Multiple sequence alignment - TraesCS7D01G052700

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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 TraesCS7D01G052700 chr7D 100.000 2504 0 0 1 2504 27489464 27486961 0.000000e+00 4625.0
1 TraesCS7D01G052700 chr7D 85.494 972 77 48 879 1825 27549262 27548330 0.000000e+00 955.0
2 TraesCS7D01G052700 chr7D 92.245 490 29 4 1878 2361 27548327 27547841 0.000000e+00 686.0
3 TraesCS7D01G052700 chr7D 85.827 127 11 6 52 175 93031226 93031104 7.270000e-26 128.0
4 TraesCS7D01G052700 chr7D 89.899 99 5 3 1548 1642 27548645 27548548 3.380000e-24 122.0
5 TraesCS7D01G052700 chr7D 78.125 128 16 6 414 535 30123729 30123608 1.240000e-08 71.3
6 TraesCS7D01G052700 chr4A 88.388 1421 105 27 243 1651 704251418 704250046 0.000000e+00 1655.0
7 TraesCS7D01G052700 chr4A 88.418 967 57 24 697 1651 704170532 704169609 0.000000e+00 1114.0
8 TraesCS7D01G052700 chr4A 88.406 966 59 23 697 1651 704224276 704223353 0.000000e+00 1114.0
9 TraesCS7D01G052700 chr4A 88.901 919 56 20 743 1651 704197464 704196582 0.000000e+00 1090.0
10 TraesCS7D01G052700 chr4A 86.228 973 73 31 1436 2361 704168741 704167783 0.000000e+00 998.0
11 TraesCS7D01G052700 chr4A 81.818 924 89 50 879 1763 704280300 704279417 0.000000e+00 702.0
12 TraesCS7D01G052700 chr4A 91.960 398 25 4 1966 2361 704279212 704278820 3.640000e-153 551.0
13 TraesCS7D01G052700 chr4A 92.800 250 13 2 2112 2361 704169173 704168929 8.520000e-95 357.0
14 TraesCS7D01G052700 chr4A 92.800 250 13 2 2112 2361 704249609 704249365 8.520000e-95 357.0
15 TraesCS7D01G052700 chr4A 92.400 250 13 3 2112 2361 704196146 704195903 3.960000e-93 351.0
16 TraesCS7D01G052700 chr4A 92.400 250 13 3 2112 2361 704222917 704222674 3.960000e-93 351.0
17 TraesCS7D01G052700 chr4A 89.493 276 27 2 391 666 704224548 704224275 5.130000e-92 348.0
18 TraesCS7D01G052700 chr4A 87.781 311 21 8 1785 2086 704249906 704249604 5.130000e-92 348.0
19 TraesCS7D01G052700 chr4A 87.460 311 21 8 1785 2086 704169469 704169168 2.380000e-90 342.0
20 TraesCS7D01G052700 chr4A 89.130 276 28 2 391 666 704170804 704170531 2.380000e-90 342.0
21 TraesCS7D01G052700 chr4A 87.460 311 21 8 1785 2086 704196442 704196141 2.380000e-90 342.0
22 TraesCS7D01G052700 chr4A 87.460 311 21 8 1785 2086 704223213 704222912 2.380000e-90 342.0
23 TraesCS7D01G052700 chr4A 79.792 480 83 9 1040 1506 703742390 703742868 1.110000e-88 337.0
24 TraesCS7D01G052700 chr4A 91.139 158 13 1 243 399 704172581 704172424 1.950000e-51 213.0
25 TraesCS7D01G052700 chr4A 91.139 158 13 1 243 399 704199446 704199289 1.950000e-51 213.0
26 TraesCS7D01G052700 chr4A 86.224 196 24 3 54 248 704226592 704226399 2.520000e-50 209.0
27 TraesCS7D01G052700 chr4A 90.506 158 14 1 243 399 704226325 704226168 9.080000e-50 207.0
28 TraesCS7D01G052700 chr4A 85.204 196 25 4 54 248 704172846 704172654 5.460000e-47 198.0
29 TraesCS7D01G052700 chr4A 82.234 197 15 9 53 248 704251670 704251493 4.310000e-33 152.0
30 TraesCS7D01G052700 chr4A 79.290 169 21 12 1600 1763 704169622 704169463 3.410000e-19 106.0
31 TraesCS7D01G052700 chr4A 79.290 169 21 12 1600 1763 704196595 704196436 3.410000e-19 106.0
32 TraesCS7D01G052700 chr4A 79.290 169 21 12 1600 1763 704223366 704223207 3.410000e-19 106.0
33 TraesCS7D01G052700 chr4A 79.290 169 21 12 1600 1763 704250059 704249900 3.410000e-19 106.0
34 TraesCS7D01G052700 chr7A 90.276 689 37 15 974 1642 27974446 27973768 0.000000e+00 874.0
35 TraesCS7D01G052700 chr7A 85.804 796 71 26 879 1651 27983933 27983157 0.000000e+00 806.0
36 TraesCS7D01G052700 chr7A 89.726 438 30 6 1869 2302 27982935 27982509 1.690000e-151 545.0
37 TraesCS7D01G052700 chr7A 84.120 233 25 11 1600 1825 27983170 27982943 5.420000e-52 215.0
38 TraesCS7D01G052700 chrUn 87.500 120 14 1 54 173 93876299 93876181 1.210000e-28 137.0
39 TraesCS7D01G052700 chr2A 86.066 122 16 1 52 173 733522149 733522269 2.020000e-26 130.0
40 TraesCS7D01G052700 chr2A 84.874 119 17 1 53 171 439374710 439374593 4.380000e-23 119.0
41 TraesCS7D01G052700 chr5A 85.981 107 11 3 68 173 679133759 679133656 7.320000e-21 111.0
42 TraesCS7D01G052700 chr2D 81.967 122 21 1 52 173 578922704 578922584 4.410000e-18 102.0
43 TraesCS7D01G052700 chr2D 100.000 28 0 0 508 535 179330585 179330558 5.000000e-03 52.8
44 TraesCS7D01G052700 chr7B 93.182 44 3 0 3 46 683450363 683450406 5.780000e-07 65.8
45 TraesCS7D01G052700 chr3D 92.857 42 3 0 503 544 506208280 506208239 7.480000e-06 62.1
46 TraesCS7D01G052700 chr3A 94.872 39 2 0 503 541 715820820 715820858 7.480000e-06 62.1
47 TraesCS7D01G052700 chr1D 76.562 128 19 7 421 545 396220670 396220789 2.690000e-05 60.2


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 TraesCS7D01G052700 chr7D 27486961 27489464 2503 True 4625.000000 4625 100.000000 1 2504 1 chr7D.!!$R1 2503
1 TraesCS7D01G052700 chr7D 27547841 27549262 1421 True 587.666667 955 89.212667 879 2361 3 chr7D.!!$R4 1482
2 TraesCS7D01G052700 chr4A 704278820 704280300 1480 True 626.500000 702 86.889000 879 2361 2 chr4A.!!$R5 1482
3 TraesCS7D01G052700 chr4A 704249365 704251670 2305 True 523.600000 1655 86.098600 53 2361 5 chr4A.!!$R4 2308
4 TraesCS7D01G052700 chr4A 704167783 704172846 5063 True 458.750000 1114 87.458625 54 2361 8 chr4A.!!$R1 2307
5 TraesCS7D01G052700 chr4A 704195903 704199446 3543 True 420.400000 1090 87.838000 243 2361 5 chr4A.!!$R2 2118
6 TraesCS7D01G052700 chr4A 704222674 704226592 3918 True 382.428571 1114 87.682714 54 2361 7 chr4A.!!$R3 2307
7 TraesCS7D01G052700 chr7A 27973768 27974446 678 True 874.000000 874 90.276000 974 1642 1 chr7A.!!$R1 668
8 TraesCS7D01G052700 chr7A 27982509 27983933 1424 True 522.000000 806 86.550000 879 2302 3 chr7A.!!$R2 1423

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
22 23 0.091176 GTGCAAATTGTAAAGCGCGC 59.909 50.0 26.66 26.66 0.0 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 3672 0.105593 TCATCTTCTCCGAGCATGGC 59.894 55.0 0.0 0.0 0.0 4.4 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
21 22 1.685302 AGTGCAAATTGTAAAGCGCG 58.315 45.000 0.00 0.00 41.96 6.86
22 23 0.091176 GTGCAAATTGTAAAGCGCGC 59.909 50.000 26.66 26.66 0.00 6.86
23 24 1.333584 TGCAAATTGTAAAGCGCGCG 61.334 50.000 28.44 28.44 0.00 6.86
24 25 1.336821 CAAATTGTAAAGCGCGCGC 59.663 52.632 45.10 45.10 42.33 6.86
40 41 3.918544 GCAATCCAGCGCCCTAAA 58.081 55.556 2.29 0.00 0.00 1.85
41 42 2.419057 GCAATCCAGCGCCCTAAAT 58.581 52.632 2.29 0.00 0.00 1.40
42 43 0.746659 GCAATCCAGCGCCCTAAATT 59.253 50.000 2.29 0.00 0.00 1.82
43 44 1.136891 GCAATCCAGCGCCCTAAATTT 59.863 47.619 2.29 0.00 0.00 1.82
44 45 2.813061 CAATCCAGCGCCCTAAATTTG 58.187 47.619 2.29 0.00 0.00 2.32
45 46 0.746659 ATCCAGCGCCCTAAATTTGC 59.253 50.000 2.29 0.00 0.00 3.68
46 47 0.610509 TCCAGCGCCCTAAATTTGCA 60.611 50.000 2.29 0.00 0.00 4.08
47 48 0.179129 CCAGCGCCCTAAATTTGCAG 60.179 55.000 2.29 0.00 0.00 4.41
48 49 0.803380 CAGCGCCCTAAATTTGCAGC 60.803 55.000 2.29 4.65 0.00 5.25
49 50 1.215117 GCGCCCTAAATTTGCAGCA 59.785 52.632 0.00 0.00 0.00 4.41
50 51 0.179103 GCGCCCTAAATTTGCAGCAT 60.179 50.000 0.00 0.00 0.00 3.79
51 52 1.563111 CGCCCTAAATTTGCAGCATG 58.437 50.000 0.00 0.00 40.87 4.06
107 108 2.638744 GCTTTTGCTGGAGCTGTCT 58.361 52.632 0.00 0.00 43.35 3.41
123 124 1.303806 TCTGGCGCCTAAAAACCCC 60.304 57.895 29.70 0.00 0.00 4.95
124 125 2.283316 TGGCGCCTAAAAACCCCC 60.283 61.111 29.70 0.00 0.00 5.40
140 141 1.154112 CCCAAATTTTAGCGCGCGT 60.154 52.632 32.35 20.00 0.00 6.01
153 154 0.785979 CGCGCGTAGTAGTTTTTGGT 59.214 50.000 24.19 0.00 0.00 3.67
156 157 2.053627 CGCGTAGTAGTTTTTGGTCGT 58.946 47.619 0.00 0.00 0.00 4.34
161 162 4.741676 CGTAGTAGTTTTTGGTCGTCTGTT 59.258 41.667 0.00 0.00 0.00 3.16
189 190 1.079543 CTCACCGGCTGAAGTCCAG 60.080 63.158 0.00 0.00 45.67 3.86
209 210 3.372206 CAGCTCTATTTCCCAACGAGTTG 59.628 47.826 8.87 8.87 40.13 3.16
306 388 5.489792 TGAAATATGGATGGGCTCTAGAC 57.510 43.478 0.00 0.00 0.00 2.59
355 439 2.444388 TCTAAGGGCCGATGACTAGGTA 59.556 50.000 0.00 0.00 0.00 3.08
361 445 1.329256 CCGATGACTAGGTAGTGGGG 58.671 60.000 0.00 0.00 36.50 4.96
369 453 6.303903 TGACTAGGTAGTGGGGAATTTAAC 57.696 41.667 0.00 0.00 36.50 2.01
377 461 3.621682 TGGGGAATTTAACACCACCTT 57.378 42.857 0.00 0.00 35.76 3.50
379 463 4.668636 TGGGGAATTTAACACCACCTTAG 58.331 43.478 0.00 0.00 35.76 2.18
411 2126 8.614469 ATTAGAGTTGAGATGCCTTTATAAGC 57.386 34.615 0.00 0.00 0.00 3.09
412 2127 5.053145 AGAGTTGAGATGCCTTTATAAGCG 58.947 41.667 0.00 0.00 0.00 4.68
457 2172 3.078837 GAGAATAAAAGTGGTTCCCGCA 58.921 45.455 0.00 0.00 36.32 5.69
458 2173 3.694566 GAGAATAAAAGTGGTTCCCGCAT 59.305 43.478 0.00 0.00 36.32 4.73
465 2180 2.044946 GGTTCCCGCATGCTCCTT 60.045 61.111 17.13 0.00 0.00 3.36
467 2182 2.125147 TTCCCGCATGCTCCTTCG 60.125 61.111 17.13 0.00 0.00 3.79
468 2183 4.838152 TCCCGCATGCTCCTTCGC 62.838 66.667 17.13 0.00 0.00 4.70
472 2187 3.885521 GCATGCTCCTTCGCTGCC 61.886 66.667 11.37 0.00 32.01 4.85
473 2188 2.437180 CATGCTCCTTCGCTGCCA 60.437 61.111 0.00 0.00 0.00 4.92
554 2269 4.668177 CGTGCGTTTACTTGATGGTTAAGG 60.668 45.833 0.00 0.00 0.00 2.69
763 2480 9.554395 AAACAAAAACAGAAAAGAAAAGAAGGA 57.446 25.926 0.00 0.00 0.00 3.36
764 2481 8.763049 ACAAAAACAGAAAAGAAAAGAAGGAG 57.237 30.769 0.00 0.00 0.00 3.69
765 2482 7.819415 ACAAAAACAGAAAAGAAAAGAAGGAGG 59.181 33.333 0.00 0.00 0.00 4.30
766 2483 7.718334 AAAACAGAAAAGAAAAGAAGGAGGA 57.282 32.000 0.00 0.00 0.00 3.71
767 2484 7.718334 AAACAGAAAAGAAAAGAAGGAGGAA 57.282 32.000 0.00 0.00 0.00 3.36
768 2485 7.718334 AACAGAAAAGAAAAGAAGGAGGAAA 57.282 32.000 0.00 0.00 0.00 3.13
811 2528 3.941188 CCGCATATGGGCCGGACT 61.941 66.667 7.57 0.00 31.88 3.85
969 2701 5.045651 TCAGCAATCTTCCTCTTCCATGTTA 60.046 40.000 0.00 0.00 0.00 2.41
988 2720 5.183228 TGTTACTATAAAAGCAGAGCACCC 58.817 41.667 0.00 0.00 0.00 4.61
990 2722 2.846827 ACTATAAAAGCAGAGCACCCCT 59.153 45.455 0.00 0.00 0.00 4.79
991 2723 2.134789 ATAAAAGCAGAGCACCCCTG 57.865 50.000 0.00 0.00 34.88 4.45
993 2725 1.719063 AAAAGCAGAGCACCCCTGGA 61.719 55.000 0.00 0.00 32.51 3.86
994 2726 2.417558 AAAGCAGAGCACCCCTGGAC 62.418 60.000 0.00 0.00 32.51 4.02
995 2727 4.767255 GCAGAGCACCCCTGGACG 62.767 72.222 0.00 0.00 32.51 4.79
996 2728 4.767255 CAGAGCACCCCTGGACGC 62.767 72.222 0.00 0.00 0.00 5.19
1029 2761 2.921069 GCAACTCTCGTCAAGTCGCTTA 60.921 50.000 0.00 0.00 0.00 3.09
1084 2816 0.106708 GCTGATGGCATCCTTCGGTA 59.893 55.000 23.92 3.22 41.35 4.02
1347 3115 1.116536 TGTTCCGGTACTGCCACTCA 61.117 55.000 12.78 0.00 36.97 3.41
1547 3338 2.508891 GCGCATCGAGTCGGAGTTG 61.509 63.158 13.54 6.97 0.00 3.16
1548 3339 2.508891 CGCATCGAGTCGGAGTTGC 61.509 63.158 13.54 14.95 0.00 4.17
1556 3347 5.258456 TCGAGTCGGAGTTGCTATTAATT 57.742 39.130 13.54 0.00 0.00 1.40
1557 3348 5.041287 TCGAGTCGGAGTTGCTATTAATTG 58.959 41.667 13.54 0.00 0.00 2.32
1561 3352 6.047231 AGTCGGAGTTGCTATTAATTGTACC 58.953 40.000 0.00 0.00 0.00 3.34
1591 3382 2.159627 CCAAGTAACAGGTGATCAACGC 59.840 50.000 4.80 0.00 0.00 4.84
1628 3422 0.868406 CGAGACCAACAAGAACAGGC 59.132 55.000 0.00 0.00 0.00 4.85
1633 3427 0.443869 CCAACAAGAACAGGCGATCG 59.556 55.000 11.69 11.69 0.00 3.69
1670 3526 9.525409 GGACGAGTATAATGTTACAATAACAGT 57.475 33.333 7.43 7.14 33.18 3.55
1679 3535 7.686438 ATGTTACAATAACAGTTGATCAGCA 57.314 32.000 12.41 0.00 33.18 4.41
1680 3536 7.132694 TGTTACAATAACAGTTGATCAGCAG 57.867 36.000 12.41 6.37 33.37 4.24
1681 3537 6.934083 TGTTACAATAACAGTTGATCAGCAGA 59.066 34.615 12.41 0.00 33.37 4.26
1682 3538 7.443879 TGTTACAATAACAGTTGATCAGCAGAA 59.556 33.333 12.41 0.00 33.37 3.02
1683 3539 6.492007 ACAATAACAGTTGATCAGCAGAAG 57.508 37.500 12.41 1.58 33.37 2.85
1684 3540 5.413833 ACAATAACAGTTGATCAGCAGAAGG 59.586 40.000 12.41 0.00 33.37 3.46
1685 3541 3.498774 AACAGTTGATCAGCAGAAGGT 57.501 42.857 12.41 0.00 0.00 3.50
1710 3569 1.262824 GCGAAGACGATCGATGGACG 61.263 60.000 24.34 19.24 45.48 4.79
1711 3570 1.262824 CGAAGACGATCGATGGACGC 61.263 60.000 24.34 5.29 45.48 5.19
1712 3571 0.935366 GAAGACGATCGATGGACGCC 60.935 60.000 24.34 0.00 42.26 5.68
1713 3572 2.663630 AAGACGATCGATGGACGCCG 62.664 60.000 24.34 7.39 42.26 6.46
1714 3573 3.177272 GACGATCGATGGACGCCGA 62.177 63.158 24.34 0.00 42.26 5.54
1715 3574 2.427575 CGATCGATGGACGCCGAG 60.428 66.667 10.26 0.00 42.26 4.63
1716 3575 2.731348 GATCGATGGACGCCGAGC 60.731 66.667 0.54 0.00 42.26 5.03
1717 3576 4.286320 ATCGATGGACGCCGAGCC 62.286 66.667 0.00 0.00 42.26 4.70
1720 3579 2.969238 GATGGACGCCGAGCCATG 60.969 66.667 17.99 0.00 44.60 3.66
1721 3580 4.552365 ATGGACGCCGAGCCATGG 62.552 66.667 7.63 7.63 43.04 3.66
1727 3586 4.864334 GCCGAGCCATGGACAGGG 62.864 72.222 18.40 11.47 34.91 4.45
1758 3645 5.766150 AGATATGTCTGAGTCTGTACAGC 57.234 43.478 18.45 12.92 34.57 4.40
1759 3646 4.582656 AGATATGTCTGAGTCTGTACAGCC 59.417 45.833 18.45 6.95 34.57 4.85
1760 3647 1.995376 TGTCTGAGTCTGTACAGCCA 58.005 50.000 18.45 13.68 34.57 4.75
1761 3648 2.529632 TGTCTGAGTCTGTACAGCCAT 58.470 47.619 18.45 6.02 34.57 4.40
1762 3649 2.232208 TGTCTGAGTCTGTACAGCCATG 59.768 50.000 18.45 7.11 34.57 3.66
1763 3650 2.493675 GTCTGAGTCTGTACAGCCATGA 59.506 50.000 18.45 9.21 34.57 3.07
1764 3651 3.131933 GTCTGAGTCTGTACAGCCATGAT 59.868 47.826 18.45 0.00 34.57 2.45
1765 3652 3.771479 TCTGAGTCTGTACAGCCATGATT 59.229 43.478 18.45 0.00 34.57 2.57
1766 3653 3.865446 TGAGTCTGTACAGCCATGATTG 58.135 45.455 18.45 0.00 0.00 2.67
1767 3654 2.611292 GAGTCTGTACAGCCATGATTGC 59.389 50.000 18.45 0.00 0.00 3.56
1768 3655 2.238144 AGTCTGTACAGCCATGATTGCT 59.762 45.455 18.45 0.00 40.41 3.91
1769 3656 3.012518 GTCTGTACAGCCATGATTGCTT 58.987 45.455 18.45 0.00 36.81 3.91
1770 3657 3.441572 GTCTGTACAGCCATGATTGCTTT 59.558 43.478 18.45 0.00 36.81 3.51
1771 3658 3.691118 TCTGTACAGCCATGATTGCTTTC 59.309 43.478 18.45 0.00 36.81 2.62
1772 3659 2.754552 TGTACAGCCATGATTGCTTTCC 59.245 45.455 0.00 0.00 36.81 3.13
1773 3660 1.927487 ACAGCCATGATTGCTTTCCA 58.073 45.000 0.00 0.00 36.81 3.53
1774 3661 1.822990 ACAGCCATGATTGCTTTCCAG 59.177 47.619 0.00 0.00 36.81 3.86
1776 3663 0.179092 GCCATGATTGCTTTCCAGCC 60.179 55.000 0.00 0.00 46.74 4.85
1777 3664 1.187974 CCATGATTGCTTTCCAGCCA 58.812 50.000 0.00 0.00 46.74 4.75
1778 3665 1.760613 CCATGATTGCTTTCCAGCCAT 59.239 47.619 0.00 0.00 46.74 4.40
1779 3666 2.483013 CCATGATTGCTTTCCAGCCATG 60.483 50.000 0.00 0.00 46.74 3.66
1780 3667 1.187974 TGATTGCTTTCCAGCCATGG 58.812 50.000 7.63 7.63 46.74 3.66
1781 3668 0.179092 GATTGCTTTCCAGCCATGGC 60.179 55.000 30.12 30.12 46.74 4.40
1782 3669 1.619807 ATTGCTTTCCAGCCATGGCC 61.620 55.000 33.14 16.18 46.74 5.36
1825 3741 3.300239 AGGACGAGGAAGCTATGTACT 57.700 47.619 0.00 0.00 0.00 2.73
1826 3742 2.952978 AGGACGAGGAAGCTATGTACTG 59.047 50.000 0.00 0.00 0.00 2.74
1827 3743 2.688958 GGACGAGGAAGCTATGTACTGT 59.311 50.000 0.00 0.00 0.00 3.55
1828 3744 3.130693 GGACGAGGAAGCTATGTACTGTT 59.869 47.826 0.00 0.00 0.00 3.16
1829 3745 4.381718 GGACGAGGAAGCTATGTACTGTTT 60.382 45.833 0.00 0.00 0.00 2.83
1840 3756 5.105064 GCTATGTACTGTTTACAAGGAGGGA 60.105 44.000 0.00 0.00 0.00 4.20
1843 3759 4.841813 TGTACTGTTTACAAGGAGGGATCA 59.158 41.667 0.00 0.00 0.00 2.92
1897 3813 1.165270 ACCGGCTGTAAATCTGCAAC 58.835 50.000 0.00 0.00 41.72 4.17
1902 3818 3.638484 GGCTGTAAATCTGCAACGTTTT 58.362 40.909 0.00 0.00 41.72 2.43
1926 3848 4.317278 CGTTGTTTTGCATGCTTTGTACTG 60.317 41.667 20.33 0.00 0.00 2.74
1931 3853 5.964887 TTTGCATGCTTTGTACTGTTTTC 57.035 34.783 20.33 0.00 0.00 2.29
1956 3879 7.918562 TCTTGTTTTGTTAATGGAGCTTTGTAC 59.081 33.333 0.00 0.00 0.00 2.90
2026 3985 6.011481 AGGAATCCTCTAAATCGTACCTAGG 58.989 44.000 7.41 7.41 0.00 3.02
2276 4240 2.651455 CTCACCATAGGTCACCGTAGA 58.349 52.381 0.00 0.00 31.02 2.59
2279 4243 2.099263 CACCATAGGTCACCGTAGAGTG 59.901 54.545 0.00 0.00 39.20 3.51
2280 4244 2.291411 ACCATAGGTCACCGTAGAGTGT 60.291 50.000 0.00 0.00 38.91 3.55
2281 4245 2.358267 CCATAGGTCACCGTAGAGTGTC 59.642 54.545 0.00 0.00 38.91 3.67
2282 4246 1.730501 TAGGTCACCGTAGAGTGTCG 58.269 55.000 0.00 0.00 38.91 4.35
2283 4247 1.154073 GGTCACCGTAGAGTGTCGC 60.154 63.158 0.00 0.00 38.91 5.19
2371 4335 3.289525 GGTACCTGCAGCGAGTCT 58.710 61.111 8.66 0.00 0.00 3.24
2372 4336 1.153745 GGTACCTGCAGCGAGTCTG 60.154 63.158 8.66 0.00 45.62 3.51
2374 4338 0.809385 GTACCTGCAGCGAGTCTGTA 59.191 55.000 8.66 0.00 44.66 2.74
2377 4341 4.097218 TGCAGCGAGTCTGTAGGT 57.903 55.556 0.00 0.00 44.66 3.08
2378 4342 3.259592 TGCAGCGAGTCTGTAGGTA 57.740 52.632 0.00 0.00 44.66 3.08
2381 4345 0.377554 CAGCGAGTCTGTAGGTACGG 59.622 60.000 0.00 0.00 38.02 4.02
2383 4347 1.726265 CGAGTCTGTAGGTACGGCC 59.274 63.158 0.00 0.00 32.63 6.13
2385 4349 0.682209 GAGTCTGTAGGTACGGCCCA 60.682 60.000 0.00 0.00 38.26 5.36
2387 4351 2.056223 TCTGTAGGTACGGCCCAGC 61.056 63.158 0.00 0.00 38.26 4.85
2388 4352 2.038329 TGTAGGTACGGCCCAGCT 59.962 61.111 8.61 8.61 38.26 4.24
2389 4353 0.754217 CTGTAGGTACGGCCCAGCTA 60.754 60.000 0.00 1.50 38.26 3.32
2390 4354 0.324552 TGTAGGTACGGCCCAGCTAA 60.325 55.000 11.43 2.29 38.26 3.09
2391 4355 1.046204 GTAGGTACGGCCCAGCTAAT 58.954 55.000 11.43 0.00 38.26 1.73
2393 4357 1.300697 GGTACGGCCCAGCTAATCG 60.301 63.158 0.00 0.00 0.00 3.34
2394 4358 1.440476 GTACGGCCCAGCTAATCGT 59.560 57.895 0.00 8.26 37.78 3.73
2396 4360 2.067091 TACGGCCCAGCTAATCGTCG 62.067 60.000 0.00 1.24 35.60 5.12
2398 4362 2.202878 GCCCAGCTAATCGTCGCA 60.203 61.111 0.00 0.00 0.00 5.10
2399 4363 2.526120 GCCCAGCTAATCGTCGCAC 61.526 63.158 0.00 0.00 0.00 5.34
2400 4364 2.230940 CCCAGCTAATCGTCGCACG 61.231 63.158 2.79 2.79 44.19 5.34
2401 4365 2.230940 CCAGCTAATCGTCGCACGG 61.231 63.158 8.46 0.00 42.81 4.94
2402 4366 2.582498 AGCTAATCGTCGCACGGC 60.582 61.111 8.46 4.77 42.81 5.68
2403 4367 2.582498 GCTAATCGTCGCACGGCT 60.582 61.111 8.46 0.61 42.81 5.52
2405 4369 2.277692 TAATCGTCGCACGGCTCG 60.278 61.111 8.46 0.00 42.81 5.03
2406 4370 3.744749 TAATCGTCGCACGGCTCGG 62.745 63.158 8.46 0.00 42.81 4.63
2418 4382 4.319133 GCTCGGCCATTTTCCTGA 57.681 55.556 2.24 0.00 0.00 3.86
2419 4383 2.101700 GCTCGGCCATTTTCCTGAG 58.898 57.895 2.24 0.00 0.00 3.35
2421 4385 1.378514 TCGGCCATTTTCCTGAGCC 60.379 57.895 2.24 0.00 40.33 4.70
2422 4386 3.200522 GGCCATTTTCCTGAGCCG 58.799 61.111 0.00 0.00 33.18 5.52
2423 4387 2.418083 GGCCATTTTCCTGAGCCGG 61.418 63.158 0.00 0.00 33.18 6.13
2424 4388 2.418083 GCCATTTTCCTGAGCCGGG 61.418 63.158 2.18 0.00 0.00 5.73
2425 4389 2.418083 CCATTTTCCTGAGCCGGGC 61.418 63.158 12.11 12.11 0.00 6.13
2427 4391 1.379044 ATTTTCCTGAGCCGGGCTG 60.379 57.895 29.31 13.22 39.88 4.85
2428 4392 1.852157 ATTTTCCTGAGCCGGGCTGA 61.852 55.000 29.31 18.70 39.88 4.26
2429 4393 2.063015 TTTTCCTGAGCCGGGCTGAA 62.063 55.000 29.31 20.48 39.88 3.02
2431 4395 3.710722 CCTGAGCCGGGCTGAACT 61.711 66.667 29.31 0.48 39.88 3.01
2432 4396 2.435586 CTGAGCCGGGCTGAACTG 60.436 66.667 29.31 12.34 39.88 3.16
2434 4398 2.435059 GAGCCGGGCTGAACTGTC 60.435 66.667 29.31 6.31 39.88 3.51
2438 4402 2.125912 CGGGCTGAACTGTCTCCG 60.126 66.667 0.00 0.00 0.00 4.63
2439 4403 2.932234 CGGGCTGAACTGTCTCCGT 61.932 63.158 0.00 0.00 32.13 4.69
2440 4404 1.079750 GGGCTGAACTGTCTCCGTC 60.080 63.158 0.00 0.00 0.00 4.79
2441 4405 1.666011 GGCTGAACTGTCTCCGTCA 59.334 57.895 0.00 0.00 0.00 4.35
2442 4406 0.667792 GGCTGAACTGTCTCCGTCAC 60.668 60.000 0.00 0.00 0.00 3.67
2443 4407 1.004277 GCTGAACTGTCTCCGTCACG 61.004 60.000 0.00 0.00 0.00 4.35
2444 4408 0.311165 CTGAACTGTCTCCGTCACGT 59.689 55.000 0.00 0.00 0.00 4.49
2446 4410 0.663568 GAACTGTCTCCGTCACGTGG 60.664 60.000 17.00 0.00 0.00 4.94
2447 4411 1.105167 AACTGTCTCCGTCACGTGGA 61.105 55.000 17.00 4.09 0.00 4.02
2448 4412 1.081376 CTGTCTCCGTCACGTGGAC 60.081 63.158 17.00 14.66 43.36 4.02
2449 4413 1.516365 CTGTCTCCGTCACGTGGACT 61.516 60.000 17.00 0.00 44.68 3.85
2452 4416 2.592574 TCCGTCACGTGGACTCGT 60.593 61.111 17.00 0.00 44.68 4.18
2453 4417 2.126417 CTCCGTCACGTGGACTCGTT 62.126 60.000 17.00 0.00 44.68 3.85
2454 4418 0.884259 TCCGTCACGTGGACTCGTTA 60.884 55.000 17.00 4.14 44.68 3.18
2455 4419 0.040157 CCGTCACGTGGACTCGTTAA 60.040 55.000 17.00 0.00 44.68 2.01
2456 4420 1.401931 CCGTCACGTGGACTCGTTAAT 60.402 52.381 17.00 0.00 44.68 1.40
2457 4421 1.647213 CGTCACGTGGACTCGTTAATG 59.353 52.381 17.00 0.00 44.68 1.90
2458 4422 1.389106 GTCACGTGGACTCGTTAATGC 59.611 52.381 17.00 0.00 43.46 3.56
2460 4424 0.390735 ACGTGGACTCGTTAATGCCC 60.391 55.000 0.00 0.00 41.37 5.36
2461 4425 0.390603 CGTGGACTCGTTAATGCCCA 60.391 55.000 0.00 0.00 0.00 5.36
2462 4426 1.084289 GTGGACTCGTTAATGCCCAC 58.916 55.000 13.90 13.90 37.50 4.61
2463 4427 0.035820 TGGACTCGTTAATGCCCACC 60.036 55.000 0.00 0.00 0.00 4.61
2464 4428 0.252197 GGACTCGTTAATGCCCACCT 59.748 55.000 0.00 0.00 0.00 4.00
2465 4429 1.369625 GACTCGTTAATGCCCACCTG 58.630 55.000 0.00 0.00 0.00 4.00
2466 4430 0.035439 ACTCGTTAATGCCCACCTGG 60.035 55.000 0.00 0.00 37.09 4.45
2476 4440 3.721706 CCACCTGGCCAGTCCCTC 61.722 72.222 30.63 0.00 0.00 4.30
2477 4441 2.930019 CACCTGGCCAGTCCCTCA 60.930 66.667 30.63 0.00 0.00 3.86
2480 4444 0.253160 ACCTGGCCAGTCCCTCATAA 60.253 55.000 30.63 0.00 0.00 1.90
2482 4446 1.496429 CCTGGCCAGTCCCTCATAAAT 59.504 52.381 30.63 0.00 0.00 1.40
2486 4450 3.136443 TGGCCAGTCCCTCATAAATGTAG 59.864 47.826 0.00 0.00 0.00 2.74
2487 4451 3.142174 GCCAGTCCCTCATAAATGTAGC 58.858 50.000 0.00 0.00 0.00 3.58
2489 4453 4.636249 CCAGTCCCTCATAAATGTAGCTC 58.364 47.826 0.00 0.00 0.00 4.09
2490 4454 4.503991 CCAGTCCCTCATAAATGTAGCTCC 60.504 50.000 0.00 0.00 0.00 4.70
2491 4455 4.101585 CAGTCCCTCATAAATGTAGCTCCA 59.898 45.833 0.00 0.00 0.00 3.86
2494 4458 4.101585 TCCCTCATAAATGTAGCTCCACAG 59.898 45.833 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.425404 CGCGCTTTACAATTTGCACTAT 58.575 40.909 5.56 0.00 0.00 2.12
1 2 2.845486 CGCGCTTTACAATTTGCACTA 58.155 42.857 5.56 0.00 0.00 2.74
2 3 1.685302 CGCGCTTTACAATTTGCACT 58.315 45.000 5.56 0.00 0.00 4.40
3 4 0.091176 GCGCGCTTTACAATTTGCAC 59.909 50.000 26.67 0.00 0.00 4.57
4 5 1.333584 CGCGCGCTTTACAATTTGCA 61.334 50.000 30.48 0.00 0.00 4.08
5 6 1.336821 CGCGCGCTTTACAATTTGC 59.663 52.632 30.48 0.00 0.00 3.68
6 7 1.336821 GCGCGCGCTTTACAATTTG 59.663 52.632 44.38 10.35 38.26 2.32
7 8 3.748856 GCGCGCGCTTTACAATTT 58.251 50.000 44.38 0.00 38.26 1.82
23 24 0.746659 AATTTAGGGCGCTGGATTGC 59.253 50.000 14.51 0.00 0.00 3.56
24 25 2.813061 CAAATTTAGGGCGCTGGATTG 58.187 47.619 14.51 9.37 0.00 2.67
25 26 1.136891 GCAAATTTAGGGCGCTGGATT 59.863 47.619 14.51 10.22 0.00 3.01
26 27 0.746659 GCAAATTTAGGGCGCTGGAT 59.253 50.000 14.51 4.23 0.00 3.41
27 28 0.610509 TGCAAATTTAGGGCGCTGGA 60.611 50.000 14.51 1.70 0.00 3.86
28 29 0.179129 CTGCAAATTTAGGGCGCTGG 60.179 55.000 14.51 0.00 0.00 4.85
29 30 0.803380 GCTGCAAATTTAGGGCGCTG 60.803 55.000 14.51 0.00 0.00 5.18
30 31 1.250154 TGCTGCAAATTTAGGGCGCT 61.250 50.000 7.64 8.86 0.00 5.92
31 32 0.179103 ATGCTGCAAATTTAGGGCGC 60.179 50.000 6.36 0.00 0.00 6.53
32 33 1.563111 CATGCTGCAAATTTAGGGCG 58.437 50.000 6.36 0.00 0.00 6.13
33 34 1.292992 GCATGCTGCAAATTTAGGGC 58.707 50.000 11.37 0.00 44.26 5.19
34 35 1.135024 ACGCATGCTGCAAATTTAGGG 60.135 47.619 17.13 4.02 45.36 3.53
35 36 1.921887 CACGCATGCTGCAAATTTAGG 59.078 47.619 17.13 0.00 45.36 2.69
48 49 2.098426 AAAAGGGTTGGGCACGCATG 62.098 55.000 0.00 0.00 40.92 4.06
49 50 1.406860 AAAAAGGGTTGGGCACGCAT 61.407 50.000 0.00 0.00 40.92 4.73
50 51 2.060980 AAAAAGGGTTGGGCACGCA 61.061 52.632 0.00 0.00 40.92 5.24
51 52 2.818841 AAAAAGGGTTGGGCACGC 59.181 55.556 0.00 0.00 38.67 5.34
70 71 3.009723 AGCTGTAAAATAGTGCATGCGT 58.990 40.909 14.09 5.32 0.00 5.24
107 108 2.283316 GGGGGTTTTTAGGCGCCA 60.283 61.111 31.54 12.31 39.18 5.69
114 115 4.316645 GCGCTAAAATTTGGGGGTTTTTA 58.683 39.130 0.00 0.00 0.00 1.52
123 124 1.201987 ACTACGCGCGCTAAAATTTGG 60.202 47.619 32.58 12.39 0.00 3.28
124 125 2.153680 ACTACGCGCGCTAAAATTTG 57.846 45.000 32.58 13.34 0.00 2.32
140 141 5.051816 CCAACAGACGACCAAAAACTACTA 58.948 41.667 0.00 0.00 0.00 1.82
224 225 8.227791 CGTACAAATTAGAAGCATGTGTTAACT 58.772 33.333 7.22 0.00 0.00 2.24
338 422 0.556747 ACTACCTAGTCATCGGCCCT 59.443 55.000 0.00 0.00 0.00 5.19
344 428 5.632034 AAATTCCCCACTACCTAGTCATC 57.368 43.478 0.00 0.00 33.46 2.92
355 439 2.449345 AGGTGGTGTTAAATTCCCCACT 59.551 45.455 7.03 0.00 43.98 4.00
361 445 6.909909 CCACTTCTAAGGTGGTGTTAAATTC 58.090 40.000 4.87 0.00 46.42 2.17
377 461 6.183360 GGCATCTCAACTCTAATCCACTTCTA 60.183 42.308 0.00 0.00 0.00 2.10
379 463 4.813697 GGCATCTCAACTCTAATCCACTTC 59.186 45.833 0.00 0.00 0.00 3.01
457 2172 2.437359 GTGGCAGCGAAGGAGCAT 60.437 61.111 0.00 0.00 40.15 3.79
465 2180 4.961511 GTGTGGACGTGGCAGCGA 62.962 66.667 14.63 0.00 35.59 4.93
467 2182 3.649986 GTGTGTGGACGTGGCAGC 61.650 66.667 0.00 0.00 0.00 5.25
468 2183 1.568612 GATGTGTGTGGACGTGGCAG 61.569 60.000 0.00 0.00 0.00 4.85
472 2187 3.309682 GGAATATGATGTGTGTGGACGTG 59.690 47.826 0.00 0.00 0.00 4.49
473 2188 3.055458 TGGAATATGATGTGTGTGGACGT 60.055 43.478 0.00 0.00 0.00 4.34
483 2198 4.698780 CGGCTTGATCATGGAATATGATGT 59.301 41.667 10.35 0.00 38.73 3.06
518 2233 0.806102 ACGCACGCATGACATAGGTC 60.806 55.000 0.00 0.00 44.57 3.85
767 2484 4.035091 GCCCTGCTTTTCAATTTCGTTTTT 59.965 37.500 0.00 0.00 0.00 1.94
768 2485 3.559655 GCCCTGCTTTTCAATTTCGTTTT 59.440 39.130 0.00 0.00 0.00 2.43
778 2495 2.203625 GGGGTGCCCTGCTTTTCA 60.204 61.111 7.26 0.00 41.34 2.69
779 2496 3.373565 CGGGGTGCCCTGCTTTTC 61.374 66.667 7.26 0.00 42.67 2.29
830 2547 2.356382 TGATCCAAGAACAAACGCGTTT 59.644 40.909 30.36 30.36 0.00 3.60
845 2562 2.153898 CTTGGGTTGGGCCTGATCCA 62.154 60.000 4.53 6.74 37.43 3.41
969 2701 2.846827 AGGGGTGCTCTGCTTTTATAGT 59.153 45.455 0.00 0.00 0.00 2.12
990 2722 4.927782 GTGGTGCTGGTGCGTCCA 62.928 66.667 0.65 0.65 45.01 4.02
995 2727 4.629115 GTTGCGTGGTGCTGGTGC 62.629 66.667 0.00 0.00 46.63 5.01
996 2728 2.896801 GAGTTGCGTGGTGCTGGTG 61.897 63.158 0.00 0.00 46.63 4.17
997 2729 2.591715 GAGTTGCGTGGTGCTGGT 60.592 61.111 0.00 0.00 46.63 4.00
998 2730 2.281070 AGAGTTGCGTGGTGCTGG 60.281 61.111 0.00 0.00 46.63 4.85
999 2731 2.661566 CGAGAGTTGCGTGGTGCTG 61.662 63.158 0.00 0.00 46.63 4.41
1000 2732 2.356313 CGAGAGTTGCGTGGTGCT 60.356 61.111 0.00 0.00 46.63 4.40
1029 2761 0.962356 CTGCCTGCTGGGTTTCGATT 60.962 55.000 12.06 0.00 37.43 3.34
1144 2876 0.388649 CTGAAGTACGCCGTCAGCTT 60.389 55.000 0.00 0.00 41.66 3.74
1389 3157 1.524482 GAGCCTCAAGAGCCGGAAT 59.476 57.895 5.05 0.00 0.00 3.01
1425 3193 0.178987 ATCCGTCAGGGCGTATCTCT 60.179 55.000 0.00 0.00 38.33 3.10
1514 3297 4.625781 CGCGACGGCTAGGGCTAC 62.626 72.222 0.00 0.00 38.73 3.58
1547 3338 5.399604 AGCGTTTCGGTACAATTAATAGC 57.600 39.130 0.00 0.00 35.27 2.97
1548 3339 5.521010 TGGAGCGTTTCGGTACAATTAATAG 59.479 40.000 3.79 0.00 45.32 1.73
1556 3347 0.390124 ACTTGGAGCGTTTCGGTACA 59.610 50.000 2.11 2.11 46.64 2.90
1557 3348 2.352503 TACTTGGAGCGTTTCGGTAC 57.647 50.000 0.00 0.00 37.83 3.34
1561 3352 1.459592 CCTGTTACTTGGAGCGTTTCG 59.540 52.381 0.00 0.00 0.00 3.46
1628 3422 2.278206 CCTGCACCTCGTCGATCG 60.278 66.667 9.36 9.36 41.41 3.69
1633 3427 1.303799 TACTCGTCCTGCACCTCGTC 61.304 60.000 0.00 0.00 0.00 4.20
1670 3526 2.362736 GCATGACCTTCTGCTGATCAA 58.637 47.619 0.00 0.00 35.49 2.57
1678 3534 0.737367 TCTTCGCGCATGACCTTCTG 60.737 55.000 8.75 0.00 0.00 3.02
1679 3535 0.737715 GTCTTCGCGCATGACCTTCT 60.738 55.000 8.75 0.00 0.00 2.85
1680 3536 1.710339 GTCTTCGCGCATGACCTTC 59.290 57.895 8.75 0.00 0.00 3.46
1681 3537 2.094659 CGTCTTCGCGCATGACCTT 61.095 57.895 8.75 0.00 0.00 3.50
1682 3538 2.284798 ATCGTCTTCGCGCATGACCT 62.285 55.000 8.75 0.00 36.96 3.85
1683 3539 1.812214 GATCGTCTTCGCGCATGACC 61.812 60.000 8.75 0.00 36.96 4.02
1684 3540 1.555538 GATCGTCTTCGCGCATGAC 59.444 57.895 8.75 11.14 36.96 3.06
1685 3541 1.939299 CGATCGTCTTCGCGCATGA 60.939 57.895 8.75 0.00 36.96 3.07
1692 3548 1.262824 GCGTCCATCGATCGTCTTCG 61.263 60.000 15.94 14.70 42.86 3.79
1710 3569 4.864334 CCCTGTCCATGGCTCGGC 62.864 72.222 6.96 0.00 0.00 5.54
1711 3570 4.864334 GCCCTGTCCATGGCTCGG 62.864 72.222 6.96 7.70 44.46 4.63
1716 3575 1.077212 CTTCCTGCCCTGTCCATGG 60.077 63.158 4.97 4.97 0.00 3.66
1717 3576 1.751927 GCTTCCTGCCCTGTCCATG 60.752 63.158 0.00 0.00 35.15 3.66
1718 3577 2.207501 CTGCTTCCTGCCCTGTCCAT 62.208 60.000 0.00 0.00 42.00 3.41
1719 3578 2.853542 TGCTTCCTGCCCTGTCCA 60.854 61.111 0.00 0.00 42.00 4.02
1720 3579 1.919600 ATCTGCTTCCTGCCCTGTCC 61.920 60.000 0.00 0.00 42.00 4.02
1721 3580 0.833287 TATCTGCTTCCTGCCCTGTC 59.167 55.000 0.00 0.00 42.00 3.51
1722 3581 1.142465 CATATCTGCTTCCTGCCCTGT 59.858 52.381 0.00 0.00 42.00 4.00
1723 3582 1.142465 ACATATCTGCTTCCTGCCCTG 59.858 52.381 0.00 0.00 42.00 4.45
1758 3645 1.187974 TGGCTGGAAAGCAATCATGG 58.812 50.000 0.00 0.00 36.33 3.66
1759 3646 2.483013 CCATGGCTGGAAAGCAATCATG 60.483 50.000 0.00 4.63 46.37 3.07
1760 3647 1.760613 CCATGGCTGGAAAGCAATCAT 59.239 47.619 0.00 0.00 46.37 2.45
1761 3648 1.187974 CCATGGCTGGAAAGCAATCA 58.812 50.000 0.00 0.00 46.37 2.57
1762 3649 0.179092 GCCATGGCTGGAAAGCAATC 60.179 55.000 29.98 0.00 46.37 2.67
1763 3650 1.619807 GGCCATGGCTGGAAAGCAAT 61.620 55.000 34.70 0.00 46.37 3.56
1764 3651 2.285024 GGCCATGGCTGGAAAGCAA 61.285 57.895 34.70 0.00 46.37 3.91
1765 3652 2.681064 GGCCATGGCTGGAAAGCA 60.681 61.111 34.70 0.00 46.37 3.91
1766 3653 3.830192 CGGCCATGGCTGGAAAGC 61.830 66.667 34.36 16.37 46.37 3.51
1767 3654 2.045045 TCGGCCATGGCTGGAAAG 60.045 61.111 38.90 21.52 46.37 2.62
1768 3655 2.045045 CTCGGCCATGGCTGGAAA 60.045 61.111 38.90 22.89 46.37 3.13
1769 3656 4.802051 GCTCGGCCATGGCTGGAA 62.802 66.667 38.90 23.59 46.37 3.53
1784 3671 0.106335 CATCTTCTCCGAGCATGGCT 59.894 55.000 0.00 0.00 43.88 4.75
1785 3672 0.105593 TCATCTTCTCCGAGCATGGC 59.894 55.000 0.00 0.00 0.00 4.40
1825 3741 5.014123 ACAGAATGATCCCTCCTTGTAAACA 59.986 40.000 0.00 0.00 39.69 2.83
1826 3742 5.501156 ACAGAATGATCCCTCCTTGTAAAC 58.499 41.667 0.00 0.00 39.69 2.01
1827 3743 5.779241 ACAGAATGATCCCTCCTTGTAAA 57.221 39.130 0.00 0.00 39.69 2.01
1828 3744 5.964477 ACTACAGAATGATCCCTCCTTGTAA 59.036 40.000 0.00 0.00 39.69 2.41
1829 3745 5.363868 CACTACAGAATGATCCCTCCTTGTA 59.636 44.000 0.00 0.00 39.69 2.41
1840 3756 4.152402 GCGAACACAACACTACAGAATGAT 59.848 41.667 0.00 0.00 39.69 2.45
1843 3759 2.806244 GGCGAACACAACACTACAGAAT 59.194 45.455 0.00 0.00 0.00 2.40
1897 3813 2.281234 AGCATGCAAAACAACGAAAACG 59.719 40.909 21.98 0.00 0.00 3.60
1902 3818 2.886081 ACAAAGCATGCAAAACAACGA 58.114 38.095 21.98 0.00 0.00 3.85
1926 3848 7.770801 AGCTCCATTAACAAAACAAGAAAAC 57.229 32.000 0.00 0.00 0.00 2.43
1931 3853 7.920682 AGTACAAAGCTCCATTAACAAAACAAG 59.079 33.333 0.00 0.00 0.00 3.16
1956 3879 8.497554 CGGTTAGAGTTGCTCTTACTAGTATAG 58.502 40.741 2.79 5.98 42.22 1.31
1961 3884 5.814764 TCGGTTAGAGTTGCTCTTACTAG 57.185 43.478 12.86 8.92 41.50 2.57
1964 3923 4.098196 AGGATCGGTTAGAGTTGCTCTTAC 59.902 45.833 3.87 5.48 41.50 2.34
2016 3975 7.889073 AGATTATAAGAGATTGCCTAGGTACGA 59.111 37.037 11.31 0.00 0.00 3.43
2055 4014 4.160329 TCAGGGAGATTGCGGAGTAATAT 58.840 43.478 0.00 0.00 44.30 1.28
2065 4027 9.323985 GAGTATATTTATCATCAGGGAGATTGC 57.676 37.037 0.00 0.00 33.72 3.56
2276 4240 4.063967 TTCATCGGCGGCGACACT 62.064 61.111 37.06 18.88 0.00 3.55
2279 4243 2.673114 TTTGTTCATCGGCGGCGAC 61.673 57.895 37.06 24.02 0.00 5.19
2280 4244 2.357638 TTTGTTCATCGGCGGCGA 60.358 55.556 36.40 36.40 0.00 5.54
2281 4245 2.202298 GTTTGTTCATCGGCGGCG 60.202 61.111 27.15 27.15 0.00 6.46
2282 4246 1.001745 GTTGTTTGTTCATCGGCGGC 61.002 55.000 7.21 0.00 0.00 6.53
2283 4247 0.724453 CGTTGTTTGTTCATCGGCGG 60.724 55.000 7.21 0.00 0.00 6.13
2363 4327 1.375098 GCCGTACCTACAGACTCGCT 61.375 60.000 0.00 0.00 0.00 4.93
2364 4328 1.063811 GCCGTACCTACAGACTCGC 59.936 63.158 0.00 0.00 0.00 5.03
2365 4329 1.722636 GGGCCGTACCTACAGACTCG 61.723 65.000 0.00 0.00 39.10 4.18
2366 4330 0.682209 TGGGCCGTACCTACAGACTC 60.682 60.000 0.00 0.00 39.10 3.36
2367 4331 0.683504 CTGGGCCGTACCTACAGACT 60.684 60.000 0.00 0.00 39.10 3.24
2368 4332 1.814527 CTGGGCCGTACCTACAGAC 59.185 63.158 0.00 0.00 39.10 3.51
2369 4333 2.056223 GCTGGGCCGTACCTACAGA 61.056 63.158 7.06 0.00 39.10 3.41
2370 4334 0.754217 TAGCTGGGCCGTACCTACAG 60.754 60.000 0.00 0.00 39.10 2.74
2371 4335 0.324552 TTAGCTGGGCCGTACCTACA 60.325 55.000 0.00 0.00 39.10 2.74
2372 4336 1.000618 GATTAGCTGGGCCGTACCTAC 59.999 57.143 0.00 0.00 39.10 3.18
2374 4338 1.745320 CGATTAGCTGGGCCGTACCT 61.745 60.000 0.00 0.00 39.10 3.08
2375 4339 1.300697 CGATTAGCTGGGCCGTACC 60.301 63.158 0.00 0.00 37.93 3.34
2376 4340 0.596859 GACGATTAGCTGGGCCGTAC 60.597 60.000 0.00 0.00 33.32 3.67
2377 4341 1.737816 GACGATTAGCTGGGCCGTA 59.262 57.895 0.00 0.00 33.32 4.02
2378 4342 2.499685 GACGATTAGCTGGGCCGT 59.500 61.111 0.00 0.11 36.08 5.68
2381 4345 2.202878 TGCGACGATTAGCTGGGC 60.203 61.111 0.00 0.00 0.00 5.36
2383 4347 2.230940 CCGTGCGACGATTAGCTGG 61.231 63.158 0.00 0.00 46.05 4.85
2385 4349 2.582498 GCCGTGCGACGATTAGCT 60.582 61.111 0.00 0.00 46.05 3.32
2387 4351 2.286559 CGAGCCGTGCGACGATTAG 61.287 63.158 0.00 0.00 46.05 1.73
2388 4352 2.277692 CGAGCCGTGCGACGATTA 60.278 61.111 0.00 0.00 46.05 1.75
2401 4365 1.997928 GCTCAGGAAAATGGCCGAGC 61.998 60.000 8.89 8.89 41.26 5.03
2402 4366 1.379642 GGCTCAGGAAAATGGCCGAG 61.380 60.000 0.00 0.00 33.30 4.63
2403 4367 1.378514 GGCTCAGGAAAATGGCCGA 60.379 57.895 0.00 0.00 33.30 5.54
2405 4369 2.418083 CCGGCTCAGGAAAATGGCC 61.418 63.158 0.00 0.00 39.43 5.36
2406 4370 2.418083 CCCGGCTCAGGAAAATGGC 61.418 63.158 0.00 0.00 0.00 4.40
2407 4371 2.418083 GCCCGGCTCAGGAAAATGG 61.418 63.158 0.71 0.00 0.00 3.16
2410 4374 2.034066 CAGCCCGGCTCAGGAAAA 59.966 61.111 9.68 0.00 36.40 2.29
2413 4377 3.706373 GTTCAGCCCGGCTCAGGA 61.706 66.667 9.68 0.63 36.40 3.86
2414 4378 3.710722 AGTTCAGCCCGGCTCAGG 61.711 66.667 9.68 0.00 36.40 3.86
2415 4379 2.435586 CAGTTCAGCCCGGCTCAG 60.436 66.667 9.68 0.00 36.40 3.35
2416 4380 3.240134 GACAGTTCAGCCCGGCTCA 62.240 63.158 9.68 0.00 36.40 4.26
2417 4381 2.435059 GACAGTTCAGCCCGGCTC 60.435 66.667 9.68 0.00 36.40 4.70
2418 4382 2.925170 AGACAGTTCAGCCCGGCT 60.925 61.111 5.94 5.94 40.77 5.52
2419 4383 2.435059 GAGACAGTTCAGCCCGGC 60.435 66.667 0.00 0.00 0.00 6.13
2421 4385 2.125912 CGGAGACAGTTCAGCCCG 60.126 66.667 0.00 0.00 0.00 6.13
2422 4386 1.079750 GACGGAGACAGTTCAGCCC 60.080 63.158 0.00 0.00 0.00 5.19
2423 4387 0.667792 GTGACGGAGACAGTTCAGCC 60.668 60.000 0.00 0.00 30.17 4.85
2424 4388 1.004277 CGTGACGGAGACAGTTCAGC 61.004 60.000 0.00 0.00 30.17 4.26
2425 4389 0.311165 ACGTGACGGAGACAGTTCAG 59.689 55.000 10.66 0.00 30.17 3.02
2427 4391 0.663568 CCACGTGACGGAGACAGTTC 60.664 60.000 19.30 0.00 30.17 3.01
2428 4392 1.105167 TCCACGTGACGGAGACAGTT 61.105 55.000 19.30 0.00 30.17 3.16
2429 4393 1.527611 TCCACGTGACGGAGACAGT 60.528 57.895 19.30 0.00 30.17 3.55
2431 4395 3.036577 GTCCACGTGACGGAGACA 58.963 61.111 19.30 0.00 34.68 3.41
2438 4402 1.389106 GCATTAACGAGTCCACGTGAC 59.611 52.381 19.30 13.24 45.83 3.67
2439 4403 1.670674 GGCATTAACGAGTCCACGTGA 60.671 52.381 19.30 0.00 45.83 4.35
2440 4404 0.719465 GGCATTAACGAGTCCACGTG 59.281 55.000 9.08 9.08 45.83 4.49
2442 4406 0.390603 TGGGCATTAACGAGTCCACG 60.391 55.000 0.00 0.00 39.31 4.94
2443 4407 1.084289 GTGGGCATTAACGAGTCCAC 58.916 55.000 11.08 11.08 37.98 4.02
2444 4408 0.035820 GGTGGGCATTAACGAGTCCA 60.036 55.000 0.00 0.00 0.00 4.02
2446 4410 1.369625 CAGGTGGGCATTAACGAGTC 58.630 55.000 0.00 0.00 0.00 3.36
2447 4411 0.035439 CCAGGTGGGCATTAACGAGT 60.035 55.000 0.00 0.00 0.00 4.18
2448 4412 2.780595 CCAGGTGGGCATTAACGAG 58.219 57.895 0.00 0.00 0.00 4.18
2460 4424 0.982852 TATGAGGGACTGGCCAGGTG 60.983 60.000 35.42 13.63 41.55 4.00
2461 4425 0.253160 TTATGAGGGACTGGCCAGGT 60.253 55.000 35.42 21.31 41.55 4.00
2462 4426 0.918983 TTTATGAGGGACTGGCCAGG 59.081 55.000 35.42 18.18 41.55 4.45
2463 4427 2.092212 ACATTTATGAGGGACTGGCCAG 60.092 50.000 31.60 31.60 41.55 4.85
2464 4428 1.922447 ACATTTATGAGGGACTGGCCA 59.078 47.619 4.71 4.71 41.55 5.36
2465 4429 2.736670 ACATTTATGAGGGACTGGCC 57.263 50.000 0.00 0.00 41.55 5.36
2466 4430 3.142174 GCTACATTTATGAGGGACTGGC 58.858 50.000 0.00 0.00 41.55 4.85
2467 4431 4.503991 GGAGCTACATTTATGAGGGACTGG 60.504 50.000 0.00 0.00 41.55 4.00
2468 4432 4.101585 TGGAGCTACATTTATGAGGGACTG 59.898 45.833 0.00 0.00 41.55 3.51
2470 4434 4.141711 TGTGGAGCTACATTTATGAGGGAC 60.142 45.833 0.00 0.00 0.00 4.46
2471 4435 4.037222 TGTGGAGCTACATTTATGAGGGA 58.963 43.478 0.00 0.00 0.00 4.20
2472 4436 4.384056 CTGTGGAGCTACATTTATGAGGG 58.616 47.826 0.00 0.00 0.00 4.30
2474 4438 3.492383 CGCTGTGGAGCTACATTTATGAG 59.508 47.826 0.00 0.00 43.77 2.90
2476 4440 3.001634 CACGCTGTGGAGCTACATTTATG 59.998 47.826 0.00 0.00 43.77 1.90
2477 4441 3.198068 CACGCTGTGGAGCTACATTTAT 58.802 45.455 0.00 0.00 43.77 1.40
2480 4444 1.021390 GCACGCTGTGGAGCTACATT 61.021 55.000 0.00 0.00 43.77 2.71
2482 4446 2.048222 GCACGCTGTGGAGCTACA 60.048 61.111 0.00 0.00 43.77 2.74


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

AutoCloner maintained by Alex Coulton.