Multiple sequence alignment - TraesCS1B01G366300

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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 TraesCS1B01G366300 chr1B 100.000 2548 0 0 1 2548 597457919 597455372 0.000000e+00 4706.0
1 TraesCS1B01G366300 chr1B 76.157 281 59 5 117 391 397659624 397659346 9.500000e-30 141.0
2 TraesCS1B01G366300 chr1D 88.554 1922 152 32 654 2548 439875280 439873400 0.000000e+00 2268.0
3 TraesCS1B01G366300 chr1D 85.156 640 83 5 1 633 439875903 439875269 0.000000e+00 645.0
4 TraesCS1B01G366300 chr1D 76.891 238 50 5 157 392 291850706 291850940 2.060000e-26 130.0
5 TraesCS1B01G366300 chr1A 91.917 866 46 5 853 1711 537967167 537966319 0.000000e+00 1190.0
6 TraesCS1B01G366300 chr1A 84.421 475 59 11 1 469 537967845 537967380 1.070000e-123 453.0
7 TraesCS1B01G366300 chr1A 76.589 299 60 8 102 392 107469204 107469500 3.390000e-34 156.0
8 TraesCS1B01G366300 chr1A 80.105 191 35 3 1807 1995 285456850 285456661 3.420000e-29 139.0
9 TraesCS1B01G366300 chr1A 86.585 82 9 2 745 826 537967251 537967172 3.490000e-14 89.8
10 TraesCS1B01G366300 chr1A 93.220 59 3 1 736 793 537967906 537967848 4.520000e-13 86.1
11 TraesCS1B01G366300 chr2B 78.537 820 147 21 1748 2547 763066499 763067309 1.750000e-141 512.0
12 TraesCS1B01G366300 chr7B 85.434 357 37 5 1295 1643 303138651 303139000 8.670000e-95 357.0
13 TraesCS1B01G366300 chr7B 79.528 381 64 14 1746 2118 205777953 205777579 2.510000e-65 259.0
14 TraesCS1B01G366300 chr7B 75.497 302 66 8 98 392 588294338 588294638 9.500000e-30 141.0
15 TraesCS1B01G366300 chr7B 76.562 256 53 5 168 417 604117662 604117408 1.590000e-27 134.0
16 TraesCS1B01G366300 chr7B 84.746 59 8 1 1789 1846 85789611 85789669 9.850000e-05 58.4
17 TraesCS1B01G366300 chr6D 88.722 266 30 0 1001 1266 464116967 464117232 2.440000e-85 326.0
18 TraesCS1B01G366300 chr6D 89.444 180 15 3 1369 1546 464117452 464117629 9.170000e-55 224.0
19 TraesCS1B01G366300 chr6D 84.286 70 9 2 2480 2548 398182568 398182636 1.640000e-07 67.6
20 TraesCS1B01G366300 chr5A 81.265 427 45 10 1225 1643 154716897 154716498 1.900000e-81 313.0
21 TraesCS1B01G366300 chr5A 75.850 294 63 7 258 549 703469244 703468957 2.640000e-30 143.0
22 TraesCS1B01G366300 chr5A 75.486 257 49 11 1856 2107 675310241 675309994 2.070000e-21 113.0
23 TraesCS1B01G366300 chr5A 97.059 34 0 1 535 568 445249386 445249354 3.540000e-04 56.5
24 TraesCS1B01G366300 chr5A 80.822 73 13 1 1748 1819 603384691 603384763 3.540000e-04 56.5
25 TraesCS1B01G366300 chr6B 89.744 195 20 0 1000 1194 707500080 707500274 1.510000e-62 250.0
26 TraesCS1B01G366300 chr6B 88.889 180 17 3 1369 1546 707442317 707442495 4.270000e-53 219.0
27 TraesCS1B01G366300 chr6B 88.333 180 17 3 1369 1546 707506067 707506244 1.990000e-51 213.0
28 TraesCS1B01G366300 chr4A 75.270 647 97 22 1938 2548 576607119 576607738 1.510000e-62 250.0
29 TraesCS1B01G366300 chr4A 100.000 28 0 0 1965 1992 120954353 120954380 5.000000e-03 52.8
30 TraesCS1B01G366300 chr6A 91.160 181 14 2 1367 1546 610642752 610642931 7.040000e-61 244.0
31 TraesCS1B01G366300 chr6A 94.595 37 0 2 1956 1992 65231438 65231472 3.540000e-04 56.5
32 TraesCS1B01G366300 chr7A 79.167 336 58 9 1748 2079 521922553 521922880 3.300000e-54 222.0
33 TraesCS1B01G366300 chr7A 91.111 45 4 0 1975 2019 48970367 48970323 7.610000e-06 62.1
34 TraesCS1B01G366300 chr3D 87.861 173 19 2 1371 1542 604448115 604448286 4.300000e-48 202.0
35 TraesCS1B01G366300 chr2A 78.676 272 52 2 998 1263 758056065 758055794 2.610000e-40 176.0
36 TraesCS1B01G366300 chr3A 76.817 289 59 5 1729 2010 82399900 82400187 3.390000e-34 156.0
37 TraesCS1B01G366300 chr5D 73.349 424 91 18 154 573 445729087 445729492 1.230000e-28 137.0
38 TraesCS1B01G366300 chr2D 76.446 242 47 9 277 516 546776894 546777127 3.440000e-24 122.0
39 TraesCS1B01G366300 chr2D 78.814 118 20 5 1728 1841 80824951 80824835 9.780000e-10 75.0
40 TraesCS1B01G366300 chr4D 88.571 70 8 0 2479 2548 131275303 131275234 4.520000e-13 86.1
41 TraesCS1B01G366300 chr5B 85.366 82 11 1 2468 2548 712705119 712705038 1.620000e-12 84.2
42 TraesCS1B01G366300 chr5B 89.583 48 5 0 526 573 405699849 405699802 7.610000e-06 62.1
43 TraesCS1B01G366300 chr5B 86.275 51 6 1 1789 1838 642884415 642884465 1.000000e-03 54.7
44 TraesCS1B01G366300 chr4B 79.279 111 18 2 2443 2548 166829938 166830048 3.520000e-09 73.1


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 TraesCS1B01G366300 chr1B 597455372 597457919 2547 True 4706.000 4706 100.00000 1 2548 1 chr1B.!!$R2 2547
1 TraesCS1B01G366300 chr1D 439873400 439875903 2503 True 1456.500 2268 86.85500 1 2548 2 chr1D.!!$R1 2547
2 TraesCS1B01G366300 chr1A 537966319 537967906 1587 True 454.725 1190 89.03575 1 1711 4 chr1A.!!$R2 1710
3 TraesCS1B01G366300 chr2B 763066499 763067309 810 False 512.000 512 78.53700 1748 2547 1 chr2B.!!$F1 799
4 TraesCS1B01G366300 chr6D 464116967 464117629 662 False 275.000 326 89.08300 1001 1546 2 chr6D.!!$F2 545
5 TraesCS1B01G366300 chr4A 576607119 576607738 619 False 250.000 250 75.27000 1938 2548 1 chr4A.!!$F2 610

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
586 659 0.247736 ACGAGGAATGCCAGTCAGTC 59.752 55.0 0.0 0.0 38.94 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2452 2804 0.034476 CAGCTCACAGAGAAGTGGCA 59.966 55.0 0.0 0.0 39.93 4.92 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
80 142 1.007502 GTGCCGCATCAACAAAGCA 60.008 52.632 0.00 0.00 0.00 3.91
113 175 1.071019 CATCGTGTTCGGACGTCAGG 61.071 60.000 18.91 8.75 40.34 3.86
115 177 2.028484 GTGTTCGGACGTCAGGCA 59.972 61.111 18.91 13.03 0.00 4.75
132 194 3.936203 AAACCGCACCGCCTCTGA 61.936 61.111 0.00 0.00 0.00 3.27
136 198 2.125552 CGCACCGCCTCTGATGAA 60.126 61.111 0.00 0.00 0.00 2.57
138 200 1.219124 GCACCGCCTCTGATGAAGA 59.781 57.895 0.00 0.00 0.00 2.87
139 201 1.086634 GCACCGCCTCTGATGAAGAC 61.087 60.000 0.00 0.00 0.00 3.01
144 211 1.402852 CGCCTCTGATGAAGACGACAA 60.403 52.381 0.00 0.00 0.00 3.18
146 213 2.353208 GCCTCTGATGAAGACGACAAGT 60.353 50.000 0.00 0.00 0.00 3.16
156 223 2.805353 CGACAAGTCTCACGCCGG 60.805 66.667 0.00 0.00 0.00 6.13
183 250 1.135199 GCATCATTTGGGCAGACACAG 60.135 52.381 0.00 0.00 0.00 3.66
191 258 1.133513 TGGGCAGACACAGTGGATTTT 60.134 47.619 5.31 0.00 0.00 1.82
194 261 2.622942 GGCAGACACAGTGGATTTTTGA 59.377 45.455 5.31 0.00 0.00 2.69
201 268 3.563808 CACAGTGGATTTTTGACGGAAGA 59.436 43.478 0.00 0.00 0.00 2.87
210 277 6.316390 GGATTTTTGACGGAAGATGTATGACT 59.684 38.462 0.00 0.00 0.00 3.41
215 282 4.202020 TGACGGAAGATGTATGACTGCTAC 60.202 45.833 0.00 0.00 0.00 3.58
221 288 1.741528 TGTATGACTGCTACCGTCGA 58.258 50.000 0.00 0.00 34.17 4.20
232 299 2.776370 TACCGTCGAGTGGCCTCCTT 62.776 60.000 3.32 0.00 33.93 3.36
238 305 3.978571 GAGTGGCCTCCTTTCGGGC 62.979 68.421 3.32 0.00 46.89 6.13
264 331 4.404654 GCGCAAGTTGGAAGGCCG 62.405 66.667 0.30 0.00 41.68 6.13
266 333 2.551912 CGCAAGTTGGAAGGCCGTT 61.552 57.895 4.75 0.00 36.79 4.44
267 334 1.739667 GCAAGTTGGAAGGCCGTTT 59.260 52.632 4.75 0.00 36.79 3.60
268 335 0.318699 GCAAGTTGGAAGGCCGTTTC 60.319 55.000 4.75 0.00 36.79 2.78
283 355 0.537653 GTTTCCTCCTTAGAGCCGCT 59.462 55.000 0.00 0.00 38.96 5.52
286 358 0.324368 TCCTCCTTAGAGCCGCTTGA 60.324 55.000 0.00 0.00 38.96 3.02
304 377 1.289800 GAAACGAGCTCCGGGTCAAC 61.290 60.000 8.47 0.00 43.93 3.18
305 378 2.035237 AAACGAGCTCCGGGTCAACA 62.035 55.000 8.47 0.00 43.93 3.33
323 396 5.026121 TCAACAGATCTGAAGGTGTAGGAT 58.974 41.667 29.27 0.00 0.00 3.24
326 399 4.098654 ACAGATCTGAAGGTGTAGGATTCG 59.901 45.833 29.27 0.00 0.00 3.34
365 438 1.609794 GGAGAAGGTGGGAGGTCGT 60.610 63.158 0.00 0.00 0.00 4.34
384 457 2.971598 CGGATGGGAGCTTGTGGGT 61.972 63.158 0.00 0.00 0.00 4.51
392 465 4.366684 GCTTGTGGGTGGAGGGGG 62.367 72.222 0.00 0.00 0.00 5.40
411 484 0.613292 GCTGGACTGGAGGAGAGTGA 60.613 60.000 0.00 0.00 0.00 3.41
418 491 1.824230 CTGGAGGAGAGTGAAGTGGAG 59.176 57.143 0.00 0.00 0.00 3.86
421 494 2.520069 GAGGAGAGTGAAGTGGAGTGA 58.480 52.381 0.00 0.00 0.00 3.41
422 495 2.894126 GAGGAGAGTGAAGTGGAGTGAA 59.106 50.000 0.00 0.00 0.00 3.18
423 496 3.309296 AGGAGAGTGAAGTGGAGTGAAA 58.691 45.455 0.00 0.00 0.00 2.69
424 497 3.906846 AGGAGAGTGAAGTGGAGTGAAAT 59.093 43.478 0.00 0.00 0.00 2.17
425 498 5.087323 AGGAGAGTGAAGTGGAGTGAAATA 58.913 41.667 0.00 0.00 0.00 1.40
437 510 3.455327 GAGTGAAATACGGCTAGGGTTC 58.545 50.000 0.00 0.00 0.00 3.62
469 542 2.861147 GGATAGGGTCCCACTTATGC 57.139 55.000 11.55 0.84 41.50 3.14
479 552 1.270839 CCCACTTATGCGGGGTATCAG 60.271 57.143 0.00 0.00 38.95 2.90
482 555 3.513912 CCACTTATGCGGGGTATCAGATA 59.486 47.826 0.00 0.00 0.00 1.98
490 563 1.352083 GGGTATCAGATAGGCCAGCA 58.648 55.000 5.01 0.00 0.00 4.41
506 579 1.380246 GCATGGGCTGGATCCAACA 60.380 57.895 17.00 15.13 37.87 3.33
507 580 0.757935 GCATGGGCTGGATCCAACAT 60.758 55.000 17.00 16.67 37.87 2.71
510 583 2.129785 GGGCTGGATCCAACATGGC 61.130 63.158 17.00 15.74 37.47 4.40
513 586 1.825191 CTGGATCCAACATGGCGGG 60.825 63.158 17.00 0.00 37.47 6.13
535 608 3.387947 CCGGGGTACGTCCAAGCT 61.388 66.667 0.00 0.00 42.24 3.74
539 612 1.078637 GGGTACGTCCAAGCTTCCC 60.079 63.158 0.00 0.00 38.11 3.97
540 613 1.078637 GGTACGTCCAAGCTTCCCC 60.079 63.158 0.00 0.00 35.97 4.81
547 620 0.764890 TCCAAGCTTCCCCATATCCG 59.235 55.000 0.00 0.00 0.00 4.18
548 621 0.474184 CCAAGCTTCCCCATATCCGT 59.526 55.000 0.00 0.00 0.00 4.69
550 623 1.417890 CAAGCTTCCCCATATCCGTCT 59.582 52.381 0.00 0.00 0.00 4.18
553 626 1.001406 GCTTCCCCATATCCGTCTCAG 59.999 57.143 0.00 0.00 0.00 3.35
568 641 4.142491 CCGTCTCAGATATGAGCTGGATAC 60.142 50.000 17.79 7.85 35.97 2.24
572 645 4.013050 TCAGATATGAGCTGGATACGAGG 58.987 47.826 0.00 0.00 42.51 4.63
581 654 1.414181 CTGGATACGAGGAATGCCAGT 59.586 52.381 0.00 0.00 38.41 4.00
586 659 0.247736 ACGAGGAATGCCAGTCAGTC 59.752 55.000 0.00 0.00 38.94 3.51
588 661 1.738365 CGAGGAATGCCAGTCAGTCTG 60.738 57.143 0.00 0.00 39.56 3.51
611 684 4.211920 GTCATTCGGGATTAAAATGGGGA 58.788 43.478 0.00 0.00 32.49 4.81
613 686 4.079443 TCATTCGGGATTAAAATGGGGAGT 60.079 41.667 0.00 0.00 32.49 3.85
615 688 4.325084 TCGGGATTAAAATGGGGAGTTT 57.675 40.909 0.00 0.00 0.00 2.66
625 698 1.231928 GGGGAGTTTGGTTGGGTGT 59.768 57.895 0.00 0.00 0.00 4.16
631 704 3.133901 GGAGTTTGGTTGGGTGTCAATTT 59.866 43.478 0.00 0.00 37.73 1.82
632 705 4.383661 GGAGTTTGGTTGGGTGTCAATTTT 60.384 41.667 0.00 0.00 37.73 1.82
633 706 5.172687 AGTTTGGTTGGGTGTCAATTTTT 57.827 34.783 0.00 0.00 37.73 1.94
654 727 6.978343 TTTTATCCGAATACACTGAACAGG 57.022 37.500 6.76 0.00 0.00 4.00
655 728 5.670792 TTATCCGAATACACTGAACAGGT 57.329 39.130 6.76 4.44 0.00 4.00
656 729 6.778834 TTATCCGAATACACTGAACAGGTA 57.221 37.500 6.76 6.28 0.00 3.08
657 730 4.713824 TCCGAATACACTGAACAGGTAG 57.286 45.455 6.76 0.00 0.00 3.18
658 731 3.119245 TCCGAATACACTGAACAGGTAGC 60.119 47.826 6.76 0.00 0.00 3.58
659 732 3.368013 CCGAATACACTGAACAGGTAGCA 60.368 47.826 6.76 0.00 0.00 3.49
660 733 4.242475 CGAATACACTGAACAGGTAGCAA 58.758 43.478 6.76 0.00 0.00 3.91
661 734 4.870426 CGAATACACTGAACAGGTAGCAAT 59.130 41.667 6.76 0.00 0.00 3.56
662 735 5.351465 CGAATACACTGAACAGGTAGCAATT 59.649 40.000 6.76 0.00 0.00 2.32
663 736 6.128282 CGAATACACTGAACAGGTAGCAATTT 60.128 38.462 6.76 0.00 0.00 1.82
671 744 2.482721 ACAGGTAGCAATTTTTCGTCCG 59.517 45.455 0.00 0.00 0.00 4.79
703 776 2.342279 CCGTCCAGGCGTTTGAGA 59.658 61.111 3.11 0.00 0.00 3.27
724 797 1.437160 GGTATCGGCGGTTCGGTTA 59.563 57.895 7.21 0.00 0.00 2.85
778 907 1.371512 CGCATGCGCTTGTTTCCAA 60.372 52.632 29.09 0.00 35.30 3.53
781 910 1.192980 GCATGCGCTTGTTTCCAAAAG 59.807 47.619 22.50 0.00 34.30 2.27
821 950 2.814280 TGGACTCGTGGAGAAAGAAC 57.186 50.000 0.00 0.00 33.32 3.01
903 1049 0.390735 CCTGCAGCAAAAGGCCATTC 60.391 55.000 8.66 0.00 46.50 2.67
926 1072 4.543692 CCATCAAAAGCAGTTCAGTTCAG 58.456 43.478 0.00 0.00 0.00 3.02
990 1144 2.677337 CGTTGCATACACCACATCATCA 59.323 45.455 0.00 0.00 0.00 3.07
1266 1423 0.036875 GCAAGTGCCTCCTGGTAAGT 59.963 55.000 0.00 0.00 35.27 2.24
1267 1424 1.545651 GCAAGTGCCTCCTGGTAAGTT 60.546 52.381 0.00 0.00 35.27 2.66
1269 1426 3.335579 CAAGTGCCTCCTGGTAAGTTAC 58.664 50.000 4.32 4.32 35.27 2.50
1300 1458 1.779569 TTTCTCAAGCGTCCGTCTTC 58.220 50.000 0.00 0.00 0.00 2.87
1334 1623 0.606401 GTGTGGGCTTGCTGCTAGAA 60.606 55.000 15.16 0.00 42.39 2.10
1362 1654 1.377725 CCCTGTGATGTGACCCTGC 60.378 63.158 0.00 0.00 0.00 4.85
1584 1876 1.073177 GCTCAAGCGCTACGGTAAAA 58.927 50.000 12.05 0.00 36.27 1.52
1608 1900 8.579682 AAAAGAAGCTGCAAATAAAAGTAGTG 57.420 30.769 1.02 0.00 0.00 2.74
1650 1945 9.157104 TGATGCACTTCGTAATAAATAAAGTGA 57.843 29.630 15.55 3.84 46.09 3.41
1724 2022 1.474330 ATGAGACCGGCCAAATTTCC 58.526 50.000 0.00 0.00 0.00 3.13
1733 2044 0.735978 GCCAAATTTCCTTTCCGCGG 60.736 55.000 22.12 22.12 0.00 6.46
1769 2080 2.270850 GCCATCCAACGCTACCCA 59.729 61.111 0.00 0.00 0.00 4.51
1777 2088 5.105106 CCATCCAACGCTACCCATATACATA 60.105 44.000 0.00 0.00 0.00 2.29
1819 2131 9.529325 CTAATCAGATGAAATTCATGCAAACAT 57.471 29.630 13.82 0.00 37.20 2.71
1838 2150 8.794406 GCAAACATGGTAGATTTTATACAAACG 58.206 33.333 0.00 0.00 0.00 3.60
1840 2152 8.795842 AACATGGTAGATTTTATACAAACGGA 57.204 30.769 0.00 0.00 0.00 4.69
1980 2293 2.628657 CGACGGATCCCTTTATCTTCCT 59.371 50.000 6.06 0.00 0.00 3.36
2040 2362 1.153025 GGGTACATTCTTCCCCCGC 60.153 63.158 0.00 0.00 35.52 6.13
2128 2453 2.187163 GGGTACTTCAGCCGGAGC 59.813 66.667 5.05 0.00 34.44 4.70
2129 2454 2.656069 GGGTACTTCAGCCGGAGCA 61.656 63.158 5.05 0.00 43.56 4.26
2151 2476 2.202756 GGTGCCTACTCCGCTTCG 60.203 66.667 0.00 0.00 0.00 3.79
2185 2510 2.280797 GGTCAGCGTTGGTCTGCA 60.281 61.111 0.00 0.00 0.00 4.41
2192 2517 1.436195 GCGTTGGTCTGCACTGAACA 61.436 55.000 0.00 0.00 0.00 3.18
2203 2528 0.532862 CACTGAACAGGGCAAGTCGT 60.533 55.000 6.76 0.00 0.00 4.34
2243 2580 1.460699 GCTTTCCAGGGACCCAAGT 59.539 57.895 14.60 0.00 0.00 3.16
2333 2680 1.725164 GTCGATTTCCGCGTCTTTCTT 59.275 47.619 4.92 0.00 38.37 2.52
2335 2682 1.266404 CGATTTCCGCGTCTTTCTTCG 60.266 52.381 4.92 0.41 0.00 3.79
2406 2756 1.077285 CTCATCCATGGCAGCCACA 60.077 57.895 19.10 3.79 35.80 4.17
2435 2786 1.586541 CACTGTGCTCTCCTGCGTA 59.413 57.895 0.00 0.00 35.36 4.42
2447 2799 1.183549 CCTGCGTACCTACTTGGAGT 58.816 55.000 0.00 0.00 39.71 3.85
2452 2804 3.828451 TGCGTACCTACTTGGAGTAACTT 59.172 43.478 0.00 0.00 39.71 2.66
2459 2811 3.577805 ACTTGGAGTAACTTGCCACTT 57.422 42.857 0.00 0.00 0.00 3.16
2472 2829 0.034616 GCCACTTCTCTGTGAGCTGT 59.965 55.000 0.00 0.00 40.12 4.40
2487 2844 2.001361 GCTGTAGCGGCGAGTTCCTA 62.001 60.000 12.98 0.00 0.00 2.94
2494 2851 0.320073 CGGCGAGTTCCTAAACCACA 60.320 55.000 0.00 0.00 35.92 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 102 1.367471 CAGAGTTGGGAGTGCGACA 59.633 57.895 0.00 0.00 0.00 4.35
80 142 2.071540 CACGATGACAGATGCACAACT 58.928 47.619 0.00 0.00 0.00 3.16
91 153 0.386352 GACGTCCGAACACGATGACA 60.386 55.000 3.51 0.00 42.69 3.58
115 177 3.254024 ATCAGAGGCGGTGCGGTTT 62.254 57.895 0.00 0.00 0.00 3.27
138 200 2.050351 CGGCGTGAGACTTGTCGT 60.050 61.111 0.00 0.00 36.51 4.34
139 201 2.543687 ATCCGGCGTGAGACTTGTCG 62.544 60.000 6.01 0.00 36.51 4.35
144 211 0.955178 CATAGATCCGGCGTGAGACT 59.045 55.000 6.01 9.09 36.51 3.24
146 213 1.106944 TGCATAGATCCGGCGTGAGA 61.107 55.000 6.01 0.00 0.00 3.27
156 223 4.077108 TCTGCCCAAATGATGCATAGATC 58.923 43.478 0.00 0.00 33.97 2.75
183 250 4.766404 ACATCTTCCGTCAAAAATCCAC 57.234 40.909 0.00 0.00 0.00 4.02
191 258 3.195610 AGCAGTCATACATCTTCCGTCAA 59.804 43.478 0.00 0.00 0.00 3.18
194 261 3.068307 GGTAGCAGTCATACATCTTCCGT 59.932 47.826 0.00 0.00 0.00 4.69
201 268 2.290916 CTCGACGGTAGCAGTCATACAT 59.709 50.000 14.19 0.00 38.46 2.29
210 277 3.755628 GGCCACTCGACGGTAGCA 61.756 66.667 0.00 0.00 0.00 3.49
215 282 2.837371 GAAAGGAGGCCACTCGACGG 62.837 65.000 5.01 0.00 44.93 4.79
250 317 0.313987 GGAAACGGCCTTCCAACTTG 59.686 55.000 16.97 0.00 43.84 3.16
254 321 1.074248 GGAGGAAACGGCCTTCCAA 59.926 57.895 22.30 0.00 46.38 3.53
264 331 0.537653 AGCGGCTCTAAGGAGGAAAC 59.462 55.000 0.00 0.00 39.80 2.78
266 333 0.537188 CAAGCGGCTCTAAGGAGGAA 59.463 55.000 1.45 0.00 39.80 3.36
267 334 0.324368 TCAAGCGGCTCTAAGGAGGA 60.324 55.000 1.45 0.00 39.80 3.71
268 335 0.537188 TTCAAGCGGCTCTAAGGAGG 59.463 55.000 1.45 0.00 39.80 4.30
283 355 1.005394 GACCCGGAGCTCGTTTCAA 60.005 57.895 0.73 0.00 37.11 2.69
286 358 1.301479 GTTGACCCGGAGCTCGTTT 60.301 57.895 0.73 0.00 37.11 3.60
304 377 4.500545 CCGAATCCTACACCTTCAGATCTG 60.501 50.000 17.07 17.07 0.00 2.90
305 378 3.639094 CCGAATCCTACACCTTCAGATCT 59.361 47.826 0.00 0.00 0.00 2.75
365 438 2.669133 CCCACAAGCTCCCATCCGA 61.669 63.158 0.00 0.00 0.00 4.55
392 465 0.613292 TCACTCTCCTCCAGTCCAGC 60.613 60.000 0.00 0.00 0.00 4.85
411 484 3.118738 CCTAGCCGTATTTCACTCCACTT 60.119 47.826 0.00 0.00 0.00 3.16
418 491 2.558378 GGAACCCTAGCCGTATTTCAC 58.442 52.381 0.00 0.00 0.00 3.18
437 510 1.734137 CTATCCACACTCCGGTCGG 59.266 63.158 0.00 2.52 0.00 4.79
469 542 0.898320 CTGGCCTATCTGATACCCCG 59.102 60.000 3.32 0.00 0.00 5.73
490 563 0.105862 CCATGTTGGATCCAGCCCAT 60.106 55.000 24.13 18.78 40.96 4.00
496 569 2.275089 CCCGCCATGTTGGATCCA 59.725 61.111 11.44 11.44 40.96 3.41
518 591 2.847435 GAAGCTTGGACGTACCCCGG 62.847 65.000 2.10 0.00 42.24 5.73
520 593 1.078637 GGAAGCTTGGACGTACCCC 60.079 63.158 2.10 0.00 38.00 4.95
523 596 0.252197 ATGGGGAAGCTTGGACGTAC 59.748 55.000 2.10 0.00 0.00 3.67
525 598 1.141053 GATATGGGGAAGCTTGGACGT 59.859 52.381 2.10 0.00 0.00 4.34
531 604 1.694696 GAGACGGATATGGGGAAGCTT 59.305 52.381 0.00 0.00 0.00 3.74
535 608 2.767644 TCTGAGACGGATATGGGGAA 57.232 50.000 0.00 0.00 0.00 3.97
550 623 4.013050 CCTCGTATCCAGCTCATATCTGA 58.987 47.826 0.00 0.00 33.54 3.27
553 626 5.347342 CATTCCTCGTATCCAGCTCATATC 58.653 45.833 0.00 0.00 0.00 1.63
568 641 0.534412 AGACTGACTGGCATTCCTCG 59.466 55.000 2.13 0.00 0.00 4.63
581 654 1.866015 ATCCCGAATGACCAGACTGA 58.134 50.000 3.32 0.00 0.00 3.41
586 659 4.037923 CCCATTTTAATCCCGAATGACCAG 59.962 45.833 0.00 0.00 33.67 4.00
588 661 3.320826 CCCCATTTTAATCCCGAATGACC 59.679 47.826 0.00 0.00 33.67 4.02
590 663 4.079443 ACTCCCCATTTTAATCCCGAATGA 60.079 41.667 0.00 0.00 33.67 2.57
611 684 4.835284 AAAATTGACACCCAACCAAACT 57.165 36.364 0.00 0.00 37.63 2.66
631 704 6.469410 ACCTGTTCAGTGTATTCGGATAAAA 58.531 36.000 0.00 0.00 0.00 1.52
632 705 6.045072 ACCTGTTCAGTGTATTCGGATAAA 57.955 37.500 0.00 0.00 0.00 1.40
633 706 5.670792 ACCTGTTCAGTGTATTCGGATAA 57.329 39.130 0.00 0.00 0.00 1.75
634 707 5.221185 GCTACCTGTTCAGTGTATTCGGATA 60.221 44.000 0.00 0.00 0.00 2.59
635 708 4.441634 GCTACCTGTTCAGTGTATTCGGAT 60.442 45.833 0.00 0.00 0.00 4.18
636 709 3.119245 GCTACCTGTTCAGTGTATTCGGA 60.119 47.826 0.00 0.00 0.00 4.55
637 710 3.187700 GCTACCTGTTCAGTGTATTCGG 58.812 50.000 0.00 0.00 0.00 4.30
638 711 3.845178 TGCTACCTGTTCAGTGTATTCG 58.155 45.455 0.00 0.00 0.00 3.34
639 712 6.743575 AATTGCTACCTGTTCAGTGTATTC 57.256 37.500 0.00 0.00 0.00 1.75
640 713 7.524717 AAAATTGCTACCTGTTCAGTGTATT 57.475 32.000 0.00 0.00 0.00 1.89
641 714 7.524717 AAAAATTGCTACCTGTTCAGTGTAT 57.475 32.000 0.00 0.00 0.00 2.29
642 715 6.293190 CGAAAAATTGCTACCTGTTCAGTGTA 60.293 38.462 0.00 1.37 0.00 2.90
643 716 5.505654 CGAAAAATTGCTACCTGTTCAGTGT 60.506 40.000 0.00 0.34 0.00 3.55
644 717 4.911610 CGAAAAATTGCTACCTGTTCAGTG 59.088 41.667 0.00 0.00 0.00 3.66
645 718 4.578928 ACGAAAAATTGCTACCTGTTCAGT 59.421 37.500 0.00 0.00 0.00 3.41
646 719 5.108385 ACGAAAAATTGCTACCTGTTCAG 57.892 39.130 0.00 0.00 0.00 3.02
647 720 4.023536 GGACGAAAAATTGCTACCTGTTCA 60.024 41.667 0.00 0.00 0.00 3.18
648 721 4.473199 GGACGAAAAATTGCTACCTGTTC 58.527 43.478 0.00 0.00 0.00 3.18
649 722 3.058501 CGGACGAAAAATTGCTACCTGTT 60.059 43.478 0.00 0.00 0.00 3.16
650 723 2.482721 CGGACGAAAAATTGCTACCTGT 59.517 45.455 0.00 0.00 0.00 4.00
651 724 2.159572 CCGGACGAAAAATTGCTACCTG 60.160 50.000 0.00 0.00 0.00 4.00
652 725 2.081462 CCGGACGAAAAATTGCTACCT 58.919 47.619 0.00 0.00 0.00 3.08
653 726 1.131693 CCCGGACGAAAAATTGCTACC 59.868 52.381 0.73 0.00 0.00 3.18
654 727 1.808343 ACCCGGACGAAAAATTGCTAC 59.192 47.619 0.73 0.00 0.00 3.58
655 728 2.188062 ACCCGGACGAAAAATTGCTA 57.812 45.000 0.73 0.00 0.00 3.49
656 729 1.808343 GTACCCGGACGAAAAATTGCT 59.192 47.619 0.73 0.00 0.00 3.91
657 730 1.536331 TGTACCCGGACGAAAAATTGC 59.464 47.619 0.73 0.00 0.00 3.56
658 731 2.095617 GGTGTACCCGGACGAAAAATTG 60.096 50.000 0.73 0.00 0.00 2.32
659 732 2.153645 GGTGTACCCGGACGAAAAATT 58.846 47.619 0.73 0.00 0.00 1.82
660 733 1.812235 GGTGTACCCGGACGAAAAAT 58.188 50.000 0.73 0.00 0.00 1.82
661 734 3.304041 GGTGTACCCGGACGAAAAA 57.696 52.632 0.73 0.00 0.00 1.94
687 760 2.372690 CGTCTCAAACGCCTGGACG 61.373 63.158 0.00 3.14 45.76 4.79
703 776 4.197498 CGAACCGCCGATACCCGT 62.197 66.667 0.00 0.00 36.31 5.28
798 927 3.926616 TCTTTCTCCACGAGTCCATTTC 58.073 45.455 0.00 0.00 0.00 2.17
799 928 4.065789 GTTCTTTCTCCACGAGTCCATTT 58.934 43.478 0.00 0.00 0.00 2.32
800 929 3.071023 TGTTCTTTCTCCACGAGTCCATT 59.929 43.478 0.00 0.00 0.00 3.16
903 1049 3.318839 TGAACTGAACTGCTTTTGATGGG 59.681 43.478 0.00 0.00 0.00 4.00
926 1072 1.954362 ATCGAGAGGCTGCCTGTGAC 61.954 60.000 28.82 11.79 31.76 3.67
963 1109 0.958382 TGGTGTATGCAACGGGAAGC 60.958 55.000 0.00 0.00 34.35 3.86
990 1144 0.181350 GTCCGGCCATCTTTGGAGAT 59.819 55.000 2.24 0.00 46.92 2.75
1266 1423 6.538742 CGCTTGAGAAAAGATATTCCTGGTAA 59.461 38.462 0.00 0.00 0.00 2.85
1267 1424 6.049149 CGCTTGAGAAAAGATATTCCTGGTA 58.951 40.000 0.00 0.00 0.00 3.25
1269 1426 4.878397 ACGCTTGAGAAAAGATATTCCTGG 59.122 41.667 0.00 0.00 0.00 4.45
1275 1433 4.113354 GACGGACGCTTGAGAAAAGATAT 58.887 43.478 0.00 0.00 0.00 1.63
1288 1446 1.596895 GAGGAAGGAAGACGGACGCT 61.597 60.000 0.00 0.00 0.00 5.07
1300 1458 1.337260 CCACACGAGACAAGAGGAAGG 60.337 57.143 0.00 0.00 0.00 3.46
1334 1623 0.320421 CATCACAGGGGAAACGTCGT 60.320 55.000 0.00 0.00 0.00 4.34
1362 1654 1.370778 TGTTCGTCACCTACACGCG 60.371 57.895 3.53 3.53 37.18 6.01
1584 1876 7.940850 TCACTACTTTTATTTGCAGCTTCTTT 58.059 30.769 0.00 0.00 0.00 2.52
1650 1945 3.154827 ACAATCACCTCCGGTTCATTT 57.845 42.857 0.00 0.00 31.02 2.32
1657 1952 2.185004 ACTTCAACAATCACCTCCGG 57.815 50.000 0.00 0.00 0.00 5.14
1658 1953 5.178797 AGAATACTTCAACAATCACCTCCG 58.821 41.667 0.00 0.00 0.00 4.63
1662 1957 6.592607 TCGGTAAGAATACTTCAACAATCACC 59.407 38.462 0.00 0.00 37.53 4.02
1733 2044 0.527817 CCGCCTTCTATGTCCGTGTC 60.528 60.000 0.00 0.00 0.00 3.67
1741 2052 0.179020 TTGGATGGCCGCCTTCTATG 60.179 55.000 21.27 0.00 36.79 2.23
1745 2056 3.508840 CGTTGGATGGCCGCCTTC 61.509 66.667 15.47 15.47 36.79 3.46
1819 2131 6.313411 CCGTTCCGTTTGTATAAAATCTACCA 59.687 38.462 0.00 0.00 0.00 3.25
1821 2133 7.524294 TCCGTTCCGTTTGTATAAAATCTAC 57.476 36.000 0.00 0.00 0.00 2.59
1823 2135 7.041235 TGTTTCCGTTCCGTTTGTATAAAATCT 60.041 33.333 0.00 0.00 0.00 2.40
1875 2188 3.818210 ACGTGCACATGATTTTACCTTCA 59.182 39.130 18.64 0.00 0.00 3.02
1876 2189 4.419522 ACGTGCACATGATTTTACCTTC 57.580 40.909 18.64 0.00 0.00 3.46
1924 2237 7.959651 CGTAAACTAGTGTAGTGTATTCGTCTT 59.040 37.037 0.00 0.00 39.39 3.01
1973 2286 1.134159 GCTGCCAGACATGAGGAAGAT 60.134 52.381 13.52 0.00 31.67 2.40
1980 2293 4.783621 GCGGGCTGCCAGACATGA 62.784 66.667 23.18 0.00 37.76 3.07
2022 2335 1.153025 GCGGGGGAAGAATGTACCC 60.153 63.158 0.00 0.00 42.59 3.69
2040 2362 2.409870 GCCGGGCACAAGGAAGATG 61.410 63.158 15.62 0.00 0.00 2.90
2070 2392 0.607489 CACCCTCTTTGCCACTCTGG 60.607 60.000 0.00 0.00 41.55 3.86
2072 2394 1.073897 GCACCCTCTTTGCCACTCT 59.926 57.895 0.00 0.00 33.58 3.24
2114 2436 1.412710 CCTTATGCTCCGGCTGAAGTA 59.587 52.381 0.00 0.00 39.59 2.24
2115 2437 0.179000 CCTTATGCTCCGGCTGAAGT 59.821 55.000 0.00 0.00 39.59 3.01
2128 2453 0.249911 GCGGAGTAGGCACCCTTATG 60.250 60.000 0.00 0.00 34.61 1.90
2129 2454 0.398664 AGCGGAGTAGGCACCCTTAT 60.399 55.000 0.00 0.00 34.61 1.73
2151 2476 1.227497 CCCTCGCCTCAGCTTCATC 60.227 63.158 0.00 0.00 36.60 2.92
2185 2510 0.249911 GACGACTTGCCCTGTTCAGT 60.250 55.000 0.00 0.00 0.00 3.41
2192 2517 0.670546 CACAATCGACGACTTGCCCT 60.671 55.000 0.00 0.00 0.00 5.19
2203 2528 3.507924 GCCGGCATGCACAATCGA 61.508 61.111 24.80 0.00 0.00 3.59
2251 2588 4.558095 CGAGAAAAAGTAGAACACGGGAGA 60.558 45.833 0.00 0.00 0.00 3.71
2308 2655 1.069378 GACGCGGAAATCGACGAGTT 61.069 55.000 10.72 10.72 42.86 3.01
2378 2728 0.107508 CATGGATGAGGCCAGACGTT 60.108 55.000 5.01 0.00 42.15 3.99
2406 2756 2.268076 GCACAGTGGAACGGGCATT 61.268 57.895 1.84 0.00 45.86 3.56
2435 2786 2.976882 TGGCAAGTTACTCCAAGTAGGT 59.023 45.455 0.00 0.00 39.02 3.08
2447 2799 3.803715 GCTCACAGAGAAGTGGCAAGTTA 60.804 47.826 0.00 0.00 39.93 2.24
2452 2804 0.034476 CAGCTCACAGAGAAGTGGCA 59.966 55.000 0.00 0.00 39.93 4.92
2459 2811 1.938657 GCCGCTACAGCTCACAGAGA 61.939 60.000 0.00 0.00 39.32 3.10
2472 2829 0.174162 GGTTTAGGAACTCGCCGCTA 59.826 55.000 0.00 0.00 41.75 4.26
2479 2836 2.140717 CGGTGTGTGGTTTAGGAACTC 58.859 52.381 0.00 0.00 41.75 3.01
2487 2844 2.124693 CCAAGCCGGTGTGTGGTTT 61.125 57.895 1.90 0.00 0.00 3.27
2511 2868 0.825410 TAGCCCGACGGAGCAAATTA 59.175 50.000 23.48 9.12 0.00 1.40


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

AutoCloner maintained by Alex Coulton.