Multiple sequence alignment - TraesCS3A01G078100

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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 TraesCS3A01G078100 chr3A 100.000 3889 0 0 1 3889 50549168 50545280 0.000000e+00 7182.0
1 TraesCS3A01G078100 chr3A 90.335 1790 101 34 985 2746 50640589 50638844 0.000000e+00 2281.0
2 TraesCS3A01G078100 chr3A 95.511 646 24 4 110 752 712531953 712531310 0.000000e+00 1027.0
3 TraesCS3A01G078100 chr3A 86.214 515 48 11 2786 3285 50638842 50638336 1.590000e-148 536.0
4 TraesCS3A01G078100 chr3A 89.318 337 25 10 3461 3791 50638216 50637885 2.800000e-111 412.0
5 TraesCS3A01G078100 chr3B 87.028 1827 140 41 1995 3791 62215896 62214137 0.000000e+00 1971.0
6 TraesCS3A01G078100 chr3B 88.299 829 50 25 985 1793 62216913 62216112 0.000000e+00 950.0
7 TraesCS3A01G078100 chr3B 88.287 794 67 16 1231 2006 62012012 62011227 0.000000e+00 928.0
8 TraesCS3A01G078100 chr3B 91.486 646 47 4 2026 2666 62011164 62010522 0.000000e+00 881.0
9 TraesCS3A01G078100 chr3B 88.481 599 45 13 2664 3254 62010450 62009868 0.000000e+00 702.0
10 TraesCS3A01G078100 chr3B 91.729 266 13 4 940 1198 62012273 62012010 1.030000e-95 361.0
11 TraesCS3A01G078100 chr3B 88.889 261 14 7 1 248 68886382 68886124 1.360000e-79 307.0
12 TraesCS3A01G078100 chr3B 95.385 130 6 0 3663 3792 62006511 62006382 1.420000e-49 207.0
13 TraesCS3A01G078100 chr3B 91.579 95 8 0 3795 3889 803051508 803051602 8.770000e-27 132.0
14 TraesCS3A01G078100 chr3B 100.000 34 0 0 841 874 62013837 62013804 3.240000e-06 63.9
15 TraesCS3A01G078100 chr3D 89.921 1270 79 23 1995 3255 39208161 39206932 0.000000e+00 1591.0
16 TraesCS3A01G078100 chr3D 88.780 1025 72 19 985 1990 39302535 39301535 0.000000e+00 1216.0
17 TraesCS3A01G078100 chr3D 90.056 714 55 11 1307 2006 39208902 39208191 0.000000e+00 911.0
18 TraesCS3A01G078100 chr3D 88.966 725 37 11 2031 2751 39301447 39300762 0.000000e+00 856.0
19 TraesCS3A01G078100 chr3D 90.947 475 29 8 751 1217 39209422 39208954 9.170000e-176 627.0
20 TraesCS3A01G078100 chr3D 88.281 512 42 9 2784 3285 39300766 39300263 7.190000e-167 597.0
21 TraesCS3A01G078100 chr3D 91.525 413 29 6 3384 3791 39300190 39299779 7.290000e-157 564.0
22 TraesCS3A01G078100 chr3D 84.397 423 33 9 3384 3793 39206864 39206462 6.100000e-103 385.0
23 TraesCS3A01G078100 chr2A 95.814 645 24 3 110 753 745423580 745424222 0.000000e+00 1038.0
24 TraesCS3A01G078100 chr2A 88.421 95 11 0 3795 3889 196353724 196353818 8.830000e-22 115.0
25 TraesCS3A01G078100 chr2A 90.164 61 4 2 3828 3887 702570720 702570779 1.160000e-10 78.7
26 TraesCS3A01G078100 chr7A 95.164 641 29 2 110 750 117548534 117547896 0.000000e+00 1011.0
27 TraesCS3A01G078100 chr7A 94.860 642 31 2 110 751 242626017 242625378 0.000000e+00 1002.0
28 TraesCS3A01G078100 chr7A 94.704 642 32 2 110 751 242665498 242664859 0.000000e+00 996.0
29 TraesCS3A01G078100 chr7A 94.557 643 32 3 110 752 125652174 125651535 0.000000e+00 990.0
30 TraesCS3A01G078100 chr5B 90.244 779 47 8 1 753 279116017 279116792 0.000000e+00 990.0
31 TraesCS3A01G078100 chr5B 87.225 454 36 8 1037 1485 385249834 385250270 7.500000e-137 497.0
32 TraesCS3A01G078100 chr7B 90.285 772 47 12 1 747 89947354 89948122 0.000000e+00 985.0
33 TraesCS3A01G078100 chr7B 87.665 454 36 8 1036 1485 698630822 698630385 9.640000e-141 510.0
34 TraesCS3A01G078100 chr7B 89.524 105 10 1 3786 3889 327381084 327381188 8.770000e-27 132.0
35 TraesCS3A01G078100 chr7D 91.011 712 55 8 1 710 157096982 157097686 0.000000e+00 952.0
36 TraesCS3A01G078100 chr6B 87.885 454 33 8 1037 1485 68221069 68221505 7.450000e-142 514.0
37 TraesCS3A01G078100 chr6B 89.247 93 10 0 3796 3888 124796419 124796327 2.460000e-22 117.0
38 TraesCS3A01G078100 chr5A 86.564 454 39 10 1037 1485 564680197 564679761 7.560000e-132 481.0
39 TraesCS3A01G078100 chr5A 82.390 477 50 23 1265 1728 632224342 632223887 6.100000e-103 385.0
40 TraesCS3A01G078100 chr4A 85.778 450 44 8 1040 1485 661807955 661807522 3.540000e-125 459.0
41 TraesCS3A01G078100 chr4A 88.421 95 11 0 3795 3889 724689881 724689787 8.830000e-22 115.0
42 TraesCS3A01G078100 chr6D 89.583 96 10 0 3794 3889 6482993 6483088 5.280000e-24 122.0
43 TraesCS3A01G078100 chr1D 89.888 89 9 0 3801 3889 62433565 62433653 8.830000e-22 115.0


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 TraesCS3A01G078100 chr3A 50545280 50549168 3888 True 7182.000000 7182 100.000000 1 3889 1 chr3A.!!$R1 3888
1 TraesCS3A01G078100 chr3A 50637885 50640589 2704 True 1076.333333 2281 88.622333 985 3791 3 chr3A.!!$R3 2806
2 TraesCS3A01G078100 chr3A 712531310 712531953 643 True 1027.000000 1027 95.511000 110 752 1 chr3A.!!$R2 642
3 TraesCS3A01G078100 chr3B 62214137 62216913 2776 True 1460.500000 1971 87.663500 985 3791 2 chr3B.!!$R3 2806
4 TraesCS3A01G078100 chr3B 62006382 62013837 7455 True 523.816667 928 92.561333 841 3792 6 chr3B.!!$R2 2951
5 TraesCS3A01G078100 chr3D 39206462 39209422 2960 True 878.500000 1591 88.830250 751 3793 4 chr3D.!!$R1 3042
6 TraesCS3A01G078100 chr3D 39299779 39302535 2756 True 808.250000 1216 89.388000 985 3791 4 chr3D.!!$R2 2806
7 TraesCS3A01G078100 chr2A 745423580 745424222 642 False 1038.000000 1038 95.814000 110 753 1 chr2A.!!$F3 643
8 TraesCS3A01G078100 chr7A 117547896 117548534 638 True 1011.000000 1011 95.164000 110 750 1 chr7A.!!$R1 640
9 TraesCS3A01G078100 chr7A 242625378 242626017 639 True 1002.000000 1002 94.860000 110 751 1 chr7A.!!$R3 641
10 TraesCS3A01G078100 chr7A 242664859 242665498 639 True 996.000000 996 94.704000 110 751 1 chr7A.!!$R4 641
11 TraesCS3A01G078100 chr7A 125651535 125652174 639 True 990.000000 990 94.557000 110 752 1 chr7A.!!$R2 642
12 TraesCS3A01G078100 chr5B 279116017 279116792 775 False 990.000000 990 90.244000 1 753 1 chr5B.!!$F1 752
13 TraesCS3A01G078100 chr7B 89947354 89948122 768 False 985.000000 985 90.285000 1 747 1 chr7B.!!$F1 746
14 TraesCS3A01G078100 chr7D 157096982 157097686 704 False 952.000000 952 91.011000 1 710 1 chr7D.!!$F1 709

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
799 831 0.108662 ATCACTCTTGCATGCGTCGA 60.109 50.0 14.09 8.14 0.0 4.20 F
1211 2741 0.104120 TACGTGCTTCCATGATCCCG 59.896 55.0 0.00 0.00 0.0 5.14 F
1599 3170 0.105224 TGTGTGTACGGGTTCCTGTG 59.895 55.0 12.98 0.00 0.0 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2216 3974 0.324943 GGAGCTGCACTTCAGGGTTA 59.675 55.000 0.00 0.0 43.06 2.85 R
2326 4086 0.979665 CCCTGCTCTCAGTCCAAAGA 59.020 55.000 0.00 0.0 38.66 2.52 R
2918 4764 1.001048 CAAGCACTGGTGTGTTCATGG 60.001 52.381 2.64 0.0 45.44 3.66 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
84 86 3.197333 AGAGATAGAGCAAGCACACATGT 59.803 43.478 0.00 0.00 0.00 3.21
538 565 1.301637 AGCAATTTTTGGCGGTGGC 60.302 52.632 0.00 0.00 38.90 5.01
618 645 4.316205 TGTTTCTGAAACAGAGCGACTA 57.684 40.909 27.14 6.05 45.79 2.59
625 652 3.254060 GAAACAGAGCGACTATTGCAGA 58.746 45.455 0.00 0.00 33.85 4.26
633 660 5.874810 AGAGCGACTATTGCAGAAAATAACA 59.125 36.000 0.00 0.00 33.85 2.41
634 661 6.371548 AGAGCGACTATTGCAGAAAATAACAA 59.628 34.615 0.00 0.00 33.85 2.83
760 792 0.179137 GCGGTTCCCTTTGCTTATGC 60.179 55.000 0.00 0.00 40.20 3.14
797 829 3.618594 TCTTAATCACTCTTGCATGCGTC 59.381 43.478 14.09 0.00 0.00 5.19
798 830 0.723414 AATCACTCTTGCATGCGTCG 59.277 50.000 14.09 3.69 0.00 5.12
799 831 0.108662 ATCACTCTTGCATGCGTCGA 60.109 50.000 14.09 8.14 0.00 4.20
800 832 0.733909 TCACTCTTGCATGCGTCGAG 60.734 55.000 21.76 21.76 0.00 4.04
919 2442 4.873129 CATACACGAGGCCGCGCT 62.873 66.667 29.59 16.54 39.95 5.92
920 2443 4.873129 ATACACGAGGCCGCGCTG 62.873 66.667 29.59 25.31 39.95 5.18
933 2456 4.710695 CGCTGGACCGTGCGTACA 62.711 66.667 19.45 0.00 46.09 2.90
934 2457 3.110178 GCTGGACCGTGCGTACAC 61.110 66.667 4.09 0.00 43.76 2.90
1115 2644 2.526873 AGGGACGGCAAGGTCTGT 60.527 61.111 0.00 0.00 37.12 3.41
1126 2655 1.461091 AAGGTCTGTCTCGTCCGCAA 61.461 55.000 0.00 0.00 0.00 4.85
1195 2725 0.591659 TCGATCCAAGATCGGCTACG 59.408 55.000 22.65 1.73 41.45 3.51
1196 2726 0.311165 CGATCCAAGATCGGCTACGT 59.689 55.000 17.12 0.00 41.85 3.57
1197 2727 1.772182 GATCCAAGATCGGCTACGTG 58.228 55.000 0.00 0.00 41.85 4.49
1198 2728 0.249489 ATCCAAGATCGGCTACGTGC 60.249 55.000 0.00 0.00 41.85 5.34
1199 2729 1.141881 CCAAGATCGGCTACGTGCT 59.858 57.895 0.00 0.00 42.39 4.40
1200 2730 0.460284 CCAAGATCGGCTACGTGCTT 60.460 55.000 0.00 0.00 42.39 3.91
1201 2731 0.924090 CAAGATCGGCTACGTGCTTC 59.076 55.000 0.00 0.01 42.39 3.86
1202 2732 0.179108 AAGATCGGCTACGTGCTTCC 60.179 55.000 0.00 0.00 42.39 3.46
1203 2733 1.141019 GATCGGCTACGTGCTTCCA 59.859 57.895 0.00 0.00 42.39 3.53
1204 2734 0.249489 GATCGGCTACGTGCTTCCAT 60.249 55.000 0.00 0.00 42.39 3.41
1205 2735 0.530650 ATCGGCTACGTGCTTCCATG 60.531 55.000 0.00 0.00 42.39 3.66
1206 2736 1.153647 CGGCTACGTGCTTCCATGA 60.154 57.895 0.00 0.00 42.39 3.07
1207 2737 0.530650 CGGCTACGTGCTTCCATGAT 60.531 55.000 0.00 0.00 42.39 2.45
1208 2738 1.221414 GGCTACGTGCTTCCATGATC 58.779 55.000 0.00 0.00 42.39 2.92
1209 2739 1.221414 GCTACGTGCTTCCATGATCC 58.779 55.000 0.00 0.00 38.95 3.36
1210 2740 1.871080 CTACGTGCTTCCATGATCCC 58.129 55.000 0.00 0.00 0.00 3.85
1211 2741 0.104120 TACGTGCTTCCATGATCCCG 59.896 55.000 0.00 0.00 0.00 5.14
1212 2742 1.143838 CGTGCTTCCATGATCCCGA 59.856 57.895 0.00 0.00 0.00 5.14
1213 2743 0.250038 CGTGCTTCCATGATCCCGAT 60.250 55.000 0.00 0.00 0.00 4.18
1214 2744 1.517242 GTGCTTCCATGATCCCGATC 58.483 55.000 0.00 0.00 38.29 3.69
1215 2745 0.397941 TGCTTCCATGATCCCGATCC 59.602 55.000 0.00 0.00 37.02 3.36
1216 2746 0.397941 GCTTCCATGATCCCGATCCA 59.602 55.000 0.00 0.00 37.02 3.41
1217 2747 1.202806 GCTTCCATGATCCCGATCCAA 60.203 52.381 0.00 0.00 37.02 3.53
1218 2748 2.749466 GCTTCCATGATCCCGATCCAAA 60.749 50.000 0.00 0.00 37.02 3.28
1219 2749 3.554934 CTTCCATGATCCCGATCCAAAA 58.445 45.455 0.00 0.00 37.02 2.44
1220 2750 3.882102 TCCATGATCCCGATCCAAAAT 57.118 42.857 0.00 0.00 37.02 1.82
1221 2751 4.991789 TCCATGATCCCGATCCAAAATA 57.008 40.909 0.00 0.00 37.02 1.40
1222 2752 4.910195 TCCATGATCCCGATCCAAAATAG 58.090 43.478 0.00 0.00 37.02 1.73
1223 2753 4.350816 TCCATGATCCCGATCCAAAATAGT 59.649 41.667 0.00 0.00 37.02 2.12
1224 2754 5.546110 TCCATGATCCCGATCCAAAATAGTA 59.454 40.000 0.00 0.00 37.02 1.82
1225 2755 5.643777 CCATGATCCCGATCCAAAATAGTAC 59.356 44.000 0.00 0.00 37.02 2.73
1226 2756 5.880164 TGATCCCGATCCAAAATAGTACA 57.120 39.130 2.31 0.00 37.02 2.90
1227 2757 6.433847 TGATCCCGATCCAAAATAGTACAT 57.566 37.500 2.31 0.00 37.02 2.29
1228 2758 6.837312 TGATCCCGATCCAAAATAGTACATT 58.163 36.000 2.31 0.00 37.02 2.71
1229 2759 7.969004 TGATCCCGATCCAAAATAGTACATTA 58.031 34.615 2.31 0.00 37.02 1.90
1262 2824 1.073125 TCGGGATCTGAAAACTTGGCA 59.927 47.619 0.00 0.00 0.00 4.92
1279 2841 2.643933 GCATTTCTGCCTTGTCCTTC 57.356 50.000 0.00 0.00 42.88 3.46
1289 2853 3.587061 TGCCTTGTCCTTCTCTAATTGGA 59.413 43.478 0.00 0.00 0.00 3.53
1378 2946 7.718525 TCATGTGGTTGATGGATTTGAATATG 58.281 34.615 0.00 0.00 0.00 1.78
1586 3157 1.134431 TGCTATCCGATGCATGTGTGT 60.134 47.619 2.46 0.00 33.94 3.72
1591 3162 1.428370 CCGATGCATGTGTGTACGGG 61.428 60.000 2.46 0.00 35.52 5.28
1592 3163 0.739462 CGATGCATGTGTGTACGGGT 60.739 55.000 2.46 0.00 0.00 5.28
1593 3164 1.448985 GATGCATGTGTGTACGGGTT 58.551 50.000 2.46 0.00 0.00 4.11
1594 3165 1.396996 GATGCATGTGTGTACGGGTTC 59.603 52.381 2.46 0.00 0.00 3.62
1595 3166 0.604243 TGCATGTGTGTACGGGTTCC 60.604 55.000 0.00 0.00 0.00 3.62
1596 3167 0.321298 GCATGTGTGTACGGGTTCCT 60.321 55.000 0.00 0.00 0.00 3.36
1597 3168 1.438651 CATGTGTGTACGGGTTCCTG 58.561 55.000 0.00 0.00 0.00 3.86
1598 3169 1.053424 ATGTGTGTACGGGTTCCTGT 58.947 50.000 8.44 8.44 0.00 4.00
1599 3170 0.105224 TGTGTGTACGGGTTCCTGTG 59.895 55.000 12.98 0.00 0.00 3.66
1600 3171 0.105408 GTGTGTACGGGTTCCTGTGT 59.895 55.000 12.98 1.27 0.00 3.72
1601 3172 1.340889 GTGTGTACGGGTTCCTGTGTA 59.659 52.381 12.98 0.03 0.00 2.90
1602 3173 1.340889 TGTGTACGGGTTCCTGTGTAC 59.659 52.381 12.98 11.41 38.10 2.90
1603 3174 0.597568 TGTACGGGTTCCTGTGTACG 59.402 55.000 12.98 0.00 39.95 3.67
1604 3175 0.109132 GTACGGGTTCCTGTGTACGG 60.109 60.000 12.98 0.00 0.00 4.02
1612 3183 4.202441 GGTTCCTGTGTACGGTAGATCTA 58.798 47.826 0.00 0.00 0.00 1.98
1735 3347 3.549299 AAGCTTGAATGAACAGAAGCG 57.451 42.857 0.00 0.00 44.51 4.68
1782 3395 5.833131 ACCTGTGGTGTTTCAGTGAATAATT 59.167 36.000 6.36 0.00 32.98 1.40
1793 3406 8.880750 GTTTCAGTGAATAATTACCACTAGGAC 58.119 37.037 17.13 13.01 38.93 3.85
1794 3407 7.120923 TCAGTGAATAATTACCACTAGGACC 57.879 40.000 17.13 0.00 38.93 4.46
1842 3459 7.839680 TGATATAAACTAGTCCAGCATGAGA 57.160 36.000 0.00 0.00 39.69 3.27
1846 3463 4.734398 AACTAGTCCAGCATGAGAGAAG 57.266 45.455 0.00 0.00 39.69 2.85
1868 3485 4.829492 AGTTTCTCCTTGTTCTTGGGAATG 59.171 41.667 0.00 0.00 33.71 2.67
1871 3493 4.906618 TCTCCTTGTTCTTGGGAATGTAC 58.093 43.478 0.00 0.00 33.71 2.90
1948 3570 5.607119 AGTTAAATCTGCTACGGTGTTTG 57.393 39.130 0.00 0.00 0.00 2.93
2016 3766 0.247460 ATGTGCGCTTGCTCTGACTA 59.753 50.000 9.73 0.00 40.12 2.59
2019 3769 0.460811 TGCGCTTGCTCTGACTATGG 60.461 55.000 9.73 0.00 40.12 2.74
2022 3772 1.804372 CGCTTGCTCTGACTATGGTCC 60.804 57.143 6.77 0.00 41.47 4.46
2076 3828 7.381408 GTGCACATATATCGCAGTAGTTCTAAA 59.619 37.037 13.17 0.00 36.07 1.85
2077 3829 7.923878 TGCACATATATCGCAGTAGTTCTAAAA 59.076 33.333 2.80 0.00 0.00 1.52
2201 3956 2.358957 TGCTATGAGTTGTCACATGGC 58.641 47.619 0.00 0.00 44.38 4.40
2310 4070 3.181329 TGACCAGGTACAATCCAGACAT 58.819 45.455 0.00 0.00 0.00 3.06
2326 4086 0.902531 ACATCCTGGACGAATCGGTT 59.097 50.000 7.80 0.00 0.00 4.44
2335 4095 2.612221 GGACGAATCGGTTCTTTGGACT 60.612 50.000 7.80 0.00 32.00 3.85
2479 4239 2.122729 TGGGAGTGGACTGAGGGG 59.877 66.667 0.00 0.00 0.00 4.79
2519 4279 1.139256 TCGTTGCCTGGTGTAAGTTCA 59.861 47.619 0.00 0.00 0.00 3.18
2595 4365 7.919690 TCAGTTTCACTAGAACAGTTTGATTG 58.080 34.615 0.00 0.00 34.26 2.67
2605 4375 7.054491 AGAACAGTTTGATTGGTTAATTGCT 57.946 32.000 0.00 0.00 0.00 3.91
2630 4400 9.512435 CTATTTGTTTCTTCTCATGCAAATAGG 57.488 33.333 19.73 9.45 44.55 2.57
2673 4517 2.569059 AGATGCATGCTACATGACACC 58.431 47.619 20.33 0.78 0.00 4.16
2718 4562 3.164268 TGGGGATTGATTTGTGTCTTGG 58.836 45.455 0.00 0.00 0.00 3.61
2750 4594 2.158449 GGAACGATGCATATGCTACAGC 59.842 50.000 27.13 10.24 42.66 4.40
2777 4621 2.186350 TTCAAACAGCGCGCCATCTG 62.186 55.000 30.33 22.08 36.45 2.90
2831 4675 2.819984 AAAGGATGGCGCCGATGTGT 62.820 55.000 23.90 2.30 0.00 3.72
2918 4764 4.627467 GGCGTAGATTATGTGTGATGGATC 59.373 45.833 0.00 0.00 0.00 3.36
2927 4773 3.346315 TGTGTGATGGATCCATGAACAC 58.654 45.455 36.62 36.62 43.55 3.32
3102 4953 2.177734 TGCTCCTGCATGCCAAAAATA 58.822 42.857 16.68 0.00 45.31 1.40
3106 4957 4.427312 CTCCTGCATGCCAAAAATACTTC 58.573 43.478 16.68 0.00 0.00 3.01
3182 5045 3.643159 GAAAACCCAAGCATTTCGACT 57.357 42.857 0.00 0.00 0.00 4.18
3195 5058 6.656003 AGCATTTCGACTAGTACAAAAACAC 58.344 36.000 0.00 0.00 0.00 3.32
3200 5063 5.339177 TCGACTAGTACAAAAACACGTTGA 58.661 37.500 0.00 0.00 0.00 3.18
3229 5092 0.179059 TTCTGGCGCTTCAACTGTCA 60.179 50.000 7.64 0.00 0.00 3.58
3234 5097 2.287547 TGGCGCTTCAACTGTCATTTTC 60.288 45.455 7.64 0.00 0.00 2.29
3239 5102 3.057245 GCTTCAACTGTCATTTTCCCCTC 60.057 47.826 0.00 0.00 0.00 4.30
3241 5104 4.387026 TCAACTGTCATTTTCCCCTCAT 57.613 40.909 0.00 0.00 0.00 2.90
3255 5118 2.165030 CCCCTCATGAAGCACAATTGTC 59.835 50.000 8.48 4.08 0.00 3.18
3258 5121 4.008330 CCTCATGAAGCACAATTGTCTCT 58.992 43.478 8.48 6.09 0.00 3.10
3285 5148 5.657826 TTGCATTAAAATAGGCAAGAGCA 57.342 34.783 0.00 0.00 44.61 4.26
3286 5149 4.997565 TGCATTAAAATAGGCAAGAGCAC 58.002 39.130 0.00 0.00 44.61 4.40
3287 5150 4.462132 TGCATTAAAATAGGCAAGAGCACA 59.538 37.500 0.00 0.00 44.61 4.57
3288 5151 5.127519 TGCATTAAAATAGGCAAGAGCACAT 59.872 36.000 0.00 0.00 44.61 3.21
3289 5152 5.689068 GCATTAAAATAGGCAAGAGCACATC 59.311 40.000 0.00 0.00 44.61 3.06
3290 5153 6.681120 GCATTAAAATAGGCAAGAGCACATCA 60.681 38.462 0.00 0.00 44.61 3.07
3291 5154 6.832520 TTAAAATAGGCAAGAGCACATCAA 57.167 33.333 0.00 0.00 44.61 2.57
3292 5155 5.726980 AAAATAGGCAAGAGCACATCAAA 57.273 34.783 0.00 0.00 44.61 2.69
3293 5156 4.708726 AATAGGCAAGAGCACATCAAAC 57.291 40.909 0.00 0.00 44.61 2.93
3294 5157 1.985473 AGGCAAGAGCACATCAAACA 58.015 45.000 0.00 0.00 44.61 2.83
3295 5158 1.610522 AGGCAAGAGCACATCAAACAC 59.389 47.619 0.00 0.00 44.61 3.32
3296 5159 1.610522 GGCAAGAGCACATCAAACACT 59.389 47.619 0.00 0.00 44.61 3.55
3297 5160 2.813754 GGCAAGAGCACATCAAACACTA 59.186 45.455 0.00 0.00 44.61 2.74
3298 5161 3.253188 GGCAAGAGCACATCAAACACTAA 59.747 43.478 0.00 0.00 44.61 2.24
3327 5190 9.208022 TGAACATGTACAACAAAATGTTTTTCA 57.792 25.926 10.67 3.66 41.91 2.69
3367 5230 4.154015 GGTAGCCCATTTGTTTGAATTTGC 59.846 41.667 0.00 0.00 0.00 3.68
3369 5232 3.816523 AGCCCATTTGTTTGAATTTGCTG 59.183 39.130 0.00 0.00 0.00 4.41
3371 5234 4.036616 GCCCATTTGTTTGAATTTGCTGTT 59.963 37.500 0.00 0.00 0.00 3.16
3372 5235 5.750650 CCCATTTGTTTGAATTTGCTGTTC 58.249 37.500 0.00 0.00 0.00 3.18
3373 5236 5.433855 CCATTTGTTTGAATTTGCTGTTCG 58.566 37.500 0.00 0.00 0.00 3.95
3374 5237 5.006552 CCATTTGTTTGAATTTGCTGTTCGT 59.993 36.000 0.00 0.00 0.00 3.85
3375 5238 5.447478 TTTGTTTGAATTTGCTGTTCGTG 57.553 34.783 0.00 0.00 0.00 4.35
3376 5239 2.857152 TGTTTGAATTTGCTGTTCGTGC 59.143 40.909 0.00 0.00 0.00 5.34
3377 5240 2.132740 TTGAATTTGCTGTTCGTGCC 57.867 45.000 0.00 0.00 0.00 5.01
3379 5242 1.001487 TGAATTTGCTGTTCGTGCCAG 60.001 47.619 0.00 0.00 0.00 4.85
3380 5243 0.314935 AATTTGCTGTTCGTGCCAGG 59.685 50.000 0.00 0.00 0.00 4.45
3381 5244 0.537143 ATTTGCTGTTCGTGCCAGGA 60.537 50.000 0.00 0.00 0.00 3.86
3382 5245 1.444119 TTTGCTGTTCGTGCCAGGAC 61.444 55.000 0.00 0.00 29.40 3.85
3386 5249 1.927895 CTGTTCGTGCCAGGACTATC 58.072 55.000 0.00 0.00 0.00 2.08
3395 5258 2.050144 GCCAGGACTATCATCCTCCAA 58.950 52.381 0.00 0.00 46.92 3.53
3448 5311 3.120468 TGATCTTGTCTGGGATCAGGA 57.880 47.619 0.00 0.00 41.99 3.86
3459 5322 2.840651 TGGGATCAGGAACTCCTCTTTC 59.159 50.000 0.00 0.00 46.65 2.62
3495 5362 5.534654 TGTATTGAAGGTCCCTCAAAAACAG 59.465 40.000 7.00 0.00 0.00 3.16
3498 5365 4.207165 TGAAGGTCCCTCAAAAACAGAAG 58.793 43.478 0.00 0.00 0.00 2.85
3507 5376 5.239525 CCCTCAAAAACAGAAGGAAGTACTG 59.760 44.000 0.00 0.00 37.62 2.74
3527 5396 2.046892 GGTCAGCTGCCATGTCGT 60.047 61.111 18.68 0.00 0.00 4.34
3640 5520 2.601666 AGAGTGTCTGGCTCGCCA 60.602 61.111 10.64 10.64 45.02 5.69
3659 8513 0.405585 ATGGTAGTTGCCTGTTGCCT 59.594 50.000 0.00 0.00 40.16 4.75
3660 8514 0.250727 TGGTAGTTGCCTGTTGCCTC 60.251 55.000 0.00 0.00 40.16 4.70
3661 8515 0.036875 GGTAGTTGCCTGTTGCCTCT 59.963 55.000 0.00 0.00 40.16 3.69
3780 8634 3.804873 GCCATCTGTTCGGACTCTTAATC 59.195 47.826 0.00 0.00 0.00 1.75
3793 8647 8.666573 TCGGACTCTTAATCGTCTATATCAATC 58.333 37.037 4.81 0.00 0.00 2.67
3794 8648 7.636745 CGGACTCTTAATCGTCTATATCAATCG 59.363 40.741 4.81 0.00 0.00 3.34
3795 8649 8.666573 GGACTCTTAATCGTCTATATCAATCGA 58.333 37.037 0.00 0.00 35.14 3.59
3796 8650 9.697250 GACTCTTAATCGTCTATATCAATCGAG 57.303 37.037 0.00 0.00 34.20 4.04
3797 8651 9.221933 ACTCTTAATCGTCTATATCAATCGAGT 57.778 33.333 0.00 0.00 34.20 4.18
3798 8652 9.484326 CTCTTAATCGTCTATATCAATCGAGTG 57.516 37.037 6.51 6.51 34.20 3.51
3799 8653 9.000486 TCTTAATCGTCTATATCAATCGAGTGT 58.000 33.333 13.18 3.12 34.20 3.55
3800 8654 8.950403 TTAATCGTCTATATCAATCGAGTGTG 57.050 34.615 13.18 0.00 34.20 3.82
3801 8655 5.358298 TCGTCTATATCAATCGAGTGTGG 57.642 43.478 13.18 0.00 0.00 4.17
3802 8656 4.820173 TCGTCTATATCAATCGAGTGTGGT 59.180 41.667 13.18 3.34 0.00 4.16
3803 8657 5.298527 TCGTCTATATCAATCGAGTGTGGTT 59.701 40.000 13.18 0.00 0.00 3.67
3804 8658 5.977725 CGTCTATATCAATCGAGTGTGGTTT 59.022 40.000 13.18 0.00 0.00 3.27
3805 8659 6.475727 CGTCTATATCAATCGAGTGTGGTTTT 59.524 38.462 13.18 0.00 0.00 2.43
3806 8660 7.306051 CGTCTATATCAATCGAGTGTGGTTTTC 60.306 40.741 13.18 0.36 0.00 2.29
3807 8661 7.707035 GTCTATATCAATCGAGTGTGGTTTTCT 59.293 37.037 13.18 0.00 0.00 2.52
3808 8662 6.668541 ATATCAATCGAGTGTGGTTTTCTG 57.331 37.500 13.18 0.00 0.00 3.02
3809 8663 3.804036 TCAATCGAGTGTGGTTTTCTGT 58.196 40.909 13.18 0.00 0.00 3.41
3810 8664 4.951254 TCAATCGAGTGTGGTTTTCTGTA 58.049 39.130 13.18 0.00 0.00 2.74
3811 8665 4.988540 TCAATCGAGTGTGGTTTTCTGTAG 59.011 41.667 13.18 0.00 0.00 2.74
3812 8666 2.750948 TCGAGTGTGGTTTTCTGTAGC 58.249 47.619 0.00 0.00 0.00 3.58
3813 8667 2.364324 TCGAGTGTGGTTTTCTGTAGCT 59.636 45.455 0.00 0.00 0.00 3.32
3814 8668 2.731976 CGAGTGTGGTTTTCTGTAGCTC 59.268 50.000 0.00 0.00 0.00 4.09
3815 8669 3.728845 GAGTGTGGTTTTCTGTAGCTCA 58.271 45.455 0.00 0.00 0.00 4.26
3816 8670 4.127171 GAGTGTGGTTTTCTGTAGCTCAA 58.873 43.478 0.00 0.00 0.00 3.02
3817 8671 4.130118 AGTGTGGTTTTCTGTAGCTCAAG 58.870 43.478 0.00 0.00 0.00 3.02
3818 8672 2.878406 TGTGGTTTTCTGTAGCTCAAGC 59.122 45.455 0.00 0.00 42.49 4.01
3830 8684 2.535012 GCTCAAGCTATCTGGTACCC 57.465 55.000 10.07 0.00 38.21 3.69
3831 8685 1.070914 GCTCAAGCTATCTGGTACCCC 59.929 57.143 10.07 0.00 38.21 4.95
3832 8686 2.683768 CTCAAGCTATCTGGTACCCCT 58.316 52.381 10.07 0.00 0.00 4.79
3833 8687 3.041946 CTCAAGCTATCTGGTACCCCTT 58.958 50.000 10.07 0.00 0.00 3.95
3834 8688 4.223953 CTCAAGCTATCTGGTACCCCTTA 58.776 47.826 10.07 0.00 0.00 2.69
3835 8689 4.827789 TCAAGCTATCTGGTACCCCTTAT 58.172 43.478 10.07 0.07 0.00 1.73
3836 8690 4.838986 TCAAGCTATCTGGTACCCCTTATC 59.161 45.833 10.07 0.00 0.00 1.75
3837 8691 4.768807 AGCTATCTGGTACCCCTTATCT 57.231 45.455 10.07 0.00 0.00 1.98
3838 8692 5.094569 AGCTATCTGGTACCCCTTATCTT 57.905 43.478 10.07 0.00 0.00 2.40
3839 8693 5.477913 AGCTATCTGGTACCCCTTATCTTT 58.522 41.667 10.07 0.00 0.00 2.52
3840 8694 6.631107 AGCTATCTGGTACCCCTTATCTTTA 58.369 40.000 10.07 0.00 0.00 1.85
3841 8695 6.497606 AGCTATCTGGTACCCCTTATCTTTAC 59.502 42.308 10.07 0.00 0.00 2.01
3842 8696 6.295745 GCTATCTGGTACCCCTTATCTTTACC 60.296 46.154 10.07 0.00 33.99 2.85
3843 8697 4.962839 TCTGGTACCCCTTATCTTTACCA 58.037 43.478 10.07 0.00 39.90 3.25
3844 8698 5.544682 TCTGGTACCCCTTATCTTTACCAT 58.455 41.667 10.07 0.00 41.03 3.55
3845 8699 5.605488 TCTGGTACCCCTTATCTTTACCATC 59.395 44.000 10.07 0.00 41.03 3.51
3846 8700 4.661709 TGGTACCCCTTATCTTTACCATCC 59.338 45.833 10.07 0.00 37.80 3.51
3847 8701 4.661709 GGTACCCCTTATCTTTACCATCCA 59.338 45.833 0.00 0.00 33.65 3.41
3848 8702 5.312443 GGTACCCCTTATCTTTACCATCCAT 59.688 44.000 0.00 0.00 33.65 3.41
3849 8703 6.183361 GGTACCCCTTATCTTTACCATCCATT 60.183 42.308 0.00 0.00 33.65 3.16
3850 8704 6.355588 ACCCCTTATCTTTACCATCCATTT 57.644 37.500 0.00 0.00 0.00 2.32
3851 8705 6.373759 ACCCCTTATCTTTACCATCCATTTC 58.626 40.000 0.00 0.00 0.00 2.17
3852 8706 6.162241 ACCCCTTATCTTTACCATCCATTTCT 59.838 38.462 0.00 0.00 0.00 2.52
3853 8707 6.491403 CCCCTTATCTTTACCATCCATTTCTG 59.509 42.308 0.00 0.00 0.00 3.02
3854 8708 6.015940 CCCTTATCTTTACCATCCATTTCTGC 60.016 42.308 0.00 0.00 0.00 4.26
3855 8709 6.547141 CCTTATCTTTACCATCCATTTCTGCA 59.453 38.462 0.00 0.00 0.00 4.41
3856 8710 7.232127 CCTTATCTTTACCATCCATTTCTGCAT 59.768 37.037 0.00 0.00 0.00 3.96
3857 8711 6.645790 ATCTTTACCATCCATTTCTGCATC 57.354 37.500 0.00 0.00 0.00 3.91
3858 8712 4.576053 TCTTTACCATCCATTTCTGCATCG 59.424 41.667 0.00 0.00 0.00 3.84
3859 8713 1.027357 ACCATCCATTTCTGCATCGC 58.973 50.000 0.00 0.00 0.00 4.58
3860 8714 0.040692 CCATCCATTTCTGCATCGCG 60.041 55.000 0.00 0.00 0.00 5.87
3861 8715 0.939419 CATCCATTTCTGCATCGCGA 59.061 50.000 13.09 13.09 0.00 5.87
3862 8716 1.534163 CATCCATTTCTGCATCGCGAT 59.466 47.619 17.62 17.62 0.00 4.58
3863 8717 1.220529 TCCATTTCTGCATCGCGATC 58.779 50.000 20.85 14.50 0.00 3.69
3864 8718 1.202568 TCCATTTCTGCATCGCGATCT 60.203 47.619 20.85 0.00 0.00 2.75
3865 8719 1.070108 CCATTTCTGCATCGCGATCTG 60.070 52.381 20.85 12.45 0.00 2.90
3866 8720 1.596260 CATTTCTGCATCGCGATCTGT 59.404 47.619 20.85 0.00 0.00 3.41
3867 8721 1.001624 TTTCTGCATCGCGATCTGTG 58.998 50.000 20.85 11.19 0.00 3.66
3868 8722 1.423721 TTCTGCATCGCGATCTGTGC 61.424 55.000 20.85 21.59 38.05 4.57
3869 8723 2.125592 TGCATCGCGATCTGTGCA 60.126 55.556 26.30 26.30 44.50 4.57
3870 8724 2.169146 TGCATCGCGATCTGTGCAG 61.169 57.895 26.30 12.60 42.13 4.41
3871 8725 1.879884 GCATCGCGATCTGTGCAGA 60.880 57.895 23.50 4.23 42.37 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 8.724229 CAAAACATGATCATCTCTGTTAGTTGA 58.276 33.333 4.86 0.00 38.11 3.18
48 49 5.526479 GCTCTATCTCTGCAAAACATGATCA 59.474 40.000 0.00 0.00 0.00 2.92
84 86 1.617850 CCAAGGCAAATACCAAGCACA 59.382 47.619 0.00 0.00 0.00 4.57
87 89 2.353704 GGAACCAAGGCAAATACCAAGC 60.354 50.000 0.00 0.00 0.00 4.01
88 90 2.896685 TGGAACCAAGGCAAATACCAAG 59.103 45.455 0.00 0.00 0.00 3.61
89 91 2.630580 GTGGAACCAAGGCAAATACCAA 59.369 45.455 0.00 0.00 0.00 3.67
90 92 2.158385 AGTGGAACCAAGGCAAATACCA 60.158 45.455 0.00 0.00 37.80 3.25
243 270 1.004044 CAGCTGGGTGAGTTTCCTGAT 59.996 52.381 5.57 0.00 0.00 2.90
360 387 2.963371 GTTCTCAGCTCCGACCGT 59.037 61.111 0.00 0.00 0.00 4.83
561 588 3.957586 CCACCAGGCACAGCTCCA 61.958 66.667 0.00 0.00 0.00 3.86
618 645 6.173427 ACCAGGTTTGTTATTTTCTGCAAT 57.827 33.333 0.00 0.00 0.00 3.56
625 652 5.356426 GCAACTGACCAGGTTTGTTATTTT 58.644 37.500 9.87 0.00 0.00 1.82
633 660 1.528309 CCCGCAACTGACCAGGTTT 60.528 57.895 0.00 0.00 0.00 3.27
634 661 2.113139 CCCGCAACTGACCAGGTT 59.887 61.111 0.00 0.00 0.00 3.50
660 687 1.227263 CCTAACAGCCGTCGGATGG 60.227 63.158 31.20 14.95 44.23 3.51
760 792 9.202273 GAGTGATTAAGACAGGCTAATCTTATG 57.798 37.037 16.81 0.00 37.29 1.90
763 795 7.430760 AGAGTGATTAAGACAGGCTAATCTT 57.569 36.000 15.28 15.28 38.67 2.40
798 830 2.516460 TAGCCTCCGACCTCGCTC 60.516 66.667 0.00 0.00 38.18 5.03
799 831 2.829458 GTAGCCTCCGACCTCGCT 60.829 66.667 0.00 0.00 38.18 4.93
800 832 2.017559 ATTGTAGCCTCCGACCTCGC 62.018 60.000 0.00 0.00 38.18 5.03
941 2464 3.770424 GTACGCACGGTCCAACGC 61.770 66.667 0.00 0.00 37.37 4.84
942 2465 2.354891 TGTACGCACGGTCCAACG 60.355 61.111 0.00 0.00 40.31 4.10
943 2466 3.237290 GTGTACGCACGGTCCAAC 58.763 61.111 0.39 0.00 35.75 3.77
1126 2655 3.781162 TGTCGTCGTCGCGATCGT 61.781 61.111 23.33 0.00 43.07 3.73
1195 2725 1.517242 GATCGGGATCATGGAAGCAC 58.483 55.000 3.84 0.00 37.74 4.40
1196 2726 0.397941 GGATCGGGATCATGGAAGCA 59.602 55.000 10.57 0.00 39.54 3.91
1197 2727 0.397941 TGGATCGGGATCATGGAAGC 59.602 55.000 10.57 0.00 39.54 3.86
1198 2728 2.936919 TTGGATCGGGATCATGGAAG 57.063 50.000 10.57 0.00 39.54 3.46
1199 2729 3.660970 TTTTGGATCGGGATCATGGAA 57.339 42.857 10.57 0.00 39.54 3.53
1200 2730 3.882102 ATTTTGGATCGGGATCATGGA 57.118 42.857 10.57 0.00 39.54 3.41
1201 2731 4.655963 ACTATTTTGGATCGGGATCATGG 58.344 43.478 10.57 0.98 39.54 3.66
1202 2732 6.230472 TGTACTATTTTGGATCGGGATCATG 58.770 40.000 10.57 0.00 39.54 3.07
1203 2733 6.433847 TGTACTATTTTGGATCGGGATCAT 57.566 37.500 10.57 0.00 39.54 2.45
1204 2734 5.880164 TGTACTATTTTGGATCGGGATCA 57.120 39.130 10.57 0.00 39.54 2.92
1205 2735 8.095169 ACTAATGTACTATTTTGGATCGGGATC 58.905 37.037 0.00 0.00 37.11 3.36
1206 2736 7.878127 CACTAATGTACTATTTTGGATCGGGAT 59.122 37.037 0.00 0.00 0.00 3.85
1207 2737 7.070198 TCACTAATGTACTATTTTGGATCGGGA 59.930 37.037 0.00 0.00 0.00 5.14
1208 2738 7.214381 TCACTAATGTACTATTTTGGATCGGG 58.786 38.462 0.00 0.00 0.00 5.14
1209 2739 8.548721 GTTCACTAATGTACTATTTTGGATCGG 58.451 37.037 0.00 0.00 0.00 4.18
1210 2740 9.314321 AGTTCACTAATGTACTATTTTGGATCG 57.686 33.333 0.00 0.00 34.92 3.69
1213 2743 8.726988 GCAAGTTCACTAATGTACTATTTTGGA 58.273 33.333 0.00 0.00 35.57 3.53
1214 2744 7.968405 GGCAAGTTCACTAATGTACTATTTTGG 59.032 37.037 0.00 0.00 35.57 3.28
1215 2745 8.511321 TGGCAAGTTCACTAATGTACTATTTTG 58.489 33.333 0.00 0.00 35.57 2.44
1216 2746 8.630054 TGGCAAGTTCACTAATGTACTATTTT 57.370 30.769 0.00 0.00 35.57 1.82
1217 2747 8.807948 ATGGCAAGTTCACTAATGTACTATTT 57.192 30.769 0.00 0.00 35.57 1.40
1218 2748 7.224753 CGATGGCAAGTTCACTAATGTACTATT 59.775 37.037 0.00 0.00 35.57 1.73
1219 2749 6.701841 CGATGGCAAGTTCACTAATGTACTAT 59.298 38.462 0.00 0.00 35.57 2.12
1220 2750 6.040247 CGATGGCAAGTTCACTAATGTACTA 58.960 40.000 0.00 0.00 35.57 1.82
1221 2751 4.870426 CGATGGCAAGTTCACTAATGTACT 59.130 41.667 0.00 0.00 38.02 2.73
1222 2752 4.034048 CCGATGGCAAGTTCACTAATGTAC 59.966 45.833 0.00 0.00 0.00 2.90
1223 2753 4.188462 CCGATGGCAAGTTCACTAATGTA 58.812 43.478 0.00 0.00 0.00 2.29
1224 2754 3.009723 CCGATGGCAAGTTCACTAATGT 58.990 45.455 0.00 0.00 0.00 2.71
1225 2755 2.355756 CCCGATGGCAAGTTCACTAATG 59.644 50.000 0.00 0.00 0.00 1.90
1226 2756 2.238646 TCCCGATGGCAAGTTCACTAAT 59.761 45.455 0.00 0.00 0.00 1.73
1227 2757 1.626321 TCCCGATGGCAAGTTCACTAA 59.374 47.619 0.00 0.00 0.00 2.24
1228 2758 1.271856 TCCCGATGGCAAGTTCACTA 58.728 50.000 0.00 0.00 0.00 2.74
1229 2759 0.620556 ATCCCGATGGCAAGTTCACT 59.379 50.000 0.00 0.00 0.00 3.41
1262 2824 5.505181 TTAGAGAAGGACAAGGCAGAAAT 57.495 39.130 0.00 0.00 0.00 2.17
1289 2853 8.422577 AAGCCAAACAGGATTATTACTTTTCT 57.577 30.769 0.00 0.00 46.15 2.52
1378 2946 1.001706 CCAGTGCTGCATCATATGTGC 60.002 52.381 17.91 17.91 42.81 4.57
1586 3157 0.539438 ACCGTACACAGGAACCCGTA 60.539 55.000 0.00 0.00 0.00 4.02
1591 3162 5.124457 TGTTAGATCTACCGTACACAGGAAC 59.876 44.000 0.67 0.00 0.00 3.62
1592 3163 5.255687 TGTTAGATCTACCGTACACAGGAA 58.744 41.667 0.67 0.00 0.00 3.36
1593 3164 4.847198 TGTTAGATCTACCGTACACAGGA 58.153 43.478 0.67 0.00 0.00 3.86
1594 3165 5.298527 TCATGTTAGATCTACCGTACACAGG 59.701 44.000 0.67 5.22 0.00 4.00
1595 3166 6.038382 ACTCATGTTAGATCTACCGTACACAG 59.962 42.308 0.67 6.72 0.00 3.66
1596 3167 5.884232 ACTCATGTTAGATCTACCGTACACA 59.116 40.000 0.67 3.55 0.00 3.72
1597 3168 6.374565 ACTCATGTTAGATCTACCGTACAC 57.625 41.667 0.67 0.00 0.00 2.90
1598 3169 8.155510 AGATACTCATGTTAGATCTACCGTACA 58.844 37.037 0.67 4.69 0.00 2.90
1599 3170 8.444715 CAGATACTCATGTTAGATCTACCGTAC 58.555 40.741 0.67 0.00 0.00 3.67
1600 3171 7.119407 GCAGATACTCATGTTAGATCTACCGTA 59.881 40.741 0.67 0.00 0.00 4.02
1601 3172 6.072397 GCAGATACTCATGTTAGATCTACCGT 60.072 42.308 0.67 0.00 0.00 4.83
1602 3173 6.072452 TGCAGATACTCATGTTAGATCTACCG 60.072 42.308 0.67 0.00 0.00 4.02
1603 3174 7.220741 TGCAGATACTCATGTTAGATCTACC 57.779 40.000 0.67 0.00 0.00 3.18
1604 3175 7.328249 GCTTGCAGATACTCATGTTAGATCTAC 59.672 40.741 0.67 0.00 0.00 2.59
1612 3183 3.678289 TGTGCTTGCAGATACTCATGTT 58.322 40.909 0.00 0.00 0.00 2.71
1735 3347 2.229784 ACACTGCCAATAAGCTCAAAGC 59.770 45.455 0.00 0.00 42.84 3.51
1842 3459 4.166144 TCCCAAGAACAAGGAGAAACTTCT 59.834 41.667 0.00 0.00 41.00 2.85
1846 3463 4.584743 ACATTCCCAAGAACAAGGAGAAAC 59.415 41.667 0.00 0.00 33.97 2.78
1854 3471 3.572255 GGCAAGTACATTCCCAAGAACAA 59.428 43.478 0.00 0.00 33.97 2.83
1868 3485 4.159879 ACATGACACCTACTAGGCAAGTAC 59.840 45.833 0.00 0.00 39.63 2.73
1871 3493 3.895232 ACATGACACCTACTAGGCAAG 57.105 47.619 0.00 0.00 39.63 4.01
1948 3570 5.590259 AGTTATGGTCTTGTATGGCAATGTC 59.410 40.000 0.00 0.00 36.36 3.06
2003 3710 1.208052 TGGACCATAGTCAGAGCAAGC 59.792 52.381 0.00 0.00 45.48 4.01
2022 3772 4.450976 TGCTAATGTGTAAGGCCATACTG 58.549 43.478 18.39 4.24 0.00 2.74
2076 3828 0.687354 AGAGCGGTCATGGACAACTT 59.313 50.000 18.15 0.00 33.68 2.66
2077 3829 1.478510 CTAGAGCGGTCATGGACAACT 59.521 52.381 18.15 0.00 33.68 3.16
2216 3974 0.324943 GGAGCTGCACTTCAGGGTTA 59.675 55.000 0.00 0.00 43.06 2.85
2310 4070 1.263356 AAGAACCGATTCGTCCAGGA 58.737 50.000 5.20 0.00 40.04 3.86
2326 4086 0.979665 CCCTGCTCTCAGTCCAAAGA 59.020 55.000 0.00 0.00 38.66 2.52
2335 4095 3.062466 CCGACGTCCCTGCTCTCA 61.062 66.667 10.58 0.00 0.00 3.27
2519 4279 4.626042 CAAGCGCAGGAGATAAAGTAGAT 58.374 43.478 11.47 0.00 0.00 1.98
2595 4365 9.860898 ATGAGAAGAAACAAATAGCAATTAACC 57.139 29.630 0.00 0.00 0.00 2.85
2605 4375 7.975616 GCCTATTTGCATGAGAAGAAACAAATA 59.024 33.333 0.00 4.05 38.36 1.40
2630 4400 3.377172 ACTTTATGTTTGAGCGGGTATGC 59.623 43.478 0.00 0.00 0.00 3.14
2673 4517 7.329226 CCAAATTGTAACAGAAATACCTTGCTG 59.671 37.037 0.00 0.00 34.65 4.41
2718 4562 1.293924 CATCGTTCCTGCCATCAGTC 58.706 55.000 0.00 0.00 38.66 3.51
2750 4594 1.199624 GCGCTGTTTGAACCAACAAG 58.800 50.000 0.00 0.00 0.00 3.16
2831 4675 5.250235 TCAAACAAAACAGAAATACCGCA 57.750 34.783 0.00 0.00 0.00 5.69
2886 4730 9.719355 TCACACATAATCTACGCCAATAAATAT 57.281 29.630 0.00 0.00 0.00 1.28
2887 4731 9.719355 ATCACACATAATCTACGCCAATAAATA 57.281 29.630 0.00 0.00 0.00 1.40
2918 4764 1.001048 CAAGCACTGGTGTGTTCATGG 60.001 52.381 2.64 0.00 45.44 3.66
2927 4773 4.700268 TGCATAATAACAAGCACTGGTG 57.300 40.909 0.00 0.00 31.05 4.17
3006 4857 9.130312 GATAGATCTCCGTTACAACAATATGAC 57.870 37.037 0.00 0.00 0.00 3.06
3125 4988 5.706833 TGCAAATGACATGTACTTGTCTGAT 59.293 36.000 30.72 19.83 45.07 2.90
3133 4996 7.750458 CGTAGAAATTTGCAAATGACATGTACT 59.250 33.333 24.74 15.56 0.00 2.73
3153 5016 1.515081 CTTGGGTTTTCGCCGTAGAA 58.485 50.000 0.00 0.00 0.00 2.10
3182 5045 4.871557 AGCACTCAACGTGTTTTTGTACTA 59.128 37.500 0.00 0.00 45.57 1.82
3195 5058 3.492313 GCCAGAAAATAAGCACTCAACG 58.508 45.455 0.00 0.00 0.00 4.10
3200 5063 1.826385 AGCGCCAGAAAATAAGCACT 58.174 45.000 2.29 0.00 0.00 4.40
3229 5092 3.173953 TGTGCTTCATGAGGGGAAAAT 57.826 42.857 6.99 0.00 0.00 1.82
3234 5097 2.165030 GACAATTGTGCTTCATGAGGGG 59.835 50.000 17.58 0.00 0.00 4.79
3269 5132 6.208402 TGTTTGATGTGCTCTTGCCTATTTTA 59.792 34.615 0.00 0.00 38.71 1.52
3275 5138 1.610522 GTGTTTGATGTGCTCTTGCCT 59.389 47.619 0.00 0.00 38.71 4.75
3280 5143 7.607607 TGTTCATATTAGTGTTTGATGTGCTCT 59.392 33.333 0.00 0.00 0.00 4.09
3347 5210 3.816523 CAGCAAATTCAAACAAATGGGCT 59.183 39.130 0.00 0.00 32.30 5.19
3348 5211 3.565063 ACAGCAAATTCAAACAAATGGGC 59.435 39.130 0.00 0.00 0.00 5.36
3350 5213 5.006552 ACGAACAGCAAATTCAAACAAATGG 59.993 36.000 0.00 0.00 0.00 3.16
3367 5230 1.204704 TGATAGTCCTGGCACGAACAG 59.795 52.381 0.00 0.00 35.74 3.16
3369 5232 2.474816 GATGATAGTCCTGGCACGAAC 58.525 52.381 0.00 0.00 0.00 3.95
3371 5234 1.040646 GGATGATAGTCCTGGCACGA 58.959 55.000 0.00 0.00 35.32 4.35
3372 5235 1.043816 AGGATGATAGTCCTGGCACG 58.956 55.000 0.00 0.00 46.76 5.34
3401 5264 1.203287 CTGCACCTCGAAGATCTCACA 59.797 52.381 0.00 0.00 33.89 3.58
3412 5275 1.728971 GATCAAAGTGTCTGCACCTCG 59.271 52.381 0.00 0.00 46.35 4.63
3474 5339 4.803452 TCTGTTTTTGAGGGACCTTCAAT 58.197 39.130 18.83 0.00 0.00 2.57
3488 5354 6.424032 ACCTTCAGTACTTCCTTCTGTTTTT 58.576 36.000 0.00 0.00 0.00 1.94
3495 5362 3.259625 AGCTGACCTTCAGTACTTCCTTC 59.740 47.826 5.14 0.00 45.94 3.46
3498 5365 2.933056 GCAGCTGACCTTCAGTACTTCC 60.933 54.545 20.43 0.00 45.94 3.46
3507 5376 1.364626 CGACATGGCAGCTGACCTTC 61.365 60.000 19.23 9.62 0.00 3.46
3515 5384 1.089920 ATGAGAAACGACATGGCAGC 58.910 50.000 0.00 0.00 0.00 5.25
3516 5385 1.202110 GCATGAGAAACGACATGGCAG 60.202 52.381 0.00 0.00 42.53 4.85
3520 5389 3.187022 TCAACTGCATGAGAAACGACATG 59.813 43.478 0.00 0.00 44.32 3.21
3527 5396 6.829811 TGGAATCATATCAACTGCATGAGAAA 59.170 34.615 0.00 0.00 32.51 2.52
3562 5442 5.082425 AGCTGGAATGAGAAAAGTGGAATT 58.918 37.500 0.00 0.00 0.00 2.17
3780 8634 5.109662 ACCACACTCGATTGATATAGACG 57.890 43.478 10.04 0.00 0.00 4.18
3793 8647 2.731976 GAGCTACAGAAAACCACACTCG 59.268 50.000 0.00 0.00 0.00 4.18
3794 8648 3.728845 TGAGCTACAGAAAACCACACTC 58.271 45.455 0.00 0.00 0.00 3.51
3795 8649 3.838244 TGAGCTACAGAAAACCACACT 57.162 42.857 0.00 0.00 0.00 3.55
3796 8650 3.304057 GCTTGAGCTACAGAAAACCACAC 60.304 47.826 0.00 0.00 38.21 3.82
3797 8651 2.878406 GCTTGAGCTACAGAAAACCACA 59.122 45.455 0.00 0.00 38.21 4.17
3798 8652 3.544356 GCTTGAGCTACAGAAAACCAC 57.456 47.619 0.00 0.00 38.21 4.16
3825 8679 5.899631 TGGATGGTAAAGATAAGGGGTAC 57.100 43.478 0.00 0.00 0.00 3.34
3826 8680 7.352522 AGAAATGGATGGTAAAGATAAGGGGTA 59.647 37.037 0.00 0.00 0.00 3.69
3827 8681 6.162241 AGAAATGGATGGTAAAGATAAGGGGT 59.838 38.462 0.00 0.00 0.00 4.95
3828 8682 6.491403 CAGAAATGGATGGTAAAGATAAGGGG 59.509 42.308 0.00 0.00 0.00 4.79
3829 8683 6.015940 GCAGAAATGGATGGTAAAGATAAGGG 60.016 42.308 0.00 0.00 0.00 3.95
3830 8684 6.547141 TGCAGAAATGGATGGTAAAGATAAGG 59.453 38.462 0.00 0.00 0.00 2.69
3831 8685 7.572523 TGCAGAAATGGATGGTAAAGATAAG 57.427 36.000 0.00 0.00 0.00 1.73
3832 8686 7.041167 CGATGCAGAAATGGATGGTAAAGATAA 60.041 37.037 0.00 0.00 0.00 1.75
3833 8687 6.427853 CGATGCAGAAATGGATGGTAAAGATA 59.572 38.462 0.00 0.00 0.00 1.98
3834 8688 5.240183 CGATGCAGAAATGGATGGTAAAGAT 59.760 40.000 0.00 0.00 0.00 2.40
3835 8689 4.576053 CGATGCAGAAATGGATGGTAAAGA 59.424 41.667 0.00 0.00 0.00 2.52
3836 8690 4.790766 GCGATGCAGAAATGGATGGTAAAG 60.791 45.833 0.00 0.00 0.00 1.85
3837 8691 3.066621 GCGATGCAGAAATGGATGGTAAA 59.933 43.478 0.00 0.00 0.00 2.01
3838 8692 2.618241 GCGATGCAGAAATGGATGGTAA 59.382 45.455 0.00 0.00 0.00 2.85
3839 8693 2.221169 GCGATGCAGAAATGGATGGTA 58.779 47.619 0.00 0.00 0.00 3.25
3840 8694 1.027357 GCGATGCAGAAATGGATGGT 58.973 50.000 0.00 0.00 0.00 3.55
3841 8695 0.040692 CGCGATGCAGAAATGGATGG 60.041 55.000 0.00 0.00 0.00 3.51
3842 8696 0.939419 TCGCGATGCAGAAATGGATG 59.061 50.000 3.71 0.00 0.00 3.51
3843 8697 1.802960 GATCGCGATGCAGAAATGGAT 59.197 47.619 29.09 0.00 0.00 3.41
3844 8698 1.202568 AGATCGCGATGCAGAAATGGA 60.203 47.619 29.09 0.00 0.00 3.41
3845 8699 1.070108 CAGATCGCGATGCAGAAATGG 60.070 52.381 29.09 0.93 0.00 3.16
3846 8700 1.596260 ACAGATCGCGATGCAGAAATG 59.404 47.619 29.09 14.53 0.00 2.32
3847 8701 1.596260 CACAGATCGCGATGCAGAAAT 59.404 47.619 29.09 0.00 0.00 2.17
3848 8702 1.001624 CACAGATCGCGATGCAGAAA 58.998 50.000 29.09 0.00 0.00 2.52
3849 8703 1.423721 GCACAGATCGCGATGCAGAA 61.424 55.000 29.09 0.00 38.00 3.02
3850 8704 1.879884 GCACAGATCGCGATGCAGA 60.880 57.895 29.09 0.00 38.00 4.26
3851 8705 2.169146 TGCACAGATCGCGATGCAG 61.169 57.895 29.09 17.58 42.92 4.41
3852 8706 2.125592 TGCACAGATCGCGATGCA 60.126 55.556 29.09 27.46 45.45 3.96
3853 8707 1.220169 ATCTGCACAGATCGCGATGC 61.220 55.000 29.09 25.03 44.37 3.91
3854 8708 1.718178 GTATCTGCACAGATCGCGATG 59.282 52.381 29.09 17.80 44.37 3.84
3855 8709 1.338020 TGTATCTGCACAGATCGCGAT 59.662 47.619 23.97 23.97 44.37 4.58
3856 8710 0.738389 TGTATCTGCACAGATCGCGA 59.262 50.000 13.09 13.09 44.37 5.87
3857 8711 1.775869 ATGTATCTGCACAGATCGCG 58.224 50.000 16.15 0.00 44.37 5.87
3858 8712 3.310774 ACAAATGTATCTGCACAGATCGC 59.689 43.478 16.15 11.20 44.37 4.58
3859 8713 5.475273 AACAAATGTATCTGCACAGATCG 57.525 39.130 16.15 3.30 44.37 3.69


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

AutoCloner maintained by Alex Coulton.