Multiple sequence alignment - TraesCS3A01G027400

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 TraesCS3A01G027400 chr3A 100.000 4509 0 0 1 4509 14755854 14760362 0.000000e+00 8327.0
1 TraesCS3A01G027400 chr3D 96.726 2291 45 8 853 3125 6180076 6177798 0.000000e+00 3788.0
2 TraesCS3A01G027400 chr3D 98.034 763 15 0 3256 4018 6177526 6176764 0.000000e+00 1327.0
3 TraesCS3A01G027400 chr3D 96.138 725 27 1 2 725 6181037 6180313 0.000000e+00 1182.0
4 TraesCS3A01G027400 chr3D 95.266 507 20 2 4004 4508 6176731 6176227 0.000000e+00 800.0
5 TraesCS3A01G027400 chr3D 99.231 130 1 0 3129 3258 6177682 6177553 7.540000e-58 235.0
6 TraesCS3A01G027400 chr3D 96.522 115 4 0 742 856 6180328 6180214 1.660000e-44 191.0
7 TraesCS3A01G027400 chr6D 96.419 391 12 1 4119 4509 83085941 83085553 1.060000e-180 643.0
8 TraesCS3A01G027400 chr6D 94.859 389 18 1 4121 4509 388550912 388550526 1.390000e-169 606.0
9 TraesCS3A01G027400 chr2D 95.897 390 14 1 4120 4509 102816874 102817261 8.230000e-177 630.0
10 TraesCS3A01G027400 chr2D 93.830 389 22 1 4121 4509 512034372 512034758 6.500000e-163 584.0
11 TraesCS3A01G027400 chr1D 94.885 391 18 1 4119 4509 405756744 405757132 1.070000e-170 610.0
12 TraesCS3A01G027400 chr1D 86.047 86 12 0 3911 3996 481696687 481696772 4.800000e-15 93.5
13 TraesCS3A01G027400 chr1B 94.588 388 13 2 4122 4509 192148679 192149058 1.080000e-165 593.0
14 TraesCS3A01G027400 chr4A 93.798 387 22 1 4123 4509 133374764 133375148 8.410000e-162 580.0
15 TraesCS3A01G027400 chr1A 93.350 391 24 1 4119 4509 592989074 592989462 1.090000e-160 577.0
16 TraesCS3A01G027400 chr6A 89.247 93 10 0 3906 3998 506233759 506233667 2.850000e-22 117.0
17 TraesCS3A01G027400 chr7B 89.535 86 9 0 3912 3997 658764607 658764522 4.770000e-20 110.0
18 TraesCS3A01G027400 chr7B 89.189 74 8 0 3923 3996 54501898 54501971 4.800000e-15 93.5
19 TraesCS3A01G027400 chr7B 86.047 86 12 0 3911 3996 75606439 75606354 4.800000e-15 93.5
20 TraesCS3A01G027400 chr7A 89.535 86 8 1 3912 3997 78422803 78422719 1.720000e-19 108.0
21 TraesCS3A01G027400 chr4D 86.747 83 11 0 3909 3991 1640043 1639961 4.800000e-15 93.5
22 TraesCS3A01G027400 chr6B 90.909 66 6 0 3911 3976 7821339 7821404 6.210000e-14 89.8


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 TraesCS3A01G027400 chr3A 14755854 14760362 4508 False 8327.000000 8327 100.000000 1 4509 1 chr3A.!!$F1 4508
1 TraesCS3A01G027400 chr3D 6176227 6181037 4810 True 1253.833333 3788 96.986167 2 4508 6 chr3D.!!$R1 4506

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
724 726 0.247736 CCGTCTCCCCTCAGTTCAAG 59.752 60.0 0.00 0.00 0.00 3.02 F
736 738 0.318762 AGTTCAAGAGACCTCACGCC 59.681 55.0 0.00 0.00 0.00 5.68 F
2341 2502 0.035152 TTGGATCGAATGGTGCAGCT 60.035 50.0 18.08 0.00 0.00 4.24 F
2353 2514 0.609131 GTGCAGCTGCTAAAGGGGAA 60.609 55.0 36.61 12.87 42.66 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2327 2488 0.036483 TTAGCAGCTGCACCATTCGA 60.036 50.000 38.24 12.96 45.16 3.71 R
2533 2694 3.381949 GCTCATTATACGGACAGACCAC 58.618 50.000 0.00 0.00 38.90 4.16 R
3263 3565 1.823797 TGCTGCAATGCATAGACACA 58.176 45.000 8.91 0.00 38.13 3.72 R
4245 4596 1.945394 GGTGGCACATGAGATTGCTAG 59.055 52.381 20.82 0.00 44.52 3.42 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
35 36 1.005037 AAGAAGATGTCGTGCGCCA 60.005 52.632 4.18 0.00 0.00 5.69
55 56 1.736645 CCCGCGACACCTACACTTG 60.737 63.158 8.23 0.00 0.00 3.16
58 59 2.380410 GCGACACCTACACTTGCCG 61.380 63.158 0.00 0.00 0.00 5.69
63 64 1.206371 ACACCTACACTTGCCGGATAC 59.794 52.381 5.05 0.00 0.00 2.24
107 108 4.365111 TTGCCCCCTCGCAAGCAT 62.365 61.111 0.00 0.00 43.65 3.79
162 163 0.653636 GGCAATTTATTCCGACGCGA 59.346 50.000 15.93 0.00 0.00 5.87
163 164 1.263217 GGCAATTTATTCCGACGCGAT 59.737 47.619 15.93 0.00 0.00 4.58
165 166 2.298300 CAATTTATTCCGACGCGATGC 58.702 47.619 15.93 0.00 0.00 3.91
183 184 1.983119 GCCATCCCCTCCATCGAACA 61.983 60.000 0.00 0.00 0.00 3.18
224 225 3.592877 GAGGCCCTACCCTATCTACTAGT 59.407 52.174 0.00 0.00 40.58 2.57
262 263 3.785859 TCCCACCTCTGCCATCGC 61.786 66.667 0.00 0.00 0.00 4.58
335 336 3.119137 GGGCAGTTATTTCAAATCGCCTT 60.119 43.478 10.82 0.00 38.37 4.35
356 357 2.123077 CAGTTTGGGTTGGGGGCA 60.123 61.111 0.00 0.00 0.00 5.36
360 361 1.003573 TTTGGGTTGGGGGCAAAGT 59.996 52.632 0.00 0.00 0.00 2.66
423 424 1.668151 GGGGCCATCGAATACGCTC 60.668 63.158 4.39 0.00 39.58 5.03
424 425 1.069090 GGGCCATCGAATACGCTCA 59.931 57.895 4.39 0.00 39.58 4.26
432 433 4.507756 CCATCGAATACGCTCAATTTCTCA 59.492 41.667 0.00 0.00 39.58 3.27
528 530 2.249844 TTGTTGGACGTCTTCCCTTC 57.750 50.000 16.46 0.00 45.17 3.46
533 535 0.452585 GGACGTCTTCCCTTCGAGAG 59.547 60.000 16.46 0.00 38.70 3.20
535 537 1.399089 GACGTCTTCCCTTCGAGAGAG 59.601 57.143 8.70 0.00 43.69 3.20
640 642 2.017559 GCTCCAGCTCCGTAACCGAT 62.018 60.000 0.00 0.00 38.21 4.18
720 722 2.284699 CCCCGTCTCCCCTCAGTT 60.285 66.667 0.00 0.00 0.00 3.16
721 723 2.359967 CCCCGTCTCCCCTCAGTTC 61.360 68.421 0.00 0.00 0.00 3.01
722 724 1.609501 CCCGTCTCCCCTCAGTTCA 60.610 63.158 0.00 0.00 0.00 3.18
723 725 1.192146 CCCGTCTCCCCTCAGTTCAA 61.192 60.000 0.00 0.00 0.00 2.69
724 726 0.247736 CCGTCTCCCCTCAGTTCAAG 59.752 60.000 0.00 0.00 0.00 3.02
725 727 1.257743 CGTCTCCCCTCAGTTCAAGA 58.742 55.000 0.00 0.00 0.00 3.02
726 728 1.203523 CGTCTCCCCTCAGTTCAAGAG 59.796 57.143 0.00 0.00 0.00 2.85
727 729 2.530701 GTCTCCCCTCAGTTCAAGAGA 58.469 52.381 0.00 0.00 35.09 3.10
728 730 2.232696 GTCTCCCCTCAGTTCAAGAGAC 59.767 54.545 0.00 0.00 42.26 3.36
729 731 1.552792 CTCCCCTCAGTTCAAGAGACC 59.447 57.143 0.00 0.00 35.09 3.85
730 732 1.150135 TCCCCTCAGTTCAAGAGACCT 59.850 52.381 0.00 0.00 35.09 3.85
731 733 1.552792 CCCCTCAGTTCAAGAGACCTC 59.447 57.143 0.00 0.00 35.09 3.85
732 734 2.251818 CCCTCAGTTCAAGAGACCTCA 58.748 52.381 0.00 0.00 35.09 3.86
733 735 2.028567 CCCTCAGTTCAAGAGACCTCAC 60.029 54.545 0.00 0.00 35.09 3.51
734 736 2.352225 CCTCAGTTCAAGAGACCTCACG 60.352 54.545 0.00 0.00 35.09 4.35
735 737 1.000163 TCAGTTCAAGAGACCTCACGC 60.000 52.381 0.00 0.00 0.00 5.34
736 738 0.318762 AGTTCAAGAGACCTCACGCC 59.681 55.000 0.00 0.00 0.00 5.68
737 739 1.009389 GTTCAAGAGACCTCACGCCG 61.009 60.000 0.00 0.00 0.00 6.46
738 740 2.765250 TTCAAGAGACCTCACGCCGC 62.765 60.000 0.00 0.00 0.00 6.53
739 741 4.421479 AAGAGACCTCACGCCGCG 62.421 66.667 12.14 12.14 0.00 6.46
870 1013 2.571216 CCCTCGGTCGAACACACCT 61.571 63.158 0.00 0.00 0.00 4.00
899 1042 4.459089 GTGCCTCCTGCTCGTCCC 62.459 72.222 0.00 0.00 42.00 4.46
923 1066 4.530857 GTGCGTCCCCGATCCTGG 62.531 72.222 0.00 0.00 35.63 4.45
965 1108 0.842467 CAACCCCAAGACCCTCTCCT 60.842 60.000 0.00 0.00 0.00 3.69
987 1130 4.415332 GCGCGTGGTCTTCGAGGA 62.415 66.667 8.43 0.00 0.00 3.71
988 1131 2.257371 CGCGTGGTCTTCGAGGAA 59.743 61.111 0.00 0.00 0.00 3.36
1004 1147 0.533755 GGAATCGAGGTGCTGATGGG 60.534 60.000 0.00 0.00 0.00 4.00
1090 1242 1.450312 CCGCTGGACCAATCCTGTC 60.450 63.158 0.00 0.00 46.43 3.51
1160 1312 9.196552 GTTTAGTTTCTCTGCAATTTTTATGCT 57.803 29.630 0.00 0.00 44.14 3.79
1161 1313 8.746922 TTAGTTTCTCTGCAATTTTTATGCTG 57.253 30.769 0.00 0.00 44.14 4.41
1162 1314 6.752168 AGTTTCTCTGCAATTTTTATGCTGT 58.248 32.000 0.00 0.00 44.14 4.40
1163 1315 7.885297 AGTTTCTCTGCAATTTTTATGCTGTA 58.115 30.769 0.00 0.00 44.14 2.74
1244 1396 2.585330 TCTTGAAATGAACCTGCTGCA 58.415 42.857 0.88 0.88 0.00 4.41
1404 1564 1.004320 ACGCGGCATTAGGTGTTCA 60.004 52.632 12.47 0.00 0.00 3.18
1410 1570 3.625764 GCGGCATTAGGTGTTCAGAATAA 59.374 43.478 0.00 0.00 0.00 1.40
1442 1602 1.376609 GGGGTGCGTTGATGGTGATC 61.377 60.000 0.00 0.00 0.00 2.92
1537 1697 2.356432 GGGGGCTTTCTTTGGTATACGT 60.356 50.000 0.00 0.00 0.00 3.57
1709 1869 8.352942 AGGAGATTAAAAACATCAACAACTCAC 58.647 33.333 0.00 0.00 0.00 3.51
1711 1871 9.173939 GAGATTAAAAACATCAACAACTCACTG 57.826 33.333 0.00 0.00 0.00 3.66
1723 1883 0.828022 ACTCACTGGTTGACACGGAA 59.172 50.000 0.00 0.00 0.00 4.30
1729 1889 3.253188 CACTGGTTGACACGGAAATCAAT 59.747 43.478 0.00 0.00 37.19 2.57
1753 1913 1.078201 TAAGCGACAGTGCTGATGCG 61.078 55.000 6.17 7.63 46.60 4.73
1760 1920 2.124570 GTGCTGATGCGGGGACAT 60.125 61.111 0.00 0.00 43.34 3.06
1811 1971 1.376466 GCTCCTGACCTCAAAGCCA 59.624 57.895 0.00 0.00 31.97 4.75
1881 2041 7.320443 TGCTTAAAATCGCTTCAATATCACT 57.680 32.000 0.00 0.00 0.00 3.41
1968 2128 2.582052 CTGCAAAACTACTTGTCCCCA 58.418 47.619 0.00 0.00 0.00 4.96
2009 2169 2.306805 TCCTGTGCTTGTTGAGGATGAT 59.693 45.455 0.00 0.00 29.25 2.45
2017 2177 4.497674 GCTTGTTGAGGATGATGAAGATGC 60.498 45.833 0.00 0.00 0.00 3.91
2119 2280 3.520290 TTCAGTAACCCAGTGCTATCG 57.480 47.619 0.00 0.00 0.00 2.92
2265 2426 3.726190 GCTGTGCTGAAGTTAGCGAAATC 60.726 47.826 0.00 0.00 46.61 2.17
2308 2469 2.954318 CTCAAGGTATGGCAAATGGGAG 59.046 50.000 0.00 0.00 0.00 4.30
2311 2472 2.208872 AGGTATGGCAAATGGGAGAGT 58.791 47.619 0.00 0.00 0.00 3.24
2325 2486 1.068194 GGAGAGTGTCTCGTCACTTGG 60.068 57.143 10.61 0.00 46.81 3.61
2327 2488 2.490115 GAGAGTGTCTCGTCACTTGGAT 59.510 50.000 10.61 1.44 46.81 3.41
2341 2502 0.035152 TTGGATCGAATGGTGCAGCT 60.035 50.000 18.08 0.00 0.00 4.24
2353 2514 0.609131 GTGCAGCTGCTAAAGGGGAA 60.609 55.000 36.61 12.87 42.66 3.97
2361 2522 3.434167 GCTGCTAAAGGGGAAGATCATGA 60.434 47.826 0.00 0.00 0.00 3.07
2362 2523 4.387598 CTGCTAAAGGGGAAGATCATGAG 58.612 47.826 0.09 0.00 0.00 2.90
2390 2551 3.070018 AGAGCTGAAACAACAATCTCCG 58.930 45.455 0.00 0.00 0.00 4.63
2533 2694 3.679389 ACACACCTTAGCTCCTTCAATG 58.321 45.455 0.00 0.00 0.00 2.82
2821 2982 4.568152 TTGCTAGGAACTTTTTGCTGTC 57.432 40.909 0.00 0.00 41.75 3.51
2920 3081 1.988956 CCTGCTCCACTCCAGCTCT 60.989 63.158 0.00 0.00 37.79 4.09
3125 3286 4.799586 GCACCTTCAAGCAGTTCACTACTA 60.800 45.833 0.00 0.00 34.56 1.82
3126 3287 4.686554 CACCTTCAAGCAGTTCACTACTAC 59.313 45.833 0.00 0.00 34.56 2.73
3127 3288 3.921021 CCTTCAAGCAGTTCACTACTACG 59.079 47.826 0.00 0.00 34.56 3.51
3194 3467 6.091441 GTGGATTAGTGCTAGCTTATGCATAC 59.909 42.308 17.23 2.69 41.45 2.39
3263 3565 9.561069 AAATGAGTCGTTTATTATCTGGCTAAT 57.439 29.630 8.61 0.00 0.00 1.73
3378 3680 0.452184 GAGAGGCAGTCGACGAATGA 59.548 55.000 27.65 0.00 28.30 2.57
3408 3710 3.093057 TCTGAGTGATCTGTGGCTACT 57.907 47.619 0.64 0.00 0.00 2.57
3434 3736 5.129634 TCAATGAAGGTGTTAAGAAGTGCA 58.870 37.500 0.00 0.00 0.00 4.57
3444 3746 5.705905 GTGTTAAGAAGTGCAAAGGTATCCT 59.294 40.000 0.00 0.00 33.87 3.24
3675 3977 6.558909 TGCAACATATTGAAATTCGCATACA 58.441 32.000 0.00 0.00 38.15 2.29
3739 4041 2.819608 GCTCCTAGCAAATGGTTGTTCA 59.180 45.455 0.00 0.00 41.89 3.18
3889 4191 3.380637 GCCATCAAGAATCTCTGTTGCAT 59.619 43.478 0.00 0.00 0.00 3.96
3892 4194 5.105877 CCATCAAGAATCTCTGTTGCATTGT 60.106 40.000 0.00 0.00 0.00 2.71
3918 4220 1.416772 GTGGCCTATCAAGTACTCCCC 59.583 57.143 3.32 0.00 0.00 4.81
3919 4221 1.057471 GGCCTATCAAGTACTCCCCC 58.943 60.000 0.00 0.00 0.00 5.40
3991 4293 8.554490 AGGCTCTTATAAATCTTTACAGAGGA 57.446 34.615 15.77 0.00 35.69 3.71
4002 4304 6.097915 TCTTTACAGAGGAAGTACCAACAG 57.902 41.667 0.00 0.00 42.04 3.16
4095 4444 5.333798 CGGTATAAACAGTCAAGTTGGTGTG 60.334 44.000 11.21 5.76 0.00 3.82
4109 4458 4.039488 AGTTGGTGTGGATAGTACGACAAA 59.961 41.667 0.00 0.00 31.15 2.83
4112 4461 5.172934 TGGTGTGGATAGTACGACAAATTC 58.827 41.667 0.00 0.00 31.15 2.17
4116 4465 7.546667 GGTGTGGATAGTACGACAAATTCTTTA 59.453 37.037 0.00 0.00 31.15 1.85
4117 4466 8.928733 GTGTGGATAGTACGACAAATTCTTTAA 58.071 33.333 0.00 0.00 31.15 1.52
4118 4467 9.491675 TGTGGATAGTACGACAAATTCTTTAAA 57.508 29.630 0.00 0.00 0.00 1.52
4148 4499 9.440761 AAACACCCCATATATTAATTAAGCCAA 57.559 29.630 3.94 0.00 0.00 4.52
4151 4502 9.308000 CACCCCATATATTAATTAAGCCAAAGA 57.692 33.333 3.94 0.00 0.00 2.52
4152 4503 9.890915 ACCCCATATATTAATTAAGCCAAAGAA 57.109 29.630 3.94 0.00 0.00 2.52
4190 4541 5.908341 TCATTCGTTACAGCATACACCATA 58.092 37.500 0.00 0.00 0.00 2.74
4245 4596 5.358160 TCGGACCTAGTACTAAAGCTAAACC 59.642 44.000 3.76 0.00 0.00 3.27
4398 4749 5.158101 TGCAAGAAACGAATGTACGAAAA 57.842 34.783 0.00 0.00 37.03 2.29
4442 4793 7.639062 AATAGATTGATGAAGGGTGATACCT 57.361 36.000 0.00 0.00 44.56 3.08
4494 4845 3.930336 TCAGCTTCATTCACACTGGTAG 58.070 45.455 0.00 0.00 0.00 3.18
4496 4847 3.681897 CAGCTTCATTCACACTGGTAGAC 59.318 47.826 0.00 0.00 0.00 2.59
4508 4859 5.520288 CACACTGGTAGACCGATCAATAAAG 59.480 44.000 0.00 0.00 39.43 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.543687 CTTCGATGTCGCCGACCTGT 62.544 60.000 15.60 0.25 39.60 4.00
35 36 1.751349 AAGTGTAGGTGTCGCGGGTT 61.751 55.000 6.13 0.00 0.00 4.11
55 56 2.657620 GCGGTCTTCGTATCCGGC 60.658 66.667 0.00 0.00 43.77 6.13
58 59 1.022735 TCTCTGCGGTCTTCGTATCC 58.977 55.000 0.00 0.00 41.72 2.59
63 64 1.797933 CGTGTCTCTGCGGTCTTCG 60.798 63.158 0.00 0.00 42.76 3.79
107 108 1.003476 TCAGCAGCGCTCCAATCAA 60.003 52.632 7.13 0.00 36.40 2.57
162 163 1.061905 TTCGATGGAGGGGATGGCAT 61.062 55.000 0.00 0.00 0.00 4.40
163 164 1.692395 TTCGATGGAGGGGATGGCA 60.692 57.895 0.00 0.00 0.00 4.92
165 166 0.107456 CTGTTCGATGGAGGGGATGG 59.893 60.000 0.00 0.00 0.00 3.51
335 336 1.760086 CCCCAACCCAAACTGCACA 60.760 57.895 0.00 0.00 0.00 4.57
356 357 1.005394 CCCAGCGACGTACCACTTT 60.005 57.895 0.00 0.00 0.00 2.66
360 361 2.918802 AACCCCAGCGACGTACCA 60.919 61.111 0.00 0.00 0.00 3.25
528 530 2.359967 GGGTGGGGGTTCTCTCTCG 61.360 68.421 0.00 0.00 0.00 4.04
533 535 4.048470 GGCTGGGTGGGGGTTCTC 62.048 72.222 0.00 0.00 0.00 2.87
717 719 0.318762 GGCGTGAGGTCTCTTGAACT 59.681 55.000 0.00 0.00 44.09 3.01
718 720 1.009389 CGGCGTGAGGTCTCTTGAAC 61.009 60.000 0.00 0.00 0.00 3.18
719 721 1.289066 CGGCGTGAGGTCTCTTGAA 59.711 57.895 0.00 0.00 0.00 2.69
720 722 2.962569 CGGCGTGAGGTCTCTTGA 59.037 61.111 0.00 0.00 0.00 3.02
721 723 2.811317 GCGGCGTGAGGTCTCTTG 60.811 66.667 9.37 0.00 0.00 3.02
722 724 4.421479 CGCGGCGTGAGGTCTCTT 62.421 66.667 16.70 0.00 0.00 2.85
738 740 3.665675 CTTGAACCGAGGGGAGGCG 62.666 68.421 0.00 0.00 36.97 5.52
739 741 2.269241 CTTGAACCGAGGGGAGGC 59.731 66.667 0.00 0.00 36.97 4.70
740 742 2.269241 GCTTGAACCGAGGGGAGG 59.731 66.667 0.00 0.00 36.97 4.30
741 743 2.269241 GGCTTGAACCGAGGGGAG 59.731 66.667 0.00 0.00 36.97 4.30
742 744 3.327404 GGGCTTGAACCGAGGGGA 61.327 66.667 0.00 0.00 36.97 4.81
743 745 4.426313 GGGGCTTGAACCGAGGGG 62.426 72.222 0.00 0.00 40.11 4.79
744 746 3.330720 AGGGGCTTGAACCGAGGG 61.331 66.667 0.00 0.00 0.00 4.30
745 747 2.269241 GAGGGGCTTGAACCGAGG 59.731 66.667 0.00 0.00 0.00 4.63
746 748 2.125512 CGAGGGGCTTGAACCGAG 60.126 66.667 0.00 0.00 0.00 4.63
747 749 4.388499 GCGAGGGGCTTGAACCGA 62.388 66.667 0.00 0.00 39.11 4.69
853 855 1.080705 GAGGTGTGTTCGACCGAGG 60.081 63.158 0.00 0.00 38.64 4.63
861 1004 3.112709 GCTCGCCGAGGTGTGTTC 61.113 66.667 16.95 0.00 0.00 3.18
982 1125 0.387202 ATCAGCACCTCGATTCCTCG 59.613 55.000 0.00 0.00 46.41 4.63
983 1126 1.539929 CCATCAGCACCTCGATTCCTC 60.540 57.143 0.00 0.00 0.00 3.71
984 1127 0.467384 CCATCAGCACCTCGATTCCT 59.533 55.000 0.00 0.00 0.00 3.36
985 1128 0.533755 CCCATCAGCACCTCGATTCC 60.534 60.000 0.00 0.00 0.00 3.01
986 1129 1.162800 GCCCATCAGCACCTCGATTC 61.163 60.000 0.00 0.00 0.00 2.52
987 1130 1.153086 GCCCATCAGCACCTCGATT 60.153 57.895 0.00 0.00 0.00 3.34
988 1131 2.037620 GAGCCCATCAGCACCTCGAT 62.038 60.000 0.00 0.00 34.23 3.59
1004 1147 1.367659 GTGCAGATCACCTTGAGAGC 58.632 55.000 0.00 0.00 39.79 4.09
1116 1268 7.368198 ACTAAACAAGAGAAGGAAGAGAAGT 57.632 36.000 0.00 0.00 0.00 3.01
1244 1396 2.362736 CAGCAGCACAGATAATGGTGT 58.637 47.619 0.00 0.00 45.31 4.16
1404 1564 4.044191 ACCCCTTGCTAACCAACTTATTCT 59.956 41.667 0.00 0.00 0.00 2.40
1410 1570 3.745723 CACCCCTTGCTAACCAACT 57.254 52.632 0.00 0.00 0.00 3.16
1442 1602 5.389830 CGACAACAAGACAATGGTATCACAG 60.390 44.000 0.00 0.00 0.00 3.66
1669 1829 8.408043 TTTTAATCTCCTCATCAAGAAAAGCA 57.592 30.769 0.00 0.00 0.00 3.91
1709 1869 3.253188 ACATTGATTTCCGTGTCAACCAG 59.747 43.478 0.00 0.00 37.19 4.00
1711 1871 3.915437 ACATTGATTTCCGTGTCAACC 57.085 42.857 0.00 0.00 37.19 3.77
1723 1883 5.586243 AGCACTGTCGCTTATAACATTGATT 59.414 36.000 0.00 0.00 39.99 2.57
1729 1889 3.586100 TCAGCACTGTCGCTTATAACA 57.414 42.857 0.00 0.00 41.38 2.41
1753 1913 5.138758 AGGAAAGGGTAATTAATGTCCCC 57.861 43.478 18.83 14.01 40.70 4.81
1760 1920 5.451354 GGCCATGTAGGAAAGGGTAATTAA 58.549 41.667 0.00 0.00 41.22 1.40
1811 1971 8.462016 GTGTACCTTTTCTGATCTTGCAAATAT 58.538 33.333 0.00 0.00 0.00 1.28
1910 2070 6.736853 GCTGTATTGTTCACGAAATTAGACAC 59.263 38.462 0.00 0.00 0.00 3.67
1968 2128 2.500504 GAGAACTCCTTGGGTAATCCGT 59.499 50.000 0.00 0.00 38.76 4.69
2009 2169 1.260538 ACCTCTCCTGCGCATCTTCA 61.261 55.000 12.24 0.00 0.00 3.02
2017 2177 0.318441 TTCAACTCACCTCTCCTGCG 59.682 55.000 0.00 0.00 0.00 5.18
2119 2280 5.016051 TGAACTCATTCCTGCAGATAGTC 57.984 43.478 17.39 2.03 33.49 2.59
2265 2426 1.866853 GAAGGTGCCTCCGCCAAAAG 61.867 60.000 0.00 0.00 44.28 2.27
2311 2472 1.530323 TCGATCCAAGTGACGAGACA 58.470 50.000 0.00 0.00 0.00 3.41
2325 2486 1.094073 AGCAGCTGCACCATTCGATC 61.094 55.000 38.24 6.46 45.16 3.69
2327 2488 0.036483 TTAGCAGCTGCACCATTCGA 60.036 50.000 38.24 12.96 45.16 3.71
2341 2502 3.782523 ACTCATGATCTTCCCCTTTAGCA 59.217 43.478 0.00 0.00 0.00 3.49
2353 2514 5.139001 TCAGCTCTATCACACTCATGATCT 58.861 41.667 0.00 0.00 39.97 2.75
2361 2522 4.960938 TGTTGTTTCAGCTCTATCACACT 58.039 39.130 0.00 0.00 0.00 3.55
2362 2523 5.673337 TTGTTGTTTCAGCTCTATCACAC 57.327 39.130 0.00 0.00 0.00 3.82
2390 2551 5.669164 AGACTTACTCCTGTGGATTTCTC 57.331 43.478 0.00 0.00 0.00 2.87
2533 2694 3.381949 GCTCATTATACGGACAGACCAC 58.618 50.000 0.00 0.00 38.90 4.16
2821 2982 7.116948 CCACAAAATTACAGTCAGTCACTAGAG 59.883 40.741 0.00 0.00 32.21 2.43
2920 3081 3.077556 GCTGGAGCGGAGGGAAGA 61.078 66.667 0.00 0.00 0.00 2.87
3080 3241 3.807622 CGTGACAGTTTAGGCTTTCAGAA 59.192 43.478 0.00 0.00 0.00 3.02
3125 3286 7.067737 CCACCCCATATAGAAACATAAAAACGT 59.932 37.037 0.00 0.00 0.00 3.99
3126 3287 7.283580 TCCACCCCATATAGAAACATAAAAACG 59.716 37.037 0.00 0.00 0.00 3.60
3127 3288 8.528044 TCCACCCCATATAGAAACATAAAAAC 57.472 34.615 0.00 0.00 0.00 2.43
3194 3467 6.017109 AGCATTTAACCTGTGTACAACTCAAG 60.017 38.462 0.00 0.00 0.00 3.02
3263 3565 1.823797 TGCTGCAATGCATAGACACA 58.176 45.000 8.91 0.00 38.13 3.72
3405 3707 8.375506 ACTTCTTAACACCTTCATTGATGAGTA 58.624 33.333 1.30 0.00 38.19 2.59
3408 3710 6.072508 GCACTTCTTAACACCTTCATTGATGA 60.073 38.462 1.30 0.00 34.44 2.92
3434 3736 7.503902 GGCATGAATTTCTAAGAGGATACCTTT 59.496 37.037 0.00 0.00 31.76 3.11
3444 3746 5.191727 TCCCAAGGCATGAATTTCTAAGA 57.808 39.130 0.00 0.00 0.00 2.10
3675 3977 3.809832 CCGACTGAACAATGTCTTCACTT 59.190 43.478 0.00 0.00 0.00 3.16
3889 4191 3.181445 ACTTGATAGGCCACACTTGACAA 60.181 43.478 5.01 0.00 0.00 3.18
3892 4194 3.838317 AGTACTTGATAGGCCACACTTGA 59.162 43.478 5.01 0.00 0.00 3.02
3918 4220 6.436843 AATGCTCTTGTATTTCTTTACGGG 57.563 37.500 0.00 0.00 0.00 5.28
3919 4221 8.879759 TCTAAATGCTCTTGTATTTCTTTACGG 58.120 33.333 0.00 0.00 38.89 4.02
3967 4269 9.267084 CTTCCTCTGTAAAGATTTATAAGAGCC 57.733 37.037 15.67 0.00 36.27 4.70
3991 4293 9.547753 GATACATGAATATGACTGTTGGTACTT 57.452 33.333 0.00 0.00 37.73 2.24
4002 4304 6.905578 TGCATTGCAGATACATGAATATGAC 58.094 36.000 7.38 0.00 34.66 3.06
4126 4477 9.890915 TTCTTTGGCTTAATTAATATATGGGGT 57.109 29.630 0.00 0.00 0.00 4.95
4190 4541 2.871096 TTAATTCTGTTCCGCCCTGT 57.129 45.000 0.00 0.00 0.00 4.00
4245 4596 1.945394 GGTGGCACATGAGATTGCTAG 59.055 52.381 20.82 0.00 44.52 3.42
4325 4676 2.633481 TGATCTGATGGATGAGGCTCTG 59.367 50.000 16.72 0.00 34.33 3.35
4366 4717 3.888934 TCGTTTCTTGCAAATGAGAAGC 58.111 40.909 0.00 1.54 33.77 3.86
4427 4778 9.047947 GGACTTTATATAGGTATCACCCTTCAT 57.952 37.037 0.00 0.00 39.75 2.57


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

AutoCloner maintained by Alex Coulton.