Multiple sequence alignment - TraesCS1D01G378800

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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 TraesCS1D01G378800 chr1D 100.000 3248 0 0 1 3248 454768103 454771350 0.000000e+00 5999.0
1 TraesCS1D01G378800 chr1D 89.948 1731 116 29 706 2409 454458711 454457012 0.000000e+00 2180.0
2 TraesCS1D01G378800 chr1D 85.802 1620 141 32 832 2411 454493966 454492396 0.000000e+00 1635.0
3 TraesCS1D01G378800 chr1D 87.060 1507 116 40 715 2163 454812459 454813944 0.000000e+00 1629.0
4 TraesCS1D01G378800 chr1D 89.560 182 18 1 4 184 454460758 454460577 2.520000e-56 230.0
5 TraesCS1D01G378800 chr1D 80.147 272 26 11 206 461 454459228 454458969 9.260000e-41 178.0
6 TraesCS1D01G378800 chr1D 88.571 105 12 0 206 310 454494797 454494693 9.460000e-26 128.0
7 TraesCS1D01G378800 chr1D 81.818 132 16 7 2161 2287 454487563 454487435 1.590000e-18 104.0
8 TraesCS1D01G378800 chr1D 77.953 127 13 10 561 673 455776156 455776281 7.520000e-07 65.8
9 TraesCS1D01G378800 chr1A 90.022 2305 174 30 963 3248 548772380 548774647 0.000000e+00 2931.0
10 TraesCS1D01G378800 chr1A 90.151 1391 111 11 947 2320 548733316 548734697 0.000000e+00 1786.0
11 TraesCS1D01G378800 chr1A 87.777 1489 122 33 715 2163 548789044 548790512 0.000000e+00 1687.0
12 TraesCS1D01G378800 chr1A 84.049 163 19 6 41 202 548732453 548732609 2.020000e-32 150.0
13 TraesCS1D01G378800 chr1A 74.129 402 60 32 206 582 548732656 548733038 3.400000e-25 126.0
14 TraesCS1D01G378800 chr1A 85.057 87 9 3 2516 2599 480574255 480574340 5.770000e-13 86.1
15 TraesCS1D01G378800 chr1A 78.070 114 16 6 2181 2294 548777779 548777883 2.710000e-06 63.9
16 TraesCS1D01G378800 chr1B 92.277 1735 111 16 691 2411 625082290 625084015 0.000000e+00 2440.0
17 TraesCS1D01G378800 chr1B 88.492 1512 125 25 819 2320 624970667 624972139 0.000000e+00 1783.0
18 TraesCS1D01G378800 chr1B 87.517 1490 121 40 715 2163 625144939 625146404 0.000000e+00 1661.0
19 TraesCS1D01G378800 chr1B 87.085 271 21 3 206 465 625081808 625082075 8.810000e-76 294.0
20 TraesCS1D01G378800 chr1B 91.346 208 15 1 1 205 625081557 625081764 6.860000e-72 281.0
21 TraesCS1D01G378800 chr1B 95.349 43 1 1 644 685 556106669 556106627 2.090000e-07 67.6
22 TraesCS1D01G378800 chr1B 85.938 64 7 1 2164 2227 625087727 625087788 2.090000e-07 67.6
23 TraesCS1D01G378800 chr2B 81.564 179 20 7 512 678 495146738 495146561 5.650000e-28 135.0
24 TraesCS1D01G378800 chr2B 83.962 106 11 3 2499 2604 644521729 644521630 2.670000e-16 97.1
25 TraesCS1D01G378800 chrUn 83.448 145 20 3 501 644 95294219 95294360 7.310000e-27 132.0
26 TraesCS1D01G378800 chr3D 79.024 205 25 13 502 689 573906647 573906850 1.220000e-24 124.0
27 TraesCS1D01G378800 chr3D 91.071 56 5 0 2551 2606 593235065 593235010 3.470000e-10 76.8
28 TraesCS1D01G378800 chr7A 78.469 209 26 10 490 684 241724674 241724877 5.690000e-23 119.0
29 TraesCS1D01G378800 chr5A 80.769 156 23 7 501 652 469108035 469107883 7.360000e-22 115.0
30 TraesCS1D01G378800 chr3A 81.818 143 21 4 507 644 602223712 602223854 7.360000e-22 115.0
31 TraesCS1D01G378800 chr3A 78.378 185 22 13 510 679 645643249 645643068 1.590000e-18 104.0
32 TraesCS1D01G378800 chr7D 82.222 135 20 4 512 644 80766945 80767077 2.650000e-21 113.0
33 TraesCS1D01G378800 chr7D 80.597 134 25 1 512 644 595523634 595523501 5.730000e-18 102.0
34 TraesCS1D01G378800 chr7D 95.000 40 2 0 645 684 478366642 478366603 2.710000e-06 63.9
35 TraesCS1D01G378800 chr7D 81.944 72 10 3 2617 2686 181339598 181339528 1.260000e-04 58.4
36 TraesCS1D01G378800 chr4A 81.481 135 20 4 512 643 16505109 16504977 4.430000e-19 106.0
37 TraesCS1D01G378800 chr2D 79.054 148 25 5 500 644 198728535 198728679 2.670000e-16 97.1
38 TraesCS1D01G378800 chr2D 82.716 81 14 0 2524 2604 606924791 606924711 4.500000e-09 73.1
39 TraesCS1D01G378800 chr2D 96.970 33 1 0 644 676 37382147 37382115 4.530000e-04 56.5
40 TraesCS1D01G378800 chr3B 85.057 87 12 1 2519 2604 739325288 739325202 1.610000e-13 87.9
41 TraesCS1D01G378800 chr2A 97.917 48 1 0 2564 2611 719274236 719274283 2.080000e-12 84.2
42 TraesCS1D01G378800 chr2A 82.418 91 16 0 2656 2746 44395494 44395584 2.690000e-11 80.5
43 TraesCS1D01G378800 chr2A 85.135 74 10 1 2823 2896 79461009 79461081 1.250000e-09 75.0
44 TraesCS1D01G378800 chr2A 81.818 88 15 1 2517 2604 649483378 649483464 4.500000e-09 73.1
45 TraesCS1D01G378800 chr6B 75.000 196 40 6 2413 2608 699533244 699533058 7.470000e-12 82.4
46 TraesCS1D01G378800 chr5B 80.000 100 8 7 586 673 476051958 476051859 2.710000e-06 63.9
47 TraesCS1D01G378800 chr4B 96.875 32 1 0 642 673 472403940 472403971 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 TraesCS1D01G378800 chr1D 454768103 454771350 3247 False 5999.000000 5999 100.000000 1 3248 1 chr1D.!!$F1 3247
1 TraesCS1D01G378800 chr1D 454812459 454813944 1485 False 1629.000000 1629 87.060000 715 2163 1 chr1D.!!$F2 1448
2 TraesCS1D01G378800 chr1D 454492396 454494797 2401 True 881.500000 1635 87.186500 206 2411 2 chr1D.!!$R3 2205
3 TraesCS1D01G378800 chr1D 454457012 454460758 3746 True 862.666667 2180 86.551667 4 2409 3 chr1D.!!$R2 2405
4 TraesCS1D01G378800 chr1A 548789044 548790512 1468 False 1687.000000 1687 87.777000 715 2163 1 chr1A.!!$F2 1448
5 TraesCS1D01G378800 chr1A 548772380 548777883 5503 False 1497.450000 2931 84.046000 963 3248 2 chr1A.!!$F4 2285
6 TraesCS1D01G378800 chr1A 548732453 548734697 2244 False 687.333333 1786 82.776333 41 2320 3 chr1A.!!$F3 2279
7 TraesCS1D01G378800 chr1B 624970667 624972139 1472 False 1783.000000 1783 88.492000 819 2320 1 chr1B.!!$F1 1501
8 TraesCS1D01G378800 chr1B 625144939 625146404 1465 False 1661.000000 1661 87.517000 715 2163 1 chr1B.!!$F2 1448
9 TraesCS1D01G378800 chr1B 625081557 625087788 6231 False 770.650000 2440 89.161500 1 2411 4 chr1B.!!$F3 2410

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
296 1625 0.168788 CCAATGCGCGTGTTCATCTT 59.831 50.0 8.43 0.00 0.00 2.40 F
1782 3703 0.964358 CGTGGAGGTTCCGGTACTCT 60.964 60.0 11.29 6.55 40.17 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 3820 0.890683 TGCAGTCGATGAAGAGCTGA 59.109 50.0 0.00 0.00 0.0 4.26 R
2655 4654 0.585838 GTCGCCGCTAGGTAGTCTAC 59.414 60.0 0.95 0.95 40.5 2.59 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
31 32 4.319911 CCATCGATCTAGAACTCCGAGAAC 60.320 50.000 1.33 0.00 32.60 3.01
110 111 0.251916 TACCTGTTGCATAAGCGCCT 59.748 50.000 2.29 0.00 46.23 5.52
152 154 0.801251 AGCTCAGCTCGCACATTTTC 59.199 50.000 0.00 0.00 30.62 2.29
164 166 4.338118 TCGCACATTTTCTTCTTCCACTTT 59.662 37.500 0.00 0.00 0.00 2.66
167 169 6.695278 CGCACATTTTCTTCTTCCACTTTTAA 59.305 34.615 0.00 0.00 0.00 1.52
170 172 7.169813 CACATTTTCTTCTTCCACTTTTAAGCC 59.830 37.037 0.00 0.00 0.00 4.35
220 1549 1.478105 GCTACAAAGGGAATGCAAGGG 59.522 52.381 0.00 0.00 0.00 3.95
296 1625 0.168788 CCAATGCGCGTGTTCATCTT 59.831 50.000 8.43 0.00 0.00 2.40
313 1642 6.051179 TCATCTTCATCATCATCCTCATCC 57.949 41.667 0.00 0.00 0.00 3.51
323 1652 2.432146 TCATCCTCATCCTCGTCTTTGG 59.568 50.000 0.00 0.00 0.00 3.28
368 1718 4.837860 TGAATGCCATAAAATATCCCCACC 59.162 41.667 0.00 0.00 0.00 4.61
372 1722 3.778265 CCATAAAATATCCCCACCCCAG 58.222 50.000 0.00 0.00 0.00 4.45
400 1750 3.933332 GCGACCATGAGGCCTATATAAAC 59.067 47.826 4.42 0.00 39.06 2.01
620 2194 6.391227 AAAGTTTTGAACGGATCTTCATGT 57.609 33.333 0.00 0.00 36.23 3.21
659 2245 5.821516 AGAATCGTTAAGTCTCAGTCGAT 57.178 39.130 0.00 0.00 39.19 3.59
661 2247 6.030849 AGAATCGTTAAGTCTCAGTCGATTG 58.969 40.000 13.69 0.68 44.18 2.67
673 2259 5.807520 TCTCAGTCGATTGAGATTTAGCAAC 59.192 40.000 30.21 0.00 46.42 4.17
678 2264 3.541632 GATTGAGATTTAGCAACCCCGA 58.458 45.455 0.00 0.00 0.00 5.14
749 2347 7.734538 ACACATACGAAAGACAAAACAAAAG 57.265 32.000 0.00 0.00 0.00 2.27
757 2355 5.816449 AAGACAAAACAAAAGCCAAATGG 57.184 34.783 0.00 0.00 38.53 3.16
840 2697 1.702886 CTTAGCCACACTCACACTCG 58.297 55.000 0.00 0.00 0.00 4.18
841 2698 1.269723 CTTAGCCACACTCACACTCGA 59.730 52.381 0.00 0.00 0.00 4.04
842 2699 1.545841 TAGCCACACTCACACTCGAT 58.454 50.000 0.00 0.00 0.00 3.59
985 2874 5.523188 CCTAGCTAAGCATCTTCTTGAGTTG 59.477 44.000 0.00 0.00 0.00 3.16
1287 3196 3.423154 CTCGGCACTTTCACGGGC 61.423 66.667 0.00 0.00 0.00 6.13
1610 3531 1.300697 ACCTGTTCGACAAGACGGC 60.301 57.895 0.00 0.00 0.00 5.68
1696 3617 1.673665 CCGCTGCAGCTTCCTTCTT 60.674 57.895 34.22 0.00 39.32 2.52
1782 3703 0.964358 CGTGGAGGTTCCGGTACTCT 60.964 60.000 11.29 6.55 40.17 3.24
2027 3966 2.506438 CTTCGGCGTCGACCTTCC 60.506 66.667 13.73 7.97 45.92 3.46
2081 4047 3.068024 GGCATGACCAAGACAAACAAGAA 59.932 43.478 0.00 0.00 38.86 2.52
2222 4194 6.605594 AGAGATCAACTAGAAGGAGTACAAGG 59.394 42.308 0.00 0.00 0.00 3.61
2232 4204 0.176910 GAGTACAAGGAGCAGGGAGC 59.823 60.000 0.00 0.00 46.19 4.70
2305 4277 5.009410 GGTCAAAATATCAGCTGGAATCAGG 59.991 44.000 15.13 0.00 41.19 3.86
2310 4282 1.220206 CAGCTGGAATCAGGAGCGT 59.780 57.895 5.57 0.00 41.19 5.07
2340 4331 7.434492 ACTCTCATTCACGTAATAGTAATGGG 58.566 38.462 0.00 0.00 30.79 4.00
2341 4332 7.287005 ACTCTCATTCACGTAATAGTAATGGGA 59.713 37.037 0.00 0.00 35.29 4.37
2342 4333 8.014070 TCTCATTCACGTAATAGTAATGGGAA 57.986 34.615 0.00 0.00 34.86 3.97
2343 4334 8.479689 TCTCATTCACGTAATAGTAATGGGAAA 58.520 33.333 0.00 0.00 34.86 3.13
2366 4357 7.781548 AAGTAGTATATGTAGCGGGTTTTTG 57.218 36.000 0.00 0.00 0.00 2.44
2404 4395 6.884832 AGTTCCGATATGTCCATCAAACTTA 58.115 36.000 0.00 0.00 31.50 2.24
2405 4396 6.986817 AGTTCCGATATGTCCATCAAACTTAG 59.013 38.462 0.00 0.00 31.50 2.18
2407 4398 7.591421 TCCGATATGTCCATCAAACTTAGTA 57.409 36.000 0.00 0.00 0.00 1.82
2462 4454 6.148480 AGACTTGTTTATGTCTCACTTGATGC 59.852 38.462 0.00 0.00 36.84 3.91
2463 4455 5.764686 ACTTGTTTATGTCTCACTTGATGCA 59.235 36.000 0.00 0.00 0.00 3.96
2464 4456 6.262944 ACTTGTTTATGTCTCACTTGATGCAA 59.737 34.615 0.00 0.00 0.00 4.08
2474 4466 5.005682 TCTCACTTGATGCAATATTCGTTCG 59.994 40.000 0.00 0.00 0.00 3.95
2476 4468 4.957967 CACTTGATGCAATATTCGTTCGAC 59.042 41.667 0.00 0.00 0.00 4.20
2481 4473 2.095213 TGCAATATTCGTTCGACCTTGC 59.905 45.455 19.18 19.18 38.33 4.01
2482 4474 2.845764 GCAATATTCGTTCGACCTTGCG 60.846 50.000 14.69 0.00 0.00 4.85
2483 4475 2.288961 ATATTCGTTCGACCTTGCGT 57.711 45.000 0.00 0.00 0.00 5.24
2488 4480 1.593209 GTTCGACCTTGCGTGTGGA 60.593 57.895 0.00 0.00 0.00 4.02
2493 4485 2.358737 CCTTGCGTGTGGAGGTCC 60.359 66.667 0.00 0.00 0.00 4.46
2501 4493 1.098712 GTGTGGAGGTCCGTGCAAAA 61.099 55.000 0.00 0.00 39.43 2.44
2502 4494 0.394488 TGTGGAGGTCCGTGCAAAAA 60.394 50.000 0.00 0.00 39.43 1.94
2567 4566 4.906618 ACTACGTCATTTGATTGGGACTT 58.093 39.130 0.00 0.00 0.00 3.01
2568 4567 4.695455 ACTACGTCATTTGATTGGGACTTG 59.305 41.667 0.00 0.00 0.00 3.16
2569 4568 3.486383 ACGTCATTTGATTGGGACTTGT 58.514 40.909 0.00 0.00 0.00 3.16
2582 4581 6.877611 TTGGGACTTGTTTAAATCTCAGTC 57.122 37.500 0.00 1.44 0.00 3.51
2601 4600 2.160022 GTCGACTGAGACCTAGTCACAC 59.840 54.545 8.70 0.00 43.65 3.82
2607 4606 3.428532 TGAGACCTAGTCACACCCTTAC 58.571 50.000 0.00 0.00 34.60 2.34
2614 4613 7.560626 AGACCTAGTCACACCCTTACTATAAAG 59.439 40.741 0.00 0.00 34.60 1.85
2649 4648 2.332063 AGTAATGGGAGTTGCATCCG 57.668 50.000 0.25 0.00 40.56 4.18
2655 4654 0.105039 GGGAGTTGCATCCGGACTAG 59.895 60.000 6.12 0.05 40.56 2.57
2693 4692 4.034510 GCGACTATAAGCACTGAAGCAAAT 59.965 41.667 0.00 0.00 36.85 2.32
2717 4717 3.003478 CGTGCCGCCGTTATCTTC 58.997 61.111 0.00 0.00 0.00 2.87
2729 4729 3.024547 CGTTATCTTCTCTCCCTCACCA 58.975 50.000 0.00 0.00 0.00 4.17
2730 4730 3.639094 CGTTATCTTCTCTCCCTCACCAT 59.361 47.826 0.00 0.00 0.00 3.55
2735 4735 2.079170 TCTCTCCCTCACCATAGCTG 57.921 55.000 0.00 0.00 0.00 4.24
2759 4759 7.511268 TGGGCAAACCTTATCGTAGTATAAAT 58.489 34.615 0.00 0.00 41.11 1.40
2784 4784 2.812613 CGGGAGGTTTTTGTGCTAAGGA 60.813 50.000 0.00 0.00 0.00 3.36
2793 4793 0.984230 TGTGCTAAGGACTCAAGGGG 59.016 55.000 0.00 0.00 0.00 4.79
2810 4810 1.035139 GGGCCAGTGCATCCAATTAG 58.965 55.000 4.39 0.00 40.13 1.73
2828 4828 7.381408 TCCAATTAGTAACGATCGATGATGAAC 59.619 37.037 24.34 4.52 0.00 3.18
2834 4834 3.119291 ACGATCGATGATGAACAGAAGC 58.881 45.455 24.34 0.00 0.00 3.86
2835 4835 2.152678 CGATCGATGATGAACAGAAGCG 59.847 50.000 10.26 0.00 0.00 4.68
2885 4885 7.064609 AGACATACGAACACCATACAAATGAAG 59.935 37.037 0.00 0.00 34.84 3.02
2906 4906 2.890945 GGCCAAATCCAACACTACTTGT 59.109 45.455 0.00 0.00 41.74 3.16
2939 4939 3.142838 GTAGTACCCTCGGGCGCA 61.143 66.667 10.83 0.00 39.32 6.09
2946 4946 2.546494 CCCTCGGGCGCATTCATTC 61.546 63.158 10.83 0.00 0.00 2.67
2958 4963 3.787634 CGCATTCATTCGTTCTTCATTGG 59.212 43.478 0.00 0.00 0.00 3.16
2972 4977 7.222611 CGTTCTTCATTGGTTCTTTGTTCATTT 59.777 33.333 0.00 0.00 0.00 2.32
2973 4978 8.882736 GTTCTTCATTGGTTCTTTGTTCATTTT 58.117 29.630 0.00 0.00 0.00 1.82
3085 5101 6.215121 TGTTTAGTCATTGGAACATTGCTTG 58.785 36.000 0.00 0.00 39.29 4.01
3087 5103 1.987770 GTCATTGGAACATTGCTTGCG 59.012 47.619 0.00 0.00 39.29 4.85
3089 5105 2.816672 TCATTGGAACATTGCTTGCGTA 59.183 40.909 0.00 0.00 39.29 4.42
3091 5107 2.697431 TGGAACATTGCTTGCGTAAC 57.303 45.000 0.00 0.00 0.00 2.50
3094 5110 3.815962 TGGAACATTGCTTGCGTAACTTA 59.184 39.130 0.00 0.00 0.00 2.24
3095 5111 4.083537 TGGAACATTGCTTGCGTAACTTAG 60.084 41.667 0.00 0.00 0.00 2.18
3096 5112 4.153475 GGAACATTGCTTGCGTAACTTAGA 59.847 41.667 0.00 0.00 0.00 2.10
3097 5113 5.334569 GGAACATTGCTTGCGTAACTTAGAA 60.335 40.000 0.00 0.00 0.00 2.10
3098 5114 5.682943 ACATTGCTTGCGTAACTTAGAAA 57.317 34.783 0.00 0.00 0.00 2.52
3099 5115 6.067263 ACATTGCTTGCGTAACTTAGAAAA 57.933 33.333 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.010933 GGAGTTCTAGATCGATGGGTATGA 58.989 45.833 0.54 0.00 0.00 2.15
31 32 0.940126 GCCGATGGTGCTGTAGAATG 59.060 55.000 0.00 0.00 0.00 2.67
110 111 2.432444 CTGCTGACCCATTTCGGTTTA 58.568 47.619 0.00 0.00 35.79 2.01
143 144 7.306807 GCTTAAAAGTGGAAGAAGAAAATGTGC 60.307 37.037 0.00 0.00 0.00 4.57
152 154 7.334671 CCTAGTAAGGCTTAAAAGTGGAAGAAG 59.665 40.741 8.86 0.00 35.64 2.85
164 166 4.589374 GCATCTCCTCCTAGTAAGGCTTAA 59.411 45.833 8.86 0.00 43.31 1.85
167 169 2.604139 GCATCTCCTCCTAGTAAGGCT 58.396 52.381 3.95 0.00 43.31 4.58
170 172 4.822896 AGTAACGCATCTCCTCCTAGTAAG 59.177 45.833 0.00 0.00 0.00 2.34
220 1549 2.139118 GTGAGAAACTCAGAGTGCCAC 58.861 52.381 3.05 6.50 41.46 5.01
281 1610 0.721154 GATGAAGATGAACACGCGCA 59.279 50.000 5.73 0.00 0.00 6.09
283 1612 2.604462 TGATGATGAAGATGAACACGCG 59.396 45.455 3.53 3.53 0.00 6.01
296 1625 3.504375 ACGAGGATGAGGATGATGATGA 58.496 45.455 0.00 0.00 0.00 2.92
313 1642 8.947115 AGGAAATATAAAAAGACCAAAGACGAG 58.053 33.333 0.00 0.00 0.00 4.18
368 1718 0.179048 TCATGGTCGCTTATGCTGGG 60.179 55.000 0.00 0.00 36.97 4.45
372 1722 1.510480 GGCCTCATGGTCGCTTATGC 61.510 60.000 0.00 0.00 35.27 3.14
381 1731 6.959606 AGATGTTTATATAGGCCTCATGGT 57.040 37.500 9.68 0.00 35.27 3.55
504 2066 3.896888 CTGAGATCTAGCCACATCCTTCT 59.103 47.826 0.00 0.00 0.00 2.85
505 2067 3.640967 ACTGAGATCTAGCCACATCCTTC 59.359 47.826 0.00 0.00 0.00 3.46
508 2070 2.030363 CGACTGAGATCTAGCCACATCC 60.030 54.545 0.00 0.00 0.00 3.51
509 2071 2.881513 TCGACTGAGATCTAGCCACATC 59.118 50.000 0.00 0.00 0.00 3.06
558 2130 9.961266 TCGTTCTTTATTTTATATGTTGTGTCG 57.039 29.630 0.00 0.00 0.00 4.35
600 2172 7.129109 TCTTACATGAAGATCCGTTCAAAAC 57.871 36.000 0.00 0.00 39.36 2.43
631 2205 9.666626 CGACTGAGACTTAACGATTCTATATTT 57.333 33.333 0.00 0.00 0.00 1.40
636 2210 6.922247 ATCGACTGAGACTTAACGATTCTA 57.078 37.500 0.00 0.00 37.21 2.10
639 2213 5.950883 TCAATCGACTGAGACTTAACGATT 58.049 37.500 0.00 0.00 46.25 3.34
659 2245 3.426787 TTCGGGGTTGCTAAATCTCAA 57.573 42.857 0.00 0.00 0.00 3.02
661 2247 4.776795 TTTTTCGGGGTTGCTAAATCTC 57.223 40.909 0.00 0.00 0.00 2.75
701 2287 9.376075 TGTAGAGTAGATAATAGGTATACACGC 57.624 37.037 5.01 0.00 0.00 5.34
723 2318 8.829514 TTTTGTTTTGTCTTTCGTATGTGTAG 57.170 30.769 0.00 0.00 0.00 2.74
724 2319 7.429920 GCTTTTGTTTTGTCTTTCGTATGTGTA 59.570 33.333 0.00 0.00 0.00 2.90
732 2327 5.523013 TTTGGCTTTTGTTTTGTCTTTCG 57.477 34.783 0.00 0.00 0.00 3.46
757 2355 8.936864 GTTCCATATACTATTTCTACACATGGC 58.063 37.037 0.00 0.00 32.29 4.40
840 2697 0.188342 AGGAGAGGAGCTGGAGGATC 59.812 60.000 0.00 0.00 0.00 3.36
841 2698 0.188342 GAGGAGAGGAGCTGGAGGAT 59.812 60.000 0.00 0.00 0.00 3.24
842 2699 1.217747 TGAGGAGAGGAGCTGGAGGA 61.218 60.000 0.00 0.00 0.00 3.71
954 2840 6.112058 AGAAGATGCTTAGCTAGGAAAAGTG 58.888 40.000 7.11 0.00 0.00 3.16
958 2844 6.070538 ACTCAAGAAGATGCTTAGCTAGGAAA 60.071 38.462 7.11 0.00 0.00 3.13
1503 3412 3.130160 GTAGGGGACGACGACGCT 61.130 66.667 7.30 14.36 43.96 5.07
1542 3463 2.507324 GCTGAAGGAGCCGACGAC 60.507 66.667 0.00 0.00 42.54 4.34
1617 3538 4.070552 AGCTTCCCCACGTCGCTC 62.071 66.667 0.00 0.00 0.00 5.03
1647 3568 2.124736 GCGTGCTGCTTGGGGATA 60.125 61.111 0.00 0.00 41.73 2.59
1763 3684 0.964358 AGAGTACCGGAACCTCCACG 60.964 60.000 9.46 0.00 35.91 4.94
1782 3703 3.631453 CTGGCTGCTGTTCCAGTAA 57.369 52.632 0.00 0.00 43.66 2.24
1899 3820 0.890683 TGCAGTCGATGAAGAGCTGA 59.109 50.000 0.00 0.00 0.00 4.26
2048 4011 1.589196 GTCATGCCGTACTCCTCGC 60.589 63.158 0.00 0.00 0.00 5.03
2081 4047 2.514592 CGCTGGCGTCCATGGATT 60.515 61.111 19.62 0.00 30.82 3.01
2232 4204 4.329801 TGACAAGTCTATAGCGCAAATGTG 59.670 41.667 11.47 0.00 0.00 3.21
2241 4213 3.696898 CGAGTGGTGACAAGTCTATAGC 58.303 50.000 1.53 0.00 46.06 2.97
2336 4327 5.187186 CCCGCTACATATACTACTTTCCCAT 59.813 44.000 0.00 0.00 0.00 4.00
2338 4329 4.525874 ACCCGCTACATATACTACTTTCCC 59.474 45.833 0.00 0.00 0.00 3.97
2339 4330 5.718724 ACCCGCTACATATACTACTTTCC 57.281 43.478 0.00 0.00 0.00 3.13
2340 4331 8.333186 CAAAAACCCGCTACATATACTACTTTC 58.667 37.037 0.00 0.00 0.00 2.62
2341 4332 7.825761 ACAAAAACCCGCTACATATACTACTTT 59.174 33.333 0.00 0.00 0.00 2.66
2342 4333 7.333323 ACAAAAACCCGCTACATATACTACTT 58.667 34.615 0.00 0.00 0.00 2.24
2343 4334 6.881570 ACAAAAACCCGCTACATATACTACT 58.118 36.000 0.00 0.00 0.00 2.57
2417 4408 7.823076 AGTCTCAGACGACTGCTACTTAGCT 62.823 48.000 10.15 0.00 42.39 3.32
2418 4409 5.685354 AGTCTCAGACGACTGCTACTTAGC 61.685 50.000 10.15 0.98 42.39 3.09
2426 4418 2.141535 AACAAGTCTCAGACGACTGC 57.858 50.000 10.15 0.00 43.14 4.40
2455 4447 4.271049 AGGTCGAACGAATATTGCATCAAG 59.729 41.667 0.00 0.00 0.00 3.02
2462 4454 2.347452 ACGCAAGGTCGAACGAATATTG 59.653 45.455 0.00 5.86 46.39 1.90
2463 4455 2.347452 CACGCAAGGTCGAACGAATATT 59.653 45.455 0.00 0.00 46.39 1.28
2464 4456 1.924524 CACGCAAGGTCGAACGAATAT 59.075 47.619 0.00 0.00 46.39 1.28
2474 4466 2.426023 ACCTCCACACGCAAGGTC 59.574 61.111 0.00 0.00 39.17 3.85
2476 4468 2.358737 GGACCTCCACACGCAAGG 60.359 66.667 0.00 0.00 37.62 3.61
2481 4473 3.800685 TTGCACGGACCTCCACACG 62.801 63.158 0.00 0.00 35.14 4.49
2482 4474 1.098712 TTTTGCACGGACCTCCACAC 61.099 55.000 0.00 0.00 35.14 3.82
2483 4475 0.394488 TTTTTGCACGGACCTCCACA 60.394 50.000 0.00 0.00 35.14 4.17
2550 4542 8.831715 ATTTAAACAAGTCCCAATCAAATGAC 57.168 30.769 0.00 0.00 0.00 3.06
2554 4553 8.243961 TGAGATTTAAACAAGTCCCAATCAAA 57.756 30.769 0.00 0.00 0.00 2.69
2562 4561 5.927115 AGTCGACTGAGATTTAAACAAGTCC 59.073 40.000 19.30 4.19 0.00 3.85
2582 4581 1.469308 GGTGTGACTAGGTCTCAGTCG 59.531 57.143 0.00 0.00 44.44 4.18
2596 4595 9.629878 TTTTTGTTCTTTATAGTAAGGGTGTGA 57.370 29.630 0.00 0.00 0.00 3.58
2597 4596 9.673454 GTTTTTGTTCTTTATAGTAAGGGTGTG 57.327 33.333 0.00 0.00 0.00 3.82
2614 4613 8.655651 TCCCATTACTTTTGATGTTTTTGTTC 57.344 30.769 0.00 0.00 0.00 3.18
2649 4648 3.663025 CCGCTAGGTAGTCTACTAGTCC 58.337 54.545 9.85 0.00 39.07 3.85
2655 4654 0.585838 GTCGCCGCTAGGTAGTCTAC 59.414 60.000 0.95 0.95 40.50 2.59
2717 4717 1.047002 CCAGCTATGGTGAGGGAGAG 58.953 60.000 0.00 0.00 42.17 3.20
2729 4729 2.172717 ACGATAAGGTTTGCCCAGCTAT 59.827 45.455 0.00 0.00 34.66 2.97
2730 4730 1.557832 ACGATAAGGTTTGCCCAGCTA 59.442 47.619 0.00 0.00 34.66 3.32
2735 4735 7.974482 ATTTATACTACGATAAGGTTTGCCC 57.026 36.000 0.00 0.00 34.57 5.36
2759 4759 3.149005 AGCACAAAAACCTCCCGATTA 57.851 42.857 0.00 0.00 0.00 1.75
2784 4784 2.490270 GATGCACTGGCCCCTTGAGT 62.490 60.000 0.00 0.00 40.13 3.41
2793 4793 3.242739 CGTTACTAATTGGATGCACTGGC 60.243 47.826 0.00 0.00 41.68 4.85
2810 4810 5.331905 GCTTCTGTTCATCATCGATCGTTAC 60.332 44.000 15.94 2.17 0.00 2.50
2828 4828 2.888594 TCCTTCCGATTAACGCTTCTG 58.111 47.619 0.00 0.00 41.07 3.02
2834 4834 5.983720 ACATGTTAGATCCTTCCGATTAACG 59.016 40.000 0.00 0.00 42.18 3.18
2835 4835 8.358148 TCTACATGTTAGATCCTTCCGATTAAC 58.642 37.037 2.30 0.00 31.74 2.01
2885 4885 2.890945 ACAAGTAGTGTTGGATTTGGCC 59.109 45.455 0.00 0.00 37.01 5.36
2939 4939 6.824305 AGAACCAATGAAGAACGAATGAAT 57.176 33.333 0.00 0.00 0.00 2.57
2946 4946 5.577835 TGAACAAAGAACCAATGAAGAACG 58.422 37.500 0.00 0.00 0.00 3.95
3065 5081 3.119884 CGCAAGCAATGTTCCAATGACTA 60.120 43.478 0.00 0.00 0.00 2.59
3077 5093 6.984740 TTTTTCTAAGTTACGCAAGCAATG 57.015 33.333 0.00 0.00 45.62 2.82
3098 5114 7.785033 ACATTGTTCTGAAGAGTGGAATTTTT 58.215 30.769 13.25 0.00 0.00 1.94
3099 5115 7.352079 ACATTGTTCTGAAGAGTGGAATTTT 57.648 32.000 13.25 0.00 0.00 1.82
3103 5119 6.427853 CACATACATTGTTCTGAAGAGTGGAA 59.572 38.462 13.25 3.31 36.00 3.53


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

AutoCloner maintained by Alex Coulton.