Multiple sequence alignment - TraesCS2A01G025700

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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 TraesCS2A01G025700 chr2A 100.000 3497 0 0 1 3497 12104433 12100937 0.000000e+00 6458.0
1 TraesCS2A01G025700 chr2A 90.596 2467 162 28 1082 3497 12073526 12071079 0.000000e+00 3206.0
2 TraesCS2A01G025700 chr2A 88.232 1657 130 31 825 2460 12048870 12047258 0.000000e+00 1919.0
3 TraesCS2A01G025700 chr2A 90.935 1412 97 12 1127 2519 15394873 15396272 0.000000e+00 1869.0
4 TraesCS2A01G025700 chr2A 80.274 583 61 34 790 1325 747086709 747087284 1.180000e-104 390.0
5 TraesCS2A01G025700 chr2A 76.081 393 88 6 59 446 36004896 36005287 2.130000e-47 200.0
6 TraesCS2A01G025700 chr2A 83.607 61 10 0 2841 2901 565279855 565279915 1.360000e-04 58.4
7 TraesCS2A01G025700 chr2B 91.110 2126 125 30 1395 3497 17882924 17880840 0.000000e+00 2820.0
8 TraesCS2A01G025700 chr2B 91.396 1418 86 19 1123 2519 17874038 17872636 0.000000e+00 1910.0
9 TraesCS2A01G025700 chr2B 91.820 1308 87 8 1127 2416 24089531 24090836 0.000000e+00 1805.0
10 TraesCS2A01G025700 chr2B 87.561 1021 107 7 1 1009 17884393 17883381 0.000000e+00 1164.0
11 TraesCS2A01G025700 chr2B 92.989 271 12 4 1126 1396 17883304 17883041 4.230000e-104 388.0
12 TraesCS2A01G025700 chr2B 79.043 606 70 37 771 1325 752784792 752785391 2.570000e-96 363.0
13 TraesCS2A01G025700 chr2D 91.020 1715 112 19 768 2458 11510272 11508576 0.000000e+00 2276.0
14 TraesCS2A01G025700 chr2D 87.726 1711 139 41 739 2416 13421068 13422740 0.000000e+00 1930.0
15 TraesCS2A01G025700 chr2D 95.066 1216 37 7 1774 2986 11495755 11494560 0.000000e+00 1892.0
16 TraesCS2A01G025700 chr2D 92.644 1074 71 1 1395 2460 11477740 11476667 0.000000e+00 1539.0
17 TraesCS2A01G025700 chr2D 88.038 1162 123 11 1407 2552 617052665 617053826 0.000000e+00 1362.0
18 TraesCS2A01G025700 chr2D 96.855 477 15 0 3021 3497 11485810 11485334 0.000000e+00 798.0
19 TraesCS2A01G025700 chr2D 82.759 696 77 23 711 1396 11496952 11496290 6.510000e-162 580.0
20 TraesCS2A01G025700 chr2D 80.336 595 66 31 771 1325 617050974 617051557 1.510000e-108 403.0
21 TraesCS2A01G025700 chr2D 90.476 315 15 6 1083 1396 11478093 11477793 5.440000e-108 401.0
22 TraesCS2A01G025700 chr2D 78.684 380 69 11 59 430 355926941 355926566 3.490000e-60 243.0
23 TraesCS2A01G025700 chr2D 83.094 278 25 11 407 672 11510574 11510307 2.100000e-57 233.0
24 TraesCS2A01G025700 chr2D 76.986 365 79 5 88 449 313801144 313800782 1.650000e-48 204.0
25 TraesCS2A01G025700 chr2D 84.444 135 13 5 823 949 11478338 11478204 3.660000e-25 126.0
26 TraesCS2A01G025700 chr3A 78.086 397 77 10 59 449 45591338 45590946 3.490000e-60 243.0
27 TraesCS2A01G025700 chr3A 76.965 369 69 13 59 417 599980024 599980386 2.750000e-46 196.0
28 TraesCS2A01G025700 chr3B 76.904 394 83 7 59 446 372190453 372190844 2.110000e-52 217.0
29 TraesCS2A01G025700 chr5A 75.814 430 85 13 1 419 643370481 643370902 2.130000e-47 200.0
30 TraesCS2A01G025700 chr1B 75.696 395 92 4 59 449 18435493 18435099 9.900000e-46 195.0
31 TraesCS2A01G025700 chr1B 87.692 65 4 4 472 533 550376143 550376080 4.840000e-09 73.1
32 TraesCS2A01G025700 chr7D 77.193 342 71 6 93 430 154647368 154647030 3.560000e-45 193.0
33 TraesCS2A01G025700 chr5B 89.231 65 7 0 2838 2902 332293428 332293492 8.050000e-12 82.4
34 TraesCS2A01G025700 chr4D 84.615 78 12 0 465 542 109476576 109476653 1.040000e-10 78.7


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 TraesCS2A01G025700 chr2A 12100937 12104433 3496 True 6458.000000 6458 100.000000 1 3497 1 chr2A.!!$R3 3496
1 TraesCS2A01G025700 chr2A 12071079 12073526 2447 True 3206.000000 3206 90.596000 1082 3497 1 chr2A.!!$R2 2415
2 TraesCS2A01G025700 chr2A 12047258 12048870 1612 True 1919.000000 1919 88.232000 825 2460 1 chr2A.!!$R1 1635
3 TraesCS2A01G025700 chr2A 15394873 15396272 1399 False 1869.000000 1869 90.935000 1127 2519 1 chr2A.!!$F1 1392
4 TraesCS2A01G025700 chr2A 747086709 747087284 575 False 390.000000 390 80.274000 790 1325 1 chr2A.!!$F4 535
5 TraesCS2A01G025700 chr2B 17872636 17874038 1402 True 1910.000000 1910 91.396000 1123 2519 1 chr2B.!!$R1 1396
6 TraesCS2A01G025700 chr2B 24089531 24090836 1305 False 1805.000000 1805 91.820000 1127 2416 1 chr2B.!!$F1 1289
7 TraesCS2A01G025700 chr2B 17880840 17884393 3553 True 1457.333333 2820 90.553333 1 3497 3 chr2B.!!$R2 3496
8 TraesCS2A01G025700 chr2B 752784792 752785391 599 False 363.000000 363 79.043000 771 1325 1 chr2B.!!$F2 554
9 TraesCS2A01G025700 chr2D 13421068 13422740 1672 False 1930.000000 1930 87.726000 739 2416 1 chr2D.!!$F1 1677
10 TraesCS2A01G025700 chr2D 11508576 11510574 1998 True 1254.500000 2276 87.057000 407 2458 2 chr2D.!!$R6 2051
11 TraesCS2A01G025700 chr2D 11494560 11496952 2392 True 1236.000000 1892 88.912500 711 2986 2 chr2D.!!$R5 2275
12 TraesCS2A01G025700 chr2D 617050974 617053826 2852 False 882.500000 1362 84.187000 771 2552 2 chr2D.!!$F2 1781
13 TraesCS2A01G025700 chr2D 11476667 11478338 1671 True 688.666667 1539 89.188000 823 2460 3 chr2D.!!$R4 1637

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
371 374 0.107410 TTCTGGTGCGTTGGTTCTGT 60.107 50.0 0.0 0.0 0.00 3.41 F
381 384 0.400213 TTGGTTCTGTGGGGCAGTAG 59.600 55.0 0.0 0.0 45.23 2.57 F
1014 1139 0.953471 TATCACCACAACGCACCAGC 60.953 55.0 0.0 0.0 37.42 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1673 3014 0.102481 GGCGAAGACCGAGCATCTTA 59.898 55.000 0.00 0.0 41.76 2.10 R
2314 3698 1.675641 ATTCCCTCGCCAGTTGTGC 60.676 57.895 0.00 0.0 0.00 4.57 R
2732 4148 0.036732 GATCTGGCCAACACTGTGGA 59.963 55.000 7.01 0.0 41.65 4.02 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
30 31 1.302431 CATGAAGCCGTGGTGGACA 60.302 57.895 0.00 0.00 42.00 4.02
40 42 2.282462 GGTGGACACTGGCCCTTG 60.282 66.667 0.00 0.00 0.00 3.61
41 43 2.282462 GTGGACACTGGCCCTTGG 60.282 66.667 0.00 0.00 0.00 3.61
42 44 2.776526 TGGACACTGGCCCTTGGT 60.777 61.111 0.00 0.00 0.00 3.67
45 47 1.377333 GACACTGGCCCTTGGTAGC 60.377 63.158 0.00 0.00 0.00 3.58
53 55 2.365105 CCTTGGTAGCGGGAGGGA 60.365 66.667 0.00 0.00 0.00 4.20
62 64 2.825264 CGGGAGGGATCTTGCTCC 59.175 66.667 0.00 0.00 35.38 4.70
69 72 3.198872 GAGGGATCTTGCTCCGTTTTAG 58.801 50.000 0.00 0.00 36.05 1.85
85 88 5.392165 CCGTTTTAGGTGTTTTGTGAGTTCA 60.392 40.000 0.00 0.00 0.00 3.18
96 99 6.533367 TGTTTTGTGAGTTCATTTAGGTTTGC 59.467 34.615 0.00 0.00 0.00 3.68
102 105 5.992829 TGAGTTCATTTAGGTTTGCGTCTTA 59.007 36.000 0.00 0.00 0.00 2.10
119 122 3.752222 GTCTTACTCAGGAAGACGAGACA 59.248 47.826 14.30 0.00 42.39 3.41
124 127 0.962489 CAGGAAGACGAGACAGTGGT 59.038 55.000 0.00 0.00 0.00 4.16
146 149 4.156739 GTGGCTCCTTGAAGTTGGAATAAG 59.843 45.833 0.00 0.00 31.23 1.73
153 156 5.416013 CCTTGAAGTTGGAATAAGGTTCTCC 59.584 44.000 0.00 0.00 34.58 3.71
155 158 4.263771 TGAAGTTGGAATAAGGTTCTCCCC 60.264 45.833 0.00 0.00 0.00 4.81
173 176 3.766691 GCGTAGGCCCCGTTCTGA 61.767 66.667 13.33 0.00 0.00 3.27
180 183 1.153086 GCCCCGTTCTGATGATGCT 60.153 57.895 0.00 0.00 0.00 3.79
200 203 1.007964 CTAGCGTCATCAGAGGGCG 60.008 63.158 4.33 4.33 31.57 6.13
202 205 1.320344 TAGCGTCATCAGAGGGCGTT 61.320 55.000 11.21 7.35 31.57 4.84
204 207 1.298859 GCGTCATCAGAGGGCGTTTT 61.299 55.000 11.21 0.00 0.00 2.43
216 219 0.586802 GGCGTTTTGAGGTGTGTCTC 59.413 55.000 0.00 0.00 0.00 3.36
230 233 1.006805 GTCTCCGGCGGATCTCATG 60.007 63.158 31.23 16.85 0.00 3.07
253 256 4.382793 GGGATTTAGTCGGTGCTAGTCTTT 60.383 45.833 0.00 0.00 0.00 2.52
268 271 0.329261 TCTTTGGTGGATCTGCCTGG 59.671 55.000 7.43 0.00 37.63 4.45
277 280 2.945080 GATCTGCCTGGATCCATTCA 57.055 50.000 16.63 14.67 36.91 2.57
280 283 3.675348 TCTGCCTGGATCCATTCATTT 57.325 42.857 16.63 0.00 0.00 2.32
289 292 7.418254 GCCTGGATCCATTCATTTTATGTCTTT 60.418 37.037 16.63 0.00 0.00 2.52
300 303 6.922957 TCATTTTATGTCTTTGTTTGTGCCTC 59.077 34.615 0.00 0.00 0.00 4.70
303 306 7.575414 TTTATGTCTTTGTTTGTGCCTCTAA 57.425 32.000 0.00 0.00 0.00 2.10
311 314 2.286365 TTGTGCCTCTAAAGGTTGGG 57.714 50.000 0.00 0.00 45.34 4.12
317 320 2.618302 GCCTCTAAAGGTTGGGTCCTTC 60.618 54.545 0.00 0.00 45.79 3.46
319 322 2.913617 CTCTAAAGGTTGGGTCCTTCCT 59.086 50.000 0.00 0.00 45.79 3.36
320 323 4.101856 CTCTAAAGGTTGGGTCCTTCCTA 58.898 47.826 0.00 0.00 45.79 2.94
331 334 7.443477 GTTGGGTCCTTCCTATTATACTTCTC 58.557 42.308 0.00 0.00 36.25 2.87
337 340 9.921637 GTCCTTCCTATTATACTTCTCTTCATG 57.078 37.037 0.00 0.00 0.00 3.07
340 343 9.638239 CTTCCTATTATACTTCTCTTCATGAGC 57.362 37.037 0.00 0.00 42.38 4.26
341 344 8.712228 TCCTATTATACTTCTCTTCATGAGCA 57.288 34.615 0.00 0.00 42.38 4.26
343 346 9.421806 CCTATTATACTTCTCTTCATGAGCAAG 57.578 37.037 0.00 0.00 42.38 4.01
362 365 1.381165 GGGTTGTTGTTCTGGTGCGT 61.381 55.000 0.00 0.00 0.00 5.24
371 374 0.107410 TTCTGGTGCGTTGGTTCTGT 60.107 50.000 0.00 0.00 0.00 3.41
378 381 2.260869 CGTTGGTTCTGTGGGGCAG 61.261 63.158 0.00 0.00 46.34 4.85
381 384 0.400213 TTGGTTCTGTGGGGCAGTAG 59.600 55.000 0.00 0.00 45.23 2.57
393 396 1.071567 GGCAGTAGCACGACGACTTC 61.072 60.000 0.00 0.00 44.61 3.01
422 425 5.362263 TGTCTACTACAACAAGTTTGGTCC 58.638 41.667 0.00 0.00 34.29 4.46
431 434 3.056328 GTTTGGTCCAGCTCCGGC 61.056 66.667 0.00 0.00 39.06 6.13
432 435 3.565214 TTTGGTCCAGCTCCGGCA 61.565 61.111 0.00 0.00 41.70 5.69
441 444 4.168291 GCTCCGGCAAGAGAGGGG 62.168 72.222 0.00 0.00 35.82 4.79
442 445 3.474570 CTCCGGCAAGAGAGGGGG 61.475 72.222 0.00 0.00 35.82 5.40
461 464 2.429610 GGGGATAACACTCGTTGCTAGA 59.570 50.000 0.00 0.00 36.52 2.43
462 465 3.118884 GGGGATAACACTCGTTGCTAGAA 60.119 47.826 0.00 0.00 36.52 2.10
478 481 3.954904 GCTAGAAGGTCTACAGACATGGA 59.045 47.826 11.31 0.00 46.47 3.41
513 516 9.502091 TGTTATTTCTGTGTTCTTTATACTGCT 57.498 29.630 0.00 0.00 0.00 4.24
518 521 7.418337 TCTGTGTTCTTTATACTGCTATGGA 57.582 36.000 0.00 0.00 0.00 3.41
528 531 8.575649 TTTATACTGCTATGGAGTGATCGATA 57.424 34.615 0.00 0.00 0.00 2.92
596 608 5.758784 AGCGAGGTAAGTAAAGCAAATATCC 59.241 40.000 0.00 0.00 0.00 2.59
599 611 7.630924 CGAGGTAAGTAAAGCAAATATCCAAG 58.369 38.462 0.00 0.00 0.00 3.61
652 664 2.070039 CCGGCCACATCTTCCCCTA 61.070 63.158 2.24 0.00 0.00 3.53
683 695 5.316992 CCCTACCTACCTATTAGTTCCCCTA 59.683 48.000 0.00 0.00 0.00 3.53
685 697 4.749820 ACCTACCTATTAGTTCCCCTAGC 58.250 47.826 0.00 0.00 0.00 3.42
788 808 1.009675 CACACGAGTGCTTGCAACC 60.010 57.895 0.00 0.00 39.21 3.77
797 864 4.351054 CTTGCAACCGGGGAGGCT 62.351 66.667 6.32 0.00 46.52 4.58
1005 1130 2.490509 ACACTCGATCGTATCACCACAA 59.509 45.455 15.94 0.00 0.00 3.33
1014 1139 0.953471 TATCACCACAACGCACCAGC 60.953 55.000 0.00 0.00 37.42 4.85
1082 1226 3.978491 GAGCCCCGATCGCGATCA 61.978 66.667 39.26 9.34 40.82 2.92
1084 1228 3.338676 GCCCCGATCGCGATCAAC 61.339 66.667 39.26 24.85 40.82 3.18
1085 1229 2.417516 CCCCGATCGCGATCAACT 59.582 61.111 39.26 14.49 40.82 3.16
1086 1230 1.658114 CCCCGATCGCGATCAACTA 59.342 57.895 39.26 6.90 40.82 2.24
1100 1260 5.239087 GCGATCAACTACTACCTAGCTAGTT 59.761 44.000 19.31 8.10 34.02 2.24
1673 3014 2.701780 CGCCGACTACCAGCTCACT 61.702 63.158 0.00 0.00 0.00 3.41
1877 3256 2.283604 TCGCTGGTAGGTCAGGCA 60.284 61.111 0.00 0.00 35.43 4.75
2672 4076 1.541147 CGTTTTCATGGGCTCACACAT 59.459 47.619 0.00 0.00 0.00 3.21
2679 4083 1.026182 TGGGCTCACACATCGCATTC 61.026 55.000 0.00 0.00 0.00 2.67
2727 4143 1.899814 TGTCTTCCTTACGTGAGCCAT 59.100 47.619 0.96 0.00 0.00 4.40
2728 4144 2.301870 TGTCTTCCTTACGTGAGCCATT 59.698 45.455 0.96 0.00 0.00 3.16
2729 4145 2.673368 GTCTTCCTTACGTGAGCCATTG 59.327 50.000 0.96 0.00 0.00 2.82
2730 4146 2.301870 TCTTCCTTACGTGAGCCATTGT 59.698 45.455 0.96 0.00 0.00 2.71
2731 4147 2.380084 TCCTTACGTGAGCCATTGTC 57.620 50.000 0.96 0.00 0.00 3.18
2732 4148 1.899814 TCCTTACGTGAGCCATTGTCT 59.100 47.619 0.96 0.00 0.00 3.41
2733 4149 2.094182 TCCTTACGTGAGCCATTGTCTC 60.094 50.000 0.96 0.00 0.00 3.36
2734 4150 2.271800 CTTACGTGAGCCATTGTCTCC 58.728 52.381 0.00 0.00 0.00 3.71
2735 4151 1.262417 TACGTGAGCCATTGTCTCCA 58.738 50.000 0.00 0.00 0.00 3.86
2736 4152 0.320771 ACGTGAGCCATTGTCTCCAC 60.321 55.000 0.00 0.00 0.00 4.02
2737 4153 0.320683 CGTGAGCCATTGTCTCCACA 60.321 55.000 0.00 0.00 0.00 4.17
2746 4162 0.465460 TTGTCTCCACAGTGTTGGCC 60.465 55.000 0.00 0.00 36.48 5.36
2758 4174 2.306805 AGTGTTGGCCAGATCTCATTCA 59.693 45.455 5.11 0.00 0.00 2.57
2779 4195 5.849510 TCAACTGATTTAACCAAGTCTCGA 58.150 37.500 0.00 0.00 0.00 4.04
2790 4206 2.619177 CCAAGTCTCGACCGAGTGATAT 59.381 50.000 17.54 1.02 42.49 1.63
2911 4343 5.007034 TCAGATTTAGCAATCCCGTTTTCA 58.993 37.500 0.00 0.00 39.95 2.69
2928 4360 5.048504 CGTTTTCAATATGCCTATGGATGCT 60.049 40.000 0.00 0.00 0.00 3.79
2986 4421 2.190161 CGAAGCGATCGTATGGAAACA 58.810 47.619 17.81 0.00 46.52 2.83
3016 4478 4.521130 TTCTATGTTCGCTGTCAGACTT 57.479 40.909 3.32 0.00 0.00 3.01
3036 4498 6.969993 ACTTTGTAGTCCCAATGCTTTTTA 57.030 33.333 0.00 0.00 0.00 1.52
3108 4570 1.830279 TCATTGGGACGTCTCGTACT 58.170 50.000 16.46 0.00 40.97 2.73
3120 4582 4.202151 ACGTCTCGTACTTGTTAGGGTTTT 60.202 41.667 0.00 0.00 38.73 2.43
3127 4589 5.279356 CGTACTTGTTAGGGTTTTCTCTCCT 60.279 44.000 0.00 0.00 34.85 3.69
3128 4590 4.974399 ACTTGTTAGGGTTTTCTCTCCTG 58.026 43.478 0.00 0.00 32.46 3.86
3265 4728 0.313043 GACGAGGTCCTTGTCGACAA 59.687 55.000 28.07 28.07 39.53 3.18
3314 4777 2.579873 CTAGCACCTTTATGGCATGCT 58.420 47.619 18.92 14.64 46.10 3.79
3349 4812 6.382869 AACTAATAGAGCATTTGCATCCAC 57.617 37.500 5.20 0.00 45.16 4.02
3359 4822 4.931002 GCATTTGCATCCACTTTTGTACAT 59.069 37.500 0.00 0.00 41.59 2.29
3451 4914 8.655901 TGTAGATATTATAGTTCATGGCAACCA 58.344 33.333 0.00 0.00 38.19 3.67
3452 4915 9.672673 GTAGATATTATAGTTCATGGCAACCAT 57.327 33.333 0.00 0.00 46.37 3.55
3456 4919 7.986085 ATTATAGTTCATGGCAACCATAGAC 57.014 36.000 0.00 1.63 43.15 2.59
3459 4922 2.747446 GTTCATGGCAACCATAGACGTT 59.253 45.455 0.00 0.00 43.15 3.99
3473 4936 8.692141 ACCATAGACGTTTAGTTCATGGCACA 62.692 42.308 5.06 0.00 43.06 4.57
3490 4953 5.321102 TGGCACAACAAATCTTATACCTGT 58.679 37.500 0.00 0.00 31.92 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.325296 ACGGCTTCATGGACCTAGGA 60.325 55.000 17.98 0.00 0.00 2.94
10 11 2.220586 TCCACCACGGCTTCATGGA 61.221 57.895 0.00 0.00 39.46 3.41
30 31 3.717294 CCGCTACCAAGGGCCAGT 61.717 66.667 6.18 2.20 34.41 4.00
40 42 1.749033 CAAGATCCCTCCCGCTACC 59.251 63.158 0.00 0.00 0.00 3.18
41 43 1.069935 GCAAGATCCCTCCCGCTAC 59.930 63.158 0.00 0.00 0.00 3.58
42 44 1.075226 AGCAAGATCCCTCCCGCTA 60.075 57.895 0.00 0.00 29.96 4.26
45 47 2.825264 GGAGCAAGATCCCTCCCG 59.175 66.667 11.70 0.00 41.42 5.14
53 55 3.418684 ACACCTAAAACGGAGCAAGAT 57.581 42.857 0.00 0.00 0.00 2.40
62 64 5.632959 TGAACTCACAAAACACCTAAAACG 58.367 37.500 0.00 0.00 0.00 3.60
69 72 6.144078 ACCTAAATGAACTCACAAAACACC 57.856 37.500 0.00 0.00 0.00 4.16
85 88 4.935808 CCTGAGTAAGACGCAAACCTAAAT 59.064 41.667 0.00 0.00 0.00 1.40
102 105 1.883275 CACTGTCTCGTCTTCCTGAGT 59.117 52.381 0.00 0.00 33.88 3.41
119 122 0.846693 AACTTCAAGGAGCCACCACT 59.153 50.000 0.00 0.00 42.04 4.00
124 127 2.978156 ATTCCAACTTCAAGGAGCCA 57.022 45.000 0.00 0.00 34.91 4.75
131 134 5.321927 GGGAGAACCTTATTCCAACTTCAA 58.678 41.667 0.00 0.00 35.85 2.69
146 149 4.525949 GCCTACGCGGGGAGAACC 62.526 72.222 21.55 0.00 39.11 3.62
165 168 2.799412 GCTAGAAGCATCATCAGAACGG 59.201 50.000 0.00 0.00 41.89 4.44
170 173 3.089573 TGACGCTAGAAGCATCATCAG 57.910 47.619 0.00 0.00 38.63 2.90
180 183 0.747255 GCCCTCTGATGACGCTAGAA 59.253 55.000 0.00 0.00 0.00 2.10
190 193 0.693049 ACCTCAAAACGCCCTCTGAT 59.307 50.000 0.00 0.00 0.00 2.90
200 203 1.226746 CCGGAGACACACCTCAAAAC 58.773 55.000 0.00 0.00 34.94 2.43
202 205 1.070786 GCCGGAGACACACCTCAAA 59.929 57.895 5.05 0.00 34.94 2.69
204 207 3.680786 CGCCGGAGACACACCTCA 61.681 66.667 5.05 0.00 34.94 3.86
216 219 2.116983 AATCCCATGAGATCCGCCGG 62.117 60.000 0.00 0.00 0.00 6.13
230 233 2.694109 AGACTAGCACCGACTAAATCCC 59.306 50.000 0.00 0.00 0.00 3.85
253 256 2.224821 GATCCAGGCAGATCCACCA 58.775 57.895 6.33 0.00 37.31 4.17
274 277 7.271511 AGGCACAAACAAAGACATAAAATGAA 58.728 30.769 0.00 0.00 0.00 2.57
277 280 7.054491 AGAGGCACAAACAAAGACATAAAAT 57.946 32.000 0.00 0.00 0.00 1.82
280 283 7.255451 CCTTTAGAGGCACAAACAAAGACATAA 60.255 37.037 0.00 0.00 35.94 1.90
311 314 9.921637 CATGAAGAGAAGTATAATAGGAAGGAC 57.078 37.037 0.00 0.00 0.00 3.85
331 334 2.624838 ACAACAACCCTTGCTCATGAAG 59.375 45.455 0.00 0.00 0.00 3.02
337 340 1.338020 CCAGAACAACAACCCTTGCTC 59.662 52.381 0.00 0.00 0.00 4.26
340 343 1.202405 GCACCAGAACAACAACCCTTG 60.202 52.381 0.00 0.00 0.00 3.61
341 344 1.111277 GCACCAGAACAACAACCCTT 58.889 50.000 0.00 0.00 0.00 3.95
343 346 1.358759 CGCACCAGAACAACAACCC 59.641 57.895 0.00 0.00 0.00 4.11
371 374 4.063967 CGTCGTGCTACTGCCCCA 62.064 66.667 0.00 0.00 38.71 4.96
378 381 1.513586 CGGGAAGTCGTCGTGCTAC 60.514 63.158 0.00 0.00 0.00 3.58
381 384 1.445582 AATCGGGAAGTCGTCGTGC 60.446 57.895 0.00 0.00 0.00 5.34
420 423 2.283894 TCTCTTGCCGGAGCTGGA 60.284 61.111 5.05 0.00 40.80 3.86
422 425 2.186384 CCTCTCTTGCCGGAGCTG 59.814 66.667 5.05 0.00 40.80 4.24
441 444 3.795623 TCTAGCAACGAGTGTTATCCC 57.204 47.619 0.00 0.00 36.28 3.85
442 445 4.113354 CCTTCTAGCAACGAGTGTTATCC 58.887 47.826 0.00 0.00 36.28 2.59
449 452 3.418995 TGTAGACCTTCTAGCAACGAGT 58.581 45.455 0.00 0.00 28.01 4.18
450 453 3.690139 TCTGTAGACCTTCTAGCAACGAG 59.310 47.826 0.00 0.00 28.01 4.18
455 458 3.701542 CCATGTCTGTAGACCTTCTAGCA 59.298 47.826 9.37 0.00 44.15 3.49
461 464 6.814954 ATTACATCCATGTCTGTAGACCTT 57.185 37.500 9.37 0.00 44.15 3.50
462 465 6.814954 AATTACATCCATGTCTGTAGACCT 57.185 37.500 9.37 0.00 44.15 3.85
495 498 7.223582 CACTCCATAGCAGTATAAAGAACACAG 59.776 40.741 0.00 0.00 0.00 3.66
506 509 6.418946 TCTATCGATCACTCCATAGCAGTAT 58.581 40.000 0.00 0.00 0.00 2.12
528 531 3.510360 TCTTCCGAGGAAACTTTCGATCT 59.490 43.478 6.01 0.00 44.43 2.75
530 533 3.955650 TCTTCCGAGGAAACTTTCGAT 57.044 42.857 6.01 0.00 44.43 3.59
558 561 0.872021 CTCGCTATGACGTTGAGCCC 60.872 60.000 10.54 0.00 32.35 5.19
566 569 3.729716 GCTTTACTTACCTCGCTATGACG 59.270 47.826 0.00 0.00 0.00 4.35
596 608 4.862018 ACACCAACAAAACGACAATTCTTG 59.138 37.500 0.00 0.00 0.00 3.02
599 611 4.416620 TCACACCAACAAAACGACAATTC 58.583 39.130 0.00 0.00 0.00 2.17
652 664 6.164086 ACTAATAGGTAGGTAGGGGAGTACT 58.836 44.000 0.00 0.00 33.68 2.73
683 695 1.499870 CTAGGTAGGTAGGGGAGTGCT 59.500 57.143 0.00 0.00 0.00 4.40
685 697 3.979347 TCTACTAGGTAGGTAGGGGAGTG 59.021 52.174 0.00 0.00 36.83 3.51
723 742 0.662374 CTCGTACGTGCTTGAACCGT 60.662 55.000 16.05 0.00 38.53 4.83
797 864 4.243008 TGGGTCGCGTGGCTTTGA 62.243 61.111 5.77 0.00 0.00 2.69
806 873 2.183555 GGAGTTAGGTGGGTCGCG 59.816 66.667 0.00 0.00 0.00 5.87
1014 1139 0.380733 AATGACAGATGCTGCATGCG 59.619 50.000 21.53 12.75 46.63 4.73
1015 1140 1.676529 AGAATGACAGATGCTGCATGC 59.323 47.619 21.53 11.82 43.25 4.06
1064 1208 3.675563 GATCGCGATCGGGGCTCT 61.676 66.667 31.24 13.39 36.13 4.09
1065 1209 3.499929 TTGATCGCGATCGGGGCTC 62.500 63.158 36.05 24.20 40.63 4.70
1068 1212 0.663568 GTAGTTGATCGCGATCGGGG 60.664 60.000 36.05 12.81 40.63 5.73
1071 1215 2.223611 AGGTAGTAGTTGATCGCGATCG 59.776 50.000 36.05 11.69 40.63 3.69
1072 1216 3.900388 AGGTAGTAGTTGATCGCGATC 57.100 47.619 36.16 36.16 38.29 3.69
1074 1218 2.547211 GCTAGGTAGTAGTTGATCGCGA 59.453 50.000 13.09 13.09 0.00 5.87
1082 1226 3.959449 GGCCAACTAGCTAGGTAGTAGTT 59.041 47.826 29.65 16.87 37.46 2.24
1084 1228 2.553172 CGGCCAACTAGCTAGGTAGTAG 59.447 54.545 29.65 24.31 32.69 2.57
1085 1229 2.579873 CGGCCAACTAGCTAGGTAGTA 58.420 52.381 29.65 0.00 32.69 1.82
1086 1230 1.400737 CGGCCAACTAGCTAGGTAGT 58.599 55.000 25.40 25.40 34.56 2.73
1100 1260 4.118995 CGTACGTACCAGCGGCCA 62.119 66.667 19.67 0.00 35.98 5.36
1212 1387 3.648982 CAGTTTGCTGGCGTCGCA 61.649 61.111 20.50 2.50 39.01 5.10
1673 3014 0.102481 GGCGAAGACCGAGCATCTTA 59.898 55.000 0.00 0.00 41.76 2.10
1877 3256 2.125512 GCACCATCGCCGAAGAGT 60.126 61.111 0.00 0.00 0.00 3.24
2314 3698 1.675641 ATTCCCTCGCCAGTTGTGC 60.676 57.895 0.00 0.00 0.00 4.57
2634 4038 4.481930 AACGAAAACGAATCATCAAGCA 57.518 36.364 0.00 0.00 0.00 3.91
2672 4076 0.790207 GTGCGAAGAAGTGAATGCGA 59.210 50.000 0.00 0.00 0.00 5.10
2679 4083 1.157870 ACAACCCGTGCGAAGAAGTG 61.158 55.000 0.00 0.00 0.00 3.16
2727 4143 0.465460 GGCCAACACTGTGGAGACAA 60.465 55.000 13.09 0.00 46.06 3.18
2728 4144 1.148273 GGCCAACACTGTGGAGACA 59.852 57.895 13.09 0.00 41.65 3.41
2729 4145 0.886490 CTGGCCAACACTGTGGAGAC 60.886 60.000 7.01 2.87 41.65 3.36
2730 4146 1.053835 TCTGGCCAACACTGTGGAGA 61.054 55.000 7.01 0.00 41.65 3.71
2731 4147 0.037303 ATCTGGCCAACACTGTGGAG 59.963 55.000 7.01 3.83 41.65 3.86
2732 4148 0.036732 GATCTGGCCAACACTGTGGA 59.963 55.000 7.01 0.00 41.65 4.02
2733 4149 0.037303 AGATCTGGCCAACACTGTGG 59.963 55.000 7.01 0.00 42.05 4.17
2734 4150 1.271001 TGAGATCTGGCCAACACTGTG 60.271 52.381 7.01 6.19 0.00 3.66
2735 4151 1.059098 TGAGATCTGGCCAACACTGT 58.941 50.000 7.01 0.00 0.00 3.55
2736 4152 2.414994 ATGAGATCTGGCCAACACTG 57.585 50.000 7.01 0.00 0.00 3.66
2737 4153 2.306805 TGAATGAGATCTGGCCAACACT 59.693 45.455 7.01 5.86 0.00 3.55
2746 4162 8.272545 TGGTTAAATCAGTTGAATGAGATCTG 57.727 34.615 0.00 0.00 31.44 2.90
2758 4174 4.995487 GGTCGAGACTTGGTTAAATCAGTT 59.005 41.667 3.09 0.00 0.00 3.16
2911 4343 3.074985 ACACCAGCATCCATAGGCATATT 59.925 43.478 0.00 0.00 33.96 1.28
2986 4421 8.492673 TGACAGCGAACATAGAAAAAGATAAT 57.507 30.769 0.00 0.00 0.00 1.28
2992 4454 5.297547 AGTCTGACAGCGAACATAGAAAAA 58.702 37.500 10.88 0.00 0.00 1.94
3016 4478 6.268847 ACCATTAAAAAGCATTGGGACTACAA 59.731 34.615 0.00 0.00 34.41 2.41
3108 4570 5.510179 CGTACAGGAGAGAAAACCCTAACAA 60.510 44.000 0.00 0.00 0.00 2.83
3120 4582 5.511716 CCTTCTAGCTATCGTACAGGAGAGA 60.512 48.000 0.00 0.00 0.00 3.10
3127 4589 2.885266 CTGGCCTTCTAGCTATCGTACA 59.115 50.000 3.32 0.00 0.00 2.90
3128 4590 2.229302 CCTGGCCTTCTAGCTATCGTAC 59.771 54.545 3.32 0.00 0.00 3.67
3218 4680 1.530771 CCTGGGCTTGGAGGATGAG 59.469 63.158 0.00 0.00 0.00 2.90
3219 4681 2.683465 GCCTGGGCTTGGAGGATGA 61.683 63.158 4.12 0.00 38.26 2.92
3221 4683 3.424105 GGCCTGGGCTTGGAGGAT 61.424 66.667 13.80 0.00 41.60 3.24
3265 4728 1.598130 GTTGCAGCGGAGACAACCT 60.598 57.895 0.00 0.00 38.15 3.50
3314 4777 7.956328 TGCTCTATTAGTTTCTAGTGGAAGA 57.044 36.000 0.00 0.00 35.16 2.87
3349 4812 5.181811 TGCTTCCATCTGTGATGTACAAAAG 59.818 40.000 0.00 0.00 39.20 2.27
3359 4822 3.054213 TCATTCCATGCTTCCATCTGTGA 60.054 43.478 0.00 0.00 0.00 3.58
3451 4914 4.827692 TGTGCCATGAACTAAACGTCTAT 58.172 39.130 0.00 0.00 0.00 1.98
3452 4915 4.260139 TGTGCCATGAACTAAACGTCTA 57.740 40.909 0.00 0.00 0.00 2.59
3456 4919 3.617540 TGTTGTGCCATGAACTAAACG 57.382 42.857 0.00 0.00 0.00 3.60
3459 4922 6.403866 AAGATTTGTTGTGCCATGAACTAA 57.596 33.333 0.00 0.00 0.00 2.24
3473 4936 6.699575 GCCATGACAGGTATAAGATTTGTT 57.300 37.500 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.