Multiple sequence alignment - TraesCS2A01G422600

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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 TraesCS2A01G422600 chr2A 100.000 6213 0 0 1 6213 677524824 677531036 0.000000e+00 11474
1 TraesCS2A01G422600 chr2B 92.884 5635 226 63 1 5573 632915611 632921132 0.000000e+00 8022
2 TraesCS2A01G422600 chr2B 92.488 426 32 0 5788 6213 632921727 632922152 1.480000e-170 610
3 TraesCS2A01G422600 chr2B 80.074 542 66 21 3162 3684 769596902 769596384 1.270000e-96 364
4 TraesCS2A01G422600 chr2B 85.446 213 19 3 5574 5774 632921439 632921651 1.750000e-50 211
5 TraesCS2A01G422600 chr2D 91.395 2789 163 44 1 2759 533132050 533134791 0.000000e+00 3749
6 TraesCS2A01G422600 chr2D 95.315 2241 66 8 3367 5573 533135416 533137651 0.000000e+00 3520
7 TraesCS2A01G422600 chr2D 90.783 651 45 4 5578 6213 533137909 533138559 0.000000e+00 856
8 TraesCS2A01G422600 chr2D 89.299 542 31 19 2756 3297 533134911 533135425 0.000000e+00 654
9 TraesCS2A01G422600 chr6B 84.789 355 47 4 2794 3143 376338534 376338886 3.560000e-92 350
10 TraesCS2A01G422600 chr6B 79.406 539 75 21 3162 3684 376338878 376339396 1.280000e-91 348
11 TraesCS2A01G422600 chr6B 83.537 328 33 13 4908 5232 376339400 376339709 2.830000e-73 287
12 TraesCS2A01G422600 chr6B 83.699 319 31 12 4917 5232 201998805 201998505 1.320000e-71 281


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 TraesCS2A01G422600 chr2A 677524824 677531036 6212 False 11474.000000 11474 100.000000 1 6213 1 chr2A.!!$F1 6212
1 TraesCS2A01G422600 chr2B 632915611 632922152 6541 False 2947.666667 8022 90.272667 1 6213 3 chr2B.!!$F1 6212
2 TraesCS2A01G422600 chr2B 769596384 769596902 518 True 364.000000 364 80.074000 3162 3684 1 chr2B.!!$R1 522
3 TraesCS2A01G422600 chr2D 533132050 533138559 6509 False 2194.750000 3749 91.698000 1 6213 4 chr2D.!!$F1 6212
4 TraesCS2A01G422600 chr6B 376338534 376339709 1175 False 328.333333 350 82.577333 2794 5232 3 chr6B.!!$F1 2438

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
338 365 0.106519 CCATCCAAATCCCGGAGCTT 60.107 55.000 0.73 0.00 35.56 3.74 F
460 492 0.322008 CCTGCCGCTTCTTCCTTTCT 60.322 55.000 0.00 0.00 0.00 2.52 F
629 665 0.462375 GGTTTTCGGCTGGTTGGTTT 59.538 50.000 0.00 0.00 0.00 3.27 F
1011 1058 1.032794 AGAGATCAATGGCGTCGCTA 58.967 50.000 18.11 12.27 0.00 4.26 F
1257 1305 2.418976 CTCTGCATGTGACCAGTTCATG 59.581 50.000 0.00 10.48 40.98 3.07 F
2088 2139 2.076863 ACGCCAAGCACAGTAGAATTC 58.923 47.619 0.00 0.00 0.00 2.17 F
2263 2317 2.942804 TGGAAACAACTCTTCCATGCA 58.057 42.857 0.13 0.00 45.88 3.96 F
3349 3532 2.497273 GCCAAATGTGTGCTCCCTAATT 59.503 45.455 0.00 0.00 0.00 1.40 F
4579 4787 1.471676 CCTGCTATCCACTCGGTTGTC 60.472 57.143 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1232 1280 1.001746 ACTGGTCACATGCAGAGACTG 59.998 52.381 13.49 10.12 37.87 3.51 R
1472 1521 2.280797 GACACACCTGGAAGCGCA 60.281 61.111 11.47 0.00 0.00 6.09 R
2066 2117 2.823924 TTCTACTGTGCTTGGCGTTA 57.176 45.000 0.00 0.00 0.00 3.18 R
2070 2121 4.708726 ATTGAATTCTACTGTGCTTGGC 57.291 40.909 7.05 0.00 0.00 4.52 R
3061 3244 4.202430 ACGGTCCAGGTGTTAGAAGAATTT 60.202 41.667 0.00 0.00 0.00 1.82 R
3271 3454 1.252904 CCTGAATGGCCAACACAGGG 61.253 60.000 31.35 19.75 42.77 4.45 R
4100 4308 1.788258 CAGCGAAGACTGTGTCATGT 58.212 50.000 0.00 0.00 34.60 3.21 R
5005 5213 0.179234 TGCACCGGTTCAAGAACTCA 59.821 50.000 2.97 1.98 40.94 3.41 R
6134 6754 0.253044 TTCCCTGAGAAGGCGATTGG 59.747 55.000 0.00 0.00 0.00 3.16 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 24 2.503895 AGAAGGAAACATGAGGGCAG 57.496 50.000 0.00 0.00 0.00 4.85
42 44 1.001048 GCAACCCGGGTTTGTTTAGTC 60.001 52.381 36.59 15.30 36.00 2.59
76 78 1.300080 CCAAGTGGCACCAAAAGCG 60.300 57.895 15.27 0.00 0.00 4.68
78 80 3.150647 AAGTGGCACCAAAAGCGCC 62.151 57.895 15.27 0.00 44.55 6.53
104 106 6.315642 GGATTAAGAACCTGTAACTAACCAGC 59.684 42.308 0.00 0.00 0.00 4.85
127 129 1.064296 CAGCATTAGCAGCAGCAGC 59.936 57.895 3.17 0.46 45.49 5.25
128 130 1.378119 AGCATTAGCAGCAGCAGCA 60.378 52.632 12.92 0.00 45.49 4.41
129 131 1.064296 GCATTAGCAGCAGCAGCAG 59.936 57.895 12.92 0.00 45.49 4.24
130 132 1.728069 CATTAGCAGCAGCAGCAGG 59.272 57.895 12.92 0.00 45.49 4.85
131 133 1.453379 ATTAGCAGCAGCAGCAGGG 60.453 57.895 12.92 0.00 45.49 4.45
144 146 0.254178 AGCAGGGGCATCAAGTAGTG 59.746 55.000 0.00 0.00 44.61 2.74
158 160 6.080648 TCAAGTAGTGGTAGTAATATGCCG 57.919 41.667 0.00 0.00 0.00 5.69
190 192 1.925229 CAGTTTTGGTGCCACAGTTG 58.075 50.000 0.00 0.00 0.00 3.16
191 193 1.204467 CAGTTTTGGTGCCACAGTTGT 59.796 47.619 0.00 0.00 0.00 3.32
212 219 2.320745 TGGCACATAGATCAGCAGTG 57.679 50.000 0.00 0.00 0.00 3.66
215 222 2.481854 GCACATAGATCAGCAGTGAGG 58.518 52.381 10.51 0.00 35.66 3.86
218 244 2.697751 ACATAGATCAGCAGTGAGGGAC 59.302 50.000 0.00 0.00 35.66 4.46
247 273 2.583520 GCTGTCTGAGCCCTGAGG 59.416 66.667 0.00 0.00 42.54 3.86
248 274 2.289532 GCTGTCTGAGCCCTGAGGT 61.290 63.158 0.00 0.00 42.54 3.85
284 310 7.010160 TCCTCTTCTCTTCTTCTTCTTCTTCT 58.990 38.462 0.00 0.00 0.00 2.85
287 313 8.243961 TCTTCTCTTCTTCTTCTTCTTCTTCA 57.756 34.615 0.00 0.00 0.00 3.02
300 326 4.543590 TCTTCTTCACCTCCTTGTCATC 57.456 45.455 0.00 0.00 0.00 2.92
306 332 1.220206 CCTCCTTGTCATCGCTGCT 59.780 57.895 0.00 0.00 0.00 4.24
328 355 2.372264 CTGCTGTGCTACCATCCAAAT 58.628 47.619 0.00 0.00 0.00 2.32
329 356 2.357009 CTGCTGTGCTACCATCCAAATC 59.643 50.000 0.00 0.00 0.00 2.17
330 357 1.678101 GCTGTGCTACCATCCAAATCC 59.322 52.381 0.00 0.00 0.00 3.01
331 358 2.301346 CTGTGCTACCATCCAAATCCC 58.699 52.381 0.00 0.00 0.00 3.85
332 359 1.308998 GTGCTACCATCCAAATCCCG 58.691 55.000 0.00 0.00 0.00 5.14
333 360 0.182537 TGCTACCATCCAAATCCCGG 59.817 55.000 0.00 0.00 0.00 5.73
334 361 0.472471 GCTACCATCCAAATCCCGGA 59.528 55.000 0.73 0.00 36.84 5.14
335 362 1.543429 GCTACCATCCAAATCCCGGAG 60.543 57.143 0.73 0.00 35.56 4.63
336 363 0.472471 TACCATCCAAATCCCGGAGC 59.528 55.000 0.73 0.00 35.56 4.70
337 364 1.281925 ACCATCCAAATCCCGGAGCT 61.282 55.000 0.73 0.00 35.56 4.09
338 365 0.106519 CCATCCAAATCCCGGAGCTT 60.107 55.000 0.73 0.00 35.56 3.74
447 478 4.148825 CCCGTTCTCCTCCTGCCG 62.149 72.222 0.00 0.00 0.00 5.69
460 492 0.322008 CCTGCCGCTTCTTCCTTTCT 60.322 55.000 0.00 0.00 0.00 2.52
498 533 4.851214 GCGCCCTCCTCCTCCTCT 62.851 72.222 0.00 0.00 0.00 3.69
629 665 0.462375 GGTTTTCGGCTGGTTGGTTT 59.538 50.000 0.00 0.00 0.00 3.27
652 688 6.100404 TGGATTTTGGTTCTTGATTTGAGG 57.900 37.500 0.00 0.00 0.00 3.86
661 697 4.229304 TCTTGATTTGAGGGGCGATTTA 57.771 40.909 0.00 0.00 0.00 1.40
810 846 3.447229 GTCCATGTAAGAATTGGGTTGGG 59.553 47.826 0.00 0.00 0.00 4.12
858 894 1.733041 TCGAACTTTGAGCGAGCGG 60.733 57.895 0.00 0.00 0.00 5.52
1011 1058 1.032794 AGAGATCAATGGCGTCGCTA 58.967 50.000 18.11 12.27 0.00 4.26
1148 1196 6.475727 TGACGTTTCTCTTCTTCAGTTAGTTG 59.524 38.462 0.00 0.00 0.00 3.16
1222 1270 7.940850 CCAAGACTTGGTTATTTTCAGAGAAA 58.059 34.615 23.92 0.00 45.93 2.52
1223 1271 8.413229 CCAAGACTTGGTTATTTTCAGAGAAAA 58.587 33.333 23.92 7.30 45.93 2.29
1257 1305 2.418976 CTCTGCATGTGACCAGTTCATG 59.581 50.000 0.00 10.48 40.98 3.07
1261 1309 2.553602 GCATGTGACCAGTTCATGTCAA 59.446 45.455 14.01 0.00 42.67 3.18
1341 1389 3.989167 TGCTGCTTGAACATATTGTTTGC 59.011 39.130 0.00 1.79 41.28 3.68
1347 1395 5.517770 GCTTGAACATATTGTTTGCCATCTC 59.482 40.000 0.00 0.00 41.28 2.75
1353 1401 6.418101 ACATATTGTTTGCCATCTCTAGTGT 58.582 36.000 0.00 0.00 0.00 3.55
1364 1412 5.352284 CCATCTCTAGTGTGCGAAGTAATT 58.648 41.667 0.00 0.00 0.00 1.40
1380 1428 7.361457 GCGAAGTAATTTGGTGTAGTTGGTATT 60.361 37.037 0.00 0.00 0.00 1.89
1472 1521 6.491403 AGTGCTTTCTTGGTAGTGAAAATGAT 59.509 34.615 0.00 0.00 32.69 2.45
1569 1618 9.590451 CCATTGTGATTAAACAATTAGCAGAAT 57.410 29.630 3.28 0.00 46.19 2.40
1595 1644 7.893124 ATCATTAGTCCTGAAATTTGATGCT 57.107 32.000 0.00 0.00 0.00 3.79
2066 2117 6.824305 AATGCTTGTTTCTACACATTAGCT 57.176 33.333 0.00 0.00 36.07 3.32
2070 2121 6.128661 TGCTTGTTTCTACACATTAGCTAACG 60.129 38.462 8.70 2.47 36.07 3.18
2088 2139 2.076863 ACGCCAAGCACAGTAGAATTC 58.923 47.619 0.00 0.00 0.00 2.17
2095 2146 6.678900 GCCAAGCACAGTAGAATTCAATAAGG 60.679 42.308 8.44 0.00 0.00 2.69
2225 2278 6.692486 TGGAAAGTTTAGTCTGAGATCACTC 58.308 40.000 0.00 0.00 42.88 3.51
2263 2317 2.942804 TGGAAACAACTCTTCCATGCA 58.057 42.857 0.13 0.00 45.88 3.96
2269 2323 4.942761 ACAACTCTTCCATGCACAATTT 57.057 36.364 0.00 0.00 0.00 1.82
2678 2732 5.693104 CAGGAACCTGATTTGTGATTTTGTG 59.307 40.000 14.94 0.00 46.30 3.33
2831 3009 7.648142 TGTAAAGTCGCTTCATCTTTGATTTT 58.352 30.769 0.00 0.00 34.09 1.82
2837 3015 6.638468 GTCGCTTCATCTTTGATTTTCTTTGT 59.362 34.615 0.00 0.00 0.00 2.83
2840 3018 8.581263 CGCTTCATCTTTGATTTTCTTTGTATG 58.419 33.333 0.00 0.00 0.00 2.39
3015 3198 8.198109 ACACAAGTATGGTAGCTCTGTATTAAG 58.802 37.037 0.00 0.00 0.00 1.85
3142 3325 6.587608 AGTCCGTTTTACGTATTCAGGTTTAG 59.412 38.462 0.00 0.00 40.58 1.85
3143 3326 6.586082 GTCCGTTTTACGTATTCAGGTTTAGA 59.414 38.462 0.00 0.00 40.58 2.10
3144 3327 7.116233 GTCCGTTTTACGTATTCAGGTTTAGAA 59.884 37.037 0.00 0.00 40.58 2.10
3145 3328 7.655328 TCCGTTTTACGTATTCAGGTTTAGAAA 59.345 33.333 0.00 0.00 40.58 2.52
3146 3329 8.445493 CCGTTTTACGTATTCAGGTTTAGAAAT 58.555 33.333 0.00 0.00 40.58 2.17
3147 3330 9.469239 CGTTTTACGTATTCAGGTTTAGAAATC 57.531 33.333 0.00 0.00 36.74 2.17
3151 3334 7.016361 ACGTATTCAGGTTTAGAAATCATGC 57.984 36.000 0.00 0.00 0.00 4.06
3152 3335 6.823689 ACGTATTCAGGTTTAGAAATCATGCT 59.176 34.615 0.00 0.00 0.00 3.79
3153 3336 7.336931 ACGTATTCAGGTTTAGAAATCATGCTT 59.663 33.333 0.00 0.00 0.00 3.91
3154 3337 8.826710 CGTATTCAGGTTTAGAAATCATGCTTA 58.173 33.333 0.00 0.00 0.00 3.09
3156 3339 6.683974 TCAGGTTTAGAAATCATGCTTAGC 57.316 37.500 0.00 0.00 0.00 3.09
3157 3340 6.179756 TCAGGTTTAGAAATCATGCTTAGCA 58.820 36.000 10.09 10.09 44.86 3.49
3200 3383 8.568617 ACCTTCCATCAACCTATAATAGAACT 57.431 34.615 0.00 0.00 0.00 3.01
3271 3454 7.322222 GCGTTATTTGCAGATCTATGTCATTTC 59.678 37.037 0.00 0.00 0.00 2.17
3315 3498 3.488721 GCATGTCTTCCATCAGTCATTGC 60.489 47.826 0.00 0.00 0.00 3.56
3329 3512 6.325596 TCAGTCATTGCGATATATCTGTAGC 58.674 40.000 10.93 7.18 0.00 3.58
3349 3532 2.497273 GCCAAATGTGTGCTCCCTAATT 59.503 45.455 0.00 0.00 0.00 1.40
3447 3631 8.752005 AGCAGCTTATATAATTTCCAACAAGA 57.248 30.769 0.00 0.00 0.00 3.02
3629 3834 8.692710 ACTAGTGCTGTTGCTTTATGTACTATA 58.307 33.333 0.00 0.00 40.48 1.31
4007 4212 3.696548 GCTAAGCTTGGAAAGGCTACATT 59.303 43.478 14.82 0.00 46.35 2.71
4055 4260 7.500992 TGCCTTATAATAGAAAGAGTGACTGG 58.499 38.462 0.00 0.00 0.00 4.00
4100 4308 8.317891 TGAAATAAGAACTGTCGCAGAATTTA 57.682 30.769 12.77 8.23 39.69 1.40
4108 4316 4.152402 ACTGTCGCAGAATTTACATGACAC 59.848 41.667 12.77 0.00 39.69 3.67
4256 4464 4.262635 GGAAGAGTCACTGGATTCTTGTCA 60.263 45.833 7.12 0.00 46.41 3.58
4327 4535 5.394443 GGCTTGCATATTGAAGATTGACCAA 60.394 40.000 0.00 0.00 0.00 3.67
4579 4787 1.471676 CCTGCTATCCACTCGGTTGTC 60.472 57.143 0.00 0.00 0.00 3.18
4858 5066 4.811024 GGATCGATCAACACTGCATTTCTA 59.189 41.667 25.93 0.00 0.00 2.10
5219 5430 8.223769 GGCAAATATACTACATCTGAAACATCG 58.776 37.037 0.00 0.00 0.00 3.84
5342 5578 6.765915 AGGGAATAGCTTCAGATTTTGTTC 57.234 37.500 0.00 0.00 32.70 3.18
5346 5582 2.229792 AGCTTCAGATTTTGTTCCGCA 58.770 42.857 0.00 0.00 0.00 5.69
5367 5603 0.962356 CCTGCATCTTTCAGGCGGTT 60.962 55.000 0.00 0.00 43.88 4.44
5491 5727 1.742761 ACTGGCAACTCATGGATTCG 58.257 50.000 0.00 0.00 37.61 3.34
5498 5734 4.034510 GGCAACTCATGGATTCGAAAGTAG 59.965 45.833 0.00 0.00 0.00 2.57
5509 5745 5.121768 GGATTCGAAAGTAGTTGCAGCTTTA 59.878 40.000 8.85 0.00 33.22 1.85
5540 5776 6.074249 TGTCACCTTTGTTTTCGTTGAAAAAC 60.074 34.615 6.31 4.56 42.09 2.43
5543 5779 5.758784 ACCTTTGTTTTCGTTGAAAAACCAA 59.241 32.000 6.31 5.43 44.70 3.67
5557 5793 6.047870 TGAAAAACCAACATCATCTTTGTGG 58.952 36.000 0.00 0.00 0.00 4.17
5565 5801 1.214589 CATCTTTGTGGCTGGCTGC 59.785 57.895 7.96 7.96 41.94 5.25
5614 6157 7.465647 GCTGAATTTGATGTGACAGTCAGATAG 60.466 40.741 13.06 6.60 29.83 2.08
5622 6165 7.286316 TGATGTGACAGTCAGATAGATGTACAT 59.714 37.037 13.06 8.43 29.83 2.29
5667 6222 5.570589 GCTCATGCAAAATGACTTAGTCAAC 59.429 40.000 19.42 7.33 41.55 3.18
5668 6223 6.569226 GCTCATGCAAAATGACTTAGTCAACT 60.569 38.462 19.42 6.82 41.55 3.16
5669 6224 7.361201 GCTCATGCAAAATGACTTAGTCAACTA 60.361 37.037 19.42 3.74 41.55 2.24
5682 6239 8.084590 ACTTAGTCAACTAATAAACAGTGCAC 57.915 34.615 9.40 9.40 37.75 4.57
5683 6240 7.713507 ACTTAGTCAACTAATAAACAGTGCACA 59.286 33.333 21.04 0.00 37.75 4.57
5689 6246 8.286800 TCAACTAATAAACAGTGCACATTACAC 58.713 33.333 21.04 0.00 38.35 2.90
5702 6259 6.699642 GTGCACATTACACAAACCATAGTTTT 59.300 34.615 13.17 0.00 43.82 2.43
5706 6263 8.788806 CACATTACACAAACCATAGTTTTAGGA 58.211 33.333 0.00 0.00 43.82 2.94
5708 6265 9.787532 CATTACACAAACCATAGTTTTAGGATG 57.212 33.333 0.00 0.00 43.82 3.51
5733 6290 8.985805 TGATCATATTCTCATCTGAATTCAACG 58.014 33.333 9.88 0.00 37.73 4.10
5738 6295 6.471976 TTCTCATCTGAATTCAACGACAAG 57.528 37.500 9.88 5.88 0.00 3.16
5751 6308 0.032952 CGACAAGGGAGTTCCACGAA 59.967 55.000 0.00 0.00 38.24 3.85
5753 6310 2.567985 GACAAGGGAGTTCCACGAAAA 58.432 47.619 0.00 0.00 38.24 2.29
5782 6340 6.869388 GCAGATAAAACTACCTAGATGGCTAC 59.131 42.308 0.00 0.00 40.22 3.58
5829 6449 1.808945 CTGGTTGCTGATGACTGAACC 59.191 52.381 0.00 0.00 37.23 3.62
5833 6453 3.341823 GTTGCTGATGACTGAACCAGAT 58.658 45.455 0.45 0.00 35.18 2.90
5834 6454 2.981898 TGCTGATGACTGAACCAGATG 58.018 47.619 0.45 0.00 35.18 2.90
5858 6478 3.567585 TGGACAAAACATCTTCATCGCAA 59.432 39.130 0.00 0.00 0.00 4.85
5932 6552 4.501571 GCCTTAGCCAATCTACGAATCTGA 60.502 45.833 0.00 0.00 0.00 3.27
5940 6560 2.176045 TCTACGAATCTGACTTGGGCA 58.824 47.619 0.00 0.00 0.00 5.36
6045 6665 1.019278 GCGATCGACCTTTTCTGGCA 61.019 55.000 21.57 0.00 0.00 4.92
6085 6705 1.891060 GCTCGCACTTCAGGTTGTCG 61.891 60.000 0.00 0.00 0.00 4.35
6095 6715 3.050275 GGTTGTCGACCTGCTGCC 61.050 66.667 14.12 2.45 45.55 4.85
6134 6754 1.359848 CGTGAGGTAGTTCATGTGCC 58.640 55.000 0.00 0.00 31.02 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.244721 GTTGCTGCCCTCATGTTTCC 59.755 55.000 0.00 0.00 0.00 3.13
22 24 1.001048 GACTAAACAAACCCGGGTTGC 60.001 52.381 38.87 16.61 38.47 4.17
28 30 2.289547 CCAGTGTGACTAAACAAACCCG 59.710 50.000 0.00 0.00 0.00 5.28
42 44 0.820074 TTGGCCGGTTAACCAGTGTG 60.820 55.000 24.14 7.43 37.24 3.82
76 78 3.870274 AGTTACAGGTTCTTAATCCGGC 58.130 45.455 0.00 0.00 0.00 6.13
78 80 6.400568 TGGTTAGTTACAGGTTCTTAATCCG 58.599 40.000 0.00 0.00 0.00 4.18
126 128 0.749454 CCACTACTTGATGCCCCTGC 60.749 60.000 0.00 0.00 38.26 4.85
127 129 0.620556 ACCACTACTTGATGCCCCTG 59.379 55.000 0.00 0.00 0.00 4.45
128 130 2.119495 CTACCACTACTTGATGCCCCT 58.881 52.381 0.00 0.00 0.00 4.79
129 131 1.838077 ACTACCACTACTTGATGCCCC 59.162 52.381 0.00 0.00 0.00 5.80
130 132 4.748277 TTACTACCACTACTTGATGCCC 57.252 45.455 0.00 0.00 0.00 5.36
131 133 6.369065 GCATATTACTACCACTACTTGATGCC 59.631 42.308 0.00 0.00 30.96 4.40
144 146 1.334054 CGACGCGGCATATTACTACC 58.666 55.000 14.85 0.00 0.00 3.18
158 160 1.772063 AAAACTGCTGACACCGACGC 61.772 55.000 0.00 0.00 0.00 5.19
183 185 5.118286 TGATCTATGTGCCATACAACTGTG 58.882 41.667 0.00 0.00 43.77 3.66
190 192 3.744942 CACTGCTGATCTATGTGCCATAC 59.255 47.826 0.00 0.00 0.00 2.39
191 193 3.642848 TCACTGCTGATCTATGTGCCATA 59.357 43.478 0.00 0.00 0.00 2.74
203 210 2.362369 CCCGTCCCTCACTGCTGAT 61.362 63.158 0.00 0.00 0.00 2.90
205 212 3.302347 GACCCGTCCCTCACTGCTG 62.302 68.421 0.00 0.00 0.00 4.41
211 218 1.918293 ATTGCTGACCCGTCCCTCA 60.918 57.895 0.00 0.00 0.00 3.86
212 219 1.450312 CATTGCTGACCCGTCCCTC 60.450 63.158 0.00 0.00 0.00 4.30
215 222 2.045926 AGCATTGCTGACCCGTCC 60.046 61.111 11.09 0.00 37.57 4.79
245 271 1.681229 AGAGGAGAGGAGACTGACCT 58.319 55.000 0.00 0.00 44.43 3.85
246 272 2.025321 AGAAGAGGAGAGGAGACTGACC 60.025 54.545 0.00 0.00 44.43 4.02
247 273 3.054361 AGAGAAGAGGAGAGGAGACTGAC 60.054 52.174 0.00 0.00 44.43 3.51
248 274 3.189606 AGAGAAGAGGAGAGGAGACTGA 58.810 50.000 0.00 0.00 44.43 3.41
284 310 0.976641 AGCGATGACAAGGAGGTGAA 59.023 50.000 0.00 0.00 0.00 3.18
287 313 1.078848 GCAGCGATGACAAGGAGGT 60.079 57.895 4.02 0.00 0.00 3.85
306 332 1.078214 GGATGGTAGCACAGCAGCA 60.078 57.895 0.00 0.00 42.82 4.41
328 355 2.731571 CCGATGGAAAGCTCCGGGA 61.732 63.158 0.00 0.00 45.85 5.14
329 356 2.203070 CCGATGGAAAGCTCCGGG 60.203 66.667 0.00 0.00 45.85 5.73
330 357 0.177141 TAACCGATGGAAAGCTCCGG 59.823 55.000 0.00 0.00 45.85 5.14
331 358 2.018542 TTAACCGATGGAAAGCTCCG 57.981 50.000 0.00 0.00 45.85 4.63
332 359 4.202020 GGAATTTAACCGATGGAAAGCTCC 60.202 45.833 0.00 0.00 42.81 4.70
333 360 4.921547 GGAATTTAACCGATGGAAAGCTC 58.078 43.478 0.00 0.00 0.00 4.09
334 361 4.983671 GGAATTTAACCGATGGAAAGCT 57.016 40.909 0.00 0.00 0.00 3.74
356 383 3.076258 GCGCCCACTATTTTGGCCC 62.076 63.158 0.00 0.00 42.29 5.80
435 466 1.608717 GAAGAAGCGGCAGGAGGAGA 61.609 60.000 1.45 0.00 0.00 3.71
447 478 4.518590 AGAGAAGCAAAGAAAGGAAGAAGC 59.481 41.667 0.00 0.00 0.00 3.86
460 492 0.671781 GGCAGAGCGAGAGAAGCAAA 60.672 55.000 0.00 0.00 37.01 3.68
498 533 1.045350 CGGCAGGGGAGAGATTCAGA 61.045 60.000 0.00 0.00 0.00 3.27
575 610 1.458927 CAAGAAAACCTCCCCGGGT 59.541 57.895 21.85 0.00 42.05 5.28
577 612 1.304134 CCCAAGAAAACCTCCCCGG 60.304 63.158 0.00 0.00 39.35 5.73
598 634 1.154197 CGAAAACCCCGACCTTTCTC 58.846 55.000 0.00 0.00 0.00 2.87
629 665 5.011943 CCCTCAAATCAAGAACCAAAATCCA 59.988 40.000 0.00 0.00 0.00 3.41
652 688 2.823747 AGAAAACCAACCTAAATCGCCC 59.176 45.455 0.00 0.00 0.00 6.13
661 697 1.535462 CGAATCGCAGAAAACCAACCT 59.465 47.619 0.00 0.00 43.58 3.50
810 846 3.195698 GCATCGACGCCTCCAACC 61.196 66.667 0.00 0.00 0.00 3.77
858 894 2.670414 CGAGCAACAGTTCTTGATCTCC 59.330 50.000 0.00 0.00 34.93 3.71
867 903 0.784778 CGACCTTCGAGCAACAGTTC 59.215 55.000 0.00 0.00 43.74 3.01
1011 1058 2.901042 GTCCCCTCGCTTTCGGAT 59.099 61.111 0.00 0.00 36.13 4.18
1222 1270 6.656270 TCACATGCAGAGACTGATTTTACATT 59.344 34.615 2.81 0.00 32.44 2.71
1223 1271 6.093219 GTCACATGCAGAGACTGATTTTACAT 59.907 38.462 8.28 0.00 35.30 2.29
1232 1280 1.001746 ACTGGTCACATGCAGAGACTG 59.998 52.381 13.49 10.12 37.87 3.51
1233 1281 1.346062 ACTGGTCACATGCAGAGACT 58.654 50.000 13.49 0.00 37.87 3.24
1301 1349 5.887598 AGCAGCACAATCCATATCAAAGTAA 59.112 36.000 0.00 0.00 0.00 2.24
1341 1389 2.949451 ACTTCGCACACTAGAGATGG 57.051 50.000 0.00 0.00 0.00 3.51
1347 1395 4.451096 ACACCAAATTACTTCGCACACTAG 59.549 41.667 0.00 0.00 0.00 2.57
1353 1401 4.214545 CCAACTACACCAAATTACTTCGCA 59.785 41.667 0.00 0.00 0.00 5.10
1364 1412 6.584471 ATCCCATAATACCAACTACACCAA 57.416 37.500 0.00 0.00 0.00 3.67
1439 1488 9.344772 TCACTACCAAGAAAGCACTAAAAATTA 57.655 29.630 0.00 0.00 0.00 1.40
1441 1490 7.817418 TCACTACCAAGAAAGCACTAAAAAT 57.183 32.000 0.00 0.00 0.00 1.82
1458 1507 3.487544 GGAAGCGCATCATTTTCACTACC 60.488 47.826 15.31 0.00 0.00 3.18
1472 1521 2.280797 GACACACCTGGAAGCGCA 60.281 61.111 11.47 0.00 0.00 6.09
1536 1585 7.837202 ATTGTTTAATCACAATGGAATGCAG 57.163 32.000 4.99 0.00 44.19 4.41
1569 1618 9.412460 AGCATCAAATTTCAGGACTAATGATTA 57.588 29.630 0.00 0.00 0.00 1.75
1635 1684 5.626142 TGATTTAGTAGCCCAACAACTTGA 58.374 37.500 0.00 0.00 0.00 3.02
1636 1685 5.957842 TGATTTAGTAGCCCAACAACTTG 57.042 39.130 0.00 0.00 0.00 3.16
2066 2117 2.823924 TTCTACTGTGCTTGGCGTTA 57.176 45.000 0.00 0.00 0.00 3.18
2070 2121 4.708726 ATTGAATTCTACTGTGCTTGGC 57.291 40.909 7.05 0.00 0.00 4.52
2088 2139 5.221048 GCACTGTTATAGTTGCCCCTTATTG 60.221 44.000 0.00 0.00 37.60 1.90
2095 2146 4.718940 AAATGCACTGTTATAGTTGCCC 57.281 40.909 0.00 0.00 37.60 5.36
2278 2332 6.985645 ACTGCAAGCAAAGTTATCAAATCAAA 59.014 30.769 0.00 0.00 37.60 2.69
2608 2662 9.146984 CAAAAATATGATGCTGAACATGAGTTT 57.853 29.630 0.00 0.00 39.84 2.66
2678 2732 5.173774 TGATGCAGAAAGAACTGTGAAAC 57.826 39.130 0.00 0.00 39.73 2.78
2831 3009 6.658816 ACAACAATATCTGCCACATACAAAGA 59.341 34.615 0.00 0.00 0.00 2.52
2837 3015 7.109501 ACAAGTACAACAATATCTGCCACATA 58.890 34.615 0.00 0.00 0.00 2.29
2840 3018 5.880054 ACAAGTACAACAATATCTGCCAC 57.120 39.130 0.00 0.00 0.00 5.01
3061 3244 4.202430 ACGGTCCAGGTGTTAGAAGAATTT 60.202 41.667 0.00 0.00 0.00 1.82
3149 3332 4.551702 TCTAAACCTGTGATGCTAAGCA 57.448 40.909 0.00 0.00 44.86 3.91
3150 3333 5.880054 TTTCTAAACCTGTGATGCTAAGC 57.120 39.130 0.00 0.00 0.00 3.09
3151 3334 8.398665 GGTAATTTCTAAACCTGTGATGCTAAG 58.601 37.037 0.00 0.00 0.00 2.18
3152 3335 8.107095 AGGTAATTTCTAAACCTGTGATGCTAA 58.893 33.333 0.00 0.00 42.08 3.09
3153 3336 7.630082 AGGTAATTTCTAAACCTGTGATGCTA 58.370 34.615 0.00 0.00 42.08 3.49
3154 3337 6.485171 AGGTAATTTCTAAACCTGTGATGCT 58.515 36.000 0.00 0.00 42.08 3.79
3155 3338 6.759497 AGGTAATTTCTAAACCTGTGATGC 57.241 37.500 0.00 0.00 42.08 3.91
3156 3339 7.393234 TGGAAGGTAATTTCTAAACCTGTGATG 59.607 37.037 0.00 0.00 42.86 3.07
3157 3340 7.466804 TGGAAGGTAATTTCTAAACCTGTGAT 58.533 34.615 0.00 0.00 42.86 3.06
3158 3341 6.843752 TGGAAGGTAATTTCTAAACCTGTGA 58.156 36.000 0.00 0.00 42.86 3.58
3159 3342 7.393234 TGATGGAAGGTAATTTCTAAACCTGTG 59.607 37.037 0.00 0.00 42.86 3.66
3160 3343 7.466804 TGATGGAAGGTAATTTCTAAACCTGT 58.533 34.615 0.00 0.00 42.86 4.00
3200 3383 7.495606 AGAAACAAATATCTGCATGTCATACGA 59.504 33.333 0.00 0.00 0.00 3.43
3271 3454 1.252904 CCTGAATGGCCAACACAGGG 61.253 60.000 31.35 19.75 42.77 4.45
3315 3498 6.401474 GCACACATTTGGCTACAGATATATCG 60.401 42.308 7.08 5.26 0.00 2.92
3329 3512 4.220382 TCAAATTAGGGAGCACACATTTGG 59.780 41.667 8.59 0.00 34.02 3.28
3349 3532 7.585286 GCAATCTGCAAATAGACATTTTCAA 57.415 32.000 0.00 0.00 44.26 2.69
3447 3631 3.149196 AGAAGGCGTCATTCACATGTTT 58.851 40.909 0.00 0.00 0.00 2.83
3941 4146 4.730657 CAAACAAGGAATGCTCATCAGAC 58.269 43.478 0.00 0.00 0.00 3.51
3999 4204 7.826690 TCCTTTTAAATTGTCTGAATGTAGCC 58.173 34.615 0.00 0.00 0.00 3.93
4007 4212 7.872483 GGCAATCTTTCCTTTTAAATTGTCTGA 59.128 33.333 0.00 0.00 0.00 3.27
4055 4260 7.391148 TTTCAGGACAATTTCAGCCTATTAC 57.609 36.000 0.00 0.00 0.00 1.89
4062 4267 7.540055 CAGTTCTTATTTCAGGACAATTTCAGC 59.460 37.037 0.00 0.00 0.00 4.26
4100 4308 1.788258 CAGCGAAGACTGTGTCATGT 58.212 50.000 0.00 0.00 34.60 3.21
4108 4316 3.051327 CTGAGATATGCAGCGAAGACTG 58.949 50.000 0.00 0.00 40.80 3.51
4256 4464 4.207891 ACGAGAGCACAATAAAGGTGAT 57.792 40.909 0.00 0.00 38.54 3.06
4579 4787 2.121116 ACTTGACACAGACGAAGACG 57.879 50.000 0.00 0.00 45.75 4.18
5005 5213 0.179234 TGCACCGGTTCAAGAACTCA 59.821 50.000 2.97 1.98 40.94 3.41
5219 5430 4.106909 CCAGTACAAACCAAACGGAAAAC 58.893 43.478 0.00 0.00 0.00 2.43
5291 5504 9.849166 TTTATATTTACAGTTTAAAGCAGCCAC 57.151 29.630 0.00 0.00 0.00 5.01
5342 5578 1.651240 CTGAAAGATGCAGGGTGCGG 61.651 60.000 0.00 0.00 41.71 5.69
5367 5603 4.009675 AGGCGAACATTTCTAGCATGAAA 58.990 39.130 0.00 6.60 39.79 2.69
5461 5697 6.071728 CCATGAGTTGCCAGTTAGAGATTTTT 60.072 38.462 0.00 0.00 0.00 1.94
5491 5727 8.290325 ACAACTTATAAAGCTGCAACTACTTTC 58.710 33.333 1.02 0.00 35.38 2.62
5498 5734 5.048713 AGGTGACAACTTATAAAGCTGCAAC 60.049 40.000 1.02 0.00 0.00 4.17
5509 5745 6.445357 ACGAAAACAAAGGTGACAACTTAT 57.555 33.333 6.08 0.00 0.00 1.73
5540 5776 2.094390 CCAGCCACAAAGATGATGTTGG 60.094 50.000 0.00 0.00 0.00 3.77
5543 5779 1.180029 GCCAGCCACAAAGATGATGT 58.820 50.000 0.00 0.00 0.00 3.06
5557 5793 1.288127 CTGAACCTTTGCAGCCAGC 59.712 57.895 0.00 0.00 45.96 4.85
5565 5801 5.772521 CCATACTGAAAACCTGAACCTTTG 58.227 41.667 0.00 0.00 0.00 2.77
5657 6212 7.713507 TGTGCACTGTTTATTAGTTGACTAAGT 59.286 33.333 19.41 0.00 41.24 2.24
5667 6222 8.901748 GTTTGTGTAATGTGCACTGTTTATTAG 58.098 33.333 19.41 0.00 37.70 1.73
5668 6223 7.863375 GGTTTGTGTAATGTGCACTGTTTATTA 59.137 33.333 19.41 10.19 37.70 0.98
5669 6224 6.699642 GGTTTGTGTAATGTGCACTGTTTATT 59.300 34.615 19.41 11.22 37.70 1.40
5682 6239 9.787532 CATCCTAAAACTATGGTTTGTGTAATG 57.212 33.333 8.06 5.68 43.90 1.90
5683 6240 9.747898 TCATCCTAAAACTATGGTTTGTGTAAT 57.252 29.630 8.06 0.00 43.90 1.89
5708 6265 9.201127 TCGTTGAATTCAGATGAGAATATGATC 57.799 33.333 8.41 0.00 37.24 2.92
5731 6288 1.111116 TCGTGGAACTCCCTTGTCGT 61.111 55.000 0.00 0.00 35.38 4.34
5733 6290 2.249844 TTTCGTGGAACTCCCTTGTC 57.750 50.000 0.00 0.00 35.38 3.18
5738 6295 2.074576 GCTAGTTTTCGTGGAACTCCC 58.925 52.381 4.58 0.00 38.28 4.30
5753 6310 7.256012 GCCATCTAGGTAGTTTTATCTGCTAGT 60.256 40.741 0.00 0.00 40.61 2.57
5782 6340 5.124297 TGACCTGCAAATGTAATCAGTGATG 59.876 40.000 6.34 0.00 0.00 3.07
5809 6429 1.808945 GGTTCAGTCATCAGCAACCAG 59.191 52.381 0.00 0.00 37.13 4.00
5829 6449 6.505044 TGAAGATGTTTTGTCCATCATCTG 57.495 37.500 7.18 0.00 43.80 2.90
5833 6453 4.142622 GCGATGAAGATGTTTTGTCCATCA 60.143 41.667 0.00 0.00 40.93 3.07
5834 6454 4.142622 TGCGATGAAGATGTTTTGTCCATC 60.143 41.667 0.00 0.00 39.19 3.51
5845 6465 6.195983 GCTAGTTTCATTTTGCGATGAAGATG 59.804 38.462 9.11 0.00 44.33 2.90
5858 6478 3.421844 GTGGTCCAGGCTAGTTTCATTT 58.578 45.455 0.00 0.00 0.00 2.32
5932 6552 0.827507 ATGAAAAGCCGTGCCCAAGT 60.828 50.000 0.00 0.00 0.00 3.16
6045 6665 3.318017 CTTGAGGAACTTCGTCATCGTT 58.682 45.455 13.55 0.00 41.55 3.85
6085 6705 2.527951 ATTCACTCGGGCAGCAGGTC 62.528 60.000 0.00 0.00 0.00 3.85
6095 6715 2.076863 GGACAAGGTTGATTCACTCGG 58.923 52.381 0.00 0.00 0.00 4.63
6134 6754 0.253044 TTCCCTGAGAAGGCGATTGG 59.747 55.000 0.00 0.00 0.00 3.16
6178 6798 2.029918 GGATTCAAAACAGGACTGTGGC 60.030 50.000 5.63 0.00 44.13 5.01


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

AutoCloner maintained by Alex Coulton.