Multiple sequence alignment - TraesCS6D01G040100

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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 TraesCS6D01G040100 chr6D 100.000 2968 0 0 1 2968 16374609 16377576 0.000000e+00 5481.0
1 TraesCS6D01G040100 chr6D 86.389 1058 82 24 1971 2968 14438884 14439939 0.000000e+00 1099.0
2 TraesCS6D01G040100 chr6D 86.066 1055 83 25 1971 2968 14484909 14485956 0.000000e+00 1075.0
3 TraesCS6D01G040100 chr6D 89.548 641 65 2 1337 1976 14940626 14939987 0.000000e+00 811.0
4 TraesCS6D01G040100 chr6D 83.673 637 98 6 1337 1970 14435631 14436264 1.970000e-166 595.0
5 TraesCS6D01G040100 chr6D 83.420 579 82 13 525 1095 14727354 14726782 2.620000e-145 525.0
6 TraesCS6D01G040100 chr6D 96.667 240 8 0 1097 1336 48073574 48073813 1.660000e-107 399.0
7 TraesCS6D01G040100 chr6D 95.455 242 11 0 1095 1336 284074778 284075019 1.290000e-103 387.0
8 TraesCS6D01G040100 chr6D 88.288 111 13 0 2853 2963 15355953 15355843 1.860000e-27 134.0
9 TraesCS6D01G040100 chr6B 94.455 1010 36 5 1975 2968 28729782 28728777 0.000000e+00 1537.0
10 TraesCS6D01G040100 chr6B 95.956 643 23 3 1337 1976 28730466 28729824 0.000000e+00 1040.0
11 TraesCS6D01G040100 chr6B 84.476 1050 79 33 1975 2968 26501729 26502750 0.000000e+00 959.0
12 TraesCS6D01G040100 chr6B 97.387 421 11 0 1556 1976 28495978 28496398 0.000000e+00 717.0
13 TraesCS6D01G040100 chr6B 86.092 568 65 11 530 1096 26500507 26501061 1.520000e-167 599.0
14 TraesCS6D01G040100 chr6B 95.418 371 17 0 2142 2512 28502198 28502568 2.550000e-165 592.0
15 TraesCS6D01G040100 chr6B 83.141 694 56 22 1971 2605 26489820 26490511 7.130000e-161 577.0
16 TraesCS6D01G040100 chr6B 89.027 483 24 5 373 855 28495505 28495958 3.320000e-159 571.0
17 TraesCS6D01G040100 chr6B 88.387 465 45 5 639 1095 28730920 28730457 4.320000e-153 551.0
18 TraesCS6D01G040100 chr6B 79.332 779 124 25 1341 2090 27058345 27057575 2.040000e-141 512.0
19 TraesCS6D01G040100 chr6B 81.201 633 117 2 1341 1972 26291852 26292483 2.640000e-140 508.0
20 TraesCS6D01G040100 chr6B 86.400 375 19 9 1 361 28494874 28495230 6.000000e-102 381.0
21 TraesCS6D01G040100 chr6B 86.217 341 16 12 39 361 28731716 28731389 1.020000e-89 340.0
22 TraesCS6D01G040100 chr6B 88.841 233 10 3 373 601 28731133 28730913 3.770000e-69 272.0
23 TraesCS6D01G040100 chr6B 87.701 187 7 1 1975 2145 28496436 28496622 1.390000e-48 204.0
24 TraesCS6D01G040100 chr6B 100.000 47 0 0 1 47 28739538 28739492 1.470000e-13 87.9
25 TraesCS6D01G040100 chr6A 86.711 1061 76 25 1971 2968 15686074 15687132 0.000000e+00 1118.0
26 TraesCS6D01G040100 chr6A 82.749 1055 86 42 1975 2967 15923999 15922979 0.000000e+00 852.0
27 TraesCS6D01G040100 chr6A 90.338 621 58 2 1337 1956 15924705 15924086 0.000000e+00 813.0
28 TraesCS6D01G040100 chr6A 85.240 542 67 10 531 1062 15647260 15647798 2.010000e-151 545.0
29 TraesCS6D01G040100 chr6A 83.595 573 76 14 535 1095 15873216 15872650 3.390000e-144 521.0
30 TraesCS6D01G040100 chr6A 96.203 316 11 1 2653 2968 16652586 16652900 1.580000e-142 516.0
31 TraesCS6D01G040100 chr6A 81.359 633 110 8 1342 1970 15906411 15905783 2.640000e-140 508.0
32 TraesCS6D01G040100 chr6A 82.013 606 90 17 487 1086 16628934 16629526 5.710000e-137 497.0
33 TraesCS6D01G040100 chr6A 85.523 373 15 12 2 361 16651355 16651701 1.310000e-93 353.0
34 TraesCS6D01G040100 chr6A 83.824 340 39 8 2635 2968 15688963 15689292 2.870000e-80 309.0
35 TraesCS6D01G040100 chr6A 96.450 169 6 0 2139 2307 15688365 15688533 2.250000e-71 279.0
36 TraesCS6D01G040100 chr6A 89.189 111 12 0 2853 2963 15937738 15937628 3.990000e-29 139.0
37 TraesCS6D01G040100 chr5D 86.016 851 53 27 1975 2768 27984277 27983436 0.000000e+00 852.0
38 TraesCS6D01G040100 chr5D 88.530 619 65 6 1337 1952 27978776 27978161 0.000000e+00 745.0
39 TraesCS6D01G040100 chr5D 89.827 521 50 3 576 1095 27979285 27978767 0.000000e+00 665.0
40 TraesCS6D01G040100 chr4B 87.840 625 66 9 1339 1956 575726639 575727260 0.000000e+00 725.0
41 TraesCS6D01G040100 chr4B 87.633 566 60 10 535 1095 575726086 575726646 0.000000e+00 649.0
42 TraesCS6D01G040100 chr1B 83.494 624 95 8 1337 1956 48061816 48061197 2.570000e-160 575.0
43 TraesCS6D01G040100 chr1B 83.420 579 85 10 526 1099 48062375 48061803 7.290000e-146 527.0
44 TraesCS6D01G040100 chr1D 96.281 242 9 0 1095 1336 393730977 393730736 5.960000e-107 398.0
45 TraesCS6D01G040100 chr1D 95.868 242 10 0 1095 1336 155778551 155778792 2.770000e-105 392.0
46 TraesCS6D01G040100 chr7D 96.281 242 7 1 1095 1336 561742474 561742713 2.140000e-106 396.0
47 TraesCS6D01G040100 chr7D 85.246 183 15 3 105 275 182428550 182428732 8.450000e-41 178.0
48 TraesCS6D01G040100 chr2D 95.473 243 10 1 1095 1336 49068734 49068492 1.290000e-103 387.0
49 TraesCS6D01G040100 chr4D 95.041 242 12 0 1095 1336 16113808 16113567 6.000000e-102 381.0
50 TraesCS6D01G040100 chr4D 95.021 241 11 1 1097 1336 501177714 501177474 7.770000e-101 377.0
51 TraesCS6D01G040100 chr3D 95.000 240 10 2 1098 1336 18664392 18664630 2.790000e-100 375.0
52 TraesCS6D01G040100 chr2B 89.655 116 10 2 140 255 789453596 789453709 2.380000e-31 147.0
53 TraesCS6D01G040100 chr5B 91.304 69 6 0 130 198 432157610 432157678 8.760000e-16 95.3


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 TraesCS6D01G040100 chr6D 16374609 16377576 2967 False 5481.000000 5481 100.00000 1 2968 1 chr6D.!!$F2 2967
1 TraesCS6D01G040100 chr6D 14484909 14485956 1047 False 1075.000000 1075 86.06600 1971 2968 1 chr6D.!!$F1 997
2 TraesCS6D01G040100 chr6D 14435631 14439939 4308 False 847.000000 1099 85.03100 1337 2968 2 chr6D.!!$F5 1631
3 TraesCS6D01G040100 chr6D 14939987 14940626 639 True 811.000000 811 89.54800 1337 1976 1 chr6D.!!$R2 639
4 TraesCS6D01G040100 chr6D 14726782 14727354 572 True 525.000000 525 83.42000 525 1095 1 chr6D.!!$R1 570
5 TraesCS6D01G040100 chr6B 26500507 26502750 2243 False 779.000000 959 85.28400 530 2968 2 chr6B.!!$F4 2438
6 TraesCS6D01G040100 chr6B 28728777 28731716 2939 True 748.000000 1537 90.77120 39 2968 5 chr6B.!!$R3 2929
7 TraesCS6D01G040100 chr6B 26489820 26490511 691 False 577.000000 577 83.14100 1971 2605 1 chr6B.!!$F2 634
8 TraesCS6D01G040100 chr6B 27057575 27058345 770 True 512.000000 512 79.33200 1341 2090 1 chr6B.!!$R1 749
9 TraesCS6D01G040100 chr6B 26291852 26292483 631 False 508.000000 508 81.20100 1341 1972 1 chr6B.!!$F1 631
10 TraesCS6D01G040100 chr6B 28494874 28496622 1748 False 468.250000 717 90.12875 1 2145 4 chr6B.!!$F5 2144
11 TraesCS6D01G040100 chr6A 15922979 15924705 1726 True 832.500000 852 86.54350 1337 2967 2 chr6A.!!$R4 1630
12 TraesCS6D01G040100 chr6A 15686074 15689292 3218 False 568.666667 1118 88.99500 1971 2968 3 chr6A.!!$F3 997
13 TraesCS6D01G040100 chr6A 15647260 15647798 538 False 545.000000 545 85.24000 531 1062 1 chr6A.!!$F1 531
14 TraesCS6D01G040100 chr6A 15872650 15873216 566 True 521.000000 521 83.59500 535 1095 1 chr6A.!!$R1 560
15 TraesCS6D01G040100 chr6A 15905783 15906411 628 True 508.000000 508 81.35900 1342 1970 1 chr6A.!!$R2 628
16 TraesCS6D01G040100 chr6A 16628934 16629526 592 False 497.000000 497 82.01300 487 1086 1 chr6A.!!$F2 599
17 TraesCS6D01G040100 chr6A 16651355 16652900 1545 False 434.500000 516 90.86300 2 2968 2 chr6A.!!$F4 2966
18 TraesCS6D01G040100 chr5D 27983436 27984277 841 True 852.000000 852 86.01600 1975 2768 1 chr5D.!!$R1 793
19 TraesCS6D01G040100 chr5D 27978161 27979285 1124 True 705.000000 745 89.17850 576 1952 2 chr5D.!!$R2 1376
20 TraesCS6D01G040100 chr4B 575726086 575727260 1174 False 687.000000 725 87.73650 535 1956 2 chr4B.!!$F1 1421
21 TraesCS6D01G040100 chr1B 48061197 48062375 1178 True 551.000000 575 83.45700 526 1956 2 chr1B.!!$R1 1430

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
604 930 0.257616 CCTTCTCCTCCTCTCCTCGT 59.742 60.0 0.0 0.0 0.0 4.18 F
1209 1657 0.110056 CAGTCAAACGAGCACATGGC 60.110 55.0 0.0 0.0 45.3 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1410 1861 0.251832 ATCCTCGACACAGGGACACT 60.252 55.0 0.0 0.0 33.81 3.55 R
2151 5286 0.877071 CGTTGCCATGAAAGCAGACT 59.123 50.0 0.0 0.0 42.17 3.24 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
57 58 6.039717 GGTTGCATCATGGTGTGTATCTTAAT 59.960 38.462 8.00 0.00 0.00 1.40
62 63 8.620416 GCATCATGGTGTGTATCTTAATTGTTA 58.380 33.333 8.00 0.00 0.00 2.41
85 86 9.632807 GTTATGGACATGCTTTAAATGTTGTAA 57.367 29.630 0.00 0.00 38.37 2.41
138 143 6.241645 AGCTAAAAAGCTGTGGAATTCTAGT 58.758 36.000 5.23 0.00 44.44 2.57
235 251 2.276740 CCTTGAGGCCATGGGTCC 59.723 66.667 15.13 7.13 34.82 4.46
236 252 2.615465 CCTTGAGGCCATGGGTCCA 61.615 63.158 15.13 0.00 34.82 4.02
237 253 1.077212 CTTGAGGCCATGGGTCCAG 60.077 63.158 15.13 0.00 0.00 3.86
238 254 2.563013 CTTGAGGCCATGGGTCCAGG 62.563 65.000 15.13 0.00 0.00 4.45
239 255 3.017581 GAGGCCATGGGTCCAGGT 61.018 66.667 15.13 0.00 0.00 4.00
240 256 3.017581 AGGCCATGGGTCCAGGTC 61.018 66.667 15.13 2.14 0.00 3.85
241 257 4.129148 GGCCATGGGTCCAGGTCC 62.129 72.222 15.13 0.00 0.00 4.46
242 258 3.338250 GCCATGGGTCCAGGTCCA 61.338 66.667 15.13 5.95 37.46 4.02
243 259 2.917897 GCCATGGGTCCAGGTCCAA 61.918 63.158 15.13 0.00 36.54 3.53
244 260 1.304282 CCATGGGTCCAGGTCCAAG 59.696 63.158 2.85 2.93 36.54 3.61
245 261 1.304282 CATGGGTCCAGGTCCAAGG 59.696 63.158 4.97 0.00 36.54 3.61
246 262 2.616458 ATGGGTCCAGGTCCAAGGC 61.616 63.158 4.97 0.00 36.54 4.35
247 263 4.048470 GGGTCCAGGTCCAAGGCC 62.048 72.222 4.97 0.00 0.00 5.19
248 264 3.256960 GGTCCAGGTCCAAGGCCA 61.257 66.667 5.01 0.00 0.00 5.36
288 312 2.350522 CCATCTTCTCCAAACACTCGG 58.649 52.381 0.00 0.00 0.00 4.63
371 396 0.881118 GAAAGCTTCGTCCATTGGCA 59.119 50.000 0.00 0.00 0.00 4.92
468 779 1.180029 GATTGCAGCCCATTCACACT 58.820 50.000 0.00 0.00 0.00 3.55
581 907 3.839432 CCTCCGAAGCTCCGTCCC 61.839 72.222 0.00 0.00 0.00 4.46
595 921 1.996187 GTCCCCACCCTTCTCCTCC 60.996 68.421 0.00 0.00 0.00 4.30
596 922 2.184631 TCCCCACCCTTCTCCTCCT 61.185 63.158 0.00 0.00 0.00 3.69
602 928 0.634465 ACCCTTCTCCTCCTCTCCTC 59.366 60.000 0.00 0.00 0.00 3.71
603 929 0.467290 CCCTTCTCCTCCTCTCCTCG 60.467 65.000 0.00 0.00 0.00 4.63
604 930 0.257616 CCTTCTCCTCCTCTCCTCGT 59.742 60.000 0.00 0.00 0.00 4.18
665 1024 3.061848 CGCCGCAGACCCCATTTT 61.062 61.111 0.00 0.00 0.00 1.82
678 1037 1.389555 CCATTTTCCCGAACCCTAGC 58.610 55.000 0.00 0.00 0.00 3.42
686 1045 1.215647 CGAACCCTAGCAGCTTCGT 59.784 57.895 0.00 0.00 32.65 3.85
1004 1452 0.877649 CCCATCGTCTCCAAGATGCG 60.878 60.000 0.33 0.00 41.98 4.73
1086 1534 1.438562 GCCTACTCTCGTCGGACCTC 61.439 65.000 1.91 0.00 0.00 3.85
1088 1536 1.152989 CTACTCTCGTCGGACCTCGG 61.153 65.000 1.91 0.00 39.77 4.63
1118 1566 4.939509 TTTTTGGAACATAGACGCTAGC 57.060 40.909 4.06 4.06 39.30 3.42
1119 1567 3.603158 TTTGGAACATAGACGCTAGCA 57.397 42.857 16.45 0.00 39.30 3.49
1120 1568 2.871182 TGGAACATAGACGCTAGCAG 57.129 50.000 16.45 10.16 0.00 4.24
1121 1569 1.202417 TGGAACATAGACGCTAGCAGC 60.202 52.381 16.45 5.57 38.02 5.25
1141 1589 4.863152 GCGTCCGGCTTTAACTTAATAA 57.137 40.909 0.00 0.00 39.11 1.40
1142 1590 5.220557 GCGTCCGGCTTTAACTTAATAAA 57.779 39.130 0.00 0.00 39.11 1.40
1143 1591 5.260900 GCGTCCGGCTTTAACTTAATAAAG 58.739 41.667 0.00 4.78 42.93 1.85
1161 1609 4.326255 CCACCAGGCAGAATCCAC 57.674 61.111 0.00 0.00 0.00 4.02
1162 1610 1.379916 CCACCAGGCAGAATCCACA 59.620 57.895 0.00 0.00 0.00 4.17
1163 1611 0.962356 CCACCAGGCAGAATCCACAC 60.962 60.000 0.00 0.00 0.00 3.82
1164 1612 0.250858 CACCAGGCAGAATCCACACA 60.251 55.000 0.00 0.00 0.00 3.72
1165 1613 0.700564 ACCAGGCAGAATCCACACAT 59.299 50.000 0.00 0.00 0.00 3.21
1166 1614 1.915489 ACCAGGCAGAATCCACACATA 59.085 47.619 0.00 0.00 0.00 2.29
1167 1615 2.092753 ACCAGGCAGAATCCACACATAG 60.093 50.000 0.00 0.00 0.00 2.23
1168 1616 2.171237 CCAGGCAGAATCCACACATAGA 59.829 50.000 0.00 0.00 0.00 1.98
1169 1617 3.464907 CAGGCAGAATCCACACATAGAG 58.535 50.000 0.00 0.00 0.00 2.43
1170 1618 3.110705 AGGCAGAATCCACACATAGAGT 58.889 45.455 0.00 0.00 0.00 3.24
1171 1619 3.133721 AGGCAGAATCCACACATAGAGTC 59.866 47.826 0.00 0.00 0.00 3.36
1172 1620 3.133721 GGCAGAATCCACACATAGAGTCT 59.866 47.826 0.00 0.00 37.91 3.24
1173 1621 4.383552 GGCAGAATCCACACATAGAGTCTT 60.384 45.833 0.00 0.00 35.39 3.01
1174 1622 5.163405 GGCAGAATCCACACATAGAGTCTTA 60.163 44.000 0.00 0.00 35.39 2.10
1175 1623 5.751028 GCAGAATCCACACATAGAGTCTTAC 59.249 44.000 0.00 0.00 35.39 2.34
1176 1624 6.628175 GCAGAATCCACACATAGAGTCTTACA 60.628 42.308 0.00 0.00 35.39 2.41
1177 1625 7.323420 CAGAATCCACACATAGAGTCTTACAA 58.677 38.462 0.00 0.00 35.39 2.41
1178 1626 7.490725 CAGAATCCACACATAGAGTCTTACAAG 59.509 40.741 0.00 0.00 35.39 3.16
1179 1627 5.073311 TCCACACATAGAGTCTTACAAGC 57.927 43.478 0.00 0.00 0.00 4.01
1180 1628 4.081642 TCCACACATAGAGTCTTACAAGCC 60.082 45.833 0.00 0.00 0.00 4.35
1181 1629 4.322725 CCACACATAGAGTCTTACAAGCCA 60.323 45.833 0.00 0.00 0.00 4.75
1182 1630 5.237815 CACACATAGAGTCTTACAAGCCAA 58.762 41.667 0.00 0.00 0.00 4.52
1183 1631 5.700832 CACACATAGAGTCTTACAAGCCAAA 59.299 40.000 0.00 0.00 0.00 3.28
1184 1632 6.372659 CACACATAGAGTCTTACAAGCCAAAT 59.627 38.462 0.00 0.00 0.00 2.32
1185 1633 7.549134 CACACATAGAGTCTTACAAGCCAAATA 59.451 37.037 0.00 0.00 0.00 1.40
1186 1634 8.100791 ACACATAGAGTCTTACAAGCCAAATAA 58.899 33.333 0.00 0.00 0.00 1.40
1187 1635 8.946085 CACATAGAGTCTTACAAGCCAAATAAA 58.054 33.333 0.00 0.00 0.00 1.40
1188 1636 9.167311 ACATAGAGTCTTACAAGCCAAATAAAG 57.833 33.333 0.00 0.00 0.00 1.85
1189 1637 9.383519 CATAGAGTCTTACAAGCCAAATAAAGA 57.616 33.333 0.00 0.00 0.00 2.52
1190 1638 7.674471 AGAGTCTTACAAGCCAAATAAAGAC 57.326 36.000 5.16 5.16 41.86 3.01
1191 1639 7.224297 AGAGTCTTACAAGCCAAATAAAGACA 58.776 34.615 13.62 0.00 43.24 3.41
1192 1640 7.389053 AGAGTCTTACAAGCCAAATAAAGACAG 59.611 37.037 13.62 0.00 43.24 3.51
1193 1641 6.998673 AGTCTTACAAGCCAAATAAAGACAGT 59.001 34.615 13.62 0.00 43.24 3.55
1194 1642 7.173390 AGTCTTACAAGCCAAATAAAGACAGTC 59.827 37.037 13.62 0.00 43.24 3.51
1195 1643 6.995686 TCTTACAAGCCAAATAAAGACAGTCA 59.004 34.615 2.66 0.00 0.00 3.41
1196 1644 7.500892 TCTTACAAGCCAAATAAAGACAGTCAA 59.499 33.333 2.66 0.00 0.00 3.18
1197 1645 6.463995 ACAAGCCAAATAAAGACAGTCAAA 57.536 33.333 2.66 0.00 0.00 2.69
1198 1646 6.273071 ACAAGCCAAATAAAGACAGTCAAAC 58.727 36.000 2.66 0.00 0.00 2.93
1199 1647 5.108385 AGCCAAATAAAGACAGTCAAACG 57.892 39.130 2.66 0.00 0.00 3.60
1200 1648 4.819630 AGCCAAATAAAGACAGTCAAACGA 59.180 37.500 2.66 0.00 0.00 3.85
1201 1649 5.049405 AGCCAAATAAAGACAGTCAAACGAG 60.049 40.000 2.66 0.00 0.00 4.18
1202 1650 5.147162 CCAAATAAAGACAGTCAAACGAGC 58.853 41.667 2.66 0.00 0.00 5.03
1203 1651 5.277779 CCAAATAAAGACAGTCAAACGAGCA 60.278 40.000 2.66 0.00 0.00 4.26
1204 1652 4.992381 ATAAAGACAGTCAAACGAGCAC 57.008 40.909 2.66 0.00 0.00 4.40
1205 1653 2.309528 AAGACAGTCAAACGAGCACA 57.690 45.000 2.66 0.00 0.00 4.57
1206 1654 2.533266 AGACAGTCAAACGAGCACAT 57.467 45.000 2.66 0.00 0.00 3.21
1207 1655 2.138320 AGACAGTCAAACGAGCACATG 58.862 47.619 2.66 0.00 0.00 3.21
1208 1656 1.195448 GACAGTCAAACGAGCACATGG 59.805 52.381 0.00 0.00 0.00 3.66
1209 1657 0.110056 CAGTCAAACGAGCACATGGC 60.110 55.000 0.00 0.00 45.30 4.40
1221 1669 3.075866 GCACATGGCTCAAGATAAAGC 57.924 47.619 0.00 0.00 40.25 3.51
1222 1670 2.686915 GCACATGGCTCAAGATAAAGCT 59.313 45.455 0.00 0.00 40.25 3.74
1223 1671 3.879295 GCACATGGCTCAAGATAAAGCTA 59.121 43.478 0.00 0.00 40.25 3.32
1224 1672 4.336433 GCACATGGCTCAAGATAAAGCTAA 59.664 41.667 0.00 0.00 40.25 3.09
1225 1673 5.505324 GCACATGGCTCAAGATAAAGCTAAG 60.505 44.000 0.00 0.00 40.25 2.18
1226 1674 5.587844 CACATGGCTCAAGATAAAGCTAAGT 59.412 40.000 0.00 0.00 38.58 2.24
1227 1675 6.763135 CACATGGCTCAAGATAAAGCTAAGTA 59.237 38.462 0.00 0.00 38.58 2.24
1228 1676 6.989169 ACATGGCTCAAGATAAAGCTAAGTAG 59.011 38.462 0.00 0.00 38.58 2.57
1229 1677 6.791867 TGGCTCAAGATAAAGCTAAGTAGA 57.208 37.500 0.00 0.00 38.58 2.59
1230 1678 7.366847 TGGCTCAAGATAAAGCTAAGTAGAT 57.633 36.000 0.00 0.00 38.58 1.98
1231 1679 7.437748 TGGCTCAAGATAAAGCTAAGTAGATC 58.562 38.462 0.00 0.00 38.58 2.75
1232 1680 6.584563 GGCTCAAGATAAAGCTAAGTAGATCG 59.415 42.308 0.00 0.00 38.58 3.69
1233 1681 6.088883 GCTCAAGATAAAGCTAAGTAGATCGC 59.911 42.308 0.00 0.00 35.60 4.58
1234 1682 7.039313 TCAAGATAAAGCTAAGTAGATCGCA 57.961 36.000 0.00 0.00 0.00 5.10
1235 1683 7.142021 TCAAGATAAAGCTAAGTAGATCGCAG 58.858 38.462 0.00 0.00 0.00 5.18
1236 1684 5.465935 AGATAAAGCTAAGTAGATCGCAGC 58.534 41.667 0.00 0.00 0.00 5.25
1237 1685 2.517650 AAGCTAAGTAGATCGCAGCC 57.482 50.000 0.00 0.00 32.58 4.85
1238 1686 1.403814 AGCTAAGTAGATCGCAGCCA 58.596 50.000 0.00 0.00 32.58 4.75
1239 1687 1.067821 AGCTAAGTAGATCGCAGCCAC 59.932 52.381 0.00 0.00 32.58 5.01
1240 1688 1.202417 GCTAAGTAGATCGCAGCCACA 60.202 52.381 0.00 0.00 0.00 4.17
1241 1689 2.738643 GCTAAGTAGATCGCAGCCACAA 60.739 50.000 0.00 0.00 0.00 3.33
1242 1690 2.015736 AAGTAGATCGCAGCCACAAG 57.984 50.000 0.00 0.00 0.00 3.16
1243 1691 0.898320 AGTAGATCGCAGCCACAAGT 59.102 50.000 0.00 0.00 0.00 3.16
1244 1692 1.276421 AGTAGATCGCAGCCACAAGTT 59.724 47.619 0.00 0.00 0.00 2.66
1245 1693 1.661112 GTAGATCGCAGCCACAAGTTC 59.339 52.381 0.00 0.00 0.00 3.01
1246 1694 1.016130 AGATCGCAGCCACAAGTTCG 61.016 55.000 0.00 0.00 0.00 3.95
1247 1695 1.970917 GATCGCAGCCACAAGTTCGG 61.971 60.000 0.00 0.00 0.00 4.30
1248 1696 2.731691 ATCGCAGCCACAAGTTCGGT 62.732 55.000 0.00 0.00 0.00 4.69
1249 1697 1.666553 CGCAGCCACAAGTTCGGTA 60.667 57.895 0.00 0.00 0.00 4.02
1250 1698 1.225376 CGCAGCCACAAGTTCGGTAA 61.225 55.000 0.00 0.00 0.00 2.85
1251 1699 0.237498 GCAGCCACAAGTTCGGTAAC 59.763 55.000 0.00 0.00 35.72 2.50
1252 1700 1.588674 CAGCCACAAGTTCGGTAACA 58.411 50.000 0.00 0.00 38.12 2.41
1253 1701 1.263217 CAGCCACAAGTTCGGTAACAC 59.737 52.381 0.00 0.00 38.12 3.32
1254 1702 1.134340 AGCCACAAGTTCGGTAACACA 60.134 47.619 0.00 0.00 38.12 3.72
1255 1703 1.671845 GCCACAAGTTCGGTAACACAA 59.328 47.619 0.00 0.00 38.12 3.33
1256 1704 2.097791 GCCACAAGTTCGGTAACACAAA 59.902 45.455 0.00 0.00 38.12 2.83
1257 1705 3.243267 GCCACAAGTTCGGTAACACAAAT 60.243 43.478 0.00 0.00 38.12 2.32
1258 1706 4.286910 CCACAAGTTCGGTAACACAAATG 58.713 43.478 0.00 0.00 38.12 2.32
1259 1707 3.728718 CACAAGTTCGGTAACACAAATGC 59.271 43.478 0.00 0.00 38.12 3.56
1260 1708 3.378742 ACAAGTTCGGTAACACAAATGCA 59.621 39.130 0.00 0.00 38.12 3.96
1261 1709 3.896648 AGTTCGGTAACACAAATGCAG 57.103 42.857 0.00 0.00 38.12 4.41
1262 1710 3.472652 AGTTCGGTAACACAAATGCAGA 58.527 40.909 0.00 0.00 38.12 4.26
1263 1711 3.880490 AGTTCGGTAACACAAATGCAGAA 59.120 39.130 0.00 0.00 38.12 3.02
1264 1712 3.889196 TCGGTAACACAAATGCAGAAC 57.111 42.857 0.00 0.00 0.00 3.01
1265 1713 3.206964 TCGGTAACACAAATGCAGAACA 58.793 40.909 0.00 0.00 0.00 3.18
1266 1714 3.818210 TCGGTAACACAAATGCAGAACAT 59.182 39.130 0.00 0.00 42.30 2.71
1267 1715 4.083537 TCGGTAACACAAATGCAGAACATC 60.084 41.667 0.00 0.00 38.34 3.06
1268 1716 4.320129 CGGTAACACAAATGCAGAACATCA 60.320 41.667 0.00 0.00 38.34 3.07
1269 1717 5.527951 GGTAACACAAATGCAGAACATCAA 58.472 37.500 0.00 0.00 38.34 2.57
1270 1718 5.630680 GGTAACACAAATGCAGAACATCAAG 59.369 40.000 0.00 0.00 38.34 3.02
1271 1719 4.247267 ACACAAATGCAGAACATCAAGG 57.753 40.909 0.00 0.00 38.34 3.61
1272 1720 2.991190 CACAAATGCAGAACATCAAGGC 59.009 45.455 0.00 0.00 38.34 4.35
1273 1721 2.028748 ACAAATGCAGAACATCAAGGCC 60.029 45.455 0.00 0.00 38.34 5.19
1274 1722 1.927487 AATGCAGAACATCAAGGCCA 58.073 45.000 5.01 0.00 38.34 5.36
1275 1723 1.927487 ATGCAGAACATCAAGGCCAA 58.073 45.000 5.01 0.00 31.52 4.52
1276 1724 1.702182 TGCAGAACATCAAGGCCAAA 58.298 45.000 5.01 0.00 0.00 3.28
1277 1725 1.614903 TGCAGAACATCAAGGCCAAAG 59.385 47.619 5.01 0.00 0.00 2.77
1278 1726 1.670967 GCAGAACATCAAGGCCAAAGC 60.671 52.381 5.01 0.00 38.76 3.51
1279 1727 1.891150 CAGAACATCAAGGCCAAAGCT 59.109 47.619 5.01 0.00 39.73 3.74
1280 1728 3.084039 CAGAACATCAAGGCCAAAGCTA 58.916 45.455 5.01 0.00 39.73 3.32
1281 1729 3.128242 CAGAACATCAAGGCCAAAGCTAG 59.872 47.826 5.01 0.00 39.73 3.42
1282 1730 1.467920 ACATCAAGGCCAAAGCTAGC 58.532 50.000 6.62 6.62 39.73 3.42
1283 1731 1.272092 ACATCAAGGCCAAAGCTAGCA 60.272 47.619 18.83 0.00 39.73 3.49
1284 1732 1.820519 CATCAAGGCCAAAGCTAGCAA 59.179 47.619 18.83 0.00 39.73 3.91
1285 1733 1.993956 TCAAGGCCAAAGCTAGCAAA 58.006 45.000 18.83 0.00 39.73 3.68
1286 1734 2.315176 TCAAGGCCAAAGCTAGCAAAA 58.685 42.857 18.83 0.00 39.73 2.44
1287 1735 2.035832 TCAAGGCCAAAGCTAGCAAAAC 59.964 45.455 18.83 1.74 39.73 2.43
1288 1736 0.598065 AGGCCAAAGCTAGCAAAACG 59.402 50.000 18.83 0.86 39.73 3.60
1289 1737 0.596082 GGCCAAAGCTAGCAAAACGA 59.404 50.000 18.83 0.00 39.73 3.85
1290 1738 1.401539 GGCCAAAGCTAGCAAAACGAG 60.402 52.381 18.83 0.00 39.73 4.18
1291 1739 1.401539 GCCAAAGCTAGCAAAACGAGG 60.402 52.381 18.83 9.45 35.50 4.63
1292 1740 2.151202 CCAAAGCTAGCAAAACGAGGA 58.849 47.619 18.83 0.00 0.00 3.71
1293 1741 2.160417 CCAAAGCTAGCAAAACGAGGAG 59.840 50.000 18.83 0.00 0.00 3.69
1294 1742 2.100605 AAGCTAGCAAAACGAGGAGG 57.899 50.000 18.83 0.00 0.00 4.30
1295 1743 1.267121 AGCTAGCAAAACGAGGAGGA 58.733 50.000 18.83 0.00 0.00 3.71
1296 1744 1.834263 AGCTAGCAAAACGAGGAGGAT 59.166 47.619 18.83 0.00 0.00 3.24
1297 1745 2.159028 AGCTAGCAAAACGAGGAGGATC 60.159 50.000 18.83 0.00 0.00 3.36
1298 1746 2.418746 GCTAGCAAAACGAGGAGGATCA 60.419 50.000 10.63 0.00 36.25 2.92
1299 1747 3.742640 GCTAGCAAAACGAGGAGGATCAT 60.743 47.826 10.63 0.00 36.25 2.45
1300 1748 2.636830 AGCAAAACGAGGAGGATCATG 58.363 47.619 0.00 0.00 36.25 3.07
1301 1749 1.672881 GCAAAACGAGGAGGATCATGG 59.327 52.381 0.00 0.00 36.25 3.66
1302 1750 2.941415 GCAAAACGAGGAGGATCATGGT 60.941 50.000 0.00 0.00 40.23 3.55
1303 1751 2.679837 CAAAACGAGGAGGATCATGGTG 59.320 50.000 0.00 0.00 36.68 4.17
1304 1752 0.179000 AACGAGGAGGATCATGGTGC 59.821 55.000 0.00 0.00 36.68 5.01
1305 1753 0.977627 ACGAGGAGGATCATGGTGCA 60.978 55.000 0.00 0.00 36.24 4.57
1306 1754 0.249784 CGAGGAGGATCATGGTGCAG 60.250 60.000 0.00 0.00 36.25 4.41
1307 1755 0.534652 GAGGAGGATCATGGTGCAGC 60.535 60.000 9.47 9.47 36.25 5.25
1308 1756 1.527844 GGAGGATCATGGTGCAGCC 60.528 63.158 14.36 5.89 36.25 4.85
1316 1764 2.276409 TGGTGCAGCCATCATCCC 59.724 61.111 14.36 0.00 43.61 3.85
1317 1765 2.311070 TGGTGCAGCCATCATCCCT 61.311 57.895 14.36 0.00 43.61 4.20
1318 1766 1.076485 GGTGCAGCCATCATCCCTT 60.076 57.895 4.03 0.00 37.17 3.95
1319 1767 1.389609 GGTGCAGCCATCATCCCTTG 61.390 60.000 4.03 0.00 37.17 3.61
1320 1768 1.755395 TGCAGCCATCATCCCTTGC 60.755 57.895 0.00 0.00 0.00 4.01
1321 1769 2.496291 GCAGCCATCATCCCTTGCC 61.496 63.158 0.00 0.00 0.00 4.52
1322 1770 2.191513 CAGCCATCATCCCTTGCCG 61.192 63.158 0.00 0.00 0.00 5.69
1323 1771 3.599704 GCCATCATCCCTTGCCGC 61.600 66.667 0.00 0.00 0.00 6.53
1324 1772 3.282157 CCATCATCCCTTGCCGCG 61.282 66.667 0.00 0.00 0.00 6.46
1325 1773 3.957535 CATCATCCCTTGCCGCGC 61.958 66.667 0.00 0.00 0.00 6.86
1410 1861 1.134818 ACTGCGATATTGTCAAGCCGA 60.135 47.619 7.83 0.00 0.00 5.54
1637 4672 2.764010 TGCTTTGTCTAAGGCTCCGATA 59.236 45.455 0.00 0.00 39.43 2.92
2048 5153 2.017559 AACTGGACGCGGGCTATCTC 62.018 60.000 12.47 0.00 0.00 2.75
2151 5286 9.868160 TCATTCCTTAGAGAAGATATCAGTGTA 57.132 33.333 5.32 0.00 34.25 2.90
2190 5325 4.694339 ACGTTTATCTAGCATGTTCCCTC 58.306 43.478 0.00 0.00 0.00 4.30
2931 6115 2.550978 CAGGGATAACTAACCGTGCTG 58.449 52.381 0.00 0.00 35.76 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 8.147058 ACAACATTTAAAGCATGTCCATAACAA 58.853 29.630 0.00 0.00 42.37 2.83
62 63 9.206870 CTTTTACAACATTTAAAGCATGTCCAT 57.793 29.630 5.99 0.00 33.54 3.41
93 94 9.878667 TTAGCTATGTATACACTACTTTTGCAA 57.121 29.630 7.96 0.00 0.00 4.08
231 247 3.256960 TGGCCTTGGACCTGGACC 61.257 66.667 3.32 8.34 0.00 4.46
232 248 2.352805 CTGGCCTTGGACCTGGAC 59.647 66.667 3.32 5.75 0.00 4.02
233 249 2.935481 CCTGGCCTTGGACCTGGA 60.935 66.667 3.32 0.00 46.44 3.86
235 251 2.352805 GACCTGGCCTTGGACCTG 59.647 66.667 19.76 0.00 0.00 4.00
236 252 2.936032 GGACCTGGCCTTGGACCT 60.936 66.667 22.02 3.83 36.67 3.85
237 253 3.256960 TGGACCTGGCCTTGGACC 61.257 66.667 22.33 22.33 39.32 4.46
238 254 2.352805 CTGGACCTGGCCTTGGAC 59.647 66.667 19.76 14.04 0.00 4.02
239 255 2.935481 CCTGGACCTGGCCTTGGA 60.935 66.667 19.76 0.00 0.00 3.53
240 256 4.748144 GCCTGGACCTGGCCTTGG 62.748 72.222 27.74 9.23 41.62 3.61
246 262 4.394712 GTGTCGGCCTGGACCTGG 62.395 72.222 13.02 13.02 36.07 4.45
247 263 2.469465 AATGTGTCGGCCTGGACCTG 62.469 60.000 0.00 0.00 36.07 4.00
248 264 2.185310 GAATGTGTCGGCCTGGACCT 62.185 60.000 0.00 0.00 36.07 3.85
288 312 1.405933 GCTGGGGGCAATGACAAAATC 60.406 52.381 0.00 0.00 41.35 2.17
335 360 2.202570 CGCATTGGCAGAAGCAGC 60.203 61.111 8.28 0.00 44.61 5.25
361 386 4.142609 TCTTACATCTCTGCCAATGGAC 57.857 45.455 2.05 0.00 0.00 4.02
362 387 4.842531 TTCTTACATCTCTGCCAATGGA 57.157 40.909 2.05 0.00 0.00 3.41
363 388 7.756395 ATATTTCTTACATCTCTGCCAATGG 57.244 36.000 0.00 0.00 0.00 3.16
468 779 2.191908 GTGTCTGTGGTGGTGGCA 59.808 61.111 0.00 0.00 0.00 4.92
581 907 0.689412 GGAGAGGAGGAGAAGGGTGG 60.689 65.000 0.00 0.00 0.00 4.61
665 1024 1.612442 AAGCTGCTAGGGTTCGGGA 60.612 57.895 0.90 0.00 0.00 5.14
678 1037 1.444553 GTCCTCCACGACGAAGCTG 60.445 63.158 0.00 0.00 0.00 4.24
932 1380 4.292178 GGCGGGCGATCTCAGGAG 62.292 72.222 0.00 0.00 0.00 3.69
1004 1452 0.753867 GAAGAGGGGCAGGTAGTAGC 59.246 60.000 0.00 0.00 0.00 3.58
1098 1546 3.932710 CTGCTAGCGTCTATGTTCCAAAA 59.067 43.478 10.77 0.00 0.00 2.44
1099 1547 3.521560 CTGCTAGCGTCTATGTTCCAAA 58.478 45.455 10.77 0.00 0.00 3.28
1100 1548 2.738643 GCTGCTAGCGTCTATGTTCCAA 60.739 50.000 10.77 0.00 0.00 3.53
1101 1549 1.202417 GCTGCTAGCGTCTATGTTCCA 60.202 52.381 10.77 0.00 0.00 3.53
1102 1550 1.492720 GCTGCTAGCGTCTATGTTCC 58.507 55.000 10.77 0.00 0.00 3.62
1120 1568 4.863152 TTATTAAGTTAAAGCCGGACGC 57.137 40.909 5.05 0.00 37.98 5.19
1144 1592 0.962356 GTGTGGATTCTGCCTGGTGG 60.962 60.000 0.00 0.00 0.00 4.61
1145 1593 0.250858 TGTGTGGATTCTGCCTGGTG 60.251 55.000 0.00 0.00 0.00 4.17
1146 1594 0.700564 ATGTGTGGATTCTGCCTGGT 59.299 50.000 0.00 0.00 0.00 4.00
1147 1595 2.171237 TCTATGTGTGGATTCTGCCTGG 59.829 50.000 0.00 0.00 0.00 4.45
1148 1596 3.118482 ACTCTATGTGTGGATTCTGCCTG 60.118 47.826 0.00 0.00 0.00 4.85
1149 1597 3.110705 ACTCTATGTGTGGATTCTGCCT 58.889 45.455 0.00 0.00 0.00 4.75
1150 1598 3.133721 AGACTCTATGTGTGGATTCTGCC 59.866 47.826 0.00 0.00 0.00 4.85
1151 1599 4.399004 AGACTCTATGTGTGGATTCTGC 57.601 45.455 0.00 0.00 0.00 4.26
1152 1600 6.867550 TGTAAGACTCTATGTGTGGATTCTG 58.132 40.000 0.00 0.00 27.79 3.02
1153 1601 7.482169 TTGTAAGACTCTATGTGTGGATTCT 57.518 36.000 0.00 0.00 0.00 2.40
1154 1602 6.256757 GCTTGTAAGACTCTATGTGTGGATTC 59.743 42.308 0.00 0.00 0.00 2.52
1155 1603 6.109359 GCTTGTAAGACTCTATGTGTGGATT 58.891 40.000 0.00 0.00 0.00 3.01
1156 1604 5.395768 GGCTTGTAAGACTCTATGTGTGGAT 60.396 44.000 0.00 0.00 0.00 3.41
1157 1605 4.081642 GGCTTGTAAGACTCTATGTGTGGA 60.082 45.833 0.00 0.00 0.00 4.02
1158 1606 4.184629 GGCTTGTAAGACTCTATGTGTGG 58.815 47.826 0.00 0.00 0.00 4.17
1159 1607 4.820897 TGGCTTGTAAGACTCTATGTGTG 58.179 43.478 0.00 0.00 34.24 3.82
1160 1608 5.483685 TTGGCTTGTAAGACTCTATGTGT 57.516 39.130 0.00 0.00 34.24 3.72
1161 1609 6.992063 ATTTGGCTTGTAAGACTCTATGTG 57.008 37.500 0.00 0.00 34.24 3.21
1162 1610 9.167311 CTTTATTTGGCTTGTAAGACTCTATGT 57.833 33.333 0.00 0.00 34.24 2.29
1163 1611 9.383519 TCTTTATTTGGCTTGTAAGACTCTATG 57.616 33.333 0.00 0.00 34.24 2.23
1164 1612 9.384764 GTCTTTATTTGGCTTGTAAGACTCTAT 57.615 33.333 0.00 0.00 38.77 1.98
1165 1613 8.372459 TGTCTTTATTTGGCTTGTAAGACTCTA 58.628 33.333 0.00 0.00 41.09 2.43
1166 1614 7.224297 TGTCTTTATTTGGCTTGTAAGACTCT 58.776 34.615 0.00 0.00 41.09 3.24
1167 1615 7.173390 ACTGTCTTTATTTGGCTTGTAAGACTC 59.827 37.037 0.00 0.00 41.09 3.36
1168 1616 6.998673 ACTGTCTTTATTTGGCTTGTAAGACT 59.001 34.615 0.00 0.00 41.09 3.24
1169 1617 7.041372 TGACTGTCTTTATTTGGCTTGTAAGAC 60.041 37.037 9.51 0.00 40.96 3.01
1170 1618 6.995686 TGACTGTCTTTATTTGGCTTGTAAGA 59.004 34.615 9.51 0.00 0.00 2.10
1171 1619 7.202016 TGACTGTCTTTATTTGGCTTGTAAG 57.798 36.000 9.51 0.00 0.00 2.34
1172 1620 7.575414 TTGACTGTCTTTATTTGGCTTGTAA 57.425 32.000 9.51 0.00 0.00 2.41
1173 1621 7.422399 GTTTGACTGTCTTTATTTGGCTTGTA 58.578 34.615 9.51 0.00 0.00 2.41
1174 1622 6.273071 GTTTGACTGTCTTTATTTGGCTTGT 58.727 36.000 9.51 0.00 0.00 3.16
1175 1623 5.399301 CGTTTGACTGTCTTTATTTGGCTTG 59.601 40.000 9.51 0.00 0.00 4.01
1176 1624 5.298276 TCGTTTGACTGTCTTTATTTGGCTT 59.702 36.000 9.51 0.00 0.00 4.35
1177 1625 4.819630 TCGTTTGACTGTCTTTATTTGGCT 59.180 37.500 9.51 0.00 0.00 4.75
1178 1626 5.103290 TCGTTTGACTGTCTTTATTTGGC 57.897 39.130 9.51 0.00 0.00 4.52
1179 1627 5.147162 GCTCGTTTGACTGTCTTTATTTGG 58.853 41.667 9.51 0.00 0.00 3.28
1180 1628 5.621228 GTGCTCGTTTGACTGTCTTTATTTG 59.379 40.000 9.51 0.00 0.00 2.32
1181 1629 5.295787 TGTGCTCGTTTGACTGTCTTTATTT 59.704 36.000 9.51 0.00 0.00 1.40
1182 1630 4.814234 TGTGCTCGTTTGACTGTCTTTATT 59.186 37.500 9.51 0.00 0.00 1.40
1183 1631 4.377021 TGTGCTCGTTTGACTGTCTTTAT 58.623 39.130 9.51 0.00 0.00 1.40
1184 1632 3.787785 TGTGCTCGTTTGACTGTCTTTA 58.212 40.909 9.51 0.00 0.00 1.85
1185 1633 2.627945 TGTGCTCGTTTGACTGTCTTT 58.372 42.857 9.51 0.00 0.00 2.52
1186 1634 2.309528 TGTGCTCGTTTGACTGTCTT 57.690 45.000 9.51 0.00 0.00 3.01
1187 1635 2.138320 CATGTGCTCGTTTGACTGTCT 58.862 47.619 9.51 0.00 0.00 3.41
1188 1636 1.195448 CCATGTGCTCGTTTGACTGTC 59.805 52.381 0.00 0.00 0.00 3.51
1189 1637 1.229428 CCATGTGCTCGTTTGACTGT 58.771 50.000 0.00 0.00 0.00 3.55
1190 1638 0.110056 GCCATGTGCTCGTTTGACTG 60.110 55.000 0.00 0.00 36.87 3.51
1191 1639 2.247790 GCCATGTGCTCGTTTGACT 58.752 52.632 0.00 0.00 36.87 3.41
1192 1640 4.847255 GCCATGTGCTCGTTTGAC 57.153 55.556 0.00 0.00 36.87 3.18
1201 1649 2.686915 AGCTTTATCTTGAGCCATGTGC 59.313 45.455 0.00 0.00 39.71 4.57
1202 1650 5.587844 ACTTAGCTTTATCTTGAGCCATGTG 59.412 40.000 0.00 0.00 39.71 3.21
1203 1651 5.749462 ACTTAGCTTTATCTTGAGCCATGT 58.251 37.500 0.00 0.00 39.71 3.21
1204 1652 7.212976 TCTACTTAGCTTTATCTTGAGCCATG 58.787 38.462 0.00 0.00 39.71 3.66
1205 1653 7.366847 TCTACTTAGCTTTATCTTGAGCCAT 57.633 36.000 0.00 0.00 39.71 4.40
1206 1654 6.791867 TCTACTTAGCTTTATCTTGAGCCA 57.208 37.500 0.00 0.00 39.71 4.75
1207 1655 6.584563 CGATCTACTTAGCTTTATCTTGAGCC 59.415 42.308 0.00 0.00 39.71 4.70
1208 1656 6.088883 GCGATCTACTTAGCTTTATCTTGAGC 59.911 42.308 0.00 0.00 39.17 4.26
1209 1657 7.142021 TGCGATCTACTTAGCTTTATCTTGAG 58.858 38.462 0.00 0.00 0.00 3.02
1210 1658 7.039313 TGCGATCTACTTAGCTTTATCTTGA 57.961 36.000 0.00 0.00 0.00 3.02
1211 1659 6.128956 GCTGCGATCTACTTAGCTTTATCTTG 60.129 42.308 0.00 0.00 0.00 3.02
1212 1660 5.923684 GCTGCGATCTACTTAGCTTTATCTT 59.076 40.000 0.00 0.00 0.00 2.40
1213 1661 5.465935 GCTGCGATCTACTTAGCTTTATCT 58.534 41.667 0.00 0.00 0.00 1.98
1214 1662 4.623595 GGCTGCGATCTACTTAGCTTTATC 59.376 45.833 0.00 0.00 34.89 1.75
1215 1663 4.039245 TGGCTGCGATCTACTTAGCTTTAT 59.961 41.667 0.00 0.00 34.89 1.40
1216 1664 3.383505 TGGCTGCGATCTACTTAGCTTTA 59.616 43.478 0.00 0.00 34.89 1.85
1217 1665 2.168521 TGGCTGCGATCTACTTAGCTTT 59.831 45.455 0.00 0.00 34.89 3.51
1218 1666 1.757118 TGGCTGCGATCTACTTAGCTT 59.243 47.619 0.00 0.00 34.89 3.74
1219 1667 1.067821 GTGGCTGCGATCTACTTAGCT 59.932 52.381 0.00 0.00 34.89 3.32
1220 1668 1.202417 TGTGGCTGCGATCTACTTAGC 60.202 52.381 0.00 0.00 0.00 3.09
1221 1669 2.871182 TGTGGCTGCGATCTACTTAG 57.129 50.000 0.00 0.00 0.00 2.18
1222 1670 2.496070 ACTTGTGGCTGCGATCTACTTA 59.504 45.455 0.00 0.00 0.00 2.24
1223 1671 1.276421 ACTTGTGGCTGCGATCTACTT 59.724 47.619 0.00 0.00 0.00 2.24
1224 1672 0.898320 ACTTGTGGCTGCGATCTACT 59.102 50.000 0.00 0.00 0.00 2.57
1225 1673 1.661112 GAACTTGTGGCTGCGATCTAC 59.339 52.381 0.00 0.00 0.00 2.59
1226 1674 1.735700 CGAACTTGTGGCTGCGATCTA 60.736 52.381 0.00 0.00 0.00 1.98
1227 1675 1.016130 CGAACTTGTGGCTGCGATCT 61.016 55.000 0.00 0.00 0.00 2.75
1228 1676 1.421485 CGAACTTGTGGCTGCGATC 59.579 57.895 0.00 0.00 0.00 3.69
1229 1677 2.034879 CCGAACTTGTGGCTGCGAT 61.035 57.895 0.00 0.00 0.00 4.58
1230 1678 2.089887 TACCGAACTTGTGGCTGCGA 62.090 55.000 0.00 0.00 0.00 5.10
1231 1679 1.225376 TTACCGAACTTGTGGCTGCG 61.225 55.000 0.00 0.00 0.00 5.18
1232 1680 0.237498 GTTACCGAACTTGTGGCTGC 59.763 55.000 0.00 0.00 32.40 5.25
1233 1681 1.263217 GTGTTACCGAACTTGTGGCTG 59.737 52.381 0.00 0.00 36.45 4.85
1234 1682 1.134340 TGTGTTACCGAACTTGTGGCT 60.134 47.619 0.00 0.00 36.45 4.75
1235 1683 1.301423 TGTGTTACCGAACTTGTGGC 58.699 50.000 0.00 0.00 36.45 5.01
1236 1684 4.286910 CATTTGTGTTACCGAACTTGTGG 58.713 43.478 0.00 0.00 36.45 4.17
1237 1685 3.728718 GCATTTGTGTTACCGAACTTGTG 59.271 43.478 0.00 0.00 36.45 3.33
1238 1686 3.378742 TGCATTTGTGTTACCGAACTTGT 59.621 39.130 0.00 0.00 36.45 3.16
1239 1687 3.958704 TGCATTTGTGTTACCGAACTTG 58.041 40.909 0.00 0.00 36.45 3.16
1240 1688 3.880490 TCTGCATTTGTGTTACCGAACTT 59.120 39.130 0.00 0.00 36.45 2.66
1241 1689 3.472652 TCTGCATTTGTGTTACCGAACT 58.527 40.909 0.00 0.00 36.45 3.01
1242 1690 3.889196 TCTGCATTTGTGTTACCGAAC 57.111 42.857 0.00 0.00 36.00 3.95
1243 1691 3.628032 TGTTCTGCATTTGTGTTACCGAA 59.372 39.130 0.00 0.00 0.00 4.30
1244 1692 3.206964 TGTTCTGCATTTGTGTTACCGA 58.793 40.909 0.00 0.00 0.00 4.69
1245 1693 3.617540 TGTTCTGCATTTGTGTTACCG 57.382 42.857 0.00 0.00 0.00 4.02
1246 1694 5.119931 TGATGTTCTGCATTTGTGTTACC 57.880 39.130 0.00 0.00 38.06 2.85
1247 1695 5.630680 CCTTGATGTTCTGCATTTGTGTTAC 59.369 40.000 0.00 0.00 38.06 2.50
1248 1696 5.771469 CCTTGATGTTCTGCATTTGTGTTA 58.229 37.500 0.00 0.00 38.06 2.41
1249 1697 4.624015 CCTTGATGTTCTGCATTTGTGTT 58.376 39.130 0.00 0.00 38.06 3.32
1250 1698 3.553508 GCCTTGATGTTCTGCATTTGTGT 60.554 43.478 0.00 0.00 38.06 3.72
1251 1699 2.991190 GCCTTGATGTTCTGCATTTGTG 59.009 45.455 0.00 0.00 38.06 3.33
1252 1700 2.028748 GGCCTTGATGTTCTGCATTTGT 60.029 45.455 0.00 0.00 38.06 2.83
1253 1701 2.028839 TGGCCTTGATGTTCTGCATTTG 60.029 45.455 3.32 0.00 38.06 2.32
1254 1702 2.250031 TGGCCTTGATGTTCTGCATTT 58.750 42.857 3.32 0.00 38.06 2.32
1255 1703 1.927487 TGGCCTTGATGTTCTGCATT 58.073 45.000 3.32 0.00 38.06 3.56
1256 1704 1.927487 TTGGCCTTGATGTTCTGCAT 58.073 45.000 3.32 0.00 41.24 3.96
1257 1705 1.614903 CTTTGGCCTTGATGTTCTGCA 59.385 47.619 3.32 0.00 0.00 4.41
1258 1706 1.670967 GCTTTGGCCTTGATGTTCTGC 60.671 52.381 3.32 0.00 0.00 4.26
1259 1707 1.891150 AGCTTTGGCCTTGATGTTCTG 59.109 47.619 3.32 0.00 39.73 3.02
1260 1708 2.299326 AGCTTTGGCCTTGATGTTCT 57.701 45.000 3.32 0.00 39.73 3.01
1261 1709 2.159324 GCTAGCTTTGGCCTTGATGTTC 60.159 50.000 7.70 0.00 39.73 3.18
1262 1710 1.821136 GCTAGCTTTGGCCTTGATGTT 59.179 47.619 7.70 0.00 39.73 2.71
1263 1711 1.272092 TGCTAGCTTTGGCCTTGATGT 60.272 47.619 17.23 0.00 39.73 3.06
1264 1712 1.466856 TGCTAGCTTTGGCCTTGATG 58.533 50.000 17.23 0.00 39.73 3.07
1265 1713 2.220653 TTGCTAGCTTTGGCCTTGAT 57.779 45.000 17.23 0.00 39.73 2.57
1266 1714 1.993956 TTTGCTAGCTTTGGCCTTGA 58.006 45.000 17.23 0.00 39.73 3.02
1267 1715 2.407090 GTTTTGCTAGCTTTGGCCTTG 58.593 47.619 17.23 0.00 39.73 3.61
1268 1716 1.000274 CGTTTTGCTAGCTTTGGCCTT 60.000 47.619 17.23 0.00 39.73 4.35
1269 1717 0.598065 CGTTTTGCTAGCTTTGGCCT 59.402 50.000 17.23 0.00 39.73 5.19
1270 1718 0.596082 TCGTTTTGCTAGCTTTGGCC 59.404 50.000 17.23 0.00 39.73 5.36
1271 1719 1.401539 CCTCGTTTTGCTAGCTTTGGC 60.402 52.381 17.23 1.79 39.06 4.52
1272 1720 2.151202 TCCTCGTTTTGCTAGCTTTGG 58.849 47.619 17.23 8.43 0.00 3.28
1273 1721 2.160417 CCTCCTCGTTTTGCTAGCTTTG 59.840 50.000 17.23 1.58 0.00 2.77
1274 1722 2.038557 TCCTCCTCGTTTTGCTAGCTTT 59.961 45.455 17.23 0.00 0.00 3.51
1275 1723 1.623811 TCCTCCTCGTTTTGCTAGCTT 59.376 47.619 17.23 0.00 0.00 3.74
1276 1724 1.267121 TCCTCCTCGTTTTGCTAGCT 58.733 50.000 17.23 0.00 0.00 3.32
1277 1725 2.205911 GATCCTCCTCGTTTTGCTAGC 58.794 52.381 8.10 8.10 0.00 3.42
1278 1726 3.526931 TGATCCTCCTCGTTTTGCTAG 57.473 47.619 0.00 0.00 0.00 3.42
1279 1727 3.432186 CCATGATCCTCCTCGTTTTGCTA 60.432 47.826 0.00 0.00 0.00 3.49
1280 1728 2.636830 CATGATCCTCCTCGTTTTGCT 58.363 47.619 0.00 0.00 0.00 3.91
1281 1729 1.672881 CCATGATCCTCCTCGTTTTGC 59.327 52.381 0.00 0.00 0.00 3.68
1282 1730 2.679837 CACCATGATCCTCCTCGTTTTG 59.320 50.000 0.00 0.00 0.00 2.44
1283 1731 2.941415 GCACCATGATCCTCCTCGTTTT 60.941 50.000 0.00 0.00 0.00 2.43
1284 1732 1.407437 GCACCATGATCCTCCTCGTTT 60.407 52.381 0.00 0.00 0.00 3.60
1285 1733 0.179000 GCACCATGATCCTCCTCGTT 59.821 55.000 0.00 0.00 0.00 3.85
1286 1734 0.977627 TGCACCATGATCCTCCTCGT 60.978 55.000 0.00 0.00 0.00 4.18
1287 1735 0.249784 CTGCACCATGATCCTCCTCG 60.250 60.000 0.00 0.00 0.00 4.63
1288 1736 0.534652 GCTGCACCATGATCCTCCTC 60.535 60.000 0.00 0.00 0.00 3.71
1289 1737 1.530771 GCTGCACCATGATCCTCCT 59.469 57.895 0.00 0.00 0.00 3.69
1290 1738 1.527844 GGCTGCACCATGATCCTCC 60.528 63.158 0.50 0.00 38.86 4.30
1291 1739 1.225426 TGGCTGCACCATGATCCTC 59.775 57.895 0.50 0.00 46.36 3.71
1292 1740 3.418687 TGGCTGCACCATGATCCT 58.581 55.556 0.50 0.00 46.36 3.24
1300 1748 1.076485 AAGGGATGATGGCTGCACC 60.076 57.895 0.50 0.00 39.84 5.01
1301 1749 2.012902 GCAAGGGATGATGGCTGCAC 62.013 60.000 0.50 0.00 0.00 4.57
1302 1750 1.755395 GCAAGGGATGATGGCTGCA 60.755 57.895 0.50 0.00 0.00 4.41
1303 1751 2.496291 GGCAAGGGATGATGGCTGC 61.496 63.158 0.00 0.00 0.00 5.25
1304 1752 2.191513 CGGCAAGGGATGATGGCTG 61.192 63.158 0.00 0.00 0.00 4.85
1305 1753 2.194056 CGGCAAGGGATGATGGCT 59.806 61.111 0.00 0.00 0.00 4.75
1306 1754 3.599704 GCGGCAAGGGATGATGGC 61.600 66.667 0.00 0.00 0.00 4.40
1307 1755 3.282157 CGCGGCAAGGGATGATGG 61.282 66.667 0.00 0.00 34.27 3.51
1308 1756 3.957535 GCGCGGCAAGGGATGATG 61.958 66.667 8.83 0.00 34.27 3.07
1320 1768 3.499737 GACATGGTGAAGGCGCGG 61.500 66.667 8.83 0.00 0.00 6.46
1321 1769 3.853330 CGACATGGTGAAGGCGCG 61.853 66.667 0.00 0.00 0.00 6.86
1322 1770 3.499737 CCGACATGGTGAAGGCGC 61.500 66.667 0.00 0.00 0.00 6.53
1323 1771 3.499737 GCCGACATGGTGAAGGCG 61.500 66.667 0.00 0.00 41.21 5.52
1324 1772 1.926511 CTTGCCGACATGGTGAAGGC 61.927 60.000 10.76 10.76 41.23 4.35
1325 1773 1.308069 CCTTGCCGACATGGTGAAGG 61.308 60.000 0.00 0.00 40.78 3.46
1326 1774 2.174334 CCTTGCCGACATGGTGAAG 58.826 57.895 0.00 0.00 41.21 3.02
1327 1775 4.395519 CCTTGCCGACATGGTGAA 57.604 55.556 0.00 0.00 41.21 3.18
1331 1779 0.392863 TGATCACCTTGCCGACATGG 60.393 55.000 1.92 1.92 44.74 3.66
1332 1780 1.399440 CTTGATCACCTTGCCGACATG 59.601 52.381 0.00 0.00 0.00 3.21
1333 1781 1.742761 CTTGATCACCTTGCCGACAT 58.257 50.000 0.00 0.00 0.00 3.06
1334 1782 0.955428 GCTTGATCACCTTGCCGACA 60.955 55.000 0.00 0.00 0.00 4.35
1335 1783 1.648467 GGCTTGATCACCTTGCCGAC 61.648 60.000 10.97 0.00 33.96 4.79
1410 1861 0.251832 ATCCTCGACACAGGGACACT 60.252 55.000 0.00 0.00 33.81 3.55
1637 4672 3.840666 TGTCCTTAGAAATCCTGAGCAGT 59.159 43.478 0.00 0.00 0.00 4.40
2151 5286 0.877071 CGTTGCCATGAAAGCAGACT 59.123 50.000 0.00 0.00 42.17 3.24


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

AutoCloner maintained by Alex Coulton.