Multiple sequence alignment - TraesCS4B01G291700

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 TraesCS4B01G291700 chr4B 100.000 4548 0 0 1 4548 577004186 576999639 0.000000e+00 8399
1 TraesCS4B01G291700 chr4B 95.537 717 28 4 1 714 186604097 186604812 0.000000e+00 1144
2 TraesCS4B01G291700 chr4D 91.597 2523 168 31 2056 4548 461491560 461489052 0.000000e+00 3445
3 TraesCS4B01G291700 chr4D 95.270 909 37 6 724 1632 461493186 461492284 0.000000e+00 1435
4 TraesCS4B01G291700 chr4D 94.253 261 14 1 1628 1887 461492051 461491791 9.170000e-107 398
5 TraesCS4B01G291700 chr4A 91.379 2517 173 28 2056 4548 7166057 7168553 0.000000e+00 3406
6 TraesCS4B01G291700 chr4A 94.654 823 27 5 769 1581 7164667 7165482 0.000000e+00 1260
7 TraesCS4B01G291700 chr4A 90.447 492 30 8 1554 2040 7165485 7165964 2.310000e-177 632
8 TraesCS4B01G291700 chr3B 96.806 720 17 4 1 716 533025267 533024550 0.000000e+00 1197
9 TraesCS4B01G291700 chr6B 96.095 717 23 5 1 714 478476892 478477606 0.000000e+00 1164
10 TraesCS4B01G291700 chr6B 95.688 719 25 4 1 715 47223436 47222720 0.000000e+00 1151
11 TraesCS4B01G291700 chr6B 95.543 718 29 1 1 715 176276359 176277076 0.000000e+00 1146
12 TraesCS4B01G291700 chr6D 95.978 721 20 5 2 718 353103265 353103980 0.000000e+00 1162
13 TraesCS4B01G291700 chr5A 95.950 716 25 3 1 713 35738606 35739320 0.000000e+00 1158
14 TraesCS4B01G291700 chr1B 95.543 718 28 4 1 715 52692444 52691728 0.000000e+00 1146
15 TraesCS4B01G291700 chr1B 95.676 717 24 3 1 714 676206959 676207671 0.000000e+00 1146


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 TraesCS4B01G291700 chr4B 576999639 577004186 4547 True 8399.000000 8399 100.000000 1 4548 1 chr4B.!!$R1 4547
1 TraesCS4B01G291700 chr4B 186604097 186604812 715 False 1144.000000 1144 95.537000 1 714 1 chr4B.!!$F1 713
2 TraesCS4B01G291700 chr4D 461489052 461493186 4134 True 1759.333333 3445 93.706667 724 4548 3 chr4D.!!$R1 3824
3 TraesCS4B01G291700 chr4A 7164667 7168553 3886 False 1766.000000 3406 92.160000 769 4548 3 chr4A.!!$F1 3779
4 TraesCS4B01G291700 chr3B 533024550 533025267 717 True 1197.000000 1197 96.806000 1 716 1 chr3B.!!$R1 715
5 TraesCS4B01G291700 chr6B 478476892 478477606 714 False 1164.000000 1164 96.095000 1 714 1 chr6B.!!$F2 713
6 TraesCS4B01G291700 chr6B 47222720 47223436 716 True 1151.000000 1151 95.688000 1 715 1 chr6B.!!$R1 714
7 TraesCS4B01G291700 chr6B 176276359 176277076 717 False 1146.000000 1146 95.543000 1 715 1 chr6B.!!$F1 714
8 TraesCS4B01G291700 chr6D 353103265 353103980 715 False 1162.000000 1162 95.978000 2 718 1 chr6D.!!$F1 716
9 TraesCS4B01G291700 chr5A 35738606 35739320 714 False 1158.000000 1158 95.950000 1 713 1 chr5A.!!$F1 712
10 TraesCS4B01G291700 chr1B 52691728 52692444 716 True 1146.000000 1146 95.543000 1 715 1 chr1B.!!$R1 714
11 TraesCS4B01G291700 chr1B 676206959 676207671 712 False 1146.000000 1146 95.676000 1 714 1 chr1B.!!$F1 713

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
277 278 0.036765 CGGCTGGTGGTACTTAGCAA 60.037 55.000 11.27 0.0 37.89 3.91 F
751 755 0.971386 GTTCGTTGTAGGGACCTGGA 59.029 55.000 0.00 0.0 0.00 3.86 F
1492 1502 0.037605 CGAGCTAAACTGGGTCGGTT 60.038 55.000 7.30 0.0 46.49 4.44 F
2702 3071 1.610673 TGCCCACTCCCTCACTCTC 60.611 63.158 0.00 0.0 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1462 1472 0.179111 TTTAGCTCGATGTGGCTCCG 60.179 55.000 0.0 0.0 39.65 4.63 R
2396 2765 1.606737 GCAAGCGAAAGTCTCCTCACT 60.607 52.381 0.0 0.0 0.00 3.41 R
2784 3153 0.907486 TCTGGCTCATTGGAGAGGTG 59.093 55.000 0.0 0.0 44.26 4.00 R
4036 4414 0.386113 GCCTCTACAGGTCGATGGAC 59.614 60.000 0.0 0.0 42.74 4.02 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
92 93 0.809385 CTCTTCGCCGTGTCTTCCTA 59.191 55.000 0.00 0.00 0.00 2.94
155 156 0.321346 TCATCTTGCACGGAGCTTCA 59.679 50.000 0.00 0.00 45.94 3.02
161 162 1.301716 GCACGGAGCTTCAGTGGAA 60.302 57.895 15.66 0.00 41.75 3.53
273 274 0.604578 GTGTCGGCTGGTGGTACTTA 59.395 55.000 0.00 0.00 0.00 2.24
277 278 0.036765 CGGCTGGTGGTACTTAGCAA 60.037 55.000 11.27 0.00 37.89 3.91
284 285 3.007635 GGTGGTACTTAGCAACATGGTC 58.992 50.000 0.00 0.00 40.87 4.02
534 535 1.165270 GTTAGGTTTGGCTGCGATGT 58.835 50.000 0.00 0.00 0.00 3.06
574 575 1.233285 GCTATCTGCGCCCCTTCATG 61.233 60.000 4.18 0.00 0.00 3.07
624 625 7.224167 GCGGCTTTAGTCTTACTGTTGTATTAT 59.776 37.037 0.00 0.00 0.00 1.28
749 753 2.833631 AAGTTCGTTGTAGGGACCTG 57.166 50.000 0.00 0.00 0.00 4.00
751 755 0.971386 GTTCGTTGTAGGGACCTGGA 59.029 55.000 0.00 0.00 0.00 3.86
752 756 1.345415 GTTCGTTGTAGGGACCTGGAA 59.655 52.381 0.00 0.00 0.00 3.53
754 758 1.345415 TCGTTGTAGGGACCTGGAAAC 59.655 52.381 0.00 2.39 0.00 2.78
846 850 6.899393 TCAAGAAAATTAGTCTGTGCCAAT 57.101 33.333 0.00 0.00 0.00 3.16
857 861 5.238583 AGTCTGTGCCAATCAGTTACTAAC 58.761 41.667 0.00 0.00 34.86 2.34
946 956 5.163447 TGACGTCTGTTCCCTTTCCATATAG 60.163 44.000 17.92 0.00 0.00 1.31
1034 1044 1.229082 TCCTCGGGGCAGTACTTGT 60.229 57.895 0.00 0.00 0.00 3.16
1492 1502 0.037605 CGAGCTAAACTGGGTCGGTT 60.038 55.000 7.30 0.00 46.49 4.44
1705 1988 7.125659 CCAACTCCCCTAAATAACAATGGAAAT 59.874 37.037 0.00 0.00 0.00 2.17
1753 2036 9.397280 TGTCATATACTCATATAGGTAGCTCAC 57.603 37.037 0.00 0.00 0.00 3.51
1762 2045 8.341892 TCATATAGGTAGCTCACTCTACATTG 57.658 38.462 0.00 0.00 40.42 2.82
1784 2067 5.981174 TGTCGTAGAATACACTGTTTTTGC 58.019 37.500 0.00 0.00 43.24 3.68
1864 2148 3.075283 TGGCATTACAAAGAGGAAGGGAA 59.925 43.478 0.00 0.00 0.00 3.97
1868 2152 5.944007 GCATTACAAAGAGGAAGGGAAGTAA 59.056 40.000 0.00 0.00 0.00 2.24
1879 2163 6.486056 AGGAAGGGAAGTAATTTTCTCCTTC 58.514 40.000 19.51 19.51 43.98 3.46
2017 2302 2.290464 TCGGCCGGTAACCATTTATTG 58.710 47.619 27.83 0.00 0.00 1.90
2027 2312 6.617879 GGTAACCATTTATTGTGGACAAGAC 58.382 40.000 0.00 0.00 39.47 3.01
2028 2313 6.433093 GGTAACCATTTATTGTGGACAAGACT 59.567 38.462 0.00 0.00 39.47 3.24
2029 2314 5.964958 ACCATTTATTGTGGACAAGACTG 57.035 39.130 0.00 0.00 39.47 3.51
2030 2315 5.630121 ACCATTTATTGTGGACAAGACTGA 58.370 37.500 0.00 0.00 39.47 3.41
2031 2316 5.707298 ACCATTTATTGTGGACAAGACTGAG 59.293 40.000 0.00 0.00 39.47 3.35
2032 2317 5.939883 CCATTTATTGTGGACAAGACTGAGA 59.060 40.000 0.00 0.00 39.47 3.27
2034 2319 7.361542 CCATTTATTGTGGACAAGACTGAGAAG 60.362 40.741 0.00 0.00 39.47 2.85
2037 2360 3.300388 TGTGGACAAGACTGAGAAGAGT 58.700 45.455 0.00 0.00 0.00 3.24
2043 2366 6.042093 TGGACAAGACTGAGAAGAGTAACAAT 59.958 38.462 0.00 0.00 0.00 2.71
2085 2448 2.159352 TGCCTCAAATTGCATGACGATG 60.159 45.455 0.00 0.00 31.31 3.84
2133 2499 7.049799 ACTAGCTCCTTAAGAGATGATGAAC 57.950 40.000 3.36 0.00 46.50 3.18
2137 2503 5.682471 GCTCCTTAAGAGATGATGAACGGAA 60.682 44.000 3.36 0.00 46.50 4.30
2181 2547 9.512748 AGGCTAGAGGGTCAATATGATAATATT 57.487 33.333 0.00 0.00 0.00 1.28
2245 2613 8.246180 AGGTGATGCAATACACTTCTAAAATTG 58.754 33.333 17.07 0.00 37.22 2.32
2246 2614 8.243426 GGTGATGCAATACACTTCTAAAATTGA 58.757 33.333 17.07 0.00 37.22 2.57
2326 2695 8.895932 AAAATACAACAATCTAGAAATGTCGC 57.104 30.769 13.19 0.00 0.00 5.19
2343 2712 7.581011 AATGTCGCAATGGATTTAAGAAAAC 57.419 32.000 0.00 0.00 0.00 2.43
2345 2714 4.862574 GTCGCAATGGATTTAAGAAAACCC 59.137 41.667 0.00 0.00 0.00 4.11
2346 2715 3.857093 CGCAATGGATTTAAGAAAACCCG 59.143 43.478 0.00 0.00 0.00 5.28
2347 2716 3.616821 GCAATGGATTTAAGAAAACCCGC 59.383 43.478 0.00 0.00 0.00 6.13
2349 2718 5.233988 CAATGGATTTAAGAAAACCCGCAA 58.766 37.500 0.00 0.00 0.00 4.85
2353 2722 4.556233 GATTTAAGAAAACCCGCAAAGCT 58.444 39.130 0.00 0.00 0.00 3.74
2396 2765 2.738587 TTTTACAGGTCCTGCCAACA 57.261 45.000 19.40 3.83 40.61 3.33
2441 2810 3.262151 TCATATGTTCGGTTGTCTTGGGA 59.738 43.478 1.90 0.00 0.00 4.37
2468 2837 3.584848 AGTCAGCTACCATCAAAGAAGGT 59.415 43.478 0.00 0.00 37.42 3.50
2469 2838 4.042187 AGTCAGCTACCATCAAAGAAGGTT 59.958 41.667 0.00 0.00 35.22 3.50
2477 2846 3.181477 CCATCAAAGAAGGTTTGTGCACA 60.181 43.478 17.42 17.42 0.00 4.57
2595 2964 5.221028 CGAAAGGCTATCACAAATATTGCCA 60.221 40.000 11.89 0.00 44.55 4.92
2609 2978 1.981256 TTGCCAACAAGAGGGAAGAC 58.019 50.000 0.00 0.00 32.37 3.01
2702 3071 1.610673 TGCCCACTCCCTCACTCTC 60.611 63.158 0.00 0.00 0.00 3.20
2753 3122 2.110213 GTTGGGGCACACGAGACA 59.890 61.111 0.00 0.00 0.00 3.41
2784 3153 2.839486 TATCACCTTCATGATCCGGC 57.161 50.000 0.00 0.00 39.97 6.13
2858 3227 3.119388 TCAATATGCTGCTTTGCTTCCAC 60.119 43.478 0.00 0.00 0.00 4.02
2873 3242 5.049167 TGCTTCCACATTTGATTCAAACAC 58.951 37.500 13.80 0.00 36.13 3.32
3110 3479 1.430992 ACCAGGGTTACCATATCCCG 58.569 55.000 2.98 0.00 45.27 5.14
3134 3503 6.035758 CGAAAGGCTGGAAAGTAAGTACATAC 59.964 42.308 0.00 0.00 0.00 2.39
3187 3557 5.249393 ACTTCCCAAGAACTCTATCACACAT 59.751 40.000 0.00 0.00 0.00 3.21
3520 3890 0.820871 TTGCCAAAAACGTCCAAGCT 59.179 45.000 0.00 0.00 0.00 3.74
3525 3895 3.735514 GCCAAAAACGTCCAAGCTAACAA 60.736 43.478 0.00 0.00 0.00 2.83
3537 3907 4.695455 CCAAGCTAACAATATGGATACCGG 59.305 45.833 0.00 0.00 32.82 5.28
3560 3930 3.496331 ACAGGTTAAACCCATGACAAGG 58.504 45.455 0.00 0.00 39.75 3.61
3589 3959 8.728337 ATTATGATGATACATGCATGGTCTAC 57.272 34.615 29.41 20.97 0.00 2.59
3605 3975 6.674694 TGGTCTACGTTATGAAGACTAGAC 57.325 41.667 13.56 7.19 39.65 2.59
3668 4039 1.410153 GCTATTCCATGTTGGGCTTGG 59.590 52.381 0.00 0.00 42.09 3.61
3676 4047 1.367346 TGTTGGGCTTGGGAGATACA 58.633 50.000 0.00 0.00 0.00 2.29
3806 4178 6.889301 CACAGGATGCAATGGTAATTCTAT 57.111 37.500 0.00 0.00 42.53 1.98
3895 4273 4.301072 TTTTACTCTCTTCCATGTGGGG 57.699 45.455 0.00 0.00 37.22 4.96
3904 4282 2.505982 CATGTGGGGCCTAGTCGG 59.494 66.667 0.84 0.00 0.00 4.79
3909 4287 1.306654 TGGGGCCTAGTCGGTGATT 60.307 57.895 0.84 0.00 34.25 2.57
3920 4298 7.416326 GGCCTAGTCGGTGATTAAAATTTGAAT 60.416 37.037 0.00 0.00 34.25 2.57
3982 4360 4.637534 GGATTGCATAGAAGTGCTCTTTCA 59.362 41.667 2.00 0.00 45.27 2.69
4001 4379 5.933187 TTCAATTGAACTACGCTAAGCAA 57.067 34.783 16.91 0.00 0.00 3.91
4003 4381 7.603963 TTCAATTGAACTACGCTAAGCAATA 57.396 32.000 16.91 0.00 0.00 1.90
4005 4383 5.637104 ATTGAACTACGCTAAGCAATACG 57.363 39.130 0.00 0.00 0.00 3.06
4008 4386 3.093717 ACTACGCTAAGCAATACGCAT 57.906 42.857 0.00 0.00 46.13 4.73
4011 4389 4.680110 ACTACGCTAAGCAATACGCATAAG 59.320 41.667 0.00 0.00 46.13 1.73
4021 4399 3.830744 ATACGCATAAGTAGTTGGGCA 57.169 42.857 8.24 0.00 0.00 5.36
4024 4402 2.093181 ACGCATAAGTAGTTGGGCATGA 60.093 45.455 0.00 0.00 0.00 3.07
4036 4414 2.358957 TGGGCATGACAAAGAAGATCG 58.641 47.619 0.00 0.00 0.00 3.69
4090 4468 4.440829 GGCCCCGGATGCCTCAAA 62.441 66.667 23.24 0.00 45.70 2.69
4093 4471 2.406616 CCCCGGATGCCTCAAAACG 61.407 63.158 0.73 0.00 0.00 3.60
4095 4473 1.369091 CCCGGATGCCTCAAAACGAG 61.369 60.000 0.73 0.00 41.89 4.18
4096 4474 0.391130 CCGGATGCCTCAAAACGAGA 60.391 55.000 0.00 0.00 45.45 4.04
4199 4588 5.566469 TCGGGAGTTTTTAGTGATCCAAAT 58.434 37.500 0.00 0.00 0.00 2.32
4281 4670 3.366396 TCCTCTTTTCTCATCCTACGCT 58.634 45.455 0.00 0.00 0.00 5.07
4287 4676 2.437085 TCTCATCCTACGCTCTCCAA 57.563 50.000 0.00 0.00 0.00 3.53
4332 4724 9.585369 TTGGGATGCAGATACATTAAAATATCA 57.415 29.630 10.41 0.00 31.34 2.15
4421 4814 8.570068 TGGGAACTAACCAACTAATAAATGTC 57.430 34.615 0.00 0.00 34.44 3.06
4422 4815 8.164733 TGGGAACTAACCAACTAATAAATGTCA 58.835 33.333 0.00 0.00 34.44 3.58
4489 4883 2.513753 TGGTAGCCAATTGTCCAAGTG 58.486 47.619 4.43 0.71 36.28 3.16
4508 4902 2.721090 GTGCAAGAGTTTTTAGCAAGCG 59.279 45.455 0.00 0.00 36.91 4.68
4510 4904 2.973879 GCAAGAGTTTTTAGCAAGCGAC 59.026 45.455 0.00 0.00 0.00 5.19
4531 4925 8.429641 AGCGACTATTTTCCCTTAAATAGATGA 58.570 33.333 18.07 0.00 44.96 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 0.036952 CCACAATCACCACGAGAGCT 60.037 55.000 0.00 0.00 0.00 4.09
155 156 2.821969 GGCATGACTTGACATTTCCACT 59.178 45.455 0.00 0.00 31.51 4.00
273 274 0.037303 CACCTCAGGACCATGTTGCT 59.963 55.000 0.00 0.00 0.00 3.91
277 278 2.768527 CTGATACACCTCAGGACCATGT 59.231 50.000 0.00 0.00 39.20 3.21
284 285 0.179100 CGCCACTGATACACCTCAGG 60.179 60.000 6.10 0.00 45.67 3.86
366 367 1.725557 GCTCGGTCCAGCTATCGTCA 61.726 60.000 6.17 0.00 36.38 4.35
534 535 2.241176 CCTGGGCCTAATACCAAACAGA 59.759 50.000 4.53 0.00 36.09 3.41
574 575 4.498345 CGTCTAAGCCACTCTATCCAGTTC 60.498 50.000 0.00 0.00 0.00 3.01
624 625 9.567776 TGATTATTCTCACAAGACCTTACAAAA 57.432 29.630 0.00 0.00 0.00 2.44
649 650 4.761745 CGATGCATACGGTCACTTTATTG 58.238 43.478 0.00 0.00 0.00 1.90
659 660 1.758440 ATCTGGGCGATGCATACGGT 61.758 55.000 16.56 0.00 0.00 4.83
718 722 7.248437 CCTACAACGAACTTTTTGAAAGAACT 58.752 34.615 7.37 0.00 0.00 3.01
719 723 6.471198 CCCTACAACGAACTTTTTGAAAGAAC 59.529 38.462 7.37 1.03 0.00 3.01
720 724 6.374894 TCCCTACAACGAACTTTTTGAAAGAA 59.625 34.615 7.37 0.00 0.00 2.52
721 725 5.881443 TCCCTACAACGAACTTTTTGAAAGA 59.119 36.000 7.37 0.00 0.00 2.52
722 726 5.969435 GTCCCTACAACGAACTTTTTGAAAG 59.031 40.000 0.00 0.00 0.00 2.62
723 727 5.163632 GGTCCCTACAACGAACTTTTTGAAA 60.164 40.000 0.00 0.00 0.00 2.69
724 728 4.336153 GGTCCCTACAACGAACTTTTTGAA 59.664 41.667 0.00 0.00 0.00 2.69
725 729 3.878699 GGTCCCTACAACGAACTTTTTGA 59.121 43.478 0.00 0.00 0.00 2.69
726 730 3.881089 AGGTCCCTACAACGAACTTTTTG 59.119 43.478 0.00 0.00 0.00 2.44
727 731 3.881089 CAGGTCCCTACAACGAACTTTTT 59.119 43.478 0.00 0.00 0.00 1.94
728 732 3.473625 CAGGTCCCTACAACGAACTTTT 58.526 45.455 0.00 0.00 0.00 2.27
732 736 0.971386 TCCAGGTCCCTACAACGAAC 59.029 55.000 0.00 0.00 0.00 3.95
733 737 1.719529 TTCCAGGTCCCTACAACGAA 58.280 50.000 0.00 0.00 0.00 3.85
751 755 1.228862 AATGCGGCAGGGAAGGTTT 60.229 52.632 9.25 0.00 0.00 3.27
752 756 1.678970 GAATGCGGCAGGGAAGGTT 60.679 57.895 9.25 0.00 0.00 3.50
754 758 2.830370 GGAATGCGGCAGGGAAGG 60.830 66.667 9.25 0.00 0.00 3.46
846 850 6.922957 ACGATGGTAAAAACGTTAGTAACTGA 59.077 34.615 11.17 0.00 35.47 3.41
857 861 3.296943 CGATTTGCACGATGGTAAAAACG 59.703 43.478 0.00 0.00 0.00 3.60
946 956 6.089954 GGGTGTTGTGTACTCGAAGTTTATAC 59.910 42.308 0.00 0.00 0.00 1.47
1034 1044 1.334556 CAACTGCAGCTACAAGCAACA 59.665 47.619 15.27 0.00 45.56 3.33
1212 1222 1.754234 GGTAGAGACCGGGCCGTAA 60.754 63.158 26.32 0.00 35.52 3.18
1237 1247 2.452813 CCGTCGGCGATCCAAACAG 61.453 63.158 12.93 0.00 41.33 3.16
1284 1294 1.661617 CCGTCGTTGCCGAATATGAAA 59.338 47.619 0.00 0.00 46.26 2.69
1305 1315 2.544685 CCTGTCTGCGTCAAGATTAGG 58.455 52.381 0.00 0.00 31.32 2.69
1308 1318 2.846371 GCCTGTCTGCGTCAAGATT 58.154 52.632 0.00 0.00 0.00 2.40
1377 1387 3.123620 CTGCGGACCAGCTTCAGC 61.124 66.667 3.85 3.85 42.49 4.26
1422 1432 2.287909 GCAGACGTATCTCCTCACCATC 60.288 54.545 0.00 0.00 30.42 3.51
1462 1472 0.179111 TTTAGCTCGATGTGGCTCCG 60.179 55.000 0.00 0.00 39.65 4.63
1762 2045 6.071463 CAGCAAAAACAGTGTATTCTACGAC 58.929 40.000 0.00 0.00 0.00 4.34
1784 2067 5.473931 ACTCTATTAGTGAACAGTGTGCAG 58.526 41.667 3.44 0.00 36.93 4.41
1879 2163 4.049186 CGTAACCATCCTCTCAATAACCG 58.951 47.826 0.00 0.00 0.00 4.44
1977 2261 7.201670 CGGCCGATTTTAGATTACCTAGTTTTT 60.202 37.037 24.07 0.00 0.00 1.94
1996 2280 2.882137 CAATAAATGGTTACCGGCCGAT 59.118 45.455 30.73 14.28 0.00 4.18
1997 2281 2.290464 CAATAAATGGTTACCGGCCGA 58.710 47.619 30.73 3.89 0.00 5.54
2017 2302 5.221263 TGTTACTCTTCTCAGTCTTGTCCAC 60.221 44.000 0.00 0.00 0.00 4.02
2066 2429 3.770263 ACATCGTCATGCAATTTGAGG 57.230 42.857 0.00 0.00 32.57 3.86
2067 2430 4.325204 CCAAACATCGTCATGCAATTTGAG 59.675 41.667 0.00 0.00 30.37 3.02
2085 2448 9.331282 AGTATGCTCATCTCTAAATTACCAAAC 57.669 33.333 0.00 0.00 0.00 2.93
2133 2499 6.581166 GCCTTTTACACAAGTAGAAAATTCCG 59.419 38.462 0.00 0.00 0.00 4.30
2137 2503 9.220767 CTCTAGCCTTTTACACAAGTAGAAAAT 57.779 33.333 0.00 0.00 0.00 1.82
2181 2547 8.328758 CAATTATCTTATATAAGGTGCCCCTCA 58.671 37.037 19.98 0.73 41.56 3.86
2200 2568 7.246674 TCACCTTGCGAGAAATACAATTATC 57.753 36.000 1.22 0.00 0.00 1.75
2207 2575 2.677836 TGCATCACCTTGCGAGAAATAC 59.322 45.455 1.22 0.00 45.77 1.89
2211 2579 1.825090 ATTGCATCACCTTGCGAGAA 58.175 45.000 1.22 0.00 45.77 2.87
2216 2584 3.441572 AGAAGTGTATTGCATCACCTTGC 59.558 43.478 11.67 0.00 43.07 4.01
2309 2678 5.185454 TCCATTGCGACATTTCTAGATTGT 58.815 37.500 8.22 8.22 0.00 2.71
2326 2695 4.815269 TGCGGGTTTTCTTAAATCCATTG 58.185 39.130 0.00 0.00 43.53 2.82
2343 2712 4.493547 TCATTTCAAATTAGCTTTGCGGG 58.506 39.130 0.00 0.00 43.32 6.13
2345 2714 7.023575 ACTACTCATTTCAAATTAGCTTTGCG 58.976 34.615 0.00 0.00 43.32 4.85
2346 2715 8.642020 CAACTACTCATTTCAAATTAGCTTTGC 58.358 33.333 0.00 0.00 43.32 3.68
2347 2716 9.897744 TCAACTACTCATTTCAAATTAGCTTTG 57.102 29.630 0.00 0.00 44.70 2.77
2396 2765 1.606737 GCAAGCGAAAGTCTCCTCACT 60.607 52.381 0.00 0.00 0.00 3.41
2441 2810 4.284490 TCTTTGATGGTAGCTGACTCTTGT 59.716 41.667 0.00 0.00 0.00 3.16
2468 2837 6.449635 AGAGTAACAAAATCTGTGCACAAA 57.550 33.333 21.98 8.53 38.67 2.83
2469 2838 6.264832 CAAGAGTAACAAAATCTGTGCACAA 58.735 36.000 21.98 12.25 38.67 3.33
2477 2846 4.767409 GCCTTCCCAAGAGTAACAAAATCT 59.233 41.667 0.00 0.00 0.00 2.40
2595 2964 3.041946 ACAGTGAGTCTTCCCTCTTGTT 58.958 45.455 0.00 0.00 30.88 2.83
2702 3071 2.348498 CGTGTTGTCCACAATGTCTTCG 60.348 50.000 0.00 0.00 44.78 3.79
2753 3122 5.489792 TGAAGGTGATAAGAGCAGAAGTT 57.510 39.130 0.00 0.00 0.00 2.66
2784 3153 0.907486 TCTGGCTCATTGGAGAGGTG 59.093 55.000 0.00 0.00 44.26 4.00
2837 3206 3.184541 GTGGAAGCAAAGCAGCATATTG 58.815 45.455 0.00 0.00 36.85 1.90
2839 3208 2.449464 TGTGGAAGCAAAGCAGCATAT 58.551 42.857 0.00 0.00 36.85 1.78
2858 3227 9.480053 AGAAATTACCAGTGTTTGAATCAAATG 57.520 29.630 11.87 6.29 35.74 2.32
2873 3242 6.414732 TCCATGGTGTAGAAGAAATTACCAG 58.585 40.000 12.58 0.00 41.05 4.00
2953 3322 6.968131 GAGCATCTTTTGGGTTTTTATTCC 57.032 37.500 0.00 0.00 0.00 3.01
3110 3479 6.877322 TGTATGTACTTACTTTCCAGCCTTTC 59.123 38.462 17.09 0.00 0.00 2.62
3499 3869 1.470805 GCTTGGACGTTTTTGGCAAGT 60.471 47.619 0.00 0.00 0.00 3.16
3520 3890 5.367352 ACCTGTTCCGGTATCCATATTGTTA 59.633 40.000 0.00 0.00 34.94 2.41
3525 3895 6.293698 GTTTAACCTGTTCCGGTATCCATAT 58.706 40.000 0.00 0.00 35.89 1.78
3537 3907 4.022329 CCTTGTCATGGGTTTAACCTGTTC 60.022 45.833 14.27 0.00 38.64 3.18
3560 3930 9.350357 GACCATGCATGTATCATCATAATTTTC 57.650 33.333 24.58 0.00 0.00 2.29
3644 4014 1.024271 CCCAACATGGAATAGCGTGG 58.976 55.000 0.00 0.00 40.96 4.94
3895 4273 6.431198 TCAAATTTTAATCACCGACTAGGC 57.569 37.500 0.00 0.00 46.52 3.93
3920 4298 5.453339 CGACCCTTCCATCAAGCTAGATTTA 60.453 44.000 0.00 0.00 0.00 1.40
3982 4360 5.501897 GCGTATTGCTTAGCGTAGTTCAATT 60.502 40.000 0.00 0.00 41.73 2.32
4001 4379 3.830744 TGCCCAACTACTTATGCGTAT 57.169 42.857 0.00 0.00 0.00 3.06
4003 4381 2.093181 TCATGCCCAACTACTTATGCGT 60.093 45.455 0.00 0.00 0.00 5.24
4005 4383 3.278574 TGTCATGCCCAACTACTTATGC 58.721 45.455 0.00 0.00 0.00 3.14
4008 4386 5.235850 TCTTTGTCATGCCCAACTACTTA 57.764 39.130 0.00 0.00 0.00 2.24
4011 4389 4.072131 TCTTCTTTGTCATGCCCAACTAC 58.928 43.478 0.00 0.00 0.00 2.73
4021 4399 4.115516 CGATGGACGATCTTCTTTGTCAT 58.884 43.478 0.00 0.00 45.77 3.06
4024 4402 3.868757 TCGATGGACGATCTTCTTTGT 57.131 42.857 0.00 0.00 46.45 2.83
4036 4414 0.386113 GCCTCTACAGGTCGATGGAC 59.614 60.000 0.00 0.00 42.74 4.02
4047 4425 0.391228 TTCAAGCACACGCCTCTACA 59.609 50.000 0.00 0.00 39.83 2.74
4080 4458 4.691216 ACTAGTTTCTCGTTTTGAGGCATC 59.309 41.667 0.00 0.00 45.32 3.91
4199 4588 7.785028 ACAGAGTACCATGTCCATCTTCTTATA 59.215 37.037 0.00 0.00 0.00 0.98
4287 4676 9.305555 CATCCCAAGATTAATCCATATTTGACT 57.694 33.333 11.92 0.00 0.00 3.41
4453 4846 4.874396 GGCTACCAACAATAGGACTTGTAC 59.126 45.833 0.00 0.00 38.38 2.90
4489 4883 2.973879 GTCGCTTGCTAAAAACTCTTGC 59.026 45.455 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.