Multiple sequence alignment - TraesCS5B01G394500

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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 TraesCS5B01G394500 chr5B 100.000 3600 0 0 1 3600 572360676 572364275 0.000000e+00 6649.0
1 TraesCS5B01G394500 chr5B 82.561 453 62 15 3151 3598 572378743 572379183 2.030000e-102 383.0
2 TraesCS5B01G394500 chr5B 89.496 238 23 2 3341 3577 572390287 572390523 2.100000e-77 300.0
3 TraesCS5B01G394500 chr5B 91.463 82 5 2 830 911 572361477 572361556 1.060000e-20 111.0
4 TraesCS5B01G394500 chr5B 91.463 82 5 2 802 881 572361505 572361586 1.060000e-20 111.0
5 TraesCS5B01G394500 chr5D 88.614 2907 189 66 162 3006 465009166 465011992 0.000000e+00 3404.0
6 TraesCS5B01G394500 chr5D 91.803 488 25 9 3108 3585 465011992 465012474 0.000000e+00 665.0
7 TraesCS5B01G394500 chr5D 86.014 429 41 10 3163 3590 465021847 465022257 3.300000e-120 442.0
8 TraesCS5B01G394500 chr5D 88.703 239 25 2 3340 3577 465031248 465031485 1.260000e-74 291.0
9 TraesCS5B01G394500 chr5A 88.120 1894 112 63 35 1889 585413505 585415324 0.000000e+00 2146.0
10 TraesCS5B01G394500 chr5A 89.615 597 48 8 2387 2972 585415811 585416404 0.000000e+00 747.0
11 TraesCS5B01G394500 chr5A 92.540 496 17 7 3108 3585 585416498 585416991 0.000000e+00 693.0
12 TraesCS5B01G394500 chr5A 91.507 471 36 4 1934 2401 585415327 585415796 0.000000e+00 645.0
13 TraesCS5B01G394500 chr5A 82.863 461 53 23 3149 3599 585420930 585421374 1.210000e-104 390.0
14 TraesCS5B01G394500 chr5A 89.732 224 21 2 3342 3564 585429919 585430141 5.880000e-73 285.0
15 TraesCS5B01G394500 chr5A 94.215 121 6 1 2994 3114 32796131 32796250 2.210000e-42 183.0
16 TraesCS5B01G394500 chr5A 94.059 101 6 0 3149 3249 585428904 585429004 1.730000e-33 154.0
17 TraesCS5B01G394500 chr6B 96.296 108 4 0 3003 3110 23766472 23766365 1.030000e-40 178.0
18 TraesCS5B01G394500 chr3B 95.495 111 5 0 3002 3112 526281010 526281120 1.030000e-40 178.0
19 TraesCS5B01G394500 chr6A 93.913 115 7 0 3002 3116 596351528 596351414 1.330000e-39 174.0
20 TraesCS5B01G394500 chr6A 94.444 36 1 1 2013 2048 467743180 467743146 2.000000e-03 54.7
21 TraesCS5B01G394500 chr6D 93.277 119 5 3 2995 3113 3196493 3196378 4.780000e-39 172.0
22 TraesCS5B01G394500 chr2A 93.220 118 7 1 3003 3120 17612865 17612981 4.780000e-39 172.0
23 TraesCS5B01G394500 chr1A 93.220 118 7 1 2993 3109 507077245 507077362 4.780000e-39 172.0
24 TraesCS5B01G394500 chr1A 92.500 120 8 1 3003 3121 387511355 387511474 1.720000e-38 171.0
25 TraesCS5B01G394500 chr1B 92.500 120 7 1 3002 3119 405127468 405127349 1.720000e-38 171.0


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 TraesCS5B01G394500 chr5B 572360676 572364275 3599 False 2290.333333 6649 94.308667 1 3600 3 chr5B.!!$F3 3599
1 TraesCS5B01G394500 chr5D 465009166 465012474 3308 False 2034.500000 3404 90.208500 162 3585 2 chr5D.!!$F3 3423
2 TraesCS5B01G394500 chr5A 585413505 585421374 7869 False 924.200000 2146 88.929000 35 3599 5 chr5A.!!$F2 3564
3 TraesCS5B01G394500 chr5A 585428904 585430141 1237 False 219.500000 285 91.895500 3149 3564 2 chr5A.!!$F3 415

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
19 20 1.032794 CAGGATGATTGCAGCAGCAT 58.967 50.0 4.01 11.44 46.43 3.79 F
1720 1804 0.036388 TGAACCCTTGGATCAGCGTC 60.036 55.0 0.00 0.00 29.57 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1917 2004 0.750850 TGGCTATTCTCCTGGTACGC 59.249 55.0 0.00 0.00 0.00 4.42 R
3091 3285 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.0 14.79 0.04 33.41 4.30 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
18 19 2.489040 CAGGATGATTGCAGCAGCA 58.511 52.632 0.00 0.00 45.70 4.41
19 20 1.032794 CAGGATGATTGCAGCAGCAT 58.967 50.000 4.01 11.44 46.43 3.79
20 21 2.227194 CAGGATGATTGCAGCAGCATA 58.773 47.619 4.01 0.00 46.43 3.14
21 22 2.226674 CAGGATGATTGCAGCAGCATAG 59.773 50.000 4.01 3.76 46.43 2.23
22 23 4.914047 CAGGATGATTGCAGCAGCATAGG 61.914 52.174 4.01 3.20 46.43 2.57
24 25 7.995063 CAGGATGATTGCAGCAGCATAGGTA 62.995 48.000 4.01 0.00 46.43 3.08
33 34 4.872691 GCAGCAGCATAGGTAATATACAGG 59.127 45.833 0.00 0.00 41.58 4.00
52 53 3.132289 CAGGCAAGGTAATCGAAGGTAGA 59.868 47.826 0.00 0.00 0.00 2.59
93 94 6.899075 TGTAATACTAGAGCAGTAAAAGGGGA 59.101 38.462 0.00 0.00 43.00 4.81
115 116 4.349365 AGGAGAAAGAACAGAGGGAGTAG 58.651 47.826 0.00 0.00 0.00 2.57
499 521 3.771160 GGGTCGATCTGCCGTGGT 61.771 66.667 0.00 0.00 0.00 4.16
598 628 3.157949 GCCCTTCTCCTCCCTCGG 61.158 72.222 0.00 0.00 0.00 4.63
793 825 5.376854 TGCCACTCTCTGCTTTTATTTTC 57.623 39.130 0.00 0.00 0.00 2.29
838 871 4.812476 CGTCTCGGCCCGCATCAA 62.812 66.667 0.00 0.00 0.00 2.57
839 872 3.195698 GTCTCGGCCCGCATCAAC 61.196 66.667 0.00 0.00 0.00 3.18
840 873 4.467084 TCTCGGCCCGCATCAACC 62.467 66.667 0.00 0.00 0.00 3.77
850 883 3.781307 CATCAACCGAGGCCCCGA 61.781 66.667 8.85 0.00 0.00 5.14
851 884 3.782443 ATCAACCGAGGCCCCGAC 61.782 66.667 8.85 0.00 0.00 4.79
922 955 3.646715 CCCAGAAACCGGCCCTGA 61.647 66.667 16.91 0.00 0.00 3.86
924 957 2.747855 CAGAAACCGGCCCTGAGC 60.748 66.667 0.00 0.00 42.60 4.26
940 989 1.569479 GAGCCGACTGTGTTTGCTCC 61.569 60.000 0.00 0.00 41.95 4.70
957 1013 2.125350 CGTGAGAGCTTCCCTGGC 60.125 66.667 0.00 0.00 0.00 4.85
982 1038 2.757508 CTCCTCTCCAGCTCGGCA 60.758 66.667 0.00 0.00 33.14 5.69
995 1051 2.658548 TCGGCAAGAGAGCAGAGAA 58.341 52.632 0.00 0.00 33.83 2.87
999 1055 2.777094 GGCAAGAGAGCAGAGAAAACT 58.223 47.619 0.00 0.00 35.83 2.66
1006 1062 1.936547 GAGCAGAGAAAACTATGGCGG 59.063 52.381 0.00 0.00 0.00 6.13
1030 1086 2.123640 CGGAGGAGGAGGGGAGAC 60.124 72.222 0.00 0.00 0.00 3.36
1166 1222 1.464593 ACGAAGGGGAAAAGGGGGA 60.465 57.895 0.00 0.00 0.00 4.81
1342 1401 3.032339 CGCTCTACGCCTACCTCC 58.968 66.667 0.00 0.00 34.21 4.30
1509 1568 1.416772 GACCCTCCTTACCTGGTATGC 59.583 57.143 7.50 0.00 0.00 3.14
1511 1570 2.127708 CCCTCCTTACCTGGTATGCTT 58.872 52.381 7.50 0.00 0.00 3.91
1516 1575 3.054655 TCCTTACCTGGTATGCTTTCCAC 60.055 47.826 7.50 0.00 0.00 4.02
1517 1576 3.279434 CTTACCTGGTATGCTTTCCACC 58.721 50.000 7.50 0.00 0.00 4.61
1518 1577 1.072266 ACCTGGTATGCTTTCCACCA 58.928 50.000 0.00 0.00 40.01 4.17
1519 1578 1.640670 ACCTGGTATGCTTTCCACCAT 59.359 47.619 0.00 0.00 41.38 3.55
1520 1579 2.849943 ACCTGGTATGCTTTCCACCATA 59.150 45.455 0.00 0.00 41.38 2.74
1521 1580 3.117888 ACCTGGTATGCTTTCCACCATAG 60.118 47.826 0.00 0.00 41.38 2.23
1522 1581 3.136443 CCTGGTATGCTTTCCACCATAGA 59.864 47.826 0.00 0.00 41.38 1.98
1523 1582 4.202503 CCTGGTATGCTTTCCACCATAGAT 60.203 45.833 0.00 0.00 41.38 1.98
1524 1583 5.380043 CTGGTATGCTTTCCACCATAGATT 58.620 41.667 0.00 0.00 41.38 2.40
1525 1584 5.132502 TGGTATGCTTTCCACCATAGATTG 58.867 41.667 0.00 0.00 37.42 2.67
1539 1598 6.547141 CACCATAGATTGCCTCCTTTGATTTA 59.453 38.462 0.00 0.00 0.00 1.40
1540 1599 7.232127 CACCATAGATTGCCTCCTTTGATTTAT 59.768 37.037 0.00 0.00 0.00 1.40
1541 1600 8.448008 ACCATAGATTGCCTCCTTTGATTTATA 58.552 33.333 0.00 0.00 0.00 0.98
1545 1604 8.457238 AGATTGCCTCCTTTGATTTATACTTC 57.543 34.615 0.00 0.00 0.00 3.01
1551 1610 7.065923 GCCTCCTTTGATTTATACTTCGTTCTT 59.934 37.037 0.00 0.00 0.00 2.52
1557 1616 7.290857 TGATTTATACTTCGTTCTTGAGCAC 57.709 36.000 0.00 0.00 0.00 4.40
1560 1619 2.890808 ACTTCGTTCTTGAGCACAGA 57.109 45.000 0.00 0.00 0.00 3.41
1561 1627 3.179443 ACTTCGTTCTTGAGCACAGAA 57.821 42.857 0.00 0.00 0.00 3.02
1562 1628 3.531538 ACTTCGTTCTTGAGCACAGAAA 58.468 40.909 0.00 0.00 0.00 2.52
1564 1630 4.212214 ACTTCGTTCTTGAGCACAGAAATC 59.788 41.667 0.00 0.00 0.00 2.17
1574 1640 5.258841 TGAGCACAGAAATCCAGATTTGAT 58.741 37.500 10.26 0.00 40.77 2.57
1653 1732 3.760035 GGTCTCCTTCCTCGCGCA 61.760 66.667 8.75 0.00 0.00 6.09
1720 1804 0.036388 TGAACCCTTGGATCAGCGTC 60.036 55.000 0.00 0.00 29.57 5.19
1751 1835 6.127479 GGATCTAACTAGAATCCGATGCATCT 60.127 42.308 23.73 7.79 35.69 2.90
1752 1836 6.018589 TCTAACTAGAATCCGATGCATCTG 57.981 41.667 23.73 17.77 0.00 2.90
1759 1843 1.372582 TCCGATGCATCTGTTCTTGC 58.627 50.000 23.73 0.00 39.33 4.01
1766 1850 5.558463 CGATGCATCTGTTCTTGCTTGATAG 60.558 44.000 23.73 0.00 39.60 2.08
1767 1851 4.582869 TGCATCTGTTCTTGCTTGATAGT 58.417 39.130 0.00 0.00 39.60 2.12
1768 1852 5.733676 TGCATCTGTTCTTGCTTGATAGTA 58.266 37.500 0.00 0.00 39.60 1.82
1797 1882 2.099405 CATTGTAAAAGGGGTGCCGAT 58.901 47.619 0.00 0.00 0.00 4.18
1801 1886 2.040012 TGTAAAAGGGGTGCCGATTGTA 59.960 45.455 0.00 0.00 0.00 2.41
1809 1894 1.064060 GGTGCCGATTGTATGTGCTTC 59.936 52.381 0.00 0.00 0.00 3.86
1811 1896 0.304705 GCCGATTGTATGTGCTTCCG 59.695 55.000 0.00 0.00 0.00 4.30
1836 1921 6.238981 GGGTTGGATTTTGTTTTGCAATCAAT 60.239 34.615 15.04 5.10 36.89 2.57
1889 1976 9.896645 CCTATTACTATCAACAATCCATGCTAT 57.103 33.333 0.00 0.00 0.00 2.97
1899 1986 7.280876 TCAACAATCCATGCTATTACTTCTCAC 59.719 37.037 0.00 0.00 0.00 3.51
1917 2004 6.539649 TCTCACAAGACTTTTAACATTCGG 57.460 37.500 0.00 0.00 0.00 4.30
1919 2006 3.906008 CACAAGACTTTTAACATTCGGCG 59.094 43.478 0.00 0.00 0.00 6.46
1924 2011 3.401182 ACTTTTAACATTCGGCGTACCA 58.599 40.909 6.85 0.00 34.57 3.25
1951 2038 1.954651 GCCATAGGCGTTCGTAGGC 60.955 63.158 0.00 0.00 39.62 3.93
1956 2043 4.832608 GGCGTTCGTAGGCTGGGG 62.833 72.222 6.68 0.00 35.54 4.96
1968 2055 2.923035 CTGGGGGTGTGGTTGTCA 59.077 61.111 0.00 0.00 0.00 3.58
1998 2085 3.793797 ACCCACTTTGCTTTGTAACAC 57.206 42.857 0.00 0.00 0.00 3.32
2037 2124 7.994911 ACTCCTCTTTATCAATGCAATGATACA 59.005 33.333 21.44 15.32 40.92 2.29
2175 2263 7.595130 GCAGTTTATTTTCATCTTTCGAAACCT 59.405 33.333 6.47 0.00 32.27 3.50
2202 2290 2.857186 TGTGCCTCTTCTTGTATGCA 57.143 45.000 0.00 0.00 0.00 3.96
2232 2320 9.508567 GGTCTCTCTTAAAAATTGTATGCAATC 57.491 33.333 9.60 0.00 43.89 2.67
2329 2419 2.226437 AGCGTGATTGTAACTTTGCTGG 59.774 45.455 0.00 0.00 0.00 4.85
2349 2440 5.106673 GCTGGGAACATTACTAGTGTTGTTC 60.107 44.000 27.85 27.85 44.48 3.18
2359 2450 9.639601 CATTACTAGTGTTGTTCTGTGAGATAA 57.360 33.333 5.39 0.00 0.00 1.75
2364 2455 7.194607 AGTGTTGTTCTGTGAGATAACAATG 57.805 36.000 0.00 0.00 42.97 2.82
2394 2514 7.753580 ACCGAAATTTGTCTTTCCGAATAATTC 59.246 33.333 0.00 0.00 32.60 2.17
2417 2537 7.234187 TCGTTTGTTCTCTAATGCATATGAC 57.766 36.000 6.97 0.00 0.00 3.06
2420 2540 7.848051 CGTTTGTTCTCTAATGCATATGACTTC 59.152 37.037 6.97 0.00 0.00 3.01
2454 2574 0.034896 GGCGAAGTTCAGAAGGACCA 59.965 55.000 3.32 0.00 0.00 4.02
2497 2617 3.373565 CCCTGCGGTTTCAAGCCC 61.374 66.667 0.00 0.00 0.00 5.19
2554 2674 0.528924 TCACGAACTATGACCCGGTG 59.471 55.000 0.00 0.00 0.00 4.94
2608 2728 2.570135 GCCTCCATTTAGCCTTCTGAG 58.430 52.381 0.00 0.00 0.00 3.35
2613 2733 2.570135 CATTTAGCCTTCTGAGGAGGC 58.430 52.381 24.55 24.55 46.74 4.70
2618 2738 1.994507 CCTTCTGAGGAGGCTGCCT 60.995 63.158 23.64 23.64 46.74 4.75
2619 2739 1.221293 CTTCTGAGGAGGCTGCCTG 59.779 63.158 28.82 11.57 38.73 4.85
2633 2753 3.114616 CCTGTGGCGCTTGTCGAG 61.115 66.667 7.64 0.00 41.67 4.04
2637 2757 2.125552 TGGCGCTTGTCGAGATGG 60.126 61.111 7.64 0.00 41.67 3.51
2669 2790 2.424557 TCGTCCTATGGATACTCTCGC 58.575 52.381 0.00 0.00 32.73 5.03
2713 2834 5.785112 GGTAAACACGAATTTAGCACGTAAC 59.215 40.000 15.53 0.00 40.60 2.50
2714 2835 5.406767 AAACACGAATTTAGCACGTAACA 57.593 34.783 0.00 0.00 38.47 2.41
2731 2853 9.119329 GCACGTAACATTTTTGTTTGATACATA 57.881 29.630 0.00 0.00 36.44 2.29
2778 2900 2.749621 GGTGAACCAGATTCTTCGCAAT 59.250 45.455 0.00 0.00 38.25 3.56
2784 2906 6.150976 TGAACCAGATTCTTCGCAATTGTAAT 59.849 34.615 7.40 0.27 38.25 1.89
2806 2929 0.190815 ACCTGTTTTGAGCCCCCATT 59.809 50.000 0.00 0.00 0.00 3.16
2856 2979 1.071228 ACGTTACCACTTTCCTGGGAC 59.929 52.381 0.00 0.00 35.34 4.46
2861 2984 2.414612 ACCACTTTCCTGGGACAACTA 58.585 47.619 0.00 0.00 38.70 2.24
2864 2987 3.139077 CACTTTCCTGGGACAACTACAC 58.861 50.000 0.00 0.00 38.70 2.90
2895 3018 6.883217 AGATTGAACTTCTGAACATGCTACAT 59.117 34.615 0.00 0.00 0.00 2.29
2897 3020 6.968131 TGAACTTCTGAACATGCTACATAC 57.032 37.500 0.00 0.00 0.00 2.39
2898 3021 6.463360 TGAACTTCTGAACATGCTACATACA 58.537 36.000 0.00 0.00 0.00 2.29
2899 3022 6.368791 TGAACTTCTGAACATGCTACATACAC 59.631 38.462 0.00 0.00 0.00 2.90
2900 3023 5.793817 ACTTCTGAACATGCTACATACACA 58.206 37.500 0.00 0.00 0.00 3.72
2901 3024 6.409704 ACTTCTGAACATGCTACATACACAT 58.590 36.000 0.00 0.00 0.00 3.21
2904 3027 6.585416 TCTGAACATGCTACATACACATGAT 58.415 36.000 0.00 0.00 43.04 2.45
2905 3028 6.480981 TCTGAACATGCTACATACACATGATG 59.519 38.462 0.00 0.00 43.04 3.07
2907 3030 5.294734 ACATGCTACATACACATGATGGA 57.705 39.130 0.00 0.00 43.04 3.41
2933 3064 2.954318 ACCGAACATACTACACGGCTAT 59.046 45.455 0.00 0.00 46.18 2.97
2934 3065 4.136796 ACCGAACATACTACACGGCTATA 58.863 43.478 0.00 0.00 46.18 1.31
2972 3103 4.332543 CGCTACATCTTTATTGGAAGCACA 59.667 41.667 0.00 0.00 31.37 4.57
3006 3200 4.816786 GCCAGTGCTACTAGTACTACTC 57.183 50.000 6.51 0.97 39.17 2.59
3007 3201 3.565063 GCCAGTGCTACTAGTACTACTCC 59.435 52.174 6.51 3.70 39.17 3.85
3008 3202 3.808726 CCAGTGCTACTAGTACTACTCCG 59.191 52.174 6.51 0.00 39.17 4.63
3010 3204 4.507388 CAGTGCTACTAGTACTACTCCGTC 59.493 50.000 6.51 0.00 39.17 4.79
3011 3205 3.807071 GTGCTACTAGTACTACTCCGTCC 59.193 52.174 0.00 0.00 0.00 4.79
3012 3206 3.056304 GCTACTAGTACTACTCCGTCCG 58.944 54.545 0.00 0.00 0.00 4.79
3013 3207 3.491792 GCTACTAGTACTACTCCGTCCGT 60.492 52.174 0.00 0.00 0.00 4.69
3014 3208 3.618690 ACTAGTACTACTCCGTCCGTT 57.381 47.619 0.00 0.00 0.00 4.44
3015 3209 3.526534 ACTAGTACTACTCCGTCCGTTC 58.473 50.000 0.00 0.00 0.00 3.95
3016 3210 1.363744 AGTACTACTCCGTCCGTTCG 58.636 55.000 0.00 0.00 0.00 3.95
3027 3221 2.331194 CGTCCGTTCGGAATTACTTGT 58.669 47.619 15.59 0.00 35.89 3.16
3028 3222 2.343544 CGTCCGTTCGGAATTACTTGTC 59.656 50.000 15.59 0.00 35.89 3.18
3029 3223 3.582780 GTCCGTTCGGAATTACTTGTCT 58.417 45.455 15.59 0.00 35.89 3.41
3030 3224 3.611549 GTCCGTTCGGAATTACTTGTCTC 59.388 47.826 15.59 0.00 35.89 3.36
3031 3225 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
3032 3226 3.495193 CGTTCGGAATTACTTGTCTCGA 58.505 45.455 0.00 0.00 0.00 4.04
3033 3227 3.916172 CGTTCGGAATTACTTGTCTCGAA 59.084 43.478 0.00 0.00 33.66 3.71
3034 3228 4.383649 CGTTCGGAATTACTTGTCTCGAAA 59.616 41.667 0.00 0.00 37.00 3.46
3035 3229 5.107760 CGTTCGGAATTACTTGTCTCGAAAA 60.108 40.000 0.00 0.00 37.00 2.29
3036 3230 6.400727 CGTTCGGAATTACTTGTCTCGAAAAT 60.401 38.462 0.00 0.00 37.00 1.82
3037 3231 6.403333 TCGGAATTACTTGTCTCGAAAATG 57.597 37.500 0.00 0.00 0.00 2.32
3038 3232 5.350365 TCGGAATTACTTGTCTCGAAAATGG 59.650 40.000 0.00 0.00 0.00 3.16
3039 3233 5.350365 CGGAATTACTTGTCTCGAAAATGGA 59.650 40.000 0.00 0.00 0.00 3.41
3040 3234 6.037172 CGGAATTACTTGTCTCGAAAATGGAT 59.963 38.462 0.00 0.00 0.00 3.41
3041 3235 7.189512 GGAATTACTTGTCTCGAAAATGGATG 58.810 38.462 0.00 0.00 0.00 3.51
3042 3236 7.148239 GGAATTACTTGTCTCGAAAATGGATGT 60.148 37.037 0.00 0.00 0.00 3.06
3043 3237 8.786826 AATTACTTGTCTCGAAAATGGATGTA 57.213 30.769 0.00 0.00 0.00 2.29
3044 3238 8.964476 ATTACTTGTCTCGAAAATGGATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
3045 3239 6.910536 ACTTGTCTCGAAAATGGATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
3046 3240 6.644347 ACTTGTCTCGAAAATGGATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
3047 3241 7.782049 ACTTGTCTCGAAAATGGATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
3048 3242 7.923344 ACTTGTCTCGAAAATGGATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
3049 3243 7.582667 TGTCTCGAAAATGGATGTATCTAGA 57.417 36.000 0.00 0.00 0.00 2.43
3050 3244 8.183104 TGTCTCGAAAATGGATGTATCTAGAT 57.817 34.615 10.73 10.73 0.00 1.98
3051 3245 8.300286 TGTCTCGAAAATGGATGTATCTAGATC 58.700 37.037 8.95 2.00 0.00 2.75
3052 3246 8.519526 GTCTCGAAAATGGATGTATCTAGATCT 58.480 37.037 8.95 0.00 0.00 2.75
3053 3247 9.740710 TCTCGAAAATGGATGTATCTAGATCTA 57.259 33.333 8.95 1.69 0.00 1.98
3081 3275 8.684973 ATACGTTTAGATACATCTATTTCCGC 57.315 34.615 0.00 0.00 39.02 5.54
3082 3276 5.628193 ACGTTTAGATACATCTATTTCCGCG 59.372 40.000 0.00 0.00 39.02 6.46
3083 3277 5.854866 CGTTTAGATACATCTATTTCCGCGA 59.145 40.000 8.23 0.00 39.02 5.87
3084 3278 6.183359 CGTTTAGATACATCTATTTCCGCGAC 60.183 42.308 8.23 0.00 39.02 5.19
3085 3279 4.848562 AGATACATCTATTTCCGCGACA 57.151 40.909 8.23 0.00 34.85 4.35
3086 3280 5.196341 AGATACATCTATTTCCGCGACAA 57.804 39.130 8.23 0.00 34.85 3.18
3087 3281 5.223382 AGATACATCTATTTCCGCGACAAG 58.777 41.667 8.23 0.00 34.85 3.16
3088 3282 3.247006 ACATCTATTTCCGCGACAAGT 57.753 42.857 8.23 0.00 0.00 3.16
3089 3283 4.380841 ACATCTATTTCCGCGACAAGTA 57.619 40.909 8.23 0.00 0.00 2.24
3090 3284 4.751060 ACATCTATTTCCGCGACAAGTAA 58.249 39.130 8.23 0.00 0.00 2.24
3091 3285 5.357257 ACATCTATTTCCGCGACAAGTAAT 58.643 37.500 8.23 0.00 0.00 1.89
3092 3286 5.815740 ACATCTATTTCCGCGACAAGTAATT 59.184 36.000 8.23 0.00 0.00 1.40
3093 3287 5.961395 TCTATTTCCGCGACAAGTAATTC 57.039 39.130 8.23 0.00 0.00 2.17
3094 3288 4.807304 TCTATTTCCGCGACAAGTAATTCC 59.193 41.667 8.23 0.00 0.00 3.01
3095 3289 1.352114 TTCCGCGACAAGTAATTCCG 58.648 50.000 8.23 0.00 0.00 4.30
3096 3290 0.527113 TCCGCGACAAGTAATTCCGA 59.473 50.000 8.23 0.00 0.00 4.55
3097 3291 1.067706 TCCGCGACAAGTAATTCCGAA 60.068 47.619 8.23 0.00 0.00 4.30
3098 3292 1.060122 CCGCGACAAGTAATTCCGAAC 59.940 52.381 8.23 0.00 0.00 3.95
3099 3293 1.266211 CGCGACAAGTAATTCCGAACG 60.266 52.381 0.00 0.00 0.00 3.95
3100 3294 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
3101 3295 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
3102 3296 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
3103 3297 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
3104 3298 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3105 3299 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
3106 3300 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
3107 3301 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
3108 3302 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
3121 3315 3.576648 GAGGGAGTAGTTGACAAACGAG 58.423 50.000 0.00 0.00 41.45 4.18
3198 3402 1.079405 GACGATGAGAACGGGGCAA 60.079 57.895 0.00 0.00 34.93 4.52
3234 3438 3.062466 TAGTCGCTCACGCTGCCT 61.062 61.111 0.00 0.00 39.84 4.75
3292 3811 3.626680 TAGCACAGCCGCTCACGTC 62.627 63.158 0.00 0.00 42.62 4.34
3304 3831 1.154197 CTCACGTCAGTCGGTAGTGA 58.846 55.000 0.00 0.00 44.69 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.872691 CCTGTATATTACCTATGCTGCTGC 59.127 45.833 8.89 8.89 40.20 5.25
11 12 4.872691 GCCTGTATATTACCTATGCTGCTG 59.127 45.833 0.00 0.00 0.00 4.41
12 13 4.532126 TGCCTGTATATTACCTATGCTGCT 59.468 41.667 0.00 0.00 0.00 4.24
13 14 4.832248 TGCCTGTATATTACCTATGCTGC 58.168 43.478 0.00 0.00 0.00 5.25
14 15 5.877012 CCTTGCCTGTATATTACCTATGCTG 59.123 44.000 0.00 0.00 0.00 4.41
15 16 5.548056 ACCTTGCCTGTATATTACCTATGCT 59.452 40.000 0.00 0.00 0.00 3.79
16 17 5.805728 ACCTTGCCTGTATATTACCTATGC 58.194 41.667 0.00 0.00 0.00 3.14
17 18 9.601217 GATTACCTTGCCTGTATATTACCTATG 57.399 37.037 0.00 0.00 0.00 2.23
18 19 8.475639 CGATTACCTTGCCTGTATATTACCTAT 58.524 37.037 0.00 0.00 0.00 2.57
19 20 7.670979 TCGATTACCTTGCCTGTATATTACCTA 59.329 37.037 0.00 0.00 0.00 3.08
20 21 6.495872 TCGATTACCTTGCCTGTATATTACCT 59.504 38.462 0.00 0.00 0.00 3.08
21 22 6.694447 TCGATTACCTTGCCTGTATATTACC 58.306 40.000 0.00 0.00 0.00 2.85
22 23 7.331193 CCTTCGATTACCTTGCCTGTATATTAC 59.669 40.741 0.00 0.00 0.00 1.89
23 24 7.015877 ACCTTCGATTACCTTGCCTGTATATTA 59.984 37.037 0.00 0.00 0.00 0.98
24 25 6.183361 ACCTTCGATTACCTTGCCTGTATATT 60.183 38.462 0.00 0.00 0.00 1.28
25 26 5.307196 ACCTTCGATTACCTTGCCTGTATAT 59.693 40.000 0.00 0.00 0.00 0.86
26 27 4.652421 ACCTTCGATTACCTTGCCTGTATA 59.348 41.667 0.00 0.00 0.00 1.47
27 28 3.454812 ACCTTCGATTACCTTGCCTGTAT 59.545 43.478 0.00 0.00 0.00 2.29
28 29 2.835764 ACCTTCGATTACCTTGCCTGTA 59.164 45.455 0.00 0.00 0.00 2.74
29 30 1.628846 ACCTTCGATTACCTTGCCTGT 59.371 47.619 0.00 0.00 0.00 4.00
30 31 2.403252 ACCTTCGATTACCTTGCCTG 57.597 50.000 0.00 0.00 0.00 4.85
31 32 3.371965 TCTACCTTCGATTACCTTGCCT 58.628 45.455 0.00 0.00 0.00 4.75
32 33 3.814005 TCTACCTTCGATTACCTTGCC 57.186 47.619 0.00 0.00 0.00 4.52
33 34 6.759827 TGTTTATCTACCTTCGATTACCTTGC 59.240 38.462 0.00 0.00 0.00 4.01
66 67 8.867097 CCCCTTTTACTGCTCTAGTATTACATA 58.133 37.037 0.00 0.00 41.36 2.29
67 68 7.567622 TCCCCTTTTACTGCTCTAGTATTACAT 59.432 37.037 0.00 0.00 41.36 2.29
77 78 2.192263 CTCCTCCCCTTTTACTGCTCT 58.808 52.381 0.00 0.00 0.00 4.09
88 89 2.545810 CTCTGTTCTTTCTCCTCCCCT 58.454 52.381 0.00 0.00 0.00 4.79
89 90 1.557371 CCTCTGTTCTTTCTCCTCCCC 59.443 57.143 0.00 0.00 0.00 4.81
93 94 3.268034 ACTCCCTCTGTTCTTTCTCCT 57.732 47.619 0.00 0.00 0.00 3.69
115 116 1.559682 TGATGTCAGCCCTAAACCTCC 59.440 52.381 0.00 0.00 0.00 4.30
363 364 1.594833 CCGATCCGGTTTGGTCTGA 59.405 57.895 10.36 0.00 42.73 3.27
440 452 4.135153 CTCCGTGCGGTGAGGAGG 62.135 72.222 10.60 0.00 45.77 4.30
530 552 3.989595 GTAGCATTCGCGCTCGCC 61.990 66.667 5.56 0.00 42.62 5.54
531 553 3.989595 GGTAGCATTCGCGCTCGC 61.990 66.667 5.56 3.90 42.62 5.03
532 554 2.278857 AGGTAGCATTCGCGCTCG 60.279 61.111 5.56 0.00 42.62 5.03
533 555 2.296480 CGAGGTAGCATTCGCGCTC 61.296 63.158 5.56 0.00 42.62 5.03
534 556 2.278857 CGAGGTAGCATTCGCGCT 60.279 61.111 5.56 0.00 45.49 5.92
646 676 3.438615 ATCTCCCGTCCTCCTCCCG 62.439 68.421 0.00 0.00 0.00 5.14
650 680 2.835431 CGCATCTCCCGTCCTCCT 60.835 66.667 0.00 0.00 0.00 3.69
894 927 2.890766 TTTCTGGGCCTCGGTGGAC 61.891 63.158 4.53 0.00 45.48 4.02
921 954 1.862806 GAGCAAACACAGTCGGCTC 59.137 57.895 0.00 0.00 43.41 4.70
922 955 1.598130 GGAGCAAACACAGTCGGCT 60.598 57.895 0.00 0.00 37.56 5.52
924 957 1.594293 ACGGAGCAAACACAGTCGG 60.594 57.895 0.00 0.00 0.00 4.79
940 989 2.125350 GCCAGGGAAGCTCTCACG 60.125 66.667 0.00 0.00 30.05 4.35
982 1038 4.512484 GCCATAGTTTTCTCTGCTCTCTT 58.488 43.478 0.00 0.00 0.00 2.85
990 1046 0.462047 CGCCCGCCATAGTTTTCTCT 60.462 55.000 0.00 0.00 0.00 3.10
1166 1222 1.162085 AGCTCCACCCCTTCTCCTT 59.838 57.895 0.00 0.00 0.00 3.36
1342 1401 3.854669 ATCCGGGCTGCTCTTCCG 61.855 66.667 0.00 7.91 43.05 4.30
1509 1568 3.117738 AGGAGGCAATCTATGGTGGAAAG 60.118 47.826 0.00 0.00 0.00 2.62
1511 1570 2.492025 AGGAGGCAATCTATGGTGGAA 58.508 47.619 0.00 0.00 0.00 3.53
1516 1575 7.771927 ATAAATCAAAGGAGGCAATCTATGG 57.228 36.000 0.00 0.00 0.00 2.74
1517 1576 9.512588 AGTATAAATCAAAGGAGGCAATCTATG 57.487 33.333 0.00 0.00 0.00 2.23
1519 1578 9.561069 GAAGTATAAATCAAAGGAGGCAATCTA 57.439 33.333 0.00 0.00 0.00 1.98
1520 1579 7.227512 CGAAGTATAAATCAAAGGAGGCAATCT 59.772 37.037 0.00 0.00 0.00 2.40
1521 1580 7.012421 ACGAAGTATAAATCAAAGGAGGCAATC 59.988 37.037 0.00 0.00 41.94 2.67
1522 1581 6.828785 ACGAAGTATAAATCAAAGGAGGCAAT 59.171 34.615 0.00 0.00 41.94 3.56
1523 1582 6.177610 ACGAAGTATAAATCAAAGGAGGCAA 58.822 36.000 0.00 0.00 41.94 4.52
1524 1583 5.741011 ACGAAGTATAAATCAAAGGAGGCA 58.259 37.500 0.00 0.00 41.94 4.75
1525 1584 6.539103 AGAACGAAGTATAAATCAAAGGAGGC 59.461 38.462 0.00 0.00 45.00 4.70
1539 1598 4.521130 TCTGTGCTCAAGAACGAAGTAT 57.479 40.909 0.00 0.00 45.00 2.12
1540 1599 4.316205 TTCTGTGCTCAAGAACGAAGTA 57.684 40.909 0.00 0.00 45.00 2.24
1545 1604 2.807967 TGGATTTCTGTGCTCAAGAACG 59.192 45.455 0.00 0.00 0.00 3.95
1551 1610 4.654915 TCAAATCTGGATTTCTGTGCTCA 58.345 39.130 5.68 0.00 38.84 4.26
1557 1616 8.869897 CACAATTCAATCAAATCTGGATTTCTG 58.130 33.333 5.68 4.89 38.84 3.02
1560 1619 7.604927 CACCACAATTCAATCAAATCTGGATTT 59.395 33.333 3.06 3.06 41.33 2.17
1561 1627 7.038870 TCACCACAATTCAATCAAATCTGGATT 60.039 33.333 0.00 0.00 35.43 3.01
1562 1628 6.438108 TCACCACAATTCAATCAAATCTGGAT 59.562 34.615 0.00 0.00 0.00 3.41
1564 1630 6.028146 TCACCACAATTCAATCAAATCTGG 57.972 37.500 0.00 0.00 0.00 3.86
1574 1640 4.909696 ACAACGAATCACCACAATTCAA 57.090 36.364 0.00 0.00 33.60 2.69
1697 1781 1.815003 GCTGATCCAAGGGTTCAGTTG 59.185 52.381 19.27 2.38 45.92 3.16
1720 1804 5.238868 TCGGATTCTAGTTAGATCCAAGACG 59.761 44.000 13.55 0.00 33.44 4.18
1751 1835 6.595326 CCATGAAGTACTATCAAGCAAGAACA 59.405 38.462 0.00 0.00 0.00 3.18
1752 1836 6.457528 GCCATGAAGTACTATCAAGCAAGAAC 60.458 42.308 18.08 0.00 33.05 3.01
1759 1843 6.932356 ACAATGCCATGAAGTACTATCAAG 57.068 37.500 0.00 0.00 0.00 3.02
1766 1850 5.394115 CCCCTTTTACAATGCCATGAAGTAC 60.394 44.000 0.00 0.00 0.00 2.73
1767 1851 4.709397 CCCCTTTTACAATGCCATGAAGTA 59.291 41.667 0.00 0.00 0.00 2.24
1768 1852 3.515104 CCCCTTTTACAATGCCATGAAGT 59.485 43.478 0.00 0.00 0.00 3.01
1797 1882 1.529226 CAACCCGGAAGCACATACAA 58.471 50.000 0.73 0.00 0.00 2.41
1801 1886 3.166434 TCCAACCCGGAAGCACAT 58.834 55.556 0.73 0.00 42.52 3.21
1809 1894 1.870402 GCAAAACAAAATCCAACCCGG 59.130 47.619 0.00 0.00 0.00 5.73
1811 1896 4.578105 TGATTGCAAAACAAAATCCAACCC 59.422 37.500 1.71 0.00 42.86 4.11
1836 1921 4.658063 ACCCGAAATCATACTGTTTTCCA 58.342 39.130 0.00 0.00 34.33 3.53
1854 1939 7.223260 TGTTGATAGTAATAGGTGATACCCG 57.777 40.000 0.00 0.00 39.75 5.28
1899 1986 4.141855 ACGCCGAATGTTAAAAGTCTTG 57.858 40.909 0.00 0.00 0.00 3.02
1917 2004 0.750850 TGGCTATTCTCCTGGTACGC 59.249 55.000 0.00 0.00 0.00 4.42
1919 2006 3.055747 GCCTATGGCTATTCTCCTGGTAC 60.056 52.174 0.73 0.00 46.69 3.34
1941 2028 3.387947 ACCCCCAGCCTACGAACG 61.388 66.667 0.00 0.00 0.00 3.95
1951 2038 1.106944 GTTGACAACCACACCCCCAG 61.107 60.000 7.10 0.00 0.00 4.45
1956 2043 1.546476 TGGTTTGTTGACAACCACACC 59.454 47.619 15.59 16.88 34.49 4.16
1968 2055 2.705730 GCAAAGTGGGTTTGGTTTGTT 58.294 42.857 0.04 0.00 45.10 2.83
1998 2085 4.457834 AAGAGGAGTTTCACATAGGTCG 57.542 45.455 0.00 0.00 0.00 4.79
2037 2124 5.511202 CCCCATGAATACACAAAAGCTTTGT 60.511 40.000 13.54 10.01 0.00 2.83
2080 2168 5.774878 TCGATCTACCGAGATGTAATACG 57.225 43.478 0.00 0.00 42.80 3.06
2175 2263 4.910195 ACAAGAAGAGGCACATCATGTAA 58.090 39.130 0.00 0.00 0.00 2.41
2202 2290 9.860898 GCATACAATTTTTAAGAGAGACCATTT 57.139 29.630 0.00 0.00 0.00 2.32
2242 2331 3.433274 ACACATTCTGATGCTAACACACG 59.567 43.478 0.00 0.00 36.72 4.49
2349 2440 5.407502 TCGGTACACATTGTTATCTCACAG 58.592 41.667 0.00 0.00 0.00 3.66
2359 2450 6.385649 AAGACAAATTTCGGTACACATTGT 57.614 33.333 0.00 0.00 32.68 2.71
2364 2455 4.211794 TCGGAAAGACAAATTTCGGTACAC 59.788 41.667 0.00 0.00 39.59 2.90
2394 2514 7.239166 AGTCATATGCATTAGAGAACAAACG 57.761 36.000 3.54 0.00 0.00 3.60
2417 2537 1.538950 GCCTGGCAGAAGAAGTTGAAG 59.461 52.381 17.94 0.00 0.00 3.02
2420 2540 0.603707 TCGCCTGGCAGAAGAAGTTG 60.604 55.000 20.29 0.00 0.00 3.16
2497 2617 0.588252 CCAGTTTGTTCGAGTGCTGG 59.412 55.000 8.44 8.44 37.71 4.85
2554 2674 1.302832 CCAGCCACCAAGTCTGTCC 60.303 63.158 0.00 0.00 0.00 4.02
2591 2711 2.774234 CCTCCTCAGAAGGCTAAATGGA 59.226 50.000 0.00 0.00 43.02 3.41
2618 2738 1.737735 CATCTCGACAAGCGCCACA 60.738 57.895 2.29 0.00 40.61 4.17
2619 2739 2.456119 CCATCTCGACAAGCGCCAC 61.456 63.158 2.29 0.00 40.61 5.01
2623 2743 0.803768 CTGTCCCATCTCGACAAGCG 60.804 60.000 0.00 0.00 39.66 4.68
2630 2750 0.179100 AACATCGCTGTCCCATCTCG 60.179 55.000 0.00 0.00 33.36 4.04
2633 2753 0.460284 ACGAACATCGCTGTCCCATC 60.460 55.000 0.00 0.00 45.12 3.51
2637 2757 3.782042 GGACGAACATCGCTGTCC 58.218 61.111 0.00 0.00 45.12 4.02
2651 2772 3.759086 TCATGCGAGAGTATCCATAGGAC 59.241 47.826 0.00 0.00 32.98 3.85
2669 2790 3.945921 ACCAGACTGAAAGATGCATCATG 59.054 43.478 27.81 14.36 37.43 3.07
2731 2853 6.694877 ATACGTGAGAGTACACATACACAT 57.305 37.500 0.00 0.00 40.34 3.21
2738 2860 5.247862 TCACCTAATACGTGAGAGTACACA 58.752 41.667 0.00 0.00 40.34 3.72
2741 2863 5.124457 TGGTTCACCTAATACGTGAGAGTAC 59.876 44.000 0.00 0.00 41.10 2.73
2778 2900 5.007682 GGGCTCAAAACAGGTAGATTACAA 58.992 41.667 0.00 0.00 0.00 2.41
2784 2906 0.696501 GGGGGCTCAAAACAGGTAGA 59.303 55.000 0.00 0.00 0.00 2.59
2846 2969 2.040939 TCGTGTAGTTGTCCCAGGAAA 58.959 47.619 0.00 0.00 0.00 3.13
2856 2979 6.712241 AGTTCAATCTCAATCGTGTAGTTG 57.288 37.500 0.00 0.00 0.00 3.16
2861 2984 5.541845 TCAGAAGTTCAATCTCAATCGTGT 58.458 37.500 5.50 0.00 0.00 4.49
2864 2987 6.471976 TGTTCAGAAGTTCAATCTCAATCG 57.528 37.500 5.50 0.00 0.00 3.34
2895 3018 1.686587 CGGTAGGCTCCATCATGTGTA 59.313 52.381 0.00 0.00 0.00 2.90
2897 3020 0.752658 TCGGTAGGCTCCATCATGTG 59.247 55.000 0.00 0.00 0.00 3.21
2898 3021 1.139058 GTTCGGTAGGCTCCATCATGT 59.861 52.381 0.00 0.00 0.00 3.21
2899 3022 1.138859 TGTTCGGTAGGCTCCATCATG 59.861 52.381 0.00 0.00 0.00 3.07
2900 3023 1.496060 TGTTCGGTAGGCTCCATCAT 58.504 50.000 0.00 0.00 0.00 2.45
2901 3024 1.496060 ATGTTCGGTAGGCTCCATCA 58.504 50.000 0.00 0.00 0.00 3.07
2904 3027 2.154567 AGTATGTTCGGTAGGCTCCA 57.845 50.000 0.00 0.00 0.00 3.86
2905 3028 2.954318 TGTAGTATGTTCGGTAGGCTCC 59.046 50.000 0.00 0.00 0.00 4.70
2907 3030 2.357009 CGTGTAGTATGTTCGGTAGGCT 59.643 50.000 0.00 0.00 0.00 4.58
2933 3064 2.782222 GCGATGGAGCTCCCGTGTA 61.782 63.158 29.95 11.51 37.93 2.90
2934 3065 4.148825 GCGATGGAGCTCCCGTGT 62.149 66.667 29.95 13.22 37.93 4.49
3007 3201 2.331194 ACAAGTAATTCCGAACGGACG 58.669 47.619 15.63 1.96 45.11 4.79
3008 3202 3.582780 AGACAAGTAATTCCGAACGGAC 58.417 45.455 15.63 5.16 45.11 4.79
3010 3204 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
3011 3205 3.495193 TCGAGACAAGTAATTCCGAACG 58.505 45.455 0.00 0.00 0.00 3.95
3012 3206 5.834239 TTTCGAGACAAGTAATTCCGAAC 57.166 39.130 0.00 0.00 34.86 3.95
3013 3207 6.128391 CCATTTTCGAGACAAGTAATTCCGAA 60.128 38.462 0.00 0.00 33.57 4.30
3014 3208 5.350365 CCATTTTCGAGACAAGTAATTCCGA 59.650 40.000 0.00 0.00 0.00 4.55
3015 3209 5.350365 TCCATTTTCGAGACAAGTAATTCCG 59.650 40.000 0.00 0.00 0.00 4.30
3016 3210 6.737254 TCCATTTTCGAGACAAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
3018 3212 7.687941 ACATCCATTTTCGAGACAAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
3019 3213 8.964476 ATACATCCATTTTCGAGACAAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
3020 3214 8.258007 AGATACATCCATTTTCGAGACAAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
3021 3215 7.782049 AGATACATCCATTTTCGAGACAAGTA 58.218 34.615 0.00 0.00 0.00 2.24
3022 3216 6.644347 AGATACATCCATTTTCGAGACAAGT 58.356 36.000 0.00 0.00 0.00 3.16
3023 3217 8.138074 TCTAGATACATCCATTTTCGAGACAAG 58.862 37.037 0.00 0.00 0.00 3.16
3024 3218 8.007405 TCTAGATACATCCATTTTCGAGACAA 57.993 34.615 0.00 0.00 0.00 3.18
3025 3219 7.582667 TCTAGATACATCCATTTTCGAGACA 57.417 36.000 0.00 0.00 0.00 3.41
3026 3220 8.519526 AGATCTAGATACATCCATTTTCGAGAC 58.480 37.037 4.89 0.00 0.00 3.36
3027 3221 8.642935 AGATCTAGATACATCCATTTTCGAGA 57.357 34.615 4.89 0.00 0.00 4.04
3055 3249 9.136952 GCGGAAATAGATGTATCTAAACGTATT 57.863 33.333 5.75 0.00 42.20 1.89
3056 3250 7.484007 CGCGGAAATAGATGTATCTAAACGTAT 59.516 37.037 0.00 0.00 42.20 3.06
3057 3251 6.798476 CGCGGAAATAGATGTATCTAAACGTA 59.202 38.462 0.00 0.00 42.20 3.57
3058 3252 5.628193 CGCGGAAATAGATGTATCTAAACGT 59.372 40.000 0.00 0.00 42.20 3.99
3059 3253 5.854866 TCGCGGAAATAGATGTATCTAAACG 59.145 40.000 6.13 8.75 42.20 3.60
3060 3254 6.639686 TGTCGCGGAAATAGATGTATCTAAAC 59.360 38.462 6.13 0.00 42.20 2.01
3061 3255 6.741109 TGTCGCGGAAATAGATGTATCTAAA 58.259 36.000 6.13 0.00 42.20 1.85
3062 3256 6.321848 TGTCGCGGAAATAGATGTATCTAA 57.678 37.500 6.13 0.00 42.20 2.10
3063 3257 5.952526 TGTCGCGGAAATAGATGTATCTA 57.047 39.130 6.13 4.22 43.00 1.98
3064 3258 4.848562 TGTCGCGGAAATAGATGTATCT 57.151 40.909 6.13 0.00 40.86 1.98
3065 3259 4.982916 ACTTGTCGCGGAAATAGATGTATC 59.017 41.667 6.13 0.00 0.00 2.24
3066 3260 4.945246 ACTTGTCGCGGAAATAGATGTAT 58.055 39.130 6.13 0.00 0.00 2.29
3067 3261 4.380841 ACTTGTCGCGGAAATAGATGTA 57.619 40.909 6.13 0.00 0.00 2.29
3068 3262 3.247006 ACTTGTCGCGGAAATAGATGT 57.753 42.857 6.13 0.00 0.00 3.06
3069 3263 5.907197 ATTACTTGTCGCGGAAATAGATG 57.093 39.130 6.13 0.00 0.00 2.90
3070 3264 5.465724 GGAATTACTTGTCGCGGAAATAGAT 59.534 40.000 6.13 0.00 0.00 1.98
3071 3265 4.807304 GGAATTACTTGTCGCGGAAATAGA 59.193 41.667 6.13 0.00 0.00 1.98
3072 3266 4.317839 CGGAATTACTTGTCGCGGAAATAG 60.318 45.833 6.13 0.00 0.00 1.73
3073 3267 3.552699 CGGAATTACTTGTCGCGGAAATA 59.447 43.478 6.13 0.00 0.00 1.40
3074 3268 2.350498 CGGAATTACTTGTCGCGGAAAT 59.650 45.455 6.13 0.00 0.00 2.17
3075 3269 1.727880 CGGAATTACTTGTCGCGGAAA 59.272 47.619 6.13 0.00 0.00 3.13
3076 3270 1.067706 TCGGAATTACTTGTCGCGGAA 60.068 47.619 6.13 0.00 0.00 4.30
3077 3271 0.527113 TCGGAATTACTTGTCGCGGA 59.473 50.000 6.13 0.00 0.00 5.54
3078 3272 1.060122 GTTCGGAATTACTTGTCGCGG 59.940 52.381 6.13 0.00 0.00 6.46
3079 3273 1.266211 CGTTCGGAATTACTTGTCGCG 60.266 52.381 0.00 0.00 0.00 5.87
3080 3274 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
3081 3275 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
3082 3276 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
3083 3277 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
3084 3278 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3085 3279 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3086 3280 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
3087 3281 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3088 3282 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3089 3283 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
3090 3284 1.341778 ACTACTCCCTCCGTTCGGAAT 60.342 52.381 14.79 2.09 33.41 3.01
3091 3285 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
3092 3286 0.038744 AACTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
3093 3287 0.172803 CAACTACTCCCTCCGTTCGG 59.827 60.000 4.74 4.74 0.00 4.30
3094 3288 1.135460 GTCAACTACTCCCTCCGTTCG 60.135 57.143 0.00 0.00 0.00 3.95
3095 3289 1.891150 TGTCAACTACTCCCTCCGTTC 59.109 52.381 0.00 0.00 0.00 3.95
3096 3290 2.005370 TGTCAACTACTCCCTCCGTT 57.995 50.000 0.00 0.00 0.00 4.44
3097 3291 2.005370 TTGTCAACTACTCCCTCCGT 57.995 50.000 0.00 0.00 0.00 4.69
3098 3292 2.685100 GTTTGTCAACTACTCCCTCCG 58.315 52.381 0.00 0.00 0.00 4.63
3099 3293 2.298163 TCGTTTGTCAACTACTCCCTCC 59.702 50.000 0.00 0.00 0.00 4.30
3100 3294 3.576648 CTCGTTTGTCAACTACTCCCTC 58.423 50.000 0.00 0.00 0.00 4.30
3101 3295 2.288886 GCTCGTTTGTCAACTACTCCCT 60.289 50.000 0.00 0.00 0.00 4.20
3102 3296 2.067013 GCTCGTTTGTCAACTACTCCC 58.933 52.381 0.00 0.00 0.00 4.30
3103 3297 2.067013 GGCTCGTTTGTCAACTACTCC 58.933 52.381 0.00 0.00 0.00 3.85
3104 3298 2.750948 TGGCTCGTTTGTCAACTACTC 58.249 47.619 0.00 0.00 0.00 2.59
3105 3299 2.902705 TGGCTCGTTTGTCAACTACT 57.097 45.000 0.00 0.00 0.00 2.57
3106 3300 3.955771 TTTGGCTCGTTTGTCAACTAC 57.044 42.857 0.00 0.00 0.00 2.73
3107 3301 4.664188 GTTTTTGGCTCGTTTGTCAACTA 58.336 39.130 0.00 0.00 0.00 2.24
3108 3302 3.507786 GTTTTTGGCTCGTTTGTCAACT 58.492 40.909 0.00 0.00 0.00 3.16
3121 3315 0.666374 ACACAGGCTACGTTTTTGGC 59.334 50.000 0.00 0.00 0.00 4.52
3234 3438 2.358615 CTGTGCAGGGCGTTGCTA 60.359 61.111 12.79 3.10 44.38 3.49
3292 3811 2.210961 TCGAGCTATCACTACCGACTG 58.789 52.381 0.00 0.00 0.00 3.51
3304 3831 0.394565 GGCCTTCCACATCGAGCTAT 59.605 55.000 0.00 0.00 0.00 2.97
3330 3857 3.129913 GAGGTACGTACGCGCCCAT 62.130 63.158 16.72 2.68 42.83 4.00


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

AutoCloner maintained by Alex Coulton.