Multiple sequence alignment - TraesCS2B01G532000

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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 TraesCS2B01G532000 chr2B 100.000 3504 0 0 1 3504 727655470 727651967 0.000000e+00 6471.0
1 TraesCS2B01G532000 chr2B 88.563 1399 124 18 1110 2506 727681300 727679936 0.000000e+00 1664.0
2 TraesCS2B01G532000 chr2B 81.110 847 128 18 924 1754 763805002 763805832 0.000000e+00 649.0
3 TraesCS2B01G532000 chr2B 76.895 541 105 15 1749 2279 727241337 727241867 4.430000e-74 289.0
4 TraesCS2B01G532000 chr2B 75.000 328 49 19 739 1065 727681677 727681382 1.710000e-23 121.0
5 TraesCS2B01G532000 chr2D 91.523 2489 145 23 215 2669 598747852 598745396 0.000000e+00 3367.0
6 TraesCS2B01G532000 chr2D 89.107 1478 119 20 1087 2556 598803288 598801845 0.000000e+00 1799.0
7 TraesCS2B01G532000 chr2D 87.162 148 14 3 694 836 598803794 598803647 2.800000e-36 163.0
8 TraesCS2B01G532000 chr2A 91.182 1962 116 30 737 2672 733030067 733028137 0.000000e+00 2612.0
9 TraesCS2B01G532000 chr2A 88.413 1424 120 25 1087 2506 733041081 733039699 0.000000e+00 1674.0
10 TraesCS2B01G532000 chr2A 89.655 551 29 7 215 742 733032326 733031781 0.000000e+00 676.0
11 TraesCS2B01G532000 chr2A 76.770 551 106 16 1740 2279 732987801 732988340 4.430000e-74 289.0
12 TraesCS2B01G532000 chr2A 86.139 202 6 10 3275 3474 733028145 733027964 7.670000e-47 198.0
13 TraesCS2B01G532000 chr2A 87.162 148 14 3 694 836 733041640 733041493 2.800000e-36 163.0
14 TraesCS2B01G532000 chr2A 97.778 90 1 1 42 131 499577132 499577220 1.680000e-33 154.0
15 TraesCS2B01G532000 chr2A 100.000 36 0 0 3469 3504 30047099 30047064 2.260000e-07 67.6
16 TraesCS2B01G532000 chr6D 92.881 604 38 5 2674 3275 32910793 32910193 0.000000e+00 872.0
17 TraesCS2B01G532000 chr6D 90.879 603 47 4 2674 3275 396541552 396542147 0.000000e+00 802.0
18 TraesCS2B01G532000 chr7D 92.384 604 41 3 2674 3275 63008625 63008025 0.000000e+00 856.0
19 TraesCS2B01G532000 chr7D 86.813 182 16 5 240 420 426305346 426305172 2.760000e-46 196.0
20 TraesCS2B01G532000 chr7D 88.312 154 17 1 237 389 563910627 563910780 2.150000e-42 183.0
21 TraesCS2B01G532000 chr7D 100.000 37 0 0 3468 3504 551584153 551584189 6.280000e-08 69.4
22 TraesCS2B01G532000 chr5D 92.027 602 42 4 2675 3275 313080650 313080054 0.000000e+00 841.0
23 TraesCS2B01G532000 chr5D 85.443 158 18 2 237 389 401838124 401838281 3.620000e-35 159.0
24 TraesCS2B01G532000 chr1D 91.074 605 46 4 2674 3275 88279963 88280562 0.000000e+00 811.0
25 TraesCS2B01G532000 chr1D 89.011 182 19 1 240 420 287226570 287226389 1.270000e-54 224.0
26 TraesCS2B01G532000 chr3B 90.909 605 51 2 2672 3275 572800462 572801063 0.000000e+00 809.0
27 TraesCS2B01G532000 chr3B 100.000 86 0 0 42 127 440124960 440125045 3.620000e-35 159.0
28 TraesCS2B01G532000 chr5B 90.713 603 52 2 2674 3275 381750042 381749443 0.000000e+00 800.0
29 TraesCS2B01G532000 chr5B 100.000 88 0 0 42 129 655846764 655846851 2.800000e-36 163.0
30 TraesCS2B01G532000 chr5B 100.000 86 0 0 42 127 336100323 336100238 3.620000e-35 159.0
31 TraesCS2B01G532000 chr5B 100.000 37 0 0 3468 3504 48852315 48852279 6.280000e-08 69.4
32 TraesCS2B01G532000 chr5B 97.059 34 1 0 2000 2033 417153665 417153698 1.360000e-04 58.4
33 TraesCS2B01G532000 chr5A 90.150 599 54 3 2680 3275 334342482 334341886 0.000000e+00 774.0
34 TraesCS2B01G532000 chr3A 89.786 607 51 10 2674 3275 658498945 658498345 0.000000e+00 767.0
35 TraesCS2B01G532000 chr3A 97.436 39 1 0 3466 3504 442902133 442902171 2.260000e-07 67.6
36 TraesCS2B01G532000 chr3D 88.649 185 20 1 237 420 557023810 557023994 1.270000e-54 224.0
37 TraesCS2B01G532000 chr3D 95.455 44 2 0 3461 3504 332149102 332149059 1.740000e-08 71.3
38 TraesCS2B01G532000 chr7A 96.842 95 1 1 42 134 75054370 75054276 1.300000e-34 158.0
39 TraesCS2B01G532000 chr7A 97.619 42 0 1 3464 3504 220405120 220405161 1.740000e-08 71.3
40 TraesCS2B01G532000 chr4A 100.000 85 0 0 42 126 16024432 16024348 1.300000e-34 158.0
41 TraesCS2B01G532000 chrUn 100.000 82 0 0 42 123 223389892 223389811 6.060000e-33 152.0
42 TraesCS2B01G532000 chrUn 89.362 47 4 1 2000 2046 122077656 122077701 1.360000e-04 58.4
43 TraesCS2B01G532000 chr6B 95.789 95 3 1 42 136 389440571 389440664 6.060000e-33 152.0
44 TraesCS2B01G532000 chr6B 94.737 38 0 1 3469 3504 258855876 258855913 1.360000e-04 58.4
45 TraesCS2B01G532000 chr6A 92.661 109 2 6 42 148 218752045 218751941 6.060000e-33 152.0
46 TraesCS2B01G532000 chr6A 75.649 308 59 15 1358 1654 565108758 565109060 4.720000e-29 139.0
47 TraesCS2B01G532000 chr6A 75.325 308 60 15 1358 1654 565057707 565058009 2.190000e-27 134.0
48 TraesCS2B01G532000 chr7B 91.489 47 4 0 3458 3504 13708684 13708730 8.120000e-07 65.8
49 TraesCS2B01G532000 chr7B 97.222 36 1 0 3469 3504 729388424 729388459 1.050000e-05 62.1


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 TraesCS2B01G532000 chr2B 727651967 727655470 3503 True 6471.0 6471 100.0000 1 3504 1 chr2B.!!$R1 3503
1 TraesCS2B01G532000 chr2B 727679936 727681677 1741 True 892.5 1664 81.7815 739 2506 2 chr2B.!!$R2 1767
2 TraesCS2B01G532000 chr2B 763805002 763805832 830 False 649.0 649 81.1100 924 1754 1 chr2B.!!$F2 830
3 TraesCS2B01G532000 chr2B 727241337 727241867 530 False 289.0 289 76.8950 1749 2279 1 chr2B.!!$F1 530
4 TraesCS2B01G532000 chr2D 598745396 598747852 2456 True 3367.0 3367 91.5230 215 2669 1 chr2D.!!$R1 2454
5 TraesCS2B01G532000 chr2D 598801845 598803794 1949 True 981.0 1799 88.1345 694 2556 2 chr2D.!!$R2 1862
6 TraesCS2B01G532000 chr2A 733027964 733032326 4362 True 1162.0 2612 88.9920 215 3474 3 chr2A.!!$R2 3259
7 TraesCS2B01G532000 chr2A 733039699 733041640 1941 True 918.5 1674 87.7875 694 2506 2 chr2A.!!$R3 1812
8 TraesCS2B01G532000 chr2A 732987801 732988340 539 False 289.0 289 76.7700 1740 2279 1 chr2A.!!$F2 539
9 TraesCS2B01G532000 chr6D 32910193 32910793 600 True 872.0 872 92.8810 2674 3275 1 chr6D.!!$R1 601
10 TraesCS2B01G532000 chr6D 396541552 396542147 595 False 802.0 802 90.8790 2674 3275 1 chr6D.!!$F1 601
11 TraesCS2B01G532000 chr7D 63008025 63008625 600 True 856.0 856 92.3840 2674 3275 1 chr7D.!!$R1 601
12 TraesCS2B01G532000 chr5D 313080054 313080650 596 True 841.0 841 92.0270 2675 3275 1 chr5D.!!$R1 600
13 TraesCS2B01G532000 chr1D 88279963 88280562 599 False 811.0 811 91.0740 2674 3275 1 chr1D.!!$F1 601
14 TraesCS2B01G532000 chr3B 572800462 572801063 601 False 809.0 809 90.9090 2672 3275 1 chr3B.!!$F2 603
15 TraesCS2B01G532000 chr5B 381749443 381750042 599 True 800.0 800 90.7130 2674 3275 1 chr5B.!!$R3 601
16 TraesCS2B01G532000 chr5A 334341886 334342482 596 True 774.0 774 90.1500 2680 3275 1 chr5A.!!$R1 595
17 TraesCS2B01G532000 chr3A 658498345 658498945 600 True 767.0 767 89.7860 2674 3275 1 chr3A.!!$R1 601

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
110 111 0.032615 TGTGCTGGTTCCCCAAAACT 60.033 50.0 0.0 0.0 41.27 2.66 F
187 188 0.038892 GTGAGGTTCGTCCGTGCTAA 60.039 55.0 0.0 0.0 41.99 3.09 F
822 2578 0.883153 TTACAAGTCCGAGCACGCTA 59.117 50.0 0.0 0.0 38.29 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1041 2934 0.324614 TGTGAGGTGCAGGTGTATGG 59.675 55.000 0.0 0.0 0.00 2.74 R
1522 3471 1.299648 CGCCATGAACCCTTCCTGA 59.700 57.895 0.0 0.0 0.00 3.86 R
2677 4683 0.664767 GAGCTCGACTCGTTTGCAGT 60.665 55.000 0.0 0.0 35.18 4.40 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.812577 CCAAATTTTCTGCCGACCC 57.187 52.632 0.00 0.00 0.00 4.46
19 20 0.965439 CCAAATTTTCTGCCGACCCA 59.035 50.000 0.00 0.00 0.00 4.51
20 21 1.342819 CCAAATTTTCTGCCGACCCAA 59.657 47.619 0.00 0.00 0.00 4.12
21 22 2.224161 CCAAATTTTCTGCCGACCCAAA 60.224 45.455 0.00 0.00 0.00 3.28
22 23 3.556843 CCAAATTTTCTGCCGACCCAAAT 60.557 43.478 0.00 0.00 0.00 2.32
23 24 3.592898 AATTTTCTGCCGACCCAAATC 57.407 42.857 0.00 0.00 0.00 2.17
24 25 2.286365 TTTTCTGCCGACCCAAATCT 57.714 45.000 0.00 0.00 0.00 2.40
25 26 1.533625 TTTCTGCCGACCCAAATCTG 58.466 50.000 0.00 0.00 0.00 2.90
26 27 0.400213 TTCTGCCGACCCAAATCTGT 59.600 50.000 0.00 0.00 0.00 3.41
27 28 0.400213 TCTGCCGACCCAAATCTGTT 59.600 50.000 0.00 0.00 0.00 3.16
28 29 0.523072 CTGCCGACCCAAATCTGTTG 59.477 55.000 0.00 0.00 0.00 3.33
29 30 0.179004 TGCCGACCCAAATCTGTTGT 60.179 50.000 0.00 0.00 0.00 3.32
30 31 0.240945 GCCGACCCAAATCTGTTGTG 59.759 55.000 0.00 0.00 0.00 3.33
31 32 0.881118 CCGACCCAAATCTGTTGTGG 59.119 55.000 0.00 0.00 0.00 4.17
34 35 2.744062 CCCAAATCTGTTGTGGGCA 58.256 52.632 0.99 0.00 45.42 5.36
35 36 1.269012 CCCAAATCTGTTGTGGGCAT 58.731 50.000 0.99 0.00 45.42 4.40
36 37 1.205417 CCCAAATCTGTTGTGGGCATC 59.795 52.381 0.99 0.00 45.42 3.91
37 38 1.894466 CCAAATCTGTTGTGGGCATCA 59.106 47.619 0.00 0.00 0.00 3.07
38 39 2.299582 CCAAATCTGTTGTGGGCATCAA 59.700 45.455 0.00 0.00 0.00 2.57
39 40 3.055675 CCAAATCTGTTGTGGGCATCAAT 60.056 43.478 0.00 0.00 0.00 2.57
40 41 4.178540 CAAATCTGTTGTGGGCATCAATC 58.821 43.478 0.00 0.00 0.00 2.67
41 42 2.885135 TCTGTTGTGGGCATCAATCT 57.115 45.000 0.00 0.00 0.00 2.40
42 43 3.998913 TCTGTTGTGGGCATCAATCTA 57.001 42.857 0.00 0.00 0.00 1.98
43 44 4.508551 TCTGTTGTGGGCATCAATCTAT 57.491 40.909 0.00 0.00 0.00 1.98
44 45 4.858850 TCTGTTGTGGGCATCAATCTATT 58.141 39.130 0.00 0.00 0.00 1.73
45 46 4.641541 TCTGTTGTGGGCATCAATCTATTG 59.358 41.667 0.00 0.00 39.10 1.90
46 47 4.343231 TGTTGTGGGCATCAATCTATTGT 58.657 39.130 2.80 0.00 38.84 2.71
47 48 5.504853 TGTTGTGGGCATCAATCTATTGTA 58.495 37.500 2.80 0.00 38.84 2.41
48 49 5.948758 TGTTGTGGGCATCAATCTATTGTAA 59.051 36.000 2.80 0.00 38.84 2.41
49 50 6.127758 TGTTGTGGGCATCAATCTATTGTAAC 60.128 38.462 2.80 0.00 38.84 2.50
50 51 5.504853 TGTGGGCATCAATCTATTGTAACA 58.495 37.500 2.80 0.00 38.84 2.41
51 52 5.356751 TGTGGGCATCAATCTATTGTAACAC 59.643 40.000 2.80 7.02 38.84 3.32
52 53 5.356751 GTGGGCATCAATCTATTGTAACACA 59.643 40.000 2.80 0.00 38.84 3.72
53 54 5.948758 TGGGCATCAATCTATTGTAACACAA 59.051 36.000 2.80 0.00 42.95 3.33
54 55 6.127758 TGGGCATCAATCTATTGTAACACAAC 60.128 38.462 2.80 0.00 41.40 3.32
55 56 6.265577 GGCATCAATCTATTGTAACACAACC 58.734 40.000 2.80 0.00 41.40 3.77
56 57 6.127758 GGCATCAATCTATTGTAACACAACCA 60.128 38.462 2.80 0.00 41.40 3.67
57 58 7.416664 GGCATCAATCTATTGTAACACAACCAT 60.417 37.037 2.80 0.00 41.40 3.55
58 59 7.975616 GCATCAATCTATTGTAACACAACCATT 59.024 33.333 2.80 0.00 41.40 3.16
83 84 9.744125 TTATATATAATGAGATAAGCCACCCCT 57.256 33.333 0.81 0.00 0.00 4.79
85 86 7.682787 ATATAATGAGATAAGCCACCCCTAG 57.317 40.000 0.00 0.00 0.00 3.02
86 87 3.637821 ATGAGATAAGCCACCCCTAGA 57.362 47.619 0.00 0.00 0.00 2.43
87 88 2.964209 TGAGATAAGCCACCCCTAGAG 58.036 52.381 0.00 0.00 0.00 2.43
88 89 2.252714 GAGATAAGCCACCCCTAGAGG 58.747 57.143 0.00 0.00 0.00 3.69
99 100 2.377136 CCTAGAGGGTTGTGCTGGT 58.623 57.895 0.00 0.00 0.00 4.00
100 101 0.693049 CCTAGAGGGTTGTGCTGGTT 59.307 55.000 0.00 0.00 0.00 3.67
101 102 1.339151 CCTAGAGGGTTGTGCTGGTTC 60.339 57.143 0.00 0.00 0.00 3.62
102 103 0.690762 TAGAGGGTTGTGCTGGTTCC 59.309 55.000 0.00 0.00 0.00 3.62
103 104 1.603739 GAGGGTTGTGCTGGTTCCC 60.604 63.158 0.00 0.00 38.50 3.97
104 105 2.600470 GGGTTGTGCTGGTTCCCC 60.600 66.667 0.00 0.00 32.66 4.81
105 106 2.197324 GGTTGTGCTGGTTCCCCA 59.803 61.111 0.00 0.00 38.87 4.96
106 107 1.456705 GGTTGTGCTGGTTCCCCAA 60.457 57.895 0.00 0.00 41.27 4.12
107 108 1.045911 GGTTGTGCTGGTTCCCCAAA 61.046 55.000 0.00 0.00 41.27 3.28
108 109 0.827368 GTTGTGCTGGTTCCCCAAAA 59.173 50.000 0.00 0.00 41.27 2.44
109 110 0.827368 TTGTGCTGGTTCCCCAAAAC 59.173 50.000 0.00 0.00 41.27 2.43
110 111 0.032615 TGTGCTGGTTCCCCAAAACT 60.033 50.000 0.00 0.00 41.27 2.66
111 112 1.119684 GTGCTGGTTCCCCAAAACTT 58.880 50.000 0.00 0.00 41.27 2.66
112 113 2.312390 GTGCTGGTTCCCCAAAACTTA 58.688 47.619 0.00 0.00 41.27 2.24
113 114 2.897326 GTGCTGGTTCCCCAAAACTTAT 59.103 45.455 0.00 0.00 41.27 1.73
114 115 3.323691 GTGCTGGTTCCCCAAAACTTATT 59.676 43.478 0.00 0.00 41.27 1.40
115 116 3.323403 TGCTGGTTCCCCAAAACTTATTG 59.677 43.478 0.00 0.00 41.27 1.90
116 117 3.323691 GCTGGTTCCCCAAAACTTATTGT 59.676 43.478 0.00 0.00 41.27 2.71
117 118 4.560716 GCTGGTTCCCCAAAACTTATTGTC 60.561 45.833 0.00 0.00 41.27 3.18
118 119 4.810345 TGGTTCCCCAAAACTTATTGTCT 58.190 39.130 0.00 0.00 37.98 3.41
119 120 5.212745 TGGTTCCCCAAAACTTATTGTCTT 58.787 37.500 0.00 0.00 37.98 3.01
120 121 6.374588 TGGTTCCCCAAAACTTATTGTCTTA 58.625 36.000 0.00 0.00 37.98 2.10
121 122 6.265876 TGGTTCCCCAAAACTTATTGTCTTAC 59.734 38.462 0.00 0.00 37.98 2.34
122 123 6.265876 GGTTCCCCAAAACTTATTGTCTTACA 59.734 38.462 0.00 0.00 0.00 2.41
123 124 6.887626 TCCCCAAAACTTATTGTCTTACAC 57.112 37.500 0.00 0.00 0.00 2.90
124 125 5.771165 TCCCCAAAACTTATTGTCTTACACC 59.229 40.000 0.00 0.00 0.00 4.16
125 126 5.335348 CCCCAAAACTTATTGTCTTACACCG 60.335 44.000 0.00 0.00 0.00 4.94
126 127 5.470777 CCCAAAACTTATTGTCTTACACCGA 59.529 40.000 0.00 0.00 0.00 4.69
127 128 6.150474 CCCAAAACTTATTGTCTTACACCGAT 59.850 38.462 0.00 0.00 0.00 4.18
128 129 7.241376 CCAAAACTTATTGTCTTACACCGATC 58.759 38.462 0.00 0.00 0.00 3.69
129 130 6.642683 AAACTTATTGTCTTACACCGATCG 57.357 37.500 8.51 8.51 0.00 3.69
130 131 5.320549 ACTTATTGTCTTACACCGATCGT 57.679 39.130 15.09 0.00 0.00 3.73
131 132 5.717119 ACTTATTGTCTTACACCGATCGTT 58.283 37.500 15.09 0.00 0.00 3.85
132 133 5.803967 ACTTATTGTCTTACACCGATCGTTC 59.196 40.000 15.09 0.00 0.00 3.95
133 134 3.928727 TTGTCTTACACCGATCGTTCT 57.071 42.857 15.09 0.00 0.00 3.01
134 135 3.482722 TGTCTTACACCGATCGTTCTC 57.517 47.619 15.09 0.00 0.00 2.87
135 136 2.815503 TGTCTTACACCGATCGTTCTCA 59.184 45.455 15.09 0.00 0.00 3.27
136 137 3.442625 TGTCTTACACCGATCGTTCTCAT 59.557 43.478 15.09 0.00 0.00 2.90
137 138 4.637091 TGTCTTACACCGATCGTTCTCATA 59.363 41.667 15.09 0.00 0.00 2.15
138 139 5.298527 TGTCTTACACCGATCGTTCTCATAT 59.701 40.000 15.09 0.00 0.00 1.78
139 140 6.183360 TGTCTTACACCGATCGTTCTCATATT 60.183 38.462 15.09 0.00 0.00 1.28
140 141 7.012610 TGTCTTACACCGATCGTTCTCATATTA 59.987 37.037 15.09 0.00 0.00 0.98
141 142 8.021973 GTCTTACACCGATCGTTCTCATATTAT 58.978 37.037 15.09 0.00 0.00 1.28
142 143 9.223099 TCTTACACCGATCGTTCTCATATTATA 57.777 33.333 15.09 0.00 0.00 0.98
144 145 9.999009 TTACACCGATCGTTCTCATATTATATC 57.001 33.333 15.09 0.00 0.00 1.63
145 146 8.051901 ACACCGATCGTTCTCATATTATATCA 57.948 34.615 15.09 0.00 0.00 2.15
146 147 8.687242 ACACCGATCGTTCTCATATTATATCAT 58.313 33.333 15.09 0.00 0.00 2.45
149 150 9.335891 CCGATCGTTCTCATATTATATCATAGC 57.664 37.037 15.09 0.00 0.00 2.97
150 151 9.884465 CGATCGTTCTCATATTATATCATAGCA 57.116 33.333 7.03 0.00 0.00 3.49
159 160 9.269453 TCATATTATATCATAGCAATGCTCTGC 57.731 33.333 12.53 2.72 40.44 4.26
165 166 3.812019 GCAATGCTCTGCTGCGCT 61.812 61.111 9.73 0.00 39.34 5.92
166 167 2.403987 CAATGCTCTGCTGCGCTC 59.596 61.111 9.73 0.28 35.36 5.03
167 168 2.046604 AATGCTCTGCTGCGCTCA 60.047 55.556 9.73 5.80 35.36 4.26
168 169 2.107292 AATGCTCTGCTGCGCTCAG 61.107 57.895 19.51 19.51 43.16 3.35
169 170 2.799814 AATGCTCTGCTGCGCTCAGT 62.800 55.000 22.82 7.42 42.29 3.41
170 171 3.488978 GCTCTGCTGCGCTCAGTG 61.489 66.667 22.82 21.42 42.29 3.66
171 172 2.260743 CTCTGCTGCGCTCAGTGA 59.739 61.111 22.82 3.76 42.29 3.41
172 173 1.806351 CTCTGCTGCGCTCAGTGAG 60.806 63.158 22.82 16.21 42.29 3.51
173 174 2.814341 CTGCTGCGCTCAGTGAGG 60.814 66.667 21.54 12.43 42.29 3.86
174 175 3.586461 CTGCTGCGCTCAGTGAGGT 62.586 63.158 21.54 0.00 42.29 3.85
175 176 2.358003 GCTGCGCTCAGTGAGGTT 60.358 61.111 21.54 0.00 42.29 3.50
176 177 2.386660 GCTGCGCTCAGTGAGGTTC 61.387 63.158 21.54 4.31 42.29 3.62
177 178 2.049156 TGCGCTCAGTGAGGTTCG 60.049 61.111 21.54 16.62 0.00 3.95
178 179 2.049063 GCGCTCAGTGAGGTTCGT 60.049 61.111 21.54 0.00 0.00 3.85
179 180 2.089349 GCGCTCAGTGAGGTTCGTC 61.089 63.158 21.54 9.13 0.00 4.20
180 181 1.444553 CGCTCAGTGAGGTTCGTCC 60.445 63.158 21.54 2.15 0.00 4.79
181 182 1.444553 GCTCAGTGAGGTTCGTCCG 60.445 63.158 21.54 0.00 41.99 4.79
182 183 1.957562 CTCAGTGAGGTTCGTCCGT 59.042 57.895 12.67 0.00 41.99 4.69
183 184 0.387367 CTCAGTGAGGTTCGTCCGTG 60.387 60.000 12.67 0.00 41.99 4.94
184 185 2.022129 CAGTGAGGTTCGTCCGTGC 61.022 63.158 0.00 0.00 41.99 5.34
185 186 2.201022 AGTGAGGTTCGTCCGTGCT 61.201 57.895 0.00 0.00 41.99 4.40
186 187 0.892358 AGTGAGGTTCGTCCGTGCTA 60.892 55.000 0.00 0.00 41.99 3.49
187 188 0.038892 GTGAGGTTCGTCCGTGCTAA 60.039 55.000 0.00 0.00 41.99 3.09
188 189 0.892755 TGAGGTTCGTCCGTGCTAAT 59.107 50.000 0.00 0.00 41.99 1.73
189 190 1.274167 TGAGGTTCGTCCGTGCTAATT 59.726 47.619 0.00 0.00 41.99 1.40
190 191 2.492881 TGAGGTTCGTCCGTGCTAATTA 59.507 45.455 0.00 0.00 41.99 1.40
191 192 3.056678 TGAGGTTCGTCCGTGCTAATTAA 60.057 43.478 0.00 0.00 41.99 1.40
192 193 3.518590 AGGTTCGTCCGTGCTAATTAAG 58.481 45.455 0.00 0.00 41.99 1.85
193 194 4.227777 AGGTTCGTCCGTGCTAATTAAGC 61.228 47.826 0.00 0.00 46.02 3.09
204 205 4.469625 GCTAATTAAGCGCTTTACCCTC 57.530 45.455 30.13 10.41 42.53 4.30
205 206 3.875134 GCTAATTAAGCGCTTTACCCTCA 59.125 43.478 30.13 4.97 42.53 3.86
206 207 4.515567 GCTAATTAAGCGCTTTACCCTCAT 59.484 41.667 30.13 2.19 42.53 2.90
207 208 5.008712 GCTAATTAAGCGCTTTACCCTCATT 59.991 40.000 30.13 11.53 42.53 2.57
208 209 5.914898 AATTAAGCGCTTTACCCTCATTT 57.085 34.783 30.13 7.98 0.00 2.32
209 210 5.914898 ATTAAGCGCTTTACCCTCATTTT 57.085 34.783 30.13 0.44 0.00 1.82
210 211 5.715434 TTAAGCGCTTTACCCTCATTTTT 57.285 34.783 30.13 0.00 0.00 1.94
211 212 6.821031 TTAAGCGCTTTACCCTCATTTTTA 57.179 33.333 30.13 0.97 0.00 1.52
212 213 4.696899 AGCGCTTTACCCTCATTTTTAC 57.303 40.909 2.64 0.00 0.00 2.01
213 214 4.076394 AGCGCTTTACCCTCATTTTTACA 58.924 39.130 2.64 0.00 0.00 2.41
306 308 3.633525 TGGATGCAATTATCTTGCCACTC 59.366 43.478 7.42 2.63 44.32 3.51
322 331 3.034635 CCACTCCAACTGCTATCCTACT 58.965 50.000 0.00 0.00 0.00 2.57
334 343 4.116238 GCTATCCTACTGTCAGTTTCTGC 58.884 47.826 11.54 5.38 0.00 4.26
399 408 1.080995 AGCGTCTGAAGCTTGATCGC 61.081 55.000 20.81 20.81 43.24 4.58
465 478 1.294659 GCATCCGCGGATCATCCTTC 61.295 60.000 37.10 15.75 33.30 3.46
557 587 8.880878 TGATCGATTCAGGAAACGAAATTATA 57.119 30.769 16.36 0.00 45.90 0.98
578 608 0.887387 GATCTCTCTCCCCGTCTCCG 60.887 65.000 0.00 0.00 0.00 4.63
687 723 3.460857 ACCCGCTCTAGTCAAATGATC 57.539 47.619 0.00 0.00 0.00 2.92
691 727 3.487574 CCGCTCTAGTCAAATGATCGAAC 59.512 47.826 0.00 0.00 0.00 3.95
813 2569 2.601763 GCAGATACCGTTTACAAGTCCG 59.398 50.000 0.00 0.00 0.00 4.79
822 2578 0.883153 TTACAAGTCCGAGCACGCTA 59.117 50.000 0.00 0.00 38.29 4.26
870 2679 3.118956 ACCTGTCGAATCAATCAGTCTCC 60.119 47.826 0.00 0.00 0.00 3.71
876 2685 3.743584 CGAATCAATCAGTCTCCTGCCAT 60.744 47.826 0.00 0.00 38.66 4.40
878 2687 1.137675 TCAATCAGTCTCCTGCCATCG 59.862 52.381 0.00 0.00 38.66 3.84
886 2695 1.412710 TCTCCTGCCATCGTTATCACC 59.587 52.381 0.00 0.00 0.00 4.02
908 2717 1.490490 TCTTCCCGCTGAGCCATTTAT 59.510 47.619 0.00 0.00 0.00 1.40
910 2719 3.135712 TCTTCCCGCTGAGCCATTTATTA 59.864 43.478 0.00 0.00 0.00 0.98
911 2720 3.126001 TCCCGCTGAGCCATTTATTAG 57.874 47.619 0.00 0.00 0.00 1.73
912 2721 2.703536 TCCCGCTGAGCCATTTATTAGA 59.296 45.455 0.00 0.00 0.00 2.10
913 2722 3.135712 TCCCGCTGAGCCATTTATTAGAA 59.864 43.478 0.00 0.00 0.00 2.10
915 2724 4.130118 CCGCTGAGCCATTTATTAGAAGT 58.870 43.478 0.00 0.00 0.00 3.01
916 2725 5.297547 CCGCTGAGCCATTTATTAGAAGTA 58.702 41.667 0.00 0.00 0.00 2.24
919 2728 7.145985 CGCTGAGCCATTTATTAGAAGTACTA 58.854 38.462 0.00 0.00 0.00 1.82
920 2729 7.115095 CGCTGAGCCATTTATTAGAAGTACTAC 59.885 40.741 0.00 0.00 0.00 2.73
922 2731 9.469807 CTGAGCCATTTATTAGAAGTACTACAG 57.530 37.037 0.00 0.00 0.00 2.74
995 2882 1.724082 GCAAGAAGTCGTTGAGAGCTC 59.276 52.381 5.27 5.27 0.00 4.09
1041 2934 3.664107 TGTCACTGCAACTGGTAAGATC 58.336 45.455 0.00 0.00 0.00 2.75
1057 2950 1.765314 AGATCCATACACCTGCACCTC 59.235 52.381 0.00 0.00 0.00 3.85
1324 3266 1.596260 GACGACGTGGTCATCGAGATA 59.404 52.381 23.70 0.00 40.86 1.98
1522 3471 3.117512 AGGTGTCCATGAACAAGAAGGTT 60.118 43.478 0.00 0.00 0.00 3.50
1671 3620 2.736347 GCTGGAGAAGTACCTCTACCA 58.264 52.381 1.07 6.82 33.79 3.25
1673 3622 3.025262 CTGGAGAAGTACCTCTACCACC 58.975 54.545 1.07 0.00 33.79 4.61
1675 3624 3.012502 TGGAGAAGTACCTCTACCACCAT 59.987 47.826 1.07 0.00 33.79 3.55
1684 3633 0.419865 TCTACCACCATGGGGAAGGA 59.580 55.000 18.14 7.12 43.37 3.36
1720 3669 3.010226 CGGGGAGGAGAGGAGGGAA 62.010 68.421 0.00 0.00 0.00 3.97
1729 3678 0.031616 AGAGGAGGGAAAGGCTCGAT 60.032 55.000 0.00 0.00 0.00 3.59
1786 3735 2.147387 GGGGATCCGGTACCTGCAT 61.147 63.158 10.90 0.00 0.00 3.96
1978 3927 3.473647 CCGGAGCTCTGGATGGCA 61.474 66.667 34.60 0.00 45.36 4.92
2140 4131 1.217057 AGGGGGACATGGAGTGCATT 61.217 55.000 0.00 0.00 40.89 3.56
2143 4134 1.098050 GGGACATGGAGTGCATTGTC 58.902 55.000 14.46 14.46 40.89 3.18
2230 4221 4.254709 TGCGTGCAGTTCCAGCCT 62.255 61.111 0.00 0.00 0.00 4.58
2326 4317 2.577059 CACTATGTGTCGGGCGGT 59.423 61.111 0.00 0.00 0.00 5.68
2356 4347 4.681978 GGCTGGGCGTTGTCGAGT 62.682 66.667 0.00 0.00 39.71 4.18
2357 4348 3.414700 GCTGGGCGTTGTCGAGTG 61.415 66.667 0.00 0.00 39.71 3.51
2358 4349 2.738521 CTGGGCGTTGTCGAGTGG 60.739 66.667 0.00 0.00 39.71 4.00
2359 4350 4.980805 TGGGCGTTGTCGAGTGGC 62.981 66.667 0.00 0.00 39.71 5.01
2360 4351 4.980805 GGGCGTTGTCGAGTGGCA 62.981 66.667 0.00 0.00 39.71 4.92
2361 4352 3.712881 GGCGTTGTCGAGTGGCAC 61.713 66.667 10.29 10.29 39.71 5.01
2362 4353 3.712881 GCGTTGTCGAGTGGCACC 61.713 66.667 15.27 4.98 39.71 5.01
2363 4354 3.403057 CGTTGTCGAGTGGCACCG 61.403 66.667 15.27 17.17 39.71 4.94
2364 4355 3.041940 GTTGTCGAGTGGCACCGG 61.042 66.667 22.21 0.00 0.00 5.28
2365 4356 4.980805 TTGTCGAGTGGCACCGGC 62.981 66.667 20.93 20.93 40.13 6.13
2469 4466 0.729116 CCGAGTGATGCAATGGTGAC 59.271 55.000 0.00 0.00 0.00 3.67
2723 4729 0.035881 TTGGAGTTGGCTCAGCTCAG 59.964 55.000 16.61 0.00 42.19 3.35
2729 4735 0.392595 TTGGCTCAGCTCAGCTCATG 60.393 55.000 10.24 0.00 36.40 3.07
2749 4755 2.096268 TGTGAAAATTCAAGCGAGCTCG 60.096 45.455 31.37 31.37 39.21 5.03
2797 4803 2.820059 AGAACATGACTCGTGCTCAA 57.180 45.000 0.00 0.00 0.00 3.02
2822 4828 3.869832 TGTAACGATCTCGAGTCGATCTT 59.130 43.478 30.46 21.08 41.40 2.40
2915 4925 5.049405 GTGAATATACTGGGAATCTTTGCCG 60.049 44.000 0.00 0.00 45.31 5.69
2916 4926 1.680338 ATACTGGGAATCTTTGCCGC 58.320 50.000 0.00 0.00 45.31 6.53
2922 4932 2.426738 TGGGAATCTTTGCCGCAAATAG 59.573 45.455 18.59 8.61 45.31 1.73
2931 4941 8.621532 ATCTTTGCCGCAAATAGAAGATATTA 57.378 30.769 18.59 0.00 33.46 0.98
2986 4997 7.120432 AGGTCAAATCTTCTCTGCACTTAATTC 59.880 37.037 0.00 0.00 0.00 2.17
3147 5161 1.340405 ACATTGGCTCAAGATCGGCTT 60.340 47.619 0.00 0.00 37.29 4.35
3275 5289 0.627986 AGCTTTCCTTGCAGCCCTAT 59.372 50.000 0.00 0.00 36.62 2.57
3276 5290 1.006400 AGCTTTCCTTGCAGCCCTATT 59.994 47.619 0.00 0.00 36.62 1.73
3277 5291 2.242196 AGCTTTCCTTGCAGCCCTATTA 59.758 45.455 0.00 0.00 36.62 0.98
3278 5292 2.620585 GCTTTCCTTGCAGCCCTATTAG 59.379 50.000 0.00 0.00 0.00 1.73
3279 5293 3.217626 CTTTCCTTGCAGCCCTATTAGG 58.782 50.000 2.43 2.43 34.30 2.69
3302 5316 5.221382 GGGATCCAATAGTACGAGCTACAAA 60.221 44.000 15.23 0.00 0.00 2.83
3313 5327 2.221055 CGAGCTACAAACAGAACCACAC 59.779 50.000 0.00 0.00 0.00 3.82
3321 5335 2.525105 ACAGAACCACACCCAAACTT 57.475 45.000 0.00 0.00 0.00 2.66
3327 5341 2.758130 ACCACACCCAAACTTCCAAAT 58.242 42.857 0.00 0.00 0.00 2.32
3328 5342 3.917300 ACCACACCCAAACTTCCAAATA 58.083 40.909 0.00 0.00 0.00 1.40
3329 5343 4.488770 ACCACACCCAAACTTCCAAATAT 58.511 39.130 0.00 0.00 0.00 1.28
3330 5344 4.526650 ACCACACCCAAACTTCCAAATATC 59.473 41.667 0.00 0.00 0.00 1.63
3331 5345 4.772100 CCACACCCAAACTTCCAAATATCT 59.228 41.667 0.00 0.00 0.00 1.98
3332 5346 5.105756 CCACACCCAAACTTCCAAATATCTC 60.106 44.000 0.00 0.00 0.00 2.75
3333 5347 5.476599 CACACCCAAACTTCCAAATATCTCA 59.523 40.000 0.00 0.00 0.00 3.27
3334 5348 5.476945 ACACCCAAACTTCCAAATATCTCAC 59.523 40.000 0.00 0.00 0.00 3.51
3335 5349 5.016831 ACCCAAACTTCCAAATATCTCACC 58.983 41.667 0.00 0.00 0.00 4.02
3336 5350 4.402474 CCCAAACTTCCAAATATCTCACCC 59.598 45.833 0.00 0.00 0.00 4.61
3337 5351 4.402474 CCAAACTTCCAAATATCTCACCCC 59.598 45.833 0.00 0.00 0.00 4.95
3338 5352 3.953542 ACTTCCAAATATCTCACCCCC 57.046 47.619 0.00 0.00 0.00 5.40
3339 5353 3.474920 ACTTCCAAATATCTCACCCCCT 58.525 45.455 0.00 0.00 0.00 4.79
3340 5354 4.641868 ACTTCCAAATATCTCACCCCCTA 58.358 43.478 0.00 0.00 0.00 3.53
3341 5355 4.412528 ACTTCCAAATATCTCACCCCCTAC 59.587 45.833 0.00 0.00 0.00 3.18
3342 5356 4.295905 TCCAAATATCTCACCCCCTACT 57.704 45.455 0.00 0.00 0.00 2.57
3343 5357 3.973973 TCCAAATATCTCACCCCCTACTG 59.026 47.826 0.00 0.00 0.00 2.74
3344 5358 3.716872 CCAAATATCTCACCCCCTACTGT 59.283 47.826 0.00 0.00 0.00 3.55
3345 5359 4.202367 CCAAATATCTCACCCCCTACTGTC 60.202 50.000 0.00 0.00 0.00 3.51
3346 5360 3.993658 ATATCTCACCCCCTACTGTCA 57.006 47.619 0.00 0.00 0.00 3.58
3347 5361 2.166907 ATCTCACCCCCTACTGTCAG 57.833 55.000 0.00 0.00 0.00 3.51
3348 5362 0.041238 TCTCACCCCCTACTGTCAGG 59.959 60.000 4.53 0.00 35.26 3.86
3387 5401 1.362932 AGAGCAGGAGAGGGGAGTTAA 59.637 52.381 0.00 0.00 0.00 2.01
3388 5402 1.483004 GAGCAGGAGAGGGGAGTTAAC 59.517 57.143 0.00 0.00 0.00 2.01
3389 5403 1.203313 AGCAGGAGAGGGGAGTTAACA 60.203 52.381 8.61 0.00 0.00 2.41
3390 5404 1.840635 GCAGGAGAGGGGAGTTAACAT 59.159 52.381 8.61 0.00 0.00 2.71
3391 5405 3.039011 GCAGGAGAGGGGAGTTAACATA 58.961 50.000 8.61 0.00 0.00 2.29
3392 5406 3.648545 GCAGGAGAGGGGAGTTAACATAT 59.351 47.826 8.61 0.00 0.00 1.78
3435 5449 3.384467 ACAGGAACATGACCAAACAAAGG 59.616 43.478 0.00 0.00 0.00 3.11
3478 5492 9.218440 GACCACTATTACTACTACTAGATGACC 57.782 40.741 0.00 0.00 0.00 4.02
3479 5493 8.721479 ACCACTATTACTACTACTAGATGACCA 58.279 37.037 0.00 0.00 0.00 4.02
3480 5494 9.221933 CCACTATTACTACTACTAGATGACCAG 57.778 40.741 0.00 0.00 0.00 4.00
3481 5495 9.781633 CACTATTACTACTACTAGATGACCAGT 57.218 37.037 0.00 0.00 0.00 4.00
3484 5498 5.838531 ACTACTACTAGATGACCAGTTGC 57.161 43.478 0.00 0.00 0.00 4.17
3485 5499 3.784701 ACTACTAGATGACCAGTTGCG 57.215 47.619 0.00 0.00 0.00 4.85
3486 5500 2.159226 ACTACTAGATGACCAGTTGCGC 60.159 50.000 0.00 0.00 0.00 6.09
3487 5501 0.108138 ACTAGATGACCAGTTGCGCC 60.108 55.000 4.18 0.00 0.00 6.53
3488 5502 0.108186 CTAGATGACCAGTTGCGCCA 60.108 55.000 4.18 0.00 0.00 5.69
3489 5503 0.323302 TAGATGACCAGTTGCGCCAA 59.677 50.000 4.18 0.00 0.00 4.52
3490 5504 0.537143 AGATGACCAGTTGCGCCAAA 60.537 50.000 4.18 0.00 0.00 3.28
3491 5505 0.527565 GATGACCAGTTGCGCCAAAT 59.472 50.000 4.18 0.00 0.00 2.32
3492 5506 0.244450 ATGACCAGTTGCGCCAAATG 59.756 50.000 4.18 8.94 38.85 2.32
3493 5507 0.821301 TGACCAGTTGCGCCAAATGA 60.821 50.000 17.38 0.56 41.15 2.57
3494 5508 0.387239 GACCAGTTGCGCCAAATGAC 60.387 55.000 17.38 9.82 41.15 3.06
3495 5509 1.442520 CCAGTTGCGCCAAATGACG 60.443 57.895 17.38 3.04 41.15 4.35
3502 5516 2.712077 CGCCAAATGACGCAAAGAC 58.288 52.632 0.00 0.00 0.00 3.01
3503 5517 0.729140 CGCCAAATGACGCAAAGACC 60.729 55.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.965439 TGGGTCGGCAGAAAATTTGG 59.035 50.000 0.00 0.00 0.00 3.28
1 2 2.810439 TTGGGTCGGCAGAAAATTTG 57.190 45.000 0.00 0.00 0.00 2.32
2 3 3.578282 AGATTTGGGTCGGCAGAAAATTT 59.422 39.130 0.00 0.00 0.00 1.82
3 4 3.056607 CAGATTTGGGTCGGCAGAAAATT 60.057 43.478 0.00 0.00 0.00 1.82
4 5 2.493278 CAGATTTGGGTCGGCAGAAAAT 59.507 45.455 0.00 0.00 0.00 1.82
5 6 1.885887 CAGATTTGGGTCGGCAGAAAA 59.114 47.619 0.00 0.00 0.00 2.29
7 8 0.400213 ACAGATTTGGGTCGGCAGAA 59.600 50.000 0.00 0.00 0.00 3.02
8 9 0.400213 AACAGATTTGGGTCGGCAGA 59.600 50.000 0.00 0.00 0.00 4.26
9 10 0.523072 CAACAGATTTGGGTCGGCAG 59.477 55.000 0.00 0.00 0.00 4.85
10 11 0.179004 ACAACAGATTTGGGTCGGCA 60.179 50.000 0.00 0.00 0.00 5.69
11 12 0.240945 CACAACAGATTTGGGTCGGC 59.759 55.000 0.00 0.00 0.00 5.54
12 13 0.881118 CCACAACAGATTTGGGTCGG 59.119 55.000 0.00 0.00 0.00 4.79
13 14 0.881118 CCCACAACAGATTTGGGTCG 59.119 55.000 0.00 0.00 44.56 4.79
17 18 1.894466 TGATGCCCACAACAGATTTGG 59.106 47.619 0.00 0.00 0.00 3.28
18 19 3.663995 TTGATGCCCACAACAGATTTG 57.336 42.857 0.00 0.00 29.45 2.32
19 20 4.091549 AGATTGATGCCCACAACAGATTT 58.908 39.130 0.00 0.00 29.45 2.17
20 21 3.705051 AGATTGATGCCCACAACAGATT 58.295 40.909 0.00 0.00 29.45 2.40
21 22 3.377253 AGATTGATGCCCACAACAGAT 57.623 42.857 0.00 0.00 29.45 2.90
22 23 2.885135 AGATTGATGCCCACAACAGA 57.115 45.000 0.00 0.00 29.45 3.41
23 24 4.400251 ACAATAGATTGATGCCCACAACAG 59.600 41.667 9.21 0.00 40.14 3.16
24 25 4.343231 ACAATAGATTGATGCCCACAACA 58.657 39.130 9.21 0.00 40.14 3.33
25 26 4.989279 ACAATAGATTGATGCCCACAAC 57.011 40.909 9.21 0.00 40.14 3.32
26 27 5.948758 TGTTACAATAGATTGATGCCCACAA 59.051 36.000 9.21 0.00 40.14 3.33
27 28 5.356751 GTGTTACAATAGATTGATGCCCACA 59.643 40.000 9.21 0.70 40.14 4.17
28 29 5.356751 TGTGTTACAATAGATTGATGCCCAC 59.643 40.000 9.21 8.18 40.14 4.61
29 30 5.504853 TGTGTTACAATAGATTGATGCCCA 58.495 37.500 9.21 0.00 40.14 5.36
30 31 6.265577 GTTGTGTTACAATAGATTGATGCCC 58.734 40.000 9.21 0.00 40.59 5.36
31 32 6.127758 TGGTTGTGTTACAATAGATTGATGCC 60.128 38.462 9.21 1.50 40.59 4.40
32 33 6.851609 TGGTTGTGTTACAATAGATTGATGC 58.148 36.000 9.21 0.00 40.59 3.91
57 58 9.744125 AGGGGTGGCTTATCTCATTATATATAA 57.256 33.333 7.62 7.62 0.00 0.98
59 60 9.386122 CTAGGGGTGGCTTATCTCATTATATAT 57.614 37.037 0.00 0.00 0.00 0.86
60 61 8.574853 TCTAGGGGTGGCTTATCTCATTATATA 58.425 37.037 0.00 0.00 0.00 0.86
61 62 7.430844 TCTAGGGGTGGCTTATCTCATTATAT 58.569 38.462 0.00 0.00 0.00 0.86
62 63 6.811574 TCTAGGGGTGGCTTATCTCATTATA 58.188 40.000 0.00 0.00 0.00 0.98
63 64 5.665701 TCTAGGGGTGGCTTATCTCATTAT 58.334 41.667 0.00 0.00 0.00 1.28
64 65 5.087323 CTCTAGGGGTGGCTTATCTCATTA 58.913 45.833 0.00 0.00 0.00 1.90
65 66 3.906846 CTCTAGGGGTGGCTTATCTCATT 59.093 47.826 0.00 0.00 0.00 2.57
66 67 3.515562 CTCTAGGGGTGGCTTATCTCAT 58.484 50.000 0.00 0.00 0.00 2.90
67 68 2.426414 CCTCTAGGGGTGGCTTATCTCA 60.426 54.545 0.00 0.00 0.00 3.27
68 69 2.252714 CCTCTAGGGGTGGCTTATCTC 58.747 57.143 0.00 0.00 0.00 2.75
69 70 2.407340 CCTCTAGGGGTGGCTTATCT 57.593 55.000 0.00 0.00 0.00 1.98
81 82 0.693049 AACCAGCACAACCCTCTAGG 59.307 55.000 0.00 0.00 43.78 3.02
82 83 1.339151 GGAACCAGCACAACCCTCTAG 60.339 57.143 0.00 0.00 0.00 2.43
83 84 0.690762 GGAACCAGCACAACCCTCTA 59.309 55.000 0.00 0.00 0.00 2.43
84 85 1.456287 GGAACCAGCACAACCCTCT 59.544 57.895 0.00 0.00 0.00 3.69
85 86 4.081050 GGAACCAGCACAACCCTC 57.919 61.111 0.00 0.00 0.00 4.30
98 99 7.143340 GTGTAAGACAATAAGTTTTGGGGAAC 58.857 38.462 0.00 0.00 0.00 3.62
99 100 6.265876 GGTGTAAGACAATAAGTTTTGGGGAA 59.734 38.462 0.00 0.00 0.00 3.97
100 101 5.771165 GGTGTAAGACAATAAGTTTTGGGGA 59.229 40.000 0.00 0.00 0.00 4.81
101 102 5.335348 CGGTGTAAGACAATAAGTTTTGGGG 60.335 44.000 0.00 0.00 0.00 4.96
102 103 5.470777 TCGGTGTAAGACAATAAGTTTTGGG 59.529 40.000 0.00 0.00 0.00 4.12
103 104 6.548441 TCGGTGTAAGACAATAAGTTTTGG 57.452 37.500 0.00 0.00 0.00 3.28
104 105 6.953743 CGATCGGTGTAAGACAATAAGTTTTG 59.046 38.462 7.38 0.00 0.00 2.44
105 106 6.647895 ACGATCGGTGTAAGACAATAAGTTTT 59.352 34.615 20.98 0.00 0.00 2.43
106 107 6.161381 ACGATCGGTGTAAGACAATAAGTTT 58.839 36.000 20.98 0.00 0.00 2.66
107 108 5.717119 ACGATCGGTGTAAGACAATAAGTT 58.283 37.500 20.98 0.00 0.00 2.66
108 109 5.320549 ACGATCGGTGTAAGACAATAAGT 57.679 39.130 20.98 0.00 0.00 2.24
109 110 6.034591 AGAACGATCGGTGTAAGACAATAAG 58.965 40.000 20.98 0.00 0.00 1.73
110 111 5.957798 AGAACGATCGGTGTAAGACAATAA 58.042 37.500 20.98 0.00 0.00 1.40
111 112 5.124297 TGAGAACGATCGGTGTAAGACAATA 59.876 40.000 20.98 0.00 0.00 1.90
112 113 4.082408 TGAGAACGATCGGTGTAAGACAAT 60.082 41.667 20.98 0.00 0.00 2.71
113 114 3.253921 TGAGAACGATCGGTGTAAGACAA 59.746 43.478 20.98 0.00 0.00 3.18
114 115 2.815503 TGAGAACGATCGGTGTAAGACA 59.184 45.455 20.98 2.40 0.00 3.41
115 116 3.482722 TGAGAACGATCGGTGTAAGAC 57.517 47.619 20.98 0.00 0.00 3.01
116 117 6.387041 AATATGAGAACGATCGGTGTAAGA 57.613 37.500 20.98 1.33 0.00 2.10
118 119 9.999009 GATATAATATGAGAACGATCGGTGTAA 57.001 33.333 20.98 4.56 0.00 2.41
119 120 9.169592 TGATATAATATGAGAACGATCGGTGTA 57.830 33.333 20.98 1.21 0.00 2.90
120 121 8.051901 TGATATAATATGAGAACGATCGGTGT 57.948 34.615 20.98 12.31 0.00 4.16
123 124 9.335891 GCTATGATATAATATGAGAACGATCGG 57.664 37.037 20.98 1.23 0.00 4.18
124 125 9.884465 TGCTATGATATAATATGAGAACGATCG 57.116 33.333 14.88 14.88 0.00 3.69
160 161 2.049156 CGAACCTCACTGAGCGCA 60.049 61.111 11.47 0.00 0.00 6.09
161 162 2.049063 ACGAACCTCACTGAGCGC 60.049 61.111 0.00 0.00 0.00 5.92
162 163 1.444553 GGACGAACCTCACTGAGCG 60.445 63.158 0.00 2.14 35.41 5.03
163 164 1.444553 CGGACGAACCTCACTGAGC 60.445 63.158 0.00 0.00 36.31 4.26
164 165 0.387367 CACGGACGAACCTCACTGAG 60.387 60.000 0.00 0.00 36.31 3.35
165 166 1.658114 CACGGACGAACCTCACTGA 59.342 57.895 0.00 0.00 36.31 3.41
166 167 2.022129 GCACGGACGAACCTCACTG 61.022 63.158 0.00 0.00 36.31 3.66
167 168 0.892358 TAGCACGGACGAACCTCACT 60.892 55.000 0.00 0.00 36.31 3.41
168 169 0.038892 TTAGCACGGACGAACCTCAC 60.039 55.000 0.00 0.00 36.31 3.51
169 170 0.892755 ATTAGCACGGACGAACCTCA 59.107 50.000 0.00 0.00 36.31 3.86
170 171 2.005971 AATTAGCACGGACGAACCTC 57.994 50.000 0.00 0.00 36.31 3.85
171 172 3.518590 CTTAATTAGCACGGACGAACCT 58.481 45.455 0.00 0.00 36.31 3.50
172 173 3.920112 CTTAATTAGCACGGACGAACC 57.080 47.619 0.00 0.00 0.00 3.62
183 184 3.875134 TGAGGGTAAAGCGCTTAATTAGC 59.125 43.478 25.33 20.40 46.83 3.09
184 185 6.619801 AATGAGGGTAAAGCGCTTAATTAG 57.380 37.500 25.33 0.00 40.72 1.73
185 186 7.399245 AAAATGAGGGTAAAGCGCTTAATTA 57.601 32.000 25.33 9.72 40.72 1.40
186 187 5.914898 AAATGAGGGTAAAGCGCTTAATT 57.085 34.783 25.33 10.89 40.72 1.40
187 188 5.914898 AAAATGAGGGTAAAGCGCTTAAT 57.085 34.783 25.33 11.73 40.72 1.40
188 189 5.715434 AAAAATGAGGGTAAAGCGCTTAA 57.285 34.783 25.33 3.74 40.72 1.85
189 190 5.706369 TGTAAAAATGAGGGTAAAGCGCTTA 59.294 36.000 25.33 5.95 40.72 3.09
190 191 4.521256 TGTAAAAATGAGGGTAAAGCGCTT 59.479 37.500 18.98 18.98 40.72 4.68
191 192 4.076394 TGTAAAAATGAGGGTAAAGCGCT 58.924 39.130 2.64 2.64 43.54 5.92
192 193 4.428615 TGTAAAAATGAGGGTAAAGCGC 57.571 40.909 0.00 0.00 0.00 5.92
193 194 4.857037 GCTTGTAAAAATGAGGGTAAAGCG 59.143 41.667 0.00 0.00 0.00 4.68
194 195 5.778862 TGCTTGTAAAAATGAGGGTAAAGC 58.221 37.500 0.00 0.00 38.34 3.51
195 196 5.863935 GCTGCTTGTAAAAATGAGGGTAAAG 59.136 40.000 0.00 0.00 0.00 1.85
196 197 5.303078 TGCTGCTTGTAAAAATGAGGGTAAA 59.697 36.000 0.00 0.00 0.00 2.01
197 198 4.830046 TGCTGCTTGTAAAAATGAGGGTAA 59.170 37.500 0.00 0.00 0.00 2.85
198 199 4.402829 TGCTGCTTGTAAAAATGAGGGTA 58.597 39.130 0.00 0.00 0.00 3.69
199 200 3.230134 TGCTGCTTGTAAAAATGAGGGT 58.770 40.909 0.00 0.00 0.00 4.34
200 201 3.841643 CTGCTGCTTGTAAAAATGAGGG 58.158 45.455 0.00 0.00 0.00 4.30
201 202 3.248266 GCTGCTGCTTGTAAAAATGAGG 58.752 45.455 8.53 0.00 36.03 3.86
202 203 2.912967 CGCTGCTGCTTGTAAAAATGAG 59.087 45.455 14.03 0.00 36.97 2.90
203 204 2.921912 GCGCTGCTGCTTGTAAAAATGA 60.922 45.455 14.03 0.00 36.97 2.57
204 205 1.387756 GCGCTGCTGCTTGTAAAAATG 59.612 47.619 14.03 0.00 36.97 2.32
205 206 1.270550 AGCGCTGCTGCTTGTAAAAAT 59.729 42.857 10.39 0.00 44.46 1.82
206 207 0.667993 AGCGCTGCTGCTTGTAAAAA 59.332 45.000 10.39 0.00 44.46 1.94
207 208 2.330254 AGCGCTGCTGCTTGTAAAA 58.670 47.368 10.39 0.00 44.46 1.52
208 209 4.063529 AGCGCTGCTGCTTGTAAA 57.936 50.000 10.39 0.00 44.46 2.01
285 287 3.005155 GGAGTGGCAAGATAATTGCATCC 59.995 47.826 13.94 12.89 46.58 3.51
286 288 3.633525 TGGAGTGGCAAGATAATTGCATC 59.366 43.478 13.94 8.49 46.58 3.91
306 308 3.449018 ACTGACAGTAGGATAGCAGTTGG 59.551 47.826 6.24 0.00 33.19 3.77
322 331 2.330440 TTGAGCAGCAGAAACTGACA 57.670 45.000 2.81 0.00 40.25 3.58
349 358 5.298347 TGCAGATTCAGAGAAGCATAGATG 58.702 41.667 0.00 0.00 0.00 2.90
465 478 7.976734 ACAGAAAAGGAATCTATTCTAGACACG 59.023 37.037 0.00 0.00 37.69 4.49
484 497 4.644234 TCCATCAACTGCTCAAACAGAAAA 59.356 37.500 0.00 0.00 40.25 2.29
557 587 0.476771 GAGACGGGGAGAGAGATCCT 59.523 60.000 0.00 0.00 39.50 3.24
608 639 6.757478 GGTGGACTGTAGCTACTCTTTTTATC 59.243 42.308 23.84 9.67 0.00 1.75
687 723 1.652124 CATACTCGGTTTGACGGTTCG 59.348 52.381 0.00 0.00 0.00 3.95
691 727 1.393539 CTTGCATACTCGGTTTGACGG 59.606 52.381 0.00 0.00 0.00 4.79
822 2578 3.592898 TGACGATACTGATTGCTGTGT 57.407 42.857 0.00 0.00 0.00 3.72
836 2592 3.928727 TCGACAGGTAAAGTTGACGAT 57.071 42.857 0.00 0.00 36.79 3.73
870 2679 3.117491 AGATGGTGATAACGATGGCAG 57.883 47.619 0.00 0.00 0.00 4.85
876 2685 1.202486 GCGGGAAGATGGTGATAACGA 60.202 52.381 0.00 0.00 0.00 3.85
878 2687 2.158957 TCAGCGGGAAGATGGTGATAAC 60.159 50.000 0.00 0.00 37.66 1.89
886 2695 0.465097 AATGGCTCAGCGGGAAGATG 60.465 55.000 0.00 0.00 37.65 2.90
913 2722 9.448587 AGGGTTAATAATCATTCCTGTAGTACT 57.551 33.333 0.00 0.00 0.00 2.73
916 2725 8.557450 ACAAGGGTTAATAATCATTCCTGTAGT 58.443 33.333 0.00 0.00 0.00 2.73
919 2728 7.557719 CAGACAAGGGTTAATAATCATTCCTGT 59.442 37.037 3.14 0.00 0.00 4.00
920 2729 7.775093 TCAGACAAGGGTTAATAATCATTCCTG 59.225 37.037 4.33 4.33 0.00 3.86
922 2731 7.013369 GGTCAGACAAGGGTTAATAATCATTCC 59.987 40.741 2.17 0.00 0.00 3.01
983 2868 2.351244 ATGCCCGAGCTCTCAACGA 61.351 57.895 12.85 0.00 40.80 3.85
1041 2934 0.324614 TGTGAGGTGCAGGTGTATGG 59.675 55.000 0.00 0.00 0.00 2.74
1057 2950 9.429359 AGACAGTTAAAATCTACTCATTCTGTG 57.571 33.333 0.00 0.00 33.55 3.66
1084 3013 6.436532 AGCTGATGAAAAATTGATCAAGGACT 59.563 34.615 14.54 0.00 0.00 3.85
1324 3266 2.125766 GAAACTTCTCCACGGGGCCT 62.126 60.000 0.00 0.00 0.00 5.19
1522 3471 1.299648 CGCCATGAACCCTTCCTGA 59.700 57.895 0.00 0.00 0.00 3.86
1624 3573 4.895889 CCATTCTCCAGGTACTCATAGACA 59.104 45.833 0.00 0.00 34.60 3.41
1671 3620 1.995626 CCGTCTCCTTCCCCATGGT 60.996 63.158 11.73 0.00 0.00 3.55
1673 3622 2.190578 GCCGTCTCCTTCCCCATG 59.809 66.667 0.00 0.00 0.00 3.66
1675 3624 4.689549 TCGCCGTCTCCTTCCCCA 62.690 66.667 0.00 0.00 0.00 4.96
1720 3669 2.125106 GTCCGCCAATCGAGCCTT 60.125 61.111 0.00 0.00 41.67 4.35
1729 3678 2.591429 CTGTGCAGTGTCCGCCAA 60.591 61.111 0.00 0.00 0.00 4.52
1762 3711 3.221389 TACCGGATCCCCTTCGCG 61.221 66.667 9.46 0.00 0.00 5.87
1786 3735 2.745698 CTGTGCTGGCACTCCTCA 59.254 61.111 23.30 5.19 46.30 3.86
1995 3944 1.615107 GAAGCTGTACACGTCGCACC 61.615 60.000 7.48 0.00 0.00 5.01
2455 4452 1.381522 CATCCGTCACCATTGCATCA 58.618 50.000 0.00 0.00 0.00 3.07
2469 4466 1.605710 GATCAATGGACTTGGCATCCG 59.394 52.381 2.85 0.00 39.30 4.18
2570 4575 8.637986 TGCTAATTTACAAAACATTCCTGACTT 58.362 29.630 0.00 0.00 0.00 3.01
2571 4576 8.177119 TGCTAATTTACAAAACATTCCTGACT 57.823 30.769 0.00 0.00 0.00 3.41
2572 4577 8.986477 ATGCTAATTTACAAAACATTCCTGAC 57.014 30.769 0.00 0.00 0.00 3.51
2677 4683 0.664767 GAGCTCGACTCGTTTGCAGT 60.665 55.000 0.00 0.00 35.18 4.40
2723 4729 3.825308 TCGCTTGAATTTTCACATGAGC 58.175 40.909 0.00 5.14 36.83 4.26
2729 4735 2.157668 TCGAGCTCGCTTGAATTTTCAC 59.842 45.455 30.97 0.00 36.71 3.18
2797 4803 2.998670 TCGACTCGAGATCGTTACAAGT 59.001 45.455 25.67 0.00 40.50 3.16
2886 4895 9.277783 CAAAGATTCCCAGTATATTCACCTTAG 57.722 37.037 0.00 0.00 0.00 2.18
2899 4909 0.539438 TTGCGGCAAAGATTCCCAGT 60.539 50.000 13.93 0.00 0.00 4.00
2922 4932 8.753175 GTGGTCGACTATGTGTTTAATATCTTC 58.247 37.037 16.46 0.00 0.00 2.87
2931 4941 2.400399 CACGTGGTCGACTATGTGTTT 58.600 47.619 33.81 10.41 38.87 2.83
2986 4997 4.822036 TTACCAACGAACATGGAAACTG 57.178 40.909 0.00 0.00 40.56 3.16
3095 5106 6.144724 GCTCGATTTTAGCTCGACAGAATATT 59.855 38.462 0.00 0.00 40.01 1.28
3147 5161 1.241165 TGTAGCTCGACCGAGAAACA 58.759 50.000 21.91 19.24 44.53 2.83
3275 5289 4.737578 AGCTCGTACTATTGGATCCCTAA 58.262 43.478 9.90 0.00 0.00 2.69
3276 5290 4.383931 AGCTCGTACTATTGGATCCCTA 57.616 45.455 9.90 0.00 0.00 3.53
3277 5291 3.246416 AGCTCGTACTATTGGATCCCT 57.754 47.619 9.90 0.00 0.00 4.20
3278 5292 3.825014 TGTAGCTCGTACTATTGGATCCC 59.175 47.826 9.90 0.00 32.19 3.85
3279 5293 5.449107 TTGTAGCTCGTACTATTGGATCC 57.551 43.478 4.20 4.20 32.19 3.36
3280 5294 6.270815 TGTTTGTAGCTCGTACTATTGGATC 58.729 40.000 0.00 0.00 32.19 3.36
3281 5295 6.096423 TCTGTTTGTAGCTCGTACTATTGGAT 59.904 38.462 0.00 0.00 32.19 3.41
3282 5296 5.416639 TCTGTTTGTAGCTCGTACTATTGGA 59.583 40.000 0.00 0.00 32.19 3.53
3302 5316 2.375146 GAAGTTTGGGTGTGGTTCTGT 58.625 47.619 0.00 0.00 0.00 3.41
3313 5327 4.402474 GGGTGAGATATTTGGAAGTTTGGG 59.598 45.833 0.00 0.00 0.00 4.12
3321 5335 3.973973 CAGTAGGGGGTGAGATATTTGGA 59.026 47.826 0.00 0.00 0.00 3.53
3327 5341 2.091278 CCTGACAGTAGGGGGTGAGATA 60.091 54.545 0.93 0.00 34.06 1.98
3328 5342 1.343478 CCTGACAGTAGGGGGTGAGAT 60.343 57.143 0.93 0.00 34.06 2.75
3329 5343 0.041238 CCTGACAGTAGGGGGTGAGA 59.959 60.000 0.93 0.00 34.06 3.27
3330 5344 1.617947 GCCTGACAGTAGGGGGTGAG 61.618 65.000 0.93 0.00 38.32 3.51
3331 5345 1.612442 GCCTGACAGTAGGGGGTGA 60.612 63.158 0.93 0.00 38.32 4.02
3332 5346 1.903877 CTGCCTGACAGTAGGGGGTG 61.904 65.000 0.93 0.00 41.86 4.61
3333 5347 1.613630 CTGCCTGACAGTAGGGGGT 60.614 63.158 0.93 0.00 41.86 4.95
3334 5348 3.313874 CTGCCTGACAGTAGGGGG 58.686 66.667 0.93 0.00 41.86 5.40
3342 5356 2.588596 CACGTGTGCTGCCTGACA 60.589 61.111 7.58 0.00 0.00 3.58
3391 5405 8.734386 CCTGTTTATTTTGCTAAGACTTGAGAT 58.266 33.333 0.00 0.00 0.00 2.75
3392 5406 7.936847 TCCTGTTTATTTTGCTAAGACTTGAGA 59.063 33.333 0.00 0.00 0.00 3.27
3435 5449 1.669211 GGTCTAAGTGGTGTCGAGTGC 60.669 57.143 0.00 0.00 0.00 4.40
3474 5488 0.821301 TCATTTGGCGCAACTGGTCA 60.821 50.000 10.83 0.00 0.00 4.02
3475 5489 0.387239 GTCATTTGGCGCAACTGGTC 60.387 55.000 10.83 0.00 0.00 4.02
3476 5490 1.659794 GTCATTTGGCGCAACTGGT 59.340 52.632 10.83 0.00 0.00 4.00
3477 5491 1.442520 CGTCATTTGGCGCAACTGG 60.443 57.895 10.83 0.00 35.94 4.00
3478 5492 4.135570 CGTCATTTGGCGCAACTG 57.864 55.556 10.83 6.66 35.94 3.16
3485 5499 3.107017 GGTCTTTGCGTCATTTGGC 57.893 52.632 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.