Multiple sequence alignment - TraesCS7B01G159000

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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 TraesCS7B01G159000 chr7B 100.000 4097 0 0 1 4097 216089363 216085267 0.000000e+00 7566.0
1 TraesCS7B01G159000 chr7B 84.783 138 19 2 1 137 466712009 466712145 1.990000e-28 137.0
2 TraesCS7B01G159000 chr7B 87.368 95 11 1 2375 2469 450642308 450642215 1.560000e-19 108.0
3 TraesCS7B01G159000 chr7B 100.000 28 0 0 2372 2399 672653242 672653215 7.000000e-03 52.8
4 TraesCS7B01G159000 chr7D 93.480 2684 101 37 253 2918 239776545 239773918 0.000000e+00 3919.0
5 TraesCS7B01G159000 chr7D 93.342 766 16 10 2948 3705 239773915 239773177 0.000000e+00 1099.0
6 TraesCS7B01G159000 chr7D 82.586 379 47 15 128 500 548706822 548707187 2.380000e-82 316.0
7 TraesCS7B01G159000 chr7D 77.009 448 69 27 217 642 560289694 560290129 4.120000e-55 226.0
8 TraesCS7B01G159000 chr7A 92.341 2572 113 30 1 2556 258368517 258371020 0.000000e+00 3581.0
9 TraesCS7B01G159000 chr7A 95.430 941 26 7 2608 3533 258371021 258371959 0.000000e+00 1483.0
10 TraesCS7B01G159000 chr7A 81.984 383 54 10 131 505 219400197 219400572 1.110000e-80 311.0
11 TraesCS7B01G159000 chr7A 83.465 127 5 5 3688 3811 258372039 258372152 2.010000e-18 104.0
12 TraesCS7B01G159000 chr1A 82.984 382 47 18 131 504 456287669 456287298 3.050000e-86 329.0
13 TraesCS7B01G159000 chr1A 85.612 139 14 6 3 137 488106724 488106860 1.540000e-29 141.0
14 TraesCS7B01G159000 chr6B 81.773 406 60 13 131 529 468308582 468308184 1.100000e-85 327.0
15 TraesCS7B01G159000 chr6B 84.892 139 18 3 1 137 138299521 138299384 1.990000e-28 137.0
16 TraesCS7B01G159000 chr5B 83.024 377 42 17 130 500 65495956 65496316 5.110000e-84 322.0
17 TraesCS7B01G159000 chr5B 100.000 30 0 0 2370 2399 540361842 540361813 5.720000e-04 56.5
18 TraesCS7B01G159000 chr3A 83.815 346 49 7 162 502 606721676 606722019 5.110000e-84 322.0
19 TraesCS7B01G159000 chr3A 83.946 299 41 6 279 571 728575769 728575472 3.120000e-71 279.0
20 TraesCS7B01G159000 chr3A 81.169 308 49 9 217 520 728545600 728545298 5.290000e-59 239.0
21 TraesCS7B01G159000 chr3D 81.890 381 59 10 131 506 95486275 95486650 3.070000e-81 313.0
22 TraesCS7B01G159000 chr3D 80.342 351 47 19 272 611 441569028 441568689 3.160000e-61 246.0
23 TraesCS7B01G159000 chr3D 92.105 38 3 0 2363 2400 611910876 611910913 2.000000e-03 54.7
24 TraesCS7B01G159000 chr2A 83.095 349 50 8 162 504 101029455 101029800 3.980000e-80 309.0
25 TraesCS7B01G159000 chr2A 86.029 136 13 6 4 136 712860575 712860443 1.540000e-29 141.0
26 TraesCS7B01G159000 chr2D 82.986 288 41 5 258 540 50159247 50158963 1.890000e-63 254.0
27 TraesCS7B01G159000 chr2D 87.209 86 10 1 2371 2456 160215173 160215089 3.370000e-16 97.1
28 TraesCS7B01G159000 chr4D 85.507 138 16 4 1 136 414059763 414059898 1.540000e-29 141.0
29 TraesCS7B01G159000 chr3B 86.923 130 12 5 10 136 753210343 753210216 1.540000e-29 141.0
30 TraesCS7B01G159000 chr3B 85.507 138 15 5 1 136 631958838 631958704 5.520000e-29 139.0
31 TraesCS7B01G159000 chr1B 86.719 128 14 3 10 136 597158537 597158412 5.520000e-29 139.0
32 TraesCS7B01G159000 chr5A 86.139 101 10 4 2372 2470 51690151 51690053 5.600000e-19 106.0
33 TraesCS7B01G159000 chr5D 83.838 99 14 2 2372 2470 61715092 61714996 4.360000e-15 93.5
34 TraesCS7B01G159000 chr4A 92.063 63 4 1 2391 2453 548532346 548532285 2.030000e-13 87.9


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 TraesCS7B01G159000 chr7B 216085267 216089363 4096 True 7566.000000 7566 100.000 1 4097 1 chr7B.!!$R1 4096
1 TraesCS7B01G159000 chr7D 239773177 239776545 3368 True 2509.000000 3919 93.411 253 3705 2 chr7D.!!$R1 3452
2 TraesCS7B01G159000 chr7A 258368517 258372152 3635 False 1722.666667 3581 90.412 1 3811 3 chr7A.!!$F2 3810

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
795 810 0.669077 CAGCCCCTACAGCGTAGTAG 59.331 60.0 12.54 8.79 40.87 2.57 F
1520 1543 0.036010 GCTATCATGATCGGTGGGGG 60.036 60.0 12.53 0.00 0.00 5.40 F
2578 2607 0.466007 TGTGTGTGCCATCTGCTTGT 60.466 50.0 0.00 0.00 42.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1652 1676 1.335964 CGATGCGTACGAGGGAATGAT 60.336 52.381 21.65 0.0 0.00 2.45 R
2692 2725 2.301870 TGTTGAACGGAGTGGCTAAGAT 59.698 45.455 0.00 0.0 45.00 2.40 R
4029 4112 0.035317 ATTGACCTCACAAGCAGCGA 59.965 50.000 0.00 0.0 33.22 4.93 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
145 148 9.454859 TGTTTCAAATATTTGTTTGGTTTCCTT 57.545 25.926 23.95 0.00 39.10 3.36
192 195 9.769093 TTTTCTTTTGTTTGTTTTCGTTTTCAA 57.231 22.222 0.00 0.00 0.00 2.69
673 684 2.034221 GCCTTCAGCGAGGGGTTT 59.966 61.111 8.36 0.00 37.29 3.27
675 686 2.335712 CCTTCAGCGAGGGGTTTGC 61.336 63.158 0.00 0.00 36.35 3.68
677 688 1.301677 CTTCAGCGAGGGGTTTGCTC 61.302 60.000 0.00 0.00 45.06 4.26
708 722 2.061773 CTTAATGCGAGACATAGGGCG 58.938 52.381 0.00 0.00 38.34 6.13
711 725 4.221422 GCGAGACATAGGGCGCCA 62.221 66.667 30.85 9.36 43.33 5.69
793 808 2.058595 CCAGCCCCTACAGCGTAGT 61.059 63.158 12.54 0.85 34.64 2.73
794 809 0.754217 CCAGCCCCTACAGCGTAGTA 60.754 60.000 12.54 1.87 34.64 1.82
795 810 0.669077 CAGCCCCTACAGCGTAGTAG 59.331 60.000 12.54 8.79 40.87 2.57
925 940 3.373565 CCCAACGCCCAAAGCCTC 61.374 66.667 0.00 0.00 38.78 4.70
1017 1040 0.603707 CCATGGATCCCGATTCGGTG 60.604 60.000 22.83 14.45 46.80 4.94
1312 1335 3.941188 AGGTCTGCACCACCCACG 61.941 66.667 6.48 0.00 46.68 4.94
1320 1343 4.752879 ACCACCCACGCGATTCGG 62.753 66.667 15.93 9.05 43.86 4.30
1367 1390 9.010029 GTCCAATATTTCTCTTGTTTGGTTCTA 57.990 33.333 0.00 0.00 36.02 2.10
1392 1415 5.384063 ACGTGCTGATCTGATCCTATTAG 57.616 43.478 14.71 6.41 0.00 1.73
1405 1428 7.892771 TCTGATCCTATTAGCTGTGATCACTAT 59.107 37.037 25.55 13.94 37.49 2.12
1430 1453 3.003897 CGATCCTTCGTTTGGTTCCAAAA 59.996 43.478 17.04 2.10 40.53 2.44
1449 1472 5.221165 CCAAAATCCCAAATCATACGGTACC 60.221 44.000 0.16 0.16 0.00 3.34
1450 1473 4.781775 AATCCCAAATCATACGGTACCA 57.218 40.909 13.54 0.00 0.00 3.25
1483 1506 0.811281 GGAAGGCCCTCAATTTCGTG 59.189 55.000 3.19 0.00 0.00 4.35
1486 1509 0.322546 AGGCCCTCAATTTCGTGTCC 60.323 55.000 0.00 0.00 0.00 4.02
1488 1511 1.794222 CCCTCAATTTCGTGTCCGC 59.206 57.895 0.00 0.00 0.00 5.54
1520 1543 0.036010 GCTATCATGATCGGTGGGGG 60.036 60.000 12.53 0.00 0.00 5.40
1608 1632 2.930826 TGTTTGGACCTGGAGACTTC 57.069 50.000 0.00 0.00 0.00 3.01
1652 1676 8.945195 TTATAGATCTTTATCCCGGAACTGTA 57.055 34.615 0.73 0.00 31.98 2.74
1662 1686 2.224305 CCCGGAACTGTATCATTCCCTC 60.224 54.545 0.73 0.00 41.26 4.30
1752 1776 7.898014 ACTTTTCCTTGAGGTAATTTCAGTT 57.102 32.000 0.00 0.00 36.34 3.16
1769 1793 7.459394 TTTCAGTTCGTGTAGTTCTTTACAG 57.541 36.000 0.00 0.00 34.41 2.74
1853 1877 1.442769 TTGGTGCTGATCGCTCTTTC 58.557 50.000 10.16 0.00 40.11 2.62
2113 2139 4.695455 ACGATATTTGCTGTAGTGTTGCTT 59.305 37.500 0.00 0.00 0.00 3.91
2117 2143 7.748683 CGATATTTGCTGTAGTGTTGCTTTTTA 59.251 33.333 0.00 0.00 0.00 1.52
2118 2144 9.405587 GATATTTGCTGTAGTGTTGCTTTTTAA 57.594 29.630 0.00 0.00 0.00 1.52
2119 2145 9.757227 ATATTTGCTGTAGTGTTGCTTTTTAAA 57.243 25.926 0.00 0.00 0.00 1.52
2120 2146 7.891183 TTTGCTGTAGTGTTGCTTTTTAAAA 57.109 28.000 0.00 0.00 0.00 1.52
2121 2147 7.891183 TTGCTGTAGTGTTGCTTTTTAAAAA 57.109 28.000 12.62 12.62 0.00 1.94
2293 2319 8.299570 TCTATTGAAGTTTCATTGCTTCCTTTC 58.700 33.333 0.00 0.00 40.07 2.62
2507 2534 2.798976 TGAAACAATTCACCTGCTGC 57.201 45.000 0.00 0.00 40.59 5.25
2576 2605 0.885879 CATGTGTGTGCCATCTGCTT 59.114 50.000 0.00 0.00 42.00 3.91
2578 2607 0.466007 TGTGTGTGCCATCTGCTTGT 60.466 50.000 0.00 0.00 42.00 3.16
2606 2635 7.715482 ACCCTATTTGTAGGAAATTACCCTTT 58.285 34.615 4.83 0.00 39.60 3.11
2616 2645 9.146984 GTAGGAAATTACCCTTTTAATTGCAAC 57.853 33.333 0.00 0.00 32.95 4.17
2620 2649 7.553504 AATTACCCTTTTAATTGCAACTCCT 57.446 32.000 0.00 0.00 31.69 3.69
2705 2738 4.130118 CCATTACACATCTTAGCCACTCC 58.870 47.826 0.00 0.00 0.00 3.85
2717 2750 1.414919 AGCCACTCCGTTCAACAGTTA 59.585 47.619 0.00 0.00 0.00 2.24
2730 2763 7.243487 CGTTCAACAGTTACATGCTTTATGAT 58.757 34.615 0.00 0.00 39.21 2.45
2792 2825 5.826737 AGATGGTCCTTGATCAATGTGATTC 59.173 40.000 8.96 3.39 37.20 2.52
2897 2930 1.270147 GCAGGTCTGTGTCTTAACGGT 60.270 52.381 0.00 0.00 0.00 4.83
2922 2956 3.873952 GAGAGGTTGCATGGAAGTACATC 59.126 47.826 0.00 0.00 0.00 3.06
2932 2966 5.277345 GCATGGAAGTACATCGTTATGTTCC 60.277 44.000 0.00 0.00 44.07 3.62
2975 3009 6.267699 AGGGAAATTTTCTTAGTTGTCCTTGG 59.732 38.462 8.93 0.00 0.00 3.61
3196 3233 2.159296 ACTCTTTGTTTGTTCGCCAACC 60.159 45.455 0.00 0.00 31.20 3.77
3485 3529 6.073440 CCTGCAATTTTGGATTGTTTTCAGAG 60.073 38.462 0.00 0.00 0.00 3.35
3526 3570 2.687935 CAAACCGGCTTAATATGGCTGT 59.312 45.455 0.00 0.00 33.41 4.40
3527 3571 2.729028 ACCGGCTTAATATGGCTGTT 57.271 45.000 0.00 0.00 33.41 3.16
3528 3572 2.572290 ACCGGCTTAATATGGCTGTTC 58.428 47.619 0.00 0.00 33.41 3.18
3529 3573 1.531149 CCGGCTTAATATGGCTGTTCG 59.469 52.381 0.00 0.00 33.41 3.95
3530 3574 2.210116 CGGCTTAATATGGCTGTTCGT 58.790 47.619 0.00 0.00 0.00 3.85
3531 3575 2.612212 CGGCTTAATATGGCTGTTCGTT 59.388 45.455 0.00 0.00 0.00 3.85
3532 3576 3.546020 CGGCTTAATATGGCTGTTCGTTG 60.546 47.826 0.00 0.00 0.00 4.10
3533 3577 3.363178 GCTTAATATGGCTGTTCGTTGC 58.637 45.455 0.00 0.00 0.00 4.17
3534 3578 3.065371 GCTTAATATGGCTGTTCGTTGCT 59.935 43.478 0.00 0.00 0.00 3.91
3535 3579 4.438744 GCTTAATATGGCTGTTCGTTGCTT 60.439 41.667 0.00 0.00 0.00 3.91
3536 3580 5.220777 GCTTAATATGGCTGTTCGTTGCTTA 60.221 40.000 0.00 0.00 0.00 3.09
3537 3581 6.676943 GCTTAATATGGCTGTTCGTTGCTTAA 60.677 38.462 0.00 0.00 0.00 1.85
3538 3582 5.835113 AATATGGCTGTTCGTTGCTTAAT 57.165 34.783 0.00 0.00 0.00 1.40
3539 3583 6.935741 AATATGGCTGTTCGTTGCTTAATA 57.064 33.333 0.00 0.00 0.00 0.98
3540 3584 7.510549 AATATGGCTGTTCGTTGCTTAATAT 57.489 32.000 0.00 0.00 0.00 1.28
3541 3585 4.614555 TGGCTGTTCGTTGCTTAATATG 57.385 40.909 0.00 0.00 0.00 1.78
3542 3586 3.376859 TGGCTGTTCGTTGCTTAATATGG 59.623 43.478 0.00 0.00 0.00 2.74
3543 3587 3.363178 GCTGTTCGTTGCTTAATATGGC 58.637 45.455 0.00 0.00 0.00 4.40
3544 3588 3.065371 GCTGTTCGTTGCTTAATATGGCT 59.935 43.478 0.00 0.00 0.00 4.75
3545 3589 4.591202 CTGTTCGTTGCTTAATATGGCTG 58.409 43.478 0.00 0.00 0.00 4.85
3584 3628 1.198178 TGTTCTGCGGTTTTAATCGGC 59.802 47.619 0.00 0.00 32.01 5.54
3589 3633 0.316689 GCGGTTTTAATCGGCGATGG 60.317 55.000 24.73 7.97 32.01 3.51
3620 3664 0.466189 CCCGGCCTATTTGTGCATCT 60.466 55.000 0.00 0.00 0.00 2.90
3637 3681 3.119743 GCATCTCTGTTGCTTGCATAACA 60.120 43.478 10.16 10.16 37.14 2.41
3638 3682 4.616604 GCATCTCTGTTGCTTGCATAACAA 60.617 41.667 11.30 3.50 36.47 2.83
3674 3718 2.989639 CCGTCTGGCTTGGGATGA 59.010 61.111 0.00 0.00 0.00 2.92
3675 3719 1.299648 CCGTCTGGCTTGGGATGAA 59.700 57.895 0.00 0.00 0.00 2.57
3676 3720 1.026718 CCGTCTGGCTTGGGATGAAC 61.027 60.000 0.00 0.00 0.00 3.18
3677 3721 1.026718 CGTCTGGCTTGGGATGAACC 61.027 60.000 0.00 0.00 38.08 3.62
3678 3722 0.038166 GTCTGGCTTGGGATGAACCA 59.962 55.000 0.00 0.00 41.20 3.67
3679 3723 2.877975 CTGGCTTGGGATGAACCAG 58.122 57.895 0.00 0.00 42.47 4.00
3705 3749 0.234884 GAAACGTGAAAGTGGCTCGG 59.765 55.000 0.00 0.00 0.00 4.63
3708 3788 2.671177 CGTGAAAGTGGCTCGGCTG 61.671 63.158 0.00 0.00 0.00 4.85
3718 3798 2.425592 CTCGGCTGGACAACCACA 59.574 61.111 0.00 0.00 41.77 4.17
3745 3827 5.335127 GTGTGACATTTCATAACTGCCATC 58.665 41.667 0.00 0.00 33.11 3.51
3746 3828 5.008980 TGTGACATTTCATAACTGCCATCA 58.991 37.500 0.00 0.00 33.11 3.07
3747 3829 5.106197 TGTGACATTTCATAACTGCCATCAC 60.106 40.000 0.00 0.00 33.11 3.06
3748 3830 4.398988 TGACATTTCATAACTGCCATCACC 59.601 41.667 0.00 0.00 0.00 4.02
3749 3831 3.701040 ACATTTCATAACTGCCATCACCC 59.299 43.478 0.00 0.00 0.00 4.61
3750 3832 3.448093 TTTCATAACTGCCATCACCCA 57.552 42.857 0.00 0.00 0.00 4.51
3751 3833 3.668141 TTCATAACTGCCATCACCCAT 57.332 42.857 0.00 0.00 0.00 4.00
3752 3834 3.213206 TCATAACTGCCATCACCCATC 57.787 47.619 0.00 0.00 0.00 3.51
3783 3865 3.830121 AGCCCATCTTCATCATCCTTTC 58.170 45.455 0.00 0.00 0.00 2.62
3798 3881 1.072965 CCTTTCTGGAAGTGCCACTCT 59.927 52.381 0.00 0.00 43.33 3.24
3806 3889 2.365941 GGAAGTGCCACTCTACCCTATC 59.634 54.545 0.00 0.00 36.34 2.08
3811 3894 5.407049 AGTGCCACTCTACCCTATCATAAT 58.593 41.667 0.00 0.00 0.00 1.28
3812 3895 5.846714 AGTGCCACTCTACCCTATCATAATT 59.153 40.000 0.00 0.00 0.00 1.40
3813 3896 6.014156 AGTGCCACTCTACCCTATCATAATTC 60.014 42.308 0.00 0.00 0.00 2.17
3814 3897 5.843969 TGCCACTCTACCCTATCATAATTCA 59.156 40.000 0.00 0.00 0.00 2.57
3815 3898 6.501805 TGCCACTCTACCCTATCATAATTCAT 59.498 38.462 0.00 0.00 0.00 2.57
3816 3899 7.678171 TGCCACTCTACCCTATCATAATTCATA 59.322 37.037 0.00 0.00 0.00 2.15
3817 3900 8.540388 GCCACTCTACCCTATCATAATTCATAA 58.460 37.037 0.00 0.00 0.00 1.90
3841 3924 8.485976 AAGACTTATTCATGTTAGAGCAACTC 57.514 34.615 0.00 0.00 38.05 3.01
3842 3925 7.846066 AGACTTATTCATGTTAGAGCAACTCT 58.154 34.615 2.23 2.23 43.83 3.24
3843 3926 8.317679 AGACTTATTCATGTTAGAGCAACTCTT 58.682 33.333 1.88 0.00 41.50 2.85
3844 3927 9.587772 GACTTATTCATGTTAGAGCAACTCTTA 57.412 33.333 1.88 0.00 41.50 2.10
3845 3928 9.944376 ACTTATTCATGTTAGAGCAACTCTTAA 57.056 29.630 1.88 0.00 41.50 1.85
3847 3930 6.706055 TTCATGTTAGAGCAACTCTTAACG 57.294 37.500 1.88 0.00 41.50 3.18
3848 3931 4.625742 TCATGTTAGAGCAACTCTTAACGC 59.374 41.667 1.88 0.00 41.50 4.84
3849 3932 2.984471 TGTTAGAGCAACTCTTAACGCG 59.016 45.455 3.53 3.53 41.50 6.01
3850 3933 2.273370 TAGAGCAACTCTTAACGCGG 57.727 50.000 12.47 0.00 41.50 6.46
3851 3934 1.014564 AGAGCAACTCTTAACGCGGC 61.015 55.000 12.47 0.00 37.60 6.53
3852 3935 2.095843 GCAACTCTTAACGCGGCG 59.904 61.111 22.36 22.36 0.00 6.46
3853 3936 2.377310 GCAACTCTTAACGCGGCGA 61.377 57.895 30.94 4.11 0.00 5.54
3854 3937 1.414897 CAACTCTTAACGCGGCGAC 59.585 57.895 30.94 0.11 0.00 5.19
3855 3938 1.735559 AACTCTTAACGCGGCGACC 60.736 57.895 30.94 0.00 0.00 4.79
3856 3939 2.884207 CTCTTAACGCGGCGACCC 60.884 66.667 30.94 0.00 0.00 4.46
3857 3940 3.636313 CTCTTAACGCGGCGACCCA 62.636 63.158 30.94 8.67 0.00 4.51
3858 3941 2.739287 CTTAACGCGGCGACCCAA 60.739 61.111 30.94 14.66 0.00 4.12
3859 3942 2.280660 TTAACGCGGCGACCCAAA 60.281 55.556 30.94 11.85 0.00 3.28
3860 3943 2.503034 CTTAACGCGGCGACCCAAAC 62.503 60.000 30.94 0.00 0.00 2.93
3873 3956 4.622456 CAAACGGGCACGCGCTTT 62.622 61.111 9.12 0.00 46.04 3.51
3874 3957 4.322385 AAACGGGCACGCGCTTTC 62.322 61.111 9.12 0.00 46.04 2.62
3880 3963 3.411351 GCACGCGCTTTCTCCGAA 61.411 61.111 5.73 0.00 34.30 4.30
3881 3964 2.950172 GCACGCGCTTTCTCCGAAA 61.950 57.895 5.73 0.00 34.30 3.46
3882 3965 1.154654 CACGCGCTTTCTCCGAAAC 60.155 57.895 5.73 0.00 0.00 2.78
3883 3966 2.315386 ACGCGCTTTCTCCGAAACC 61.315 57.895 5.73 0.00 0.00 3.27
3884 3967 2.314647 CGCGCTTTCTCCGAAACCA 61.315 57.895 5.56 0.00 0.00 3.67
3885 3968 1.206831 GCGCTTTCTCCGAAACCAC 59.793 57.895 0.00 0.00 0.00 4.16
3886 3969 1.491563 CGCTTTCTCCGAAACCACG 59.508 57.895 0.00 0.00 0.00 4.94
3887 3970 1.219522 CGCTTTCTCCGAAACCACGT 61.220 55.000 0.00 0.00 0.00 4.49
3888 3971 0.942252 GCTTTCTCCGAAACCACGTT 59.058 50.000 0.00 0.00 0.00 3.99
3889 3972 1.333791 GCTTTCTCCGAAACCACGTTG 60.334 52.381 0.00 0.00 0.00 4.10
3890 3973 1.263217 CTTTCTCCGAAACCACGTTGG 59.737 52.381 2.92 2.92 45.02 3.77
3891 3974 1.161563 TTCTCCGAAACCACGTTGGC 61.162 55.000 4.23 0.00 42.67 4.52
3892 3975 2.592287 TCCGAAACCACGTTGGCC 60.592 61.111 0.00 0.00 42.67 5.36
3893 3976 4.020378 CCGAAACCACGTTGGCCG 62.020 66.667 0.00 5.81 42.67 6.13
3894 3977 2.968156 CGAAACCACGTTGGCCGA 60.968 61.111 0.00 0.00 42.67 5.54
3895 3978 2.535788 CGAAACCACGTTGGCCGAA 61.536 57.895 0.00 0.00 42.67 4.30
3896 3979 1.728672 GAAACCACGTTGGCCGAAA 59.271 52.632 0.00 0.00 42.67 3.46
3897 3980 0.593008 GAAACCACGTTGGCCGAAAC 60.593 55.000 0.00 0.00 42.67 2.78
3898 3981 1.313812 AAACCACGTTGGCCGAAACA 61.314 50.000 0.00 0.00 42.67 2.83
3899 3982 1.720694 AACCACGTTGGCCGAAACAG 61.721 55.000 0.00 0.00 42.67 3.16
3900 3983 1.890041 CCACGTTGGCCGAAACAGA 60.890 57.895 0.00 0.00 40.70 3.41
3901 3984 1.278637 CACGTTGGCCGAAACAGAC 59.721 57.895 0.00 0.00 40.70 3.51
3902 3985 1.145377 ACGTTGGCCGAAACAGACT 59.855 52.632 0.00 0.00 40.70 3.24
3903 3986 0.390124 ACGTTGGCCGAAACAGACTA 59.610 50.000 0.00 0.00 40.70 2.59
3904 3987 1.202557 ACGTTGGCCGAAACAGACTAA 60.203 47.619 0.00 0.00 40.70 2.24
3905 3988 2.073816 CGTTGGCCGAAACAGACTAAT 58.926 47.619 0.00 0.00 39.56 1.73
3906 3989 2.482721 CGTTGGCCGAAACAGACTAATT 59.517 45.455 0.00 0.00 39.56 1.40
3907 3990 3.680937 CGTTGGCCGAAACAGACTAATTA 59.319 43.478 0.00 0.00 39.56 1.40
3908 3991 4.152759 CGTTGGCCGAAACAGACTAATTAA 59.847 41.667 0.00 0.00 39.56 1.40
3909 3992 5.334260 CGTTGGCCGAAACAGACTAATTAAA 60.334 40.000 0.00 0.00 39.56 1.52
3910 3993 5.616488 TGGCCGAAACAGACTAATTAAAC 57.384 39.130 0.00 0.00 0.00 2.01
3911 3994 5.064558 TGGCCGAAACAGACTAATTAAACA 58.935 37.500 0.00 0.00 0.00 2.83
3912 3995 5.708230 TGGCCGAAACAGACTAATTAAACAT 59.292 36.000 0.00 0.00 0.00 2.71
3913 3996 6.879993 TGGCCGAAACAGACTAATTAAACATA 59.120 34.615 0.00 0.00 0.00 2.29
3914 3997 7.065324 TGGCCGAAACAGACTAATTAAACATAG 59.935 37.037 0.00 0.00 0.00 2.23
3915 3998 7.065443 GGCCGAAACAGACTAATTAAACATAGT 59.935 37.037 0.00 0.18 35.13 2.12
3916 3999 8.448615 GCCGAAACAGACTAATTAAACATAGTT 58.551 33.333 0.00 0.00 32.66 2.24
3932 4015 7.681939 AACATAGTTATACATAAATGGCCGG 57.318 36.000 0.00 0.00 0.00 6.13
3933 4016 5.646360 ACATAGTTATACATAAATGGCCGGC 59.354 40.000 21.18 21.18 0.00 6.13
3934 4017 3.418047 AGTTATACATAAATGGCCGGCC 58.582 45.455 39.40 39.40 0.00 6.13
3944 4027 4.660938 GGCCGGCCAAGTCCACTT 62.661 66.667 40.73 0.00 36.45 3.16
3945 4028 2.349755 GCCGGCCAAGTCCACTTA 59.650 61.111 18.11 0.00 34.28 2.24
3946 4029 1.302993 GCCGGCCAAGTCCACTTAA 60.303 57.895 18.11 0.00 34.28 1.85
3947 4030 0.891904 GCCGGCCAAGTCCACTTAAA 60.892 55.000 18.11 0.00 34.28 1.52
3948 4031 0.879090 CCGGCCAAGTCCACTTAAAC 59.121 55.000 2.24 0.00 34.28 2.01
3949 4032 1.600023 CGGCCAAGTCCACTTAAACA 58.400 50.000 2.24 0.00 34.28 2.83
3950 4033 1.950909 CGGCCAAGTCCACTTAAACAA 59.049 47.619 2.24 0.00 34.28 2.83
3951 4034 2.287368 CGGCCAAGTCCACTTAAACAAC 60.287 50.000 2.24 0.00 34.28 3.32
3952 4035 2.956333 GGCCAAGTCCACTTAAACAACT 59.044 45.455 0.00 0.00 34.28 3.16
3953 4036 4.139038 GGCCAAGTCCACTTAAACAACTA 58.861 43.478 0.00 0.00 34.28 2.24
3954 4037 4.215613 GGCCAAGTCCACTTAAACAACTAG 59.784 45.833 0.00 0.00 34.28 2.57
3955 4038 5.061179 GCCAAGTCCACTTAAACAACTAGA 58.939 41.667 0.00 0.00 34.28 2.43
3956 4039 5.529800 GCCAAGTCCACTTAAACAACTAGAA 59.470 40.000 0.00 0.00 34.28 2.10
3957 4040 6.038936 GCCAAGTCCACTTAAACAACTAGAAA 59.961 38.462 0.00 0.00 34.28 2.52
3958 4041 7.415877 GCCAAGTCCACTTAAACAACTAGAAAA 60.416 37.037 0.00 0.00 34.28 2.29
3959 4042 8.630037 CCAAGTCCACTTAAACAACTAGAAAAT 58.370 33.333 0.00 0.00 34.28 1.82
3986 4069 3.685836 AAACACTAATAAATCGCCCGC 57.314 42.857 0.00 0.00 0.00 6.13
3987 4070 2.319136 ACACTAATAAATCGCCCGCA 57.681 45.000 0.00 0.00 0.00 5.69
3988 4071 1.937899 ACACTAATAAATCGCCCGCAC 59.062 47.619 0.00 0.00 0.00 5.34
3989 4072 1.070843 CACTAATAAATCGCCCGCACG 60.071 52.381 0.00 0.00 0.00 5.34
3990 4073 0.110823 CTAATAAATCGCCCGCACGC 60.111 55.000 0.00 0.00 0.00 5.34
3991 4074 1.500512 TAATAAATCGCCCGCACGCC 61.501 55.000 0.00 0.00 0.00 5.68
3992 4075 4.761845 TAAATCGCCCGCACGCCA 62.762 61.111 0.00 0.00 0.00 5.69
4000 4083 3.454573 CCGCACGCCACCCTAGTA 61.455 66.667 0.00 0.00 0.00 1.82
4001 4084 2.104331 CGCACGCCACCCTAGTAG 59.896 66.667 0.00 0.00 0.00 2.57
4002 4085 2.412323 CGCACGCCACCCTAGTAGA 61.412 63.158 0.00 0.00 0.00 2.59
4003 4086 1.141234 GCACGCCACCCTAGTAGAC 59.859 63.158 0.00 0.00 0.00 2.59
4004 4087 1.814527 CACGCCACCCTAGTAGACC 59.185 63.158 0.00 0.00 0.00 3.85
4005 4088 1.751927 ACGCCACCCTAGTAGACCG 60.752 63.158 0.00 0.00 0.00 4.79
4006 4089 2.813200 GCCACCCTAGTAGACCGC 59.187 66.667 0.00 0.00 0.00 5.68
4007 4090 2.794028 GCCACCCTAGTAGACCGCC 61.794 68.421 0.00 0.00 0.00 6.13
4008 4091 1.076192 CCACCCTAGTAGACCGCCT 60.076 63.158 0.00 0.00 0.00 5.52
4009 4092 0.686769 CCACCCTAGTAGACCGCCTT 60.687 60.000 0.00 0.00 0.00 4.35
4010 4093 0.460311 CACCCTAGTAGACCGCCTTG 59.540 60.000 0.00 0.00 0.00 3.61
4011 4094 1.328430 ACCCTAGTAGACCGCCTTGC 61.328 60.000 0.00 0.00 0.00 4.01
4012 4095 1.442148 CCTAGTAGACCGCCTTGCC 59.558 63.158 0.00 0.00 0.00 4.52
4013 4096 1.442148 CTAGTAGACCGCCTTGCCC 59.558 63.158 0.00 0.00 0.00 5.36
4014 4097 1.001248 TAGTAGACCGCCTTGCCCT 59.999 57.895 0.00 0.00 0.00 5.19
4015 4098 0.616679 TAGTAGACCGCCTTGCCCTT 60.617 55.000 0.00 0.00 0.00 3.95
4016 4099 1.745489 GTAGACCGCCTTGCCCTTG 60.745 63.158 0.00 0.00 0.00 3.61
4017 4100 3.622060 TAGACCGCCTTGCCCTTGC 62.622 63.158 0.00 0.00 38.26 4.01
4021 4104 3.741476 CGCCTTGCCCTTGCTGTC 61.741 66.667 0.00 0.00 38.71 3.51
4022 4105 2.598394 GCCTTGCCCTTGCTGTCA 60.598 61.111 0.00 0.00 38.71 3.58
4023 4106 1.980772 GCCTTGCCCTTGCTGTCAT 60.981 57.895 0.00 0.00 38.71 3.06
4024 4107 1.941999 GCCTTGCCCTTGCTGTCATC 61.942 60.000 0.00 0.00 38.71 2.92
4025 4108 1.651240 CCTTGCCCTTGCTGTCATCG 61.651 60.000 0.00 0.00 38.71 3.84
4026 4109 0.957395 CTTGCCCTTGCTGTCATCGT 60.957 55.000 0.00 0.00 38.71 3.73
4027 4110 0.955428 TTGCCCTTGCTGTCATCGTC 60.955 55.000 0.00 0.00 38.71 4.20
4028 4111 2.109126 GCCCTTGCTGTCATCGTCC 61.109 63.158 0.00 0.00 33.53 4.79
4029 4112 1.599047 CCCTTGCTGTCATCGTCCT 59.401 57.895 0.00 0.00 0.00 3.85
4030 4113 0.460987 CCCTTGCTGTCATCGTCCTC 60.461 60.000 0.00 0.00 0.00 3.71
4031 4114 0.803768 CCTTGCTGTCATCGTCCTCG 60.804 60.000 0.00 0.00 38.55 4.63
4032 4115 1.416813 CTTGCTGTCATCGTCCTCGC 61.417 60.000 0.00 0.00 36.96 5.03
4033 4116 1.877576 TTGCTGTCATCGTCCTCGCT 61.878 55.000 0.00 0.00 36.96 4.93
4034 4117 1.875813 GCTGTCATCGTCCTCGCTG 60.876 63.158 0.00 0.00 36.96 5.18
4035 4118 1.875813 CTGTCATCGTCCTCGCTGC 60.876 63.158 0.00 0.00 33.91 5.25
4036 4119 2.276863 CTGTCATCGTCCTCGCTGCT 62.277 60.000 0.00 0.00 33.91 4.24
4037 4120 1.153745 GTCATCGTCCTCGCTGCTT 60.154 57.895 0.00 0.00 33.91 3.91
4038 4121 1.153765 TCATCGTCCTCGCTGCTTG 60.154 57.895 0.00 0.00 33.91 4.01
4039 4122 1.446792 CATCGTCCTCGCTGCTTGT 60.447 57.895 0.00 0.00 36.96 3.16
4040 4123 1.446792 ATCGTCCTCGCTGCTTGTG 60.447 57.895 0.00 0.00 36.96 3.33
4041 4124 1.877576 ATCGTCCTCGCTGCTTGTGA 61.878 55.000 0.00 0.00 36.96 3.58
4045 4128 3.867771 CTCGCTGCTTGTGAGGTC 58.132 61.111 11.30 0.00 46.48 3.85
4046 4129 1.005748 CTCGCTGCTTGTGAGGTCA 60.006 57.895 11.30 0.00 46.48 4.02
4047 4130 0.601046 CTCGCTGCTTGTGAGGTCAA 60.601 55.000 11.30 0.00 46.48 3.18
4048 4131 0.035317 TCGCTGCTTGTGAGGTCAAT 59.965 50.000 0.00 0.00 0.00 2.57
4049 4132 0.167470 CGCTGCTTGTGAGGTCAATG 59.833 55.000 0.00 0.00 0.00 2.82
4050 4133 1.527034 GCTGCTTGTGAGGTCAATGA 58.473 50.000 0.00 0.00 0.00 2.57
4051 4134 1.881973 GCTGCTTGTGAGGTCAATGAA 59.118 47.619 0.00 0.00 0.00 2.57
4052 4135 2.095364 GCTGCTTGTGAGGTCAATGAAG 60.095 50.000 0.00 0.00 0.00 3.02
4053 4136 3.405831 CTGCTTGTGAGGTCAATGAAGA 58.594 45.455 0.00 0.00 0.00 2.87
4054 4137 3.141398 TGCTTGTGAGGTCAATGAAGAC 58.859 45.455 0.00 0.00 37.80 3.01
4055 4138 2.158449 GCTTGTGAGGTCAATGAAGACG 59.842 50.000 0.00 0.00 39.42 4.18
4056 4139 1.795768 TGTGAGGTCAATGAAGACGC 58.204 50.000 0.00 0.00 39.42 5.19
4057 4140 0.716108 GTGAGGTCAATGAAGACGCG 59.284 55.000 3.53 3.53 39.42 6.01
4058 4141 0.389817 TGAGGTCAATGAAGACGCGG 60.390 55.000 12.47 0.00 39.42 6.46
4059 4142 1.696832 GAGGTCAATGAAGACGCGGC 61.697 60.000 12.47 7.86 39.42 6.53
4060 4143 1.741770 GGTCAATGAAGACGCGGCT 60.742 57.895 9.84 9.84 39.42 5.52
4061 4144 1.298859 GGTCAATGAAGACGCGGCTT 61.299 55.000 30.81 30.81 39.42 4.35
4062 4145 0.179215 GTCAATGAAGACGCGGCTTG 60.179 55.000 35.74 19.62 0.00 4.01
4063 4146 0.320334 TCAATGAAGACGCGGCTTGA 60.320 50.000 35.74 27.17 0.00 3.02
4064 4147 0.729116 CAATGAAGACGCGGCTTGAT 59.271 50.000 35.74 28.36 0.00 2.57
4065 4148 1.933181 CAATGAAGACGCGGCTTGATA 59.067 47.619 35.74 18.70 0.00 2.15
4066 4149 1.858091 ATGAAGACGCGGCTTGATAG 58.142 50.000 35.74 0.00 0.00 2.08
4067 4150 0.179111 TGAAGACGCGGCTTGATAGG 60.179 55.000 35.74 0.00 0.00 2.57
4068 4151 1.491505 GAAGACGCGGCTTGATAGGC 61.492 60.000 35.74 13.17 43.21 3.93
4069 4152 2.925162 AAGACGCGGCTTGATAGGCC 62.925 60.000 29.74 0.00 43.72 5.19
4074 4157 4.445699 GGCTTGATAGGCCGTCAG 57.554 61.111 12.66 9.13 40.92 3.51
4075 4158 1.227674 GGCTTGATAGGCCGTCAGG 60.228 63.158 15.77 15.77 40.92 3.86
4076 4159 1.227674 GCTTGATAGGCCGTCAGGG 60.228 63.158 19.67 14.49 38.20 4.45
4086 4169 4.436998 CGTCAGGGCAGTCGGGAC 62.437 72.222 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
259 262 6.993786 TGAATAAGCATTCGGACAATGTTA 57.006 33.333 0.00 0.00 43.06 2.41
408 413 9.934190 AAATGTTGAACAAGTATTTGAAAATGC 57.066 25.926 0.62 0.00 37.73 3.56
633 644 4.047125 CCACTTGTCCCGGCCCAT 62.047 66.667 0.00 0.00 0.00 4.00
673 684 2.130272 TTAAGCGAGAGAGAGGAGCA 57.870 50.000 0.00 0.00 0.00 4.26
675 686 3.011949 GCATTAAGCGAGAGAGAGGAG 57.988 52.381 0.00 0.00 0.00 3.69
733 748 0.953960 CGCTGGGCTAGTTTTCCGTT 60.954 55.000 0.00 0.00 0.00 4.44
734 749 1.375523 CGCTGGGCTAGTTTTCCGT 60.376 57.895 0.00 0.00 0.00 4.69
925 940 1.078214 TTTGGAGCTCTGGATGCGG 60.078 57.895 14.64 0.00 35.28 5.69
985 1008 4.247380 CATGGCCTCTCCCTCGCC 62.247 72.222 3.32 0.00 43.32 5.54
986 1009 4.247380 CCATGGCCTCTCCCTCGC 62.247 72.222 3.32 0.00 0.00 5.03
987 1010 1.825281 GATCCATGGCCTCTCCCTCG 61.825 65.000 6.96 0.00 0.00 4.63
988 1011 1.487850 GGATCCATGGCCTCTCCCTC 61.488 65.000 6.96 0.00 0.00 4.30
1367 1390 2.660572 AGGATCAGATCAGCACGTACT 58.339 47.619 12.66 0.00 0.00 2.73
1371 1394 4.082300 AGCTAATAGGATCAGATCAGCACG 60.082 45.833 17.61 2.74 0.00 5.34
1430 1453 3.714798 AGTGGTACCGTATGATTTGGGAT 59.285 43.478 7.57 0.00 0.00 3.85
1483 1506 0.233332 GCAAAGCATAGATCGCGGAC 59.767 55.000 6.13 0.00 0.00 4.79
1486 1509 2.989166 TGATAGCAAAGCATAGATCGCG 59.011 45.455 0.00 0.00 0.00 5.87
1488 1511 6.291690 CGATCATGATAGCAAAGCATAGATCG 60.292 42.308 21.82 21.82 39.91 3.69
1520 1543 8.643324 ACAGGGATATAGATTAAGTTGACAGAC 58.357 37.037 0.00 0.00 0.00 3.51
1608 1632 7.658261 TCTATAAATGTCCACTTGTCGGATAG 58.342 38.462 0.00 0.00 34.32 2.08
1652 1676 1.335964 CGATGCGTACGAGGGAATGAT 60.336 52.381 21.65 0.00 0.00 2.45
1662 1686 1.876714 CCCAAGGACGATGCGTACG 60.877 63.158 11.84 11.84 46.41 3.67
1752 1776 5.475909 ACAGATCCTGTAAAGAACTACACGA 59.524 40.000 0.00 0.00 43.46 4.35
1769 1793 5.501156 ACAGACTAAAATCCCAACAGATCC 58.499 41.667 0.00 0.00 0.00 3.36
2125 2151 8.721478 GCTCACATTATCGGTATCACAATTATT 58.279 33.333 0.00 0.00 0.00 1.40
2127 2153 7.213678 TGCTCACATTATCGGTATCACAATTA 58.786 34.615 0.00 0.00 0.00 1.40
2128 2154 6.054941 TGCTCACATTATCGGTATCACAATT 58.945 36.000 0.00 0.00 0.00 2.32
2129 2155 5.610398 TGCTCACATTATCGGTATCACAAT 58.390 37.500 0.00 0.00 0.00 2.71
2293 2319 2.827322 TGCATGGTGAAAGGAATTCTGG 59.173 45.455 5.23 0.00 38.92 3.86
2353 2379 9.106070 GGAGTATTTGTTATTCTAAACGACCAT 57.894 33.333 0.00 0.00 31.76 3.55
2502 2529 5.977635 AGATACAACTACACATAAGCAGCA 58.022 37.500 0.00 0.00 0.00 4.41
2692 2725 2.301870 TGTTGAACGGAGTGGCTAAGAT 59.698 45.455 0.00 0.00 45.00 2.40
2705 2738 6.598525 TCATAAAGCATGTAACTGTTGAACG 58.401 36.000 2.69 0.00 35.96 3.95
2717 2750 5.769367 CAGCATAAGCATCATAAAGCATGT 58.231 37.500 0.00 0.00 45.49 3.21
2792 2825 4.217983 ACACTCTTCTAAGGACCAGTAACG 59.782 45.833 0.00 0.00 0.00 3.18
2897 2930 3.228188 ACTTCCATGCAACCTCTCAAA 57.772 42.857 0.00 0.00 0.00 2.69
2922 2956 6.591834 AGATCAGAAAGACAAGGAACATAACG 59.408 38.462 0.00 0.00 0.00 3.18
2932 2966 5.157940 TCCCTTGAGATCAGAAAGACAAG 57.842 43.478 0.00 0.00 35.84 3.16
2975 3009 4.279420 AGAAAAGACTCCAAATCCTTGTGC 59.721 41.667 0.00 0.00 0.00 4.57
3485 3529 4.742201 TTCGTCTGCAGCCGGAGC 62.742 66.667 18.07 9.42 40.32 4.70
3526 3570 4.201773 CGAACAGCCATATTAAGCAACGAA 60.202 41.667 0.00 0.00 0.00 3.85
3527 3571 3.308595 CGAACAGCCATATTAAGCAACGA 59.691 43.478 0.00 0.00 0.00 3.85
3528 3572 3.063452 ACGAACAGCCATATTAAGCAACG 59.937 43.478 0.00 0.00 0.00 4.10
3529 3573 4.616181 ACGAACAGCCATATTAAGCAAC 57.384 40.909 0.00 0.00 0.00 4.17
3530 3574 4.457603 ACAACGAACAGCCATATTAAGCAA 59.542 37.500 0.00 0.00 0.00 3.91
3531 3575 4.006989 ACAACGAACAGCCATATTAAGCA 58.993 39.130 0.00 0.00 0.00 3.91
3532 3576 4.342772 CACAACGAACAGCCATATTAAGC 58.657 43.478 0.00 0.00 0.00 3.09
3533 3577 4.142708 TGCACAACGAACAGCCATATTAAG 60.143 41.667 0.00 0.00 0.00 1.85
3534 3578 3.753797 TGCACAACGAACAGCCATATTAA 59.246 39.130 0.00 0.00 0.00 1.40
3535 3579 3.339141 TGCACAACGAACAGCCATATTA 58.661 40.909 0.00 0.00 0.00 0.98
3536 3580 2.158559 TGCACAACGAACAGCCATATT 58.841 42.857 0.00 0.00 0.00 1.28
3537 3581 1.739466 CTGCACAACGAACAGCCATAT 59.261 47.619 0.00 0.00 0.00 1.78
3538 3582 1.155889 CTGCACAACGAACAGCCATA 58.844 50.000 0.00 0.00 0.00 2.74
3539 3583 0.534877 TCTGCACAACGAACAGCCAT 60.535 50.000 0.00 0.00 0.00 4.40
3540 3584 0.746204 TTCTGCACAACGAACAGCCA 60.746 50.000 0.00 0.00 0.00 4.75
3541 3585 0.317020 GTTCTGCACAACGAACAGCC 60.317 55.000 10.70 0.00 39.36 4.85
3542 3586 3.148823 GTTCTGCACAACGAACAGC 57.851 52.632 10.70 0.00 39.36 4.40
3605 3649 3.733077 GCAACAGAGATGCACAAATAGGC 60.733 47.826 0.00 0.00 43.29 3.93
3637 3681 2.297315 GGCTGCTTTTAGTTTCCTGCTT 59.703 45.455 0.00 0.00 0.00 3.91
3638 3682 1.889170 GGCTGCTTTTAGTTTCCTGCT 59.111 47.619 0.00 0.00 0.00 4.24
3674 3718 1.210967 TCACGTTTCTGGGAACTGGTT 59.789 47.619 0.00 0.00 0.00 3.67
3675 3719 0.834612 TCACGTTTCTGGGAACTGGT 59.165 50.000 0.00 0.00 0.00 4.00
3676 3720 1.961793 TTCACGTTTCTGGGAACTGG 58.038 50.000 0.00 0.00 0.00 4.00
3677 3721 2.943033 ACTTTCACGTTTCTGGGAACTG 59.057 45.455 0.00 0.00 0.00 3.16
3678 3722 2.943033 CACTTTCACGTTTCTGGGAACT 59.057 45.455 0.00 0.00 0.00 3.01
3679 3723 2.032924 CCACTTTCACGTTTCTGGGAAC 59.967 50.000 0.00 0.00 0.00 3.62
3705 3749 3.749981 CCAGTGTGGTTGTCCAGC 58.250 61.111 0.00 0.00 45.24 4.85
3718 3798 4.216257 GCAGTTATGAAATGTCACACCAGT 59.784 41.667 0.00 0.00 36.31 4.00
3745 3827 1.303309 GCTTTGAGGATCGATGGGTG 58.697 55.000 0.54 0.00 38.61 4.61
3746 3828 0.181350 GGCTTTGAGGATCGATGGGT 59.819 55.000 0.54 0.00 38.61 4.51
3747 3829 0.536006 GGGCTTTGAGGATCGATGGG 60.536 60.000 0.54 0.00 38.61 4.00
3748 3830 0.181114 TGGGCTTTGAGGATCGATGG 59.819 55.000 0.54 0.00 38.61 3.51
3749 3831 2.149578 GATGGGCTTTGAGGATCGATG 58.850 52.381 0.54 0.00 38.61 3.84
3750 3832 2.053244 AGATGGGCTTTGAGGATCGAT 58.947 47.619 0.00 0.00 38.61 3.59
3751 3833 1.500474 AGATGGGCTTTGAGGATCGA 58.500 50.000 0.00 0.00 38.61 3.59
3752 3834 2.216898 GAAGATGGGCTTTGAGGATCG 58.783 52.381 0.00 0.00 35.38 3.69
3815 3898 9.587772 GAGTTGCTCTAACATGAATAAGTCTTA 57.412 33.333 0.00 0.00 41.88 2.10
3816 3899 8.317679 AGAGTTGCTCTAACATGAATAAGTCTT 58.682 33.333 0.00 0.00 39.28 3.01
3817 3900 7.846066 AGAGTTGCTCTAACATGAATAAGTCT 58.154 34.615 0.00 0.18 39.28 3.24
3818 3901 8.485976 AAGAGTTGCTCTAACATGAATAAGTC 57.514 34.615 0.00 0.00 40.28 3.01
3819 3902 9.944376 TTAAGAGTTGCTCTAACATGAATAAGT 57.056 29.630 0.00 0.00 40.28 2.24
3821 3904 8.869897 CGTTAAGAGTTGCTCTAACATGAATAA 58.130 33.333 0.00 0.00 40.28 1.40
3822 3905 7.010183 GCGTTAAGAGTTGCTCTAACATGAATA 59.990 37.037 0.00 0.00 40.28 1.75
3823 3906 6.183360 GCGTTAAGAGTTGCTCTAACATGAAT 60.183 38.462 0.00 0.00 40.28 2.57
3824 3907 5.120208 GCGTTAAGAGTTGCTCTAACATGAA 59.880 40.000 0.00 0.00 40.28 2.57
3825 3908 4.625742 GCGTTAAGAGTTGCTCTAACATGA 59.374 41.667 0.00 0.00 40.28 3.07
3826 3909 4.490959 CGCGTTAAGAGTTGCTCTAACATG 60.491 45.833 0.00 0.00 40.28 3.21
3827 3910 3.612860 CGCGTTAAGAGTTGCTCTAACAT 59.387 43.478 0.00 0.00 40.28 2.71
3828 3911 2.984471 CGCGTTAAGAGTTGCTCTAACA 59.016 45.455 0.00 0.00 40.28 2.41
3829 3912 2.344741 CCGCGTTAAGAGTTGCTCTAAC 59.655 50.000 4.92 4.46 40.28 2.34
3830 3913 2.602878 CCGCGTTAAGAGTTGCTCTAA 58.397 47.619 4.92 0.00 40.28 2.10
3831 3914 1.734707 GCCGCGTTAAGAGTTGCTCTA 60.735 52.381 4.92 0.00 40.28 2.43
3832 3915 1.014564 GCCGCGTTAAGAGTTGCTCT 61.015 55.000 4.92 0.00 43.37 4.09
3833 3916 1.420312 GCCGCGTTAAGAGTTGCTC 59.580 57.895 4.92 0.00 0.00 4.26
3834 3917 2.380410 CGCCGCGTTAAGAGTTGCT 61.380 57.895 4.92 0.00 0.00 3.91
3835 3918 2.095843 CGCCGCGTTAAGAGTTGC 59.904 61.111 4.92 0.00 0.00 4.17
3836 3919 1.414897 GTCGCCGCGTTAAGAGTTG 59.585 57.895 13.39 0.00 0.00 3.16
3837 3920 1.735559 GGTCGCCGCGTTAAGAGTT 60.736 57.895 13.39 0.00 0.00 3.01
3838 3921 2.126189 GGTCGCCGCGTTAAGAGT 60.126 61.111 13.39 0.00 0.00 3.24
3839 3922 2.884207 GGGTCGCCGCGTTAAGAG 60.884 66.667 13.39 0.00 0.00 2.85
3840 3923 2.712325 TTTGGGTCGCCGCGTTAAGA 62.712 55.000 13.39 0.00 0.00 2.10
3841 3924 2.319096 TTTGGGTCGCCGCGTTAAG 61.319 57.895 13.39 0.00 0.00 1.85
3842 3925 2.280660 TTTGGGTCGCCGCGTTAA 60.281 55.556 13.39 1.49 0.00 2.01
3843 3926 3.043121 GTTTGGGTCGCCGCGTTA 61.043 61.111 13.39 0.00 0.00 3.18
3856 3939 4.622456 AAAGCGCGTGCCCGTTTG 62.622 61.111 19.02 0.00 44.31 2.93
3857 3940 4.322385 GAAAGCGCGTGCCCGTTT 62.322 61.111 19.02 11.97 44.31 3.60
3863 3946 2.950172 TTTCGGAGAAAGCGCGTGC 61.950 57.895 14.39 14.39 45.90 5.34
3864 3947 1.154654 GTTTCGGAGAAAGCGCGTG 60.155 57.895 8.43 0.00 45.90 5.34
3865 3948 2.315386 GGTTTCGGAGAAAGCGCGT 61.315 57.895 8.43 0.00 45.90 6.01
3866 3949 2.314647 TGGTTTCGGAGAAAGCGCG 61.315 57.895 16.49 0.00 45.90 6.86
3867 3950 1.206831 GTGGTTTCGGAGAAAGCGC 59.793 57.895 18.11 18.11 45.90 5.92
3868 3951 1.219522 ACGTGGTTTCGGAGAAAGCG 61.220 55.000 16.49 13.15 45.90 4.68
3869 3952 0.942252 AACGTGGTTTCGGAGAAAGC 59.058 50.000 15.25 15.25 45.90 3.51
3870 3953 1.263217 CCAACGTGGTTTCGGAGAAAG 59.737 52.381 0.00 0.00 35.15 2.62
3871 3954 1.301423 CCAACGTGGTTTCGGAGAAA 58.699 50.000 0.00 0.00 35.15 2.52
3872 3955 1.161563 GCCAACGTGGTTTCGGAGAA 61.162 55.000 0.00 0.00 40.58 2.87
3873 3956 1.595929 GCCAACGTGGTTTCGGAGA 60.596 57.895 0.00 0.00 40.46 3.71
3874 3957 2.613506 GGCCAACGTGGTTTCGGAG 61.614 63.158 0.00 0.00 40.46 4.63
3875 3958 2.592287 GGCCAACGTGGTTTCGGA 60.592 61.111 0.00 0.00 40.46 4.55
3876 3959 4.020378 CGGCCAACGTGGTTTCGG 62.020 66.667 2.24 0.00 40.46 4.30
3877 3960 2.049475 TTTCGGCCAACGTGGTTTCG 62.049 55.000 2.24 0.10 44.69 3.46
3878 3961 0.593008 GTTTCGGCCAACGTGGTTTC 60.593 55.000 2.24 0.00 44.69 2.78
3879 3962 1.313812 TGTTTCGGCCAACGTGGTTT 61.314 50.000 2.24 0.00 44.69 3.27
3880 3963 1.720694 CTGTTTCGGCCAACGTGGTT 61.721 55.000 2.24 0.00 44.69 3.67
3881 3964 2.124653 TGTTTCGGCCAACGTGGT 60.125 55.556 2.24 0.00 44.69 4.16
3882 3965 1.890041 TCTGTTTCGGCCAACGTGG 60.890 57.895 2.24 0.00 44.69 4.94
3883 3966 1.157870 AGTCTGTTTCGGCCAACGTG 61.158 55.000 2.24 0.00 44.69 4.49
3884 3967 0.390124 TAGTCTGTTTCGGCCAACGT 59.610 50.000 2.24 0.00 44.69 3.99
3885 3968 1.504359 TTAGTCTGTTTCGGCCAACG 58.496 50.000 2.24 0.00 46.11 4.10
3886 3969 5.616488 TTAATTAGTCTGTTTCGGCCAAC 57.384 39.130 2.24 0.30 0.00 3.77
3887 3970 5.531659 TGTTTAATTAGTCTGTTTCGGCCAA 59.468 36.000 2.24 0.00 0.00 4.52
3888 3971 5.064558 TGTTTAATTAGTCTGTTTCGGCCA 58.935 37.500 2.24 0.00 0.00 5.36
3889 3972 5.616488 TGTTTAATTAGTCTGTTTCGGCC 57.384 39.130 0.00 0.00 0.00 6.13
3890 3973 7.971455 ACTATGTTTAATTAGTCTGTTTCGGC 58.029 34.615 0.00 0.00 0.00 5.54
3906 3989 9.221933 CCGGCCATTTATGTATAACTATGTTTA 57.778 33.333 2.24 0.00 0.00 2.01
3907 3990 7.308951 GCCGGCCATTTATGTATAACTATGTTT 60.309 37.037 18.11 0.00 0.00 2.83
3908 3991 6.150474 GCCGGCCATTTATGTATAACTATGTT 59.850 38.462 18.11 0.00 0.00 2.71
3909 3992 5.646360 GCCGGCCATTTATGTATAACTATGT 59.354 40.000 18.11 0.00 0.00 2.29
3910 3993 5.065988 GGCCGGCCATTTATGTATAACTATG 59.934 44.000 40.73 0.00 35.81 2.23
3911 3994 5.190677 GGCCGGCCATTTATGTATAACTAT 58.809 41.667 40.73 0.00 35.81 2.12
3912 3995 4.041815 TGGCCGGCCATTTATGTATAACTA 59.958 41.667 44.23 16.09 41.89 2.24
3913 3996 3.181438 TGGCCGGCCATTTATGTATAACT 60.181 43.478 44.23 0.00 41.89 2.24
3914 3997 3.150767 TGGCCGGCCATTTATGTATAAC 58.849 45.455 44.23 13.60 41.89 1.89
3915 3998 3.510531 TGGCCGGCCATTTATGTATAA 57.489 42.857 44.23 17.60 41.89 0.98
3916 3999 3.181438 ACTTGGCCGGCCATTTATGTATA 60.181 43.478 46.94 28.07 46.64 1.47
3917 4000 2.238521 CTTGGCCGGCCATTTATGTAT 58.761 47.619 46.94 0.00 46.64 2.29
3918 4001 1.064314 ACTTGGCCGGCCATTTATGTA 60.064 47.619 46.94 29.61 46.64 2.29
3919 4002 0.324275 ACTTGGCCGGCCATTTATGT 60.324 50.000 46.94 32.98 46.64 2.29
3920 4003 0.385390 GACTTGGCCGGCCATTTATG 59.615 55.000 46.94 32.37 46.64 1.90
3921 4004 0.755327 GGACTTGGCCGGCCATTTAT 60.755 55.000 46.94 31.40 46.64 1.40
3922 4005 1.379309 GGACTTGGCCGGCCATTTA 60.379 57.895 46.94 31.93 46.64 1.40
3923 4006 2.679996 GGACTTGGCCGGCCATTT 60.680 61.111 46.94 35.63 46.64 2.32
3924 4007 3.978193 TGGACTTGGCCGGCCATT 61.978 61.111 46.94 36.01 46.64 3.16
3925 4008 4.740822 GTGGACTTGGCCGGCCAT 62.741 66.667 46.94 34.74 46.64 4.40
3927 4010 2.757980 TTAAGTGGACTTGGCCGGCC 62.758 60.000 39.40 39.40 37.40 6.13
3928 4011 0.891904 TTTAAGTGGACTTGGCCGGC 60.892 55.000 21.18 21.18 37.40 6.13
3929 4012 0.879090 GTTTAAGTGGACTTGGCCGG 59.121 55.000 0.00 0.00 37.40 6.13
3930 4013 1.600023 TGTTTAAGTGGACTTGGCCG 58.400 50.000 0.00 0.00 37.40 6.13
3931 4014 2.956333 AGTTGTTTAAGTGGACTTGGCC 59.044 45.455 0.00 0.00 37.40 5.36
3932 4015 5.061179 TCTAGTTGTTTAAGTGGACTTGGC 58.939 41.667 2.14 0.00 37.40 4.52
3933 4016 7.562454 TTTCTAGTTGTTTAAGTGGACTTGG 57.438 36.000 2.14 0.00 37.40 3.61
3964 4047 4.082679 TGCGGGCGATTTATTAGTGTTTTT 60.083 37.500 0.00 0.00 0.00 1.94
3965 4048 3.440872 TGCGGGCGATTTATTAGTGTTTT 59.559 39.130 0.00 0.00 0.00 2.43
3966 4049 3.011119 TGCGGGCGATTTATTAGTGTTT 58.989 40.909 0.00 0.00 0.00 2.83
3967 4050 2.353579 GTGCGGGCGATTTATTAGTGTT 59.646 45.455 0.00 0.00 0.00 3.32
3968 4051 1.937899 GTGCGGGCGATTTATTAGTGT 59.062 47.619 0.00 0.00 0.00 3.55
3969 4052 1.070843 CGTGCGGGCGATTTATTAGTG 60.071 52.381 0.00 0.00 0.00 2.74
3970 4053 1.214367 CGTGCGGGCGATTTATTAGT 58.786 50.000 0.00 0.00 0.00 2.24
3971 4054 0.110823 GCGTGCGGGCGATTTATTAG 60.111 55.000 0.00 0.00 0.00 1.73
3972 4055 1.500512 GGCGTGCGGGCGATTTATTA 61.501 55.000 0.00 0.00 0.00 0.98
3973 4056 2.713154 GCGTGCGGGCGATTTATT 59.287 55.556 0.00 0.00 0.00 1.40
3974 4057 3.276846 GGCGTGCGGGCGATTTAT 61.277 61.111 0.00 0.00 0.00 1.40
3975 4058 4.761845 TGGCGTGCGGGCGATTTA 62.762 61.111 0.00 0.00 46.04 1.40
3983 4066 3.426117 CTACTAGGGTGGCGTGCGG 62.426 68.421 0.00 0.00 0.00 5.69
3984 4067 2.104331 CTACTAGGGTGGCGTGCG 59.896 66.667 0.00 0.00 0.00 5.34
3985 4068 1.141234 GTCTACTAGGGTGGCGTGC 59.859 63.158 0.00 0.00 0.00 5.34
3986 4069 1.814527 GGTCTACTAGGGTGGCGTG 59.185 63.158 0.00 0.00 0.00 5.34
3987 4070 1.751927 CGGTCTACTAGGGTGGCGT 60.752 63.158 0.00 0.00 0.00 5.68
3988 4071 3.117372 CGGTCTACTAGGGTGGCG 58.883 66.667 0.00 0.00 0.00 5.69
3989 4072 2.794028 GGCGGTCTACTAGGGTGGC 61.794 68.421 0.00 0.00 0.00 5.01
3990 4073 0.686769 AAGGCGGTCTACTAGGGTGG 60.687 60.000 0.00 0.00 0.00 4.61
3991 4074 0.460311 CAAGGCGGTCTACTAGGGTG 59.540 60.000 0.00 0.00 0.00 4.61
3992 4075 1.328430 GCAAGGCGGTCTACTAGGGT 61.328 60.000 0.00 0.00 0.00 4.34
3993 4076 1.442148 GCAAGGCGGTCTACTAGGG 59.558 63.158 0.00 0.00 0.00 3.53
3994 4077 1.442148 GGCAAGGCGGTCTACTAGG 59.558 63.158 0.00 0.00 0.00 3.02
3995 4078 1.043673 AGGGCAAGGCGGTCTACTAG 61.044 60.000 0.00 0.00 0.00 2.57
3996 4079 0.616679 AAGGGCAAGGCGGTCTACTA 60.617 55.000 0.00 0.00 0.00 1.82
3997 4080 1.918800 AAGGGCAAGGCGGTCTACT 60.919 57.895 0.00 0.00 0.00 2.57
3998 4081 1.745489 CAAGGGCAAGGCGGTCTAC 60.745 63.158 0.00 0.00 0.00 2.59
3999 4082 2.668632 CAAGGGCAAGGCGGTCTA 59.331 61.111 0.00 0.00 0.00 2.59
4004 4087 3.741476 GACAGCAAGGGCAAGGCG 61.741 66.667 0.00 0.00 44.61 5.52
4005 4088 1.941999 GATGACAGCAAGGGCAAGGC 61.942 60.000 0.00 0.00 44.61 4.35
4006 4089 1.651240 CGATGACAGCAAGGGCAAGG 61.651 60.000 0.00 0.00 44.61 3.61
4007 4090 0.957395 ACGATGACAGCAAGGGCAAG 60.957 55.000 0.00 0.00 44.61 4.01
4008 4091 0.955428 GACGATGACAGCAAGGGCAA 60.955 55.000 0.00 0.00 44.61 4.52
4009 4092 1.375908 GACGATGACAGCAAGGGCA 60.376 57.895 0.00 0.00 44.61 5.36
4010 4093 2.109126 GGACGATGACAGCAAGGGC 61.109 63.158 0.00 0.00 41.61 5.19
4011 4094 0.460987 GAGGACGATGACAGCAAGGG 60.461 60.000 0.00 0.00 0.00 3.95
4012 4095 0.803768 CGAGGACGATGACAGCAAGG 60.804 60.000 0.00 0.00 42.66 3.61
4013 4096 1.416813 GCGAGGACGATGACAGCAAG 61.417 60.000 0.00 0.00 42.66 4.01
4014 4097 1.446099 GCGAGGACGATGACAGCAA 60.446 57.895 0.00 0.00 42.66 3.91
4015 4098 2.181777 GCGAGGACGATGACAGCA 59.818 61.111 0.00 0.00 42.66 4.41
4016 4099 2.492090 AGCGAGGACGATGACAGC 59.508 61.111 0.00 0.00 42.66 4.40
4022 4105 1.446792 CACAAGCAGCGAGGACGAT 60.447 57.895 0.00 0.00 42.66 3.73
4023 4106 2.049156 CACAAGCAGCGAGGACGA 60.049 61.111 0.00 0.00 42.66 4.20
4024 4107 2.049156 TCACAAGCAGCGAGGACG 60.049 61.111 0.00 0.00 42.93 4.79
4025 4108 3.867771 CTCACAAGCAGCGAGGAC 58.132 61.111 0.00 0.00 0.00 3.85
4028 4111 0.601046 TTGACCTCACAAGCAGCGAG 60.601 55.000 0.00 0.00 0.00 5.03
4029 4112 0.035317 ATTGACCTCACAAGCAGCGA 59.965 50.000 0.00 0.00 33.22 4.93
4030 4113 0.167470 CATTGACCTCACAAGCAGCG 59.833 55.000 0.00 0.00 33.22 5.18
4031 4114 1.527034 TCATTGACCTCACAAGCAGC 58.473 50.000 0.00 0.00 33.22 5.25
4032 4115 3.188048 GTCTTCATTGACCTCACAAGCAG 59.812 47.826 0.00 0.00 33.22 4.24
4033 4116 3.141398 GTCTTCATTGACCTCACAAGCA 58.859 45.455 0.00 0.00 33.22 3.91
4034 4117 2.158449 CGTCTTCATTGACCTCACAAGC 59.842 50.000 0.00 0.00 33.70 4.01
4035 4118 2.158449 GCGTCTTCATTGACCTCACAAG 59.842 50.000 0.00 0.00 33.70 3.16
4036 4119 2.143122 GCGTCTTCATTGACCTCACAA 58.857 47.619 0.00 0.00 33.70 3.33
4037 4120 1.795768 GCGTCTTCATTGACCTCACA 58.204 50.000 0.00 0.00 33.70 3.58
4038 4121 0.716108 CGCGTCTTCATTGACCTCAC 59.284 55.000 0.00 0.00 33.70 3.51
4039 4122 0.389817 CCGCGTCTTCATTGACCTCA 60.390 55.000 4.92 0.00 33.70 3.86
4040 4123 1.696832 GCCGCGTCTTCATTGACCTC 61.697 60.000 4.92 0.00 33.70 3.85
4041 4124 1.741770 GCCGCGTCTTCATTGACCT 60.742 57.895 4.92 0.00 33.70 3.85
4042 4125 1.298859 AAGCCGCGTCTTCATTGACC 61.299 55.000 4.92 0.00 33.70 4.02
4043 4126 0.179215 CAAGCCGCGTCTTCATTGAC 60.179 55.000 0.00 0.00 0.00 3.18
4044 4127 0.320334 TCAAGCCGCGTCTTCATTGA 60.320 50.000 0.00 0.00 0.00 2.57
4045 4128 0.729116 ATCAAGCCGCGTCTTCATTG 59.271 50.000 0.00 0.00 0.00 2.82
4046 4129 2.205074 CTATCAAGCCGCGTCTTCATT 58.795 47.619 0.00 0.00 0.00 2.57
4047 4130 1.539065 CCTATCAAGCCGCGTCTTCAT 60.539 52.381 0.00 0.00 0.00 2.57
4048 4131 0.179111 CCTATCAAGCCGCGTCTTCA 60.179 55.000 0.00 0.00 0.00 3.02
4049 4132 1.491505 GCCTATCAAGCCGCGTCTTC 61.492 60.000 0.00 0.00 0.00 2.87
4050 4133 1.521681 GCCTATCAAGCCGCGTCTT 60.522 57.895 4.92 0.00 0.00 3.01
4051 4134 2.107141 GCCTATCAAGCCGCGTCT 59.893 61.111 4.92 0.00 0.00 4.18
4052 4135 2.967615 GGCCTATCAAGCCGCGTC 60.968 66.667 4.92 0.00 41.41 5.19
4058 4141 1.227674 CCCTGACGGCCTATCAAGC 60.228 63.158 0.00 0.00 0.00 4.01
4069 4152 4.436998 GTCCCGACTGCCCTGACG 62.437 72.222 0.00 0.00 0.00 4.35
4070 4153 4.436998 CGTCCCGACTGCCCTGAC 62.437 72.222 0.00 0.00 0.00 3.51
4075 4158 4.681978 ACAAGCGTCCCGACTGCC 62.682 66.667 7.66 0.00 33.56 4.85
4076 4159 3.414700 CACAAGCGTCCCGACTGC 61.415 66.667 4.27 4.27 0.00 4.40
4077 4160 1.734477 CTCACAAGCGTCCCGACTG 60.734 63.158 0.00 0.00 0.00 3.51
4078 4161 2.651361 CTCACAAGCGTCCCGACT 59.349 61.111 0.00 0.00 0.00 4.18
4079 4162 2.432628 CCTCACAAGCGTCCCGAC 60.433 66.667 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.