Multiple sequence alignment - TraesCS4A01G102900

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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 TraesCS4A01G102900 chr4A 100.000 4550 0 0 1 4550 115785784 115790333 0.000000e+00 8403
1 TraesCS4A01G102900 chr4A 78.935 864 156 20 2497 3344 900679 901532 8.550000e-157 564
2 TraesCS4A01G102900 chr4D 95.287 4562 169 20 1 4550 349192833 349188306 0.000000e+00 7191
3 TraesCS4A01G102900 chr4D 79.258 863 152 22 2497 3344 630149 630999 1.100000e-160 577
4 TraesCS4A01G102900 chr4B 93.507 4605 187 46 1 4550 431798610 431794063 0.000000e+00 6745
5 TraesCS4A01G102900 chr4B 79.143 863 153 22 2497 3344 1244574 1243724 5.110000e-159 571
6 TraesCS4A01G102900 chr4B 77.556 851 147 27 2526 3342 654130706 654131546 1.480000e-129 473
7 TraesCS4A01G102900 chr4B 80.914 613 95 15 2526 3119 654125471 654126080 8.920000e-127 464
8 TraesCS4A01G102900 chr4B 75.793 851 169 18 2526 3344 638987543 638988388 3.300000e-106 396
9 TraesCS4A01G102900 chr5A 77.119 826 169 20 2529 3344 540053610 540054425 1.150000e-125 460
10 TraesCS4A01G102900 chr3A 79.937 633 104 19 2510 3129 546572733 546572111 1.160000e-120 444
11 TraesCS4A01G102900 chr3B 79.463 633 107 19 2510 3129 142722734 142722112 1.170000e-115 427


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 TraesCS4A01G102900 chr4A 115785784 115790333 4549 False 8403 8403 100.000 1 4550 1 chr4A.!!$F2 4549
1 TraesCS4A01G102900 chr4A 900679 901532 853 False 564 564 78.935 2497 3344 1 chr4A.!!$F1 847
2 TraesCS4A01G102900 chr4D 349188306 349192833 4527 True 7191 7191 95.287 1 4550 1 chr4D.!!$R1 4549
3 TraesCS4A01G102900 chr4D 630149 630999 850 False 577 577 79.258 2497 3344 1 chr4D.!!$F1 847
4 TraesCS4A01G102900 chr4B 431794063 431798610 4547 True 6745 6745 93.507 1 4550 1 chr4B.!!$R2 4549
5 TraesCS4A01G102900 chr4B 1243724 1244574 850 True 571 571 79.143 2497 3344 1 chr4B.!!$R1 847
6 TraesCS4A01G102900 chr4B 654130706 654131546 840 False 473 473 77.556 2526 3342 1 chr4B.!!$F3 816
7 TraesCS4A01G102900 chr4B 654125471 654126080 609 False 464 464 80.914 2526 3119 1 chr4B.!!$F2 593
8 TraesCS4A01G102900 chr4B 638987543 638988388 845 False 396 396 75.793 2526 3344 1 chr4B.!!$F1 818
9 TraesCS4A01G102900 chr5A 540053610 540054425 815 False 460 460 77.119 2529 3344 1 chr5A.!!$F1 815
10 TraesCS4A01G102900 chr3A 546572111 546572733 622 True 444 444 79.937 2510 3129 1 chr3A.!!$R1 619
11 TraesCS4A01G102900 chr3B 142722112 142722734 622 True 427 427 79.463 2510 3129 1 chr3B.!!$R1 619

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
835 867 0.033601 ACTCCCTCTGCTCATCTCGT 60.034 55.000 0.00 0.00 0.00 4.18 F
905 937 0.536260 GCACTCTGGTGATGCTCTCT 59.464 55.000 0.00 0.00 45.61 3.10 F
956 992 0.684805 CTCCGTGGCCTCCTTCTAGT 60.685 60.000 3.32 0.00 0.00 2.57 F
1462 1498 1.140804 GAGCTCAGGGAGTTCTCGC 59.859 63.158 9.40 8.51 37.04 5.03 F
2315 2357 0.744771 GGGTTCATCGCCTTCAGGAC 60.745 60.000 0.00 0.00 37.39 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1743 1779 0.398696 TCAAGGGCTTGGCGTCTTTA 59.601 50.000 0.00 0.00 40.78 1.85 R
2049 2085 1.826720 TCCTTGTACACCGGTATGGAC 59.173 52.381 6.87 2.96 42.00 4.02 R
2221 2263 2.127232 GACCTTTGAACTGCGCGC 60.127 61.111 27.26 27.26 0.00 6.86 R
3414 3490 0.900647 ACAGGCTACGCTGAACCTCT 60.901 55.000 0.00 0.00 0.00 3.69 R
3766 3854 0.601311 CTGGAGTATAAGCCGCTGCC 60.601 60.000 0.00 0.00 38.69 4.85 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
31 32 6.349033 CGGGAAAAGAAAAGGAATGTACGAAT 60.349 38.462 0.00 0.00 0.00 3.34
45 47 4.160635 GAATTGCGCCCGGTCGTG 62.161 66.667 6.80 0.00 0.00 4.35
134 136 1.990614 GGAGACTTCCTCGGCCCTT 60.991 63.158 0.00 0.00 42.89 3.95
150 157 1.377333 CTTTCCTTCCCACCGAGCC 60.377 63.158 0.00 0.00 0.00 4.70
151 158 3.248446 TTTCCTTCCCACCGAGCCG 62.248 63.158 0.00 0.00 0.00 5.52
152 159 4.689549 TCCTTCCCACCGAGCCGA 62.690 66.667 0.00 0.00 0.00 5.54
153 160 4.148825 CCTTCCCACCGAGCCGAG 62.149 72.222 0.00 0.00 0.00 4.63
154 161 4.821589 CTTCCCACCGAGCCGAGC 62.822 72.222 0.00 0.00 0.00 5.03
176 183 0.321564 CAGCACAATGGTCGAGGGAA 60.322 55.000 0.00 0.00 0.00 3.97
179 186 1.890876 CACAATGGTCGAGGGAACAA 58.109 50.000 0.00 0.00 44.54 2.83
215 222 2.312390 GTTCCTAAACAAAGGGCCACA 58.688 47.619 6.18 0.00 37.24 4.17
216 223 1.989706 TCCTAAACAAAGGGCCACAC 58.010 50.000 6.18 0.00 37.24 3.82
269 282 1.201855 GCAGTCGTTTTCATCTGCGAG 60.202 52.381 0.00 0.00 42.51 5.03
296 309 1.094785 CCGTGGGATTTGACATGTCC 58.905 55.000 22.85 7.68 0.00 4.02
299 312 2.793831 GGGATTTGACATGTCCCGG 58.206 57.895 22.85 0.00 41.99 5.73
324 337 1.067516 CCACAACAGAAAAGGTGCCTG 59.932 52.381 0.00 0.00 0.00 4.85
325 338 0.746659 ACAACAGAAAAGGTGCCTGC 59.253 50.000 0.00 0.00 0.00 4.85
335 348 2.813042 GTGCCTGCTGCTCTCGTC 60.813 66.667 0.00 0.00 42.00 4.20
366 380 0.687354 CTGGCCTCAGTGTTGGTACT 59.313 55.000 3.32 0.00 36.30 2.73
367 381 1.899814 CTGGCCTCAGTGTTGGTACTA 59.100 52.381 3.32 0.00 36.30 1.82
368 382 1.621814 TGGCCTCAGTGTTGGTACTAC 59.378 52.381 3.32 0.00 0.00 2.73
369 383 1.621814 GGCCTCAGTGTTGGTACTACA 59.378 52.381 0.00 0.00 0.00 2.74
370 384 2.353803 GGCCTCAGTGTTGGTACTACAG 60.354 54.545 0.00 0.00 0.00 2.74
405 419 2.080693 GTGCCACGGAACATGACAATA 58.919 47.619 0.00 0.00 0.00 1.90
412 426 4.007659 ACGGAACATGACAATAAGAACCC 58.992 43.478 0.00 0.00 0.00 4.11
413 427 4.006989 CGGAACATGACAATAAGAACCCA 58.993 43.478 0.00 0.00 0.00 4.51
414 428 4.094887 CGGAACATGACAATAAGAACCCAG 59.905 45.833 0.00 0.00 0.00 4.45
416 430 5.476945 GGAACATGACAATAAGAACCCAGTT 59.523 40.000 0.00 0.00 0.00 3.16
417 431 5.964958 ACATGACAATAAGAACCCAGTTG 57.035 39.130 0.00 0.00 0.00 3.16
418 432 5.385198 ACATGACAATAAGAACCCAGTTGT 58.615 37.500 0.00 0.00 35.87 3.32
419 433 5.833131 ACATGACAATAAGAACCCAGTTGTT 59.167 36.000 0.00 0.00 33.55 2.83
420 434 5.766150 TGACAATAAGAACCCAGTTGTTG 57.234 39.130 0.55 0.00 33.55 3.33
421 435 5.441500 TGACAATAAGAACCCAGTTGTTGA 58.558 37.500 0.55 0.00 33.55 3.18
422 436 5.298276 TGACAATAAGAACCCAGTTGTTGAC 59.702 40.000 0.55 0.00 33.55 3.18
423 437 5.197451 ACAATAAGAACCCAGTTGTTGACA 58.803 37.500 0.55 0.00 31.63 3.58
424 438 5.067283 ACAATAAGAACCCAGTTGTTGACAC 59.933 40.000 0.55 0.00 31.63 3.67
444 459 5.542779 ACACTTGACAGTAAAAGAGCCTAG 58.457 41.667 3.03 0.00 0.00 3.02
472 487 1.342082 CGGTCCGTTCATCACACGTC 61.342 60.000 2.08 0.00 35.81 4.34
475 490 2.019408 CCGTTCATCACACGTCGCA 61.019 57.895 0.00 0.00 35.81 5.10
510 525 8.231837 TCGCCTTGTCTTTGTTTAACAATATAC 58.768 33.333 11.50 10.19 38.00 1.47
528 543 8.443160 ACAATATACATGTTGACGTTTCTTCAG 58.557 33.333 2.30 0.00 33.73 3.02
615 632 2.027192 ACGGCATTAGAAAGCTCCTGAA 60.027 45.455 0.00 0.00 0.00 3.02
643 660 2.483876 GCAAACAAGGAAAAAGCTCCC 58.516 47.619 0.00 0.00 35.95 4.30
678 696 2.856760 TCAAGCCTATCTCTCCACCT 57.143 50.000 0.00 0.00 0.00 4.00
679 697 2.392662 TCAAGCCTATCTCTCCACCTG 58.607 52.381 0.00 0.00 0.00 4.00
680 698 2.023984 TCAAGCCTATCTCTCCACCTGA 60.024 50.000 0.00 0.00 0.00 3.86
681 699 2.364970 CAAGCCTATCTCTCCACCTGAG 59.635 54.545 0.00 0.00 42.90 3.35
760 782 0.742281 CCACCACATCCAAGAGCTCG 60.742 60.000 8.37 0.00 0.00 5.03
784 810 3.837213 AAACCAAGCATCGATTCACTG 57.163 42.857 0.00 0.00 0.00 3.66
829 861 0.323451 TCGCTAACTCCCTCTGCTCA 60.323 55.000 0.00 0.00 0.00 4.26
832 864 2.038659 GCTAACTCCCTCTGCTCATCT 58.961 52.381 0.00 0.00 0.00 2.90
833 865 2.035832 GCTAACTCCCTCTGCTCATCTC 59.964 54.545 0.00 0.00 0.00 2.75
834 866 1.110442 AACTCCCTCTGCTCATCTCG 58.890 55.000 0.00 0.00 0.00 4.04
835 867 0.033601 ACTCCCTCTGCTCATCTCGT 60.034 55.000 0.00 0.00 0.00 4.18
836 868 1.110442 CTCCCTCTGCTCATCTCGTT 58.890 55.000 0.00 0.00 0.00 3.85
886 918 3.120199 CCACCTCTACAAAAGCAATCGTG 60.120 47.826 0.00 0.00 0.00 4.35
905 937 0.536260 GCACTCTGGTGATGCTCTCT 59.464 55.000 0.00 0.00 45.61 3.10
948 984 1.617947 ATGAAGACCTCCGTGGCCTC 61.618 60.000 3.32 0.00 40.22 4.70
951 987 3.003763 GACCTCCGTGGCCTCCTT 61.004 66.667 3.32 0.00 40.22 3.36
956 992 0.684805 CTCCGTGGCCTCCTTCTAGT 60.685 60.000 3.32 0.00 0.00 2.57
1088 1124 2.743538 GTTTACCCCCGCGGACAC 60.744 66.667 30.73 5.81 34.64 3.67
1423 1459 2.084681 GTGCTCGTCAACGGGTACG 61.085 63.158 7.86 0.00 44.68 3.67
1461 1497 1.813192 GGAGCTCAGGGAGTTCTCG 59.187 63.158 17.19 0.00 39.34 4.04
1462 1498 1.140804 GAGCTCAGGGAGTTCTCGC 59.859 63.158 9.40 8.51 37.04 5.03
1476 1512 3.553437 CTCGCTGAACGTCACCGGT 62.553 63.158 0.00 0.00 44.19 5.28
1478 1514 3.712881 GCTGAACGTCACCGGTGC 61.713 66.667 30.25 22.27 38.78 5.01
1656 1692 2.180204 CCGGATCAACATGGGCGTC 61.180 63.158 0.00 0.00 0.00 5.19
1782 1818 4.340263 TGACGATCAAATACGACGAGAAG 58.660 43.478 0.00 0.00 0.00 2.85
1794 1830 2.103340 GAGAAGTCGGCGCTCTCC 59.897 66.667 7.64 2.01 0.00 3.71
2013 2049 3.998672 GGGTCGGTGGTGCTCGAA 61.999 66.667 0.00 0.00 37.14 3.71
2049 2085 1.885388 TGACACGTTCAACCGGCTG 60.885 57.895 0.00 0.00 0.00 4.85
2148 2184 3.723348 GAGGACAACGCGTTGCCC 61.723 66.667 42.76 41.27 42.49 5.36
2315 2357 0.744771 GGGTTCATCGCCTTCAGGAC 60.745 60.000 0.00 0.00 37.39 3.85
3414 3490 3.587933 GTGCCCGTGAAAACGCCA 61.588 61.111 0.00 0.00 0.00 5.69
3569 3648 0.798776 AGCCAAAAGATGCTTCGTCG 59.201 50.000 0.00 0.00 32.94 5.12
3581 3660 1.121967 GCTTCGTCGACGTTGTACAAG 59.878 52.381 34.40 27.93 40.80 3.16
3653 3735 6.252281 TGACAAACGATGTACAAACTTTCAC 58.748 36.000 0.00 0.00 44.12 3.18
3674 3756 9.582431 TTTCACGTAGAAGAAAGTTATATCAGG 57.418 33.333 0.00 0.00 37.57 3.86
3703 3785 7.597743 GTGATGTATAACGTACCAATAAGGAGG 59.402 40.741 0.00 0.00 41.22 4.30
3739 3821 6.385649 TGATTTCACAAAAGTAACCTCACC 57.614 37.500 0.00 0.00 0.00 4.02
3765 3853 6.129179 TGGATATGTATATGATCGGCAGAGA 58.871 40.000 0.00 0.00 0.00 3.10
3766 3854 6.264067 TGGATATGTATATGATCGGCAGAGAG 59.736 42.308 0.00 0.00 0.00 3.20
3807 3906 3.929610 GGATGAGTATAAGCAGAATCGCC 59.070 47.826 0.00 0.00 0.00 5.54
3863 3972 1.446907 GAGGTGTCACTGCATTCAGG 58.553 55.000 2.35 0.00 44.54 3.86
3917 4027 3.834231 ACTGCAGTAAATGGGCAAGAAAT 59.166 39.130 20.16 0.00 37.06 2.17
4106 4216 3.468140 GTCTACTCCCCCGTGGCC 61.468 72.222 0.00 0.00 0.00 5.36
4128 4238 6.166982 GCCATCTAATACTCAATCACTACCC 58.833 44.000 0.00 0.00 0.00 3.69
4196 4306 1.101049 AGCACCGTCCCACAAACTTG 61.101 55.000 0.00 0.00 0.00 3.16
4253 4363 1.810151 GCTACGACCAAAAGCCATTCA 59.190 47.619 0.00 0.00 0.00 2.57
4313 4423 2.969628 AAGGCACGTAGAGGATCAAG 57.030 50.000 0.00 0.00 37.82 3.02
4328 4438 4.840115 AGGATCAAGAAATGAAGCCCAAAA 59.160 37.500 0.00 0.00 42.54 2.44
4445 4555 3.390967 TCTCAATGGACACCAAGACAGAA 59.609 43.478 0.00 0.00 36.95 3.02
4475 4585 3.059257 GGGTTGTTGCTTTTATTTTGCCG 60.059 43.478 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 136 3.702048 CGGCTCGGTGGGAAGGAA 61.702 66.667 0.00 0.00 0.00 3.36
150 157 1.915614 GACCATTGTGCTGTGGCTCG 61.916 60.000 0.00 0.00 39.13 5.03
151 158 1.878775 GACCATTGTGCTGTGGCTC 59.121 57.895 0.00 0.00 39.13 4.70
152 159 1.968017 CGACCATTGTGCTGTGGCT 60.968 57.895 0.00 0.00 39.13 4.75
153 160 1.915614 CTCGACCATTGTGCTGTGGC 61.916 60.000 0.00 0.00 39.13 5.01
154 161 1.300971 CCTCGACCATTGTGCTGTGG 61.301 60.000 0.00 0.00 41.35 4.17
155 162 1.300971 CCCTCGACCATTGTGCTGTG 61.301 60.000 0.00 0.00 0.00 3.66
176 183 3.130280 ACGTAAAGGGGAACGATTTGT 57.870 42.857 1.45 0.00 41.55 2.83
179 186 2.303890 AGGAACGTAAAGGGGAACGATT 59.696 45.455 1.45 0.00 41.55 3.34
215 222 2.661709 CGCATTTTGTCGTGTGAATCGT 60.662 45.455 0.00 0.00 0.00 3.73
216 223 1.898079 CGCATTTTGTCGTGTGAATCG 59.102 47.619 0.00 0.00 0.00 3.34
240 247 2.875933 TGAAAACGACTGCGAGGAAAAT 59.124 40.909 0.00 0.00 41.64 1.82
269 282 0.591170 CAAATCCCACGGTGACACAC 59.409 55.000 10.28 0.00 0.00 3.82
296 309 2.690653 TTTCTGTTGTGGCCTCCCGG 62.691 60.000 3.32 0.00 0.00 5.73
299 312 0.961753 CCTTTTCTGTTGTGGCCTCC 59.038 55.000 3.32 0.00 0.00 4.30
324 337 0.667792 AAAGGTTCGACGAGAGCAGC 60.668 55.000 0.00 0.00 0.00 5.25
325 338 1.721926 GAAAAGGTTCGACGAGAGCAG 59.278 52.381 0.00 0.00 0.00 4.24
335 348 1.270839 TGAGGCCAGAGAAAAGGTTCG 60.271 52.381 5.01 0.00 38.90 3.95
366 380 5.953548 TGGCACTAGGAATTACTGTACTGTA 59.046 40.000 8.40 8.40 0.00 2.74
367 381 4.775780 TGGCACTAGGAATTACTGTACTGT 59.224 41.667 10.46 10.46 0.00 3.55
368 382 5.109903 GTGGCACTAGGAATTACTGTACTG 58.890 45.833 11.13 0.00 0.00 2.74
369 383 4.142227 CGTGGCACTAGGAATTACTGTACT 60.142 45.833 16.72 0.00 0.00 2.73
370 384 4.110482 CGTGGCACTAGGAATTACTGTAC 58.890 47.826 16.72 0.00 0.00 2.90
405 419 3.366052 AGTGTCAACAACTGGGTTCTT 57.634 42.857 0.00 0.00 0.00 2.52
412 426 5.794687 TTACTGTCAAGTGTCAACAACTG 57.205 39.130 0.00 0.00 37.19 3.16
413 427 6.653320 TCTTTTACTGTCAAGTGTCAACAACT 59.347 34.615 0.00 0.00 37.19 3.16
414 428 6.837992 TCTTTTACTGTCAAGTGTCAACAAC 58.162 36.000 0.00 0.00 37.19 3.32
416 430 5.064707 GCTCTTTTACTGTCAAGTGTCAACA 59.935 40.000 0.00 0.00 37.19 3.33
417 431 5.502606 GCTCTTTTACTGTCAAGTGTCAAC 58.497 41.667 0.00 0.00 37.19 3.18
418 432 4.574828 GGCTCTTTTACTGTCAAGTGTCAA 59.425 41.667 0.00 0.00 37.19 3.18
419 433 4.127171 GGCTCTTTTACTGTCAAGTGTCA 58.873 43.478 0.00 0.00 37.19 3.58
420 434 4.381411 AGGCTCTTTTACTGTCAAGTGTC 58.619 43.478 0.00 0.00 37.19 3.67
421 435 4.423625 AGGCTCTTTTACTGTCAAGTGT 57.576 40.909 0.00 0.00 37.19 3.55
422 436 4.932200 CCTAGGCTCTTTTACTGTCAAGTG 59.068 45.833 0.00 0.00 37.19 3.16
423 437 4.838986 TCCTAGGCTCTTTTACTGTCAAGT 59.161 41.667 2.96 0.00 40.67 3.16
424 438 5.407407 TCCTAGGCTCTTTTACTGTCAAG 57.593 43.478 2.96 0.00 0.00 3.02
510 525 4.151335 CCTCTCTGAAGAAACGTCAACATG 59.849 45.833 0.00 0.00 0.00 3.21
528 543 5.520649 GGTAAATTTCTCGTGTGATCCTCTC 59.479 44.000 0.00 0.00 0.00 3.20
615 632 0.178947 TTCCTTGTTTGCGGGGGAAT 60.179 50.000 0.00 0.00 32.03 3.01
678 696 6.155737 TGTCATTTTCTCAGGATCTCATCTCA 59.844 38.462 0.00 0.00 0.00 3.27
679 697 6.479660 GTGTCATTTTCTCAGGATCTCATCTC 59.520 42.308 0.00 0.00 0.00 2.75
680 698 6.347696 GTGTCATTTTCTCAGGATCTCATCT 58.652 40.000 0.00 0.00 0.00 2.90
681 699 5.526846 GGTGTCATTTTCTCAGGATCTCATC 59.473 44.000 0.00 0.00 0.00 2.92
682 700 5.435291 GGTGTCATTTTCTCAGGATCTCAT 58.565 41.667 0.00 0.00 0.00 2.90
760 782 3.914364 GTGAATCGATGCTTGGTTTTGAC 59.086 43.478 4.68 0.00 0.00 3.18
784 810 2.504175 TGCTAATACCCACAGGAAGGAC 59.496 50.000 0.00 0.00 36.73 3.85
829 861 3.627577 ACACTTGTTGCTTGAAACGAGAT 59.372 39.130 14.06 1.47 42.09 2.75
832 864 2.744741 TGACACTTGTTGCTTGAAACGA 59.255 40.909 0.00 0.00 32.47 3.85
833 865 3.129852 TGACACTTGTTGCTTGAAACG 57.870 42.857 0.00 0.00 32.47 3.60
834 866 4.485163 AGTTGACACTTGTTGCTTGAAAC 58.515 39.130 0.00 0.00 0.00 2.78
835 867 4.458989 AGAGTTGACACTTGTTGCTTGAAA 59.541 37.500 0.00 0.00 31.22 2.69
836 868 4.009675 AGAGTTGACACTTGTTGCTTGAA 58.990 39.130 0.00 0.00 31.22 2.69
886 918 0.536260 AGAGAGCATCACCAGAGTGC 59.464 55.000 0.00 0.00 44.16 4.40
905 937 2.988684 GGATGGCGGCACAAACCA 60.989 61.111 16.34 0.00 37.99 3.67
948 984 2.125106 GCACGGGGCACTAGAAGG 60.125 66.667 0.00 0.00 43.97 3.46
1088 1124 2.482333 CCGCAGAGGACGAGGTAGG 61.482 68.421 0.00 0.00 45.00 3.18
1243 1279 3.186047 CGCGGACCGGTAAAGCTG 61.186 66.667 17.22 10.42 0.00 4.24
1278 1314 2.098831 GGCGAACGTGTAGGAAGCC 61.099 63.158 0.00 0.00 36.08 4.35
1478 1514 3.958147 AAGGCGATCACCAGCGTGG 62.958 63.158 1.91 2.92 45.02 4.94
1590 1626 4.446413 CCGGTGTACTGGACGGCC 62.446 72.222 0.00 0.00 45.36 6.13
1639 1675 2.180204 GGACGCCCATGTTGATCCG 61.180 63.158 0.00 0.00 0.00 4.18
1656 1692 4.856801 CCGGGCGTGATCTTGGGG 62.857 72.222 0.00 0.00 0.00 4.96
1743 1779 0.398696 TCAAGGGCTTGGCGTCTTTA 59.601 50.000 0.00 0.00 40.78 1.85
1788 1824 2.102553 GTGTACGCGGAGGAGAGC 59.897 66.667 12.47 0.00 0.00 4.09
2049 2085 1.826720 TCCTTGTACACCGGTATGGAC 59.173 52.381 6.87 2.96 42.00 4.02
2148 2184 2.809601 CCGTTGAGGAAGCCGTCG 60.810 66.667 0.00 0.00 45.00 5.12
2221 2263 2.127232 GACCTTTGAACTGCGCGC 60.127 61.111 27.26 27.26 0.00 6.86
3414 3490 0.900647 ACAGGCTACGCTGAACCTCT 60.901 55.000 0.00 0.00 0.00 3.69
3453 3529 3.857854 GTCATGGCAGCAGCGTCG 61.858 66.667 0.00 0.00 43.41 5.12
3458 3534 1.604308 TTGGTGGTCATGGCAGCAG 60.604 57.895 0.00 0.00 0.00 4.24
3459 3535 1.902918 GTTGGTGGTCATGGCAGCA 60.903 57.895 0.00 0.00 0.00 4.41
3460 3536 1.181098 AAGTTGGTGGTCATGGCAGC 61.181 55.000 0.00 0.00 0.00 5.25
3569 3648 1.864711 TGCTTCAGCTTGTACAACGTC 59.135 47.619 3.59 0.00 42.66 4.34
3581 3660 5.739752 TTGACATATACATGTGCTTCAGC 57.260 39.130 9.11 0.00 45.58 4.26
3653 3735 9.666626 CACTACCTGATATAACTTTCTTCTACG 57.333 37.037 0.00 0.00 0.00 3.51
3673 3755 9.403110 CTTATTGGTACGTTATACATCACTACC 57.597 37.037 0.00 0.00 0.00 3.18
3674 3756 9.403110 CCTTATTGGTACGTTATACATCACTAC 57.597 37.037 0.00 0.00 0.00 2.73
3685 3767 5.716228 TCTGTTCCTCCTTATTGGTACGTTA 59.284 40.000 0.00 0.00 37.07 3.18
3686 3768 4.529377 TCTGTTCCTCCTTATTGGTACGTT 59.471 41.667 0.00 0.00 37.07 3.99
3687 3769 4.091549 TCTGTTCCTCCTTATTGGTACGT 58.908 43.478 0.00 0.00 37.07 3.57
3703 3785 6.808008 TTGTGAAATCAGGAGAATCTGTTC 57.192 37.500 0.00 0.00 36.25 3.18
3739 3821 6.752168 TCTGCCGATCATATACATATCCATG 58.248 40.000 0.00 0.00 38.21 3.66
3765 3853 1.048724 TGGAGTATAAGCCGCTGCCT 61.049 55.000 0.00 0.00 38.69 4.75
3766 3854 0.601311 CTGGAGTATAAGCCGCTGCC 60.601 60.000 0.00 0.00 38.69 4.85
3807 3906 0.798776 GTCTCGGCCTTGTTCACATG 59.201 55.000 0.00 0.00 0.00 3.21
3863 3972 9.453572 TCACTTATATCCATGAAATATTCTGCC 57.546 33.333 0.00 0.00 0.00 4.85
3905 4015 2.463752 ACAGCATGATTTCTTGCCCAT 58.536 42.857 13.09 0.00 44.97 4.00
3964 4074 8.169839 TCGAGTTTAACAGACTCATTTATTCG 57.830 34.615 6.60 0.00 42.85 3.34
4106 4216 8.415950 AGAGGGTAGTGATTGAGTATTAGATG 57.584 38.462 0.00 0.00 0.00 2.90
4128 4238 3.429684 GGAAAGCGGAAGGAAGAGTAGAG 60.430 52.174 0.00 0.00 0.00 2.43
4184 4294 2.484770 CGAGGTTCTCAAGTTTGTGGGA 60.485 50.000 0.00 0.00 0.00 4.37
4196 4306 2.478200 GGTTCTCATCGACGAGGTTCTC 60.478 54.545 8.88 0.06 33.59 2.87
4253 4363 2.380064 TTGTGCCCCTCAGTTTCAAT 57.620 45.000 0.00 0.00 0.00 2.57
4313 4423 3.653344 GGTGTCTTTTGGGCTTCATTTC 58.347 45.455 0.00 0.00 0.00 2.17
4328 4438 0.396435 TTCTGGCAATGTCGGTGTCT 59.604 50.000 0.00 0.00 0.00 3.41
4445 4555 0.853530 AAGCAACAACCCTCTCCCTT 59.146 50.000 0.00 0.00 0.00 3.95
4475 4585 1.017387 CTTGCGATTACTTCCAGGGC 58.983 55.000 0.00 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.