Multiple sequence alignment - TraesCS2D01G369900

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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 TraesCS2D01G369900 chr2D 100.000 3368 0 0 1 3368 474510836 474514203 0.000000e+00 6220
1 TraesCS2D01G369900 chr2B 92.264 3322 204 25 1 3310 555383411 555386691 0.000000e+00 4662
2 TraesCS2D01G369900 chr2A 95.567 2662 86 10 523 3170 616991696 616994339 0.000000e+00 4233
3 TraesCS2D01G369900 chr6D 86.310 336 40 5 1501 1833 307517590 307517258 8.880000e-96 361
4 TraesCS2D01G369900 chr6A 85.714 336 42 5 1501 1833 444674675 444674343 1.920000e-92 350
5 TraesCS2D01G369900 chr6A 83.237 173 29 0 1610 1782 535403366 535403194 3.480000e-35 159
6 TraesCS2D01G369900 chr7A 83.333 186 30 1 1598 1783 135689654 135689470 1.610000e-38 171


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 TraesCS2D01G369900 chr2D 474510836 474514203 3367 False 6220 6220 100.000 1 3368 1 chr2D.!!$F1 3367
1 TraesCS2D01G369900 chr2B 555383411 555386691 3280 False 4662 4662 92.264 1 3310 1 chr2B.!!$F1 3309
2 TraesCS2D01G369900 chr2A 616991696 616994339 2643 False 4233 4233 95.567 523 3170 1 chr2A.!!$F1 2647

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
138 139 0.035458 AGCAACTGTAGAGCACACCC 59.965 55.0 0.0 0.0 32.33 4.61 F
409 412 0.042731 TCTCGAAGGAGGGGGTCAAT 59.957 55.0 0.0 0.0 40.85 2.57 F
1890 1905 0.171231 CTTCCTGCTCGTCGTCATCA 59.829 55.0 0.0 0.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1713 1.078759 CATCCTCTGCGGTGTCGAAC 61.079 60.0 0.00 0.0 39.0 3.95 R
2307 2322 0.321671 CTGAAGAAGAGGTTGCCGGA 59.678 55.0 5.05 0.0 0.0 5.14 R
2879 2908 0.541863 AAAGGGCCTGATACTGACCG 59.458 55.0 6.92 0.0 0.0 4.79 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
22 23 3.613193 CGAATAATATCCGGCCTCAACGA 60.613 47.826 0.00 0.00 0.00 3.85
55 56 2.757917 GCGAGGGAGAGGAGCACT 60.758 66.667 0.00 0.00 0.00 4.40
66 67 1.228245 GGAGCACTGCTTCACCCAA 60.228 57.895 4.67 0.00 39.88 4.12
68 69 0.595095 GAGCACTGCTTCACCCAAAG 59.405 55.000 4.67 0.00 39.88 2.77
120 121 2.125512 GGCGCACCTCCACACTAG 60.126 66.667 10.83 0.00 0.00 2.57
123 124 1.005037 CGCACCTCCACACTAGCAA 60.005 57.895 0.00 0.00 0.00 3.91
124 125 1.291877 CGCACCTCCACACTAGCAAC 61.292 60.000 0.00 0.00 0.00 4.17
127 128 1.070758 CACCTCCACACTAGCAACTGT 59.929 52.381 0.00 0.00 0.00 3.55
129 130 2.563179 ACCTCCACACTAGCAACTGTAG 59.437 50.000 0.00 0.00 0.00 2.74
133 134 2.029020 CCACACTAGCAACTGTAGAGCA 60.029 50.000 0.00 0.00 0.00 4.26
138 139 0.035458 AGCAACTGTAGAGCACACCC 59.965 55.000 0.00 0.00 32.33 4.61
141 142 0.317479 AACTGTAGAGCACACCCGAC 59.683 55.000 0.00 0.00 32.33 4.79
151 152 4.203076 CACCCGACCCCGATCGAC 62.203 72.222 18.66 4.19 45.13 4.20
160 161 4.129737 CCGATCGACGTGCAGGGT 62.130 66.667 18.66 0.00 40.78 4.34
161 162 2.880879 CGATCGACGTGCAGGGTG 60.881 66.667 10.26 2.59 37.22 4.61
176 177 4.796231 GTGTCGGATCCGCGTGCT 62.796 66.667 29.62 0.00 39.59 4.40
184 185 1.211818 GATCCGCGTGCTCTCATCAC 61.212 60.000 4.92 0.00 0.00 3.06
193 194 1.065926 TGCTCTCATCACCACACCATC 60.066 52.381 0.00 0.00 0.00 3.51
194 195 1.065926 GCTCTCATCACCACACCATCA 60.066 52.381 0.00 0.00 0.00 3.07
196 197 3.678289 CTCTCATCACCACACCATCAAA 58.322 45.455 0.00 0.00 0.00 2.69
206 207 4.080638 ACCACACCATCAAACAAAAACCAT 60.081 37.500 0.00 0.00 0.00 3.55
208 209 5.114780 CACACCATCAAACAAAAACCATCA 58.885 37.500 0.00 0.00 0.00 3.07
210 211 5.990996 ACACCATCAAACAAAAACCATCATC 59.009 36.000 0.00 0.00 0.00 2.92
212 213 4.091800 CCATCAAACAAAAACCATCATCGC 59.908 41.667 0.00 0.00 0.00 4.58
214 215 4.942852 TCAAACAAAAACCATCATCGCTT 58.057 34.783 0.00 0.00 0.00 4.68
217 218 2.095263 ACAAAAACCATCATCGCTTCCG 60.095 45.455 0.00 0.00 0.00 4.30
233 235 0.683179 TCCGATGACTGTCCGACCAT 60.683 55.000 5.17 0.00 0.00 3.55
234 236 0.249073 CCGATGACTGTCCGACCATC 60.249 60.000 5.17 1.12 33.86 3.51
250 252 4.363999 GACCATCGTATCAACAAGAGAGG 58.636 47.826 0.00 0.00 0.00 3.69
257 259 4.504461 CGTATCAACAAGAGAGGAAATCCG 59.496 45.833 0.00 0.00 42.08 4.18
267 269 2.028020 AGAGGAAATCCGTGACACCTTC 60.028 50.000 0.00 0.00 42.08 3.46
280 283 2.036098 CCTTCAGTGCATGGCCCA 59.964 61.111 0.00 0.00 0.00 5.36
281 284 1.380785 CCTTCAGTGCATGGCCCAT 60.381 57.895 0.00 0.00 0.00 4.00
295 298 1.134946 GGCCCATTGTCATAACAGTGC 59.865 52.381 0.00 0.00 40.69 4.40
297 300 3.278574 GCCCATTGTCATAACAGTGCTA 58.721 45.455 0.00 0.00 40.69 3.49
300 303 3.313526 CCATTGTCATAACAGTGCTAGCC 59.686 47.826 13.29 3.49 40.69 3.93
303 306 1.134788 GTCATAACAGTGCTAGCCGGT 60.135 52.381 13.29 7.68 0.00 5.28
311 314 2.355986 TGCTAGCCGGTGGTAGTGG 61.356 63.158 13.29 0.00 43.11 4.00
315 318 0.542467 TAGCCGGTGGTAGTGGTGAA 60.542 55.000 1.90 0.00 0.00 3.18
320 323 0.613777 GGTGGTAGTGGTGAAGAGGG 59.386 60.000 0.00 0.00 0.00 4.30
321 324 1.640917 GTGGTAGTGGTGAAGAGGGA 58.359 55.000 0.00 0.00 0.00 4.20
327 330 1.713647 AGTGGTGAAGAGGGAGAGAGA 59.286 52.381 0.00 0.00 0.00 3.10
331 334 2.291930 GGTGAAGAGGGAGAGAGAGGAA 60.292 54.545 0.00 0.00 0.00 3.36
337 340 1.119684 GGGAGAGAGAGGAAGAAGGC 58.880 60.000 0.00 0.00 0.00 4.35
339 342 2.091555 GGGAGAGAGAGGAAGAAGGCTA 60.092 54.545 0.00 0.00 0.00 3.93
345 348 2.586357 GGAAGAAGGCTAGCGGCG 60.586 66.667 9.00 0.51 42.94 6.46
370 373 3.344137 TTCCCCCTTGCATCGCCTC 62.344 63.158 0.00 0.00 0.00 4.70
376 379 1.523258 CTTGCATCGCCTCAGAGGG 60.523 63.158 18.83 8.49 35.37 4.30
379 382 1.522580 GCATCGCCTCAGAGGGAAC 60.523 63.158 18.83 7.00 35.37 3.62
393 396 1.516603 GGAACACTAGCGCCGTCTC 60.517 63.158 2.29 0.74 0.00 3.36
406 409 2.416432 CGTCTCGAAGGAGGGGGTC 61.416 68.421 0.00 0.00 40.85 4.46
407 410 1.305046 GTCTCGAAGGAGGGGGTCA 60.305 63.158 0.00 0.00 40.85 4.02
409 412 0.042731 TCTCGAAGGAGGGGGTCAAT 59.957 55.000 0.00 0.00 40.85 2.57
419 422 1.075536 AGGGGGTCAATTCGAGCTTTT 59.924 47.619 0.00 0.00 42.06 2.27
424 427 4.504858 GGGTCAATTCGAGCTTTTCTCTA 58.495 43.478 0.00 0.00 42.06 2.43
448 451 3.647590 ACGGGAGTGGAGTTACCTTTTTA 59.352 43.478 0.00 0.00 44.82 1.52
450 453 5.484998 ACGGGAGTGGAGTTACCTTTTTATA 59.515 40.000 0.00 0.00 44.82 0.98
451 454 6.013466 ACGGGAGTGGAGTTACCTTTTTATAA 60.013 38.462 0.00 0.00 44.82 0.98
453 456 6.827251 GGGAGTGGAGTTACCTTTTTATAAGG 59.173 42.308 0.00 0.00 43.05 2.69
454 457 6.827251 GGAGTGGAGTTACCTTTTTATAAGGG 59.173 42.308 6.42 1.46 41.71 3.95
456 459 5.359009 GTGGAGTTACCTTTTTATAAGGGCC 59.641 44.000 6.42 0.00 41.71 5.80
459 462 2.860817 ACCTTTTTATAAGGGCCCCC 57.139 50.000 21.43 0.00 41.71 5.40
480 483 2.622903 TAGCCGATGAACCTTCGCCG 62.623 60.000 0.00 0.00 35.31 6.46
481 484 2.890474 CCGATGAACCTTCGCCGG 60.890 66.667 0.00 0.00 38.02 6.13
511 514 2.159986 GCATTTGCGAACGTTTTCATGG 60.160 45.455 0.46 0.00 0.00 3.66
512 515 1.482278 TTTGCGAACGTTTTCATGGC 58.518 45.000 0.46 0.53 0.00 4.40
515 518 1.000827 TGCGAACGTTTTCATGGCATT 60.001 42.857 0.46 0.00 0.00 3.56
518 521 3.670991 GCGAACGTTTTCATGGCATTTTA 59.329 39.130 0.46 0.00 0.00 1.52
519 522 4.201485 GCGAACGTTTTCATGGCATTTTAG 60.201 41.667 0.46 0.00 0.00 1.85
520 523 4.915085 CGAACGTTTTCATGGCATTTTAGT 59.085 37.500 0.46 0.00 0.00 2.24
521 524 5.059221 CGAACGTTTTCATGGCATTTTAGTC 59.941 40.000 0.46 0.00 0.00 2.59
541 544 1.470051 GTGTGTGGGGTGACTGTTTT 58.530 50.000 0.00 0.00 0.00 2.43
566 569 9.611284 TTTTCAGAACAACATGATATTTTCTCG 57.389 29.630 0.00 0.00 0.00 4.04
592 595 4.580167 TGAAACCTCAAAACTGTCATCCTG 59.420 41.667 0.00 0.00 0.00 3.86
615 618 4.183865 CCAGAAAATGTCATGTCGCTCTA 58.816 43.478 0.00 0.00 0.00 2.43
654 657 4.318546 CCGACACAACTAAAACTACACAGC 60.319 45.833 0.00 0.00 0.00 4.40
664 667 7.085746 ACTAAAACTACACAGCAAAAACGTTT 58.914 30.769 7.96 7.96 0.00 3.60
683 686 1.452108 GAAATGCCACCCTCTCCCG 60.452 63.158 0.00 0.00 0.00 5.14
711 714 4.399934 ACGGCAACCAAATATAATTTCCGT 59.600 37.500 8.45 8.45 41.10 4.69
712 715 5.105675 ACGGCAACCAAATATAATTTCCGTT 60.106 36.000 8.45 1.09 42.97 4.44
761 764 3.298958 GAGTCCATGCTCGTGGGA 58.701 61.111 8.16 0.00 39.80 4.37
791 795 0.953471 CGACCACGATCTTTTGCCCA 60.953 55.000 0.00 0.00 42.66 5.36
984 988 1.883084 ATTTTCCTAGCGCCGCGAG 60.883 57.895 18.91 12.50 0.00 5.03
1308 1320 1.410004 TCTTCCCCTTCGCGTATGAT 58.590 50.000 5.77 0.00 0.00 2.45
1309 1321 1.068588 TCTTCCCCTTCGCGTATGATG 59.931 52.381 5.77 0.23 0.00 3.07
1310 1322 1.068588 CTTCCCCTTCGCGTATGATGA 59.931 52.381 5.77 0.00 0.00 2.92
1890 1905 0.171231 CTTCCTGCTCGTCGTCATCA 59.829 55.000 0.00 0.00 0.00 3.07
2299 2314 1.218875 GACGTCGGACACAACATGCA 61.219 55.000 9.10 0.00 0.00 3.96
2312 2327 3.187058 ATGCAATGACGTTCCGGC 58.813 55.556 0.00 0.00 34.27 6.13
2324 2339 1.157585 GTTCCGGCAACCTCTTCTTC 58.842 55.000 0.00 0.00 0.00 2.87
2325 2340 0.762418 TTCCGGCAACCTCTTCTTCA 59.238 50.000 0.00 0.00 0.00 3.02
2326 2341 0.321671 TCCGGCAACCTCTTCTTCAG 59.678 55.000 0.00 0.00 0.00 3.02
2399 2417 7.642071 AAACATGCATACACATTCAAAGTTC 57.358 32.000 0.00 0.00 0.00 3.01
2646 2666 5.046529 CAGTCAATCTCTCCTCCATTTACG 58.953 45.833 0.00 0.00 0.00 3.18
2711 2737 7.334171 AGTCTTAAAAGTTTGTTTGCTGCAAAT 59.666 29.630 28.21 13.71 38.00 2.32
2817 2846 9.023962 TGAAACATTCCAGCTATTAATTGTTCT 57.976 29.630 0.00 0.00 0.00 3.01
2879 2908 3.242518 GGTACATTTTCTTGGCTTTCGC 58.757 45.455 0.00 0.00 0.00 4.70
2906 2935 1.341080 ATCAGGCCCTTTGTGTTTGG 58.659 50.000 0.00 0.00 0.00 3.28
2931 2960 7.310237 GGTTAGAGTTCTGAACCAGGTACAATA 60.310 40.741 16.48 0.00 41.93 1.90
2932 2961 6.875972 AGAGTTCTGAACCAGGTACAATAT 57.124 37.500 16.48 0.00 31.51 1.28
3057 3086 2.093973 AGTCGATTGTGCTACTTCTGGG 60.094 50.000 0.00 0.00 0.00 4.45
3058 3087 1.899814 TCGATTGTGCTACTTCTGGGT 59.100 47.619 0.00 0.00 0.00 4.51
3074 3103 1.271871 TGGGTTGATCCATCGTTTGCT 60.272 47.619 0.00 0.00 38.11 3.91
3084 3113 6.483307 TGATCCATCGTTTGCTTATTTCCTAG 59.517 38.462 0.00 0.00 0.00 3.02
3150 3179 5.476091 AGGGCTAGTGATAAGTATTGAGC 57.524 43.478 0.00 0.00 0.00 4.26
3174 3203 2.639347 TCCTCATCTTTTGGTGAGAGCA 59.361 45.455 7.77 0.00 43.50 4.26
3182 3211 5.003804 TCTTTTGGTGAGAGCAATAACTCC 58.996 41.667 0.00 0.00 35.34 3.85
3183 3212 3.350219 TTGGTGAGAGCAATAACTCCC 57.650 47.619 0.00 0.00 37.39 4.30
3198 3227 2.991250 ACTCCCGATTTGGTGAAGATG 58.009 47.619 0.00 0.00 35.15 2.90
3211 3240 1.087501 GAAGATGGCTTTGACGACCC 58.912 55.000 0.00 0.00 33.61 4.46
3228 3257 2.227388 GACCCTTCTGCAAACATGTGAG 59.773 50.000 0.00 0.00 0.00 3.51
3234 3263 5.632347 CCTTCTGCAAACATGTGAGAAATTC 59.368 40.000 0.00 0.00 0.00 2.17
3244 3273 7.219484 ACATGTGAGAAATTCTGGGTTTTAG 57.781 36.000 0.00 0.00 0.00 1.85
3257 3286 7.548196 TCTGGGTTTTAGCAATAGTTATTCG 57.452 36.000 0.00 0.00 0.00 3.34
3260 3289 8.514330 TGGGTTTTAGCAATAGTTATTCGAAT 57.486 30.769 16.15 16.15 0.00 3.34
3310 3339 2.433664 GCGAACCCGACCACGAAT 60.434 61.111 0.00 0.00 42.66 3.34
3311 3340 1.153784 GCGAACCCGACCACGAATA 60.154 57.895 0.00 0.00 42.66 1.75
3312 3341 0.529119 GCGAACCCGACCACGAATAT 60.529 55.000 0.00 0.00 42.66 1.28
3313 3342 1.930567 CGAACCCGACCACGAATATT 58.069 50.000 0.00 0.00 42.66 1.28
3314 3343 1.591158 CGAACCCGACCACGAATATTG 59.409 52.381 0.00 0.00 42.66 1.90
3315 3344 2.736081 CGAACCCGACCACGAATATTGA 60.736 50.000 0.00 0.00 42.66 2.57
3316 3345 3.264104 GAACCCGACCACGAATATTGAA 58.736 45.455 0.00 0.00 42.66 2.69
3317 3346 2.901249 ACCCGACCACGAATATTGAAG 58.099 47.619 0.00 0.00 42.66 3.02
3318 3347 2.210116 CCCGACCACGAATATTGAAGG 58.790 52.381 0.00 0.00 42.66 3.46
3319 3348 2.159014 CCCGACCACGAATATTGAAGGA 60.159 50.000 0.00 0.00 42.66 3.36
3320 3349 2.864343 CCGACCACGAATATTGAAGGAC 59.136 50.000 0.00 0.00 42.66 3.85
3321 3350 3.517602 CGACCACGAATATTGAAGGACA 58.482 45.455 0.00 0.00 42.66 4.02
3322 3351 3.551890 CGACCACGAATATTGAAGGACAG 59.448 47.826 0.00 0.00 42.66 3.51
3323 3352 4.504858 GACCACGAATATTGAAGGACAGT 58.495 43.478 0.00 0.00 0.00 3.55
3324 3353 5.657474 GACCACGAATATTGAAGGACAGTA 58.343 41.667 0.00 0.00 0.00 2.74
3325 3354 6.045072 ACCACGAATATTGAAGGACAGTAA 57.955 37.500 0.00 0.00 0.00 2.24
3326 3355 6.469410 ACCACGAATATTGAAGGACAGTAAA 58.531 36.000 0.00 0.00 0.00 2.01
3327 3356 6.938030 ACCACGAATATTGAAGGACAGTAAAA 59.062 34.615 0.00 0.00 0.00 1.52
3328 3357 7.119262 ACCACGAATATTGAAGGACAGTAAAAG 59.881 37.037 0.00 0.00 0.00 2.27
3329 3358 7.333423 CCACGAATATTGAAGGACAGTAAAAGA 59.667 37.037 0.00 0.00 0.00 2.52
3330 3359 8.883731 CACGAATATTGAAGGACAGTAAAAGAT 58.116 33.333 0.00 0.00 0.00 2.40
3339 3368 9.924650 TGAAGGACAGTAAAAGATAGTCTAAAC 57.075 33.333 0.00 0.00 0.00 2.01
3352 3381 9.495382 AAGATAGTCTAAACTAGATTGGGTTCT 57.505 33.333 0.00 0.00 41.22 3.01
3353 3382 9.138596 AGATAGTCTAAACTAGATTGGGTTCTC 57.861 37.037 0.00 0.00 41.22 2.87
3354 3383 6.210287 AGTCTAAACTAGATTGGGTTCTCG 57.790 41.667 0.00 0.00 37.13 4.04
3355 3384 5.950549 AGTCTAAACTAGATTGGGTTCTCGA 59.049 40.000 0.00 0.00 37.13 4.04
3356 3385 6.436532 AGTCTAAACTAGATTGGGTTCTCGAA 59.563 38.462 0.00 0.00 37.13 3.71
3357 3386 6.752815 GTCTAAACTAGATTGGGTTCTCGAAG 59.247 42.308 0.00 0.00 37.13 3.79
3358 3387 5.740290 AAACTAGATTGGGTTCTCGAAGA 57.260 39.130 0.00 0.00 0.00 2.87
3359 3388 5.941555 AACTAGATTGGGTTCTCGAAGAT 57.058 39.130 0.00 0.00 33.89 2.40
3360 3389 5.269505 ACTAGATTGGGTTCTCGAAGATG 57.730 43.478 0.00 0.00 33.89 2.90
3361 3390 2.911484 AGATTGGGTTCTCGAAGATGC 58.089 47.619 0.00 0.00 33.89 3.91
3362 3391 1.594862 GATTGGGTTCTCGAAGATGCG 59.405 52.381 0.00 0.00 33.89 4.73
3363 3392 1.019278 TTGGGTTCTCGAAGATGCGC 61.019 55.000 0.00 0.00 33.89 6.09
3364 3393 1.447838 GGGTTCTCGAAGATGCGCA 60.448 57.895 14.96 14.96 33.89 6.09
3365 3394 0.811616 GGGTTCTCGAAGATGCGCAT 60.812 55.000 25.66 25.66 33.89 4.73
3366 3395 1.009829 GGTTCTCGAAGATGCGCATT 58.990 50.000 26.12 10.69 33.89 3.56
3367 3396 2.201732 GGTTCTCGAAGATGCGCATTA 58.798 47.619 26.12 7.21 33.89 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.828022 TGTCGTTGAGGCCGGATATT 59.172 50.000 5.05 0.00 0.00 1.28
11 12 2.106683 GGGAATGTCGTTGAGGCCG 61.107 63.158 0.00 0.00 0.00 6.13
19 20 2.926242 ACCACCGGGGAATGTCGT 60.926 61.111 4.41 0.00 41.15 4.34
22 23 4.360405 GCCACCACCGGGGAATGT 62.360 66.667 4.41 0.00 41.15 2.71
55 56 1.228552 GGAGCCTTTGGGTGAAGCA 60.229 57.895 0.00 0.00 31.55 3.91
77 78 0.464036 TAGCTCAATGCCACGGGTAG 59.536 55.000 0.00 0.00 44.23 3.18
120 121 1.291877 CGGGTGTGCTCTACAGTTGC 61.292 60.000 0.00 0.00 40.69 4.17
123 124 1.533469 GGTCGGGTGTGCTCTACAGT 61.533 60.000 0.00 0.00 40.69 3.55
124 125 1.215647 GGTCGGGTGTGCTCTACAG 59.784 63.158 0.00 0.00 40.69 2.74
127 128 2.682494 GGGGTCGGGTGTGCTCTA 60.682 66.667 0.00 0.00 0.00 2.43
133 134 4.746309 TCGATCGGGGTCGGGTGT 62.746 66.667 16.41 0.00 41.74 4.16
141 142 4.873129 CCTGCACGTCGATCGGGG 62.873 72.222 16.41 9.95 43.98 5.73
151 152 2.509336 GATCCGACACCCTGCACG 60.509 66.667 0.00 0.00 0.00 5.34
153 154 3.770040 CGGATCCGACACCCTGCA 61.770 66.667 30.62 0.00 42.83 4.41
160 161 4.492160 GAGCACGCGGATCCGACA 62.492 66.667 37.64 0.00 42.83 4.35
161 162 4.194720 AGAGCACGCGGATCCGAC 62.195 66.667 37.64 25.45 42.83 4.79
176 177 3.181446 TGTTTGATGGTGTGGTGATGAGA 60.181 43.478 0.00 0.00 0.00 3.27
184 185 3.866651 TGGTTTTTGTTTGATGGTGTGG 58.133 40.909 0.00 0.00 0.00 4.17
193 194 4.150451 GGAAGCGATGATGGTTTTTGTTTG 59.850 41.667 0.00 0.00 0.00 2.93
194 195 4.306600 GGAAGCGATGATGGTTTTTGTTT 58.693 39.130 0.00 0.00 0.00 2.83
196 197 2.095263 CGGAAGCGATGATGGTTTTTGT 60.095 45.455 0.00 0.00 0.00 2.83
208 209 0.103208 GGACAGTCATCGGAAGCGAT 59.897 55.000 2.17 0.00 0.00 4.58
210 211 1.874019 CGGACAGTCATCGGAAGCG 60.874 63.158 2.17 0.00 0.00 4.68
212 213 0.179134 GGTCGGACAGTCATCGGAAG 60.179 60.000 10.76 0.00 30.62 3.46
214 215 0.683179 ATGGTCGGACAGTCATCGGA 60.683 55.000 10.76 0.00 0.00 4.55
217 218 0.456221 ACGATGGTCGGACAGTCATC 59.544 55.000 10.76 12.07 45.59 2.92
220 221 1.674441 TGATACGATGGTCGGACAGTC 59.326 52.381 10.76 6.24 45.59 3.51
223 224 1.819903 TGTTGATACGATGGTCGGACA 59.180 47.619 10.76 0.00 45.59 4.02
225 226 2.756207 TCTTGTTGATACGATGGTCGGA 59.244 45.455 4.28 0.00 45.59 4.55
233 235 5.661458 GGATTTCCTCTCTTGTTGATACGA 58.339 41.667 0.00 0.00 0.00 3.43
234 236 4.504461 CGGATTTCCTCTCTTGTTGATACG 59.496 45.833 0.00 0.00 0.00 3.06
250 252 2.480419 CACTGAAGGTGTCACGGATTTC 59.520 50.000 0.00 0.00 40.79 2.17
257 259 0.877071 CCATGCACTGAAGGTGTCAC 59.123 55.000 0.00 0.00 46.86 3.67
267 269 1.252215 TGACAATGGGCCATGCACTG 61.252 55.000 22.01 16.88 30.56 3.66
280 283 3.198068 CGGCTAGCACTGTTATGACAAT 58.802 45.455 18.24 0.00 34.85 2.71
281 284 2.616960 CGGCTAGCACTGTTATGACAA 58.383 47.619 18.24 0.00 34.85 3.18
295 298 0.968901 TCACCACTACCACCGGCTAG 60.969 60.000 0.00 0.00 0.00 3.42
297 300 1.827399 CTTCACCACTACCACCGGCT 61.827 60.000 0.00 0.00 0.00 5.52
300 303 0.246635 CCTCTTCACCACTACCACCG 59.753 60.000 0.00 0.00 0.00 4.94
303 306 1.431633 TCTCCCTCTTCACCACTACCA 59.568 52.381 0.00 0.00 0.00 3.25
311 314 2.818751 TCCTCTCTCTCCCTCTTCAC 57.181 55.000 0.00 0.00 0.00 3.18
315 318 2.244769 CCTTCTTCCTCTCTCTCCCTCT 59.755 54.545 0.00 0.00 0.00 3.69
320 323 2.623416 GCTAGCCTTCTTCCTCTCTCTC 59.377 54.545 2.29 0.00 0.00 3.20
321 324 2.666317 GCTAGCCTTCTTCCTCTCTCT 58.334 52.381 2.29 0.00 0.00 3.10
327 330 2.904131 GCCGCTAGCCTTCTTCCT 59.096 61.111 9.66 0.00 34.35 3.36
331 334 2.833582 TAGCGCCGCTAGCCTTCT 60.834 61.111 15.99 4.02 40.44 2.85
362 365 0.460987 GTGTTCCCTCTGAGGCGATG 60.461 60.000 18.51 4.79 32.73 3.84
364 367 0.039180 TAGTGTTCCCTCTGAGGCGA 59.961 55.000 18.51 13.59 32.73 5.54
370 373 1.153549 GGCGCTAGTGTTCCCTCTG 60.154 63.158 7.64 0.00 0.00 3.35
376 379 1.868251 CGAGACGGCGCTAGTGTTC 60.868 63.158 6.90 7.36 0.00 3.18
379 382 1.583967 CTTCGAGACGGCGCTAGTG 60.584 63.158 6.90 0.00 0.00 2.74
393 396 0.462047 CGAATTGACCCCCTCCTTCG 60.462 60.000 0.00 0.00 30.95 3.79
419 422 0.697079 ACTCCACTCCCGTGTAGAGA 59.303 55.000 5.97 0.00 39.55 3.10
424 427 2.359088 GGTAACTCCACTCCCGTGT 58.641 57.895 0.00 0.00 39.55 4.49
453 456 2.752807 TTCATCGGCTAAGGGGGCC 61.753 63.158 0.00 0.00 45.57 5.80
454 457 1.526225 GTTCATCGGCTAAGGGGGC 60.526 63.158 0.00 0.00 0.00 5.80
456 459 0.546598 AAGGTTCATCGGCTAAGGGG 59.453 55.000 0.00 0.00 0.00 4.79
459 462 0.931005 GCGAAGGTTCATCGGCTAAG 59.069 55.000 0.00 0.00 40.54 2.18
461 464 4.827481 GCGAAGGTTCATCGGCTA 57.173 55.556 0.00 0.00 40.54 3.93
464 467 2.890474 CCGGCGAAGGTTCATCGG 60.890 66.667 9.30 6.41 40.54 4.18
465 468 2.845752 TTCCCGGCGAAGGTTCATCG 62.846 60.000 9.30 0.00 42.99 3.84
467 470 1.078426 CTTCCCGGCGAAGGTTCAT 60.078 57.895 19.42 0.00 43.80 2.57
468 471 2.345991 CTTCCCGGCGAAGGTTCA 59.654 61.111 19.42 0.00 43.80 3.18
480 483 2.981302 GCAAATGCCACCCTTCCC 59.019 61.111 0.00 0.00 34.31 3.97
481 484 1.531739 TTCGCAAATGCCACCCTTCC 61.532 55.000 0.00 0.00 37.91 3.46
486 489 0.596341 AAACGTTCGCAAATGCCACC 60.596 50.000 0.00 0.00 37.91 4.61
511 514 1.199097 CCCCACACACGACTAAAATGC 59.801 52.381 0.00 0.00 0.00 3.56
512 515 2.225491 CACCCCACACACGACTAAAATG 59.775 50.000 0.00 0.00 0.00 2.32
515 518 1.121378 TCACCCCACACACGACTAAA 58.879 50.000 0.00 0.00 0.00 1.85
518 521 1.760875 AGTCACCCCACACACGACT 60.761 57.895 0.00 0.00 32.19 4.18
519 522 1.594293 CAGTCACCCCACACACGAC 60.594 63.158 0.00 0.00 0.00 4.34
520 523 1.618876 AACAGTCACCCCACACACGA 61.619 55.000 0.00 0.00 0.00 4.35
521 524 0.746563 AAACAGTCACCCCACACACG 60.747 55.000 0.00 0.00 0.00 4.49
541 544 8.236586 CCGAGAAAATATCATGTTGTTCTGAAA 58.763 33.333 0.00 0.00 0.00 2.69
566 569 5.335976 GGATGACAGTTTTGAGGTTTCATCC 60.336 44.000 10.99 10.99 46.51 3.51
592 595 1.470098 AGCGACATGACATTTTCTGGC 59.530 47.619 0.00 0.00 0.00 4.85
615 618 2.173143 TGTCGGGGGTAACAGTTTCTTT 59.827 45.455 0.00 0.00 39.74 2.52
654 657 3.242576 GGGTGGCATTTCAAACGTTTTTG 60.243 43.478 11.66 1.66 43.17 2.44
664 667 1.691219 GGGAGAGGGTGGCATTTCA 59.309 57.895 0.00 0.00 0.00 2.69
683 686 0.454196 ATATTTGGTTGCCGTTCGCC 59.546 50.000 0.00 0.00 36.24 5.54
958 962 1.193426 GCGCTAGGAAAATGATCGCTC 59.807 52.381 0.00 0.00 38.29 5.03
1047 1051 2.930019 CACCTCCTGCCAGTCCCA 60.930 66.667 0.00 0.00 0.00 4.37
1185 1189 2.987547 GACGTGGTCCGGTGGAGA 60.988 66.667 0.00 0.00 42.24 3.71
1233 1245 2.997897 AAAGACCGAGGCGAGGCT 60.998 61.111 0.00 0.00 0.00 4.58
1698 1713 1.078759 CATCCTCTGCGGTGTCGAAC 61.079 60.000 0.00 0.00 39.00 3.95
1890 1905 2.781595 AAGTTTGCGGAGGCGACGAT 62.782 55.000 0.00 0.00 44.10 3.73
2307 2322 0.321671 CTGAAGAAGAGGTTGCCGGA 59.678 55.000 5.05 0.00 0.00 5.14
2312 2327 2.354604 GGAGGAGCTGAAGAAGAGGTTG 60.355 54.545 0.00 0.00 0.00 3.77
2324 2339 0.979665 TGTTTCTGGAGGAGGAGCTG 59.020 55.000 0.00 0.00 0.00 4.24
2325 2340 0.980423 GTGTTTCTGGAGGAGGAGCT 59.020 55.000 0.00 0.00 0.00 4.09
2326 2341 0.687354 TGTGTTTCTGGAGGAGGAGC 59.313 55.000 0.00 0.00 0.00 4.70
2646 2666 5.865552 AGACATTCAACATGTGCTAAAATGC 59.134 36.000 0.00 3.13 31.52 3.56
2691 2711 5.642919 TGAGATTTGCAGCAAACAAACTTTT 59.357 32.000 22.92 4.33 39.65 2.27
2711 2737 7.996385 TCACATAGAAGTATGAAACGATGAGA 58.004 34.615 0.00 0.00 38.76 3.27
2817 2846 4.832248 AGCAACTTACAAGTAGCATAGCA 58.168 39.130 0.00 0.00 38.57 3.49
2879 2908 0.541863 AAAGGGCCTGATACTGACCG 59.458 55.000 6.92 0.00 0.00 4.79
2906 2935 5.464030 TGTACCTGGTTCAGAACTCTAAC 57.536 43.478 13.13 6.38 32.44 2.34
2922 2951 6.454223 AACATATCCTGCCATATTGTACCT 57.546 37.500 0.00 0.00 0.00 3.08
3057 3086 5.743872 GGAAATAAGCAAACGATGGATCAAC 59.256 40.000 0.00 0.00 0.00 3.18
3058 3087 5.652014 AGGAAATAAGCAAACGATGGATCAA 59.348 36.000 0.00 0.00 0.00 2.57
3074 3103 7.989947 ACAGTGATAAGGACCTAGGAAATAA 57.010 36.000 17.98 0.00 0.00 1.40
3084 3113 5.763698 GGGCTATAAAACAGTGATAAGGACC 59.236 44.000 0.00 0.00 0.00 4.46
3146 3175 2.373169 ACCAAAAGATGAGGACAGCTCA 59.627 45.455 0.00 0.00 42.17 4.26
3150 3179 4.252073 CTCTCACCAAAAGATGAGGACAG 58.748 47.826 1.66 0.00 42.25 3.51
3174 3203 5.174037 TCTTCACCAAATCGGGAGTTATT 57.826 39.130 0.00 0.00 40.22 1.40
3182 3211 1.755179 AGCCATCTTCACCAAATCGG 58.245 50.000 0.00 0.00 42.50 4.18
3183 3212 3.191162 TCAAAGCCATCTTCACCAAATCG 59.809 43.478 0.00 0.00 0.00 3.34
3198 3227 1.578206 GCAGAAGGGTCGTCAAAGCC 61.578 60.000 0.00 0.00 37.06 4.35
3211 3240 6.362551 CAGAATTTCTCACATGTTTGCAGAAG 59.637 38.462 0.00 0.00 30.63 2.85
3234 3263 7.548196 TCGAATAACTATTGCTAAAACCCAG 57.452 36.000 0.00 0.00 0.00 4.45
3244 3273 7.012421 ACCCTCTTGAATTCGAATAACTATTGC 59.988 37.037 11.83 0.00 0.00 3.56
3257 3286 4.941873 ACCGTCAATAACCCTCTTGAATTC 59.058 41.667 0.00 0.00 33.45 2.17
3260 3289 3.071892 ACACCGTCAATAACCCTCTTGAA 59.928 43.478 0.00 0.00 33.45 2.69
3313 3342 9.924650 GTTTAGACTATCTTTTACTGTCCTTCA 57.075 33.333 0.00 0.00 0.00 3.02
3326 3355 9.495382 AGAACCCAATCTAGTTTAGACTATCTT 57.505 33.333 0.00 0.00 37.71 2.40
3327 3356 9.138596 GAGAACCCAATCTAGTTTAGACTATCT 57.861 37.037 0.00 0.00 37.71 1.98
3328 3357 8.077386 CGAGAACCCAATCTAGTTTAGACTATC 58.923 40.741 0.00 0.00 37.71 2.08
3329 3358 7.778853 TCGAGAACCCAATCTAGTTTAGACTAT 59.221 37.037 0.00 0.00 37.71 2.12
3330 3359 7.114754 TCGAGAACCCAATCTAGTTTAGACTA 58.885 38.462 0.00 0.00 37.69 2.59
3331 3360 5.950549 TCGAGAACCCAATCTAGTTTAGACT 59.049 40.000 0.00 0.00 37.69 3.24
3332 3361 6.205101 TCGAGAACCCAATCTAGTTTAGAC 57.795 41.667 0.00 0.00 37.69 2.59
3333 3362 6.662234 TCTTCGAGAACCCAATCTAGTTTAGA 59.338 38.462 0.00 0.00 39.50 2.10
3334 3363 6.864342 TCTTCGAGAACCCAATCTAGTTTAG 58.136 40.000 0.00 0.00 0.00 1.85
3335 3364 6.845758 TCTTCGAGAACCCAATCTAGTTTA 57.154 37.500 0.00 0.00 0.00 2.01
3336 3365 5.740290 TCTTCGAGAACCCAATCTAGTTT 57.260 39.130 0.00 0.00 0.00 2.66
3337 3366 5.665459 CATCTTCGAGAACCCAATCTAGTT 58.335 41.667 0.00 0.00 0.00 2.24
3338 3367 4.442192 GCATCTTCGAGAACCCAATCTAGT 60.442 45.833 0.00 0.00 0.00 2.57
3339 3368 4.054671 GCATCTTCGAGAACCCAATCTAG 58.945 47.826 0.00 0.00 0.00 2.43
3340 3369 3.490933 CGCATCTTCGAGAACCCAATCTA 60.491 47.826 0.00 0.00 0.00 1.98
3341 3370 2.739932 CGCATCTTCGAGAACCCAATCT 60.740 50.000 0.00 0.00 0.00 2.40
3342 3371 1.594862 CGCATCTTCGAGAACCCAATC 59.405 52.381 0.00 0.00 0.00 2.67
3343 3372 1.656652 CGCATCTTCGAGAACCCAAT 58.343 50.000 0.00 0.00 0.00 3.16
3344 3373 1.019278 GCGCATCTTCGAGAACCCAA 61.019 55.000 0.30 0.00 0.00 4.12
3345 3374 1.447838 GCGCATCTTCGAGAACCCA 60.448 57.895 0.30 0.00 0.00 4.51
3346 3375 0.811616 ATGCGCATCTTCGAGAACCC 60.812 55.000 19.28 0.00 0.00 4.11
3347 3376 1.009829 AATGCGCATCTTCGAGAACC 58.990 50.000 25.53 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.