Multiple sequence alignment - TraesCS4A01G147300

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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 TraesCS4A01G147300 chr4A 100.000 2438 0 0 1 2438 262786068 262788505 0.000000e+00 4503.0
1 TraesCS4A01G147300 chr4A 85.269 930 119 16 1518 2438 309531547 309530627 0.000000e+00 942.0
2 TraesCS4A01G147300 chr4A 83.333 918 133 20 1518 2431 80834920 80834019 0.000000e+00 830.0
3 TraesCS4A01G147300 chr4A 83.745 689 60 24 4 654 297866855 297866181 2.680000e-169 604.0
4 TraesCS4A01G147300 chr4A 83.237 692 66 21 1 654 297883233 297882554 7.510000e-165 590.0
5 TraesCS4A01G147300 chr4A 87.500 456 46 11 1 454 368553651 368553205 1.290000e-142 516.0
6 TraesCS4A01G147300 chr4A 79.909 657 76 38 1 619 428532046 428532684 4.820000e-117 431.0
7 TraesCS4A01G147300 chr4A 79.542 655 76 35 1 619 428502006 428502638 4.850000e-112 414.0
8 TraesCS4A01G147300 chr7A 90.402 969 81 7 1478 2436 112636333 112637299 0.000000e+00 1264.0
9 TraesCS4A01G147300 chr7A 82.365 981 133 33 1478 2438 515484154 515485114 0.000000e+00 817.0
10 TraesCS4A01G147300 chr7A 82.481 919 138 23 1518 2431 261349827 261350727 0.000000e+00 784.0
11 TraesCS4A01G147300 chr7A 88.713 443 42 7 11 451 391581124 391580688 3.570000e-148 534.0
12 TraesCS4A01G147300 chr7A 86.598 97 7 6 597 689 353716972 353716878 4.290000e-18 102.0
13 TraesCS4A01G147300 chr7A 93.750 48 3 0 768 815 444382778 444382825 3.360000e-09 73.1
14 TraesCS4A01G147300 chr7A 78.723 94 18 2 723 815 355011364 355011272 7.280000e-06 62.1
15 TraesCS4A01G147300 chr1A 85.629 1176 130 12 85 1231 44438972 44437807 0.000000e+00 1199.0
16 TraesCS4A01G147300 chr1A 85.235 1192 129 23 78 1234 44451954 44450775 0.000000e+00 1182.0
17 TraesCS4A01G147300 chr1A 88.539 445 41 7 1 440 79769425 79769864 4.620000e-147 531.0
18 TraesCS4A01G147300 chr1A 92.308 156 11 1 1317 1472 98983337 98983183 1.130000e-53 220.0
19 TraesCS4A01G147300 chr1A 90.683 161 13 2 1317 1477 98929127 98928969 1.900000e-51 213.0
20 TraesCS4A01G147300 chr1A 84.507 142 11 7 454 592 374850267 374850134 1.970000e-26 130.0
21 TraesCS4A01G147300 chr1A 100.000 31 0 0 733 763 346156427 346156457 9.420000e-05 58.4
22 TraesCS4A01G147300 chr6A 85.399 1178 127 13 78 1225 209756606 209757768 0.000000e+00 1181.0
23 TraesCS4A01G147300 chr6A 83.099 923 131 23 1519 2431 310997521 310996614 0.000000e+00 817.0
24 TraesCS4A01G147300 chr6A 85.260 692 51 22 1 654 573098924 573099602 0.000000e+00 665.0
25 TraesCS4A01G147300 chr6A 88.914 442 40 7 3 440 56139754 56140190 9.920000e-149 536.0
26 TraesCS4A01G147300 chr6A 87.417 453 54 3 1 451 492910605 492910154 3.590000e-143 518.0
27 TraesCS4A01G147300 chr6A 87.033 455 50 7 1 454 305514337 305513891 2.800000e-139 505.0
28 TraesCS4A01G147300 chr5A 86.195 891 103 18 1518 2398 373893134 373894014 0.000000e+00 946.0
29 TraesCS4A01G147300 chr5A 83.099 923 129 22 1519 2431 412784209 412785114 0.000000e+00 815.0
30 TraesCS4A01G147300 chr5A 92.683 41 3 0 1109 1149 358282326 358282366 2.620000e-05 60.2
31 TraesCS4A01G147300 chr2A 82.298 966 135 27 1492 2436 286162779 286161829 0.000000e+00 804.0
32 TraesCS4A01G147300 chr2A 80.460 87 13 3 732 815 182451098 182451013 2.020000e-06 63.9
33 TraesCS4A01G147300 chr2A 79.167 96 15 5 723 815 317959041 317959134 7.280000e-06 62.1
34 TraesCS4A01G147300 chr3A 88.565 446 47 4 1 444 252886002 252885559 2.760000e-149 538.0
35 TraesCS4A01G147300 chr3A 88.341 446 48 4 1 444 252897498 252897055 1.280000e-147 532.0
36 TraesCS4A01G147300 chr3A 87.892 446 50 4 1 444 252747975 252747532 2.780000e-144 521.0
37 TraesCS4A01G147300 chr3A 86.982 169 13 7 454 619 453427019 453427181 5.350000e-42 182.0
38 TraesCS4A01G147300 chr3A 89.655 58 2 3 717 770 286414966 286415023 1.210000e-08 71.3
39 TraesCS4A01G147300 chr3A 80.612 98 13 4 732 828 334614251 334614343 1.210000e-08 71.3
40 TraesCS4A01G147300 chr3A 91.667 48 4 0 768 815 293929462 293929415 1.560000e-07 67.6
41 TraesCS4A01G147300 chr3A 100.000 28 0 0 787 814 205805673 205805700 4.000000e-03 52.8
42 TraesCS4A01G147300 chr7B 100.000 33 0 0 1106 1138 169816224 169816256 7.280000e-06 62.1
43 TraesCS4A01G147300 chr7B 100.000 33 0 0 1106 1138 349572563 349572595 7.280000e-06 62.1
44 TraesCS4A01G147300 chr2B 100.000 33 0 0 1106 1138 492406012 492405980 7.280000e-06 62.1
45 TraesCS4A01G147300 chr2B 100.000 33 0 0 1106 1138 492413615 492413583 7.280000e-06 62.1
46 TraesCS4A01G147300 chr1B 100.000 33 0 0 1106 1138 300396436 300396404 7.280000e-06 62.1
47 TraesCS4A01G147300 chr1B 100.000 31 0 0 1108 1138 670096744 670096774 9.420000e-05 58.4
48 TraesCS4A01G147300 chr1B 96.970 33 1 0 1106 1138 670104208 670104240 3.390000e-04 56.5


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 TraesCS4A01G147300 chr4A 262786068 262788505 2437 False 4503 4503 100.000 1 2438 1 chr4A.!!$F1 2437
1 TraesCS4A01G147300 chr4A 309530627 309531547 920 True 942 942 85.269 1518 2438 1 chr4A.!!$R4 920
2 TraesCS4A01G147300 chr4A 80834019 80834920 901 True 830 830 83.333 1518 2431 1 chr4A.!!$R1 913
3 TraesCS4A01G147300 chr4A 297866181 297866855 674 True 604 604 83.745 4 654 1 chr4A.!!$R2 650
4 TraesCS4A01G147300 chr4A 297882554 297883233 679 True 590 590 83.237 1 654 1 chr4A.!!$R3 653
5 TraesCS4A01G147300 chr4A 428532046 428532684 638 False 431 431 79.909 1 619 1 chr4A.!!$F3 618
6 TraesCS4A01G147300 chr4A 428502006 428502638 632 False 414 414 79.542 1 619 1 chr4A.!!$F2 618
7 TraesCS4A01G147300 chr7A 112636333 112637299 966 False 1264 1264 90.402 1478 2436 1 chr7A.!!$F1 958
8 TraesCS4A01G147300 chr7A 515484154 515485114 960 False 817 817 82.365 1478 2438 1 chr7A.!!$F4 960
9 TraesCS4A01G147300 chr7A 261349827 261350727 900 False 784 784 82.481 1518 2431 1 chr7A.!!$F2 913
10 TraesCS4A01G147300 chr1A 44437807 44438972 1165 True 1199 1199 85.629 85 1231 1 chr1A.!!$R1 1146
11 TraesCS4A01G147300 chr1A 44450775 44451954 1179 True 1182 1182 85.235 78 1234 1 chr1A.!!$R2 1156
12 TraesCS4A01G147300 chr6A 209756606 209757768 1162 False 1181 1181 85.399 78 1225 1 chr6A.!!$F2 1147
13 TraesCS4A01G147300 chr6A 310996614 310997521 907 True 817 817 83.099 1519 2431 1 chr6A.!!$R2 912
14 TraesCS4A01G147300 chr6A 573098924 573099602 678 False 665 665 85.260 1 654 1 chr6A.!!$F3 653
15 TraesCS4A01G147300 chr5A 373893134 373894014 880 False 946 946 86.195 1518 2398 1 chr5A.!!$F2 880
16 TraesCS4A01G147300 chr5A 412784209 412785114 905 False 815 815 83.099 1519 2431 1 chr5A.!!$F3 912
17 TraesCS4A01G147300 chr2A 286161829 286162779 950 True 804 804 82.298 1492 2436 1 chr2A.!!$R2 944

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
815 903 0.771127 CCTCCTCCCTCTCGATCTCT 59.229 60.0 0.0 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 2118 1.533625 CATTTGTCACCGTGGTGGAT 58.466 50.0 18.47 5.89 45.43 3.41 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
31 32 6.715264 ACGTTCCAGAAGACTTCCATATTTTT 59.285 34.615 11.67 0.00 0.00 1.94
57 58 2.287547 CCTCCGTGTGTTTCATTTGTGG 60.288 50.000 0.00 0.00 0.00 4.17
58 59 2.616376 CTCCGTGTGTTTCATTTGTGGA 59.384 45.455 0.00 0.00 0.00 4.02
63 64 4.370917 GTGTGTTTCATTTGTGGATGCTT 58.629 39.130 0.00 0.00 0.00 3.91
305 324 5.180492 CCATGCCTTTTGTACTTCGAGTTTA 59.820 40.000 0.00 0.00 0.00 2.01
376 433 7.070322 CCTCCAATAATCCTCATCATTTTTGGT 59.930 37.037 11.83 0.00 40.50 3.67
526 609 6.468212 CCCCTAACCTCCCTTTCTTTTCTTTA 60.468 42.308 0.00 0.00 0.00 1.85
528 611 8.333984 CCCTAACCTCCCTTTCTTTTCTTTATA 58.666 37.037 0.00 0.00 0.00 0.98
529 612 9.922477 CCTAACCTCCCTTTCTTTTCTTTATAT 57.078 33.333 0.00 0.00 0.00 0.86
569 656 9.695155 TTTTATTTATCCTTCTTTAGAGTGGGG 57.305 33.333 0.00 0.00 0.00 4.96
570 657 5.710409 TTTATCCTTCTTTAGAGTGGGGG 57.290 43.478 0.00 0.00 0.00 5.40
654 742 2.063378 GCAGTCCTCTAGGCCAGCT 61.063 63.158 5.01 0.00 34.44 4.24
662 750 2.759973 TAGGCCAGCTCAGTCCCG 60.760 66.667 5.01 0.00 0.00 5.14
815 903 0.771127 CCTCCTCCCTCTCGATCTCT 59.229 60.000 0.00 0.00 0.00 3.10
819 907 1.133945 CCTCCCTCTCGATCTCTCACA 60.134 57.143 0.00 0.00 0.00 3.58
885 973 4.172512 CTCCAGCCAGCGAGCCAT 62.173 66.667 0.00 0.00 0.00 4.40
996 1084 3.068691 CCCCGACTTCGCTCTCCA 61.069 66.667 0.00 0.00 38.18 3.86
1029 1120 4.814294 CCGGCGACCACCTACAGC 62.814 72.222 9.30 0.00 0.00 4.40
1058 1149 1.153823 GAGCCGTCTCTTTAGCGCA 60.154 57.895 11.47 0.00 36.42 6.09
1099 1190 1.913451 CTTCGTCGTCCGTCTCTGCT 61.913 60.000 0.00 0.00 37.94 4.24
1143 1234 4.020617 CGCCCAACCTCCAGCTCA 62.021 66.667 0.00 0.00 0.00 4.26
1150 1241 3.699894 CCTCCAGCTCACGCCTGT 61.700 66.667 0.00 0.00 36.60 4.00
1160 1251 3.314331 ACGCCTGTGTCCCTCCAG 61.314 66.667 0.00 0.00 0.00 3.86
1167 1258 0.977627 TGTGTCCCTCCAGCATCGAT 60.978 55.000 0.00 0.00 0.00 3.59
1202 1293 1.536073 CCTCCACGTCCTCTGCTTCA 61.536 60.000 0.00 0.00 0.00 3.02
1231 1322 4.003788 CCGTGCTCCTCCCGTTGT 62.004 66.667 0.00 0.00 0.00 3.32
1234 1325 1.841663 CGTGCTCCTCCCGTTGTTTG 61.842 60.000 0.00 0.00 0.00 2.93
1235 1326 1.228124 TGCTCCTCCCGTTGTTTGG 60.228 57.895 0.00 0.00 0.00 3.28
1236 1327 1.228154 GCTCCTCCCGTTGTTTGGT 60.228 57.895 0.00 0.00 0.00 3.67
1237 1328 1.235281 GCTCCTCCCGTTGTTTGGTC 61.235 60.000 0.00 0.00 0.00 4.02
1238 1329 0.396811 CTCCTCCCGTTGTTTGGTCT 59.603 55.000 0.00 0.00 0.00 3.85
1239 1330 0.841289 TCCTCCCGTTGTTTGGTCTT 59.159 50.000 0.00 0.00 0.00 3.01
1240 1331 1.202722 TCCTCCCGTTGTTTGGTCTTC 60.203 52.381 0.00 0.00 0.00 2.87
1241 1332 1.235724 CTCCCGTTGTTTGGTCTTCC 58.764 55.000 0.00 0.00 0.00 3.46
1242 1333 0.841289 TCCCGTTGTTTGGTCTTCCT 59.159 50.000 0.00 0.00 34.23 3.36
1243 1334 1.213430 TCCCGTTGTTTGGTCTTCCTT 59.787 47.619 0.00 0.00 34.23 3.36
1244 1335 2.438763 TCCCGTTGTTTGGTCTTCCTTA 59.561 45.455 0.00 0.00 34.23 2.69
1245 1336 2.551032 CCCGTTGTTTGGTCTTCCTTAC 59.449 50.000 0.00 0.00 34.23 2.34
1246 1337 2.551032 CCGTTGTTTGGTCTTCCTTACC 59.449 50.000 0.00 0.00 37.53 2.85
1247 1338 2.551032 CGTTGTTTGGTCTTCCTTACCC 59.449 50.000 0.00 0.00 36.06 3.69
1248 1339 3.558033 GTTGTTTGGTCTTCCTTACCCA 58.442 45.455 0.00 0.00 36.06 4.51
1249 1340 3.217681 TGTTTGGTCTTCCTTACCCAC 57.782 47.619 0.00 0.00 36.06 4.61
1250 1341 2.158579 TGTTTGGTCTTCCTTACCCACC 60.159 50.000 0.00 0.00 36.06 4.61
1251 1342 2.107726 GTTTGGTCTTCCTTACCCACCT 59.892 50.000 0.00 0.00 36.06 4.00
1252 1343 3.278987 TTGGTCTTCCTTACCCACCTA 57.721 47.619 0.00 0.00 36.06 3.08
1253 1344 3.502051 TGGTCTTCCTTACCCACCTAT 57.498 47.619 0.00 0.00 36.06 2.57
1254 1345 3.381335 TGGTCTTCCTTACCCACCTATC 58.619 50.000 0.00 0.00 36.06 2.08
1255 1346 3.246203 TGGTCTTCCTTACCCACCTATCA 60.246 47.826 0.00 0.00 36.06 2.15
1256 1347 3.388350 GGTCTTCCTTACCCACCTATCAG 59.612 52.174 0.00 0.00 0.00 2.90
1257 1348 3.388350 GTCTTCCTTACCCACCTATCAGG 59.612 52.174 0.00 0.00 42.49 3.86
1263 1354 2.822399 CCACCTATCAGGGACGCC 59.178 66.667 0.00 0.00 40.58 5.68
1264 1355 2.063979 CCACCTATCAGGGACGCCA 61.064 63.158 0.00 0.00 40.58 5.69
1265 1356 1.410850 CCACCTATCAGGGACGCCAT 61.411 60.000 0.00 0.00 40.58 4.40
1266 1357 0.250038 CACCTATCAGGGACGCCATG 60.250 60.000 4.47 4.47 40.58 3.66
1267 1358 1.372683 CCTATCAGGGACGCCATGG 59.627 63.158 7.63 7.63 35.84 3.66
1268 1359 1.302033 CTATCAGGGACGCCATGGC 60.302 63.158 27.67 27.67 35.84 4.40
1269 1360 1.762522 CTATCAGGGACGCCATGGCT 61.763 60.000 33.07 20.54 35.84 4.75
1270 1361 2.043604 TATCAGGGACGCCATGGCTG 62.044 60.000 33.07 26.84 35.84 4.85
1285 1376 4.431131 CTGCCGCCCCATGGAGTT 62.431 66.667 15.22 0.00 0.00 3.01
1286 1377 3.944250 CTGCCGCCCCATGGAGTTT 62.944 63.158 15.22 0.00 0.00 2.66
1287 1378 3.140814 GCCGCCCCATGGAGTTTC 61.141 66.667 15.22 0.00 0.00 2.78
1288 1379 2.354729 CCGCCCCATGGAGTTTCA 59.645 61.111 15.22 0.00 0.00 2.69
1289 1380 1.076777 CCGCCCCATGGAGTTTCAT 60.077 57.895 15.22 0.00 0.00 2.57
1290 1381 1.103398 CCGCCCCATGGAGTTTCATC 61.103 60.000 15.22 0.00 0.00 2.92
1291 1382 1.439353 CGCCCCATGGAGTTTCATCG 61.439 60.000 15.22 0.00 0.00 3.84
1292 1383 1.103398 GCCCCATGGAGTTTCATCGG 61.103 60.000 15.22 3.12 0.00 4.18
1293 1384 1.103398 CCCCATGGAGTTTCATCGGC 61.103 60.000 15.22 0.00 0.00 5.54
1294 1385 1.103398 CCCATGGAGTTTCATCGGCC 61.103 60.000 15.22 0.00 0.00 6.13
1295 1386 1.103398 CCATGGAGTTTCATCGGCCC 61.103 60.000 5.56 0.00 0.00 5.80
1296 1387 0.394216 CATGGAGTTTCATCGGCCCA 60.394 55.000 0.00 0.00 0.00 5.36
1297 1388 0.552848 ATGGAGTTTCATCGGCCCAT 59.447 50.000 0.00 0.00 0.00 4.00
1298 1389 1.208706 TGGAGTTTCATCGGCCCATA 58.791 50.000 0.00 0.00 0.00 2.74
1299 1390 1.774254 TGGAGTTTCATCGGCCCATAT 59.226 47.619 0.00 0.00 0.00 1.78
1300 1391 2.224523 TGGAGTTTCATCGGCCCATATC 60.225 50.000 0.00 0.00 0.00 1.63
1301 1392 2.039084 GGAGTTTCATCGGCCCATATCT 59.961 50.000 0.00 0.00 0.00 1.98
1302 1393 3.070018 GAGTTTCATCGGCCCATATCTG 58.930 50.000 0.00 0.00 0.00 2.90
1303 1394 2.154462 GTTTCATCGGCCCATATCTGG 58.846 52.381 0.00 0.00 42.73 3.86
1309 1400 3.249189 GCCCATATCTGGCCGGGA 61.249 66.667 12.87 6.17 43.33 5.14
1310 1401 2.829384 GCCCATATCTGGCCGGGAA 61.829 63.158 12.87 0.00 43.33 3.97
1311 1402 1.073199 CCCATATCTGGCCGGGAAC 59.927 63.158 12.87 0.00 41.62 3.62
1312 1403 1.073199 CCATATCTGGCCGGGAACC 59.927 63.158 12.87 0.00 40.07 3.62
1313 1404 1.705002 CCATATCTGGCCGGGAACCA 61.705 60.000 12.87 0.30 42.78 3.67
1314 1405 3.210264 CCATATCTGGCCGGGAACCAA 62.210 57.143 12.87 0.00 42.78 3.67
1315 1406 4.669721 CCATATCTGGCCGGGAACCAAA 62.670 54.545 12.87 0.00 42.78 3.28
1324 1415 3.053896 GGAACCAAACGAGCCCCG 61.054 66.667 0.00 0.00 45.44 5.73
1345 1436 3.667282 CTGCTGCTGCCGCTGTTT 61.667 61.111 16.81 0.00 38.71 2.83
1346 1437 3.203546 CTGCTGCTGCCGCTGTTTT 62.204 57.895 16.81 0.00 38.71 2.43
1347 1438 2.028043 GCTGCTGCCGCTGTTTTT 59.972 55.556 8.89 0.00 37.41 1.94
1348 1439 2.018324 GCTGCTGCCGCTGTTTTTC 61.018 57.895 8.89 0.00 37.41 2.29
1349 1440 1.372128 CTGCTGCCGCTGTTTTTCC 60.372 57.895 0.70 0.00 36.97 3.13
1350 1441 2.049156 GCTGCCGCTGTTTTTCCC 60.049 61.111 0.00 0.00 0.00 3.97
1351 1442 2.564721 GCTGCCGCTGTTTTTCCCT 61.565 57.895 0.00 0.00 0.00 4.20
1352 1443 1.581447 CTGCCGCTGTTTTTCCCTC 59.419 57.895 0.00 0.00 0.00 4.30
1353 1444 0.890996 CTGCCGCTGTTTTTCCCTCT 60.891 55.000 0.00 0.00 0.00 3.69
1354 1445 1.172180 TGCCGCTGTTTTTCCCTCTG 61.172 55.000 0.00 0.00 0.00 3.35
1355 1446 1.172812 GCCGCTGTTTTTCCCTCTGT 61.173 55.000 0.00 0.00 0.00 3.41
1356 1447 0.875059 CCGCTGTTTTTCCCTCTGTC 59.125 55.000 0.00 0.00 0.00 3.51
1357 1448 1.593196 CGCTGTTTTTCCCTCTGTCA 58.407 50.000 0.00 0.00 0.00 3.58
1358 1449 1.946768 CGCTGTTTTTCCCTCTGTCAA 59.053 47.619 0.00 0.00 0.00 3.18
1359 1450 2.357637 CGCTGTTTTTCCCTCTGTCAAA 59.642 45.455 0.00 0.00 0.00 2.69
1360 1451 3.706698 GCTGTTTTTCCCTCTGTCAAAC 58.293 45.455 0.00 0.00 0.00 2.93
1361 1452 3.792124 GCTGTTTTTCCCTCTGTCAAACG 60.792 47.826 0.00 0.00 31.24 3.60
1362 1453 3.611970 TGTTTTTCCCTCTGTCAAACGA 58.388 40.909 0.00 0.00 31.24 3.85
1363 1454 4.011023 TGTTTTTCCCTCTGTCAAACGAA 58.989 39.130 0.00 0.00 31.24 3.85
1364 1455 4.642885 TGTTTTTCCCTCTGTCAAACGAAT 59.357 37.500 0.00 0.00 31.24 3.34
1365 1456 4.829064 TTTTCCCTCTGTCAAACGAATG 57.171 40.909 0.00 0.00 0.00 2.67
1366 1457 3.762407 TTCCCTCTGTCAAACGAATGA 57.238 42.857 0.00 0.00 0.00 2.57
1367 1458 3.762407 TCCCTCTGTCAAACGAATGAA 57.238 42.857 0.00 0.00 0.00 2.57
1368 1459 3.399330 TCCCTCTGTCAAACGAATGAAC 58.601 45.455 0.00 0.00 0.00 3.18
1369 1460 3.138304 CCCTCTGTCAAACGAATGAACA 58.862 45.455 0.00 0.00 0.00 3.18
1370 1461 3.058914 CCCTCTGTCAAACGAATGAACAC 60.059 47.826 0.00 0.00 0.00 3.32
1371 1462 3.058914 CCTCTGTCAAACGAATGAACACC 60.059 47.826 0.00 0.00 0.00 4.16
1372 1463 3.804036 TCTGTCAAACGAATGAACACCT 58.196 40.909 0.00 0.00 0.00 4.00
1373 1464 4.196193 TCTGTCAAACGAATGAACACCTT 58.804 39.130 0.00 0.00 0.00 3.50
1374 1465 4.272504 TCTGTCAAACGAATGAACACCTTC 59.727 41.667 0.00 0.00 0.00 3.46
1375 1466 3.314080 TGTCAAACGAATGAACACCTTCC 59.686 43.478 0.00 0.00 0.00 3.46
1376 1467 2.882137 TCAAACGAATGAACACCTTCCC 59.118 45.455 0.00 0.00 0.00 3.97
1377 1468 1.905637 AACGAATGAACACCTTCCCC 58.094 50.000 0.00 0.00 0.00 4.81
1378 1469 0.321298 ACGAATGAACACCTTCCCCG 60.321 55.000 0.00 0.00 0.00 5.73
1379 1470 1.024579 CGAATGAACACCTTCCCCGG 61.025 60.000 0.00 0.00 0.00 5.73
1380 1471 0.326927 GAATGAACACCTTCCCCGGA 59.673 55.000 0.73 0.00 0.00 5.14
1381 1472 0.328258 AATGAACACCTTCCCCGGAG 59.672 55.000 0.73 0.00 0.00 4.63
1382 1473 0.546747 ATGAACACCTTCCCCGGAGA 60.547 55.000 0.73 0.00 0.00 3.71
1383 1474 1.295746 GAACACCTTCCCCGGAGAC 59.704 63.158 0.73 0.00 0.00 3.36
1384 1475 1.152096 AACACCTTCCCCGGAGACT 60.152 57.895 0.73 0.00 0.00 3.24
1385 1476 1.481056 AACACCTTCCCCGGAGACTG 61.481 60.000 0.73 0.00 0.00 3.51
1386 1477 3.003763 ACCTTCCCCGGAGACTGC 61.004 66.667 0.73 0.00 0.00 4.40
1387 1478 3.787001 CCTTCCCCGGAGACTGCC 61.787 72.222 0.73 0.00 0.00 4.85
1388 1479 3.003173 CTTCCCCGGAGACTGCCA 61.003 66.667 0.73 0.00 0.00 4.92
1389 1480 2.528127 TTCCCCGGAGACTGCCAA 60.528 61.111 0.73 0.00 0.00 4.52
1390 1481 2.527951 CTTCCCCGGAGACTGCCAAG 62.528 65.000 0.73 0.00 0.00 3.61
1391 1482 3.003173 CCCCGGAGACTGCCAAGA 61.003 66.667 0.73 0.00 0.00 3.02
1392 1483 2.266055 CCCGGAGACTGCCAAGAC 59.734 66.667 0.73 0.00 0.00 3.01
1393 1484 2.266055 CCGGAGACTGCCAAGACC 59.734 66.667 0.00 0.00 0.00 3.85
1394 1485 2.125912 CGGAGACTGCCAAGACCG 60.126 66.667 0.00 0.00 34.31 4.79
1395 1486 2.932234 CGGAGACTGCCAAGACCGT 61.932 63.158 0.00 0.00 35.36 4.83
1396 1487 1.371558 GGAGACTGCCAAGACCGTT 59.628 57.895 0.00 0.00 0.00 4.44
1397 1488 0.670854 GGAGACTGCCAAGACCGTTC 60.671 60.000 0.00 0.00 0.00 3.95
1398 1489 0.033504 GAGACTGCCAAGACCGTTCA 59.966 55.000 0.00 0.00 0.00 3.18
1399 1490 0.034059 AGACTGCCAAGACCGTTCAG 59.966 55.000 0.00 0.00 0.00 3.02
1401 1492 1.371183 CTGCCAAGACCGTTCAGGA 59.629 57.895 0.00 0.00 45.00 3.86
1402 1493 0.036010 CTGCCAAGACCGTTCAGGAT 60.036 55.000 0.00 0.00 45.00 3.24
1403 1494 0.400213 TGCCAAGACCGTTCAGGATT 59.600 50.000 0.00 0.00 45.00 3.01
1404 1495 1.087501 GCCAAGACCGTTCAGGATTC 58.912 55.000 0.00 0.00 45.00 2.52
1405 1496 1.359848 CCAAGACCGTTCAGGATTCG 58.640 55.000 0.00 0.00 45.00 3.34
1406 1497 0.721718 CAAGACCGTTCAGGATTCGC 59.278 55.000 0.00 0.00 45.00 4.70
1407 1498 0.391263 AAGACCGTTCAGGATTCGCC 60.391 55.000 0.00 0.00 45.00 5.54
1408 1499 1.079405 GACCGTTCAGGATTCGCCA 60.079 57.895 0.00 0.00 45.00 5.69
1409 1500 0.672401 GACCGTTCAGGATTCGCCAA 60.672 55.000 0.00 0.00 45.00 4.52
1410 1501 0.673644 ACCGTTCAGGATTCGCCAAG 60.674 55.000 0.00 0.00 45.00 3.61
1411 1502 0.673644 CCGTTCAGGATTCGCCAAGT 60.674 55.000 0.00 0.00 45.00 3.16
1412 1503 1.404986 CCGTTCAGGATTCGCCAAGTA 60.405 52.381 0.00 0.00 45.00 2.24
1413 1504 1.659098 CGTTCAGGATTCGCCAAGTAC 59.341 52.381 0.00 0.00 40.02 2.73
1414 1505 2.007608 GTTCAGGATTCGCCAAGTACC 58.992 52.381 0.00 0.00 40.02 3.34
1415 1506 0.174845 TCAGGATTCGCCAAGTACCG 59.825 55.000 0.00 0.00 40.02 4.02
1416 1507 0.810031 CAGGATTCGCCAAGTACCGG 60.810 60.000 0.00 0.00 40.02 5.28
1417 1508 1.219935 GGATTCGCCAAGTACCGGT 59.780 57.895 13.98 13.98 36.34 5.28
1418 1509 0.392060 GGATTCGCCAAGTACCGGTT 60.392 55.000 15.04 0.00 36.34 4.44
1419 1510 1.004595 GATTCGCCAAGTACCGGTTC 58.995 55.000 15.04 8.12 0.00 3.62
1420 1511 0.738412 ATTCGCCAAGTACCGGTTCG 60.738 55.000 15.04 7.54 0.00 3.95
1421 1512 1.804396 TTCGCCAAGTACCGGTTCGA 61.804 55.000 15.04 9.89 0.00 3.71
1422 1513 1.804326 CGCCAAGTACCGGTTCGAG 60.804 63.158 15.04 5.63 0.00 4.04
1423 1514 1.291272 GCCAAGTACCGGTTCGAGT 59.709 57.895 15.04 0.00 0.00 4.18
1424 1515 0.527565 GCCAAGTACCGGTTCGAGTA 59.472 55.000 15.04 0.00 0.00 2.59
1425 1516 1.733718 GCCAAGTACCGGTTCGAGTAC 60.734 57.143 15.04 2.91 39.31 2.73
1426 1517 1.466360 CCAAGTACCGGTTCGAGTACG 60.466 57.143 15.04 3.41 42.92 3.67
1437 1528 2.214387 TCGAGTACGACTATCGCTGA 57.786 50.000 0.00 0.00 45.12 4.26
1438 1529 2.752121 TCGAGTACGACTATCGCTGAT 58.248 47.619 0.00 0.00 45.12 2.90
1439 1530 3.905784 TCGAGTACGACTATCGCTGATA 58.094 45.455 0.00 0.00 45.12 2.15
1440 1531 3.672397 TCGAGTACGACTATCGCTGATAC 59.328 47.826 0.00 0.00 45.12 2.24
1441 1532 3.181532 CGAGTACGACTATCGCTGATACC 60.182 52.174 0.00 0.00 45.12 2.73
1442 1533 3.072944 AGTACGACTATCGCTGATACCC 58.927 50.000 0.00 0.00 45.12 3.69
1443 1534 1.245732 ACGACTATCGCTGATACCCC 58.754 55.000 0.00 0.00 45.12 4.95
1444 1535 0.168348 CGACTATCGCTGATACCCCG 59.832 60.000 0.00 0.00 31.14 5.73
1445 1536 1.531423 GACTATCGCTGATACCCCGA 58.469 55.000 0.00 0.00 35.29 5.14
1446 1537 1.469308 GACTATCGCTGATACCCCGAG 59.531 57.143 0.00 0.00 34.21 4.63
1447 1538 0.811915 CTATCGCTGATACCCCGAGG 59.188 60.000 0.00 0.00 40.04 4.63
1448 1539 0.402887 TATCGCTGATACCCCGAGGA 59.597 55.000 0.00 0.00 36.73 3.71
1449 1540 1.179814 ATCGCTGATACCCCGAGGAC 61.180 60.000 0.00 0.00 36.73 3.85
1450 1541 2.125326 CGCTGATACCCCGAGGACA 61.125 63.158 0.00 0.00 36.73 4.02
1451 1542 1.442148 GCTGATACCCCGAGGACAC 59.558 63.158 0.00 0.00 36.73 3.67
1452 1543 2.029307 GCTGATACCCCGAGGACACC 62.029 65.000 0.00 0.00 36.73 4.16
1453 1544 0.686441 CTGATACCCCGAGGACACCA 60.686 60.000 0.00 0.00 36.73 4.17
1454 1545 0.252330 TGATACCCCGAGGACACCAA 60.252 55.000 0.00 0.00 36.73 3.67
1455 1546 0.464452 GATACCCCGAGGACACCAAG 59.536 60.000 0.00 0.00 36.73 3.61
1456 1547 0.252558 ATACCCCGAGGACACCAAGT 60.253 55.000 0.00 0.00 36.73 3.16
1457 1548 1.189524 TACCCCGAGGACACCAAGTG 61.190 60.000 0.00 0.00 36.66 3.16
1474 1565 1.139308 TGTACGAATACACCCGGCG 59.861 57.895 0.00 0.00 36.34 6.46
1475 1566 1.311651 TGTACGAATACACCCGGCGA 61.312 55.000 9.30 0.00 36.34 5.54
1476 1567 0.031178 GTACGAATACACCCGGCGAT 59.969 55.000 9.30 0.00 0.00 4.58
1477 1568 1.266718 GTACGAATACACCCGGCGATA 59.733 52.381 9.30 0.00 0.00 2.92
1478 1569 0.031178 ACGAATACACCCGGCGATAC 59.969 55.000 9.30 0.00 0.00 2.24
1479 1570 0.665369 CGAATACACCCGGCGATACC 60.665 60.000 9.30 0.00 0.00 2.73
1480 1571 0.320160 GAATACACCCGGCGATACCC 60.320 60.000 9.30 0.00 33.26 3.69
1481 1572 1.761500 AATACACCCGGCGATACCCC 61.761 60.000 9.30 0.00 33.26 4.95
1490 1581 2.994699 CGATACCCCAAGGCACCA 59.005 61.111 0.00 0.00 36.11 4.17
1516 1608 2.416296 CGTAAGTTCCTCGCCATGTACA 60.416 50.000 0.00 0.00 0.00 2.90
1549 1648 4.692625 ACGACTACTATGTGAACGTGTACT 59.307 41.667 0.00 0.00 0.00 2.73
1563 1662 2.040544 GTACTCGACGACCCCGGAA 61.041 63.158 0.73 0.00 40.78 4.30
1574 1675 1.003928 GACCCCGGAAACCTATGTTGT 59.996 52.381 0.73 0.00 34.13 3.32
1585 1686 2.006888 CCTATGTTGTGCCAAGTACCG 58.993 52.381 0.00 0.00 0.00 4.02
1604 1707 1.635663 GCCTCGTTGACCCGAACATG 61.636 60.000 0.00 0.00 36.24 3.21
1615 1718 4.007659 GACCCGAACATGTACAGGAAAAT 58.992 43.478 15.54 0.00 0.00 1.82
1633 1736 3.536956 AATGTGTACCACTACCATCGG 57.463 47.619 0.00 0.00 35.11 4.18
1698 1805 2.041350 ACTTCCTCTACTTCCCTCGACA 59.959 50.000 0.00 0.00 0.00 4.35
1714 1821 2.281208 CAAACTCGAACCGCCCCA 60.281 61.111 0.00 0.00 0.00 4.96
1724 1831 2.676121 CCGCCCCAGAAATGCACA 60.676 61.111 0.00 0.00 0.00 4.57
1743 1850 4.449743 GCACACTTCAAAGGTATAACGTCA 59.550 41.667 0.00 0.00 0.00 4.35
1792 1903 6.041423 TGTGATGTGTTGTATGAGATGTCT 57.959 37.500 0.00 0.00 0.00 3.41
1810 1921 1.031235 CTGTGTTTGCACCATGTCCA 58.969 50.000 0.00 0.00 44.65 4.02
1832 1943 5.183140 CCAAATTGATCCTTGTACGTTCCTT 59.817 40.000 0.00 0.00 0.00 3.36
1899 2013 0.606401 ACCATCCTTGCTTGACACGG 60.606 55.000 0.00 0.00 39.07 4.94
2000 2118 2.349755 GCCGTGGCACCCTTTCTA 59.650 61.111 12.86 0.00 41.49 2.10
2178 2306 4.926832 CGGAATGGTTATTTGTTGTTTCCC 59.073 41.667 0.00 0.00 0.00 3.97
2230 2358 5.201243 AGTTTACTTTTGCCTCACCTCTTT 58.799 37.500 0.00 0.00 0.00 2.52
2284 2413 7.829378 GTACATAACCAGGAGTGAACTAAAG 57.171 40.000 0.00 0.00 0.00 1.85
2295 2424 7.118390 CAGGAGTGAACTAAAGAATCGAATGTT 59.882 37.037 0.00 0.00 0.00 2.71
2374 2504 1.368579 GTTGCACTTTGCCATGCCT 59.631 52.632 0.00 0.00 44.23 4.75
2387 2517 2.417787 GCCATGCCTTGCCTCTTTAAAG 60.418 50.000 9.04 9.04 0.00 1.85
2398 2528 2.487762 CCTCTTTAAAGCGGACATGCAA 59.512 45.455 17.72 0.00 32.62 4.08
2416 2546 4.487019 TGCAACATACTTGATTGTGCATG 58.513 39.130 0.00 0.00 30.49 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.723616 TCACAAAAATATGGAAGTCTTCTGGAA 59.276 33.333 12.31 0.00 0.00 3.53
31 32 0.537653 TGAAACACACGGAGGTCACA 59.462 50.000 0.00 0.00 0.00 3.58
73 74 7.545615 GCATGATGATATGATGTGATGCAAAAT 59.454 33.333 0.00 0.00 35.97 1.82
82 83 6.699575 ATGATGGCATGATGATATGATGTG 57.300 37.500 3.81 0.00 32.31 3.21
124 125 9.007901 AGATCTATGCCATTTATTTAGTTGAGC 57.992 33.333 0.00 0.00 0.00 4.26
241 258 8.257306 GTGTGTTTATGGGTGATTCCAAATTAT 58.743 33.333 0.00 0.00 40.62 1.28
244 261 5.779771 AGTGTGTTTATGGGTGATTCCAAAT 59.220 36.000 0.00 0.00 40.62 2.32
305 324 5.796424 ATTGCAGACAAGATTTGAAGGTT 57.204 34.783 0.00 0.00 39.69 3.50
437 495 2.912967 GTGCACAAGATTGCGAGATTTG 59.087 45.455 13.17 0.00 46.20 2.32
568 655 1.411074 GGTCTCTCTTCTCTCTCCCCC 60.411 61.905 0.00 0.00 0.00 5.40
569 656 1.286553 TGGTCTCTCTTCTCTCTCCCC 59.713 57.143 0.00 0.00 0.00 4.81
570 657 2.654863 CTGGTCTCTCTTCTCTCTCCC 58.345 57.143 0.00 0.00 0.00 4.30
571 658 2.024414 GCTGGTCTCTCTTCTCTCTCC 58.976 57.143 0.00 0.00 0.00 3.71
654 742 1.613610 CTAGAGGGTCCGGGACTGA 59.386 63.158 25.39 6.93 32.47 3.41
664 752 3.882137 TAGGTGGGCCTAGAGGGT 58.118 61.111 4.53 0.00 44.90 4.34
717 805 0.470833 AGGGAGTGAGATGGGATCGG 60.471 60.000 0.00 0.00 0.00 4.18
783 871 3.525545 GGAGGGGGTCGAGCGTAC 61.526 72.222 8.77 1.25 0.00 3.67
819 907 4.335647 CAAGAGGTGGCTGCGGGT 62.336 66.667 0.00 0.00 0.00 5.28
852 940 1.079127 GAGCTTGCTAGTGGCGGAA 60.079 57.895 0.00 0.00 45.43 4.30
859 947 1.601171 CTGGCTGGAGCTTGCTAGT 59.399 57.895 10.80 0.00 41.70 2.57
962 1050 2.737830 GGCAGCGATAGAGGGTCC 59.262 66.667 0.00 0.00 39.76 4.46
1046 1137 0.603065 TGTGCTCTGCGCTAAAGAGA 59.397 50.000 23.23 10.39 43.27 3.10
1143 1234 3.314331 CTGGAGGGACACAGGCGT 61.314 66.667 0.00 0.00 33.09 5.68
1150 1241 0.687427 TCATCGATGCTGGAGGGACA 60.687 55.000 20.81 0.00 0.00 4.02
1160 1251 1.826024 AGGTGGTCCTCATCGATGC 59.174 57.895 20.81 6.37 40.58 3.91
1182 1273 1.534235 AAGCAGAGGACGTGGAGGT 60.534 57.895 0.00 0.00 0.00 3.85
1220 1311 0.841289 AAGACCAAACAACGGGAGGA 59.159 50.000 0.00 0.00 0.00 3.71
1225 1316 2.551032 GGTAAGGAAGACCAAACAACGG 59.449 50.000 0.00 0.00 36.91 4.44
1226 1317 2.551032 GGGTAAGGAAGACCAAACAACG 59.449 50.000 0.00 0.00 38.86 4.10
1231 1322 2.424793 AGGTGGGTAAGGAAGACCAAA 58.575 47.619 0.00 0.00 38.86 3.28
1234 1325 3.381335 TGATAGGTGGGTAAGGAAGACC 58.619 50.000 0.00 0.00 36.12 3.85
1235 1326 3.388350 CCTGATAGGTGGGTAAGGAAGAC 59.612 52.174 0.00 0.00 0.00 3.01
1236 1327 3.632645 CCCTGATAGGTGGGTAAGGAAGA 60.633 52.174 0.00 0.00 38.65 2.87
1237 1328 2.706190 CCCTGATAGGTGGGTAAGGAAG 59.294 54.545 0.00 0.00 38.65 3.46
1238 1329 2.319747 TCCCTGATAGGTGGGTAAGGAA 59.680 50.000 0.00 0.00 43.74 3.36
1239 1330 1.941682 TCCCTGATAGGTGGGTAAGGA 59.058 52.381 0.00 0.00 43.74 3.36
1240 1331 2.047830 GTCCCTGATAGGTGGGTAAGG 58.952 57.143 0.00 0.00 43.74 2.69
1241 1332 1.687123 CGTCCCTGATAGGTGGGTAAG 59.313 57.143 0.00 0.00 43.74 2.34
1242 1333 1.784358 CGTCCCTGATAGGTGGGTAA 58.216 55.000 0.00 0.00 43.74 2.85
1243 1334 0.757935 GCGTCCCTGATAGGTGGGTA 60.758 60.000 0.00 0.00 43.74 3.69
1244 1335 2.064581 GCGTCCCTGATAGGTGGGT 61.065 63.158 0.00 0.00 43.74 4.51
1245 1336 2.808206 GGCGTCCCTGATAGGTGGG 61.808 68.421 0.00 0.00 44.66 4.61
1246 1337 1.410850 ATGGCGTCCCTGATAGGTGG 61.411 60.000 0.00 0.00 31.93 4.61
1247 1338 0.250038 CATGGCGTCCCTGATAGGTG 60.250 60.000 0.00 0.00 31.93 4.00
1248 1339 1.410850 CCATGGCGTCCCTGATAGGT 61.411 60.000 0.00 0.00 31.93 3.08
1249 1340 1.372683 CCATGGCGTCCCTGATAGG 59.627 63.158 0.00 0.00 34.30 2.57
1250 1341 1.302033 GCCATGGCGTCCCTGATAG 60.302 63.158 23.48 0.00 0.00 2.08
1251 1342 2.828868 GCCATGGCGTCCCTGATA 59.171 61.111 23.48 0.00 0.00 2.15
1268 1359 3.944250 AAACTCCATGGGGCGGCAG 62.944 63.158 13.00 2.48 0.00 4.85
1269 1360 3.936772 GAAACTCCATGGGGCGGCA 62.937 63.158 13.00 0.00 0.00 5.69
1270 1361 3.140814 GAAACTCCATGGGGCGGC 61.141 66.667 13.00 0.00 0.00 6.53
1271 1362 1.076777 ATGAAACTCCATGGGGCGG 60.077 57.895 13.00 2.43 0.00 6.13
1272 1363 1.439353 CGATGAAACTCCATGGGGCG 61.439 60.000 13.00 1.40 0.00 6.13
1273 1364 1.103398 CCGATGAAACTCCATGGGGC 61.103 60.000 13.00 0.00 38.34 5.80
1274 1365 1.103398 GCCGATGAAACTCCATGGGG 61.103 60.000 11.11 11.11 41.12 4.96
1275 1366 1.103398 GGCCGATGAAACTCCATGGG 61.103 60.000 13.02 5.22 42.90 4.00
1276 1367 1.103398 GGGCCGATGAAACTCCATGG 61.103 60.000 4.97 4.97 0.00 3.66
1277 1368 0.394216 TGGGCCGATGAAACTCCATG 60.394 55.000 0.00 0.00 0.00 3.66
1278 1369 0.552848 ATGGGCCGATGAAACTCCAT 59.447 50.000 0.00 0.00 0.00 3.41
1279 1370 1.208706 TATGGGCCGATGAAACTCCA 58.791 50.000 11.03 0.00 0.00 3.86
1280 1371 2.039084 AGATATGGGCCGATGAAACTCC 59.961 50.000 11.03 0.00 0.00 3.85
1281 1372 3.070018 CAGATATGGGCCGATGAAACTC 58.930 50.000 11.03 0.00 0.00 3.01
1282 1373 2.224621 CCAGATATGGGCCGATGAAACT 60.225 50.000 11.03 1.67 0.00 2.66
1283 1374 2.154462 CCAGATATGGGCCGATGAAAC 58.846 52.381 11.03 0.00 0.00 2.78
1284 1375 1.545428 GCCAGATATGGGCCGATGAAA 60.545 52.381 11.03 0.00 45.87 2.69
1285 1376 0.036732 GCCAGATATGGGCCGATGAA 59.963 55.000 11.03 0.00 45.87 2.57
1286 1377 1.679311 GCCAGATATGGGCCGATGA 59.321 57.895 11.03 0.00 45.87 2.92
1287 1378 4.308526 GCCAGATATGGGCCGATG 57.691 61.111 11.03 0.00 45.87 3.84
1293 1384 1.073199 GTTCCCGGCCAGATATGGG 59.927 63.158 8.78 3.75 43.36 4.00
1294 1385 1.073199 GGTTCCCGGCCAGATATGG 59.927 63.158 2.24 0.69 0.00 2.74
1295 1386 0.182537 TTGGTTCCCGGCCAGATATG 59.817 55.000 2.24 0.00 37.31 1.78
1296 1387 0.923358 TTTGGTTCCCGGCCAGATAT 59.077 50.000 2.24 0.00 37.31 1.63
1297 1388 0.034863 GTTTGGTTCCCGGCCAGATA 60.035 55.000 2.24 0.00 37.31 1.98
1298 1389 1.304134 GTTTGGTTCCCGGCCAGAT 60.304 57.895 2.24 0.00 37.31 2.90
1299 1390 2.114411 GTTTGGTTCCCGGCCAGA 59.886 61.111 2.24 0.00 37.31 3.86
1300 1391 3.361977 CGTTTGGTTCCCGGCCAG 61.362 66.667 2.24 0.00 37.31 4.85
1301 1392 3.835790 CTCGTTTGGTTCCCGGCCA 62.836 63.158 2.24 0.00 0.00 5.36
1302 1393 3.053896 CTCGTTTGGTTCCCGGCC 61.054 66.667 0.00 0.00 0.00 6.13
1303 1394 3.733960 GCTCGTTTGGTTCCCGGC 61.734 66.667 0.00 0.00 0.00 6.13
1304 1395 3.053896 GGCTCGTTTGGTTCCCGG 61.054 66.667 0.00 0.00 0.00 5.73
1305 1396 3.053896 GGGCTCGTTTGGTTCCCG 61.054 66.667 0.00 0.00 0.00 5.14
1306 1397 2.675423 GGGGCTCGTTTGGTTCCC 60.675 66.667 0.00 0.00 36.25 3.97
1307 1398 3.053896 CGGGGCTCGTTTGGTTCC 61.054 66.667 0.00 0.00 0.00 3.62
1333 1424 2.049156 GGGAAAAACAGCGGCAGC 60.049 61.111 0.00 0.00 45.58 5.25
1334 1425 0.890996 AGAGGGAAAAACAGCGGCAG 60.891 55.000 1.45 0.00 0.00 4.85
1335 1426 1.150536 AGAGGGAAAAACAGCGGCA 59.849 52.632 1.45 0.00 0.00 5.69
1336 1427 1.172812 ACAGAGGGAAAAACAGCGGC 61.173 55.000 0.00 0.00 0.00 6.53
1337 1428 0.875059 GACAGAGGGAAAAACAGCGG 59.125 55.000 0.00 0.00 0.00 5.52
1338 1429 1.593196 TGACAGAGGGAAAAACAGCG 58.407 50.000 0.00 0.00 0.00 5.18
1339 1430 3.706698 GTTTGACAGAGGGAAAAACAGC 58.293 45.455 0.00 0.00 32.34 4.40
1340 1431 3.625764 TCGTTTGACAGAGGGAAAAACAG 59.374 43.478 0.00 0.00 31.69 3.16
1341 1432 3.611970 TCGTTTGACAGAGGGAAAAACA 58.388 40.909 0.00 0.00 31.69 2.83
1342 1433 4.625972 TTCGTTTGACAGAGGGAAAAAC 57.374 40.909 0.00 0.00 0.00 2.43
1343 1434 4.884744 TCATTCGTTTGACAGAGGGAAAAA 59.115 37.500 0.00 0.00 0.00 1.94
1344 1435 4.456535 TCATTCGTTTGACAGAGGGAAAA 58.543 39.130 0.00 0.00 0.00 2.29
1345 1436 4.079980 TCATTCGTTTGACAGAGGGAAA 57.920 40.909 0.00 0.00 0.00 3.13
1346 1437 3.762407 TCATTCGTTTGACAGAGGGAA 57.238 42.857 0.00 0.00 0.00 3.97
1347 1438 3.181459 TGTTCATTCGTTTGACAGAGGGA 60.181 43.478 0.00 0.00 0.00 4.20
1348 1439 3.058914 GTGTTCATTCGTTTGACAGAGGG 60.059 47.826 0.00 0.00 0.00 4.30
1349 1440 3.058914 GGTGTTCATTCGTTTGACAGAGG 60.059 47.826 0.00 0.00 0.00 3.69
1350 1441 3.809832 AGGTGTTCATTCGTTTGACAGAG 59.190 43.478 0.00 0.00 0.00 3.35
1351 1442 3.804036 AGGTGTTCATTCGTTTGACAGA 58.196 40.909 0.00 0.00 0.00 3.41
1352 1443 4.527564 GAAGGTGTTCATTCGTTTGACAG 58.472 43.478 0.00 0.00 32.36 3.51
1353 1444 3.314080 GGAAGGTGTTCATTCGTTTGACA 59.686 43.478 0.00 0.00 35.53 3.58
1354 1445 3.304458 GGGAAGGTGTTCATTCGTTTGAC 60.304 47.826 0.00 0.00 35.53 3.18
1355 1446 2.882137 GGGAAGGTGTTCATTCGTTTGA 59.118 45.455 0.00 0.00 35.53 2.69
1356 1447 2.030274 GGGGAAGGTGTTCATTCGTTTG 60.030 50.000 0.00 0.00 35.53 2.93
1357 1448 2.235891 GGGGAAGGTGTTCATTCGTTT 58.764 47.619 0.00 0.00 35.53 3.60
1358 1449 1.880646 CGGGGAAGGTGTTCATTCGTT 60.881 52.381 0.00 0.00 35.53 3.85
1359 1450 0.321298 CGGGGAAGGTGTTCATTCGT 60.321 55.000 0.00 0.00 35.53 3.85
1360 1451 1.024579 CCGGGGAAGGTGTTCATTCG 61.025 60.000 0.00 0.00 35.53 3.34
1361 1452 0.326927 TCCGGGGAAGGTGTTCATTC 59.673 55.000 0.00 0.00 33.93 2.67
1362 1453 0.328258 CTCCGGGGAAGGTGTTCATT 59.672 55.000 0.00 0.00 33.93 2.57
1363 1454 0.546747 TCTCCGGGGAAGGTGTTCAT 60.547 55.000 0.00 0.00 33.93 2.57
1364 1455 1.152204 TCTCCGGGGAAGGTGTTCA 60.152 57.895 0.00 0.00 33.93 3.18
1365 1456 1.192803 AGTCTCCGGGGAAGGTGTTC 61.193 60.000 5.00 0.00 0.00 3.18
1366 1457 1.152096 AGTCTCCGGGGAAGGTGTT 60.152 57.895 5.00 0.00 0.00 3.32
1367 1458 1.913762 CAGTCTCCGGGGAAGGTGT 60.914 63.158 5.00 0.00 0.00 4.16
1368 1459 2.982130 CAGTCTCCGGGGAAGGTG 59.018 66.667 5.00 0.00 0.00 4.00
1369 1460 3.003763 GCAGTCTCCGGGGAAGGT 61.004 66.667 5.00 0.00 0.00 3.50
1370 1461 3.787001 GGCAGTCTCCGGGGAAGG 61.787 72.222 5.00 1.36 0.00 3.46
1371 1462 2.527951 CTTGGCAGTCTCCGGGGAAG 62.528 65.000 5.00 2.33 0.00 3.46
1372 1463 2.528127 TTGGCAGTCTCCGGGGAA 60.528 61.111 5.00 0.00 0.00 3.97
1373 1464 3.003173 CTTGGCAGTCTCCGGGGA 61.003 66.667 0.00 0.00 0.00 4.81
1374 1465 3.003173 TCTTGGCAGTCTCCGGGG 61.003 66.667 0.00 0.00 0.00 5.73
1375 1466 2.266055 GTCTTGGCAGTCTCCGGG 59.734 66.667 0.00 0.00 0.00 5.73
1376 1467 2.266055 GGTCTTGGCAGTCTCCGG 59.734 66.667 0.00 0.00 0.00 5.14
1377 1468 2.125912 CGGTCTTGGCAGTCTCCG 60.126 66.667 7.73 7.73 0.00 4.63
1378 1469 0.670854 GAACGGTCTTGGCAGTCTCC 60.671 60.000 0.00 0.00 0.00 3.71
1379 1470 0.033504 TGAACGGTCTTGGCAGTCTC 59.966 55.000 0.33 0.00 0.00 3.36
1380 1471 0.034059 CTGAACGGTCTTGGCAGTCT 59.966 55.000 0.33 0.00 0.00 3.24
1381 1472 0.951040 CCTGAACGGTCTTGGCAGTC 60.951 60.000 0.33 0.00 0.00 3.51
1382 1473 1.071471 CCTGAACGGTCTTGGCAGT 59.929 57.895 0.33 0.00 0.00 4.40
1383 1474 0.036010 ATCCTGAACGGTCTTGGCAG 60.036 55.000 0.33 0.00 0.00 4.85
1384 1475 0.400213 AATCCTGAACGGTCTTGGCA 59.600 50.000 0.33 0.00 0.00 4.92
1385 1476 1.087501 GAATCCTGAACGGTCTTGGC 58.912 55.000 0.33 0.00 0.00 4.52
1386 1477 1.359848 CGAATCCTGAACGGTCTTGG 58.640 55.000 0.33 4.23 0.00 3.61
1387 1478 0.721718 GCGAATCCTGAACGGTCTTG 59.278 55.000 0.33 0.00 0.00 3.02
1388 1479 0.391263 GGCGAATCCTGAACGGTCTT 60.391 55.000 0.33 0.00 0.00 3.01
1389 1480 1.218316 GGCGAATCCTGAACGGTCT 59.782 57.895 0.33 0.00 0.00 3.85
1390 1481 0.672401 TTGGCGAATCCTGAACGGTC 60.672 55.000 0.00 0.00 35.26 4.79
1391 1482 0.673644 CTTGGCGAATCCTGAACGGT 60.674 55.000 0.00 0.00 35.26 4.83
1392 1483 0.673644 ACTTGGCGAATCCTGAACGG 60.674 55.000 0.00 0.00 35.26 4.44
1393 1484 1.659098 GTACTTGGCGAATCCTGAACG 59.341 52.381 0.00 0.00 35.26 3.95
1394 1485 2.007608 GGTACTTGGCGAATCCTGAAC 58.992 52.381 0.00 0.00 35.26 3.18
1395 1486 1.404986 CGGTACTTGGCGAATCCTGAA 60.405 52.381 0.00 0.00 35.26 3.02
1396 1487 0.174845 CGGTACTTGGCGAATCCTGA 59.825 55.000 0.00 0.00 35.26 3.86
1397 1488 0.810031 CCGGTACTTGGCGAATCCTG 60.810 60.000 0.00 0.00 35.26 3.86
1398 1489 1.262640 ACCGGTACTTGGCGAATCCT 61.263 55.000 4.49 0.00 35.26 3.24
1399 1490 0.392060 AACCGGTACTTGGCGAATCC 60.392 55.000 8.00 0.00 0.00 3.01
1400 1491 1.004595 GAACCGGTACTTGGCGAATC 58.995 55.000 8.00 0.00 0.00 2.52
1401 1492 0.738412 CGAACCGGTACTTGGCGAAT 60.738 55.000 8.00 0.00 0.00 3.34
1402 1493 1.373246 CGAACCGGTACTTGGCGAA 60.373 57.895 8.00 0.00 0.00 4.70
1403 1494 2.203972 CTCGAACCGGTACTTGGCGA 62.204 60.000 8.00 9.77 0.00 5.54
1404 1495 1.804326 CTCGAACCGGTACTTGGCG 60.804 63.158 8.00 5.52 0.00 5.69
1405 1496 0.527565 TACTCGAACCGGTACTTGGC 59.472 55.000 8.00 0.00 0.00 4.52
1406 1497 1.466360 CGTACTCGAACCGGTACTTGG 60.466 57.143 8.00 0.00 39.71 3.61
1407 1498 1.464608 TCGTACTCGAACCGGTACTTG 59.535 52.381 8.00 0.00 43.34 3.16
1408 1499 1.808411 TCGTACTCGAACCGGTACTT 58.192 50.000 8.00 0.00 43.34 2.24
1409 1500 3.532896 TCGTACTCGAACCGGTACT 57.467 52.632 8.00 0.00 43.34 2.73
1418 1509 2.214387 TCAGCGATAGTCGTACTCGA 57.786 50.000 5.72 0.00 42.81 4.04
1419 1510 3.181532 GGTATCAGCGATAGTCGTACTCG 60.182 52.174 1.11 0.00 42.81 4.18
1420 1511 3.124976 GGGTATCAGCGATAGTCGTACTC 59.875 52.174 1.11 0.00 42.81 2.59
1421 1512 3.072944 GGGTATCAGCGATAGTCGTACT 58.927 50.000 1.11 0.00 42.81 2.73
1422 1513 2.161211 GGGGTATCAGCGATAGTCGTAC 59.839 54.545 1.11 0.00 42.81 3.67
1423 1514 2.430465 GGGGTATCAGCGATAGTCGTA 58.570 52.381 1.11 0.00 42.81 3.43
1424 1515 1.245732 GGGGTATCAGCGATAGTCGT 58.754 55.000 1.11 0.00 42.81 4.34
1425 1516 0.168348 CGGGGTATCAGCGATAGTCG 59.832 60.000 0.00 0.00 43.89 4.18
1426 1517 1.469308 CTCGGGGTATCAGCGATAGTC 59.531 57.143 0.00 0.00 39.35 2.59
1427 1518 1.535833 CTCGGGGTATCAGCGATAGT 58.464 55.000 0.00 0.00 39.35 2.12
1428 1519 0.811915 CCTCGGGGTATCAGCGATAG 59.188 60.000 0.00 0.00 0.00 2.08
1429 1520 0.402887 TCCTCGGGGTATCAGCGATA 59.597 55.000 0.00 0.00 0.00 2.92
1430 1521 1.153061 TCCTCGGGGTATCAGCGAT 59.847 57.895 0.00 0.00 0.00 4.58
1431 1522 1.826921 GTCCTCGGGGTATCAGCGA 60.827 63.158 0.00 0.00 0.00 4.93
1432 1523 2.125326 TGTCCTCGGGGTATCAGCG 61.125 63.158 0.00 0.00 0.00 5.18
1433 1524 1.442148 GTGTCCTCGGGGTATCAGC 59.558 63.158 0.00 0.00 0.00 4.26
1434 1525 0.686441 TGGTGTCCTCGGGGTATCAG 60.686 60.000 0.00 0.00 0.00 2.90
1435 1526 0.252330 TTGGTGTCCTCGGGGTATCA 60.252 55.000 0.00 0.00 0.00 2.15
1436 1527 0.464452 CTTGGTGTCCTCGGGGTATC 59.536 60.000 0.00 0.00 0.00 2.24
1437 1528 0.252558 ACTTGGTGTCCTCGGGGTAT 60.253 55.000 0.00 0.00 0.00 2.73
1438 1529 1.156803 ACTTGGTGTCCTCGGGGTA 59.843 57.895 0.00 0.00 0.00 3.69
1439 1530 2.122547 ACTTGGTGTCCTCGGGGT 60.123 61.111 0.00 0.00 0.00 4.95
1440 1531 1.189524 TACACTTGGTGTCCTCGGGG 61.190 60.000 6.59 0.00 43.92 5.73
1441 1532 0.037605 GTACACTTGGTGTCCTCGGG 60.038 60.000 6.59 0.00 43.92 5.14
1442 1533 0.388134 CGTACACTTGGTGTCCTCGG 60.388 60.000 6.59 0.00 43.92 4.63
1443 1534 0.594602 TCGTACACTTGGTGTCCTCG 59.405 55.000 6.59 10.39 43.92 4.63
1444 1535 2.806608 TTCGTACACTTGGTGTCCTC 57.193 50.000 6.59 0.00 43.92 3.71
1445 1536 3.575256 TGTATTCGTACACTTGGTGTCCT 59.425 43.478 6.59 0.00 43.92 3.85
1446 1537 3.676646 GTGTATTCGTACACTTGGTGTCC 59.323 47.826 6.59 0.00 43.92 4.02
1447 1538 3.676646 GGTGTATTCGTACACTTGGTGTC 59.323 47.826 15.75 0.00 43.92 3.67
1449 1540 2.997986 GGGTGTATTCGTACACTTGGTG 59.002 50.000 15.75 0.00 46.92 4.17
1450 1541 2.353011 CGGGTGTATTCGTACACTTGGT 60.353 50.000 15.75 0.00 46.92 3.67
1451 1542 2.264813 CGGGTGTATTCGTACACTTGG 58.735 52.381 15.75 4.91 46.92 3.61
1452 1543 2.264813 CCGGGTGTATTCGTACACTTG 58.735 52.381 15.75 9.83 46.92 3.16
1453 1544 1.404583 GCCGGGTGTATTCGTACACTT 60.405 52.381 15.75 0.00 46.92 3.16
1454 1545 0.174162 GCCGGGTGTATTCGTACACT 59.826 55.000 15.75 0.00 46.92 3.55
1456 1547 1.139308 CGCCGGGTGTATTCGTACA 59.861 57.895 2.18 0.00 0.00 2.90
1457 1548 0.031178 ATCGCCGGGTGTATTCGTAC 59.969 55.000 2.18 0.00 0.00 3.67
1458 1549 1.266718 GTATCGCCGGGTGTATTCGTA 59.733 52.381 2.18 0.00 0.00 3.43
1459 1550 0.031178 GTATCGCCGGGTGTATTCGT 59.969 55.000 2.18 0.00 0.00 3.85
1460 1551 0.665369 GGTATCGCCGGGTGTATTCG 60.665 60.000 2.18 0.00 0.00 3.34
1461 1552 0.320160 GGGTATCGCCGGGTGTATTC 60.320 60.000 2.18 0.00 38.44 1.75
1462 1553 1.750297 GGGTATCGCCGGGTGTATT 59.250 57.895 2.18 0.00 38.44 1.89
1463 1554 2.212110 GGGGTATCGCCGGGTGTAT 61.212 63.158 2.18 2.95 38.44 2.29
1464 1555 2.839162 GGGGTATCGCCGGGTGTA 60.839 66.667 2.18 0.00 38.44 2.90
1466 1557 3.750373 CTTGGGGTATCGCCGGGTG 62.750 68.421 2.18 0.00 39.47 4.61
1467 1558 3.476419 CTTGGGGTATCGCCGGGT 61.476 66.667 2.18 0.00 39.47 5.28
1468 1559 4.250305 CCTTGGGGTATCGCCGGG 62.250 72.222 2.18 0.00 39.47 5.73
1469 1560 4.929707 GCCTTGGGGTATCGCCGG 62.930 72.222 0.00 0.00 39.47 6.13
1470 1561 4.169696 TGCCTTGGGGTATCGCCG 62.170 66.667 0.00 0.00 39.47 6.46
1471 1562 2.516225 GTGCCTTGGGGTATCGCC 60.516 66.667 0.00 0.00 36.97 5.54
1472 1563 2.516225 GGTGCCTTGGGGTATCGC 60.516 66.667 0.00 0.00 34.45 4.58
1473 1564 0.819259 CATGGTGCCTTGGGGTATCG 60.819 60.000 0.00 0.00 30.52 2.92
1474 1565 0.468029 CCATGGTGCCTTGGGGTATC 60.468 60.000 13.59 0.00 37.53 2.24
1475 1566 0.923729 TCCATGGTGCCTTGGGGTAT 60.924 55.000 19.16 0.00 40.42 2.73
1476 1567 1.542628 TCCATGGTGCCTTGGGGTA 60.543 57.895 19.16 2.12 40.42 3.69
1477 1568 2.863484 TCCATGGTGCCTTGGGGT 60.863 61.111 19.16 0.00 40.42 4.95
1478 1569 2.362889 GTCCATGGTGCCTTGGGG 60.363 66.667 19.16 3.33 40.42 4.96
1479 1570 2.191786 TACGTCCATGGTGCCTTGGG 62.192 60.000 19.16 9.55 40.42 4.12
1480 1571 0.322098 TTACGTCCATGGTGCCTTGG 60.322 55.000 12.58 14.86 41.10 3.61
1481 1572 1.086696 CTTACGTCCATGGTGCCTTG 58.913 55.000 12.58 0.00 0.00 3.61
1490 1581 0.175073 GGCGAGGAACTTACGTCCAT 59.825 55.000 0.00 0.00 41.55 3.41
1516 1608 4.026228 CACATAGTAGTCGTACACGTCGAT 60.026 45.833 0.00 0.00 39.45 3.59
1549 1648 2.762969 TAGGTTTCCGGGGTCGTCGA 62.763 60.000 0.00 0.00 33.95 4.20
1574 1675 2.874664 AACGAGGCGGTACTTGGCA 61.875 57.895 13.05 0.00 0.00 4.92
1585 1686 1.375523 ATGTTCGGGTCAACGAGGC 60.376 57.895 0.00 0.00 44.47 4.70
1633 1736 7.337436 AGTGGAAGTAGTTGTACTATCAGTCTC 59.663 40.741 0.00 0.00 38.66 3.36
1698 1805 2.032071 CTGGGGCGGTTCGAGTTT 59.968 61.111 0.00 0.00 0.00 2.66
1714 1821 7.573096 CGTTATACCTTTGAAGTGTGCATTTCT 60.573 37.037 8.49 0.00 0.00 2.52
1724 1831 5.632347 CGTCTTGACGTTATACCTTTGAAGT 59.368 40.000 14.18 0.00 0.00 3.01
1762 1870 6.313658 TCTCATACAACACATCACAAGCATAC 59.686 38.462 0.00 0.00 0.00 2.39
1792 1903 1.827344 TTTGGACATGGTGCAAACACA 59.173 42.857 11.24 0.00 45.84 3.72
1810 1921 5.768164 ACAAGGAACGTACAAGGATCAATTT 59.232 36.000 0.00 0.00 0.00 1.82
1832 1943 1.598676 CGAGACGACGACAAGGAAACA 60.599 52.381 0.00 0.00 35.09 2.83
1899 2013 2.227194 CAAAAGGTAGTGTGGTGGGAC 58.773 52.381 0.00 0.00 0.00 4.46
1937 2052 2.762327 ACAACATATCGGTTCCGGTAGT 59.238 45.455 11.37 6.19 0.00 2.73
2000 2118 1.533625 CATTTGTCACCGTGGTGGAT 58.466 50.000 18.47 5.89 45.43 3.41
2048 2168 9.311916 GCATATCCAAGTTTATGCAATTTTACA 57.688 29.630 11.49 0.00 46.36 2.41
2122 2248 7.122650 CCCCACATGTCATTTAGTAATTGAAGT 59.877 37.037 8.65 6.18 0.00 3.01
2131 2259 5.891551 GGTAAATCCCCACATGTCATTTAGT 59.108 40.000 0.00 0.00 0.00 2.24
2178 2306 7.812669 ACATTTTAGGAAATTTTAAGTGAGGCG 59.187 33.333 0.00 0.00 33.25 5.52
2295 2424 5.211454 CAAGTTGCATATTGACGAAACACA 58.789 37.500 5.67 0.00 0.00 3.72
2374 2504 2.264005 TGTCCGCTTTAAAGAGGCAA 57.736 45.000 27.71 17.44 44.54 4.52
2387 2517 1.737236 TCAAGTATGTTGCATGTCCGC 59.263 47.619 0.00 0.00 0.00 5.54
2398 2528 4.928601 GCATCATGCACAATCAAGTATGT 58.071 39.130 4.20 0.00 44.26 2.29
2416 2546 4.114058 ACACAAGCATAAACATGGCATC 57.886 40.909 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.