Multiple sequence alignment - TraesCS5B01G484300

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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 TraesCS5B01G484300 chr5B 100.000 4459 0 0 1 4459 655902184 655897726 0.000000e+00 8235.0
1 TraesCS5B01G484300 chr5B 81.495 2221 314 58 882 3047 640491870 640489692 0.000000e+00 1735.0
2 TraesCS5B01G484300 chr5B 84.021 582 76 8 3098 3672 640489257 640488686 1.090000e-150 544.0
3 TraesCS5B01G484300 chr5B 82.126 414 62 8 3667 4072 640476719 640476310 1.190000e-90 344.0
4 TraesCS5B01G484300 chr5B 72.846 383 68 30 120 476 297811809 297811437 1.020000e-16 99.0
5 TraesCS5B01G484300 chr5B 100.000 29 0 0 4032 4060 262129627 262129655 2.000000e-03 54.7
6 TraesCS5B01G484300 chr5D 92.295 3777 244 27 716 4459 520580833 520577071 0.000000e+00 5319.0
7 TraesCS5B01G484300 chr5D 82.709 2215 286 52 943 3100 509651677 509649503 0.000000e+00 1879.0
8 TraesCS5B01G484300 chr5D 82.260 1009 132 22 3098 4072 509648966 509647971 0.000000e+00 828.0
9 TraesCS5B01G484300 chr5D 78.343 688 101 29 30 695 520585333 520584672 6.950000e-108 401.0
10 TraesCS5B01G484300 chr5D 74.809 262 45 20 40 286 309887176 309886921 1.020000e-16 99.0
11 TraesCS5B01G484300 chr5A 88.433 3778 335 55 1 3718 648771984 648768249 0.000000e+00 4462.0
12 TraesCS5B01G484300 chr5A 89.867 750 72 4 3712 4459 648746537 648745790 0.000000e+00 961.0
13 TraesCS5B01G484300 chr1D 79.359 1686 239 53 1467 3096 440581287 440582919 0.000000e+00 1085.0
14 TraesCS5B01G484300 chr1D 81.377 988 151 25 2132 3100 440576278 440577251 0.000000e+00 774.0
15 TraesCS5B01G484300 chr1D 82.117 699 101 18 2393 3078 440647484 440648171 1.080000e-160 577.0
16 TraesCS5B01G484300 chr1D 81.687 415 66 7 2687 3099 440567061 440567467 1.990000e-88 337.0
17 TraesCS5B01G484300 chr1D 79.149 235 31 13 150 374 476815381 476815607 3.590000e-31 147.0
18 TraesCS5B01G484300 chr1A 79.231 1690 241 56 1470 3100 537441466 537439828 0.000000e+00 1075.0
19 TraesCS5B01G484300 chr1A 75.918 245 43 14 175 408 72773868 72774107 1.310000e-20 111.0
20 TraesCS5B01G484300 chr1B 76.137 1693 284 64 1467 3100 597982818 597984449 0.000000e+00 778.0
21 TraesCS5B01G484300 chr1B 78.687 990 172 31 2132 3100 597961721 597962692 1.360000e-174 623.0
22 TraesCS5B01G484300 chr1B 100.000 29 0 0 4032 4060 391829402 391829374 2.000000e-03 54.7
23 TraesCS5B01G484300 chr7A 92.434 304 21 2 716 1017 28209390 28209087 2.460000e-117 433.0
24 TraesCS5B01G484300 chr7D 76.667 690 92 35 30 660 364370052 364370731 7.200000e-83 318.0
25 TraesCS5B01G484300 chr7D 75.321 312 56 19 80 378 70113633 70113330 3.620000e-26 130.0
26 TraesCS5B01G484300 chr3B 78.632 234 32 14 176 399 262738635 262738860 6.010000e-29 139.0
27 TraesCS5B01G484300 chr3B 92.105 38 3 0 4023 4060 102941722 102941759 2.000000e-03 54.7
28 TraesCS5B01G484300 chr3B 100.000 29 0 0 4032 4060 491609193 491609165 2.000000e-03 54.7
29 TraesCS5B01G484300 chr4A 80.838 167 25 7 160 322 548310006 548310169 1.680000e-24 124.0
30 TraesCS5B01G484300 chr6B 76.285 253 45 12 177 418 20094971 20094723 2.180000e-23 121.0
31 TraesCS5B01G484300 chr2D 75.180 278 46 17 177 437 63755851 63755580 4.720000e-20 110.0
32 TraesCS5B01G484300 chr6D 97.059 34 1 0 4029 4062 373408783 373408816 1.730000e-04 58.4
33 TraesCS5B01G484300 chrUn 96.875 32 1 0 4029 4060 239341478 239341509 2.000000e-03 54.7


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 TraesCS5B01G484300 chr5B 655897726 655902184 4458 True 8235.0 8235 100.0000 1 4459 1 chr5B.!!$R3 4458
1 TraesCS5B01G484300 chr5B 640488686 640491870 3184 True 1139.5 1735 82.7580 882 3672 2 chr5B.!!$R4 2790
2 TraesCS5B01G484300 chr5D 520577071 520585333 8262 True 2860.0 5319 85.3190 30 4459 2 chr5D.!!$R3 4429
3 TraesCS5B01G484300 chr5D 509647971 509651677 3706 True 1353.5 1879 82.4845 943 4072 2 chr5D.!!$R2 3129
4 TraesCS5B01G484300 chr5A 648768249 648771984 3735 True 4462.0 4462 88.4330 1 3718 1 chr5A.!!$R2 3717
5 TraesCS5B01G484300 chr5A 648745790 648746537 747 True 961.0 961 89.8670 3712 4459 1 chr5A.!!$R1 747
6 TraesCS5B01G484300 chr1D 440581287 440582919 1632 False 1085.0 1085 79.3590 1467 3096 1 chr1D.!!$F3 1629
7 TraesCS5B01G484300 chr1D 440576278 440577251 973 False 774.0 774 81.3770 2132 3100 1 chr1D.!!$F2 968
8 TraesCS5B01G484300 chr1D 440647484 440648171 687 False 577.0 577 82.1170 2393 3078 1 chr1D.!!$F4 685
9 TraesCS5B01G484300 chr1A 537439828 537441466 1638 True 1075.0 1075 79.2310 1470 3100 1 chr1A.!!$R1 1630
10 TraesCS5B01G484300 chr1B 597982818 597984449 1631 False 778.0 778 76.1370 1467 3100 1 chr1B.!!$F2 1633
11 TraesCS5B01G484300 chr1B 597961721 597962692 971 False 623.0 623 78.6870 2132 3100 1 chr1B.!!$F1 968
12 TraesCS5B01G484300 chr7D 364370052 364370731 679 False 318.0 318 76.6670 30 660 1 chr7D.!!$F1 630

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
580 747 0.872021 GTACTGATCGGGCAAGCGAG 60.872 60.0 6.47 0.00 0.00 5.03 F
1623 5652 0.398696 TTTGGCCTTCTTGACGCCTA 59.601 50.0 3.32 0.44 43.42 3.93 F
1706 5758 1.462616 TCCAAATGATCCAACAGCCG 58.537 50.0 0.00 0.00 0.00 5.52 F
2896 6982 2.239907 GAGCCCAAGATAGGTGAAAGGT 59.760 50.0 0.00 0.00 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1695 5747 1.001020 TCATTGCCGGCTGTTGGAT 60.001 52.632 29.7 8.94 0.0 3.41 R
2736 6819 0.618458 CGGTGATTTCTTCCCTCCCA 59.382 55.000 0.0 0.00 0.0 4.37 R
3107 7740 0.663153 GCGGGAATGATGGTGTTAGC 59.337 55.000 0.0 0.00 0.0 3.09 R
3738 8390 0.175073 GTGTTTCTCCCGTCGCCTAT 59.825 55.000 0.0 0.00 0.0 2.57 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
112 118 6.483307 TCACGAACTTCTTTTGAATCTCATGT 59.517 34.615 0.00 0.00 37.85 3.21
115 121 7.095187 ACGAACTTCTTTTGAATCTCATGTACC 60.095 37.037 0.00 0.00 37.85 3.34
227 234 8.446273 TCAAAATCGATGAACTCTTCTCAAATC 58.554 33.333 0.00 0.00 0.00 2.17
232 239 8.000780 TCGATGAACTCTTCTCAAATCTGATA 57.999 34.615 0.00 0.00 0.00 2.15
234 241 9.258826 CGATGAACTCTTCTCAAATCTGATAAT 57.741 33.333 0.00 0.00 0.00 1.28
371 516 8.606040 ATCATTGAACGTTTTCCAAATTTGAT 57.394 26.923 19.86 6.17 0.00 2.57
372 517 7.849496 TCATTGAACGTTTTCCAAATTTGATG 58.151 30.769 19.86 10.08 0.00 3.07
373 518 7.708322 TCATTGAACGTTTTCCAAATTTGATGA 59.292 29.630 19.86 12.06 0.00 2.92
374 519 8.497554 CATTGAACGTTTTCCAAATTTGATGAT 58.502 29.630 19.86 0.00 0.00 2.45
375 520 8.430801 TTGAACGTTTTCCAAATTTGATGATT 57.569 26.923 19.86 4.53 0.00 2.57
376 521 8.430801 TGAACGTTTTCCAAATTTGATGATTT 57.569 26.923 19.86 3.84 0.00 2.17
377 522 8.887717 TGAACGTTTTCCAAATTTGATGATTTT 58.112 25.926 19.86 4.43 0.00 1.82
461 627 7.014134 TCCAAATTCATGCTCTGTTTTAGAACA 59.986 33.333 0.00 0.00 43.23 3.18
524 691 6.519679 TTAGTAGTCAACAAGGCTAATCGA 57.480 37.500 0.00 0.00 35.90 3.59
530 697 6.582636 AGTCAACAAGGCTAATCGATCAATA 58.417 36.000 0.00 0.00 0.00 1.90
534 701 7.933577 TCAACAAGGCTAATCGATCAATAGAAT 59.066 33.333 0.00 0.00 0.00 2.40
543 710 4.617959 TCGATCAATAGAATGACCGTTCC 58.382 43.478 0.00 0.00 37.60 3.62
546 713 4.819105 TCAATAGAATGACCGTTCCAGT 57.181 40.909 0.00 0.00 0.00 4.00
548 715 3.543680 ATAGAATGACCGTTCCAGTGG 57.456 47.619 1.40 1.40 0.00 4.00
571 738 8.173130 GTGGTTTATTTTAGTTGTACTGATCGG 58.827 37.037 0.00 0.00 0.00 4.18
574 741 3.965379 TTTAGTTGTACTGATCGGGCA 57.035 42.857 6.47 1.68 0.00 5.36
580 747 0.872021 GTACTGATCGGGCAAGCGAG 60.872 60.000 6.47 0.00 0.00 5.03
709 1895 5.278315 GGGAAAAAGAACGTTGTATCAGCTT 60.278 40.000 5.00 0.00 0.00 3.74
746 4744 2.614057 CGCCAAATAGGAAGGTGCTTAG 59.386 50.000 0.00 0.00 41.22 2.18
757 4755 2.906354 AGGTGCTTAGCTTATTCCGTG 58.094 47.619 5.60 0.00 0.00 4.94
758 4756 2.236395 AGGTGCTTAGCTTATTCCGTGT 59.764 45.455 5.60 0.00 0.00 4.49
759 4757 2.351726 GGTGCTTAGCTTATTCCGTGTG 59.648 50.000 5.60 0.00 0.00 3.82
772 4770 2.267961 GTGTGGAGGTTAGGCCCG 59.732 66.667 0.00 0.00 38.26 6.13
849 4849 7.550551 TCAATAGTCTTCCTCATCAATCAACAC 59.449 37.037 0.00 0.00 0.00 3.32
960 4966 0.889306 GGACGCTCTGACAGTTACCT 59.111 55.000 1.59 0.00 0.00 3.08
979 4985 5.209818 ACCTGTTTCAGTTTCAGACGATA 57.790 39.130 0.00 0.00 0.00 2.92
998 5004 8.325787 AGACGATACACTCCTAGATCTATCATT 58.674 37.037 2.11 0.00 0.00 2.57
1039 5045 2.711922 GCGAGGGACTGGTCATCGT 61.712 63.158 20.30 2.22 41.55 3.73
1062 5068 1.527433 CCCTCGATGCGCTATCCTCA 61.527 60.000 9.73 0.00 31.82 3.86
1122 5128 4.057428 GGCCTCGTGTGTCGCTCT 62.057 66.667 0.00 0.00 39.67 4.09
1209 5215 0.618458 TCCTAAAGGGCGATGCTGTT 59.382 50.000 0.00 0.00 35.41 3.16
1232 5238 1.437986 GCGAGATGGCGAAGGTAGT 59.562 57.895 0.00 0.00 0.00 2.73
1234 5240 0.738975 CGAGATGGCGAAGGTAGTCA 59.261 55.000 0.00 0.00 0.00 3.41
1273 5279 3.296709 CTCAGGGTGTTCGTCGGGG 62.297 68.421 0.00 0.00 0.00 5.73
1493 5504 7.494625 TCTTTTAGCAACAATAGTAGGGAATCG 59.505 37.037 0.00 0.00 0.00 3.34
1496 5507 3.248602 GCAACAATAGTAGGGAATCGCTG 59.751 47.826 10.25 0.00 0.00 5.18
1536 5550 7.719193 TCATTAATATTGGTGGGACATGTACAG 59.281 37.037 10.99 0.00 44.52 2.74
1604 5633 4.540502 AGTATCCCTTCCTTTAAGCTTGGT 59.459 41.667 9.86 0.00 33.49 3.67
1618 5647 1.269778 GCTTGGTTTGGCCTTCTTGAC 60.270 52.381 3.32 0.00 38.35 3.18
1623 5652 0.398696 TTTGGCCTTCTTGACGCCTA 59.601 50.000 3.32 0.44 43.42 3.93
1652 5681 7.970061 TCAAAGTGAGATTTGAAGTGTGAAAAG 59.030 33.333 0.00 0.00 44.14 2.27
1679 5710 5.863935 GCAATATTCCAAGTTGTTGACCTTC 59.136 40.000 1.45 0.00 35.46 3.46
1682 5713 7.839680 ATATTCCAAGTTGTTGACCTTCTTT 57.160 32.000 1.45 0.00 35.46 2.52
1695 5747 4.648762 TGACCTTCTTTTGCTTCCAAATGA 59.351 37.500 0.00 0.00 40.40 2.57
1706 5758 1.462616 TCCAAATGATCCAACAGCCG 58.537 50.000 0.00 0.00 0.00 5.52
1791 5845 4.218417 ACAATTTCATAGGCAGTGTTCCAC 59.782 41.667 0.00 0.00 34.10 4.02
1814 5869 4.151883 TCAAACCTAGAGCAAGCCAAAAT 58.848 39.130 0.00 0.00 0.00 1.82
1844 5900 6.028987 GCTGAAATCTGAATTGAAGAAGAGC 58.971 40.000 0.00 0.00 0.00 4.09
1906 5962 6.267471 ACACAATTACTGGTTTCAATGTGGAT 59.733 34.615 7.39 0.00 0.00 3.41
1926 5982 6.767902 GTGGATGTGCTTTCTTATCAGGATAA 59.232 38.462 2.08 2.08 0.00 1.75
2106 6165 3.194116 CAGTAGATTGCCAACTGCCATTT 59.806 43.478 0.00 0.00 40.16 2.32
2159 6222 5.069383 TGCTGTTGCTAATCATGCCATTTAT 59.931 36.000 0.00 0.00 40.48 1.40
2205 6268 4.529769 TGTTGGACAAAAATGGATGCCATA 59.470 37.500 0.00 0.00 44.40 2.74
2279 6343 4.337555 GGCAACATTGATGCTATGTCTTCT 59.662 41.667 17.05 0.00 43.34 2.85
2280 6344 5.528690 GGCAACATTGATGCTATGTCTTCTA 59.471 40.000 17.05 0.00 43.34 2.10
2339 6403 6.590068 AGTCTCATCATTCCACTTATCAAGG 58.410 40.000 0.00 0.00 0.00 3.61
2375 6439 8.322091 ACTATGTTTCTAGAAGCAGGTTTACAT 58.678 33.333 23.74 19.33 35.08 2.29
2431 6497 5.848406 ACAACAGTCTCTTCACTAGAAAGG 58.152 41.667 0.00 0.00 32.35 3.11
2454 6520 2.364324 CCAACGCTAGTGGGATAGCTAA 59.636 50.000 8.42 0.00 44.55 3.09
2471 6537 2.357009 GCTAAGCACCTCACCATCATTG 59.643 50.000 0.00 0.00 0.00 2.82
2553 6620 9.944376 TGTATAAGAATTTAGTGAGCAGAGTTT 57.056 29.630 0.00 0.00 0.00 2.66
2700 6782 5.760743 GCCAGATTTTAAGTGGTCTAGGATC 59.239 44.000 0.00 0.00 33.51 3.36
2705 6787 8.925338 AGATTTTAAGTGGTCTAGGATCGTAAT 58.075 33.333 0.00 0.00 0.00 1.89
2733 6816 4.221262 ACTCTAATGCAACACATGGCAAAT 59.779 37.500 0.00 0.00 44.20 2.32
2736 6819 6.876155 TCTAATGCAACACATGGCAAATATT 58.124 32.000 0.00 0.00 44.20 1.28
2797 6881 9.072375 CCTACTAGAGTATGACATCATTGAAGA 57.928 37.037 0.00 0.00 37.76 2.87
2896 6982 2.239907 GAGCCCAAGATAGGTGAAAGGT 59.760 50.000 0.00 0.00 0.00 3.50
2903 6989 6.284459 CCAAGATAGGTGAAAGGTGTATCTC 58.716 44.000 0.00 0.00 30.76 2.75
2973 7062 8.429641 TCAGATATACTAATTGGGACCAAAGAC 58.570 37.037 8.00 0.00 39.55 3.01
3087 7178 9.616634 GGCATGATAATAAGTGTATCATTTGTG 57.383 33.333 0.00 0.00 43.16 3.33
3197 7835 4.597004 TGACTACCCTTCGACTTGTATCT 58.403 43.478 0.00 0.00 0.00 1.98
3309 7947 2.571653 CTCACCATGAGGGAACTAACCA 59.428 50.000 0.00 0.00 44.43 3.67
3373 8011 6.671190 TGCACTATTGTTTCTTGATCAACTG 58.329 36.000 3.38 0.00 0.00 3.16
3376 8014 6.800408 CACTATTGTTTCTTGATCAACTGCAG 59.200 38.462 13.48 13.48 0.00 4.41
3418 8056 4.381292 GGCAAAATTCACCAGGATCAAGAG 60.381 45.833 0.00 0.00 0.00 2.85
3463 8108 6.384224 ACGAGTGTTGTGTCGATTAATAAGA 58.616 36.000 0.00 0.00 39.53 2.10
3485 8130 2.499693 TCCGACAATGACCATGCTCTTA 59.500 45.455 0.00 0.00 0.00 2.10
3523 8168 8.133024 AGAGGATAGATTATTCAGTGTGATCC 57.867 38.462 0.00 0.00 0.00 3.36
3524 8169 6.929625 AGGATAGATTATTCAGTGTGATCCG 58.070 40.000 0.00 0.00 36.31 4.18
3640 8285 5.974108 TCTGTACCAATTCTAGCTTGTACC 58.026 41.667 0.00 0.00 0.00 3.34
3688 8333 5.148651 ACCTTTGTCTCTAGCGTTGTATT 57.851 39.130 0.00 0.00 0.00 1.89
3732 8384 6.826893 TGCTTGTTGAAATAAAGAACTTGC 57.173 33.333 0.00 0.00 0.00 4.01
3737 8389 8.912787 TTGTTGAAATAAAGAACTTGCGTTAA 57.087 26.923 0.00 0.00 32.39 2.01
3738 8390 8.912787 TGTTGAAATAAAGAACTTGCGTTAAA 57.087 26.923 0.00 0.00 32.39 1.52
3760 8412 1.006571 GCGACGGGAGAAACACTCA 60.007 57.895 0.00 0.00 46.54 3.41
3764 8416 3.243301 GCGACGGGAGAAACACTCATATA 60.243 47.826 0.00 0.00 46.54 0.86
3818 8483 1.405526 GGTACGCTGCATCTTCTTGGA 60.406 52.381 0.00 0.00 0.00 3.53
3841 8506 9.791801 TGGATGCTACATAATTATCTTGCTAAA 57.208 29.630 8.18 0.00 0.00 1.85
4030 8696 3.714798 TCAGGGACTAGGTTCAACTTTGT 59.285 43.478 0.00 0.00 36.02 2.83
4108 8774 2.964464 TGTCCCGTTGTACTTTAGTGGA 59.036 45.455 0.00 0.00 0.00 4.02
4139 8805 8.710835 TGATTACTAATGAAGCGAATACACAA 57.289 30.769 0.00 0.00 0.00 3.33
4180 8846 1.478105 GCTGAAACAAATAGGGCCTGG 59.522 52.381 18.53 5.52 0.00 4.45
4186 8852 1.417890 ACAAATAGGGCCTGGATCTCG 59.582 52.381 18.53 0.23 0.00 4.04
4197 8863 2.092968 CCTGGATCTCGGTGATTTGGAA 60.093 50.000 0.00 0.00 35.14 3.53
4206 8872 9.219603 GATCTCGGTGATTTGGAATTTGATATA 57.780 33.333 0.00 0.00 35.14 0.86
4283 8949 4.458989 GCCATTTGACTTAACCATGAGTCA 59.541 41.667 10.13 10.13 46.80 3.41
4345 9011 4.099266 AGTTTGAGCAGTGCCAAATTTGTA 59.901 37.500 24.82 3.07 33.78 2.41
4400 9066 6.400568 CATTTCCATTTCCATTGTTGTAGCT 58.599 36.000 0.00 0.00 0.00 3.32
4414 9080 7.440505 TTGTTGTAGCTAATGGGATTACCTA 57.559 36.000 0.00 0.00 41.11 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 77 7.090953 AGTTCGTGAATTCAAAAGGTACAAA 57.909 32.000 10.35 0.00 0.00 2.83
78 84 8.393395 TCAAAAGAAGTTCGTGAATTCAAAAG 57.607 30.769 10.35 5.15 0.00 2.27
112 118 9.936759 AAAAAGTTCACAAATTTGAAGAAGGTA 57.063 25.926 24.64 4.66 36.15 3.08
342 487 9.500864 AAATTTGGAAAACGTTCAATGATTTTG 57.499 25.926 0.00 0.00 35.25 2.44
350 495 8.430801 AATCATCAAATTTGGAAAACGTTCAA 57.569 26.923 17.90 0.00 35.25 2.69
500 667 7.108841 TCGATTAGCCTTGTTGACTACTAAT 57.891 36.000 0.00 0.00 34.05 1.73
546 713 7.334921 CCCGATCAGTACAACTAAAATAAACCA 59.665 37.037 0.00 0.00 0.00 3.67
548 715 7.148373 TGCCCGATCAGTACAACTAAAATAAAC 60.148 37.037 0.00 0.00 0.00 2.01
571 738 2.306581 GCTCTATCGCTCGCTTGCC 61.307 63.158 0.00 0.00 0.00 4.52
574 741 1.281353 CTCGCTCTATCGCTCGCTT 59.719 57.895 0.00 0.00 0.00 4.68
580 747 0.305313 AACTCGACTCGCTCTATCGC 59.695 55.000 0.00 0.00 35.82 4.58
582 749 2.867368 TGAGAACTCGACTCGCTCTATC 59.133 50.000 0.00 0.00 37.22 2.08
641 821 1.102222 GGCGTTGGGTTGTTGTACCA 61.102 55.000 0.00 0.00 40.09 3.25
680 860 4.993029 ACAACGTTCTTTTTCCCATCAA 57.007 36.364 0.00 0.00 0.00 2.57
681 861 5.765677 TGATACAACGTTCTTTTTCCCATCA 59.234 36.000 0.00 0.00 0.00 3.07
683 863 5.335661 GCTGATACAACGTTCTTTTTCCCAT 60.336 40.000 0.00 0.00 0.00 4.00
709 1895 1.273048 TGGCGCTTAAGGAAGAACGTA 59.727 47.619 7.64 0.00 34.25 3.57
746 4744 2.109425 AACCTCCACACGGAATAAGC 57.891 50.000 0.00 0.00 42.21 3.09
757 4755 3.793888 CCCGGGCCTAACCTCCAC 61.794 72.222 8.08 0.00 39.10 4.02
758 4756 4.014075 TCCCGGGCCTAACCTCCA 62.014 66.667 18.49 0.00 39.10 3.86
759 4757 3.477346 GTCCCGGGCCTAACCTCC 61.477 72.222 18.49 0.00 39.10 4.30
787 4785 3.535280 TTTGTTGAGAAAACCAAGGGC 57.465 42.857 0.00 0.00 0.00 5.19
810 4808 4.112331 AGACTATTGAGGGGCCTACTTTT 58.888 43.478 0.84 0.00 0.00 2.27
814 4812 2.369203 GGAAGACTATTGAGGGGCCTAC 59.631 54.545 0.84 0.00 0.00 3.18
815 4813 2.250273 AGGAAGACTATTGAGGGGCCTA 59.750 50.000 0.84 0.00 0.00 3.93
824 4824 7.201679 GGTGTTGATTGATGAGGAAGACTATTG 60.202 40.741 0.00 0.00 0.00 1.90
825 4825 6.825721 GGTGTTGATTGATGAGGAAGACTATT 59.174 38.462 0.00 0.00 0.00 1.73
849 4849 2.578664 GCCATCGGCCTTTTTGGG 59.421 61.111 0.00 0.00 44.06 4.12
960 4966 5.597806 AGTGTATCGTCTGAAACTGAAACA 58.402 37.500 0.00 0.00 0.00 2.83
979 4985 7.244558 TCCATCAATGATAGATCTAGGAGTGT 58.755 38.462 8.70 0.00 0.00 3.55
998 5004 2.974148 GCGCCGCATCATCCATCA 60.974 61.111 3.15 0.00 0.00 3.07
1062 5068 0.527817 CGCCGAGCCTAACGAAGATT 60.528 55.000 0.00 0.00 0.00 2.40
1084 5090 1.300465 CGCCCATGAGGACATCGAG 60.300 63.158 0.00 0.00 38.24 4.04
1172 5178 3.750371 AGGAACACGGAATCATGTTTGA 58.250 40.909 4.05 0.00 39.13 2.69
1179 5185 2.617021 GCCCTTTAGGAACACGGAATCA 60.617 50.000 0.00 0.00 38.24 2.57
1182 5188 0.320946 CGCCCTTTAGGAACACGGAA 60.321 55.000 0.00 0.00 38.24 4.30
1273 5279 2.009774 CTCATCGGTGACAAACATCCC 58.990 52.381 0.00 0.00 0.00 3.85
1468 5477 7.630924 CGATTCCCTACTATTGTTGCTAAAAG 58.369 38.462 0.00 0.00 0.00 2.27
1618 5647 7.225538 ACTTCAAATCTCACTTTGATATAGGCG 59.774 37.037 0.56 0.00 42.87 5.52
1623 5652 8.853077 TCACACTTCAAATCTCACTTTGATAT 57.147 30.769 0.56 0.00 42.87 1.63
1644 5673 7.230849 ACTTGGAATATTGCATCTTTTCACA 57.769 32.000 10.71 0.00 0.00 3.58
1647 5676 8.437742 CAACAACTTGGAATATTGCATCTTTTC 58.562 33.333 10.71 0.00 0.00 2.29
1648 5677 8.149647 TCAACAACTTGGAATATTGCATCTTTT 58.850 29.630 10.71 0.00 0.00 2.27
1649 5678 7.599998 GTCAACAACTTGGAATATTGCATCTTT 59.400 33.333 10.71 1.96 0.00 2.52
1652 5681 5.807011 GGTCAACAACTTGGAATATTGCATC 59.193 40.000 10.71 0.00 0.00 3.91
1679 5710 5.299148 TGTTGGATCATTTGGAAGCAAAAG 58.701 37.500 0.00 0.00 0.00 2.27
1682 5713 3.306225 GCTGTTGGATCATTTGGAAGCAA 60.306 43.478 0.00 0.00 0.00 3.91
1695 5747 1.001020 TCATTGCCGGCTGTTGGAT 60.001 52.632 29.70 8.94 0.00 3.41
1706 5758 1.538047 TCAAAGAGTGCCTCATTGCC 58.462 50.000 12.49 0.00 38.54 4.52
1718 5770 8.193438 GGGGATACTCAATTCAATTTCAAAGAG 58.807 37.037 0.00 0.00 36.63 2.85
1791 5845 2.479566 TGGCTTGCTCTAGGTTTGAG 57.520 50.000 0.00 0.00 34.87 3.02
1814 5869 6.491062 TCTTCAATTCAGATTTCAGCCAAAGA 59.509 34.615 0.00 0.00 0.00 2.52
1829 5884 5.356190 CCTTATGCAGCTCTTCTTCAATTCA 59.644 40.000 0.00 0.00 0.00 2.57
1830 5885 5.356470 ACCTTATGCAGCTCTTCTTCAATTC 59.644 40.000 0.00 0.00 0.00 2.17
1866 5922 7.115236 CAGTAATTGTGTTTTGTGTGATGATGG 59.885 37.037 0.00 0.00 0.00 3.51
1906 5962 7.044181 CAGAGTTATCCTGATAAGAAAGCACA 58.956 38.462 0.00 0.00 34.27 4.57
1926 5982 8.911918 TTACAACACATGTTAAATACCAGAGT 57.088 30.769 0.00 0.00 43.63 3.24
2284 6348 5.509501 GCAAGATTCCCACATTTGTTCTCAA 60.510 40.000 0.00 0.00 0.00 3.02
2294 6358 2.905415 TTCAGGCAAGATTCCCACAT 57.095 45.000 0.00 0.00 0.00 3.21
2339 6403 9.078753 GCTTCTAGAAACATAGTCAAACTCTAC 57.921 37.037 6.63 0.00 0.00 2.59
2375 6439 6.715280 AGAGGATTTCAAGAACAAGATAGCA 58.285 36.000 0.00 0.00 0.00 3.49
2424 6489 2.232941 CCACTAGCGTTGGACCTTTCTA 59.767 50.000 0.00 0.00 0.00 2.10
2431 6497 1.538419 GCTATCCCACTAGCGTTGGAC 60.538 57.143 0.00 0.00 37.74 4.02
2454 6520 3.719268 TTACAATGATGGTGAGGTGCT 57.281 42.857 0.00 0.00 0.00 4.40
2497 6564 7.455953 TCTTCTACCAGCATGATATACCTTGAT 59.544 37.037 0.00 0.00 39.69 2.57
2667 6743 5.241506 CCACTTAAAATCTGGCAGAAGTCAA 59.758 40.000 22.84 12.22 0.00 3.18
2700 6782 6.976349 TGTGTTGCATTAGAGTACCTATTACG 59.024 38.462 0.00 0.00 35.61 3.18
2705 6787 5.670485 CCATGTGTTGCATTAGAGTACCTA 58.330 41.667 0.00 0.00 35.19 3.08
2733 6816 3.118038 CGGTGATTTCTTCCCTCCCAATA 60.118 47.826 0.00 0.00 0.00 1.90
2736 6819 0.618458 CGGTGATTTCTTCCCTCCCA 59.382 55.000 0.00 0.00 0.00 4.37
2797 6881 9.220767 GACTTGACAAAAGACTATCTGGTATTT 57.779 33.333 0.00 0.00 32.93 1.40
2912 7000 2.897326 GGGTGGCTAACATTCTTGGTTT 59.103 45.455 0.00 0.00 0.00 3.27
2973 7062 5.712217 TGAAAGTCAACTACAACAAGTCG 57.288 39.130 0.00 0.00 0.00 4.18
3107 7740 0.663153 GCGGGAATGATGGTGTTAGC 59.337 55.000 0.00 0.00 0.00 3.09
3110 7743 1.750778 GAATGCGGGAATGATGGTGTT 59.249 47.619 0.00 0.00 0.00 3.32
3197 7835 1.302511 GCTGAAGACCCCGAAGCAA 60.303 57.895 0.00 0.00 34.01 3.91
3299 7937 5.682730 GCTCTCAAGGATAGTGGTTAGTTCC 60.683 48.000 0.00 0.00 0.00 3.62
3305 7943 2.093235 GCAGCTCTCAAGGATAGTGGTT 60.093 50.000 0.00 0.00 0.00 3.67
3309 7947 1.127343 GGGCAGCTCTCAAGGATAGT 58.873 55.000 0.00 0.00 0.00 2.12
3418 8056 0.745845 ATCCCACTTGAGCGTCATGC 60.746 55.000 0.00 0.00 46.98 4.06
3463 8108 1.487976 AGAGCATGGTCATTGTCGGAT 59.512 47.619 25.71 0.00 0.00 4.18
3565 8210 9.125026 GAACTATCACAAACATAAGGATCCATT 57.875 33.333 15.82 8.04 0.00 3.16
3645 8290 7.352079 AGGTATTAAAATGCATCTGAAAGGG 57.648 36.000 0.00 0.00 0.00 3.95
3732 8384 1.066002 TCTCCCGTCGCCTATTTAACG 59.934 52.381 0.00 0.00 35.01 3.18
3737 8389 0.899720 TGTTTCTCCCGTCGCCTATT 59.100 50.000 0.00 0.00 0.00 1.73
3738 8390 0.175073 GTGTTTCTCCCGTCGCCTAT 59.825 55.000 0.00 0.00 0.00 2.57
3760 8412 9.554053 AAGAGAGTTACTATGGAAGCCATATAT 57.446 33.333 6.62 2.10 44.33 0.86
3764 8416 6.567602 AAAGAGAGTTACTATGGAAGCCAT 57.432 37.500 4.18 4.18 46.99 4.40
3795 8447 1.726853 AGAAGATGCAGCGTACCAAC 58.273 50.000 0.00 0.00 0.00 3.77
3841 8506 6.887626 TTGGCTACTCCGTTAAAGATTTTT 57.112 33.333 0.00 0.00 37.80 1.94
3863 8528 4.600062 AGTTCAAAGAGTCACCAACCTTT 58.400 39.130 0.00 0.00 32.15 3.11
3958 8623 1.192146 TCTAGCCAAGTTCGCAGGGT 61.192 55.000 0.00 0.00 36.95 4.34
4113 8779 8.710835 TGTGTATTCGCTTCATTAGTAATCAA 57.289 30.769 0.00 0.00 0.00 2.57
4139 8805 5.471456 CAGCTTCAACTTCTACCAAATCAGT 59.529 40.000 0.00 0.00 0.00 3.41
4180 8846 5.818136 TCAAATTCCAAATCACCGAGATC 57.182 39.130 0.00 0.00 35.39 2.75
4214 8880 9.847224 TTAGAGTTGAAGAACTTACAGGAAATT 57.153 29.630 0.00 0.00 42.80 1.82
4223 8889 6.169557 TGCACCTTAGAGTTGAAGAACTTA 57.830 37.500 0.00 0.00 42.80 2.24
4239 8905 2.301346 CAAGAGAGTTGGTTGCACCTT 58.699 47.619 6.83 0.00 39.58 3.50
4254 8920 3.826157 TGGTTAAGTCAAATGGCCAAGAG 59.174 43.478 10.96 1.70 0.00 2.85
4257 8923 4.155709 TCATGGTTAAGTCAAATGGCCAA 58.844 39.130 10.96 0.00 0.00 4.52
4368 9034 5.640158 ATGGAAATGGAAATGGCAATCAT 57.360 34.783 0.00 0.00 37.79 2.45


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

AutoCloner maintained by Alex Coulton.