Multiple sequence alignment - TraesCS6A01G412700

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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 TraesCS6A01G412700 chr6A 100.000 5773 0 0 1 5773 614166567 614160795 0.000000e+00 10661.0
1 TraesCS6A01G412700 chr6D 97.038 3275 79 10 2512 5773 468097868 468094599 0.000000e+00 5494.0
2 TraesCS6A01G412700 chr6D 91.407 1187 85 12 1227 2408 468059582 468058408 0.000000e+00 1611.0
3 TraesCS6A01G412700 chr6D 90.150 1137 108 4 3625 4759 468168870 468167736 0.000000e+00 1476.0
4 TraesCS6A01G412700 chr6D 90.917 1101 87 10 1 1096 468185971 468184879 0.000000e+00 1467.0
5 TraesCS6A01G412700 chr6D 88.936 1184 124 4 1227 2408 468099045 468097867 0.000000e+00 1454.0
6 TraesCS6A01G412700 chr6D 89.622 1137 112 6 3625 4758 468057401 468056268 0.000000e+00 1441.0
7 TraesCS6A01G412700 chr6D 88.153 1148 119 11 1 1139 468100826 468099687 0.000000e+00 1351.0
8 TraesCS6A01G412700 chr6D 85.835 1186 147 15 3742 4910 468147033 468145852 0.000000e+00 1240.0
9 TraesCS6A01G412700 chr6D 82.997 1141 175 12 1277 2410 468170940 468169812 0.000000e+00 1014.0
10 TraesCS6A01G412700 chr6D 85.161 465 51 9 684 1139 468060915 468060460 1.470000e-125 460.0
11 TraesCS6A01G412700 chr6D 85.177 452 56 6 712 1160 468171427 468170984 2.450000e-123 453.0
12 TraesCS6A01G412700 chr6D 87.532 385 28 14 2512 2882 468058409 468058031 1.490000e-115 427.0
13 TraesCS6A01G412700 chr6D 88.043 368 29 8 2515 2877 468169813 468169456 6.920000e-114 422.0
14 TraesCS6A01G412700 chr6D 85.912 362 41 6 721 1077 468664369 468664013 1.520000e-100 377.0
15 TraesCS6A01G412700 chr6D 90.717 237 20 1 2895 3131 468169465 468169231 1.210000e-81 315.0
16 TraesCS6A01G412700 chr6D 83.959 293 33 6 3141 3423 468169191 468168903 9.530000e-68 268.0
17 TraesCS6A01G412700 chr6D 84.343 198 25 4 3229 3424 468057626 468057433 7.640000e-44 189.0
18 TraesCS6A01G412700 chr6B 87.685 1283 137 15 3651 4917 714340805 714339528 0.000000e+00 1474.0
19 TraesCS6A01G412700 chr6B 88.235 1020 113 7 3742 4758 714330687 714329672 0.000000e+00 1212.0
20 TraesCS6A01G412700 chr6B 81.068 1405 201 41 1518 2882 714342902 714341523 0.000000e+00 1061.0
21 TraesCS6A01G412700 chr6B 84.141 908 101 27 1 894 714343765 714342887 0.000000e+00 839.0
22 TraesCS6A01G412700 chr6B 84.234 444 56 13 658 1096 714336870 714336436 2.490000e-113 420.0
23 TraesCS6A01G412700 chr6B 92.336 274 21 0 317 590 714410825 714410552 1.950000e-104 390.0
24 TraesCS6A01G412700 chr6B 76.648 728 145 17 1356 2075 714409603 714408893 4.220000e-101 379.0
25 TraesCS6A01G412700 chr6B 86.349 315 32 4 3141 3447 714341125 714340814 3.330000e-87 333.0
26 TraesCS6A01G412700 chr6B 89.143 175 15 4 3446 3617 664448194 664448021 1.260000e-51 215.0
27 TraesCS6A01G412700 chr6B 90.756 119 9 2 3016 3133 714341279 714341162 2.150000e-34 158.0
28 TraesCS6A01G412700 chrUn 89.798 1137 109 6 3625 4759 346081819 346080688 0.000000e+00 1450.0
29 TraesCS6A01G412700 chrUn 88.911 1010 107 5 3742 4749 310899428 310900434 0.000000e+00 1240.0
30 TraesCS6A01G412700 chrUn 84.794 1164 131 26 1 1154 210220346 210219219 0.000000e+00 1127.0
31 TraesCS6A01G412700 chrUn 81.722 1138 173 17 1277 2408 210219169 210218061 0.000000e+00 917.0
32 TraesCS6A01G412700 chrUn 86.102 590 64 7 509 1096 75283431 75284004 2.290000e-173 619.0
33 TraesCS6A01G412700 chrUn 86.201 587 63 7 512 1096 327314414 327313844 2.290000e-173 619.0
34 TraesCS6A01G412700 chrUn 92.308 390 26 3 1 388 75283009 75283396 8.450000e-153 551.0
35 TraesCS6A01G412700 chrUn 92.308 390 26 3 1 388 327314839 327314452 8.450000e-153 551.0
36 TraesCS6A01G412700 chrUn 91.971 274 22 0 317 590 211919251 211919524 9.070000e-103 385.0
37 TraesCS6A01G412700 chrUn 76.648 728 145 17 1356 2075 211920473 211921183 4.220000e-101 379.0
38 TraesCS6A01G412700 chrUn 85.970 335 38 5 786 1119 211919524 211919850 3.310000e-92 350.0
39 TraesCS6A01G412700 chrUn 91.371 197 17 0 394 590 479932512 479932316 2.650000e-68 270.0
40 TraesCS6A01G412700 chrUn 85.507 69 9 1 5191 5258 79769871 79769939 2.890000e-08 71.3
41 TraesCS6A01G412700 chr2B 85.794 1077 149 3 3690 4763 118631788 118632863 0.000000e+00 1138.0
42 TraesCS6A01G412700 chr2B 91.071 168 13 2 3446 3612 150942314 150942480 5.820000e-55 226.0
43 TraesCS6A01G412700 chr2A 82.951 305 44 2 1779 2075 77538316 77538620 9.530000e-68 268.0
44 TraesCS6A01G412700 chr2A 91.667 120 9 1 2407 2526 227627532 227627414 1.290000e-36 165.0
45 TraesCS6A01G412700 chr2D 82.508 303 47 1 1779 2075 76871693 76871995 1.600000e-65 261.0
46 TraesCS6A01G412700 chr2D 93.913 115 7 0 2407 2521 525935417 525935531 2.140000e-39 174.0
47 TraesCS6A01G412700 chr2D 93.913 115 6 1 2403 2516 14813413 14813527 7.690000e-39 172.0
48 TraesCS6A01G412700 chr3B 94.152 171 7 2 3447 3616 487497388 487497556 2.060000e-64 257.0
49 TraesCS6A01G412700 chr5B 91.176 170 13 2 3447 3615 514067823 514067991 4.500000e-56 230.0
50 TraesCS6A01G412700 chr5B 90.643 171 14 2 3447 3616 41990147 41989978 5.820000e-55 226.0
51 TraesCS6A01G412700 chr5B 90.588 170 12 4 3448 3616 563604260 563604426 7.530000e-54 222.0
52 TraesCS6A01G412700 chr5B 96.262 107 4 0 2407 2513 650990197 650990091 5.950000e-40 176.0
53 TraesCS6A01G412700 chr1B 90.000 170 16 1 3443 3612 527287157 527287325 9.740000e-53 219.0
54 TraesCS6A01G412700 chr4B 89.474 171 16 2 3446 3616 604540714 604540882 1.260000e-51 215.0
55 TraesCS6A01G412700 chr4B 93.860 114 7 0 2403 2516 416442710 416442597 7.690000e-39 172.0
56 TraesCS6A01G412700 chr7D 86.047 172 15 8 5506 5670 254171517 254171348 5.950000e-40 176.0
57 TraesCS6A01G412700 chr7D 91.270 126 8 3 2392 2517 478908758 478908880 9.950000e-38 169.0
58 TraesCS6A01G412700 chr7B 95.413 109 5 0 2406 2514 741544745 741544853 2.140000e-39 174.0
59 TraesCS6A01G412700 chr7B 91.870 123 8 2 2395 2517 58655888 58656008 2.770000e-38 171.0
60 TraesCS6A01G412700 chr7B 86.316 95 10 2 5678 5772 231414852 231414761 3.680000e-17 100.0
61 TraesCS6A01G412700 chr7B 100.000 29 0 0 1519 1547 84453582 84453554 3.000000e-03 54.7
62 TraesCS6A01G412700 chr1D 92.562 121 9 0 2397 2517 471123005 471123125 2.140000e-39 174.0
63 TraesCS6A01G412700 chr7A 97.183 71 2 0 5589 5659 272517286 272517216 2.830000e-23 121.0
64 TraesCS6A01G412700 chr7A 87.342 79 10 0 5679 5757 272496910 272496832 2.220000e-14 91.6
65 TraesCS6A01G412700 chr7A 94.118 51 3 0 5441 5491 272517347 272517297 1.720000e-10 78.7
66 TraesCS6A01G412700 chr3A 96.226 53 2 0 5615 5667 684694087 684694139 2.870000e-13 87.9


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 TraesCS6A01G412700 chr6A 614160795 614166567 5772 True 10661.000000 10661 100.000000 1 5773 1 chr6A.!!$R1 5772
1 TraesCS6A01G412700 chr6D 468094599 468100826 6227 True 2766.333333 5494 91.375667 1 5773 3 chr6D.!!$R5 5772
2 TraesCS6A01G412700 chr6D 468184879 468185971 1092 True 1467.000000 1467 90.917000 1 1096 1 chr6D.!!$R2 1095
3 TraesCS6A01G412700 chr6D 468145852 468147033 1181 True 1240.000000 1240 85.835000 3742 4910 1 chr6D.!!$R1 1168
4 TraesCS6A01G412700 chr6D 468056268 468060915 4647 True 825.600000 1611 87.613000 684 4758 5 chr6D.!!$R4 4074
5 TraesCS6A01G412700 chr6D 468167736 468171427 3691 True 658.000000 1476 86.840500 712 4759 6 chr6D.!!$R6 4047
6 TraesCS6A01G412700 chr6B 714329672 714330687 1015 True 1212.000000 1212 88.235000 3742 4758 1 chr6B.!!$R2 1016
7 TraesCS6A01G412700 chr6B 714336436 714343765 7329 True 714.166667 1474 85.705500 1 4917 6 chr6B.!!$R3 4916
8 TraesCS6A01G412700 chr6B 714408893 714410825 1932 True 384.500000 390 84.492000 317 2075 2 chr6B.!!$R4 1758
9 TraesCS6A01G412700 chrUn 346080688 346081819 1131 True 1450.000000 1450 89.798000 3625 4759 1 chrUn.!!$R1 1134
10 TraesCS6A01G412700 chrUn 310899428 310900434 1006 False 1240.000000 1240 88.911000 3742 4749 1 chrUn.!!$F2 1007
11 TraesCS6A01G412700 chrUn 210218061 210220346 2285 True 1022.000000 1127 83.258000 1 2408 2 chrUn.!!$R3 2407
12 TraesCS6A01G412700 chrUn 75283009 75284004 995 False 585.000000 619 89.205000 1 1096 2 chrUn.!!$F3 1095
13 TraesCS6A01G412700 chrUn 327313844 327314839 995 True 585.000000 619 89.254500 1 1096 2 chrUn.!!$R4 1095
14 TraesCS6A01G412700 chrUn 211919251 211921183 1932 False 371.333333 385 84.863000 317 2075 3 chrUn.!!$F4 1758
15 TraesCS6A01G412700 chr2B 118631788 118632863 1075 False 1138.000000 1138 85.794000 3690 4763 1 chr2B.!!$F1 1073

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
883 976 0.321671 CCTTGTCCTCCTTTCAGCGA 59.678 55.000 0.00 0.00 0.00 4.93 F
1178 1283 0.183014 AGGATGGATGGAGCTTGCTG 59.817 55.000 0.00 0.00 0.00 4.41 F
1640 2551 0.250901 TCCTGCCTTTCAGACCTTGC 60.251 55.000 0.00 0.00 45.72 4.01 F
2210 3129 0.538584 ATCAATGAGTGCGAGCTCCA 59.461 50.000 8.47 4.37 34.74 3.86 F
2915 4008 1.154035 GCCGAAATGTTTGGAGGCG 60.154 57.895 0.00 0.00 34.94 5.52 F
3616 4982 0.481128 CCCTGTAACCAAACACCCCT 59.519 55.000 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2496 3536 0.331954 AGCTACTCCCTCCGTTCTGA 59.668 55.000 0.00 0.0 0.00 3.27 R
2915 4008 1.135333 CTCTAAGACCGGGAGTTCTGC 59.865 57.143 6.32 0.0 0.00 4.26 R
3597 4963 0.481128 AGGGGTGTTTGGTTACAGGG 59.519 55.000 0.00 0.0 0.00 4.45 R
3616 4982 2.570098 TCCTACCTCAGGGTCTCTACA 58.430 52.381 0.00 0.0 45.98 2.74 R
4635 6006 5.292101 CGATCCCTGTCAAACTATCAAGAAC 59.708 44.000 0.00 0.0 0.00 3.01 R
5140 6535 1.066143 CCAGGACGTTAGGATGCAGTT 60.066 52.381 0.00 0.0 0.00 3.16 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
82 85 4.746535 TGTATGAACACCATATCACGGT 57.253 40.909 0.00 0.00 39.69 4.83
248 255 3.198635 CCTCTATTATGATCATGGCCCGT 59.801 47.826 18.72 0.00 0.00 5.28
271 280 6.702282 CGTCTCTTAGAAAACAGAAAGAAGGT 59.298 38.462 0.00 0.00 0.00 3.50
396 409 7.452880 AAAAACAATTCTCCTCAATCGATCA 57.547 32.000 0.00 0.00 0.00 2.92
466 481 7.055378 AGAAGATGCATTTCTAAAGCAGAGAT 58.945 34.615 17.22 0.00 42.14 2.75
536 614 6.715347 ATGTGTTCCAGCTTTTCTTTTAGT 57.285 33.333 0.00 0.00 0.00 2.24
586 664 8.244113 ACTAATTAAGTGCATTCTTTTGTAGCC 58.756 33.333 0.00 0.00 36.93 3.93
595 673 2.858745 TCTTTTGTAGCCTGTGGAACC 58.141 47.619 0.00 0.00 34.36 3.62
629 709 9.478019 CAAATAAACAAGCGTCTTATAGTGAAG 57.522 33.333 0.00 0.00 0.00 3.02
633 713 6.458232 ACAAGCGTCTTATAGTGAAGAGAT 57.542 37.500 0.00 0.00 36.13 2.75
715 796 4.637534 ACCGTCGACGCTACCAATATATAT 59.362 41.667 31.73 0.00 38.18 0.86
768 849 4.537015 CTTAATTAGCTTTGCGCCCATAC 58.463 43.478 4.18 0.00 40.39 2.39
825 912 3.640407 ACCAGCATGACCACGCCT 61.640 61.111 0.00 0.00 39.69 5.52
854 941 3.884704 ATTCCCAGCCGCTGCCAAA 62.885 57.895 15.36 8.57 38.69 3.28
867 954 3.092301 GCTGCCAAAAATCCTACTCCTT 58.908 45.455 0.00 0.00 0.00 3.36
868 955 3.119352 GCTGCCAAAAATCCTACTCCTTG 60.119 47.826 0.00 0.00 0.00 3.61
883 976 0.321671 CCTTGTCCTCCTTTCAGCGA 59.678 55.000 0.00 0.00 0.00 4.93
902 995 2.799917 CGACGATTCCTCACTTGATCCC 60.800 54.545 0.00 0.00 0.00 3.85
1065 1158 2.099921 CGACTCCTTCAATCCTCATCGT 59.900 50.000 0.00 0.00 0.00 3.73
1097 1190 3.490078 GCTGACAGCAGAGTATACCAGTC 60.490 52.174 22.62 0.00 45.17 3.51
1123 1218 0.675837 CGAGGAGTACGACAGGGTGA 60.676 60.000 0.00 0.00 0.00 4.02
1139 1234 2.552809 GGGTGAAGGTAGGCCGTTTTAA 60.553 50.000 0.00 0.00 40.50 1.52
1144 1239 6.340522 GTGAAGGTAGGCCGTTTTAATACTA 58.659 40.000 0.00 0.00 40.50 1.82
1146 1241 4.953667 AGGTAGGCCGTTTTAATACTAGC 58.046 43.478 0.00 0.00 40.50 3.42
1147 1242 4.652881 AGGTAGGCCGTTTTAATACTAGCT 59.347 41.667 0.00 0.00 40.50 3.32
1164 1269 6.472686 ACTAGCTAAAACTGAGGTAGGATG 57.527 41.667 12.14 0.00 45.29 3.51
1168 1273 5.059833 GCTAAAACTGAGGTAGGATGGATG 58.940 45.833 0.00 0.00 0.00 3.51
1173 1278 1.221523 TGAGGTAGGATGGATGGAGCT 59.778 52.381 0.00 0.00 0.00 4.09
1177 1282 1.419387 GTAGGATGGATGGAGCTTGCT 59.581 52.381 0.00 0.00 0.00 3.91
1178 1283 0.183014 AGGATGGATGGAGCTTGCTG 59.817 55.000 0.00 0.00 0.00 4.41
1210 1811 7.989416 AGACTATCATTGGAGTACTAGTAGC 57.011 40.000 1.87 0.00 0.00 3.58
1246 2148 7.221452 CGTACTATGGTTTACTGTGTGGTAATC 59.779 40.741 0.00 0.00 32.64 1.75
1247 2149 7.253905 ACTATGGTTTACTGTGTGGTAATCT 57.746 36.000 0.00 0.00 32.64 2.40
1279 2182 8.018520 TGATTTTTACACGGTGCTGTAATTAAG 58.981 33.333 8.30 0.00 36.67 1.85
1284 2187 8.550710 TTACACGGTGCTGTAATTAAGTAATT 57.449 30.769 8.30 2.11 39.14 1.40
1285 2188 9.650539 TTACACGGTGCTGTAATTAAGTAATTA 57.349 29.630 8.30 0.33 37.16 1.40
1286 2189 8.550710 ACACGGTGCTGTAATTAAGTAATTAA 57.449 30.769 8.30 0.00 39.17 1.40
1287 2190 9.169592 ACACGGTGCTGTAATTAAGTAATTAAT 57.830 29.630 8.30 2.38 39.17 1.40
1288 2191 9.433317 CACGGTGCTGTAATTAAGTAATTAATG 57.567 33.333 8.81 0.00 39.17 1.90
1303 2206 8.673626 AGTAATTAATGTTGCATTTGTCTTCG 57.326 30.769 0.00 0.00 0.00 3.79
1304 2207 8.511321 AGTAATTAATGTTGCATTTGTCTTCGA 58.489 29.630 0.00 0.00 0.00 3.71
1305 2208 7.566858 AATTAATGTTGCATTTGTCTTCGAC 57.433 32.000 0.00 0.00 0.00 4.20
1306 2209 3.559238 ATGTTGCATTTGTCTTCGACC 57.441 42.857 0.00 0.00 0.00 4.79
1307 2210 2.293170 TGTTGCATTTGTCTTCGACCA 58.707 42.857 0.00 0.00 0.00 4.02
1328 2231 5.658190 ACCATAAATTAATGCAGCCAGAGTT 59.342 36.000 0.00 0.00 0.00 3.01
1329 2232 6.183360 ACCATAAATTAATGCAGCCAGAGTTC 60.183 38.462 0.00 0.00 0.00 3.01
1333 2244 1.531423 AATGCAGCCAGAGTTCAGTG 58.469 50.000 0.00 0.00 0.00 3.66
1336 2247 0.871057 GCAGCCAGAGTTCAGTGAAC 59.129 55.000 25.51 25.51 42.25 3.18
1350 2261 4.617959 TCAGTGAACTTTGGAGTAGAACG 58.382 43.478 0.00 0.00 34.21 3.95
1358 2269 3.795623 TTGGAGTAGAACGCTGGATAC 57.204 47.619 0.00 0.00 0.00 2.24
1485 2396 6.153340 CCAAGAATCAACATATGAAGTTGGGT 59.847 38.462 10.38 0.00 44.84 4.51
1486 2397 6.764308 AGAATCAACATATGAAGTTGGGTG 57.236 37.500 10.38 0.00 44.84 4.61
1500 2411 1.573108 TGGGTGAGAAGATGAGTCCC 58.427 55.000 0.00 0.00 0.00 4.46
1638 2549 1.627834 CTCTCCTGCCTTTCAGACCTT 59.372 52.381 0.00 0.00 45.72 3.50
1640 2551 0.250901 TCCTGCCTTTCAGACCTTGC 60.251 55.000 0.00 0.00 45.72 4.01
1746 2660 4.643387 ACCGTGCTTGGTCTGGCC 62.643 66.667 0.00 0.00 37.91 5.36
1757 2671 2.265367 TGGTCTGGCCTTCACTATGAA 58.735 47.619 3.32 0.00 38.35 2.57
1761 2675 3.437049 GTCTGGCCTTCACTATGAACAAC 59.563 47.826 3.32 0.00 32.21 3.32
1776 2690 8.349983 ACTATGAACAACAATAACACCTTGTTC 58.650 33.333 12.92 12.92 46.73 3.18
1993 2909 1.102809 CAACAGCTCCTGTGCCAACA 61.103 55.000 0.00 0.00 44.62 3.33
2016 2932 1.213296 CTACTGGCCAGGGGTATGTT 58.787 55.000 35.42 15.23 0.00 2.71
2040 2956 0.830444 AGTGCTGGGACCACTACGAA 60.830 55.000 0.00 0.00 41.47 3.85
2164 3082 6.583562 AGGAACTCCATCTTACTTTTATCCG 58.416 40.000 0.00 0.00 38.89 4.18
2179 3097 5.570234 TTTATCCGTGCCTTTGTATTTCC 57.430 39.130 0.00 0.00 0.00 3.13
2203 3122 4.400845 CTTTTCAGACATCAATGAGTGCG 58.599 43.478 0.00 0.00 0.00 5.34
2210 3129 0.538584 ATCAATGAGTGCGAGCTCCA 59.461 50.000 8.47 4.37 34.74 3.86
2270 3189 9.178758 CAAAAATAAGTTAGGAGGCTATGACTT 57.821 33.333 12.17 12.17 0.00 3.01
2417 3457 9.577337 TTATATACTCCTATCTACTCCCTCTGT 57.423 37.037 0.00 0.00 0.00 3.41
2418 3458 6.790177 ATACTCCTATCTACTCCCTCTGTT 57.210 41.667 0.00 0.00 0.00 3.16
2419 3459 5.056553 ACTCCTATCTACTCCCTCTGTTC 57.943 47.826 0.00 0.00 0.00 3.18
2420 3460 4.069304 CTCCTATCTACTCCCTCTGTTCG 58.931 52.174 0.00 0.00 0.00 3.95
2421 3461 3.150767 CCTATCTACTCCCTCTGTTCGG 58.849 54.545 0.00 0.00 0.00 4.30
2422 3462 3.181442 CCTATCTACTCCCTCTGTTCGGA 60.181 52.174 0.00 0.00 0.00 4.55
2423 3463 2.893215 TCTACTCCCTCTGTTCGGAA 57.107 50.000 0.00 0.00 0.00 4.30
2424 3464 3.383698 TCTACTCCCTCTGTTCGGAAT 57.616 47.619 0.00 0.00 0.00 3.01
2425 3465 3.709587 TCTACTCCCTCTGTTCGGAATT 58.290 45.455 0.00 0.00 0.00 2.17
2426 3466 4.863548 TCTACTCCCTCTGTTCGGAATTA 58.136 43.478 0.00 0.00 0.00 1.40
2427 3467 3.889520 ACTCCCTCTGTTCGGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
2428 3468 3.442076 ACTCCCTCTGTTCGGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
2429 3469 3.838903 ACTCCCTCTGTTCGGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
2430 3470 4.184629 CTCCCTCTGTTCGGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
2431 3471 3.581332 TCCCTCTGTTCGGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
2432 3472 3.933332 CCCTCTGTTCGGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
2433 3473 3.612860 CCTCTGTTCGGAATTACTTGTCG 59.387 47.826 0.00 0.00 0.00 4.35
2434 3474 4.235360 CTCTGTTCGGAATTACTTGTCGT 58.765 43.478 0.00 0.00 0.00 4.34
2435 3475 5.375417 TCTGTTCGGAATTACTTGTCGTA 57.625 39.130 0.00 0.00 0.00 3.43
2436 3476 5.396484 TCTGTTCGGAATTACTTGTCGTAG 58.604 41.667 0.00 0.00 0.00 3.51
2437 3477 5.181811 TCTGTTCGGAATTACTTGTCGTAGA 59.818 40.000 0.00 0.00 0.00 2.59
2438 3478 5.771469 TGTTCGGAATTACTTGTCGTAGAA 58.229 37.500 0.00 0.00 39.69 2.10
2439 3479 6.215121 TGTTCGGAATTACTTGTCGTAGAAA 58.785 36.000 0.00 0.00 39.69 2.52
2440 3480 6.869913 TGTTCGGAATTACTTGTCGTAGAAAT 59.130 34.615 0.00 0.00 39.69 2.17
2441 3481 6.880822 TCGGAATTACTTGTCGTAGAAATG 57.119 37.500 0.00 0.00 39.69 2.32
2442 3482 5.808540 TCGGAATTACTTGTCGTAGAAATGG 59.191 40.000 0.00 0.00 39.69 3.16
2443 3483 5.808540 CGGAATTACTTGTCGTAGAAATGGA 59.191 40.000 0.00 0.00 39.69 3.41
2444 3484 6.479001 CGGAATTACTTGTCGTAGAAATGGAT 59.521 38.462 0.00 0.00 39.69 3.41
2445 3485 7.516785 CGGAATTACTTGTCGTAGAAATGGATG 60.517 40.741 0.00 0.00 39.69 3.51
2446 3486 7.280205 GGAATTACTTGTCGTAGAAATGGATGT 59.720 37.037 0.00 0.00 39.69 3.06
2447 3487 9.309516 GAATTACTTGTCGTAGAAATGGATGTA 57.690 33.333 0.00 0.00 39.69 2.29
2448 3488 9.832445 AATTACTTGTCGTAGAAATGGATGTAT 57.168 29.630 0.00 0.00 39.69 2.29
2449 3489 8.867112 TTACTTGTCGTAGAAATGGATGTATC 57.133 34.615 0.00 0.00 39.69 2.24
2450 3490 7.113658 ACTTGTCGTAGAAATGGATGTATCT 57.886 36.000 0.00 0.00 39.69 1.98
2451 3491 8.234136 ACTTGTCGTAGAAATGGATGTATCTA 57.766 34.615 0.00 0.00 39.69 1.98
2452 3492 8.353684 ACTTGTCGTAGAAATGGATGTATCTAG 58.646 37.037 0.00 0.00 39.69 2.43
2453 3493 7.818997 TGTCGTAGAAATGGATGTATCTAGT 57.181 36.000 0.00 0.00 39.69 2.57
2454 3494 7.872881 TGTCGTAGAAATGGATGTATCTAGTC 58.127 38.462 0.00 0.00 39.69 2.59
2455 3495 7.501225 TGTCGTAGAAATGGATGTATCTAGTCA 59.499 37.037 0.00 0.00 39.69 3.41
2456 3496 8.516234 GTCGTAGAAATGGATGTATCTAGTCAT 58.484 37.037 0.00 0.00 39.69 3.06
2457 3497 9.078990 TCGTAGAAATGGATGTATCTAGTCATT 57.921 33.333 0.00 0.00 0.00 2.57
2458 3498 9.698309 CGTAGAAATGGATGTATCTAGTCATTT 57.302 33.333 0.00 0.00 37.48 2.32
2485 3525 6.759497 AGTTCTAGGTACATCCATTTTTGC 57.241 37.500 0.00 0.00 39.02 3.68
2486 3526 5.354234 AGTTCTAGGTACATCCATTTTTGCG 59.646 40.000 0.00 0.00 39.02 4.85
2487 3527 5.092554 TCTAGGTACATCCATTTTTGCGA 57.907 39.130 0.00 0.00 39.02 5.10
2488 3528 4.873827 TCTAGGTACATCCATTTTTGCGAC 59.126 41.667 0.00 0.00 39.02 5.19
2489 3529 3.417101 AGGTACATCCATTTTTGCGACA 58.583 40.909 0.00 0.00 39.02 4.35
2490 3530 3.823873 AGGTACATCCATTTTTGCGACAA 59.176 39.130 0.00 0.00 39.02 3.18
2491 3531 4.082787 AGGTACATCCATTTTTGCGACAAG 60.083 41.667 0.00 0.00 39.02 3.16
2492 3532 4.320935 GGTACATCCATTTTTGCGACAAGT 60.321 41.667 0.00 0.00 35.97 3.16
2493 3533 5.106475 GGTACATCCATTTTTGCGACAAGTA 60.106 40.000 0.00 0.00 35.97 2.24
2494 3534 5.446143 ACATCCATTTTTGCGACAAGTAA 57.554 34.783 0.00 0.00 0.00 2.24
2495 3535 6.024552 ACATCCATTTTTGCGACAAGTAAT 57.975 33.333 0.00 0.00 0.00 1.89
2496 3536 6.454795 ACATCCATTTTTGCGACAAGTAATT 58.545 32.000 0.00 0.00 0.00 1.40
2497 3537 6.586082 ACATCCATTTTTGCGACAAGTAATTC 59.414 34.615 0.00 0.00 0.00 2.17
2498 3538 6.078202 TCCATTTTTGCGACAAGTAATTCA 57.922 33.333 0.00 0.00 0.00 2.57
2499 3539 6.148948 TCCATTTTTGCGACAAGTAATTCAG 58.851 36.000 0.00 0.00 0.00 3.02
2500 3540 6.016693 TCCATTTTTGCGACAAGTAATTCAGA 60.017 34.615 0.00 0.00 0.00 3.27
2501 3541 6.640499 CCATTTTTGCGACAAGTAATTCAGAA 59.360 34.615 0.00 0.00 0.00 3.02
2502 3542 7.358352 CCATTTTTGCGACAAGTAATTCAGAAC 60.358 37.037 0.00 0.00 0.00 3.01
2503 3543 4.383774 TTGCGACAAGTAATTCAGAACG 57.616 40.909 0.00 0.00 0.00 3.95
2504 3544 2.734606 TGCGACAAGTAATTCAGAACGG 59.265 45.455 0.00 0.00 0.00 4.44
2505 3545 2.991190 GCGACAAGTAATTCAGAACGGA 59.009 45.455 0.00 0.00 0.00 4.69
2506 3546 3.060895 GCGACAAGTAATTCAGAACGGAG 59.939 47.826 0.00 0.00 0.00 4.63
2507 3547 3.612860 CGACAAGTAATTCAGAACGGAGG 59.387 47.826 0.00 0.00 0.00 4.30
2508 3548 3.933332 GACAAGTAATTCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
2509 3549 3.581332 ACAAGTAATTCAGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
2510 3550 4.184629 CAAGTAATTCAGAACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
2511 3551 3.442076 AGTAATTCAGAACGGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
2512 3552 4.607239 AGTAATTCAGAACGGAGGGAGTA 58.393 43.478 0.00 0.00 0.00 2.59
2651 3727 5.597182 TCCCGAGTATAACTAGCAGAACATT 59.403 40.000 0.00 0.00 0.00 2.71
2915 4008 1.154035 GCCGAAATGTTTGGAGGCG 60.154 57.895 0.00 0.00 34.94 5.52
2955 4048 6.874288 AGAGTCCAAATTTGAAAGTCTCAG 57.126 37.500 19.86 0.00 34.81 3.35
2967 4060 4.401519 TGAAAGTCTCAGTATACCCGGAAG 59.598 45.833 0.73 0.00 0.00 3.46
3112 4346 1.292242 AGGCAGAAGGAGTAGGGATGA 59.708 52.381 0.00 0.00 0.00 2.92
3163 4427 4.470304 ACAAACTCCTAGATGTAACCCTCC 59.530 45.833 0.00 0.00 0.00 4.30
3167 4431 4.353191 ACTCCTAGATGTAACCCTCCGATA 59.647 45.833 0.00 0.00 0.00 2.92
3309 4664 3.744238 TTCTCACGTGGATGTCTTTGA 57.256 42.857 17.00 0.00 0.00 2.69
3310 4665 3.744238 TCTCACGTGGATGTCTTTGAA 57.256 42.857 17.00 0.00 0.00 2.69
3351 4706 9.671279 TTCATATGTGACACTAATGACAAATCT 57.329 29.630 17.61 0.00 31.84 2.40
3535 4901 7.696981 TCAGTAGAGTCTTTTTCTAGTCCCTA 58.303 38.462 0.00 0.00 30.30 3.53
3551 4917 5.906254 AGTCCCTATAGAATAAGTCCCTCC 58.094 45.833 0.00 0.00 0.00 4.30
3565 4931 4.172807 AGTCCCTCCTGTTTGGTTACATA 58.827 43.478 0.00 0.00 37.07 2.29
3584 4950 6.749036 ACATAGGGACTTATAGGGACTTTG 57.251 41.667 0.00 0.00 39.49 2.77
3616 4982 0.481128 CCCTGTAACCAAACACCCCT 59.519 55.000 0.00 0.00 0.00 4.79
3621 4987 3.047115 TGTAACCAAACACCCCTGTAGA 58.953 45.455 0.00 0.00 0.00 2.59
3794 5164 7.558444 GGTGGAATAGGTGGTGTTTTTATCATA 59.442 37.037 0.00 0.00 0.00 2.15
3846 5216 7.407337 TCGCAAAGAGAAAAAGAAAACTAGAC 58.593 34.615 0.00 0.00 0.00 2.59
4331 5702 7.716799 ACCAGCAAATATACTTTTGGATGAA 57.283 32.000 2.22 0.00 37.13 2.57
4821 6207 4.933065 AGGAAACTATGGATGGGACAATGC 60.933 45.833 0.00 0.00 41.13 3.56
4901 6288 6.405842 GCCCTTTGTCCCAAGAAAATATGTAG 60.406 42.308 0.00 0.00 0.00 2.74
5026 6421 5.567037 TTAGTGTATAGGGCATGCATCTT 57.433 39.130 21.36 1.53 31.44 2.40
5082 6477 2.613026 TGACATTGTTCACCAGTCGT 57.387 45.000 0.00 0.00 32.08 4.34
5086 6481 4.056050 GACATTGTTCACCAGTCGTAACT 58.944 43.478 0.00 0.00 35.60 2.24
5123 6518 4.731483 GCATGCATCAAAATAAGCGACTGA 60.731 41.667 14.21 0.00 0.00 3.41
5124 6519 5.516996 CATGCATCAAAATAAGCGACTGAT 58.483 37.500 0.00 0.00 0.00 2.90
5135 6530 2.476051 GACTGATTGCACCGCGTG 59.524 61.111 4.92 4.73 36.51 5.34
5286 6681 7.435784 TCGAAACAAAAAGGTTTAATTACTGCC 59.564 33.333 0.00 0.00 40.85 4.85
5413 8770 6.307077 GTGACTTGTTTTGGTACAGTTTTGTC 59.693 38.462 0.00 0.00 42.39 3.18
5670 9027 0.378257 ATCAAACACATCGGATGCGC 59.622 50.000 17.61 0.00 0.00 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 59 5.500131 CGTGATATGGTGTTCATACAACGTG 60.500 44.000 0.00 0.00 45.25 4.49
151 154 4.366267 AGCATATAGGTTATGGAGGAGGG 58.634 47.826 0.00 0.00 0.00 4.30
248 255 6.924060 CGACCTTCTTTCTGTTTTCTAAGAGA 59.076 38.462 0.00 0.00 32.33 3.10
271 280 6.093495 CCAATAAGATAAGAAAGGTTGCACGA 59.907 38.462 0.00 0.00 0.00 4.35
350 359 0.686789 TCTGCTAGCTTGCTCCACAA 59.313 50.000 20.64 0.00 36.62 3.33
396 409 3.431346 CCATCTGATCGAGGAACACATGT 60.431 47.826 0.00 0.00 0.00 3.21
466 481 3.581332 TCTCTTTCTAAAAGGGCTCCGAA 59.419 43.478 0.00 0.00 0.00 4.30
510 587 6.715347 AAAAGAAAAGCTGGAACACATACT 57.285 33.333 0.00 0.00 0.00 2.12
514 591 7.633193 TTACTAAAAGAAAAGCTGGAACACA 57.367 32.000 0.00 0.00 0.00 3.72
536 614 6.317893 GTCAAGAAGGAAAGTTGACACCTTTA 59.682 38.462 9.08 0.00 46.18 1.85
595 673 2.656422 CGCTTGTTTATTTGAAGTGGCG 59.344 45.455 0.00 0.00 0.00 5.69
715 796 4.381612 CGGGCTTACTGAGTCATCTAAACA 60.382 45.833 0.00 0.00 0.00 2.83
762 843 4.348168 AGCTAACTTGGTCTATGGTATGGG 59.652 45.833 0.00 0.00 0.00 4.00
795 876 1.313772 TGCTGGTGTATGTTTTGCGT 58.686 45.000 0.00 0.00 0.00 5.24
825 912 1.682849 CTGGGAATGGGGTCACGAA 59.317 57.895 0.00 0.00 0.00 3.85
829 916 3.727258 CGGCTGGGAATGGGGTCA 61.727 66.667 0.00 0.00 0.00 4.02
854 941 4.081695 AGGAGGACAAGGAGTAGGATTT 57.918 45.455 0.00 0.00 0.00 2.17
867 954 1.176619 TCGTCGCTGAAAGGAGGACA 61.177 55.000 0.00 0.00 0.00 4.02
868 955 0.173708 ATCGTCGCTGAAAGGAGGAC 59.826 55.000 0.00 0.00 33.28 3.85
883 976 1.137086 CGGGATCAAGTGAGGAATCGT 59.863 52.381 0.00 0.00 0.00 3.73
1011 1104 2.032681 AAGCCCTCACGGAAGCAC 59.967 61.111 0.00 0.00 0.00 4.40
1065 1158 1.667830 GCTGTCAGCAACGTAGGCA 60.668 57.895 20.16 0.29 41.89 4.75
1077 1170 3.969553 AGACTGGTATACTCTGCTGTCA 58.030 45.455 14.62 0.00 0.00 3.58
1078 1171 4.882427 TGTAGACTGGTATACTCTGCTGTC 59.118 45.833 2.25 5.92 0.00 3.51
1084 1177 5.998981 CCTCGAATGTAGACTGGTATACTCT 59.001 44.000 2.25 0.70 0.00 3.24
1097 1190 3.002451 CCTGTCGTACTCCTCGAATGTAG 59.998 52.174 0.00 0.00 39.01 2.74
1123 1218 5.129980 AGCTAGTATTAAAACGGCCTACCTT 59.870 40.000 0.00 0.00 0.00 3.50
1139 1234 7.233757 CCATCCTACCTCAGTTTTAGCTAGTAT 59.766 40.741 0.00 0.00 0.00 2.12
1144 1239 4.362677 TCCATCCTACCTCAGTTTTAGCT 58.637 43.478 0.00 0.00 0.00 3.32
1146 1241 5.366768 TCCATCCATCCTACCTCAGTTTTAG 59.633 44.000 0.00 0.00 0.00 1.85
1147 1242 5.285401 TCCATCCATCCTACCTCAGTTTTA 58.715 41.667 0.00 0.00 0.00 1.52
1173 1278 8.815912 TCCAATGATAGTCTTATATAGCAGCAA 58.184 33.333 0.00 0.00 0.00 3.91
1187 1788 7.747155 TGCTACTAGTACTCCAATGATAGTC 57.253 40.000 0.00 0.00 0.00 2.59
1189 1790 9.456147 ACTATGCTACTAGTACTCCAATGATAG 57.544 37.037 0.00 3.31 30.16 2.08
1217 1818 5.801947 CCACACAGTAAACCATAGTACGTAC 59.198 44.000 18.10 18.10 0.00 3.67
1219 1820 4.281688 ACCACACAGTAAACCATAGTACGT 59.718 41.667 0.00 0.00 0.00 3.57
1221 1822 8.255905 AGATTACCACACAGTAAACCATAGTAC 58.744 37.037 0.00 0.00 35.90 2.73
1222 1823 8.370266 AGATTACCACACAGTAAACCATAGTA 57.630 34.615 0.00 0.00 35.90 1.82
1246 2148 8.181573 ACAGCACCGTGTAAAAATCATTAATAG 58.818 33.333 0.00 0.00 0.00 1.73
1247 2149 8.046294 ACAGCACCGTGTAAAAATCATTAATA 57.954 30.769 0.00 0.00 0.00 0.98
1279 2182 8.667987 TCGAAGACAAATGCAACATTAATTAC 57.332 30.769 0.00 0.00 0.00 1.89
1299 2202 5.215160 GGCTGCATTAATTTATGGTCGAAG 58.785 41.667 6.57 0.00 0.00 3.79
1301 2204 4.203226 TGGCTGCATTAATTTATGGTCGA 58.797 39.130 6.57 0.00 0.00 4.20
1303 2206 5.300286 ACTCTGGCTGCATTAATTTATGGTC 59.700 40.000 6.57 0.00 0.00 4.02
1304 2207 5.203528 ACTCTGGCTGCATTAATTTATGGT 58.796 37.500 6.57 0.00 0.00 3.55
1305 2208 5.779529 ACTCTGGCTGCATTAATTTATGG 57.220 39.130 6.57 0.00 0.00 2.74
1306 2209 6.798482 TGAACTCTGGCTGCATTAATTTATG 58.202 36.000 0.50 0.00 0.00 1.90
1307 2210 6.604795 ACTGAACTCTGGCTGCATTAATTTAT 59.395 34.615 0.50 0.00 0.00 1.40
1328 2231 4.617959 CGTTCTACTCCAAAGTTCACTGA 58.382 43.478 0.00 0.00 36.92 3.41
1329 2232 3.184581 GCGTTCTACTCCAAAGTTCACTG 59.815 47.826 0.00 0.00 36.92 3.66
1333 2244 2.737252 CCAGCGTTCTACTCCAAAGTTC 59.263 50.000 0.00 0.00 36.92 3.01
1336 2247 2.743636 TCCAGCGTTCTACTCCAAAG 57.256 50.000 0.00 0.00 0.00 2.77
1348 2259 4.508128 CGCCGTGGTATCCAGCGT 62.508 66.667 12.16 0.00 41.26 5.07
1350 2261 1.743995 AAACGCCGTGGTATCCAGC 60.744 57.895 0.00 0.00 32.34 4.85
1358 2269 1.970917 GATGAGCTCAAACGCCGTGG 61.971 60.000 22.50 0.00 0.00 4.94
1485 2396 3.772025 GGAAGAAGGGACTCATCTTCTCA 59.228 47.826 17.45 0.00 46.13 3.27
1486 2397 4.030216 AGGAAGAAGGGACTCATCTTCTC 58.970 47.826 17.45 9.51 46.13 2.87
1500 2411 1.730772 CGCTCTGTCGACAGGAAGAAG 60.731 57.143 37.82 28.93 43.91 2.85
1504 2415 2.082629 TTGCGCTCTGTCGACAGGAA 62.083 55.000 37.82 23.00 43.91 3.36
1668 2582 1.606313 CCCCTTGCATGACCCGTTT 60.606 57.895 0.00 0.00 0.00 3.60
1746 2660 8.099364 AGGTGTTATTGTTGTTCATAGTGAAG 57.901 34.615 0.00 0.00 37.00 3.02
1761 2675 5.766150 TGGTCTTGAACAAGGTGTTATTG 57.234 39.130 13.46 0.00 41.28 1.90
1993 2909 2.159101 TACCCCTGGCCAGTAGTCGT 62.159 60.000 30.63 19.35 0.00 4.34
2000 2916 1.322538 GCAAACATACCCCTGGCCAG 61.323 60.000 26.87 26.87 0.00 4.85
2016 2932 1.827789 GTGGTCCCAGCACTTGCAA 60.828 57.895 3.62 0.00 42.83 4.08
2040 2956 0.981183 TGACGATGTAAGGGTTGCCT 59.019 50.000 0.00 0.00 0.00 4.75
2123 3039 4.716784 AGTTCCTATATGAGCAGTGTGGAA 59.283 41.667 0.00 0.00 0.00 3.53
2124 3040 4.290093 AGTTCCTATATGAGCAGTGTGGA 58.710 43.478 0.00 0.00 0.00 4.02
2130 3046 5.999205 AGATGGAGTTCCTATATGAGCAG 57.001 43.478 0.00 0.00 36.82 4.24
2159 3077 3.547746 GGGAAATACAAAGGCACGGATA 58.452 45.455 0.00 0.00 0.00 2.59
2162 3080 0.815095 GGGGAAATACAAAGGCACGG 59.185 55.000 0.00 0.00 0.00 4.94
2164 3082 4.039852 TGAAAAGGGGAAATACAAAGGCAC 59.960 41.667 0.00 0.00 0.00 5.01
2179 3097 4.380233 GCACTCATTGATGTCTGAAAAGGG 60.380 45.833 0.00 0.00 0.00 3.95
2203 3122 3.460857 AGGATACAAATCGTGGAGCTC 57.539 47.619 4.71 4.71 41.41 4.09
2210 3129 2.550978 CGGAGCAAGGATACAAATCGT 58.449 47.619 0.00 0.00 41.41 3.73
2270 3189 5.480073 CCTTTCATTCCTGGTTTACATGGAA 59.520 40.000 0.00 0.00 39.24 3.53
2408 3448 4.184629 CAAGTAATTCCGAACAGAGGGAG 58.815 47.826 0.00 0.00 33.01 4.30
2409 3449 3.581332 ACAAGTAATTCCGAACAGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
2410 3450 3.933332 GACAAGTAATTCCGAACAGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
2411 3451 3.612860 CGACAAGTAATTCCGAACAGAGG 59.387 47.826 0.00 0.00 0.00 3.69
2412 3452 4.235360 ACGACAAGTAATTCCGAACAGAG 58.765 43.478 0.00 0.00 0.00 3.35
2413 3453 4.247267 ACGACAAGTAATTCCGAACAGA 57.753 40.909 0.00 0.00 0.00 3.41
2414 3454 5.396484 TCTACGACAAGTAATTCCGAACAG 58.604 41.667 0.00 0.00 34.45 3.16
2415 3455 5.375417 TCTACGACAAGTAATTCCGAACA 57.625 39.130 0.00 0.00 34.45 3.18
2416 3456 6.695292 TTTCTACGACAAGTAATTCCGAAC 57.305 37.500 0.00 0.00 34.45 3.95
2417 3457 6.311935 CCATTTCTACGACAAGTAATTCCGAA 59.688 38.462 0.00 0.00 34.45 4.30
2418 3458 5.808540 CCATTTCTACGACAAGTAATTCCGA 59.191 40.000 0.00 0.00 34.45 4.55
2419 3459 5.808540 TCCATTTCTACGACAAGTAATTCCG 59.191 40.000 0.00 0.00 34.45 4.30
2420 3460 7.280205 ACATCCATTTCTACGACAAGTAATTCC 59.720 37.037 0.00 0.00 34.45 3.01
2421 3461 8.197988 ACATCCATTTCTACGACAAGTAATTC 57.802 34.615 0.00 0.00 34.45 2.17
2422 3462 9.832445 ATACATCCATTTCTACGACAAGTAATT 57.168 29.630 0.00 0.00 34.45 1.40
2423 3463 9.477484 GATACATCCATTTCTACGACAAGTAAT 57.523 33.333 0.00 0.00 34.45 1.89
2424 3464 8.692710 AGATACATCCATTTCTACGACAAGTAA 58.307 33.333 0.00 0.00 34.45 2.24
2425 3465 8.234136 AGATACATCCATTTCTACGACAAGTA 57.766 34.615 0.00 0.00 0.00 2.24
2426 3466 7.113658 AGATACATCCATTTCTACGACAAGT 57.886 36.000 0.00 0.00 0.00 3.16
2427 3467 8.353684 ACTAGATACATCCATTTCTACGACAAG 58.646 37.037 0.00 0.00 0.00 3.16
2428 3468 8.234136 ACTAGATACATCCATTTCTACGACAA 57.766 34.615 0.00 0.00 0.00 3.18
2429 3469 7.501225 TGACTAGATACATCCATTTCTACGACA 59.499 37.037 0.00 0.00 0.00 4.35
2430 3470 7.872881 TGACTAGATACATCCATTTCTACGAC 58.127 38.462 0.00 0.00 0.00 4.34
2431 3471 8.637196 ATGACTAGATACATCCATTTCTACGA 57.363 34.615 0.00 0.00 0.00 3.43
2432 3472 9.698309 AAATGACTAGATACATCCATTTCTACG 57.302 33.333 0.00 0.00 31.07 3.51
2459 3499 8.736244 GCAAAAATGGATGTACCTAGAACTAAA 58.264 33.333 0.00 0.00 39.86 1.85
2460 3500 7.065324 CGCAAAAATGGATGTACCTAGAACTAA 59.935 37.037 0.00 0.00 39.86 2.24
2461 3501 6.537301 CGCAAAAATGGATGTACCTAGAACTA 59.463 38.462 0.00 0.00 39.86 2.24
2462 3502 5.354234 CGCAAAAATGGATGTACCTAGAACT 59.646 40.000 0.00 0.00 39.86 3.01
2463 3503 5.353123 TCGCAAAAATGGATGTACCTAGAAC 59.647 40.000 0.00 0.00 39.86 3.01
2464 3504 5.353123 GTCGCAAAAATGGATGTACCTAGAA 59.647 40.000 0.00 0.00 39.86 2.10
2465 3505 4.873827 GTCGCAAAAATGGATGTACCTAGA 59.126 41.667 0.00 0.00 39.86 2.43
2466 3506 4.634004 TGTCGCAAAAATGGATGTACCTAG 59.366 41.667 0.00 0.00 39.86 3.02
2467 3507 4.580868 TGTCGCAAAAATGGATGTACCTA 58.419 39.130 0.00 0.00 39.86 3.08
2468 3508 3.417101 TGTCGCAAAAATGGATGTACCT 58.583 40.909 0.00 0.00 39.86 3.08
2469 3509 3.840890 TGTCGCAAAAATGGATGTACC 57.159 42.857 0.00 0.00 39.54 3.34
2470 3510 4.794169 ACTTGTCGCAAAAATGGATGTAC 58.206 39.130 0.00 0.00 0.00 2.90
2471 3511 6.561737 TTACTTGTCGCAAAAATGGATGTA 57.438 33.333 0.00 0.00 0.00 2.29
2472 3512 5.446143 TTACTTGTCGCAAAAATGGATGT 57.554 34.783 0.00 0.00 0.00 3.06
2473 3513 6.585702 TGAATTACTTGTCGCAAAAATGGATG 59.414 34.615 0.00 0.00 0.00 3.51
2474 3514 6.686630 TGAATTACTTGTCGCAAAAATGGAT 58.313 32.000 0.00 0.00 0.00 3.41
2475 3515 6.016693 TCTGAATTACTTGTCGCAAAAATGGA 60.017 34.615 0.00 0.00 0.00 3.41
2476 3516 6.148948 TCTGAATTACTTGTCGCAAAAATGG 58.851 36.000 0.00 0.00 0.00 3.16
2477 3517 7.493313 GTTCTGAATTACTTGTCGCAAAAATG 58.507 34.615 0.00 0.00 0.00 2.32
2478 3518 6.359617 CGTTCTGAATTACTTGTCGCAAAAAT 59.640 34.615 0.00 0.00 0.00 1.82
2479 3519 5.679355 CGTTCTGAATTACTTGTCGCAAAAA 59.321 36.000 0.00 0.00 0.00 1.94
2480 3520 5.201910 CGTTCTGAATTACTTGTCGCAAAA 58.798 37.500 0.00 0.00 0.00 2.44
2481 3521 4.319190 CCGTTCTGAATTACTTGTCGCAAA 60.319 41.667 0.00 0.00 0.00 3.68
2482 3522 3.185594 CCGTTCTGAATTACTTGTCGCAA 59.814 43.478 0.00 0.00 0.00 4.85
2483 3523 2.734606 CCGTTCTGAATTACTTGTCGCA 59.265 45.455 0.00 0.00 0.00 5.10
2484 3524 2.991190 TCCGTTCTGAATTACTTGTCGC 59.009 45.455 0.00 0.00 0.00 5.19
2485 3525 3.612860 CCTCCGTTCTGAATTACTTGTCG 59.387 47.826 0.00 0.00 0.00 4.35
2486 3526 3.933332 CCCTCCGTTCTGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
2487 3527 3.581332 TCCCTCCGTTCTGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
2488 3528 4.184629 CTCCCTCCGTTCTGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
2489 3529 3.838903 ACTCCCTCCGTTCTGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
2490 3530 3.442076 ACTCCCTCCGTTCTGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
2491 3531 3.889520 ACTCCCTCCGTTCTGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
2492 3532 3.383825 GCTACTCCCTCCGTTCTGAATTA 59.616 47.826 0.00 0.00 0.00 1.40
2493 3533 2.168728 GCTACTCCCTCCGTTCTGAATT 59.831 50.000 0.00 0.00 0.00 2.17
2494 3534 1.757699 GCTACTCCCTCCGTTCTGAAT 59.242 52.381 0.00 0.00 0.00 2.57
2495 3535 1.183549 GCTACTCCCTCCGTTCTGAA 58.816 55.000 0.00 0.00 0.00 3.02
2496 3536 0.331954 AGCTACTCCCTCCGTTCTGA 59.668 55.000 0.00 0.00 0.00 3.27
2497 3537 2.054232 TAGCTACTCCCTCCGTTCTG 57.946 55.000 0.00 0.00 0.00 3.02
2498 3538 2.822707 TTAGCTACTCCCTCCGTTCT 57.177 50.000 0.00 0.00 0.00 3.01
2499 3539 4.143543 ACTATTAGCTACTCCCTCCGTTC 58.856 47.826 0.00 0.00 0.00 3.95
2500 3540 4.181799 ACTATTAGCTACTCCCTCCGTT 57.818 45.455 0.00 0.00 0.00 4.44
2501 3541 3.880168 ACTATTAGCTACTCCCTCCGT 57.120 47.619 0.00 0.00 0.00 4.69
2502 3542 4.649692 TGTACTATTAGCTACTCCCTCCG 58.350 47.826 0.00 0.00 0.00 4.63
2503 3543 5.011586 CCTGTACTATTAGCTACTCCCTCC 58.988 50.000 0.00 0.00 0.00 4.30
2504 3544 5.878627 TCCTGTACTATTAGCTACTCCCTC 58.121 45.833 0.00 0.00 0.00 4.30
2505 3545 5.926580 TCCTGTACTATTAGCTACTCCCT 57.073 43.478 0.00 0.00 0.00 4.20
2506 3546 6.376018 CAGATCCTGTACTATTAGCTACTCCC 59.624 46.154 0.00 0.00 0.00 4.30
2507 3547 7.169591 TCAGATCCTGTACTATTAGCTACTCC 58.830 42.308 0.00 0.00 32.61 3.85
2508 3548 8.624367 TTCAGATCCTGTACTATTAGCTACTC 57.376 38.462 0.00 0.00 32.61 2.59
2509 3549 9.238368 GATTCAGATCCTGTACTATTAGCTACT 57.762 37.037 0.00 0.00 32.61 2.57
2510 3550 9.238368 AGATTCAGATCCTGTACTATTAGCTAC 57.762 37.037 0.00 0.00 32.44 3.58
2512 3552 9.238368 GTAGATTCAGATCCTGTACTATTAGCT 57.762 37.037 0.00 0.00 32.44 3.32
2651 3727 2.511218 ACCAGATAGACCGGTACCTACA 59.489 50.000 7.34 0.00 0.00 2.74
2915 4008 1.135333 CTCTAAGACCGGGAGTTCTGC 59.865 57.143 6.32 0.00 0.00 4.26
2955 4048 5.295152 CCATGAGTTTACTTCCGGGTATAC 58.705 45.833 0.00 2.45 0.00 1.47
2967 4060 7.824779 AGATCTAGAAAACACCCATGAGTTTAC 59.175 37.037 0.00 0.00 36.98 2.01
3112 4346 1.146982 ACCCTGGCCACAATAAACACT 59.853 47.619 0.00 0.00 0.00 3.55
3163 4427 3.797039 TGACCCAAAGCTGAGAATATCG 58.203 45.455 0.00 0.00 0.00 2.92
3167 4431 5.128919 GTGATATGACCCAAAGCTGAGAAT 58.871 41.667 0.00 0.00 0.00 2.40
3285 4640 5.530915 TCAAAGACATCCACGTGAGAAAAAT 59.469 36.000 19.30 0.36 0.00 1.82
3351 4706 3.275143 CCCACACGCTGGTTAATTCATA 58.725 45.455 0.00 0.00 38.60 2.15
3411 4768 2.736670 AAGACCCACTATCCAATGGC 57.263 50.000 0.00 0.00 34.37 4.40
3450 4814 2.192861 TCCCTTGCAACCAAGCACG 61.193 57.895 0.00 0.00 45.65 5.34
3454 4818 2.039084 AGTCTAGTCCCTTGCAACCAAG 59.961 50.000 0.00 0.00 46.38 3.61
3505 4870 6.783482 ACTAGAAAAAGACTCTACTGAAGGGT 59.217 38.462 0.00 0.00 43.68 4.34
3506 4871 7.234661 ACTAGAAAAAGACTCTACTGAAGGG 57.765 40.000 0.00 0.00 0.00 3.95
3508 4873 7.177744 AGGGACTAGAAAAAGACTCTACTGAAG 59.822 40.741 0.00 0.00 36.02 3.02
3509 4874 7.011382 AGGGACTAGAAAAAGACTCTACTGAA 58.989 38.462 0.00 0.00 36.02 3.02
3535 4901 5.731678 ACCAAACAGGAGGGACTTATTCTAT 59.268 40.000 0.00 0.00 41.55 1.98
3551 4917 7.931948 CCTATAAGTCCCTATGTAACCAAACAG 59.068 40.741 0.00 0.00 31.70 3.16
3565 4931 6.464530 AAAACAAAGTCCCTATAAGTCCCT 57.535 37.500 0.00 0.00 0.00 4.20
3584 4950 6.350629 TGGTTACAGGGACTAGACTAAAAC 57.649 41.667 0.00 0.47 36.02 2.43
3597 4963 0.481128 AGGGGTGTTTGGTTACAGGG 59.519 55.000 0.00 0.00 0.00 4.45
3616 4982 2.570098 TCCTACCTCAGGGTCTCTACA 58.430 52.381 0.00 0.00 45.98 2.74
3621 4987 3.246167 ACTGATTTCCTACCTCAGGGTCT 60.246 47.826 0.00 0.00 45.98 3.85
3642 5008 6.183360 TGCTTTGTTTTGTTTCACAATAGCAC 60.183 34.615 13.22 0.00 39.44 4.40
3794 5164 6.137104 AGAATAAGGAATGATATGGCTGCT 57.863 37.500 0.00 0.00 0.00 4.24
3846 5216 5.640732 CCCACCGTTCTTCTCATAAAATTG 58.359 41.667 0.00 0.00 0.00 2.32
3900 5270 5.679638 GCTTGAGCTTCTCCTTTTCAAACAA 60.680 40.000 0.00 0.00 38.21 2.83
4475 5846 6.207417 CCAAGATGACAACTCCAAAACTGTAT 59.793 38.462 0.00 0.00 0.00 2.29
4617 5988 6.012508 TCAAGAACCTCCAAATCTCCAGTTAT 60.013 38.462 0.00 0.00 0.00 1.89
4635 6006 5.292101 CGATCCCTGTCAAACTATCAAGAAC 59.708 44.000 0.00 0.00 0.00 3.01
4821 6207 7.010697 TCCACAACAGCAATACAAATATACG 57.989 36.000 0.00 0.00 0.00 3.06
4901 6288 7.345192 CAGTAAACACACTCAATGAGTTACAC 58.655 38.462 13.99 6.25 41.37 2.90
5026 6421 3.788227 ACTTTTGACCAGCCATAGTGA 57.212 42.857 0.00 0.00 0.00 3.41
5076 6471 8.813282 TGCATACATATTAACAAGTTACGACTG 58.187 33.333 0.00 0.00 35.91 3.51
5086 6481 9.813446 TTTTGATGCATGCATACATATTAACAA 57.187 25.926 32.27 23.34 36.70 2.83
5114 6509 2.680913 GCGGTGCAATCAGTCGCTT 61.681 57.895 0.00 0.00 40.51 4.68
5116 6511 4.505217 CGCGGTGCAATCAGTCGC 62.505 66.667 0.00 0.00 40.37 5.19
5139 6534 2.271800 CAGGACGTTAGGATGCAGTTC 58.728 52.381 0.00 0.00 0.00 3.01
5140 6535 1.066143 CCAGGACGTTAGGATGCAGTT 60.066 52.381 0.00 0.00 0.00 3.16
5266 6661 6.223120 AGCTGGCAGTAATTAAACCTTTTTG 58.777 36.000 17.16 0.00 0.00 2.44
5423 8780 2.643551 CTCTAACAAACGGGATGGCAT 58.356 47.619 0.00 0.00 0.00 4.40
5426 8783 2.107950 TGCTCTAACAAACGGGATGG 57.892 50.000 0.00 0.00 0.00 3.51
5459 8816 6.127647 GGCATTTGTGACTCCAAATTAGATGA 60.128 38.462 0.00 0.00 41.79 2.92
5484 8841 4.675029 AAACGACCCGGTCAGCGG 62.675 66.667 17.87 8.80 32.09 5.52
5496 8853 5.534407 TGTTGTAGATGCTCTAACAAACGA 58.466 37.500 0.00 0.00 29.58 3.85
5498 8855 6.080406 GCTTGTTGTAGATGCTCTAACAAAC 58.920 40.000 0.00 9.43 32.49 2.93
5526 8883 4.156008 GGCGTTTGTGACTCCAAATTAGAT 59.844 41.667 0.00 0.00 36.75 1.98
5660 9017 4.891727 GGTGACCGCGCATCCGAT 62.892 66.667 8.75 0.00 36.29 4.18


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

AutoCloner maintained by Alex Coulton.