Multiple sequence alignment - TraesCS1D01G122900

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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 TraesCS1D01G122900 chr1D 100.000 2438 0 0 1 2438 123892862 123890425 0.000000e+00 4503.0
1 TraesCS1D01G122900 chr1D 93.109 595 37 2 1846 2438 157970238 157969646 0.000000e+00 869.0
2 TraesCS1D01G122900 chr1B 87.937 1202 136 9 646 1845 183887653 183886459 0.000000e+00 1408.0
3 TraesCS1D01G122900 chr1B 88.945 398 40 3 4 398 183888048 183887652 2.820000e-134 488.0
4 TraesCS1D01G122900 chr2D 94.454 595 31 2 1846 2438 157433127 157433721 0.000000e+00 915.0
5 TraesCS1D01G122900 chr2D 93.109 595 38 2 1846 2438 284267222 284267815 0.000000e+00 869.0
6 TraesCS1D01G122900 chr2D 72.498 1069 263 25 55 1104 624775725 624776781 1.410000e-82 316.0
7 TraesCS1D01G122900 chr2D 74.123 228 58 1 827 1053 2280590 2280817 2.580000e-15 93.5
8 TraesCS1D01G122900 chr2B 93.445 595 33 4 1846 2438 413156109 413156699 0.000000e+00 878.0
9 TraesCS1D01G122900 chr2B 93.277 595 36 3 1846 2438 364176729 364176137 0.000000e+00 874.0
10 TraesCS1D01G122900 chr2B 71.111 450 118 10 617 1058 441858621 441859066 1.540000e-17 100.0
11 TraesCS1D01G122900 chr3D 93.277 595 36 3 1846 2438 267790886 267790294 0.000000e+00 874.0
12 TraesCS1D01G122900 chr6D 93.109 595 37 3 1846 2438 418422827 418422235 0.000000e+00 869.0
13 TraesCS1D01G122900 chr6D 93.098 594 37 3 1847 2438 394319707 394320298 0.000000e+00 867.0
14 TraesCS1D01G122900 chr4A 93.109 595 36 4 1846 2438 100425528 100426119 0.000000e+00 867.0
15 TraesCS1D01G122900 chr5B 72.197 1320 308 50 27 1316 222123670 222124960 1.390000e-92 350.0
16 TraesCS1D01G122900 chr2A 71.578 1052 266 27 22 1055 461603902 461604938 3.110000e-64 255.0
17 TraesCS1D01G122900 chr7B 82.488 217 28 4 1626 1840 709601912 709602120 5.350000e-42 182.0
18 TraesCS1D01G122900 chr5A 71.059 774 209 13 346 1111 354696244 354697010 8.960000e-40 174.0
19 TraesCS1D01G122900 chr5A 77.640 161 34 2 952 1111 72591322 72591163 2.000000e-16 97.1
20 TraesCS1D01G122900 chrUn 76.667 270 62 1 843 1111 442193881 442194150 5.430000e-32 148.0
21 TraesCS1D01G122900 chr5D 98.305 59 1 0 1786 1844 525968095 525968037 1.190000e-18 104.0
22 TraesCS1D01G122900 chr7D 90.625 64 2 4 1786 1846 80435902 80435840 5.590000e-12 82.4


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 TraesCS1D01G122900 chr1D 123890425 123892862 2437 True 4503 4503 100.000 1 2438 1 chr1D.!!$R1 2437
1 TraesCS1D01G122900 chr1D 157969646 157970238 592 True 869 869 93.109 1846 2438 1 chr1D.!!$R2 592
2 TraesCS1D01G122900 chr1B 183886459 183888048 1589 True 948 1408 88.441 4 1845 2 chr1B.!!$R1 1841
3 TraesCS1D01G122900 chr2D 157433127 157433721 594 False 915 915 94.454 1846 2438 1 chr2D.!!$F2 592
4 TraesCS1D01G122900 chr2D 284267222 284267815 593 False 869 869 93.109 1846 2438 1 chr2D.!!$F3 592
5 TraesCS1D01G122900 chr2D 624775725 624776781 1056 False 316 316 72.498 55 1104 1 chr2D.!!$F4 1049
6 TraesCS1D01G122900 chr2B 413156109 413156699 590 False 878 878 93.445 1846 2438 1 chr2B.!!$F1 592
7 TraesCS1D01G122900 chr2B 364176137 364176729 592 True 874 874 93.277 1846 2438 1 chr2B.!!$R1 592
8 TraesCS1D01G122900 chr3D 267790294 267790886 592 True 874 874 93.277 1846 2438 1 chr3D.!!$R1 592
9 TraesCS1D01G122900 chr6D 418422235 418422827 592 True 869 869 93.109 1846 2438 1 chr6D.!!$R1 592
10 TraesCS1D01G122900 chr6D 394319707 394320298 591 False 867 867 93.098 1847 2438 1 chr6D.!!$F1 591
11 TraesCS1D01G122900 chr4A 100425528 100426119 591 False 867 867 93.109 1846 2438 1 chr4A.!!$F1 592
12 TraesCS1D01G122900 chr5B 222123670 222124960 1290 False 350 350 72.197 27 1316 1 chr5B.!!$F1 1289
13 TraesCS1D01G122900 chr2A 461603902 461604938 1036 False 255 255 71.578 22 1055 1 chr2A.!!$F1 1033

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
331 339 0.543174 AGGACACAGGACTCCACCTC 60.543 60.0 0.0 0.0 38.32 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 1620 0.179094 TTGTTGTCTTCAGCGACGGT 60.179 50.0 0.0 0.0 36.71 4.83 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
116 117 6.672218 TGATAAACTTAGAAGGGAGGACATCA 59.328 38.462 0.00 0.00 0.00 3.07
119 120 3.777522 ACTTAGAAGGGAGGACATCAAGG 59.222 47.826 0.00 0.00 0.00 3.61
126 127 2.103941 GGGAGGACATCAAGGCTCTTAG 59.896 54.545 0.00 0.00 0.00 2.18
144 149 8.897752 GGCTCTTAGTGACAAAATTATGAAGAT 58.102 33.333 0.00 0.00 0.00 2.40
163 168 0.548031 TAATTGCTGGCTGGAGAGGG 59.452 55.000 0.00 0.00 0.00 4.30
230 235 8.531982 CATGCCTAGCTAGTATTCCTATTTACA 58.468 37.037 19.31 0.04 0.00 2.41
274 280 5.124457 CCCTAAATGGCCATTAAGATGATCG 59.876 44.000 30.84 9.70 35.16 3.69
331 339 0.543174 AGGACACAGGACTCCACCTC 60.543 60.000 0.00 0.00 38.32 3.85
332 340 0.832135 GGACACAGGACTCCACCTCA 60.832 60.000 0.00 0.00 38.32 3.86
339 347 3.075582 ACAGGACTCCACCTCACTAACTA 59.924 47.826 0.00 0.00 38.32 2.24
406 414 5.015178 TCCCAACCTCCAAGACATTAATCTT 59.985 40.000 0.00 0.00 39.60 2.40
412 420 5.163581 CCTCCAAGACATTAATCTTTGCCTG 60.164 44.000 0.00 0.00 36.78 4.85
419 427 3.297134 TTAATCTTTGCCTGCTAGGGG 57.703 47.619 4.65 0.00 35.37 4.79
450 458 7.070821 GGTTAAAAGGTACTATGAGGAGGATGA 59.929 40.741 0.00 0.00 38.49 2.92
464 472 4.106341 AGGAGGATGAGAAACCTTGGAAAA 59.894 41.667 0.00 0.00 36.57 2.29
478 486 9.884636 AAACCTTGGAAAATTATTATTAGGCAC 57.115 29.630 0.00 0.00 0.00 5.01
493 501 1.423541 AGGCACAAGTACATGTTGGGA 59.576 47.619 2.30 0.00 28.97 4.37
508 516 5.649970 TGTTGGGAAAACCTAACCTCTTA 57.350 39.130 11.68 0.00 41.11 2.10
512 520 4.262617 GGGAAAACCTAACCTCTTAGCTG 58.737 47.826 0.00 0.00 35.85 4.24
516 524 5.346181 AAACCTAACCTCTTAGCTGCTAG 57.654 43.478 9.62 0.00 0.00 3.42
517 525 3.983821 ACCTAACCTCTTAGCTGCTAGT 58.016 45.455 9.62 1.53 0.00 2.57
521 529 4.399004 AACCTCTTAGCTGCTAGTCATG 57.601 45.455 9.62 2.23 0.00 3.07
535 543 3.576078 AGTCATGACCAAAACACCTCA 57.424 42.857 22.21 0.00 0.00 3.86
537 545 4.277476 AGTCATGACCAAAACACCTCAAA 58.723 39.130 22.21 0.00 0.00 2.69
550 558 4.546674 ACACCTCAAAATTCTGGAAAGGT 58.453 39.130 0.00 0.00 36.10 3.50
553 561 4.342092 ACCTCAAAATTCTGGAAAGGTGTG 59.658 41.667 3.68 0.00 34.46 3.82
571 579 4.220382 GGTGTGAAATCCATCATCCAAACA 59.780 41.667 0.00 0.00 0.00 2.83
577 585 7.277098 GTGAAATCCATCATCCAAACATTGAAG 59.723 37.037 0.00 0.00 0.00 3.02
595 603 9.699410 ACATTGAAGTTTGGATATAGATGGAAA 57.301 29.630 0.00 0.00 0.00 3.13
602 610 6.590656 TTGGATATAGATGGAAAGTTGGGT 57.409 37.500 0.00 0.00 0.00 4.51
603 611 6.187727 TGGATATAGATGGAAAGTTGGGTC 57.812 41.667 0.00 0.00 0.00 4.46
604 612 5.669904 TGGATATAGATGGAAAGTTGGGTCA 59.330 40.000 0.00 0.00 0.00 4.02
605 613 5.998363 GGATATAGATGGAAAGTTGGGTCAC 59.002 44.000 0.00 0.00 0.00 3.67
609 618 2.243602 TGGAAAGTTGGGTCACGTAC 57.756 50.000 0.00 0.00 0.00 3.67
645 654 2.158579 GGGAGGACACTTGGTTTGGTAA 60.159 50.000 0.00 0.00 0.00 2.85
687 697 7.093156 CCAATTCTGGCCTATCTACATCATCTA 60.093 40.741 3.32 0.00 35.39 1.98
721 731 2.865119 AATGCATCTGTGAGGTGTGA 57.135 45.000 0.00 0.00 0.00 3.58
777 787 5.473066 ACTTTTGATGAGAAAATGGTGGG 57.527 39.130 0.00 0.00 0.00 4.61
780 790 2.710377 TGATGAGAAAATGGTGGGACG 58.290 47.619 0.00 0.00 0.00 4.79
788 798 2.175035 AATGGTGGGACGGTGGTACG 62.175 60.000 0.00 0.00 40.31 3.67
817 827 6.610020 TGGTAGAAATAGCTAGTAGGCTCAAA 59.390 38.462 0.00 0.00 42.97 2.69
907 917 8.154856 TCCCTATACCATGTCATTAACTTTAGC 58.845 37.037 0.00 0.00 0.00 3.09
916 927 4.511826 GTCATTAACTTTAGCGGGATCCAG 59.488 45.833 15.23 11.38 0.00 3.86
946 957 9.667107 CTTTACATTCCTAGTGTCTGGAAATTA 57.333 33.333 0.00 0.00 44.34 1.40
995 1007 1.444895 GGCTGATGGCGCAAAACAG 60.445 57.895 10.83 13.62 42.94 3.16
1058 1070 5.841810 CAAGCCTTTGGATTGTGTTTTCTA 58.158 37.500 6.44 0.00 43.22 2.10
1117 1129 4.409718 TGTGTAGTGGCTAAAGTTGTCA 57.590 40.909 0.00 0.00 0.00 3.58
1137 1149 8.999431 GTTGTCAGGTCTTTCATTAGTAATCAA 58.001 33.333 0.00 0.00 0.00 2.57
1179 1191 8.831550 GGAAACAACTTTGAATCTATAGCTAGG 58.168 37.037 0.00 0.00 0.00 3.02
1189 1201 7.280356 TGAATCTATAGCTAGGTTTTTGGTCC 58.720 38.462 0.00 0.00 28.11 4.46
1210 1222 4.522789 TCCCCAATAACAAAAACTCTGCTC 59.477 41.667 0.00 0.00 0.00 4.26
1229 1241 7.615403 TCTGCTCTGAATAATGTTACTTCTGT 58.385 34.615 0.00 0.00 0.00 3.41
1230 1242 8.749354 TCTGCTCTGAATAATGTTACTTCTGTA 58.251 33.333 0.00 0.00 0.00 2.74
1231 1243 8.932945 TGCTCTGAATAATGTTACTTCTGTAG 57.067 34.615 0.00 0.00 0.00 2.74
1232 1244 7.492669 TGCTCTGAATAATGTTACTTCTGTAGC 59.507 37.037 0.00 0.00 0.00 3.58
1262 1274 5.161358 GGGGCTTTCGAAACTTAGAAATTG 58.839 41.667 6.47 0.00 36.02 2.32
1299 1311 9.360093 GATGATACGATTTGGTCCTCTATTAAG 57.640 37.037 0.00 0.00 0.00 1.85
1316 1328 4.890158 TTAAGCAGGTCATGAGACTGAA 57.110 40.909 24.32 11.61 44.36 3.02
1318 1330 1.973515 AGCAGGTCATGAGACTGAACA 59.026 47.619 24.32 0.00 44.36 3.18
1320 1332 2.676839 GCAGGTCATGAGACTGAACATG 59.323 50.000 24.32 9.45 44.36 3.21
1328 1340 5.188359 TCATGAGACTGAACATGAGGATGAA 59.812 40.000 0.00 0.00 44.86 2.57
1331 1343 5.702670 TGAGACTGAACATGAGGATGAAAAC 59.297 40.000 0.00 0.00 33.36 2.43
1351 1363 2.704596 ACATCCTGGATCATCCTGTCTG 59.295 50.000 6.13 6.65 37.46 3.51
1352 1364 2.557555 TCCTGGATCATCCTGTCTGT 57.442 50.000 4.96 0.00 37.46 3.41
1359 1371 2.532250 TCATCCTGTCTGTGGAGCTA 57.468 50.000 0.00 0.00 36.99 3.32
1419 1431 3.257933 GTTCTGCAACGCCCTCTG 58.742 61.111 0.00 0.00 0.00 3.35
1433 1445 1.277273 CCCTCTGCTGATCACAAGTGA 59.723 52.381 5.24 5.24 44.59 3.41
1434 1446 5.812043 GCCCTCTGCTGATCACAAGTGAT 62.812 52.174 15.06 15.06 44.24 3.06
1447 1459 0.541863 AAGTGATTAGGCTCGTGGGG 59.458 55.000 0.00 0.00 0.00 4.96
1450 1462 1.335132 TGATTAGGCTCGTGGGGGTC 61.335 60.000 0.00 0.00 0.00 4.46
1451 1463 1.003051 ATTAGGCTCGTGGGGGTCT 59.997 57.895 0.00 0.00 0.00 3.85
1459 1471 0.616395 TCGTGGGGGTCTGATGCTAA 60.616 55.000 0.00 0.00 0.00 3.09
1465 1477 2.303311 GGGGGTCTGATGCTAATACCTC 59.697 54.545 0.00 0.00 0.00 3.85
1484 1496 4.554036 GACCCCTGGCGCCATCTC 62.554 72.222 32.87 17.50 0.00 2.75
1496 1508 1.335780 CGCCATCTCAAGATCTCGGAG 60.336 57.143 15.03 15.03 31.21 4.63
1499 1511 1.617850 CATCTCAAGATCTCGGAGGGG 59.382 57.143 18.96 10.92 31.21 4.79
1500 1512 0.105964 TCTCAAGATCTCGGAGGGGG 60.106 60.000 18.96 1.45 0.00 5.40
1521 1533 1.819305 GCTGCAAGACTCCTCCCAAAA 60.819 52.381 0.00 0.00 34.07 2.44
1545 1557 2.445274 GCGTGATGCTCGAGACAAA 58.555 52.632 18.75 4.27 41.73 2.83
1562 1574 1.064654 CAAATCGAAGCTGCTTAGCCC 59.935 52.381 15.95 1.62 34.90 5.19
1566 1578 1.219393 GAAGCTGCTTAGCCCGACT 59.781 57.895 15.95 0.00 34.90 4.18
1590 1602 3.644606 CTGGGTGCCTGCTGGTCT 61.645 66.667 11.69 0.00 35.27 3.85
1603 1615 1.903877 CTGGTCTCCACAAGCCGGAT 61.904 60.000 5.05 0.00 32.36 4.18
1623 1635 2.355837 GCACCGTCGCTGAAGACA 60.356 61.111 0.00 0.00 40.98 3.41
1624 1636 1.954146 GCACCGTCGCTGAAGACAA 60.954 57.895 0.00 0.00 40.98 3.18
1631 1643 0.944386 TCGCTGAAGACAACAAAGGC 59.056 50.000 0.00 0.00 0.00 4.35
1649 1661 1.603455 CGATGCCCACCCAACAAGT 60.603 57.895 0.00 0.00 0.00 3.16
1657 1669 1.206849 CCACCCAACAAGTGTGCTTTT 59.793 47.619 0.00 0.00 33.20 2.27
1667 1679 7.009174 CCAACAAGTGTGCTTTTAGTAGTTTTG 59.991 37.037 0.00 0.00 31.49 2.44
1671 1683 8.921670 CAAGTGTGCTTTTAGTAGTTTTGTTTT 58.078 29.630 0.00 0.00 31.49 2.43
1703 1715 0.321653 GACATGGGTCGCCAGAACTT 60.322 55.000 0.00 0.00 33.68 2.66
1712 1724 3.253432 GGTCGCCAGAACTTTTTCAGATT 59.747 43.478 0.00 0.00 33.72 2.40
1714 1726 4.676924 GTCGCCAGAACTTTTTCAGATTTG 59.323 41.667 0.00 0.00 33.72 2.32
1715 1727 4.338118 TCGCCAGAACTTTTTCAGATTTGT 59.662 37.500 0.00 0.00 33.72 2.83
1716 1728 5.529430 TCGCCAGAACTTTTTCAGATTTGTA 59.471 36.000 0.00 0.00 33.72 2.41
1717 1729 5.853282 CGCCAGAACTTTTTCAGATTTGTAG 59.147 40.000 0.00 0.00 33.72 2.74
1719 1731 6.152379 CCAGAACTTTTTCAGATTTGTAGCC 58.848 40.000 0.00 0.00 33.72 3.93
1720 1732 5.853282 CAGAACTTTTTCAGATTTGTAGCCG 59.147 40.000 0.00 0.00 33.72 5.52
1722 1734 3.821033 ACTTTTTCAGATTTGTAGCCGCT 59.179 39.130 0.00 0.00 0.00 5.52
1730 1742 5.053145 CAGATTTGTAGCCGCTCTCTTTAT 58.947 41.667 0.00 0.00 0.00 1.40
1737 1749 4.737855 AGCCGCTCTCTTTATCTTTGTA 57.262 40.909 0.00 0.00 0.00 2.41
1738 1750 5.086104 AGCCGCTCTCTTTATCTTTGTAA 57.914 39.130 0.00 0.00 0.00 2.41
1760 1772 2.125773 TCTGTCGAACTACCCCTCTC 57.874 55.000 0.00 0.00 0.00 3.20
1771 1783 1.679898 CCCCTCTCAGTGGGTTGAC 59.320 63.158 11.05 0.00 43.09 3.18
1772 1784 1.127567 CCCCTCTCAGTGGGTTGACA 61.128 60.000 11.05 0.00 43.09 3.58
1837 1849 4.484912 GAGAGGCCTCCCTATTCTTCTAA 58.515 47.826 29.54 0.00 43.12 2.10
1925 1937 7.281324 CGTATTAGTAGGCTAGCTAGTGATCAT 59.719 40.741 21.62 5.63 0.00 2.45
1946 1958 7.490962 TCATTCAGTAACTTGTAAACACTGG 57.509 36.000 0.00 0.00 37.72 4.00
1984 1996 5.924825 AGGAACTGCTAGTAACTTGTAAACG 59.075 40.000 0.00 0.00 37.18 3.60
1985 1997 5.693555 GGAACTGCTAGTAACTTGTAAACGT 59.306 40.000 0.00 0.00 0.00 3.99
1994 2006 7.230466 AGTAACTTGTAAACGTTGAGAACAG 57.770 36.000 0.00 0.00 0.00 3.16
2112 2124 6.662414 TTAGTAGCCGAAATTCACAATCAG 57.338 37.500 0.00 0.00 0.00 2.90
2166 2178 8.638873 ACATGTTAATGCATCTCAATGATTCAT 58.361 29.630 15.36 0.00 39.96 2.57
2273 2288 5.105752 GGCTAACATTCAGTACAGAGTGAG 58.894 45.833 16.07 6.48 36.37 3.51
2284 2301 7.148641 TCAGTACAGAGTGAGAGAAATTTGTC 58.851 38.462 7.23 7.23 31.13 3.18
2301 2318 9.736023 GAAATTTGTCTGTGAAGTCTACAATTT 57.264 29.630 0.00 0.00 30.76 1.82
2353 2370 3.245016 TGCTGGAACCATGAGAATGAACT 60.245 43.478 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.509575 AGTGCTGGCAGCTATCTCTATAC 59.490 47.826 36.50 23.50 42.97 1.47
19 20 7.049799 ACATTCTAAGATAGAGAGGAAGTGC 57.950 40.000 0.00 0.00 35.96 4.40
85 86 9.225682 TCCTCCCTTCTAAGTTTATCATAATGT 57.774 33.333 0.00 0.00 0.00 2.71
116 117 8.635765 TTCATAATTTTGTCACTAAGAGCCTT 57.364 30.769 0.00 0.00 0.00 4.35
144 149 0.548031 CCCTCTCCAGCCAGCAATTA 59.452 55.000 0.00 0.00 0.00 1.40
237 242 6.215227 TGGCCATTTAGGGAATTTGAAGAAAT 59.785 34.615 0.00 0.00 38.09 2.17
274 280 3.132646 AGACAGTGAGCCATCTGAGAATC 59.867 47.826 0.00 0.00 35.84 2.52
412 420 2.031870 CTTTTAACCCATGCCCCTAGC 58.968 52.381 0.00 0.00 44.14 3.42
419 427 5.531287 CCTCATAGTACCTTTTAACCCATGC 59.469 44.000 0.00 0.00 0.00 4.06
421 429 6.101296 CCTCCTCATAGTACCTTTTAACCCAT 59.899 42.308 0.00 0.00 0.00 4.00
473 481 1.423541 TCCCAACATGTACTTGTGCCT 59.576 47.619 14.52 0.00 0.00 4.75
474 482 1.904287 TCCCAACATGTACTTGTGCC 58.096 50.000 14.52 0.00 0.00 5.01
475 483 4.048504 GTTTTCCCAACATGTACTTGTGC 58.951 43.478 14.52 0.00 0.00 4.57
478 486 6.443792 GTTAGGTTTTCCCAACATGTACTTG 58.556 40.000 0.00 7.18 40.43 3.16
488 496 4.352893 AGCTAAGAGGTTAGGTTTTCCCAA 59.647 41.667 0.00 0.00 43.08 4.12
489 497 3.914435 AGCTAAGAGGTTAGGTTTTCCCA 59.086 43.478 0.00 0.00 43.08 4.37
490 498 4.262617 CAGCTAAGAGGTTAGGTTTTCCC 58.737 47.826 0.00 0.00 43.08 3.97
493 501 4.642466 AGCAGCTAAGAGGTTAGGTTTT 57.358 40.909 0.00 0.00 43.08 2.43
508 516 3.077359 GTTTTGGTCATGACTAGCAGCT 58.923 45.455 24.50 0.00 0.00 4.24
512 520 3.412386 AGGTGTTTTGGTCATGACTAGC 58.588 45.455 24.50 13.17 0.00 3.42
516 524 4.647424 TTTGAGGTGTTTTGGTCATGAC 57.353 40.909 17.91 17.91 0.00 3.06
517 525 5.867903 ATTTTGAGGTGTTTTGGTCATGA 57.132 34.783 0.00 0.00 0.00 3.07
521 529 5.049828 CCAGAATTTTGAGGTGTTTTGGTC 58.950 41.667 0.00 0.00 0.00 4.02
535 543 6.099557 TGGATTTCACACCTTTCCAGAATTTT 59.900 34.615 0.00 0.00 32.80 1.82
537 545 5.147032 TGGATTTCACACCTTTCCAGAATT 58.853 37.500 0.00 0.00 32.80 2.17
550 558 6.210984 TCAATGTTTGGATGATGGATTTCACA 59.789 34.615 0.00 0.00 0.00 3.58
553 561 7.325694 ACTTCAATGTTTGGATGATGGATTTC 58.674 34.615 0.00 0.00 0.00 2.17
571 579 9.927081 ACTTTCCATCTATATCCAAACTTCAAT 57.073 29.630 0.00 0.00 0.00 2.57
577 585 6.833933 ACCCAACTTTCCATCTATATCCAAAC 59.166 38.462 0.00 0.00 0.00 2.93
583 591 5.130477 ACGTGACCCAACTTTCCATCTATAT 59.870 40.000 0.00 0.00 0.00 0.86
602 610 6.548441 CCAAAATCTAACTTTGGTACGTGA 57.452 37.500 0.00 0.00 45.21 4.35
721 731 6.838382 AGTAAGTTTTAGGTTGTGGTCATCT 58.162 36.000 0.00 0.00 0.00 2.90
772 782 2.573083 TTCGTACCACCGTCCCACC 61.573 63.158 0.00 0.00 0.00 4.61
773 783 1.373371 GTTCGTACCACCGTCCCAC 60.373 63.158 0.00 0.00 0.00 4.61
777 787 0.881118 TACCAGTTCGTACCACCGTC 59.119 55.000 0.00 0.00 0.00 4.79
780 790 3.665745 TTTCTACCAGTTCGTACCACC 57.334 47.619 0.00 0.00 0.00 4.61
788 798 6.265876 AGCCTACTAGCTATTTCTACCAGTTC 59.734 42.308 0.00 0.00 42.70 3.01
817 827 4.054359 AGAGTCTGGGTCAGTATTGAGT 57.946 45.455 0.00 0.00 32.98 3.41
907 917 0.251916 TGTAAAGTGGCTGGATCCCG 59.748 55.000 9.90 3.53 0.00 5.14
916 927 4.631813 CAGACACTAGGAATGTAAAGTGGC 59.368 45.833 6.31 2.84 46.35 5.01
946 957 0.121197 TGGATCCTGGGGGAACTCTT 59.879 55.000 14.23 0.00 45.78 2.85
995 1007 7.940137 TCCTAAGGTTATCTCTAGTCATCAGTC 59.060 40.741 0.00 0.00 0.00 3.51
1056 1068 7.283807 TGTGTGATGGATTCATTTTCCTCATAG 59.716 37.037 0.00 0.00 36.54 2.23
1058 1070 5.953548 TGTGTGATGGATTCATTTTCCTCAT 59.046 36.000 0.00 0.00 36.54 2.90
1117 1129 9.401058 CTGGAATTGATTACTAATGAAAGACCT 57.599 33.333 0.00 0.00 0.00 3.85
1137 1149 7.637511 AGTTGTTTCCAATATCTCTCTGGAAT 58.362 34.615 6.64 0.00 46.07 3.01
1152 1164 9.383519 CTAGCTATAGATTCAAAGTTGTTTCCA 57.616 33.333 3.21 0.00 0.00 3.53
1189 1201 5.241506 TCAGAGCAGAGTTTTTGTTATTGGG 59.758 40.000 0.00 0.00 0.00 4.12
1210 1222 7.225538 CAGGGCTACAGAAGTAACATTATTCAG 59.774 40.741 0.00 0.00 0.00 3.02
1262 1274 9.950680 ACCAAATCGTATCATCAAAAATCATAC 57.049 29.630 0.00 0.00 0.00 2.39
1276 1288 7.152645 TGCTTAATAGAGGACCAAATCGTATC 58.847 38.462 0.00 0.00 0.00 2.24
1281 1293 5.685728 ACCTGCTTAATAGAGGACCAAATC 58.314 41.667 0.00 0.00 0.00 2.17
1299 1311 2.462456 TGTTCAGTCTCATGACCTGC 57.538 50.000 11.25 2.17 43.91 4.85
1328 1340 3.784763 AGACAGGATGATCCAGGATGTTT 59.215 43.478 14.90 1.60 39.61 2.83
1331 1343 2.704596 ACAGACAGGATGATCCAGGATG 59.295 50.000 14.90 11.01 39.61 3.51
1351 1363 0.313672 CTCGATCTGCCTAGCTCCAC 59.686 60.000 0.00 0.00 0.00 4.02
1352 1364 0.183731 TCTCGATCTGCCTAGCTCCA 59.816 55.000 0.00 0.00 0.00 3.86
1359 1371 0.754957 CCTCCAGTCTCGATCTGCCT 60.755 60.000 10.90 0.00 0.00 4.75
1402 1414 2.970974 GCAGAGGGCGTTGCAGAAC 61.971 63.158 8.68 0.00 40.02 3.01
1415 1427 4.809958 CCTAATCACTTGTGATCAGCAGAG 59.190 45.833 15.48 7.40 0.00 3.35
1416 1428 4.763073 CCTAATCACTTGTGATCAGCAGA 58.237 43.478 15.48 0.00 0.00 4.26
1419 1431 3.539604 AGCCTAATCACTTGTGATCAGC 58.460 45.455 15.48 16.58 0.00 4.26
1433 1445 1.003051 AGACCCCCACGAGCCTAAT 59.997 57.895 0.00 0.00 0.00 1.73
1434 1446 1.987855 CAGACCCCCACGAGCCTAA 60.988 63.158 0.00 0.00 0.00 2.69
1447 1459 2.891580 TCCGAGGTATTAGCATCAGACC 59.108 50.000 0.00 0.00 0.00 3.85
1450 1462 2.028930 GGGTCCGAGGTATTAGCATCAG 60.029 54.545 0.00 0.00 0.00 2.90
1451 1463 1.968493 GGGTCCGAGGTATTAGCATCA 59.032 52.381 0.00 0.00 0.00 3.07
1459 1471 2.446036 GCCAGGGGTCCGAGGTAT 60.446 66.667 0.00 0.00 0.00 2.73
1499 1511 2.270527 GGAGGAGTCTTGCAGCCC 59.729 66.667 0.00 0.00 0.00 5.19
1500 1512 2.129555 TTGGGAGGAGTCTTGCAGCC 62.130 60.000 0.00 0.00 0.00 4.85
1502 1514 2.276732 TTTTGGGAGGAGTCTTGCAG 57.723 50.000 0.00 0.00 0.00 4.41
1503 1515 2.746279 TTTTTGGGAGGAGTCTTGCA 57.254 45.000 0.00 0.00 0.00 4.08
1536 1548 1.067565 AGCAGCTTCGATTTGTCTCGA 60.068 47.619 0.00 0.00 45.32 4.04
1537 1549 1.354040 AGCAGCTTCGATTTGTCTCG 58.646 50.000 0.00 0.00 39.99 4.04
1545 1557 3.816064 GTCGGGCTAAGCAGCTTCGAT 62.816 57.143 12.07 0.00 46.37 3.59
1562 1574 2.125912 CACCCAGAGCCGAAGTCG 60.126 66.667 0.00 0.00 39.44 4.18
1586 1598 1.026718 CAATCCGGCTTGTGGAGACC 61.027 60.000 9.92 0.00 39.30 3.85
1603 1615 2.664851 CTTCAGCGACGGTGCCAA 60.665 61.111 21.69 11.09 34.65 4.52
1607 1619 0.874175 TGTTGTCTTCAGCGACGGTG 60.874 55.000 20.57 20.57 36.71 4.94
1608 1620 0.179094 TTGTTGTCTTCAGCGACGGT 60.179 50.000 0.00 0.00 36.71 4.83
1609 1621 0.934496 TTTGTTGTCTTCAGCGACGG 59.066 50.000 0.00 0.00 36.71 4.79
1612 1624 0.944386 GCCTTTGTTGTCTTCAGCGA 59.056 50.000 0.00 0.00 0.00 4.93
1616 1628 1.266718 GCATCGCCTTTGTTGTCTTCA 59.733 47.619 0.00 0.00 0.00 3.02
1631 1643 1.603455 ACTTGTTGGGTGGGCATCG 60.603 57.895 0.00 0.00 0.00 3.84
1644 1656 7.153217 ACAAAACTACTAAAAGCACACTTGT 57.847 32.000 0.00 0.00 35.85 3.16
1649 1661 7.036829 GGGAAAACAAAACTACTAAAAGCACA 58.963 34.615 0.00 0.00 0.00 4.57
1657 1669 5.133153 AGGACAGGGGAAAACAAAACTACTA 59.867 40.000 0.00 0.00 0.00 1.82
1698 1710 4.617223 GCGGCTACAAATCTGAAAAAGTTC 59.383 41.667 0.00 0.00 0.00 3.01
1703 1715 3.674997 AGAGCGGCTACAAATCTGAAAA 58.325 40.909 0.60 0.00 0.00 2.29
1712 1724 4.737855 AAGATAAAGAGAGCGGCTACAA 57.262 40.909 0.60 0.00 0.00 2.41
1714 1726 4.434520 ACAAAGATAAAGAGAGCGGCTAC 58.565 43.478 0.60 0.00 0.00 3.58
1715 1727 4.737855 ACAAAGATAAAGAGAGCGGCTA 57.262 40.909 0.60 0.00 0.00 3.93
1716 1728 3.618690 ACAAAGATAAAGAGAGCGGCT 57.381 42.857 0.00 0.00 0.00 5.52
1717 1729 5.993106 ATTACAAAGATAAAGAGAGCGGC 57.007 39.130 0.00 0.00 0.00 6.53
1719 1731 8.660373 ACAGAAATTACAAAGATAAAGAGAGCG 58.340 33.333 0.00 0.00 0.00 5.03
1720 1732 9.980780 GACAGAAATTACAAAGATAAAGAGAGC 57.019 33.333 0.00 0.00 0.00 4.09
1722 1734 9.923143 TCGACAGAAATTACAAAGATAAAGAGA 57.077 29.630 0.00 0.00 0.00 3.10
1730 1742 6.647895 GGGTAGTTCGACAGAAATTACAAAGA 59.352 38.462 0.00 0.00 38.23 2.52
1737 1749 3.838903 AGAGGGGTAGTTCGACAGAAATT 59.161 43.478 0.00 0.00 38.23 1.82
1738 1750 3.442076 AGAGGGGTAGTTCGACAGAAAT 58.558 45.455 0.00 0.00 38.23 2.17
1760 1772 5.734720 AGTATGAATAGTGTCAACCCACTG 58.265 41.667 4.17 0.00 45.08 3.66
1768 1780 8.458573 AAACCAACAAAGTATGAATAGTGTCA 57.541 30.769 0.00 0.00 0.00 3.58
1771 1783 9.912634 AATGAAACCAACAAAGTATGAATAGTG 57.087 29.630 0.00 0.00 0.00 2.74
1772 1784 9.912634 CAATGAAACCAACAAAGTATGAATAGT 57.087 29.630 0.00 0.00 0.00 2.12
1778 1790 8.815141 TTCATCAATGAAACCAACAAAGTATG 57.185 30.769 2.97 0.00 43.26 2.39
1925 1937 4.577283 GCCCAGTGTTTACAAGTTACTGAA 59.423 41.667 0.00 0.00 40.80 3.02
1946 1958 3.447742 CAGTTCCTTGTTTCTGTTTGCC 58.552 45.455 0.00 0.00 0.00 4.52
1984 1996 8.610896 CATGATCCTTATTTCTCTGTTCTCAAC 58.389 37.037 0.00 0.00 0.00 3.18
1985 1997 8.324306 ACATGATCCTTATTTCTCTGTTCTCAA 58.676 33.333 0.00 0.00 0.00 3.02
1994 2006 6.127925 TGTGCACAACATGATCCTTATTTCTC 60.128 38.462 19.28 0.00 32.36 2.87
2098 2110 6.887376 TCGTACTAGCTGATTGTGAATTTC 57.113 37.500 0.00 0.00 0.00 2.17
2112 2124 7.154435 TCTTATGTATGGGAATCGTACTAGC 57.846 40.000 0.00 0.00 38.39 3.42
2211 2223 9.965824 CATGTTAGTAGGAAGAACAAATGTTTT 57.034 29.630 0.00 0.00 38.56 2.43
2212 2224 8.576442 CCATGTTAGTAGGAAGAACAAATGTTT 58.424 33.333 0.00 0.00 38.56 2.83
2273 2288 7.715265 TGTAGACTTCACAGACAAATTTCTC 57.285 36.000 0.00 0.00 0.00 2.87
2284 2301 6.203530 TGCAAGAGAAATTGTAGACTTCACAG 59.796 38.462 0.00 0.00 32.56 3.66
2301 2318 3.188159 ACCACTTACGTTTGCAAGAGA 57.812 42.857 0.00 0.00 0.00 3.10
2331 2348 3.084039 GTTCATTCTCATGGTTCCAGCA 58.916 45.455 0.00 0.00 0.00 4.41
2353 2370 3.779738 TGGATGTTCCTCCATCATGTGTA 59.220 43.478 3.83 0.00 42.47 2.90
2378 2395 6.283694 TCGAGAGAAGACCAAATCATATTGG 58.716 40.000 4.58 4.58 46.19 3.16


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

AutoCloner maintained by Alex Coulton.