Multiple sequence alignment - TraesCS7D01G171000

Loading Multiple Alignment...

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 TraesCS7D01G171000 chr7D 100.000 5329 0 0 1 5329 123322218 123327546 0.000000e+00 9841.0
1 TraesCS7D01G171000 chr7D 89.856 1735 90 30 2494 4174 123382390 123384092 0.000000e+00 2150.0
2 TraesCS7D01G171000 chr7D 92.121 330 19 6 4279 4602 123384091 123384419 4.860000e-125 459.0
3 TraesCS7D01G171000 chr7D 95.238 42 2 0 2302 2343 435437673 435437714 3.440000e-07 67.6
4 TraesCS7D01G171000 chr7D 90.476 42 3 1 2431 2471 123382304 123382345 3.000000e-03 54.7
5 TraesCS7D01G171000 chr7B 90.544 2242 130 36 1833 4013 84564176 84566396 0.000000e+00 2891.0
6 TraesCS7D01G171000 chr7B 91.165 1562 100 19 2468 4011 84522710 84524251 0.000000e+00 2085.0
7 TraesCS7D01G171000 chr7B 92.379 1076 33 22 768 1811 84562787 84563845 0.000000e+00 1487.0
8 TraesCS7D01G171000 chr7B 87.214 1267 136 18 2763 4017 84635616 84636868 0.000000e+00 1419.0
9 TraesCS7D01G171000 chr7B 88.216 908 54 21 524 1421 84520720 84521584 0.000000e+00 1035.0
10 TraesCS7D01G171000 chr7B 87.879 561 47 14 4302 4846 84644137 84644692 1.620000e-179 640.0
11 TraesCS7D01G171000 chr7B 81.447 760 101 25 4279 5020 84567407 84568144 2.140000e-163 586.0
12 TraesCS7D01G171000 chr7B 84.659 528 66 7 1 522 84520163 84520681 3.680000e-141 512.0
13 TraesCS7D01G171000 chr7B 77.451 714 114 19 1 705 84561366 84562041 3.010000e-102 383.0
14 TraesCS7D01G171000 chr7B 80.371 377 42 16 1914 2267 84634863 84635230 1.900000e-64 257.0
15 TraesCS7D01G171000 chr7B 79.070 430 41 26 1682 2077 84521838 84522252 3.190000e-62 250.0
16 TraesCS7D01G171000 chr7B 90.850 153 14 0 3466 3618 84636280 84636432 7.000000e-49 206.0
17 TraesCS7D01G171000 chr7B 89.796 147 11 4 5186 5329 84645233 84645378 9.110000e-43 185.0
18 TraesCS7D01G171000 chr7B 88.235 153 9 3 4026 4174 84643960 84644107 1.970000e-39 174.0
19 TraesCS7D01G171000 chr7B 95.370 108 5 0 2468 2575 84635302 84635409 7.100000e-39 172.0
20 TraesCS7D01G171000 chr7B 96.907 97 2 1 2602 2697 84635405 84635501 1.540000e-35 161.0
21 TraesCS7D01G171000 chr7B 91.228 114 8 2 4176 4289 34609752 34609641 2.570000e-33 154.0
22 TraesCS7D01G171000 chr7B 96.250 80 2 1 695 773 84562437 84562516 4.330000e-26 130.0
23 TraesCS7D01G171000 chr7B 100.000 29 0 0 5301 5329 333351502 333351474 3.000000e-03 54.7
24 TraesCS7D01G171000 chr7A 84.932 2044 170 73 245 2232 126175437 126177398 0.000000e+00 1941.0
25 TraesCS7D01G171000 chr7A 89.793 1450 86 23 2592 4017 126177672 126179083 0.000000e+00 1801.0
26 TraesCS7D01G171000 chr7A 91.873 1255 89 3 2758 4011 126142767 126144009 0.000000e+00 1740.0
27 TraesCS7D01G171000 chr7A 87.154 794 64 17 4279 5047 126185499 126186279 0.000000e+00 867.0
28 TraesCS7D01G171000 chr7A 78.679 1060 122 59 4279 5261 126144394 126145426 1.270000e-170 610.0
29 TraesCS7D01G171000 chr7A 84.182 550 61 20 1141 1681 126140045 126140577 1.320000e-140 510.0
30 TraesCS7D01G171000 chr7A 82.672 479 43 23 1811 2260 126141797 126142264 6.470000e-104 388.0
31 TraesCS7D01G171000 chr7A 87.676 284 17 6 2498 2765 126142327 126142608 1.110000e-81 315.0
32 TraesCS7D01G171000 chr7A 77.165 254 49 9 217 466 526620993 526621241 7.200000e-29 139.0
33 TraesCS7D01G171000 chrUn 100.000 386 0 0 3578 3963 480568364 480567979 0.000000e+00 713.0
34 TraesCS7D01G171000 chrUn 77.435 421 83 11 56 473 33187397 33187808 1.920000e-59 241.0
35 TraesCS7D01G171000 chrUn 93.750 64 2 1 2365 2428 103105963 103106024 1.580000e-15 95.3
36 TraesCS7D01G171000 chr6B 76.000 575 101 23 3141 3689 634308451 634309014 4.090000e-66 263.0
37 TraesCS7D01G171000 chr6B 79.221 231 46 2 3754 3983 634309435 634309664 5.520000e-35 159.0
38 TraesCS7D01G171000 chr6B 92.188 64 3 1 2365 2428 64320367 64320428 7.350000e-14 89.8
39 TraesCS7D01G171000 chr6B 78.070 114 14 7 2310 2417 5729617 5729725 1.600000e-05 62.1
40 TraesCS7D01G171000 chr6D 77.570 428 85 10 51 474 315365838 315366258 1.150000e-61 248.0
41 TraesCS7D01G171000 chr6A 77.622 429 82 13 51 474 452304284 452304703 1.150000e-61 248.0
42 TraesCS7D01G171000 chr6A 74.603 630 109 30 3146 3735 564096543 564097161 4.150000e-56 230.0
43 TraesCS7D01G171000 chr6A 80.087 231 44 2 3754 3983 564097603 564097832 2.550000e-38 171.0
44 TraesCS7D01G171000 chr6A 80.612 98 10 5 5108 5198 549363655 549363560 3.440000e-07 67.6
45 TraesCS7D01G171000 chr3D 76.963 382 76 11 95 473 22053365 22053737 1.950000e-49 207.0
46 TraesCS7D01G171000 chr3D 92.683 41 3 0 2300 2340 40173899 40173939 5.760000e-05 60.2
47 TraesCS7D01G171000 chr2D 77.596 366 66 14 114 475 627929496 627929143 1.950000e-49 207.0
48 TraesCS7D01G171000 chr2D 91.453 117 9 1 4173 4289 444766894 444767009 5.520000e-35 159.0
49 TraesCS7D01G171000 chr2A 74.891 458 95 12 51 501 713218663 713219107 1.960000e-44 191.0
50 TraesCS7D01G171000 chr2A 78.231 147 30 2 4388 4532 602717874 602717728 5.680000e-15 93.5
51 TraesCS7D01G171000 chr5A 96.078 102 4 0 4173 4274 64655827 64655928 3.300000e-37 167.0
52 TraesCS7D01G171000 chr3B 74.528 424 85 18 55 473 577529815 577529410 4.270000e-36 163.0
53 TraesCS7D01G171000 chr3B 82.692 104 13 5 5099 5198 779715690 779715792 2.640000e-13 87.9
54 TraesCS7D01G171000 chr3B 86.957 69 8 1 5099 5167 798325322 798325255 5.720000e-10 76.8
55 TraesCS7D01G171000 chr1A 74.232 423 92 16 56 473 6440441 6440851 1.540000e-35 161.0
56 TraesCS7D01G171000 chr1A 79.070 129 25 2 3455 3582 90109689 90109816 2.640000e-13 87.9
57 TraesCS7D01G171000 chr1A 87.719 57 7 0 5104 5160 32458623 32458679 3.440000e-07 67.6
58 TraesCS7D01G171000 chr5D 90.244 123 11 1 4161 4282 449260193 449260315 5.520000e-35 159.0
59 TraesCS7D01G171000 chr5D 88.618 123 12 2 4159 4280 114006085 114005964 1.200000e-31 148.0
60 TraesCS7D01G171000 chr5D 87.143 70 4 3 2359 2428 292715817 292715881 2.060000e-09 75.0
61 TraesCS7D01G171000 chr3A 91.964 112 9 0 4176 4287 746352859 746352748 1.990000e-34 158.0
62 TraesCS7D01G171000 chr3A 91.818 110 7 2 4165 4274 265545028 265545135 9.240000e-33 152.0
63 TraesCS7D01G171000 chr3A 89.394 66 7 0 5264 5329 11968643 11968708 3.420000e-12 84.2
64 TraesCS7D01G171000 chr3A 95.122 41 2 0 2303 2343 699566755 699566795 1.240000e-06 65.8
65 TraesCS7D01G171000 chr4A 90.598 117 9 2 4176 4292 152742124 152742010 2.570000e-33 154.0
66 TraesCS7D01G171000 chr4A 92.063 63 4 1 2367 2429 597867938 597867999 2.640000e-13 87.9
67 TraesCS7D01G171000 chr1B 90.678 118 8 2 4173 4290 488126024 488126138 2.570000e-33 154.0
68 TraesCS7D01G171000 chr1B 91.667 48 3 1 2300 2346 648708058 648708105 1.240000e-06 65.8
69 TraesCS7D01G171000 chr4D 80.000 200 35 5 229 427 433702655 433702460 5.560000e-30 143.0
70 TraesCS7D01G171000 chr4D 85.526 76 5 3 2367 2442 31822040 31822109 2.060000e-09 75.0
71 TraesCS7D01G171000 chr4B 79.851 134 7 15 2306 2428 188176939 188176815 4.420000e-11 80.5
72 TraesCS7D01G171000 chr5B 77.500 120 16 7 2308 2421 449613306 449613192 1.600000e-05 62.1
73 TraesCS7D01G171000 chr2B 97.143 35 1 0 2309 2343 171023193 171023159 5.760000e-05 60.2


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 TraesCS7D01G171000 chr7D 123322218 123327546 5328 False 9841.0 9841 100.000000 1 5329 1 chr7D.!!$F1 5328
1 TraesCS7D01G171000 chr7D 123382304 123384419 2115 False 887.9 2150 90.817667 2431 4602 3 chr7D.!!$F3 2171
2 TraesCS7D01G171000 chr7B 84561366 84568144 6778 False 1095.4 2891 87.614200 1 5020 5 chr7B.!!$F2 5019
3 TraesCS7D01G171000 chr7B 84520163 84524251 4088 False 970.5 2085 85.777500 1 4011 4 chr7B.!!$F1 4010
4 TraesCS7D01G171000 chr7B 84634863 84636868 2005 False 443.0 1419 90.142400 1914 4017 5 chr7B.!!$F3 2103
5 TraesCS7D01G171000 chr7B 84643960 84645378 1418 False 333.0 640 88.636667 4026 5329 3 chr7B.!!$F4 1303
6 TraesCS7D01G171000 chr7A 126175437 126179083 3646 False 1871.0 1941 87.362500 245 4017 2 chr7A.!!$F4 3772
7 TraesCS7D01G171000 chr7A 126185499 126186279 780 False 867.0 867 87.154000 4279 5047 1 chr7A.!!$F1 768
8 TraesCS7D01G171000 chr7A 126140045 126145426 5381 False 712.6 1740 85.016400 1141 5261 5 chr7A.!!$F3 4120
9 TraesCS7D01G171000 chr6B 634308451 634309664 1213 False 211.0 263 77.610500 3141 3983 2 chr6B.!!$F3 842
10 TraesCS7D01G171000 chr6A 564096543 564097832 1289 False 200.5 230 77.345000 3146 3983 2 chr6A.!!$F2 837

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
140 144 0.030235 GCGTGTGGAGGTTTGTTTCC 59.970 55.000 0.0 0.00 0.00 3.13 F
144 148 0.584876 GTGGAGGTTTGTTTCCGACG 59.415 55.000 0.0 0.00 36.22 5.12 F
309 313 0.913205 TTCCTATGGTGCCGCCTTAA 59.087 50.000 0.0 0.00 38.35 1.85 F
889 1628 1.132168 ACCCACCCCCTATCTAATCCC 60.132 57.143 0.0 0.00 0.00 3.85 F
1319 2085 1.227943 GCTGCTGTGGGTGAAGACA 60.228 57.895 0.0 0.00 0.00 3.41 F
2919 5831 1.609501 TTACCTCGCTGCTCTGGGT 60.610 57.895 0.0 3.26 0.00 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 3697 0.233848 CCCGTGTACGTTTGCAGTTC 59.766 55.000 0.00 0.0 37.74 3.01 R
1873 4088 1.587946 CAAGAACAACCAAACGCTTGC 59.412 47.619 0.00 0.0 0.00 4.01 R
2085 4371 3.624777 ACTGACATTGCCCTTATCTTGG 58.375 45.455 0.00 0.0 0.00 3.61 R
2820 5732 0.319641 GCGATCGATAGTTGGGGGAC 60.320 60.000 21.57 0.0 37.40 4.46 R
3068 5991 1.153745 GCCAAACGTGTGTTGCCAA 60.154 52.632 4.73 0.0 38.62 4.52 R
4796 9204 0.811281 ATTGCTGGCTTCGCTAAACC 59.189 50.000 0.00 0.0 0.00 3.27 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
26 27 6.681729 TGTGTCTCTTTAGGGTTTGTATCT 57.318 37.500 0.00 0.00 0.00 1.98
27 28 7.074653 TGTGTCTCTTTAGGGTTTGTATCTT 57.925 36.000 0.00 0.00 0.00 2.40
28 29 7.159372 TGTGTCTCTTTAGGGTTTGTATCTTC 58.841 38.462 0.00 0.00 0.00 2.87
29 30 7.159372 GTGTCTCTTTAGGGTTTGTATCTTCA 58.841 38.462 0.00 0.00 0.00 3.02
30 31 7.660208 GTGTCTCTTTAGGGTTTGTATCTTCAA 59.340 37.037 0.00 0.00 0.00 2.69
41 45 4.377839 TGTATCTTCAAGAAGGCGAGAG 57.622 45.455 9.73 0.00 38.88 3.20
47 51 0.243907 CAAGAAGGCGAGAGAACGGA 59.756 55.000 0.00 0.00 0.00 4.69
77 81 5.728741 ACTGAAGATGGGATAAAGTTCTCCT 59.271 40.000 4.85 0.00 0.00 3.69
79 83 5.726308 TGAAGATGGGATAAAGTTCTCCTCA 59.274 40.000 4.85 2.74 0.00 3.86
89 93 7.673926 GGATAAAGTTCTCCTCATCTATCTCCT 59.326 40.741 0.00 0.00 0.00 3.69
93 97 6.414732 AGTTCTCCTCATCTATCTCCTATCG 58.585 44.000 0.00 0.00 0.00 2.92
109 113 0.459899 ATCGCGATGGTGCTTGTAGA 59.540 50.000 23.04 0.00 0.00 2.59
117 121 0.520404 GGTGCTTGTAGAGTCGTCGA 59.480 55.000 0.00 0.00 0.00 4.20
140 144 0.030235 GCGTGTGGAGGTTTGTTTCC 59.970 55.000 0.00 0.00 0.00 3.13
142 146 1.670791 GTGTGGAGGTTTGTTTCCGA 58.329 50.000 0.00 0.00 36.22 4.55
144 148 0.584876 GTGGAGGTTTGTTTCCGACG 59.415 55.000 0.00 0.00 36.22 5.12
177 181 5.799213 AGATTCTGTCGGATTTTGTCTTCT 58.201 37.500 0.00 0.00 0.00 2.85
186 190 4.697352 CGGATTTTGTCTTCTGTGGATCTT 59.303 41.667 0.00 0.00 0.00 2.40
192 196 3.326006 TGTCTTCTGTGGATCTTCTTGCT 59.674 43.478 0.00 0.00 0.00 3.91
195 199 4.285517 TCTTCTGTGGATCTTCTTGCTTCT 59.714 41.667 0.00 0.00 0.00 2.85
207 211 3.884895 TCTTGCTTCTGGTCTTTGTTCA 58.115 40.909 0.00 0.00 0.00 3.18
215 219 4.380531 TCTGGTCTTTGTTCATCTGTGTC 58.619 43.478 0.00 0.00 0.00 3.67
248 252 6.332976 ACAGGTTGGATCCTTTCAATCTAT 57.667 37.500 14.23 0.00 33.10 1.98
264 268 6.522946 TCAATCTATGCTTCTCTTCATCAGG 58.477 40.000 0.00 0.00 0.00 3.86
278 282 3.950397 TCATCAGGGACGCTTGTTATTT 58.050 40.909 0.00 0.00 0.00 1.40
290 294 3.836949 CTTGTTATTTTGGTGCGCTGAT 58.163 40.909 9.73 0.00 0.00 2.90
309 313 0.913205 TTCCTATGGTGCCGCCTTAA 59.087 50.000 0.00 0.00 38.35 1.85
325 329 4.662145 GCCTTAACACAATGATTTCTCGG 58.338 43.478 0.00 0.00 0.00 4.63
326 330 4.156008 GCCTTAACACAATGATTTCTCGGT 59.844 41.667 0.00 0.00 0.00 4.69
349 354 6.239204 GGTTGTCTAAACAATAAGGTTTGCCT 60.239 38.462 0.00 0.00 46.58 4.75
357 362 2.478335 TAAGGTTTGCCTGGCTCCGG 62.478 60.000 21.03 0.00 46.33 5.14
416 421 1.531149 CTCCGGTGCTTGTAGTTGTTG 59.469 52.381 0.00 0.00 0.00 3.33
418 423 1.263217 CCGGTGCTTGTAGTTGTTGTC 59.737 52.381 0.00 0.00 0.00 3.18
429 434 4.591498 TGTAGTTGTTGTCAGGTGGTCTAT 59.409 41.667 0.00 0.00 0.00 1.98
451 456 8.553153 TCTATGGACCTGGATGTAATGTTTTTA 58.447 33.333 0.00 0.00 0.00 1.52
457 462 9.832445 GACCTGGATGTAATGTTTTTATCTCTA 57.168 33.333 0.00 0.00 0.00 2.43
586 633 4.824479 TTCAGATAGGTGACTTGCATCA 57.176 40.909 0.00 0.00 43.67 3.07
609 658 4.220602 AGCAACTCTCTCTCTTTCTTCCTC 59.779 45.833 0.00 0.00 0.00 3.71
615 664 4.045334 TCTCTCTCTTTCTTCCTCTCCCTT 59.955 45.833 0.00 0.00 0.00 3.95
622 671 1.208706 CTTCCTCTCCCTTTCCCTCC 58.791 60.000 0.00 0.00 0.00 4.30
627 676 2.357569 CCTCTCCCTTTCCCTCCAAATG 60.358 54.545 0.00 0.00 0.00 2.32
684 734 2.172851 ATCAGGAAAACCGTACGCAA 57.827 45.000 10.49 0.00 0.00 4.85
804 1537 3.545703 CGCCTTTGATCTGGTCCTTAAT 58.454 45.455 0.00 0.00 0.00 1.40
805 1538 3.947834 CGCCTTTGATCTGGTCCTTAATT 59.052 43.478 0.00 0.00 0.00 1.40
806 1539 5.123227 CGCCTTTGATCTGGTCCTTAATTA 58.877 41.667 0.00 0.00 0.00 1.40
807 1540 5.237344 CGCCTTTGATCTGGTCCTTAATTAG 59.763 44.000 0.00 0.00 0.00 1.73
889 1628 1.132168 ACCCACCCCCTATCTAATCCC 60.132 57.143 0.00 0.00 0.00 3.85
902 1641 9.945904 CCCTATCTAATCCCTAGTTTAATTCAC 57.054 37.037 0.00 0.00 0.00 3.18
950 1706 1.269998 GCACGCGGTTCTATCCTCTAT 59.730 52.381 12.47 0.00 0.00 1.98
951 1707 2.486982 GCACGCGGTTCTATCCTCTATA 59.513 50.000 12.47 0.00 0.00 1.31
953 1709 3.752222 CACGCGGTTCTATCCTCTATACT 59.248 47.826 12.47 0.00 0.00 2.12
954 1710 4.002316 ACGCGGTTCTATCCTCTATACTC 58.998 47.826 12.47 0.00 0.00 2.59
955 1711 4.001652 CGCGGTTCTATCCTCTATACTCA 58.998 47.826 0.00 0.00 0.00 3.41
956 1712 4.093703 CGCGGTTCTATCCTCTATACTCAG 59.906 50.000 0.00 0.00 0.00 3.35
982 1743 3.006967 CCGGCCTATATATATGCACCTCC 59.993 52.174 18.19 3.72 0.00 4.30
1081 1847 1.672030 CGTGCTCCTGTTGGCATCA 60.672 57.895 0.00 0.00 40.66 3.07
1319 2085 1.227943 GCTGCTGTGGGTGAAGACA 60.228 57.895 0.00 0.00 0.00 3.41
1400 2166 1.982073 GCGGCGTGCTCAAGCTTATT 61.982 55.000 9.37 0.00 42.66 1.40
1562 2344 7.337942 AGTTTCACATGAGGTTTCCATCTTATC 59.662 37.037 0.00 0.00 0.00 1.75
1643 2429 2.627945 TCCATGGCGAAACATACAGTC 58.372 47.619 6.96 0.00 0.00 3.51
1873 4088 7.805071 GCAATATCAAATAGAAACGGGAATCAG 59.195 37.037 0.00 0.00 0.00 2.90
2085 4371 9.832445 TCAGAACTTATAATCCATAACAACTCC 57.168 33.333 0.00 0.00 0.00 3.85
2270 4562 7.118390 GCACGCCTTATCATTATCAAATACTCT 59.882 37.037 0.00 0.00 0.00 3.24
2271 4563 8.651588 CACGCCTTATCATTATCAAATACTCTC 58.348 37.037 0.00 0.00 0.00 3.20
2312 4604 8.858094 AGTATCTAAACTTTAGTATTCCCTCCG 58.142 37.037 8.16 0.00 0.00 4.63
2421 4713 6.037786 TGAGACACTTATTTTGAGACGGAT 57.962 37.500 0.00 0.00 0.00 4.18
2429 4721 2.961526 TTTGAGACGGATGGAGTAGC 57.038 50.000 0.00 0.00 0.00 3.58
2575 5266 7.324616 CGTTTCATTTTTCTCCTCTGAAATGAC 59.675 37.037 9.19 1.42 43.93 3.06
2620 5311 6.377912 TCTTCAATGTTCCCCTTCCTTTTAA 58.622 36.000 0.00 0.00 0.00 1.52
2820 5732 3.777465 TTACGAATTCCGGACAGAGAG 57.223 47.619 1.83 0.00 43.93 3.20
2919 5831 1.609501 TTACCTCGCTGCTCTGGGT 60.610 57.895 0.00 3.26 0.00 4.51
2979 5891 3.797796 TCATCAAGAACGTCGTCGAAAAA 59.202 39.130 9.47 0.00 40.62 1.94
3068 5991 8.455903 AAACATGAAGCATGCATATAGTAGTT 57.544 30.769 21.98 10.65 44.80 2.24
3332 6281 3.294493 GGCACTCGGGCTGCAAAA 61.294 61.111 11.15 0.00 39.42 2.44
3402 6363 3.204827 GCCTACTACGCCGTCCGA 61.205 66.667 0.00 0.00 41.02 4.55
3432 6393 2.577772 AGAAGTCCCTAGAGGCCAAT 57.422 50.000 5.01 0.00 34.51 3.16
3438 6399 2.797278 CCTAGAGGCCAATCCGCGT 61.797 63.158 5.01 0.00 39.89 6.01
3963 7452 1.287815 CTACGTGAACGCCACCAGA 59.712 57.895 0.00 0.00 42.76 3.86
4024 7513 8.248117 CCATTAATTGGTTACTACGTATAGGC 57.752 38.462 0.00 0.00 40.99 3.93
4042 7546 6.016276 GTATAGGCCATACAATCCAACTTTGG 60.016 42.308 5.01 1.13 42.94 3.28
4081 8443 4.202441 CGAGAGATCCATGGAAATTGGTT 58.798 43.478 20.67 0.00 35.64 3.67
4111 8473 5.703978 AACCATTGTTGATGTTCGATGAA 57.296 34.783 0.00 0.00 33.71 2.57
4150 8512 6.593268 TTTCCATGATTCTTGCATTCTTCA 57.407 33.333 0.00 0.00 0.00 3.02
4172 8536 1.271926 GCCACTCCCACCATAAGTGTT 60.272 52.381 0.00 0.00 45.74 3.32
4173 8537 2.026636 GCCACTCCCACCATAAGTGTTA 60.027 50.000 0.00 0.00 45.74 2.41
4174 8538 3.371595 GCCACTCCCACCATAAGTGTTAT 60.372 47.826 0.00 0.00 45.74 1.89
4175 8539 4.855340 CCACTCCCACCATAAGTGTTATT 58.145 43.478 0.00 0.00 45.74 1.40
4176 8540 4.881850 CCACTCCCACCATAAGTGTTATTC 59.118 45.833 0.00 0.00 45.74 1.75
4177 8541 4.881850 CACTCCCACCATAAGTGTTATTCC 59.118 45.833 0.00 0.00 45.74 3.01
4178 8542 4.079958 ACTCCCACCATAAGTGTTATTCCC 60.080 45.833 0.00 0.00 45.74 3.97
4179 8543 4.116113 TCCCACCATAAGTGTTATTCCCT 58.884 43.478 0.00 0.00 45.74 4.20
4180 8544 4.165372 TCCCACCATAAGTGTTATTCCCTC 59.835 45.833 0.00 0.00 45.74 4.30
4181 8545 4.461198 CCACCATAAGTGTTATTCCCTCC 58.539 47.826 0.00 0.00 45.74 4.30
4182 8546 4.127171 CACCATAAGTGTTATTCCCTCCG 58.873 47.826 0.00 0.00 41.93 4.63
4183 8547 3.778629 ACCATAAGTGTTATTCCCTCCGT 59.221 43.478 0.00 0.00 0.00 4.69
4184 8548 4.226620 ACCATAAGTGTTATTCCCTCCGTT 59.773 41.667 0.00 0.00 0.00 4.44
4185 8549 4.814771 CCATAAGTGTTATTCCCTCCGTTC 59.185 45.833 0.00 0.00 0.00 3.95
4186 8550 5.424757 CATAAGTGTTATTCCCTCCGTTCA 58.575 41.667 0.00 0.00 0.00 3.18
4187 8551 3.329929 AGTGTTATTCCCTCCGTTCAC 57.670 47.619 0.00 0.00 0.00 3.18
4188 8552 2.904434 AGTGTTATTCCCTCCGTTCACT 59.096 45.455 0.00 0.00 0.00 3.41
4189 8553 3.326880 AGTGTTATTCCCTCCGTTCACTT 59.673 43.478 0.00 0.00 32.15 3.16
4190 8554 4.070009 GTGTTATTCCCTCCGTTCACTTT 58.930 43.478 0.00 0.00 0.00 2.66
4191 8555 4.517832 GTGTTATTCCCTCCGTTCACTTTT 59.482 41.667 0.00 0.00 0.00 2.27
4192 8556 5.702209 GTGTTATTCCCTCCGTTCACTTTTA 59.298 40.000 0.00 0.00 0.00 1.52
4193 8557 6.373495 GTGTTATTCCCTCCGTTCACTTTTAT 59.627 38.462 0.00 0.00 0.00 1.40
4194 8558 7.550196 GTGTTATTCCCTCCGTTCACTTTTATA 59.450 37.037 0.00 0.00 0.00 0.98
4195 8559 8.102047 TGTTATTCCCTCCGTTCACTTTTATAA 58.898 33.333 0.00 0.00 0.00 0.98
4196 8560 8.610035 GTTATTCCCTCCGTTCACTTTTATAAG 58.390 37.037 0.00 0.00 37.40 1.73
4197 8561 5.750352 TCCCTCCGTTCACTTTTATAAGT 57.250 39.130 0.00 0.00 45.40 2.24
4198 8562 5.727434 TCCCTCCGTTCACTTTTATAAGTC 58.273 41.667 0.00 0.00 42.67 3.01
4199 8563 4.565564 CCCTCCGTTCACTTTTATAAGTCG 59.434 45.833 0.00 0.00 42.67 4.18
4200 8564 5.166398 CCTCCGTTCACTTTTATAAGTCGT 58.834 41.667 0.00 0.00 42.67 4.34
4201 8565 5.636543 CCTCCGTTCACTTTTATAAGTCGTT 59.363 40.000 0.00 0.00 42.67 3.85
4202 8566 6.146673 CCTCCGTTCACTTTTATAAGTCGTTT 59.853 38.462 0.00 0.00 42.67 3.60
4203 8567 7.109006 TCCGTTCACTTTTATAAGTCGTTTC 57.891 36.000 0.00 0.00 42.67 2.78
4204 8568 6.700960 TCCGTTCACTTTTATAAGTCGTTTCA 59.299 34.615 0.00 0.00 42.67 2.69
4205 8569 7.007697 CCGTTCACTTTTATAAGTCGTTTCAG 58.992 38.462 0.00 0.00 42.67 3.02
4206 8570 7.095940 CCGTTCACTTTTATAAGTCGTTTCAGA 60.096 37.037 0.00 0.00 42.67 3.27
4207 8571 7.734726 CGTTCACTTTTATAAGTCGTTTCAGAC 59.265 37.037 0.00 0.00 42.67 3.51
4208 8572 8.545420 GTTCACTTTTATAAGTCGTTTCAGACA 58.455 33.333 0.00 0.00 42.67 3.41
4209 8573 8.651391 TCACTTTTATAAGTCGTTTCAGACAA 57.349 30.769 0.00 0.00 42.67 3.18
4210 8574 9.100554 TCACTTTTATAAGTCGTTTCAGACAAA 57.899 29.630 0.00 0.00 42.67 2.83
4211 8575 9.878599 CACTTTTATAAGTCGTTTCAGACAAAT 57.121 29.630 0.00 0.00 42.67 2.32
4212 8576 9.878599 ACTTTTATAAGTCGTTTCAGACAAATG 57.121 29.630 0.00 0.00 40.60 2.32
4224 8588 6.395426 TTCAGACAAATGAAATTGAGCTGT 57.605 33.333 0.00 0.00 36.10 4.40
4225 8589 6.395426 TCAGACAAATGAAATTGAGCTGTT 57.605 33.333 0.00 0.00 36.10 3.16
4226 8590 6.808829 TCAGACAAATGAAATTGAGCTGTTT 58.191 32.000 0.00 0.00 36.10 2.83
4227 8591 7.267128 TCAGACAAATGAAATTGAGCTGTTTT 58.733 30.769 0.00 0.00 36.10 2.43
4228 8592 8.412456 TCAGACAAATGAAATTGAGCTGTTTTA 58.588 29.630 0.00 0.00 36.10 1.52
4229 8593 8.482429 CAGACAAATGAAATTGAGCTGTTTTAC 58.518 33.333 0.00 0.00 36.10 2.01
4230 8594 8.196771 AGACAAATGAAATTGAGCTGTTTTACA 58.803 29.630 0.00 0.00 36.10 2.41
4231 8595 8.891671 ACAAATGAAATTGAGCTGTTTTACAT 57.108 26.923 0.00 0.00 36.10 2.29
4232 8596 9.979578 ACAAATGAAATTGAGCTGTTTTACATA 57.020 25.926 0.00 0.00 36.10 2.29
4235 8599 9.630098 AATGAAATTGAGCTGTTTTACATAGTG 57.370 29.630 0.00 0.00 33.44 2.74
4236 8600 8.165239 TGAAATTGAGCTGTTTTACATAGTGT 57.835 30.769 0.00 0.00 0.00 3.55
4237 8601 8.289618 TGAAATTGAGCTGTTTTACATAGTGTC 58.710 33.333 0.00 0.00 0.00 3.67
4238 8602 7.986085 AATTGAGCTGTTTTACATAGTGTCT 57.014 32.000 0.00 0.00 0.00 3.41
4239 8603 6.785488 TTGAGCTGTTTTACATAGTGTCTG 57.215 37.500 0.00 0.00 0.00 3.51
4240 8604 6.096673 TGAGCTGTTTTACATAGTGTCTGA 57.903 37.500 0.00 0.00 0.00 3.27
4241 8605 6.521162 TGAGCTGTTTTACATAGTGTCTGAA 58.479 36.000 0.00 0.00 0.00 3.02
4242 8606 6.989759 TGAGCTGTTTTACATAGTGTCTGAAA 59.010 34.615 0.00 0.00 0.00 2.69
4243 8607 7.042051 TGAGCTGTTTTACATAGTGTCTGAAAC 60.042 37.037 0.00 0.00 32.90 2.78
4244 8608 6.765989 AGCTGTTTTACATAGTGTCTGAAACA 59.234 34.615 0.02 13.57 36.43 2.83
4245 8609 7.445402 AGCTGTTTTACATAGTGTCTGAAACAT 59.555 33.333 14.16 0.00 40.80 2.71
4246 8610 7.746475 GCTGTTTTACATAGTGTCTGAAACATC 59.254 37.037 14.16 9.83 40.80 3.06
4247 8611 8.902540 TGTTTTACATAGTGTCTGAAACATCT 57.097 30.769 0.02 0.00 40.80 2.90
4248 8612 9.990360 TGTTTTACATAGTGTCTGAAACATCTA 57.010 29.630 0.02 0.00 40.80 1.98
4250 8614 9.990360 TTTTACATAGTGTCTGAAACATCTACA 57.010 29.630 0.02 0.00 40.80 2.74
4251 8615 9.990360 TTTACATAGTGTCTGAAACATCTACAA 57.010 29.630 0.02 0.00 40.80 2.41
4252 8616 9.990360 TTACATAGTGTCTGAAACATCTACAAA 57.010 29.630 0.02 0.00 40.80 2.83
4253 8617 8.539770 ACATAGTGTCTGAAACATCTACAAAG 57.460 34.615 0.02 0.00 40.80 2.77
4254 8618 5.931441 AGTGTCTGAAACATCTACAAAGC 57.069 39.130 0.02 0.00 40.80 3.51
4255 8619 4.757149 AGTGTCTGAAACATCTACAAAGCC 59.243 41.667 0.02 0.00 40.80 4.35
4256 8620 4.757149 GTGTCTGAAACATCTACAAAGCCT 59.243 41.667 0.00 0.00 40.80 4.58
4257 8621 5.239525 GTGTCTGAAACATCTACAAAGCCTT 59.760 40.000 0.00 0.00 40.80 4.35
4258 8622 6.426937 GTGTCTGAAACATCTACAAAGCCTTA 59.573 38.462 0.00 0.00 40.80 2.69
4259 8623 7.119846 GTGTCTGAAACATCTACAAAGCCTTAT 59.880 37.037 0.00 0.00 40.80 1.73
4260 8624 8.318412 TGTCTGAAACATCTACAAAGCCTTATA 58.682 33.333 0.00 0.00 31.20 0.98
4261 8625 9.162764 GTCTGAAACATCTACAAAGCCTTATAA 57.837 33.333 0.00 0.00 0.00 0.98
4262 8626 9.733556 TCTGAAACATCTACAAAGCCTTATAAA 57.266 29.630 0.00 0.00 0.00 1.40
4267 8631 9.515226 AACATCTACAAAGCCTTATAAAAGTGA 57.485 29.630 0.00 0.00 0.00 3.41
4268 8632 9.515226 ACATCTACAAAGCCTTATAAAAGTGAA 57.485 29.630 0.00 0.00 0.00 3.18
4269 8633 9.774742 CATCTACAAAGCCTTATAAAAGTGAAC 57.225 33.333 0.00 0.00 0.00 3.18
4270 8634 8.911918 TCTACAAAGCCTTATAAAAGTGAACA 57.088 30.769 0.00 0.00 0.00 3.18
4271 8635 8.999431 TCTACAAAGCCTTATAAAAGTGAACAG 58.001 33.333 0.00 0.00 0.00 3.16
4272 8636 7.817418 ACAAAGCCTTATAAAAGTGAACAGA 57.183 32.000 0.00 0.00 0.00 3.41
4273 8637 7.875971 ACAAAGCCTTATAAAAGTGAACAGAG 58.124 34.615 0.00 0.00 0.00 3.35
4274 8638 7.719633 ACAAAGCCTTATAAAAGTGAACAGAGA 59.280 33.333 0.00 0.00 0.00 3.10
4275 8639 7.674471 AAGCCTTATAAAAGTGAACAGAGAC 57.326 36.000 0.00 0.00 0.00 3.36
4276 8640 6.769512 AGCCTTATAAAAGTGAACAGAGACA 58.230 36.000 0.00 0.00 0.00 3.41
4277 8641 6.876257 AGCCTTATAAAAGTGAACAGAGACAG 59.124 38.462 0.00 0.00 0.00 3.51
4289 8653 5.698089 TGAACAGAGACAGTAGCTGATTTTG 59.302 40.000 0.00 0.00 35.18 2.44
4305 8669 4.837860 TGATTTTGTAGGCCAGTGGATTTT 59.162 37.500 15.20 0.00 0.00 1.82
4384 8763 5.181245 CCAAGTGTATCATAATTAAGGGCGG 59.819 44.000 0.00 0.00 0.00 6.13
4385 8764 5.562298 AGTGTATCATAATTAAGGGCGGT 57.438 39.130 0.00 0.00 0.00 5.68
4497 8888 3.642901 CACCGTAGTGCGCTTCTAT 57.357 52.632 9.73 0.00 37.14 1.98
4506 8897 1.321743 GTGCGCTTCTATGTTCTGTCG 59.678 52.381 9.73 0.00 0.00 4.35
4559 8952 6.097696 GCTTGACTAAGAATTCTCTACCCTCT 59.902 42.308 8.78 0.00 35.92 3.69
4608 9001 3.181510 CCATCATCGTATGCGTCGATCTA 60.182 47.826 2.37 3.77 44.49 1.98
4651 9044 4.398988 TCATCTTAACCACATCCATGCAAC 59.601 41.667 0.00 0.00 0.00 4.17
4653 9046 1.458398 TAACCACATCCATGCAACCG 58.542 50.000 0.00 0.00 0.00 4.44
4658 9051 1.334556 CACATCCATGCAACCGGTATG 59.665 52.381 8.00 8.38 39.11 2.39
4659 9052 1.211703 ACATCCATGCAACCGGTATGA 59.788 47.619 15.96 4.13 41.61 2.15
4660 9053 2.296792 CATCCATGCAACCGGTATGAA 58.703 47.619 15.96 8.40 41.61 2.57
4734 9140 4.149598 GGTGGGAGTAAAACTGGAAATGT 58.850 43.478 0.00 0.00 0.00 2.71
4737 9143 3.826729 GGGAGTAAAACTGGAAATGTGCT 59.173 43.478 0.00 0.00 0.00 4.40
4855 9314 1.903860 TGTTGAATACTAGGGTGCGGT 59.096 47.619 0.00 0.00 0.00 5.68
4856 9315 2.277084 GTTGAATACTAGGGTGCGGTG 58.723 52.381 0.00 0.00 0.00 4.94
4959 9423 9.677567 TCTTGTTTATTTCTTTCTCCATTTTCG 57.322 29.630 0.00 0.00 0.00 3.46
5056 9573 4.781775 TCTCTTGGGTTTCACTGGTTTA 57.218 40.909 0.00 0.00 0.00 2.01
5174 9691 9.522804 TTAACATTTTCTAAACACATGGTCAAC 57.477 29.630 0.00 0.00 0.00 3.18
5175 9692 7.346751 ACATTTTCTAAACACATGGTCAACT 57.653 32.000 0.00 0.00 0.00 3.16
5217 9832 6.628919 ACATACTTTTAAACACAGGGTCAC 57.371 37.500 0.00 0.00 0.00 3.67
5218 9833 6.123651 ACATACTTTTAAACACAGGGTCACA 58.876 36.000 0.00 0.00 0.00 3.58
5219 9834 6.775629 ACATACTTTTAAACACAGGGTCACAT 59.224 34.615 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.336887 CCGTTCTCTCGCCTTCTTGAA 60.337 52.381 0.00 0.00 0.00 2.69
27 28 0.243907 CCGTTCTCTCGCCTTCTTGA 59.756 55.000 0.00 0.00 0.00 3.02
28 29 0.243907 TCCGTTCTCTCGCCTTCTTG 59.756 55.000 0.00 0.00 0.00 3.02
29 30 0.966920 TTCCGTTCTCTCGCCTTCTT 59.033 50.000 0.00 0.00 0.00 2.52
30 31 0.966920 TTTCCGTTCTCTCGCCTTCT 59.033 50.000 0.00 0.00 0.00 2.85
41 45 3.433615 CCATCTTCAGTGAGTTTCCGTTC 59.566 47.826 0.00 0.00 0.00 3.95
47 51 6.784031 ACTTTATCCCATCTTCAGTGAGTTT 58.216 36.000 0.00 0.00 0.00 2.66
77 81 3.879892 CCATCGCGATAGGAGATAGATGA 59.120 47.826 23.22 0.00 36.94 2.92
79 83 3.629855 CACCATCGCGATAGGAGATAGAT 59.370 47.826 31.08 13.52 33.01 1.98
89 93 1.679153 TCTACAAGCACCATCGCGATA 59.321 47.619 23.22 1.31 36.85 2.92
93 97 1.281899 GACTCTACAAGCACCATCGC 58.718 55.000 0.00 0.00 0.00 4.58
109 113 3.292936 ACACGCCCTTCGACGACT 61.293 61.111 0.00 0.00 41.67 4.18
117 121 1.528309 CAAACCTCCACACGCCCTT 60.528 57.895 0.00 0.00 0.00 3.95
140 144 1.124462 GAATCTTGCGAGATCCGTCG 58.876 55.000 17.02 0.22 41.78 5.12
142 146 1.478510 ACAGAATCTTGCGAGATCCGT 59.521 47.619 17.02 11.18 41.78 4.69
144 148 2.123342 CGACAGAATCTTGCGAGATCC 58.877 52.381 17.02 4.23 41.78 3.36
167 171 5.009010 GCAAGAAGATCCACAGAAGACAAAA 59.991 40.000 0.00 0.00 0.00 2.44
177 181 2.373169 ACCAGAAGCAAGAAGATCCACA 59.627 45.455 0.00 0.00 0.00 4.17
186 190 3.884895 TGAACAAAGACCAGAAGCAAGA 58.115 40.909 0.00 0.00 0.00 3.02
192 196 4.780815 ACACAGATGAACAAAGACCAGAA 58.219 39.130 0.00 0.00 0.00 3.02
195 199 3.476552 GGACACAGATGAACAAAGACCA 58.523 45.455 0.00 0.00 0.00 4.02
207 211 2.229062 CTGTAGACACACGGACACAGAT 59.771 50.000 0.00 0.00 36.37 2.90
215 219 0.677288 TCCAACCTGTAGACACACGG 59.323 55.000 0.00 0.00 0.00 4.94
248 252 1.205655 CGTCCCTGATGAAGAGAAGCA 59.794 52.381 0.00 0.00 0.00 3.91
264 268 2.324860 GCACCAAAATAACAAGCGTCC 58.675 47.619 0.00 0.00 0.00 4.79
278 282 1.667236 CATAGGAATCAGCGCACCAA 58.333 50.000 11.47 0.00 0.00 3.67
290 294 0.913205 TTAAGGCGGCACCATAGGAA 59.087 50.000 13.08 0.00 43.14 3.36
309 313 4.389374 AGACAACCGAGAAATCATTGTGT 58.611 39.130 0.00 0.00 33.76 3.72
357 362 0.030908 CGTCATCGCTCCTCCCTTAC 59.969 60.000 0.00 0.00 0.00 2.34
429 434 7.410174 AGATAAAAACATTACATCCAGGTCCA 58.590 34.615 0.00 0.00 0.00 4.02
532 577 8.377799 CCCCGGGTTTATAGTGTTTAATATACT 58.622 37.037 21.85 0.00 32.44 2.12
586 633 4.159557 AGGAAGAAAGAGAGAGAGTTGCT 58.840 43.478 0.00 0.00 0.00 3.91
609 658 2.907458 ACATTTGGAGGGAAAGGGAG 57.093 50.000 0.00 0.00 0.00 4.30
615 664 1.283613 ACGGCATACATTTGGAGGGAA 59.716 47.619 0.00 0.00 0.00 3.97
622 671 4.221342 GCATGACATACGGCATACATTTG 58.779 43.478 0.00 0.00 0.00 2.32
684 734 4.868314 ACCTTCAGTTACTCGCTAGTTT 57.132 40.909 0.00 0.00 37.15 2.66
804 1537 5.720202 CATACTGGACTGCTGTGTTACTAA 58.280 41.667 0.00 0.00 0.00 2.24
805 1538 4.381612 GCATACTGGACTGCTGTGTTACTA 60.382 45.833 0.00 0.00 35.49 1.82
806 1539 3.617531 GCATACTGGACTGCTGTGTTACT 60.618 47.826 0.00 0.00 35.49 2.24
807 1540 2.673368 GCATACTGGACTGCTGTGTTAC 59.327 50.000 0.00 0.00 35.49 2.50
902 1641 3.873952 GCAGTGCTGAGGGTTCTAATTAG 59.126 47.826 8.18 6.11 0.00 1.73
982 1743 3.264897 GTATCAGCACGGCCGCAG 61.265 66.667 28.58 20.09 0.00 5.18
1081 1847 2.882876 CCGGTCTGTCGGTCGATT 59.117 61.111 0.00 0.00 44.60 3.34
1319 2085 4.351054 CCGAGCTTGGCCAAGGGT 62.351 66.667 39.51 27.57 38.80 4.34
1400 2166 2.772077 TACCTTGCATGGCGTTTCTA 57.228 45.000 18.17 0.00 0.00 2.10
1521 2303 2.931325 TGAAACTGCACGAACGTACTTT 59.069 40.909 0.00 0.00 0.00 2.66
1643 2429 0.895530 TTCGCAACTACTCCAGGAGG 59.104 55.000 21.31 6.30 33.35 4.30
1799 3694 1.301423 GTGTACGTTTGCAGTTCCCA 58.699 50.000 0.00 0.00 0.00 4.37
1802 3697 0.233848 CCCGTGTACGTTTGCAGTTC 59.766 55.000 0.00 0.00 37.74 3.01
1873 4088 1.587946 CAAGAACAACCAAACGCTTGC 59.412 47.619 0.00 0.00 0.00 4.01
2085 4371 3.624777 ACTGACATTGCCCTTATCTTGG 58.375 45.455 0.00 0.00 0.00 3.61
2293 4585 4.781621 AGGACGGAGGGAATACTAAAGTTT 59.218 41.667 0.00 0.00 0.00 2.66
2297 4589 6.872585 TTTTAGGACGGAGGGAATACTAAA 57.127 37.500 0.00 0.00 0.00 1.85
2303 4595 6.771267 GTCATTTATTTTAGGACGGAGGGAAT 59.229 38.462 0.00 0.00 0.00 3.01
2306 4598 5.681639 AGTCATTTATTTTAGGACGGAGGG 58.318 41.667 0.00 0.00 33.84 4.30
2310 4602 7.611213 AGTTGAGTCATTTATTTTAGGACGG 57.389 36.000 0.00 0.00 33.84 4.79
2405 4697 5.463724 GCTACTCCATCCGTCTCAAAATAAG 59.536 44.000 0.00 0.00 0.00 1.73
2421 4713 4.714632 ACTAAAACAAAGCTGCTACTCCA 58.285 39.130 0.90 0.00 0.00 3.86
2620 5311 2.616842 GTGTTTTCCACGTCACTCCAAT 59.383 45.455 0.00 0.00 33.61 3.16
2787 5699 4.091365 GGAATTCGTAATTTGCCTGCAAAC 59.909 41.667 18.62 7.20 46.80 2.93
2820 5732 0.319641 GCGATCGATAGTTGGGGGAC 60.320 60.000 21.57 0.00 37.40 4.46
2919 5831 3.980698 AGGCTAGTTTGGAGGCCATAATA 59.019 43.478 5.01 0.00 46.23 0.98
2979 5891 2.821969 GAGGAATTTCATGTGCCAGTGT 59.178 45.455 0.00 0.00 0.00 3.55
3068 5991 1.153745 GCCAAACGTGTGTTGCCAA 60.154 52.632 4.73 0.00 38.62 4.52
3318 6267 1.507141 CGTTCTTTTGCAGCCCGAGT 61.507 55.000 0.00 0.00 0.00 4.18
3402 6363 1.080434 GGACTTCTTCAGCGCGTCT 60.080 57.895 8.43 1.94 0.00 4.18
4017 7506 6.970484 CAAAGTTGGATTGTATGGCCTATAC 58.030 40.000 3.32 11.03 41.68 1.47
4042 7546 1.389106 CTCGCACTACGGCTAAACAAC 59.611 52.381 0.00 0.00 43.89 3.32
4047 7551 1.602851 GATCTCTCGCACTACGGCTAA 59.397 52.381 0.00 0.00 43.89 3.09
4109 8471 2.813779 AATGCTCGAACGCAGATTTC 57.186 45.000 5.54 0.00 44.10 2.17
4110 8472 2.159517 GGAAATGCTCGAACGCAGATTT 60.160 45.455 5.54 2.31 44.10 2.17
4111 8473 1.398390 GGAAATGCTCGAACGCAGATT 59.602 47.619 5.54 3.38 44.10 2.40
4150 8512 1.064463 CACTTATGGTGGGAGTGGCAT 60.064 52.381 0.00 0.00 41.90 4.40
4172 8536 7.854337 ACTTATAAAAGTGAACGGAGGGAATA 58.146 34.615 0.00 0.00 44.40 1.75
4173 8537 6.718294 ACTTATAAAAGTGAACGGAGGGAAT 58.282 36.000 0.00 0.00 44.40 3.01
4174 8538 6.117975 ACTTATAAAAGTGAACGGAGGGAA 57.882 37.500 0.00 0.00 44.40 3.97
4175 8539 5.622914 CGACTTATAAAAGTGAACGGAGGGA 60.623 44.000 0.00 0.00 46.09 4.20
4176 8540 4.565564 CGACTTATAAAAGTGAACGGAGGG 59.434 45.833 0.00 0.00 46.09 4.30
4177 8541 5.166398 ACGACTTATAAAAGTGAACGGAGG 58.834 41.667 0.00 0.00 46.09 4.30
4178 8542 6.701432 AACGACTTATAAAAGTGAACGGAG 57.299 37.500 0.00 0.00 46.09 4.63
4179 8543 6.700960 TGAAACGACTTATAAAAGTGAACGGA 59.299 34.615 0.00 0.00 46.09 4.69
4180 8544 6.879962 TGAAACGACTTATAAAAGTGAACGG 58.120 36.000 0.00 0.00 46.09 4.44
4181 8545 7.734726 GTCTGAAACGACTTATAAAAGTGAACG 59.265 37.037 0.00 0.00 46.09 3.95
4182 8546 8.545420 TGTCTGAAACGACTTATAAAAGTGAAC 58.455 33.333 0.00 0.00 46.09 3.18
4183 8547 8.651391 TGTCTGAAACGACTTATAAAAGTGAA 57.349 30.769 0.00 0.00 46.09 3.18
4184 8548 8.651391 TTGTCTGAAACGACTTATAAAAGTGA 57.349 30.769 0.00 0.00 46.09 3.41
4185 8549 9.878599 ATTTGTCTGAAACGACTTATAAAAGTG 57.121 29.630 0.00 0.00 46.09 3.16
4192 8556 9.398170 CAATTTCATTTGTCTGAAACGACTTAT 57.602 29.630 1.68 0.00 45.21 1.73
4193 8557 8.616942 TCAATTTCATTTGTCTGAAACGACTTA 58.383 29.630 1.68 0.00 45.21 2.24
4194 8558 7.479980 TCAATTTCATTTGTCTGAAACGACTT 58.520 30.769 1.68 0.00 45.21 3.01
4195 8559 7.026631 TCAATTTCATTTGTCTGAAACGACT 57.973 32.000 1.68 0.00 45.21 4.18
4196 8560 6.129352 GCTCAATTTCATTTGTCTGAAACGAC 60.129 38.462 1.68 0.00 45.21 4.34
4197 8561 5.914635 GCTCAATTTCATTTGTCTGAAACGA 59.085 36.000 1.68 2.14 45.21 3.85
4198 8562 5.916883 AGCTCAATTTCATTTGTCTGAAACG 59.083 36.000 1.68 0.00 45.21 3.60
4199 8563 6.698766 ACAGCTCAATTTCATTTGTCTGAAAC 59.301 34.615 1.68 0.00 45.21 2.78
4200 8564 6.808829 ACAGCTCAATTTCATTTGTCTGAAA 58.191 32.000 2.11 2.11 46.13 2.69
4201 8565 6.395426 ACAGCTCAATTTCATTTGTCTGAA 57.605 33.333 12.42 0.00 34.98 3.02
4202 8566 6.395426 AACAGCTCAATTTCATTTGTCTGA 57.605 33.333 12.42 0.00 34.98 3.27
4203 8567 7.473027 AAAACAGCTCAATTTCATTTGTCTG 57.527 32.000 0.00 0.00 35.95 3.51
4204 8568 8.196771 TGTAAAACAGCTCAATTTCATTTGTCT 58.803 29.630 0.00 0.00 0.00 3.41
4205 8569 8.351495 TGTAAAACAGCTCAATTTCATTTGTC 57.649 30.769 0.00 0.00 0.00 3.18
4206 8570 8.891671 ATGTAAAACAGCTCAATTTCATTTGT 57.108 26.923 0.00 0.00 0.00 2.83
4209 8573 9.630098 CACTATGTAAAACAGCTCAATTTCATT 57.370 29.630 0.00 0.00 0.00 2.57
4210 8574 8.796475 ACACTATGTAAAACAGCTCAATTTCAT 58.204 29.630 0.00 0.00 0.00 2.57
4211 8575 8.165239 ACACTATGTAAAACAGCTCAATTTCA 57.835 30.769 0.00 0.00 0.00 2.69
4212 8576 8.507249 AGACACTATGTAAAACAGCTCAATTTC 58.493 33.333 0.00 0.00 0.00 2.17
4213 8577 8.292448 CAGACACTATGTAAAACAGCTCAATTT 58.708 33.333 0.00 0.00 0.00 1.82
4214 8578 7.661437 TCAGACACTATGTAAAACAGCTCAATT 59.339 33.333 0.00 0.00 0.00 2.32
4215 8579 7.161404 TCAGACACTATGTAAAACAGCTCAAT 58.839 34.615 0.00 0.00 0.00 2.57
4216 8580 6.521162 TCAGACACTATGTAAAACAGCTCAA 58.479 36.000 0.00 0.00 0.00 3.02
4217 8581 6.096673 TCAGACACTATGTAAAACAGCTCA 57.903 37.500 0.00 0.00 0.00 4.26
4218 8582 7.042051 TGTTTCAGACACTATGTAAAACAGCTC 60.042 37.037 10.38 0.00 32.93 4.09
4219 8583 6.765989 TGTTTCAGACACTATGTAAAACAGCT 59.234 34.615 10.38 0.00 32.93 4.24
4220 8584 6.954944 TGTTTCAGACACTATGTAAAACAGC 58.045 36.000 10.38 0.00 32.93 4.40
4221 8585 8.993121 AGATGTTTCAGACACTATGTAAAACAG 58.007 33.333 15.76 0.00 42.04 3.16
4222 8586 8.902540 AGATGTTTCAGACACTATGTAAAACA 57.097 30.769 14.16 14.16 42.04 2.83
4224 8588 9.990360 TGTAGATGTTTCAGACACTATGTAAAA 57.010 29.630 0.00 0.00 42.04 1.52
4225 8589 9.990360 TTGTAGATGTTTCAGACACTATGTAAA 57.010 29.630 0.00 0.00 42.04 2.01
4226 8590 9.990360 TTTGTAGATGTTTCAGACACTATGTAA 57.010 29.630 0.00 0.00 42.04 2.41
4227 8591 9.639601 CTTTGTAGATGTTTCAGACACTATGTA 57.360 33.333 0.00 0.00 42.04 2.29
4228 8592 7.118390 GCTTTGTAGATGTTTCAGACACTATGT 59.882 37.037 0.00 0.00 42.04 2.29
4229 8593 7.413438 GGCTTTGTAGATGTTTCAGACACTATG 60.413 40.741 0.00 0.00 42.04 2.23
4230 8594 6.595716 GGCTTTGTAGATGTTTCAGACACTAT 59.404 38.462 0.00 0.00 42.04 2.12
4231 8595 5.932303 GGCTTTGTAGATGTTTCAGACACTA 59.068 40.000 0.00 0.00 42.04 2.74
4232 8596 4.757149 GGCTTTGTAGATGTTTCAGACACT 59.243 41.667 0.00 0.00 42.04 3.55
4233 8597 4.757149 AGGCTTTGTAGATGTTTCAGACAC 59.243 41.667 0.00 0.00 42.04 3.67
4234 8598 4.973168 AGGCTTTGTAGATGTTTCAGACA 58.027 39.130 0.00 0.00 43.71 3.41
4235 8599 5.948992 AAGGCTTTGTAGATGTTTCAGAC 57.051 39.130 0.00 0.00 0.00 3.51
4236 8600 9.733556 TTTATAAGGCTTTGTAGATGTTTCAGA 57.266 29.630 4.45 0.00 0.00 3.27
4241 8605 9.515226 TCACTTTTATAAGGCTTTGTAGATGTT 57.485 29.630 4.45 0.00 35.61 2.71
4242 8606 9.515226 TTCACTTTTATAAGGCTTTGTAGATGT 57.485 29.630 4.45 1.05 35.61 3.06
4243 8607 9.774742 GTTCACTTTTATAAGGCTTTGTAGATG 57.225 33.333 4.45 0.00 35.61 2.90
4244 8608 9.515226 TGTTCACTTTTATAAGGCTTTGTAGAT 57.485 29.630 4.45 0.00 35.61 1.98
4245 8609 8.911918 TGTTCACTTTTATAAGGCTTTGTAGA 57.088 30.769 4.45 0.00 35.61 2.59
4246 8610 8.999431 TCTGTTCACTTTTATAAGGCTTTGTAG 58.001 33.333 4.45 0.00 35.61 2.74
4247 8611 8.911918 TCTGTTCACTTTTATAAGGCTTTGTA 57.088 30.769 4.45 0.00 35.61 2.41
4248 8612 7.719633 TCTCTGTTCACTTTTATAAGGCTTTGT 59.280 33.333 4.45 0.00 35.61 2.83
4249 8613 8.017946 GTCTCTGTTCACTTTTATAAGGCTTTG 58.982 37.037 4.45 0.00 35.61 2.77
4250 8614 7.719633 TGTCTCTGTTCACTTTTATAAGGCTTT 59.280 33.333 4.45 0.00 35.61 3.51
4251 8615 7.224297 TGTCTCTGTTCACTTTTATAAGGCTT 58.776 34.615 4.58 4.58 35.61 4.35
4252 8616 6.769512 TGTCTCTGTTCACTTTTATAAGGCT 58.230 36.000 0.00 0.00 35.61 4.58
4253 8617 6.651225 ACTGTCTCTGTTCACTTTTATAAGGC 59.349 38.462 0.00 0.00 35.61 4.35
4254 8618 9.360093 CTACTGTCTCTGTTCACTTTTATAAGG 57.640 37.037 0.00 0.00 35.61 2.69
4255 8619 8.865001 GCTACTGTCTCTGTTCACTTTTATAAG 58.135 37.037 0.00 0.00 37.40 1.73
4256 8620 8.585881 AGCTACTGTCTCTGTTCACTTTTATAA 58.414 33.333 0.00 0.00 0.00 0.98
4257 8621 8.029522 CAGCTACTGTCTCTGTTCACTTTTATA 58.970 37.037 0.00 0.00 0.00 0.98
4258 8622 6.870965 CAGCTACTGTCTCTGTTCACTTTTAT 59.129 38.462 0.00 0.00 0.00 1.40
4259 8623 6.040504 TCAGCTACTGTCTCTGTTCACTTTTA 59.959 38.462 8.44 0.00 32.61 1.52
4260 8624 5.053145 CAGCTACTGTCTCTGTTCACTTTT 58.947 41.667 0.00 0.00 0.00 2.27
4261 8625 4.342378 TCAGCTACTGTCTCTGTTCACTTT 59.658 41.667 8.44 0.00 32.61 2.66
4262 8626 3.891977 TCAGCTACTGTCTCTGTTCACTT 59.108 43.478 8.44 0.00 32.61 3.16
4263 8627 3.491342 TCAGCTACTGTCTCTGTTCACT 58.509 45.455 8.44 0.00 32.61 3.41
4264 8628 3.924918 TCAGCTACTGTCTCTGTTCAC 57.075 47.619 8.44 0.00 32.61 3.18
4265 8629 5.474578 AAATCAGCTACTGTCTCTGTTCA 57.525 39.130 8.44 0.00 32.61 3.18
4266 8630 5.698545 ACAAAATCAGCTACTGTCTCTGTTC 59.301 40.000 8.44 0.00 32.61 3.18
4267 8631 5.615289 ACAAAATCAGCTACTGTCTCTGTT 58.385 37.500 8.44 0.12 32.61 3.16
4268 8632 5.220710 ACAAAATCAGCTACTGTCTCTGT 57.779 39.130 8.44 0.00 32.61 3.41
4269 8633 5.809562 CCTACAAAATCAGCTACTGTCTCTG 59.190 44.000 0.00 3.64 32.61 3.35
4270 8634 5.625656 GCCTACAAAATCAGCTACTGTCTCT 60.626 44.000 0.00 0.00 32.61 3.10
4271 8635 4.568760 GCCTACAAAATCAGCTACTGTCTC 59.431 45.833 0.00 0.00 32.61 3.36
4272 8636 4.508662 GCCTACAAAATCAGCTACTGTCT 58.491 43.478 0.00 0.00 32.61 3.41
4273 8637 3.623510 GGCCTACAAAATCAGCTACTGTC 59.376 47.826 0.00 0.00 32.61 3.51
4274 8638 3.009033 TGGCCTACAAAATCAGCTACTGT 59.991 43.478 3.32 0.00 32.61 3.55
4275 8639 3.609853 TGGCCTACAAAATCAGCTACTG 58.390 45.455 3.32 0.00 0.00 2.74
4276 8640 3.264450 ACTGGCCTACAAAATCAGCTACT 59.736 43.478 3.32 0.00 0.00 2.57
4277 8641 3.375299 CACTGGCCTACAAAATCAGCTAC 59.625 47.826 3.32 0.00 0.00 3.58
4325 8704 9.649167 GATTGAATCATGATTGAGTTCCTTTTT 57.351 29.630 25.37 0.00 34.73 1.94
4445 8831 2.840651 AGACCCGATGAGATTTCTGGTT 59.159 45.455 0.00 0.00 0.00 3.67
4496 8887 7.667043 TTATTAGCAAACTTCGACAGAACAT 57.333 32.000 0.00 0.00 32.15 2.71
4497 8888 7.386573 TCATTATTAGCAAACTTCGACAGAACA 59.613 33.333 0.00 0.00 32.15 3.18
4567 8960 9.649167 GATGATGGTGAAAGAAAGAAAAATCAT 57.351 29.630 0.00 0.00 34.61 2.45
4608 9001 1.137697 TCATGAGCATGGATGAGGCT 58.862 50.000 10.31 0.00 46.87 4.58
4698 9092 2.552743 CTCCCACCGGTTTTTCTTCTTC 59.447 50.000 2.97 0.00 0.00 2.87
4699 9093 2.092049 ACTCCCACCGGTTTTTCTTCTT 60.092 45.455 2.97 0.00 0.00 2.52
4700 9094 1.493446 ACTCCCACCGGTTTTTCTTCT 59.507 47.619 2.97 0.00 0.00 2.85
4701 9095 1.977056 ACTCCCACCGGTTTTTCTTC 58.023 50.000 2.97 0.00 0.00 2.87
4703 9097 3.581265 TTTACTCCCACCGGTTTTTCT 57.419 42.857 2.97 0.00 0.00 2.52
4734 9140 2.368548 TCTGCTTTCAACTAGGTCAGCA 59.631 45.455 5.84 5.84 35.95 4.41
4737 9143 2.634940 AGCTCTGCTTTCAACTAGGTCA 59.365 45.455 0.00 0.00 33.89 4.02
4796 9204 0.811281 ATTGCTGGCTTCGCTAAACC 59.189 50.000 0.00 0.00 0.00 3.27
4855 9314 4.100498 CCGGCTCTTTTCCCTATAAGTACA 59.900 45.833 0.00 0.00 0.00 2.90
4856 9315 4.100653 ACCGGCTCTTTTCCCTATAAGTAC 59.899 45.833 0.00 0.00 0.00 2.73
5021 9496 6.456795 ACCCAAGAGAAAAGAAGAAAAGTG 57.543 37.500 0.00 0.00 0.00 3.16
5022 9497 7.178451 TGAAACCCAAGAGAAAAGAAGAAAAGT 59.822 33.333 0.00 0.00 0.00 2.66
5023 9498 7.489435 GTGAAACCCAAGAGAAAAGAAGAAAAG 59.511 37.037 0.00 0.00 0.00 2.27
5145 9662 9.906660 GACCATGTGTTTAGAAAATGTTAATCA 57.093 29.630 0.00 0.00 0.00 2.57
5188 9803 9.974980 ACCCTGTGTTTAAAAGTATGTTAAATG 57.025 29.630 0.00 0.00 39.73 2.32
5198 9813 6.538945 AAATGTGACCCTGTGTTTAAAAGT 57.461 33.333 0.00 0.00 0.00 2.66
5288 9906 8.109705 ACTGAAAAATGTTGCATGTGTATAGA 57.890 30.769 0.00 0.00 0.00 1.98
5293 9911 6.572519 AGTAACTGAAAAATGTTGCATGTGT 58.427 32.000 0.00 0.00 32.56 3.72
5300 9918 8.920665 TGTTGAACAAGTAACTGAAAAATGTTG 58.079 29.630 0.00 0.00 30.37 3.33


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

AutoCloner maintained by Alex Coulton.