Multiple sequence alignment - TraesCS5A01G289000

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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 TraesCS5A01G289000 chr5A 100.000 2754 0 0 1 2754 495927859 495925106 0.000000e+00 5086.0
1 TraesCS5A01G289000 chr5A 87.148 1066 114 11 723 1785 495907045 495906000 0.000000e+00 1188.0
2 TraesCS5A01G289000 chr5A 80.525 1258 165 39 703 1913 495903385 495902161 0.000000e+00 893.0
3 TraesCS5A01G289000 chr5A 85.504 814 97 10 1108 1913 495910272 495909472 0.000000e+00 830.0
4 TraesCS5A01G289000 chr5A 93.372 347 20 2 767 1112 495912260 495911916 6.800000e-141 510.0
5 TraesCS5A01G289000 chr5A 88.316 291 22 9 493 782 495918441 495918162 3.400000e-89 339.0
6 TraesCS5A01G289000 chr5A 98.919 185 2 0 2474 2658 18658770 18658586 5.680000e-87 331.0
7 TraesCS5A01G289000 chr5A 89.216 102 6 2 398 499 495903747 495903651 3.720000e-24 122.0
8 TraesCS5A01G289000 chr5D 92.797 1416 78 14 502 1915 393904224 393902831 0.000000e+00 2028.0
9 TraesCS5A01G289000 chr5D 88.053 1423 100 39 499 1905 393908266 393906898 0.000000e+00 1622.0
10 TraesCS5A01G289000 chr5D 88.220 1180 110 11 735 1905 393901085 393899926 0.000000e+00 1382.0
11 TraesCS5A01G289000 chr5D 82.305 1232 152 29 703 1913 393897360 393896174 0.000000e+00 1007.0
12 TraesCS5A01G289000 chr5D 78.764 1149 193 31 708 1832 393881637 393880516 0.000000e+00 723.0
13 TraesCS5A01G289000 chr5D 89.850 532 21 13 1 503 393908833 393908306 0.000000e+00 652.0
14 TraesCS5A01G289000 chr5D 87.149 498 29 20 1 494 393905307 393904841 1.450000e-147 532.0
15 TraesCS5A01G289000 chr5D 88.811 429 40 5 2045 2471 393906469 393906891 1.130000e-143 520.0
16 TraesCS5A01G289000 chr5D 89.524 315 22 5 2156 2467 393902523 393902829 3.330000e-104 388.0
17 TraesCS5A01G289000 chr5D 87.000 200 14 8 499 698 393897594 393897407 5.970000e-52 215.0
18 TraesCS5A01G289000 chr5D 90.714 140 11 2 9 147 393938287 393938149 4.680000e-43 185.0
19 TraesCS5A01G289000 chr5D 88.235 102 7 2 398 499 393897724 393897628 1.730000e-22 117.0
20 TraesCS5A01G289000 chr5B 90.559 1430 99 18 499 1915 473783055 473781649 0.000000e+00 1860.0
21 TraesCS5A01G289000 chr5B 88.820 1136 87 18 804 1915 473773811 473772692 0.000000e+00 1358.0
22 TraesCS5A01G289000 chr5B 81.605 1234 161 30 703 1913 473766323 473765133 0.000000e+00 961.0
23 TraesCS5A01G289000 chr5B 89.427 454 21 11 64 503 473783532 473783092 5.190000e-152 547.0
24 TraesCS5A01G289000 chr5B 88.889 414 40 4 2061 2471 473781240 473781650 3.170000e-139 505.0
25 TraesCS5A01G289000 chr5B 86.863 373 31 9 2046 2416 473770459 473770815 4.270000e-108 401.0
26 TraesCS5A01G289000 chr5B 84.910 391 32 14 69 453 473775708 473775339 1.200000e-98 370.0
27 TraesCS5A01G289000 chr5B 91.045 201 9 4 499 698 473766562 473766370 2.100000e-66 263.0
28 TraesCS5A01G289000 chr5B 86.631 187 10 9 501 686 473773977 473773805 2.800000e-45 193.0
29 TraesCS5A01G289000 chr5B 94.048 84 5 0 64 147 473790361 473790278 8.010000e-26 128.0
30 TraesCS5A01G289000 chr5B 98.148 54 1 0 8 61 473783712 473783659 8.120000e-16 95.3
31 TraesCS5A01G289000 chr5B 93.333 45 2 1 1974 2018 559212105 559212148 6.370000e-07 65.8
32 TraesCS5A01G289000 chr3A 95.652 207 9 0 2461 2667 9970137 9970343 1.580000e-87 333.0
33 TraesCS5A01G289000 chr3A 97.297 185 5 0 2474 2658 68866487 68866671 5.730000e-82 315.0
34 TraesCS5A01G289000 chr3A 97.368 38 1 0 1974 2011 703893358 703893395 6.370000e-07 65.8
35 TraesCS5A01G289000 chr7A 95.588 204 9 0 2464 2667 51360563 51360360 7.350000e-86 327.0
36 TraesCS5A01G289000 chr7A 96.809 188 6 0 2474 2661 685390933 685390746 5.730000e-82 315.0
37 TraesCS5A01G289000 chr7A 100.000 34 0 0 1978 2011 506964060 506964093 2.290000e-06 63.9
38 TraesCS5A01G289000 chr3B 95.588 204 8 1 2464 2667 696703890 696703688 2.640000e-85 326.0
39 TraesCS5A01G289000 chr1A 97.354 189 4 1 2474 2661 483658537 483658725 1.230000e-83 320.0
40 TraesCS5A01G289000 chr1A 93.103 203 12 2 2465 2667 44363222 44363422 2.070000e-76 296.0
41 TraesCS5A01G289000 chr6A 96.774 186 6 0 2474 2659 17942643 17942828 7.410000e-81 311.0
42 TraesCS5A01G289000 chr6A 100.000 34 0 0 1978 2011 503487071 503487104 2.290000e-06 63.9
43 TraesCS5A01G289000 chrUn 88.696 115 13 0 2053 2167 97362050 97362164 1.030000e-29 141.0
44 TraesCS5A01G289000 chrUn 100.000 34 0 0 1978 2011 474962466 474962499 2.290000e-06 63.9
45 TraesCS5A01G289000 chr6D 90.000 110 9 2 2058 2167 427717442 427717335 1.030000e-29 141.0
46 TraesCS5A01G289000 chr3D 87.500 120 13 2 2046 2164 550654563 550654445 1.330000e-28 137.0
47 TraesCS5A01G289000 chr4A 86.667 120 14 2 2046 2164 552857232 552857350 6.190000e-27 132.0
48 TraesCS5A01G289000 chr7D 86.087 115 15 1 2053 2167 548086283 548086170 3.720000e-24 122.0
49 TraesCS5A01G289000 chr7D 85.000 120 16 2 2046 2164 29717711 29717829 1.340000e-23 121.0
50 TraesCS5A01G289000 chr7D 84.252 127 17 3 2046 2171 498727279 498727403 1.340000e-23 121.0
51 TraesCS5A01G289000 chr7D 100.000 31 0 0 2376 2406 629651847 629651817 1.070000e-04 58.4
52 TraesCS5A01G289000 chr2A 85.470 117 15 2 2052 2167 150494259 150494144 1.340000e-23 121.0
53 TraesCS5A01G289000 chr2A 97.368 38 0 1 1978 2014 765874948 765874985 2.290000e-06 63.9
54 TraesCS5A01G289000 chr2D 100.000 34 0 0 1978 2011 25038671 25038704 2.290000e-06 63.9
55 TraesCS5A01G289000 chr1D 100.000 34 0 0 1978 2011 246416403 246416370 2.290000e-06 63.9
56 TraesCS5A01G289000 chr1D 100.000 34 0 0 1978 2011 411155374 411155407 2.290000e-06 63.9


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 TraesCS5A01G289000 chr5A 495925106 495927859 2753 True 5086.000000 5086 100.000000 1 2754 1 chr5A.!!$R3 2753
1 TraesCS5A01G289000 chr5A 495902161 495912260 10099 True 708.600000 1188 87.153000 398 1913 5 chr5A.!!$R4 1515
2 TraesCS5A01G289000 chr5D 393896174 393908833 12659 True 944.375000 2028 87.951125 1 1915 8 chr5D.!!$R3 1914
3 TraesCS5A01G289000 chr5D 393880516 393881637 1121 True 723.000000 723 78.764000 708 1832 1 chr5D.!!$R1 1124
4 TraesCS5A01G289000 chr5D 393902523 393906891 4368 False 454.000000 520 89.167500 2045 2471 2 chr5D.!!$F1 426
5 TraesCS5A01G289000 chr5B 473781649 473783712 2063 True 834.100000 1860 92.711333 8 1915 3 chr5B.!!$R4 1907
6 TraesCS5A01G289000 chr5B 473772692 473775708 3016 True 640.333333 1358 86.787000 69 1915 3 chr5B.!!$R3 1846
7 TraesCS5A01G289000 chr5B 473765133 473766562 1429 True 612.000000 961 86.325000 499 1913 2 chr5B.!!$R2 1414

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
592 6395 0.107017 CCAAGTCGGCCATGAGGAAT 60.107 55.0 2.24 0.0 36.89 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2192 12184 0.105778 GGCCTCTGCATGACTAGACC 59.894 60.0 0.0 0.0 40.13 3.85 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
86 213 2.447244 AAGGAAGACAGCACGAAGAG 57.553 50.000 0.00 0.00 0.00 2.85
172 310 3.751175 TGGCAAAGACTATTCAAAGTCCG 59.249 43.478 0.54 0.00 45.86 4.79
312 460 3.898482 ACTTGGTGCATTATTAGACCCC 58.102 45.455 0.00 0.00 0.00 4.95
337 485 2.973316 AAATCGCCAAACCGCCGAC 61.973 57.895 0.00 0.00 33.46 4.79
567 6370 1.830408 CCCTCCTCCAGCTCCTACG 60.830 68.421 0.00 0.00 0.00 3.51
581 6384 0.737219 CCTACGTACCTCCAAGTCGG 59.263 60.000 0.00 0.00 0.00 4.79
590 6393 1.612146 TCCAAGTCGGCCATGAGGA 60.612 57.895 2.24 0.00 36.89 3.71
592 6395 0.107017 CCAAGTCGGCCATGAGGAAT 60.107 55.000 2.24 0.00 36.89 3.01
593 6396 1.019673 CAAGTCGGCCATGAGGAATG 58.980 55.000 2.24 0.00 36.89 2.67
594 6397 0.911769 AAGTCGGCCATGAGGAATGA 59.088 50.000 2.24 0.00 38.72 2.57
595 6398 1.135094 AGTCGGCCATGAGGAATGAT 58.865 50.000 2.24 0.00 38.72 2.45
596 6399 1.202734 AGTCGGCCATGAGGAATGATG 60.203 52.381 2.24 0.00 38.72 3.07
597 6400 0.839277 TCGGCCATGAGGAATGATGT 59.161 50.000 2.24 0.00 38.72 3.06
598 6401 1.202687 TCGGCCATGAGGAATGATGTC 60.203 52.381 2.24 0.00 38.72 3.06
599 6402 1.475571 CGGCCATGAGGAATGATGTCA 60.476 52.381 2.24 0.00 38.72 3.58
600 6403 2.812983 CGGCCATGAGGAATGATGTCAT 60.813 50.000 2.24 0.00 38.72 3.06
638 10479 1.134995 CAATCCACAGTCGCAGCTAGA 60.135 52.381 0.00 0.00 0.00 2.43
639 10480 0.743688 ATCCACAGTCGCAGCTAGAG 59.256 55.000 0.00 0.00 0.00 2.43
654 10495 0.480690 TAGAGCTAGCTCCTCCCCTG 59.519 60.000 35.58 0.00 43.70 4.45
658 10499 1.191489 GCTAGCTCCTCCCCTGGATC 61.191 65.000 7.70 0.00 35.30 3.36
718 10601 7.430441 TCTGACTGTAAGCGTATTATAATGCA 58.570 34.615 13.12 0.00 37.60 3.96
840 10731 5.695851 TCTGTTTCCATTGCTCTTCTTTC 57.304 39.130 0.00 0.00 0.00 2.62
934 10829 3.127895 CGGATTTCAAATACGGCCTTTCA 59.872 43.478 6.87 0.00 0.00 2.69
1167 11084 1.444119 GCACCACAGCGAGGAACAAA 61.444 55.000 0.00 0.00 0.00 2.83
1461 11383 0.104120 CTATGATTGTCGGCCGGTCA 59.896 55.000 27.83 22.94 0.00 4.02
1472 11400 1.202132 CGGCCGGTCATAACATTTGTG 60.202 52.381 20.10 0.00 0.00 3.33
1483 11411 6.368516 GTCATAACATTTGTGTTTGGATTGGG 59.631 38.462 0.00 0.00 33.59 4.12
1489 11424 2.956132 TGTGTTTGGATTGGGTGATGT 58.044 42.857 0.00 0.00 0.00 3.06
1558 11495 1.526887 CGTGTACACAGTTGGAAGCAG 59.473 52.381 24.98 1.01 0.00 4.24
1561 11498 0.764890 TACACAGTTGGAAGCAGCCT 59.235 50.000 0.00 0.00 0.00 4.58
1562 11499 0.106519 ACACAGTTGGAAGCAGCCTT 60.107 50.000 0.00 0.00 0.00 4.35
1563 11500 1.142870 ACACAGTTGGAAGCAGCCTTA 59.857 47.619 0.00 0.00 0.00 2.69
1564 11501 2.229792 CACAGTTGGAAGCAGCCTTAA 58.770 47.619 0.00 0.00 0.00 1.85
1576 11515 2.359214 GCAGCCTTAATTAGCTCCCAAC 59.641 50.000 0.00 0.00 37.18 3.77
1719 11666 4.074259 TGTAGTAACTGTCTGCGGAAGTA 58.926 43.478 0.00 0.00 0.00 2.24
1761 11708 2.605837 TTGTAAGTGTTCTGCCGACA 57.394 45.000 0.00 0.00 0.00 4.35
1799 11790 9.774413 AATACCGTAATTCCAAAGTAGAATAGG 57.226 33.333 0.00 0.00 32.80 2.57
1842 11833 2.289382 TGATTGCAAGTTGGAGCGTCTA 60.289 45.455 4.94 0.00 0.00 2.59
1861 11852 6.183359 GCGTCTATGTCTCTACTGTGTTTTTC 60.183 42.308 0.00 0.00 0.00 2.29
1905 11896 6.403333 TGAAACTATGCTAACGTTGATCAC 57.597 37.500 11.99 0.00 0.00 3.06
1906 11897 5.929415 TGAAACTATGCTAACGTTGATCACA 59.071 36.000 11.99 2.07 0.00 3.58
1907 11898 6.425417 TGAAACTATGCTAACGTTGATCACAA 59.575 34.615 11.99 0.00 0.00 3.33
1924 11915 9.513906 TTGATCACAACCATATTCTACTTTTCA 57.486 29.630 0.00 0.00 0.00 2.69
1953 11944 9.391006 TCACACTTTTCATTTAAACTCTACTGT 57.609 29.630 0.00 0.00 0.00 3.55
1954 11945 9.438291 CACACTTTTCATTTAAACTCTACTGTG 57.562 33.333 0.00 0.00 0.00 3.66
1955 11946 9.174166 ACACTTTTCATTTAAACTCTACTGTGT 57.826 29.630 0.00 0.00 0.00 3.72
1962 11953 9.997482 TCATTTAAACTCTACTGTGTTTTTCAC 57.003 29.630 0.00 0.00 46.31 3.18
1977 11968 8.075593 GTGTTTTTCACATTTTATGCACATCT 57.924 30.769 0.00 0.00 45.51 2.90
1978 11969 9.190858 GTGTTTTTCACATTTTATGCACATCTA 57.809 29.630 0.00 0.00 45.51 1.98
1979 11970 9.409312 TGTTTTTCACATTTTATGCACATCTAG 57.591 29.630 0.00 0.00 0.00 2.43
1980 11971 9.624697 GTTTTTCACATTTTATGCACATCTAGA 57.375 29.630 0.00 0.00 0.00 2.43
1982 11973 9.791820 TTTTCACATTTTATGCACATCTAGATG 57.208 29.630 27.63 27.63 44.15 2.90
1997 11988 7.579589 CATCTAGATGTGCAATAACTAGAGC 57.420 40.000 22.42 0.00 41.37 4.09
1998 11989 6.715347 TCTAGATGTGCAATAACTAGAGCA 57.285 37.500 12.40 0.00 35.96 4.26
1999 11990 7.295322 TCTAGATGTGCAATAACTAGAGCAT 57.705 36.000 12.40 0.00 39.43 3.79
2000 11991 8.409358 TCTAGATGTGCAATAACTAGAGCATA 57.591 34.615 12.40 0.00 39.43 3.14
2001 11992 9.029368 TCTAGATGTGCAATAACTAGAGCATAT 57.971 33.333 12.40 2.60 40.71 1.78
2019 12010 9.033711 AGAGCATATCTAGATGTGACATTATGT 57.966 33.333 27.97 0.00 36.10 2.29
2041 12032 7.848223 TGTCAATAACTAGACATGACATTGG 57.152 36.000 15.93 0.00 43.79 3.16
2042 12033 7.394016 TGTCAATAACTAGACATGACATTGGT 58.606 34.615 15.93 0.00 43.79 3.67
2043 12034 7.334171 TGTCAATAACTAGACATGACATTGGTG 59.666 37.037 15.93 0.00 43.79 4.17
2044 12035 6.823182 TCAATAACTAGACATGACATTGGTGG 59.177 38.462 0.00 0.00 0.00 4.61
2045 12036 4.640771 AACTAGACATGACATTGGTGGT 57.359 40.909 0.00 0.00 0.00 4.16
2046 12037 4.207891 ACTAGACATGACATTGGTGGTC 57.792 45.455 0.00 0.00 35.83 4.02
2047 12038 2.099141 AGACATGACATTGGTGGTCG 57.901 50.000 0.00 0.00 38.10 4.79
2048 12039 0.447801 GACATGACATTGGTGGTCGC 59.552 55.000 0.00 0.00 38.10 5.19
2051 12042 2.047655 GACATTGGTGGTCGCCGA 60.048 61.111 0.00 0.00 0.00 5.54
2055 12046 2.332654 ATTGGTGGTCGCCGAAAGC 61.333 57.895 0.00 0.00 38.52 3.51
2056 12047 3.758973 TTGGTGGTCGCCGAAAGCA 62.759 57.895 0.00 0.00 44.04 3.91
2068 12059 3.418619 CGCCGAAAGCATGAAATAAATCG 59.581 43.478 0.00 0.00 44.04 3.34
2077 12068 9.956720 AAAGCATGAAATAAATCGAGGAATAAG 57.043 29.630 0.00 0.00 0.00 1.73
2082 12073 6.202188 TGAAATAAATCGAGGAATAAGGCGAC 59.798 38.462 0.00 0.00 35.44 5.19
2089 12080 1.564348 AGGAATAAGGCGACCACCAAT 59.436 47.619 0.00 0.00 0.00 3.16
2092 12083 2.038387 ATAAGGCGACCACCAATGTC 57.962 50.000 0.00 0.00 0.00 3.06
2100 12091 3.254060 CGACCACCAATGTCAAGTCTAG 58.746 50.000 0.00 0.00 32.91 2.43
2119 12110 1.903183 AGGACTTGAACTCTAGTGGGC 59.097 52.381 0.00 0.00 32.36 5.36
2121 12112 2.093921 GGACTTGAACTCTAGTGGGCTC 60.094 54.545 0.00 0.00 32.36 4.70
2124 12115 0.039180 TGAACTCTAGTGGGCTCGGA 59.961 55.000 0.00 0.00 0.00 4.55
2131 12122 4.534401 GTGGGCTCGGAATACCAC 57.466 61.111 8.91 8.91 45.56 4.16
2133 12124 3.619475 TGGGCTCGGAATACCACTA 57.381 52.632 0.00 0.00 35.59 2.74
2148 12139 7.093421 GGAATACCACTATCCTACTAACCATCC 60.093 44.444 0.00 0.00 35.97 3.51
2151 12142 5.365895 ACCACTATCCTACTAACCATCCAAC 59.634 44.000 0.00 0.00 0.00 3.77
2154 12145 4.772886 ATCCTACTAACCATCCAACCAC 57.227 45.455 0.00 0.00 0.00 4.16
2156 12147 3.517901 TCCTACTAACCATCCAACCACAG 59.482 47.826 0.00 0.00 0.00 3.66
2157 12148 2.879103 ACTAACCATCCAACCACAGG 57.121 50.000 0.00 0.00 0.00 4.00
2158 12149 2.062636 ACTAACCATCCAACCACAGGT 58.937 47.619 0.00 0.00 37.65 4.00
2192 12184 3.917380 TCTTTTCTTTGTTGTTGTGTGCG 59.083 39.130 0.00 0.00 0.00 5.34
2193 12185 2.270275 TTCTTTGTTGTTGTGTGCGG 57.730 45.000 0.00 0.00 0.00 5.69
2209 12201 0.249238 GCGGTCTAGTCATGCAGAGG 60.249 60.000 0.00 0.00 0.00 3.69
2211 12203 0.105778 GGTCTAGTCATGCAGAGGCC 59.894 60.000 0.00 0.00 40.13 5.19
2214 12206 1.381191 TAGTCATGCAGAGGCCGGA 60.381 57.895 5.05 0.00 40.13 5.14
2227 12219 1.082117 GGCCGGACATGTACTCGTTG 61.082 60.000 5.05 0.00 0.00 4.10
2229 12221 1.625616 CCGGACATGTACTCGTTGTC 58.374 55.000 6.49 2.72 0.00 3.18
2277 12269 8.780846 TTATGTGTCGATAAAAAGCTCCTTTA 57.219 30.769 0.00 4.04 31.99 1.85
2389 12382 4.730487 GCCATGTGAGTTGAGGCT 57.270 55.556 0.00 0.00 42.01 4.58
2392 12385 1.945394 GCCATGTGAGTTGAGGCTATG 59.055 52.381 0.00 0.00 42.01 2.23
2471 12464 6.866480 AGCAGATGAACTTCAGAAAAACAAA 58.134 32.000 0.00 0.00 0.00 2.83
2472 12465 6.753744 AGCAGATGAACTTCAGAAAAACAAAC 59.246 34.615 0.00 0.00 0.00 2.93
2473 12466 6.291269 GCAGATGAACTTCAGAAAAACAAACG 60.291 38.462 0.00 0.00 0.00 3.60
2474 12467 6.197096 CAGATGAACTTCAGAAAAACAAACGG 59.803 38.462 0.00 0.00 0.00 4.44
2475 12468 4.739195 TGAACTTCAGAAAAACAAACGGG 58.261 39.130 0.00 0.00 0.00 5.28
2476 12469 4.459685 TGAACTTCAGAAAAACAAACGGGA 59.540 37.500 0.00 0.00 0.00 5.14
2477 12470 5.047943 TGAACTTCAGAAAAACAAACGGGAA 60.048 36.000 0.00 0.00 0.00 3.97
2478 12471 5.592104 ACTTCAGAAAAACAAACGGGAAT 57.408 34.783 0.00 0.00 0.00 3.01
2479 12472 5.348164 ACTTCAGAAAAACAAACGGGAATG 58.652 37.500 0.00 0.00 0.00 2.67
2480 12473 4.993029 TCAGAAAAACAAACGGGAATGT 57.007 36.364 0.00 0.00 0.00 2.71
2481 12474 4.927422 TCAGAAAAACAAACGGGAATGTC 58.073 39.130 0.00 0.00 0.00 3.06
2483 12476 5.823570 TCAGAAAAACAAACGGGAATGTCTA 59.176 36.000 0.00 0.00 0.00 2.59
2484 12477 6.319152 TCAGAAAAACAAACGGGAATGTCTAA 59.681 34.615 0.00 0.00 0.00 2.10
2485 12478 6.636850 CAGAAAAACAAACGGGAATGTCTAAG 59.363 38.462 0.00 0.00 0.00 2.18
2486 12479 5.447624 AAAACAAACGGGAATGTCTAAGG 57.552 39.130 0.00 0.00 0.00 2.69
2487 12480 2.433436 ACAAACGGGAATGTCTAAGGC 58.567 47.619 0.00 0.00 0.00 4.35
2488 12481 2.224670 ACAAACGGGAATGTCTAAGGCA 60.225 45.455 0.00 0.00 0.00 4.75
2489 12482 2.109425 AACGGGAATGTCTAAGGCAC 57.891 50.000 0.00 0.00 0.00 5.01
2490 12483 0.981183 ACGGGAATGTCTAAGGCACA 59.019 50.000 0.00 0.00 0.00 4.57
2491 12484 1.559682 ACGGGAATGTCTAAGGCACAT 59.440 47.619 0.00 0.00 35.94 3.21
2492 12485 2.213499 CGGGAATGTCTAAGGCACATC 58.787 52.381 0.00 0.00 33.12 3.06
2493 12486 2.158900 CGGGAATGTCTAAGGCACATCT 60.159 50.000 0.00 0.00 33.12 2.90
2494 12487 3.069586 CGGGAATGTCTAAGGCACATCTA 59.930 47.826 0.00 0.00 33.12 1.98
2495 12488 4.636249 GGGAATGTCTAAGGCACATCTAG 58.364 47.826 0.00 0.00 33.12 2.43
2496 12489 4.345257 GGGAATGTCTAAGGCACATCTAGA 59.655 45.833 0.00 0.00 33.12 2.43
2497 12490 5.012561 GGGAATGTCTAAGGCACATCTAGAT 59.987 44.000 0.00 0.00 33.12 1.98
2498 12491 5.931146 GGAATGTCTAAGGCACATCTAGATG 59.069 44.000 27.63 27.63 44.15 2.90
2513 12506 5.215252 TCTAGATGTGCCCTACTTATTGC 57.785 43.478 0.00 0.00 0.00 3.56
2514 12507 3.931907 AGATGTGCCCTACTTATTGCA 57.068 42.857 0.00 0.00 0.00 4.08
2515 12508 4.443978 AGATGTGCCCTACTTATTGCAT 57.556 40.909 0.00 0.00 35.96 3.96
2516 12509 5.567037 AGATGTGCCCTACTTATTGCATA 57.433 39.130 0.00 0.00 35.96 3.14
2517 12510 6.131972 AGATGTGCCCTACTTATTGCATAT 57.868 37.500 0.00 0.00 38.10 1.78
2518 12511 6.176183 AGATGTGCCCTACTTATTGCATATC 58.824 40.000 10.77 10.77 46.39 1.63
2519 12512 5.567037 TGTGCCCTACTTATTGCATATCT 57.433 39.130 0.00 0.00 35.96 1.98
2520 12513 6.680148 TGTGCCCTACTTATTGCATATCTA 57.320 37.500 0.00 0.00 35.96 1.98
2521 12514 7.073457 TGTGCCCTACTTATTGCATATCTAA 57.927 36.000 0.00 0.00 35.96 2.10
2522 12515 7.161404 TGTGCCCTACTTATTGCATATCTAAG 58.839 38.462 0.00 0.00 35.96 2.18
2523 12516 7.162082 GTGCCCTACTTATTGCATATCTAAGT 58.838 38.462 12.94 12.94 38.75 2.24
2524 12517 7.118390 GTGCCCTACTTATTGCATATCTAAGTG 59.882 40.741 15.91 9.44 36.60 3.16
2525 12518 7.016170 TGCCCTACTTATTGCATATCTAAGTGA 59.984 37.037 15.91 5.61 36.60 3.41
2526 12519 7.547370 GCCCTACTTATTGCATATCTAAGTGAG 59.453 40.741 15.91 9.97 36.60 3.51
2527 12520 8.589338 CCCTACTTATTGCATATCTAAGTGAGT 58.411 37.037 15.91 0.00 36.60 3.41
2528 12521 9.416794 CCTACTTATTGCATATCTAAGTGAGTG 57.583 37.037 15.91 7.92 36.60 3.51
2536 12529 7.559486 TGCATATCTAAGTGAGTGAATCAAGT 58.441 34.615 0.00 0.00 40.43 3.16
2542 12535 9.814899 ATCTAAGTGAGTGAATCAAGTATGAAG 57.185 33.333 0.00 0.00 40.43 3.02
2548 12541 7.604164 GTGAGTGAATCAAGTATGAAGAGGAAA 59.396 37.037 0.00 0.00 40.43 3.13
2549 12542 8.156820 TGAGTGAATCAAGTATGAAGAGGAAAA 58.843 33.333 0.00 0.00 39.49 2.29
2550 12543 8.558973 AGTGAATCAAGTATGAAGAGGAAAAG 57.441 34.615 0.00 0.00 39.49 2.27
2551 12544 8.378565 AGTGAATCAAGTATGAAGAGGAAAAGA 58.621 33.333 0.00 0.00 39.49 2.52
2552 12545 9.003658 GTGAATCAAGTATGAAGAGGAAAAGAA 57.996 33.333 0.00 0.00 39.49 2.52
2553 12546 9.573166 TGAATCAAGTATGAAGAGGAAAAGAAA 57.427 29.630 0.00 0.00 39.49 2.52
2578 12571 9.810545 AAAAAGAAAAAGAAAATATCCACACGA 57.189 25.926 0.00 0.00 0.00 4.35
2579 12572 9.810545 AAAAGAAAAAGAAAATATCCACACGAA 57.189 25.926 0.00 0.00 0.00 3.85
2580 12573 9.981114 AAAGAAAAAGAAAATATCCACACGAAT 57.019 25.926 0.00 0.00 0.00 3.34
2581 12574 9.626045 AAGAAAAAGAAAATATCCACACGAATC 57.374 29.630 0.00 0.00 0.00 2.52
2582 12575 9.014297 AGAAAAAGAAAATATCCACACGAATCT 57.986 29.630 0.00 0.00 0.00 2.40
2583 12576 9.278734 GAAAAAGAAAATATCCACACGAATCTC 57.721 33.333 0.00 0.00 0.00 2.75
2585 12578 7.921786 AAGAAAATATCCACACGAATCTCAA 57.078 32.000 0.00 0.00 0.00 3.02
2586 12579 7.308782 AGAAAATATCCACACGAATCTCAAC 57.691 36.000 0.00 0.00 0.00 3.18
2587 12580 5.718649 AAATATCCACACGAATCTCAACG 57.281 39.130 0.00 0.00 0.00 4.10
2588 12581 2.743636 ATCCACACGAATCTCAACGT 57.256 45.000 0.00 0.00 43.50 3.99
2589 12582 3.861276 ATCCACACGAATCTCAACGTA 57.139 42.857 0.00 0.00 40.76 3.57
2590 12583 3.646611 TCCACACGAATCTCAACGTAA 57.353 42.857 0.00 0.00 40.76 3.18
2591 12584 3.571571 TCCACACGAATCTCAACGTAAG 58.428 45.455 0.00 0.00 40.76 2.34
2594 12587 4.265556 CCACACGAATCTCAACGTAAGATC 59.734 45.833 12.34 6.90 40.76 2.75
2595 12588 4.857037 CACACGAATCTCAACGTAAGATCA 59.143 41.667 12.34 0.00 40.76 2.92
2596 12589 5.344933 CACACGAATCTCAACGTAAGATCAA 59.655 40.000 12.34 0.00 40.76 2.57
2599 12592 6.253512 CACGAATCTCAACGTAAGATCAATGA 59.746 38.462 12.34 0.00 40.76 2.57
2600 12593 6.980978 ACGAATCTCAACGTAAGATCAATGAT 59.019 34.615 12.34 0.00 40.92 2.45
2601 12594 8.135529 ACGAATCTCAACGTAAGATCAATGATA 58.864 33.333 12.34 0.00 40.92 2.15
2628 12621 8.668510 AAGACTTAGATGTGCAATACTTATGG 57.331 34.615 0.00 0.00 0.00 2.74
2687 12721 9.295214 GAAAAACAAAGAAAAGAAGAGAGAAGG 57.705 33.333 0.00 0.00 0.00 3.46
2690 12724 8.581253 AACAAAGAAAAGAAGAGAGAAGGAAA 57.419 30.769 0.00 0.00 0.00 3.13
2691 12725 8.219546 ACAAAGAAAAGAAGAGAGAAGGAAAG 57.780 34.615 0.00 0.00 0.00 2.62
2692 12726 7.284261 ACAAAGAAAAGAAGAGAGAAGGAAAGG 59.716 37.037 0.00 0.00 0.00 3.11
2695 12729 7.394016 AGAAAAGAAGAGAGAAGGAAAGGATC 58.606 38.462 0.00 0.00 0.00 3.36
2696 12730 6.694445 AAAGAAGAGAGAAGGAAAGGATCA 57.306 37.500 0.00 0.00 0.00 2.92
2698 12732 6.048732 AGAAGAGAGAAGGAAAGGATCAAC 57.951 41.667 0.00 0.00 0.00 3.18
2699 12733 4.464069 AGAGAGAAGGAAAGGATCAACG 57.536 45.455 0.00 0.00 0.00 4.10
2701 12735 2.303022 AGAGAAGGAAAGGATCAACGCA 59.697 45.455 0.00 0.00 0.00 5.24
2702 12736 3.074412 GAGAAGGAAAGGATCAACGCAA 58.926 45.455 0.00 0.00 0.00 4.85
2704 12738 2.859165 AGGAAAGGATCAACGCAAGA 57.141 45.000 0.00 0.00 43.62 3.02
2705 12739 2.427506 AGGAAAGGATCAACGCAAGAC 58.572 47.619 0.00 0.00 43.62 3.01
2716 12750 3.241177 GCAAGACGAACGACCCAC 58.759 61.111 0.14 0.00 0.00 4.61
2717 12751 1.300697 GCAAGACGAACGACCCACT 60.301 57.895 0.14 0.00 0.00 4.00
2718 12752 0.038892 GCAAGACGAACGACCCACTA 60.039 55.000 0.14 0.00 0.00 2.74
2719 12753 1.694639 CAAGACGAACGACCCACTAC 58.305 55.000 0.14 0.00 0.00 2.73
2721 12755 0.879765 AGACGAACGACCCACTACAG 59.120 55.000 0.14 0.00 0.00 2.74
2722 12756 0.731855 GACGAACGACCCACTACAGC 60.732 60.000 0.14 0.00 0.00 4.40
2723 12757 1.287815 CGAACGACCCACTACAGCA 59.712 57.895 0.00 0.00 0.00 4.41
2724 12758 0.319211 CGAACGACCCACTACAGCAA 60.319 55.000 0.00 0.00 0.00 3.91
2725 12759 1.145803 GAACGACCCACTACAGCAAC 58.854 55.000 0.00 0.00 0.00 4.17
2726 12760 0.250166 AACGACCCACTACAGCAACC 60.250 55.000 0.00 0.00 0.00 3.77
2730 12764 0.249398 ACCCACTACAGCAACCGATC 59.751 55.000 0.00 0.00 0.00 3.69
2732 12766 1.338674 CCCACTACAGCAACCGATCAA 60.339 52.381 0.00 0.00 0.00 2.57
2734 12768 2.412870 CACTACAGCAACCGATCAACA 58.587 47.619 0.00 0.00 0.00 3.33
2735 12769 2.805671 CACTACAGCAACCGATCAACAA 59.194 45.455 0.00 0.00 0.00 2.83
2736 12770 3.436704 CACTACAGCAACCGATCAACAAT 59.563 43.478 0.00 0.00 0.00 2.71
2737 12771 4.072131 ACTACAGCAACCGATCAACAATT 58.928 39.130 0.00 0.00 0.00 2.32
2738 12772 5.121611 CACTACAGCAACCGATCAACAATTA 59.878 40.000 0.00 0.00 0.00 1.40
2741 12775 3.190327 CAGCAACCGATCAACAATTACCA 59.810 43.478 0.00 0.00 0.00 3.25
2743 12777 3.672241 GCAACCGATCAACAATTACCACC 60.672 47.826 0.00 0.00 0.00 4.61
2745 12779 2.289819 ACCGATCAACAATTACCACCGT 60.290 45.455 0.00 0.00 0.00 4.83
2746 12780 2.350498 CCGATCAACAATTACCACCGTC 59.650 50.000 0.00 0.00 0.00 4.79
2747 12781 2.028763 CGATCAACAATTACCACCGTCG 59.971 50.000 0.00 0.00 0.00 5.12
2748 12782 2.529780 TCAACAATTACCACCGTCGT 57.470 45.000 0.00 0.00 0.00 4.34
2751 12785 2.529780 ACAATTACCACCGTCGTTGA 57.470 45.000 0.00 0.00 0.00 3.18
2752 12786 2.137523 ACAATTACCACCGTCGTTGAC 58.862 47.619 0.00 0.00 0.00 3.18
2753 12787 2.136728 CAATTACCACCGTCGTTGACA 58.863 47.619 0.00 0.00 32.09 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 235 2.474526 GCGAATGTCGACATGAAACTGG 60.475 50.000 30.57 16.72 43.74 4.00
172 310 1.252904 TGATTTGCTTGAGCCCTGCC 61.253 55.000 0.00 0.00 41.18 4.85
312 460 0.386731 GGTTTGGCGATTTGACACCG 60.387 55.000 0.00 0.00 32.88 4.94
567 6370 0.462047 CATGGCCGACTTGGAGGTAC 60.462 60.000 0.00 0.00 42.00 3.34
581 6384 3.635373 ACAATGACATCATTCCTCATGGC 59.365 43.478 4.08 0.00 44.10 4.40
590 6393 3.365264 GCGTGTGTGACAATGACATCATT 60.365 43.478 1.11 1.11 46.62 2.57
592 6395 1.530720 GCGTGTGTGACAATGACATCA 59.469 47.619 0.00 0.00 0.00 3.07
593 6396 1.800586 AGCGTGTGTGACAATGACATC 59.199 47.619 0.00 0.00 0.00 3.06
594 6397 1.882912 AGCGTGTGTGACAATGACAT 58.117 45.000 0.00 0.00 0.00 3.06
595 6398 1.597195 GAAGCGTGTGTGACAATGACA 59.403 47.619 0.00 0.00 0.00 3.58
596 6399 1.069906 GGAAGCGTGTGTGACAATGAC 60.070 52.381 0.00 0.00 0.00 3.06
597 6400 1.225855 GGAAGCGTGTGTGACAATGA 58.774 50.000 0.00 0.00 0.00 2.57
598 6401 0.943673 TGGAAGCGTGTGTGACAATG 59.056 50.000 0.00 0.00 0.00 2.82
599 6402 0.944386 GTGGAAGCGTGTGTGACAAT 59.056 50.000 0.00 0.00 0.00 2.71
600 6403 0.391793 TGTGGAAGCGTGTGTGACAA 60.392 50.000 0.00 0.00 0.00 3.18
638 10479 1.673928 ATCCAGGGGAGGAGCTAGCT 61.674 60.000 19.45 19.45 41.90 3.32
639 10480 1.152139 ATCCAGGGGAGGAGCTAGC 60.152 63.158 6.62 6.62 41.90 3.42
654 10495 0.462759 CTGCCTCGGAAGGTTGATCC 60.463 60.000 0.00 0.00 45.34 3.36
658 10499 2.747855 GGCTGCCTCGGAAGGTTG 60.748 66.667 12.43 0.00 45.34 3.77
840 10731 8.059798 AGACTTTGATCACCATTCCATTAAAG 57.940 34.615 0.00 0.00 32.23 1.85
934 10829 1.341531 CCAAGACTTGGTCTGTCGACT 59.658 52.381 23.92 0.00 42.59 4.18
947 10845 1.609794 GGAGGGGTCGACCAAGACT 60.610 63.158 34.40 24.80 42.91 3.24
1152 11066 0.588252 CTGGTTTGTTCCTCGCTGTG 59.412 55.000 0.00 0.00 0.00 3.66
1284 11201 3.884900 GCGTCTGCGTACCCAAAT 58.115 55.556 0.00 0.00 40.81 2.32
1360 11281 1.595466 GCCATCTGCTTCTCCATCTG 58.405 55.000 0.00 0.00 36.87 2.90
1364 11285 2.586245 CCGCCATCTGCTTCTCCA 59.414 61.111 0.00 0.00 38.05 3.86
1472 11400 2.420022 CTCGACATCACCCAATCCAAAC 59.580 50.000 0.00 0.00 0.00 2.93
1483 11411 2.857152 GAGCTCATCAACTCGACATCAC 59.143 50.000 9.40 0.00 0.00 3.06
1489 11424 2.441410 ACTCAGAGCTCATCAACTCGA 58.559 47.619 17.77 0.00 37.99 4.04
1558 11495 4.762251 CCATAGTTGGGAGCTAATTAAGGC 59.238 45.833 0.00 0.00 39.56 4.35
1576 11515 5.523916 GGTGATGCTGTTTACAGTACCATAG 59.476 44.000 11.23 0.00 45.45 2.23
1655 11602 5.351465 ACATTAACATCTAACAGTGCCTTCG 59.649 40.000 0.00 0.00 0.00 3.79
1750 11697 2.157668 CGCCATATATTGTCGGCAGAAC 59.842 50.000 11.25 0.00 45.14 3.01
1761 11708 8.259411 TGGAATTACGGTATTACGCCATATATT 58.741 33.333 0.00 0.00 37.37 1.28
1799 11790 4.569966 CAGTGTGAGATGAATAGAAGTGCC 59.430 45.833 0.00 0.00 0.00 5.01
1842 11833 7.014711 TCTCTGAGAAAAACACAGTAGAGACAT 59.985 37.037 4.57 0.00 38.15 3.06
1880 11871 7.119116 TGTGATCAACGTTAGCATAGTTTCATT 59.881 33.333 0.00 0.00 0.00 2.57
1907 11898 9.520515 AGTGTGAAATGAAAAGTAGAATATGGT 57.479 29.630 0.00 0.00 0.00 3.55
1927 11918 9.391006 ACAGTAGAGTTTAAATGAAAAGTGTGA 57.609 29.630 0.00 0.00 0.00 3.58
1928 11919 9.438291 CACAGTAGAGTTTAAATGAAAAGTGTG 57.562 33.333 11.02 11.02 32.88 3.82
1929 11920 9.174166 ACACAGTAGAGTTTAAATGAAAAGTGT 57.826 29.630 0.00 0.00 0.00 3.55
1953 11944 9.409312 CTAGATGTGCATAAAATGTGAAAAACA 57.591 29.630 0.00 0.00 44.79 2.83
1954 11945 9.624697 TCTAGATGTGCATAAAATGTGAAAAAC 57.375 29.630 0.00 0.00 0.00 2.43
1956 11947 9.791820 CATCTAGATGTGCATAAAATGTGAAAA 57.208 29.630 22.42 0.00 34.23 2.29
1973 11964 7.150640 TGCTCTAGTTATTGCACATCTAGATG 58.849 38.462 27.63 27.63 44.15 2.90
1974 11965 7.295322 TGCTCTAGTTATTGCACATCTAGAT 57.705 36.000 0.00 0.00 37.20 1.98
1975 11966 6.715347 TGCTCTAGTTATTGCACATCTAGA 57.285 37.500 0.00 0.00 36.64 2.43
1976 11967 9.299963 GATATGCTCTAGTTATTGCACATCTAG 57.700 37.037 0.00 0.00 36.69 2.43
1977 11968 9.029368 AGATATGCTCTAGTTATTGCACATCTA 57.971 33.333 5.90 0.00 44.54 1.98
1978 11969 7.905265 AGATATGCTCTAGTTATTGCACATCT 58.095 34.615 2.31 2.31 42.53 2.90
1979 11970 9.299963 CTAGATATGCTCTAGTTATTGCACATC 57.700 37.037 0.00 0.00 45.79 3.06
1993 11984 9.033711 ACATAATGTCACATCTAGATATGCTCT 57.966 33.333 6.10 0.00 38.06 4.09
1994 11985 9.299963 GACATAATGTCACATCTAGATATGCTC 57.700 37.037 6.10 3.13 46.22 4.26
2018 12009 7.201644 CCACCAATGTCATGTCTAGTTATTGAC 60.202 40.741 0.00 9.42 37.73 3.18
2019 12010 6.823182 CCACCAATGTCATGTCTAGTTATTGA 59.177 38.462 0.00 0.00 0.00 2.57
2020 12011 6.599244 ACCACCAATGTCATGTCTAGTTATTG 59.401 38.462 0.00 0.00 0.00 1.90
2021 12012 6.721318 ACCACCAATGTCATGTCTAGTTATT 58.279 36.000 0.00 0.00 0.00 1.40
2022 12013 6.313519 ACCACCAATGTCATGTCTAGTTAT 57.686 37.500 0.00 0.00 0.00 1.89
2023 12014 5.623596 CGACCACCAATGTCATGTCTAGTTA 60.624 44.000 0.00 0.00 32.91 2.24
2024 12015 4.579869 GACCACCAATGTCATGTCTAGTT 58.420 43.478 0.00 0.00 32.91 2.24
2025 12016 3.368427 CGACCACCAATGTCATGTCTAGT 60.368 47.826 0.00 0.00 32.91 2.57
2026 12017 3.190079 CGACCACCAATGTCATGTCTAG 58.810 50.000 0.00 0.00 32.91 2.43
2027 12018 2.676750 GCGACCACCAATGTCATGTCTA 60.677 50.000 0.00 0.00 32.91 2.59
2028 12019 1.945819 GCGACCACCAATGTCATGTCT 60.946 52.381 0.00 0.00 32.91 3.41
2029 12020 0.447801 GCGACCACCAATGTCATGTC 59.552 55.000 0.00 0.00 32.91 3.06
2030 12021 0.960364 GGCGACCACCAATGTCATGT 60.960 55.000 0.00 0.00 32.91 3.21
2031 12022 1.802636 GGCGACCACCAATGTCATG 59.197 57.895 0.00 0.00 32.91 3.07
2032 12023 1.745115 CGGCGACCACCAATGTCAT 60.745 57.895 0.00 0.00 32.91 3.06
2033 12024 2.358125 CGGCGACCACCAATGTCA 60.358 61.111 0.00 0.00 32.91 3.58
2034 12025 1.231958 TTTCGGCGACCACCAATGTC 61.232 55.000 10.16 0.00 0.00 3.06
2035 12026 1.228003 TTTCGGCGACCACCAATGT 60.228 52.632 10.16 0.00 0.00 2.71
2036 12027 1.501741 CTTTCGGCGACCACCAATG 59.498 57.895 10.16 0.00 0.00 2.82
2037 12028 2.332654 GCTTTCGGCGACCACCAAT 61.333 57.895 10.16 0.00 0.00 3.16
2038 12029 2.975799 GCTTTCGGCGACCACCAA 60.976 61.111 10.16 0.00 0.00 3.67
2039 12030 3.545124 ATGCTTTCGGCGACCACCA 62.545 57.895 10.16 5.05 45.43 4.17
2040 12031 2.746277 ATGCTTTCGGCGACCACC 60.746 61.111 10.16 0.00 45.43 4.61
2041 12032 1.573829 TTCATGCTTTCGGCGACCAC 61.574 55.000 10.16 1.59 45.43 4.16
2042 12033 0.886938 TTTCATGCTTTCGGCGACCA 60.887 50.000 10.16 7.90 45.43 4.02
2043 12034 0.451783 ATTTCATGCTTTCGGCGACC 59.548 50.000 10.16 1.19 45.43 4.79
2044 12035 3.398954 TTATTTCATGCTTTCGGCGAC 57.601 42.857 10.16 0.00 45.43 5.19
2045 12036 4.597079 GATTTATTTCATGCTTTCGGCGA 58.403 39.130 4.99 4.99 45.43 5.54
2046 12037 3.418619 CGATTTATTTCATGCTTTCGGCG 59.581 43.478 0.00 0.00 45.43 6.46
2047 12038 4.597079 TCGATTTATTTCATGCTTTCGGC 58.403 39.130 0.00 0.00 42.22 5.54
2048 12039 5.007626 TCCTCGATTTATTTCATGCTTTCGG 59.992 40.000 0.00 0.00 0.00 4.30
2051 12042 9.956720 CTTATTCCTCGATTTATTTCATGCTTT 57.043 29.630 0.00 0.00 0.00 3.51
2055 12046 7.017645 CGCCTTATTCCTCGATTTATTTCATG 58.982 38.462 0.00 0.00 0.00 3.07
2056 12047 6.934645 TCGCCTTATTCCTCGATTTATTTCAT 59.065 34.615 0.00 0.00 0.00 2.57
2068 12059 0.539986 TGGTGGTCGCCTTATTCCTC 59.460 55.000 2.07 0.00 0.00 3.71
2077 12068 0.889186 ACTTGACATTGGTGGTCGCC 60.889 55.000 0.00 0.00 38.10 5.54
2082 12073 3.261897 AGTCCTAGACTTGACATTGGTGG 59.738 47.826 0.00 0.00 40.28 4.61
2100 12091 1.903183 AGCCCACTAGAGTTCAAGTCC 59.097 52.381 0.00 0.00 0.00 3.85
2106 12097 1.183549 TTCCGAGCCCACTAGAGTTC 58.816 55.000 0.00 0.00 0.00 3.01
2119 12110 6.150809 GGTTAGTAGGATAGTGGTATTCCGAG 59.849 46.154 0.00 0.00 36.30 4.63
2121 12112 5.771666 TGGTTAGTAGGATAGTGGTATTCCG 59.228 44.000 0.00 0.00 36.30 4.30
2124 12115 7.310634 TGGATGGTTAGTAGGATAGTGGTATT 58.689 38.462 0.00 0.00 0.00 1.89
2131 12122 5.365605 TGTGGTTGGATGGTTAGTAGGATAG 59.634 44.000 0.00 0.00 0.00 2.08
2133 12124 4.108570 TGTGGTTGGATGGTTAGTAGGAT 58.891 43.478 0.00 0.00 0.00 3.24
2154 12145 0.385390 AAGAAGCGCAAACCAACCTG 59.615 50.000 11.47 0.00 0.00 4.00
2156 12147 1.858458 GAAAAGAAGCGCAAACCAACC 59.142 47.619 11.47 0.00 0.00 3.77
2157 12148 2.809446 AGAAAAGAAGCGCAAACCAAC 58.191 42.857 11.47 0.00 0.00 3.77
2158 12149 3.518634 AAGAAAAGAAGCGCAAACCAA 57.481 38.095 11.47 0.00 0.00 3.67
2159 12150 3.186119 CAAAGAAAAGAAGCGCAAACCA 58.814 40.909 11.47 0.00 0.00 3.67
2160 12151 3.186909 ACAAAGAAAAGAAGCGCAAACC 58.813 40.909 11.47 0.00 0.00 3.27
2164 12155 3.502191 ACAACAAAGAAAAGAAGCGCA 57.498 38.095 11.47 0.00 0.00 6.09
2167 12158 5.668621 GCACACAACAACAAAGAAAAGAAGC 60.669 40.000 0.00 0.00 0.00 3.86
2192 12184 0.105778 GGCCTCTGCATGACTAGACC 59.894 60.000 0.00 0.00 40.13 3.85
2193 12185 0.249238 CGGCCTCTGCATGACTAGAC 60.249 60.000 0.00 0.00 40.13 2.59
2209 12201 0.389426 ACAACGAGTACATGTCCGGC 60.389 55.000 0.00 0.00 0.00 6.13
2214 12206 3.746045 ACAAGGACAACGAGTACATGT 57.254 42.857 2.69 2.69 38.14 3.21
2227 12219 9.553064 AATATCACATCAAGAGAATACAAGGAC 57.447 33.333 0.00 0.00 0.00 3.85
2268 12260 7.923414 AGTTGTATTTTTCGATAAAGGAGCT 57.077 32.000 7.13 0.00 0.00 4.09
2296 12288 3.058224 GTCACACCAAAGCAATACTCACC 60.058 47.826 0.00 0.00 0.00 4.02
2298 12290 3.814625 TGTCACACCAAAGCAATACTCA 58.185 40.909 0.00 0.00 0.00 3.41
2303 12295 2.694628 ACACATGTCACACCAAAGCAAT 59.305 40.909 0.00 0.00 0.00 3.56
2357 12350 6.888632 ACTCACATGGCTAATTTTCAGATCTT 59.111 34.615 0.00 0.00 0.00 2.40
2389 12382 9.693739 AAATCCATTTACACACAGGATTACATA 57.306 29.630 5.52 0.00 45.61 2.29
2392 12385 8.050778 TCAAATCCATTTACACACAGGATTAC 57.949 34.615 5.52 0.00 45.61 1.89
2471 12464 0.981183 TGTGCCTTAGACATTCCCGT 59.019 50.000 0.00 0.00 0.00 5.28
2472 12465 2.158900 AGATGTGCCTTAGACATTCCCG 60.159 50.000 0.00 0.00 34.10 5.14
2473 12466 3.567478 AGATGTGCCTTAGACATTCCC 57.433 47.619 0.00 0.00 34.10 3.97
2474 12467 5.537300 TCTAGATGTGCCTTAGACATTCC 57.463 43.478 0.00 0.00 34.10 3.01
2489 12482 5.641209 GCAATAAGTAGGGCACATCTAGATG 59.359 44.000 27.63 27.63 44.15 2.90
2490 12483 5.307976 TGCAATAAGTAGGGCACATCTAGAT 59.692 40.000 0.00 0.00 0.00 1.98
2491 12484 4.653801 TGCAATAAGTAGGGCACATCTAGA 59.346 41.667 0.00 0.00 0.00 2.43
2492 12485 4.960938 TGCAATAAGTAGGGCACATCTAG 58.039 43.478 0.00 0.00 0.00 2.43
2493 12486 5.567037 ATGCAATAAGTAGGGCACATCTA 57.433 39.130 0.00 0.00 39.34 1.98
2494 12487 3.931907 TGCAATAAGTAGGGCACATCT 57.068 42.857 0.00 0.00 0.00 2.90
2495 12488 6.176183 AGATATGCAATAAGTAGGGCACATC 58.824 40.000 0.00 0.00 39.73 3.06
2496 12489 6.131972 AGATATGCAATAAGTAGGGCACAT 57.868 37.500 0.00 0.00 39.34 3.21
2497 12490 5.567037 AGATATGCAATAAGTAGGGCACA 57.433 39.130 0.00 0.00 39.34 4.57
2498 12491 7.118390 CACTTAGATATGCAATAAGTAGGGCAC 59.882 40.741 13.38 0.00 37.59 5.01
2499 12492 7.016170 TCACTTAGATATGCAATAAGTAGGGCA 59.984 37.037 13.38 0.00 37.59 5.36
2500 12493 7.386851 TCACTTAGATATGCAATAAGTAGGGC 58.613 38.462 13.38 0.00 37.59 5.19
2501 12494 8.589338 ACTCACTTAGATATGCAATAAGTAGGG 58.411 37.037 13.38 11.21 37.59 3.53
2502 12495 9.416794 CACTCACTTAGATATGCAATAAGTAGG 57.583 37.037 13.38 11.78 37.59 3.18
2509 12502 8.969260 TTGATTCACTCACTTAGATATGCAAT 57.031 30.769 0.00 0.00 32.17 3.56
2510 12503 8.043113 ACTTGATTCACTCACTTAGATATGCAA 58.957 33.333 0.00 0.00 32.17 4.08
2511 12504 7.559486 ACTTGATTCACTCACTTAGATATGCA 58.441 34.615 0.00 0.00 32.17 3.96
2512 12505 9.703892 ATACTTGATTCACTCACTTAGATATGC 57.296 33.333 0.00 0.00 32.17 3.14
2516 12509 9.814899 CTTCATACTTGATTCACTCACTTAGAT 57.185 33.333 0.00 0.00 32.17 1.98
2517 12510 9.025041 TCTTCATACTTGATTCACTCACTTAGA 57.975 33.333 0.00 0.00 32.17 2.10
2518 12511 9.299963 CTCTTCATACTTGATTCACTCACTTAG 57.700 37.037 0.00 0.00 32.17 2.18
2519 12512 8.253810 CCTCTTCATACTTGATTCACTCACTTA 58.746 37.037 0.00 0.00 32.17 2.24
2520 12513 7.038729 TCCTCTTCATACTTGATTCACTCACTT 60.039 37.037 0.00 0.00 32.17 3.16
2521 12514 6.438741 TCCTCTTCATACTTGATTCACTCACT 59.561 38.462 0.00 0.00 32.17 3.41
2522 12515 6.634805 TCCTCTTCATACTTGATTCACTCAC 58.365 40.000 0.00 0.00 32.17 3.51
2523 12516 6.857437 TCCTCTTCATACTTGATTCACTCA 57.143 37.500 0.00 0.00 0.00 3.41
2524 12517 8.553459 TTTTCCTCTTCATACTTGATTCACTC 57.447 34.615 0.00 0.00 0.00 3.51
2525 12518 8.378565 TCTTTTCCTCTTCATACTTGATTCACT 58.621 33.333 0.00 0.00 0.00 3.41
2526 12519 8.553459 TCTTTTCCTCTTCATACTTGATTCAC 57.447 34.615 0.00 0.00 0.00 3.18
2527 12520 9.573166 TTTCTTTTCCTCTTCATACTTGATTCA 57.427 29.630 0.00 0.00 0.00 2.57
2552 12545 9.810545 TCGTGTGGATATTTTCTTTTTCTTTTT 57.189 25.926 0.00 0.00 0.00 1.94
2553 12546 9.810545 TTCGTGTGGATATTTTCTTTTTCTTTT 57.189 25.926 0.00 0.00 0.00 2.27
2554 12547 9.981114 ATTCGTGTGGATATTTTCTTTTTCTTT 57.019 25.926 0.00 0.00 0.00 2.52
2555 12548 9.626045 GATTCGTGTGGATATTTTCTTTTTCTT 57.374 29.630 0.00 0.00 0.00 2.52
2558 12551 8.792633 TGAGATTCGTGTGGATATTTTCTTTTT 58.207 29.630 0.00 0.00 0.00 1.94
2560 12553 7.921786 TGAGATTCGTGTGGATATTTTCTTT 57.078 32.000 0.00 0.00 0.00 2.52
2562 12555 6.036083 CGTTGAGATTCGTGTGGATATTTTCT 59.964 38.462 0.00 0.00 0.00 2.52
2563 12556 6.183360 ACGTTGAGATTCGTGTGGATATTTTC 60.183 38.462 0.00 0.00 38.85 2.29
2564 12557 5.642063 ACGTTGAGATTCGTGTGGATATTTT 59.358 36.000 0.00 0.00 38.85 1.82
2566 12559 4.755411 ACGTTGAGATTCGTGTGGATATT 58.245 39.130 0.00 0.00 38.85 1.28
2567 12560 4.386867 ACGTTGAGATTCGTGTGGATAT 57.613 40.909 0.00 0.00 38.85 1.63
2569 12562 2.743636 ACGTTGAGATTCGTGTGGAT 57.256 45.000 0.00 0.00 38.85 3.41
2570 12563 3.253921 TCTTACGTTGAGATTCGTGTGGA 59.746 43.478 0.00 0.00 40.50 4.02
2572 12565 4.857037 TGATCTTACGTTGAGATTCGTGTG 59.143 41.667 13.35 0.00 40.50 3.82
2573 12566 5.055642 TGATCTTACGTTGAGATTCGTGT 57.944 39.130 13.35 0.00 40.50 4.49
2576 12569 6.812481 TCATTGATCTTACGTTGAGATTCG 57.188 37.500 13.35 5.46 34.13 3.34
2603 12596 7.227512 GCCATAAGTATTGCACATCTAAGTCTT 59.772 37.037 0.00 0.00 0.00 3.01
2604 12597 6.708054 GCCATAAGTATTGCACATCTAAGTCT 59.292 38.462 0.00 0.00 0.00 3.24
2605 12598 6.483307 TGCCATAAGTATTGCACATCTAAGTC 59.517 38.462 0.00 0.00 30.49 3.01
2606 12599 6.356556 TGCCATAAGTATTGCACATCTAAGT 58.643 36.000 0.00 0.00 30.49 2.24
2615 12608 6.173427 TCTAGATGTGCCATAAGTATTGCA 57.827 37.500 0.00 0.00 32.69 4.08
2616 12609 7.069852 CATCTAGATGTGCCATAAGTATTGC 57.930 40.000 22.42 0.00 34.23 3.56
2642 12635 8.652463 TGTTTTTCTTTACAGTTTTGCTAAAGC 58.348 29.630 0.00 0.00 42.50 3.51
2646 12639 9.915629 TCTTTGTTTTTCTTTACAGTTTTGCTA 57.084 25.926 0.00 0.00 0.00 3.49
2648 12641 9.871299 TTTCTTTGTTTTTCTTTACAGTTTTGC 57.129 25.926 0.00 0.00 0.00 3.68
2661 12654 9.295214 CCTTCTCTCTTCTTTTCTTTGTTTTTC 57.705 33.333 0.00 0.00 0.00 2.29
2663 12656 8.581253 TCCTTCTCTCTTCTTTTCTTTGTTTT 57.419 30.769 0.00 0.00 0.00 2.43
2664 12657 8.581253 TTCCTTCTCTCTTCTTTTCTTTGTTT 57.419 30.769 0.00 0.00 0.00 2.83
2667 12701 7.500559 TCCTTTCCTTCTCTCTTCTTTTCTTTG 59.499 37.037 0.00 0.00 0.00 2.77
2681 12715 2.699954 TGCGTTGATCCTTTCCTTCTC 58.300 47.619 0.00 0.00 0.00 2.87
2682 12716 2.859165 TGCGTTGATCCTTTCCTTCT 57.141 45.000 0.00 0.00 0.00 2.85
2683 12717 3.074412 TCTTGCGTTGATCCTTTCCTTC 58.926 45.455 0.00 0.00 0.00 3.46
2684 12718 2.814336 GTCTTGCGTTGATCCTTTCCTT 59.186 45.455 0.00 0.00 0.00 3.36
2686 12720 1.128692 CGTCTTGCGTTGATCCTTTCC 59.871 52.381 0.00 0.00 35.54 3.13
2687 12721 2.066262 TCGTCTTGCGTTGATCCTTTC 58.934 47.619 0.00 0.00 42.13 2.62
2690 12724 1.429463 GTTCGTCTTGCGTTGATCCT 58.571 50.000 0.00 0.00 42.13 3.24
2691 12725 0.093026 CGTTCGTCTTGCGTTGATCC 59.907 55.000 0.00 0.00 42.13 3.36
2692 12726 1.057636 TCGTTCGTCTTGCGTTGATC 58.942 50.000 0.00 0.00 42.13 2.92
2695 12729 1.200839 GGTCGTTCGTCTTGCGTTG 59.799 57.895 0.00 0.00 42.13 4.10
2696 12730 1.952635 GGGTCGTTCGTCTTGCGTT 60.953 57.895 0.00 0.00 42.13 4.84
2698 12732 2.355363 TGGGTCGTTCGTCTTGCG 60.355 61.111 0.00 0.00 43.01 4.85
2699 12733 0.038892 TAGTGGGTCGTTCGTCTTGC 60.039 55.000 0.00 0.00 0.00 4.01
2701 12735 1.268899 CTGTAGTGGGTCGTTCGTCTT 59.731 52.381 0.00 0.00 0.00 3.01
2702 12736 0.879765 CTGTAGTGGGTCGTTCGTCT 59.120 55.000 0.00 0.00 0.00 4.18
2703 12737 0.731855 GCTGTAGTGGGTCGTTCGTC 60.732 60.000 0.00 0.00 0.00 4.20
2704 12738 1.288127 GCTGTAGTGGGTCGTTCGT 59.712 57.895 0.00 0.00 0.00 3.85
2705 12739 0.319211 TTGCTGTAGTGGGTCGTTCG 60.319 55.000 0.00 0.00 0.00 3.95
2706 12740 1.145803 GTTGCTGTAGTGGGTCGTTC 58.854 55.000 0.00 0.00 0.00 3.95
2707 12741 0.250166 GGTTGCTGTAGTGGGTCGTT 60.250 55.000 0.00 0.00 0.00 3.85
2708 12742 1.370064 GGTTGCTGTAGTGGGTCGT 59.630 57.895 0.00 0.00 0.00 4.34
2709 12743 1.736645 CGGTTGCTGTAGTGGGTCG 60.737 63.158 0.00 0.00 0.00 4.79
2710 12744 0.249398 ATCGGTTGCTGTAGTGGGTC 59.751 55.000 0.00 0.00 0.00 4.46
2711 12745 0.249398 GATCGGTTGCTGTAGTGGGT 59.751 55.000 0.00 0.00 0.00 4.51
2712 12746 0.249120 TGATCGGTTGCTGTAGTGGG 59.751 55.000 0.00 0.00 0.00 4.61
2713 12747 1.732259 GTTGATCGGTTGCTGTAGTGG 59.268 52.381 0.00 0.00 0.00 4.00
2714 12748 2.412870 TGTTGATCGGTTGCTGTAGTG 58.587 47.619 0.00 0.00 0.00 2.74
2715 12749 2.831685 TGTTGATCGGTTGCTGTAGT 57.168 45.000 0.00 0.00 0.00 2.73
2716 12750 4.685169 AATTGTTGATCGGTTGCTGTAG 57.315 40.909 0.00 0.00 0.00 2.74
2717 12751 4.393680 GGTAATTGTTGATCGGTTGCTGTA 59.606 41.667 0.00 0.00 0.00 2.74
2718 12752 3.190535 GGTAATTGTTGATCGGTTGCTGT 59.809 43.478 0.00 0.00 0.00 4.40
2719 12753 3.190327 TGGTAATTGTTGATCGGTTGCTG 59.810 43.478 0.00 0.00 0.00 4.41
2721 12755 3.498082 GTGGTAATTGTTGATCGGTTGC 58.502 45.455 0.00 0.00 0.00 4.17
2722 12756 3.425625 CGGTGGTAATTGTTGATCGGTTG 60.426 47.826 0.00 0.00 0.00 3.77
2723 12757 2.745281 CGGTGGTAATTGTTGATCGGTT 59.255 45.455 0.00 0.00 0.00 4.44
2724 12758 2.289819 ACGGTGGTAATTGTTGATCGGT 60.290 45.455 0.00 0.00 0.00 4.69
2725 12759 2.350498 GACGGTGGTAATTGTTGATCGG 59.650 50.000 0.00 0.00 0.00 4.18
2726 12760 2.028763 CGACGGTGGTAATTGTTGATCG 59.971 50.000 0.00 0.00 0.00 3.69
2730 12764 2.544686 TCAACGACGGTGGTAATTGTTG 59.455 45.455 13.91 0.00 37.23 3.33
2732 12766 2.137523 GTCAACGACGGTGGTAATTGT 58.862 47.619 13.91 0.00 0.00 2.71
2734 12768 2.529780 TGTCAACGACGGTGGTAATT 57.470 45.000 13.91 0.00 34.95 1.40


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

AutoCloner maintained by Alex Coulton.