Multiple sequence alignment - TraesCS3A01G291300

Loading Multiple Alignment...

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 TraesCS3A01G291300 chr3A 100.000 4364 0 0 1 4364 521602957 521598594 0.000000e+00 8059.0
1 TraesCS3A01G291300 chr3A 97.975 889 17 1 1 889 547191047 547190160 0.000000e+00 1541.0
2 TraesCS3A01G291300 chr3D 94.356 1630 63 12 976 2587 401051151 401049533 0.000000e+00 2473.0
3 TraesCS3A01G291300 chr3D 95.638 596 22 2 3084 3679 401049010 401048419 0.000000e+00 953.0
4 TraesCS3A01G291300 chr3D 96.253 427 15 1 2652 3077 401049535 401049109 0.000000e+00 699.0
5 TraesCS3A01G291300 chr3D 79.227 414 52 19 3973 4359 401031521 401031115 1.560000e-64 257.0
6 TraesCS3A01G291300 chr3D 92.857 84 6 0 3872 3955 401047911 401047828 5.930000e-24 122.0
7 TraesCS3A01G291300 chr3B 94.331 1376 48 8 1712 3077 526809919 526808564 0.000000e+00 2082.0
8 TraesCS3A01G291300 chr3B 94.845 679 33 1 988 1664 526810605 526809927 0.000000e+00 1059.0
9 TraesCS3A01G291300 chr3B 93.765 417 20 3 3270 3684 526808337 526807925 4.790000e-174 621.0
10 TraesCS3A01G291300 chr3B 89.643 280 19 5 4094 4364 526806680 526806402 8.980000e-92 348.0
11 TraesCS3A01G291300 chr3B 93.333 135 5 3 3084 3217 526808465 526808334 3.440000e-46 196.0
12 TraesCS3A01G291300 chr3B 88.235 136 12 2 3675 3810 526807886 526807755 4.520000e-35 159.0
13 TraesCS3A01G291300 chr3B 87.387 111 13 1 3910 4020 526807556 526807447 4.580000e-25 126.0
14 TraesCS3A01G291300 chr3B 75.829 211 36 7 3677 3887 556434461 556434266 4.650000e-15 93.5
15 TraesCS3A01G291300 chr2A 98.307 886 13 2 1 886 763256373 763257256 0.000000e+00 1552.0
16 TraesCS3A01G291300 chr1B 98.081 886 16 1 1 886 678137906 678138790 0.000000e+00 1541.0
17 TraesCS3A01G291300 chr1B 97.856 886 19 0 1 886 90182891 90183776 0.000000e+00 1531.0
18 TraesCS3A01G291300 chr1B 97.643 891 19 2 1 891 404477664 404476776 0.000000e+00 1528.0
19 TraesCS3A01G291300 chr6B 97.968 886 18 0 1 886 645573936 645574821 0.000000e+00 1537.0
20 TraesCS3A01G291300 chr2B 97.968 886 18 0 1 886 742106005 742105120 0.000000e+00 1537.0
21 TraesCS3A01G291300 chr4B 97.968 886 17 1 1 886 347642677 347643561 0.000000e+00 1535.0
22 TraesCS3A01G291300 chr5B 97.856 886 19 0 1 886 629143706 629144591 0.000000e+00 1531.0
23 TraesCS3A01G291300 chr5B 80.571 175 30 3 3719 3891 256919965 256919793 9.850000e-27 132.0
24 TraesCS3A01G291300 chr1A 80.717 223 36 4 3675 3892 303735744 303735964 2.700000e-37 167.0
25 TraesCS3A01G291300 chr1A 96.970 33 1 0 892 924 555654471 555654439 6.100000e-04 56.5
26 TraesCS3A01G291300 chr2D 79.724 217 29 9 3675 3891 593231964 593232165 4.550000e-30 143.0
27 TraesCS3A01G291300 chr4A 81.461 178 21 6 3711 3888 742813599 742813764 7.610000e-28 135.0
28 TraesCS3A01G291300 chr7D 87.755 98 12 0 3791 3888 134775383 134775286 9.920000e-22 115.0
29 TraesCS3A01G291300 chr7D 85.333 75 6 3 3677 3750 559460778 559460848 6.050000e-09 73.1
30 TraesCS3A01G291300 chr6A 79.375 160 23 7 3627 3778 98181482 98181325 2.150000e-18 104.0
31 TraesCS3A01G291300 chr7A 73.711 194 34 8 3685 3877 644134454 644134631 4.710000e-05 60.2


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 TraesCS3A01G291300 chr3A 521598594 521602957 4363 True 8059.000000 8059 100.000000 1 4364 1 chr3A.!!$R1 4363
1 TraesCS3A01G291300 chr3A 547190160 547191047 887 True 1541.000000 1541 97.975000 1 889 1 chr3A.!!$R2 888
2 TraesCS3A01G291300 chr3D 401047828 401051151 3323 True 1061.750000 2473 94.776000 976 3955 4 chr3D.!!$R2 2979
3 TraesCS3A01G291300 chr3B 526806402 526810605 4203 True 655.857143 2082 91.648429 988 4364 7 chr3B.!!$R2 3376
4 TraesCS3A01G291300 chr2A 763256373 763257256 883 False 1552.000000 1552 98.307000 1 886 1 chr2A.!!$F1 885
5 TraesCS3A01G291300 chr1B 678137906 678138790 884 False 1541.000000 1541 98.081000 1 886 1 chr1B.!!$F2 885
6 TraesCS3A01G291300 chr1B 90182891 90183776 885 False 1531.000000 1531 97.856000 1 886 1 chr1B.!!$F1 885
7 TraesCS3A01G291300 chr1B 404476776 404477664 888 True 1528.000000 1528 97.643000 1 891 1 chr1B.!!$R1 890
8 TraesCS3A01G291300 chr6B 645573936 645574821 885 False 1537.000000 1537 97.968000 1 886 1 chr6B.!!$F1 885
9 TraesCS3A01G291300 chr2B 742105120 742106005 885 True 1537.000000 1537 97.968000 1 886 1 chr2B.!!$R1 885
10 TraesCS3A01G291300 chr4B 347642677 347643561 884 False 1535.000000 1535 97.968000 1 886 1 chr4B.!!$F1 885
11 TraesCS3A01G291300 chr5B 629143706 629144591 885 False 1531.000000 1531 97.856000 1 886 1 chr5B.!!$F1 885

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
974 978 0.033504 AGCAGTCTTGTACCCACACG 59.966 55.0 0.00 0.0 33.30 4.49 F
1491 1495 0.322322 TTGGAATGTCGCGGTTAGGT 59.678 50.0 6.13 0.0 0.00 3.08 F
1639 1646 1.053424 TTCCGGCAGTTTAGGTCAGT 58.947 50.0 0.00 0.0 0.00 3.41 F
2816 2843 0.396811 AGTTCCTACCACACCAGTGC 59.603 55.0 0.00 0.0 44.53 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2789 2816 0.517316 GTGGTAGGAACTGCTTTGCG 59.483 55.000 0.0 0.0 42.03 4.85 R
2816 2843 2.022764 TGTTGACGCATGGTAGATGG 57.977 50.000 0.0 0.0 0.00 3.51 R
3105 3226 2.441750 AGCTCCTCAAAACAGTACCCAA 59.558 45.455 0.0 0.0 0.00 4.12 R
3971 4563 0.102481 CCAGACGACAATCTACGGGG 59.898 60.000 0.0 0.0 0.00 5.73 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
75 76 1.072331 ACAAAAGTGCAGATCCCGTCT 59.928 47.619 0.00 0.00 37.80 4.18
255 256 3.209410 GGATCAGAGCATGGACGAAATT 58.791 45.455 0.00 0.00 0.00 1.82
886 890 7.094118 ACCAACTGAGACATTAGAAGTAGAGAC 60.094 40.741 0.00 0.00 0.00 3.36
889 893 9.914834 AACTGAGACATTAGAAGTAGAGACTAT 57.085 33.333 0.00 0.00 33.58 2.12
890 894 9.555727 ACTGAGACATTAGAAGTAGAGACTATC 57.444 37.037 0.00 0.00 33.58 2.08
891 895 8.911918 TGAGACATTAGAAGTAGAGACTATCC 57.088 38.462 0.00 0.00 33.58 2.59
892 896 8.495260 TGAGACATTAGAAGTAGAGACTATCCA 58.505 37.037 0.00 0.00 33.58 3.41
893 897 8.685838 AGACATTAGAAGTAGAGACTATCCAC 57.314 38.462 0.00 0.00 33.58 4.02
894 898 8.499406 AGACATTAGAAGTAGAGACTATCCACT 58.501 37.037 0.00 0.00 33.58 4.00
895 899 9.781633 GACATTAGAAGTAGAGACTATCCACTA 57.218 37.037 0.00 0.00 33.58 2.74
898 902 9.747898 ATTAGAAGTAGAGACTATCCACTATGG 57.252 37.037 0.00 0.00 34.83 2.74
899 903 7.395525 AGAAGTAGAGACTATCCACTATGGA 57.604 40.000 0.00 0.00 42.93 3.41
900 904 7.458397 AGAAGTAGAGACTATCCACTATGGAG 58.542 42.308 3.57 0.00 42.33 3.86
901 905 7.293771 AGAAGTAGAGACTATCCACTATGGAGA 59.706 40.741 3.57 0.00 42.33 3.71
902 906 7.995663 AAGTAGAGACTATCCACTATGGAGAT 58.004 38.462 3.57 0.00 42.33 2.75
903 907 9.118367 AAGTAGAGACTATCCACTATGGAGATA 57.882 37.037 3.57 0.00 42.33 1.98
915 919 9.656323 TCCACTATGGAGATAGTAACATAAACT 57.344 33.333 0.00 0.00 42.67 2.66
929 933 9.798994 AGTAACATAAACTAGTAACATCGGAAG 57.201 33.333 0.00 0.00 0.00 3.46
930 934 9.578439 GTAACATAAACTAGTAACATCGGAAGT 57.422 33.333 0.00 0.00 0.00 3.01
943 947 9.283420 GTAACATCGGAAGTTACTACTCTTTAC 57.717 37.037 22.30 2.05 44.82 2.01
944 948 7.700022 ACATCGGAAGTTACTACTCTTTACT 57.300 36.000 0.00 0.00 31.99 2.24
945 949 7.760437 ACATCGGAAGTTACTACTCTTTACTC 58.240 38.462 0.00 0.00 31.99 2.59
946 950 6.749923 TCGGAAGTTACTACTCTTTACTCC 57.250 41.667 0.00 0.00 31.99 3.85
947 951 5.649831 TCGGAAGTTACTACTCTTTACTCCC 59.350 44.000 0.00 0.00 31.99 4.30
948 952 5.163571 CGGAAGTTACTACTCTTTACTCCCC 60.164 48.000 0.00 0.00 31.99 4.81
949 953 5.718607 GGAAGTTACTACTCTTTACTCCCCA 59.281 44.000 0.00 0.00 31.99 4.96
950 954 6.383436 GGAAGTTACTACTCTTTACTCCCCAT 59.617 42.308 0.00 0.00 31.99 4.00
951 955 7.092979 GGAAGTTACTACTCTTTACTCCCCATT 60.093 40.741 0.00 0.00 31.99 3.16
952 956 8.906238 AAGTTACTACTCTTTACTCCCCATTA 57.094 34.615 0.00 0.00 31.99 1.90
953 957 9.503369 AAGTTACTACTCTTTACTCCCCATTAT 57.497 33.333 0.00 0.00 31.99 1.28
954 958 8.925338 AGTTACTACTCTTTACTCCCCATTATG 58.075 37.037 0.00 0.00 0.00 1.90
955 959 8.921205 GTTACTACTCTTTACTCCCCATTATGA 58.079 37.037 0.00 0.00 0.00 2.15
956 960 7.604657 ACTACTCTTTACTCCCCATTATGAG 57.395 40.000 0.00 0.00 34.73 2.90
957 961 5.297569 ACTCTTTACTCCCCATTATGAGC 57.702 43.478 0.00 0.00 31.65 4.26
958 962 4.721776 ACTCTTTACTCCCCATTATGAGCA 59.278 41.667 0.00 0.00 31.65 4.26
959 963 5.163258 ACTCTTTACTCCCCATTATGAGCAG 60.163 44.000 0.00 0.00 31.65 4.24
960 964 4.721776 TCTTTACTCCCCATTATGAGCAGT 59.278 41.667 0.00 0.00 31.65 4.40
961 965 4.689612 TTACTCCCCATTATGAGCAGTC 57.310 45.455 0.00 0.00 31.65 3.51
962 966 2.769209 ACTCCCCATTATGAGCAGTCT 58.231 47.619 0.00 0.00 31.65 3.24
963 967 3.118531 ACTCCCCATTATGAGCAGTCTT 58.881 45.455 0.00 0.00 31.65 3.01
964 968 3.118112 ACTCCCCATTATGAGCAGTCTTG 60.118 47.826 0.00 0.00 31.65 3.02
965 969 2.846206 TCCCCATTATGAGCAGTCTTGT 59.154 45.455 0.00 0.00 0.00 3.16
966 970 4.037222 TCCCCATTATGAGCAGTCTTGTA 58.963 43.478 0.00 0.00 0.00 2.41
967 971 4.130118 CCCCATTATGAGCAGTCTTGTAC 58.870 47.826 0.00 0.00 0.00 2.90
968 972 4.130118 CCCATTATGAGCAGTCTTGTACC 58.870 47.826 0.00 0.00 0.00 3.34
969 973 4.130118 CCATTATGAGCAGTCTTGTACCC 58.870 47.826 0.00 0.00 0.00 3.69
970 974 4.384098 CCATTATGAGCAGTCTTGTACCCA 60.384 45.833 0.00 0.00 0.00 4.51
971 975 2.770164 ATGAGCAGTCTTGTACCCAC 57.230 50.000 0.00 0.00 0.00 4.61
972 976 1.419381 TGAGCAGTCTTGTACCCACA 58.581 50.000 0.00 0.00 0.00 4.17
973 977 1.070134 TGAGCAGTCTTGTACCCACAC 59.930 52.381 0.00 0.00 33.30 3.82
974 978 0.033504 AGCAGTCTTGTACCCACACG 59.966 55.000 0.00 0.00 33.30 4.49
982 986 1.057471 TGTACCCACACGGATCCAAA 58.943 50.000 13.41 0.00 34.64 3.28
1044 1048 1.486310 TCCTTGAGATCCGGACCAATG 59.514 52.381 6.12 8.98 0.00 2.82
1062 1066 1.375523 GGAAGGTCGCATCCAACGT 60.376 57.895 0.00 0.00 35.71 3.99
1064 1068 0.389948 GAAGGTCGCATCCAACGTCT 60.390 55.000 0.00 0.00 0.00 4.18
1199 1203 2.046892 CCAGGGTGAACGAGCCAG 60.047 66.667 0.00 0.00 45.68 4.85
1240 1244 2.630098 CCGCATCTATTTCCTCCTCTCA 59.370 50.000 0.00 0.00 0.00 3.27
1247 1251 5.975113 TCTATTTCCTCCTCTCATCCTGAT 58.025 41.667 0.00 0.00 0.00 2.90
1248 1252 7.108667 TCTATTTCCTCCTCTCATCCTGATA 57.891 40.000 0.00 0.00 0.00 2.15
1406 1410 1.144503 CTATCTGCCCTGGATTTGCCT 59.855 52.381 0.00 0.00 37.63 4.75
1483 1487 1.359848 ACGTCTGATTGGAATGTCGC 58.640 50.000 0.00 0.00 0.00 5.19
1491 1495 0.322322 TTGGAATGTCGCGGTTAGGT 59.678 50.000 6.13 0.00 0.00 3.08
1492 1496 1.184431 TGGAATGTCGCGGTTAGGTA 58.816 50.000 6.13 0.00 0.00 3.08
1493 1497 1.135024 TGGAATGTCGCGGTTAGGTAC 60.135 52.381 6.13 0.00 0.00 3.34
1591 1598 4.136796 ACTAAGTGCAAGAGTGAAATGCA 58.863 39.130 0.00 0.00 46.97 3.96
1639 1646 1.053424 TTCCGGCAGTTTAGGTCAGT 58.947 50.000 0.00 0.00 0.00 3.41
1667 1676 4.525100 GCTATTAGGCCAGCTCTAACTACT 59.475 45.833 5.01 0.00 34.86 2.57
1702 1711 5.175127 TGCATTACACTAGTACCACATGTG 58.825 41.667 19.31 19.31 32.59 3.21
1710 1719 5.817296 CACTAGTACCACATGTGCACATTAT 59.183 40.000 29.48 17.76 33.61 1.28
1714 1723 5.887598 AGTACCACATGTGCACATTATCAAT 59.112 36.000 29.48 14.92 33.61 2.57
1717 1726 4.269123 CCACATGTGCACATTATCAATTGC 59.731 41.667 29.48 0.00 33.61 3.56
1721 1730 4.554292 TGTGCACATTATCAATTGCGTTT 58.446 34.783 17.42 0.00 37.82 3.60
1798 1810 8.721478 TGTAATTCTGAATGCTCACTTTAGAAC 58.279 33.333 3.22 0.00 0.00 3.01
1808 1820 3.993081 CTCACTTTAGAACACTCTGCCAG 59.007 47.826 0.00 0.00 32.70 4.85
1896 1908 7.324856 TGTTGTCATTCACATTATTTGCGTTAC 59.675 33.333 0.00 0.00 33.90 2.50
2032 2052 7.664318 TGATTTTGCAGACTATCATATCATGCT 59.336 33.333 0.00 0.00 33.47 3.79
2244 2264 2.147958 GTCGCACATTTAGGTGGAACA 58.852 47.619 0.00 0.00 39.98 3.18
2326 2346 4.917906 ACTTTCCCTTCAGAATGCTAGT 57.082 40.909 0.00 0.00 34.76 2.57
2437 2462 7.833285 ACTGGGTCTTGTTGTATGTATTTTT 57.167 32.000 0.00 0.00 0.00 1.94
2526 2551 3.436470 GCTCTGGCCCCTCCAATTTATAA 60.436 47.826 0.00 0.00 46.01 0.98
2527 2552 4.145052 CTCTGGCCCCTCCAATTTATAAC 58.855 47.826 0.00 0.00 46.01 1.89
2558 2585 5.900437 TCTTTCTTTCTCTAGTACCCTCCA 58.100 41.667 0.00 0.00 0.00 3.86
2580 2607 6.205853 TCCAATACATATTTATTGTCACGGCC 59.794 38.462 16.64 0.00 37.64 6.13
2713 2740 4.757149 GGAACATGTAGGATAAGTGGCATC 59.243 45.833 0.00 0.00 0.00 3.91
2789 2816 6.992063 TTAGAAGAAGAATGTCATGAAGGC 57.008 37.500 0.00 0.00 0.00 4.35
2816 2843 0.396811 AGTTCCTACCACACCAGTGC 59.603 55.000 0.00 0.00 44.53 4.40
2935 2963 3.071023 AGGTGTGATTGTATATCCACCCG 59.929 47.826 15.58 0.00 38.75 5.28
3077 3105 5.105752 ACTTCGCTGTCATTCAGAACTATC 58.894 41.667 0.00 0.00 46.27 2.08
3078 3106 4.991153 TCGCTGTCATTCAGAACTATCT 57.009 40.909 0.00 0.00 46.27 1.98
3079 3107 5.330455 TCGCTGTCATTCAGAACTATCTT 57.670 39.130 0.00 0.00 46.27 2.40
3080 3108 5.724328 TCGCTGTCATTCAGAACTATCTTT 58.276 37.500 0.00 0.00 46.27 2.52
3081 3109 6.166279 TCGCTGTCATTCAGAACTATCTTTT 58.834 36.000 0.00 0.00 46.27 2.27
3082 3110 6.091305 TCGCTGTCATTCAGAACTATCTTTTG 59.909 38.462 0.00 0.00 46.27 2.44
3105 3226 5.429762 TGAGATTCAGGGGATATTTGAGTGT 59.570 40.000 0.00 0.00 0.00 3.55
3112 3233 4.079958 AGGGGATATTTGAGTGTTGGGTAC 60.080 45.833 0.00 0.00 0.00 3.34
3260 3381 3.826729 AGCCTTTGTTATCCTGTTGGAAC 59.173 43.478 0.00 0.00 46.80 3.62
3329 3450 6.477688 GCATTGTGATGAAATATTCTTGGTGG 59.522 38.462 0.00 0.00 35.16 4.61
3379 3500 9.797556 TTTCAGGTTAGAAAAGTTTTAAGCTTC 57.202 29.630 0.00 0.00 34.77 3.86
3434 3555 1.737793 GGCATCCACAAGGTTTCTACG 59.262 52.381 0.00 0.00 35.89 3.51
3511 3632 8.908678 CGTGATTTATCCATGCAATATTTTCTG 58.091 33.333 0.00 0.00 0.00 3.02
3516 3637 4.522114 TCCATGCAATATTTTCTGTCCGA 58.478 39.130 0.00 0.00 0.00 4.55
3561 3684 7.957484 CAGTTCAGTGCTTGTGTGTATATTAAC 59.043 37.037 0.00 0.00 0.00 2.01
3608 3731 0.610232 GATGGCATCCATAGGGTGGC 60.610 60.000 16.75 15.21 45.26 5.01
3609 3732 3.014015 GATGGCATCCATAGGGTGGCT 62.014 57.143 21.35 8.98 45.26 4.75
3660 3783 6.440436 GTTAACAATACAACCAACAATCGGT 58.560 36.000 0.00 0.00 38.85 4.69
3682 3852 6.062095 GGTTATAAGGAGTTGCCATGTACAT 58.938 40.000 1.41 1.41 40.02 2.29
3751 3921 6.144078 ACTTTACAACCTCACAAATTGTCC 57.856 37.500 0.00 0.00 37.68 4.02
3753 3923 5.766150 TTACAACCTCACAAATTGTCCTG 57.234 39.130 0.00 0.00 37.68 3.86
3754 3924 3.897239 ACAACCTCACAAATTGTCCTGA 58.103 40.909 0.00 0.00 30.82 3.86
3770 3940 1.943116 CTGAGGCTCGTACTGCAGCT 61.943 60.000 15.27 0.00 35.82 4.24
3772 3942 1.938657 GAGGCTCGTACTGCAGCTGA 61.939 60.000 20.43 8.31 35.82 4.26
3781 3951 4.038361 CGTACTGCAGCTGACTACTAATG 58.962 47.826 20.43 0.00 0.00 1.90
3788 3958 4.932200 GCAGCTGACTACTAATGAACAGTT 59.068 41.667 20.43 0.00 0.00 3.16
3811 4001 5.559148 TGCTTCTTTTCTCTCTCCTCTTT 57.441 39.130 0.00 0.00 0.00 2.52
3814 4004 5.994668 GCTTCTTTTCTCTCTCCTCTTTTCA 59.005 40.000 0.00 0.00 0.00 2.69
3815 4005 6.073276 GCTTCTTTTCTCTCTCCTCTTTTCAC 60.073 42.308 0.00 0.00 0.00 3.18
3824 4014 5.244178 TCTCTCCTCTTTTCACTACTCCAAC 59.756 44.000 0.00 0.00 0.00 3.77
3831 4021 6.588204 TCTTTTCACTACTCCAACTAAGCAA 58.412 36.000 0.00 0.00 0.00 3.91
3832 4022 7.051623 TCTTTTCACTACTCCAACTAAGCAAA 58.948 34.615 0.00 0.00 0.00 3.68
3833 4023 6.861065 TTTCACTACTCCAACTAAGCAAAG 57.139 37.500 0.00 0.00 0.00 2.77
3834 4024 5.801531 TCACTACTCCAACTAAGCAAAGA 57.198 39.130 0.00 0.00 0.00 2.52
3835 4025 6.360370 TCACTACTCCAACTAAGCAAAGAT 57.640 37.500 0.00 0.00 0.00 2.40
3836 4026 7.476540 TCACTACTCCAACTAAGCAAAGATA 57.523 36.000 0.00 0.00 0.00 1.98
3837 4027 7.548097 TCACTACTCCAACTAAGCAAAGATAG 58.452 38.462 0.00 0.00 0.00 2.08
3870 4462 7.380423 AGTCCTTATAGCCTGTTTATGTCAT 57.620 36.000 0.00 0.00 0.00 3.06
3908 4500 6.921307 GCTCTAAGTTTTCTAGGCTGTATCTC 59.079 42.308 0.00 0.00 0.00 2.75
3926 4518 2.965831 TCTCTGTCTTGGTGTAGCAGTT 59.034 45.455 0.00 0.00 0.00 3.16
3983 4575 2.590092 GCCAGCCCCGTAGATTGT 59.410 61.111 0.00 0.00 0.00 2.71
3988 4580 0.683504 AGCCCCGTAGATTGTCGTCT 60.684 55.000 0.00 0.00 0.00 4.18
3993 4585 0.866061 CGTAGATTGTCGTCTGGCGG 60.866 60.000 0.30 0.00 41.72 6.13
4009 4601 0.582005 GCGGATTGCGACTGTTATCC 59.418 55.000 0.29 0.00 34.51 2.59
4011 4603 2.545113 GCGGATTGCGACTGTTATCCTA 60.545 50.000 0.29 0.00 35.47 2.94
4020 4612 2.630580 GACTGTTATCCTAGGGCAGAGG 59.369 54.545 21.60 8.56 35.17 3.69
4021 4613 1.974236 CTGTTATCCTAGGGCAGAGGG 59.026 57.143 9.46 0.00 34.56 4.30
4023 4615 2.022428 TGTTATCCTAGGGCAGAGGGAA 60.022 50.000 9.46 0.00 34.56 3.97
4025 4617 0.104725 ATCCTAGGGCAGAGGGAAGG 60.105 60.000 9.46 0.00 34.56 3.46
4034 5316 1.488393 GCAGAGGGAAGGCTATGAAGT 59.512 52.381 0.00 0.00 0.00 3.01
4053 5351 1.127951 GTTCCGTCCGTGCTTGTTATG 59.872 52.381 0.00 0.00 0.00 1.90
4057 5355 0.793861 GTCCGTGCTTGTTATGCGAA 59.206 50.000 0.00 0.00 0.00 4.70
4066 5364 4.036262 TGCTTGTTATGCGAACTGAAGTTT 59.964 37.500 0.00 0.00 38.56 2.66
4079 5377 1.333619 TGAAGTTTTGACTGCCGCTTC 59.666 47.619 0.00 0.00 34.61 3.86
4080 5378 1.604278 GAAGTTTTGACTGCCGCTTCT 59.396 47.619 0.00 0.00 32.21 2.85
4081 5379 1.230324 AGTTTTGACTGCCGCTTCTC 58.770 50.000 0.00 0.00 0.00 2.87
4082 5380 1.202698 AGTTTTGACTGCCGCTTCTCT 60.203 47.619 0.00 0.00 0.00 3.10
4083 5381 1.604278 GTTTTGACTGCCGCTTCTCTT 59.396 47.619 0.00 0.00 0.00 2.85
4084 5382 2.806244 GTTTTGACTGCCGCTTCTCTTA 59.194 45.455 0.00 0.00 0.00 2.10
4085 5383 2.080286 TTGACTGCCGCTTCTCTTAC 57.920 50.000 0.00 0.00 0.00 2.34
4086 5384 0.246635 TGACTGCCGCTTCTCTTACC 59.753 55.000 0.00 0.00 0.00 2.85
4087 5385 0.533032 GACTGCCGCTTCTCTTACCT 59.467 55.000 0.00 0.00 0.00 3.08
4088 5386 0.977395 ACTGCCGCTTCTCTTACCTT 59.023 50.000 0.00 0.00 0.00 3.50
4089 5387 1.338200 ACTGCCGCTTCTCTTACCTTG 60.338 52.381 0.00 0.00 0.00 3.61
4090 5388 0.973632 TGCCGCTTCTCTTACCTTGA 59.026 50.000 0.00 0.00 0.00 3.02
4091 5389 1.555075 TGCCGCTTCTCTTACCTTGAT 59.445 47.619 0.00 0.00 0.00 2.57
4092 5390 2.205911 GCCGCTTCTCTTACCTTGATC 58.794 52.381 0.00 0.00 0.00 2.92
4102 5400 0.613260 TACCTTGATCGCTGCCTGTT 59.387 50.000 0.00 0.00 0.00 3.16
4117 5415 2.029020 GCCTGTTTTGTCTTTGGGGATC 60.029 50.000 0.00 0.00 0.00 3.36
4127 5425 2.107031 TCTTTGGGGATCGATGCATCAT 59.893 45.455 25.70 17.33 0.00 2.45
4135 5433 4.440525 GGGATCGATGCATCATTGTTTGTT 60.441 41.667 25.70 3.43 0.00 2.83
4188 5486 3.689347 TGCTTGCCTTGATGTAATGTCT 58.311 40.909 0.00 0.00 0.00 3.41
4195 5493 4.119862 CCTTGATGTAATGTCTACGGTGG 58.880 47.826 0.00 0.00 0.00 4.61
4205 5503 3.981211 TGTCTACGGTGGTGTAAGAAAC 58.019 45.455 0.00 0.00 0.00 2.78
4220 5518 4.640771 AAGAAACTCTGGCTGATGGTAA 57.359 40.909 0.00 0.00 0.00 2.85
4227 5525 2.169561 TCTGGCTGATGGTAATGCGTAA 59.830 45.455 0.00 0.00 0.00 3.18
4246 5544 9.719355 ATGCGTAACCTGTTTATTATATCATCA 57.281 29.630 0.00 0.00 0.00 3.07
4247 5545 8.984764 TGCGTAACCTGTTTATTATATCATCAC 58.015 33.333 0.00 0.00 0.00 3.06
4248 5546 9.204570 GCGTAACCTGTTTATTATATCATCACT 57.795 33.333 0.00 0.00 0.00 3.41
4258 5556 9.923143 TTTATTATATCATCACTCTAACCACGG 57.077 33.333 0.00 0.00 0.00 4.94
4284 5590 6.277605 ACGTATGACAATATTTCATCCGACA 58.722 36.000 20.93 4.95 35.48 4.35
4295 5601 1.135112 TCATCCGACACTGAACCATCG 60.135 52.381 0.00 0.00 0.00 3.84
4327 5633 5.758296 TCAAACAGTATCCAACTTCACACTC 59.242 40.000 0.00 0.00 35.76 3.51
4346 5652 2.673368 CTCTTGCATCGGTAACTTCACC 59.327 50.000 0.00 0.00 35.04 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 5.834460 TCCTAATGTCTCAGTTGGTAGGTA 58.166 41.667 0.00 0.00 0.00 3.08
104 105 5.164620 TCACTCACCAAGATTGCTATTCA 57.835 39.130 0.00 0.00 0.00 2.57
147 148 1.252215 TGGAGGAACGACACGCCATA 61.252 55.000 0.00 0.00 0.00 2.74
255 256 3.757947 TCCTCAACCTCTACCATCTCA 57.242 47.619 0.00 0.00 0.00 3.27
775 779 4.675303 CCTCCCACCTCCCACCCA 62.675 72.222 0.00 0.00 0.00 4.51
889 893 9.656323 AGTTTATGTTACTATCTCCATAGTGGA 57.344 33.333 5.12 0.00 45.98 4.02
903 907 9.798994 CTTCCGATGTTACTAGTTTATGTTACT 57.201 33.333 0.00 0.00 0.00 2.24
904 908 9.578439 ACTTCCGATGTTACTAGTTTATGTTAC 57.422 33.333 0.00 0.00 0.00 2.50
907 911 9.578439 GTAACTTCCGATGTTACTAGTTTATGT 57.422 33.333 21.61 0.00 43.56 2.29
917 921 9.283420 GTAAAGAGTAGTAACTTCCGATGTTAC 57.717 37.037 21.46 21.46 45.81 2.50
918 922 9.236006 AGTAAAGAGTAGTAACTTCCGATGTTA 57.764 33.333 3.37 3.37 35.56 2.41
919 923 8.120140 AGTAAAGAGTAGTAACTTCCGATGTT 57.880 34.615 5.14 5.14 35.56 2.71
920 924 7.148103 GGAGTAAAGAGTAGTAACTTCCGATGT 60.148 40.741 0.00 0.00 35.56 3.06
921 925 7.194962 GGAGTAAAGAGTAGTAACTTCCGATG 58.805 42.308 0.00 0.00 35.56 3.84
922 926 6.320926 GGGAGTAAAGAGTAGTAACTTCCGAT 59.679 42.308 0.00 0.00 35.56 4.18
923 927 5.649831 GGGAGTAAAGAGTAGTAACTTCCGA 59.350 44.000 0.00 0.00 35.56 4.55
924 928 5.163571 GGGGAGTAAAGAGTAGTAACTTCCG 60.164 48.000 0.00 0.00 36.79 4.30
925 929 5.718607 TGGGGAGTAAAGAGTAGTAACTTCC 59.281 44.000 0.00 0.00 35.56 3.46
926 930 6.847421 TGGGGAGTAAAGAGTAGTAACTTC 57.153 41.667 0.00 0.00 35.56 3.01
927 931 7.809880 AATGGGGAGTAAAGAGTAGTAACTT 57.190 36.000 0.00 0.00 35.56 2.66
928 932 8.925338 CATAATGGGGAGTAAAGAGTAGTAACT 58.075 37.037 0.00 0.00 39.21 2.24
929 933 8.921205 TCATAATGGGGAGTAAAGAGTAGTAAC 58.079 37.037 0.00 0.00 0.00 2.50
930 934 9.144298 CTCATAATGGGGAGTAAAGAGTAGTAA 57.856 37.037 0.00 0.00 0.00 2.24
931 935 7.232941 GCTCATAATGGGGAGTAAAGAGTAGTA 59.767 40.741 0.00 0.00 33.66 1.82
932 936 6.042208 GCTCATAATGGGGAGTAAAGAGTAGT 59.958 42.308 0.00 0.00 33.66 2.73
933 937 6.042093 TGCTCATAATGGGGAGTAAAGAGTAG 59.958 42.308 0.00 0.00 33.66 2.57
934 938 5.903010 TGCTCATAATGGGGAGTAAAGAGTA 59.097 40.000 0.00 0.00 33.66 2.59
935 939 4.721776 TGCTCATAATGGGGAGTAAAGAGT 59.278 41.667 0.00 0.00 33.66 3.24
936 940 5.296151 TGCTCATAATGGGGAGTAAAGAG 57.704 43.478 0.00 0.00 33.66 2.85
937 941 5.296151 CTGCTCATAATGGGGAGTAAAGA 57.704 43.478 0.00 0.00 31.02 2.52
943 947 3.118112 ACAAGACTGCTCATAATGGGGAG 60.118 47.826 0.00 0.00 42.53 4.30
944 948 2.846206 ACAAGACTGCTCATAATGGGGA 59.154 45.455 0.00 0.00 0.00 4.81
945 949 3.287867 ACAAGACTGCTCATAATGGGG 57.712 47.619 0.00 0.00 0.00 4.96
946 950 4.130118 GGTACAAGACTGCTCATAATGGG 58.870 47.826 0.00 0.00 0.00 4.00
947 951 4.130118 GGGTACAAGACTGCTCATAATGG 58.870 47.826 0.00 0.00 0.00 3.16
948 952 4.572389 GTGGGTACAAGACTGCTCATAATG 59.428 45.833 0.00 0.00 0.00 1.90
949 953 4.225042 TGTGGGTACAAGACTGCTCATAAT 59.775 41.667 0.00 0.00 32.88 1.28
950 954 3.580895 TGTGGGTACAAGACTGCTCATAA 59.419 43.478 0.00 0.00 32.88 1.90
951 955 3.056107 GTGTGGGTACAAGACTGCTCATA 60.056 47.826 0.00 0.00 38.82 2.15
952 956 1.977854 TGTGGGTACAAGACTGCTCAT 59.022 47.619 0.00 0.00 32.88 2.90
953 957 1.070134 GTGTGGGTACAAGACTGCTCA 59.930 52.381 0.00 0.00 38.82 4.26
954 958 1.797025 GTGTGGGTACAAGACTGCTC 58.203 55.000 0.00 0.00 38.82 4.26
955 959 0.033504 CGTGTGGGTACAAGACTGCT 59.966 55.000 0.00 0.00 38.37 4.24
956 960 0.949105 CCGTGTGGGTACAAGACTGC 60.949 60.000 0.00 0.00 38.37 4.40
957 961 0.677288 TCCGTGTGGGTACAAGACTG 59.323 55.000 0.00 0.00 38.37 3.51
958 962 1.549170 GATCCGTGTGGGTACAAGACT 59.451 52.381 0.00 0.00 38.37 3.24
959 963 1.405121 GGATCCGTGTGGGTACAAGAC 60.405 57.143 0.00 0.00 38.37 3.01
960 964 0.899720 GGATCCGTGTGGGTACAAGA 59.100 55.000 0.00 0.00 38.37 3.02
961 965 0.611200 TGGATCCGTGTGGGTACAAG 59.389 55.000 7.39 0.00 35.73 3.16
962 966 2.761324 TGGATCCGTGTGGGTACAA 58.239 52.632 7.39 0.00 35.73 2.41
963 967 1.057471 TTTGGATCCGTGTGGGTACA 58.943 50.000 7.39 0.00 37.46 2.90
964 968 1.445871 GTTTGGATCCGTGTGGGTAC 58.554 55.000 7.39 0.00 37.00 3.34
965 969 0.037139 CGTTTGGATCCGTGTGGGTA 60.037 55.000 7.39 0.00 37.00 3.69
966 970 1.302192 CGTTTGGATCCGTGTGGGT 60.302 57.895 7.39 0.00 37.00 4.51
967 971 2.038269 CCGTTTGGATCCGTGTGGG 61.038 63.158 7.39 0.63 37.49 4.61
968 972 1.004320 TCCGTTTGGATCCGTGTGG 60.004 57.895 7.39 6.91 40.17 4.17
969 973 4.685447 TCCGTTTGGATCCGTGTG 57.315 55.556 7.39 0.00 40.17 3.82
982 986 0.537188 ATTTCATCCGCTGAGTCCGT 59.463 50.000 0.00 0.00 34.68 4.69
1007 1011 3.965888 GAGTCAGGGCAACTCCAAT 57.034 52.632 3.34 0.00 37.72 3.16
1044 1048 1.359459 GACGTTGGATGCGACCTTCC 61.359 60.000 0.00 0.00 36.18 3.46
1062 1066 2.279810 TTGTCGGGGCGTCATCAGA 61.280 57.895 0.00 0.00 0.00 3.27
1064 1068 2.047655 GTTGTCGGGGCGTCATCA 60.048 61.111 0.00 0.00 0.00 3.07
1173 1177 0.771755 GTTCACCCTGGGGAGAAACT 59.228 55.000 18.88 0.00 44.16 2.66
1240 1244 7.542025 GTCTGCAGAAACAATTTTATCAGGAT 58.458 34.615 20.19 0.00 0.00 3.24
1247 1251 4.320202 GCCTCGTCTGCAGAAACAATTTTA 60.320 41.667 20.19 0.00 0.00 1.52
1248 1252 3.550842 GCCTCGTCTGCAGAAACAATTTT 60.551 43.478 20.19 0.00 0.00 1.82
1491 1495 9.720769 GGCCTGCTTTAATCAATTATAGTAGTA 57.279 33.333 0.00 0.00 34.65 1.82
1492 1496 8.217799 TGGCCTGCTTTAATCAATTATAGTAGT 58.782 33.333 3.32 0.00 34.65 2.73
1493 1497 8.621532 TGGCCTGCTTTAATCAATTATAGTAG 57.378 34.615 3.32 9.65 35.48 2.57
1515 1522 1.372128 CCGCAAGACAAAAGCTGGC 60.372 57.895 0.00 0.00 43.02 4.85
1516 1523 0.883833 ATCCGCAAGACAAAAGCTGG 59.116 50.000 0.00 0.00 43.02 4.85
1591 1598 7.568199 AACTGCAAAGTACTGTCAAAGTTAT 57.432 32.000 0.00 0.00 40.56 1.89
1721 1730 2.497675 TGCAGTTAGCCCAACAACAAAA 59.502 40.909 2.02 0.00 44.83 2.44
1732 1743 0.602562 TGCCACAATTGCAGTTAGCC 59.397 50.000 5.05 0.00 44.83 3.93
1798 1810 3.996150 AAATTGTTGTCTGGCAGAGTG 57.004 42.857 19.38 0.00 0.00 3.51
1808 1820 7.257722 TCAAGTGAAGAGGAAAAATTGTTGTC 58.742 34.615 0.00 0.00 0.00 3.18
1845 1857 8.849168 CATTACATTAGTGAATATCTTGGGCAA 58.151 33.333 0.00 0.00 0.00 4.52
1896 1908 2.949106 CAAGCCGAAGTGCCTGTG 59.051 61.111 0.00 0.00 0.00 3.66
2104 2124 6.317140 CCATCACAGCAATCTACAAACATAGT 59.683 38.462 0.00 0.00 0.00 2.12
2188 2208 1.364626 CCATTGTCTGTCTCGGCAGC 61.365 60.000 0.00 0.00 36.49 5.25
2326 2346 2.368548 TCTGCTCCAGAAACAGCTACAA 59.631 45.455 0.00 0.00 37.57 2.41
2363 2383 7.858052 CTGTAAACAGGACAATTGAAATCAC 57.142 36.000 13.59 0.51 40.20 3.06
2437 2462 2.798283 CCGTCGAGCAAAGTAGAAAACA 59.202 45.455 0.00 0.00 0.00 2.83
2501 2526 2.454468 TGGAGGGGCCAGAGCTTA 59.546 61.111 4.39 0.00 43.33 3.09
2526 2551 6.879400 ACTAGAGAAAGAAAGAACACACTGT 58.121 36.000 0.00 0.00 0.00 3.55
2527 2552 7.382759 GGTACTAGAGAAAGAAAGAACACACTG 59.617 40.741 0.00 0.00 0.00 3.66
2558 2585 7.817418 AAGGCCGTGACAATAAATATGTATT 57.183 32.000 0.00 0.00 0.00 1.89
2606 2633 6.857848 TCCCTCCAATACATATTAATTGCCA 58.142 36.000 0.00 0.00 32.79 4.92
2607 2634 6.948309 ACTCCCTCCAATACATATTAATTGCC 59.052 38.462 0.00 0.00 32.79 4.52
2713 2740 7.186804 GTCTGTTCGAGAGAGAGAAATAGAAG 58.813 42.308 0.00 0.00 43.69 2.85
2753 2780 9.340695 CATTCTTCTTCTAATATAGAGCGACAG 57.659 37.037 0.00 0.00 35.96 3.51
2789 2816 0.517316 GTGGTAGGAACTGCTTTGCG 59.483 55.000 0.00 0.00 42.03 4.85
2816 2843 2.022764 TGTTGACGCATGGTAGATGG 57.977 50.000 0.00 0.00 0.00 3.51
2842 2869 7.869429 TCTTAGTTTAGGTTAGTCTTCAAACGG 59.131 37.037 0.00 0.00 32.54 4.44
2846 2874 8.169977 TCGTCTTAGTTTAGGTTAGTCTTCAA 57.830 34.615 0.00 0.00 0.00 2.69
3058 3086 6.091305 TCAAAAGATAGTTCTGAATGACAGCG 59.909 38.462 0.00 0.00 45.38 5.18
3077 3105 7.559170 ACTCAAATATCCCCTGAATCTCAAAAG 59.441 37.037 0.00 0.00 0.00 2.27
3078 3106 7.340232 CACTCAAATATCCCCTGAATCTCAAAA 59.660 37.037 0.00 0.00 0.00 2.44
3079 3107 6.830324 CACTCAAATATCCCCTGAATCTCAAA 59.170 38.462 0.00 0.00 0.00 2.69
3080 3108 6.069440 ACACTCAAATATCCCCTGAATCTCAA 60.069 38.462 0.00 0.00 0.00 3.02
3081 3109 5.429762 ACACTCAAATATCCCCTGAATCTCA 59.570 40.000 0.00 0.00 0.00 3.27
3082 3110 5.934781 ACACTCAAATATCCCCTGAATCTC 58.065 41.667 0.00 0.00 0.00 2.75
3088 3208 3.290710 CCCAACACTCAAATATCCCCTG 58.709 50.000 0.00 0.00 0.00 4.45
3105 3226 2.441750 AGCTCCTCAAAACAGTACCCAA 59.558 45.455 0.00 0.00 0.00 4.12
3112 3233 6.566197 AAATACTGAAGCTCCTCAAAACAG 57.434 37.500 0.00 0.00 0.00 3.16
3215 3336 4.905429 TGCTACTGCTGAACTGGATTAAA 58.095 39.130 0.00 0.00 40.48 1.52
3329 3450 4.823790 AACACGGTTAATTTGGTGAGTC 57.176 40.909 0.00 0.00 34.59 3.36
3345 3466 9.511144 AAACTTTTCTAACCTGAAAATAACACG 57.489 29.630 0.00 0.00 42.63 4.49
3379 3500 2.630098 TCCAATTCTCGATCAGCCCTAG 59.370 50.000 0.00 0.00 0.00 3.02
3434 3555 4.339814 AGCAGATGTGTAGGCTAGTTACTC 59.660 45.833 0.00 5.41 34.25 2.59
3516 3637 2.660802 CGTTACCGGCAGGAAGGT 59.339 61.111 10.86 0.82 44.08 3.50
3561 3684 6.281848 ACAACACACGAACACAATAGTAAG 57.718 37.500 0.00 0.00 0.00 2.34
3660 3783 6.894682 TGATGTACATGGCAACTCCTTATAA 58.105 36.000 14.43 0.00 35.26 0.98
3712 3882 9.617523 GGTTGTAAAGTAGGCCAACTATTATTA 57.382 33.333 5.01 0.00 37.80 0.98
3713 3883 8.333984 AGGTTGTAAAGTAGGCCAACTATTATT 58.666 33.333 5.01 0.00 37.80 1.40
3714 3884 7.868974 AGGTTGTAAAGTAGGCCAACTATTAT 58.131 34.615 5.01 0.00 37.80 1.28
3751 3921 1.518133 GCTGCAGTACGAGCCTCAG 60.518 63.158 16.64 3.62 0.00 3.35
3753 3923 1.518133 CAGCTGCAGTACGAGCCTC 60.518 63.158 16.64 0.00 35.69 4.70
3754 3924 1.979155 TCAGCTGCAGTACGAGCCT 60.979 57.895 16.64 0.00 35.69 4.58
3770 3940 7.217200 AGAAGCAAACTGTTCATTAGTAGTCA 58.783 34.615 0.00 0.00 0.00 3.41
3772 3942 8.451908 AAAGAAGCAAACTGTTCATTAGTAGT 57.548 30.769 0.00 0.00 0.00 2.73
3781 3951 6.370433 AGAGAGAAAAGAAGCAAACTGTTC 57.630 37.500 0.00 0.00 33.30 3.18
3788 3958 5.559148 AAGAGGAGAGAGAAAAGAAGCAA 57.441 39.130 0.00 0.00 0.00 3.91
3811 4001 6.169557 TCTTTGCTTAGTTGGAGTAGTGAA 57.830 37.500 0.00 0.00 0.00 3.18
3814 4004 7.719871 TCTATCTTTGCTTAGTTGGAGTAGT 57.280 36.000 0.00 0.00 0.00 2.73
3880 4472 5.241662 ACAGCCTAGAAAACTTAGAGCAAG 58.758 41.667 0.00 0.00 40.38 4.01
3896 4488 3.701542 CACCAAGACAGAGATACAGCCTA 59.298 47.826 0.00 0.00 0.00 3.93
3900 4492 4.158579 TGCTACACCAAGACAGAGATACAG 59.841 45.833 0.00 0.00 0.00 2.74
3908 4500 1.532868 GCAACTGCTACACCAAGACAG 59.467 52.381 0.00 0.00 38.21 3.51
3926 4518 2.031012 CTCCTTGTGTCGGCTGCA 59.969 61.111 0.50 0.00 0.00 4.41
3961 4553 2.270874 ATCTACGGGGCTGGCCAAAG 62.271 60.000 22.68 14.81 37.98 2.77
3969 4561 0.683504 AGACGACAATCTACGGGGCT 60.684 55.000 0.00 0.00 0.00 5.19
3971 4563 0.102481 CCAGACGACAATCTACGGGG 59.898 60.000 0.00 0.00 0.00 5.73
3988 4580 0.107897 ATAACAGTCGCAATCCGCCA 60.108 50.000 0.00 0.00 37.30 5.69
3993 4585 3.654414 CCCTAGGATAACAGTCGCAATC 58.346 50.000 11.48 0.00 0.00 2.67
4003 4595 2.400467 TCCCTCTGCCCTAGGATAAC 57.600 55.000 11.48 0.00 36.08 1.89
4004 4596 2.427889 CCTTCCCTCTGCCCTAGGATAA 60.428 54.545 11.48 0.00 36.08 1.75
4009 4601 0.105453 TAGCCTTCCCTCTGCCCTAG 60.105 60.000 0.00 0.00 0.00 3.02
4011 4603 1.059006 CATAGCCTTCCCTCTGCCCT 61.059 60.000 0.00 0.00 0.00 5.19
4020 4612 2.552031 GACGGAACTTCATAGCCTTCC 58.448 52.381 0.00 0.00 0.00 3.46
4021 4613 2.552031 GGACGGAACTTCATAGCCTTC 58.448 52.381 0.00 0.00 0.00 3.46
4023 4615 0.460311 CGGACGGAACTTCATAGCCT 59.540 55.000 0.00 0.00 0.00 4.58
4025 4617 1.278238 CACGGACGGAACTTCATAGC 58.722 55.000 0.00 0.00 0.00 2.97
4034 5316 1.434555 CATAACAAGCACGGACGGAA 58.565 50.000 0.00 0.00 0.00 4.30
4053 5351 2.376032 GCAGTCAAAACTTCAGTTCGC 58.624 47.619 0.00 0.00 37.25 4.70
4057 5355 0.663153 GCGGCAGTCAAAACTTCAGT 59.337 50.000 0.00 0.00 31.71 3.41
4066 5364 1.337823 GGTAAGAGAAGCGGCAGTCAA 60.338 52.381 1.45 0.00 0.00 3.18
4079 5377 1.137872 AGGCAGCGATCAAGGTAAGAG 59.862 52.381 0.00 0.00 0.00 2.85
4080 5378 1.134699 CAGGCAGCGATCAAGGTAAGA 60.135 52.381 0.00 0.00 0.00 2.10
4081 5379 1.293924 CAGGCAGCGATCAAGGTAAG 58.706 55.000 0.00 0.00 0.00 2.34
4082 5380 0.613260 ACAGGCAGCGATCAAGGTAA 59.387 50.000 0.00 0.00 0.00 2.85
4083 5381 0.613260 AACAGGCAGCGATCAAGGTA 59.387 50.000 0.00 0.00 0.00 3.08
4084 5382 0.250901 AAACAGGCAGCGATCAAGGT 60.251 50.000 0.00 0.00 0.00 3.50
4085 5383 0.883833 AAAACAGGCAGCGATCAAGG 59.116 50.000 0.00 0.00 0.00 3.61
4086 5384 1.267806 ACAAAACAGGCAGCGATCAAG 59.732 47.619 0.00 0.00 0.00 3.02
4087 5385 1.266718 GACAAAACAGGCAGCGATCAA 59.733 47.619 0.00 0.00 0.00 2.57
4088 5386 0.874390 GACAAAACAGGCAGCGATCA 59.126 50.000 0.00 0.00 0.00 2.92
4089 5387 1.160137 AGACAAAACAGGCAGCGATC 58.840 50.000 0.00 0.00 0.00 3.69
4090 5388 1.609208 AAGACAAAACAGGCAGCGAT 58.391 45.000 0.00 0.00 0.00 4.58
4091 5389 1.065401 CAAAGACAAAACAGGCAGCGA 59.935 47.619 0.00 0.00 0.00 4.93
4092 5390 1.480205 CAAAGACAAAACAGGCAGCG 58.520 50.000 0.00 0.00 0.00 5.18
4102 5400 2.091541 GCATCGATCCCCAAAGACAAA 58.908 47.619 0.00 0.00 0.00 2.83
4117 5415 3.782369 CGAGAACAAACAATGATGCATCG 59.218 43.478 21.34 10.11 0.00 3.84
4127 5425 2.907634 TGCACCTACGAGAACAAACAA 58.092 42.857 0.00 0.00 0.00 2.83
4135 5433 4.081697 TCAAAGATTGATGCACCTACGAGA 60.082 41.667 0.00 0.00 34.08 4.04
4188 5486 3.006110 CCAGAGTTTCTTACACCACCGTA 59.994 47.826 0.00 0.00 0.00 4.02
4195 5493 3.686726 CCATCAGCCAGAGTTTCTTACAC 59.313 47.826 0.00 0.00 0.00 2.90
4205 5503 1.224075 CGCATTACCATCAGCCAGAG 58.776 55.000 0.00 0.00 0.00 3.35
4220 5518 9.719355 TGATGATATAATAAACAGGTTACGCAT 57.281 29.630 0.00 0.00 0.00 4.73
4244 5542 1.896220 ACGTACCGTGGTTAGAGTGA 58.104 50.000 0.00 0.00 39.18 3.41
4245 5543 3.374988 TCATACGTACCGTGGTTAGAGTG 59.625 47.826 0.00 0.00 41.39 3.51
4246 5544 3.375299 GTCATACGTACCGTGGTTAGAGT 59.625 47.826 0.00 0.00 41.39 3.24
4247 5545 3.374988 TGTCATACGTACCGTGGTTAGAG 59.625 47.826 0.00 0.00 41.39 2.43
4248 5546 3.342719 TGTCATACGTACCGTGGTTAGA 58.657 45.455 0.00 0.00 41.39 2.10
4249 5547 3.763097 TGTCATACGTACCGTGGTTAG 57.237 47.619 0.00 0.00 41.39 2.34
4250 5548 4.717233 ATTGTCATACGTACCGTGGTTA 57.283 40.909 0.00 0.00 41.39 2.85
4251 5549 3.598019 ATTGTCATACGTACCGTGGTT 57.402 42.857 0.00 0.00 41.39 3.67
4253 5551 5.749588 TGAAATATTGTCATACGTACCGTGG 59.250 40.000 0.00 0.00 41.39 4.94
4254 5552 6.815672 TGAAATATTGTCATACGTACCGTG 57.184 37.500 0.00 0.00 41.39 4.94
4255 5553 6.643770 GGATGAAATATTGTCATACGTACCGT 59.356 38.462 0.00 0.00 44.35 4.83
4256 5554 7.045725 GGATGAAATATTGTCATACGTACCG 57.954 40.000 0.00 0.00 35.84 4.02
4265 5571 5.729510 TCAGTGTCGGATGAAATATTGTCA 58.270 37.500 0.00 0.00 0.00 3.58
4270 5576 5.097742 TGGTTCAGTGTCGGATGAAATAT 57.902 39.130 0.00 0.00 37.19 1.28
4284 5590 0.620556 ATCAAGGGCGATGGTTCAGT 59.379 50.000 0.00 0.00 0.00 3.41
4295 5601 3.620488 TGGATACTGTTTGATCAAGGGC 58.380 45.455 8.41 4.26 37.61 5.19
4327 5633 2.699954 AGGTGAAGTTACCGATGCAAG 58.300 47.619 0.00 0.00 45.56 4.01


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

AutoCloner maintained by Alex Coulton.