Multiple sequence alignment - TraesCS1A01G118400

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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 TraesCS1A01G118400 chr1A 100.000 3633 0 0 1 3633 127078643 127075011 0.000000e+00 6709.0
1 TraesCS1A01G118400 chr1A 100.000 421 0 0 3975 4395 127074669 127074249 0.000000e+00 778.0
2 TraesCS1A01G118400 chr1D 94.102 2204 60 25 1 2180 116006398 116004241 0.000000e+00 3286.0
3 TraesCS1A01G118400 chr1D 95.592 1157 42 3 2297 3451 116004120 116002971 0.000000e+00 1845.0
4 TraesCS1A01G118400 chr1D 91.489 94 3 2 2177 2266 116004209 116004117 1.660000e-24 124.0
5 TraesCS1A01G118400 chr1D 83.838 99 9 3 3450 3546 454458912 454458819 2.180000e-13 87.9
6 TraesCS1A01G118400 chr1B 93.858 2133 76 22 65 2180 177839288 177837194 0.000000e+00 3162.0
7 TraesCS1A01G118400 chr1B 95.311 1301 45 7 2177 3470 177837162 177835871 0.000000e+00 2050.0
8 TraesCS1A01G118400 chr1B 87.665 227 28 0 4166 4392 651293419 651293193 9.370000e-67 265.0
9 TraesCS1A01G118400 chr1B 88.830 188 21 0 4050 4237 177835184 177834997 9.510000e-57 231.0
10 TraesCS1A01G118400 chr1B 91.209 91 4 2 3547 3633 436689115 436689025 2.150000e-23 121.0
11 TraesCS1A01G118400 chr1B 90.217 92 4 3 3547 3633 601106867 601106776 9.990000e-22 115.0
12 TraesCS1A01G118400 chr1B 84.158 101 8 3 3448 3546 6543495 6543401 1.680000e-14 91.6
13 TraesCS1A01G118400 chr4B 82.656 369 41 10 4047 4394 548766315 548765949 5.520000e-79 305.0
14 TraesCS1A01G118400 chr4D 82.466 365 43 9 4050 4394 441900398 441900035 2.570000e-77 300.0
15 TraesCS1A01G118400 chr4D 86.869 99 6 4 3450 3546 117421191 117421284 2.160000e-18 104.0
16 TraesCS1A01G118400 chr6D 88.106 227 27 0 4166 4392 220294784 220295010 2.010000e-68 270.0
17 TraesCS1A01G118400 chr5D 88.158 228 26 1 4166 4392 218611996 218612223 2.010000e-68 270.0
18 TraesCS1A01G118400 chr5D 90.000 90 5 2 3547 3632 412100133 412100222 3.590000e-21 113.0
19 TraesCS1A01G118400 chr5D 95.238 63 3 0 1753 1815 66756451 66756513 2.800000e-17 100.0
20 TraesCS1A01G118400 chr5D 84.375 96 15 0 1720 1815 457777221 457777316 1.300000e-15 95.3
21 TraesCS1A01G118400 chr2D 80.822 365 50 11 4050 4394 83552696 83553060 7.250000e-68 268.0
22 TraesCS1A01G118400 chr2D 80.845 355 54 9 4050 4392 10816649 10816297 2.610000e-67 267.0
23 TraesCS1A01G118400 chr3D 87.946 224 27 0 4169 4392 522162741 522162518 9.370000e-67 265.0
24 TraesCS1A01G118400 chr3D 76.294 367 52 19 1466 1821 81207160 81207502 3.520000e-36 163.0
25 TraesCS1A01G118400 chr3D 81.068 206 24 8 1118 1311 81206732 81206934 2.740000e-32 150.0
26 TraesCS1A01G118400 chr3A 80.968 310 45 8 4093 4392 108382586 108382891 2.640000e-57 233.0
27 TraesCS1A01G118400 chr3A 89.431 123 13 0 1699 1821 95477817 95477939 5.890000e-34 156.0
28 TraesCS1A01G118400 chr3A 85.000 100 10 2 3447 3546 108467796 108467702 3.620000e-16 97.1
29 TraesCS1A01G118400 chr3A 86.747 83 10 1 1466 1547 95477584 95477666 1.680000e-14 91.6
30 TraesCS1A01G118400 chr3B 76.022 367 53 20 1466 1821 126920987 126921329 1.640000e-34 158.0
31 TraesCS1A01G118400 chr3B 96.875 32 0 1 1903 1934 820478049 820478019 8.000000e-03 52.8
32 TraesCS1A01G118400 chr6B 91.209 91 4 2 3547 3633 705861819 705861909 2.150000e-23 121.0
33 TraesCS1A01G118400 chr6B 94.444 36 1 1 1895 1930 641751968 641752002 2.000000e-03 54.7
34 TraesCS1A01G118400 chr5A 91.111 90 4 2 3547 3632 475324404 475324493 7.720000e-23 119.0
35 TraesCS1A01G118400 chr5A 90.110 91 5 2 3547 3633 688327083 688327173 9.990000e-22 115.0
36 TraesCS1A01G118400 chr5A 91.304 69 6 0 1753 1821 57375669 57375601 1.300000e-15 95.3
37 TraesCS1A01G118400 chr5A 83.333 96 16 0 1720 1815 575658615 575658710 6.050000e-14 89.8
38 TraesCS1A01G118400 chr6A 90.110 91 5 2 3547 3633 91902442 91902532 9.990000e-22 115.0
39 TraesCS1A01G118400 chr7B 89.888 89 5 2 3547 3633 735002783 735002697 1.290000e-20 111.0
40 TraesCS1A01G118400 chr7B 87.000 100 5 5 3445 3542 337023468 337023375 6.010000e-19 106.0
41 TraesCS1A01G118400 chr7B 92.308 39 1 2 506 544 462058144 462058108 2.000000e-03 54.7
42 TraesCS1A01G118400 chrUn 89.011 91 6 2 3547 3633 479167368 479167458 4.650000e-20 110.0
43 TraesCS1A01G118400 chrUn 85.577 104 7 3 3445 3546 100087309 100087212 7.780000e-18 102.0
44 TraesCS1A01G118400 chr7A 87.879 99 5 4 3450 3546 103151241 103151148 4.650000e-20 110.0
45 TraesCS1A01G118400 chr5B 86.139 101 6 5 3448 3546 665813249 665813155 7.780000e-18 102.0
46 TraesCS1A01G118400 chr5B 92.754 69 5 0 1753 1821 64265122 64265054 2.800000e-17 100.0
47 TraesCS1A01G118400 chr5B 84.375 96 15 0 1720 1815 559992274 559992369 1.300000e-15 95.3
48 TraesCS1A01G118400 chr4A 86.139 101 7 4 3448 3546 15773563 15773658 7.780000e-18 102.0


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 TraesCS1A01G118400 chr1A 127074249 127078643 4394 True 3743.500000 6709 100.000000 1 4395 2 chr1A.!!$R1 4394
1 TraesCS1A01G118400 chr1D 116002971 116006398 3427 True 1751.666667 3286 93.727667 1 3451 3 chr1D.!!$R2 3450
2 TraesCS1A01G118400 chr1B 177834997 177839288 4291 True 1814.333333 3162 92.666333 65 4237 3 chr1B.!!$R5 4172

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
625 647 0.596082 AACGTTAATGCTGCACCACC 59.404 50.0 3.57 0.0 0.00 4.61 F
2014 2049 0.605319 ATGGTTTGGTGATCGTGCGT 60.605 50.0 0.00 0.0 0.00 5.24 F
2574 2649 0.771127 ACCAGCTCTAGTTTTGGCCA 59.229 50.0 0.00 0.0 33.98 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2287 2361 0.598680 AGCATCACTCGCCGCTAATC 60.599 55.0 0.00 0.0 31.60 1.75 R
2883 2959 0.173255 TCATGAGACGAATGCGCTGA 59.827 50.0 9.73 0.0 42.48 4.26 R
4142 4407 0.037697 TCGGGTGACAATGACGAAGG 60.038 55.0 0.00 0.0 0.00 3.46 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
71 78 0.605589 AGCAGTACTGAGTGGTGAGC 59.394 55.000 27.08 7.50 35.38 4.26
75 82 3.490078 GCAGTACTGAGTGGTGAGCTATC 60.490 52.174 27.08 0.00 0.00 2.08
76 83 3.951037 CAGTACTGAGTGGTGAGCTATCT 59.049 47.826 18.45 0.00 0.00 1.98
94 101 8.169977 AGCTATCTCTCAAAAACAATGAACAA 57.830 30.769 0.00 0.00 0.00 2.83
95 102 8.800332 AGCTATCTCTCAAAAACAATGAACAAT 58.200 29.630 0.00 0.00 0.00 2.71
175 188 1.537202 GTACAGACAAGGCCAAAGCAG 59.463 52.381 5.01 0.00 42.56 4.24
503 525 2.443394 GGATCGGTGATGGAGGGCA 61.443 63.158 0.00 0.00 0.00 5.36
624 646 1.724654 CGAACGTTAATGCTGCACCAC 60.725 52.381 3.57 0.71 0.00 4.16
625 647 0.596082 AACGTTAATGCTGCACCACC 59.404 50.000 3.57 0.00 0.00 4.61
626 648 1.241315 ACGTTAATGCTGCACCACCC 61.241 55.000 3.57 0.00 0.00 4.61
627 649 1.890174 GTTAATGCTGCACCACCCC 59.110 57.895 3.57 0.00 0.00 4.95
628 650 1.304879 TTAATGCTGCACCACCCCC 60.305 57.895 3.57 0.00 0.00 5.40
629 651 2.086599 TTAATGCTGCACCACCCCCA 62.087 55.000 3.57 0.00 0.00 4.96
630 652 2.779742 TAATGCTGCACCACCCCCAC 62.780 60.000 3.57 0.00 0.00 4.61
813 839 3.117888 GGAGGGATGGAGCAAAGTTGATA 60.118 47.826 0.00 0.00 0.00 2.15
814 840 4.526970 GAGGGATGGAGCAAAGTTGATAA 58.473 43.478 0.00 0.00 0.00 1.75
842 868 5.263599 TGGACTGGAATGCAAATATCAGTT 58.736 37.500 11.05 0.00 35.87 3.16
859 885 1.078497 TTGGAACTGGCATCGCGAT 60.078 52.632 17.62 17.62 0.00 4.58
871 897 2.284627 GCATCGCGATGAAAAATTGTGC 60.285 45.455 44.20 26.98 41.20 4.57
897 923 1.536073 CCCAAGGTCACGAGCAGAGA 61.536 60.000 0.00 0.00 0.00 3.10
1069 1103 4.892965 GCACCCACACCAGCACCA 62.893 66.667 0.00 0.00 0.00 4.17
1070 1104 2.595463 CACCCACACCAGCACCAG 60.595 66.667 0.00 0.00 0.00 4.00
1071 1105 4.586235 ACCCACACCAGCACCAGC 62.586 66.667 0.00 0.00 42.56 4.85
1072 1106 4.584518 CCCACACCAGCACCAGCA 62.585 66.667 0.00 0.00 45.49 4.41
1073 1107 3.289834 CCACACCAGCACCAGCAC 61.290 66.667 0.00 0.00 45.49 4.40
1074 1108 3.289834 CACACCAGCACCAGCACC 61.290 66.667 0.00 0.00 45.49 5.01
1075 1109 3.807839 ACACCAGCACCAGCACCA 61.808 61.111 0.00 0.00 45.49 4.17
1076 1110 2.981909 CACCAGCACCAGCACCAG 60.982 66.667 0.00 0.00 45.49 4.00
1077 1111 4.962836 ACCAGCACCAGCACCAGC 62.963 66.667 0.00 0.00 45.49 4.85
1078 1112 4.960866 CCAGCACCAGCACCAGCA 62.961 66.667 0.00 0.00 45.49 4.41
1079 1113 3.667282 CAGCACCAGCACCAGCAC 61.667 66.667 0.00 0.00 45.49 4.40
1080 1114 4.962836 AGCACCAGCACCAGCACC 62.963 66.667 0.00 0.00 45.49 5.01
1082 1116 2.519063 CACCAGCACCAGCACCAA 60.519 61.111 0.00 0.00 45.49 3.67
1195 1229 2.036098 TTCGAGGACACCGCCCTA 59.964 61.111 0.00 0.00 33.36 3.53
1667 1701 1.385743 GTGTTAGCTACGTGTTGCTCG 59.614 52.381 12.03 0.00 41.56 5.03
1825 1860 1.271926 CGTCCCCTGGAGGTGAATTTT 60.272 52.381 0.00 0.00 33.46 1.82
1844 1879 2.900716 TTTTGGGCCTTTTGTGCTAC 57.099 45.000 4.53 0.00 0.00 3.58
1854 1889 5.451381 GGCCTTTTGTGCTACTTTACAGTTT 60.451 40.000 0.00 0.00 34.06 2.66
1866 1901 6.569179 ACTTTACAGTTTAAATCCGCATGT 57.431 33.333 0.00 0.00 0.00 3.21
1878 1913 2.879070 CGCATGTCGCTGCATCTCC 61.879 63.158 0.00 0.00 42.40 3.71
1887 1922 1.375098 GCTGCATCTCCTGTTGCTCC 61.375 60.000 0.00 0.00 39.08 4.70
2011 2046 1.739466 CTGGATGGTTTGGTGATCGTG 59.261 52.381 0.00 0.00 0.00 4.35
2014 2049 0.605319 ATGGTTTGGTGATCGTGCGT 60.605 50.000 0.00 0.00 0.00 5.24
2105 2140 5.415077 AGTGATATATAAGGAACTCGGACCG 59.585 44.000 7.84 7.84 38.49 4.79
2108 2143 1.047034 ATAAGGAACTCGGACCGGGG 61.047 60.000 20.08 12.16 38.49 5.73
2267 2341 9.337396 TGCTAGTTAAACAGAAATCTCAGAAAA 57.663 29.630 0.00 0.00 0.00 2.29
2299 2374 3.990469 AGATGTAAATGATTAGCGGCGAG 59.010 43.478 12.98 0.00 0.00 5.03
2377 2452 6.779860 ACATGATTAGGGTTGAAACTAGTGT 58.220 36.000 0.00 0.00 0.00 3.55
2420 2495 2.036217 TGACAGCAAGCCATTTTCCTTG 59.964 45.455 0.00 0.00 40.97 3.61
2426 2501 3.731089 CAAGCCATTTTCCTTGCTTTCA 58.269 40.909 0.00 0.00 41.83 2.69
2448 2523 4.744795 AACTCACAGAAGACAGAAGTGT 57.255 40.909 0.00 0.00 40.71 3.55
2452 2527 5.163364 ACTCACAGAAGACAGAAGTGTTGAT 60.163 40.000 0.00 0.00 36.88 2.57
2453 2528 5.674525 TCACAGAAGACAGAAGTGTTGATT 58.325 37.500 0.00 0.00 36.88 2.57
2454 2529 5.525012 TCACAGAAGACAGAAGTGTTGATTG 59.475 40.000 0.00 0.00 36.88 2.67
2455 2530 5.295292 CACAGAAGACAGAAGTGTTGATTGT 59.705 40.000 0.00 0.00 36.88 2.71
2456 2531 5.525378 ACAGAAGACAGAAGTGTTGATTGTC 59.475 40.000 0.00 0.00 36.88 3.18
2458 2533 5.988561 AGAAGACAGAAGTGTTGATTGTCTC 59.011 40.000 5.97 1.60 45.52 3.36
2506 2581 4.216042 TCCTGTGCTGTTTCATGTGTAATG 59.784 41.667 0.00 0.00 0.00 1.90
2530 2605 5.047377 GTGAATTGAATGGCTTAGGGAAACA 60.047 40.000 0.00 0.00 0.00 2.83
2540 2615 4.398358 GGCTTAGGGAAACAGGACAATAAC 59.602 45.833 0.00 0.00 0.00 1.89
2574 2649 0.771127 ACCAGCTCTAGTTTTGGCCA 59.229 50.000 0.00 0.00 33.98 5.36
2675 2751 7.015389 AGTGTACTCTTATTGTATTAGGAGGGC 59.985 40.741 0.00 0.00 31.46 5.19
2693 2769 3.381590 AGGGCTCAACAAACTTTCTGTTC 59.618 43.478 0.00 0.00 38.03 3.18
2705 2781 8.889717 ACAAACTTTCTGTTCGAGAAGAAATTA 58.110 29.630 19.11 4.35 41.86 1.40
2808 2884 8.918202 TGTTATTAGATTTCGGGCTTCATTAT 57.082 30.769 0.00 0.00 0.00 1.28
2877 2953 2.622942 GACCTGCAGAATGTTTGTGGAA 59.377 45.455 17.39 0.00 39.31 3.53
2883 2959 3.181476 GCAGAATGTTTGTGGAAACCTGT 60.181 43.478 0.00 0.00 40.81 4.00
2916 2992 3.932089 GTCTCATGAAAAGCTCTGAGGTC 59.068 47.826 10.15 0.00 36.59 3.85
2942 3018 7.228108 CGTCAATCTAGGTACACATAACTCCTA 59.772 40.741 0.00 0.00 28.62 2.94
3285 3361 4.696877 TGTGATGCTTCAGAAATACACCTG 59.303 41.667 1.91 0.00 30.85 4.00
3462 3558 8.640063 TGCTATATTATGTACTCCTTCCGTTA 57.360 34.615 0.00 0.00 0.00 3.18
3501 3764 8.853077 TTTCTAGATACTGCATTCCAATATGG 57.147 34.615 0.00 0.00 39.43 2.74
3523 3786 5.527214 TGGATTACATACGGAGCAAAATGAG 59.473 40.000 0.00 0.00 0.00 2.90
3524 3787 5.758296 GGATTACATACGGAGCAAAATGAGA 59.242 40.000 0.00 0.00 0.00 3.27
3525 3788 6.260050 GGATTACATACGGAGCAAAATGAGAA 59.740 38.462 0.00 0.00 0.00 2.87
3526 3789 7.041098 GGATTACATACGGAGCAAAATGAGAAT 60.041 37.037 0.00 0.00 0.00 2.40
3527 3790 5.741388 ACATACGGAGCAAAATGAGAATC 57.259 39.130 0.00 0.00 0.00 2.52
3528 3791 5.431765 ACATACGGAGCAAAATGAGAATCT 58.568 37.500 0.00 0.00 34.92 2.40
3529 3792 6.582636 ACATACGGAGCAAAATGAGAATCTA 58.417 36.000 0.00 0.00 34.92 1.98
3530 3793 6.480320 ACATACGGAGCAAAATGAGAATCTAC 59.520 38.462 0.00 0.00 34.92 2.59
3531 3794 4.832248 ACGGAGCAAAATGAGAATCTACA 58.168 39.130 0.00 0.00 34.92 2.74
3532 3795 4.631813 ACGGAGCAAAATGAGAATCTACAC 59.368 41.667 0.00 0.00 34.92 2.90
3533 3796 4.872691 CGGAGCAAAATGAGAATCTACACT 59.127 41.667 0.00 0.00 34.92 3.55
3534 3797 5.006165 CGGAGCAAAATGAGAATCTACACTC 59.994 44.000 0.00 0.00 34.92 3.51
3535 3798 6.112058 GGAGCAAAATGAGAATCTACACTCT 58.888 40.000 0.00 0.00 34.92 3.24
3536 3799 6.036953 GGAGCAAAATGAGAATCTACACTCTG 59.963 42.308 0.00 0.00 34.92 3.35
3537 3800 6.705302 AGCAAAATGAGAATCTACACTCTGA 58.295 36.000 0.00 0.00 34.92 3.27
3538 3801 7.164122 AGCAAAATGAGAATCTACACTCTGAA 58.836 34.615 0.00 0.00 34.92 3.02
3539 3802 7.118971 AGCAAAATGAGAATCTACACTCTGAAC 59.881 37.037 0.00 0.00 34.92 3.18
3540 3803 7.118971 GCAAAATGAGAATCTACACTCTGAACT 59.881 37.037 0.00 0.00 34.92 3.01
3541 3804 9.645059 CAAAATGAGAATCTACACTCTGAACTA 57.355 33.333 0.00 0.00 34.92 2.24
3542 3805 9.646427 AAAATGAGAATCTACACTCTGAACTAC 57.354 33.333 0.00 0.00 34.92 2.73
3543 3806 6.424176 TGAGAATCTACACTCTGAACTACG 57.576 41.667 0.00 0.00 34.92 3.51
3544 3807 5.938710 TGAGAATCTACACTCTGAACTACGT 59.061 40.000 0.00 0.00 34.92 3.57
3545 3808 6.092396 TGAGAATCTACACTCTGAACTACGTC 59.908 42.308 0.00 0.00 34.92 4.34
3546 3809 5.938710 AGAATCTACACTCTGAACTACGTCA 59.061 40.000 0.00 0.00 0.00 4.35
3547 3810 6.600032 AGAATCTACACTCTGAACTACGTCAT 59.400 38.462 0.00 0.00 0.00 3.06
3548 3811 6.761099 ATCTACACTCTGAACTACGTCATT 57.239 37.500 0.00 0.00 0.00 2.57
3549 3812 6.179504 TCTACACTCTGAACTACGTCATTC 57.820 41.667 0.00 0.00 0.00 2.67
3550 3813 4.175787 ACACTCTGAACTACGTCATTCC 57.824 45.455 0.00 0.00 0.00 3.01
3551 3814 3.572682 ACACTCTGAACTACGTCATTCCA 59.427 43.478 0.00 0.00 0.00 3.53
3552 3815 4.038763 ACACTCTGAACTACGTCATTCCAA 59.961 41.667 0.00 0.00 0.00 3.53
3553 3816 5.171476 CACTCTGAACTACGTCATTCCAAT 58.829 41.667 0.00 0.00 0.00 3.16
3554 3817 6.071560 ACACTCTGAACTACGTCATTCCAATA 60.072 38.462 0.00 0.00 0.00 1.90
3555 3818 6.980978 CACTCTGAACTACGTCATTCCAATAT 59.019 38.462 0.00 0.00 0.00 1.28
3556 3819 6.980978 ACTCTGAACTACGTCATTCCAATATG 59.019 38.462 0.00 0.00 0.00 1.78
3557 3820 6.280643 TCTGAACTACGTCATTCCAATATGG 58.719 40.000 0.00 0.00 39.43 2.74
3558 3821 6.097696 TCTGAACTACGTCATTCCAATATGGA 59.902 38.462 0.00 0.00 46.61 3.41
3592 3855 7.093333 TGGAGCAAAATGAGAATCTACACTCTA 60.093 37.037 0.00 0.00 34.92 2.43
3996 4261 2.668250 TCGATATAAACACGGCGGATG 58.332 47.619 13.24 3.44 0.00 3.51
3998 4263 2.407361 CGATATAAACACGGCGGATGTC 59.593 50.000 13.24 3.57 0.00 3.06
4006 4271 1.401552 CACGGCGGATGTCATTGAAAT 59.598 47.619 13.24 0.00 0.00 2.17
4008 4273 2.159393 ACGGCGGATGTCATTGAAATTG 60.159 45.455 13.24 0.00 0.00 2.32
4010 4275 2.417107 GGCGGATGTCATTGAAATTGCA 60.417 45.455 13.71 0.00 0.00 4.08
4011 4276 2.855963 GCGGATGTCATTGAAATTGCAG 59.144 45.455 9.09 0.00 0.00 4.41
4013 4278 3.855379 CGGATGTCATTGAAATTGCAGTG 59.145 43.478 2.46 2.46 0.00 3.66
4015 4280 5.472148 GGATGTCATTGAAATTGCAGTGAA 58.528 37.500 12.89 5.06 36.47 3.18
4018 4283 7.118680 GGATGTCATTGAAATTGCAGTGAATTT 59.881 33.333 12.89 10.93 36.47 1.82
4019 4284 7.410800 TGTCATTGAAATTGCAGTGAATTTC 57.589 32.000 12.89 21.47 46.14 2.17
4024 4289 2.900122 ATTGCAGTGAATTTCGTCCG 57.100 45.000 0.00 0.00 0.00 4.79
4025 4290 0.237235 TTGCAGTGAATTTCGTCCGC 59.763 50.000 0.00 0.00 0.00 5.54
4026 4291 0.602638 TGCAGTGAATTTCGTCCGCT 60.603 50.000 0.00 0.00 0.00 5.52
4027 4292 0.179215 GCAGTGAATTTCGTCCGCTG 60.179 55.000 0.00 0.00 40.33 5.18
4028 4293 1.428448 CAGTGAATTTCGTCCGCTGA 58.572 50.000 0.00 0.00 39.91 4.26
4029 4294 1.391485 CAGTGAATTTCGTCCGCTGAG 59.609 52.381 0.00 0.00 39.91 3.35
4030 4295 0.721718 GTGAATTTCGTCCGCTGAGG 59.278 55.000 0.00 0.00 42.97 3.86
4033 4298 1.838073 AATTTCGTCCGCTGAGGGGT 61.838 55.000 15.63 0.00 41.52 4.95
4036 4301 3.382832 CGTCCGCTGAGGGGTCTT 61.383 66.667 15.63 0.00 41.52 3.01
4037 4302 2.050350 CGTCCGCTGAGGGGTCTTA 61.050 63.158 15.63 0.00 41.52 2.10
4038 4303 1.392710 CGTCCGCTGAGGGGTCTTAT 61.393 60.000 15.63 0.00 41.52 1.73
4039 4304 1.700955 GTCCGCTGAGGGGTCTTATA 58.299 55.000 15.63 0.00 41.52 0.98
4042 4307 3.071167 GTCCGCTGAGGGGTCTTATATTT 59.929 47.826 15.63 0.00 41.52 1.40
4043 4308 3.714798 TCCGCTGAGGGGTCTTATATTTT 59.285 43.478 15.63 0.00 41.52 1.82
4044 4309 4.903049 TCCGCTGAGGGGTCTTATATTTTA 59.097 41.667 15.63 0.00 41.52 1.52
4045 4310 5.546499 TCCGCTGAGGGGTCTTATATTTTAT 59.454 40.000 15.63 0.00 41.52 1.40
4046 4311 6.043938 TCCGCTGAGGGGTCTTATATTTTATT 59.956 38.462 15.63 0.00 41.52 1.40
4047 4312 6.149474 CCGCTGAGGGGTCTTATATTTTATTG 59.851 42.308 7.49 0.00 35.97 1.90
4048 4313 6.934645 CGCTGAGGGGTCTTATATTTTATTGA 59.065 38.462 0.00 0.00 0.00 2.57
4049 4314 7.444183 CGCTGAGGGGTCTTATATTTTATTGAA 59.556 37.037 0.00 0.00 0.00 2.69
4050 4315 9.301897 GCTGAGGGGTCTTATATTTTATTGAAT 57.698 33.333 0.00 0.00 0.00 2.57
4152 4417 1.183549 ACGGCTACTCCTTCGTCATT 58.816 50.000 0.00 0.00 0.00 2.57
4156 4421 2.094182 GGCTACTCCTTCGTCATTGTCA 60.094 50.000 0.00 0.00 0.00 3.58
4157 4422 2.924290 GCTACTCCTTCGTCATTGTCAC 59.076 50.000 0.00 0.00 0.00 3.67
4160 4425 0.037697 TCCTTCGTCATTGTCACCCG 60.038 55.000 0.00 0.00 0.00 5.28
4164 4429 0.677288 TCGTCATTGTCACCCGACTT 59.323 50.000 0.00 0.00 43.06 3.01
4238 4503 3.680786 CCGCCTGACACTCACGGA 61.681 66.667 0.00 0.00 38.00 4.69
4239 4504 2.573869 CGCCTGACACTCACGGAT 59.426 61.111 0.00 0.00 0.00 4.18
4240 4505 1.807165 CGCCTGACACTCACGGATG 60.807 63.158 0.00 0.00 0.00 3.51
4241 4506 1.591703 GCCTGACACTCACGGATGA 59.408 57.895 0.00 0.00 0.00 2.92
4242 4507 0.176680 GCCTGACACTCACGGATGAT 59.823 55.000 0.00 0.00 33.22 2.45
4243 4508 1.804372 GCCTGACACTCACGGATGATC 60.804 57.143 0.00 0.00 33.22 2.92
4244 4509 1.202463 CCTGACACTCACGGATGATCC 60.202 57.143 0.08 0.08 33.22 3.36
4245 4510 1.753649 CTGACACTCACGGATGATCCT 59.246 52.381 10.18 0.00 33.30 3.24
4246 4511 1.751351 TGACACTCACGGATGATCCTC 59.249 52.381 10.18 0.00 33.30 3.71
4247 4512 2.028130 GACACTCACGGATGATCCTCT 58.972 52.381 10.18 0.00 33.30 3.69
4248 4513 2.028130 ACACTCACGGATGATCCTCTC 58.972 52.381 10.18 0.00 33.30 3.20
4249 4514 1.339610 CACTCACGGATGATCCTCTCC 59.660 57.143 10.18 0.00 33.30 3.71
4252 4517 2.653702 CGGATGATCCTCTCCGCC 59.346 66.667 10.18 0.00 46.87 6.13
4253 4518 1.905843 CGGATGATCCTCTCCGCCT 60.906 63.158 10.18 0.00 46.87 5.52
4254 4519 1.872197 CGGATGATCCTCTCCGCCTC 61.872 65.000 10.18 0.00 46.87 4.70
4255 4520 1.540435 GGATGATCCTCTCCGCCTCC 61.540 65.000 3.71 0.00 32.53 4.30
4256 4521 0.541764 GATGATCCTCTCCGCCTCCT 60.542 60.000 0.00 0.00 0.00 3.69
4257 4522 0.541764 ATGATCCTCTCCGCCTCCTC 60.542 60.000 0.00 0.00 0.00 3.71
4258 4523 1.906333 GATCCTCTCCGCCTCCTCC 60.906 68.421 0.00 0.00 0.00 4.30
4259 4524 2.366153 GATCCTCTCCGCCTCCTCCT 62.366 65.000 0.00 0.00 0.00 3.69
4260 4525 2.655077 ATCCTCTCCGCCTCCTCCTG 62.655 65.000 0.00 0.00 0.00 3.86
4261 4526 3.535962 CTCTCCGCCTCCTCCTGC 61.536 72.222 0.00 0.00 0.00 4.85
4302 4567 4.742201 CACCGAGGACGTGGGCTG 62.742 72.222 0.00 0.00 37.88 4.85
4307 4572 4.974438 AGGACGTGGGCTGGGGAA 62.974 66.667 0.00 0.00 0.00 3.97
4308 4573 4.410400 GGACGTGGGCTGGGGAAG 62.410 72.222 0.00 0.00 0.00 3.46
4309 4574 3.319198 GACGTGGGCTGGGGAAGA 61.319 66.667 0.00 0.00 0.00 2.87
4310 4575 3.316573 GACGTGGGCTGGGGAAGAG 62.317 68.421 0.00 0.00 0.00 2.85
4311 4576 3.003173 CGTGGGCTGGGGAAGAGA 61.003 66.667 0.00 0.00 0.00 3.10
4312 4577 2.993853 GTGGGCTGGGGAAGAGAG 59.006 66.667 0.00 0.00 0.00 3.20
4313 4578 3.011517 TGGGCTGGGGAAGAGAGC 61.012 66.667 0.00 0.00 0.00 4.09
4314 4579 3.011517 GGGCTGGGGAAGAGAGCA 61.012 66.667 0.00 0.00 34.20 4.26
4315 4580 2.588989 GGCTGGGGAAGAGAGCAG 59.411 66.667 0.00 0.00 34.20 4.24
4316 4581 2.124778 GCTGGGGAAGAGAGCAGC 60.125 66.667 0.00 0.00 32.70 5.25
4317 4582 2.186384 CTGGGGAAGAGAGCAGCG 59.814 66.667 0.00 0.00 0.00 5.18
4318 4583 3.382803 CTGGGGAAGAGAGCAGCGG 62.383 68.421 0.00 0.00 0.00 5.52
4319 4584 3.394836 GGGGAAGAGAGCAGCGGT 61.395 66.667 0.00 0.00 0.00 5.68
4320 4585 2.185608 GGGAAGAGAGCAGCGGTC 59.814 66.667 0.00 0.43 0.00 4.79
4321 4586 2.202676 GGAAGAGAGCAGCGGTCG 60.203 66.667 0.00 0.00 35.00 4.79
4322 4587 2.569134 GAAGAGAGCAGCGGTCGT 59.431 61.111 0.00 0.00 35.00 4.34
4323 4588 1.080434 GAAGAGAGCAGCGGTCGTT 60.080 57.895 0.00 1.71 35.00 3.85
4324 4589 0.170561 GAAGAGAGCAGCGGTCGTTA 59.829 55.000 0.00 0.00 35.00 3.18
4325 4590 0.171455 AAGAGAGCAGCGGTCGTTAG 59.829 55.000 0.00 0.00 35.00 2.34
4326 4591 0.677098 AGAGAGCAGCGGTCGTTAGA 60.677 55.000 0.00 0.00 35.00 2.10
4327 4592 0.248296 GAGAGCAGCGGTCGTTAGAG 60.248 60.000 0.00 0.00 35.00 2.43
4328 4593 1.226717 GAGCAGCGGTCGTTAGAGG 60.227 63.158 0.00 0.00 0.00 3.69
4329 4594 2.886124 GCAGCGGTCGTTAGAGGC 60.886 66.667 0.00 0.00 0.00 4.70
4330 4595 2.579787 CAGCGGTCGTTAGAGGCG 60.580 66.667 0.00 0.00 33.65 5.52
4331 4596 3.060615 AGCGGTCGTTAGAGGCGT 61.061 61.111 0.00 0.00 33.65 5.68
4332 4597 2.578981 GCGGTCGTTAGAGGCGTC 60.579 66.667 0.00 0.00 0.00 5.19
4333 4598 2.277120 CGGTCGTTAGAGGCGTCG 60.277 66.667 0.00 0.00 0.00 5.12
4334 4599 2.873288 GGTCGTTAGAGGCGTCGT 59.127 61.111 0.00 0.00 0.00 4.34
4335 4600 1.226239 GGTCGTTAGAGGCGTCGTC 60.226 63.158 0.00 0.00 0.00 4.20
4336 4601 1.579626 GTCGTTAGAGGCGTCGTCG 60.580 63.158 0.00 7.53 40.37 5.12
4337 4602 2.029288 TCGTTAGAGGCGTCGTCGT 61.029 57.895 15.68 0.00 39.49 4.34
4338 4603 1.154338 CGTTAGAGGCGTCGTCGTT 60.154 57.895 3.66 0.00 39.49 3.85
4339 4604 1.393597 CGTTAGAGGCGTCGTCGTTG 61.394 60.000 3.66 0.00 39.49 4.10
4340 4605 1.069378 GTTAGAGGCGTCGTCGTTGG 61.069 60.000 3.66 0.00 39.49 3.77
4341 4606 2.807631 TTAGAGGCGTCGTCGTTGGC 62.808 60.000 3.66 5.21 39.49 4.52
4362 4627 4.933064 GGCGGCGATCTCGGTGAG 62.933 72.222 12.98 0.00 40.23 3.51
4363 4628 4.933064 GCGGCGATCTCGGTGAGG 62.933 72.222 12.98 0.00 40.23 3.86
4364 4629 4.271816 CGGCGATCTCGGTGAGGG 62.272 72.222 0.00 0.00 40.23 4.30
4365 4630 2.833582 GGCGATCTCGGTGAGGGA 60.834 66.667 1.34 0.00 40.23 4.20
4366 4631 2.413765 GCGATCTCGGTGAGGGAC 59.586 66.667 1.34 0.00 40.23 4.46
4367 4632 3.121019 CGATCTCGGTGAGGGACC 58.879 66.667 0.00 0.00 42.07 4.46
4368 4633 1.753078 CGATCTCGGTGAGGGACCA 60.753 63.158 0.00 0.00 46.55 4.02
4369 4634 1.109920 CGATCTCGGTGAGGGACCAT 61.110 60.000 0.00 0.00 46.55 3.55
4370 4635 1.123928 GATCTCGGTGAGGGACCATT 58.876 55.000 0.00 0.00 46.55 3.16
4371 4636 1.069358 GATCTCGGTGAGGGACCATTC 59.931 57.143 0.00 0.00 46.55 2.67
4372 4637 0.976073 TCTCGGTGAGGGACCATTCC 60.976 60.000 0.00 0.00 46.55 3.01
4373 4638 0.978146 CTCGGTGAGGGACCATTCCT 60.978 60.000 0.00 0.00 46.55 3.36
4374 4639 0.976073 TCGGTGAGGGACCATTCCTC 60.976 60.000 3.37 3.37 46.55 3.71
4377 4642 3.309582 GAGGGACCATTCCTCGCA 58.690 61.111 0.00 0.00 42.38 5.10
4378 4643 1.144936 GAGGGACCATTCCTCGCAG 59.855 63.158 0.00 0.00 42.38 5.18
4379 4644 1.613630 AGGGACCATTCCTCGCAGT 60.614 57.895 0.00 0.00 42.38 4.40
4380 4645 0.325296 AGGGACCATTCCTCGCAGTA 60.325 55.000 0.00 0.00 42.38 2.74
4381 4646 0.179081 GGGACCATTCCTCGCAGTAC 60.179 60.000 0.00 0.00 42.38 2.73
4382 4647 0.179081 GGACCATTCCTCGCAGTACC 60.179 60.000 0.00 0.00 39.13 3.34
4383 4648 0.824759 GACCATTCCTCGCAGTACCT 59.175 55.000 0.00 0.00 0.00 3.08
4384 4649 0.537188 ACCATTCCTCGCAGTACCTG 59.463 55.000 0.00 0.00 34.12 4.00
4385 4650 0.179073 CCATTCCTCGCAGTACCTGG 60.179 60.000 0.00 0.00 31.21 4.45
4386 4651 0.811616 CATTCCTCGCAGTACCTGGC 60.812 60.000 0.00 0.00 31.21 4.85
4387 4652 1.972660 ATTCCTCGCAGTACCTGGCC 61.973 60.000 0.00 0.00 31.21 5.36
4388 4653 3.390521 CCTCGCAGTACCTGGCCA 61.391 66.667 4.71 4.71 31.21 5.36
4389 4654 2.735772 CCTCGCAGTACCTGGCCAT 61.736 63.158 5.51 0.00 31.21 4.40
4390 4655 1.227380 CTCGCAGTACCTGGCCATC 60.227 63.158 5.51 0.00 31.21 3.51
4391 4656 1.680522 CTCGCAGTACCTGGCCATCT 61.681 60.000 5.51 0.00 31.21 2.90
4392 4657 1.221840 CGCAGTACCTGGCCATCTT 59.778 57.895 5.51 0.00 31.21 2.40
4393 4658 0.811616 CGCAGTACCTGGCCATCTTC 60.812 60.000 5.51 0.00 31.21 2.87
4394 4659 0.543749 GCAGTACCTGGCCATCTTCT 59.456 55.000 5.51 0.00 31.21 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 8.943909 ACTAATAGTACTTGCCAACAATCTAC 57.056 34.615 0.00 0.00 34.61 2.59
65 72 6.372659 TCATTGTTTTTGAGAGATAGCTCACC 59.627 38.462 11.20 2.14 44.08 4.02
96 103 9.244292 TGTCAGCGGTAAGATTTATCTATCTAT 57.756 33.333 0.00 0.00 35.76 1.98
97 104 8.512956 GTGTCAGCGGTAAGATTTATCTATCTA 58.487 37.037 0.00 0.00 35.76 1.98
98 105 7.371936 GTGTCAGCGGTAAGATTTATCTATCT 58.628 38.462 0.00 0.00 35.76 1.98
99 106 6.305877 CGTGTCAGCGGTAAGATTTATCTATC 59.694 42.308 0.00 0.00 35.76 2.08
116 123 1.201921 CCGATTTTACAGCGTGTCAGC 60.202 52.381 0.00 0.00 37.41 4.26
152 159 2.427506 CTTTGGCCTTGTCTGTACTCC 58.572 52.381 3.32 0.00 0.00 3.85
153 160 1.807142 GCTTTGGCCTTGTCTGTACTC 59.193 52.381 3.32 0.00 0.00 2.59
286 308 1.759459 ATCGAATCGGCTTCCCTCCC 61.759 60.000 1.76 0.00 0.00 4.30
793 819 4.018050 ACTTATCAACTTTGCTCCATCCCT 60.018 41.667 0.00 0.00 0.00 4.20
813 839 2.957402 TGCATTCCAGTCCAAGACTT 57.043 45.000 0.00 0.00 41.37 3.01
814 840 2.957402 TTGCATTCCAGTCCAAGACT 57.043 45.000 0.00 0.00 44.44 3.24
842 868 1.815003 CATCGCGATGCCAGTTCCA 60.815 57.895 33.70 0.00 31.39 3.53
859 885 4.755411 TGGGTTTTACGCACAATTTTTCA 58.245 34.783 0.00 0.00 36.06 2.69
871 897 1.796459 CTCGTGACCTTGGGTTTTACG 59.204 52.381 12.39 12.39 38.32 3.18
897 923 2.492090 GCGCTCTGACACTCGGAT 59.508 61.111 0.00 0.00 30.24 4.18
1057 1091 3.289834 GGTGCTGGTGCTGGTGTG 61.290 66.667 0.00 0.00 40.48 3.82
1068 1102 2.263741 GGAGTTGGTGCTGGTGCTG 61.264 63.158 0.00 0.00 40.48 4.41
1069 1103 2.113986 GGAGTTGGTGCTGGTGCT 59.886 61.111 0.00 0.00 40.48 4.40
1070 1104 1.968540 GAGGAGTTGGTGCTGGTGC 60.969 63.158 0.00 0.00 40.20 5.01
1071 1105 1.302832 GGAGGAGTTGGTGCTGGTG 60.303 63.158 0.00 0.00 0.00 4.17
1072 1106 1.462238 AGGAGGAGTTGGTGCTGGT 60.462 57.895 0.00 0.00 0.00 4.00
1073 1107 1.298014 GAGGAGGAGTTGGTGCTGG 59.702 63.158 0.00 0.00 0.00 4.85
1074 1108 1.197430 AGGAGGAGGAGTTGGTGCTG 61.197 60.000 0.00 0.00 0.00 4.41
1075 1109 0.907230 GAGGAGGAGGAGTTGGTGCT 60.907 60.000 0.00 0.00 0.00 4.40
1076 1110 1.599576 GAGGAGGAGGAGTTGGTGC 59.400 63.158 0.00 0.00 0.00 5.01
1077 1111 0.252467 AGGAGGAGGAGGAGTTGGTG 60.252 60.000 0.00 0.00 0.00 4.17
1078 1112 0.041982 GAGGAGGAGGAGGAGTTGGT 59.958 60.000 0.00 0.00 0.00 3.67
1079 1113 0.338120 AGAGGAGGAGGAGGAGTTGG 59.662 60.000 0.00 0.00 0.00 3.77
1080 1114 1.830477 CAAGAGGAGGAGGAGGAGTTG 59.170 57.143 0.00 0.00 0.00 3.16
1081 1115 1.899438 GCAAGAGGAGGAGGAGGAGTT 60.899 57.143 0.00 0.00 0.00 3.01
1082 1116 0.325203 GCAAGAGGAGGAGGAGGAGT 60.325 60.000 0.00 0.00 0.00 3.85
1319 1353 1.608717 GGAAGGAGCGAGAGAAGGCA 61.609 60.000 0.00 0.00 0.00 4.75
1667 1701 2.649034 TCGTCAGAACCCACGAGC 59.351 61.111 0.00 0.00 40.05 5.03
1825 1860 2.393646 AGTAGCACAAAAGGCCCAAAA 58.606 42.857 0.00 0.00 0.00 2.44
1844 1879 5.732647 CGACATGCGGATTTAAACTGTAAAG 59.267 40.000 0.00 0.00 36.03 1.85
1866 1901 1.742880 GCAACAGGAGATGCAGCGA 60.743 57.895 0.00 0.00 42.50 4.93
1887 1922 7.440523 ACTTAAACAAAAGGACATAGCTGAG 57.559 36.000 0.00 0.00 0.00 3.35
2011 2046 7.357287 GCAAAGATAAACTGAAACTAACAACGC 60.357 37.037 0.00 0.00 0.00 4.84
2014 2049 9.515020 CAAGCAAAGATAAACTGAAACTAACAA 57.485 29.630 0.00 0.00 0.00 2.83
2108 2143 6.366061 GTGTAAGAAATTTTCATGTTCAGCCC 59.634 38.462 11.53 0.00 0.00 5.19
2269 2343 9.869844 CCGCTAATCATTTACATCTCTTTTAAG 57.130 33.333 0.00 0.00 0.00 1.85
2286 2360 0.875908 GCATCACTCGCCGCTAATCA 60.876 55.000 0.00 0.00 0.00 2.57
2287 2361 0.598680 AGCATCACTCGCCGCTAATC 60.599 55.000 0.00 0.00 31.60 1.75
2288 2362 0.598680 GAGCATCACTCGCCGCTAAT 60.599 55.000 0.00 0.00 35.18 1.73
2289 2363 1.226974 GAGCATCACTCGCCGCTAA 60.227 57.895 0.00 0.00 35.18 3.09
2377 2452 6.818644 GTCAGAAACAAATATCAGTGCTCCTA 59.181 38.462 0.00 0.00 0.00 2.94
2420 2495 4.572389 TCTGTCTTCTGTGAGTTTGAAAGC 59.428 41.667 0.00 0.00 0.00 3.51
2426 2501 5.091261 ACACTTCTGTCTTCTGTGAGTTT 57.909 39.130 0.00 0.00 33.41 2.66
2448 2523 5.384336 TCCATTTCCACAAGAGACAATCAA 58.616 37.500 0.00 0.00 0.00 2.57
2452 2527 5.246981 AGATCCATTTCCACAAGAGACAA 57.753 39.130 0.00 0.00 0.00 3.18
2453 2528 4.916041 AGATCCATTTCCACAAGAGACA 57.084 40.909 0.00 0.00 0.00 3.41
2454 2529 5.495640 AGAAGATCCATTTCCACAAGAGAC 58.504 41.667 0.00 0.00 0.00 3.36
2455 2530 5.768980 AGAAGATCCATTTCCACAAGAGA 57.231 39.130 0.00 0.00 0.00 3.10
2456 2531 6.317391 GGTAAGAAGATCCATTTCCACAAGAG 59.683 42.308 0.00 0.00 0.00 2.85
2457 2532 6.180472 GGTAAGAAGATCCATTTCCACAAGA 58.820 40.000 0.00 0.00 0.00 3.02
2458 2533 5.945784 TGGTAAGAAGATCCATTTCCACAAG 59.054 40.000 0.00 0.00 0.00 3.16
2506 2581 5.047377 TGTTTCCCTAAGCCATTCAATTCAC 60.047 40.000 0.00 0.00 0.00 3.18
2530 2605 4.702131 GGCACAATTCTCAGTTATTGTCCT 59.298 41.667 5.33 0.00 41.65 3.85
2540 2615 2.012673 GCTGGTAGGCACAATTCTCAG 58.987 52.381 0.00 0.00 0.00 3.35
2574 2649 7.234355 AGATACAAAAGTCTGGAGGAAAATGT 58.766 34.615 0.00 0.00 0.00 2.71
2675 2751 5.718649 TCTCGAACAGAAAGTTTGTTGAG 57.281 39.130 0.00 3.79 41.51 3.02
2693 2769 9.503427 AAAGTTCAACTTGTTAATTTCTTCTCG 57.497 29.630 2.78 0.00 38.66 4.04
2705 2781 3.591196 TGCAGCAAAGTTCAACTTGTT 57.409 38.095 2.78 0.00 38.66 2.83
2781 2857 7.639113 ATGAAGCCCGAAATCTAATAACAAA 57.361 32.000 0.00 0.00 0.00 2.83
2808 2884 4.985538 AGAGCCAACCTTTTACAGAATCA 58.014 39.130 0.00 0.00 0.00 2.57
2877 2953 1.291877 GACGAATGCGCTGACAGGTT 61.292 55.000 9.73 0.00 42.48 3.50
2883 2959 0.173255 TCATGAGACGAATGCGCTGA 59.827 50.000 9.73 0.00 42.48 4.26
2916 2992 6.039493 AGGAGTTATGTGTACCTAGATTGACG 59.961 42.308 0.00 0.00 0.00 4.35
2942 3018 5.765182 CCACTAGTCTGAAAAACAAGGTCAT 59.235 40.000 0.00 0.00 0.00 3.06
3001 3077 3.969976 AGAGCAGCCAGATTTATCCAGTA 59.030 43.478 0.00 0.00 0.00 2.74
3016 3092 0.534412 TGCAGGTAGAAGAGAGCAGC 59.466 55.000 0.00 0.00 0.00 5.25
3285 3361 7.112148 CAGTCTTATTTTTCAAGAACGAACTGC 59.888 37.037 0.00 0.00 33.95 4.40
3493 3756 5.487433 TGCTCCGTATGTAATCCATATTGG 58.513 41.667 0.00 0.00 38.29 3.16
3501 3764 6.844696 TCTCATTTTGCTCCGTATGTAATC 57.155 37.500 0.00 0.00 0.00 1.75
3503 3766 7.047891 AGATTCTCATTTTGCTCCGTATGTAA 58.952 34.615 0.00 0.00 0.00 2.41
3531 3794 7.898710 CCATATTGGAATGACGTAGTTCAGAGT 60.899 40.741 12.70 1.44 40.56 3.24
3532 3795 6.422100 CCATATTGGAATGACGTAGTTCAGAG 59.578 42.308 12.70 0.02 40.56 3.35
3533 3796 6.097696 TCCATATTGGAATGACGTAGTTCAGA 59.902 38.462 12.70 3.26 45.00 3.27
3534 3797 6.280643 TCCATATTGGAATGACGTAGTTCAG 58.719 40.000 12.70 0.00 45.00 3.02
3535 3798 6.228616 TCCATATTGGAATGACGTAGTTCA 57.771 37.500 12.70 0.00 45.00 3.18
3549 3812 7.943079 TTGCTCCATATGTAATCCATATTGG 57.057 36.000 1.24 0.00 42.87 3.16
3552 3815 9.758021 TCATTTTGCTCCATATGTAATCCATAT 57.242 29.630 1.24 0.00 45.67 1.78
3553 3816 9.234827 CTCATTTTGCTCCATATGTAATCCATA 57.765 33.333 1.24 0.00 40.27 2.74
3554 3817 7.946219 TCTCATTTTGCTCCATATGTAATCCAT 59.054 33.333 1.24 0.00 37.58 3.41
3555 3818 7.289310 TCTCATTTTGCTCCATATGTAATCCA 58.711 34.615 1.24 0.00 0.00 3.41
3556 3819 7.750229 TCTCATTTTGCTCCATATGTAATCC 57.250 36.000 1.24 0.00 0.00 3.01
3557 3820 9.837525 GATTCTCATTTTGCTCCATATGTAATC 57.162 33.333 1.24 0.00 0.00 1.75
3558 3821 9.584008 AGATTCTCATTTTGCTCCATATGTAAT 57.416 29.630 1.24 0.00 0.00 1.89
3559 3822 8.985315 AGATTCTCATTTTGCTCCATATGTAA 57.015 30.769 1.24 0.00 0.00 2.41
3560 3823 9.494271 GTAGATTCTCATTTTGCTCCATATGTA 57.506 33.333 1.24 0.00 0.00 2.29
3561 3824 7.994911 TGTAGATTCTCATTTTGCTCCATATGT 59.005 33.333 1.24 0.00 0.00 2.29
3562 3825 8.288208 GTGTAGATTCTCATTTTGCTCCATATG 58.712 37.037 0.00 0.00 0.00 1.78
3563 3826 8.216423 AGTGTAGATTCTCATTTTGCTCCATAT 58.784 33.333 0.00 0.00 0.00 1.78
3564 3827 7.568349 AGTGTAGATTCTCATTTTGCTCCATA 58.432 34.615 0.00 0.00 0.00 2.74
3565 3828 6.421485 AGTGTAGATTCTCATTTTGCTCCAT 58.579 36.000 0.00 0.00 0.00 3.41
3566 3829 5.809001 AGTGTAGATTCTCATTTTGCTCCA 58.191 37.500 0.00 0.00 0.00 3.86
3567 3830 6.112058 AGAGTGTAGATTCTCATTTTGCTCC 58.888 40.000 0.00 0.00 33.63 4.70
3568 3831 8.709386 TTAGAGTGTAGATTCTCATTTTGCTC 57.291 34.615 0.00 0.00 33.63 4.26
3569 3832 8.940952 GTTTAGAGTGTAGATTCTCATTTTGCT 58.059 33.333 0.00 0.00 33.63 3.91
3570 3833 8.940952 AGTTTAGAGTGTAGATTCTCATTTTGC 58.059 33.333 0.00 0.00 33.63 3.68
3576 3839 9.688091 AGACATAGTTTAGAGTGTAGATTCTCA 57.312 33.333 0.00 0.00 33.63 3.27
3977 4242 2.400399 ACATCCGCCGTGTTTATATCG 58.600 47.619 0.00 0.00 0.00 2.92
3988 4253 2.453080 CAATTTCAATGACATCCGCCG 58.547 47.619 0.00 0.00 0.00 6.46
3990 4255 2.855963 CTGCAATTTCAATGACATCCGC 59.144 45.455 0.00 0.00 0.00 5.54
3996 4261 6.144402 ACGAAATTCACTGCAATTTCAATGAC 59.856 34.615 17.43 0.00 46.56 3.06
3998 4263 6.400303 GGACGAAATTCACTGCAATTTCAATG 60.400 38.462 17.43 7.50 46.56 2.82
4006 4271 0.237235 GCGGACGAAATTCACTGCAA 59.763 50.000 13.30 0.00 35.13 4.08
4008 4273 0.179215 CAGCGGACGAAATTCACTGC 60.179 55.000 11.20 11.20 35.23 4.40
4010 4275 1.673033 CCTCAGCGGACGAAATTCACT 60.673 52.381 0.00 0.00 33.16 3.41
4011 4276 0.721718 CCTCAGCGGACGAAATTCAC 59.278 55.000 0.00 0.00 33.16 3.18
4013 4278 1.090052 CCCCTCAGCGGACGAAATTC 61.090 60.000 0.00 0.00 33.16 2.17
4015 4280 2.240162 GACCCCTCAGCGGACGAAAT 62.240 60.000 0.00 0.00 33.16 2.17
4018 4283 2.488771 TAAGACCCCTCAGCGGACGA 62.489 60.000 0.00 0.00 33.16 4.20
4019 4284 1.392710 ATAAGACCCCTCAGCGGACG 61.393 60.000 0.00 0.00 33.16 4.79
4020 4285 1.700955 TATAAGACCCCTCAGCGGAC 58.299 55.000 0.00 0.00 33.16 4.79
4021 4286 2.696526 ATATAAGACCCCTCAGCGGA 57.303 50.000 0.00 0.00 33.16 5.54
4022 4287 3.771577 AAATATAAGACCCCTCAGCGG 57.228 47.619 0.00 0.00 0.00 5.52
4023 4288 6.934645 TCAATAAAATATAAGACCCCTCAGCG 59.065 38.462 0.00 0.00 0.00 5.18
4024 4289 8.691661 TTCAATAAAATATAAGACCCCTCAGC 57.308 34.615 0.00 0.00 0.00 4.26
4106 4371 1.831106 TGACATTGGCTACGAGGTCAT 59.169 47.619 0.00 0.00 44.42 3.06
4133 4398 1.135083 CAATGACGAAGGAGTAGCCGT 60.135 52.381 0.00 0.00 43.43 5.68
4134 4399 1.135083 ACAATGACGAAGGAGTAGCCG 60.135 52.381 0.00 0.00 43.43 5.52
4139 4404 1.002087 GGGTGACAATGACGAAGGAGT 59.998 52.381 0.00 0.00 0.00 3.85
4142 4407 0.037697 TCGGGTGACAATGACGAAGG 60.038 55.000 0.00 0.00 0.00 3.46
4160 4425 2.027625 CCAAGCCCGACGACAAGTC 61.028 63.158 0.00 0.00 46.16 3.01
4230 4495 1.698506 GGAGAGGATCATCCGTGAGT 58.301 55.000 3.23 0.00 42.75 3.41
4237 4502 0.541764 AGGAGGCGGAGAGGATCATC 60.542 60.000 0.00 0.00 37.82 2.92
4238 4503 0.541764 GAGGAGGCGGAGAGGATCAT 60.542 60.000 0.00 0.00 37.82 2.45
4239 4504 1.152652 GAGGAGGCGGAGAGGATCA 60.153 63.158 0.00 0.00 37.82 2.92
4240 4505 1.906333 GGAGGAGGCGGAGAGGATC 60.906 68.421 0.00 0.00 0.00 3.36
4241 4506 2.200092 GGAGGAGGCGGAGAGGAT 59.800 66.667 0.00 0.00 0.00 3.24
4242 4507 3.024356 AGGAGGAGGCGGAGAGGA 61.024 66.667 0.00 0.00 0.00 3.71
4243 4508 2.837291 CAGGAGGAGGCGGAGAGG 60.837 72.222 0.00 0.00 0.00 3.69
4244 4509 3.535962 GCAGGAGGAGGCGGAGAG 61.536 72.222 0.00 0.00 0.00 3.20
4285 4550 4.742201 CAGCCCACGTCCTCGGTG 62.742 72.222 0.00 0.00 41.85 4.94
4290 4555 4.974438 TTCCCCAGCCCACGTCCT 62.974 66.667 0.00 0.00 0.00 3.85
4291 4556 4.410400 CTTCCCCAGCCCACGTCC 62.410 72.222 0.00 0.00 0.00 4.79
4292 4557 3.316573 CTCTTCCCCAGCCCACGTC 62.317 68.421 0.00 0.00 0.00 4.34
4293 4558 3.322466 CTCTTCCCCAGCCCACGT 61.322 66.667 0.00 0.00 0.00 4.49
4294 4559 3.003173 TCTCTTCCCCAGCCCACG 61.003 66.667 0.00 0.00 0.00 4.94
4295 4560 2.993853 CTCTCTTCCCCAGCCCAC 59.006 66.667 0.00 0.00 0.00 4.61
4296 4561 3.011517 GCTCTCTTCCCCAGCCCA 61.012 66.667 0.00 0.00 0.00 5.36
4297 4562 3.011517 TGCTCTCTTCCCCAGCCC 61.012 66.667 0.00 0.00 31.68 5.19
4298 4563 2.588989 CTGCTCTCTTCCCCAGCC 59.411 66.667 0.00 0.00 31.68 4.85
4299 4564 2.124778 GCTGCTCTCTTCCCCAGC 60.125 66.667 0.00 0.00 43.10 4.85
4300 4565 2.186384 CGCTGCTCTCTTCCCCAG 59.814 66.667 0.00 0.00 0.00 4.45
4301 4566 3.393970 CCGCTGCTCTCTTCCCCA 61.394 66.667 0.00 0.00 0.00 4.96
4302 4567 3.378399 GACCGCTGCTCTCTTCCCC 62.378 68.421 0.00 0.00 0.00 4.81
4303 4568 2.185608 GACCGCTGCTCTCTTCCC 59.814 66.667 0.00 0.00 0.00 3.97
4304 4569 2.202676 CGACCGCTGCTCTCTTCC 60.203 66.667 0.00 0.00 0.00 3.46
4305 4570 0.170561 TAACGACCGCTGCTCTCTTC 59.829 55.000 0.00 0.00 0.00 2.87
4306 4571 0.171455 CTAACGACCGCTGCTCTCTT 59.829 55.000 0.00 0.00 0.00 2.85
4307 4572 0.677098 TCTAACGACCGCTGCTCTCT 60.677 55.000 0.00 0.00 0.00 3.10
4308 4573 0.248296 CTCTAACGACCGCTGCTCTC 60.248 60.000 0.00 0.00 0.00 3.20
4309 4574 1.658686 CCTCTAACGACCGCTGCTCT 61.659 60.000 0.00 0.00 0.00 4.09
4310 4575 1.226717 CCTCTAACGACCGCTGCTC 60.227 63.158 0.00 0.00 0.00 4.26
4311 4576 2.885861 CCTCTAACGACCGCTGCT 59.114 61.111 0.00 0.00 0.00 4.24
4312 4577 2.886124 GCCTCTAACGACCGCTGC 60.886 66.667 0.00 0.00 0.00 5.25
4313 4578 2.579787 CGCCTCTAACGACCGCTG 60.580 66.667 0.00 0.00 0.00 5.18
4314 4579 3.048941 GACGCCTCTAACGACCGCT 62.049 63.158 0.00 0.00 0.00 5.52
4315 4580 2.578981 GACGCCTCTAACGACCGC 60.579 66.667 0.00 0.00 0.00 5.68
4316 4581 2.277120 CGACGCCTCTAACGACCG 60.277 66.667 0.00 0.00 0.00 4.79
4317 4582 1.226239 GACGACGCCTCTAACGACC 60.226 63.158 0.00 0.00 0.00 4.79
4318 4583 1.579626 CGACGACGCCTCTAACGAC 60.580 63.158 0.00 0.00 0.00 4.34
4319 4584 1.568612 AACGACGACGCCTCTAACGA 61.569 55.000 7.30 0.00 43.96 3.85
4320 4585 1.154338 AACGACGACGCCTCTAACG 60.154 57.895 7.30 0.00 43.96 3.18
4321 4586 1.069378 CCAACGACGACGCCTCTAAC 61.069 60.000 7.30 0.00 43.96 2.34
4322 4587 1.210931 CCAACGACGACGCCTCTAA 59.789 57.895 7.30 0.00 43.96 2.10
4323 4588 2.872557 CCAACGACGACGCCTCTA 59.127 61.111 7.30 0.00 43.96 2.43
4324 4589 4.719369 GCCAACGACGACGCCTCT 62.719 66.667 7.30 0.00 43.96 3.69
4345 4610 4.933064 CTCACCGAGATCGCCGCC 62.933 72.222 0.00 0.00 38.18 6.13
4346 4611 4.933064 CCTCACCGAGATCGCCGC 62.933 72.222 0.00 0.00 38.18 6.53
4347 4612 4.271816 CCCTCACCGAGATCGCCG 62.272 72.222 0.00 3.98 38.18 6.46
4348 4613 2.833582 TCCCTCACCGAGATCGCC 60.834 66.667 0.00 0.00 38.18 5.54
4349 4614 2.413765 GTCCCTCACCGAGATCGC 59.586 66.667 0.00 0.00 38.18 4.58
4350 4615 3.121019 GGTCCCTCACCGAGATCG 58.879 66.667 0.00 0.00 34.56 3.69
4360 4625 1.144936 CTGCGAGGAATGGTCCCTC 59.855 63.158 0.00 0.00 46.30 4.30
4361 4626 0.325296 TACTGCGAGGAATGGTCCCT 60.325 55.000 0.00 0.00 46.30 4.20
4362 4627 0.179081 GTACTGCGAGGAATGGTCCC 60.179 60.000 0.00 0.00 46.30 4.46
4363 4628 0.179081 GGTACTGCGAGGAATGGTCC 60.179 60.000 0.00 0.00 45.35 4.46
4364 4629 0.824759 AGGTACTGCGAGGAATGGTC 59.175 55.000 0.00 0.00 37.18 4.02
4365 4630 2.992476 AGGTACTGCGAGGAATGGT 58.008 52.632 0.00 0.00 37.18 3.55


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

AutoCloner maintained by Alex Coulton.