Multiple sequence alignment - TraesCS1B01G387500

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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 TraesCS1B01G387500 chr1B 100.000 3223 0 0 1 3223 621948601 621945379 0.000000e+00 5952
1 TraesCS1B01G387500 chr1B 76.060 1061 231 19 1147 2194 130010125 130011175 6.120000e-147 531
2 TraesCS1B01G387500 chr1A 91.884 3228 240 13 1 3223 546504805 546501595 0.000000e+00 4490
3 TraesCS1B01G387500 chr1D 93.467 2801 173 9 235 3029 451942063 451939267 0.000000e+00 4150
4 TraesCS1B01G387500 chr1D 76.635 1040 222 19 1147 2174 79115821 79116851 3.630000e-154 555
5 TraesCS1B01G387500 chr1D 92.965 199 12 2 3025 3223 451884622 451884426 4.070000e-74 289
6 TraesCS1B01G387500 chr1D 93.023 172 10 2 2 172 451942237 451942067 1.920000e-62 250
7 TraesCS1B01G387500 chr6D 84.142 618 80 10 1360 1976 361520411 361521011 1.670000e-162 582
8 TraesCS1B01G387500 chr6B 83.254 633 85 11 1360 1991 543213231 543213843 2.170000e-156 562
9 TraesCS1B01G387500 chr6A 82.808 634 89 11 1360 1991 502671532 502672147 1.690000e-152 549
10 TraesCS1B01G387500 chr4A 74.194 589 136 10 1587 2173 726576664 726576090 6.950000e-57 231
11 TraesCS1B01G387500 chr7D 73.544 601 129 20 1582 2173 11261486 11262065 5.450000e-48 202
12 TraesCS1B01G387500 chr7A 73.640 478 98 19 1582 2051 10380939 10381396 3.330000e-35 159


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 TraesCS1B01G387500 chr1B 621945379 621948601 3222 True 5952 5952 100.000 1 3223 1 chr1B.!!$R1 3222
1 TraesCS1B01G387500 chr1B 130010125 130011175 1050 False 531 531 76.060 1147 2194 1 chr1B.!!$F1 1047
2 TraesCS1B01G387500 chr1A 546501595 546504805 3210 True 4490 4490 91.884 1 3223 1 chr1A.!!$R1 3222
3 TraesCS1B01G387500 chr1D 451939267 451942237 2970 True 2200 4150 93.245 2 3029 2 chr1D.!!$R2 3027
4 TraesCS1B01G387500 chr1D 79115821 79116851 1030 False 555 555 76.635 1147 2174 1 chr1D.!!$F1 1027
5 TraesCS1B01G387500 chr6D 361520411 361521011 600 False 582 582 84.142 1360 1976 1 chr6D.!!$F1 616
6 TraesCS1B01G387500 chr6B 543213231 543213843 612 False 562 562 83.254 1360 1991 1 chr6B.!!$F1 631
7 TraesCS1B01G387500 chr6A 502671532 502672147 615 False 549 549 82.808 1360 1991 1 chr6A.!!$F1 631
8 TraesCS1B01G387500 chr4A 726576090 726576664 574 True 231 231 74.194 1587 2173 1 chr4A.!!$R1 586
9 TraesCS1B01G387500 chr7D 11261486 11262065 579 False 202 202 73.544 1582 2173 1 chr7D.!!$F1 591

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
947 962 0.036010 CATGCGTCCTTTCCCTCACT 60.036 55.0 0.0 0.0 0.0 3.41 F
1576 1594 0.250124 CCAAGGTGGCAGTAACGACA 60.250 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2093 1.688197 CCCTTCACTTGCCACAACATT 59.312 47.619 0.0 0.0 0.0 2.71 R
3047 3068 2.371841 TGTTCCACTTGCCTCATGTACT 59.628 45.455 0.0 0.0 0.0 2.73 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
33 34 9.275398 CTATGTTATATTAAACCGGTGGCTTTA 57.725 33.333 8.52 0.00 0.00 1.85
103 105 4.840680 TGGACCATCCATCGAAGATCTATT 59.159 41.667 0.00 0.00 42.67 1.73
110 112 3.307975 CCATCGAAGATCTATTGGCCCAT 60.308 47.826 0.00 0.00 45.12 4.00
111 113 3.407424 TCGAAGATCTATTGGCCCATG 57.593 47.619 0.00 0.00 0.00 3.66
116 118 5.376625 GAAGATCTATTGGCCCATGTACAA 58.623 41.667 0.00 0.00 0.00 2.41
183 185 6.162777 AGTAGAGAAACTCTCAAGCACAATC 58.837 40.000 4.51 0.00 45.73 2.67
216 218 1.635663 CGAGATCCAACAACCCACGC 61.636 60.000 0.00 0.00 0.00 5.34
299 301 6.156748 ACACTATTGGGAAACTTTGGAAAC 57.843 37.500 0.00 0.00 0.00 2.78
305 307 6.413783 TTGGGAAACTTTGGAAACTTATCC 57.586 37.500 0.00 0.00 40.10 2.59
317 319 4.142381 GGAAACTTATCCTTGCTCGCAAAT 60.142 41.667 5.77 0.43 36.50 2.32
335 337 5.564651 CGCAAATGACCACTAACTCCAAATT 60.565 40.000 0.00 0.00 0.00 1.82
361 363 4.607235 CGCGAGTGAATTACAAGAAACAAC 59.393 41.667 0.00 0.00 0.00 3.32
424 426 5.186021 TGTTTGACACATAACCACCACTTTT 59.814 36.000 0.00 0.00 0.00 2.27
425 427 5.923733 TTGACACATAACCACCACTTTTT 57.076 34.783 0.00 0.00 0.00 1.94
440 442 7.201875 CCACCACTTTTTAGACAATGGTAAAGT 60.202 37.037 0.00 0.00 38.38 2.66
482 484 1.223187 CGTTGGGACTAAAGCGTGTT 58.777 50.000 0.00 0.00 0.00 3.32
483 485 1.600485 CGTTGGGACTAAAGCGTGTTT 59.400 47.619 0.00 0.00 0.00 2.83
484 486 2.601266 CGTTGGGACTAAAGCGTGTTTG 60.601 50.000 0.00 0.00 0.00 2.93
485 487 1.600023 TGGGACTAAAGCGTGTTTGG 58.400 50.000 0.00 0.00 0.00 3.28
486 488 1.134037 TGGGACTAAAGCGTGTTTGGT 60.134 47.619 1.93 1.93 0.00 3.67
487 489 1.951602 GGGACTAAAGCGTGTTTGGTT 59.048 47.619 3.59 0.00 0.00 3.67
488 490 2.031420 GGGACTAAAGCGTGTTTGGTTC 60.031 50.000 3.59 1.95 0.00 3.62
489 491 2.349155 GGACTAAAGCGTGTTTGGTTCG 60.349 50.000 3.59 0.00 0.00 3.95
490 492 2.540931 GACTAAAGCGTGTTTGGTTCGA 59.459 45.455 3.59 0.00 0.00 3.71
491 493 2.542595 ACTAAAGCGTGTTTGGTTCGAG 59.457 45.455 0.00 0.00 0.00 4.04
492 494 1.658994 AAAGCGTGTTTGGTTCGAGA 58.341 45.000 0.00 0.00 0.00 4.04
493 495 1.658994 AAGCGTGTTTGGTTCGAGAA 58.341 45.000 0.00 0.00 0.00 2.87
502 504 1.803334 TGGTTCGAGAATTTGACCGG 58.197 50.000 0.00 0.00 0.00 5.28
542 556 4.149511 TGGGATAACATTGATTCGCAGA 57.850 40.909 0.00 0.00 0.00 4.26
601 615 1.335496 GGCTAAAGCGTGTTTTGACCA 59.665 47.619 0.00 0.00 43.26 4.02
616 630 6.098124 TGTTTTGACCAAGAATCTGACCATTT 59.902 34.615 0.00 0.00 0.00 2.32
625 639 7.308435 CAAGAATCTGACCATTTGGAGTAAAC 58.692 38.462 3.01 0.00 38.94 2.01
668 682 4.705337 TTGGTGTCTAAAGCGTGTTTTT 57.295 36.364 0.00 0.00 0.00 1.94
712 727 0.602905 GCTAAGGCGTGTGTGACCTT 60.603 55.000 0.00 0.00 45.62 3.50
719 734 2.611971 GGCGTGTGTGACCTTGAATCTA 60.612 50.000 0.00 0.00 0.00 1.98
721 736 3.496884 GCGTGTGTGACCTTGAATCTAAA 59.503 43.478 0.00 0.00 0.00 1.85
734 749 9.495572 ACCTTGAATCTAAAAGTTGAGACTAAG 57.504 33.333 0.00 0.00 34.21 2.18
737 752 7.450074 TGAATCTAAAAGTTGAGACTAAGGCA 58.550 34.615 0.00 0.00 34.21 4.75
746 761 2.301870 TGAGACTAAGGCACATTTCGGT 59.698 45.455 0.00 0.00 0.00 4.69
794 809 9.434420 GTTTATTTTGGGATGACATTGATTGAA 57.566 29.630 0.00 0.00 0.00 2.69
800 815 6.131264 TGGGATGACATTGATTGAAAGCTAT 58.869 36.000 0.00 0.00 0.00 2.97
831 846 9.445786 CATTTCGGGATAACACATAACATTAAC 57.554 33.333 0.00 0.00 0.00 2.01
835 850 8.208224 TCGGGATAACACATAACATTAACTCAT 58.792 33.333 0.00 0.00 0.00 2.90
904 919 2.714793 CCTAAATAGGGGTAGGGTTGGG 59.285 54.545 0.00 0.00 39.86 4.12
947 962 0.036010 CATGCGTCCTTTCCCTCACT 60.036 55.000 0.00 0.00 0.00 3.41
965 980 0.743097 CTAGTAGTGCCACCGTACCC 59.257 60.000 0.00 0.00 0.00 3.69
1047 1062 3.117738 CCCCTACTTTGATGGCTTGAGAT 60.118 47.826 0.00 0.00 0.00 2.75
1063 1078 1.696884 GAGATCAGTTCTCCCCATCCC 59.303 57.143 0.00 0.00 44.46 3.85
1114 1129 1.001631 TCCAATCTCGGAGGAGCCA 59.998 57.895 4.96 0.00 40.26 4.75
1121 1136 1.535444 TCGGAGGAGCCACAAAGGA 60.535 57.895 0.00 0.00 41.22 3.36
1139 1154 1.480954 GGACTAGAATGAGGGCGTCAA 59.519 52.381 14.47 0.00 39.19 3.18
1198 1213 4.157289 CACACTTTCAAGATTGCTGGCTAT 59.843 41.667 0.00 0.00 0.00 2.97
1220 1235 3.567579 CTTCAAAGGGGCCTCGGCA 62.568 63.158 10.51 0.00 44.11 5.69
1243 1258 1.585006 CAGGTACTTGTCGTCCGCT 59.415 57.895 0.00 0.00 34.60 5.52
1249 1264 1.961277 CTTGTCGTCCGCTGCCTTT 60.961 57.895 0.00 0.00 0.00 3.11
1271 1286 0.322322 TGTCGGCGGATACTTTTGGT 59.678 50.000 7.21 0.00 0.00 3.67
1327 1342 2.421529 GGAAAATGGGGACTATGCGTCT 60.422 50.000 0.00 0.00 42.44 4.18
1331 1346 3.685139 ATGGGGACTATGCGTCTATTG 57.315 47.619 0.00 0.00 42.44 1.90
1344 1359 3.304057 GCGTCTATTGCCCTAGATTTTGC 60.304 47.826 0.00 0.00 30.75 3.68
1357 1372 1.537202 GATTTTGCGAGCACCAACTCT 59.463 47.619 0.00 0.00 34.35 3.24
1371 1386 0.251653 AACTCTGAGGTGAGGGCGTA 60.252 55.000 9.85 0.00 38.32 4.42
1381 1396 0.896940 TGAGGGCGTACTTCGAGGTT 60.897 55.000 5.17 0.00 42.86 3.50
1387 1402 2.423538 GGCGTACTTCGAGGTTAGGTTA 59.576 50.000 5.17 0.00 42.86 2.85
1389 1404 3.689346 CGTACTTCGAGGTTAGGTTAGC 58.311 50.000 5.17 0.00 42.86 3.09
1393 1408 2.062971 TCGAGGTTAGGTTAGCCGAT 57.937 50.000 0.00 0.00 40.50 4.18
1430 1445 0.895100 GCCATTGGTGTTGCTCTCCA 60.895 55.000 4.26 0.00 37.84 3.86
1509 1527 1.079405 AACCATCGGTGTACCTGCG 60.079 57.895 0.00 0.00 35.34 5.18
1576 1594 0.250124 CCAAGGTGGCAGTAACGACA 60.250 55.000 0.00 0.00 0.00 4.35
1626 1644 6.887545 CCCTCAGACCTATCTAATAATCTCGT 59.112 42.308 0.00 0.00 32.25 4.18
1654 1672 2.187896 TTAAGGCGGGGGAGGAAACG 62.188 60.000 0.00 0.00 0.00 3.60
2075 2093 9.868160 TTATCACTTCTCCAGATAGAATAGACA 57.132 33.333 0.00 0.00 35.04 3.41
2080 2098 8.986991 ACTTCTCCAGATAGAATAGACAATGTT 58.013 33.333 0.00 0.00 35.04 2.71
2179 2197 1.134848 TCCCGCAAAATTTAGCATGCC 60.135 47.619 15.66 0.00 35.41 4.40
2181 2199 0.922717 CGCAAAATTTAGCATGCCCG 59.077 50.000 15.66 0.00 35.41 6.13
2188 2206 0.679640 TTTAGCATGCCCGTCCTTGG 60.680 55.000 15.66 0.00 0.00 3.61
2194 2212 2.437895 GCCCGTCCTTGGTTAGCC 60.438 66.667 0.00 0.00 0.00 3.93
2225 2243 6.036408 GCTAATGAACATTTGGCTTCCAATTC 59.964 38.462 5.37 2.02 43.55 2.17
2233 2251 2.956132 TGGCTTCCAATTCAGTTTCCA 58.044 42.857 0.00 0.00 0.00 3.53
2374 2392 9.593134 CTACAAGATTGCTACTGTTCTCTAAAT 57.407 33.333 0.00 0.00 0.00 1.40
2543 2562 7.505248 ACTTCTGCAACTCTATCATCAGAGATA 59.495 37.037 7.12 0.00 44.11 1.98
2629 2648 8.833493 TCTATGCAAGATGTCTTTGATATTGTG 58.167 33.333 0.00 0.00 33.11 3.33
2667 2686 8.047310 GGTCGGAATATTGGACAATAGGATATT 58.953 37.037 14.76 1.35 36.79 1.28
2674 2693 7.639062 ATTGGACAATAGGATATTCCAGACT 57.361 36.000 0.00 0.00 39.61 3.24
2679 2698 9.495572 GGACAATAGGATATTCCAGACTAAAAG 57.504 37.037 0.00 0.00 39.61 2.27
2701 2720 9.860898 AAAAGATTCATCAATAGGTAGTTTTGC 57.139 29.630 0.00 0.00 0.00 3.68
2714 2733 6.182627 AGGTAGTTTTGCTTCATCATCATGA 58.817 36.000 0.00 0.00 37.24 3.07
2727 2746 6.481643 TCATCATCATGACATGCCTCATTAT 58.518 36.000 10.76 0.00 33.80 1.28
2757 2776 5.957798 TCTGAAGCAATTCAATAGCCAAAG 58.042 37.500 0.00 0.00 0.00 2.77
2764 2783 5.232838 GCAATTCAATAGCCAAAGCACATAC 59.767 40.000 0.00 0.00 43.56 2.39
2875 2894 8.000709 TCTATATTGAAAGGCCACATGATTTCT 58.999 33.333 5.01 0.00 33.74 2.52
2877 2896 8.716674 ATATTGAAAGGCCACATGATTTCTAT 57.283 30.769 5.01 9.95 33.74 1.98
2900 2919 1.106285 CATCTAAAAGGTGCAGGGGC 58.894 55.000 0.00 0.00 41.68 5.80
2913 2932 1.133356 GCAGGGGCATTAGGAGGATTT 60.133 52.381 0.00 0.00 40.72 2.17
2964 2983 1.843851 GGAATATCTGTCCCCACACCA 59.156 52.381 0.00 0.00 0.00 4.17
2986 3005 5.393461 CCATAGAAGCTCCAAAATCAACACC 60.393 44.000 0.00 0.00 0.00 4.16
3017 3038 8.593492 TCAAATCACCTACATTGAGAATATCG 57.407 34.615 0.00 0.00 0.00 2.92
3062 3083 4.163078 AGAGCAATAGTACATGAGGCAAGT 59.837 41.667 0.00 0.00 0.00 3.16
3074 3095 4.508551 TGAGGCAAGTGGAACATATCAT 57.491 40.909 0.00 0.00 44.52 2.45
3105 3126 6.611381 TGTCATCTGCTATAACTTTTTGCAC 58.389 36.000 0.00 0.00 0.00 4.57
3146 3167 9.369904 TCTTTATTCTTGGCAAAATAATGAAGC 57.630 29.630 22.71 0.00 32.79 3.86
3155 3176 6.071221 TGGCAAAATAATGAAGCTGTGAGAAT 60.071 34.615 0.00 0.00 0.00 2.40
3216 3237 4.970662 AACAATGATGCATCACCACTAC 57.029 40.909 30.92 0.75 40.03 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.739498 AAGCCACCGGTTTAATATAACATAG 57.261 36.000 2.97 0.00 0.00 2.23
8 9 9.624373 TTAAAGCCACCGGTTTAATATAACATA 57.376 29.630 2.97 0.00 43.50 2.29
9 10 8.522542 TTAAAGCCACCGGTTTAATATAACAT 57.477 30.769 2.97 0.00 43.50 2.71
33 34 5.606749 AGGAGGCTAAAAACCCAGAAAATTT 59.393 36.000 0.00 0.00 0.00 1.82
92 94 3.131709 ACATGGGCCAATAGATCTTCG 57.868 47.619 11.89 0.00 0.00 3.79
103 105 3.737559 AGAGAAATTGTACATGGGCCA 57.262 42.857 9.61 9.61 0.00 5.36
183 185 0.399454 ATCTCGAATGGATGGCCTGG 59.601 55.000 3.32 0.00 34.31 4.45
249 251 7.369551 TCTAAGTGGGAAATACGATAATGGT 57.630 36.000 0.00 0.00 0.00 3.55
277 279 6.405278 AGTTTCCAAAGTTTCCCAATAGTG 57.595 37.500 0.00 0.00 0.00 2.74
299 301 3.242870 GGTCATTTGCGAGCAAGGATAAG 60.243 47.826 10.52 0.00 37.24 1.73
305 307 0.877071 AGTGGTCATTTGCGAGCAAG 59.123 50.000 10.52 0.96 44.41 4.01
317 319 4.062293 CGTGAATTTGGAGTTAGTGGTCA 58.938 43.478 0.00 0.00 0.00 4.02
361 363 7.827236 TGGTTTACTGATAATCTAACCTTGTGG 59.173 37.037 0.00 0.00 36.76 4.17
424 426 7.331687 GCCTAAACGTACTTTACCATTGTCTAA 59.668 37.037 0.00 0.00 0.00 2.10
425 427 6.813152 GCCTAAACGTACTTTACCATTGTCTA 59.187 38.462 0.00 0.00 0.00 2.59
440 442 4.023021 GGTCATTTTTGTGGCCTAAACGTA 60.023 41.667 3.32 0.00 40.74 3.57
482 484 2.147958 CCGGTCAAATTCTCGAACCAA 58.852 47.619 0.00 0.00 0.00 3.67
483 485 1.071071 ACCGGTCAAATTCTCGAACCA 59.929 47.619 0.00 0.00 0.00 3.67
484 486 1.463444 CACCGGTCAAATTCTCGAACC 59.537 52.381 2.59 0.00 0.00 3.62
485 487 1.463444 CCACCGGTCAAATTCTCGAAC 59.537 52.381 2.59 0.00 0.00 3.95
486 488 1.609580 CCCACCGGTCAAATTCTCGAA 60.610 52.381 2.59 0.00 0.00 3.71
487 489 0.036765 CCCACCGGTCAAATTCTCGA 60.037 55.000 2.59 0.00 0.00 4.04
488 490 0.036765 TCCCACCGGTCAAATTCTCG 60.037 55.000 2.59 0.00 0.00 4.04
489 491 1.003233 AGTCCCACCGGTCAAATTCTC 59.997 52.381 2.59 0.00 0.00 2.87
490 492 1.064825 AGTCCCACCGGTCAAATTCT 58.935 50.000 2.59 0.00 0.00 2.40
491 493 2.773993 TAGTCCCACCGGTCAAATTC 57.226 50.000 2.59 0.00 0.00 2.17
492 494 3.181437 ACTTTAGTCCCACCGGTCAAATT 60.181 43.478 2.59 0.00 0.00 1.82
493 495 2.374170 ACTTTAGTCCCACCGGTCAAAT 59.626 45.455 2.59 0.00 0.00 2.32
502 504 3.306019 CCCAAAATGCACTTTAGTCCCAC 60.306 47.826 0.00 0.00 0.00 4.61
542 556 5.155643 GTGTTATCCAAAACCGCGTTTTAT 58.844 37.500 15.54 10.95 42.78 1.40
601 615 7.234355 AGTTTACTCCAAATGGTCAGATTCTT 58.766 34.615 0.00 0.00 36.34 2.52
616 630 9.137459 TGTTATCCAAAAATGAAGTTTACTCCA 57.863 29.630 0.00 0.00 0.00 3.86
625 639 9.439500 ACCAATCAATGTTATCCAAAAATGAAG 57.561 29.630 0.00 0.00 0.00 3.02
649 663 3.065648 TCCAAAAACACGCTTTAGACACC 59.934 43.478 0.00 0.00 0.00 4.16
668 682 7.255555 GCCATGAATCAATGTATGTGTTATCCA 60.256 37.037 0.00 0.00 0.00 3.41
712 727 7.387948 GTGCCTTAGTCTCAACTTTTAGATTCA 59.612 37.037 0.00 0.00 36.92 2.57
719 734 6.513393 CGAAATGTGCCTTAGTCTCAACTTTT 60.513 38.462 0.00 0.00 36.92 2.27
721 736 4.452455 CGAAATGTGCCTTAGTCTCAACTT 59.548 41.667 0.00 0.00 36.92 2.66
734 749 1.635663 CCAGACGACCGAAATGTGCC 61.636 60.000 0.00 0.00 0.00 5.01
737 752 1.375523 GGCCAGACGACCGAAATGT 60.376 57.895 0.00 0.00 0.00 2.71
746 761 1.195442 TACACCCAATGGCCAGACGA 61.195 55.000 13.05 0.00 33.59 4.20
794 809 1.070134 TCCCGAAATGCGCTATAGCTT 59.930 47.619 21.98 9.74 39.32 3.74
800 815 2.206750 GTGTTATCCCGAAATGCGCTA 58.793 47.619 9.73 0.00 39.11 4.26
831 846 9.988350 ACAATTAAAACACGCTTTATCTATGAG 57.012 29.630 0.00 0.00 0.00 2.90
852 867 5.717119 AGTACTAACGGTCGATTCACAATT 58.283 37.500 0.00 0.00 0.00 2.32
861 876 2.534298 CTCTCGAGTACTAACGGTCGA 58.466 52.381 13.13 0.00 39.04 4.20
920 935 0.255890 AAAGGACGCATGGCTATGGT 59.744 50.000 12.41 7.94 34.79 3.55
929 944 1.482593 CTAGTGAGGGAAAGGACGCAT 59.517 52.381 0.00 0.00 0.00 4.73
930 945 0.895530 CTAGTGAGGGAAAGGACGCA 59.104 55.000 0.00 0.00 0.00 5.24
947 962 0.684153 GGGGTACGGTGGCACTACTA 60.684 60.000 18.45 1.59 0.00 1.82
974 989 0.748005 ATGGTGATGTTAGGGCGCAC 60.748 55.000 10.83 5.15 0.00 5.34
980 995 2.242196 AGGGGTTGATGGTGATGTTAGG 59.758 50.000 0.00 0.00 0.00 2.69
1047 1062 0.252513 TTCGGGATGGGGAGAACTGA 60.253 55.000 0.00 0.00 0.00 3.41
1063 1078 1.555967 AATTCATGGGGGTGGTTTCG 58.444 50.000 0.00 0.00 0.00 3.46
1114 1129 2.093447 CGCCCTCATTCTAGTCCTTTGT 60.093 50.000 0.00 0.00 0.00 2.83
1121 1136 1.899814 TGTTGACGCCCTCATTCTAGT 59.100 47.619 0.00 0.00 0.00 2.57
1139 1154 1.076024 AGAAGGGGTGCACAATGATGT 59.924 47.619 20.43 0.00 41.61 3.06
1220 1235 1.338769 GGACGACAAGTACCTGCCAAT 60.339 52.381 0.00 0.00 0.00 3.16
1249 1264 2.276201 CAAAAGTATCCGCCGACATCA 58.724 47.619 0.00 0.00 0.00 3.07
1271 1286 1.479323 GTCGGGGTAGTACTCAATGCA 59.521 52.381 0.00 0.00 0.00 3.96
1327 1342 2.878406 GCTCGCAAAATCTAGGGCAATA 59.122 45.455 0.00 0.00 0.00 1.90
1331 1346 0.378610 GTGCTCGCAAAATCTAGGGC 59.621 55.000 0.00 0.00 0.00 5.19
1344 1359 0.668706 CACCTCAGAGTTGGTGCTCG 60.669 60.000 0.00 0.00 45.68 5.03
1357 1372 1.592400 CGAAGTACGCCCTCACCTCA 61.592 60.000 0.00 0.00 34.51 3.86
1371 1386 1.475682 CGGCTAACCTAACCTCGAAGT 59.524 52.381 0.00 0.00 0.00 3.01
1381 1396 1.491668 TGGCTTGATCGGCTAACCTA 58.508 50.000 9.73 0.00 0.00 3.08
1387 1402 1.589716 GCTTGTTGGCTTGATCGGCT 61.590 55.000 9.73 0.00 0.00 5.52
1389 1404 0.169672 CAGCTTGTTGGCTTGATCGG 59.830 55.000 0.00 0.00 41.00 4.18
1393 1408 2.554636 CGGCAGCTTGTTGGCTTGA 61.555 57.895 9.04 0.00 41.00 3.02
1430 1445 5.065988 AGCGAAACACTATCGGCATATTTTT 59.934 36.000 0.00 0.00 40.54 1.94
1435 1450 2.361119 AGAGCGAAACACTATCGGCATA 59.639 45.455 0.00 0.00 40.54 3.14
1509 1527 1.463674 AATCGCAAGGTTGTCATCCC 58.536 50.000 0.00 0.00 40.80 3.85
1576 1594 3.256631 GCACTTGGATGTCAATGGAAGTT 59.743 43.478 0.00 0.00 34.45 2.66
1626 1644 3.644738 CTCCCCCGCCTTAAGTAATTCTA 59.355 47.826 0.97 0.00 0.00 2.10
1654 1672 4.878397 CCTCTAACCTTGAATGTGACATCC 59.122 45.833 0.00 0.00 0.00 3.51
2074 2092 2.546373 CCCTTCACTTGCCACAACATTG 60.546 50.000 0.00 0.00 0.00 2.82
2075 2093 1.688197 CCCTTCACTTGCCACAACATT 59.312 47.619 0.00 0.00 0.00 2.71
2080 2098 1.886222 GCATACCCTTCACTTGCCACA 60.886 52.381 0.00 0.00 0.00 4.17
2151 2169 5.010213 TGCTAAATTTTGCGGGACTTAGTTT 59.990 36.000 17.66 0.00 0.00 2.66
2194 2212 8.025445 GGAAGCCAAATGTTCATTAGCTATATG 58.975 37.037 17.27 2.09 0.00 1.78
2225 2243 6.211587 TGGCAGAAATATCATTGGAAACTG 57.788 37.500 0.00 0.00 0.00 3.16
2233 2251 3.567164 CCGCTCTTGGCAGAAATATCATT 59.433 43.478 0.00 0.00 41.91 2.57
2350 2368 8.854614 AATTTAGAGAACAGTAGCAATCTTGT 57.145 30.769 0.00 0.00 0.00 3.16
2355 2373 9.553064 CCATAGAATTTAGAGAACAGTAGCAAT 57.447 33.333 0.00 0.00 0.00 3.56
2362 2380 9.658799 TCAAAGACCATAGAATTTAGAGAACAG 57.341 33.333 0.00 0.00 0.00 3.16
2424 2443 5.627499 TGATAAATTCAAGGAGCACACAC 57.373 39.130 0.00 0.00 0.00 3.82
2543 2562 6.126536 ACAAATCCTCTCTTGCTCCTATCAAT 60.127 38.462 0.00 0.00 0.00 2.57
2629 2648 6.202954 CCAATATTCCGACCTACTTCAATCAC 59.797 42.308 0.00 0.00 0.00 3.06
2667 2686 8.772250 ACCTATTGATGAATCTTTTAGTCTGGA 58.228 33.333 0.00 0.00 0.00 3.86
2679 2698 8.677300 TGAAGCAAAACTACCTATTGATGAATC 58.323 33.333 0.00 0.00 0.00 2.52
2701 2720 4.134563 TGAGGCATGTCATGATGATGAAG 58.865 43.478 17.24 0.00 40.39 3.02
2714 2733 6.124340 TCAGATTGTGAATAATGAGGCATGT 58.876 36.000 0.00 0.00 29.64 3.21
2727 2746 7.031372 GCTATTGAATTGCTTCAGATTGTGAA 58.969 34.615 4.38 0.00 42.19 3.18
2757 2776 4.502259 CCCAGTCTCTCTATTGGTATGTGC 60.502 50.000 0.00 0.00 0.00 4.57
2790 2809 2.894765 TCACACGTAAGAGATGGGTCAA 59.105 45.455 0.00 0.00 43.62 3.18
2875 2894 5.014123 CCCCTGCACCTTTTAGATGGATATA 59.986 44.000 0.00 0.00 0.00 0.86
2877 2896 3.138283 CCCCTGCACCTTTTAGATGGATA 59.862 47.826 0.00 0.00 0.00 2.59
2900 2919 8.698210 TGAAATCAATTGGAAATCCTCCTAATG 58.302 33.333 5.42 0.00 45.64 1.90
2935 2954 4.956075 GGGGACAGATATTCCAACAACAAT 59.044 41.667 0.00 0.00 34.45 2.71
2938 2957 3.694566 GTGGGGACAGATATTCCAACAAC 59.305 47.826 0.00 0.00 44.46 3.32
2964 2983 5.183904 GTGGTGTTGATTTTGGAGCTTCTAT 59.816 40.000 0.00 0.00 0.00 1.98
2986 3005 6.375174 TCTCAATGTAGGTGATTTGAATGGTG 59.625 38.462 0.00 0.00 0.00 4.17
3047 3068 2.371841 TGTTCCACTTGCCTCATGTACT 59.628 45.455 0.00 0.00 0.00 2.73
3051 3072 4.201657 TGATATGTTCCACTTGCCTCATG 58.798 43.478 0.00 0.00 0.00 3.07
3053 3074 3.998913 TGATATGTTCCACTTGCCTCA 57.001 42.857 0.00 0.00 0.00 3.86
3124 3145 7.760794 CACAGCTTCATTATTTTGCCAAGAATA 59.239 33.333 0.00 0.00 0.00 1.75
3155 3176 8.212995 TGGCATGATGATACTCTTCAAGATAAA 58.787 33.333 0.00 0.00 34.79 1.40
3203 3224 2.831685 AAACTCGTAGTGGTGATGCA 57.168 45.000 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.