Multiple sequence alignment - TraesCS1B01G034200

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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 TraesCS1B01G034200 chr1B 100.000 2216 0 0 1 2216 16481557 16479342 0.000000e+00 4093.0
1 TraesCS1B01G034200 chr1B 87.872 907 47 21 1342 2216 16647074 16646199 0.000000e+00 1007.0
2 TraesCS1B01G034200 chr1B 88.457 771 44 19 217 947 16653316 16652551 0.000000e+00 889.0
3 TraesCS1B01G034200 chr1B 96.196 368 9 2 980 1344 16652551 16652186 4.070000e-167 597.0
4 TraesCS1B01G034200 chr1B 87.638 453 29 12 1 426 16653456 16653004 3.280000e-138 501.0
5 TraesCS1B01G034200 chr1D 92.185 1817 82 31 443 2216 11126507 11124708 0.000000e+00 2514.0
6 TraesCS1B01G034200 chr1D 90.508 1475 61 29 724 2163 11042944 11041514 0.000000e+00 1875.0
7 TraesCS1B01G034200 chr1D 89.987 1488 68 24 712 2163 11091670 11090228 0.000000e+00 1847.0
8 TraesCS1B01G034200 chr1D 89.826 747 43 14 1 718 11045367 11044625 0.000000e+00 928.0
9 TraesCS1B01G034200 chr1D 89.149 470 23 12 1 443 11128325 11127857 5.340000e-156 560.0
10 TraesCS1B01G034200 chr1D 87.339 387 34 11 454 831 11202514 11202134 1.570000e-116 429.0
11 TraesCS1B01G034200 chr1D 90.036 281 25 3 148 426 11045093 11044814 5.820000e-96 361.0
12 TraesCS1B01G034200 chr1D 89.130 92 9 1 145 235 11127948 11127857 1.800000e-21 113.0
13 TraesCS1B01G034200 chr1A 90.182 1487 78 27 776 2216 22631678 22633142 0.000000e+00 1875.0
14 TraesCS1B01G034200 chr1A 85.770 1033 84 31 321 1314 12679693 12680701 0.000000e+00 1035.0
15 TraesCS1B01G034200 chr1A 94.967 457 20 3 321 777 22631121 22631574 0.000000e+00 713.0
16 TraesCS1B01G034200 chr1A 91.471 340 17 6 1816 2154 12688629 12688957 7.210000e-125 457.0
17 TraesCS1B01G034200 chr1A 86.527 334 33 6 985 1314 13281674 13281349 7.520000e-95 357.0
18 TraesCS1B01G034200 chr1A 93.617 141 5 2 1686 1826 12686574 12686710 8.020000e-50 207.0
19 TraesCS1B01G034200 chr1A 89.157 83 7 2 138 218 22631248 22631330 3.890000e-18 102.0
20 TraesCS1B01G034200 chrUn 88.737 1021 56 24 1 965 351922866 351921849 0.000000e+00 1194.0
21 TraesCS1B01G034200 chrUn 86.527 334 33 6 985 1314 261624300 261624625 7.520000e-95 357.0
22 TraesCS1B01G034200 chrUn 89.643 280 28 1 148 426 351922589 351922310 2.710000e-94 355.0
23 TraesCS1B01G034200 chrUn 95.349 43 1 1 1426 1468 326549467 326549426 1.420000e-07 67.6
24 TraesCS1B01G034200 chr7B 85.770 1033 84 31 321 1314 192779214 192780222 0.000000e+00 1035.0
25 TraesCS1B01G034200 chr7B 93.617 141 5 2 1686 1826 192786095 192786231 8.020000e-50 207.0
26 TraesCS1B01G034200 chr2B 85.770 1033 84 31 321 1314 47191070 47190062 0.000000e+00 1035.0
27 TraesCS1B01G034200 chr2B 93.617 141 5 2 1686 1826 47184189 47184053 8.020000e-50 207.0
28 TraesCS1B01G034200 chr7A 92.000 50 2 2 1426 1473 164195451 164195402 3.950000e-08 69.4
29 TraesCS1B01G034200 chr5D 92.000 50 2 2 1426 1473 391806016 391806065 3.950000e-08 69.4
30 TraesCS1B01G034200 chr7D 88.889 54 4 2 1426 1477 26785788 26785841 5.110000e-07 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 TraesCS1B01G034200 chr1B 16479342 16481557 2215 True 4093.000000 4093 100.000000 1 2216 1 chr1B.!!$R1 2215
1 TraesCS1B01G034200 chr1B 16646199 16647074 875 True 1007.000000 1007 87.872000 1342 2216 1 chr1B.!!$R2 874
2 TraesCS1B01G034200 chr1B 16652186 16653456 1270 True 662.333333 889 90.763667 1 1344 3 chr1B.!!$R3 1343
3 TraesCS1B01G034200 chr1D 11090228 11091670 1442 True 1847.000000 1847 89.987000 712 2163 1 chr1D.!!$R1 1451
4 TraesCS1B01G034200 chr1D 11124708 11128325 3617 True 1062.333333 2514 90.154667 1 2216 3 chr1D.!!$R4 2215
5 TraesCS1B01G034200 chr1D 11041514 11045367 3853 True 1054.666667 1875 90.123333 1 2163 3 chr1D.!!$R3 2162
6 TraesCS1B01G034200 chr1A 12679693 12680701 1008 False 1035.000000 1035 85.770000 321 1314 1 chr1A.!!$F1 993
7 TraesCS1B01G034200 chr1A 22631121 22633142 2021 False 896.666667 1875 91.435333 138 2216 3 chr1A.!!$F3 2078
8 TraesCS1B01G034200 chr1A 12686574 12688957 2383 False 332.000000 457 92.544000 1686 2154 2 chr1A.!!$F2 468
9 TraesCS1B01G034200 chrUn 351921849 351922866 1017 True 774.500000 1194 89.190000 1 965 2 chrUn.!!$R2 964
10 TraesCS1B01G034200 chr7B 192779214 192780222 1008 False 1035.000000 1035 85.770000 321 1314 1 chr7B.!!$F1 993
11 TraesCS1B01G034200 chr2B 47190062 47191070 1008 True 1035.000000 1035 85.770000 321 1314 1 chr2B.!!$R2 993

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
649 2030 0.476338 TAGGTTGCTTGCTTGACCCA 59.524 50.0 8.79 0.0 32.53 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 7241 0.114364 AATTTTCCCCACCTTCCGCT 59.886 50.0 0.0 0.0 0.0 5.52 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
40 41 5.983540 TGGAAACAAAAACCTTATTGTGCT 58.016 33.333 0.00 0.00 39.57 4.40
112 113 1.604593 AGGGCTTTGCAGATGCGTT 60.605 52.632 0.00 0.00 45.83 4.84
144 145 6.998074 CACCTACATGCTCCTATAAATTTCCA 59.002 38.462 0.00 0.00 0.00 3.53
149 150 8.682936 ACATGCTCCTATAAATTTCCAGTAAG 57.317 34.615 0.00 0.00 0.00 2.34
152 153 7.280356 TGCTCCTATAAATTTCCAGTAAGTCC 58.720 38.462 0.00 0.00 0.00 3.85
153 154 7.092623 TGCTCCTATAAATTTCCAGTAAGTCCA 60.093 37.037 0.00 0.00 0.00 4.02
155 156 9.277783 CTCCTATAAATTTCCAGTAAGTCCATG 57.722 37.037 0.00 0.00 0.00 3.66
156 157 8.998814 TCCTATAAATTTCCAGTAAGTCCATGA 58.001 33.333 0.00 0.00 0.00 3.07
164 165 8.792830 TTTCCAGTAAGTCCATGATTTTCTAG 57.207 34.615 0.00 0.00 0.00 2.43
165 166 7.733773 TCCAGTAAGTCCATGATTTTCTAGA 57.266 36.000 0.00 0.00 0.00 2.43
166 167 7.786030 TCCAGTAAGTCCATGATTTTCTAGAG 58.214 38.462 0.00 0.00 0.00 2.43
167 168 7.619698 TCCAGTAAGTCCATGATTTTCTAGAGA 59.380 37.037 0.00 0.00 0.00 3.10
168 169 7.708752 CCAGTAAGTCCATGATTTTCTAGAGAC 59.291 40.741 0.00 0.00 0.00 3.36
169 170 8.474025 CAGTAAGTCCATGATTTTCTAGAGACT 58.526 37.037 0.00 2.15 34.94 3.24
170 171 9.702253 AGTAAGTCCATGATTTTCTAGAGACTA 57.298 33.333 7.27 0.00 33.21 2.59
171 172 9.738832 GTAAGTCCATGATTTTCTAGAGACTAC 57.261 37.037 7.27 4.16 33.21 2.73
172 173 7.962995 AGTCCATGATTTTCTAGAGACTACA 57.037 36.000 5.48 0.00 31.84 2.74
174 175 8.986991 AGTCCATGATTTTCTAGAGACTACATT 58.013 33.333 5.48 0.00 31.84 2.71
200 201 6.739331 AATAGGTCCATAGTTTCTGGAGAG 57.261 41.667 0.00 0.00 43.33 3.20
201 202 4.338795 AGGTCCATAGTTTCTGGAGAGA 57.661 45.455 0.00 0.00 43.33 3.10
202 203 4.889780 AGGTCCATAGTTTCTGGAGAGAT 58.110 43.478 0.00 0.00 43.33 2.75
203 204 6.031964 AGGTCCATAGTTTCTGGAGAGATA 57.968 41.667 0.00 0.00 43.33 1.98
205 206 7.079048 AGGTCCATAGTTTCTGGAGAGATAAT 58.921 38.462 0.00 0.00 43.33 1.28
206 207 8.235230 AGGTCCATAGTTTCTGGAGAGATAATA 58.765 37.037 0.00 0.00 43.33 0.98
207 208 9.041354 GGTCCATAGTTTCTGGAGAGATAATAT 57.959 37.037 0.00 0.00 43.33 1.28
271 272 7.565323 AGCAAATCCATGATTTTCTAGAGAC 57.435 36.000 0.00 0.00 39.82 3.36
272 273 7.344913 AGCAAATCCATGATTTTCTAGAGACT 58.655 34.615 0.00 0.00 39.82 3.24
273 274 8.489489 AGCAAATCCATGATTTTCTAGAGACTA 58.511 33.333 0.00 0.00 39.82 2.59
274 275 8.555361 GCAAATCCATGATTTTCTAGAGACTAC 58.445 37.037 0.00 0.00 39.82 2.73
275 276 9.605275 CAAATCCATGATTTTCTAGAGACTACA 57.395 33.333 0.00 0.00 39.82 2.74
276 277 9.829507 AAATCCATGATTTTCTAGAGACTACAG 57.170 33.333 0.00 0.00 38.89 2.74
277 278 7.962995 TCCATGATTTTCTAGAGACTACAGT 57.037 36.000 0.00 0.00 0.00 3.55
279 280 9.647918 TCCATGATTTTCTAGAGACTACAGTAT 57.352 33.333 0.00 0.00 0.00 2.12
304 305 9.813826 ATAATAAATCCATAGTTTTCTGGGGAG 57.186 33.333 0.00 0.00 37.07 4.30
311 312 8.757307 TCCATAGTTTTCTGGGGAGATAATAT 57.243 34.615 0.00 0.00 32.41 1.28
312 313 9.182642 TCCATAGTTTTCTGGGGAGATAATATT 57.817 33.333 0.00 0.00 32.41 1.28
392 523 8.997621 TCATGTGACTACACTTTAATAAGTCC 57.002 34.615 0.00 0.00 42.67 3.85
393 524 8.590204 TCATGTGACTACACTTTAATAAGTCCA 58.410 33.333 0.00 0.00 42.67 4.02
394 525 9.383519 CATGTGACTACACTTTAATAAGTCCAT 57.616 33.333 0.00 0.00 42.67 3.41
409 540 7.979786 ATAAGTCCATAGTTTTCTGGAGAGA 57.020 36.000 0.00 0.00 42.10 3.10
410 541 6.882768 AAGTCCATAGTTTTCTGGAGAGAT 57.117 37.500 0.00 0.00 42.10 2.75
411 542 7.979786 AAGTCCATAGTTTTCTGGAGAGATA 57.020 36.000 0.00 0.00 42.10 1.98
412 543 7.979786 AGTCCATAGTTTTCTGGAGAGATAA 57.020 36.000 0.00 0.00 42.10 1.75
413 544 8.560124 AGTCCATAGTTTTCTGGAGAGATAAT 57.440 34.615 0.00 0.00 42.10 1.28
437 568 9.734984 AATATTATTATCCTTCCGGTAACTTGG 57.265 33.333 0.00 0.00 0.00 3.61
438 569 6.564557 TTATTATCCTTCCGGTAACTTGGT 57.435 37.500 0.00 0.00 0.00 3.67
439 570 4.476628 TTATCCTTCCGGTAACTTGGTC 57.523 45.455 0.00 0.00 0.00 4.02
442 573 1.270465 CCTTCCGGTAACTTGGTCGTT 60.270 52.381 0.00 0.00 0.00 3.85
443 574 2.029110 CCTTCCGGTAACTTGGTCGTTA 60.029 50.000 0.00 0.00 0.00 3.18
444 575 3.554752 CCTTCCGGTAACTTGGTCGTTAA 60.555 47.826 0.00 0.00 31.73 2.01
445 576 3.742433 TCCGGTAACTTGGTCGTTAAA 57.258 42.857 0.00 0.00 31.73 1.52
446 577 4.270245 TCCGGTAACTTGGTCGTTAAAT 57.730 40.909 0.00 0.00 31.73 1.40
447 578 3.995705 TCCGGTAACTTGGTCGTTAAATG 59.004 43.478 0.00 0.00 31.73 2.32
449 580 4.143052 CCGGTAACTTGGTCGTTAAATGAC 60.143 45.833 0.00 1.40 31.73 3.06
450 581 4.448395 CGGTAACTTGGTCGTTAAATGACA 59.552 41.667 10.32 0.00 35.87 3.58
451 582 5.121142 CGGTAACTTGGTCGTTAAATGACAT 59.879 40.000 10.32 0.00 35.87 3.06
452 583 6.347888 CGGTAACTTGGTCGTTAAATGACATT 60.348 38.462 10.32 0.00 35.87 2.71
453 584 7.148606 CGGTAACTTGGTCGTTAAATGACATTA 60.149 37.037 0.00 0.00 35.87 1.90
456 587 7.129109 ACTTGGTCGTTAAATGACATTACAG 57.871 36.000 0.00 0.00 35.87 2.74
457 588 6.708949 ACTTGGTCGTTAAATGACATTACAGT 59.291 34.615 0.00 0.00 35.87 3.55
458 589 7.874016 ACTTGGTCGTTAAATGACATTACAGTA 59.126 33.333 0.00 0.00 35.87 2.74
459 590 8.604640 TTGGTCGTTAAATGACATTACAGTAA 57.395 30.769 0.00 0.00 35.87 2.24
461 592 7.874016 TGGTCGTTAAATGACATTACAGTAAGT 59.126 33.333 0.00 0.00 35.87 2.24
463 594 8.378421 GTCGTTAAATGACATTACAGTAAGTCC 58.622 37.037 0.00 2.72 34.36 3.85
465 596 8.879759 CGTTAAATGACATTACAGTAAGTCCAT 58.120 33.333 0.00 8.41 0.00 3.41
466 597 9.988350 GTTAAATGACATTACAGTAAGTCCATG 57.012 33.333 0.00 5.36 0.00 3.66
467 598 9.952030 TTAAATGACATTACAGTAAGTCCATGA 57.048 29.630 0.00 3.56 0.00 3.07
470 601 9.466497 AATGACATTACAGTAAGTCCATGATTT 57.534 29.630 14.98 0.00 0.00 2.17
619 1996 5.240183 AGCATTCAAGACCATATCAATTCGG 59.760 40.000 0.00 0.00 0.00 4.30
625 2004 2.224606 ACCATATCAATTCGGCAGCTG 58.775 47.619 10.11 10.11 0.00 4.24
649 2030 0.476338 TAGGTTGCTTGCTTGACCCA 59.524 50.000 8.79 0.00 32.53 4.51
721 3779 3.192212 ACGTGTACCTTGCTACTAGAACC 59.808 47.826 0.00 0.00 0.00 3.62
722 3780 3.428589 CGTGTACCTTGCTACTAGAACCC 60.429 52.174 0.00 0.00 0.00 4.11
807 3971 5.645929 ACTCGACCAATGTGTTATGCAAATA 59.354 36.000 0.00 0.00 0.00 1.40
821 3985 3.138304 TGCAAATAAAGTCTCACGCACT 58.862 40.909 0.00 0.00 0.00 4.40
892 4091 3.317149 CCGTCCATTAATCGGTGAGTAGA 59.683 47.826 6.02 0.00 39.51 2.59
897 4096 6.255887 GTCCATTAATCGGTGAGTAGAAACTG 59.744 42.308 4.51 0.00 35.56 3.16
898 4097 6.153851 TCCATTAATCGGTGAGTAGAAACTGA 59.846 38.462 4.51 0.00 35.56 3.41
899 4098 6.986817 CCATTAATCGGTGAGTAGAAACTGAT 59.013 38.462 0.00 0.00 42.83 2.90
902 4101 5.923733 ATCGGTGAGTAGAAACTGATCTT 57.076 39.130 0.00 0.00 37.80 2.40
903 4102 5.312120 TCGGTGAGTAGAAACTGATCTTC 57.688 43.478 0.00 0.00 35.56 2.87
904 4103 5.010933 TCGGTGAGTAGAAACTGATCTTCT 58.989 41.667 0.00 0.00 35.56 2.85
969 4197 4.870123 AGCTAGCTCTGATTGATCGATT 57.130 40.909 12.68 0.00 0.00 3.34
1018 4246 0.809385 GATGAGTTCCTCCGACGACA 59.191 55.000 0.00 0.00 0.00 4.35
1273 4504 2.229675 TAGATGCTGGCTCACGAATG 57.770 50.000 0.00 0.00 0.00 2.67
1337 4572 4.083484 GCTTAATCGGTGCTTAAAGTGTGT 60.083 41.667 0.00 0.00 0.00 3.72
1338 4573 3.896648 AATCGGTGCTTAAAGTGTGTG 57.103 42.857 0.00 0.00 0.00 3.82
1473 4711 0.616395 TGCAGAGACCGGGGTAATCA 60.616 55.000 6.32 0.00 0.00 2.57
1478 4716 2.966516 AGAGACCGGGGTAATCATTCTC 59.033 50.000 6.32 5.56 0.00 2.87
1502 4744 8.339344 TCTAAAAGAAATCATGTGCTTGATCA 57.661 30.769 0.00 0.00 35.29 2.92
1529 4773 9.219603 GTCAGTTATGTATGTATATGTGCCAAT 57.780 33.333 0.00 0.00 0.00 3.16
1552 4796 2.304761 TGTGAAGTTCCATCCAGGGTAC 59.695 50.000 0.00 0.00 38.24 3.34
1580 4851 9.515226 TTAAGACAAGCCTAATTAAATCTGTGT 57.485 29.630 0.00 0.00 0.00 3.72
1628 4899 1.879380 CGAGCAATCCCAAGTTCACAA 59.121 47.619 0.00 0.00 0.00 3.33
1656 4928 8.306038 TCAATTTTAATCACCAATTCTGGACAG 58.694 33.333 0.00 0.00 46.92 3.51
1657 4929 5.643379 TTTAATCACCAATTCTGGACAGC 57.357 39.130 0.00 0.00 46.92 4.40
1754 5030 1.134788 CCTAAGGAAACGACCGAGCAT 60.135 52.381 0.00 0.00 34.73 3.79
1789 5065 3.482783 GCTTGCGCGTGAGGTCTC 61.483 66.667 8.43 0.00 0.00 3.36
1790 5066 2.049156 CTTGCGCGTGAGGTCTCA 60.049 61.111 8.43 0.00 37.24 3.27
1966 7170 2.703536 TGAGAGAAGCACAAGGGTGTTA 59.296 45.455 0.00 0.00 46.95 2.41
1967 7171 3.244215 TGAGAGAAGCACAAGGGTGTTAG 60.244 47.826 0.00 0.00 46.95 2.34
1968 7172 2.706190 AGAGAAGCACAAGGGTGTTAGT 59.294 45.455 0.00 0.00 46.95 2.24
1969 7173 3.136626 AGAGAAGCACAAGGGTGTTAGTT 59.863 43.478 0.00 0.00 46.95 2.24
2017 7221 7.327975 ACATCAGTAGTCGATAAAATTCACCA 58.672 34.615 0.00 0.00 0.00 4.17
2018 7222 7.492669 ACATCAGTAGTCGATAAAATTCACCAG 59.507 37.037 0.00 0.00 0.00 4.00
2019 7223 5.810587 TCAGTAGTCGATAAAATTCACCAGC 59.189 40.000 0.00 0.00 0.00 4.85
2020 7224 4.804139 AGTAGTCGATAAAATTCACCAGCG 59.196 41.667 0.00 0.00 0.00 5.18
2036 7241 2.767536 GCGAGCATTGCCTTGAGTA 58.232 52.632 4.70 0.00 40.55 2.59
2053 7258 0.037160 GTAGCGGAAGGTGGGGAAAA 59.963 55.000 0.00 0.00 44.53 2.29
2054 7259 0.996583 TAGCGGAAGGTGGGGAAAAT 59.003 50.000 0.00 0.00 44.53 1.82
2069 7274 5.183969 GGGGAAAATTAGTCTTAAGCGAGT 58.816 41.667 0.00 0.00 0.00 4.18
2070 7275 6.070653 TGGGGAAAATTAGTCTTAAGCGAGTA 60.071 38.462 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.099266 TGCACAAGAGCACAATAAGGTTTT 59.901 37.500 0.00 0.00 40.11 2.43
29 30 2.163010 CCTGCACAAGAGCACAATAAGG 59.837 50.000 0.00 0.00 40.11 2.69
40 41 4.574674 AGTAATTGGATCCTGCACAAGA 57.425 40.909 14.23 0.00 0.00 3.02
112 113 3.792736 GCATGTAGGTGCCCGGGA 61.793 66.667 29.31 6.60 39.18 5.14
124 125 8.275040 ACTTACTGGAAATTTATAGGAGCATGT 58.725 33.333 0.00 0.00 0.00 3.21
136 137 9.093458 AGAAAATCATGGACTTACTGGAAATTT 57.907 29.630 0.00 0.00 0.00 1.82
144 145 8.602472 AGTCTCTAGAAAATCATGGACTTACT 57.398 34.615 0.00 0.00 30.00 2.24
174 175 9.535170 CTCTCCAGAAACTATGGACCTATTATA 57.465 37.037 0.00 0.00 41.96 0.98
176 177 7.592736 TCTCTCCAGAAACTATGGACCTATTA 58.407 38.462 0.00 0.00 41.96 0.98
177 178 6.444704 TCTCTCCAGAAACTATGGACCTATT 58.555 40.000 0.00 0.00 41.96 1.73
178 179 6.031964 TCTCTCCAGAAACTATGGACCTAT 57.968 41.667 0.00 0.00 41.96 2.57
179 180 5.467668 TCTCTCCAGAAACTATGGACCTA 57.532 43.478 0.00 0.00 41.96 3.08
181 182 6.732896 TTATCTCTCCAGAAACTATGGACC 57.267 41.667 0.00 0.00 41.96 4.46
245 246 9.282569 GTCTCTAGAAAATCATGGATTTGCTAT 57.717 33.333 16.09 0.11 43.71 2.97
246 247 8.489489 AGTCTCTAGAAAATCATGGATTTGCTA 58.511 33.333 15.29 15.29 43.71 3.49
249 250 9.605275 TGTAGTCTCTAGAAAATCATGGATTTG 57.395 33.333 5.07 0.00 40.77 2.32
252 253 8.546083 ACTGTAGTCTCTAGAAAATCATGGAT 57.454 34.615 0.00 0.00 0.00 3.41
279 280 9.009675 TCTCCCCAGAAAACTATGGATTTATTA 57.990 33.333 0.00 0.00 39.02 0.98
280 281 7.882755 TCTCCCCAGAAAACTATGGATTTATT 58.117 34.615 0.00 0.00 39.02 1.40
282 283 6.901615 TCTCCCCAGAAAACTATGGATTTA 57.098 37.500 0.00 0.00 39.02 1.40
284 285 7.465900 TTATCTCCCCAGAAAACTATGGATT 57.534 36.000 0.00 0.00 39.02 3.01
285 286 7.654287 ATTATCTCCCCAGAAAACTATGGAT 57.346 36.000 0.00 0.00 39.02 3.41
286 287 8.757307 ATATTATCTCCCCAGAAAACTATGGA 57.243 34.615 0.00 0.00 39.02 3.41
311 312 7.781693 ACTACCGACTTACCAGAAGGATAATAA 59.218 37.037 0.00 0.00 38.69 1.40
312 313 7.293073 ACTACCGACTTACCAGAAGGATAATA 58.707 38.462 0.00 0.00 38.69 0.98
313 314 6.134754 ACTACCGACTTACCAGAAGGATAAT 58.865 40.000 0.00 0.00 38.69 1.28
314 315 5.513233 ACTACCGACTTACCAGAAGGATAA 58.487 41.667 0.00 0.00 38.69 1.75
315 316 5.121380 ACTACCGACTTACCAGAAGGATA 57.879 43.478 0.00 0.00 38.69 2.59
318 319 5.649782 TTAACTACCGACTTACCAGAAGG 57.350 43.478 0.00 0.00 42.21 3.46
319 320 9.813446 ATTATTTAACTACCGACTTACCAGAAG 57.187 33.333 0.00 0.00 0.00 2.85
383 514 9.488762 TCTCTCCAGAAAACTATGGACTTATTA 57.511 33.333 0.00 0.00 40.70 0.98
384 515 8.380742 TCTCTCCAGAAAACTATGGACTTATT 57.619 34.615 0.00 0.00 40.70 1.40
385 516 7.979786 TCTCTCCAGAAAACTATGGACTTAT 57.020 36.000 0.00 0.00 40.70 1.73
386 517 7.979786 ATCTCTCCAGAAAACTATGGACTTA 57.020 36.000 0.00 0.00 40.70 2.24
388 519 7.979786 TTATCTCTCCAGAAAACTATGGACT 57.020 36.000 0.00 0.00 40.70 3.85
418 549 7.752515 TAACGACCAAGTTACCGGAAGGATAA 61.753 42.308 9.46 0.00 44.08 1.75
419 550 6.328981 TAACGACCAAGTTACCGGAAGGATA 61.329 44.000 9.46 0.00 44.08 2.59
420 551 5.596362 TAACGACCAAGTTACCGGAAGGAT 61.596 45.833 9.46 0.00 44.08 3.24
422 553 2.029110 TAACGACCAAGTTACCGGAAGG 60.029 50.000 9.46 2.52 45.55 3.46
424 555 3.742433 TTAACGACCAAGTTACCGGAA 57.258 42.857 9.46 0.00 36.44 4.30
425 556 3.742433 TTTAACGACCAAGTTACCGGA 57.258 42.857 9.46 0.00 36.44 5.14
426 557 3.995705 TCATTTAACGACCAAGTTACCGG 59.004 43.478 0.00 0.00 36.44 5.28
427 558 4.448395 TGTCATTTAACGACCAAGTTACCG 59.552 41.667 0.00 0.00 36.44 4.02
428 559 5.927954 TGTCATTTAACGACCAAGTTACC 57.072 39.130 0.00 0.00 36.44 2.85
429 560 8.497554 TGTAATGTCATTTAACGACCAAGTTAC 58.502 33.333 2.79 6.76 36.44 2.50
431 562 7.227910 ACTGTAATGTCATTTAACGACCAAGTT 59.772 33.333 2.79 0.00 38.07 2.66
434 565 8.604640 TTACTGTAATGTCATTTAACGACCAA 57.395 30.769 2.79 0.00 32.15 3.67
435 566 7.874016 ACTTACTGTAATGTCATTTAACGACCA 59.126 33.333 2.79 0.00 32.15 4.02
436 567 8.248117 ACTTACTGTAATGTCATTTAACGACC 57.752 34.615 2.79 0.00 32.15 4.79
437 568 8.378421 GGACTTACTGTAATGTCATTTAACGAC 58.622 37.037 20.96 0.00 0.00 4.34
438 569 8.089597 TGGACTTACTGTAATGTCATTTAACGA 58.910 33.333 20.96 0.00 0.00 3.85
439 570 8.246908 TGGACTTACTGTAATGTCATTTAACG 57.753 34.615 20.96 0.00 0.00 3.18
443 574 9.466497 AATCATGGACTTACTGTAATGTCATTT 57.534 29.630 20.96 10.01 0.00 2.32
444 575 9.466497 AAATCATGGACTTACTGTAATGTCATT 57.534 29.630 20.96 3.06 0.00 2.57
445 576 9.113838 GAAATCATGGACTTACTGTAATGTCAT 57.886 33.333 20.96 13.56 0.00 3.06
446 577 7.552687 GGAAATCATGGACTTACTGTAATGTCA 59.447 37.037 20.96 12.40 0.00 3.58
447 578 7.770897 AGGAAATCATGGACTTACTGTAATGTC 59.229 37.037 15.62 15.62 0.00 3.06
449 580 7.923888 CAGGAAATCATGGACTTACTGTAATG 58.076 38.462 0.00 0.00 0.00 1.90
463 594 5.350504 AGTGTAGTCTCCAGGAAATCATG 57.649 43.478 0.00 0.00 0.00 3.07
465 596 8.783660 ATTATAGTGTAGTCTCCAGGAAATCA 57.216 34.615 0.00 0.00 0.00 2.57
468 599 9.710818 ACTTATTATAGTGTAGTCTCCAGGAAA 57.289 33.333 0.00 0.00 0.00 3.13
470 601 9.352191 GAACTTATTATAGTGTAGTCTCCAGGA 57.648 37.037 0.00 0.00 0.00 3.86
619 1996 2.694760 GCAACCTACAGGCAGCTGC 61.695 63.158 30.88 30.88 39.32 5.25
625 2004 0.242017 CAAGCAAGCAACCTACAGGC 59.758 55.000 0.00 0.00 39.32 4.85
721 3779 4.183223 TCATTTTCCCATCCATGGTAGG 57.817 45.455 12.58 14.41 46.65 3.18
722 3780 4.038402 GCTTCATTTTCCCATCCATGGTAG 59.962 45.833 12.58 5.40 46.65 3.18
821 3985 1.980951 GCCGATGATTGAGTTGCGCA 61.981 55.000 5.66 5.66 0.00 6.09
897 4096 8.534778 CAGCAACAAACTAAACAAAAGAAGATC 58.465 33.333 0.00 0.00 0.00 2.75
898 4097 8.250332 TCAGCAACAAACTAAACAAAAGAAGAT 58.750 29.630 0.00 0.00 0.00 2.40
899 4098 7.598278 TCAGCAACAAACTAAACAAAAGAAGA 58.402 30.769 0.00 0.00 0.00 2.87
902 4101 8.770438 ATTTCAGCAACAAACTAAACAAAAGA 57.230 26.923 0.00 0.00 0.00 2.52
903 4102 9.900264 GTATTTCAGCAACAAACTAAACAAAAG 57.100 29.630 0.00 0.00 0.00 2.27
904 4103 8.874816 GGTATTTCAGCAACAAACTAAACAAAA 58.125 29.630 0.00 0.00 0.00 2.44
969 4197 6.711277 AGCACTGGTTGATAACTTTAGATCA 58.289 36.000 0.00 0.00 0.00 2.92
975 4203 4.890088 TCGTAGCACTGGTTGATAACTTT 58.110 39.130 0.00 0.00 0.00 2.66
1018 4246 0.391263 GTCTTCTTTCCACCGGCGAT 60.391 55.000 9.30 0.00 0.00 4.58
1304 4539 2.095853 CACCGATTAAGCACACATGACC 59.904 50.000 0.00 0.00 0.00 4.02
1337 4572 2.552599 TCCACAACACCGATTAAGCA 57.447 45.000 0.00 0.00 0.00 3.91
1338 4573 3.907894 TTTCCACAACACCGATTAAGC 57.092 42.857 0.00 0.00 0.00 3.09
1473 4711 9.017509 TCAAGCACATGATTTCTTTTAGAGAAT 57.982 29.630 0.00 0.00 43.65 2.40
1478 4716 8.242053 ACTGATCAAGCACATGATTTCTTTTAG 58.758 33.333 0.00 0.00 40.08 1.85
1502 4744 7.962441 TGGCACATATACATACATAACTGACT 58.038 34.615 0.00 0.00 0.00 3.41
1529 4773 1.630369 CCCTGGATGGAACTTCACAGA 59.370 52.381 0.00 0.00 38.35 3.41
1575 4846 4.276431 TGCATGGCATTGACATATACACAG 59.724 41.667 4.27 0.00 31.71 3.66
1628 4899 8.306761 GTCCAGAATTGGTGATTAAAATTGAGT 58.693 33.333 0.00 0.00 45.26 3.41
1656 4928 7.142306 ACTTTTTAGAGGAAAGGTATTTCGC 57.858 36.000 0.00 0.00 44.87 4.70
1721 4993 5.336531 CGTTTCCTTAGGTACACATCTCTGT 60.337 44.000 0.00 0.00 35.44 3.41
1722 4994 5.103000 CGTTTCCTTAGGTACACATCTCTG 58.897 45.833 0.00 0.00 0.00 3.35
1754 5030 3.251479 AGCACACGAAGCATCATTAGA 57.749 42.857 0.00 0.00 0.00 2.10
1877 7081 2.614969 AGCTTGGGAGGGATGCCA 60.615 61.111 5.86 0.00 0.00 4.92
1923 7127 1.946156 ACATGCATCGTAGCGAGCG 60.946 57.895 0.00 0.00 39.91 5.03
1966 7170 2.703007 AGCAGAGAGGTGTTCTTGAACT 59.297 45.455 13.65 0.00 35.87 3.01
1967 7171 3.118905 AGCAGAGAGGTGTTCTTGAAC 57.881 47.619 6.56 6.56 35.87 3.18
1968 7172 3.134623 TGAAGCAGAGAGGTGTTCTTGAA 59.865 43.478 0.00 0.00 35.87 2.69
1969 7173 2.700371 TGAAGCAGAGAGGTGTTCTTGA 59.300 45.455 0.00 0.00 35.87 3.02
2017 7221 0.250234 TACTCAAGGCAATGCTCGCT 59.750 50.000 4.82 0.00 0.00 4.93
2018 7222 0.654683 CTACTCAAGGCAATGCTCGC 59.345 55.000 4.82 0.00 0.00 5.03
2019 7223 0.654683 GCTACTCAAGGCAATGCTCG 59.345 55.000 4.82 0.00 0.00 5.03
2020 7224 0.654683 CGCTACTCAAGGCAATGCTC 59.345 55.000 4.82 0.00 0.00 4.26
2036 7241 0.114364 AATTTTCCCCACCTTCCGCT 59.886 50.000 0.00 0.00 0.00 5.52
2069 7274 6.908820 CGTCATCGCAACACTAAGTAACTATA 59.091 38.462 0.00 0.00 0.00 1.31
2070 7275 5.742453 CGTCATCGCAACACTAAGTAACTAT 59.258 40.000 0.00 0.00 0.00 2.12
2170 7375 5.550290 TGAGAAATGCATGAGACAAGTGTA 58.450 37.500 0.00 0.00 0.00 2.90
2177 7382 7.935338 TTTTTCTTTGAGAAATGCATGAGAC 57.065 32.000 0.00 0.00 43.06 3.36


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

AutoCloner maintained by Alex Coulton.