Multiple sequence alignment - TraesCS2D01G252100

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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 TraesCS2D01G252100 chr2D 100.000 3564 0 0 1 3564 302254502 302250939 0.000000e+00 6582.0
1 TraesCS2D01G252100 chr2B 93.111 3208 75 35 1 3151 357924889 357921771 0.000000e+00 4566.0
2 TraesCS2D01G252100 chr2B 83.150 273 20 7 3259 3526 357921667 357921416 3.580000e-55 226.0
3 TraesCS2D01G252100 chr2A 93.750 2240 51 24 358 2572 379159569 379157394 0.000000e+00 3278.0
4 TraesCS2D01G252100 chr2A 96.674 481 10 2 2677 3151 379157029 379156549 0.000000e+00 795.0
5 TraesCS2D01G252100 chr2A 88.704 301 25 3 3259 3559 379156443 379156152 3.380000e-95 359.0
6 TraesCS2D01G252100 chr5D 80.856 397 53 16 1236 1631 488677622 488677996 1.250000e-74 291.0
7 TraesCS2D01G252100 chr5A 80.750 400 49 19 1234 1631 609619358 609619731 1.620000e-73 287.0
8 TraesCS2D01G252100 chr5B 80.151 398 51 19 1236 1631 601864722 601865093 4.530000e-69 272.0
9 TraesCS2D01G252100 chr5B 87.879 66 8 0 3156 3221 73356132 73356067 1.060000e-10 78.7
10 TraesCS2D01G252100 chr3D 95.455 44 1 1 3187 3230 456153933 456153975 6.380000e-08 69.4
11 TraesCS2D01G252100 chr1D 94.595 37 0 2 3194 3230 470921224 470921258 4.970000e-04 56.5


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 TraesCS2D01G252100 chr2D 302250939 302254502 3563 True 6582.000000 6582 100.000000 1 3564 1 chr2D.!!$R1 3563
1 TraesCS2D01G252100 chr2B 357921416 357924889 3473 True 2396.000000 4566 88.130500 1 3526 2 chr2B.!!$R1 3525
2 TraesCS2D01G252100 chr2A 379156152 379159569 3417 True 1477.333333 3278 93.042667 358 3559 3 chr2A.!!$R1 3201

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
744 752 0.037605 CCGATAGAATGGTACGCCCC 60.038 60.0 0.0 0.0 39.76 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2588 2664 0.046397 ATGCTCCCTCCCCCTAAAGT 59.954 55.0 0.0 0.0 0.0 2.66 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
42 43 1.390565 CAGGACGACTGGTAGTAGGG 58.609 60.000 0.00 0.00 43.70 3.53
50 51 3.094572 GACTGGTAGTAGGGTTGCACTA 58.905 50.000 0.00 0.00 0.00 2.74
59 60 1.356527 GGGTTGCACTAACTACCGCG 61.357 60.000 0.00 0.00 39.31 6.46
60 61 1.356527 GGTTGCACTAACTACCGCGG 61.357 60.000 26.86 26.86 39.31 6.46
94 95 1.737793 CCAAGGCACAATACGGTTCTC 59.262 52.381 0.00 0.00 0.00 2.87
113 114 1.065564 TCGGGGTTTATGGGGTTTACG 60.066 52.381 0.00 0.00 0.00 3.18
115 116 2.093890 GGGGTTTATGGGGTTTACGTG 58.906 52.381 0.00 0.00 0.00 4.49
168 169 0.324275 TTTACCTACCTACCGCCGGT 60.324 55.000 15.63 15.63 40.16 5.28
170 171 2.624674 TACCTACCTACCGCCGGTCC 62.625 65.000 14.44 0.00 37.09 4.46
171 172 2.123982 CTACCTACCGCCGGTCCT 60.124 66.667 14.44 0.00 37.09 3.85
173 174 2.012902 CTACCTACCGCCGGTCCTTG 62.013 65.000 14.44 1.95 37.09 3.61
176 177 3.659089 CTACCGCCGGTCCTTGTGG 62.659 68.421 14.44 6.37 37.09 4.17
180 181 4.778143 GCCGGTCCTTGTGGCGAT 62.778 66.667 1.90 0.00 39.30 4.58
181 182 2.897207 CCGGTCCTTGTGGCGATA 59.103 61.111 0.00 0.00 0.00 2.92
182 183 1.227263 CCGGTCCTTGTGGCGATAG 60.227 63.158 0.00 0.00 0.00 2.08
183 184 1.227263 CGGTCCTTGTGGCGATAGG 60.227 63.158 0.00 0.00 0.00 2.57
184 185 1.672854 CGGTCCTTGTGGCGATAGGA 61.673 60.000 0.00 0.00 35.75 2.94
186 187 0.527817 GTCCTTGTGGCGATAGGACG 60.528 60.000 14.24 0.00 45.95 4.79
187 188 0.968901 TCCTTGTGGCGATAGGACGT 60.969 55.000 0.00 0.00 33.23 4.34
188 189 0.108329 CCTTGTGGCGATAGGACGTT 60.108 55.000 0.00 0.00 35.59 3.99
189 190 1.674817 CCTTGTGGCGATAGGACGTTT 60.675 52.381 0.00 0.00 35.59 3.60
190 191 2.417651 CCTTGTGGCGATAGGACGTTTA 60.418 50.000 0.00 0.00 35.59 2.01
191 192 2.572191 TGTGGCGATAGGACGTTTAG 57.428 50.000 0.00 0.00 35.59 1.85
192 193 1.206523 GTGGCGATAGGACGTTTAGC 58.793 55.000 0.00 0.00 35.59 3.09
193 194 0.818938 TGGCGATAGGACGTTTAGCA 59.181 50.000 0.00 0.00 35.59 3.49
194 195 1.206523 GGCGATAGGACGTTTAGCAC 58.793 55.000 0.00 0.00 35.59 4.40
195 196 1.470285 GGCGATAGGACGTTTAGCACA 60.470 52.381 0.00 0.00 35.59 4.57
196 197 1.852895 GCGATAGGACGTTTAGCACAG 59.147 52.381 0.00 0.00 35.59 3.66
197 198 2.460918 CGATAGGACGTTTAGCACAGG 58.539 52.381 0.00 0.00 0.00 4.00
198 199 2.159282 CGATAGGACGTTTAGCACAGGT 60.159 50.000 0.00 0.00 0.00 4.00
199 200 3.445857 GATAGGACGTTTAGCACAGGTC 58.554 50.000 0.00 0.00 0.00 3.85
200 201 1.045407 AGGACGTTTAGCACAGGTCA 58.955 50.000 0.00 0.00 31.85 4.02
224 225 0.738975 TAAGACAGGAGATGACGGCG 59.261 55.000 4.80 4.80 0.00 6.46
226 227 1.226717 GACAGGAGATGACGGCGAC 60.227 63.158 16.62 8.59 0.00 5.19
247 248 4.945246 ACTGCCTTAACATACCACTATCG 58.055 43.478 0.00 0.00 0.00 2.92
250 251 4.202182 TGCCTTAACATACCACTATCGACC 60.202 45.833 0.00 0.00 0.00 4.79
251 252 4.798593 GCCTTAACATACCACTATCGACCC 60.799 50.000 0.00 0.00 0.00 4.46
252 253 4.262335 CCTTAACATACCACTATCGACCCC 60.262 50.000 0.00 0.00 0.00 4.95
253 254 2.464796 ACATACCACTATCGACCCCA 57.535 50.000 0.00 0.00 0.00 4.96
254 255 2.317040 ACATACCACTATCGACCCCAG 58.683 52.381 0.00 0.00 0.00 4.45
255 256 1.000955 CATACCACTATCGACCCCAGC 59.999 57.143 0.00 0.00 0.00 4.85
256 257 0.757935 TACCACTATCGACCCCAGCC 60.758 60.000 0.00 0.00 0.00 4.85
257 258 2.063979 CCACTATCGACCCCAGCCA 61.064 63.158 0.00 0.00 0.00 4.75
258 259 1.410850 CCACTATCGACCCCAGCCAT 61.411 60.000 0.00 0.00 0.00 4.40
306 309 6.877611 TTTTAAACCAGAGTCAGATCCAAC 57.122 37.500 0.00 0.00 0.00 3.77
307 310 5.825593 TTAAACCAGAGTCAGATCCAACT 57.174 39.130 0.00 0.00 0.00 3.16
308 311 6.928348 TTAAACCAGAGTCAGATCCAACTA 57.072 37.500 0.00 0.00 0.00 2.24
309 312 5.825593 AAACCAGAGTCAGATCCAACTAA 57.174 39.130 0.00 0.00 0.00 2.24
310 313 5.825593 AACCAGAGTCAGATCCAACTAAA 57.174 39.130 0.00 0.00 0.00 1.85
311 314 5.153950 ACCAGAGTCAGATCCAACTAAAC 57.846 43.478 0.00 0.00 0.00 2.01
312 315 4.841246 ACCAGAGTCAGATCCAACTAAACT 59.159 41.667 0.00 0.00 0.00 2.66
313 316 5.308237 ACCAGAGTCAGATCCAACTAAACTT 59.692 40.000 0.00 0.00 0.00 2.66
314 317 6.183361 ACCAGAGTCAGATCCAACTAAACTTT 60.183 38.462 0.00 0.00 0.00 2.66
315 318 7.016268 ACCAGAGTCAGATCCAACTAAACTTTA 59.984 37.037 0.00 0.00 0.00 1.85
316 319 8.043710 CCAGAGTCAGATCCAACTAAACTTTAT 58.956 37.037 0.00 0.00 0.00 1.40
317 320 9.092876 CAGAGTCAGATCCAACTAAACTTTATC 57.907 37.037 0.00 0.00 0.00 1.75
318 321 8.816894 AGAGTCAGATCCAACTAAACTTTATCA 58.183 33.333 0.00 0.00 0.00 2.15
319 322 9.436957 GAGTCAGATCCAACTAAACTTTATCAA 57.563 33.333 0.00 0.00 0.00 2.57
320 323 9.793259 AGTCAGATCCAACTAAACTTTATCAAA 57.207 29.630 0.00 0.00 0.00 2.69
343 346 6.375945 AAAGTCAAAACATCAAATTTGGCC 57.624 33.333 17.90 0.00 40.98 5.36
349 352 3.683365 ACATCAAATTTGGCCTCCAAC 57.317 42.857 17.90 0.00 43.82 3.77
350 353 3.242011 ACATCAAATTTGGCCTCCAACT 58.758 40.909 17.90 0.00 43.82 3.16
374 377 1.510204 CTCGCGACAGAGACGTCAC 60.510 63.158 19.50 12.15 40.57 3.67
450 455 1.340600 CGGAGAGAGAGACCTTGGACT 60.341 57.143 0.00 0.00 0.00 3.85
483 488 2.774951 CGTCGTCGCCGTGATGAAC 61.775 63.158 5.42 0.75 44.07 3.18
572 577 4.251909 CGTCGCGCGCATGTACAG 62.252 66.667 32.61 13.04 0.00 2.74
573 578 3.179265 GTCGCGCGCATGTACAGT 61.179 61.111 32.61 0.00 0.00 3.55
574 579 1.870458 GTCGCGCGCATGTACAGTA 60.870 57.895 32.61 0.00 0.00 2.74
575 580 1.870458 TCGCGCGCATGTACAGTAC 60.870 57.895 32.61 3.49 0.00 2.73
718 726 2.044650 ACGGGCTACTCGCTACCA 60.045 61.111 0.00 0.00 39.13 3.25
743 751 0.669625 GCCGATAGAATGGTACGCCC 60.670 60.000 0.00 0.00 39.76 6.13
744 752 0.037605 CCGATAGAATGGTACGCCCC 60.038 60.000 0.00 0.00 39.76 5.80
745 753 0.966920 CGATAGAATGGTACGCCCCT 59.033 55.000 0.00 0.00 39.76 4.79
746 754 1.067776 CGATAGAATGGTACGCCCCTC 60.068 57.143 0.00 0.00 39.76 4.30
877 904 2.329399 ACCTCCCCTCTCTCCCTCC 61.329 68.421 0.00 0.00 0.00 4.30
879 906 2.018086 CTCCCCTCTCTCCCTCCCT 61.018 68.421 0.00 0.00 0.00 4.20
917 944 1.915769 GTGCTCCCTCCACTCCACT 60.916 63.158 0.00 0.00 0.00 4.00
918 945 1.610673 TGCTCCCTCCACTCCACTC 60.611 63.158 0.00 0.00 0.00 3.51
919 946 2.363172 GCTCCCTCCACTCCACTCC 61.363 68.421 0.00 0.00 0.00 3.85
920 947 1.079256 CTCCCTCCACTCCACTCCA 59.921 63.158 0.00 0.00 0.00 3.86
1521 1590 3.288308 CTGCTCTTCACGCGGAGGT 62.288 63.158 12.47 0.00 35.81 3.85
1693 1762 0.822532 ACAAGGACGACTCGGTCACT 60.823 55.000 2.98 0.00 38.70 3.41
1747 1816 1.448717 GGCTTCCTTCACCGAGCTC 60.449 63.158 2.73 2.73 35.53 4.09
2014 2083 1.347817 CGCACTTCTCCTTCTCGCAC 61.348 60.000 0.00 0.00 0.00 5.34
2391 2466 1.474077 CTTTTGGATGCTGGTAGGTGC 59.526 52.381 0.00 0.00 0.00 5.01
2648 2724 4.926238 CAGGTGTCAATTCACTACTCACTC 59.074 45.833 0.00 0.00 38.28 3.51
2658 2734 2.875933 CACTACTCACTCGAGAGGGATC 59.124 54.545 21.68 0.00 40.59 3.36
2966 3308 9.965824 TCCAGAATTTCTTTGTAGATGTTTTTC 57.034 29.630 0.00 0.00 0.00 2.29
3151 3497 7.980742 AAGTGAAATGTTTCGAAACTTAACC 57.019 32.000 33.94 21.64 40.01 2.85
3152 3498 6.500910 AGTGAAATGTTTCGAAACTTAACCC 58.499 36.000 33.94 20.58 40.01 4.11
3153 3499 6.095720 AGTGAAATGTTTCGAAACTTAACCCA 59.904 34.615 33.94 22.47 40.01 4.51
3157 3548 4.984205 TGTTTCGAAACTTAACCCAACAC 58.016 39.130 33.94 11.00 39.59 3.32
3176 3567 2.452813 CCCTCATTTGTCCGCGTCG 61.453 63.158 4.92 0.00 0.00 5.12
3211 3602 1.213430 TGTATCCGAACCCCCAAATCC 59.787 52.381 0.00 0.00 0.00 3.01
3212 3603 1.213430 GTATCCGAACCCCCAAATCCA 59.787 52.381 0.00 0.00 0.00 3.41
3213 3604 0.933700 ATCCGAACCCCCAAATCCAT 59.066 50.000 0.00 0.00 0.00 3.41
3214 3605 0.033601 TCCGAACCCCCAAATCCATG 60.034 55.000 0.00 0.00 0.00 3.66
3215 3606 1.675720 CCGAACCCCCAAATCCATGC 61.676 60.000 0.00 0.00 0.00 4.06
3216 3607 0.969917 CGAACCCCCAAATCCATGCA 60.970 55.000 0.00 0.00 0.00 3.96
3217 3608 1.274712 GAACCCCCAAATCCATGCAA 58.725 50.000 0.00 0.00 0.00 4.08
3218 3609 0.983467 AACCCCCAAATCCATGCAAC 59.017 50.000 0.00 0.00 0.00 4.17
3219 3610 0.909133 ACCCCCAAATCCATGCAACC 60.909 55.000 0.00 0.00 0.00 3.77
3220 3611 1.625417 CCCCCAAATCCATGCAACCC 61.625 60.000 0.00 0.00 0.00 4.11
3221 3612 1.625417 CCCCAAATCCATGCAACCCC 61.625 60.000 0.00 0.00 0.00 4.95
3222 3613 0.908656 CCCAAATCCATGCAACCCCA 60.909 55.000 0.00 0.00 0.00 4.96
3223 3614 0.982704 CCAAATCCATGCAACCCCAA 59.017 50.000 0.00 0.00 0.00 4.12
3224 3615 1.560611 CCAAATCCATGCAACCCCAAT 59.439 47.619 0.00 0.00 0.00 3.16
3225 3616 2.634600 CAAATCCATGCAACCCCAATG 58.365 47.619 0.00 0.00 0.00 2.82
3226 3617 0.542805 AATCCATGCAACCCCAATGC 59.457 50.000 0.00 0.00 44.08 3.56
3232 3623 2.843669 GCAACCCCAATGCAACATG 58.156 52.632 0.00 0.00 43.29 3.21
3233 3624 0.321021 GCAACCCCAATGCAACATGA 59.679 50.000 0.00 0.00 43.29 3.07
3234 3625 1.065998 GCAACCCCAATGCAACATGAT 60.066 47.619 0.00 0.00 43.29 2.45
3235 3626 2.896168 CAACCCCAATGCAACATGATC 58.104 47.619 0.00 0.00 0.00 2.92
3236 3627 2.234168 CAACCCCAATGCAACATGATCA 59.766 45.455 0.00 0.00 0.00 2.92
3237 3628 2.538222 ACCCCAATGCAACATGATCAA 58.462 42.857 0.00 0.00 0.00 2.57
3238 3629 2.905085 ACCCCAATGCAACATGATCAAA 59.095 40.909 0.00 0.00 0.00 2.69
3239 3630 3.327172 ACCCCAATGCAACATGATCAAAA 59.673 39.130 0.00 0.00 0.00 2.44
3240 3631 4.019141 ACCCCAATGCAACATGATCAAAAT 60.019 37.500 0.00 0.00 0.00 1.82
3241 3632 5.189342 ACCCCAATGCAACATGATCAAAATA 59.811 36.000 0.00 0.00 0.00 1.40
3242 3633 5.756347 CCCCAATGCAACATGATCAAAATAG 59.244 40.000 0.00 0.00 0.00 1.73
3243 3634 6.342906 CCCAATGCAACATGATCAAAATAGT 58.657 36.000 0.00 0.00 0.00 2.12
3244 3635 7.417683 CCCCAATGCAACATGATCAAAATAGTA 60.418 37.037 0.00 0.00 0.00 1.82
3245 3636 7.436080 CCCAATGCAACATGATCAAAATAGTAC 59.564 37.037 0.00 0.00 0.00 2.73
3246 3637 7.166307 CCAATGCAACATGATCAAAATAGTACG 59.834 37.037 0.00 0.00 0.00 3.67
3247 3638 6.735678 TGCAACATGATCAAAATAGTACGT 57.264 33.333 0.00 0.00 0.00 3.57
3248 3639 7.835634 TGCAACATGATCAAAATAGTACGTA 57.164 32.000 0.00 0.00 0.00 3.57
3249 3640 7.680982 TGCAACATGATCAAAATAGTACGTAC 58.319 34.615 18.10 18.10 0.00 3.67
3250 3641 7.332182 TGCAACATGATCAAAATAGTACGTACA 59.668 33.333 26.55 13.44 0.00 2.90
3251 3642 8.335356 GCAACATGATCAAAATAGTACGTACAT 58.665 33.333 26.55 15.00 0.00 2.29
3285 3676 2.678190 GCATAGTTCATAGATCGGGGGC 60.678 54.545 0.00 0.00 0.00 5.80
3287 3678 0.399949 AGTTCATAGATCGGGGGCCA 60.400 55.000 4.39 0.00 0.00 5.36
3288 3679 0.250338 GTTCATAGATCGGGGGCCAC 60.250 60.000 4.39 0.00 0.00 5.01
3289 3680 0.692756 TTCATAGATCGGGGGCCACA 60.693 55.000 7.65 0.00 0.00 4.17
3290 3681 0.473694 TCATAGATCGGGGGCCACAT 60.474 55.000 7.65 0.00 0.00 3.21
3291 3682 0.321919 CATAGATCGGGGGCCACATG 60.322 60.000 7.65 0.00 0.00 3.21
3293 3684 2.613576 TAGATCGGGGGCCACATGGA 62.614 60.000 7.65 0.00 37.39 3.41
3294 3685 2.778278 ATCGGGGGCCACATGGAT 60.778 61.111 7.65 3.00 37.39 3.41
3295 3686 2.754664 GATCGGGGGCCACATGGATC 62.755 65.000 7.65 12.28 37.39 3.36
3296 3687 4.935495 CGGGGGCCACATGGATCG 62.935 72.222 7.65 0.00 37.39 3.69
3316 3708 3.068574 GAGCTCCTCGTACGACTCT 57.931 57.895 15.28 8.57 0.00 3.24
3318 3710 1.062845 GCTCCTCGTACGACTCTGC 59.937 63.158 15.28 12.29 0.00 4.26
3423 3815 1.609794 GAGGACGGGGAAGTGGAGT 60.610 63.158 0.00 0.00 0.00 3.85
3432 3824 0.898789 GGAAGTGGAGTGGACGAGGA 60.899 60.000 0.00 0.00 0.00 3.71
3437 3829 2.025226 AGTGGAGTGGACGAGGAGATTA 60.025 50.000 0.00 0.00 0.00 1.75
3453 3845 4.262420 GGAGATTATGAGGAGAGTGGAAGC 60.262 50.000 0.00 0.00 0.00 3.86
3455 3847 0.747255 TATGAGGAGAGTGGAAGCGC 59.253 55.000 0.00 0.00 0.00 5.92
3479 3871 1.303282 GGCTAGGGTTTGGTCCAGG 59.697 63.158 0.00 0.00 0.00 4.45
3494 3886 2.370849 GTCCAGGTGGAGTTTTAGTGGA 59.629 50.000 0.00 0.00 46.49 4.02
3498 3890 3.071023 CAGGTGGAGTTTTAGTGGAGTCA 59.929 47.826 0.00 0.00 0.00 3.41
3517 3913 3.249189 GGTGGGTCAGAGTGGGCA 61.249 66.667 0.00 0.00 0.00 5.36
3536 3932 4.944372 GATCCTACGTGGCCGCCG 62.944 72.222 11.56 12.14 37.70 6.46
3559 3955 1.200519 CCGGACCTTCCTGTATTCCA 58.799 55.000 0.00 0.00 33.30 3.53
3560 3956 1.134491 CCGGACCTTCCTGTATTCCAC 60.134 57.143 0.00 0.00 33.30 4.02
3561 3957 1.134491 CGGACCTTCCTGTATTCCACC 60.134 57.143 0.00 0.00 33.30 4.61
3562 3958 1.212195 GGACCTTCCTGTATTCCACCC 59.788 57.143 0.00 0.00 32.53 4.61
3563 3959 1.212195 GACCTTCCTGTATTCCACCCC 59.788 57.143 0.00 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.812571 CTGGTGGTAGGATGCACAAAC 59.187 52.381 0.00 0.00 0.00 2.93
28 29 0.892755 TGCAACCCTACTACCAGTCG 59.107 55.000 0.00 0.00 0.00 4.18
29 30 1.900486 AGTGCAACCCTACTACCAGTC 59.100 52.381 0.00 0.00 37.80 3.51
36 37 2.494870 CGGTAGTTAGTGCAACCCTACT 59.505 50.000 11.54 4.52 37.80 2.57
42 43 0.388907 TCCGCGGTAGTTAGTGCAAC 60.389 55.000 27.15 0.00 37.41 4.17
60 61 1.686428 GCCTTGGGAGGGGAAGAATTC 60.686 57.143 0.00 0.00 43.50 2.17
94 95 1.339920 ACGTAAACCCCATAAACCCCG 60.340 52.381 0.00 0.00 0.00 5.73
113 114 3.009115 TGGCAGTAGGGAGGGCAC 61.009 66.667 0.00 0.00 31.66 5.01
115 116 4.182433 GCTGGCAGTAGGGAGGGC 62.182 72.222 17.16 0.00 0.00 5.19
168 169 0.968901 ACGTCCTATCGCCACAAGGA 60.969 55.000 0.00 0.00 37.07 3.36
170 171 1.722011 AAACGTCCTATCGCCACAAG 58.278 50.000 0.00 0.00 0.00 3.16
171 172 2.883574 CTAAACGTCCTATCGCCACAA 58.116 47.619 0.00 0.00 0.00 3.33
173 174 1.206523 GCTAAACGTCCTATCGCCAC 58.793 55.000 0.00 0.00 0.00 5.01
176 177 1.852895 CTGTGCTAAACGTCCTATCGC 59.147 52.381 0.00 0.00 0.00 4.58
177 178 2.159282 ACCTGTGCTAAACGTCCTATCG 60.159 50.000 0.00 0.00 0.00 2.92
178 179 3.119245 TGACCTGTGCTAAACGTCCTATC 60.119 47.826 0.00 0.00 0.00 2.08
179 180 2.829720 TGACCTGTGCTAAACGTCCTAT 59.170 45.455 0.00 0.00 0.00 2.57
180 181 2.230508 CTGACCTGTGCTAAACGTCCTA 59.769 50.000 0.00 0.00 0.00 2.94
181 182 1.000955 CTGACCTGTGCTAAACGTCCT 59.999 52.381 0.00 0.00 0.00 3.85
182 183 1.270147 ACTGACCTGTGCTAAACGTCC 60.270 52.381 0.00 0.00 0.00 4.79
183 184 2.059541 GACTGACCTGTGCTAAACGTC 58.940 52.381 0.00 0.00 0.00 4.34
184 185 1.411246 TGACTGACCTGTGCTAAACGT 59.589 47.619 0.00 0.00 0.00 3.99
185 186 2.148916 TGACTGACCTGTGCTAAACG 57.851 50.000 0.00 0.00 0.00 3.60
186 187 5.348997 GTCTTATGACTGACCTGTGCTAAAC 59.651 44.000 1.60 0.00 39.94 2.01
187 188 5.011635 TGTCTTATGACTGACCTGTGCTAAA 59.988 40.000 9.87 0.00 43.29 1.85
188 189 4.526650 TGTCTTATGACTGACCTGTGCTAA 59.473 41.667 9.87 0.00 43.29 3.09
189 190 4.086457 TGTCTTATGACTGACCTGTGCTA 58.914 43.478 9.87 0.00 43.29 3.49
190 191 2.899900 TGTCTTATGACTGACCTGTGCT 59.100 45.455 9.87 0.00 43.29 4.40
191 192 3.257393 CTGTCTTATGACTGACCTGTGC 58.743 50.000 9.87 0.00 42.42 4.57
192 193 3.511540 TCCTGTCTTATGACTGACCTGTG 59.488 47.826 14.74 0.97 42.42 3.66
193 194 3.766591 CTCCTGTCTTATGACTGACCTGT 59.233 47.826 14.74 0.00 42.42 4.00
194 195 4.019858 TCTCCTGTCTTATGACTGACCTG 58.980 47.826 14.74 1.82 42.42 4.00
195 196 4.323569 TCTCCTGTCTTATGACTGACCT 57.676 45.455 14.74 0.00 42.42 3.85
196 197 4.646945 TCATCTCCTGTCTTATGACTGACC 59.353 45.833 14.74 0.00 42.42 4.02
197 198 5.587289 GTCATCTCCTGTCTTATGACTGAC 58.413 45.833 14.74 11.85 43.07 3.51
198 199 4.336713 CGTCATCTCCTGTCTTATGACTGA 59.663 45.833 14.74 8.57 43.82 3.41
199 200 4.498850 CCGTCATCTCCTGTCTTATGACTG 60.499 50.000 9.87 9.00 43.82 3.51
200 201 3.634448 CCGTCATCTCCTGTCTTATGACT 59.366 47.826 9.87 0.00 43.82 3.41
224 225 4.982916 CGATAGTGGTATGTTAAGGCAGTC 59.017 45.833 0.00 0.00 0.00 3.51
226 227 4.982916 GTCGATAGTGGTATGTTAAGGCAG 59.017 45.833 0.00 0.00 37.40 4.85
316 319 7.967303 GCCAAATTTGATGTTTTGACTTTTTGA 59.033 29.630 19.86 0.00 35.34 2.69
317 320 7.220491 GGCCAAATTTGATGTTTTGACTTTTTG 59.780 33.333 19.86 0.00 35.34 2.44
318 321 7.122501 AGGCCAAATTTGATGTTTTGACTTTTT 59.877 29.630 19.86 0.00 35.34 1.94
319 322 6.602803 AGGCCAAATTTGATGTTTTGACTTTT 59.397 30.769 19.86 0.00 35.34 2.27
320 323 6.121590 AGGCCAAATTTGATGTTTTGACTTT 58.878 32.000 19.86 0.00 35.34 2.66
321 324 5.683681 AGGCCAAATTTGATGTTTTGACTT 58.316 33.333 19.86 0.00 35.34 3.01
322 325 5.294734 AGGCCAAATTTGATGTTTTGACT 57.705 34.783 19.86 5.36 35.34 3.41
349 352 0.462225 TCTCTGTCGCGAGGTCCTAG 60.462 60.000 10.24 1.51 0.00 3.02
350 353 0.743701 GTCTCTGTCGCGAGGTCCTA 60.744 60.000 10.24 0.00 0.00 2.94
374 377 0.884704 CCGTATCCTGGAAATGCCCG 60.885 60.000 0.00 0.00 34.97 6.13
483 488 2.429351 GCTCGCTGTCAGACGTTCG 61.429 63.158 3.32 0.00 0.00 3.95
484 489 2.429351 CGCTCGCTGTCAGACGTTC 61.429 63.158 3.32 3.24 0.00 3.95
485 490 2.429236 CGCTCGCTGTCAGACGTT 60.429 61.111 3.32 0.00 0.00 3.99
486 491 3.315769 CTCGCTCGCTGTCAGACGT 62.316 63.158 3.32 0.00 0.00 4.34
571 576 3.303593 CGAATCGGCACATAGTACGTACT 60.304 47.826 29.62 29.62 40.24 2.73
572 577 2.969306 CGAATCGGCACATAGTACGTAC 59.031 50.000 18.10 18.10 0.00 3.67
573 578 2.613595 ACGAATCGGCACATAGTACGTA 59.386 45.455 7.80 0.00 0.00 3.57
574 579 1.402968 ACGAATCGGCACATAGTACGT 59.597 47.619 7.80 0.00 0.00 3.57
575 580 2.115348 ACGAATCGGCACATAGTACG 57.885 50.000 7.80 0.00 0.00 3.67
579 584 0.043053 CGCAACGAATCGGCACATAG 60.043 55.000 7.80 0.00 0.00 2.23
718 726 1.204146 ACCATTCTATCGGCCACACT 58.796 50.000 2.24 0.00 0.00 3.55
743 751 2.758737 AACGAGGCGGTAGGGAGG 60.759 66.667 0.00 0.00 0.00 4.30
744 752 2.783288 GGAACGAGGCGGTAGGGAG 61.783 68.421 0.00 0.00 0.00 4.30
745 753 2.757099 GGAACGAGGCGGTAGGGA 60.757 66.667 0.00 0.00 0.00 4.20
917 944 3.170672 CTGGGGCGATGGGATGGA 61.171 66.667 0.00 0.00 0.00 3.41
918 945 4.275508 CCTGGGGCGATGGGATGG 62.276 72.222 0.00 0.00 0.00 3.51
919 946 4.275508 CCCTGGGGCGATGGGATG 62.276 72.222 4.27 0.00 43.47 3.51
1747 1816 2.825836 GCCGCCAATCCAGTGAGG 60.826 66.667 0.00 0.00 39.47 3.86
1942 2011 0.392193 ATAAGCTGAAGTGCTGCGCT 60.392 50.000 10.42 10.42 45.13 5.92
2014 2083 1.518572 GACGGGCATGTAGTGGTCG 60.519 63.158 0.00 0.00 0.00 4.79
2391 2466 3.242543 GCGTATGCATTTGGAGAGTTCAG 60.243 47.826 3.54 0.00 42.15 3.02
2588 2664 0.046397 ATGCTCCCTCCCCCTAAAGT 59.954 55.000 0.00 0.00 0.00 2.66
2648 2724 2.289694 ACACCAAAACAGATCCCTCTCG 60.290 50.000 0.00 0.00 0.00 4.04
2658 2734 2.100749 GGGGAACAGAACACCAAAACAG 59.899 50.000 0.00 0.00 0.00 3.16
2926 3268 1.140589 CTGGACTGCGCCTCTACTG 59.859 63.158 4.18 0.00 0.00 2.74
3137 3483 3.380954 GGGTGTTGGGTTAAGTTTCGAAA 59.619 43.478 6.47 6.47 0.00 3.46
3151 3497 1.256812 GGACAAATGAGGGGTGTTGG 58.743 55.000 0.00 0.00 0.00 3.77
3152 3498 0.881118 CGGACAAATGAGGGGTGTTG 59.119 55.000 0.00 0.00 0.00 3.33
3153 3499 0.893727 GCGGACAAATGAGGGGTGTT 60.894 55.000 0.00 0.00 0.00 3.32
3157 3548 2.046314 ACGCGGACAAATGAGGGG 60.046 61.111 12.47 0.00 0.00 4.79
3191 3582 1.213430 GGATTTGGGGGTTCGGATACA 59.787 52.381 0.00 0.00 0.00 2.29
3192 3583 1.213430 TGGATTTGGGGGTTCGGATAC 59.787 52.381 0.00 0.00 0.00 2.24
3197 3588 0.969917 TGCATGGATTTGGGGGTTCG 60.970 55.000 0.00 0.00 0.00 3.95
3214 3605 0.321021 TCATGTTGCATTGGGGTTGC 59.679 50.000 0.00 0.00 40.55 4.17
3215 3606 2.234168 TGATCATGTTGCATTGGGGTTG 59.766 45.455 0.00 0.00 0.00 3.77
3216 3607 2.538222 TGATCATGTTGCATTGGGGTT 58.462 42.857 0.00 0.00 0.00 4.11
3217 3608 2.234896 TGATCATGTTGCATTGGGGT 57.765 45.000 0.00 0.00 0.00 4.95
3218 3609 3.613494 TTTGATCATGTTGCATTGGGG 57.387 42.857 0.00 0.00 0.00 4.96
3219 3610 6.342906 ACTATTTTGATCATGTTGCATTGGG 58.657 36.000 0.00 0.00 0.00 4.12
3220 3611 7.166307 CGTACTATTTTGATCATGTTGCATTGG 59.834 37.037 0.00 0.00 0.00 3.16
3221 3612 7.697710 ACGTACTATTTTGATCATGTTGCATTG 59.302 33.333 0.00 0.00 0.00 2.82
3222 3613 7.761409 ACGTACTATTTTGATCATGTTGCATT 58.239 30.769 0.00 0.00 0.00 3.56
3223 3614 7.320443 ACGTACTATTTTGATCATGTTGCAT 57.680 32.000 0.00 0.00 0.00 3.96
3224 3615 6.735678 ACGTACTATTTTGATCATGTTGCA 57.264 33.333 0.00 0.00 0.00 4.08
3225 3616 7.680982 TGTACGTACTATTTTGATCATGTTGC 58.319 34.615 25.12 0.00 0.00 4.17
3239 3630 8.770828 GCCATGTTCAATTTATGTACGTACTAT 58.229 33.333 25.12 18.19 32.40 2.12
3240 3631 7.764901 TGCCATGTTCAATTTATGTACGTACTA 59.235 33.333 25.12 12.85 32.40 1.82
3241 3632 6.596106 TGCCATGTTCAATTTATGTACGTACT 59.404 34.615 25.12 13.70 32.40 2.73
3242 3633 6.777101 TGCCATGTTCAATTTATGTACGTAC 58.223 36.000 18.90 18.90 32.40 3.67
3243 3634 6.986904 TGCCATGTTCAATTTATGTACGTA 57.013 33.333 0.00 0.00 32.40 3.57
3244 3635 5.888691 TGCCATGTTCAATTTATGTACGT 57.111 34.783 0.00 0.00 32.40 3.57
3245 3636 7.639039 ACTATGCCATGTTCAATTTATGTACG 58.361 34.615 0.00 0.00 32.40 3.67
3246 3637 9.450807 GAACTATGCCATGTTCAATTTATGTAC 57.549 33.333 12.25 0.00 41.35 2.90
3247 3638 9.183368 TGAACTATGCCATGTTCAATTTATGTA 57.817 29.630 15.57 0.00 46.17 2.29
3248 3639 8.065473 TGAACTATGCCATGTTCAATTTATGT 57.935 30.769 15.57 0.00 46.17 2.29
3257 3648 5.349817 CCGATCTATGAACTATGCCATGTTC 59.650 44.000 10.94 10.94 41.87 3.18
3263 3654 2.093447 CCCCCGATCTATGAACTATGCC 60.093 54.545 0.00 0.00 0.00 4.40
3285 3676 1.953138 GAGCTCGCGATCCATGTGG 60.953 63.158 10.36 0.00 0.00 4.17
3287 3678 2.419198 GGAGCTCGCGATCCATGT 59.581 61.111 21.13 0.00 45.12 3.21
3318 3710 4.096003 ATTGGGACACCCTCGCGG 62.096 66.667 6.13 0.00 45.70 6.46
3327 3719 1.607071 CCCGTGGATCATTGGGACA 59.393 57.895 9.22 0.00 44.88 4.02
3403 3795 1.305046 TCCACTTCCCCGTCCTCTC 60.305 63.158 0.00 0.00 0.00 3.20
3423 3815 3.138468 TCTCCTCATAATCTCCTCGTCCA 59.862 47.826 0.00 0.00 0.00 4.02
3432 3824 3.320541 CGCTTCCACTCTCCTCATAATCT 59.679 47.826 0.00 0.00 0.00 2.40
3437 3829 1.519719 GCGCTTCCACTCTCCTCAT 59.480 57.895 0.00 0.00 0.00 2.90
3479 3871 3.557264 CCCTGACTCCACTAAAACTCCAC 60.557 52.174 0.00 0.00 0.00 4.02
3494 3886 0.833834 CACTCTGACCCACCCTGACT 60.834 60.000 0.00 0.00 0.00 3.41
3498 3890 2.203998 CCCACTCTGACCCACCCT 60.204 66.667 0.00 0.00 0.00 4.34
3517 3913 3.537874 GCGGCCACGTAGGATCCT 61.538 66.667 20.48 20.48 43.45 3.24
3536 3932 1.673808 ATACAGGAAGGTCCGGACGC 61.674 60.000 27.68 19.96 42.75 5.19
3541 3937 1.134491 GGTGGAATACAGGAAGGTCCG 60.134 57.143 0.00 0.00 42.75 4.79


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

AutoCloner maintained by Alex Coulton.