Multiple sequence alignment - TraesCS1B01G083600

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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 TraesCS1B01G083600 chr1B 100.000 2468 0 0 1 2468 67541950 67539483 0.000000e+00 4558.0
1 TraesCS1B01G083600 chr1B 97.647 85 1 1 302 386 427472241 427472158 7.110000e-31 145.0
2 TraesCS1B01G083600 chr1B 96.512 86 3 0 301 386 427468757 427468672 2.560000e-30 143.0
3 TraesCS1B01G083600 chr1D 93.144 846 24 4 1650 2468 47879320 47878482 0.000000e+00 1210.0
4 TraesCS1B01G083600 chr1D 91.370 533 23 10 867 1385 47879966 47879443 0.000000e+00 708.0
5 TraesCS1B01G083600 chr1D 87.791 516 36 10 302 813 47880472 47879980 1.650000e-161 579.0
6 TraesCS1B01G083600 chr1D 97.619 84 2 0 303 386 315607965 315607882 7.110000e-31 145.0
7 TraesCS1B01G083600 chr1D 92.391 92 4 1 129 220 47880769 47880681 7.160000e-26 128.0
8 TraesCS1B01G083600 chr1D 82.270 141 9 7 1431 1557 47879444 47879306 9.330000e-20 108.0
9 TraesCS1B01G083600 chr1D 95.238 42 1 1 223 264 47880649 47880609 5.700000e-07 65.8
10 TraesCS1B01G083600 chr1D 93.478 46 0 3 220 265 47933139 47933097 5.700000e-07 65.8
11 TraesCS1B01G083600 chr1D 100.000 30 0 0 191 220 47933217 47933188 3.430000e-04 56.5
12 TraesCS1B01G083600 chr1A 92.234 837 33 7 1653 2468 47805689 47804864 0.000000e+00 1157.0
13 TraesCS1B01G083600 chr1A 85.538 1051 65 43 489 1490 47806788 47805776 0.000000e+00 1018.0
14 TraesCS1B01G083600 chr1A 90.179 224 15 3 3 220 47812982 47812760 4.020000e-73 285.0
15 TraesCS1B01G083600 chr1A 89.545 220 16 5 3 220 47812494 47812280 3.130000e-69 272.0
16 TraesCS1B01G083600 chr1A 87.500 152 14 4 302 451 47806939 47806791 1.170000e-38 171.0
17 TraesCS1B01G083600 chr5D 87.567 563 27 15 1922 2468 371468823 371468288 1.620000e-171 612.0
18 TraesCS1B01G083600 chr5D 91.262 103 5 3 302 401 539481252 539481151 1.190000e-28 137.0
19 TraesCS1B01G083600 chr5A 93.684 285 15 3 1922 2205 427869994 427869712 8.160000e-115 424.0
20 TraesCS1B01G083600 chr5A 88.298 94 7 3 1554 1645 299619419 299619328 2.590000e-20 110.0
21 TraesCS1B01G083600 chr5A 92.647 68 4 1 2040 2106 474540958 474540891 2.020000e-16 97.1
22 TraesCS1B01G083600 chr5A 94.231 52 2 1 2257 2307 474540690 474540639 7.320000e-11 78.7
23 TraesCS1B01G083600 chr5A 97.561 41 0 1 2428 2468 474540456 474540417 4.400000e-08 69.4
24 TraesCS1B01G083600 chr3B 96.629 89 3 0 302 390 617415055 617414967 5.500000e-32 148.0
25 TraesCS1B01G083600 chr3B 94.444 90 4 1 297 385 659068019 659068108 1.190000e-28 137.0
26 TraesCS1B01G083600 chr7D 95.506 89 4 0 298 386 590446690 590446778 2.560000e-30 143.0
27 TraesCS1B01G083600 chr4A 88.506 87 9 1 1561 1647 565745686 565745601 1.210000e-18 104.0


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 TraesCS1B01G083600 chr1B 67539483 67541950 2467 True 4558.000000 4558 100.000000 1 2468 1 chr1B.!!$R1 2467
1 TraesCS1B01G083600 chr1D 47878482 47880769 2287 True 466.466667 1210 90.367333 129 2468 6 chr1D.!!$R2 2339
2 TraesCS1B01G083600 chr1A 47804864 47806939 2075 True 782.000000 1157 88.424000 302 2468 3 chr1A.!!$R1 2166
3 TraesCS1B01G083600 chr1A 47812280 47812982 702 True 278.500000 285 89.862000 3 220 2 chr1A.!!$R2 217
4 TraesCS1B01G083600 chr5D 371468288 371468823 535 True 612.000000 612 87.567000 1922 2468 1 chr5D.!!$R1 546

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
904 1080 0.105778 CGAATTCCTCTCCCTCTGGC 59.894 60.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 1993 0.921896 AATACCATGGCTCTGTGGCT 59.078 50.0 13.04 0.0 42.34 4.75 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
124 126 8.761575 ATGAAGTAATTTGCCTTTGTAACATG 57.238 30.769 0.00 0.00 0.00 3.21
281 381 4.036380 TGTGTGTGTACATATCTAGGCTCG 59.964 45.833 0.00 0.00 39.39 5.03
298 398 6.385649 AGGCTCGTTTGTATTTTCTTTCAA 57.614 33.333 0.00 0.00 0.00 2.69
300 400 5.629435 GGCTCGTTTGTATTTTCTTTCAAGG 59.371 40.000 0.00 0.00 0.00 3.61
303 403 7.434013 GCTCGTTTGTATTTTCTTTCAAGGAAA 59.566 33.333 0.00 0.00 37.87 3.13
304 404 9.296400 CTCGTTTGTATTTTCTTTCAAGGAAAA 57.704 29.630 9.64 9.64 43.65 2.29
305 405 9.640963 TCGTTTGTATTTTCTTTCAAGGAAAAA 57.359 25.926 11.10 2.47 43.06 1.94
405 561 4.734402 GCTTTGTGTCACTTGCTTCATTCA 60.734 41.667 4.27 0.00 0.00 2.57
407 563 2.287644 TGTGTCACTTGCTTCATTCACG 59.712 45.455 4.27 0.00 0.00 4.35
408 564 1.872952 TGTCACTTGCTTCATTCACGG 59.127 47.619 0.00 0.00 0.00 4.94
409 565 0.874390 TCACTTGCTTCATTCACGGC 59.126 50.000 0.00 0.00 0.00 5.68
417 573 6.369890 ACTTGCTTCATTCACGGCTATATATG 59.630 38.462 0.00 0.00 0.00 1.78
418 574 5.793817 TGCTTCATTCACGGCTATATATGT 58.206 37.500 0.00 0.00 0.00 2.29
423 579 8.926715 TTCATTCACGGCTATATATGTGATAC 57.073 34.615 11.26 0.00 40.67 2.24
425 581 7.973944 TCATTCACGGCTATATATGTGATACAC 59.026 37.037 11.26 0.00 40.67 2.90
438 594 3.957497 TGTGATACACCAAACAAAAGCCT 59.043 39.130 0.00 0.00 32.73 4.58
445 601 2.695147 ACCAAACAAAAGCCTTCCTCTG 59.305 45.455 0.00 0.00 0.00 3.35
451 607 0.621082 AAAGCCTTCCTCTGCCTACC 59.379 55.000 0.00 0.00 0.00 3.18
452 608 0.252927 AAGCCTTCCTCTGCCTACCT 60.253 55.000 0.00 0.00 0.00 3.08
454 610 0.753867 GCCTTCCTCTGCCTACCTAC 59.246 60.000 0.00 0.00 0.00 3.18
456 612 1.033574 CTTCCTCTGCCTACCTACCG 58.966 60.000 0.00 0.00 0.00 4.02
457 613 0.627451 TTCCTCTGCCTACCTACCGA 59.373 55.000 0.00 0.00 0.00 4.69
458 614 0.183014 TCCTCTGCCTACCTACCGAG 59.817 60.000 0.00 0.00 0.00 4.63
459 615 1.457009 CCTCTGCCTACCTACCGAGC 61.457 65.000 0.00 0.00 0.00 5.03
461 617 0.465824 TCTGCCTACCTACCGAGCTC 60.466 60.000 2.73 2.73 0.00 4.09
491 647 1.062440 TCAATTATCAGCGTGCAAGCG 59.938 47.619 18.93 13.60 43.00 4.68
495 651 1.078201 TATCAGCGTGCAAGCGAGTG 61.078 55.000 18.93 12.07 43.00 3.51
504 660 3.722082 CGTGCAAGCGAGTGATTAGTTTC 60.722 47.826 0.00 0.00 0.00 2.78
511 668 7.059602 GCAAGCGAGTGATTAGTTTCTTTTAAC 59.940 37.037 0.00 0.00 0.00 2.01
543 700 3.118519 TCCTTCCATTACTTAACCTCGCC 60.119 47.826 0.00 0.00 0.00 5.54
613 777 6.043243 TCCTTTCCACCAGGATATCATTAGTC 59.957 42.308 4.83 0.00 45.26 2.59
652 816 9.671279 CCATTCATGCATTATTATACTACTCCA 57.329 33.333 0.00 0.00 0.00 3.86
722 893 0.666274 TTGTCGCGTAGAGGCACAAG 60.666 55.000 5.77 0.00 44.70 3.16
732 903 3.660111 GGCACAAGCGGCGAAAGT 61.660 61.111 12.98 1.07 43.41 2.66
805 981 4.449068 CAGGTAGTGCTGCTAATAATTCCG 59.551 45.833 0.00 0.00 0.00 4.30
865 1041 0.666577 CTGCAAGCAGAAAAGGCAGC 60.667 55.000 16.75 0.00 46.30 5.25
890 1066 4.549458 CTGTTTGTGATTGCTTCCGAATT 58.451 39.130 0.00 0.00 0.00 2.17
892 1068 3.848272 TTGTGATTGCTTCCGAATTCC 57.152 42.857 0.00 0.00 0.00 3.01
904 1080 0.105778 CGAATTCCTCTCCCTCTGGC 59.894 60.000 0.00 0.00 0.00 4.85
1070 1265 6.146184 CACACGATCCGATTATATCTTGCTTT 59.854 38.462 0.00 0.00 0.00 3.51
1085 1280 4.837972 CTTGCTTTAAGAGGAAGGTAGCT 58.162 43.478 0.00 0.00 46.63 3.32
1086 1281 4.207891 TGCTTTAAGAGGAAGGTAGCTG 57.792 45.455 0.00 0.00 0.00 4.24
1087 1282 3.055094 TGCTTTAAGAGGAAGGTAGCTGG 60.055 47.826 0.00 0.00 0.00 4.85
1088 1283 3.197983 GCTTTAAGAGGAAGGTAGCTGGA 59.802 47.826 0.00 0.00 0.00 3.86
1089 1284 4.682050 GCTTTAAGAGGAAGGTAGCTGGAG 60.682 50.000 0.00 0.00 0.00 3.86
1174 1373 1.078918 CATGTGCGGCAGGAGAAGA 60.079 57.895 1.18 0.00 0.00 2.87
1209 1408 1.286880 CCAACAAGAAGCCGCCAAG 59.713 57.895 0.00 0.00 0.00 3.61
1238 1455 2.479730 CCGTGAAGAGTATCGGTGAAGG 60.480 54.545 0.00 0.00 42.67 3.46
1242 1459 4.339814 GTGAAGAGTATCGGTGAAGGAGAT 59.660 45.833 0.00 0.00 42.67 2.75
1251 1468 5.521906 TCGGTGAAGGAGATAAGATCAAG 57.478 43.478 0.00 0.00 0.00 3.02
1383 1600 1.067915 GCTGTGCGTCTTCTCTTCTCT 60.068 52.381 0.00 0.00 0.00 3.10
1384 1601 2.594321 CTGTGCGTCTTCTCTTCTCTG 58.406 52.381 0.00 0.00 0.00 3.35
1385 1602 1.957177 TGTGCGTCTTCTCTTCTCTGT 59.043 47.619 0.00 0.00 0.00 3.41
1424 1641 7.377131 GCTTGATTTGAGAGTTTAGTTTGTGTC 59.623 37.037 0.00 0.00 0.00 3.67
1426 1643 8.142994 TGATTTGAGAGTTTAGTTTGTGTCTC 57.857 34.615 0.00 0.00 0.00 3.36
1427 1644 7.987458 TGATTTGAGAGTTTAGTTTGTGTCTCT 59.013 33.333 0.00 0.00 35.41 3.10
1428 1645 7.539712 TTTGAGAGTTTAGTTTGTGTCTCTG 57.460 36.000 0.00 0.00 33.31 3.35
1429 1646 6.465439 TGAGAGTTTAGTTTGTGTCTCTGA 57.535 37.500 0.00 0.00 33.31 3.27
1490 1707 8.072567 GGAAATAAAGATGTGTGCTCATATGTC 58.927 37.037 2.52 0.00 0.00 3.06
1502 1727 3.614092 CTCATATGTCCCACAAGCTTGT 58.386 45.455 26.36 26.36 43.36 3.16
1542 1773 7.445402 ACAATCAAATATATAGTCCAGCCACAC 59.555 37.037 0.00 0.00 0.00 3.82
1543 1774 6.493189 TCAAATATATAGTCCAGCCACACA 57.507 37.500 0.00 0.00 0.00 3.72
1544 1775 7.078249 TCAAATATATAGTCCAGCCACACAT 57.922 36.000 0.00 0.00 0.00 3.21
1545 1776 7.517320 TCAAATATATAGTCCAGCCACACATT 58.483 34.615 0.00 0.00 0.00 2.71
1546 1777 7.998383 TCAAATATATAGTCCAGCCACACATTT 59.002 33.333 0.00 0.00 0.00 2.32
1552 1783 4.215109 AGTCCAGCCACACATTTAAAACT 58.785 39.130 0.00 0.00 0.00 2.66
1553 1784 4.037923 AGTCCAGCCACACATTTAAAACTG 59.962 41.667 0.00 0.00 0.00 3.16
1556 1787 5.105146 TCCAGCCACACATTTAAAACTGTTT 60.105 36.000 0.00 0.00 0.00 2.83
1560 1791 7.064490 CAGCCACACATTTAAAACTGTTTTTCT 59.936 33.333 22.07 6.38 36.32 2.52
1580 1811 3.694734 CTTTTGACGAAAAAGCAGCAGA 58.305 40.909 12.70 0.00 46.13 4.26
1581 1812 3.988379 TTTGACGAAAAAGCAGCAGAT 57.012 38.095 0.00 0.00 0.00 2.90
1582 1813 3.988379 TTGACGAAAAAGCAGCAGATT 57.012 38.095 0.00 0.00 0.00 2.40
1583 1814 3.272439 TGACGAAAAAGCAGCAGATTG 57.728 42.857 0.00 0.00 0.00 2.67
1584 1815 1.981533 GACGAAAAAGCAGCAGATTGC 59.018 47.619 0.00 0.00 45.46 3.56
1600 1831 7.997107 GCAGATTGCTGATTTTCATTGATAA 57.003 32.000 0.00 0.00 45.17 1.75
1601 1832 8.415192 GCAGATTGCTGATTTTCATTGATAAA 57.585 30.769 0.00 0.00 45.17 1.40
1602 1833 8.540492 GCAGATTGCTGATTTTCATTGATAAAG 58.460 33.333 0.00 0.00 45.17 1.85
1603 1834 9.582431 CAGATTGCTGATTTTCATTGATAAAGT 57.418 29.630 0.00 0.00 45.17 2.66
1604 1835 9.582431 AGATTGCTGATTTTCATTGATAAAGTG 57.418 29.630 0.00 0.00 0.00 3.16
1605 1836 8.712285 ATTGCTGATTTTCATTGATAAAGTGG 57.288 30.769 0.00 0.00 0.00 4.00
1606 1837 7.230849 TGCTGATTTTCATTGATAAAGTGGT 57.769 32.000 0.00 0.00 0.00 4.16
1607 1838 8.347004 TGCTGATTTTCATTGATAAAGTGGTA 57.653 30.769 0.00 0.00 0.00 3.25
1608 1839 8.461222 TGCTGATTTTCATTGATAAAGTGGTAG 58.539 33.333 0.00 0.00 0.00 3.18
1609 1840 8.677300 GCTGATTTTCATTGATAAAGTGGTAGA 58.323 33.333 0.00 0.00 0.00 2.59
1620 1851 9.841295 TTGATAAAGTGGTAGAAGTAAACAGTT 57.159 29.630 0.00 0.00 0.00 3.16
1624 1855 8.658499 AAAGTGGTAGAAGTAAACAGTTACAG 57.342 34.615 0.00 0.00 41.88 2.74
1625 1856 6.756221 AGTGGTAGAAGTAAACAGTTACAGG 58.244 40.000 0.00 0.00 41.88 4.00
1626 1857 5.407691 GTGGTAGAAGTAAACAGTTACAGGC 59.592 44.000 0.00 0.00 41.88 4.85
1627 1858 4.934001 GGTAGAAGTAAACAGTTACAGGCC 59.066 45.833 0.00 0.00 41.88 5.19
1628 1859 4.699925 AGAAGTAAACAGTTACAGGCCA 57.300 40.909 5.01 0.00 41.88 5.36
1629 1860 4.386711 AGAAGTAAACAGTTACAGGCCAC 58.613 43.478 5.01 0.00 41.88 5.01
1630 1861 4.102681 AGAAGTAAACAGTTACAGGCCACT 59.897 41.667 5.01 0.00 41.88 4.00
1643 1874 3.312736 AGGCCACTGAAAGGAAAAGAA 57.687 42.857 5.01 0.00 39.30 2.52
1644 1875 3.642141 AGGCCACTGAAAGGAAAAGAAA 58.358 40.909 5.01 0.00 39.30 2.52
1645 1876 4.030216 AGGCCACTGAAAGGAAAAGAAAA 58.970 39.130 5.01 0.00 39.30 2.29
1646 1877 4.469586 AGGCCACTGAAAGGAAAAGAAAAA 59.530 37.500 5.01 0.00 39.30 1.94
1647 1878 4.811024 GGCCACTGAAAGGAAAAGAAAAAG 59.189 41.667 0.00 0.00 39.30 2.27
1648 1879 5.419542 GCCACTGAAAGGAAAAGAAAAAGT 58.580 37.500 0.00 0.00 39.30 2.66
1722 1976 4.530161 ACTAGAAGATGCAGGAACAGAGTT 59.470 41.667 0.00 0.00 0.00 3.01
1723 1977 4.363991 AGAAGATGCAGGAACAGAGTTT 57.636 40.909 0.00 0.00 0.00 2.66
1724 1978 4.723309 AGAAGATGCAGGAACAGAGTTTT 58.277 39.130 0.00 0.00 0.00 2.43
1725 1979 5.136105 AGAAGATGCAGGAACAGAGTTTTT 58.864 37.500 0.00 0.00 0.00 1.94
1763 2023 2.424601 CACAGAGCCATGGTATTGGTTG 59.575 50.000 14.67 5.43 39.11 3.77
1836 2108 0.104672 TCCTGAACTTCCACTCCCCA 60.105 55.000 0.00 0.00 0.00 4.96
1877 2149 2.096496 CGAATTCAGCGCCATTCTTCTT 59.904 45.455 17.66 0.00 0.00 2.52
1900 2172 1.645455 CATTGCGCCAGAATCTCCG 59.355 57.895 4.18 0.00 0.00 4.63
1911 2183 3.889538 CCAGAATCTCCGTATACCTGTCA 59.110 47.826 0.00 0.00 0.00 3.58
2250 2522 1.819903 GCCTTATAGAGCCGAGGTAGG 59.180 57.143 0.00 0.00 0.00 3.18
2267 2539 2.666272 AGGACACTCTCACTCACAGA 57.334 50.000 0.00 0.00 0.00 3.41
2271 2543 0.109365 CACTCTCACTCACAGAGGCG 60.109 60.000 1.96 0.00 41.66 5.52
2344 2631 0.404040 TTTCTGTTCCCCAGCGGATT 59.596 50.000 0.00 0.00 41.63 3.01
2379 2666 7.041098 GGTGAACAAGATGTCAGTAACTCAATT 60.041 37.037 0.00 0.00 0.00 2.32
2389 2676 9.783081 ATGTCAGTAACTCAATTGCATATATCA 57.217 29.630 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.425577 AAAACCTGAACGATGATTGAGC 57.574 40.909 0.00 0.00 0.00 4.26
63 64 9.487790 TTTGGTCCAATGTAGAATTGATTTTTC 57.512 29.630 4.80 0.00 0.00 2.29
137 139 6.870971 TTGCGTATTTGACCTTAAAACTCT 57.129 33.333 0.00 0.00 0.00 3.24
148 150 6.853872 TGTTCTTGTGTATTTGCGTATTTGAC 59.146 34.615 0.00 0.00 0.00 3.18
220 227 9.944376 AATGTCACTCTAACACATGTACTATTT 57.056 29.630 0.00 0.00 31.00 1.40
265 318 8.813643 AAATACAAACGAGCCTAGATATGTAC 57.186 34.615 0.00 0.00 0.00 2.90
271 371 7.606456 TGAAAGAAAATACAAACGAGCCTAGAT 59.394 33.333 0.00 0.00 0.00 1.98
272 372 6.932400 TGAAAGAAAATACAAACGAGCCTAGA 59.068 34.615 0.00 0.00 0.00 2.43
298 398 2.443416 GGTGGGCGATTACTTTTTCCT 58.557 47.619 0.00 0.00 0.00 3.36
300 400 1.808343 ACGGTGGGCGATTACTTTTTC 59.192 47.619 0.00 0.00 0.00 2.29
303 403 0.675522 CCACGGTGGGCGATTACTTT 60.676 55.000 19.63 0.00 32.67 2.66
304 404 1.078708 CCACGGTGGGCGATTACTT 60.079 57.895 19.63 0.00 32.67 2.24
305 405 2.582436 CCACGGTGGGCGATTACT 59.418 61.111 19.63 0.00 32.67 2.24
359 515 3.011119 CGTCTAGCTCAGTTGGTAGAGT 58.989 50.000 0.00 0.00 44.42 3.24
405 561 6.599356 TTGGTGTATCACATATATAGCCGT 57.401 37.500 2.41 0.00 35.86 5.68
407 563 8.615878 TTGTTTGGTGTATCACATATATAGCC 57.384 34.615 2.41 0.00 35.86 3.93
417 573 4.584327 AGGCTTTTGTTTGGTGTATCAC 57.416 40.909 0.00 0.00 0.00 3.06
418 574 4.038642 GGAAGGCTTTTGTTTGGTGTATCA 59.961 41.667 0.00 0.00 0.00 2.15
423 579 2.695147 AGAGGAAGGCTTTTGTTTGGTG 59.305 45.455 0.00 0.00 0.00 4.17
425 581 2.546584 GCAGAGGAAGGCTTTTGTTTGG 60.547 50.000 0.00 0.00 0.00 3.28
438 594 0.627451 TCGGTAGGTAGGCAGAGGAA 59.373 55.000 0.00 0.00 0.00 3.36
445 601 0.386113 CTTGAGCTCGGTAGGTAGGC 59.614 60.000 9.64 0.00 32.30 3.93
451 607 1.079503 GCAAACCTTGAGCTCGGTAG 58.920 55.000 13.02 10.20 32.07 3.18
452 608 0.685097 AGCAAACCTTGAGCTCGGTA 59.315 50.000 13.02 0.00 32.05 4.02
454 610 2.166270 GAGCAAACCTTGAGCTCGG 58.834 57.895 9.64 7.71 44.37 4.63
457 613 5.012239 TGATAATTGAGCAAACCTTGAGCT 58.988 37.500 0.00 0.00 42.17 4.09
458 614 5.314923 TGATAATTGAGCAAACCTTGAGC 57.685 39.130 0.00 0.00 0.00 4.26
459 615 5.338365 GCTGATAATTGAGCAAACCTTGAG 58.662 41.667 0.00 0.00 35.15 3.02
461 617 4.100529 CGCTGATAATTGAGCAAACCTTG 58.899 43.478 0.00 0.00 34.69 3.61
491 647 8.617290 TCCAGGTTAAAAGAAACTAATCACTC 57.383 34.615 0.00 0.00 0.00 3.51
543 700 1.250328 TGCTTTGGTGATTCTGCTGG 58.750 50.000 0.00 0.00 0.00 4.85
582 746 1.850345 TCCTGGTGGAAAGGAACAACT 59.150 47.619 0.00 0.00 40.95 3.16
583 747 2.358322 TCCTGGTGGAAAGGAACAAC 57.642 50.000 0.00 0.00 40.95 3.32
584 748 4.290985 TGATATCCTGGTGGAAAGGAACAA 59.709 41.667 0.00 0.00 46.76 2.83
652 816 6.143496 CACTGACGCGTCTATATTTGTCTAT 58.857 40.000 36.27 6.98 0.00 1.98
722 893 4.404654 CTGCCCAACTTTCGCCGC 62.405 66.667 0.00 0.00 0.00 6.53
792 968 2.634600 ACGGTTGCGGAATTATTAGCA 58.365 42.857 0.00 3.98 37.89 3.49
793 969 3.685836 AACGGTTGCGGAATTATTAGC 57.314 42.857 0.00 0.00 0.00 3.09
794 970 4.496840 GGGAAACGGTTGCGGAATTATTAG 60.497 45.833 0.00 0.00 0.00 1.73
795 971 3.377798 GGGAAACGGTTGCGGAATTATTA 59.622 43.478 0.00 0.00 0.00 0.98
805 981 4.700365 GCTGCGGGAAACGGTTGC 62.700 66.667 0.00 0.00 44.51 4.17
848 1024 1.373873 GGCTGCCTTTTCTGCTTGC 60.374 57.895 12.43 0.00 0.00 4.01
849 1025 1.080974 CGGCTGCCTTTTCTGCTTG 60.081 57.895 17.92 0.00 0.00 4.01
850 1026 2.924105 GCGGCTGCCTTTTCTGCTT 61.924 57.895 17.92 0.00 33.98 3.91
852 1028 3.368571 AGCGGCTGCCTTTTCTGC 61.369 61.111 15.55 11.43 44.31 4.26
853 1029 1.799258 AACAGCGGCTGCCTTTTCTG 61.799 55.000 28.80 18.40 44.31 3.02
854 1030 1.109323 AAACAGCGGCTGCCTTTTCT 61.109 50.000 28.80 5.52 44.31 2.52
855 1031 0.940991 CAAACAGCGGCTGCCTTTTC 60.941 55.000 28.80 3.15 44.31 2.29
865 1041 1.666888 GGAAGCAATCACAAACAGCGG 60.667 52.381 0.00 0.00 0.00 5.52
890 1066 2.043852 GTCGCCAGAGGGAGAGGA 60.044 66.667 0.00 0.00 44.15 3.71
892 1068 2.716017 GGTGTCGCCAGAGGGAGAG 61.716 68.421 0.00 0.00 44.15 3.20
904 1080 2.048023 TGGTAGGCGGTAGGTGTCG 61.048 63.158 0.00 0.00 0.00 4.35
1070 1265 3.759815 ACTCCAGCTACCTTCCTCTTA 57.240 47.619 0.00 0.00 0.00 2.10
1085 1280 1.908619 TGAAAGATGCAGGCTACTCCA 59.091 47.619 0.00 0.00 37.29 3.86
1086 1281 2.559440 CTGAAAGATGCAGGCTACTCC 58.441 52.381 0.00 0.00 34.07 3.85
1087 1282 1.939255 GCTGAAAGATGCAGGCTACTC 59.061 52.381 0.00 0.00 34.07 2.59
1088 1283 1.558756 AGCTGAAAGATGCAGGCTACT 59.441 47.619 0.00 0.00 34.07 2.57
1089 1284 1.669779 CAGCTGAAAGATGCAGGCTAC 59.330 52.381 8.42 0.00 46.61 3.58
1174 1373 0.982852 TGGTTGATCCTCTGCCGGAT 60.983 55.000 5.05 0.00 46.28 4.18
1209 1408 3.682921 GATACTCTTCACGGTCGTCTTC 58.317 50.000 0.00 0.00 0.00 2.87
1238 1455 7.902403 CGCAGTTTTTCTTCTTGATCTTATCTC 59.098 37.037 0.00 0.00 0.00 2.75
1242 1459 6.706270 AGTCGCAGTTTTTCTTCTTGATCTTA 59.294 34.615 0.00 0.00 0.00 2.10
1251 1468 3.498397 TCCATGAGTCGCAGTTTTTCTTC 59.502 43.478 0.00 0.00 0.00 2.87
1365 1582 1.957177 ACAGAGAAGAGAAGACGCACA 59.043 47.619 0.00 0.00 0.00 4.57
1366 1583 2.715737 ACAGAGAAGAGAAGACGCAC 57.284 50.000 0.00 0.00 0.00 5.34
1406 1623 6.465439 TCAGAGACACAAACTAAACTCTCA 57.535 37.500 0.00 0.00 33.35 3.27
1426 1643 7.093354 TGAGACAAGCTAAAACTACTCATCAG 58.907 38.462 0.00 0.00 0.00 2.90
1427 1644 6.993079 TGAGACAAGCTAAAACTACTCATCA 58.007 36.000 0.00 0.00 0.00 3.07
1428 1645 7.815068 TCTTGAGACAAGCTAAAACTACTCATC 59.185 37.037 6.62 0.00 34.07 2.92
1429 1646 7.671302 TCTTGAGACAAGCTAAAACTACTCAT 58.329 34.615 6.62 0.00 34.07 2.90
1511 1736 9.419297 GCTGGACTATATATTTGATTGTTCGTA 57.581 33.333 0.00 0.00 0.00 3.43
1514 1745 8.507249 GTGGCTGGACTATATATTTGATTGTTC 58.493 37.037 0.00 0.00 0.00 3.18
1529 1760 5.240623 CAGTTTTAAATGTGTGGCTGGACTA 59.759 40.000 0.00 0.00 0.00 2.59
1530 1761 4.037923 CAGTTTTAAATGTGTGGCTGGACT 59.962 41.667 0.00 0.00 0.00 3.85
1531 1762 4.202111 ACAGTTTTAAATGTGTGGCTGGAC 60.202 41.667 2.90 0.00 35.69 4.02
1560 1791 3.773860 TCTGCTGCTTTTTCGTCAAAA 57.226 38.095 0.00 0.00 33.12 2.44
1563 1794 2.605338 GCAATCTGCTGCTTTTTCGTCA 60.605 45.455 0.00 0.00 40.96 4.35
1576 1807 7.997107 TTATCAATGAAAATCAGCAATCTGC 57.003 32.000 0.00 0.00 45.46 4.26
1577 1808 9.582431 ACTTTATCAATGAAAATCAGCAATCTG 57.418 29.630 0.00 0.00 41.67 2.90
1578 1809 9.582431 CACTTTATCAATGAAAATCAGCAATCT 57.418 29.630 0.00 0.00 0.00 2.40
1579 1810 8.814235 CCACTTTATCAATGAAAATCAGCAATC 58.186 33.333 0.00 0.00 0.00 2.67
1580 1811 8.316214 ACCACTTTATCAATGAAAATCAGCAAT 58.684 29.630 0.00 0.00 0.00 3.56
1581 1812 7.669427 ACCACTTTATCAATGAAAATCAGCAA 58.331 30.769 0.00 0.00 0.00 3.91
1582 1813 7.230849 ACCACTTTATCAATGAAAATCAGCA 57.769 32.000 0.00 0.00 0.00 4.41
1583 1814 8.677300 TCTACCACTTTATCAATGAAAATCAGC 58.323 33.333 0.00 0.00 0.00 4.26
1594 1825 9.841295 AACTGTTTACTTCTACCACTTTATCAA 57.159 29.630 0.00 0.00 0.00 2.57
1598 1829 9.754382 CTGTAACTGTTTACTTCTACCACTTTA 57.246 33.333 0.00 0.00 38.78 1.85
1599 1830 7.713942 CCTGTAACTGTTTACTTCTACCACTTT 59.286 37.037 0.00 0.00 38.78 2.66
1600 1831 7.215085 CCTGTAACTGTTTACTTCTACCACTT 58.785 38.462 0.00 0.00 38.78 3.16
1601 1832 6.740681 GCCTGTAACTGTTTACTTCTACCACT 60.741 42.308 0.00 0.00 38.78 4.00
1602 1833 5.407691 GCCTGTAACTGTTTACTTCTACCAC 59.592 44.000 0.00 0.00 38.78 4.16
1603 1834 5.511888 GGCCTGTAACTGTTTACTTCTACCA 60.512 44.000 0.00 0.00 38.78 3.25
1604 1835 4.934001 GGCCTGTAACTGTTTACTTCTACC 59.066 45.833 0.00 0.00 38.78 3.18
1605 1836 5.407691 GTGGCCTGTAACTGTTTACTTCTAC 59.592 44.000 3.32 0.00 38.78 2.59
1606 1837 5.306160 AGTGGCCTGTAACTGTTTACTTCTA 59.694 40.000 3.32 0.00 38.78 2.10
1607 1838 4.102681 AGTGGCCTGTAACTGTTTACTTCT 59.897 41.667 3.32 0.00 38.78 2.85
1608 1839 4.213482 CAGTGGCCTGTAACTGTTTACTTC 59.787 45.833 11.84 0.00 39.17 3.01
1609 1840 4.134563 CAGTGGCCTGTAACTGTTTACTT 58.865 43.478 11.84 0.00 39.17 2.24
1610 1841 3.389983 TCAGTGGCCTGTAACTGTTTACT 59.610 43.478 17.79 0.00 43.49 2.24
1611 1842 3.735591 TCAGTGGCCTGTAACTGTTTAC 58.264 45.455 17.79 0.00 43.49 2.01
1612 1843 4.425180 TTCAGTGGCCTGTAACTGTTTA 57.575 40.909 17.79 5.37 43.49 2.01
1613 1844 3.290948 TTCAGTGGCCTGTAACTGTTT 57.709 42.857 17.79 0.00 43.49 2.83
1614 1845 3.214328 CTTTCAGTGGCCTGTAACTGTT 58.786 45.455 17.79 0.00 43.49 3.16
1615 1846 2.487265 CCTTTCAGTGGCCTGTAACTGT 60.487 50.000 17.79 0.00 43.49 3.55
1616 1847 2.154462 CCTTTCAGTGGCCTGTAACTG 58.846 52.381 13.50 13.50 44.23 3.16
1617 1848 2.054799 TCCTTTCAGTGGCCTGTAACT 58.945 47.619 3.32 0.00 39.82 2.24
1618 1849 2.561478 TCCTTTCAGTGGCCTGTAAC 57.439 50.000 3.32 0.00 39.82 2.50
1619 1850 3.586470 TTTCCTTTCAGTGGCCTGTAA 57.414 42.857 3.32 0.00 39.82 2.41
1620 1851 3.137544 TCTTTTCCTTTCAGTGGCCTGTA 59.862 43.478 3.32 0.00 39.82 2.74
1621 1852 2.091885 TCTTTTCCTTTCAGTGGCCTGT 60.092 45.455 3.32 0.00 39.82 4.00
1622 1853 2.586425 TCTTTTCCTTTCAGTGGCCTG 58.414 47.619 3.32 0.00 40.25 4.85
1623 1854 3.312736 TTCTTTTCCTTTCAGTGGCCT 57.687 42.857 3.32 0.00 0.00 5.19
1624 1855 4.400529 TTTTCTTTTCCTTTCAGTGGCC 57.599 40.909 0.00 0.00 0.00 5.36
1625 1856 5.291858 CACTTTTTCTTTTCCTTTCAGTGGC 59.708 40.000 0.00 0.00 0.00 5.01
1626 1857 6.630071 TCACTTTTTCTTTTCCTTTCAGTGG 58.370 36.000 0.00 0.00 31.85 4.00
1627 1858 8.193438 AGATCACTTTTTCTTTTCCTTTCAGTG 58.807 33.333 0.00 0.00 0.00 3.66
1628 1859 8.298729 AGATCACTTTTTCTTTTCCTTTCAGT 57.701 30.769 0.00 0.00 0.00 3.41
1644 1875 9.956720 CTGTCAGAAACAATTTTAGATCACTTT 57.043 29.630 0.00 0.00 37.45 2.66
1645 1876 8.571336 CCTGTCAGAAACAATTTTAGATCACTT 58.429 33.333 0.00 0.00 37.45 3.16
1646 1877 7.308830 GCCTGTCAGAAACAATTTTAGATCACT 60.309 37.037 0.00 0.00 37.45 3.41
1647 1878 6.803807 GCCTGTCAGAAACAATTTTAGATCAC 59.196 38.462 0.00 0.00 37.45 3.06
1648 1879 6.071952 GGCCTGTCAGAAACAATTTTAGATCA 60.072 38.462 0.00 0.00 37.45 2.92
1739 1993 0.921896 AATACCATGGCTCTGTGGCT 59.078 50.000 13.04 0.00 42.34 4.75
1744 1998 1.406539 GCAACCAATACCATGGCTCTG 59.593 52.381 13.04 6.10 44.75 3.35
1763 2023 4.515191 TGGCAATATTAAGATTCCAGTCGC 59.485 41.667 8.84 2.38 0.00 5.19
1836 2108 1.506262 GGCGTTTGATGCCGTGAAT 59.494 52.632 0.00 0.00 40.96 2.57
1877 2149 1.001020 ATTCTGGCGCAATGGACCA 60.001 52.632 10.83 0.00 0.00 4.02
1900 2172 3.532542 GGGCAGAAGTTGACAGGTATAC 58.467 50.000 0.00 0.00 36.08 1.47
1911 2183 2.529389 ACGGAGGGGGCAGAAGTT 60.529 61.111 0.00 0.00 0.00 2.66
2145 2417 4.065088 GTTGCTCACATGTGAAGGACTTA 58.935 43.478 27.63 4.78 39.39 2.24
2217 2489 7.222000 GCTCTATAAGGCAGACTATTACACT 57.778 40.000 0.00 0.00 0.00 3.55
2250 2522 1.067915 GCCTCTGTGAGTGAGAGTGTC 60.068 57.143 0.00 0.00 36.04 3.67
2344 2631 5.169992 ACATCTTGTTCACCATCATCAGA 57.830 39.130 0.00 0.00 0.00 3.27
2379 2666 7.521871 TTTGTGTTGCCATATGATATATGCA 57.478 32.000 3.65 0.80 0.00 3.96
2389 2676 6.835488 ACTTCATCCTATTTGTGTTGCCATAT 59.165 34.615 0.00 0.00 0.00 1.78
2402 2689 5.364157 AGAACCGAAGCTACTTCATCCTATT 59.636 40.000 7.99 0.00 40.17 1.73
2404 2691 4.098044 CAGAACCGAAGCTACTTCATCCTA 59.902 45.833 7.99 0.00 40.17 2.94
2407 2694 4.109050 CTCAGAACCGAAGCTACTTCATC 58.891 47.826 7.99 3.25 40.17 2.92


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

AutoCloner maintained by Alex Coulton.