Multiple sequence alignment - TraesCS6A01G082200

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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 TraesCS6A01G082200 chr6A 100.000 3576 0 0 1 3576 51395913 51399488 0.000000e+00 6604.0
1 TraesCS6A01G082200 chr6A 78.336 1094 174 36 1135 2205 51373566 51374619 0.000000e+00 649.0
2 TraesCS6A01G082200 chr6A 77.123 883 148 34 1197 2034 846607 847480 2.520000e-126 462.0
3 TraesCS6A01G082200 chr6B 86.008 2866 253 64 743 3576 90099882 90102631 0.000000e+00 2935.0
4 TraesCS6A01G082200 chr6B 79.059 1041 175 30 1239 2262 89903906 89904920 0.000000e+00 675.0
5 TraesCS6A01G082200 chr6B 80.396 454 59 20 228 664 689211803 689211363 5.760000e-83 318.0
6 TraesCS6A01G082200 chr6B 91.071 56 5 0 687 742 90099448 90099503 3.830000e-10 76.8
7 TraesCS6A01G082200 chr6D 90.630 1302 90 22 1166 2439 38875540 38876837 0.000000e+00 1700.0
8 TraesCS6A01G082200 chr6D 89.325 1096 91 14 2502 3576 38876866 38877956 0.000000e+00 1352.0
9 TraesCS6A01G082200 chr6D 78.992 1190 200 36 1204 2371 38635807 38636968 0.000000e+00 767.0
10 TraesCS6A01G082200 chr6D 79.310 1160 187 35 1239 2371 38816375 38817508 0.000000e+00 763.0
11 TraesCS6A01G082200 chr6D 77.336 1156 189 48 1203 2323 1998025 1996908 1.820000e-172 616.0
12 TraesCS6A01G082200 chr6D 78.537 820 134 29 1389 2201 38752551 38753335 5.330000e-138 501.0
13 TraesCS6A01G082200 chr6D 81.593 565 95 4 1797 2360 38827277 38827833 3.250000e-125 459.0
14 TraesCS6A01G082200 chr6D 94.007 267 16 0 690 956 38858855 38859121 4.300000e-109 405.0
15 TraesCS6A01G082200 chr6D 97.163 141 4 0 3047 3187 38804609 38804749 4.610000e-59 239.0
16 TraesCS6A01G082200 chr6D 83.333 138 21 1 1788 1925 38647516 38647651 3.750000e-25 126.0
17 TraesCS6A01G082200 chr7A 89.883 682 47 6 1 664 49584442 49583765 0.000000e+00 857.0
18 TraesCS6A01G082200 chr7A 85.283 265 28 10 402 664 633417582 633417327 2.740000e-66 263.0
19 TraesCS6A01G082200 chrUn 79.184 1177 201 32 1204 2360 76982328 76981176 0.000000e+00 776.0
20 TraesCS6A01G082200 chrUn 79.184 1177 201 32 1204 2360 261142467 261141315 0.000000e+00 776.0
21 TraesCS6A01G082200 chrUn 84.288 681 70 14 1 664 7181100 7180440 6.520000e-177 630.0
22 TraesCS6A01G082200 chr5A 82.628 685 82 30 1 664 654878156 654877488 4.010000e-159 571.0
23 TraesCS6A01G082200 chr5B 82.370 692 74 18 1 664 610015838 610016509 3.120000e-155 558.0
24 TraesCS6A01G082200 chr5B 79.613 672 102 31 1 663 3552110 3551465 1.960000e-122 449.0
25 TraesCS6A01G082200 chr5B 81.190 420 49 17 260 664 321025958 321025554 9.640000e-81 311.0
26 TraesCS6A01G082200 chr4B 82.258 682 55 31 1 664 85591449 85592082 2.440000e-146 529.0
27 TraesCS6A01G082200 chr3B 80.631 666 73 41 1 664 820313177 820313788 6.990000e-127 464.0
28 TraesCS6A01G082200 chr3B 89.558 249 21 3 1 249 812791690 812791447 9.640000e-81 311.0
29 TraesCS6A01G082200 chr3B 89.862 217 17 4 451 664 711757057 711757271 1.260000e-69 274.0
30 TraesCS6A01G082200 chr7B 82.600 477 46 19 1 477 725315604 725315165 1.560000e-103 387.0
31 TraesCS6A01G082200 chr4A 83.750 400 50 10 277 664 734932658 734933054 7.300000e-97 364.0
32 TraesCS6A01G082200 chr1B 83.832 334 46 6 334 664 642808770 642809098 9.640000e-81 311.0


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 TraesCS6A01G082200 chr6A 51395913 51399488 3575 False 6604.0 6604 100.0000 1 3576 1 chr6A.!!$F3 3575
1 TraesCS6A01G082200 chr6A 51373566 51374619 1053 False 649.0 649 78.3360 1135 2205 1 chr6A.!!$F2 1070
2 TraesCS6A01G082200 chr6A 846607 847480 873 False 462.0 462 77.1230 1197 2034 1 chr6A.!!$F1 837
3 TraesCS6A01G082200 chr6B 90099448 90102631 3183 False 1505.9 2935 88.5395 687 3576 2 chr6B.!!$F2 2889
4 TraesCS6A01G082200 chr6B 89903906 89904920 1014 False 675.0 675 79.0590 1239 2262 1 chr6B.!!$F1 1023
5 TraesCS6A01G082200 chr6D 38875540 38877956 2416 False 1526.0 1700 89.9775 1166 3576 2 chr6D.!!$F8 2410
6 TraesCS6A01G082200 chr6D 38635807 38636968 1161 False 767.0 767 78.9920 1204 2371 1 chr6D.!!$F1 1167
7 TraesCS6A01G082200 chr6D 38816375 38817508 1133 False 763.0 763 79.3100 1239 2371 1 chr6D.!!$F5 1132
8 TraesCS6A01G082200 chr6D 1996908 1998025 1117 True 616.0 616 77.3360 1203 2323 1 chr6D.!!$R1 1120
9 TraesCS6A01G082200 chr6D 38752551 38753335 784 False 501.0 501 78.5370 1389 2201 1 chr6D.!!$F3 812
10 TraesCS6A01G082200 chr6D 38827277 38827833 556 False 459.0 459 81.5930 1797 2360 1 chr6D.!!$F6 563
11 TraesCS6A01G082200 chr7A 49583765 49584442 677 True 857.0 857 89.8830 1 664 1 chr7A.!!$R1 663
12 TraesCS6A01G082200 chrUn 76981176 76982328 1152 True 776.0 776 79.1840 1204 2360 1 chrUn.!!$R2 1156
13 TraesCS6A01G082200 chrUn 261141315 261142467 1152 True 776.0 776 79.1840 1204 2360 1 chrUn.!!$R3 1156
14 TraesCS6A01G082200 chrUn 7180440 7181100 660 True 630.0 630 84.2880 1 664 1 chrUn.!!$R1 663
15 TraesCS6A01G082200 chr5A 654877488 654878156 668 True 571.0 571 82.6280 1 664 1 chr5A.!!$R1 663
16 TraesCS6A01G082200 chr5B 610015838 610016509 671 False 558.0 558 82.3700 1 664 1 chr5B.!!$F1 663
17 TraesCS6A01G082200 chr5B 3551465 3552110 645 True 449.0 449 79.6130 1 663 1 chr5B.!!$R1 662
18 TraesCS6A01G082200 chr4B 85591449 85592082 633 False 529.0 529 82.2580 1 664 1 chr4B.!!$F1 663
19 TraesCS6A01G082200 chr3B 820313177 820313788 611 False 464.0 464 80.6310 1 664 1 chr3B.!!$F2 663

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
752 844 0.026803 GCATCGATCTGAAACCACGC 59.973 55.0 0.0 0.0 0.0 5.34 F
2443 3046 0.097674 GTGTCGCTGATGCCACAATC 59.902 55.0 0.0 0.0 41.6 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2471 3074 0.106719 AACACAATCCTATGCCCCGG 60.107 55.000 0.00 0.0 0.0 5.73 R
3329 3947 1.000843 GTGTCTTTTCCATTGGCCACC 59.999 52.381 3.88 0.0 0.0 4.61 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
27 28 2.037144 AGGTACTCACGGAACACAAGT 58.963 47.619 0.00 0.00 0.00 3.16
226 230 3.828023 GGTGGTGGGTGGGTGGTT 61.828 66.667 0.00 0.00 0.00 3.67
258 262 2.112297 GGTTGGGAAGTGTGGCGA 59.888 61.111 0.00 0.00 0.00 5.54
529 621 7.545615 CGTGCTGCAATAGATACCATATAGAAA 59.454 37.037 2.77 0.00 0.00 2.52
573 665 3.005791 TCTCGATGTATTGATCGGTGCAT 59.994 43.478 0.00 1.36 44.41 3.96
602 694 9.334947 GGCACGTATATATAAGTATAGAGGTGA 57.665 37.037 18.98 0.00 45.04 4.02
641 733 0.104409 AGAGGAAACAGGAGGTGGGT 60.104 55.000 0.00 0.00 0.00 4.51
664 756 5.397534 GTCCTACACGCAAATATACACGTAG 59.602 44.000 0.00 0.00 36.91 3.51
665 757 5.296531 TCCTACACGCAAATATACACGTAGA 59.703 40.000 0.00 0.00 36.91 2.59
666 758 5.624081 CCTACACGCAAATATACACGTAGAG 59.376 44.000 0.00 0.00 36.91 2.43
667 759 5.239359 ACACGCAAATATACACGTAGAGA 57.761 39.130 0.00 0.00 36.91 3.10
668 760 5.643664 ACACGCAAATATACACGTAGAGAA 58.356 37.500 0.00 0.00 36.91 2.87
669 761 6.094719 ACACGCAAATATACACGTAGAGAAA 58.905 36.000 0.00 0.00 36.91 2.52
670 762 6.587226 ACACGCAAATATACACGTAGAGAAAA 59.413 34.615 0.00 0.00 36.91 2.29
671 763 7.111139 CACGCAAATATACACGTAGAGAAAAG 58.889 38.462 0.00 0.00 36.91 2.27
672 764 7.008901 CACGCAAATATACACGTAGAGAAAAGA 59.991 37.037 0.00 0.00 36.91 2.52
673 765 7.220300 ACGCAAATATACACGTAGAGAAAAGAG 59.780 37.037 0.00 0.00 36.91 2.85
674 766 7.306051 CGCAAATATACACGTAGAGAAAAGAGG 60.306 40.741 0.00 0.00 0.00 3.69
675 767 7.516943 GCAAATATACACGTAGAGAAAAGAGGC 60.517 40.741 0.00 0.00 0.00 4.70
676 768 2.745515 ACACGTAGAGAAAAGAGGCC 57.254 50.000 0.00 0.00 0.00 5.19
677 769 2.249139 ACACGTAGAGAAAAGAGGCCT 58.751 47.619 3.86 3.86 0.00 5.19
678 770 2.028930 ACACGTAGAGAAAAGAGGCCTG 60.029 50.000 12.00 0.00 0.00 4.85
679 771 1.550976 ACGTAGAGAAAAGAGGCCTGG 59.449 52.381 12.00 0.00 0.00 4.45
680 772 1.740718 CGTAGAGAAAAGAGGCCTGGC 60.741 57.143 12.00 11.05 0.00 4.85
695 787 2.027100 GCCTGGCCAAGTAGTAACTCTT 60.027 50.000 7.01 0.00 33.75 2.85
742 834 2.558378 CAAGTGTGGATGCATCGATCT 58.442 47.619 20.15 15.06 0.00 2.75
745 837 2.169144 AGTGTGGATGCATCGATCTGAA 59.831 45.455 20.15 0.00 0.00 3.02
746 838 2.938451 GTGTGGATGCATCGATCTGAAA 59.062 45.455 20.15 0.00 0.00 2.69
747 839 2.938451 TGTGGATGCATCGATCTGAAAC 59.062 45.455 20.15 3.68 0.00 2.78
748 840 2.289002 GTGGATGCATCGATCTGAAACC 59.711 50.000 20.15 3.77 0.00 3.27
749 841 2.093021 TGGATGCATCGATCTGAAACCA 60.093 45.455 20.15 6.48 0.00 3.67
750 842 2.289002 GGATGCATCGATCTGAAACCAC 59.711 50.000 20.15 0.00 0.00 4.16
751 843 1.358877 TGCATCGATCTGAAACCACG 58.641 50.000 0.00 0.00 0.00 4.94
752 844 0.026803 GCATCGATCTGAAACCACGC 59.973 55.000 0.00 0.00 0.00 5.34
753 845 1.358877 CATCGATCTGAAACCACGCA 58.641 50.000 0.00 0.00 0.00 5.24
754 846 1.731709 CATCGATCTGAAACCACGCAA 59.268 47.619 0.00 0.00 0.00 4.85
756 848 0.179215 CGATCTGAAACCACGCAAGC 60.179 55.000 0.00 0.00 45.62 4.01
768 1240 2.094659 CGCAAGCTCAATCGACGGT 61.095 57.895 0.00 0.00 0.00 4.83
779 1251 0.679002 ATCGACGGTCTCCTCGGAAA 60.679 55.000 6.57 0.00 0.00 3.13
792 1264 2.939103 CCTCGGAAATGTAAAGCCTCTG 59.061 50.000 0.00 0.00 0.00 3.35
802 1274 5.429681 TGTAAAGCCTCTGCATTAACCTA 57.570 39.130 0.00 0.00 41.13 3.08
803 1275 5.428253 TGTAAAGCCTCTGCATTAACCTAG 58.572 41.667 0.00 0.00 41.13 3.02
804 1276 2.629336 AGCCTCTGCATTAACCTAGC 57.371 50.000 0.00 0.00 41.13 3.42
817 1289 7.223971 TGCATTAACCTAGCAGTAATTAACTCG 59.776 37.037 0.00 0.00 35.76 4.18
827 1299 6.089150 AGCAGTAATTAACTCGTTCTCGAAAC 59.911 38.462 0.00 0.00 45.61 2.78
830 1302 8.270799 CAGTAATTAACTCGTTCTCGAAACAAA 58.729 33.333 9.90 0.00 45.61 2.83
831 1303 8.485591 AGTAATTAACTCGTTCTCGAAACAAAG 58.514 33.333 9.90 8.64 45.61 2.77
856 1328 1.003118 ACTTAATCAACTCGGCCTGCA 59.997 47.619 0.00 0.00 0.00 4.41
860 1332 1.028330 ATCAACTCGGCCTGCATGTG 61.028 55.000 0.00 0.00 0.00 3.21
861 1333 3.058160 AACTCGGCCTGCATGTGC 61.058 61.111 0.00 0.00 42.50 4.57
862 1334 3.557903 AACTCGGCCTGCATGTGCT 62.558 57.895 0.00 0.00 42.66 4.40
863 1335 3.200593 CTCGGCCTGCATGTGCTC 61.201 66.667 0.00 0.00 42.66 4.26
864 1336 3.963687 CTCGGCCTGCATGTGCTCA 62.964 63.158 0.00 0.00 42.66 4.26
865 1337 3.506096 CGGCCTGCATGTGCTCAG 61.506 66.667 0.00 0.00 42.66 3.35
875 1347 2.741228 GCATGTGCTCAGTTCTAGAGGG 60.741 54.545 0.00 0.00 38.21 4.30
907 1379 2.223144 CGCTGGACTTCGTTTGAATTGA 59.777 45.455 0.00 0.00 32.61 2.57
912 1384 3.966218 GGACTTCGTTTGAATTGAACACG 59.034 43.478 6.20 6.20 32.61 4.49
914 1386 4.833126 ACTTCGTTTGAATTGAACACGAG 58.167 39.130 12.01 10.05 40.68 4.18
957 1429 4.488136 TTGCCGGGCATCTCGCAT 62.488 61.111 24.49 0.00 45.17 4.73
958 1430 3.993614 TTGCCGGGCATCTCGCATT 62.994 57.895 24.49 0.00 45.17 3.56
959 1431 3.654020 GCCGGGCATCTCGCATTC 61.654 66.667 15.62 0.00 45.17 2.67
960 1432 2.203056 CCGGGCATCTCGCATTCA 60.203 61.111 0.00 0.00 45.17 2.57
961 1433 1.598962 CCGGGCATCTCGCATTCAT 60.599 57.895 0.00 0.00 45.17 2.57
962 1434 1.168407 CCGGGCATCTCGCATTCATT 61.168 55.000 0.00 0.00 45.17 2.57
963 1435 0.236711 CGGGCATCTCGCATTCATTC 59.763 55.000 0.00 0.00 45.17 2.67
964 1436 1.602311 GGGCATCTCGCATTCATTCT 58.398 50.000 0.00 0.00 45.17 2.40
965 1437 1.534595 GGGCATCTCGCATTCATTCTC 59.465 52.381 0.00 0.00 45.17 2.87
966 1438 1.194098 GGCATCTCGCATTCATTCTCG 59.806 52.381 0.00 0.00 45.17 4.04
1029 1501 2.237392 GCTCTTACCATTCTGTCCCACT 59.763 50.000 0.00 0.00 0.00 4.00
1032 1504 2.642171 TACCATTCTGTCCCACTCCT 57.358 50.000 0.00 0.00 0.00 3.69
1033 1505 2.642171 ACCATTCTGTCCCACTCCTA 57.358 50.000 0.00 0.00 0.00 2.94
1034 1506 2.188817 ACCATTCTGTCCCACTCCTAC 58.811 52.381 0.00 0.00 0.00 3.18
1037 1509 0.252558 TTCTGTCCCACTCCTACCCC 60.253 60.000 0.00 0.00 0.00 4.95
1038 1510 2.038329 TGTCCCACTCCTACCCCG 59.962 66.667 0.00 0.00 0.00 5.73
1039 1511 2.762875 GTCCCACTCCTACCCCGG 60.763 72.222 0.00 0.00 0.00 5.73
1040 1512 4.791069 TCCCACTCCTACCCCGGC 62.791 72.222 0.00 0.00 0.00 6.13
1086 1558 0.104855 TCGGCGATCCTCCATTCTTG 59.895 55.000 4.99 0.00 0.00 3.02
1107 1581 9.661563 TTCTTGGATCAGTACGTTTATGTAATT 57.338 29.630 0.00 0.00 0.00 1.40
1129 1603 1.905215 AGATATGCTTCCCCTGATCGG 59.095 52.381 0.00 0.00 0.00 4.18
1130 1604 0.326264 ATATGCTTCCCCTGATCGGC 59.674 55.000 0.00 0.00 0.00 5.54
1182 1675 1.683011 GGTATCACCCAATGCTGCACT 60.683 52.381 3.57 0.00 30.04 4.40
1183 1676 2.094675 GTATCACCCAATGCTGCACTT 58.905 47.619 3.57 0.00 0.00 3.16
1193 1686 4.337274 CCAATGCTGCACTTCATCTCATAA 59.663 41.667 3.57 0.00 0.00 1.90
1299 1795 4.373116 GCGCCTCCACCAAGTCGA 62.373 66.667 0.00 0.00 0.00 4.20
1322 1818 1.557099 TCAACTCCGGTGCAGATAGT 58.443 50.000 0.00 0.00 0.00 2.12
1385 1881 1.595929 GACAACTCCCAACGGCGAA 60.596 57.895 16.62 0.00 0.00 4.70
1462 1964 3.343941 CCCTAATGGTTTTGACGAGGA 57.656 47.619 0.00 0.00 0.00 3.71
1464 1966 4.270008 CCCTAATGGTTTTGACGAGGATT 58.730 43.478 0.00 0.00 0.00 3.01
1522 2024 2.744307 GATACCGGGCCGAGCGTTAG 62.744 65.000 30.79 11.41 0.00 2.34
1531 2033 0.736325 CCGAGCGTTAGGGTTCAGTG 60.736 60.000 0.00 0.00 0.00 3.66
1562 2064 1.271856 TCATTGACCAGCCCGAGTTA 58.728 50.000 0.00 0.00 0.00 2.24
1631 2169 4.262592 GGTTCTTTTGATGGCCAGTTTGAT 60.263 41.667 13.05 0.00 0.00 2.57
1736 2301 1.376037 GGCCGTGAACAAGGAGGAG 60.376 63.158 10.64 0.00 31.21 3.69
1742 2307 0.547712 TGAACAAGGAGGAGGAGGGG 60.548 60.000 0.00 0.00 0.00 4.79
1933 2501 1.894466 CTTTGGCACCATGAATGTGGA 59.106 47.619 0.00 0.00 42.02 4.02
1982 2550 3.386486 AGACGACATCAAAGCAAACGTA 58.614 40.909 0.00 0.00 32.88 3.57
1987 2555 4.142902 CGACATCAAAGCAAACGTATTCCT 60.143 41.667 0.00 0.00 0.00 3.36
1990 2558 3.745799 TCAAAGCAAACGTATTCCTGGA 58.254 40.909 0.00 0.00 0.00 3.86
2012 2580 5.351740 GGACTTGCTTACTTTCATCTACACC 59.648 44.000 0.00 0.00 0.00 4.16
2035 2609 1.473677 TGGAATGCCTGAATTCAAGCG 59.526 47.619 21.06 8.19 38.14 4.68
2040 2620 0.874390 GCCTGAATTCAAGCGTGACA 59.126 50.000 13.05 0.00 31.90 3.58
2082 2683 4.002982 CACCGAAGAGGATGACATGAAAA 58.997 43.478 0.00 0.00 45.00 2.29
2135 2736 4.036144 GCAGAAAGATATGGTCTCCAAAGC 59.964 45.833 0.00 0.00 36.95 3.51
2282 2883 2.998772 ACTAGCACAAATTTGCACACG 58.001 42.857 18.12 6.92 45.62 4.49
2379 2980 2.183478 TGCTTCCTGAATCGCTTGAA 57.817 45.000 0.00 0.00 0.00 2.69
2402 3005 8.370940 TGAATTCTAGACCTATGGTTCATGATC 58.629 37.037 7.05 0.00 35.25 2.92
2406 3009 5.093236 AGACCTATGGTTCATGATCCCTA 57.907 43.478 18.25 12.48 35.25 3.53
2437 3040 4.527564 GTTATTATTGTGTCGCTGATGCC 58.472 43.478 0.00 0.00 35.36 4.40
2438 3041 2.106477 TTATTGTGTCGCTGATGCCA 57.894 45.000 0.00 0.00 35.36 4.92
2439 3042 1.368641 TATTGTGTCGCTGATGCCAC 58.631 50.000 0.00 0.00 35.36 5.01
2440 3043 0.606130 ATTGTGTCGCTGATGCCACA 60.606 50.000 0.00 0.00 37.94 4.17
2441 3044 0.817229 TTGTGTCGCTGATGCCACAA 60.817 50.000 8.12 8.12 41.60 3.33
2442 3045 0.606130 TGTGTCGCTGATGCCACAAT 60.606 50.000 0.00 0.00 41.60 2.71
2443 3046 0.097674 GTGTCGCTGATGCCACAATC 59.902 55.000 0.00 0.00 41.60 2.67
2444 3047 1.026182 TGTCGCTGATGCCACAATCC 61.026 55.000 0.00 0.00 37.36 3.01
2445 3048 0.745845 GTCGCTGATGCCACAATCCT 60.746 55.000 0.00 0.00 35.36 3.24
2446 3049 0.829990 TCGCTGATGCCACAATCCTA 59.170 50.000 0.00 0.00 35.36 2.94
2448 3051 1.534163 CGCTGATGCCACAATCCTATG 59.466 52.381 0.00 0.00 35.36 2.23
2449 3052 2.807837 CGCTGATGCCACAATCCTATGA 60.808 50.000 0.00 0.00 35.36 2.15
2450 3053 2.551459 GCTGATGCCACAATCCTATGAC 59.449 50.000 0.00 0.00 0.00 3.06
2452 3055 4.395625 CTGATGCCACAATCCTATGACAT 58.604 43.478 0.00 0.00 0.00 3.06
2453 3056 4.139038 TGATGCCACAATCCTATGACATG 58.861 43.478 0.00 0.00 0.00 3.21
2454 3057 2.300433 TGCCACAATCCTATGACATGC 58.700 47.619 0.00 0.00 0.00 4.06
2460 3063 5.532032 CCACAATCCTATGACATGCACAATA 59.468 40.000 0.00 0.00 0.00 1.90
2466 3069 5.817296 TCCTATGACATGCACAATACTGTTC 59.183 40.000 0.00 0.00 31.64 3.18
2467 3070 4.604843 ATGACATGCACAATACTGTTCG 57.395 40.909 0.00 0.00 31.64 3.95
2468 3071 3.658709 TGACATGCACAATACTGTTCGA 58.341 40.909 0.00 0.00 31.64 3.71
2469 3072 3.431912 TGACATGCACAATACTGTTCGAC 59.568 43.478 0.00 0.00 31.64 4.20
2470 3073 2.742053 ACATGCACAATACTGTTCGACC 59.258 45.455 0.00 0.00 31.64 4.79
2471 3074 1.803334 TGCACAATACTGTTCGACCC 58.197 50.000 0.00 0.00 31.64 4.46
2472 3075 1.084289 GCACAATACTGTTCGACCCC 58.916 55.000 0.00 0.00 31.64 4.95
2473 3076 1.355971 CACAATACTGTTCGACCCCG 58.644 55.000 0.00 0.00 31.64 5.73
2474 3077 0.248289 ACAATACTGTTCGACCCCGG 59.752 55.000 0.00 0.00 36.24 5.73
2475 3078 0.461339 CAATACTGTTCGACCCCGGG 60.461 60.000 15.80 15.80 36.24 5.73
2476 3079 1.619807 AATACTGTTCGACCCCGGGG 61.620 60.000 39.18 39.18 42.03 5.73
2480 3083 3.472726 GTTCGACCCCGGGGCATA 61.473 66.667 40.67 22.10 39.32 3.14
2481 3084 3.158648 TTCGACCCCGGGGCATAG 61.159 66.667 40.67 26.54 39.32 2.23
2484 3087 2.529389 GACCCCGGGGCATAGGAT 60.529 66.667 40.67 19.20 39.32 3.24
2485 3088 2.038762 ACCCCGGGGCATAGGATT 60.039 61.111 40.67 15.28 39.32 3.01
2486 3089 2.411765 GACCCCGGGGCATAGGATTG 62.412 65.000 40.67 12.33 39.32 2.67
2487 3090 2.460853 CCCCGGGGCATAGGATTGT 61.461 63.158 31.01 0.00 0.00 2.71
2488 3091 1.228245 CCCGGGGCATAGGATTGTG 60.228 63.158 14.71 0.00 0.00 3.33
2489 3092 1.531748 CCGGGGCATAGGATTGTGT 59.468 57.895 0.00 0.00 0.00 3.72
2490 3093 0.106719 CCGGGGCATAGGATTGTGTT 60.107 55.000 0.00 0.00 0.00 3.32
2491 3094 1.024271 CGGGGCATAGGATTGTGTTG 58.976 55.000 0.00 0.00 0.00 3.33
2492 3095 1.408127 CGGGGCATAGGATTGTGTTGA 60.408 52.381 0.00 0.00 0.00 3.18
2493 3096 2.749466 CGGGGCATAGGATTGTGTTGAT 60.749 50.000 0.00 0.00 0.00 2.57
2494 3097 2.624838 GGGGCATAGGATTGTGTTGATG 59.375 50.000 0.00 0.00 0.00 3.07
2495 3098 3.290710 GGGCATAGGATTGTGTTGATGT 58.709 45.455 0.00 0.00 0.00 3.06
2496 3099 3.316308 GGGCATAGGATTGTGTTGATGTC 59.684 47.826 0.00 0.00 0.00 3.06
2497 3100 4.202441 GGCATAGGATTGTGTTGATGTCT 58.798 43.478 0.00 0.00 0.00 3.41
2498 3101 4.641989 GGCATAGGATTGTGTTGATGTCTT 59.358 41.667 0.00 0.00 0.00 3.01
2514 3117 7.334844 TGATGTCTTATGTCTACCACTACTG 57.665 40.000 0.00 0.00 0.00 2.74
2518 3121 6.128090 TGTCTTATGTCTACCACTACTGTTCG 60.128 42.308 0.00 0.00 0.00 3.95
2520 3123 4.966965 ATGTCTACCACTACTGTTCGAG 57.033 45.455 0.00 0.00 0.00 4.04
2525 3128 5.008331 TCTACCACTACTGTTCGAGATGTT 58.992 41.667 0.00 0.00 0.00 2.71
2530 3133 3.990469 ACTACTGTTCGAGATGTTTGCTG 59.010 43.478 0.00 0.00 0.00 4.41
2532 3135 3.466836 ACTGTTCGAGATGTTTGCTGAA 58.533 40.909 0.00 0.00 0.00 3.02
2535 3138 5.877012 ACTGTTCGAGATGTTTGCTGAATAT 59.123 36.000 0.00 0.00 0.00 1.28
2542 3145 8.461222 TCGAGATGTTTGCTGAATATTGAAATT 58.539 29.630 0.00 0.00 0.00 1.82
2637 3240 8.285776 ACGTTGAAATGTTGAGATGAAATTTC 57.714 30.769 11.41 11.41 37.62 2.17
2688 3293 2.618241 TCAGCTGCAGGTGTAAAAACTG 59.382 45.455 37.07 21.72 43.46 3.16
2689 3294 2.618241 CAGCTGCAGGTGTAAAAACTGA 59.382 45.455 32.68 0.00 38.61 3.41
2710 3315 1.261619 CCAGCAGTGTTCAAGTTCGTC 59.738 52.381 0.00 0.00 0.00 4.20
2713 3318 1.933853 GCAGTGTTCAAGTTCGTCAGT 59.066 47.619 0.00 0.00 0.00 3.41
2717 3322 4.745125 CAGTGTTCAAGTTCGTCAGTATGT 59.255 41.667 0.00 0.00 37.40 2.29
2719 3324 6.419710 CAGTGTTCAAGTTCGTCAGTATGTTA 59.580 38.462 0.00 0.00 37.40 2.41
2733 3338 3.568853 AGTATGTTACCTTCTCCGATCCG 59.431 47.826 0.00 0.00 0.00 4.18
2751 3356 1.475571 CCGATTGAGGGTGCATGATGA 60.476 52.381 0.00 0.00 0.00 2.92
2755 3360 2.531522 TGAGGGTGCATGATGATACG 57.468 50.000 0.00 0.00 0.00 3.06
2760 3365 4.569943 AGGGTGCATGATGATACGAATAC 58.430 43.478 0.00 0.00 0.00 1.89
2779 3384 6.607004 AATACCCTAGATAAATCTCGTGGG 57.393 41.667 17.20 17.20 42.59 4.61
2852 3457 4.823790 AAACGACCACACATTTTACTCC 57.176 40.909 0.00 0.00 0.00 3.85
2857 3462 4.093408 CGACCACACATTTTACTCCAGATG 59.907 45.833 0.00 0.00 0.00 2.90
2872 3477 3.068732 TCCAGATGATTGTCGACATCCTC 59.931 47.826 20.80 18.46 42.38 3.71
2890 3495 8.899427 ACATCCTCTGATACATAACTGATTTG 57.101 34.615 0.00 0.00 0.00 2.32
2891 3496 8.489489 ACATCCTCTGATACATAACTGATTTGT 58.511 33.333 0.00 0.00 0.00 2.83
2892 3497 9.334947 CATCCTCTGATACATAACTGATTTGTT 57.665 33.333 0.00 0.00 0.00 2.83
2938 3547 8.959705 ATAACCATAACTAAACTCAGTTAGCC 57.040 34.615 0.00 0.00 42.63 3.93
2946 3555 7.719871 ACTAAACTCAGTTAGCCTCATTCTA 57.280 36.000 0.00 0.00 34.92 2.10
2947 3556 7.777095 ACTAAACTCAGTTAGCCTCATTCTAG 58.223 38.462 0.00 0.00 34.92 2.43
2951 3560 3.386078 TCAGTTAGCCTCATTCTAGCAGG 59.614 47.826 0.00 0.00 0.00 4.85
2954 3563 1.871418 AGCCTCATTCTAGCAGGACA 58.129 50.000 0.00 0.00 0.00 4.02
2955 3564 1.761784 AGCCTCATTCTAGCAGGACAG 59.238 52.381 0.00 0.00 0.00 3.51
2956 3565 1.759445 GCCTCATTCTAGCAGGACAGA 59.241 52.381 0.00 0.00 0.00 3.41
2957 3566 2.368221 GCCTCATTCTAGCAGGACAGAT 59.632 50.000 0.00 0.00 0.00 2.90
2958 3567 3.554752 GCCTCATTCTAGCAGGACAGATC 60.555 52.174 0.00 0.00 0.00 2.75
2959 3568 3.305267 CCTCATTCTAGCAGGACAGATCG 60.305 52.174 0.00 0.00 0.00 3.69
2978 3589 2.028567 TCGTGCAATCCATGTACACTGA 60.029 45.455 0.00 0.00 44.04 3.41
2990 3601 2.294074 GTACACTGAACAGGGCACAAA 58.706 47.619 3.83 0.00 34.48 2.83
3018 3629 6.253013 TCGATACAAGTAACATGTACAGACG 58.747 40.000 0.00 0.00 36.19 4.18
3023 3634 2.500098 AGTAACATGTACAGACGGCCAT 59.500 45.455 2.24 0.00 0.00 4.40
3031 3642 0.532573 ACAGACGGCCATGTGACTAG 59.467 55.000 1.68 0.00 0.00 2.57
3034 3645 1.079127 ACGGCCATGTGACTAGTGC 60.079 57.895 0.00 0.00 0.00 4.40
3103 3714 8.304596 TGGCTATTACCTTTACATAGAAGATCG 58.695 37.037 0.00 0.00 0.00 3.69
3201 3816 4.081972 TGCCTTAAGCTACTTCTGAGACAG 60.082 45.833 0.00 0.00 44.23 3.51
3202 3817 4.081917 GCCTTAAGCTACTTCTGAGACAGT 60.082 45.833 0.00 3.52 38.99 3.55
3203 3818 5.125739 GCCTTAAGCTACTTCTGAGACAGTA 59.874 44.000 0.00 5.04 38.99 2.74
3210 3826 6.887545 AGCTACTTCTGAGACAGTACTATGTT 59.112 38.462 0.00 0.00 32.25 2.71
3222 3840 6.461640 ACAGTACTATGTTCCTTTACCACAC 58.538 40.000 0.00 0.00 0.00 3.82
3249 3867 1.271434 GGAACTCCACCCCTCAAAGTC 60.271 57.143 0.00 0.00 35.64 3.01
3334 3952 1.271840 TGACAGGGTCATAGGGTGGC 61.272 60.000 0.00 0.00 37.67 5.01
3354 3972 3.244526 GGCCAATGGAAAAGACACCAAAT 60.245 43.478 2.05 0.00 39.69 2.32
3478 4101 6.956202 ACACCATGTATGTACTAGGTAGTC 57.044 41.667 0.00 0.00 37.73 2.59
3497 4122 5.695851 AGTCATTGTTTAAGCAACCTCTG 57.304 39.130 6.91 2.30 33.97 3.35
3516 4141 5.310409 TCTGTCTTTGGGGGATTATGATC 57.690 43.478 0.00 0.00 0.00 2.92
3525 4150 8.518720 TTTGGGGGATTATGATCTATGACTAA 57.481 34.615 0.00 0.00 32.66 2.24
3526 4151 7.739995 TGGGGGATTATGATCTATGACTAAG 57.260 40.000 0.00 0.00 32.66 2.18
3528 4153 8.406643 TGGGGGATTATGATCTATGACTAAGTA 58.593 37.037 0.00 0.00 32.66 2.24
3529 4154 8.697292 GGGGGATTATGATCTATGACTAAGTAC 58.303 40.741 0.00 0.00 32.66 2.73
3530 4155 8.697292 GGGGATTATGATCTATGACTAAGTACC 58.303 40.741 0.00 0.00 32.66 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 3.891400 CGTTCGCCGGTCCCGATA 61.891 66.667 7.42 0.00 42.83 2.92
217 219 3.292159 GCAACCCGAACCACCCAC 61.292 66.667 0.00 0.00 0.00 4.61
238 242 1.152756 GCCACACTTCCCAACCTGT 60.153 57.895 0.00 0.00 0.00 4.00
240 244 2.113139 CGCCACACTTCCCAACCT 59.887 61.111 0.00 0.00 0.00 3.50
439 472 4.738998 TGCCGCCACCATCCCTTG 62.739 66.667 0.00 0.00 0.00 3.61
479 542 2.553685 CCTAAAACCCTAAAGCCACCGT 60.554 50.000 0.00 0.00 0.00 4.83
483 546 3.264964 ACGATCCTAAAACCCTAAAGCCA 59.735 43.478 0.00 0.00 0.00 4.75
529 621 1.561076 TGCACAGCCCATATCTTGTCT 59.439 47.619 0.00 0.00 0.00 3.41
573 665 9.557061 CCTCTATACTTATATATACGTGCCTGA 57.443 37.037 11.18 4.86 0.00 3.86
602 694 5.186021 CCTCTGTATAGTTGAGGTTGTGACT 59.814 44.000 0.00 0.00 41.64 3.41
604 696 5.330233 TCCTCTGTATAGTTGAGGTTGTGA 58.670 41.667 12.57 0.00 45.46 3.58
641 733 4.374843 ACGTGTATATTTGCGTGTAGGA 57.625 40.909 0.00 0.00 36.16 2.94
649 741 7.516943 GCCTCTTTTCTCTACGTGTATATTTGC 60.517 40.741 0.00 0.00 0.00 3.68
664 756 4.328041 GGCCAGGCCTCTTTTCTC 57.672 61.111 24.99 0.00 46.69 2.87
671 763 5.554384 GAGTTACTACTTGGCCAGGCCTC 62.554 56.522 31.51 12.49 41.57 4.70
672 764 3.745836 GAGTTACTACTTGGCCAGGCCT 61.746 54.545 31.51 14.21 41.57 5.19
673 765 1.407025 GAGTTACTACTTGGCCAGGCC 60.407 57.143 25.54 25.54 41.45 5.19
674 766 1.555533 AGAGTTACTACTTGGCCAGGC 59.444 52.381 16.02 1.26 33.84 4.85
675 767 3.676324 CGAAGAGTTACTACTTGGCCAGG 60.676 52.174 14.35 14.35 33.84 4.45
676 768 3.512680 CGAAGAGTTACTACTTGGCCAG 58.487 50.000 5.11 2.72 33.84 4.85
677 769 2.232941 CCGAAGAGTTACTACTTGGCCA 59.767 50.000 0.00 0.00 33.84 5.36
678 770 2.233186 ACCGAAGAGTTACTACTTGGCC 59.767 50.000 0.00 0.00 33.84 5.36
679 771 3.057033 TCACCGAAGAGTTACTACTTGGC 60.057 47.826 2.72 0.00 33.84 4.52
680 772 4.458295 TCTCACCGAAGAGTTACTACTTGG 59.542 45.833 4.39 1.11 36.97 3.61
681 773 5.392286 GTCTCACCGAAGAGTTACTACTTG 58.608 45.833 4.39 0.00 36.97 3.16
682 774 4.458642 GGTCTCACCGAAGAGTTACTACTT 59.541 45.833 4.39 0.00 36.97 2.24
683 775 4.009002 GGTCTCACCGAAGAGTTACTACT 58.991 47.826 4.39 0.00 36.97 2.57
684 776 4.009002 AGGTCTCACCGAAGAGTTACTAC 58.991 47.826 4.39 0.00 44.90 2.73
685 777 4.008330 CAGGTCTCACCGAAGAGTTACTA 58.992 47.826 4.39 0.00 44.90 1.82
691 783 0.814457 CTCCAGGTCTCACCGAAGAG 59.186 60.000 0.00 0.00 44.90 2.85
695 787 1.000771 CTCCTCCAGGTCTCACCGA 60.001 63.158 0.00 0.00 44.90 4.69
724 816 1.758862 TCAGATCGATGCATCCACACT 59.241 47.619 20.87 11.85 0.00 3.55
726 818 2.938451 GTTTCAGATCGATGCATCCACA 59.062 45.455 20.87 5.64 0.00 4.17
735 827 2.002586 CTTGCGTGGTTTCAGATCGAT 58.997 47.619 0.00 0.00 0.00 3.59
742 834 1.266718 GATTGAGCTTGCGTGGTTTCA 59.733 47.619 0.00 0.00 0.00 2.69
745 837 0.602638 TCGATTGAGCTTGCGTGGTT 60.603 50.000 0.00 0.00 0.00 3.67
746 838 1.005037 TCGATTGAGCTTGCGTGGT 60.005 52.632 0.00 0.00 0.00 4.16
747 839 1.421485 GTCGATTGAGCTTGCGTGG 59.579 57.895 0.00 0.00 0.00 4.94
748 840 1.057822 CGTCGATTGAGCTTGCGTG 59.942 57.895 0.00 0.00 0.00 5.34
749 841 2.094659 CCGTCGATTGAGCTTGCGT 61.095 57.895 0.00 0.00 0.00 5.24
750 842 2.014093 GACCGTCGATTGAGCTTGCG 62.014 60.000 0.00 0.00 0.00 4.85
751 843 0.737715 AGACCGTCGATTGAGCTTGC 60.738 55.000 0.00 0.00 0.00 4.01
752 844 1.272781 GAGACCGTCGATTGAGCTTG 58.727 55.000 0.00 0.00 0.00 4.01
753 845 0.173708 GGAGACCGTCGATTGAGCTT 59.826 55.000 0.00 0.00 0.00 3.74
754 846 0.681564 AGGAGACCGTCGATTGAGCT 60.682 55.000 0.00 0.00 0.00 4.09
755 847 0.248702 GAGGAGACCGTCGATTGAGC 60.249 60.000 0.00 0.00 0.00 4.26
756 848 3.928343 GAGGAGACCGTCGATTGAG 57.072 57.895 0.00 0.00 0.00 3.02
768 1240 2.838202 AGGCTTTACATTTCCGAGGAGA 59.162 45.455 0.00 0.00 0.00 3.71
779 1251 4.860022 AGGTTAATGCAGAGGCTTTACAT 58.140 39.130 0.00 0.00 38.79 2.29
792 1264 7.224167 ACGAGTTAATTACTGCTAGGTTAATGC 59.776 37.037 0.00 0.00 37.17 3.56
802 1274 5.306532 TCGAGAACGAGTTAATTACTGCT 57.693 39.130 0.00 0.00 43.81 4.24
827 1299 6.143919 GGCCGAGTTGATTAAGTTTTTCTTTG 59.856 38.462 0.00 0.00 37.56 2.77
830 1302 5.048713 CAGGCCGAGTTGATTAAGTTTTTCT 60.049 40.000 0.00 0.00 0.00 2.52
831 1303 5.154222 CAGGCCGAGTTGATTAAGTTTTTC 58.846 41.667 0.00 0.00 0.00 2.29
856 1328 2.114616 CCCCTCTAGAACTGAGCACAT 58.885 52.381 0.00 0.00 0.00 3.21
860 1332 0.741915 CGTCCCCTCTAGAACTGAGC 59.258 60.000 0.00 0.00 0.00 4.26
861 1333 1.064611 TCCGTCCCCTCTAGAACTGAG 60.065 57.143 0.00 0.00 0.00 3.35
862 1334 0.997363 TCCGTCCCCTCTAGAACTGA 59.003 55.000 0.00 0.00 0.00 3.41
863 1335 1.394618 CTCCGTCCCCTCTAGAACTG 58.605 60.000 0.00 0.00 0.00 3.16
864 1336 0.259356 CCTCCGTCCCCTCTAGAACT 59.741 60.000 0.00 0.00 0.00 3.01
865 1337 0.258194 TCCTCCGTCCCCTCTAGAAC 59.742 60.000 0.00 0.00 0.00 3.01
907 1379 2.050351 CCTCGTCGTGCTCGTGTT 60.050 61.111 8.17 0.00 38.33 3.32
912 1384 1.153997 GGAGAACCTCGTCGTGCTC 60.154 63.158 4.57 4.57 37.66 4.26
914 1386 1.444553 CTGGAGAACCTCGTCGTGC 60.445 63.158 0.00 0.00 37.04 5.34
955 1427 8.433893 GCATATATATAGCAGCGAGAATGAATG 58.566 37.037 10.46 0.00 0.00 2.67
956 1428 8.531622 GCATATATATAGCAGCGAGAATGAAT 57.468 34.615 10.46 0.00 0.00 2.57
957 1429 7.936950 GCATATATATAGCAGCGAGAATGAA 57.063 36.000 10.46 0.00 0.00 2.57
965 1437 3.914966 GGTAGCGCATATATATAGCAGCG 59.085 47.826 22.43 22.43 46.99 5.18
966 1438 5.127693 AGGTAGCGCATATATATAGCAGC 57.872 43.478 11.47 17.38 0.00 5.25
1007 1479 1.559682 TGGGACAGAATGGTAAGAGCC 59.440 52.381 0.00 0.00 43.62 4.70
1050 1522 1.081376 GATCACCGCCGTATCTCCG 60.081 63.158 0.00 0.00 0.00 4.63
1051 1523 1.081376 CGATCACCGCCGTATCTCC 60.081 63.158 0.00 0.00 0.00 3.71
1052 1524 1.081376 CCGATCACCGCCGTATCTC 60.081 63.158 0.00 0.00 36.84 2.75
1053 1525 3.039988 CCGATCACCGCCGTATCT 58.960 61.111 0.00 0.00 36.84 1.98
1054 1526 2.733593 GCCGATCACCGCCGTATC 60.734 66.667 0.00 0.00 36.84 2.24
1055 1527 4.640855 CGCCGATCACCGCCGTAT 62.641 66.667 0.00 0.00 34.19 3.06
1060 1532 4.286320 AGGATCGCCGATCACCGC 62.286 66.667 26.64 10.74 40.50 5.68
1064 1536 0.318441 GAATGGAGGATCGCCGATCA 59.682 55.000 26.64 8.94 40.50 2.92
1065 1537 0.605589 AGAATGGAGGATCGCCGATC 59.394 55.000 18.56 18.56 39.96 3.69
1098 1570 9.739276 CAGGGGAAGCATATCTAAATTACATAA 57.261 33.333 0.00 0.00 0.00 1.90
1107 1581 3.515502 CCGATCAGGGGAAGCATATCTAA 59.484 47.826 0.00 0.00 35.97 2.10
1110 1584 1.677217 GCCGATCAGGGGAAGCATATC 60.677 57.143 5.87 0.00 41.48 1.63
1123 1597 0.679505 CGAAATCTAGGGGCCGATCA 59.320 55.000 0.00 0.00 0.00 2.92
1129 1603 3.194005 TGATGAACGAAATCTAGGGGC 57.806 47.619 0.00 0.00 0.00 5.80
1130 1604 6.543831 AGAAAATGATGAACGAAATCTAGGGG 59.456 38.462 0.00 0.00 0.00 4.79
1193 1686 4.697514 AGCTGCGAGAAACACATATATGT 58.302 39.130 12.75 12.75 42.84 2.29
1244 1740 2.010145 TGAGAGATACGCCAGCAAAC 57.990 50.000 0.00 0.00 0.00 2.93
1299 1795 1.003355 CTGCACCGGAGTTGATGGT 60.003 57.895 9.46 0.00 36.10 3.55
1322 1818 1.695242 ACAACGATCAAGTGGTACCCA 59.305 47.619 10.07 0.00 0.00 4.51
1385 1881 3.515502 TGAAAGGACGAGACTTGATCCAT 59.484 43.478 11.62 0.79 33.33 3.41
1522 2024 0.179018 ACTGAAGGCACACTGAACCC 60.179 55.000 0.00 0.00 0.00 4.11
1531 2033 2.622942 TGGTCAATGAAACTGAAGGCAC 59.377 45.455 0.00 0.00 0.00 5.01
1631 2169 8.854614 TTTCAAAAACCTCCTTTTTCATGAAA 57.145 26.923 16.91 16.91 39.61 2.69
1723 2261 0.547712 CCCCTCCTCCTCCTTGTTCA 60.548 60.000 0.00 0.00 0.00 3.18
1742 2307 0.672401 TGAATGGAAGAACGGCGGTC 60.672 55.000 18.98 18.98 0.00 4.79
1750 2315 2.491693 GGCAATTCGGTGAATGGAAGAA 59.508 45.455 0.00 0.00 32.14 2.52
1933 2501 2.143122 CAACACTGGACGTAGCATTGT 58.857 47.619 0.00 0.00 0.00 2.71
1946 2514 4.546570 TGTCGTCTATCTTGACAACACTG 58.453 43.478 0.00 0.00 39.50 3.66
1982 2550 4.985538 TGAAAGTAAGCAAGTCCAGGAAT 58.014 39.130 0.00 0.00 0.00 3.01
1987 2555 5.932303 GTGTAGATGAAAGTAAGCAAGTCCA 59.068 40.000 0.00 0.00 0.00 4.02
1990 2558 4.929808 CGGTGTAGATGAAAGTAAGCAAGT 59.070 41.667 0.00 0.00 0.00 3.16
2012 2580 3.794475 GCTTGAATTCAGGCATTCCATCG 60.794 47.826 31.07 0.00 46.60 3.84
2035 2609 1.662629 CAGTCTCATCGCCATTGTCAC 59.337 52.381 0.00 0.00 0.00 3.67
2040 2620 2.169144 TGTCATCAGTCTCATCGCCATT 59.831 45.455 0.00 0.00 0.00 3.16
2135 2736 3.571828 TCTCTTCACAGACTGACTTGAGG 59.428 47.826 10.08 3.48 0.00 3.86
2282 2883 1.883021 CCCATCAGCCGTGAAAACC 59.117 57.895 0.00 0.00 35.88 3.27
2379 2980 6.214412 GGGATCATGAACCATAGGTCTAGAAT 59.786 42.308 22.18 0.00 33.12 2.40
2429 3032 2.551459 GTCATAGGATTGTGGCATCAGC 59.449 50.000 0.00 0.00 41.10 4.26
2437 3040 4.968812 TTGTGCATGTCATAGGATTGTG 57.031 40.909 0.00 0.00 0.00 3.33
2438 3041 6.261603 CAGTATTGTGCATGTCATAGGATTGT 59.738 38.462 0.00 0.00 0.00 2.71
2439 3042 6.261603 ACAGTATTGTGCATGTCATAGGATTG 59.738 38.462 0.00 0.00 35.83 2.67
2440 3043 6.359804 ACAGTATTGTGCATGTCATAGGATT 58.640 36.000 0.00 0.00 35.83 3.01
2441 3044 5.933617 ACAGTATTGTGCATGTCATAGGAT 58.066 37.500 0.00 0.00 35.83 3.24
2442 3045 5.357742 ACAGTATTGTGCATGTCATAGGA 57.642 39.130 0.00 0.00 35.83 2.94
2443 3046 5.277011 CGAACAGTATTGTGCATGTCATAGG 60.277 44.000 0.00 0.00 37.67 2.57
2444 3047 5.519927 TCGAACAGTATTGTGCATGTCATAG 59.480 40.000 0.00 0.00 37.67 2.23
2445 3048 5.290885 GTCGAACAGTATTGTGCATGTCATA 59.709 40.000 0.00 0.00 37.67 2.15
2446 3049 4.093408 GTCGAACAGTATTGTGCATGTCAT 59.907 41.667 0.00 0.00 37.67 3.06
2448 3051 3.181520 GGTCGAACAGTATTGTGCATGTC 60.182 47.826 0.00 0.00 37.67 3.06
2449 3052 2.742053 GGTCGAACAGTATTGTGCATGT 59.258 45.455 0.00 0.00 37.67 3.21
2450 3053 2.095853 GGGTCGAACAGTATTGTGCATG 59.904 50.000 1.31 0.00 37.67 4.06
2452 3055 1.609580 GGGGTCGAACAGTATTGTGCA 60.610 52.381 1.31 0.00 37.67 4.57
2453 3056 1.084289 GGGGTCGAACAGTATTGTGC 58.916 55.000 1.31 0.00 37.67 4.57
2454 3057 1.355971 CGGGGTCGAACAGTATTGTG 58.644 55.000 1.31 0.00 37.67 3.33
2467 3070 2.154074 AATCCTATGCCCCGGGGTC 61.154 63.158 39.80 30.55 37.65 4.46
2468 3071 2.038762 AATCCTATGCCCCGGGGT 60.039 61.111 39.80 24.60 37.65 4.95
2469 3072 2.436109 CAATCCTATGCCCCGGGG 59.564 66.667 37.09 37.09 38.57 5.73
2470 3073 1.228245 CACAATCCTATGCCCCGGG 60.228 63.158 15.80 15.80 0.00 5.73
2471 3074 0.106719 AACACAATCCTATGCCCCGG 60.107 55.000 0.00 0.00 0.00 5.73
2472 3075 1.024271 CAACACAATCCTATGCCCCG 58.976 55.000 0.00 0.00 0.00 5.73
2473 3076 2.435372 TCAACACAATCCTATGCCCC 57.565 50.000 0.00 0.00 0.00 5.80
2474 3077 3.290710 ACATCAACACAATCCTATGCCC 58.709 45.455 0.00 0.00 0.00 5.36
2475 3078 4.202441 AGACATCAACACAATCCTATGCC 58.798 43.478 0.00 0.00 0.00 4.40
2476 3079 5.824904 AAGACATCAACACAATCCTATGC 57.175 39.130 0.00 0.00 0.00 3.14
2477 3080 8.442632 ACATAAGACATCAACACAATCCTATG 57.557 34.615 0.00 0.00 0.00 2.23
2478 3081 8.489489 AGACATAAGACATCAACACAATCCTAT 58.511 33.333 0.00 0.00 0.00 2.57
2479 3082 7.851228 AGACATAAGACATCAACACAATCCTA 58.149 34.615 0.00 0.00 0.00 2.94
2480 3083 6.715280 AGACATAAGACATCAACACAATCCT 58.285 36.000 0.00 0.00 0.00 3.24
2481 3084 6.992063 AGACATAAGACATCAACACAATCC 57.008 37.500 0.00 0.00 0.00 3.01
2482 3085 7.549134 TGGTAGACATAAGACATCAACACAATC 59.451 37.037 0.00 0.00 0.00 2.67
2483 3086 7.334421 GTGGTAGACATAAGACATCAACACAAT 59.666 37.037 0.00 0.00 0.00 2.71
2484 3087 6.649141 GTGGTAGACATAAGACATCAACACAA 59.351 38.462 0.00 0.00 0.00 3.33
2485 3088 6.014584 AGTGGTAGACATAAGACATCAACACA 60.015 38.462 0.00 0.00 0.00 3.72
2486 3089 6.398918 AGTGGTAGACATAAGACATCAACAC 58.601 40.000 0.00 0.00 0.00 3.32
2487 3090 6.605471 AGTGGTAGACATAAGACATCAACA 57.395 37.500 0.00 0.00 0.00 3.33
2488 3091 7.702772 CAGTAGTGGTAGACATAAGACATCAAC 59.297 40.741 0.00 0.00 0.00 3.18
2489 3092 7.396339 ACAGTAGTGGTAGACATAAGACATCAA 59.604 37.037 1.92 0.00 0.00 2.57
2490 3093 6.890268 ACAGTAGTGGTAGACATAAGACATCA 59.110 38.462 1.92 0.00 0.00 3.07
2491 3094 7.336161 ACAGTAGTGGTAGACATAAGACATC 57.664 40.000 1.92 0.00 0.00 3.06
2492 3095 7.415318 CGAACAGTAGTGGTAGACATAAGACAT 60.415 40.741 1.92 0.00 0.00 3.06
2493 3096 6.128090 CGAACAGTAGTGGTAGACATAAGACA 60.128 42.308 1.92 0.00 0.00 3.41
2494 3097 6.093219 TCGAACAGTAGTGGTAGACATAAGAC 59.907 42.308 1.92 0.00 0.00 3.01
2495 3098 6.175471 TCGAACAGTAGTGGTAGACATAAGA 58.825 40.000 1.92 0.00 0.00 2.10
2496 3099 6.315642 TCTCGAACAGTAGTGGTAGACATAAG 59.684 42.308 1.92 0.00 0.00 1.73
2497 3100 6.175471 TCTCGAACAGTAGTGGTAGACATAA 58.825 40.000 1.92 0.00 0.00 1.90
2498 3101 5.737860 TCTCGAACAGTAGTGGTAGACATA 58.262 41.667 1.92 0.00 0.00 2.29
2514 3117 6.775088 TCAATATTCAGCAAACATCTCGAAC 58.225 36.000 0.00 0.00 0.00 3.95
2525 3128 9.000486 TGCATTTCAAATTTCAATATTCAGCAA 58.000 25.926 0.00 0.00 0.00 3.91
2530 3133 9.828852 TTTGCTGCATTTCAAATTTCAATATTC 57.171 25.926 1.84 0.00 0.00 1.75
2567 3170 9.878667 TCAAATGAATTCAAGCAAATCACATAT 57.121 25.926 13.09 0.00 0.00 1.78
2574 3177 7.335673 TGCATGATCAAATGAATTCAAGCAAAT 59.664 29.630 13.09 3.04 35.90 2.32
2610 3213 8.728088 AATTTCATCTCAACATTTCAACGTAC 57.272 30.769 0.00 0.00 0.00 3.67
2613 3216 7.113404 ACGAAATTTCATCTCAACATTTCAACG 59.887 33.333 17.99 0.93 34.74 4.10
2637 3240 1.507630 CATGGATGCACCCAACACG 59.492 57.895 2.29 0.00 40.04 4.49
2676 3281 3.626028 CTGCTGGTCAGTTTTTACACC 57.374 47.619 0.00 0.00 38.02 4.16
2688 3293 1.261619 CGAACTTGAACACTGCTGGTC 59.738 52.381 0.00 0.00 34.28 4.02
2689 3294 1.299541 CGAACTTGAACACTGCTGGT 58.700 50.000 0.00 0.00 0.00 4.00
2697 3302 5.693104 GGTAACATACTGACGAACTTGAACA 59.307 40.000 0.00 0.00 0.00 3.18
2698 3303 5.924825 AGGTAACATACTGACGAACTTGAAC 59.075 40.000 0.00 0.00 41.41 3.18
2700 3305 5.717078 AGGTAACATACTGACGAACTTGA 57.283 39.130 0.00 0.00 41.41 3.02
2710 3315 4.556898 CGGATCGGAGAAGGTAACATACTG 60.557 50.000 0.00 0.00 43.58 2.74
2713 3318 3.824133 TCGGATCGGAGAAGGTAACATA 58.176 45.455 0.00 0.00 43.58 2.29
2717 3322 3.293337 TCAATCGGATCGGAGAAGGTAA 58.707 45.455 9.03 0.00 43.58 2.85
2719 3324 1.683917 CTCAATCGGATCGGAGAAGGT 59.316 52.381 9.03 0.00 43.58 3.50
2733 3338 3.434641 CGTATCATCATGCACCCTCAATC 59.565 47.826 0.00 0.00 0.00 2.67
2751 3356 8.675504 CACGAGATTTATCTAGGGTATTCGTAT 58.324 37.037 0.00 0.00 37.25 3.06
2755 3360 6.210984 ACCCACGAGATTTATCTAGGGTATTC 59.789 42.308 20.10 0.00 46.37 1.75
2760 3365 5.279356 GGTTACCCACGAGATTTATCTAGGG 60.279 48.000 16.72 16.72 43.63 3.53
2779 3384 7.209471 TGTTTGGTATCACTGATTTGGTTAC 57.791 36.000 0.00 0.00 0.00 2.50
2827 3432 5.754778 AGTAAAATGTGTGGTCGTTTTAGC 58.245 37.500 0.00 0.00 38.55 3.09
2831 3436 4.200874 TGGAGTAAAATGTGTGGTCGTTT 58.799 39.130 0.00 0.00 0.00 3.60
2852 3457 4.049869 CAGAGGATGTCGACAATCATCTG 58.950 47.826 32.64 32.64 43.55 2.90
2857 3462 5.188327 TGTATCAGAGGATGTCGACAATC 57.812 43.478 24.13 19.59 34.89 2.67
2917 3526 6.640518 TGAGGCTAACTGAGTTTAGTTATGG 58.359 40.000 1.97 0.00 41.04 2.74
2938 3547 3.317711 ACGATCTGTCCTGCTAGAATGAG 59.682 47.826 0.00 0.00 0.00 2.90
2946 3555 0.251354 ATTGCACGATCTGTCCTGCT 59.749 50.000 0.00 0.00 37.31 4.24
2947 3556 0.654683 GATTGCACGATCTGTCCTGC 59.345 55.000 0.00 0.00 37.05 4.85
2951 3560 2.283298 ACATGGATTGCACGATCTGTC 58.717 47.619 0.00 0.00 0.00 3.51
2954 3563 3.118629 AGTGTACATGGATTGCACGATCT 60.119 43.478 0.00 0.00 35.46 2.75
2955 3564 3.001634 CAGTGTACATGGATTGCACGATC 59.998 47.826 0.00 0.00 35.46 3.69
2956 3565 2.938451 CAGTGTACATGGATTGCACGAT 59.062 45.455 0.00 0.00 35.46 3.73
2957 3566 2.028567 TCAGTGTACATGGATTGCACGA 60.029 45.455 0.00 0.00 35.46 4.35
2958 3567 2.345876 TCAGTGTACATGGATTGCACG 58.654 47.619 0.00 0.00 35.46 5.34
2959 3568 3.501828 TGTTCAGTGTACATGGATTGCAC 59.498 43.478 0.00 0.00 0.00 4.57
2978 3589 0.537143 TCGAGCATTTGTGCCCTGTT 60.537 50.000 0.00 0.00 34.90 3.16
2990 3601 6.569780 TGTACATGTTACTTGTATCGAGCAT 58.430 36.000 2.30 0.00 32.56 3.79
3001 3612 2.300723 TGGCCGTCTGTACATGTTACTT 59.699 45.455 2.30 0.00 0.00 2.24
3006 3617 0.613260 ACATGGCCGTCTGTACATGT 59.387 50.000 2.69 2.69 46.41 3.21
3018 3629 0.174845 TACGCACTAGTCACATGGCC 59.825 55.000 0.00 0.00 0.00 5.36
3023 3634 1.542915 GGTTCCTACGCACTAGTCACA 59.457 52.381 0.00 0.00 0.00 3.58
3031 3642 3.493503 GCTGTATAATGGTTCCTACGCAC 59.506 47.826 0.00 0.00 0.00 5.34
3034 3645 5.196341 TGAGCTGTATAATGGTTCCTACG 57.804 43.478 0.00 0.00 0.00 3.51
3103 3714 3.309954 GTCGCCAATCCTGAATTACTGAC 59.690 47.826 0.00 0.00 0.00 3.51
3201 3816 8.090214 TGTTAGTGTGGTAAAGGAACATAGTAC 58.910 37.037 0.00 0.00 0.00 2.73
3202 3817 8.192743 TGTTAGTGTGGTAAAGGAACATAGTA 57.807 34.615 0.00 0.00 0.00 1.82
3203 3818 7.069877 TGTTAGTGTGGTAAAGGAACATAGT 57.930 36.000 0.00 0.00 0.00 2.12
3210 3826 5.131475 AGTTCCTTGTTAGTGTGGTAAAGGA 59.869 40.000 0.00 0.00 41.00 3.36
3222 3840 1.985895 AGGGGTGGAGTTCCTTGTTAG 59.014 52.381 0.00 0.00 36.82 2.34
3329 3947 1.000843 GTGTCTTTTCCATTGGCCACC 59.999 52.381 3.88 0.00 0.00 4.61
3334 3952 4.040217 TCCATTTGGTGTCTTTTCCATTGG 59.960 41.667 0.00 0.00 38.05 3.16
3336 3954 5.885449 TTCCATTTGGTGTCTTTTCCATT 57.115 34.783 0.00 0.00 36.34 3.16
3354 3972 9.695526 CTACATGAATTGAAACTTGATTTTCCA 57.304 29.630 0.00 0.00 35.01 3.53
3478 4101 5.695851 AGACAGAGGTTGCTTAAACAATG 57.304 39.130 0.00 0.00 40.86 2.82
3497 4122 6.881602 GTCATAGATCATAATCCCCCAAAGAC 59.118 42.308 0.00 0.00 31.78 3.01
3526 4151 6.875076 TGTGCTCCTCTTATTTAGAAGGTAC 58.125 40.000 0.00 0.00 30.91 3.34
3528 4153 5.104735 CCTGTGCTCCTCTTATTTAGAAGGT 60.105 44.000 0.00 0.00 30.91 3.50
3529 4154 5.104735 ACCTGTGCTCCTCTTATTTAGAAGG 60.105 44.000 0.00 0.00 30.91 3.46
3530 4155 5.814705 CACCTGTGCTCCTCTTATTTAGAAG 59.185 44.000 0.00 0.00 30.91 2.85


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

AutoCloner maintained by Alex Coulton.