Multiple sequence alignment - TraesCS2D01G383200

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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 TraesCS2D01G383200 chr2D 100.000 2489 0 0 1 2489 487492419 487494907 0.000000e+00 4597.0
1 TraesCS2D01G383200 chr2D 89.241 158 15 2 125 281 549021009 549020853 1.950000e-46 196.0
2 TraesCS2D01G383200 chr2D 86.076 158 21 1 125 281 551152202 551152359 4.260000e-38 169.0
3 TraesCS2D01G383200 chr2B 88.828 1835 105 27 165 1943 572155502 572157292 0.000000e+00 2161.0
4 TraesCS2D01G383200 chr2B 89.234 548 18 21 1948 2489 572157497 572158009 0.000000e+00 647.0
5 TraesCS2D01G383200 chr2B 99.010 101 1 0 2 102 572155367 572155467 5.470000e-42 182.0
6 TraesCS2D01G383200 chr2A 88.173 1877 89 53 532 2335 632506560 632508376 0.000000e+00 2113.0
7 TraesCS2D01G383200 chr2A 93.333 90 6 0 2400 2489 632508400 632508489 1.550000e-27 134.0
8 TraesCS2D01G383200 chr4D 88.125 160 17 2 123 281 75266906 75266748 3.270000e-44 189.0
9 TraesCS2D01G383200 chr7A 88.742 151 15 2 131 281 719336325 719336177 1.520000e-42 183.0
10 TraesCS2D01G383200 chr7A 86.585 164 20 2 119 281 597552833 597552995 1.970000e-41 180.0
11 TraesCS2D01G383200 chr3A 86.538 156 20 1 131 286 607058423 607058577 1.180000e-38 171.0
12 TraesCS2D01G383200 chr3A 84.756 164 23 2 119 281 478426330 478426492 1.980000e-36 163.0
13 TraesCS2D01G383200 chr1D 85.625 160 21 2 123 281 462491083 462490925 1.530000e-37 167.0
14 TraesCS2D01G383200 chr1B 88.732 71 7 1 44 113 297727293 297727223 4.410000e-13 86.1
15 TraesCS2D01G383200 chr3D 100.000 30 0 0 54 83 61188678 61188649 3.460000e-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 TraesCS2D01G383200 chr2D 487492419 487494907 2488 False 4597.000000 4597 100.000000 1 2489 1 chr2D.!!$F1 2488
1 TraesCS2D01G383200 chr2B 572155367 572158009 2642 False 996.666667 2161 92.357333 2 2489 3 chr2B.!!$F1 2487
2 TraesCS2D01G383200 chr2A 632506560 632508489 1929 False 1123.500000 2113 90.753000 532 2489 2 chr2A.!!$F1 1957

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
451 457 0.043053 CGCGTAATTGCATCGACAGG 60.043 55.0 0.0 0.0 34.15 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2019 2298 0.042731 TCCTTCCTAGGTGGGGACTG 59.957 60.0 18.72 0.0 42.6 3.51 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
102 103 7.159322 AGCTACGTCTTATATTGTGGGATAG 57.841 40.000 0.00 0.00 0.00 2.08
104 105 7.450634 AGCTACGTCTTATATTGTGGGATAGAA 59.549 37.037 0.00 0.00 0.00 2.10
105 106 7.755822 GCTACGTCTTATATTGTGGGATAGAAG 59.244 40.741 0.00 0.00 33.97 2.85
106 107 6.994221 ACGTCTTATATTGTGGGATAGAAGG 58.006 40.000 0.00 0.00 33.66 3.46
108 109 7.039644 ACGTCTTATATTGTGGGATAGAAGGAG 60.040 40.741 0.00 0.00 33.66 3.69
110 111 9.310449 GTCTTATATTGTGGGATAGAAGGAGTA 57.690 37.037 0.00 0.00 33.66 2.59
111 112 9.535170 TCTTATATTGTGGGATAGAAGGAGTAG 57.465 37.037 0.00 0.00 33.66 2.57
112 113 9.315363 CTTATATTGTGGGATAGAAGGAGTAGT 57.685 37.037 0.00 0.00 30.77 2.73
113 114 9.670442 TTATATTGTGGGATAGAAGGAGTAGTT 57.330 33.333 0.00 0.00 0.00 2.24
114 115 6.893020 ATTGTGGGATAGAAGGAGTAGTTT 57.107 37.500 0.00 0.00 0.00 2.66
115 116 5.934402 TGTGGGATAGAAGGAGTAGTTTC 57.066 43.478 0.00 0.00 0.00 2.78
116 117 5.590818 TGTGGGATAGAAGGAGTAGTTTCT 58.409 41.667 0.00 0.00 37.42 2.52
117 118 6.023603 TGTGGGATAGAAGGAGTAGTTTCTT 58.976 40.000 0.00 0.00 35.42 2.52
118 119 6.154706 TGTGGGATAGAAGGAGTAGTTTCTTC 59.845 42.308 6.53 6.53 37.68 2.87
119 120 6.381707 GTGGGATAGAAGGAGTAGTTTCTTCT 59.618 42.308 16.32 16.32 46.04 2.85
126 127 8.673456 AGAAGGAGTAGTTTCTTCTATTTCCT 57.327 34.615 12.59 0.00 43.53 3.36
127 128 8.755028 AGAAGGAGTAGTTTCTTCTATTTCCTC 58.245 37.037 12.59 0.00 43.53 3.71
129 130 6.097129 AGGAGTAGTTTCTTCTATTTCCTCGG 59.903 42.308 0.00 0.00 34.67 4.63
130 131 6.127394 GGAGTAGTTTCTTCTATTTCCTCGGT 60.127 42.308 0.00 0.00 0.00 4.69
132 133 5.087391 AGTTTCTTCTATTTCCTCGGTCC 57.913 43.478 0.00 0.00 0.00 4.46
133 134 4.778427 AGTTTCTTCTATTTCCTCGGTCCT 59.222 41.667 0.00 0.00 0.00 3.85
135 136 6.439692 AGTTTCTTCTATTTCCTCGGTCCTAA 59.560 38.462 0.00 0.00 0.00 2.69
136 137 6.862469 TTCTTCTATTTCCTCGGTCCTAAA 57.138 37.500 0.00 0.00 0.00 1.85
137 138 7.433537 TTCTTCTATTTCCTCGGTCCTAAAT 57.566 36.000 0.00 0.00 0.00 1.40
138 139 8.543293 TTCTTCTATTTCCTCGGTCCTAAATA 57.457 34.615 0.00 0.00 0.00 1.40
139 140 8.722622 TCTTCTATTTCCTCGGTCCTAAATAT 57.277 34.615 0.00 0.00 0.00 1.28
140 141 9.818270 TCTTCTATTTCCTCGGTCCTAAATATA 57.182 33.333 0.00 0.00 0.00 0.86
143 144 9.818270 TCTATTTCCTCGGTCCTAAATATAAGA 57.182 33.333 0.00 0.00 0.00 2.10
144 145 9.857957 CTATTTCCTCGGTCCTAAATATAAGAC 57.142 37.037 0.00 0.00 0.00 3.01
145 146 6.661304 TTCCTCGGTCCTAAATATAAGACC 57.339 41.667 0.00 0.00 44.42 3.85
146 147 5.961897 TCCTCGGTCCTAAATATAAGACCT 58.038 41.667 6.48 0.00 45.45 3.85
147 148 6.379579 TCCTCGGTCCTAAATATAAGACCTT 58.620 40.000 6.48 0.00 45.45 3.50
148 149 6.267014 TCCTCGGTCCTAAATATAAGACCTTG 59.733 42.308 6.48 0.00 45.45 3.61
149 150 6.041751 CCTCGGTCCTAAATATAAGACCTTGT 59.958 42.308 6.48 0.00 45.45 3.16
150 151 7.232127 CCTCGGTCCTAAATATAAGACCTTGTA 59.768 40.741 6.48 0.00 45.45 2.41
151 152 8.174733 TCGGTCCTAAATATAAGACCTTGTAG 57.825 38.462 6.48 0.00 45.45 2.74
152 153 8.000709 TCGGTCCTAAATATAAGACCTTGTAGA 58.999 37.037 6.48 0.00 45.45 2.59
153 154 8.298140 CGGTCCTAAATATAAGACCTTGTAGAG 58.702 40.741 6.48 0.00 45.45 2.43
154 155 9.364653 GGTCCTAAATATAAGACCTTGTAGAGA 57.635 37.037 0.80 0.00 44.46 3.10
167 168 8.697292 AGACCTTGTAGAGATTTTACTATGGAC 58.303 37.037 0.00 0.00 0.00 4.02
275 276 9.946165 AAAAAGTCTTGTATTTAGAAACGAAGG 57.054 29.630 0.00 0.00 0.00 3.46
276 277 7.668525 AAGTCTTGTATTTAGAAACGAAGGG 57.331 36.000 0.00 0.00 0.00 3.95
277 278 7.001099 AGTCTTGTATTTAGAAACGAAGGGA 57.999 36.000 0.00 0.00 0.00 4.20
278 279 7.097834 AGTCTTGTATTTAGAAACGAAGGGAG 58.902 38.462 0.00 0.00 0.00 4.30
279 280 6.872547 GTCTTGTATTTAGAAACGAAGGGAGT 59.127 38.462 0.00 0.00 0.00 3.85
280 281 8.031277 GTCTTGTATTTAGAAACGAAGGGAGTA 58.969 37.037 0.00 0.00 0.00 2.59
281 282 8.755977 TCTTGTATTTAGAAACGAAGGGAGTAT 58.244 33.333 0.00 0.00 0.00 2.12
319 324 8.830580 CACTCAAACACTATTACATTATGGGAG 58.169 37.037 0.00 0.00 0.00 4.30
352 358 2.104170 ACTAGCTAGCTGTGGTCCTTC 58.896 52.381 27.68 0.00 0.00 3.46
402 408 1.379843 ATTTGGACATCCCACGGCC 60.380 57.895 0.00 0.00 46.62 6.13
405 411 1.622607 TTGGACATCCCACGGCCTAG 61.623 60.000 0.00 0.00 46.62 3.02
423 429 1.800805 AGACTCCGTCAACATGCAAG 58.199 50.000 0.00 0.00 34.60 4.01
424 430 1.070758 AGACTCCGTCAACATGCAAGT 59.929 47.619 0.00 0.00 34.60 3.16
425 431 1.873591 GACTCCGTCAACATGCAAGTT 59.126 47.619 0.51 0.51 32.09 2.66
428 434 2.549754 CTCCGTCAACATGCAAGTTCTT 59.450 45.455 3.95 0.00 0.00 2.52
445 451 2.514902 TCTTTTGCGCGTAATTGCATC 58.485 42.857 11.23 0.00 41.42 3.91
451 457 0.043053 CGCGTAATTGCATCGACAGG 60.043 55.000 0.00 0.00 34.15 4.00
457 463 2.209838 ATTGCATCGACAGGAGTACG 57.790 50.000 0.00 0.00 0.00 3.67
461 467 1.135489 GCATCGACAGGAGTACGTGAA 60.135 52.381 0.00 0.00 36.05 3.18
467 473 4.880120 TCGACAGGAGTACGTGAATCTATT 59.120 41.667 0.00 0.00 36.05 1.73
469 475 5.455849 CGACAGGAGTACGTGAATCTATTTG 59.544 44.000 0.00 0.00 36.05 2.32
470 476 6.282199 ACAGGAGTACGTGAATCTATTTGT 57.718 37.500 0.00 0.00 36.05 2.83
471 477 7.400599 ACAGGAGTACGTGAATCTATTTGTA 57.599 36.000 0.00 0.00 36.05 2.41
472 478 7.256286 ACAGGAGTACGTGAATCTATTTGTAC 58.744 38.462 0.00 0.00 36.05 2.90
473 479 7.122353 ACAGGAGTACGTGAATCTATTTGTACT 59.878 37.037 0.00 12.33 43.61 2.73
474 480 7.432545 CAGGAGTACGTGAATCTATTTGTACTG 59.567 40.741 15.22 0.00 41.68 2.74
475 481 7.338703 AGGAGTACGTGAATCTATTTGTACTGA 59.661 37.037 15.22 0.00 41.68 3.41
476 482 8.136165 GGAGTACGTGAATCTATTTGTACTGAT 58.864 37.037 15.22 0.00 41.68 2.90
483 489 6.883756 TGAATCTATTTGTACTGATTGTGGCA 59.116 34.615 0.00 0.00 30.41 4.92
484 490 6.932356 ATCTATTTGTACTGATTGTGGCAG 57.068 37.500 0.00 0.00 39.26 4.85
506 512 3.078836 CAGGCCAGCCAAATGGGG 61.079 66.667 12.03 0.00 40.97 4.96
520 526 3.782443 GGGGGTAGTGTGGCGGAG 61.782 72.222 0.00 0.00 0.00 4.63
621 636 3.570975 ACCGAAAACCAGGTAAAATCACC 59.429 43.478 0.00 0.00 39.30 4.02
639 654 8.932945 AAATCACCTCAAAAGAAGAAGAAAAC 57.067 30.769 0.00 0.00 0.00 2.43
680 695 4.007659 ACAAATACCCCACACGAAATCTC 58.992 43.478 0.00 0.00 0.00 2.75
691 706 0.539051 CGAAATCTCCTCCTGCCAGT 59.461 55.000 0.00 0.00 0.00 4.00
748 763 4.546570 GAACCTTCCTTTCATCAAAACGG 58.453 43.478 0.00 0.00 0.00 4.44
771 786 1.222115 ACGACGAGCTGCAGGAAAAC 61.222 55.000 17.12 0.00 0.00 2.43
773 788 0.235926 GACGAGCTGCAGGAAAACAC 59.764 55.000 17.12 0.00 0.00 3.32
774 789 0.463654 ACGAGCTGCAGGAAAACACA 60.464 50.000 17.12 0.00 0.00 3.72
775 790 0.877071 CGAGCTGCAGGAAAACACAT 59.123 50.000 17.12 0.00 0.00 3.21
777 792 1.881973 GAGCTGCAGGAAAACACATCA 59.118 47.619 17.12 0.00 0.00 3.07
779 794 2.694628 AGCTGCAGGAAAACACATCAAA 59.305 40.909 17.12 0.00 0.00 2.69
780 795 3.132646 AGCTGCAGGAAAACACATCAAAA 59.867 39.130 17.12 0.00 0.00 2.44
958 978 1.258445 GCTCGTCCAGGAAAGGAGGA 61.258 60.000 12.95 5.42 46.93 3.71
1494 1535 2.900273 GCCAGGTGGTAGCATCGA 59.100 61.111 0.00 0.00 37.57 3.59
1495 1536 1.447643 GCCAGGTGGTAGCATCGAT 59.552 57.895 0.00 0.00 37.57 3.59
1629 1702 3.420893 TGATTCATCTTCCTGCCGTTTT 58.579 40.909 0.00 0.00 0.00 2.43
1702 1780 4.039609 ACTCATCTATGGATTGTCGATGCA 59.960 41.667 0.00 0.00 40.59 3.96
1704 1782 5.173664 TCATCTATGGATTGTCGATGCATC 58.826 41.667 17.10 17.10 42.42 3.91
1870 1948 3.335579 ACACAAAAGGTTCTATCGGAGC 58.664 45.455 0.00 0.00 0.00 4.70
1871 1949 3.244422 ACACAAAAGGTTCTATCGGAGCA 60.244 43.478 0.00 0.00 0.00 4.26
1939 2018 7.414098 GCCTAGAAATTTCTCACGAGCAAAATA 60.414 37.037 23.70 1.42 38.70 1.40
1943 2022 8.660373 AGAAATTTCTCACGAGCAAAATACTAG 58.340 33.333 15.11 0.00 29.94 2.57
1944 2023 5.779806 TTTCTCACGAGCAAAATACTAGC 57.220 39.130 0.00 0.00 0.00 3.42
2018 2297 0.537653 GCCACTCAGTTACTCCTCCC 59.462 60.000 0.00 0.00 0.00 4.30
2019 2298 1.196012 CCACTCAGTTACTCCTCCCC 58.804 60.000 0.00 0.00 0.00 4.81
2020 2299 1.552486 CCACTCAGTTACTCCTCCCCA 60.552 57.143 0.00 0.00 0.00 4.96
2021 2300 1.827969 CACTCAGTTACTCCTCCCCAG 59.172 57.143 0.00 0.00 0.00 4.45
2117 2396 1.296145 GTCACGCACGCATGATTCG 60.296 57.895 0.00 0.00 0.00 3.34
2118 2397 2.645628 CACGCACGCATGATTCGC 60.646 61.111 0.00 0.00 0.00 4.70
2119 2398 3.864686 ACGCACGCATGATTCGCC 61.865 61.111 0.00 0.00 0.00 5.54
2120 2399 3.566853 CGCACGCATGATTCGCCT 61.567 61.111 0.00 0.00 0.00 5.52
2121 2400 2.325857 GCACGCATGATTCGCCTC 59.674 61.111 0.00 0.00 0.00 4.70
2433 2735 2.744377 TGGAATTCCACCGCGACA 59.256 55.556 23.63 0.00 42.01 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.576662 TCTTACCTATCTCTAGGAAATGCG 57.423 41.667 5.70 0.00 46.66 4.73
102 103 7.703197 CGAGGAAATAGAAGAAACTACTCCTTC 59.297 40.741 0.00 0.00 37.77 3.46
104 105 6.097129 CCGAGGAAATAGAAGAAACTACTCCT 59.903 42.308 0.00 0.00 39.08 3.69
105 106 6.127394 ACCGAGGAAATAGAAGAAACTACTCC 60.127 42.308 0.00 0.00 32.40 3.85
106 107 6.865411 ACCGAGGAAATAGAAGAAACTACTC 58.135 40.000 0.00 0.00 0.00 2.59
108 109 6.041511 GGACCGAGGAAATAGAAGAAACTAC 58.958 44.000 0.00 0.00 0.00 2.73
110 111 4.778427 AGGACCGAGGAAATAGAAGAAACT 59.222 41.667 0.00 0.00 0.00 2.66
111 112 5.087391 AGGACCGAGGAAATAGAAGAAAC 57.913 43.478 0.00 0.00 0.00 2.78
112 113 6.862469 TTAGGACCGAGGAAATAGAAGAAA 57.138 37.500 0.00 0.00 0.00 2.52
113 114 6.862469 TTTAGGACCGAGGAAATAGAAGAA 57.138 37.500 0.00 0.00 0.00 2.52
114 115 8.722622 ATATTTAGGACCGAGGAAATAGAAGA 57.277 34.615 0.00 0.00 29.76 2.87
117 118 9.818270 TCTTATATTTAGGACCGAGGAAATAGA 57.182 33.333 0.00 0.00 29.76 1.98
118 119 9.857957 GTCTTATATTTAGGACCGAGGAAATAG 57.142 37.037 0.00 0.00 30.29 1.73
119 120 8.810041 GGTCTTATATTTAGGACCGAGGAAATA 58.190 37.037 8.38 0.00 42.62 1.40
120 121 7.677892 GGTCTTATATTTAGGACCGAGGAAAT 58.322 38.462 8.38 0.00 42.62 2.17
122 123 6.661304 GGTCTTATATTTAGGACCGAGGAA 57.339 41.667 8.38 0.00 42.62 3.36
140 141 9.268282 TCCATAGTAAAATCTCTACAAGGTCTT 57.732 33.333 0.00 0.00 0.00 3.01
141 142 8.697292 GTCCATAGTAAAATCTCTACAAGGTCT 58.303 37.037 0.00 0.00 0.00 3.85
142 143 8.697292 AGTCCATAGTAAAATCTCTACAAGGTC 58.303 37.037 0.00 0.00 0.00 3.85
143 144 8.611051 AGTCCATAGTAAAATCTCTACAAGGT 57.389 34.615 0.00 0.00 0.00 3.50
144 145 9.968870 GTAGTCCATAGTAAAATCTCTACAAGG 57.031 37.037 0.00 0.00 0.00 3.61
162 163 9.520515 ACTCATTTTTCTTTGTATGTAGTCCAT 57.479 29.630 0.00 0.00 37.58 3.41
163 164 8.783093 CACTCATTTTTCTTTGTATGTAGTCCA 58.217 33.333 0.00 0.00 0.00 4.02
273 274 9.802039 TTGAGTGTTTGTTTTATTATACTCCCT 57.198 29.630 0.00 0.00 34.06 4.20
319 324 7.593273 CACAGCTAGCTAGTTTATACTCATCAC 59.407 40.741 18.86 0.26 35.78 3.06
423 429 2.047769 TGCAATTACGCGCAAAAGAAC 58.952 42.857 5.73 0.00 34.59 3.01
424 430 2.407521 TGCAATTACGCGCAAAAGAA 57.592 40.000 5.73 0.00 34.59 2.52
425 431 2.514902 GATGCAATTACGCGCAAAAGA 58.485 42.857 5.73 0.00 42.37 2.52
428 434 0.444260 TCGATGCAATTACGCGCAAA 59.556 45.000 5.73 0.20 42.37 3.68
445 451 4.815040 ATAGATTCACGTACTCCTGTCG 57.185 45.455 0.00 0.00 0.00 4.35
451 457 9.517609 AATCAGTACAAATAGATTCACGTACTC 57.482 33.333 0.00 0.00 37.93 2.59
457 463 7.148255 TGCCACAATCAGTACAAATAGATTCAC 60.148 37.037 0.00 0.00 0.00 3.18
461 467 6.653020 TCTGCCACAATCAGTACAAATAGAT 58.347 36.000 0.00 0.00 33.48 1.98
467 473 3.253188 GCTTTCTGCCACAATCAGTACAA 59.747 43.478 0.00 0.00 35.15 2.41
469 475 2.813754 TGCTTTCTGCCACAATCAGTAC 59.186 45.455 0.00 0.00 42.00 2.73
470 476 3.076621 CTGCTTTCTGCCACAATCAGTA 58.923 45.455 0.00 0.00 42.00 2.74
471 477 1.884579 CTGCTTTCTGCCACAATCAGT 59.115 47.619 0.00 0.00 42.00 3.41
472 478 1.201647 CCTGCTTTCTGCCACAATCAG 59.798 52.381 0.00 0.00 42.00 2.90
473 479 1.250328 CCTGCTTTCTGCCACAATCA 58.750 50.000 0.00 0.00 42.00 2.57
474 480 0.108945 GCCTGCTTTCTGCCACAATC 60.109 55.000 0.00 0.00 42.00 2.67
475 481 1.538687 GGCCTGCTTTCTGCCACAAT 61.539 55.000 0.00 0.00 44.70 2.71
476 482 2.202395 GGCCTGCTTTCTGCCACAA 61.202 57.895 0.00 0.00 44.70 3.33
483 489 0.543646 ATTTGGCTGGCCTGCTTTCT 60.544 50.000 30.65 13.21 36.94 2.52
484 490 0.390735 CATTTGGCTGGCCTGCTTTC 60.391 55.000 30.65 16.88 36.94 2.62
492 498 1.758122 CTACCCCCATTTGGCTGGC 60.758 63.158 0.00 0.00 34.77 4.85
494 500 0.039618 ACACTACCCCCATTTGGCTG 59.960 55.000 0.00 0.00 0.00 4.85
520 526 0.588252 CCATGATTTCATCCGTCGGC 59.412 55.000 6.34 0.00 33.61 5.54
521 527 1.867233 GTCCATGATTTCATCCGTCGG 59.133 52.381 4.39 4.39 33.61 4.79
523 529 2.614057 GTGGTCCATGATTTCATCCGTC 59.386 50.000 0.00 0.00 33.61 4.79
524 530 2.643551 GTGGTCCATGATTTCATCCGT 58.356 47.619 0.00 0.00 33.61 4.69
525 531 1.599071 CGTGGTCCATGATTTCATCCG 59.401 52.381 4.96 0.00 33.61 4.18
526 532 2.614057 GTCGTGGTCCATGATTTCATCC 59.386 50.000 16.92 0.00 33.61 3.51
527 533 2.614057 GGTCGTGGTCCATGATTTCATC 59.386 50.000 16.92 3.07 33.61 2.92
529 535 1.674519 CGGTCGTGGTCCATGATTTCA 60.675 52.381 16.92 0.00 31.77 2.69
621 636 7.326063 ACGTGTTTGTTTTCTTCTTCTTTTGAG 59.674 33.333 0.00 0.00 0.00 3.02
639 654 4.822036 TGTCTGGGATTTTACGTGTTTG 57.178 40.909 0.00 0.00 0.00 2.93
748 763 0.944311 TCCTGCAGCTCGTCGTTTTC 60.944 55.000 8.66 0.00 0.00 2.29
777 792 9.406828 GCGTTTTTGAGATCCTACTAAAATTTT 57.593 29.630 8.75 8.75 0.00 1.82
779 794 7.535997 GGCGTTTTTGAGATCCTACTAAAATT 58.464 34.615 0.00 0.00 0.00 1.82
780 795 6.183360 CGGCGTTTTTGAGATCCTACTAAAAT 60.183 38.462 0.00 0.00 0.00 1.82
843 858 0.250770 GTGGGGGAAGTGGACTGTTC 60.251 60.000 0.00 0.00 0.00 3.18
1464 1505 1.675641 CCTGGCGAACCCCTTCTTG 60.676 63.158 0.00 0.00 33.59 3.02
1494 1535 0.112801 GACTCCTAGGCCTACGGGAT 59.887 60.000 18.62 10.60 33.58 3.85
1495 1536 1.535685 GACTCCTAGGCCTACGGGA 59.464 63.158 17.59 17.59 33.58 5.14
1629 1702 2.394632 ACCGCATCCATCCACTAGTTA 58.605 47.619 0.00 0.00 0.00 2.24
1739 1817 2.468777 CAGATTTGTCAACAGCAAACGC 59.531 45.455 0.00 0.00 38.44 4.84
1939 2018 1.672881 GAATTCAATGGCGCTGCTAGT 59.327 47.619 7.64 0.00 0.00 2.57
1943 2022 1.205657 CATGAATTCAATGGCGCTGC 58.794 50.000 13.09 0.00 0.00 5.25
1944 2023 1.202371 AGCATGAATTCAATGGCGCTG 60.202 47.619 13.09 5.43 0.00 5.18
2018 2297 0.983378 CCTTCCTAGGTGGGGACTGG 60.983 65.000 9.08 0.00 36.74 4.00
2019 2298 0.042731 TCCTTCCTAGGTGGGGACTG 59.957 60.000 18.72 0.00 42.60 3.51
2020 2299 0.797579 TTCCTTCCTAGGTGGGGACT 59.202 55.000 18.72 0.00 42.60 3.85
2021 2300 1.205055 CTTCCTTCCTAGGTGGGGAC 58.795 60.000 18.72 0.00 42.60 4.46
2038 2317 3.286329 AGTTTGTACCGTTCCCAACTT 57.714 42.857 0.00 0.00 0.00 2.66
2039 2318 3.286329 AAGTTTGTACCGTTCCCAACT 57.714 42.857 0.00 0.00 0.00 3.16
2040 2319 4.024641 CAGTAAGTTTGTACCGTTCCCAAC 60.025 45.833 0.00 0.00 0.00 3.77
2041 2320 4.128643 CAGTAAGTTTGTACCGTTCCCAA 58.871 43.478 0.00 0.00 0.00 4.12
2119 2398 2.742372 CTCCAACCAACCGCCGAG 60.742 66.667 0.00 0.00 0.00 4.63
2211 2496 1.447217 CATCACGCCTATGGAGCCA 59.553 57.895 0.00 0.00 0.00 4.75
2212 2497 1.963338 GCATCACGCCTATGGAGCC 60.963 63.158 0.00 0.00 32.94 4.70
2248 2538 4.077188 GTGCTCGTTGGCTGTCGC 62.077 66.667 0.00 0.00 0.00 5.19
2397 2697 2.332654 CCGGAAGAAAAGGGTGCCG 61.333 63.158 0.00 0.00 38.54 5.69
2398 2698 1.228459 ACCGGAAGAAAAGGGTGCC 60.228 57.895 9.46 0.00 0.00 5.01
2402 2704 2.215942 ATTCCACCGGAAGAAAAGGG 57.784 50.000 9.46 0.00 45.48 3.95


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

AutoCloner maintained by Alex Coulton.