Multiple sequence alignment - TraesCS6A01G392100

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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 TraesCS6A01G392100 chr6A 100.000 3260 0 0 1 3260 606769192 606765933 0 6021
1 TraesCS6A01G392100 chr6D 93.497 1138 60 13 2130 3260 460573347 460572217 0 1679
2 TraesCS6A01G392100 chr6D 87.620 1349 81 26 105 1391 460575467 460574143 0 1487
3 TraesCS6A01G392100 chr6D 92.875 786 34 15 1330 2105 460574254 460573481 0 1122
4 TraesCS6A01G392100 chr6B 93.052 1137 66 11 2130 3260 701661250 701660121 0 1650
5 TraesCS6A01G392100 chr6B 84.948 1342 94 44 97 1391 701663301 701662021 0 1260
6 TraesCS6A01G392100 chr6B 91.791 804 50 10 1330 2126 701662133 701661339 0 1105


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 TraesCS6A01G392100 chr6A 606765933 606769192 3259 True 6021.000000 6021 100.000000 1 3260 1 chr6A.!!$R1 3259
1 TraesCS6A01G392100 chr6D 460572217 460575467 3250 True 1429.333333 1679 91.330667 105 3260 3 chr6D.!!$R1 3155
2 TraesCS6A01G392100 chr6B 701660121 701663301 3180 True 1338.333333 1650 89.930333 97 3260 3 chr6B.!!$R1 3163

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
31 32 0.031994 GTTGCAATTCACGGGCACTT 59.968 50.0 0.59 0.0 37.26 3.16 F
90 91 0.038890 TGCATCGTTCCCAATTCCCA 59.961 50.0 0.00 0.0 0.00 4.37 F
1745 1841 0.034896 TTCAGGCCCGACAGAAGAAC 59.965 55.0 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1218 1306 0.539051 GCTGCTGTGACTGGAGGTAT 59.461 55.0 12.4 0.0 0.00 2.73 R
1798 1895 0.767375 ACAAGATGGTGGTGCTGAGT 59.233 50.0 0.0 0.0 0.00 3.41 R
3130 3349 1.159713 TGCGTCAGTGGCTGTTTCTG 61.160 55.0 0.0 0.0 32.61 3.02 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.267188 CATCTGTTGCAATTCACGGG 57.733 50.000 0.59 0.00 0.00 5.28
27 28 0.527565 ATCTGTTGCAATTCACGGGC 59.472 50.000 0.59 0.00 0.00 6.13
28 29 0.821301 TCTGTTGCAATTCACGGGCA 60.821 50.000 0.59 0.00 35.41 5.36
29 30 0.664166 CTGTTGCAATTCACGGGCAC 60.664 55.000 0.59 0.00 37.26 5.01
30 31 1.106351 TGTTGCAATTCACGGGCACT 61.106 50.000 0.59 0.00 37.26 4.40
31 32 0.031994 GTTGCAATTCACGGGCACTT 59.968 50.000 0.59 0.00 37.26 3.16
32 33 0.749649 TTGCAATTCACGGGCACTTT 59.250 45.000 0.00 0.00 37.26 2.66
33 34 1.610363 TGCAATTCACGGGCACTTTA 58.390 45.000 0.00 0.00 31.58 1.85
34 35 1.268352 TGCAATTCACGGGCACTTTAC 59.732 47.619 0.00 0.00 31.58 2.01
35 36 1.402325 GCAATTCACGGGCACTTTACC 60.402 52.381 0.00 0.00 0.00 2.85
36 37 1.883275 CAATTCACGGGCACTTTACCA 59.117 47.619 0.00 0.00 0.00 3.25
37 38 1.821216 ATTCACGGGCACTTTACCAG 58.179 50.000 0.00 0.00 0.00 4.00
38 39 0.470766 TTCACGGGCACTTTACCAGT 59.529 50.000 0.00 0.00 35.89 4.00
54 55 1.581934 CAGTGCAACAGGAACGAAGA 58.418 50.000 0.00 0.00 41.43 2.87
55 56 1.939934 CAGTGCAACAGGAACGAAGAA 59.060 47.619 0.00 0.00 41.43 2.52
56 57 2.032549 CAGTGCAACAGGAACGAAGAAG 60.033 50.000 0.00 0.00 41.43 2.85
57 58 2.158957 AGTGCAACAGGAACGAAGAAGA 60.159 45.455 0.00 0.00 41.43 2.87
58 59 2.808543 GTGCAACAGGAACGAAGAAGAT 59.191 45.455 0.00 0.00 36.32 2.40
59 60 3.251004 GTGCAACAGGAACGAAGAAGATT 59.749 43.478 0.00 0.00 36.32 2.40
60 61 3.498397 TGCAACAGGAACGAAGAAGATTC 59.502 43.478 0.00 0.00 0.00 2.52
61 62 3.423645 GCAACAGGAACGAAGAAGATTCG 60.424 47.826 8.35 8.35 46.36 3.34
70 71 4.175473 CGAAGAAGATTCGTGCTGATTC 57.825 45.455 1.99 0.00 37.18 2.52
71 72 3.862267 CGAAGAAGATTCGTGCTGATTCT 59.138 43.478 1.99 0.00 38.61 2.40
72 73 4.259730 CGAAGAAGATTCGTGCTGATTCTG 60.260 45.833 1.99 0.00 37.38 3.02
73 74 2.935201 AGAAGATTCGTGCTGATTCTGC 59.065 45.455 8.46 8.46 37.38 4.26
74 75 2.391616 AGATTCGTGCTGATTCTGCA 57.608 45.000 13.50 13.50 36.28 4.41
75 76 2.915349 AGATTCGTGCTGATTCTGCAT 58.085 42.857 19.34 5.43 40.15 3.96
76 77 2.871022 AGATTCGTGCTGATTCTGCATC 59.129 45.455 19.34 13.23 40.15 3.91
77 78 1.001624 TTCGTGCTGATTCTGCATCG 58.998 50.000 19.34 20.99 40.15 3.84
78 79 0.108662 TCGTGCTGATTCTGCATCGT 60.109 50.000 24.46 0.00 40.15 3.73
79 80 0.723414 CGTGCTGATTCTGCATCGTT 59.277 50.000 19.34 0.00 40.15 3.85
80 81 1.267235 CGTGCTGATTCTGCATCGTTC 60.267 52.381 19.34 7.14 40.15 3.95
81 82 1.063174 GTGCTGATTCTGCATCGTTCC 59.937 52.381 19.34 4.11 40.15 3.62
82 83 0.659957 GCTGATTCTGCATCGTTCCC 59.340 55.000 10.32 0.00 34.08 3.97
83 84 2.013563 GCTGATTCTGCATCGTTCCCA 61.014 52.381 10.32 0.00 34.08 4.37
84 85 2.358957 CTGATTCTGCATCGTTCCCAA 58.641 47.619 0.00 0.00 34.08 4.12
85 86 2.947652 CTGATTCTGCATCGTTCCCAAT 59.052 45.455 0.00 0.00 34.08 3.16
86 87 3.355378 TGATTCTGCATCGTTCCCAATT 58.645 40.909 0.00 0.00 34.08 2.32
87 88 3.378112 TGATTCTGCATCGTTCCCAATTC 59.622 43.478 0.00 0.00 34.08 2.17
88 89 1.750193 TCTGCATCGTTCCCAATTCC 58.250 50.000 0.00 0.00 0.00 3.01
89 90 0.740737 CTGCATCGTTCCCAATTCCC 59.259 55.000 0.00 0.00 0.00 3.97
90 91 0.038890 TGCATCGTTCCCAATTCCCA 59.961 50.000 0.00 0.00 0.00 4.37
91 92 1.341877 TGCATCGTTCCCAATTCCCAT 60.342 47.619 0.00 0.00 0.00 4.00
92 93 1.067516 GCATCGTTCCCAATTCCCATG 59.932 52.381 0.00 0.00 0.00 3.66
93 94 2.653726 CATCGTTCCCAATTCCCATGA 58.346 47.619 0.00 0.00 0.00 3.07
94 95 2.889170 TCGTTCCCAATTCCCATGAA 57.111 45.000 0.00 0.00 34.33 2.57
95 96 2.442413 TCGTTCCCAATTCCCATGAAC 58.558 47.619 0.00 0.00 32.13 3.18
126 127 0.511653 CGCAGCATCATGATCTTCCG 59.488 55.000 4.86 3.26 0.00 4.30
147 148 2.978010 CCGTTTTGGAGCGCTGGT 60.978 61.111 18.48 0.00 42.00 4.00
154 155 0.902984 TTGGAGCGCTGGTTCCTCTA 60.903 55.000 18.48 0.00 43.45 2.43
156 157 0.466124 GGAGCGCTGGTTCCTCTATT 59.534 55.000 18.48 0.00 40.18 1.73
157 158 1.539280 GGAGCGCTGGTTCCTCTATTC 60.539 57.143 18.48 0.00 40.18 1.75
161 162 1.269309 CGCTGGTTCCTCTATTCCTCG 60.269 57.143 0.00 0.00 0.00 4.63
167 168 0.465642 TCCTCTATTCCTCGCTCGCA 60.466 55.000 0.00 0.00 0.00 5.10
172 173 1.524355 CTATTCCTCGCTCGCATGTTG 59.476 52.381 0.00 0.00 0.00 3.33
186 191 0.680921 ATGTTGTCCGCCCCAGATTG 60.681 55.000 0.00 0.00 0.00 2.67
189 194 0.107214 TTGTCCGCCCCAGATTGATC 60.107 55.000 0.00 0.00 0.00 2.92
244 249 2.640302 GCTCCGACAGGTCAGCAGA 61.640 63.158 6.82 0.00 37.34 4.26
375 388 0.610687 CTCCTCCATCCTTATCCGGC 59.389 60.000 0.00 0.00 0.00 6.13
471 500 4.980805 GGAAGCACCGCGTGTCCA 62.981 66.667 4.92 0.00 35.75 4.02
472 501 2.742372 GAAGCACCGCGTGTCCAT 60.742 61.111 4.92 0.00 35.75 3.41
516 547 2.363795 ACCAGAGATTCCGGGCGA 60.364 61.111 0.00 0.00 0.00 5.54
517 548 1.749334 GACCAGAGATTCCGGGCGAT 61.749 60.000 0.00 0.00 0.00 4.58
530 567 1.298859 GGGCGATGACAAGAAACGCT 61.299 55.000 0.00 0.00 46.71 5.07
531 568 0.179215 GGCGATGACAAGAAACGCTG 60.179 55.000 0.00 0.00 46.71 5.18
568 616 0.752658 TAGGTGCACATCCAGATCCG 59.247 55.000 20.43 0.00 0.00 4.18
600 648 1.568597 TCCATGAATTACCACCCCAGG 59.431 52.381 0.00 0.00 0.00 4.45
601 649 1.402787 CATGAATTACCACCCCAGGC 58.597 55.000 0.00 0.00 0.00 4.85
602 650 0.261696 ATGAATTACCACCCCAGGCC 59.738 55.000 0.00 0.00 0.00 5.19
603 651 1.076265 GAATTACCACCCCAGGCCC 60.076 63.158 0.00 0.00 0.00 5.80
604 652 1.859735 AATTACCACCCCAGGCCCA 60.860 57.895 0.00 0.00 0.00 5.36
605 653 1.874299 AATTACCACCCCAGGCCCAG 61.874 60.000 0.00 0.00 0.00 4.45
638 686 7.061789 GGTTAAAACTTAAAACGCCATGATCAG 59.938 37.037 0.09 0.00 0.00 2.90
698 746 4.040755 ACTGCCATGATTCTACCTACCTT 58.959 43.478 0.00 0.00 0.00 3.50
699 747 4.141620 ACTGCCATGATTCTACCTACCTTG 60.142 45.833 0.00 0.00 0.00 3.61
700 748 4.037222 TGCCATGATTCTACCTACCTTGA 58.963 43.478 0.00 0.00 0.00 3.02
701 749 4.141711 TGCCATGATTCTACCTACCTTGAC 60.142 45.833 0.00 0.00 0.00 3.18
717 770 3.118702 CCTTGACTGAGCTCACTGATCAT 60.119 47.826 13.74 0.00 40.58 2.45
718 771 4.505808 CTTGACTGAGCTCACTGATCATT 58.494 43.478 13.74 0.00 40.58 2.57
753 821 4.019174 TCTATCAGCACACTCATCAGTCA 58.981 43.478 0.00 0.00 0.00 3.41
821 899 2.697644 CCAGCCCTTCCCTCCCAT 60.698 66.667 0.00 0.00 0.00 4.00
822 900 2.599597 CAGCCCTTCCCTCCCATG 59.400 66.667 0.00 0.00 0.00 3.66
825 903 3.099171 CCCTTCCCTCCCATGCAA 58.901 61.111 0.00 0.00 0.00 4.08
843 921 1.538687 AAGCAAGCAAGCCCATCCAC 61.539 55.000 0.00 0.00 34.23 4.02
847 925 2.825836 GCAAGCCCATCCACCTCG 60.826 66.667 0.00 0.00 0.00 4.63
853 931 2.669133 CCCATCCACCTCGGCTCAA 61.669 63.158 0.00 0.00 33.14 3.02
859 937 0.742281 CCACCTCGGCTCAATGACAG 60.742 60.000 0.00 0.00 0.00 3.51
860 938 0.247460 CACCTCGGCTCAATGACAGA 59.753 55.000 0.00 0.00 0.00 3.41
861 939 0.247736 ACCTCGGCTCAATGACAGAC 59.752 55.000 0.00 0.00 0.00 3.51
862 940 0.247460 CCTCGGCTCAATGACAGACA 59.753 55.000 0.00 0.00 0.00 3.41
896 974 1.375268 GTGAGTGCACCTCCAGCTC 60.375 63.158 14.63 2.88 39.65 4.09
899 977 1.908340 GAGTGCACCTCCAGCTCCAT 61.908 60.000 14.63 0.00 33.79 3.41
901 979 0.610232 GTGCACCTCCAGCTCCATTT 60.610 55.000 5.22 0.00 0.00 2.32
902 980 0.609957 TGCACCTCCAGCTCCATTTG 60.610 55.000 0.00 0.00 0.00 2.32
961 1039 2.170397 ACACAGTCAGACAACATCCACA 59.830 45.455 2.66 0.00 0.00 4.17
987 1072 3.399440 AGACAAGGAAGCAGTGAAGAG 57.601 47.619 0.00 0.00 0.00 2.85
988 1073 2.703007 AGACAAGGAAGCAGTGAAGAGT 59.297 45.455 0.00 0.00 0.00 3.24
1052 1137 1.547372 CATGTTCAAAGGGGCCAAGAG 59.453 52.381 4.39 0.00 0.00 2.85
1054 1139 1.777878 TGTTCAAAGGGGCCAAGAGTA 59.222 47.619 4.39 0.00 0.00 2.59
1091 1179 2.429930 CAGTGGCGGGACCTTTGA 59.570 61.111 0.00 0.00 40.22 2.69
1155 1243 2.772691 GCTCGACGAGAACCCCGAT 61.773 63.158 28.43 0.00 0.00 4.18
1230 1318 2.494445 CGCGCATACCTCCAGTCA 59.506 61.111 8.75 0.00 0.00 3.41
1250 1338 2.728383 GCAGCAGCAGCAACAACG 60.728 61.111 4.63 0.00 45.49 4.10
1253 1341 1.819208 AGCAGCAGCAACAACGACA 60.819 52.632 3.17 0.00 45.49 4.35
1257 1345 1.029408 AGCAGCAACAACGACAACCA 61.029 50.000 0.00 0.00 0.00 3.67
1278 1366 2.514592 CATGCCGGCGATCAGGTT 60.515 61.111 23.90 0.00 0.00 3.50
1299 1388 5.334724 GGTTCTTCTTCTTGCTGATCTTGTG 60.335 44.000 0.00 0.00 0.00 3.33
1307 1396 1.338484 TGCTGATCTTGTGGTCTCTGC 60.338 52.381 0.00 0.00 34.38 4.26
1308 1397 1.066286 GCTGATCTTGTGGTCTCTGCT 60.066 52.381 0.00 0.00 32.02 4.24
1335 1424 5.083533 TCCTCTCTTGATGCTTCTTCTTC 57.916 43.478 0.88 0.00 0.00 2.87
1336 1425 4.081198 TCCTCTCTTGATGCTTCTTCTTCC 60.081 45.833 0.88 0.00 0.00 3.46
1337 1426 4.080975 CCTCTCTTGATGCTTCTTCTTCCT 60.081 45.833 0.88 0.00 0.00 3.36
1338 1427 4.829968 TCTCTTGATGCTTCTTCTTCCTG 58.170 43.478 0.88 0.00 0.00 3.86
1339 1428 3.341823 TCTTGATGCTTCTTCTTCCTGC 58.658 45.455 0.88 0.00 0.00 4.85
1340 1429 3.008813 TCTTGATGCTTCTTCTTCCTGCT 59.991 43.478 0.88 0.00 0.00 4.24
1341 1430 2.708051 TGATGCTTCTTCTTCCTGCTG 58.292 47.619 0.88 0.00 0.00 4.41
1342 1431 2.303890 TGATGCTTCTTCTTCCTGCTGA 59.696 45.455 0.88 0.00 0.00 4.26
1343 1432 3.054582 TGATGCTTCTTCTTCCTGCTGAT 60.055 43.478 0.88 0.00 0.00 2.90
1344 1433 2.983229 TGCTTCTTCTTCCTGCTGATC 58.017 47.619 0.00 0.00 0.00 2.92
1345 1434 2.570752 TGCTTCTTCTTCCTGCTGATCT 59.429 45.455 0.00 0.00 0.00 2.75
1346 1435 3.008813 TGCTTCTTCTTCCTGCTGATCTT 59.991 43.478 0.00 0.00 0.00 2.40
1347 1436 3.374678 GCTTCTTCTTCCTGCTGATCTTG 59.625 47.826 0.00 0.00 0.00 3.02
1348 1437 4.577875 CTTCTTCTTCCTGCTGATCTTGT 58.422 43.478 0.00 0.00 0.00 3.16
1349 1438 5.728471 CTTCTTCTTCCTGCTGATCTTGTA 58.272 41.667 0.00 0.00 0.00 2.41
1350 1439 5.336150 TCTTCTTCCTGCTGATCTTGTAG 57.664 43.478 0.00 0.00 0.00 2.74
1351 1440 4.774726 TCTTCTTCCTGCTGATCTTGTAGT 59.225 41.667 0.00 0.00 0.00 2.73
1352 1441 4.727507 TCTTCCTGCTGATCTTGTAGTC 57.272 45.455 0.00 0.00 0.00 2.59
1353 1442 4.348486 TCTTCCTGCTGATCTTGTAGTCT 58.652 43.478 0.00 0.00 0.00 3.24
1354 1443 4.400884 TCTTCCTGCTGATCTTGTAGTCTC 59.599 45.833 0.00 0.00 0.00 3.36
1355 1444 3.974719 TCCTGCTGATCTTGTAGTCTCT 58.025 45.455 0.00 0.00 0.00 3.10
1356 1445 4.348486 TCCTGCTGATCTTGTAGTCTCTT 58.652 43.478 0.00 0.00 0.00 2.85
1357 1446 4.774726 TCCTGCTGATCTTGTAGTCTCTTT 59.225 41.667 0.00 0.00 0.00 2.52
1358 1447 5.105554 TCCTGCTGATCTTGTAGTCTCTTTC 60.106 44.000 0.00 0.00 0.00 2.62
1359 1448 5.337089 CCTGCTGATCTTGTAGTCTCTTTCA 60.337 44.000 0.00 0.00 0.00 2.69
1360 1449 6.291648 TGCTGATCTTGTAGTCTCTTTCAT 57.708 37.500 0.00 0.00 0.00 2.57
1361 1450 6.336566 TGCTGATCTTGTAGTCTCTTTCATC 58.663 40.000 0.00 0.00 0.00 2.92
1362 1451 6.154192 TGCTGATCTTGTAGTCTCTTTCATCT 59.846 38.462 0.00 0.00 0.00 2.90
1363 1452 6.697019 GCTGATCTTGTAGTCTCTTTCATCTC 59.303 42.308 0.00 0.00 0.00 2.75
1364 1453 7.106439 TGATCTTGTAGTCTCTTTCATCTCC 57.894 40.000 0.00 0.00 0.00 3.71
1365 1454 6.894654 TGATCTTGTAGTCTCTTTCATCTCCT 59.105 38.462 0.00 0.00 0.00 3.69
1366 1455 6.767524 TCTTGTAGTCTCTTTCATCTCCTC 57.232 41.667 0.00 0.00 0.00 3.71
1367 1456 6.489603 TCTTGTAGTCTCTTTCATCTCCTCT 58.510 40.000 0.00 0.00 0.00 3.69
1368 1457 6.601613 TCTTGTAGTCTCTTTCATCTCCTCTC 59.398 42.308 0.00 0.00 0.00 3.20
1369 1458 6.073447 TGTAGTCTCTTTCATCTCCTCTCT 57.927 41.667 0.00 0.00 0.00 3.10
1370 1459 6.489603 TGTAGTCTCTTTCATCTCCTCTCTT 58.510 40.000 0.00 0.00 0.00 2.85
1371 1460 5.920193 AGTCTCTTTCATCTCCTCTCTTG 57.080 43.478 0.00 0.00 0.00 3.02
1372 1461 5.579047 AGTCTCTTTCATCTCCTCTCTTGA 58.421 41.667 0.00 0.00 0.00 3.02
1373 1462 6.197168 AGTCTCTTTCATCTCCTCTCTTGAT 58.803 40.000 0.00 0.00 0.00 2.57
1374 1463 6.097270 AGTCTCTTTCATCTCCTCTCTTGATG 59.903 42.308 0.00 0.00 38.97 3.07
1375 1464 6.096705 GTCTCTTTCATCTCCTCTCTTGATGA 59.903 42.308 0.00 0.00 43.02 2.92
1376 1465 6.840181 TCTCTTTCATCTCCTCTCTTGATGAT 59.160 38.462 5.85 0.00 43.78 2.45
1377 1466 6.818233 TCTTTCATCTCCTCTCTTGATGATG 58.182 40.000 5.85 0.00 43.78 3.07
1378 1467 4.603989 TCATCTCCTCTCTTGATGATGC 57.396 45.455 0.00 0.00 40.81 3.91
1379 1468 4.224762 TCATCTCCTCTCTTGATGATGCT 58.775 43.478 0.00 0.00 40.81 3.79
1380 1469 4.654724 TCATCTCCTCTCTTGATGATGCTT 59.345 41.667 0.00 0.00 40.81 3.91
1381 1470 4.669206 TCTCCTCTCTTGATGATGCTTC 57.331 45.455 0.00 0.00 0.00 3.86
1382 1471 4.288398 TCTCCTCTCTTGATGATGCTTCT 58.712 43.478 0.88 0.00 0.00 2.85
1383 1472 4.715792 TCTCCTCTCTTGATGATGCTTCTT 59.284 41.667 0.88 0.00 0.00 2.52
1384 1473 5.021033 TCCTCTCTTGATGATGCTTCTTC 57.979 43.478 8.16 8.16 0.00 2.87
1385 1474 4.715792 TCCTCTCTTGATGATGCTTCTTCT 59.284 41.667 14.19 0.00 0.00 2.85
1386 1475 5.189342 TCCTCTCTTGATGATGCTTCTTCTT 59.811 40.000 14.19 0.00 0.00 2.52
1465 1558 2.814336 CCCCTTGCTTGACTTTGTACTC 59.186 50.000 0.00 0.00 0.00 2.59
1604 1697 2.571216 CCTCCCGGTTGTCGACAGT 61.571 63.158 19.11 0.00 42.43 3.55
1607 1700 3.041940 CCGGTTGTCGACAGTGCC 61.042 66.667 19.11 19.36 42.43 5.01
1611 1704 4.980805 TTGTCGACAGTGCCCGCC 62.981 66.667 19.11 0.00 0.00 6.13
1616 1709 4.760047 GACAGTGCCCGCCGATGT 62.760 66.667 0.00 0.00 0.00 3.06
1642 1735 0.179197 GTCGTCGTCAAGAGCGATCA 60.179 55.000 2.38 0.00 40.59 2.92
1691 1784 1.903955 GCTCCTCCCCCTTCTCTCTTT 60.904 57.143 0.00 0.00 0.00 2.52
1702 1795 7.406151 TCCCCCTTCTCTCTTTATCTGTTTTAT 59.594 37.037 0.00 0.00 0.00 1.40
1703 1796 8.055790 CCCCCTTCTCTCTTTATCTGTTTTATT 58.944 37.037 0.00 0.00 0.00 1.40
1704 1797 9.467796 CCCCTTCTCTCTTTATCTGTTTTATTT 57.532 33.333 0.00 0.00 0.00 1.40
1729 1822 0.667993 CAACTCTTTGCCGCCTTTCA 59.332 50.000 0.00 0.00 0.00 2.69
1745 1841 0.034896 TTCAGGCCCGACAGAAGAAC 59.965 55.000 0.00 0.00 0.00 3.01
1746 1842 0.832135 TCAGGCCCGACAGAAGAACT 60.832 55.000 0.00 0.00 0.00 3.01
1751 1848 2.483106 GGCCCGACAGAAGAACTAAAAC 59.517 50.000 0.00 0.00 0.00 2.43
1772 1869 8.655651 AAAACAGACAGAAAAAGAAAACACAA 57.344 26.923 0.00 0.00 0.00 3.33
1798 1895 5.645929 CACACCCACATATACAAGTTGCTAA 59.354 40.000 1.81 0.00 0.00 3.09
1839 1936 7.539712 TGTGTTTGCTAATCTAGTTGCTATC 57.460 36.000 0.00 0.00 0.00 2.08
1942 2039 5.413213 CCGGTAATTGTTGTTTCCACTCATA 59.587 40.000 0.00 0.00 0.00 2.15
2089 2189 8.433126 CAAGTAATAGGTGAGTAACAGAAAACG 58.567 37.037 0.00 0.00 0.00 3.60
2105 2205 2.427410 CGCGACAAAACCAGCAGC 60.427 61.111 0.00 0.00 0.00 5.25
2106 2206 2.427410 GCGACAAAACCAGCAGCG 60.427 61.111 0.00 0.00 0.00 5.18
2109 2209 0.238289 CGACAAAACCAGCAGCGAAT 59.762 50.000 0.00 0.00 0.00 3.34
2115 2215 0.877071 AACCAGCAGCGAATGACTTG 59.123 50.000 0.00 0.00 0.00 3.16
2122 2222 5.696270 CCAGCAGCGAATGACTTGTATATAA 59.304 40.000 0.00 0.00 0.00 0.98
2126 2226 8.307483 AGCAGCGAATGACTTGTATATAATACT 58.693 33.333 0.00 0.00 0.00 2.12
2179 2390 5.856126 TGGAGTATGTTTCAAGCTTAACG 57.144 39.130 0.00 0.00 0.00 3.18
2336 2549 3.258971 ACTTTGAGTAGCAGGCAGATC 57.741 47.619 0.00 0.00 0.00 2.75
2357 2570 9.877178 CAGATCCTATAGTCTGTAAAAGTGTTT 57.123 33.333 10.76 0.00 37.62 2.83
2358 2571 9.877178 AGATCCTATAGTCTGTAAAAGTGTTTG 57.123 33.333 0.00 0.00 0.00 2.93
2359 2572 7.900782 TCCTATAGTCTGTAAAAGTGTTTGC 57.099 36.000 0.00 0.00 0.00 3.68
2360 2573 7.446769 TCCTATAGTCTGTAAAAGTGTTTGCA 58.553 34.615 0.00 0.00 37.05 4.08
2366 2579 5.235305 CTGTAAAAGTGTTTGCAGTCTGT 57.765 39.130 0.93 0.00 46.50 3.41
2367 2580 6.358118 CTGTAAAAGTGTTTGCAGTCTGTA 57.642 37.500 0.93 0.00 46.50 2.74
2368 2581 6.935741 TGTAAAAGTGTTTGCAGTCTGTAT 57.064 33.333 0.93 0.00 34.82 2.29
2369 2582 6.954944 TGTAAAAGTGTTTGCAGTCTGTATC 58.045 36.000 0.93 0.00 34.82 2.24
2370 2583 4.732285 AAAGTGTTTGCAGTCTGTATCG 57.268 40.909 0.93 0.00 0.00 2.92
2371 2584 2.069273 AGTGTTTGCAGTCTGTATCGC 58.931 47.619 0.93 1.09 0.00 4.58
2372 2585 1.798223 GTGTTTGCAGTCTGTATCGCA 59.202 47.619 0.93 0.00 0.00 5.10
2451 2664 3.859411 GCTTCTGCTCTGTACTGTACT 57.141 47.619 17.98 0.00 36.03 2.73
2454 2667 4.559704 GCTTCTGCTCTGTACTGTACTGTT 60.560 45.833 17.98 0.00 36.03 3.16
2465 2680 4.617253 ACTGTACTGTTTGGTATCTGCA 57.383 40.909 0.00 0.00 0.00 4.41
2468 2683 4.062293 TGTACTGTTTGGTATCTGCACAC 58.938 43.478 0.00 0.00 0.00 3.82
2498 2714 2.995283 TCCATGAGCAATGACTTCCAG 58.005 47.619 0.00 0.00 38.72 3.86
2506 2722 2.096496 GCAATGACTTCCAGATTCCACG 59.904 50.000 0.00 0.00 0.00 4.94
2508 2724 0.036388 TGACTTCCAGATTCCACGGC 60.036 55.000 0.00 0.00 0.00 5.68
2513 2729 0.690192 TCCAGATTCCACGGCAAGAA 59.310 50.000 0.00 0.00 0.00 2.52
2514 2730 1.073125 TCCAGATTCCACGGCAAGAAA 59.927 47.619 0.00 0.00 0.00 2.52
2518 2734 2.955660 AGATTCCACGGCAAGAAAAACA 59.044 40.909 0.00 0.00 0.00 2.83
2523 2739 3.680458 TCCACGGCAAGAAAAACAAAAAC 59.320 39.130 0.00 0.00 0.00 2.43
2528 2744 5.641636 ACGGCAAGAAAAACAAAAACTCATT 59.358 32.000 0.00 0.00 0.00 2.57
2529 2745 5.958949 CGGCAAGAAAAACAAAAACTCATTG 59.041 36.000 0.00 0.00 0.00 2.82
2562 2778 4.352001 AGAGGAATGGAGGCAATATGCTTA 59.648 41.667 2.00 0.00 44.28 3.09
2624 2840 1.081906 GCAGCCACGTGTGTTCATG 60.082 57.895 15.65 4.84 36.71 3.07
2635 2851 3.436359 CGTGTGTTCATGGACAATGATGA 59.564 43.478 8.85 0.00 44.84 2.92
2640 2856 9.006839 GTGTGTTCATGGACAATGATGATATAT 57.993 33.333 8.85 0.00 44.84 0.86
2666 2882 3.074412 CGGTTTCCAGAAGCAGTACAAT 58.926 45.455 0.00 0.00 0.00 2.71
2678 2894 8.110612 CAGAAGCAGTACAATAGTTTTATCACG 58.889 37.037 0.00 0.00 0.00 4.35
2697 2913 6.308371 TCACGAAAGATGTATAGCACGATA 57.692 37.500 0.00 0.00 0.00 2.92
2780 2996 0.321671 TGCCCTAGACACTCAACAGC 59.678 55.000 0.00 0.00 0.00 4.40
2788 3004 1.115930 ACACTCAACAGCCGAGGACT 61.116 55.000 0.00 0.00 34.66 3.85
2789 3005 0.888619 CACTCAACAGCCGAGGACTA 59.111 55.000 0.00 0.00 34.66 2.59
2849 3068 7.100458 ACAGTGCCTTTATTTATTGGACATC 57.900 36.000 0.00 0.00 0.00 3.06
2902 3121 3.744426 GTGTGCCATACGAAAACTACAGT 59.256 43.478 0.00 0.00 0.00 3.55
2926 3145 2.751806 GACAATGCAAGAGAAAGGAGGG 59.248 50.000 0.00 0.00 0.00 4.30
2962 3181 6.950842 TGAATGCCCATACCAGAGAATATAG 58.049 40.000 0.00 0.00 0.00 1.31
3113 3332 3.578716 CCTCTACTTGTTGACCTTCTCCA 59.421 47.826 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.733389 GCCCGTGAATTGCAACAGATG 60.733 52.381 0.00 0.00 0.00 2.90
8 9 0.527565 GCCCGTGAATTGCAACAGAT 59.472 50.000 0.00 0.00 0.00 2.90
9 10 0.821301 TGCCCGTGAATTGCAACAGA 60.821 50.000 0.00 0.00 30.85 3.41
10 11 0.664166 GTGCCCGTGAATTGCAACAG 60.664 55.000 0.00 0.00 36.65 3.16
11 12 1.106351 AGTGCCCGTGAATTGCAACA 61.106 50.000 0.00 0.00 36.65 3.33
12 13 0.031994 AAGTGCCCGTGAATTGCAAC 59.968 50.000 0.00 0.00 36.65 4.17
13 14 0.749649 AAAGTGCCCGTGAATTGCAA 59.250 45.000 0.00 0.00 36.65 4.08
14 15 1.268352 GTAAAGTGCCCGTGAATTGCA 59.732 47.619 0.00 0.00 0.00 4.08
15 16 1.402325 GGTAAAGTGCCCGTGAATTGC 60.402 52.381 0.00 0.00 0.00 3.56
16 17 1.883275 TGGTAAAGTGCCCGTGAATTG 59.117 47.619 0.00 0.00 0.00 2.32
17 18 2.159382 CTGGTAAAGTGCCCGTGAATT 58.841 47.619 0.00 0.00 0.00 2.17
18 19 1.073284 ACTGGTAAAGTGCCCGTGAAT 59.927 47.619 0.00 0.00 37.88 2.57
19 20 0.470766 ACTGGTAAAGTGCCCGTGAA 59.529 50.000 0.00 0.00 37.88 3.18
20 21 2.138595 ACTGGTAAAGTGCCCGTGA 58.861 52.632 0.00 0.00 37.88 4.35
21 22 4.792087 ACTGGTAAAGTGCCCGTG 57.208 55.556 0.00 0.00 37.88 4.94
28 29 2.949644 GTTCCTGTTGCACTGGTAAAGT 59.050 45.455 10.43 0.00 40.93 2.66
29 30 2.032030 CGTTCCTGTTGCACTGGTAAAG 60.032 50.000 10.43 5.04 38.25 1.85
30 31 1.944024 CGTTCCTGTTGCACTGGTAAA 59.056 47.619 10.43 0.00 38.25 2.01
31 32 1.139256 TCGTTCCTGTTGCACTGGTAA 59.861 47.619 10.43 4.00 38.25 2.85
32 33 0.753867 TCGTTCCTGTTGCACTGGTA 59.246 50.000 10.43 1.55 38.25 3.25
33 34 0.107410 TTCGTTCCTGTTGCACTGGT 60.107 50.000 10.43 0.00 38.25 4.00
34 35 0.588252 CTTCGTTCCTGTTGCACTGG 59.412 55.000 0.00 0.00 38.41 4.00
35 36 1.581934 TCTTCGTTCCTGTTGCACTG 58.418 50.000 0.00 0.00 0.00 3.66
36 37 2.158957 TCTTCTTCGTTCCTGTTGCACT 60.159 45.455 0.00 0.00 0.00 4.40
37 38 2.210116 TCTTCTTCGTTCCTGTTGCAC 58.790 47.619 0.00 0.00 0.00 4.57
38 39 2.613026 TCTTCTTCGTTCCTGTTGCA 57.387 45.000 0.00 0.00 0.00 4.08
39 40 3.423645 CGAATCTTCTTCGTTCCTGTTGC 60.424 47.826 0.00 0.00 37.18 4.17
40 41 4.313522 CGAATCTTCTTCGTTCCTGTTG 57.686 45.455 0.00 0.00 37.18 3.33
49 50 3.862267 AGAATCAGCACGAATCTTCTTCG 59.138 43.478 5.87 5.87 46.36 3.79
50 51 4.493872 GCAGAATCAGCACGAATCTTCTTC 60.494 45.833 0.00 0.00 31.06 2.87
51 52 3.373439 GCAGAATCAGCACGAATCTTCTT 59.627 43.478 0.00 0.00 31.06 2.52
52 53 2.935201 GCAGAATCAGCACGAATCTTCT 59.065 45.455 0.00 0.00 31.06 2.85
53 54 2.674852 TGCAGAATCAGCACGAATCTTC 59.325 45.455 0.00 0.00 37.02 2.87
54 55 2.703416 TGCAGAATCAGCACGAATCTT 58.297 42.857 0.00 0.00 37.02 2.40
55 56 2.391616 TGCAGAATCAGCACGAATCT 57.608 45.000 0.00 0.00 37.02 2.40
56 57 2.348311 CGATGCAGAATCAGCACGAATC 60.348 50.000 1.57 0.00 45.95 2.52
57 58 1.596260 CGATGCAGAATCAGCACGAAT 59.404 47.619 1.57 0.00 45.95 3.34
58 59 1.001624 CGATGCAGAATCAGCACGAA 58.998 50.000 1.57 0.00 45.95 3.85
59 60 0.108662 ACGATGCAGAATCAGCACGA 60.109 50.000 21.31 0.00 45.95 4.35
60 61 0.723414 AACGATGCAGAATCAGCACG 59.277 50.000 16.04 16.04 45.95 5.34
61 62 1.063174 GGAACGATGCAGAATCAGCAC 59.937 52.381 1.57 0.00 45.95 4.40
63 64 0.659957 GGGAACGATGCAGAATCAGC 59.340 55.000 0.00 0.00 34.68 4.26
64 65 2.028420 TGGGAACGATGCAGAATCAG 57.972 50.000 0.00 0.00 34.68 2.90
65 66 2.488204 TTGGGAACGATGCAGAATCA 57.512 45.000 0.00 0.00 34.68 2.57
66 67 3.243201 GGAATTGGGAACGATGCAGAATC 60.243 47.826 0.00 0.00 33.59 2.52
67 68 2.689983 GGAATTGGGAACGATGCAGAAT 59.310 45.455 0.00 0.00 33.59 2.40
68 69 2.091541 GGAATTGGGAACGATGCAGAA 58.908 47.619 0.00 0.00 33.59 3.02
69 70 1.681780 GGGAATTGGGAACGATGCAGA 60.682 52.381 0.00 0.00 33.59 4.26
70 71 0.740737 GGGAATTGGGAACGATGCAG 59.259 55.000 0.00 0.00 33.59 4.41
71 72 0.038890 TGGGAATTGGGAACGATGCA 59.961 50.000 0.00 0.00 33.59 3.96
72 73 1.067516 CATGGGAATTGGGAACGATGC 59.932 52.381 0.00 0.00 33.59 3.91
73 74 2.653726 TCATGGGAATTGGGAACGATG 58.346 47.619 0.00 0.00 33.59 3.84
74 75 3.023832 GTTCATGGGAATTGGGAACGAT 58.976 45.455 0.00 0.00 35.05 3.73
75 76 2.442413 GTTCATGGGAATTGGGAACGA 58.558 47.619 0.00 0.00 35.05 3.85
76 77 2.939460 GTTCATGGGAATTGGGAACG 57.061 50.000 0.00 0.00 35.05 3.95
77 78 1.476488 CCGTTCATGGGAATTGGGAAC 59.524 52.381 0.00 0.00 35.05 3.62
78 79 1.846007 CCGTTCATGGGAATTGGGAA 58.154 50.000 0.00 0.00 35.05 3.97
79 80 3.586843 CCGTTCATGGGAATTGGGA 57.413 52.632 0.00 0.00 35.05 4.37
88 89 1.303309 GCAGAATCTCCCGTTCATGG 58.697 55.000 0.00 0.00 0.00 3.66
89 90 0.933097 CGCAGAATCTCCCGTTCATG 59.067 55.000 0.00 0.00 0.00 3.07
90 91 0.811616 GCGCAGAATCTCCCGTTCAT 60.812 55.000 0.30 0.00 0.00 2.57
91 92 1.447838 GCGCAGAATCTCCCGTTCA 60.448 57.895 0.30 0.00 0.00 3.18
92 93 1.424493 CTGCGCAGAATCTCCCGTTC 61.424 60.000 33.66 0.00 0.00 3.95
93 94 1.448540 CTGCGCAGAATCTCCCGTT 60.449 57.895 33.66 0.00 0.00 4.44
94 95 2.185350 CTGCGCAGAATCTCCCGT 59.815 61.111 33.66 0.00 0.00 5.28
95 96 3.267860 GCTGCGCAGAATCTCCCG 61.268 66.667 40.21 12.59 0.00 5.14
147 148 0.669077 GCGAGCGAGGAATAGAGGAA 59.331 55.000 0.00 0.00 0.00 3.36
154 155 0.391661 ACAACATGCGAGCGAGGAAT 60.392 50.000 0.00 0.00 0.00 3.01
156 157 1.446099 GACAACATGCGAGCGAGGA 60.446 57.895 0.00 0.00 0.00 3.71
157 158 2.456119 GGACAACATGCGAGCGAGG 61.456 63.158 0.00 0.00 0.00 4.63
161 162 4.166011 GGCGGACAACATGCGAGC 62.166 66.667 0.00 0.00 46.80 5.03
167 168 0.680921 CAATCTGGGGCGGACAACAT 60.681 55.000 0.00 0.00 0.00 2.71
172 173 1.227973 GGATCAATCTGGGGCGGAC 60.228 63.158 0.00 0.00 0.00 4.79
186 191 2.776072 CACGGTTTCGCGTGGATC 59.224 61.111 5.77 0.00 40.63 3.36
343 356 3.003763 AGGAGTGCCGACCCTTCC 61.004 66.667 0.00 0.00 39.96 3.46
471 500 0.392998 GTGGATTGACGTGGAGCCAT 60.393 55.000 7.86 0.00 0.00 4.40
472 501 1.003839 GTGGATTGACGTGGAGCCA 60.004 57.895 0.00 0.00 0.00 4.75
474 503 1.009829 GATGTGGATTGACGTGGAGC 58.990 55.000 0.00 0.00 0.00 4.70
516 547 3.265791 GGATCTCAGCGTTTCTTGTCAT 58.734 45.455 0.00 0.00 0.00 3.06
517 548 2.037121 TGGATCTCAGCGTTTCTTGTCA 59.963 45.455 0.00 0.00 0.00 3.58
530 567 4.593206 ACCTAACTCACAAGTTGGATCTCA 59.407 41.667 7.96 0.00 44.40 3.27
531 568 4.932200 CACCTAACTCACAAGTTGGATCTC 59.068 45.833 7.96 0.00 44.40 2.75
568 616 1.852157 TTCATGGAGGCTGGGGTGAC 61.852 60.000 0.00 0.00 0.00 3.67
602 650 0.114364 AGTTTTAACCCCTGGCCTGG 59.886 55.000 21.51 21.51 0.00 4.45
603 651 2.009681 AAGTTTTAACCCCTGGCCTG 57.990 50.000 3.32 2.54 0.00 4.85
604 652 3.907459 TTAAGTTTTAACCCCTGGCCT 57.093 42.857 3.32 0.00 0.00 5.19
605 653 4.634199 GTTTTAAGTTTTAACCCCTGGCC 58.366 43.478 0.00 0.00 0.00 5.36
606 654 4.300803 CGTTTTAAGTTTTAACCCCTGGC 58.699 43.478 0.00 0.00 0.00 4.85
638 686 4.666253 TGGCAGAAGCTGGGTGGC 62.666 66.667 9.19 9.19 41.70 5.01
698 746 3.512724 TGAATGATCAGTGAGCTCAGTCA 59.487 43.478 21.41 18.24 42.87 3.41
699 747 4.114073 CTGAATGATCAGTGAGCTCAGTC 58.886 47.826 21.41 15.11 46.60 3.51
700 748 4.126208 CTGAATGATCAGTGAGCTCAGT 57.874 45.455 18.89 18.75 46.60 3.41
717 770 9.920133 GTGTGCTGATAGATAAATATCTCTGAA 57.080 33.333 6.22 0.00 41.85 3.02
718 771 9.306777 AGTGTGCTGATAGATAAATATCTCTGA 57.693 33.333 6.22 0.00 41.85 3.27
734 802 3.197116 TGATGACTGATGAGTGTGCTGAT 59.803 43.478 0.00 0.00 30.16 2.90
753 821 4.841422 CTGAGATCCCACTTTGACTTGAT 58.159 43.478 0.00 0.00 0.00 2.57
811 886 0.612732 CTTGCTTGCATGGGAGGGAA 60.613 55.000 1.34 0.00 0.00 3.97
820 898 1.550130 ATGGGCTTGCTTGCTTGCAT 61.550 50.000 5.15 0.00 42.96 3.96
821 899 2.162338 GATGGGCTTGCTTGCTTGCA 62.162 55.000 10.93 0.27 41.65 4.08
822 900 1.447314 GATGGGCTTGCTTGCTTGC 60.447 57.895 1.96 0.00 0.00 4.01
825 903 1.980772 GTGGATGGGCTTGCTTGCT 60.981 57.895 1.96 0.00 0.00 3.91
843 921 0.247460 TGTCTGTCATTGAGCCGAGG 59.753 55.000 0.00 0.00 0.00 4.63
847 925 2.615912 GCCTATTGTCTGTCATTGAGCC 59.384 50.000 0.00 0.00 0.00 4.70
853 931 3.746751 GCTCCATGCCTATTGTCTGTCAT 60.747 47.826 0.00 0.00 35.15 3.06
859 937 2.357009 CACTTGCTCCATGCCTATTGTC 59.643 50.000 0.00 0.00 42.00 3.18
860 938 2.025981 TCACTTGCTCCATGCCTATTGT 60.026 45.455 0.00 0.00 42.00 2.71
861 939 2.617308 CTCACTTGCTCCATGCCTATTG 59.383 50.000 0.00 0.00 42.00 1.90
862 940 2.240667 ACTCACTTGCTCCATGCCTATT 59.759 45.455 0.00 0.00 42.00 1.73
880 958 1.908340 ATGGAGCTGGAGGTGCACTC 61.908 60.000 17.98 11.88 46.01 3.51
881 959 1.495579 AATGGAGCTGGAGGTGCACT 61.496 55.000 17.98 2.27 46.01 4.40
882 960 0.610232 AAATGGAGCTGGAGGTGCAC 60.610 55.000 8.80 8.80 46.01 4.57
961 1039 2.684881 CACTGCTTCCTTGTCTTGTGTT 59.315 45.455 0.00 0.00 0.00 3.32
987 1072 0.034059 ACGCCATGGATGCTAGCTAC 59.966 55.000 18.40 9.57 0.00 3.58
988 1073 0.033920 CACGCCATGGATGCTAGCTA 59.966 55.000 18.40 2.58 0.00 3.32
1052 1137 2.101750 GCTCTACCTCTTCTGGCCTTAC 59.898 54.545 3.32 0.00 0.00 2.34
1054 1139 1.199615 GCTCTACCTCTTCTGGCCTT 58.800 55.000 3.32 0.00 0.00 4.35
1155 1243 2.040988 TCCCCGGAGATGATGGCA 60.041 61.111 0.73 0.00 0.00 4.92
1218 1306 0.539051 GCTGCTGTGACTGGAGGTAT 59.461 55.000 12.40 0.00 0.00 2.73
1230 1318 2.122797 TTGTTGCTGCTGCTGCTGT 61.123 52.632 27.67 0.00 39.81 4.40
1250 1338 2.120909 CCGGCATGGGATGGTTGTC 61.121 63.158 0.00 0.00 0.00 3.18
1257 1345 3.541950 CTGATCGCCGGCATGGGAT 62.542 63.158 28.98 20.58 38.63 3.85
1278 1366 4.202398 ACCACAAGATCAGCAAGAAGAAGA 60.202 41.667 0.00 0.00 0.00 2.87
1299 1388 1.956477 GAGAGGAGATGAGCAGAGACC 59.044 57.143 0.00 0.00 0.00 3.85
1307 1396 4.342951 AGAAGCATCAAGAGAGGAGATGAG 59.657 45.833 5.88 0.00 41.18 2.90
1308 1397 4.288398 AGAAGCATCAAGAGAGGAGATGA 58.712 43.478 5.88 0.00 41.18 2.92
1335 1424 4.734398 AAGAGACTACAAGATCAGCAGG 57.266 45.455 0.00 0.00 0.00 4.85
1336 1425 5.718146 TGAAAGAGACTACAAGATCAGCAG 58.282 41.667 0.00 0.00 0.00 4.24
1337 1426 5.728637 TGAAAGAGACTACAAGATCAGCA 57.271 39.130 0.00 0.00 0.00 4.41
1338 1427 6.572519 AGATGAAAGAGACTACAAGATCAGC 58.427 40.000 0.00 0.00 0.00 4.26
1339 1428 7.068593 AGGAGATGAAAGAGACTACAAGATCAG 59.931 40.741 0.00 0.00 0.00 2.90
1340 1429 6.894654 AGGAGATGAAAGAGACTACAAGATCA 59.105 38.462 0.00 0.00 0.00 2.92
1341 1430 7.285401 AGAGGAGATGAAAGAGACTACAAGATC 59.715 40.741 0.00 0.00 0.00 2.75
1342 1431 7.125391 AGAGGAGATGAAAGAGACTACAAGAT 58.875 38.462 0.00 0.00 0.00 2.40
1343 1432 6.489603 AGAGGAGATGAAAGAGACTACAAGA 58.510 40.000 0.00 0.00 0.00 3.02
1344 1433 6.603201 AGAGAGGAGATGAAAGAGACTACAAG 59.397 42.308 0.00 0.00 0.00 3.16
1345 1434 6.489603 AGAGAGGAGATGAAAGAGACTACAA 58.510 40.000 0.00 0.00 0.00 2.41
1346 1435 6.073447 AGAGAGGAGATGAAAGAGACTACA 57.927 41.667 0.00 0.00 0.00 2.74
1347 1436 6.601613 TCAAGAGAGGAGATGAAAGAGACTAC 59.398 42.308 0.00 0.00 0.00 2.73
1348 1437 6.726379 TCAAGAGAGGAGATGAAAGAGACTA 58.274 40.000 0.00 0.00 0.00 2.59
1349 1438 5.579047 TCAAGAGAGGAGATGAAAGAGACT 58.421 41.667 0.00 0.00 0.00 3.24
1350 1439 5.913137 TCAAGAGAGGAGATGAAAGAGAC 57.087 43.478 0.00 0.00 0.00 3.36
1351 1440 6.193504 TCATCAAGAGAGGAGATGAAAGAGA 58.806 40.000 0.00 0.00 43.56 3.10
1352 1441 6.468333 TCATCAAGAGAGGAGATGAAAGAG 57.532 41.667 0.00 0.00 43.56 2.85
1358 1447 4.610605 AGCATCATCAAGAGAGGAGATG 57.389 45.455 0.00 0.00 38.06 2.90
1359 1448 4.903049 AGAAGCATCATCAAGAGAGGAGAT 59.097 41.667 0.00 0.00 38.06 2.75
1360 1449 4.288398 AGAAGCATCATCAAGAGAGGAGA 58.712 43.478 0.00 0.00 38.06 3.71
1361 1450 4.675976 AGAAGCATCATCAAGAGAGGAG 57.324 45.455 0.00 0.00 38.06 3.69
1362 1451 4.715792 AGAAGAAGCATCATCAAGAGAGGA 59.284 41.667 0.00 0.00 39.13 3.71
1363 1452 5.026038 AGAAGAAGCATCATCAAGAGAGG 57.974 43.478 0.00 0.00 0.00 3.69
1364 1453 5.524646 GGAAGAAGAAGCATCATCAAGAGAG 59.475 44.000 0.00 0.00 0.00 3.20
1365 1454 5.189342 AGGAAGAAGAAGCATCATCAAGAGA 59.811 40.000 0.00 0.00 0.00 3.10
1366 1455 5.294799 CAGGAAGAAGAAGCATCATCAAGAG 59.705 44.000 0.00 0.00 0.00 2.85
1367 1456 5.183969 CAGGAAGAAGAAGCATCATCAAGA 58.816 41.667 0.00 0.00 0.00 3.02
1368 1457 4.201930 GCAGGAAGAAGAAGCATCATCAAG 60.202 45.833 0.00 0.00 0.00 3.02
1369 1458 3.693085 GCAGGAAGAAGAAGCATCATCAA 59.307 43.478 0.00 0.00 0.00 2.57
1370 1459 3.054582 AGCAGGAAGAAGAAGCATCATCA 60.055 43.478 0.00 0.00 0.00 3.07
1371 1460 3.312973 CAGCAGGAAGAAGAAGCATCATC 59.687 47.826 0.00 0.00 0.00 2.92
1372 1461 3.054582 TCAGCAGGAAGAAGAAGCATCAT 60.055 43.478 0.00 0.00 0.00 2.45
1373 1462 2.303890 TCAGCAGGAAGAAGAAGCATCA 59.696 45.455 0.00 0.00 0.00 3.07
1374 1463 2.983229 TCAGCAGGAAGAAGAAGCATC 58.017 47.619 0.00 0.00 0.00 3.91
1375 1464 3.200385 AGATCAGCAGGAAGAAGAAGCAT 59.800 43.478 0.00 0.00 0.00 3.79
1376 1465 2.570752 AGATCAGCAGGAAGAAGAAGCA 59.429 45.455 0.00 0.00 0.00 3.91
1377 1466 3.264998 AGATCAGCAGGAAGAAGAAGC 57.735 47.619 0.00 0.00 0.00 3.86
1378 1467 4.577875 ACAAGATCAGCAGGAAGAAGAAG 58.422 43.478 0.00 0.00 0.00 2.85
1379 1468 4.630644 ACAAGATCAGCAGGAAGAAGAA 57.369 40.909 0.00 0.00 0.00 2.52
1380 1469 4.774726 ACTACAAGATCAGCAGGAAGAAGA 59.225 41.667 0.00 0.00 0.00 2.87
1381 1470 5.083533 ACTACAAGATCAGCAGGAAGAAG 57.916 43.478 0.00 0.00 0.00 2.85
1382 1471 4.774726 AGACTACAAGATCAGCAGGAAGAA 59.225 41.667 0.00 0.00 0.00 2.52
1383 1472 4.348486 AGACTACAAGATCAGCAGGAAGA 58.652 43.478 0.00 0.00 0.00 2.87
1384 1473 4.402155 AGAGACTACAAGATCAGCAGGAAG 59.598 45.833 0.00 0.00 0.00 3.46
1385 1474 4.159321 CAGAGACTACAAGATCAGCAGGAA 59.841 45.833 0.00 0.00 0.00 3.36
1386 1475 3.698539 CAGAGACTACAAGATCAGCAGGA 59.301 47.826 0.00 0.00 0.00 3.86
1502 1595 4.451150 GGCGTCGACATGGCCTCA 62.451 66.667 21.43 0.00 43.52 3.86
1571 1664 3.655810 GAGGCCTGACACGAGCTGG 62.656 68.421 12.00 0.00 0.00 4.85
1616 1709 2.906388 TTGACGACGACCCCGACA 60.906 61.111 0.00 0.00 39.50 4.35
1702 1795 2.223386 GCGGCAAAGAGTTGTGTGTAAA 60.223 45.455 0.00 0.00 37.06 2.01
1703 1796 1.332375 GCGGCAAAGAGTTGTGTGTAA 59.668 47.619 0.00 0.00 37.06 2.41
1704 1797 0.941542 GCGGCAAAGAGTTGTGTGTA 59.058 50.000 0.00 0.00 37.06 2.90
1705 1798 1.724582 GGCGGCAAAGAGTTGTGTGT 61.725 55.000 3.07 0.00 37.06 3.72
1729 1822 1.640917 TTAGTTCTTCTGTCGGGCCT 58.359 50.000 0.84 0.00 0.00 5.19
1732 1825 4.448060 GTCTGTTTTAGTTCTTCTGTCGGG 59.552 45.833 0.00 0.00 0.00 5.14
1745 1841 9.405587 TGTGTTTTCTTTTTCTGTCTGTTTTAG 57.594 29.630 0.00 0.00 0.00 1.85
1746 1842 9.751542 TTGTGTTTTCTTTTTCTGTCTGTTTTA 57.248 25.926 0.00 0.00 0.00 1.52
1751 1848 6.089417 GTGGTTGTGTTTTCTTTTTCTGTCTG 59.911 38.462 0.00 0.00 0.00 3.51
1772 1869 4.331968 CAACTTGTATATGTGGGTGTGGT 58.668 43.478 0.00 0.00 0.00 4.16
1798 1895 0.767375 ACAAGATGGTGGTGCTGAGT 59.233 50.000 0.00 0.00 0.00 3.41
1804 1901 1.682854 AGCAAACACAAGATGGTGGTG 59.317 47.619 0.00 0.00 37.84 4.17
1806 1903 4.460382 AGATTAGCAAACACAAGATGGTGG 59.540 41.667 0.00 0.00 43.08 4.61
1977 2074 2.813754 GTTGGCATCACATGTGTGTACT 59.186 45.455 24.63 4.09 45.76 2.73
2089 2189 2.387125 TTCGCTGCTGGTTTTGTCGC 62.387 55.000 0.00 0.00 0.00 5.19
2122 2222 8.114102 TCGATGTTAAGGGGATGATAGTAGTAT 58.886 37.037 0.00 0.00 0.00 2.12
2126 2226 6.312529 AGTCGATGTTAAGGGGATGATAGTA 58.687 40.000 0.00 0.00 0.00 1.82
2128 2228 5.730296 AGTCGATGTTAAGGGGATGATAG 57.270 43.478 0.00 0.00 0.00 2.08
2179 2390 6.483640 CCTGTTAGCAGTGTTTAGAATATCCC 59.516 42.308 5.81 0.00 41.02 3.85
2336 2549 7.387948 ACTGCAAACACTTTTACAGACTATAGG 59.612 37.037 4.43 0.00 38.06 2.57
2389 2602 4.460731 ACAAGGAAAAGCTCTCCTAAATGC 59.539 41.667 15.83 0.00 42.77 3.56
2391 2604 8.164070 TCTTTACAAGGAAAAGCTCTCCTAAAT 58.836 33.333 15.83 8.49 42.77 1.40
2444 2657 4.202315 TGTGCAGATACCAAACAGTACAGT 60.202 41.667 0.00 0.00 0.00 3.55
2445 2658 4.152402 GTGTGCAGATACCAAACAGTACAG 59.848 45.833 0.00 0.00 0.00 2.74
2451 2664 2.535012 TCGTGTGCAGATACCAAACA 57.465 45.000 0.00 0.00 0.00 2.83
2454 2667 3.818210 ACATTTTCGTGTGCAGATACCAA 59.182 39.130 0.00 0.00 0.00 3.67
2498 2714 3.363341 TGTTTTTCTTGCCGTGGAATC 57.637 42.857 0.00 0.00 0.00 2.52
2506 2722 6.841119 ACAATGAGTTTTTGTTTTTCTTGCC 58.159 32.000 0.00 0.00 33.64 4.52
2528 2744 7.811282 TGCCTCCATTCCTCTTAAATATTACA 58.189 34.615 0.00 0.00 0.00 2.41
2529 2745 8.691661 TTGCCTCCATTCCTCTTAAATATTAC 57.308 34.615 0.00 0.00 0.00 1.89
2534 2750 6.210185 GCATATTGCCTCCATTCCTCTTAAAT 59.790 38.462 0.00 0.00 37.42 1.40
2538 2754 3.139770 AGCATATTGCCTCCATTCCTCTT 59.860 43.478 0.00 0.00 46.52 2.85
2542 2758 5.789643 TTTAAGCATATTGCCTCCATTCC 57.210 39.130 0.00 0.00 46.52 3.01
2568 2784 5.419788 TCATGATCAATTTATAGGCATGCCC 59.580 40.000 33.14 15.39 36.58 5.36
2615 2831 9.223099 GATATATCATCATTGTCCATGAACACA 57.777 33.333 7.89 0.00 45.45 3.72
2624 2840 8.948631 AACCGTATGATATATCATCATTGTCC 57.051 34.615 27.58 10.12 43.72 4.02
2635 2851 7.004555 TGCTTCTGGAAACCGTATGATATAT 57.995 36.000 0.00 0.00 0.00 0.86
2640 2856 2.301870 ACTGCTTCTGGAAACCGTATGA 59.698 45.455 0.00 0.00 0.00 2.15
2722 2938 7.487484 TGCACTTCTTGTTGTTAATCATGAAA 58.513 30.769 0.00 0.00 31.08 2.69
2738 2954 3.279434 AGGAACTTCGTTTGCACTTCTT 58.721 40.909 0.00 0.00 27.25 2.52
2780 2996 3.862642 GCTCAAAGGCATATAGTCCTCGG 60.863 52.174 0.00 0.00 0.00 4.63
2788 3004 7.408756 AAAATGAAGTGCTCAAAGGCATATA 57.591 32.000 0.00 0.00 44.34 0.86
2789 3005 5.927281 AAATGAAGTGCTCAAAGGCATAT 57.073 34.783 0.00 0.00 44.34 1.78
2825 3043 6.096846 GGATGTCCAATAAATAAAGGCACTGT 59.903 38.462 0.00 0.00 35.23 3.55
2849 3068 3.057736 CCTGAAGTGCTCAAAGATGTTGG 60.058 47.826 0.00 0.00 32.17 3.77
2902 3121 4.323792 CCTCCTTTCTCTTGCATTGTCCTA 60.324 45.833 0.00 0.00 0.00 2.94
2926 3145 2.028420 GGCATTCATTGGCCTTTTCC 57.972 50.000 3.32 0.00 46.74 3.13
2962 3181 4.886579 AGTTCCTTCACATTTGAATTGGC 58.113 39.130 0.00 0.00 41.05 4.52
3113 3332 4.412796 TTCTGCTGCTAGTATTGCATCT 57.587 40.909 0.00 0.00 39.86 2.90
3130 3349 1.159713 TGCGTCAGTGGCTGTTTCTG 61.160 55.000 0.00 0.00 32.61 3.02


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

AutoCloner maintained by Alex Coulton.