Multiple sequence alignment - TraesCS2A01G395400

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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 TraesCS2A01G395400 chr2A 100.000 3896 0 0 1 3896 647344252 647348147 0.000000e+00 7195
1 TraesCS2A01G395400 chr2B 91.927 3964 160 56 19 3896 589210746 589214635 0.000000e+00 5400
2 TraesCS2A01G395400 chr2D 94.036 3085 87 37 859 3896 502108896 502111930 0.000000e+00 4588
3 TraesCS2A01G395400 chr2D 85.119 672 51 21 17 670 502108043 502108683 3.280000e-180 641
4 TraesCS2A01G395400 chr1D 94.403 536 24 3 2692 3227 215044106 215043577 0.000000e+00 819
5 TraesCS2A01G395400 chr1D 89.147 129 13 1 2727 2855 113492871 113492998 4.030000e-35 159
6 TraesCS2A01G395400 chr5D 94.574 129 7 0 2727 2855 321681930 321682058 2.370000e-47 200
7 TraesCS2A01G395400 chr4D 92.248 129 10 0 2727 2855 227830190 227830062 2.390000e-42 183
8 TraesCS2A01G395400 chr6D 92.800 125 9 0 2692 2816 101397236 101397360 8.600000e-42 182
9 TraesCS2A01G395400 chr6D 90.698 129 12 0 2727 2855 185870425 185870297 5.180000e-39 172
10 TraesCS2A01G395400 chr3A 91.473 129 11 0 2727 2855 58310019 58309891 1.110000e-40 178


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 TraesCS2A01G395400 chr2A 647344252 647348147 3895 False 7195.0 7195 100.0000 1 3896 1 chr2A.!!$F1 3895
1 TraesCS2A01G395400 chr2B 589210746 589214635 3889 False 5400.0 5400 91.9270 19 3896 1 chr2B.!!$F1 3877
2 TraesCS2A01G395400 chr2D 502108043 502111930 3887 False 2614.5 4588 89.5775 17 3896 2 chr2D.!!$F1 3879
3 TraesCS2A01G395400 chr1D 215043577 215044106 529 True 819.0 819 94.4030 2692 3227 1 chr1D.!!$R1 535

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
233 247 0.179163 CCTTTCGCCGAATGGAAAGC 60.179 55.0 23.16 0.0 44.83 3.51 F
708 763 0.249398 CCTCCCCACAGGTAAGTTCG 59.751 60.0 0.00 0.0 36.75 3.95 F
1749 1864 0.250295 CCACTTCCACGGCTTCTTCA 60.250 55.0 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 1758 0.680280 GTAGAGTGGAGGAGACGGCA 60.680 60.0 0.0 0.0 0.0 5.69 R
2334 2449 0.182061 TGGATGCCTCAATCTCTGCC 59.818 55.0 0.0 0.0 0.0 4.85 R
3520 3647 0.034670 ATCTCTTCCCTTGCAGCCAC 60.035 55.0 0.0 0.0 0.0 5.01 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
120 121 0.462047 CTACCGCCACCAATCTGGAC 60.462 60.000 0.00 0.00 40.96 4.02
121 122 1.195442 TACCGCCACCAATCTGGACA 61.195 55.000 0.00 0.00 40.96 4.02
126 127 1.895131 GCCACCAATCTGGACAACAAT 59.105 47.619 0.00 0.00 40.96 2.71
128 129 3.701040 GCCACCAATCTGGACAACAATAT 59.299 43.478 0.00 0.00 40.96 1.28
146 147 6.123651 ACAATATAATTGTTTCCCACCGCTA 58.876 36.000 0.00 0.00 0.00 4.26
147 148 6.038936 ACAATATAATTGTTTCCCACCGCTAC 59.961 38.462 0.00 0.00 0.00 3.58
148 149 1.541379 AATTGTTTCCCACCGCTACC 58.459 50.000 0.00 0.00 0.00 3.18
149 150 0.402504 ATTGTTTCCCACCGCTACCA 59.597 50.000 0.00 0.00 0.00 3.25
150 151 0.250553 TTGTTTCCCACCGCTACCAG 60.251 55.000 0.00 0.00 0.00 4.00
151 152 1.373812 GTTTCCCACCGCTACCAGT 59.626 57.895 0.00 0.00 0.00 4.00
152 153 0.250597 GTTTCCCACCGCTACCAGTT 60.251 55.000 0.00 0.00 0.00 3.16
153 154 0.250553 TTTCCCACCGCTACCAGTTG 60.251 55.000 0.00 0.00 0.00 3.16
154 155 1.412453 TTCCCACCGCTACCAGTTGT 61.412 55.000 0.00 0.00 0.00 3.32
155 156 0.542467 TCCCACCGCTACCAGTTGTA 60.542 55.000 0.00 0.00 0.00 2.41
156 157 0.539986 CCCACCGCTACCAGTTGTAT 59.460 55.000 0.00 0.00 0.00 2.29
157 158 1.758280 CCCACCGCTACCAGTTGTATA 59.242 52.381 0.00 0.00 0.00 1.47
158 159 2.223971 CCCACCGCTACCAGTTGTATAG 60.224 54.545 0.00 0.00 0.00 1.31
159 160 2.470821 CACCGCTACCAGTTGTATAGC 58.529 52.381 0.00 0.00 38.36 2.97
160 161 2.100916 CACCGCTACCAGTTGTATAGCT 59.899 50.000 0.00 0.00 39.36 3.32
161 162 3.317149 CACCGCTACCAGTTGTATAGCTA 59.683 47.826 0.00 0.00 39.36 3.32
162 163 3.568853 ACCGCTACCAGTTGTATAGCTAG 59.431 47.826 0.00 0.00 39.36 3.42
163 164 3.057456 CCGCTACCAGTTGTATAGCTAGG 60.057 52.174 0.00 0.00 39.36 3.02
233 247 0.179163 CCTTTCGCCGAATGGAAAGC 60.179 55.000 23.16 0.00 44.83 3.51
302 317 4.107051 GCGTGCATGCACAGGGAC 62.107 66.667 40.95 24.51 46.47 4.46
304 319 3.064324 GTGCATGCACAGGGACCC 61.064 66.667 39.12 14.86 45.53 4.46
346 361 1.150536 ACCCGCAAACATCACCTGT 59.849 52.632 0.00 0.00 40.84 4.00
359 374 5.676552 ACATCACCTGTTGTTGTTGTAGTA 58.323 37.500 0.00 0.00 34.99 1.82
369 384 7.428020 TGTTGTTGTTGTAGTACCAGTACTAG 58.572 38.462 16.15 0.00 45.97 2.57
370 385 7.068593 TGTTGTTGTTGTAGTACCAGTACTAGT 59.931 37.037 16.15 0.00 45.97 2.57
371 386 8.567948 GTTGTTGTTGTAGTACCAGTACTAGTA 58.432 37.037 16.15 0.00 45.97 1.82
395 410 1.852067 GAAATTCACGCGCCTGTGGT 61.852 55.000 5.73 0.00 40.31 4.16
396 411 2.128853 AAATTCACGCGCCTGTGGTG 62.129 55.000 5.73 10.32 40.31 4.17
397 412 3.825160 ATTCACGCGCCTGTGGTGT 62.825 57.895 5.73 0.00 40.31 4.16
462 488 2.652530 CGTCTCCGGGGAAAACGA 59.347 61.111 5.00 0.00 35.45 3.85
525 567 2.674380 CACAGCAAGGCAGGTCCC 60.674 66.667 0.00 0.00 34.51 4.46
526 568 3.971702 ACAGCAAGGCAGGTCCCC 61.972 66.667 0.00 0.00 34.51 4.81
527 569 3.655211 CAGCAAGGCAGGTCCCCT 61.655 66.667 0.00 0.00 34.51 4.79
637 679 0.867746 CACACCATTCACTCACCACG 59.132 55.000 0.00 0.00 0.00 4.94
708 763 0.249398 CCTCCCCACAGGTAAGTTCG 59.751 60.000 0.00 0.00 36.75 3.95
713 768 1.337823 CCCACAGGTAAGTTCGAGGTG 60.338 57.143 0.00 0.00 0.00 4.00
724 779 1.292061 TTCGAGGTGAACAAACACGG 58.708 50.000 0.00 0.00 41.12 4.94
725 780 0.531090 TCGAGGTGAACAAACACGGG 60.531 55.000 0.00 0.00 41.12 5.28
857 930 1.870064 AGGGGAAGCAATTGAATGGG 58.130 50.000 10.34 0.00 0.00 4.00
928 1013 1.602416 GCGTTCGGAGCTAGTATTCCC 60.602 57.143 0.00 0.00 0.00 3.97
952 1037 4.880537 CTGCCTGCCTACCGCGAG 62.881 72.222 8.23 0.00 42.08 5.03
990 1078 1.074850 CCTCTTCCCTCCTCCTCCC 60.075 68.421 0.00 0.00 0.00 4.30
991 1079 1.456705 CTCTTCCCTCCTCCTCCCG 60.457 68.421 0.00 0.00 0.00 5.14
993 1081 3.684628 TTCCCTCCTCCTCCCGCT 61.685 66.667 0.00 0.00 0.00 5.52
1152 1267 2.996395 CTGGAGAGGTGGCAGCAT 59.004 61.111 20.04 6.81 0.00 3.79
1643 1758 2.047274 CAACTCCATCACGGCCGT 60.047 61.111 28.70 28.70 33.14 5.68
1749 1864 0.250295 CCACTTCCACGGCTTCTTCA 60.250 55.000 0.00 0.00 0.00 3.02
2017 2132 1.687840 CACCATACCGGGTCCCAGA 60.688 63.158 9.12 0.00 39.79 3.86
2079 2194 1.548973 CCGCTAACATCGCCATCGTC 61.549 60.000 0.00 0.00 36.96 4.20
2241 2356 1.005394 ACCGTTTACGCAGTCCCTG 60.005 57.895 0.00 0.00 43.93 4.45
2334 2449 3.932626 CAGAATGATCAGCTGCAGAGCG 61.933 54.545 20.43 4.33 45.68 5.03
2660 2775 2.568090 GGCAAACATGTCGGCCAG 59.432 61.111 27.04 0.00 45.70 4.85
3006 3127 1.133790 GATTGGCAAGGTGTGATGAGC 59.866 52.381 5.96 0.00 0.00 4.26
3007 3128 0.111061 TTGGCAAGGTGTGATGAGCT 59.889 50.000 0.00 0.00 0.00 4.09
3008 3129 0.111061 TGGCAAGGTGTGATGAGCTT 59.889 50.000 0.00 0.00 33.94 3.74
3012 3133 3.549299 CAAGGTGTGATGAGCTTGTTC 57.451 47.619 0.00 0.00 43.45 3.18
3106 3228 6.417044 ACATTATTACGCTACTGATTGTCGTC 59.583 38.462 0.00 0.00 32.58 4.20
3202 3324 5.235516 GCTACATACACTTGTACACAGGTT 58.764 41.667 0.00 0.00 33.67 3.50
3208 3330 5.093849 ACACTTGTACACAGGTTGTAGTT 57.906 39.130 0.00 0.00 41.58 2.24
3209 3331 4.873827 ACACTTGTACACAGGTTGTAGTTG 59.126 41.667 0.00 0.00 41.58 3.16
3210 3332 4.873827 CACTTGTACACAGGTTGTAGTTGT 59.126 41.667 0.00 0.00 41.58 3.32
3316 3438 0.584876 GGTTTTCCTTCGTGACGTGG 59.415 55.000 4.40 9.09 36.94 4.94
3372 3496 5.106442 TGGTCATGCTTGTACGTAATACTG 58.894 41.667 0.00 0.00 34.56 2.74
3373 3497 4.506654 GGTCATGCTTGTACGTAATACTGG 59.493 45.833 0.00 0.00 34.56 4.00
3374 3498 5.107133 GTCATGCTTGTACGTAATACTGGT 58.893 41.667 0.00 0.00 34.56 4.00
3375 3499 6.267817 GTCATGCTTGTACGTAATACTGGTA 58.732 40.000 0.00 0.00 34.56 3.25
3376 3500 6.417044 GTCATGCTTGTACGTAATACTGGTAG 59.583 42.308 0.00 0.00 34.56 3.18
3377 3501 5.252969 TGCTTGTACGTAATACTGGTAGG 57.747 43.478 0.00 0.00 34.56 3.18
3378 3502 4.949238 TGCTTGTACGTAATACTGGTAGGA 59.051 41.667 0.00 0.00 34.56 2.94
3379 3503 5.066893 TGCTTGTACGTAATACTGGTAGGAG 59.933 44.000 0.00 0.00 34.56 3.69
3380 3504 5.067023 GCTTGTACGTAATACTGGTAGGAGT 59.933 44.000 0.00 0.00 34.56 3.85
3412 3536 8.851541 TTTTGGAAGTTTATATGTTACTCCGT 57.148 30.769 0.00 0.00 0.00 4.69
3413 3537 9.941325 TTTTGGAAGTTTATATGTTACTCCGTA 57.059 29.630 0.00 0.00 0.00 4.02
3414 3538 8.931385 TTGGAAGTTTATATGTTACTCCGTAC 57.069 34.615 0.00 0.00 0.00 3.67
3426 3550 1.336125 ACTCCGTACAATAGTAGCGGC 59.664 52.381 0.00 0.00 40.98 6.53
3508 3635 6.549912 GGTAATATTACCGATCGCCTTTTT 57.450 37.500 25.21 1.39 43.30 1.94
3516 3643 1.135689 CGATCGCCTTTTTGAGTTGGG 60.136 52.381 0.26 0.00 0.00 4.12
3520 3647 0.969149 GCCTTTTTGAGTTGGGAGGG 59.031 55.000 0.00 0.00 0.00 4.30
3527 3654 3.927481 GAGTTGGGAGGGTGGCTGC 62.927 68.421 0.00 0.00 0.00 5.25
3531 3658 4.748144 GGGAGGGTGGCTGCAAGG 62.748 72.222 0.50 0.00 0.00 3.61
3561 3693 2.161410 GGTGCACGAAATGACATGCTAA 59.839 45.455 11.45 0.00 38.90 3.09
3563 3695 3.787634 GTGCACGAAATGACATGCTAATG 59.212 43.478 0.00 0.00 38.90 1.90
3597 3735 4.446371 CTGGCCTCAAAAGTATCCTACTG 58.554 47.826 3.32 0.00 39.39 2.74
3602 3749 4.383552 CCTCAAAAGTATCCTACTGCTGCT 60.384 45.833 0.00 0.00 39.39 4.24
3603 3750 4.507710 TCAAAAGTATCCTACTGCTGCTG 58.492 43.478 4.89 4.89 39.39 4.41
3604 3751 2.611225 AAGTATCCTACTGCTGCTGC 57.389 50.000 8.89 8.89 39.39 5.25
3605 3752 1.786937 AGTATCCTACTGCTGCTGCT 58.213 50.000 17.00 0.00 37.69 4.24
3606 3753 1.411977 AGTATCCTACTGCTGCTGCTG 59.588 52.381 18.66 18.66 42.70 4.41
3607 3754 0.105593 TATCCTACTGCTGCTGCTGC 59.894 55.000 22.51 22.51 41.07 5.25
3608 3755 1.624479 ATCCTACTGCTGCTGCTGCT 61.624 55.000 27.67 14.24 41.07 4.24
3609 3756 2.107292 CCTACTGCTGCTGCTGCTG 61.107 63.158 27.75 27.75 41.07 4.41
3734 3881 0.320073 TTTGGTAGTGGAACGAGGCG 60.320 55.000 0.00 0.00 45.86 5.52
3866 4013 0.179129 GTGATTGCCATTTCCTGCGG 60.179 55.000 0.00 0.00 0.00 5.69
3889 4036 0.937304 CCATTACGGATTCGCTGGTG 59.063 55.000 0.00 0.00 40.63 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 4.778143 GGTGGCGGTAGGGCTGTG 62.778 72.222 0.00 0.00 42.84 3.66
120 121 5.518487 GCGGTGGGAAACAATTATATTGTTG 59.482 40.000 16.04 5.68 41.30 3.33
121 122 5.420739 AGCGGTGGGAAACAATTATATTGTT 59.579 36.000 11.01 11.01 43.72 2.83
126 127 4.080469 TGGTAGCGGTGGGAAACAATTATA 60.080 41.667 0.00 0.00 0.00 0.98
128 129 2.040012 TGGTAGCGGTGGGAAACAATTA 59.960 45.455 0.00 0.00 0.00 1.40
138 139 2.802057 GCTATACAACTGGTAGCGGTGG 60.802 54.545 7.26 6.98 34.92 4.61
146 147 5.593502 GTGTACTCCTAGCTATACAACTGGT 59.406 44.000 6.51 0.00 29.71 4.00
147 148 5.009811 GGTGTACTCCTAGCTATACAACTGG 59.990 48.000 11.41 0.70 33.36 4.00
148 149 5.593095 TGGTGTACTCCTAGCTATACAACTG 59.407 44.000 17.10 0.00 36.42 3.16
149 150 5.763355 TGGTGTACTCCTAGCTATACAACT 58.237 41.667 17.10 0.00 36.42 3.16
150 151 6.461110 TTGGTGTACTCCTAGCTATACAAC 57.539 41.667 14.75 11.68 36.08 3.32
151 152 7.014326 CAGATTGGTGTACTCCTAGCTATACAA 59.986 40.741 14.25 0.00 29.16 2.41
152 153 6.490381 CAGATTGGTGTACTCCTAGCTATACA 59.510 42.308 14.25 0.00 29.16 2.29
153 154 6.490721 ACAGATTGGTGTACTCCTAGCTATAC 59.509 42.308 14.25 0.00 29.16 1.47
154 155 6.611785 ACAGATTGGTGTACTCCTAGCTATA 58.388 40.000 14.25 0.00 29.16 1.31
155 156 5.459505 ACAGATTGGTGTACTCCTAGCTAT 58.540 41.667 14.25 2.63 29.16 2.97
156 157 4.868268 ACAGATTGGTGTACTCCTAGCTA 58.132 43.478 14.25 0.00 29.16 3.32
157 158 3.714144 ACAGATTGGTGTACTCCTAGCT 58.286 45.455 14.75 12.22 30.10 3.32
158 159 4.081642 TCAACAGATTGGTGTACTCCTAGC 60.082 45.833 14.75 10.16 36.24 3.42
159 160 5.661056 TCAACAGATTGGTGTACTCCTAG 57.339 43.478 14.75 3.57 36.24 3.02
160 161 7.727578 TTATCAACAGATTGGTGTACTCCTA 57.272 36.000 14.75 7.98 36.24 2.94
161 162 6.620877 TTATCAACAGATTGGTGTACTCCT 57.379 37.500 14.75 0.00 36.24 3.69
162 163 7.681939 TTTTATCAACAGATTGGTGTACTCC 57.318 36.000 7.03 7.03 36.24 3.85
233 247 2.778928 CGATTTCTAGAAGTCGCAGTCG 59.221 50.000 29.62 12.52 42.03 4.18
346 361 7.587037 ACTAGTACTGGTACTACAACAACAA 57.413 36.000 10.57 0.00 43.98 2.83
347 362 7.939039 ACTACTAGTACTGGTACTACAACAACA 59.061 37.037 14.52 0.00 43.98 3.33
359 374 7.311408 GTGAATTTCGAACTACTAGTACTGGT 58.689 38.462 16.68 16.68 0.00 4.00
369 384 1.526384 GGCGCGTGAATTTCGAACTAC 60.526 52.381 8.43 0.00 0.00 2.73
370 385 0.717224 GGCGCGTGAATTTCGAACTA 59.283 50.000 8.43 0.00 0.00 2.24
371 386 0.949105 AGGCGCGTGAATTTCGAACT 60.949 50.000 8.43 0.00 0.00 3.01
395 410 1.363807 CACTCACCTGCGAGTCACA 59.636 57.895 0.00 0.00 44.49 3.58
396 411 1.373497 CCACTCACCTGCGAGTCAC 60.373 63.158 0.00 0.00 44.49 3.67
397 412 3.051210 CCACTCACCTGCGAGTCA 58.949 61.111 0.00 0.00 44.49 3.41
448 474 2.436115 GCCTCGTTTTCCCCGGAG 60.436 66.667 0.73 0.00 0.00 4.63
455 481 1.334689 CCTGGTTTTCGCCTCGTTTTC 60.335 52.381 0.00 0.00 0.00 2.29
461 487 3.431725 CCGCCTGGTTTTCGCCTC 61.432 66.667 0.00 0.00 0.00 4.70
543 585 2.284699 AGACGACCAAGGGGGAGG 60.285 66.667 0.00 0.00 41.15 4.30
544 586 2.660064 CCAGACGACCAAGGGGGAG 61.660 68.421 0.00 0.00 41.15 4.30
545 587 2.606519 CCAGACGACCAAGGGGGA 60.607 66.667 0.00 0.00 41.15 4.81
546 588 2.606519 TCCAGACGACCAAGGGGG 60.607 66.667 0.00 0.00 44.81 5.40
547 589 2.660064 CCTCCAGACGACCAAGGGG 61.660 68.421 0.00 0.00 41.29 4.79
548 590 1.608717 CTCCTCCAGACGACCAAGGG 61.609 65.000 0.00 0.00 0.00 3.95
637 679 1.128513 GCTAAAATAAATGCGCGGGC 58.871 50.000 18.81 18.81 40.52 6.13
691 746 1.263356 CTCGAACTTACCTGTGGGGA 58.737 55.000 0.00 0.00 38.76 4.81
692 747 0.249398 CCTCGAACTTACCTGTGGGG 59.751 60.000 0.00 0.00 41.89 4.96
693 748 0.974383 ACCTCGAACTTACCTGTGGG 59.026 55.000 0.00 0.00 38.88 4.61
694 749 1.616865 TCACCTCGAACTTACCTGTGG 59.383 52.381 0.00 0.00 0.00 4.17
695 750 3.380479 TTCACCTCGAACTTACCTGTG 57.620 47.619 0.00 0.00 0.00 3.66
708 763 1.098712 TGCCCGTGTTTGTTCACCTC 61.099 55.000 0.00 0.00 35.18 3.85
713 768 2.725641 GGGTGCCCGTGTTTGTTC 59.274 61.111 0.00 0.00 0.00 3.18
760 815 1.954651 GCATTACCTCTACGGCGGC 60.955 63.158 13.24 0.00 35.61 6.53
769 824 3.554337 CCACCCGTATACAGCATTACCTC 60.554 52.174 3.32 0.00 0.00 3.85
857 930 3.058224 GCTATAAACGGGTGCCATTCATC 60.058 47.826 0.00 0.00 0.00 2.92
953 1038 3.902086 GGTAGACGGAGGCGCTCC 61.902 72.222 7.64 11.60 46.44 4.70
1281 1396 1.990060 CCCGGAGAAGAAGGGCTGA 60.990 63.158 0.73 0.00 38.51 4.26
1368 1483 1.822613 CTGAATCAGCGGCATGGCT 60.823 57.895 18.09 3.98 46.13 4.75
1643 1758 0.680280 GTAGAGTGGAGGAGACGGCA 60.680 60.000 0.00 0.00 0.00 5.69
1857 1972 3.716006 GCGCGCTTGAGAGTTGCA 61.716 61.111 26.67 0.00 0.00 4.08
1956 2071 3.469970 TGCTGGGACGATGCCGAT 61.470 61.111 0.00 0.00 39.50 4.18
2017 2132 1.141881 GCGTGATGTCGTGGAGGAT 59.858 57.895 0.00 0.00 0.00 3.24
2193 2308 2.433664 GTTACGGCGGTCACCTGG 60.434 66.667 13.24 0.00 0.00 4.45
2292 2407 1.069258 GTGGTACTCTATGCCGGCC 59.931 63.158 26.77 6.44 35.35 6.13
2334 2449 0.182061 TGGATGCCTCAATCTCTGCC 59.818 55.000 0.00 0.00 0.00 4.85
2494 2609 2.125753 CTCCTGCTCCACGAGTGC 60.126 66.667 0.00 0.00 35.49 4.40
3007 3128 9.640963 GCTTTACTACTAGATCAAGAAGAACAA 57.359 33.333 0.00 0.00 0.00 2.83
3008 3129 9.026121 AGCTTTACTACTAGATCAAGAAGAACA 57.974 33.333 0.00 0.00 0.00 3.18
3009 3130 9.863845 AAGCTTTACTACTAGATCAAGAAGAAC 57.136 33.333 0.00 0.00 0.00 3.01
3012 3133 9.458374 GCTAAGCTTTACTACTAGATCAAGAAG 57.542 37.037 3.20 0.00 0.00 2.85
3106 3228 2.344142 GCAACAGGTGACAAAAACAACG 59.656 45.455 0.00 0.00 0.00 4.10
3202 3324 3.899360 ACTACTTGGGCAGTACAACTACA 59.101 43.478 0.00 0.00 36.88 2.74
3332 3454 2.989166 GACCAACTACTTTTACCGACGG 59.011 50.000 13.61 13.61 0.00 4.79
3372 3496 8.859236 AACTTCCAAAATTTACTACTCCTACC 57.141 34.615 0.00 0.00 0.00 3.18
3407 3531 1.607628 AGCCGCTACTATTGTACGGAG 59.392 52.381 22.15 2.60 41.40 4.63
3408 3532 1.683943 AGCCGCTACTATTGTACGGA 58.316 50.000 22.15 0.00 41.40 4.69
3409 3533 2.124903 CAAGCCGCTACTATTGTACGG 58.875 52.381 17.23 17.23 41.59 4.02
3410 3534 2.805845 ACAAGCCGCTACTATTGTACG 58.194 47.619 0.00 0.00 34.26 3.67
3411 3535 3.930848 ACAACAAGCCGCTACTATTGTAC 59.069 43.478 8.81 0.00 34.92 2.90
3412 3536 4.196626 ACAACAAGCCGCTACTATTGTA 57.803 40.909 8.81 0.00 34.92 2.41
3413 3537 3.053831 ACAACAAGCCGCTACTATTGT 57.946 42.857 0.00 0.00 37.47 2.71
3414 3538 3.483574 CGAACAACAAGCCGCTACTATTG 60.484 47.826 0.00 0.00 0.00 1.90
3446 3571 1.515081 CAAGGGGCAACAAAGCAATG 58.485 50.000 0.00 0.00 39.74 2.82
3492 3619 3.048337 ACTCAAAAAGGCGATCGGTAA 57.952 42.857 18.30 0.00 0.00 2.85
3495 3622 1.135689 CCAACTCAAAAAGGCGATCGG 60.136 52.381 18.30 0.00 0.00 4.18
3508 3635 2.121963 AGCCACCCTCCCAACTCA 60.122 61.111 0.00 0.00 0.00 3.41
3516 3643 3.210012 TTCCCTTGCAGCCACCCTC 62.210 63.158 0.00 0.00 0.00 4.30
3520 3647 0.034670 ATCTCTTCCCTTGCAGCCAC 60.035 55.000 0.00 0.00 0.00 5.01
3527 3654 1.457346 GTGCACCATCTCTTCCCTTG 58.543 55.000 5.22 0.00 0.00 3.61
3531 3658 1.808411 TTTCGTGCACCATCTCTTCC 58.192 50.000 12.15 0.00 0.00 3.46
3561 3693 2.675423 CCAGCCAGTGCAGCACAT 60.675 61.111 27.35 9.83 41.13 3.21
3609 3756 2.866085 AATCGGAGAGTGCAGCCAGC 62.866 60.000 0.00 0.00 43.63 4.85
3610 3757 0.392193 AAATCGGAGAGTGCAGCCAG 60.392 55.000 0.00 0.00 43.63 4.85
3611 3758 0.674581 CAAATCGGAGAGTGCAGCCA 60.675 55.000 0.00 0.00 43.63 4.75
3734 3881 0.876342 GCACTACAGGCATAGGCGAC 60.876 60.000 0.00 0.00 42.47 5.19
3738 3885 1.208052 ACACAGCACTACAGGCATAGG 59.792 52.381 1.51 0.00 0.00 2.57
3797 3944 0.955428 TAAGCAACCGAGGCAAGCAG 60.955 55.000 0.00 0.00 0.00 4.24
3866 4013 2.935955 CGAATCCGTAATGGGCGC 59.064 61.111 0.00 0.00 38.76 6.53


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

AutoCloner maintained by Alex Coulton.