Multiple sequence alignment - TraesCS7A01G209800

Loading Multiple Alignment...

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 TraesCS7A01G209800 chr7A 100.000 3312 0 0 1 3312 172416914 172420225 0.000000e+00 6117
1 TraesCS7A01G209800 chr7A 85.000 220 23 10 2392 2607 172420506 172420293 7.200000e-52 215
2 TraesCS7A01G209800 chr7A 81.992 261 39 7 2391 2648 639585909 639586164 7.200000e-52 215
3 TraesCS7A01G209800 chr7D 94.615 1467 68 6 925 2382 169823924 169825388 0.000000e+00 2261
4 TraesCS7A01G209800 chr7D 91.266 229 17 3 230 456 169822999 169823226 3.210000e-80 309
5 TraesCS7A01G209800 chr7D 95.604 182 7 1 687 867 169823454 169823635 1.160000e-74 291
6 TraesCS7A01G209800 chr7D 90.732 205 12 7 1 201 169822800 169823001 1.960000e-67 267
7 TraesCS7A01G209800 chr7D 83.226 155 5 6 555 688 169823218 169823372 4.490000e-24 122
8 TraesCS7A01G209800 chr7B 93.678 1044 56 7 925 1962 135528312 135529351 0.000000e+00 1554
9 TraesCS7A01G209800 chr7B 85.699 909 79 23 1 865 135527139 135528040 0.000000e+00 911
10 TraesCS7A01G209800 chr7B 94.815 405 20 1 1966 2369 135529429 135529833 6.030000e-177 630
11 TraesCS7A01G209800 chr6A 95.770 922 39 0 2391 3312 523827735 523826814 0.000000e+00 1487
12 TraesCS7A01G209800 chr2D 94.828 580 30 0 2733 3312 160801033 160801612 0.000000e+00 905
13 TraesCS7A01G209800 chr2D 94.540 348 16 3 2391 2736 160800626 160800972 4.860000e-148 534
14 TraesCS7A01G209800 chr4B 93.933 511 31 0 2733 3243 38319434 38319944 0.000000e+00 773
15 TraesCS7A01G209800 chr4B 90.138 578 54 2 2738 3312 376416683 376416106 0.000000e+00 749
16 TraesCS7A01G209800 chr4B 90.323 341 25 2 2396 2736 376417081 376416749 1.090000e-119 440
17 TraesCS7A01G209800 chr3B 93.346 511 34 0 2736 3246 72947141 72946631 0.000000e+00 756
18 TraesCS7A01G209800 chr4A 92.172 511 33 1 2733 3243 489438518 489439021 0.000000e+00 715
19 TraesCS7A01G209800 chr3D 83.026 271 37 8 2389 2655 43454762 43455027 1.540000e-58 237
20 TraesCS7A01G209800 chr1D 81.041 269 41 9 2391 2655 302254139 302253877 4.330000e-49 206
21 TraesCS7A01G209800 chr4D 80.669 269 41 10 2391 2655 228529213 228529474 7.250000e-47 198
22 TraesCS7A01G209800 chr5A 79.699 266 50 4 2391 2655 314162389 314162651 4.360000e-44 189
23 TraesCS7A01G209800 chr2B 86.614 127 17 0 2990 3116 27898948 27899074 1.240000e-29 141
24 TraesCS7A01G209800 chr2A 85.039 127 19 0 2990 3116 17741250 17741376 2.680000e-26 130


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 TraesCS7A01G209800 chr7A 172416914 172420225 3311 False 6117.000000 6117 100.000000 1 3312 1 chr7A.!!$F1 3311
1 TraesCS7A01G209800 chr7D 169822800 169825388 2588 False 650.000000 2261 91.088600 1 2382 5 chr7D.!!$F1 2381
2 TraesCS7A01G209800 chr7B 135527139 135529833 2694 False 1031.666667 1554 91.397333 1 2369 3 chr7B.!!$F1 2368
3 TraesCS7A01G209800 chr6A 523826814 523827735 921 True 1487.000000 1487 95.770000 2391 3312 1 chr6A.!!$R1 921
4 TraesCS7A01G209800 chr2D 160800626 160801612 986 False 719.500000 905 94.684000 2391 3312 2 chr2D.!!$F1 921
5 TraesCS7A01G209800 chr4B 38319434 38319944 510 False 773.000000 773 93.933000 2733 3243 1 chr4B.!!$F1 510
6 TraesCS7A01G209800 chr4B 376416106 376417081 975 True 594.500000 749 90.230500 2396 3312 2 chr4B.!!$R1 916
7 TraesCS7A01G209800 chr3B 72946631 72947141 510 True 756.000000 756 93.346000 2736 3246 1 chr3B.!!$R1 510
8 TraesCS7A01G209800 chr4A 489438518 489439021 503 False 715.000000 715 92.172000 2733 3243 1 chr4A.!!$F1 510

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
439 479 0.172578 TGAGGAAGTCGCCACATACG 59.827 55.0 0.0 0.0 0.00 3.06 F
457 497 0.240145 CGTCTCGTAGTTGACAGGCA 59.760 55.0 0.0 0.0 33.51 4.75 F
1563 1984 0.316204 CACCTTTGCTTCAGGCCTTG 59.684 55.0 0.0 0.0 40.92 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1455 1869 0.036388 GCATGACCTGAGTCGGGAAA 60.036 55.0 25.39 12.07 46.74 3.13 R
2296 2796 0.828677 GTACTTAGCCACCACCGGAT 59.171 55.0 9.46 0.00 0.00 4.18 R
2949 3519 0.892063 GAGAAGGAGGTCGTTGAGCT 59.108 55.0 0.00 0.00 43.43 4.09 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
130 135 6.971527 TTGATTCATGACATTGGCAATTTC 57.028 33.333 17.35 17.35 0.00 2.17
149 154 9.195411 GCAATTTCTACTTGTCAAATTGATGAA 57.805 29.630 22.02 0.00 44.79 2.57
154 159 4.222336 ACTTGTCAAATTGATGAACCCCA 58.778 39.130 0.00 0.00 0.00 4.96
159 164 3.055963 TCAAATTGATGAACCCCACATGC 60.056 43.478 0.00 0.00 0.00 4.06
176 181 0.955178 TGCCGGCGAAAGAAAAATCA 59.045 45.000 23.90 0.00 0.00 2.57
177 182 1.335506 TGCCGGCGAAAGAAAAATCAC 60.336 47.619 23.90 0.00 0.00 3.06
206 211 7.873699 AAGAACTTGGTACTATATATGGGCT 57.126 36.000 0.80 0.00 0.00 5.19
207 212 7.873699 AGAACTTGGTACTATATATGGGCTT 57.126 36.000 0.80 0.00 0.00 4.35
208 213 7.680730 AGAACTTGGTACTATATATGGGCTTG 58.319 38.462 0.80 0.00 0.00 4.01
209 214 7.512746 AGAACTTGGTACTATATATGGGCTTGA 59.487 37.037 0.80 0.00 0.00 3.02
210 215 7.626999 ACTTGGTACTATATATGGGCTTGAA 57.373 36.000 0.80 0.00 0.00 2.69
211 216 7.450903 ACTTGGTACTATATATGGGCTTGAAC 58.549 38.462 0.80 0.00 0.00 3.18
212 217 6.368779 TGGTACTATATATGGGCTTGAACC 57.631 41.667 0.80 0.12 0.00 3.62
219 224 4.735358 GGGCTTGAACCCCGGGAC 62.735 72.222 26.32 13.80 45.00 4.46
220 225 4.735358 GGCTTGAACCCCGGGACC 62.735 72.222 26.32 11.15 0.00 4.46
221 226 4.735358 GCTTGAACCCCGGGACCC 62.735 72.222 26.32 10.74 0.00 4.46
222 227 2.933834 CTTGAACCCCGGGACCCT 60.934 66.667 26.32 1.92 0.00 4.34
223 228 2.931649 TTGAACCCCGGGACCCTC 60.932 66.667 26.32 13.00 0.00 4.30
224 229 3.795977 TTGAACCCCGGGACCCTCA 62.796 63.158 26.32 15.63 0.00 3.86
225 230 2.931649 GAACCCCGGGACCCTCAA 60.932 66.667 26.32 0.00 0.00 3.02
226 231 2.933834 AACCCCGGGACCCTCAAG 60.934 66.667 26.32 4.48 0.00 3.02
252 291 3.293337 AGTTTGGTTGTTGGGACTTACC 58.707 45.455 0.00 0.00 34.09 2.85
280 320 2.627699 CCACCACACCAAATAGTGCTTT 59.372 45.455 0.00 0.00 41.67 3.51
338 378 6.375377 TGAGAAACACACTACAAACACAAAC 58.625 36.000 0.00 0.00 0.00 2.93
339 379 6.017026 TGAGAAACACACTACAAACACAAACA 60.017 34.615 0.00 0.00 0.00 2.83
350 390 4.393680 ACAAACACAAACACTCACATACGT 59.606 37.500 0.00 0.00 0.00 3.57
368 408 2.032071 GCACGCACACCCTACCTT 59.968 61.111 0.00 0.00 0.00 3.50
392 432 3.117208 ACCCTACACCTATGAGTACCTCC 60.117 52.174 0.00 0.00 0.00 4.30
409 449 2.005451 CTCCAAGAGATTGAGCCAACG 58.995 52.381 0.00 0.00 0.00 4.10
423 463 4.054671 GAGCCAACGGATCTTAGATTGAG 58.945 47.826 0.00 0.00 34.95 3.02
429 469 5.523438 ACGGATCTTAGATTGAGGAAGTC 57.477 43.478 0.00 0.00 0.00 3.01
432 472 3.802948 TCTTAGATTGAGGAAGTCGCC 57.197 47.619 0.00 0.00 0.00 5.54
433 473 3.096852 TCTTAGATTGAGGAAGTCGCCA 58.903 45.455 0.00 0.00 0.00 5.69
439 479 0.172578 TGAGGAAGTCGCCACATACG 59.827 55.000 0.00 0.00 0.00 3.06
452 492 3.423571 CCACATACGTCTCGTAGTTGAC 58.576 50.000 0.00 0.00 45.45 3.18
454 494 4.089341 CACATACGTCTCGTAGTTGACAG 58.911 47.826 0.00 0.00 45.45 3.51
455 495 3.126514 ACATACGTCTCGTAGTTGACAGG 59.873 47.826 0.00 0.00 45.45 4.00
456 496 0.240411 ACGTCTCGTAGTTGACAGGC 59.760 55.000 0.00 0.00 38.73 4.85
457 497 0.240145 CGTCTCGTAGTTGACAGGCA 59.760 55.000 0.00 0.00 33.51 4.75
458 498 1.699343 GTCTCGTAGTTGACAGGCAC 58.301 55.000 0.00 0.00 33.91 5.01
460 500 1.344942 CTCGTAGTTGACAGGCACGC 61.345 60.000 0.00 0.00 32.85 5.34
463 510 0.882927 GTAGTTGACAGGCACGCCAA 60.883 55.000 11.35 0.00 38.92 4.52
472 519 2.244651 GGCACGCCAAGCTATACCG 61.245 63.158 2.36 0.00 35.81 4.02
486 533 7.254455 CCAAGCTATACCGTTGAAAGAATAGTG 60.254 40.741 0.00 0.00 0.00 2.74
489 536 6.074994 GCTATACCGTTGAAAGAATAGTGTCG 60.075 42.308 0.00 0.00 0.00 4.35
497 544 3.528597 AAGAATAGTGTCGAAGAGGCC 57.471 47.619 0.00 0.00 36.95 5.19
498 545 1.405821 AGAATAGTGTCGAAGAGGCCG 59.594 52.381 0.00 0.00 36.95 6.13
500 547 1.392710 ATAGTGTCGAAGAGGCCGGG 61.393 60.000 2.18 0.00 36.95 5.73
521 572 5.695816 CGGGAGAAATCAAAGAAAATGCAAA 59.304 36.000 0.00 0.00 0.00 3.68
522 573 6.346838 CGGGAGAAATCAAAGAAAATGCAAAC 60.347 38.462 0.00 0.00 0.00 2.93
526 577 6.260714 AGAAATCAAAGAAAATGCAAACCCAC 59.739 34.615 0.00 0.00 0.00 4.61
568 620 2.204136 TGGGTGGGCAGGTCTCAT 60.204 61.111 0.00 0.00 0.00 2.90
624 677 8.200364 AGTTCGTAGTTAAGTGCAAACTTTTA 57.800 30.769 7.54 0.00 38.18 1.52
680 753 7.026562 TGGCGATGTATTTTCATGTTTACTTG 58.973 34.615 0.00 0.00 0.00 3.16
732 888 1.401761 TGGGTGCACATCAATATGCC 58.598 50.000 20.43 7.61 41.33 4.40
762 918 4.699925 TGTAGTTGTTTTCCCTACTGCT 57.300 40.909 0.00 0.00 33.75 4.24
870 1284 3.739300 TCTACTTGCAACTTTGTACGAGC 59.261 43.478 0.00 0.00 0.00 5.03
945 1359 9.110502 GGTAAGATTAACTTCAATCTAACCCAG 57.889 37.037 0.00 0.00 43.01 4.45
948 1362 8.152023 AGATTAACTTCAATCTAACCCAGACT 57.848 34.615 0.00 0.00 42.22 3.24
954 1368 3.056107 TCAATCTAACCCAGACTTGTCCG 60.056 47.826 0.00 0.00 35.62 4.79
960 1374 1.247567 CCCAGACTTGTCCGCAATTT 58.752 50.000 0.00 0.00 33.65 1.82
968 1382 3.880490 ACTTGTCCGCAATTTGTTGTCTA 59.120 39.130 0.00 0.00 33.65 2.59
998 1412 8.764524 ATCACTTCTGACTTGTATACTGAAAC 57.235 34.615 4.17 0.00 0.00 2.78
1008 1422 7.327975 ACTTGTATACTGAAACGATGGATGAA 58.672 34.615 4.17 0.00 0.00 2.57
1012 1426 4.008074 ACTGAAACGATGGATGAACTGT 57.992 40.909 0.00 0.00 0.00 3.55
1014 1428 2.483877 TGAAACGATGGATGAACTGTGC 59.516 45.455 0.00 0.00 0.00 4.57
1022 1436 1.490490 GGATGAACTGTGCCCTCCATA 59.510 52.381 0.74 0.00 0.00 2.74
1063 1477 2.808543 GGACAGTCCATGTTGTTGAGAC 59.191 50.000 15.43 0.00 44.17 3.36
1082 1496 5.877012 TGAGACAAATATCTTCTTCTGCCAC 59.123 40.000 0.00 0.00 0.00 5.01
1125 1539 1.324134 GCACATTATGCGCGCAATTTT 59.676 42.857 39.68 24.35 46.55 1.82
1471 1885 2.094390 CGTTATTTCCCGACTCAGGTCA 60.094 50.000 0.00 0.00 42.21 4.02
1484 1898 1.959042 CAGGTCATGCATCCTGTACC 58.041 55.000 21.14 12.79 44.19 3.34
1485 1899 0.839946 AGGTCATGCATCCTGTACCC 59.160 55.000 6.15 0.00 32.29 3.69
1487 1901 2.047061 GGTCATGCATCCTGTACCCTA 58.953 52.381 0.00 0.00 0.00 3.53
1489 1903 2.047061 TCATGCATCCTGTACCCTACC 58.953 52.381 0.00 0.00 0.00 3.18
1490 1904 1.768275 CATGCATCCTGTACCCTACCA 59.232 52.381 0.00 0.00 0.00 3.25
1491 1905 2.190398 TGCATCCTGTACCCTACCAT 57.810 50.000 0.00 0.00 0.00 3.55
1492 1906 2.487775 TGCATCCTGTACCCTACCATT 58.512 47.619 0.00 0.00 0.00 3.16
1493 1907 3.659841 TGCATCCTGTACCCTACCATTA 58.340 45.455 0.00 0.00 0.00 1.90
1494 1908 3.646162 TGCATCCTGTACCCTACCATTAG 59.354 47.826 0.00 0.00 0.00 1.73
1495 1909 3.557264 GCATCCTGTACCCTACCATTAGC 60.557 52.174 0.00 0.00 0.00 3.09
1496 1910 3.700863 TCCTGTACCCTACCATTAGCT 57.299 47.619 0.00 0.00 0.00 3.32
1497 1911 3.573695 TCCTGTACCCTACCATTAGCTC 58.426 50.000 0.00 0.00 0.00 4.09
1502 1916 5.741011 TGTACCCTACCATTAGCTCTTTTG 58.259 41.667 0.00 0.00 0.00 2.44
1506 1920 5.710567 ACCCTACCATTAGCTCTTTTGTTTC 59.289 40.000 0.00 0.00 0.00 2.78
1508 1928 7.110155 CCCTACCATTAGCTCTTTTGTTTCTA 58.890 38.462 0.00 0.00 0.00 2.10
1519 1939 9.305925 AGCTCTTTTGTTTCTACATTTTTCTTG 57.694 29.630 0.00 0.00 33.44 3.02
1520 1940 8.058328 GCTCTTTTGTTTCTACATTTTTCTTGC 58.942 33.333 0.00 0.00 33.44 4.01
1563 1984 0.316204 CACCTTTGCTTCAGGCCTTG 59.684 55.000 0.00 0.00 40.92 3.61
1722 2143 2.348404 GGATTACGCTCGTACTCGTCTC 60.348 54.545 11.71 6.91 39.79 3.36
1905 2326 0.541063 TGTACGACTCCCTCAAGCCA 60.541 55.000 0.00 0.00 0.00 4.75
1932 2353 4.073293 TCTTGTTGGTTCTCTTGAGGTC 57.927 45.455 0.00 0.00 0.00 3.85
2071 2571 2.252072 TAACGATGGGTGCTGGGCTC 62.252 60.000 0.00 0.00 0.00 4.70
2227 2727 2.877691 GCCAACATCCTTCGTGCC 59.122 61.111 0.00 0.00 0.00 5.01
2296 2796 3.007506 TCGTCTTTGGCAAGAAGTATGGA 59.992 43.478 0.00 0.00 40.90 3.41
2315 2815 0.828677 ATCCGGTGGTGGCTAAGTAC 59.171 55.000 0.00 0.00 0.00 2.73
2382 2882 7.927629 GCTTTTGAATAAAATCTGCCATATGGA 59.072 33.333 26.47 9.60 35.39 3.41
2383 2883 9.472361 CTTTTGAATAAAATCTGCCATATGGAG 57.528 33.333 26.47 18.23 35.39 3.86
2384 2884 8.537728 TTTGAATAAAATCTGCCATATGGAGT 57.462 30.769 26.47 0.42 37.39 3.85
2385 2885 9.639563 TTTGAATAAAATCTGCCATATGGAGTA 57.360 29.630 26.47 9.27 37.39 2.59
2386 2886 9.812347 TTGAATAAAATCTGCCATATGGAGTAT 57.188 29.630 26.47 11.20 37.39 2.12
2387 2887 9.234827 TGAATAAAATCTGCCATATGGAGTATG 57.765 33.333 26.47 9.36 39.95 2.39
2472 2973 6.454795 ACAAATTTGTGCCGAAAACTATCAT 58.545 32.000 22.71 0.00 40.49 2.45
2519 3020 6.575162 AACTACCATGTCTCAAAAATGTCC 57.425 37.500 0.00 0.00 0.00 4.02
2551 3052 7.229907 ACCTTTTCTAAACGCCTTTCTGATAAA 59.770 33.333 0.00 0.00 0.00 1.40
2677 3180 4.019771 ACCTCTTCTCCCTGAAACAGATTC 60.020 45.833 0.00 0.00 38.60 2.52
2794 3364 2.124983 CGAGCTGGTGGATGGTGG 60.125 66.667 0.00 0.00 0.00 4.61
2799 3369 1.922057 CTGGTGGATGGTGGCCATA 59.078 57.895 9.72 0.77 45.26 2.74
2840 3410 2.104359 ATGGCATCCAACCACCCCAA 62.104 55.000 0.00 0.00 40.82 4.12
2949 3519 0.945099 CGCTCTGTAGCCATCTCGTA 59.055 55.000 0.00 0.00 46.68 3.43
3266 3843 3.049674 CGCTCAAAGCCTCCGCAA 61.050 61.111 0.00 0.00 38.18 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 135 5.476599 TGGGGTTCATCAATTTGACAAGTAG 59.523 40.000 0.15 0.00 0.00 2.57
154 159 0.671251 TTTTTCTTTCGCCGGCATGT 59.329 45.000 28.98 0.00 0.00 3.21
159 164 2.697431 TGTGATTTTTCTTTCGCCGG 57.303 45.000 0.00 0.00 0.00 6.13
203 208 4.735358 GGTCCCGGGGTTCAAGCC 62.735 72.222 23.50 8.03 34.31 4.35
204 209 4.735358 GGGTCCCGGGGTTCAAGC 62.735 72.222 23.50 10.56 0.00 4.01
205 210 2.933834 AGGGTCCCGGGGTTCAAG 60.934 66.667 23.50 0.00 0.00 3.02
206 211 2.931649 GAGGGTCCCGGGGTTCAA 60.932 66.667 23.50 0.00 0.00 2.69
207 212 3.795977 TTGAGGGTCCCGGGGTTCA 62.796 63.158 23.50 16.09 0.00 3.18
208 213 2.931649 TTGAGGGTCCCGGGGTTC 60.932 66.667 23.50 13.60 0.00 3.62
209 214 2.933834 CTTGAGGGTCCCGGGGTT 60.934 66.667 23.50 3.29 0.00 4.11
212 217 1.632018 TATTGCTTGAGGGTCCCGGG 61.632 60.000 16.85 16.85 0.00 5.73
213 218 0.179045 CTATTGCTTGAGGGTCCCGG 60.179 60.000 0.99 0.00 0.00 5.73
214 219 0.541863 ACTATTGCTTGAGGGTCCCG 59.458 55.000 0.99 0.00 0.00 5.14
215 220 2.755103 CAAACTATTGCTTGAGGGTCCC 59.245 50.000 0.00 0.00 0.00 4.46
216 221 2.755103 CCAAACTATTGCTTGAGGGTCC 59.245 50.000 0.00 0.00 35.10 4.46
217 222 3.421844 ACCAAACTATTGCTTGAGGGTC 58.578 45.455 0.00 0.00 35.10 4.46
218 223 3.525800 ACCAAACTATTGCTTGAGGGT 57.474 42.857 0.00 0.00 35.10 4.34
219 224 3.573967 ACAACCAAACTATTGCTTGAGGG 59.426 43.478 4.19 0.00 36.20 4.30
220 225 4.853924 ACAACCAAACTATTGCTTGAGG 57.146 40.909 4.19 0.00 36.20 3.86
221 226 4.984161 CCAACAACCAAACTATTGCTTGAG 59.016 41.667 4.19 0.00 36.20 3.02
222 227 4.202202 CCCAACAACCAAACTATTGCTTGA 60.202 41.667 4.19 0.00 36.20 3.02
223 228 4.057432 CCCAACAACCAAACTATTGCTTG 58.943 43.478 0.00 0.00 37.86 4.01
224 229 3.964031 TCCCAACAACCAAACTATTGCTT 59.036 39.130 0.00 0.00 35.10 3.91
225 230 3.320826 GTCCCAACAACCAAACTATTGCT 59.679 43.478 0.00 0.00 35.10 3.91
226 231 3.320826 AGTCCCAACAACCAAACTATTGC 59.679 43.478 0.00 0.00 35.10 3.56
227 232 5.529581 AAGTCCCAACAACCAAACTATTG 57.470 39.130 0.00 0.00 36.25 1.90
228 233 5.537295 GGTAAGTCCCAACAACCAAACTATT 59.463 40.000 0.00 0.00 35.09 1.73
241 246 3.181441 GGTGGTAACTTGGTAAGTCCCAA 60.181 47.826 12.03 0.00 41.34 4.12
252 291 4.825085 ACTATTTGGTGTGGTGGTAACTTG 59.175 41.667 0.00 0.00 37.61 3.16
280 320 7.804476 AAGTTGCACTTATCTCCCTAGAGACTA 60.804 40.741 0.00 0.00 40.45 2.59
310 350 6.858993 TGTGTTTGTAGTGTGTTTCTCAAAAC 59.141 34.615 0.00 0.00 44.18 2.43
350 390 1.473497 TAAGGTAGGGTGTGCGTGCA 61.473 55.000 0.00 0.00 0.00 4.57
368 408 5.739143 AGGTACTCATAGGTGTAGGGTTA 57.261 43.478 0.00 0.00 0.00 2.85
392 432 2.099141 TCCGTTGGCTCAATCTCTTG 57.901 50.000 0.00 0.00 0.00 3.02
409 449 4.303282 GCGACTTCCTCAATCTAAGATCC 58.697 47.826 0.00 0.00 0.00 3.36
423 463 0.172803 AGACGTATGTGGCGACTTCC 59.827 55.000 0.00 0.00 31.22 3.46
429 469 0.376152 ACTACGAGACGTATGTGGCG 59.624 55.000 4.56 0.00 41.53 5.69
432 472 4.074466 TGTCAACTACGAGACGTATGTG 57.926 45.455 4.56 6.33 41.53 3.21
433 473 3.126514 CCTGTCAACTACGAGACGTATGT 59.873 47.826 4.56 0.00 41.53 2.29
439 479 1.699343 GTGCCTGTCAACTACGAGAC 58.301 55.000 0.00 0.00 35.37 3.36
452 492 1.160329 GGTATAGCTTGGCGTGCCTG 61.160 60.000 12.84 6.29 36.94 4.85
454 494 2.244651 CGGTATAGCTTGGCGTGCC 61.245 63.158 3.30 3.30 0.00 5.01
455 495 1.087771 AACGGTATAGCTTGGCGTGC 61.088 55.000 0.00 0.00 0.00 5.34
456 496 0.650512 CAACGGTATAGCTTGGCGTG 59.349 55.000 0.00 0.00 0.00 5.34
457 497 0.533491 TCAACGGTATAGCTTGGCGT 59.467 50.000 0.00 0.00 0.00 5.68
458 498 1.647346 TTCAACGGTATAGCTTGGCG 58.353 50.000 0.00 0.00 0.00 5.69
460 500 6.761714 ACTATTCTTTCAACGGTATAGCTTGG 59.238 38.462 0.00 0.00 0.00 3.61
463 510 6.875076 ACACTATTCTTTCAACGGTATAGCT 58.125 36.000 0.00 0.00 0.00 3.32
472 519 5.163943 GCCTCTTCGACACTATTCTTTCAAC 60.164 44.000 0.00 0.00 0.00 3.18
486 533 1.885163 TTTCTCCCGGCCTCTTCGAC 61.885 60.000 0.00 0.00 0.00 4.20
489 536 0.541863 TGATTTCTCCCGGCCTCTTC 59.458 55.000 0.00 0.00 0.00 2.87
497 544 4.808558 TGCATTTTCTTTGATTTCTCCCG 58.191 39.130 0.00 0.00 0.00 5.14
498 545 6.073058 GGTTTGCATTTTCTTTGATTTCTCCC 60.073 38.462 0.00 0.00 0.00 4.30
500 547 6.482973 TGGGTTTGCATTTTCTTTGATTTCTC 59.517 34.615 0.00 0.00 0.00 2.87
521 572 1.909302 CTAGACTTGACATGGGTGGGT 59.091 52.381 0.00 0.00 0.00 4.51
522 573 2.093447 GTCTAGACTTGACATGGGTGGG 60.093 54.545 15.91 0.00 34.80 4.61
568 620 1.902508 CAGAGGCTAGGTTCCTTGTCA 59.097 52.381 7.52 0.00 33.24 3.58
624 677 5.011125 CGGTCAGTAGGAGGTTGATGATATT 59.989 44.000 0.00 0.00 0.00 1.28
645 718 2.676632 TACATCGCCAACATTACGGT 57.323 45.000 0.00 0.00 0.00 4.83
706 862 7.377398 GCATATTGATGTGCACCCAAATAATA 58.623 34.615 20.66 13.83 43.34 0.98
732 888 9.977762 GTAGGGAAAACAACTACATATTTAACG 57.022 33.333 0.00 0.00 37.58 3.18
777 933 6.359804 AGGATGAGTGCAGCAGAAAATATTA 58.640 36.000 0.00 0.00 30.33 0.98
911 1325 6.636562 TGAAGTTAATCTTACCCGCAAAAA 57.363 33.333 0.00 0.00 36.40 1.94
912 1326 6.636562 TTGAAGTTAATCTTACCCGCAAAA 57.363 33.333 0.00 0.00 36.40 2.44
913 1327 6.657541 AGATTGAAGTTAATCTTACCCGCAAA 59.342 34.615 0.00 0.00 43.08 3.68
914 1328 6.177610 AGATTGAAGTTAATCTTACCCGCAA 58.822 36.000 0.00 0.00 43.08 4.85
915 1329 5.741011 AGATTGAAGTTAATCTTACCCGCA 58.259 37.500 0.00 0.00 43.08 5.69
916 1330 7.628235 GTTAGATTGAAGTTAATCTTACCCGC 58.372 38.462 6.35 0.00 43.08 6.13
920 1334 9.886132 TCTGGGTTAGATTGAAGTTAATCTTAC 57.114 33.333 6.35 7.48 43.08 2.34
921 1335 9.886132 GTCTGGGTTAGATTGAAGTTAATCTTA 57.114 33.333 6.35 0.00 43.08 2.10
922 1336 8.606830 AGTCTGGGTTAGATTGAAGTTAATCTT 58.393 33.333 6.35 0.00 43.08 2.40
923 1337 8.152023 AGTCTGGGTTAGATTGAAGTTAATCT 57.848 34.615 6.30 6.30 46.27 2.40
924 1338 8.669243 CAAGTCTGGGTTAGATTGAAGTTAATC 58.331 37.037 0.00 0.00 37.83 1.75
925 1339 8.164070 ACAAGTCTGGGTTAGATTGAAGTTAAT 58.836 33.333 0.00 0.00 37.83 1.40
926 1340 7.514721 ACAAGTCTGGGTTAGATTGAAGTTAA 58.485 34.615 0.00 0.00 37.83 2.01
927 1341 7.074653 ACAAGTCTGGGTTAGATTGAAGTTA 57.925 36.000 0.00 0.00 37.83 2.24
928 1342 5.941788 ACAAGTCTGGGTTAGATTGAAGTT 58.058 37.500 0.00 0.00 37.83 2.66
929 1343 5.513267 GGACAAGTCTGGGTTAGATTGAAGT 60.513 44.000 0.00 0.00 37.83 3.01
930 1344 4.938226 GGACAAGTCTGGGTTAGATTGAAG 59.062 45.833 0.00 0.00 37.83 3.02
931 1345 4.562757 CGGACAAGTCTGGGTTAGATTGAA 60.563 45.833 1.01 0.00 37.83 2.69
932 1346 3.056107 CGGACAAGTCTGGGTTAGATTGA 60.056 47.826 1.01 0.00 37.83 2.57
945 1359 3.042887 GACAACAAATTGCGGACAAGTC 58.957 45.455 0.00 0.00 39.69 3.01
948 1362 4.096532 TGTTAGACAACAAATTGCGGACAA 59.903 37.500 0.00 0.00 41.69 3.18
954 1368 6.672147 AGTGATCTGTTAGACAACAAATTGC 58.328 36.000 0.00 0.00 43.92 3.56
988 1402 6.756542 CACAGTTCATCCATCGTTTCAGTATA 59.243 38.462 0.00 0.00 0.00 1.47
992 1406 3.425359 GCACAGTTCATCCATCGTTTCAG 60.425 47.826 0.00 0.00 0.00 3.02
998 1412 0.107508 AGGGCACAGTTCATCCATCG 60.108 55.000 0.00 0.00 0.00 3.84
1022 1436 1.064906 CATGGAGCTTCTGGACCACAT 60.065 52.381 0.00 0.00 35.19 3.21
1059 1473 5.006165 CGTGGCAGAAGAAGATATTTGTCTC 59.994 44.000 0.00 0.00 0.00 3.36
1063 1477 5.111989 TCTCGTGGCAGAAGAAGATATTTG 58.888 41.667 0.00 0.00 0.00 2.32
1082 1496 5.961843 GCATTGTTGATTACATGACTTCTCG 59.038 40.000 0.00 0.00 36.44 4.04
1125 1539 5.408299 CGTCTGATGGTATTTTGTCACAGAA 59.592 40.000 0.00 0.00 35.47 3.02
1455 1869 0.036388 GCATGACCTGAGTCGGGAAA 60.036 55.000 25.39 12.07 46.74 3.13
1471 1885 2.190398 TGGTAGGGTACAGGATGCAT 57.810 50.000 0.00 0.00 42.53 3.96
1480 1894 5.742063 ACAAAAGAGCTAATGGTAGGGTAC 58.258 41.667 0.00 0.00 0.00 3.34
1484 1898 7.606456 TGTAGAAACAAAAGAGCTAATGGTAGG 59.394 37.037 0.00 0.00 30.91 3.18
1485 1899 8.547967 TGTAGAAACAAAAGAGCTAATGGTAG 57.452 34.615 0.00 0.00 30.91 3.18
1487 1901 8.409358 AATGTAGAAACAAAAGAGCTAATGGT 57.591 30.769 0.00 0.00 39.58 3.55
1493 1907 9.305925 CAAGAAAAATGTAGAAACAAAAGAGCT 57.694 29.630 0.00 0.00 39.58 4.09
1494 1908 8.058328 GCAAGAAAAATGTAGAAACAAAAGAGC 58.942 33.333 0.00 0.00 39.58 4.09
1495 1909 8.542953 GGCAAGAAAAATGTAGAAACAAAAGAG 58.457 33.333 0.00 0.00 39.58 2.85
1496 1910 8.037758 TGGCAAGAAAAATGTAGAAACAAAAGA 58.962 29.630 0.00 0.00 39.58 2.52
1497 1911 8.195617 TGGCAAGAAAAATGTAGAAACAAAAG 57.804 30.769 0.00 0.00 39.58 2.27
1502 1916 7.945033 TTCATGGCAAGAAAAATGTAGAAAC 57.055 32.000 2.14 0.00 0.00 2.78
1506 1920 7.298507 CCATTTCATGGCAAGAAAAATGTAG 57.701 36.000 20.15 7.69 44.70 2.74
1519 1939 5.751990 GAAATCATTCAGTCCATTTCATGGC 59.248 40.000 0.00 0.00 41.55 4.40
1520 1940 6.127281 TGGAAATCATTCAGTCCATTTCATGG 60.127 38.462 0.00 0.00 43.50 3.66
1563 1984 2.034685 GTGGTCCTTGAAGGCAAAGTTC 59.965 50.000 6.30 0.00 34.61 3.01
1785 2206 1.143183 GGCGAGGGTCTTGCGATAA 59.857 57.895 0.00 0.00 41.49 1.75
1905 2326 1.141053 AGAGAACCAACAAGAACCGCT 59.859 47.619 0.00 0.00 0.00 5.52
1932 2353 6.817765 ACAGAAACAATGGTATGGTTACTG 57.182 37.500 0.00 0.00 34.34 2.74
2071 2571 2.607187 GTATCAATGGGATACGAGGCG 58.393 52.381 0.00 0.00 46.44 5.52
2296 2796 0.828677 GTACTTAGCCACCACCGGAT 59.171 55.000 9.46 0.00 0.00 4.18
2315 2815 2.550830 ATTTAGCCCTACAGCATCCG 57.449 50.000 0.00 0.00 34.23 4.18
2519 3020 3.435671 AGGCGTTTAGAAAAGGTGAATCG 59.564 43.478 0.00 0.00 0.00 3.34
2551 3052 1.526917 GCTTACATGCGGGCCATCT 60.527 57.895 4.39 0.00 29.71 2.90
2677 3180 2.359900 CTCGAGGAAATGTCCCAAAGG 58.640 52.381 3.91 0.00 46.30 3.11
2794 3364 2.106332 CCACGGACGAGGTATGGC 59.894 66.667 0.00 0.00 0.00 4.40
2799 3369 3.681835 GCTCACCACGGACGAGGT 61.682 66.667 8.01 8.01 39.63 3.85
2819 3389 2.120909 GGGTGGTTGGATGCCATCG 61.121 63.158 0.00 0.00 37.98 3.84
2949 3519 0.892063 GAGAAGGAGGTCGTTGAGCT 59.108 55.000 0.00 0.00 43.43 4.09
3266 3843 1.541588 GCCAACGCCATTCTTTCTCTT 59.458 47.619 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.