Multiple sequence alignment - TraesCS1B01G386800

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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 TraesCS1B01G386800 chr1B 100.000 2924 0 0 1 2924 621259835 621262758 0.000000e+00 5400.0
1 TraesCS1B01G386800 chr1B 89.326 1068 80 16 883 1943 621409696 621408656 0.000000e+00 1310.0
2 TraesCS1B01G386800 chr1B 87.195 164 21 0 29 192 378925096 378925259 1.380000e-43 187.0
3 TraesCS1B01G386800 chr1B 82.707 133 12 8 2256 2386 621351917 621352040 1.110000e-19 108.0
4 TraesCS1B01G386800 chr1B 85.185 81 5 4 2181 2257 621351752 621351829 3.120000e-10 76.8
5 TraesCS1B01G386800 chr1D 89.322 2154 141 41 1 2142 451638033 451635957 0.000000e+00 2621.0
6 TraesCS1B01G386800 chr1D 90.119 1093 75 14 883 1969 451782195 451781130 0.000000e+00 1389.0
7 TraesCS1B01G386800 chr1D 87.335 379 28 8 1889 2256 451634472 451634103 1.620000e-112 416.0
8 TraesCS1B01G386800 chr1D 88.571 210 11 4 2719 2923 451633322 451633121 2.910000e-60 243.0
9 TraesCS1B01G386800 chr1D 89.444 180 18 1 13 192 279132625 279132803 2.930000e-55 226.0
10 TraesCS1B01G386800 chr1D 89.143 175 19 0 18 192 279134149 279134323 4.910000e-53 219.0
11 TraesCS1B01G386800 chr1D 81.600 125 13 9 2259 2381 451777228 451777112 8.630000e-16 95.3
12 TraesCS1B01G386800 chr1D 85.333 75 4 5 2181 2251 451777413 451777342 1.450000e-08 71.3
13 TraesCS1B01G386800 chr1A 89.165 2095 150 34 1 2073 546225989 546223950 0.000000e+00 2540.0
14 TraesCS1B01G386800 chr1A 90.850 1071 73 8 907 1969 546231915 546230862 0.000000e+00 1411.0
15 TraesCS1B01G386800 chr1A 87.173 803 78 12 1 795 299726266 299725481 0.000000e+00 889.0
16 TraesCS1B01G386800 chr1A 83.065 124 11 9 2259 2380 546228886 546228771 1.430000e-18 104.0
17 TraesCS1B01G386800 chr1A 85.185 81 5 5 2181 2257 546229039 546228962 3.120000e-10 76.8
18 TraesCS1B01G386800 chr5A 92.240 683 44 3 1185 1864 11311054 11310378 0.000000e+00 959.0
19 TraesCS1B01G386800 chr2A 92.676 669 40 4 1199 1864 770129775 770129113 0.000000e+00 955.0
20 TraesCS1B01G386800 chr4D 88.476 781 76 7 19 795 462844256 462843486 0.000000e+00 931.0
21 TraesCS1B01G386800 chr7B 86.184 304 34 5 166 465 618764204 618763905 3.640000e-84 322.0
22 TraesCS1B01G386800 chr7B 85.016 307 39 4 163 465 618331738 618332041 3.660000e-79 305.0
23 TraesCS1B01G386800 chr3B 84.839 310 46 1 1 309 630381148 630380839 7.870000e-81 311.0
24 TraesCS1B01G386800 chr7A 83.333 354 31 9 1270 1622 675441687 675441361 4.740000e-78 302.0
25 TraesCS1B01G386800 chr2D 84.404 109 16 1 1437 1545 181192232 181192339 3.990000e-19 106.0
26 TraesCS1B01G386800 chrUn 86.885 61 6 2 2511 2570 46187597 46187656 1.880000e-07 67.6
27 TraesCS1B01G386800 chr3D 81.818 77 13 1 2500 2575 386775241 386775165 2.430000e-06 63.9
28 TraesCS1B01G386800 chr3D 97.059 34 1 0 638 671 593804401 593804434 1.130000e-04 58.4


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 TraesCS1B01G386800 chr1B 621259835 621262758 2923 False 5400.000000 5400 100.000000 1 2924 1 chr1B.!!$F2 2923
1 TraesCS1B01G386800 chr1B 621408656 621409696 1040 True 1310.000000 1310 89.326000 883 1943 1 chr1B.!!$R1 1060
2 TraesCS1B01G386800 chr1D 451633121 451638033 4912 True 1093.333333 2621 88.409333 1 2923 3 chr1D.!!$R1 2922
3 TraesCS1B01G386800 chr1D 451777112 451782195 5083 True 518.533333 1389 85.684000 883 2381 3 chr1D.!!$R2 1498
4 TraesCS1B01G386800 chr1D 279132625 279134323 1698 False 222.500000 226 89.293500 13 192 2 chr1D.!!$F1 179
5 TraesCS1B01G386800 chr1A 546223950 546231915 7965 True 1032.950000 2540 87.066250 1 2380 4 chr1A.!!$R2 2379
6 TraesCS1B01G386800 chr1A 299725481 299726266 785 True 889.000000 889 87.173000 1 795 1 chr1A.!!$R1 794
7 TraesCS1B01G386800 chr5A 11310378 11311054 676 True 959.000000 959 92.240000 1185 1864 1 chr5A.!!$R1 679
8 TraesCS1B01G386800 chr2A 770129113 770129775 662 True 955.000000 955 92.676000 1199 1864 1 chr2A.!!$R1 665
9 TraesCS1B01G386800 chr4D 462843486 462844256 770 True 931.000000 931 88.476000 19 795 1 chr4D.!!$R1 776

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
46 48 0.165944 GGGTTCATTTGTCTCGCACG 59.834 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 8952 0.03467 ATTGCCAGGAGAAGAGCACC 60.035 55.0 0.0 0.0 34.37 5.01 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
34 36 2.125512 GTCTCGCGCTGGGTTCAT 60.126 61.111 5.56 0.00 0.00 2.57
46 48 0.165944 GGGTTCATTTGTCTCGCACG 59.834 55.000 0.00 0.00 0.00 5.34
80 82 0.322456 TCTCCATCAACCAAAGCCCG 60.322 55.000 0.00 0.00 0.00 6.13
95 97 2.963854 CCGCACGCATCTAGCCAG 60.964 66.667 0.00 0.00 41.38 4.85
143 145 0.392998 GAATCCTCCGCACCACACAT 60.393 55.000 0.00 0.00 0.00 3.21
148 150 0.321210 CTCCGCACCACACATACCAA 60.321 55.000 0.00 0.00 0.00 3.67
150 152 1.173043 CCGCACCACACATACCAAAT 58.827 50.000 0.00 0.00 0.00 2.32
151 153 2.027100 TCCGCACCACACATACCAAATA 60.027 45.455 0.00 0.00 0.00 1.40
172 174 8.540492 CAAATATACTCGTAGTTGACATGTTCC 58.460 37.037 0.00 0.00 32.91 3.62
173 175 3.314541 ACTCGTAGTTGACATGTTCCC 57.685 47.619 0.00 0.00 0.00 3.97
196 198 3.683822 GTGAGCTCTGAAATCTTCTGTGG 59.316 47.826 16.19 0.00 0.00 4.17
206 208 5.726308 TGAAATCTTCTGTGGGGAGAGAATA 59.274 40.000 0.00 0.00 0.00 1.75
211 213 5.726308 TCTTCTGTGGGGAGAGAATATTTCA 59.274 40.000 0.00 0.00 0.00 2.69
220 222 4.636206 GGAGAGAATATTTCACCAAACGCT 59.364 41.667 0.00 0.00 0.00 5.07
222 224 6.018669 GGAGAGAATATTTCACCAAACGCTAG 60.019 42.308 0.00 0.00 0.00 3.42
248 250 6.241645 AGAACATTCTTCTTTTACCTGGGAG 58.758 40.000 0.00 0.00 32.55 4.30
250 252 4.202567 ACATTCTTCTTTTACCTGGGAGCA 60.203 41.667 0.00 0.00 0.00 4.26
258 260 3.418684 TTACCTGGGAGCAGAGTTTTC 57.581 47.619 0.00 0.00 0.00 2.29
270 272 6.808704 GGAGCAGAGTTTTCCACAATAATTTC 59.191 38.462 0.00 0.00 0.00 2.17
286 288 2.787473 TTTCCATGAAGCCGAGTCAT 57.213 45.000 0.00 0.00 36.11 3.06
292 294 2.591571 TGAAGCCGAGTCATGATCTG 57.408 50.000 0.00 0.00 0.00 2.90
321 323 0.991920 ATCCCGACAAACCATCCAGT 59.008 50.000 0.00 0.00 0.00 4.00
329 331 0.251787 AAACCATCCAGTCAAGCCCC 60.252 55.000 0.00 0.00 0.00 5.80
375 377 2.963498 TTCTATACGCGGATCTCACG 57.037 50.000 7.35 0.00 0.00 4.35
380 382 0.659427 TACGCGGATCTCACGGTAAG 59.341 55.000 12.47 0.00 0.00 2.34
393 395 2.161609 CACGGTAAGCATCCCACTTTTC 59.838 50.000 0.00 0.00 0.00 2.29
424 426 1.672356 GCCCAACTGTCAGCGATGT 60.672 57.895 0.00 0.00 0.00 3.06
446 448 1.885887 TGTTGTGCAAAGAGGTATGCC 59.114 47.619 0.00 0.00 41.87 4.40
448 450 0.676466 TGTGCAAAGAGGTATGCCGG 60.676 55.000 0.00 0.00 41.87 6.13
453 455 0.532862 AAAGAGGTATGCCGGCGATG 60.533 55.000 23.90 0.00 40.50 3.84
454 456 2.357517 GAGGTATGCCGGCGATGG 60.358 66.667 23.90 0.00 40.50 3.51
468 470 2.421424 GGCGATGGCAAGGATATCAATC 59.579 50.000 4.83 0.00 42.47 2.67
481 483 2.572191 ATCAATCGGCAAGCACAATG 57.428 45.000 0.00 0.00 0.00 2.82
488 490 1.667151 GCAAGCACAATGCCTCCAA 59.333 52.632 0.00 0.00 46.52 3.53
492 494 2.226962 AGCACAATGCCTCCAATCTT 57.773 45.000 0.00 0.00 46.52 2.40
496 498 3.428045 GCACAATGCCTCCAATCTTACAC 60.428 47.826 0.00 0.00 37.42 2.90
497 499 3.009723 ACAATGCCTCCAATCTTACACG 58.990 45.455 0.00 0.00 0.00 4.49
498 500 3.270027 CAATGCCTCCAATCTTACACGA 58.730 45.455 0.00 0.00 0.00 4.35
499 501 3.845781 ATGCCTCCAATCTTACACGAT 57.154 42.857 0.00 0.00 0.00 3.73
500 502 3.627395 TGCCTCCAATCTTACACGATT 57.373 42.857 0.00 0.00 34.07 3.34
501 503 3.270027 TGCCTCCAATCTTACACGATTG 58.730 45.455 6.56 6.56 46.15 2.67
522 524 1.270518 ACGATCCCATGTAGCAGATGC 60.271 52.381 0.00 0.00 42.49 3.91
574 576 1.969589 GTTACCAACCCTGCACCCG 60.970 63.158 0.00 0.00 0.00 5.28
599 601 7.093727 CGTAAGGTCTCATCATAACATCCCTAT 60.094 40.741 0.00 0.00 0.00 2.57
600 602 9.256228 GTAAGGTCTCATCATAACATCCCTATA 57.744 37.037 0.00 0.00 0.00 1.31
631 633 4.822036 TTGTCCAACCAAATGTTAGTCG 57.178 40.909 0.00 0.00 34.69 4.18
636 638 4.039973 TCCAACCAAATGTTAGTCGTCTCT 59.960 41.667 0.00 0.00 34.69 3.10
639 641 3.179830 CCAAATGTTAGTCGTCTCTCCG 58.820 50.000 0.00 0.00 0.00 4.63
652 654 4.946157 TCGTCTCTCCGTTACCTATTCTTT 59.054 41.667 0.00 0.00 0.00 2.52
681 684 3.926616 ACCTTGTTTCAGTATGTCTCGG 58.073 45.455 0.00 0.00 37.40 4.63
699 702 3.947834 CTCGGCCTTCAATTATTGACCTT 59.052 43.478 7.19 0.00 39.87 3.50
701 704 3.694072 CGGCCTTCAATTATTGACCTTCA 59.306 43.478 7.19 0.00 39.87 3.02
711 714 7.178983 TCAATTATTGACCTTCAGATTTGGCTT 59.821 33.333 3.20 0.00 34.08 4.35
714 717 2.108075 TGACCTTCAGATTTGGCTTGGA 59.892 45.455 0.00 0.00 0.00 3.53
721 724 4.012374 TCAGATTTGGCTTGGATGACTTC 58.988 43.478 0.00 0.00 0.00 3.01
722 725 3.760151 CAGATTTGGCTTGGATGACTTCA 59.240 43.478 0.00 0.00 0.00 3.02
737 740 2.744202 GACTTCACAGTTCGGCATTGAT 59.256 45.455 0.00 0.00 31.22 2.57
744 747 5.589855 TCACAGTTCGGCATTGATAATTGAT 59.410 36.000 0.00 0.00 0.00 2.57
745 748 6.095300 TCACAGTTCGGCATTGATAATTGATT 59.905 34.615 0.00 0.00 0.00 2.57
746 749 7.281999 TCACAGTTCGGCATTGATAATTGATTA 59.718 33.333 0.00 0.00 0.00 1.75
747 750 7.588854 CACAGTTCGGCATTGATAATTGATTAG 59.411 37.037 0.00 0.00 0.00 1.73
748 751 7.080099 CAGTTCGGCATTGATAATTGATTAGG 58.920 38.462 0.00 0.00 0.00 2.69
749 752 6.207417 AGTTCGGCATTGATAATTGATTAGGG 59.793 38.462 0.00 0.00 0.00 3.53
750 753 5.875224 TCGGCATTGATAATTGATTAGGGA 58.125 37.500 0.00 0.00 0.00 4.20
751 754 6.303054 TCGGCATTGATAATTGATTAGGGAA 58.697 36.000 0.00 0.00 0.00 3.97
752 755 6.775142 TCGGCATTGATAATTGATTAGGGAAA 59.225 34.615 0.00 0.00 0.00 3.13
753 756 7.451255 TCGGCATTGATAATTGATTAGGGAAAT 59.549 33.333 0.00 0.00 0.00 2.17
754 757 8.739039 CGGCATTGATAATTGATTAGGGAAATA 58.261 33.333 0.00 0.00 0.00 1.40
801 804 3.499338 AGTGATTCAGGAATTGCCAACA 58.501 40.909 0.00 0.00 40.02 3.33
856 859 2.611518 GTCAGATTTGAGGTCGAGTGG 58.388 52.381 0.00 0.00 32.98 4.00
925 931 1.334243 CGTAACAAAAAGGAACCGCCA 59.666 47.619 0.00 0.00 40.02 5.69
926 932 2.734670 GTAACAAAAAGGAACCGCCAC 58.265 47.619 0.00 0.00 40.02 5.01
942 949 3.474570 ACGCTCAGGGGATCTGGC 61.475 66.667 0.00 0.00 43.53 4.85
944 951 4.247380 GCTCAGGGGATCTGGCGG 62.247 72.222 0.00 0.00 43.53 6.13
945 952 4.247380 CTCAGGGGATCTGGCGGC 62.247 72.222 0.00 0.00 43.53 6.53
986 1010 0.738412 ACGCCATCCTACCGTTTTCG 60.738 55.000 0.00 0.00 43.67 3.46
989 1013 1.287425 CCATCCTACCGTTTTCGCTC 58.713 55.000 0.00 0.00 42.58 5.03
991 1015 1.134788 CATCCTACCGTTTTCGCTCCT 60.135 52.381 0.00 0.00 42.58 3.69
992 1016 0.529378 TCCTACCGTTTTCGCTCCTC 59.471 55.000 0.00 0.00 42.58 3.71
993 1017 0.801067 CCTACCGTTTTCGCTCCTCG 60.801 60.000 0.00 0.00 42.58 4.63
994 1018 1.411493 CTACCGTTTTCGCTCCTCGC 61.411 60.000 0.00 0.00 42.58 5.03
995 1019 1.870055 TACCGTTTTCGCTCCTCGCT 61.870 55.000 0.00 0.00 42.58 4.93
996 1020 2.730672 CCGTTTTCGCTCCTCGCTG 61.731 63.158 0.00 0.00 42.58 5.18
1096 1120 2.512515 GCATCTGCCTCGACCACC 60.513 66.667 0.00 0.00 34.31 4.61
1867 8871 1.417890 CCACCGGCATCTCCTATTTCT 59.582 52.381 0.00 0.00 0.00 2.52
1948 8952 4.160635 GCCGCCATGGTTTCGTCG 62.161 66.667 14.67 6.92 41.21 5.12
1977 10714 0.824109 TCCTGGCAATCTGGAGTACG 59.176 55.000 0.00 0.00 38.38 3.67
1982 10719 3.623703 TGGCAATCTGGAGTACGTACTA 58.376 45.455 27.44 13.06 36.50 1.82
1983 10720 3.630769 TGGCAATCTGGAGTACGTACTAG 59.369 47.826 27.44 21.23 36.50 2.57
1987 10724 5.277731 GCAATCTGGAGTACGTACTAGTACC 60.278 48.000 27.44 22.83 45.91 3.34
2023 10760 1.587034 GCGTCCGAAAACTATTCCTCG 59.413 52.381 0.00 0.00 0.00 4.63
2034 10771 0.535335 TATTCCTCGGTCCAGTGCAC 59.465 55.000 9.40 9.40 0.00 4.57
2064 10871 5.119588 TGCTTGATTATTATTACTACGCCGC 59.880 40.000 0.00 0.00 0.00 6.53
2086 10893 7.123830 CCGCTTAGTTATTTAATTCGGAACTG 58.876 38.462 0.00 0.00 33.84 3.16
2153 14446 9.798994 GACGTGAATCCTTTTCTAGATAAGTTA 57.201 33.333 18.13 9.06 0.00 2.24
2173 14470 5.128827 AGTTAATCCTACTGATCCTCGCAAA 59.871 40.000 0.00 0.00 31.61 3.68
2174 14471 4.487714 AATCCTACTGATCCTCGCAAAA 57.512 40.909 0.00 0.00 31.61 2.44
2213 14510 2.887783 TGATATTCAGAGGAGTCGAGCC 59.112 50.000 0.00 0.00 0.00 4.70
2214 14511 2.437085 TATTCAGAGGAGTCGAGCCA 57.563 50.000 6.98 0.00 0.00 4.75
2257 14661 4.757657 TGCGGTAGCTTGTTTTCAAAGATA 59.242 37.500 0.00 0.00 45.42 1.98
2328 14733 7.205737 TGCGACAAGGACTCGTATAATTATA 57.794 36.000 0.81 0.81 33.51 0.98
2352 14757 5.847670 AGATTCACGAGAAGTACAAAAGC 57.152 39.130 1.01 0.00 37.14 3.51
2353 14758 5.297547 AGATTCACGAGAAGTACAAAAGCA 58.702 37.500 1.01 0.00 37.14 3.91
2354 14759 5.934625 AGATTCACGAGAAGTACAAAAGCAT 59.065 36.000 1.01 0.00 37.14 3.79
2356 14761 3.994392 TCACGAGAAGTACAAAAGCATCC 59.006 43.478 0.00 0.00 0.00 3.51
2357 14762 3.125316 CACGAGAAGTACAAAAGCATCCC 59.875 47.826 0.00 0.00 0.00 3.85
2359 14764 3.751175 CGAGAAGTACAAAAGCATCCCAA 59.249 43.478 0.00 0.00 0.00 4.12
2360 14765 4.378459 CGAGAAGTACAAAAGCATCCCAAC 60.378 45.833 0.00 0.00 0.00 3.77
2361 14766 4.729868 AGAAGTACAAAAGCATCCCAACT 58.270 39.130 0.00 0.00 0.00 3.16
2402 14807 4.213700 CGAGAGCGCCGTCTAATC 57.786 61.111 2.29 0.00 0.00 1.75
2403 14808 1.370657 CGAGAGCGCCGTCTAATCC 60.371 63.158 2.29 0.00 0.00 3.01
2404 14809 1.370657 GAGAGCGCCGTCTAATCCG 60.371 63.158 2.29 0.00 0.00 4.18
2405 14810 2.061182 GAGAGCGCCGTCTAATCCGT 62.061 60.000 2.29 0.00 0.00 4.69
2406 14811 1.657794 GAGCGCCGTCTAATCCGTC 60.658 63.158 2.29 0.00 0.00 4.79
2407 14812 2.657620 GCGCCGTCTAATCCGTCC 60.658 66.667 0.00 0.00 0.00 4.79
2408 14813 3.117372 CGCCGTCTAATCCGTCCT 58.883 61.111 0.00 0.00 0.00 3.85
2409 14814 1.299165 CGCCGTCTAATCCGTCCTG 60.299 63.158 0.00 0.00 0.00 3.86
2410 14815 1.721664 CGCCGTCTAATCCGTCCTGA 61.722 60.000 0.00 0.00 0.00 3.86
2411 14816 0.674534 GCCGTCTAATCCGTCCTGAT 59.325 55.000 0.00 0.00 0.00 2.90
2412 14817 1.603172 GCCGTCTAATCCGTCCTGATG 60.603 57.143 0.00 0.00 0.00 3.07
2413 14818 1.954382 CCGTCTAATCCGTCCTGATGA 59.046 52.381 0.00 0.00 0.00 2.92
2414 14819 2.361119 CCGTCTAATCCGTCCTGATGAA 59.639 50.000 0.00 0.00 0.00 2.57
2415 14820 3.372954 CGTCTAATCCGTCCTGATGAAC 58.627 50.000 0.00 0.00 0.00 3.18
2416 14821 3.181490 CGTCTAATCCGTCCTGATGAACA 60.181 47.826 0.00 0.00 0.00 3.18
2417 14822 4.676986 CGTCTAATCCGTCCTGATGAACAA 60.677 45.833 0.00 0.00 0.00 2.83
2418 14823 5.175859 GTCTAATCCGTCCTGATGAACAAA 58.824 41.667 0.00 0.00 0.00 2.83
2419 14824 5.817816 GTCTAATCCGTCCTGATGAACAAAT 59.182 40.000 0.00 0.00 0.00 2.32
2420 14825 6.316390 GTCTAATCCGTCCTGATGAACAAATT 59.684 38.462 0.00 0.00 0.00 1.82
2421 14826 5.567138 AATCCGTCCTGATGAACAAATTC 57.433 39.130 0.00 0.00 35.18 2.17
2437 14842 9.835389 TGAACAAATTCAAAGAGGATCAAAAAT 57.165 25.926 0.00 0.00 41.99 1.82
2439 14844 9.835389 AACAAATTCAAAGAGGATCAAAAATCA 57.165 25.926 0.00 0.00 37.82 2.57
2440 14845 9.835389 ACAAATTCAAAGAGGATCAAAAATCAA 57.165 25.926 0.00 0.00 37.82 2.57
2451 14856 7.795047 AGGATCAAAAATCAAAAGACCAACTT 58.205 30.769 0.00 0.00 40.98 2.66
2465 14870 2.484264 ACCAACTTGAAGATAAGCACGC 59.516 45.455 0.00 0.00 0.00 5.34
2467 14872 1.739067 ACTTGAAGATAAGCACGCCC 58.261 50.000 0.00 0.00 0.00 6.13
2470 14875 0.107703 TGAAGATAAGCACGCCCCTG 60.108 55.000 0.00 0.00 0.00 4.45
2471 14876 1.440145 GAAGATAAGCACGCCCCTGC 61.440 60.000 0.00 0.00 37.44 4.85
2485 14890 1.636988 CCCTGCGAGTACTAAAACCG 58.363 55.000 0.00 0.00 0.00 4.44
2489 14894 4.427312 CCTGCGAGTACTAAAACCGTAAT 58.573 43.478 0.00 0.00 0.00 1.89
2490 14895 4.501921 CCTGCGAGTACTAAAACCGTAATC 59.498 45.833 0.00 0.00 0.00 1.75
2495 14900 5.741040 CGAGTACTAAAACCGTAATCTGTCC 59.259 44.000 0.00 0.00 31.75 4.02
2500 14905 2.865343 AACCGTAATCTGTCCGCTAG 57.135 50.000 0.00 0.00 0.00 3.42
2507 14930 4.912766 CGTAATCTGTCCGCTAGAATTCTC 59.087 45.833 12.24 0.00 0.00 2.87
2508 14931 5.505819 CGTAATCTGTCCGCTAGAATTCTCA 60.506 44.000 12.24 1.55 0.00 3.27
2520 14943 2.978452 AATTCTCATCCTCGCCGCCG 62.978 60.000 0.00 0.00 0.00 6.46
2534 14957 4.133796 GCCGGCCATTGGAGCAAC 62.134 66.667 18.11 0.00 0.00 4.17
2535 14958 2.676121 CCGGCCATTGGAGCAACA 60.676 61.111 6.95 0.00 0.00 3.33
2536 14959 2.703798 CCGGCCATTGGAGCAACAG 61.704 63.158 6.95 0.00 0.00 3.16
2537 14960 2.703798 CGGCCATTGGAGCAACAGG 61.704 63.158 6.95 0.00 0.00 4.00
2538 14961 2.575461 GCCATTGGAGCAACAGGC 59.425 61.111 6.95 0.00 39.45 4.85
2547 14970 2.045536 GCAACAGGCAGAGGGAGG 60.046 66.667 0.00 0.00 43.97 4.30
2548 14971 2.045536 CAACAGGCAGAGGGAGGC 60.046 66.667 0.00 0.00 0.00 4.70
2549 14972 3.710722 AACAGGCAGAGGGAGGCG 61.711 66.667 0.00 0.00 36.55 5.52
2550 14973 4.704103 ACAGGCAGAGGGAGGCGA 62.704 66.667 0.00 0.00 36.55 5.54
2551 14974 3.393970 CAGGCAGAGGGAGGCGAA 61.394 66.667 0.00 0.00 36.55 4.70
2552 14975 2.366167 AGGCAGAGGGAGGCGAAT 60.366 61.111 0.00 0.00 36.55 3.34
2553 14976 2.110006 GGCAGAGGGAGGCGAATC 59.890 66.667 0.00 0.00 0.00 2.52
2554 14977 2.110006 GCAGAGGGAGGCGAATCC 59.890 66.667 0.00 0.00 38.76 3.01
2555 14978 2.735772 GCAGAGGGAGGCGAATCCA 61.736 63.158 8.41 0.00 41.52 3.41
2556 14979 1.144936 CAGAGGGAGGCGAATCCAC 59.855 63.158 8.41 2.68 41.52 4.02
2557 14980 1.306141 AGAGGGAGGCGAATCCACA 60.306 57.895 8.41 0.00 41.52 4.17
2558 14981 1.144936 GAGGGAGGCGAATCCACAG 59.855 63.158 8.41 0.00 41.52 3.66
2559 14982 1.306141 AGGGAGGCGAATCCACAGA 60.306 57.895 8.41 0.00 41.52 3.41
2560 14983 1.153349 GGGAGGCGAATCCACAGAC 60.153 63.158 8.41 0.00 41.52 3.51
2561 14984 1.617947 GGGAGGCGAATCCACAGACT 61.618 60.000 8.41 0.00 41.52 3.24
2562 14985 0.179097 GGAGGCGAATCCACAGACTC 60.179 60.000 1.72 0.00 39.34 3.36
2563 14986 0.526524 GAGGCGAATCCACAGACTCG 60.527 60.000 0.00 0.00 44.32 4.18
2565 14988 4.094684 CGAATCCACAGACTCGCC 57.905 61.111 0.00 0.00 34.68 5.54
2566 14989 1.874019 CGAATCCACAGACTCGCCG 60.874 63.158 0.00 0.00 34.68 6.46
2567 14990 1.519455 GAATCCACAGACTCGCCGG 60.519 63.158 0.00 0.00 0.00 6.13
2568 14991 3.665675 AATCCACAGACTCGCCGGC 62.666 63.158 19.07 19.07 0.00 6.13
2575 14998 3.285215 GACTCGCCGGCGGAGATA 61.285 66.667 44.95 26.86 40.25 1.98
2576 14999 2.831742 ACTCGCCGGCGGAGATAA 60.832 61.111 44.95 26.09 40.25 1.75
2577 15000 2.345880 GACTCGCCGGCGGAGATAAA 62.346 60.000 44.95 25.32 40.25 1.40
2578 15001 1.661821 CTCGCCGGCGGAGATAAAG 60.662 63.158 44.95 30.04 40.25 1.85
2579 15002 3.338676 CGCCGGCGGAGATAAAGC 61.339 66.667 40.50 10.57 35.56 3.51
2580 15003 3.338676 GCCGGCGGAGATAAAGCG 61.339 66.667 33.44 0.00 0.00 4.68
2581 15004 2.661866 CCGGCGGAGATAAAGCGG 60.662 66.667 24.41 0.00 0.00 5.52
2582 15005 2.661866 CGGCGGAGATAAAGCGGG 60.662 66.667 0.00 0.00 0.00 6.13
2583 15006 2.280865 GGCGGAGATAAAGCGGGG 60.281 66.667 0.00 0.00 0.00 5.73
2584 15007 2.803817 GGCGGAGATAAAGCGGGGA 61.804 63.158 0.00 0.00 0.00 4.81
2585 15008 1.301009 GCGGAGATAAAGCGGGGAG 60.301 63.158 0.00 0.00 0.00 4.30
2586 15009 1.745320 GCGGAGATAAAGCGGGGAGA 61.745 60.000 0.00 0.00 0.00 3.71
2587 15010 0.315568 CGGAGATAAAGCGGGGAGAG 59.684 60.000 0.00 0.00 0.00 3.20
2588 15011 1.705873 GGAGATAAAGCGGGGAGAGA 58.294 55.000 0.00 0.00 0.00 3.10
2589 15012 1.341852 GGAGATAAAGCGGGGAGAGAC 59.658 57.143 0.00 0.00 0.00 3.36
2590 15013 2.312390 GAGATAAAGCGGGGAGAGACT 58.688 52.381 0.00 0.00 0.00 3.24
2593 15199 3.519913 AGATAAAGCGGGGAGAGACTTTT 59.480 43.478 0.00 0.00 34.39 2.27
2597 15203 2.104170 AGCGGGGAGAGACTTTTCTAG 58.896 52.381 0.00 0.00 29.47 2.43
2607 15213 3.654414 AGACTTTTCTAGTGGTCTTGCG 58.346 45.455 0.00 0.00 37.17 4.85
2611 15217 3.577649 TTTCTAGTGGTCTTGCGAGAG 57.422 47.619 3.10 0.00 31.07 3.20
2612 15218 1.464734 TCTAGTGGTCTTGCGAGAGG 58.535 55.000 3.10 0.00 31.07 3.69
2614 15220 0.970937 TAGTGGTCTTGCGAGAGGGG 60.971 60.000 3.10 0.00 31.07 4.79
2615 15221 2.119611 TGGTCTTGCGAGAGGGGA 59.880 61.111 3.10 0.00 31.07 4.81
2616 15222 1.535444 TGGTCTTGCGAGAGGGGAA 60.535 57.895 3.10 0.00 31.07 3.97
2617 15223 1.125093 TGGTCTTGCGAGAGGGGAAA 61.125 55.000 3.10 0.00 31.07 3.13
2618 15224 0.391793 GGTCTTGCGAGAGGGGAAAG 60.392 60.000 3.10 0.00 31.07 2.62
2619 15225 0.608640 GTCTTGCGAGAGGGGAAAGA 59.391 55.000 3.10 0.00 31.07 2.52
2620 15226 1.002087 GTCTTGCGAGAGGGGAAAGAA 59.998 52.381 3.10 0.00 31.07 2.52
2621 15227 1.697432 TCTTGCGAGAGGGGAAAGAAA 59.303 47.619 0.00 0.00 0.00 2.52
2622 15228 2.079925 CTTGCGAGAGGGGAAAGAAAG 58.920 52.381 0.00 0.00 0.00 2.62
2623 15229 1.348064 TGCGAGAGGGGAAAGAAAGA 58.652 50.000 0.00 0.00 0.00 2.52
2624 15230 1.909302 TGCGAGAGGGGAAAGAAAGAT 59.091 47.619 0.00 0.00 0.00 2.40
2625 15231 3.104512 TGCGAGAGGGGAAAGAAAGATA 58.895 45.455 0.00 0.00 0.00 1.98
2626 15232 3.711704 TGCGAGAGGGGAAAGAAAGATAT 59.288 43.478 0.00 0.00 0.00 1.63
2627 15233 4.164221 TGCGAGAGGGGAAAGAAAGATATT 59.836 41.667 0.00 0.00 0.00 1.28
2628 15234 5.126779 GCGAGAGGGGAAAGAAAGATATTT 58.873 41.667 0.00 0.00 0.00 1.40
2629 15235 5.590663 GCGAGAGGGGAAAGAAAGATATTTT 59.409 40.000 0.00 0.00 0.00 1.82
2664 15271 1.334419 CCTTGACAAGAAGCTTGTGCG 60.334 52.381 16.99 0.00 45.42 5.34
2679 15286 0.451135 GTGCGTCAACGTGATTCAGC 60.451 55.000 4.29 0.00 42.22 4.26
2681 15288 0.234625 GCGTCAACGTGATTCAGCAA 59.765 50.000 4.29 0.00 42.22 3.91
2682 15289 1.333702 GCGTCAACGTGATTCAGCAAA 60.334 47.619 4.29 0.00 42.22 3.68
2683 15290 2.563976 CGTCAACGTGATTCAGCAAAG 58.436 47.619 0.00 0.00 34.11 2.77
2684 15291 2.662791 CGTCAACGTGATTCAGCAAAGG 60.663 50.000 0.00 0.00 34.11 3.11
2686 15293 2.548057 TCAACGTGATTCAGCAAAGGAC 59.452 45.455 0.00 0.00 0.00 3.85
2740 15439 8.579850 TGATATGATGAAAGGCTAAACAGTTT 57.420 30.769 3.49 3.49 0.00 2.66
2832 15538 2.197792 CATGCAAACATGCGTGCTAT 57.802 45.000 18.84 10.10 46.75 2.97
2833 15539 2.114056 CATGCAAACATGCGTGCTATC 58.886 47.619 18.84 0.00 46.75 2.08
2834 15540 0.096802 TGCAAACATGCGTGCTATCG 59.903 50.000 18.84 0.00 41.48 2.92
2878 15584 1.633945 ACACCACAACTATTCTCCCCC 59.366 52.381 0.00 0.00 0.00 5.40
2892 15598 3.854856 CCCCCACAACACACTTGG 58.145 61.111 0.00 0.00 0.00 3.61
2923 15630 3.020274 GCCTCTTTTCATTCTTCCCTCC 58.980 50.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.469251 GCGCGAGACAGTGGAATTCTA 60.469 52.381 12.10 0.00 0.00 2.10
10 12 2.049156 CAGCGCGAGACAGTGGAA 60.049 61.111 12.10 0.00 0.00 3.53
34 36 1.153329 AACACCCGTGCGAGACAAA 60.153 52.632 0.00 0.00 0.00 2.83
46 48 3.350219 TGGAGATTTAGCAGAACACCC 57.650 47.619 0.00 0.00 0.00 4.61
80 82 3.634072 CGCTGGCTAGATGCGTGC 61.634 66.667 0.00 0.00 44.00 5.34
143 145 8.689061 ACATGTCAACTACGAGTATATTTGGTA 58.311 33.333 0.00 0.00 0.00 3.25
148 150 7.208080 GGGAACATGTCAACTACGAGTATATT 58.792 38.462 0.00 0.00 0.00 1.28
150 152 5.220912 CGGGAACATGTCAACTACGAGTATA 60.221 44.000 0.00 0.00 0.00 1.47
151 153 4.439700 CGGGAACATGTCAACTACGAGTAT 60.440 45.833 0.00 0.00 0.00 2.12
172 174 2.928757 CAGAAGATTTCAGAGCTCACGG 59.071 50.000 17.77 5.05 0.00 4.94
173 175 3.367327 CACAGAAGATTTCAGAGCTCACG 59.633 47.826 17.77 6.66 0.00 4.35
196 198 4.201920 GCGTTTGGTGAAATATTCTCTCCC 60.202 45.833 12.28 7.49 0.00 4.30
206 208 4.819630 TGTTCTTCTAGCGTTTGGTGAAAT 59.180 37.500 0.00 0.00 0.00 2.17
211 213 4.642429 AGAATGTTCTTCTAGCGTTTGGT 58.358 39.130 0.00 0.00 32.55 3.67
235 237 3.425162 AACTCTGCTCCCAGGTAAAAG 57.575 47.619 0.00 0.00 39.61 2.27
248 250 6.454795 TGGAAATTATTGTGGAAAACTCTGC 58.545 36.000 0.00 0.00 0.00 4.26
250 252 8.421249 TCATGGAAATTATTGTGGAAAACTCT 57.579 30.769 0.00 0.00 0.00 3.24
258 260 4.097741 TCGGCTTCATGGAAATTATTGTGG 59.902 41.667 0.00 0.00 0.00 4.17
286 288 2.959030 CGGGATCTTCCAGTACAGATCA 59.041 50.000 17.84 0.00 45.09 2.92
291 293 2.225382 TGTCGGGATCTTCCAGTACA 57.775 50.000 0.00 0.00 38.64 2.90
292 294 3.259902 GTTTGTCGGGATCTTCCAGTAC 58.740 50.000 0.00 0.00 38.64 2.73
321 323 0.341258 AGATGAGGAGAGGGGCTTGA 59.659 55.000 0.00 0.00 0.00 3.02
329 331 9.904198 TGATGATAGATACTAAGATGAGGAGAG 57.096 37.037 0.00 0.00 0.00 3.20
375 377 3.686016 TGAGAAAAGTGGGATGCTTACC 58.314 45.455 0.00 0.00 0.00 2.85
380 382 4.550422 GAACTTTGAGAAAAGTGGGATGC 58.450 43.478 4.71 0.00 41.76 3.91
393 395 2.035066 CAGTTGGGCTTGGAACTTTGAG 59.965 50.000 0.00 0.00 29.73 3.02
424 426 2.813754 GCATACCTCTTTGCACAACAGA 59.186 45.455 0.00 0.00 38.72 3.41
446 448 0.320683 TGATATCCTTGCCATCGCCG 60.321 55.000 0.00 0.00 0.00 6.46
448 450 2.094894 CGATTGATATCCTTGCCATCGC 59.905 50.000 0.00 0.00 0.00 4.58
453 455 1.896220 TGCCGATTGATATCCTTGCC 58.104 50.000 0.00 0.00 0.00 4.52
454 456 2.351157 GCTTGCCGATTGATATCCTTGC 60.351 50.000 0.00 0.00 0.00 4.01
457 459 2.158769 TGTGCTTGCCGATTGATATCCT 60.159 45.455 0.00 0.00 0.00 3.24
488 490 3.383505 TGGGATCGTCAATCGTGTAAGAT 59.616 43.478 0.00 0.00 40.80 2.40
492 494 2.429250 ACATGGGATCGTCAATCGTGTA 59.571 45.455 0.00 0.00 40.80 2.90
496 498 2.061773 GCTACATGGGATCGTCAATCG 58.938 52.381 0.00 0.00 41.41 3.34
497 499 3.062763 CTGCTACATGGGATCGTCAATC 58.937 50.000 0.00 0.00 0.00 2.67
498 500 2.700371 TCTGCTACATGGGATCGTCAAT 59.300 45.455 0.00 0.00 0.00 2.57
499 501 2.107366 TCTGCTACATGGGATCGTCAA 58.893 47.619 0.00 0.00 0.00 3.18
500 502 1.775385 TCTGCTACATGGGATCGTCA 58.225 50.000 0.00 0.00 0.00 4.35
501 503 2.681706 CATCTGCTACATGGGATCGTC 58.318 52.381 0.00 0.00 0.00 4.20
502 504 1.270518 GCATCTGCTACATGGGATCGT 60.271 52.381 0.00 0.00 38.21 3.73
503 505 1.270465 TGCATCTGCTACATGGGATCG 60.270 52.381 3.53 0.00 42.66 3.69
522 524 3.622612 TGCGTCACATCTTATTGACCATG 59.377 43.478 0.00 0.00 39.22 3.66
574 576 6.426646 AGGGATGTTATGATGAGACCTTAC 57.573 41.667 0.00 0.00 0.00 2.34
606 608 7.175990 ACGACTAACATTTGGTTGGACAAATAT 59.824 33.333 4.10 0.71 46.27 1.28
607 609 6.487331 ACGACTAACATTTGGTTGGACAAATA 59.513 34.615 4.10 0.00 46.27 1.40
609 611 4.641094 ACGACTAACATTTGGTTGGACAAA 59.359 37.500 0.00 0.00 43.69 2.83
636 638 9.822185 GGTCTTATAAAAAGAATAGGTAACGGA 57.178 33.333 0.00 0.00 46.39 4.69
681 684 6.705863 ATCTGAAGGTCAATAATTGAAGGC 57.294 37.500 0.00 0.00 42.15 4.35
699 702 3.726557 AGTCATCCAAGCCAAATCTGA 57.273 42.857 0.00 0.00 0.00 3.27
701 704 3.760684 GTGAAGTCATCCAAGCCAAATCT 59.239 43.478 0.00 0.00 0.00 2.40
711 714 1.608025 GCCGAACTGTGAAGTCATCCA 60.608 52.381 0.00 0.00 0.00 3.41
714 717 2.479566 ATGCCGAACTGTGAAGTCAT 57.520 45.000 0.00 0.00 0.00 3.06
721 724 5.233957 TCAATTATCAATGCCGAACTGTG 57.766 39.130 0.00 0.00 0.00 3.66
722 725 6.455360 AATCAATTATCAATGCCGAACTGT 57.545 33.333 0.00 0.00 0.00 3.55
737 740 7.441157 CGCAGTGTCTATTTCCCTAATCAATTA 59.559 37.037 0.00 0.00 0.00 1.40
744 747 2.235155 TGCGCAGTGTCTATTTCCCTAA 59.765 45.455 5.66 0.00 0.00 2.69
745 748 1.828595 TGCGCAGTGTCTATTTCCCTA 59.171 47.619 5.66 0.00 0.00 3.53
746 749 0.613260 TGCGCAGTGTCTATTTCCCT 59.387 50.000 5.66 0.00 0.00 4.20
747 750 1.009829 CTGCGCAGTGTCTATTTCCC 58.990 55.000 29.24 0.00 0.00 3.97
748 751 2.010145 TCTGCGCAGTGTCTATTTCC 57.990 50.000 34.70 0.00 0.00 3.13
749 752 4.331168 AGAATTCTGCGCAGTGTCTATTTC 59.669 41.667 34.70 24.01 0.00 2.17
750 753 4.256920 AGAATTCTGCGCAGTGTCTATTT 58.743 39.130 34.70 18.05 0.00 1.40
751 754 3.866651 AGAATTCTGCGCAGTGTCTATT 58.133 40.909 34.70 24.33 0.00 1.73
752 755 3.452474 GAGAATTCTGCGCAGTGTCTAT 58.548 45.455 34.70 18.50 0.00 1.98
753 756 2.732282 CGAGAATTCTGCGCAGTGTCTA 60.732 50.000 34.70 14.63 0.00 2.59
754 757 1.719600 GAGAATTCTGCGCAGTGTCT 58.280 50.000 34.70 30.74 0.00 3.41
755 758 0.368227 CGAGAATTCTGCGCAGTGTC 59.632 55.000 34.70 27.26 0.00 3.67
831 834 4.712337 ACTCGACCTCAAATCTGACCTAAT 59.288 41.667 0.00 0.00 0.00 1.73
925 931 3.474570 GCCAGATCCCCTGAGCGT 61.475 66.667 0.00 0.00 45.78 5.07
989 1013 2.409870 GGTTCCATTGGCAGCGAGG 61.410 63.158 0.00 0.00 0.00 4.63
991 1015 2.361104 GGGTTCCATTGGCAGCGA 60.361 61.111 0.00 0.00 0.00 4.93
992 1016 2.676121 TGGGTTCCATTGGCAGCG 60.676 61.111 0.00 0.00 0.00 5.18
993 1017 1.598701 GACTGGGTTCCATTGGCAGC 61.599 60.000 7.68 2.35 30.82 5.25
994 1018 0.038744 AGACTGGGTTCCATTGGCAG 59.961 55.000 0.00 2.21 30.82 4.85
995 1019 0.251297 CAGACTGGGTTCCATTGGCA 60.251 55.000 0.00 0.00 30.82 4.92
996 1020 0.967380 CCAGACTGGGTTCCATTGGC 60.967 60.000 14.26 0.00 32.67 4.52
1183 1207 4.247380 GCCTGAGGCTGATCCCGG 62.247 72.222 17.96 0.00 46.69 5.73
1193 1220 4.527583 GCGAGCCTGAGCCTGAGG 62.528 72.222 0.00 0.00 41.25 3.86
1375 1402 2.081425 CTCGCCTCCTCCATCTTCCG 62.081 65.000 0.00 0.00 0.00 4.30
1867 8871 3.103289 GCACACGATGTCGACGCA 61.103 61.111 11.62 0.00 43.02 5.24
1948 8952 0.034670 ATTGCCAGGAGAAGAGCACC 60.035 55.000 0.00 0.00 34.37 5.01
1974 10711 6.881065 GGGATCATACATGGTACTAGTACGTA 59.119 42.308 23.40 19.65 36.94 3.57
1977 10714 5.709164 ACGGGATCATACATGGTACTAGTAC 59.291 44.000 22.53 22.53 35.40 2.73
1982 10719 3.510360 GCTACGGGATCATACATGGTACT 59.490 47.826 0.00 0.00 0.00 2.73
1983 10720 3.672511 CGCTACGGGATCATACATGGTAC 60.673 52.174 0.00 0.00 0.00 3.34
1987 10724 2.596452 GACGCTACGGGATCATACATG 58.404 52.381 0.00 0.00 0.00 3.21
2023 10760 0.955919 GCAAGTAGGTGCACTGGACC 60.956 60.000 17.98 11.72 44.29 4.46
2064 10871 8.665685 ACAGCAGTTCCGAATTAAATAACTAAG 58.334 33.333 0.00 0.00 0.00 2.18
2086 10893 7.573968 AATTTACAAATCATCTCCCTACAGC 57.426 36.000 0.00 0.00 0.00 4.40
2153 14446 4.487714 TTTTGCGAGGATCAGTAGGATT 57.512 40.909 0.00 0.00 36.00 3.01
2204 14501 1.646189 GTCCTTGATTGGCTCGACTC 58.354 55.000 0.00 0.00 0.00 3.36
2205 14502 0.250513 GGTCCTTGATTGGCTCGACT 59.749 55.000 0.00 0.00 0.00 4.18
2206 14503 0.250513 AGGTCCTTGATTGGCTCGAC 59.749 55.000 0.00 0.00 0.00 4.20
2207 14504 1.860641 TAGGTCCTTGATTGGCTCGA 58.139 50.000 0.00 0.00 0.00 4.04
2208 14505 2.678336 GTTTAGGTCCTTGATTGGCTCG 59.322 50.000 0.00 0.00 0.00 5.03
2209 14506 2.678336 CGTTTAGGTCCTTGATTGGCTC 59.322 50.000 0.00 0.00 0.00 4.70
2210 14507 2.711542 CGTTTAGGTCCTTGATTGGCT 58.288 47.619 0.00 0.00 0.00 4.75
2211 14508 1.132453 GCGTTTAGGTCCTTGATTGGC 59.868 52.381 0.00 0.00 0.00 4.52
2212 14509 1.743394 GGCGTTTAGGTCCTTGATTGG 59.257 52.381 0.00 0.00 0.00 3.16
2213 14510 2.711542 AGGCGTTTAGGTCCTTGATTG 58.288 47.619 0.00 0.00 0.00 2.67
2214 14511 3.434940 AAGGCGTTTAGGTCCTTGATT 57.565 42.857 0.00 0.00 38.66 2.57
2257 14661 9.419297 GAAAGGTTTAAAAACTTGTGAAGAAGT 57.581 29.630 6.42 0.00 38.89 3.01
2328 14733 6.260050 TGCTTTTGTACTTCTCGTGAATCTTT 59.740 34.615 0.00 0.00 0.00 2.52
2338 14743 4.762251 AGTTGGGATGCTTTTGTACTTCTC 59.238 41.667 0.00 0.00 0.00 2.87
2385 14790 1.370657 GGATTAGACGGCGCTCTCG 60.371 63.158 6.90 4.93 39.07 4.04
2401 14806 4.014569 TGAATTTGTTCATCAGGACGGA 57.985 40.909 0.00 0.00 0.00 4.69
2402 14807 4.764679 TTGAATTTGTTCATCAGGACGG 57.235 40.909 0.00 0.00 0.00 4.79
2403 14808 6.000891 TCTTTGAATTTGTTCATCAGGACG 57.999 37.500 0.00 0.00 0.00 4.79
2404 14809 6.207417 TCCTCTTTGAATTTGTTCATCAGGAC 59.793 38.462 8.21 0.00 31.14 3.85
2405 14810 6.306199 TCCTCTTTGAATTTGTTCATCAGGA 58.694 36.000 8.21 8.21 32.47 3.86
2406 14811 6.579666 TCCTCTTTGAATTTGTTCATCAGG 57.420 37.500 0.00 0.00 0.00 3.86
2407 14812 7.823665 TGATCCTCTTTGAATTTGTTCATCAG 58.176 34.615 0.00 0.00 0.00 2.90
2408 14813 7.764141 TGATCCTCTTTGAATTTGTTCATCA 57.236 32.000 0.00 0.00 0.00 3.07
2409 14814 9.480053 TTTTGATCCTCTTTGAATTTGTTCATC 57.520 29.630 0.00 0.00 0.00 2.92
2410 14815 9.835389 TTTTTGATCCTCTTTGAATTTGTTCAT 57.165 25.926 0.00 0.00 0.00 2.57
2411 14816 9.835389 ATTTTTGATCCTCTTTGAATTTGTTCA 57.165 25.926 0.00 0.00 0.00 3.18
2413 14818 9.835389 TGATTTTTGATCCTCTTTGAATTTGTT 57.165 25.926 0.00 0.00 0.00 2.83
2414 14819 9.835389 TTGATTTTTGATCCTCTTTGAATTTGT 57.165 25.926 0.00 0.00 0.00 2.83
2419 14824 9.533253 GTCTTTTGATTTTTGATCCTCTTTGAA 57.467 29.630 0.00 0.00 0.00 2.69
2420 14825 8.143835 GGTCTTTTGATTTTTGATCCTCTTTGA 58.856 33.333 0.00 0.00 0.00 2.69
2421 14826 7.927629 TGGTCTTTTGATTTTTGATCCTCTTTG 59.072 33.333 0.00 0.00 0.00 2.77
2422 14827 8.021898 TGGTCTTTTGATTTTTGATCCTCTTT 57.978 30.769 0.00 0.00 0.00 2.52
2423 14828 7.601705 TGGTCTTTTGATTTTTGATCCTCTT 57.398 32.000 0.00 0.00 0.00 2.85
2424 14829 7.288621 AGTTGGTCTTTTGATTTTTGATCCTCT 59.711 33.333 0.00 0.00 0.00 3.69
2431 14836 8.477984 TCTTCAAGTTGGTCTTTTGATTTTTG 57.522 30.769 2.34 0.00 33.63 2.44
2436 14841 7.231317 TGCTTATCTTCAAGTTGGTCTTTTGAT 59.769 33.333 2.34 0.51 33.63 2.57
2437 14842 6.545666 TGCTTATCTTCAAGTTGGTCTTTTGA 59.454 34.615 2.34 0.00 33.63 2.69
2439 14844 6.513393 CGTGCTTATCTTCAAGTTGGTCTTTT 60.513 38.462 2.34 0.00 33.63 2.27
2440 14845 5.049405 CGTGCTTATCTTCAAGTTGGTCTTT 60.049 40.000 2.34 0.00 33.63 2.52
2451 14856 0.107703 CAGGGGCGTGCTTATCTTCA 60.108 55.000 0.00 0.00 0.00 3.02
2465 14870 1.738030 CGGTTTTAGTACTCGCAGGGG 60.738 57.143 0.00 0.00 0.00 4.79
2467 14872 2.358939 ACGGTTTTAGTACTCGCAGG 57.641 50.000 0.00 0.00 0.00 4.85
2470 14875 5.098211 ACAGATTACGGTTTTAGTACTCGC 58.902 41.667 0.00 0.00 31.63 5.03
2471 14876 5.741040 GGACAGATTACGGTTTTAGTACTCG 59.259 44.000 0.00 0.00 31.63 4.18
2475 14880 4.158394 AGCGGACAGATTACGGTTTTAGTA 59.842 41.667 0.00 0.00 34.39 1.82
2485 14890 5.833082 TGAGAATTCTAGCGGACAGATTAC 58.167 41.667 8.25 0.00 0.00 1.89
2489 14894 3.319405 GGATGAGAATTCTAGCGGACAGA 59.681 47.826 8.25 0.00 0.00 3.41
2490 14895 3.320541 AGGATGAGAATTCTAGCGGACAG 59.679 47.826 8.25 0.00 0.00 3.51
2495 14900 2.323959 GCGAGGATGAGAATTCTAGCG 58.676 52.381 8.25 7.24 0.00 4.26
2500 14905 1.224722 GGCGGCGAGGATGAGAATTC 61.225 60.000 12.98 0.00 0.00 2.17
2520 14943 3.010413 GCCTGTTGCTCCAATGGCC 62.010 63.158 0.00 0.00 38.71 5.36
2521 14944 2.221906 CTGCCTGTTGCTCCAATGGC 62.222 60.000 13.96 13.96 42.02 4.40
2522 14945 0.609957 TCTGCCTGTTGCTCCAATGG 60.610 55.000 0.00 0.00 42.00 3.16
2523 14946 0.809385 CTCTGCCTGTTGCTCCAATG 59.191 55.000 0.00 0.00 42.00 2.82
2524 14947 0.323178 CCTCTGCCTGTTGCTCCAAT 60.323 55.000 0.00 0.00 42.00 3.16
2525 14948 1.073722 CCTCTGCCTGTTGCTCCAA 59.926 57.895 0.00 0.00 42.00 3.53
2526 14949 2.752358 CCTCTGCCTGTTGCTCCA 59.248 61.111 0.00 0.00 42.00 3.86
2527 14950 2.045536 CCCTCTGCCTGTTGCTCC 60.046 66.667 0.00 0.00 42.00 4.70
2528 14951 1.078567 CTCCCTCTGCCTGTTGCTC 60.079 63.158 0.00 0.00 42.00 4.26
2529 14952 2.600729 CCTCCCTCTGCCTGTTGCT 61.601 63.158 0.00 0.00 42.00 3.91
2530 14953 2.045536 CCTCCCTCTGCCTGTTGC 60.046 66.667 0.00 0.00 41.77 4.17
2531 14954 2.045536 GCCTCCCTCTGCCTGTTG 60.046 66.667 0.00 0.00 0.00 3.33
2532 14955 3.710722 CGCCTCCCTCTGCCTGTT 61.711 66.667 0.00 0.00 0.00 3.16
2533 14956 4.704103 TCGCCTCCCTCTGCCTGT 62.704 66.667 0.00 0.00 0.00 4.00
2534 14957 2.657102 GATTCGCCTCCCTCTGCCTG 62.657 65.000 0.00 0.00 0.00 4.85
2535 14958 2.366167 ATTCGCCTCCCTCTGCCT 60.366 61.111 0.00 0.00 0.00 4.75
2536 14959 2.110006 GATTCGCCTCCCTCTGCC 59.890 66.667 0.00 0.00 0.00 4.85
2537 14960 2.110006 GGATTCGCCTCCCTCTGC 59.890 66.667 0.00 0.00 0.00 4.26
2538 14961 1.144936 GTGGATTCGCCTCCCTCTG 59.855 63.158 1.25 0.00 37.63 3.35
2539 14962 1.306141 TGTGGATTCGCCTCCCTCT 60.306 57.895 1.25 0.00 37.63 3.69
2540 14963 1.144936 CTGTGGATTCGCCTCCCTC 59.855 63.158 1.25 0.00 37.63 4.30
2541 14964 1.306141 TCTGTGGATTCGCCTCCCT 60.306 57.895 1.25 0.00 37.63 4.20
2542 14965 1.153349 GTCTGTGGATTCGCCTCCC 60.153 63.158 1.25 0.00 37.63 4.30
2543 14966 0.179097 GAGTCTGTGGATTCGCCTCC 60.179 60.000 0.00 0.00 37.63 4.30
2544 14967 0.526524 CGAGTCTGTGGATTCGCCTC 60.527 60.000 0.00 0.00 42.75 4.70
2545 14968 1.513158 CGAGTCTGTGGATTCGCCT 59.487 57.895 0.00 0.00 42.75 5.52
2546 14969 4.094684 CGAGTCTGTGGATTCGCC 57.905 61.111 0.00 0.00 42.75 5.54
2549 14972 1.519455 CCGGCGAGTCTGTGGATTC 60.519 63.158 9.30 0.00 0.00 2.52
2550 14973 2.579201 CCGGCGAGTCTGTGGATT 59.421 61.111 9.30 0.00 0.00 3.01
2551 14974 4.148825 GCCGGCGAGTCTGTGGAT 62.149 66.667 12.58 0.00 0.00 3.41
2562 14985 3.338676 GCTTTATCTCCGCCGGCG 61.339 66.667 41.00 41.00 39.44 6.46
2563 14986 3.338676 CGCTTTATCTCCGCCGGC 61.339 66.667 19.07 19.07 0.00 6.13
2564 14987 2.661866 CCGCTTTATCTCCGCCGG 60.662 66.667 0.00 0.00 0.00 6.13
2565 14988 2.661866 CCCGCTTTATCTCCGCCG 60.662 66.667 0.00 0.00 0.00 6.46
2566 14989 2.280865 CCCCGCTTTATCTCCGCC 60.281 66.667 0.00 0.00 0.00 6.13
2567 14990 1.301009 CTCCCCGCTTTATCTCCGC 60.301 63.158 0.00 0.00 0.00 5.54
2568 14991 0.315568 CTCTCCCCGCTTTATCTCCG 59.684 60.000 0.00 0.00 0.00 4.63
2569 14992 1.341852 GTCTCTCCCCGCTTTATCTCC 59.658 57.143 0.00 0.00 0.00 3.71
2570 14993 2.312390 AGTCTCTCCCCGCTTTATCTC 58.688 52.381 0.00 0.00 0.00 2.75
2571 14994 2.463047 AGTCTCTCCCCGCTTTATCT 57.537 50.000 0.00 0.00 0.00 1.98
2572 14995 3.545366 AAAGTCTCTCCCCGCTTTATC 57.455 47.619 0.00 0.00 30.45 1.75
2573 14996 3.519913 AGAAAAGTCTCTCCCCGCTTTAT 59.480 43.478 0.00 0.00 31.78 1.40
2574 14997 2.904434 AGAAAAGTCTCTCCCCGCTTTA 59.096 45.455 0.00 0.00 31.78 1.85
2575 14998 1.700186 AGAAAAGTCTCTCCCCGCTTT 59.300 47.619 0.00 0.00 33.20 3.51
2576 14999 1.353091 AGAAAAGTCTCTCCCCGCTT 58.647 50.000 0.00 0.00 0.00 4.68
2577 15000 2.104170 CTAGAAAAGTCTCTCCCCGCT 58.896 52.381 0.00 0.00 35.12 5.52
2578 15001 1.826096 ACTAGAAAAGTCTCTCCCCGC 59.174 52.381 0.00 0.00 35.12 6.13
2579 15002 2.166664 CCACTAGAAAAGTCTCTCCCCG 59.833 54.545 0.00 0.00 35.76 5.73
2580 15003 3.174779 ACCACTAGAAAAGTCTCTCCCC 58.825 50.000 0.00 0.00 35.76 4.81
2581 15004 4.090819 AGACCACTAGAAAAGTCTCTCCC 58.909 47.826 0.00 0.00 34.53 4.30
2582 15005 5.474825 CAAGACCACTAGAAAAGTCTCTCC 58.525 45.833 0.00 0.00 38.61 3.71
2583 15006 4.926832 GCAAGACCACTAGAAAAGTCTCTC 59.073 45.833 0.00 0.00 38.61 3.20
2584 15007 4.559704 CGCAAGACCACTAGAAAAGTCTCT 60.560 45.833 0.00 0.00 38.61 3.10
2585 15008 3.675698 CGCAAGACCACTAGAAAAGTCTC 59.324 47.826 0.00 0.00 38.61 3.36
2586 15009 3.321111 TCGCAAGACCACTAGAAAAGTCT 59.679 43.478 0.00 0.00 45.01 3.24
2587 15010 3.650139 TCGCAAGACCACTAGAAAAGTC 58.350 45.455 0.00 0.00 45.01 3.01
2588 15011 3.321111 TCTCGCAAGACCACTAGAAAAGT 59.679 43.478 0.00 0.00 45.01 2.66
2589 15012 3.914312 TCTCGCAAGACCACTAGAAAAG 58.086 45.455 0.00 0.00 45.01 2.27
2590 15013 3.306088 CCTCTCGCAAGACCACTAGAAAA 60.306 47.826 0.00 0.00 45.01 2.29
2593 15199 1.464734 CCTCTCGCAAGACCACTAGA 58.535 55.000 0.00 0.00 45.01 2.43
2597 15203 1.827399 TTCCCCTCTCGCAAGACCAC 61.827 60.000 0.00 0.00 45.01 4.16
2653 15259 0.654472 CACGTTGACGCACAAGCTTC 60.654 55.000 0.00 0.00 44.43 3.86
2664 15271 2.548057 TCCTTTGCTGAATCACGTTGAC 59.452 45.455 0.00 0.00 0.00 3.18
2679 15286 1.133482 AGACTTTGTGGGGGTCCTTTG 60.133 52.381 0.00 0.00 0.00 2.77
2681 15288 1.231963 AAGACTTTGTGGGGGTCCTT 58.768 50.000 0.00 0.00 0.00 3.36
2682 15289 1.231963 AAAGACTTTGTGGGGGTCCT 58.768 50.000 0.00 0.00 0.00 3.85
2683 15290 2.082140 AAAAGACTTTGTGGGGGTCC 57.918 50.000 0.06 0.00 0.00 4.46
2706 15382 5.180117 GCCTTTCATCATATCATAGCAACGT 59.820 40.000 0.00 0.00 0.00 3.99
2707 15383 5.410746 AGCCTTTCATCATATCATAGCAACG 59.589 40.000 0.00 0.00 0.00 4.10
2708 15384 6.814506 AGCCTTTCATCATATCATAGCAAC 57.185 37.500 0.00 0.00 0.00 4.17
2710 15386 7.938490 TGTTTAGCCTTTCATCATATCATAGCA 59.062 33.333 0.00 0.00 0.00 3.49
2711 15387 8.327941 TGTTTAGCCTTTCATCATATCATAGC 57.672 34.615 0.00 0.00 0.00 2.97
2714 15390 8.757982 AACTGTTTAGCCTTTCATCATATCAT 57.242 30.769 0.00 0.00 0.00 2.45
2716 15392 8.462016 ACAAACTGTTTAGCCTTTCATCATATC 58.538 33.333 5.31 0.00 0.00 1.63
2717 15393 8.353423 ACAAACTGTTTAGCCTTTCATCATAT 57.647 30.769 5.31 0.00 0.00 1.78
2723 15422 6.329496 CAAGAACAAACTGTTTAGCCTTTCA 58.671 36.000 5.31 0.00 41.28 2.69
2771 15477 1.762370 TGCTGCTGCTTGCCTATACTA 59.238 47.619 17.00 0.00 42.00 1.82
2772 15478 0.543277 TGCTGCTGCTTGCCTATACT 59.457 50.000 17.00 0.00 42.00 2.12
2773 15479 0.659957 GTGCTGCTGCTTGCCTATAC 59.340 55.000 17.00 0.00 42.00 1.47
2798 15504 1.154225 CATGAACAAACGCTCCGGC 60.154 57.895 0.00 0.00 0.00 6.13
2878 15584 0.525242 CGCAACCAAGTGTGTTGTGG 60.525 55.000 13.75 0.00 45.71 4.17
2879 15585 2.942545 CGCAACCAAGTGTGTTGTG 58.057 52.632 11.66 10.83 44.69 3.33
2892 15598 1.336755 TGAAAAGAGGCTTTCCGCAAC 59.663 47.619 0.00 0.00 41.67 4.17


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

AutoCloner maintained by Alex Coulton.