Multiple sequence alignment - TraesCS7D01G466600

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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 TraesCS7D01G466600 chr7D 100.000 2462 0 0 1 2462 580382452 580379991 0.000000e+00 4547.0
1 TraesCS7D01G466600 chr7D 88.847 529 34 8 1722 2250 459782532 459783035 5.780000e-176 627.0
2 TraesCS7D01G466600 chr7D 88.817 465 52 0 1000 1464 562148731 562148267 2.750000e-159 571.0
3 TraesCS7D01G466600 chr7D 89.414 444 47 0 998 1441 562149189 562148746 5.950000e-156 560.0
4 TraesCS7D01G466600 chr7D 86.166 506 68 2 970 1473 572757357 572757862 1.660000e-151 545.0
5 TraesCS7D01G466600 chr7D 91.542 201 9 6 2267 2462 459783021 459783218 1.120000e-68 270.0
6 TraesCS7D01G466600 chr7B 87.103 1070 64 25 637 1690 647070868 647069857 0.000000e+00 1144.0
7 TraesCS7D01G466600 chr7B 92.697 712 36 7 1722 2423 318416427 318415722 0.000000e+00 1013.0
8 TraesCS7D01G466600 chr7B 89.837 492 49 1 976 1466 632337625 632337134 4.470000e-177 630.0
9 TraesCS7D01G466600 chr7B 89.796 490 48 2 980 1467 630552387 630552876 5.780000e-176 627.0
10 TraesCS7D01G466600 chr7B 87.324 497 61 2 970 1464 630310663 630311159 3.550000e-158 568.0
11 TraesCS7D01G466600 chr7B 89.209 139 11 2 90 224 647071354 647071216 1.170000e-38 171.0
12 TraesCS7D01G466600 chr7B 79.608 255 32 11 347 588 647071118 647070871 5.450000e-37 165.0
13 TraesCS7D01G466600 chr7B 89.706 68 7 0 406 473 632338449 632338382 1.210000e-13 87.9
14 TraesCS7D01G466600 chrUn 96.148 675 18 3 1796 2462 24306973 24307647 0.000000e+00 1096.0
15 TraesCS7D01G466600 chrUn 93.447 351 23 0 1722 2072 322140980 322140630 2.810000e-144 521.0
16 TraesCS7D01G466600 chr7A 89.642 531 42 3 1722 2250 300167214 300167733 0.000000e+00 664.0
17 TraesCS7D01G466600 chr7A 88.577 499 56 1 969 1466 663498347 663497849 2.710000e-169 604.0
18 TraesCS7D01G466600 chr7A 88.372 473 53 1 1001 1473 647917222 647916752 3.550000e-158 568.0
19 TraesCS7D01G466600 chr7A 93.814 194 9 3 2268 2458 300167720 300167913 3.100000e-74 289.0
20 TraesCS7D01G466600 chr7A 92.462 199 12 3 2267 2462 717917309 717917111 5.180000e-72 281.0
21 TraesCS7D01G466600 chr4D 88.847 529 34 8 1722 2250 498625434 498625937 5.780000e-176 627.0
22 TraesCS7D01G466600 chr4D 84.151 530 59 11 592 1105 228952117 228952637 7.910000e-135 490.0
23 TraesCS7D01G466600 chr4D 93.401 197 10 3 2267 2462 498625923 498626117 3.100000e-74 289.0
24 TraesCS7D01G466600 chr3D 85.255 529 61 10 592 1104 3572117 3572644 1.680000e-146 529.0
25 TraesCS7D01G466600 chr3D 84.528 530 52 15 592 1105 573060349 573060864 4.730000e-137 497.0
26 TraesCS7D01G466600 chr3D 83.176 529 65 16 592 1105 21114418 21114937 1.720000e-126 462.0
27 TraesCS7D01G466600 chr5B 93.447 351 23 0 1722 2072 513808971 513808621 2.810000e-144 521.0
28 TraesCS7D01G466600 chr5B 88.274 452 29 9 1722 2172 2618495 2618923 1.010000e-143 520.0
29 TraesCS7D01G466600 chr5B 94.521 292 9 4 2174 2462 2622577 2622864 6.250000e-121 444.0
30 TraesCS7D01G466600 chr2D 84.340 530 58 11 592 1105 629235794 629235274 1.700000e-136 496.0
31 TraesCS7D01G466600 chr2D 83.962 530 55 13 592 1105 487757270 487757785 4.760000e-132 481.0
32 TraesCS7D01G466600 chr2D 83.774 530 61 11 592 1105 40772730 40773250 1.710000e-131 479.0
33 TraesCS7D01G466600 chr6D 83.932 529 61 13 592 1105 244273046 244273565 3.680000e-133 484.0
34 TraesCS7D01G466600 chr1D 83.774 530 61 11 592 1105 951140 951660 1.710000e-131 479.0
35 TraesCS7D01G466600 chr3B 90.107 374 26 8 1881 2250 709520744 709521110 2.220000e-130 475.0
36 TraesCS7D01G466600 chr3B 88.725 204 12 3 2267 2459 709521096 709521299 3.160000e-59 239.0
37 TraesCS7D01G466600 chr5A 84.742 485 51 17 1984 2462 643566087 643566554 4.800000e-127 464.0
38 TraesCS7D01G466600 chr5A 84.337 249 19 4 1722 1970 643565276 643565504 2.460000e-55 226.0
39 TraesCS7D01G466600 chr1A 90.090 333 25 5 1716 2046 558265646 558265320 2.260000e-115 425.0
40 TraesCS7D01G466600 chr1B 89.655 319 22 8 1881 2196 302212928 302213238 1.770000e-106 396.0
41 TraesCS7D01G466600 chr1B 87.107 318 32 7 797 1105 646284500 646284817 3.900000e-93 351.0
42 TraesCS7D01G466600 chr2A 90.391 281 17 2 1723 2002 699381706 699381977 6.470000e-96 361.0
43 TraesCS7D01G466600 chr2A 94.211 190 10 1 2274 2462 699381976 699382165 3.100000e-74 289.0


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 TraesCS7D01G466600 chr7D 580379991 580382452 2461 True 4547.000000 4547 100.000000 1 2462 1 chr7D.!!$R1 2461
1 TraesCS7D01G466600 chr7D 562148267 562149189 922 True 565.500000 571 89.115500 998 1464 2 chr7D.!!$R2 466
2 TraesCS7D01G466600 chr7D 572757357 572757862 505 False 545.000000 545 86.166000 970 1473 1 chr7D.!!$F1 503
3 TraesCS7D01G466600 chr7D 459782532 459783218 686 False 448.500000 627 90.194500 1722 2462 2 chr7D.!!$F2 740
4 TraesCS7D01G466600 chr7B 318415722 318416427 705 True 1013.000000 1013 92.697000 1722 2423 1 chr7B.!!$R1 701
5 TraesCS7D01G466600 chr7B 647069857 647071354 1497 True 493.333333 1144 85.306667 90 1690 3 chr7B.!!$R3 1600
6 TraesCS7D01G466600 chr7B 632337134 632338449 1315 True 358.950000 630 89.771500 406 1466 2 chr7B.!!$R2 1060
7 TraesCS7D01G466600 chrUn 24306973 24307647 674 False 1096.000000 1096 96.148000 1796 2462 1 chrUn.!!$F1 666
8 TraesCS7D01G466600 chr7A 300167214 300167913 699 False 476.500000 664 91.728000 1722 2458 2 chr7A.!!$F1 736
9 TraesCS7D01G466600 chr4D 228952117 228952637 520 False 490.000000 490 84.151000 592 1105 1 chr4D.!!$F1 513
10 TraesCS7D01G466600 chr4D 498625434 498626117 683 False 458.000000 627 91.124000 1722 2462 2 chr4D.!!$F2 740
11 TraesCS7D01G466600 chr3D 3572117 3572644 527 False 529.000000 529 85.255000 592 1104 1 chr3D.!!$F1 512
12 TraesCS7D01G466600 chr3D 573060349 573060864 515 False 497.000000 497 84.528000 592 1105 1 chr3D.!!$F3 513
13 TraesCS7D01G466600 chr3D 21114418 21114937 519 False 462.000000 462 83.176000 592 1105 1 chr3D.!!$F2 513
14 TraesCS7D01G466600 chr5B 2618495 2622864 4369 False 482.000000 520 91.397500 1722 2462 2 chr5B.!!$F1 740
15 TraesCS7D01G466600 chr2D 629235274 629235794 520 True 496.000000 496 84.340000 592 1105 1 chr2D.!!$R1 513
16 TraesCS7D01G466600 chr2D 487757270 487757785 515 False 481.000000 481 83.962000 592 1105 1 chr2D.!!$F2 513
17 TraesCS7D01G466600 chr2D 40772730 40773250 520 False 479.000000 479 83.774000 592 1105 1 chr2D.!!$F1 513
18 TraesCS7D01G466600 chr6D 244273046 244273565 519 False 484.000000 484 83.932000 592 1105 1 chr6D.!!$F1 513
19 TraesCS7D01G466600 chr1D 951140 951660 520 False 479.000000 479 83.774000 592 1105 1 chr1D.!!$F1 513
20 TraesCS7D01G466600 chr3B 709520744 709521299 555 False 357.000000 475 89.416000 1881 2459 2 chr3B.!!$F1 578
21 TraesCS7D01G466600 chr5A 643565276 643566554 1278 False 345.000000 464 84.539500 1722 2462 2 chr5A.!!$F1 740

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
132 136 0.032678 CCCAATCCACTCCGATCGAG 59.967 60.0 18.66 14.23 44.95 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 2534 0.249911 AATACGATGGAAGAGGCCGC 60.25 55.0 0.0 0.0 0.0 6.53 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
20 21 3.060000 GGCCCACGTAAAGCCCAC 61.060 66.667 10.73 0.00 41.00 4.61
21 22 3.060000 GCCCACGTAAAGCCCACC 61.060 66.667 0.00 0.00 0.00 4.61
22 23 2.754375 CCCACGTAAAGCCCACCT 59.246 61.111 0.00 0.00 0.00 4.00
23 24 1.376812 CCCACGTAAAGCCCACCTC 60.377 63.158 0.00 0.00 0.00 3.85
24 25 1.740296 CCACGTAAAGCCCACCTCG 60.740 63.158 0.00 0.00 0.00 4.63
25 26 2.047560 ACGTAAAGCCCACCTCGC 60.048 61.111 0.00 0.00 0.00 5.03
26 27 2.047655 CGTAAAGCCCACCTCGCA 60.048 61.111 0.00 0.00 0.00 5.10
27 28 2.100631 CGTAAAGCCCACCTCGCAG 61.101 63.158 0.00 0.00 0.00 5.18
28 29 2.046314 TAAAGCCCACCTCGCAGC 60.046 61.111 0.00 0.00 0.00 5.25
29 30 2.592993 TAAAGCCCACCTCGCAGCT 61.593 57.895 0.00 0.00 37.10 4.24
30 31 2.803155 TAAAGCCCACCTCGCAGCTG 62.803 60.000 10.11 10.11 35.30 4.24
34 35 2.749044 CCACCTCGCAGCTGCAAT 60.749 61.111 36.03 16.54 42.21 3.56
35 36 2.338015 CCACCTCGCAGCTGCAATT 61.338 57.895 36.03 15.75 42.21 2.32
36 37 1.136147 CACCTCGCAGCTGCAATTC 59.864 57.895 36.03 8.88 42.21 2.17
37 38 2.042831 ACCTCGCAGCTGCAATTCC 61.043 57.895 36.03 8.11 42.21 3.01
38 39 2.768492 CCTCGCAGCTGCAATTCCC 61.768 63.158 36.03 7.35 42.21 3.97
39 40 2.751436 TCGCAGCTGCAATTCCCC 60.751 61.111 36.03 6.57 42.21 4.81
40 41 3.830192 CGCAGCTGCAATTCCCCC 61.830 66.667 36.03 5.81 42.21 5.40
41 42 2.681064 GCAGCTGCAATTCCCCCA 60.681 61.111 33.36 0.00 41.59 4.96
42 43 3.010413 GCAGCTGCAATTCCCCCAC 62.010 63.158 33.36 0.00 41.59 4.61
43 44 1.607178 CAGCTGCAATTCCCCCACA 60.607 57.895 0.00 0.00 0.00 4.17
44 45 1.607467 AGCTGCAATTCCCCCACAC 60.607 57.895 1.02 0.00 0.00 3.82
45 46 2.993471 GCTGCAATTCCCCCACACG 61.993 63.158 0.00 0.00 0.00 4.49
46 47 2.988684 TGCAATTCCCCCACACGC 60.989 61.111 0.00 0.00 0.00 5.34
47 48 2.988684 GCAATTCCCCCACACGCA 60.989 61.111 0.00 0.00 0.00 5.24
48 49 2.350458 GCAATTCCCCCACACGCAT 61.350 57.895 0.00 0.00 0.00 4.73
49 50 1.809207 CAATTCCCCCACACGCATC 59.191 57.895 0.00 0.00 0.00 3.91
50 51 1.748879 AATTCCCCCACACGCATCG 60.749 57.895 0.00 0.00 0.00 3.84
51 52 2.191786 AATTCCCCCACACGCATCGA 62.192 55.000 0.00 0.00 0.00 3.59
52 53 2.869503 ATTCCCCCACACGCATCGAC 62.870 60.000 0.00 0.00 0.00 4.20
56 57 4.735132 CCACACGCATCGACCCGT 62.735 66.667 6.39 6.39 38.35 5.28
57 58 2.179767 CACACGCATCGACCCGTA 59.820 61.111 11.23 0.00 35.69 4.02
58 59 2.156446 CACACGCATCGACCCGTAC 61.156 63.158 11.23 0.00 35.69 3.67
59 60 2.947621 CACGCATCGACCCGTACG 60.948 66.667 8.69 8.69 35.69 3.67
60 61 4.842091 ACGCATCGACCCGTACGC 62.842 66.667 10.49 0.00 35.69 4.42
61 62 4.547905 CGCATCGACCCGTACGCT 62.548 66.667 10.49 0.00 0.00 5.07
62 63 2.654404 GCATCGACCCGTACGCTC 60.654 66.667 10.49 5.43 0.00 5.03
63 64 3.108343 CATCGACCCGTACGCTCT 58.892 61.111 10.49 0.00 0.00 4.09
64 65 1.432251 CATCGACCCGTACGCTCTT 59.568 57.895 10.49 0.00 0.00 2.85
65 66 0.591741 CATCGACCCGTACGCTCTTC 60.592 60.000 10.49 1.79 0.00 2.87
66 67 0.747283 ATCGACCCGTACGCTCTTCT 60.747 55.000 10.49 0.00 0.00 2.85
67 68 1.226323 CGACCCGTACGCTCTTCTG 60.226 63.158 10.49 0.00 0.00 3.02
68 69 1.881602 GACCCGTACGCTCTTCTGT 59.118 57.895 10.49 0.00 0.00 3.41
69 70 0.243095 GACCCGTACGCTCTTCTGTT 59.757 55.000 10.49 0.00 0.00 3.16
70 71 0.243095 ACCCGTACGCTCTTCTGTTC 59.757 55.000 10.49 0.00 0.00 3.18
71 72 0.797249 CCCGTACGCTCTTCTGTTCG 60.797 60.000 10.49 0.00 0.00 3.95
72 73 1.403972 CCGTACGCTCTTCTGTTCGC 61.404 60.000 10.49 0.00 0.00 4.70
73 74 1.403972 CGTACGCTCTTCTGTTCGCC 61.404 60.000 0.52 0.00 0.00 5.54
74 75 0.109226 GTACGCTCTTCTGTTCGCCT 60.109 55.000 0.00 0.00 0.00 5.52
75 76 1.131883 GTACGCTCTTCTGTTCGCCTA 59.868 52.381 0.00 0.00 0.00 3.93
76 77 0.171455 ACGCTCTTCTGTTCGCCTAG 59.829 55.000 0.00 0.00 0.00 3.02
77 78 0.452184 CGCTCTTCTGTTCGCCTAGA 59.548 55.000 0.00 0.00 0.00 2.43
78 79 1.532921 CGCTCTTCTGTTCGCCTAGAG 60.533 57.143 0.00 0.00 36.33 2.43
79 80 1.474879 GCTCTTCTGTTCGCCTAGAGT 59.525 52.381 0.00 0.00 35.81 3.24
80 81 2.683867 GCTCTTCTGTTCGCCTAGAGTA 59.316 50.000 0.00 0.00 35.81 2.59
81 82 3.316868 GCTCTTCTGTTCGCCTAGAGTAT 59.683 47.826 0.00 0.00 35.81 2.12
82 83 4.515944 GCTCTTCTGTTCGCCTAGAGTATA 59.484 45.833 0.00 0.00 35.81 1.47
83 84 5.008811 GCTCTTCTGTTCGCCTAGAGTATAA 59.991 44.000 0.00 0.00 35.81 0.98
84 85 6.459848 GCTCTTCTGTTCGCCTAGAGTATAAA 60.460 42.308 0.00 0.00 35.81 1.40
85 86 7.400599 TCTTCTGTTCGCCTAGAGTATAAAA 57.599 36.000 0.00 0.00 0.00 1.52
86 87 8.008513 TCTTCTGTTCGCCTAGAGTATAAAAT 57.991 34.615 0.00 0.00 0.00 1.82
87 88 8.475639 TCTTCTGTTCGCCTAGAGTATAAAATT 58.524 33.333 0.00 0.00 0.00 1.82
88 89 8.644318 TTCTGTTCGCCTAGAGTATAAAATTC 57.356 34.615 0.00 0.00 0.00 2.17
132 136 0.032678 CCCAATCCACTCCGATCGAG 59.967 60.000 18.66 14.23 44.95 4.04
140 144 2.101582 CCACTCCGATCGAGAAAATCCT 59.898 50.000 18.66 0.00 41.63 3.24
145 149 1.132588 GATCGAGAAAATCCTCCGCG 58.867 55.000 0.00 0.00 0.00 6.46
147 151 0.744874 TCGAGAAAATCCTCCGCGAT 59.255 50.000 8.23 0.00 0.00 4.58
154 158 0.249911 AATCCTCCGCGATACAAGCC 60.250 55.000 8.23 0.00 0.00 4.35
163 167 1.001268 GCGATACAAGCCTCGATCTCA 60.001 52.381 0.00 0.00 37.05 3.27
210 215 2.890474 CCCGCCGTCGATTTCCTG 60.890 66.667 0.00 0.00 38.10 3.86
212 217 2.452813 CCGCCGTCGATTTCCTGTG 61.453 63.158 0.00 0.00 38.10 3.66
220 225 0.322456 CGATTTCCTGTGCCCCAAGA 60.322 55.000 0.00 0.00 0.00 3.02
224 229 4.504864 CGATTTCCTGTGCCCCAAGATATA 60.505 45.833 0.00 0.00 0.00 0.86
225 230 4.437682 TTTCCTGTGCCCCAAGATATAG 57.562 45.455 0.00 0.00 0.00 1.31
226 231 3.344535 TCCTGTGCCCCAAGATATAGA 57.655 47.619 0.00 0.00 0.00 1.98
228 233 3.584406 TCCTGTGCCCCAAGATATAGATG 59.416 47.826 0.00 0.00 0.00 2.90
229 234 3.307975 CCTGTGCCCCAAGATATAGATGG 60.308 52.174 0.00 0.00 0.00 3.51
231 236 4.178339 TGTGCCCCAAGATATAGATGGAT 58.822 43.478 3.14 0.00 0.00 3.41
233 238 3.054139 TGCCCCAAGATATAGATGGATGC 60.054 47.826 3.14 5.80 0.00 3.91
234 239 3.801698 CCCCAAGATATAGATGGATGCG 58.198 50.000 3.14 0.00 0.00 4.73
235 240 3.198635 CCCCAAGATATAGATGGATGCGT 59.801 47.826 3.14 0.00 0.00 5.24
236 241 4.186926 CCCAAGATATAGATGGATGCGTG 58.813 47.826 3.14 0.00 0.00 5.34
237 242 4.081476 CCCAAGATATAGATGGATGCGTGA 60.081 45.833 3.14 0.00 0.00 4.35
238 243 5.396101 CCCAAGATATAGATGGATGCGTGAT 60.396 44.000 3.14 0.00 0.00 3.06
239 244 6.111382 CCAAGATATAGATGGATGCGTGATT 58.889 40.000 0.00 0.00 0.00 2.57
241 246 7.437565 CCAAGATATAGATGGATGCGTGATTAG 59.562 40.741 0.00 0.00 0.00 1.73
242 247 7.888250 AGATATAGATGGATGCGTGATTAGA 57.112 36.000 0.00 0.00 0.00 2.10
243 248 8.476064 AGATATAGATGGATGCGTGATTAGAT 57.524 34.615 0.00 0.00 0.00 1.98
244 249 8.358895 AGATATAGATGGATGCGTGATTAGATG 58.641 37.037 0.00 0.00 0.00 2.90
245 250 4.879197 AGATGGATGCGTGATTAGATGA 57.121 40.909 0.00 0.00 0.00 2.92
246 251 5.417754 AGATGGATGCGTGATTAGATGAT 57.582 39.130 0.00 0.00 0.00 2.45
247 252 5.176592 AGATGGATGCGTGATTAGATGATG 58.823 41.667 0.00 0.00 0.00 3.07
248 253 4.605640 TGGATGCGTGATTAGATGATGA 57.394 40.909 0.00 0.00 0.00 2.92
249 254 4.563061 TGGATGCGTGATTAGATGATGAG 58.437 43.478 0.00 0.00 0.00 2.90
251 256 4.993584 GGATGCGTGATTAGATGATGAGTT 59.006 41.667 0.00 0.00 0.00 3.01
252 257 5.468072 GGATGCGTGATTAGATGATGAGTTT 59.532 40.000 0.00 0.00 0.00 2.66
253 258 5.723492 TGCGTGATTAGATGATGAGTTTG 57.277 39.130 0.00 0.00 0.00 2.93
255 260 6.337356 TGCGTGATTAGATGATGAGTTTGTA 58.663 36.000 0.00 0.00 0.00 2.41
256 261 6.816140 TGCGTGATTAGATGATGAGTTTGTAA 59.184 34.615 0.00 0.00 0.00 2.41
257 262 7.495606 TGCGTGATTAGATGATGAGTTTGTAAT 59.504 33.333 0.00 0.00 0.00 1.89
264 290 9.739276 TTAGATGATGAGTTTGTAATTCACCTT 57.261 29.630 0.00 0.00 0.00 3.50
272 298 4.695217 TTGTAATTCACCTTGGCGATTC 57.305 40.909 0.00 0.00 0.00 2.52
285 311 1.658114 CGATTCCCGTAGATCCGCA 59.342 57.895 0.00 0.00 0.00 5.69
292 318 0.167033 CCGTAGATCCGCAGAGATCG 59.833 60.000 0.00 0.00 46.06 3.69
301 327 4.147449 CAGAGATCGCCGTGCCCA 62.147 66.667 0.00 0.00 0.00 5.36
302 328 3.157252 AGAGATCGCCGTGCCCAT 61.157 61.111 0.00 0.00 0.00 4.00
303 329 2.969238 GAGATCGCCGTGCCCATG 60.969 66.667 0.00 0.00 0.00 3.66
304 330 4.552365 AGATCGCCGTGCCCATGG 62.552 66.667 4.14 4.14 40.47 3.66
305 331 4.856801 GATCGCCGTGCCCATGGT 62.857 66.667 11.73 0.00 39.68 3.55
306 332 4.424711 ATCGCCGTGCCCATGGTT 62.425 61.111 11.73 0.00 39.68 3.67
307 333 3.936772 ATCGCCGTGCCCATGGTTT 62.937 57.895 11.73 0.00 39.68 3.27
308 334 2.544590 ATCGCCGTGCCCATGGTTTA 62.545 55.000 11.73 0.00 39.68 2.01
309 335 2.118404 CGCCGTGCCCATGGTTTAT 61.118 57.895 11.73 0.00 39.68 1.40
310 336 1.437160 GCCGTGCCCATGGTTTATG 59.563 57.895 11.73 1.81 39.68 1.90
311 337 1.034838 GCCGTGCCCATGGTTTATGA 61.035 55.000 11.73 0.00 39.21 2.15
312 338 1.691196 CCGTGCCCATGGTTTATGAT 58.309 50.000 11.73 0.00 39.21 2.45
313 339 2.031120 CCGTGCCCATGGTTTATGATT 58.969 47.619 11.73 0.00 39.21 2.57
314 340 2.430332 CCGTGCCCATGGTTTATGATTT 59.570 45.455 11.73 0.00 39.21 2.17
315 341 3.118811 CCGTGCCCATGGTTTATGATTTT 60.119 43.478 11.73 0.00 39.21 1.82
316 342 3.864583 CGTGCCCATGGTTTATGATTTTG 59.135 43.478 11.73 0.00 39.21 2.44
317 343 4.620332 CGTGCCCATGGTTTATGATTTTGT 60.620 41.667 11.73 0.00 39.21 2.83
318 344 5.244755 GTGCCCATGGTTTATGATTTTGTT 58.755 37.500 11.73 0.00 39.21 2.83
319 345 5.704978 GTGCCCATGGTTTATGATTTTGTTT 59.295 36.000 11.73 0.00 39.21 2.83
320 346 5.704515 TGCCCATGGTTTATGATTTTGTTTG 59.295 36.000 11.73 0.00 39.21 2.93
321 347 5.704978 GCCCATGGTTTATGATTTTGTTTGT 59.295 36.000 11.73 0.00 39.21 2.83
322 348 6.876257 GCCCATGGTTTATGATTTTGTTTGTA 59.124 34.615 11.73 0.00 39.21 2.41
323 349 7.552330 GCCCATGGTTTATGATTTTGTTTGTAT 59.448 33.333 11.73 0.00 39.21 2.29
338 364 9.674068 TTTTGTTTGTATATATGCTGGTAGACA 57.326 29.630 2.37 0.00 0.00 3.41
353 379 3.614616 GGTAGACAGAAAACATCGAGCTG 59.385 47.826 0.00 0.00 0.00 4.24
359 385 2.225019 AGAAAACATCGAGCTGCTGTTG 59.775 45.455 7.01 7.64 37.03 3.33
360 386 1.882912 AAACATCGAGCTGCTGTTGA 58.117 45.000 7.01 2.21 37.03 3.18
378 404 4.018506 TGTTGAGGGATCATTGGTGTATGT 60.019 41.667 0.00 0.00 0.00 2.29
385 411 2.989909 TCATTGGTGTATGTGCTCCTG 58.010 47.619 0.00 0.00 0.00 3.86
399 425 2.373169 TGCTCCTGGTCAATTCTGTTCT 59.627 45.455 0.00 0.00 0.00 3.01
433 459 3.322254 GTCCCGTGATGGTTCATCTAGAT 59.678 47.826 0.00 0.00 41.06 1.98
462 490 9.495754 GTTGATTAGAATTTTACTGATCAGTGC 57.504 33.333 33.76 17.13 42.52 4.40
466 494 4.946157 AGAATTTTACTGATCAGTGCTGGG 59.054 41.667 33.76 6.47 42.52 4.45
490 518 1.335872 GCCGTGGTGGATTCTTGTTTG 60.336 52.381 0.00 0.00 42.00 2.93
492 520 2.031157 CCGTGGTGGATTCTTGTTTGTC 60.031 50.000 0.00 0.00 42.00 3.18
493 521 2.349438 CGTGGTGGATTCTTGTTTGTCG 60.349 50.000 0.00 0.00 0.00 4.35
505 533 0.593128 GTTTGTCGCTGCACCAGATT 59.407 50.000 0.00 0.00 32.44 2.40
506 534 1.804151 GTTTGTCGCTGCACCAGATTA 59.196 47.619 0.00 0.00 32.44 1.75
507 535 2.401583 TTGTCGCTGCACCAGATTAT 57.598 45.000 0.00 0.00 32.44 1.28
508 536 2.401583 TGTCGCTGCACCAGATTATT 57.598 45.000 0.00 0.00 32.44 1.40
512 540 2.092968 TCGCTGCACCAGATTATTCCTT 60.093 45.455 0.00 0.00 32.44 3.36
520 548 2.423947 CCAGATTATTCCTTGGCTGGCT 60.424 50.000 2.00 0.00 36.80 4.75
521 549 2.883386 CAGATTATTCCTTGGCTGGCTC 59.117 50.000 2.00 0.00 0.00 4.70
532 560 1.005805 TGGCTGGCTCATGGTGTTAAT 59.994 47.619 2.00 0.00 0.00 1.40
533 561 1.678101 GGCTGGCTCATGGTGTTAATC 59.322 52.381 0.00 0.00 0.00 1.75
535 563 2.615912 GCTGGCTCATGGTGTTAATCTC 59.384 50.000 0.00 0.00 0.00 2.75
536 564 3.209410 CTGGCTCATGGTGTTAATCTCC 58.791 50.000 0.00 0.00 0.00 3.71
544 572 4.220693 TGGTGTTAATCTCCATGGTCTG 57.779 45.455 12.58 3.75 35.16 3.51
545 573 2.945668 GGTGTTAATCTCCATGGTCTGC 59.054 50.000 12.58 0.00 0.00 4.26
546 574 2.945668 GTGTTAATCTCCATGGTCTGCC 59.054 50.000 12.58 0.00 0.00 4.85
567 606 4.640201 GCCACTCTGCCTTATTGTTATTCA 59.360 41.667 0.00 0.00 0.00 2.57
590 636 7.993101 TCAATCTCTTTCTGCTAATTTGGATG 58.007 34.615 0.00 0.00 0.00 3.51
605 651 2.172679 TGGATGGACGTAGTACTGCAA 58.827 47.619 11.70 0.00 45.52 4.08
618 664 8.195436 ACGTAGTACTGCAATTGTATGTTAGAT 58.805 33.333 11.70 0.00 41.94 1.98
624 670 7.755591 ACTGCAATTGTATGTTAGATTCACAG 58.244 34.615 7.40 3.20 0.00 3.66
654 700 1.920574 CGCAGTTAGATCGACCTGTTG 59.079 52.381 2.54 0.00 0.00 3.33
829 890 6.000891 TCACATTGCTTCATGACTTTGTAC 57.999 37.500 0.00 0.00 0.00 2.90
835 896 4.154737 TGCTTCATGACTTTGTACATCTGC 59.845 41.667 0.00 0.00 0.00 4.26
848 909 3.543680 ACATCTGCTTGTATACGCCTT 57.456 42.857 0.00 0.00 0.00 4.35
892 954 6.541641 TGCTTTGTTTGCAATTTCCAACTATT 59.458 30.769 0.00 0.00 37.51 1.73
911 1194 8.817100 CAACTATTCGTATCTGTTGCAAGATTA 58.183 33.333 6.23 0.00 37.98 1.75
925 1208 7.970061 TGTTGCAAGATTAAGATTATTGCTGTC 59.030 33.333 0.00 1.86 44.99 3.51
929 1212 9.230932 GCAAGATTAAGATTATTGCTGTCTTTC 57.769 33.333 1.20 0.00 42.24 2.62
958 1298 8.229811 TCGTGTCTTTCTTGATTTGTTCATATG 58.770 33.333 0.00 0.00 33.34 1.78
972 1312 4.248859 GTTCATATGCGCCTGACATATCT 58.751 43.478 4.18 0.00 38.38 1.98
981 1333 4.142600 GCGCCTGACATATCTTGTTTTCTT 60.143 41.667 0.00 0.00 39.18 2.52
1029 1838 1.699730 TTGTGAAGACTCTCACCGGA 58.300 50.000 9.46 0.00 44.30 5.14
1164 2201 3.147595 CTCGAGGATGGCCGGACA 61.148 66.667 15.46 15.46 39.96 4.02
1218 2255 1.203441 TCCATCTGGTGCTCAGGCTT 61.203 55.000 7.57 0.00 43.53 4.35
1266 2303 1.002134 CCTCACCGGCAAGACCATT 60.002 57.895 0.00 0.00 39.03 3.16
1473 2510 2.125912 CAGTGAGTTCTCCGGGCG 60.126 66.667 0.00 0.00 0.00 6.13
1475 2512 2.182030 GTGAGTTCTCCGGGCGAG 59.818 66.667 0.00 0.00 40.30 5.03
1476 2513 2.282958 TGAGTTCTCCGGGCGAGT 60.283 61.111 0.00 0.00 39.84 4.18
1477 2514 1.906824 TGAGTTCTCCGGGCGAGTT 60.907 57.895 0.00 0.00 39.84 3.01
1478 2515 1.153804 GAGTTCTCCGGGCGAGTTC 60.154 63.158 0.00 0.00 39.84 3.01
1479 2516 2.125633 GTTCTCCGGGCGAGTTCC 60.126 66.667 0.00 0.00 39.84 3.62
1480 2517 3.387947 TTCTCCGGGCGAGTTCCC 61.388 66.667 0.00 0.00 43.02 3.97
1487 2524 3.081409 GGCGAGTTCCCCAGGCTA 61.081 66.667 0.00 0.00 0.00 3.93
1488 2525 2.187163 GCGAGTTCCCCAGGCTAC 59.813 66.667 0.00 0.00 0.00 3.58
1489 2526 2.901042 CGAGTTCCCCAGGCTACC 59.099 66.667 0.00 0.00 0.00 3.18
1490 2527 1.686110 CGAGTTCCCCAGGCTACCT 60.686 63.158 0.00 0.00 0.00 3.08
1519 2556 2.224066 CGGCCTCTTCCATCGTATTCTT 60.224 50.000 0.00 0.00 0.00 2.52
1524 2561 5.354234 GCCTCTTCCATCGTATTCTTTTTGA 59.646 40.000 0.00 0.00 0.00 2.69
1585 2622 8.800370 TTATGTGCCATTTGTTAGAACATCTA 57.200 30.769 0.00 0.00 38.95 1.98
1590 2627 5.979517 GCCATTTGTTAGAACATCTATTGCC 59.020 40.000 0.00 0.00 38.95 4.52
1611 2648 0.739112 CCTTCGAGCAGCTTGGTCTC 60.739 60.000 9.98 3.77 42.30 3.36
1613 2650 2.492449 TTCGAGCAGCTTGGTCTCCG 62.492 60.000 9.98 0.24 42.30 4.63
1644 2684 7.435068 TCTTATTCTGTAACTGGCTGTTTTC 57.565 36.000 15.08 9.49 39.89 2.29
1648 2688 2.880890 CTGTAACTGGCTGTTTTCTGCT 59.119 45.455 15.08 0.00 42.95 4.24
1669 2716 2.990284 TGGTCCCCTTTTCTGGTTATCA 59.010 45.455 0.00 0.00 0.00 2.15
1672 2719 4.569865 GGTCCCCTTTTCTGGTTATCACAT 60.570 45.833 0.00 0.00 0.00 3.21
1675 2722 6.486993 GTCCCCTTTTCTGGTTATCACATATC 59.513 42.308 0.00 0.00 0.00 1.63
1694 2741 9.322773 CACATATCCTCATATGACATGTATTCC 57.677 37.037 0.00 0.00 43.37 3.01
1695 2742 9.050154 ACATATCCTCATATGACATGTATTCCA 57.950 33.333 0.00 0.00 43.37 3.53
1696 2743 9.895138 CATATCCTCATATGACATGTATTCCAA 57.105 33.333 0.00 0.00 43.37 3.53
1699 2746 9.818270 ATCCTCATATGACATGTATTCCAAAAT 57.182 29.630 0.00 0.00 0.00 1.82
1700 2747 9.645128 TCCTCATATGACATGTATTCCAAAATT 57.355 29.630 0.00 0.00 0.00 1.82
1737 2784 1.062880 ACACGACGCGAATTTTTGTGT 59.937 42.857 15.93 13.72 37.97 3.72
1755 2802 1.980232 TCATGGTACCACGCGAGGT 60.980 57.895 30.48 30.48 45.72 3.85
1762 2809 1.657094 GTACCACGCGAGGTTGTTATG 59.343 52.381 32.59 7.08 43.08 1.90
1938 2993 6.534793 CAGGTTACCATTCAATGCAATTAACC 59.465 38.462 3.51 14.74 32.46 2.85
2090 3716 4.888823 TGCTCCAATTCTTGCTTGCATATA 59.111 37.500 0.00 0.00 0.00 0.86
2251 7569 1.704641 AAGGCTCCTTGAACCAAACC 58.295 50.000 0.00 0.00 34.60 3.27
2413 7782 2.267188 TAGACGACAAATCCGTTCGG 57.733 50.000 4.74 4.74 40.67 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.300634 GGGCTTTACGTGGGCCTAA 59.699 57.895 21.33 0.00 44.70 2.69
1 2 1.919308 TGGGCTTTACGTGGGCCTA 60.919 57.895 23.09 16.92 46.53 3.93
2 3 3.253838 TGGGCTTTACGTGGGCCT 61.254 61.111 23.09 0.00 46.53 5.19
3 4 3.060000 GTGGGCTTTACGTGGGCC 61.060 66.667 18.58 18.58 46.56 5.80
4 5 3.060000 GGTGGGCTTTACGTGGGC 61.060 66.667 0.00 0.21 0.00 5.36
5 6 1.376812 GAGGTGGGCTTTACGTGGG 60.377 63.158 0.00 0.00 0.00 4.61
6 7 1.740296 CGAGGTGGGCTTTACGTGG 60.740 63.158 0.00 0.00 0.00 4.94
7 8 2.388232 GCGAGGTGGGCTTTACGTG 61.388 63.158 0.00 0.00 0.00 4.49
8 9 2.047560 GCGAGGTGGGCTTTACGT 60.048 61.111 0.00 0.00 0.00 3.57
9 10 2.047655 TGCGAGGTGGGCTTTACG 60.048 61.111 0.00 0.00 0.00 3.18
10 11 2.399356 GCTGCGAGGTGGGCTTTAC 61.399 63.158 0.00 0.00 0.00 2.01
11 12 2.046314 GCTGCGAGGTGGGCTTTA 60.046 61.111 0.00 0.00 0.00 1.85
12 13 3.958860 AGCTGCGAGGTGGGCTTT 61.959 61.111 0.00 0.00 0.00 3.51
13 14 4.711949 CAGCTGCGAGGTGGGCTT 62.712 66.667 0.00 0.00 39.87 4.35
17 18 2.262471 GAATTGCAGCTGCGAGGTGG 62.262 60.000 31.23 0.00 43.49 4.61
18 19 1.136147 GAATTGCAGCTGCGAGGTG 59.864 57.895 31.23 9.95 45.86 4.00
19 20 2.042831 GGAATTGCAGCTGCGAGGT 61.043 57.895 31.23 22.24 45.83 3.85
20 21 2.768492 GGGAATTGCAGCTGCGAGG 61.768 63.158 31.23 0.00 45.83 4.63
21 22 2.768492 GGGGAATTGCAGCTGCGAG 61.768 63.158 31.23 0.00 45.83 5.03
22 23 2.751436 GGGGAATTGCAGCTGCGA 60.751 61.111 30.31 30.31 45.83 5.10
23 24 3.830192 GGGGGAATTGCAGCTGCG 61.830 66.667 32.11 0.00 45.83 5.18
24 25 2.681064 TGGGGGAATTGCAGCTGC 60.681 61.111 31.89 31.89 42.50 5.25
25 26 1.607178 TGTGGGGGAATTGCAGCTG 60.607 57.895 10.11 10.11 0.00 4.24
26 27 1.607467 GTGTGGGGGAATTGCAGCT 60.607 57.895 0.00 0.00 0.00 4.24
27 28 2.973082 GTGTGGGGGAATTGCAGC 59.027 61.111 0.00 0.00 0.00 5.25
28 29 2.993471 GCGTGTGGGGGAATTGCAG 61.993 63.158 0.00 0.00 0.00 4.41
29 30 2.988684 GCGTGTGGGGGAATTGCA 60.989 61.111 0.00 0.00 0.00 4.08
30 31 2.283472 GATGCGTGTGGGGGAATTGC 62.283 60.000 0.00 0.00 0.00 3.56
31 32 1.809207 GATGCGTGTGGGGGAATTG 59.191 57.895 0.00 0.00 0.00 2.32
32 33 1.748879 CGATGCGTGTGGGGGAATT 60.749 57.895 0.00 0.00 0.00 2.17
33 34 2.124736 CGATGCGTGTGGGGGAAT 60.125 61.111 0.00 0.00 0.00 3.01
34 35 3.315140 TCGATGCGTGTGGGGGAA 61.315 61.111 0.00 0.00 0.00 3.97
35 36 4.077184 GTCGATGCGTGTGGGGGA 62.077 66.667 0.00 0.00 0.00 4.81
39 40 3.345209 TACGGGTCGATGCGTGTGG 62.345 63.158 0.00 0.00 0.00 4.17
40 41 2.156446 GTACGGGTCGATGCGTGTG 61.156 63.158 0.00 0.00 0.00 3.82
41 42 2.180017 GTACGGGTCGATGCGTGT 59.820 61.111 0.00 0.00 0.00 4.49
42 43 2.947621 CGTACGGGTCGATGCGTG 60.948 66.667 7.57 0.00 0.00 5.34
43 44 4.842091 GCGTACGGGTCGATGCGT 62.842 66.667 18.39 0.00 0.00 5.24
44 45 4.547905 AGCGTACGGGTCGATGCG 62.548 66.667 18.39 0.00 0.00 4.73
45 46 2.654404 GAGCGTACGGGTCGATGC 60.654 66.667 18.39 0.00 32.77 3.91
50 51 0.243095 AACAGAAGAGCGTACGGGTC 59.757 55.000 18.39 12.44 43.56 4.46
51 52 0.243095 GAACAGAAGAGCGTACGGGT 59.757 55.000 18.39 3.09 0.00 5.28
52 53 0.797249 CGAACAGAAGAGCGTACGGG 60.797 60.000 18.39 0.00 0.00 5.28
53 54 1.403972 GCGAACAGAAGAGCGTACGG 61.404 60.000 18.39 0.23 0.00 4.02
54 55 1.403972 GGCGAACAGAAGAGCGTACG 61.404 60.000 11.84 11.84 0.00 3.67
55 56 0.109226 AGGCGAACAGAAGAGCGTAC 60.109 55.000 0.00 0.00 0.00 3.67
56 57 1.400846 CTAGGCGAACAGAAGAGCGTA 59.599 52.381 0.00 0.00 0.00 4.42
57 58 0.171455 CTAGGCGAACAGAAGAGCGT 59.829 55.000 0.00 0.00 0.00 5.07
58 59 0.452184 TCTAGGCGAACAGAAGAGCG 59.548 55.000 0.00 0.00 0.00 5.03
59 60 1.474879 ACTCTAGGCGAACAGAAGAGC 59.525 52.381 0.00 0.00 37.75 4.09
60 61 6.621316 TTATACTCTAGGCGAACAGAAGAG 57.379 41.667 0.00 0.00 39.65 2.85
61 62 7.400599 TTTTATACTCTAGGCGAACAGAAGA 57.599 36.000 0.00 0.00 0.00 2.87
62 63 8.649973 AATTTTATACTCTAGGCGAACAGAAG 57.350 34.615 0.00 0.00 0.00 2.85
63 64 7.709613 GGAATTTTATACTCTAGGCGAACAGAA 59.290 37.037 0.00 0.00 0.00 3.02
64 65 7.208080 GGAATTTTATACTCTAGGCGAACAGA 58.792 38.462 0.00 0.00 0.00 3.41
65 66 6.424207 GGGAATTTTATACTCTAGGCGAACAG 59.576 42.308 0.00 0.00 0.00 3.16
66 67 6.285990 GGGAATTTTATACTCTAGGCGAACA 58.714 40.000 0.00 0.00 0.00 3.18
67 68 5.699915 GGGGAATTTTATACTCTAGGCGAAC 59.300 44.000 0.00 0.00 0.00 3.95
68 69 5.221783 GGGGGAATTTTATACTCTAGGCGAA 60.222 44.000 0.00 0.00 0.00 4.70
69 70 4.285260 GGGGGAATTTTATACTCTAGGCGA 59.715 45.833 0.00 0.00 0.00 5.54
70 71 4.041198 TGGGGGAATTTTATACTCTAGGCG 59.959 45.833 0.00 0.00 0.00 5.52
71 72 5.163131 TGTGGGGGAATTTTATACTCTAGGC 60.163 44.000 0.00 0.00 0.00 3.93
72 73 6.296803 GTGTGGGGGAATTTTATACTCTAGG 58.703 44.000 0.00 0.00 0.00 3.02
73 74 5.989777 CGTGTGGGGGAATTTTATACTCTAG 59.010 44.000 0.00 0.00 0.00 2.43
74 75 5.685599 GCGTGTGGGGGAATTTTATACTCTA 60.686 44.000 0.00 0.00 0.00 2.43
75 76 4.777463 CGTGTGGGGGAATTTTATACTCT 58.223 43.478 0.00 0.00 0.00 3.24
76 77 3.314357 GCGTGTGGGGGAATTTTATACTC 59.686 47.826 0.00 0.00 0.00 2.59
77 78 3.284617 GCGTGTGGGGGAATTTTATACT 58.715 45.455 0.00 0.00 0.00 2.12
78 79 3.018149 TGCGTGTGGGGGAATTTTATAC 58.982 45.455 0.00 0.00 0.00 1.47
79 80 3.367646 TGCGTGTGGGGGAATTTTATA 57.632 42.857 0.00 0.00 0.00 0.98
80 81 2.223803 TGCGTGTGGGGGAATTTTAT 57.776 45.000 0.00 0.00 0.00 1.40
81 82 2.096248 GATGCGTGTGGGGGAATTTTA 58.904 47.619 0.00 0.00 0.00 1.52
82 83 0.894835 GATGCGTGTGGGGGAATTTT 59.105 50.000 0.00 0.00 0.00 1.82
83 84 1.312371 CGATGCGTGTGGGGGAATTT 61.312 55.000 0.00 0.00 0.00 1.82
84 85 1.748879 CGATGCGTGTGGGGGAATT 60.749 57.895 0.00 0.00 0.00 2.17
85 86 2.124736 CGATGCGTGTGGGGGAAT 60.125 61.111 0.00 0.00 0.00 3.01
86 87 3.315140 TCGATGCGTGTGGGGGAA 61.315 61.111 0.00 0.00 0.00 3.97
87 88 4.077184 GTCGATGCGTGTGGGGGA 62.077 66.667 0.00 0.00 0.00 4.81
132 136 2.032808 GCTTGTATCGCGGAGGATTTTC 60.033 50.000 6.13 0.00 0.00 2.29
140 144 1.452953 ATCGAGGCTTGTATCGCGGA 61.453 55.000 6.13 0.00 38.79 5.54
145 149 2.295909 AGCTGAGATCGAGGCTTGTATC 59.704 50.000 0.77 4.17 0.00 2.24
147 151 1.678627 GAGCTGAGATCGAGGCTTGTA 59.321 52.381 0.77 0.00 35.01 2.41
199 203 0.608035 TTGGGGCACAGGAAATCGAC 60.608 55.000 0.00 0.00 0.00 4.20
207 211 3.307975 CCATCTATATCTTGGGGCACAGG 60.308 52.174 0.00 0.00 0.00 4.00
210 215 4.521146 CATCCATCTATATCTTGGGGCAC 58.479 47.826 0.00 0.00 0.00 5.01
212 217 3.549794 GCATCCATCTATATCTTGGGGC 58.450 50.000 0.00 0.00 0.00 5.80
220 225 8.242729 TCATCTAATCACGCATCCATCTATAT 57.757 34.615 0.00 0.00 0.00 0.86
224 229 4.879197 TCATCTAATCACGCATCCATCT 57.121 40.909 0.00 0.00 0.00 2.90
225 230 5.173664 TCATCATCTAATCACGCATCCATC 58.826 41.667 0.00 0.00 0.00 3.51
226 231 5.156608 TCATCATCTAATCACGCATCCAT 57.843 39.130 0.00 0.00 0.00 3.41
228 233 4.564041 ACTCATCATCTAATCACGCATCC 58.436 43.478 0.00 0.00 0.00 3.51
229 234 6.018425 ACAAACTCATCATCTAATCACGCATC 60.018 38.462 0.00 0.00 0.00 3.91
231 236 5.178061 ACAAACTCATCATCTAATCACGCA 58.822 37.500 0.00 0.00 0.00 5.24
233 238 9.855361 GAATTACAAACTCATCATCTAATCACG 57.145 33.333 0.00 0.00 0.00 4.35
237 242 9.911788 AGGTGAATTACAAACTCATCATCTAAT 57.088 29.630 0.00 0.00 0.00 1.73
238 243 9.739276 AAGGTGAATTACAAACTCATCATCTAA 57.261 29.630 0.00 0.00 28.69 2.10
239 244 9.166173 CAAGGTGAATTACAAACTCATCATCTA 57.834 33.333 0.00 0.00 28.69 1.98
241 246 7.253422 CCAAGGTGAATTACAAACTCATCATC 58.747 38.462 0.00 0.00 0.00 2.92
242 247 6.350445 GCCAAGGTGAATTACAAACTCATCAT 60.350 38.462 0.00 0.00 0.00 2.45
243 248 5.048083 GCCAAGGTGAATTACAAACTCATCA 60.048 40.000 0.00 0.00 0.00 3.07
244 249 5.402398 GCCAAGGTGAATTACAAACTCATC 58.598 41.667 0.00 0.00 0.00 2.92
245 250 4.082787 CGCCAAGGTGAATTACAAACTCAT 60.083 41.667 0.00 0.00 0.00 2.90
246 251 3.252215 CGCCAAGGTGAATTACAAACTCA 59.748 43.478 0.00 0.00 0.00 3.41
247 252 3.500680 TCGCCAAGGTGAATTACAAACTC 59.499 43.478 0.00 0.00 0.00 3.01
248 253 3.482436 TCGCCAAGGTGAATTACAAACT 58.518 40.909 0.00 0.00 0.00 2.66
249 254 3.907894 TCGCCAAGGTGAATTACAAAC 57.092 42.857 0.00 0.00 0.00 2.93
251 256 3.442273 GGAATCGCCAAGGTGAATTACAA 59.558 43.478 6.43 0.00 38.20 2.41
252 257 3.013921 GGAATCGCCAAGGTGAATTACA 58.986 45.455 6.43 0.00 38.20 2.41
253 258 2.357952 GGGAATCGCCAAGGTGAATTAC 59.642 50.000 6.43 3.10 38.20 1.89
255 260 1.474330 GGGAATCGCCAAGGTGAATT 58.526 50.000 6.43 2.28 38.20 2.17
256 261 0.748005 CGGGAATCGCCAAGGTGAAT 60.748 55.000 6.43 0.00 38.20 2.57
257 262 1.376683 CGGGAATCGCCAAGGTGAA 60.377 57.895 6.43 0.00 38.20 3.18
264 290 1.802337 CGGATCTACGGGAATCGCCA 61.802 60.000 0.00 0.00 43.89 5.69
272 298 0.523966 GATCTCTGCGGATCTACGGG 59.476 60.000 0.00 0.00 39.06 5.28
285 311 3.157252 ATGGGCACGGCGATCTCT 61.157 61.111 16.62 0.00 0.00 3.10
292 318 1.034838 TCATAAACCATGGGCACGGC 61.035 55.000 18.09 0.00 35.16 5.68
312 338 9.674068 TGTCTACCAGCATATATACAAACAAAA 57.326 29.630 0.00 0.00 0.00 2.44
313 339 9.325198 CTGTCTACCAGCATATATACAAACAAA 57.675 33.333 0.00 0.00 33.59 2.83
314 340 8.700973 TCTGTCTACCAGCATATATACAAACAA 58.299 33.333 0.00 0.00 41.25 2.83
315 341 8.245195 TCTGTCTACCAGCATATATACAAACA 57.755 34.615 0.00 0.00 41.25 2.83
316 342 9.542462 TTTCTGTCTACCAGCATATATACAAAC 57.458 33.333 0.00 0.00 41.25 2.93
318 344 9.542462 GTTTTCTGTCTACCAGCATATATACAA 57.458 33.333 0.00 0.00 41.25 2.41
319 345 8.700973 TGTTTTCTGTCTACCAGCATATATACA 58.299 33.333 0.00 0.00 41.25 2.29
320 346 9.712305 ATGTTTTCTGTCTACCAGCATATATAC 57.288 33.333 0.00 0.00 41.25 1.47
321 347 9.929180 GATGTTTTCTGTCTACCAGCATATATA 57.071 33.333 0.00 0.00 41.25 0.86
322 348 7.600375 CGATGTTTTCTGTCTACCAGCATATAT 59.400 37.037 0.00 0.00 41.25 0.86
323 349 6.923508 CGATGTTTTCTGTCTACCAGCATATA 59.076 38.462 0.00 0.00 41.25 0.86
324 350 5.755375 CGATGTTTTCTGTCTACCAGCATAT 59.245 40.000 0.00 0.00 41.25 1.78
325 351 5.105513 TCGATGTTTTCTGTCTACCAGCATA 60.106 40.000 0.00 0.00 41.25 3.14
326 352 3.935203 CGATGTTTTCTGTCTACCAGCAT 59.065 43.478 0.00 0.00 41.25 3.79
327 353 3.006430 TCGATGTTTTCTGTCTACCAGCA 59.994 43.478 0.00 0.00 41.25 4.41
328 354 3.585862 TCGATGTTTTCTGTCTACCAGC 58.414 45.455 0.00 0.00 41.25 4.85
329 355 3.614616 GCTCGATGTTTTCTGTCTACCAG 59.385 47.826 0.00 0.00 42.97 4.00
330 356 3.258372 AGCTCGATGTTTTCTGTCTACCA 59.742 43.478 0.00 0.00 0.00 3.25
331 357 3.614616 CAGCTCGATGTTTTCTGTCTACC 59.385 47.826 0.00 0.00 0.00 3.18
332 358 3.061429 GCAGCTCGATGTTTTCTGTCTAC 59.939 47.826 0.00 0.00 0.00 2.59
333 359 3.056536 AGCAGCTCGATGTTTTCTGTCTA 60.057 43.478 0.00 0.00 0.00 2.59
334 360 2.072298 GCAGCTCGATGTTTTCTGTCT 58.928 47.619 0.00 0.00 0.00 3.41
335 361 2.072298 AGCAGCTCGATGTTTTCTGTC 58.928 47.619 0.00 0.00 0.00 3.51
336 362 1.802960 CAGCAGCTCGATGTTTTCTGT 59.197 47.619 0.00 0.00 0.00 3.41
337 363 1.802960 ACAGCAGCTCGATGTTTTCTG 59.197 47.619 0.00 0.00 43.15 3.02
338 364 2.175878 ACAGCAGCTCGATGTTTTCT 57.824 45.000 0.00 0.00 43.15 2.52
344 370 1.088340 CCCTCAACAGCAGCTCGATG 61.088 60.000 0.00 0.00 36.94 3.84
345 371 1.220206 CCCTCAACAGCAGCTCGAT 59.780 57.895 0.00 0.00 0.00 3.59
353 379 1.747355 CACCAATGATCCCTCAACAGC 59.253 52.381 0.00 0.00 34.37 4.40
359 385 2.880890 GCACATACACCAATGATCCCTC 59.119 50.000 0.00 0.00 0.00 4.30
360 386 2.511218 AGCACATACACCAATGATCCCT 59.489 45.455 0.00 0.00 0.00 4.20
378 404 2.373169 AGAACAGAATTGACCAGGAGCA 59.627 45.455 0.00 0.00 0.00 4.26
385 411 7.487189 CAGCAATTTCATAGAACAGAATTGACC 59.513 37.037 10.33 0.00 0.00 4.02
399 425 3.342377 TCACGGGACAGCAATTTCATA 57.658 42.857 0.00 0.00 0.00 2.15
453 481 2.672908 CAGGCCCAGCACTGATCA 59.327 61.111 0.00 0.00 36.86 2.92
466 494 3.134127 GAATCCACCACGGCAGGC 61.134 66.667 0.00 0.00 33.14 4.85
478 506 1.266718 TGCAGCGACAAACAAGAATCC 59.733 47.619 0.00 0.00 0.00 3.01
490 518 1.599542 GGAATAATCTGGTGCAGCGAC 59.400 52.381 11.91 0.00 0.00 5.19
492 520 1.959042 AGGAATAATCTGGTGCAGCG 58.041 50.000 11.91 6.42 0.00 5.18
493 521 2.360165 CCAAGGAATAATCTGGTGCAGC 59.640 50.000 9.47 9.47 0.00 5.25
505 533 1.133699 CCATGAGCCAGCCAAGGAATA 60.134 52.381 0.00 0.00 0.00 1.75
506 534 0.396695 CCATGAGCCAGCCAAGGAAT 60.397 55.000 0.00 0.00 0.00 3.01
507 535 1.000521 CCATGAGCCAGCCAAGGAA 60.001 57.895 0.00 0.00 0.00 3.36
508 536 2.233566 ACCATGAGCCAGCCAAGGA 61.234 57.895 0.00 0.00 0.00 3.36
512 540 0.403655 TTAACACCATGAGCCAGCCA 59.596 50.000 0.00 0.00 0.00 4.75
539 567 0.543749 ATAAGGCAGAGTGGCAGACC 59.456 55.000 3.09 0.00 46.46 3.85
540 568 2.012673 CAATAAGGCAGAGTGGCAGAC 58.987 52.381 3.09 0.00 46.46 3.51
541 569 1.630369 ACAATAAGGCAGAGTGGCAGA 59.370 47.619 3.09 0.00 46.46 4.26
542 570 2.119801 ACAATAAGGCAGAGTGGCAG 57.880 50.000 3.09 0.00 46.46 4.85
544 572 4.640201 TGAATAACAATAAGGCAGAGTGGC 59.360 41.667 0.00 0.00 44.10 5.01
545 573 6.757897 TTGAATAACAATAAGGCAGAGTGG 57.242 37.500 0.00 0.00 33.18 4.00
567 606 7.067981 GTCCATCCAAATTAGCAGAAAGAGATT 59.932 37.037 0.00 0.00 0.00 2.40
590 636 5.107133 ACATACAATTGCAGTACTACGTCC 58.893 41.667 5.05 0.00 0.00 4.79
624 670 3.302480 CGATCTAACTGCGGCACATTAAC 60.302 47.826 0.00 0.00 0.00 2.01
634 680 1.920574 CAACAGGTCGATCTAACTGCG 59.079 52.381 12.00 0.48 34.40 5.18
688 736 6.935208 ACTGGAAGACAATCTAACTGTTTACC 59.065 38.462 0.00 0.00 37.43 2.85
829 890 4.211374 GGTAAAGGCGTATACAAGCAGATG 59.789 45.833 3.32 0.00 34.54 2.90
835 896 3.250040 GGCATGGTAAAGGCGTATACAAG 59.750 47.826 3.32 0.00 0.00 3.16
848 909 4.460263 AGCAAGATAAATCGGCATGGTAA 58.540 39.130 10.75 0.00 35.42 2.85
892 954 9.764363 ATAATCTTAATCTTGCAACAGATACGA 57.236 29.630 0.00 0.00 32.84 3.43
911 1194 6.312426 CACGAGAGAAAGACAGCAATAATCTT 59.688 38.462 0.00 0.00 34.11 2.40
925 1208 6.777526 AATCAAGAAAGACACGAGAGAAAG 57.222 37.500 0.00 0.00 0.00 2.62
929 1212 5.914085 ACAAATCAAGAAAGACACGAGAG 57.086 39.130 0.00 0.00 0.00 3.20
958 1298 3.375299 AGAAAACAAGATATGTCAGGCGC 59.625 43.478 0.00 0.00 42.99 6.53
972 1312 9.376075 TGAATAGTTGAAATTGCAAGAAAACAA 57.624 25.926 4.94 4.46 0.00 2.83
981 1333 6.151480 TCTGCATCTGAATAGTTGAAATTGCA 59.849 34.615 0.00 0.00 35.35 4.08
1029 1838 3.744660 GACCTCAAGTGTGATGGTCTTT 58.255 45.455 13.54 0.00 42.64 2.52
1113 2150 1.875813 GATGAGACGCTGCTGGTCG 60.876 63.158 0.00 0.00 39.38 4.79
1164 2201 6.769822 CCTTCTGGATATTGTAATCAGCAAGT 59.230 38.462 0.00 0.00 34.57 3.16
1218 2255 3.405093 GATCTGCATGCCACCCCGA 62.405 63.158 16.68 2.43 0.00 5.14
1293 2330 3.436704 TCTTCGCCTTCACATTGTCAATC 59.563 43.478 0.00 0.00 0.00 2.67
1473 2510 4.482431 AGGTAGCCTGGGGAACTC 57.518 61.111 0.00 0.00 29.57 3.01
1493 2530 3.764160 GATGGAAGAGGCCGCCAGG 62.764 68.421 13.15 0.00 41.62 4.45
1494 2531 2.203126 GATGGAAGAGGCCGCCAG 60.203 66.667 13.15 0.00 34.74 4.85
1495 2532 4.161295 CGATGGAAGAGGCCGCCA 62.161 66.667 13.15 7.54 35.91 5.69
1496 2533 2.100879 ATACGATGGAAGAGGCCGCC 62.101 60.000 1.49 0.00 0.00 6.13
1497 2534 0.249911 AATACGATGGAAGAGGCCGC 60.250 55.000 0.00 0.00 0.00 6.53
1498 2535 1.341531 AGAATACGATGGAAGAGGCCG 59.658 52.381 0.00 0.00 0.00 6.13
1519 2556 9.814899 ATGACACAAAACTTGACATAATCAAAA 57.185 25.926 0.00 0.00 46.80 2.44
1524 2561 5.858049 CGCATGACACAAAACTTGACATAAT 59.142 36.000 0.00 0.00 0.00 1.28
1538 2575 2.135139 GAGTTTCAGACGCATGACACA 58.865 47.619 0.00 0.00 33.29 3.72
1585 2622 2.821366 CTGCTCGAAGGCGGCAAT 60.821 61.111 13.08 0.00 41.01 3.56
1590 2627 3.494336 CCAAGCTGCTCGAAGGCG 61.494 66.667 1.00 0.00 39.35 5.52
1611 2648 5.235186 CAGTTACAGAATAAGATTCAGGCGG 59.765 44.000 2.27 0.00 0.00 6.13
1613 2650 5.008118 GCCAGTTACAGAATAAGATTCAGGC 59.992 44.000 2.27 0.00 0.00 4.85
1669 2716 9.050154 TGGAATACATGTCATATGAGGATATGT 57.950 33.333 19.86 19.86 45.29 2.29
1698 2745 8.804743 CGTCGTGTGTGAATCTACTTTATAAAT 58.195 33.333 0.00 0.00 0.00 1.40
1699 2746 7.201376 GCGTCGTGTGTGAATCTACTTTATAAA 60.201 37.037 0.00 0.00 0.00 1.40
1700 2747 6.252015 GCGTCGTGTGTGAATCTACTTTATAA 59.748 38.462 0.00 0.00 0.00 0.98
1701 2748 5.740569 GCGTCGTGTGTGAATCTACTTTATA 59.259 40.000 0.00 0.00 0.00 0.98
1702 2749 4.561606 GCGTCGTGTGTGAATCTACTTTAT 59.438 41.667 0.00 0.00 0.00 1.40
1703 2750 3.916172 GCGTCGTGTGTGAATCTACTTTA 59.084 43.478 0.00 0.00 0.00 1.85
1704 2751 2.729882 GCGTCGTGTGTGAATCTACTTT 59.270 45.455 0.00 0.00 0.00 2.66
1705 2752 2.325761 GCGTCGTGTGTGAATCTACTT 58.674 47.619 0.00 0.00 0.00 2.24
1706 2753 1.728179 CGCGTCGTGTGTGAATCTACT 60.728 52.381 0.00 0.00 0.00 2.57
1707 2754 0.633733 CGCGTCGTGTGTGAATCTAC 59.366 55.000 0.00 0.00 0.00 2.59
1708 2755 0.518195 TCGCGTCGTGTGTGAATCTA 59.482 50.000 5.77 0.00 0.00 1.98
1709 2756 0.318360 TTCGCGTCGTGTGTGAATCT 60.318 50.000 5.77 0.00 31.37 2.40
1710 2757 0.713883 ATTCGCGTCGTGTGTGAATC 59.286 50.000 5.77 0.00 41.37 2.52
1711 2758 1.144969 AATTCGCGTCGTGTGTGAAT 58.855 45.000 5.77 7.08 45.66 2.57
1712 2759 0.931702 AAATTCGCGTCGTGTGTGAA 59.068 45.000 5.77 3.59 39.85 3.18
1713 2760 0.931702 AAAATTCGCGTCGTGTGTGA 59.068 45.000 5.77 0.00 0.00 3.58
1714 2761 1.442813 CAAAAATTCGCGTCGTGTGTG 59.557 47.619 5.77 0.00 0.00 3.82
1715 2762 1.062880 ACAAAAATTCGCGTCGTGTGT 59.937 42.857 5.77 2.01 0.00 3.72
1716 2763 1.442813 CACAAAAATTCGCGTCGTGTG 59.557 47.619 5.77 9.54 0.00 3.82
1717 2764 1.062880 ACACAAAAATTCGCGTCGTGT 59.937 42.857 5.77 7.47 0.00 4.49
1718 2765 1.701431 GACACAAAAATTCGCGTCGTG 59.299 47.619 5.77 0.00 0.00 4.35
1719 2766 1.328069 TGACACAAAAATTCGCGTCGT 59.672 42.857 5.77 0.00 0.00 4.34
1720 2767 2.011932 TGACACAAAAATTCGCGTCG 57.988 45.000 5.77 0.00 0.00 5.12
1737 2784 1.537814 AACCTCGCGTGGTACCATGA 61.538 55.000 33.81 22.20 39.83 3.07
1755 2802 2.665649 ATCGTCGGTCAGCATAACAA 57.334 45.000 0.00 0.00 0.00 2.83
1762 2809 0.807667 AGCATCAATCGTCGGTCAGC 60.808 55.000 0.00 0.00 0.00 4.26
1938 2993 1.956629 ATACGGCCCAGGTCACGAAG 61.957 60.000 0.00 0.00 0.00 3.79
2054 3678 2.136298 TGGAGCAACAACTTTCACCA 57.864 45.000 0.00 0.00 0.00 4.17
2090 3716 2.031120 CAAGGTTGTGGGTGAACATGT 58.969 47.619 0.00 0.00 0.00 3.21
2269 7595 7.985476 CAAAGAGAAGTTACTTTGGTTCAAGA 58.015 34.615 19.04 0.00 44.95 3.02


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

AutoCloner maintained by Alex Coulton.