Multiple sequence alignment - TraesCS3A01G503100

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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 TraesCS3A01G503100 chr3A 100.000 5093 0 0 1 5093 726016598 726021690 0.000000e+00 9406.0
1 TraesCS3A01G503100 chr3D 91.687 3729 196 54 1 3703 595015869 595019509 0.000000e+00 5064.0
2 TraesCS3A01G503100 chr3D 90.584 1232 75 18 3826 5030 595019507 595020724 0.000000e+00 1594.0
3 TraesCS3A01G503100 chr3D 89.041 73 3 1 5026 5093 595020752 595020824 9.090000e-13 86.1
4 TraesCS3A01G503100 chr3B 89.832 3757 250 64 24 3703 798457763 798461464 0.000000e+00 4700.0
5 TraesCS3A01G503100 chr3B 88.583 981 70 19 3826 4793 798461462 798462413 0.000000e+00 1153.0
6 TraesCS3A01G503100 chr3B 90.374 187 14 2 4909 5092 798462407 798462592 5.090000e-60 243.0
7 TraesCS3A01G503100 chr4D 100.000 127 0 0 3702 3828 306860403 306860277 8.520000e-58 235.0
8 TraesCS3A01G503100 chr1B 98.496 133 1 1 3701 3833 543038775 543038906 3.070000e-57 233.0
9 TraesCS3A01G503100 chr1A 98.485 132 2 0 3701 3832 486045772 486045903 3.070000e-57 233.0
10 TraesCS3A01G503100 chr6B 98.473 131 2 0 3701 3831 207511028 207510898 1.100000e-56 231.0
11 TraesCS3A01G503100 chr6B 92.810 153 8 3 3680 3831 10221083 10220933 8.590000e-53 219.0
12 TraesCS3A01G503100 chr2B 95.714 140 6 0 3697 3836 721714784 721714645 5.130000e-55 226.0
13 TraesCS3A01G503100 chr7D 93.878 147 5 3 3702 3848 425229713 425229855 8.590000e-53 219.0
14 TraesCS3A01G503100 chr5D 93.878 147 5 3 3702 3848 162219775 162219917 8.590000e-53 219.0
15 TraesCS3A01G503100 chr5A 93.878 147 5 2 3702 3848 12509190 12509332 8.590000e-53 219.0


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 TraesCS3A01G503100 chr3A 726016598 726021690 5092 False 9406.000000 9406 100.000000 1 5093 1 chr3A.!!$F1 5092
1 TraesCS3A01G503100 chr3D 595015869 595020824 4955 False 2248.033333 5064 90.437333 1 5093 3 chr3D.!!$F1 5092
2 TraesCS3A01G503100 chr3B 798457763 798462592 4829 False 2032.000000 4700 89.596333 24 5092 3 chr3B.!!$F1 5068

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
890 935 0.725118 CTCTCCGACGACAACGACAC 60.725 60.0 0.0 0.0 42.66 3.67 F
1488 1557 0.178921 AGTCCTCTGAGGTGAAGCCA 60.179 55.0 22.5 0.0 40.61 4.75 F
2249 2323 0.250338 ACGGAAGCCTCTGTTCAACC 60.250 55.0 0.0 0.0 38.00 3.77 F
3529 3629 0.322975 GCCGCCTACAGATGATGGAT 59.677 55.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 1823 0.179100 AATCGACACGGCCTCATCAG 60.179 55.0 0.00 0.00 0.00 2.90 R
3147 3235 0.251386 TCTTCCTGAGCTCGTGGACT 60.251 55.0 22.82 0.00 0.00 3.85 R
3704 3826 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.20 R
4800 4951 0.182537 ATTATAAGCAGGGCACGCCA 59.817 50.0 10.83 0.00 37.98 5.69 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
39 40 4.144727 GAGAGGAGAGGGGGCGGA 62.145 72.222 0.00 0.00 0.00 5.54
86 87 1.264557 CAAAATTGTACGCGACCACCA 59.735 47.619 15.93 0.00 0.00 4.17
139 158 0.919289 TTCCTCCCTCCCAATCCCAC 60.919 60.000 0.00 0.00 0.00 4.61
147 166 1.006998 CTCCCAATCCCACATCCCAAA 59.993 52.381 0.00 0.00 0.00 3.28
148 167 1.650700 TCCCAATCCCACATCCCAAAT 59.349 47.619 0.00 0.00 0.00 2.32
151 170 2.041701 CAATCCCACATCCCAAATCCC 58.958 52.381 0.00 0.00 0.00 3.85
152 171 1.624173 ATCCCACATCCCAAATCCCT 58.376 50.000 0.00 0.00 0.00 4.20
378 400 1.209504 TGCGCATCTAGCTAGGGTTTT 59.790 47.619 20.58 0.00 42.61 2.43
383 405 3.458189 CATCTAGCTAGGGTTTTCGGTG 58.542 50.000 20.58 0.00 0.00 4.94
539 578 2.987547 TTCCTCGTCCTCCGCGTT 60.988 61.111 4.92 0.00 36.19 4.84
880 925 3.141488 CCCACTCCCTCTCCGACG 61.141 72.222 0.00 0.00 0.00 5.12
881 926 2.045242 CCACTCCCTCTCCGACGA 60.045 66.667 0.00 0.00 0.00 4.20
883 928 1.674651 CACTCCCTCTCCGACGACA 60.675 63.158 0.00 0.00 0.00 4.35
884 929 1.074423 ACTCCCTCTCCGACGACAA 59.926 57.895 0.00 0.00 0.00 3.18
886 931 2.178521 CCCTCTCCGACGACAACG 59.821 66.667 0.00 0.00 45.75 4.10
887 932 2.330372 CCCTCTCCGACGACAACGA 61.330 63.158 0.00 0.00 42.66 3.85
889 934 1.572941 CTCTCCGACGACAACGACA 59.427 57.895 0.00 0.00 42.66 4.35
890 935 0.725118 CTCTCCGACGACAACGACAC 60.725 60.000 0.00 0.00 42.66 3.67
891 936 1.728426 CTCCGACGACAACGACACC 60.728 63.158 0.00 0.00 42.66 4.16
892 937 3.095278 CCGACGACAACGACACCG 61.095 66.667 0.00 0.00 42.66 4.94
893 938 3.749373 CGACGACAACGACACCGC 61.749 66.667 0.00 0.00 42.66 5.68
894 939 2.656007 GACGACAACGACACCGCA 60.656 61.111 0.00 0.00 42.66 5.69
895 940 2.645510 GACGACAACGACACCGCAG 61.646 63.158 0.00 0.00 42.66 5.18
896 941 2.354188 CGACAACGACACCGCAGA 60.354 61.111 0.00 0.00 42.66 4.26
897 942 2.645510 CGACAACGACACCGCAGAC 61.646 63.158 0.00 0.00 42.66 3.51
898 943 1.299926 GACAACGACACCGCAGACT 60.300 57.895 0.00 0.00 39.95 3.24
899 944 1.276145 GACAACGACACCGCAGACTC 61.276 60.000 0.00 0.00 39.95 3.36
909 954 2.202324 GCAGACTCCGACGACGAC 60.202 66.667 9.28 0.00 42.66 4.34
1198 1261 0.606604 GCCGTGGGACTTCTTAGACA 59.393 55.000 0.00 0.00 0.00 3.41
1218 1281 3.385749 CTTCACGCCCACGCCCTAT 62.386 63.158 0.00 0.00 45.53 2.57
1229 1292 1.146263 CGCCCTATGACCAGTTCCC 59.854 63.158 0.00 0.00 0.00 3.97
1389 1452 0.681175 GGCCAGCAAAACCATCAACT 59.319 50.000 0.00 0.00 0.00 3.16
1392 1455 2.224018 GCCAGCAAAACCATCAACTTCA 60.224 45.455 0.00 0.00 0.00 3.02
1398 1461 1.238439 AACCATCAACTTCAGCCGTG 58.762 50.000 0.00 0.00 0.00 4.94
1413 1476 1.338200 GCCGTGGTTGAAGATCAGAGT 60.338 52.381 0.00 0.00 0.00 3.24
1455 1518 0.620556 CTGGTCCTACCACCAATGCT 59.379 55.000 0.00 0.00 44.79 3.79
1457 1520 3.074578 TGGTCCTACCACCAATGCTGG 62.075 57.143 0.00 0.00 44.79 4.85
1465 1528 3.078836 CCAATGCTGGGCCCAAGG 61.079 66.667 28.29 16.99 39.30 3.61
1466 1529 3.078836 CAATGCTGGGCCCAAGGG 61.079 66.667 28.29 16.15 38.57 3.95
1488 1557 0.178921 AGTCCTCTGAGGTGAAGCCA 60.179 55.000 22.50 0.00 40.61 4.75
1489 1558 0.687354 GTCCTCTGAGGTGAAGCCAA 59.313 55.000 22.50 0.00 40.61 4.52
1551 1620 0.366871 CGCTGTCAAGGAACGATTCG 59.633 55.000 4.14 4.14 0.00 3.34
1626 1695 0.250640 CAGTGAGCTTGAAGGGTGCT 60.251 55.000 0.00 0.00 40.02 4.40
1647 1716 2.071778 ACTTTGGTGACATTGCTGGT 57.928 45.000 0.00 0.00 42.32 4.00
1676 1748 6.941857 ACTCCTCCAATAAGAAGAAGAAGAC 58.058 40.000 0.00 0.00 0.00 3.01
1679 1751 5.105310 CCTCCAATAAGAAGAAGAAGACGGA 60.105 44.000 0.00 0.00 0.00 4.69
1727 1799 4.577677 TGTTGGCGGCAGCTCCAA 62.578 61.111 25.26 13.45 44.37 3.53
1728 1800 3.064324 GTTGGCGGCAGCTCCAAT 61.064 61.111 18.61 0.00 43.43 3.16
1732 1804 4.802051 GCGGCAGCTCCAATGGGA 62.802 66.667 0.00 0.00 42.29 4.37
1733 1805 2.045045 CGGCAGCTCCAATGGGAA 60.045 61.111 0.00 0.00 44.38 3.97
1751 1823 0.603975 AAGAAGAAGGGTGCTGCGAC 60.604 55.000 0.00 0.00 0.00 5.19
1763 1835 3.362399 CTGCGACTGATGAGGCCGT 62.362 63.158 0.00 0.00 0.00 5.68
1775 1847 3.186047 GGCCGTGTCGATTGTCGG 61.186 66.667 13.35 13.35 44.86 4.79
1814 1886 2.591429 CCACGGCAAGTCAGTGCA 60.591 61.111 0.00 0.00 46.81 4.57
1825 1897 3.129502 CAGTGCAGTCGGCCATGG 61.130 66.667 7.63 7.63 43.89 3.66
1828 1900 4.429522 TGCAGTCGGCCATGGCAT 62.430 61.111 36.56 17.32 43.89 4.40
1832 1904 1.001020 AGTCGGCCATGGCATTGAA 60.001 52.632 36.56 14.66 44.11 2.69
2048 2120 7.222611 AGCAACACATGTCTGAAATTTTGTTAC 59.777 33.333 8.37 1.27 0.00 2.50
2059 2133 7.014711 TCTGAAATTTTGTTACATGGGCAAGTA 59.985 33.333 0.00 0.00 0.00 2.24
2186 2260 0.961753 GGGAAAGGTGCTCAAGGTTG 59.038 55.000 0.00 0.00 0.00 3.77
2193 2267 3.793144 GCTCAAGGTTGCCGAGCG 61.793 66.667 0.00 0.00 42.42 5.03
2216 2290 1.033746 CAGCTTCATCGGCCAATGGT 61.034 55.000 3.24 0.00 0.00 3.55
2237 2311 1.464997 AGAGAAAATCGCAACGGAAGC 59.535 47.619 0.00 0.00 0.00 3.86
2249 2323 0.250338 ACGGAAGCCTCTGTTCAACC 60.250 55.000 0.00 0.00 38.00 3.77
2336 2410 3.558505 CACATCAACAAGCTACAAGTGC 58.441 45.455 0.00 0.00 0.00 4.40
2421 2495 2.117865 AGGATGAAGAGAAGCTGAGGG 58.882 52.381 0.00 0.00 0.00 4.30
2456 2530 3.388024 AGAAGTACAACAGGCTGAAGTCA 59.612 43.478 23.66 5.54 0.00 3.41
2495 2569 1.660355 GCCGGATGCGATAGAGACA 59.340 57.895 8.71 0.00 39.76 3.41
2621 2695 7.458397 TGTACCCTCAACTTGTTGATCTTATT 58.542 34.615 15.35 2.39 0.00 1.40
2638 2724 7.663081 TGATCTTATTCAAGGGTATGATGAAGC 59.337 37.037 0.00 0.00 36.59 3.86
2642 2728 4.679373 TCAAGGGTATGATGAAGCTCTC 57.321 45.455 0.00 0.00 0.00 3.20
2643 2729 4.293494 TCAAGGGTATGATGAAGCTCTCT 58.707 43.478 0.00 0.00 0.00 3.10
2644 2730 4.718774 TCAAGGGTATGATGAAGCTCTCTT 59.281 41.667 0.00 0.00 34.68 2.85
2645 2731 4.953940 AGGGTATGATGAAGCTCTCTTC 57.046 45.455 0.00 0.00 46.85 2.87
2646 2732 3.645687 AGGGTATGATGAAGCTCTCTTCC 59.354 47.826 0.00 0.00 46.28 3.46
2647 2733 3.645687 GGGTATGATGAAGCTCTCTTCCT 59.354 47.826 0.00 0.00 46.28 3.36
2648 2734 4.502950 GGGTATGATGAAGCTCTCTTCCTG 60.503 50.000 0.00 0.00 46.28 3.86
2649 2735 3.842007 ATGATGAAGCTCTCTTCCTGG 57.158 47.619 0.00 0.00 46.28 4.45
2650 2736 2.544721 TGATGAAGCTCTCTTCCTGGT 58.455 47.619 0.00 0.00 46.28 4.00
2651 2737 2.909006 TGATGAAGCTCTCTTCCTGGTT 59.091 45.455 0.00 0.00 46.28 3.67
2652 2738 3.055530 TGATGAAGCTCTCTTCCTGGTTC 60.056 47.826 0.00 0.00 46.28 3.62
2653 2739 1.625818 TGAAGCTCTCTTCCTGGTTCC 59.374 52.381 0.00 0.00 46.28 3.62
2654 2740 1.625818 GAAGCTCTCTTCCTGGTTCCA 59.374 52.381 0.00 0.00 42.18 3.53
2655 2741 1.274712 AGCTCTCTTCCTGGTTCCAG 58.725 55.000 11.52 11.52 0.00 3.86
2656 2742 0.980423 GCTCTCTTCCTGGTTCCAGT 59.020 55.000 16.33 0.00 32.56 4.00
2657 2743 1.349357 GCTCTCTTCCTGGTTCCAGTT 59.651 52.381 16.33 0.00 32.56 3.16
2709 2795 4.989044 ACAAAACCTTTAAACTGACCACG 58.011 39.130 0.00 0.00 0.00 4.94
2711 2797 1.223187 ACCTTTAAACTGACCACGCG 58.777 50.000 3.53 3.53 0.00 6.01
2729 2815 1.774639 CGCATTGCTGCTCTTGTTTT 58.225 45.000 7.12 0.00 46.65 2.43
2993 3081 3.699134 GATGGTTCCCCGAGGTGCC 62.699 68.421 0.00 0.00 0.00 5.01
3147 3235 5.233902 GTCGATCGACTACTTCTACAAGCTA 59.766 44.000 34.97 0.00 41.57 3.32
3234 3322 0.879090 GGGACTACAACAAAAGGCGG 59.121 55.000 0.00 0.00 0.00 6.13
3396 3496 1.810853 GCATGTCCATTTTGCGGCC 60.811 57.895 0.00 0.00 0.00 6.13
3492 3592 3.204827 GCGCGCATCAGGACCAAT 61.205 61.111 29.10 0.00 0.00 3.16
3498 3598 1.452651 CATCAGGACCAATGGCGCT 60.453 57.895 7.64 0.00 0.00 5.92
3506 3606 3.570638 CAATGGCGCTGGAGCTCG 61.571 66.667 7.64 0.00 39.32 5.03
3524 3624 3.536917 CGGGCCGCCTACAGATGA 61.537 66.667 15.42 0.00 0.00 2.92
3525 3625 2.872388 CGGGCCGCCTACAGATGAT 61.872 63.158 15.42 0.00 0.00 2.45
3526 3626 1.302033 GGGCCGCCTACAGATGATG 60.302 63.158 9.86 0.00 0.00 3.07
3527 3627 1.302033 GGCCGCCTACAGATGATGG 60.302 63.158 0.71 0.00 0.00 3.51
3528 3628 1.748403 GCCGCCTACAGATGATGGA 59.252 57.895 0.00 0.00 0.00 3.41
3529 3629 0.322975 GCCGCCTACAGATGATGGAT 59.677 55.000 0.00 0.00 0.00 3.41
3530 3630 1.674221 GCCGCCTACAGATGATGGATC 60.674 57.143 0.00 0.00 0.00 3.36
3531 3631 1.898472 CCGCCTACAGATGATGGATCT 59.102 52.381 0.00 0.00 42.70 2.75
3545 3645 2.141535 GGATCTGAATCCGAGGTTCG 57.858 55.000 0.00 0.00 42.16 3.95
3581 3681 1.081094 GGCTGATGGCATGTTTTTGC 58.919 50.000 3.81 0.00 44.01 3.68
3582 3682 1.608542 GGCTGATGGCATGTTTTTGCA 60.609 47.619 3.81 0.00 44.59 4.08
3583 3683 1.730064 GCTGATGGCATGTTTTTGCAG 59.270 47.619 3.81 5.16 44.59 4.41
3584 3684 2.610976 GCTGATGGCATGTTTTTGCAGA 60.611 45.455 3.81 0.00 44.59 4.26
3585 3685 3.250744 CTGATGGCATGTTTTTGCAGAG 58.749 45.455 3.81 0.00 44.59 3.35
3587 3687 0.680618 TGGCATGTTTTTGCAGAGGG 59.319 50.000 0.00 0.00 44.59 4.30
3598 3713 1.967319 TGCAGAGGGTTTTGTGACTC 58.033 50.000 0.00 0.00 0.00 3.36
3633 3753 1.285078 GGGGGTAGTGCTGGAGATTTT 59.715 52.381 0.00 0.00 0.00 1.82
3642 3762 4.275936 AGTGCTGGAGATTTTTGTGTGTAC 59.724 41.667 0.00 0.00 0.00 2.90
3656 3778 7.609760 TTTGTGTGTACATAGATCATTGGTC 57.390 36.000 0.00 0.00 36.53 4.02
3677 3799 2.102578 CATTCTGGGGTTTAGGCCTTG 58.897 52.381 12.58 0.00 0.00 3.61
3703 3825 4.036734 TCCTACGAACGATTATGGTGGTAC 59.963 45.833 0.14 0.00 0.00 3.34
3704 3826 4.037208 CCTACGAACGATTATGGTGGTACT 59.963 45.833 0.14 0.00 0.00 2.73
3705 3827 4.037858 ACGAACGATTATGGTGGTACTC 57.962 45.455 0.14 0.00 0.00 2.59
3706 3828 3.181483 ACGAACGATTATGGTGGTACTCC 60.181 47.826 0.14 0.00 43.26 3.85
3707 3829 3.725490 GAACGATTATGGTGGTACTCCC 58.275 50.000 0.00 0.00 42.10 4.30
3708 3830 3.042059 ACGATTATGGTGGTACTCCCT 57.958 47.619 0.00 0.00 42.10 4.20
3709 3831 2.963782 ACGATTATGGTGGTACTCCCTC 59.036 50.000 0.00 0.00 42.10 4.30
3710 3832 2.299297 CGATTATGGTGGTACTCCCTCC 59.701 54.545 0.00 0.00 45.59 4.30
3713 3835 3.613527 GGTGGTACTCCCTCCGTC 58.386 66.667 0.00 0.00 37.14 4.79
3714 3836 2.056815 GGTGGTACTCCCTCCGTCC 61.057 68.421 0.00 0.00 37.14 4.79
3715 3837 2.044650 TGGTACTCCCTCCGTCCG 60.045 66.667 0.00 0.00 0.00 4.79
3716 3838 2.832201 GGTACTCCCTCCGTCCGG 60.832 72.222 0.00 0.00 0.00 5.14
3717 3839 2.273449 GTACTCCCTCCGTCCGGA 59.727 66.667 0.00 0.00 42.90 5.14
3718 3840 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
3719 3841 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
3720 3842 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
3721 3843 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
3722 3844 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
3723 3845 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
3724 3846 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
3725 3847 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
3726 3848 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
3727 3849 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
3728 3850 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
3729 3851 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
3730 3852 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
3731 3853 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
3732 3854 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
3733 3855 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
3734 3856 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
3735 3857 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
3736 3858 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
3737 3859 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
3738 3860 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
3739 3861 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
3740 3862 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
3746 3868 7.614494 ACTTGTCATCAAAATGGATAAAAGGG 58.386 34.615 0.00 0.00 33.42 3.95
3747 3869 6.543430 TGTCATCAAAATGGATAAAAGGGG 57.457 37.500 0.00 0.00 33.42 4.79
3748 3870 6.259893 TGTCATCAAAATGGATAAAAGGGGA 58.740 36.000 0.00 0.00 33.42 4.81
3749 3871 6.902416 TGTCATCAAAATGGATAAAAGGGGAT 59.098 34.615 0.00 0.00 33.42 3.85
3750 3872 8.064389 TGTCATCAAAATGGATAAAAGGGGATA 58.936 33.333 0.00 0.00 33.42 2.59
3751 3873 9.093458 GTCATCAAAATGGATAAAAGGGGATAT 57.907 33.333 0.00 0.00 33.42 1.63
3760 3882 8.534954 TGGATAAAAGGGGATATATCTAGACG 57.465 38.462 12.42 0.00 0.00 4.18
3761 3883 8.120538 TGGATAAAAGGGGATATATCTAGACGT 58.879 37.037 12.42 0.00 0.00 4.34
3762 3884 9.638176 GGATAAAAGGGGATATATCTAGACGTA 57.362 37.037 12.42 0.00 0.00 3.57
3807 3929 9.918630 CTCTTTTTATCCATTTTGATGACAAGT 57.081 29.630 0.00 0.00 37.32 3.16
3814 3936 8.915871 ATCCATTTTGATGACAAGTATTTTCG 57.084 30.769 0.00 0.00 37.32 3.46
3815 3937 7.312154 TCCATTTTGATGACAAGTATTTTCGG 58.688 34.615 0.00 0.00 37.32 4.30
3816 3938 7.175816 TCCATTTTGATGACAAGTATTTTCGGA 59.824 33.333 0.00 0.00 37.32 4.55
3817 3939 7.273381 CCATTTTGATGACAAGTATTTTCGGAC 59.727 37.037 0.00 0.00 37.32 4.79
3818 3940 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
3819 3941 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
3820 3942 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
3821 3943 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
3822 3944 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
3823 3945 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
3824 3946 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
3825 3947 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
3826 3948 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
3827 3949 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
3844 3968 8.527810 GGAGGGAGTAGATTAGATAGAATGTTG 58.472 40.741 0.00 0.00 0.00 3.33
3878 4002 3.153919 GGTTTTTACTGATGGTGCCTGA 58.846 45.455 0.00 0.00 0.00 3.86
3881 4005 3.788227 TTTACTGATGGTGCCTGACTT 57.212 42.857 0.00 0.00 0.00 3.01
3922 4047 2.294233 GGAGCTGCAAATGTTTCAGTGA 59.706 45.455 0.00 0.00 0.00 3.41
3938 4069 7.392953 TGTTTCAGTGATGCTCCAATTAATACA 59.607 33.333 0.00 0.00 0.00 2.29
3946 4077 8.785946 TGATGCTCCAATTAATACATGTACATG 58.214 33.333 29.97 29.97 44.15 3.21
4001 4132 6.364165 CGATCTTCATTTCAGCAATGTGTTTT 59.636 34.615 0.00 0.00 42.79 2.43
4009 4140 4.454678 TCAGCAATGTGTTTTGAGAGAGT 58.545 39.130 0.00 0.00 0.00 3.24
4013 4144 6.634436 CAGCAATGTGTTTTGAGAGAGTTAAC 59.366 38.462 0.00 0.00 0.00 2.01
4061 4192 5.833400 CGCTACTTCGCATTATGTTTTTC 57.167 39.130 0.00 0.00 0.00 2.29
4073 4206 9.128107 CGCATTATGTTTTTCTAACTGTGAATT 57.872 29.630 0.00 0.00 0.00 2.17
4120 4253 0.596600 CGGCATGGCTTCATTGCATC 60.597 55.000 18.09 0.00 34.04 3.91
4133 4266 4.142038 TCATTGCATCATTCCAGGATCTG 58.858 43.478 0.00 0.00 0.00 2.90
4142 4275 5.384336 TCATTCCAGGATCTGAAAAACACA 58.616 37.500 0.00 0.00 32.44 3.72
4146 4279 6.088016 TCCAGGATCTGAAAAACACAAATG 57.912 37.500 0.00 0.00 32.44 2.32
4147 4280 5.598005 TCCAGGATCTGAAAAACACAAATGT 59.402 36.000 0.00 0.00 35.23 2.71
4148 4281 5.693104 CCAGGATCTGAAAAACACAAATGTG 59.307 40.000 11.83 11.83 41.83 3.21
4197 4334 0.788391 GTTCATCGTCGTCGCCTTTT 59.212 50.000 0.00 0.00 36.96 2.27
4229 4367 2.037381 GTGCCTATACTGACCCCTAAGC 59.963 54.545 0.00 0.00 0.00 3.09
4230 4368 1.272769 GCCTATACTGACCCCTAAGCG 59.727 57.143 0.00 0.00 0.00 4.68
4231 4369 1.272769 CCTATACTGACCCCTAAGCGC 59.727 57.143 0.00 0.00 0.00 5.92
4232 4370 1.961394 CTATACTGACCCCTAAGCGCA 59.039 52.381 11.47 0.00 0.00 6.09
4233 4371 1.200519 ATACTGACCCCTAAGCGCAA 58.799 50.000 11.47 0.00 0.00 4.85
4234 4372 0.535335 TACTGACCCCTAAGCGCAAG 59.465 55.000 11.47 6.47 43.44 4.01
4235 4373 1.450312 CTGACCCCTAAGCGCAAGG 60.450 63.158 19.12 19.12 38.28 3.61
4278 4416 1.351017 TCCTCACTGGACCCAACATTC 59.649 52.381 0.00 0.00 40.56 2.67
4280 4418 0.036164 TCACTGGACCCAACATTCCG 59.964 55.000 0.00 0.00 34.24 4.30
4410 4551 4.224594 TCTCAGCATCTCCTGAACAATTCT 59.775 41.667 0.00 0.00 41.02 2.40
4486 4631 3.103793 CGAACCGCAACTTCTATTGTG 57.896 47.619 0.00 0.00 39.35 3.33
4493 4638 2.673368 GCAACTTCTATTGTGAGGGTCG 59.327 50.000 0.00 0.00 31.83 4.79
4495 4640 2.180276 ACTTCTATTGTGAGGGTCGCT 58.820 47.619 0.00 0.00 0.00 4.93
4504 4649 1.180456 TGAGGGTCGCTGTTCGGTTA 61.180 55.000 0.00 0.00 39.05 2.85
4559 4704 2.672651 CGGTGCTGGCATGAACCA 60.673 61.111 12.68 0.00 35.33 3.67
4576 4721 2.248248 ACCACCTCGTCTGAAGAATCA 58.752 47.619 0.00 0.00 0.00 2.57
4588 4733 0.257039 AAGAATCATCCGCCTTGGCT 59.743 50.000 10.12 0.00 37.80 4.75
4648 4799 1.071605 CTTGCTGTCGCTTGTACTCC 58.928 55.000 0.00 0.00 36.97 3.85
4804 4955 2.911198 CGCAATCGTAAAACTGGCG 58.089 52.632 0.00 0.00 36.93 5.69
4805 4956 0.165079 CGCAATCGTAAAACTGGCGT 59.835 50.000 0.00 0.00 38.36 5.68
4816 4967 2.124570 CTGGCGTGCCCTGCTTAT 60.125 61.111 8.69 0.00 34.56 1.73
4822 4973 2.550208 GGCGTGCCCTGCTTATAATAGT 60.550 50.000 0.00 0.00 0.00 2.12
4828 4979 4.346709 TGCCCTGCTTATAATAGTACAGCA 59.653 41.667 5.93 5.93 38.16 4.41
4832 4983 6.463049 CCCTGCTTATAATAGTACAGCACTGT 60.463 42.308 8.57 8.57 46.87 3.55
4836 4987 8.692710 TGCTTATAATAGTACAGCACTGTAGTT 58.307 33.333 20.18 13.18 44.75 2.24
4872 5023 2.083774 CTTGGTTCAGTGTGTGTGTGT 58.916 47.619 0.00 0.00 0.00 3.72
4873 5024 1.447945 TGGTTCAGTGTGTGTGTGTG 58.552 50.000 0.00 0.00 0.00 3.82
4876 5027 0.801872 TTCAGTGTGTGTGTGTGTGC 59.198 50.000 0.00 0.00 0.00 4.57
4877 5028 0.321122 TCAGTGTGTGTGTGTGTGCA 60.321 50.000 0.00 0.00 0.00 4.57
4878 5029 0.734309 CAGTGTGTGTGTGTGTGCAT 59.266 50.000 0.00 0.00 0.00 3.96
4881 5032 0.731994 TGTGTGTGTGTGTGCATGAC 59.268 50.000 0.00 0.00 0.00 3.06
4882 5033 0.731994 GTGTGTGTGTGTGCATGACA 59.268 50.000 0.00 0.00 0.00 3.58
4883 5034 1.015868 TGTGTGTGTGTGCATGACAG 58.984 50.000 0.00 0.00 34.28 3.51
4893 5044 2.104622 TGTGCATGACAGGAAGTTCAGA 59.895 45.455 5.01 0.00 0.00 3.27
4936 5087 5.631026 TCAAATTTGTAGCGCTGAAATCTC 58.369 37.500 22.90 2.19 0.00 2.75
4991 5142 3.364460 TGATTCCCACACCATCGATTT 57.636 42.857 0.00 0.00 0.00 2.17
5023 5174 1.066002 ACTGAAGTGCACACAACATGC 59.934 47.619 21.04 0.00 43.68 4.06
5046 5229 5.671329 GCGTGTTGCTAAATTAAGGACTGAG 60.671 44.000 0.00 0.00 41.73 3.35
5080 5268 4.030216 CCTGGGTTATTATTGGCAGGTTT 58.970 43.478 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.294512 CGGCTTTTCCTTTTCTTCTGCT 59.705 45.455 0.00 0.00 0.00 4.24
70 71 0.389426 GAGTGGTGGTCGCGTACAAT 60.389 55.000 5.77 0.00 0.00 2.71
86 87 2.172679 GGAGACGAGAAAGGAAGGAGT 58.827 52.381 0.00 0.00 0.00 3.85
139 158 0.468029 CCGGGAAGGGATTTGGGATG 60.468 60.000 0.00 0.00 35.97 3.51
361 383 2.158943 ACCGAAAACCCTAGCTAGATGC 60.159 50.000 22.70 3.33 43.29 3.91
363 385 2.158943 GCACCGAAAACCCTAGCTAGAT 60.159 50.000 22.70 6.99 0.00 1.98
378 400 2.646175 CGAAGGGAGAAGGCACCGA 61.646 63.158 0.00 0.00 0.00 4.69
383 405 2.188207 GAGGCGAAGGGAGAAGGC 59.812 66.667 0.00 0.00 0.00 4.35
828 873 4.144727 GAGGAGGAGGAGGCCGGA 62.145 72.222 5.05 0.00 0.00 5.14
833 878 2.443016 CGGTGGAGGAGGAGGAGG 60.443 72.222 0.00 0.00 0.00 4.30
859 904 1.000486 CGGAGAGGGAGTGGGAGAA 60.000 63.158 0.00 0.00 0.00 2.87
880 925 1.276145 GAGTCTGCGGTGTCGTTGTC 61.276 60.000 0.00 0.00 38.89 3.18
881 926 1.299926 GAGTCTGCGGTGTCGTTGT 60.300 57.895 0.00 0.00 38.89 3.32
883 928 2.338984 GGAGTCTGCGGTGTCGTT 59.661 61.111 0.00 0.00 38.89 3.85
884 929 4.039357 CGGAGTCTGCGGTGTCGT 62.039 66.667 5.76 0.00 38.89 4.34
886 931 2.126424 GTCGGAGTCTGCGGTGTC 60.126 66.667 14.16 0.00 0.00 3.67
887 932 4.039357 CGTCGGAGTCTGCGGTGT 62.039 66.667 14.16 0.00 0.00 4.16
889 934 3.735029 GTCGTCGGAGTCTGCGGT 61.735 66.667 14.16 0.00 0.00 5.68
890 935 4.813526 CGTCGTCGGAGTCTGCGG 62.814 72.222 14.16 0.00 0.00 5.69
891 936 3.785499 TCGTCGTCGGAGTCTGCG 61.785 66.667 7.54 7.54 37.69 5.18
892 937 2.202324 GTCGTCGTCGGAGTCTGC 60.202 66.667 1.55 0.00 37.69 4.26
893 938 2.096030 CGTCGTCGTCGGAGTCTG 59.904 66.667 3.90 0.00 37.69 3.51
894 939 2.048784 TCGTCGTCGTCGGAGTCT 60.049 61.111 11.74 0.00 38.33 3.24
895 940 2.394912 CTCGTCGTCGTCGGAGTC 59.605 66.667 11.74 0.00 38.33 3.36
896 941 3.786586 GCTCGTCGTCGTCGGAGT 61.787 66.667 11.74 0.00 38.33 3.85
897 942 3.785499 TGCTCGTCGTCGTCGGAG 61.785 66.667 11.74 8.43 38.33 4.63
898 943 4.081030 GTGCTCGTCGTCGTCGGA 62.081 66.667 11.74 0.00 38.33 4.55
1198 1261 4.778143 GGGCGTGGGCGTGAAGAT 62.778 66.667 0.00 0.00 41.24 2.40
1378 1441 1.608590 CACGGCTGAAGTTGATGGTTT 59.391 47.619 0.00 0.00 0.00 3.27
1380 1443 0.606401 CCACGGCTGAAGTTGATGGT 60.606 55.000 0.00 0.00 0.00 3.55
1389 1452 1.071542 TGATCTTCAACCACGGCTGAA 59.928 47.619 0.00 2.14 0.00 3.02
1392 1455 0.976641 TCTGATCTTCAACCACGGCT 59.023 50.000 0.00 0.00 0.00 5.52
1398 1461 3.999663 CCTTCACACTCTGATCTTCAACC 59.000 47.826 0.00 0.00 0.00 3.77
1413 1476 1.352083 CTGGTCTCTTCCCCTTCACA 58.648 55.000 0.00 0.00 0.00 3.58
1458 1521 4.475135 GAGGACTCGCCCTTGGGC 62.475 72.222 20.15 20.15 36.49 5.36
1461 1524 1.515020 CTCAGAGGACTCGCCCTTG 59.485 63.158 0.00 0.00 36.49 3.61
1462 1525 1.684049 CCTCAGAGGACTCGCCCTT 60.684 63.158 11.62 0.00 37.67 3.95
1463 1526 2.043450 CCTCAGAGGACTCGCCCT 60.043 66.667 11.62 0.00 37.67 5.19
1464 1527 2.363147 ACCTCAGAGGACTCGCCC 60.363 66.667 24.45 0.00 37.67 6.13
1465 1528 1.251527 TTCACCTCAGAGGACTCGCC 61.252 60.000 24.45 0.00 37.67 5.54
1466 1529 0.172352 CTTCACCTCAGAGGACTCGC 59.828 60.000 24.45 0.00 37.67 5.03
1467 1530 0.172352 GCTTCACCTCAGAGGACTCG 59.828 60.000 24.45 9.49 37.67 4.18
1469 1532 0.178921 TGGCTTCACCTCAGAGGACT 60.179 55.000 24.45 0.00 37.67 3.85
1470 1533 0.687354 TTGGCTTCACCTCAGAGGAC 59.313 55.000 24.45 6.57 37.67 3.85
1488 1557 2.579860 ACCAGATGATCCCTTGCTCTTT 59.420 45.455 0.00 0.00 0.00 2.52
1489 1558 2.092538 CACCAGATGATCCCTTGCTCTT 60.093 50.000 0.00 0.00 0.00 2.85
1626 1695 3.317711 CACCAGCAATGTCACCAAAGTTA 59.682 43.478 0.00 0.00 0.00 2.24
1647 1716 3.587061 TCTTCTTATTGGAGGAGTTGCCA 59.413 43.478 0.00 0.00 40.02 4.92
1660 1729 5.582665 GCACATCCGTCTTCTTCTTCTTATT 59.417 40.000 0.00 0.00 0.00 1.40
1662 1731 4.495422 GCACATCCGTCTTCTTCTTCTTA 58.505 43.478 0.00 0.00 0.00 2.10
1727 1799 1.005215 CAGCACCCTTCTTCTTCCCAT 59.995 52.381 0.00 0.00 0.00 4.00
1728 1800 0.401738 CAGCACCCTTCTTCTTCCCA 59.598 55.000 0.00 0.00 0.00 4.37
1731 1803 0.320771 TCGCAGCACCCTTCTTCTTC 60.321 55.000 0.00 0.00 0.00 2.87
1732 1804 0.603975 GTCGCAGCACCCTTCTTCTT 60.604 55.000 0.00 0.00 0.00 2.52
1733 1805 1.004440 GTCGCAGCACCCTTCTTCT 60.004 57.895 0.00 0.00 0.00 2.85
1751 1823 0.179100 AATCGACACGGCCTCATCAG 60.179 55.000 0.00 0.00 0.00 2.90
1763 1835 0.246360 ATCTGCACCGACAATCGACA 59.754 50.000 0.00 0.00 43.74 4.35
1794 1866 1.893808 CACTGACTTGCCGTGGCTT 60.894 57.895 12.84 0.00 42.51 4.35
1814 1886 1.001020 TTCAATGCCATGGCCGACT 60.001 52.632 33.44 13.05 41.09 4.18
1825 1897 1.129437 GAAGGACTCGCTGTTCAATGC 59.871 52.381 0.00 0.00 0.00 3.56
1828 1900 2.440539 GAGAAGGACTCGCTGTTCAA 57.559 50.000 0.00 0.00 35.84 2.69
1851 1923 1.918262 TCTCTCTCCCCATTGTGCAAT 59.082 47.619 0.00 0.00 0.00 3.56
2048 2120 3.511146 ACCTTTCAATGTACTTGCCCATG 59.489 43.478 0.00 0.00 34.66 3.66
2059 2133 8.896744 CATAATATGTCAGTCACCTTTCAATGT 58.103 33.333 0.00 0.00 0.00 2.71
2193 2267 1.308069 TTGGCCGATGAAGCTGAAGC 61.308 55.000 0.00 0.00 42.49 3.86
2216 2290 2.671396 GCTTCCGTTGCGATTTTCTCTA 59.329 45.455 0.00 0.00 0.00 2.43
2237 2311 1.352083 TCTCCAGGGTTGAACAGAGG 58.648 55.000 0.00 0.00 0.00 3.69
2249 2323 2.158986 CCATACACAGAGCTTCTCCAGG 60.159 54.545 0.00 0.00 0.00 4.45
2421 2495 7.360438 CCTGTTGTACTTCTTTTCATACAGAGC 60.360 40.741 0.00 0.00 34.02 4.09
2456 2530 0.608640 CTGCCCCTTGTTCGTCTAGT 59.391 55.000 0.00 0.00 0.00 2.57
2495 2569 4.498520 CGCACCGACGATCTGGCT 62.499 66.667 0.00 0.00 34.06 4.75
2606 2680 8.328758 TCATACCCTTGAATAAGATCAACAAGT 58.671 33.333 0.00 0.00 37.02 3.16
2621 2695 4.293494 AGAGAGCTTCATCATACCCTTGA 58.707 43.478 0.00 0.00 0.00 3.02
2643 2729 6.646429 TGGAACAACAACTGGAACCAGGAA 62.646 45.833 22.40 0.00 41.81 3.36
2644 2730 5.222109 TGGAACAACAACTGGAACCAGGA 62.222 47.826 22.40 0.00 41.81 3.86
2645 2731 2.948147 TGGAACAACAACTGGAACCAGG 60.948 50.000 22.40 9.98 41.81 4.45
2646 2732 2.099098 GTGGAACAACAACTGGAACCAG 59.901 50.000 17.94 17.94 44.16 4.00
2647 2733 2.096248 GTGGAACAACAACTGGAACCA 58.904 47.619 0.00 0.00 44.16 3.67
2648 2734 2.863401 GTGGAACAACAACTGGAACC 57.137 50.000 0.00 0.00 44.16 3.62
2709 2795 0.665369 AAACAAGAGCAGCAATGCGC 60.665 50.000 12.63 12.63 40.27 6.09
3147 3235 0.251386 TCTTCCTGAGCTCGTGGACT 60.251 55.000 22.82 0.00 0.00 3.85
3315 3415 2.169978 CCTCCTCATCTTGTGCAGATCA 59.830 50.000 0.00 0.00 40.67 2.92
3526 3626 1.409427 ACGAACCTCGGATTCAGATCC 59.591 52.381 0.67 0.00 45.59 3.36
3527 3627 2.733517 GACGAACCTCGGATTCAGATC 58.266 52.381 0.67 0.00 45.59 2.75
3528 3628 1.065701 CGACGAACCTCGGATTCAGAT 59.934 52.381 0.67 0.00 45.59 2.90
3529 3629 0.450583 CGACGAACCTCGGATTCAGA 59.549 55.000 0.67 0.00 45.59 3.27
3530 3630 2.945315 CGACGAACCTCGGATTCAG 58.055 57.895 0.67 0.00 45.59 3.02
3545 3645 3.499737 CAAGATGTGGCCGCCGAC 61.500 66.667 15.15 5.09 0.00 4.79
3558 3658 1.927487 AAACATGCCATCAGCCAAGA 58.073 45.000 0.00 0.00 42.71 3.02
3575 3675 3.513515 AGTCACAAAACCCTCTGCAAAAA 59.486 39.130 0.00 0.00 0.00 1.94
3581 3681 2.408050 CTCGAGTCACAAAACCCTCTG 58.592 52.381 3.62 0.00 0.00 3.35
3582 3682 1.344763 CCTCGAGTCACAAAACCCTCT 59.655 52.381 12.31 0.00 0.00 3.69
3583 3683 1.070289 ACCTCGAGTCACAAAACCCTC 59.930 52.381 12.31 0.00 0.00 4.30
3584 3684 1.129058 ACCTCGAGTCACAAAACCCT 58.871 50.000 12.31 0.00 0.00 4.34
3585 3685 1.226746 CACCTCGAGTCACAAAACCC 58.773 55.000 12.31 0.00 0.00 4.11
3587 3687 1.949465 ACCACCTCGAGTCACAAAAC 58.051 50.000 12.31 0.00 0.00 2.43
3598 3713 1.455959 CCCCTCCTCTACCACCTCG 60.456 68.421 0.00 0.00 0.00 4.63
3633 3753 6.112734 GGACCAATGATCTATGTACACACAA 58.887 40.000 0.00 0.00 38.42 3.33
3703 3825 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
3704 3826 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
3705 3827 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
3706 3828 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
3707 3829 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
3708 3830 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
3709 3831 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
3710 3832 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
3711 3833 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
3712 3834 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
3713 3835 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
3714 3836 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
3720 3842 8.748412 CCCTTTTATCCATTTTGATGACAAGTA 58.252 33.333 0.00 0.00 37.32 2.24
3721 3843 7.310609 CCCCTTTTATCCATTTTGATGACAAGT 60.311 37.037 0.00 0.00 37.32 3.16
3722 3844 7.043565 CCCCTTTTATCCATTTTGATGACAAG 58.956 38.462 0.00 0.00 37.32 3.16
3723 3845 6.728164 TCCCCTTTTATCCATTTTGATGACAA 59.272 34.615 0.00 0.00 0.00 3.18
3724 3846 6.259893 TCCCCTTTTATCCATTTTGATGACA 58.740 36.000 0.00 0.00 0.00 3.58
3725 3847 6.790232 TCCCCTTTTATCCATTTTGATGAC 57.210 37.500 0.00 0.00 0.00 3.06
3734 3856 9.148879 CGTCTAGATATATCCCCTTTTATCCAT 57.851 37.037 9.18 0.00 0.00 3.41
3735 3857 8.120538 ACGTCTAGATATATCCCCTTTTATCCA 58.879 37.037 9.18 0.00 0.00 3.41
3736 3858 8.536340 ACGTCTAGATATATCCCCTTTTATCC 57.464 38.462 9.18 0.00 0.00 2.59
3781 3903 9.918630 ACTTGTCATCAAAATGGATAAAAAGAG 57.081 29.630 0.00 0.00 33.42 2.85
3789 3911 7.975616 CCGAAAATACTTGTCATCAAAATGGAT 59.024 33.333 0.00 0.00 33.42 3.41
3790 3912 7.175816 TCCGAAAATACTTGTCATCAAAATGGA 59.824 33.333 0.00 0.00 33.42 3.41
3791 3913 7.273381 GTCCGAAAATACTTGTCATCAAAATGG 59.727 37.037 0.00 0.00 33.42 3.16
3792 3914 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
3793 3915 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
3794 3916 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
3795 3917 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
3796 3918 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
3797 3919 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
3798 3920 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
3799 3921 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
3800 3922 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
3801 3923 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
3802 3924 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
3803 3925 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
3804 3926 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
3805 3927 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
3806 3928 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
3807 3929 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
3808 3930 1.755380 CTACTCCCTCCGTCCGAAAAT 59.245 52.381 0.00 0.00 0.00 1.82
3809 3931 1.180029 CTACTCCCTCCGTCCGAAAA 58.820 55.000 0.00 0.00 0.00 2.29
3810 3932 0.329261 TCTACTCCCTCCGTCCGAAA 59.671 55.000 0.00 0.00 0.00 3.46
3811 3933 0.549950 ATCTACTCCCTCCGTCCGAA 59.450 55.000 0.00 0.00 0.00 4.30
3812 3934 0.549950 AATCTACTCCCTCCGTCCGA 59.450 55.000 0.00 0.00 0.00 4.55
3813 3935 2.152830 CTAATCTACTCCCTCCGTCCG 58.847 57.143 0.00 0.00 0.00 4.79
3814 3936 3.505480 TCTAATCTACTCCCTCCGTCC 57.495 52.381 0.00 0.00 0.00 4.79
3815 3937 6.052405 TCTATCTAATCTACTCCCTCCGTC 57.948 45.833 0.00 0.00 0.00 4.79
3816 3938 6.451292 TTCTATCTAATCTACTCCCTCCGT 57.549 41.667 0.00 0.00 0.00 4.69
3817 3939 6.887545 ACATTCTATCTAATCTACTCCCTCCG 59.112 42.308 0.00 0.00 0.00 4.63
3818 3940 8.527810 CAACATTCTATCTAATCTACTCCCTCC 58.472 40.741 0.00 0.00 0.00 4.30
3819 3941 8.527810 CCAACATTCTATCTAATCTACTCCCTC 58.472 40.741 0.00 0.00 0.00 4.30
3820 3942 8.013667 ACCAACATTCTATCTAATCTACTCCCT 58.986 37.037 0.00 0.00 0.00 4.20
3821 3943 8.091449 CACCAACATTCTATCTAATCTACTCCC 58.909 40.741 0.00 0.00 0.00 4.30
3822 3944 8.643324 ACACCAACATTCTATCTAATCTACTCC 58.357 37.037 0.00 0.00 0.00 3.85
3827 3949 8.462016 GCAAAACACCAACATTCTATCTAATCT 58.538 33.333 0.00 0.00 0.00 2.40
3844 3968 4.803613 CAGTAAAAACCTCTGCAAAACACC 59.196 41.667 0.00 0.00 0.00 4.16
3878 4002 3.452627 CCTCTACTGAGCAATGGGTAAGT 59.547 47.826 0.00 0.00 39.55 2.24
3881 4005 2.398588 CCCTCTACTGAGCAATGGGTA 58.601 52.381 0.00 0.00 38.93 3.69
3922 4047 7.725397 ACCATGTACATGTATTAATTGGAGCAT 59.275 33.333 29.25 9.61 37.11 3.79
3938 4069 9.494271 GATGAAGTATCATGTAACCATGTACAT 57.506 33.333 1.41 1.41 46.30 2.29
3946 4077 9.601217 AGTAAGTTGATGAAGTATCATGTAACC 57.399 33.333 0.00 0.00 46.30 2.85
4001 4132 6.479990 CACAATGTGAACTGTTAACTCTCTCA 59.520 38.462 7.78 7.95 35.23 3.27
4061 4192 7.010923 GGAGCTGTCATTAGAATTCACAGTTAG 59.989 40.741 18.71 6.85 37.41 2.34
4073 4206 4.041567 TGTTTCAAGGGAGCTGTCATTAGA 59.958 41.667 0.00 0.00 0.00 2.10
4120 4253 5.710513 TGTGTTTTTCAGATCCTGGAATG 57.289 39.130 0.00 3.01 28.16 2.67
4197 4334 6.270815 GTCAGTATAGGCACGAATGTAAAGA 58.729 40.000 0.00 0.00 0.00 2.52
4235 4373 3.090219 ATAGAGGGTCCGTTGCGCC 62.090 63.158 4.18 0.00 0.00 6.53
4236 4374 1.883084 CATAGAGGGTCCGTTGCGC 60.883 63.158 0.00 0.00 0.00 6.09
4246 4384 2.315176 CAGTGAGGAGACCATAGAGGG 58.685 57.143 0.00 0.00 43.89 4.30
4278 4416 3.557595 GTGGATGACTGAAGCTTATTCGG 59.442 47.826 0.00 0.00 0.00 4.30
4280 4418 5.505324 GCATGTGGATGACTGAAGCTTATTC 60.505 44.000 0.00 0.00 0.00 1.75
4427 4568 2.352814 CGAAATAGAATCTCGCGGGGAT 60.353 50.000 5.94 7.96 0.00 3.85
4470 4615 2.009774 CCCTCACAATAGAAGTTGCGG 58.990 52.381 0.00 0.00 32.32 5.69
4485 4630 1.180456 TAACCGAACAGCGACCCTCA 61.180 55.000 0.00 0.00 44.57 3.86
4486 4631 0.735287 GTAACCGAACAGCGACCCTC 60.735 60.000 0.00 0.00 44.57 4.30
4493 4638 1.337447 TGCTACAGGTAACCGAACAGC 60.337 52.381 0.00 0.00 37.17 4.40
4495 4640 1.965643 ACTGCTACAGGTAACCGAACA 59.034 47.619 0.00 0.00 35.51 3.18
4504 4649 1.121407 TGGCTGTGACTGCTACAGGT 61.121 55.000 14.04 0.00 44.36 4.00
4559 4704 2.099921 CGGATGATTCTTCAGACGAGGT 59.900 50.000 0.00 0.00 37.20 3.85
4654 4805 4.344865 ATGGAAAGCACCCGCCGT 62.345 61.111 0.00 0.00 39.83 5.68
4666 4817 2.695666 GGTTCTCCTCATCTCGATGGAA 59.304 50.000 7.03 0.78 39.24 3.53
4735 4886 1.169661 TGCAGGTAAGGCCACAAACG 61.170 55.000 5.01 0.00 40.61 3.60
4770 4921 2.665649 TGCGTCCGATACAACTCATT 57.334 45.000 0.00 0.00 0.00 2.57
4800 4951 0.182537 ATTATAAGCAGGGCACGCCA 59.817 50.000 10.83 0.00 37.98 5.69
4801 4952 2.076863 CTATTATAAGCAGGGCACGCC 58.923 52.381 0.00 0.00 0.00 5.68
4803 4954 4.878439 TGTACTATTATAAGCAGGGCACG 58.122 43.478 0.00 0.00 0.00 5.34
4804 4955 4.691216 GCTGTACTATTATAAGCAGGGCAC 59.309 45.833 0.00 0.00 34.01 5.01
4805 4956 4.346709 TGCTGTACTATTATAAGCAGGGCA 59.653 41.667 0.00 0.00 38.88 5.36
4816 4967 8.033038 CCTTTCAACTACAGTGCTGTACTATTA 58.967 37.037 7.87 0.00 44.42 0.98
4822 4973 4.682778 ACCTTTCAACTACAGTGCTGTA 57.317 40.909 11.07 11.07 44.42 2.74
4872 5023 2.104622 TCTGAACTTCCTGTCATGCACA 59.895 45.455 0.00 0.00 0.00 4.57
4873 5024 2.481952 GTCTGAACTTCCTGTCATGCAC 59.518 50.000 0.00 0.00 0.00 4.57
4876 5027 3.007290 TCCTGTCTGAACTTCCTGTCATG 59.993 47.826 0.00 0.00 0.00 3.07
4877 5028 3.242867 TCCTGTCTGAACTTCCTGTCAT 58.757 45.455 0.00 0.00 0.00 3.06
4878 5029 2.677914 TCCTGTCTGAACTTCCTGTCA 58.322 47.619 0.00 0.00 0.00 3.58
4881 5032 3.332919 CACATCCTGTCTGAACTTCCTG 58.667 50.000 0.00 0.00 0.00 3.86
4882 5033 2.304180 CCACATCCTGTCTGAACTTCCT 59.696 50.000 0.00 0.00 0.00 3.36
4883 5034 2.039084 ACCACATCCTGTCTGAACTTCC 59.961 50.000 0.00 0.00 0.00 3.46
4893 5044 1.004560 CTGCGTGACCACATCCTGT 60.005 57.895 0.85 0.00 0.00 4.00
4907 5058 2.104144 GCGCTACAAATTTGATCTGCG 58.896 47.619 28.18 28.18 44.10 5.18
4936 5087 2.810439 TTTTGCCCAACATTTCCTCG 57.190 45.000 0.00 0.00 0.00 4.63
4966 5117 3.141398 CGATGGTGTGGGAATCATAAGG 58.859 50.000 0.00 0.00 0.00 2.69
4971 5122 3.364460 AAATCGATGGTGTGGGAATCA 57.636 42.857 0.00 0.00 0.00 2.57
4991 5142 5.588246 TGTGCACTTCAGTCTTTTGTGATAA 59.412 36.000 19.41 0.00 0.00 1.75
5023 5174 5.408604 ACTCAGTCCTTAATTTAGCAACACG 59.591 40.000 0.00 0.00 0.00 4.49
5046 5229 2.124151 CCCAGGGGCATGCACTAC 60.124 66.667 21.47 3.60 0.00 2.73


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

AutoCloner maintained by Alex Coulton.