Multiple sequence alignment - TraesCS6B01G107600

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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 TraesCS6B01G107600 chr6B 100.000 5332 0 0 1 5332 88222035 88216704 0.000000e+00 9847.0
1 TraesCS6B01G107600 chrUn 91.594 2748 168 22 2604 5332 134268024 134270727 0.000000e+00 3736.0
2 TraesCS6B01G107600 chrUn 92.887 1940 129 5 2604 4543 134253806 134251876 0.000000e+00 2809.0
3 TraesCS6B01G107600 chrUn 84.590 1804 249 23 2715 4499 108321786 108323579 0.000000e+00 1764.0
4 TraesCS6B01G107600 chrUn 86.808 1084 89 25 1 1065 134255889 134254841 0.000000e+00 1160.0
5 TraesCS6B01G107600 chrUn 86.728 1085 88 26 1 1065 134265941 134266989 0.000000e+00 1155.0
6 TraesCS6B01G107600 chrUn 93.623 737 43 3 1091 1823 134254887 134254151 0.000000e+00 1098.0
7 TraesCS6B01G107600 chrUn 93.623 737 43 3 1091 1823 134266943 134267679 0.000000e+00 1098.0
8 TraesCS6B01G107600 chrUn 88.298 846 85 9 1091 1927 108319583 108320423 0.000000e+00 1002.0
9 TraesCS6B01G107600 chrUn 87.768 466 55 2 601 1065 108319165 108319629 1.310000e-150 544.0
10 TraesCS6B01G107600 chrUn 82.044 685 57 27 4641 5309 108323915 108324549 1.700000e-144 523.0
11 TraesCS6B01G107600 chrUn 89.080 348 33 3 1885 2231 134254153 134253810 1.370000e-115 427.0
12 TraesCS6B01G107600 chrUn 89.080 348 33 3 1885 2231 134267677 134268020 1.370000e-115 427.0
13 TraesCS6B01G107600 chrUn 82.472 445 51 11 118 548 108318719 108319150 1.090000e-96 364.0
14 TraesCS6B01G107600 chrUn 81.683 404 36 13 2272 2675 108320684 108321049 8.680000e-78 302.0
15 TraesCS6B01G107600 chrUn 86.275 102 14 0 5030 5131 108428971 108428870 1.570000e-20 111.0
16 TraesCS6B01G107600 chr5A 92.787 1941 126 7 2604 4543 706083193 706085120 0.000000e+00 2796.0
17 TraesCS6B01G107600 chr5A 84.109 1806 253 25 2715 4499 705844013 705842221 0.000000e+00 1714.0
18 TraesCS6B01G107600 chr5A 89.972 1087 86 13 1 1065 706081074 706082159 0.000000e+00 1382.0
19 TraesCS6B01G107600 chr5A 93.234 739 46 3 1091 1825 706082113 706082851 0.000000e+00 1085.0
20 TraesCS6B01G107600 chr5A 85.893 957 99 20 1091 2041 705846250 705845324 0.000000e+00 987.0
21 TraesCS6B01G107600 chr5A 83.307 635 81 15 454 1064 705846838 705846205 3.610000e-156 562.0
22 TraesCS6B01G107600 chr5A 91.124 338 21 3 4654 4991 705841771 705841443 2.930000e-122 449.0
23 TraesCS6B01G107600 chr5A 88.761 347 35 3 1885 2231 706082847 706083189 6.380000e-114 422.0
24 TraesCS6B01G107600 chr5A 88.852 305 32 2 1334 1637 705555890 705556193 1.810000e-99 374.0
25 TraesCS6B01G107600 chr5A 84.456 386 38 11 173 548 705550509 705550882 1.410000e-95 361.0
26 TraesCS6B01G107600 chr5A 83.455 411 39 6 2265 2675 705845170 705844789 6.570000e-94 355.0
27 TraesCS6B01G107600 chr5A 83.554 377 58 4 691 1065 705550985 705551359 3.060000e-92 350.0
28 TraesCS6B01G107600 chr5A 86.290 248 24 5 1091 1338 705551313 705551550 1.470000e-65 261.0
29 TraesCS6B01G107600 chr5A 81.277 235 37 3 5030 5257 705566170 705566404 3.280000e-42 183.0
30 TraesCS6B01G107600 chr4B 91.877 1859 137 8 2604 4458 666583004 666581156 0.000000e+00 2584.0
31 TraesCS6B01G107600 chr4B 84.778 1800 250 17 2715 4499 625975255 625977045 0.000000e+00 1784.0
32 TraesCS6B01G107600 chr4B 84.109 1806 253 25 2715 4499 665877028 665875236 0.000000e+00 1714.0
33 TraesCS6B01G107600 chr4B 89.534 1051 87 13 33 1065 666585085 666584040 0.000000e+00 1310.0
34 TraesCS6B01G107600 chr4B 92.287 739 53 3 1091 1825 666584086 666583348 0.000000e+00 1046.0
35 TraesCS6B01G107600 chr4B 86.207 957 101 18 1091 2041 665879270 665878339 0.000000e+00 1007.0
36 TraesCS6B01G107600 chr4B 85.922 689 91 4 1091 1775 665552677 665553363 0.000000e+00 730.0
37 TraesCS6B01G107600 chr4B 82.265 733 104 15 118 832 665551812 665552536 1.270000e-170 610.0
38 TraesCS6B01G107600 chr4B 83.281 634 82 14 454 1064 665879857 665879225 3.610000e-156 562.0
39 TraesCS6B01G107600 chr4B 87.469 407 50 1 654 1060 625973068 625973473 8.090000e-128 468.0
40 TraesCS6B01G107600 chr4B 91.420 338 20 3 4654 4991 665874785 665874457 6.300000e-124 455.0
41 TraesCS6B01G107600 chr4B 89.685 349 30 4 1885 2231 666583352 666583008 1.760000e-119 440.0
42 TraesCS6B01G107600 chr4B 88.715 319 27 3 4641 4959 666579403 666579094 1.080000e-101 381.0
43 TraesCS6B01G107600 chr4B 86.455 347 39 4 2326 2672 665557793 665558131 1.810000e-99 374.0
44 TraesCS6B01G107600 chr4B 83.455 411 39 6 2265 2675 665878185 665877804 6.570000e-94 355.0
45 TraesCS6B01G107600 chr4B 88.557 201 15 2 4791 4991 195445721 195445913 2.480000e-58 237.0
46 TraesCS6B01G107600 chr4B 88.050 159 11 3 4840 4991 625978578 625978735 1.180000e-41 182.0
47 TraesCS6B01G107600 chr4B 87.050 139 15 2 4853 4991 625874036 625874171 2.570000e-33 154.0
48 TraesCS6B01G107600 chr4B 100.000 29 0 0 4547 4575 666579596 666579568 3.000000e-03 54.7
49 TraesCS6B01G107600 chr5D 79.459 1811 349 21 2737 4534 355203668 355205468 0.000000e+00 1262.0
50 TraesCS6B01G107600 chr5D 75.472 477 83 25 2246 2712 355200997 355201449 9.050000e-48 202.0
51 TraesCS6B01G107600 chr5D 93.069 101 7 0 1 101 503681358 503681458 1.200000e-31 148.0
52 TraesCS6B01G107600 chr5D 93.069 101 7 0 1 101 532939409 532939309 1.200000e-31 148.0
53 TraesCS6B01G107600 chr4A 83.239 883 131 11 1542 2416 658402656 658401783 0.000000e+00 795.0
54 TraesCS6B01G107600 chr6A 83.091 550 68 20 1545 2079 50355954 50355415 1.340000e-130 477.0
55 TraesCS6B01G107600 chr6A 83.398 259 34 2 2075 2324 50348989 50348731 1.150000e-56 231.0
56 TraesCS6B01G107600 chr6A 84.615 104 16 0 2311 2414 158908620 158908723 2.630000e-18 104.0
57 TraesCS6B01G107600 chr5B 87.838 222 19 2 4770 4991 490727243 490727456 2.460000e-63 254.0
58 TraesCS6B01G107600 chr6D 86.937 222 18 4 4770 4991 417348842 417348632 6.900000e-59 239.0
59 TraesCS6B01G107600 chr7D 93.069 101 7 0 1 101 561639115 561639215 1.200000e-31 148.0
60 TraesCS6B01G107600 chr7D 93.069 101 7 0 1 101 597424337 597424437 1.200000e-31 148.0
61 TraesCS6B01G107600 chr1D 93.069 101 7 0 1 101 61573866 61573766 1.200000e-31 148.0


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 TraesCS6B01G107600 chr6B 88216704 88222035 5331 True 9847.000000 9847 100.000000 1 5332 1 chr6B.!!$R1 5331
1 TraesCS6B01G107600 chrUn 134265941 134270727 4786 False 1604.000000 3736 90.256250 1 5332 4 chrUn.!!$F2 5331
2 TraesCS6B01G107600 chrUn 134251876 134255889 4013 True 1373.500000 2809 90.599500 1 4543 4 chrUn.!!$R2 4542
3 TraesCS6B01G107600 chrUn 108318719 108324549 5830 False 749.833333 1764 84.475833 118 5309 6 chrUn.!!$F1 5191
4 TraesCS6B01G107600 chr5A 706081074 706085120 4046 False 1421.250000 2796 91.188500 1 4543 4 chr5A.!!$F4 4542
5 TraesCS6B01G107600 chr5A 705841443 705846838 5395 True 813.400000 1714 85.577600 454 4991 5 chr5A.!!$R1 4537
6 TraesCS6B01G107600 chr5A 705550509 705551550 1041 False 324.000000 361 84.766667 173 1338 3 chr5A.!!$F3 1165
7 TraesCS6B01G107600 chr4B 666579094 666585085 5991 True 969.283333 2584 92.016333 33 4959 6 chr4B.!!$R2 4926
8 TraesCS6B01G107600 chr4B 665874457 665879857 5400 True 818.600000 1714 85.694400 454 4991 5 chr4B.!!$R1 4537
9 TraesCS6B01G107600 chr4B 625973068 625978735 5667 False 811.333333 1784 86.765667 654 4991 3 chr4B.!!$F4 4337
10 TraesCS6B01G107600 chr4B 665551812 665553363 1551 False 670.000000 730 84.093500 118 1775 2 chr4B.!!$F5 1657
11 TraesCS6B01G107600 chr5D 355200997 355205468 4471 False 732.000000 1262 77.465500 2246 4534 2 chr5D.!!$F2 2288
12 TraesCS6B01G107600 chr4A 658401783 658402656 873 True 795.000000 795 83.239000 1542 2416 1 chr4A.!!$R1 874
13 TraesCS6B01G107600 chr6A 50355415 50355954 539 True 477.000000 477 83.091000 1545 2079 1 chr6A.!!$R2 534

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
96 97 3.262915 AGAGAGAGCACCACAAGCTAAAT 59.737 43.478 0.00 0.00 43.58 1.40 F
1521 1576 1.133945 TCTGCTCGAGCTACTCCTCAT 60.134 52.381 35.27 0.00 42.66 2.90 F
2291 2609 1.168714 GGTGCTTTAACCTGCAGGAG 58.831 55.000 39.19 25.46 40.06 3.69 F
3530 6130 0.759436 GATCACCGCTTCCCCCTCTA 60.759 60.000 0.00 0.00 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 1782 0.178767 TCATCGCCATCCCAGTTCTG 59.821 55.000 0.0 0.0 0.00 3.02 R
2362 2680 1.000955 TCTTCCGAACACTTCTGAGCC 59.999 52.381 0.0 0.0 0.00 4.70 R
3812 6412 1.112916 TGCCGACTCCTCTTGTGTGA 61.113 55.000 0.0 0.0 0.00 3.58 R
5061 9601 1.410004 ACACCAAACTCCAGAGTCGA 58.590 50.000 0.0 0.0 41.58 4.20 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
48 49 4.202245 TCCACCATTGCTTGTACTAGTC 57.798 45.455 0.00 0.00 0.00 2.59
62 63 7.813148 GCTTGTACTAGTCTGTCAAGAATACAA 59.187 37.037 22.39 13.26 38.06 2.41
96 97 3.262915 AGAGAGAGCACCACAAGCTAAAT 59.737 43.478 0.00 0.00 43.58 1.40
113 114 6.311735 AGCTAAATACCTTCTTTGTTGGGAA 58.688 36.000 0.00 0.00 0.00 3.97
128 129 4.286808 TGTTGGGAACTCTCATCTGAATCA 59.713 41.667 0.00 0.00 0.00 2.57
149 154 7.573968 ATCATTTTTATAGTCCAGTTGCTCC 57.426 36.000 0.00 0.00 0.00 4.70
151 156 6.599244 TCATTTTTATAGTCCAGTTGCTCCAG 59.401 38.462 0.00 0.00 0.00 3.86
163 170 5.525378 CCAGTTGCTCCAGTATATGTTCTTC 59.475 44.000 0.00 0.00 0.00 2.87
218 228 3.822167 TGAATGAGACTGCTGATTTTGCA 59.178 39.130 0.00 0.00 38.81 4.08
221 231 4.859304 TGAGACTGCTGATTTTGCATTT 57.141 36.364 0.00 0.00 39.86 2.32
259 273 6.018425 GTCGCATGATCTCTTGTTTCATATGT 60.018 38.462 1.90 0.00 0.00 2.29
329 351 3.820467 CAGGTTGACACTCTTTAATGCCA 59.180 43.478 0.00 0.00 0.00 4.92
330 352 4.278170 CAGGTTGACACTCTTTAATGCCAA 59.722 41.667 0.00 0.00 0.00 4.52
479 506 8.819974 GTTTATCCATTTGGTAAAAGCATCATG 58.180 33.333 0.00 0.00 36.34 3.07
489 516 6.435591 TGGTAAAAGCATCATGAAATGGTACA 59.564 34.615 0.00 0.00 46.73 2.90
558 585 6.874288 GCAATCCTGCTCAGTTTTATAGAT 57.126 37.500 0.00 0.00 45.74 1.98
606 653 8.720562 TCCATCATGATTTGTAAATACTATGCG 58.279 33.333 5.16 0.00 0.00 4.73
706 753 7.264947 CCCAAAACTACAAATCAGACTGTTTT 58.735 34.615 1.59 4.00 36.84 2.43
735 782 6.006275 ACACTGATGTATATTTTCTGGGCT 57.994 37.500 0.00 0.00 37.26 5.19
740 787 8.275040 ACTGATGTATATTTTCTGGGCTTTAGT 58.725 33.333 0.00 0.00 0.00 2.24
749 796 8.757164 ATTTTCTGGGCTTTAGTTTAATTTCG 57.243 30.769 0.00 0.00 0.00 3.46
754 801 7.229907 TCTGGGCTTTAGTTTAATTTCGTCTTT 59.770 33.333 0.00 0.00 0.00 2.52
822 871 4.156556 TCTTCTTCCCTTTTGATGCATTCG 59.843 41.667 0.00 0.00 0.00 3.34
866 915 6.173339 AGTTGTATTGATTTCATGTCGGAGT 58.827 36.000 0.00 0.00 0.00 3.85
875 924 7.432869 TGATTTCATGTCGGAGTTTTCAATTT 58.567 30.769 0.00 0.00 0.00 1.82
968 1021 8.147704 CACTATAATTGGTTTTCTGGTGGTTTT 58.852 33.333 0.00 0.00 0.00 2.43
982 1035 9.974980 TTCTGGTGGTTTTCTTTCAATATTAAC 57.025 29.630 0.00 0.00 0.00 2.01
987 1040 7.753580 GTGGTTTTCTTTCAATATTAACCGAGG 59.246 37.037 8.71 0.00 37.07 4.63
1011 1064 4.256920 GTGCTTAACTCATGTCACAGGAT 58.743 43.478 0.00 0.00 0.00 3.24
1032 1085 4.471904 TTGGACCAGTGATAGTGATGAC 57.528 45.455 0.00 0.00 0.00 3.06
1033 1086 2.427095 TGGACCAGTGATAGTGATGACG 59.573 50.000 0.00 0.00 0.00 4.35
1034 1087 2.223829 GGACCAGTGATAGTGATGACGG 60.224 54.545 0.00 0.00 0.00 4.79
1035 1088 2.427453 GACCAGTGATAGTGATGACGGT 59.573 50.000 0.00 0.00 32.16 4.83
1036 1089 2.166459 ACCAGTGATAGTGATGACGGTG 59.834 50.000 0.00 0.00 29.83 4.94
1037 1090 2.427095 CCAGTGATAGTGATGACGGTGA 59.573 50.000 0.00 0.00 0.00 4.02
1038 1091 3.068732 CCAGTGATAGTGATGACGGTGAT 59.931 47.826 0.00 0.00 0.00 3.06
1039 1092 4.278419 CCAGTGATAGTGATGACGGTGATA 59.722 45.833 0.00 0.00 0.00 2.15
1040 1093 5.221244 CCAGTGATAGTGATGACGGTGATAA 60.221 44.000 0.00 0.00 0.00 1.75
1041 1094 5.917447 CAGTGATAGTGATGACGGTGATAAG 59.083 44.000 0.00 0.00 0.00 1.73
1042 1095 5.594725 AGTGATAGTGATGACGGTGATAAGT 59.405 40.000 0.00 0.00 0.00 2.24
1043 1096 6.096987 AGTGATAGTGATGACGGTGATAAGTT 59.903 38.462 0.00 0.00 0.00 2.66
1044 1097 6.757010 GTGATAGTGATGACGGTGATAAGTTT 59.243 38.462 0.00 0.00 0.00 2.66
1045 1098 6.756542 TGATAGTGATGACGGTGATAAGTTTG 59.243 38.462 0.00 0.00 0.00 2.93
1046 1099 5.147330 AGTGATGACGGTGATAAGTTTGA 57.853 39.130 0.00 0.00 0.00 2.69
1047 1100 5.171476 AGTGATGACGGTGATAAGTTTGAG 58.829 41.667 0.00 0.00 0.00 3.02
1048 1101 4.929808 GTGATGACGGTGATAAGTTTGAGT 59.070 41.667 0.00 0.00 0.00 3.41
1049 1102 4.929211 TGATGACGGTGATAAGTTTGAGTG 59.071 41.667 0.00 0.00 0.00 3.51
1050 1103 3.659786 TGACGGTGATAAGTTTGAGTGG 58.340 45.455 0.00 0.00 0.00 4.00
1051 1104 3.000727 GACGGTGATAAGTTTGAGTGGG 58.999 50.000 0.00 0.00 0.00 4.61
1052 1105 2.635915 ACGGTGATAAGTTTGAGTGGGA 59.364 45.455 0.00 0.00 0.00 4.37
1053 1106 3.000727 CGGTGATAAGTTTGAGTGGGAC 58.999 50.000 0.00 0.00 0.00 4.46
1054 1107 3.556213 CGGTGATAAGTTTGAGTGGGACA 60.556 47.826 0.00 0.00 0.00 4.02
1055 1108 4.003648 GGTGATAAGTTTGAGTGGGACAG 58.996 47.826 0.00 0.00 41.80 3.51
1057 1110 4.452455 GTGATAAGTTTGAGTGGGACAGTG 59.548 45.833 0.00 0.00 45.14 3.66
1058 1111 4.346709 TGATAAGTTTGAGTGGGACAGTGA 59.653 41.667 0.00 0.00 45.14 3.41
1059 1112 3.864789 AAGTTTGAGTGGGACAGTGAT 57.135 42.857 0.00 0.00 45.14 3.06
1060 1113 4.974645 AAGTTTGAGTGGGACAGTGATA 57.025 40.909 0.00 0.00 45.14 2.15
1061 1114 4.543590 AGTTTGAGTGGGACAGTGATAG 57.456 45.455 0.00 0.00 45.14 2.08
1062 1115 3.904339 AGTTTGAGTGGGACAGTGATAGT 59.096 43.478 0.00 0.00 45.14 2.12
1063 1116 3.961480 TTGAGTGGGACAGTGATAGTG 57.039 47.619 0.00 0.00 45.14 2.74
1064 1117 3.169512 TGAGTGGGACAGTGATAGTGA 57.830 47.619 0.00 0.00 45.14 3.41
1065 1118 3.713003 TGAGTGGGACAGTGATAGTGAT 58.287 45.455 0.00 0.00 45.14 3.06
1066 1119 3.448660 TGAGTGGGACAGTGATAGTGATG 59.551 47.826 0.00 0.00 45.14 3.07
1067 1120 3.701542 GAGTGGGACAGTGATAGTGATGA 59.298 47.826 0.00 0.00 45.14 2.92
1068 1121 4.293494 AGTGGGACAGTGATAGTGATGAT 58.707 43.478 0.00 0.00 42.47 2.45
1069 1122 5.458595 AGTGGGACAGTGATAGTGATGATA 58.541 41.667 0.00 0.00 42.47 2.15
1070 1123 5.538053 AGTGGGACAGTGATAGTGATGATAG 59.462 44.000 0.00 0.00 42.47 2.08
1071 1124 5.303078 GTGGGACAGTGATAGTGATGATAGT 59.697 44.000 0.00 0.00 41.80 2.12
1072 1125 5.302823 TGGGACAGTGATAGTGATGATAGTG 59.697 44.000 0.00 0.00 0.00 2.74
1073 1126 5.536538 GGGACAGTGATAGTGATGATAGTGA 59.463 44.000 0.00 0.00 0.00 3.41
1074 1127 6.210385 GGGACAGTGATAGTGATGATAGTGAT 59.790 42.308 0.00 0.00 0.00 3.06
1075 1128 7.394641 GGGACAGTGATAGTGATGATAGTGATA 59.605 40.741 0.00 0.00 0.00 2.15
1076 1129 8.797438 GGACAGTGATAGTGATGATAGTGATAA 58.203 37.037 0.00 0.00 0.00 1.75
1077 1130 9.838975 GACAGTGATAGTGATGATAGTGATAAG 57.161 37.037 0.00 0.00 0.00 1.73
1078 1131 9.360901 ACAGTGATAGTGATGATAGTGATAAGT 57.639 33.333 0.00 0.00 0.00 2.24
1085 1138 8.939201 AGTGATGATAGTGATAAGTTTGAGTG 57.061 34.615 0.00 0.00 0.00 3.51
1086 1139 7.984050 AGTGATGATAGTGATAAGTTTGAGTGG 59.016 37.037 0.00 0.00 0.00 4.00
1087 1140 7.225538 GTGATGATAGTGATAAGTTTGAGTGGG 59.774 40.741 0.00 0.00 0.00 4.61
1088 1141 6.867519 TGATAGTGATAAGTTTGAGTGGGA 57.132 37.500 0.00 0.00 0.00 4.37
1089 1142 7.437713 TGATAGTGATAAGTTTGAGTGGGAT 57.562 36.000 0.00 0.00 0.00 3.85
1090 1143 8.547481 TGATAGTGATAAGTTTGAGTGGGATA 57.453 34.615 0.00 0.00 0.00 2.59
1091 1144 8.642432 TGATAGTGATAAGTTTGAGTGGGATAG 58.358 37.037 0.00 0.00 0.00 2.08
1092 1145 6.875972 AGTGATAAGTTTGAGTGGGATAGT 57.124 37.500 0.00 0.00 0.00 2.12
1093 1146 6.644347 AGTGATAAGTTTGAGTGGGATAGTG 58.356 40.000 0.00 0.00 0.00 2.74
1094 1147 6.440647 AGTGATAAGTTTGAGTGGGATAGTGA 59.559 38.462 0.00 0.00 0.00 3.41
1095 1148 7.126421 AGTGATAAGTTTGAGTGGGATAGTGAT 59.874 37.037 0.00 0.00 0.00 3.06
1096 1149 8.421784 GTGATAAGTTTGAGTGGGATAGTGATA 58.578 37.037 0.00 0.00 0.00 2.15
1097 1150 8.642432 TGATAAGTTTGAGTGGGATAGTGATAG 58.358 37.037 0.00 0.00 0.00 2.08
1098 1151 6.875972 AAGTTTGAGTGGGATAGTGATAGT 57.124 37.500 0.00 0.00 0.00 2.12
1099 1152 6.227298 AGTTTGAGTGGGATAGTGATAGTG 57.773 41.667 0.00 0.00 0.00 2.74
1100 1153 5.958380 AGTTTGAGTGGGATAGTGATAGTGA 59.042 40.000 0.00 0.00 0.00 3.41
1101 1154 6.613271 AGTTTGAGTGGGATAGTGATAGTGAT 59.387 38.462 0.00 0.00 0.00 3.06
1102 1155 6.410942 TTGAGTGGGATAGTGATAGTGATG 57.589 41.667 0.00 0.00 0.00 3.07
1103 1156 5.705400 TGAGTGGGATAGTGATAGTGATGA 58.295 41.667 0.00 0.00 0.00 2.92
1206 1259 2.028476 CCCATCCACACTCGTAAGTCAA 60.028 50.000 0.00 0.00 31.71 3.18
1246 1300 2.964740 GCGCAAGAGCTATCCATGATA 58.035 47.619 0.30 0.00 43.02 2.15
1289 1343 9.679661 ATGGTGTGATATTTGTTCATGTAACTA 57.320 29.630 0.00 0.00 38.99 2.24
1388 1442 2.076863 CCCAAAAGAGATGGTCGTGAC 58.923 52.381 0.00 0.00 36.14 3.67
1501 1556 2.704596 AGGACATAGTGATGCAGATGCT 59.295 45.455 6.35 0.00 42.66 3.79
1521 1576 1.133945 TCTGCTCGAGCTACTCCTCAT 60.134 52.381 35.27 0.00 42.66 2.90
1609 1668 1.444836 TGGCAAGGGTCGTTTATTCG 58.555 50.000 0.00 0.00 0.00 3.34
1645 1704 1.561076 TGCAGGCACTAGGTGATGATT 59.439 47.619 1.57 0.00 36.02 2.57
1667 1732 4.558226 ATGCAGTGGACAATCACTCTAA 57.442 40.909 0.00 0.00 45.24 2.10
1670 1735 5.316167 TGCAGTGGACAATCACTCTAATTT 58.684 37.500 0.00 0.00 45.24 1.82
1677 1742 5.183904 GGACAATCACTCTAATTTTGGCTGT 59.816 40.000 0.00 0.00 0.00 4.40
1679 1744 7.383102 ACAATCACTCTAATTTTGGCTGTAG 57.617 36.000 0.00 0.00 0.00 2.74
1706 1771 5.061853 CCCTAGTGTTGAAGATGATGATGG 58.938 45.833 0.00 0.00 0.00 3.51
1717 1782 7.993101 TGAAGATGATGATGGTCTTGATTTTC 58.007 34.615 0.00 0.00 32.67 2.29
1751 1816 3.244078 GGCGATGATGATACTGGTGGTAA 60.244 47.826 0.00 0.00 33.74 2.85
1817 1885 6.701340 TCTTATCTCTAGTTCAGCAGCAAAA 58.299 36.000 0.00 0.00 0.00 2.44
1917 2003 7.171508 TGTTTTGAGCTTTCATCAGTGTAGTAG 59.828 37.037 0.00 0.00 0.00 2.57
1918 2004 4.748892 TGAGCTTTCATCAGTGTAGTAGC 58.251 43.478 0.00 0.00 0.00 3.58
1919 2005 4.220602 TGAGCTTTCATCAGTGTAGTAGCA 59.779 41.667 0.00 0.00 0.00 3.49
1920 2006 5.105187 TGAGCTTTCATCAGTGTAGTAGCAT 60.105 40.000 0.00 0.00 0.00 3.79
1921 2007 5.738909 AGCTTTCATCAGTGTAGTAGCATT 58.261 37.500 0.00 0.00 0.00 3.56
1922 2008 6.176183 AGCTTTCATCAGTGTAGTAGCATTT 58.824 36.000 0.00 0.00 0.00 2.32
1946 2032 5.125257 TCATTGTGAAGTTTGAGCACTTGAA 59.875 36.000 0.00 0.00 37.11 2.69
1947 2033 5.384063 TTGTGAAGTTTGAGCACTTGAAA 57.616 34.783 0.00 0.00 37.11 2.69
1960 2053 8.044060 TGAGCACTTGAAATTTTCTACATAGG 57.956 34.615 10.33 0.00 0.00 2.57
2047 2351 6.127793 ACGTTAGACAATACCTCCTACAGAT 58.872 40.000 0.00 0.00 0.00 2.90
2062 2366 9.667107 CCTCCTACAGATTAATCAAACAAACTA 57.333 33.333 17.56 0.00 0.00 2.24
2154 2460 5.092554 TCTGTCAGACACCACTTGTTTTA 57.907 39.130 0.00 0.00 39.17 1.52
2158 2464 5.758296 TGTCAGACACCACTTGTTTTATCTC 59.242 40.000 0.00 0.00 39.17 2.75
2239 2557 8.450578 TGCTACAAGAAAATTATATCAGGTGG 57.549 34.615 0.00 0.00 0.00 4.61
2244 2562 9.308000 ACAAGAAAATTATATCAGGTGGTTGAA 57.692 29.630 0.00 0.00 0.00 2.69
2267 2585 9.817809 TGAACCAAGAGAAGATATTACACATAC 57.182 33.333 0.00 0.00 0.00 2.39
2291 2609 1.168714 GGTGCTTTAACCTGCAGGAG 58.831 55.000 39.19 25.46 40.06 3.69
2294 2612 1.699634 TGCTTTAACCTGCAGGAGTCT 59.300 47.619 39.19 20.84 38.94 3.24
2301 2619 3.252974 ACCTGCAGGAGTCTAAATTCG 57.747 47.619 39.19 8.02 38.94 3.34
2327 2645 7.431084 GTGCAACGGTTATGGTTTTTGATATAG 59.569 37.037 0.00 0.00 0.00 1.31
2362 2680 9.645059 CCAAGATATAGTGTACAATCATACTGG 57.355 37.037 0.00 1.96 0.00 4.00
2372 2690 3.521126 ACAATCATACTGGGCTCAGAAGT 59.479 43.478 23.49 0.22 43.49 3.01
2376 2694 3.055819 TCATACTGGGCTCAGAAGTGTTC 60.056 47.826 23.49 0.00 43.49 3.18
2458 2776 8.974292 AGCTGGACCTAAATAATTCTATCCTA 57.026 34.615 0.00 0.00 0.00 2.94
2495 2814 3.571119 CTGCAACCCAGCTCTTCG 58.429 61.111 0.00 0.00 34.21 3.79
2510 2829 3.680196 GCTCTTCGCTTCTCCATAAAGGT 60.680 47.826 0.00 0.00 35.46 3.50
2512 2831 2.691409 TCGCTTCTCCATAAAGGTGG 57.309 50.000 0.00 0.00 40.76 4.61
2531 2850 2.025981 TGGGTTGAGAACTAGCATGCAT 60.026 45.455 21.98 7.68 0.00 3.96
2539 2858 5.163269 TGAGAACTAGCATGCATGTTAGGAT 60.163 40.000 37.77 30.06 43.30 3.24
2547 2866 4.735578 GCATGCATGTTAGGATGAACAAGG 60.736 45.833 26.79 0.00 42.39 3.61
2552 2871 5.183904 GCATGTTAGGATGAACAAGGTCTTT 59.816 40.000 0.00 0.00 42.39 2.52
2662 2985 7.665690 ACCACATTAATTAGTTGCATCAAACA 58.334 30.769 0.00 0.00 32.21 2.83
2663 2986 8.147058 ACCACATTAATTAGTTGCATCAAACAA 58.853 29.630 0.00 0.00 32.21 2.83
2666 2989 8.367156 ACATTAATTAGTTGCATCAAACAACCT 58.633 29.630 3.18 0.00 46.85 3.50
2701 3024 4.187694 CTCAGGAAAGCAACATCTACCTC 58.812 47.826 0.00 0.00 0.00 3.85
2722 5285 6.838612 ACCTCTTAGAGCTGACATCTAATCTT 59.161 38.462 3.26 0.00 38.30 2.40
2733 5296 6.003326 TGACATCTAATCTTGGCTTTTGTCA 58.997 36.000 0.00 0.00 38.75 3.58
2799 5362 3.529533 AGAAGATCAACTCATTGCGAGG 58.470 45.455 0.00 0.00 46.98 4.63
2806 5369 1.153107 CTCATTGCGAGGCATGGGA 60.153 57.895 0.00 0.00 38.76 4.37
2822 5385 5.105228 GGCATGGGATTTTCTGAAGATGAAA 60.105 40.000 0.00 0.00 0.00 2.69
2847 5410 6.204688 ACAAACATGGCTATTACGATATGTGG 59.795 38.462 0.00 0.00 0.00 4.17
2848 5411 5.483685 ACATGGCTATTACGATATGTGGT 57.516 39.130 0.00 0.00 0.00 4.16
2849 5412 6.599356 ACATGGCTATTACGATATGTGGTA 57.401 37.500 0.00 0.00 0.00 3.25
2850 5413 7.182817 ACATGGCTATTACGATATGTGGTAT 57.817 36.000 0.00 0.00 0.00 2.73
2851 5414 7.041721 ACATGGCTATTACGATATGTGGTATG 58.958 38.462 0.00 0.00 0.00 2.39
2852 5415 5.416083 TGGCTATTACGATATGTGGTATGC 58.584 41.667 0.00 0.00 0.00 3.14
2853 5416 4.809426 GGCTATTACGATATGTGGTATGCC 59.191 45.833 0.00 0.00 0.00 4.40
2872 5463 1.087771 CGTATGCCTCCGTTTGACCC 61.088 60.000 0.00 0.00 0.00 4.46
2957 5549 2.961741 GGTGTGGATGCTGATCTCTCTA 59.038 50.000 0.00 0.00 0.00 2.43
2986 5578 5.124457 GGTTGACTCAATTAGTGCATCACAT 59.876 40.000 0.00 0.00 39.07 3.21
2991 5583 7.553760 TGACTCAATTAGTGCATCACATGTTAT 59.446 33.333 0.00 0.00 39.07 1.89
3330 5930 2.957402 TCAATGACCCAAGTGCTTCT 57.043 45.000 0.00 0.00 0.00 2.85
3370 5970 9.457436 GGACCACCTTATTTCTACTATGAAAAA 57.543 33.333 0.00 0.00 39.08 1.94
3413 6013 4.439563 GGTGTATGGGCGAAAATTACAAGG 60.440 45.833 0.00 0.00 0.00 3.61
3417 6017 4.674281 TGGGCGAAAATTACAAGGTTTT 57.326 36.364 0.00 0.00 0.00 2.43
3431 6031 8.833231 TTACAAGGTTTTTGTTTGACATTCAA 57.167 26.923 0.00 0.00 34.03 2.69
3444 6044 3.066621 TGACATTCAACCAGAGTTTGTGC 59.933 43.478 0.00 0.00 32.45 4.57
3463 6063 3.999001 GTGCATTCTCTTCATCTGTGTGA 59.001 43.478 0.00 0.00 0.00 3.58
3523 6123 1.646189 GAGAACAGATCACCGCTTCC 58.354 55.000 0.00 0.00 0.00 3.46
3530 6130 0.759436 GATCACCGCTTCCCCCTCTA 60.759 60.000 0.00 0.00 0.00 2.43
3561 6161 3.569491 ACCATATTTGAGGCATTCCCTG 58.431 45.455 0.00 0.00 46.60 4.45
3571 6171 4.166725 TGAGGCATTCCCTGATTACAAGAT 59.833 41.667 0.00 0.00 46.60 2.40
3607 6207 1.001406 GGACCAGAGAACACACCTCAG 59.999 57.143 0.00 0.00 33.25 3.35
3659 6259 2.125512 ACAGAACGGATCCAGCGC 60.126 61.111 13.41 0.00 0.00 5.92
3719 6319 6.316140 GTGTACAGAAATATGTCAGGCATGAA 59.684 38.462 0.92 0.00 38.47 2.57
3869 6469 1.833630 TCTCTCGGCAACTCATTCCAT 59.166 47.619 0.00 0.00 0.00 3.41
3877 6477 3.005684 GGCAACTCATTCCATGTTGACAA 59.994 43.478 8.94 0.00 45.88 3.18
3907 6507 2.332063 CACTTGTCAGTGTCAAGGGT 57.668 50.000 26.63 10.88 44.96 4.34
3933 6533 3.586470 TTCCCAATGGTGTTACTGTGT 57.414 42.857 0.00 0.00 0.00 3.72
3955 6555 1.067354 GTCCTTGTTCACCGGTATCGT 60.067 52.381 6.87 0.00 33.95 3.73
4035 6635 6.712095 TGTTGAGATATGCAAAGCTAATAGGG 59.288 38.462 0.00 0.00 0.00 3.53
4102 6702 7.165460 TGATTGAGATTGCTGATGTGAAATT 57.835 32.000 0.00 0.00 0.00 1.82
4152 6752 5.067954 ACGTTAGTAGATTTGGTGGCTTTT 58.932 37.500 0.00 0.00 0.00 2.27
4164 6764 4.730966 TGGTGGCTTTTACTTGGTGATTA 58.269 39.130 0.00 0.00 0.00 1.75
4196 6796 4.821805 CCATGTAATAATCTTGCCGGAAGT 59.178 41.667 5.05 0.00 32.90 3.01
4201 6801 2.871096 AATCTTGCCGGAAGTAACCA 57.129 45.000 5.05 0.00 32.90 3.67
4240 6840 1.377536 GAGGGCAAGCACTCATCTTC 58.622 55.000 18.86 0.00 45.31 2.87
4246 6846 2.481952 GCAAGCACTCATCTTCGTTCTT 59.518 45.455 0.00 0.00 0.00 2.52
4291 6897 1.281899 GTCAAGTCAGCTATGGCGAC 58.718 55.000 14.78 14.78 44.37 5.19
4326 6934 3.128938 CCGCTGTAGTACCTATGCTATCC 59.871 52.174 0.00 0.00 0.00 2.59
4327 6935 3.756963 CGCTGTAGTACCTATGCTATCCA 59.243 47.826 0.00 0.00 0.00 3.41
4428 7038 8.680903 AGAAAGATCACATTAACATTTAGCTGG 58.319 33.333 0.00 0.00 0.00 4.85
4431 7041 8.757982 AGATCACATTAACATTTAGCTGGATT 57.242 30.769 0.00 0.00 0.00 3.01
4519 7130 4.141298 CCCTTCAAATCTTCCAGAGCCTAT 60.141 45.833 0.00 0.00 0.00 2.57
4536 7147 3.697166 CCTATTTTTGTACAGGCAGGGT 58.303 45.455 0.00 0.00 0.00 4.34
4625 8852 4.084011 TGAATGAATGGATATCGCCACA 57.916 40.909 0.00 0.00 41.56 4.17
4632 8859 6.272318 TGAATGGATATCGCCACAAAATTTC 58.728 36.000 0.00 0.00 41.56 2.17
4636 8863 7.581213 TGGATATCGCCACAAAATTTCTAAT 57.419 32.000 0.00 0.00 31.66 1.73
4744 9106 8.127150 TCACTATTTCTCTTGAACTCTCATCA 57.873 34.615 0.00 0.00 31.02 3.07
4772 9134 1.442526 GAATCCAGCATGACAGCCGG 61.443 60.000 0.00 0.00 39.69 6.13
4788 9150 1.238439 CCGGCAGTGTTGTTCTTCAT 58.762 50.000 0.00 0.00 0.00 2.57
4800 9162 6.922957 GTGTTGTTCTTCATTCTAATTTGGCA 59.077 34.615 0.00 0.00 0.00 4.92
4813 9175 7.792374 TCTAATTTGGCAATAGTCATCTGAC 57.208 36.000 0.00 2.01 45.08 3.51
5020 9560 8.857098 AGTGAGACACTGTTTTTATCTGTACTA 58.143 33.333 3.54 0.00 43.63 1.82
5054 9594 5.689383 TTCAGAATGTACTTGCTTGTTCC 57.311 39.130 0.00 0.00 37.40 3.62
5055 9595 4.713553 TCAGAATGTACTTGCTTGTTCCA 58.286 39.130 0.00 0.00 37.40 3.53
5056 9596 5.316167 TCAGAATGTACTTGCTTGTTCCAT 58.684 37.500 0.00 0.00 37.40 3.41
5057 9597 5.181811 TCAGAATGTACTTGCTTGTTCCATG 59.818 40.000 0.00 0.00 37.40 3.66
5058 9598 5.048504 CAGAATGTACTTGCTTGTTCCATGT 60.049 40.000 0.00 0.00 0.00 3.21
5059 9599 4.771590 ATGTACTTGCTTGTTCCATGTG 57.228 40.909 0.00 0.00 0.00 3.21
5060 9600 3.550820 TGTACTTGCTTGTTCCATGTGT 58.449 40.909 0.00 0.00 0.00 3.72
5061 9601 3.951037 TGTACTTGCTTGTTCCATGTGTT 59.049 39.130 0.00 0.00 0.00 3.32
5062 9602 3.715628 ACTTGCTTGTTCCATGTGTTC 57.284 42.857 0.00 0.00 0.00 3.18
5187 9742 7.896782 GGATTTTAACGAGTCGAGTTTATGTTC 59.103 37.037 21.50 4.77 33.42 3.18
5195 9750 8.618677 ACGAGTCGAGTTTATGTTCTTGATATA 58.381 33.333 21.50 0.00 0.00 0.86
5299 9860 4.453136 GCAACCTTAGGTATGACGAAAACA 59.547 41.667 3.55 0.00 33.12 2.83
5314 9875 6.811170 TGACGAAAACAGATTTCTTTTGCTTT 59.189 30.769 2.04 0.00 44.35 3.51
5317 9878 7.117667 ACGAAAACAGATTTCTTTTGCTTTTGT 59.882 29.630 2.04 0.00 44.35 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.508551 AGCAATGGTGGATCAGATACAA 57.491 40.909 0.00 0.00 0.00 2.41
48 49 7.976175 TGCTATACAGACTTGTATTCTTGACAG 59.024 37.037 5.61 0.00 45.92 3.51
96 97 4.410883 TGAGAGTTCCCAACAAAGAAGGTA 59.589 41.667 0.00 0.00 0.00 3.08
128 129 6.485171 ACTGGAGCAACTGGACTATAAAAAT 58.515 36.000 0.00 0.00 0.00 1.82
142 147 6.341316 TCAGAAGAACATATACTGGAGCAAC 58.659 40.000 0.00 0.00 0.00 4.17
163 170 7.201767 GGGTCCAGAATGTCTCAAATAAATCAG 60.202 40.741 0.00 0.00 0.00 2.90
176 184 3.769844 TCAACTCTAGGGTCCAGAATGTC 59.230 47.826 0.00 0.00 0.00 3.06
177 185 3.791320 TCAACTCTAGGGTCCAGAATGT 58.209 45.455 0.00 0.00 0.00 2.71
221 231 2.159490 TCATGCGACAGTCGTAATTCGA 60.159 45.455 23.62 12.10 46.83 3.71
259 273 4.983538 GTGTCAATGCATCAACATGAACAA 59.016 37.500 14.91 0.00 31.16 2.83
479 506 5.643777 ACAAGCACTACTGATGTACCATTTC 59.356 40.000 0.00 0.00 0.00 2.17
489 516 9.726438 AAGATTAACTAAACAAGCACTACTGAT 57.274 29.630 0.00 0.00 0.00 2.90
712 759 6.006275 AGCCCAGAAAATATACATCAGTGT 57.994 37.500 0.00 0.00 42.39 3.55
740 787 7.562454 ACCTCTGTCAAAAGACGAAATTAAA 57.438 32.000 0.00 0.00 0.00 1.52
749 796 3.142174 CCCTCAACCTCTGTCAAAAGAC 58.858 50.000 0.00 0.00 0.00 3.01
754 801 1.352083 CTCCCCTCAACCTCTGTCAA 58.648 55.000 0.00 0.00 0.00 3.18
761 808 1.850345 TGAACAAACTCCCCTCAACCT 59.150 47.619 0.00 0.00 0.00 3.50
822 871 8.819643 ACAACTACATTTGACTCTAGAGTTTC 57.180 34.615 25.86 14.83 42.66 2.78
849 898 6.384258 TTGAAAACTCCGACATGAAATCAA 57.616 33.333 0.00 0.00 0.00 2.57
860 909 8.792633 ACAAGATATCAAAATTGAAAACTCCGA 58.207 29.630 5.32 0.00 41.13 4.55
866 915 8.149647 ACAGCCACAAGATATCAAAATTGAAAA 58.850 29.630 5.32 0.00 41.13 2.29
875 924 3.758023 CCACAACAGCCACAAGATATCAA 59.242 43.478 5.32 0.00 0.00 2.57
943 996 7.849322 AAACCACCAGAAAACCAATTATAGT 57.151 32.000 0.00 0.00 0.00 2.12
953 1006 8.887036 ATATTGAAAGAAAACCACCAGAAAAC 57.113 30.769 0.00 0.00 0.00 2.43
968 1021 5.353123 GCACACCTCGGTTAATATTGAAAGA 59.647 40.000 0.00 0.00 0.00 2.52
982 1035 2.002586 CATGAGTTAAGCACACCTCGG 58.997 52.381 0.00 0.00 0.00 4.63
987 1040 3.187227 CCTGTGACATGAGTTAAGCACAC 59.813 47.826 0.00 0.00 33.30 3.82
1011 1064 3.119137 CGTCATCACTATCACTGGTCCAA 60.119 47.826 0.00 0.00 0.00 3.53
1032 1085 3.000727 GTCCCACTCAAACTTATCACCG 58.999 50.000 0.00 0.00 0.00 4.94
1033 1086 4.003648 CTGTCCCACTCAAACTTATCACC 58.996 47.826 0.00 0.00 0.00 4.02
1034 1087 4.452455 CACTGTCCCACTCAAACTTATCAC 59.548 45.833 0.00 0.00 0.00 3.06
1035 1088 4.346709 TCACTGTCCCACTCAAACTTATCA 59.653 41.667 0.00 0.00 0.00 2.15
1036 1089 4.894784 TCACTGTCCCACTCAAACTTATC 58.105 43.478 0.00 0.00 0.00 1.75
1037 1090 4.974645 TCACTGTCCCACTCAAACTTAT 57.025 40.909 0.00 0.00 0.00 1.73
1038 1091 4.974645 ATCACTGTCCCACTCAAACTTA 57.025 40.909 0.00 0.00 0.00 2.24
1039 1092 3.864789 ATCACTGTCCCACTCAAACTT 57.135 42.857 0.00 0.00 0.00 2.66
1040 1093 3.904339 ACTATCACTGTCCCACTCAAACT 59.096 43.478 0.00 0.00 0.00 2.66
1041 1094 3.997021 CACTATCACTGTCCCACTCAAAC 59.003 47.826 0.00 0.00 0.00 2.93
1042 1095 3.901222 TCACTATCACTGTCCCACTCAAA 59.099 43.478 0.00 0.00 0.00 2.69
1043 1096 3.506398 TCACTATCACTGTCCCACTCAA 58.494 45.455 0.00 0.00 0.00 3.02
1044 1097 3.169512 TCACTATCACTGTCCCACTCA 57.830 47.619 0.00 0.00 0.00 3.41
1045 1098 3.701542 TCATCACTATCACTGTCCCACTC 59.298 47.826 0.00 0.00 0.00 3.51
1046 1099 3.713003 TCATCACTATCACTGTCCCACT 58.287 45.455 0.00 0.00 0.00 4.00
1047 1100 4.679373 ATCATCACTATCACTGTCCCAC 57.321 45.455 0.00 0.00 0.00 4.61
1048 1101 5.302823 CACTATCATCACTATCACTGTCCCA 59.697 44.000 0.00 0.00 0.00 4.37
1049 1102 5.536538 TCACTATCATCACTATCACTGTCCC 59.463 44.000 0.00 0.00 0.00 4.46
1050 1103 6.641169 TCACTATCATCACTATCACTGTCC 57.359 41.667 0.00 0.00 0.00 4.02
1051 1104 9.838975 CTTATCACTATCATCACTATCACTGTC 57.161 37.037 0.00 0.00 0.00 3.51
1052 1105 9.360901 ACTTATCACTATCATCACTATCACTGT 57.639 33.333 0.00 0.00 0.00 3.55
1060 1113 7.984050 CCACTCAAACTTATCACTATCATCACT 59.016 37.037 0.00 0.00 0.00 3.41
1061 1114 7.225538 CCCACTCAAACTTATCACTATCATCAC 59.774 40.741 0.00 0.00 0.00 3.06
1062 1115 7.125659 TCCCACTCAAACTTATCACTATCATCA 59.874 37.037 0.00 0.00 0.00 3.07
1063 1116 7.500992 TCCCACTCAAACTTATCACTATCATC 58.499 38.462 0.00 0.00 0.00 2.92
1064 1117 7.437713 TCCCACTCAAACTTATCACTATCAT 57.562 36.000 0.00 0.00 0.00 2.45
1065 1118 6.867519 TCCCACTCAAACTTATCACTATCA 57.132 37.500 0.00 0.00 0.00 2.15
1066 1119 8.643324 ACTATCCCACTCAAACTTATCACTATC 58.357 37.037 0.00 0.00 0.00 2.08
1067 1120 8.424918 CACTATCCCACTCAAACTTATCACTAT 58.575 37.037 0.00 0.00 0.00 2.12
1068 1121 7.618117 TCACTATCCCACTCAAACTTATCACTA 59.382 37.037 0.00 0.00 0.00 2.74
1069 1122 6.440647 TCACTATCCCACTCAAACTTATCACT 59.559 38.462 0.00 0.00 0.00 3.41
1070 1123 6.640518 TCACTATCCCACTCAAACTTATCAC 58.359 40.000 0.00 0.00 0.00 3.06
1071 1124 6.867519 TCACTATCCCACTCAAACTTATCA 57.132 37.500 0.00 0.00 0.00 2.15
1072 1125 8.643324 ACTATCACTATCCCACTCAAACTTATC 58.357 37.037 0.00 0.00 0.00 1.75
1073 1126 8.424918 CACTATCACTATCCCACTCAAACTTAT 58.575 37.037 0.00 0.00 0.00 1.73
1074 1127 7.618117 TCACTATCACTATCCCACTCAAACTTA 59.382 37.037 0.00 0.00 0.00 2.24
1075 1128 6.440647 TCACTATCACTATCCCACTCAAACTT 59.559 38.462 0.00 0.00 0.00 2.66
1076 1129 5.958380 TCACTATCACTATCCCACTCAAACT 59.042 40.000 0.00 0.00 0.00 2.66
1077 1130 6.222038 TCACTATCACTATCCCACTCAAAC 57.778 41.667 0.00 0.00 0.00 2.93
1078 1131 6.611236 TCATCACTATCACTATCCCACTCAAA 59.389 38.462 0.00 0.00 0.00 2.69
1079 1132 6.040955 GTCATCACTATCACTATCCCACTCAA 59.959 42.308 0.00 0.00 0.00 3.02
1080 1133 5.536538 GTCATCACTATCACTATCCCACTCA 59.463 44.000 0.00 0.00 0.00 3.41
1081 1134 5.536538 TGTCATCACTATCACTATCCCACTC 59.463 44.000 0.00 0.00 0.00 3.51
1082 1135 5.458595 TGTCATCACTATCACTATCCCACT 58.541 41.667 0.00 0.00 0.00 4.00
1083 1136 5.303078 ACTGTCATCACTATCACTATCCCAC 59.697 44.000 0.00 0.00 0.00 4.61
1084 1137 5.302823 CACTGTCATCACTATCACTATCCCA 59.697 44.000 0.00 0.00 0.00 4.37
1085 1138 5.536538 TCACTGTCATCACTATCACTATCCC 59.463 44.000 0.00 0.00 0.00 3.85
1086 1139 6.641169 TCACTGTCATCACTATCACTATCC 57.359 41.667 0.00 0.00 0.00 2.59
1087 1140 9.838975 CTTATCACTGTCATCACTATCACTATC 57.161 37.037 0.00 0.00 0.00 2.08
1088 1141 9.360901 ACTTATCACTGTCATCACTATCACTAT 57.639 33.333 0.00 0.00 0.00 2.12
1089 1142 8.753497 ACTTATCACTGTCATCACTATCACTA 57.247 34.615 0.00 0.00 0.00 2.74
1090 1143 7.652524 ACTTATCACTGTCATCACTATCACT 57.347 36.000 0.00 0.00 0.00 3.41
1091 1144 8.598924 CAAACTTATCACTGTCATCACTATCAC 58.401 37.037 0.00 0.00 0.00 3.06
1092 1145 8.531146 TCAAACTTATCACTGTCATCACTATCA 58.469 33.333 0.00 0.00 0.00 2.15
1093 1146 8.932945 TCAAACTTATCACTGTCATCACTATC 57.067 34.615 0.00 0.00 0.00 2.08
1094 1147 8.535335 ACTCAAACTTATCACTGTCATCACTAT 58.465 33.333 0.00 0.00 0.00 2.12
1095 1148 7.814587 CACTCAAACTTATCACTGTCATCACTA 59.185 37.037 0.00 0.00 0.00 2.74
1096 1149 6.648310 CACTCAAACTTATCACTGTCATCACT 59.352 38.462 0.00 0.00 0.00 3.41
1097 1150 6.128445 CCACTCAAACTTATCACTGTCATCAC 60.128 42.308 0.00 0.00 0.00 3.06
1098 1151 5.934043 CCACTCAAACTTATCACTGTCATCA 59.066 40.000 0.00 0.00 0.00 3.07
1099 1152 5.352569 CCCACTCAAACTTATCACTGTCATC 59.647 44.000 0.00 0.00 0.00 2.92
1100 1153 5.013079 TCCCACTCAAACTTATCACTGTCAT 59.987 40.000 0.00 0.00 0.00 3.06
1101 1154 4.346709 TCCCACTCAAACTTATCACTGTCA 59.653 41.667 0.00 0.00 0.00 3.58
1102 1155 4.691216 GTCCCACTCAAACTTATCACTGTC 59.309 45.833 0.00 0.00 0.00 3.51
1103 1156 4.102524 TGTCCCACTCAAACTTATCACTGT 59.897 41.667 0.00 0.00 0.00 3.55
1206 1259 7.881643 TGCGCTGAAATACAAAATTTATGTT 57.118 28.000 9.73 0.00 32.27 2.71
1289 1343 4.540099 TCCACCCATCCAAACTCTTTAGAT 59.460 41.667 0.00 0.00 0.00 1.98
1301 1355 1.607071 CCGTTGATCCACCCATCCA 59.393 57.895 0.00 0.00 0.00 3.41
1302 1356 1.152963 CCCGTTGATCCACCCATCC 60.153 63.158 0.00 0.00 0.00 3.51
1303 1357 1.152963 CCCCGTTGATCCACCCATC 60.153 63.158 0.00 0.00 0.00 3.51
1425 1479 9.927668 AACACAAACAGGATAAATAAAATGGAG 57.072 29.630 0.00 0.00 0.00 3.86
1471 1526 4.095483 GCATCACTATGTCCTGAAAACAGG 59.905 45.833 9.67 9.67 37.35 4.00
1475 1530 5.164620 TCTGCATCACTATGTCCTGAAAA 57.835 39.130 0.00 0.00 35.38 2.29
1501 1556 0.253327 TGAGGAGTAGCTCGAGCAGA 59.747 55.000 36.87 22.71 45.16 4.26
1562 1621 9.713740 GAATCAAGAGCAGTACAGAATAAATTG 57.286 33.333 0.00 0.00 0.00 2.32
1609 1668 3.490419 GCCTGCATTTCACATCTCAATCC 60.490 47.826 0.00 0.00 0.00 3.01
1645 1704 5.675684 TTAGAGTGATTGTCCACTGCATA 57.324 39.130 0.88 0.00 46.45 3.14
1688 1753 5.645067 TCAAGACCATCATCATCTTCAACAC 59.355 40.000 0.00 0.00 30.17 3.32
1706 1771 5.105997 CCATCCCAGTTCTGAAAATCAAGAC 60.106 44.000 1.00 0.00 0.00 3.01
1717 1782 0.178767 TCATCGCCATCCCAGTTCTG 59.821 55.000 0.00 0.00 0.00 3.02
1841 1910 6.717997 TGCATGGCAAAGATCTCACATATATT 59.282 34.615 0.00 0.00 34.76 1.28
1852 1921 1.180029 AGGTGTGCATGGCAAAGATC 58.820 50.000 0.00 0.00 41.47 2.75
1917 2003 4.746115 TGCTCAAACTTCACAATGAAATGC 59.254 37.500 0.00 0.00 35.73 3.56
1918 2004 5.981315 AGTGCTCAAACTTCACAATGAAATG 59.019 36.000 0.00 0.00 35.73 2.32
1919 2005 6.152932 AGTGCTCAAACTTCACAATGAAAT 57.847 33.333 0.00 0.00 35.73 2.17
1920 2006 5.581126 AGTGCTCAAACTTCACAATGAAA 57.419 34.783 0.00 0.00 35.73 2.69
1921 2007 5.125257 TCAAGTGCTCAAACTTCACAATGAA 59.875 36.000 0.00 0.00 38.34 2.57
1922 2008 4.639755 TCAAGTGCTCAAACTTCACAATGA 59.360 37.500 0.00 0.00 38.34 2.57
1947 2033 9.479549 ACATGGTGAAAATCCTATGTAGAAAAT 57.520 29.630 0.00 0.00 30.85 1.82
2018 2322 8.752187 TGTAGGAGGTATTGTCTAACGTTATTT 58.248 33.333 8.76 0.00 0.00 1.40
2069 2373 9.220906 AGGACAATAATACACCCAGTTTCTATA 57.779 33.333 0.00 0.00 0.00 1.31
2080 2386 5.897377 AACAAGCAGGACAATAATACACC 57.103 39.130 0.00 0.00 0.00 4.16
2126 2432 6.299141 ACAAGTGGTGTCTGACAGAAATTAT 58.701 36.000 11.41 0.00 34.38 1.28
2137 2443 5.063204 TGGAGATAAAACAAGTGGTGTCTG 58.937 41.667 0.00 0.00 40.60 3.51
2154 2460 7.893124 ATTCAAATGCATAAGAACTGGAGAT 57.107 32.000 13.91 0.00 0.00 2.75
2192 2506 6.886459 AGCAACATAACTCCACAAGTCATAAT 59.114 34.615 0.00 0.00 37.17 1.28
2196 2510 4.085357 AGCAACATAACTCCACAAGTCA 57.915 40.909 0.00 0.00 37.17 3.41
2239 2557 8.547967 TGTGTAATATCTTCTCTTGGTTCAAC 57.452 34.615 0.00 0.00 0.00 3.18
2267 2585 4.130118 CCTGCAGGTTAAAGCACCTATAG 58.870 47.826 25.53 0.00 46.27 1.31
2270 2588 1.982226 TCCTGCAGGTTAAAGCACCTA 59.018 47.619 31.58 5.39 46.27 3.08
2272 2590 1.168714 CTCCTGCAGGTTAAAGCACC 58.831 55.000 31.58 0.00 36.62 5.01
2289 2607 2.735134 ACCGTTGCACGAATTTAGACTC 59.265 45.455 9.75 0.00 46.05 3.36
2291 2609 3.531262 AACCGTTGCACGAATTTAGAC 57.469 42.857 9.75 0.00 46.05 2.59
2294 2612 3.752222 ACCATAACCGTTGCACGAATTTA 59.248 39.130 9.75 5.50 46.05 1.40
2301 2619 3.707793 TCAAAAACCATAACCGTTGCAC 58.292 40.909 0.00 0.00 0.00 4.57
2327 2645 9.865321 TTGTACACTATATCTTGGACTACAAAC 57.135 33.333 0.00 0.00 38.91 2.93
2362 2680 1.000955 TCTTCCGAACACTTCTGAGCC 59.999 52.381 0.00 0.00 0.00 4.70
2372 2690 7.159372 AGTTTAGCTTCTAATTCTTCCGAACA 58.841 34.615 0.00 0.00 30.67 3.18
2376 2694 7.596749 TCAAGTTTAGCTTCTAATTCTTCCG 57.403 36.000 0.00 0.00 34.69 4.30
2458 2776 4.732784 CAGCACAAACTTTACAACAGTGT 58.267 39.130 0.00 0.00 42.09 3.55
2492 2811 2.355716 CCCACCTTTATGGAGAAGCGAA 60.356 50.000 0.00 0.00 43.02 4.70
2495 2814 2.755103 CAACCCACCTTTATGGAGAAGC 59.245 50.000 0.00 0.00 43.02 3.86
2510 2829 1.350684 TGCATGCTAGTTCTCAACCCA 59.649 47.619 20.33 0.00 0.00 4.51
2512 2831 3.012518 ACATGCATGCTAGTTCTCAACC 58.987 45.455 26.53 0.00 0.00 3.77
2531 2850 7.741785 TCTTAAAGACCTTGTTCATCCTAACA 58.258 34.615 0.00 0.00 37.58 2.41
2662 2985 1.850345 TGAGGTTGGTCTTGGAAGGTT 59.150 47.619 0.00 0.00 0.00 3.50
2663 2986 1.421646 CTGAGGTTGGTCTTGGAAGGT 59.578 52.381 0.00 0.00 0.00 3.50
2666 2989 1.814429 TCCTGAGGTTGGTCTTGGAA 58.186 50.000 0.00 0.00 0.00 3.53
2701 3024 5.695816 GCCAAGATTAGATGTCAGCTCTAAG 59.304 44.000 0.00 0.00 38.30 2.18
2722 5285 3.243704 GCACAAAGGTATGACAAAAGCCA 60.244 43.478 0.00 0.00 0.00 4.75
2733 5296 5.354234 CGTAGAAAATCCTGCACAAAGGTAT 59.646 40.000 0.00 0.00 38.58 2.73
2799 5362 5.587388 TTCATCTTCAGAAAATCCCATGC 57.413 39.130 0.00 0.00 0.00 4.06
2806 5369 7.172019 GCCATGTTTGTTTCATCTTCAGAAAAT 59.828 33.333 0.00 0.00 36.80 1.82
2822 5385 6.204688 CCACATATCGTAATAGCCATGTTTGT 59.795 38.462 0.00 0.00 0.00 2.83
2851 5414 1.448893 TCAAACGGAGGCATACGGC 60.449 57.895 8.32 0.00 36.93 5.68
2852 5415 1.087771 GGTCAAACGGAGGCATACGG 61.088 60.000 8.32 0.00 36.93 4.02
2853 5416 1.087771 GGGTCAAACGGAGGCATACG 61.088 60.000 0.00 0.00 39.32 3.06
2872 5463 6.098017 GCCTTTTCCATGAAGAAAGAATGAG 58.902 40.000 13.53 3.11 37.09 2.90
2918 5509 6.070194 TCCACACCTGGGAAAATTTTAAACAA 60.070 34.615 2.75 0.00 38.25 2.83
2927 5519 1.077663 AGCATCCACACCTGGGAAAAT 59.922 47.619 0.00 0.00 38.09 1.82
2934 5526 1.485480 AGAGATCAGCATCCACACCTG 59.515 52.381 0.00 0.00 0.00 4.00
2957 5549 7.557358 TGATGCACTAATTGAGTCAACCAATAT 59.443 33.333 7.96 0.00 35.64 1.28
3290 5890 3.223940 TGGTCCCCTATAACCAGGAAA 57.776 47.619 0.00 0.00 40.60 3.13
3321 5921 4.570930 GGTAGCTAGTTCAAGAAGCACTT 58.429 43.478 0.00 0.00 38.75 3.16
3330 5930 1.547372 GTGGTCCGGTAGCTAGTTCAA 59.453 52.381 0.00 0.00 0.00 2.69
3370 5970 2.424842 TTTTGGAGCTCGGGCCACAT 62.425 55.000 2.00 0.00 39.73 3.21
3431 6031 3.498774 AGAGAATGCACAAACTCTGGT 57.501 42.857 11.24 0.00 38.14 4.00
3463 6063 1.372501 TCCCCTTTTCCTAGCAGCTT 58.627 50.000 0.00 0.00 0.00 3.74
3491 6091 2.955660 TCTGTTCTCGGTTGGCAAATTT 59.044 40.909 0.00 0.00 0.00 1.82
3523 6123 1.279749 GGTCTTTGGGGGTAGAGGGG 61.280 65.000 0.00 0.00 0.00 4.79
3530 6130 3.309848 CCTCAAATATGGTCTTTGGGGGT 60.310 47.826 6.77 0.00 46.26 4.95
3561 6161 2.722094 TGGCCACCACATCTTGTAATC 58.278 47.619 0.00 0.00 0.00 1.75
3607 6207 2.412770 GCCATACATGTTTGCAAGCAAC 59.587 45.455 20.20 6.43 35.46 4.17
3719 6319 4.021719 CAGACAAGGTTCCATTTTGAGCAT 60.022 41.667 0.00 0.00 0.00 3.79
3812 6412 1.112916 TGCCGACTCCTCTTGTGTGA 61.113 55.000 0.00 0.00 0.00 3.58
3869 6469 2.610374 GTGGTAAGCGACTTTGTCAACA 59.390 45.455 0.00 0.00 32.09 3.33
3877 6477 2.102588 ACTGACAAGTGGTAAGCGACTT 59.897 45.455 0.00 0.00 42.99 3.01
3900 6500 3.164268 CATTGGGAAACATGACCCTTGA 58.836 45.455 20.93 11.83 45.74 3.02
3901 6501 2.234414 CCATTGGGAAACATGACCCTTG 59.766 50.000 20.93 18.01 45.74 3.61
3902 6502 2.158173 ACCATTGGGAAACATGACCCTT 60.158 45.455 20.93 10.88 45.74 3.95
3907 6507 4.522405 CAGTAACACCATTGGGAAACATGA 59.478 41.667 7.78 0.00 38.05 3.07
3933 6533 2.610976 CGATACCGGTGAACAAGGACAA 60.611 50.000 19.93 0.00 0.00 3.18
3955 6555 1.279271 GCAAAGCAACCTCTCCTCCTA 59.721 52.381 0.00 0.00 0.00 2.94
4035 6635 3.084786 CCCACCAACTCCTCAAAATCTC 58.915 50.000 0.00 0.00 0.00 2.75
4071 6671 2.095617 CAGCAATCTCAATCAACGTGCA 60.096 45.455 0.00 0.00 32.98 4.57
4102 6702 5.301045 GATGCAATTTCATCATCCTTGAGGA 59.699 40.000 12.47 1.54 40.68 3.71
4130 6730 5.622770 AAAAGCCACCAAATCTACTAACG 57.377 39.130 0.00 0.00 0.00 3.18
4152 6752 1.211949 GCTGCCCCTAATCACCAAGTA 59.788 52.381 0.00 0.00 0.00 2.24
4240 6840 7.813148 TCAAGATCCTAAAGTAGTCAAAGAACG 59.187 37.037 0.00 0.00 0.00 3.95
4246 6846 7.764443 CGGAATTCAAGATCCTAAAGTAGTCAA 59.236 37.037 7.93 0.00 33.36 3.18
4439 7049 7.339212 TGAACATGCCATAACTTAGTTAGCAAT 59.661 33.333 18.39 10.22 34.54 3.56
4451 7061 8.196771 TCCAAATAAAGATGAACATGCCATAAC 58.803 33.333 0.00 0.00 0.00 1.89
4459 7069 8.992073 GTGCTTTTTCCAAATAAAGATGAACAT 58.008 29.630 0.00 0.00 34.11 2.71
4519 7130 2.445682 ACACCCTGCCTGTACAAAAA 57.554 45.000 0.00 0.00 0.00 1.94
4536 7147 5.626142 ACCACATCAGGTGTACAAATTACA 58.374 37.500 0.00 0.00 46.44 2.41
4632 8859 8.730680 ACAAACCTGCAAGTTGATACTTATTAG 58.269 33.333 7.16 0.00 42.67 1.73
4636 8863 6.296026 AGACAAACCTGCAAGTTGATACTTA 58.704 36.000 7.16 0.00 42.67 2.24
4744 9106 6.598457 GCTGTCATGCTGGATTCAGATATAAT 59.402 38.462 4.75 0.00 43.49 1.28
4772 9134 7.115378 CCAAATTAGAATGAAGAACAACACTGC 59.885 37.037 0.00 0.00 0.00 4.40
4788 9150 7.283127 GGTCAGATGACTATTGCCAAATTAGAA 59.717 37.037 12.43 0.00 44.20 2.10
4800 9162 6.421485 AGATTTGCAAGGTCAGATGACTATT 58.579 36.000 12.43 5.72 44.20 1.73
4813 9175 4.977963 CACAAGTGTTGTAGATTTGCAAGG 59.022 41.667 0.00 0.00 43.23 3.61
4835 9358 7.744087 AAACAGTAGCATTAATCACAACTCA 57.256 32.000 0.00 0.00 0.00 3.41
4862 9385 9.905713 TCACTGCTAAACTCTTGGAATAATAAT 57.094 29.630 0.00 0.00 0.00 1.28
4925 9455 8.102047 TCCATGCATTTTATCAAACTTCCAAAT 58.898 29.630 0.00 0.00 0.00 2.32
5025 9565 6.699575 AGCAAGTACATTCTGAAACAAAGT 57.300 33.333 0.00 0.00 0.00 2.66
5054 9594 2.732412 ACTCCAGAGTCGAACACATG 57.268 50.000 0.00 0.00 36.92 3.21
5055 9595 3.393800 CAAACTCCAGAGTCGAACACAT 58.606 45.455 0.00 0.00 41.58 3.21
5056 9596 2.483013 CCAAACTCCAGAGTCGAACACA 60.483 50.000 0.00 0.00 41.58 3.72
5057 9597 2.135933 CCAAACTCCAGAGTCGAACAC 58.864 52.381 0.00 0.00 41.58 3.32
5058 9598 1.760613 ACCAAACTCCAGAGTCGAACA 59.239 47.619 0.00 0.00 41.58 3.18
5059 9599 2.135933 CACCAAACTCCAGAGTCGAAC 58.864 52.381 0.00 0.00 41.58 3.95
5060 9600 1.760613 ACACCAAACTCCAGAGTCGAA 59.239 47.619 0.00 0.00 41.58 3.71
5061 9601 1.410004 ACACCAAACTCCAGAGTCGA 58.590 50.000 0.00 0.00 41.58 4.20
5062 9602 2.557056 TCTACACCAAACTCCAGAGTCG 59.443 50.000 0.00 0.00 41.58 4.18
5195 9750 3.197766 TCCGGATGCAGTCTACAAGAAAT 59.802 43.478 0.00 0.00 0.00 2.17
5299 9860 6.873076 TGTGACAACAAAAGCAAAAGAAATCT 59.127 30.769 0.00 0.00 31.82 2.40


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

AutoCloner maintained by Alex Coulton.