Multiple sequence alignment - TraesCS5B01G347900

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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 TraesCS5B01G347900 chr5B 100.000 5396 0 0 1 5396 528779704 528785099 0.000000e+00 9965.0
1 TraesCS5B01G347900 chr5B 89.024 492 51 1 2742 3233 528781800 528782288 1.660000e-169 606.0
2 TraesCS5B01G347900 chr5B 89.024 492 51 1 2097 2585 528782445 528782936 1.660000e-169 606.0
3 TraesCS5B01G347900 chr5B 98.621 145 2 0 2593 2737 528782437 528782581 1.930000e-64 257.0
4 TraesCS5B01G347900 chr5B 86.603 209 28 0 3311 3519 528782447 528782655 1.170000e-56 231.0
5 TraesCS5B01G347900 chr5B 86.603 209 28 0 2744 2952 528783014 528783222 1.170000e-56 231.0
6 TraesCS5B01G347900 chr5B 85.326 184 21 1 3259 3442 528782260 528782437 9.230000e-43 185.0
7 TraesCS5B01G347900 chr5B 85.326 184 21 1 2557 2734 528782962 528783145 9.230000e-43 185.0
8 TraesCS5B01G347900 chr5A 94.599 2018 92 7 2734 4747 549354358 549356362 0.000000e+00 3107.0
9 TraesCS5B01G347900 chr5A 93.876 1927 73 14 815 2737 549352617 549354502 0.000000e+00 2863.0
10 TraesCS5B01G347900 chr5A 87.016 878 56 29 6 829 549351726 549352599 0.000000e+00 937.0
11 TraesCS5B01G347900 chr5A 90.328 548 31 10 4859 5396 549357128 549357663 0.000000e+00 699.0
12 TraesCS5B01G347900 chr5A 89.697 495 45 3 2742 3233 549353859 549354350 1.280000e-175 627.0
13 TraesCS5B01G347900 chr5A 87.602 492 58 1 2097 2585 549354366 549354857 7.840000e-158 568.0
14 TraesCS5B01G347900 chr5A 81.595 326 50 4 17 333 549359945 549360269 1.490000e-65 261.0
15 TraesCS5B01G347900 chr5A 82.661 248 43 0 3272 3519 549353822 549354069 2.530000e-53 220.0
16 TraesCS5B01G347900 chr5A 88.304 171 14 1 2557 2721 549354883 549355053 3.300000e-47 200.0
17 TraesCS5B01G347900 chr5A 94.118 119 4 2 4737 4855 549356844 549356959 1.540000e-40 178.0
18 TraesCS5B01G347900 chr5D 93.258 2032 97 18 739 2737 435512309 435514333 0.000000e+00 2957.0
19 TraesCS5B01G347900 chr5D 94.653 1571 74 6 3183 4746 435514746 435516313 0.000000e+00 2427.0
20 TraesCS5B01G347900 chr5D 97.846 557 12 0 2734 3290 435514189 435514745 0.000000e+00 963.0
21 TraesCS5B01G347900 chr5D 89.583 672 33 15 4739 5396 435516746 435517394 0.000000e+00 819.0
22 TraesCS5B01G347900 chr5D 90.650 492 43 1 2742 3233 435513693 435514181 0.000000e+00 651.0
23 TraesCS5B01G347900 chr5D 85.413 617 56 9 61 672 435492972 435493559 1.280000e-170 610.0
24 TraesCS5B01G347900 chr5D 88.821 492 52 1 2097 2585 435514197 435514688 7.730000e-168 601.0
25 TraesCS5B01G347900 chr5D 85.057 261 33 1 3259 3519 435514153 435514407 1.490000e-65 261.0
26 TraesCS5B01G347900 chr5D 88.038 209 25 0 2744 2952 435514874 435515082 1.160000e-61 248.0
27 TraesCS5B01G347900 chr5D 79.437 355 67 5 27 378 435519346 435519697 4.170000e-61 246.0
28 TraesCS5B01G347900 chr5D 84.274 248 39 0 3272 3519 435513656 435513903 5.400000e-60 243.0
29 TraesCS5B01G347900 chr5D 87.500 184 17 1 2557 2734 435514822 435515005 1.970000e-49 207.0
30 TraesCS5B01G347900 chr5D 91.241 137 12 0 2601 2737 435513693 435513829 2.570000e-43 187.0
31 TraesCS5B01G347900 chr5D 95.370 108 5 0 3183 3290 435514692 435514799 7.190000e-39 172.0
32 TraesCS5B01G347900 chr1B 89.784 832 85 0 3237 4068 259513572 259514403 0.000000e+00 1066.0
33 TraesCS5B01G347900 chr1B 84.753 446 44 7 2314 2735 259513333 259513778 5.000000e-115 425.0
34 TraesCS5B01G347900 chr1B 88.306 248 29 0 2060 2307 259513607 259513854 1.140000e-76 298.0
35 TraesCS5B01G347900 chr1B 90.909 209 19 0 2744 2952 259513646 259513854 1.140000e-71 281.0
36 TraesCS5B01G347900 chr1B 86.869 198 11 6 4151 4336 259514639 259514833 1.970000e-49 207.0
37 TraesCS5B01G347900 chr1A 88.822 832 90 1 3237 4068 236719778 236720606 0.000000e+00 1018.0
38 TraesCS5B01G347900 chr1A 85.682 440 45 6 2314 2735 236719545 236719984 1.070000e-121 448.0
39 TraesCS5B01G347900 chr1A 88.583 254 28 1 2060 2312 236719813 236720066 1.890000e-79 307.0
40 TraesCS5B01G347900 chr1A 90.698 215 19 1 2744 2957 236719852 236720066 8.850000e-73 285.0
41 TraesCS5B01G347900 chr1A 93.333 165 8 1 1900 2061 236719431 236719595 1.940000e-59 241.0
42 TraesCS5B01G347900 chr1A 88.172 186 7 3 4151 4336 236720842 236721012 1.970000e-49 207.0
43 TraesCS5B01G347900 chr3B 82.000 250 35 8 133 379 752285698 752285940 2.550000e-48 204.0
44 TraesCS5B01G347900 chr6D 86.000 100 14 0 131 230 448646854 448646755 2.060000e-19 108.0
45 TraesCS5B01G347900 chr6A 85.000 100 15 0 131 230 594721520 594721421 9.560000e-18 102.0
46 TraesCS5B01G347900 chr3D 81.633 98 18 0 144 241 14042044 14041947 1.250000e-11 82.4


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 TraesCS5B01G347900 chr5B 528779704 528785099 5395 False 1533.250000 9965 90.065875 1 5396 8 chr5B.!!$F1 5395
1 TraesCS5B01G347900 chr5A 549351726 549360269 8543 False 966.000000 3107 88.979600 6 5396 10 chr5A.!!$F1 5390
2 TraesCS5B01G347900 chr5D 435512309 435519697 7388 False 767.846154 2957 89.671385 27 5396 13 chr5D.!!$F2 5369
3 TraesCS5B01G347900 chr5D 435492972 435493559 587 False 610.000000 610 85.413000 61 672 1 chr5D.!!$F1 611
4 TraesCS5B01G347900 chr1B 259513333 259514833 1500 False 455.400000 1066 88.124200 2060 4336 5 chr1B.!!$F1 2276
5 TraesCS5B01G347900 chr1A 236719431 236721012 1581 False 417.666667 1018 89.215000 1900 4336 6 chr1A.!!$F1 2436

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
829 885 0.179468 GGCCAGCGGTCCAACTTATA 59.821 55.0 0.00 0.0 0.00 0.98 F
1674 1802 0.105593 ACGAGCATATGACCAGGCAG 59.894 55.0 6.97 0.0 0.00 4.85 F
2358 2486 0.250513 ATGGCCTTGGAAGTCGAGTC 59.749 55.0 3.32 0.0 0.00 3.36 F
2762 2911 0.039618 TTCCTTCCATTGCCTGGGTC 59.960 55.0 0.00 0.0 45.98 4.46 F
2764 2913 0.251742 CCTTCCATTGCCTGGGTCAA 60.252 55.0 0.00 0.0 45.98 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2162 0.036388 GTCGACTTCCAAGGCCATGA 60.036 55.000 10.18 0.00 0.00 3.07 R
2732 2881 0.105964 TGGAAGGAACACGTCACCAG 59.894 55.000 0.00 0.00 0.00 4.00 R
4133 4519 0.043334 ACCTCCAGCAGATAGTGGGT 59.957 55.000 0.00 0.00 34.27 4.51 R
4374 4808 0.240945 ATTTCTTTGCGTTGCCGGAG 59.759 50.000 5.05 0.00 35.23 4.63 R
4593 5031 1.726791 CGAACATGACACTGCAGTACC 59.273 52.381 21.20 14.48 0.00 3.34 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
19 20 1.570813 TCGTCGCAATCATGGTGATC 58.429 50.000 0.00 0.00 35.76 2.92
23 24 2.874086 GTCGCAATCATGGTGATCATCA 59.126 45.455 11.92 11.92 35.76 3.07
62 66 2.125912 CGCAGAGGAGTTGGGTCG 60.126 66.667 0.00 0.00 0.00 4.79
69 73 1.219935 GGAGTTGGGTCGCGGTATT 59.780 57.895 6.13 0.00 0.00 1.89
80 84 1.154205 CGCGGTATTGGAGAAGGCTG 61.154 60.000 0.00 0.00 0.00 4.85
83 87 1.207089 CGGTATTGGAGAAGGCTGTGA 59.793 52.381 0.00 0.00 0.00 3.58
97 101 2.224018 GGCTGTGAACAAAATGGCTCAA 60.224 45.455 0.00 0.00 0.00 3.02
272 276 2.202756 GTGCTTAGGCGGTCCTCG 60.203 66.667 0.00 0.00 43.06 4.63
285 292 1.683707 TCCTCGCTCTCAGCCACAT 60.684 57.895 0.00 0.00 38.18 3.21
390 397 1.870055 ATGAGCAAACAGGCGGCAAG 61.870 55.000 13.08 5.73 39.27 4.01
401 408 2.941616 GCGGCAAGGATGGGCAAAA 61.942 57.895 0.00 0.00 31.22 2.44
477 496 3.071206 GAGTGCTCCCGCTCCTCA 61.071 66.667 0.00 0.00 41.64 3.86
539 559 1.142097 GAGCGCTCACTCCCCTAAC 59.858 63.158 31.91 0.00 0.00 2.34
563 583 0.390472 CTCGGTTCTGGGTTCTCTGC 60.390 60.000 0.00 0.00 0.00 4.26
565 585 0.671781 CGGTTCTGGGTTCTCTGCTG 60.672 60.000 0.00 0.00 0.00 4.41
566 586 0.322008 GGTTCTGGGTTCTCTGCTGG 60.322 60.000 0.00 0.00 0.00 4.85
567 587 0.398318 GTTCTGGGTTCTCTGCTGGT 59.602 55.000 0.00 0.00 0.00 4.00
568 588 0.397941 TTCTGGGTTCTCTGCTGGTG 59.602 55.000 0.00 0.00 0.00 4.17
584 604 2.204090 TGGGTGGGGGAGAGGAAC 60.204 66.667 0.00 0.00 0.00 3.62
611 631 1.299850 TCAGCGGCGAACGGATATG 60.300 57.895 12.98 0.00 44.51 1.78
686 706 2.016704 CTCGAGCAACACGAAGCGT 61.017 57.895 0.00 0.00 42.36 5.07
687 707 1.935065 CTCGAGCAACACGAAGCGTC 61.935 60.000 0.00 0.00 38.32 5.19
705 751 2.202676 GCGCAGGAAGACGAGAGG 60.203 66.667 0.30 0.00 0.00 3.69
708 754 2.355193 GCAGGAAGACGAGAGGCCT 61.355 63.158 3.86 3.86 43.69 5.19
715 761 3.637694 GGAAGACGAGAGGCCTACTATTT 59.362 47.826 4.42 0.00 43.69 1.40
786 842 0.249911 AGCGTGTCCAACTTGTCTCC 60.250 55.000 0.00 0.00 0.00 3.71
803 859 1.000145 CCCCACCGCCTTACCAAAT 60.000 57.895 0.00 0.00 0.00 2.32
811 867 1.806623 CGCCTTACCAAATCTCTCCGG 60.807 57.143 0.00 0.00 0.00 5.14
829 885 0.179468 GGCCAGCGGTCCAACTTATA 59.821 55.000 0.00 0.00 0.00 0.98
830 886 1.202770 GGCCAGCGGTCCAACTTATAT 60.203 52.381 0.00 0.00 0.00 0.86
831 887 2.038033 GGCCAGCGGTCCAACTTATATA 59.962 50.000 0.00 0.00 0.00 0.86
832 888 3.495453 GGCCAGCGGTCCAACTTATATAA 60.495 47.826 0.00 0.00 0.00 0.98
833 889 4.131596 GCCAGCGGTCCAACTTATATAAA 58.868 43.478 0.00 0.00 0.00 1.40
911 998 0.244178 GTCTCGAACCTTCTCGCCTT 59.756 55.000 0.00 0.00 38.73 4.35
921 1008 1.137282 CTTCTCGCCTTCTCTAACCCC 59.863 57.143 0.00 0.00 0.00 4.95
922 1009 1.035932 TCTCGCCTTCTCTAACCCCG 61.036 60.000 0.00 0.00 0.00 5.73
923 1010 2.202892 CGCCTTCTCTAACCCCGC 60.203 66.667 0.00 0.00 0.00 6.13
1209 1322 1.067821 GTCATCTCCGATTTCTCCGCT 59.932 52.381 0.00 0.00 0.00 5.52
1210 1323 1.338337 TCATCTCCGATTTCTCCGCTC 59.662 52.381 0.00 0.00 0.00 5.03
1305 1418 2.034179 CGCCGACCACTACAAGATGATA 59.966 50.000 0.00 0.00 0.00 2.15
1362 1490 2.034048 GAATCGAGGAGGACCAGGCC 62.034 65.000 0.00 0.00 38.94 5.19
1438 1566 1.044790 CCTGCTAAGGGGGCATTTGG 61.045 60.000 0.00 0.00 40.27 3.28
1467 1595 4.137872 GGGCTGCGCATGTGCAAT 62.138 61.111 31.75 0.00 45.74 3.56
1485 1613 1.673767 ATCTTTGCTTGGGAGGGAGA 58.326 50.000 0.00 0.00 0.00 3.71
1531 1659 2.164422 CTCTACACGCAGGAACAGATGA 59.836 50.000 0.00 0.00 0.00 2.92
1575 1703 2.221918 GGAGGTGGATGGTTCCGAT 58.778 57.895 0.00 0.00 45.89 4.18
1576 1704 0.179045 GGAGGTGGATGGTTCCGATG 60.179 60.000 0.00 0.00 45.89 3.84
1577 1705 0.830648 GAGGTGGATGGTTCCGATGA 59.169 55.000 0.00 0.00 45.89 2.92
1581 1709 1.065418 GTGGATGGTTCCGATGAGGTT 60.065 52.381 0.00 0.00 45.89 3.50
1584 1712 2.555199 GATGGTTCCGATGAGGTTGAG 58.445 52.381 0.00 0.00 41.99 3.02
1658 1786 7.761038 TCTATGGAGATAATGAGCTTTACGA 57.239 36.000 0.00 0.00 0.00 3.43
1672 1800 2.526304 TTACGAGCATATGACCAGGC 57.474 50.000 6.97 0.00 0.00 4.85
1674 1802 0.105593 ACGAGCATATGACCAGGCAG 59.894 55.000 6.97 0.00 0.00 4.85
1681 1809 1.567357 TATGACCAGGCAGCACTACA 58.433 50.000 0.00 0.00 0.00 2.74
1704 1832 1.502163 GCCACATATGTCAGAGGCGC 61.502 60.000 16.55 0.00 31.88 6.53
1714 1842 4.804420 AGAGGCGCCATCCTGGGA 62.804 66.667 31.54 0.00 38.19 4.37
1715 1843 4.247380 GAGGCGCCATCCTGGGAG 62.247 72.222 31.54 0.00 38.19 4.30
1738 1866 4.374707 GCTACGATTATTTCCGCAACTACG 60.375 45.833 0.00 0.00 0.00 3.51
1740 1868 3.549070 ACGATTATTTCCGCAACTACGAC 59.451 43.478 0.00 0.00 34.06 4.34
1744 1872 1.621107 TTTCCGCAACTACGACGATC 58.379 50.000 0.00 0.00 34.06 3.69
1759 1887 4.051237 CGACGATCTGGAGATGCATTTTA 58.949 43.478 0.00 0.00 34.37 1.52
1764 1892 5.178996 CGATCTGGAGATGCATTTTAGGAAG 59.821 44.000 0.00 0.00 34.37 3.46
1788 1916 2.562738 TCACTTCCTCTGCGAAGATGAA 59.437 45.455 10.36 10.36 41.57 2.57
1830 1958 2.082629 TTGTCTTCCAGAGCGACGCA 62.083 55.000 23.70 0.00 0.00 5.24
1938 2066 6.509418 TTTATGTACCAAAGGAATGAGCAC 57.491 37.500 0.00 0.00 0.00 4.40
2080 2208 4.096003 CAGGGGGTTCCGCGATGT 62.096 66.667 8.23 0.00 41.60 3.06
2131 2259 3.139077 CCTGGGTCAAGTAACAAGTGTC 58.861 50.000 0.00 0.00 0.00 3.67
2154 2282 1.817740 GCTTCAACACAACAGGGGCTA 60.818 52.381 0.00 0.00 0.00 3.93
2262 2390 5.182570 TCAAACTGCTCAAAATCCTGAGATG 59.817 40.000 4.81 0.00 44.82 2.90
2358 2486 0.250513 ATGGCCTTGGAAGTCGAGTC 59.749 55.000 3.32 0.00 0.00 3.36
2440 2589 1.448893 GGGAATGGTCGCGTGCTTA 60.449 57.895 5.77 0.00 0.00 3.09
2470 2619 4.202503 TGTCTTTTCCTCATCTTCAAGGCT 60.203 41.667 0.00 0.00 32.37 4.58
2735 2884 3.846360 CCGTGAAGGTACTAAAGTCTGG 58.154 50.000 0.00 0.00 38.49 3.86
2736 2885 3.257624 CCGTGAAGGTACTAAAGTCTGGT 59.742 47.826 0.00 0.00 38.49 4.00
2737 2886 4.235360 CGTGAAGGTACTAAAGTCTGGTG 58.765 47.826 0.00 0.00 38.49 4.17
2738 2887 4.022589 CGTGAAGGTACTAAAGTCTGGTGA 60.023 45.833 0.00 0.00 38.49 4.02
2739 2888 5.228665 GTGAAGGTACTAAAGTCTGGTGAC 58.771 45.833 0.00 0.00 38.49 3.67
2740 2889 4.022589 TGAAGGTACTAAAGTCTGGTGACG 60.023 45.833 0.00 0.00 43.45 4.35
2741 2890 3.494332 AGGTACTAAAGTCTGGTGACGT 58.506 45.455 0.00 0.00 42.76 4.34
2742 2891 3.255149 AGGTACTAAAGTCTGGTGACGTG 59.745 47.826 0.00 0.00 42.76 4.49
2743 2892 5.231561 AGGTACTAAAGTCTGGTGACGTGT 61.232 45.833 0.00 0.00 42.76 4.49
2744 2893 6.674760 AGGTACTAAAGTCTGGTGACGTGTT 61.675 44.000 0.00 0.00 42.76 3.32
2745 2894 8.393793 AGGTACTAAAGTCTGGTGACGTGTTC 62.394 46.154 0.00 0.00 42.76 3.18
2748 2897 3.680842 GTCTGGTGACGTGTTCCTT 57.319 52.632 0.00 0.00 33.15 3.36
2749 2898 1.499049 GTCTGGTGACGTGTTCCTTC 58.501 55.000 0.00 0.00 33.15 3.46
2750 2899 0.391597 TCTGGTGACGTGTTCCTTCC 59.608 55.000 0.00 0.00 0.00 3.46
2751 2900 0.105964 CTGGTGACGTGTTCCTTCCA 59.894 55.000 0.00 0.00 0.00 3.53
2752 2901 0.762418 TGGTGACGTGTTCCTTCCAT 59.238 50.000 0.00 0.00 0.00 3.41
2753 2902 1.142060 TGGTGACGTGTTCCTTCCATT 59.858 47.619 0.00 0.00 0.00 3.16
2754 2903 1.535462 GGTGACGTGTTCCTTCCATTG 59.465 52.381 0.00 0.00 0.00 2.82
2755 2904 1.069227 GTGACGTGTTCCTTCCATTGC 60.069 52.381 0.00 0.00 0.00 3.56
2756 2905 0.521735 GACGTGTTCCTTCCATTGCC 59.478 55.000 0.00 0.00 0.00 4.52
2757 2906 0.110486 ACGTGTTCCTTCCATTGCCT 59.890 50.000 0.00 0.00 0.00 4.75
2758 2907 0.523072 CGTGTTCCTTCCATTGCCTG 59.477 55.000 0.00 0.00 0.00 4.85
2760 2909 0.251742 TGTTCCTTCCATTGCCTGGG 60.252 55.000 0.00 0.00 45.98 4.45
2761 2910 0.251787 GTTCCTTCCATTGCCTGGGT 60.252 55.000 0.00 0.00 45.98 4.51
2762 2911 0.039618 TTCCTTCCATTGCCTGGGTC 59.960 55.000 0.00 0.00 45.98 4.46
2763 2912 1.139498 TCCTTCCATTGCCTGGGTCA 61.139 55.000 0.00 0.00 45.98 4.02
2764 2913 0.251742 CCTTCCATTGCCTGGGTCAA 60.252 55.000 0.00 0.00 45.98 3.18
2765 2914 1.180029 CTTCCATTGCCTGGGTCAAG 58.820 55.000 0.00 0.00 45.98 3.02
2766 2915 0.482446 TTCCATTGCCTGGGTCAAGT 59.518 50.000 0.00 0.00 45.98 3.16
2767 2916 1.367346 TCCATTGCCTGGGTCAAGTA 58.633 50.000 0.00 0.00 45.98 2.24
2768 2917 1.707989 TCCATTGCCTGGGTCAAGTAA 59.292 47.619 0.00 0.00 45.98 2.24
2769 2918 1.818674 CCATTGCCTGGGTCAAGTAAC 59.181 52.381 0.00 0.00 41.82 2.50
2770 2919 2.513753 CATTGCCTGGGTCAAGTAACA 58.486 47.619 0.00 0.00 0.00 2.41
2771 2920 2.738587 TTGCCTGGGTCAAGTAACAA 57.261 45.000 0.00 0.00 0.00 2.83
2772 2921 2.738587 TGCCTGGGTCAAGTAACAAA 57.261 45.000 0.00 0.00 0.00 2.83
2773 2922 2.582052 TGCCTGGGTCAAGTAACAAAG 58.418 47.619 0.00 0.00 0.00 2.77
2774 2923 1.886542 GCCTGGGTCAAGTAACAAAGG 59.113 52.381 0.00 0.00 0.00 3.11
2775 2924 2.751816 GCCTGGGTCAAGTAACAAAGGT 60.752 50.000 0.00 0.00 0.00 3.50
2776 2925 3.562182 CCTGGGTCAAGTAACAAAGGTT 58.438 45.455 0.00 0.00 41.06 3.50
2777 2926 3.568430 CCTGGGTCAAGTAACAAAGGTTC 59.432 47.826 0.00 0.00 38.45 3.62
2778 2927 4.461198 CTGGGTCAAGTAACAAAGGTTCT 58.539 43.478 0.00 0.00 38.45 3.01
2779 2928 4.204012 TGGGTCAAGTAACAAAGGTTCTG 58.796 43.478 0.00 0.00 38.45 3.02
2780 2929 3.004419 GGGTCAAGTAACAAAGGTTCTGC 59.996 47.826 0.00 0.00 38.45 4.26
2781 2930 3.883489 GGTCAAGTAACAAAGGTTCTGCT 59.117 43.478 0.00 0.00 38.45 4.24
2782 2931 4.338400 GGTCAAGTAACAAAGGTTCTGCTT 59.662 41.667 0.00 0.00 38.45 3.91
2783 2932 5.505819 GGTCAAGTAACAAAGGTTCTGCTTC 60.506 44.000 0.00 0.00 38.45 3.86
2784 2933 5.065988 GTCAAGTAACAAAGGTTCTGCTTCA 59.934 40.000 0.00 0.00 38.45 3.02
2785 2934 5.650266 TCAAGTAACAAAGGTTCTGCTTCAA 59.350 36.000 0.00 0.00 38.45 2.69
2786 2935 5.500645 AGTAACAAAGGTTCTGCTTCAAC 57.499 39.130 0.00 0.00 38.45 3.18
2787 2936 4.947388 AGTAACAAAGGTTCTGCTTCAACA 59.053 37.500 0.00 0.00 38.45 3.33
2788 2937 3.782889 ACAAAGGTTCTGCTTCAACAC 57.217 42.857 0.00 0.00 0.00 3.32
2789 2938 3.088532 ACAAAGGTTCTGCTTCAACACA 58.911 40.909 0.00 0.00 0.00 3.72
2790 2939 3.509575 ACAAAGGTTCTGCTTCAACACAA 59.490 39.130 0.00 0.00 0.00 3.33
2791 2940 3.782889 AAGGTTCTGCTTCAACACAAC 57.217 42.857 0.00 0.00 0.00 3.32
2792 2941 2.722094 AGGTTCTGCTTCAACACAACA 58.278 42.857 0.00 0.00 0.00 3.33
2793 2942 2.684881 AGGTTCTGCTTCAACACAACAG 59.315 45.455 0.00 0.00 0.00 3.16
2794 2943 2.223572 GGTTCTGCTTCAACACAACAGG 60.224 50.000 0.00 0.00 0.00 4.00
2795 2944 1.679139 TCTGCTTCAACACAACAGGG 58.321 50.000 0.00 0.00 0.00 4.45
2796 2945 0.670162 CTGCTTCAACACAACAGGGG 59.330 55.000 0.00 0.00 0.00 4.79
2797 2946 1.363807 GCTTCAACACAACAGGGGC 59.636 57.895 0.00 0.00 0.00 5.80
2798 2947 1.109323 GCTTCAACACAACAGGGGCT 61.109 55.000 0.00 0.00 0.00 5.19
2799 2948 0.670162 CTTCAACACAACAGGGGCTG 59.330 55.000 0.00 0.00 37.52 4.85
2800 2949 1.391157 TTCAACACAACAGGGGCTGC 61.391 55.000 0.00 0.00 34.37 5.25
2801 2950 2.126596 CAACACAACAGGGGCTGCA 61.127 57.895 0.50 0.00 34.37 4.41
2802 2951 1.381056 AACACAACAGGGGCTGCAA 60.381 52.632 0.50 0.00 34.37 4.08
2803 2952 1.394266 AACACAACAGGGGCTGCAAG 61.394 55.000 0.50 0.00 34.37 4.01
2825 2974 3.487207 GCTTTTGCTAAGAACACACTTGC 59.513 43.478 3.72 0.00 43.35 4.01
2826 2975 4.671377 CTTTTGCTAAGAACACACTTGCA 58.329 39.130 0.00 0.00 34.70 4.08
2827 2976 4.916983 TTTGCTAAGAACACACTTGCAT 57.083 36.364 0.00 0.00 35.60 3.96
2828 2977 4.488126 TTGCTAAGAACACACTTGCATC 57.512 40.909 0.00 0.00 35.60 3.91
2829 2978 3.475575 TGCTAAGAACACACTTGCATCA 58.524 40.909 0.00 0.00 33.11 3.07
2830 2979 3.882288 TGCTAAGAACACACTTGCATCAA 59.118 39.130 0.00 0.00 33.11 2.57
2831 2980 4.023792 TGCTAAGAACACACTTGCATCAAG 60.024 41.667 5.13 5.13 45.85 3.02
2832 2981 3.996150 AAGAACACACTTGCATCAAGG 57.004 42.857 10.80 3.36 44.81 3.61
2833 2982 1.610522 AGAACACACTTGCATCAAGGC 59.389 47.619 10.80 0.00 44.81 4.35
2834 2983 1.610522 GAACACACTTGCATCAAGGCT 59.389 47.619 10.80 0.00 44.81 4.58
2835 2984 1.696063 ACACACTTGCATCAAGGCTT 58.304 45.000 10.80 0.00 44.81 4.35
2836 2985 1.338973 ACACACTTGCATCAAGGCTTG 59.661 47.619 21.17 21.17 44.81 4.01
2837 2986 1.610038 CACACTTGCATCAAGGCTTGA 59.390 47.619 30.29 30.29 44.81 3.02
2838 2987 2.034939 CACACTTGCATCAAGGCTTGAA 59.965 45.455 31.57 14.63 44.81 2.69
2839 2988 2.035066 ACACTTGCATCAAGGCTTGAAC 59.965 45.455 31.57 25.41 44.81 3.18
2840 2989 2.034939 CACTTGCATCAAGGCTTGAACA 59.965 45.455 31.57 27.42 44.81 3.18
2841 2990 2.694628 ACTTGCATCAAGGCTTGAACAA 59.305 40.909 30.71 30.71 44.81 2.83
2842 2991 2.798976 TGCATCAAGGCTTGAACAAC 57.201 45.000 31.57 20.64 43.95 3.32
2843 2992 1.340889 TGCATCAAGGCTTGAACAACC 59.659 47.619 31.57 18.04 43.95 3.77
2844 2993 1.615392 GCATCAAGGCTTGAACAACCT 59.385 47.619 31.57 13.14 43.95 3.50
2845 2994 2.819608 GCATCAAGGCTTGAACAACCTA 59.180 45.455 31.57 8.69 43.95 3.08
2846 2995 3.119708 GCATCAAGGCTTGAACAACCTAG 60.120 47.826 31.57 15.18 43.95 3.02
2847 2996 3.140325 TCAAGGCTTGAACAACCTAGG 57.860 47.619 26.78 7.41 36.59 3.02
2848 2997 2.708861 TCAAGGCTTGAACAACCTAGGA 59.291 45.455 26.78 0.00 36.59 2.94
2849 2998 3.137544 TCAAGGCTTGAACAACCTAGGAA 59.862 43.478 26.78 0.00 36.59 3.36
2850 2999 3.425162 AGGCTTGAACAACCTAGGAAG 57.575 47.619 17.98 8.56 29.98 3.46
2851 3000 7.729079 TCAAGGCTTGAACAACCTAGGAAGG 62.729 48.000 26.78 6.66 42.08 3.46
2889 3038 1.122019 AGTCTGGTCGGCCTCAAACT 61.122 55.000 7.97 2.26 35.27 2.66
3021 3170 4.528596 AGTCTAGTTGATAGTGTTGCAGGT 59.471 41.667 0.00 0.00 32.85 4.00
3221 3370 3.341823 CACTGGCTGTTAATCAGAGCTT 58.658 45.455 8.63 0.00 46.27 3.74
3267 3524 1.154035 GCATGCACCGGCTGTTAAC 60.154 57.895 14.21 0.00 41.91 2.01
3398 3655 4.021807 TGCTGAGAACACATTTGCATCAAT 60.022 37.500 0.00 0.00 0.00 2.57
3427 3684 2.111878 CTAGGAAGGGCGCCATGG 59.888 66.667 30.85 7.63 0.00 3.66
3435 3692 2.203070 GGCGCCATGGAGGTACTG 60.203 66.667 24.80 0.00 41.55 2.74
3483 3749 6.475504 TGAAAATCTTGAGATAGTGCCTGAA 58.524 36.000 0.00 0.00 33.73 3.02
3558 3824 1.137282 GGGTCTTCTCACCTTCGGATC 59.863 57.143 0.00 0.00 36.57 3.36
3560 3826 1.743958 GTCTTCTCACCTTCGGATCGA 59.256 52.381 0.00 0.00 0.00 3.59
3664 3930 2.339769 AGCACTCTGTTTCTACCCCTT 58.660 47.619 0.00 0.00 0.00 3.95
3945 4211 4.926238 GGTATATCGCATCTTGTTCCTGAG 59.074 45.833 0.00 0.00 0.00 3.35
3954 4220 5.374921 CATCTTGTTCCTGAGATGGCTATT 58.625 41.667 5.63 0.00 43.43 1.73
3970 4236 2.094545 GCTATTTTGTTGCCTGACCCTG 60.095 50.000 0.00 0.00 0.00 4.45
4133 4519 4.367039 ACCGATCTTCCAAGGAAAGAAA 57.633 40.909 2.78 0.00 33.34 2.52
4236 4670 0.386478 GCAGCAGCAGTAACAACAGC 60.386 55.000 0.00 0.00 41.58 4.40
4358 4792 4.914291 CGTTTGGAAGAACGGTGC 57.086 55.556 2.48 0.00 46.29 5.01
4374 4808 4.451652 GCGGCGCACAAGCTCTTC 62.452 66.667 29.21 0.00 39.10 2.87
4383 4817 0.603975 ACAAGCTCTTCTCCGGCAAC 60.604 55.000 0.00 0.00 0.00 4.17
4453 4888 1.801309 GCAGCTGGTTGGCGGTAAAA 61.801 55.000 17.12 0.00 37.29 1.52
4501 4936 1.801913 CTTGGAGAAGGCGTCGTCG 60.802 63.158 0.00 0.00 40.37 5.12
4534 4972 3.734231 TCGCTTCGTTTGAGTCTAGTTTG 59.266 43.478 0.00 0.00 0.00 2.93
4539 4977 6.677187 GCTTCGTTTGAGTCTAGTTTGGTTTT 60.677 38.462 0.00 0.00 0.00 2.43
4593 5031 5.709164 AGAAGTGAGGATGGAACTTGAAATG 59.291 40.000 0.00 0.00 34.37 2.32
4622 5060 0.391130 TGTCATGTTCGTGGCTAGCC 60.391 55.000 27.71 27.71 0.00 3.93
4634 5072 3.866883 TGGCTAGCCATAACTTTTTGC 57.133 42.857 32.88 1.83 41.89 3.68
4678 5116 6.251376 GCACGAATTCTACCAATGATTTTGTC 59.749 38.462 3.52 0.00 0.00 3.18
4680 5118 8.023128 CACGAATTCTACCAATGATTTTGTCTT 58.977 33.333 3.52 0.00 0.00 3.01
4682 5120 9.065871 CGAATTCTACCAATGATTTTGTCTTTC 57.934 33.333 3.52 0.00 0.00 2.62
4683 5121 9.358872 GAATTCTACCAATGATTTTGTCTTTCC 57.641 33.333 0.00 0.00 0.00 3.13
4684 5122 7.831691 TTCTACCAATGATTTTGTCTTTCCA 57.168 32.000 0.00 0.00 0.00 3.53
4685 5123 7.831691 TCTACCAATGATTTTGTCTTTCCAA 57.168 32.000 0.00 0.00 0.00 3.53
4733 5171 1.021202 TTGGGTTCGCTCAGTGTTTG 58.979 50.000 0.00 0.00 0.00 2.93
4794 5746 4.792704 GCCACATTCAGATGAAACGTGTTT 60.793 41.667 19.09 0.00 38.64 2.83
4826 5778 2.811431 TGTTCCACTAGCCATTTGTTCG 59.189 45.455 0.00 0.00 0.00 3.95
4867 5982 5.583495 AGAGTACTGTTTCATATCAGTCGC 58.417 41.667 0.00 0.00 42.77 5.19
4876 5991 4.356405 TCATATCAGTCGCCCATTGATT 57.644 40.909 0.00 0.00 33.61 2.57
4922 6038 9.450807 CGGGAATTCTATCATGTTATTTTGAAC 57.549 33.333 5.23 0.00 0.00 3.18
4944 6060 8.664798 TGAACGTGTTCAGAAGGAATAAATATG 58.335 33.333 11.21 0.00 43.90 1.78
4945 6061 8.561738 AACGTGTTCAGAAGGAATAAATATGT 57.438 30.769 0.00 0.00 37.93 2.29
4946 6062 8.561738 ACGTGTTCAGAAGGAATAAATATGTT 57.438 30.769 0.00 0.00 37.93 2.71
5076 6196 5.263968 TCAATTCATACGGGAGAGAAGTC 57.736 43.478 0.00 0.00 0.00 3.01
5146 6266 7.922382 ACCTAGATATTGTGCTGGCTATAAAT 58.078 34.615 0.00 0.00 0.00 1.40
5188 6308 3.091545 TGATTTCTTTGATCACAGGGGC 58.908 45.455 8.97 0.00 0.00 5.80
5191 6311 2.905415 TCTTTGATCACAGGGGCAAT 57.095 45.000 8.97 0.00 0.00 3.56
5231 6353 4.148563 TCTCTTTGAGAGACGAGTTTCG 57.851 45.455 3.62 0.00 45.77 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.134848 TGATCACCATGATTGCGACGA 60.135 47.619 0.00 0.00 37.20 4.20
2 3 2.874086 TGATGATCACCATGATTGCGAC 59.126 45.455 0.00 0.00 37.20 5.19
3 4 2.874086 GTGATGATCACCATGATTGCGA 59.126 45.455 14.48 0.00 41.37 5.10
4 5 2.349155 CGTGATGATCACCATGATTGCG 60.349 50.000 19.01 1.20 44.20 4.85
15 16 5.582269 GTGAGATCCTTTTTCGTGATGATCA 59.418 40.000 0.00 0.00 32.90 2.92
19 20 5.808042 ATGTGAGATCCTTTTTCGTGATG 57.192 39.130 0.00 0.00 0.00 3.07
23 24 4.152402 CGTGAATGTGAGATCCTTTTTCGT 59.848 41.667 0.00 0.00 0.00 3.85
25 26 4.083324 TGCGTGAATGTGAGATCCTTTTTC 60.083 41.667 0.00 0.00 0.00 2.29
62 66 0.107654 ACAGCCTTCTCCAATACCGC 60.108 55.000 0.00 0.00 0.00 5.68
69 73 2.727123 TTTGTTCACAGCCTTCTCCA 57.273 45.000 0.00 0.00 0.00 3.86
80 84 3.319122 AGGACTTGAGCCATTTTGTTCAC 59.681 43.478 0.00 0.00 0.00 3.18
83 87 2.036346 GCAGGACTTGAGCCATTTTGTT 59.964 45.455 0.00 0.00 0.00 2.83
97 101 0.693049 CTACCAGTTTGGGCAGGACT 59.307 55.000 0.00 0.00 43.37 3.85
125 129 1.944676 CATTCGCCTCGACGCCTAC 60.945 63.158 0.63 0.00 34.89 3.18
244 248 3.932580 CTAAGCACGCTGCCGGACA 62.933 63.158 5.05 1.09 46.52 4.02
343 350 2.270205 CCACCATCGGCAGCTTCT 59.730 61.111 0.00 0.00 0.00 2.85
362 369 3.144506 CCTGTTTGCTCATTCTGTGTCT 58.855 45.455 0.00 0.00 0.00 3.41
401 408 1.270550 CTTGGTGCGAATCTTGGCTTT 59.729 47.619 0.00 0.00 32.75 3.51
525 544 0.470341 GATGGGTTAGGGGAGTGAGC 59.530 60.000 0.00 0.00 0.00 4.26
526 545 2.043227 GAGATGGGTTAGGGGAGTGAG 58.957 57.143 0.00 0.00 0.00 3.51
563 583 3.011517 CTCTCCCCCACCCACCAG 61.012 72.222 0.00 0.00 0.00 4.00
565 585 3.883822 TTCCTCTCCCCCACCCACC 62.884 68.421 0.00 0.00 0.00 4.61
566 586 2.204090 TTCCTCTCCCCCACCCAC 60.204 66.667 0.00 0.00 0.00 4.61
567 587 2.204090 GTTCCTCTCCCCCACCCA 60.204 66.667 0.00 0.00 0.00 4.51
568 588 3.400054 CGTTCCTCTCCCCCACCC 61.400 72.222 0.00 0.00 0.00 4.61
648 668 1.202290 GGAAATGAATGCACGGCGATT 60.202 47.619 16.62 2.15 0.00 3.34
686 706 3.040414 CTCTCGTCTTCCTGCGCGA 62.040 63.158 12.10 0.00 0.00 5.87
687 707 2.578178 CTCTCGTCTTCCTGCGCG 60.578 66.667 0.00 0.00 0.00 6.86
689 709 2.202676 GCCTCTCGTCTTCCTGCG 60.203 66.667 0.00 0.00 0.00 5.18
691 711 0.741915 GTAGGCCTCTCGTCTTCCTG 59.258 60.000 9.68 0.00 0.00 3.86
692 712 0.626916 AGTAGGCCTCTCGTCTTCCT 59.373 55.000 9.68 0.00 0.00 3.36
694 714 4.338682 TCAAATAGTAGGCCTCTCGTCTTC 59.661 45.833 9.68 0.00 0.00 2.87
698 744 2.358267 CGTCAAATAGTAGGCCTCTCGT 59.642 50.000 9.68 0.00 0.00 4.18
699 745 2.859032 GCGTCAAATAGTAGGCCTCTCG 60.859 54.545 9.68 6.46 0.00 4.04
705 751 1.202382 ACGGAGCGTCAAATAGTAGGC 60.202 52.381 0.00 0.00 33.69 3.93
708 754 1.917273 GCACGGAGCGTCAAATAGTA 58.083 50.000 0.00 0.00 38.32 1.82
786 842 0.034477 AGATTTGGTAAGGCGGTGGG 60.034 55.000 0.00 0.00 0.00 4.61
811 867 2.256117 ATATAAGTTGGACCGCTGGC 57.744 50.000 0.00 0.00 0.00 4.85
1246 1359 1.548719 TGAATCCTCGTGGTACCAGTG 59.451 52.381 16.93 11.48 34.23 3.66
1372 1500 3.759828 CTTTGCTTGCGCTTGCGC 61.760 61.111 29.59 29.59 43.34 6.09
1373 1501 3.101428 CCTTTGCTTGCGCTTGCG 61.101 61.111 9.73 10.90 43.34 4.85
1374 1502 2.735857 CCCTTTGCTTGCGCTTGC 60.736 61.111 9.73 13.68 36.97 4.01
1375 1503 2.735857 GCCCTTTGCTTGCGCTTG 60.736 61.111 9.73 1.85 36.87 4.01
1376 1504 3.216944 CTGCCCTTTGCTTGCGCTT 62.217 57.895 9.73 0.00 42.00 4.68
1386 1514 1.073897 GGTGCTGTCTCTGCCCTTT 59.926 57.895 0.00 0.00 0.00 3.11
1467 1595 1.444933 TTCTCCCTCCCAAGCAAAGA 58.555 50.000 0.00 0.00 0.00 2.52
1478 1606 3.008485 ACAGATGAACACCTTTCTCCCTC 59.992 47.826 0.00 0.00 0.00 4.30
1479 1607 2.982488 ACAGATGAACACCTTTCTCCCT 59.018 45.455 0.00 0.00 0.00 4.20
1557 1685 0.179045 CATCGGAACCATCCACCTCC 60.179 60.000 0.00 0.00 46.97 4.30
1569 1697 1.447838 GCGCTCAACCTCATCGGAA 60.448 57.895 0.00 0.00 36.31 4.30
1611 1739 1.293924 CCCTCTTGCAATACTCGCAG 58.706 55.000 0.00 0.00 41.18 5.18
1658 1786 0.465097 GTGCTGCCTGGTCATATGCT 60.465 55.000 0.00 0.00 0.00 3.79
1681 1809 1.134699 CCTCTGACATATGTGGCACGT 60.135 52.381 14.43 17.65 38.84 4.49
1714 1842 3.793559 AGTTGCGGAAATAATCGTAGCT 58.206 40.909 0.00 0.00 0.00 3.32
1715 1843 4.374707 CGTAGTTGCGGAAATAATCGTAGC 60.375 45.833 0.00 0.00 0.00 3.58
1716 1844 4.971830 TCGTAGTTGCGGAAATAATCGTAG 59.028 41.667 0.00 0.00 0.00 3.51
1738 1866 4.450419 CCTAAAATGCATCTCCAGATCGTC 59.550 45.833 0.00 0.00 31.21 4.20
1740 1868 4.635223 TCCTAAAATGCATCTCCAGATCG 58.365 43.478 0.00 0.00 31.21 3.69
1744 1872 4.785301 TCCTTCCTAAAATGCATCTCCAG 58.215 43.478 0.00 0.00 0.00 3.86
1788 1916 0.751643 ACTTCTTGGCCAAACACGCT 60.752 50.000 20.91 0.00 0.00 5.07
1830 1958 4.283363 AGCATTGTGTCTGTTGATCTCT 57.717 40.909 0.00 0.00 0.00 3.10
1873 2001 1.599047 CATTCCTCTGGGCACGAGT 59.401 57.895 6.98 0.00 35.07 4.18
1938 2066 4.228097 CTGCCGCGCCTTTGATCG 62.228 66.667 0.00 0.00 0.00 3.69
1973 2101 2.235650 CTGTCAGGTCTGTCATGGTGAT 59.764 50.000 0.00 0.00 0.00 3.06
2034 2162 0.036388 GTCGACTTCCAAGGCCATGA 60.036 55.000 10.18 0.00 0.00 3.07
2080 2208 4.773674 AGGGAACAATGATTCATCAGCAAA 59.226 37.500 0.00 0.00 40.64 3.68
2131 2259 0.670162 CCCTGTTGTGTTGAAGCAGG 59.330 55.000 0.00 0.00 44.51 4.85
2214 2342 4.040095 GGCCGACCAGAATATAGTACCTTT 59.960 45.833 0.00 0.00 35.26 3.11
2262 2390 3.244770 TGGAAGTGGAAACATGAGGTACC 60.245 47.826 2.73 2.73 46.14 3.34
2358 2486 0.392998 AAGGCCCTGCAACACTATCG 60.393 55.000 0.00 0.00 0.00 2.92
2440 2589 8.010733 TGAAGATGAGGAAAAGACAATTGTTT 57.989 30.769 13.36 3.77 0.00 2.83
2470 2619 4.146245 TCCTAGCATCAGGAATATCCCA 57.854 45.455 0.00 0.00 41.88 4.37
2730 2879 1.499049 GAAGGAACACGTCACCAGAC 58.501 55.000 0.00 0.00 41.46 3.51
2731 2880 0.391597 GGAAGGAACACGTCACCAGA 59.608 55.000 0.00 0.00 0.00 3.86
2732 2881 0.105964 TGGAAGGAACACGTCACCAG 59.894 55.000 0.00 0.00 0.00 4.00
2733 2882 0.762418 ATGGAAGGAACACGTCACCA 59.238 50.000 0.00 0.00 32.69 4.17
2734 2883 1.535462 CAATGGAAGGAACACGTCACC 59.465 52.381 0.00 0.00 0.00 4.02
2735 2884 1.069227 GCAATGGAAGGAACACGTCAC 60.069 52.381 0.00 0.00 0.00 3.67
2736 2885 1.234821 GCAATGGAAGGAACACGTCA 58.765 50.000 0.00 0.00 0.00 4.35
2737 2886 0.521735 GGCAATGGAAGGAACACGTC 59.478 55.000 0.00 0.00 0.00 4.34
2738 2887 0.110486 AGGCAATGGAAGGAACACGT 59.890 50.000 0.00 0.00 0.00 4.49
2739 2888 0.523072 CAGGCAATGGAAGGAACACG 59.477 55.000 0.00 0.00 0.00 4.49
2750 2899 2.513753 TGTTACTTGACCCAGGCAATG 58.486 47.619 0.00 0.00 0.00 2.82
2751 2900 2.969821 TGTTACTTGACCCAGGCAAT 57.030 45.000 0.00 0.00 0.00 3.56
2752 2901 2.738587 TTGTTACTTGACCCAGGCAA 57.261 45.000 0.00 0.00 0.00 4.52
2753 2902 2.582052 CTTTGTTACTTGACCCAGGCA 58.418 47.619 0.00 0.00 0.00 4.75
2754 2903 1.886542 CCTTTGTTACTTGACCCAGGC 59.113 52.381 0.00 0.00 0.00 4.85
2755 2904 3.223674 ACCTTTGTTACTTGACCCAGG 57.776 47.619 0.00 0.00 0.00 4.45
2756 2905 4.275936 CAGAACCTTTGTTACTTGACCCAG 59.724 45.833 0.00 0.00 33.97 4.45
2757 2906 4.204012 CAGAACCTTTGTTACTTGACCCA 58.796 43.478 0.00 0.00 33.97 4.51
2758 2907 3.004419 GCAGAACCTTTGTTACTTGACCC 59.996 47.826 0.00 0.00 33.97 4.46
2759 2908 3.883489 AGCAGAACCTTTGTTACTTGACC 59.117 43.478 0.00 0.00 33.97 4.02
2760 2909 5.065988 TGAAGCAGAACCTTTGTTACTTGAC 59.934 40.000 0.00 0.00 33.97 3.18
2761 2910 5.189928 TGAAGCAGAACCTTTGTTACTTGA 58.810 37.500 0.00 0.00 33.97 3.02
2762 2911 5.499139 TGAAGCAGAACCTTTGTTACTTG 57.501 39.130 0.00 0.00 33.97 3.16
2763 2912 5.417580 TGTTGAAGCAGAACCTTTGTTACTT 59.582 36.000 0.00 0.00 33.97 2.24
2764 2913 4.947388 TGTTGAAGCAGAACCTTTGTTACT 59.053 37.500 0.00 0.00 33.97 2.24
2765 2914 5.034797 GTGTTGAAGCAGAACCTTTGTTAC 58.965 41.667 0.00 0.00 33.97 2.50
2766 2915 4.702612 TGTGTTGAAGCAGAACCTTTGTTA 59.297 37.500 0.00 0.00 33.97 2.41
2767 2916 3.509575 TGTGTTGAAGCAGAACCTTTGTT 59.490 39.130 0.00 0.00 37.42 2.83
2768 2917 3.088532 TGTGTTGAAGCAGAACCTTTGT 58.911 40.909 0.00 0.00 0.00 2.83
2769 2918 3.781079 TGTGTTGAAGCAGAACCTTTG 57.219 42.857 0.00 0.00 0.00 2.77
2770 2919 3.509575 TGTTGTGTTGAAGCAGAACCTTT 59.490 39.130 5.03 0.00 40.53 3.11
2771 2920 3.088532 TGTTGTGTTGAAGCAGAACCTT 58.911 40.909 5.03 0.00 40.53 3.50
2772 2921 2.684881 CTGTTGTGTTGAAGCAGAACCT 59.315 45.455 5.03 0.00 40.53 3.50
2773 2922 2.223572 CCTGTTGTGTTGAAGCAGAACC 60.224 50.000 5.03 0.00 40.53 3.62
2774 2923 2.223572 CCCTGTTGTGTTGAAGCAGAAC 60.224 50.000 1.01 1.01 41.29 3.01
2775 2924 2.023673 CCCTGTTGTGTTGAAGCAGAA 58.976 47.619 0.00 0.00 0.00 3.02
2776 2925 1.679139 CCCTGTTGTGTTGAAGCAGA 58.321 50.000 0.00 0.00 0.00 4.26
2777 2926 0.670162 CCCCTGTTGTGTTGAAGCAG 59.330 55.000 0.00 0.00 0.00 4.24
2778 2927 1.391157 GCCCCTGTTGTGTTGAAGCA 61.391 55.000 0.00 0.00 0.00 3.91
2779 2928 1.109323 AGCCCCTGTTGTGTTGAAGC 61.109 55.000 0.00 0.00 0.00 3.86
2780 2929 0.670162 CAGCCCCTGTTGTGTTGAAG 59.330 55.000 0.00 0.00 0.00 3.02
2781 2930 1.391157 GCAGCCCCTGTTGTGTTGAA 61.391 55.000 0.00 0.00 33.43 2.69
2782 2931 1.827789 GCAGCCCCTGTTGTGTTGA 60.828 57.895 0.00 0.00 33.43 3.18
2783 2932 1.674764 TTGCAGCCCCTGTTGTGTTG 61.675 55.000 0.00 0.00 33.43 3.33
2784 2933 1.381056 TTGCAGCCCCTGTTGTGTT 60.381 52.632 0.00 0.00 33.43 3.32
2785 2934 1.829533 CTTGCAGCCCCTGTTGTGT 60.830 57.895 0.00 0.00 33.43 3.72
2786 2935 3.045142 CTTGCAGCCCCTGTTGTG 58.955 61.111 0.00 0.00 33.43 3.33
2787 2936 2.914097 GCTTGCAGCCCCTGTTGT 60.914 61.111 0.00 0.00 34.48 3.32
2788 2937 1.751349 AAAGCTTGCAGCCCCTGTTG 61.751 55.000 0.00 0.00 43.77 3.33
2789 2938 1.050421 AAAAGCTTGCAGCCCCTGTT 61.050 50.000 0.00 0.00 43.77 3.16
2790 2939 1.458209 AAAAGCTTGCAGCCCCTGT 60.458 52.632 0.00 0.00 43.77 4.00
2791 2940 1.005394 CAAAAGCTTGCAGCCCCTG 60.005 57.895 0.00 0.00 43.77 4.45
2792 2941 3.463345 CAAAAGCTTGCAGCCCCT 58.537 55.556 0.00 0.00 43.77 4.79
2800 2949 4.925068 AGTGTGTTCTTAGCAAAAGCTTG 58.075 39.130 0.00 0.00 35.49 4.01
2801 2950 5.343249 CAAGTGTGTTCTTAGCAAAAGCTT 58.657 37.500 0.00 0.00 0.00 3.74
2802 2951 4.734695 GCAAGTGTGTTCTTAGCAAAAGCT 60.735 41.667 0.00 0.00 0.00 3.74
2803 2952 3.487207 GCAAGTGTGTTCTTAGCAAAAGC 59.513 43.478 0.00 0.00 0.00 3.51
2804 2953 4.671377 TGCAAGTGTGTTCTTAGCAAAAG 58.329 39.130 0.00 0.00 32.87 2.27
2805 2954 4.710423 TGCAAGTGTGTTCTTAGCAAAA 57.290 36.364 0.00 0.00 32.87 2.44
2806 2955 4.337836 TGATGCAAGTGTGTTCTTAGCAAA 59.662 37.500 0.00 0.00 36.21 3.68
2807 2956 3.882288 TGATGCAAGTGTGTTCTTAGCAA 59.118 39.130 0.00 0.00 36.21 3.91
2808 2957 3.475575 TGATGCAAGTGTGTTCTTAGCA 58.524 40.909 0.00 0.00 36.63 3.49
2809 2958 4.470462 CTTGATGCAAGTGTGTTCTTAGC 58.530 43.478 0.00 0.00 36.79 3.09
2810 2959 4.614535 GCCTTGATGCAAGTGTGTTCTTAG 60.615 45.833 6.44 0.00 39.58 2.18
2811 2960 3.253188 GCCTTGATGCAAGTGTGTTCTTA 59.747 43.478 6.44 0.00 39.58 2.10
2812 2961 2.035066 GCCTTGATGCAAGTGTGTTCTT 59.965 45.455 6.44 0.00 39.58 2.52
2813 2962 1.610522 GCCTTGATGCAAGTGTGTTCT 59.389 47.619 6.44 0.00 39.58 3.01
2814 2963 1.610522 AGCCTTGATGCAAGTGTGTTC 59.389 47.619 6.44 0.00 39.58 3.18
2815 2964 1.696063 AGCCTTGATGCAAGTGTGTT 58.304 45.000 6.44 0.00 39.58 3.32
2816 2965 1.338973 CAAGCCTTGATGCAAGTGTGT 59.661 47.619 0.00 0.00 39.58 3.72
2817 2966 1.610038 TCAAGCCTTGATGCAAGTGTG 59.390 47.619 2.24 2.24 39.58 3.82
2818 2967 1.985473 TCAAGCCTTGATGCAAGTGT 58.015 45.000 2.24 0.00 39.58 3.55
2819 2968 2.034939 TGTTCAAGCCTTGATGCAAGTG 59.965 45.455 8.18 0.00 39.58 3.16
2820 2969 2.309613 TGTTCAAGCCTTGATGCAAGT 58.690 42.857 8.18 0.00 39.58 3.16
2821 2970 3.054878 GTTGTTCAAGCCTTGATGCAAG 58.945 45.455 18.86 0.00 39.84 4.01
2822 2971 2.224018 GGTTGTTCAAGCCTTGATGCAA 60.224 45.455 8.18 13.20 39.84 4.08
2823 2972 1.340889 GGTTGTTCAAGCCTTGATGCA 59.659 47.619 8.18 7.94 39.84 3.96
2824 2973 1.615392 AGGTTGTTCAAGCCTTGATGC 59.385 47.619 8.18 5.38 39.84 3.91
2825 2974 3.441572 CCTAGGTTGTTCAAGCCTTGATG 59.558 47.826 8.18 0.00 39.84 3.07
2826 2975 3.330701 TCCTAGGTTGTTCAAGCCTTGAT 59.669 43.478 8.18 0.00 39.84 2.57
2827 2976 2.708861 TCCTAGGTTGTTCAAGCCTTGA 59.291 45.455 9.08 2.24 38.04 3.02
2828 2977 3.140325 TCCTAGGTTGTTCAAGCCTTG 57.860 47.619 9.08 0.00 34.07 3.61
2829 2978 3.498661 CCTTCCTAGGTTGTTCAAGCCTT 60.499 47.826 9.08 0.00 36.74 4.35
2830 2979 2.040412 CCTTCCTAGGTTGTTCAAGCCT 59.960 50.000 9.08 10.19 36.74 4.58
2831 2980 2.437413 CCTTCCTAGGTTGTTCAAGCC 58.563 52.381 9.08 4.22 36.74 4.35
2832 2981 2.437413 CCCTTCCTAGGTTGTTCAAGC 58.563 52.381 9.08 6.63 40.19 4.01
2833 2982 2.224769 TGCCCTTCCTAGGTTGTTCAAG 60.225 50.000 9.08 3.65 40.19 3.02
2834 2983 1.777878 TGCCCTTCCTAGGTTGTTCAA 59.222 47.619 9.08 0.00 40.19 2.69
2835 2984 1.073284 GTGCCCTTCCTAGGTTGTTCA 59.927 52.381 9.08 0.28 40.19 3.18
2836 2985 1.613520 GGTGCCCTTCCTAGGTTGTTC 60.614 57.143 9.08 0.00 40.19 3.18
2837 2986 0.404426 GGTGCCCTTCCTAGGTTGTT 59.596 55.000 9.08 0.00 40.19 2.83
2838 2987 0.770557 TGGTGCCCTTCCTAGGTTGT 60.771 55.000 9.08 0.00 40.19 3.32
2839 2988 0.625849 ATGGTGCCCTTCCTAGGTTG 59.374 55.000 9.08 2.72 40.19 3.77
2840 2989 0.625849 CATGGTGCCCTTCCTAGGTT 59.374 55.000 9.08 0.00 40.19 3.50
2841 2990 0.253160 TCATGGTGCCCTTCCTAGGT 60.253 55.000 9.08 0.00 40.19 3.08
2842 2991 0.918983 TTCATGGTGCCCTTCCTAGG 59.081 55.000 0.82 0.82 41.60 3.02
2843 2992 1.133976 CCTTCATGGTGCCCTTCCTAG 60.134 57.143 0.00 0.00 0.00 3.02
2844 2993 0.918983 CCTTCATGGTGCCCTTCCTA 59.081 55.000 0.00 0.00 0.00 2.94
2845 2994 1.693640 CCTTCATGGTGCCCTTCCT 59.306 57.895 0.00 0.00 0.00 3.36
2846 2995 4.344237 CCTTCATGGTGCCCTTCC 57.656 61.111 0.00 0.00 0.00 3.46
2855 3004 5.420409 GACCAGACTTTAGTACCTTCATGG 58.580 45.833 0.00 0.00 42.93 3.66
2856 3005 5.103000 CGACCAGACTTTAGTACCTTCATG 58.897 45.833 0.00 0.00 0.00 3.07
2857 3006 4.159879 CCGACCAGACTTTAGTACCTTCAT 59.840 45.833 0.00 0.00 0.00 2.57
2858 3007 3.508793 CCGACCAGACTTTAGTACCTTCA 59.491 47.826 0.00 0.00 0.00 3.02
2859 3008 3.675502 GCCGACCAGACTTTAGTACCTTC 60.676 52.174 0.00 0.00 0.00 3.46
2860 3009 2.233186 GCCGACCAGACTTTAGTACCTT 59.767 50.000 0.00 0.00 0.00 3.50
2861 3010 1.823610 GCCGACCAGACTTTAGTACCT 59.176 52.381 0.00 0.00 0.00 3.08
2862 3011 1.134877 GGCCGACCAGACTTTAGTACC 60.135 57.143 0.00 0.00 35.26 3.34
2863 3012 1.823610 AGGCCGACCAGACTTTAGTAC 59.176 52.381 0.00 0.00 39.06 2.73
2864 3013 2.097825 GAGGCCGACCAGACTTTAGTA 58.902 52.381 0.00 0.00 39.06 1.82
2865 3014 0.896226 GAGGCCGACCAGACTTTAGT 59.104 55.000 0.00 0.00 39.06 2.24
2866 3015 0.895530 TGAGGCCGACCAGACTTTAG 59.104 55.000 0.00 0.00 39.06 1.85
2867 3016 1.344065 TTGAGGCCGACCAGACTTTA 58.656 50.000 0.00 0.00 39.06 1.85
2868 3017 0.472471 TTTGAGGCCGACCAGACTTT 59.528 50.000 0.00 0.00 39.06 2.66
2869 3018 0.250338 GTTTGAGGCCGACCAGACTT 60.250 55.000 0.00 0.00 39.06 3.01
2870 3019 1.122019 AGTTTGAGGCCGACCAGACT 61.122 55.000 11.36 11.36 39.06 3.24
2871 3020 0.951040 CAGTTTGAGGCCGACCAGAC 60.951 60.000 0.00 2.70 39.06 3.51
2889 3038 5.663106 AGGTACTATCTCAGGATTTTCAGCA 59.337 40.000 0.00 0.00 36.02 4.41
3021 3170 5.545063 TGACACTTGATGACTGTAAAGGA 57.455 39.130 0.00 0.00 0.00 3.36
3221 3370 0.618458 ATGCTTCGCAGAACCCCTTA 59.382 50.000 0.00 0.00 45.90 2.69
3267 3524 1.746516 GCAGAATCCCTTGAGCTCTGG 60.747 57.143 16.19 16.20 36.00 3.86
3398 3655 1.003580 CCTTCCTAGGTTGCTGAAGCA 59.996 52.381 9.08 0.00 41.90 3.91
3405 3662 2.824489 GCGCCCTTCCTAGGTTGC 60.824 66.667 9.08 6.59 40.19 4.17
3427 3684 4.174762 GACCGACAAGAATTCAGTACCTC 58.825 47.826 8.44 0.00 0.00 3.85
3435 3692 2.228103 GGTTTGGGACCGACAAGAATTC 59.772 50.000 0.00 0.00 39.00 2.17
3483 3749 1.886655 GCCTCGGTGGAAGTGGAAAAT 60.887 52.381 0.00 0.00 38.35 1.82
3558 3824 3.217599 TCTCTTGTCGATTGAGGTTCG 57.782 47.619 10.78 0.00 37.94 3.95
3560 3826 6.051717 CCATTATCTCTTGTCGATTGAGGTT 58.948 40.000 10.78 4.32 0.00 3.50
3664 3930 3.256704 AGGACCCACCAGAAACAAGATA 58.743 45.455 0.00 0.00 42.04 1.98
3789 4055 0.968405 GCATTCTTTCCACAAGGGCA 59.032 50.000 0.00 0.00 36.21 5.36
3879 4145 6.892456 AGAGATACTCTGAAGTACCAATGACA 59.108 38.462 0.25 0.00 40.74 3.58
3954 4220 0.257328 TCACAGGGTCAGGCAACAAA 59.743 50.000 0.00 0.00 41.41 2.83
3970 4236 1.576421 CAAGTTCGGCCTGCTTCAC 59.424 57.895 0.00 0.00 0.00 3.18
3979 4245 2.521958 TAGGCCTCAGCAAGTTCGGC 62.522 60.000 9.68 0.00 42.56 5.54
4133 4519 0.043334 ACCTCCAGCAGATAGTGGGT 59.957 55.000 0.00 0.00 34.27 4.51
4236 4670 8.638685 ACTTTGATGTCTTCTTTGATTGTTTG 57.361 30.769 0.00 0.00 0.00 2.93
4358 4792 2.734673 GAGAAGAGCTTGTGCGCCG 61.735 63.158 4.18 0.00 45.42 6.46
4365 4799 1.630244 CGTTGCCGGAGAAGAGCTTG 61.630 60.000 5.05 0.00 0.00 4.01
4374 4808 0.240945 ATTTCTTTGCGTTGCCGGAG 59.759 50.000 5.05 0.00 35.23 4.63
4383 4817 5.486706 GCAAAATGATGCTATTTCTTTGCG 58.513 37.500 0.00 0.00 43.06 4.85
4501 4936 2.563471 ACGAAGCGACCTTCTACATC 57.437 50.000 0.00 0.00 44.24 3.06
4534 4972 4.210328 CCAGCAAAAATTCGGTACAAAACC 59.790 41.667 0.00 0.00 45.77 3.27
4539 4977 4.657436 AAACCAGCAAAAATTCGGTACA 57.343 36.364 0.00 0.00 0.00 2.90
4593 5031 1.726791 CGAACATGACACTGCAGTACC 59.273 52.381 21.20 14.48 0.00 3.34
4622 5060 7.417612 ACAGTCTACACTTGCAAAAAGTTATG 58.582 34.615 0.00 0.00 0.00 1.90
4631 5069 6.092122 GTGCAATATACAGTCTACACTTGCAA 59.908 38.462 8.05 0.00 39.47 4.08
4634 5072 6.033966 TCGTGCAATATACAGTCTACACTTG 58.966 40.000 0.00 0.00 0.00 3.16
4696 5134 9.796120 CGAACCCAATAAAAATTTGCTATAGAA 57.204 29.630 3.21 0.00 0.00 2.10
4707 5145 4.522789 ACACTGAGCGAACCCAATAAAAAT 59.477 37.500 0.00 0.00 0.00 1.82
4712 5150 2.811431 CAAACACTGAGCGAACCCAATA 59.189 45.455 0.00 0.00 0.00 1.90
4794 5746 6.539173 TGGCTAGTGGAACAGATAAGAAAAA 58.461 36.000 0.00 0.00 41.80 1.94
4798 5750 5.957771 AATGGCTAGTGGAACAGATAAGA 57.042 39.130 0.00 0.00 41.80 2.10
4799 5751 5.882557 ACAAATGGCTAGTGGAACAGATAAG 59.117 40.000 0.00 0.00 41.80 1.73
4804 5756 3.120199 CGAACAAATGGCTAGTGGAACAG 60.120 47.826 0.00 0.00 41.80 3.16
4867 5982 5.519927 GCGAAAATTACCTTCAATCAATGGG 59.480 40.000 0.00 0.00 0.00 4.00
4922 6038 9.840427 AAAACATATTTATTCCTTCTGAACACG 57.160 29.630 0.00 0.00 35.31 4.49
4945 6061 9.280174 CCCTTACACAGAGTATTAGAAACAAAA 57.720 33.333 0.00 0.00 31.53 2.44
4946 6062 8.434392 ACCCTTACACAGAGTATTAGAAACAAA 58.566 33.333 0.00 0.00 31.53 2.83
5146 6266 6.459670 TCACAGCCAAATATCTACGTTCTA 57.540 37.500 0.00 0.00 0.00 2.10
5188 6308 5.826737 AGATTCAGCCAGATGGACTTTATTG 59.173 40.000 2.18 0.00 37.39 1.90
5191 6311 4.718774 AGAGATTCAGCCAGATGGACTTTA 59.281 41.667 2.18 0.00 37.39 1.85
5229 6351 9.529325 CAGGTTATCTGAAAAACATATAGACGA 57.471 33.333 0.00 0.00 46.18 4.20
5230 6352 8.765219 CCAGGTTATCTGAAAAACATATAGACG 58.235 37.037 0.00 0.00 46.18 4.18
5231 6353 9.057089 CCCAGGTTATCTGAAAAACATATAGAC 57.943 37.037 0.00 0.00 46.18 2.59
5233 6355 8.980481 ACCCAGGTTATCTGAAAAACATATAG 57.020 34.615 0.00 0.00 46.18 1.31
5235 6357 7.557719 CAGACCCAGGTTATCTGAAAAACATAT 59.442 37.037 6.74 0.00 46.18 1.78
5236 6358 6.884295 CAGACCCAGGTTATCTGAAAAACATA 59.116 38.462 6.74 0.00 46.18 2.29
5237 6359 5.711976 CAGACCCAGGTTATCTGAAAAACAT 59.288 40.000 6.74 0.00 46.18 2.71
5238 6360 5.070001 CAGACCCAGGTTATCTGAAAAACA 58.930 41.667 6.74 0.00 46.18 2.83
5239 6361 5.313712 TCAGACCCAGGTTATCTGAAAAAC 58.686 41.667 11.30 0.00 44.49 2.43
5244 6372 4.782691 TGATTTCAGACCCAGGTTATCTGA 59.217 41.667 10.10 10.10 46.18 3.27


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

AutoCloner maintained by Alex Coulton.