Multiple sequence alignment - TraesCS7B01G309600

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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 TraesCS7B01G309600 chr7B 100.000 4050 0 0 1 4050 553638822 553634773 0.000000e+00 7480.0
1 TraesCS7B01G309600 chr7D 90.995 2021 85 45 118 2077 520414437 520412453 0.000000e+00 2634.0
2 TraesCS7B01G309600 chr7D 89.517 849 51 18 2878 3702 520411576 520410742 0.000000e+00 1040.0
3 TraesCS7B01G309600 chr7D 89.189 592 38 7 2248 2834 520412269 520411699 0.000000e+00 715.0
4 TraesCS7B01G309600 chr7D 92.616 474 19 8 911 1371 638016620 638017090 0.000000e+00 667.0
5 TraesCS7B01G309600 chr7D 89.706 204 20 1 2240 2442 638017832 638018035 4.020000e-65 259.0
6 TraesCS7B01G309600 chr7D 96.970 132 3 1 2112 2242 251035919 251036050 1.890000e-53 220.0
7 TraesCS7B01G309600 chr7D 90.291 103 8 2 3766 3868 459429428 459429328 2.540000e-27 134.0
8 TraesCS7B01G309600 chr7D 87.931 116 5 2 1 116 520414702 520414596 1.180000e-25 128.0
9 TraesCS7B01G309600 chr7D 97.368 38 1 0 2833 2870 520411640 520411603 9.400000e-07 65.8
10 TraesCS7B01G309600 chr7A 89.647 2038 109 32 118 2076 596731591 596729577 0.000000e+00 2501.0
11 TraesCS7B01G309600 chr7A 87.205 1610 115 47 2240 3776 596729323 596727732 0.000000e+00 1748.0
12 TraesCS7B01G309600 chr7A 95.578 995 33 7 1095 2086 517128098 517129084 0.000000e+00 1583.0
13 TraesCS7B01G309600 chr7A 96.212 132 5 0 2111 2242 442265750 442265881 2.450000e-52 217.0
14 TraesCS7B01G309600 chr7A 83.429 175 12 6 3878 4050 596727718 596727559 3.260000e-31 147.0
15 TraesCS7B01G309600 chr6B 94.874 995 41 8 1095 2085 103259395 103260383 0.000000e+00 1546.0
16 TraesCS7B01G309600 chr6B 93.706 143 9 0 2113 2255 15392224 15392082 8.820000e-52 215.0
17 TraesCS7B01G309600 chr6B 93.750 96 5 1 3771 3866 507505787 507505881 4.220000e-30 143.0
18 TraesCS7B01G309600 chrUn 94.758 992 45 6 1095 2085 184899845 184900830 0.000000e+00 1537.0
19 TraesCS7B01G309600 chrUn 92.944 992 64 4 1095 2085 227524517 227525503 0.000000e+00 1439.0
20 TraesCS7B01G309600 chrUn 94.444 738 35 5 1349 2085 218749864 218749132 0.000000e+00 1131.0
21 TraesCS7B01G309600 chr2B 94.758 992 45 6 1095 2085 755391625 755390640 0.000000e+00 1537.0
22 TraesCS7B01G309600 chr2B 87.789 475 38 9 911 1371 227175246 227174778 4.610000e-149 538.0
23 TraesCS7B01G309600 chr2B 89.706 204 20 1 2240 2442 102555327 102555530 4.020000e-65 259.0
24 TraesCS7B01G309600 chr5B 94.456 992 49 5 1095 2085 553580054 553579068 0.000000e+00 1522.0
25 TraesCS7B01G309600 chr2A 94.254 992 51 5 1095 2085 82805698 82804712 0.000000e+00 1511.0
26 TraesCS7B01G309600 chr4B 95.483 642 22 3 1444 2085 619768444 619769078 0.000000e+00 1018.0
27 TraesCS7B01G309600 chr4B 90.291 103 8 2 3771 3872 179437356 179437457 2.540000e-27 134.0
28 TraesCS7B01G309600 chr3B 91.688 385 29 3 1095 1478 406134659 406134277 7.710000e-147 531.0
29 TraesCS7B01G309600 chr3B 89.855 207 20 1 2240 2445 738227490 738227284 8.630000e-67 265.0
30 TraesCS7B01G309600 chr3B 92.784 97 4 3 3775 3868 66572269 66572365 1.960000e-28 137.0
31 TraesCS7B01G309600 chr3B 89.720 107 9 2 3774 3879 43050405 43050300 7.060000e-28 135.0
32 TraesCS7B01G309600 chr2D 91.176 204 17 1 2240 2442 166479234 166479437 3.990000e-70 276.0
33 TraesCS7B01G309600 chr2D 97.638 127 3 0 2116 2242 340252868 340252742 6.820000e-53 219.0
34 TraesCS7B01G309600 chr2D 90.385 104 8 2 3765 3868 591362883 591362782 7.060000e-28 135.0
35 TraesCS7B01G309600 chr6A 90.196 204 19 1 2240 2442 413097843 413097640 8.630000e-67 265.0
36 TraesCS7B01G309600 chr6A 96.970 132 4 0 2111 2242 506234751 506234620 5.270000e-54 222.0
37 TraesCS7B01G309600 chr5A 89.756 205 19 2 2240 2442 687891170 687891374 1.120000e-65 261.0
38 TraesCS7B01G309600 chr5D 89.706 204 20 1 2240 2442 300555474 300555271 4.020000e-65 259.0
39 TraesCS7B01G309600 chr4A 98.425 127 2 0 2116 2242 735001559 735001685 1.460000e-54 224.0
40 TraesCS7B01G309600 chr6D 97.638 127 3 0 2116 2242 272859228 272859354 6.820000e-53 219.0
41 TraesCS7B01G309600 chr3D 96.875 128 4 0 2115 2242 606951435 606951308 8.820000e-52 215.0
42 TraesCS7B01G309600 chr3D 96.154 130 5 0 2114 2243 267286537 267286408 3.170000e-51 213.0
43 TraesCS7B01G309600 chr1B 95.506 89 4 0 3775 3863 164770366 164770454 4.220000e-30 143.0
44 TraesCS7B01G309600 chr4D 93.684 95 4 1 3775 3867 449455616 449455710 1.520000e-29 141.0
45 TraesCS7B01G309600 chr4D 93.548 93 5 1 3771 3863 10971527 10971618 1.960000e-28 137.0


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 TraesCS7B01G309600 chr7B 553634773 553638822 4049 True 7480.000000 7480 100.000000 1 4050 1 chr7B.!!$R1 4049
1 TraesCS7B01G309600 chr7D 520410742 520414702 3960 True 916.560000 2634 91.000000 1 3702 5 chr7D.!!$R2 3701
2 TraesCS7B01G309600 chr7D 638016620 638018035 1415 False 463.000000 667 91.161000 911 2442 2 chr7D.!!$F2 1531
3 TraesCS7B01G309600 chr7A 517128098 517129084 986 False 1583.000000 1583 95.578000 1095 2086 1 chr7A.!!$F2 991
4 TraesCS7B01G309600 chr7A 596727559 596731591 4032 True 1465.333333 2501 86.760333 118 4050 3 chr7A.!!$R1 3932
5 TraesCS7B01G309600 chr6B 103259395 103260383 988 False 1546.000000 1546 94.874000 1095 2085 1 chr6B.!!$F1 990
6 TraesCS7B01G309600 chrUn 184899845 184900830 985 False 1537.000000 1537 94.758000 1095 2085 1 chrUn.!!$F1 990
7 TraesCS7B01G309600 chrUn 227524517 227525503 986 False 1439.000000 1439 92.944000 1095 2085 1 chrUn.!!$F2 990
8 TraesCS7B01G309600 chrUn 218749132 218749864 732 True 1131.000000 1131 94.444000 1349 2085 1 chrUn.!!$R1 736
9 TraesCS7B01G309600 chr2B 755390640 755391625 985 True 1537.000000 1537 94.758000 1095 2085 1 chr2B.!!$R2 990
10 TraesCS7B01G309600 chr5B 553579068 553580054 986 True 1522.000000 1522 94.456000 1095 2085 1 chr5B.!!$R1 990
11 TraesCS7B01G309600 chr2A 82804712 82805698 986 True 1511.000000 1511 94.254000 1095 2085 1 chr2A.!!$R1 990
12 TraesCS7B01G309600 chr4B 619768444 619769078 634 False 1018.000000 1018 95.483000 1444 2085 1 chr4B.!!$F2 641

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
274 435 0.103208 GCCTGATCTCGTCGTCCAAT 59.897 55.000 0.0 0.0 0.0 3.16 F
982 1175 1.379843 CCCAGAAATCCCCAACCCG 60.380 63.158 0.0 0.0 0.0 5.28 F
2128 2649 1.829222 TGAATTGTACTCCCTCCGTCC 59.171 52.381 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2226 2747 0.185416 GATCTACTCCCTCCGTCCCA 59.815 60.0 0.0 0.0 0.00 4.37 R
2227 2748 0.185416 TGATCTACTCCCTCCGTCCC 59.815 60.0 0.0 0.0 0.00 4.46 R
3945 4625 0.615850 AACAAGAGTAGGGGCTCTGC 59.384 55.0 0.0 0.0 44.34 4.26 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
67 68 5.168569 TGAGCTCTGTAAAATAGAACCACG 58.831 41.667 16.19 0.00 0.00 4.94
68 69 5.148651 AGCTCTGTAAAATAGAACCACGT 57.851 39.130 0.00 0.00 0.00 4.49
69 70 5.548406 AGCTCTGTAAAATAGAACCACGTT 58.452 37.500 0.00 0.00 0.00 3.99
70 71 5.638234 AGCTCTGTAAAATAGAACCACGTTC 59.362 40.000 0.00 0.00 42.25 3.95
71 72 5.444218 GCTCTGTAAAATAGAACCACGTTCG 60.444 44.000 0.00 0.00 45.96 3.95
72 73 5.771469 TCTGTAAAATAGAACCACGTTCGA 58.229 37.500 0.00 0.00 45.96 3.71
73 74 5.630680 TCTGTAAAATAGAACCACGTTCGAC 59.369 40.000 0.00 0.00 45.96 4.20
84 85 0.935196 ACGTTCGACAACTTCCAAGC 59.065 50.000 0.00 0.00 0.00 4.01
92 93 2.887152 GACAACTTCCAAGCATGTCCTT 59.113 45.455 11.94 0.00 38.88 3.36
93 94 2.624838 ACAACTTCCAAGCATGTCCTTG 59.375 45.455 6.19 6.19 41.40 3.61
105 106 1.352083 TGTCCTTGGCTACTCTTGCT 58.648 50.000 0.00 0.00 0.00 3.91
106 107 1.699634 TGTCCTTGGCTACTCTTGCTT 59.300 47.619 0.00 0.00 0.00 3.91
107 108 2.903784 TGTCCTTGGCTACTCTTGCTTA 59.096 45.455 0.00 0.00 0.00 3.09
108 109 3.055819 TGTCCTTGGCTACTCTTGCTTAG 60.056 47.826 0.00 0.00 0.00 2.18
109 110 3.055747 GTCCTTGGCTACTCTTGCTTAGT 60.056 47.826 0.00 0.00 0.00 2.24
110 111 4.159879 GTCCTTGGCTACTCTTGCTTAGTA 59.840 45.833 0.00 0.00 0.00 1.82
111 112 4.402793 TCCTTGGCTACTCTTGCTTAGTAG 59.597 45.833 13.22 13.22 46.09 2.57
112 113 4.442192 CCTTGGCTACTCTTGCTTAGTAGG 60.442 50.000 16.97 4.75 44.36 3.18
114 115 4.863548 TGGCTACTCTTGCTTAGTAGGTA 58.136 43.478 16.97 6.33 44.36 3.08
115 116 5.455872 TGGCTACTCTTGCTTAGTAGGTAT 58.544 41.667 16.97 0.00 44.36 2.73
116 117 5.897824 TGGCTACTCTTGCTTAGTAGGTATT 59.102 40.000 16.97 0.00 44.36 1.89
122 278 6.668283 ACTCTTGCTTAGTAGGTATTCTTCCA 59.332 38.462 0.00 0.00 0.00 3.53
163 319 1.659335 CGTTTGCTGCACCTTGCTG 60.659 57.895 0.00 0.08 45.31 4.41
210 371 0.961019 ACACGCTGTTCATGCCATTT 59.039 45.000 0.00 0.00 0.00 2.32
217 378 3.118884 GCTGTTCATGCCATTTCCAGATT 60.119 43.478 0.00 0.00 0.00 2.40
220 381 4.773674 TGTTCATGCCATTTCCAGATTCTT 59.226 37.500 0.00 0.00 0.00 2.52
241 402 3.711059 ATACGTCCCCGACCTCGCT 62.711 63.158 0.00 0.00 38.18 4.93
253 414 2.712539 CTCGCTCAGTCGATCGCT 59.287 61.111 11.09 8.28 37.87 4.93
274 435 0.103208 GCCTGATCTCGTCGTCCAAT 59.897 55.000 0.00 0.00 0.00 3.16
292 453 2.060050 ATGACCGAGAGTTCCGAGAT 57.940 50.000 0.00 0.00 0.00 2.75
332 493 2.525629 TGGGCTCCGGTCAAGACA 60.526 61.111 0.00 0.00 0.00 3.41
530 694 7.525688 TTTGATTTCTAGCATCGTAGTCAAG 57.474 36.000 0.00 0.00 0.00 3.02
550 714 6.260493 GTCAAGTAGGAGTATGATACGACAGT 59.740 42.308 0.00 0.00 0.00 3.55
552 716 6.177310 AGTAGGAGTATGATACGACAGTCT 57.823 41.667 0.00 0.00 0.00 3.24
553 717 6.593807 AGTAGGAGTATGATACGACAGTCTT 58.406 40.000 0.00 0.00 0.00 3.01
577 741 9.384764 CTTTGCTAGATAAGTTTATATAGGCCC 57.615 37.037 0.00 1.52 36.15 5.80
578 742 7.108841 TGCTAGATAAGTTTATATAGGCCCG 57.891 40.000 0.00 0.00 36.15 6.13
591 758 2.594592 GCCCGGCTGACAAGTGTT 60.595 61.111 0.71 0.00 0.00 3.32
592 759 2.193536 GCCCGGCTGACAAGTGTTT 61.194 57.895 0.71 0.00 0.00 2.83
710 877 4.815308 CAGATTTGACCTAGATCCAAGCTG 59.185 45.833 2.04 2.04 33.22 4.24
720 887 5.420104 CCTAGATCCAAGCTGAAATTTGGTT 59.580 40.000 0.00 0.00 43.43 3.67
817 996 2.048597 GTGGACGGATGCGTGTGA 60.049 61.111 19.71 0.00 0.00 3.58
896 1078 2.885861 CTTGACCGGTCCTCCTCG 59.114 66.667 31.19 9.49 0.00 4.63
931 1117 1.926426 AACCTAGCCATCAGCCCACC 61.926 60.000 0.00 0.00 45.47 4.61
932 1118 2.074948 CCTAGCCATCAGCCCACCT 61.075 63.158 0.00 0.00 45.47 4.00
933 1119 1.449353 CTAGCCATCAGCCCACCTC 59.551 63.158 0.00 0.00 45.47 3.85
982 1175 1.379843 CCCAGAAATCCCCAACCCG 60.380 63.158 0.00 0.00 0.00 5.28
1839 2092 3.314635 CCATTCCATCTTGCTAACTGCTC 59.685 47.826 0.00 0.00 43.37 4.26
2119 2640 9.204570 ACAACTATTGTGTAGTGAATTGTACTC 57.795 33.333 0.00 0.00 43.48 2.59
2121 2642 7.328737 ACTATTGTGTAGTGAATTGTACTCCC 58.671 38.462 0.00 0.00 0.00 4.30
2122 2643 5.818678 TTGTGTAGTGAATTGTACTCCCT 57.181 39.130 0.00 0.00 0.00 4.20
2123 2644 5.401531 TGTGTAGTGAATTGTACTCCCTC 57.598 43.478 0.00 0.00 0.00 4.30
2124 2645 4.222145 TGTGTAGTGAATTGTACTCCCTCC 59.778 45.833 0.00 0.00 0.00 4.30
2126 2647 2.537143 AGTGAATTGTACTCCCTCCGT 58.463 47.619 0.00 0.00 0.00 4.69
2127 2648 2.496470 AGTGAATTGTACTCCCTCCGTC 59.504 50.000 0.00 0.00 0.00 4.79
2128 2649 1.829222 TGAATTGTACTCCCTCCGTCC 59.171 52.381 0.00 0.00 0.00 4.79
2132 2653 2.905415 TGTACTCCCTCCGTCCTAAA 57.095 50.000 0.00 0.00 0.00 1.85
2139 2660 4.192317 CTCCCTCCGTCCTAAAATTCTTG 58.808 47.826 0.00 0.00 0.00 3.02
2141 2662 3.939592 CCCTCCGTCCTAAAATTCTTGTC 59.060 47.826 0.00 0.00 0.00 3.18
2143 2664 5.246307 CCTCCGTCCTAAAATTCTTGTCTT 58.754 41.667 0.00 0.00 0.00 3.01
2145 2666 6.535508 CCTCCGTCCTAAAATTCTTGTCTTAG 59.464 42.308 0.00 0.00 0.00 2.18
2148 2669 8.319146 TCCGTCCTAAAATTCTTGTCTTAGATT 58.681 33.333 0.00 0.00 0.00 2.40
2149 2670 8.947115 CCGTCCTAAAATTCTTGTCTTAGATTT 58.053 33.333 0.00 0.00 0.00 2.17
2150 2671 9.760660 CGTCCTAAAATTCTTGTCTTAGATTTG 57.239 33.333 0.00 0.00 0.00 2.32
2175 2696 9.803315 TGTCTAAATACAGATGTATCAAGTCAC 57.197 33.333 5.97 3.82 40.10 3.67
2176 2697 8.959058 GTCTAAATACAGATGTATCAAGTCACG 58.041 37.037 5.97 0.00 40.10 4.35
2177 2698 8.683615 TCTAAATACAGATGTATCAAGTCACGT 58.316 33.333 5.97 0.00 40.10 4.49
2178 2699 9.302345 CTAAATACAGATGTATCAAGTCACGTT 57.698 33.333 5.97 0.00 40.10 3.99
2179 2700 8.547967 AAATACAGATGTATCAAGTCACGTTT 57.452 30.769 5.97 0.00 40.10 3.60
2180 2701 8.547967 AATACAGATGTATCAAGTCACGTTTT 57.452 30.769 5.97 0.00 40.10 2.43
2181 2702 9.647797 AATACAGATGTATCAAGTCACGTTTTA 57.352 29.630 5.97 0.00 40.10 1.52
2182 2703 7.582435 ACAGATGTATCAAGTCACGTTTTAG 57.418 36.000 0.00 0.00 0.00 1.85
2183 2704 7.152645 ACAGATGTATCAAGTCACGTTTTAGT 58.847 34.615 0.00 0.00 0.00 2.24
2184 2705 8.301720 ACAGATGTATCAAGTCACGTTTTAGTA 58.698 33.333 0.00 0.00 0.00 1.82
2185 2706 9.302345 CAGATGTATCAAGTCACGTTTTAGTAT 57.698 33.333 0.00 0.00 0.00 2.12
2186 2707 9.871238 AGATGTATCAAGTCACGTTTTAGTATT 57.129 29.630 0.00 0.00 0.00 1.89
2196 2717 9.962783 AGTCACGTTTTAGTATTAGATACATCC 57.037 33.333 0.00 0.00 38.21 3.51
2197 2718 9.740239 GTCACGTTTTAGTATTAGATACATCCA 57.260 33.333 0.00 0.00 38.21 3.41
2230 2751 9.898152 AACAAATTTAAGACAAGAATTTTGGGA 57.102 25.926 0.00 0.00 33.39 4.37
2231 2752 9.325198 ACAAATTTAAGACAAGAATTTTGGGAC 57.675 29.630 0.00 0.00 33.39 4.46
2232 2753 8.487176 CAAATTTAAGACAAGAATTTTGGGACG 58.513 33.333 0.00 0.00 32.35 4.79
2233 2754 5.699097 TTAAGACAAGAATTTTGGGACGG 57.301 39.130 0.00 0.00 0.00 4.79
2234 2755 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2235 2756 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2236 2757 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2237 2758 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2238 2759 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2258 2779 3.055963 GGAGTAGATCAGATGGCATGGAG 60.056 52.174 3.81 0.00 0.00 3.86
2324 2847 3.892284 TCTTGGCCTTTGTTTGTCTGTA 58.108 40.909 3.32 0.00 0.00 2.74
2333 2856 5.231991 CCTTTGTTTGTCTGTAATGTTGTGC 59.768 40.000 0.00 0.00 0.00 4.57
2353 2876 2.405025 GCGCAGTGCAAATGTAGAAAAC 59.595 45.455 16.83 0.00 45.45 2.43
2378 2901 4.806247 CACACTAACCTACTGCTGCTATTC 59.194 45.833 0.00 0.00 0.00 1.75
2434 2957 5.048504 TGCTTTTGTCATGACATTCTTCTCC 60.049 40.000 28.32 12.14 41.52 3.71
2509 3032 0.874390 TTGTCCTGACAATGAAGCGC 59.126 50.000 8.58 0.00 45.42 5.92
2566 3089 2.050350 CAGCATGGGGAAGCAGGTG 61.050 63.158 0.00 0.00 0.00 4.00
2567 3090 2.233566 AGCATGGGGAAGCAGGTGA 61.234 57.895 0.00 0.00 0.00 4.02
2570 3093 0.329261 CATGGGGAAGCAGGTGAGAA 59.671 55.000 0.00 0.00 0.00 2.87
2592 3115 1.604604 TGCTGCTGGTTGGAAGTTAC 58.395 50.000 0.00 0.00 0.00 2.50
2649 3172 2.828874 GCTTTCTGCAAGATCTCTGC 57.171 50.000 17.68 17.68 46.36 4.26
2652 3175 3.057736 GCTTTCTGCAAGATCTCTGCAAA 60.058 43.478 23.58 17.73 46.36 3.68
2655 3178 4.959596 TCTGCAAGATCTCTGCAAAATC 57.040 40.909 23.58 0.00 38.67 2.17
2656 3179 4.329392 TCTGCAAGATCTCTGCAAAATCA 58.671 39.130 23.58 10.18 38.67 2.57
2679 3202 2.290197 TGCAAAATTCTTTCCATGCCCC 60.290 45.455 0.00 0.00 33.01 5.80
2680 3203 2.290197 GCAAAATTCTTTCCATGCCCCA 60.290 45.455 0.00 0.00 0.00 4.96
2682 3205 4.591929 CAAAATTCTTTCCATGCCCCATT 58.408 39.130 0.00 0.00 0.00 3.16
2712 3235 8.249466 CATTACAGGTTTAATGCCGATTGATCG 61.249 40.741 6.41 6.41 38.73 3.69
2752 3284 2.701423 TCACTTGTACTACTTGGTGCCA 59.299 45.455 0.00 0.00 0.00 4.92
2757 3289 2.280628 GTACTACTTGGTGCCATGAGC 58.719 52.381 10.54 0.00 44.14 4.26
2759 3291 0.749454 CTACTTGGTGCCATGAGCCC 60.749 60.000 10.54 0.91 42.71 5.19
2761 3293 3.925630 CTTGGTGCCATGAGCCCGT 62.926 63.158 0.00 0.00 42.71 5.28
2762 3294 4.720902 TGGTGCCATGAGCCCGTG 62.721 66.667 0.00 0.00 42.71 4.94
2763 3295 4.408821 GGTGCCATGAGCCCGTGA 62.409 66.667 0.00 0.00 42.71 4.35
2764 3296 2.821366 GTGCCATGAGCCCGTGAG 60.821 66.667 0.00 0.00 42.71 3.51
2817 3352 6.003950 TCCTGATTGAACTTTCCTACTTTGG 58.996 40.000 0.00 0.00 0.00 3.28
2874 3494 4.392940 AGCTAGCATGTCATTATTGGTCC 58.607 43.478 18.83 0.00 0.00 4.46
2916 3555 6.434028 AGCAAGCTTTTTAACATCATACCAGA 59.566 34.615 0.00 0.00 0.00 3.86
2960 3599 6.183359 GCACTTCAAAAGTTAGCGAATTTACG 60.183 38.462 0.00 0.00 40.46 3.18
2975 3614 6.908284 GCGAATTTACGATATTTTGGCTTACA 59.092 34.615 0.00 0.00 35.09 2.41
2976 3615 7.589954 GCGAATTTACGATATTTTGGCTTACAT 59.410 33.333 0.00 0.00 35.09 2.29
3007 3648 5.664294 TGCAATTTCCAATGCAGAAGTAT 57.336 34.783 0.00 0.00 46.87 2.12
3025 3666 0.336392 ATGGAGGAAAGAAAGGCCCC 59.664 55.000 0.00 0.00 0.00 5.80
3034 3675 1.979155 GAAAGGCCCCTCAACCAGC 60.979 63.158 0.00 0.00 0.00 4.85
3084 3726 0.827925 TCCCTGTGTCGCTCTTCTGT 60.828 55.000 0.00 0.00 0.00 3.41
3097 3739 4.681835 CTCTTCTGTGAGCCAAAGATTG 57.318 45.455 0.00 0.00 26.81 2.67
3208 3873 1.019673 TAGTAGCTTCCGTACGCTGG 58.980 55.000 10.49 2.50 37.05 4.85
3222 3887 0.110688 CGCTGGTCATTTGTCACGTG 60.111 55.000 9.94 9.94 0.00 4.49
3287 3952 0.468226 TGGGACTCGTGCAACTCTTT 59.532 50.000 0.00 0.00 31.75 2.52
3397 4072 9.791820 TCATCTTTTGCTGTTCAAATATATGTG 57.208 29.630 0.00 0.00 43.53 3.21
3417 4092 4.520111 TGTGAAGTTCAGATTTGGTCCATG 59.480 41.667 5.62 0.00 0.00 3.66
3419 4094 5.241506 GTGAAGTTCAGATTTGGTCCATGAA 59.758 40.000 5.62 2.10 0.00 2.57
3478 4154 4.270008 GCCCAATACTAGACAACACCATT 58.730 43.478 0.00 0.00 0.00 3.16
3513 4189 1.082756 GACAGTTTTGGTCGCGCTG 60.083 57.895 5.56 3.32 0.00 5.18
3635 4311 6.887545 TCCCTATGTTGGTCGTTATTTGATTT 59.112 34.615 0.00 0.00 0.00 2.17
3684 4360 3.837355 ACTTGGGATTCTTTTGCACTCT 58.163 40.909 0.00 0.00 0.00 3.24
3689 4365 4.635765 TGGGATTCTTTTGCACTCTTATCG 59.364 41.667 0.00 0.00 0.00 2.92
3703 4379 6.675728 GCACTCTTATCGTGGAGGAAAATTTC 60.676 42.308 0.00 0.00 34.22 2.17
3742 4419 5.817296 ACTTGTGGAATTTCCTTTGCTTTTC 59.183 36.000 16.25 0.00 37.46 2.29
3743 4420 5.612725 TGTGGAATTTCCTTTGCTTTTCT 57.387 34.783 16.25 0.00 37.46 2.52
3750 4428 3.120321 TCCTTTGCTTTTCTCGTGCTA 57.880 42.857 0.00 0.00 0.00 3.49
3776 4454 7.518161 TCAAACGTTCATCTGAATTCATGTAC 58.482 34.615 8.96 8.44 36.33 2.90
3778 4456 6.893958 ACGTTCATCTGAATTCATGTACTC 57.106 37.500 8.96 0.00 36.33 2.59
3779 4457 5.812642 ACGTTCATCTGAATTCATGTACTCC 59.187 40.000 8.96 0.00 36.33 3.85
3780 4458 5.235186 CGTTCATCTGAATTCATGTACTCCC 59.765 44.000 8.96 0.00 36.33 4.30
3781 4459 6.352516 GTTCATCTGAATTCATGTACTCCCT 58.647 40.000 8.96 0.00 36.33 4.20
3782 4460 6.166984 TCATCTGAATTCATGTACTCCCTC 57.833 41.667 8.96 0.00 0.00 4.30
3783 4461 5.070981 TCATCTGAATTCATGTACTCCCTCC 59.929 44.000 8.96 0.00 0.00 4.30
3786 4464 5.070981 TCTGAATTCATGTACTCCCTCCATC 59.929 44.000 8.96 0.00 0.00 3.51
3787 4465 4.103153 TGAATTCATGTACTCCCTCCATCC 59.897 45.833 3.38 0.00 0.00 3.51
3789 4467 1.293763 TCATGTACTCCCTCCATCCCA 59.706 52.381 0.00 0.00 0.00 4.37
3790 4468 2.089982 TCATGTACTCCCTCCATCCCAT 60.090 50.000 0.00 0.00 0.00 4.00
3791 4469 3.143933 TCATGTACTCCCTCCATCCCATA 59.856 47.826 0.00 0.00 0.00 2.74
3792 4470 3.717507 TGTACTCCCTCCATCCCATAA 57.282 47.619 0.00 0.00 0.00 1.90
3793 4471 4.228237 TGTACTCCCTCCATCCCATAAT 57.772 45.455 0.00 0.00 0.00 1.28
3794 4472 3.909995 TGTACTCCCTCCATCCCATAATG 59.090 47.826 0.00 0.00 0.00 1.90
3795 4473 3.080660 ACTCCCTCCATCCCATAATGT 57.919 47.619 0.00 0.00 0.00 2.71
3796 4474 4.228237 ACTCCCTCCATCCCATAATGTA 57.772 45.455 0.00 0.00 0.00 2.29
3797 4475 4.577096 ACTCCCTCCATCCCATAATGTAA 58.423 43.478 0.00 0.00 0.00 2.41
3798 4476 4.599241 ACTCCCTCCATCCCATAATGTAAG 59.401 45.833 0.00 0.00 0.00 2.34
3799 4477 4.838403 TCCCTCCATCCCATAATGTAAGA 58.162 43.478 0.00 0.00 0.00 2.10
3800 4478 4.597507 TCCCTCCATCCCATAATGTAAGAC 59.402 45.833 0.00 0.00 0.00 3.01
3801 4479 4.563580 CCCTCCATCCCATAATGTAAGACG 60.564 50.000 0.00 0.00 0.00 4.18
3802 4480 4.563580 CCTCCATCCCATAATGTAAGACGG 60.564 50.000 0.00 0.00 0.00 4.79
3803 4481 3.971305 TCCATCCCATAATGTAAGACGGT 59.029 43.478 0.00 0.00 0.00 4.83
3804 4482 4.410883 TCCATCCCATAATGTAAGACGGTT 59.589 41.667 0.00 0.00 0.00 4.44
3805 4483 5.104277 TCCATCCCATAATGTAAGACGGTTT 60.104 40.000 0.00 0.00 0.00 3.27
3806 4484 5.592688 CCATCCCATAATGTAAGACGGTTTT 59.407 40.000 0.00 0.00 0.00 2.43
3807 4485 6.096282 CCATCCCATAATGTAAGACGGTTTTT 59.904 38.462 0.00 0.00 0.00 1.94
3808 4486 6.503589 TCCCATAATGTAAGACGGTTTTTG 57.496 37.500 0.00 0.00 0.00 2.44
3809 4487 6.239396 TCCCATAATGTAAGACGGTTTTTGA 58.761 36.000 0.00 0.00 0.00 2.69
3810 4488 6.149807 TCCCATAATGTAAGACGGTTTTTGAC 59.850 38.462 0.00 0.00 0.00 3.18
3811 4489 6.150474 CCCATAATGTAAGACGGTTTTTGACT 59.850 38.462 0.00 0.00 0.00 3.41
3812 4490 7.241376 CCATAATGTAAGACGGTTTTTGACTC 58.759 38.462 0.00 0.00 0.00 3.36
3813 4491 7.119262 CCATAATGTAAGACGGTTTTTGACTCT 59.881 37.037 0.00 0.00 0.00 3.24
3814 4492 9.146984 CATAATGTAAGACGGTTTTTGACTCTA 57.853 33.333 0.00 0.00 0.00 2.43
3815 4493 7.653767 AATGTAAGACGGTTTTTGACTCTAG 57.346 36.000 0.00 0.00 0.00 2.43
3816 4494 6.152932 TGTAAGACGGTTTTTGACTCTAGT 57.847 37.500 0.00 0.00 0.00 2.57
3817 4495 5.981315 TGTAAGACGGTTTTTGACTCTAGTG 59.019 40.000 0.00 0.00 0.00 2.74
3818 4496 4.667519 AGACGGTTTTTGACTCTAGTGT 57.332 40.909 0.00 0.00 0.00 3.55
3819 4497 5.779529 AGACGGTTTTTGACTCTAGTGTA 57.220 39.130 0.00 0.00 0.00 2.90
3820 4498 5.770417 AGACGGTTTTTGACTCTAGTGTAG 58.230 41.667 0.00 0.00 0.00 2.74
3821 4499 5.301298 AGACGGTTTTTGACTCTAGTGTAGT 59.699 40.000 0.00 0.00 0.00 2.73
3822 4500 5.287226 ACGGTTTTTGACTCTAGTGTAGTG 58.713 41.667 0.00 0.00 0.00 2.74
3823 4501 5.163478 ACGGTTTTTGACTCTAGTGTAGTGT 60.163 40.000 0.00 0.00 35.42 3.55
3824 4502 5.401674 CGGTTTTTGACTCTAGTGTAGTGTC 59.598 44.000 0.00 8.55 45.01 3.67
3853 4531 4.995124 CGTCTTATATTATGGGACGGAGG 58.005 47.826 17.59 0.00 43.69 4.30
3854 4532 4.142227 CGTCTTATATTATGGGACGGAGGG 60.142 50.000 17.59 0.46 43.69 4.30
3855 4533 5.021458 GTCTTATATTATGGGACGGAGGGA 58.979 45.833 0.00 0.00 0.00 4.20
3856 4534 5.482878 GTCTTATATTATGGGACGGAGGGAA 59.517 44.000 0.00 0.00 0.00 3.97
3857 4535 6.156429 GTCTTATATTATGGGACGGAGGGAAT 59.844 42.308 0.00 0.00 0.00 3.01
3858 4536 7.343833 GTCTTATATTATGGGACGGAGGGAATA 59.656 40.741 0.00 0.00 0.00 1.75
3859 4537 7.563924 TCTTATATTATGGGACGGAGGGAATAG 59.436 40.741 0.00 0.00 0.00 1.73
3860 4538 3.339713 TTATGGGACGGAGGGAATAGT 57.660 47.619 0.00 0.00 0.00 2.12
3861 4539 2.191981 ATGGGACGGAGGGAATAGTT 57.808 50.000 0.00 0.00 0.00 2.24
3862 4540 1.961133 TGGGACGGAGGGAATAGTTT 58.039 50.000 0.00 0.00 0.00 2.66
3863 4541 2.271777 TGGGACGGAGGGAATAGTTTT 58.728 47.619 0.00 0.00 0.00 2.43
3864 4542 2.026636 TGGGACGGAGGGAATAGTTTTG 60.027 50.000 0.00 0.00 0.00 2.44
3865 4543 2.026542 GGGACGGAGGGAATAGTTTTGT 60.027 50.000 0.00 0.00 0.00 2.83
3866 4544 3.198417 GGGACGGAGGGAATAGTTTTGTA 59.802 47.826 0.00 0.00 0.00 2.41
3867 4545 4.323715 GGGACGGAGGGAATAGTTTTGTAA 60.324 45.833 0.00 0.00 0.00 2.41
3868 4546 5.434408 GGACGGAGGGAATAGTTTTGTAAT 58.566 41.667 0.00 0.00 0.00 1.89
3869 4547 5.884232 GGACGGAGGGAATAGTTTTGTAATT 59.116 40.000 0.00 0.00 0.00 1.40
3870 4548 6.376299 GGACGGAGGGAATAGTTTTGTAATTT 59.624 38.462 0.00 0.00 0.00 1.82
3871 4549 7.387119 ACGGAGGGAATAGTTTTGTAATTTC 57.613 36.000 0.00 0.00 0.00 2.17
3872 4550 6.943718 ACGGAGGGAATAGTTTTGTAATTTCA 59.056 34.615 0.00 0.00 0.00 2.69
3873 4551 7.614192 ACGGAGGGAATAGTTTTGTAATTTCAT 59.386 33.333 0.00 0.00 0.00 2.57
3874 4552 9.116067 CGGAGGGAATAGTTTTGTAATTTCATA 57.884 33.333 0.00 0.00 0.00 2.15
3897 4575 9.999660 CATAGGATAGGATTCAAGATGATATGG 57.000 37.037 0.00 0.00 0.00 2.74
3903 4581 4.391216 GGATTCAAGATGATATGGCACTCG 59.609 45.833 0.00 0.00 0.00 4.18
3945 4625 9.350357 CCTATTCATGTGTTTTTGAGAATTCTG 57.650 33.333 14.00 0.00 0.00 3.02
3947 4627 6.146601 TCATGTGTTTTTGAGAATTCTGCA 57.853 33.333 14.00 8.03 0.00 4.41
3954 4634 0.254178 TGAGAATTCTGCAGAGCCCC 59.746 55.000 17.43 7.83 0.00 5.80
3961 4641 0.041833 TCTGCAGAGCCCCTACTCTT 59.958 55.000 13.74 0.00 44.76 2.85
3962 4642 0.177604 CTGCAGAGCCCCTACTCTTG 59.822 60.000 8.42 0.00 44.76 3.02
3976 4656 2.576615 ACTCTTGTTTGCTTCCTCACC 58.423 47.619 0.00 0.00 0.00 4.02
3982 4662 1.604278 GTTTGCTTCCTCACCTGTCAC 59.396 52.381 0.00 0.00 0.00 3.67
3999 4679 4.228912 GTCACTTGACAATCCAAACTGG 57.771 45.455 4.43 0.00 44.18 4.00
4000 4680 2.622942 TCACTTGACAATCCAAACTGGC 59.377 45.455 0.00 0.00 37.47 4.85
4001 4681 2.361757 CACTTGACAATCCAAACTGGCA 59.638 45.455 0.00 0.00 37.47 4.92
4002 4682 3.006110 CACTTGACAATCCAAACTGGCAT 59.994 43.478 0.00 0.00 37.47 4.40
4003 4683 4.218200 CACTTGACAATCCAAACTGGCATA 59.782 41.667 0.00 0.00 37.47 3.14
4004 4684 5.018809 ACTTGACAATCCAAACTGGCATAT 58.981 37.500 0.00 0.00 37.47 1.78
4005 4685 5.126061 ACTTGACAATCCAAACTGGCATATC 59.874 40.000 0.00 0.00 37.47 1.63
4006 4686 3.953612 TGACAATCCAAACTGGCATATCC 59.046 43.478 0.00 0.00 37.47 2.59
4007 4687 3.953612 GACAATCCAAACTGGCATATCCA 59.046 43.478 0.00 0.00 44.18 3.41
4008 4688 4.352009 ACAATCCAAACTGGCATATCCAA 58.648 39.130 0.00 0.00 46.01 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 2.290641 ACATGCTTGGAAGTTGTCGAAC 59.709 45.455 4.44 0.00 0.00 3.95
68 69 2.548057 GACATGCTTGGAAGTTGTCGAA 59.452 45.455 4.44 0.00 34.26 3.71
69 70 2.143122 GACATGCTTGGAAGTTGTCGA 58.857 47.619 4.44 0.00 34.26 4.20
70 71 1.197721 GGACATGCTTGGAAGTTGTCG 59.802 52.381 4.44 0.00 39.77 4.35
71 72 2.508526 AGGACATGCTTGGAAGTTGTC 58.491 47.619 4.44 12.51 38.96 3.18
72 73 2.624838 CAAGGACATGCTTGGAAGTTGT 59.375 45.455 5.29 0.00 0.00 3.32
73 74 3.293311 CAAGGACATGCTTGGAAGTTG 57.707 47.619 5.29 0.00 0.00 3.16
84 85 2.012673 GCAAGAGTAGCCAAGGACATG 58.987 52.381 0.00 0.00 0.00 3.21
92 93 3.709587 ACCTACTAAGCAAGAGTAGCCA 58.290 45.455 12.04 0.00 43.40 4.75
93 94 6.265876 AGAATACCTACTAAGCAAGAGTAGCC 59.734 42.308 12.04 2.50 43.40 3.93
105 106 8.890410 ACAGTACTTGGAAGAATACCTACTAA 57.110 34.615 0.00 0.00 0.00 2.24
106 107 8.890410 AACAGTACTTGGAAGAATACCTACTA 57.110 34.615 0.00 0.00 0.00 1.82
107 108 7.453752 TGAACAGTACTTGGAAGAATACCTACT 59.546 37.037 0.00 0.00 0.00 2.57
108 109 7.544915 GTGAACAGTACTTGGAAGAATACCTAC 59.455 40.741 0.00 0.00 0.00 3.18
109 110 7.453752 AGTGAACAGTACTTGGAAGAATACCTA 59.546 37.037 0.00 0.00 0.00 3.08
110 111 6.270231 AGTGAACAGTACTTGGAAGAATACCT 59.730 38.462 0.00 0.00 0.00 3.08
111 112 6.465084 AGTGAACAGTACTTGGAAGAATACC 58.535 40.000 0.00 0.00 0.00 2.73
112 113 8.923683 GTTAGTGAACAGTACTTGGAAGAATAC 58.076 37.037 0.00 0.00 35.48 1.89
114 115 6.935208 GGTTAGTGAACAGTACTTGGAAGAAT 59.065 38.462 0.00 0.00 37.29 2.40
115 116 6.126997 TGGTTAGTGAACAGTACTTGGAAGAA 60.127 38.462 0.00 0.00 37.29 2.52
116 117 5.364446 TGGTTAGTGAACAGTACTTGGAAGA 59.636 40.000 0.00 0.00 37.29 2.87
122 278 5.278660 CGGTAGTGGTTAGTGAACAGTACTT 60.279 44.000 15.37 0.00 37.29 2.24
163 319 1.024271 TGCTTGTTGTCAGTTCAGGC 58.976 50.000 0.00 0.00 35.33 4.85
186 347 0.179225 GCATGAACAGCGTGTTACCG 60.179 55.000 0.00 0.00 41.28 4.02
210 371 3.134081 GGGGACGTATTCAAGAATCTGGA 59.866 47.826 0.00 0.00 32.50 3.86
241 402 2.755876 AGGCCAGCGATCGACTGA 60.756 61.111 29.03 0.00 37.32 3.41
253 414 2.415608 GGACGACGAGATCAGGCCA 61.416 63.158 5.01 0.00 31.45 5.36
274 435 1.095600 CATCTCGGAACTCTCGGTCA 58.904 55.000 0.00 0.00 0.00 4.02
332 493 3.155167 GACCGCCCCTTCCGAGAT 61.155 66.667 0.00 0.00 0.00 2.75
430 594 0.520404 TCTCGCACTCGAACAGGTAC 59.480 55.000 0.00 0.00 44.98 3.34
530 694 6.864360 AAGACTGTCGTATCATACTCCTAC 57.136 41.667 1.52 0.00 0.00 3.18
552 716 8.038944 CGGGCCTATATAAACTTATCTAGCAAA 58.961 37.037 0.84 0.00 0.00 3.68
553 717 7.364408 CCGGGCCTATATAAACTTATCTAGCAA 60.364 40.741 0.84 0.00 0.00 3.91
573 737 4.643387 ACACTTGTCAGCCGGGCC 62.643 66.667 17.02 0.00 0.00 5.80
574 738 1.734388 AAAACACTTGTCAGCCGGGC 61.734 55.000 12.11 12.11 0.00 6.13
575 739 0.744281 AAAAACACTTGTCAGCCGGG 59.256 50.000 2.18 0.00 0.00 5.73
576 740 1.838913 CAAAAACACTTGTCAGCCGG 58.161 50.000 0.00 0.00 0.00 6.13
577 741 1.199624 GCAAAAACACTTGTCAGCCG 58.800 50.000 0.00 0.00 0.00 5.52
578 742 2.584492 AGCAAAAACACTTGTCAGCC 57.416 45.000 0.00 0.00 0.00 4.85
591 758 3.343617 CATACGGGAGAAGGAAGCAAAA 58.656 45.455 0.00 0.00 0.00 2.44
592 759 2.939640 GCATACGGGAGAAGGAAGCAAA 60.940 50.000 0.00 0.00 0.00 3.68
720 887 8.200024 TCCATCTAAAACAATGGGAAATTTGA 57.800 30.769 0.00 0.00 42.31 2.69
798 977 3.311110 ACACGCATCCGTCCACCT 61.311 61.111 0.00 0.00 46.39 4.00
817 996 4.681978 GTTCGGCTCGGGCACACT 62.682 66.667 10.74 0.00 40.87 3.55
1879 2132 5.966742 AATGGCTTAACAAGGAGTTCTTC 57.033 39.130 0.00 0.00 41.64 2.87
2094 2615 8.656849 GGAGTACAATTCACTACACAATAGTTG 58.343 37.037 0.00 0.00 0.00 3.16
2119 2640 3.939592 GACAAGAATTTTAGGACGGAGGG 59.060 47.826 0.00 0.00 0.00 4.30
2121 2642 7.321153 TCTAAGACAAGAATTTTAGGACGGAG 58.679 38.462 0.00 0.00 0.00 4.63
2122 2643 7.235935 TCTAAGACAAGAATTTTAGGACGGA 57.764 36.000 0.00 0.00 0.00 4.69
2123 2644 8.494016 AATCTAAGACAAGAATTTTAGGACGG 57.506 34.615 0.00 0.00 0.00 4.79
2124 2645 9.760660 CAAATCTAAGACAAGAATTTTAGGACG 57.239 33.333 0.00 0.00 0.00 4.79
2149 2670 9.803315 GTGACTTGATACATCTGTATTTAGACA 57.197 33.333 14.44 12.43 40.99 3.41
2150 2671 8.959058 CGTGACTTGATACATCTGTATTTAGAC 58.041 37.037 14.44 10.85 40.99 2.59
2152 2673 8.858003 ACGTGACTTGATACATCTGTATTTAG 57.142 34.615 4.44 7.42 40.99 1.85
2154 2675 8.547967 AAACGTGACTTGATACATCTGTATTT 57.452 30.769 4.44 0.00 40.99 1.40
2155 2676 8.547967 AAAACGTGACTTGATACATCTGTATT 57.452 30.769 4.44 0.00 40.99 1.89
2156 2677 9.302345 CTAAAACGTGACTTGATACATCTGTAT 57.698 33.333 2.53 2.53 43.38 2.29
2157 2678 8.301720 ACTAAAACGTGACTTGATACATCTGTA 58.698 33.333 0.00 0.00 34.67 2.74
2158 2679 7.152645 ACTAAAACGTGACTTGATACATCTGT 58.847 34.615 0.00 0.00 0.00 3.41
2159 2680 7.582435 ACTAAAACGTGACTTGATACATCTG 57.418 36.000 0.00 0.00 0.00 2.90
2160 2681 9.871238 AATACTAAAACGTGACTTGATACATCT 57.129 29.630 0.00 0.00 0.00 2.90
2170 2691 9.962783 GGATGTATCTAATACTAAAACGTGACT 57.037 33.333 0.00 0.00 36.70 3.41
2171 2692 9.740239 TGGATGTATCTAATACTAAAACGTGAC 57.260 33.333 0.00 0.00 36.70 3.67
2204 2725 9.898152 TCCCAAAATTCTTGTCTTAAATTTGTT 57.102 25.926 0.00 0.00 33.95 2.83
2205 2726 9.325198 GTCCCAAAATTCTTGTCTTAAATTTGT 57.675 29.630 0.00 0.00 33.95 2.83
2206 2727 8.487176 CGTCCCAAAATTCTTGTCTTAAATTTG 58.513 33.333 0.00 0.00 33.95 2.32
2207 2728 7.655732 CCGTCCCAAAATTCTTGTCTTAAATTT 59.344 33.333 0.00 0.00 34.86 1.82
2208 2729 7.014808 TCCGTCCCAAAATTCTTGTCTTAAATT 59.985 33.333 0.00 0.00 0.00 1.82
2209 2730 6.492087 TCCGTCCCAAAATTCTTGTCTTAAAT 59.508 34.615 0.00 0.00 0.00 1.40
2210 2731 5.828859 TCCGTCCCAAAATTCTTGTCTTAAA 59.171 36.000 0.00 0.00 0.00 1.52
2211 2732 5.378332 TCCGTCCCAAAATTCTTGTCTTAA 58.622 37.500 0.00 0.00 0.00 1.85
2212 2733 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2213 2734 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2214 2735 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2215 2736 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2216 2737 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2217 2738 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2218 2739 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2219 2740 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2220 2741 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2221 2742 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2222 2743 1.838077 CTACTCCCTCCGTCCCAAAAT 59.162 52.381 0.00 0.00 0.00 1.82
2223 2744 1.203212 TCTACTCCCTCCGTCCCAAAA 60.203 52.381 0.00 0.00 0.00 2.44
2224 2745 0.410663 TCTACTCCCTCCGTCCCAAA 59.589 55.000 0.00 0.00 0.00 3.28
2225 2746 0.635009 ATCTACTCCCTCCGTCCCAA 59.365 55.000 0.00 0.00 0.00 4.12
2226 2747 0.185416 GATCTACTCCCTCCGTCCCA 59.815 60.000 0.00 0.00 0.00 4.37
2227 2748 0.185416 TGATCTACTCCCTCCGTCCC 59.815 60.000 0.00 0.00 0.00 4.46
2228 2749 1.143277 TCTGATCTACTCCCTCCGTCC 59.857 57.143 0.00 0.00 0.00 4.79
2229 2750 2.642154 TCTGATCTACTCCCTCCGTC 57.358 55.000 0.00 0.00 0.00 4.79
2230 2751 2.489985 CCATCTGATCTACTCCCTCCGT 60.490 54.545 0.00 0.00 0.00 4.69
2231 2752 2.166829 CCATCTGATCTACTCCCTCCG 58.833 57.143 0.00 0.00 0.00 4.63
2232 2753 1.899142 GCCATCTGATCTACTCCCTCC 59.101 57.143 0.00 0.00 0.00 4.30
2233 2754 2.603021 TGCCATCTGATCTACTCCCTC 58.397 52.381 0.00 0.00 0.00 4.30
2234 2755 2.783379 TGCCATCTGATCTACTCCCT 57.217 50.000 0.00 0.00 0.00 4.20
2235 2756 2.027377 CCATGCCATCTGATCTACTCCC 60.027 54.545 0.00 0.00 0.00 4.30
2236 2757 2.902486 TCCATGCCATCTGATCTACTCC 59.098 50.000 0.00 0.00 0.00 3.85
2237 2758 3.577848 ACTCCATGCCATCTGATCTACTC 59.422 47.826 0.00 0.00 0.00 2.59
2238 2759 3.585360 ACTCCATGCCATCTGATCTACT 58.415 45.455 0.00 0.00 0.00 2.57
2258 2779 8.135529 ACAAAATCTTTTCAAACTAGTGCCTAC 58.864 33.333 0.00 0.00 0.00 3.18
2333 2856 2.979813 GGTTTTCTACATTTGCACTGCG 59.020 45.455 0.00 0.00 0.00 5.18
2348 2871 3.501062 GCAGTAGGTTAGTGTGGGTTTTC 59.499 47.826 0.00 0.00 0.00 2.29
2353 2876 1.676014 GCAGCAGTAGGTTAGTGTGGG 60.676 57.143 0.00 0.00 0.00 4.61
2378 2901 3.181493 GCTTTTGTGATGGCATACCTGAG 60.181 47.826 0.00 0.00 36.63 3.35
2434 2957 5.063944 CCAGAAGACAGGAACATCAAATACG 59.936 44.000 0.00 0.00 0.00 3.06
2566 3089 1.888512 TCCAACCAGCAGCAAATTCTC 59.111 47.619 0.00 0.00 0.00 2.87
2567 3090 1.999648 TCCAACCAGCAGCAAATTCT 58.000 45.000 0.00 0.00 0.00 2.40
2570 3093 1.708341 ACTTCCAACCAGCAGCAAAT 58.292 45.000 0.00 0.00 0.00 2.32
2649 3172 7.249186 TGGAAAGAATTTTGCACTGATTTTG 57.751 32.000 0.00 0.00 39.27 2.44
2652 3175 5.410439 GCATGGAAAGAATTTTGCACTGATT 59.590 36.000 0.00 0.00 45.54 2.57
2655 3178 3.434299 GGCATGGAAAGAATTTTGCACTG 59.566 43.478 0.00 0.00 45.54 3.66
2656 3179 3.557686 GGGCATGGAAAGAATTTTGCACT 60.558 43.478 0.00 0.00 45.54 4.40
2667 3190 3.017048 TGACTAATGGGGCATGGAAAG 57.983 47.619 0.00 0.00 0.00 2.62
2679 3202 7.011950 TCGGCATTAAACCTGTAATGACTAATG 59.988 37.037 8.71 0.00 44.27 1.90
2680 3203 7.051623 TCGGCATTAAACCTGTAATGACTAAT 58.948 34.615 8.71 0.00 44.27 1.73
2682 3205 5.979993 TCGGCATTAAACCTGTAATGACTA 58.020 37.500 8.71 0.00 44.27 2.59
2728 3251 4.315803 GCACCAAGTAGTACAAGTGACAT 58.684 43.478 16.90 0.00 0.00 3.06
2757 3289 1.402968 CAATTCTGATTGCCTCACGGG 59.597 52.381 0.00 0.00 36.54 5.28
2759 3291 3.426695 GGTTCAATTCTGATTGCCTCACG 60.427 47.826 0.00 0.00 41.94 4.35
2761 3293 3.091545 GGGTTCAATTCTGATTGCCTCA 58.908 45.455 0.00 0.00 41.94 3.86
2762 3294 3.129988 CAGGGTTCAATTCTGATTGCCTC 59.870 47.826 0.00 0.00 41.94 4.70
2763 3295 3.094572 CAGGGTTCAATTCTGATTGCCT 58.905 45.455 0.00 0.00 41.94 4.75
2764 3296 2.827921 ACAGGGTTCAATTCTGATTGCC 59.172 45.455 0.00 0.00 41.94 4.52
2765 3297 3.507233 TCACAGGGTTCAATTCTGATTGC 59.493 43.478 0.00 0.00 41.94 3.56
2766 3298 5.710513 TTCACAGGGTTCAATTCTGATTG 57.289 39.130 0.00 0.00 43.24 2.67
2767 3299 5.337009 GCATTCACAGGGTTCAATTCTGATT 60.337 40.000 0.00 0.00 33.19 2.57
2768 3300 4.159135 GCATTCACAGGGTTCAATTCTGAT 59.841 41.667 0.00 0.00 33.19 2.90
2817 3352 9.968870 CCTAAACAGATATAGTTTACTCCAGAC 57.031 37.037 8.24 0.00 39.65 3.51
2916 3555 5.410602 AGTGCAGATCCTAGGGAGAATATT 58.589 41.667 9.46 0.00 34.05 1.28
2960 3599 6.729187 AGCGAAGAATGTAAGCCAAAATATC 58.271 36.000 0.00 0.00 0.00 1.63
2967 3606 1.468520 GCAAGCGAAGAATGTAAGCCA 59.531 47.619 0.00 0.00 0.00 4.75
2975 3614 3.940209 TGGAAATTGCAAGCGAAGAAT 57.060 38.095 4.94 0.00 0.00 2.40
2976 3615 3.724508 TTGGAAATTGCAAGCGAAGAA 57.275 38.095 4.94 0.00 0.00 2.52
3007 3648 0.776080 AGGGGCCTTTCTTTCCTCCA 60.776 55.000 0.84 0.00 0.00 3.86
3025 3666 1.089920 CTTTGGATCCGCTGGTTGAG 58.910 55.000 7.39 0.00 0.00 3.02
3034 3675 0.940126 CGCCTCAATCTTTGGATCCG 59.060 55.000 7.39 0.00 0.00 4.18
3084 3726 6.916360 AATAAAACCTCAATCTTTGGCTCA 57.084 33.333 0.00 0.00 0.00 4.26
3208 3873 3.944422 ACAGAACACGTGACAAATGAC 57.056 42.857 25.01 4.02 0.00 3.06
3222 3887 5.915758 CACTCTCACAGTACTACAACAGAAC 59.084 44.000 0.00 0.00 32.21 3.01
3287 3952 2.018355 TGGAGTAGGTGGTAGCAACA 57.982 50.000 13.33 0.00 0.00 3.33
3396 4071 4.984295 TCATGGACCAAATCTGAACTTCA 58.016 39.130 0.00 0.00 0.00 3.02
3397 4072 5.703876 GTTCATGGACCAAATCTGAACTTC 58.296 41.667 22.95 5.56 41.41 3.01
3417 4092 6.759497 AAATGTTGCCTAGTATTGGAGTTC 57.241 37.500 0.00 0.00 0.00 3.01
3446 4122 4.038642 GTCTAGTATTGGGCCTCAAGAGAG 59.961 50.000 4.53 3.78 38.95 3.20
3447 4123 3.961408 GTCTAGTATTGGGCCTCAAGAGA 59.039 47.826 4.53 4.93 38.95 3.10
3448 4124 3.706594 TGTCTAGTATTGGGCCTCAAGAG 59.293 47.826 4.53 2.77 38.95 2.85
3493 4169 1.082756 GCGCGACCAAAACTGTCTG 60.083 57.895 12.10 0.00 0.00 3.51
3494 4170 1.227556 AGCGCGACCAAAACTGTCT 60.228 52.632 12.10 0.00 0.00 3.41
3496 4172 3.022287 CAGCGCGACCAAAACTGT 58.978 55.556 12.10 0.00 0.00 3.55
3499 4175 2.427410 CAGCAGCGCGACCAAAAC 60.427 61.111 12.10 0.00 0.00 2.43
3501 4177 4.927782 ACCAGCAGCGCGACCAAA 62.928 61.111 12.10 0.00 0.00 3.28
3513 4189 2.798976 TGAAATCACTTTGCACCAGC 57.201 45.000 0.00 0.00 42.57 4.85
3575 4251 4.739793 TCCAAATCCTCCACAAATTCTGT 58.260 39.130 0.00 0.00 39.56 3.41
3653 4329 7.494298 GCAAAAGAATCCCAAGTAAAAAGTTGA 59.506 33.333 0.00 0.00 0.00 3.18
3654 4330 7.279758 TGCAAAAGAATCCCAAGTAAAAAGTTG 59.720 33.333 0.00 0.00 0.00 3.16
3658 4334 6.883744 AGTGCAAAAGAATCCCAAGTAAAAA 58.116 32.000 0.00 0.00 0.00 1.94
3703 4379 3.753272 CCACAAGTGGTTTGAGTAGATGG 59.247 47.826 11.08 0.00 45.53 3.51
3742 4419 3.859961 AGATGAACGTTTGATAGCACGAG 59.140 43.478 0.46 0.00 39.76 4.18
3743 4420 3.612423 CAGATGAACGTTTGATAGCACGA 59.388 43.478 0.46 0.00 39.76 4.35
3750 4428 7.149569 ACATGAATTCAGATGAACGTTTGAT 57.850 32.000 14.54 0.00 36.80 2.57
3776 4454 4.846367 TCTTACATTATGGGATGGAGGGAG 59.154 45.833 0.00 0.00 0.00 4.30
3778 4456 4.563580 CGTCTTACATTATGGGATGGAGGG 60.564 50.000 0.00 0.00 0.00 4.30
3779 4457 4.563580 CCGTCTTACATTATGGGATGGAGG 60.564 50.000 13.77 4.26 35.71 4.30
3780 4458 4.040461 ACCGTCTTACATTATGGGATGGAG 59.960 45.833 20.86 2.95 36.78 3.86
3781 4459 3.971305 ACCGTCTTACATTATGGGATGGA 59.029 43.478 20.86 2.52 36.78 3.41
3782 4460 4.351874 ACCGTCTTACATTATGGGATGG 57.648 45.455 15.91 15.91 38.58 3.51
3783 4461 6.693315 AAAACCGTCTTACATTATGGGATG 57.307 37.500 0.00 0.00 0.00 3.51
3786 4464 6.150474 AGTCAAAAACCGTCTTACATTATGGG 59.850 38.462 0.00 0.00 0.00 4.00
3787 4465 7.119262 AGAGTCAAAAACCGTCTTACATTATGG 59.881 37.037 0.00 0.00 0.00 2.74
3789 4467 9.367444 CTAGAGTCAAAAACCGTCTTACATTAT 57.633 33.333 0.00 0.00 0.00 1.28
3790 4468 8.362639 ACTAGAGTCAAAAACCGTCTTACATTA 58.637 33.333 0.00 0.00 0.00 1.90
3791 4469 7.170998 CACTAGAGTCAAAAACCGTCTTACATT 59.829 37.037 0.00 0.00 0.00 2.71
3792 4470 6.645415 CACTAGAGTCAAAAACCGTCTTACAT 59.355 38.462 0.00 0.00 0.00 2.29
3793 4471 5.981315 CACTAGAGTCAAAAACCGTCTTACA 59.019 40.000 0.00 0.00 0.00 2.41
3794 4472 5.981915 ACACTAGAGTCAAAAACCGTCTTAC 59.018 40.000 0.00 0.00 0.00 2.34
3795 4473 6.152932 ACACTAGAGTCAAAAACCGTCTTA 57.847 37.500 0.00 0.00 0.00 2.10
3796 4474 5.019785 ACACTAGAGTCAAAAACCGTCTT 57.980 39.130 0.00 0.00 0.00 3.01
3797 4475 4.667519 ACACTAGAGTCAAAAACCGTCT 57.332 40.909 0.00 0.00 0.00 4.18
3798 4476 5.401674 CACTACACTAGAGTCAAAAACCGTC 59.598 44.000 0.00 0.00 0.00 4.79
3799 4477 5.163478 ACACTACACTAGAGTCAAAAACCGT 60.163 40.000 0.00 0.00 0.00 4.83
3800 4478 5.287226 ACACTACACTAGAGTCAAAAACCG 58.713 41.667 0.00 0.00 0.00 4.44
3801 4479 6.766452 GACACTACACTAGAGTCAAAAACC 57.234 41.667 0.00 0.00 43.19 3.27
3826 4504 7.274447 TCCGTCCCATAATATAAGACGTTTTT 58.726 34.615 17.31 0.00 46.62 1.94
3827 4505 6.819284 TCCGTCCCATAATATAAGACGTTTT 58.181 36.000 17.31 0.00 46.62 2.43
3828 4506 6.409524 TCCGTCCCATAATATAAGACGTTT 57.590 37.500 17.31 0.00 46.62 3.60
3829 4507 5.047519 CCTCCGTCCCATAATATAAGACGTT 60.048 44.000 17.31 0.00 46.62 3.99
3830 4508 4.461781 CCTCCGTCCCATAATATAAGACGT 59.538 45.833 17.31 0.00 46.62 4.34
3832 4510 5.021458 TCCCTCCGTCCCATAATATAAGAC 58.979 45.833 0.00 0.00 0.00 3.01
3833 4511 5.279562 TCCCTCCGTCCCATAATATAAGA 57.720 43.478 0.00 0.00 0.00 2.10
3834 4512 6.561519 ATTCCCTCCGTCCCATAATATAAG 57.438 41.667 0.00 0.00 0.00 1.73
3835 4513 7.194050 ACTATTCCCTCCGTCCCATAATATAA 58.806 38.462 0.00 0.00 0.00 0.98
3836 4514 6.748969 ACTATTCCCTCCGTCCCATAATATA 58.251 40.000 0.00 0.00 0.00 0.86
3837 4515 5.600749 ACTATTCCCTCCGTCCCATAATAT 58.399 41.667 0.00 0.00 0.00 1.28
3838 4516 5.019657 ACTATTCCCTCCGTCCCATAATA 57.980 43.478 0.00 0.00 0.00 0.98
3839 4517 3.870559 ACTATTCCCTCCGTCCCATAAT 58.129 45.455 0.00 0.00 0.00 1.28
3840 4518 3.339713 ACTATTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
3841 4519 3.339713 AACTATTCCCTCCGTCCCATA 57.660 47.619 0.00 0.00 0.00 2.74
3842 4520 2.191981 AACTATTCCCTCCGTCCCAT 57.808 50.000 0.00 0.00 0.00 4.00
3843 4521 1.961133 AAACTATTCCCTCCGTCCCA 58.039 50.000 0.00 0.00 0.00 4.37
3844 4522 2.026542 ACAAAACTATTCCCTCCGTCCC 60.027 50.000 0.00 0.00 0.00 4.46
3845 4523 3.345508 ACAAAACTATTCCCTCCGTCC 57.654 47.619 0.00 0.00 0.00 4.79
3846 4524 6.997239 AATTACAAAACTATTCCCTCCGTC 57.003 37.500 0.00 0.00 0.00 4.79
3847 4525 6.943718 TGAAATTACAAAACTATTCCCTCCGT 59.056 34.615 0.00 0.00 0.00 4.69
3848 4526 7.385778 TGAAATTACAAAACTATTCCCTCCG 57.614 36.000 0.00 0.00 0.00 4.63
3871 4549 9.999660 CCATATCATCTTGAATCCTATCCTATG 57.000 37.037 0.00 0.00 0.00 2.23
3872 4550 8.658619 GCCATATCATCTTGAATCCTATCCTAT 58.341 37.037 0.00 0.00 0.00 2.57
3873 4551 7.624879 TGCCATATCATCTTGAATCCTATCCTA 59.375 37.037 0.00 0.00 0.00 2.94
3874 4552 6.446110 TGCCATATCATCTTGAATCCTATCCT 59.554 38.462 0.00 0.00 0.00 3.24
3875 4553 6.541641 GTGCCATATCATCTTGAATCCTATCC 59.458 42.308 0.00 0.00 0.00 2.59
3876 4554 7.337167 AGTGCCATATCATCTTGAATCCTATC 58.663 38.462 0.00 0.00 0.00 2.08
3890 4568 4.152647 AGTAGGATTCGAGTGCCATATCA 58.847 43.478 0.00 0.00 0.00 2.15
3893 4571 5.353394 AAAAGTAGGATTCGAGTGCCATA 57.647 39.130 0.00 0.00 0.00 2.74
3895 4573 3.695830 AAAAGTAGGATTCGAGTGCCA 57.304 42.857 0.00 0.00 0.00 4.92
3918 4598 8.526147 AGAATTCTCAAAAACACATGAATAGGG 58.474 33.333 0.88 0.00 0.00 3.53
3945 4625 0.615850 AACAAGAGTAGGGGCTCTGC 59.384 55.000 0.00 0.00 44.34 4.26
3947 4627 1.003696 GCAAACAAGAGTAGGGGCTCT 59.996 52.381 0.00 0.00 46.82 4.09
3954 4634 3.748568 GGTGAGGAAGCAAACAAGAGTAG 59.251 47.826 0.00 0.00 0.00 2.57
3961 4641 1.211703 TGACAGGTGAGGAAGCAAACA 59.788 47.619 0.00 0.00 0.00 2.83
3962 4642 1.604278 GTGACAGGTGAGGAAGCAAAC 59.396 52.381 0.00 0.00 0.00 2.93
3982 4662 3.947910 ATGCCAGTTTGGATTGTCAAG 57.052 42.857 0.00 0.00 40.96 3.02
3998 4678 3.005155 GGACAAATCAGCTTGGATATGCC 59.995 47.826 0.00 0.00 37.10 4.40
3999 4679 3.887716 AGGACAAATCAGCTTGGATATGC 59.112 43.478 0.00 0.00 0.00 3.14
4000 4680 6.294473 AGTAGGACAAATCAGCTTGGATATG 58.706 40.000 0.00 0.00 0.00 1.78
4001 4681 6.506538 AGTAGGACAAATCAGCTTGGATAT 57.493 37.500 0.00 0.00 0.00 1.63
4002 4682 5.957771 AGTAGGACAAATCAGCTTGGATA 57.042 39.130 0.00 0.00 0.00 2.59
4003 4683 4.851639 AGTAGGACAAATCAGCTTGGAT 57.148 40.909 0.00 0.00 0.00 3.41
4004 4684 5.023452 TCTAGTAGGACAAATCAGCTTGGA 58.977 41.667 0.00 0.00 0.00 3.53
4005 4685 5.344743 TCTAGTAGGACAAATCAGCTTGG 57.655 43.478 0.00 0.00 0.00 3.61
4006 4686 5.689514 CGATCTAGTAGGACAAATCAGCTTG 59.310 44.000 0.00 0.00 0.00 4.01
4007 4687 5.361285 ACGATCTAGTAGGACAAATCAGCTT 59.639 40.000 0.00 0.00 0.00 3.74
4008 4688 4.890581 ACGATCTAGTAGGACAAATCAGCT 59.109 41.667 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.