Multiple sequence alignment - TraesCS5D01G440700

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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 TraesCS5D01G440700 chr5D 100.000 2863 0 0 1 2863 493832640 493835502 0.000000e+00 5288.0
1 TraesCS5D01G440700 chr5D 92.857 294 21 0 2395 2688 494053341 494053048 7.330000e-116 427.0
2 TraesCS5D01G440700 chr5D 96.842 190 4 2 2669 2856 412360772 412360961 1.660000e-82 316.0
3 TraesCS5D01G440700 chr5D 92.742 124 9 0 2565 2688 494042345 494042222 2.270000e-41 180.0
4 TraesCS5D01G440700 chr5A 88.503 1296 82 28 723 2001 616878429 616879674 0.000000e+00 1506.0
5 TraesCS5D01G440700 chr5A 92.776 526 29 2 2163 2688 616879832 616880348 0.000000e+00 752.0
6 TraesCS5D01G440700 chr5A 87.151 537 44 13 2162 2688 616909058 616909579 1.140000e-163 586.0
7 TraesCS5D01G440700 chr5A 93.537 294 19 0 2395 2688 616914042 616914335 3.390000e-119 438.0
8 TraesCS5D01G440700 chr5A 91.186 295 24 2 2395 2688 616919404 616919697 1.600000e-107 399.0
9 TraesCS5D01G440700 chr5A 98.883 179 2 0 2685 2863 702454490 702454312 1.280000e-83 320.0
10 TraesCS5D01G440700 chr5A 98.333 180 1 2 2678 2857 32839939 32840116 5.950000e-82 315.0
11 TraesCS5D01G440700 chr5A 99.419 172 1 0 2684 2855 476123641 476123812 2.140000e-81 313.0
12 TraesCS5D01G440700 chr5B 89.120 1204 71 27 680 1870 609598461 609599617 0.000000e+00 1443.0
13 TraesCS5D01G440700 chr5B 91.196 443 27 8 99 541 609597812 609598242 2.460000e-165 592.0
14 TraesCS5D01G440700 chr5B 85.283 530 47 17 2162 2688 609927131 609927632 4.230000e-143 518.0
15 TraesCS5D01G440700 chr5B 88.189 381 31 4 2178 2554 609599900 609600270 2.620000e-120 442.0
16 TraesCS5D01G440700 chr5B 92.177 294 23 0 2395 2688 609935245 609935538 1.590000e-112 416.0
17 TraesCS5D01G440700 chr5B 87.543 289 26 5 2401 2688 609848138 609848417 2.750000e-85 326.0
18 TraesCS5D01G440700 chr5B 96.226 106 3 1 564 669 609598236 609598340 3.790000e-39 172.0
19 TraesCS5D01G440700 chr5B 79.200 250 39 7 2267 2513 610085045 610085284 8.210000e-36 161.0
20 TraesCS5D01G440700 chr5B 82.500 160 24 4 998 1153 441811990 441811831 1.380000e-28 137.0
21 TraesCS5D01G440700 chr5B 83.077 130 9 6 1950 2078 609599744 609599861 3.900000e-19 106.0
22 TraesCS5D01G440700 chr5B 97.872 47 1 0 2032 2078 609604625 609604671 6.570000e-12 82.4
23 TraesCS5D01G440700 chr5B 97.872 47 1 0 2032 2078 609926851 609926897 6.570000e-12 82.4
24 TraesCS5D01G440700 chr3D 99.252 401 3 0 978 1378 471044606 471044206 0.000000e+00 725.0
25 TraesCS5D01G440700 chr2D 98.343 181 1 2 2684 2863 33774448 33774627 1.660000e-82 316.0
26 TraesCS5D01G440700 chr2D 80.000 200 40 0 1595 1794 15967048 15967247 6.390000e-32 148.0
27 TraesCS5D01G440700 chr2A 100.000 171 0 0 2685 2855 2261360 2261190 1.660000e-82 316.0
28 TraesCS5D01G440700 chr1D 99.419 172 1 0 2685 2856 469836086 469836257 2.140000e-81 313.0
29 TraesCS5D01G440700 chr1D 86.538 156 21 0 1001 1156 63543583 63543738 3.790000e-39 172.0
30 TraesCS5D01G440700 chr4A 99.419 172 0 1 2688 2859 536870013 536869843 7.700000e-81 311.0
31 TraesCS5D01G440700 chr3B 97.283 184 3 2 2680 2862 242488454 242488272 7.700000e-81 311.0
32 TraesCS5D01G440700 chr1B 87.179 156 20 0 1001 1156 101519246 101519401 8.150000e-41 178.0
33 TraesCS5D01G440700 chr1B 86.335 161 22 0 1001 1161 101591796 101591636 2.930000e-40 176.0
34 TraesCS5D01G440700 chr1A 86.709 158 17 3 1001 1156 61575846 61576001 3.790000e-39 172.0
35 TraesCS5D01G440700 chr7A 80.690 145 28 0 1009 1153 708116337 708116193 2.330000e-21 113.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G440700 chr5D 493832640 493835502 2862 False 5288.0 5288 100.0000 1 2863 1 chr5D.!!$F2 2862
1 TraesCS5D01G440700 chr5A 616878429 616880348 1919 False 1129.0 1506 90.6395 723 2688 2 chr5A.!!$F6 1965
2 TraesCS5D01G440700 chr5A 616909058 616909579 521 False 586.0 586 87.1510 2162 2688 1 chr5A.!!$F3 526
3 TraesCS5D01G440700 chr5B 609597812 609600270 2458 False 551.0 1443 89.5616 99 2554 5 chr5B.!!$F5 2455
4 TraesCS5D01G440700 chr5B 609926851 609927632 781 False 300.2 518 91.5775 2032 2688 2 chr5B.!!$F6 656

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
778 888 0.041238 AGGGCTAGTGCTGGTAGACA 59.959 55.0 0.0 0.0 39.59 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 2038 0.03759 AATGTAACCTGGCAGGCGAA 59.962 50.0 33.04 15.91 39.63 4.7 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
20 21 3.515602 ACCCAAGAAACAGAGCAAGAT 57.484 42.857 0.00 0.00 0.00 2.40
21 22 3.152341 ACCCAAGAAACAGAGCAAGATG 58.848 45.455 0.00 0.00 0.00 2.90
22 23 3.181440 ACCCAAGAAACAGAGCAAGATGA 60.181 43.478 0.00 0.00 0.00 2.92
23 24 4.015084 CCCAAGAAACAGAGCAAGATGAT 58.985 43.478 0.00 0.00 0.00 2.45
24 25 4.461781 CCCAAGAAACAGAGCAAGATGATT 59.538 41.667 0.00 0.00 0.00 2.57
25 26 5.649395 CCCAAGAAACAGAGCAAGATGATTA 59.351 40.000 0.00 0.00 0.00 1.75
26 27 6.151648 CCCAAGAAACAGAGCAAGATGATTAA 59.848 38.462 0.00 0.00 0.00 1.40
27 28 7.309377 CCCAAGAAACAGAGCAAGATGATTAAA 60.309 37.037 0.00 0.00 0.00 1.52
28 29 8.248945 CCAAGAAACAGAGCAAGATGATTAAAT 58.751 33.333 0.00 0.00 0.00 1.40
29 30 9.286946 CAAGAAACAGAGCAAGATGATTAAATC 57.713 33.333 0.00 0.00 0.00 2.17
30 31 8.571461 AGAAACAGAGCAAGATGATTAAATCA 57.429 30.769 0.00 0.00 44.55 2.57
46 47 2.127271 ATCATGCCAACATGGTTCGA 57.873 45.000 6.22 0.00 45.64 3.71
47 48 2.445427 ATCATGCCAACATGGTTCGAA 58.555 42.857 6.22 0.00 45.64 3.71
48 49 2.164219 ATCATGCCAACATGGTTCGAAC 59.836 45.455 20.14 20.14 45.64 3.95
49 50 0.521291 ATGCCAACATGGTTCGAACG 59.479 50.000 21.34 10.81 40.46 3.95
50 51 0.816018 TGCCAACATGGTTCGAACGT 60.816 50.000 21.34 11.45 40.46 3.99
51 52 0.110373 GCCAACATGGTTCGAACGTC 60.110 55.000 21.34 9.69 40.46 4.34
52 53 0.515564 CCAACATGGTTCGAACGTCC 59.484 55.000 21.34 9.19 31.35 4.79
53 54 0.162933 CAACATGGTTCGAACGTCCG 59.837 55.000 21.34 12.17 0.00 4.79
54 55 0.249573 AACATGGTTCGAACGTCCGT 60.250 50.000 21.34 12.77 0.00 4.69
55 56 0.665369 ACATGGTTCGAACGTCCGTC 60.665 55.000 21.34 7.55 0.00 4.79
56 57 0.665068 CATGGTTCGAACGTCCGTCA 60.665 55.000 21.34 12.91 0.00 4.35
57 58 0.388134 ATGGTTCGAACGTCCGTCAG 60.388 55.000 21.34 0.00 0.00 3.51
58 59 2.370393 GGTTCGAACGTCCGTCAGC 61.370 63.158 21.34 1.08 0.00 4.26
59 60 2.049802 TTCGAACGTCCGTCAGCC 60.050 61.111 0.00 0.00 0.00 4.85
60 61 2.847754 TTCGAACGTCCGTCAGCCA 61.848 57.895 0.00 0.00 0.00 4.75
61 62 2.352704 TTCGAACGTCCGTCAGCCAA 62.353 55.000 0.00 0.00 0.00 4.52
62 63 2.372690 CGAACGTCCGTCAGCCAAG 61.373 63.158 0.00 0.00 0.00 3.61
63 64 1.006571 GAACGTCCGTCAGCCAAGA 60.007 57.895 0.00 0.00 0.00 3.02
64 65 0.389948 GAACGTCCGTCAGCCAAGAT 60.390 55.000 0.00 0.00 0.00 2.40
65 66 0.892755 AACGTCCGTCAGCCAAGATA 59.107 50.000 0.00 0.00 0.00 1.98
66 67 0.172803 ACGTCCGTCAGCCAAGATAC 59.827 55.000 0.00 0.00 0.00 2.24
67 68 0.172578 CGTCCGTCAGCCAAGATACA 59.827 55.000 0.00 0.00 0.00 2.29
68 69 1.799181 CGTCCGTCAGCCAAGATACAG 60.799 57.143 0.00 0.00 0.00 2.74
69 70 0.175760 TCCGTCAGCCAAGATACAGC 59.824 55.000 0.00 0.00 0.00 4.40
70 71 1.148157 CCGTCAGCCAAGATACAGCG 61.148 60.000 0.00 0.00 0.00 5.18
71 72 1.756375 CGTCAGCCAAGATACAGCGC 61.756 60.000 0.00 0.00 0.00 5.92
72 73 0.460987 GTCAGCCAAGATACAGCGCT 60.461 55.000 2.64 2.64 0.00 5.92
73 74 0.179100 TCAGCCAAGATACAGCGCTC 60.179 55.000 7.13 0.00 0.00 5.03
74 75 1.144936 AGCCAAGATACAGCGCTCC 59.855 57.895 7.13 0.00 0.00 4.70
75 76 1.153369 GCCAAGATACAGCGCTCCA 60.153 57.895 7.13 0.00 0.00 3.86
76 77 0.744414 GCCAAGATACAGCGCTCCAA 60.744 55.000 7.13 0.00 0.00 3.53
77 78 1.009829 CCAAGATACAGCGCTCCAAC 58.990 55.000 7.13 0.00 0.00 3.77
78 79 1.009829 CAAGATACAGCGCTCCAACC 58.990 55.000 7.13 0.00 0.00 3.77
79 80 0.613260 AAGATACAGCGCTCCAACCA 59.387 50.000 7.13 0.00 0.00 3.67
80 81 0.108138 AGATACAGCGCTCCAACCAC 60.108 55.000 7.13 0.00 0.00 4.16
81 82 0.108138 GATACAGCGCTCCAACCACT 60.108 55.000 7.13 0.00 0.00 4.00
82 83 0.391661 ATACAGCGCTCCAACCACTG 60.392 55.000 7.13 0.00 0.00 3.66
84 85 4.335647 AGCGCTCCAACCACTGGG 62.336 66.667 2.64 0.00 46.44 4.45
87 88 4.284550 GCTCCAACCACTGGGCCA 62.285 66.667 5.85 5.85 46.44 5.36
88 89 2.520458 CTCCAACCACTGGGCCAA 59.480 61.111 8.04 0.00 46.44 4.52
89 90 1.077265 CTCCAACCACTGGGCCAAT 59.923 57.895 8.04 0.00 46.44 3.16
90 91 0.542702 CTCCAACCACTGGGCCAATT 60.543 55.000 8.04 0.00 46.44 2.32
91 92 0.105246 TCCAACCACTGGGCCAATTT 60.105 50.000 8.04 0.00 46.44 1.82
92 93 0.764271 CCAACCACTGGGCCAATTTT 59.236 50.000 8.04 0.00 42.17 1.82
93 94 1.142667 CCAACCACTGGGCCAATTTTT 59.857 47.619 8.04 0.00 42.17 1.94
145 146 7.924412 ACAAAATTTCTATATCTGCCATGCTTG 59.076 33.333 0.00 0.00 0.00 4.01
155 156 1.269883 TGCCATGCTTGCAGAAAACAG 60.270 47.619 0.87 0.00 34.05 3.16
222 223 5.580661 ACAAATTTGCAATGCTTTTTCCAC 58.419 33.333 18.12 0.00 0.00 4.02
232 233 3.971150 TGCTTTTTCCACCACATTTACG 58.029 40.909 0.00 0.00 0.00 3.18
241 242 1.000717 ACCACATTTACGCAGCCAAAC 60.001 47.619 0.00 0.00 0.00 2.93
258 259 9.023967 GCAGCCAAACTAAAATATTTCTATGTG 57.976 33.333 0.10 0.00 0.00 3.21
283 284 3.445096 GCCATGCTTGTAGGAAAAGTGAT 59.555 43.478 0.00 0.00 0.00 3.06
284 285 4.082026 GCCATGCTTGTAGGAAAAGTGATT 60.082 41.667 0.00 0.00 0.00 2.57
314 315 1.192090 CAAAATTTGCGCAGGTTTCGG 59.808 47.619 11.31 8.22 0.00 4.30
349 350 9.733556 TTATTAAACTTTCAAGTGGAGCATAGA 57.266 29.630 0.00 0.00 39.66 1.98
419 420 4.348754 TCCTGCAATCATGACCATCAGATA 59.651 41.667 14.15 3.76 0.00 1.98
420 421 5.013808 TCCTGCAATCATGACCATCAGATAT 59.986 40.000 14.15 0.00 0.00 1.63
421 422 6.214005 TCCTGCAATCATGACCATCAGATATA 59.786 38.462 14.15 0.00 0.00 0.86
477 478 6.585702 TCGCCATGTTGAAATTTCTTGTTATG 59.414 34.615 18.64 14.10 0.00 1.90
488 489 9.585099 GAAATTTCTTGTTATGTATCATGGCAA 57.415 29.630 11.05 0.00 0.00 4.52
495 496 5.008514 TGTTATGTATCATGGCAATTCGTGG 59.991 40.000 0.00 0.00 0.00 4.94
498 499 0.396139 ATCATGGCAATTCGTGGGCT 60.396 50.000 0.00 0.00 0.00 5.19
500 501 1.133823 TCATGGCAATTCGTGGGCTAT 60.134 47.619 0.00 0.00 0.00 2.97
501 502 1.682854 CATGGCAATTCGTGGGCTATT 59.317 47.619 0.00 0.00 0.00 1.73
509 510 0.912487 TCGTGGGCTATTTGTCCCCT 60.912 55.000 0.00 0.00 40.46 4.79
513 514 2.241430 GTGGGCTATTTGTCCCCTTAGT 59.759 50.000 0.00 0.00 40.46 2.24
578 579 2.350498 GCGCGGTAATAGTGTTGTTCAT 59.650 45.455 8.83 0.00 0.00 2.57
668 669 4.220693 GCCTCTTTTGGCCCATTATTTT 57.779 40.909 0.00 0.00 46.82 1.82
669 670 4.588899 GCCTCTTTTGGCCCATTATTTTT 58.411 39.130 0.00 0.00 46.82 1.94
670 671 4.635765 GCCTCTTTTGGCCCATTATTTTTC 59.364 41.667 0.00 0.00 46.82 2.29
672 673 6.475504 CCTCTTTTGGCCCATTATTTTTCTT 58.524 36.000 0.00 0.00 0.00 2.52
675 676 9.500785 CTCTTTTGGCCCATTATTTTTCTTTTA 57.499 29.630 0.00 0.00 0.00 1.52
676 677 9.500785 TCTTTTGGCCCATTATTTTTCTTTTAG 57.499 29.630 0.00 0.00 0.00 1.85
678 679 6.365970 TGGCCCATTATTTTTCTTTTAGCA 57.634 33.333 0.00 0.00 0.00 3.49
710 820 1.561769 ATCCACACATCCCTGCCGAA 61.562 55.000 0.00 0.00 0.00 4.30
711 821 1.746615 CCACACATCCCTGCCGAAG 60.747 63.158 0.00 0.00 0.00 3.79
712 822 1.003355 CACACATCCCTGCCGAAGT 60.003 57.895 0.00 0.00 0.00 3.01
713 823 1.003355 ACACATCCCTGCCGAAGTG 60.003 57.895 0.00 0.00 37.46 3.16
714 824 2.045926 ACATCCCTGCCGAAGTGC 60.046 61.111 0.00 0.00 0.00 4.40
715 825 2.825836 CATCCCTGCCGAAGTGCC 60.826 66.667 0.00 0.00 0.00 5.01
716 826 4.473520 ATCCCTGCCGAAGTGCCG 62.474 66.667 0.00 0.00 0.00 5.69
774 884 1.879575 AATCAGGGCTAGTGCTGGTA 58.120 50.000 0.00 0.00 39.59 3.25
775 885 1.418334 ATCAGGGCTAGTGCTGGTAG 58.582 55.000 0.00 0.00 39.59 3.18
776 886 0.335019 TCAGGGCTAGTGCTGGTAGA 59.665 55.000 0.00 0.00 39.59 2.59
777 887 0.461961 CAGGGCTAGTGCTGGTAGAC 59.538 60.000 0.00 0.00 39.59 2.59
778 888 0.041238 AGGGCTAGTGCTGGTAGACA 59.959 55.000 0.00 0.00 39.59 3.41
839 949 2.691526 ACGTGTCACCTCACTTCAACTA 59.308 45.455 0.00 0.00 36.33 2.24
850 960 4.127171 TCACTTCAACTAGTCAAAGCACC 58.873 43.478 14.14 0.00 0.00 5.01
855 965 4.127171 TCAACTAGTCAAAGCACCAAGTC 58.873 43.478 0.00 0.00 0.00 3.01
872 982 1.199327 AGTCTCATGGTGTACGACGTG 59.801 52.381 11.56 3.19 0.00 4.49
882 992 1.269206 TGTACGACGTGTTGGACCTTC 60.269 52.381 11.56 0.00 0.00 3.46
899 1017 2.503765 CCTTCCCTTCTTTCTCCTCTCC 59.496 54.545 0.00 0.00 0.00 3.71
902 1020 2.115427 CCCTTCTTTCTCCTCTCCCTC 58.885 57.143 0.00 0.00 0.00 4.30
903 1021 2.115427 CCTTCTTTCTCCTCTCCCTCC 58.885 57.143 0.00 0.00 0.00 4.30
909 1027 1.074623 CTCCTCTCCCTCCCATGCT 60.075 63.158 0.00 0.00 0.00 3.79
923 1041 4.728772 TCCCATGCTGTATAAATCAAGGG 58.271 43.478 1.22 1.22 0.00 3.95
926 1044 3.660970 TGCTGTATAAATCAAGGGGCA 57.339 42.857 0.00 0.00 0.00 5.36
954 1072 3.689649 GTGAGAATTCCGCATAAACCAGT 59.310 43.478 0.65 0.00 0.00 4.00
964 1082 1.212935 CATAAACCAGTGGAGGGGAGG 59.787 57.143 18.40 0.00 0.00 4.30
965 1083 0.549169 TAAACCAGTGGAGGGGAGGG 60.549 60.000 18.40 0.00 0.00 4.30
966 1084 2.355484 AAACCAGTGGAGGGGAGGGA 62.355 60.000 18.40 0.00 0.00 4.20
967 1085 2.366167 CCAGTGGAGGGGAGGGAG 60.366 72.222 1.68 0.00 0.00 4.30
970 1088 3.403558 GTGGAGGGGAGGGAGCAC 61.404 72.222 0.00 0.00 0.00 4.40
989 1107 0.249784 CCGTCATCCATCAGCAGAGG 60.250 60.000 0.00 0.00 0.00 3.69
993 1111 2.036217 GTCATCCATCAGCAGAGGAGAG 59.964 54.545 0.00 0.00 34.40 3.20
1020 1139 4.025401 GCGCCGGTGAAGGTGTTG 62.025 66.667 21.76 0.00 43.39 3.33
1155 1274 0.669625 ACCTCGCCAGAAACGTAAGC 60.670 55.000 0.00 0.00 45.62 3.09
1163 1282 1.944024 CAGAAACGTAAGCACACCCAA 59.056 47.619 0.00 0.00 45.62 4.12
1164 1283 2.552315 CAGAAACGTAAGCACACCCAAT 59.448 45.455 0.00 0.00 45.62 3.16
1166 1285 1.530323 AACGTAAGCACACCCAATCC 58.470 50.000 0.00 0.00 45.62 3.01
1167 1286 0.690762 ACGTAAGCACACCCAATCCT 59.309 50.000 0.00 0.00 45.62 3.24
1169 1288 1.338674 CGTAAGCACACCCAATCCTCA 60.339 52.381 0.00 0.00 0.00 3.86
1170 1289 2.359900 GTAAGCACACCCAATCCTCAG 58.640 52.381 0.00 0.00 0.00 3.35
1175 1295 0.610232 ACACCCAATCCTCAGCTTGC 60.610 55.000 0.00 0.00 0.00 4.01
1184 1304 2.929830 CTCAGCTTGCAGCAGAGTT 58.070 52.632 16.78 0.00 46.01 3.01
1185 1305 1.236628 CTCAGCTTGCAGCAGAGTTT 58.763 50.000 16.78 0.00 46.01 2.66
1186 1306 0.949397 TCAGCTTGCAGCAGAGTTTG 59.051 50.000 10.16 1.13 45.56 2.93
1187 1307 0.039437 CAGCTTGCAGCAGAGTTTGG 60.039 55.000 10.16 0.00 45.56 3.28
1188 1308 0.179009 AGCTTGCAGCAGAGTTTGGA 60.179 50.000 10.16 0.00 45.56 3.53
1189 1309 0.240411 GCTTGCAGCAGAGTTTGGAG 59.760 55.000 0.00 0.00 41.89 3.86
1190 1310 1.888215 CTTGCAGCAGAGTTTGGAGA 58.112 50.000 0.00 0.00 0.00 3.71
1191 1311 2.224606 CTTGCAGCAGAGTTTGGAGAA 58.775 47.619 0.00 0.00 0.00 2.87
1192 1312 2.346766 TGCAGCAGAGTTTGGAGAAA 57.653 45.000 0.00 0.00 0.00 2.52
1193 1313 2.867624 TGCAGCAGAGTTTGGAGAAAT 58.132 42.857 0.00 0.00 0.00 2.17
1194 1314 2.816087 TGCAGCAGAGTTTGGAGAAATC 59.184 45.455 0.00 0.00 0.00 2.17
1195 1315 2.163211 GCAGCAGAGTTTGGAGAAATCC 59.837 50.000 0.00 0.00 0.00 3.01
1196 1316 2.751806 CAGCAGAGTTTGGAGAAATCCC 59.248 50.000 0.00 0.00 0.00 3.85
1207 1327 5.333566 TGGAGAAATCCCTAAGTTTTGGT 57.666 39.130 0.00 0.00 0.00 3.67
1208 1328 5.076873 TGGAGAAATCCCTAAGTTTTGGTG 58.923 41.667 0.00 0.00 0.00 4.17
1214 1342 4.919774 TCCCTAAGTTTTGGTGCATAGA 57.080 40.909 0.00 0.00 0.00 1.98
1221 1349 4.000988 AGTTTTGGTGCATAGAACTACCG 58.999 43.478 7.71 0.00 35.98 4.02
1228 1356 1.935300 GCATAGAACTACCGCCGGATG 60.935 57.143 11.71 1.63 0.00 3.51
1229 1357 0.317479 ATAGAACTACCGCCGGATGC 59.683 55.000 11.71 0.00 0.00 3.91
1230 1358 0.754217 TAGAACTACCGCCGGATGCT 60.754 55.000 11.71 0.75 38.05 3.79
1259 1389 3.861840 TCATAACTCTGCTTTTCTCCGG 58.138 45.455 0.00 0.00 0.00 5.14
1329 1459 5.432885 TCTTCCGTCAGTTTTCAATTTCC 57.567 39.130 0.00 0.00 0.00 3.13
1347 1477 9.889128 TCAATTTCCTATTGATTTTCAAATCCC 57.111 29.630 9.33 0.00 43.19 3.85
1356 1486 7.801716 TTGATTTTCAAATCCCTATACTCCG 57.198 36.000 9.33 0.00 43.19 4.63
1357 1487 6.895782 TGATTTTCAAATCCCTATACTCCGT 58.104 36.000 9.33 0.00 43.19 4.69
1358 1488 8.025270 TGATTTTCAAATCCCTATACTCCGTA 57.975 34.615 9.33 0.00 43.19 4.02
1359 1489 7.929785 TGATTTTCAAATCCCTATACTCCGTAC 59.070 37.037 9.33 0.00 43.19 3.67
1360 1490 7.427989 TTTTCAAATCCCTATACTCCGTACT 57.572 36.000 0.00 0.00 0.00 2.73
1361 1491 6.401047 TTCAAATCCCTATACTCCGTACTG 57.599 41.667 0.00 0.00 0.00 2.74
1362 1492 5.698104 TCAAATCCCTATACTCCGTACTGA 58.302 41.667 0.00 0.00 0.00 3.41
1365 1495 7.289317 TCAAATCCCTATACTCCGTACTGATTT 59.711 37.037 0.00 0.00 31.97 2.17
1375 1505 4.421058 TCCGTACTGATTTTGAGATCACG 58.579 43.478 0.00 0.00 32.82 4.35
1393 1523 9.190858 GAGATCACGGAATTATATATGCATCTC 57.809 37.037 0.19 0.00 0.00 2.75
1399 1532 6.980978 CGGAATTATATATGCATCTCCGTCTT 59.019 38.462 0.19 0.00 39.72 3.01
1487 1620 2.269241 GAAGGCGACCCCAAGGAG 59.731 66.667 0.00 0.00 36.73 3.69
1724 1857 1.920835 GGACCTCAGCCACTTCCCT 60.921 63.158 0.00 0.00 0.00 4.20
1796 1929 2.813908 CGTGTTAGGGCGTGGCTC 60.814 66.667 0.00 0.00 0.00 4.70
1811 1944 4.775746 CTCGAGGAGCTGTTCGAC 57.224 61.111 13.46 0.00 40.55 4.20
1919 2084 9.396022 AGGTTACATTATGTGGTGAGAAATAAG 57.604 33.333 8.26 0.00 0.00 1.73
1928 2094 2.656002 GTGAGAAATAAGAAGGGGCCC 58.344 52.381 17.12 17.12 0.00 5.80
1996 2176 7.099764 TCTCACCACAGACTTTCTTATCAATC 58.900 38.462 0.00 0.00 0.00 2.67
2001 2181 8.986991 ACCACAGACTTTCTTATCAATCTAGAT 58.013 33.333 0.00 0.00 0.00 1.98
2002 2182 9.829507 CCACAGACTTTCTTATCAATCTAGATT 57.170 33.333 12.37 12.37 0.00 2.40
2006 2186 9.336171 AGACTTTCTTATCAATCTAGATTTGCC 57.664 33.333 15.49 0.00 0.00 4.52
2011 2191 6.868864 TCTTATCAATCTAGATTTGCCGCTAC 59.131 38.462 15.49 0.00 0.00 3.58
2012 2192 4.672587 TCAATCTAGATTTGCCGCTACT 57.327 40.909 15.49 0.00 0.00 2.57
2016 2196 7.217200 TCAATCTAGATTTGCCGCTACTATTT 58.783 34.615 15.49 0.00 0.00 1.40
2017 2197 7.171508 TCAATCTAGATTTGCCGCTACTATTTG 59.828 37.037 15.49 0.61 0.00 2.32
2019 2199 6.759272 TCTAGATTTGCCGCTACTATTTGAT 58.241 36.000 0.00 0.00 0.00 2.57
2020 2200 7.892609 TCTAGATTTGCCGCTACTATTTGATA 58.107 34.615 0.00 0.00 0.00 2.15
2022 2202 7.190920 AGATTTGCCGCTACTATTTGATAAC 57.809 36.000 0.00 0.00 0.00 1.89
2023 2203 6.992715 AGATTTGCCGCTACTATTTGATAACT 59.007 34.615 0.00 0.00 0.00 2.24
2024 2204 6.995511 TTTGCCGCTACTATTTGATAACTT 57.004 33.333 0.00 0.00 0.00 2.66
2025 2205 5.984233 TGCCGCTACTATTTGATAACTTG 57.016 39.130 0.00 0.00 0.00 3.16
2026 2206 5.424757 TGCCGCTACTATTTGATAACTTGT 58.575 37.500 0.00 0.00 0.00 3.16
2027 2207 5.522460 TGCCGCTACTATTTGATAACTTGTC 59.478 40.000 0.00 0.00 0.00 3.18
2028 2208 5.522460 GCCGCTACTATTTGATAACTTGTCA 59.478 40.000 0.00 0.00 0.00 3.58
2029 2209 6.036735 GCCGCTACTATTTGATAACTTGTCAA 59.963 38.462 0.00 0.00 34.01 3.18
2078 2258 5.990408 ACTCTGTTTTATGCTCTGTTTTCG 58.010 37.500 0.00 0.00 0.00 3.46
2082 2262 6.480651 TCTGTTTTATGCTCTGTTTTCGTACA 59.519 34.615 0.00 0.00 0.00 2.90
2134 2406 3.385755 ACCAACTGAGCTTTCTTTGCAAT 59.614 39.130 0.00 0.00 0.00 3.56
2157 2429 3.126858 GGCACACATGACACAACGATAAT 59.873 43.478 0.00 0.00 32.03 1.28
2264 2614 3.791973 TGGAACACAACAATGACCAAC 57.208 42.857 0.00 0.00 31.00 3.77
2299 2649 5.518848 TGCTCAATGCTAAACCAATATGG 57.481 39.130 0.00 0.00 42.60 2.74
2374 2728 4.803426 CAGTCCAGCGGCCGAGAC 62.803 72.222 33.48 29.17 0.00 3.36
2435 2796 3.345808 GCGAGCGCAAACACCAGA 61.346 61.111 11.47 0.00 41.49 3.86
2486 2847 2.758327 TCCTGCAGGTACGCCGAT 60.758 61.111 31.58 0.00 40.50 4.18
2603 2967 4.382320 GGCGGGGTCTGCACGTTA 62.382 66.667 1.01 0.00 0.00 3.18
2712 3076 2.311294 CGTAGCTAGCCCAACATGC 58.689 57.895 12.13 0.00 0.00 4.06
2713 3077 1.160329 CGTAGCTAGCCCAACATGCC 61.160 60.000 12.13 0.00 0.00 4.40
2714 3078 0.107214 GTAGCTAGCCCAACATGCCA 60.107 55.000 12.13 0.00 0.00 4.92
2715 3079 0.181114 TAGCTAGCCCAACATGCCAG 59.819 55.000 12.13 0.00 0.00 4.85
2716 3080 2.123428 GCTAGCCCAACATGCCAGG 61.123 63.158 2.29 0.00 0.00 4.45
2717 3081 1.454479 CTAGCCCAACATGCCAGGG 60.454 63.158 12.20 12.20 45.68 4.45
2718 3082 2.215451 CTAGCCCAACATGCCAGGGT 62.215 60.000 16.46 11.28 44.69 4.34
2719 3083 2.497792 TAGCCCAACATGCCAGGGTG 62.498 60.000 16.46 0.00 44.69 4.61
2720 3084 2.681064 CCCAACATGCCAGGGTGG 60.681 66.667 6.42 6.42 41.55 4.61
2721 3085 2.118076 CCAACATGCCAGGGTGGT 59.882 61.111 4.99 0.00 40.46 4.16
2722 3086 1.978617 CCAACATGCCAGGGTGGTC 60.979 63.158 4.99 0.00 40.46 4.02
2723 3087 1.978617 CAACATGCCAGGGTGGTCC 60.979 63.158 0.00 0.00 40.46 4.46
2724 3088 2.468868 AACATGCCAGGGTGGTCCA 61.469 57.895 0.00 0.00 40.46 4.02
2725 3089 2.361610 CATGCCAGGGTGGTCCAC 60.362 66.667 14.13 14.13 40.46 4.02
2740 3104 5.083533 TGGTCCACCAATGCAAAATATTC 57.916 39.130 0.00 0.00 44.35 1.75
2741 3105 4.529769 TGGTCCACCAATGCAAAATATTCA 59.470 37.500 0.00 0.00 44.35 2.57
2742 3106 4.869861 GGTCCACCAATGCAAAATATTCAC 59.130 41.667 0.00 0.00 35.64 3.18
2743 3107 5.477510 GTCCACCAATGCAAAATATTCACA 58.522 37.500 0.00 0.00 0.00 3.58
2744 3108 6.108015 GTCCACCAATGCAAAATATTCACAT 58.892 36.000 0.00 0.00 0.00 3.21
2745 3109 7.264221 GTCCACCAATGCAAAATATTCACATA 58.736 34.615 0.00 0.00 0.00 2.29
2746 3110 7.763528 GTCCACCAATGCAAAATATTCACATAA 59.236 33.333 0.00 0.00 0.00 1.90
2747 3111 8.316946 TCCACCAATGCAAAATATTCACATAAA 58.683 29.630 0.00 0.00 0.00 1.40
2748 3112 9.111613 CCACCAATGCAAAATATTCACATAAAT 57.888 29.630 0.00 0.00 0.00 1.40
2813 3177 5.966968 ATATTATGGGGAAATTCCAGGGT 57.033 39.130 14.68 0.00 38.64 4.34
2814 3178 3.396685 TTATGGGGAAATTCCAGGGTG 57.603 47.619 14.68 0.00 38.64 4.61
2815 3179 0.339510 ATGGGGAAATTCCAGGGTGG 59.660 55.000 14.68 0.00 38.64 4.61
2816 3180 1.077298 TGGGGAAATTCCAGGGTGGT 61.077 55.000 14.68 0.00 38.64 4.16
2817 3181 0.324368 GGGGAAATTCCAGGGTGGTC 60.324 60.000 14.68 0.00 38.64 4.02
2818 3182 0.324368 GGGAAATTCCAGGGTGGTCC 60.324 60.000 14.68 0.00 38.64 4.46
2819 3183 0.407918 GGAAATTCCAGGGTGGTCCA 59.592 55.000 7.23 0.00 39.03 4.02
2820 3184 1.007118 GGAAATTCCAGGGTGGTCCAT 59.993 52.381 7.23 0.00 39.03 3.41
2821 3185 2.102578 GAAATTCCAGGGTGGTCCATG 58.897 52.381 0.00 0.00 44.12 3.66
2832 3196 3.495729 GTCCATGGACCACCCTGT 58.504 61.111 31.37 0.00 39.08 4.00
2833 3197 1.299976 GTCCATGGACCACCCTGTC 59.700 63.158 31.37 5.53 39.08 3.51
2839 3203 3.647771 GACCACCCTGTCCACCCC 61.648 72.222 0.00 0.00 0.00 4.95
2842 3206 2.124085 CACCCTGTCCACCCCCTA 59.876 66.667 0.00 0.00 0.00 3.53
2843 3207 1.995626 CACCCTGTCCACCCCCTAG 60.996 68.421 0.00 0.00 0.00 3.02
2844 3208 2.181773 ACCCTGTCCACCCCCTAGA 61.182 63.158 0.00 0.00 0.00 2.43
2845 3209 1.318380 CCCTGTCCACCCCCTAGAT 59.682 63.158 0.00 0.00 0.00 1.98
2846 3210 0.566176 CCCTGTCCACCCCCTAGATA 59.434 60.000 0.00 0.00 0.00 1.98
2847 3211 1.718280 CCTGTCCACCCCCTAGATAC 58.282 60.000 0.00 0.00 0.00 2.24
2848 3212 1.329256 CTGTCCACCCCCTAGATACG 58.671 60.000 0.00 0.00 0.00 3.06
2849 3213 0.757935 TGTCCACCCCCTAGATACGC 60.758 60.000 0.00 0.00 0.00 4.42
2850 3214 1.152398 TCCACCCCCTAGATACGCC 60.152 63.158 0.00 0.00 0.00 5.68
2851 3215 1.458777 CCACCCCCTAGATACGCCA 60.459 63.158 0.00 0.00 0.00 5.69
2852 3216 1.746517 CACCCCCTAGATACGCCAC 59.253 63.158 0.00 0.00 0.00 5.01
2853 3217 0.759436 CACCCCCTAGATACGCCACT 60.759 60.000 0.00 0.00 0.00 4.00
2854 3218 0.759436 ACCCCCTAGATACGCCACTG 60.759 60.000 0.00 0.00 0.00 3.66
2855 3219 1.367840 CCCCTAGATACGCCACTGC 59.632 63.158 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.152341 CATCTTGCTCTGTTTCTTGGGT 58.848 45.455 0.00 0.00 0.00 4.51
1 2 3.415212 TCATCTTGCTCTGTTTCTTGGG 58.585 45.455 0.00 0.00 0.00 4.12
2 3 5.640189 AATCATCTTGCTCTGTTTCTTGG 57.360 39.130 0.00 0.00 0.00 3.61
3 4 9.286946 GATTTAATCATCTTGCTCTGTTTCTTG 57.713 33.333 0.00 0.00 0.00 3.02
4 5 9.017509 TGATTTAATCATCTTGCTCTGTTTCTT 57.982 29.630 3.20 0.00 33.59 2.52
5 6 8.571461 TGATTTAATCATCTTGCTCTGTTTCT 57.429 30.769 3.20 0.00 33.59 2.52
6 7 9.234384 CATGATTTAATCATCTTGCTCTGTTTC 57.766 33.333 16.59 0.00 46.62 2.78
7 8 7.705325 GCATGATTTAATCATCTTGCTCTGTTT 59.295 33.333 16.59 0.00 46.62 2.83
8 9 7.201145 GCATGATTTAATCATCTTGCTCTGTT 58.799 34.615 16.59 0.00 46.62 3.16
9 10 6.238953 GGCATGATTTAATCATCTTGCTCTGT 60.239 38.462 22.86 0.00 46.62 3.41
10 11 6.150318 GGCATGATTTAATCATCTTGCTCTG 58.850 40.000 22.86 12.02 46.62 3.35
11 12 5.831525 TGGCATGATTTAATCATCTTGCTCT 59.168 36.000 22.86 1.04 46.62 4.09
12 13 6.080648 TGGCATGATTTAATCATCTTGCTC 57.919 37.500 22.86 16.39 46.62 4.26
13 14 6.127281 TGTTGGCATGATTTAATCATCTTGCT 60.127 34.615 22.86 2.27 46.62 3.91
14 15 6.044046 TGTTGGCATGATTTAATCATCTTGC 58.956 36.000 16.59 17.60 46.62 4.01
30 31 0.521291 CGTTCGAACCATGTTGGCAT 59.479 50.000 22.07 0.00 42.67 4.40
31 32 0.816018 ACGTTCGAACCATGTTGGCA 60.816 50.000 22.07 0.00 42.67 4.92
32 33 0.110373 GACGTTCGAACCATGTTGGC 60.110 55.000 22.07 5.71 42.67 4.52
33 34 0.515564 GGACGTTCGAACCATGTTGG 59.484 55.000 22.07 8.93 45.02 3.77
34 35 0.162933 CGGACGTTCGAACCATGTTG 59.837 55.000 22.07 9.64 0.00 3.33
35 36 0.249573 ACGGACGTTCGAACCATGTT 60.250 50.000 25.79 0.00 0.00 2.71
36 37 0.665369 GACGGACGTTCGAACCATGT 60.665 55.000 25.79 14.25 0.00 3.21
37 38 0.665068 TGACGGACGTTCGAACCATG 60.665 55.000 25.79 11.07 0.00 3.66
38 39 0.388134 CTGACGGACGTTCGAACCAT 60.388 55.000 25.79 10.95 0.00 3.55
39 40 1.008194 CTGACGGACGTTCGAACCA 60.008 57.895 25.79 15.83 0.00 3.67
40 41 2.370393 GCTGACGGACGTTCGAACC 61.370 63.158 25.79 11.91 0.00 3.62
41 42 2.370393 GGCTGACGGACGTTCGAAC 61.370 63.158 25.79 18.47 0.00 3.95
42 43 2.049802 GGCTGACGGACGTTCGAA 60.050 61.111 25.79 9.81 0.00 3.71
43 44 2.742710 CTTGGCTGACGGACGTTCGA 62.743 60.000 25.79 0.00 0.00 3.71
44 45 2.355363 TTGGCTGACGGACGTTCG 60.355 61.111 16.31 16.31 0.00 3.95
45 46 0.389948 ATCTTGGCTGACGGACGTTC 60.390 55.000 0.00 0.00 0.00 3.95
46 47 0.892755 TATCTTGGCTGACGGACGTT 59.107 50.000 0.00 0.00 0.00 3.99
47 48 0.172803 GTATCTTGGCTGACGGACGT 59.827 55.000 0.00 0.00 0.00 4.34
48 49 0.172578 TGTATCTTGGCTGACGGACG 59.827 55.000 0.00 0.00 0.00 4.79
49 50 1.927895 CTGTATCTTGGCTGACGGAC 58.072 55.000 0.00 0.00 0.00 4.79
50 51 0.175760 GCTGTATCTTGGCTGACGGA 59.824 55.000 0.00 0.00 0.00 4.69
51 52 1.148157 CGCTGTATCTTGGCTGACGG 61.148 60.000 0.00 0.00 0.00 4.79
52 53 1.756375 GCGCTGTATCTTGGCTGACG 61.756 60.000 0.00 0.00 0.00 4.35
53 54 0.460987 AGCGCTGTATCTTGGCTGAC 60.461 55.000 10.39 0.00 31.74 3.51
54 55 0.179100 GAGCGCTGTATCTTGGCTGA 60.179 55.000 18.48 0.00 33.40 4.26
55 56 1.156645 GGAGCGCTGTATCTTGGCTG 61.157 60.000 18.48 0.00 33.40 4.85
56 57 1.144936 GGAGCGCTGTATCTTGGCT 59.855 57.895 18.48 0.00 36.51 4.75
57 58 0.744414 TTGGAGCGCTGTATCTTGGC 60.744 55.000 18.48 0.00 0.00 4.52
58 59 1.009829 GTTGGAGCGCTGTATCTTGG 58.990 55.000 18.48 0.00 0.00 3.61
59 60 1.009829 GGTTGGAGCGCTGTATCTTG 58.990 55.000 18.48 0.00 0.00 3.02
60 61 0.613260 TGGTTGGAGCGCTGTATCTT 59.387 50.000 18.48 0.00 0.00 2.40
61 62 0.108138 GTGGTTGGAGCGCTGTATCT 60.108 55.000 18.48 0.00 0.00 1.98
62 63 0.108138 AGTGGTTGGAGCGCTGTATC 60.108 55.000 18.48 0.00 34.85 2.24
63 64 0.391661 CAGTGGTTGGAGCGCTGTAT 60.392 55.000 18.48 0.00 45.92 2.29
64 65 1.005037 CAGTGGTTGGAGCGCTGTA 60.005 57.895 18.48 0.00 45.92 2.74
65 66 2.281070 CAGTGGTTGGAGCGCTGT 60.281 61.111 18.48 0.00 45.92 4.40
74 75 2.636647 AAAAATTGGCCCAGTGGTTG 57.363 45.000 8.74 0.00 0.00 3.77
96 97 9.461312 TTGTAGTGATAGCATGGAAAATTTAGT 57.539 29.630 0.00 0.00 0.00 2.24
113 114 9.851686 TGGCAGATATAGAAATTTTGTAGTGAT 57.148 29.630 0.00 0.00 0.00 3.06
114 115 9.851686 ATGGCAGATATAGAAATTTTGTAGTGA 57.148 29.630 0.00 0.00 0.00 3.41
124 125 5.074804 TGCAAGCATGGCAGATATAGAAAT 58.925 37.500 0.00 0.00 42.69 2.17
222 223 1.269448 AGTTTGGCTGCGTAAATGTGG 59.731 47.619 4.43 0.00 0.00 4.17
232 233 9.023967 CACATAGAAATATTTTAGTTTGGCTGC 57.976 33.333 1.43 0.00 0.00 5.25
258 259 3.005791 ACTTTTCCTACAAGCATGGCAAC 59.994 43.478 0.00 0.00 0.00 4.17
266 267 4.630069 TCGCTAATCACTTTTCCTACAAGC 59.370 41.667 0.00 0.00 0.00 4.01
283 284 4.032900 TGCGCAAATTTTGTTTTTCGCTAA 59.967 33.333 22.42 8.74 41.57 3.09
284 285 3.551890 TGCGCAAATTTTGTTTTTCGCTA 59.448 34.783 22.42 12.23 41.57 4.26
331 332 7.869429 ACAAATTTTCTATGCTCCACTTGAAAG 59.131 33.333 0.00 0.00 0.00 2.62
336 337 8.409358 AAGTACAAATTTTCTATGCTCCACTT 57.591 30.769 0.00 0.00 0.00 3.16
451 452 4.549458 ACAAGAAATTTCAACATGGCGAG 58.451 39.130 19.99 0.72 0.00 5.03
477 478 1.001378 GCCCACGAATTGCCATGATAC 60.001 52.381 0.00 0.00 0.00 2.24
488 489 1.409661 GGGGACAAATAGCCCACGAAT 60.410 52.381 0.00 0.00 46.57 3.34
495 496 5.995565 AAAAACTAAGGGGACAAATAGCC 57.004 39.130 0.00 0.00 0.00 3.93
552 553 3.003482 ACAACACTATTACCGCGCAAAAA 59.997 39.130 8.75 0.00 0.00 1.94
553 554 2.548904 ACAACACTATTACCGCGCAAAA 59.451 40.909 8.75 0.00 0.00 2.44
554 555 2.144730 ACAACACTATTACCGCGCAAA 58.855 42.857 8.75 0.00 0.00 3.68
555 556 1.798283 ACAACACTATTACCGCGCAA 58.202 45.000 8.75 0.00 0.00 4.85
556 557 1.727880 GAACAACACTATTACCGCGCA 59.272 47.619 8.75 0.00 0.00 6.09
557 558 1.727880 TGAACAACACTATTACCGCGC 59.272 47.619 0.00 0.00 0.00 6.86
558 559 3.615056 TGATGAACAACACTATTACCGCG 59.385 43.478 0.00 0.00 0.00 6.46
559 560 5.501715 CATGATGAACAACACTATTACCGC 58.498 41.667 0.00 0.00 0.00 5.68
560 561 5.504010 GCCATGATGAACAACACTATTACCG 60.504 44.000 0.00 0.00 0.00 4.02
561 562 5.356751 TGCCATGATGAACAACACTATTACC 59.643 40.000 0.00 0.00 0.00 2.85
562 563 6.435430 TGCCATGATGAACAACACTATTAC 57.565 37.500 0.00 0.00 0.00 1.89
563 564 7.459795 TTTGCCATGATGAACAACACTATTA 57.540 32.000 0.00 0.00 0.00 0.98
564 565 5.981088 TTGCCATGATGAACAACACTATT 57.019 34.783 0.00 0.00 0.00 1.73
565 566 5.981088 TTTGCCATGATGAACAACACTAT 57.019 34.783 0.00 0.00 0.00 2.12
664 665 3.972502 GCGTCACGTGCTAAAAGAAAAAT 59.027 39.130 11.67 0.00 0.00 1.82
668 669 1.259507 GTGCGTCACGTGCTAAAAGAA 59.740 47.619 11.67 0.00 0.00 2.52
669 670 0.856641 GTGCGTCACGTGCTAAAAGA 59.143 50.000 11.67 0.00 0.00 2.52
670 671 0.859232 AGTGCGTCACGTGCTAAAAG 59.141 50.000 11.67 0.00 39.64 2.27
672 673 0.249114 TGAGTGCGTCACGTGCTAAA 60.249 50.000 11.67 0.00 39.64 1.85
675 676 1.734477 GATGAGTGCGTCACGTGCT 60.734 57.895 11.67 0.70 38.28 4.40
676 677 2.730672 GGATGAGTGCGTCACGTGC 61.731 63.158 11.67 5.23 38.28 5.34
678 679 1.372997 GTGGATGAGTGCGTCACGT 60.373 57.895 0.00 0.00 38.28 4.49
710 820 2.115911 CCTCTACTCGCTCGGCACT 61.116 63.158 0.00 0.00 0.00 4.40
711 821 2.409651 CCTCTACTCGCTCGGCAC 59.590 66.667 0.00 0.00 0.00 5.01
712 822 3.518998 GCCTCTACTCGCTCGGCA 61.519 66.667 0.00 0.00 40.41 5.69
713 823 2.851071 ATGCCTCTACTCGCTCGGC 61.851 63.158 0.00 0.00 41.06 5.54
714 824 1.007964 CATGCCTCTACTCGCTCGG 60.008 63.158 0.00 0.00 0.00 4.63
715 825 0.317436 GACATGCCTCTACTCGCTCG 60.317 60.000 0.00 0.00 0.00 5.03
716 826 0.031449 GGACATGCCTCTACTCGCTC 59.969 60.000 0.00 0.00 0.00 5.03
717 827 0.396417 AGGACATGCCTCTACTCGCT 60.396 55.000 3.16 0.00 46.97 4.93
718 828 2.119886 AGGACATGCCTCTACTCGC 58.880 57.895 3.16 0.00 46.97 5.03
774 884 3.004419 TCGTCGTCTGAATTGTCTTGTCT 59.996 43.478 0.00 0.00 0.00 3.41
775 885 3.119792 GTCGTCGTCTGAATTGTCTTGTC 59.880 47.826 0.00 0.00 0.00 3.18
776 886 3.050619 GTCGTCGTCTGAATTGTCTTGT 58.949 45.455 0.00 0.00 0.00 3.16
777 887 3.309388 AGTCGTCGTCTGAATTGTCTTG 58.691 45.455 0.00 0.00 0.00 3.02
778 888 3.644884 AGTCGTCGTCTGAATTGTCTT 57.355 42.857 0.00 0.00 0.00 3.01
839 949 3.144506 CATGAGACTTGGTGCTTTGACT 58.855 45.455 0.00 0.00 0.00 3.41
850 960 2.251040 CGTCGTACACCATGAGACTTG 58.749 52.381 0.00 0.00 0.00 3.16
855 965 1.719246 CAACACGTCGTACACCATGAG 59.281 52.381 0.00 0.00 0.00 2.90
872 982 3.413327 GAGAAAGAAGGGAAGGTCCAAC 58.587 50.000 0.00 0.00 38.64 3.77
882 992 2.115427 GAGGGAGAGGAGAAAGAAGGG 58.885 57.143 0.00 0.00 0.00 3.95
899 1017 4.763793 CCTTGATTTATACAGCATGGGAGG 59.236 45.833 0.00 0.00 43.62 4.30
902 1020 3.828451 CCCCTTGATTTATACAGCATGGG 59.172 47.826 17.21 17.21 43.62 4.00
903 1021 3.256631 GCCCCTTGATTTATACAGCATGG 59.743 47.826 2.82 2.82 43.62 3.66
909 1027 2.424234 GCCCTGCCCCTTGATTTATACA 60.424 50.000 0.00 0.00 0.00 2.29
923 1041 2.044946 AATTCTCACGGCCCTGCC 60.045 61.111 0.00 0.00 46.75 4.85
926 1044 2.584608 CGGAATTCTCACGGCCCT 59.415 61.111 5.23 0.00 0.00 5.19
954 1072 4.741239 GGTGCTCCCTCCCCTCCA 62.741 72.222 0.00 0.00 0.00 3.86
964 1082 0.531532 CTGATGGATGACGGTGCTCC 60.532 60.000 0.00 0.00 0.00 4.70
965 1083 1.156645 GCTGATGGATGACGGTGCTC 61.157 60.000 0.00 0.00 0.00 4.26
966 1084 1.153289 GCTGATGGATGACGGTGCT 60.153 57.895 0.00 0.00 0.00 4.40
967 1085 1.434622 CTGCTGATGGATGACGGTGC 61.435 60.000 0.00 0.00 0.00 5.01
970 1088 0.249784 CCTCTGCTGATGGATGACGG 60.250 60.000 0.00 0.00 0.00 4.79
989 1107 3.270839 GCGCCATGCTCTGCTCTC 61.271 66.667 0.00 0.00 41.73 3.20
1109 1228 1.527433 GCCCTTGTGCTCCTTGGAAC 61.527 60.000 0.00 0.00 0.00 3.62
1155 1274 1.171308 CAAGCTGAGGATTGGGTGTG 58.829 55.000 0.00 0.00 35.46 3.82
1175 1295 2.751806 GGGATTTCTCCAAACTCTGCTG 59.248 50.000 0.00 0.00 44.08 4.41
1184 1304 5.538433 CACCAAAACTTAGGGATTTCTCCAA 59.462 40.000 0.00 0.00 44.08 3.53
1185 1305 5.076873 CACCAAAACTTAGGGATTTCTCCA 58.923 41.667 0.00 0.00 44.08 3.86
1186 1306 4.082190 GCACCAAAACTTAGGGATTTCTCC 60.082 45.833 0.00 0.00 41.26 3.71
1187 1307 4.522789 TGCACCAAAACTTAGGGATTTCTC 59.477 41.667 0.00 0.00 0.00 2.87
1188 1308 4.479158 TGCACCAAAACTTAGGGATTTCT 58.521 39.130 0.00 0.00 0.00 2.52
1189 1309 4.864704 TGCACCAAAACTTAGGGATTTC 57.135 40.909 0.00 0.00 0.00 2.17
1190 1310 6.252995 TCTATGCACCAAAACTTAGGGATTT 58.747 36.000 0.00 0.00 0.00 2.17
1191 1311 5.826643 TCTATGCACCAAAACTTAGGGATT 58.173 37.500 0.00 0.00 0.00 3.01
1192 1312 5.450818 TCTATGCACCAAAACTTAGGGAT 57.549 39.130 0.00 0.00 0.00 3.85
1193 1313 4.919774 TCTATGCACCAAAACTTAGGGA 57.080 40.909 0.00 0.00 0.00 4.20
1194 1314 5.010282 AGTTCTATGCACCAAAACTTAGGG 58.990 41.667 0.00 0.00 0.00 3.53
1195 1315 6.093633 GGTAGTTCTATGCACCAAAACTTAGG 59.906 42.308 9.90 0.00 32.71 2.69
1196 1316 6.183360 CGGTAGTTCTATGCACCAAAACTTAG 60.183 42.308 9.90 0.00 32.71 2.18
1207 1327 1.038681 TCCGGCGGTAGTTCTATGCA 61.039 55.000 27.32 0.00 0.00 3.96
1208 1328 0.317479 ATCCGGCGGTAGTTCTATGC 59.683 55.000 27.32 0.00 0.00 3.14
1221 1349 1.311859 TGAATCAATCAGCATCCGGC 58.688 50.000 0.00 0.00 45.30 6.13
1228 1356 6.374565 AAGCAGAGTTATGAATCAATCAGC 57.625 37.500 0.00 0.00 42.53 4.26
1229 1357 8.675504 AGAAAAGCAGAGTTATGAATCAATCAG 58.324 33.333 0.00 0.00 42.53 2.90
1230 1358 8.571461 AGAAAAGCAGAGTTATGAATCAATCA 57.429 30.769 0.00 0.00 43.67 2.57
1347 1477 8.568794 TGATCTCAAAATCAGTACGGAGTATAG 58.431 37.037 1.40 0.00 36.66 1.31
1349 1479 7.203910 GTGATCTCAAAATCAGTACGGAGTAT 58.796 38.462 1.40 0.00 37.97 2.12
1351 1481 5.411781 GTGATCTCAAAATCAGTACGGAGT 58.588 41.667 1.40 0.00 39.56 3.85
1352 1482 4.500837 CGTGATCTCAAAATCAGTACGGAG 59.499 45.833 1.40 0.00 36.36 4.63
1354 1484 3.551890 CCGTGATCTCAAAATCAGTACGG 59.448 47.826 0.00 0.00 36.85 4.02
1356 1486 6.910536 ATTCCGTGATCTCAAAATCAGTAC 57.089 37.500 0.00 0.00 36.36 2.73
1358 1488 9.784531 ATATAATTCCGTGATCTCAAAATCAGT 57.215 29.630 0.00 0.00 36.36 3.41
1365 1495 9.317936 GATGCATATATAATTCCGTGATCTCAA 57.682 33.333 0.00 0.00 0.00 3.02
1375 1505 8.200792 AGAAGACGGAGATGCATATATAATTCC 58.799 37.037 0.00 0.00 0.00 3.01
1393 1523 1.803943 CGGGACTCTGAGAAGACGG 59.196 63.158 12.44 0.00 0.00 4.79
1590 1723 2.655685 GATCTTCTCGTCGGGCGC 60.656 66.667 0.00 0.00 41.07 6.53
1724 1857 1.204704 CCCATGAAGTAGTGCGTCTCA 59.795 52.381 0.00 0.00 0.00 3.27
1796 1929 1.153939 CCTGTCGAACAGCTCCTCG 60.154 63.158 7.51 7.51 44.63 4.63
1811 1944 4.697756 TTCTTGACGGCGGGCCTG 62.698 66.667 13.24 7.41 0.00 4.85
1883 2038 0.037590 AATGTAACCTGGCAGGCGAA 59.962 50.000 33.04 15.91 39.63 4.70
1891 2046 5.097742 TCTCACCACATAATGTAACCTGG 57.902 43.478 0.00 0.00 0.00 4.45
1919 2084 2.108250 TCTTATTGCATAGGGCCCCTTC 59.892 50.000 21.43 6.02 43.89 3.46
1928 2094 5.882557 AGTCAACCTTGGTCTTATTGCATAG 59.117 40.000 0.00 0.00 0.00 2.23
1996 2176 8.436200 GTTATCAAATAGTAGCGGCAAATCTAG 58.564 37.037 1.45 0.00 0.00 2.43
2001 2181 6.373216 ACAAGTTATCAAATAGTAGCGGCAAA 59.627 34.615 1.45 0.00 0.00 3.68
2002 2182 5.878116 ACAAGTTATCAAATAGTAGCGGCAA 59.122 36.000 1.45 0.00 0.00 4.52
2004 2184 5.522460 TGACAAGTTATCAAATAGTAGCGGC 59.478 40.000 0.00 0.00 0.00 6.53
2006 2186 7.111139 CGTTGACAAGTTATCAAATAGTAGCG 58.889 38.462 0.00 0.00 37.80 4.26
2011 2191 6.831769 AGCACGTTGACAAGTTATCAAATAG 58.168 36.000 0.00 0.00 37.80 1.73
2012 2192 6.649141 AGAGCACGTTGACAAGTTATCAAATA 59.351 34.615 0.00 0.00 37.80 1.40
2016 2196 3.740832 CAGAGCACGTTGACAAGTTATCA 59.259 43.478 0.00 0.00 0.00 2.15
2017 2197 3.741344 ACAGAGCACGTTGACAAGTTATC 59.259 43.478 0.00 0.00 0.00 1.75
2019 2199 3.173668 ACAGAGCACGTTGACAAGTTA 57.826 42.857 0.00 0.00 0.00 2.24
2020 2200 2.024176 ACAGAGCACGTTGACAAGTT 57.976 45.000 0.00 0.00 0.00 2.66
2022 2202 3.063997 AGAAAACAGAGCACGTTGACAAG 59.936 43.478 0.00 0.00 0.00 3.16
2023 2203 3.006940 AGAAAACAGAGCACGTTGACAA 58.993 40.909 0.00 0.00 0.00 3.18
2024 2204 2.351418 CAGAAAACAGAGCACGTTGACA 59.649 45.455 0.00 0.00 0.00 3.58
2025 2205 2.607635 TCAGAAAACAGAGCACGTTGAC 59.392 45.455 0.00 0.00 0.00 3.18
2026 2206 2.866156 CTCAGAAAACAGAGCACGTTGA 59.134 45.455 0.00 0.00 0.00 3.18
2027 2207 2.609459 ACTCAGAAAACAGAGCACGTTG 59.391 45.455 0.00 0.00 35.28 4.10
2028 2208 2.906354 ACTCAGAAAACAGAGCACGTT 58.094 42.857 0.00 0.00 35.28 3.99
2029 2209 2.604046 ACTCAGAAAACAGAGCACGT 57.396 45.000 0.00 0.00 35.28 4.49
2134 2406 0.462759 TCGTTGTGTCATGTGTGCCA 60.463 50.000 0.00 0.00 0.00 4.92
2150 2422 4.908601 TCCCATTGATGCCTATTATCGT 57.091 40.909 0.00 0.00 0.00 3.73
2157 2429 3.620488 GTCTTGTTCCCATTGATGCCTA 58.380 45.455 0.00 0.00 0.00 3.93
2186 2533 4.268884 CAGTCGAAATAAAGAGCTACTGGC 59.731 45.833 0.00 0.00 42.19 4.85
2256 2606 2.670148 GGCGAGGAGGGTTGGTCAT 61.670 63.158 0.00 0.00 0.00 3.06
2299 2649 4.213270 TCCTGTGTGACACGATTTGATTTC 59.787 41.667 11.51 0.00 37.14 2.17
2374 2728 2.577112 CCGTGTAGTGAGCGAGCG 60.577 66.667 0.00 0.00 0.00 5.03
2426 2787 3.868985 ACGGCGGGTCTGGTGTTT 61.869 61.111 13.24 0.00 0.00 2.83
2692 3056 1.146263 ATGTTGGGCTAGCTACGCC 59.854 57.895 15.72 19.98 46.83 5.68
2693 3057 1.776034 GCATGTTGGGCTAGCTACGC 61.776 60.000 15.72 6.93 0.00 4.42
2694 3058 1.160329 GGCATGTTGGGCTAGCTACG 61.160 60.000 15.72 1.04 0.00 3.51
2695 3059 0.107214 TGGCATGTTGGGCTAGCTAC 60.107 55.000 15.72 10.98 0.00 3.58
2696 3060 0.181114 CTGGCATGTTGGGCTAGCTA 59.819 55.000 15.72 0.96 33.06 3.32
2697 3061 1.077212 CTGGCATGTTGGGCTAGCT 60.077 57.895 15.72 0.00 33.06 3.32
2698 3062 2.123428 CCTGGCATGTTGGGCTAGC 61.123 63.158 6.04 6.04 38.40 3.42
2699 3063 1.454479 CCCTGGCATGTTGGGCTAG 60.454 63.158 6.83 0.00 39.31 3.42
2700 3064 2.237965 ACCCTGGCATGTTGGGCTA 61.238 57.895 16.24 0.00 44.56 3.93
2701 3065 3.593680 ACCCTGGCATGTTGGGCT 61.594 61.111 16.24 5.04 44.56 5.19
2702 3066 3.384532 CACCCTGGCATGTTGGGC 61.385 66.667 16.24 0.00 44.56 5.36
2703 3067 2.681064 CCACCCTGGCATGTTGGG 60.681 66.667 15.17 15.17 46.07 4.12
2704 3068 1.978617 GACCACCCTGGCATGTTGG 60.979 63.158 4.83 4.83 42.67 3.77
2705 3069 1.978617 GGACCACCCTGGCATGTTG 60.979 63.158 0.00 0.00 42.67 3.33
2706 3070 2.440599 GGACCACCCTGGCATGTT 59.559 61.111 0.00 0.00 42.67 2.71
2707 3071 2.858476 TGGACCACCCTGGCATGT 60.858 61.111 0.00 0.00 42.67 3.21
2708 3072 2.361610 GTGGACCACCCTGGCATG 60.362 66.667 14.16 0.00 42.67 4.06
2718 3082 4.529769 TGAATATTTTGCATTGGTGGACCA 59.470 37.500 0.00 0.00 45.94 4.02
2719 3083 4.869861 GTGAATATTTTGCATTGGTGGACC 59.130 41.667 0.00 0.00 0.00 4.46
2720 3084 5.477510 TGTGAATATTTTGCATTGGTGGAC 58.522 37.500 0.00 0.00 0.00 4.02
2721 3085 5.735285 TGTGAATATTTTGCATTGGTGGA 57.265 34.783 0.00 0.00 0.00 4.02
2722 3086 8.489990 TTTATGTGAATATTTTGCATTGGTGG 57.510 30.769 0.00 0.00 0.00 4.61
2787 3151 9.321500 ACCCTGGAATTTCCCCATAATATATAT 57.678 33.333 12.90 0.00 35.03 0.86
2788 3152 8.565239 CACCCTGGAATTTCCCCATAATATATA 58.435 37.037 12.90 0.00 35.03 0.86
2789 3153 7.421684 CACCCTGGAATTTCCCCATAATATAT 58.578 38.462 12.90 0.00 35.03 0.86
2790 3154 6.240733 CCACCCTGGAATTTCCCCATAATATA 60.241 42.308 12.90 0.00 40.96 0.86
2791 3155 5.461018 CCACCCTGGAATTTCCCCATAATAT 60.461 44.000 12.90 0.00 40.96 1.28
2792 3156 4.140805 CCACCCTGGAATTTCCCCATAATA 60.141 45.833 12.90 0.00 40.96 0.98
2793 3157 3.375207 CCACCCTGGAATTTCCCCATAAT 60.375 47.826 12.90 0.00 40.96 1.28
2794 3158 2.023501 CCACCCTGGAATTTCCCCATAA 60.024 50.000 12.90 0.00 40.96 1.90
2795 3159 1.573376 CCACCCTGGAATTTCCCCATA 59.427 52.381 12.90 0.00 40.96 2.74
2796 3160 0.339510 CCACCCTGGAATTTCCCCAT 59.660 55.000 12.90 0.00 40.96 4.00
2797 3161 1.077298 ACCACCCTGGAATTTCCCCA 61.077 55.000 12.90 0.00 40.96 4.96
2798 3162 0.324368 GACCACCCTGGAATTTCCCC 60.324 60.000 12.90 0.00 40.96 4.81
2799 3163 0.324368 GGACCACCCTGGAATTTCCC 60.324 60.000 12.90 0.00 40.96 3.97
2800 3164 0.407918 TGGACCACCCTGGAATTTCC 59.592 55.000 8.59 8.59 40.96 3.13
2801 3165 2.102578 CATGGACCACCCTGGAATTTC 58.897 52.381 0.00 0.00 40.96 2.17
2802 3166 2.236489 CATGGACCACCCTGGAATTT 57.764 50.000 0.00 0.00 40.96 1.82
2822 3186 3.647771 GGGGTGGACAGGGTGGTC 61.648 72.222 0.00 0.00 37.06 4.02
2824 3188 3.572715 TAGGGGGTGGACAGGGTGG 62.573 68.421 0.00 0.00 0.00 4.61
2825 3189 1.995626 CTAGGGGGTGGACAGGGTG 60.996 68.421 0.00 0.00 0.00 4.61
2826 3190 1.537478 ATCTAGGGGGTGGACAGGGT 61.537 60.000 0.00 0.00 0.00 4.34
2827 3191 0.566176 TATCTAGGGGGTGGACAGGG 59.434 60.000 0.00 0.00 0.00 4.45
2828 3192 1.718280 GTATCTAGGGGGTGGACAGG 58.282 60.000 0.00 0.00 0.00 4.00
2829 3193 1.329256 CGTATCTAGGGGGTGGACAG 58.671 60.000 0.00 0.00 0.00 3.51
2830 3194 0.757935 GCGTATCTAGGGGGTGGACA 60.758 60.000 0.00 0.00 0.00 4.02
2831 3195 1.470165 GGCGTATCTAGGGGGTGGAC 61.470 65.000 0.00 0.00 0.00 4.02
2832 3196 1.152398 GGCGTATCTAGGGGGTGGA 60.152 63.158 0.00 0.00 0.00 4.02
2833 3197 1.458777 TGGCGTATCTAGGGGGTGG 60.459 63.158 0.00 0.00 0.00 4.61
2834 3198 0.759436 AGTGGCGTATCTAGGGGGTG 60.759 60.000 0.00 0.00 0.00 4.61
2835 3199 0.759436 CAGTGGCGTATCTAGGGGGT 60.759 60.000 0.00 0.00 0.00 4.95
2836 3200 2.050269 CAGTGGCGTATCTAGGGGG 58.950 63.158 0.00 0.00 0.00 5.40
2837 3201 1.367840 GCAGTGGCGTATCTAGGGG 59.632 63.158 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.