Multiple sequence alignment - TraesCS5B01G168900

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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 TraesCS5B01G168900 chr5B 100.000 4191 0 0 1 4191 313149035 313153225 0.000000e+00 7740.0
1 TraesCS5B01G168900 chr5A 86.519 1936 132 53 2 1891 364709502 364711354 0.000000e+00 2010.0
2 TraesCS5B01G168900 chr5A 95.864 822 31 3 1944 2763 364711365 364712185 0.000000e+00 1327.0
3 TraesCS5B01G168900 chr5A 94.040 453 25 2 2922 3373 364712184 364712635 0.000000e+00 686.0
4 TraesCS5B01G168900 chr5A 83.144 528 54 20 3677 4191 364713470 364713975 2.300000e-122 449.0
5 TraesCS5B01G168900 chr5A 95.062 162 8 0 2762 2923 320214244 320214405 5.380000e-64 255.0
6 TraesCS5B01G168900 chr5A 90.710 183 17 0 3370 3552 364712715 364712897 1.160000e-60 244.0
7 TraesCS5B01G168900 chr5A 91.525 59 3 2 771 828 44801145 44801088 3.470000e-11 80.5
8 TraesCS5B01G168900 chr5D 93.630 1193 61 9 2922 4108 276310139 276311322 0.000000e+00 1768.0
9 TraesCS5B01G168900 chr5D 92.897 1070 48 11 830 1874 276307692 276308758 0.000000e+00 1530.0
10 TraesCS5B01G168900 chr5D 95.845 746 28 3 2021 2763 276309395 276310140 0.000000e+00 1203.0
11 TraesCS5B01G168900 chr5D 88.567 586 35 16 196 774 276307104 276307664 0.000000e+00 682.0
12 TraesCS5B01G168900 chr5D 100.000 54 0 0 1946 1999 276309060 276309113 2.670000e-17 100.0
13 TraesCS5B01G168900 chr2D 94.611 167 7 2 2762 2928 296364209 296364045 1.500000e-64 257.0
14 TraesCS5B01G168900 chr2B 94.611 167 7 2 2762 2928 366017519 366017683 1.500000e-64 257.0
15 TraesCS5B01G168900 chr4D 95.062 162 8 0 2762 2923 34661688 34661527 5.380000e-64 255.0
16 TraesCS5B01G168900 chr4D 94.479 163 9 0 2762 2924 64390632 64390470 6.960000e-63 252.0
17 TraesCS5B01G168900 chr3D 95.062 162 8 0 2762 2923 187836308 187836469 5.380000e-64 255.0
18 TraesCS5B01G168900 chr2A 94.512 164 9 0 2760 2923 342647397 342647560 1.930000e-63 254.0
19 TraesCS5B01G168900 chr3B 93.976 166 9 1 2758 2923 654649875 654649711 2.500000e-62 250.0
20 TraesCS5B01G168900 chr3B 91.379 58 4 1 772 828 135685091 135685034 1.250000e-10 78.7
21 TraesCS5B01G168900 chr4A 88.718 195 16 6 2753 2946 405565350 405565161 2.520000e-57 233.0
22 TraesCS5B01G168900 chr1D 96.296 54 1 1 775 828 9865183 9865131 2.080000e-13 87.9
23 TraesCS5B01G168900 chr1D 92.593 54 4 0 775 828 358222554 358222607 1.250000e-10 78.7
24 TraesCS5B01G168900 chr7B 94.444 54 3 0 775 828 537747042 537746989 2.690000e-12 84.2
25 TraesCS5B01G168900 chr7A 97.917 48 1 0 781 828 652009320 652009273 2.690000e-12 84.2
26 TraesCS5B01G168900 chr1B 94.545 55 2 1 775 829 2525822 2525769 2.690000e-12 84.2
27 TraesCS5B01G168900 chr1A 94.444 54 3 0 775 828 493203442 493203389 2.690000e-12 84.2
28 TraesCS5B01G168900 chr6A 90.323 62 2 3 770 827 459871485 459871546 1.250000e-10 78.7
29 TraesCS5B01G168900 chr4B 92.308 39 3 0 1284 1322 615710258 615710296 5.850000e-04 56.5


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 TraesCS5B01G168900 chr5B 313149035 313153225 4190 False 7740.0 7740 100.0000 1 4191 1 chr5B.!!$F1 4190
1 TraesCS5B01G168900 chr5A 364709502 364713975 4473 False 943.2 2010 90.0554 2 4191 5 chr5A.!!$F2 4189
2 TraesCS5B01G168900 chr5D 276307104 276311322 4218 False 1056.6 1768 94.1878 196 4108 5 chr5D.!!$F1 3912

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
573 604 0.038166 TACGGGTCGTGGTACTTCCT 59.962 55.0 3.03 0.0 41.39 3.36 F
723 755 0.460311 CGATTTCCTAGCTCGTGGGT 59.540 55.0 0.00 0.0 0.00 4.51 F
1907 1972 0.179018 GATCACCATAGCACACCCCC 60.179 60.0 0.00 0.0 0.00 5.40 F
1923 1988 0.257039 CCCCCTCCTGTTGATTGGAG 59.743 60.0 0.00 0.0 46.91 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1904 1969 0.257039 CTCCAATCAACAGGAGGGGG 59.743 60.000 0.0 0.0 46.11 5.40 R
1909 1974 1.067295 ACTGCCTCCAATCAACAGGA 58.933 50.000 0.0 0.0 32.60 3.86 R
3139 3698 1.739049 CTCATCCTCCTCAGCCGAC 59.261 63.158 0.0 0.0 0.00 4.79 R
3744 4909 2.654863 CCAGATACACCAACCAATCCC 58.345 52.381 0.0 0.0 0.00 3.85 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
38 39 3.050619 CGTCTGTTAGAGTGAACGCTTT 58.949 45.455 0.00 0.00 31.59 3.51
43 44 6.019318 GTCTGTTAGAGTGAACGCTTTAAACA 60.019 38.462 0.00 0.00 31.59 2.83
49 50 3.558418 AGTGAACGCTTTAAACACGTGAT 59.442 39.130 25.01 7.78 40.44 3.06
65 66 2.673893 CGTGATGTGACGATTCCTCCAA 60.674 50.000 0.00 0.00 42.10 3.53
82 83 0.586319 CAACACCAAGATTCGTGCGT 59.414 50.000 0.00 0.00 33.09 5.24
85 86 1.148310 CACCAAGATTCGTGCGTCTT 58.852 50.000 0.00 0.00 35.15 3.01
95 96 0.638746 CGTGCGTCTTATCCAACGAC 59.361 55.000 0.00 0.00 41.29 4.34
104 105 1.996786 TATCCAACGACGGGAGCGAC 61.997 60.000 0.00 0.00 37.96 5.19
138 139 4.806342 TTTCTAAAAACCTGACGTCTGC 57.194 40.909 17.92 0.00 0.00 4.26
157 158 6.366332 CGTCTGCTGTATAGTCTTTGAGTTTT 59.634 38.462 0.00 0.00 0.00 2.43
223 231 4.092091 CGTTTGCTTAGCCTACTCTTTCAG 59.908 45.833 0.29 0.00 0.00 3.02
344 352 4.105697 ACCAGAAACCTAAACAGAATCCCA 59.894 41.667 0.00 0.00 0.00 4.37
345 353 5.076873 CCAGAAACCTAAACAGAATCCCAA 58.923 41.667 0.00 0.00 0.00 4.12
346 354 5.048013 CCAGAAACCTAAACAGAATCCCAAC 60.048 44.000 0.00 0.00 0.00 3.77
347 355 5.048013 CAGAAACCTAAACAGAATCCCAACC 60.048 44.000 0.00 0.00 0.00 3.77
348 356 3.451402 ACCTAAACAGAATCCCAACCC 57.549 47.619 0.00 0.00 0.00 4.11
375 383 4.738998 CCGCAGCCAATCCCACCA 62.739 66.667 0.00 0.00 0.00 4.17
416 430 1.038130 CCCAATCTCGACTCCTCCGT 61.038 60.000 0.00 0.00 0.00 4.69
490 512 3.787001 CCTCTCCCCTGGTTCGGC 61.787 72.222 0.00 0.00 0.00 5.54
505 527 1.884926 CGGCGCCCATCTCTCTTTC 60.885 63.158 23.46 0.00 0.00 2.62
507 529 0.531753 GGCGCCCATCTCTCTTTCTC 60.532 60.000 18.11 0.00 0.00 2.87
521 543 0.599558 TTTCTCCGTCGGTTCATCGT 59.400 50.000 11.88 0.00 0.00 3.73
523 545 0.956902 TCTCCGTCGGTTCATCGTGA 60.957 55.000 11.88 0.00 0.00 4.35
536 558 3.760035 CGTGACTAGGCGGCTGGT 61.760 66.667 27.89 27.89 0.00 4.00
555 586 1.684983 GTTTCTCATCGGATCGGGGTA 59.315 52.381 0.00 0.00 0.00 3.69
556 587 1.325355 TTCTCATCGGATCGGGGTAC 58.675 55.000 0.00 0.00 0.00 3.34
557 588 0.887836 TCTCATCGGATCGGGGTACG 60.888 60.000 0.00 0.00 46.11 3.67
558 589 1.863662 CTCATCGGATCGGGGTACGG 61.864 65.000 0.00 0.00 44.45 4.02
559 590 2.599578 ATCGGATCGGGGTACGGG 60.600 66.667 0.00 0.00 44.45 5.28
560 591 3.441712 ATCGGATCGGGGTACGGGT 62.442 63.158 0.00 0.00 44.45 5.28
567 598 2.362375 GGGGTACGGGTCGTGGTA 60.362 66.667 3.03 0.00 41.39 3.25
573 604 0.038166 TACGGGTCGTGGTACTTCCT 59.962 55.000 3.03 0.00 41.39 3.36
584 615 1.271217 GGTACTTCCTGGCTCGGTTTT 60.271 52.381 0.00 0.00 0.00 2.43
595 627 0.798776 CTCGGTTTTCGCTGATGCTT 59.201 50.000 0.00 0.00 39.05 3.91
636 668 4.748503 TTACGATTGTAGTCGCAAATCG 57.251 40.909 13.67 13.67 45.12 3.34
653 685 1.629013 TCGCAACTGCTAGTTCATCG 58.371 50.000 0.00 4.46 36.03 3.84
661 693 1.201098 GCTAGTTCATCGCCGTCGTC 61.201 60.000 0.00 0.00 36.96 4.20
675 707 3.928375 GCCGTCGTCTTTGTAAGGAAATA 59.072 43.478 0.00 0.00 0.00 1.40
676 708 4.201656 GCCGTCGTCTTTGTAAGGAAATAC 60.202 45.833 0.00 0.00 0.00 1.89
678 710 5.579511 CCGTCGTCTTTGTAAGGAAATACAT 59.420 40.000 0.00 0.00 35.80 2.29
679 711 6.753279 CCGTCGTCTTTGTAAGGAAATACATA 59.247 38.462 0.00 0.00 35.80 2.29
680 712 7.253883 CCGTCGTCTTTGTAAGGAAATACATAC 60.254 40.741 0.00 0.00 35.80 2.39
681 713 7.487189 CGTCGTCTTTGTAAGGAAATACATACT 59.513 37.037 0.00 0.00 35.80 2.12
682 714 9.793252 GTCGTCTTTGTAAGGAAATACATACTA 57.207 33.333 0.00 0.00 35.80 1.82
683 715 9.793252 TCGTCTTTGTAAGGAAATACATACTAC 57.207 33.333 0.00 0.00 35.80 2.73
684 716 9.798994 CGTCTTTGTAAGGAAATACATACTACT 57.201 33.333 0.00 0.00 35.80 2.57
704 736 1.470890 TGTATTACTTTGCGCCCAAGC 59.529 47.619 14.66 1.45 37.71 4.01
723 755 0.460311 CGATTTCCTAGCTCGTGGGT 59.540 55.000 0.00 0.00 0.00 4.51
727 759 3.536956 TTTCCTAGCTCGTGGGTTATG 57.463 47.619 0.00 0.00 0.00 1.90
728 760 2.154567 TCCTAGCTCGTGGGTTATGT 57.845 50.000 0.00 0.00 0.00 2.29
738 770 6.927381 AGCTCGTGGGTTATGTATTTATGTAC 59.073 38.462 0.00 0.00 0.00 2.90
746 778 7.012610 GGGTTATGTATTTATGTACGCTGGTTT 59.987 37.037 0.00 0.00 0.00 3.27
761 793 2.986479 CTGGTTTTAGTGGCGAATTTGC 59.014 45.455 9.36 9.36 0.00 3.68
774 806 3.565482 GCGAATTTGCCATCTAGGATTGA 59.435 43.478 6.38 0.00 41.22 2.57
776 808 4.818546 CGAATTTGCCATCTAGGATTGACT 59.181 41.667 0.00 0.00 41.22 3.41
778 810 3.845781 TTGCCATCTAGGATTGACTCC 57.154 47.619 0.00 0.00 45.33 3.85
779 811 2.050144 TGCCATCTAGGATTGACTCCC 58.950 52.381 0.00 0.00 46.27 4.30
780 812 2.334023 GCCATCTAGGATTGACTCCCT 58.666 52.381 0.00 0.00 46.27 4.20
781 813 2.301583 GCCATCTAGGATTGACTCCCTC 59.698 54.545 0.00 0.00 46.27 4.30
782 814 3.855668 CCATCTAGGATTGACTCCCTCT 58.144 50.000 0.00 0.00 46.27 3.69
784 816 4.222336 CATCTAGGATTGACTCCCTCTGT 58.778 47.826 0.00 0.00 46.27 3.41
785 817 5.389520 CATCTAGGATTGACTCCCTCTGTA 58.610 45.833 0.00 0.00 46.27 2.74
786 818 5.467668 TCTAGGATTGACTCCCTCTGTAA 57.532 43.478 0.00 0.00 46.27 2.41
787 819 5.838955 TCTAGGATTGACTCCCTCTGTAAA 58.161 41.667 0.00 0.00 46.27 2.01
788 820 4.828072 AGGATTGACTCCCTCTGTAAAC 57.172 45.455 0.00 0.00 46.27 2.01
789 821 4.430441 AGGATTGACTCCCTCTGTAAACT 58.570 43.478 0.00 0.00 46.27 2.66
790 822 5.590818 AGGATTGACTCCCTCTGTAAACTA 58.409 41.667 0.00 0.00 46.27 2.24
791 823 6.023603 AGGATTGACTCCCTCTGTAAACTAA 58.976 40.000 0.00 0.00 46.27 2.24
792 824 6.674419 AGGATTGACTCCCTCTGTAAACTAAT 59.326 38.462 0.00 0.00 46.27 1.73
793 825 7.844779 AGGATTGACTCCCTCTGTAAACTAATA 59.155 37.037 0.00 0.00 46.27 0.98
794 826 8.652290 GGATTGACTCCCTCTGTAAACTAATAT 58.348 37.037 0.00 0.00 38.19 1.28
798 830 9.931698 TGACTCCCTCTGTAAACTAATATAAGA 57.068 33.333 0.00 0.00 0.00 2.10
800 832 9.145442 ACTCCCTCTGTAAACTAATATAAGACC 57.855 37.037 0.00 0.00 0.00 3.85
801 833 9.369672 CTCCCTCTGTAAACTAATATAAGACCT 57.630 37.037 0.00 0.00 0.00 3.85
802 834 9.725206 TCCCTCTGTAAACTAATATAAGACCTT 57.275 33.333 0.00 0.00 0.00 3.50
822 854 9.756571 AGACCTTTTAGATCTCTACTTTAGTGA 57.243 33.333 0.00 0.00 33.41 3.41
858 890 4.937620 GTCTTAATGCCAGATTGTGAGTCA 59.062 41.667 0.00 0.00 0.00 3.41
859 891 5.587844 GTCTTAATGCCAGATTGTGAGTCAT 59.412 40.000 0.00 0.00 0.00 3.06
860 892 5.587443 TCTTAATGCCAGATTGTGAGTCATG 59.413 40.000 0.00 0.00 0.00 3.07
865 897 3.607741 CCAGATTGTGAGTCATGAGCTT 58.392 45.455 0.00 0.00 0.00 3.74
875 907 4.398988 TGAGTCATGAGCTTGTGTTTGTTT 59.601 37.500 0.00 0.00 0.00 2.83
883 915 3.035942 GCTTGTGTTTGTTTGCTAGTCG 58.964 45.455 0.00 0.00 0.00 4.18
916 948 3.616379 CACCAGATTTCTTCGAGCTTCTC 59.384 47.826 0.00 0.00 0.00 2.87
967 999 3.514309 ACCTCTTACTATGCTTCCGTGTT 59.486 43.478 0.00 0.00 0.00 3.32
1108 1141 6.476896 CGTCAAGTCTACCGTTTTGTTTTTA 58.523 36.000 0.00 0.00 0.00 1.52
1126 1159 5.744666 TTTTATTATGCCGGCTACACTTC 57.255 39.130 29.70 0.00 0.00 3.01
1138 1171 5.524646 CCGGCTACACTTCGGATAAATTAAA 59.475 40.000 0.00 0.00 45.96 1.52
1357 1415 1.354040 CTGACGTTGACTGGATCAGC 58.646 55.000 0.00 0.00 38.99 4.26
1378 1436 2.603560 CGCGTCCTGAATTAAAGAGGTC 59.396 50.000 0.00 0.00 0.00 3.85
1394 1452 3.124560 GAGGTCGTTAATCTTGCTAGCC 58.875 50.000 13.29 0.00 0.00 3.93
1473 1531 5.163581 GCATTGGCAGTTTCTGATCAACTAT 60.164 40.000 0.00 0.00 40.72 2.12
1526 1584 7.339482 GGGAATTTAGTGTGTAGGAATTCTCT 58.661 38.462 5.23 3.70 35.40 3.10
1548 1606 2.548057 TGTGATTTCAGCTTCGTCCAAC 59.452 45.455 0.00 0.00 0.00 3.77
1892 1957 9.753674 AAAGAATAAAAGAGGTATGGTTGATCA 57.246 29.630 0.00 0.00 0.00 2.92
1893 1958 8.738645 AGAATAAAAGAGGTATGGTTGATCAC 57.261 34.615 0.00 0.00 0.00 3.06
1904 1969 2.017049 GGTTGATCACCATAGCACACC 58.983 52.381 0.00 0.00 46.42 4.16
1905 1970 2.017049 GTTGATCACCATAGCACACCC 58.983 52.381 0.00 0.00 0.00 4.61
1906 1971 0.546122 TGATCACCATAGCACACCCC 59.454 55.000 0.00 0.00 0.00 4.95
1907 1972 0.179018 GATCACCATAGCACACCCCC 60.179 60.000 0.00 0.00 0.00 5.40
1922 1987 2.397815 CCCCCTCCTGTTGATTGGA 58.602 57.895 0.00 0.00 0.00 3.53
1923 1988 0.257039 CCCCCTCCTGTTGATTGGAG 59.743 60.000 0.00 0.00 46.91 3.86
1926 1991 3.963733 CTCCTGTTGATTGGAGGCA 57.036 52.632 0.00 0.00 44.44 4.75
1927 1992 1.747709 CTCCTGTTGATTGGAGGCAG 58.252 55.000 0.00 0.00 44.44 4.85
1928 1993 1.004044 CTCCTGTTGATTGGAGGCAGT 59.996 52.381 0.00 0.00 44.44 4.40
1929 1994 2.237143 CTCCTGTTGATTGGAGGCAGTA 59.763 50.000 0.00 0.00 44.44 2.74
1930 1995 2.846206 TCCTGTTGATTGGAGGCAGTAT 59.154 45.455 0.00 0.00 0.00 2.12
1931 1996 2.947652 CCTGTTGATTGGAGGCAGTATG 59.052 50.000 0.00 0.00 40.87 2.39
2048 2604 6.398234 TGTGTATAAGGTGCATGTTTTGTT 57.602 33.333 0.00 0.00 0.00 2.83
2068 2624 4.022416 TGTTTAGTGTTTTATGGCAGCCAG 60.022 41.667 21.51 0.00 36.75 4.85
2118 2675 7.172875 GCAGTGATGATTCTTCATGTAGCTAAT 59.827 37.037 0.00 0.00 42.73 1.73
2172 2729 8.619546 ACTCTTTCTTCTTCAGTTGAGAAAATG 58.380 33.333 0.00 0.00 0.00 2.32
2185 2742 6.209391 AGTTGAGAAAATGTGATTACCTTGGG 59.791 38.462 0.00 0.00 0.00 4.12
2276 2833 7.275341 TGTGTCAATTGAATCACTGTTTTTCAC 59.725 33.333 22.53 15.96 0.00 3.18
2427 2986 5.761165 TGCATCCATGTATCTTCACAATG 57.239 39.130 0.00 0.00 30.84 2.82
2638 3197 6.887376 TCTTTGTGCTACAGAAATATCGAC 57.113 37.500 0.00 0.00 0.00 4.20
2711 3270 7.175467 TGAAACAAATACAAGATGCTCTGTCAT 59.825 33.333 0.00 0.00 0.00 3.06
2766 3325 5.358090 GGTAACTCACTAGCCAATTACTCC 58.642 45.833 0.00 0.00 0.00 3.85
2767 3326 4.489306 AACTCACTAGCCAATTACTCCC 57.511 45.455 0.00 0.00 0.00 4.30
2768 3327 3.725634 ACTCACTAGCCAATTACTCCCT 58.274 45.455 0.00 0.00 0.00 4.20
2769 3328 3.707102 ACTCACTAGCCAATTACTCCCTC 59.293 47.826 0.00 0.00 0.00 4.30
2770 3329 3.039011 TCACTAGCCAATTACTCCCTCC 58.961 50.000 0.00 0.00 0.00 4.30
2771 3330 2.040178 ACTAGCCAATTACTCCCTCCG 58.960 52.381 0.00 0.00 0.00 4.63
2772 3331 2.040178 CTAGCCAATTACTCCCTCCGT 58.960 52.381 0.00 0.00 0.00 4.69
2773 3332 1.286248 AGCCAATTACTCCCTCCGTT 58.714 50.000 0.00 0.00 0.00 4.44
2774 3333 1.209747 AGCCAATTACTCCCTCCGTTC 59.790 52.381 0.00 0.00 0.00 3.95
2775 3334 1.746171 GCCAATTACTCCCTCCGTTCC 60.746 57.143 0.00 0.00 0.00 3.62
2776 3335 1.838077 CCAATTACTCCCTCCGTTCCT 59.162 52.381 0.00 0.00 0.00 3.36
2777 3336 3.036091 CCAATTACTCCCTCCGTTCCTA 58.964 50.000 0.00 0.00 0.00 2.94
2778 3337 3.453353 CCAATTACTCCCTCCGTTCCTAA 59.547 47.826 0.00 0.00 0.00 2.69
2779 3338 4.080751 CCAATTACTCCCTCCGTTCCTAAA 60.081 45.833 0.00 0.00 0.00 1.85
2780 3339 5.397559 CCAATTACTCCCTCCGTTCCTAAAT 60.398 44.000 0.00 0.00 0.00 1.40
2781 3340 6.183361 CCAATTACTCCCTCCGTTCCTAAATA 60.183 42.308 0.00 0.00 0.00 1.40
2782 3341 7.450903 CAATTACTCCCTCCGTTCCTAAATAT 58.549 38.462 0.00 0.00 0.00 1.28
2783 3342 8.591072 CAATTACTCCCTCCGTTCCTAAATATA 58.409 37.037 0.00 0.00 0.00 0.86
2784 3343 8.731591 ATTACTCCCTCCGTTCCTAAATATAA 57.268 34.615 0.00 0.00 0.00 0.98
2785 3344 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2786 3345 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2787 3346 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2788 3347 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2789 3348 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2790 3349 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2791 3350 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
2792 3351 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
2808 3367 7.693969 AGTCTTTTTAGAGATTCCAATGTGG 57.306 36.000 0.00 0.00 39.43 4.17
2809 3368 7.461749 AGTCTTTTTAGAGATTCCAATGTGGA 58.538 34.615 0.00 0.00 46.61 4.02
2823 3382 1.842052 TGTGGACTACATACGGAGCA 58.158 50.000 0.00 0.00 33.42 4.26
2824 3383 2.172679 TGTGGACTACATACGGAGCAA 58.827 47.619 0.00 0.00 33.42 3.91
2825 3384 2.563620 TGTGGACTACATACGGAGCAAA 59.436 45.455 0.00 0.00 33.42 3.68
2826 3385 3.007074 TGTGGACTACATACGGAGCAAAA 59.993 43.478 0.00 0.00 33.42 2.44
2827 3386 4.189231 GTGGACTACATACGGAGCAAAAT 58.811 43.478 0.00 0.00 0.00 1.82
2828 3387 4.034048 GTGGACTACATACGGAGCAAAATG 59.966 45.833 0.00 0.00 0.00 2.32
2829 3388 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
2830 3389 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
2831 3390 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
2832 3391 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
2833 3392 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
2834 3393 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
2835 3394 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
2836 3395 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
2837 3396 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
2838 3397 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
2839 3398 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
2840 3399 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
2841 3400 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
2913 3472 9.291664 CTCTAGAAAGACTTGTATTTAGGAACG 57.708 37.037 0.00 0.00 0.00 3.95
2914 3473 8.248945 TCTAGAAAGACTTGTATTTAGGAACGG 58.751 37.037 0.00 0.00 0.00 4.44
2915 3474 7.001099 AGAAAGACTTGTATTTAGGAACGGA 57.999 36.000 0.00 0.00 0.00 4.69
2916 3475 7.621796 AGAAAGACTTGTATTTAGGAACGGAT 58.378 34.615 0.00 0.00 0.00 4.18
2917 3476 7.549488 AGAAAGACTTGTATTTAGGAACGGATG 59.451 37.037 0.00 0.00 0.00 3.51
2918 3477 5.671493 AGACTTGTATTTAGGAACGGATGG 58.329 41.667 0.00 0.00 0.00 3.51
2919 3478 5.424252 AGACTTGTATTTAGGAACGGATGGA 59.576 40.000 0.00 0.00 0.00 3.41
2920 3479 5.671493 ACTTGTATTTAGGAACGGATGGAG 58.329 41.667 0.00 0.00 0.00 3.86
3040 3599 1.625818 GAAGAGTTGGAGGGAGCAGAA 59.374 52.381 0.00 0.00 0.00 3.02
3092 3651 8.382030 TGTAACTATTCCTATTCATACGACGA 57.618 34.615 0.00 0.00 0.00 4.20
3269 3831 4.794278 TCCGACTAACACTTGCTAATCA 57.206 40.909 0.00 0.00 0.00 2.57
3314 3876 7.669304 TGAAGTGATCTCAAATTTTATGGGTCA 59.331 33.333 0.00 0.00 0.00 4.02
3318 3880 7.542130 GTGATCTCAAATTTTATGGGTCAACAC 59.458 37.037 0.00 0.00 0.00 3.32
3424 4069 4.949856 TCATTAGATTTTTCTGGGTCTGGC 59.050 41.667 0.00 0.00 0.00 4.85
3427 4072 2.158325 AGATTTTTCTGGGTCTGGCCAA 60.158 45.455 7.01 0.00 39.65 4.52
3627 4791 1.225855 TAAGTTCAGCTGCACCAACG 58.774 50.000 13.13 0.00 0.00 4.10
3628 4792 1.447317 AAGTTCAGCTGCACCAACGG 61.447 55.000 13.13 0.00 0.00 4.44
3638 4802 1.202463 TGCACCAACGGAAACAATTGG 60.202 47.619 10.83 0.70 46.71 3.16
3651 4815 4.460948 AACAATTGGCACATTCAGGATC 57.539 40.909 10.83 0.00 39.30 3.36
3652 4816 3.433343 ACAATTGGCACATTCAGGATCA 58.567 40.909 10.83 0.00 39.30 2.92
3670 4834 7.235399 TCAGGATCAATGTAGACCAATATGCTA 59.765 37.037 0.00 0.00 0.00 3.49
3675 4839 7.441836 TCAATGTAGACCAATATGCTACGAAT 58.558 34.615 0.00 0.00 37.82 3.34
3725 4890 6.127810 AGAACATATGTCATGCACATTGTC 57.872 37.500 9.23 0.00 43.89 3.18
3744 4909 4.645535 TGTCACAATGAGGAAAAGGAGAG 58.354 43.478 0.00 0.00 0.00 3.20
3747 4920 3.009473 CACAATGAGGAAAAGGAGAGGGA 59.991 47.826 0.00 0.00 0.00 4.20
3806 4979 4.028993 AGATGTTTGTACGGTGGGATTT 57.971 40.909 0.00 0.00 0.00 2.17
3933 5106 2.424793 TGTTCTATAACCCCATCCCCC 58.575 52.381 0.00 0.00 34.49 5.40
3934 5107 2.020441 TGTTCTATAACCCCATCCCCCT 60.020 50.000 0.00 0.00 34.49 4.79
3935 5108 2.375509 GTTCTATAACCCCATCCCCCTG 59.624 54.545 0.00 0.00 0.00 4.45
3937 5110 2.020441 TCTATAACCCCATCCCCCTGTT 60.020 50.000 0.00 0.00 0.00 3.16
3938 5111 1.706539 ATAACCCCATCCCCCTGTTT 58.293 50.000 0.00 0.00 0.00 2.83
3944 5117 1.229145 CATCCCCCTGTTTTGGGCA 60.229 57.895 0.00 0.00 45.78 5.36
3983 5156 6.366877 TGCGTTCTAGACATGGTTACTTAAAC 59.633 38.462 0.00 0.00 37.36 2.01
3985 5158 7.756722 GCGTTCTAGACATGGTTACTTAAACTA 59.243 37.037 0.00 0.00 38.23 2.24
3994 5167 7.920738 CATGGTTACTTAAACTATGCCTTCTC 58.079 38.462 2.00 0.00 46.12 2.87
3995 5168 7.011499 TGGTTACTTAAACTATGCCTTCTCA 57.989 36.000 0.00 0.00 38.23 3.27
4004 5183 7.530426 AAACTATGCCTTCTCATTTGTCTTT 57.470 32.000 0.00 0.00 0.00 2.52
4005 5184 6.749923 ACTATGCCTTCTCATTTGTCTTTC 57.250 37.500 0.00 0.00 0.00 2.62
4007 5186 3.831323 TGCCTTCTCATTTGTCTTTCCA 58.169 40.909 0.00 0.00 0.00 3.53
4065 5244 0.843309 TGCAGTTTCTGGGAGGAACA 59.157 50.000 0.00 0.00 31.21 3.18
4089 5269 7.173390 ACAACATACAAGAAGGTTAGCTTCTTC 59.827 37.037 29.32 5.09 45.89 2.87
4113 5293 1.528586 CATGCATGTACTAAGCGAGCC 59.471 52.381 18.91 0.00 0.00 4.70
4135 5315 2.045242 CTGCTGGAGCCACTGCAT 60.045 61.111 9.62 0.00 42.98 3.96
4145 5331 2.759114 CACTGCATGGACCTGGGT 59.241 61.111 0.00 0.00 0.00 4.51
4157 5343 4.800554 CTGGGTGTCAGGACCAAC 57.199 61.111 0.00 0.00 39.76 3.77
4181 5367 3.388024 GGGTGGTGCTATCACTGATAGAA 59.612 47.826 24.66 14.94 43.17 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.840271 TCACTCTAACAGACGTCCAGATA 58.160 43.478 13.01 3.78 0.00 1.98
10 11 3.687125 TCACTCTAACAGACGTCCAGAT 58.313 45.455 13.01 2.67 0.00 2.90
15 16 1.977412 GCGTTCACTCTAACAGACGTC 59.023 52.381 7.70 7.70 0.00 4.34
19 20 6.019318 GTGTTTAAAGCGTTCACTCTAACAGA 60.019 38.462 0.00 0.00 0.00 3.41
21 22 5.276489 CGTGTTTAAAGCGTTCACTCTAACA 60.276 40.000 0.00 0.00 0.00 2.41
38 39 3.676172 GGAATCGTCACATCACGTGTTTA 59.324 43.478 16.51 0.00 46.44 2.01
43 44 1.135083 GGAGGAATCGTCACATCACGT 60.135 52.381 5.28 0.00 40.79 4.49
49 50 1.270625 GGTGTTGGAGGAATCGTCACA 60.271 52.381 5.28 0.00 0.00 3.58
65 66 0.033504 AGACGCACGAATCTTGGTGT 59.966 50.000 0.00 0.00 38.86 4.16
82 83 0.458669 GCTCCCGTCGTTGGATAAGA 59.541 55.000 0.00 0.00 0.00 2.10
85 86 1.750018 TCGCTCCCGTCGTTGGATA 60.750 57.895 0.00 0.00 35.54 2.59
104 105 6.416750 AGGTTTTTAGAAAATTCAAGCGAACG 59.583 34.615 0.00 0.00 32.81 3.95
112 113 7.414436 CAGACGTCAGGTTTTTAGAAAATTCA 58.586 34.615 19.50 0.00 0.00 2.57
178 182 3.575965 AACGCACCCTCAATCAATTTC 57.424 42.857 0.00 0.00 0.00 2.17
180 184 2.095263 CGAAACGCACCCTCAATCAATT 60.095 45.455 0.00 0.00 0.00 2.32
182 186 0.871722 CGAAACGCACCCTCAATCAA 59.128 50.000 0.00 0.00 0.00 2.57
183 187 0.250124 ACGAAACGCACCCTCAATCA 60.250 50.000 0.00 0.00 0.00 2.57
191 195 1.670326 CTAAGCAAACGAAACGCACC 58.330 50.000 0.00 0.00 0.00 5.01
223 231 2.047560 GTACCCCACACGGTGAGC 60.048 66.667 16.29 0.00 36.56 4.26
453 468 4.301027 GGTAGGGGCGCGGATCTG 62.301 72.222 8.83 0.00 0.00 2.90
490 512 0.249238 CGGAGAAAGAGAGATGGGCG 60.249 60.000 0.00 0.00 0.00 6.13
505 527 0.797249 GTCACGATGAACCGACGGAG 60.797 60.000 23.38 6.78 0.00 4.63
507 529 0.448990 TAGTCACGATGAACCGACGG 59.551 55.000 13.61 13.61 33.56 4.79
521 543 1.192146 AGAAACCAGCCGCCTAGTCA 61.192 55.000 0.00 0.00 0.00 3.41
523 545 1.192146 TGAGAAACCAGCCGCCTAGT 61.192 55.000 0.00 0.00 0.00 2.57
536 558 1.684983 GTACCCCGATCCGATGAGAAA 59.315 52.381 0.00 0.00 0.00 2.52
555 586 1.228675 AGGAAGTACCACGACCCGT 60.229 57.895 0.00 0.00 42.36 5.28
556 587 1.214589 CAGGAAGTACCACGACCCG 59.785 63.158 0.00 0.00 42.04 5.28
557 588 1.595357 CCAGGAAGTACCACGACCC 59.405 63.158 0.00 0.00 42.04 4.46
558 589 1.079336 GCCAGGAAGTACCACGACC 60.079 63.158 0.00 0.00 42.04 4.79
559 590 0.108756 GAGCCAGGAAGTACCACGAC 60.109 60.000 0.00 0.00 42.04 4.34
560 591 1.592400 CGAGCCAGGAAGTACCACGA 61.592 60.000 0.00 0.00 42.04 4.35
567 598 0.602905 CGAAAACCGAGCCAGGAAGT 60.603 55.000 1.68 0.00 41.76 3.01
573 604 1.003839 ATCAGCGAAAACCGAGCCA 60.004 52.632 0.00 0.00 41.76 4.75
636 668 0.375106 GGCGATGAACTAGCAGTTGC 59.625 55.000 6.31 0.00 38.80 4.17
653 685 1.787012 TTCCTTACAAAGACGACGGC 58.213 50.000 0.00 0.00 0.00 5.68
675 707 5.751990 GGCGCAAAGTAATACAGTAGTATGT 59.248 40.000 10.83 0.00 40.00 2.29
676 708 5.176958 GGGCGCAAAGTAATACAGTAGTATG 59.823 44.000 10.83 0.00 40.00 2.39
678 710 4.160065 TGGGCGCAAAGTAATACAGTAGTA 59.840 41.667 10.83 0.00 34.10 1.82
679 711 3.055675 TGGGCGCAAAGTAATACAGTAGT 60.056 43.478 10.83 0.00 0.00 2.73
680 712 3.527533 TGGGCGCAAAGTAATACAGTAG 58.472 45.455 10.83 0.00 0.00 2.57
681 713 3.613494 TGGGCGCAAAGTAATACAGTA 57.387 42.857 10.83 0.00 0.00 2.74
682 714 2.483014 TGGGCGCAAAGTAATACAGT 57.517 45.000 10.83 0.00 0.00 3.55
683 715 2.477863 GCTTGGGCGCAAAGTAATACAG 60.478 50.000 17.59 3.40 0.00 2.74
684 716 1.470890 GCTTGGGCGCAAAGTAATACA 59.529 47.619 17.59 0.00 0.00 2.29
685 717 2.188837 GCTTGGGCGCAAAGTAATAC 57.811 50.000 17.59 3.33 0.00 1.89
704 736 0.460311 ACCCACGAGCTAGGAAATCG 59.540 55.000 0.00 0.00 42.04 3.34
727 759 7.404203 CCACTAAAACCAGCGTACATAAATAC 58.596 38.462 0.00 0.00 0.00 1.89
728 760 6.037391 GCCACTAAAACCAGCGTACATAAATA 59.963 38.462 0.00 0.00 0.00 1.40
774 806 9.145442 GGTCTTATATTAGTTTACAGAGGGAGT 57.855 37.037 0.00 0.00 0.00 3.85
776 808 9.725206 AAGGTCTTATATTAGTTTACAGAGGGA 57.275 33.333 0.00 0.00 0.00 4.20
796 828 9.756571 TCACTAAAGTAGAGATCTAAAAGGTCT 57.243 33.333 0.00 0.00 0.00 3.85
806 838 8.846211 AGCACTTAGATCACTAAAGTAGAGATC 58.154 37.037 12.23 12.23 46.58 2.75
807 839 8.629158 CAGCACTTAGATCACTAAAGTAGAGAT 58.371 37.037 0.00 0.00 38.54 2.75
808 840 7.415765 GCAGCACTTAGATCACTAAAGTAGAGA 60.416 40.741 0.00 0.00 38.01 3.10
809 841 6.695278 GCAGCACTTAGATCACTAAAGTAGAG 59.305 42.308 0.00 0.00 38.01 2.43
810 842 6.565234 GCAGCACTTAGATCACTAAAGTAGA 58.435 40.000 0.00 0.00 38.01 2.59
811 843 5.457148 CGCAGCACTTAGATCACTAAAGTAG 59.543 44.000 0.00 0.00 38.01 2.57
812 844 5.105877 ACGCAGCACTTAGATCACTAAAGTA 60.106 40.000 0.00 0.00 38.01 2.24
813 845 4.177026 CGCAGCACTTAGATCACTAAAGT 58.823 43.478 0.00 0.00 38.01 2.66
814 846 4.177026 ACGCAGCACTTAGATCACTAAAG 58.823 43.478 0.00 0.00 38.01 1.85
815 847 4.082190 AGACGCAGCACTTAGATCACTAAA 60.082 41.667 0.00 0.00 38.01 1.85
816 848 3.444034 AGACGCAGCACTTAGATCACTAA 59.556 43.478 0.00 0.00 37.13 2.24
817 849 3.017442 AGACGCAGCACTTAGATCACTA 58.983 45.455 0.00 0.00 0.00 2.74
818 850 1.821753 AGACGCAGCACTTAGATCACT 59.178 47.619 0.00 0.00 0.00 3.41
819 851 2.285827 AGACGCAGCACTTAGATCAC 57.714 50.000 0.00 0.00 0.00 3.06
820 852 4.450082 TTAAGACGCAGCACTTAGATCA 57.550 40.909 0.00 0.00 33.16 2.92
821 853 4.318404 GCATTAAGACGCAGCACTTAGATC 60.318 45.833 8.44 0.00 33.16 2.75
822 854 3.557595 GCATTAAGACGCAGCACTTAGAT 59.442 43.478 8.44 4.75 33.16 1.98
823 855 2.930040 GCATTAAGACGCAGCACTTAGA 59.070 45.455 8.44 3.19 33.16 2.10
824 856 2.030946 GGCATTAAGACGCAGCACTTAG 59.969 50.000 8.44 2.14 33.16 2.18
825 857 2.006888 GGCATTAAGACGCAGCACTTA 58.993 47.619 5.31 5.31 0.00 2.24
826 858 0.804989 GGCATTAAGACGCAGCACTT 59.195 50.000 6.98 6.98 0.00 3.16
827 859 0.321564 TGGCATTAAGACGCAGCACT 60.322 50.000 0.00 0.00 0.00 4.40
831 863 2.679837 ACAATCTGGCATTAAGACGCAG 59.320 45.455 0.00 0.00 0.00 5.18
858 890 3.806625 AGCAAACAAACACAAGCTCAT 57.193 38.095 0.00 0.00 0.00 2.90
859 891 3.694072 ACTAGCAAACAAACACAAGCTCA 59.306 39.130 0.00 0.00 33.83 4.26
860 892 4.282873 GACTAGCAAACAAACACAAGCTC 58.717 43.478 0.00 0.00 33.83 4.09
916 948 5.817296 TCATTCACCGGACAATTATGAGAAG 59.183 40.000 9.46 0.00 0.00 2.85
967 999 1.496060 ATATGGACTCGGAACCTGCA 58.504 50.000 0.00 0.00 0.00 4.41
1108 1141 1.540363 CCGAAGTGTAGCCGGCATAAT 60.540 52.381 31.54 10.73 36.62 1.28
1113 1146 0.103572 TTATCCGAAGTGTAGCCGGC 59.896 55.000 21.89 21.89 42.70 6.13
1126 1159 9.450807 CAGTTAGCATTTCCTTTAATTTATCCG 57.549 33.333 0.00 0.00 0.00 4.18
1138 1171 3.008049 ACGTTCTCCAGTTAGCATTTCCT 59.992 43.478 0.00 0.00 0.00 3.36
1154 1187 2.657237 CCTCCCAGCGAACGTTCT 59.343 61.111 24.80 5.45 0.00 3.01
1251 1309 3.771216 AGTTGGAGAACATGGCAAATCT 58.229 40.909 0.00 0.00 34.17 2.40
1346 1404 2.583593 GGACGCGCTGATCCAGTC 60.584 66.667 5.73 8.70 34.87 3.51
1357 1415 2.603560 GACCTCTTTAATTCAGGACGCG 59.396 50.000 3.53 3.53 0.00 6.01
1359 1417 3.846360 ACGACCTCTTTAATTCAGGACG 58.154 45.455 14.01 14.01 46.60 4.79
1378 1436 7.891183 ATTATACAGGCTAGCAAGATTAACG 57.109 36.000 18.24 0.00 0.00 3.18
1394 1452 8.998989 CGTGCATTCAACAACTTAATTATACAG 58.001 33.333 0.00 0.00 0.00 2.74
1526 1584 2.844946 TGGACGAAGCTGAAATCACAA 58.155 42.857 0.00 0.00 0.00 3.33
1548 1606 6.660887 ACAAAGTTTGCACACCAAATAAAG 57.339 33.333 15.59 0.00 44.61 1.85
1584 1642 6.648192 CAGACTATGAAAGAAAGGACAGGAT 58.352 40.000 0.00 0.00 0.00 3.24
1587 1645 5.486526 AGCAGACTATGAAAGAAAGGACAG 58.513 41.667 0.00 0.00 0.00 3.51
1603 1661 2.627515 TGCAACTTCAGAAGCAGACT 57.372 45.000 10.33 0.00 32.48 3.24
1904 1969 0.257039 CTCCAATCAACAGGAGGGGG 59.743 60.000 0.00 0.00 46.11 5.40
1905 1970 3.890527 CTCCAATCAACAGGAGGGG 57.109 57.895 0.00 0.00 46.11 4.79
1909 1974 1.067295 ACTGCCTCCAATCAACAGGA 58.933 50.000 0.00 0.00 32.60 3.86
1910 1975 2.787473 TACTGCCTCCAATCAACAGG 57.213 50.000 0.00 0.00 32.60 4.00
1911 1976 2.357009 GCATACTGCCTCCAATCAACAG 59.643 50.000 0.00 0.00 37.42 3.16
1912 1977 2.025981 AGCATACTGCCTCCAATCAACA 60.026 45.455 0.00 0.00 46.52 3.33
1913 1978 2.648059 AGCATACTGCCTCCAATCAAC 58.352 47.619 0.00 0.00 46.52 3.18
1914 1979 3.370840 AAGCATACTGCCTCCAATCAA 57.629 42.857 0.00 0.00 46.52 2.57
1915 1980 3.370840 AAAGCATACTGCCTCCAATCA 57.629 42.857 0.00 0.00 46.52 2.57
1916 1981 3.950395 AGAAAAGCATACTGCCTCCAATC 59.050 43.478 0.00 0.00 46.52 2.67
1917 1982 3.950395 GAGAAAAGCATACTGCCTCCAAT 59.050 43.478 0.00 0.00 46.52 3.16
1918 1983 3.244875 TGAGAAAAGCATACTGCCTCCAA 60.245 43.478 0.00 0.00 46.52 3.53
1919 1984 2.305635 TGAGAAAAGCATACTGCCTCCA 59.694 45.455 0.00 0.00 46.52 3.86
1920 1985 2.991250 TGAGAAAAGCATACTGCCTCC 58.009 47.619 0.00 0.00 46.52 4.30
1921 1986 4.457257 ACTTTGAGAAAAGCATACTGCCTC 59.543 41.667 0.00 0.00 46.52 4.70
1922 1987 4.401925 ACTTTGAGAAAAGCATACTGCCT 58.598 39.130 0.00 0.00 46.52 4.75
1923 1988 4.773323 ACTTTGAGAAAAGCATACTGCC 57.227 40.909 0.00 0.00 46.52 4.85
1924 1989 8.642020 CATTTTACTTTGAGAAAAGCATACTGC 58.358 33.333 0.00 0.00 45.46 4.40
1925 1990 9.132521 CCATTTTACTTTGAGAAAAGCATACTG 57.867 33.333 0.00 0.00 33.18 2.74
1926 1991 8.860088 ACCATTTTACTTTGAGAAAAGCATACT 58.140 29.630 0.00 0.00 33.18 2.12
1930 1995 9.691362 GATTACCATTTTACTTTGAGAAAAGCA 57.309 29.630 0.00 0.00 33.18 3.91
1931 1996 9.691362 TGATTACCATTTTACTTTGAGAAAAGC 57.309 29.630 0.00 0.00 33.18 3.51
1939 2004 9.965824 ACAGAAGTTGATTACCATTTTACTTTG 57.034 29.630 0.00 0.00 0.00 2.77
2048 2604 2.491693 GCTGGCTGCCATAAAACACTAA 59.508 45.455 23.64 0.00 35.15 2.24
2068 2624 6.525628 GCTTTAAGTAAAATGACGGTAAAGGC 59.474 38.462 0.00 0.00 35.05 4.35
2172 2729 5.765182 CCAGATAACATCCCAAGGTAATCAC 59.235 44.000 0.00 0.00 0.00 3.06
2185 2742 9.236006 ACATAATAATGAAGGCCAGATAACATC 57.764 33.333 5.01 0.00 36.54 3.06
2276 2833 1.538512 CAATGATTGGATAGCCGCTGG 59.461 52.381 2.16 0.00 36.79 4.85
2474 3033 3.999001 TCAATGCATCAACAGTCTCTGTC 59.001 43.478 0.00 0.00 44.62 3.51
2568 3127 7.669304 TCAATTCCATGAAACAATTAGTGGAGA 59.331 33.333 0.00 0.00 35.09 3.71
2638 3197 3.692791 TCCATAGTCTTGTCGACATCG 57.307 47.619 20.80 13.70 45.32 3.84
2761 3320 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
2762 3321 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
2763 3322 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2764 3323 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2765 3324 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2766 3325 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
2782 3341 9.231297 CCACATTGGAATCTCTAAAAAGACTTA 57.769 33.333 0.00 0.00 40.96 2.24
2783 3342 7.944554 TCCACATTGGAATCTCTAAAAAGACTT 59.055 33.333 0.00 0.00 45.00 3.01
2784 3343 7.461749 TCCACATTGGAATCTCTAAAAAGACT 58.538 34.615 0.00 0.00 45.00 3.24
2785 3344 7.687941 TCCACATTGGAATCTCTAAAAAGAC 57.312 36.000 0.00 0.00 45.00 3.01
2799 3358 3.367321 TCCGTATGTAGTCCACATTGGA 58.633 45.455 6.85 6.85 46.01 3.53
2800 3359 3.717707 CTCCGTATGTAGTCCACATTGG 58.282 50.000 0.00 0.00 46.01 3.16
2801 3360 3.123804 GCTCCGTATGTAGTCCACATTG 58.876 50.000 0.00 0.00 46.01 2.82
2802 3361 2.764010 TGCTCCGTATGTAGTCCACATT 59.236 45.455 0.00 0.00 46.01 2.71
2804 3363 1.842052 TGCTCCGTATGTAGTCCACA 58.158 50.000 0.00 0.00 42.69 4.17
2805 3364 2.953466 TTGCTCCGTATGTAGTCCAC 57.047 50.000 0.00 0.00 0.00 4.02
2806 3365 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
2807 3366 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
2808 3367 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
2809 3368 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
2810 3369 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
2811 3370 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
2812 3371 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
2813 3372 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
2814 3373 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
2815 3374 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
2816 3375 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
2817 3376 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
2818 3377 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
2819 3378 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
2887 3446 9.291664 CGTTCCTAAATACAAGTCTTTCTAGAG 57.708 37.037 0.00 0.00 0.00 2.43
2888 3447 8.248945 CCGTTCCTAAATACAAGTCTTTCTAGA 58.751 37.037 0.00 0.00 0.00 2.43
2889 3448 8.248945 TCCGTTCCTAAATACAAGTCTTTCTAG 58.751 37.037 0.00 0.00 0.00 2.43
2890 3449 8.125978 TCCGTTCCTAAATACAAGTCTTTCTA 57.874 34.615 0.00 0.00 0.00 2.10
2891 3450 7.001099 TCCGTTCCTAAATACAAGTCTTTCT 57.999 36.000 0.00 0.00 0.00 2.52
2892 3451 7.201617 CCATCCGTTCCTAAATACAAGTCTTTC 60.202 40.741 0.00 0.00 0.00 2.62
2893 3452 6.598064 CCATCCGTTCCTAAATACAAGTCTTT 59.402 38.462 0.00 0.00 0.00 2.52
2894 3453 6.070424 TCCATCCGTTCCTAAATACAAGTCTT 60.070 38.462 0.00 0.00 0.00 3.01
2895 3454 5.424252 TCCATCCGTTCCTAAATACAAGTCT 59.576 40.000 0.00 0.00 0.00 3.24
2896 3455 5.667466 TCCATCCGTTCCTAAATACAAGTC 58.333 41.667 0.00 0.00 0.00 3.01
2897 3456 5.189145 ACTCCATCCGTTCCTAAATACAAGT 59.811 40.000 0.00 0.00 0.00 3.16
2898 3457 5.671493 ACTCCATCCGTTCCTAAATACAAG 58.329 41.667 0.00 0.00 0.00 3.16
2899 3458 5.687166 ACTCCATCCGTTCCTAAATACAA 57.313 39.130 0.00 0.00 0.00 2.41
2900 3459 5.303589 CCTACTCCATCCGTTCCTAAATACA 59.696 44.000 0.00 0.00 0.00 2.29
2901 3460 5.537674 TCCTACTCCATCCGTTCCTAAATAC 59.462 44.000 0.00 0.00 0.00 1.89
2902 3461 5.708544 TCCTACTCCATCCGTTCCTAAATA 58.291 41.667 0.00 0.00 0.00 1.40
2903 3462 4.553678 TCCTACTCCATCCGTTCCTAAAT 58.446 43.478 0.00 0.00 0.00 1.40
2904 3463 3.985127 TCCTACTCCATCCGTTCCTAAA 58.015 45.455 0.00 0.00 0.00 1.85
2905 3464 3.675348 TCCTACTCCATCCGTTCCTAA 57.325 47.619 0.00 0.00 0.00 2.69
2906 3465 3.897657 ATCCTACTCCATCCGTTCCTA 57.102 47.619 0.00 0.00 0.00 2.94
2907 3466 2.777459 ATCCTACTCCATCCGTTCCT 57.223 50.000 0.00 0.00 0.00 3.36
2908 3467 3.840124 AAATCCTACTCCATCCGTTCC 57.160 47.619 0.00 0.00 0.00 3.62
2909 3468 6.097915 TCATAAATCCTACTCCATCCGTTC 57.902 41.667 0.00 0.00 0.00 3.95
2910 3469 6.498651 AGATCATAAATCCTACTCCATCCGTT 59.501 38.462 0.00 0.00 0.00 4.44
2911 3470 6.019748 AGATCATAAATCCTACTCCATCCGT 58.980 40.000 0.00 0.00 0.00 4.69
2912 3471 6.537453 AGATCATAAATCCTACTCCATCCG 57.463 41.667 0.00 0.00 0.00 4.18
2913 3472 7.108847 CCAAGATCATAAATCCTACTCCATCC 58.891 42.308 0.00 0.00 0.00 3.51
2914 3473 7.108847 CCCAAGATCATAAATCCTACTCCATC 58.891 42.308 0.00 0.00 0.00 3.51
2915 3474 6.012157 CCCCAAGATCATAAATCCTACTCCAT 60.012 42.308 0.00 0.00 0.00 3.41
2916 3475 5.310594 CCCCAAGATCATAAATCCTACTCCA 59.689 44.000 0.00 0.00 0.00 3.86
2917 3476 5.310857 ACCCCAAGATCATAAATCCTACTCC 59.689 44.000 0.00 0.00 0.00 3.85
2918 3477 6.441088 ACCCCAAGATCATAAATCCTACTC 57.559 41.667 0.00 0.00 0.00 2.59
2919 3478 6.848562 AACCCCAAGATCATAAATCCTACT 57.151 37.500 0.00 0.00 0.00 2.57
2920 3479 8.437575 TCTAAACCCCAAGATCATAAATCCTAC 58.562 37.037 0.00 0.00 0.00 3.18
3130 3689 2.734673 CTCAGCCGACGCTTTCTGC 61.735 63.158 0.00 0.00 45.55 4.26
3139 3698 1.739049 CTCATCCTCCTCAGCCGAC 59.261 63.158 0.00 0.00 0.00 4.79
3269 3831 5.594317 ACTTCAATTACCAAACTCAGCAAGT 59.406 36.000 0.00 0.00 41.10 3.16
3627 4791 3.006752 TCCTGAATGTGCCAATTGTTTCC 59.993 43.478 4.43 0.00 0.00 3.13
3628 4792 4.255833 TCCTGAATGTGCCAATTGTTTC 57.744 40.909 4.43 0.94 0.00 2.78
3638 4802 4.274459 GGTCTACATTGATCCTGAATGTGC 59.726 45.833 16.29 8.81 42.63 4.57
3651 4815 7.658179 ATTCGTAGCATATTGGTCTACATTG 57.342 36.000 0.00 0.00 34.02 2.82
3652 4816 8.559536 CAAATTCGTAGCATATTGGTCTACATT 58.440 33.333 0.00 0.00 34.02 2.71
3703 4868 5.740569 GTGACAATGTGCATGACATATGTTC 59.259 40.000 10.30 4.23 45.12 3.18
3725 4890 3.009473 TCCCTCTCCTTTTCCTCATTGTG 59.991 47.826 0.00 0.00 0.00 3.33
3744 4909 2.654863 CCAGATACACCAACCAATCCC 58.345 52.381 0.00 0.00 0.00 3.85
3747 4920 4.608170 AATCCCAGATACACCAACCAAT 57.392 40.909 0.00 0.00 0.00 3.16
3890 5063 8.613060 ACATAGCATTCGATTGACAAGAATAT 57.387 30.769 11.36 0.00 33.75 1.28
3891 5064 8.437360 AACATAGCATTCGATTGACAAGAATA 57.563 30.769 11.36 0.00 33.75 1.75
3892 5065 6.932356 ACATAGCATTCGATTGACAAGAAT 57.068 33.333 11.36 0.00 35.24 2.40
3893 5066 6.595326 AGAACATAGCATTCGATTGACAAGAA 59.405 34.615 11.36 0.00 0.00 2.52
3901 5074 6.879458 GGGGTTATAGAACATAGCATTCGATT 59.121 38.462 2.17 0.00 37.29 3.34
3910 5083 4.227527 GGGGGATGGGGTTATAGAACATAG 59.772 50.000 2.17 0.00 37.29 2.23
3944 5117 0.905337 AACGCAGGAGAAGGCTACCT 60.905 55.000 0.00 0.00 33.87 3.08
3983 5156 5.649395 TGGAAAGACAAATGAGAAGGCATAG 59.351 40.000 0.00 0.00 0.00 2.23
3985 5158 4.219288 GTGGAAAGACAAATGAGAAGGCAT 59.781 41.667 0.00 0.00 0.00 4.40
3987 5160 3.569701 TGTGGAAAGACAAATGAGAAGGC 59.430 43.478 0.00 0.00 0.00 4.35
3988 5161 4.022849 GGTGTGGAAAGACAAATGAGAAGG 60.023 45.833 0.00 0.00 0.00 3.46
3989 5162 4.580167 TGGTGTGGAAAGACAAATGAGAAG 59.420 41.667 0.00 0.00 0.00 2.85
3990 5163 4.531854 TGGTGTGGAAAGACAAATGAGAA 58.468 39.130 0.00 0.00 0.00 2.87
3992 5165 4.763793 AGATGGTGTGGAAAGACAAATGAG 59.236 41.667 0.00 0.00 0.00 2.90
3994 5167 5.458041 AAGATGGTGTGGAAAGACAAATG 57.542 39.130 0.00 0.00 0.00 2.32
3995 5168 4.524328 GGAAGATGGTGTGGAAAGACAAAT 59.476 41.667 0.00 0.00 0.00 2.32
4004 5183 4.018490 CAAATGATGGAAGATGGTGTGGA 58.982 43.478 0.00 0.00 0.00 4.02
4005 5184 4.018490 TCAAATGATGGAAGATGGTGTGG 58.982 43.478 0.00 0.00 0.00 4.17
4007 5186 5.512298 TGATCAAATGATGGAAGATGGTGT 58.488 37.500 0.00 0.00 34.37 4.16
4089 5269 3.447742 TCGCTTAGTACATGCATGAGTG 58.552 45.455 32.75 23.18 0.00 3.51
4156 5342 0.615331 CAGTGATAGCACCACCCAGT 59.385 55.000 7.66 0.00 46.32 4.00
4157 5343 0.904649 TCAGTGATAGCACCACCCAG 59.095 55.000 7.66 0.00 46.32 4.45


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

AutoCloner maintained by Alex Coulton.