Multiple sequence alignment - TraesCS4D01G205200

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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 TraesCS4D01G205200 chr4D 100.000 4976 0 0 1 4976 352755793 352750818 0.000000e+00 9190.0
1 TraesCS4D01G205200 chr4D 91.703 458 28 4 268 715 30195019 30195476 1.180000e-175 627.0
2 TraesCS4D01G205200 chr4A 95.542 2445 63 19 1847 4267 112769471 112771893 0.000000e+00 3869.0
3 TraesCS4D01G205200 chr4A 92.846 1328 63 14 7 1319 112766913 112768223 0.000000e+00 1897.0
4 TraesCS4D01G205200 chr4A 92.164 536 27 9 1320 1848 112768820 112769347 0.000000e+00 743.0
5 TraesCS4D01G205200 chr4A 92.222 450 26 3 275 715 572846014 572845565 3.270000e-176 628.0
6 TraesCS4D01G205200 chr4A 83.552 687 85 17 4292 4976 728124269 728124929 7.080000e-173 617.0
7 TraesCS4D01G205200 chr4B 93.136 2637 124 23 15 2608 436312563 436309941 0.000000e+00 3814.0
8 TraesCS4D01G205200 chr4B 94.268 1640 66 16 2643 4267 436309942 436308316 0.000000e+00 2483.0
9 TraesCS4D01G205200 chr4B 88.571 140 16 0 4837 4976 656868339 656868200 2.380000e-38 171.0
10 TraesCS4D01G205200 chr4B 80.952 84 15 1 1829 1911 41531500 41531417 1.160000e-06 65.8
11 TraesCS4D01G205200 chr3B 89.520 687 70 2 4291 4976 749283455 749282770 0.000000e+00 869.0
12 TraesCS4D01G205200 chr3B 82.899 690 105 11 4292 4976 761738054 761738735 4.260000e-170 608.0
13 TraesCS4D01G205200 chr3B 82.571 700 104 10 4292 4974 94682953 94682255 7.130000e-168 601.0
14 TraesCS4D01G205200 chr3B 82.353 85 12 3 1829 1911 637089698 637089781 2.490000e-08 71.3
15 TraesCS4D01G205200 chr3B 93.478 46 0 1 275 317 613811866 613811821 1.160000e-06 65.8
16 TraesCS4D01G205200 chr5D 85.820 677 86 3 4292 4967 424050522 424051189 0.000000e+00 710.0
17 TraesCS4D01G205200 chr7A 85.079 697 88 7 4292 4975 65493822 65493129 0.000000e+00 697.0
18 TraesCS4D01G205200 chr3A 85.000 680 98 3 4292 4967 746539371 746540050 0.000000e+00 688.0
19 TraesCS4D01G205200 chr3A 93.478 46 0 1 275 317 605241241 605241196 1.160000e-06 65.8
20 TraesCS4D01G205200 chr2A 84.840 686 71 11 4292 4976 654864844 654864191 0.000000e+00 660.0
21 TraesCS4D01G205200 chr2A 84.195 677 90 10 4292 4967 423770581 423769921 4.200000e-180 641.0
22 TraesCS4D01G205200 chr7B 83.768 690 90 10 4292 4965 703520200 703519517 7.030000e-178 634.0
23 TraesCS4D01G205200 chr1B 83.796 685 89 13 4292 4967 676250394 676251065 9.090000e-177 630.0
24 TraesCS4D01G205200 chr1B 91.429 455 27 5 273 715 344375640 344375186 9.160000e-172 614.0
25 TraesCS4D01G205200 chr1B 90.989 455 30 6 271 715 434429747 434429294 1.980000e-168 603.0
26 TraesCS4D01G205200 chr1A 91.170 453 29 6 273 715 400955573 400956024 5.510000e-169 604.0
27 TraesCS4D01G205200 chr1A 88.742 453 28 14 273 715 482767992 482768431 2.640000e-147 532.0
28 TraesCS4D01G205200 chr1A 80.488 82 15 1 1829 1909 350017099 350017180 1.500000e-05 62.1
29 TraesCS4D01G205200 chr1D 90.949 453 30 6 273 715 321710603 321710152 2.560000e-167 599.0
30 TraesCS4D01G205200 chr1D 90.110 455 33 6 273 715 271837819 271837365 9.290000e-162 580.0
31 TraesCS4D01G205200 chr1D 88.143 447 31 10 274 715 382719801 382720230 3.440000e-141 512.0
32 TraesCS4D01G205200 chr6D 83.871 93 13 2 1821 1912 330111502 330111411 2.470000e-13 87.9
33 TraesCS4D01G205200 chr6D 81.395 86 12 3 1829 1912 451854836 451854919 3.210000e-07 67.6
34 TraesCS4D01G205200 chr6D 80.899 89 12 4 1819 1906 343295636 343295720 1.160000e-06 65.8
35 TraesCS4D01G205200 chr3D 82.353 85 12 3 1829 1911 477907360 477907443 2.490000e-08 71.3
36 TraesCS4D01G205200 chr3D 93.478 46 0 1 275 317 462246628 462246583 1.160000e-06 65.8
37 TraesCS4D01G205200 chr3D 93.478 46 0 1 275 317 462455385 462455340 1.160000e-06 65.8


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 TraesCS4D01G205200 chr4D 352750818 352755793 4975 True 9190.000000 9190 100.000000 1 4976 1 chr4D.!!$R1 4975
1 TraesCS4D01G205200 chr4A 112766913 112771893 4980 False 2169.666667 3869 93.517333 7 4267 3 chr4A.!!$F2 4260
2 TraesCS4D01G205200 chr4A 728124269 728124929 660 False 617.000000 617 83.552000 4292 4976 1 chr4A.!!$F1 684
3 TraesCS4D01G205200 chr4B 436308316 436312563 4247 True 3148.500000 3814 93.702000 15 4267 2 chr4B.!!$R3 4252
4 TraesCS4D01G205200 chr3B 749282770 749283455 685 True 869.000000 869 89.520000 4291 4976 1 chr3B.!!$R3 685
5 TraesCS4D01G205200 chr3B 761738054 761738735 681 False 608.000000 608 82.899000 4292 4976 1 chr3B.!!$F2 684
6 TraesCS4D01G205200 chr3B 94682255 94682953 698 True 601.000000 601 82.571000 4292 4974 1 chr3B.!!$R1 682
7 TraesCS4D01G205200 chr5D 424050522 424051189 667 False 710.000000 710 85.820000 4292 4967 1 chr5D.!!$F1 675
8 TraesCS4D01G205200 chr7A 65493129 65493822 693 True 697.000000 697 85.079000 4292 4975 1 chr7A.!!$R1 683
9 TraesCS4D01G205200 chr3A 746539371 746540050 679 False 688.000000 688 85.000000 4292 4967 1 chr3A.!!$F1 675
10 TraesCS4D01G205200 chr2A 654864191 654864844 653 True 660.000000 660 84.840000 4292 4976 1 chr2A.!!$R2 684
11 TraesCS4D01G205200 chr2A 423769921 423770581 660 True 641.000000 641 84.195000 4292 4967 1 chr2A.!!$R1 675
12 TraesCS4D01G205200 chr7B 703519517 703520200 683 True 634.000000 634 83.768000 4292 4965 1 chr7B.!!$R1 673
13 TraesCS4D01G205200 chr1B 676250394 676251065 671 False 630.000000 630 83.796000 4292 4967 1 chr1B.!!$F1 675

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
734 735 0.119358 AGCAACTAGGGAGGGAAGGT 59.881 55.000 0.00 0.0 0.0 3.50 F
1232 1258 0.532862 AGAGTGTTGTTCGCCTGTGG 60.533 55.000 0.00 0.0 0.0 4.17 F
1738 2371 0.031994 GGGGTGCACATTGTTGACAC 59.968 55.000 20.43 0.0 34.7 3.67 F
3289 4068 1.279271 ACCGCTTTCTATTCACAGGCT 59.721 47.619 0.00 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1573 2202 2.558359 GCAACCAGTCTACTTTTGGCAT 59.442 45.455 0.00 0.0 35.35 4.40 R
2480 3249 3.898123 ACTTCAGCACAGTTTCCTCTAGA 59.102 43.478 0.00 0.0 0.00 2.43 R
3513 4293 2.324541 TGGTAATGCACAAAAAGGCCT 58.675 42.857 0.00 0.0 0.00 5.19 R
4938 5796 0.249489 ATCGGGTACGCTTGAGCATC 60.249 55.000 8.43 0.0 42.21 3.91 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
265 266 0.951040 CCCGACACCTCAAGCTCAAC 60.951 60.000 0.00 0.00 0.00 3.18
726 727 1.729586 AGTTCACCAGCAACTAGGGA 58.270 50.000 0.00 0.00 32.08 4.20
727 728 1.625818 AGTTCACCAGCAACTAGGGAG 59.374 52.381 0.00 0.00 32.08 4.30
728 729 0.984230 TTCACCAGCAACTAGGGAGG 59.016 55.000 0.00 0.00 0.00 4.30
729 730 0.909610 TCACCAGCAACTAGGGAGGG 60.910 60.000 0.00 0.00 0.00 4.30
730 731 0.909610 CACCAGCAACTAGGGAGGGA 60.910 60.000 0.00 0.00 0.00 4.20
731 732 0.178873 ACCAGCAACTAGGGAGGGAA 60.179 55.000 0.00 0.00 0.00 3.97
732 733 0.543749 CCAGCAACTAGGGAGGGAAG 59.456 60.000 0.00 0.00 0.00 3.46
734 735 0.119358 AGCAACTAGGGAGGGAAGGT 59.881 55.000 0.00 0.00 0.00 3.50
737 739 2.829023 CAACTAGGGAGGGAAGGTGTA 58.171 52.381 0.00 0.00 0.00 2.90
765 769 3.562779 TTCCGTCGCCGTGTTCTCC 62.563 63.158 0.00 0.00 0.00 3.71
774 781 1.470112 GCCGTGTTCTCCTCTAGCTTC 60.470 57.143 0.00 0.00 0.00 3.86
809 816 2.597305 GTCGTGTCCATGTGTATCGTTC 59.403 50.000 0.00 0.00 0.00 3.95
872 879 3.129287 GTGATGGACGGCTTTGATTTCAT 59.871 43.478 0.00 0.00 0.00 2.57
880 887 5.418676 ACGGCTTTGATTTCATTTAATGGG 58.581 37.500 5.02 0.00 0.00 4.00
890 900 7.454380 TGATTTCATTTAATGGGAGAGGTTGTT 59.546 33.333 5.02 0.00 0.00 2.83
1038 1060 1.741770 GATGCGTTTGGCCTCTCGT 60.742 57.895 3.32 0.00 42.61 4.18
1042 1064 1.006102 CGTTTGGCCTCTCGTCACT 60.006 57.895 3.32 0.00 0.00 3.41
1105 1127 6.149973 CAGTAAGCAATCATCCTCTGTTTTCA 59.850 38.462 0.00 0.00 0.00 2.69
1123 1145 2.354729 CCCCATTCCCGTGCTTGA 59.645 61.111 0.00 0.00 0.00 3.02
1129 1151 3.194542 CCCATTCCCGTGCTTGAATAAAA 59.805 43.478 0.00 0.00 30.31 1.52
1130 1152 4.141959 CCCATTCCCGTGCTTGAATAAAAT 60.142 41.667 0.00 0.00 30.31 1.82
1131 1153 4.805192 CCATTCCCGTGCTTGAATAAAATG 59.195 41.667 0.00 0.00 30.31 2.32
1132 1154 3.502191 TCCCGTGCTTGAATAAAATGC 57.498 42.857 0.00 0.00 0.00 3.56
1134 1156 3.509575 TCCCGTGCTTGAATAAAATGCTT 59.490 39.130 0.00 0.00 0.00 3.91
1136 1158 3.613737 CCGTGCTTGAATAAAATGCTTGG 59.386 43.478 0.00 0.00 0.00 3.61
1137 1159 4.236935 CGTGCTTGAATAAAATGCTTGGT 58.763 39.130 0.00 0.00 0.00 3.67
1138 1160 5.398169 CGTGCTTGAATAAAATGCTTGGTA 58.602 37.500 0.00 0.00 0.00 3.25
1139 1161 5.286082 CGTGCTTGAATAAAATGCTTGGTAC 59.714 40.000 0.00 0.00 0.00 3.34
1140 1162 6.389906 GTGCTTGAATAAAATGCTTGGTACT 58.610 36.000 0.00 0.00 0.00 2.73
1141 1163 6.528072 GTGCTTGAATAAAATGCTTGGTACTC 59.472 38.462 0.00 0.00 0.00 2.59
1193 1219 7.438160 GTGATTATGGTGACGATTATTGTCTGA 59.562 37.037 13.14 0.00 37.26 3.27
1194 1220 8.150296 TGATTATGGTGACGATTATTGTCTGAT 58.850 33.333 13.14 5.75 37.26 2.90
1203 1229 4.926238 CGATTATTGTCTGATACCTCTGGC 59.074 45.833 0.00 0.00 0.00 4.85
1232 1258 0.532862 AGAGTGTTGTTCGCCTGTGG 60.533 55.000 0.00 0.00 0.00 4.17
1359 1987 4.020662 GCCTGCTACTGATAGGAGCTTTAT 60.021 45.833 13.71 0.00 43.68 1.40
1410 2038 1.555075 ACACCACGGATGCTTCATACT 59.445 47.619 1.64 0.00 0.00 2.12
1411 2039 2.764010 ACACCACGGATGCTTCATACTA 59.236 45.455 1.64 0.00 0.00 1.82
1412 2040 3.123804 CACCACGGATGCTTCATACTAC 58.876 50.000 1.64 0.00 0.00 2.73
1517 2146 3.052455 TGCCGACTGATTATGTGTGTT 57.948 42.857 0.00 0.00 0.00 3.32
1538 2167 7.222417 TGTGTTGATGAAAACTAATTGTTGCTG 59.778 33.333 0.00 0.00 39.13 4.41
1544 2173 6.686630 TGAAAACTAATTGTTGCTGTATGGG 58.313 36.000 0.00 0.00 39.13 4.00
1562 2191 2.224892 TGGGCAGTACAATTTGTAGCCA 60.225 45.455 27.64 17.44 42.58 4.75
1568 2197 5.689819 CAGTACAATTTGTAGCCACAAGTC 58.310 41.667 9.49 0.00 45.17 3.01
1573 2202 2.823924 TTGTAGCCACAAGTCGCTTA 57.176 45.000 0.00 0.00 39.75 3.09
1665 2294 7.812690 TTATCATCTTGGATGAAATGTCTGG 57.187 36.000 13.15 0.00 0.00 3.86
1666 2295 5.183530 TCATCTTGGATGAAATGTCTGGT 57.816 39.130 7.64 0.00 0.00 4.00
1667 2296 4.945543 TCATCTTGGATGAAATGTCTGGTG 59.054 41.667 7.64 0.00 0.00 4.17
1738 2371 0.031994 GGGGTGCACATTGTTGACAC 59.968 55.000 20.43 0.00 34.70 3.67
1805 2438 6.646240 TGCAGTTTGCCTCTTCATTTTAATTC 59.354 34.615 0.00 0.00 44.23 2.17
1994 2754 4.110482 CTCATGCTGCCTTTTAAATCTGC 58.890 43.478 0.00 0.00 0.00 4.26
2139 2899 9.120538 GAAGGTATCTATGCCATTTTTGAACTA 57.879 33.333 0.00 0.00 34.71 2.24
2149 2909 4.024048 CCATTTTTGAACTAGTGTGACGCT 60.024 41.667 3.41 3.41 0.00 5.07
2150 2910 4.530094 TTTTTGAACTAGTGTGACGCTG 57.470 40.909 9.23 1.65 0.00 5.18
2151 2911 2.882927 TTGAACTAGTGTGACGCTGT 57.117 45.000 9.23 2.29 0.00 4.40
2152 2912 2.882927 TGAACTAGTGTGACGCTGTT 57.117 45.000 9.23 10.74 0.00 3.16
2387 3156 1.614317 GGAAGGGTATGCACACTGCTT 60.614 52.381 0.00 0.00 45.31 3.91
2480 3249 7.341256 ACTGAGAATTCATGATTGCCATTTACT 59.659 33.333 8.44 0.00 31.94 2.24
2557 3326 1.539280 GCCGCTGATACTCCTTCCTTC 60.539 57.143 0.00 0.00 0.00 3.46
2579 3348 4.163458 TCCTCAACTGAAACTACCTTGTGT 59.837 41.667 0.00 0.00 0.00 3.72
2618 3387 5.126067 AGAGTAAAGTGCACAGAAACACAT 58.874 37.500 21.04 0.00 39.30 3.21
2761 3532 1.795768 ACTGACAATGCTGGTGTACG 58.204 50.000 0.00 0.00 0.00 3.67
2862 3633 9.661563 CAATGTGTTAAGAGGTACCTACATTAA 57.338 33.333 26.76 21.79 36.20 1.40
3284 4063 6.905609 GCTACATTTTACCGCTTTCTATTCAC 59.094 38.462 0.00 0.00 0.00 3.18
3289 4068 1.279271 ACCGCTTTCTATTCACAGGCT 59.721 47.619 0.00 0.00 0.00 4.58
3441 4221 3.650139 ACTATGTGAACAGACCACGAAC 58.350 45.455 0.00 0.00 37.34 3.95
3462 4242 6.635239 CGAACGTCATAATCAAAGGTGTTTTT 59.365 34.615 0.00 0.00 0.00 1.94
3543 4325 3.411446 TGTGCATTACCAAGTCAGGAAG 58.589 45.455 0.00 0.00 0.00 3.46
3547 4329 2.561478 TTACCAAGTCAGGAAGTGCC 57.439 50.000 0.00 0.00 0.00 5.01
3768 4553 7.288810 ACTATTTGGATTTGAGCAGTGAAAA 57.711 32.000 0.00 0.00 0.00 2.29
3887 4672 2.480419 CACCGTCTGCTTGGACTTTAAG 59.520 50.000 0.00 0.00 34.38 1.85
4067 4855 6.760298 CACTTCTCTCTTTGCATCTTGCTATA 59.240 38.462 0.75 0.00 45.31 1.31
4100 4888 2.610479 CGAATAGTGACGGCATGCCTAT 60.610 50.000 33.07 21.79 0.00 2.57
4252 5043 1.820519 ACGCCGGAGTAATGTGAACTA 59.179 47.619 9.91 0.00 0.00 2.24
4262 5053 7.538575 GGAGTAATGTGAACTAAAGTACGGTA 58.461 38.462 0.00 0.00 0.00 4.02
4263 5054 8.193438 GGAGTAATGTGAACTAAAGTACGGTAT 58.807 37.037 0.00 0.00 0.00 2.73
4268 5059 8.922058 ATGTGAACTAAAGTACGGTATTACTG 57.078 34.615 0.94 0.94 32.39 2.74
4269 5060 7.885297 TGTGAACTAAAGTACGGTATTACTGT 58.115 34.615 12.72 12.72 41.33 3.55
4270 5061 8.359642 TGTGAACTAAAGTACGGTATTACTGTT 58.640 33.333 13.31 0.00 38.84 3.16
4271 5062 9.840427 GTGAACTAAAGTACGGTATTACTGTTA 57.160 33.333 13.31 0.09 38.84 2.41
4279 5070 9.573133 AAGTACGGTATTACTGTTAACATGTAC 57.427 33.333 13.31 9.38 38.84 2.90
4280 5071 8.190784 AGTACGGTATTACTGTTAACATGTACC 58.809 37.037 13.31 15.82 38.84 3.34
4281 5072 7.174107 ACGGTATTACTGTTAACATGTACCT 57.826 36.000 22.62 14.33 32.95 3.08
4282 5073 7.037438 ACGGTATTACTGTTAACATGTACCTG 58.963 38.462 22.62 19.61 32.95 4.00
4283 5074 7.037438 CGGTATTACTGTTAACATGTACCTGT 58.963 38.462 22.62 14.19 0.00 4.00
4284 5075 8.190122 CGGTATTACTGTTAACATGTACCTGTA 58.810 37.037 22.62 13.48 0.00 2.74
4285 5076 9.305925 GGTATTACTGTTAACATGTACCTGTAC 57.694 37.037 20.38 16.25 36.63 2.90
4377 5168 2.437359 ATGAAGCTGCTCACCGCC 60.437 61.111 1.00 0.00 38.05 6.13
4557 5351 2.933878 AAACCTCGCTCAACGCACCA 62.934 55.000 0.00 0.00 43.23 4.17
4601 5395 3.399181 GTCCATGGGCTCGGTGGA 61.399 66.667 9.76 6.43 39.61 4.02
4681 5484 2.721167 CGGATCGGCTTCAGGACCA 61.721 63.158 0.00 0.00 0.00 4.02
4745 5560 4.760047 AGTGGTGATCGCGGTGGC 62.760 66.667 6.13 0.00 0.00 5.01
4946 5804 1.612146 TCCGGGACCTGATGCTCAA 60.612 57.895 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.055470 TATGGCTTCCCAAGGGGCG 62.055 63.158 5.08 0.00 46.14 6.13
1 2 1.455773 GTATGGCTTCCCAAGGGGC 60.456 63.158 5.08 1.34 46.14 5.80
2 3 1.152963 CGTATGGCTTCCCAAGGGG 60.153 63.158 5.08 0.00 46.14 4.79
3 4 0.179045 CTCGTATGGCTTCCCAAGGG 60.179 60.000 0.00 0.00 46.14 3.95
4 5 0.815615 GCTCGTATGGCTTCCCAAGG 60.816 60.000 0.00 0.00 46.14 3.61
5 6 0.815615 GGCTCGTATGGCTTCCCAAG 60.816 60.000 0.00 0.00 46.14 3.61
8 9 1.227674 CAGGCTCGTATGGCTTCCC 60.228 63.158 0.00 0.00 41.04 3.97
426 427 2.158645 GCTCTTCTTGTTCTTCTTCCGC 59.841 50.000 0.00 0.00 0.00 5.54
726 727 2.866454 ACCCTAGAGATACACCTTCCCT 59.134 50.000 0.00 0.00 0.00 4.20
727 728 3.331718 ACCCTAGAGATACACCTTCCC 57.668 52.381 0.00 0.00 0.00 3.97
728 729 3.642377 GGAACCCTAGAGATACACCTTCC 59.358 52.174 0.00 0.00 0.00 3.46
729 730 3.318557 CGGAACCCTAGAGATACACCTTC 59.681 52.174 0.00 0.00 0.00 3.46
730 731 3.297736 CGGAACCCTAGAGATACACCTT 58.702 50.000 0.00 0.00 0.00 3.50
731 732 2.244252 ACGGAACCCTAGAGATACACCT 59.756 50.000 0.00 0.00 0.00 4.00
732 733 2.622470 GACGGAACCCTAGAGATACACC 59.378 54.545 0.00 0.00 0.00 4.16
734 735 2.569059 CGACGGAACCCTAGAGATACA 58.431 52.381 0.00 0.00 0.00 2.29
737 739 1.108132 GGCGACGGAACCCTAGAGAT 61.108 60.000 0.00 0.00 0.00 2.75
765 769 1.337260 ACGGCAACACAGAAGCTAGAG 60.337 52.381 0.00 0.00 0.00 2.43
774 781 3.403057 CGACCGACGGCAACACAG 61.403 66.667 15.39 0.00 38.46 3.66
809 816 1.897615 AGGCGCGCTACCTACCTAG 60.898 63.158 32.29 0.00 35.10 3.02
872 879 5.300792 GTCACAAACAACCTCTCCCATTAAA 59.699 40.000 0.00 0.00 0.00 1.52
880 887 4.442706 TGAGAAGTCACAAACAACCTCTC 58.557 43.478 0.00 0.00 0.00 3.20
890 900 4.020751 AGCTAGCAGATTGAGAAGTCACAA 60.021 41.667 18.83 0.00 30.10 3.33
992 1005 1.061411 CGCAACATCATCGGCAGTG 59.939 57.895 0.00 0.00 0.00 3.66
993 1006 1.079197 TCGCAACATCATCGGCAGT 60.079 52.632 0.00 0.00 0.00 4.40
1105 1127 2.035626 CAAGCACGGGAATGGGGT 59.964 61.111 0.00 0.00 0.00 4.95
1123 1145 8.686334 CATACAAGGAGTACCAAGCATTTTATT 58.314 33.333 0.00 0.00 38.94 1.40
1129 1151 3.545703 GCATACAAGGAGTACCAAGCAT 58.454 45.455 0.00 0.00 38.94 3.79
1130 1152 2.676750 CGCATACAAGGAGTACCAAGCA 60.677 50.000 0.00 0.00 38.94 3.91
1131 1153 1.933853 CGCATACAAGGAGTACCAAGC 59.066 52.381 0.00 0.00 38.94 4.01
1132 1154 3.520290 TCGCATACAAGGAGTACCAAG 57.480 47.619 0.00 0.00 38.94 3.61
1134 1156 3.028130 TCATCGCATACAAGGAGTACCA 58.972 45.455 0.00 0.00 38.94 3.25
1136 1158 5.050091 CCAATTCATCGCATACAAGGAGTAC 60.050 44.000 0.00 0.00 35.05 2.73
1137 1159 5.056480 CCAATTCATCGCATACAAGGAGTA 58.944 41.667 0.00 0.00 37.06 2.59
1138 1160 3.879295 CCAATTCATCGCATACAAGGAGT 59.121 43.478 0.00 0.00 0.00 3.85
1139 1161 3.879295 ACCAATTCATCGCATACAAGGAG 59.121 43.478 0.00 0.00 0.00 3.69
1140 1162 3.627123 CACCAATTCATCGCATACAAGGA 59.373 43.478 0.00 0.00 0.00 3.36
1141 1163 3.793129 GCACCAATTCATCGCATACAAGG 60.793 47.826 0.00 0.00 0.00 3.61
1193 1219 0.678395 CGAGCATGAGCCAGAGGTAT 59.322 55.000 0.00 0.00 43.56 2.73
1194 1220 0.395724 TCGAGCATGAGCCAGAGGTA 60.396 55.000 0.00 0.00 43.56 3.08
1203 1229 2.360553 ACAACACTCTCGAGCATGAG 57.639 50.000 19.04 9.76 37.33 2.90
1232 1258 1.202405 CCACACCCAAACAACTTCAGC 60.202 52.381 0.00 0.00 0.00 4.26
1359 1987 8.547481 TGTAACTGTCCAGAGGAATCATATTA 57.453 34.615 0.40 0.00 31.38 0.98
1372 2000 3.684788 GGTGTTGCTATGTAACTGTCCAG 59.315 47.826 0.00 0.00 0.00 3.86
1410 2038 7.333423 CCGTGATAAAGTTCTCAAAAGATGGTA 59.667 37.037 0.00 0.00 0.00 3.25
1411 2039 6.149474 CCGTGATAAAGTTCTCAAAAGATGGT 59.851 38.462 0.00 0.00 0.00 3.55
1412 2040 6.403636 CCCGTGATAAAGTTCTCAAAAGATGG 60.404 42.308 0.00 0.00 0.00 3.51
1517 2146 8.028354 CCATACAGCAACAATTAGTTTTCATCA 58.972 33.333 0.00 0.00 38.74 3.07
1538 2167 4.036380 GGCTACAAATTGTACTGCCCATAC 59.964 45.833 19.71 1.68 37.89 2.39
1544 2173 4.023193 ACTTGTGGCTACAAATTGTACTGC 60.023 41.667 16.89 5.38 45.53 4.40
1562 2191 2.884639 ACTTTTGGCATAAGCGACTTGT 59.115 40.909 16.21 0.00 43.41 3.16
1568 2197 3.063997 CCAGTCTACTTTTGGCATAAGCG 59.936 47.826 16.21 8.87 43.41 4.68
1573 2202 2.558359 GCAACCAGTCTACTTTTGGCAT 59.442 45.455 0.00 0.00 35.35 4.40
1634 2263 5.114764 TCATCCAAGATGATAAAGTGCCA 57.885 39.130 3.17 0.00 0.00 4.92
1665 2294 9.736023 AACTAGAGATGAAAACAAATTGTTCAC 57.264 29.630 12.11 9.53 40.14 3.18
1738 2371 3.057104 TGTGTATGTGTACTTCAGGTCCG 60.057 47.826 0.00 0.00 0.00 4.79
1805 2438 7.306213 AGTCGAACATATATGGTGATCTTACG 58.694 38.462 16.96 8.32 0.00 3.18
2029 2789 8.772250 TGATAACCCTGACAAAAGAATCTAGAT 58.228 33.333 0.00 0.00 0.00 1.98
2149 2909 4.944619 TTACAATTCCATGTGGCAAACA 57.055 36.364 0.00 0.00 44.79 2.83
2150 2910 6.165577 AGATTTACAATTCCATGTGGCAAAC 58.834 36.000 0.00 0.00 34.75 2.93
2151 2911 6.357579 AGATTTACAATTCCATGTGGCAAA 57.642 33.333 0.00 0.00 34.75 3.68
2152 2912 5.999205 AGATTTACAATTCCATGTGGCAA 57.001 34.783 0.00 0.00 34.75 4.52
2387 3156 6.096164 AGGTTACACCCAAGATAGTAGGTA 57.904 41.667 0.00 0.00 39.75 3.08
2480 3249 3.898123 ACTTCAGCACAGTTTCCTCTAGA 59.102 43.478 0.00 0.00 0.00 2.43
2557 3326 4.451900 ACACAAGGTAGTTTCAGTTGAGG 58.548 43.478 0.00 0.00 0.00 3.86
2618 3387 8.096621 TGTGGTTTATCACATTATCCCTAAGA 57.903 34.615 0.00 0.00 42.05 2.10
2694 3463 9.807921 ATGAGAGATTAGGGTTTTTCTTTTACA 57.192 29.630 0.00 0.00 0.00 2.41
2697 3466 8.712228 ACATGAGAGATTAGGGTTTTTCTTTT 57.288 30.769 0.00 0.00 0.00 2.27
2701 3470 9.232473 ACTAAACATGAGAGATTAGGGTTTTTC 57.768 33.333 0.00 0.00 31.25 2.29
3284 4063 4.997395 TGCAGTTCTTAGTTTAAGAGCCTG 59.003 41.667 15.78 15.78 44.16 4.85
3289 4068 9.772973 TTGTCTAATGCAGTTCTTAGTTTAAGA 57.227 29.630 0.00 0.00 42.68 2.10
3462 4242 6.488006 AGAAACCAGTCTACGACACTAGTTAA 59.512 38.462 0.00 0.00 34.60 2.01
3463 4243 6.000219 AGAAACCAGTCTACGACACTAGTTA 59.000 40.000 0.00 0.00 34.60 2.24
3464 4244 4.826183 AGAAACCAGTCTACGACACTAGTT 59.174 41.667 0.00 0.00 34.60 2.24
3465 4245 4.396522 AGAAACCAGTCTACGACACTAGT 58.603 43.478 0.00 0.00 34.60 2.57
3466 4246 5.867166 GTAGAAACCAGTCTACGACACTAG 58.133 45.833 0.00 0.00 40.37 2.57
3513 4293 2.324541 TGGTAATGCACAAAAAGGCCT 58.675 42.857 0.00 0.00 0.00 5.19
3514 4294 2.829741 TGGTAATGCACAAAAAGGCC 57.170 45.000 0.00 0.00 0.00 5.19
3515 4295 3.727726 ACTTGGTAATGCACAAAAAGGC 58.272 40.909 0.00 0.00 0.00 4.35
3516 4296 4.942852 TGACTTGGTAATGCACAAAAAGG 58.057 39.130 0.00 0.00 0.00 3.11
3517 4297 4.984161 CCTGACTTGGTAATGCACAAAAAG 59.016 41.667 0.00 0.00 0.00 2.27
3518 4298 4.646945 TCCTGACTTGGTAATGCACAAAAA 59.353 37.500 0.00 0.00 0.00 1.94
3543 4325 6.002062 AGATAAATAGCTAATTTGCGGCAC 57.998 37.500 0.05 0.00 38.29 5.01
3547 4329 8.987599 TCGAAAAGATAAATAGCTAATTTGCG 57.012 30.769 6.23 3.65 38.29 4.85
3592 4375 9.928236 GACTATTCTGATGCTATTTCAAGAAAC 57.072 33.333 0.00 0.00 32.51 2.78
3887 4672 8.942338 AAAAGGGACAAAATCAGTTAAGAAAC 57.058 30.769 0.00 0.00 35.72 2.78
4067 4855 4.566987 GTCACTATTCGGTCCTGTTCTTT 58.433 43.478 0.00 0.00 0.00 2.52
4100 4888 4.641541 CAGATGGCTGTTTGGATAACATGA 59.358 41.667 0.00 0.00 37.37 3.07
4273 5064 7.095481 GAGCATCATACAATGTACAGGTACATG 60.095 40.741 21.94 17.75 44.50 3.21
4274 5065 6.931281 GAGCATCATACAATGTACAGGTACAT 59.069 38.462 17.10 17.10 45.90 2.29
4275 5066 6.127196 TGAGCATCATACAATGTACAGGTACA 60.127 38.462 14.06 14.06 44.99 2.90
4276 5067 6.280643 TGAGCATCATACAATGTACAGGTAC 58.719 40.000 11.17 2.66 42.56 3.34
4277 5068 6.478512 TGAGCATCATACAATGTACAGGTA 57.521 37.500 11.30 11.30 42.56 3.08
4278 5069 5.357742 TGAGCATCATACAATGTACAGGT 57.642 39.130 0.33 4.94 42.56 4.00
4425 5216 1.296715 GATGCCGTGGAGGAACTGT 59.703 57.895 0.00 0.00 41.55 3.55
4672 5466 0.396435 ATCGTTGCTGTGGTCCTGAA 59.604 50.000 0.00 0.00 0.00 3.02
4681 5484 2.742372 GGGCACGATCGTTGCTGT 60.742 61.111 28.70 5.42 0.00 4.40
4745 5560 2.584418 CGCCTGCATCCTCAGTCG 60.584 66.667 0.00 0.00 32.32 4.18
4835 5693 1.141053 GGAGCGAAGAACCCCATGTAT 59.859 52.381 0.00 0.00 0.00 2.29
4901 5759 4.250305 AGGACACCAGCGGCGTTT 62.250 61.111 9.37 0.00 0.00 3.60
4938 5796 0.249489 ATCGGGTACGCTTGAGCATC 60.249 55.000 8.43 0.00 42.21 3.91
4946 5804 1.035932 AGTACTGCATCGGGTACGCT 61.036 55.000 8.43 0.00 41.94 5.07


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

AutoCloner maintained by Alex Coulton.