Multiple sequence alignment - TraesCS2D01G120200

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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 TraesCS2D01G120200 chr2D 100.000 5333 0 0 2122 7454 69509244 69503912 0.000000e+00 9849.0
1 TraesCS2D01G120200 chr2D 100.000 1521 0 0 1 1521 69511365 69509845 0.000000e+00 2809.0
2 TraesCS2D01G120200 chr2D 95.775 71 3 0 3065 3135 69508230 69508160 1.700000e-21 115.0
3 TraesCS2D01G120200 chr2D 95.775 71 3 0 3136 3206 69508301 69508231 1.700000e-21 115.0
4 TraesCS2D01G120200 chr2D 100.000 29 0 0 693 721 69510640 69510612 4.000000e-03 54.7
5 TraesCS2D01G120200 chr2D 100.000 29 0 0 726 754 69510673 69510645 4.000000e-03 54.7
6 TraesCS2D01G120200 chr2B 93.200 2250 98 22 5150 7370 105910553 105908330 0.000000e+00 3256.0
7 TraesCS2D01G120200 chr2B 92.024 1329 69 15 3815 5121 105911964 105910651 0.000000e+00 1832.0
8 TraesCS2D01G120200 chr2B 94.975 1015 47 3 2122 3135 105913500 105912489 0.000000e+00 1589.0
9 TraesCS2D01G120200 chr2B 94.807 597 17 8 3136 3724 105912559 105911969 0.000000e+00 918.0
10 TraesCS2D01G120200 chr2B 85.132 760 57 29 726 1450 105915284 105914546 0.000000e+00 726.0
11 TraesCS2D01G120200 chr2B 88.966 435 44 4 292 725 105915683 105915252 1.100000e-147 534.0
12 TraesCS2D01G120200 chr2B 94.245 278 14 2 7 282 105916191 105915914 2.490000e-114 424.0
13 TraesCS2D01G120200 chr2B 98.667 75 1 0 7380 7454 105908283 105908209 4.690000e-27 134.0
14 TraesCS2D01G120200 chr2B 94.872 39 2 0 5121 5159 105910604 105910566 2.250000e-05 62.1
15 TraesCS2D01G120200 chr2A 94.862 1635 51 13 5246 6857 69326629 69325005 0.000000e+00 2523.0
16 TraesCS2D01G120200 chr2A 94.350 1522 70 6 2133 3654 69330585 69329080 0.000000e+00 2320.0
17 TraesCS2D01G120200 chr2A 94.343 1096 51 9 3815 4907 69328823 69327736 0.000000e+00 1670.0
18 TraesCS2D01G120200 chr2A 92.375 682 42 6 6780 7454 69325014 69324336 0.000000e+00 963.0
19 TraesCS2D01G120200 chr2A 82.127 442 41 16 4 410 69334522 69334084 1.990000e-90 344.0
20 TraesCS2D01G120200 chr2A 91.705 217 10 4 4911 5121 69327096 69326882 2.030000e-75 294.0
21 TraesCS2D01G120200 chr2A 92.500 200 6 3 1141 1340 69331737 69331547 2.050000e-70 278.0
22 TraesCS2D01G120200 chr2A 95.833 120 5 0 5130 5249 69326829 69326710 2.120000e-45 195.0
23 TraesCS2D01G120200 chr2A 95.506 89 4 0 3637 3725 69328909 69328821 7.800000e-30 143.0
24 TraesCS2D01G120200 chr2A 97.222 72 2 0 3064 3135 69329584 69329513 1.020000e-23 122.0
25 TraesCS2D01G120200 chr2A 94.286 70 4 0 3136 3205 69329654 69329585 2.840000e-19 108.0
26 TraesCS2D01G120200 chr4D 81.931 725 109 16 2140 2858 173572943 173573651 1.790000e-165 593.0
27 TraesCS2D01G120200 chr4A 81.481 729 106 16 2140 2861 227093922 227093216 8.390000e-159 571.0
28 TraesCS2D01G120200 chr4A 86.842 114 7 5 3720 3828 133061493 133061383 3.650000e-23 121.0
29 TraesCS2D01G120200 chr4B 81.044 728 116 16 2140 2861 246319269 246318558 1.820000e-155 560.0
30 TraesCS2D01G120200 chr7B 87.861 173 15 1 3149 3321 628988101 628987935 1.640000e-46 198.0
31 TraesCS2D01G120200 chr7B 94.828 58 3 0 3078 3135 628988101 628988044 2.860000e-14 91.6
32 TraesCS2D01G120200 chr5D 90.816 98 4 2 3723 3816 65990491 65990587 7.850000e-25 126.0
33 TraesCS2D01G120200 chr5D 90.816 98 4 2 3723 3816 558970435 558970531 7.850000e-25 126.0
34 TraesCS2D01G120200 chr5A 90.722 97 5 2 3723 3816 239529841 239529936 7.850000e-25 126.0
35 TraesCS2D01G120200 chr5A 88.462 104 7 2 3720 3819 593472224 593472326 3.650000e-23 121.0
36 TraesCS2D01G120200 chr5B 89.216 102 6 2 3720 3817 316712602 316712702 1.020000e-23 122.0
37 TraesCS2D01G120200 chr7D 87.850 107 7 3 3723 3824 168579919 168580024 3.650000e-23 121.0
38 TraesCS2D01G120200 chr7D 89.796 98 5 2 3723 3816 454663644 454663740 3.650000e-23 121.0
39 TraesCS2D01G120200 chr3D 88.235 102 8 4 3723 3822 92122349 92122250 1.310000e-22 119.0
40 TraesCS2D01G120200 chr3D 89.130 46 4 1 4970 5015 118540060 118540016 1.000000e-03 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G120200 chr2D 69503912 69511365 7453 True 2166.233333 9849 98.591667 1 7454 6 chr2D.!!$R1 7453
1 TraesCS2D01G120200 chr2B 105908209 105916191 7982 True 1052.788889 3256 92.987556 7 7454 9 chr2B.!!$R1 7447
2 TraesCS2D01G120200 chr2A 69324336 69334522 10186 True 814.545455 2523 93.191727 4 7454 11 chr2A.!!$R1 7450
3 TraesCS2D01G120200 chr4D 173572943 173573651 708 False 593.000000 593 81.931000 2140 2858 1 chr4D.!!$F1 718
4 TraesCS2D01G120200 chr4A 227093216 227093922 706 True 571.000000 571 81.481000 2140 2861 1 chr4A.!!$R2 721
5 TraesCS2D01G120200 chr4B 246318558 246319269 711 True 560.000000 560 81.044000 2140 2861 1 chr4B.!!$R1 721

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
285 302 0.193574 TATCACATCCCCCTCCCCTC 59.806 60.000 0.00 0.0 0.00 4.30 F
734 1022 0.381089 GCGTACAGTAGACCGCAGAT 59.619 55.000 8.72 0.0 45.12 2.90 F
1216 3123 0.178950 AGAGAGACACAGGTGCAGGA 60.179 55.000 0.00 0.0 0.00 3.86 F
2165 4899 1.082104 GCAAGGCACGTACAGCAAC 60.082 57.895 9.23 0.0 0.00 4.17 F
3737 6669 0.531200 GTGTTACTCCCTCTGTCCCG 59.469 60.000 0.00 0.0 0.00 5.14 F
3818 6750 0.042131 TTGGGACGGAGGGAGTACAT 59.958 55.000 0.00 0.0 0.00 2.29 F
4988 8573 0.248289 AACTAGCATAACGCCCGTGT 59.752 50.000 0.00 0.0 44.04 4.49 F
6128 9943 0.825425 TTTTCCCGCTTGCCATGTCA 60.825 50.000 0.00 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1122 1489 0.387202 CAGCGGAGTGGAGTATGAGG 59.613 60.0 0.00 0.00 0.00 3.86 R
2487 5224 0.317160 CTCGACCAGCTACACCACAA 59.683 55.0 0.00 0.00 0.00 3.33 R
2500 5237 0.378962 CACCTCGATCAGACTCGACC 59.621 60.0 0.00 0.00 42.38 4.79 R
3799 6731 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.0 0.00 0.00 0.00 4.12 R
5159 8847 0.392998 GGATTTTCTCCCTGCAGCGA 60.393 55.0 8.66 4.15 38.19 4.93 R
5634 9441 1.601419 TACGGCTAGCACCCACTGAC 61.601 60.0 18.24 0.00 0.00 3.51 R
6411 10227 0.511653 GTTGTTTCGAAGAGCGTCCC 59.488 55.0 0.00 0.00 41.80 4.46 R
7255 11153 0.323725 ACAAGATGTGTCCATGGGGC 60.324 55.0 13.02 6.08 34.38 5.80 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 81 6.947733 ACAATTGTCATCTTCCTTAACCATCA 59.052 34.615 4.92 0.00 0.00 3.07
105 106 1.765904 TGAGCTGTGGTGGTTCTGTAA 59.234 47.619 0.00 0.00 0.00 2.41
176 187 0.433492 CGTCGCGTCGAAGTCAAAAT 59.567 50.000 20.81 0.00 37.72 1.82
224 237 2.222027 CATATTTGCTCCGTCCCCTTC 58.778 52.381 0.00 0.00 0.00 3.46
229 242 3.083997 CTCCGTCCCCTTCCCCTG 61.084 72.222 0.00 0.00 0.00 4.45
257 274 0.958091 GTTGCCAGGCACAACATACA 59.042 50.000 15.89 0.00 45.35 2.29
285 302 0.193574 TATCACATCCCCCTCCCCTC 59.806 60.000 0.00 0.00 0.00 4.30
286 303 1.913321 ATCACATCCCCCTCCCCTCA 61.913 60.000 0.00 0.00 0.00 3.86
408 649 4.518211 GGAGCAAGTAATCATCCCATGAAG 59.482 45.833 0.00 0.00 43.50 3.02
522 805 9.974980 TCTTCTCCCAAAACATAAATTTACAAC 57.025 29.630 0.00 0.00 0.00 3.32
526 810 6.421202 TCCCAAAACATAAATTTACAACGTGC 59.579 34.615 0.00 0.00 0.00 5.34
538 822 3.827008 ACAACGTGCCATCATCTCTAT 57.173 42.857 0.00 0.00 0.00 1.98
539 823 4.142609 ACAACGTGCCATCATCTCTATT 57.857 40.909 0.00 0.00 0.00 1.73
552 836 4.893524 TCATCTCTATTGTACCACCGTCAT 59.106 41.667 0.00 0.00 0.00 3.06
561 845 4.808558 TGTACCACCGTCATACAGTTTAC 58.191 43.478 0.00 0.00 0.00 2.01
596 881 1.665442 GGTTCCATGCACACAACCC 59.335 57.895 10.25 0.00 33.42 4.11
597 882 0.827507 GGTTCCATGCACACAACCCT 60.828 55.000 10.25 0.00 33.42 4.34
598 883 1.546773 GGTTCCATGCACACAACCCTA 60.547 52.381 10.25 0.00 33.42 3.53
599 884 2.446435 GTTCCATGCACACAACCCTAT 58.554 47.619 0.00 0.00 0.00 2.57
606 891 2.004733 GCACACAACCCTATAACGACC 58.995 52.381 0.00 0.00 0.00 4.79
608 896 2.997986 CACACAACCCTATAACGACCAC 59.002 50.000 0.00 0.00 0.00 4.16
645 933 3.194968 TCGCTTTCGATAAGAACCCTCTT 59.805 43.478 10.34 0.00 41.35 2.85
652 940 5.258841 TCGATAAGAACCCTCTTACAGTCA 58.741 41.667 0.00 0.00 44.94 3.41
658 946 2.789409 CCCTCTTACAGTCAAAGGGG 57.211 55.000 6.26 1.37 43.24 4.79
722 1010 2.096335 TGTACATACACCTCGCGTACAG 59.904 50.000 5.77 0.00 37.95 2.74
725 1013 2.353889 ACATACACCTCGCGTACAGTAG 59.646 50.000 5.77 0.00 0.00 2.57
726 1014 2.385013 TACACCTCGCGTACAGTAGA 57.615 50.000 5.77 0.00 0.00 2.59
727 1015 0.801251 ACACCTCGCGTACAGTAGAC 59.199 55.000 5.77 0.00 0.00 2.59
730 1018 1.297451 CTCGCGTACAGTAGACCGC 60.297 63.158 5.77 4.38 42.53 5.68
732 1020 1.582937 CGCGTACAGTAGACCGCAG 60.583 63.158 12.87 4.11 46.02 5.18
733 1021 1.798735 GCGTACAGTAGACCGCAGA 59.201 57.895 8.72 0.00 45.12 4.26
734 1022 0.381089 GCGTACAGTAGACCGCAGAT 59.619 55.000 8.72 0.00 45.12 2.90
735 1023 1.860399 GCGTACAGTAGACCGCAGATG 60.860 57.143 8.72 0.00 45.12 2.90
736 1024 1.400846 CGTACAGTAGACCGCAGATGT 59.599 52.381 0.00 0.00 0.00 3.06
738 1026 3.545624 CGTACAGTAGACCGCAGATGTAC 60.546 52.174 0.00 0.00 0.00 2.90
739 1027 2.443416 ACAGTAGACCGCAGATGTACA 58.557 47.619 0.00 0.00 0.00 2.90
740 1028 3.024547 ACAGTAGACCGCAGATGTACAT 58.975 45.455 8.43 8.43 0.00 2.29
741 1029 4.204799 ACAGTAGACCGCAGATGTACATA 58.795 43.478 8.71 0.00 0.00 2.29
743 1031 4.036380 CAGTAGACCGCAGATGTACATACA 59.964 45.833 8.71 0.00 40.98 2.29
744 1032 3.438297 AGACCGCAGATGTACATACAC 57.562 47.619 8.71 0.00 39.30 2.90
749 1037 2.128035 GCAGATGTACATACACCTCGC 58.872 52.381 8.71 4.98 39.30 5.03
751 1039 2.022195 AGATGTACATACACCTCGCGT 58.978 47.619 8.71 0.00 39.30 6.01
753 1041 2.830772 TGTACATACACCTCGCGTAC 57.169 50.000 5.77 0.00 34.40 3.67
754 1042 2.358957 TGTACATACACCTCGCGTACT 58.641 47.619 5.77 0.00 34.80 2.73
755 1043 3.530535 TGTACATACACCTCGCGTACTA 58.469 45.455 5.77 0.00 34.80 1.82
756 1044 4.129380 TGTACATACACCTCGCGTACTAT 58.871 43.478 5.77 0.00 34.80 2.12
757 1045 3.620929 ACATACACCTCGCGTACTATG 57.379 47.619 5.77 8.04 0.00 2.23
758 1046 3.208594 ACATACACCTCGCGTACTATGA 58.791 45.455 5.77 0.00 0.00 2.15
761 1049 5.471116 ACATACACCTCGCGTACTATGAATA 59.529 40.000 5.77 0.00 0.00 1.75
772 1060 7.271868 TCGCGTACTATGAATATCATTTTACCG 59.728 37.037 5.77 6.79 38.26 4.02
796 1084 2.635444 CCTTAAAAATATCACCGCGCG 58.365 47.619 25.67 25.67 0.00 6.86
826 1115 2.476241 CACGCAAGCCCTTTTGAAATTC 59.524 45.455 0.00 0.00 45.62 2.17
827 1116 1.720852 CGCAAGCCCTTTTGAAATTCG 59.279 47.619 0.00 0.00 0.00 3.34
828 1117 2.754472 GCAAGCCCTTTTGAAATTCGT 58.246 42.857 0.00 0.00 0.00 3.85
852 1141 8.879759 CGTATTAGGCAAAAGATTCTAAGTTCA 58.120 33.333 0.00 0.00 0.00 3.18
883 1183 8.885722 ACTATAAACGAAAGAAACAACAAGACA 58.114 29.630 0.00 0.00 0.00 3.41
900 1200 7.725818 ACAAGACATATCATGAGCATACTTG 57.274 36.000 21.72 21.72 37.56 3.16
920 1220 4.617253 TGCATAACATATACCCGCTCTT 57.383 40.909 0.00 0.00 0.00 2.85
953 1261 1.537289 CCGTCCGCACATCGATTACG 61.537 60.000 0.00 0.00 41.67 3.18
996 1305 4.387862 AGGATACGTCAACATCACGAAAAC 59.612 41.667 0.00 0.00 46.39 2.43
1002 1311 1.978097 CAACATCACGAAAACGCCATG 59.022 47.619 0.00 0.00 0.00 3.66
1003 1312 1.234821 ACATCACGAAAACGCCATGT 58.765 45.000 0.00 0.00 0.00 3.21
1072 1384 7.589574 AAACGCAAACCAATAATCAAATACC 57.410 32.000 0.00 0.00 0.00 2.73
1122 1489 9.590451 TTTTTATCATGATGCATTTTCCTCTTC 57.410 29.630 18.72 0.00 0.00 2.87
1125 1492 4.885907 TCATGATGCATTTTCCTCTTCCTC 59.114 41.667 0.00 0.00 0.00 3.71
1126 1493 4.305539 TGATGCATTTTCCTCTTCCTCA 57.694 40.909 0.00 0.00 0.00 3.86
1128 1495 6.005066 TGATGCATTTTCCTCTTCCTCATA 57.995 37.500 0.00 0.00 0.00 2.15
1129 1496 5.824624 TGATGCATTTTCCTCTTCCTCATAC 59.175 40.000 0.00 0.00 0.00 2.39
1131 1498 5.431765 TGCATTTTCCTCTTCCTCATACTC 58.568 41.667 0.00 0.00 0.00 2.59
1132 1499 4.819088 GCATTTTCCTCTTCCTCATACTCC 59.181 45.833 0.00 0.00 0.00 3.85
1134 1501 5.422214 TTTTCCTCTTCCTCATACTCCAC 57.578 43.478 0.00 0.00 0.00 4.02
1135 1502 4.338795 TTCCTCTTCCTCATACTCCACT 57.661 45.455 0.00 0.00 0.00 4.00
1136 1503 3.904717 TCCTCTTCCTCATACTCCACTC 58.095 50.000 0.00 0.00 0.00 3.51
1139 3046 1.067821 CTTCCTCATACTCCACTCCGC 59.932 57.143 0.00 0.00 0.00 5.54
1210 3117 1.077828 TCCATCCAGAGAGACACAGGT 59.922 52.381 0.00 0.00 0.00 4.00
1216 3123 0.178950 AGAGAGACACAGGTGCAGGA 60.179 55.000 0.00 0.00 0.00 3.86
1253 3160 2.092861 TCCGAGTCAAAACCAGAACCAA 60.093 45.455 0.00 0.00 0.00 3.67
1340 3253 4.767255 CCCCTCACTCGCAGGCAC 62.767 72.222 0.00 0.00 0.00 5.01
1504 4238 4.112341 GACCCGTCCGTCCGTCAG 62.112 72.222 0.00 0.00 0.00 3.51
1505 4239 4.962836 ACCCGTCCGTCCGTCAGT 62.963 66.667 0.00 0.00 0.00 3.41
1506 4240 4.112341 CCCGTCCGTCCGTCAGTC 62.112 72.222 0.00 0.00 0.00 3.51
1507 4241 4.112341 CCGTCCGTCCGTCAGTCC 62.112 72.222 0.00 0.00 0.00 3.85
1509 4243 3.360340 GTCCGTCCGTCAGTCCGT 61.360 66.667 0.00 0.00 0.00 4.69
1510 4244 3.052082 TCCGTCCGTCAGTCCGTC 61.052 66.667 0.00 0.00 0.00 4.79
1512 4246 4.112341 CGTCCGTCAGTCCGTCCC 62.112 72.222 0.00 0.00 0.00 4.46
1513 4247 3.756727 GTCCGTCAGTCCGTCCCC 61.757 72.222 0.00 0.00 0.00 4.81
1514 4248 4.289101 TCCGTCAGTCCGTCCCCA 62.289 66.667 0.00 0.00 0.00 4.96
1515 4249 3.075005 CCGTCAGTCCGTCCCCAT 61.075 66.667 0.00 0.00 0.00 4.00
1516 4250 2.184322 CGTCAGTCCGTCCCCATG 59.816 66.667 0.00 0.00 0.00 3.66
1518 4252 2.687200 TCAGTCCGTCCCCATGGG 60.687 66.667 25.30 25.30 46.11 4.00
1519 4253 4.489771 CAGTCCGTCCCCATGGGC 62.490 72.222 26.87 12.01 43.94 5.36
1520 4254 4.741239 AGTCCGTCCCCATGGGCT 62.741 66.667 26.87 13.02 43.94 5.19
2165 4899 1.082104 GCAAGGCACGTACAGCAAC 60.082 57.895 9.23 0.00 0.00 4.17
2375 5109 2.099263 CGTCTTCGACTACATGGTCCAT 59.901 50.000 0.00 0.00 39.71 3.41
2447 5184 2.620585 GGTCAAGATCCCATTTAGCTGC 59.379 50.000 0.00 0.00 0.00 5.25
2487 5224 9.647797 TGACAAATTATATTACTTCGAGTGTGT 57.352 29.630 3.81 0.00 0.00 3.72
2500 5237 1.867233 GAGTGTGTTGTGGTGTAGCTG 59.133 52.381 0.00 0.00 0.00 4.24
2662 5406 3.434984 GTGTGCTGAAGATTGGAGACTTC 59.565 47.826 0.00 0.00 41.67 3.01
2716 5460 2.579787 CCGATGACCAGTCGCGTC 60.580 66.667 5.77 0.00 37.75 5.19
2881 5625 4.545823 TGGAACACTTGCTCTTTTAACG 57.454 40.909 0.00 0.00 0.00 3.18
2945 5689 5.163913 GCTGAAGTACTGTTCATAGCTTGTG 60.164 44.000 0.00 0.00 35.88 3.33
2962 5706 4.571919 CTTGTGAACCATTCCATGCAAAT 58.428 39.130 0.00 0.00 0.00 2.32
2979 5723 8.491152 CCATGCAAATCACGTTAACATTTTAAA 58.509 29.630 6.39 0.00 0.00 1.52
3053 5797 7.451732 AGAGCATGTTCAGATAGAATAAGCAT 58.548 34.615 12.41 0.00 42.27 3.79
3115 5859 2.076863 GAAATTGACCCGGTGTCTCAG 58.923 52.381 19.61 0.00 44.75 3.35
3158 5902 3.247006 TGTTCTTTATCAGAGGCGGAC 57.753 47.619 0.00 0.00 31.12 4.79
3214 5958 3.902218 ACCACACATATTTCCCATCCAG 58.098 45.455 0.00 0.00 0.00 3.86
3572 6316 2.309528 TGGCTACCAGTATCTTTGCG 57.690 50.000 0.00 0.00 0.00 4.85
3586 6330 8.491152 CAGTATCTTTGCGAATATTTAGACTGG 58.509 37.037 5.41 0.00 0.00 4.00
3610 6354 9.460019 TGGATACTTGAAAATCATACATGTGAA 57.540 29.630 9.11 0.00 37.61 3.18
3670 6602 6.229936 ACCGAATCAGTGCCTAATACTTTA 57.770 37.500 0.00 0.00 0.00 1.85
3728 6660 8.336801 ACTTCAATTCTATTTGTGTTACTCCC 57.663 34.615 0.00 0.00 0.00 4.30
3729 6661 8.164070 ACTTCAATTCTATTTGTGTTACTCCCT 58.836 33.333 0.00 0.00 0.00 4.20
3731 6663 7.918076 TCAATTCTATTTGTGTTACTCCCTCT 58.082 34.615 0.00 0.00 0.00 3.69
3732 6664 7.824289 TCAATTCTATTTGTGTTACTCCCTCTG 59.176 37.037 0.00 0.00 0.00 3.35
3734 6666 6.282199 TCTATTTGTGTTACTCCCTCTGTC 57.718 41.667 0.00 0.00 0.00 3.51
3735 6667 3.764237 TTTGTGTTACTCCCTCTGTCC 57.236 47.619 0.00 0.00 0.00 4.02
3736 6668 1.640917 TGTGTTACTCCCTCTGTCCC 58.359 55.000 0.00 0.00 0.00 4.46
3737 6669 0.531200 GTGTTACTCCCTCTGTCCCG 59.469 60.000 0.00 0.00 0.00 5.14
3739 6671 1.203087 TGTTACTCCCTCTGTCCCGAA 60.203 52.381 0.00 0.00 0.00 4.30
3740 6672 1.897802 GTTACTCCCTCTGTCCCGAAA 59.102 52.381 0.00 0.00 0.00 3.46
3741 6673 2.500504 GTTACTCCCTCTGTCCCGAAAT 59.499 50.000 0.00 0.00 0.00 2.17
3742 6674 2.544844 ACTCCCTCTGTCCCGAAATA 57.455 50.000 0.00 0.00 0.00 1.40
3743 6675 2.829023 ACTCCCTCTGTCCCGAAATAA 58.171 47.619 0.00 0.00 0.00 1.40
3744 6676 2.766828 ACTCCCTCTGTCCCGAAATAAG 59.233 50.000 0.00 0.00 0.00 1.73
3745 6677 2.766828 CTCCCTCTGTCCCGAAATAAGT 59.233 50.000 0.00 0.00 0.00 2.24
3746 6678 2.500098 TCCCTCTGTCCCGAAATAAGTG 59.500 50.000 0.00 0.00 0.00 3.16
3747 6679 2.236395 CCCTCTGTCCCGAAATAAGTGT 59.764 50.000 0.00 0.00 0.00 3.55
3748 6680 3.522553 CCTCTGTCCCGAAATAAGTGTC 58.477 50.000 0.00 0.00 0.00 3.67
3749 6681 3.195825 CCTCTGTCCCGAAATAAGTGTCT 59.804 47.826 0.00 0.00 0.00 3.41
3750 6682 4.425520 CTCTGTCCCGAAATAAGTGTCTC 58.574 47.826 0.00 0.00 0.00 3.36
3751 6683 3.830178 TCTGTCCCGAAATAAGTGTCTCA 59.170 43.478 0.00 0.00 0.00 3.27
3752 6684 4.282449 TCTGTCCCGAAATAAGTGTCTCAA 59.718 41.667 0.00 0.00 0.00 3.02
3753 6685 4.312443 TGTCCCGAAATAAGTGTCTCAAC 58.688 43.478 0.00 0.00 0.00 3.18
3754 6686 4.039973 TGTCCCGAAATAAGTGTCTCAACT 59.960 41.667 0.00 0.00 0.00 3.16
3755 6687 4.995487 GTCCCGAAATAAGTGTCTCAACTT 59.005 41.667 0.00 0.00 42.89 2.66
3756 6688 5.120363 GTCCCGAAATAAGTGTCTCAACTTC 59.880 44.000 0.00 0.00 40.77 3.01
3757 6689 4.994852 CCCGAAATAAGTGTCTCAACTTCA 59.005 41.667 0.00 0.00 40.77 3.02
3758 6690 5.120830 CCCGAAATAAGTGTCTCAACTTCAG 59.879 44.000 0.00 0.00 40.77 3.02
3759 6691 5.696724 CCGAAATAAGTGTCTCAACTTCAGT 59.303 40.000 0.00 0.00 40.77 3.41
3760 6692 6.866770 CCGAAATAAGTGTCTCAACTTCAGTA 59.133 38.462 0.00 0.00 40.77 2.74
3761 6693 7.148787 CCGAAATAAGTGTCTCAACTTCAGTAC 60.149 40.741 0.00 0.00 40.77 2.73
3762 6694 7.595502 CGAAATAAGTGTCTCAACTTCAGTACT 59.404 37.037 0.00 0.00 40.77 2.73
3763 6695 9.909644 GAAATAAGTGTCTCAACTTCAGTACTA 57.090 33.333 0.00 0.00 40.77 1.82
3766 6698 9.915629 ATAAGTGTCTCAACTTCAGTACTAAAG 57.084 33.333 4.07 4.07 40.77 1.85
3767 6699 7.349412 AGTGTCTCAACTTCAGTACTAAAGT 57.651 36.000 5.52 5.52 37.32 2.66
3768 6700 8.461249 AGTGTCTCAACTTCAGTACTAAAGTA 57.539 34.615 11.93 0.00 34.71 2.24
3804 6736 9.362151 ACTAAAATTGAGACACTTATTTTGGGA 57.638 29.630 0.00 0.00 34.64 4.37
3805 6737 9.626045 CTAAAATTGAGACACTTATTTTGGGAC 57.374 33.333 0.00 0.00 33.59 4.46
3806 6738 5.880054 ATTGAGACACTTATTTTGGGACG 57.120 39.130 0.00 0.00 0.00 4.79
3807 6739 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
3808 6740 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
3809 6741 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
3810 6742 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3811 6743 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
3812 6744 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3813 6745 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
3814 6746 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
3815 6747 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3816 6748 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
3817 6749 0.178926 TTTGGGACGGAGGGAGTACA 60.179 55.000 0.00 0.00 0.00 2.90
3818 6750 0.042131 TTGGGACGGAGGGAGTACAT 59.958 55.000 0.00 0.00 0.00 2.29
3822 6754 2.629051 GGACGGAGGGAGTACATTTTG 58.371 52.381 0.00 0.00 0.00 2.44
3945 6883 1.729586 TTAAGCTATGCGGATCCCCT 58.270 50.000 6.06 0.00 0.00 4.79
4002 6940 3.445008 TGCAACCATATTTAAGCCCCAA 58.555 40.909 0.00 0.00 0.00 4.12
4095 7033 4.411540 ACACTCCTATCAATTGATCCTGCT 59.588 41.667 23.95 3.15 36.05 4.24
4115 7053 4.506838 CTGATCGTTTAACAGCTACTGC 57.493 45.455 0.00 0.00 34.37 4.40
4221 7166 6.096705 TCTCAAATCGTTGGATAAATTGGCAT 59.903 34.615 0.00 0.00 35.29 4.40
4229 7174 6.016360 CGTTGGATAAATTGGCATAAGGATGA 60.016 38.462 0.00 0.00 34.73 2.92
4397 7342 6.181908 TCATTGGAATCACATTGAGATCACA 58.818 36.000 0.00 0.00 0.00 3.58
4408 7353 7.547019 TCACATTGAGATCACAGTATCTTGTTC 59.453 37.037 0.00 0.00 36.33 3.18
4633 7581 4.551702 TCTACATTGCTGCTCCTTGTTA 57.448 40.909 0.00 0.00 0.00 2.41
4636 7584 4.445452 ACATTGCTGCTCCTTGTTATTG 57.555 40.909 0.00 0.00 0.00 1.90
4653 7602 5.177881 TGTTATTGCACCGTACTTACAACTG 59.822 40.000 0.00 0.00 0.00 3.16
4665 7614 6.183360 CGTACTTACAACTGACACCTTTTTGT 60.183 38.462 0.00 0.00 34.79 2.83
4698 7647 5.296035 CACAGTTCTTTAAAACGGAACCTCT 59.704 40.000 12.65 0.00 39.82 3.69
4909 8494 5.049954 TCACAACCTAGAAATGTAAACACGC 60.050 40.000 0.00 0.00 0.00 5.34
4988 8573 0.248289 AACTAGCATAACGCCCGTGT 59.752 50.000 0.00 0.00 44.04 4.49
5020 8605 5.988561 TGGAACCACAAAAATAATTGCACTC 59.011 36.000 0.00 0.00 33.52 3.51
5115 8712 2.029649 GCACCATGACAAGATTTGCAGT 60.030 45.455 0.00 0.00 0.00 4.40
5128 8816 3.595819 GCAGTGGCATGGAGGAAC 58.404 61.111 0.00 0.00 40.72 3.62
5159 8847 0.995675 CATGGGGATTGGGGAGGAGT 60.996 60.000 0.00 0.00 0.00 3.85
5169 8879 4.154347 GGAGGAGTCGCTGCAGGG 62.154 72.222 23.98 23.98 0.00 4.45
5443 9250 5.527033 AGAGAAAAGTGCTGAAGAAATTGC 58.473 37.500 0.00 0.00 0.00 3.56
5483 9290 9.134055 GTAGAGTTAGGAATACAGTTACAGGAT 57.866 37.037 0.00 0.00 0.00 3.24
5528 9335 2.170187 AGGAGCCTACTTCTGCAGAATG 59.830 50.000 28.57 22.67 40.87 2.67
5570 9377 4.749245 AACAGGAAAGCATAACTTGACG 57.251 40.909 0.00 0.00 39.09 4.35
5634 9441 8.574196 ACATTTCTTTGATTCAAAAGGTAACG 57.426 30.769 12.62 0.54 46.39 3.18
5867 9674 5.382664 TTCTCCACCTCTTAACCTTGTTT 57.617 39.130 0.00 0.00 0.00 2.83
5910 9725 5.691754 GCACTGTATAAATTGCTTATTGGCC 59.308 40.000 0.00 0.00 32.28 5.36
5995 9810 3.060020 GACAAGGACGCGGGATCGA 62.060 63.158 12.47 0.00 39.00 3.59
6128 9943 0.825425 TTTTCCCGCTTGCCATGTCA 60.825 50.000 0.00 0.00 0.00 3.58
6411 10227 2.286184 CCAGAAACGGAAACACAAGTCG 60.286 50.000 0.00 0.00 0.00 4.18
6545 10361 5.428131 GGAAGCTGGGGAGATCTGATTATAT 59.572 44.000 0.00 0.00 0.00 0.86
6732 10558 7.066525 TCGTTTGAGTGAGTAATGGAACTTTTT 59.933 33.333 0.00 0.00 0.00 1.94
6750 10576 3.712016 TTTAGGTCTACTTGGCATGCA 57.288 42.857 21.36 2.54 0.00 3.96
6755 10581 2.154462 GTCTACTTGGCATGCAACTGT 58.846 47.619 21.36 12.26 0.00 3.55
6756 10582 2.095567 GTCTACTTGGCATGCAACTGTG 60.096 50.000 21.36 5.34 0.00 3.66
6875 10770 5.983540 TGTTTGGTCCAGCTTTATGTTTTT 58.016 33.333 0.00 0.00 0.00 1.94
7022 10920 9.956720 GGCAATATTTCTGCATATATATGTTCC 57.043 33.333 21.10 7.93 41.78 3.62
7083 10981 2.546795 GGTTGTATCTCCTCATGGCGAG 60.547 54.545 0.00 0.00 41.89 5.03
7087 10985 1.184322 ATCTCCTCATGGCGAGCGAT 61.184 55.000 0.00 0.00 40.78 4.58
7099 10997 1.139734 GAGCGATGCCGAGAGTGAA 59.860 57.895 0.00 0.00 38.22 3.18
7130 11028 1.698067 TTCTTCCCGGAAACCGTGGT 61.698 55.000 0.73 0.00 46.80 4.16
7134 11032 2.047560 CCGGAAACCGTGGTCCTC 60.048 66.667 0.00 0.00 46.80 3.71
7159 11057 2.034878 CAGATGTCATCTTCCCGGAGA 58.965 52.381 12.88 0.00 37.58 3.71
7168 11066 0.889306 CTTCCCGGAGAACGAAGTCT 59.111 55.000 0.73 0.00 45.00 3.24
7442 11381 4.127040 AGCGTCTGGAGCAGCTCG 62.127 66.667 16.47 6.20 34.48 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 2.876550 CCACCACAGCTCATGTATGATG 59.123 50.000 0.00 0.00 41.41 3.07
80 81 2.573462 AGAACCACCACAGCTCATGTAT 59.427 45.455 0.00 0.00 41.41 2.29
105 106 1.873903 GCACGTGTCACATTCCTGTCT 60.874 52.381 18.38 0.00 31.62 3.41
176 187 1.982958 GGAGGAGTGGAACCCAACTAA 59.017 52.381 0.00 0.00 37.80 2.24
224 237 1.218316 GCAACCTACGAGTCAGGGG 59.782 63.158 1.84 0.00 37.51 4.79
229 242 1.448013 GCCTGGCAACCTACGAGTC 60.448 63.158 15.17 0.00 0.00 3.36
257 274 2.225908 GGGGGATGTGATAGGGGTAGAT 60.226 54.545 0.00 0.00 0.00 1.98
422 704 7.282585 TCCAGACCCACTTAATGAAATCATAG 58.717 38.462 0.00 0.00 35.10 2.23
501 784 6.421202 GCACGTTGTAAATTTATGTTTTGGGA 59.579 34.615 0.31 0.00 0.00 4.37
522 805 3.990469 GGTACAATAGAGATGATGGCACG 59.010 47.826 0.00 0.00 0.00 5.34
526 810 4.039245 ACGGTGGTACAATAGAGATGATGG 59.961 45.833 0.00 0.00 44.16 3.51
538 822 4.339872 AAACTGTATGACGGTGGTACAA 57.660 40.909 0.00 0.00 44.16 2.41
539 823 4.523943 AGTAAACTGTATGACGGTGGTACA 59.476 41.667 12.01 0.00 37.84 2.90
575 860 1.825622 TTGTGTGCATGGAACCGCA 60.826 52.632 0.00 0.00 33.31 5.69
606 891 0.439985 CGATGGCAAGTTCAGACGTG 59.560 55.000 0.00 0.00 38.15 4.49
608 896 1.016130 AGCGATGGCAAGTTCAGACG 61.016 55.000 1.50 0.00 43.41 4.18
634 922 4.202472 CCCTTTGACTGTAAGAGGGTTCTT 60.202 45.833 11.91 0.00 45.45 2.52
645 933 1.069513 CACACGTCCCCTTTGACTGTA 59.930 52.381 0.00 0.00 32.97 2.74
652 940 2.279935 TAAATGCACACGTCCCCTTT 57.720 45.000 0.00 0.00 0.00 3.11
658 946 4.090930 ACGTACAAGATAAATGCACACGTC 59.909 41.667 0.00 0.00 35.40 4.34
691 979 2.159156 GGTGTATGTACATCTGCGGTCA 60.159 50.000 12.68 0.00 38.63 4.02
722 1010 4.288531 GTGTATGTACATCTGCGGTCTAC 58.711 47.826 12.68 2.11 38.63 2.59
725 1013 2.100916 AGGTGTATGTACATCTGCGGTC 59.899 50.000 12.68 0.00 45.39 4.79
726 1014 2.100916 GAGGTGTATGTACATCTGCGGT 59.899 50.000 12.68 0.00 46.97 5.68
727 1015 2.743938 GAGGTGTATGTACATCTGCGG 58.256 52.381 12.68 0.00 46.97 5.69
730 1018 2.223502 ACGCGAGGTGTATGTACATCTG 60.224 50.000 15.93 5.02 46.97 2.90
732 1020 2.486951 ACGCGAGGTGTATGTACATC 57.513 50.000 15.93 5.06 38.63 3.06
733 1021 2.947652 AGTACGCGAGGTGTATGTACAT 59.052 45.455 15.93 13.93 38.24 2.29
734 1022 2.358957 AGTACGCGAGGTGTATGTACA 58.641 47.619 15.93 0.00 38.24 2.90
735 1023 4.212004 TCATAGTACGCGAGGTGTATGTAC 59.788 45.833 15.93 0.59 36.52 2.90
736 1024 4.379652 TCATAGTACGCGAGGTGTATGTA 58.620 43.478 15.93 0.00 32.62 2.29
738 1026 3.891056 TCATAGTACGCGAGGTGTATG 57.109 47.619 15.93 12.10 31.13 2.39
739 1027 6.373495 TGATATTCATAGTACGCGAGGTGTAT 59.627 38.462 15.93 6.15 31.13 2.29
740 1028 5.702209 TGATATTCATAGTACGCGAGGTGTA 59.298 40.000 15.93 0.00 0.00 2.90
741 1029 4.517832 TGATATTCATAGTACGCGAGGTGT 59.482 41.667 15.93 0.00 0.00 4.16
743 1031 5.899120 ATGATATTCATAGTACGCGAGGT 57.101 39.130 15.93 0.00 34.88 3.85
744 1032 7.582435 AAAATGATATTCATAGTACGCGAGG 57.418 36.000 15.93 0.00 35.76 4.63
749 1037 8.572976 CGACGGTAAAATGATATTCATAGTACG 58.427 37.037 0.00 0.00 35.76 3.67
751 1039 7.543172 GGCGACGGTAAAATGATATTCATAGTA 59.457 37.037 0.00 0.00 35.76 1.82
753 1041 6.590292 AGGCGACGGTAAAATGATATTCATAG 59.410 38.462 0.00 0.00 35.76 2.23
754 1042 6.460781 AGGCGACGGTAAAATGATATTCATA 58.539 36.000 0.00 0.00 35.76 2.15
755 1043 5.305585 AGGCGACGGTAAAATGATATTCAT 58.694 37.500 0.00 0.00 39.09 2.57
756 1044 4.699637 AGGCGACGGTAAAATGATATTCA 58.300 39.130 0.00 0.00 0.00 2.57
757 1045 5.668558 AAGGCGACGGTAAAATGATATTC 57.331 39.130 0.00 0.00 0.00 1.75
758 1046 7.556733 TTTAAGGCGACGGTAAAATGATATT 57.443 32.000 0.00 0.00 0.00 1.28
761 1049 5.883503 TTTTAAGGCGACGGTAAAATGAT 57.116 34.783 8.37 0.00 32.96 2.45
772 1060 3.614588 GCGGTGATATTTTTAAGGCGAC 58.385 45.455 0.00 0.00 0.00 5.19
807 1096 1.720852 CGAATTTCAAAAGGGCTTGCG 59.279 47.619 0.00 0.00 0.00 4.85
826 1115 8.879759 TGAACTTAGAATCTTTTGCCTAATACG 58.120 33.333 0.00 0.00 0.00 3.06
852 1141 9.843334 TGTTGTTTCTTTCGTTTATAGTTTGTT 57.157 25.926 0.00 0.00 0.00 2.83
865 1154 8.229811 TCATGATATGTCTTGTTGTTTCTTTCG 58.770 33.333 0.00 0.00 32.80 3.46
866 1155 9.552114 CTCATGATATGTCTTGTTGTTTCTTTC 57.448 33.333 0.00 0.00 32.80 2.62
900 1200 7.041644 TGTTTAAAGAGCGGGTATATGTTATGC 60.042 37.037 0.00 0.00 0.00 3.14
912 1212 6.183360 ACGGTTATATTTGTTTAAAGAGCGGG 60.183 38.462 0.00 0.00 0.00 6.13
913 1213 6.778108 ACGGTTATATTTGTTTAAAGAGCGG 58.222 36.000 0.00 0.00 0.00 5.52
915 1215 6.903479 CGGACGGTTATATTTGTTTAAAGAGC 59.097 38.462 0.00 0.00 0.00 4.09
920 1220 5.410746 TGTGCGGACGGTTATATTTGTTTAA 59.589 36.000 1.60 0.00 0.00 1.52
971 1279 2.098607 TCGTGATGTTGACGTATCCTCC 59.901 50.000 0.00 0.00 38.04 4.30
977 1285 2.097299 GCGTTTTCGTGATGTTGACGTA 60.097 45.455 0.00 0.00 46.03 3.57
996 1305 3.831883 CCTTGGATCCACATGGCG 58.168 61.111 15.91 0.00 34.44 5.69
1002 1311 1.828979 TTTTACCGCCTTGGATCCAC 58.171 50.000 15.91 1.76 42.00 4.02
1003 1312 2.588464 TTTTTACCGCCTTGGATCCA 57.412 45.000 11.44 11.44 42.00 3.41
1101 1468 5.455872 AGGAAGAGGAAAATGCATCATGAT 58.544 37.500 1.18 1.18 0.00 2.45
1103 1470 4.643334 TGAGGAAGAGGAAAATGCATCATG 59.357 41.667 0.00 0.00 0.00 3.07
1122 1489 0.387202 CAGCGGAGTGGAGTATGAGG 59.613 60.000 0.00 0.00 0.00 3.86
1125 1492 3.352447 CACAGCGGAGTGGAGTATG 57.648 57.895 0.00 0.00 35.88 2.39
1139 3046 1.148310 CTACAACAGAACCGCCACAG 58.852 55.000 0.00 0.00 0.00 3.66
1151 3058 2.033372 TCACGTTCCTGTCCTACAACA 58.967 47.619 0.00 0.00 0.00 3.33
1152 3059 2.223876 TGTCACGTTCCTGTCCTACAAC 60.224 50.000 0.00 0.00 0.00 3.32
1153 3060 2.033372 TGTCACGTTCCTGTCCTACAA 58.967 47.619 0.00 0.00 0.00 2.41
1216 3123 4.008933 GACGGGTGTGCTCCTGCT 62.009 66.667 0.00 0.00 40.48 4.24
1226 3133 1.226030 GGTTTTGACTCGGACGGGTG 61.226 60.000 0.23 0.00 0.00 4.61
1361 3274 1.836166 GGGGTGGGGAGTAGTAAAGTC 59.164 57.143 0.00 0.00 0.00 3.01
2165 4899 4.728102 TCCCGCGCCTTGTACACG 62.728 66.667 0.00 0.00 0.00 4.49
2447 5184 2.183478 TTGTCACTATGTGGCTGTGG 57.817 50.000 3.97 0.00 39.12 4.17
2479 5216 0.859232 GCTACACCACAACACACTCG 59.141 55.000 0.00 0.00 0.00 4.18
2487 5224 0.317160 CTCGACCAGCTACACCACAA 59.683 55.000 0.00 0.00 0.00 3.33
2500 5237 0.378962 CACCTCGATCAGACTCGACC 59.621 60.000 0.00 0.00 42.38 4.79
2662 5406 2.049433 AAGAACGACGCCAGACCG 60.049 61.111 0.00 0.00 0.00 4.79
2716 5460 1.211969 CCGGTACCAGAGTGTCACG 59.788 63.158 13.54 0.00 0.00 4.35
2878 5622 8.349983 AGAATCAACTTTAGTAACATTTGCGTT 58.650 29.630 0.00 0.00 0.00 4.84
2879 5623 7.803189 CAGAATCAACTTTAGTAACATTTGCGT 59.197 33.333 0.00 0.00 0.00 5.24
2881 5625 9.463443 AACAGAATCAACTTTAGTAACATTTGC 57.537 29.630 0.00 0.00 0.00 3.68
2945 5689 3.181397 CGTGATTTGCATGGAATGGTTC 58.819 45.455 0.00 0.00 46.86 3.62
2962 5706 6.261381 AGACCTGCTTTAAAATGTTAACGTGA 59.739 34.615 0.00 0.00 0.00 4.35
2979 5723 1.005630 GTCTTGCACGAGACCTGCT 60.006 57.895 7.23 0.00 40.10 4.24
3134 5878 3.751175 CCGCCTCTGATAAAGAACAACAA 59.249 43.478 0.00 0.00 33.37 2.83
3151 5895 0.618968 ATTTCTCTCTGGGTCCGCCT 60.619 55.000 0.00 0.00 34.45 5.52
3158 5902 1.407437 CCGGGTCAATTTCTCTCTGGG 60.407 57.143 0.00 0.00 0.00 4.45
3488 6232 5.792712 AGGACCAAAGGGCATAGTATATGAT 59.207 40.000 0.00 0.00 37.90 2.45
3489 6233 5.162637 AGGACCAAAGGGCATAGTATATGA 58.837 41.667 0.00 0.00 37.90 2.15
3490 6234 5.505181 AGGACCAAAGGGCATAGTATATG 57.495 43.478 0.00 0.00 37.90 1.78
3492 6236 8.745149 TTTATAGGACCAAAGGGCATAGTATA 57.255 34.615 0.00 0.00 27.51 1.47
3493 6237 7.642094 TTTATAGGACCAAAGGGCATAGTAT 57.358 36.000 0.00 0.00 27.51 2.12
3494 6238 7.454553 TTTTATAGGACCAAAGGGCATAGTA 57.545 36.000 0.00 0.00 27.51 1.82
3495 6239 5.987019 TTTATAGGACCAAAGGGCATAGT 57.013 39.130 0.00 0.00 27.51 2.12
3496 6240 5.241728 GCTTTTATAGGACCAAAGGGCATAG 59.758 44.000 0.00 0.00 27.51 2.23
3620 6364 7.425577 GCTTCAGCATTTCCATTAAACTTTT 57.574 32.000 0.00 0.00 41.59 2.27
3646 6390 4.755266 AGTATTAGGCACTGATTCGGTT 57.245 40.909 0.00 0.00 41.52 4.44
3670 6602 4.221262 AGGTATGAACTGCAAACATGCAAT 59.779 37.500 4.93 0.00 44.88 3.56
3727 6659 3.195825 AGACACTTATTTCGGGACAGAGG 59.804 47.826 0.00 0.00 0.00 3.69
3728 6660 4.082190 TGAGACACTTATTTCGGGACAGAG 60.082 45.833 0.00 0.00 0.00 3.35
3729 6661 3.830178 TGAGACACTTATTTCGGGACAGA 59.170 43.478 0.00 0.00 0.00 3.41
3731 6663 4.039973 AGTTGAGACACTTATTTCGGGACA 59.960 41.667 0.00 0.00 0.00 4.02
3732 6664 4.566987 AGTTGAGACACTTATTTCGGGAC 58.433 43.478 0.00 0.00 0.00 4.46
3734 6666 4.994852 TGAAGTTGAGACACTTATTTCGGG 59.005 41.667 0.00 0.00 37.11 5.14
3735 6667 5.696724 ACTGAAGTTGAGACACTTATTTCGG 59.303 40.000 0.00 0.00 37.11 4.30
3736 6668 6.771188 ACTGAAGTTGAGACACTTATTTCG 57.229 37.500 0.00 0.00 37.11 3.46
3737 6669 8.819643 AGTACTGAAGTTGAGACACTTATTTC 57.180 34.615 0.00 0.00 37.11 2.17
3740 6672 9.915629 CTTTAGTACTGAAGTTGAGACACTTAT 57.084 33.333 17.11 0.00 37.11 1.73
3741 6673 8.910944 ACTTTAGTACTGAAGTTGAGACACTTA 58.089 33.333 23.39 0.00 36.19 2.24
3742 6674 7.783042 ACTTTAGTACTGAAGTTGAGACACTT 58.217 34.615 23.39 1.46 36.19 3.16
3743 6675 7.349412 ACTTTAGTACTGAAGTTGAGACACT 57.651 36.000 23.39 2.11 36.19 3.55
3744 6676 8.504812 GTACTTTAGTACTGAAGTTGAGACAC 57.495 38.462 30.84 20.39 45.47 3.67
3778 6710 9.362151 TCCCAAAATAAGTGTCTCAATTTTAGT 57.638 29.630 0.00 0.00 31.97 2.24
3779 6711 9.626045 GTCCCAAAATAAGTGTCTCAATTTTAG 57.374 33.333 0.00 0.00 31.97 1.85
3780 6712 8.293867 CGTCCCAAAATAAGTGTCTCAATTTTA 58.706 33.333 0.00 0.00 31.97 1.52
3781 6713 7.145323 CGTCCCAAAATAAGTGTCTCAATTTT 58.855 34.615 0.00 0.00 33.07 1.82
3782 6714 6.294508 CCGTCCCAAAATAAGTGTCTCAATTT 60.295 38.462 0.00 0.00 0.00 1.82
3783 6715 5.183140 CCGTCCCAAAATAAGTGTCTCAATT 59.817 40.000 0.00 0.00 0.00 2.32
3784 6716 4.700213 CCGTCCCAAAATAAGTGTCTCAAT 59.300 41.667 0.00 0.00 0.00 2.57
3785 6717 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3786 6718 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
3787 6719 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
3788 6720 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
3789 6721 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
3790 6722 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
3791 6723 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3792 6724 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3793 6725 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3794 6726 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3795 6727 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3796 6728 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3797 6729 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3798 6730 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
3799 6731 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
3800 6732 0.042131 AATGTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
3801 6733 1.201424 AAATGTACTCCCTCCGTCCC 58.799 55.000 0.00 0.00 0.00 4.46
3802 6734 2.235402 TCAAAATGTACTCCCTCCGTCC 59.765 50.000 0.00 0.00 0.00 4.79
3803 6735 3.604875 TCAAAATGTACTCCCTCCGTC 57.395 47.619 0.00 0.00 0.00 4.79
3804 6736 3.326880 ACTTCAAAATGTACTCCCTCCGT 59.673 43.478 0.00 0.00 0.00 4.69
3805 6737 3.684788 CACTTCAAAATGTACTCCCTCCG 59.315 47.826 0.00 0.00 0.00 4.63
3806 6738 4.906618 TCACTTCAAAATGTACTCCCTCC 58.093 43.478 0.00 0.00 0.00 4.30
3807 6739 9.482627 CTATATCACTTCAAAATGTACTCCCTC 57.517 37.037 0.00 0.00 0.00 4.30
3808 6740 8.993424 ACTATATCACTTCAAAATGTACTCCCT 58.007 33.333 0.00 0.00 0.00 4.20
3896 6834 7.575414 TTATGCAACTGTTCTACCTGAAAAA 57.425 32.000 0.00 0.00 36.30 1.94
4002 6940 0.533308 TTCGCCTTTTGTACGGCTGT 60.533 50.000 2.42 2.42 44.11 4.40
4110 7048 8.956533 TTACATCACTATTTAATGCAGCAGTA 57.043 30.769 0.00 0.00 0.00 2.74
4202 7147 6.068010 TCCTTATGCCAATTTATCCAACGAT 58.932 36.000 0.00 0.00 0.00 3.73
4397 7342 6.948886 TCTGTACAGAGGAAGAACAAGATACT 59.051 38.462 21.74 0.00 32.82 2.12
4602 7550 6.931281 GGAGCAGCAATGTAGATACTTCATAA 59.069 38.462 0.00 0.00 0.00 1.90
4603 7551 6.268617 AGGAGCAGCAATGTAGATACTTCATA 59.731 38.462 0.00 0.00 0.00 2.15
4633 7581 3.744426 GTCAGTTGTAAGTACGGTGCAAT 59.256 43.478 0.00 0.00 0.00 3.56
4636 7584 2.473984 GTGTCAGTTGTAAGTACGGTGC 59.526 50.000 0.00 0.00 0.00 5.01
4653 7602 5.354792 TGTGTTGGTAGTACAAAAAGGTGTC 59.645 40.000 2.06 0.00 32.75 3.67
4665 7614 7.011295 CCGTTTTAAAGAACTGTGTTGGTAGTA 59.989 37.037 0.00 0.00 0.00 1.82
4698 7647 1.739466 GACTTGATGGATCGCAAGCAA 59.261 47.619 16.70 6.79 43.99 3.91
4909 8494 3.983344 GTGCATGCTTTCTAAAACCACTG 59.017 43.478 20.33 0.00 0.00 3.66
4988 8573 5.543507 ATTTTTGTGGTTCCATAGCAACA 57.456 34.783 0.00 0.00 35.72 3.33
5115 8712 1.001764 CTGCTGTTCCTCCATGCCA 60.002 57.895 0.00 0.00 0.00 4.92
5127 8815 1.376424 CCCATGCTTCGACTGCTGT 60.376 57.895 10.38 0.00 0.00 4.40
5128 8816 2.110967 CCCCATGCTTCGACTGCTG 61.111 63.158 10.38 6.61 0.00 4.41
5159 8847 0.392998 GGATTTTCTCCCTGCAGCGA 60.393 55.000 8.66 4.15 38.19 4.93
5423 9230 4.446719 CCAGCAATTTCTTCAGCACTTTTC 59.553 41.667 0.00 0.00 0.00 2.29
5426 9233 3.225104 TCCAGCAATTTCTTCAGCACTT 58.775 40.909 0.00 0.00 0.00 3.16
5443 9250 9.629878 TTCCTAACTCTACTCTATAACTTCCAG 57.370 37.037 0.00 0.00 0.00 3.86
5483 9290 9.754382 CCTACGGCAAACTAGATTTTAGTATAA 57.246 33.333 0.00 0.00 0.00 0.98
5487 9294 6.290294 TCCTACGGCAAACTAGATTTTAGT 57.710 37.500 0.00 0.00 0.00 2.24
5528 9335 3.687572 ATCAAGTTCATCGAAGCATGC 57.312 42.857 10.51 10.51 0.00 4.06
5529 9336 6.110543 TGTTATCAAGTTCATCGAAGCATG 57.889 37.500 0.00 0.00 0.00 4.06
5530 9337 5.295292 CCTGTTATCAAGTTCATCGAAGCAT 59.705 40.000 0.00 0.00 0.00 3.79
5531 9338 4.631377 CCTGTTATCAAGTTCATCGAAGCA 59.369 41.667 0.00 0.00 0.00 3.91
5634 9441 1.601419 TACGGCTAGCACCCACTGAC 61.601 60.000 18.24 0.00 0.00 3.51
6113 9928 3.818787 GCTGACATGGCAAGCGGG 61.819 66.667 1.11 0.00 0.00 6.13
6128 9943 2.095567 CAGATTAGCGTTTGCAACAGCT 60.096 45.455 25.09 25.09 46.23 4.24
6300 10116 0.518636 TACTGAACGAAGACGGGTCG 59.481 55.000 0.00 3.50 44.46 4.79
6411 10227 0.511653 GTTGTTTCGAAGAGCGTCCC 59.488 55.000 0.00 0.00 41.80 4.46
6681 10507 9.645059 GAATCTAACATGACATATAGCTGCTTA 57.355 33.333 7.79 0.56 0.00 3.09
6732 10558 2.571653 AGTTGCATGCCAAGTAGACCTA 59.428 45.455 16.68 0.00 35.35 3.08
6750 10576 8.693625 AGTAAGAGTTAACAGTAAGTCACAGTT 58.306 33.333 8.61 0.00 40.72 3.16
6755 10581 7.046292 TGCAGTAAGAGTTAACAGTAAGTCA 57.954 36.000 8.61 0.00 40.72 3.41
6756 10582 7.146648 ACTGCAGTAAGAGTTAACAGTAAGTC 58.853 38.462 20.16 0.00 39.19 3.01
6837 10731 8.243961 TGGACCAAACATCAGATTTAAGAAAA 57.756 30.769 0.00 0.00 0.00 2.29
6875 10770 7.732025 TCTACAACTTGTGAAGTCATAAAGGA 58.268 34.615 4.57 0.00 41.91 3.36
6933 10831 3.204526 CTGAAGGGCAATGCAACAAAAA 58.795 40.909 7.79 0.00 0.00 1.94
6934 10832 2.170187 ACTGAAGGGCAATGCAACAAAA 59.830 40.909 7.79 0.00 0.00 2.44
6935 10833 1.761784 ACTGAAGGGCAATGCAACAAA 59.238 42.857 7.79 0.00 0.00 2.83
6947 10845 4.553323 CATTTTGCTGAAGAACTGAAGGG 58.447 43.478 0.00 0.00 0.00 3.95
7046 10944 0.393808 AACCTTCGGGCACGCATTAT 60.394 50.000 1.67 0.00 40.69 1.28
7083 10981 1.009829 AAATTCACTCTCGGCATCGC 58.990 50.000 0.00 0.00 36.13 4.58
7087 10985 0.796312 GCGAAAATTCACTCTCGGCA 59.204 50.000 0.00 0.00 0.00 5.69
7090 10988 1.346365 TCGGCGAAAATTCACTCTCG 58.654 50.000 7.35 0.00 0.00 4.04
7099 10997 1.400494 CGGGAAGAAATCGGCGAAAAT 59.600 47.619 15.93 2.30 0.00 1.82
7130 11028 1.126488 GATGACATCTGCAGGGAGGA 58.874 55.000 15.13 0.00 0.00 3.71
7134 11032 1.476471 GGGAAGATGACATCTGCAGGG 60.476 57.143 22.56 9.34 40.13 4.45
7159 11057 2.685100 GAAATCGACCCAGACTTCGTT 58.315 47.619 0.00 0.00 36.60 3.85
7168 11066 1.445410 CGACAGCGAAATCGACCCA 60.445 57.895 7.06 0.00 40.86 4.51
7255 11153 0.323725 ACAAGATGTGTCCATGGGGC 60.324 55.000 13.02 6.08 34.38 5.80


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

AutoCloner maintained by Alex Coulton.