Multiple sequence alignment - TraesCS7B01G272900

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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 TraesCS7B01G272900 chr7B 100.000 4412 0 0 1 4412 500733768 500729357 0.000000e+00 8148.0
1 TraesCS7B01G272900 chr7D 89.089 2218 110 45 8 2170 476690919 476688779 0.000000e+00 2634.0
2 TraesCS7B01G272900 chr7D 91.486 1750 93 29 2303 4035 476687955 476686245 0.000000e+00 2355.0
3 TraesCS7B01G272900 chr7D 93.960 149 4 2 4261 4408 476685876 476685732 2.070000e-53 220.0
4 TraesCS7B01G272900 chr7D 86.802 197 17 3 2242 2429 476688478 476688282 1.240000e-50 211.0
5 TraesCS7B01G272900 chr7D 89.076 119 9 3 2057 2175 476688601 476688487 1.280000e-30 145.0
6 TraesCS7B01G272900 chr7D 90.909 66 6 0 4049 4114 476686116 476686051 6.080000e-14 89.8
7 TraesCS7B01G272900 chr7A 85.959 1517 126 42 2535 4004 519132881 519134357 0.000000e+00 1541.0
8 TraesCS7B01G272900 chr7A 85.309 776 52 19 786 1509 519130859 519131624 0.000000e+00 745.0
9 TraesCS7B01G272900 chr7A 79.920 503 31 35 8 452 519130082 519130572 5.540000e-79 305.0
10 TraesCS7B01G272900 chr7A 87.500 64 6 2 4202 4264 519139758 519139820 6.120000e-09 73.1
11 TraesCS7B01G272900 chr3B 89.163 203 22 0 1061 1263 149453779 149453981 2.040000e-63 254.0
12 TraesCS7B01G272900 chr3D 88.177 203 24 0 1061 1263 98871950 98872152 4.410000e-60 243.0
13 TraesCS7B01G272900 chr3A 84.615 247 34 4 1019 1263 116518936 116519180 4.410000e-60 243.0
14 TraesCS7B01G272900 chr6B 85.366 205 30 0 1059 1263 642915740 642915944 3.460000e-51 213.0
15 TraesCS7B01G272900 chr6A 85.366 205 30 0 1059 1263 571795525 571795729 3.460000e-51 213.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G272900 chr7B 500729357 500733768 4411 True 8148.000000 8148 100.000000 1 4412 1 chr7B.!!$R1 4411
1 TraesCS7B01G272900 chr7D 476685732 476690919 5187 True 942.466667 2634 90.220333 8 4408 6 chr7D.!!$R1 4400
2 TraesCS7B01G272900 chr7A 519130082 519134357 4275 False 863.666667 1541 83.729333 8 4004 3 chr7A.!!$F2 3996

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
434 513 0.096454 GTGCGACGCCAAGGTTAATC 59.904 55.0 18.69 0.0 0.0 1.75 F
1445 1650 0.320374 TTCTGCTACTTGGGACGTGG 59.680 55.0 0.00 0.0 0.0 4.94 F
1486 1691 0.742990 TCGGTTGCTTCTTATGGCGG 60.743 55.0 0.00 0.0 0.0 6.13 F
2525 3717 0.878523 TTGGAAGCCGTTGTCTGTCG 60.879 55.0 0.00 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1486 1691 0.318762 AAGCAGAGTCCGTGACTTCC 59.681 55.0 7.80 0.00 43.53 3.46 R
2615 3807 0.178767 CCTCATTGGATCAGGACGCA 59.821 55.0 0.00 0.00 38.35 5.24 R
2715 3907 0.260230 AAGAGGATCCAGAGCTCGGA 59.740 55.0 23.38 23.38 36.84 4.55 R
4376 5816 0.034337 CAGTGCAATGCAAAGGCCTT 59.966 50.0 13.78 13.78 41.47 4.35 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
263 329 1.501741 GAAAGAAAGCGCGATGGCA 59.498 52.632 12.10 0.00 39.92 4.92
342 408 2.238847 GACCGTGCTGTGCTGGGATA 62.239 60.000 6.49 0.00 0.00 2.59
393 459 1.623542 AATACCGTGTCTGCCCCTCC 61.624 60.000 0.00 0.00 0.00 4.30
401 467 4.077184 CTGCCCCTCCACGCGTAA 62.077 66.667 13.44 1.59 0.00 3.18
434 513 0.096454 GTGCGACGCCAAGGTTAATC 59.904 55.000 18.69 0.00 0.00 1.75
459 538 1.210478 GCCAGATTTGGTCTCAGCCTA 59.790 52.381 3.90 0.00 46.80 3.93
485 564 3.882888 GGCCGAATGTCTTTTCCATATCA 59.117 43.478 0.00 0.00 0.00 2.15
552 635 7.469260 GTGTACATTGGAAATACACACATACC 58.531 38.462 0.00 0.00 45.23 2.73
575 658 3.837213 ACATTGGAATGCTCAAGAACG 57.163 42.857 0.00 0.00 40.04 3.95
598 682 2.494059 TGCTTGGACGGAAAAGAAGAG 58.506 47.619 0.00 0.00 0.00 2.85
627 745 9.439500 AATTAAATCACTTCCAAAACATCATGG 57.561 29.630 0.00 0.00 38.09 3.66
628 746 6.669125 AAATCACTTCCAAAACATCATGGA 57.331 33.333 0.00 0.00 43.84 3.41
629 747 6.862469 AATCACTTCCAAAACATCATGGAT 57.138 33.333 0.00 0.00 44.83 3.41
630 748 5.902613 TCACTTCCAAAACATCATGGATC 57.097 39.130 0.00 0.00 44.83 3.36
631 749 5.573219 TCACTTCCAAAACATCATGGATCT 58.427 37.500 0.00 0.00 44.83 2.75
632 750 5.649395 TCACTTCCAAAACATCATGGATCTC 59.351 40.000 0.00 0.00 44.83 2.75
633 751 5.651139 CACTTCCAAAACATCATGGATCTCT 59.349 40.000 0.00 0.00 44.83 3.10
634 752 5.884792 ACTTCCAAAACATCATGGATCTCTC 59.115 40.000 0.00 0.00 44.83 3.20
635 753 5.705397 TCCAAAACATCATGGATCTCTCT 57.295 39.130 0.00 0.00 40.74 3.10
636 754 5.678583 TCCAAAACATCATGGATCTCTCTC 58.321 41.667 0.00 0.00 40.74 3.20
641 759 5.329191 ACATCATGGATCTCTCTCTCTCT 57.671 43.478 0.00 0.00 0.00 3.10
648 766 3.636764 GGATCTCTCTCTCTCTTTGACCC 59.363 52.174 0.00 0.00 0.00 4.46
663 781 2.253610 TGACCCAACCGTACAGAATCT 58.746 47.619 0.00 0.00 0.00 2.40
719 870 0.544595 ACGGGAAGGTGGTAAGAGCT 60.545 55.000 0.00 0.00 0.00 4.09
797 951 1.740296 GCCGAGCGTTTAAGCCAGA 60.740 57.895 0.00 0.00 38.01 3.86
846 1000 1.661463 TCAGACTGCCAATTCCTCCT 58.339 50.000 0.00 0.00 0.00 3.69
847 1001 1.988107 TCAGACTGCCAATTCCTCCTT 59.012 47.619 0.00 0.00 0.00 3.36
848 1002 2.026822 TCAGACTGCCAATTCCTCCTTC 60.027 50.000 0.00 0.00 0.00 3.46
849 1003 1.283321 AGACTGCCAATTCCTCCTTCC 59.717 52.381 0.00 0.00 0.00 3.46
856 1010 1.139853 CAATTCCTCCTTCCTCCTCCG 59.860 57.143 0.00 0.00 0.00 4.63
884 1038 5.771165 TCCTCCCCACAAATACTAAACAAAC 59.229 40.000 0.00 0.00 0.00 2.93
890 1044 5.221342 CCACAAATACTAAACAAACCAGCCA 60.221 40.000 0.00 0.00 0.00 4.75
891 1045 5.920273 CACAAATACTAAACAAACCAGCCAG 59.080 40.000 0.00 0.00 0.00 4.85
916 1070 2.159028 TCGAGCGAGAGATTGAGAGAGA 60.159 50.000 0.00 0.00 34.41 3.10
917 1071 2.221749 CGAGCGAGAGATTGAGAGAGAG 59.778 54.545 0.00 0.00 30.80 3.20
1280 1447 3.382083 GGTAACCCATCCAACCAATCT 57.618 47.619 0.00 0.00 32.04 2.40
1282 1449 3.447229 GGTAACCCATCCAACCAATCTTG 59.553 47.826 0.00 0.00 32.04 3.02
1348 1538 1.469940 CCGATATATCTGCGAGGCCAC 60.470 57.143 5.01 0.00 0.00 5.01
1365 1555 2.126071 CGTAGCACCTGACACCCG 60.126 66.667 0.00 0.00 0.00 5.28
1366 1556 2.632544 CGTAGCACCTGACACCCGA 61.633 63.158 0.00 0.00 0.00 5.14
1367 1557 1.215647 GTAGCACCTGACACCCGAG 59.784 63.158 0.00 0.00 0.00 4.63
1369 1559 2.435120 TAGCACCTGACACCCGAGGA 62.435 60.000 0.00 0.00 33.16 3.71
1424 1629 2.802816 GCTCGTGTGTTTGATCTGACTT 59.197 45.455 0.00 0.00 0.00 3.01
1445 1650 0.320374 TTCTGCTACTTGGGACGTGG 59.680 55.000 0.00 0.00 0.00 4.94
1452 1657 3.901797 CTTGGGACGTGGGTGCTCC 62.902 68.421 0.00 0.00 34.50 4.70
1457 1662 2.280592 ACGTGGGTGCTCCGTTTC 60.281 61.111 0.00 0.00 38.76 2.78
1474 1679 0.881118 TTCTGCTTGGATTCGGTTGC 59.119 50.000 0.00 0.00 0.00 4.17
1479 1684 1.541588 GCTTGGATTCGGTTGCTTCTT 59.458 47.619 0.00 0.00 0.00 2.52
1480 1685 2.747446 GCTTGGATTCGGTTGCTTCTTA 59.253 45.455 0.00 0.00 0.00 2.10
1484 1689 2.033424 GGATTCGGTTGCTTCTTATGGC 59.967 50.000 0.00 0.00 0.00 4.40
1485 1690 1.083489 TTCGGTTGCTTCTTATGGCG 58.917 50.000 0.00 0.00 0.00 5.69
1486 1691 0.742990 TCGGTTGCTTCTTATGGCGG 60.743 55.000 0.00 0.00 0.00 6.13
1494 1699 2.280628 CTTCTTATGGCGGGAAGTCAC 58.719 52.381 0.00 0.00 37.24 3.67
1498 1703 1.952102 TATGGCGGGAAGTCACGGAC 61.952 60.000 4.94 0.00 44.19 4.79
1539 1744 1.857837 CGTGGCGATTTTGTTGCTTTT 59.142 42.857 0.00 0.00 37.39 2.27
1540 1745 3.046390 CGTGGCGATTTTGTTGCTTTTA 58.954 40.909 0.00 0.00 37.39 1.52
1541 1746 3.672867 CGTGGCGATTTTGTTGCTTTTAT 59.327 39.130 0.00 0.00 37.39 1.40
1593 1798 3.706698 GATGCGCTGTACTCTACATCAA 58.293 45.455 9.73 0.00 38.15 2.57
1598 1803 4.733815 GCGCTGTACTCTACATCAAAGCTA 60.734 45.833 0.00 0.00 38.15 3.32
1621 1826 4.104383 TGGTTCTGGAGCAATTTCTCTT 57.896 40.909 5.08 0.00 33.70 2.85
1624 1829 5.221303 TGGTTCTGGAGCAATTTCTCTTTTG 60.221 40.000 5.08 0.00 33.70 2.44
1673 1880 3.378512 TCTCTAGGAATGCTGTGGTGAT 58.621 45.455 0.00 0.00 0.00 3.06
1678 1885 4.525912 AGGAATGCTGTGGTGATTTTTC 57.474 40.909 0.00 0.00 0.00 2.29
1684 1891 3.243501 TGCTGTGGTGATTTTTCTTGCTC 60.244 43.478 0.00 0.00 0.00 4.26
1746 1953 3.575805 TCTCCTTTGCTTTTGGTTGGAT 58.424 40.909 0.00 0.00 0.00 3.41
1747 1954 3.966665 TCTCCTTTGCTTTTGGTTGGATT 59.033 39.130 0.00 0.00 0.00 3.01
1748 1955 4.408596 TCTCCTTTGCTTTTGGTTGGATTT 59.591 37.500 0.00 0.00 0.00 2.17
1774 1981 8.785329 TTTTTCTTGTTTGCCTTTAGTTGAAT 57.215 26.923 0.00 0.00 0.00 2.57
1834 2057 3.115554 GGCTGTTTTTGTGTCATGTCAC 58.884 45.455 15.09 15.09 38.63 3.67
1953 2186 1.140052 TCGAACTGTTTGCTCCTTGGA 59.860 47.619 2.78 0.00 0.00 3.53
2004 2239 1.128809 TCGGTTGCCAAGTAAGGGGA 61.129 55.000 0.00 0.00 0.00 4.81
2014 2249 1.305886 AGTAAGGGGAAATGGGGTCC 58.694 55.000 0.00 0.00 0.00 4.46
2175 2897 4.749099 GGTGCAGAAAATATTGTGTTTGCA 59.251 37.500 7.68 7.68 37.91 4.08
2195 2917 3.244976 CACGGAACATTTCAATTGCCTC 58.755 45.455 0.00 0.00 0.00 4.70
2198 2920 4.156008 ACGGAACATTTCAATTGCCTCTAC 59.844 41.667 0.00 0.00 0.00 2.59
2199 2921 4.396166 CGGAACATTTCAATTGCCTCTACT 59.604 41.667 0.00 0.00 0.00 2.57
2201 2923 6.095377 GGAACATTTCAATTGCCTCTACTTG 58.905 40.000 0.00 0.00 0.00 3.16
2202 2924 5.649782 ACATTTCAATTGCCTCTACTTGG 57.350 39.130 0.00 0.00 0.00 3.61
2203 2925 5.324409 ACATTTCAATTGCCTCTACTTGGA 58.676 37.500 0.00 0.00 0.00 3.53
2204 2926 5.954150 ACATTTCAATTGCCTCTACTTGGAT 59.046 36.000 0.00 0.00 0.00 3.41
2205 2927 7.118723 ACATTTCAATTGCCTCTACTTGGATA 58.881 34.615 0.00 0.00 0.00 2.59
2206 2928 7.615365 ACATTTCAATTGCCTCTACTTGGATAA 59.385 33.333 0.00 0.00 0.00 1.75
2207 2929 7.630242 TTTCAATTGCCTCTACTTGGATAAG 57.370 36.000 0.00 0.00 39.86 1.73
2209 2931 7.432148 TCAATTGCCTCTACTTGGATAAGTA 57.568 36.000 0.00 0.00 45.07 2.24
2210 2932 7.272978 TCAATTGCCTCTACTTGGATAAGTAC 58.727 38.462 0.00 0.00 45.07 2.73
2211 2933 5.609533 TTGCCTCTACTTGGATAAGTACC 57.390 43.478 0.00 0.00 45.07 3.34
2212 2934 4.880164 TGCCTCTACTTGGATAAGTACCT 58.120 43.478 0.00 0.00 45.07 3.08
2213 2935 5.278061 TGCCTCTACTTGGATAAGTACCTT 58.722 41.667 0.00 0.00 45.07 3.50
2214 2936 5.724854 TGCCTCTACTTGGATAAGTACCTTT 59.275 40.000 0.00 0.00 45.07 3.11
2215 2937 6.214819 TGCCTCTACTTGGATAAGTACCTTTT 59.785 38.462 0.00 0.00 45.07 2.27
2216 2938 7.110810 GCCTCTACTTGGATAAGTACCTTTTT 58.889 38.462 0.00 0.00 45.07 1.94
2270 2992 9.337396 TCACATAAGCTTTTTCTCAAGAACTTA 57.663 29.630 3.20 0.00 33.13 2.24
2360 3549 4.555262 TGGAAATCGCCACATTTCTTTTC 58.445 39.130 7.10 0.00 41.00 2.29
2400 3592 6.138761 GCTGATGCTTCAATTATTTCGGTAG 58.861 40.000 3.65 0.00 36.03 3.18
2411 3603 8.617809 TCAATTATTTCGGTAGATTTTAGTGGC 58.382 33.333 0.00 0.00 0.00 5.01
2514 3706 6.524101 TGGTCAATTTTATAGTTGGAAGCC 57.476 37.500 0.00 0.00 0.00 4.35
2525 3717 0.878523 TTGGAAGCCGTTGTCTGTCG 60.879 55.000 0.00 0.00 0.00 4.35
2547 3739 3.193267 GCACCTACATTTCCTTTGCATGA 59.807 43.478 0.00 0.00 0.00 3.07
2598 3790 5.630121 TGTTTGTCTGTATTTCAGGGATGT 58.370 37.500 0.00 0.00 43.76 3.06
2601 3793 7.390440 TGTTTGTCTGTATTTCAGGGATGTAAG 59.610 37.037 0.00 0.00 43.76 2.34
2615 3807 1.729586 TGTAAGCCTCCTCCACAAGT 58.270 50.000 0.00 0.00 0.00 3.16
2664 3856 2.659428 GCAAGCCCCTGTTCTTCATAT 58.341 47.619 0.00 0.00 0.00 1.78
2715 3907 2.294078 CCCTGCGTCCTCCTCCTTT 61.294 63.158 0.00 0.00 0.00 3.11
2799 3991 4.073201 GGAAGCTCCCTCATCCCA 57.927 61.111 0.00 0.00 0.00 4.37
2805 3997 1.759881 CTCCCTCATCCCATGGCTC 59.240 63.158 6.09 0.00 0.00 4.70
2814 4006 1.075601 TCCCATGGCTCAAGAACCTT 58.924 50.000 6.09 0.00 0.00 3.50
2817 4009 2.556114 CCCATGGCTCAAGAACCTTTCT 60.556 50.000 6.09 0.00 43.15 2.52
2826 4018 2.552743 CAAGAACCTTTCTTCGAACCCC 59.447 50.000 0.00 0.00 46.62 4.95
3123 4315 4.396790 ACGTACAACCTTGTTTCACACAAT 59.603 37.500 0.00 0.00 44.72 2.71
3126 4318 4.023291 ACAACCTTGTTTCACACAATCCT 58.977 39.130 0.00 0.00 44.72 3.24
3207 4399 2.427320 CCGGTGATGGGCGATCAT 59.573 61.111 15.38 0.00 43.20 2.45
3246 4438 2.502947 TGTCCAGATGGAGATGGTTGAG 59.497 50.000 0.65 0.00 46.49 3.02
3252 4444 2.308722 GGAGATGGTTGAGGGGGCA 61.309 63.158 0.00 0.00 0.00 5.36
3264 4456 1.758122 GGGGGCAGCGGATGATTTT 60.758 57.895 0.00 0.00 0.00 1.82
3270 4462 1.404583 GCAGCGGATGATTTTGCCTTT 60.405 47.619 0.00 0.00 0.00 3.11
3303 4495 2.807622 GGCAACAATGGATCGCCC 59.192 61.111 0.00 0.00 36.73 6.13
3415 4607 2.507471 GGAGAACCACCCTTCTGATGAT 59.493 50.000 0.00 0.00 35.97 2.45
3416 4608 3.539604 GAGAACCACCCTTCTGATGATG 58.460 50.000 0.00 0.00 30.21 3.07
3417 4609 3.184628 AGAACCACCCTTCTGATGATGA 58.815 45.455 0.00 0.00 0.00 2.92
3420 4612 3.117745 ACCACCCTTCTGATGATGATGA 58.882 45.455 0.00 0.00 0.00 2.92
3423 4615 4.202430 CCACCCTTCTGATGATGATGATGA 60.202 45.833 0.00 0.00 0.00 2.92
3426 4618 5.309806 ACCCTTCTGATGATGATGATGATGA 59.690 40.000 0.00 0.00 0.00 2.92
3458 4654 0.605589 CTGTCTCTTCTTCGCCTGGT 59.394 55.000 0.00 0.00 0.00 4.00
3459 4655 0.318441 TGTCTCTTCTTCGCCTGGTG 59.682 55.000 0.00 0.00 0.00 4.17
3460 4656 0.390472 GTCTCTTCTTCGCCTGGTGG 60.390 60.000 7.51 0.00 0.00 4.61
3471 4667 1.474330 GCCTGGTGGGTTTATCCTTG 58.526 55.000 0.00 0.00 37.43 3.61
3479 4675 6.655930 TGGTGGGTTTATCCTTGATACTTAC 58.344 40.000 0.00 0.00 36.25 2.34
3482 4678 7.282450 GGTGGGTTTATCCTTGATACTTACTTG 59.718 40.741 0.00 0.00 36.25 3.16
3483 4679 7.282450 GTGGGTTTATCCTTGATACTTACTTGG 59.718 40.741 0.00 0.00 36.25 3.61
3487 4683 7.504926 TTATCCTTGATACTTACTTGGGTGT 57.495 36.000 0.00 0.00 0.00 4.16
3490 4714 3.880047 TGATACTTACTTGGGTGTCGG 57.120 47.619 0.00 0.00 0.00 4.79
3519 4743 3.188159 TCTACAAGCTCGGTGTTTGTT 57.812 42.857 15.53 3.36 45.62 2.83
3520 4744 3.537580 TCTACAAGCTCGGTGTTTGTTT 58.462 40.909 15.53 0.00 45.62 2.83
3521 4745 2.559998 ACAAGCTCGGTGTTTGTTTG 57.440 45.000 6.48 0.00 45.62 2.93
3522 4746 1.816224 ACAAGCTCGGTGTTTGTTTGT 59.184 42.857 6.48 0.00 45.62 2.83
3748 4976 2.026356 TGAAGAAATGGAATGGCGGAGA 60.026 45.455 0.00 0.00 0.00 3.71
3749 4977 3.217626 GAAGAAATGGAATGGCGGAGAT 58.782 45.455 0.00 0.00 0.00 2.75
3754 4982 2.260844 TGGAATGGCGGAGATCATTC 57.739 50.000 7.32 7.32 43.54 2.67
3765 4994 4.793028 GCGGAGATCATTCGTCATCAGTAA 60.793 45.833 0.00 0.00 0.00 2.24
3813 5042 3.382546 GGCCATTTATCATGTGCTCTTGT 59.617 43.478 0.00 0.00 0.00 3.16
3821 5050 5.847111 ATCATGTGCTCTTGTAATGCAAT 57.153 34.783 0.00 0.00 38.50 3.56
3822 5051 4.989044 TCATGTGCTCTTGTAATGCAATG 58.011 39.130 0.00 0.00 38.50 2.82
3823 5052 3.220507 TGTGCTCTTGTAATGCAATGC 57.779 42.857 0.00 0.00 38.50 3.56
3824 5053 2.557490 TGTGCTCTTGTAATGCAATGCA 59.443 40.909 11.44 11.44 44.86 3.96
3825 5054 3.005578 TGTGCTCTTGTAATGCAATGCAA 59.994 39.130 13.45 5.15 43.62 4.08
3826 5055 3.989167 GTGCTCTTGTAATGCAATGCAAA 59.011 39.130 13.45 0.27 43.62 3.68
3827 5056 3.989167 TGCTCTTGTAATGCAATGCAAAC 59.011 39.130 13.45 14.20 43.62 2.93
3828 5057 3.989167 GCTCTTGTAATGCAATGCAAACA 59.011 39.130 13.45 16.74 43.62 2.83
3833 5062 4.691175 TGTAATGCAATGCAAACACAAGT 58.309 34.783 13.45 0.00 43.62 3.16
3897 5138 1.209127 GGGTGTGCGTTGTATGTGC 59.791 57.895 0.00 0.00 0.00 4.57
3923 5169 6.015519 TGGACCGTTCATTCATTGATTCTTTT 60.016 34.615 0.00 0.00 33.34 2.27
3940 5186 6.463995 TTCTTTTGTGTCTTTGCTGGTTAT 57.536 33.333 0.00 0.00 0.00 1.89
3941 5187 6.463995 TCTTTTGTGTCTTTGCTGGTTATT 57.536 33.333 0.00 0.00 0.00 1.40
3942 5188 6.272318 TCTTTTGTGTCTTTGCTGGTTATTG 58.728 36.000 0.00 0.00 0.00 1.90
3943 5189 4.582701 TTGTGTCTTTGCTGGTTATTGG 57.417 40.909 0.00 0.00 0.00 3.16
3944 5190 3.561143 TGTGTCTTTGCTGGTTATTGGT 58.439 40.909 0.00 0.00 0.00 3.67
3945 5191 3.957497 TGTGTCTTTGCTGGTTATTGGTT 59.043 39.130 0.00 0.00 0.00 3.67
3946 5192 4.202101 TGTGTCTTTGCTGGTTATTGGTTG 60.202 41.667 0.00 0.00 0.00 3.77
3968 5216 8.635328 GGTTGGAGTTGTTAGAAATTCCTTTTA 58.365 33.333 0.00 0.00 36.98 1.52
3969 5217 9.459640 GTTGGAGTTGTTAGAAATTCCTTTTAC 57.540 33.333 0.00 0.00 36.98 2.01
3990 5238 5.096443 ACTCATCTTCTTGTTGGATCCTC 57.904 43.478 14.23 6.93 0.00 3.71
4000 5248 1.480954 GTTGGATCCTCTCAGCGGTAA 59.519 52.381 14.23 0.00 0.00 2.85
4004 5252 1.751924 GATCCTCTCAGCGGTAACTGT 59.248 52.381 0.00 0.00 38.84 3.55
4005 5253 1.629043 TCCTCTCAGCGGTAACTGTT 58.371 50.000 0.00 0.00 38.84 3.16
4006 5254 1.272490 TCCTCTCAGCGGTAACTGTTG 59.728 52.381 2.69 0.00 38.84 3.33
4007 5255 1.673033 CCTCTCAGCGGTAACTGTTGG 60.673 57.143 2.69 0.00 38.84 3.77
4010 5258 0.882927 TCAGCGGTAACTGTTGGTGC 60.883 55.000 2.69 4.12 38.84 5.01
4011 5259 1.147376 AGCGGTAACTGTTGGTGCA 59.853 52.632 2.69 0.00 0.00 4.57
4015 5265 2.226912 GCGGTAACTGTTGGTGCAAATA 59.773 45.455 2.69 0.00 0.00 1.40
4017 5267 3.500680 CGGTAACTGTTGGTGCAAATAGT 59.499 43.478 2.69 0.00 0.00 2.12
4035 5285 6.500684 AATAGTTTTACCAGTGTGCTGATG 57.499 37.500 0.00 0.00 45.28 3.07
4036 5286 2.554032 AGTTTTACCAGTGTGCTGATGC 59.446 45.455 0.00 0.00 45.28 3.91
4037 5287 1.155889 TTTACCAGTGTGCTGATGCG 58.844 50.000 0.00 0.00 45.28 4.73
4038 5288 0.320050 TTACCAGTGTGCTGATGCGA 59.680 50.000 0.00 0.00 45.28 5.10
4039 5289 0.320050 TACCAGTGTGCTGATGCGAA 59.680 50.000 0.00 0.00 45.28 4.70
4042 5292 0.952497 CAGTGTGCTGATGCGAAGGT 60.952 55.000 0.00 0.00 45.28 3.50
4043 5293 0.952497 AGTGTGCTGATGCGAAGGTG 60.952 55.000 0.00 0.00 43.34 4.00
4044 5294 0.950555 GTGTGCTGATGCGAAGGTGA 60.951 55.000 0.00 0.00 43.34 4.02
4045 5295 0.671472 TGTGCTGATGCGAAGGTGAG 60.671 55.000 0.00 0.00 43.34 3.51
4046 5296 0.671781 GTGCTGATGCGAAGGTGAGT 60.672 55.000 0.00 0.00 43.34 3.41
4047 5297 0.035317 TGCTGATGCGAAGGTGAGTT 59.965 50.000 0.00 0.00 43.34 3.01
4069 5434 3.074390 TCCACAAGATGATGTTTCCAGGT 59.926 43.478 0.00 0.00 0.00 4.00
4070 5435 3.192001 CCACAAGATGATGTTTCCAGGTG 59.808 47.826 0.00 0.00 0.00 4.00
4075 5440 0.038166 TGATGTTTCCAGGTGGAGGC 59.962 55.000 0.00 0.00 46.36 4.70
4130 5513 5.648330 AAACTAGTGTCTTCCTTTCCCTT 57.352 39.130 0.00 0.00 0.00 3.95
4131 5514 4.625607 ACTAGTGTCTTCCTTTCCCTTG 57.374 45.455 0.00 0.00 0.00 3.61
4132 5515 3.974642 ACTAGTGTCTTCCTTTCCCTTGT 59.025 43.478 0.00 0.00 0.00 3.16
4133 5516 3.953542 AGTGTCTTCCTTTCCCTTGTT 57.046 42.857 0.00 0.00 0.00 2.83
4134 5517 3.555966 AGTGTCTTCCTTTCCCTTGTTG 58.444 45.455 0.00 0.00 0.00 3.33
4135 5518 2.034685 GTGTCTTCCTTTCCCTTGTTGC 59.965 50.000 0.00 0.00 0.00 4.17
4136 5519 2.306847 GTCTTCCTTTCCCTTGTTGCA 58.693 47.619 0.00 0.00 0.00 4.08
4137 5520 2.294512 GTCTTCCTTTCCCTTGTTGCAG 59.705 50.000 0.00 0.00 0.00 4.41
4138 5521 2.091885 TCTTCCTTTCCCTTGTTGCAGT 60.092 45.455 0.00 0.00 0.00 4.40
4139 5522 1.981256 TCCTTTCCCTTGTTGCAGTC 58.019 50.000 0.00 0.00 0.00 3.51
4140 5523 0.961753 CCTTTCCCTTGTTGCAGTCC 59.038 55.000 0.00 0.00 0.00 3.85
4141 5524 1.691196 CTTTCCCTTGTTGCAGTCCA 58.309 50.000 0.00 0.00 0.00 4.02
4142 5525 2.031120 CTTTCCCTTGTTGCAGTCCAA 58.969 47.619 0.00 0.00 0.00 3.53
4143 5526 1.691196 TTCCCTTGTTGCAGTCCAAG 58.309 50.000 13.11 13.11 38.21 3.61
4144 5527 0.550914 TCCCTTGTTGCAGTCCAAGT 59.449 50.000 16.70 0.00 37.05 3.16
4145 5528 1.064017 TCCCTTGTTGCAGTCCAAGTT 60.064 47.619 16.70 0.00 37.05 2.66
4146 5529 1.756538 CCCTTGTTGCAGTCCAAGTTT 59.243 47.619 16.70 0.00 37.05 2.66
4147 5530 2.955660 CCCTTGTTGCAGTCCAAGTTTA 59.044 45.455 16.70 0.00 37.05 2.01
4148 5531 3.004734 CCCTTGTTGCAGTCCAAGTTTAG 59.995 47.826 16.70 6.19 37.05 1.85
4149 5532 3.632145 CCTTGTTGCAGTCCAAGTTTAGT 59.368 43.478 16.70 0.00 37.05 2.24
4150 5533 4.097892 CCTTGTTGCAGTCCAAGTTTAGTT 59.902 41.667 16.70 0.00 37.05 2.24
4151 5534 4.630894 TGTTGCAGTCCAAGTTTAGTTG 57.369 40.909 0.00 0.00 33.21 3.16
4152 5535 4.265893 TGTTGCAGTCCAAGTTTAGTTGA 58.734 39.130 0.00 0.00 33.21 3.18
4153 5536 4.702612 TGTTGCAGTCCAAGTTTAGTTGAA 59.297 37.500 0.00 0.00 33.21 2.69
4154 5537 5.359576 TGTTGCAGTCCAAGTTTAGTTGAAT 59.640 36.000 0.00 0.00 33.21 2.57
4155 5538 6.127479 TGTTGCAGTCCAAGTTTAGTTGAATT 60.127 34.615 0.00 0.00 33.21 2.17
4156 5539 6.463995 TGCAGTCCAAGTTTAGTTGAATTT 57.536 33.333 0.00 0.00 0.00 1.82
4157 5540 6.503524 TGCAGTCCAAGTTTAGTTGAATTTC 58.496 36.000 0.00 0.00 0.00 2.17
4158 5541 5.920840 GCAGTCCAAGTTTAGTTGAATTTCC 59.079 40.000 0.00 0.00 0.00 3.13
4159 5542 6.142817 CAGTCCAAGTTTAGTTGAATTTCCG 58.857 40.000 0.00 0.00 0.00 4.30
4160 5543 5.240844 AGTCCAAGTTTAGTTGAATTTCCGG 59.759 40.000 0.00 0.00 0.00 5.14
4161 5544 5.239963 GTCCAAGTTTAGTTGAATTTCCGGA 59.760 40.000 0.00 0.00 0.00 5.14
4162 5545 5.239963 TCCAAGTTTAGTTGAATTTCCGGAC 59.760 40.000 1.83 0.00 0.00 4.79
4163 5546 5.009210 CCAAGTTTAGTTGAATTTCCGGACA 59.991 40.000 1.83 0.00 0.00 4.02
4164 5547 6.460399 CCAAGTTTAGTTGAATTTCCGGACAA 60.460 38.462 1.83 1.49 0.00 3.18
4165 5548 6.313744 AGTTTAGTTGAATTTCCGGACAAG 57.686 37.500 1.83 0.00 0.00 3.16
4166 5549 6.059484 AGTTTAGTTGAATTTCCGGACAAGA 58.941 36.000 1.83 0.00 0.00 3.02
4167 5550 6.544564 AGTTTAGTTGAATTTCCGGACAAGAA 59.455 34.615 1.83 0.00 0.00 2.52
4168 5551 6.945938 TTAGTTGAATTTCCGGACAAGAAA 57.054 33.333 1.83 0.00 37.61 2.52
4169 5552 7.519032 TTAGTTGAATTTCCGGACAAGAAAT 57.481 32.000 1.83 0.00 43.95 2.17
4175 5558 2.418368 TCCGGACAAGAAATCCATGG 57.582 50.000 4.97 4.97 35.83 3.66
4202 5585 4.179579 GCTGCCGCCGTCATTTCC 62.180 66.667 0.00 0.00 0.00 3.13
4210 5593 2.753966 CCGTCATTTCCGCCTGCAG 61.754 63.158 6.78 6.78 0.00 4.41
4211 5594 2.753966 CGTCATTTCCGCCTGCAGG 61.754 63.158 29.34 29.34 38.53 4.85
4225 5608 4.662961 CAGGCGCCGACACTGTCA 62.663 66.667 23.20 0.00 32.09 3.58
4258 5641 1.298993 CAGTCTCAGCTGCCACCAT 59.701 57.895 9.47 0.00 0.00 3.55
4259 5642 0.538584 CAGTCTCAGCTGCCACCATA 59.461 55.000 9.47 0.00 0.00 2.74
4289 5728 0.538287 GGCCCCAGCTAATCATGACC 60.538 60.000 0.00 0.00 39.73 4.02
4326 5766 3.062763 AGTGCTTCAGATCGAACAACAG 58.937 45.455 0.00 0.00 0.00 3.16
4333 5773 0.179205 GATCGAACAACAGCAGCAGC 60.179 55.000 0.00 0.00 42.56 5.25
4336 5776 1.501337 CGAACAACAGCAGCAGCAGA 61.501 55.000 3.17 0.00 45.49 4.26
4375 5815 1.276421 GTAGACAGGCCAGCTGAAAGA 59.724 52.381 17.39 0.00 34.07 2.52
4376 5816 0.767375 AGACAGGCCAGCTGAAAGAA 59.233 50.000 17.39 0.00 34.07 2.52
4377 5817 1.143684 AGACAGGCCAGCTGAAAGAAA 59.856 47.619 17.39 0.00 34.07 2.52
4378 5818 1.538950 GACAGGCCAGCTGAAAGAAAG 59.461 52.381 17.39 0.00 34.07 2.62
4408 5848 5.009510 TGCATTGCACTGTAGTATTGTTTGT 59.990 36.000 7.38 0.00 31.71 2.83
4409 5849 6.205658 TGCATTGCACTGTAGTATTGTTTGTA 59.794 34.615 7.38 0.00 31.71 2.41
4410 5850 6.523201 GCATTGCACTGTAGTATTGTTTGTAC 59.477 38.462 3.15 0.00 0.00 2.90
4411 5851 7.580600 CATTGCACTGTAGTATTGTTTGTACA 58.419 34.615 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
416 495 0.036765 AGATTAACCTTGGCGTCGCA 60.037 50.000 20.50 2.14 0.00 5.10
459 538 2.290896 TGGAAAAGACATTCGGCCTGAT 60.291 45.455 0.00 0.00 0.00 2.90
474 553 1.295792 GCGGACGCTGATATGGAAAA 58.704 50.000 9.76 0.00 38.26 2.29
485 564 1.068417 TACAAACTGTGCGGACGCT 59.932 52.632 18.04 0.00 42.51 5.07
552 635 4.651994 GTTCTTGAGCATTCCAATGTACG 58.348 43.478 1.37 0.00 38.65 3.67
575 658 4.000988 TCTTCTTTTCCGTCCAAGCATAC 58.999 43.478 0.00 0.00 0.00 2.39
621 739 6.266103 GTCAAAGAGAGAGAGAGATCCATGAT 59.734 42.308 0.00 0.00 0.00 2.45
622 740 5.593909 GTCAAAGAGAGAGAGAGATCCATGA 59.406 44.000 0.00 0.00 0.00 3.07
623 741 5.221303 GGTCAAAGAGAGAGAGAGATCCATG 60.221 48.000 0.00 0.00 0.00 3.66
624 742 4.895297 GGTCAAAGAGAGAGAGAGATCCAT 59.105 45.833 0.00 0.00 0.00 3.41
625 743 4.277476 GGTCAAAGAGAGAGAGAGATCCA 58.723 47.826 0.00 0.00 0.00 3.41
626 744 3.636764 GGGTCAAAGAGAGAGAGAGATCC 59.363 52.174 0.00 0.00 0.00 3.36
627 745 4.277476 TGGGTCAAAGAGAGAGAGAGATC 58.723 47.826 0.00 0.00 0.00 2.75
628 746 4.329638 TGGGTCAAAGAGAGAGAGAGAT 57.670 45.455 0.00 0.00 0.00 2.75
629 747 3.816398 TGGGTCAAAGAGAGAGAGAGA 57.184 47.619 0.00 0.00 0.00 3.10
630 748 3.056179 GGTTGGGTCAAAGAGAGAGAGAG 60.056 52.174 0.00 0.00 0.00 3.20
631 749 2.900546 GGTTGGGTCAAAGAGAGAGAGA 59.099 50.000 0.00 0.00 0.00 3.10
632 750 2.353208 CGGTTGGGTCAAAGAGAGAGAG 60.353 54.545 0.00 0.00 0.00 3.20
633 751 1.618837 CGGTTGGGTCAAAGAGAGAGA 59.381 52.381 0.00 0.00 0.00 3.10
634 752 1.344763 ACGGTTGGGTCAAAGAGAGAG 59.655 52.381 0.00 0.00 0.00 3.20
635 753 1.420430 ACGGTTGGGTCAAAGAGAGA 58.580 50.000 0.00 0.00 0.00 3.10
636 754 2.036733 TGTACGGTTGGGTCAAAGAGAG 59.963 50.000 0.00 0.00 0.00 3.20
641 759 3.071892 AGATTCTGTACGGTTGGGTCAAA 59.928 43.478 0.64 0.00 0.00 2.69
675 793 2.833943 ACCCTCCGAGTTTATTTACGGT 59.166 45.455 0.00 0.00 44.72 4.83
687 838 0.609662 TTCCCGTTTTACCCTCCGAG 59.390 55.000 0.00 0.00 0.00 4.63
688 839 0.609662 CTTCCCGTTTTACCCTCCGA 59.390 55.000 0.00 0.00 0.00 4.55
743 894 6.981559 GGTGCGAAATGCCCTTTATTTATTTA 59.018 34.615 0.00 0.00 45.60 1.40
744 895 5.815222 GGTGCGAAATGCCCTTTATTTATTT 59.185 36.000 0.00 0.00 45.60 1.40
745 896 5.356426 GGTGCGAAATGCCCTTTATTTATT 58.644 37.500 0.00 0.00 45.60 1.40
746 897 4.202212 GGGTGCGAAATGCCCTTTATTTAT 60.202 41.667 0.00 0.00 45.60 1.40
747 898 3.131400 GGGTGCGAAATGCCCTTTATTTA 59.869 43.478 0.00 0.00 45.60 1.40
771 922 2.867333 TAAACGCTCGGCTCAGCTCG 62.867 60.000 0.00 0.00 37.25 5.03
797 951 2.267006 CCTCATGCCGCTGTCTGT 59.733 61.111 0.00 0.00 0.00 3.41
846 1000 0.324460 GGAGGAAGACGGAGGAGGAA 60.324 60.000 0.00 0.00 0.00 3.36
847 1001 1.306970 GGAGGAAGACGGAGGAGGA 59.693 63.158 0.00 0.00 0.00 3.71
848 1002 1.758906 GGGAGGAAGACGGAGGAGG 60.759 68.421 0.00 0.00 0.00 4.30
849 1003 1.758906 GGGGAGGAAGACGGAGGAG 60.759 68.421 0.00 0.00 0.00 3.69
856 1010 5.431179 TTAGTATTTGTGGGGAGGAAGAC 57.569 43.478 0.00 0.00 0.00 3.01
884 1038 3.570638 CGCTCGATTGCTGGCTGG 61.571 66.667 0.00 0.00 0.00 4.85
890 1044 1.406898 TCAATCTCTCGCTCGATTGCT 59.593 47.619 12.53 0.00 43.73 3.91
891 1045 1.786004 CTCAATCTCTCGCTCGATTGC 59.214 52.381 12.53 0.00 43.73 3.56
963 1120 3.215245 GCTGGATCTGCGAGGTCT 58.785 61.111 0.00 0.00 0.00 3.85
1083 1250 2.809601 CTCCGCCGGTTGTTCTCG 60.810 66.667 1.63 0.00 0.00 4.04
1273 1440 1.446907 CGAGCAAGAGCAAGATTGGT 58.553 50.000 0.00 0.00 45.49 3.67
1276 1443 1.367659 GAGCGAGCAAGAGCAAGATT 58.632 50.000 0.00 0.00 45.49 2.40
1277 1444 0.461693 GGAGCGAGCAAGAGCAAGAT 60.462 55.000 0.00 0.00 45.49 2.40
1278 1445 1.079543 GGAGCGAGCAAGAGCAAGA 60.080 57.895 0.00 0.00 45.49 3.02
1280 1447 1.079543 GAGGAGCGAGCAAGAGCAA 60.080 57.895 0.00 0.00 45.49 3.91
1282 1449 2.202864 GGAGGAGCGAGCAAGAGC 60.203 66.667 0.00 0.00 42.56 4.09
1348 1538 2.126071 CGGGTGTCAGGTGCTACG 60.126 66.667 0.00 0.00 0.00 3.51
1424 1629 1.045407 ACGTCCCAAGTAGCAGAACA 58.955 50.000 0.00 0.00 0.00 3.18
1445 1650 1.576421 CAAGCAGAAACGGAGCACC 59.424 57.895 0.00 0.00 0.00 5.01
1452 1657 1.156736 ACCGAATCCAAGCAGAAACG 58.843 50.000 0.00 0.00 0.00 3.60
1457 1662 0.883833 AAGCAACCGAATCCAAGCAG 59.116 50.000 0.00 0.00 0.00 4.24
1474 1679 2.280628 GTGACTTCCCGCCATAAGAAG 58.719 52.381 0.00 0.00 42.19 2.85
1479 1684 1.683025 TCCGTGACTTCCCGCCATA 60.683 57.895 0.00 0.00 0.00 2.74
1480 1685 3.000819 TCCGTGACTTCCCGCCAT 61.001 61.111 0.00 0.00 0.00 4.40
1484 1689 1.213013 CAGAGTCCGTGACTTCCCG 59.787 63.158 7.80 0.00 43.53 5.14
1485 1690 1.079750 GCAGAGTCCGTGACTTCCC 60.080 63.158 7.80 0.00 43.53 3.97
1486 1691 0.318762 AAGCAGAGTCCGTGACTTCC 59.681 55.000 7.80 0.00 43.53 3.46
1494 1699 1.275291 TCCTAAACCAAGCAGAGTCCG 59.725 52.381 0.00 0.00 0.00 4.79
1498 1703 2.424956 GGCATTCCTAAACCAAGCAGAG 59.575 50.000 0.00 0.00 0.00 3.35
1539 1744 5.991606 CGCATCCAAGAACATTCCTCTAATA 59.008 40.000 0.00 0.00 0.00 0.98
1540 1745 4.818546 CGCATCCAAGAACATTCCTCTAAT 59.181 41.667 0.00 0.00 0.00 1.73
1541 1746 4.191544 CGCATCCAAGAACATTCCTCTAA 58.808 43.478 0.00 0.00 0.00 2.10
1593 1798 3.439857 TTGCTCCAGAACCATTAGCTT 57.560 42.857 0.00 0.00 34.28 3.74
1598 1803 4.670765 AGAGAAATTGCTCCAGAACCATT 58.329 39.130 10.04 0.00 35.49 3.16
1647 1853 4.287067 ACCACAGCATTCCTAGAGAAAGAA 59.713 41.667 0.00 0.00 38.21 2.52
1649 1855 3.937706 CACCACAGCATTCCTAGAGAAAG 59.062 47.826 0.00 0.00 38.21 2.62
1651 1857 3.173151 TCACCACAGCATTCCTAGAGAA 58.827 45.455 0.00 0.00 39.32 2.87
1653 1859 3.834489 ATCACCACAGCATTCCTAGAG 57.166 47.619 0.00 0.00 0.00 2.43
1655 1861 5.416952 AGAAAAATCACCACAGCATTCCTAG 59.583 40.000 0.00 0.00 0.00 3.02
1666 1873 6.348868 CCTCTAAGAGCAAGAAAAATCACCAC 60.349 42.308 0.00 0.00 0.00 4.16
1673 1880 7.721399 AGAACAATCCTCTAAGAGCAAGAAAAA 59.279 33.333 0.00 0.00 0.00 1.94
1678 1885 5.353678 CCAAGAACAATCCTCTAAGAGCAAG 59.646 44.000 0.00 0.00 0.00 4.01
1684 1891 4.272018 CGCATCCAAGAACAATCCTCTAAG 59.728 45.833 0.00 0.00 0.00 2.18
1834 2057 0.826715 TCTTGAATCTCCAGCTCCGG 59.173 55.000 0.00 0.00 0.00 5.14
1995 2230 1.305886 GGACCCCATTTCCCCTTACT 58.694 55.000 0.00 0.00 0.00 2.24
2004 2239 3.542969 AAAACTAGCTGGACCCCATTT 57.457 42.857 3.17 0.00 30.82 2.32
2014 2249 4.503714 TCCCCATTCCTAAAACTAGCTG 57.496 45.455 0.00 0.00 0.00 4.24
2054 2289 6.817765 CTAAATCAGGAGGTTGCTAAAACA 57.182 37.500 0.00 0.00 0.00 2.83
2154 2875 5.903764 GTGCAAACACAATATTTTCTGCA 57.096 34.783 0.00 0.00 46.61 4.41
2175 2897 3.157087 AGAGGCAATTGAAATGTTCCGT 58.843 40.909 10.34 0.00 0.00 4.69
2216 2938 9.005777 AGTACTTATCCAAGTTATTCGCAAAAA 57.994 29.630 0.00 0.00 42.51 1.94
2217 2939 8.556213 AGTACTTATCCAAGTTATTCGCAAAA 57.444 30.769 0.00 0.00 42.51 2.44
2218 2940 8.556213 AAGTACTTATCCAAGTTATTCGCAAA 57.444 30.769 6.26 0.00 42.51 3.68
2219 2941 8.556213 AAAGTACTTATCCAAGTTATTCGCAA 57.444 30.769 8.92 0.00 42.51 4.85
2220 2942 7.820386 TGAAAGTACTTATCCAAGTTATTCGCA 59.180 33.333 8.92 0.00 42.51 5.10
2221 2943 8.114905 GTGAAAGTACTTATCCAAGTTATTCGC 58.885 37.037 8.92 1.19 42.51 4.70
2222 2944 9.146984 TGTGAAAGTACTTATCCAAGTTATTCG 57.853 33.333 8.92 0.00 42.51 3.34
2227 2949 8.947115 GCTTATGTGAAAGTACTTATCCAAGTT 58.053 33.333 8.92 0.00 42.51 2.66
2228 2950 8.322091 AGCTTATGTGAAAGTACTTATCCAAGT 58.678 33.333 8.92 0.00 46.77 3.16
2229 2951 8.723942 AGCTTATGTGAAAGTACTTATCCAAG 57.276 34.615 8.92 8.89 37.81 3.61
2230 2952 9.515226 AAAGCTTATGTGAAAGTACTTATCCAA 57.485 29.630 8.92 0.00 0.00 3.53
2231 2953 9.515226 AAAAGCTTATGTGAAAGTACTTATCCA 57.485 29.630 8.92 6.05 0.00 3.41
2236 2958 9.120538 TGAGAAAAAGCTTATGTGAAAGTACTT 57.879 29.630 1.12 1.12 0.00 2.24
2237 2959 8.677148 TGAGAAAAAGCTTATGTGAAAGTACT 57.323 30.769 0.00 0.00 0.00 2.73
2238 2960 9.387123 CTTGAGAAAAAGCTTATGTGAAAGTAC 57.613 33.333 0.00 0.00 0.00 2.73
2239 2961 9.337396 TCTTGAGAAAAAGCTTATGTGAAAGTA 57.663 29.630 0.00 0.00 0.00 2.24
2240 2962 8.225603 TCTTGAGAAAAAGCTTATGTGAAAGT 57.774 30.769 0.00 0.00 0.00 2.66
2278 3000 9.836864 TTGATCATGCAAGAAACTAGTATACAT 57.163 29.630 5.50 0.00 0.00 2.29
2280 3002 9.922305 GTTTGATCATGCAAGAAACTAGTATAC 57.078 33.333 0.00 0.00 0.00 1.47
2400 3592 6.270815 TGTAGTCTATCACGCCACTAAAATC 58.729 40.000 0.00 0.00 0.00 2.17
2411 3603 8.581057 AATAGCTGAAAATGTAGTCTATCACG 57.419 34.615 0.00 0.00 0.00 4.35
2477 3669 3.797451 TTGACCAAACGGTTTTTACCC 57.203 42.857 2.79 0.00 36.70 3.69
2500 3692 4.250464 CAGACAACGGCTTCCAACTATAA 58.750 43.478 0.00 0.00 0.00 0.98
2514 3706 0.318360 TGTAGGTGCGACAGACAACG 60.318 55.000 0.00 0.00 0.00 4.10
2525 3717 3.193267 TCATGCAAAGGAAATGTAGGTGC 59.807 43.478 0.00 0.00 0.00 5.01
2598 3790 0.324943 GCACTTGTGGAGGAGGCTTA 59.675 55.000 2.81 0.00 0.00 3.09
2601 3793 2.743928 CGCACTTGTGGAGGAGGC 60.744 66.667 2.81 0.00 0.00 4.70
2615 3807 0.178767 CCTCATTGGATCAGGACGCA 59.821 55.000 0.00 0.00 38.35 5.24
2655 3847 1.070758 GGGCTCGGCTGATATGAAGAA 59.929 52.381 0.00 0.00 0.00 2.52
2715 3907 0.260230 AAGAGGATCCAGAGCTCGGA 59.740 55.000 23.38 23.38 36.84 4.55
2814 4006 2.159382 GCAAATGAGGGGTTCGAAGAA 58.841 47.619 0.00 0.00 45.90 2.52
2817 4009 0.404040 AGGCAAATGAGGGGTTCGAA 59.596 50.000 0.00 0.00 0.00 3.71
2826 4018 0.914644 TGGAGGAGGAGGCAAATGAG 59.085 55.000 0.00 0.00 0.00 2.90
2859 4051 4.125703 CTCCATTGAAGTAGAGATGGTGC 58.874 47.826 0.00 0.00 39.95 5.01
3144 4336 4.421479 CACGCCCTCGACGAGCTT 62.421 66.667 19.55 0.54 39.41 3.74
3246 4438 1.758122 AAAATCATCCGCTGCCCCC 60.758 57.895 0.00 0.00 0.00 5.40
3252 4444 1.205417 CCAAAGGCAAAATCATCCGCT 59.795 47.619 0.00 0.00 0.00 5.52
3270 4462 3.052954 CCATTGCTGTTGCTGCCA 58.947 55.556 0.00 0.00 40.48 4.92
3303 4495 3.136123 CATGCCTTCACCAGCCCG 61.136 66.667 0.00 0.00 0.00 6.13
3318 4510 1.128188 GTATCCGCTCCCCTTCCCAT 61.128 60.000 0.00 0.00 0.00 4.00
3415 4607 3.630312 CACTTGTGGCATCATCATCATCA 59.370 43.478 0.00 0.00 0.00 3.07
3416 4608 3.630769 ACACTTGTGGCATCATCATCATC 59.369 43.478 5.72 0.00 0.00 2.92
3417 4609 3.628008 ACACTTGTGGCATCATCATCAT 58.372 40.909 5.72 0.00 0.00 2.45
3420 4612 3.014623 CAGACACTTGTGGCATCATCAT 58.985 45.455 9.44 0.00 0.00 2.45
3423 4615 2.039480 AGACAGACACTTGTGGCATCAT 59.961 45.455 9.44 0.00 0.00 2.45
3426 4618 1.696336 AGAGACAGACACTTGTGGCAT 59.304 47.619 9.44 0.00 0.00 4.40
3458 4654 7.343357 CCAAGTAAGTATCAAGGATAAACCCA 58.657 38.462 0.00 0.00 40.05 4.51
3459 4655 6.771267 CCCAAGTAAGTATCAAGGATAAACCC 59.229 42.308 0.00 0.00 40.05 4.11
3460 4656 7.282450 CACCCAAGTAAGTATCAAGGATAAACC 59.718 40.741 0.00 0.00 39.35 3.27
3471 4667 3.446516 AGACCGACACCCAAGTAAGTATC 59.553 47.826 0.00 0.00 0.00 2.24
3479 4675 0.321671 ACATCAGACCGACACCCAAG 59.678 55.000 0.00 0.00 0.00 3.61
3482 4678 0.608640 AGAACATCAGACCGACACCC 59.391 55.000 0.00 0.00 0.00 4.61
3483 4679 2.230508 TGTAGAACATCAGACCGACACC 59.769 50.000 0.00 0.00 0.00 4.16
3487 4683 2.826128 AGCTTGTAGAACATCAGACCGA 59.174 45.455 0.00 0.00 0.00 4.69
3490 4714 3.182967 CCGAGCTTGTAGAACATCAGAC 58.817 50.000 0.00 0.00 0.00 3.51
3519 4743 3.231818 ACTCCCTTCTCTCTTTCGACAA 58.768 45.455 0.00 0.00 0.00 3.18
3520 4744 2.877866 ACTCCCTTCTCTCTTTCGACA 58.122 47.619 0.00 0.00 0.00 4.35
3521 4745 3.256136 TCAACTCCCTTCTCTCTTTCGAC 59.744 47.826 0.00 0.00 0.00 4.20
3522 4746 3.497332 TCAACTCCCTTCTCTCTTTCGA 58.503 45.455 0.00 0.00 0.00 3.71
3748 4976 5.220739 GCTTTGCTTACTGATGACGAATGAT 60.221 40.000 0.00 0.00 0.00 2.45
3749 4977 4.093408 GCTTTGCTTACTGATGACGAATGA 59.907 41.667 0.00 0.00 0.00 2.57
3754 4982 2.738846 ACTGCTTTGCTTACTGATGACG 59.261 45.455 0.00 0.00 0.00 4.35
3813 5042 5.814188 TGAAACTTGTGTTTGCATTGCATTA 59.186 32.000 12.95 0.82 45.36 1.90
3821 5050 4.233789 GACAACTGAAACTTGTGTTTGCA 58.766 39.130 0.00 0.00 45.36 4.08
3822 5051 3.612423 GGACAACTGAAACTTGTGTTTGC 59.388 43.478 0.00 0.00 45.36 3.68
3823 5052 5.059404 AGGACAACTGAAACTTGTGTTTG 57.941 39.130 0.00 0.00 45.36 2.93
3825 5054 4.764823 TCAAGGACAACTGAAACTTGTGTT 59.235 37.500 0.00 0.00 39.49 3.32
3826 5055 4.331968 TCAAGGACAACTGAAACTTGTGT 58.668 39.130 0.00 0.00 39.49 3.72
3827 5056 4.963276 TCAAGGACAACTGAAACTTGTG 57.037 40.909 0.00 0.00 39.49 3.33
3828 5057 6.998074 TCATATCAAGGACAACTGAAACTTGT 59.002 34.615 0.00 0.00 39.49 3.16
3833 5062 6.533730 ACAGTCATATCAAGGACAACTGAAA 58.466 36.000 6.61 0.00 38.89 2.69
3897 5138 4.637534 AGAATCAATGAATGAACGGTCCAG 59.362 41.667 0.00 0.00 42.54 3.86
3923 5169 3.561143 ACCAATAACCAGCAAAGACACA 58.439 40.909 0.00 0.00 0.00 3.72
3940 5186 6.133356 AGGAATTTCTAACAACTCCAACCAA 58.867 36.000 0.00 0.00 0.00 3.67
3941 5187 5.701224 AGGAATTTCTAACAACTCCAACCA 58.299 37.500 0.00 0.00 0.00 3.67
3942 5188 6.650427 AAGGAATTTCTAACAACTCCAACC 57.350 37.500 0.00 0.00 0.00 3.77
3943 5189 9.459640 GTAAAAGGAATTTCTAACAACTCCAAC 57.540 33.333 0.00 0.00 32.27 3.77
3944 5190 9.416284 AGTAAAAGGAATTTCTAACAACTCCAA 57.584 29.630 0.00 0.00 32.27 3.53
3945 5191 8.990163 AGTAAAAGGAATTTCTAACAACTCCA 57.010 30.769 0.00 0.00 32.27 3.86
3946 5192 9.063615 TGAGTAAAAGGAATTTCTAACAACTCC 57.936 33.333 12.46 0.00 32.11 3.85
3968 5216 4.782156 AGAGGATCCAACAAGAAGATGAGT 59.218 41.667 15.82 0.00 33.66 3.41
3969 5217 5.105023 TGAGAGGATCCAACAAGAAGATGAG 60.105 44.000 15.82 0.00 33.66 2.90
3990 5238 1.148310 CACCAACAGTTACCGCTGAG 58.852 55.000 0.00 0.00 39.62 3.35
4000 5248 5.361285 TGGTAAAACTATTTGCACCAACAGT 59.639 36.000 0.00 0.00 36.30 3.55
4004 5252 5.361285 ACACTGGTAAAACTATTTGCACCAA 59.639 36.000 8.54 0.00 37.81 3.67
4005 5253 4.890581 ACACTGGTAAAACTATTTGCACCA 59.109 37.500 0.00 7.45 36.66 4.17
4006 5254 5.219633 CACACTGGTAAAACTATTTGCACC 58.780 41.667 0.00 0.00 33.33 5.01
4007 5255 4.679654 GCACACTGGTAAAACTATTTGCAC 59.320 41.667 0.00 0.00 33.33 4.57
4010 5258 6.312399 TCAGCACACTGGTAAAACTATTTG 57.688 37.500 0.00 0.00 44.59 2.32
4011 5259 6.570378 GCATCAGCACACTGGTAAAACTATTT 60.570 38.462 0.00 0.00 44.59 1.40
4015 5265 2.554032 GCATCAGCACACTGGTAAAACT 59.446 45.455 0.00 0.00 44.59 2.66
4017 5267 1.535028 CGCATCAGCACACTGGTAAAA 59.465 47.619 0.00 0.00 44.59 1.52
4035 5285 0.868406 CTTGTGGAACTCACCTTCGC 59.132 55.000 0.00 0.00 45.48 4.70
4036 5286 2.526304 TCTTGTGGAACTCACCTTCG 57.474 50.000 0.00 0.00 45.48 3.79
4037 5287 4.008074 TCATCTTGTGGAACTCACCTTC 57.992 45.455 0.00 0.00 45.48 3.46
4038 5288 4.202503 ACATCATCTTGTGGAACTCACCTT 60.203 41.667 0.00 0.00 45.48 3.50
4039 5289 3.328931 ACATCATCTTGTGGAACTCACCT 59.671 43.478 0.00 0.00 45.48 4.00
4042 5292 4.761739 GGAAACATCATCTTGTGGAACTCA 59.238 41.667 0.00 0.00 38.04 3.41
4043 5293 4.761739 TGGAAACATCATCTTGTGGAACTC 59.238 41.667 0.00 0.00 33.42 3.01
4044 5294 4.728772 TGGAAACATCATCTTGTGGAACT 58.271 39.130 0.00 0.00 33.42 3.01
4045 5295 4.082571 CCTGGAAACATCATCTTGTGGAAC 60.083 45.833 0.00 0.00 41.51 3.62
4046 5296 4.081406 CCTGGAAACATCATCTTGTGGAA 58.919 43.478 0.00 0.00 41.51 3.53
4047 5297 3.074390 ACCTGGAAACATCATCTTGTGGA 59.926 43.478 0.00 0.00 41.51 4.02
4054 5419 2.648059 CCTCCACCTGGAAACATCATC 58.352 52.381 0.00 0.00 44.91 2.92
4057 5422 0.329596 AGCCTCCACCTGGAAACATC 59.670 55.000 0.00 0.00 44.91 3.06
4075 5440 1.005215 ACCTCCAAGATCCAGGCAAAG 59.995 52.381 0.00 0.00 0.00 2.77
4081 5446 5.070001 TGTTTAAACACCTCCAAGATCCAG 58.930 41.667 17.01 0.00 33.17 3.86
4121 5504 0.961753 GGACTGCAACAAGGGAAAGG 59.038 55.000 0.00 0.00 0.00 3.11
4130 5513 4.265893 TCAACTAAACTTGGACTGCAACA 58.734 39.130 0.00 0.00 0.00 3.33
4131 5514 4.893424 TCAACTAAACTTGGACTGCAAC 57.107 40.909 0.00 0.00 0.00 4.17
4132 5515 6.463995 AATTCAACTAAACTTGGACTGCAA 57.536 33.333 0.00 0.00 0.00 4.08
4133 5516 6.460953 GGAAATTCAACTAAACTTGGACTGCA 60.461 38.462 0.00 0.00 0.00 4.41
4134 5517 5.920840 GGAAATTCAACTAAACTTGGACTGC 59.079 40.000 0.00 0.00 0.00 4.40
4135 5518 6.142817 CGGAAATTCAACTAAACTTGGACTG 58.857 40.000 0.00 0.00 0.00 3.51
4136 5519 5.240844 CCGGAAATTCAACTAAACTTGGACT 59.759 40.000 0.00 0.00 0.00 3.85
4137 5520 5.239963 TCCGGAAATTCAACTAAACTTGGAC 59.760 40.000 0.00 0.00 0.00 4.02
4138 5521 5.239963 GTCCGGAAATTCAACTAAACTTGGA 59.760 40.000 5.23 0.00 0.00 3.53
4139 5522 5.009210 TGTCCGGAAATTCAACTAAACTTGG 59.991 40.000 5.23 0.00 0.00 3.61
4140 5523 6.067263 TGTCCGGAAATTCAACTAAACTTG 57.933 37.500 5.23 0.00 0.00 3.16
4141 5524 6.544564 TCTTGTCCGGAAATTCAACTAAACTT 59.455 34.615 5.23 0.00 0.00 2.66
4142 5525 6.059484 TCTTGTCCGGAAATTCAACTAAACT 58.941 36.000 5.23 0.00 0.00 2.66
4143 5526 6.308371 TCTTGTCCGGAAATTCAACTAAAC 57.692 37.500 5.23 0.00 0.00 2.01
4144 5527 6.945938 TTCTTGTCCGGAAATTCAACTAAA 57.054 33.333 5.23 0.00 0.00 1.85
4145 5528 6.945938 TTTCTTGTCCGGAAATTCAACTAA 57.054 33.333 5.23 0.00 0.00 2.24
4146 5529 6.150474 GGATTTCTTGTCCGGAAATTCAACTA 59.850 38.462 5.23 0.00 41.59 2.24
4147 5530 5.048013 GGATTTCTTGTCCGGAAATTCAACT 60.048 40.000 5.23 0.00 41.59 3.16
4148 5531 5.161358 GGATTTCTTGTCCGGAAATTCAAC 58.839 41.667 5.23 0.00 41.59 3.18
4149 5532 4.830046 TGGATTTCTTGTCCGGAAATTCAA 59.170 37.500 5.23 5.24 42.33 2.69
4150 5533 4.402829 TGGATTTCTTGTCCGGAAATTCA 58.597 39.130 5.23 3.88 42.75 2.57
4151 5534 5.343249 CATGGATTTCTTGTCCGGAAATTC 58.657 41.667 5.23 0.65 41.59 2.17
4152 5535 4.160252 CCATGGATTTCTTGTCCGGAAATT 59.840 41.667 5.23 0.00 41.59 1.82
4153 5536 3.701040 CCATGGATTTCTTGTCCGGAAAT 59.299 43.478 5.23 0.73 43.40 2.17
4154 5537 3.088532 CCATGGATTTCTTGTCCGGAAA 58.911 45.455 5.23 0.00 38.64 3.13
4155 5538 2.041081 ACCATGGATTTCTTGTCCGGAA 59.959 45.455 21.47 0.00 38.64 4.30
4156 5539 1.633432 ACCATGGATTTCTTGTCCGGA 59.367 47.619 21.47 0.00 38.64 5.14
4157 5540 2.017049 GACCATGGATTTCTTGTCCGG 58.983 52.381 21.47 0.00 38.64 5.14
4158 5541 2.939103 GAGACCATGGATTTCTTGTCCG 59.061 50.000 21.47 0.00 38.64 4.79
4159 5542 4.227864 AGAGACCATGGATTTCTTGTCC 57.772 45.455 21.47 0.00 36.26 4.02
4160 5543 5.163814 CGAAAGAGACCATGGATTTCTTGTC 60.164 44.000 21.47 18.33 0.00 3.18
4161 5544 4.697352 CGAAAGAGACCATGGATTTCTTGT 59.303 41.667 21.47 13.18 0.00 3.16
4162 5545 4.095483 CCGAAAGAGACCATGGATTTCTTG 59.905 45.833 21.47 11.92 0.00 3.02
4163 5546 4.265073 CCGAAAGAGACCATGGATTTCTT 58.735 43.478 21.47 19.29 0.00 2.52
4164 5547 3.878778 CCGAAAGAGACCATGGATTTCT 58.121 45.455 21.47 11.33 0.00 2.52
4165 5548 2.356069 GCCGAAAGAGACCATGGATTTC 59.644 50.000 21.47 19.30 0.00 2.17
4166 5549 2.025887 AGCCGAAAGAGACCATGGATTT 60.026 45.455 21.47 13.14 0.00 2.17
4167 5550 1.561542 AGCCGAAAGAGACCATGGATT 59.438 47.619 21.47 5.48 0.00 3.01
4168 5551 1.134280 CAGCCGAAAGAGACCATGGAT 60.134 52.381 21.47 6.30 0.00 3.41
4169 5552 0.250234 CAGCCGAAAGAGACCATGGA 59.750 55.000 21.47 0.00 0.00 3.41
4210 5593 3.490759 CATGACAGTGTCGGCGCC 61.491 66.667 19.07 19.07 34.95 6.53
4211 5594 4.152625 GCATGACAGTGTCGGCGC 62.153 66.667 19.78 16.65 34.95 6.53
4212 5595 2.733671 CTGCATGACAGTGTCGGCG 61.734 63.158 25.40 18.91 41.86 6.46
4213 5596 3.171987 CTGCATGACAGTGTCGGC 58.828 61.111 24.84 24.84 41.86 5.54
4241 5624 0.539051 GTATGGTGGCAGCTGAGACT 59.461 55.000 20.43 0.33 0.00 3.24
4258 5641 2.039191 GGGGCCTGGGGTATGGTA 60.039 66.667 0.84 0.00 0.00 3.25
4259 5642 4.379467 TGGGGCCTGGGGTATGGT 62.379 66.667 0.84 0.00 0.00 3.55
4289 5728 6.738114 TGAAGCACTAATTTTTGAGACAAGG 58.262 36.000 0.00 0.00 0.00 3.61
4375 5815 0.760572 AGTGCAATGCAAAGGCCTTT 59.239 45.000 25.47 25.47 41.47 3.11
4376 5816 0.034337 CAGTGCAATGCAAAGGCCTT 59.966 50.000 13.78 13.78 41.47 4.35
4377 5817 1.117142 ACAGTGCAATGCAAAGGCCT 61.117 50.000 15.18 0.00 41.47 5.19
4378 5818 0.602562 TACAGTGCAATGCAAAGGCC 59.397 50.000 15.18 0.00 41.47 5.19


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

AutoCloner maintained by Alex Coulton.