Multiple sequence alignment - TraesCS4A01G337200

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 TraesCS4A01G337200 chr4A 100.000 1747 0 0 847 2593 619369909 619371655 0.000000e+00 3227.0
1 TraesCS4A01G337200 chr4A 100.000 501 0 0 1 501 619369063 619369563 0.000000e+00 926.0
2 TraesCS4A01G337200 chr4A 83.376 776 74 33 875 1618 619333592 619334344 0.000000e+00 667.0
3 TraesCS4A01G337200 chr4A 80.405 592 83 23 1020 1593 619312346 619312922 1.110000e-113 420.0
4 TraesCS4A01G337200 chr5D 87.287 1762 103 47 878 2593 548479558 548481244 0.000000e+00 1901.0
5 TraesCS4A01G337200 chr5D 85.750 793 63 28 861 1618 548460447 548461224 0.000000e+00 793.0
6 TraesCS4A01G337200 chr5D 80.943 509 53 27 1 499 548478705 548479179 1.900000e-96 363.0
7 TraesCS4A01G337200 chr5D 81.718 454 45 16 1 449 548468555 548468975 6.870000e-91 344.0
8 TraesCS4A01G337200 chr5D 86.842 152 11 8 1457 1603 548374458 548374605 7.430000e-36 161.0
9 TraesCS4A01G337200 chr5B 86.591 1760 113 54 878 2578 692691084 692692779 0.000000e+00 1829.0
10 TraesCS4A01G337200 chr5B 82.803 628 60 22 1003 1596 692678727 692679340 3.830000e-143 518.0
11 TraesCS4A01G337200 chr5B 86.022 279 27 8 1 277 692690298 692690566 3.260000e-74 289.0
12 TraesCS4A01G337200 chr5B 77.586 290 37 11 874 1149 692648715 692648990 1.610000e-32 150.0
13 TraesCS4A01G337200 chr4B 88.000 475 41 8 2130 2593 650179605 650180074 4.880000e-152 547.0
14 TraesCS4A01G337200 chr4B 87.789 475 42 7 2130 2593 650049548 650050017 2.270000e-150 542.0
15 TraesCS4A01G337200 chr4B 87.158 475 45 7 2130 2593 650059157 650059626 2.290000e-145 525.0
16 TraesCS4A01G337200 chr4B 86.947 475 45 8 2130 2593 650117945 650118413 3.830000e-143 518.0
17 TraesCS4A01G337200 chr6B 85.895 475 49 9 2130 2593 49267852 49268319 8.340000e-135 490.0
18 TraesCS4A01G337200 chr1B 87.850 321 31 5 2130 2442 538494144 538494464 1.130000e-98 370.0
19 TraesCS4A01G337200 chr2B 78.846 156 16 10 2 157 134257280 134257142 3.550000e-14 89.8


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 TraesCS4A01G337200 chr4A 619369063 619371655 2592 False 2076.5 3227 100.0000 1 2593 2 chr4A.!!$F3 2592
1 TraesCS4A01G337200 chr4A 619333592 619334344 752 False 667.0 667 83.3760 875 1618 1 chr4A.!!$F2 743
2 TraesCS4A01G337200 chr4A 619312346 619312922 576 False 420.0 420 80.4050 1020 1593 1 chr4A.!!$F1 573
3 TraesCS4A01G337200 chr5D 548478705 548481244 2539 False 1132.0 1901 84.1150 1 2593 2 chr5D.!!$F4 2592
4 TraesCS4A01G337200 chr5D 548460447 548461224 777 False 793.0 793 85.7500 861 1618 1 chr5D.!!$F2 757
5 TraesCS4A01G337200 chr5B 692690298 692692779 2481 False 1059.0 1829 86.3065 1 2578 2 chr5B.!!$F3 2577
6 TraesCS4A01G337200 chr5B 692678727 692679340 613 False 518.0 518 82.8030 1003 1596 1 chr5B.!!$F2 593

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
500 517 0.240945 CAACGAATTGGCACACCTCC 59.759 55.0 0.0 0.0 39.29 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1618 1767 0.321671 TGGTTTCTCGAGCTCAAGGG 59.678 55.0 15.4 0.0 0.0 3.95 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
70 72 8.691661 TTAGCCTAGACTCAATGAAAAAGTTT 57.308 30.769 0.00 0.00 0.00 2.66
106 108 8.461249 AATGAAATGACATCCCTTTCTCTATG 57.539 34.615 0.00 0.00 31.66 2.23
125 127 7.506261 TCTCTATGGAACTAAGACACCTATTCC 59.494 40.741 0.00 0.00 36.86 3.01
141 143 9.343994 ACACCTATTCCCATGATATTTCTATCT 57.656 33.333 0.00 0.00 35.69 1.98
174 176 8.636213 CCAAAGAAGCCTTCATATGAAACATAT 58.364 33.333 18.47 5.12 33.07 1.78
175 177 9.674824 CAAAGAAGCCTTCATATGAAACATATC 57.325 33.333 18.47 12.71 33.07 1.63
207 209 9.897744 CAGTTTTCTTAATGAATACTCTTTGCA 57.102 29.630 7.35 0.00 42.33 4.08
242 244 1.337384 TATGTGCATCCTCGGGTGCT 61.337 55.000 20.82 4.86 41.78 4.40
244 246 4.100084 TGCATCCTCGGGTGCTGG 62.100 66.667 20.82 0.00 41.78 4.85
288 298 7.201644 CCATAATCTCAAGTCGCACTTTTACAT 60.202 37.037 0.00 0.00 36.03 2.29
293 303 6.910433 TCTCAAGTCGCACTTTTACATTTTTC 59.090 34.615 0.00 0.00 36.03 2.29
294 304 6.791303 TCAAGTCGCACTTTTACATTTTTCT 58.209 32.000 0.00 0.00 36.03 2.52
295 305 7.254852 TCAAGTCGCACTTTTACATTTTTCTT 58.745 30.769 0.00 0.00 36.03 2.52
296 306 7.757624 TCAAGTCGCACTTTTACATTTTTCTTT 59.242 29.630 0.00 0.00 36.03 2.52
297 307 8.379902 CAAGTCGCACTTTTACATTTTTCTTTT 58.620 29.630 0.00 0.00 36.03 2.27
298 308 7.894847 AGTCGCACTTTTACATTTTTCTTTTG 58.105 30.769 0.00 0.00 0.00 2.44
300 310 5.611200 CGCACTTTTACATTTTTCTTTTGCG 59.389 36.000 0.00 0.00 41.49 4.85
303 313 7.318674 GCACTTTTACATTTTTCTTTTGCGATG 59.681 33.333 0.00 0.00 0.00 3.84
304 314 8.538856 CACTTTTACATTTTTCTTTTGCGATGA 58.461 29.630 0.00 0.00 0.00 2.92
305 315 8.539674 ACTTTTACATTTTTCTTTTGCGATGAC 58.460 29.630 0.00 0.00 0.00 3.06
306 316 7.993821 TTTACATTTTTCTTTTGCGATGACA 57.006 28.000 0.00 0.00 0.00 3.58
307 317 5.888412 ACATTTTTCTTTTGCGATGACAC 57.112 34.783 0.00 0.00 0.00 3.67
308 318 5.591099 ACATTTTTCTTTTGCGATGACACT 58.409 33.333 0.00 0.00 0.00 3.55
309 319 6.042143 ACATTTTTCTTTTGCGATGACACTT 58.958 32.000 0.00 0.00 0.00 3.16
310 320 6.534793 ACATTTTTCTTTTGCGATGACACTTT 59.465 30.769 0.00 0.00 0.00 2.66
311 321 6.959671 TTTTTCTTTTGCGATGACACTTTT 57.040 29.167 0.00 0.00 0.00 2.27
312 322 8.538856 CATTTTTCTTTTGCGATGACACTTTTA 58.461 29.630 0.00 0.00 0.00 1.52
313 323 7.444558 TTTTCTTTTGCGATGACACTTTTAC 57.555 32.000 0.00 0.00 0.00 2.01
314 324 5.743026 TCTTTTGCGATGACACTTTTACA 57.257 34.783 0.00 0.00 0.00 2.41
315 325 6.312399 TCTTTTGCGATGACACTTTTACAT 57.688 33.333 0.00 0.00 0.00 2.29
316 326 6.734137 TCTTTTGCGATGACACTTTTACATT 58.266 32.000 0.00 0.00 0.00 2.71
317 327 6.855914 TCTTTTGCGATGACACTTTTACATTC 59.144 34.615 0.00 0.00 0.00 2.67
318 328 5.940192 TTGCGATGACACTTTTACATTCT 57.060 34.783 0.00 0.00 0.00 2.40
319 329 5.940192 TGCGATGACACTTTTACATTCTT 57.060 34.783 0.00 0.00 0.00 2.52
320 330 6.312399 TGCGATGACACTTTTACATTCTTT 57.688 33.333 0.00 0.00 0.00 2.52
321 331 6.734137 TGCGATGACACTTTTACATTCTTTT 58.266 32.000 0.00 0.00 0.00 2.27
322 332 6.855914 TGCGATGACACTTTTACATTCTTTTC 59.144 34.615 0.00 0.00 0.00 2.29
323 333 7.078228 GCGATGACACTTTTACATTCTTTTCT 58.922 34.615 0.00 0.00 0.00 2.52
324 334 8.227791 GCGATGACACTTTTACATTCTTTTCTA 58.772 33.333 0.00 0.00 0.00 2.10
325 335 9.530129 CGATGACACTTTTACATTCTTTTCTAC 57.470 33.333 0.00 0.00 0.00 2.59
376 388 1.066787 GTCAAGTGAGTAGGGTGCTCC 60.067 57.143 0.00 0.00 32.31 4.70
448 461 2.011222 GTCGAAAACCACACTTCCACA 58.989 47.619 0.00 0.00 0.00 4.17
449 462 2.011222 TCGAAAACCACACTTCCACAC 58.989 47.619 0.00 0.00 0.00 3.82
450 463 1.064952 CGAAAACCACACTTCCACACC 59.935 52.381 0.00 0.00 0.00 4.16
451 464 1.407618 GAAAACCACACTTCCACACCC 59.592 52.381 0.00 0.00 0.00 4.61
491 508 2.287547 CCACACTTCCACAACGAATTGG 60.288 50.000 0.00 0.00 40.42 3.16
500 517 0.240945 CAACGAATTGGCACACCTCC 59.759 55.000 0.00 0.00 39.29 4.30
905 943 2.664851 CACGCCGAGCCAAGAACA 60.665 61.111 0.00 0.00 0.00 3.18
906 944 2.357517 ACGCCGAGCCAAGAACAG 60.358 61.111 0.00 0.00 0.00 3.16
934 980 4.267536 CATTCTGCATCTTTCTTCCTCCA 58.732 43.478 0.00 0.00 0.00 3.86
971 1017 1.533469 CCTCCGTCAGAACCTCCGTT 61.533 60.000 0.00 0.00 33.88 4.44
1137 1201 2.450243 GACACCCCCTCCTCCTCA 59.550 66.667 0.00 0.00 0.00 3.86
1144 1208 1.003442 CCCTCCTCCTCATCCACCA 59.997 63.158 0.00 0.00 0.00 4.17
1145 1209 0.621571 CCCTCCTCCTCATCCACCAA 60.622 60.000 0.00 0.00 0.00 3.67
1146 1210 0.543749 CCTCCTCCTCATCCACCAAC 59.456 60.000 0.00 0.00 0.00 3.77
1201 1289 7.501559 ACTTCCTCATCACAATTCATATGAAGG 59.498 37.037 21.97 18.09 37.48 3.46
1244 1340 4.452455 ACATACTAACAGCAAGCAGAACAC 59.548 41.667 0.00 0.00 0.00 3.32
1248 1344 1.884235 ACAGCAAGCAGAACACCTAC 58.116 50.000 0.00 0.00 0.00 3.18
1252 1348 0.673644 CAAGCAGAACACCTACCGGG 60.674 60.000 6.32 0.00 41.89 5.73
1256 1352 0.903454 CAGAACACCTACCGGGGTCT 60.903 60.000 6.32 0.00 46.56 3.85
1308 1422 1.671742 GAGGACAAGGCGAGAACCA 59.328 57.895 0.00 0.00 0.00 3.67
1380 1497 1.135083 GGATCAAGACCTTCTTCGCGA 60.135 52.381 3.71 3.71 33.78 5.87
1381 1498 2.482142 GGATCAAGACCTTCTTCGCGAT 60.482 50.000 10.88 0.00 33.78 4.58
1597 1744 1.955778 CACCTGCATCAACTGACCAAA 59.044 47.619 0.00 0.00 0.00 3.28
1602 1749 3.141398 TGCATCAACTGACCAAACTCTC 58.859 45.455 0.00 0.00 0.00 3.20
1618 1767 2.760799 TCCTGCCATTGCCATGCC 60.761 61.111 0.00 0.00 36.33 4.40
1622 1771 3.085296 GCCATTGCCATGCCCCTT 61.085 61.111 0.00 0.00 0.00 3.95
1799 1949 7.672983 AGCATATGCATAGGTTTGTGTATAC 57.327 36.000 28.62 0.00 45.16 1.47
1828 1988 5.071250 TGGAGTGGAGTTGTGTACATACTTT 59.929 40.000 12.99 3.09 0.00 2.66
1829 1989 6.268158 TGGAGTGGAGTTGTGTACATACTTTA 59.732 38.462 12.99 5.19 0.00 1.85
1977 2144 2.046604 CTGCTGCTGCTGCTGGTA 60.047 61.111 27.67 10.41 40.48 3.25
1978 2145 2.359107 TGCTGCTGCTGCTGGTAC 60.359 61.111 27.67 7.80 40.48 3.34
1991 2158 6.280643 TGCTGCTGGTACTACAATAATAGTG 58.719 40.000 0.00 0.00 36.09 2.74
2027 2195 6.353323 TCAAGTCTTCATGTTTGTTGGACTA 58.647 36.000 0.00 0.00 0.00 2.59
2028 2196 6.998074 TCAAGTCTTCATGTTTGTTGGACTAT 59.002 34.615 0.00 0.00 0.00 2.12
2029 2197 8.154203 TCAAGTCTTCATGTTTGTTGGACTATA 58.846 33.333 0.00 0.00 0.00 1.31
2106 2286 3.754323 TGGTTAAGGCCAATTAACTCGTG 59.246 43.478 20.85 0.00 42.63 4.35
2112 2292 2.412325 GGCCAATTAACTCGTGTGTTCG 60.412 50.000 0.00 0.00 0.00 3.95
2121 2301 2.551032 ACTCGTGTGTTCGTCATAGACA 59.449 45.455 0.00 0.00 32.09 3.41
2123 2303 3.498082 TCGTGTGTTCGTCATAGACATG 58.502 45.455 0.00 0.00 32.09 3.21
2126 2306 1.933853 GTGTTCGTCATAGACATGGCC 59.066 52.381 0.00 0.00 32.87 5.36
2129 2317 1.775385 TCGTCATAGACATGGCCAGA 58.225 50.000 13.05 0.00 32.87 3.86
2253 2448 5.238650 TGCTTTAAGCTTAGACAAGGAACAC 59.761 40.000 18.20 2.82 42.97 3.32
2291 2487 1.636988 ACGTCGACCCGATCAAAATC 58.363 50.000 10.58 0.00 38.42 2.17
2342 2538 5.048846 ACTAAAGTGTTCACATGGAAGGT 57.951 39.130 5.74 0.00 35.82 3.50
2345 2541 3.059352 AGTGTTCACATGGAAGGTAGC 57.941 47.619 5.74 0.00 35.82 3.58
2347 2543 1.985159 TGTTCACATGGAAGGTAGCCT 59.015 47.619 0.00 0.00 35.82 4.58
2350 2546 4.192317 GTTCACATGGAAGGTAGCCTTAG 58.808 47.826 0.00 0.00 44.82 2.18
2357 2553 7.556275 CACATGGAAGGTAGCCTTAGAAAAATA 59.444 37.037 0.00 0.00 44.82 1.40
2398 2594 7.503521 TTGATAGTGCAATTCACACACTAAA 57.496 32.000 10.04 0.00 46.67 1.85
2479 2681 5.705609 ATCACCAACCACTGATTAACAAC 57.294 39.130 0.00 0.00 0.00 3.32
2529 2731 4.085357 AGAAACAGTGATGTGCCACTAA 57.915 40.909 0.00 0.00 44.87 2.24
2552 2754 2.316792 CTACTGTTGGAACGTGACTCG 58.683 52.381 0.00 0.00 46.00 4.18
2554 2756 1.557443 CTGTTGGAACGTGACTCGCC 61.557 60.000 0.00 0.00 44.19 5.54
2579 2781 7.308830 CCACTTAGCTTCTTTATTATCATGGGC 60.309 40.741 0.00 0.00 0.00 5.36
2589 2791 8.224025 TCTTTATTATCATGGGCACTTAATCCA 58.776 33.333 0.00 0.00 34.79 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 45 8.273780 ACTTTTTCATTGAGTCTAGGCTAATG 57.726 34.615 15.01 15.01 0.00 1.90
70 72 8.324306 GGGATGTCATTTCATTCATAGGATAGA 58.676 37.037 0.00 0.00 0.00 1.98
106 108 5.130477 TCATGGGAATAGGTGTCTTAGTTCC 59.870 44.000 0.00 0.00 35.52 3.62
141 143 7.833682 TCATATGAAGGCTTCTTTGGTTCATAA 59.166 33.333 26.26 3.52 41.22 1.90
221 223 0.882042 CACCCGAGGATGCACATAGC 60.882 60.000 0.00 0.00 45.96 2.97
222 224 0.882042 GCACCCGAGGATGCACATAG 60.882 60.000 3.05 0.00 41.65 2.23
223 225 1.146041 GCACCCGAGGATGCACATA 59.854 57.895 3.05 0.00 41.65 2.29
224 226 2.124570 GCACCCGAGGATGCACAT 60.125 61.111 3.05 0.00 41.65 3.21
225 227 3.321648 AGCACCCGAGGATGCACA 61.322 61.111 11.59 0.00 44.59 4.57
242 244 3.379445 GAACTCTCCCGGTCGCCA 61.379 66.667 0.00 0.00 0.00 5.69
244 246 1.737008 GTTGAACTCTCCCGGTCGC 60.737 63.158 0.00 0.00 0.00 5.19
245 247 1.080025 GGTTGAACTCTCCCGGTCG 60.080 63.158 0.00 0.00 0.00 4.79
288 298 6.959671 AAAAGTGTCATCGCAAAAGAAAAA 57.040 29.167 0.00 0.00 0.00 1.94
293 303 6.857964 AGAATGTAAAAGTGTCATCGCAAAAG 59.142 34.615 0.00 0.00 0.00 2.27
294 304 6.734137 AGAATGTAAAAGTGTCATCGCAAAA 58.266 32.000 0.00 0.00 0.00 2.44
295 305 6.312399 AGAATGTAAAAGTGTCATCGCAAA 57.688 33.333 0.00 0.00 0.00 3.68
296 306 5.940192 AGAATGTAAAAGTGTCATCGCAA 57.060 34.783 0.00 0.00 0.00 4.85
297 307 5.940192 AAGAATGTAAAAGTGTCATCGCA 57.060 34.783 0.00 0.00 0.00 5.10
298 308 7.078228 AGAAAAGAATGTAAAAGTGTCATCGC 58.922 34.615 0.00 0.00 0.00 4.58
362 372 2.351244 CGCAGGAGCACCCTACTCA 61.351 63.158 0.00 0.00 45.60 3.41
466 479 2.438411 TCGTTGTGGAAGTGTGGTTTT 58.562 42.857 0.00 0.00 0.00 2.43
468 481 2.116827 TTCGTTGTGGAAGTGTGGTT 57.883 45.000 0.00 0.00 0.00 3.67
471 484 2.858260 GCCAATTCGTTGTGGAAGTGTG 60.858 50.000 5.40 0.00 39.61 3.82
472 485 1.336755 GCCAATTCGTTGTGGAAGTGT 59.663 47.619 5.40 0.00 39.61 3.55
473 486 1.336440 TGCCAATTCGTTGTGGAAGTG 59.664 47.619 5.40 0.00 40.60 3.16
474 487 1.336755 GTGCCAATTCGTTGTGGAAGT 59.663 47.619 5.40 0.00 37.03 3.01
475 488 1.336440 TGTGCCAATTCGTTGTGGAAG 59.664 47.619 5.40 0.00 37.03 3.46
846 863 1.895798 GGGAAAGGGAGCAAAGGAAAG 59.104 52.381 0.00 0.00 0.00 2.62
847 864 1.503347 AGGGAAAGGGAGCAAAGGAAA 59.497 47.619 0.00 0.00 0.00 3.13
849 866 1.158007 AAGGGAAAGGGAGCAAAGGA 58.842 50.000 0.00 0.00 0.00 3.36
854 887 0.112412 GGAACAAGGGAAAGGGAGCA 59.888 55.000 0.00 0.00 0.00 4.26
855 888 0.612174 GGGAACAAGGGAAAGGGAGC 60.612 60.000 0.00 0.00 0.00 4.70
857 890 1.785353 CGGGGAACAAGGGAAAGGGA 61.785 60.000 0.00 0.00 0.00 4.20
858 891 1.304134 CGGGGAACAAGGGAAAGGG 60.304 63.158 0.00 0.00 0.00 3.95
859 892 0.893727 CACGGGGAACAAGGGAAAGG 60.894 60.000 0.00 0.00 0.00 3.11
905 943 4.660168 AGAAAGATGCAGAATGGTGTTCT 58.340 39.130 0.00 0.00 35.86 3.01
906 944 5.382618 AAGAAAGATGCAGAATGGTGTTC 57.617 39.130 0.00 0.00 35.86 3.18
934 980 1.285373 AGGGTACAGAGGATGAGACGT 59.715 52.381 0.00 0.00 0.00 4.34
1114 1178 3.721706 GGAGGGGGTGTCAGCCTG 61.722 72.222 20.17 0.00 35.71 4.85
1119 1183 1.826384 ATGAGGAGGAGGGGGTGTCA 61.826 60.000 0.00 0.00 0.00 3.58
1137 1201 2.282180 GCCGTGGTGTTGGTGGAT 60.282 61.111 0.00 0.00 0.00 3.41
1163 1239 5.597182 GTGATGAGGAAGTACATACCCTGTA 59.403 44.000 0.00 0.00 39.39 2.74
1201 1289 1.026718 GCAGTACCTGTGGCATGGAC 61.027 60.000 14.93 3.08 33.43 4.02
1244 1340 2.628657 CTCTGAAATAGACCCCGGTAGG 59.371 54.545 0.00 0.00 37.24 3.18
1248 1344 2.625790 CTCTCTCTGAAATAGACCCCGG 59.374 54.545 0.00 0.00 0.00 5.73
1252 1348 2.544903 GCGCCTCTCTCTGAAATAGACC 60.545 54.545 0.00 0.00 0.00 3.85
1254 1350 1.683917 GGCGCCTCTCTCTGAAATAGA 59.316 52.381 22.15 0.00 0.00 1.98
1256 1352 0.385751 CGGCGCCTCTCTCTGAAATA 59.614 55.000 26.68 0.00 0.00 1.40
1358 1475 1.208293 GCGAAGAAGGTCTTGATCCCT 59.792 52.381 0.00 0.00 36.73 4.20
1380 1497 2.478890 CCTCCTCGCCGTCGTACAT 61.479 63.158 0.00 0.00 36.96 2.29
1381 1498 3.129502 CCTCCTCGCCGTCGTACA 61.130 66.667 0.00 0.00 36.96 2.90
1597 1744 0.395311 CATGGCAATGGCAGGAGAGT 60.395 55.000 16.47 0.00 42.32 3.24
1618 1767 0.321671 TGGTTTCTCGAGCTCAAGGG 59.678 55.000 15.40 0.00 0.00 3.95
1622 1771 0.976641 ATGGTGGTTTCTCGAGCTCA 59.023 50.000 15.40 0.00 0.00 4.26
1672 1821 6.672266 AGAACTAAAAGATGAGACCAGTCA 57.328 37.500 0.00 0.00 0.00 3.41
1675 1824 6.370166 GTGGAAGAACTAAAAGATGAGACCAG 59.630 42.308 0.00 0.00 0.00 4.00
1678 1827 5.927115 ACGTGGAAGAACTAAAAGATGAGAC 59.073 40.000 0.00 0.00 0.00 3.36
1799 1949 3.685139 ACACAACTCCACTCCACATAG 57.315 47.619 0.00 0.00 0.00 2.23
1828 1988 3.133003 GCTGAAGCTCCCACAATCTACTA 59.867 47.826 0.00 0.00 38.21 1.82
1829 1989 2.093235 GCTGAAGCTCCCACAATCTACT 60.093 50.000 0.00 0.00 38.21 2.57
1976 2143 9.845740 ATGATTTGCACCACTATTATTGTAGTA 57.154 29.630 0.00 0.00 33.29 1.82
1977 2144 8.752005 ATGATTTGCACCACTATTATTGTAGT 57.248 30.769 0.00 0.00 35.34 2.73
1978 2145 9.669353 GAATGATTTGCACCACTATTATTGTAG 57.331 33.333 0.00 0.00 0.00 2.74
1991 2158 5.125100 TGAAGACTTGAATGATTTGCACC 57.875 39.130 0.00 0.00 0.00 5.01
2062 2230 6.776116 ACCATTATGCAGTACTAGCAGTAGTA 59.224 38.462 19.77 9.04 46.36 1.82
2063 2231 5.598830 ACCATTATGCAGTACTAGCAGTAGT 59.401 40.000 19.77 12.27 46.36 2.73
2064 2232 6.090483 ACCATTATGCAGTACTAGCAGTAG 57.910 41.667 19.77 12.10 46.36 2.57
2065 2233 6.479972 AACCATTATGCAGTACTAGCAGTA 57.520 37.500 19.77 12.93 46.36 2.74
2066 2234 5.359194 AACCATTATGCAGTACTAGCAGT 57.641 39.130 19.77 11.98 46.36 4.40
2067 2235 6.425114 CCTTAACCATTATGCAGTACTAGCAG 59.575 42.308 19.77 11.51 46.36 4.24
2106 2286 1.933853 GGCCATGTCTATGACGAACAC 59.066 52.381 0.00 0.00 36.36 3.32
2112 2292 2.149578 GCATCTGGCCATGTCTATGAC 58.850 52.381 5.51 0.00 36.36 3.06
2126 2306 2.501261 CATGTACCATCTGGGCATCTG 58.499 52.381 0.54 0.00 42.05 2.90
2129 2317 0.552363 TGCATGTACCATCTGGGCAT 59.448 50.000 0.54 2.38 42.05 4.40
2177 2372 9.815936 GGACTGCAAAAGATTATTTTTCATTTG 57.184 29.630 0.00 0.00 35.79 2.32
2235 2430 6.321181 TGAATTTGTGTTCCTTGTCTAAGCTT 59.679 34.615 3.48 3.48 32.40 3.74
2253 2448 5.169561 CGACGTTTGACTTTGTCTGAATTTG 59.830 40.000 0.00 0.00 33.15 2.32
2291 2487 6.992063 ACTGCTTACTGTTGAATTATCTGG 57.008 37.500 0.00 0.00 0.00 3.86
2310 2506 9.329913 CATGTGAACACTTTAGTTTTATACTGC 57.670 33.333 6.51 0.00 37.73 4.40
2320 2516 5.048846 ACCTTCCATGTGAACACTTTAGT 57.951 39.130 6.51 0.00 0.00 2.24
2321 2517 5.122396 GCTACCTTCCATGTGAACACTTTAG 59.878 44.000 6.51 0.36 0.00 1.85
2324 2520 3.412386 GCTACCTTCCATGTGAACACTT 58.588 45.455 6.51 0.00 0.00 3.16
2383 2579 9.759259 CACATATAGTGTTTAGTGTGTGAATTG 57.241 33.333 0.00 0.00 43.40 2.32
2442 2644 5.163652 GGTTGGTGATATTGACTGGTTAAGC 60.164 44.000 0.00 0.00 0.00 3.09
2479 2681 9.135843 TCTTATTACAAAGATACAGTGTCAACG 57.864 33.333 0.00 0.00 30.54 4.10
2506 2708 4.085357 AGTGGCACATCACTGTTTCTTA 57.915 40.909 21.41 0.00 45.27 2.10
2507 2709 2.936202 AGTGGCACATCACTGTTTCTT 58.064 42.857 21.41 0.00 45.27 2.52
2508 2710 2.645838 AGTGGCACATCACTGTTTCT 57.354 45.000 21.41 0.00 45.27 2.52
2509 2711 4.726416 CATTAGTGGCACATCACTGTTTC 58.274 43.478 21.41 0.00 46.29 2.78
2510 2712 3.057315 GCATTAGTGGCACATCACTGTTT 60.057 43.478 21.41 0.00 46.29 2.83
2529 2731 2.037251 AGTCACGTTCCAACAGTAGCAT 59.963 45.455 0.00 0.00 0.00 3.79
2552 2754 7.308830 CCCATGATAATAAAGAAGCTAAGTGGC 60.309 40.741 0.00 0.00 0.00 5.01
2554 2756 7.229306 TGCCCATGATAATAAAGAAGCTAAGTG 59.771 37.037 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.