Multiple sequence alignment - TraesCS7D01G491900

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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 TraesCS7D01G491900 chr7D 100.000 4057 0 0 1 4057 600872620 600876676 0.000000e+00 7492.0
1 TraesCS7D01G491900 chr7D 81.886 806 114 23 2088 2882 600702613 600701829 0.000000e+00 651.0
2 TraesCS7D01G491900 chr7D 81.799 478 59 8 1 452 61292332 61292807 3.830000e-100 375.0
3 TraesCS7D01G491900 chr7D 92.105 228 18 0 1298 1525 600703333 600703106 5.060000e-84 322.0
4 TraesCS7D01G491900 chr7D 78.105 475 82 16 1001 1460 600748481 600748948 8.590000e-72 281.0
5 TraesCS7D01G491900 chr7D 88.372 129 15 0 1072 1200 600703563 600703435 5.430000e-34 156.0
6 TraesCS7D01G491900 chr7D 82.313 147 21 5 1058 1200 17762562 17762417 5.510000e-24 122.0
7 TraesCS7D01G491900 chr7B 89.458 1385 94 30 1708 3077 680096277 680097624 0.000000e+00 1701.0
8 TraesCS7D01G491900 chr7B 86.517 712 54 9 1 678 680094535 680095238 0.000000e+00 745.0
9 TraesCS7D01G491900 chr7B 88.182 550 43 14 707 1243 680095234 680095774 1.590000e-178 636.0
10 TraesCS7D01G491900 chr7B 81.850 573 89 12 2315 2880 679998393 679997829 6.140000e-128 468.0
11 TraesCS7D01G491900 chr7B 90.690 290 24 2 1270 1559 680095767 680096053 2.290000e-102 383.0
12 TraesCS7D01G491900 chr7B 82.201 427 49 11 1087 1503 679930885 679930476 3.880000e-90 342.0
13 TraesCS7D01G491900 chr7B 89.823 226 21 2 1282 1506 679987242 679987466 5.130000e-74 289.0
14 TraesCS7D01G491900 chr7B 87.200 250 29 3 1 248 54558475 54558227 8.590000e-72 281.0
15 TraesCS7D01G491900 chr7B 88.158 228 25 2 226 452 510630916 510630690 1.860000e-68 270.0
16 TraesCS7D01G491900 chr7B 87.069 232 29 1 1799 2029 679930393 679930162 1.120000e-65 261.0
17 TraesCS7D01G491900 chr7B 87.336 229 28 1 1805 2032 680004250 680004022 1.120000e-65 261.0
18 TraesCS7D01G491900 chr7B 93.023 43 3 0 3867 3909 699819256 699819214 3.390000e-06 63.9
19 TraesCS7D01G491900 chr7B 89.362 47 4 1 3880 3925 81695607 81695561 1.580000e-04 58.4
20 TraesCS7D01G491900 chr7A 86.540 1263 85 29 3 1221 692795804 692797025 0.000000e+00 1312.0
21 TraesCS7D01G491900 chr7A 93.649 866 36 3 3193 4057 692810036 692810883 0.000000e+00 1277.0
22 TraesCS7D01G491900 chr7A 85.038 1183 115 18 1799 2975 692769682 692770808 0.000000e+00 1147.0
23 TraesCS7D01G491900 chr7A 94.522 712 35 3 1292 2000 692799533 692800243 0.000000e+00 1096.0
24 TraesCS7D01G491900 chr7A 96.595 558 19 0 2553 3110 692809480 692810037 0.000000e+00 926.0
25 TraesCS7D01G491900 chr7A 95.564 541 24 0 2017 2557 692800304 692800844 0.000000e+00 867.0
26 TraesCS7D01G491900 chr7A 82.086 815 113 25 2079 2882 692522308 692521516 0.000000e+00 665.0
27 TraesCS7D01G491900 chr7A 81.773 609 95 13 2287 2887 692613462 692614062 2.820000e-136 496.0
28 TraesCS7D01G491900 chr7A 90.795 239 18 3 1291 1525 692523098 692522860 2.350000e-82 316.0
29 TraesCS7D01G491900 chr7A 88.608 237 24 1 1275 1508 692762385 692762621 6.640000e-73 285.0
30 TraesCS7D01G491900 chr7A 90.863 197 18 0 1299 1495 692616817 692616621 8.650000e-67 265.0
31 TraesCS7D01G491900 chr7A 83.732 209 22 6 1044 1246 692762115 692762317 1.930000e-43 187.0
32 TraesCS7D01G491900 chr7A 88.406 138 12 1 1904 2037 692616260 692616123 3.240000e-36 163.0
33 TraesCS7D01G491900 chr7A 93.333 90 6 0 3107 3196 223532985 223532896 2.540000e-27 134.0
34 TraesCS7D01G491900 chr7A 84.496 129 20 0 1072 1200 692617081 692616953 1.180000e-25 128.0
35 TraesCS7D01G491900 chr7A 83.212 137 17 5 676 808 692761801 692761935 1.980000e-23 121.0
36 TraesCS7D01G491900 chr7A 88.119 101 8 3 3012 3110 692770810 692770908 2.560000e-22 117.0
37 TraesCS7D01G491900 chr3D 85.841 452 60 4 1 449 511529052 511529502 1.020000e-130 477.0
38 TraesCS7D01G491900 chr3D 82.700 526 83 5 2361 2885 12385826 12386344 1.030000e-125 460.0
39 TraesCS7D01G491900 chr3D 92.391 92 7 0 3105 3196 113456636 113456545 9.150000e-27 132.0
40 TraesCS7D01G491900 chr3D 77.876 113 20 4 3809 3919 34698344 34698453 9.410000e-07 65.8
41 TraesCS7D01G491900 chr6D 82.881 479 54 11 1 453 67688330 67688806 4.880000e-109 405.0
42 TraesCS7D01G491900 chr6D 94.318 88 5 0 3109 3196 67915700 67915787 7.070000e-28 135.0
43 TraesCS7D01G491900 chr1B 82.737 475 54 13 1 449 638063703 638064175 8.170000e-107 398.0
44 TraesCS7D01G491900 chr1B 80.585 479 62 12 1 452 675592416 675592890 1.400000e-89 340.0
45 TraesCS7D01G491900 chr1B 90.222 225 19 3 226 449 531690219 531690441 1.430000e-74 291.0
46 TraesCS7D01G491900 chrUn 82.008 478 54 10 1 449 63016088 63016562 1.060000e-100 377.0
47 TraesCS7D01G491900 chrUn 95.402 87 4 0 3108 3194 12907587 12907673 5.470000e-29 139.0
48 TraesCS7D01G491900 chr1D 81.723 476 58 14 1 449 227114165 227114638 1.780000e-98 370.0
49 TraesCS7D01G491900 chr1D 81.818 429 49 10 1 403 29562621 29563046 2.340000e-87 333.0
50 TraesCS7D01G491900 chr2D 88.095 252 25 5 1 249 22933886 22934135 1.100000e-75 294.0
51 TraesCS7D01G491900 chr2D 100.000 30 0 0 3880 3909 552623253 552623282 5.660000e-04 56.5
52 TraesCS7D01G491900 chr4A 88.393 224 25 1 226 449 605538385 605538607 6.680000e-68 268.0
53 TraesCS7D01G491900 chr4A 82.993 147 20 5 1058 1200 715912678 715912823 1.180000e-25 128.0
54 TraesCS7D01G491900 chr4A 85.965 114 14 2 1088 1200 715641590 715641478 1.980000e-23 121.0
55 TraesCS7D01G491900 chr4B 94.565 92 5 0 3108 3199 585960628 585960719 4.230000e-30 143.0
56 TraesCS7D01G491900 chr4B 94.505 91 4 1 3108 3197 138846363 138846453 5.470000e-29 139.0
57 TraesCS7D01G491900 chr4B 92.683 41 3 0 3878 3918 463076060 463076020 4.380000e-05 60.2
58 TraesCS7D01G491900 chr6B 94.382 89 5 0 3106 3194 702688136 702688048 1.970000e-28 137.0
59 TraesCS7D01G491900 chr6A 95.349 86 4 0 3109 3194 473616532 473616617 1.970000e-28 137.0
60 TraesCS7D01G491900 chr6A 90.698 43 4 0 3867 3909 548240692 548240650 1.580000e-04 58.4
61 TraesCS7D01G491900 chr6A 100.000 29 0 0 3881 3909 587639625 587639597 2.000000e-03 54.7
62 TraesCS7D01G491900 chr2B 93.333 90 6 0 3107 3196 785746847 785746758 2.540000e-27 134.0
63 TraesCS7D01G491900 chr2B 78.448 116 17 6 3806 3919 493655499 493655608 7.280000e-08 69.4
64 TraesCS7D01G491900 chr3B 91.209 91 8 0 1101 1191 17689172 17689082 1.530000e-24 124.0
65 TraesCS7D01G491900 chr4D 100.000 28 0 0 3882 3909 28898090 28898117 7.000000e-03 52.8


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 TraesCS7D01G491900 chr7D 600872620 600876676 4056 False 7492.000000 7492 100.000000 1 4057 1 chr7D.!!$F3 4056
1 TraesCS7D01G491900 chr7D 600701829 600703563 1734 True 376.333333 651 87.454333 1072 2882 3 chr7D.!!$R2 1810
2 TraesCS7D01G491900 chr7B 680094535 680097624 3089 False 866.250000 1701 88.711750 1 3077 4 chr7B.!!$F2 3076
3 TraesCS7D01G491900 chr7B 679997829 679998393 564 True 468.000000 468 81.850000 2315 2880 1 chr7B.!!$R4 565
4 TraesCS7D01G491900 chr7B 679930162 679930885 723 True 301.500000 342 84.635000 1087 2029 2 chr7B.!!$R7 942
5 TraesCS7D01G491900 chr7A 692809480 692810883 1403 False 1101.500000 1277 95.122000 2553 4057 2 chr7A.!!$F5 1504
6 TraesCS7D01G491900 chr7A 692795804 692800844 5040 False 1091.666667 1312 92.208667 3 2557 3 chr7A.!!$F4 2554
7 TraesCS7D01G491900 chr7A 692769682 692770908 1226 False 632.000000 1147 86.578500 1799 3110 2 chr7A.!!$F3 1311
8 TraesCS7D01G491900 chr7A 692613462 692614062 600 False 496.000000 496 81.773000 2287 2887 1 chr7A.!!$F1 600
9 TraesCS7D01G491900 chr7A 692521516 692523098 1582 True 490.500000 665 86.440500 1291 2882 2 chr7A.!!$R2 1591
10 TraesCS7D01G491900 chr3D 12385826 12386344 518 False 460.000000 460 82.700000 2361 2885 1 chr3D.!!$F1 524

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
36 38 0.325765 GGGAGTGGGAAGAGGTAGCT 60.326 60.000 0.00 0.00 0.0 3.32 F
1324 3842 0.323629 GGAGTTTGATGGACCGGACA 59.676 55.000 9.46 7.37 0.0 4.02 F
2247 5212 1.000896 CCGGGCCTTCAACCTCATT 60.001 57.895 0.84 0.00 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 4488 0.032267 AGCGGGAAATAGCGAGCTAC 59.968 55.0 6.99 0.0 38.61 3.58 R
2262 5227 0.179092 AGCGTACCGGATTGTTAGCC 60.179 55.0 9.46 0.0 0.00 3.93 R
3179 6177 0.535797 CCCACTACTCCCTCCGTTTC 59.464 60.0 0.00 0.0 0.00 2.78 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
36 38 0.325765 GGGAGTGGGAAGAGGTAGCT 60.326 60.000 0.00 0.00 0.00 3.32
87 89 2.692368 GGCTGGGAGGTGGGATGA 60.692 66.667 0.00 0.00 0.00 2.92
140 142 2.493973 CAGTCAGCCTCCTCTCGC 59.506 66.667 0.00 0.00 0.00 5.03
144 146 2.262915 CAGCCTCCTCTCGCGTTT 59.737 61.111 5.77 0.00 0.00 3.60
148 150 0.949105 GCCTCCTCTCGCGTTTTTCA 60.949 55.000 5.77 0.00 0.00 2.69
158 160 1.069906 CGCGTTTTTCAGTGAAGAGGG 60.070 52.381 5.56 4.10 0.00 4.30
163 165 1.518367 TTTCAGTGAAGAGGGGGTGT 58.482 50.000 5.56 0.00 0.00 4.16
234 236 4.292178 GATCCTGCCGGCGAGGAG 62.292 72.222 35.06 23.53 43.02 3.69
268 295 4.092816 CGAACCGGATAAAAATCAAACCG 58.907 43.478 9.46 0.00 40.03 4.44
276 303 7.044576 CCGGATAAAAATCAAACCGAAAATACG 60.045 37.037 0.00 0.00 42.40 3.06
292 319 4.976224 AATACGCCTGAAATTTGTACCC 57.024 40.909 0.00 0.00 0.00 3.69
300 327 5.163550 GCCTGAAATTTGTACCCAGAATACC 60.164 44.000 0.00 0.00 0.00 2.73
367 394 1.074727 TCTTCCAAAAATGCCCCTCGA 59.925 47.619 0.00 0.00 0.00 4.04
382 409 4.618693 GCCCCTCGAGCTCTGTTATAATAC 60.619 50.000 12.85 0.00 0.00 1.89
394 421 6.610456 TCTGTTATAATACACGTGACGTCAA 58.390 36.000 25.01 4.26 38.32 3.18
396 423 5.283482 TGTTATAATACACGTGACGTCAACG 59.717 40.000 27.26 27.26 38.32 4.10
410 437 4.787381 CGTCAACGTATTGCATTGGATA 57.213 40.909 0.00 0.00 35.63 2.59
433 460 2.331805 CGTCGAATCCGCTCCGAT 59.668 61.111 0.00 0.00 34.71 4.18
435 462 1.359117 GTCGAATCCGCTCCGATGA 59.641 57.895 0.00 0.00 34.71 2.92
452 479 0.821517 TGAACGGTGCATATCGACCT 59.178 50.000 12.67 0.00 33.73 3.85
505 540 7.979444 TTGGTCTACATTCTCGAAGAAAAAT 57.021 32.000 2.21 0.00 37.82 1.82
651 694 2.995466 CGTGTCCCGTAGAGTAAACA 57.005 50.000 0.00 0.00 0.00 2.83
652 695 3.287312 CGTGTCCCGTAGAGTAAACAA 57.713 47.619 0.00 0.00 0.00 2.83
653 696 3.641648 CGTGTCCCGTAGAGTAAACAAA 58.358 45.455 0.00 0.00 0.00 2.83
654 697 3.426525 CGTGTCCCGTAGAGTAAACAAAC 59.573 47.826 0.00 0.00 0.00 2.93
655 698 4.370917 GTGTCCCGTAGAGTAAACAAACA 58.629 43.478 0.00 0.00 0.00 2.83
656 699 4.209911 GTGTCCCGTAGAGTAAACAAACAC 59.790 45.833 0.00 0.00 0.00 3.32
657 700 4.141981 TGTCCCGTAGAGTAAACAAACACA 60.142 41.667 0.00 0.00 0.00 3.72
658 701 4.992951 GTCCCGTAGAGTAAACAAACACAT 59.007 41.667 0.00 0.00 0.00 3.21
659 702 6.158598 GTCCCGTAGAGTAAACAAACACATA 58.841 40.000 0.00 0.00 0.00 2.29
660 703 6.646240 GTCCCGTAGAGTAAACAAACACATAA 59.354 38.462 0.00 0.00 0.00 1.90
661 704 7.171337 GTCCCGTAGAGTAAACAAACACATAAA 59.829 37.037 0.00 0.00 0.00 1.40
662 705 7.879160 TCCCGTAGAGTAAACAAACACATAAAT 59.121 33.333 0.00 0.00 0.00 1.40
663 706 8.508875 CCCGTAGAGTAAACAAACACATAAATT 58.491 33.333 0.00 0.00 0.00 1.82
664 707 9.537848 CCGTAGAGTAAACAAACACATAAATTC 57.462 33.333 0.00 0.00 0.00 2.17
665 708 9.537848 CGTAGAGTAAACAAACACATAAATTCC 57.462 33.333 0.00 0.00 0.00 3.01
668 711 9.912634 AGAGTAAACAAACACATAAATTCCATG 57.087 29.630 0.00 0.00 0.00 3.66
669 712 8.532977 AGTAAACAAACACATAAATTCCATGC 57.467 30.769 0.00 0.00 0.00 4.06
670 713 8.147058 AGTAAACAAACACATAAATTCCATGCA 58.853 29.630 0.00 0.00 0.00 3.96
671 714 7.798596 AAACAAACACATAAATTCCATGCAA 57.201 28.000 0.00 0.00 0.00 4.08
672 715 7.798596 AACAAACACATAAATTCCATGCAAA 57.201 28.000 0.00 0.00 0.00 3.68
673 716 7.798596 ACAAACACATAAATTCCATGCAAAA 57.201 28.000 0.00 0.00 0.00 2.44
674 717 8.218338 ACAAACACATAAATTCCATGCAAAAA 57.782 26.923 0.00 0.00 0.00 1.94
728 771 6.291637 GCGAAAAAGAAAGTTTGGAAAGCTAC 60.292 38.462 0.00 0.00 35.87 3.58
769 812 3.403624 GATCAGGTGCCTGGTCCA 58.596 61.111 18.29 0.41 45.69 4.02
868 926 1.221840 CGGGCAGCTTGACCTGTAT 59.778 57.895 6.50 0.00 45.79 2.29
903 961 2.089734 GCATCGATCGAAAGCTACATCG 59.910 50.000 28.16 9.49 39.60 3.84
913 971 2.575694 AGCTACATCGAGAAGCACAG 57.424 50.000 16.04 0.00 38.75 3.66
948 1006 2.566724 AGTCTTCTTTCTCTGGAGCCAG 59.433 50.000 10.29 10.29 44.86 4.85
965 1023 2.482142 GCCAGTGAATCTCGGGTCTTAG 60.482 54.545 3.68 0.00 0.00 2.18
981 1039 6.580788 GGGTCTTAGTTAATCAAGTAGGGAC 58.419 44.000 0.00 0.00 0.00 4.46
992 1053 1.218316 GTAGGGACTTCAGGCGGTG 59.782 63.158 0.00 0.00 41.75 4.94
1248 1448 4.747218 TGCTCTTGCATGCATCCA 57.253 50.000 23.37 13.05 45.31 3.41
1249 1449 2.964343 TGCTCTTGCATGCATCCAA 58.036 47.368 23.37 5.27 45.31 3.53
1264 1464 7.333423 GCATGCATCCAATTTTTCATATAGCAT 59.667 33.333 14.21 0.00 38.23 3.79
1265 1465 8.869897 CATGCATCCAATTTTTCATATAGCATC 58.130 33.333 0.00 0.00 35.86 3.91
1266 1466 7.953752 TGCATCCAATTTTTCATATAGCATCA 58.046 30.769 0.00 0.00 0.00 3.07
1267 1467 8.590204 TGCATCCAATTTTTCATATAGCATCAT 58.410 29.630 0.00 0.00 0.00 2.45
1281 1481 8.886719 CATATAGCATCATACTTGTATGTTGGG 58.113 37.037 22.60 12.59 31.31 4.12
1317 3835 1.066430 GGTGCGTAGGAGTTTGATGGA 60.066 52.381 0.00 0.00 0.00 3.41
1324 3842 0.323629 GGAGTTTGATGGACCGGACA 59.676 55.000 9.46 7.37 0.00 4.02
1325 3843 1.271163 GGAGTTTGATGGACCGGACAA 60.271 52.381 9.46 0.00 0.00 3.18
1646 4358 4.901881 CGTTAAAAACCTGAATGTCGTGTC 59.098 41.667 0.00 0.00 0.00 3.67
1654 4366 4.338118 ACCTGAATGTCGTGTCAACAATTT 59.662 37.500 0.00 0.00 0.00 1.82
1701 4413 1.302033 CCCTCACAGGCTCACACAC 60.302 63.158 0.00 0.00 32.73 3.82
1752 4464 2.956333 TCGGCTAAGCTATGCACTTCTA 59.044 45.455 12.04 0.00 0.00 2.10
1757 4469 1.941325 AGCTATGCACTTCTAACGCC 58.059 50.000 0.00 0.00 0.00 5.68
1772 4484 6.325919 TCTAACGCCAAACTGAAAATGATT 57.674 33.333 0.00 0.00 0.00 2.57
1776 4488 7.406799 AACGCCAAACTGAAAATGATTTTAG 57.593 32.000 2.71 4.75 37.95 1.85
1871 4587 3.282021 GGGCTTGTTCAAGAGCATGATA 58.718 45.455 15.52 0.00 40.63 2.15
1890 4606 2.030958 GGACCCAAGTACAACGGCG 61.031 63.158 4.80 4.80 0.00 6.46
1958 4674 3.323115 TCAGTCAGACACTCAAGAGCATT 59.677 43.478 2.66 0.00 30.26 3.56
2196 5161 4.103928 ACCTACCTCCCCGGCCAT 62.104 66.667 2.24 0.00 35.61 4.40
2212 5177 1.064654 GCCATCATTTCGAGACCAAGC 59.935 52.381 0.00 0.00 0.00 4.01
2215 5180 1.428448 TCATTTCGAGACCAAGCACG 58.572 50.000 0.00 0.00 0.00 5.34
2247 5212 1.000896 CCGGGCCTTCAACCTCATT 60.001 57.895 0.84 0.00 0.00 2.57
2342 5309 6.595326 TCTGTGATGTTGATACATTTCTCACC 59.405 38.462 0.00 0.00 44.90 4.02
2474 5449 3.423154 GTCCTTTCGCTGGGCACG 61.423 66.667 0.00 0.00 0.00 5.34
2642 5617 2.047274 TTCCAGGCGCTACACTGC 60.047 61.111 7.64 0.00 33.43 4.40
2771 5752 2.260869 GGCGTTGCTGAAGAGGCAA 61.261 57.895 0.00 0.00 45.70 4.52
2804 5785 3.265791 GAACATCGAGACAGGCAAGAAT 58.734 45.455 0.00 0.00 0.00 2.40
2982 5977 2.613595 CGCCATCAAGTGCTAATGCTTA 59.386 45.455 0.00 0.00 40.48 3.09
3049 6047 8.277270 TGATATCGTCGATATTTGTTGTACAC 57.723 34.615 24.69 11.23 35.64 2.90
3081 6079 5.597813 AAAGATGTTGAATCTCGTCACAC 57.402 39.130 0.00 0.00 0.00 3.82
3115 6113 7.880160 TGCATTGCAATATAAACTACTTCCT 57.120 32.000 12.53 0.00 34.76 3.36
3116 6114 7.930217 TGCATTGCAATATAAACTACTTCCTC 58.070 34.615 12.53 0.00 34.76 3.71
3117 6115 7.013274 TGCATTGCAATATAAACTACTTCCTCC 59.987 37.037 12.53 0.00 34.76 4.30
3118 6116 7.576236 CATTGCAATATAAACTACTTCCTCCG 58.424 38.462 12.53 0.00 0.00 4.63
3119 6117 6.229936 TGCAATATAAACTACTTCCTCCGT 57.770 37.500 0.00 0.00 0.00 4.69
3120 6118 6.646267 TGCAATATAAACTACTTCCTCCGTT 58.354 36.000 0.00 0.00 0.00 4.44
3121 6119 6.759827 TGCAATATAAACTACTTCCTCCGTTC 59.240 38.462 0.00 0.00 0.00 3.95
3122 6120 6.985059 GCAATATAAACTACTTCCTCCGTTCT 59.015 38.462 0.00 0.00 0.00 3.01
3123 6121 8.139989 GCAATATAAACTACTTCCTCCGTTCTA 58.860 37.037 0.00 0.00 0.00 2.10
3129 6127 8.999220 AAACTACTTCCTCCGTTCTAAAATAG 57.001 34.615 0.00 0.00 0.00 1.73
3130 6128 7.951347 ACTACTTCCTCCGTTCTAAAATAGA 57.049 36.000 0.00 0.00 0.00 1.98
3131 6129 8.536340 ACTACTTCCTCCGTTCTAAAATAGAT 57.464 34.615 0.00 0.00 34.22 1.98
3132 6130 8.414778 ACTACTTCCTCCGTTCTAAAATAGATG 58.585 37.037 0.00 0.00 34.22 2.90
3133 6131 7.419711 ACTTCCTCCGTTCTAAAATAGATGA 57.580 36.000 0.00 0.00 34.22 2.92
3134 6132 8.024145 ACTTCCTCCGTTCTAAAATAGATGAT 57.976 34.615 0.00 0.00 34.22 2.45
3135 6133 8.487028 ACTTCCTCCGTTCTAAAATAGATGATT 58.513 33.333 0.00 0.00 34.22 2.57
3136 6134 8.888579 TTCCTCCGTTCTAAAATAGATGATTC 57.111 34.615 0.00 0.00 34.22 2.52
3137 6135 8.018537 TCCTCCGTTCTAAAATAGATGATTCA 57.981 34.615 0.00 0.00 34.22 2.57
3138 6136 8.482943 TCCTCCGTTCTAAAATAGATGATTCAA 58.517 33.333 0.00 0.00 34.22 2.69
3139 6137 8.552034 CCTCCGTTCTAAAATAGATGATTCAAC 58.448 37.037 0.00 0.00 34.22 3.18
3140 6138 9.319143 CTCCGTTCTAAAATAGATGATTCAACT 57.681 33.333 1.83 1.83 34.22 3.16
3141 6139 9.667107 TCCGTTCTAAAATAGATGATTCAACTT 57.333 29.630 1.47 0.00 34.22 2.66
3157 6155 9.719355 TGATTCAACTTTATACTAACTTCAGCA 57.281 29.630 0.00 0.00 0.00 4.41
3158 6156 9.974750 GATTCAACTTTATACTAACTTCAGCAC 57.025 33.333 0.00 0.00 0.00 4.40
3159 6157 8.896320 TTCAACTTTATACTAACTTCAGCACA 57.104 30.769 0.00 0.00 0.00 4.57
3160 6158 8.896320 TCAACTTTATACTAACTTCAGCACAA 57.104 30.769 0.00 0.00 0.00 3.33
3161 6159 9.332502 TCAACTTTATACTAACTTCAGCACAAA 57.667 29.630 0.00 0.00 0.00 2.83
3162 6160 9.599322 CAACTTTATACTAACTTCAGCACAAAG 57.401 33.333 0.00 0.00 0.00 2.77
3163 6161 8.904099 ACTTTATACTAACTTCAGCACAAAGT 57.096 30.769 0.00 0.00 38.59 2.66
3164 6162 9.338622 ACTTTATACTAACTTCAGCACAAAGTT 57.661 29.630 13.41 13.41 46.04 2.66
3165 6163 9.599322 CTTTATACTAACTTCAGCACAAAGTTG 57.401 33.333 16.70 11.14 44.47 3.16
3166 6164 4.900635 ACTAACTTCAGCACAAAGTTGG 57.099 40.909 16.70 16.08 44.47 3.77
3167 6165 3.632145 ACTAACTTCAGCACAAAGTTGGG 59.368 43.478 18.92 13.99 44.70 4.12
3168 6166 2.143876 ACTTCAGCACAAAGTTGGGT 57.856 45.000 0.00 0.00 33.19 4.51
3169 6167 2.024414 ACTTCAGCACAAAGTTGGGTC 58.976 47.619 0.00 0.00 33.19 4.46
3170 6168 2.023673 CTTCAGCACAAAGTTGGGTCA 58.976 47.619 0.00 0.00 33.05 4.02
3171 6169 2.363306 TCAGCACAAAGTTGGGTCAT 57.637 45.000 0.00 0.00 33.05 3.06
3172 6170 2.229792 TCAGCACAAAGTTGGGTCATC 58.770 47.619 0.00 0.00 33.05 2.92
3173 6171 2.158623 TCAGCACAAAGTTGGGTCATCT 60.159 45.455 0.00 0.00 33.05 2.90
3174 6172 3.072330 TCAGCACAAAGTTGGGTCATCTA 59.928 43.478 0.00 0.00 33.05 1.98
3175 6173 4.012374 CAGCACAAAGTTGGGTCATCTAT 58.988 43.478 0.00 0.00 33.05 1.98
3176 6174 4.460382 CAGCACAAAGTTGGGTCATCTATT 59.540 41.667 0.00 0.00 33.05 1.73
3177 6175 5.047802 CAGCACAAAGTTGGGTCATCTATTT 60.048 40.000 0.00 0.00 33.05 1.40
3178 6176 5.539955 AGCACAAAGTTGGGTCATCTATTTT 59.460 36.000 0.00 0.00 33.05 1.82
3179 6177 5.634859 GCACAAAGTTGGGTCATCTATTTTG 59.365 40.000 0.00 0.00 33.05 2.44
3180 6178 6.516527 GCACAAAGTTGGGTCATCTATTTTGA 60.517 38.462 0.00 0.00 33.05 2.69
3181 6179 7.432869 CACAAAGTTGGGTCATCTATTTTGAA 58.567 34.615 0.00 0.00 0.00 2.69
3182 6180 7.925483 CACAAAGTTGGGTCATCTATTTTGAAA 59.075 33.333 0.00 0.00 0.00 2.69
3183 6181 7.926018 ACAAAGTTGGGTCATCTATTTTGAAAC 59.074 33.333 0.00 0.00 0.00 2.78
3184 6182 6.254281 AGTTGGGTCATCTATTTTGAAACG 57.746 37.500 0.00 0.00 0.00 3.60
3185 6183 5.183140 AGTTGGGTCATCTATTTTGAAACGG 59.817 40.000 0.00 0.00 0.00 4.44
3186 6184 4.912586 TGGGTCATCTATTTTGAAACGGA 58.087 39.130 0.00 0.00 0.00 4.69
3187 6185 4.941263 TGGGTCATCTATTTTGAAACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
3188 6186 4.335594 GGGTCATCTATTTTGAAACGGAGG 59.664 45.833 0.00 0.00 0.00 4.30
3189 6187 4.335594 GGTCATCTATTTTGAAACGGAGGG 59.664 45.833 0.00 0.00 0.00 4.30
3190 6188 5.183228 GTCATCTATTTTGAAACGGAGGGA 58.817 41.667 0.00 0.00 0.00 4.20
3191 6189 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
3192 6190 4.903045 TCTATTTTGAAACGGAGGGAGT 57.097 40.909 0.00 0.00 0.00 3.85
3193 6191 6.155565 TCATCTATTTTGAAACGGAGGGAGTA 59.844 38.462 0.00 0.00 0.00 2.59
3216 6214 1.377725 GGTGACCTGTGCATCTGGG 60.378 63.158 13.77 6.46 39.12 4.45
3221 6219 0.840288 ACCTGTGCATCTGGGTGGTA 60.840 55.000 13.77 0.00 39.12 3.25
3330 6328 4.618920 ACATACTTATAGAAAGGGGGCG 57.381 45.455 0.00 0.00 0.00 6.13
3560 6558 5.590663 GGGAGTCCCTCAGATTTCATTTTAC 59.409 44.000 22.04 0.00 41.34 2.01
3567 6565 6.434028 CCCTCAGATTTCATTTTACAGAACCA 59.566 38.462 0.00 0.00 0.00 3.67
3601 6599 9.826574 TTACGGCTACTGAACATAAAAATAGAT 57.173 29.630 0.00 0.00 0.00 1.98
3616 6614 7.660030 AAAAATAGATGGGGTTTGATACCTG 57.340 36.000 0.00 0.00 46.86 4.00
3668 6666 9.436957 AACCAAACACTACTATTAGAACTGATG 57.563 33.333 0.00 0.00 0.00 3.07
3714 6713 5.241506 CCTTTTCTCCTTTCTTATGTGCACA 59.758 40.000 24.08 24.08 0.00 4.57
3758 6757 7.591006 ACTAATTTCATGCATGCAGAAAAAG 57.409 32.000 30.86 29.50 35.20 2.27
3834 6833 2.734606 TGTTTTGTATCTCAAGCCGTCG 59.265 45.455 0.00 0.00 37.35 5.12
3894 6893 7.655732 TCATCACGACAAGATCTTCAAAACTAA 59.344 33.333 4.57 0.00 0.00 2.24
3895 6894 7.780008 TCACGACAAGATCTTCAAAACTAAA 57.220 32.000 4.57 0.00 0.00 1.85
3896 6895 8.378172 TCACGACAAGATCTTCAAAACTAAAT 57.622 30.769 4.57 0.00 0.00 1.40
3897 6896 8.495949 TCACGACAAGATCTTCAAAACTAAATC 58.504 33.333 4.57 0.00 0.00 2.17
3898 6897 8.499162 CACGACAAGATCTTCAAAACTAAATCT 58.501 33.333 4.57 0.00 0.00 2.40
3899 6898 8.713271 ACGACAAGATCTTCAAAACTAAATCTC 58.287 33.333 4.57 0.00 0.00 2.75
3900 6899 8.712363 CGACAAGATCTTCAAAACTAAATCTCA 58.288 33.333 4.57 0.00 0.00 3.27
3919 6918 9.745880 AAATCTCATGTTGATATTTTCTGATGC 57.254 29.630 0.00 0.00 31.72 3.91
3925 6924 8.600625 CATGTTGATATTTTCTGATGCCTTTTG 58.399 33.333 0.00 0.00 0.00 2.44
3947 6946 1.548719 GGGGGCCAAAAGTTATCACAC 59.451 52.381 4.39 0.00 0.00 3.82
4006 7005 5.921976 TGTAAGTTACCATGTTGTCTACACG 59.078 40.000 10.51 0.00 40.19 4.49
4014 7013 7.355332 ACCATGTTGTCTACACGTAAAATAC 57.645 36.000 0.00 0.00 40.19 1.89
4016 7015 7.117236 ACCATGTTGTCTACACGTAAAATACAG 59.883 37.037 0.00 0.00 40.19 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.301738 CCTCTTCCCACTCCCCACC 61.302 68.421 0.00 0.00 0.00 4.61
36 38 2.860009 CCTATAGCCACGAGGTGAGTA 58.140 52.381 0.00 0.00 35.23 2.59
71 73 2.592308 GTCATCCCACCTCCCAGC 59.408 66.667 0.00 0.00 0.00 4.85
140 142 1.880027 CCCCCTCTTCACTGAAAAACG 59.120 52.381 0.00 0.00 0.00 3.60
144 146 1.142870 CACACCCCCTCTTCACTGAAA 59.857 52.381 0.00 0.00 0.00 2.69
148 150 0.191064 TCTCACACCCCCTCTTCACT 59.809 55.000 0.00 0.00 0.00 3.41
158 160 2.262915 CCTCACGCTCTCACACCC 59.737 66.667 0.00 0.00 0.00 4.61
163 165 0.250234 CCAATTCCCTCACGCTCTCA 59.750 55.000 0.00 0.00 0.00 3.27
233 235 1.066645 CCGGTTCGCTAGGGTTTTACT 60.067 52.381 6.70 0.00 0.00 2.24
234 236 1.066929 TCCGGTTCGCTAGGGTTTTAC 60.067 52.381 0.00 1.91 0.00 2.01
268 295 5.803461 GGGTACAAATTTCAGGCGTATTTTC 59.197 40.000 0.00 0.00 0.00 2.29
276 303 5.163550 GGTATTCTGGGTACAAATTTCAGGC 60.164 44.000 0.00 0.00 0.00 4.85
292 319 7.386299 CCTCTCAAATATTTCGAGGGTATTCTG 59.614 40.741 23.55 8.66 38.04 3.02
300 327 7.500559 AGATTTTCCCTCTCAAATATTTCGAGG 59.499 37.037 23.98 23.98 40.68 4.63
351 378 0.967380 AGCTCGAGGGGCATTTTTGG 60.967 55.000 15.58 0.00 0.00 3.28
353 380 0.329596 AGAGCTCGAGGGGCATTTTT 59.670 50.000 15.58 0.00 0.00 1.94
367 394 5.163683 ACGTCACGTGTATTATAACAGAGCT 60.164 40.000 16.51 0.00 39.18 4.09
394 421 4.072131 GGTCCATATCCAATGCAATACGT 58.928 43.478 0.00 0.00 0.00 3.57
396 423 4.072131 ACGGTCCATATCCAATGCAATAC 58.928 43.478 0.00 0.00 0.00 1.89
410 437 2.106332 GCGGATTCGACGGTCCAT 59.894 61.111 16.72 0.00 39.00 3.41
433 460 0.821517 AGGTCGATATGCACCGTTCA 59.178 50.000 0.00 0.00 37.79 3.18
435 462 0.535335 ACAGGTCGATATGCACCGTT 59.465 50.000 0.00 0.00 37.79 4.44
452 479 5.751586 AGTGGTTCAAAGAGTCCTTTTACA 58.248 37.500 0.00 0.00 40.42 2.41
505 540 6.192970 AGAAGTTTCTCCTCCAGAATTTCA 57.807 37.500 0.00 0.00 41.02 2.69
559 594 2.953648 TGTCGTAGCTGGAAATATCGGA 59.046 45.455 0.00 0.00 0.00 4.55
703 746 4.566759 AGCTTTCCAAACTTTCTTTTTCGC 59.433 37.500 0.00 0.00 0.00 4.70
728 771 2.637025 CCGGTTTTGTGGTGCTCG 59.363 61.111 0.00 0.00 0.00 5.03
769 812 1.332686 GTTTCGCGGTCCAGTTTCTTT 59.667 47.619 6.13 0.00 0.00 2.52
903 961 1.446966 GGTCTCGCCTGTGCTTCTC 60.447 63.158 0.00 0.00 34.43 2.87
913 971 2.126031 GACTCCGTTGGTCTCGCC 60.126 66.667 0.00 0.00 37.90 5.54
948 1006 6.570692 TGATTAACTAAGACCCGAGATTCAC 58.429 40.000 0.00 0.00 0.00 3.18
965 1023 4.876679 GCCTGAAGTCCCTACTTGATTAAC 59.123 45.833 0.00 0.00 46.09 2.01
981 1039 2.429930 TGGGAACACCGCCTGAAG 59.570 61.111 0.00 0.00 44.64 3.02
992 1053 1.228552 ATGGCCGGCATATGGGAAC 60.229 57.895 30.85 7.78 0.00 3.62
1205 1272 5.928839 GCAGGTTGATACTCTGTATGTATGG 59.071 44.000 0.00 0.00 31.55 2.74
1264 1464 5.187381 TCGTTACCCCAACATACAAGTATGA 59.813 40.000 23.02 0.33 44.22 2.15
1265 1465 5.421277 TCGTTACCCCAACATACAAGTATG 58.579 41.667 16.47 16.47 46.24 2.39
1266 1466 5.188359 ACTCGTTACCCCAACATACAAGTAT 59.812 40.000 0.00 0.00 36.92 2.12
1267 1467 4.527816 ACTCGTTACCCCAACATACAAGTA 59.472 41.667 0.00 0.00 36.92 2.24
1268 1468 3.325716 ACTCGTTACCCCAACATACAAGT 59.674 43.478 0.00 0.00 36.92 3.16
1269 1469 3.934068 ACTCGTTACCCCAACATACAAG 58.066 45.455 0.00 0.00 36.92 3.16
1270 1470 4.066490 CAACTCGTTACCCCAACATACAA 58.934 43.478 0.00 0.00 36.92 2.41
1277 1477 1.477195 CCCAACAACTCGTTACCCCAA 60.477 52.381 0.00 0.00 35.52 4.12
1281 1481 1.232119 CACCCCAACAACTCGTTACC 58.768 55.000 0.00 0.00 35.52 2.85
1317 3835 1.949847 CTGCGATCCTCTTGTCCGGT 61.950 60.000 0.00 0.00 0.00 5.28
1324 3842 3.632604 TCGAAGTAATCTGCGATCCTCTT 59.367 43.478 0.00 0.00 45.57 2.85
1325 3843 3.215151 TCGAAGTAATCTGCGATCCTCT 58.785 45.455 0.00 0.00 45.57 3.69
1586 4298 3.715495 CATAAGCTCAGGTACAGCTCTG 58.285 50.000 6.65 4.76 46.96 3.35
1588 4300 2.478831 GCATAAGCTCAGGTACAGCTC 58.521 52.381 6.65 0.00 46.96 4.09
1624 4336 5.812652 TGACACGACATTCAGGTTTTTAAC 58.187 37.500 0.00 0.00 0.00 2.01
1646 4358 8.505625 CACCCCTAATTTCATTGAAAATTGTTG 58.494 33.333 15.34 6.68 38.82 3.33
1654 4366 4.412060 ACCCACCCCTAATTTCATTGAA 57.588 40.909 0.00 0.00 0.00 2.69
1685 4397 1.436600 GATGTGTGTGAGCCTGTGAG 58.563 55.000 0.00 0.00 0.00 3.51
1701 4413 1.000506 AGTTTTTGCTGCTGCTGGATG 59.999 47.619 17.00 0.00 40.48 3.51
1752 4464 6.983890 ACTAAAATCATTTTCAGTTTGGCGTT 59.016 30.769 0.00 0.00 34.19 4.84
1757 4469 9.055248 CGAGCTACTAAAATCATTTTCAGTTTG 57.945 33.333 0.00 0.00 34.19 2.93
1772 4484 3.797865 GCGGGAAATAGCGAGCTACTAAA 60.798 47.826 6.99 0.00 0.00 1.85
1776 4488 0.032267 AGCGGGAAATAGCGAGCTAC 59.968 55.000 6.99 0.00 38.61 3.58
1871 4587 1.373812 GCCGTTGTACTTGGGTCCT 59.626 57.895 0.00 0.00 0.00 3.85
1890 4606 2.433318 GACCGAGTGCAGGTGCTC 60.433 66.667 0.00 0.00 43.01 4.26
1958 4674 1.052617 TGTCGAAAGTGGGGATGACA 58.947 50.000 0.00 0.00 34.27 3.58
2196 5161 1.000394 TCGTGCTTGGTCTCGAAATGA 60.000 47.619 0.00 0.00 0.00 2.57
2212 5177 1.281656 GGGTCTTGCCGTTTTCGTG 59.718 57.895 0.00 0.00 42.35 4.35
2215 5180 2.622962 CCCGGGTCTTGCCGTTTTC 61.623 63.158 14.18 0.00 38.44 2.29
2262 5227 0.179092 AGCGTACCGGATTGTTAGCC 60.179 55.000 9.46 0.00 0.00 3.93
2342 5309 3.752747 TCTGTGCACATCCATGTAAGTTG 59.247 43.478 22.00 3.63 39.39 3.16
2516 5491 1.899437 CGAGAAGGCCCCACTTGCTA 61.899 60.000 0.00 0.00 0.00 3.49
2642 5617 1.297451 GTAGCGCCTGTCGTAGTCG 60.297 63.158 2.29 0.00 41.07 4.18
2719 5700 1.774254 TGAGCCTTTTGAGGTTCTCCA 59.226 47.619 10.07 0.00 39.51 3.86
2771 5752 1.202639 TCGATGTTCACCTTGCACACT 60.203 47.619 0.00 0.00 0.00 3.55
2804 5785 1.227664 CCTCTCTAGGTCGGGCTCA 59.772 63.158 0.00 0.00 38.19 4.26
2939 5921 4.032900 CGTAGGTCATCAAATTCGAACAGG 59.967 45.833 0.00 0.00 0.00 4.00
3049 6047 8.937932 CGAGATTCAACATCTTTATTTAAAGCG 58.062 33.333 5.39 2.68 41.77 4.68
3081 6079 2.144833 TTGCAATGCAACCTCGCTGG 62.145 55.000 17.55 0.00 43.99 4.85
3110 6108 8.894768 AATCATCTATTTTAGAACGGAGGAAG 57.105 34.615 0.00 0.00 38.50 3.46
3111 6109 8.482943 TGAATCATCTATTTTAGAACGGAGGAA 58.517 33.333 0.00 0.00 38.50 3.36
3112 6110 8.018537 TGAATCATCTATTTTAGAACGGAGGA 57.981 34.615 0.00 0.00 38.50 3.71
3113 6111 8.552034 GTTGAATCATCTATTTTAGAACGGAGG 58.448 37.037 0.00 0.00 38.50 4.30
3114 6112 9.319143 AGTTGAATCATCTATTTTAGAACGGAG 57.681 33.333 0.00 0.00 38.50 4.63
3115 6113 9.667107 AAGTTGAATCATCTATTTTAGAACGGA 57.333 29.630 0.00 0.00 38.50 4.69
3131 6129 9.719355 TGCTGAAGTTAGTATAAAGTTGAATCA 57.281 29.630 0.00 0.00 0.00 2.57
3132 6130 9.974750 GTGCTGAAGTTAGTATAAAGTTGAATC 57.025 33.333 0.00 0.00 0.00 2.52
3133 6131 9.502091 TGTGCTGAAGTTAGTATAAAGTTGAAT 57.498 29.630 0.00 0.00 0.00 2.57
3134 6132 8.896320 TGTGCTGAAGTTAGTATAAAGTTGAA 57.104 30.769 0.00 0.00 0.00 2.69
3135 6133 8.896320 TTGTGCTGAAGTTAGTATAAAGTTGA 57.104 30.769 0.00 0.00 0.00 3.18
3136 6134 9.599322 CTTTGTGCTGAAGTTAGTATAAAGTTG 57.401 33.333 0.00 0.00 37.02 3.16
3137 6135 9.338622 ACTTTGTGCTGAAGTTAGTATAAAGTT 57.661 29.630 10.97 0.00 45.21 2.66
3138 6136 8.904099 ACTTTGTGCTGAAGTTAGTATAAAGT 57.096 30.769 10.97 10.97 43.91 2.66
3139 6137 9.599322 CAACTTTGTGCTGAAGTTAGTATAAAG 57.401 33.333 10.74 10.00 43.44 1.85
3140 6138 8.564574 CCAACTTTGTGCTGAAGTTAGTATAAA 58.435 33.333 10.74 0.00 43.44 1.40
3141 6139 7.174253 CCCAACTTTGTGCTGAAGTTAGTATAA 59.826 37.037 10.74 0.00 43.44 0.98
3142 6140 6.653320 CCCAACTTTGTGCTGAAGTTAGTATA 59.347 38.462 10.74 0.00 43.44 1.47
3143 6141 5.473504 CCCAACTTTGTGCTGAAGTTAGTAT 59.526 40.000 10.74 0.00 43.44 2.12
3144 6142 4.819630 CCCAACTTTGTGCTGAAGTTAGTA 59.180 41.667 10.74 0.00 43.44 1.82
3145 6143 3.632145 CCCAACTTTGTGCTGAAGTTAGT 59.368 43.478 10.74 0.00 43.44 2.24
3146 6144 3.632145 ACCCAACTTTGTGCTGAAGTTAG 59.368 43.478 10.74 8.83 43.44 2.34
3147 6145 3.626930 ACCCAACTTTGTGCTGAAGTTA 58.373 40.909 10.74 0.00 43.44 2.24
3148 6146 2.427095 GACCCAACTTTGTGCTGAAGTT 59.573 45.455 6.79 6.79 45.49 2.66
3149 6147 2.024414 GACCCAACTTTGTGCTGAAGT 58.976 47.619 0.00 0.00 38.92 3.01
3150 6148 2.023673 TGACCCAACTTTGTGCTGAAG 58.976 47.619 0.00 0.00 0.00 3.02
3151 6149 2.136298 TGACCCAACTTTGTGCTGAA 57.864 45.000 0.00 0.00 0.00 3.02
3152 6150 2.158623 AGATGACCCAACTTTGTGCTGA 60.159 45.455 0.00 0.00 0.00 4.26
3153 6151 2.233271 AGATGACCCAACTTTGTGCTG 58.767 47.619 0.00 0.00 0.00 4.41
3154 6152 2.664402 AGATGACCCAACTTTGTGCT 57.336 45.000 0.00 0.00 0.00 4.40
3155 6153 5.391312 AAATAGATGACCCAACTTTGTGC 57.609 39.130 0.00 0.00 0.00 4.57
3156 6154 6.980593 TCAAAATAGATGACCCAACTTTGTG 58.019 36.000 0.00 0.00 0.00 3.33
3157 6155 7.595819 TTCAAAATAGATGACCCAACTTTGT 57.404 32.000 0.00 0.00 0.00 2.83
3158 6156 7.114811 CGTTTCAAAATAGATGACCCAACTTTG 59.885 37.037 0.00 0.00 0.00 2.77
3159 6157 7.145323 CGTTTCAAAATAGATGACCCAACTTT 58.855 34.615 0.00 0.00 0.00 2.66
3160 6158 6.294508 CCGTTTCAAAATAGATGACCCAACTT 60.295 38.462 0.00 0.00 0.00 2.66
3161 6159 5.183140 CCGTTTCAAAATAGATGACCCAACT 59.817 40.000 0.00 0.00 0.00 3.16
3162 6160 5.182380 TCCGTTTCAAAATAGATGACCCAAC 59.818 40.000 0.00 0.00 0.00 3.77
3163 6161 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
3164 6162 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
3165 6163 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
3166 6164 4.335594 CCCTCCGTTTCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
3167 6165 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
3168 6166 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
3169 6167 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
3170 6168 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
3171 6169 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
3172 6170 5.581085 CACTACTCCCTCCGTTTCAAAATAG 59.419 44.000 0.00 0.00 0.00 1.73
3173 6171 5.484715 CACTACTCCCTCCGTTTCAAAATA 58.515 41.667 0.00 0.00 0.00 1.40
3174 6172 4.324267 CACTACTCCCTCCGTTTCAAAAT 58.676 43.478 0.00 0.00 0.00 1.82
3175 6173 3.495453 CCACTACTCCCTCCGTTTCAAAA 60.495 47.826 0.00 0.00 0.00 2.44
3176 6174 2.038033 CCACTACTCCCTCCGTTTCAAA 59.962 50.000 0.00 0.00 0.00 2.69
3177 6175 1.621814 CCACTACTCCCTCCGTTTCAA 59.378 52.381 0.00 0.00 0.00 2.69
3178 6176 1.263356 CCACTACTCCCTCCGTTTCA 58.737 55.000 0.00 0.00 0.00 2.69
3179 6177 0.535797 CCCACTACTCCCTCCGTTTC 59.464 60.000 0.00 0.00 0.00 2.78
3180 6178 0.908180 CCCCACTACTCCCTCCGTTT 60.908 60.000 0.00 0.00 0.00 3.60
3181 6179 1.305887 CCCCACTACTCCCTCCGTT 60.306 63.158 0.00 0.00 0.00 4.44
3182 6180 2.363361 CCCCACTACTCCCTCCGT 59.637 66.667 0.00 0.00 0.00 4.69
3183 6181 2.058595 CACCCCACTACTCCCTCCG 61.059 68.421 0.00 0.00 0.00 4.63
3184 6182 0.976590 GTCACCCCACTACTCCCTCC 60.977 65.000 0.00 0.00 0.00 4.30
3185 6183 0.976590 GGTCACCCCACTACTCCCTC 60.977 65.000 0.00 0.00 0.00 4.30
3186 6184 1.080538 GGTCACCCCACTACTCCCT 59.919 63.158 0.00 0.00 0.00 4.20
3187 6185 1.080538 AGGTCACCCCACTACTCCC 59.919 63.158 0.00 0.00 34.66 4.30
3188 6186 0.544595 ACAGGTCACCCCACTACTCC 60.545 60.000 0.00 0.00 34.66 3.85
3189 6187 0.608640 CACAGGTCACCCCACTACTC 59.391 60.000 0.00 0.00 34.66 2.59
3190 6188 1.481056 GCACAGGTCACCCCACTACT 61.481 60.000 0.00 0.00 34.66 2.57
3191 6189 1.003718 GCACAGGTCACCCCACTAC 60.004 63.158 0.00 0.00 34.66 2.73
3192 6190 0.840288 ATGCACAGGTCACCCCACTA 60.840 55.000 0.00 0.00 34.66 2.74
3193 6191 2.129555 GATGCACAGGTCACCCCACT 62.130 60.000 0.00 0.00 34.66 4.00
3216 6214 4.000988 ACGGACATCACAAATCTTACCAC 58.999 43.478 0.00 0.00 0.00 4.16
3221 6219 6.915843 GTGTTTTAACGGACATCACAAATCTT 59.084 34.615 0.00 0.00 0.00 2.40
3281 6279 7.039574 TGTGTACTTAGTGGCAACTAATGTCTA 60.040 37.037 14.16 5.32 45.59 2.59
3330 6328 1.459592 GCATATGACATTCGGGTACGC 59.540 52.381 6.97 0.00 40.69 4.42
3342 6340 5.634859 CCCAAACAAAGTTTCTGCATATGAC 59.365 40.000 6.97 0.00 0.00 3.06
3424 6422 8.040716 TCCACATGTGTAGTGATATATCGTAG 57.959 38.462 23.79 3.07 39.30 3.51
3473 6471 7.872113 ATGGAAAGGCTTCTAATAGAGTTTG 57.128 36.000 0.00 0.00 0.00 2.93
3546 6544 7.432869 TGGTTGGTTCTGTAAAATGAAATCTG 58.567 34.615 0.00 0.00 0.00 2.90
3560 6558 1.535462 CCGTAAAGCTGGTTGGTTCTG 59.465 52.381 0.00 0.00 35.02 3.02
3567 6565 1.621814 TCAGTAGCCGTAAAGCTGGTT 59.378 47.619 0.00 0.00 44.67 3.67
3668 6666 2.023181 CGCCACGTACATGCATGC 59.977 61.111 26.53 11.82 0.00 4.06
3866 6865 7.173907 AGTTTTGAAGATCTTGTCGTGATGAAT 59.826 33.333 14.00 0.00 0.00 2.57
3872 6871 8.499162 AGATTTAGTTTTGAAGATCTTGTCGTG 58.501 33.333 14.00 0.00 0.00 4.35
3873 6872 8.608844 AGATTTAGTTTTGAAGATCTTGTCGT 57.391 30.769 14.00 0.00 0.00 4.34
3894 6893 8.358148 GGCATCAGAAAATATCAACATGAGATT 58.642 33.333 0.00 0.00 39.70 2.40
3895 6894 7.724506 AGGCATCAGAAAATATCAACATGAGAT 59.275 33.333 0.00 5.16 28.05 2.75
3896 6895 7.058525 AGGCATCAGAAAATATCAACATGAGA 58.941 34.615 0.00 0.00 0.00 3.27
3897 6896 7.273320 AGGCATCAGAAAATATCAACATGAG 57.727 36.000 0.00 0.00 0.00 2.90
3898 6897 7.649533 AAGGCATCAGAAAATATCAACATGA 57.350 32.000 0.00 0.00 0.00 3.07
3899 6898 8.600625 CAAAAGGCATCAGAAAATATCAACATG 58.399 33.333 0.00 0.00 0.00 3.21
3900 6899 8.316214 ACAAAAGGCATCAGAAAATATCAACAT 58.684 29.630 0.00 0.00 0.00 2.71
3901 6900 7.599621 CACAAAAGGCATCAGAAAATATCAACA 59.400 33.333 0.00 0.00 0.00 3.33
3902 6901 7.063780 CCACAAAAGGCATCAGAAAATATCAAC 59.936 37.037 0.00 0.00 0.00 3.18
3903 6902 7.098477 CCACAAAAGGCATCAGAAAATATCAA 58.902 34.615 0.00 0.00 0.00 2.57
3904 6903 6.351202 CCCACAAAAGGCATCAGAAAATATCA 60.351 38.462 0.00 0.00 0.00 2.15
3905 6904 6.044682 CCCACAAAAGGCATCAGAAAATATC 58.955 40.000 0.00 0.00 0.00 1.63
3906 6905 5.104817 CCCCACAAAAGGCATCAGAAAATAT 60.105 40.000 0.00 0.00 0.00 1.28
3907 6906 4.222588 CCCCACAAAAGGCATCAGAAAATA 59.777 41.667 0.00 0.00 0.00 1.40
3908 6907 3.008266 CCCCACAAAAGGCATCAGAAAAT 59.992 43.478 0.00 0.00 0.00 1.82
3919 6918 2.225792 TTTTGGCCCCCACAAAAGG 58.774 52.632 0.00 0.00 41.39 3.11
3925 6924 1.548719 GTGATAACTTTTGGCCCCCAC 59.451 52.381 0.00 0.00 30.78 4.61
3947 6946 4.689071 TGTGATAAGTTACATAGCCCACG 58.311 43.478 0.00 0.00 0.00 4.94
3981 6980 6.089016 CGTGTAGACAACATGGTAACTTACAG 59.911 42.308 0.00 0.00 41.10 2.74
3982 6981 5.921976 CGTGTAGACAACATGGTAACTTACA 59.078 40.000 0.00 0.00 41.10 2.41
3983 6982 6.385537 CGTGTAGACAACATGGTAACTTAC 57.614 41.667 0.00 0.00 41.10 2.34
4014 7013 6.364701 TGGAAGAACCATATTTATGTCCCTG 58.635 40.000 0.00 0.00 44.64 4.45


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

AutoCloner maintained by Alex Coulton.