Multiple sequence alignment - TraesCS4D01G199700

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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 TraesCS4D01G199700 chr4D 100.000 3819 0 0 1 3819 346455180 346451362 0.000000e+00 7053.0
1 TraesCS4D01G199700 chr4D 92.208 77 6 0 3275 3351 346451837 346451761 4.030000e-20 110.0
2 TraesCS4D01G199700 chr4D 92.208 77 6 0 3344 3420 346451906 346451830 4.030000e-20 110.0
3 TraesCS4D01G199700 chr4B 93.377 1676 89 9 1445 3115 427498410 427496752 0.000000e+00 2460.0
4 TraesCS4D01G199700 chr4B 88.862 1230 52 32 85 1281 427499859 427498682 0.000000e+00 1434.0
5 TraesCS4D01G199700 chr4B 93.595 484 15 7 3344 3819 427496594 427496119 0.000000e+00 708.0
6 TraesCS4D01G199700 chr4B 89.634 164 10 2 1273 1436 427498662 427498506 6.470000e-48 202.0
7 TraesCS4D01G199700 chr4B 90.714 140 9 2 3212 3351 427496657 427496522 2.340000e-42 183.0
8 TraesCS4D01G199700 chr4B 78.977 176 17 12 1018 1193 385957548 385957703 6.750000e-18 102.0
9 TraesCS4D01G199700 chr4B 91.549 71 3 2 3111 3181 427496725 427496658 1.130000e-15 95.3
10 TraesCS4D01G199700 chr4A 94.249 1617 74 7 1568 3182 119081288 119082887 0.000000e+00 2453.0
11 TraesCS4D01G199700 chr4A 87.604 1323 56 37 1 1228 119079674 119080983 0.000000e+00 1435.0
12 TraesCS4D01G199700 chr4A 92.276 479 16 3 3344 3819 119083143 119083603 0.000000e+00 660.0
13 TraesCS4D01G199700 chr4A 97.959 147 3 0 3181 3327 119083049 119083195 4.900000e-64 255.0
14 TraesCS4D01G199700 chr4A 85.321 109 12 3 1373 1481 119081187 119081291 4.030000e-20 110.0
15 TraesCS4D01G199700 chr4A 79.775 178 12 13 1018 1193 538908630 538908475 1.450000e-19 108.0
16 TraesCS4D01G199700 chr4A 95.000 40 2 0 3098 3137 614706420 614706381 3.180000e-06 63.9
17 TraesCS4D01G199700 chr5A 87.050 139 12 2 1090 1228 692541494 692541626 6.610000e-33 152.0
18 TraesCS4D01G199700 chr5A 85.612 139 14 2 1090 1228 692548063 692548195 1.430000e-29 141.0
19 TraesCS4D01G199700 chr2B 80.682 176 14 10 1018 1193 17219896 17219741 6.700000e-23 119.0
20 TraesCS4D01G199700 chr2B 80.682 176 14 10 1018 1193 414953270 414953425 6.700000e-23 119.0
21 TraesCS4D01G199700 chr2B 83.333 132 8 6 1018 1149 127202947 127203064 4.030000e-20 110.0
22 TraesCS4D01G199700 chr6B 95.918 49 2 0 3180 3228 213239647 213239695 3.160000e-11 80.5
23 TraesCS4D01G199700 chr3D 93.182 44 3 0 3094 3137 435451254 435451297 8.860000e-07 65.8
24 TraesCS4D01G199700 chr6A 93.182 44 2 1 3094 3137 454653999 454654041 3.180000e-06 63.9
25 TraesCS4D01G199700 chr6A 92.683 41 3 0 3098 3138 591381867 591381907 4.120000e-05 60.2
26 TraesCS4D01G199700 chr5D 95.000 40 2 0 3098 3137 61066477 61066438 3.180000e-06 63.9
27 TraesCS4D01G199700 chr5B 95.000 40 2 0 3098 3137 69548050 69548089 3.180000e-06 63.9
28 TraesCS4D01G199700 chr3B 92.857 42 3 0 3098 3139 630499868 630499909 1.150000e-05 62.1


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 TraesCS4D01G199700 chr4D 346451362 346455180 3818 True 2424.333333 7053 94.805333 1 3819 3 chr4D.!!$R1 3818
1 TraesCS4D01G199700 chr4B 427496119 427499859 3740 True 847.050000 2460 91.288500 85 3819 6 chr4B.!!$R1 3734
2 TraesCS4D01G199700 chr4A 119079674 119083603 3929 False 982.600000 2453 91.481800 1 3819 5 chr4A.!!$F1 3818

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
87 99 0.246374 CAACGACTCGAACGATTGCG 60.246 55.0 16.43 4.95 44.79 4.85 F
699 758 0.454117 GGAGAAACGGACGAGTCGAC 60.454 60.0 21.50 13.62 0.00 4.20 F
1600 1882 0.108041 TAAATCCGACTCCGTTGCCC 60.108 55.0 0.00 0.00 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 1870 0.605319 TGATGTTGGGCAACGGAGTC 60.605 55.0 0.00 0.0 45.00 3.36 R
2153 2435 1.252904 TGCATTTTCTCCAGCCCTGC 61.253 55.0 0.00 0.0 0.00 4.85 R
3338 3820 0.839946 ACCTTGACCAAGCTGTCACT 59.160 50.0 6.39 0.0 44.55 3.41 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
45 46 1.069296 CGCGAAGAAATGGACTTGCAA 60.069 47.619 0.00 0.00 0.00 4.08
87 99 0.246374 CAACGACTCGAACGATTGCG 60.246 55.000 16.43 4.95 44.79 4.85
203 215 3.945285 ACGAACCAAACATCAAGTGAAGT 59.055 39.130 0.00 0.00 0.00 3.01
311 324 2.541178 CGCACGATACCAAGAGACTACC 60.541 54.545 0.00 0.00 0.00 3.18
463 488 2.603473 ACGTACCAGCTGAGGGCA 60.603 61.111 17.39 0.00 44.79 5.36
695 754 1.532316 TGGGGAGAAACGGACGAGT 60.532 57.895 0.00 0.00 0.00 4.18
699 758 0.454117 GGAGAAACGGACGAGTCGAC 60.454 60.000 21.50 13.62 0.00 4.20
896 970 3.240069 CGTTACGTACTTCCTCCAAGTG 58.760 50.000 0.00 0.00 45.60 3.16
906 980 1.743252 CTCCAAGTGCGCCTTCCTC 60.743 63.158 4.18 0.00 0.00 3.71
958 1036 1.768684 TTCGCTCAGGCACCTCCTTT 61.769 55.000 0.00 0.00 44.75 3.11
971 1049 1.076187 CCTCCTTTTCCTTCCTTGGCT 59.924 52.381 0.00 0.00 0.00 4.75
1262 1402 3.200483 CCTTACCATAACCTAACCACGC 58.800 50.000 0.00 0.00 0.00 5.34
1281 1421 1.339610 GCTCTCTGTCTCACACACACT 59.660 52.381 0.00 0.00 0.00 3.55
1282 1422 2.223923 GCTCTCTGTCTCACACACACTT 60.224 50.000 0.00 0.00 0.00 3.16
1283 1423 3.379240 CTCTCTGTCTCACACACACTTG 58.621 50.000 0.00 0.00 0.00 3.16
1284 1424 2.760650 TCTCTGTCTCACACACACTTGT 59.239 45.455 0.00 0.00 35.84 3.16
1285 1425 3.195610 TCTCTGTCTCACACACACTTGTT 59.804 43.478 0.00 0.00 31.66 2.83
1286 1426 4.401202 TCTCTGTCTCACACACACTTGTTA 59.599 41.667 0.00 0.00 31.66 2.41
1287 1427 4.430007 TCTGTCTCACACACACTTGTTAC 58.570 43.478 0.00 0.00 31.66 2.50
1309 1473 6.256912 ACTTACTTAGTGAGTACTGCAGAC 57.743 41.667 23.35 14.11 40.51 3.51
1315 1479 4.775058 AGTGAGTACTGCAGACTTGTAG 57.225 45.455 23.35 0.00 42.11 2.74
1328 1492 8.344446 TGCAGACTTGTAGTATGTTCTTAGTA 57.656 34.615 3.73 0.00 39.48 1.82
1366 1530 1.399440 TGCTCATGCTTGCTTCGATTC 59.601 47.619 0.00 0.00 40.48 2.52
1400 1595 2.496899 AATGGGTGACAGTCCATCAC 57.503 50.000 9.85 0.00 42.43 3.06
1436 1631 5.946972 AGGTGATCTGGGTATAGAATCTACG 59.053 44.000 0.00 0.00 0.00 3.51
1437 1632 5.125739 GGTGATCTGGGTATAGAATCTACGG 59.874 48.000 0.00 0.00 0.00 4.02
1438 1633 5.944599 GTGATCTGGGTATAGAATCTACGGA 59.055 44.000 0.00 0.00 0.00 4.69
1439 1634 6.433404 GTGATCTGGGTATAGAATCTACGGAA 59.567 42.308 0.00 0.00 0.00 4.30
1440 1635 7.122948 GTGATCTGGGTATAGAATCTACGGAAT 59.877 40.741 0.00 0.00 0.00 3.01
1441 1636 8.333984 TGATCTGGGTATAGAATCTACGGAATA 58.666 37.037 0.00 0.00 0.00 1.75
1442 1637 8.754991 ATCTGGGTATAGAATCTACGGAATAG 57.245 38.462 0.00 0.00 0.00 1.73
1477 1759 5.489792 TGCTCTAATCTGAATATGGGACC 57.510 43.478 0.00 0.00 0.00 4.46
1495 1777 2.681344 GACCGAATCCCATACCAAACAC 59.319 50.000 0.00 0.00 0.00 3.32
1504 1786 2.552315 CCATACCAAACACTCGCACTTT 59.448 45.455 0.00 0.00 0.00 2.66
1522 1804 7.646130 TCGCACTTTGAAAGTTTAAATAGGTTG 59.354 33.333 8.03 0.00 40.46 3.77
1587 1869 1.925185 GGAAGTCGCTGTCGTAAATCC 59.075 52.381 0.00 0.00 36.96 3.01
1588 1870 1.582502 GAAGTCGCTGTCGTAAATCCG 59.417 52.381 0.00 0.00 36.96 4.18
1600 1882 0.108041 TAAATCCGACTCCGTTGCCC 60.108 55.000 0.00 0.00 0.00 5.36
1602 1884 2.119484 AATCCGACTCCGTTGCCCAA 62.119 55.000 0.00 0.00 0.00 4.12
1625 1907 7.013942 CCAACATCATCCATCATAACAGTGAAT 59.986 37.037 0.00 0.00 0.00 2.57
1690 1972 0.960861 GTTGCCAGGAAGCCAGTACC 60.961 60.000 0.00 0.00 0.00 3.34
1876 2158 1.558233 ACCAGTACTGTGGCCTACTC 58.442 55.000 21.18 0.00 41.90 2.59
1893 2175 2.973945 ACTCTAAATGTTGGACGGCTC 58.026 47.619 0.00 0.00 0.00 4.70
1906 2188 3.274288 GGACGGCTCATGATTTCTTCTT 58.726 45.455 0.00 0.00 0.00 2.52
1956 2238 3.640498 CCATGCATAGGAAGAGTGAGAGA 59.360 47.826 0.00 0.00 0.00 3.10
1979 2261 4.038402 ACTTCATTTCTTTGACTTGCAGGG 59.962 41.667 0.00 0.00 0.00 4.45
1996 2278 2.278330 GGGTTCCCAGGCAAGCAAG 61.278 63.158 2.59 0.00 0.00 4.01
1997 2279 2.653115 GTTCCCAGGCAAGCAAGC 59.347 61.111 0.00 0.00 0.00 4.01
1998 2280 2.198150 TTCCCAGGCAAGCAAGCA 59.802 55.556 2.78 0.00 35.83 3.91
1999 2281 1.457267 TTCCCAGGCAAGCAAGCAA 60.457 52.632 2.78 0.00 35.83 3.91
2000 2282 1.047596 TTCCCAGGCAAGCAAGCAAA 61.048 50.000 2.78 0.00 35.83 3.68
2001 2283 1.301165 CCCAGGCAAGCAAGCAAAC 60.301 57.895 2.78 0.00 35.83 2.93
2002 2284 1.442567 CCAGGCAAGCAAGCAAACA 59.557 52.632 2.78 0.00 35.83 2.83
2003 2285 0.179078 CCAGGCAAGCAAGCAAACAA 60.179 50.000 2.78 0.00 35.83 2.83
2068 2350 3.570926 AGTCACTGATTTGCATGCTTG 57.429 42.857 20.33 5.08 0.00 4.01
2153 2435 2.174360 TCAGAGAGTGGTGGAGACATG 58.826 52.381 0.00 0.00 46.14 3.21
2500 2783 1.002430 CTCTGAGCACTGGTTTAGCCA 59.998 52.381 0.00 0.00 46.95 4.75
2524 2807 1.434188 TGTTCATGGACAGGTCAGGT 58.566 50.000 1.52 0.00 0.00 4.00
2525 2808 1.774254 TGTTCATGGACAGGTCAGGTT 59.226 47.619 1.52 0.00 0.00 3.50
2526 2809 2.224523 TGTTCATGGACAGGTCAGGTTC 60.225 50.000 1.52 0.00 0.00 3.62
2527 2810 0.984230 TCATGGACAGGTCAGGTTCC 59.016 55.000 1.41 0.00 0.00 3.62
2564 2847 4.261801 TCTGCATACTTTAGGTTCTTGGC 58.738 43.478 0.00 0.00 0.00 4.52
2608 2892 0.613260 AGCTGTGAATTACTCCGGCA 59.387 50.000 0.00 0.00 32.14 5.69
2631 2915 5.371115 AACGTTGGTCTTATTGTGAATGG 57.629 39.130 0.00 0.00 0.00 3.16
2660 2945 4.974368 TGGCACCGTCCATTTTATTTAG 57.026 40.909 0.00 0.00 0.00 1.85
2757 3042 1.269723 GAAAGGGCGGAAAGTTTGGAG 59.730 52.381 0.00 0.00 0.00 3.86
2880 3165 0.036105 TGATGCCAGTTGATGCGTCT 60.036 50.000 7.58 0.00 42.62 4.18
2952 3238 2.046285 CATTGCCCGGTTCAGGACC 61.046 63.158 0.00 0.00 45.55 4.46
2977 3264 2.318908 TGGTTGCATCTCTTTTTGCCT 58.681 42.857 0.00 0.00 38.08 4.75
3096 3384 4.937015 GGAACTGCAATGCCAAAACATAAT 59.063 37.500 1.53 0.00 0.00 1.28
3158 3477 7.766736 ATTACCCCCTCTGTAAAGAAATAGT 57.233 36.000 0.00 0.00 32.37 2.12
3159 3478 8.865244 ATTACCCCCTCTGTAAAGAAATAGTA 57.135 34.615 0.00 0.00 32.37 1.82
3346 3828 8.657074 AGATATAGATAGATACGAGTGACAGC 57.343 38.462 0.00 0.00 0.00 4.40
3347 3829 8.482943 AGATATAGATAGATACGAGTGACAGCT 58.517 37.037 0.00 0.00 0.00 4.24
3348 3830 9.104965 GATATAGATAGATACGAGTGACAGCTT 57.895 37.037 0.00 0.00 0.00 3.74
3349 3831 5.431420 AGATAGATACGAGTGACAGCTTG 57.569 43.478 0.00 0.00 0.00 4.01
3350 3832 2.949451 AGATACGAGTGACAGCTTGG 57.051 50.000 0.00 0.00 0.00 3.61
3351 3833 2.171840 AGATACGAGTGACAGCTTGGT 58.828 47.619 0.00 0.00 0.00 3.67
3352 3834 2.164624 AGATACGAGTGACAGCTTGGTC 59.835 50.000 0.00 0.00 38.29 4.02
3353 3835 1.324383 TACGAGTGACAGCTTGGTCA 58.676 50.000 2.87 2.87 45.06 4.02
3359 3841 1.679139 TGACAGCTTGGTCAAGGTTG 58.321 50.000 12.07 10.38 45.80 3.77
3360 3842 1.211703 TGACAGCTTGGTCAAGGTTGA 59.788 47.619 12.07 0.00 45.80 3.18
3361 3843 2.297701 GACAGCTTGGTCAAGGTTGAA 58.702 47.619 12.07 0.00 45.80 2.69
3362 3844 2.887152 GACAGCTTGGTCAAGGTTGAAT 59.113 45.455 12.07 0.34 45.80 2.57
3363 3845 4.072131 GACAGCTTGGTCAAGGTTGAATA 58.928 43.478 12.07 0.00 45.80 1.75
3364 3846 4.469657 ACAGCTTGGTCAAGGTTGAATAA 58.530 39.130 12.07 0.00 45.80 1.40
3365 3847 5.079643 ACAGCTTGGTCAAGGTTGAATAAT 58.920 37.500 12.07 0.00 45.80 1.28
3366 3848 5.539955 ACAGCTTGGTCAAGGTTGAATAATT 59.460 36.000 12.07 0.00 45.80 1.40
3367 3849 6.041979 ACAGCTTGGTCAAGGTTGAATAATTT 59.958 34.615 12.07 0.00 45.80 1.82
3368 3850 7.232534 ACAGCTTGGTCAAGGTTGAATAATTTA 59.767 33.333 12.07 0.00 45.80 1.40
3369 3851 8.087750 CAGCTTGGTCAAGGTTGAATAATTTAA 58.912 33.333 12.07 0.00 45.80 1.52
3370 3852 8.088365 AGCTTGGTCAAGGTTGAATAATTTAAC 58.912 33.333 9.32 0.00 45.80 2.01
3371 3853 7.870445 GCTTGGTCAAGGTTGAATAATTTAACA 59.130 33.333 12.02 0.00 39.21 2.41
3372 3854 9.927668 CTTGGTCAAGGTTGAATAATTTAACAT 57.072 29.630 2.94 0.00 39.21 2.71
3373 3855 9.703892 TTGGTCAAGGTTGAATAATTTAACATG 57.296 29.630 0.00 0.00 39.21 3.21
3374 3856 7.816995 TGGTCAAGGTTGAATAATTTAACATGC 59.183 33.333 0.00 0.00 39.21 4.06
3375 3857 7.816995 GGTCAAGGTTGAATAATTTAACATGCA 59.183 33.333 0.00 0.00 39.21 3.96
3376 3858 9.369904 GTCAAGGTTGAATAATTTAACATGCAT 57.630 29.630 0.00 0.00 39.21 3.96
3377 3859 9.941325 TCAAGGTTGAATAATTTAACATGCATT 57.059 25.926 0.00 0.00 33.55 3.56
3504 3986 2.808543 AGAACTGAAGATCGCAAACCAC 59.191 45.455 0.00 0.00 0.00 4.16
3712 4199 1.265454 AAGGGAGGGTCGTGTCATCC 61.265 60.000 0.00 0.00 0.00 3.51
3752 4242 2.489722 CTCATCTTGTCCAGACTGTCGA 59.510 50.000 1.52 0.00 32.83 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 7.042658 AGTCCATTTCTTCGCGATTAAGTAATC 60.043 37.037 10.88 0.00 38.89 1.75
45 46 6.197168 TGCATTCTTGGGAATTAGGATTTCT 58.803 36.000 0.00 0.00 39.87 2.52
87 99 4.664891 GCAATGCTTTCTCGTGATTTTTGC 60.665 41.667 0.00 0.00 0.00 3.68
161 173 6.193514 TCGTGAAATGTGTACGGAATAGTA 57.806 37.500 0.00 0.00 38.29 1.82
203 215 1.669760 CCGTGGTTTCTTGGCGCTA 60.670 57.895 7.64 0.00 0.00 4.26
376 396 3.275848 TCTCCTTCTTCTTCTTCCCCA 57.724 47.619 0.00 0.00 0.00 4.96
379 402 6.597672 GGAATTCTTCTCCTTCTTCTTCTTCC 59.402 42.308 5.23 0.00 0.00 3.46
606 638 1.690985 CACTTCCCTCCCTCCCTCC 60.691 68.421 0.00 0.00 0.00 4.30
695 754 2.378084 CGGAGTCGTCTCGTGTCGA 61.378 63.158 2.82 2.82 41.26 4.20
717 776 0.108019 GGAGTCGTGGACAAAAGGGT 59.892 55.000 0.00 0.00 34.60 4.34
896 970 1.003233 AAAGTCCAGAGGAAGGCGC 60.003 57.895 0.00 0.00 31.38 6.53
927 1005 2.928757 CCTGAGCGAATTTCACAGAGAG 59.071 50.000 13.23 0.00 0.00 3.20
936 1014 0.678048 GGAGGTGCCTGAGCGAATTT 60.678 55.000 0.00 0.00 44.31 1.82
958 1036 2.034066 CGGCAGCCAAGGAAGGAA 59.966 61.111 13.30 0.00 0.00 3.36
1236 1376 3.434596 GGTTAGGTTATGGTAAGGCTGGG 60.435 52.174 0.00 0.00 0.00 4.45
1262 1402 3.181482 ACAAGTGTGTGTGAGACAGAGAG 60.181 47.826 0.00 0.00 36.31 3.20
1281 1421 7.944061 TGCAGTACTCACTAAGTAAGTAACAA 58.056 34.615 0.00 0.00 42.11 2.83
1282 1422 7.446319 TCTGCAGTACTCACTAAGTAAGTAACA 59.554 37.037 14.67 0.00 42.11 2.41
1283 1423 7.750014 GTCTGCAGTACTCACTAAGTAAGTAAC 59.250 40.741 14.67 0.00 42.11 2.50
1284 1424 7.664731 AGTCTGCAGTACTCACTAAGTAAGTAA 59.335 37.037 14.67 0.00 42.11 2.24
1285 1425 7.166851 AGTCTGCAGTACTCACTAAGTAAGTA 58.833 38.462 14.67 0.00 42.11 2.24
1286 1426 6.005198 AGTCTGCAGTACTCACTAAGTAAGT 58.995 40.000 14.67 0.00 42.11 2.24
1287 1427 6.503589 AGTCTGCAGTACTCACTAAGTAAG 57.496 41.667 14.67 0.00 42.11 2.34
1328 1492 7.307632 GCATGAGCACGATTACATAATTTCTCT 60.308 37.037 0.00 0.00 41.58 3.10
1366 1530 8.224389 TGTCACCCATTTATTTACAGATGATG 57.776 34.615 0.00 0.00 0.00 3.07
1400 1595 5.221501 ACCCAGATCACCTTGTCAAATTTTG 60.222 40.000 2.59 2.59 0.00 2.44
1452 1734 6.205658 GGTCCCATATTCAGATTAGAGCAAAC 59.794 42.308 0.00 0.00 0.00 2.93
1477 1759 2.607635 CGAGTGTTTGGTATGGGATTCG 59.392 50.000 0.00 0.00 0.00 3.34
1489 1771 3.758300 ACTTTCAAAGTGCGAGTGTTTG 58.242 40.909 0.68 0.00 41.01 2.93
1495 1777 7.360361 ACCTATTTAAACTTTCAAAGTGCGAG 58.640 34.615 2.78 0.00 41.91 5.03
1504 1786 6.492087 CCCAGTCCAACCTATTTAAACTTTCA 59.508 38.462 0.00 0.00 0.00 2.69
1534 1816 5.111989 ACATCATCAGTCATAACCGTGAAG 58.888 41.667 0.00 0.00 0.00 3.02
1540 1822 6.676456 GCAGTGAAACATCATCAGTCATAACC 60.676 42.308 0.00 0.00 41.43 2.85
1545 1827 3.749609 CAGCAGTGAAACATCATCAGTCA 59.250 43.478 0.00 0.00 41.43 3.41
1587 1869 1.635663 GATGTTGGGCAACGGAGTCG 61.636 60.000 0.00 0.00 45.00 4.18
1588 1870 0.605319 TGATGTTGGGCAACGGAGTC 60.605 55.000 0.00 0.00 45.00 3.36
1600 1882 6.930667 TCACTGTTATGATGGATGATGTTG 57.069 37.500 0.00 0.00 0.00 3.33
1602 1884 7.284820 TGATTCACTGTTATGATGGATGATGT 58.715 34.615 0.00 0.00 0.00 3.06
1690 1972 2.540361 GCTATTGCTGCCAGTTCATTCG 60.540 50.000 0.00 0.00 36.03 3.34
1725 2007 7.054491 AGCTGGTTGTTGAAATACTGAAATT 57.946 32.000 0.00 0.00 0.00 1.82
1727 2009 5.592282 TGAGCTGGTTGTTGAAATACTGAAA 59.408 36.000 0.00 0.00 0.00 2.69
1864 2146 3.941483 CCAACATTTAGAGTAGGCCACAG 59.059 47.826 5.01 0.00 0.00 3.66
1876 2158 3.270027 TCATGAGCCGTCCAACATTTAG 58.730 45.455 0.00 0.00 0.00 1.85
1893 2175 9.701098 TGGAAAATTTCAGAAGAAGAAATCATG 57.299 29.630 8.09 0.00 42.98 3.07
1906 2188 3.243359 ACAGCCCTGGAAAATTTCAGA 57.757 42.857 8.09 0.00 33.11 3.27
1956 2238 4.038402 CCCTGCAAGTCAAAGAAATGAAGT 59.962 41.667 0.00 0.00 0.00 3.01
1996 2278 5.831997 ACAAGGTACTCAAAGATTGTTTGC 58.168 37.500 1.54 0.00 38.49 3.68
1997 2279 8.190784 AGAAACAAGGTACTCAAAGATTGTTTG 58.809 33.333 16.00 0.00 45.64 2.93
1999 2281 7.013369 GGAGAAACAAGGTACTCAAAGATTGTT 59.987 37.037 0.00 0.00 38.49 2.83
2000 2282 6.486993 GGAGAAACAAGGTACTCAAAGATTGT 59.513 38.462 0.00 0.00 38.49 2.71
2001 2283 6.486657 TGGAGAAACAAGGTACTCAAAGATTG 59.513 38.462 0.00 0.00 38.49 2.67
2002 2284 6.601332 TGGAGAAACAAGGTACTCAAAGATT 58.399 36.000 0.00 0.00 38.49 2.40
2003 2285 6.187727 TGGAGAAACAAGGTACTCAAAGAT 57.812 37.500 0.00 0.00 38.49 2.40
2068 2350 2.140717 CCGTGTTCCACCTGAGTAAAC 58.859 52.381 0.00 0.00 0.00 2.01
2153 2435 1.252904 TGCATTTTCTCCAGCCCTGC 61.253 55.000 0.00 0.00 0.00 4.85
2500 2783 2.639347 TGACCTGTCCATGAACATCAGT 59.361 45.455 0.00 0.00 0.00 3.41
2524 2807 3.557898 GCAGAGTGGTGATCAAGAAGGAA 60.558 47.826 0.00 0.00 0.00 3.36
2525 2808 2.027745 GCAGAGTGGTGATCAAGAAGGA 60.028 50.000 0.00 0.00 0.00 3.36
2526 2809 2.289882 TGCAGAGTGGTGATCAAGAAGG 60.290 50.000 0.00 0.00 0.00 3.46
2527 2810 3.049708 TGCAGAGTGGTGATCAAGAAG 57.950 47.619 0.00 0.00 0.00 2.85
2608 2892 5.300792 ACCATTCACAATAAGACCAACGTTT 59.699 36.000 0.00 0.00 0.00 3.60
2631 2915 3.660111 GACGGTGCCAAGTGCCAC 61.660 66.667 0.00 0.00 40.16 5.01
2660 2945 4.474226 AGAATGAAACGCTTGTCAACTC 57.526 40.909 0.00 0.00 0.00 3.01
2757 3042 5.722021 TTCCTTCACCTTAAAATGGAAGC 57.278 39.130 0.00 0.00 34.96 3.86
2854 3139 1.527034 TCAACTGGCATCACTGAAGC 58.473 50.000 0.00 0.00 0.00 3.86
2880 3165 3.071479 GGGCAACTTCAACATAACGAGA 58.929 45.455 0.00 0.00 0.00 4.04
2984 3271 2.979814 AAAGGCAACACAAACTTCCC 57.020 45.000 0.00 0.00 41.41 3.97
3096 3384 7.411808 AGATCACTACTTTACAGAGGGAGTAA 58.588 38.462 0.00 0.00 0.00 2.24
3336 3818 1.143305 CTTGACCAAGCTGTCACTCG 58.857 55.000 6.39 0.00 44.55 4.18
3337 3819 1.202698 ACCTTGACCAAGCTGTCACTC 60.203 52.381 6.39 0.00 44.55 3.51
3338 3820 0.839946 ACCTTGACCAAGCTGTCACT 59.160 50.000 6.39 0.00 44.55 3.41
3339 3821 1.334869 CAACCTTGACCAAGCTGTCAC 59.665 52.381 6.39 0.00 44.55 3.67
3340 3822 1.211703 TCAACCTTGACCAAGCTGTCA 59.788 47.619 2.87 2.87 43.26 3.58
3341 3823 1.967319 TCAACCTTGACCAAGCTGTC 58.033 50.000 4.31 0.00 37.11 3.51
3342 3824 2.435372 TTCAACCTTGACCAAGCTGT 57.565 45.000 4.31 0.00 36.83 4.40
3343 3825 5.649782 ATTATTCAACCTTGACCAAGCTG 57.350 39.130 4.31 4.48 36.83 4.24
3344 3826 6.670695 AAATTATTCAACCTTGACCAAGCT 57.329 33.333 4.31 0.00 36.83 3.74
3345 3827 7.870445 TGTTAAATTATTCAACCTTGACCAAGC 59.130 33.333 4.31 0.00 36.83 4.01
3346 3828 9.927668 ATGTTAAATTATTCAACCTTGACCAAG 57.072 29.630 2.89 2.89 36.83 3.61
3347 3829 9.703892 CATGTTAAATTATTCAACCTTGACCAA 57.296 29.630 0.00 0.00 36.83 3.67
3348 3830 7.816995 GCATGTTAAATTATTCAACCTTGACCA 59.183 33.333 0.00 0.00 36.83 4.02
3349 3831 7.816995 TGCATGTTAAATTATTCAACCTTGACC 59.183 33.333 0.00 0.00 36.83 4.02
3350 3832 8.755696 TGCATGTTAAATTATTCAACCTTGAC 57.244 30.769 0.00 0.00 36.83 3.18
3351 3833 9.941325 AATGCATGTTAAATTATTCAACCTTGA 57.059 25.926 0.00 0.00 34.92 3.02
3394 3876 7.875041 GCCAAGTTGTCACTCATATCTGTATAT 59.125 37.037 1.45 0.00 30.45 0.86
3395 3877 7.069950 AGCCAAGTTGTCACTCATATCTGTATA 59.930 37.037 1.45 0.00 30.45 1.47
3396 3878 6.051717 GCCAAGTTGTCACTCATATCTGTAT 58.948 40.000 1.45 0.00 30.45 2.29
3397 3879 5.187772 AGCCAAGTTGTCACTCATATCTGTA 59.812 40.000 1.45 0.00 30.45 2.74
3398 3880 4.019860 AGCCAAGTTGTCACTCATATCTGT 60.020 41.667 1.45 0.00 30.45 3.41
3399 3881 4.511527 AGCCAAGTTGTCACTCATATCTG 58.488 43.478 1.45 0.00 30.45 2.90
3400 3882 4.833478 AGCCAAGTTGTCACTCATATCT 57.167 40.909 1.45 0.00 30.45 1.98
3401 3883 5.521735 CAGTAGCCAAGTTGTCACTCATATC 59.478 44.000 1.45 0.00 30.45 1.63
3402 3884 5.423015 CAGTAGCCAAGTTGTCACTCATAT 58.577 41.667 1.45 0.00 30.45 1.78
3403 3885 4.322725 CCAGTAGCCAAGTTGTCACTCATA 60.323 45.833 1.45 0.00 30.45 2.15
3404 3886 3.557898 CCAGTAGCCAAGTTGTCACTCAT 60.558 47.826 1.45 0.00 30.45 2.90
3405 3887 2.224281 CCAGTAGCCAAGTTGTCACTCA 60.224 50.000 1.45 0.00 30.45 3.41
3504 3986 1.401552 CATGCATGTTACCCCTCGTTG 59.598 52.381 18.91 0.00 0.00 4.10
3568 4055 1.901085 GGCCGACTCCAGATGAACT 59.099 57.895 0.00 0.00 0.00 3.01
3712 4199 2.684843 GCAGGCCAAGCAGAAGACG 61.685 63.158 14.58 0.00 0.00 4.18
3752 4242 1.228003 TGTCCGTGGGCAATTCGTT 60.228 52.632 0.00 0.00 0.00 3.85
3788 4278 2.557920 ACCAAAGCAGGAAGAGACTG 57.442 50.000 0.00 0.00 38.95 3.51


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

AutoCloner maintained by Alex Coulton.