Multiple sequence alignment - TraesCS4A01G009200

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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 TraesCS4A01G009200 chr4A 100.000 6033 0 0 1 6033 5530802 5524770 0.000000e+00 11141.0
1 TraesCS4A01G009200 chr4A 98.627 801 11 0 1 801 203204121 203203321 0.000000e+00 1419.0
2 TraesCS4A01G009200 chr4A 98.377 801 13 0 1 801 5538507 5537707 0.000000e+00 1408.0
3 TraesCS4A01G009200 chr4D 95.697 2022 70 4 2027 4042 464754449 464756459 0.000000e+00 3236.0
4 TraesCS4A01G009200 chr4D 91.387 1161 73 14 802 1959 464753313 464754449 0.000000e+00 1565.0
5 TraesCS4A01G009200 chr4D 88.515 862 51 12 4103 4932 464756448 464757293 0.000000e+00 1000.0
6 TraesCS4A01G009200 chr4B 92.465 2097 110 22 875 2957 581159086 581161148 0.000000e+00 2953.0
7 TraesCS4A01G009200 chr4B 92.088 1959 94 23 2986 4904 581161143 581163080 0.000000e+00 2702.0
8 TraesCS4A01G009200 chr4B 78.993 1033 169 32 4957 5963 625981268 625980258 0.000000e+00 662.0
9 TraesCS4A01G009200 chr4B 82.022 267 39 6 5090 5352 665968770 665969031 1.020000e-52 219.0
10 TraesCS4A01G009200 chr3A 94.070 978 49 4 3070 4042 218263951 218264924 0.000000e+00 1476.0
11 TraesCS4A01G009200 chr3A 98.252 801 14 0 1 801 361525822 361526622 0.000000e+00 1402.0
12 TraesCS4A01G009200 chr3A 97.896 808 17 0 1 808 361533847 361534654 0.000000e+00 1399.0
13 TraesCS4A01G009200 chr3A 94.499 909 44 2 3139 4042 218313683 218314590 0.000000e+00 1397.0
14 TraesCS4A01G009200 chr3A 98.127 801 15 0 1 801 361518082 361518882 0.000000e+00 1397.0
15 TraesCS4A01G009200 chr3A 87.399 865 76 15 4103 4957 218314579 218315420 0.000000e+00 963.0
16 TraesCS4A01G009200 chr3A 91.176 374 30 2 4103 4473 218264913 218265286 6.980000e-139 505.0
17 TraesCS4A01G009200 chr3A 94.286 315 17 1 3070 3384 218313366 218313679 1.180000e-131 481.0
18 TraesCS4A01G009200 chr5A 98.377 801 12 1 1 801 66949062 66949861 0.000000e+00 1406.0
19 TraesCS4A01G009200 chr6A 98.130 802 15 0 1 802 380393368 380392567 0.000000e+00 1399.0
20 TraesCS4A01G009200 chr6A 98.127 801 15 0 1 801 513855435 513856235 0.000000e+00 1397.0
21 TraesCS4A01G009200 chr2A 98.127 801 15 0 1 801 553919610 553920410 0.000000e+00 1397.0
22 TraesCS4A01G009200 chr2D 83.195 601 73 12 5302 5874 614376976 614377576 5.360000e-145 525.0
23 TraesCS4A01G009200 chr1D 75.796 785 151 25 5124 5885 460533834 460533066 1.600000e-95 361.0
24 TraesCS4A01G009200 chr1D 75.450 778 151 26 5131 5885 490370442 490369682 5.790000e-90 342.0
25 TraesCS4A01G009200 chr7A 85.374 294 29 5 5073 5353 5744722 5744430 5.910000e-75 292.0
26 TraesCS4A01G009200 chr6B 79.147 422 49 22 4306 4713 71578686 71578290 7.760000e-64 255.0
27 TraesCS4A01G009200 chr7B 96.875 32 0 1 1120 1151 556676891 556676861 1.100000e-02 52.8


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 TraesCS4A01G009200 chr4A 5524770 5530802 6032 True 11141.000000 11141 100.000000 1 6033 1 chr4A.!!$R1 6032
1 TraesCS4A01G009200 chr4A 203203321 203204121 800 True 1419.000000 1419 98.627000 1 801 1 chr4A.!!$R3 800
2 TraesCS4A01G009200 chr4A 5537707 5538507 800 True 1408.000000 1408 98.377000 1 801 1 chr4A.!!$R2 800
3 TraesCS4A01G009200 chr4D 464753313 464757293 3980 False 1933.666667 3236 91.866333 802 4932 3 chr4D.!!$F1 4130
4 TraesCS4A01G009200 chr4B 581159086 581163080 3994 False 2827.500000 2953 92.276500 875 4904 2 chr4B.!!$F2 4029
5 TraesCS4A01G009200 chr4B 625980258 625981268 1010 True 662.000000 662 78.993000 4957 5963 1 chr4B.!!$R1 1006
6 TraesCS4A01G009200 chr3A 361525822 361526622 800 False 1402.000000 1402 98.252000 1 801 1 chr3A.!!$F2 800
7 TraesCS4A01G009200 chr3A 361533847 361534654 807 False 1399.000000 1399 97.896000 1 808 1 chr3A.!!$F3 807
8 TraesCS4A01G009200 chr3A 361518082 361518882 800 False 1397.000000 1397 98.127000 1 801 1 chr3A.!!$F1 800
9 TraesCS4A01G009200 chr3A 218263951 218265286 1335 False 990.500000 1476 92.623000 3070 4473 2 chr3A.!!$F4 1403
10 TraesCS4A01G009200 chr3A 218313366 218315420 2054 False 947.000000 1397 92.061333 3070 4957 3 chr3A.!!$F5 1887
11 TraesCS4A01G009200 chr5A 66949062 66949861 799 False 1406.000000 1406 98.377000 1 801 1 chr5A.!!$F1 800
12 TraesCS4A01G009200 chr6A 380392567 380393368 801 True 1399.000000 1399 98.130000 1 802 1 chr6A.!!$R1 801
13 TraesCS4A01G009200 chr6A 513855435 513856235 800 False 1397.000000 1397 98.127000 1 801 1 chr6A.!!$F1 800
14 TraesCS4A01G009200 chr2A 553919610 553920410 800 False 1397.000000 1397 98.127000 1 801 1 chr2A.!!$F1 800
15 TraesCS4A01G009200 chr2D 614376976 614377576 600 False 525.000000 525 83.195000 5302 5874 1 chr2D.!!$F1 572
16 TraesCS4A01G009200 chr1D 460533066 460533834 768 True 361.000000 361 75.796000 5124 5885 1 chr1D.!!$R1 761
17 TraesCS4A01G009200 chr1D 490369682 490370442 760 True 342.000000 342 75.450000 5131 5885 1 chr1D.!!$R2 754

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
878 879 0.106318 ATGATGCTGGGGAAGAAGGC 60.106 55.000 0.0 0.0 0.00 4.35 F
1590 1607 0.259647 CCAGGCATTGGGAAGATCCA 59.740 55.000 0.0 0.0 43.75 3.41 F
1728 1745 2.028476 TGGTGGATTGATTCGTTCGAGT 60.028 45.455 0.0 0.0 0.00 4.18 F
2498 2522 1.066787 GCTGTTCTTCGCCCTTCTAGT 60.067 52.381 0.0 0.0 0.00 2.57 F
4153 4432 0.598065 AGCAAAACCCGAATGCAGAC 59.402 50.000 0.0 0.0 42.45 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 1790 0.517316 GATCGCCGTATCCATTTGGC 59.483 55.000 0.00 0.0 44.09 4.52 R
2427 2451 0.978151 AGCCAATTTCATGCCAGCAA 59.022 45.000 0.00 0.0 0.00 3.91 R
3388 3667 2.094026 TCTGTGATGCAACAGCTACGAT 60.094 45.455 12.79 0.0 45.93 3.73 R
4414 4696 0.111253 CTTGAGTTGGCTGGAGGGTT 59.889 55.000 0.00 0.0 0.00 4.11 R
5413 5756 0.032130 TCGATCGCATTACTGAGGGC 59.968 55.000 11.09 0.0 0.00 5.19 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
469 470 5.163237 GGCTTAGGGTTTAGGTCATATGTGA 60.163 44.000 1.90 0.00 0.00 3.58
511 512 8.219868 TGAGGATTTTGGAGCATATCATTAAGA 58.780 33.333 0.00 0.00 0.00 2.10
680 681 2.777692 TCTTGAAGGAGTTCCCACAACT 59.222 45.455 0.00 0.00 37.41 3.16
695 696 3.511146 CCACAACTTTTAGTCCATGCCAT 59.489 43.478 0.00 0.00 0.00 4.40
834 835 2.550208 GGCAGACGAGGGAGAAGAAAAA 60.550 50.000 0.00 0.00 0.00 1.94
842 843 3.841255 GAGGGAGAAGAAAAAGAGAGGGA 59.159 47.826 0.00 0.00 0.00 4.20
843 844 3.843619 AGGGAGAAGAAAAAGAGAGGGAG 59.156 47.826 0.00 0.00 0.00 4.30
844 845 3.054728 GGGAGAAGAAAAAGAGAGGGAGG 60.055 52.174 0.00 0.00 0.00 4.30
845 846 3.841255 GGAGAAGAAAAAGAGAGGGAGGA 59.159 47.826 0.00 0.00 0.00 3.71
848 849 3.569135 AGAAAAAGAGAGGGAGGAGGA 57.431 47.619 0.00 0.00 0.00 3.71
858 859 0.340208 GGGAGGAGGAAAGAGGAGGA 59.660 60.000 0.00 0.00 0.00 3.71
863 864 3.973305 GAGGAGGAAAGAGGAGGAATGAT 59.027 47.826 0.00 0.00 0.00 2.45
873 874 1.478288 GGAGGAATGATGCTGGGGAAG 60.478 57.143 0.00 0.00 0.00 3.46
878 879 0.106318 ATGATGCTGGGGAAGAAGGC 60.106 55.000 0.00 0.00 0.00 4.35
885 886 0.323360 TGGGGAAGAAGGCATTTCCG 60.323 55.000 8.09 0.00 43.05 4.30
899 900 0.945265 TTTCCGGCTAAACGTGTCGG 60.945 55.000 10.87 10.87 41.80 4.79
900 901 3.484547 CCGGCTAAACGTGTCGGC 61.485 66.667 4.38 0.00 34.17 5.54
901 902 2.735478 CGGCTAAACGTGTCGGCA 60.735 61.111 4.66 0.00 0.00 5.69
903 904 1.713830 GGCTAAACGTGTCGGCATC 59.286 57.895 0.00 0.00 0.00 3.91
947 948 2.030562 CGGACGAGCACAACCCTT 59.969 61.111 0.00 0.00 0.00 3.95
949 950 1.070786 GGACGAGCACAACCCTTGA 59.929 57.895 0.00 0.00 0.00 3.02
983 984 2.281692 ACACGGCCCGTTTAACCC 60.282 61.111 5.76 0.00 38.32 4.11
990 991 1.304547 CCCGTTTAACCCCATGCCA 60.305 57.895 0.00 0.00 0.00 4.92
991 992 1.319614 CCCGTTTAACCCCATGCCAG 61.320 60.000 0.00 0.00 0.00 4.85
992 993 1.319614 CCGTTTAACCCCATGCCAGG 61.320 60.000 0.00 0.00 0.00 4.45
993 994 0.610785 CGTTTAACCCCATGCCAGGT 60.611 55.000 0.00 0.00 38.27 4.00
1035 1036 2.843545 GTTGGCCAGGTTCAGGGA 59.156 61.111 5.11 0.00 0.00 4.20
1038 1039 4.048470 GGCCAGGTTCAGGGACCC 62.048 72.222 0.59 0.59 40.73 4.46
1040 1041 2.539081 GCCAGGTTCAGGGACCCTT 61.539 63.158 11.56 0.00 40.73 3.95
1042 1043 0.842467 CCAGGTTCAGGGACCCTTCT 60.842 60.000 11.56 3.39 40.73 2.85
1043 1044 1.554822 CCAGGTTCAGGGACCCTTCTA 60.555 57.143 11.56 0.00 40.73 2.10
1044 1045 1.555533 CAGGTTCAGGGACCCTTCTAC 59.444 57.143 11.56 9.05 40.73 2.59
1045 1046 1.437547 AGGTTCAGGGACCCTTCTACT 59.562 52.381 11.56 4.43 40.73 2.57
1057 1058 5.447757 GACCCTTCTACTACTGTACTCCAT 58.552 45.833 0.00 0.00 0.00 3.41
1059 1060 5.044328 ACCCTTCTACTACTGTACTCCATCA 60.044 44.000 0.00 0.00 0.00 3.07
1063 1064 5.437946 TCTACTACTGTACTCCATCACCAG 58.562 45.833 0.00 0.00 0.00 4.00
1164 1166 4.278513 CCGCAACCTCAACCCCCA 62.279 66.667 0.00 0.00 0.00 4.96
1176 1185 3.171388 CCCCCATTCCTCCCTCCG 61.171 72.222 0.00 0.00 0.00 4.63
1296 1305 1.802337 CTATCATCCGTCCCCGCGAA 61.802 60.000 8.23 0.00 0.00 4.70
1298 1307 2.040009 ATCATCCGTCCCCGCGAATT 62.040 55.000 8.23 0.00 0.00 2.17
1300 1309 3.750373 ATCCGTCCCCGCGAATTGG 62.750 63.158 8.23 0.00 0.00 3.16
1378 1387 2.433318 GACCTCGGTGAGCTGCAC 60.433 66.667 1.02 0.00 46.98 4.57
1390 1399 1.399791 GAGCTGCACTTGATAGCAACC 59.600 52.381 1.02 0.00 40.73 3.77
1427 1436 4.026886 GGTTTTGCATTTCGTGTTCTGAAC 60.027 41.667 13.49 13.49 0.00 3.18
1446 1456 3.505464 ACGAGATTCGATTCGGAACTT 57.495 42.857 15.73 0.00 43.74 2.66
1454 1464 5.403897 TTCGATTCGGAACTTTCATATGC 57.596 39.130 6.18 0.00 0.00 3.14
1540 1557 5.124457 GTGATTAGCATCTGATGTGGTTTGT 59.876 40.000 18.19 0.19 0.00 2.83
1590 1607 0.259647 CCAGGCATTGGGAAGATCCA 59.740 55.000 0.00 0.00 43.75 3.41
1643 1660 2.743928 GTGCGCTCCCCTGTCTTG 60.744 66.667 9.73 0.00 0.00 3.02
1666 1683 6.361433 TGTCCTTGTTTATTGTCTTTCTCCA 58.639 36.000 0.00 0.00 0.00 3.86
1672 1689 9.533253 CTTGTTTATTGTCTTTCTCCAAAACAT 57.467 29.630 0.00 0.00 0.00 2.71
1674 1691 9.959749 TGTTTATTGTCTTTCTCCAAAACATAC 57.040 29.630 0.00 0.00 0.00 2.39
1675 1692 9.113876 GTTTATTGTCTTTCTCCAAAACATACG 57.886 33.333 0.00 0.00 0.00 3.06
1728 1745 2.028476 TGGTGGATTGATTCGTTCGAGT 60.028 45.455 0.00 0.00 0.00 4.18
1773 1790 4.000557 GTGGTGACGCTGTGCACG 62.001 66.667 13.13 8.32 38.02 5.34
1871 1888 7.759489 TGGTTTCTTGTAATTCTGTAGCATT 57.241 32.000 0.00 0.00 0.00 3.56
1875 1892 6.647212 TCTTGTAATTCTGTAGCATTGACG 57.353 37.500 0.00 0.00 0.00 4.35
1971 1990 3.996150 CCAATCCATGGTTAGTGATGC 57.004 47.619 12.58 0.00 44.85 3.91
2498 2522 1.066787 GCTGTTCTTCGCCCTTCTAGT 60.067 52.381 0.00 0.00 0.00 2.57
2531 2555 7.615365 TGCTATCTGAATGTTACCCAGAAAAAT 59.385 33.333 0.00 0.00 39.94 1.82
2550 2574 9.030301 AGAAAAATGTTGAAAAGGTATTGTTCG 57.970 29.630 0.00 0.00 32.73 3.95
2608 2632 6.182634 CGTAGGCAAATTACGTGTTATCTTG 58.817 40.000 0.00 0.00 39.13 3.02
2614 2638 6.464834 GCAAATTACGTGTTATCTTGCTACAC 59.535 38.462 0.00 0.00 38.96 2.90
2845 2871 7.231467 TCTTAGCTTGTTTTTGATACCCTTCT 58.769 34.615 0.00 0.00 0.00 2.85
2936 2962 6.177610 GGTGGAGGTGTCTGACAAAATTATA 58.822 40.000 12.81 0.00 0.00 0.98
3346 3620 5.125356 TGTGTAATCATCTTTCGCCATCAT 58.875 37.500 0.00 0.00 0.00 2.45
3350 3624 7.489113 GTGTAATCATCTTTCGCCATCATTTTT 59.511 33.333 0.00 0.00 0.00 1.94
3363 3637 7.446319 TCGCCATCATTTTTGAGATGATATCTT 59.554 33.333 3.98 0.00 43.28 2.40
3480 3759 2.158623 TGCAAAATGACAGTGTCTCCCT 60.159 45.455 23.29 4.01 33.15 4.20
3481 3760 2.887152 GCAAAATGACAGTGTCTCCCTT 59.113 45.455 23.29 9.22 33.15 3.95
3550 3829 3.010420 GCCTGGTGACTTACAAATCTCC 58.990 50.000 0.00 0.00 0.00 3.71
3639 3918 0.681175 ACAATGAGTTTTGCAGGCCC 59.319 50.000 0.00 0.00 0.00 5.80
3796 4075 7.813148 GCTGTTAACAGTAGTATTCTGAGAACA 59.187 37.037 30.90 0.00 45.45 3.18
3812 4091 7.542890 TCTGAGAACAGACAAAGATACTCATC 58.457 38.462 0.00 0.00 46.55 2.92
4074 4353 3.008375 AGCAAGGAGATAACTGTTGCTGA 59.992 43.478 14.85 0.00 44.43 4.26
4085 4364 1.272490 CTGTTGCTGAGGGTTCTCGTA 59.728 52.381 0.00 0.00 42.79 3.43
4153 4432 0.598065 AGCAAAACCCGAATGCAGAC 59.402 50.000 0.00 0.00 42.45 3.51
4263 4542 2.012673 GCAACTCTCTGGCGATGATTT 58.987 47.619 0.00 0.00 0.00 2.17
4354 4633 1.936547 GCAGATGATTTCCTCGGTGAC 59.063 52.381 0.00 0.00 0.00 3.67
4456 4738 2.211250 ATTGCTCAATGTCTGCCACT 57.789 45.000 0.00 0.00 0.00 4.00
4495 4783 3.209410 CAGTCATAAGATGGTGGCTTCC 58.791 50.000 0.00 0.00 0.00 3.46
4498 4786 1.942657 CATAAGATGGTGGCTTCCGTG 59.057 52.381 0.00 0.00 0.00 4.94
4579 4867 4.991687 GCATACTTCATCTAGTAGTTGCCC 59.008 45.833 3.68 0.00 34.32 5.36
4609 4909 2.217750 TGGGTCAGTTTGATGTTGTCG 58.782 47.619 0.00 0.00 0.00 4.35
4616 4916 0.313672 TTTGATGTTGTCGCAAGGGC 59.686 50.000 0.00 0.00 38.47 5.19
4617 4917 0.821301 TTGATGTTGTCGCAAGGGCA 60.821 50.000 0.00 0.00 41.24 5.36
4619 4919 1.514678 GATGTTGTCGCAAGGGCACA 61.515 55.000 0.00 0.00 41.24 4.57
4677 4978 6.365520 AGTCTTGAAGATTGGTTAACACCTT 58.634 36.000 8.10 4.56 44.61 3.50
4710 5011 2.100749 TCACGTGTTCTCAGTGATGTGT 59.899 45.455 16.51 0.00 39.63 3.72
4728 5029 4.693283 TGTGTCTCGATGACTTGAAACTT 58.307 39.130 13.65 0.00 45.54 2.66
4729 5030 4.507756 TGTGTCTCGATGACTTGAAACTTG 59.492 41.667 13.65 0.00 45.54 3.16
4732 5033 4.985409 GTCTCGATGACTTGAAACTTGTCT 59.015 41.667 7.50 0.00 42.21 3.41
4761 5062 6.428159 CCAAATAGACAGTTTGTAGAGCAGTT 59.572 38.462 0.00 0.00 35.35 3.16
4800 5119 2.294233 TCTTGTGCAGTTTGAAGGATGC 59.706 45.455 0.00 0.00 39.14 3.91
4802 5121 1.610038 TGTGCAGTTTGAAGGATGCTG 59.390 47.619 0.00 0.00 39.42 4.41
4887 5206 2.514824 GGCTAAGGGGCGCTGAAG 60.515 66.667 7.64 7.32 0.00 3.02
4914 5233 3.133003 TCCTCGGGCTTCTTAGAAATCTG 59.867 47.826 0.00 0.00 0.00 2.90
4932 5255 2.197324 TGGAAGGCGCAGGGTTTT 59.803 55.556 10.83 0.00 0.00 2.43
4959 5282 1.475280 CGACGACTTTCCCCATGACTA 59.525 52.381 0.00 0.00 0.00 2.59
4965 5288 5.189145 ACGACTTTCCCCATGACTAATTAGT 59.811 40.000 18.05 18.05 39.71 2.24
4973 5296 5.380043 CCCATGACTAATTAGTTCCAGCAT 58.620 41.667 18.96 13.72 36.50 3.79
4977 5300 5.109210 TGACTAATTAGTTCCAGCATCGTG 58.891 41.667 18.96 0.00 36.50 4.35
4983 5306 1.065491 AGTTCCAGCATCGTGCCAATA 60.065 47.619 6.39 0.00 46.52 1.90
4984 5307 1.742831 GTTCCAGCATCGTGCCAATAA 59.257 47.619 6.39 0.00 46.52 1.40
4992 5315 5.045215 AGCATCGTGCCAATAATTTCAATG 58.955 37.500 6.39 0.00 46.52 2.82
4993 5316 4.318263 GCATCGTGCCAATAATTTCAATGC 60.318 41.667 0.00 0.00 37.42 3.56
4995 5318 5.008619 TCGTGCCAATAATTTCAATGCAT 57.991 34.783 0.00 0.00 0.00 3.96
4998 5321 5.117584 GTGCCAATAATTTCAATGCATCCA 58.882 37.500 0.00 0.00 0.00 3.41
5001 5324 6.093771 TGCCAATAATTTCAATGCATCCAAAC 59.906 34.615 0.00 0.00 0.00 2.93
5009 5332 7.649533 TTTCAATGCATCCAAACATCTCTAT 57.350 32.000 0.00 0.00 0.00 1.98
5015 5338 6.124340 TGCATCCAAACATCTCTATGTGAAT 58.876 36.000 0.00 0.00 45.79 2.57
5019 5342 8.562892 CATCCAAACATCTCTATGTGAATAACC 58.437 37.037 0.00 0.00 45.79 2.85
5020 5343 7.629157 TCCAAACATCTCTATGTGAATAACCA 58.371 34.615 0.00 0.00 45.79 3.67
5021 5344 8.274322 TCCAAACATCTCTATGTGAATAACCAT 58.726 33.333 0.00 0.00 45.79 3.55
5028 5351 9.770097 ATCTCTATGTGAATAACCATTACACTG 57.230 33.333 0.00 0.00 33.41 3.66
5029 5352 8.977412 TCTCTATGTGAATAACCATTACACTGA 58.023 33.333 0.00 0.00 33.41 3.41
5050 5378 9.770503 CACTGAATGAAGATAGAAGAAATGTTG 57.229 33.333 0.00 0.00 0.00 3.33
5052 5380 9.985318 CTGAATGAAGATAGAAGAAATGTTGTC 57.015 33.333 0.00 0.00 0.00 3.18
5055 5383 9.730705 AATGAAGATAGAAGAAATGTTGTCTCA 57.269 29.630 0.00 0.00 0.00 3.27
5070 5398 5.811613 TGTTGTCTCAAATTTTCAAAGCCAG 59.188 36.000 0.00 0.00 0.00 4.85
5078 5406 7.765307 TCAAATTTTCAAAGCCAGCTAGATAG 58.235 34.615 0.00 0.00 0.00 2.08
5080 5408 7.709149 AATTTTCAAAGCCAGCTAGATAGTT 57.291 32.000 0.00 0.00 0.00 2.24
5082 5410 7.524717 TTTTCAAAGCCAGCTAGATAGTTTT 57.475 32.000 0.00 0.00 0.00 2.43
5087 5415 4.310769 AGCCAGCTAGATAGTTTTATGCG 58.689 43.478 0.00 0.00 0.00 4.73
5088 5416 4.039245 AGCCAGCTAGATAGTTTTATGCGA 59.961 41.667 0.00 0.00 0.00 5.10
5099 5427 5.857822 AGTTTTATGCGACTCCAAAGTAC 57.142 39.130 0.00 0.00 35.28 2.73
5100 5428 5.302360 AGTTTTATGCGACTCCAAAGTACA 58.698 37.500 0.00 0.00 35.28 2.90
5102 5430 6.430000 AGTTTTATGCGACTCCAAAGTACATT 59.570 34.615 0.00 0.00 35.28 2.71
5103 5431 6.811253 TTTATGCGACTCCAAAGTACATTT 57.189 33.333 0.00 0.00 35.28 2.32
5104 5432 4.685169 ATGCGACTCCAAAGTACATTTG 57.315 40.909 0.00 3.45 46.62 2.32
5139 5467 4.837972 TCATCATACCCACGAATTGTCAA 58.162 39.130 0.00 0.00 0.00 3.18
5140 5468 4.634004 TCATCATACCCACGAATTGTCAAC 59.366 41.667 0.00 0.00 0.00 3.18
5147 5475 3.255642 CCCACGAATTGTCAACCATTTCT 59.744 43.478 0.00 0.00 33.32 2.52
5158 5486 3.369756 TCAACCATTTCTTCATACGCGAC 59.630 43.478 15.93 0.00 0.00 5.19
5163 5491 0.388778 TTCTTCATACGCGACGGCAA 60.389 50.000 15.93 0.00 39.92 4.52
5170 5498 4.368808 CGCGACGGCAACCAACTG 62.369 66.667 0.00 0.00 39.92 3.16
5171 5499 4.683334 GCGACGGCAACCAACTGC 62.683 66.667 0.00 0.00 41.85 4.40
5173 5501 2.616330 CGACGGCAACCAACTGCAT 61.616 57.895 0.00 0.00 44.52 3.96
5175 5503 0.168128 GACGGCAACCAACTGCATAC 59.832 55.000 0.00 0.00 44.52 2.39
5182 5510 3.853307 GCAACCAACTGCATACACTTCAC 60.853 47.826 0.00 0.00 42.17 3.18
5184 5512 3.403038 ACCAACTGCATACACTTCACTC 58.597 45.455 0.00 0.00 0.00 3.51
5204 5532 1.873591 CCGAACCTTCAAGTTCAGGTG 59.126 52.381 4.31 0.00 45.27 4.00
5206 5534 2.576615 GAACCTTCAAGTTCAGGTGCT 58.423 47.619 4.31 0.00 43.05 4.40
5292 5620 2.419324 CCTGAATCAGCAAGTCAAGCTC 59.581 50.000 4.40 0.00 41.14 4.09
5306 5634 2.169352 TCAAGCTCCATAGTCTCCAAGC 59.831 50.000 0.00 0.00 0.00 4.01
5334 5662 3.815401 GAGAAAAACCAGCAGCAGAGTAA 59.185 43.478 0.00 0.00 0.00 2.24
5357 5688 3.019564 CCAGAAGGGGTCATCATTGTTC 58.980 50.000 0.00 0.00 0.00 3.18
5372 5703 6.662414 TCATTGTTCTTGATAAGTAAGCGG 57.338 37.500 0.00 0.00 0.00 5.52
5373 5704 6.170506 TCATTGTTCTTGATAAGTAAGCGGT 58.829 36.000 0.00 0.00 0.00 5.68
5413 5756 2.777832 CCTTGAGGTCTCCCTGAAAG 57.222 55.000 0.00 0.00 42.86 2.62
5433 5785 1.772182 CCCTCAGTAATGCGATCGAC 58.228 55.000 21.57 10.98 0.00 4.20
5436 5788 2.791560 CCTCAGTAATGCGATCGACTTG 59.208 50.000 21.57 8.14 0.00 3.16
5494 5846 1.134128 TGAATCCCATCACCATCCACG 60.134 52.381 0.00 0.00 0.00 4.94
5531 5883 3.645212 CTGGAGGAGGAAATCAGCAGATA 59.355 47.826 0.00 0.00 33.08 1.98
5547 5899 5.756833 CAGCAGATACATGAGCAATACAGAA 59.243 40.000 0.00 0.00 0.00 3.02
5604 5967 0.318441 CACTCCACCTTCGCTTGAGA 59.682 55.000 0.00 0.00 0.00 3.27
5637 6000 0.036388 GTGGTGACATCCATGGTCGT 60.036 55.000 12.58 10.14 46.14 4.34
5638 6001 0.036483 TGGTGACATCCATGGTCGTG 60.036 55.000 12.58 11.79 38.10 4.35
5640 6003 1.078497 TGACATCCATGGTCGTGGC 60.078 57.895 12.58 12.09 39.19 5.01
5657 6023 1.686587 TGGCGTCGATCCTTATCATGT 59.313 47.619 0.00 0.00 31.93 3.21
5700 6072 3.753272 CAGTAAACAGAATCACCCACCAG 59.247 47.826 0.00 0.00 0.00 4.00
5701 6073 3.394606 AGTAAACAGAATCACCCACCAGT 59.605 43.478 0.00 0.00 0.00 4.00
5714 6086 1.151668 CACCAGTGTGCTAGTCTTGC 58.848 55.000 0.00 0.00 35.31 4.01
5773 6151 1.379843 GATGGCCCAATCCCACGTT 60.380 57.895 0.00 0.00 34.68 3.99
5776 6154 2.696759 GGCCCAATCCCACGTTTCG 61.697 63.158 0.00 0.00 0.00 3.46
5833 6211 2.125952 CAGATGCAGACCACGCGA 60.126 61.111 15.93 0.00 0.00 5.87
5858 6236 2.035940 AGGGCTTCTCGTCGGAGT 59.964 61.111 0.00 0.00 41.26 3.85
5860 6238 0.748729 AGGGCTTCTCGTCGGAGTAG 60.749 60.000 0.00 0.00 41.26 2.57
5882 6260 2.514160 AGGAGGTGAAAACCAAGGAAGT 59.486 45.455 0.00 0.00 0.00 3.01
5906 6296 1.511305 GTCTCCGCCATGAAGTCGA 59.489 57.895 0.00 0.00 0.00 4.20
5910 6300 2.885644 CGCCATGAAGTCGACGGG 60.886 66.667 10.46 9.14 0.00 5.28
5941 6331 4.131088 GAGTCGACGGCCCAGGTC 62.131 72.222 10.46 0.00 0.00 3.85
5944 6334 3.458163 TCGACGGCCCAGGTCATC 61.458 66.667 9.55 0.00 34.04 2.92
5954 6344 0.176680 CCAGGTCATCGGGTTGAGAG 59.823 60.000 0.00 0.00 0.00 3.20
5972 6362 4.812476 CGGCGAGCGAACCATGGA 62.812 66.667 21.47 0.00 0.00 3.41
5973 6363 2.892425 GGCGAGCGAACCATGGAG 60.892 66.667 21.47 10.47 0.00 3.86
5974 6364 3.567797 GCGAGCGAACCATGGAGC 61.568 66.667 21.47 19.84 0.00 4.70
5975 6365 3.257561 CGAGCGAACCATGGAGCG 61.258 66.667 21.47 21.24 34.34 5.03
5979 6369 3.501396 CGAACCATGGAGCGCATT 58.499 55.556 21.47 0.00 0.00 3.56
5980 6370 1.353103 CGAACCATGGAGCGCATTC 59.647 57.895 21.47 9.62 0.00 2.67
5981 6371 1.729881 GAACCATGGAGCGCATTCC 59.270 57.895 21.47 9.86 37.77 3.01
5986 6376 2.586245 TGGAGCGCATTCCAGAGG 59.414 61.111 13.98 0.00 42.24 3.69
5987 6377 1.989508 TGGAGCGCATTCCAGAGGA 60.990 57.895 13.98 0.00 42.24 3.71
5988 6378 1.227497 GGAGCGCATTCCAGAGGAG 60.227 63.158 11.47 0.00 37.20 3.69
5989 6379 1.227497 GAGCGCATTCCAGAGGAGG 60.227 63.158 11.47 0.00 31.21 4.30
5990 6380 2.203126 GCGCATTCCAGAGGAGGG 60.203 66.667 0.30 0.00 31.21 4.30
5991 6381 2.203126 CGCATTCCAGAGGAGGGC 60.203 66.667 0.00 0.00 31.21 5.19
5992 6382 2.203126 GCATTCCAGAGGAGGGCG 60.203 66.667 0.00 0.00 31.21 6.13
5993 6383 2.203126 CATTCCAGAGGAGGGCGC 60.203 66.667 0.00 0.00 31.21 6.53
5994 6384 3.854669 ATTCCAGAGGAGGGCGCG 61.855 66.667 0.00 0.00 31.21 6.86
6018 6408 4.838486 GCGGCAGTCGTCGAGGAG 62.838 72.222 8.30 0.00 45.23 3.69
6019 6409 4.838486 CGGCAGTCGTCGAGGAGC 62.838 72.222 8.30 9.31 45.23 4.70
6020 6410 4.500116 GGCAGTCGTCGAGGAGCC 62.500 72.222 18.82 18.82 34.71 4.70
6021 6411 3.749064 GCAGTCGTCGAGGAGCCA 61.749 66.667 8.30 0.00 0.00 4.75
6022 6412 2.487428 CAGTCGTCGAGGAGCCAG 59.513 66.667 8.30 0.00 0.00 4.85
6023 6413 3.444805 AGTCGTCGAGGAGCCAGC 61.445 66.667 8.30 0.00 0.00 4.85
6024 6414 4.500116 GTCGTCGAGGAGCCAGCC 62.500 72.222 8.30 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
371 372 1.068948 TAGCCACTGCCAAACCCTAA 58.931 50.000 0.00 0.00 38.69 2.69
469 470 2.979678 TCCTCAGCTACTTTCCCACTTT 59.020 45.455 0.00 0.00 0.00 2.66
680 681 4.776837 ACAATGGAATGGCATGGACTAAAA 59.223 37.500 0.00 0.00 0.00 1.52
695 696 6.459024 CGTTTCAGGTAAGTTCAACAATGGAA 60.459 38.462 0.00 0.00 0.00 3.53
818 819 3.259625 CCTCTCTTTTTCTTCTCCCTCGT 59.740 47.826 0.00 0.00 0.00 4.18
834 835 1.290732 CCTCTTTCCTCCTCCCTCTCT 59.709 57.143 0.00 0.00 0.00 3.10
842 843 3.498614 TCATTCCTCCTCTTTCCTCCT 57.501 47.619 0.00 0.00 0.00 3.69
843 844 3.747069 GCATCATTCCTCCTCTTTCCTCC 60.747 52.174 0.00 0.00 0.00 4.30
844 845 3.136260 AGCATCATTCCTCCTCTTTCCTC 59.864 47.826 0.00 0.00 0.00 3.71
845 846 3.117963 CAGCATCATTCCTCCTCTTTCCT 60.118 47.826 0.00 0.00 0.00 3.36
848 849 2.091994 CCCAGCATCATTCCTCCTCTTT 60.092 50.000 0.00 0.00 0.00 2.52
858 859 1.687368 GCCTTCTTCCCCAGCATCATT 60.687 52.381 0.00 0.00 0.00 2.57
863 864 0.114954 AAATGCCTTCTTCCCCAGCA 59.885 50.000 0.00 0.00 37.94 4.41
873 874 1.202143 CGTTTAGCCGGAAATGCCTTC 60.202 52.381 5.05 0.00 0.00 3.46
878 879 1.201877 CGACACGTTTAGCCGGAAATG 60.202 52.381 5.05 5.90 0.00 2.32
885 886 1.713830 GATGCCGACACGTTTAGCC 59.286 57.895 0.00 0.00 0.00 3.93
928 929 4.980805 GGGTTGTGCTCGTCCGCA 62.981 66.667 0.00 0.00 37.62 5.69
934 935 3.972227 CCTCAAGGGTTGTGCTCG 58.028 61.111 0.00 0.00 0.00 5.03
947 948 3.164977 TGGCCCGTGACAACCTCA 61.165 61.111 0.00 0.00 0.00 3.86
949 950 2.847234 TCTGGCCCGTGACAACCT 60.847 61.111 0.00 0.00 0.00 3.50
1031 1032 3.857420 AGTACAGTAGTAGAAGGGTCCCT 59.143 47.826 3.85 3.85 33.87 4.20
1035 1036 4.942363 TGGAGTACAGTAGTAGAAGGGT 57.058 45.455 0.00 0.00 0.00 4.34
1038 1039 5.886474 TGGTGATGGAGTACAGTAGTAGAAG 59.114 44.000 0.00 0.00 0.00 2.85
1040 1041 5.045066 ACTGGTGATGGAGTACAGTAGTAGA 60.045 44.000 0.00 0.00 40.31 2.59
1042 1043 5.188988 ACTGGTGATGGAGTACAGTAGTA 57.811 43.478 0.00 0.00 40.31 1.82
1043 1044 4.017808 GACTGGTGATGGAGTACAGTAGT 58.982 47.826 0.00 0.00 41.98 2.73
1044 1045 4.017126 TGACTGGTGATGGAGTACAGTAG 58.983 47.826 0.00 0.00 41.98 2.57
1045 1046 3.762288 GTGACTGGTGATGGAGTACAGTA 59.238 47.826 0.00 0.00 41.98 2.74
1057 1058 1.271840 GGGCCATAGGTGACTGGTGA 61.272 60.000 4.39 0.00 43.88 4.02
1059 1060 0.844661 TTGGGCCATAGGTGACTGGT 60.845 55.000 7.26 0.00 43.88 4.00
1063 1064 1.032114 GCAGTTGGGCCATAGGTGAC 61.032 60.000 7.26 0.19 0.00 3.67
1104 1106 0.026544 GTCGGAGTCGTCGATGTCTC 59.973 60.000 19.66 19.66 38.93 3.36
1146 1148 4.280019 GGGGGTTGAGGTTGCGGT 62.280 66.667 0.00 0.00 0.00 5.68
1147 1149 3.583882 ATGGGGGTTGAGGTTGCGG 62.584 63.158 0.00 0.00 0.00 5.69
1148 1150 1.595093 GAATGGGGGTTGAGGTTGCG 61.595 60.000 0.00 0.00 0.00 4.85
1149 1151 1.257750 GGAATGGGGGTTGAGGTTGC 61.258 60.000 0.00 0.00 0.00 4.17
1150 1152 0.409484 AGGAATGGGGGTTGAGGTTG 59.591 55.000 0.00 0.00 0.00 3.77
1184 1193 1.001641 GCTGATGGGAAGTGGTGCT 60.002 57.895 0.00 0.00 0.00 4.40
1315 1324 4.421479 AGGAAGTCGGCGTCAGCG 62.421 66.667 6.85 0.00 46.35 5.18
1318 1327 2.867855 AAGCAGGAAGTCGGCGTCA 61.868 57.895 6.85 0.00 41.48 4.35
1396 1405 3.181495 ACGAAATGCAAAACCTTTGACGA 60.181 39.130 3.35 0.00 0.00 4.20
1427 1436 3.857665 TGAAAGTTCCGAATCGAATCTCG 59.142 43.478 3.36 3.63 42.10 4.04
1446 1456 5.104151 TCCATACTGAACTTGGGCATATGAA 60.104 40.000 6.97 0.00 0.00 2.57
1454 1464 3.763897 CCCTTTTCCATACTGAACTTGGG 59.236 47.826 0.00 0.00 0.00 4.12
1531 1541 1.018148 CACCTGCGTTACAAACCACA 58.982 50.000 0.00 0.00 0.00 4.17
1540 1557 2.967397 CGGTCTCCACCTGCGTTA 59.033 61.111 0.00 0.00 41.17 3.18
1590 1607 1.000955 GATCTAATGCCCGGTCGACAT 59.999 52.381 18.91 0.00 0.00 3.06
1629 1646 1.831652 AAGGACAAGACAGGGGAGCG 61.832 60.000 0.00 0.00 0.00 5.03
1630 1647 0.322008 CAAGGACAAGACAGGGGAGC 60.322 60.000 0.00 0.00 0.00 4.70
1643 1660 6.877611 TGGAGAAAGACAATAAACAAGGAC 57.122 37.500 0.00 0.00 0.00 3.85
1666 1683 6.806249 CAGTGGCAAAATGATACGTATGTTTT 59.194 34.615 13.97 15.70 0.00 2.43
1672 1689 3.373748 CAGCAGTGGCAAAATGATACGTA 59.626 43.478 0.00 0.00 44.61 3.57
1673 1690 2.162208 CAGCAGTGGCAAAATGATACGT 59.838 45.455 0.00 0.00 44.61 3.57
1674 1691 2.478370 CCAGCAGTGGCAAAATGATACG 60.478 50.000 0.00 0.00 44.61 3.06
1675 1692 3.155093 CCAGCAGTGGCAAAATGATAC 57.845 47.619 0.00 0.00 44.61 2.24
1704 1721 2.094258 CGAACGAATCAATCCACCACAG 59.906 50.000 0.00 0.00 0.00 3.66
1728 1745 3.576078 ACCTGATCACAACCAAGAACA 57.424 42.857 0.00 0.00 0.00 3.18
1773 1790 0.517316 GATCGCCGTATCCATTTGGC 59.483 55.000 0.00 0.00 44.09 4.52
1857 1874 6.163476 ACTCAACGTCAATGCTACAGAATTA 58.837 36.000 0.00 0.00 0.00 1.40
1871 1888 2.148916 ATCAGCGAAACTCAACGTCA 57.851 45.000 0.00 0.00 0.00 4.35
1875 1892 4.154195 ACATGGTAATCAGCGAAACTCAAC 59.846 41.667 0.00 0.00 0.00 3.18
1970 1989 5.748152 TGCAGTTACAACAAAAGAGAAATGC 59.252 36.000 0.00 0.00 38.11 3.56
1971 1990 7.195646 TCTGCAGTTACAACAAAAGAGAAATG 58.804 34.615 14.67 0.00 0.00 2.32
2427 2451 0.978151 AGCCAATTTCATGCCAGCAA 59.022 45.000 0.00 0.00 0.00 3.91
2436 2460 4.998671 TTCAACAGTGAAGCCAATTTCA 57.001 36.364 0.00 0.00 38.88 2.69
2498 2522 6.338146 GGTAACATTCAGATAGCACACTGTA 58.662 40.000 0.00 0.00 35.84 2.74
2531 2555 6.539464 AGTGTACGAACAATACCTTTTCAACA 59.461 34.615 0.00 0.00 37.36 3.33
2566 2590 5.450965 GCCTACGTCAGCACCTATAAAAGTA 60.451 44.000 0.00 0.00 0.00 2.24
2599 2623 8.100791 ACTTAAGGAATGTGTAGCAAGATAACA 58.899 33.333 7.53 0.00 0.00 2.41
3061 3087 8.972127 TCTCTAATCTGCTTTATTAGTCACAGT 58.028 33.333 10.85 0.00 37.89 3.55
3137 3163 9.520515 ACACACATCCTTAATTTAAGTCTGAAT 57.479 29.630 13.68 4.03 33.96 2.57
3186 3460 2.524569 ATCCCTTTTTGCCACGTTTG 57.475 45.000 0.00 0.00 0.00 2.93
3369 3643 9.450807 GCTACGATATAAAACAGCAATTCAAAT 57.549 29.630 0.00 0.00 0.00 2.32
3388 3667 2.094026 TCTGTGATGCAACAGCTACGAT 60.094 45.455 12.79 0.00 45.93 3.73
3394 3673 2.291465 TGAACTTCTGTGATGCAACAGC 59.709 45.455 12.79 2.31 45.93 4.40
3480 3759 3.888323 TGATGGAACTGCTTGCTTACAAA 59.112 39.130 0.00 0.00 34.74 2.83
3481 3760 3.485394 TGATGGAACTGCTTGCTTACAA 58.515 40.909 0.00 0.00 0.00 2.41
3550 3829 7.912778 TTTATTTGGGGGATGAATAAAGAGG 57.087 36.000 0.00 0.00 32.98 3.69
3639 3918 4.778213 TCCCTTTCCATGTTATCTCCTG 57.222 45.455 0.00 0.00 0.00 3.86
3796 4075 6.510879 TGTACACGATGAGTATCTTTGTCT 57.489 37.500 0.00 0.00 34.93 3.41
4074 4353 4.091549 TCCACAATTACTACGAGAACCCT 58.908 43.478 0.00 0.00 0.00 4.34
4153 4432 1.208358 CGGCTGTGTGCATCTTGTG 59.792 57.895 0.00 0.00 45.15 3.33
4208 4487 2.778299 ACAGGAAGCTTGCGAACAATA 58.222 42.857 12.66 0.00 34.61 1.90
4263 4542 3.603158 TTTTACTACGAGGCTGCATCA 57.397 42.857 15.07 0.00 0.00 3.07
4302 4581 0.813184 ACCATTGCCATCAGAAAGCG 59.187 50.000 0.00 0.00 0.00 4.68
4331 4610 3.068732 TCACCGAGGAAATCATCTGCTAG 59.931 47.826 0.00 0.00 0.00 3.42
4354 4633 1.303309 GCTTCCTGATCGGATTGTGG 58.697 55.000 2.08 0.00 42.70 4.17
4414 4696 0.111253 CTTGAGTTGGCTGGAGGGTT 59.889 55.000 0.00 0.00 0.00 4.11
4456 4738 0.693622 TGGAAGGTAATGTTCCGCCA 59.306 50.000 0.00 0.00 45.75 5.69
4495 4783 1.012086 CATCAGTCCATTCTGGCACG 58.988 55.000 0.00 0.00 37.47 5.34
4498 4786 1.307097 GCTCATCAGTCCATTCTGGC 58.693 55.000 0.00 0.00 37.47 4.85
4593 4893 2.290367 CCTTGCGACAACATCAAACTGA 59.710 45.455 0.00 0.00 0.00 3.41
4609 4909 0.459489 TGACTTTGTTGTGCCCTTGC 59.541 50.000 0.00 0.00 38.26 4.01
4616 4916 3.441496 AACATGCCTGACTTTGTTGTG 57.559 42.857 0.00 0.00 31.45 3.33
4617 4917 4.207165 ACTAACATGCCTGACTTTGTTGT 58.793 39.130 0.00 0.00 34.39 3.32
4619 4919 4.644685 ACAACTAACATGCCTGACTTTGTT 59.355 37.500 0.00 0.00 36.37 2.83
4710 5011 5.201713 AGACAAGTTTCAAGTCATCGAGA 57.798 39.130 0.00 0.00 34.80 4.04
4732 5033 8.755028 TGCTCTACAAACTGTCTATTTGGTATA 58.245 33.333 2.84 0.00 40.64 1.47
4742 5043 4.672587 TCAACTGCTCTACAAACTGTCT 57.327 40.909 0.00 0.00 0.00 3.41
4748 5049 9.494271 GATATAATCCATCAACTGCTCTACAAA 57.506 33.333 0.00 0.00 0.00 2.83
4756 5057 8.709386 AGATTACGATATAATCCATCAACTGC 57.291 34.615 0.00 0.00 35.19 4.40
4761 5062 8.093927 TGCACAAGATTACGATATAATCCATCA 58.906 33.333 0.00 0.00 35.19 3.07
4800 5119 5.940192 TTAGGAGCAACATGTAACAACAG 57.060 39.130 0.00 0.00 0.00 3.16
4802 5121 7.367285 TCATTTTAGGAGCAACATGTAACAAC 58.633 34.615 0.00 0.00 0.00 3.32
4877 5196 2.435059 GGAGTGTCTTCAGCGCCC 60.435 66.667 2.29 0.00 0.00 6.13
4887 5206 1.135333 CTAAGAAGCCCGAGGAGTGTC 59.865 57.143 0.00 0.00 0.00 3.67
4914 5233 0.891904 TAAAACCCTGCGCCTTCCAC 60.892 55.000 4.18 0.00 0.00 4.02
4932 5255 2.295885 GGGGAAAGTCGTCGATCTCTA 58.704 52.381 0.00 0.00 0.00 2.43
4959 5282 2.017049 GGCACGATGCTGGAACTAATT 58.983 47.619 9.31 0.00 44.28 1.40
4965 5288 2.121291 TTATTGGCACGATGCTGGAA 57.879 45.000 9.31 2.53 44.28 3.53
4973 5296 4.446994 TGCATTGAAATTATTGGCACGA 57.553 36.364 0.00 0.00 0.00 4.35
4977 5300 6.093771 TGTTTGGATGCATTGAAATTATTGGC 59.906 34.615 0.00 0.00 0.00 4.52
4983 5306 6.942976 AGAGATGTTTGGATGCATTGAAATT 58.057 32.000 0.00 0.00 0.00 1.82
4984 5307 6.540438 AGAGATGTTTGGATGCATTGAAAT 57.460 33.333 0.00 0.00 0.00 2.17
4992 5315 6.630444 ATTCACATAGAGATGTTTGGATGC 57.370 37.500 0.00 0.00 44.18 3.91
4993 5316 8.562892 GGTTATTCACATAGAGATGTTTGGATG 58.437 37.037 0.00 0.00 44.18 3.51
4995 5318 7.629157 TGGTTATTCACATAGAGATGTTTGGA 58.371 34.615 0.00 0.00 44.18 3.53
5001 5324 9.770097 AGTGTAATGGTTATTCACATAGAGATG 57.230 33.333 0.00 0.00 39.16 2.90
5009 5332 8.628630 TTCATTCAGTGTAATGGTTATTCACA 57.371 30.769 12.43 0.00 37.44 3.58
5023 5346 9.512588 AACATTTCTTCTATCTTCATTCAGTGT 57.487 29.630 0.00 0.00 0.00 3.55
5024 5347 9.770503 CAACATTTCTTCTATCTTCATTCAGTG 57.229 33.333 0.00 0.00 0.00 3.66
5025 5348 9.512588 ACAACATTTCTTCTATCTTCATTCAGT 57.487 29.630 0.00 0.00 0.00 3.41
5029 5352 9.730705 TGAGACAACATTTCTTCTATCTTCATT 57.269 29.630 0.00 0.00 0.00 2.57
5046 5374 5.728471 TGGCTTTGAAAATTTGAGACAACA 58.272 33.333 0.00 0.00 0.00 3.33
5047 5375 5.277011 GCTGGCTTTGAAAATTTGAGACAAC 60.277 40.000 0.00 0.00 0.00 3.32
5048 5376 4.810491 GCTGGCTTTGAAAATTTGAGACAA 59.190 37.500 0.00 0.00 0.00 3.18
5050 5378 4.625028 AGCTGGCTTTGAAAATTTGAGAC 58.375 39.130 0.00 0.00 0.00 3.36
5052 5380 6.017400 TCTAGCTGGCTTTGAAAATTTGAG 57.983 37.500 0.00 0.00 0.00 3.02
5055 5383 7.709149 ACTATCTAGCTGGCTTTGAAAATTT 57.291 32.000 0.00 0.00 0.00 1.82
5065 5393 4.039245 TCGCATAAAACTATCTAGCTGGCT 59.961 41.667 0.00 0.00 0.00 4.75
5070 5398 5.529791 TGGAGTCGCATAAAACTATCTAGC 58.470 41.667 0.00 0.00 0.00 3.42
5078 5406 5.600908 TGTACTTTGGAGTCGCATAAAAC 57.399 39.130 0.00 0.00 37.33 2.43
5080 5408 6.428465 TCAAATGTACTTTGGAGTCGCATAAA 59.572 34.615 14.02 0.00 43.71 1.40
5082 5410 5.483811 TCAAATGTACTTTGGAGTCGCATA 58.516 37.500 14.02 0.00 43.71 3.14
5087 5415 8.324163 ACTGTTATCAAATGTACTTTGGAGTC 57.676 34.615 14.02 5.14 43.71 3.36
5088 5416 8.691661 AACTGTTATCAAATGTACTTTGGAGT 57.308 30.769 14.02 1.75 43.71 3.85
5102 5430 8.052141 TGGGTATGATGAATGAACTGTTATCAA 58.948 33.333 6.93 0.00 0.00 2.57
5103 5431 7.498900 GTGGGTATGATGAATGAACTGTTATCA 59.501 37.037 5.64 5.64 0.00 2.15
5104 5432 7.307396 CGTGGGTATGATGAATGAACTGTTATC 60.307 40.741 0.00 0.00 0.00 1.75
5106 5434 5.815222 CGTGGGTATGATGAATGAACTGTTA 59.185 40.000 0.00 0.00 0.00 2.41
5107 5435 4.635765 CGTGGGTATGATGAATGAACTGTT 59.364 41.667 0.00 0.00 0.00 3.16
5108 5436 4.081142 TCGTGGGTATGATGAATGAACTGT 60.081 41.667 0.00 0.00 0.00 3.55
5109 5437 4.441792 TCGTGGGTATGATGAATGAACTG 58.558 43.478 0.00 0.00 0.00 3.16
5111 5439 6.183360 ACAATTCGTGGGTATGATGAATGAAC 60.183 38.462 0.00 0.00 30.94 3.18
5112 5440 5.885352 ACAATTCGTGGGTATGATGAATGAA 59.115 36.000 0.00 0.00 30.94 2.57
5113 5441 5.436175 ACAATTCGTGGGTATGATGAATGA 58.564 37.500 0.00 0.00 30.94 2.57
5114 5442 5.296531 TGACAATTCGTGGGTATGATGAATG 59.703 40.000 0.00 0.00 30.94 2.67
5115 5443 5.436175 TGACAATTCGTGGGTATGATGAAT 58.564 37.500 0.00 0.00 31.63 2.57
5116 5444 4.837972 TGACAATTCGTGGGTATGATGAA 58.162 39.130 0.00 0.00 0.00 2.57
5117 5445 4.479786 TGACAATTCGTGGGTATGATGA 57.520 40.909 0.00 0.00 0.00 2.92
5118 5446 4.201910 GGTTGACAATTCGTGGGTATGATG 60.202 45.833 0.00 0.00 0.00 3.07
5119 5447 3.945285 GGTTGACAATTCGTGGGTATGAT 59.055 43.478 0.00 0.00 0.00 2.45
5120 5448 3.244596 TGGTTGACAATTCGTGGGTATGA 60.245 43.478 0.00 0.00 0.00 2.15
5121 5449 3.078097 TGGTTGACAATTCGTGGGTATG 58.922 45.455 0.00 0.00 0.00 2.39
5122 5450 3.426787 TGGTTGACAATTCGTGGGTAT 57.573 42.857 0.00 0.00 0.00 2.73
5139 5467 1.924524 CGTCGCGTATGAAGAAATGGT 59.075 47.619 5.77 0.00 0.00 3.55
5140 5468 1.257936 CCGTCGCGTATGAAGAAATGG 59.742 52.381 5.77 0.00 0.00 3.16
5147 5475 2.095847 GGTTGCCGTCGCGTATGAA 61.096 57.895 5.77 0.00 38.08 2.57
5158 5486 0.109781 GTGTATGCAGTTGGTTGCCG 60.110 55.000 0.00 0.00 43.43 5.69
5163 5491 3.403038 GAGTGAAGTGTATGCAGTTGGT 58.597 45.455 8.74 0.00 38.30 3.67
5170 5498 2.000447 GGTTCGGAGTGAAGTGTATGC 59.000 52.381 0.00 0.00 37.23 3.14
5171 5499 3.594603 AGGTTCGGAGTGAAGTGTATG 57.405 47.619 0.00 0.00 37.23 2.39
5173 5501 2.960384 TGAAGGTTCGGAGTGAAGTGTA 59.040 45.455 0.00 0.00 37.23 2.90
5175 5503 2.526304 TGAAGGTTCGGAGTGAAGTG 57.474 50.000 0.00 0.00 37.23 3.16
5184 5512 1.873591 CACCTGAACTTGAAGGTTCGG 59.126 52.381 7.06 7.06 44.63 4.30
5204 5532 5.003804 TCCTTCTTTAGTTGGTGATGAAGC 58.996 41.667 0.00 0.00 29.23 3.86
5206 5534 5.560724 CCTCCTTCTTTAGTTGGTGATGAA 58.439 41.667 0.00 0.00 0.00 2.57
5245 5573 1.423584 ATGATGGTCGTGGCTATCCA 58.576 50.000 0.00 0.00 40.85 3.41
5292 5620 2.239654 TCCCTTTGCTTGGAGACTATGG 59.760 50.000 0.00 0.00 0.00 2.74
5306 5634 2.546584 GCTGCTGGTTTTTCTCCCTTTG 60.547 50.000 0.00 0.00 0.00 2.77
5334 5662 1.064166 CAATGATGACCCCTTCTGGCT 60.064 52.381 0.00 0.00 0.00 4.75
5357 5688 4.511826 GGATGGAACCGCTTACTTATCAAG 59.488 45.833 0.00 0.00 0.00 3.02
5372 5703 2.790433 TGTGCAAGTTAGGGATGGAAC 58.210 47.619 0.00 0.00 0.00 3.62
5373 5704 3.153919 GTTGTGCAAGTTAGGGATGGAA 58.846 45.455 0.00 0.00 0.00 3.53
5411 5742 1.539065 CGATCGCATTACTGAGGGCTT 60.539 52.381 0.26 0.00 0.00 4.35
5413 5756 0.032130 TCGATCGCATTACTGAGGGC 59.968 55.000 11.09 0.00 0.00 5.19
5433 5785 2.094854 GCAATCTCTTTGGGTGCTCAAG 60.095 50.000 0.00 0.00 35.75 3.02
5436 5788 0.813821 GGCAATCTCTTTGGGTGCTC 59.186 55.000 0.00 0.00 35.75 4.26
5531 5883 4.202441 GGTGGATTCTGTATTGCTCATGT 58.798 43.478 0.00 0.00 0.00 3.21
5604 5967 1.078823 TCACCACTGTGGATCTACCCT 59.921 52.381 32.30 5.12 40.96 4.34
5625 5988 2.125147 ACGCCACGACCATGGATG 60.125 61.111 21.47 12.68 43.02 3.51
5637 6000 1.686587 ACATGATAAGGATCGACGCCA 59.313 47.619 0.00 0.00 34.49 5.69
5638 6001 2.061773 CACATGATAAGGATCGACGCC 58.938 52.381 0.00 0.00 34.49 5.68
5640 6003 2.472861 GCACACATGATAAGGATCGACG 59.527 50.000 0.00 0.00 34.49 5.12
5686 6058 0.250901 GCACACTGGTGGGTGATTCT 60.251 55.000 2.31 0.00 45.38 2.40
5690 6062 0.762842 ACTAGCACACTGGTGGGTGA 60.763 55.000 2.31 0.00 45.38 4.02
5714 6086 3.964909 GTGGAAACAACAGCCTAAAGTG 58.035 45.455 0.00 0.00 46.06 3.16
5773 6151 2.564975 GCCGTCTTCTCGTCCGAA 59.435 61.111 0.00 0.00 0.00 4.30
5833 6211 1.592223 CGAGAAGCCCTCCTCGTTT 59.408 57.895 0.00 0.00 44.99 3.60
5839 6217 2.754658 TCCGACGAGAAGCCCTCC 60.755 66.667 0.00 0.00 38.71 4.30
5840 6218 0.747283 TACTCCGACGAGAAGCCCTC 60.747 60.000 0.00 0.00 38.52 4.30
5842 6220 0.747283 TCTACTCCGACGAGAAGCCC 60.747 60.000 0.00 0.00 38.52 5.19
5858 6236 3.593942 TCCTTGGTTTTCACCTCCTCTA 58.406 45.455 0.00 0.00 44.61 2.43
5860 6238 2.951229 TCCTTGGTTTTCACCTCCTC 57.049 50.000 0.00 0.00 44.61 3.71
5938 6328 1.519455 CGCTCTCAACCCGATGACC 60.519 63.158 0.00 0.00 0.00 4.02
5941 6331 2.892425 GCCGCTCTCAACCCGATG 60.892 66.667 0.00 0.00 0.00 3.84
5963 6353 1.031571 TGGAATGCGCTCCATGGTTC 61.032 55.000 13.98 6.80 40.71 3.62
5964 6354 1.001020 TGGAATGCGCTCCATGGTT 60.001 52.632 13.98 0.00 40.71 3.67
5965 6355 1.452651 CTGGAATGCGCTCCATGGT 60.453 57.895 17.78 0.00 44.59 3.55
5966 6356 1.153107 TCTGGAATGCGCTCCATGG 60.153 57.895 17.78 4.97 44.59 3.66
5967 6357 1.164662 CCTCTGGAATGCGCTCCATG 61.165 60.000 17.78 13.33 44.59 3.66
5968 6358 1.147824 CCTCTGGAATGCGCTCCAT 59.852 57.895 17.78 0.00 44.59 3.41
5969 6359 1.964608 CTCCTCTGGAATGCGCTCCA 61.965 60.000 16.68 16.68 43.45 3.86
5970 6360 1.227497 CTCCTCTGGAATGCGCTCC 60.227 63.158 9.73 9.14 35.88 4.70
5971 6361 1.227497 CCTCCTCTGGAATGCGCTC 60.227 63.158 9.73 0.00 0.00 5.03
5972 6362 2.739996 CCCTCCTCTGGAATGCGCT 61.740 63.158 9.73 0.00 0.00 5.92
5973 6363 2.203126 CCCTCCTCTGGAATGCGC 60.203 66.667 0.00 0.00 0.00 6.09
5974 6364 2.203126 GCCCTCCTCTGGAATGCG 60.203 66.667 0.00 0.00 0.00 4.73
5975 6365 2.203126 CGCCCTCCTCTGGAATGC 60.203 66.667 0.00 0.00 0.00 3.56
5976 6366 2.203126 GCGCCCTCCTCTGGAATG 60.203 66.667 0.00 0.00 0.00 2.67
5977 6367 3.854669 CGCGCCCTCCTCTGGAAT 61.855 66.667 0.00 0.00 0.00 3.01
6001 6391 4.838486 CTCCTCGACGACTGCCGC 62.838 72.222 0.00 0.00 43.32 6.53
6002 6392 4.838486 GCTCCTCGACGACTGCCG 62.838 72.222 0.00 0.00 45.44 5.69
6003 6393 4.500116 GGCTCCTCGACGACTGCC 62.500 72.222 13.01 13.01 0.00 4.85
6004 6394 3.691744 CTGGCTCCTCGACGACTGC 62.692 68.421 0.00 0.00 0.00 4.40
6005 6395 2.487428 CTGGCTCCTCGACGACTG 59.513 66.667 0.00 0.00 0.00 3.51
6006 6396 3.444805 GCTGGCTCCTCGACGACT 61.445 66.667 0.00 0.00 0.00 4.18
6007 6397 4.500116 GGCTGGCTCCTCGACGAC 62.500 72.222 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.