Multiple sequence alignment - TraesCS1A01G129100

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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 TraesCS1A01G129100 chr1A 100.000 3623 0 0 1 3623 163384900 163381278 0.000000e+00 6691
1 TraesCS1A01G129100 chr1D 93.685 2882 114 23 1 2854 134681293 134684134 0.000000e+00 4252
2 TraesCS1A01G129100 chr1D 87.288 236 10 7 2854 3088 249487613 249487397 6.010000e-63 252
3 TraesCS1A01G129100 chr1B 94.368 2184 73 15 694 2853 201775004 201777161 0.000000e+00 3306
4 TraesCS1A01G129100 chr1B 93.072 433 28 1 220 650 201774576 201775008 1.840000e-177 632
5 TraesCS1A01G129100 chr1B 82.766 441 48 10 2911 3346 623364964 623365381 5.720000e-98 368
6 TraesCS1A01G129100 chr1B 93.274 223 15 0 1 223 201760691 201760913 2.700000e-86 329
7 TraesCS1A01G129100 chr7B 91.772 790 28 7 2851 3623 72305022 72304253 0.000000e+00 1064
8 TraesCS1A01G129100 chr4B 90.343 787 39 11 2854 3623 510386003 510386769 0.000000e+00 998
9 TraesCS1A01G129100 chr4B 86.772 189 25 0 2138 2326 412778111 412777923 1.020000e-50 211
10 TraesCS1A01G129100 chr4B 84.100 239 13 10 2853 3090 633617570 633617784 1.320000e-49 207
11 TraesCS1A01G129100 chr6A 89.520 792 43 11 2851 3623 23449952 23449182 0.000000e+00 966
12 TraesCS1A01G129100 chr6A 79.599 549 68 20 2851 3380 143073650 143074173 1.600000e-93 353
13 TraesCS1A01G129100 chr5B 85.478 785 76 14 2853 3620 384367811 384367048 0.000000e+00 784
14 TraesCS1A01G129100 chr5B 88.981 481 20 10 2851 3318 356265855 356266315 6.790000e-157 564
15 TraesCS1A01G129100 chr5A 86.275 510 26 6 2852 3348 704693153 704693631 6.940000e-142 514
16 TraesCS1A01G129100 chr5A 79.927 548 67 22 2851 3380 650516324 650515802 2.660000e-96 363
17 TraesCS1A01G129100 chr2B 83.168 505 53 11 2853 3345 479657087 479656603 2.000000e-117 433
18 TraesCS1A01G129100 chr6B 83.135 504 54 11 2848 3346 18850718 18850241 7.190000e-117 431
19 TraesCS1A01G129100 chr5D 78.674 694 94 30 2851 3518 388601986 388601321 2.600000e-111 412
20 TraesCS1A01G129100 chr3D 88.235 289 28 3 3233 3518 21411366 21411081 1.250000e-89 340
21 TraesCS1A01G129100 chr3D 88.235 289 28 4 3233 3518 21433912 21433627 1.250000e-89 340
22 TraesCS1A01G129100 chr4D 87.197 289 31 3 3233 3518 315359852 315360137 1.250000e-84 324
23 TraesCS1A01G129100 chr4D 86.243 189 26 0 2138 2326 334962736 334962548 4.740000e-49 206
24 TraesCS1A01G129100 chr3B 82.842 373 46 6 3094 3450 143598171 143598541 5.840000e-83 318
25 TraesCS1A01G129100 chr2D 86.897 290 30 5 3233 3518 179878039 179877754 5.840000e-83 318
26 TraesCS1A01G129100 chr4A 86.243 189 26 0 2138 2326 138418991 138419179 4.740000e-49 206


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 TraesCS1A01G129100 chr1A 163381278 163384900 3622 True 6691 6691 100.000 1 3623 1 chr1A.!!$R1 3622
1 TraesCS1A01G129100 chr1D 134681293 134684134 2841 False 4252 4252 93.685 1 2854 1 chr1D.!!$F1 2853
2 TraesCS1A01G129100 chr1B 201774576 201777161 2585 False 1969 3306 93.720 220 2853 2 chr1B.!!$F3 2633
3 TraesCS1A01G129100 chr7B 72304253 72305022 769 True 1064 1064 91.772 2851 3623 1 chr7B.!!$R1 772
4 TraesCS1A01G129100 chr4B 510386003 510386769 766 False 998 998 90.343 2854 3623 1 chr4B.!!$F1 769
5 TraesCS1A01G129100 chr6A 23449182 23449952 770 True 966 966 89.520 2851 3623 1 chr6A.!!$R1 772
6 TraesCS1A01G129100 chr6A 143073650 143074173 523 False 353 353 79.599 2851 3380 1 chr6A.!!$F1 529
7 TraesCS1A01G129100 chr5B 384367048 384367811 763 True 784 784 85.478 2853 3620 1 chr5B.!!$R1 767
8 TraesCS1A01G129100 chr5A 650515802 650516324 522 True 363 363 79.927 2851 3380 1 chr5A.!!$R1 529
9 TraesCS1A01G129100 chr5D 388601321 388601986 665 True 412 412 78.674 2851 3518 1 chr5D.!!$R1 667

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
407 408 0.033642 GCGTTAGCTACATCCTCCCC 59.966 60.000 0.0 0.0 41.01 4.81 F
884 906 0.108396 GCCCAGCCCACAAACATTTT 59.892 50.000 0.0 0.0 0.00 1.82 F
1376 1432 1.229400 AGGGAACAGGAAGGCCGTA 60.229 57.895 0.0 0.0 39.96 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 1704 1.020437 GGCATGCTCTCTGGTAAAGC 58.980 55.0 18.92 0.00 36.56 3.51 R
2029 2094 1.252175 TGGCATTTTGCTAGGCGAAA 58.748 45.0 7.29 7.29 44.56 3.46 R
2950 3019 0.541392 ATGAACTACAGCCCATCGCA 59.459 50.0 0.00 0.00 41.38 5.10 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
106 107 1.227823 TGTTGGGTCGCAACCTCTG 60.228 57.895 25.02 0.00 45.66 3.35
138 139 2.156917 ACGACCACGAACATCTCTACA 58.843 47.619 0.00 0.00 42.66 2.74
159 160 0.399075 CGACCACAACCTTTACCCCT 59.601 55.000 0.00 0.00 0.00 4.79
162 163 2.107726 GACCACAACCTTTACCCCTCTT 59.892 50.000 0.00 0.00 0.00 2.85
163 164 2.158519 ACCACAACCTTTACCCCTCTTG 60.159 50.000 0.00 0.00 0.00 3.02
164 165 1.886542 CACAACCTTTACCCCTCTTGC 59.113 52.381 0.00 0.00 0.00 4.01
165 166 1.497286 ACAACCTTTACCCCTCTTGCA 59.503 47.619 0.00 0.00 0.00 4.08
167 168 2.755103 CAACCTTTACCCCTCTTGCATC 59.245 50.000 0.00 0.00 0.00 3.91
206 207 1.001378 GCTTGCTCAAAACACGACCAT 60.001 47.619 0.00 0.00 0.00 3.55
253 254 2.107041 CTTCGTGCCACCCACTGGTA 62.107 60.000 0.00 0.00 45.57 3.25
310 311 2.123854 TCCCTCCATCCTCGACCG 60.124 66.667 0.00 0.00 0.00 4.79
345 346 1.135915 GCCACAACATCAACAACCACA 59.864 47.619 0.00 0.00 0.00 4.17
364 365 2.027192 ACAATATGCTTGACCACCGTCT 60.027 45.455 0.00 0.00 39.94 4.18
407 408 0.033642 GCGTTAGCTACATCCTCCCC 59.966 60.000 0.00 0.00 41.01 4.81
436 437 0.398318 ACTGGCTTCCTTGACCACTC 59.602 55.000 0.00 0.00 0.00 3.51
445 446 1.609061 CCTTGACCACTCGCTCAATGT 60.609 52.381 0.00 0.00 0.00 2.71
464 465 2.289631 TGTCAGCAACTTCCACGATGAT 60.290 45.455 0.00 0.00 0.00 2.45
481 482 7.147976 CACGATGATATCTAAGGTCATTCACA 58.852 38.462 3.98 0.00 33.03 3.58
501 502 3.854669 CCTGCCGCTACTCCTGGG 61.855 72.222 0.00 0.00 0.00 4.45
540 541 3.055819 ACACTGACATCGTCATTAGCCTT 60.056 43.478 0.00 0.00 41.94 4.35
549 550 1.207329 GTCATTAGCCTTCCCGTCACT 59.793 52.381 0.00 0.00 0.00 3.41
550 551 1.906574 TCATTAGCCTTCCCGTCACTT 59.093 47.619 0.00 0.00 0.00 3.16
558 559 1.052124 TTCCCGTCACTTGTCACCCT 61.052 55.000 0.00 0.00 0.00 4.34
663 666 5.010922 TGCCTGTTTAAGCAATGACAGAAAT 59.989 36.000 10.63 0.00 41.46 2.17
732 752 9.128107 GTTTTGCATCATAATTTATCCCGTATG 57.872 33.333 0.00 0.00 0.00 2.39
781 802 5.633830 AATAATATTTGGATCAGCGGCAG 57.366 39.130 1.45 0.00 0.00 4.85
809 830 4.216042 TGAGCACATACACAGTCCATTTTG 59.784 41.667 0.00 0.00 0.00 2.44
862 884 2.202756 GGCCTTCTGTACCGAGCG 60.203 66.667 0.00 0.00 0.00 5.03
881 903 2.604382 GGCCCAGCCCACAAACAT 60.604 61.111 0.00 0.00 44.06 2.71
882 904 2.216331 GGCCCAGCCCACAAACATT 61.216 57.895 0.00 0.00 44.06 2.71
883 905 1.754107 GCCCAGCCCACAAACATTT 59.246 52.632 0.00 0.00 0.00 2.32
884 906 0.108396 GCCCAGCCCACAAACATTTT 59.892 50.000 0.00 0.00 0.00 1.82
885 907 1.881591 CCCAGCCCACAAACATTTTG 58.118 50.000 0.00 0.00 0.00 2.44
886 908 1.542987 CCCAGCCCACAAACATTTTGG 60.543 52.381 3.82 1.32 0.00 3.28
893 915 4.622260 CCACAAACATTTTGGGATTCCT 57.378 40.909 2.01 0.00 0.00 3.36
894 916 4.971939 CCACAAACATTTTGGGATTCCTT 58.028 39.130 2.01 0.00 0.00 3.36
977 1033 2.760385 CCCCTCGACCTCCCTCAC 60.760 72.222 0.00 0.00 0.00 3.51
1082 1138 2.101575 CGTCGCGCAGGTAGCTAA 59.898 61.111 8.75 0.00 42.61 3.09
1376 1432 1.229400 AGGGAACAGGAAGGCCGTA 60.229 57.895 0.00 0.00 39.96 4.02
1496 1552 5.716228 TGAATTGCCATTCACCTTGTTAGAT 59.284 36.000 9.05 0.00 43.32 1.98
1522 1578 5.997746 CCTTTCCTTTGAGAACAGTGTGATA 59.002 40.000 0.00 0.00 0.00 2.15
1524 1580 7.824289 CCTTTCCTTTGAGAACAGTGTGATATA 59.176 37.037 0.00 0.00 0.00 0.86
1525 1581 8.547967 TTTCCTTTGAGAACAGTGTGATATAC 57.452 34.615 0.00 0.00 0.00 1.47
1645 1704 5.358442 CCCCTACAGCTATAGCAGTATACTG 59.642 48.000 24.91 25.68 41.17 2.74
1715 1774 1.618343 TGCACTACACTCTGCTGCTAA 59.382 47.619 0.00 0.00 34.29 3.09
1718 1777 3.124297 GCACTACACTCTGCTGCTAAAAG 59.876 47.826 0.00 0.00 0.00 2.27
1755 1814 2.886523 CTGTGTGTGGAATGTTCACCAT 59.113 45.455 0.00 0.00 38.48 3.55
1768 1827 5.692115 TGTTCACCATTATGCTTCCTAGA 57.308 39.130 0.00 0.00 0.00 2.43
1833 1892 6.400727 CCGTTTGGAAGAGTTGTATTTACTCG 60.401 42.308 0.00 0.00 41.53 4.18
1877 1936 3.297134 TTTCCTTCTTTGTCAGGTGCT 57.703 42.857 0.00 0.00 0.00 4.40
1897 1956 7.394359 AGGTGCTATTTACAATGTTTGTCATCT 59.606 33.333 0.00 0.00 44.12 2.90
1939 1998 6.752815 TGGTTTAAAGTCGAATTTGGTTGTTC 59.247 34.615 20.25 4.91 0.00 3.18
1986 2045 7.864108 TTATTGTATTCATGTCACTTCCCTG 57.136 36.000 0.00 0.00 0.00 4.45
1987 2046 3.609853 TGTATTCATGTCACTTCCCTGC 58.390 45.455 0.00 0.00 0.00 4.85
1999 2058 3.055963 CACTTCCCTGCAATTGCCAAATA 60.056 43.478 26.94 7.59 41.18 1.40
2029 2094 6.931281 TCTGTTCGAGAAATTTCTTCATGTCT 59.069 34.615 21.33 0.00 37.73 3.41
2051 2116 1.067915 TCGCCTAGCAAAATGCCAAAC 60.068 47.619 0.00 0.00 46.52 2.93
2137 2202 4.002982 TGTGGTTGACTATGACTCAATGC 58.997 43.478 0.00 0.00 30.46 3.56
2217 2282 1.180456 TTGTTCGCCCTCGTACCAGA 61.180 55.000 0.00 0.00 35.51 3.86
2441 2506 6.834876 TCTTCTGAATTGATCAACATTGACG 58.165 36.000 11.07 5.57 40.49 4.35
2444 2509 4.725359 TGAATTGATCAACATTGACGCTG 58.275 39.130 11.07 0.00 40.49 5.18
2514 2579 0.250234 TGCAGATCTTCTTGGACCCG 59.750 55.000 0.00 0.00 0.00 5.28
2631 2696 4.191544 CCGAAACTGCTTGAAGATCCATA 58.808 43.478 0.00 0.00 0.00 2.74
2634 2699 6.183360 CCGAAACTGCTTGAAGATCCATATTT 60.183 38.462 0.00 0.00 0.00 1.40
2698 2763 1.268743 GCTTGCTTGAGCTCGTTGTTT 60.269 47.619 9.64 0.00 42.66 2.83
2727 2792 9.071221 CGGATCATGTATTCGAAAAATCAAAAA 57.929 29.630 0.00 0.00 39.08 1.94
2775 2840 7.948278 ATATTTGCTAGTTCGAGATGGTAAC 57.052 36.000 0.00 0.00 0.00 2.50
2823 2888 9.458374 GAGCTTTAAATTAAGTTGCACTTGTTA 57.542 29.630 10.59 5.34 39.11 2.41
2840 2905 7.381079 CACTTGTTATATTTACGTGACGAGTG 58.619 38.462 13.70 6.32 40.84 3.51
2901 2966 6.779860 TCCATACTTCTAAAAACTTCTGCCT 58.220 36.000 0.00 0.00 0.00 4.75
2950 3019 4.154918 CACGAAGCTAAAATTCAGGAAGCT 59.845 41.667 0.00 0.00 45.12 3.74
2999 3070 1.346068 GCGATAGATTCCCAGCTTCCT 59.654 52.381 0.00 0.00 39.76 3.36
3011 3082 2.554032 CCAGCTTCCTGTTTTCGTGAAT 59.446 45.455 0.00 0.00 37.38 2.57
3012 3083 3.365364 CCAGCTTCCTGTTTTCGTGAATC 60.365 47.826 0.00 0.00 37.38 2.52
3013 3084 3.499918 CAGCTTCCTGTTTTCGTGAATCT 59.500 43.478 0.00 0.00 34.31 2.40
3014 3085 3.499918 AGCTTCCTGTTTTCGTGAATCTG 59.500 43.478 0.00 0.00 0.00 2.90
3015 3086 3.498397 GCTTCCTGTTTTCGTGAATCTGA 59.502 43.478 0.00 0.00 0.00 3.27
3016 3087 4.024048 GCTTCCTGTTTTCGTGAATCTGAA 60.024 41.667 0.00 0.00 0.00 3.02
3017 3088 5.673337 TTCCTGTTTTCGTGAATCTGAAG 57.327 39.130 0.00 0.00 0.00 3.02
3018 3089 3.498397 TCCTGTTTTCGTGAATCTGAAGC 59.502 43.478 0.00 0.00 0.00 3.86
3019 3090 3.499918 CCTGTTTTCGTGAATCTGAAGCT 59.500 43.478 0.00 0.00 0.00 3.74
3020 3091 4.461405 CTGTTTTCGTGAATCTGAAGCTG 58.539 43.478 0.00 0.00 0.00 4.24
3021 3092 3.876914 TGTTTTCGTGAATCTGAAGCTGT 59.123 39.130 0.00 0.00 0.00 4.40
3022 3093 4.335315 TGTTTTCGTGAATCTGAAGCTGTT 59.665 37.500 0.00 0.00 0.00 3.16
3023 3094 5.163663 TGTTTTCGTGAATCTGAAGCTGTTT 60.164 36.000 0.00 0.00 0.00 2.83
3024 3095 5.499139 TTTCGTGAATCTGAAGCTGTTTT 57.501 34.783 0.00 0.00 0.00 2.43
3025 3096 4.732285 TCGTGAATCTGAAGCTGTTTTC 57.268 40.909 0.00 0.00 0.00 2.29
3026 3097 3.184379 TCGTGAATCTGAAGCTGTTTTCG 59.816 43.478 0.00 0.00 0.00 3.46
3027 3098 3.059597 CGTGAATCTGAAGCTGTTTTCGT 60.060 43.478 0.00 0.00 0.00 3.85
3028 3099 4.214437 GTGAATCTGAAGCTGTTTTCGTG 58.786 43.478 0.00 0.00 0.00 4.35
3029 3100 4.024893 GTGAATCTGAAGCTGTTTTCGTGA 60.025 41.667 0.00 0.00 0.00 4.35
3030 3101 4.574421 TGAATCTGAAGCTGTTTTCGTGAA 59.426 37.500 0.00 0.00 0.00 3.18
3092 3166 3.750639 AGAAAAACGTTTCGCTCAACA 57.249 38.095 15.01 0.00 46.56 3.33
3223 3327 5.465390 CCAAATCGTTGACTCAACTACAGAA 59.535 40.000 17.81 0.17 41.62 3.02
3231 3335 1.005394 CAACTACAGAACCGGCCGT 60.005 57.895 26.12 6.07 0.00 5.68
3376 3481 2.118513 AGGAGTGGCACGAGGACT 59.881 61.111 12.71 4.48 0.00 3.85
3382 3487 3.755628 GGCACGAGGACTACCGCA 61.756 66.667 0.00 0.00 41.83 5.69
3519 3627 4.566545 TGTTGTGTGCAAATTCCTACAG 57.433 40.909 0.00 0.00 36.22 2.74
3521 3629 5.126779 TGTTGTGTGCAAATTCCTACAGTA 58.873 37.500 0.00 0.00 36.22 2.74
3531 3639 7.769044 TGCAAATTCCTACAGTAGAACCTATTC 59.231 37.037 9.38 0.00 34.78 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.680786 CGAGGGGACGTGAGCACA 61.681 66.667 0.00 0.00 0.00 4.57
20 21 2.066393 AATGCTGCTAGCGAGGGGA 61.066 57.895 10.77 1.92 46.26 4.81
100 101 2.972505 CGCCGCAAACACAGAGGT 60.973 61.111 0.00 0.00 0.00 3.85
106 107 4.364409 GGTCGTCGCCGCAAACAC 62.364 66.667 0.00 0.00 0.00 3.32
138 139 0.109153 GGGTAAAGGTTGTGGTCGGT 59.891 55.000 0.00 0.00 0.00 4.69
159 160 1.446099 GACGTCGCCTGATGCAAGA 60.446 57.895 0.00 0.00 41.33 3.02
162 163 2.027073 GTTGACGTCGCCTGATGCA 61.027 57.895 11.62 0.00 41.33 3.96
163 164 1.687494 GAGTTGACGTCGCCTGATGC 61.687 60.000 11.62 0.00 34.28 3.91
164 165 1.078759 GGAGTTGACGTCGCCTGATG 61.079 60.000 11.62 0.00 37.15 3.07
165 166 1.215647 GGAGTTGACGTCGCCTGAT 59.784 57.895 11.62 0.00 0.00 2.90
167 168 2.805353 CGGAGTTGACGTCGCCTG 60.805 66.667 11.62 1.13 0.00 4.85
253 254 2.376109 CTTGGAAGAAGGCATGCTGAT 58.624 47.619 18.92 3.71 0.00 2.90
345 346 2.027192 ACAGACGGTGGTCAAGCATATT 60.027 45.455 0.00 0.00 45.92 1.28
364 365 2.291209 TCGAGTACACACCCCTTACA 57.709 50.000 0.00 0.00 0.00 2.41
407 408 1.556911 AGGAAGCCAGTATGACCACTG 59.443 52.381 0.00 0.00 44.60 3.66
436 437 1.135859 GGAAGTTGCTGACATTGAGCG 60.136 52.381 0.00 0.00 39.47 5.03
445 446 2.768253 ATCATCGTGGAAGTTGCTGA 57.232 45.000 0.00 0.00 0.00 4.26
464 465 5.614308 CAGGCATGTGAATGACCTTAGATA 58.386 41.667 0.00 0.00 0.00 1.98
540 541 1.052124 AAGGGTGACAAGTGACGGGA 61.052 55.000 0.00 0.00 0.00 5.14
600 603 7.049133 CCCATGATTGATTTGCTTTATTGGAA 58.951 34.615 0.00 0.00 0.00 3.53
703 723 6.642131 CGGGATAAATTATGATGCAAAACAGG 59.358 38.462 0.00 0.00 0.00 4.00
788 809 4.144297 ACAAAATGGACTGTGTATGTGCT 58.856 39.130 0.00 0.00 0.00 4.40
878 900 7.226059 AGGTCTATAAGGAATCCCAAAATGT 57.774 36.000 0.00 0.00 33.88 2.71
885 907 9.819267 CGATTTTATAGGTCTATAAGGAATCCC 57.181 37.037 18.16 0.00 38.70 3.85
894 916 9.986157 AGTGGGATACGATTTTATAGGTCTATA 57.014 33.333 0.00 0.00 37.60 1.31
1082 1138 1.004979 ACGTGAGACTAGAGGGCTTCT 59.995 52.381 4.03 4.03 40.06 2.85
1093 1149 0.747255 AACAGCAGTGACGTGAGACT 59.253 50.000 0.00 0.00 0.00 3.24
1356 1412 2.895424 CGGCCTTCCTGTTCCCTGT 61.895 63.158 0.00 0.00 0.00 4.00
1496 1552 4.640201 CACACTGTTCTCAAAGGAAAGGAA 59.360 41.667 0.00 0.00 0.00 3.36
1524 1580 8.982723 ACTCCTATGTGAAATACTGATTACTGT 58.017 33.333 0.00 0.00 0.00 3.55
1555 1614 1.741706 CGGACTAGCGAACTTACTCCA 59.258 52.381 0.00 0.00 0.00 3.86
1645 1704 1.020437 GGCATGCTCTCTGGTAAAGC 58.980 55.000 18.92 0.00 36.56 3.51
1715 1774 4.870426 CACAGAGGTATCGCATTGTACTTT 59.130 41.667 0.00 0.00 0.00 2.66
1718 1777 3.551890 CACACAGAGGTATCGCATTGTAC 59.448 47.826 0.00 0.00 0.00 2.90
1768 1827 5.511363 AGAGTACAGCATCCTAGTTGTAGT 58.489 41.667 0.00 0.00 40.22 2.73
1849 1908 8.413229 CACCTGACAAAGAAGGAAATAAGAAAA 58.587 33.333 0.00 0.00 37.01 2.29
1986 2045 6.197096 CGAACAGAGTATTATTTGGCAATTGC 59.803 38.462 22.47 22.47 41.14 3.56
1987 2046 7.471721 TCGAACAGAGTATTATTTGGCAATTG 58.528 34.615 0.00 0.00 0.00 2.32
1999 2058 8.833231 TGAAGAAATTTCTCGAACAGAGTATT 57.167 30.769 20.71 0.62 46.86 1.89
2029 2094 1.252175 TGGCATTTTGCTAGGCGAAA 58.748 45.000 7.29 7.29 44.56 3.46
2137 2202 5.288015 TGTTGCAACAATAACAACATCCTG 58.712 37.500 29.36 0.00 46.33 3.86
2217 2282 2.571212 TCATGAACAGCGGTCAAAGTT 58.429 42.857 0.00 0.00 0.00 2.66
2422 2487 4.216042 ACAGCGTCAATGTTGATCAATTCA 59.784 37.500 12.12 6.31 39.73 2.57
2472 2537 6.292114 GCAACAACACCAGTAAAATAAACAGC 60.292 38.462 0.00 0.00 0.00 4.40
2514 2579 1.668751 TCTGTGTTGTTGCGTTCCTTC 59.331 47.619 0.00 0.00 0.00 3.46
2631 2696 6.100134 ACAAGAGGGCCAATATGCAAATAAAT 59.900 34.615 6.18 0.00 0.00 1.40
2634 2699 4.545678 ACAAGAGGGCCAATATGCAAATA 58.454 39.130 6.18 0.00 0.00 1.40
2698 2763 6.983890 TGATTTTTCGAATACATGATCCGAGA 59.016 34.615 0.00 0.00 0.00 4.04
2727 2792 4.443978 AGGTTTGGCATCACAGCTATAT 57.556 40.909 0.00 0.00 30.63 0.86
2775 2840 6.291269 GCTCAAAATTCAACACTTTTCACTCG 60.291 38.462 0.00 0.00 0.00 4.18
2823 2888 5.571741 CAGTGTTCACTCGTCACGTAAATAT 59.428 40.000 0.00 0.00 37.20 1.28
2827 2892 2.355444 TCAGTGTTCACTCGTCACGTAA 59.645 45.455 0.00 0.00 37.20 3.18
2830 2895 1.268589 ACTCAGTGTTCACTCGTCACG 60.269 52.381 2.22 0.00 37.20 4.35
2840 2905 1.348036 ACAGGCCCTAACTCAGTGTTC 59.652 52.381 0.00 0.00 39.89 3.18
2901 2966 4.697756 CCGTTCGGGCTGCCTTCA 62.698 66.667 19.68 0.00 0.00 3.02
2906 2971 2.534903 GCTAATCCGTTCGGGCTGC 61.535 63.158 11.37 7.37 34.94 5.25
2950 3019 0.541392 ATGAACTACAGCCCATCGCA 59.459 50.000 0.00 0.00 41.38 5.10
2983 3054 4.589908 GAAAACAGGAAGCTGGGAATCTA 58.410 43.478 0.00 0.00 0.00 1.98
2999 3070 3.876914 ACAGCTTCAGATTCACGAAAACA 59.123 39.130 0.00 0.00 0.00 2.83
3011 3082 4.212004 CAGATTCACGAAAACAGCTTCAGA 59.788 41.667 0.00 0.00 0.00 3.27
3012 3083 4.212004 TCAGATTCACGAAAACAGCTTCAG 59.788 41.667 0.00 0.00 0.00 3.02
3013 3084 4.126437 TCAGATTCACGAAAACAGCTTCA 58.874 39.130 0.00 0.00 0.00 3.02
3014 3085 4.732285 TCAGATTCACGAAAACAGCTTC 57.268 40.909 0.00 0.00 0.00 3.86
3015 3086 4.555511 GCTTCAGATTCACGAAAACAGCTT 60.556 41.667 0.00 0.00 0.00 3.74
3016 3087 3.058639 GCTTCAGATTCACGAAAACAGCT 60.059 43.478 0.00 0.00 0.00 4.24
3017 3088 3.058639 AGCTTCAGATTCACGAAAACAGC 60.059 43.478 0.00 0.00 0.00 4.40
3018 3089 4.461405 CAGCTTCAGATTCACGAAAACAG 58.539 43.478 0.00 0.00 0.00 3.16
3019 3090 3.303990 GCAGCTTCAGATTCACGAAAACA 60.304 43.478 0.00 0.00 0.00 2.83
3020 3091 3.058639 AGCAGCTTCAGATTCACGAAAAC 60.059 43.478 0.00 0.00 0.00 2.43
3021 3092 3.141398 AGCAGCTTCAGATTCACGAAAA 58.859 40.909 0.00 0.00 0.00 2.29
3022 3093 2.771089 AGCAGCTTCAGATTCACGAAA 58.229 42.857 0.00 0.00 0.00 3.46
3023 3094 2.462456 AGCAGCTTCAGATTCACGAA 57.538 45.000 0.00 0.00 0.00 3.85
3024 3095 2.071540 CAAGCAGCTTCAGATTCACGA 58.928 47.619 4.07 0.00 0.00 4.35
3025 3096 1.802960 ACAAGCAGCTTCAGATTCACG 59.197 47.619 4.07 0.00 0.00 4.35
3026 3097 3.911661 AACAAGCAGCTTCAGATTCAC 57.088 42.857 4.07 0.00 0.00 3.18
3027 3098 6.579666 AAATAACAAGCAGCTTCAGATTCA 57.420 33.333 4.07 0.00 0.00 2.57
3028 3099 6.684555 CGTAAATAACAAGCAGCTTCAGATTC 59.315 38.462 4.07 0.00 0.00 2.52
3029 3100 6.403636 CCGTAAATAACAAGCAGCTTCAGATT 60.404 38.462 4.07 2.02 0.00 2.40
3030 3101 5.065218 CCGTAAATAACAAGCAGCTTCAGAT 59.935 40.000 4.07 0.00 0.00 2.90
3223 3327 3.674050 ATAGACTGGGACGGCCGGT 62.674 63.158 31.76 17.59 39.14 5.28
3231 3335 1.682451 CGGCGGGAAATAGACTGGGA 61.682 60.000 0.00 0.00 0.00 4.37
3370 3475 1.255667 TTGGAGGTGCGGTAGTCCTC 61.256 60.000 0.00 0.00 44.78 3.71
3376 3481 0.906066 TTATGCTTGGAGGTGCGGTA 59.094 50.000 0.00 0.00 0.00 4.02
3519 3627 6.554334 TGCACAACAAAGAATAGGTTCTAC 57.446 37.500 0.00 0.00 43.80 2.59
3521 3629 6.463995 TTTGCACAACAAAGAATAGGTTCT 57.536 33.333 0.00 0.00 46.50 3.01
3598 3709 0.911525 AGCACTCATGGCAGTACCCT 60.912 55.000 0.00 0.00 37.83 4.34


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

AutoCloner maintained by Alex Coulton.