Multiple sequence alignment - TraesCS4A01G193000

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 TraesCS4A01G193000 chr4A 100.000 3089 0 0 1 3089 473947623 473944535 0.000000e+00 5705
1 TraesCS4A01G193000 chr4D 93.232 2231 123 11 1 2223 101435334 101437544 0.000000e+00 3258
2 TraesCS4A01G193000 chr4D 88.034 585 41 12 2225 2783 101437654 101438235 0.000000e+00 665
3 TraesCS4A01G193000 chr4D 79.588 583 75 20 90 631 14648170 14648749 8.090000e-101 377
4 TraesCS4A01G193000 chr4D 78.522 582 84 23 90 631 266955362 266955942 8.200000e-91 344
5 TraesCS4A01G193000 chr4B 93.722 1975 110 5 728 2695 145370948 145372915 0.000000e+00 2948
6 TraesCS4A01G193000 chr4B 85.802 648 63 13 1 643 145370293 145370916 0.000000e+00 660
7 TraesCS4A01G193000 chr4B 78.947 399 33 26 2697 3087 145372959 145373314 1.110000e-54 224
8 TraesCS4A01G193000 chr4B 76.009 446 86 15 190 619 159636330 159635890 8.680000e-51 211
9 TraesCS4A01G193000 chr1A 82.202 545 72 17 90 612 399194720 399194179 2.190000e-121 446
10 TraesCS4A01G193000 chr6B 79.598 647 89 22 1 619 341545268 341545899 1.020000e-114 424
11 TraesCS4A01G193000 chr6B 76.861 497 111 4 1571 2065 542585795 542586289 8.440000e-71 278
12 TraesCS4A01G193000 chr6B 82.659 173 19 8 464 631 197820207 197820041 3.210000e-30 143
13 TraesCS4A01G193000 chr3D 81.004 558 73 17 89 619 61178106 61177555 2.220000e-111 412
14 TraesCS4A01G193000 chr6A 80.600 567 76 18 80 619 34418296 34418855 1.030000e-109 407
15 TraesCS4A01G193000 chr6A 76.779 534 117 5 1571 2102 502366779 502367307 3.010000e-75 292
16 TraesCS4A01G193000 chr5D 80.247 567 78 18 80 619 189246630 189247189 2.230000e-106 396
17 TraesCS4A01G193000 chr5D 87.342 158 14 6 464 619 434557174 434557327 3.170000e-40 176
18 TraesCS4A01G193000 chr5D 78.788 231 26 16 2823 3032 505117379 505117607 1.930000e-27 134
19 TraesCS4A01G193000 chr3A 78.899 545 83 24 111 630 210116463 210115926 1.060000e-89 340
20 TraesCS4A01G193000 chr6D 77.062 497 110 4 1571 2065 361380293 361380787 1.810000e-72 283
21 TraesCS4A01G193000 chr6D 84.277 159 18 7 463 618 58712861 58713015 6.900000e-32 148
22 TraesCS4A01G193000 chr2B 75.893 560 91 31 91 614 719160574 719160023 2.380000e-61 246
23 TraesCS4A01G193000 chr2B 90.984 122 7 4 493 613 233577306 233577424 8.860000e-36 161
24 TraesCS4A01G193000 chr2B 77.606 259 43 12 464 712 140789846 140789593 3.210000e-30 143
25 TraesCS4A01G193000 chr5B 77.586 232 26 17 2823 3032 634974486 634974713 1.950000e-22 117


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 TraesCS4A01G193000 chr4A 473944535 473947623 3088 True 5705.000000 5705 100.000 1 3089 1 chr4A.!!$R1 3088
1 TraesCS4A01G193000 chr4D 101435334 101438235 2901 False 1961.500000 3258 90.633 1 2783 2 chr4D.!!$F3 2782
2 TraesCS4A01G193000 chr4D 14648170 14648749 579 False 377.000000 377 79.588 90 631 1 chr4D.!!$F1 541
3 TraesCS4A01G193000 chr4D 266955362 266955942 580 False 344.000000 344 78.522 90 631 1 chr4D.!!$F2 541
4 TraesCS4A01G193000 chr4B 145370293 145373314 3021 False 1277.333333 2948 86.157 1 3087 3 chr4B.!!$F1 3086
5 TraesCS4A01G193000 chr1A 399194179 399194720 541 True 446.000000 446 82.202 90 612 1 chr1A.!!$R1 522
6 TraesCS4A01G193000 chr6B 341545268 341545899 631 False 424.000000 424 79.598 1 619 1 chr6B.!!$F1 618
7 TraesCS4A01G193000 chr3D 61177555 61178106 551 True 412.000000 412 81.004 89 619 1 chr3D.!!$R1 530
8 TraesCS4A01G193000 chr6A 34418296 34418855 559 False 407.000000 407 80.600 80 619 1 chr6A.!!$F1 539
9 TraesCS4A01G193000 chr6A 502366779 502367307 528 False 292.000000 292 76.779 1571 2102 1 chr6A.!!$F2 531
10 TraesCS4A01G193000 chr5D 189246630 189247189 559 False 396.000000 396 80.247 80 619 1 chr5D.!!$F1 539
11 TraesCS4A01G193000 chr3A 210115926 210116463 537 True 340.000000 340 78.899 111 630 1 chr3A.!!$R1 519
12 TraesCS4A01G193000 chr2B 719160023 719160574 551 True 246.000000 246 75.893 91 614 1 chr2B.!!$R2 523

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
49 51 0.679321 CCTCCTTTGCCTTGAGCTCC 60.679 60.0 12.15 0.0 44.23 4.70 F
84 86 1.018910 ACAACTTTACCACGTGTGCC 58.981 50.0 15.65 0.0 0.00 5.01 F
1348 1424 0.594602 CCCGTCAGTGTTCGACTACA 59.405 55.0 10.81 0.0 31.73 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1161 1237 0.970937 TGGCTCCGTCAGGGTAGAAG 60.971 60.000 0.00 0.00 38.33 2.85 R
1764 1840 1.063642 TCACCACCAAAATCACCCACA 60.064 47.619 0.00 0.00 0.00 4.17 R
2865 3102 0.544833 TAACTGGACCGGCCCACTTA 60.545 55.000 4.87 4.98 34.97 2.24 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
49 51 0.679321 CCTCCTTTGCCTTGAGCTCC 60.679 60.000 12.15 0.00 44.23 4.70
55 57 2.202676 GCCTTGAGCTCCTCGACG 60.203 66.667 12.15 0.00 38.99 5.12
67 69 1.215382 CTCGACGGGAGCATCAACA 59.785 57.895 0.00 0.00 35.63 3.33
74 76 2.812011 ACGGGAGCATCAACAACTTTAC 59.188 45.455 0.00 0.00 36.25 2.01
75 77 2.161609 CGGGAGCATCAACAACTTTACC 59.838 50.000 0.00 0.00 36.25 2.85
76 78 3.153919 GGGAGCATCAACAACTTTACCA 58.846 45.455 0.00 0.00 36.25 3.25
84 86 1.018910 ACAACTTTACCACGTGTGCC 58.981 50.000 15.65 0.00 0.00 5.01
126 128 2.329379 GAAGTACCTCAACAGCGACAG 58.671 52.381 0.00 0.00 0.00 3.51
163 168 5.878669 TGAAGATGATGAGGACTTCAACATG 59.121 40.000 13.91 0.00 45.88 3.21
164 169 4.778579 AGATGATGAGGACTTCAACATGG 58.221 43.478 13.91 0.00 45.88 3.66
255 260 1.757118 ACCCATCTCATCGACATCGTT 59.243 47.619 0.54 0.00 40.80 3.85
325 340 1.502039 AGTCTCACCCCGGATATGGTA 59.498 52.381 0.73 0.00 32.32 3.25
327 342 2.701951 GTCTCACCCCGGATATGGTAAA 59.298 50.000 0.73 0.00 32.32 2.01
357 372 1.947456 GGCCGTGAAATATGAGGAACC 59.053 52.381 0.00 0.00 0.00 3.62
360 375 3.873910 CCGTGAAATATGAGGAACCAGT 58.126 45.455 0.00 0.00 0.00 4.00
374 389 1.949799 ACCAGTGAGAAGGAGAGCAT 58.050 50.000 0.00 0.00 0.00 3.79
386 401 2.634940 AGGAGAGCATAATACACCGCAT 59.365 45.455 0.00 0.00 0.00 4.73
412 427 3.068590 ACAAAGAACTGGAAGCCACATTG 59.931 43.478 0.00 0.00 37.60 2.82
524 591 4.595762 TCTAGAGCGTGGTTTTGTACTT 57.404 40.909 0.00 0.00 0.00 2.24
527 594 4.547406 AGAGCGTGGTTTTGTACTTTTC 57.453 40.909 0.00 0.00 0.00 2.29
534 601 6.309494 GCGTGGTTTTGTACTTTTCTTTCTTT 59.691 34.615 0.00 0.00 0.00 2.52
764 840 1.228063 CCAATCTGGCCAGATCCCG 60.228 63.158 41.33 31.35 46.75 5.14
875 951 1.515020 CTCCTCCTCTGCCGACTTG 59.485 63.158 0.00 0.00 0.00 3.16
942 1018 1.961394 TCCTCGACAAAGCTGTGTACT 59.039 47.619 10.23 0.00 35.30 2.73
1129 1205 3.350909 TTCGTCCAGTCGGCCATCG 62.351 63.158 2.24 0.00 40.90 3.84
1161 1237 1.065928 CTACGACTGGACCATCCGC 59.934 63.158 13.55 0.00 40.17 5.54
1185 1261 0.907704 ACCCTGACGGAGCCAACATA 60.908 55.000 0.00 0.00 34.64 2.29
1224 1300 4.405173 GTGTCGGTTTCGCGCGAC 62.405 66.667 35.02 22.94 39.51 5.19
1237 1313 4.373116 GCGACCTCACGGGCAAGA 62.373 66.667 0.00 0.00 38.74 3.02
1238 1314 2.125912 CGACCTCACGGGCAAGAG 60.126 66.667 0.00 0.00 38.74 2.85
1239 1315 2.435059 GACCTCACGGGCAAGAGC 60.435 66.667 0.00 0.00 38.64 4.09
1240 1316 3.240134 GACCTCACGGGCAAGAGCA 62.240 63.158 0.00 0.00 44.61 4.26
1241 1317 2.032528 CCTCACGGGCAAGAGCAA 59.967 61.111 0.00 0.00 44.61 3.91
1270 1346 1.890979 CGGGCATCCTGTGATCTGC 60.891 63.158 0.00 0.00 0.00 4.26
1324 1400 5.903810 AGAGTATTTGGTATCCGTCTCAAC 58.096 41.667 0.00 0.00 0.00 3.18
1333 1409 2.424302 CGTCTCAACCAACCCCGT 59.576 61.111 0.00 0.00 0.00 5.28
1337 1413 1.052124 TCTCAACCAACCCCGTCAGT 61.052 55.000 0.00 0.00 0.00 3.41
1348 1424 0.594602 CCCGTCAGTGTTCGACTACA 59.405 55.000 10.81 0.00 31.73 2.74
1349 1425 1.001048 CCCGTCAGTGTTCGACTACAA 60.001 52.381 10.81 0.00 31.73 2.41
1368 1444 5.880054 ACAATAATCGTGTTTTCCCAGAG 57.120 39.130 0.00 0.00 0.00 3.35
1422 1498 2.843701 CTGGAAGCATCAGGGTACATC 58.156 52.381 0.00 0.00 0.00 3.06
1491 1567 1.133407 TCGCAGGTGACAAAAACAACC 59.867 47.619 0.00 0.00 0.00 3.77
1590 1666 0.944386 ACGTGACATTCAGTGTTGGC 59.056 50.000 0.00 0.00 42.36 4.52
1650 1726 1.363744 GATCACCTGTCTTTGAGGCG 58.636 55.000 0.00 0.00 33.39 5.52
1654 1730 0.832135 ACCTGTCTTTGAGGCGGAGA 60.832 55.000 0.00 0.00 33.39 3.71
1675 1751 4.596643 AGATGTATGGAGGGATGAAGGAAG 59.403 45.833 0.00 0.00 0.00 3.46
1740 1816 4.800582 GCTTTCAAGGCCTTACTGCATTTT 60.801 41.667 20.00 0.00 32.08 1.82
1764 1840 5.480422 TGTATATACCGACTCATTGCCTGAT 59.520 40.000 10.38 0.00 32.10 2.90
1824 1900 0.108662 GGCATTTACTTGTGGCTGCC 60.109 55.000 12.87 12.87 42.00 4.85
1842 1918 2.773661 TGCCGATAGATATGCCATGGAT 59.226 45.455 18.40 8.90 39.76 3.41
1962 2038 3.395858 CTTAAGGAAGCGTGCATTGAG 57.604 47.619 0.00 0.00 0.00 3.02
2040 2116 3.222603 TCTCAAAAGAACTTGCCCTTCC 58.777 45.455 0.00 0.00 0.00 3.46
2254 2438 5.221244 GCACCTTTTGTCAAACTACTGGATT 60.221 40.000 0.00 0.00 0.00 3.01
2257 2441 5.534654 CCTTTTGTCAAACTACTGGATTCCA 59.465 40.000 5.05 5.05 0.00 3.53
2426 2617 6.537566 CAAATATCATCTGGCGCATAGTTAC 58.462 40.000 10.83 0.00 0.00 2.50
2431 2622 1.215655 CTGGCGCATAGTTACCGAGC 61.216 60.000 10.83 0.00 0.00 5.03
2462 2653 5.049267 TGCATCGTCTGTTAAACTTTTACCC 60.049 40.000 0.00 0.00 0.00 3.69
2627 2819 9.937175 GTTCAAGGTTATTTATGTTATCTGCTC 57.063 33.333 0.00 0.00 0.00 4.26
2768 3005 5.247564 ACGGGTTATAGATTGCTGCCTTATA 59.752 40.000 0.00 0.00 0.00 0.98
2796 3033 6.734137 ACAGAGAGTAATTCAGAATAGCTCG 58.266 40.000 15.61 8.64 31.35 5.03
2797 3034 5.629020 CAGAGAGTAATTCAGAATAGCTCGC 59.371 44.000 16.17 16.17 31.35 5.03
2798 3035 5.534654 AGAGAGTAATTCAGAATAGCTCGCT 59.465 40.000 18.76 18.76 32.00 4.93
2800 3037 6.578023 AGAGTAATTCAGAATAGCTCGCTTT 58.422 36.000 15.61 0.00 31.35 3.51
2801 3038 7.044798 AGAGTAATTCAGAATAGCTCGCTTTT 58.955 34.615 15.61 0.00 31.35 2.27
2802 3039 7.550906 AGAGTAATTCAGAATAGCTCGCTTTTT 59.449 33.333 15.61 0.00 31.35 1.94
2824 3061 4.928661 TTTGAGACAAAGAATAGCTCGC 57.071 40.909 0.00 0.00 0.00 5.03
2825 3062 3.876274 TGAGACAAAGAATAGCTCGCT 57.124 42.857 0.00 0.00 0.00 4.93
2826 3063 4.193826 TGAGACAAAGAATAGCTCGCTT 57.806 40.909 0.00 0.00 0.00 4.68
2827 3064 5.324784 TGAGACAAAGAATAGCTCGCTTA 57.675 39.130 0.00 0.00 0.00 3.09
2828 3065 5.907207 TGAGACAAAGAATAGCTCGCTTAT 58.093 37.500 0.00 0.00 0.00 1.73
2829 3066 7.039313 TGAGACAAAGAATAGCTCGCTTATA 57.961 36.000 0.00 0.00 0.00 0.98
2830 3067 7.142021 TGAGACAAAGAATAGCTCGCTTATAG 58.858 38.462 0.00 0.00 0.00 1.31
2831 3068 5.923684 AGACAAAGAATAGCTCGCTTATAGC 59.076 40.000 0.00 0.00 40.40 2.97
2854 3091 2.353607 GTAGGTCGCGATCGCCTG 60.354 66.667 32.63 20.49 40.56 4.85
2857 3094 2.060004 TAGGTCGCGATCGCCTGAAG 62.060 60.000 32.63 19.01 40.56 3.02
2858 3095 3.621394 GTCGCGATCGCCTGAAGC 61.621 66.667 32.63 11.49 37.98 3.86
2877 3114 1.397390 CGACCTATAAGTGGGCCGGT 61.397 60.000 1.90 0.00 0.00 5.28
2885 3122 1.205460 AAGTGGGCCGGTCCAGTTAT 61.205 55.000 40.53 22.92 45.67 1.89
2891 3128 2.443416 GGCCGGTCCAGTTATTTCTTT 58.557 47.619 1.90 0.00 34.01 2.52
2894 3131 3.254903 GCCGGTCCAGTTATTTCTTTGTT 59.745 43.478 1.90 0.00 0.00 2.83
2895 3132 4.794169 CCGGTCCAGTTATTTCTTTGTTG 58.206 43.478 0.00 0.00 0.00 3.33
2900 3137 6.366061 GGTCCAGTTATTTCTTTGTTGCATTC 59.634 38.462 0.00 0.00 0.00 2.67
2901 3138 7.147976 GTCCAGTTATTTCTTTGTTGCATTCT 58.852 34.615 0.00 0.00 0.00 2.40
2905 3142 9.033481 CAGTTATTTCTTTGTTGCATTCTTTCA 57.967 29.630 0.00 0.00 0.00 2.69
2918 3155 5.874261 TGCATTCTTTCATTCACTACGATGA 59.126 36.000 0.00 0.00 0.00 2.92
2921 3158 7.912250 GCATTCTTTCATTCACTACGATGATTT 59.088 33.333 0.00 0.00 0.00 2.17
3010 3253 7.495135 AAAAATCGAGCATTTGGAAAATGTT 57.505 28.000 12.82 7.91 34.69 2.71
3011 3254 8.600449 AAAAATCGAGCATTTGGAAAATGTTA 57.400 26.923 12.82 0.00 34.69 2.41
3012 3255 8.600449 AAAATCGAGCATTTGGAAAATGTTAA 57.400 26.923 12.82 2.05 34.69 2.01
3013 3256 7.581011 AATCGAGCATTTGGAAAATGTTAAC 57.419 32.000 12.82 0.00 0.00 2.01
3014 3257 6.078202 TCGAGCATTTGGAAAATGTTAACA 57.922 33.333 11.41 11.41 0.00 2.41
3015 3258 5.918011 TCGAGCATTTGGAAAATGTTAACAC 59.082 36.000 11.22 0.00 0.00 3.32
3016 3259 5.689514 CGAGCATTTGGAAAATGTTAACACA 59.310 36.000 11.22 0.70 37.31 3.72
3017 3260 6.129115 CGAGCATTTGGAAAATGTTAACACAG 60.129 38.462 11.22 0.00 35.94 3.66
3018 3261 6.581712 AGCATTTGGAAAATGTTAACACAGT 58.418 32.000 11.22 0.00 35.94 3.55
3019 3262 6.479660 AGCATTTGGAAAATGTTAACACAGTG 59.520 34.615 11.22 0.00 35.94 3.66
3020 3263 6.257630 GCATTTGGAAAATGTTAACACAGTGT 59.742 34.615 11.22 0.00 35.94 3.55
3021 3264 7.436673 GCATTTGGAAAATGTTAACACAGTGTA 59.563 33.333 11.22 0.00 35.94 2.90
3022 3265 8.751335 CATTTGGAAAATGTTAACACAGTGTAC 58.249 33.333 11.22 2.93 35.94 2.90
3025 3268 8.057536 TGGAAAATGTTAACACAGTGTACTTT 57.942 30.769 11.22 4.41 35.94 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.134574 TGAAATACCTTGTTCCACGCT 57.865 42.857 0.00 0.00 0.00 5.07
17 19 5.654209 AGGCAAAGGAGGAAGAATGAAATAC 59.346 40.000 0.00 0.00 0.00 1.89
23 25 3.424703 TCAAGGCAAAGGAGGAAGAATG 58.575 45.455 0.00 0.00 0.00 2.67
24 26 3.694926 CTCAAGGCAAAGGAGGAAGAAT 58.305 45.455 0.00 0.00 0.00 2.40
49 51 0.389817 TTGTTGATGCTCCCGTCGAG 60.390 55.000 0.00 0.00 42.04 4.04
55 57 3.057526 GTGGTAAAGTTGTTGATGCTCCC 60.058 47.826 0.00 0.00 0.00 4.30
67 69 1.305201 CAGGCACACGTGGTAAAGTT 58.695 50.000 21.57 0.00 0.00 2.66
74 76 4.935495 ACCTGCAGGCACACGTGG 62.935 66.667 33.06 7.01 39.32 4.94
75 77 3.653009 CACCTGCAGGCACACGTG 61.653 66.667 33.06 18.15 39.32 4.49
76 78 4.935495 CCACCTGCAGGCACACGT 62.935 66.667 33.06 9.33 39.32 4.49
84 86 1.488705 TAACTCCCCACCACCTGCAG 61.489 60.000 6.78 6.78 0.00 4.41
126 128 5.816258 TCATCATCTTCATTGAAGCTGACTC 59.184 40.000 26.69 0.00 44.03 3.36
163 168 1.617850 TGTTCATGCCACCATTGTTCC 59.382 47.619 0.00 0.00 0.00 3.62
164 169 2.035704 TGTGTTCATGCCACCATTGTTC 59.964 45.455 11.36 0.00 31.71 3.18
255 260 5.414360 CAGCTATGTTGAAAGCAGACTCTA 58.586 41.667 0.00 0.00 41.32 2.43
325 340 4.657436 TTTCACGGCCATTAGTGTTTTT 57.343 36.364 2.24 0.00 39.25 1.94
327 342 5.650266 TCATATTTCACGGCCATTAGTGTTT 59.350 36.000 2.24 0.00 39.25 2.83
357 372 5.982516 GTGTATTATGCTCTCCTTCTCACTG 59.017 44.000 0.00 0.00 0.00 3.66
360 375 4.038042 CGGTGTATTATGCTCTCCTTCTCA 59.962 45.833 0.00 0.00 0.00 3.27
374 389 6.651643 AGTTCTTTGTTGTATGCGGTGTATTA 59.348 34.615 0.00 0.00 0.00 0.98
386 401 3.630312 GTGGCTTCCAGTTCTTTGTTGTA 59.370 43.478 0.00 0.00 32.34 2.41
485 550 7.171678 CGCTCTAGATTATACAAAAGGGAAAGG 59.828 40.741 0.00 0.00 0.00 3.11
524 591 5.582950 TCCATCCCTGAGAAAGAAAGAAA 57.417 39.130 0.00 0.00 0.00 2.52
527 594 4.263683 ACCTTCCATCCCTGAGAAAGAAAG 60.264 45.833 0.00 0.00 0.00 2.62
534 601 4.788075 TCATTAAACCTTCCATCCCTGAGA 59.212 41.667 0.00 0.00 0.00 3.27
852 928 3.160748 GGCAGAGGAGGAGGAGGC 61.161 72.222 0.00 0.00 0.00 4.70
875 951 1.448013 GCGAGTGGAGTACCTTGGC 60.448 63.158 0.00 0.00 37.04 4.52
942 1018 4.276183 CGGATCTGAGAATACGAGAGGAAA 59.724 45.833 0.00 0.00 34.82 3.13
1059 1135 1.064296 CCCGACGATCTCCAAGACG 59.936 63.158 0.00 0.00 0.00 4.18
1161 1237 0.970937 TGGCTCCGTCAGGGTAGAAG 60.971 60.000 0.00 0.00 38.33 2.85
1226 1302 2.032528 CCTTGCTCTTGCCCGTGA 59.967 61.111 0.00 0.00 38.71 4.35
1270 1346 4.181578 CCAGTATCCTTGTTAACCAGTCG 58.818 47.826 2.48 0.00 0.00 4.18
1313 1389 1.683441 GGGGTTGGTTGAGACGGAT 59.317 57.895 0.00 0.00 0.00 4.18
1316 1392 1.666872 GACGGGGTTGGTTGAGACG 60.667 63.158 0.00 0.00 0.00 4.18
1324 1400 1.959226 CGAACACTGACGGGGTTGG 60.959 63.158 6.65 1.11 42.32 3.77
1333 1409 5.798434 CACGATTATTGTAGTCGAACACTGA 59.202 40.000 8.54 0.00 39.86 3.41
1337 1413 7.359431 GGAAAACACGATTATTGTAGTCGAACA 60.359 37.037 8.54 0.00 39.86 3.18
1348 1424 5.181245 CACACTCTGGGAAAACACGATTATT 59.819 40.000 0.00 0.00 0.00 1.40
1349 1425 4.695455 CACACTCTGGGAAAACACGATTAT 59.305 41.667 0.00 0.00 0.00 1.28
1368 1444 3.263425 TCCTTTCAATAGACCCTCCACAC 59.737 47.826 0.00 0.00 0.00 3.82
1379 1455 4.440880 CTCCAGCTCACTCCTTTCAATAG 58.559 47.826 0.00 0.00 0.00 1.73
1380 1456 3.369892 GCTCCAGCTCACTCCTTTCAATA 60.370 47.826 0.00 0.00 38.21 1.90
1416 1492 6.283694 TGTCAAGCTATCATCCTTGATGTAC 58.716 40.000 6.38 0.00 46.24 2.90
1422 1498 6.688637 TCAATTGTCAAGCTATCATCCTTG 57.311 37.500 5.13 0.00 39.74 3.61
1491 1567 1.065854 ACCTTGATTTCAGAGCTCCCG 60.066 52.381 10.93 1.67 0.00 5.14
1590 1666 1.667830 TGCGGCAAAAGTCTCTCCG 60.668 57.895 0.00 0.00 42.68 4.63
1650 1726 3.262915 CCTTCATCCCTCCATACATCTCC 59.737 52.174 0.00 0.00 0.00 3.71
1654 1730 3.654806 CCTTCCTTCATCCCTCCATACAT 59.345 47.826 0.00 0.00 0.00 2.29
1675 1751 3.274288 CTGTAATGGACTCTGCCTTTCC 58.726 50.000 0.00 0.00 0.00 3.13
1740 1816 4.830600 TCAGGCAATGAGTCGGTATATACA 59.169 41.667 14.70 0.00 32.77 2.29
1764 1840 1.063642 TCACCACCAAAATCACCCACA 60.064 47.619 0.00 0.00 0.00 4.17
1842 1918 6.939730 TGTTTTGACATATCAACTTCAGCCTA 59.060 34.615 0.00 0.00 44.66 3.93
1962 2038 6.429385 CCATCTCATCCTTAGAGGCAATAAAC 59.571 42.308 0.00 0.00 34.61 2.01
2004 2080 8.837389 GTTCTTTTGAGATTACTGTAACCTTGT 58.163 33.333 1.73 0.00 0.00 3.16
2081 2157 1.070445 ATGAGCTGCTCACCTATGCTC 59.930 52.381 32.54 2.83 43.63 4.26
2133 2209 8.821894 AGCTAGCTTTTCATACGATTTAAGAAG 58.178 33.333 12.68 0.00 0.00 2.85
2156 2232 4.098807 GCTGCTCTAGGAAACTAACTAGCT 59.901 45.833 0.00 0.00 43.83 3.32
2254 2438 3.138304 CCTGACGTTCAACAATTCTGGA 58.862 45.455 0.00 0.00 0.00 3.86
2257 2441 2.878406 CACCCTGACGTTCAACAATTCT 59.122 45.455 0.00 0.00 0.00 2.40
2258 2442 2.616842 ACACCCTGACGTTCAACAATTC 59.383 45.455 0.00 0.00 0.00 2.17
2264 2448 2.011222 GTTCAACACCCTGACGTTCAA 58.989 47.619 0.00 0.00 0.00 2.69
2426 2617 0.664466 ACGATGCATATGTCGCTCGG 60.664 55.000 13.84 0.00 41.31 4.63
2431 2622 5.232202 AGTTTAACAGACGATGCATATGTCG 59.768 40.000 20.02 14.13 43.13 4.35
2462 2653 8.045176 AGTTTTCTGAAATAGGAATCCGAAAG 57.955 34.615 3.31 0.00 32.74 2.62
2500 2691 4.606961 CGTTCACCAAATTGTTGTAGCTT 58.393 39.130 0.00 0.00 32.40 3.74
2503 2694 3.958704 TGCGTTCACCAAATTGTTGTAG 58.041 40.909 0.00 0.00 32.40 2.74
2533 2724 1.596260 CAGGCTTCAGTGCATGATACG 59.404 52.381 0.00 0.00 46.12 3.06
2573 2765 5.669798 AGGCATAACAAATAGGAATCCCT 57.330 39.130 0.00 0.00 46.62 4.20
2627 2819 9.988350 ACATAACTGAAATTAAGCTGTTTATCG 57.012 29.630 0.00 0.00 0.00 2.92
2654 2849 5.814188 TGCATGAAGTTCATCTCAGTATGAC 59.186 40.000 15.60 1.92 35.77 3.06
2745 2982 2.550830 AGGCAGCAATCTATAACCCG 57.449 50.000 0.00 0.00 0.00 5.28
2775 3012 5.768317 AGCGAGCTATTCTGAATTACTCTC 58.232 41.667 20.62 16.19 0.00 3.20
2801 3038 5.470098 AGCGAGCTATTCTTTGTCTCAAAAA 59.530 36.000 0.00 0.00 0.00 1.94
2802 3039 4.997395 AGCGAGCTATTCTTTGTCTCAAAA 59.003 37.500 0.00 0.00 0.00 2.44
2803 3040 4.569943 AGCGAGCTATTCTTTGTCTCAAA 58.430 39.130 0.00 0.00 0.00 2.69
2804 3041 4.193826 AGCGAGCTATTCTTTGTCTCAA 57.806 40.909 0.00 0.00 0.00 3.02
2805 3042 3.876274 AGCGAGCTATTCTTTGTCTCA 57.124 42.857 0.00 0.00 0.00 3.27
2807 3044 5.923684 GCTATAAGCGAGCTATTCTTTGTCT 59.076 40.000 0.00 0.00 36.96 3.41
2823 3060 2.666069 CGACCTACAGCTCGCTATAAGC 60.666 54.545 0.00 0.00 40.14 3.09
2824 3061 3.190314 CGACCTACAGCTCGCTATAAG 57.810 52.381 0.00 0.00 0.00 1.73
2831 3068 1.369448 GATCGCGACCTACAGCTCG 60.369 63.158 12.93 0.00 0.00 5.03
2832 3069 1.369448 CGATCGCGACCTACAGCTC 60.369 63.158 12.93 0.55 40.82 4.09
2833 3070 2.716244 CGATCGCGACCTACAGCT 59.284 61.111 12.93 0.00 40.82 4.24
2834 3071 3.025176 GCGATCGCGACCTACAGC 61.025 66.667 26.12 7.26 40.82 4.40
2835 3072 2.353607 GGCGATCGCGACCTACAG 60.354 66.667 31.76 0.00 40.51 2.74
2854 3091 1.540580 GGCCCACTTATAGGTCGCTTC 60.541 57.143 0.00 0.00 0.00 3.86
2857 3094 1.300697 CGGCCCACTTATAGGTCGC 60.301 63.158 0.00 0.00 45.35 5.19
2865 3102 0.544833 TAACTGGACCGGCCCACTTA 60.545 55.000 4.87 4.98 34.97 2.24
2877 3114 7.288810 AGAATGCAACAAAGAAATAACTGGA 57.711 32.000 0.00 0.00 0.00 3.86
2885 3122 7.765360 AGTGAATGAAAGAATGCAACAAAGAAA 59.235 29.630 0.00 0.00 0.00 2.52
2891 3128 5.468409 TCGTAGTGAATGAAAGAATGCAACA 59.532 36.000 0.00 0.00 0.00 3.33
2894 3131 5.874261 TCATCGTAGTGAATGAAAGAATGCA 59.126 36.000 0.00 0.00 0.00 3.96
2895 3132 6.349973 TCATCGTAGTGAATGAAAGAATGC 57.650 37.500 0.00 0.00 0.00 3.56
2989 3232 7.116233 GTGTTAACATTTTCCAAATGCTCGATT 59.884 33.333 12.26 0.00 0.00 3.34
2996 3239 7.769272 ACACTGTGTTAACATTTTCCAAATG 57.231 32.000 12.26 8.17 35.22 2.32
3001 3244 8.920509 AAAAGTACACTGTGTTAACATTTTCC 57.079 30.769 19.73 0.00 35.22 3.13


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

AutoCloner maintained by Alex Coulton.