462 24.34 0.00 42.21 2.40
1310 1479 1.343377 GGCAATGGGGAAGGAAAGGAT 60.343 52.381 0.00 0.00 0.00 3.24
1330 1499 2.443957 AAAAGCTCAGAAACGCCGCG 62.444 55.000 12.14 12.14 0.00 6.46
1332 1501 2.571206 GTAAAAAGCTCAGAAACGCCG 58.429 47.619 0.00 0.00 0.00 6.46
1333 1502 2.292292 TGGTAAAAAGCTCAGAAACGCC 59.708 45.455 0.00 0.00 0.00 5.68
1334 1503 3.297472 GTGGTAAAAAGCTCAGAAACGC 58.703 45.455 0.00 0.00 0.00 4.84
1335 1504 3.314080 TGGTGGTAAAAAGCTCAGAAACG 59.686 43.478 0.00 0.00 0.00 3.60
1336 1505 4.607955 GTGGTGGTAAAAAGCTCAGAAAC 58.392 43.478 0.00 0.00 0.00 2.78
1337 1506 3.314080 CGTGGTGGTAAAAAGCTCAGAAA 59.686 43.478 0.00 0.00 0.00 2.52
1338 1507 2.875933 CGTGGTGGTAAAAAGCTCAGAA 59.124 45.455 0.00 0.00 0.00 3.02
1339 1508 2.158871 ACGTGGTGGTAAAAAGCTCAGA 60.159 45.455 0.00 0.00 0.00 3.27
1340 1509 2.218603 ACGTGGTGGTAAAAAGCTCAG 58.781 47.619 0.00 0.00 0.00 3.35
1341 1510 2.335316 ACGTGGTGGTAAAAAGCTCA 57.665 45.000 0.00 0.00 0.00 4.26
1342 1511 3.368495 CAAACGTGGTGGTAAAAAGCTC 58.632 45.455 0.00 0.00 0.00 4.09
1343 1512 2.480587 GCAAACGTGGTGGTAAAAAGCT 60.481 45.455 0.00 0.00 0.00 3.74
1344 1513 1.855978 GCAAACGTGGTGGTAAAAAGC 59.144 47.619 0.00 0.00 0.00 3.51
1345 1514 3.066203 AGAGCAAACGTGGTGGTAAAAAG 59.934 43.478 4.36 0.00 35.00 2.27
1346 1515 3.018149 AGAGCAAACGTGGTGGTAAAAA 58.982 40.909 4.36 0.00 35.00 1.94
1347 1516 2.356382 CAGAGCAAACGTGGTGGTAAAA 59.644 45.455 4.36 0.00 35.00 1.52
1348 1517 1.944024 CAGAGCAAACGTGGTGGTAAA 59.056 47.619 4.36 0.00 35.00 2.01
1349 1518 1.139256 TCAGAGCAAACGTGGTGGTAA 59.861 47.619 4.36 0.00 35.00 2.85
1350 1519 0.753867 TCAGAGCAAACGTGGTGGTA 59.246 50.000 4.36 0.00 35.00 3.25
1351 1520 0.107410 TTCAGAGCAAACGTGGTGGT 60.107 50.000 4.04 4.04 35.00 4.16
1352 1521 0.307760 GTTCAGAGCAAACGTGGTGG 59.692 55.000 0.00 0.00 35.00 4.61
1353 1522 1.299541 AGTTCAGAGCAAACGTGGTG 58.700 50.000 0.00 0.00 35.00 4.17
1354 1523 2.902705 TAGTTCAGAGCAAACGTGGT 57.097 45.000 0.00 0.00 38.47 4.16
1382 1577 3.584834 CGATGACTGTGTGATGTGGTAA 58.415 45.455 0.00 0.00 0.00 2.85
1383 1578 2.673893 GCGATGACTGTGTGATGTGGTA 60.674 50.000 0.00 0.00 0.00 3.25
1386 1581 0.723414 GGCGATGACTGTGTGATGTG 59.277 55.000 0.00 0.00 0.00 3.21
1389 1584 0.737367 CACGGCGATGACTGTGTGAT 60.737 55.000 16.62 0.00 41.21 3.06
1393 1588 2.094659 GTCCACGGCGATGACTGTG 61.095 63.158 16.62 0.00 44.92 3.66
1499 1709 2.486592 TGCAGTTGATGATTGCTCTGTG 59.513 45.455 0.00 0.00 41.23 3.66
1500 1710 2.786777 TGCAGTTGATGATTGCTCTGT 58.213 42.857 0.00 0.00 41.23 3.41
1512 1722 3.425577 CAAGTCTTGCTTTGCAGTTGA 57.574 42.857 0.00 0.00 40.61 3.18
1526 1736 9.746457 AAATTAAATAAGAGGAGAAGCAAGTCT 57.254 29.630 0.00 0.00 0.00 3.24
1539 1749 7.165812 CGTGAAATGGGCGAAATTAAATAAGAG 59.834 37.037 0.00 0.00 0.00 2.85
1541 1751 6.198216 CCGTGAAATGGGCGAAATTAAATAAG 59.802 38.462 0.00 0.00 40.17 1.73
1544 1754 4.429108 CCGTGAAATGGGCGAAATTAAAT 58.571 39.130 0.00 0.00 40.17 1.40
1548 1758 0.108851 GCCGTGAAATGGGCGAAATT 60.109 50.000 0.00 0.00 45.58 1.82
1844 2076 5.745294 CACAGGTGAAAGAAAACAATCAGTG 59.255 40.000 0.00 0.00 0.00 3.66
1933 2168 0.970937 CCTTGAGGAGGTCGTAGCCA 60.971 60.000 0.00 0.00 40.95 4.75
1974 2209 6.772233 AGAAAACATAGGTATGTATGCATGCA 59.228 34.615 25.04 25.04 45.55 3.96
1975 2210 7.206981 AGAAAACATAGGTATGTATGCATGC 57.793 36.000 11.82 11.82 45.55 4.06
1976 2211 8.292448 GGAAGAAAACATAGGTATGTATGCATG 58.708 37.037 10.16 0.00 45.55 4.06
1977 2212 7.998383 TGGAAGAAAACATAGGTATGTATGCAT 59.002 33.333 3.79 3.79 45.55 3.96
1985 2220 8.522830 CACAAATGTGGAAGAAAACATAGGTAT 58.477 33.333 5.63 0.00 42.10 2.73
1987 2222 6.738453 GCACAAATGTGGAAGAAAACATAGGT 60.738 38.462 14.85 0.00 45.72 3.08
1990 2225 6.183360 ACAGCACAAATGTGGAAGAAAACATA 60.183 34.615 14.85 0.00 45.72 2.29
1993 2228 4.268405 CACAGCACAAATGTGGAAGAAAAC 59.732 41.667 14.85 0.00 45.72 2.43
2012 2247 4.331992 CAGCCAGAATAATGACTGACACAG 59.668 45.833 0.00 0.00 36.38 3.66
2017 2252 4.962362 TCTACCAGCCAGAATAATGACTGA 59.038 41.667 0.00 0.00 36.38 3.41
2018 2253 5.282055 TCTACCAGCCAGAATAATGACTG 57.718 43.478 0.00 0.00 0.00 3.51
2019 2254 5.189736 TGTTCTACCAGCCAGAATAATGACT 59.810 40.000 0.00 0.00 34.67 3.41
2020 2255 5.428253 TGTTCTACCAGCCAGAATAATGAC 58.572 41.667 0.00 0.00 34.67 3.06
2021 2256 5.692115 TGTTCTACCAGCCAGAATAATGA 57.308 39.130 0.00 0.00 34.67 2.57
2022 2257 5.824624 ACATGTTCTACCAGCCAGAATAATG 59.175 40.000 0.00 0.00 36.27 1.90
2023 2258 6.006275 ACATGTTCTACCAGCCAGAATAAT 57.994 37.500 0.00 0.00 34.67 1.28
2024 2259 5.428253 GACATGTTCTACCAGCCAGAATAA 58.572 41.667 0.00 0.00 34.67 1.40
2025 2260 4.141711 GGACATGTTCTACCAGCCAGAATA 60.142 45.833 0.00 0.00 34.67 1.75
2026 2261 3.370953 GGACATGTTCTACCAGCCAGAAT 60.371 47.826 0.00 0.00 34.67 2.40
2027 2262 2.027192 GGACATGTTCTACCAGCCAGAA 60.027 50.000 0.00 0.00 0.00 3.02
2028 2263 1.555075 GGACATGTTCTACCAGCCAGA 59.445 52.381 0.00 0.00 0.00 3.86
2029 2264 1.278985 TGGACATGTTCTACCAGCCAG 59.721 52.381 5.55 0.00 0.00 4.85
2030 2265 1.357137 TGGACATGTTCTACCAGCCA 58.643 50.000 5.55 0.00 0.00 4.75
2031 2266 2.489938 TTGGACATGTTCTACCAGCC 57.510 50.000 5.55 0.00 33.85 4.85
2032 2267 2.098117 GCATTGGACATGTTCTACCAGC 59.902 50.000 5.55 3.04 33.85 4.85
2033 2268 3.614092 AGCATTGGACATGTTCTACCAG 58.386 45.455 5.55 0.00 33.85 4.00
2034 2269 3.609853 GAGCATTGGACATGTTCTACCA 58.390 45.455 5.55 2.54 0.00 3.25
2035 2270 2.945668 GGAGCATTGGACATGTTCTACC 59.054 50.000 5.55 0.00 31.26 3.18
2036 2271 2.945668 GGGAGCATTGGACATGTTCTAC 59.054 50.000 5.55 0.00 31.26 2.59
2037 2272 2.575735 TGGGAGCATTGGACATGTTCTA 59.424 45.455 5.55 0.00 31.26 2.10
2042 2277 2.133281 TTCTGGGAGCATTGGACATG 57.867 50.000 0.00 0.00 0.00 3.21
2064 2299 8.980143 AAAACGTTCATGGAAATTAGTAATGG 57.020 30.769 0.00 0.00 0.00 3.16
2082 2317 1.880027 GACTCATGGCCTGAAAACGTT 59.120 47.619 3.32 0.00 32.14 3.99
2146 2381 1.692042 CCTGCTGATCCTCTGGGGT 60.692 63.158 0.00 0.00 36.25 4.95
2180 2415 3.740115 CTCGAGTGAAGAAAAGGGGAAA 58.260 45.455 3.62 0.00 0.00 3.13
2254 2489 1.174712 ACTGTCGCAGCAAAGGCAAT 61.175 50.000 6.74 0.00 44.61 3.56
2295 2530 8.614469 ATCCATCTTATTAACTGAGCTTTAGC 57.386 34.615 0.00 0.00 42.49 3.09
2495 2736 1.069823 AGGTATCAGCTGCAGGATTCG 59.930 52.381 17.12 0.00 0.00 3.34
2527 2768 2.364002 TGTCCCCAGCAAAAAGTTAAGC 59.636 45.455 0.00 0.00 0.00 3.09
2583 2824 1.277557 TCCTTGCTCTGAAGAGGCTTC 59.722 52.381 9.32 0.00 42.29 3.86
2637 2878 2.190578 CATGGAGGGTCCTTCGGC 59.809 66.667 0.00 0.00 37.46 5.54
2640 2881 1.452833 GCTGCATGGAGGGTCCTTC 60.453 63.158 16.65 0.00 37.46 3.46
2673 2914 2.125147 GCAGCTATGTGGTCCGCA 60.125 61.111 7.77 7.77 0.00 5.69
2682 2923 2.233654 GCCGTCGACAGCAGCTATG 61.234 63.158 18.70 0.00 0.00 2.23
3030 3271 2.088423 CGACACAAGAGCTACTCCTCT 58.912 52.381 0.00 0.00 43.81 3.69
3341 3582 9.251792 CTTTTCTCATGAGATCTGATGAACTAG 57.748 37.037 25.64 12.96 37.29 2.57
3411 3653 6.364435 GTGTCTGCATCATCTTTTTCTTTTCC 59.636 38.462 0.00 0.00 0.00 3.13
3526 3768 4.031652 GCAAACATTCTATCGCGCAATTTT 59.968 37.500 8.75 0.00 0.00 1.82
3571 3814 8.302515 AGCAAACATTTTATCTGGAATCATCT 57.697 30.769 0.00 0.00 0.00 2.90
3637 3881 1.882623 GATTTCAATGGCTCGGATCCC 59.117 52.381 6.06 0.00 0.00 3.85
3685 3930 1.381928 TAGCAGTAGGAAGACGGGCG 61.382 60.000 0.00 0.00 32.10 6.13
3880 4125 2.066262 AGTACGTTGCTGACAATTCCG 58.934 47.619 0.00 0.00 38.27 4.30


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

AutoCloner maintained by Alex Coulton.