Multiple sequence alignment - TraesCS5B01G409700

Loading Multiple Alignment...

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 TraesCS5B01G409700 chr5B 100.000 4100 0 0 1 4100 584887997 584883898 0.000000e+00 7572
1 TraesCS5B01G409700 chr5B 100.000 220 0 0 4491 4710 584883507 584883288 1.580000e-109 407
2 TraesCS5B01G409700 chr5D 94.423 3317 139 18 808 4100 477315430 477312136 0.000000e+00 5059
3 TraesCS5B01G409700 chr5D 88.668 503 45 5 12 512 355454789 355455281 1.880000e-168 603
4 TraesCS5B01G409700 chr5D 95.238 210 9 1 4501 4710 477311833 477311625 9.770000e-87 331
5 TraesCS5B01G409700 chr5A 91.727 3481 195 43 589 4039 596523993 596520576 0.000000e+00 4747
6 TraesCS5B01G409700 chr3B 97.069 580 14 3 11 589 815965730 815966307 0.000000e+00 974
7 TraesCS5B01G409700 chr3B 89.535 258 24 3 1 256 119310124 119309868 1.630000e-84 324
8 TraesCS5B01G409700 chr7B 96.277 591 20 2 1 590 692302483 692301894 0.000000e+00 968
9 TraesCS5B01G409700 chr7B 96.271 590 18 3 1 588 730403561 730402974 0.000000e+00 965
10 TraesCS5B01G409700 chr7B 81.347 193 28 8 406 592 715971625 715971815 2.940000e-32 150
11 TraesCS5B01G409700 chr2B 95.953 593 22 2 1 591 572756063 572756655 0.000000e+00 961
12 TraesCS5B01G409700 chr6A 90.780 282 22 3 10 288 564261766 564261486 1.600000e-99 374
13 TraesCS5B01G409700 chrUn 81.347 193 28 8 406 592 390364364 390364174 2.940000e-32 150
14 TraesCS5B01G409700 chrUn 81.250 192 29 7 406 592 176284152 176283963 1.060000e-31 148
15 TraesCS5B01G409700 chrUn 81.250 192 29 7 406 592 396162025 396161836 1.060000e-31 148


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 TraesCS5B01G409700 chr5B 584883288 584887997 4709 True 3989.5 7572 100.0000 1 4710 2 chr5B.!!$R1 4709
1 TraesCS5B01G409700 chr5D 477311625 477315430 3805 True 2695.0 5059 94.8305 808 4710 2 chr5D.!!$R1 3902
2 TraesCS5B01G409700 chr5A 596520576 596523993 3417 True 4747.0 4747 91.7270 589 4039 1 chr5A.!!$R1 3450
3 TraesCS5B01G409700 chr3B 815965730 815966307 577 False 974.0 974 97.0690 11 589 1 chr3B.!!$F1 578
4 TraesCS5B01G409700 chr7B 692301894 692302483 589 True 968.0 968 96.2770 1 590 1 chr7B.!!$R1 589
5 TraesCS5B01G409700 chr7B 730402974 730403561 587 True 965.0 965 96.2710 1 588 1 chr7B.!!$R2 587
6 TraesCS5B01G409700 chr2B 572756063 572756655 592 False 961.0 961 95.9530 1 591 1 chr2B.!!$F1 590

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
831 842 0.036164 TGCCTAAACACGCCATCACT 59.964 50.0 0.0 0.0 0.00 3.41 F
1513 1537 0.110056 CACCACGCTGCTCATGTTTC 60.110 55.0 0.0 0.0 0.00 2.78 F
1591 1616 0.543749 GGTGATTGACCAGGGAGAGG 59.456 60.0 0.0 0.0 45.34 3.69 F
2894 2919 0.621082 GGCCAAGCTCTAAACTCCCT 59.379 55.0 0.0 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2289 2314 0.250124 TGAAAACATCCGGTGCGACT 60.250 50.0 0.00 0.00 0.00 4.18 R
3127 3152 1.798234 TTGCACACACCTGAGCATGC 61.798 55.0 10.51 10.51 42.66 4.06 R
3148 3173 2.095567 CCATGAAAGAGGAAGTTGCGTG 60.096 50.0 0.00 0.00 0.00 5.34 R
4639 4683 0.371645 GACGACGACGACGACCTATT 59.628 55.0 25.15 2.32 42.66 1.73 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
47 48 2.118513 AGTGGTGAGAGCTCCGGT 59.881 61.111 10.93 0.00 0.00 5.28
98 99 3.652000 GGGTTTTGCGTCGCCGAA 61.652 61.111 15.88 6.90 35.63 4.30
131 132 1.301716 GCGCAGTGAACTCAAGGGA 60.302 57.895 0.30 0.00 0.00 4.20
255 256 1.112916 TTGACAGAGAGGGACACGCA 61.113 55.000 0.00 0.00 0.00 5.24
256 257 1.112916 TGACAGAGAGGGACACGCAA 61.113 55.000 0.00 0.00 0.00 4.85
403 404 2.424842 ATCGCTGAAGCCACCCCAAA 62.425 55.000 0.00 0.00 37.91 3.28
600 602 8.865090 AGTGGTTTTGGTATATTCATGTTTTGA 58.135 29.630 0.00 0.00 0.00 2.69
620 622 9.198065 GTTTTGAAACAATGTTCAGAAATTTCG 57.802 29.630 12.42 7.92 38.69 3.46
624 626 9.311916 TGAAACAATGTTCAGAAATTTCGAAAT 57.688 25.926 17.60 17.60 32.56 2.17
826 837 2.033448 CCCTGCCTAAACACGCCA 59.967 61.111 0.00 0.00 0.00 5.69
831 842 0.036164 TGCCTAAACACGCCATCACT 59.964 50.000 0.00 0.00 0.00 3.41
962 985 0.804933 GCACGACACCTTATCCGGTC 60.805 60.000 0.00 0.00 34.29 4.79
1103 1127 1.338890 GCTACCTCCTCCTGAACCCC 61.339 65.000 0.00 0.00 0.00 4.95
1318 1342 3.148279 GGGAGACGGCGAGGATGT 61.148 66.667 16.62 0.00 0.00 3.06
1489 1513 3.823304 GTGCTTGTTCCTCCTTCTGAATT 59.177 43.478 0.00 0.00 0.00 2.17
1498 1522 1.071542 TCCTTCTGAATTGCGACACCA 59.928 47.619 0.00 0.00 0.00 4.17
1513 1537 0.110056 CACCACGCTGCTCATGTTTC 60.110 55.000 0.00 0.00 0.00 2.78
1560 1585 4.021280 TCTGCTTATGCTTTTTGGATTGCA 60.021 37.500 1.96 0.00 40.48 4.08
1591 1616 0.543749 GGTGATTGACCAGGGAGAGG 59.456 60.000 0.00 0.00 45.34 3.69
1925 1950 2.685388 GGGAAGCATTAGGAAGCAAGAC 59.315 50.000 0.00 0.00 0.00 3.01
1999 2024 0.687354 GGTGCCGGATATGAGGTGAT 59.313 55.000 5.05 0.00 0.00 3.06
2029 2054 1.269726 CGATGCAATACATTTGCCCCC 60.270 52.381 7.76 0.00 44.32 5.40
2032 2057 1.980765 TGCAATACATTTGCCCCCAAA 59.019 42.857 7.76 0.00 44.32 3.28
2034 2059 3.009916 TGCAATACATTTGCCCCCAAATT 59.990 39.130 7.76 0.00 46.66 1.82
2036 2061 4.587891 CAATACATTTGCCCCCAAATTGT 58.412 39.130 0.00 4.86 46.66 2.71
2037 2062 2.857186 ACATTTGCCCCCAAATTGTC 57.143 45.000 0.00 0.00 46.66 3.18
2044 2069 1.067846 GCCCCCAAATTGTCGTTCTTC 60.068 52.381 0.00 0.00 0.00 2.87
2061 2086 4.207891 TCTTCCCTTCTCAGCATGTTAC 57.792 45.455 0.00 0.00 37.40 2.50
2062 2087 3.582647 TCTTCCCTTCTCAGCATGTTACA 59.417 43.478 0.00 0.00 37.40 2.41
2063 2088 4.225942 TCTTCCCTTCTCAGCATGTTACAT 59.774 41.667 0.00 0.00 37.40 2.29
2064 2089 4.574674 TCCCTTCTCAGCATGTTACATT 57.425 40.909 0.00 0.00 37.40 2.71
2065 2090 5.692115 TCCCTTCTCAGCATGTTACATTA 57.308 39.130 0.00 0.00 37.40 1.90
2066 2091 6.061022 TCCCTTCTCAGCATGTTACATTAA 57.939 37.500 0.00 0.00 37.40 1.40
2067 2092 6.480763 TCCCTTCTCAGCATGTTACATTAAA 58.519 36.000 0.00 0.00 37.40 1.52
2068 2093 6.945435 TCCCTTCTCAGCATGTTACATTAAAA 59.055 34.615 0.00 0.00 37.40 1.52
2069 2094 7.450014 TCCCTTCTCAGCATGTTACATTAAAAA 59.550 33.333 0.00 0.00 37.40 1.94
2070 2095 8.253113 CCCTTCTCAGCATGTTACATTAAAAAT 58.747 33.333 0.00 0.00 37.40 1.82
2094 2119 4.081406 TGCTTGATATGTTGCAGGTCTTT 58.919 39.130 0.00 0.00 0.00 2.52
2097 2122 5.355350 GCTTGATATGTTGCAGGTCTTTACT 59.645 40.000 0.00 0.00 0.00 2.24
2106 2131 1.134491 CAGGTCTTTACTAAGGGCCCG 60.134 57.143 18.44 4.53 31.54 6.13
2109 2134 1.829849 GTCTTTACTAAGGGCCCGTCT 59.170 52.381 15.74 6.38 32.02 4.18
2142 2167 2.436115 GGCCTTGCTGGTCGGTAC 60.436 66.667 0.00 0.00 38.35 3.34
2289 2314 3.708631 TGAAACCCAAAGGCATTTTCTCA 59.291 39.130 0.00 0.00 36.11 3.27
2313 2338 2.418628 CGCACCGGATGTTTTCAATACT 59.581 45.455 9.46 0.00 0.00 2.12
2328 2353 6.801539 TTCAATACTGAAGTCCATGTCAAC 57.198 37.500 0.00 0.00 36.62 3.18
2377 2402 2.303311 GGAGAGGTAACCACTTTGCTCT 59.697 50.000 0.00 0.00 37.17 4.09
2624 2649 3.634910 GTGAAGGACCTTTTAACTTGGCA 59.365 43.478 8.49 0.00 0.00 4.92
2682 2707 1.880027 ACGGAACATTCTTGCCACTTC 59.120 47.619 0.00 0.00 0.00 3.01
2894 2919 0.621082 GGCCAAGCTCTAAACTCCCT 59.379 55.000 0.00 0.00 0.00 4.20
2971 2996 4.078922 TCTGGATCTCAAGGTCAGGACTAT 60.079 45.833 0.00 0.00 0.00 2.12
2973 2998 5.777449 TGGATCTCAAGGTCAGGACTATAA 58.223 41.667 0.00 0.00 0.00 0.98
3091 3116 0.821517 TCGTGTATGCTGGATTCGGT 59.178 50.000 0.00 0.00 0.00 4.69
3127 3152 3.426859 CGACCTGCATTAGCTATCTTTCG 59.573 47.826 0.00 0.00 42.74 3.46
3161 3194 0.380378 TGCAAACACGCAACTTCCTC 59.620 50.000 0.00 0.00 39.45 3.71
3178 3211 4.021102 TCCTCTTTCATGGTTGTCTTCC 57.979 45.455 0.00 0.00 0.00 3.46
3197 3230 6.872020 GTCTTCCACAAGCACTGTATTAACTA 59.128 38.462 0.00 0.00 36.10 2.24
3198 3231 7.549488 GTCTTCCACAAGCACTGTATTAACTAT 59.451 37.037 0.00 0.00 36.10 2.12
3269 3302 2.444421 ACTACAGTAGTTGTCGGAGGG 58.556 52.381 7.48 0.00 41.29 4.30
3275 3308 1.204231 GTAGTTGTCGGAGGGAAGTCC 59.796 57.143 0.00 0.00 0.00 3.85
3287 3320 1.613255 GGGAAGTCCAATCGAGCCAAA 60.613 52.381 0.00 0.00 37.91 3.28
3389 3422 2.386661 AATCAAGTACTGCGTGAGGG 57.613 50.000 0.00 0.00 38.86 4.30
3394 3427 0.456221 AGTACTGCGTGAGGGATTCG 59.544 55.000 0.00 0.00 0.00 3.34
3402 3435 2.664698 GCGTGAGGGATTCGTTTTGTTC 60.665 50.000 0.00 0.00 0.00 3.18
3422 3455 2.037121 TCGGTTGAGATTGCTGAAGACA 59.963 45.455 0.00 0.00 0.00 3.41
3423 3456 2.158449 CGGTTGAGATTGCTGAAGACAC 59.842 50.000 0.00 0.00 0.00 3.67
3440 3473 2.772568 CACGCAGGTGTTGAATTGAA 57.227 45.000 0.00 0.00 39.38 2.69
3465 3498 3.769844 TGGTTCATAGACAAGTCCCTCTC 59.230 47.826 0.00 0.00 0.00 3.20
3467 3500 3.646736 TCATAGACAAGTCCCTCTCGA 57.353 47.619 0.00 0.00 0.00 4.04
3537 3571 8.570488 TGCAATTGGACTATGTATTCATCATTC 58.430 33.333 7.72 0.00 35.70 2.67
3541 3575 7.379059 TGGACTATGTATTCATCATTCAGGT 57.621 36.000 0.00 0.00 35.70 4.00
3545 3579 8.899427 ACTATGTATTCATCATTCAGGTCAAG 57.101 34.615 0.00 0.00 35.70 3.02
3620 3658 5.757850 AAAGGAAACTGATGTTGTCACTC 57.242 39.130 0.00 0.00 42.68 3.51
3628 3666 6.227298 ACTGATGTTGTCACTCTATTAGGG 57.773 41.667 0.00 0.00 32.22 3.53
3878 3921 1.963515 GTGGTGGAGCAAGAATGGTTT 59.036 47.619 0.00 0.00 37.41 3.27
4087 4131 1.196808 GCCCGTGTTGTACTCAATGTG 59.803 52.381 0.00 0.00 35.92 3.21
4089 4133 1.196808 CCGTGTTGTACTCAATGTGGC 59.803 52.381 0.00 0.00 35.92 5.01
4538 4582 3.477224 TTTTTGCACTGGCGGCGAC 62.477 57.895 12.98 9.31 45.35 5.19
4555 4599 2.286242 GCGACGACGACTTAGATCATCA 60.286 50.000 12.29 0.00 42.66 3.07
4583 4627 3.637273 GTGCTCCTCCCCACCGTT 61.637 66.667 0.00 0.00 0.00 4.44
4621 4665 4.452733 CCCGTCTCCGTCTTGCCC 62.453 72.222 0.00 0.00 0.00 5.36
4639 4683 1.078918 CGCCTTGTCTCCAGCATCA 60.079 57.895 0.00 0.00 0.00 3.07
4688 4732 0.035534 ACAAGCATCATACGGCCACA 60.036 50.000 2.24 0.00 0.00 4.17
4689 4733 0.659427 CAAGCATCATACGGCCACAG 59.341 55.000 2.24 0.00 0.00 3.66
4690 4734 0.253044 AAGCATCATACGGCCACAGT 59.747 50.000 2.24 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 0.955905 CATTGATGGCCGATGCATCA 59.044 50.000 25.70 7.89 40.13 3.07
98 99 1.741770 GCGCACGTCTCCCAGATTT 60.742 57.895 0.30 0.00 0.00 2.17
131 132 6.072119 CGTTTATAAAAAGCTCTTGTCCCCTT 60.072 38.462 0.00 0.00 0.00 3.95
255 256 5.241728 CCGTTTCTCCCTCTCAATTTTCTTT 59.758 40.000 0.00 0.00 0.00 2.52
256 257 4.762251 CCGTTTCTCCCTCTCAATTTTCTT 59.238 41.667 0.00 0.00 0.00 2.52
403 404 2.505628 TCGCATTTTTGTGTGTGCAT 57.494 40.000 0.00 0.00 37.44 3.96
473 474 5.432390 TGTATTAATTTGGGCTACAGGGGTA 59.568 40.000 0.00 0.00 0.00 3.69
514 516 3.822735 TGGATGAAAGCAACTTGAGAAGG 59.177 43.478 0.00 0.00 0.00 3.46
596 598 8.694975 TCGAAATTTCTGAACATTGTTTCAAA 57.305 26.923 15.92 4.15 35.07 2.69
627 629 9.603921 ATTGTGAACATTTTCAAAGAACTGAAT 57.396 25.926 0.00 0.00 43.52 2.57
628 630 9.434420 AATTGTGAACATTTTCAAAGAACTGAA 57.566 25.926 0.00 0.00 43.52 3.02
629 631 9.434420 AAATTGTGAACATTTTCAAAGAACTGA 57.566 25.926 0.00 0.00 43.52 3.41
769 780 6.632834 CGGCCAGTCGAGATTTTATTTAAATG 59.367 38.462 11.05 0.00 36.59 2.32
770 781 6.540914 TCGGCCAGTCGAGATTTTATTTAAAT 59.459 34.615 2.24 5.89 35.33 1.40
772 783 5.421277 TCGGCCAGTCGAGATTTTATTTAA 58.579 37.500 2.24 0.00 34.82 1.52
773 784 5.013568 TCGGCCAGTCGAGATTTTATTTA 57.986 39.130 2.24 0.00 34.82 1.40
774 785 3.869065 TCGGCCAGTCGAGATTTTATTT 58.131 40.909 2.24 0.00 34.82 1.40
785 796 0.179056 ACCCATAATTCGGCCAGTCG 60.179 55.000 2.24 0.00 0.00 4.18
815 826 4.804139 CCTAGTTAGTGATGGCGTGTTTAG 59.196 45.833 0.00 0.00 0.00 1.85
826 837 4.674281 GCTACAAGGCCTAGTTAGTGAT 57.326 45.455 5.16 0.00 0.00 3.06
902 921 6.112058 AGTGAAGTGAGAGGCAAATATCTTC 58.888 40.000 0.00 0.00 0.00 2.87
1103 1127 4.087892 CGGTGGCAGGTCCTGGAG 62.088 72.222 20.72 0.00 35.26 3.86
1498 1522 0.035317 TGAGGAAACATGAGCAGCGT 59.965 50.000 0.00 0.00 0.00 5.07
1506 1530 3.504863 CGGAAGCATTTGAGGAAACATG 58.495 45.455 0.00 0.00 0.00 3.21
1513 1537 1.098050 CTTCCCGGAAGCATTTGAGG 58.902 55.000 14.34 0.00 32.78 3.86
1537 1561 4.021280 TGCAATCCAAAAAGCATAAGCAGA 60.021 37.500 0.00 0.00 45.49 4.26
1538 1562 4.247258 TGCAATCCAAAAAGCATAAGCAG 58.753 39.130 0.00 0.00 45.49 4.24
1560 1585 1.304381 AATCACCGTGCCTGCCATT 60.304 52.632 0.00 0.00 0.00 3.16
1591 1616 2.886124 GAAGTAGTGGCTCGGCGC 60.886 66.667 0.00 0.00 38.13 6.53
1999 2024 3.669536 TGTATTGCATCGAAGGTGACAA 58.330 40.909 0.00 0.00 0.00 3.18
2010 2035 1.761784 TGGGGGCAAATGTATTGCATC 59.238 47.619 14.34 6.40 46.58 3.91
2011 2036 1.876849 TGGGGGCAAATGTATTGCAT 58.123 45.000 14.34 0.00 46.58 3.96
2029 2054 4.515191 TGAGAAGGGAAGAACGACAATTTG 59.485 41.667 0.00 0.00 0.00 2.32
2032 2057 3.866449 GCTGAGAAGGGAAGAACGACAAT 60.866 47.826 0.00 0.00 0.00 2.71
2034 2059 1.000955 GCTGAGAAGGGAAGAACGACA 59.999 52.381 0.00 0.00 0.00 4.35
2036 2061 1.338107 TGCTGAGAAGGGAAGAACGA 58.662 50.000 0.00 0.00 0.00 3.85
2037 2062 2.005451 CATGCTGAGAAGGGAAGAACG 58.995 52.381 0.00 0.00 0.00 3.95
2044 2069 6.757897 TTTAATGTAACATGCTGAGAAGGG 57.242 37.500 0.00 0.00 0.00 3.95
2061 2086 8.657729 TGCAACATATCAAGCACATTTTTAATG 58.342 29.630 0.00 0.00 31.05 1.90
2062 2087 8.774890 TGCAACATATCAAGCACATTTTTAAT 57.225 26.923 0.00 0.00 31.05 1.40
2063 2088 7.331440 CCTGCAACATATCAAGCACATTTTTAA 59.669 33.333 0.00 0.00 32.87 1.52
2064 2089 6.812656 CCTGCAACATATCAAGCACATTTTTA 59.187 34.615 0.00 0.00 32.87 1.52
2065 2090 5.640357 CCTGCAACATATCAAGCACATTTTT 59.360 36.000 0.00 0.00 32.87 1.94
2066 2091 5.172934 CCTGCAACATATCAAGCACATTTT 58.827 37.500 0.00 0.00 32.87 1.82
2067 2092 4.221262 ACCTGCAACATATCAAGCACATTT 59.779 37.500 0.00 0.00 32.87 2.32
2068 2093 3.765511 ACCTGCAACATATCAAGCACATT 59.234 39.130 0.00 0.00 32.87 2.71
2069 2094 3.359033 ACCTGCAACATATCAAGCACAT 58.641 40.909 0.00 0.00 32.87 3.21
2070 2095 2.749076 GACCTGCAACATATCAAGCACA 59.251 45.455 0.00 0.00 32.87 4.57
2080 2105 4.589908 CCCTTAGTAAAGACCTGCAACAT 58.410 43.478 0.00 0.00 34.37 2.71
2094 2119 1.648116 ACAAAGACGGGCCCTTAGTA 58.352 50.000 22.43 0.00 0.00 1.82
2097 2122 1.407712 GCATACAAAGACGGGCCCTTA 60.408 52.381 22.43 0.00 0.00 2.69
2148 2173 4.759096 GCCACGTGCACGCCAATC 62.759 66.667 37.35 18.68 44.43 2.67
2154 2179 2.239341 AAATCATCGCCACGTGCACG 62.239 55.000 35.99 35.99 46.33 5.34
2193 2218 3.028366 GCTTCCGGTCGCAGAAAGC 62.028 63.158 0.00 3.33 39.69 3.51
2289 2314 0.250124 TGAAAACATCCGGTGCGACT 60.250 50.000 0.00 0.00 0.00 4.18
2313 2338 0.762418 ACCGGTTGACATGGACTTCA 59.238 50.000 0.00 0.00 0.00 3.02
2328 2353 4.825634 TCATAGTACTCCATGTAGAACCGG 59.174 45.833 0.00 0.00 0.00 5.28
2971 2996 9.965824 GTCTTCAAAATGGAAAGACTGAATTTA 57.034 29.630 7.12 0.00 0.00 1.40
2973 2998 8.010733 TGTCTTCAAAATGGAAAGACTGAATT 57.989 30.769 13.70 0.00 31.79 2.17
3091 3116 2.027073 GGTCGTCAACATGAGCGCA 61.027 57.895 11.47 0.00 0.00 6.09
3127 3152 1.798234 TTGCACACACCTGAGCATGC 61.798 55.000 10.51 10.51 42.66 4.06
3148 3173 2.095567 CCATGAAAGAGGAAGTTGCGTG 60.096 50.000 0.00 0.00 0.00 5.34
3151 3176 3.319122 ACAACCATGAAAGAGGAAGTTGC 59.681 43.478 0.00 0.00 37.27 4.17
3161 3194 4.794003 GCTTGTGGAAGACAACCATGAAAG 60.794 45.833 0.00 0.00 39.78 2.62
3197 3230 9.476202 GAGCAAAGTAAACCAGAAATTTGTAAT 57.524 29.630 0.00 0.00 31.84 1.89
3198 3231 8.691797 AGAGCAAAGTAAACCAGAAATTTGTAA 58.308 29.630 0.00 0.00 31.84 2.41
3269 3302 4.082787 TCAATTTTGGCTCGATTGGACTTC 60.083 41.667 0.00 0.00 32.91 3.01
3275 3308 7.116662 TCAGAAAATTCAATTTTGGCTCGATTG 59.883 33.333 12.95 0.00 42.15 2.67
3287 3320 7.972277 CGGTTCATCTCATCAGAAAATTCAATT 59.028 33.333 0.00 0.00 30.24 2.32
3341 3374 6.474140 TCTACTGTTTTCTCACCAACACTA 57.526 37.500 0.00 0.00 0.00 2.74
3389 3422 4.461992 TCTCAACCGAACAAAACGAATC 57.538 40.909 0.00 0.00 0.00 2.52
3394 3427 3.730715 CAGCAATCTCAACCGAACAAAAC 59.269 43.478 0.00 0.00 0.00 2.43
3402 3435 2.158449 GTGTCTTCAGCAATCTCAACCG 59.842 50.000 0.00 0.00 0.00 4.44
3422 3455 2.297701 ACTTCAATTCAACACCTGCGT 58.702 42.857 0.00 0.00 0.00 5.24
3423 3456 3.044986 CAACTTCAATTCAACACCTGCG 58.955 45.455 0.00 0.00 0.00 5.18
3434 3467 7.040409 GGACTTGTCTATGAACCAACTTCAATT 60.040 37.037 0.61 0.00 42.37 2.32
3440 3473 3.910627 AGGGACTTGTCTATGAACCAACT 59.089 43.478 0.61 0.00 27.25 3.16
3465 3498 7.602517 AGAATGTAAGATTTCCTGTTCTTCG 57.397 36.000 0.00 0.00 34.22 3.79
3545 3579 4.367450 TGTACAATTCCTTGCAAGCAAAC 58.633 39.130 21.43 8.25 35.69 2.93
3620 3658 8.506168 TTTATCACTTTGTTCTGCCCTAATAG 57.494 34.615 0.00 0.00 0.00 1.73
3683 3721 8.006027 GCTTCAGCAATTTTGAAAATTCAGTAC 58.994 33.333 12.58 1.95 41.59 2.73
4490 4534 3.861840 TGGATTTTCATCTCCTGTCGTC 58.138 45.455 0.00 0.00 32.47 4.20
4491 4535 3.981071 TGGATTTTCATCTCCTGTCGT 57.019 42.857 0.00 0.00 32.47 4.34
4492 4536 3.375299 GGTTGGATTTTCATCTCCTGTCG 59.625 47.826 0.00 0.00 32.47 4.35
4493 4537 4.593956 AGGTTGGATTTTCATCTCCTGTC 58.406 43.478 0.00 0.00 32.47 3.51
4494 4538 4.593956 GAGGTTGGATTTTCATCTCCTGT 58.406 43.478 0.00 0.00 30.70 4.00
4495 4539 3.624861 CGAGGTTGGATTTTCATCTCCTG 59.375 47.826 0.00 0.00 30.70 3.86
4496 4540 3.370953 CCGAGGTTGGATTTTCATCTCCT 60.371 47.826 0.00 0.00 32.07 3.69
4497 4541 2.945668 CCGAGGTTGGATTTTCATCTCC 59.054 50.000 0.00 0.00 0.00 3.71
4498 4542 3.610911 ACCGAGGTTGGATTTTCATCTC 58.389 45.455 0.00 0.00 0.00 2.75
4499 4543 3.721087 ACCGAGGTTGGATTTTCATCT 57.279 42.857 0.00 0.00 0.00 2.90
4531 4575 2.643764 ATCTAAGTCGTCGTCGCCGC 62.644 60.000 0.00 0.00 36.96 6.53
4536 4580 4.496183 GTGTTGATGATCTAAGTCGTCGTC 59.504 45.833 0.00 0.00 37.02 4.20
4538 4582 4.497251 CAGTGTTGATGATCTAAGTCGTCG 59.503 45.833 0.00 0.00 37.02 5.12
4555 4599 3.161557 GGAGCACCTCCCAGTGTT 58.838 61.111 0.00 0.00 44.36 3.32
4583 4627 1.248785 ACGAAGGGAGCGAGCAACTA 61.249 55.000 0.00 0.00 0.00 2.24
4621 4665 0.674581 TTGATGCTGGAGACAAGGCG 60.675 55.000 0.00 0.00 42.06 5.52
4639 4683 0.371645 GACGACGACGACGACCTATT 59.628 55.000 25.15 2.32 42.66 1.73


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

AutoCloner maintained by Alex Coulton.