Multiple sequence alignment - TraesCS6D01G069900

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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 TraesCS6D01G069900 chr6D 100.000 4921 0 0 1 4921 35001028 34996108 0.000000e+00 9088
1 TraesCS6D01G069900 chr6B 87.533 2615 219 44 2017 4553 72378514 72375929 0.000000e+00 2924
2 TraesCS6D01G069900 chr6B 88.089 2057 131 48 4 2011 72380741 72378750 0.000000e+00 2337
3 TraesCS6D01G069900 chr6A 86.400 2625 228 56 2017 4556 39180151 39177571 0.000000e+00 2750
4 TraesCS6D01G069900 chr6A 88.599 1263 72 40 775 2012 39181404 39180189 0.000000e+00 1469
5 TraesCS6D01G069900 chr6A 86.463 229 14 5 4691 4918 39177481 39177269 8.240000e-58 235
6 TraesCS6D01G069900 chr6A 79.695 197 36 4 438 630 1899050 1898854 6.640000e-29 139
7 TraesCS6D01G069900 chr3A 84.486 593 67 12 67 656 655651472 655652042 3.330000e-156 562
8 TraesCS6D01G069900 chr7B 82.780 633 75 19 27 645 84454881 84454269 7.250000e-148 534
9 TraesCS6D01G069900 chr5B 80.343 641 86 25 27 659 488850839 488850231 2.700000e-122 449
10 TraesCS6D01G069900 chr1A 83.753 437 43 9 244 659 522240431 522240002 5.970000e-104 388
11 TraesCS6D01G069900 chr1A 78.550 331 58 11 102 421 11936905 11937233 6.460000e-49 206
12 TraesCS6D01G069900 chr1A 90.678 118 9 1 1242 1357 300859823 300859706 6.600000e-34 156
13 TraesCS6D01G069900 chr1A 88.710 124 6 4 1240 1355 520122817 520122940 1.430000e-30 145
14 TraesCS6D01G069900 chr1A 87.500 120 15 0 1453 1572 520122996 520123115 6.640000e-29 139
15 TraesCS6D01G069900 chr1A 87.611 113 14 0 1453 1565 300859639 300859527 1.110000e-26 132
16 TraesCS6D01G069900 chr1A 86.408 103 4 8 2032 2129 300859050 300858953 2.420000e-18 104
17 TraesCS6D01G069900 chr4A 86.416 346 35 9 226 567 708429597 708429934 7.780000e-98 368
18 TraesCS6D01G069900 chr1D 81.292 449 61 12 1687 2115 246937543 246937988 4.720000e-90 342
19 TraesCS6D01G069900 chr1D 89.916 119 5 3 1240 1351 423764015 423764133 3.970000e-31 147
20 TraesCS6D01G069900 chr1D 91.429 105 9 0 1242 1346 246937161 246937265 1.430000e-30 145
21 TraesCS6D01G069900 chr1D 87.931 116 14 0 1453 1568 423764199 423764314 2.390000e-28 137
22 TraesCS6D01G069900 chr1B 77.982 327 52 12 1242 1565 331146661 331146352 2.340000e-43 187
23 TraesCS6D01G069900 chr1B 88.525 122 7 3 1240 1354 573215958 573216079 1.850000e-29 141
24 TraesCS6D01G069900 chr1B 84.615 130 20 0 1453 1582 573216149 573216278 4.000000e-26 130
25 TraesCS6D01G069900 chr5D 80.000 160 26 5 102 258 24967548 24967392 4.030000e-21 113


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 TraesCS6D01G069900 chr6D 34996108 35001028 4920 True 9088.000000 9088 100.0000 1 4921 1 chr6D.!!$R1 4920
1 TraesCS6D01G069900 chr6B 72375929 72380741 4812 True 2630.500000 2924 87.8110 4 4553 2 chr6B.!!$R1 4549
2 TraesCS6D01G069900 chr6A 39177269 39181404 4135 True 1484.666667 2750 87.1540 775 4918 3 chr6A.!!$R2 4143
3 TraesCS6D01G069900 chr3A 655651472 655652042 570 False 562.000000 562 84.4860 67 656 1 chr3A.!!$F1 589
4 TraesCS6D01G069900 chr7B 84454269 84454881 612 True 534.000000 534 82.7800 27 645 1 chr7B.!!$R1 618
5 TraesCS6D01G069900 chr5B 488850231 488850839 608 True 449.000000 449 80.3430 27 659 1 chr5B.!!$R1 632
6 TraesCS6D01G069900 chr1D 246937161 246937988 827 False 243.500000 342 86.3605 1242 2115 2 chr1D.!!$F1 873

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
907 955 0.464036 TGCGTAGGTAAGCCTCCATG 59.536 55.0 0.00 0.0 45.64 3.66 F
1644 1732 0.097674 CCGTTTCGACGTAGACCGAT 59.902 55.0 15.39 0.0 40.70 4.18 F
2151 2479 0.179034 GAGCTACCATGCCTCCCTTG 60.179 60.0 0.00 0.0 0.00 3.61 F
2669 3021 0.108186 CGGAGCTGGTCTACAATGCA 60.108 55.0 6.83 0.0 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2501 2853 0.111061 TTGTCTGGGCATTGCTCACT 59.889 50.0 7.23 0.00 32.27 3.41 R
2554 2906 0.539438 GGTGTTGGGACCAGATGCAA 60.539 55.0 0.00 0.00 35.88 4.08 R
3778 4148 0.257039 ACACCAAGGAGGGATGCATC 59.743 55.0 18.81 18.81 43.89 3.91 R
4389 4798 0.472925 TAACCAGACCAGGAGGCACA 60.473 55.0 0.00 0.00 39.06 4.57 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
42 43 1.073763 TGTCAAGACCACCCCTGAATG 59.926 52.381 0.00 0.00 0.00 2.67
48 49 1.478105 GACCACCCCTGAATGCATTTC 59.522 52.381 14.33 7.58 34.72 2.17
51 52 2.026641 CACCCCTGAATGCATTTCGAT 58.973 47.619 14.33 0.00 37.13 3.59
52 53 2.026641 ACCCCTGAATGCATTTCGATG 58.973 47.619 14.33 5.61 37.13 3.84
64 65 9.264782 GAATGCATTTCGATGGTTTTAAAAATG 57.735 29.630 14.33 1.82 37.23 2.32
73 74 9.092876 TCGATGGTTTTAAAAATGGAAATATGC 57.907 29.630 1.31 0.00 0.00 3.14
126 127 8.772705 GTGCAAAAATGGTAGAAAAATCATGAA 58.227 29.630 0.00 0.00 0.00 2.57
207 212 3.640967 AGCCTTTCTTTGTATTGTTGGCA 59.359 39.130 0.00 0.00 40.18 4.92
304 318 5.592688 TCAGATTTTTCACGGGAGTTCTTTT 59.407 36.000 0.00 0.00 44.67 2.27
306 320 6.198966 CAGATTTTTCACGGGAGTTCTTTTTG 59.801 38.462 0.00 0.00 44.67 2.44
318 332 7.217200 GGGAGTTCTTTTTGGAAAGCTTTATT 58.783 34.615 12.68 0.00 41.63 1.40
320 334 7.385205 GGAGTTCTTTTTGGAAAGCTTTATTCC 59.615 37.037 12.68 10.28 45.39 3.01
334 348 5.484290 AGCTTTATTCCAGTACACCAGTAGT 59.516 40.000 0.00 0.00 34.19 2.73
346 360 5.560966 ACACCAGTAGTTCAAGTTTGTTG 57.439 39.130 0.00 0.00 0.00 3.33
533 561 3.871594 GACCAGGTGATAAATCCGACTTG 59.128 47.826 0.00 0.00 0.00 3.16
608 636 4.711846 TGGATGAGTTGTACTGTCTAGCAT 59.288 41.667 0.00 0.00 0.00 3.79
631 659 1.226379 CACGGCGTGGCAATCAATC 60.226 57.895 31.19 0.00 0.00 2.67
665 693 4.065281 GACCTCCCGTGTCCCGTG 62.065 72.222 0.00 0.00 33.66 4.94
686 714 3.510753 TGCACGGTAGTTAATCCACAGTA 59.489 43.478 0.00 0.00 0.00 2.74
765 795 1.270199 GCGAGAGATGCATGGATCACT 60.270 52.381 26.58 24.94 0.00 3.41
769 799 2.133553 GAGATGCATGGATCACTGTCG 58.866 52.381 26.58 0.00 0.00 4.35
819 866 1.418342 CCGGCGTAATTGTGGTCGAG 61.418 60.000 6.01 0.00 0.00 4.04
821 868 1.017177 GGCGTAATTGTGGTCGAGCA 61.017 55.000 14.39 14.39 0.00 4.26
900 948 4.733405 GCATTTGTTTATGCGTAGGTAAGC 59.267 41.667 0.00 0.00 41.24 3.09
901 949 4.950434 TTTGTTTATGCGTAGGTAAGCC 57.050 40.909 0.00 0.00 0.00 4.35
902 950 8.329637 GCATTTGTTTATGCGTAGGTAAGCCT 62.330 42.308 0.00 0.00 43.52 4.58
903 951 3.788937 TGTTTATGCGTAGGTAAGCCTC 58.211 45.455 0.00 0.00 45.64 4.70
906 954 1.424638 ATGCGTAGGTAAGCCTCCAT 58.575 50.000 0.00 0.00 45.64 3.41
907 955 0.464036 TGCGTAGGTAAGCCTCCATG 59.536 55.000 0.00 0.00 45.64 3.66
908 956 0.464452 GCGTAGGTAAGCCTCCATGT 59.536 55.000 0.00 0.00 45.64 3.21
909 957 1.538419 GCGTAGGTAAGCCTCCATGTC 60.538 57.143 0.00 0.00 45.64 3.06
910 958 1.754803 CGTAGGTAAGCCTCCATGTCA 59.245 52.381 0.00 0.00 45.64 3.58
911 959 2.167693 CGTAGGTAAGCCTCCATGTCAA 59.832 50.000 0.00 0.00 45.64 3.18
912 960 3.181465 CGTAGGTAAGCCTCCATGTCAAT 60.181 47.826 0.00 0.00 45.64 2.57
913 961 3.287867 AGGTAAGCCTCCATGTCAATG 57.712 47.619 0.00 0.00 42.67 2.82
933 981 0.812412 GCCGCGGCACCTATTTTAGA 60.812 55.000 43.55 0.00 41.49 2.10
962 1010 2.748058 CTTGTAACCCAGCCGCACCT 62.748 60.000 0.00 0.00 0.00 4.00
974 1036 2.980233 GCACCTCACCACCACAGC 60.980 66.667 0.00 0.00 0.00 4.40
1017 1079 1.267121 AGATGGACAAGTACTGCCGT 58.733 50.000 0.00 0.00 0.00 5.68
1038 1103 2.766400 CGTCGCTCTGTCCTCCCTC 61.766 68.421 0.00 0.00 0.00 4.30
1044 1109 1.305633 TCTGTCCTCCCTCCTGCTG 60.306 63.158 0.00 0.00 0.00 4.41
1185 1256 4.569228 CCCTTCCCTATATACGCTGGTCTA 60.569 50.000 0.00 0.00 0.00 2.59
1360 1435 2.906354 GGTACGCCATCATCTTCTGTT 58.094 47.619 0.00 0.00 34.09 3.16
1361 1436 2.866762 GGTACGCCATCATCTTCTGTTC 59.133 50.000 0.00 0.00 34.09 3.18
1362 1437 3.430929 GGTACGCCATCATCTTCTGTTCT 60.431 47.826 0.00 0.00 34.09 3.01
1365 1440 3.055530 ACGCCATCATCTTCTGTTCTCTT 60.056 43.478 0.00 0.00 0.00 2.85
1427 1515 0.811616 GCTCGCCGTCATTTCCATCT 60.812 55.000 0.00 0.00 0.00 2.90
1428 1516 1.656652 CTCGCCGTCATTTCCATCTT 58.343 50.000 0.00 0.00 0.00 2.40
1430 1518 2.006888 TCGCCGTCATTTCCATCTTTC 58.993 47.619 0.00 0.00 0.00 2.62
1431 1519 1.064060 CGCCGTCATTTCCATCTTTCC 59.936 52.381 0.00 0.00 0.00 3.13
1432 1520 2.091541 GCCGTCATTTCCATCTTTCCA 58.908 47.619 0.00 0.00 0.00 3.53
1433 1521 2.689983 GCCGTCATTTCCATCTTTCCAT 59.310 45.455 0.00 0.00 0.00 3.41
1434 1522 3.489738 GCCGTCATTTCCATCTTTCCATG 60.490 47.826 0.00 0.00 0.00 3.66
1591 1679 4.020543 CAGAGCTACAAACTCCTACTCCT 58.979 47.826 0.00 0.00 34.56 3.69
1592 1680 4.097286 CAGAGCTACAAACTCCTACTCCTC 59.903 50.000 0.00 0.00 34.56 3.71
1593 1681 3.367321 AGCTACAAACTCCTACTCCTCC 58.633 50.000 0.00 0.00 0.00 4.30
1594 1682 3.097614 GCTACAAACTCCTACTCCTCCA 58.902 50.000 0.00 0.00 0.00 3.86
1596 1684 4.442192 GCTACAAACTCCTACTCCTCCATG 60.442 50.000 0.00 0.00 0.00 3.66
1600 1688 2.324541 ACTCCTACTCCTCCATGCATC 58.675 52.381 0.00 0.00 0.00 3.91
1603 1691 2.702478 TCCTACTCCTCCATGCATCTTG 59.298 50.000 0.00 0.00 0.00 3.02
1613 1701 3.200605 TCCATGCATCTTGCTTCTTCCTA 59.799 43.478 0.00 0.00 45.31 2.94
1617 1705 2.685388 GCATCTTGCTTCTTCCTAACCC 59.315 50.000 0.00 0.00 40.96 4.11
1626 1714 2.294132 CTTCCTAACCCGACCTCGCC 62.294 65.000 0.00 0.00 38.18 5.54
1631 1719 2.490993 TAACCCGACCTCGCCGTTTC 62.491 60.000 4.40 0.00 38.18 2.78
1634 1722 3.170585 CGACCTCGCCGTTTCGAC 61.171 66.667 0.00 0.00 34.46 4.20
1636 1724 3.886329 GACCTCGCCGTTTCGACGT 62.886 63.158 0.00 0.00 33.95 4.34
1637 1725 2.176546 CCTCGCCGTTTCGACGTA 59.823 61.111 0.00 0.00 33.95 3.57
1639 1727 1.133253 CTCGCCGTTTCGACGTAGA 59.867 57.895 0.00 0.00 33.95 2.59
1641 1729 2.148365 CGCCGTTTCGACGTAGACC 61.148 63.158 0.00 0.00 0.00 3.85
1642 1730 2.148365 GCCGTTTCGACGTAGACCG 61.148 63.158 0.00 4.00 44.03 4.79
1643 1731 1.497278 CCGTTTCGACGTAGACCGA 59.503 57.895 15.39 5.83 40.70 4.69
1644 1732 0.097674 CCGTTTCGACGTAGACCGAT 59.902 55.000 15.39 0.00 40.70 4.18
1645 1733 1.466360 CCGTTTCGACGTAGACCGATT 60.466 52.381 15.39 0.00 40.70 3.34
1646 1734 1.576246 CGTTTCGACGTAGACCGATTG 59.424 52.381 10.20 0.00 40.70 2.67
1650 1738 4.880886 TTCGACGTAGACCGATTGATTA 57.119 40.909 0.00 0.00 40.70 1.75
1964 2057 1.226974 GCTCGGCGACAGCTTCATA 60.227 57.895 4.99 0.00 44.37 2.15
2013 2288 7.540055 GCAAAACATGGTCTCTTAGAATTCTTG 59.460 37.037 14.36 7.50 0.00 3.02
2151 2479 0.179034 GAGCTACCATGCCTCCCTTG 60.179 60.000 0.00 0.00 0.00 3.61
2245 2575 1.140312 AAACTCTGACCAGGAAGGCA 58.860 50.000 0.00 0.00 43.14 4.75
2315 2645 1.006571 TCGTGGACGGACTTGCTTC 60.007 57.895 0.00 0.00 40.29 3.86
2456 2808 5.645497 CACCTATAACTTCTTGCTTGAAGCT 59.355 40.000 18.94 8.93 45.20 3.74
2503 2855 4.760047 GTCATCGGTGGCGGCAGT 62.760 66.667 13.91 0.00 0.00 4.40
2531 2883 2.637382 TGCCCAGACAATGAAGTACTCA 59.363 45.455 0.00 0.00 38.81 3.41
2540 2892 7.604164 CAGACAATGAAGTACTCAACATACCTT 59.396 37.037 0.00 0.00 37.67 3.50
2543 2895 8.594550 ACAATGAAGTACTCAACATACCTTAGT 58.405 33.333 0.00 0.00 37.67 2.24
2554 2906 2.226962 TACCTTAGTCGCAAGGAGGT 57.773 50.000 14.76 9.14 46.94 3.85
2594 2946 3.204827 AGCGGCATCATGAACGGC 61.205 61.111 18.30 18.30 0.00 5.68
2669 3021 0.108186 CGGAGCTGGTCTACAATGCA 60.108 55.000 6.83 0.00 0.00 3.96
2734 3086 0.747283 CCTAGCTCTACACCGACCGT 60.747 60.000 0.00 0.00 0.00 4.83
2777 3129 7.352719 ACTTTTGTTTTGTTAAATTGCGACA 57.647 28.000 0.00 0.00 0.00 4.35
3012 3371 7.301868 ACTTGTTGATTACAAATCCAATGGT 57.698 32.000 0.00 0.00 45.69 3.55
3013 3372 7.378181 ACTTGTTGATTACAAATCCAATGGTC 58.622 34.615 0.00 0.00 45.69 4.02
3014 3373 5.948588 TGTTGATTACAAATCCAATGGTCG 58.051 37.500 0.00 0.00 37.77 4.79
3015 3374 5.475220 TGTTGATTACAAATCCAATGGTCGT 59.525 36.000 0.00 0.00 37.77 4.34
3016 3375 6.655425 TGTTGATTACAAATCCAATGGTCGTA 59.345 34.615 0.00 0.00 37.77 3.43
3191 3556 2.549329 ACGCTAAAAACGACCGGATTTT 59.451 40.909 9.46 12.27 0.00 1.82
3198 3563 5.556355 AAAACGACCGGATTTTATCTTCC 57.444 39.130 9.46 0.00 0.00 3.46
3218 3583 1.942657 CGTGGGAAGCATATGGTTGAG 59.057 52.381 24.07 7.31 35.69 3.02
3244 3609 2.175530 GACTGGTCGATGTACTGTCG 57.824 55.000 12.93 12.93 40.30 4.35
3277 3642 6.018433 AGGTACCAGATTAGCAAATGGAAT 57.982 37.500 15.94 0.00 36.62 3.01
3310 3675 5.712152 AAGAAACGGCTCTTGAATTTGAT 57.288 34.783 0.88 0.00 34.31 2.57
3409 3776 7.503566 CACATTCTACACCCAGATATTTCCAAT 59.496 37.037 0.00 0.00 0.00 3.16
3554 3923 0.324285 CAGAAGCTCAAGTGAGGCCT 59.676 55.000 3.86 3.86 42.29 5.19
3640 4010 0.745845 CTTTCAGATGGGACGGGCTG 60.746 60.000 0.00 0.00 0.00 4.85
3747 4117 4.842531 TGCATTTCTACTGGATCCTTCA 57.157 40.909 14.23 0.00 0.00 3.02
3754 4124 0.622665 ACTGGATCCTTCAAGCTGGG 59.377 55.000 14.23 0.00 0.00 4.45
3769 4139 0.798776 CTGGGCACTTTGTAAGCTCG 59.201 55.000 0.00 0.00 0.00 5.03
3778 4148 5.668866 GCACTTTGTAAGCTCGTGAACATAG 60.669 44.000 0.00 0.00 0.00 2.23
3806 4176 4.631234 TCCCTCCTTGGTGTCTTATATGT 58.369 43.478 0.00 0.00 0.00 2.29
3881 4251 0.251297 ACCAGCCTTGCATTGCACTA 60.251 50.000 11.66 0.00 38.71 2.74
3925 4295 2.166664 AGTCTCCGGCAAGTTAGATGAC 59.833 50.000 0.00 0.00 0.00 3.06
3930 4300 2.612972 CCGGCAAGTTAGATGACACACT 60.613 50.000 0.00 0.00 0.00 3.55
3941 4311 7.540299 GTTAGATGACACACTAACTCTAGCTT 58.460 38.462 18.89 0.00 42.63 3.74
3952 4322 9.857957 ACACTAACTCTAGCTTTATTGTACTTC 57.142 33.333 0.00 0.00 0.00 3.01
3992 4365 4.837896 TGTACCATCTGCGAGAAGATAG 57.162 45.455 0.00 0.00 35.09 2.08
4013 4386 4.135306 AGATGGTGATCATGATTCAGTGC 58.865 43.478 10.14 0.00 35.97 4.40
4022 4395 3.640498 TCATGATTCAGTGCAAAACCCAA 59.360 39.130 0.00 0.00 0.00 4.12
4023 4396 4.283978 TCATGATTCAGTGCAAAACCCAAT 59.716 37.500 0.00 0.00 0.00 3.16
4031 4404 2.490115 GTGCAAAACCCAATATCCGACA 59.510 45.455 0.00 0.00 0.00 4.35
4038 4411 4.431416 ACCCAATATCCGACATTTGCTA 57.569 40.909 0.00 0.00 0.00 3.49
4045 4418 6.808008 ATATCCGACATTTGCTAATTGGAG 57.192 37.500 10.48 0.00 0.00 3.86
4052 4425 4.223477 ACATTTGCTAATTGGAGTTGGCAT 59.777 37.500 0.00 0.00 43.60 4.40
4096 4484 2.568956 TGCTCTGGCAGAGTTGTATTCT 59.431 45.455 37.14 0.00 44.12 2.40
4127 4515 0.179004 TGGTTTGGTCGATGTGCCTT 60.179 50.000 0.00 0.00 0.00 4.35
4131 4519 3.071479 GTTTGGTCGATGTGCCTTCTTA 58.929 45.455 0.00 0.00 0.00 2.10
4133 4521 1.291132 GGTCGATGTGCCTTCTTAGC 58.709 55.000 0.00 0.00 0.00 3.09
4144 4532 2.271800 CCTTCTTAGCGTGTGTCATCC 58.728 52.381 0.00 0.00 0.00 3.51
4151 4557 3.238108 AGCGTGTGTCATCCTTTCTAG 57.762 47.619 0.00 0.00 0.00 2.43
4166 4572 9.612620 CATCCTTTCTAGTAATTTTGTTGTGTC 57.387 33.333 0.00 0.00 0.00 3.67
4190 4598 7.224753 GTCAATCCTCGATGTTTTGAATAGCTA 59.775 37.037 0.00 0.00 0.00 3.32
4217 4625 3.838244 TTGTGTTGTTACAGAGAGCCT 57.162 42.857 0.00 0.00 34.24 4.58
4231 4639 3.957497 AGAGAGCCTGGTGTAACTGATAG 59.043 47.826 0.00 0.00 36.74 2.08
4257 4665 8.633561 GCTTCTTGGTATTAATATGCTTCCTTT 58.366 33.333 0.00 0.00 0.00 3.11
4291 4700 8.976986 AAAAATCATCACTTCAGTGCTAAATC 57.023 30.769 1.74 0.00 45.25 2.17
4294 4703 3.350219 TCACTTCAGTGCTAAATCCCC 57.650 47.619 1.74 0.00 45.25 4.81
4295 4704 2.026262 TCACTTCAGTGCTAAATCCCCC 60.026 50.000 1.74 0.00 45.25 5.40
4332 4741 4.807304 TCTTATTTCCGCCGAGTGAATTAC 59.193 41.667 0.00 0.00 0.00 1.89
4346 4755 6.910536 AGTGAATTACTCGTCATTGATTCC 57.089 37.500 0.00 0.00 33.17 3.01
4347 4756 6.644347 AGTGAATTACTCGTCATTGATTCCT 58.356 36.000 0.00 0.00 33.17 3.36
4348 4757 7.106239 AGTGAATTACTCGTCATTGATTCCTT 58.894 34.615 0.00 0.00 33.17 3.36
4370 4779 2.217510 TGCTACCCTTCTTCGTCTCT 57.782 50.000 0.00 0.00 0.00 3.10
4372 4781 1.819903 GCTACCCTTCTTCGTCTCTGT 59.180 52.381 0.00 0.00 0.00 3.41
4376 4785 2.224917 ACCCTTCTTCGTCTCTGTCTCT 60.225 50.000 0.00 0.00 0.00 3.10
4377 4786 3.009253 ACCCTTCTTCGTCTCTGTCTCTA 59.991 47.826 0.00 0.00 0.00 2.43
4389 4798 4.534500 TCTCTGTCTCTAGTGACCTCTCTT 59.466 45.833 19.48 0.00 36.21 2.85
4400 4809 1.197430 ACCTCTCTTGTGCCTCCTGG 61.197 60.000 0.00 0.00 0.00 4.45
4402 4811 0.248843 CTCTCTTGTGCCTCCTGGTC 59.751 60.000 0.00 0.00 35.27 4.02
4428 4837 2.949447 ACCTTTTGCACCTCTCATTGT 58.051 42.857 0.00 0.00 0.00 2.71
4441 4850 1.112315 TCATTGTTTGTGGCCGCCTT 61.112 50.000 15.15 0.00 0.00 4.35
4444 4853 1.112113 TTGTTTGTGGCCGCCTTAAA 58.888 45.000 15.15 4.91 0.00 1.52
4446 4855 1.480954 TGTTTGTGGCCGCCTTAAAAA 59.519 42.857 15.15 4.09 0.00 1.94
4472 4881 5.572252 ACCAAGGTGGGTCGATAAAATTTA 58.428 37.500 0.00 0.00 43.37 1.40
4482 4891 8.192110 TGGGTCGATAAAATTTATAGCAAAACC 58.808 33.333 0.00 2.86 0.00 3.27
4506 4921 6.371389 CGAAGACAAAAGAAACATTACTCCC 58.629 40.000 0.00 0.00 0.00 4.30
4508 4923 6.635030 AGACAAAAGAAACATTACTCCCAC 57.365 37.500 0.00 0.00 0.00 4.61
4511 4926 5.008316 ACAAAAGAAACATTACTCCCACGTC 59.992 40.000 0.00 0.00 0.00 4.34
4524 4945 1.442769 CCACGTCAAAGGTCCAGATG 58.557 55.000 0.00 0.00 0.00 2.90
4531 4952 4.437390 CGTCAAAGGTCCAGATGTAAATGC 60.437 45.833 0.00 0.00 0.00 3.56
4544 4965 7.816031 CCAGATGTAAATGCTTTTTCATGAAGT 59.184 33.333 17.92 0.00 34.25 3.01
4552 4973 9.979578 AAATGCTTTTTCATGAAGTATGTTACA 57.020 25.926 8.41 1.59 38.01 2.41
4576 4997 9.778741 ACATACTTCTTGTCTTAGATTTGTCAA 57.221 29.630 0.00 0.00 0.00 3.18
4583 5004 9.645059 TCTTGTCTTAGATTTGTCAAGATAGTG 57.355 33.333 7.76 0.00 37.13 2.74
4584 5005 9.645059 CTTGTCTTAGATTTGTCAAGATAGTGA 57.355 33.333 4.21 0.00 35.69 3.41
4585 5006 8.988064 TGTCTTAGATTTGTCAAGATAGTGAC 57.012 34.615 0.00 0.00 46.74 3.67
4633 5054 9.144298 TCTTAGACAAGTAATACTAATGGGAGG 57.856 37.037 0.00 0.00 33.20 4.30
4634 5055 6.749036 AGACAAGTAATACTAATGGGAGGG 57.251 41.667 0.00 0.00 0.00 4.30
4635 5056 6.449956 AGACAAGTAATACTAATGGGAGGGA 58.550 40.000 0.00 0.00 0.00 4.20
4636 5057 6.555360 AGACAAGTAATACTAATGGGAGGGAG 59.445 42.308 0.00 0.00 0.00 4.30
4639 5060 7.289549 ACAAGTAATACTAATGGGAGGGAGTAC 59.710 40.741 0.00 0.00 0.00 2.73
4655 5076 7.982354 GGAGGGAGTACTATATTTGTATCATGC 59.018 40.741 0.00 0.00 0.00 4.06
4656 5077 8.435931 AGGGAGTACTATATTTGTATCATGCA 57.564 34.615 0.00 0.00 0.00 3.96
4657 5078 9.051259 AGGGAGTACTATATTTGTATCATGCAT 57.949 33.333 0.00 0.00 0.00 3.96
4670 5091 6.172630 TGTATCATGCATATACACATCACCC 58.827 40.000 17.66 0.06 35.44 4.61
4671 5092 4.980339 TCATGCATATACACATCACCCT 57.020 40.909 0.00 0.00 0.00 4.34
4674 5095 7.019656 TCATGCATATACACATCACCCTAAT 57.980 36.000 0.00 0.00 0.00 1.73
4676 5097 7.944000 TCATGCATATACACATCACCCTAATTT 59.056 33.333 0.00 0.00 0.00 1.82
4678 5099 6.489700 TGCATATACACATCACCCTAATTTGG 59.510 38.462 0.00 0.00 0.00 3.28
4679 5100 6.490040 GCATATACACATCACCCTAATTTGGT 59.510 38.462 5.19 0.00 36.21 3.67
4680 5101 7.014230 GCATATACACATCACCCTAATTTGGTT 59.986 37.037 5.19 0.00 32.46 3.67
4681 5102 6.773976 ATACACATCACCCTAATTTGGTTG 57.226 37.500 5.19 1.08 32.46 3.77
4683 5104 2.831526 ACATCACCCTAATTTGGTTGGC 59.168 45.455 3.80 0.00 32.46 4.52
4684 5105 2.990740 TCACCCTAATTTGGTTGGCT 57.009 45.000 3.80 0.00 32.46 4.75
4685 5106 3.252554 TCACCCTAATTTGGTTGGCTT 57.747 42.857 3.80 0.00 32.46 4.35
4686 5107 2.896685 TCACCCTAATTTGGTTGGCTTG 59.103 45.455 3.80 0.00 32.46 4.01
4687 5108 2.896685 CACCCTAATTTGGTTGGCTTGA 59.103 45.455 5.19 0.00 32.46 3.02
4688 5109 2.897326 ACCCTAATTTGGTTGGCTTGAC 59.103 45.455 5.19 0.00 29.75 3.18
4690 5111 2.094752 CCTAATTTGGTTGGCTTGACGG 60.095 50.000 0.00 0.00 0.00 4.79
4691 5112 1.698506 AATTTGGTTGGCTTGACGGA 58.301 45.000 0.00 0.00 0.00 4.69
4699 5122 2.060050 TGGCTTGACGGAAAAGGAAA 57.940 45.000 0.00 0.00 0.00 3.13
4705 5128 2.227194 TGACGGAAAAGGAAAAGGAGC 58.773 47.619 0.00 0.00 0.00 4.70
4734 5157 0.244994 AGTAGACGAGCAGCACAAGG 59.755 55.000 0.00 0.00 0.00 3.61
4739 5162 0.035317 ACGAGCAGCACAAGGATCAA 59.965 50.000 0.00 0.00 0.00 2.57
4766 5189 0.383231 CCAAGCCAAGAATCGCATCC 59.617 55.000 0.00 0.00 0.00 3.51
4767 5190 1.386533 CAAGCCAAGAATCGCATCCT 58.613 50.000 0.00 0.00 0.00 3.24
4768 5191 1.332997 CAAGCCAAGAATCGCATCCTC 59.667 52.381 0.00 0.00 0.00 3.71
4769 5192 0.835941 AGCCAAGAATCGCATCCTCT 59.164 50.000 0.00 0.00 0.00 3.69
4770 5193 1.202627 AGCCAAGAATCGCATCCTCTC 60.203 52.381 0.00 0.00 0.00 3.20
4771 5194 1.876322 CCAAGAATCGCATCCTCTCC 58.124 55.000 0.00 0.00 0.00 3.71
4772 5195 1.139654 CCAAGAATCGCATCCTCTCCA 59.860 52.381 0.00 0.00 0.00 3.86
4773 5196 2.208431 CAAGAATCGCATCCTCTCCAC 58.792 52.381 0.00 0.00 0.00 4.02
4774 5197 1.489481 AGAATCGCATCCTCTCCACA 58.511 50.000 0.00 0.00 0.00 4.17
4775 5198 1.137872 AGAATCGCATCCTCTCCACAC 59.862 52.381 0.00 0.00 0.00 3.82
4776 5199 0.904649 AATCGCATCCTCTCCACACA 59.095 50.000 0.00 0.00 0.00 3.72
4777 5200 1.126488 ATCGCATCCTCTCCACACAT 58.874 50.000 0.00 0.00 0.00 3.21
4778 5201 0.176449 TCGCATCCTCTCCACACATG 59.824 55.000 0.00 0.00 0.00 3.21
4779 5202 1.434622 CGCATCCTCTCCACACATGC 61.435 60.000 0.00 0.00 37.16 4.06
4780 5203 1.434622 GCATCCTCTCCACACATGCG 61.435 60.000 0.00 0.00 31.19 4.73
4781 5204 0.107993 CATCCTCTCCACACATGCGT 60.108 55.000 0.00 0.00 0.00 5.24
4823 5246 1.671379 GGTCCACGCTGTTTCCTCC 60.671 63.158 0.00 0.00 0.00 4.30
4837 5260 2.356667 CTCCTTTGGCCCCACCTC 59.643 66.667 0.00 0.00 40.22 3.85
4846 5269 2.973899 CCCCACCTCTCAGTGTCG 59.026 66.667 0.00 0.00 35.93 4.35
4847 5270 2.262915 CCCACCTCTCAGTGTCGC 59.737 66.667 0.00 0.00 35.93 5.19
4849 5272 2.645567 CACCTCTCAGTGTCGCGT 59.354 61.111 5.77 0.00 32.89 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 7.357951 TCCATTTTTAAAACCATCGAAATGC 57.642 32.000 0.00 0.00 34.71 3.56
48 49 8.055402 CGCATATTTCCATTTTTAAAACCATCG 58.945 33.333 0.00 0.00 0.00 3.84
51 52 7.872993 TGTCGCATATTTCCATTTTTAAAACCA 59.127 29.630 0.00 0.00 0.00 3.67
52 53 8.245701 TGTCGCATATTTCCATTTTTAAAACC 57.754 30.769 0.00 0.00 0.00 3.27
64 65 7.865707 AGAGTTTTATCATGTCGCATATTTCC 58.134 34.615 0.00 0.00 0.00 3.13
100 101 8.309163 TCATGATTTTTCTACCATTTTTGCAC 57.691 30.769 0.00 0.00 0.00 4.57
167 169 4.249661 AGGCTTTTCTTCGCAAAAACAAA 58.750 34.783 0.00 0.00 0.00 2.83
170 172 4.822107 GAAAGGCTTTTCTTCGCAAAAAC 58.178 39.130 14.66 0.00 39.66 2.43
281 291 5.438761 AAAGAACTCCCGTGAAAAATCTG 57.561 39.130 0.00 0.00 0.00 2.90
306 320 5.007682 TGGTGTACTGGAATAAAGCTTTCC 58.992 41.667 16.57 11.95 42.52 3.13
318 332 4.220724 ACTTGAACTACTGGTGTACTGGA 58.779 43.478 0.00 0.00 0.00 3.86
320 334 5.815740 ACAAACTTGAACTACTGGTGTACTG 59.184 40.000 0.00 0.00 0.00 2.74
326 340 4.850680 TCCAACAAACTTGAACTACTGGT 58.149 39.130 0.00 0.00 0.00 4.00
509 533 2.104967 TCGGATTTATCACCTGGTCGT 58.895 47.619 0.00 0.00 0.00 4.34
533 561 9.834628 TTGTATCGATTTTATCTTTTGAACACC 57.165 29.630 1.71 0.00 0.00 4.16
596 624 3.490933 GCCGTGATTCATGCTAGACAGTA 60.491 47.826 0.00 0.00 0.00 2.74
608 636 1.643868 GATTGCCACGCCGTGATTCA 61.644 55.000 20.57 10.56 35.23 2.57
662 690 1.657094 GTGGATTAACTACCGTGCACG 59.343 52.381 31.77 31.77 39.44 5.34
663 691 2.671396 CTGTGGATTAACTACCGTGCAC 59.329 50.000 6.82 6.82 34.11 4.57
664 692 2.300723 ACTGTGGATTAACTACCGTGCA 59.699 45.455 0.00 0.00 0.00 4.57
665 693 2.968675 ACTGTGGATTAACTACCGTGC 58.031 47.619 0.00 0.00 0.00 5.34
686 714 2.947652 CGGCATTCTTCATCAGTCCAAT 59.052 45.455 0.00 0.00 0.00 3.16
716 745 0.823356 GCCCCGGTACAATGATGCAT 60.823 55.000 0.00 0.00 0.00 3.96
740 769 4.615815 ATGCATCTCTCGCCGGCC 62.616 66.667 23.46 4.19 0.00 6.13
765 795 3.307906 AAGGCGGCTACCACGACA 61.308 61.111 13.71 0.00 43.13 4.35
769 799 2.125106 CTCCAAGGCGGCTACCAC 60.125 66.667 13.71 0.00 33.14 4.16
910 958 3.714487 AATAGGTGCCGCGGCCATT 62.714 57.895 44.42 31.96 41.09 3.16
911 959 3.714487 AAATAGGTGCCGCGGCCAT 62.714 57.895 44.42 33.53 41.09 4.40
912 960 2.538512 TAAAATAGGTGCCGCGGCCA 62.539 55.000 44.42 30.09 41.09 5.36
913 961 1.782028 CTAAAATAGGTGCCGCGGCC 61.782 60.000 44.42 33.85 41.09 6.13
914 962 0.812412 TCTAAAATAGGTGCCGCGGC 60.812 55.000 42.35 42.35 42.35 6.53
915 963 0.935196 GTCTAAAATAGGTGCCGCGG 59.065 55.000 24.05 24.05 0.00 6.46
916 964 0.575390 CGTCTAAAATAGGTGCCGCG 59.425 55.000 0.00 0.00 0.00 6.46
948 996 4.643387 GTGAGGTGCGGCTGGGTT 62.643 66.667 0.00 0.00 0.00 4.11
962 1010 3.569210 CAGGGGCTGTGGTGGTGA 61.569 66.667 0.00 0.00 0.00 4.02
1017 1079 2.750637 GAGGACAGAGCGACGGGA 60.751 66.667 0.00 0.00 0.00 5.14
1044 1109 0.104671 GAGACAGGCAGCAGAGGATC 59.895 60.000 0.00 0.00 0.00 3.36
1185 1256 1.736645 CCGCCAACGAACGATGACT 60.737 57.895 6.08 0.00 43.93 3.41
1230 1302 1.383456 GCCTCTGCAACACACACCAA 61.383 55.000 0.00 0.00 37.47 3.67
1355 1430 7.147880 GGCATAGGTAAGTAAGAAGAGAACAGA 60.148 40.741 0.00 0.00 0.00 3.41
1357 1432 6.405508 CGGCATAGGTAAGTAAGAAGAGAACA 60.406 42.308 0.00 0.00 0.00 3.18
1358 1433 5.978322 CGGCATAGGTAAGTAAGAAGAGAAC 59.022 44.000 0.00 0.00 0.00 3.01
1360 1435 4.583489 CCGGCATAGGTAAGTAAGAAGAGA 59.417 45.833 0.00 0.00 0.00 3.10
1361 1436 4.583489 TCCGGCATAGGTAAGTAAGAAGAG 59.417 45.833 0.00 0.00 0.00 2.85
1362 1437 4.539726 TCCGGCATAGGTAAGTAAGAAGA 58.460 43.478 0.00 0.00 0.00 2.87
1365 1440 2.626743 GCTCCGGCATAGGTAAGTAAGA 59.373 50.000 0.00 0.00 38.54 2.10
1412 1500 2.091541 TGGAAAGATGGAAATGACGGC 58.908 47.619 0.00 0.00 0.00 5.68
1427 1515 1.628340 ACGGACAGACATCCATGGAAA 59.372 47.619 20.67 0.00 38.87 3.13
1428 1516 1.207089 GACGGACAGACATCCATGGAA 59.793 52.381 20.67 1.96 38.87 3.53
1430 1518 0.528466 CGACGGACAGACATCCATGG 60.528 60.000 4.97 4.97 38.87 3.66
1431 1519 0.455815 TCGACGGACAGACATCCATG 59.544 55.000 0.00 0.00 38.87 3.66
1432 1520 0.741326 CTCGACGGACAGACATCCAT 59.259 55.000 0.00 0.00 38.87 3.41
1433 1521 1.934220 GCTCGACGGACAGACATCCA 61.934 60.000 0.00 0.00 38.87 3.41
1434 1522 1.226717 GCTCGACGGACAGACATCC 60.227 63.158 0.00 0.00 35.16 3.51
1469 1557 1.604378 CAGGAAGTTGCCGATCCCT 59.396 57.895 0.00 0.00 33.55 4.20
1509 1597 2.983592 GTTGCGGGGGTTGAGGTG 60.984 66.667 0.00 0.00 0.00 4.00
1577 1665 2.237143 TGCATGGAGGAGTAGGAGTTTG 59.763 50.000 0.00 0.00 0.00 2.93
1586 1674 3.491208 GCAAGATGCATGGAGGAGT 57.509 52.632 2.46 0.00 44.26 3.85
1596 1684 2.685388 GGGTTAGGAAGAAGCAAGATGC 59.315 50.000 0.00 0.00 45.46 3.91
1600 1688 2.347731 GTCGGGTTAGGAAGAAGCAAG 58.652 52.381 0.00 0.00 0.00 4.01
1603 1691 0.903236 AGGTCGGGTTAGGAAGAAGC 59.097 55.000 0.00 0.00 0.00 3.86
1613 1701 3.871248 GAAACGGCGAGGTCGGGTT 62.871 63.158 16.62 0.00 40.23 4.11
1617 1705 3.170585 GTCGAAACGGCGAGGTCG 61.171 66.667 16.62 18.68 41.49 4.79
1631 1719 3.003068 AGGTAATCAATCGGTCTACGTCG 59.997 47.826 0.00 0.00 44.69 5.12
1634 1722 4.042398 CACAGGTAATCAATCGGTCTACG 58.958 47.826 0.00 0.00 46.11 3.51
1636 1724 5.186215 TCAACACAGGTAATCAATCGGTCTA 59.814 40.000 0.00 0.00 0.00 2.59
1637 1725 4.020573 TCAACACAGGTAATCAATCGGTCT 60.021 41.667 0.00 0.00 0.00 3.85
1639 1727 4.280436 TCAACACAGGTAATCAATCGGT 57.720 40.909 0.00 0.00 0.00 4.69
1641 1729 4.496341 GCCATCAACACAGGTAATCAATCG 60.496 45.833 0.00 0.00 0.00 3.34
1642 1730 4.641989 AGCCATCAACACAGGTAATCAATC 59.358 41.667 0.00 0.00 0.00 2.67
1643 1731 4.400251 CAGCCATCAACACAGGTAATCAAT 59.600 41.667 0.00 0.00 0.00 2.57
1644 1732 3.758023 CAGCCATCAACACAGGTAATCAA 59.242 43.478 0.00 0.00 0.00 2.57
1645 1733 3.346315 CAGCCATCAACACAGGTAATCA 58.654 45.455 0.00 0.00 0.00 2.57
1646 1734 2.684881 CCAGCCATCAACACAGGTAATC 59.315 50.000 0.00 0.00 0.00 1.75
1650 1738 1.604593 GCCAGCCATCAACACAGGT 60.605 57.895 0.00 0.00 0.00 4.00
1964 2057 2.280186 GCGAAATCCTCCGGCGAT 60.280 61.111 9.30 0.00 0.00 4.58
2151 2479 2.356069 GCCATGTAAGCAAGAAGGTAGC 59.644 50.000 0.00 0.00 0.00 3.58
2219 2549 3.345808 GGTCAGAGTTTGCGCGCA 61.346 61.111 33.09 33.09 0.00 6.09
2245 2575 3.288308 CTGCTCCTTCACGGTCGCT 62.288 63.158 0.00 0.00 33.48 4.93
2296 2626 1.006102 AAGCAAGTCCGTCCACGAG 60.006 57.895 0.00 0.00 43.02 4.18
2315 2645 2.854777 CGCTCTTGGACTCGATAAACAG 59.145 50.000 0.00 0.00 0.00 3.16
2351 2681 9.209175 CACTAAGTTAGTTGAAAGCTAGTTCAT 57.791 33.333 13.00 0.00 37.36 2.57
2415 2766 2.107726 AGGTGTCCTACAAAGGGGAAAC 59.892 50.000 0.00 0.00 43.84 2.78
2456 2808 4.028490 GACACCGGGTCCATGCCA 62.028 66.667 6.32 0.00 40.83 4.92
2501 2853 0.111061 TTGTCTGGGCATTGCTCACT 59.889 50.000 7.23 0.00 32.27 3.41
2503 2855 1.179152 CATTGTCTGGGCATTGCTCA 58.821 50.000 11.44 11.44 36.30 4.26
2531 2883 3.118738 CCTCCTTGCGACTAAGGTATGTT 60.119 47.826 11.65 0.00 45.94 2.71
2554 2906 0.539438 GGTGTTGGGACCAGATGCAA 60.539 55.000 0.00 0.00 35.88 4.08
2594 2946 4.488126 TTTGAGCTTTTCCTTGATGACG 57.512 40.909 0.00 0.00 0.00 4.35
2669 3021 3.693085 GCTTCATGATGTCATTGACCAGT 59.307 43.478 14.05 0.61 33.61 4.00
2718 3070 0.892358 TTGACGGTCGGTGTAGAGCT 60.892 55.000 3.34 0.00 36.57 4.09
2723 3075 4.567971 ACAAATATTTGACGGTCGGTGTA 58.432 39.130 30.18 0.00 40.55 2.90
2725 3077 4.083749 TGAACAAATATTTGACGGTCGGTG 60.084 41.667 30.18 5.19 40.55 4.94
2770 3122 0.871722 CATCGTCCCTTTTGTCGCAA 59.128 50.000 0.00 0.00 0.00 4.85
2777 3129 6.488683 TCAATTAGTGAAACATCGTCCCTTTT 59.511 34.615 0.00 0.00 41.43 2.27
2956 3309 6.764877 ACTAACATTACGCCTAATGATTCG 57.235 37.500 18.60 9.77 41.31 3.34
2999 3358 5.710099 ACTTCATTACGACCATTGGATTTGT 59.290 36.000 10.37 0.40 0.00 2.83
3000 3359 6.194796 ACTTCATTACGACCATTGGATTTG 57.805 37.500 10.37 0.00 0.00 2.32
3001 3360 6.834168 AACTTCATTACGACCATTGGATTT 57.166 33.333 10.37 0.00 0.00 2.17
3002 3361 6.834168 AAACTTCATTACGACCATTGGATT 57.166 33.333 10.37 0.00 0.00 3.01
3003 3362 8.519799 AATAAACTTCATTACGACCATTGGAT 57.480 30.769 10.37 0.00 0.00 3.41
3004 3363 7.608376 TGAATAAACTTCATTACGACCATTGGA 59.392 33.333 10.37 0.00 0.00 3.53
3005 3364 7.757526 TGAATAAACTTCATTACGACCATTGG 58.242 34.615 0.00 0.00 0.00 3.16
3006 3365 9.225201 CATGAATAAACTTCATTACGACCATTG 57.775 33.333 0.00 0.00 37.06 2.82
3007 3366 8.405531 CCATGAATAAACTTCATTACGACCATT 58.594 33.333 0.00 0.00 37.06 3.16
3008 3367 7.013274 CCCATGAATAAACTTCATTACGACCAT 59.987 37.037 0.00 0.00 37.06 3.55
3009 3368 6.317642 CCCATGAATAAACTTCATTACGACCA 59.682 38.462 0.00 0.00 37.06 4.02
3010 3369 6.540914 TCCCATGAATAAACTTCATTACGACC 59.459 38.462 0.00 0.00 37.06 4.79
3011 3370 7.280205 ACTCCCATGAATAAACTTCATTACGAC 59.720 37.037 0.00 0.00 37.06 4.34
3012 3371 7.335627 ACTCCCATGAATAAACTTCATTACGA 58.664 34.615 0.00 0.00 37.06 3.43
3013 3372 7.553881 ACTCCCATGAATAAACTTCATTACG 57.446 36.000 0.00 0.00 37.06 3.18
3016 3375 9.699410 TCATTACTCCCATGAATAAACTTCATT 57.301 29.630 0.00 0.00 37.06 2.57
3145 3510 4.850680 TGGTTACAAGTTGGTCAGTTTCT 58.149 39.130 7.96 0.00 0.00 2.52
3172 3537 6.115450 AGATAAAATCCGGTCGTTTTTAGC 57.885 37.500 16.02 15.69 33.59 3.09
3198 3563 1.942657 CTCAACCATATGCTTCCCACG 59.057 52.381 0.00 0.00 0.00 4.94
3202 3567 2.648059 AGCACTCAACCATATGCTTCC 58.352 47.619 0.00 0.00 46.06 3.46
3244 3609 6.767902 TGCTAATCTGGTACCTTCATCAAATC 59.232 38.462 14.36 0.00 0.00 2.17
3277 3642 5.305585 AGAGCCGTTTCTTACTCAAAATGA 58.694 37.500 0.00 0.00 0.00 2.57
3382 3749 6.157820 TGGAAATATCTGGGTGTAGAATGTGA 59.842 38.462 0.00 0.00 0.00 3.58
3409 3776 5.603596 GCCCATTCATGAAATGCTATTCAA 58.396 37.500 13.09 0.00 46.21 2.69
3554 3923 4.024048 GGAGAAGCGTGACAAAGAATTGAA 60.024 41.667 0.00 0.00 38.94 2.69
3640 4010 1.268079 GGCAGGCTTGTGAAGTTCTTC 59.732 52.381 4.17 5.70 0.00 2.87
3747 4117 0.961753 GCTTACAAAGTGCCCAGCTT 59.038 50.000 0.00 0.00 0.00 3.74
3754 4124 2.286833 TGTTCACGAGCTTACAAAGTGC 59.713 45.455 0.00 0.00 33.28 4.40
3769 4139 3.072184 AGGAGGGATGCATCTATGTTCAC 59.928 47.826 25.28 6.71 0.00 3.18
3778 4148 0.257039 ACACCAAGGAGGGATGCATC 59.743 55.000 18.81 18.81 43.89 3.91
3806 4176 7.308770 CCAATATCAACTTCAGTTCAAGAGCAA 60.309 37.037 0.00 0.00 35.83 3.91
3881 4251 4.141413 TGGGTTATGCTACTGATCATGCTT 60.141 41.667 13.90 10.98 0.00 3.91
3925 4295 9.640963 AAGTACAATAAAGCTAGAGTTAGTGTG 57.359 33.333 20.31 9.18 38.54 3.82
3941 4311 5.941647 GCTACCCCACAAAGAAGTACAATAA 59.058 40.000 0.00 0.00 0.00 1.40
3952 4322 4.222124 ACAATAGAGCTACCCCACAAAG 57.778 45.455 0.00 0.00 0.00 2.77
3992 4365 3.881089 TGCACTGAATCATGATCACCATC 59.119 43.478 9.06 2.96 31.94 3.51
4013 4386 4.566360 GCAAATGTCGGATATTGGGTTTTG 59.434 41.667 0.48 0.00 0.00 2.44
4022 4395 6.299141 ACTCCAATTAGCAAATGTCGGATAT 58.701 36.000 0.00 0.00 0.00 1.63
4023 4396 5.680619 ACTCCAATTAGCAAATGTCGGATA 58.319 37.500 0.00 0.00 0.00 2.59
4031 4404 4.223477 ACATGCCAACTCCAATTAGCAAAT 59.777 37.500 0.00 0.00 29.94 2.32
4038 4411 3.196254 GGAATGACATGCCAACTCCAATT 59.804 43.478 7.68 0.00 0.00 2.32
4045 4418 2.450476 AGAAGGGAATGACATGCCAAC 58.550 47.619 14.81 4.93 32.31 3.77
4052 4425 3.588842 ACATCTCCAAGAAGGGAATGACA 59.411 43.478 0.00 0.00 36.27 3.58
4096 4484 3.562141 CGACCAAACCATGACAACACTAA 59.438 43.478 0.00 0.00 0.00 2.24
4127 4515 3.258372 AGAAAGGATGACACACGCTAAGA 59.742 43.478 0.00 0.00 0.00 2.10
4131 4519 2.563179 ACTAGAAAGGATGACACACGCT 59.437 45.455 0.00 0.00 0.00 5.07
4133 4521 7.596749 AAATTACTAGAAAGGATGACACACG 57.403 36.000 0.00 0.00 0.00 4.49
4151 4557 6.664515 TCGAGGATTGACACAACAAAATTAC 58.335 36.000 0.00 0.00 33.44 1.89
4166 4572 6.369059 AGCTATTCAAAACATCGAGGATTG 57.631 37.500 3.06 8.95 0.00 2.67
4190 4598 7.066284 GGCTCTCTGTAACAACACAATATCAAT 59.934 37.037 0.00 0.00 0.00 2.57
4198 4606 2.224281 CCAGGCTCTCTGTAACAACACA 60.224 50.000 0.00 0.00 41.83 3.72
4208 4616 1.895798 TCAGTTACACCAGGCTCTCTG 59.104 52.381 0.00 0.00 43.00 3.35
4217 4625 4.286032 ACCAAGAAGCTATCAGTTACACCA 59.714 41.667 0.00 0.00 0.00 4.17
4231 4639 7.751768 AGGAAGCATATTAATACCAAGAAGC 57.248 36.000 0.00 0.00 0.00 3.86
4308 4717 2.579207 TCACTCGGCGGAAATAAGAG 57.421 50.000 7.21 0.00 35.28 2.85
4312 4721 4.365723 GAGTAATTCACTCGGCGGAAATA 58.634 43.478 7.21 0.00 44.19 1.40
4313 4722 3.195661 GAGTAATTCACTCGGCGGAAAT 58.804 45.455 7.21 0.00 44.19 2.17
4332 4741 3.438087 AGCAACAAGGAATCAATGACGAG 59.562 43.478 0.00 0.00 0.00 4.18
4341 4750 3.956744 AGAAGGGTAGCAACAAGGAATC 58.043 45.455 0.00 0.00 0.00 2.52
4343 4752 3.751518 GAAGAAGGGTAGCAACAAGGAA 58.248 45.455 0.00 0.00 0.00 3.36
4344 4753 2.289444 CGAAGAAGGGTAGCAACAAGGA 60.289 50.000 0.00 0.00 0.00 3.36
4346 4755 2.737252 GACGAAGAAGGGTAGCAACAAG 59.263 50.000 0.00 0.00 0.00 3.16
4347 4756 2.367567 AGACGAAGAAGGGTAGCAACAA 59.632 45.455 0.00 0.00 0.00 2.83
4348 4757 1.968493 AGACGAAGAAGGGTAGCAACA 59.032 47.619 0.00 0.00 0.00 3.33
4370 4779 4.075682 CACAAGAGAGGTCACTAGAGACA 58.924 47.826 19.98 0.00 40.29 3.41
4372 4781 3.085533 GCACAAGAGAGGTCACTAGAGA 58.914 50.000 0.00 0.00 0.00 3.10
4376 4785 2.171840 GAGGCACAAGAGAGGTCACTA 58.828 52.381 0.00 0.00 0.00 2.74
4377 4786 0.972883 GAGGCACAAGAGAGGTCACT 59.027 55.000 0.00 0.00 0.00 3.41
4389 4798 0.472925 TAACCAGACCAGGAGGCACA 60.473 55.000 0.00 0.00 39.06 4.57
4400 4809 2.552743 GAGGTGCAAAAGGTAACCAGAC 59.447 50.000 0.00 0.00 35.01 3.51
4402 4811 2.814336 GAGAGGTGCAAAAGGTAACCAG 59.186 50.000 0.00 0.00 35.01 4.00
4428 4837 2.365617 TCATTTTTAAGGCGGCCACAAA 59.634 40.909 23.09 16.89 0.00 2.83
4472 4881 6.385649 TTCTTTTGTCTTCGGTTTTGCTAT 57.614 33.333 0.00 0.00 0.00 2.97
4482 4891 6.017440 TGGGAGTAATGTTTCTTTTGTCTTCG 60.017 38.462 0.00 0.00 0.00 3.79
4506 4921 2.169832 ACATCTGGACCTTTGACGTG 57.830 50.000 0.00 0.00 0.00 4.49
4508 4923 4.437390 GCATTTACATCTGGACCTTTGACG 60.437 45.833 0.00 0.00 0.00 4.35
4511 4926 5.649782 AAGCATTTACATCTGGACCTTTG 57.350 39.130 0.00 0.00 0.00 2.77
4557 4978 9.645059 CACTATCTTGACAAATCTAAGACAAGA 57.355 33.333 0.00 0.00 45.38 3.02
4559 4980 9.424319 GTCACTATCTTGACAAATCTAAGACAA 57.576 33.333 0.00 0.00 44.62 3.18
4560 4981 8.988064 GTCACTATCTTGACAAATCTAAGACA 57.012 34.615 0.00 0.00 44.62 3.41
4607 5028 9.144298 CCTCCCATTAGTATTACTTGTCTAAGA 57.856 37.037 0.85 0.00 37.36 2.10
4608 5029 8.368668 CCCTCCCATTAGTATTACTTGTCTAAG 58.631 40.741 0.85 0.00 39.86 2.18
4609 5030 8.069356 TCCCTCCCATTAGTATTACTTGTCTAA 58.931 37.037 0.85 0.00 0.00 2.10
4610 5031 7.598248 TCCCTCCCATTAGTATTACTTGTCTA 58.402 38.462 0.85 0.00 0.00 2.59
4611 5032 6.449956 TCCCTCCCATTAGTATTACTTGTCT 58.550 40.000 0.85 0.00 0.00 3.41
4612 5033 6.326843 ACTCCCTCCCATTAGTATTACTTGTC 59.673 42.308 0.85 0.00 0.00 3.18
4613 5034 6.210522 ACTCCCTCCCATTAGTATTACTTGT 58.789 40.000 0.85 0.00 0.00 3.16
4614 5035 6.749036 ACTCCCTCCCATTAGTATTACTTG 57.251 41.667 0.85 0.00 0.00 3.16
4615 5036 7.602868 AGTACTCCCTCCCATTAGTATTACTT 58.397 38.462 0.85 0.00 0.00 2.24
4616 5037 7.176909 AGTACTCCCTCCCATTAGTATTACT 57.823 40.000 1.30 1.30 0.00 2.24
4621 5042 9.543231 CAAATATAGTACTCCCTCCCATTAGTA 57.457 37.037 0.00 0.00 0.00 1.82
4622 5043 8.017251 ACAAATATAGTACTCCCTCCCATTAGT 58.983 37.037 0.00 0.00 0.00 2.24
4623 5044 8.437274 ACAAATATAGTACTCCCTCCCATTAG 57.563 38.462 0.00 0.00 0.00 1.73
4625 5046 8.990693 ATACAAATATAGTACTCCCTCCCATT 57.009 34.615 0.00 0.00 0.00 3.16
4626 5047 8.184249 TGATACAAATATAGTACTCCCTCCCAT 58.816 37.037 0.00 0.00 0.00 4.00
4627 5048 7.541074 TGATACAAATATAGTACTCCCTCCCA 58.459 38.462 0.00 0.00 0.00 4.37
4628 5049 8.478877 CATGATACAAATATAGTACTCCCTCCC 58.521 40.741 0.00 0.00 0.00 4.30
4629 5050 7.982354 GCATGATACAAATATAGTACTCCCTCC 59.018 40.741 0.00 0.00 0.00 4.30
4630 5051 8.531982 TGCATGATACAAATATAGTACTCCCTC 58.468 37.037 0.00 0.00 0.00 4.30
4631 5052 8.435931 TGCATGATACAAATATAGTACTCCCT 57.564 34.615 0.00 0.00 0.00 4.20
4655 5076 8.463930 AACCAAATTAGGGTGATGTGTATATG 57.536 34.615 2.70 0.00 39.01 1.78
4666 5087 2.896685 TCAAGCCAACCAAATTAGGGTG 59.103 45.455 2.70 0.00 46.21 4.61
4667 5088 2.897326 GTCAAGCCAACCAAATTAGGGT 59.103 45.455 0.00 0.00 41.41 4.34
4670 5091 2.817258 TCCGTCAAGCCAACCAAATTAG 59.183 45.455 0.00 0.00 0.00 1.73
4671 5092 2.865079 TCCGTCAAGCCAACCAAATTA 58.135 42.857 0.00 0.00 0.00 1.40
4674 5095 1.475403 TTTCCGTCAAGCCAACCAAA 58.525 45.000 0.00 0.00 0.00 3.28
4676 5097 1.028905 CTTTTCCGTCAAGCCAACCA 58.971 50.000 0.00 0.00 0.00 3.67
4678 5099 1.314730 TCCTTTTCCGTCAAGCCAAC 58.685 50.000 0.00 0.00 0.00 3.77
4679 5100 2.060050 TTCCTTTTCCGTCAAGCCAA 57.940 45.000 0.00 0.00 0.00 4.52
4680 5101 2.060050 TTTCCTTTTCCGTCAAGCCA 57.940 45.000 0.00 0.00 0.00 4.75
4681 5102 2.288213 CCTTTTCCTTTTCCGTCAAGCC 60.288 50.000 0.00 0.00 0.00 4.35
4683 5104 3.304726 GCTCCTTTTCCTTTTCCGTCAAG 60.305 47.826 0.00 0.00 0.00 3.02
4684 5105 2.621526 GCTCCTTTTCCTTTTCCGTCAA 59.378 45.455 0.00 0.00 0.00 3.18
4685 5106 2.227194 GCTCCTTTTCCTTTTCCGTCA 58.773 47.619 0.00 0.00 0.00 4.35
4686 5107 1.197036 CGCTCCTTTTCCTTTTCCGTC 59.803 52.381 0.00 0.00 0.00 4.79
4687 5108 1.235724 CGCTCCTTTTCCTTTTCCGT 58.764 50.000 0.00 0.00 0.00 4.69
4688 5109 0.521735 CCGCTCCTTTTCCTTTTCCG 59.478 55.000 0.00 0.00 0.00 4.30
4690 5111 1.540267 GTCCCGCTCCTTTTCCTTTTC 59.460 52.381 0.00 0.00 0.00 2.29
4691 5112 1.617322 GTCCCGCTCCTTTTCCTTTT 58.383 50.000 0.00 0.00 0.00 2.27
4699 5122 0.896940 TACTCAACGTCCCGCTCCTT 60.897 55.000 0.00 0.00 0.00 3.36
4705 5128 0.096628 CTCGTCTACTCAACGTCCCG 59.903 60.000 0.00 0.00 40.86 5.14
4721 5144 0.445436 GTTGATCCTTGTGCTGCTCG 59.555 55.000 0.00 0.00 0.00 5.03
4734 5157 1.092345 GGCTTGGCTCGAGGTTGATC 61.092 60.000 15.58 0.00 0.00 2.92
4739 5162 1.768684 TTCTTGGCTTGGCTCGAGGT 61.769 55.000 15.58 0.00 0.00 3.85
4774 5197 4.489771 GGGCCCTAGCACGCATGT 62.490 66.667 17.04 0.00 42.56 3.21
4780 5203 1.377333 GTCAAGTGGGCCCTAGCAC 60.377 63.158 25.70 13.19 45.43 4.40
4781 5204 2.602676 GGTCAAGTGGGCCCTAGCA 61.603 63.158 25.70 0.00 42.56 3.49
4782 5205 2.258748 GAGGTCAAGTGGGCCCTAGC 62.259 65.000 25.70 13.43 38.76 3.42
4783 5206 0.618968 AGAGGTCAAGTGGGCCCTAG 60.619 60.000 25.70 10.21 0.00 3.02
4784 5207 0.617820 GAGAGGTCAAGTGGGCCCTA 60.618 60.000 25.70 6.58 0.00 3.53
4785 5208 1.920835 GAGAGGTCAAGTGGGCCCT 60.921 63.158 25.70 0.00 0.00 5.19
4823 5246 1.001641 CTGAGAGGTGGGGCCAAAG 60.002 63.158 4.39 0.00 40.61 2.77
4837 5260 3.061674 GCGTTACGCGACACTGAG 58.938 61.111 15.43 0.00 44.55 3.35
4847 5270 0.027586 GCCAAATAGCAGGCGTTACG 59.972 55.000 0.00 0.00 41.70 3.18
4861 5284 1.173043 CGCCACCTTTATGAGCCAAA 58.827 50.000 0.00 0.00 0.00 3.28
4864 5287 1.823899 CCCGCCACCTTTATGAGCC 60.824 63.158 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.