Multiple sequence alignment - TraesCS6D01G113700

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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 TraesCS6D01G113700 chr6D 100.000 3436 0 0 1 3436 81151622 81148187 0.000000e+00 6346
1 TraesCS6D01G113700 chr6D 94.756 1125 12 5 2279 3356 400785765 400786889 0.000000e+00 1707
2 TraesCS6D01G113700 chr6D 100.000 404 0 0 3686 4089 81147937 81147534 0.000000e+00 747
3 TraesCS6D01G113700 chr6D 94.819 386 9 1 3686 4071 469312414 469312788 3.520000e-165 592
4 TraesCS6D01G113700 chr6D 77.288 295 51 12 18 302 81110994 81110706 4.230000e-35 159
5 TraesCS6D01G113700 chr7D 97.098 2378 36 9 1081 3436 370966230 370963864 0.000000e+00 3978
6 TraesCS6D01G113700 chr7D 99.010 404 4 0 3686 4089 370961968 370961565 0.000000e+00 725
7 TraesCS6D01G113700 chr7D 95.596 386 6 1 3686 4071 510432715 510432341 3.490000e-170 608
8 TraesCS6D01G113700 chr2D 96.175 2379 27 9 1081 3436 459830858 459833195 0.000000e+00 3831
9 TraesCS6D01G113700 chr2D 95.537 1994 40 12 1081 3049 155549162 155547193 0.000000e+00 3144
10 TraesCS6D01G113700 chr2D 91.088 2390 104 47 1081 3403 632025041 632022694 0.000000e+00 3133
11 TraesCS6D01G113700 chr2D 97.593 1205 20 3 1081 2284 114802129 114803325 0.000000e+00 2056
12 TraesCS6D01G113700 chr2D 97.927 386 8 0 3686 4071 114804681 114805066 0.000000e+00 669
13 TraesCS6D01G113700 chr2D 98.387 372 6 0 3686 4057 459833076 459833447 0.000000e+00 654
14 TraesCS6D01G113700 chr2D 100.000 95 0 0 3979 4073 459833421 459833515 4.200000e-40 176
15 TraesCS6D01G113700 chr3D 94.869 2397 63 22 1081 3434 114397630 114395251 0.000000e+00 3690
16 TraesCS6D01G113700 chr3D 95.676 2336 30 9 1081 3385 595953694 595951399 0.000000e+00 3688
17 TraesCS6D01G113700 chr3D 98.515 404 6 0 3686 4089 114394676 114394273 0.000000e+00 713
18 TraesCS6D01G113700 chr3D 97.816 412 9 0 3023 3434 114395613 114395202 0.000000e+00 712
19 TraesCS6D01G113700 chr3D 97.698 391 9 0 3686 4076 595950994 595950604 0.000000e+00 673
20 TraesCS6D01G113700 chr3D 94.000 400 10 11 3686 4071 406150478 406150079 9.790000e-166 593
21 TraesCS6D01G113700 chr3D 93.000 400 14 10 3686 4071 66255500 66255899 4.590000e-159 571
22 TraesCS6D01G113700 chr4D 95.149 2309 43 10 1081 3352 414636101 414633825 0.000000e+00 3579
23 TraesCS6D01G113700 chr4D 96.853 1271 18 4 2188 3436 469103037 469104307 0.000000e+00 2106
24 TraesCS6D01G113700 chr1A 93.367 2382 75 17 1080 3436 1315708 1318031 0.000000e+00 3446
25 TraesCS6D01G113700 chr7A 92.450 2371 108 30 1081 3436 100756027 100753713 0.000000e+00 3321
26 TraesCS6D01G113700 chr7A 94.871 2125 65 7 1349 3436 652923887 652926004 0.000000e+00 3280
27 TraesCS6D01G113700 chr5D 98.008 1205 16 2 1081 2284 58672898 58671701 0.000000e+00 2085
28 TraesCS6D01G113700 chr5D 95.058 1214 26 5 2257 3436 384157595 384158808 0.000000e+00 1879
29 TraesCS6D01G113700 chr5D 97.927 386 7 1 3686 4071 58670514 58670130 0.000000e+00 667
30 TraesCS6D01G113700 chr5D 81.786 571 61 20 2782 3317 51563579 51564141 4.850000e-119 438
31 TraesCS6D01G113700 chr5D 97.814 183 4 0 3252 3434 384159476 384159658 2.370000e-82 316
32 TraesCS6D01G113700 chr1D 95.305 1214 23 5 2257 3436 276512390 276511177 0.000000e+00 1895
33 TraesCS6D01G113700 chr1D 91.694 614 17 6 2840 3419 414457592 414456979 0.000000e+00 821
34 TraesCS6D01G113700 chr6A 93.013 1188 31 11 1967 3120 555216336 555215167 0.000000e+00 1687
35 TraesCS6D01G113700 chr6A 91.769 1057 85 2 13 1068 97723451 97722396 0.000000e+00 1469
36 TraesCS6D01G113700 chr6A 79.602 201 25 8 624 821 97628938 97628751 3.320000e-26 130


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 TraesCS6D01G113700 chr6D 81147534 81151622 4088 True 3546.500000 6346 100.000000 1 4089 2 chr6D.!!$R2 4088
1 TraesCS6D01G113700 chr6D 400785765 400786889 1124 False 1707.000000 1707 94.756000 2279 3356 1 chr6D.!!$F1 1077
2 TraesCS6D01G113700 chr7D 370961565 370966230 4665 True 2351.500000 3978 98.054000 1081 4089 2 chr7D.!!$R2 3008
3 TraesCS6D01G113700 chr2D 155547193 155549162 1969 True 3144.000000 3144 95.537000 1081 3049 1 chr2D.!!$R1 1968
4 TraesCS6D01G113700 chr2D 632022694 632025041 2347 True 3133.000000 3133 91.088000 1081 3403 1 chr2D.!!$R2 2322
5 TraesCS6D01G113700 chr2D 459830858 459833515 2657 False 1553.666667 3831 98.187333 1081 4073 3 chr2D.!!$F2 2992
6 TraesCS6D01G113700 chr2D 114802129 114805066 2937 False 1362.500000 2056 97.760000 1081 4071 2 chr2D.!!$F1 2990
7 TraesCS6D01G113700 chr3D 595950604 595953694 3090 True 2180.500000 3688 96.687000 1081 4076 2 chr3D.!!$R3 2995
8 TraesCS6D01G113700 chr3D 114394273 114397630 3357 True 1705.000000 3690 97.066667 1081 4089 3 chr3D.!!$R2 3008
9 TraesCS6D01G113700 chr4D 414633825 414636101 2276 True 3579.000000 3579 95.149000 1081 3352 1 chr4D.!!$R1 2271
10 TraesCS6D01G113700 chr4D 469103037 469104307 1270 False 2106.000000 2106 96.853000 2188 3436 1 chr4D.!!$F1 1248
11 TraesCS6D01G113700 chr1A 1315708 1318031 2323 False 3446.000000 3446 93.367000 1080 3436 1 chr1A.!!$F1 2356
12 TraesCS6D01G113700 chr7A 100753713 100756027 2314 True 3321.000000 3321 92.450000 1081 3436 1 chr7A.!!$R1 2355
13 TraesCS6D01G113700 chr7A 652923887 652926004 2117 False 3280.000000 3280 94.871000 1349 3436 1 chr7A.!!$F1 2087
14 TraesCS6D01G113700 chr5D 58670130 58672898 2768 True 1376.000000 2085 97.967500 1081 4071 2 chr5D.!!$R1 2990
15 TraesCS6D01G113700 chr5D 384157595 384159658 2063 False 1097.500000 1879 96.436000 2257 3436 2 chr5D.!!$F2 1179
16 TraesCS6D01G113700 chr5D 51563579 51564141 562 False 438.000000 438 81.786000 2782 3317 1 chr5D.!!$F1 535
17 TraesCS6D01G113700 chr1D 276511177 276512390 1213 True 1895.000000 1895 95.305000 2257 3436 1 chr1D.!!$R1 1179
18 TraesCS6D01G113700 chr1D 414456979 414457592 613 True 821.000000 821 91.694000 2840 3419 1 chr1D.!!$R2 579
19 TraesCS6D01G113700 chr6A 555215167 555216336 1169 True 1687.000000 1687 93.013000 1967 3120 1 chr6A.!!$R3 1153
20 TraesCS6D01G113700 chr6A 97722396 97723451 1055 True 1469.000000 1469 91.769000 13 1068 1 chr6A.!!$R2 1055

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
613 615 0.180406 ATGCATTACCCACCTCGTCC 59.820 55.0 0.00 0.0 0.0 4.79 F
997 999 0.525668 AATCGATCGACACGCTCACC 60.526 55.0 22.06 0.0 0.0 4.02 F
1404 1426 0.679640 CTCTCTCTGGCTCTGGTCGT 60.680 60.0 0.00 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2561 2805 2.310538 CTTGGGAATATTGTCCTGGGC 58.689 52.381 0.00 0.0 37.85 5.36 R
2948 3214 3.891366 ACTTCAAATACTGCAAACTGCCT 59.109 39.130 0.00 0.0 44.23 4.75 R
3199 3678 4.156455 AGGGTGCCATAGTTAACATCAG 57.844 45.455 8.61 0.0 0.00 2.90 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
43 45 7.972832 TTGTATGAGTCGGTGAAACTAAATT 57.027 32.000 0.00 0.00 36.74 1.82
91 93 8.136057 AGTAGAATAACAAATGCAGAGAATCG 57.864 34.615 0.00 0.00 42.67 3.34
95 97 8.180267 AGAATAACAAATGCAGAGAATCGAAAG 58.820 33.333 0.00 0.00 42.67 2.62
130 132 9.686683 AAAATTAGAGTGTTACATATCAGGCTT 57.313 29.630 0.00 0.00 0.00 4.35
148 150 8.815565 TCAGGCTTATAGAGAGGTGATATAAG 57.184 38.462 6.78 6.78 40.26 1.73
161 163 4.452455 GGTGATATAAGCTGCGCAATAAGT 59.548 41.667 13.05 0.00 0.00 2.24
164 166 7.394872 GTGATATAAGCTGCGCAATAAGTATC 58.605 38.462 13.05 16.25 0.00 2.24
171 173 1.539496 GCGCAATAAGTATCGACCCCA 60.539 52.381 0.30 0.00 0.00 4.96
196 198 0.324368 ATGGCCAGTACACGAGAGGA 60.324 55.000 13.05 0.00 0.00 3.71
217 219 4.412207 GACTCACAATTATTTTGGCCGAC 58.588 43.478 0.00 0.00 0.00 4.79
304 306 3.378427 GGCATTAGGAATGACACTTCCAC 59.622 47.826 14.96 3.93 46.47 4.02
311 313 4.020573 AGGAATGACACTTCCACGAATGTA 60.021 41.667 14.96 0.00 46.02 2.29
320 322 3.819564 TCCACGAATGTATCTCCCAAG 57.180 47.619 0.00 0.00 0.00 3.61
325 327 3.117888 ACGAATGTATCTCCCAAGGCATT 60.118 43.478 0.00 0.00 0.00 3.56
337 339 3.160777 CAAGGCATTTGGATTGCTCTC 57.839 47.619 0.00 0.00 40.03 3.20
352 354 5.465532 TTGCTCTCTTATAGATGCTCTGG 57.534 43.478 0.00 0.00 32.41 3.86
372 374 2.159142 GGAGCCTCTGCATCCAATTTTG 60.159 50.000 0.00 0.00 41.13 2.44
373 375 1.206371 AGCCTCTGCATCCAATTTTGC 59.794 47.619 0.00 0.00 41.13 3.68
375 377 1.134610 CCTCTGCATCCAATTTTGCCC 60.135 52.381 0.00 0.00 38.08 5.36
396 398 2.289694 CCTACAACTCACCTTGGGTCAG 60.290 54.545 0.00 0.00 31.02 3.51
404 406 0.763223 ACCTTGGGTCAGAACTCGGT 60.763 55.000 0.00 0.00 0.00 4.69
413 415 2.231478 GTCAGAACTCGGTCAGGAATCA 59.769 50.000 0.00 0.00 0.00 2.57
427 429 4.931601 TCAGGAATCAAACACATCGAAGAG 59.068 41.667 0.00 0.00 43.63 2.85
452 454 8.773216 AGAAGAATCTATAAACCAAGGCTTACT 58.227 33.333 0.00 0.00 32.88 2.24
456 458 5.671493 TCTATAAACCAAGGCTTACTGCTC 58.329 41.667 0.00 0.00 42.39 4.26
463 465 3.341823 CAAGGCTTACTGCTCATCTTGT 58.658 45.455 0.00 0.00 42.39 3.16
468 470 4.382040 GGCTTACTGCTCATCTTGTACAGA 60.382 45.833 0.00 0.00 42.39 3.41
494 496 0.686224 TTTTCCTTTGCCCATGCTGG 59.314 50.000 0.00 0.00 38.71 4.85
516 518 1.740718 GCAGTTCACCCCGATTCTCTC 60.741 57.143 0.00 0.00 0.00 3.20
610 612 1.676006 GGAAATGCATTACCCACCTCG 59.324 52.381 13.39 0.00 0.00 4.63
613 615 0.180406 ATGCATTACCCACCTCGTCC 59.820 55.000 0.00 0.00 0.00 4.79
634 636 6.253727 CGTCCTGTATCACTGTCTGTAATTTC 59.746 42.308 0.00 0.00 0.00 2.17
645 647 7.441157 CACTGTCTGTAATTTCAGTGTAGGAAA 59.559 37.037 11.33 0.00 46.92 3.13
646 648 8.157476 ACTGTCTGTAATTTCAGTGTAGGAAAT 58.843 33.333 11.33 0.00 44.52 2.17
649 651 7.606456 GTCTGTAATTTCAGTGTAGGAAATGGA 59.394 37.037 11.33 0.00 42.48 3.41
663 665 3.244181 GGAAATGGATGTGTTTGTGGCTT 60.244 43.478 0.00 0.00 0.00 4.35
708 710 9.144085 CGAATTATCTGCGACTTAAACAAATAC 57.856 33.333 0.00 0.00 0.00 1.89
716 718 4.495184 CGACTTAAACAAATACGATGGCCC 60.495 45.833 0.00 0.00 0.00 5.80
791 793 3.305539 CCCATTGTGTGCACATATATGCC 60.306 47.826 24.69 8.68 45.50 4.40
794 796 3.280197 TGTGTGCACATATATGCCAGT 57.720 42.857 24.69 0.00 45.50 4.00
795 797 2.944349 TGTGTGCACATATATGCCAGTG 59.056 45.455 24.69 4.80 45.50 3.66
797 799 4.126437 GTGTGCACATATATGCCAGTGTA 58.874 43.478 24.69 0.50 45.50 2.90
802 804 6.595326 GTGCACATATATGCCAGTGTACATAT 59.405 38.462 13.17 16.05 45.50 1.78
857 859 2.640316 ACCACAGAGACCTTTTGACC 57.360 50.000 0.00 0.00 0.00 4.02
929 931 1.448540 GATGCCACACACTCCTCCG 60.449 63.158 0.00 0.00 0.00 4.63
936 938 2.039624 ACACTCCTCCGGCATCCT 59.960 61.111 0.00 0.00 0.00 3.24
990 992 2.186076 GTGTCTCCAATCGATCGACAC 58.814 52.381 22.06 22.64 44.91 3.67
996 998 0.567968 CAATCGATCGACACGCTCAC 59.432 55.000 22.06 0.00 0.00 3.51
997 999 0.525668 AATCGATCGACACGCTCACC 60.526 55.000 22.06 0.00 0.00 4.02
1000 1002 4.129737 ATCGACACGCTCACCCCG 62.130 66.667 0.00 0.00 0.00 5.73
1004 1006 4.657824 ACACGCTCACCCCGAACG 62.658 66.667 0.00 0.00 39.16 3.95
1010 1012 3.296709 CTCACCCCGAACGACCTGG 62.297 68.421 0.00 0.00 0.00 4.45
1062 1064 1.807165 CGATCCATCCATAGCCGCG 60.807 63.158 0.00 0.00 0.00 6.46
1124 1126 2.065899 TTTGTGGCTAGGTTTGCAGT 57.934 45.000 0.00 0.00 0.00 4.40
1404 1426 0.679640 CTCTCTCTGGCTCTGGTCGT 60.680 60.000 0.00 0.00 0.00 4.34
1883 1945 6.127786 TGTTCATTGTTCATGTTCACTGTTCA 60.128 34.615 0.00 1.10 34.06 3.18
1884 1946 6.638096 TCATTGTTCATGTTCACTGTTCAT 57.362 33.333 0.00 0.00 34.06 2.57
1885 1947 7.041635 TCATTGTTCATGTTCACTGTTCATT 57.958 32.000 0.00 0.00 34.06 2.57
1886 1948 6.919115 TCATTGTTCATGTTCACTGTTCATTG 59.081 34.615 0.00 0.00 34.06 2.82
1887 1949 5.833406 TGTTCATGTTCACTGTTCATTGT 57.167 34.783 0.00 0.00 0.00 2.71
1888 1950 6.206395 TGTTCATGTTCACTGTTCATTGTT 57.794 33.333 0.00 0.00 0.00 2.83
1889 1951 6.264832 TGTTCATGTTCACTGTTCATTGTTC 58.735 36.000 0.00 0.00 0.00 3.18
2561 2805 5.248640 AGGATGTGAACAACCTACTTGATG 58.751 41.667 10.28 0.00 45.75 3.07
2917 3161 5.647658 GTGATTTGTAATCTGACCATGTGGA 59.352 40.000 5.96 0.00 38.94 4.02
2918 3162 5.882000 TGATTTGTAATCTGACCATGTGGAG 59.118 40.000 5.96 0.00 38.94 3.86
2919 3163 4.908601 TTGTAATCTGACCATGTGGAGT 57.091 40.909 5.96 0.00 38.94 3.85
2920 3164 4.908601 TGTAATCTGACCATGTGGAGTT 57.091 40.909 5.96 0.00 38.94 3.01
2922 3166 5.245531 TGTAATCTGACCATGTGGAGTTTC 58.754 41.667 5.96 0.00 38.94 2.78
2924 3168 3.126001 TCTGACCATGTGGAGTTTCAC 57.874 47.619 5.96 0.00 38.94 3.18
2948 3214 5.222079 TGGCTTGTAATGTGTGAACTAGA 57.778 39.130 0.00 0.00 0.00 2.43
3421 5297 2.797278 CGCCGAGGCACCCTAGATT 61.797 63.158 15.03 0.00 42.06 2.40
3807 8168 8.314751 ACCCTAGATGATCAAATTAGGTTATCG 58.685 37.037 20.38 12.15 31.06 2.92
3900 8408 6.543735 AGAAAATTAGGAGCCACAACTAACT 58.456 36.000 0.00 0.00 30.33 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.407202 ACTCATACAAAGGTCATCACTTACC 58.593 40.000 0.00 0.00 35.91 2.85
5 6 6.253727 CGACTCATACAAAGGTCATCACTTAC 59.746 42.308 0.00 0.00 0.00 2.34
6 7 6.330278 CGACTCATACAAAGGTCATCACTTA 58.670 40.000 0.00 0.00 0.00 2.24
7 8 5.171476 CGACTCATACAAAGGTCATCACTT 58.829 41.667 0.00 0.00 0.00 3.16
8 9 4.382040 CCGACTCATACAAAGGTCATCACT 60.382 45.833 0.00 0.00 0.00 3.41
9 10 3.865745 CCGACTCATACAAAGGTCATCAC 59.134 47.826 0.00 0.00 0.00 3.06
10 11 3.513912 ACCGACTCATACAAAGGTCATCA 59.486 43.478 0.00 0.00 0.00 3.07
11 12 3.865745 CACCGACTCATACAAAGGTCATC 59.134 47.826 0.00 0.00 0.00 2.92
16 17 4.315803 AGTTTCACCGACTCATACAAAGG 58.684 43.478 0.00 0.00 0.00 3.11
76 78 6.259608 ACCTATCTTTCGATTCTCTGCATTTG 59.740 38.462 0.00 0.00 0.00 2.32
111 113 9.015367 TCTCTATAAGCCTGATATGTAACACTC 57.985 37.037 0.00 0.00 0.00 3.51
130 132 6.685527 CGCAGCTTATATCACCTCTCTATA 57.314 41.667 0.00 0.00 0.00 1.31
152 154 2.519377 TGGGGTCGATACTTATTGCG 57.481 50.000 0.00 0.00 0.00 4.85
161 163 2.224670 GGCCATAACAATGGGGTCGATA 60.225 50.000 0.00 0.00 41.94 2.92
164 166 0.395036 TGGCCATAACAATGGGGTCG 60.395 55.000 0.00 0.00 41.94 4.79
171 173 3.196901 TCTCGTGTACTGGCCATAACAAT 59.803 43.478 18.93 0.00 0.00 2.71
196 198 3.823873 TGTCGGCCAAAATAATTGTGAGT 59.176 39.130 2.24 0.00 0.00 3.41
238 240 4.113354 GTTCTCTCGGTGTTATGATGGAC 58.887 47.826 0.00 0.00 0.00 4.02
245 247 6.459066 CATATCATGGTTCTCTCGGTGTTAT 58.541 40.000 0.00 0.00 0.00 1.89
302 304 2.213499 GCCTTGGGAGATACATTCGTG 58.787 52.381 0.00 0.00 0.00 4.35
304 306 2.620251 TGCCTTGGGAGATACATTCG 57.380 50.000 0.00 0.00 0.00 3.34
320 322 6.000219 TCTATAAGAGAGCAATCCAAATGCC 59.000 40.000 0.00 0.00 44.91 4.40
325 327 6.430962 AGCATCTATAAGAGAGCAATCCAA 57.569 37.500 6.84 0.00 37.70 3.53
352 354 2.737679 GCAAAATTGGATGCAGAGGCTC 60.738 50.000 6.34 6.34 42.12 4.70
372 374 0.322546 CCAAGGTGAGTTGTAGGGGC 60.323 60.000 0.00 0.00 0.00 5.80
373 375 0.328258 CCCAAGGTGAGTTGTAGGGG 59.672 60.000 0.00 0.00 0.00 4.79
375 377 1.697432 TGACCCAAGGTGAGTTGTAGG 59.303 52.381 0.00 0.00 35.25 3.18
396 398 3.186613 GTGTTTGATTCCTGACCGAGTTC 59.813 47.826 0.00 0.00 0.00 3.01
404 406 4.893608 TCTTCGATGTGTTTGATTCCTGA 58.106 39.130 0.00 0.00 0.00 3.86
427 429 8.831550 CAGTAAGCCTTGGTTTATAGATTCTTC 58.168 37.037 0.00 0.00 0.00 2.87
452 454 5.984695 AACTAGTCTGTACAAGATGAGCA 57.015 39.130 0.00 0.00 37.23 4.26
494 496 0.321653 AGAATCGGGGTGAACTGCAC 60.322 55.000 0.00 0.00 46.98 4.57
506 508 3.243805 ACATCTGCATCTGAGAGAATCGG 60.244 47.826 2.91 0.00 42.67 4.18
508 510 5.358090 TCAACATCTGCATCTGAGAGAATC 58.642 41.667 2.91 0.00 0.00 2.52
542 544 6.687081 TTTGGTACTACAAAACTTGGACTG 57.313 37.500 0.00 0.00 37.40 3.51
578 580 1.125633 GCATTTCCCCAAGGATGCAT 58.874 50.000 0.00 0.00 44.43 3.96
607 609 2.750166 ACAGACAGTGATACAGGACGAG 59.250 50.000 0.00 0.00 0.00 4.18
610 612 7.097192 TGAAATTACAGACAGTGATACAGGAC 58.903 38.462 0.00 0.00 0.00 3.85
634 636 5.241506 ACAAACACATCCATTTCCTACACTG 59.758 40.000 0.00 0.00 0.00 3.66
645 647 1.619827 CCAAGCCACAAACACATCCAT 59.380 47.619 0.00 0.00 0.00 3.41
646 648 1.039068 CCAAGCCACAAACACATCCA 58.961 50.000 0.00 0.00 0.00 3.41
649 651 1.047596 TGCCCAAGCCACAAACACAT 61.048 50.000 0.00 0.00 38.69 3.21
663 665 3.558033 TCGTAGTATATCTGTGTGCCCA 58.442 45.455 0.00 0.00 0.00 5.36
708 710 3.822735 AGATTAACAATCATGGGCCATCG 59.177 43.478 18.16 12.59 40.42 3.84
795 797 9.825391 CGAGAAACGTATTGTTGTTATATGTAC 57.175 33.333 0.00 0.00 40.84 2.90
891 893 1.512734 GAGCCAAGTTGAATGCGCG 60.513 57.895 0.00 0.00 0.00 6.86
893 895 1.135315 CGGAGCCAAGTTGAATGCG 59.865 57.895 3.87 5.65 0.00 4.73
929 931 2.373707 ACTGCTCCCTCAGGATGCC 61.374 63.158 0.00 0.00 42.93 4.40
936 938 2.283604 TACGCCACTGCTCCCTCA 60.284 61.111 0.00 0.00 34.43 3.86
963 965 1.375523 GATTGGAGACACGGCCGTT 60.376 57.895 32.11 20.44 42.67 4.44
968 970 0.380733 TCGATCGATTGGAGACACGG 59.619 55.000 15.15 0.00 42.67 4.94
973 975 0.248498 GCGTGTCGATCGATTGGAGA 60.248 55.000 22.50 3.20 0.00 3.71
996 998 1.449601 CATTCCAGGTCGTTCGGGG 60.450 63.158 0.00 0.00 0.00 5.73
997 999 1.449601 CCATTCCAGGTCGTTCGGG 60.450 63.158 0.00 0.00 0.00 5.14
1000 1002 1.026718 CCTGCCATTCCAGGTCGTTC 61.027 60.000 0.10 0.00 45.87 3.95
1010 1012 1.658673 GCTATGCAGCCTGCCATTC 59.341 57.895 15.29 0.00 44.23 2.67
1044 1046 1.807165 CGCGGCTATGGATGGATCG 60.807 63.158 0.00 0.00 0.00 3.69
1068 1070 0.965866 ATTGACTCTCCCTGACGCGA 60.966 55.000 15.93 0.00 0.00 5.87
1069 1071 0.108615 AATTGACTCTCCCTGACGCG 60.109 55.000 3.53 3.53 0.00 6.01
1070 1072 1.363744 CAATTGACTCTCCCTGACGC 58.636 55.000 0.00 0.00 0.00 5.19
1071 1073 1.338105 TGCAATTGACTCTCCCTGACG 60.338 52.381 10.34 0.00 0.00 4.35
1072 1074 2.479566 TGCAATTGACTCTCCCTGAC 57.520 50.000 10.34 0.00 0.00 3.51
1073 1075 2.639347 TCTTGCAATTGACTCTCCCTGA 59.361 45.455 10.34 0.00 0.00 3.86
1074 1076 3.063510 TCTTGCAATTGACTCTCCCTG 57.936 47.619 10.34 0.00 0.00 4.45
1075 1077 3.795688 TTCTTGCAATTGACTCTCCCT 57.204 42.857 10.34 0.00 0.00 4.20
1076 1078 3.057245 GGTTTCTTGCAATTGACTCTCCC 60.057 47.826 10.34 0.00 0.00 4.30
1077 1079 3.569701 TGGTTTCTTGCAATTGACTCTCC 59.430 43.478 10.34 2.96 0.00 3.71
1078 1080 4.540824 GTGGTTTCTTGCAATTGACTCTC 58.459 43.478 10.34 0.00 0.00 3.20
1124 1126 7.095523 GCAACAGATTAACGACTTGGTAGTTTA 60.096 37.037 0.00 0.00 33.77 2.01
1255 1258 4.927782 TTTGCCTGTCCGCACGCT 62.928 61.111 0.00 0.00 38.83 5.07
1404 1426 2.962569 CTGGCTTCTCACCGACGA 59.037 61.111 0.00 0.00 0.00 4.20
1884 1946 9.768662 CCTTTAACTAAACTACTAGGTGAACAA 57.231 33.333 0.00 0.00 0.00 2.83
1885 1947 8.927411 ACCTTTAACTAAACTACTAGGTGAACA 58.073 33.333 0.00 0.00 0.00 3.18
1888 1950 9.813826 AGTACCTTTAACTAAACTACTAGGTGA 57.186 33.333 0.00 0.00 0.00 4.02
1889 1951 9.852091 CAGTACCTTTAACTAAACTACTAGGTG 57.148 37.037 0.00 0.00 0.00 4.00
2561 2805 2.310538 CTTGGGAATATTGTCCTGGGC 58.689 52.381 0.00 0.00 37.85 5.36
2924 3168 4.771590 AGTTCACACATTACAAGCCATG 57.228 40.909 0.00 0.00 0.00 3.66
2948 3214 3.891366 ACTTCAAATACTGCAAACTGCCT 59.109 39.130 0.00 0.00 44.23 4.75
3199 3678 4.156455 AGGGTGCCATAGTTAACATCAG 57.844 45.455 8.61 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.