Multiple sequence alignment - TraesCS2B01G483000

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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 TraesCS2B01G483000 chr2B 100.000 2261 0 0 1 2261 680445086 680447346 0.000000e+00 4176.0
1 TraesCS2B01G483000 chr2B 83.682 478 50 13 982 1449 680322523 680322982 2.080000e-115 425.0
2 TraesCS2B01G483000 chr2B 80.247 486 49 20 982 1457 680408969 680409417 2.800000e-84 322.0
3 TraesCS2B01G483000 chr2B 80.043 466 45 24 899 1353 680308624 680309052 3.650000e-78 302.0
4 TraesCS2B01G483000 chr2B 85.638 188 16 8 899 1079 680074664 680074847 1.070000e-43 187.0
5 TraesCS2B01G483000 chr2A 91.424 1271 76 13 710 1963 707235529 707236783 0.000000e+00 1712.0
6 TraesCS2B01G483000 chr2A 93.499 723 30 8 712 1427 707221827 707222539 0.000000e+00 1059.0
7 TraesCS2B01G483000 chr2A 86.293 642 71 10 21 647 2742397 2741758 0.000000e+00 682.0
8 TraesCS2B01G483000 chr2A 94.209 449 21 2 1742 2189 707225832 707226276 0.000000e+00 680.0
9 TraesCS2B01G483000 chr2A 84.770 696 63 15 772 1457 707105022 707105684 0.000000e+00 658.0
10 TraesCS2B01G483000 chr2A 91.239 331 22 4 1419 1746 707222675 707223001 5.730000e-121 444.0
11 TraesCS2B01G483000 chr2A 83.444 453 53 12 982 1429 707077470 707077905 3.500000e-108 401.0
12 TraesCS2B01G483000 chr2A 84.866 337 40 6 1849 2185 707106708 707107033 1.670000e-86 329.0
13 TraesCS2B01G483000 chr2A 89.873 237 20 2 1955 2191 707242218 707242450 3.650000e-78 302.0
14 TraesCS2B01G483000 chr2A 76.686 519 67 33 897 1406 707064204 707064677 2.900000e-59 239.0
15 TraesCS2B01G483000 chr2D 92.023 1053 53 10 710 1758 567677614 567678639 0.000000e+00 1450.0
16 TraesCS2B01G483000 chr2D 93.654 457 21 4 1742 2195 567679265 567679716 0.000000e+00 676.0
17 TraesCS2B01G483000 chr2D 92.727 275 13 5 1923 2196 567932469 567932737 7.570000e-105 390.0
18 TraesCS2B01G483000 chr2D 89.109 303 16 3 1627 1928 567806165 567806451 5.940000e-96 361.0
19 TraesCS2B01G483000 chr2D 79.550 489 48 12 982 1457 567594842 567595291 3.650000e-78 302.0
20 TraesCS2B01G483000 chr2D 79.412 476 49 19 993 1457 567642038 567642475 7.900000e-75 291.0
21 TraesCS2B01G483000 chr2D 92.147 191 12 3 931 1118 567805955 567806145 1.330000e-67 267.0
22 TraesCS2B01G483000 chr2D 97.500 120 3 0 710 829 567802790 567802909 2.940000e-49 206.0
23 TraesCS2B01G483000 chr2D 77.428 381 52 20 973 1353 567589844 567590190 1.770000e-46 196.0
24 TraesCS2B01G483000 chr2D 77.262 409 38 28 897 1291 567584593 567584960 2.960000e-44 189.0
25 TraesCS2B01G483000 chr2D 85.638 188 16 6 899 1079 567057391 567057574 1.070000e-43 187.0
26 TraesCS2B01G483000 chr2D 97.619 84 2 0 820 903 567804071 567804154 6.510000e-31 145.0
27 TraesCS2B01G483000 chr6A 86.061 660 74 13 17 662 608656643 608655988 0.000000e+00 693.0
28 TraesCS2B01G483000 chr5D 85.802 655 65 20 23 657 498464493 498465139 0.000000e+00 669.0
29 TraesCS2B01G483000 chr5D 83.614 653 88 11 21 658 438401379 438400731 1.490000e-166 595.0
30 TraesCS2B01G483000 chr5D 100.000 28 0 0 1103 1130 379839766 379839739 4.000000e-03 52.8
31 TraesCS2B01G483000 chr7A 85.891 645 70 14 21 647 510900606 510901247 0.000000e+00 667.0
32 TraesCS2B01G483000 chr7A 84.954 658 75 14 21 658 142951038 142950385 0.000000e+00 645.0
33 TraesCS2B01G483000 chr7A 85.185 648 73 17 20 653 729559666 729559028 0.000000e+00 643.0
34 TraesCS2B01G483000 chr7A 93.103 58 4 0 2201 2258 701462996 701463053 4.000000e-13 86.1
35 TraesCS2B01G483000 chr7A 86.538 52 6 1 1616 1667 74598577 74598627 3.140000e-04 56.5
36 TraesCS2B01G483000 chr7D 85.168 654 79 11 18 657 635663030 635663679 0.000000e+00 654.0
37 TraesCS2B01G483000 chr5B 84.533 653 79 13 21 657 668107156 668107802 5.300000e-176 627.0
38 TraesCS2B01G483000 chr1D 84.101 673 71 17 21 670 445097048 445096389 3.190000e-173 617.0
39 TraesCS2B01G483000 chr1B 83.920 653 87 11 21 659 22398570 22399218 1.920000e-170 608.0
40 TraesCS2B01G483000 chr1B 83.717 651 87 12 21 657 22518515 22519160 4.160000e-167 597.0
41 TraesCS2B01G483000 chr1B 83.902 615 79 6 37 645 433138754 433138154 9.060000e-159 569.0
42 TraesCS2B01G483000 chr5A 82.695 653 95 13 20 658 635280891 635281539 4.220000e-157 564.0
43 TraesCS2B01G483000 chr5A 91.228 57 4 1 1612 1668 487950222 487950167 2.410000e-10 76.8
44 TraesCS2B01G483000 chr3A 86.564 521 54 7 141 649 711257142 711256626 5.450000e-156 560.0
45 TraesCS2B01G483000 chr3A 94.872 39 2 0 1614 1652 7443860 7443898 6.740000e-06 62.1
46 TraesCS2B01G483000 chr3D 86.151 491 53 8 183 662 79442115 79441629 1.200000e-142 516.0
47 TraesCS2B01G483000 chr3D 92.308 52 2 1 2198 2249 48417662 48417711 3.120000e-09 73.1
48 TraesCS2B01G483000 chrUn 89.286 56 5 1 2194 2249 90937238 90937292 4.030000e-08 69.4


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 TraesCS2B01G483000 chr2B 680445086 680447346 2260 False 4176.000000 4176 100.000000 1 2261 1 chr2B.!!$F5 2260
1 TraesCS2B01G483000 chr2A 707235529 707236783 1254 False 1712.000000 1712 91.424000 710 1963 1 chr2A.!!$F3 1253
2 TraesCS2B01G483000 chr2A 707221827 707226276 4449 False 727.666667 1059 92.982333 712 2189 3 chr2A.!!$F6 1477
3 TraesCS2B01G483000 chr2A 2741758 2742397 639 True 682.000000 682 86.293000 21 647 1 chr2A.!!$R1 626
4 TraesCS2B01G483000 chr2A 707105022 707107033 2011 False 493.500000 658 84.818000 772 2185 2 chr2A.!!$F5 1413
5 TraesCS2B01G483000 chr2D 567677614 567679716 2102 False 1063.000000 1450 92.838500 710 2195 2 chr2D.!!$F7 1485
6 TraesCS2B01G483000 chr2D 567802790 567806451 3661 False 244.750000 361 94.093750 710 1928 4 chr2D.!!$F8 1218
7 TraesCS2B01G483000 chr6A 608655988 608656643 655 True 693.000000 693 86.061000 17 662 1 chr6A.!!$R1 645
8 TraesCS2B01G483000 chr5D 498464493 498465139 646 False 669.000000 669 85.802000 23 657 1 chr5D.!!$F1 634
9 TraesCS2B01G483000 chr5D 438400731 438401379 648 True 595.000000 595 83.614000 21 658 1 chr5D.!!$R2 637
10 TraesCS2B01G483000 chr7A 510900606 510901247 641 False 667.000000 667 85.891000 21 647 1 chr7A.!!$F2 626
11 TraesCS2B01G483000 chr7A 142950385 142951038 653 True 645.000000 645 84.954000 21 658 1 chr7A.!!$R1 637
12 TraesCS2B01G483000 chr7A 729559028 729559666 638 True 643.000000 643 85.185000 20 653 1 chr7A.!!$R2 633
13 TraesCS2B01G483000 chr7D 635663030 635663679 649 False 654.000000 654 85.168000 18 657 1 chr7D.!!$F1 639
14 TraesCS2B01G483000 chr5B 668107156 668107802 646 False 627.000000 627 84.533000 21 657 1 chr5B.!!$F1 636
15 TraesCS2B01G483000 chr1D 445096389 445097048 659 True 617.000000 617 84.101000 21 670 1 chr1D.!!$R1 649
16 TraesCS2B01G483000 chr1B 22398570 22399218 648 False 608.000000 608 83.920000 21 659 1 chr1B.!!$F1 638
17 TraesCS2B01G483000 chr1B 22518515 22519160 645 False 597.000000 597 83.717000 21 657 1 chr1B.!!$F2 636
18 TraesCS2B01G483000 chr1B 433138154 433138754 600 True 569.000000 569 83.902000 37 645 1 chr1B.!!$R1 608
19 TraesCS2B01G483000 chr5A 635280891 635281539 648 False 564.000000 564 82.695000 20 658 1 chr5A.!!$F1 638
20 TraesCS2B01G483000 chr3A 711256626 711257142 516 True 560.000000 560 86.564000 141 649 1 chr3A.!!$R1 508

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
439 472 0.61326 TCTGGTGCGCTGGTCTTATT 59.387 50.0 9.73 0.0 0.0 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2213 9754 0.119358 AGAGGCTGGGGTCTTAACCT 59.881 55.0 0.0 0.0 45.66 3.5 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 125 2.364973 TAGGCCATGGAGGTGCGA 60.365 61.111 18.40 0.00 40.61 5.10
157 172 4.466898 GGAGGGACCCCGTTCTTA 57.533 61.111 7.00 0.00 41.95 2.10
211 230 2.046314 CGGCGGTGATGTCCCTTT 60.046 61.111 0.00 0.00 0.00 3.11
271 302 1.739667 CATCATCGGAGGGCGTGTA 59.260 57.895 0.00 0.00 0.00 2.90
298 331 0.744874 GTCTCCATCGGATCCACGAA 59.255 55.000 13.41 0.00 46.92 3.85
315 348 1.996898 CGAAATTCGATCGGTGTTGGA 59.003 47.619 16.41 0.00 43.74 3.53
385 418 5.370679 GTGTTTACAGGTTTGACCCTTCTA 58.629 41.667 0.00 0.00 39.75 2.10
394 427 5.482878 AGGTTTGACCCTTCTAATCTACGAA 59.517 40.000 0.00 0.00 39.75 3.85
435 468 1.599606 CTACTCTGGTGCGCTGGTCT 61.600 60.000 9.73 0.00 0.00 3.85
439 472 0.613260 TCTGGTGCGCTGGTCTTATT 59.387 50.000 9.73 0.00 0.00 1.40
544 579 1.004560 CTTTGGCTCGCTCTGGTGA 60.005 57.895 0.00 0.00 0.00 4.02
572 607 1.982395 TCGCTAGGTGGTCCACAGG 60.982 63.158 23.48 12.93 35.86 4.00
578 613 3.064324 GTGGTCCACAGGCATGGC 61.064 66.667 17.59 12.14 39.85 4.40
769 815 1.479323 CAAATGGAAGCATGGGTCTGG 59.521 52.381 0.00 0.00 0.00 3.86
964 3960 1.029408 TCAAACGCAGCCACACAACT 61.029 50.000 0.00 0.00 0.00 3.16
966 3962 0.748005 AAACGCAGCCACACAACTCT 60.748 50.000 0.00 0.00 0.00 3.24
967 3963 1.439353 AACGCAGCCACACAACTCTG 61.439 55.000 0.00 0.00 0.00 3.35
979 3982 5.292765 CACACAACTCTGTCTCAGTACATT 58.707 41.667 0.00 0.00 31.64 2.71
1089 4092 0.178903 ACCAGAAGGACCAGGCACTA 60.179 55.000 0.00 0.00 35.49 2.74
1407 4412 6.418226 CCTTAATGAGCGTCTGTATCAACTAC 59.582 42.308 0.00 0.00 0.00 2.73
1450 4600 9.396022 TCTTTCAGTTCATGTTCTAGTTTTTCT 57.604 29.630 0.00 0.00 0.00 2.52
1460 4610 6.055588 TGTTCTAGTTTTTCTGTTCCTCTGG 58.944 40.000 0.00 0.00 0.00 3.86
1572 4731 6.450545 TCAGGAGCTTGTATCATCGATTTAG 58.549 40.000 0.00 0.00 0.00 1.85
1605 4764 2.837947 TGATCACAAGGTCCCATCTCT 58.162 47.619 0.00 0.00 0.00 3.10
1610 4769 0.179936 CAAGGTCCCATCTCTGGAGC 59.820 60.000 0.35 0.35 46.37 4.70
1615 4775 2.505819 GGTCCCATCTCTGGAGCTTTTA 59.494 50.000 1.44 0.00 46.37 1.52
1619 4779 5.298026 GTCCCATCTCTGGAGCTTTTATTTC 59.702 44.000 0.00 0.00 46.37 2.17
1656 4824 3.802866 AGCTTCCTCTCCGATTTTCATC 58.197 45.455 0.00 0.00 0.00 2.92
1668 4836 5.476599 TCCGATTTTCATCAACAGAAACCAT 59.523 36.000 0.00 0.00 34.94 3.55
1735 4919 2.551355 ACGACGACACATGATCTGAG 57.449 50.000 0.00 0.00 0.00 3.35
1823 8484 2.263895 TCCTACAGCCCACCATACTT 57.736 50.000 0.00 0.00 0.00 2.24
1883 9415 3.487544 GGAATTCGTTTCTACTGGCATGC 60.488 47.826 9.90 9.90 34.56 4.06
1910 9449 0.107703 TTTGAGGCGAGCTGGTATGG 60.108 55.000 0.00 0.00 0.00 2.74
2030 9571 4.384547 GCACATATCCAAAACCACGAAAAC 59.615 41.667 0.00 0.00 0.00 2.43
2041 9582 3.888583 ACCACGAAAACAAGGGAAACTA 58.111 40.909 0.00 0.00 0.00 2.24
2107 9648 6.207417 ACCTTTCATGTTCTTCAATGGTGTAG 59.793 38.462 0.00 0.00 0.00 2.74
2123 9664 3.808174 GGTGTAGTTTGAGTCACTGAACC 59.192 47.826 0.00 0.00 0.00 3.62
2124 9665 3.489785 GTGTAGTTTGAGTCACTGAACCG 59.510 47.826 0.00 0.00 0.00 4.44
2125 9666 3.382227 TGTAGTTTGAGTCACTGAACCGA 59.618 43.478 0.00 0.00 0.00 4.69
2126 9667 3.753294 AGTTTGAGTCACTGAACCGAT 57.247 42.857 0.00 0.00 0.00 4.18
2158 9699 0.251916 CAACCCAGGTCCGCTTGATA 59.748 55.000 0.00 0.00 0.00 2.15
2159 9700 1.134098 CAACCCAGGTCCGCTTGATAT 60.134 52.381 0.00 0.00 0.00 1.63
2160 9701 1.213296 ACCCAGGTCCGCTTGATATT 58.787 50.000 0.00 0.00 0.00 1.28
2161 9702 1.564348 ACCCAGGTCCGCTTGATATTT 59.436 47.619 0.00 0.00 0.00 1.40
2191 9732 5.535753 TGATCAGAATAGAATTCGAGGCA 57.464 39.130 0.00 0.00 0.00 4.75
2193 9734 4.327982 TCAGAATAGAATTCGAGGCAGG 57.672 45.455 0.00 0.00 0.00 4.85
2194 9735 2.805099 CAGAATAGAATTCGAGGCAGGC 59.195 50.000 0.00 0.00 0.00 4.85
2195 9736 1.795286 GAATAGAATTCGAGGCAGGCG 59.205 52.381 0.00 0.00 0.00 5.52
2196 9737 1.040646 ATAGAATTCGAGGCAGGCGA 58.959 50.000 0.00 0.00 35.76 5.54
2197 9738 1.040646 TAGAATTCGAGGCAGGCGAT 58.959 50.000 0.00 0.00 37.64 4.58
2198 9739 0.179000 AGAATTCGAGGCAGGCGATT 59.821 50.000 0.00 0.00 37.64 3.34
2199 9740 1.017387 GAATTCGAGGCAGGCGATTT 58.983 50.000 0.00 0.00 37.64 2.17
2200 9741 1.401905 GAATTCGAGGCAGGCGATTTT 59.598 47.619 0.00 0.00 37.64 1.82
2201 9742 1.463674 ATTCGAGGCAGGCGATTTTT 58.536 45.000 0.00 0.00 37.64 1.94
2223 9764 6.474140 TTTTTGGAAAAGGAGGTTAAGACC 57.526 37.500 0.00 0.00 46.92 3.85
2232 9773 2.698168 GGTTAAGACCCCAGCCTCT 58.302 57.895 0.00 0.00 40.25 3.69
2233 9774 0.253327 GGTTAAGACCCCAGCCTCTG 59.747 60.000 0.00 0.00 40.25 3.35
2234 9775 0.393132 GTTAAGACCCCAGCCTCTGC 60.393 60.000 0.00 0.00 37.95 4.26
2235 9776 0.840288 TTAAGACCCCAGCCTCTGCA 60.840 55.000 0.00 0.00 41.13 4.41
2236 9777 0.621571 TAAGACCCCAGCCTCTGCAT 60.622 55.000 0.00 0.00 41.13 3.96
2237 9778 1.919600 AAGACCCCAGCCTCTGCATC 61.920 60.000 0.00 0.00 41.13 3.91
2238 9779 2.611800 ACCCCAGCCTCTGCATCA 60.612 61.111 0.00 0.00 41.13 3.07
2239 9780 2.202236 GACCCCAGCCTCTGCATCAA 62.202 60.000 0.00 0.00 41.13 2.57
2240 9781 1.229359 CCCCAGCCTCTGCATCAAT 59.771 57.895 0.00 0.00 41.13 2.57
2241 9782 0.822532 CCCCAGCCTCTGCATCAATC 60.823 60.000 0.00 0.00 41.13 2.67
2242 9783 1.164662 CCCAGCCTCTGCATCAATCG 61.165 60.000 0.00 0.00 41.13 3.34
2243 9784 0.179065 CCAGCCTCTGCATCAATCGA 60.179 55.000 0.00 0.00 41.13 3.59
2244 9785 1.542767 CCAGCCTCTGCATCAATCGAT 60.543 52.381 0.00 0.00 41.13 3.59
2245 9786 2.289257 CCAGCCTCTGCATCAATCGATA 60.289 50.000 0.00 0.00 41.13 2.92
2246 9787 2.735663 CAGCCTCTGCATCAATCGATAC 59.264 50.000 0.00 0.00 41.13 2.24
2247 9788 2.366590 AGCCTCTGCATCAATCGATACA 59.633 45.455 0.00 0.00 41.13 2.29
2248 9789 3.007723 AGCCTCTGCATCAATCGATACAT 59.992 43.478 0.00 0.00 41.13 2.29
2249 9790 4.221482 AGCCTCTGCATCAATCGATACATA 59.779 41.667 0.00 0.00 41.13 2.29
2250 9791 5.105023 AGCCTCTGCATCAATCGATACATAT 60.105 40.000 0.00 0.00 41.13 1.78
2251 9792 5.006455 GCCTCTGCATCAATCGATACATATG 59.994 44.000 0.00 0.00 37.47 1.78
2252 9793 5.522824 CCTCTGCATCAATCGATACATATGG 59.477 44.000 7.80 0.00 0.00 2.74
2253 9794 6.041423 TCTGCATCAATCGATACATATGGT 57.959 37.500 7.80 0.00 0.00 3.55
2254 9795 6.101997 TCTGCATCAATCGATACATATGGTC 58.898 40.000 7.80 4.11 0.00 4.02
2255 9796 5.792741 TGCATCAATCGATACATATGGTCA 58.207 37.500 7.80 0.00 0.00 4.02
2256 9797 6.408869 TGCATCAATCGATACATATGGTCAT 58.591 36.000 7.80 0.00 0.00 3.06
2257 9798 6.536224 TGCATCAATCGATACATATGGTCATC 59.464 38.462 7.80 5.99 0.00 2.92
2258 9799 6.760298 GCATCAATCGATACATATGGTCATCT 59.240 38.462 7.80 0.00 0.00 2.90
2259 9800 7.279536 GCATCAATCGATACATATGGTCATCTT 59.720 37.037 7.80 0.00 0.00 2.40
2260 9801 9.159364 CATCAATCGATACATATGGTCATCTTT 57.841 33.333 7.80 1.87 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.222872 AGAGATGGAAGAATAGGTGCTTAATG 58.777 38.462 0.00 0.00 0.00 1.90
2 3 6.814954 AGAGATGGAAGAATAGGTGCTTAA 57.185 37.500 0.00 0.00 0.00 1.85
3 4 6.814954 AAGAGATGGAAGAATAGGTGCTTA 57.185 37.500 0.00 0.00 0.00 3.09
5 6 5.397334 GGAAAGAGATGGAAGAATAGGTGCT 60.397 44.000 0.00 0.00 0.00 4.40
6 7 4.819088 GGAAAGAGATGGAAGAATAGGTGC 59.181 45.833 0.00 0.00 0.00 5.01
7 8 6.245890 AGGAAAGAGATGGAAGAATAGGTG 57.754 41.667 0.00 0.00 0.00 4.00
8 9 5.368230 GGAGGAAAGAGATGGAAGAATAGGT 59.632 44.000 0.00 0.00 0.00 3.08
9 10 5.606329 AGGAGGAAAGAGATGGAAGAATAGG 59.394 44.000 0.00 0.00 0.00 2.57
10 11 6.554605 AGAGGAGGAAAGAGATGGAAGAATAG 59.445 42.308 0.00 0.00 0.00 1.73
11 12 6.448202 AGAGGAGGAAAGAGATGGAAGAATA 58.552 40.000 0.00 0.00 0.00 1.75
12 13 5.287864 AGAGGAGGAAAGAGATGGAAGAAT 58.712 41.667 0.00 0.00 0.00 2.40
13 14 4.693420 AGAGGAGGAAAGAGATGGAAGAA 58.307 43.478 0.00 0.00 0.00 2.52
14 15 4.344938 AGAGGAGGAAAGAGATGGAAGA 57.655 45.455 0.00 0.00 0.00 2.87
15 16 5.896678 TCTTAGAGGAGGAAAGAGATGGAAG 59.103 44.000 0.00 0.00 0.00 3.46
157 172 5.180492 TCAAGACGCCGAATTTAACAAGAAT 59.820 36.000 0.00 0.00 0.00 2.40
211 230 6.386927 AGAACATGGGAGACATTATTCCTACA 59.613 38.462 0.00 0.00 37.84 2.74
297 330 3.053831 AGTCCAACACCGATCGAATTT 57.946 42.857 18.66 2.82 0.00 1.82
298 331 2.762535 AGTCCAACACCGATCGAATT 57.237 45.000 18.66 4.60 0.00 2.17
315 348 4.524328 GGATTCAAACAGATCCACCAAAGT 59.476 41.667 0.00 0.00 33.55 2.66
385 418 7.921786 TCACCAATGAAGAAATTCGTAGATT 57.078 32.000 0.00 0.00 35.04 2.40
394 427 4.529377 AGCAACCATCACCAATGAAGAAAT 59.471 37.500 0.00 0.00 38.69 2.17
435 468 4.119862 GTCGTCATGCTAAGGCTCAATAA 58.880 43.478 0.00 0.00 39.59 1.40
439 472 1.186200 AGTCGTCATGCTAAGGCTCA 58.814 50.000 0.00 0.00 39.59 4.26
544 579 1.404391 CCACCTAGCGACGACTACAAT 59.596 52.381 0.00 0.00 0.00 2.71
572 607 9.403110 CAGAGATAATAAAAATTACAGCCATGC 57.597 33.333 0.00 0.00 0.00 4.06
964 3960 4.861196 AGGCTCTAATGTACTGAGACAGA 58.139 43.478 5.76 0.00 38.26 3.41
966 3962 3.954904 GGAGGCTCTAATGTACTGAGACA 59.045 47.826 15.23 0.00 38.26 3.41
967 3963 3.319689 GGGAGGCTCTAATGTACTGAGAC 59.680 52.174 15.23 0.00 36.17 3.36
979 3982 2.247699 TTGCTAACTGGGAGGCTCTA 57.752 50.000 15.23 3.15 0.00 2.43
1407 4412 7.042335 ACTGAAAGAAAATACAGACGATAGGG 58.958 38.462 0.00 0.00 37.86 3.53
1450 4600 5.694995 ACTGAAAGAAAATCCAGAGGAACA 58.305 37.500 0.00 0.00 37.43 3.18
1495 4645 9.918630 GACAAAGTAGTACTTATTAGGTTGACA 57.081 33.333 15.84 0.00 37.47 3.58
1552 4711 8.804688 AAGTACTAAATCGATGATACAAGCTC 57.195 34.615 0.00 0.00 0.00 4.09
1572 4731 5.934625 ACCTTGTGATCAAGTGATGAAGTAC 59.065 40.000 0.00 0.00 46.70 2.73
1683 4851 5.492855 TTCTGCTTGCCCTTAGTAGTTTA 57.507 39.130 0.00 0.00 0.00 2.01
1735 4919 4.985538 TGGGTATATCTCATTTTGCTCCC 58.014 43.478 0.00 0.00 0.00 4.30
1823 8484 7.469537 TTTTCTTTTACCAGAACAACTCCAA 57.530 32.000 0.00 0.00 32.28 3.53
1883 9415 4.576463 ACCAGCTCGCCTCAAATTAAATAG 59.424 41.667 0.00 0.00 0.00 1.73
1910 9449 9.751542 AACGCTTTGATATATCCTATATGTAGC 57.248 33.333 10.25 6.41 0.00 3.58
2030 9571 5.805728 ACCTGTATCAAGTAGTTTCCCTTG 58.194 41.667 0.00 0.00 39.50 3.61
2107 9648 2.408704 CGATCGGTTCAGTGACTCAAAC 59.591 50.000 7.38 0.03 0.00 2.93
2123 9664 1.226575 TTGCTACACCGCTCGATCG 60.227 57.895 9.36 9.36 0.00 3.69
2124 9665 1.146358 GGTTGCTACACCGCTCGATC 61.146 60.000 0.00 0.00 0.00 3.69
2125 9666 1.153628 GGTTGCTACACCGCTCGAT 60.154 57.895 0.00 0.00 0.00 3.59
2126 9667 2.260434 GGTTGCTACACCGCTCGA 59.740 61.111 0.00 0.00 0.00 4.04
2160 9701 8.996271 CGAATTCTATTCTGATCAATGGATGAA 58.004 33.333 3.52 0.00 42.54 2.57
2161 9702 8.370182 TCGAATTCTATTCTGATCAATGGATGA 58.630 33.333 3.52 0.00 43.67 2.92
2200 9741 5.364446 GGGTCTTAACCTCCTTTTCCAAAAA 59.636 40.000 0.00 0.00 45.66 1.94
2201 9742 4.897076 GGGTCTTAACCTCCTTTTCCAAAA 59.103 41.667 0.00 0.00 45.66 2.44
2202 9743 4.476297 GGGTCTTAACCTCCTTTTCCAAA 58.524 43.478 0.00 0.00 45.66 3.28
2203 9744 3.181426 GGGGTCTTAACCTCCTTTTCCAA 60.181 47.826 0.00 0.00 45.66 3.53
2204 9745 2.377531 GGGGTCTTAACCTCCTTTTCCA 59.622 50.000 0.00 0.00 45.66 3.53
2205 9746 2.377531 TGGGGTCTTAACCTCCTTTTCC 59.622 50.000 0.00 0.00 46.61 3.13
2206 9747 3.687125 CTGGGGTCTTAACCTCCTTTTC 58.313 50.000 0.00 0.00 46.61 2.29
2207 9748 2.225041 GCTGGGGTCTTAACCTCCTTTT 60.225 50.000 0.00 0.00 46.61 2.27
2208 9749 1.354705 GCTGGGGTCTTAACCTCCTTT 59.645 52.381 0.00 0.00 46.61 3.11
2209 9750 0.992695 GCTGGGGTCTTAACCTCCTT 59.007 55.000 0.00 0.00 46.61 3.36
2210 9751 0.914902 GGCTGGGGTCTTAACCTCCT 60.915 60.000 0.00 0.00 46.61 3.69
2211 9752 0.914902 AGGCTGGGGTCTTAACCTCC 60.915 60.000 0.00 0.00 46.61 4.30
2213 9754 0.119358 AGAGGCTGGGGTCTTAACCT 59.881 55.000 0.00 0.00 45.66 3.50
2214 9755 0.253327 CAGAGGCTGGGGTCTTAACC 59.747 60.000 0.00 0.00 45.65 2.85
2215 9756 0.393132 GCAGAGGCTGGGGTCTTAAC 60.393 60.000 0.00 0.00 36.96 2.01
2216 9757 0.840288 TGCAGAGGCTGGGGTCTTAA 60.840 55.000 0.00 0.00 41.91 1.85
2217 9758 0.621571 ATGCAGAGGCTGGGGTCTTA 60.622 55.000 0.00 0.00 41.91 2.10
2218 9759 1.919600 GATGCAGAGGCTGGGGTCTT 61.920 60.000 0.00 0.00 41.91 3.01
2219 9760 2.285969 ATGCAGAGGCTGGGGTCT 60.286 61.111 0.00 0.00 41.91 3.85
2220 9761 2.191641 GATGCAGAGGCTGGGGTC 59.808 66.667 0.00 0.00 41.91 4.46
2221 9762 1.578215 ATTGATGCAGAGGCTGGGGT 61.578 55.000 0.00 0.00 41.91 4.95
2222 9763 0.822532 GATTGATGCAGAGGCTGGGG 60.823 60.000 0.00 0.00 41.91 4.96
2223 9764 1.164662 CGATTGATGCAGAGGCTGGG 61.165 60.000 0.00 0.00 41.91 4.45
2224 9765 0.179065 TCGATTGATGCAGAGGCTGG 60.179 55.000 0.00 0.00 41.91 4.85
2225 9766 1.880271 ATCGATTGATGCAGAGGCTG 58.120 50.000 0.00 0.00 41.91 4.85
2226 9767 2.366590 TGTATCGATTGATGCAGAGGCT 59.633 45.455 9.48 0.00 41.50 4.58
2227 9768 2.759191 TGTATCGATTGATGCAGAGGC 58.241 47.619 9.48 0.00 41.50 4.70
2233 9774 6.760298 AGATGACCATATGTATCGATTGATGC 59.240 38.462 1.71 4.86 37.68 3.91
2234 9775 8.713737 AAGATGACCATATGTATCGATTGATG 57.286 34.615 1.71 2.58 35.99 3.07


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

AutoCloner maintained by Alex Coulton.