Multiple sequence alignment - TraesCS4A01G200800

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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 TraesCS4A01G200800 chr4A 100.000 5426 0 0 737 6162 489436938 489431513 0.000000e+00 10021.0
1 TraesCS4A01G200800 chr4A 100.000 262 0 0 1 262 489437674 489437413 9.290000e-133 484.0
2 TraesCS4A01G200800 chr4A 76.744 430 66 20 3041 3462 16247383 16247786 6.260000e-50 209.0
3 TraesCS4A01G200800 chr4A 87.117 163 20 1 3717 3878 568900358 568900520 3.790000e-42 183.0
4 TraesCS4A01G200800 chr4B 93.818 2572 97 31 931 3477 130622726 130625260 0.000000e+00 3812.0
5 TraesCS4A01G200800 chr4B 94.751 1886 48 20 3879 5747 130625400 130627251 0.000000e+00 2887.0
6 TraesCS4A01G200800 chr4B 96.565 262 3 2 1 262 130621841 130622096 4.410000e-116 429.0
7 TraesCS4A01G200800 chr4B 90.182 275 18 6 5888 6162 130627442 130627707 3.530000e-92 350.0
8 TraesCS4A01G200800 chr4B 77.030 431 63 25 3041 3462 563628420 563628017 1.350000e-51 215.0
9 TraesCS4A01G200800 chr4B 94.286 140 2 5 737 871 130622260 130622398 6.260000e-50 209.0
10 TraesCS4A01G200800 chr4B 93.878 49 3 0 3667 3715 130625350 130625398 2.380000e-09 75.0
11 TraesCS4A01G200800 chr4D 94.631 1881 45 23 3879 5746 93070156 93071993 0.000000e+00 2863.0
12 TraesCS4A01G200800 chr4D 93.552 1799 64 23 1856 3642 93068358 93070116 0.000000e+00 2632.0
13 TraesCS4A01G200800 chr4D 94.682 1053 40 12 738 1789 93067317 93068354 0.000000e+00 1620.0
14 TraesCS4A01G200800 chr4D 88.288 333 23 7 5830 6162 93075634 93075950 9.690000e-103 385.0
15 TraesCS4A01G200800 chr4D 91.710 193 5 4 81 262 93066966 93067158 2.200000e-64 257.0
16 TraesCS4A01G200800 chr4D 77.209 430 64 23 3041 3462 450332084 450331681 2.890000e-53 220.0
17 TraesCS4A01G200800 chr4D 90.566 53 1 2 3667 3715 93070102 93070154 3.990000e-07 67.6
18 TraesCS4A01G200800 chr2D 94.848 330 10 3 1333 1656 81515467 81515139 5.510000e-140 508.0
19 TraesCS4A01G200800 chr2D 96.364 110 4 0 3174 3283 81515148 81515039 1.360000e-41 182.0
20 TraesCS4A01G200800 chr6B 92.638 326 11 3 1333 1655 615607840 615607525 2.020000e-124 457.0
21 TraesCS4A01G200800 chr6B 90.332 331 15 4 1333 1656 507373160 507373480 9.550000e-113 418.0
22 TraesCS4A01G200800 chr6B 96.262 107 4 0 3174 3280 507373471 507373577 6.350000e-40 176.0
23 TraesCS4A01G200800 chr6B 92.661 109 8 0 3175 3283 615607532 615607424 2.300000e-34 158.0
24 TraesCS4A01G200800 chr5B 92.638 326 11 3 1333 1655 625119812 625119497 2.020000e-124 457.0
25 TraesCS4A01G200800 chr5B 92.638 326 11 3 1333 1655 628699361 628699046 2.020000e-124 457.0
26 TraesCS4A01G200800 chr5B 86.747 166 18 4 3717 3880 611866685 611866522 1.360000e-41 182.0
27 TraesCS4A01G200800 chr5B 85.549 173 20 5 3711 3880 457986944 457987114 6.350000e-40 176.0
28 TraesCS4A01G200800 chr5B 94.495 109 6 0 3175 3283 625119504 625119396 1.060000e-37 169.0
29 TraesCS4A01G200800 chr5B 92.661 109 8 0 3175 3283 628699053 628698945 2.300000e-34 158.0
30 TraesCS4A01G200800 chr7A 92.212 321 12 3 1338 1655 487478230 487478540 5.670000e-120 442.0
31 TraesCS4A01G200800 chr7A 94.340 106 6 0 3175 3280 487478533 487478638 4.940000e-36 163.0
32 TraesCS4A01G200800 chr7A 83.158 95 16 0 3370 3464 8916177 8916271 3.060000e-13 87.9
33 TraesCS4A01G200800 chr5D 86.391 169 21 2 3713 3880 374607438 374607605 3.790000e-42 183.0
34 TraesCS4A01G200800 chr7D 86.667 165 20 2 3717 3880 543097056 543097219 1.360000e-41 182.0
35 TraesCS4A01G200800 chr7D 98.361 61 1 0 4335 4395 477932152 477932212 2.350000e-19 108.0
36 TraesCS4A01G200800 chr7D 85.263 95 14 0 3370 3464 8479804 8479898 1.410000e-16 99.0
37 TraesCS4A01G200800 chr3B 86.747 166 18 4 3717 3880 673289448 673289285 1.360000e-41 182.0
38 TraesCS4A01G200800 chr3B 96.774 62 2 0 4335 4396 624317595 624317534 3.040000e-18 104.0
39 TraesCS4A01G200800 chr2A 85.714 168 23 1 3714 3880 598639892 598639725 6.350000e-40 176.0
40 TraesCS4A01G200800 chr2A 96.774 62 2 0 4335 4396 138533223 138533284 3.040000e-18 104.0
41 TraesCS4A01G200800 chr1B 86.145 166 19 4 3717 3880 643105736 643105899 6.350000e-40 176.0
42 TraesCS4A01G200800 chr1B 85.088 114 10 4 4335 4446 342973262 342973154 6.530000e-20 110.0
43 TraesCS4A01G200800 chr2B 84.181 177 22 6 3717 3889 556659198 556659024 3.820000e-37 167.0
44 TraesCS4A01G200800 chr1D 86.842 114 8 4 4335 4446 269726487 269726379 3.020000e-23 121.0
45 TraesCS4A01G200800 chr1A 86.842 114 8 4 4335 4446 333135671 333135563 3.020000e-23 121.0
46 TraesCS4A01G200800 chr3A 96.774 62 2 0 4335 4396 612524274 612524213 3.040000e-18 104.0


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 TraesCS4A01G200800 chr4A 489431513 489437674 6161 True 5252.500000 10021 100.000000 1 6162 2 chr4A.!!$R1 6161
1 TraesCS4A01G200800 chr4B 130621841 130627707 5866 False 1293.666667 3812 93.913333 1 6162 6 chr4B.!!$F1 6161
2 TraesCS4A01G200800 chr4D 93066966 93075950 8984 False 1304.100000 2863 92.238167 81 6162 6 chr4D.!!$F1 6081

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
955 1240 1.480545 AGTGCACATACGGACATAGCA 59.519 47.619 21.04 0.0 0.00 3.49 F
957 1242 2.285220 GTGCACATACGGACATAGCAAG 59.715 50.000 13.17 0.0 31.78 4.01 F
2589 2888 1.202405 GGTGTTGTTTGTTGAGGCCAG 60.202 52.381 5.01 0.0 0.00 4.85 F
3675 3991 1.145571 TTTTGTGGGGAGCTAGGTGT 58.854 50.000 0.00 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 2205 2.556622 CACTACCAAAATCGCCAGGTTT 59.443 45.455 0.0 0.0 35.62 3.27 R
2591 2890 3.480505 AGTTAAAGGTGGCTTGTACGT 57.519 42.857 0.0 0.0 0.00 3.57 R
3983 4316 0.599558 ATGAGCATTGTGTGTGTGCC 59.400 50.000 0.0 0.0 39.62 5.01 R
5316 5670 1.080498 ACACCCCCAATGACCTAGAGA 59.920 52.381 0.0 0.0 0.00 3.10 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 5.124036 TCTTTTAGAGAGAGAGAGAGGGG 57.876 47.826 0.00 0.00 0.00 4.79
39 40 3.963476 TTTAGAGAGAGAGAGAGGGGG 57.037 52.381 0.00 0.00 0.00 5.40
67 68 8.306038 AGAGAGAGATTACTTATATGCAAGCTG 58.694 37.037 0.00 0.00 0.00 4.24
69 70 9.083422 AGAGAGATTACTTATATGCAAGCTGTA 57.917 33.333 0.00 0.00 0.00 2.74
70 71 9.134734 GAGAGATTACTTATATGCAAGCTGTAC 57.865 37.037 0.00 0.00 0.00 2.90
858 875 1.536709 GGTCAAAGCCACAACAAGCTG 60.537 52.381 0.00 0.00 39.87 4.24
871 888 3.137446 ACAAGCTGCACTGAAGAAGAT 57.863 42.857 1.02 0.00 0.00 2.40
873 890 4.841422 ACAAGCTGCACTGAAGAAGATAT 58.159 39.130 1.02 0.00 0.00 1.63
875 892 6.590068 ACAAGCTGCACTGAAGAAGATATAT 58.410 36.000 1.02 0.00 0.00 0.86
876 893 7.730084 ACAAGCTGCACTGAAGAAGATATATA 58.270 34.615 1.02 0.00 0.00 0.86
877 894 8.206867 ACAAGCTGCACTGAAGAAGATATATAA 58.793 33.333 1.02 0.00 0.00 0.98
878 895 9.217278 CAAGCTGCACTGAAGAAGATATATAAT 57.783 33.333 1.02 0.00 0.00 1.28
879 896 9.790344 AAGCTGCACTGAAGAAGATATATAATT 57.210 29.630 1.02 0.00 0.00 1.40
880 897 9.217278 AGCTGCACTGAAGAAGATATATAATTG 57.783 33.333 1.02 0.00 0.00 2.32
881 898 9.212641 GCTGCACTGAAGAAGATATATAATTGA 57.787 33.333 0.00 0.00 0.00 2.57
896 913 9.713684 ATATATAATTGAAGAGAGAGAGAGGGG 57.286 37.037 0.00 0.00 0.00 4.79
955 1240 1.480545 AGTGCACATACGGACATAGCA 59.519 47.619 21.04 0.00 0.00 3.49
957 1242 2.285220 GTGCACATACGGACATAGCAAG 59.715 50.000 13.17 0.00 31.78 4.01
1152 1437 3.340928 CAACATGATGCTCCTCAACTCA 58.659 45.455 0.00 0.00 0.00 3.41
1420 1705 3.643554 GGTACCACCTTGGGGCGT 61.644 66.667 7.15 0.00 43.37 5.68
1503 1788 2.627737 GCTCGACGAGGTGGTGAGT 61.628 63.158 25.31 0.00 0.00 3.41
1727 2012 6.199937 TGACGAGGTCAGTAATTAACCTAC 57.800 41.667 7.22 4.21 43.43 3.18
1735 2020 7.177392 AGGTCAGTAATTAACCTACGTACACTT 59.823 37.037 5.66 0.00 41.61 3.16
1794 2079 8.856153 TGTTAAGAAATGTCCTGCTTTATACA 57.144 30.769 0.00 0.00 0.00 2.29
1882 2168 5.726980 TTGCTGCTTAGGAATTGTTGATT 57.273 34.783 0.00 0.00 0.00 2.57
1919 2205 8.370940 TGGAAAACAAGGCATATTTGACAAATA 58.629 29.630 20.13 20.13 37.71 1.40
1926 2212 6.877236 AGGCATATTTGACAAATAAACCTGG 58.123 36.000 27.87 15.31 39.40 4.45
1934 2220 5.226396 TGACAAATAAACCTGGCGATTTTG 58.774 37.500 0.00 2.62 0.00 2.44
1970 2256 5.126061 ACATTCAACATTGCCCTCTGAATAC 59.874 40.000 0.00 0.00 35.50 1.89
2020 2306 9.950496 TCTGATATTTCCTTGCCTCTATAATTC 57.050 33.333 0.00 0.00 0.00 2.17
2048 2334 8.903820 AGAAAGTGTTATTGAAAGTATATGGGC 58.096 33.333 0.00 0.00 0.00 5.36
2223 2509 6.455647 TGCACCAACTATATATTCTCTTCGG 58.544 40.000 0.00 0.00 0.00 4.30
2224 2510 6.266786 TGCACCAACTATATATTCTCTTCGGA 59.733 38.462 0.00 0.00 0.00 4.55
2258 2549 3.764237 ACACCGTCCAGTATTGTCTTT 57.236 42.857 0.00 0.00 0.00 2.52
2259 2550 4.081322 ACACCGTCCAGTATTGTCTTTT 57.919 40.909 0.00 0.00 0.00 2.27
2260 2551 5.217978 ACACCGTCCAGTATTGTCTTTTA 57.782 39.130 0.00 0.00 0.00 1.52
2261 2552 5.613329 ACACCGTCCAGTATTGTCTTTTAA 58.387 37.500 0.00 0.00 0.00 1.52
2295 2586 9.704098 GCAGAATTACAGCTACAGTTAATTAAC 57.296 33.333 18.77 18.77 36.46 2.01
2298 2589 7.781548 ATTACAGCTACAGTTAATTAACGGG 57.218 36.000 25.60 20.97 40.96 5.28
2301 2592 4.034048 CAGCTACAGTTAATTAACGGGCAG 59.966 45.833 25.60 21.99 40.96 4.85
2397 2696 8.950208 AGATTATAAAAGTGACAAGTCTAGCC 57.050 34.615 1.53 0.00 0.00 3.93
2589 2888 1.202405 GGTGTTGTTTGTTGAGGCCAG 60.202 52.381 5.01 0.00 0.00 4.85
2590 2889 1.476488 GTGTTGTTTGTTGAGGCCAGT 59.524 47.619 5.01 0.00 0.00 4.00
2591 2890 2.685897 GTGTTGTTTGTTGAGGCCAGTA 59.314 45.455 5.01 0.00 0.00 2.74
2592 2891 2.685897 TGTTGTTTGTTGAGGCCAGTAC 59.314 45.455 5.01 0.00 0.00 2.73
2801 3108 8.450578 TCATGCTTTGAGTTTTTCTTCTTCTA 57.549 30.769 0.00 0.00 0.00 2.10
2858 3169 9.851686 TCTCCATATAAATAAGAAATGCAGTGT 57.148 29.630 0.00 0.00 0.00 3.55
2871 3182 2.228925 TGCAGTGTAGCATGCTTTTGA 58.771 42.857 28.02 4.26 42.98 2.69
2894 3205 8.728337 TGATAAAATCCACTTGATTCTCTCAG 57.272 34.615 0.00 0.00 42.97 3.35
2946 3258 9.959721 ATGATAAACACAATCCAAAGTAGTACT 57.040 29.630 0.00 0.00 0.00 2.73
2998 3310 9.886132 AACACTAGTAATCAACCCACTAATTAG 57.114 33.333 11.05 11.05 0.00 1.73
3484 3796 2.614987 GCTTCACACATGCTCTCCTCTT 60.615 50.000 0.00 0.00 0.00 2.85
3520 3836 8.386606 ACTACTTACGTACTTCGATGACTTTAG 58.613 37.037 5.16 0.00 42.86 1.85
3526 3842 2.205074 CTTCGATGACTTTAGCGCCAT 58.795 47.619 2.29 0.00 0.00 4.40
3674 3990 2.286365 TTTTTGTGGGGAGCTAGGTG 57.714 50.000 0.00 0.00 0.00 4.00
3675 3991 1.145571 TTTTGTGGGGAGCTAGGTGT 58.854 50.000 0.00 0.00 0.00 4.16
3676 3992 2.032965 TTTGTGGGGAGCTAGGTGTA 57.967 50.000 0.00 0.00 0.00 2.90
3677 3993 2.263895 TTGTGGGGAGCTAGGTGTAT 57.736 50.000 0.00 0.00 0.00 2.29
3678 3994 2.263895 TGTGGGGAGCTAGGTGTATT 57.736 50.000 0.00 0.00 0.00 1.89
3679 3995 1.837439 TGTGGGGAGCTAGGTGTATTG 59.163 52.381 0.00 0.00 0.00 1.90
3680 3996 1.838077 GTGGGGAGCTAGGTGTATTGT 59.162 52.381 0.00 0.00 0.00 2.71
3702 4022 5.362717 TGTACAGGTGAACTCCATCGATAAT 59.637 40.000 0.00 0.00 0.00 1.28
3715 4035 8.353684 ACTCCATCGATAATTGAACTACAGTAG 58.646 37.037 6.00 6.00 0.00 2.57
3716 4036 8.234136 TCCATCGATAATTGAACTACAGTAGT 57.766 34.615 7.48 7.48 41.73 2.73
3717 4037 9.346005 TCCATCGATAATTGAACTACAGTAGTA 57.654 33.333 13.87 0.00 38.26 1.82
3718 4038 9.395707 CCATCGATAATTGAACTACAGTAGTAC 57.604 37.037 13.87 0.00 38.26 2.73
3721 4041 8.834465 TCGATAATTGAACTACAGTAGTACTCC 58.166 37.037 13.87 4.86 38.26 3.85
3722 4042 8.074972 CGATAATTGAACTACAGTAGTACTCCC 58.925 40.741 13.87 2.63 38.26 4.30
3723 4043 9.134055 GATAATTGAACTACAGTAGTACTCCCT 57.866 37.037 13.87 0.00 38.26 4.20
3724 4044 7.407393 AATTGAACTACAGTAGTACTCCCTC 57.593 40.000 13.87 7.21 38.26 4.30
3725 4045 5.775813 TGAACTACAGTAGTACTCCCTCT 57.224 43.478 13.87 0.00 38.26 3.69
3726 4046 5.498393 TGAACTACAGTAGTACTCCCTCTG 58.502 45.833 13.87 7.15 38.26 3.35
3727 4047 3.888583 ACTACAGTAGTACTCCCTCTGC 58.111 50.000 11.84 0.00 37.23 4.26
3728 4048 3.524380 ACTACAGTAGTACTCCCTCTGCT 59.476 47.826 11.84 0.00 37.23 4.24
3729 4049 3.459710 ACAGTAGTACTCCCTCTGCTT 57.540 47.619 0.00 0.00 0.00 3.91
3730 4050 3.780626 ACAGTAGTACTCCCTCTGCTTT 58.219 45.455 0.00 0.00 0.00 3.51
3731 4051 3.764972 ACAGTAGTACTCCCTCTGCTTTC 59.235 47.826 0.00 0.00 0.00 2.62
3732 4052 3.764434 CAGTAGTACTCCCTCTGCTTTCA 59.236 47.826 0.00 0.00 0.00 2.69
3733 4053 4.220821 CAGTAGTACTCCCTCTGCTTTCAA 59.779 45.833 0.00 0.00 0.00 2.69
3734 4054 4.838986 AGTAGTACTCCCTCTGCTTTCAAA 59.161 41.667 0.00 0.00 0.00 2.69
3735 4055 4.917906 AGTACTCCCTCTGCTTTCAAAT 57.082 40.909 0.00 0.00 0.00 2.32
3736 4056 6.668283 AGTAGTACTCCCTCTGCTTTCAAATA 59.332 38.462 0.00 0.00 0.00 1.40
3737 4057 6.567602 AGTACTCCCTCTGCTTTCAAATAT 57.432 37.500 0.00 0.00 0.00 1.28
3738 4058 6.963322 AGTACTCCCTCTGCTTTCAAATATT 58.037 36.000 0.00 0.00 0.00 1.28
3739 4059 7.406104 AGTACTCCCTCTGCTTTCAAATATTT 58.594 34.615 0.00 0.00 0.00 1.40
3740 4060 6.521151 ACTCCCTCTGCTTTCAAATATTTG 57.479 37.500 20.13 20.13 39.48 2.32
3741 4061 6.012745 ACTCCCTCTGCTTTCAAATATTTGT 58.987 36.000 23.95 1.02 39.18 2.83
3742 4062 6.494835 ACTCCCTCTGCTTTCAAATATTTGTT 59.505 34.615 23.95 0.00 39.18 2.83
3743 4063 7.015584 ACTCCCTCTGCTTTCAAATATTTGTTT 59.984 33.333 23.95 0.00 39.18 2.83
3744 4064 7.734942 TCCCTCTGCTTTCAAATATTTGTTTT 58.265 30.769 23.95 0.00 39.18 2.43
3745 4065 8.210265 TCCCTCTGCTTTCAAATATTTGTTTTT 58.790 29.630 23.95 0.00 39.18 1.94
3746 4066 8.498358 CCCTCTGCTTTCAAATATTTGTTTTTC 58.502 33.333 23.95 13.01 39.18 2.29
3747 4067 9.264719 CCTCTGCTTTCAAATATTTGTTTTTCT 57.735 29.630 23.95 0.00 39.18 2.52
3793 4113 4.273148 ACGAAGTAAAATGAGTGAGCCT 57.727 40.909 0.00 0.00 41.94 4.58
3794 4114 5.401531 ACGAAGTAAAATGAGTGAGCCTA 57.598 39.130 0.00 0.00 41.94 3.93
3795 4115 5.978814 ACGAAGTAAAATGAGTGAGCCTAT 58.021 37.500 0.00 0.00 41.94 2.57
3796 4116 7.108841 ACGAAGTAAAATGAGTGAGCCTATA 57.891 36.000 0.00 0.00 41.94 1.31
3797 4117 6.979238 ACGAAGTAAAATGAGTGAGCCTATAC 59.021 38.462 0.00 0.00 41.94 1.47
3798 4118 7.147880 ACGAAGTAAAATGAGTGAGCCTATACT 60.148 37.037 0.00 0.00 41.94 2.12
3799 4119 7.380065 CGAAGTAAAATGAGTGAGCCTATACTC 59.620 40.741 0.00 0.00 42.77 2.59
3800 4120 7.906199 AGTAAAATGAGTGAGCCTATACTCT 57.094 36.000 9.27 0.00 42.86 3.24
3801 4121 8.998277 AGTAAAATGAGTGAGCCTATACTCTA 57.002 34.615 9.27 0.00 42.86 2.43
3802 4122 9.422681 AGTAAAATGAGTGAGCCTATACTCTAA 57.577 33.333 9.27 0.00 42.86 2.10
3809 4129 9.588096 TGAGTGAGCCTATACTCTAAAATATGA 57.412 33.333 9.27 0.00 42.86 2.15
3810 4130 9.849166 GAGTGAGCCTATACTCTAAAATATGAC 57.151 37.037 0.00 0.00 40.06 3.06
3811 4131 9.594936 AGTGAGCCTATACTCTAAAATATGACT 57.405 33.333 0.00 0.00 37.58 3.41
3844 4164 9.734620 ATCCGTATGTTGTAATCATTTGAAATG 57.265 29.630 11.54 11.54 0.00 2.32
3845 4165 8.951243 TCCGTATGTTGTAATCATTTGAAATGA 58.049 29.630 21.39 21.39 0.00 2.57
3846 4166 9.009327 CCGTATGTTGTAATCATTTGAAATGAC 57.991 33.333 21.54 11.23 0.00 3.06
3847 4167 9.773328 CGTATGTTGTAATCATTTGAAATGACT 57.227 29.630 21.54 14.37 0.00 3.41
3859 4179 9.342308 TCATTTGAAATGACTAGAAAGACAAGT 57.658 29.630 16.04 0.00 31.23 3.16
3866 4186 9.793259 AAATGACTAGAAAGACAAGTATTTGGA 57.207 29.630 0.00 0.00 38.66 3.53
3867 4187 9.793259 AATGACTAGAAAGACAAGTATTTGGAA 57.207 29.630 0.00 0.00 38.66 3.53
3868 4188 9.793259 ATGACTAGAAAGACAAGTATTTGGAAA 57.207 29.630 0.00 0.00 38.66 3.13
3869 4189 9.052759 TGACTAGAAAGACAAGTATTTGGAAAC 57.947 33.333 0.00 0.00 38.66 2.78
3870 4190 8.084590 ACTAGAAAGACAAGTATTTGGAAACG 57.915 34.615 0.00 0.00 38.66 3.60
3871 4191 6.313744 AGAAAGACAAGTATTTGGAAACGG 57.686 37.500 2.81 0.00 38.66 4.44
3872 4192 6.059484 AGAAAGACAAGTATTTGGAAACGGA 58.941 36.000 2.81 0.00 38.66 4.69
3873 4193 5.941948 AAGACAAGTATTTGGAAACGGAG 57.058 39.130 2.81 0.00 38.66 4.63
3874 4194 5.223449 AGACAAGTATTTGGAAACGGAGA 57.777 39.130 2.81 0.00 38.66 3.71
3875 4195 5.238583 AGACAAGTATTTGGAAACGGAGAG 58.761 41.667 2.81 0.00 38.66 3.20
3876 4196 5.011738 AGACAAGTATTTGGAAACGGAGAGA 59.988 40.000 2.81 0.00 38.66 3.10
3877 4197 5.238583 ACAAGTATTTGGAAACGGAGAGAG 58.761 41.667 2.81 0.00 38.66 3.20
3885 4205 8.857694 ATTTGGAAACGGAGAGAGTAATTAAA 57.142 30.769 0.00 0.00 0.00 1.52
3886 4206 8.680039 TTTGGAAACGGAGAGAGTAATTAAAA 57.320 30.769 0.00 0.00 0.00 1.52
3981 4314 5.998363 AGACATAGACATAGCACGAGATACA 59.002 40.000 0.00 0.00 0.00 2.29
3982 4315 6.003234 ACATAGACATAGCACGAGATACAC 57.997 41.667 0.00 0.00 0.00 2.90
3983 4316 3.610786 AGACATAGCACGAGATACACG 57.389 47.619 0.00 0.00 0.00 4.49
3984 4317 2.290916 AGACATAGCACGAGATACACGG 59.709 50.000 0.00 0.00 34.93 4.94
4057 4394 1.186030 CTCCATTCGTACGTGCGTAC 58.814 55.000 24.94 20.84 45.29 3.67
4119 4456 4.778415 CCTCGTGTCGCACTCCCG 62.778 72.222 8.07 0.00 31.34 5.14
4296 4634 1.881591 TTTTTACTGTTACCGCGGCT 58.118 45.000 28.58 15.49 0.00 5.52
4322 4660 3.896648 TTGATCCGTGAGAGTTTTTGC 57.103 42.857 0.00 0.00 0.00 3.68
4328 4667 2.857748 CCGTGAGAGTTTTTGCAAAACC 59.142 45.455 23.79 17.43 0.00 3.27
4334 4673 7.358352 CGTGAGAGTTTTTGCAAAACCATTATC 60.358 37.037 23.79 13.83 0.00 1.75
4501 4840 1.849976 GAAAGAGCAGCAGCAACGCT 61.850 55.000 3.17 3.81 45.49 5.07
4879 5230 1.827789 CCACCACCACCACCAACAG 60.828 63.158 0.00 0.00 0.00 3.16
5189 5540 3.837213 GCATCATGCATGGTATACCAC 57.163 47.619 26.87 15.46 44.26 4.16
5190 5541 3.415212 GCATCATGCATGGTATACCACT 58.585 45.455 26.87 13.09 44.26 4.00
5315 5669 1.889170 GGCTGCCATTAATCCTAAGCC 59.111 52.381 15.17 10.58 41.70 4.35
5316 5670 2.489802 GGCTGCCATTAATCCTAAGCCT 60.490 50.000 15.17 0.00 44.26 4.58
5324 5678 5.782845 CCATTAATCCTAAGCCTCTCTAGGT 59.217 44.000 0.00 0.00 45.64 3.08
5564 5923 9.216117 GAGTATTGTTTTTGGATACTGTACTGT 57.784 33.333 10.46 10.46 36.88 3.55
5604 5964 7.450124 TTGTAGTACTCCTCTTCACTACTTG 57.550 40.000 0.00 0.00 42.41 3.16
5736 6096 9.396022 TCTTCTACAGAAAACAGTTCATTTCTT 57.604 29.630 0.00 0.00 41.79 2.52
5747 6107 6.585416 ACAGTTCATTTCTTGCAGGAAAAAT 58.415 32.000 25.39 9.57 38.46 1.82
5749 6109 8.370182 ACAGTTCATTTCTTGCAGGAAAAATAT 58.630 29.630 25.39 8.52 38.46 1.28
5750 6110 9.211485 CAGTTCATTTCTTGCAGGAAAAATATT 57.789 29.630 25.39 8.16 38.46 1.28
5751 6111 9.211485 AGTTCATTTCTTGCAGGAAAAATATTG 57.789 29.630 25.39 18.56 38.46 1.90
5752 6112 8.992073 GTTCATTTCTTGCAGGAAAAATATTGT 58.008 29.630 25.39 6.77 38.46 2.71
5753 6113 9.558396 TTCATTTCTTGCAGGAAAAATATTGTT 57.442 25.926 25.39 6.08 38.46 2.83
5754 6114 8.991026 TCATTTCTTGCAGGAAAAATATTGTTG 58.009 29.630 25.39 16.69 38.46 3.33
5755 6115 8.776470 CATTTCTTGCAGGAAAAATATTGTTGT 58.224 29.630 25.39 4.70 38.46 3.32
5756 6116 7.712264 TTCTTGCAGGAAAAATATTGTTGTG 57.288 32.000 9.07 0.00 0.00 3.33
5757 6117 5.695816 TCTTGCAGGAAAAATATTGTTGTGC 59.304 36.000 12.56 12.56 0.00 4.57
5759 6119 4.202295 TGCAGGAAAAATATTGTTGTGCCA 60.202 37.500 15.25 5.64 0.00 4.92
5760 6120 4.937015 GCAGGAAAAATATTGTTGTGCCAT 59.063 37.500 9.74 0.00 0.00 4.40
5761 6121 6.105333 GCAGGAAAAATATTGTTGTGCCATA 58.895 36.000 9.74 0.00 0.00 2.74
5763 6123 7.280652 GCAGGAAAAATATTGTTGTGCCATATT 59.719 33.333 9.74 0.00 0.00 1.28
5764 6124 9.165035 CAGGAAAAATATTGTTGTGCCATATTT 57.835 29.630 0.00 0.00 0.00 1.40
5766 6126 9.382275 GGAAAAATATTGTTGTGCCATATTTCT 57.618 29.630 0.00 0.00 30.03 2.52
5773 6133 8.907222 ATTGTTGTGCCATATTTCTTTTCTTT 57.093 26.923 0.00 0.00 0.00 2.52
5774 6134 8.729805 TTGTTGTGCCATATTTCTTTTCTTTT 57.270 26.923 0.00 0.00 0.00 2.27
5775 6135 8.729805 TGTTGTGCCATATTTCTTTTCTTTTT 57.270 26.923 0.00 0.00 0.00 1.94
5798 6158 8.631480 TTTTTAGAAAAGGAGGATAACCAGAC 57.369 34.615 0.00 0.00 38.94 3.51
5799 6159 7.569599 TTTAGAAAAGGAGGATAACCAGACT 57.430 36.000 0.00 0.00 38.94 3.24
5800 6160 5.428184 AGAAAAGGAGGATAACCAGACTG 57.572 43.478 0.00 0.00 38.94 3.51
5803 6163 2.769209 AGGAGGATAACCAGACTGCAT 58.231 47.619 0.00 0.00 38.94 3.96
5804 6164 3.118531 AGGAGGATAACCAGACTGCATT 58.881 45.455 0.00 0.00 38.94 3.56
5805 6165 4.298626 AGGAGGATAACCAGACTGCATTA 58.701 43.478 0.00 0.00 38.94 1.90
5807 6167 5.370880 AGGAGGATAACCAGACTGCATTATT 59.629 40.000 10.09 0.00 38.94 1.40
5808 6168 5.471456 GGAGGATAACCAGACTGCATTATTG 59.529 44.000 10.09 0.00 38.94 1.90
5809 6169 4.823989 AGGATAACCAGACTGCATTATTGC 59.176 41.667 10.09 2.60 43.28 3.56
5810 6170 4.319766 GGATAACCAGACTGCATTATTGCG 60.320 45.833 10.09 3.24 43.09 4.85
5811 6171 6.482698 GGATAACCAGACTGCATTATTGCGA 61.483 44.000 10.09 0.00 43.09 5.10
5827 9670 2.158559 TGCGATGCACAAAACAGGTAT 58.841 42.857 0.00 0.00 31.71 2.73
5828 9671 2.161410 TGCGATGCACAAAACAGGTATC 59.839 45.455 0.00 0.00 31.71 2.24
5837 9754 6.883756 TGCACAAAACAGGTATCAGATAATGA 59.116 34.615 9.82 0.00 43.70 2.57
5843 9760 6.814954 ACAGGTATCAGATAATGAAGGTGT 57.185 37.500 9.82 0.00 42.53 4.16
5868 9785 4.212143 CCTTCTTGGTCATGACTCATGA 57.788 45.455 24.50 21.53 46.84 3.07
5898 9815 8.884323 AGATAAGATGATGGCAGAAGGTAATAA 58.116 33.333 0.00 0.00 0.00 1.40
5915 9864 9.762381 AAGGTAATAAAAGGAACAATCATACCA 57.238 29.630 0.00 0.00 33.24 3.25
5916 9865 9.762381 AGGTAATAAAAGGAACAATCATACCAA 57.238 29.630 0.00 0.00 33.24 3.67
5920 9869 9.533831 AATAAAAGGAACAATCATACCAAGTCT 57.466 29.630 0.00 0.00 0.00 3.24
5921 9870 6.824305 AAAGGAACAATCATACCAAGTCTG 57.176 37.500 0.00 0.00 0.00 3.51
5963 9912 3.128242 GTCATTGGAGAATTGCTGGACAG 59.872 47.826 0.00 0.00 0.00 3.51
6010 9959 8.314021 TGATAGACAACAAACATCTAGTGTCAT 58.686 33.333 8.14 1.67 41.14 3.06
6041 9990 4.154737 TGATCACACAGCAAAATGTAGCTC 59.845 41.667 0.00 0.00 39.50 4.09
6099 10048 9.372369 ACATGCTAACAGTTCTATTTCTAGTTC 57.628 33.333 0.00 0.00 0.00 3.01
6100 10049 9.371136 CATGCTAACAGTTCTATTTCTAGTTCA 57.629 33.333 0.00 0.00 0.00 3.18
6102 10051 9.204570 TGCTAACAGTTCTATTTCTAGTTCAAC 57.795 33.333 0.00 0.00 0.00 3.18
6119 10068 4.675976 TCAACGAAGACTTACAAAGGGA 57.324 40.909 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 6.097696 GCATATAAGTAATCTCTCTCTCCCCC 59.902 46.154 0.00 0.00 0.00 5.40
37 38 6.665680 TGCATATAAGTAATCTCTCTCTCCCC 59.334 42.308 0.00 0.00 0.00 4.81
38 39 7.710676 TGCATATAAGTAATCTCTCTCTCCC 57.289 40.000 0.00 0.00 0.00 4.30
39 40 7.759433 GCTTGCATATAAGTAATCTCTCTCTCC 59.241 40.741 0.00 0.00 0.00 3.71
40 41 8.522830 AGCTTGCATATAAGTAATCTCTCTCTC 58.477 37.037 0.00 0.00 0.00 3.20
41 42 8.306038 CAGCTTGCATATAAGTAATCTCTCTCT 58.694 37.037 0.00 0.00 0.00 3.10
67 68 3.245315 CGTGCTAGCCGTGCGTAC 61.245 66.667 13.29 0.19 0.00 3.67
871 888 8.119246 CCCCCTCTCTCTCTCTTCAATTATATA 58.881 40.741 0.00 0.00 0.00 0.86
873 890 6.318913 CCCCCTCTCTCTCTCTTCAATTATA 58.681 44.000 0.00 0.00 0.00 0.98
875 892 4.551671 CCCCCTCTCTCTCTCTTCAATTA 58.448 47.826 0.00 0.00 0.00 1.40
876 893 3.383223 CCCCCTCTCTCTCTCTTCAATT 58.617 50.000 0.00 0.00 0.00 2.32
877 894 3.044873 CCCCCTCTCTCTCTCTTCAAT 57.955 52.381 0.00 0.00 0.00 2.57
878 895 2.541233 CCCCCTCTCTCTCTCTTCAA 57.459 55.000 0.00 0.00 0.00 2.69
896 913 9.809096 GAAATTCTTCTTGAAATAAATCTCCCC 57.191 33.333 0.00 0.00 38.29 4.81
914 931 6.498304 CACTTGTGCACTAACTGAAATTCTT 58.502 36.000 19.41 0.00 0.00 2.52
955 1240 1.094785 CGGTCGATGGCAAAATCCTT 58.905 50.000 0.00 0.00 0.00 3.36
957 1242 1.029947 ACCGGTCGATGGCAAAATCC 61.030 55.000 0.00 0.00 0.00 3.01
1503 1788 3.555324 TCCACGCCCTTGCTCACA 61.555 61.111 0.00 0.00 34.43 3.58
1550 1835 1.402984 CCTCCTTCTTCTTGACCGACG 60.403 57.143 0.00 0.00 0.00 5.12
1842 2128 5.067954 CAGCAATTGGTGATATGATCAGGA 58.932 41.667 29.31 0.00 45.66 3.86
1845 2131 4.466827 AGCAGCAATTGGTGATATGATCA 58.533 39.130 35.28 0.00 45.66 2.92
1848 2134 4.823442 CCTAAGCAGCAATTGGTGATATGA 59.177 41.667 35.28 19.48 45.66 2.15
1849 2135 4.823442 TCCTAAGCAGCAATTGGTGATATG 59.177 41.667 35.28 24.70 45.66 1.78
1905 2191 6.559810 TCGCCAGGTTTATTTGTCAAATATG 58.440 36.000 16.82 12.32 33.64 1.78
1919 2205 2.556622 CACTACCAAAATCGCCAGGTTT 59.443 45.455 0.00 0.00 35.62 3.27
1926 2212 3.496884 TGTTCAGACACTACCAAAATCGC 59.503 43.478 0.00 0.00 0.00 4.58
1934 2220 6.373779 CAATGTTGAATGTTCAGACACTACC 58.626 40.000 10.63 0.00 38.91 3.18
1970 2256 3.873361 ACATCATCAATCTAACACTGCCG 59.127 43.478 0.00 0.00 0.00 5.69
2048 2334 5.697633 ACAAACATAGCTGAAAAGCAAATGG 59.302 36.000 0.00 3.73 35.86 3.16
2233 2519 5.416947 AGACAATACTGGACGGTGTTTATC 58.583 41.667 0.00 0.00 0.00 1.75
2259 2550 9.884636 TGTAGCTGTAATTCTGCTTTCTAATTA 57.115 29.630 0.00 0.00 46.51 1.40
2260 2551 8.792830 TGTAGCTGTAATTCTGCTTTCTAATT 57.207 30.769 0.00 0.00 46.51 1.40
2261 2552 8.043710 ACTGTAGCTGTAATTCTGCTTTCTAAT 58.956 33.333 0.00 0.00 46.51 1.73
2589 2888 4.309933 AGTTAAAGGTGGCTTGTACGTAC 58.690 43.478 18.90 18.90 0.00 3.67
2590 2889 4.605640 AGTTAAAGGTGGCTTGTACGTA 57.394 40.909 0.00 0.00 0.00 3.57
2591 2890 3.480505 AGTTAAAGGTGGCTTGTACGT 57.519 42.857 0.00 0.00 0.00 3.57
2592 2891 4.035909 ACAAAGTTAAAGGTGGCTTGTACG 59.964 41.667 0.00 0.00 0.00 3.67
2675 2974 6.985653 ACCTTCTGTACTGATAGCATATGT 57.014 37.500 4.29 0.00 0.00 2.29
2676 2975 8.341892 TCTACCTTCTGTACTGATAGCATATG 57.658 38.462 3.03 0.00 0.00 1.78
2801 3108 8.924303 ACAAACTAAAGCTCCCTAAAAAGAATT 58.076 29.630 0.00 0.00 0.00 2.17
2858 3169 7.408756 AGTGGATTTTATCAAAAGCATGCTA 57.591 32.000 23.00 5.30 38.46 3.49
2871 3182 8.547173 AGACTGAGAGAATCAAGTGGATTTTAT 58.453 33.333 0.00 0.00 46.17 1.40
2939 3251 6.878389 ACAACCACTCTCTAGTACAGTACTAC 59.122 42.308 15.43 0.00 40.14 2.73
2940 3252 6.877855 CACAACCACTCTCTAGTACAGTACTA 59.122 42.308 17.86 17.86 40.14 1.82
2941 3253 5.706369 CACAACCACTCTCTAGTACAGTACT 59.294 44.000 17.51 17.51 42.68 2.73
2942 3254 5.106237 CCACAACCACTCTCTAGTACAGTAC 60.106 48.000 2.05 2.05 33.48 2.73
2943 3255 5.008331 CCACAACCACTCTCTAGTACAGTA 58.992 45.833 0.00 0.00 33.48 2.74
2944 3256 3.827302 CCACAACCACTCTCTAGTACAGT 59.173 47.826 0.00 0.00 33.48 3.55
2945 3257 3.827302 ACCACAACCACTCTCTAGTACAG 59.173 47.826 0.00 0.00 33.48 2.74
2946 3258 3.572682 CACCACAACCACTCTCTAGTACA 59.427 47.826 0.00 0.00 33.48 2.90
3361 3673 2.820619 CGCGCTGCTCTGCATCATT 61.821 57.895 5.56 0.00 38.13 2.57
3472 3784 3.622630 ACGTAGTACAAGAGGAGAGCAT 58.377 45.455 0.38 0.00 41.94 3.79
3473 3785 3.069079 ACGTAGTACAAGAGGAGAGCA 57.931 47.619 0.38 0.00 41.94 4.26
3505 3821 1.067142 TGGCGCTAAAGTCATCGAAGT 60.067 47.619 7.64 0.00 0.00 3.01
3509 3825 3.405170 AAAATGGCGCTAAAGTCATCG 57.595 42.857 7.64 0.00 0.00 3.84
3553 3869 1.269413 ACAATTCAAGCACTGCACAGC 60.269 47.619 3.30 0.00 0.00 4.40
3554 3870 2.787601 ACAATTCAAGCACTGCACAG 57.212 45.000 3.30 0.00 0.00 3.66
3555 3871 3.446799 GAAACAATTCAAGCACTGCACA 58.553 40.909 3.30 0.00 35.54 4.57
3556 3872 2.468777 CGAAACAATTCAAGCACTGCAC 59.531 45.455 3.30 0.00 35.15 4.57
3561 3877 7.432252 CCTTATAATCCGAAACAATTCAAGCAC 59.568 37.037 0.00 0.00 35.15 4.40
3655 3971 1.497286 ACACCTAGCTCCCCACAAAAA 59.503 47.619 0.00 0.00 0.00 1.94
3656 3972 1.145571 ACACCTAGCTCCCCACAAAA 58.854 50.000 0.00 0.00 0.00 2.44
3657 3973 2.032965 TACACCTAGCTCCCCACAAA 57.967 50.000 0.00 0.00 0.00 2.83
3658 3974 2.238646 CAATACACCTAGCTCCCCACAA 59.761 50.000 0.00 0.00 0.00 3.33
3659 3975 1.837439 CAATACACCTAGCTCCCCACA 59.163 52.381 0.00 0.00 0.00 4.17
3660 3976 1.838077 ACAATACACCTAGCTCCCCAC 59.162 52.381 0.00 0.00 0.00 4.61
3661 3977 2.263895 ACAATACACCTAGCTCCCCA 57.736 50.000 0.00 0.00 0.00 4.96
3662 3978 3.036091 TGTACAATACACCTAGCTCCCC 58.964 50.000 0.00 0.00 32.89 4.81
3663 3979 3.069729 CCTGTACAATACACCTAGCTCCC 59.930 52.174 0.00 0.00 34.46 4.30
3664 3980 3.705072 ACCTGTACAATACACCTAGCTCC 59.295 47.826 0.00 0.00 34.46 4.70
3665 3981 4.401519 TCACCTGTACAATACACCTAGCTC 59.598 45.833 0.00 0.00 34.46 4.09
3666 3982 4.350245 TCACCTGTACAATACACCTAGCT 58.650 43.478 0.00 0.00 34.46 3.32
3667 3983 4.730949 TCACCTGTACAATACACCTAGC 57.269 45.455 0.00 0.00 34.46 3.42
3668 3984 6.282199 AGTTCACCTGTACAATACACCTAG 57.718 41.667 0.00 0.00 34.46 3.02
3669 3985 5.186409 GGAGTTCACCTGTACAATACACCTA 59.814 44.000 0.00 0.00 34.46 3.08
3670 3986 4.020485 GGAGTTCACCTGTACAATACACCT 60.020 45.833 0.00 0.00 34.46 4.00
3671 3987 4.251268 GGAGTTCACCTGTACAATACACC 58.749 47.826 0.00 0.00 34.46 4.16
3672 3988 4.890088 TGGAGTTCACCTGTACAATACAC 58.110 43.478 0.00 0.00 34.46 2.90
3673 3989 5.623596 CGATGGAGTTCACCTGTACAATACA 60.624 44.000 0.00 0.00 37.13 2.29
3674 3990 4.804139 CGATGGAGTTCACCTGTACAATAC 59.196 45.833 0.00 0.00 0.00 1.89
3675 3991 4.707934 TCGATGGAGTTCACCTGTACAATA 59.292 41.667 0.00 0.00 0.00 1.90
3676 3992 3.513912 TCGATGGAGTTCACCTGTACAAT 59.486 43.478 0.00 0.00 0.00 2.71
3677 3993 2.894765 TCGATGGAGTTCACCTGTACAA 59.105 45.455 0.00 0.00 0.00 2.41
3678 3994 2.521126 TCGATGGAGTTCACCTGTACA 58.479 47.619 0.00 0.00 0.00 2.90
3679 3995 3.802948 ATCGATGGAGTTCACCTGTAC 57.197 47.619 0.00 0.00 0.00 2.90
3680 3996 6.097696 TCAATTATCGATGGAGTTCACCTGTA 59.902 38.462 8.54 0.00 0.00 2.74
3702 4022 5.944599 CAGAGGGAGTACTACTGTAGTTCAA 59.055 44.000 24.09 5.36 40.14 2.69
3715 4035 7.121315 ACAAATATTTGAAAGCAGAGGGAGTAC 59.879 37.037 30.18 0.00 40.55 2.73
3716 4036 7.175104 ACAAATATTTGAAAGCAGAGGGAGTA 58.825 34.615 30.18 0.00 40.55 2.59
3717 4037 6.012745 ACAAATATTTGAAAGCAGAGGGAGT 58.987 36.000 30.18 4.10 40.55 3.85
3718 4038 6.521151 ACAAATATTTGAAAGCAGAGGGAG 57.479 37.500 30.18 3.44 40.55 4.30
3719 4039 6.916360 AACAAATATTTGAAAGCAGAGGGA 57.084 33.333 30.18 0.00 40.55 4.20
3720 4040 7.967890 AAAACAAATATTTGAAAGCAGAGGG 57.032 32.000 30.18 4.03 40.55 4.30
3721 4041 9.264719 AGAAAAACAAATATTTGAAAGCAGAGG 57.735 29.630 30.18 4.51 40.55 3.69
3764 4084 9.355215 CTCACTCATTTTACTTCGTATGTAGTT 57.645 33.333 0.00 0.00 0.00 2.24
3765 4085 7.488471 GCTCACTCATTTTACTTCGTATGTAGT 59.512 37.037 0.00 0.00 0.00 2.73
3766 4086 7.043325 GGCTCACTCATTTTACTTCGTATGTAG 60.043 40.741 0.00 0.00 0.00 2.74
3767 4087 6.755141 GGCTCACTCATTTTACTTCGTATGTA 59.245 38.462 0.00 0.00 0.00 2.29
3768 4088 5.581085 GGCTCACTCATTTTACTTCGTATGT 59.419 40.000 0.00 0.00 0.00 2.29
3769 4089 5.812642 AGGCTCACTCATTTTACTTCGTATG 59.187 40.000 0.00 0.00 0.00 2.39
3770 4090 5.978814 AGGCTCACTCATTTTACTTCGTAT 58.021 37.500 0.00 0.00 0.00 3.06
3771 4091 5.401531 AGGCTCACTCATTTTACTTCGTA 57.598 39.130 0.00 0.00 0.00 3.43
3772 4092 4.273148 AGGCTCACTCATTTTACTTCGT 57.727 40.909 0.00 0.00 0.00 3.85
3773 4093 7.203910 AGTATAGGCTCACTCATTTTACTTCG 58.796 38.462 0.00 0.00 0.00 3.79
3774 4094 8.417884 AGAGTATAGGCTCACTCATTTTACTTC 58.582 37.037 23.51 2.36 42.99 3.01
3775 4095 8.312669 AGAGTATAGGCTCACTCATTTTACTT 57.687 34.615 23.51 5.24 42.99 2.24
3776 4096 7.906199 AGAGTATAGGCTCACTCATTTTACT 57.094 36.000 23.51 5.80 42.99 2.24
3783 4103 9.588096 TCATATTTTAGAGTATAGGCTCACTCA 57.412 33.333 23.51 11.89 42.99 3.41
3784 4104 9.849166 GTCATATTTTAGAGTATAGGCTCACTC 57.151 37.037 17.25 17.25 41.25 3.51
3785 4105 9.594936 AGTCATATTTTAGAGTATAGGCTCACT 57.405 33.333 0.00 0.00 37.94 3.41
3818 4138 9.734620 CATTTCAAATGATTACAACATACGGAT 57.265 29.630 3.82 0.00 0.00 4.18
3819 4139 8.951243 TCATTTCAAATGATTACAACATACGGA 58.049 29.630 8.85 0.00 0.00 4.69
3820 4140 9.009327 GTCATTTCAAATGATTACAACATACGG 57.991 33.333 15.91 0.00 0.00 4.02
3821 4141 9.773328 AGTCATTTCAAATGATTACAACATACG 57.227 29.630 15.91 0.00 0.00 3.06
3833 4153 9.342308 ACTTGTCTTTCTAGTCATTTCAAATGA 57.658 29.630 8.85 8.85 0.00 2.57
3840 4160 9.793259 TCCAAATACTTGTCTTTCTAGTCATTT 57.207 29.630 0.00 0.00 34.37 2.32
3841 4161 9.793259 TTCCAAATACTTGTCTTTCTAGTCATT 57.207 29.630 0.00 0.00 34.37 2.57
3842 4162 9.793259 TTTCCAAATACTTGTCTTTCTAGTCAT 57.207 29.630 0.00 0.00 34.37 3.06
3843 4163 9.052759 GTTTCCAAATACTTGTCTTTCTAGTCA 57.947 33.333 0.00 0.00 34.37 3.41
3844 4164 8.221766 CGTTTCCAAATACTTGTCTTTCTAGTC 58.778 37.037 0.00 0.00 34.37 2.59
3845 4165 7.172703 CCGTTTCCAAATACTTGTCTTTCTAGT 59.827 37.037 0.00 0.00 36.28 2.57
3846 4166 7.386848 TCCGTTTCCAAATACTTGTCTTTCTAG 59.613 37.037 0.00 0.00 0.00 2.43
3847 4167 7.218614 TCCGTTTCCAAATACTTGTCTTTCTA 58.781 34.615 0.00 0.00 0.00 2.10
3848 4168 6.059484 TCCGTTTCCAAATACTTGTCTTTCT 58.941 36.000 0.00 0.00 0.00 2.52
3849 4169 6.204108 TCTCCGTTTCCAAATACTTGTCTTTC 59.796 38.462 0.00 0.00 0.00 2.62
3850 4170 6.059484 TCTCCGTTTCCAAATACTTGTCTTT 58.941 36.000 0.00 0.00 0.00 2.52
3851 4171 5.617252 TCTCCGTTTCCAAATACTTGTCTT 58.383 37.500 0.00 0.00 0.00 3.01
3852 4172 5.011738 TCTCTCCGTTTCCAAATACTTGTCT 59.988 40.000 0.00 0.00 0.00 3.41
3853 4173 5.235516 TCTCTCCGTTTCCAAATACTTGTC 58.764 41.667 0.00 0.00 0.00 3.18
3854 4174 5.221661 ACTCTCTCCGTTTCCAAATACTTGT 60.222 40.000 0.00 0.00 0.00 3.16
3855 4175 5.238583 ACTCTCTCCGTTTCCAAATACTTG 58.761 41.667 0.00 0.00 0.00 3.16
3856 4176 5.485209 ACTCTCTCCGTTTCCAAATACTT 57.515 39.130 0.00 0.00 0.00 2.24
3857 4177 6.600882 TTACTCTCTCCGTTTCCAAATACT 57.399 37.500 0.00 0.00 0.00 2.12
3858 4178 7.845066 AATTACTCTCTCCGTTTCCAAATAC 57.155 36.000 0.00 0.00 0.00 1.89
3859 4179 9.947433 TTTAATTACTCTCTCCGTTTCCAAATA 57.053 29.630 0.00 0.00 0.00 1.40
3860 4180 8.857694 TTTAATTACTCTCTCCGTTTCCAAAT 57.142 30.769 0.00 0.00 0.00 2.32
3861 4181 8.680039 TTTTAATTACTCTCTCCGTTTCCAAA 57.320 30.769 0.00 0.00 0.00 3.28
3862 4182 8.680039 TTTTTAATTACTCTCTCCGTTTCCAA 57.320 30.769 0.00 0.00 0.00 3.53
3863 4183 8.726988 CATTTTTAATTACTCTCTCCGTTTCCA 58.273 33.333 0.00 0.00 0.00 3.53
3864 4184 7.696872 GCATTTTTAATTACTCTCTCCGTTTCC 59.303 37.037 0.00 0.00 0.00 3.13
3865 4185 8.234546 TGCATTTTTAATTACTCTCTCCGTTTC 58.765 33.333 0.00 0.00 0.00 2.78
3866 4186 8.106247 TGCATTTTTAATTACTCTCTCCGTTT 57.894 30.769 0.00 0.00 0.00 3.60
3867 4187 7.681939 TGCATTTTTAATTACTCTCTCCGTT 57.318 32.000 0.00 0.00 0.00 4.44
3868 4188 7.865706 ATGCATTTTTAATTACTCTCTCCGT 57.134 32.000 0.00 0.00 0.00 4.69
3869 4189 9.226345 GAAATGCATTTTTAATTACTCTCTCCG 57.774 33.333 24.81 0.00 0.00 4.63
3885 4205 5.411977 CAGTGACAGAGAGAGAAATGCATTT 59.588 40.000 24.33 24.33 0.00 2.32
3886 4206 4.936411 CAGTGACAGAGAGAGAAATGCATT 59.064 41.667 5.99 5.99 0.00 3.56
3981 4314 1.785041 GAGCATTGTGTGTGTGCCGT 61.785 55.000 0.00 0.00 39.62 5.68
3982 4315 1.081906 GAGCATTGTGTGTGTGCCG 60.082 57.895 0.00 0.00 39.62 5.69
3983 4316 0.599558 ATGAGCATTGTGTGTGTGCC 59.400 50.000 0.00 0.00 39.62 5.01
3984 4317 1.267533 TCATGAGCATTGTGTGTGTGC 59.732 47.619 0.00 0.00 39.10 4.57
4119 4456 1.436983 GGGCGATCCGATCAACCAAC 61.437 60.000 15.84 0.87 0.00 3.77
4296 4634 3.485463 ACTCTCACGGATCAAACCAAA 57.515 42.857 0.00 0.00 0.00 3.28
4322 4660 5.181245 AGTTCGACACCTGATAATGGTTTTG 59.819 40.000 0.00 0.00 35.28 2.44
4328 4667 3.861840 ACCAGTTCGACACCTGATAATG 58.138 45.455 7.35 0.00 0.00 1.90
4334 4673 2.069273 GATGAACCAGTTCGACACCTG 58.931 52.381 6.08 0.00 42.28 4.00
4577 4916 4.003788 CAAGGACGCCTGGACGGT 62.004 66.667 13.50 0.95 37.37 4.83
5315 5669 1.765314 CACCCCCAATGACCTAGAGAG 59.235 57.143 0.00 0.00 0.00 3.20
5316 5670 1.080498 ACACCCCCAATGACCTAGAGA 59.920 52.381 0.00 0.00 0.00 3.10
5324 5678 7.644062 TCTTTACATAATTACACCCCCAATGA 58.356 34.615 0.00 0.00 0.00 2.57
5604 5964 1.156736 CGTCCATGGAACTGGAACAC 58.843 55.000 18.20 0.00 46.66 3.32
5622 5982 3.778618 TCTCATGCATCTGTTCTCTTCG 58.221 45.455 0.00 0.00 0.00 3.79
5656 6016 6.575162 ATGAGTTTTGGTTGCTAAAGGTAG 57.425 37.500 0.00 0.00 0.00 3.18
5736 6096 4.202295 TGGCACAACAATATTTTTCCTGCA 60.202 37.500 12.41 0.00 31.92 4.41
5773 6133 8.445588 AGTCTGGTTATCCTCCTTTTCTAAAAA 58.554 33.333 0.00 0.00 34.23 1.94
5774 6134 7.883311 CAGTCTGGTTATCCTCCTTTTCTAAAA 59.117 37.037 0.00 0.00 34.23 1.52
5775 6135 7.394816 CAGTCTGGTTATCCTCCTTTTCTAAA 58.605 38.462 0.00 0.00 34.23 1.85
5776 6136 6.576442 GCAGTCTGGTTATCCTCCTTTTCTAA 60.576 42.308 1.14 0.00 34.23 2.10
5778 6138 4.323868 GCAGTCTGGTTATCCTCCTTTTCT 60.324 45.833 1.14 0.00 34.23 2.52
5779 6139 3.942115 GCAGTCTGGTTATCCTCCTTTTC 59.058 47.826 1.14 0.00 34.23 2.29
5780 6140 3.330701 TGCAGTCTGGTTATCCTCCTTTT 59.669 43.478 1.14 0.00 34.23 2.27
5781 6141 2.912956 TGCAGTCTGGTTATCCTCCTTT 59.087 45.455 1.14 0.00 34.23 3.11
5785 6145 6.551385 CAATAATGCAGTCTGGTTATCCTC 57.449 41.667 1.14 0.00 34.23 3.71
5803 6163 3.005261 ACCTGTTTTGTGCATCGCAATAA 59.995 39.130 0.00 0.00 41.47 1.40
5804 6164 2.556189 ACCTGTTTTGTGCATCGCAATA 59.444 40.909 0.00 0.00 41.47 1.90
5805 6165 1.340889 ACCTGTTTTGTGCATCGCAAT 59.659 42.857 0.00 0.00 41.47 3.56
5807 6167 1.598882 TACCTGTTTTGTGCATCGCA 58.401 45.000 0.00 0.00 35.60 5.10
5808 6168 2.161410 TGATACCTGTTTTGTGCATCGC 59.839 45.455 0.00 0.00 0.00 4.58
5809 6169 3.684305 TCTGATACCTGTTTTGTGCATCG 59.316 43.478 0.00 0.00 0.00 3.84
5810 6170 5.824904 ATCTGATACCTGTTTTGTGCATC 57.175 39.130 0.00 0.00 0.00 3.91
5811 6171 7.557358 TCATTATCTGATACCTGTTTTGTGCAT 59.443 33.333 0.00 0.00 0.00 3.96
5815 9658 8.109634 ACCTTCATTATCTGATACCTGTTTTGT 58.890 33.333 0.00 0.00 32.72 2.83
5817 9660 8.109634 ACACCTTCATTATCTGATACCTGTTTT 58.890 33.333 0.00 0.00 32.72 2.43
5862 9779 6.485648 TGCCATCATCTTATCTTGTTCATGAG 59.514 38.462 0.00 0.00 0.00 2.90
5863 9780 6.358991 TGCCATCATCTTATCTTGTTCATGA 58.641 36.000 0.00 0.00 0.00 3.07
5864 9781 6.485648 TCTGCCATCATCTTATCTTGTTCATG 59.514 38.462 0.00 0.00 0.00 3.07
5865 9782 6.598503 TCTGCCATCATCTTATCTTGTTCAT 58.401 36.000 0.00 0.00 0.00 2.57
5866 9783 5.993055 TCTGCCATCATCTTATCTTGTTCA 58.007 37.500 0.00 0.00 0.00 3.18
5867 9784 6.017275 CCTTCTGCCATCATCTTATCTTGTTC 60.017 42.308 0.00 0.00 0.00 3.18
5868 9785 5.826737 CCTTCTGCCATCATCTTATCTTGTT 59.173 40.000 0.00 0.00 0.00 2.83
5875 9792 9.342308 CTTTTATTACCTTCTGCCATCATCTTA 57.658 33.333 0.00 0.00 0.00 2.10
5898 9815 5.711976 CCAGACTTGGTATGATTGTTCCTTT 59.288 40.000 0.00 0.00 39.79 3.11
5923 9872 3.506398 TGACATCTCTACTGGTGGAACA 58.494 45.455 0.00 0.00 39.98 3.18
5924 9873 4.744795 ATGACATCTCTACTGGTGGAAC 57.255 45.455 0.00 0.00 0.00 3.62
5925 9874 4.080919 CCAATGACATCTCTACTGGTGGAA 60.081 45.833 0.00 0.00 0.00 3.53
5926 9875 3.452264 CCAATGACATCTCTACTGGTGGA 59.548 47.826 0.00 0.00 0.00 4.02
5927 9876 3.452264 TCCAATGACATCTCTACTGGTGG 59.548 47.826 2.33 0.00 0.00 4.61
5928 9877 4.403752 TCTCCAATGACATCTCTACTGGTG 59.596 45.833 2.33 0.83 0.00 4.17
5929 9878 4.614475 TCTCCAATGACATCTCTACTGGT 58.386 43.478 2.33 0.00 0.00 4.00
5930 9879 5.604758 TTCTCCAATGACATCTCTACTGG 57.395 43.478 0.00 0.00 0.00 4.00
5931 9880 6.018098 GCAATTCTCCAATGACATCTCTACTG 60.018 42.308 0.00 0.00 0.00 2.74
5932 9881 6.054295 GCAATTCTCCAATGACATCTCTACT 58.946 40.000 0.00 0.00 0.00 2.57
5933 9882 6.018098 CAGCAATTCTCCAATGACATCTCTAC 60.018 42.308 0.00 0.00 0.00 2.59
5934 9883 6.053650 CAGCAATTCTCCAATGACATCTCTA 58.946 40.000 0.00 0.00 0.00 2.43
5940 9889 3.084039 GTCCAGCAATTCTCCAATGACA 58.916 45.455 0.00 0.00 0.00 3.58
5963 9912 3.124578 ACATTTTTGGGGTTGATGTGC 57.875 42.857 0.00 0.00 30.37 4.57
5990 9939 8.902540 TTTCTATGACACTAGATGTTTGTTGT 57.097 30.769 0.00 0.00 43.56 3.32
6001 9950 8.193438 TGTGTGATCAGATTTCTATGACACTAG 58.807 37.037 0.00 0.00 33.00 2.57
6002 9951 8.066612 TGTGTGATCAGATTTCTATGACACTA 57.933 34.615 0.00 0.00 33.00 2.74
6004 9953 6.238049 GCTGTGTGATCAGATTTCTATGACAC 60.238 42.308 0.00 0.00 37.61 3.67
6010 9959 7.175467 ACATTTTGCTGTGTGATCAGATTTCTA 59.825 33.333 0.00 0.00 37.61 2.10
6041 9990 1.002868 CTTGCAGTGACCTGGGAGG 60.003 63.158 0.00 0.00 42.49 4.30
6099 10048 4.154195 CCATCCCTTTGTAAGTCTTCGTTG 59.846 45.833 0.00 0.00 0.00 4.10
6100 10049 4.324267 CCATCCCTTTGTAAGTCTTCGTT 58.676 43.478 0.00 0.00 0.00 3.85
6102 10051 2.678336 GCCATCCCTTTGTAAGTCTTCG 59.322 50.000 0.00 0.00 0.00 3.79
6119 10068 2.423538 GCGTTGATAACTGGAAAGCCAT 59.576 45.455 0.00 0.00 44.91 4.40


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

AutoCloner maintained by Alex Coulton.