Multiple sequence alignment - TraesCS3D01G068000

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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 TraesCS3D01G068000 chr3D 100.000 4288 0 0 1 4288 29966419 29970706 0.000000e+00 7919.0
1 TraesCS3D01G068000 chr3D 90.083 363 27 6 2678 3033 30063090 30063450 3.020000e-126 462.0
2 TraesCS3D01G068000 chr3D 94.444 90 4 1 3185 3273 30063491 30063580 2.080000e-28 137.0
3 TraesCS3D01G068000 chr3D 89.286 56 6 0 686 741 6599636 6599691 2.140000e-08 71.3
4 TraesCS3D01G068000 chr3B 84.937 3014 226 87 2 2926 51943322 51946196 0.000000e+00 2841.0
5 TraesCS3D01G068000 chr3B 88.380 1222 72 35 1417 2600 52430678 52431867 0.000000e+00 1406.0
6 TraesCS3D01G068000 chr3B 84.666 1213 75 39 1730 2926 51225942 51227059 0.000000e+00 1107.0
7 TraesCS3D01G068000 chr3B 83.557 967 106 31 1 944 51222321 51223257 0.000000e+00 856.0
8 TraesCS3D01G068000 chr3B 86.675 818 52 29 969 1733 51224970 51225783 0.000000e+00 854.0
9 TraesCS3D01G068000 chr3B 81.121 1070 107 51 1181 2189 496063046 496064081 0.000000e+00 769.0
10 TraesCS3D01G068000 chr3B 82.253 879 121 19 2467 3327 51731271 51732132 0.000000e+00 726.0
11 TraesCS3D01G068000 chr3B 82.584 867 86 33 3452 4260 52854769 52853910 0.000000e+00 704.0
12 TraesCS3D01G068000 chr3B 88.854 323 28 7 2608 2923 52434716 52435037 1.450000e-104 390.0
13 TraesCS3D01G068000 chr3B 92.969 256 16 2 3199 3452 52854981 52854726 5.240000e-99 372.0
14 TraesCS3D01G068000 chr3B 90.602 266 17 6 1093 1354 52430403 52430664 3.170000e-91 346.0
15 TraesCS3D01G068000 chr3B 78.968 504 79 21 196 681 411839843 411839349 6.920000e-83 318.0
16 TraesCS3D01G068000 chr3B 83.163 196 20 6 4078 4260 52778135 52777940 2.650000e-37 167.0
17 TraesCS3D01G068000 chr3B 79.608 255 28 10 3024 3273 51946264 51946499 1.230000e-35 161.0
18 TraesCS3D01G068000 chr3B 84.277 159 23 2 3116 3273 52435389 52435546 2.060000e-33 154.0
19 TraesCS3D01G068000 chr3B 92.708 96 6 1 3179 3273 52779034 52778939 2.080000e-28 137.0
20 TraesCS3D01G068000 chr3B 85.047 107 11 1 4078 4179 51228189 51228295 2.110000e-18 104.0
21 TraesCS3D01G068000 chr3B 85.567 97 9 1 4078 4169 51771265 51771361 3.530000e-16 97.1
22 TraesCS3D01G068000 chr3B 83.333 108 13 1 4078 4180 51947446 51947553 1.270000e-15 95.3
23 TraesCS3D01G068000 chr3B 83.838 99 11 1 4076 4169 52436359 52436457 5.910000e-14 89.8
24 TraesCS3D01G068000 chr3B 92.982 57 4 0 2459 2515 52196110 52196166 2.750000e-12 84.2
25 TraesCS3D01G068000 chr3B 90.909 55 5 0 2374 2428 52788645 52788591 1.650000e-09 75.0
26 TraesCS3D01G068000 chr3A 86.724 821 68 18 2627 3436 41602366 41603156 0.000000e+00 874.0
27 TraesCS3D01G068000 chr3A 81.750 1063 89 52 740 1730 40913008 40914037 0.000000e+00 791.0
28 TraesCS3D01G068000 chr3A 89.917 605 50 9 2678 3273 41627884 41628486 0.000000e+00 769.0
29 TraesCS3D01G068000 chr3A 83.118 853 81 26 3452 4248 41354011 41354856 0.000000e+00 719.0
30 TraesCS3D01G068000 chr3A 84.236 628 63 20 2481 3094 40915053 40915658 2.870000e-161 579.0
31 TraesCS3D01G068000 chr3A 85.102 490 35 17 3452 3931 41603129 41603590 2.340000e-127 466.0
32 TraesCS3D01G068000 chr3A 89.552 335 28 6 3120 3453 41353727 41354055 6.630000e-113 418.0
33 TraesCS3D01G068000 chr3A 77.433 709 134 18 1 695 579647734 579648430 2.400000e-107 399.0
34 TraesCS3D01G068000 chr3A 87.000 300 17 10 2172 2462 40914598 40914884 6.920000e-83 318.0
35 TraesCS3D01G068000 chr3A 87.251 251 24 4 2611 2861 41281473 41281715 3.270000e-71 279.0
36 TraesCS3D01G068000 chr3A 90.152 132 3 5 2060 2189 40914448 40914571 3.430000e-36 163.0
37 TraesCS3D01G068000 chr3A 85.185 108 11 1 4078 4180 40917743 40917850 5.860000e-19 106.0
38 TraesCS3D01G068000 chr1D 78.161 696 122 20 7 688 127170159 127170838 2.390000e-112 416.0
39 TraesCS3D01G068000 chr5B 78.464 664 121 15 32 681 677912575 677911920 8.580000e-112 414.0
40 TraesCS3D01G068000 chr6A 77.909 679 131 17 6 677 12223892 12223226 5.160000e-109 405.0
41 TraesCS3D01G068000 chr1B 77.326 688 135 16 1 677 5035075 5035752 1.870000e-103 387.0
42 TraesCS3D01G068000 chr2B 78.420 519 84 21 196 695 51204672 51204163 3.220000e-81 313.0
43 TraesCS3D01G068000 chr2B 88.679 53 4 2 687 739 651349944 651349894 3.580000e-06 63.9
44 TraesCS3D01G068000 chr2A 76.407 551 109 14 149 682 768465285 768465831 1.170000e-70 278.0
45 TraesCS3D01G068000 chr2A 76.340 541 95 24 158 682 753968843 753968320 4.250000e-65 259.0
46 TraesCS3D01G068000 chr7A 76.753 542 96 23 158 681 42033372 42033901 4.220000e-70 276.0
47 TraesCS3D01G068000 chr2D 79.093 397 73 7 132 519 579073317 579073712 9.140000e-67 265.0
48 TraesCS3D01G068000 chr4A 76.330 545 96 26 158 684 722002229 722002758 1.180000e-65 261.0
49 TraesCS3D01G068000 chr4A 76.829 328 61 10 32 349 632849449 632849771 2.050000e-38 171.0
50 TraesCS3D01G068000 chr1A 78.238 386 68 12 1 377 4824545 4824923 2.580000e-57 233.0
51 TraesCS3D01G068000 chr4B 96.296 54 2 0 686 739 507969486 507969433 5.910000e-14 89.8
52 TraesCS3D01G068000 chr5A 91.228 57 5 0 686 742 664847551 664847607 1.280000e-10 78.7


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 TraesCS3D01G068000 chr3D 29966419 29970706 4287 False 7919.000000 7919 100.00000 1 4288 1 chr3D.!!$F2 4287
1 TraesCS3D01G068000 chr3B 51943322 51947553 4231 False 1032.433333 2841 82.62600 2 4180 3 chr3B.!!$F6 4178
2 TraesCS3D01G068000 chr3B 496063046 496064081 1035 False 769.000000 769 81.12100 1181 2189 1 chr3B.!!$F4 1008
3 TraesCS3D01G068000 chr3B 51222321 51228295 5974 False 730.250000 1107 84.98625 1 4179 4 chr3B.!!$F5 4178
4 TraesCS3D01G068000 chr3B 51731271 51732132 861 False 726.000000 726 82.25300 2467 3327 1 chr3B.!!$F1 860
5 TraesCS3D01G068000 chr3B 52853910 52854981 1071 True 538.000000 704 87.77650 3199 4260 2 chr3B.!!$R4 1061
6 TraesCS3D01G068000 chr3B 52430403 52436457 6054 False 477.160000 1406 87.19020 1093 4169 5 chr3B.!!$F7 3076
7 TraesCS3D01G068000 chr3A 41627884 41628486 602 False 769.000000 769 89.91700 2678 3273 1 chr3A.!!$F2 595
8 TraesCS3D01G068000 chr3A 41602366 41603590 1224 False 670.000000 874 85.91300 2627 3931 2 chr3A.!!$F6 1304
9 TraesCS3D01G068000 chr3A 41353727 41354856 1129 False 568.500000 719 86.33500 3120 4248 2 chr3A.!!$F5 1128
10 TraesCS3D01G068000 chr3A 579647734 579648430 696 False 399.000000 399 77.43300 1 695 1 chr3A.!!$F3 694
11 TraesCS3D01G068000 chr3A 40913008 40917850 4842 False 391.400000 791 85.66460 740 4180 5 chr3A.!!$F4 3440
12 TraesCS3D01G068000 chr1D 127170159 127170838 679 False 416.000000 416 78.16100 7 688 1 chr1D.!!$F1 681
13 TraesCS3D01G068000 chr5B 677911920 677912575 655 True 414.000000 414 78.46400 32 681 1 chr5B.!!$R1 649
14 TraesCS3D01G068000 chr6A 12223226 12223892 666 True 405.000000 405 77.90900 6 677 1 chr6A.!!$R1 671
15 TraesCS3D01G068000 chr1B 5035075 5035752 677 False 387.000000 387 77.32600 1 677 1 chr1B.!!$F1 676
16 TraesCS3D01G068000 chr2B 51204163 51204672 509 True 313.000000 313 78.42000 196 695 1 chr2B.!!$R1 499
17 TraesCS3D01G068000 chr2A 768465285 768465831 546 False 278.000000 278 76.40700 149 682 1 chr2A.!!$F1 533
18 TraesCS3D01G068000 chr2A 753968320 753968843 523 True 259.000000 259 76.34000 158 682 1 chr2A.!!$R1 524
19 TraesCS3D01G068000 chr7A 42033372 42033901 529 False 276.000000 276 76.75300 158 681 1 chr7A.!!$F1 523
20 TraesCS3D01G068000 chr4A 722002229 722002758 529 False 261.000000 261 76.33000 158 684 1 chr4A.!!$F2 526

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
112 117 0.390866 AATGTGCTGGCAGAGAGACG 60.391 55.000 20.86 0.00 0.00 4.18 F
762 810 1.662629 GTTGATGACATGTCTCCTGCG 59.337 52.381 25.55 0.00 0.00 5.18 F
1814 3862 0.107993 TGCCTCACTATGCAGCTGTC 60.108 55.000 16.64 8.39 32.77 3.51 F
1815 3863 0.177604 GCCTCACTATGCAGCTGTCT 59.822 55.000 16.64 5.47 0.00 3.41 F
1906 3955 0.258774 TCCTTAAGCAATCCCCAGGC 59.741 55.000 0.00 0.00 0.00 4.85 F
2697 7822 1.034838 TCAGCTTTGTGGTTGGCGTT 61.035 50.000 0.00 0.00 0.00 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1020 2793 0.181350 CCTCTTTTCTCGGATGGGGG 59.819 60.0 0.00 0.00 0.00 5.40 R
1906 3955 0.690411 ATGAGAGGGTGAGGCAGAGG 60.690 60.0 0.00 0.00 0.00 3.69 R
2832 7964 0.108281 GGTTCAACTCGGGGCTACTC 60.108 60.0 0.00 0.00 0.00 2.59 R
3016 8155 0.252479 AGCCAGCCATGAACTCTCAG 59.748 55.0 0.00 0.00 34.23 3.35 R
3019 8158 0.403271 AACAGCCAGCCATGAACTCT 59.597 50.0 0.00 0.00 0.00 3.24 R
4191 11001 0.251787 TCCAGAGCTGCCACTGAGTA 60.252 55.0 20.57 7.59 36.38 2.59 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
80 84 3.938963 ACGCCTTACAAACATAGGACATG 59.061 43.478 0.00 0.00 0.00 3.21
109 114 2.478989 CCAATGTGCTGGCAGAGAG 58.521 57.895 20.86 0.76 0.00 3.20
112 117 0.390866 AATGTGCTGGCAGAGAGACG 60.391 55.000 20.86 0.00 0.00 4.18
113 118 2.813042 GTGCTGGCAGAGAGACGC 60.813 66.667 20.86 1.52 0.00 5.19
208 215 3.244875 TGTGGGCATGTGACAATAAGAGT 60.245 43.478 0.00 0.00 0.00 3.24
210 217 3.008923 TGGGCATGTGACAATAAGAGTGA 59.991 43.478 0.00 0.00 0.00 3.41
297 323 6.485830 CCTGATAAAGAAGGGTATGTCTGA 57.514 41.667 0.00 0.00 0.00 3.27
451 487 4.244463 CCACAACCCCGACACGGT 62.244 66.667 9.28 0.00 46.80 4.83
530 571 4.280929 CCCACCACTATCAAGATATCGTGA 59.719 45.833 21.22 21.22 38.61 4.35
628 672 7.127186 TGGACAAATCAGTTATCTCTCCCATTA 59.873 37.037 0.00 0.00 0.00 1.90
652 700 5.127845 ACTTCTCGCAGAAAATATCTCTCCA 59.872 40.000 1.25 0.00 35.73 3.86
664 712 2.275134 TCTCTCCAGTTGCAATGCAA 57.725 45.000 17.55 17.55 46.80 4.08
705 753 5.082251 AGTAAAGATTCACCGGAAGTACC 57.918 43.478 9.46 0.00 36.25 3.34
755 803 4.371855 TCGAGGTAGTTGATGACATGTC 57.628 45.455 19.27 19.27 0.00 3.06
762 810 1.662629 GTTGATGACATGTCTCCTGCG 59.337 52.381 25.55 0.00 0.00 5.18
875 926 5.473162 TGACGATGTTTCATCAGTTCCAAAT 59.527 36.000 9.81 0.00 0.00 2.32
876 927 6.652900 TGACGATGTTTCATCAGTTCCAAATA 59.347 34.615 9.81 0.00 0.00 1.40
958 1053 2.202810 CGCCTTCGCTCCTTCTCC 60.203 66.667 0.00 0.00 0.00 3.71
961 1056 1.819905 CCTTCGCTCCTTCTCCTCC 59.180 63.158 0.00 0.00 0.00 4.30
984 2751 5.635700 CCTCTTCTTCGTCTACAAGAAAAGG 59.364 44.000 2.54 2.54 40.23 3.11
1019 2792 8.950007 AAAATTCCTTCTCTTATTTACCACCA 57.050 30.769 0.00 0.00 0.00 4.17
1020 2793 7.939784 AATTCCTTCTCTTATTTACCACCAC 57.060 36.000 0.00 0.00 0.00 4.16
1021 2794 5.431179 TCCTTCTCTTATTTACCACCACC 57.569 43.478 0.00 0.00 0.00 4.61
1022 2795 4.226620 TCCTTCTCTTATTTACCACCACCC 59.773 45.833 0.00 0.00 0.00 4.61
1055 2828 5.339423 AAAGAGGGAAGAAAAATCCTCCA 57.661 39.130 0.00 0.00 45.04 3.86
1175 2952 4.680237 CAGGACGCCGCCAACTCA 62.680 66.667 0.70 0.00 0.00 3.41
1258 3047 2.413142 GGTACGTCCGACCTCCCTG 61.413 68.421 0.00 0.00 33.86 4.45
1259 3051 2.753043 TACGTCCGACCTCCCTGC 60.753 66.667 0.00 0.00 0.00 4.85
1310 3117 3.411351 GTTTTCGCTCGCTCGCCA 61.411 61.111 0.00 0.00 0.00 5.69
1381 3188 5.736813 AGTTTGGGTGTATCAAGCGTATTA 58.263 37.500 0.00 0.00 31.97 0.98
1392 3199 8.623030 TGTATCAAGCGTATTATACTGTACACA 58.377 33.333 0.00 0.00 0.00 3.72
1396 3203 6.446781 AGCGTATTATACTGTACACACTGT 57.553 37.500 0.00 0.00 39.78 3.55
1397 3204 7.558161 AGCGTATTATACTGTACACACTGTA 57.442 36.000 0.00 0.00 41.54 2.74
1398 3205 7.988737 AGCGTATTATACTGTACACACTGTAA 58.011 34.615 0.00 0.00 40.93 2.41
1494 3310 4.059008 CTGAAAGCTTGACTAAACGAGC 57.941 45.455 0.00 0.00 44.84 5.03
1495 3311 2.806244 TGAAAGCTTGACTAAACGAGCC 59.194 45.455 0.00 0.00 45.41 4.70
1500 3316 2.095718 GCTTGACTAAACGAGCCAAAGG 60.096 50.000 0.00 0.00 40.32 3.11
1532 3370 7.891183 TCTGTAAGAAAGCTTCAGTTATGTC 57.109 36.000 0.00 0.00 42.31 3.06
1533 3371 7.441836 TCTGTAAGAAAGCTTCAGTTATGTCA 58.558 34.615 0.00 0.00 42.31 3.58
1534 3372 8.097038 TCTGTAAGAAAGCTTCAGTTATGTCAT 58.903 33.333 0.00 0.00 42.31 3.06
1535 3373 8.621532 TGTAAGAAAGCTTCAGTTATGTCATT 57.378 30.769 0.00 0.00 35.56 2.57
1536 3374 8.721478 TGTAAGAAAGCTTCAGTTATGTCATTC 58.279 33.333 0.00 0.00 35.56 2.67
1537 3375 7.992754 AAGAAAGCTTCAGTTATGTCATTCT 57.007 32.000 0.00 0.00 0.00 2.40
1538 3376 7.375106 AGAAAGCTTCAGTTATGTCATTCTG 57.625 36.000 0.00 9.88 0.00 3.02
1546 3384 6.946340 TCAGTTATGTCATTCTGTGTATGGT 58.054 36.000 13.61 0.00 0.00 3.55
1553 3391 5.105351 TGTCATTCTGTGTATGGTAGGACAG 60.105 44.000 0.00 0.00 37.72 3.51
1600 3448 6.655003 ACTTATGTCAGTATTTTGGGTGTCTG 59.345 38.462 0.00 0.00 0.00 3.51
1602 3452 4.385825 TGTCAGTATTTTGGGTGTCTGTC 58.614 43.478 0.00 0.00 0.00 3.51
1690 3545 3.282885 GAGAACAAGAATTAGCCTGGGG 58.717 50.000 0.00 0.00 0.00 4.96
1693 3548 3.087370 ACAAGAATTAGCCTGGGGAAC 57.913 47.619 0.00 0.00 0.00 3.62
1694 3549 2.378547 ACAAGAATTAGCCTGGGGAACA 59.621 45.455 0.00 0.00 0.00 3.18
1698 3553 3.138468 AGAATTAGCCTGGGGAACATACC 59.862 47.826 0.00 0.00 0.00 2.73
1754 3781 3.164268 ACAGCAGATATTTGGTTGCCAA 58.836 40.909 0.00 0.00 42.29 4.52
1813 3861 1.985614 TGCCTCACTATGCAGCTGT 59.014 52.632 16.64 0.00 32.77 4.40
1814 3862 0.107993 TGCCTCACTATGCAGCTGTC 60.108 55.000 16.64 8.39 32.77 3.51
1815 3863 0.177604 GCCTCACTATGCAGCTGTCT 59.822 55.000 16.64 5.47 0.00 3.41
1816 3864 1.937278 CCTCACTATGCAGCTGTCTG 58.063 55.000 16.64 6.12 43.16 3.51
1832 3880 6.981762 GCTGTCTGCTATATGATTATTGCT 57.018 37.500 0.00 0.00 37.43 3.91
1833 3881 6.773080 GCTGTCTGCTATATGATTATTGCTG 58.227 40.000 0.00 0.00 37.43 4.41
1835 3883 7.118825 GCTGTCTGCTATATGATTATTGCTGAA 59.881 37.037 9.30 3.11 41.92 3.02
1858 3906 7.775093 TGAATTTCCATATCCCACTTCTACAAG 59.225 37.037 0.00 0.00 35.50 3.16
1875 3924 3.577919 ACAAGTGTACCCTCTGACTTCT 58.422 45.455 0.00 0.00 0.00 2.85
1898 3947 1.635487 TGTGCCTCCTCCTTAAGCAAT 59.365 47.619 0.00 0.00 34.79 3.56
1899 3948 2.293170 GTGCCTCCTCCTTAAGCAATC 58.707 52.381 0.00 0.00 34.79 2.67
1903 3952 1.846439 CTCCTCCTTAAGCAATCCCCA 59.154 52.381 0.00 0.00 0.00 4.96
1904 3953 1.846439 TCCTCCTTAAGCAATCCCCAG 59.154 52.381 0.00 0.00 0.00 4.45
1906 3955 0.258774 TCCTTAAGCAATCCCCAGGC 59.741 55.000 0.00 0.00 0.00 4.85
1928 3980 2.191641 GCCTCACCCTCTCATGCC 59.808 66.667 0.00 0.00 0.00 4.40
2155 4220 5.643379 TGGTCATTAGTTGATTGAAAGCC 57.357 39.130 0.00 0.00 36.54 4.35
2156 4221 5.324409 TGGTCATTAGTTGATTGAAAGCCT 58.676 37.500 0.00 0.00 36.54 4.58
2157 4222 5.183713 TGGTCATTAGTTGATTGAAAGCCTG 59.816 40.000 0.00 0.00 36.54 4.85
2158 4223 5.098211 GTCATTAGTTGATTGAAAGCCTGC 58.902 41.667 0.00 0.00 36.54 4.85
2159 4224 5.012239 TCATTAGTTGATTGAAAGCCTGCT 58.988 37.500 0.00 0.00 0.00 4.24
2160 4225 5.477984 TCATTAGTTGATTGAAAGCCTGCTT 59.522 36.000 0.00 0.00 37.98 3.91
2161 4226 3.655276 AGTTGATTGAAAGCCTGCTTG 57.345 42.857 4.95 0.00 36.26 4.01
2162 4227 2.961062 AGTTGATTGAAAGCCTGCTTGT 59.039 40.909 4.95 0.00 36.26 3.16
2194 4302 1.231963 AGGTGAAAGGTTTGTCCCCT 58.768 50.000 0.00 0.00 36.75 4.79
2199 4308 3.819337 GTGAAAGGTTTGTCCCCTCTTAC 59.181 47.826 0.00 0.00 36.75 2.34
2232 4341 6.939730 TGAAAGTATTGATTTGCACTAGTCCA 59.060 34.615 0.00 0.00 0.00 4.02
2467 4584 3.910817 TGGCACATGCATGTTTTCC 57.089 47.368 29.48 26.64 44.36 3.13
2468 4585 1.046204 TGGCACATGCATGTTTTCCA 58.954 45.000 29.48 28.58 44.36 3.53
2588 4868 6.667848 TCTGTAATCCCTGACTCAAGTTATGA 59.332 38.462 0.00 0.00 36.38 2.15
2600 4880 6.711277 ACTCAAGTTATGATCCTTGCAAGTA 58.289 36.000 24.35 10.26 38.33 2.24
2601 4881 7.341805 ACTCAAGTTATGATCCTTGCAAGTAT 58.658 34.615 24.35 15.16 38.33 2.12
2602 4882 8.486210 ACTCAAGTTATGATCCTTGCAAGTATA 58.514 33.333 24.35 13.84 38.33 1.47
2603 4883 9.499479 CTCAAGTTATGATCCTTGCAAGTATAT 57.501 33.333 24.35 14.57 38.33 0.86
2697 7822 1.034838 TCAGCTTTGTGGTTGGCGTT 61.035 50.000 0.00 0.00 0.00 4.84
2775 7900 8.063200 TCAAGAGAATTAAGGACGATGAGTAA 57.937 34.615 0.00 0.00 0.00 2.24
2832 7964 4.489810 CAAGTGTGCTCTAGTTACTCTGG 58.510 47.826 0.00 0.00 0.00 3.86
2908 8043 5.692613 ATAGTCGTCTGTAAGCTGTATCC 57.307 43.478 0.00 0.00 0.00 2.59
2909 8044 3.622630 AGTCGTCTGTAAGCTGTATCCT 58.377 45.455 0.00 0.00 0.00 3.24
2990 8128 3.759418 TGTTTCTCTCGCTGATCGTAAG 58.241 45.455 0.00 0.00 39.67 2.34
3002 8140 2.159014 TGATCGTAAGTGTATGGTGCCC 60.159 50.000 0.00 0.00 39.48 5.36
3019 8158 2.997315 CCTGTGCGGTCCTCCTGA 60.997 66.667 0.00 0.00 0.00 3.86
3022 8161 1.943116 CTGTGCGGTCCTCCTGAGAG 61.943 65.000 0.00 0.00 40.09 3.20
3113 8449 3.013932 AAGCAGAGGAGGGGGCTG 61.014 66.667 0.00 0.00 36.58 4.85
3116 8452 2.439104 GCAGAGGAGGGGGCTGTAG 61.439 68.421 0.00 0.00 32.39 2.74
3139 8475 4.526970 CAGCCAGTGTTTATTGGGTATCT 58.473 43.478 0.00 0.00 41.78 1.98
3140 8476 4.949856 CAGCCAGTGTTTATTGGGTATCTT 59.050 41.667 0.00 0.00 41.78 2.40
3144 8480 7.839200 AGCCAGTGTTTATTGGGTATCTTATTT 59.161 33.333 0.00 0.00 41.88 1.40
3187 8524 2.557924 TGTTGCTTGGCTTTCCAGTATG 59.442 45.455 0.00 0.00 44.53 2.39
3230 8567 2.231964 GCAAGGCATCAGGTTCAATCAA 59.768 45.455 0.00 0.00 0.00 2.57
3242 8579 7.483307 TCAGGTTCAATCAACAAGAAAGAAAG 58.517 34.615 0.00 0.00 36.61 2.62
3309 8659 2.473576 AGGGATCGTTAGTTAGCCCT 57.526 50.000 0.00 0.00 40.97 5.19
3311 8661 3.229293 AGGGATCGTTAGTTAGCCCTAC 58.771 50.000 0.00 0.00 43.83 3.18
3331 8681 5.929992 CCTACGTCCAAGTAAACAAAGATGA 59.070 40.000 0.00 0.00 0.00 2.92
3426 8779 5.612725 TGCTTCAAACCAAAGAAATTCCT 57.387 34.783 0.00 0.00 0.00 3.36
3453 8806 3.499338 AGTTTGCCTCATTCACCAATCA 58.501 40.909 0.00 0.00 0.00 2.57
3454 8807 3.896888 AGTTTGCCTCATTCACCAATCAA 59.103 39.130 0.00 0.00 0.00 2.57
3456 8809 3.940209 TGCCTCATTCACCAATCAAAC 57.060 42.857 0.00 0.00 0.00 2.93
3457 8810 2.562298 TGCCTCATTCACCAATCAAACC 59.438 45.455 0.00 0.00 0.00 3.27
3458 8811 2.562298 GCCTCATTCACCAATCAAACCA 59.438 45.455 0.00 0.00 0.00 3.67
3459 8812 3.006752 GCCTCATTCACCAATCAAACCAA 59.993 43.478 0.00 0.00 0.00 3.67
3460 8813 4.502950 GCCTCATTCACCAATCAAACCAAA 60.503 41.667 0.00 0.00 0.00 3.28
3461 8814 5.232463 CCTCATTCACCAATCAAACCAAAG 58.768 41.667 0.00 0.00 0.00 2.77
3462 8815 5.010922 CCTCATTCACCAATCAAACCAAAGA 59.989 40.000 0.00 0.00 0.00 2.52
3463 8816 6.462768 CCTCATTCACCAATCAAACCAAAGAA 60.463 38.462 0.00 0.00 0.00 2.52
3464 8817 6.882656 TCATTCACCAATCAAACCAAAGAAA 58.117 32.000 0.00 0.00 0.00 2.52
3465 8818 7.507829 TCATTCACCAATCAAACCAAAGAAAT 58.492 30.769 0.00 0.00 0.00 2.17
3466 8819 7.992033 TCATTCACCAATCAAACCAAAGAAATT 59.008 29.630 0.00 0.00 0.00 1.82
3467 8820 7.784633 TTCACCAATCAAACCAAAGAAATTC 57.215 32.000 0.00 0.00 0.00 2.17
3468 8821 6.287525 TCACCAATCAAACCAAAGAAATTCC 58.712 36.000 0.00 0.00 0.00 3.01
3469 8822 5.469760 CACCAATCAAACCAAAGAAATTCCC 59.530 40.000 0.00 0.00 0.00 3.97
3470 8823 5.369404 ACCAATCAAACCAAAGAAATTCCCT 59.631 36.000 0.00 0.00 0.00 4.20
3471 8824 5.702209 CCAATCAAACCAAAGAAATTCCCTG 59.298 40.000 0.00 0.00 0.00 4.45
3472 8825 4.335400 TCAAACCAAAGAAATTCCCTGC 57.665 40.909 0.00 0.00 0.00 4.85
3473 8826 3.070878 TCAAACCAAAGAAATTCCCTGCC 59.929 43.478 0.00 0.00 0.00 4.85
3474 8827 1.256812 ACCAAAGAAATTCCCTGCCG 58.743 50.000 0.00 0.00 0.00 5.69
3475 8828 1.203001 ACCAAAGAAATTCCCTGCCGA 60.203 47.619 0.00 0.00 0.00 5.54
3476 8829 1.474077 CCAAAGAAATTCCCTGCCGAG 59.526 52.381 0.00 0.00 0.00 4.63
3477 8830 2.162681 CAAAGAAATTCCCTGCCGAGT 58.837 47.619 0.00 0.00 0.00 4.18
3478 8831 2.558359 CAAAGAAATTCCCTGCCGAGTT 59.442 45.455 0.00 0.00 0.00 3.01
3479 8832 2.586648 AGAAATTCCCTGCCGAGTTT 57.413 45.000 0.00 0.00 0.00 2.66
3480 8833 2.162681 AGAAATTCCCTGCCGAGTTTG 58.837 47.619 0.00 0.00 0.00 2.93
3481 8834 0.603065 AAATTCCCTGCCGAGTTTGC 59.397 50.000 0.00 0.00 0.00 3.68
3482 8835 1.250840 AATTCCCTGCCGAGTTTGCC 61.251 55.000 0.00 0.00 0.00 4.52
3483 8836 2.142292 ATTCCCTGCCGAGTTTGCCT 62.142 55.000 0.00 0.00 0.00 4.75
3484 8837 2.747855 CCCTGCCGAGTTTGCCTC 60.748 66.667 0.00 0.00 36.80 4.70
3485 8838 2.032528 CCTGCCGAGTTTGCCTCA 59.967 61.111 0.00 0.00 40.48 3.86
3529 8882 4.258702 TGTTCTGCTCTGTTCTTACTCC 57.741 45.455 0.00 0.00 0.00 3.85
3563 8921 1.172812 GGCTTGTCTTGGTCCGCTTT 61.173 55.000 0.00 0.00 0.00 3.51
3564 8922 0.238553 GCTTGTCTTGGTCCGCTTTC 59.761 55.000 0.00 0.00 0.00 2.62
3569 8927 0.391597 TCTTGGTCCGCTTTCGTTCT 59.608 50.000 0.00 0.00 0.00 3.01
3597 8992 2.291043 CCTGTGGAGTTACCGGCCT 61.291 63.158 0.00 0.00 42.61 5.19
3639 9038 1.466167 CTCATTGTTCGCACTTCTGGG 59.534 52.381 0.00 0.00 0.00 4.45
3649 9048 2.159099 CGCACTTCTGGGTCTATAGCAA 60.159 50.000 0.00 0.00 0.00 3.91
3655 9056 0.771127 TGGGTCTATAGCAATGGGCC 59.229 55.000 0.00 0.00 46.50 5.80
3664 9086 1.839424 AGCAATGGGCCTTACTTGAC 58.161 50.000 4.53 1.05 46.50 3.18
3727 9227 1.686052 GTTTTCACTGGTGATTGGCCA 59.314 47.619 0.00 0.00 39.64 5.36
3782 9297 6.293955 GCTTGCCTTGTGTGATCTTAAAAGTA 60.294 38.462 0.00 0.00 0.00 2.24
3784 9299 5.181245 TGCCTTGTGTGATCTTAAAAGTAGC 59.819 40.000 0.00 0.00 0.00 3.58
3802 10003 2.314246 AGCGAGATGGACTGATCATCA 58.686 47.619 0.00 0.00 42.38 3.07
3803 10004 2.898612 AGCGAGATGGACTGATCATCAT 59.101 45.455 0.00 0.81 42.38 2.45
3804 10005 4.085009 AGCGAGATGGACTGATCATCATA 58.915 43.478 0.00 0.00 42.38 2.15
3805 10006 4.710865 AGCGAGATGGACTGATCATCATAT 59.289 41.667 0.00 0.00 42.38 1.78
3849 10050 9.209175 CCAGATGCATGATGATCACTATATATG 57.791 37.037 2.46 0.00 0.00 1.78
3919 10121 4.393062 AGGTAATGACTTGCAATCGACTTG 59.607 41.667 0.00 0.00 37.94 3.16
3933 10135 7.386573 TGCAATCGACTTGACTTTCATTACTAA 59.613 33.333 10.52 0.00 36.97 2.24
3939 10141 8.433126 CGACTTGACTTTCATTACTAAAATCGT 58.567 33.333 0.00 0.00 0.00 3.73
3967 10274 7.695869 AATTAGTTTACATACAGCTAGTCGC 57.304 36.000 0.00 0.00 39.57 5.19
3968 10275 3.692576 AGTTTACATACAGCTAGTCGCG 58.307 45.455 0.00 0.00 45.59 5.87
3989 10314 5.174761 CGCGGAGAAGATAGATCAGAAAAAG 59.825 44.000 0.00 0.00 0.00 2.27
3990 10315 5.465056 GCGGAGAAGATAGATCAGAAAAAGG 59.535 44.000 0.00 0.00 0.00 3.11
4112 10917 2.788640 CCATTGGATGGCGCCCTTG 61.789 63.158 26.77 9.16 44.70 3.61
4145 10950 9.218440 CAGGACAAACCAATAAATATTTTTGCT 57.782 29.630 5.91 0.00 42.04 3.91
4171 10981 6.310467 TGCTAAAACACGTGTAAATTTGCAAA 59.690 30.769 29.45 15.44 30.78 3.68
4172 10982 7.148639 TGCTAAAACACGTGTAAATTTGCAAAA 60.149 29.630 29.45 17.47 30.78 2.44
4207 11017 3.710209 AAAATACTCAGTGGCAGCTCT 57.290 42.857 0.00 0.00 0.00 4.09
4212 11022 0.252479 CTCAGTGGCAGCTCTGGAAT 59.748 55.000 14.75 0.00 33.13 3.01
4221 11031 2.941720 GCAGCTCTGGAATTTAGTCCTG 59.058 50.000 0.00 0.00 38.62 3.86
4227 11037 5.071115 GCTCTGGAATTTAGTCCTGGATACT 59.929 44.000 0.00 0.00 38.62 2.12
4236 11046 1.344763 GTCCTGGATACTTGGCGCTAT 59.655 52.381 7.64 0.00 37.61 2.97
4248 11058 1.718757 GGCGCTATTCAAGGTGCTGG 61.719 60.000 7.64 0.00 38.76 4.85
4250 11060 1.009829 CGCTATTCAAGGTGCTGGAC 58.990 55.000 0.00 0.00 0.00 4.02
4261 11071 3.343941 GGTGCTGGACCTGTATGTAAA 57.656 47.619 11.48 0.00 42.25 2.01
4262 11072 3.886123 GGTGCTGGACCTGTATGTAAAT 58.114 45.455 11.48 0.00 42.25 1.40
4263 11073 5.031066 GGTGCTGGACCTGTATGTAAATA 57.969 43.478 11.48 0.00 42.25 1.40
4264 11074 5.057149 GGTGCTGGACCTGTATGTAAATAG 58.943 45.833 11.48 0.00 42.25 1.73
4265 11075 4.511826 GTGCTGGACCTGTATGTAAATAGC 59.488 45.833 0.00 0.00 0.00 2.97
4266 11076 4.163268 TGCTGGACCTGTATGTAAATAGCA 59.837 41.667 0.00 0.00 35.36 3.49
4267 11077 5.123227 GCTGGACCTGTATGTAAATAGCAA 58.877 41.667 0.00 0.00 0.00 3.91
4268 11078 5.007724 GCTGGACCTGTATGTAAATAGCAAC 59.992 44.000 0.00 0.00 0.00 4.17
4269 11079 6.056090 TGGACCTGTATGTAAATAGCAACA 57.944 37.500 0.00 0.00 0.00 3.33
4270 11080 6.477253 TGGACCTGTATGTAAATAGCAACAA 58.523 36.000 0.00 0.00 0.00 2.83
4271 11081 6.597672 TGGACCTGTATGTAAATAGCAACAAG 59.402 38.462 0.00 0.00 0.00 3.16
4272 11082 6.821665 GGACCTGTATGTAAATAGCAACAAGA 59.178 38.462 0.00 0.00 0.00 3.02
4273 11083 7.499232 GGACCTGTATGTAAATAGCAACAAGAT 59.501 37.037 0.00 0.00 0.00 2.40
4274 11084 9.542462 GACCTGTATGTAAATAGCAACAAGATA 57.458 33.333 0.00 0.00 0.00 1.98
4275 11085 9.547753 ACCTGTATGTAAATAGCAACAAGATAG 57.452 33.333 0.00 0.00 0.00 2.08
4276 11086 9.547753 CCTGTATGTAAATAGCAACAAGATAGT 57.452 33.333 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 84 1.223417 GCACATTGGCAGGCACAAAC 61.223 55.000 0.00 0.00 0.00 2.93
104 109 2.860735 GCATAACAATTCGCGTCTCTCT 59.139 45.455 5.77 0.00 0.00 3.10
112 117 0.730265 TGGGACGCATAACAATTCGC 59.270 50.000 0.00 0.00 0.00 4.70
113 118 2.854424 GCATGGGACGCATAACAATTCG 60.854 50.000 4.47 0.00 0.00 3.34
290 311 6.940867 AGCATAATCAGTGCATAATCAGACAT 59.059 34.615 0.00 0.00 44.87 3.06
351 381 7.093640 ACTCTCCTATGACAACGTAACCAAATA 60.094 37.037 0.00 0.00 0.00 1.40
451 487 0.473694 TTTCTCCTCTGGGTCTGCCA 60.474 55.000 0.00 0.00 36.17 4.92
530 571 3.055719 CGCGGGTCATGTTTGGCT 61.056 61.111 0.00 0.00 0.00 4.75
608 652 8.560124 AGAAGTAATGGGAGAGATAACTGATT 57.440 34.615 0.00 0.00 0.00 2.57
613 657 5.221263 TGCGAGAAGTAATGGGAGAGATAAC 60.221 44.000 0.00 0.00 0.00 1.89
628 672 5.127845 TGGAGAGATATTTTCTGCGAGAAGT 59.872 40.000 0.00 0.00 35.37 3.01
652 700 3.873910 TGCCCTTGCATTGCAACT 58.126 50.000 19.77 0.00 43.99 3.16
677 725 7.490000 ACTTCCGGTGAATCTTTACTATACTG 58.510 38.462 0.00 0.00 0.00 2.74
682 730 5.716228 TGGTACTTCCGGTGAATCTTTACTA 59.284 40.000 0.00 0.00 39.52 1.82
683 731 4.529377 TGGTACTTCCGGTGAATCTTTACT 59.471 41.667 0.00 0.00 39.52 2.24
684 732 4.824289 TGGTACTTCCGGTGAATCTTTAC 58.176 43.478 0.00 0.00 39.52 2.01
685 733 5.484715 CTTGGTACTTCCGGTGAATCTTTA 58.515 41.667 0.00 0.00 39.52 1.85
686 734 4.324267 CTTGGTACTTCCGGTGAATCTTT 58.676 43.478 0.00 0.00 39.52 2.52
705 753 6.092748 ACTTTTATTATGTTTGAGGCGCTTG 58.907 36.000 7.64 0.00 0.00 4.01
755 803 1.667830 TTTGTCGGAAGCGCAGGAG 60.668 57.895 11.47 0.00 0.00 3.69
762 810 1.264288 CTTGACCAGTTTGTCGGAAGC 59.736 52.381 0.00 0.00 38.11 3.86
888 939 2.508526 GCACTGGTCCAATTTCTCTGT 58.491 47.619 0.00 0.00 0.00 3.41
958 1053 5.630661 TTCTTGTAGACGAAGAAGAGGAG 57.369 43.478 0.00 0.00 35.07 3.69
961 1056 5.119434 GCCTTTTCTTGTAGACGAAGAAGAG 59.881 44.000 0.00 0.00 39.86 2.85
984 2751 5.773575 AGAGAAGGAATTTTCTTTTTCCGC 58.226 37.500 0.00 0.00 44.99 5.54
1019 2792 0.912486 CTCTTTTCTCGGATGGGGGT 59.088 55.000 0.00 0.00 0.00 4.95
1020 2793 0.181350 CCTCTTTTCTCGGATGGGGG 59.819 60.000 0.00 0.00 0.00 5.40
1021 2794 0.181350 CCCTCTTTTCTCGGATGGGG 59.819 60.000 0.00 0.00 0.00 4.96
1022 2795 1.204146 TCCCTCTTTTCTCGGATGGG 58.796 55.000 0.00 0.00 34.76 4.00
1055 2828 0.682209 TCGAGCTAGGGTTTAGCGGT 60.682 55.000 0.00 0.00 44.73 5.68
1175 2952 2.909965 GAGCGCGAGGAGGAGGAT 60.910 66.667 12.10 0.00 0.00 3.24
1310 3117 3.545703 CCCAAATCGAAGCAATCTACCT 58.454 45.455 0.00 0.00 0.00 3.08
1392 3199 1.548719 TGCGTCAGCCACTATTACAGT 59.451 47.619 0.00 0.00 44.33 3.55
1396 3203 2.093711 ACATGTGCGTCAGCCACTATTA 60.094 45.455 0.00 0.00 44.33 0.98
1397 3204 1.339055 ACATGTGCGTCAGCCACTATT 60.339 47.619 0.00 0.00 44.33 1.73
1398 3205 0.250234 ACATGTGCGTCAGCCACTAT 59.750 50.000 0.00 0.00 44.33 2.12
1403 3210 0.391130 TTCCTACATGTGCGTCAGCC 60.391 55.000 9.11 0.00 44.33 4.85
1495 3311 6.648879 TTTCTTACAGACCAAATCCCTTTG 57.351 37.500 0.00 0.00 41.22 2.77
1500 3316 5.473504 TGAAGCTTTCTTACAGACCAAATCC 59.526 40.000 0.00 0.00 31.48 3.01
1507 3323 7.385205 TGACATAACTGAAGCTTTCTTACAGAC 59.615 37.037 16.54 1.37 34.50 3.51
1532 3370 4.122776 GCTGTCCTACCATACACAGAATG 58.877 47.826 2.11 0.00 38.90 2.67
1533 3371 3.134804 GGCTGTCCTACCATACACAGAAT 59.865 47.826 2.11 0.00 38.90 2.40
1534 3372 2.500098 GGCTGTCCTACCATACACAGAA 59.500 50.000 2.11 0.00 38.90 3.02
1535 3373 2.108168 GGCTGTCCTACCATACACAGA 58.892 52.381 2.11 0.00 38.90 3.41
1536 3374 1.831106 TGGCTGTCCTACCATACACAG 59.169 52.381 0.00 0.00 39.47 3.66
1537 3375 1.945580 TGGCTGTCCTACCATACACA 58.054 50.000 0.00 0.00 0.00 3.72
1538 3376 3.560636 ATTGGCTGTCCTACCATACAC 57.439 47.619 0.00 0.00 35.42 2.90
1546 3384 5.128827 AGAAGTCGAATAATTGGCTGTCCTA 59.871 40.000 0.00 0.00 0.00 2.94
1553 3391 7.073342 AGTAAACAGAAGTCGAATAATTGGC 57.927 36.000 0.00 0.00 0.00 4.52
1690 3545 6.821665 ACATGTACAACATACAGGGTATGTTC 59.178 38.462 24.32 16.83 43.80 3.18
1693 3548 8.902540 AATACATGTACAACATACAGGGTATG 57.097 34.615 7.96 13.32 36.53 2.39
1698 3553 9.554395 TCCATAAATACATGTACAACATACAGG 57.446 33.333 7.96 2.43 36.53 4.00
1720 3575 8.680903 CAAATATCTGCTGTTTAGAAGTTCCAT 58.319 33.333 0.00 0.00 30.91 3.41
1754 3781 2.677836 CAACGTGGCTAAGCATGTACAT 59.322 45.455 1.41 1.41 0.00 2.29
1810 3858 8.543862 TTCAGCAATAATCATATAGCAGACAG 57.456 34.615 0.00 0.00 0.00 3.51
1814 3862 9.784680 GGAAATTCAGCAATAATCATATAGCAG 57.215 33.333 0.00 0.00 0.00 4.24
1815 3863 9.299465 TGGAAATTCAGCAATAATCATATAGCA 57.701 29.630 0.00 0.00 0.00 3.49
1827 3875 5.461327 AGTGGGATATGGAAATTCAGCAAT 58.539 37.500 0.00 0.00 0.00 3.56
1832 3880 7.206789 TGTAGAAGTGGGATATGGAAATTCA 57.793 36.000 0.00 0.00 0.00 2.57
1833 3881 7.775561 ACTTGTAGAAGTGGGATATGGAAATTC 59.224 37.037 4.15 0.00 41.12 2.17
1835 3883 7.213178 ACTTGTAGAAGTGGGATATGGAAAT 57.787 36.000 4.15 0.00 41.12 2.17
1858 3906 2.494073 CAGGAGAAGTCAGAGGGTACAC 59.506 54.545 0.00 0.00 0.00 2.90
1875 3924 1.573108 CTTAAGGAGGAGGCACAGGA 58.427 55.000 0.00 0.00 0.00 3.86
1906 3955 0.690411 ATGAGAGGGTGAGGCAGAGG 60.690 60.000 0.00 0.00 0.00 3.69
2155 4220 5.349817 CACCTACAAGTATCAAGACAAGCAG 59.650 44.000 0.00 0.00 0.00 4.24
2156 4221 5.011635 TCACCTACAAGTATCAAGACAAGCA 59.988 40.000 0.00 0.00 0.00 3.91
2157 4222 5.479306 TCACCTACAAGTATCAAGACAAGC 58.521 41.667 0.00 0.00 0.00 4.01
2158 4223 7.118390 CCTTTCACCTACAAGTATCAAGACAAG 59.882 40.741 0.00 0.00 0.00 3.16
2159 4224 6.934645 CCTTTCACCTACAAGTATCAAGACAA 59.065 38.462 0.00 0.00 0.00 3.18
2160 4225 6.042781 ACCTTTCACCTACAAGTATCAAGACA 59.957 38.462 0.00 0.00 0.00 3.41
2161 4226 6.465084 ACCTTTCACCTACAAGTATCAAGAC 58.535 40.000 0.00 0.00 0.00 3.01
2162 4227 6.681729 ACCTTTCACCTACAAGTATCAAGA 57.318 37.500 0.00 0.00 0.00 3.02
2199 4308 9.801714 GTGCAAATCAATACTTTCAATTTCAAG 57.198 29.630 0.00 0.00 0.00 3.02
2464 4581 8.728974 ACTAGAGAGTAGATGCCAAATGTGGAA 61.729 40.741 5.94 0.00 40.01 3.53
2465 4582 7.316377 ACTAGAGAGTAGATGCCAAATGTGGA 61.316 42.308 5.94 0.00 40.01 4.02
2466 4583 5.163364 ACTAGAGAGTAGATGCCAAATGTGG 60.163 44.000 0.00 0.00 40.37 4.17
2467 4584 5.911752 ACTAGAGAGTAGATGCCAAATGTG 58.088 41.667 0.00 0.00 32.65 3.21
2468 4585 5.896678 AGACTAGAGAGTAGATGCCAAATGT 59.103 40.000 0.00 0.00 35.45 2.71
2529 4809 0.881796 TGTGCACGTTCAAAACACCA 59.118 45.000 13.13 0.00 0.00 4.17
2534 4814 3.223423 ACAACATGTGCACGTTCAAAA 57.777 38.095 9.37 0.00 0.00 2.44
2536 4816 2.939756 AGTACAACATGTGCACGTTCAA 59.060 40.909 9.37 0.00 35.34 2.69
2538 4818 2.286833 ACAGTACAACATGTGCACGTTC 59.713 45.455 9.37 0.00 35.34 3.95
2600 4880 7.175347 AGGATCGTACATCAGTTGCATATAT 57.825 36.000 0.00 0.00 0.00 0.86
2601 4881 6.590234 AGGATCGTACATCAGTTGCATATA 57.410 37.500 0.00 0.00 0.00 0.86
2602 4882 5.474578 AGGATCGTACATCAGTTGCATAT 57.525 39.130 0.00 0.00 0.00 1.78
2603 4883 4.937201 AGGATCGTACATCAGTTGCATA 57.063 40.909 0.00 0.00 0.00 3.14
2604 4884 3.827008 AGGATCGTACATCAGTTGCAT 57.173 42.857 0.00 0.00 0.00 3.96
2614 7739 4.081365 TCTGCAATACCAAAGGATCGTACA 60.081 41.667 0.00 0.00 0.00 2.90
2775 7900 6.531503 TCAAGATTAACTGCACTAGCTAGT 57.468 37.500 20.95 20.95 42.74 2.57
2832 7964 0.108281 GGTTCAACTCGGGGCTACTC 60.108 60.000 0.00 0.00 0.00 2.59
2894 8029 9.039870 CAAAGAGATTTAGGATACAGCTTACAG 57.960 37.037 0.00 0.00 41.41 2.74
2908 8043 8.435982 AGAACTATGGATCCCAAAGAGATTTAG 58.564 37.037 9.90 0.00 36.95 1.85
2909 8044 8.213679 CAGAACTATGGATCCCAAAGAGATTTA 58.786 37.037 9.90 0.00 36.95 1.40
2955 8093 5.407995 CGAGAGAAACAAAGCAGAATCTTCT 59.592 40.000 0.00 0.00 38.25 2.85
2957 8095 4.083590 GCGAGAGAAACAAAGCAGAATCTT 60.084 41.667 0.00 0.00 0.00 2.40
3016 8155 0.252479 AGCCAGCCATGAACTCTCAG 59.748 55.000 0.00 0.00 34.23 3.35
3019 8158 0.403271 AACAGCCAGCCATGAACTCT 59.597 50.000 0.00 0.00 0.00 3.24
3022 8161 0.961019 TTCAACAGCCAGCCATGAAC 59.039 50.000 0.00 0.00 0.00 3.18
3090 8425 1.684248 CCCCCTCCTCTGCTTCAATTG 60.684 57.143 0.00 0.00 0.00 2.32
3094 8429 3.011517 GCCCCCTCCTCTGCTTCA 61.012 66.667 0.00 0.00 0.00 3.02
3113 8449 2.423538 CCCAATAAACACTGGCTGCTAC 59.576 50.000 0.00 0.00 0.00 3.58
3116 8452 1.256812 ACCCAATAAACACTGGCTGC 58.743 50.000 0.00 0.00 0.00 5.25
3156 8492 1.873698 CCAAGCAACAGCAAAGCATT 58.126 45.000 0.00 0.00 0.00 3.56
3157 8493 0.601841 GCCAAGCAACAGCAAAGCAT 60.602 50.000 0.00 0.00 0.00 3.79
3230 8567 2.952310 GTGGCTCACCTTTCTTTCTTGT 59.048 45.455 0.00 0.00 36.63 3.16
3309 8659 5.407387 GCTCATCTTTGTTTACTTGGACGTA 59.593 40.000 0.00 0.00 0.00 3.57
3311 8661 4.213270 TGCTCATCTTTGTTTACTTGGACG 59.787 41.667 0.00 0.00 0.00 4.79
3331 8681 5.426185 AGAAGAGAAAAGAGATGGAGATGCT 59.574 40.000 0.00 0.00 0.00 3.79
3453 8806 2.037121 CGGCAGGGAATTTCTTTGGTTT 59.963 45.455 0.00 0.00 0.00 3.27
3454 8807 1.618343 CGGCAGGGAATTTCTTTGGTT 59.382 47.619 0.00 0.00 0.00 3.67
3456 8809 1.474077 CTCGGCAGGGAATTTCTTTGG 59.526 52.381 0.00 0.00 0.00 3.28
3457 8810 2.162681 ACTCGGCAGGGAATTTCTTTG 58.837 47.619 0.00 0.00 0.00 2.77
3458 8811 2.586648 ACTCGGCAGGGAATTTCTTT 57.413 45.000 0.00 0.00 0.00 2.52
3459 8812 2.558359 CAAACTCGGCAGGGAATTTCTT 59.442 45.455 0.00 0.00 0.00 2.52
3460 8813 2.162681 CAAACTCGGCAGGGAATTTCT 58.837 47.619 0.00 0.00 0.00 2.52
3461 8814 1.402852 GCAAACTCGGCAGGGAATTTC 60.403 52.381 0.00 0.00 0.00 2.17
3462 8815 0.603065 GCAAACTCGGCAGGGAATTT 59.397 50.000 0.00 0.00 0.00 1.82
3463 8816 1.250840 GGCAAACTCGGCAGGGAATT 61.251 55.000 0.00 0.00 0.00 2.17
3464 8817 1.678970 GGCAAACTCGGCAGGGAAT 60.679 57.895 0.00 0.00 0.00 3.01
3465 8818 2.282180 GGCAAACTCGGCAGGGAA 60.282 61.111 0.00 0.00 0.00 3.97
3466 8819 3.249189 AGGCAAACTCGGCAGGGA 61.249 61.111 0.00 0.00 0.00 4.20
3467 8820 2.747855 GAGGCAAACTCGGCAGGG 60.748 66.667 0.00 0.00 36.29 4.45
3474 8827 4.525912 AATTGGTGAATGAGGCAAACTC 57.474 40.909 0.00 0.00 46.78 3.01
3475 8828 4.262592 GGAAATTGGTGAATGAGGCAAACT 60.263 41.667 0.00 0.00 0.00 2.66
3476 8829 3.996363 GGAAATTGGTGAATGAGGCAAAC 59.004 43.478 0.00 0.00 0.00 2.93
3477 8830 3.903090 AGGAAATTGGTGAATGAGGCAAA 59.097 39.130 0.00 0.00 0.00 3.68
3478 8831 3.258872 CAGGAAATTGGTGAATGAGGCAA 59.741 43.478 0.00 0.00 0.00 4.52
3479 8832 2.827322 CAGGAAATTGGTGAATGAGGCA 59.173 45.455 0.00 0.00 0.00 4.75
3480 8833 3.091545 TCAGGAAATTGGTGAATGAGGC 58.908 45.455 0.00 0.00 0.00 4.70
3481 8834 5.927281 ATTCAGGAAATTGGTGAATGAGG 57.073 39.130 8.61 0.00 39.04 3.86
3482 8835 9.880157 AAAATATTCAGGAAATTGGTGAATGAG 57.120 29.630 15.50 0.00 40.36 2.90
3483 8836 9.656040 CAAAATATTCAGGAAATTGGTGAATGA 57.344 29.630 15.50 5.54 40.36 2.57
3484 8837 9.439500 ACAAAATATTCAGGAAATTGGTGAATG 57.561 29.630 15.50 6.90 40.36 2.67
3529 8882 2.125350 GCCTCTGGGTGCGAAGAG 60.125 66.667 0.00 0.00 39.76 2.85
3563 8921 3.057019 CACAGGATCAAACGAAGAACGA 58.943 45.455 0.00 0.00 45.77 3.85
3569 8927 3.485463 AACTCCACAGGATCAAACGAA 57.515 42.857 0.00 0.00 0.00 3.85
3623 9021 0.468226 AGACCCAGAAGTGCGAACAA 59.532 50.000 0.00 0.00 0.00 2.83
3639 9038 4.625607 AGTAAGGCCCATTGCTATAGAC 57.374 45.455 3.21 0.00 40.92 2.59
3649 9048 4.019174 CAAGATTGTCAAGTAAGGCCCAT 58.981 43.478 0.00 0.00 0.00 4.00
3693 9120 3.315191 AGTGAAAACGTTGTTGCTGCTAT 59.685 39.130 0.00 0.00 0.00 2.97
3782 9297 2.314246 TGATGATCAGTCCATCTCGCT 58.686 47.619 0.09 0.00 40.65 4.93
3784 9299 8.022550 GCTATATATGATGATCAGTCCATCTCG 58.977 40.741 0.09 0.00 40.65 4.04
3824 10025 9.209175 CCATATATAGTGATCATCATGCATCTG 57.791 37.037 0.00 0.00 0.00 2.90
3849 10050 8.683615 AGGAAAAACCGTCAATAATAAGAATCC 58.316 33.333 0.00 0.00 44.74 3.01
3952 10259 0.663688 CTCCGCGACTAGCTGTATGT 59.336 55.000 8.23 0.00 45.59 2.29
3956 10263 0.677098 TCTTCTCCGCGACTAGCTGT 60.677 55.000 8.23 0.00 45.59 4.40
3957 10264 0.665835 ATCTTCTCCGCGACTAGCTG 59.334 55.000 8.23 0.00 45.59 4.24
3958 10265 2.147958 CTATCTTCTCCGCGACTAGCT 58.852 52.381 8.23 0.00 45.59 3.32
3959 10266 2.144730 TCTATCTTCTCCGCGACTAGC 58.855 52.381 8.23 0.00 43.95 3.42
3960 10267 3.997681 TGATCTATCTTCTCCGCGACTAG 59.002 47.826 8.23 1.57 0.00 2.57
3961 10268 3.997681 CTGATCTATCTTCTCCGCGACTA 59.002 47.826 8.23 0.00 0.00 2.59
3962 10269 2.811431 CTGATCTATCTTCTCCGCGACT 59.189 50.000 8.23 0.00 0.00 4.18
3963 10270 2.809119 TCTGATCTATCTTCTCCGCGAC 59.191 50.000 8.23 0.00 0.00 5.19
3964 10271 3.127425 TCTGATCTATCTTCTCCGCGA 57.873 47.619 8.23 0.00 0.00 5.87
3965 10272 3.906014 TTCTGATCTATCTTCTCCGCG 57.094 47.619 0.00 0.00 0.00 6.46
3966 10273 5.465056 CCTTTTTCTGATCTATCTTCTCCGC 59.535 44.000 0.00 0.00 0.00 5.54
3967 10274 6.810911 TCCTTTTTCTGATCTATCTTCTCCG 58.189 40.000 0.00 0.00 0.00 4.63
3968 10275 9.625747 ATTTCCTTTTTCTGATCTATCTTCTCC 57.374 33.333 0.00 0.00 0.00 3.71
3989 10314 4.741321 TGATCATCCAGCCAAAATTTCC 57.259 40.909 0.00 0.00 0.00 3.13
3990 10315 6.579865 AGATTGATCATCCAGCCAAAATTTC 58.420 36.000 0.00 0.00 31.20 2.17
4057 10854 7.696872 GCAGTCTATATAGCGATCGAATTACAA 59.303 37.037 21.57 0.00 0.00 2.41
4061 10858 6.443934 AGCAGTCTATATAGCGATCGAATT 57.556 37.500 21.57 5.85 0.00 2.17
4112 10917 0.467290 TTGGTTTGTCCTGCCCAGTC 60.467 55.000 0.00 0.00 37.07 3.51
4121 10926 9.824534 CAAGCAAAAATATTTATTGGTTTGTCC 57.175 29.630 23.06 7.26 41.33 4.02
4145 10950 5.805486 TGCAAATTTACACGTGTTTTAGCAA 59.195 32.000 28.55 11.07 0.00 3.91
4150 10960 7.352739 TGTTTTTGCAAATTTACACGTGTTTT 58.647 26.923 28.55 18.22 0.00 2.43
4181 10991 6.624423 AGCTGCCACTGAGTATTTTAATTTG 58.376 36.000 0.00 0.00 0.00 2.32
4191 11001 0.251787 TCCAGAGCTGCCACTGAGTA 60.252 55.000 20.57 7.59 36.38 2.59
4193 11003 0.252479 ATTCCAGAGCTGCCACTGAG 59.748 55.000 20.57 13.04 36.38 3.35
4200 11010 2.941720 CAGGACTAAATTCCAGAGCTGC 59.058 50.000 0.00 0.00 38.25 5.25
4207 11017 5.631481 GCCAAGTATCCAGGACTAAATTCCA 60.631 44.000 0.00 0.00 38.25 3.53
4212 11022 2.419574 GCGCCAAGTATCCAGGACTAAA 60.420 50.000 0.00 0.00 0.00 1.85
4221 11031 2.808543 CCTTGAATAGCGCCAAGTATCC 59.191 50.000 18.64 0.00 38.39 2.59
4227 11037 0.322456 AGCACCTTGAATAGCGCCAA 60.322 50.000 2.29 0.00 0.00 4.52
4248 11058 7.843490 TCTTGTTGCTATTTACATACAGGTC 57.157 36.000 0.00 0.00 0.00 3.85
4250 11060 9.547753 ACTATCTTGTTGCTATTTACATACAGG 57.452 33.333 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.