Multiple sequence alignment - TraesCS1A01G038900

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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 TraesCS1A01G038900 chr1A 100.000 2195 0 0 1 2195 21197467 21199661 0.000000e+00 4054.0
1 TraesCS1A01G038900 chr1A 91.538 650 36 12 1562 2195 550209248 550208602 0.000000e+00 878.0
2 TraesCS1A01G038900 chr1A 95.753 259 9 1 1458 1716 21209219 21209475 1.210000e-112 416.0
3 TraesCS1A01G038900 chr5A 88.516 1193 122 10 96 1281 480199371 480198187 0.000000e+00 1430.0
4 TraesCS1A01G038900 chr5D 87.327 1081 87 17 96 1170 379616817 379615781 0.000000e+00 1192.0
5 TraesCS1A01G038900 chr2B 83.682 1195 160 17 96 1281 493647051 493648219 0.000000e+00 1094.0
6 TraesCS1A01G038900 chr2B 90.280 751 57 8 1458 2195 18005447 18006194 0.000000e+00 968.0
7 TraesCS1A01G038900 chr2B 80.801 1198 211 14 93 1281 474891023 474892210 0.000000e+00 920.0
8 TraesCS1A01G038900 chr2B 86.885 244 26 5 1458 1698 18010435 18010675 3.590000e-68 268.0
9 TraesCS1A01G038900 chrUn 91.914 742 48 8 1456 2195 31859468 31858737 0.000000e+00 1027.0
10 TraesCS1A01G038900 chr6B 91.204 739 62 2 1458 2195 30254838 30255574 0.000000e+00 1002.0
11 TraesCS1A01G038900 chr6B 80.268 1196 220 12 93 1281 438404855 438406041 0.000000e+00 887.0
12 TraesCS1A01G038900 chr6B 90.852 634 50 7 1566 2195 716479019 716479648 0.000000e+00 843.0
13 TraesCS1A01G038900 chr6B 81.123 837 140 15 464 1289 229138015 229137186 0.000000e+00 654.0
14 TraesCS1A01G038900 chr6B 86.641 262 28 5 1458 1716 30259796 30260053 1.280000e-72 283.0
15 TraesCS1A01G038900 chr2A 90.738 745 60 8 1456 2195 6249494 6248754 0.000000e+00 985.0
16 TraesCS1A01G038900 chr4B 90.067 745 63 9 1456 2195 159521843 159522581 0.000000e+00 955.0
17 TraesCS1A01G038900 chr6A 80.050 1203 217 17 93 1288 600911562 600912748 0.000000e+00 870.0
18 TraesCS1A01G038900 chr5B 79.734 1204 218 18 93 1281 400932065 400933257 0.000000e+00 848.0
19 TraesCS1A01G038900 chr7B 79.599 1196 224 16 96 1281 402821734 402820549 0.000000e+00 839.0
20 TraesCS1A01G038900 chr7B 95.146 515 25 0 1681 2195 588832297 588832811 0.000000e+00 813.0
21 TraesCS1A01G038900 chr7B 94.369 515 29 0 1681 2195 588824310 588824824 0.000000e+00 791.0
22 TraesCS1A01G038900 chr4A 81.219 1017 181 6 98 1109 327512119 327513130 0.000000e+00 811.0
23 TraesCS1A01G038900 chr1B 87.692 260 29 2 1458 1716 553902347 553902090 1.270000e-77 300.0
24 TraesCS1A01G038900 chr1D 83.774 265 21 13 1458 1717 111537533 111537780 4.710000e-57 231.0
25 TraesCS1A01G038900 chr1D 88.298 94 11 0 1 94 299894627 299894720 1.780000e-21 113.0
26 TraesCS1A01G038900 chr2D 91.489 94 8 0 1 94 96826366 96826459 1.770000e-26 130.0
27 TraesCS1A01G038900 chr3B 89.189 74 8 0 12 85 276478559 276478486 2.320000e-15 93.5
28 TraesCS1A01G038900 chr7D 87.324 71 9 0 15 85 245379474 245379404 5.020000e-12 82.4


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 TraesCS1A01G038900 chr1A 21197467 21199661 2194 False 4054 4054 100.000 1 2195 1 chr1A.!!$F1 2194
1 TraesCS1A01G038900 chr1A 550208602 550209248 646 True 878 878 91.538 1562 2195 1 chr1A.!!$R1 633
2 TraesCS1A01G038900 chr5A 480198187 480199371 1184 True 1430 1430 88.516 96 1281 1 chr5A.!!$R1 1185
3 TraesCS1A01G038900 chr5D 379615781 379616817 1036 True 1192 1192 87.327 96 1170 1 chr5D.!!$R1 1074
4 TraesCS1A01G038900 chr2B 493647051 493648219 1168 False 1094 1094 83.682 96 1281 1 chr2B.!!$F4 1185
5 TraesCS1A01G038900 chr2B 18005447 18006194 747 False 968 968 90.280 1458 2195 1 chr2B.!!$F1 737
6 TraesCS1A01G038900 chr2B 474891023 474892210 1187 False 920 920 80.801 93 1281 1 chr2B.!!$F3 1188
7 TraesCS1A01G038900 chrUn 31858737 31859468 731 True 1027 1027 91.914 1456 2195 1 chrUn.!!$R1 739
8 TraesCS1A01G038900 chr6B 30254838 30255574 736 False 1002 1002 91.204 1458 2195 1 chr6B.!!$F1 737
9 TraesCS1A01G038900 chr6B 438404855 438406041 1186 False 887 887 80.268 93 1281 1 chr6B.!!$F3 1188
10 TraesCS1A01G038900 chr6B 716479019 716479648 629 False 843 843 90.852 1566 2195 1 chr6B.!!$F4 629
11 TraesCS1A01G038900 chr6B 229137186 229138015 829 True 654 654 81.123 464 1289 1 chr6B.!!$R1 825
12 TraesCS1A01G038900 chr2A 6248754 6249494 740 True 985 985 90.738 1456 2195 1 chr2A.!!$R1 739
13 TraesCS1A01G038900 chr4B 159521843 159522581 738 False 955 955 90.067 1456 2195 1 chr4B.!!$F1 739
14 TraesCS1A01G038900 chr6A 600911562 600912748 1186 False 870 870 80.050 93 1288 1 chr6A.!!$F1 1195
15 TraesCS1A01G038900 chr5B 400932065 400933257 1192 False 848 848 79.734 93 1281 1 chr5B.!!$F1 1188
16 TraesCS1A01G038900 chr7B 402820549 402821734 1185 True 839 839 79.599 96 1281 1 chr7B.!!$R1 1185
17 TraesCS1A01G038900 chr7B 588832297 588832811 514 False 813 813 95.146 1681 2195 1 chr7B.!!$F2 514
18 TraesCS1A01G038900 chr7B 588824310 588824824 514 False 791 791 94.369 1681 2195 1 chr7B.!!$F1 514
19 TraesCS1A01G038900 chr4A 327512119 327513130 1011 False 811 811 81.219 98 1109 1 chr4A.!!$F1 1011

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
874 905 0.171231 GCGGCACATCTTCTTTTCCC 59.829 55.0 0.0 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2062 2131 0.249398 GGCAACTGTATCCAGGTCGT 59.751 55.0 0.0 0.0 43.36 4.34 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
66 67 9.591792 TGTTTCATCATTATCACAAAAACAACA 57.408 25.926 0.00 0.00 33.76 3.33
69 70 8.672214 TCATCATTATCACAAAAACAACATCG 57.328 30.769 0.00 0.00 0.00 3.84
70 71 8.296000 TCATCATTATCACAAAAACAACATCGT 58.704 29.630 0.00 0.00 0.00 3.73
71 72 7.850268 TCATTATCACAAAAACAACATCGTG 57.150 32.000 0.00 0.00 0.00 4.35
72 73 7.421599 TCATTATCACAAAAACAACATCGTGT 58.578 30.769 0.00 0.00 0.00 4.49
73 74 8.560374 TCATTATCACAAAAACAACATCGTGTA 58.440 29.630 0.00 0.00 0.00 2.90
74 75 8.626576 CATTATCACAAAAACAACATCGTGTAC 58.373 33.333 0.00 0.00 0.00 2.90
75 76 5.804692 TCACAAAAACAACATCGTGTACT 57.195 34.783 0.00 0.00 0.00 2.73
76 77 6.905544 TCACAAAAACAACATCGTGTACTA 57.094 33.333 0.00 0.00 0.00 1.82
77 78 6.707711 TCACAAAAACAACATCGTGTACTAC 58.292 36.000 0.00 0.00 0.00 2.73
78 79 5.905181 CACAAAAACAACATCGTGTACTACC 59.095 40.000 0.00 0.00 0.00 3.18
79 80 5.818857 ACAAAAACAACATCGTGTACTACCT 59.181 36.000 0.00 0.00 0.00 3.08
80 81 6.985645 ACAAAAACAACATCGTGTACTACCTA 59.014 34.615 0.00 0.00 0.00 3.08
81 82 7.042523 ACAAAAACAACATCGTGTACTACCTAC 60.043 37.037 0.00 0.00 0.00 3.18
82 83 4.708726 ACAACATCGTGTACTACCTACC 57.291 45.455 0.00 0.00 0.00 3.18
83 84 3.445096 ACAACATCGTGTACTACCTACCC 59.555 47.826 0.00 0.00 0.00 3.69
84 85 3.370840 ACATCGTGTACTACCTACCCA 57.629 47.619 0.00 0.00 0.00 4.51
85 86 3.019564 ACATCGTGTACTACCTACCCAC 58.980 50.000 0.00 0.00 0.00 4.61
86 87 2.128771 TCGTGTACTACCTACCCACC 57.871 55.000 0.00 0.00 0.00 4.61
87 88 1.354031 TCGTGTACTACCTACCCACCA 59.646 52.381 0.00 0.00 0.00 4.17
88 89 2.025037 TCGTGTACTACCTACCCACCAT 60.025 50.000 0.00 0.00 0.00 3.55
89 90 2.762327 CGTGTACTACCTACCCACCATT 59.238 50.000 0.00 0.00 0.00 3.16
90 91 3.429822 CGTGTACTACCTACCCACCATTG 60.430 52.174 0.00 0.00 0.00 2.82
91 92 2.502538 TGTACTACCTACCCACCATTGC 59.497 50.000 0.00 0.00 0.00 3.56
94 95 2.026262 ACTACCTACCCACCATTGCTTG 60.026 50.000 0.00 0.00 0.00 4.01
117 118 5.171476 GTGAAGAAGATTGACTCCATTCGA 58.829 41.667 0.00 0.00 0.00 3.71
127 128 3.316868 TGACTCCATTCGACGTGCATATA 59.683 43.478 0.00 0.00 0.00 0.86
128 129 4.022329 TGACTCCATTCGACGTGCATATAT 60.022 41.667 0.00 0.00 0.00 0.86
129 130 5.182380 TGACTCCATTCGACGTGCATATATA 59.818 40.000 0.00 0.00 0.00 0.86
130 131 5.399858 ACTCCATTCGACGTGCATATATAC 58.600 41.667 0.00 0.00 0.00 1.47
138 139 4.559906 CGACGTGCATATATACCTTTGGGA 60.560 45.833 0.00 0.00 36.25 4.37
156 157 2.027469 GGGAAGGTTATGACAAGGTCGT 60.027 50.000 0.00 0.00 34.95 4.34
157 158 3.558533 GGGAAGGTTATGACAAGGTCGTT 60.559 47.826 0.00 0.00 34.95 3.85
159 160 4.312443 GAAGGTTATGACAAGGTCGTTGA 58.688 43.478 12.07 0.00 38.60 3.18
180 181 5.508567 TGATGGGAAATGCAAGATCAACTA 58.491 37.500 0.00 0.00 0.00 2.24
185 186 5.189180 GGAAATGCAAGATCAACTAGGAGT 58.811 41.667 0.00 0.00 0.00 3.85
267 268 1.980052 CCCTTCGCCTCTGTTGGTA 59.020 57.895 0.00 0.00 0.00 3.25
310 311 0.955919 CCAAGCCTTCGGTCAACCTC 60.956 60.000 0.00 0.00 0.00 3.85
355 357 1.597742 ATGATATTTTCGCCGCTGCT 58.402 45.000 0.00 0.00 34.43 4.24
385 387 1.463444 GTCGTTGGAAATGGTCTTCGG 59.537 52.381 0.00 0.00 32.44 4.30
436 453 3.877559 TGGCATGAGACCTAAAGATGTG 58.122 45.455 0.00 0.00 0.00 3.21
439 456 3.877559 CATGAGACCTAAAGATGTGGCA 58.122 45.455 0.00 0.00 0.00 4.92
462 479 6.983890 GCACCAAAAATCTTTGACCTTTCTAA 59.016 34.615 0.00 0.00 44.03 2.10
508 525 7.850193 AGAAGGCCTTGCATAATAATTTTTGA 58.150 30.769 26.25 0.00 0.00 2.69
604 625 0.606604 GCTCGTCAACCTCAACCCTA 59.393 55.000 0.00 0.00 0.00 3.53
633 654 5.586243 GCTTGACTCAATTACATGGAAGCTA 59.414 40.000 0.00 0.00 32.42 3.32
662 683 4.609995 CCAATACTCGGTGGCGTT 57.390 55.556 0.00 0.00 0.00 4.84
731 752 2.316108 GTTGGTGTGGAAGAATTGGGT 58.684 47.619 0.00 0.00 0.00 4.51
810 841 1.680522 GCTTCAGCGGAGAGGATGGA 61.681 60.000 0.00 0.00 0.00 3.41
874 905 0.171231 GCGGCACATCTTCTTTTCCC 59.829 55.000 0.00 0.00 0.00 3.97
880 911 3.094572 CACATCTTCTTTTCCCATGCCT 58.905 45.455 0.00 0.00 0.00 4.75
887 918 2.642311 TCTTTTCCCATGCCTCTACACA 59.358 45.455 0.00 0.00 0.00 3.72
917 948 7.773489 TGTGTGGGAAATGATTAAATCTTGA 57.227 32.000 0.00 0.00 0.00 3.02
953 985 2.098770 GTGTACATCCGGTGGACTAGAC 59.901 54.545 16.97 6.73 42.56 2.59
955 987 3.200605 TGTACATCCGGTGGACTAGACTA 59.799 47.826 16.97 0.00 42.56 2.59
967 999 3.322541 GGACTAGACTAGATTGCCTTCCC 59.677 52.174 16.55 0.27 0.00 3.97
996 1028 1.514678 GGTGGCGTGTCAATGCTTCA 61.515 55.000 0.00 0.00 38.46 3.02
1007 1039 2.842496 TCAATGCTTCAGGGATGTCTCT 59.158 45.455 0.00 0.00 0.00 3.10
1160 1192 0.904865 CTGTGGTGTCTAGCTGGGGA 60.905 60.000 0.00 0.00 0.00 4.81
1164 1196 1.992557 TGGTGTCTAGCTGGGGAAAAT 59.007 47.619 0.00 0.00 0.00 1.82
1165 1197 3.054655 GTGGTGTCTAGCTGGGGAAAATA 60.055 47.826 0.00 0.00 0.00 1.40
1234 1267 1.006758 GGCCTAGCCCTAAAACCCTTT 59.993 52.381 0.00 0.00 44.06 3.11
1245 1278 7.039011 AGCCCTAAAACCCTTTTTCTTATTCAG 60.039 37.037 0.00 0.00 36.32 3.02
1271 1306 0.250381 TTGCATGCCTTTTGCCTTGG 60.250 50.000 16.68 0.00 39.39 3.61
1300 1335 5.453567 AAATAATAATTTCTCGCCCCAGC 57.546 39.130 0.00 0.00 28.88 4.85
1301 1336 1.692411 AATAATTTCTCGCCCCAGCC 58.308 50.000 0.00 0.00 34.57 4.85
1302 1337 0.550914 ATAATTTCTCGCCCCAGCCA 59.449 50.000 0.00 0.00 34.57 4.75
1303 1338 0.107214 TAATTTCTCGCCCCAGCCAG 60.107 55.000 0.00 0.00 34.57 4.85
1304 1339 4.722700 TTTCTCGCCCCAGCCAGC 62.723 66.667 0.00 0.00 34.57 4.85
1322 1357 4.308458 CCAGGCCAACGACGGACA 62.308 66.667 5.01 0.00 35.99 4.02
1323 1358 2.738521 CAGGCCAACGACGGACAG 60.739 66.667 5.01 0.00 35.99 3.51
1324 1359 4.681978 AGGCCAACGACGGACAGC 62.682 66.667 5.01 0.00 35.99 4.40
1325 1360 4.980805 GGCCAACGACGGACAGCA 62.981 66.667 0.00 0.00 32.44 4.41
1326 1361 3.414700 GCCAACGACGGACAGCAG 61.415 66.667 0.00 0.00 0.00 4.24
1327 1362 3.414700 CCAACGACGGACAGCAGC 61.415 66.667 0.00 0.00 0.00 5.25
1328 1363 3.767230 CAACGACGGACAGCAGCG 61.767 66.667 0.00 0.00 0.00 5.18
1329 1364 4.280494 AACGACGGACAGCAGCGT 62.280 61.111 0.00 0.00 36.68 5.07
1330 1365 3.785189 AACGACGGACAGCAGCGTT 62.785 57.895 0.00 0.00 39.95 4.84
1331 1366 3.767230 CGACGGACAGCAGCGTTG 61.767 66.667 0.00 0.00 0.00 4.10
1332 1367 2.355837 GACGGACAGCAGCGTTGA 60.356 61.111 2.38 0.00 0.00 3.18
1333 1368 2.356313 ACGGACAGCAGCGTTGAG 60.356 61.111 2.38 0.00 0.00 3.02
1349 1384 2.477104 TGAGCATCACCTAGGGATCA 57.523 50.000 14.81 6.67 42.56 2.92
1350 1385 2.981921 TGAGCATCACCTAGGGATCAT 58.018 47.619 14.81 3.94 42.56 2.45
1351 1386 3.321039 TGAGCATCACCTAGGGATCATT 58.679 45.455 14.81 1.37 42.56 2.57
1352 1387 3.718434 TGAGCATCACCTAGGGATCATTT 59.282 43.478 14.81 0.00 42.56 2.32
1353 1388 4.166725 TGAGCATCACCTAGGGATCATTTT 59.833 41.667 14.81 0.00 42.56 1.82
1354 1389 5.369404 TGAGCATCACCTAGGGATCATTTTA 59.631 40.000 14.81 0.00 42.56 1.52
1355 1390 5.625150 AGCATCACCTAGGGATCATTTTAC 58.375 41.667 14.81 0.00 0.00 2.01
1356 1391 5.370880 AGCATCACCTAGGGATCATTTTACT 59.629 40.000 14.81 0.00 0.00 2.24
1357 1392 6.064717 GCATCACCTAGGGATCATTTTACTT 58.935 40.000 14.81 0.00 0.00 2.24
1358 1393 6.205658 GCATCACCTAGGGATCATTTTACTTC 59.794 42.308 14.81 0.00 0.00 3.01
1359 1394 7.512992 CATCACCTAGGGATCATTTTACTTCT 58.487 38.462 14.81 0.00 0.00 2.85
1360 1395 7.510675 TCACCTAGGGATCATTTTACTTCTT 57.489 36.000 14.81 0.00 0.00 2.52
1361 1396 7.928873 TCACCTAGGGATCATTTTACTTCTTT 58.071 34.615 14.81 0.00 0.00 2.52
1362 1397 7.829211 TCACCTAGGGATCATTTTACTTCTTTG 59.171 37.037 14.81 0.00 0.00 2.77
1363 1398 7.611855 CACCTAGGGATCATTTTACTTCTTTGT 59.388 37.037 14.81 0.00 0.00 2.83
1364 1399 7.829706 ACCTAGGGATCATTTTACTTCTTTGTC 59.170 37.037 14.81 0.00 0.00 3.18
1365 1400 7.829211 CCTAGGGATCATTTTACTTCTTTGTCA 59.171 37.037 0.00 0.00 0.00 3.58
1366 1401 7.454260 AGGGATCATTTTACTTCTTTGTCAC 57.546 36.000 0.00 0.00 0.00 3.67
1367 1402 7.234355 AGGGATCATTTTACTTCTTTGTCACT 58.766 34.615 0.00 0.00 0.00 3.41
1368 1403 8.383175 AGGGATCATTTTACTTCTTTGTCACTA 58.617 33.333 0.00 0.00 0.00 2.74
1369 1404 8.451748 GGGATCATTTTACTTCTTTGTCACTAC 58.548 37.037 0.00 0.00 0.00 2.73
1370 1405 8.999431 GGATCATTTTACTTCTTTGTCACTACA 58.001 33.333 0.00 0.00 0.00 2.74
1373 1408 9.554395 TCATTTTACTTCTTTGTCACTACATCA 57.446 29.630 0.00 0.00 34.97 3.07
1374 1409 9.817365 CATTTTACTTCTTTGTCACTACATCAG 57.183 33.333 0.00 0.00 34.97 2.90
1375 1410 7.421530 TTTACTTCTTTGTCACTACATCAGC 57.578 36.000 0.00 0.00 34.97 4.26
1376 1411 4.319177 ACTTCTTTGTCACTACATCAGCC 58.681 43.478 0.00 0.00 34.97 4.85
1377 1412 3.334583 TCTTTGTCACTACATCAGCCC 57.665 47.619 0.00 0.00 34.97 5.19
1378 1413 2.906389 TCTTTGTCACTACATCAGCCCT 59.094 45.455 0.00 0.00 34.97 5.19
1379 1414 2.768253 TTGTCACTACATCAGCCCTG 57.232 50.000 0.00 0.00 34.97 4.45
1380 1415 0.250234 TGTCACTACATCAGCCCTGC 59.750 55.000 0.00 0.00 0.00 4.85
1381 1416 0.250234 GTCACTACATCAGCCCTGCA 59.750 55.000 0.00 0.00 0.00 4.41
1382 1417 0.983467 TCACTACATCAGCCCTGCAA 59.017 50.000 0.00 0.00 0.00 4.08
1383 1418 1.561076 TCACTACATCAGCCCTGCAAT 59.439 47.619 0.00 0.00 0.00 3.56
1384 1419 1.945394 CACTACATCAGCCCTGCAATC 59.055 52.381 0.00 0.00 0.00 2.67
1385 1420 1.133976 ACTACATCAGCCCTGCAATCC 60.134 52.381 0.00 0.00 0.00 3.01
1386 1421 1.142465 CTACATCAGCCCTGCAATCCT 59.858 52.381 0.00 0.00 0.00 3.24
1387 1422 0.106819 ACATCAGCCCTGCAATCCTC 60.107 55.000 0.00 0.00 0.00 3.71
1388 1423 0.106868 CATCAGCCCTGCAATCCTCA 60.107 55.000 0.00 0.00 0.00 3.86
1389 1424 0.851469 ATCAGCCCTGCAATCCTCAT 59.149 50.000 0.00 0.00 0.00 2.90
1390 1425 0.182061 TCAGCCCTGCAATCCTCATC 59.818 55.000 0.00 0.00 0.00 2.92
1391 1426 0.822532 CAGCCCTGCAATCCTCATCC 60.823 60.000 0.00 0.00 0.00 3.51
1392 1427 1.530183 GCCCTGCAATCCTCATCCC 60.530 63.158 0.00 0.00 0.00 3.85
1393 1428 1.152368 CCCTGCAATCCTCATCCCC 59.848 63.158 0.00 0.00 0.00 4.81
1394 1429 1.648302 CCCTGCAATCCTCATCCCCA 61.648 60.000 0.00 0.00 0.00 4.96
1395 1430 0.481567 CCTGCAATCCTCATCCCCAT 59.518 55.000 0.00 0.00 0.00 4.00
1396 1431 1.617322 CTGCAATCCTCATCCCCATG 58.383 55.000 0.00 0.00 0.00 3.66
1397 1432 0.468585 TGCAATCCTCATCCCCATGC 60.469 55.000 0.00 0.00 0.00 4.06
1398 1433 1.183676 GCAATCCTCATCCCCATGCC 61.184 60.000 0.00 0.00 0.00 4.40
1399 1434 0.481567 CAATCCTCATCCCCATGCCT 59.518 55.000 0.00 0.00 0.00 4.75
1400 1435 1.133262 CAATCCTCATCCCCATGCCTT 60.133 52.381 0.00 0.00 0.00 4.35
1401 1436 0.776176 ATCCTCATCCCCATGCCTTC 59.224 55.000 0.00 0.00 0.00 3.46
1402 1437 0.327867 TCCTCATCCCCATGCCTTCT 60.328 55.000 0.00 0.00 0.00 2.85
1403 1438 0.178998 CCTCATCCCCATGCCTTCTG 60.179 60.000 0.00 0.00 0.00 3.02
1404 1439 0.841961 CTCATCCCCATGCCTTCTGA 59.158 55.000 0.00 0.00 0.00 3.27
1405 1440 1.424302 CTCATCCCCATGCCTTCTGAT 59.576 52.381 0.00 0.00 0.00 2.90
1406 1441 1.854939 TCATCCCCATGCCTTCTGATT 59.145 47.619 0.00 0.00 0.00 2.57
1407 1442 2.245546 TCATCCCCATGCCTTCTGATTT 59.754 45.455 0.00 0.00 0.00 2.17
1408 1443 2.148446 TCCCCATGCCTTCTGATTTG 57.852 50.000 0.00 0.00 0.00 2.32
1409 1444 1.117150 CCCCATGCCTTCTGATTTGG 58.883 55.000 0.00 0.00 0.00 3.28
1410 1445 1.620524 CCCCATGCCTTCTGATTTGGT 60.621 52.381 0.00 0.00 0.00 3.67
1411 1446 1.753073 CCCATGCCTTCTGATTTGGTC 59.247 52.381 0.00 0.00 0.00 4.02
1412 1447 2.449464 CCATGCCTTCTGATTTGGTCA 58.551 47.619 0.00 0.00 35.05 4.02
1413 1448 3.028850 CCATGCCTTCTGATTTGGTCAT 58.971 45.455 0.00 0.00 35.97 3.06
1414 1449 3.181479 CCATGCCTTCTGATTTGGTCATG 60.181 47.826 14.44 14.44 35.97 3.07
1415 1450 2.449464 TGCCTTCTGATTTGGTCATGG 58.551 47.619 0.00 0.00 35.97 3.66
1416 1451 1.135721 GCCTTCTGATTTGGTCATGGC 59.864 52.381 0.00 0.00 39.02 4.40
1417 1452 2.449464 CCTTCTGATTTGGTCATGGCA 58.551 47.619 0.00 0.00 35.97 4.92
1418 1453 2.827322 CCTTCTGATTTGGTCATGGCAA 59.173 45.455 0.00 0.00 35.97 4.52
1419 1454 3.367703 CCTTCTGATTTGGTCATGGCAAC 60.368 47.826 0.00 0.00 35.97 4.17
1420 1455 2.170166 TCTGATTTGGTCATGGCAACC 58.830 47.619 0.00 1.23 35.97 3.77
1421 1456 1.894466 CTGATTTGGTCATGGCAACCA 59.106 47.619 6.95 6.95 44.98 3.67
1422 1457 1.894466 TGATTTGGTCATGGCAACCAG 59.106 47.619 10.72 0.00 46.99 4.00
1423 1458 1.205417 GATTTGGTCATGGCAACCAGG 59.795 52.381 10.72 0.00 46.99 4.45
1424 1459 0.187117 TTTGGTCATGGCAACCAGGA 59.813 50.000 10.72 0.00 46.99 3.86
1425 1460 0.251297 TTGGTCATGGCAACCAGGAG 60.251 55.000 10.72 0.00 45.15 3.69
1426 1461 1.379044 GGTCATGGCAACCAGGAGG 60.379 63.158 0.42 0.00 45.15 4.30
1439 1474 2.973945 CCAGGAGGTACAACTACAAGC 58.026 52.381 0.00 0.00 0.00 4.01
1440 1475 2.301870 CCAGGAGGTACAACTACAAGCA 59.698 50.000 0.00 0.00 0.00 3.91
1441 1476 3.055094 CCAGGAGGTACAACTACAAGCAT 60.055 47.826 0.00 0.00 0.00 3.79
1442 1477 3.935203 CAGGAGGTACAACTACAAGCATG 59.065 47.826 0.00 0.00 0.00 4.06
1443 1478 2.678336 GGAGGTACAACTACAAGCATGC 59.322 50.000 10.51 10.51 0.00 4.06
1444 1479 2.678336 GAGGTACAACTACAAGCATGCC 59.322 50.000 15.66 0.00 0.00 4.40
1445 1480 2.305927 AGGTACAACTACAAGCATGCCT 59.694 45.455 15.66 0.00 0.00 4.75
1446 1481 3.517901 AGGTACAACTACAAGCATGCCTA 59.482 43.478 15.66 0.35 0.00 3.93
1447 1482 4.019681 AGGTACAACTACAAGCATGCCTAA 60.020 41.667 15.66 0.00 0.00 2.69
1448 1483 4.881850 GGTACAACTACAAGCATGCCTAAT 59.118 41.667 15.66 0.00 0.00 1.73
1449 1484 6.053005 GGTACAACTACAAGCATGCCTAATA 58.947 40.000 15.66 1.13 0.00 0.98
1450 1485 6.202954 GGTACAACTACAAGCATGCCTAATAG 59.797 42.308 15.66 13.39 0.00 1.73
1451 1486 5.126067 ACAACTACAAGCATGCCTAATAGG 58.874 41.667 15.66 0.99 38.80 2.57
1452 1487 5.104527 ACAACTACAAGCATGCCTAATAGGA 60.105 40.000 15.66 0.00 37.67 2.94
1453 1488 5.832539 ACTACAAGCATGCCTAATAGGAT 57.167 39.130 15.66 0.00 37.67 3.24
1454 1489 6.935240 ACTACAAGCATGCCTAATAGGATA 57.065 37.500 15.66 0.00 37.67 2.59
1500 1535 3.147595 CATCGAGAGGGGACGCCA 61.148 66.667 11.67 0.00 0.00 5.69
1520 1555 3.347216 CATACATGTTATAGGCAGGGGC 58.653 50.000 2.30 0.00 40.13 5.80
1523 1558 1.705002 ATGTTATAGGCAGGGGCGCA 61.705 55.000 10.83 0.00 42.47 6.09
1526 1561 1.632018 TTATAGGCAGGGGCGCAAGT 61.632 55.000 10.83 0.00 42.47 3.16
1535 1570 4.954933 GGCGCAAGTCCCTGATAA 57.045 55.556 10.83 0.00 41.68 1.75
1544 1579 4.188462 CAAGTCCCTGATAACGCATACAA 58.812 43.478 0.00 0.00 0.00 2.41
1548 1586 6.588204 AGTCCCTGATAACGCATACAATTTA 58.412 36.000 0.00 0.00 0.00 1.40
1554 1592 8.993121 CCTGATAACGCATACAATTTAGATCTT 58.007 33.333 0.00 0.00 0.00 2.40
1560 1598 8.958119 ACGCATACAATTTAGATCTTTTAGGA 57.042 30.769 0.00 0.00 0.00 2.94
1606 1644 8.742777 AGATCAAGCTAGCTAGAGATAGAATTG 58.257 37.037 25.15 7.99 36.19 2.32
1652 1691 4.110482 CCTAACTGCCAAGATACGTACAC 58.890 47.826 0.00 0.00 0.00 2.90
1653 1692 3.671008 AACTGCCAAGATACGTACACA 57.329 42.857 0.00 0.00 0.00 3.72
1662 1701 4.698583 AGATACGTACACAACTCCTGTC 57.301 45.455 0.00 0.00 35.47 3.51
1672 1711 4.521639 ACACAACTCCTGTCAAGATACGTA 59.478 41.667 0.00 0.00 35.47 3.57
1673 1712 4.857588 CACAACTCCTGTCAAGATACGTAC 59.142 45.833 0.00 0.00 35.47 3.67
1674 1713 4.521639 ACAACTCCTGTCAAGATACGTACA 59.478 41.667 0.00 0.00 29.87 2.90
1675 1714 4.698583 ACTCCTGTCAAGATACGTACAC 57.301 45.455 0.00 0.00 0.00 2.90
1676 1715 3.126514 ACTCCTGTCAAGATACGTACACG 59.873 47.826 0.00 0.00 46.33 4.49
1736 1800 4.141018 ACACCCTCCCTTAATCACAACTTT 60.141 41.667 0.00 0.00 0.00 2.66
1785 1849 5.536161 TCTTCAAAGCTTCTTGTAGGCAAAT 59.464 36.000 0.00 0.00 33.73 2.32
1961 2030 2.783135 AGGTTGTCACACCATAAGCAG 58.217 47.619 6.87 0.00 39.62 4.24
2036 2105 1.985473 TCTCAGTTGTGGCATTTGCT 58.015 45.000 2.12 0.00 41.70 3.91
2062 2131 3.369471 GCCTTGTATTCTACCTCTGTGCA 60.369 47.826 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 9.591792 TGTTGTTTTTGTGATAATGATGAAACA 57.408 25.926 0.00 0.00 34.92 2.83
43 44 9.127006 CGATGTTGTTTTTGTGATAATGATGAA 57.873 29.630 0.00 0.00 0.00 2.57
44 45 8.296000 ACGATGTTGTTTTTGTGATAATGATGA 58.704 29.630 0.00 0.00 0.00 2.92
45 46 8.367396 CACGATGTTGTTTTTGTGATAATGATG 58.633 33.333 0.00 0.00 30.17 3.07
46 47 8.081633 ACACGATGTTGTTTTTGTGATAATGAT 58.918 29.630 0.00 0.00 32.58 2.45
47 48 7.421599 ACACGATGTTGTTTTTGTGATAATGA 58.578 30.769 0.00 0.00 32.58 2.57
48 49 7.621832 ACACGATGTTGTTTTTGTGATAATG 57.378 32.000 0.00 0.00 32.58 1.90
49 50 8.564574 AGTACACGATGTTGTTTTTGTGATAAT 58.435 29.630 0.00 0.00 32.58 1.28
50 51 7.921787 AGTACACGATGTTGTTTTTGTGATAA 58.078 30.769 0.00 0.00 32.58 1.75
51 52 7.485418 AGTACACGATGTTGTTTTTGTGATA 57.515 32.000 0.00 0.00 32.58 2.15
52 53 6.371809 AGTACACGATGTTGTTTTTGTGAT 57.628 33.333 0.00 0.00 32.58 3.06
53 54 5.804692 AGTACACGATGTTGTTTTTGTGA 57.195 34.783 0.00 0.00 32.58 3.58
54 55 5.905181 GGTAGTACACGATGTTGTTTTTGTG 59.095 40.000 2.06 0.00 34.11 3.33
55 56 5.818857 AGGTAGTACACGATGTTGTTTTTGT 59.181 36.000 2.06 0.00 0.00 2.83
56 57 6.295039 AGGTAGTACACGATGTTGTTTTTG 57.705 37.500 2.06 0.00 0.00 2.44
57 58 6.424812 GGTAGGTAGTACACGATGTTGTTTTT 59.575 38.462 2.06 0.00 32.62 1.94
58 59 5.928264 GGTAGGTAGTACACGATGTTGTTTT 59.072 40.000 2.06 0.00 32.62 2.43
59 60 5.473039 GGTAGGTAGTACACGATGTTGTTT 58.527 41.667 2.06 0.00 32.62 2.83
60 61 4.082026 GGGTAGGTAGTACACGATGTTGTT 60.082 45.833 2.06 0.00 32.62 2.83
61 62 3.445096 GGGTAGGTAGTACACGATGTTGT 59.555 47.826 2.06 0.00 32.62 3.32
62 63 3.444742 TGGGTAGGTAGTACACGATGTTG 59.555 47.826 2.06 0.00 37.96 3.33
63 64 3.445096 GTGGGTAGGTAGTACACGATGTT 59.555 47.826 2.06 0.00 37.96 2.71
64 65 3.019564 GTGGGTAGGTAGTACACGATGT 58.980 50.000 2.06 0.00 37.96 3.06
65 66 2.360165 GGTGGGTAGGTAGTACACGATG 59.640 54.545 2.06 0.00 37.96 3.84
66 67 2.025037 TGGTGGGTAGGTAGTACACGAT 60.025 50.000 2.06 0.00 37.96 3.73
67 68 1.354031 TGGTGGGTAGGTAGTACACGA 59.646 52.381 2.06 0.00 37.96 4.35
68 69 1.838112 TGGTGGGTAGGTAGTACACG 58.162 55.000 2.06 0.00 37.96 4.49
69 70 3.680754 GCAATGGTGGGTAGGTAGTACAC 60.681 52.174 2.06 0.00 35.32 2.90
70 71 2.502538 GCAATGGTGGGTAGGTAGTACA 59.497 50.000 2.06 0.00 32.62 2.90
71 72 2.770232 AGCAATGGTGGGTAGGTAGTAC 59.230 50.000 0.00 0.00 0.00 2.73
72 73 3.124856 AGCAATGGTGGGTAGGTAGTA 57.875 47.619 0.00 0.00 0.00 1.82
73 74 1.966845 AGCAATGGTGGGTAGGTAGT 58.033 50.000 0.00 0.00 0.00 2.73
74 75 2.026262 ACAAGCAATGGTGGGTAGGTAG 60.026 50.000 0.00 0.00 0.00 3.18
75 76 1.989586 ACAAGCAATGGTGGGTAGGTA 59.010 47.619 0.00 0.00 0.00 3.08
76 77 0.777446 ACAAGCAATGGTGGGTAGGT 59.223 50.000 0.00 0.00 0.00 3.08
77 78 1.176527 CACAAGCAATGGTGGGTAGG 58.823 55.000 0.00 0.00 0.00 3.18
78 79 2.198827 TCACAAGCAATGGTGGGTAG 57.801 50.000 0.00 0.00 35.74 3.18
79 80 2.107378 TCTTCACAAGCAATGGTGGGTA 59.893 45.455 0.00 0.00 35.74 3.69
80 81 1.133513 TCTTCACAAGCAATGGTGGGT 60.134 47.619 0.00 0.00 35.74 4.51
81 82 1.619654 TCTTCACAAGCAATGGTGGG 58.380 50.000 0.00 0.00 35.74 4.61
82 83 2.886523 TCTTCTTCACAAGCAATGGTGG 59.113 45.455 0.00 0.00 35.74 4.61
83 84 4.778534 ATCTTCTTCACAAGCAATGGTG 57.221 40.909 0.00 0.00 36.36 4.17
84 85 4.828939 TCAATCTTCTTCACAAGCAATGGT 59.171 37.500 0.00 0.00 0.00 3.55
85 86 5.048224 AGTCAATCTTCTTCACAAGCAATGG 60.048 40.000 0.00 0.00 0.00 3.16
86 87 6.010294 AGTCAATCTTCTTCACAAGCAATG 57.990 37.500 0.00 0.00 0.00 2.82
87 88 5.182760 GGAGTCAATCTTCTTCACAAGCAAT 59.817 40.000 0.00 0.00 0.00 3.56
88 89 4.516698 GGAGTCAATCTTCTTCACAAGCAA 59.483 41.667 0.00 0.00 0.00 3.91
89 90 4.067896 GGAGTCAATCTTCTTCACAAGCA 58.932 43.478 0.00 0.00 0.00 3.91
90 91 4.067896 TGGAGTCAATCTTCTTCACAAGC 58.932 43.478 0.00 0.00 0.00 4.01
91 92 6.401903 CGAATGGAGTCAATCTTCTTCACAAG 60.402 42.308 0.00 0.00 0.00 3.16
94 95 5.062809 GTCGAATGGAGTCAATCTTCTTCAC 59.937 44.000 0.00 0.00 0.00 3.18
117 118 4.967084 TCCCAAAGGTATATATGCACGT 57.033 40.909 3.10 0.00 0.00 4.49
128 129 9.594774 GACCTTGTCATAACCTTCCCAAAGGTA 62.595 44.444 10.11 0.79 46.74 3.08
130 131 6.555152 GACCTTGTCATAACCTTCCCAAAGG 61.555 48.000 2.66 2.66 43.75 3.11
138 139 4.345859 TCAACGACCTTGTCATAACCTT 57.654 40.909 0.00 0.00 32.09 3.50
144 145 1.628340 TCCCATCAACGACCTTGTCAT 59.372 47.619 0.00 0.00 32.09 3.06
156 157 4.773674 AGTTGATCTTGCATTTCCCATCAA 59.226 37.500 0.00 0.00 0.00 2.57
157 158 4.346730 AGTTGATCTTGCATTTCCCATCA 58.653 39.130 0.00 0.00 0.00 3.07
159 160 4.891756 CCTAGTTGATCTTGCATTTCCCAT 59.108 41.667 0.00 0.00 0.00 4.00
180 181 0.251341 GGATTTGCACACCCACTCCT 60.251 55.000 0.00 0.00 0.00 3.69
185 186 1.786937 ACTTTGGATTTGCACACCCA 58.213 45.000 0.00 0.00 0.00 4.51
267 268 1.504275 ATCCTTCCAAGCAGCCCACT 61.504 55.000 0.00 0.00 0.00 4.00
310 311 1.781153 TACCCCCACAAAGGTTCCCG 61.781 60.000 0.00 0.00 37.59 5.14
318 319 2.983192 TCATTGTCTCTACCCCCACAAA 59.017 45.455 0.00 0.00 32.66 2.83
355 357 3.278668 TTTCCAACGACAACCTTGGTA 57.721 42.857 0.00 0.00 38.50 3.25
385 387 1.203287 GCAGAGTTCCAAAATGAGGCC 59.797 52.381 0.00 0.00 0.00 5.19
436 453 3.751479 AGGTCAAAGATTTTTGGTGCC 57.249 42.857 8.70 8.68 43.11 5.01
439 456 9.599866 CTTTTAGAAAGGTCAAAGATTTTTGGT 57.400 29.630 8.70 0.00 43.11 3.67
474 491 0.035458 CAAGGCCTTCTTCACGGAGT 59.965 55.000 17.29 0.00 35.02 3.85
508 525 8.893563 TTCCACCAATATCCAAATTAGAAACT 57.106 30.769 0.00 0.00 0.00 2.66
604 625 4.946157 CCATGTAATTGAGTCAAGCTCCTT 59.054 41.667 11.91 2.97 43.48 3.36
633 654 2.951642 CGAGTATTGGCCATCATTGGTT 59.048 45.455 6.09 0.00 45.57 3.67
662 683 5.357878 CCAAGAAATTGAGCACTATAAGCCA 59.642 40.000 0.00 0.00 0.00 4.75
874 905 3.548770 ACATGGATTGTGTAGAGGCATG 58.451 45.455 0.00 0.00 37.11 4.06
917 948 6.347888 CGGATGTACACCGTTTAAAATGAAGT 60.348 38.462 21.45 0.00 44.57 3.01
932 963 2.098770 GTCTAGTCCACCGGATGTACAC 59.901 54.545 9.46 0.00 32.73 2.90
953 985 2.926778 CCTGAGGGAAGGCAATCTAG 57.073 55.000 0.00 0.00 33.58 2.43
967 999 3.314331 ACGCCACCACTCCCTGAG 61.314 66.667 0.00 0.00 35.52 3.35
996 1028 2.765807 CGGGGCAGAGACATCCCT 60.766 66.667 0.00 0.00 39.95 4.20
1023 1055 9.160496 CAAGAAATCAGTAGCATAAGAGAAACT 57.840 33.333 0.00 0.00 0.00 2.66
1104 1136 2.031258 TTCGAGCAACAAGAACACCA 57.969 45.000 0.00 0.00 0.00 4.17
1196 1228 0.751643 CCAGGGGCCGAATTACAAGG 60.752 60.000 0.00 0.00 0.00 3.61
1229 1262 8.498358 GCAATTTTCACTGAATAAGAAAAAGGG 58.502 33.333 0.00 0.00 42.43 3.95
1234 1267 7.118101 GGCATGCAATTTTCACTGAATAAGAAA 59.882 33.333 21.36 0.00 0.00 2.52
1245 1278 3.557508 GCAAAAGGCATGCAATTTTCAC 58.442 40.909 22.74 16.53 43.29 3.18
1281 1316 2.173782 TGGCTGGGGCGAGAAATTATTA 59.826 45.455 0.00 0.00 39.81 0.98
1284 1319 0.107214 CTGGCTGGGGCGAGAAATTA 60.107 55.000 0.00 0.00 45.21 1.40
1287 1322 4.722700 GCTGGCTGGGGCGAGAAA 62.723 66.667 4.33 0.00 45.21 2.52
1305 1340 4.308458 TGTCCGTCGTTGGCCTGG 62.308 66.667 3.32 0.00 0.00 4.45
1306 1341 2.738521 CTGTCCGTCGTTGGCCTG 60.739 66.667 3.32 0.00 0.00 4.85
1307 1342 4.681978 GCTGTCCGTCGTTGGCCT 62.682 66.667 3.32 0.00 0.00 5.19
1308 1343 4.980805 TGCTGTCCGTCGTTGGCC 62.981 66.667 0.00 0.00 0.00 5.36
1309 1344 3.414700 CTGCTGTCCGTCGTTGGC 61.415 66.667 0.00 0.00 0.00 4.52
1310 1345 3.414700 GCTGCTGTCCGTCGTTGG 61.415 66.667 0.00 0.00 0.00 3.77
1311 1346 3.767230 CGCTGCTGTCCGTCGTTG 61.767 66.667 0.00 0.00 0.00 4.10
1312 1347 3.785189 AACGCTGCTGTCCGTCGTT 62.785 57.895 0.00 0.00 36.56 3.85
1313 1348 4.280494 AACGCTGCTGTCCGTCGT 62.280 61.111 0.00 0.00 36.56 4.34
1314 1349 3.767230 CAACGCTGCTGTCCGTCG 61.767 66.667 0.00 0.00 36.56 5.12
1315 1350 2.355837 TCAACGCTGCTGTCCGTC 60.356 61.111 0.00 0.00 36.56 4.79
1316 1351 2.356313 CTCAACGCTGCTGTCCGT 60.356 61.111 0.00 0.00 39.70 4.69
1317 1352 3.782244 GCTCAACGCTGCTGTCCG 61.782 66.667 0.00 0.00 35.14 4.79
1318 1353 1.975363 GATGCTCAACGCTGCTGTCC 61.975 60.000 0.00 0.00 40.11 4.02
1319 1354 1.293963 TGATGCTCAACGCTGCTGTC 61.294 55.000 0.00 0.00 40.11 3.51
1320 1355 1.301953 TGATGCTCAACGCTGCTGT 60.302 52.632 0.00 0.00 40.11 4.40
1321 1356 1.134075 GTGATGCTCAACGCTGCTG 59.866 57.895 0.00 0.00 40.11 4.41
1322 1357 2.037136 GGTGATGCTCAACGCTGCT 61.037 57.895 0.00 0.00 40.11 4.24
1323 1358 0.740868 TAGGTGATGCTCAACGCTGC 60.741 55.000 0.00 0.00 39.55 5.25
1324 1359 1.284657 CTAGGTGATGCTCAACGCTG 58.715 55.000 0.00 0.00 39.55 5.18
1325 1360 0.176680 CCTAGGTGATGCTCAACGCT 59.823 55.000 0.00 0.00 39.55 5.07
1326 1361 0.811616 CCCTAGGTGATGCTCAACGC 60.812 60.000 8.29 0.00 39.55 4.84
1327 1362 0.824109 TCCCTAGGTGATGCTCAACG 59.176 55.000 8.29 0.00 39.55 4.10
1328 1363 2.435805 TGATCCCTAGGTGATGCTCAAC 59.564 50.000 15.17 3.54 33.32 3.18
1329 1364 2.763039 TGATCCCTAGGTGATGCTCAA 58.237 47.619 15.17 0.00 0.00 3.02
1330 1365 2.477104 TGATCCCTAGGTGATGCTCA 57.523 50.000 15.17 7.43 0.00 4.26
1331 1366 4.363991 AAATGATCCCTAGGTGATGCTC 57.636 45.455 15.17 5.35 0.00 4.26
1332 1367 4.803329 AAAATGATCCCTAGGTGATGCT 57.197 40.909 15.17 2.72 0.00 3.79
1333 1368 5.625150 AGTAAAATGATCCCTAGGTGATGC 58.375 41.667 15.17 8.97 0.00 3.91
1334 1369 7.512992 AGAAGTAAAATGATCCCTAGGTGATG 58.487 38.462 15.17 0.00 0.00 3.07
1335 1370 7.698163 AGAAGTAAAATGATCCCTAGGTGAT 57.302 36.000 8.29 10.09 0.00 3.06
1336 1371 7.510675 AAGAAGTAAAATGATCCCTAGGTGA 57.489 36.000 8.29 5.19 0.00 4.02
1337 1372 7.611855 ACAAAGAAGTAAAATGATCCCTAGGTG 59.388 37.037 8.29 0.00 0.00 4.00
1338 1373 7.699878 ACAAAGAAGTAAAATGATCCCTAGGT 58.300 34.615 8.29 0.00 0.00 3.08
1339 1374 7.829211 TGACAAAGAAGTAAAATGATCCCTAGG 59.171 37.037 0.06 0.06 0.00 3.02
1340 1375 8.669243 GTGACAAAGAAGTAAAATGATCCCTAG 58.331 37.037 0.00 0.00 0.00 3.02
1341 1376 8.383175 AGTGACAAAGAAGTAAAATGATCCCTA 58.617 33.333 0.00 0.00 0.00 3.53
1342 1377 7.234355 AGTGACAAAGAAGTAAAATGATCCCT 58.766 34.615 0.00 0.00 0.00 4.20
1343 1378 7.454260 AGTGACAAAGAAGTAAAATGATCCC 57.546 36.000 0.00 0.00 0.00 3.85
1344 1379 8.999431 TGTAGTGACAAAGAAGTAAAATGATCC 58.001 33.333 0.00 0.00 30.68 3.36
1347 1382 9.554395 TGATGTAGTGACAAAGAAGTAAAATGA 57.446 29.630 0.00 0.00 39.59 2.57
1348 1383 9.817365 CTGATGTAGTGACAAAGAAGTAAAATG 57.183 33.333 0.00 0.00 39.59 2.32
1349 1384 8.507249 GCTGATGTAGTGACAAAGAAGTAAAAT 58.493 33.333 0.00 0.00 39.59 1.82
1350 1385 7.041372 GGCTGATGTAGTGACAAAGAAGTAAAA 60.041 37.037 0.00 0.00 39.59 1.52
1351 1386 6.426937 GGCTGATGTAGTGACAAAGAAGTAAA 59.573 38.462 0.00 0.00 39.59 2.01
1352 1387 5.932303 GGCTGATGTAGTGACAAAGAAGTAA 59.068 40.000 0.00 0.00 39.59 2.24
1353 1388 5.479306 GGCTGATGTAGTGACAAAGAAGTA 58.521 41.667 0.00 0.00 39.59 2.24
1354 1389 4.319177 GGCTGATGTAGTGACAAAGAAGT 58.681 43.478 0.00 0.00 39.59 3.01
1355 1390 3.686726 GGGCTGATGTAGTGACAAAGAAG 59.313 47.826 0.00 0.00 39.59 2.85
1356 1391 3.327757 AGGGCTGATGTAGTGACAAAGAA 59.672 43.478 0.00 0.00 39.59 2.52
1357 1392 2.906389 AGGGCTGATGTAGTGACAAAGA 59.094 45.455 0.00 0.00 39.59 2.52
1358 1393 3.005554 CAGGGCTGATGTAGTGACAAAG 58.994 50.000 0.00 0.00 39.59 2.77
1359 1394 2.875672 GCAGGGCTGATGTAGTGACAAA 60.876 50.000 0.00 0.00 39.59 2.83
1360 1395 1.339055 GCAGGGCTGATGTAGTGACAA 60.339 52.381 0.00 0.00 39.59 3.18
1361 1396 0.250234 GCAGGGCTGATGTAGTGACA 59.750 55.000 0.00 0.00 40.72 3.58
1362 1397 0.250234 TGCAGGGCTGATGTAGTGAC 59.750 55.000 0.00 0.00 0.00 3.67
1363 1398 0.983467 TTGCAGGGCTGATGTAGTGA 59.017 50.000 0.00 0.00 0.00 3.41
1364 1399 1.945394 GATTGCAGGGCTGATGTAGTG 59.055 52.381 0.00 0.00 0.00 2.74
1365 1400 1.133976 GGATTGCAGGGCTGATGTAGT 60.134 52.381 0.00 0.00 0.00 2.73
1366 1401 1.142465 AGGATTGCAGGGCTGATGTAG 59.858 52.381 0.00 0.00 0.00 2.74
1367 1402 1.141657 GAGGATTGCAGGGCTGATGTA 59.858 52.381 0.00 0.00 0.00 2.29
1368 1403 0.106819 GAGGATTGCAGGGCTGATGT 60.107 55.000 0.00 0.00 0.00 3.06
1369 1404 0.106868 TGAGGATTGCAGGGCTGATG 60.107 55.000 0.00 0.00 0.00 3.07
1370 1405 0.851469 ATGAGGATTGCAGGGCTGAT 59.149 50.000 0.00 0.00 0.00 2.90
1371 1406 0.182061 GATGAGGATTGCAGGGCTGA 59.818 55.000 0.00 0.00 0.00 4.26
1372 1407 0.822532 GGATGAGGATTGCAGGGCTG 60.823 60.000 0.00 0.00 0.00 4.85
1373 1408 1.535685 GGATGAGGATTGCAGGGCT 59.464 57.895 0.00 0.00 0.00 5.19
1374 1409 1.530183 GGGATGAGGATTGCAGGGC 60.530 63.158 0.00 0.00 0.00 5.19
1375 1410 1.152368 GGGGATGAGGATTGCAGGG 59.848 63.158 0.00 0.00 0.00 4.45
1376 1411 0.481567 ATGGGGATGAGGATTGCAGG 59.518 55.000 0.00 0.00 0.00 4.85
1377 1412 1.617322 CATGGGGATGAGGATTGCAG 58.383 55.000 0.00 0.00 0.00 4.41
1378 1413 0.468585 GCATGGGGATGAGGATTGCA 60.469 55.000 0.00 0.00 0.00 4.08
1379 1414 1.183676 GGCATGGGGATGAGGATTGC 61.184 60.000 0.00 0.00 0.00 3.56
1380 1415 0.481567 AGGCATGGGGATGAGGATTG 59.518 55.000 0.00 0.00 0.00 2.67
1381 1416 1.146566 GAAGGCATGGGGATGAGGATT 59.853 52.381 0.00 0.00 0.00 3.01
1382 1417 0.776176 GAAGGCATGGGGATGAGGAT 59.224 55.000 0.00 0.00 0.00 3.24
1383 1418 0.327867 AGAAGGCATGGGGATGAGGA 60.328 55.000 0.00 0.00 0.00 3.71
1384 1419 0.178998 CAGAAGGCATGGGGATGAGG 60.179 60.000 0.00 0.00 0.00 3.86
1385 1420 0.841961 TCAGAAGGCATGGGGATGAG 59.158 55.000 0.00 0.00 0.00 2.90
1386 1421 1.526315 ATCAGAAGGCATGGGGATGA 58.474 50.000 0.00 0.00 0.00 2.92
1387 1422 2.364324 CAAATCAGAAGGCATGGGGATG 59.636 50.000 0.00 0.00 0.00 3.51
1388 1423 2.674420 CAAATCAGAAGGCATGGGGAT 58.326 47.619 0.00 0.00 0.00 3.85
1389 1424 1.342275 CCAAATCAGAAGGCATGGGGA 60.342 52.381 0.00 0.00 0.00 4.81
1390 1425 1.117150 CCAAATCAGAAGGCATGGGG 58.883 55.000 0.00 0.00 0.00 4.96
1391 1426 1.753073 GACCAAATCAGAAGGCATGGG 59.247 52.381 0.00 0.00 32.21 4.00
1392 1427 2.449464 TGACCAAATCAGAAGGCATGG 58.551 47.619 0.00 0.00 31.91 3.66
1393 1428 3.181479 CCATGACCAAATCAGAAGGCATG 60.181 47.826 0.00 0.00 41.91 4.06
1394 1429 3.028850 CCATGACCAAATCAGAAGGCAT 58.971 45.455 0.00 0.00 41.91 4.40
1395 1430 2.449464 CCATGACCAAATCAGAAGGCA 58.551 47.619 0.00 0.00 41.91 4.75
1396 1431 1.135721 GCCATGACCAAATCAGAAGGC 59.864 52.381 0.00 0.00 41.91 4.35
1397 1432 2.449464 TGCCATGACCAAATCAGAAGG 58.551 47.619 0.00 0.00 41.91 3.46
1398 1433 3.367703 GGTTGCCATGACCAAATCAGAAG 60.368 47.826 0.00 0.00 41.91 2.85
1399 1434 2.562298 GGTTGCCATGACCAAATCAGAA 59.438 45.455 0.00 0.00 41.91 3.02
1400 1435 2.170166 GGTTGCCATGACCAAATCAGA 58.830 47.619 0.00 0.00 41.91 3.27
1401 1436 1.894466 TGGTTGCCATGACCAAATCAG 59.106 47.619 2.35 0.00 43.87 2.90
1402 1437 1.894466 CTGGTTGCCATGACCAAATCA 59.106 47.619 6.25 5.25 45.94 2.57
1403 1438 1.205417 CCTGGTTGCCATGACCAAATC 59.795 52.381 6.25 1.65 45.94 2.17
1404 1439 1.203162 TCCTGGTTGCCATGACCAAAT 60.203 47.619 6.25 0.00 45.94 2.32
1405 1440 0.187117 TCCTGGTTGCCATGACCAAA 59.813 50.000 6.25 0.00 45.94 3.28
1406 1441 0.251297 CTCCTGGTTGCCATGACCAA 60.251 55.000 6.25 1.08 45.94 3.67
1407 1442 1.379916 CTCCTGGTTGCCATGACCA 59.620 57.895 4.79 4.79 44.59 4.02
1408 1443 1.379044 CCTCCTGGTTGCCATGACC 60.379 63.158 0.00 0.00 37.69 4.02
1409 1444 0.618458 TACCTCCTGGTTGCCATGAC 59.382 55.000 0.00 0.00 46.05 3.06
1410 1445 0.618458 GTACCTCCTGGTTGCCATGA 59.382 55.000 0.00 0.00 46.05 3.07
1411 1446 0.327924 TGTACCTCCTGGTTGCCATG 59.672 55.000 0.00 0.00 46.05 3.66
1412 1447 1.072266 TTGTACCTCCTGGTTGCCAT 58.928 50.000 0.00 0.00 46.05 4.40
1413 1448 0.109723 GTTGTACCTCCTGGTTGCCA 59.890 55.000 0.00 0.00 46.05 4.92
1414 1449 0.400594 AGTTGTACCTCCTGGTTGCC 59.599 55.000 0.00 0.00 46.05 4.52
1415 1450 2.038033 TGTAGTTGTACCTCCTGGTTGC 59.962 50.000 0.00 0.00 46.05 4.17
1416 1451 4.315803 CTTGTAGTTGTACCTCCTGGTTG 58.684 47.826 0.00 0.00 46.05 3.77
1417 1452 3.244457 GCTTGTAGTTGTACCTCCTGGTT 60.244 47.826 0.00 0.00 46.05 3.67
1419 1454 2.301870 TGCTTGTAGTTGTACCTCCTGG 59.698 50.000 0.00 0.00 39.83 4.45
1420 1455 3.678056 TGCTTGTAGTTGTACCTCCTG 57.322 47.619 0.00 0.00 0.00 3.86
1421 1456 3.619979 GCATGCTTGTAGTTGTACCTCCT 60.620 47.826 11.37 0.00 0.00 3.69
1422 1457 2.678336 GCATGCTTGTAGTTGTACCTCC 59.322 50.000 11.37 0.00 0.00 4.30
1423 1458 2.678336 GGCATGCTTGTAGTTGTACCTC 59.322 50.000 18.92 0.00 0.00 3.85
1424 1459 2.305927 AGGCATGCTTGTAGTTGTACCT 59.694 45.455 18.92 0.00 0.00 3.08
1425 1460 2.711542 AGGCATGCTTGTAGTTGTACC 58.288 47.619 18.92 0.00 0.00 3.34
1426 1461 6.202954 CCTATTAGGCATGCTTGTAGTTGTAC 59.797 42.308 18.92 0.00 0.00 2.90
1427 1462 6.099125 TCCTATTAGGCATGCTTGTAGTTGTA 59.901 38.462 18.92 0.00 34.61 2.41
1428 1463 5.104527 TCCTATTAGGCATGCTTGTAGTTGT 60.105 40.000 18.92 0.00 34.61 3.32
1429 1464 5.368145 TCCTATTAGGCATGCTTGTAGTTG 58.632 41.667 18.92 5.96 34.61 3.16
1430 1465 5.630415 TCCTATTAGGCATGCTTGTAGTT 57.370 39.130 18.92 0.00 34.61 2.24
1431 1466 5.832539 ATCCTATTAGGCATGCTTGTAGT 57.167 39.130 18.92 6.58 34.61 2.73
1432 1467 7.332926 CACTTATCCTATTAGGCATGCTTGTAG 59.667 40.741 18.92 15.63 34.61 2.74
1433 1468 7.161404 CACTTATCCTATTAGGCATGCTTGTA 58.839 38.462 18.92 7.08 34.61 2.41
1434 1469 6.000219 CACTTATCCTATTAGGCATGCTTGT 59.000 40.000 18.92 6.21 34.61 3.16
1435 1470 6.000219 ACACTTATCCTATTAGGCATGCTTG 59.000 40.000 18.92 0.00 34.61 4.01
1436 1471 6.000219 CACACTTATCCTATTAGGCATGCTT 59.000 40.000 18.92 13.45 34.61 3.91
1437 1472 5.555017 CACACTTATCCTATTAGGCATGCT 58.445 41.667 18.92 6.26 34.61 3.79
1438 1473 4.154918 GCACACTTATCCTATTAGGCATGC 59.845 45.833 9.90 9.90 34.61 4.06
1439 1474 4.389992 CGCACACTTATCCTATTAGGCATG 59.610 45.833 4.73 0.00 34.61 4.06
1440 1475 4.283467 TCGCACACTTATCCTATTAGGCAT 59.717 41.667 4.73 2.99 34.61 4.40
1441 1476 3.639561 TCGCACACTTATCCTATTAGGCA 59.360 43.478 4.73 0.00 34.61 4.75
1442 1477 4.252971 TCGCACACTTATCCTATTAGGC 57.747 45.455 4.73 0.00 34.61 3.93
1443 1478 4.686554 GCTTCGCACACTTATCCTATTAGG 59.313 45.833 3.07 3.07 36.46 2.69
1444 1479 4.383052 CGCTTCGCACACTTATCCTATTAG 59.617 45.833 0.00 0.00 0.00 1.73
1445 1480 4.295870 CGCTTCGCACACTTATCCTATTA 58.704 43.478 0.00 0.00 0.00 0.98
1446 1481 3.123804 CGCTTCGCACACTTATCCTATT 58.876 45.455 0.00 0.00 0.00 1.73
1447 1482 2.545952 CCGCTTCGCACACTTATCCTAT 60.546 50.000 0.00 0.00 0.00 2.57
1448 1483 1.202371 CCGCTTCGCACACTTATCCTA 60.202 52.381 0.00 0.00 0.00 2.94
1449 1484 0.460284 CCGCTTCGCACACTTATCCT 60.460 55.000 0.00 0.00 0.00 3.24
1450 1485 0.459585 TCCGCTTCGCACACTTATCC 60.460 55.000 0.00 0.00 0.00 2.59
1451 1486 1.355971 TTCCGCTTCGCACACTTATC 58.644 50.000 0.00 0.00 0.00 1.75
1452 1487 1.803334 TTTCCGCTTCGCACACTTAT 58.197 45.000 0.00 0.00 0.00 1.73
1453 1488 1.262151 GTTTTCCGCTTCGCACACTTA 59.738 47.619 0.00 0.00 0.00 2.24
1454 1489 0.028902 GTTTTCCGCTTCGCACACTT 59.971 50.000 0.00 0.00 0.00 3.16
1500 1535 2.027192 CGCCCCTGCCTATAACATGTAT 60.027 50.000 0.00 0.00 0.00 2.29
1520 1555 0.739462 TGCGTTATCAGGGACTTGCG 60.739 55.000 0.00 0.00 34.60 4.85
1523 1558 4.481368 TTGTATGCGTTATCAGGGACTT 57.519 40.909 0.00 0.00 34.60 3.01
1526 1561 6.822442 TCTAAATTGTATGCGTTATCAGGGA 58.178 36.000 0.00 0.00 0.00 4.20
1535 1570 8.958119 TCCTAAAAGATCTAAATTGTATGCGT 57.042 30.769 0.00 0.00 0.00 5.24
1544 1579 9.500701 AACCTCTCTCTCCTAAAAGATCTAAAT 57.499 33.333 0.00 0.00 0.00 1.40
1548 1586 7.415086 TGTAACCTCTCTCTCCTAAAAGATCT 58.585 38.462 0.00 0.00 0.00 2.75
1554 1592 6.014499 CCAAGTTGTAACCTCTCTCTCCTAAA 60.014 42.308 1.45 0.00 0.00 1.85
1555 1593 5.480772 CCAAGTTGTAACCTCTCTCTCCTAA 59.519 44.000 1.45 0.00 0.00 2.69
1558 1596 3.833070 TCCAAGTTGTAACCTCTCTCTCC 59.167 47.826 1.45 0.00 0.00 3.71
1559 1597 4.767928 TCTCCAAGTTGTAACCTCTCTCTC 59.232 45.833 1.45 0.00 0.00 3.20
1560 1598 4.742012 TCTCCAAGTTGTAACCTCTCTCT 58.258 43.478 1.45 0.00 0.00 3.10
1606 1644 7.726738 AGGATAGGAGGTTTATCTCTAGTTCAC 59.273 40.741 0.00 0.00 34.39 3.18
1652 1691 4.857588 GTGTACGTATCTTGACAGGAGTTG 59.142 45.833 0.00 0.00 0.00 3.16
1653 1692 4.379186 CGTGTACGTATCTTGACAGGAGTT 60.379 45.833 0.00 0.00 31.07 3.01
1672 1711 2.904866 ATGTTTGGGCGCACGTGT 60.905 55.556 18.38 0.00 0.00 4.49
1673 1712 2.428902 CATGTTTGGGCGCACGTG 60.429 61.111 12.28 12.28 0.00 4.49
1674 1713 3.669344 CCATGTTTGGGCGCACGT 61.669 61.111 10.83 0.00 39.56 4.49
1736 1800 9.102757 GACTTCAAGCATAATCTCAACTTGATA 57.897 33.333 4.74 0.00 44.36 2.15
1785 1849 2.516906 TGCAGATGGATTCACAAAGCA 58.483 42.857 0.00 0.00 0.00 3.91
2036 2105 6.582636 CACAGAGGTAGAATACAAGGCATTA 58.417 40.000 0.00 0.00 45.43 1.90
2052 2121 2.737180 CAGGTCGTGCACAGAGGT 59.263 61.111 18.64 2.70 0.00 3.85
2062 2131 0.249398 GGCAACTGTATCCAGGTCGT 59.751 55.000 0.00 0.00 43.36 4.34
2083 2152 5.122519 TGATATCATGGTGTGCACGTAAAT 58.877 37.500 13.13 3.63 0.00 1.40


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

AutoCloner maintained by Alex Coulton.