Multiple sequence alignment - TraesCS5A01G360700

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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 TraesCS5A01G360700 chr5A 100.000 2480 0 0 1 2480 562117955 562115476 0.000000e+00 4580.0
1 TraesCS5A01G360700 chr5A 84.302 516 55 16 978 1480 562101045 562100543 4.800000e-132 481.0
2 TraesCS5A01G360700 chr5A 81.977 516 54 14 1001 1480 562108595 562108083 3.840000e-108 401.0
3 TraesCS5A01G360700 chr5A 83.849 291 26 12 985 1269 562407375 562407100 8.800000e-65 257.0
4 TraesCS5A01G360700 chr5A 94.286 35 0 1 88 120 125149548 125149514 4.000000e-03 52.8
5 TraesCS5A01G360700 chr5D 87.141 1462 86 54 46 1492 445073820 445072446 0.000000e+00 1565.0
6 TraesCS5A01G360700 chr5D 90.894 593 25 13 1895 2480 445072058 445071488 0.000000e+00 769.0
7 TraesCS5A01G360700 chr5D 85.271 516 49 19 978 1481 445056166 445055666 7.910000e-140 507.0
8 TraesCS5A01G360700 chr5D 84.646 508 46 12 1001 1480 445062924 445062421 6.210000e-131 477.0
9 TraesCS5A01G360700 chr5D 84.016 244 26 9 1540 1773 445072448 445072208 3.210000e-54 222.0
10 TraesCS5A01G360700 chr5B 86.674 893 70 22 978 1857 542331437 542330581 0.000000e+00 944.0
11 TraesCS5A01G360700 chr5B 91.446 491 23 9 1997 2480 542330376 542329898 0.000000e+00 656.0
12 TraesCS5A01G360700 chr5B 83.658 514 46 23 1001 1480 542320200 542319691 1.350000e-122 449.0
13 TraesCS5A01G360700 chr5B 82.800 500 46 20 986 1480 542295738 542295274 6.380000e-111 411.0
14 TraesCS5A01G360700 chr5B 82.770 296 31 14 985 1270 542694939 542694654 1.900000e-61 246.0
15 TraesCS5A01G360700 chr5B 73.805 481 47 40 166 597 542332541 542332091 1.560000e-22 117.0
16 TraesCS5A01G360700 chr5B 86.813 91 1 5 1899 1989 542330494 542330415 9.450000e-15 91.6
17 TraesCS5A01G360700 chr1A 94.737 38 1 1 93 129 11940848 11940811 9.580000e-05 58.4


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 TraesCS5A01G360700 chr5A 562115476 562117955 2479 True 4580.00 4580 100.000000 1 2480 1 chr5A.!!$R4 2479
1 TraesCS5A01G360700 chr5A 562100543 562101045 502 True 481.00 481 84.302000 978 1480 1 chr5A.!!$R2 502
2 TraesCS5A01G360700 chr5A 562108083 562108595 512 True 401.00 401 81.977000 1001 1480 1 chr5A.!!$R3 479
3 TraesCS5A01G360700 chr5D 445071488 445073820 2332 True 852.00 1565 87.350333 46 2480 3 chr5D.!!$R3 2434
4 TraesCS5A01G360700 chr5D 445055666 445056166 500 True 507.00 507 85.271000 978 1481 1 chr5D.!!$R1 503
5 TraesCS5A01G360700 chr5D 445062421 445062924 503 True 477.00 477 84.646000 1001 1480 1 chr5D.!!$R2 479
6 TraesCS5A01G360700 chr5B 542329898 542332541 2643 True 452.15 944 84.684500 166 2480 4 chr5B.!!$R4 2314
7 TraesCS5A01G360700 chr5B 542319691 542320200 509 True 449.00 449 83.658000 1001 1480 1 chr5B.!!$R2 479

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
333 355 0.035458 CCTGGTGAAGTGAGGTGGTC 59.965 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 2482 1.002087 AGCTACTGGTGCAGTGGTAAC 59.998 52.381 0.0 0.0 45.01 2.5 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
24 25 7.321745 ACCCGCTTTTATTGATTAGAGAAAG 57.678 36.000 0.00 0.00 0.00 2.62
25 26 7.110155 ACCCGCTTTTATTGATTAGAGAAAGA 58.890 34.615 0.00 0.00 0.00 2.52
26 27 7.065923 ACCCGCTTTTATTGATTAGAGAAAGAC 59.934 37.037 0.00 0.00 0.00 3.01
27 28 7.065803 CCCGCTTTTATTGATTAGAGAAAGACA 59.934 37.037 0.00 0.00 0.00 3.41
28 29 7.905493 CCGCTTTTATTGATTAGAGAAAGACAC 59.095 37.037 0.00 0.00 0.00 3.67
29 30 8.660373 CGCTTTTATTGATTAGAGAAAGACACT 58.340 33.333 0.00 0.00 0.00 3.55
36 37 9.956640 ATTGATTAGAGAAAGACACTTGAAGAT 57.043 29.630 0.00 0.00 0.00 2.40
37 38 9.784531 TTGATTAGAGAAAGACACTTGAAGATT 57.215 29.630 0.00 0.00 0.00 2.40
38 39 9.212641 TGATTAGAGAAAGACACTTGAAGATTG 57.787 33.333 0.00 0.00 0.00 2.67
39 40 9.429359 GATTAGAGAAAGACACTTGAAGATTGA 57.571 33.333 0.00 0.00 0.00 2.57
40 41 8.594881 TTAGAGAAAGACACTTGAAGATTGAC 57.405 34.615 0.00 0.00 0.00 3.18
41 42 6.825610 AGAGAAAGACACTTGAAGATTGACT 58.174 36.000 0.00 0.00 0.00 3.41
42 43 6.705381 AGAGAAAGACACTTGAAGATTGACTG 59.295 38.462 0.00 0.00 0.00 3.51
43 44 6.586344 AGAAAGACACTTGAAGATTGACTGA 58.414 36.000 0.00 0.00 0.00 3.41
44 45 6.481644 AGAAAGACACTTGAAGATTGACTGAC 59.518 38.462 0.00 0.00 0.00 3.51
60 61 6.321848 TGACTGACTGATAACTCGTGTTAA 57.678 37.500 13.50 0.00 41.36 2.01
64 65 6.423001 ACTGACTGATAACTCGTGTTAAAACC 59.577 38.462 13.50 5.25 41.36 3.27
137 138 9.169592 GATAGAGAGGTAGTAGGACAATACATC 57.830 40.741 0.00 0.00 32.01 3.06
143 144 7.126733 AGGTAGTAGGACAATACATCTGTCTT 58.873 38.462 3.24 0.00 42.38 3.01
144 145 7.068839 AGGTAGTAGGACAATACATCTGTCTTG 59.931 40.741 6.84 6.84 42.38 3.02
145 146 5.665459 AGTAGGACAATACATCTGTCTTGC 58.335 41.667 7.99 0.00 42.38 4.01
146 147 4.558226 AGGACAATACATCTGTCTTGCA 57.442 40.909 7.99 0.00 42.38 4.08
147 148 4.511527 AGGACAATACATCTGTCTTGCAG 58.488 43.478 7.99 0.00 46.34 4.41
148 149 4.019860 AGGACAATACATCTGTCTTGCAGT 60.020 41.667 7.99 0.00 45.23 4.40
149 150 5.187772 AGGACAATACATCTGTCTTGCAGTA 59.812 40.000 7.99 0.00 45.23 2.74
150 151 6.051717 GGACAATACATCTGTCTTGCAGTAT 58.948 40.000 7.99 0.00 45.23 2.12
151 152 7.069950 AGGACAATACATCTGTCTTGCAGTATA 59.930 37.037 7.99 0.00 45.23 1.47
152 153 7.169982 GGACAATACATCTGTCTTGCAGTATAC 59.830 40.741 7.99 0.00 45.23 1.47
153 154 6.697455 ACAATACATCTGTCTTGCAGTATACG 59.303 38.462 7.99 0.00 45.23 3.06
154 155 4.983671 ACATCTGTCTTGCAGTATACGA 57.016 40.909 0.00 0.00 45.23 3.43
155 156 5.521906 ACATCTGTCTTGCAGTATACGAT 57.478 39.130 0.00 0.00 45.23 3.73
156 157 5.524284 ACATCTGTCTTGCAGTATACGATC 58.476 41.667 0.00 0.00 45.23 3.69
216 217 3.167425 GGATCGATCGATGATGACGAAG 58.833 50.000 33.86 0.00 42.80 3.79
234 235 3.123620 GAAGCTGGCAGCAGGACG 61.124 66.667 38.09 2.37 45.56 4.79
243 244 1.812922 CAGCAGGACGCAGATGGAC 60.813 63.158 0.00 0.00 46.13 4.02
257 258 4.927425 GCAGATGGACTACGTCAACTTAAA 59.073 41.667 0.00 0.00 37.58 1.52
277 296 2.294979 AGTCGTCGTGGCAGACATATA 58.705 47.619 14.48 0.00 40.98 0.86
289 308 5.098893 GGCAGACATATAAGATACGCAGAG 58.901 45.833 0.00 0.00 0.00 3.35
327 349 0.250513 GTAGGCCCTGGTGAAGTGAG 59.749 60.000 0.00 0.00 0.00 3.51
333 355 0.035458 CCTGGTGAAGTGAGGTGGTC 59.965 60.000 0.00 0.00 0.00 4.02
336 358 1.668151 GTGAAGTGAGGTGGTCGGC 60.668 63.158 0.00 0.00 0.00 5.54
386 432 2.147150 GTTTGCTCACTCACTTCCTCC 58.853 52.381 0.00 0.00 0.00 4.30
421 471 1.363744 GTACTGACACTGCATCAGGC 58.636 55.000 17.75 8.28 46.60 4.85
422 472 0.250234 TACTGACACTGCATCAGGCC 59.750 55.000 17.75 0.00 46.60 5.19
423 473 1.002990 CTGACACTGCATCAGGCCA 60.003 57.895 5.01 0.00 43.89 5.36
424 474 0.607217 CTGACACTGCATCAGGCCAA 60.607 55.000 5.01 0.00 43.89 4.52
425 475 0.178995 TGACACTGCATCAGGCCAAA 60.179 50.000 5.01 0.00 43.89 3.28
426 476 0.524862 GACACTGCATCAGGCCAAAG 59.475 55.000 5.01 0.00 43.89 2.77
427 477 1.214589 CACTGCATCAGGCCAAAGC 59.785 57.895 5.01 3.72 43.89 3.51
467 523 0.319555 ATCTACAGTTGCACGCACGT 60.320 50.000 0.00 0.00 0.00 4.49
472 528 2.103647 AGTTGCACGCACGTGTTGA 61.104 52.632 22.66 7.89 46.90 3.18
476 532 2.323105 CACGCACGTGTTGACCAC 59.677 61.111 18.38 0.00 40.91 4.16
490 547 1.076777 ACCACCTGCATGCATACCC 60.077 57.895 22.97 0.00 0.00 3.69
500 557 3.275338 GCATACCCGCAGCTGAGC 61.275 66.667 20.43 0.85 0.00 4.26
545 613 4.085357 TGAGTCCAATGTGTGTTAGCTT 57.915 40.909 0.00 0.00 0.00 3.74
616 710 5.780984 CCGGGTGATTAGTAGGAGTATTTC 58.219 45.833 0.00 0.00 0.00 2.17
638 732 6.312399 TCGTTTTCATTTCATGCAGTACTT 57.688 33.333 0.00 0.00 0.00 2.24
641 735 8.015087 TCGTTTTCATTTCATGCAGTACTTTAG 58.985 33.333 0.00 0.00 0.00 1.85
642 736 7.803189 CGTTTTCATTTCATGCAGTACTTTAGT 59.197 33.333 0.00 0.00 0.00 2.24
645 739 6.472016 TCATTTCATGCAGTACTTTAGTCCA 58.528 36.000 0.00 0.00 0.00 4.02
646 740 6.371548 TCATTTCATGCAGTACTTTAGTCCAC 59.628 38.462 0.00 0.00 0.00 4.02
647 741 4.202245 TCATGCAGTACTTTAGTCCACC 57.798 45.455 0.00 0.00 0.00 4.61
648 742 2.736144 TGCAGTACTTTAGTCCACCG 57.264 50.000 0.00 0.00 0.00 4.94
649 743 1.274167 TGCAGTACTTTAGTCCACCGG 59.726 52.381 0.00 0.00 0.00 5.28
650 744 2.005560 GCAGTACTTTAGTCCACCGGC 61.006 57.143 0.00 0.00 0.00 6.13
651 745 0.900421 AGTACTTTAGTCCACCGGCC 59.100 55.000 0.00 0.00 0.00 6.13
668 762 2.131067 CCGCTTCCTCCTCCCTCTC 61.131 68.421 0.00 0.00 0.00 3.20
758 1103 2.023673 CAGGCGATTAATTCAAGGCCA 58.976 47.619 5.01 0.00 40.47 5.36
781 1126 6.082984 CACGCAAAAACAACAAAAGGAAATT 58.917 32.000 0.00 0.00 0.00 1.82
825 1207 2.105128 CTCGATCCACGGTGCTCC 59.895 66.667 1.68 0.00 42.82 4.70
850 1244 4.082136 CCACTCCTCCTCTTTATATACCGC 60.082 50.000 0.00 0.00 0.00 5.68
857 1251 1.680105 CTTTATATACCGCCGCGCCG 61.680 60.000 7.42 0.88 0.00 6.46
879 1273 4.947278 CGGTCGCTCGCTCGCTAG 62.947 72.222 0.00 0.00 0.00 3.42
893 1287 2.973899 CTAGCTCACACCACCGCT 59.026 61.111 0.00 0.00 36.56 5.52
894 1288 1.293498 CTAGCTCACACCACCGCTT 59.707 57.895 0.00 0.00 34.14 4.68
897 1291 2.743718 CTCACACCACCGCTTCCT 59.256 61.111 0.00 0.00 0.00 3.36
898 1292 1.071471 CTCACACCACCGCTTCCTT 59.929 57.895 0.00 0.00 0.00 3.36
925 1319 0.906756 CCACTCCCTCTGCCTCTTCA 60.907 60.000 0.00 0.00 0.00 3.02
931 1325 2.117865 CCCTCTGCCTCTTCATCTTCT 58.882 52.381 0.00 0.00 0.00 2.85
935 1329 3.448934 TCTGCCTCTTCATCTTCTTCCT 58.551 45.455 0.00 0.00 0.00 3.36
937 1331 2.503356 TGCCTCTTCATCTTCTTCCTCC 59.497 50.000 0.00 0.00 0.00 4.30
938 1332 2.503356 GCCTCTTCATCTTCTTCCTCCA 59.497 50.000 0.00 0.00 0.00 3.86
939 1333 3.681313 GCCTCTTCATCTTCTTCCTCCAC 60.681 52.174 0.00 0.00 0.00 4.02
940 1334 3.517100 CCTCTTCATCTTCTTCCTCCACA 59.483 47.826 0.00 0.00 0.00 4.17
1035 1462 3.117171 CAGTCGCACCAGCTGCTC 61.117 66.667 8.66 0.00 44.64 4.26
1192 1640 1.639298 CTACTGCCAGCGCAAGTTCC 61.639 60.000 11.47 0.00 46.66 3.62
1308 1765 3.286751 GCTCAAACTGCCACGCCA 61.287 61.111 0.00 0.00 0.00 5.69
1435 1907 2.032528 GTAGCACCACAGCAGCCA 59.967 61.111 0.00 0.00 36.85 4.75
1520 1992 2.738846 GAGGCAATATCTATGTGCACGG 59.261 50.000 13.13 5.15 40.12 4.94
1649 2126 6.388259 GATTGCTTCAGCTTATCGATCTAC 57.612 41.667 0.00 0.00 42.66 2.59
1650 2127 5.521906 TTGCTTCAGCTTATCGATCTACT 57.478 39.130 0.00 0.00 42.66 2.57
1651 2128 5.521906 TGCTTCAGCTTATCGATCTACTT 57.478 39.130 0.00 0.00 42.66 2.24
1721 2205 7.962995 AGACTGGATATATAACGGATCACAT 57.037 36.000 0.00 0.00 0.00 3.21
1820 2319 3.726291 ACAAAGAAACAACCAATCCGG 57.274 42.857 0.00 0.00 42.50 5.14
1857 2356 7.500141 TGATCAAGCATATGTATGTGTACACT 58.500 34.615 25.60 14.02 43.21 3.55
1859 2358 7.770801 TCAAGCATATGTATGTGTACACTTC 57.229 36.000 25.60 15.73 43.21 3.01
1860 2359 7.555965 TCAAGCATATGTATGTGTACACTTCT 58.444 34.615 25.60 13.25 43.21 2.85
1861 2360 7.706607 TCAAGCATATGTATGTGTACACTTCTC 59.293 37.037 25.60 15.83 43.21 2.87
1864 2382 6.360947 GCATATGTATGTGTACACTTCTCTCG 59.639 42.308 25.60 10.04 43.21 4.04
1866 2384 3.504520 TGTATGTGTACACTTCTCTCGCA 59.495 43.478 25.60 10.82 35.94 5.10
1867 2385 3.660501 ATGTGTACACTTCTCTCGCAA 57.339 42.857 25.60 2.74 0.00 4.85
1869 2387 3.381045 TGTGTACACTTCTCTCGCAAAG 58.619 45.455 25.60 0.00 0.00 2.77
1870 2388 3.181479 TGTGTACACTTCTCTCGCAAAGT 60.181 43.478 25.60 0.00 36.16 2.66
1874 2392 5.690409 TGTACACTTCTCTCGCAAAGTAAAG 59.310 40.000 0.00 0.00 34.05 1.85
1875 2393 4.694339 ACACTTCTCTCGCAAAGTAAAGT 58.306 39.130 0.00 0.00 34.05 2.66
1880 2398 8.283291 CACTTCTCTCGCAAAGTAAAGTAAAAT 58.717 33.333 0.00 0.00 34.05 1.82
1897 2445 7.807977 AGTAAAATATTACCACTCCAGCATG 57.192 36.000 0.00 0.00 41.98 4.06
1934 2482 9.144747 CATACATATAAGCAGCTTACTTACCAG 57.855 37.037 17.39 6.12 32.67 4.00
1942 2490 4.562963 GCAGCTTACTTACCAGTTACCACT 60.563 45.833 0.00 0.00 34.06 4.00
1950 2498 3.706055 CAGTTACCACTGCACCAGT 57.294 52.632 0.00 0.00 46.51 4.00
1951 2499 2.831685 CAGTTACCACTGCACCAGTA 57.168 50.000 0.00 0.00 43.43 2.74
1952 2500 2.688507 CAGTTACCACTGCACCAGTAG 58.311 52.381 0.00 0.00 43.43 2.57
1953 2501 1.002087 AGTTACCACTGCACCAGTAGC 59.998 52.381 0.00 0.00 43.43 3.58
1954 2502 1.002087 GTTACCACTGCACCAGTAGCT 59.998 52.381 0.00 0.00 43.43 3.32
1990 2538 0.396435 TCTGTCGTTGGGTGCATCTT 59.604 50.000 0.00 0.00 0.00 2.40
2032 2611 2.027625 CGTGAGGTCCGGTTCTTGC 61.028 63.158 0.00 0.00 0.00 4.01
2039 2618 2.267642 CCGGTTCTTGCCCATCGA 59.732 61.111 0.00 0.00 0.00 3.59
2040 2619 1.153168 CCGGTTCTTGCCCATCGAT 60.153 57.895 0.00 0.00 0.00 3.59
2041 2620 1.160329 CCGGTTCTTGCCCATCGATC 61.160 60.000 0.00 0.00 0.00 3.69
2042 2621 1.490693 CGGTTCTTGCCCATCGATCG 61.491 60.000 9.36 9.36 0.00 3.69
2043 2622 1.160329 GGTTCTTGCCCATCGATCGG 61.160 60.000 16.41 4.45 0.00 4.18
2045 2624 1.622607 TTCTTGCCCATCGATCGGGT 61.623 55.000 24.75 1.25 46.40 5.28
2075 2654 0.179032 TTGGAAGTTGCTTGCTCGGA 60.179 50.000 0.00 0.00 33.01 4.55
2085 2664 1.742761 CTTGCTCGGATGAACCACAT 58.257 50.000 0.00 0.00 42.47 3.21
2133 2712 3.081061 ACGGCAAAGACATCATTGCTTA 58.919 40.909 18.23 0.00 46.24 3.09
2159 2738 2.184579 GTCACCGCACCTAGCCTC 59.815 66.667 0.00 0.00 41.38 4.70
2165 2744 2.482333 CGCACCTAGCCTCGCTACT 61.482 63.158 0.00 0.00 40.44 2.57
2166 2745 1.360911 GCACCTAGCCTCGCTACTC 59.639 63.158 0.00 0.00 40.44 2.59
2167 2746 1.104577 GCACCTAGCCTCGCTACTCT 61.105 60.000 0.00 0.00 40.44 3.24
2168 2747 1.814634 GCACCTAGCCTCGCTACTCTA 60.815 57.143 0.00 0.00 40.44 2.43
2169 2748 1.874872 CACCTAGCCTCGCTACTCTAC 59.125 57.143 0.00 0.00 40.44 2.59
2196 2775 5.875359 CACAGATCAGATATCCACCATGATG 59.125 44.000 8.65 0.00 30.98 3.07
2220 2803 4.525487 TGACTAGACGTTTACTCACCCAAT 59.475 41.667 0.00 0.00 0.00 3.16
2246 2832 2.960819 ACTCGTCAATACTTGAGTGGC 58.039 47.619 0.00 0.00 41.01 5.01
2254 2840 5.049818 GTCAATACTTGAGTGGCAGATATGC 60.050 44.000 3.01 3.01 41.01 3.14
2378 2968 2.030007 TGCAAAAGTTGGTCTGCTATGC 60.030 45.455 0.00 0.00 35.78 3.14
2381 2971 2.584835 AAGTTGGTCTGCTATGCCAA 57.415 45.000 0.00 0.00 39.66 4.52
2431 3021 5.105997 GCACTGGCTGAATTAATCACTTCTT 60.106 40.000 0.00 0.00 36.96 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.065923 GTCTTTCTCTAATCAATAAAAGCGGGT 59.934 37.037 0.00 0.00 0.00 5.28
1 2 7.065803 TGTCTTTCTCTAATCAATAAAAGCGGG 59.934 37.037 0.00 0.00 0.00 6.13
2 3 7.905493 GTGTCTTTCTCTAATCAATAAAAGCGG 59.095 37.037 0.00 0.00 0.00 5.52
3 4 8.660373 AGTGTCTTTCTCTAATCAATAAAAGCG 58.340 33.333 0.00 0.00 0.00 4.68
10 11 9.956640 ATCTTCAAGTGTCTTTCTCTAATCAAT 57.043 29.630 0.00 0.00 0.00 2.57
11 12 9.784531 AATCTTCAAGTGTCTTTCTCTAATCAA 57.215 29.630 0.00 0.00 0.00 2.57
12 13 9.212641 CAATCTTCAAGTGTCTTTCTCTAATCA 57.787 33.333 0.00 0.00 0.00 2.57
13 14 9.429359 TCAATCTTCAAGTGTCTTTCTCTAATC 57.571 33.333 0.00 0.00 0.00 1.75
14 15 9.213799 GTCAATCTTCAAGTGTCTTTCTCTAAT 57.786 33.333 0.00 0.00 0.00 1.73
15 16 8.424918 AGTCAATCTTCAAGTGTCTTTCTCTAA 58.575 33.333 0.00 0.00 0.00 2.10
16 17 7.869937 CAGTCAATCTTCAAGTGTCTTTCTCTA 59.130 37.037 0.00 0.00 0.00 2.43
17 18 6.705381 CAGTCAATCTTCAAGTGTCTTTCTCT 59.295 38.462 0.00 0.00 0.00 3.10
18 19 6.703607 TCAGTCAATCTTCAAGTGTCTTTCTC 59.296 38.462 0.00 0.00 0.00 2.87
19 20 6.481644 GTCAGTCAATCTTCAAGTGTCTTTCT 59.518 38.462 0.00 0.00 0.00 2.52
20 21 6.481644 AGTCAGTCAATCTTCAAGTGTCTTTC 59.518 38.462 0.00 0.00 0.00 2.62
21 22 6.259608 CAGTCAGTCAATCTTCAAGTGTCTTT 59.740 38.462 0.00 0.00 0.00 2.52
22 23 5.757320 CAGTCAGTCAATCTTCAAGTGTCTT 59.243 40.000 0.00 0.00 0.00 3.01
23 24 5.069648 TCAGTCAGTCAATCTTCAAGTGTCT 59.930 40.000 0.00 0.00 0.00 3.41
24 25 5.292765 TCAGTCAGTCAATCTTCAAGTGTC 58.707 41.667 0.00 0.00 0.00 3.67
25 26 5.282055 TCAGTCAGTCAATCTTCAAGTGT 57.718 39.130 0.00 0.00 0.00 3.55
26 27 7.601886 AGTTATCAGTCAGTCAATCTTCAAGTG 59.398 37.037 0.00 0.00 0.00 3.16
27 28 7.675062 AGTTATCAGTCAGTCAATCTTCAAGT 58.325 34.615 0.00 0.00 0.00 3.16
28 29 7.009083 CGAGTTATCAGTCAGTCAATCTTCAAG 59.991 40.741 0.00 0.00 0.00 3.02
29 30 6.808704 CGAGTTATCAGTCAGTCAATCTTCAA 59.191 38.462 0.00 0.00 0.00 2.69
30 31 6.071896 ACGAGTTATCAGTCAGTCAATCTTCA 60.072 38.462 0.00 0.00 0.00 3.02
31 32 6.252441 CACGAGTTATCAGTCAGTCAATCTTC 59.748 42.308 0.00 0.00 0.00 2.87
32 33 6.096036 CACGAGTTATCAGTCAGTCAATCTT 58.904 40.000 0.00 0.00 0.00 2.40
33 34 5.184096 ACACGAGTTATCAGTCAGTCAATCT 59.816 40.000 0.00 0.00 0.00 2.40
34 35 5.403246 ACACGAGTTATCAGTCAGTCAATC 58.597 41.667 0.00 0.00 0.00 2.67
35 36 5.392767 ACACGAGTTATCAGTCAGTCAAT 57.607 39.130 0.00 0.00 0.00 2.57
36 37 4.848562 ACACGAGTTATCAGTCAGTCAA 57.151 40.909 0.00 0.00 0.00 3.18
37 38 4.848562 AACACGAGTTATCAGTCAGTCA 57.151 40.909 0.00 0.00 35.85 3.41
38 39 7.359014 GGTTTTAACACGAGTTATCAGTCAGTC 60.359 40.741 6.27 0.00 39.78 3.51
39 40 6.423001 GGTTTTAACACGAGTTATCAGTCAGT 59.577 38.462 6.27 0.00 39.78 3.41
40 41 6.399669 CGGTTTTAACACGAGTTATCAGTCAG 60.400 42.308 6.27 0.00 39.78 3.51
41 42 5.403166 CGGTTTTAACACGAGTTATCAGTCA 59.597 40.000 6.27 0.00 39.78 3.41
42 43 5.630680 TCGGTTTTAACACGAGTTATCAGTC 59.369 40.000 6.27 0.00 39.78 3.51
43 44 5.531634 TCGGTTTTAACACGAGTTATCAGT 58.468 37.500 6.27 0.00 39.78 3.41
44 45 6.294363 GTTCGGTTTTAACACGAGTTATCAG 58.706 40.000 6.27 2.71 39.78 2.90
60 61 3.684788 CAGATGATTTCTCGGTTCGGTTT 59.315 43.478 0.00 0.00 29.93 3.27
64 65 2.544685 AGCAGATGATTTCTCGGTTCG 58.455 47.619 0.00 0.00 29.93 3.95
121 122 6.379988 TGCAAGACAGATGTATTGTCCTACTA 59.620 38.462 18.48 0.00 45.86 1.82
143 144 3.786516 TTCCAACGATCGTATACTGCA 57.213 42.857 23.04 0.00 0.00 4.41
144 145 5.432157 CAATTTCCAACGATCGTATACTGC 58.568 41.667 23.04 0.00 0.00 4.40
145 146 5.751509 TCCAATTTCCAACGATCGTATACTG 59.248 40.000 23.04 15.66 0.00 2.74
146 147 5.909477 TCCAATTTCCAACGATCGTATACT 58.091 37.500 23.04 2.08 0.00 2.12
147 148 6.592798 TTCCAATTTCCAACGATCGTATAC 57.407 37.500 23.04 0.00 0.00 1.47
148 149 6.425721 GGATTCCAATTTCCAACGATCGTATA 59.574 38.462 23.04 7.11 31.99 1.47
149 150 5.238650 GGATTCCAATTTCCAACGATCGTAT 59.761 40.000 23.04 8.00 31.99 3.06
150 151 4.573201 GGATTCCAATTTCCAACGATCGTA 59.427 41.667 23.04 5.53 31.99 3.43
151 152 3.377172 GGATTCCAATTTCCAACGATCGT 59.623 43.478 16.60 16.60 31.99 3.73
152 153 3.376859 TGGATTCCAATTTCCAACGATCG 59.623 43.478 14.88 14.88 39.05 3.69
153 154 4.399303 ACTGGATTCCAATTTCCAACGATC 59.601 41.667 6.88 0.00 41.36 3.69
154 155 4.344104 ACTGGATTCCAATTTCCAACGAT 58.656 39.130 6.88 0.00 41.36 3.73
155 156 3.761897 ACTGGATTCCAATTTCCAACGA 58.238 40.909 6.88 0.00 41.36 3.85
156 157 5.835113 ATACTGGATTCCAATTTCCAACG 57.165 39.130 6.88 0.00 41.36 4.10
216 217 2.749441 GTCCTGCTGCCAGCTTCC 60.749 66.667 18.96 0.00 42.97 3.46
243 244 4.779136 CGACGACTTTAAGTTGACGTAG 57.221 45.455 22.26 13.59 40.89 3.51
257 258 1.103803 ATATGTCTGCCACGACGACT 58.896 50.000 0.00 0.00 36.71 4.18
277 296 3.067461 GTCCTGTCATCTCTGCGTATCTT 59.933 47.826 0.00 0.00 0.00 2.40
289 308 1.134530 CGAACTCGCGTCCTGTCATC 61.135 60.000 5.77 0.00 0.00 2.92
306 328 1.229082 ACTTCACCAGGGCCTACGA 60.229 57.895 5.28 0.00 0.00 3.43
408 458 1.530013 GCTTTGGCCTGATGCAGTGT 61.530 55.000 3.32 0.00 43.89 3.55
422 472 2.617308 CTCATATCTGCACCAGGCTTTG 59.383 50.000 0.00 0.00 45.15 2.77
423 473 2.507058 TCTCATATCTGCACCAGGCTTT 59.493 45.455 0.00 0.00 45.15 3.51
424 474 2.121948 TCTCATATCTGCACCAGGCTT 58.878 47.619 0.00 0.00 45.15 4.35
425 475 1.798626 TCTCATATCTGCACCAGGCT 58.201 50.000 0.00 0.00 45.15 4.58
426 476 2.855209 ATCTCATATCTGCACCAGGC 57.145 50.000 0.00 0.00 45.13 4.85
427 477 7.600231 AGATATATCTCATATCTGCACCAGG 57.400 40.000 9.57 0.00 39.23 4.45
428 478 9.129532 TGTAGATATATCTCATATCTGCACCAG 57.870 37.037 18.59 0.00 43.65 4.00
429 479 9.129532 CTGTAGATATATCTCATATCTGCACCA 57.870 37.037 18.59 8.25 43.65 4.17
430 480 9.130661 ACTGTAGATATATCTCATATCTGCACC 57.869 37.037 18.59 5.28 43.65 5.01
433 483 9.462174 GCAACTGTAGATATATCTCATATCTGC 57.538 37.037 18.59 16.10 40.45 4.26
467 523 0.540133 ATGCATGCAGGTGGTCAACA 60.540 50.000 26.69 0.00 0.00 3.33
472 528 1.076777 GGGTATGCATGCAGGTGGT 60.077 57.895 26.69 11.35 0.00 4.16
476 532 2.516695 TGCGGGTATGCATGCAGG 60.517 61.111 26.69 12.95 40.62 4.85
490 547 2.439761 CGTACTGTGCTCAGCTGCG 61.440 63.158 15.50 3.41 44.77 5.18
500 557 1.342082 GCAGCGTGGTACGTACTGTG 61.342 60.000 24.07 14.68 44.73 3.66
545 613 3.332421 GCATGCATGCGACAAATGA 57.668 47.368 33.99 0.00 44.67 2.57
597 665 9.362539 TGAAAACGAAATACTCCTACTAATCAC 57.637 33.333 0.00 0.00 0.00 3.06
638 732 3.305177 GAAGCGGCCGGTGGACTAA 62.305 63.158 33.14 0.00 0.00 2.24
649 743 3.855853 GAGGGAGGAGGAAGCGGC 61.856 72.222 0.00 0.00 0.00 6.53
650 744 2.042435 AGAGGGAGGAGGAAGCGG 60.042 66.667 0.00 0.00 0.00 5.52
651 745 2.131067 GGAGAGGGAGGAGGAAGCG 61.131 68.421 0.00 0.00 0.00 4.68
758 1103 5.871465 ATTTCCTTTTGTTGTTTTTGCGT 57.129 30.435 0.00 0.00 0.00 5.24
781 1126 4.143333 GCCCGCGAACCAGCTCTA 62.143 66.667 8.23 0.00 34.40 2.43
825 1207 5.047943 CGGTATATAAAGAGGAGGAGTGGTG 60.048 48.000 0.00 0.00 0.00 4.17
832 1226 2.416972 GCGGCGGTATATAAAGAGGAGG 60.417 54.545 9.78 0.00 0.00 4.30
833 1227 2.731341 CGCGGCGGTATATAAAGAGGAG 60.731 54.545 15.84 0.00 0.00 3.69
834 1228 1.200716 CGCGGCGGTATATAAAGAGGA 59.799 52.381 15.84 0.00 0.00 3.71
875 1269 2.788191 AAGCGGTGGTGTGAGCTAGC 62.788 60.000 6.62 6.62 39.25 3.42
876 1270 0.737715 GAAGCGGTGGTGTGAGCTAG 60.738 60.000 0.00 0.00 39.25 3.42
877 1271 1.292223 GAAGCGGTGGTGTGAGCTA 59.708 57.895 0.00 0.00 39.25 3.32
878 1272 2.031163 GAAGCGGTGGTGTGAGCT 59.969 61.111 0.00 0.00 42.35 4.09
879 1273 3.050275 GGAAGCGGTGGTGTGAGC 61.050 66.667 0.00 0.00 0.00 4.26
880 1274 0.951040 GAAGGAAGCGGTGGTGTGAG 60.951 60.000 0.00 0.00 0.00 3.51
881 1275 1.070786 GAAGGAAGCGGTGGTGTGA 59.929 57.895 0.00 0.00 0.00 3.58
882 1276 1.966451 GGAAGGAAGCGGTGGTGTG 60.966 63.158 0.00 0.00 0.00 3.82
925 1319 2.711009 TGTGGTTGTGGAGGAAGAAGAT 59.289 45.455 0.00 0.00 0.00 2.40
931 1325 1.525077 GCGTGTGGTTGTGGAGGAA 60.525 57.895 0.00 0.00 0.00 3.36
935 1329 4.920112 CGGGCGTGTGGTTGTGGA 62.920 66.667 0.00 0.00 0.00 4.02
937 1331 3.947841 CACGGGCGTGTGGTTGTG 61.948 66.667 0.00 0.00 40.91 3.33
958 1376 2.436115 GGGTGGAAGGTACTGCGC 60.436 66.667 0.00 0.00 40.86 6.09
1182 1630 2.734673 CGAGCTGAGGAACTTGCGC 61.735 63.158 0.00 0.00 41.55 6.09
1290 1747 2.980233 GGCGTGGCAGTTTGAGCT 60.980 61.111 0.00 0.00 0.00 4.09
1294 1751 1.926511 GAGGATGGCGTGGCAGTTTG 61.927 60.000 1.74 0.00 0.00 2.93
1295 1752 1.675641 GAGGATGGCGTGGCAGTTT 60.676 57.895 1.74 0.00 0.00 2.66
1308 1765 1.997874 GTGGGGCCAGTGAGAGGAT 60.998 63.158 4.39 0.00 0.00 3.24
1489 1961 7.332926 CACATAGATATTGCCTCTGGAATGTAC 59.667 40.741 0.00 0.00 0.00 2.90
1529 2001 2.739784 CTAGCTAGCCAGGCGCAT 59.260 61.111 12.13 0.00 41.38 4.73
1530 2002 4.227134 GCTAGCTAGCCAGGCGCA 62.227 66.667 31.67 1.50 43.39 6.09
1532 2004 2.907897 AAACGCTAGCTAGCCAGGCG 62.908 60.000 34.27 30.74 46.34 5.52
1537 2009 1.722011 TGTTGAAACGCTAGCTAGCC 58.278 50.000 34.27 22.67 46.34 3.93
1550 2022 3.698539 TGAATTGAGCACCACTTGTTGAA 59.301 39.130 0.00 0.00 0.00 2.69
1700 2178 8.417106 AGCTTATGTGATCCGTTATATATCCAG 58.583 37.037 0.00 0.00 0.00 3.86
1796 2295 5.183140 CCGGATTGGTTGTTTCTTTGTATCT 59.817 40.000 0.00 0.00 0.00 1.98
1799 2298 4.839668 CCGGATTGGTTGTTTCTTTGTA 57.160 40.909 0.00 0.00 0.00 2.41
1813 2312 9.091784 CTTGATCATTCACTATATACCGGATTG 57.908 37.037 9.46 0.00 0.00 2.67
1815 2314 7.093333 TGCTTGATCATTCACTATATACCGGAT 60.093 37.037 9.46 0.00 0.00 4.18
1827 2326 7.868775 ACACATACATATGCTTGATCATTCAC 58.131 34.615 1.58 0.00 37.19 3.18
1829 2328 8.992073 TGTACACATACATATGCTTGATCATTC 58.008 33.333 1.58 0.00 36.34 2.67
1869 2387 9.169592 TGCTGGAGTGGTAATATTTTACTTTAC 57.830 33.333 6.10 4.20 38.22 2.01
1870 2388 9.914834 ATGCTGGAGTGGTAATATTTTACTTTA 57.085 29.630 6.10 0.00 38.22 1.85
1874 2392 7.067008 ACACATGCTGGAGTGGTAATATTTTAC 59.933 37.037 0.00 0.00 39.99 2.01
1875 2393 7.066887 CACACATGCTGGAGTGGTAATATTTTA 59.933 37.037 0.00 0.00 39.99 1.52
1880 2398 3.263170 ACACACATGCTGGAGTGGTAATA 59.737 43.478 9.60 0.00 39.99 0.98
1897 2445 7.420184 TGCTTATATGTATGCATGTACACAC 57.580 36.000 10.16 0.00 37.40 3.82
1916 2464 5.246656 TGGTAACTGGTAAGTAAGCTGCTTA 59.753 40.000 17.67 17.67 34.77 3.09
1934 2482 1.002087 AGCTACTGGTGCAGTGGTAAC 59.998 52.381 0.00 0.00 45.01 2.50
1942 2490 1.546029 CACTCACTAGCTACTGGTGCA 59.454 52.381 6.25 0.00 41.64 4.57
1948 2496 3.933955 CACGTACTCACTCACTAGCTACT 59.066 47.826 0.00 0.00 0.00 2.57
1950 2498 3.931468 GACACGTACTCACTCACTAGCTA 59.069 47.826 0.00 0.00 0.00 3.32
1951 2499 2.743126 GACACGTACTCACTCACTAGCT 59.257 50.000 0.00 0.00 0.00 3.32
1952 2500 2.743126 AGACACGTACTCACTCACTAGC 59.257 50.000 0.00 0.00 0.00 3.42
1953 2501 3.747010 ACAGACACGTACTCACTCACTAG 59.253 47.826 0.00 0.00 0.00 2.57
1954 2502 3.736720 ACAGACACGTACTCACTCACTA 58.263 45.455 0.00 0.00 0.00 2.74
1990 2538 5.305644 GTCAAAGCAAGGGGATCTATCTAGA 59.694 44.000 0.00 0.00 36.65 2.43
2039 2618 2.039746 TCCAAGAAATGACACACCCGAT 59.960 45.455 0.00 0.00 0.00 4.18
2040 2619 1.418264 TCCAAGAAATGACACACCCGA 59.582 47.619 0.00 0.00 0.00 5.14
2041 2620 1.890876 TCCAAGAAATGACACACCCG 58.109 50.000 0.00 0.00 0.00 5.28
2042 2621 3.222603 ACTTCCAAGAAATGACACACCC 58.777 45.455 0.00 0.00 0.00 4.61
2043 2622 4.610945 CAACTTCCAAGAAATGACACACC 58.389 43.478 0.00 0.00 0.00 4.16
2044 2623 4.044426 GCAACTTCCAAGAAATGACACAC 58.956 43.478 0.00 0.00 0.00 3.82
2045 2624 3.953612 AGCAACTTCCAAGAAATGACACA 59.046 39.130 0.00 0.00 0.00 3.72
2075 2654 4.463891 GGTGAGAAAATGGATGTGGTTCAT 59.536 41.667 0.00 0.00 39.77 2.57
2085 2664 4.080526 GGCTAACTAGGGTGAGAAAATGGA 60.081 45.833 0.00 0.00 0.00 3.41
2159 2738 5.051153 TCTGATCTGTGTAGTAGAGTAGCG 58.949 45.833 0.00 0.00 0.00 4.26
2165 2744 6.943146 GGTGGATATCTGATCTGTGTAGTAGA 59.057 42.308 2.05 0.00 0.00 2.59
2166 2745 6.717084 TGGTGGATATCTGATCTGTGTAGTAG 59.283 42.308 2.05 0.00 0.00 2.57
2167 2746 6.610830 TGGTGGATATCTGATCTGTGTAGTA 58.389 40.000 2.05 0.00 0.00 1.82
2168 2747 5.458595 TGGTGGATATCTGATCTGTGTAGT 58.541 41.667 2.05 0.00 0.00 2.73
2169 2748 6.210185 TCATGGTGGATATCTGATCTGTGTAG 59.790 42.308 2.05 0.00 0.00 2.74
2196 2775 3.254166 TGGGTGAGTAAACGTCTAGTCAC 59.746 47.826 23.08 23.08 45.57 3.67
2246 2832 3.396560 ACATGTGTGGATCGCATATCTG 58.603 45.455 0.00 0.00 44.25 2.90
2254 2840 1.570813 ATGCGTACATGTGTGGATCG 58.429 50.000 9.11 5.02 34.35 3.69
2381 2971 2.734175 CGTGCAGTGTATGTACCATCGT 60.734 50.000 0.00 0.00 41.10 3.73
2391 2981 1.819288 AGTGCTAGTCGTGCAGTGTAT 59.181 47.619 0.00 0.00 41.85 2.29


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

AutoCloner maintained by Alex Coulton.