Multiple sequence alignment - TraesCS5A01G007500

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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 TraesCS5A01G007500 chr5A 100.000 2543 0 0 1 2543 4690934 4693476 0 4697
1 TraesCS5A01G007500 chr1A 86.801 2523 299 25 45 2542 587951510 587948997 0 2784
2 TraesCS5A01G007500 chr6B 85.770 2572 318 35 5 2542 52163315 52160758 0 2678
3 TraesCS5A01G007500 chr6B 83.872 2567 382 24 2 2543 586519168 586521727 0 2418
4 TraesCS5A01G007500 chr7A 84.418 2567 366 26 2 2543 721569362 721566805 0 2494
5 TraesCS5A01G007500 chr3A 84.262 2567 371 25 2 2543 20021643 20024201 0 2471
6 TraesCS5A01G007500 chr3A 84.760 1916 262 20 651 2542 741110551 741112460 0 1893
7 TraesCS5A01G007500 chr2B 84.190 2568 371 27 2 2543 31587822 31590380 0 2460
8 TraesCS5A01G007500 chr2B 81.552 1675 287 12 2 1657 24249884 24251555 0 1362
9 TraesCS5A01G007500 chr1B 84.112 2568 373 24 2 2543 441990986 441993544 0 2449
10 TraesCS5A01G007500 chr6A 84.067 2567 374 24 2 2542 117404716 117407273 0 2442
11 TraesCS5A01G007500 chr4A 84.985 1665 216 20 902 2542 656896064 656897718 0 1659
12 TraesCS5A01G007500 chr3B 83.418 1574 226 27 995 2543 762634452 762632889 0 1428


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 TraesCS5A01G007500 chr5A 4690934 4693476 2542 False 4697 4697 100.000 1 2543 1 chr5A.!!$F1 2542
1 TraesCS5A01G007500 chr1A 587948997 587951510 2513 True 2784 2784 86.801 45 2542 1 chr1A.!!$R1 2497
2 TraesCS5A01G007500 chr6B 52160758 52163315 2557 True 2678 2678 85.770 5 2542 1 chr6B.!!$R1 2537
3 TraesCS5A01G007500 chr6B 586519168 586521727 2559 False 2418 2418 83.872 2 2543 1 chr6B.!!$F1 2541
4 TraesCS5A01G007500 chr7A 721566805 721569362 2557 True 2494 2494 84.418 2 2543 1 chr7A.!!$R1 2541
5 TraesCS5A01G007500 chr3A 20021643 20024201 2558 False 2471 2471 84.262 2 2543 1 chr3A.!!$F1 2541
6 TraesCS5A01G007500 chr3A 741110551 741112460 1909 False 1893 1893 84.760 651 2542 1 chr3A.!!$F2 1891
7 TraesCS5A01G007500 chr2B 31587822 31590380 2558 False 2460 2460 84.190 2 2543 1 chr2B.!!$F2 2541
8 TraesCS5A01G007500 chr2B 24249884 24251555 1671 False 1362 1362 81.552 2 1657 1 chr2B.!!$F1 1655
9 TraesCS5A01G007500 chr1B 441990986 441993544 2558 False 2449 2449 84.112 2 2543 1 chr1B.!!$F1 2541
10 TraesCS5A01G007500 chr6A 117404716 117407273 2557 False 2442 2442 84.067 2 2542 1 chr6A.!!$F1 2540
11 TraesCS5A01G007500 chr4A 656896064 656897718 1654 False 1659 1659 84.985 902 2542 1 chr4A.!!$F1 1640
12 TraesCS5A01G007500 chr3B 762632889 762634452 1563 True 1428 1428 83.418 995 2543 1 chr3B.!!$R1 1548

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
517 524 0.179 ATTCGAGATCTGGTGGTGGC 59.821 55.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2436 2467 0.104462 TCCATAGCAGCCCTACCCAT 60.104 55.0 0.0 0.0 0.0 4.0 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
28 29 2.034066 CCGCACCTCACCAACCAT 59.966 61.111 0.00 0.00 0.00 3.55
103 104 3.083997 GGACCCAGCACCGGATCT 61.084 66.667 9.46 0.34 0.00 2.75
141 142 4.144727 GGAGGAGGCGAGGGGAGA 62.145 72.222 0.00 0.00 0.00 3.71
142 143 2.200092 GAGGAGGCGAGGGGAGAT 59.800 66.667 0.00 0.00 0.00 2.75
149 150 1.522580 GCGAGGGGAGATGCTTCAC 60.523 63.158 2.07 0.00 0.00 3.18
164 167 1.004394 CTTCACTTTCCCCACCTACCC 59.996 57.143 0.00 0.00 0.00 3.69
166 169 1.137594 CACTTTCCCCACCTACCCCA 61.138 60.000 0.00 0.00 0.00 4.96
172 175 0.548197 CCCCACCTACCCCAACTACA 60.548 60.000 0.00 0.00 0.00 2.74
230 233 1.295423 GAGCGTCCTAGGGTTTGCA 59.705 57.895 9.46 0.00 0.00 4.08
232 235 0.328258 AGCGTCCTAGGGTTTGCATT 59.672 50.000 9.46 0.00 0.00 3.56
239 242 3.106827 CCTAGGGTTTGCATTCCCAATT 58.893 45.455 23.03 9.74 45.64 2.32
269 272 0.776810 TGATTCCTTTGGCTGGTGGA 59.223 50.000 0.00 0.00 0.00 4.02
315 318 2.629656 CCTTCGCCCAAGTTGCTGG 61.630 63.158 0.00 0.00 36.10 4.85
319 322 2.282745 GCCCAAGTTGCTGGAGCT 60.283 61.111 0.00 0.00 42.66 4.09
421 428 4.404098 GGTGGATTCGGTGGCGGT 62.404 66.667 0.00 0.00 0.00 5.68
454 461 1.086696 CGCCAAACCAATCTCGTCAT 58.913 50.000 0.00 0.00 0.00 3.06
517 524 0.179000 ATTCGAGATCTGGTGGTGGC 59.821 55.000 0.00 0.00 0.00 5.01
561 568 3.002583 TGCTCGGGCCATGAGTGA 61.003 61.111 21.34 9.24 37.74 3.41
562 569 2.321263 CTGCTCGGGCCATGAGTGAT 62.321 60.000 21.34 0.00 37.74 3.06
567 574 1.890979 GGGCCATGAGTGATGCGAG 60.891 63.158 4.39 0.00 0.00 5.03
611 618 3.485346 GAACCGCCTCCACCACCAA 62.485 63.158 0.00 0.00 0.00 3.67
647 654 3.365265 CCAAGGGCAACACCGAGC 61.365 66.667 0.00 0.00 40.62 5.03
697 704 2.187163 GCTCCTCGTTGCCCTACC 59.813 66.667 0.00 0.00 0.00 3.18
709 716 1.069765 CCCTACCATTCGCTGCGAT 59.930 57.895 26.51 13.36 35.23 4.58
712 719 2.061773 CCTACCATTCGCTGCGATAAG 58.938 52.381 26.51 18.21 35.23 1.73
715 722 1.290203 CCATTCGCTGCGATAAGTGT 58.710 50.000 26.51 5.27 35.23 3.55
722 729 3.122278 TCGCTGCGATAAGTGTAACAAAC 59.878 43.478 22.24 0.00 41.43 2.93
739 746 5.435686 ACAAACTAGGTCATATGGCTCAA 57.564 39.130 7.36 0.00 0.00 3.02
766 773 0.695347 AAGTTCTGAGGCCTTGGGAG 59.305 55.000 6.77 0.70 0.00 4.30
769 776 0.768221 TTCTGAGGCCTTGGGAGTGT 60.768 55.000 6.77 0.00 0.00 3.55
771 778 0.250513 CTGAGGCCTTGGGAGTGTAC 59.749 60.000 6.77 0.00 0.00 2.90
772 779 1.198759 TGAGGCCTTGGGAGTGTACC 61.199 60.000 6.77 0.00 0.00 3.34
793 800 2.697751 CCCCTTCATGTGTGGTTTTCAA 59.302 45.455 0.00 0.00 0.00 2.69
796 803 4.281688 CCCTTCATGTGTGGTTTTCAATCT 59.718 41.667 0.00 0.00 0.00 2.40
856 864 4.672801 GCAGCTAAGCATAGTGTGGAAAAC 60.673 45.833 0.00 0.00 0.00 2.43
858 866 3.128764 GCTAAGCATAGTGTGGAAAACCC 59.871 47.826 0.00 0.00 0.00 4.11
877 885 6.773976 AACCCAATAATGTGGTGATTACTG 57.226 37.500 0.00 0.00 36.90 2.74
885 893 9.733556 AATAATGTGGTGATTACTGTAGTTGAA 57.266 29.630 0.00 0.00 0.00 2.69
969 979 3.254903 GGAAAAGGAAATGGCGTTGTACT 59.745 43.478 0.00 0.00 0.00 2.73
1059 1069 0.179174 GTTATGGGAAACGCTTGCCG 60.179 55.000 4.56 0.00 45.80 5.69
1086 1096 4.373156 AGAGGGGAATATTGTGGTATGC 57.627 45.455 0.00 0.00 0.00 3.14
1101 1111 3.118038 TGGTATGCATTACTCCTTGGACC 60.118 47.826 3.54 2.41 0.00 4.46
1125 1135 2.564771 TCGATTGGAGCTAAAGGCATG 58.435 47.619 0.00 0.00 44.79 4.06
1126 1136 1.002033 CGATTGGAGCTAAAGGCATGC 60.002 52.381 9.90 9.90 44.79 4.06
1137 1147 0.037975 AAGGCATGCTGGAAAAAGCG 60.038 50.000 18.92 0.00 46.65 4.68
1173 1183 4.201950 CGCAACATTCCCATAGAGAAAAGG 60.202 45.833 0.00 0.00 0.00 3.11
1186 1196 3.567164 AGAGAAAAGGTGCACTGAACATG 59.433 43.478 17.98 0.00 0.00 3.21
1188 1198 3.067180 AGAAAAGGTGCACTGAACATGTG 59.933 43.478 17.98 0.00 38.36 3.21
1242 1252 2.167281 AGAGGTGGATGAATCGACTGTG 59.833 50.000 5.58 0.00 36.05 3.66
1251 1261 3.669536 TGAATCGACTGTGCATAAACCA 58.330 40.909 0.00 0.00 0.00 3.67
1254 1264 2.959516 TCGACTGTGCATAAACCAGAG 58.040 47.619 8.15 2.69 0.00 3.35
1266 1276 7.736447 GCATAAACCAGAGTATGCTAGAATT 57.264 36.000 8.11 0.00 45.96 2.17
1278 1288 3.012518 TGCTAGAATTCTTCTTGGCTGC 58.987 45.455 14.36 6.41 41.14 5.25
1280 1290 3.631227 GCTAGAATTCTTCTTGGCTGCAT 59.369 43.478 14.36 0.00 41.14 3.96
1344 1355 9.075678 CTGGGAGAGCAAATATATGATTTCTTT 57.924 33.333 0.00 0.00 0.00 2.52
1379 1390 1.003580 AGTTGTGACTATGGGTGCTGG 59.996 52.381 0.00 0.00 33.32 4.85
1390 1401 0.961753 GGGTGCTGGGAAAAGTCAAG 59.038 55.000 0.00 0.00 0.00 3.02
1426 1437 0.803117 CAGCAGTGCATCACCTTCTG 59.197 55.000 19.20 0.00 34.49 3.02
1469 1480 6.311055 GGATTCATATCCTGCTTCTTCAAC 57.689 41.667 0.00 0.00 45.88 3.18
1491 1502 1.687493 GCAGGGGGAGACTAGTGCT 60.687 63.158 0.00 0.00 0.00 4.40
1495 1506 2.213280 GGGGAGACTAGTGCTTCCC 58.787 63.158 20.96 20.96 43.84 3.97
1496 1507 1.338890 GGGGAGACTAGTGCTTCCCC 61.339 65.000 27.69 27.69 44.32 4.81
1497 1508 1.338890 GGGAGACTAGTGCTTCCCCC 61.339 65.000 19.41 11.31 0.00 5.40
1520 1544 3.598264 CCCCCAGAACTATGATAAGGGA 58.402 50.000 0.00 0.00 36.96 4.20
1523 1547 5.790618 CCCCCAGAACTATGATAAGGGAATA 59.209 44.000 0.00 0.00 36.96 1.75
1565 1589 4.329638 TGAGAGTGAAGAAGAGGAGGAT 57.670 45.455 0.00 0.00 0.00 3.24
1582 1606 4.099727 GGAGGATAGTGAGGAAGGTAACAC 59.900 50.000 0.00 0.00 41.41 3.32
1663 1688 6.748333 TTGTGGCTCTCAATCTGATAAAAG 57.252 37.500 0.00 0.00 0.00 2.27
1667 1692 5.882557 TGGCTCTCAATCTGATAAAAGTTCC 59.117 40.000 0.00 0.00 0.00 3.62
1673 1698 7.604164 TCTCAATCTGATAAAAGTTCCTGTGAC 59.396 37.037 0.00 0.00 0.00 3.67
1676 1701 8.352201 CAATCTGATAAAAGTTCCTGTGACAAA 58.648 33.333 0.00 0.00 0.00 2.83
1679 1704 8.352201 TCTGATAAAAGTTCCTGTGACAAAATG 58.648 33.333 0.00 0.00 0.00 2.32
1680 1705 8.231692 TGATAAAAGTTCCTGTGACAAAATGA 57.768 30.769 0.00 0.00 0.00 2.57
1685 1710 5.192927 AGTTCCTGTGACAAAATGACTGAA 58.807 37.500 0.00 0.00 0.00 3.02
1695 1720 7.550551 GTGACAAAATGACTGAAGATCTGGATA 59.449 37.037 0.00 0.00 0.00 2.59
1696 1721 7.767659 TGACAAAATGACTGAAGATCTGGATAG 59.232 37.037 0.00 0.00 0.00 2.08
1697 1722 7.855375 ACAAAATGACTGAAGATCTGGATAGA 58.145 34.615 0.00 0.00 37.35 1.98
1700 1725 8.495160 AAATGACTGAAGATCTGGATAGAGAT 57.505 34.615 0.00 0.00 36.14 2.75
1703 1728 7.065504 TGACTGAAGATCTGGATAGAGATGAA 58.934 38.462 0.00 0.00 36.14 2.57
1706 1731 9.599056 ACTGAAGATCTGGATAGAGATGAAATA 57.401 33.333 0.00 0.00 36.14 1.40
1767 1792 2.979678 GCTTGGGGGATGATTACTCCTA 59.020 50.000 0.00 0.00 33.05 2.94
1772 1797 4.140204 TGGGGGATGATTACTCCTATTCCT 60.140 45.833 0.00 0.00 33.05 3.36
1792 1817 4.847512 TCCTCCCTCACCTTTGTTTATGTA 59.152 41.667 0.00 0.00 0.00 2.29
1795 1820 5.424757 TCCCTCACCTTTGTTTATGTATCG 58.575 41.667 0.00 0.00 0.00 2.92
1801 1826 6.315144 TCACCTTTGTTTATGTATCGTGATGG 59.685 38.462 0.00 0.00 0.00 3.51
1802 1827 6.315144 CACCTTTGTTTATGTATCGTGATGGA 59.685 38.462 0.00 0.00 0.00 3.41
1803 1828 7.012327 CACCTTTGTTTATGTATCGTGATGGAT 59.988 37.037 0.00 0.00 0.00 3.41
1804 1829 7.012327 ACCTTTGTTTATGTATCGTGATGGATG 59.988 37.037 0.00 0.00 0.00 3.51
1814 1839 6.492087 TGTATCGTGATGGATGTACTTATGGA 59.508 38.462 0.00 0.00 0.00 3.41
1838 1863 4.104383 TGCTTTTCCTCCTTTGTCAGAT 57.896 40.909 0.00 0.00 0.00 2.90
1856 1881 4.019174 CAGATTATGTGGTTTGGCCTTCT 58.981 43.478 3.32 0.00 38.35 2.85
1859 1884 2.683211 ATGTGGTTTGGCCTTCTCTT 57.317 45.000 3.32 0.00 38.35 2.85
1862 1887 0.850100 TGGTTTGGCCTTCTCTTCCA 59.150 50.000 3.32 0.19 38.35 3.53
1871 1896 4.473196 TGGCCTTCTCTTCCACATATTGTA 59.527 41.667 3.32 0.00 0.00 2.41
1898 1923 0.842467 AGGAGGGAACTGTGGAAGGG 60.842 60.000 0.00 0.00 44.43 3.95
1916 1941 3.053826 AGGGGGAGAAAACTGTAGTGTT 58.946 45.455 0.00 0.00 0.00 3.32
1934 1959 8.812972 TGTAGTGTTTATACAGTTGAATCTCCT 58.187 33.333 0.00 0.00 38.79 3.69
1949 1974 4.703379 ATCTCCTTCTGGATCACCAATC 57.297 45.455 0.00 0.00 46.32 2.67
1971 1996 2.636647 TGACTGCATGAGTGGTGAAA 57.363 45.000 0.00 0.00 33.83 2.69
2014 2039 0.906756 CAGAAGCTGGAGAGGGTGGA 60.907 60.000 0.00 0.00 0.00 4.02
2015 2040 0.617249 AGAAGCTGGAGAGGGTGGAG 60.617 60.000 0.00 0.00 0.00 3.86
2016 2041 0.616111 GAAGCTGGAGAGGGTGGAGA 60.616 60.000 0.00 0.00 0.00 3.71
2042 2067 1.269448 GCGGCAAACAGAATGAGGAAA 59.731 47.619 0.00 0.00 39.69 3.13
2061 2086 5.650703 AGGAAACGTAATTTGGAAGGTATGG 59.349 40.000 0.00 0.00 0.00 2.74
2108 2134 3.966006 TCTCTGCCTTATCTGATTCTGCT 59.034 43.478 0.00 0.00 0.00 4.24
2123 2149 5.934043 TGATTCTGCTATTATATTGCGTGCT 59.066 36.000 0.00 0.00 33.65 4.40
2124 2150 5.596268 TTCTGCTATTATATTGCGTGCTG 57.404 39.130 0.00 0.00 33.65 4.41
2161 2187 3.652057 AATCCCCGATGATGACTTTGT 57.348 42.857 0.00 0.00 0.00 2.83
2175 2201 8.492673 TGATGACTTTGTTACTGTTGATATCC 57.507 34.615 0.00 0.00 0.00 2.59
2190 2216 6.821160 TGTTGATATCCTGCGTGAATTAGAAA 59.179 34.615 0.00 0.00 0.00 2.52
2203 2229 9.856803 GCGTGAATTAGAAATCTCTAGAAATTC 57.143 33.333 13.37 13.37 36.01 2.17
2213 2239 7.615582 AATCTCTAGAAATTCGTTGCATGAA 57.384 32.000 0.00 4.58 0.00 2.57
2255 2284 7.665145 TCACAGAAAATAACTGTCAATGATGGA 59.335 33.333 0.00 0.00 45.15 3.41
2304 2333 5.651612 AACATGGGATGATGATAGTGGAA 57.348 39.130 0.00 0.00 0.00 3.53
2309 2338 7.832685 ACATGGGATGATGATAGTGGAAATATG 59.167 37.037 0.00 0.00 0.00 1.78
2312 2341 6.825721 GGGATGATGATAGTGGAAATATGGAC 59.174 42.308 0.00 0.00 0.00 4.02
2347 2376 7.095695 TCCTGGTTCAGTCTAAAAACAAAAG 57.904 36.000 0.00 0.00 0.00 2.27
2370 2401 6.748132 AGAAAGAAAAATCATCGCAGGAAAA 58.252 32.000 0.00 0.00 0.00 2.29
2376 2407 0.034198 TCATCGCAGGAAAACGGTGA 59.966 50.000 0.00 0.00 46.41 4.02
2378 2409 2.093921 TCATCGCAGGAAAACGGTGATA 60.094 45.455 0.00 0.00 43.95 2.15
2382 2413 3.056678 TCGCAGGAAAACGGTGATAGTTA 60.057 43.478 0.00 0.00 0.00 2.24
2393 2424 6.847421 ACGGTGATAGTTATATCCCCTAAC 57.153 41.667 0.00 0.00 34.66 2.34
2433 2464 5.688348 GACTAGAAGTCAGCACAATAACG 57.312 43.478 0.00 0.00 44.45 3.18
2434 2465 5.386958 ACTAGAAGTCAGCACAATAACGA 57.613 39.130 0.00 0.00 0.00 3.85
2436 2467 4.521130 AGAAGTCAGCACAATAACGAGA 57.479 40.909 0.00 0.00 0.00 4.04
2456 2489 0.104462 TGGGTAGGGCTGCTATGGAT 60.104 55.000 0.00 0.00 0.00 3.41
2476 2509 3.713650 TGGCAGACCTACCAGAGC 58.286 61.111 0.00 0.00 36.63 4.09
2482 2515 0.106918 AGACCTACCAGAGCGAGAGG 60.107 60.000 0.00 0.00 0.00 3.69
2483 2516 0.107116 GACCTACCAGAGCGAGAGGA 60.107 60.000 0.00 0.00 0.00 3.71
2489 2522 0.610687 CCAGAGCGAGAGGAAAACCT 59.389 55.000 0.00 0.00 0.00 3.50
2493 2526 2.368875 AGAGCGAGAGGAAAACCTGAAA 59.631 45.455 0.00 0.00 0.00 2.69
2498 2531 4.330347 GCGAGAGGAAAACCTGAAAGATAC 59.670 45.833 0.00 0.00 34.07 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 2.227089 GAGATGTTCCCACGCGTCCT 62.227 60.000 9.86 0.00 0.00 3.85
88 89 3.402681 CCAGATCCGGTGCTGGGT 61.403 66.667 27.20 0.00 46.24 4.51
141 142 0.779997 AGGTGGGGAAAGTGAAGCAT 59.220 50.000 0.00 0.00 0.00 3.79
142 143 1.073284 GTAGGTGGGGAAAGTGAAGCA 59.927 52.381 0.00 0.00 0.00 3.91
149 150 0.039180 GTTGGGGTAGGTGGGGAAAG 59.961 60.000 0.00 0.00 0.00 2.62
164 167 0.318360 TGTGCGTCTCGTGTAGTTGG 60.318 55.000 0.00 0.00 0.00 3.77
166 169 0.318445 GGTGTGCGTCTCGTGTAGTT 60.318 55.000 0.00 0.00 0.00 2.24
230 233 2.178544 CAGGAGGGGATGAATTGGGAAT 59.821 50.000 0.00 0.00 0.00 3.01
232 235 1.225373 CAGGAGGGGATGAATTGGGA 58.775 55.000 0.00 0.00 0.00 4.37
239 242 2.511218 CAAAGGAATCAGGAGGGGATGA 59.489 50.000 0.00 0.00 0.00 2.92
344 347 2.920912 ACGGTCACCCATCACGGT 60.921 61.111 0.00 0.00 36.18 4.83
379 386 4.147322 GTGTTGTCGCGCCATCCG 62.147 66.667 0.00 0.00 40.75 4.18
406 413 4.444838 CGACCGCCACCGAATCCA 62.445 66.667 0.00 0.00 36.29 3.41
435 442 1.086696 ATGACGAGATTGGTTTGGCG 58.913 50.000 0.00 0.00 0.00 5.69
445 452 3.368843 GCTGCCATACCATATGACGAGAT 60.369 47.826 3.65 0.00 0.00 2.75
517 524 1.361668 CCCATCTGTCCGCAACTTCG 61.362 60.000 0.00 0.00 0.00 3.79
547 554 2.190313 GCATCACTCATGGCCCGA 59.810 61.111 0.00 0.00 32.37 5.14
550 557 2.541120 GCTCGCATCACTCATGGCC 61.541 63.158 0.00 0.00 32.37 5.36
561 568 1.474677 CCATCTTCTCCTTGCTCGCAT 60.475 52.381 0.00 0.00 0.00 4.73
562 569 0.107993 CCATCTTCTCCTTGCTCGCA 60.108 55.000 0.00 0.00 0.00 5.10
567 574 1.821332 CCCGCCATCTTCTCCTTGC 60.821 63.158 0.00 0.00 0.00 4.01
595 602 4.265056 GTTGGTGGTGGAGGCGGT 62.265 66.667 0.00 0.00 0.00 5.68
604 611 0.612732 CATGCCCAGATGTTGGTGGT 60.613 55.000 0.00 0.00 46.25 4.16
607 614 0.612732 CCACATGCCCAGATGTTGGT 60.613 55.000 0.00 0.00 46.25 3.67
611 618 2.438975 CGCCACATGCCCAGATGT 60.439 61.111 0.00 0.00 37.01 3.06
622 629 4.196778 TTGCCCTTGGTCGCCACA 62.197 61.111 0.00 0.00 30.78 4.17
624 631 4.196778 TGTTGCCCTTGGTCGCCA 62.197 61.111 0.00 0.00 0.00 5.69
697 704 3.305897 TGTTACACTTATCGCAGCGAATG 59.694 43.478 23.76 18.96 39.99 2.67
709 716 7.767198 GCCATATGACCTAGTTTGTTACACTTA 59.233 37.037 3.65 0.00 0.00 2.24
712 719 6.113411 AGCCATATGACCTAGTTTGTTACAC 58.887 40.000 3.65 0.00 0.00 2.90
715 722 6.553953 TGAGCCATATGACCTAGTTTGTTA 57.446 37.500 3.65 0.00 0.00 2.41
722 729 4.274459 GCAAAGTTGAGCCATATGACCTAG 59.726 45.833 3.65 0.00 0.00 3.02
766 773 1.613255 CCACACATGAAGGGGGTACAC 60.613 57.143 0.00 0.00 0.00 2.90
769 776 1.451449 AACCACACATGAAGGGGGTA 58.549 50.000 14.19 0.00 0.00 3.69
771 778 1.618343 GAAAACCACACATGAAGGGGG 59.382 52.381 14.19 9.27 0.00 5.40
772 779 2.315176 TGAAAACCACACATGAAGGGG 58.685 47.619 0.00 4.48 0.00 4.79
775 782 5.242393 AGGAGATTGAAAACCACACATGAAG 59.758 40.000 0.00 0.00 0.00 3.02
814 821 7.244886 AGCTGCACACATATCAGGTATATAA 57.755 36.000 1.02 0.00 36.87 0.98
835 842 4.010349 GGTTTTCCACACTATGCTTAGCT 58.990 43.478 5.60 0.00 40.31 3.32
856 864 7.054124 ACTACAGTAATCACCACATTATTGGG 58.946 38.462 0.00 0.00 41.49 4.12
858 866 9.161629 TCAACTACAGTAATCACCACATTATTG 57.838 33.333 0.00 0.00 33.99 1.90
877 885 3.197983 ACAGTAGCATCCCCTTCAACTAC 59.802 47.826 0.00 0.00 0.00 2.73
885 893 3.130734 TCCTTAACAGTAGCATCCCCT 57.869 47.619 0.00 0.00 0.00 4.79
953 963 3.694889 GCAGTACAACGCCATTTCC 57.305 52.632 0.00 0.00 0.00 3.13
975 985 4.141181 ACATATTGAGCAGGGCCAATAGAA 60.141 41.667 6.18 0.00 36.22 2.10
1059 1069 3.633986 CCACAATATTCCCCTCTTTCAGC 59.366 47.826 0.00 0.00 0.00 4.26
1086 1096 2.280628 GAAGCGGTCCAAGGAGTAATG 58.719 52.381 0.00 0.00 0.00 1.90
1101 1111 1.594862 CCTTTAGCTCCAATCGAAGCG 59.405 52.381 0.00 0.00 0.00 4.68
1125 1135 0.955905 TAACCCACGCTTTTTCCAGC 59.044 50.000 0.00 0.00 36.33 4.85
1126 1136 1.539827 CCTAACCCACGCTTTTTCCAG 59.460 52.381 0.00 0.00 0.00 3.86
1137 1147 0.535553 TGTTGCGAACCCTAACCCAC 60.536 55.000 0.00 0.00 0.00 4.61
1173 1183 0.670162 AAGCCACATGTTCAGTGCAC 59.330 50.000 9.40 9.40 35.69 4.57
1197 1207 0.471211 TAATCCCCACTAGAGCCCCG 60.471 60.000 0.00 0.00 0.00 5.73
1242 1252 7.659390 AGAATTCTAGCATACTCTGGTTTATGC 59.341 37.037 6.06 5.60 43.92 3.14
1266 1276 3.920231 ACATCTATGCAGCCAAGAAGA 57.080 42.857 0.00 0.00 0.00 2.87
1278 1288 6.599445 AGGAGGGATTTTCTCAACATCTATG 58.401 40.000 0.00 0.00 33.18 2.23
1280 1290 6.215431 TGAAGGAGGGATTTTCTCAACATCTA 59.785 38.462 0.00 0.00 33.18 1.98
1379 1390 4.333926 CAGCAGTATAGGCTTGACTTTTCC 59.666 45.833 0.00 0.00 40.23 3.13
1390 1401 2.231215 CTGTCCACAGCAGTATAGGC 57.769 55.000 0.00 0.00 37.15 3.93
1419 1430 1.202940 GCTTTCTTGGGGACAGAAGGT 60.203 52.381 0.00 0.00 44.54 3.50
1426 1437 1.821136 CATCCTTGCTTTCTTGGGGAC 59.179 52.381 0.00 0.00 0.00 4.46
1469 1480 4.475444 TAGTCTCCCCCTGCCCCG 62.475 72.222 0.00 0.00 0.00 5.73
1500 1524 5.850046 ATTCCCTTATCATAGTTCTGGGG 57.150 43.478 0.00 0.00 34.27 4.96
1520 1544 1.912043 ACTGCAGGAAGCCTCTGTATT 59.088 47.619 19.93 0.00 44.83 1.89
1523 1547 0.901124 CTACTGCAGGAAGCCTCTGT 59.099 55.000 19.93 0.00 44.83 3.41
1565 1589 3.576982 CTGTGGTGTTACCTTCCTCACTA 59.423 47.826 0.00 0.00 39.58 2.74
1582 1606 3.260740 GTCTCAATCAGAAGCTCTGTGG 58.739 50.000 11.37 4.93 44.58 4.17
1604 1628 1.022735 CTGCATGTTCTCTGGCCATC 58.977 55.000 5.51 0.00 0.00 3.51
1663 1688 5.296780 TCTTCAGTCATTTTGTCACAGGAAC 59.703 40.000 0.00 0.00 0.00 3.62
1667 1692 6.348295 CCAGATCTTCAGTCATTTTGTCACAG 60.348 42.308 0.00 0.00 0.00 3.66
1673 1698 8.202811 TCTCTATCCAGATCTTCAGTCATTTTG 58.797 37.037 0.00 0.00 0.00 2.44
1676 1701 7.729431 TCATCTCTATCCAGATCTTCAGTCATT 59.271 37.037 0.00 0.00 30.07 2.57
1679 1704 7.523293 TTCATCTCTATCCAGATCTTCAGTC 57.477 40.000 0.00 0.00 30.07 3.51
1680 1705 7.911130 TTTCATCTCTATCCAGATCTTCAGT 57.089 36.000 0.00 0.00 30.07 3.41
1717 1742 3.148412 TGTATGCTGTTCACATTGCTGT 58.852 40.909 0.00 0.00 35.44 4.40
1721 1746 6.748658 CACCTTTATGTATGCTGTTCACATTG 59.251 38.462 0.00 0.00 34.78 2.82
1726 1751 4.588899 AGCACCTTTATGTATGCTGTTCA 58.411 39.130 0.00 0.00 46.42 3.18
1733 1758 2.958355 CCCCCAAGCACCTTTATGTATG 59.042 50.000 0.00 0.00 0.00 2.39
1767 1792 3.903530 AAACAAAGGTGAGGGAGGAAT 57.096 42.857 0.00 0.00 0.00 3.01
1772 1797 5.046159 ACGATACATAAACAAAGGTGAGGGA 60.046 40.000 0.00 0.00 0.00 4.20
1792 1817 6.419484 TTCCATAAGTACATCCATCACGAT 57.581 37.500 0.00 0.00 0.00 3.73
1795 1820 6.488006 AGCATTTCCATAAGTACATCCATCAC 59.512 38.462 0.00 0.00 0.00 3.06
1814 1839 4.895297 TCTGACAAAGGAGGAAAAGCATTT 59.105 37.500 0.00 0.00 42.41 2.32
1829 1854 4.021544 GGCCAAACCACATAATCTGACAAA 60.022 41.667 0.00 0.00 38.86 2.83
1838 1863 3.806949 AGAGAAGGCCAAACCACATAA 57.193 42.857 5.01 0.00 43.14 1.90
1856 1881 6.127054 CCTCAAGAGGTACAATATGTGGAAGA 60.127 42.308 7.98 0.00 43.61 2.87
1859 1884 5.614324 CCTCAAGAGGTACAATATGTGGA 57.386 43.478 7.98 0.00 43.61 4.02
1887 1912 1.145119 GTTTTCTCCCCCTTCCACAGT 59.855 52.381 0.00 0.00 0.00 3.55
1889 1914 1.144913 CAGTTTTCTCCCCCTTCCACA 59.855 52.381 0.00 0.00 0.00 4.17
1898 1923 8.252964 CTGTATAAACACTACAGTTTTCTCCC 57.747 38.462 0.00 0.00 41.58 4.30
1916 1941 7.733773 TCCAGAAGGAGATTCAACTGTATAA 57.266 36.000 0.00 0.00 39.61 0.98
1967 1992 5.007034 TGTCTGTGTGAAACTTCCTTTTCA 58.993 37.500 0.00 0.00 42.04 2.69
1971 1996 4.487714 TCTGTCTGTGTGAAACTTCCTT 57.512 40.909 0.00 0.00 38.04 3.36
2008 2033 2.438434 CCGCCACATTCTCCACCC 60.438 66.667 0.00 0.00 0.00 4.61
2014 2039 0.537143 TCTGTTTGCCGCCACATTCT 60.537 50.000 0.00 0.00 0.00 2.40
2015 2040 0.313672 TTCTGTTTGCCGCCACATTC 59.686 50.000 0.00 0.00 0.00 2.67
2016 2041 0.968405 ATTCTGTTTGCCGCCACATT 59.032 45.000 0.00 0.00 0.00 2.71
2042 2067 9.886132 GATATATCCATACCTTCCAAATTACGT 57.114 33.333 0.81 0.00 0.00 3.57
2108 2134 4.881920 TCAGAGCAGCACGCAATATAATA 58.118 39.130 0.00 0.00 46.13 0.98
2123 2149 0.401356 TTTGCACTCCCATCAGAGCA 59.599 50.000 0.00 0.00 38.10 4.26
2124 2150 1.674962 GATTTGCACTCCCATCAGAGC 59.325 52.381 0.00 0.00 37.39 4.09
2147 2173 6.466308 TCAACAGTAACAAAGTCATCATCG 57.534 37.500 0.00 0.00 0.00 3.84
2161 2187 4.729227 TCACGCAGGATATCAACAGTAA 57.271 40.909 4.83 0.00 0.00 2.24
2175 2201 7.993821 TTCTAGAGATTTCTAATTCACGCAG 57.006 36.000 0.00 0.00 35.55 5.18
2190 2216 7.615582 TTTCATGCAACGAATTTCTAGAGAT 57.384 32.000 0.00 0.00 0.00 2.75
2223 2252 9.846248 ATTGACAGTTATTTTCTGTGAATTAGC 57.154 29.630 3.29 0.00 43.28 3.09
2255 2284 1.575304 AGGGGCACATCATTACCCAAT 59.425 47.619 0.00 0.00 44.76 3.16
2347 2376 6.398935 CGTTTTCCTGCGATGATTTTTCTTTC 60.399 38.462 0.00 0.00 0.00 2.62
2376 2407 8.017251 ACTGGACTTGTTAGGGGATATAACTAT 58.983 37.037 0.00 0.00 34.80 2.12
2378 2409 6.210522 ACTGGACTTGTTAGGGGATATAACT 58.789 40.000 0.00 0.00 34.80 2.24
2382 2413 5.839606 GTCTACTGGACTTGTTAGGGGATAT 59.160 44.000 0.00 0.00 41.46 1.63
2426 2457 2.368875 AGCCCTACCCATCTCGTTATTG 59.631 50.000 0.00 0.00 0.00 1.90
2429 2460 1.410004 CAGCCCTACCCATCTCGTTA 58.590 55.000 0.00 0.00 0.00 3.18
2432 2463 0.827925 TAGCAGCCCTACCCATCTCG 60.828 60.000 0.00 0.00 0.00 4.04
2433 2464 1.277557 CATAGCAGCCCTACCCATCTC 59.722 57.143 0.00 0.00 0.00 2.75
2434 2465 1.356124 CATAGCAGCCCTACCCATCT 58.644 55.000 0.00 0.00 0.00 2.90
2436 2467 0.104462 TCCATAGCAGCCCTACCCAT 60.104 55.000 0.00 0.00 0.00 4.00
2482 2515 9.196552 CCTTTCATTTGTATCTTTCAGGTTTTC 57.803 33.333 0.00 0.00 0.00 2.29
2483 2516 8.150296 CCCTTTCATTTGTATCTTTCAGGTTTT 58.850 33.333 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.