Multiple sequence alignment - TraesCS4B01G356400

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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 TraesCS4B01G356400 chr4B 100.000 2506 0 0 1 2506 646969011 646966506 0.000000e+00 4628.0
1 TraesCS4B01G356400 chr4D 93.382 952 45 9 19 961 502572083 502571141 0.000000e+00 1393.0
2 TraesCS4B01G356400 chr4D 84.572 888 79 30 957 1816 502571103 502570246 0.000000e+00 828.0
3 TraesCS4B01G356400 chr4D 90.492 305 7 6 2213 2506 502569464 502569171 1.410000e-102 383.0
4 TraesCS4B01G356400 chr4D 82.276 457 42 22 1777 2215 502569973 502569538 2.370000e-95 359.0
5 TraesCS4B01G356400 chr5A 95.978 721 23 2 241 961 685989137 685988423 0.000000e+00 1166.0
6 TraesCS4B01G356400 chr5A 85.260 597 53 19 957 1522 685988385 685987793 1.290000e-162 582.0
7 TraesCS4B01G356400 chr5A 82.776 598 52 18 1632 2193 685987637 685987055 1.040000e-133 486.0
8 TraesCS4B01G356400 chr5A 80.800 250 27 11 2208 2445 685986989 685986749 2.560000e-40 176.0
9 TraesCS4B01G356400 chr7B 81.795 390 54 9 307 694 478486403 478486777 6.730000e-81 311.0
10 TraesCS4B01G356400 chr1D 80.573 314 53 7 392 701 258984140 258984449 4.170000e-58 235.0
11 TraesCS4B01G356400 chr1B 79.876 323 61 4 381 701 353942297 353941977 1.500000e-57 233.0
12 TraesCS4B01G356400 chr1A 78.526 312 63 4 392 701 341868206 341867897 4.230000e-48 202.0
13 TraesCS4B01G356400 chr1A 95.455 44 2 0 1566 1609 561070469 561070512 1.240000e-08 71.3
14 TraesCS4B01G356400 chr4A 95.652 46 2 0 1564 1609 36805133 36805178 9.610000e-10 75.0
15 TraesCS4B01G356400 chr4A 95.455 44 2 0 1566 1609 731471400 731471357 1.240000e-08 71.3
16 TraesCS4B01G356400 chrUn 93.750 48 3 0 1562 1609 37366803 37366850 3.460000e-09 73.1
17 TraesCS4B01G356400 chr5D 92.308 52 3 1 1559 1609 134485628 134485679 3.460000e-09 73.1
18 TraesCS4B01G356400 chr5D 95.455 44 2 0 1566 1609 48933796 48933753 1.240000e-08 71.3
19 TraesCS4B01G356400 chr6A 95.455 44 2 0 1566 1609 72732857 72732900 1.240000e-08 71.3
20 TraesCS4B01G356400 chr2D 95.455 44 2 0 1566 1609 178776456 178776499 1.240000e-08 71.3
21 TraesCS4B01G356400 chr2D 95.455 44 2 0 1566 1609 611793985 611793942 1.240000e-08 71.3


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 TraesCS4B01G356400 chr4B 646966506 646969011 2505 True 4628.00 4628 100.0000 1 2506 1 chr4B.!!$R1 2505
1 TraesCS4B01G356400 chr4D 502569171 502572083 2912 True 740.75 1393 87.6805 19 2506 4 chr4D.!!$R1 2487
2 TraesCS4B01G356400 chr5A 685986749 685989137 2388 True 602.50 1166 86.2035 241 2445 4 chr5A.!!$R1 2204

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
101 102 0.523519 GCAAGGAACACTAGGCTTGC 59.476 55.0 0.0 0.0 39.92 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 2584 0.18135 GGGATCTTCTTGCCGGTCAT 59.819 55.0 1.9 0.0 0.0 3.06 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
96 97 2.012673 GCTCATGCAAGGAACACTAGG 58.987 52.381 0.00 0.00 39.41 3.02
101 102 0.523519 GCAAGGAACACTAGGCTTGC 59.476 55.000 0.00 0.00 39.92 4.01
102 103 1.896220 CAAGGAACACTAGGCTTGCA 58.104 50.000 0.00 0.00 0.00 4.08
112 113 4.122776 CACTAGGCTTGCACATAGTAAGG 58.877 47.826 0.00 0.00 39.96 2.69
120 121 3.937814 TGCACATAGTAAGGGAACACAG 58.062 45.455 0.00 0.00 0.00 3.66
121 122 2.678336 GCACATAGTAAGGGAACACAGC 59.322 50.000 0.00 0.00 0.00 4.40
124 125 5.670485 CACATAGTAAGGGAACACAGCATA 58.330 41.667 0.00 0.00 0.00 3.14
125 126 5.755375 CACATAGTAAGGGAACACAGCATAG 59.245 44.000 0.00 0.00 0.00 2.23
127 128 2.092914 AGTAAGGGAACACAGCATAGGC 60.093 50.000 0.00 0.00 41.61 3.93
213 220 5.882557 AGAGTAGGCATTACATCAAACCAAG 59.117 40.000 0.00 0.00 34.56 3.61
219 226 2.851263 TACATCAAACCAAGCCGTCT 57.149 45.000 0.00 0.00 0.00 4.18
222 229 3.009723 ACATCAAACCAAGCCGTCTATG 58.990 45.455 0.00 0.00 0.00 2.23
228 235 5.527214 TCAAACCAAGCCGTCTATGATAATG 59.473 40.000 0.00 0.00 0.00 1.90
231 238 5.240891 ACCAAGCCGTCTATGATAATGATG 58.759 41.667 0.00 0.00 0.00 3.07
234 241 6.596888 CCAAGCCGTCTATGATAATGATGATT 59.403 38.462 0.00 0.00 0.00 2.57
251 258 4.824479 TGATTAACCAGACAGATCAGCA 57.176 40.909 0.00 0.00 0.00 4.41
286 293 0.529992 GTAGGCCCAATTCCTCGACG 60.530 60.000 0.00 0.00 35.21 5.12
332 339 3.054361 AGGCAGAAACTAATGGGAACGAT 60.054 43.478 0.00 0.00 0.00 3.73
349 357 5.220491 GGAACGATGCAGTAAATTCAGAGAC 60.220 44.000 0.00 0.00 0.00 3.36
373 381 1.351017 GTCAGAACAGGGGGTCAATGA 59.649 52.381 0.00 0.00 0.00 2.57
379 389 2.042944 GGGGGTCAATGAAGGGGC 60.043 66.667 0.00 0.00 0.00 5.80
791 801 2.046892 GTCCACGTCCATGCTGCT 60.047 61.111 0.00 0.00 0.00 4.24
792 802 2.046988 TCCACGTCCATGCTGCTG 60.047 61.111 0.00 0.00 0.00 4.41
793 803 3.807538 CCACGTCCATGCTGCTGC 61.808 66.667 8.89 8.89 40.20 5.25
963 1015 4.185286 GGGCCGGGTATGGGTCAC 62.185 72.222 2.18 0.00 0.00 3.67
984 1036 1.476488 GTGCGTTGGCCCAATAATTCT 59.524 47.619 0.00 0.00 38.85 2.40
1017 1069 5.608449 ACAGGCCGAAATAACCTCTTATAC 58.392 41.667 0.00 0.00 0.00 1.47
1074 1165 3.828921 ACACTTTTTAGGTCCAAGGTCC 58.171 45.455 0.00 0.00 0.00 4.46
1077 1168 0.694196 TTTTAGGTCCAAGGTCCCGG 59.306 55.000 0.00 0.00 0.00 5.73
1078 1169 1.844544 TTTAGGTCCAAGGTCCCGGC 61.845 60.000 0.00 0.00 0.00 6.13
1093 1184 3.894947 GGCGAGCGAGGAGGTCTC 61.895 72.222 0.00 0.00 44.71 3.36
1426 1524 7.775053 AAAAATCCATGTGTTACTGTGGTAT 57.225 32.000 0.00 0.00 33.47 2.73
1499 1600 6.830114 AGCGACTAGTAATAATTTGTCTGC 57.170 37.500 0.00 0.00 0.00 4.26
1504 1605 8.321716 CGACTAGTAATAATTTGTCTGCTGTTC 58.678 37.037 0.00 0.00 0.00 3.18
1510 1611 4.574599 AATTTGTCTGCTGTTCTTCACC 57.425 40.909 0.00 0.00 0.00 4.02
1511 1612 1.581934 TTGTCTGCTGTTCTTCACCG 58.418 50.000 0.00 0.00 0.00 4.94
1533 1642 1.599542 GTATCATTTGGGACGAGCTGC 59.400 52.381 0.00 0.00 0.00 5.25
1564 1691 0.680921 TGCTGCTGGGGCTACATTTC 60.681 55.000 0.00 0.00 39.59 2.17
1566 1693 1.098050 CTGCTGGGGCTACATTTCAC 58.902 55.000 0.00 0.00 39.59 3.18
1567 1694 0.698238 TGCTGGGGCTACATTTCACT 59.302 50.000 0.00 0.00 39.59 3.41
1568 1695 1.340017 TGCTGGGGCTACATTTCACTC 60.340 52.381 0.00 0.00 39.59 3.51
1569 1696 2.019156 GCTGGGGCTACATTTCACTCC 61.019 57.143 0.00 0.00 35.22 3.85
1570 1697 0.623723 TGGGGCTACATTTCACTCCC 59.376 55.000 0.00 0.00 0.00 4.30
1571 1698 0.919710 GGGGCTACATTTCACTCCCT 59.080 55.000 0.00 0.00 34.28 4.20
1572 1699 1.134068 GGGGCTACATTTCACTCCCTC 60.134 57.143 0.00 0.00 34.28 4.30
1573 1700 1.134068 GGGCTACATTTCACTCCCTCC 60.134 57.143 0.00 0.00 0.00 4.30
1574 1701 1.473434 GGCTACATTTCACTCCCTCCG 60.473 57.143 0.00 0.00 0.00 4.63
1575 1702 1.207329 GCTACATTTCACTCCCTCCGT 59.793 52.381 0.00 0.00 0.00 4.69
1576 1703 2.738964 GCTACATTTCACTCCCTCCGTC 60.739 54.545 0.00 0.00 0.00 4.79
1577 1704 1.645710 ACATTTCACTCCCTCCGTCT 58.354 50.000 0.00 0.00 0.00 4.18
1578 1705 1.550976 ACATTTCACTCCCTCCGTCTC 59.449 52.381 0.00 0.00 0.00 3.36
1579 1706 1.550524 CATTTCACTCCCTCCGTCTCA 59.449 52.381 0.00 0.00 0.00 3.27
1580 1707 1.938585 TTTCACTCCCTCCGTCTCAT 58.061 50.000 0.00 0.00 0.00 2.90
1581 1708 2.820728 TTCACTCCCTCCGTCTCATA 57.179 50.000 0.00 0.00 0.00 2.15
1582 1709 2.820728 TCACTCCCTCCGTCTCATAA 57.179 50.000 0.00 0.00 0.00 1.90
1583 1710 3.314307 TCACTCCCTCCGTCTCATAAT 57.686 47.619 0.00 0.00 0.00 1.28
1584 1711 4.448720 TCACTCCCTCCGTCTCATAATA 57.551 45.455 0.00 0.00 0.00 0.98
1585 1712 4.999310 TCACTCCCTCCGTCTCATAATAT 58.001 43.478 0.00 0.00 0.00 1.28
1586 1713 6.135819 TCACTCCCTCCGTCTCATAATATA 57.864 41.667 0.00 0.00 0.00 0.86
1587 1714 6.549242 TCACTCCCTCCGTCTCATAATATAA 58.451 40.000 0.00 0.00 0.00 0.98
1588 1715 6.659668 TCACTCCCTCCGTCTCATAATATAAG 59.340 42.308 0.00 0.00 0.00 1.73
1589 1716 6.659668 CACTCCCTCCGTCTCATAATATAAGA 59.340 42.308 0.00 0.00 0.00 2.10
1590 1717 7.176865 CACTCCCTCCGTCTCATAATATAAGAA 59.823 40.741 0.00 0.00 0.00 2.52
1591 1718 7.177041 ACTCCCTCCGTCTCATAATATAAGAAC 59.823 40.741 0.00 0.00 0.00 3.01
1592 1719 6.150641 TCCCTCCGTCTCATAATATAAGAACG 59.849 42.308 0.00 0.00 0.00 3.95
1593 1720 6.072064 CCCTCCGTCTCATAATATAAGAACGT 60.072 42.308 0.00 0.00 0.00 3.99
1594 1721 7.368833 CCTCCGTCTCATAATATAAGAACGTT 58.631 38.462 0.00 0.00 0.00 3.99
1595 1722 7.866393 CCTCCGTCTCATAATATAAGAACGTTT 59.134 37.037 0.46 0.00 0.00 3.60
1596 1723 9.245962 CTCCGTCTCATAATATAAGAACGTTTT 57.754 33.333 0.46 0.00 0.00 2.43
1597 1724 9.590451 TCCGTCTCATAATATAAGAACGTTTTT 57.410 29.630 9.22 9.22 0.00 1.94
1598 1725 9.845305 CCGTCTCATAATATAAGAACGTTTTTC 57.155 33.333 7.42 0.00 0.00 2.29
1622 1749 2.726066 GCTAGTGTTTCAGTGCAATCGC 60.726 50.000 0.00 0.00 39.24 4.58
1623 1750 1.597742 AGTGTTTCAGTGCAATCGCT 58.402 45.000 0.00 0.00 39.64 4.93
1684 1876 0.466922 CCCATGACTGAATCCCCTGC 60.467 60.000 0.00 0.00 0.00 4.85
1687 1879 0.106819 ATGACTGAATCCCCTGCTGC 60.107 55.000 0.00 0.00 0.00 5.25
1781 1973 0.467290 TTGAGCCACAACCCAACTCC 60.467 55.000 0.00 0.00 33.18 3.85
1820 2327 1.214062 GTCTGTCAGTGGAGCCTCG 59.786 63.158 0.00 0.00 0.00 4.63
1835 2342 2.229784 AGCCTCGCTGATTTTCCAAAAG 59.770 45.455 0.00 0.00 37.57 2.27
1844 2351 6.486248 GCTGATTTTCCAAAAGGAACAAAAC 58.514 36.000 0.00 0.00 0.00 2.43
1855 2362 2.097466 AGGAACAAAACTGTCGCTGTTG 59.903 45.455 6.79 0.00 32.31 3.33
1898 2405 0.317020 GTGTGCGTTGGAACTTCAGC 60.317 55.000 0.00 0.00 0.00 4.26
1912 2419 4.264460 ACTTCAGCGTCTGATTTCTCTT 57.736 40.909 9.78 0.00 40.39 2.85
1952 2474 5.109210 GTTGTTTTAGCACCTTTCAGCTTT 58.891 37.500 0.00 0.00 42.05 3.51
1977 2499 2.983229 AGAACATTACTCCAGCTGCTG 58.017 47.619 22.44 22.44 0.00 4.41
2003 2525 2.502295 GATCCCATTGGCTCAGACATC 58.498 52.381 0.00 0.00 0.00 3.06
2005 2527 1.065199 TCCCATTGGCTCAGACATCAC 60.065 52.381 0.00 0.00 0.00 3.06
2044 2584 2.752358 CTCTGCTTCACCTGGCCA 59.248 61.111 4.71 4.71 0.00 5.36
2047 2587 1.001764 CTGCTTCACCTGGCCATGA 60.002 57.895 15.66 10.19 0.00 3.07
2072 2612 2.922335 GCAAGAAGATCCCAACGCAAAC 60.922 50.000 0.00 0.00 0.00 2.93
2092 2632 2.282407 CACGCAATCACATCTCATCCA 58.718 47.619 0.00 0.00 0.00 3.41
2093 2633 2.287103 CACGCAATCACATCTCATCCAG 59.713 50.000 0.00 0.00 0.00 3.86
2094 2634 2.093288 ACGCAATCACATCTCATCCAGT 60.093 45.455 0.00 0.00 0.00 4.00
2095 2635 2.543012 CGCAATCACATCTCATCCAGTC 59.457 50.000 0.00 0.00 0.00 3.51
2096 2636 3.538591 GCAATCACATCTCATCCAGTCA 58.461 45.455 0.00 0.00 0.00 3.41
2097 2637 3.560481 GCAATCACATCTCATCCAGTCAG 59.440 47.826 0.00 0.00 0.00 3.51
2098 2638 4.127907 CAATCACATCTCATCCAGTCAGG 58.872 47.826 0.00 0.00 39.47 3.86
2126 2666 2.587956 CGTCACGTTCCACGAAGATTA 58.412 47.619 2.75 0.00 46.05 1.75
2137 2677 3.119602 CCACGAAGATTACCGAAGTCAGA 60.120 47.826 0.00 0.00 0.00 3.27
2159 2699 3.646162 ACACACAATCCACTAAGTCCAGA 59.354 43.478 0.00 0.00 0.00 3.86
2166 2706 6.777580 ACAATCCACTAAGTCCAGACAAATTT 59.222 34.615 0.00 0.00 0.00 1.82
2178 2718 1.726248 GACAAATTTGGTGCAATCCGC 59.274 47.619 21.74 0.00 42.89 5.54
2180 2720 2.224257 ACAAATTTGGTGCAATCCGCTT 60.224 40.909 21.74 0.00 43.06 4.68
2204 2744 1.667191 CAGCTTCAGTCTGCGCTGT 60.667 57.895 24.37 0.00 43.53 4.40
2275 2892 7.224753 CACTTTTCAACTGAGCTAGAACAGTAA 59.775 37.037 17.97 10.12 44.94 2.24
2333 2960 6.065374 TGCCAAAGTTAACCACTTATTCAGA 58.935 36.000 0.88 0.00 45.77 3.27
2334 2961 6.719370 TGCCAAAGTTAACCACTTATTCAGAT 59.281 34.615 0.88 0.00 45.77 2.90
2335 2962 7.232534 TGCCAAAGTTAACCACTTATTCAGATT 59.767 33.333 0.88 0.00 45.77 2.40
2336 2963 7.755373 GCCAAAGTTAACCACTTATTCAGATTC 59.245 37.037 0.88 0.00 45.77 2.52
2337 2964 8.792633 CCAAAGTTAACCACTTATTCAGATTCA 58.207 33.333 0.88 0.00 45.77 2.57
2466 3111 7.987458 GTCTTGGAATTCTATACAGTGATGGAA 59.013 37.037 5.23 0.65 31.74 3.53
2472 3117 7.741027 ATTCTATACAGTGATGGAATGCAAG 57.259 36.000 0.00 0.00 36.13 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.006989 TGCTTACGCTGATGTTGGTAATT 58.993 39.130 0.00 0.00 36.97 1.40
1 2 3.605634 TGCTTACGCTGATGTTGGTAAT 58.394 40.909 0.00 0.00 36.97 1.89
2 3 3.046968 TGCTTACGCTGATGTTGGTAA 57.953 42.857 0.00 0.00 36.97 2.85
3 4 2.753055 TGCTTACGCTGATGTTGGTA 57.247 45.000 0.00 0.00 36.97 3.25
4 5 1.890876 TTGCTTACGCTGATGTTGGT 58.109 45.000 0.00 0.00 36.97 3.67
5 6 2.162208 ACATTGCTTACGCTGATGTTGG 59.838 45.455 7.59 0.00 39.11 3.77
6 7 3.165890 CACATTGCTTACGCTGATGTTG 58.834 45.455 9.80 4.74 39.69 3.33
7 8 2.414559 GCACATTGCTTACGCTGATGTT 60.415 45.455 9.80 0.00 40.96 2.71
8 9 1.131126 GCACATTGCTTACGCTGATGT 59.869 47.619 7.59 7.59 40.96 3.06
9 10 1.130938 TGCACATTGCTTACGCTGATG 59.869 47.619 0.00 6.60 45.31 3.07
10 11 1.131126 GTGCACATTGCTTACGCTGAT 59.869 47.619 13.17 0.00 45.31 2.90
11 12 0.516877 GTGCACATTGCTTACGCTGA 59.483 50.000 13.17 0.00 45.31 4.26
12 13 0.790495 CGTGCACATTGCTTACGCTG 60.790 55.000 18.64 0.00 45.31 5.18
13 14 1.497278 CGTGCACATTGCTTACGCT 59.503 52.632 18.64 0.00 45.31 5.07
14 15 1.511887 CCGTGCACATTGCTTACGC 60.512 57.895 18.64 0.00 45.31 4.42
15 16 1.072391 TACCGTGCACATTGCTTACG 58.928 50.000 18.64 0.00 45.31 3.18
16 17 2.723618 CGTTACCGTGCACATTGCTTAC 60.724 50.000 18.64 4.21 45.31 2.34
17 18 1.461512 CGTTACCGTGCACATTGCTTA 59.538 47.619 18.64 0.00 45.31 3.09
24 25 1.584175 AATTGTCGTTACCGTGCACA 58.416 45.000 18.64 0.00 35.01 4.57
25 26 2.673976 AAATTGTCGTTACCGTGCAC 57.326 45.000 6.82 6.82 35.01 4.57
30 31 9.454585 TGATAAGATAGTAAATTGTCGTTACCG 57.545 33.333 0.00 0.00 32.83 4.02
78 79 1.630369 AGCCTAGTGTTCCTTGCATGA 59.370 47.619 0.00 0.00 0.00 3.07
95 96 2.683362 GTTCCCTTACTATGTGCAAGCC 59.317 50.000 0.00 0.00 0.00 4.35
96 97 3.127030 GTGTTCCCTTACTATGTGCAAGC 59.873 47.826 0.00 0.00 0.00 4.01
101 102 3.937814 TGCTGTGTTCCCTTACTATGTG 58.062 45.455 0.00 0.00 0.00 3.21
102 103 4.844349 ATGCTGTGTTCCCTTACTATGT 57.156 40.909 0.00 0.00 0.00 2.29
199 206 3.134574 AGACGGCTTGGTTTGATGTAA 57.865 42.857 0.00 0.00 0.00 2.41
213 220 7.549134 TGGTTAATCATCATTATCATAGACGGC 59.451 37.037 0.00 0.00 0.00 5.68
222 229 9.716531 TGATCTGTCTGGTTAATCATCATTATC 57.283 33.333 0.00 0.76 0.00 1.75
228 235 5.363101 TGCTGATCTGTCTGGTTAATCATC 58.637 41.667 1.27 0.00 0.00 2.92
231 238 4.574013 CCTTGCTGATCTGTCTGGTTAATC 59.426 45.833 1.27 0.00 0.00 1.75
234 241 3.173151 TCCTTGCTGATCTGTCTGGTTA 58.827 45.455 1.27 0.00 0.00 2.85
268 275 1.682451 CCGTCGAGGAATTGGGCCTA 61.682 60.000 4.53 0.00 45.00 3.93
286 293 1.169661 TGTGGTGGTTGCGTTGATCC 61.170 55.000 0.00 0.00 0.00 3.36
332 339 1.992667 CGCGTCTCTGAATTTACTGCA 59.007 47.619 0.00 0.00 0.00 4.41
349 357 4.760047 CCCCCTGTTCTGACCGCG 62.760 72.222 0.00 0.00 0.00 6.46
373 381 0.178961 GTGAGAAAACCCTGCCCCTT 60.179 55.000 0.00 0.00 0.00 3.95
806 816 3.291383 TTTTGCGGCGAACCCCAG 61.291 61.111 12.98 0.00 0.00 4.45
864 874 3.610669 CCCCTCCTCGGCATCTCG 61.611 72.222 0.00 0.00 0.00 4.04
963 1015 0.172352 AATTATTGGGCCAACGCACG 59.828 50.000 23.59 0.00 43.51 5.34
1007 1059 4.913968 AGCCCACCATATTGTATAAGAGGT 59.086 41.667 0.00 0.00 0.00 3.85
1017 1069 1.111116 CCAGCCAGCCCACCATATTG 61.111 60.000 0.00 0.00 0.00 1.90
1130 1221 2.504244 GCTTCGACGAGACCACCG 60.504 66.667 0.00 0.00 0.00 4.94
1333 1424 3.494336 CTTCTTGCGCCGCTCCTG 61.494 66.667 11.67 0.00 0.00 3.86
1426 1524 5.348724 GCATCAAGAACAACAGACTAATCGA 59.651 40.000 0.00 0.00 0.00 3.59
1499 1600 5.390885 CCAAATGATACACGGTGAAGAACAG 60.391 44.000 16.29 0.00 0.00 3.16
1504 1605 3.374058 GTCCCAAATGATACACGGTGAAG 59.626 47.826 16.29 0.00 0.00 3.02
1510 1611 1.593006 GCTCGTCCCAAATGATACACG 59.407 52.381 0.00 0.00 0.00 4.49
1511 1612 2.609459 CAGCTCGTCCCAAATGATACAC 59.391 50.000 0.00 0.00 0.00 2.90
1533 1642 2.138320 CCAGCAGCAGGATATACAACG 58.862 52.381 0.00 0.00 0.00 4.10
1535 1644 1.421268 CCCCAGCAGCAGGATATACAA 59.579 52.381 5.14 0.00 0.00 2.41
1539 1648 0.474466 TAGCCCCAGCAGCAGGATAT 60.474 55.000 5.14 0.00 43.56 1.63
1564 1691 6.659668 TCTTATATTATGAGACGGAGGGAGTG 59.340 42.308 0.00 0.00 0.00 3.51
1566 1693 7.540299 GTTCTTATATTATGAGACGGAGGGAG 58.460 42.308 0.00 0.00 0.00 4.30
1567 1694 6.150641 CGTTCTTATATTATGAGACGGAGGGA 59.849 42.308 0.00 0.00 0.00 4.20
1568 1695 6.072064 ACGTTCTTATATTATGAGACGGAGGG 60.072 42.308 16.71 2.79 0.00 4.30
1569 1696 6.910995 ACGTTCTTATATTATGAGACGGAGG 58.089 40.000 16.71 6.29 0.00 4.30
1570 1697 8.798748 AAACGTTCTTATATTATGAGACGGAG 57.201 34.615 0.00 6.40 0.00 4.63
1571 1698 9.590451 AAAAACGTTCTTATATTATGAGACGGA 57.410 29.630 0.00 0.00 0.00 4.69
1572 1699 9.845305 GAAAAACGTTCTTATATTATGAGACGG 57.155 33.333 0.00 8.31 0.00 4.79
1592 1719 4.728608 CACTGAAACACTAGCGTGAAAAAC 59.271 41.667 0.00 0.00 43.97 2.43
1593 1720 4.729458 GCACTGAAACACTAGCGTGAAAAA 60.729 41.667 0.00 0.00 43.97 1.94
1594 1721 3.242608 GCACTGAAACACTAGCGTGAAAA 60.243 43.478 0.00 0.00 43.97 2.29
1595 1722 2.286833 GCACTGAAACACTAGCGTGAAA 59.713 45.455 0.00 0.00 43.97 2.69
1596 1723 1.864711 GCACTGAAACACTAGCGTGAA 59.135 47.619 0.00 0.00 43.97 3.18
1597 1724 1.202475 TGCACTGAAACACTAGCGTGA 60.202 47.619 0.00 0.00 43.97 4.35
1598 1725 1.217001 TGCACTGAAACACTAGCGTG 58.783 50.000 0.00 0.00 46.63 5.34
1599 1726 1.948104 TTGCACTGAAACACTAGCGT 58.052 45.000 0.00 0.00 0.00 5.07
1600 1727 2.472886 CGATTGCACTGAAACACTAGCG 60.473 50.000 0.00 0.00 0.00 4.26
1601 1728 2.726066 GCGATTGCACTGAAACACTAGC 60.726 50.000 0.00 0.00 42.15 3.42
1602 1729 2.738846 AGCGATTGCACTGAAACACTAG 59.261 45.455 7.90 0.00 46.23 2.57
1603 1730 2.480037 CAGCGATTGCACTGAAACACTA 59.520 45.455 7.90 0.00 46.23 2.74
1604 1731 1.265095 CAGCGATTGCACTGAAACACT 59.735 47.619 7.90 0.00 46.23 3.55
1605 1732 1.264020 TCAGCGATTGCACTGAAACAC 59.736 47.619 7.90 0.00 46.23 3.32
1606 1733 1.592064 TCAGCGATTGCACTGAAACA 58.408 45.000 7.90 0.00 46.23 2.83
1607 1734 2.686558 TTCAGCGATTGCACTGAAAC 57.313 45.000 13.41 0.00 46.89 2.78
1622 1749 3.183373 GCTCAGACGTCTTTTCAGTTCAG 59.817 47.826 17.26 0.10 0.00 3.02
1623 1750 3.123804 GCTCAGACGTCTTTTCAGTTCA 58.876 45.455 17.26 0.00 0.00 3.18
1624 1751 3.385577 AGCTCAGACGTCTTTTCAGTTC 58.614 45.455 17.26 1.22 0.00 3.01
1625 1752 3.460857 AGCTCAGACGTCTTTTCAGTT 57.539 42.857 17.26 4.80 0.00 3.16
1627 1754 3.060003 CACAAGCTCAGACGTCTTTTCAG 60.060 47.826 17.26 10.49 0.00 3.02
1628 1755 2.866156 CACAAGCTCAGACGTCTTTTCA 59.134 45.455 17.26 0.00 0.00 2.69
1665 1857 0.466922 GCAGGGGATTCAGTCATGGG 60.467 60.000 0.00 0.00 0.00 4.00
1720 1912 9.908152 GCTAAACATCCAACTAATAAAACAGTT 57.092 29.630 0.00 0.00 35.38 3.16
1728 1920 9.515226 ACTGAAAAGCTAAACATCCAACTAATA 57.485 29.630 0.00 0.00 0.00 0.98
1729 1921 8.409358 ACTGAAAAGCTAAACATCCAACTAAT 57.591 30.769 0.00 0.00 0.00 1.73
1781 1973 3.240069 CAGACAACGGAACCTTACTACG 58.760 50.000 0.00 0.00 0.00 3.51
1835 2342 2.096819 TCAACAGCGACAGTTTTGTTCC 59.903 45.455 0.00 0.00 37.76 3.62
1844 2351 2.549754 AGAACCAAATCAACAGCGACAG 59.450 45.455 0.00 0.00 0.00 3.51
1855 2362 4.646572 AGTTCAGACCTCAGAACCAAATC 58.353 43.478 6.89 0.00 41.48 2.17
1898 2405 2.594654 CGTCCGAAAGAGAAATCAGACG 59.405 50.000 0.00 0.00 39.29 4.18
1912 2419 2.036217 ACAACACAAGTATCCGTCCGAA 59.964 45.455 0.00 0.00 0.00 4.30
1969 2491 4.357699 GATCCGATCCAGCAGCTG 57.642 61.111 16.23 16.23 0.00 4.24
1977 2499 0.322008 GAGCCAATGGGATCCGATCC 60.322 60.000 18.03 18.03 43.99 3.36
1978 2500 3.239861 GAGCCAATGGGATCCGATC 57.760 57.895 9.99 0.00 43.99 3.69
2044 2584 0.181350 GGGATCTTCTTGCCGGTCAT 59.819 55.000 1.90 0.00 0.00 3.06
2047 2587 0.322546 GTTGGGATCTTCTTGCCGGT 60.323 55.000 1.90 0.00 0.00 5.28
2072 2612 2.282407 TGGATGAGATGTGATTGCGTG 58.718 47.619 0.00 0.00 0.00 5.34
2092 2632 1.228583 TGACGGCTGACTCCTGACT 60.229 57.895 0.00 0.00 0.00 3.41
2093 2633 1.080434 GTGACGGCTGACTCCTGAC 60.080 63.158 0.00 0.00 0.00 3.51
2094 2634 2.626780 CGTGACGGCTGACTCCTGA 61.627 63.158 0.00 0.00 0.00 3.86
2095 2635 2.126307 CGTGACGGCTGACTCCTG 60.126 66.667 0.00 0.00 0.00 3.86
2096 2636 2.143594 GAACGTGACGGCTGACTCCT 62.144 60.000 10.66 0.00 0.00 3.69
2097 2637 1.733399 GAACGTGACGGCTGACTCC 60.733 63.158 10.66 0.00 0.00 3.85
2098 2638 1.733399 GGAACGTGACGGCTGACTC 60.733 63.158 10.66 0.00 0.00 3.36
2126 2666 2.548067 GGATTGTGTGTCTGACTTCGGT 60.548 50.000 9.51 0.00 0.00 4.69
2137 2677 3.646162 TCTGGACTTAGTGGATTGTGTGT 59.354 43.478 0.00 0.00 0.00 3.72
2159 2699 1.794512 GCGGATTGCACCAAATTTGT 58.205 45.000 16.73 2.76 45.45 2.83
2178 2718 2.686235 CAGACTGAAGCTGGACTGAAG 58.314 52.381 0.00 0.00 0.00 3.02
2180 2720 0.319728 GCAGACTGAAGCTGGACTGA 59.680 55.000 6.65 0.00 34.00 3.41
2204 2744 5.409590 TCTCAAGGGATCTAAGAGATGGA 57.590 43.478 0.00 0.00 34.53 3.41
2235 2850 8.709646 CAGTTGAAAAGTGTTACCTACATACTC 58.290 37.037 0.00 0.00 42.28 2.59
2236 2851 8.603242 CAGTTGAAAAGTGTTACCTACATACT 57.397 34.615 0.00 0.00 42.28 2.12
2275 2892 7.062322 TGGCAATCTGTCAGATTTAATGGTAT 58.938 34.615 22.89 0.00 41.90 2.73
2333 2960 3.009916 AGGCTCCTGTTGATCACTTGAAT 59.990 43.478 0.00 0.00 0.00 2.57
2334 2961 2.373169 AGGCTCCTGTTGATCACTTGAA 59.627 45.455 0.00 0.00 0.00 2.69
2335 2962 1.980765 AGGCTCCTGTTGATCACTTGA 59.019 47.619 0.00 0.00 0.00 3.02
2336 2963 2.289882 TGAGGCTCCTGTTGATCACTTG 60.290 50.000 12.86 0.00 0.00 3.16
2337 2964 1.980765 TGAGGCTCCTGTTGATCACTT 59.019 47.619 12.86 0.00 0.00 3.16
2338 2965 1.649321 TGAGGCTCCTGTTGATCACT 58.351 50.000 12.86 0.00 0.00 3.41
2445 3090 6.712095 TGCATTCCATCACTGTATAGAATTCC 59.288 38.462 0.65 0.00 0.00 3.01
2455 3100 3.693085 GTCATCTTGCATTCCATCACTGT 59.307 43.478 0.00 0.00 0.00 3.55
2466 3111 7.472334 AAAAAGGTCTATTGTCATCTTGCAT 57.528 32.000 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.