Multiple sequence alignment - TraesCS6D01G403200

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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 TraesCS6D01G403200 chr6D 100.000 6128 0 0 1 6128 471247778 471253905 0.000000e+00 11317.0
1 TraesCS6D01G403200 chr6D 94.493 454 14 3 1 451 367300980 367300535 0.000000e+00 689.0
2 TraesCS6D01G403200 chr6D 92.507 347 10 5 1 347 139581818 139582148 3.320000e-132 483.0
3 TraesCS6D01G403200 chr6D 86.538 156 1 9 560 696 139582161 139582315 2.960000e-33 154.0
4 TraesCS6D01G403200 chr6D 87.952 83 5 5 611 690 390619174 390619254 6.540000e-15 93.5
5 TraesCS6D01G403200 chr6B 90.305 2589 151 31 3579 6128 719409559 719407032 0.000000e+00 3299.0
6 TraesCS6D01G403200 chr6B 94.805 1694 71 11 1876 3561 719411291 719409607 0.000000e+00 2625.0
7 TraesCS6D01G403200 chr6B 94.493 1144 56 4 3559 4697 719440834 719441975 0.000000e+00 1757.0
8 TraesCS6D01G403200 chr6B 89.517 849 70 11 4700 5536 719442034 719442875 0.000000e+00 1057.0
9 TraesCS6D01G403200 chr6B 92.166 651 25 5 2912 3561 719440171 719440796 0.000000e+00 896.0
10 TraesCS6D01G403200 chr6B 88.434 709 76 3 990 1692 719438999 719439707 0.000000e+00 850.0
11 TraesCS6D01G403200 chr6B 96.429 224 8 0 2388 2611 719439911 719440134 2.700000e-98 370.0
12 TraesCS6D01G403200 chr6A 94.248 1721 65 9 3559 5260 615973420 615975125 0.000000e+00 2599.0
13 TraesCS6D01G403200 chr6A 97.096 1515 36 4 2050 3561 615971873 615973382 0.000000e+00 2547.0
14 TraesCS6D01G403200 chr6A 90.373 966 66 11 918 1877 615967689 615968633 0.000000e+00 1243.0
15 TraesCS6D01G403200 chr6A 88.950 181 7 7 718 889 615967398 615967574 1.730000e-50 211.0
16 TraesCS6D01G403200 chr6A 94.118 85 4 1 1970 2054 615971616 615971699 1.790000e-25 128.0
17 TraesCS6D01G403200 chr6A 92.308 39 1 2 5260 5298 592883021 592883057 3.000000e-03 54.7
18 TraesCS6D01G403200 chr7A 85.255 902 84 20 3556 4427 263718587 263719469 0.000000e+00 883.0
19 TraesCS6D01G403200 chr7A 82.459 724 91 26 2865 3567 263717773 263718481 8.790000e-168 601.0
20 TraesCS6D01G403200 chr7A 83.512 467 61 10 2380 2845 263717241 263717692 7.340000e-114 422.0
21 TraesCS6D01G403200 chr7A 83.333 228 21 4 4944 5155 263727574 263727800 1.740000e-45 195.0
22 TraesCS6D01G403200 chr7D 84.469 895 85 26 3561 4424 246813351 246814222 0.000000e+00 833.0
23 TraesCS6D01G403200 chr7D 83.217 715 90 21 2865 3561 246812528 246813230 4.030000e-176 628.0
24 TraesCS6D01G403200 chr7D 82.833 466 64 11 2381 2845 246812000 246812450 2.660000e-108 403.0
25 TraesCS6D01G403200 chr7D 90.984 244 6 1 400 643 458945079 458944852 1.280000e-81 315.0
26 TraesCS6D01G403200 chr7D 86.932 176 11 1 4971 5134 246815012 246815187 2.920000e-43 187.0
27 TraesCS6D01G403200 chr7D 100.000 36 0 0 655 690 458944821 458944786 3.960000e-07 67.6
28 TraesCS6D01G403200 chr7B 84.281 897 87 20 3556 4424 223176107 223176977 0.000000e+00 826.0
29 TraesCS6D01G403200 chr7B 85.694 720 62 20 3 688 316265180 316264468 0.000000e+00 721.0
30 TraesCS6D01G403200 chr7B 84.581 668 74 19 2865 3513 223175292 223175949 2.410000e-178 636.0
31 TraesCS6D01G403200 chr7B 83.476 466 62 11 2381 2845 223174760 223175211 2.640000e-113 420.0
32 TraesCS6D01G403200 chr7B 83.902 205 20 2 4941 5133 223178623 223178826 3.770000e-42 183.0
33 TraesCS6D01G403200 chr2D 93.704 270 8 2 1 267 350346397 350346134 4.450000e-106 396.0
34 TraesCS6D01G403200 chr2D 92.857 42 3 0 5257 5298 189359730 189359771 1.840000e-05 62.1
35 TraesCS6D01G403200 chr2D 91.111 45 1 3 5259 5302 402307958 402307916 2.390000e-04 58.4
36 TraesCS6D01G403200 chr5D 77.331 472 91 12 5660 6126 40908591 40909051 1.310000e-66 265.0
37 TraesCS6D01G403200 chr5B 74.494 494 85 31 137 604 406889011 406888533 6.310000e-40 176.0
38 TraesCS6D01G403200 chr1B 97.333 75 1 1 566 639 166588787 166588861 6.450000e-25 126.0
39 TraesCS6D01G403200 chr4A 94.595 37 0 2 5266 5302 58875427 58875393 8.580000e-04 56.5
40 TraesCS6D01G403200 chrUn 92.308 39 2 1 5260 5298 102499754 102499717 3.000000e-03 54.7
41 TraesCS6D01G403200 chr1A 100.000 29 0 0 5270 5298 337681787 337681759 3.000000e-03 54.7
42 TraesCS6D01G403200 chr3B 92.105 38 2 1 5261 5298 808897410 808897446 1.100000e-02 52.8


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 TraesCS6D01G403200 chr6D 471247778 471253905 6127 False 11317.000000 11317 100.00000 1 6128 1 chr6D.!!$F2 6127
1 TraesCS6D01G403200 chr6B 719407032 719411291 4259 True 2962.000000 3299 92.55500 1876 6128 2 chr6B.!!$R1 4252
2 TraesCS6D01G403200 chr6B 719438999 719442875 3876 False 986.000000 1757 92.20780 990 5536 5 chr6B.!!$F1 4546
3 TraesCS6D01G403200 chr6A 615967398 615975125 7727 False 1345.600000 2599 92.95700 718 5260 5 chr6A.!!$F2 4542
4 TraesCS6D01G403200 chr7A 263717241 263719469 2228 False 635.333333 883 83.74200 2380 4427 3 chr7A.!!$F2 2047
5 TraesCS6D01G403200 chr7D 246812000 246815187 3187 False 512.750000 833 84.36275 2381 5134 4 chr7D.!!$F1 2753
6 TraesCS6D01G403200 chr7B 316264468 316265180 712 True 721.000000 721 85.69400 3 688 1 chr7B.!!$R1 685
7 TraesCS6D01G403200 chr7B 223174760 223178826 4066 False 516.250000 826 84.06000 2381 5133 4 chr7B.!!$F1 2752

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
965 1092 0.039180 TCTCGTCTCCAAGGGTAGCA 59.961 55.000 0.00 0.00 0.00 3.49 F
1205 1338 0.027586 GCGCTTGCCAAGTATAACCG 59.972 55.000 6.28 1.05 0.00 4.44 F
1596 1732 0.036952 CGGAGCAGATGGACACACTT 60.037 55.000 0.00 0.00 0.00 3.16 F
1702 1838 1.068434 GCTCCTCTCTCTATGGTGCAC 59.932 57.143 8.80 8.80 39.36 4.57 F
2698 6034 0.881796 TGTCGGCTACTGTGAGAGTG 59.118 55.000 0.00 0.00 35.96 3.51 F
3018 6421 1.544724 GGTGGTTTGAAGCCATGCTA 58.455 50.000 3.54 0.00 38.25 3.49 F
4411 8008 0.895530 TGCCTCCAGAGTAGGTTTCG 59.104 55.000 0.00 0.00 36.43 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 1910 2.746277 GCGCAACCCACGGAATCT 60.746 61.111 0.30 0.0 0.00 2.40 R
2290 5500 3.791973 TGGATTGTTGCGTTTCACTTT 57.208 38.095 0.00 0.0 0.00 2.66 R
2661 5997 6.039382 AGCCGACAATAATATCCAGTTTTTCC 59.961 38.462 0.00 0.0 0.00 3.13 R
3557 6977 6.358974 TCATGAACCTTCACAGAGTTATGA 57.641 37.500 0.00 0.0 40.49 2.15 R
3969 7539 1.369625 GCAGAACATTACCAGTCCCG 58.630 55.000 0.00 0.0 0.00 5.14 R
4832 9635 1.426983 AGCTTCTGGAGGCCTTCTTTT 59.573 47.619 13.68 0.0 33.44 2.27 R
5656 10672 0.035439 CCACTTGTCACGGGCCTAAT 60.035 55.000 0.84 0.0 0.00 1.73 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
137 138 0.321021 AGCAGCACAGTCTTGAGGAG 59.679 55.000 0.00 0.00 0.00 3.69
140 141 1.739562 GCACAGTCTTGAGGAGCCG 60.740 63.158 0.00 0.00 0.00 5.52
149 150 0.396435 TTGAGGAGCCGAAGAAAGCA 59.604 50.000 0.00 0.00 0.00 3.91
158 159 1.474077 CCGAAGAAAGCAATGAAGGGG 59.526 52.381 0.00 0.00 0.00 4.79
160 161 0.890683 AAGAAAGCAATGAAGGGGCG 59.109 50.000 0.00 0.00 0.00 6.13
164 165 0.890683 AAGCAATGAAGGGGCGAAAG 59.109 50.000 0.00 0.00 0.00 2.62
251 255 4.767255 CGGCCAGAGGAGCACCAC 62.767 72.222 2.24 0.00 38.94 4.16
304 308 4.643387 GACACCCCAGCCAGCGTT 62.643 66.667 0.00 0.00 0.00 4.84
339 343 4.060667 CAATCCCGGGGCCCAAGT 62.061 66.667 26.86 3.18 0.00 3.16
356 360 0.772124 AGTCCTTGCCTTTCTCCCCA 60.772 55.000 0.00 0.00 0.00 4.96
358 362 0.112412 TCCTTGCCTTTCTCCCCAAC 59.888 55.000 0.00 0.00 0.00 3.77
432 436 2.284699 AACTCCCACCCCCGAGAG 60.285 66.667 0.00 0.00 0.00 3.20
440 444 3.537874 CCCCCGAGAGTAAGGCCG 61.538 72.222 0.00 0.00 0.00 6.13
688 725 4.129148 GCCCGGGCCTTCCATCTT 62.129 66.667 36.64 0.00 34.36 2.40
689 726 2.193248 CCCGGGCCTTCCATCTTC 59.807 66.667 8.08 0.00 34.36 2.87
690 727 2.679342 CCCGGGCCTTCCATCTTCA 61.679 63.158 8.08 0.00 34.36 3.02
691 728 1.302949 CCGGGCCTTCCATCTTCAA 59.697 57.895 0.84 0.00 34.36 2.69
692 729 0.106519 CCGGGCCTTCCATCTTCAAT 60.107 55.000 0.84 0.00 34.36 2.57
693 730 1.686115 CCGGGCCTTCCATCTTCAATT 60.686 52.381 0.84 0.00 34.36 2.32
694 731 2.102578 CGGGCCTTCCATCTTCAATTT 58.897 47.619 0.84 0.00 34.36 1.82
695 732 2.497273 CGGGCCTTCCATCTTCAATTTT 59.503 45.455 0.84 0.00 34.36 1.82
696 733 3.055891 CGGGCCTTCCATCTTCAATTTTT 60.056 43.478 0.84 0.00 34.36 1.94
739 776 7.689559 GGAACCACCTATAAGGATAAAGTCCAG 60.690 44.444 0.00 0.00 41.74 3.86
751 788 6.095377 GGATAAAGTCCAGCAAAAGTCAATG 58.905 40.000 0.00 0.00 46.96 2.82
752 789 6.294731 GGATAAAGTCCAGCAAAAGTCAATGT 60.295 38.462 0.00 0.00 46.96 2.71
754 791 4.574599 AGTCCAGCAAAAGTCAATGTTC 57.425 40.909 0.00 0.00 0.00 3.18
755 792 3.003689 AGTCCAGCAAAAGTCAATGTTCG 59.996 43.478 0.00 0.00 0.00 3.95
756 793 3.003275 GTCCAGCAAAAGTCAATGTTCGA 59.997 43.478 0.00 0.00 0.00 3.71
757 794 3.820467 TCCAGCAAAAGTCAATGTTCGAT 59.180 39.130 0.00 0.00 0.00 3.59
759 796 5.122239 TCCAGCAAAAGTCAATGTTCGATAG 59.878 40.000 0.00 0.00 0.00 2.08
774 811 0.618458 GATAGTGGTGTCCCTGCCAA 59.382 55.000 0.00 0.00 36.41 4.52
782 819 0.840617 TGTCCCTGCCAACACTTGTA 59.159 50.000 0.00 0.00 0.00 2.41
783 820 1.235724 GTCCCTGCCAACACTTGTAC 58.764 55.000 0.00 0.00 0.00 2.90
816 853 6.909550 AGGATATTGCTGACTAGTAAGAGG 57.090 41.667 11.84 0.00 31.94 3.69
817 854 5.245075 AGGATATTGCTGACTAGTAAGAGGC 59.755 44.000 11.84 4.96 31.94 4.70
821 858 3.365472 TGCTGACTAGTAAGAGGCATGA 58.635 45.455 11.84 0.00 32.70 3.07
873 914 1.218316 CACCAGCTAGGGACGAACC 59.782 63.158 0.00 0.00 43.89 3.62
889 930 2.478879 CGAACCGCCTTTGTTGAAAAGT 60.479 45.455 0.00 0.00 0.00 2.66
892 933 4.301637 ACCGCCTTTGTTGAAAAGTAAG 57.698 40.909 0.00 0.00 0.00 2.34
900 1019 8.116136 GCCTTTGTTGAAAAGTAAGAAAACATG 58.884 33.333 0.00 0.00 0.00 3.21
915 1034 4.129737 ATGCGACCGAGTCCACCG 62.130 66.667 0.00 0.00 0.00 4.94
928 1055 3.499737 CACCGCTCCCAACGCATC 61.500 66.667 0.00 0.00 0.00 3.91
955 1082 3.192466 GTCTACAGACTCTCTCGTCTCC 58.808 54.545 2.03 0.00 42.10 3.71
956 1083 2.832733 TCTACAGACTCTCTCGTCTCCA 59.167 50.000 0.00 0.00 42.10 3.86
957 1084 2.570415 ACAGACTCTCTCGTCTCCAA 57.430 50.000 0.00 0.00 42.10 3.53
959 1086 1.742831 CAGACTCTCTCGTCTCCAAGG 59.257 57.143 0.00 0.00 42.10 3.61
961 1088 0.406361 ACTCTCTCGTCTCCAAGGGT 59.594 55.000 0.00 0.00 0.00 4.34
962 1089 1.634459 ACTCTCTCGTCTCCAAGGGTA 59.366 52.381 0.00 0.00 0.00 3.69
963 1090 2.294074 CTCTCTCGTCTCCAAGGGTAG 58.706 57.143 0.00 0.00 0.00 3.18
964 1091 0.741915 CTCTCGTCTCCAAGGGTAGC 59.258 60.000 0.00 0.00 0.00 3.58
965 1092 0.039180 TCTCGTCTCCAAGGGTAGCA 59.961 55.000 0.00 0.00 0.00 3.49
966 1093 1.115467 CTCGTCTCCAAGGGTAGCAT 58.885 55.000 0.00 0.00 0.00 3.79
968 1095 1.480954 TCGTCTCCAAGGGTAGCATTC 59.519 52.381 0.00 0.00 0.00 2.67
970 1097 1.840635 GTCTCCAAGGGTAGCATTCCT 59.159 52.381 0.00 0.00 34.29 3.36
971 1098 1.839994 TCTCCAAGGGTAGCATTCCTG 59.160 52.381 0.00 0.00 32.95 3.86
980 1107 3.824810 GCATTCCTGCTGCTCCTC 58.175 61.111 0.00 0.00 45.32 3.71
981 1108 1.823041 GCATTCCTGCTGCTCCTCC 60.823 63.158 0.00 0.00 45.32 4.30
982 1109 1.913722 CATTCCTGCTGCTCCTCCT 59.086 57.895 0.00 0.00 0.00 3.69
983 1110 0.179051 CATTCCTGCTGCTCCTCCTC 60.179 60.000 0.00 0.00 0.00 3.71
984 1111 0.326427 ATTCCTGCTGCTCCTCCTCT 60.326 55.000 0.00 0.00 0.00 3.69
985 1112 0.546267 TTCCTGCTGCTCCTCCTCTT 60.546 55.000 0.00 0.00 0.00 2.85
986 1113 0.975040 TCCTGCTGCTCCTCCTCTTC 60.975 60.000 0.00 0.00 0.00 2.87
987 1114 0.977108 CCTGCTGCTCCTCCTCTTCT 60.977 60.000 0.00 0.00 0.00 2.85
988 1115 0.461135 CTGCTGCTCCTCCTCTTCTC 59.539 60.000 0.00 0.00 0.00 2.87
1021 1148 3.959991 GAAGCTCCGCCGCCTCTTT 62.960 63.158 0.00 0.00 0.00 2.52
1034 1161 2.092914 CGCCTCTTTTCCTACCATTCCT 60.093 50.000 0.00 0.00 0.00 3.36
1038 1165 4.195416 CTCTTTTCCTACCATTCCTGCTC 58.805 47.826 0.00 0.00 0.00 4.26
1065 1198 0.039180 TCCTCCTAGCCTCGAACACA 59.961 55.000 0.00 0.00 0.00 3.72
1094 1227 4.478371 CAGGGATGGCTGCAGCGA 62.478 66.667 31.19 28.73 43.26 4.93
1139 1272 4.005650 TCCTACTACGTCACGAAGAACAT 58.994 43.478 2.91 0.00 0.00 2.71
1144 1277 1.784856 ACGTCACGAAGAACATGAACG 59.215 47.619 2.91 0.05 0.00 3.95
1151 1284 2.800544 CGAAGAACATGAACGTCACCTT 59.199 45.455 0.00 0.00 0.00 3.50
1158 1291 1.006825 TGAACGTCACCTTCATCGCG 61.007 55.000 0.00 0.00 0.00 5.87
1159 1292 2.279937 GAACGTCACCTTCATCGCGC 62.280 60.000 0.00 0.00 0.00 6.86
1160 1293 2.809174 CGTCACCTTCATCGCGCA 60.809 61.111 8.75 0.00 0.00 6.09
1176 1309 2.164026 GCAGCTCTTCGGCTTCTCG 61.164 63.158 0.00 0.00 41.00 4.04
1205 1338 0.027586 GCGCTTGCCAAGTATAACCG 59.972 55.000 6.28 1.05 0.00 4.44
1231 1364 0.750546 CCCCAGGATCGACTACGTCA 60.751 60.000 0.00 0.00 40.69 4.35
1234 1367 1.092348 CAGGATCGACTACGTCACCA 58.908 55.000 0.00 0.00 40.69 4.17
1240 1373 1.973281 GACTACGTCACCACCGGGA 60.973 63.158 6.32 0.00 38.05 5.14
1267 1403 4.974438 ACGTCCCCTTCCCCTGCA 62.974 66.667 0.00 0.00 0.00 4.41
1328 1464 2.511452 CCGCCTCCATCCCCTACAG 61.511 68.421 0.00 0.00 0.00 2.74
1370 1506 2.338015 CCAGCATCGCCAGCAACTT 61.338 57.895 0.00 0.00 0.00 2.66
1373 1509 0.890542 AGCATCGCCAGCAACTTCAA 60.891 50.000 0.00 0.00 0.00 2.69
1439 1575 1.004320 CCAACAACATCCCCGACGA 60.004 57.895 0.00 0.00 0.00 4.20
1536 1672 3.971894 CCGCTAAGGGACTGGGAT 58.028 61.111 0.00 0.00 40.86 3.85
1548 1684 3.544167 CTGGGATACGCTCGCCTCG 62.544 68.421 1.04 0.00 36.01 4.63
1592 1728 2.512515 GCCGGAGCAGATGGACAC 60.513 66.667 5.05 0.00 39.53 3.67
1596 1732 0.036952 CGGAGCAGATGGACACACTT 60.037 55.000 0.00 0.00 0.00 3.16
1702 1838 1.068434 GCTCCTCTCTCTATGGTGCAC 59.932 57.143 8.80 8.80 39.36 4.57
1772 1908 7.412137 TGATTGATATTGATCTACGTTGCTG 57.588 36.000 0.00 0.00 32.79 4.41
1773 1909 5.657470 TTGATATTGATCTACGTTGCTGC 57.343 39.130 0.00 0.00 32.79 5.25
1774 1910 4.692228 TGATATTGATCTACGTTGCTGCA 58.308 39.130 0.00 0.00 32.79 4.41
1775 1911 4.746611 TGATATTGATCTACGTTGCTGCAG 59.253 41.667 10.11 10.11 32.79 4.41
1776 1912 2.741759 TTGATCTACGTTGCTGCAGA 57.258 45.000 20.43 0.00 0.00 4.26
1777 1913 2.967599 TGATCTACGTTGCTGCAGAT 57.032 45.000 20.43 1.40 0.00 2.90
1778 1914 3.251479 TGATCTACGTTGCTGCAGATT 57.749 42.857 20.43 0.00 0.00 2.40
1779 1915 3.190079 TGATCTACGTTGCTGCAGATTC 58.810 45.455 20.43 5.13 0.00 2.52
1780 1916 2.010145 TCTACGTTGCTGCAGATTCC 57.990 50.000 20.43 0.00 0.00 3.01
1819 1955 8.700439 TGCCATTTCTGCATGCATATATATAT 57.300 30.769 22.97 5.40 32.85 0.86
1895 2192 7.552687 TCCTGCAACTATATTCAAACTACTTGG 59.447 37.037 0.00 0.00 35.56 3.61
1929 2231 2.169561 TCCGAACATCCCATCATCGAAA 59.830 45.455 0.00 0.00 35.65 3.46
1957 2259 8.136800 ACACATGTATAATGTATTTGTGCATGG 58.863 33.333 14.15 8.14 46.50 3.66
2060 5269 3.119531 GGTCGATTGTCAATGGAATGCAA 60.120 43.478 11.37 0.00 0.00 4.08
2105 5315 6.971726 AAGACTACCCGATATGTACATTGA 57.028 37.500 14.77 0.00 0.00 2.57
2106 5316 7.540474 AAGACTACCCGATATGTACATTGAT 57.460 36.000 14.77 1.79 0.00 2.57
2107 5317 8.645814 AAGACTACCCGATATGTACATTGATA 57.354 34.615 14.77 0.00 0.00 2.15
2108 5318 8.824756 AGACTACCCGATATGTACATTGATAT 57.175 34.615 14.77 0.56 0.00 1.63
2159 5369 2.620585 GGTTACGACCCTAATAGCGACT 59.379 50.000 0.00 0.00 40.25 4.18
2179 5389 6.497437 CGACTTGCATGATTAATGGAATTCA 58.503 36.000 7.93 0.00 44.55 2.57
2184 5394 6.798482 TGCATGATTAATGGAATTCAGACAC 58.202 36.000 7.93 0.00 37.87 3.67
2198 5408 4.454728 TCAGACACGATCATTCATGACA 57.545 40.909 0.00 0.00 40.03 3.58
2509 5845 7.756722 CAGCAGGGTAAGAATTGTTATTTGAAG 59.243 37.037 0.00 0.00 0.00 3.02
2649 5985 4.025145 GCTAATTATTGCTCGCCGTTAAGT 60.025 41.667 0.00 0.00 0.00 2.24
2697 6033 1.617322 TTGTCGGCTACTGTGAGAGT 58.383 50.000 0.00 0.00 38.88 3.24
2698 6034 0.881796 TGTCGGCTACTGTGAGAGTG 59.118 55.000 0.00 0.00 35.96 3.51
3018 6421 1.544724 GGTGGTTTGAAGCCATGCTA 58.455 50.000 3.54 0.00 38.25 3.49
3557 6977 2.971330 TCAGAAACCCACATGCCAAAAT 59.029 40.909 0.00 0.00 0.00 1.82
3575 7116 6.294731 GCCAAAATCATAACTCTGTGAAGGTT 60.295 38.462 0.00 0.00 0.00 3.50
3778 7323 9.968743 CGTAAATCTTCTATTTGTTCACCTAAC 57.031 33.333 0.00 0.00 38.67 2.34
3807 7354 6.307800 CACTGCTTTTTAATGGGACGTTAATG 59.692 38.462 0.00 0.00 0.00 1.90
4020 7590 1.669795 CCGAATGTGCCTTTTTCTGCC 60.670 52.381 0.00 0.00 0.00 4.85
4032 7602 2.071778 TTTCTGCCCTGTTGCTTCTT 57.928 45.000 0.00 0.00 0.00 2.52
4279 7873 8.887036 TCCATGTGTTCTATATGTACATTCAC 57.113 34.615 14.77 13.22 30.15 3.18
4286 7880 9.726232 TGTTCTATATGTACATTCACGAAGTAC 57.274 33.333 14.77 7.40 41.61 2.73
4298 7892 5.585500 TCACGAAGTACTGTTGTTTATGC 57.415 39.130 0.00 0.00 41.61 3.14
4411 8008 0.895530 TGCCTCCAGAGTAGGTTTCG 59.104 55.000 0.00 0.00 36.43 3.46
4494 8098 5.152623 ACTGCAGAGTAGTTGCTGATTTA 57.847 39.130 23.35 0.00 41.35 1.40
4525 8130 6.678568 TGTTGACAATTATGGGAAATGGTT 57.321 33.333 0.00 0.00 0.00 3.67
4684 8289 5.944007 GGACTGGTTTATCTGGTAATTGTGT 59.056 40.000 0.00 0.00 0.00 3.72
4697 8302 6.296026 TGGTAATTGTGTTTCTGAGCTAGTT 58.704 36.000 0.00 0.00 0.00 2.24
4726 8387 3.002791 CTGCTCTCGGTGCTTCATAAAA 58.997 45.455 0.00 0.00 0.00 1.52
4727 8388 2.742053 TGCTCTCGGTGCTTCATAAAAC 59.258 45.455 0.00 0.00 0.00 2.43
4728 8389 2.096013 GCTCTCGGTGCTTCATAAAACC 59.904 50.000 0.00 0.00 0.00 3.27
4733 8394 3.675467 GGTGCTTCATAAAACCGCTAG 57.325 47.619 0.00 0.00 0.00 3.42
4734 8395 2.223272 GGTGCTTCATAAAACCGCTAGC 60.223 50.000 4.06 4.06 0.00 3.42
4735 8396 2.014128 TGCTTCATAAAACCGCTAGCC 58.986 47.619 9.66 0.00 0.00 3.93
4736 8397 2.289565 GCTTCATAAAACCGCTAGCCT 58.710 47.619 9.66 0.00 0.00 4.58
4737 8398 2.032178 GCTTCATAAAACCGCTAGCCTG 59.968 50.000 9.66 2.99 0.00 4.85
4832 9635 0.900421 CTCTCACTGCACTGGATCCA 59.100 55.000 15.27 15.27 0.00 3.41
4951 9782 5.730568 GCTTGCTCGTTCGATTGGATAAAAT 60.731 40.000 0.00 0.00 0.00 1.82
4952 9783 5.811399 TGCTCGTTCGATTGGATAAAATT 57.189 34.783 0.00 0.00 0.00 1.82
4967 9963 9.806448 TTGGATAAAATTATATGCTGCCTTCTA 57.194 29.630 0.00 0.00 0.00 2.10
5185 10195 4.591321 AGATCAGGGCACATTTCCTTTA 57.409 40.909 0.00 0.00 0.00 1.85
5211 10221 0.100503 GAAGCAAACACACGCCTTGT 59.899 50.000 0.00 0.00 39.97 3.16
5316 10326 6.881065 TCTGCATAGGAAATTAGATACATGCC 59.119 38.462 0.00 0.00 37.36 4.40
5420 10436 1.264020 GCGCATGACTGAAGTGAACAA 59.736 47.619 0.30 0.00 0.00 2.83
5422 10438 2.660094 CGCATGACTGAAGTGAACAACG 60.660 50.000 0.00 0.00 0.00 4.10
5423 10439 2.287915 GCATGACTGAAGTGAACAACGT 59.712 45.455 0.00 0.00 0.00 3.99
5424 10440 3.846023 GCATGACTGAAGTGAACAACGTG 60.846 47.826 0.00 0.00 0.00 4.49
5425 10441 2.967362 TGACTGAAGTGAACAACGTGT 58.033 42.857 0.00 0.00 0.00 4.49
5470 10486 3.400054 GAGGGGTTGGTAGCGGCT 61.400 66.667 7.98 7.98 0.00 5.52
5495 10511 1.117150 GCCGTGGTGGAGTTATAGGA 58.883 55.000 0.00 0.00 42.00 2.94
5496 10512 1.483415 GCCGTGGTGGAGTTATAGGAA 59.517 52.381 0.00 0.00 42.00 3.36
5572 10588 2.046507 AAGCTGCTCTTCCTGGCG 60.047 61.111 1.00 0.00 0.00 5.69
5580 10596 1.271102 GCTCTTCCTGGCGTATCCTAG 59.729 57.143 0.00 0.00 35.26 3.02
5584 10600 2.217510 TCCTGGCGTATCCTAGATCC 57.782 55.000 0.00 0.00 35.26 3.36
5590 10606 2.028020 GGCGTATCCTAGATCCCCTTTG 60.028 54.545 0.00 0.00 0.00 2.77
5607 10623 1.981256 TTGTCCTTGTTCTTCCTGCC 58.019 50.000 0.00 0.00 0.00 4.85
5643 10659 2.144450 TCCCTAGATCACTAGAGGCCA 58.856 52.381 5.01 0.00 46.34 5.36
5644 10660 2.109128 TCCCTAGATCACTAGAGGCCAG 59.891 54.545 5.01 0.00 46.34 4.85
5645 10661 2.158385 CCCTAGATCACTAGAGGCCAGT 60.158 54.545 5.01 0.00 46.34 4.00
5646 10662 2.890311 CCTAGATCACTAGAGGCCAGTG 59.110 54.545 14.17 14.17 46.34 3.66
5649 10665 3.765968 TCACTAGAGGCCAGTGACA 57.234 52.632 18.01 0.39 45.68 3.58
5650 10666 2.009681 TCACTAGAGGCCAGTGACAA 57.990 50.000 18.01 0.00 45.68 3.18
5651 10667 1.895798 TCACTAGAGGCCAGTGACAAG 59.104 52.381 18.01 2.62 45.68 3.16
5652 10668 1.620819 CACTAGAGGCCAGTGACAAGT 59.379 52.381 15.03 1.02 45.10 3.16
5653 10669 1.620819 ACTAGAGGCCAGTGACAAGTG 59.379 52.381 5.01 0.00 0.00 3.16
5662 10678 3.270877 CCAGTGACAAGTGGTATTAGGC 58.729 50.000 0.00 0.00 41.43 3.93
5663 10679 3.270877 CAGTGACAAGTGGTATTAGGCC 58.729 50.000 0.00 0.00 0.00 5.19
5686 10702 3.589988 GTGACAAGTGGTATCAGAGGTG 58.410 50.000 0.00 0.00 0.00 4.00
5704 10720 4.305524 AGGTGAGAGATCCTGGATTCAAT 58.694 43.478 11.17 1.00 32.29 2.57
5716 10732 2.766263 TGGATTCAATCTACCAGCGACT 59.234 45.455 0.00 0.00 0.00 4.18
5718 10734 3.181475 GGATTCAATCTACCAGCGACTGA 60.181 47.826 8.20 0.00 32.44 3.41
5728 10744 4.796225 GCGACTGAGCTACCAGAC 57.204 61.111 9.28 2.53 37.59 3.51
5769 10785 0.693430 AGCCATGGAGGAGCAGATCA 60.693 55.000 18.40 0.00 41.22 2.92
5779 10795 2.894387 GCAGATCACCGCTCTGGC 60.894 66.667 0.00 0.00 43.94 4.85
5792 10808 1.006571 TCTGGCGAAGACGGTCAAC 60.007 57.895 11.27 2.91 46.47 3.18
5832 10848 2.187946 CCCGCCTCGAAGCAATCT 59.812 61.111 6.84 0.00 0.00 2.40
5834 10850 0.598680 CCCGCCTCGAAGCAATCTAG 60.599 60.000 6.84 0.00 0.00 2.43
5835 10851 0.598680 CCGCCTCGAAGCAATCTAGG 60.599 60.000 6.84 5.91 42.58 3.02
5888 10904 1.407936 ACCTACATCAGCAGCTCGAT 58.592 50.000 0.00 0.00 0.00 3.59
5891 10907 2.607526 CCTACATCAGCAGCTCGATGAG 60.608 54.545 27.74 21.53 44.78 2.90
5892 10908 0.822811 ACATCAGCAGCTCGATGAGT 59.177 50.000 27.74 13.25 44.78 3.41
5898 10914 2.096442 CAGCTCGATGAGTTGCGCA 61.096 57.895 5.66 5.66 34.48 6.09
5899 10915 2.097038 AGCTCGATGAGTTGCGCAC 61.097 57.895 11.12 5.61 31.39 5.34
5900 10916 3.084579 CTCGATGAGTTGCGCACC 58.915 61.111 11.12 1.55 0.00 5.01
5901 10917 2.434185 TCGATGAGTTGCGCACCC 60.434 61.111 11.12 3.25 0.00 4.61
5902 10918 2.741985 CGATGAGTTGCGCACCCA 60.742 61.111 11.12 9.01 0.00 4.51
5903 10919 2.743752 CGATGAGTTGCGCACCCAG 61.744 63.158 11.12 0.00 0.00 4.45
5923 10939 3.866582 CCAGGTGGGCCGGATCTC 61.867 72.222 5.05 0.00 40.50 2.75
5935 10951 2.581354 GATCTCGCTGCACCCAGT 59.419 61.111 0.00 0.00 41.26 4.00
5953 10969 1.228644 TGCTTGCATTGGCTCCAGT 60.229 52.632 8.00 0.00 41.91 4.00
5956 10972 1.753073 GCTTGCATTGGCTCCAGTAAT 59.247 47.619 0.00 0.00 41.91 1.89
5960 10976 1.873591 GCATTGGCTCCAGTAATACCG 59.126 52.381 0.00 0.00 36.96 4.02
6009 11025 0.109086 AGATCCAGTCGACAACGCTG 60.109 55.000 19.50 6.55 40.45 5.18
6054 11070 0.528466 CGTCATCATCGACACTGGGG 60.528 60.000 0.00 0.00 35.54 4.96
6055 11071 0.179073 GTCATCATCGACACTGGGGG 60.179 60.000 0.00 0.00 35.88 5.40
6095 11111 1.762460 CACCCTGATACCGCCTCCT 60.762 63.158 0.00 0.00 0.00 3.69
6100 11116 0.824109 CTGATACCGCCTCCTGTCAA 59.176 55.000 0.00 0.00 0.00 3.18
6106 11122 2.360475 GCCTCCTGTCAAGGGTGC 60.360 66.667 0.00 0.00 44.62 5.01
6110 11126 1.821061 CTCCTGTCAAGGGTGCGTCT 61.821 60.000 0.00 0.00 44.62 4.18
6114 11130 1.445582 GTCAAGGGTGCGTCTACCG 60.446 63.158 0.00 0.00 41.79 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 0.319040 TCAAGACTGTGCTGCTCGAC 60.319 55.000 0.00 0.00 0.00 4.20
137 138 1.135286 CCCTTCATTGCTTTCTTCGGC 60.135 52.381 0.00 0.00 0.00 5.54
140 141 1.135286 CGCCCCTTCATTGCTTTCTTC 60.135 52.381 0.00 0.00 0.00 2.87
149 150 1.000359 CCCCTTTCGCCCCTTCATT 60.000 57.895 0.00 0.00 0.00 2.57
238 242 2.126307 CGTCGTGGTGCTCCTCTG 60.126 66.667 6.34 0.12 34.23 3.35
332 336 0.540597 AGAAAGGCAAGGACTTGGGC 60.541 55.000 13.41 6.98 40.74 5.36
339 343 0.112412 GTTGGGGAGAAAGGCAAGGA 59.888 55.000 0.00 0.00 0.00 3.36
342 346 1.901464 GCGTTGGGGAGAAAGGCAA 60.901 57.895 0.00 0.00 38.10 4.52
343 347 2.282180 GCGTTGGGGAGAAAGGCA 60.282 61.111 0.00 0.00 38.10 4.75
413 417 3.771160 CTCGGGGGTGGGAGTTCG 61.771 72.222 0.00 0.00 0.00 3.95
694 731 4.159244 TCCTCTCGGGAGAAAACAAAAA 57.841 40.909 15.72 0.00 41.86 1.94
695 732 3.849563 TCCTCTCGGGAGAAAACAAAA 57.150 42.857 15.72 0.00 41.86 2.44
696 733 3.473625 GTTCCTCTCGGGAGAAAACAAA 58.526 45.455 15.72 0.00 46.01 2.83
697 734 2.224450 GGTTCCTCTCGGGAGAAAACAA 60.224 50.000 23.47 5.15 46.01 2.83
698 735 1.346722 GGTTCCTCTCGGGAGAAAACA 59.653 52.381 23.47 0.21 46.01 2.83
699 736 1.346722 TGGTTCCTCTCGGGAGAAAAC 59.653 52.381 15.72 16.83 46.01 2.43
700 737 1.346722 GTGGTTCCTCTCGGGAGAAAA 59.653 52.381 15.72 4.82 46.01 2.29
701 738 0.974383 GTGGTTCCTCTCGGGAGAAA 59.026 55.000 15.72 0.00 46.01 2.52
702 739 0.903454 GGTGGTTCCTCTCGGGAGAA 60.903 60.000 15.72 3.31 46.01 2.87
703 740 1.305046 GGTGGTTCCTCTCGGGAGA 60.305 63.158 15.72 0.00 46.01 3.71
704 741 0.033405 TAGGTGGTTCCTCTCGGGAG 60.033 60.000 4.93 4.93 44.42 4.30
705 742 0.635009 ATAGGTGGTTCCTCTCGGGA 59.365 55.000 0.00 0.00 44.42 5.14
706 743 2.376695 TATAGGTGGTTCCTCTCGGG 57.623 55.000 0.00 0.00 44.42 5.14
707 744 2.628657 CCTTATAGGTGGTTCCTCTCGG 59.371 54.545 0.00 0.00 44.42 4.63
708 745 3.563223 TCCTTATAGGTGGTTCCTCTCG 58.437 50.000 0.00 0.00 44.42 4.04
709 746 7.290481 ACTTTATCCTTATAGGTGGTTCCTCTC 59.710 40.741 0.00 0.00 44.42 3.20
710 747 7.140304 ACTTTATCCTTATAGGTGGTTCCTCT 58.860 38.462 0.00 0.00 44.42 3.69
711 748 7.376335 ACTTTATCCTTATAGGTGGTTCCTC 57.624 40.000 0.00 0.00 44.42 3.71
712 749 6.329460 GGACTTTATCCTTATAGGTGGTTCCT 59.671 42.308 0.00 0.00 46.14 3.36
713 750 6.531923 GGACTTTATCCTTATAGGTGGTTCC 58.468 44.000 0.00 0.00 45.22 3.62
739 776 5.088739 CCACTATCGAACATTGACTTTTGC 58.911 41.667 0.00 0.00 0.00 3.68
751 788 1.739371 GCAGGGACACCACTATCGAAC 60.739 57.143 0.00 0.00 40.13 3.95
752 789 0.535335 GCAGGGACACCACTATCGAA 59.465 55.000 0.00 0.00 40.13 3.71
754 791 1.144057 GGCAGGGACACCACTATCG 59.856 63.158 0.00 0.00 40.13 2.92
755 792 0.618458 TTGGCAGGGACACCACTATC 59.382 55.000 0.00 0.00 36.55 2.08
756 793 0.328258 GTTGGCAGGGACACCACTAT 59.672 55.000 0.00 0.00 36.55 2.12
757 794 1.057275 TGTTGGCAGGGACACCACTA 61.057 55.000 0.00 0.00 36.55 2.74
759 796 2.193536 GTGTTGGCAGGGACACCAC 61.194 63.158 9.30 0.00 40.11 4.16
782 819 2.026262 AGCAATATCCTTCCAACACGGT 60.026 45.455 0.00 0.00 35.57 4.83
783 820 2.355756 CAGCAATATCCTTCCAACACGG 59.644 50.000 0.00 0.00 0.00 4.94
816 853 3.219176 TCTGGGAGGATTCATTCATGC 57.781 47.619 0.00 0.00 0.00 4.06
817 854 3.568853 GCTTCTGGGAGGATTCATTCATG 59.431 47.826 0.00 0.00 0.00 3.07
821 858 4.043596 ACTAGCTTCTGGGAGGATTCATT 58.956 43.478 0.00 0.00 0.00 2.57
873 914 6.309251 TGTTTTCTTACTTTTCAACAAAGGCG 59.691 34.615 0.00 0.00 0.00 5.52
889 930 2.991190 GACTCGGTCGCATGTTTTCTTA 59.009 45.455 0.00 0.00 0.00 2.10
892 933 0.442699 GGACTCGGTCGCATGTTTTC 59.557 55.000 0.00 0.00 32.65 2.29
947 1074 1.115467 ATGCTACCCTTGGAGACGAG 58.885 55.000 0.00 0.00 41.95 4.18
948 1075 1.480954 GAATGCTACCCTTGGAGACGA 59.519 52.381 0.00 0.00 0.00 4.20
949 1076 1.473434 GGAATGCTACCCTTGGAGACG 60.473 57.143 0.00 0.00 0.00 4.18
950 1077 1.840635 AGGAATGCTACCCTTGGAGAC 59.159 52.381 0.00 0.00 0.00 3.36
953 1080 0.255890 GCAGGAATGCTACCCTTGGA 59.744 55.000 0.00 0.00 0.00 3.53
954 1081 0.257039 AGCAGGAATGCTACCCTTGG 59.743 55.000 0.00 0.00 44.28 3.61
955 1082 1.386533 CAGCAGGAATGCTACCCTTG 58.613 55.000 1.86 0.00 44.30 3.61
956 1083 0.394899 GCAGCAGGAATGCTACCCTT 60.395 55.000 1.86 0.00 44.30 3.95
957 1084 1.225704 GCAGCAGGAATGCTACCCT 59.774 57.895 1.86 0.00 44.30 4.34
963 1090 1.823041 GGAGGAGCAGCAGGAATGC 60.823 63.158 0.00 0.00 44.18 3.56
964 1091 0.179051 GAGGAGGAGCAGCAGGAATG 60.179 60.000 0.00 0.00 0.00 2.67
965 1092 0.326427 AGAGGAGGAGCAGCAGGAAT 60.326 55.000 0.00 0.00 0.00 3.01
966 1093 0.546267 AAGAGGAGGAGCAGCAGGAA 60.546 55.000 0.00 0.00 0.00 3.36
968 1095 0.977108 AGAAGAGGAGGAGCAGCAGG 60.977 60.000 0.00 0.00 0.00 4.85
970 1097 0.975040 GGAGAAGAGGAGGAGCAGCA 60.975 60.000 0.00 0.00 0.00 4.41
971 1098 0.687427 AGGAGAAGAGGAGGAGCAGC 60.687 60.000 0.00 0.00 0.00 5.25
973 1100 1.063567 GGTAGGAGAAGAGGAGGAGCA 60.064 57.143 0.00 0.00 0.00 4.26
974 1101 1.699730 GGTAGGAGAAGAGGAGGAGC 58.300 60.000 0.00 0.00 0.00 4.70
975 1102 1.477923 CGGGTAGGAGAAGAGGAGGAG 60.478 61.905 0.00 0.00 0.00 3.69
976 1103 0.551879 CGGGTAGGAGAAGAGGAGGA 59.448 60.000 0.00 0.00 0.00 3.71
977 1104 1.110518 GCGGGTAGGAGAAGAGGAGG 61.111 65.000 0.00 0.00 0.00 4.30
978 1105 1.448922 CGCGGGTAGGAGAAGAGGAG 61.449 65.000 0.00 0.00 0.00 3.69
979 1106 1.453379 CGCGGGTAGGAGAAGAGGA 60.453 63.158 0.00 0.00 0.00 3.71
980 1107 3.121019 CGCGGGTAGGAGAAGAGG 58.879 66.667 0.00 0.00 0.00 3.69
981 1108 2.413765 GCGCGGGTAGGAGAAGAG 59.586 66.667 8.83 0.00 0.00 2.85
982 1109 3.145551 GGCGCGGGTAGGAGAAGA 61.146 66.667 8.83 0.00 0.00 2.87
983 1110 2.797278 ATGGCGCGGGTAGGAGAAG 61.797 63.158 8.83 0.00 0.00 2.85
984 1111 2.762459 ATGGCGCGGGTAGGAGAA 60.762 61.111 8.83 0.00 0.00 2.87
985 1112 3.536917 CATGGCGCGGGTAGGAGA 61.537 66.667 8.83 0.00 0.00 3.71
986 1113 4.609018 CCATGGCGCGGGTAGGAG 62.609 72.222 8.83 0.00 0.00 3.69
988 1115 4.169696 TTCCATGGCGCGGGTAGG 62.170 66.667 8.83 0.00 0.00 3.18
1021 1148 2.119495 GAGGAGCAGGAATGGTAGGAA 58.881 52.381 0.00 0.00 0.00 3.36
1034 1161 0.627768 TAGGAGGAGGAGGAGGAGCA 60.628 60.000 0.00 0.00 0.00 4.26
1038 1165 1.155155 GGCTAGGAGGAGGAGGAGG 59.845 68.421 0.00 0.00 0.00 4.30
1139 1272 1.006825 CGCGATGAAGGTGACGTTCA 61.007 55.000 20.98 20.98 38.28 3.18
1144 1277 3.084579 CTGCGCGATGAAGGTGAC 58.915 61.111 12.10 0.00 0.00 3.67
1151 1284 2.580597 CGAAGAGCTGCGCGATGA 60.581 61.111 12.10 0.00 0.00 2.92
1158 1291 2.164026 CGAGAAGCCGAAGAGCTGC 61.164 63.158 0.00 0.00 44.11 5.25
1159 1292 1.518133 CCGAGAAGCCGAAGAGCTG 60.518 63.158 0.00 0.00 44.11 4.24
1176 1309 2.886124 GCAAGCGCTCGGTAGTCC 60.886 66.667 12.06 0.00 34.30 3.85
1186 1319 0.027586 CGGTTATACTTGGCAAGCGC 59.972 55.000 26.45 0.00 36.53 5.92
1187 1320 0.027586 GCGGTTATACTTGGCAAGCG 59.972 55.000 26.45 20.16 43.79 4.68
1191 1324 1.153329 CCCGCGGTTATACTTGGCA 60.153 57.895 26.12 0.00 0.00 4.92
1328 1464 0.388263 GGTTTCTCCCGTGACGACTC 60.388 60.000 6.54 0.00 0.00 3.36
1370 1506 1.525077 GCGGTGGTGAGGTTGTTGA 60.525 57.895 0.00 0.00 0.00 3.18
1373 1509 4.619227 CGGCGGTGGTGAGGTTGT 62.619 66.667 0.00 0.00 0.00 3.32
1454 1590 1.669115 CAGGAGCAGTTGACGGTGG 60.669 63.158 0.00 0.00 0.00 4.61
1503 1639 1.218047 CGGGAATGTGCGGAAGAGA 59.782 57.895 0.00 0.00 0.00 3.10
1592 1728 3.056035 GCCGGGATTATACCTCCTAAGTG 60.056 52.174 2.18 0.00 33.05 3.16
1596 1732 3.104512 CATGCCGGGATTATACCTCCTA 58.895 50.000 5.36 0.00 33.05 2.94
1702 1838 4.755123 ACATAAAGGAAGAAACGTGTGAGG 59.245 41.667 0.00 0.00 0.00 3.86
1772 1908 2.877691 GCAACCCACGGAATCTGC 59.122 61.111 0.00 0.00 0.00 4.26
1773 1909 3.039202 GCGCAACCCACGGAATCTG 62.039 63.158 0.30 0.00 0.00 2.90
1774 1910 2.746277 GCGCAACCCACGGAATCT 60.746 61.111 0.30 0.00 0.00 2.40
1775 1911 3.810896 GGCGCAACCCACGGAATC 61.811 66.667 10.83 0.00 0.00 2.52
1776 1912 3.936772 ATGGCGCAACCCACGGAAT 62.937 57.895 10.83 0.00 37.79 3.01
1777 1913 4.652131 ATGGCGCAACCCACGGAA 62.652 61.111 10.83 0.00 37.79 4.30
1818 1954 9.131791 AGGCATTTTAATCCAAGTTAATACGAT 57.868 29.630 0.00 0.00 0.00 3.73
1819 1955 8.514330 AGGCATTTTAATCCAAGTTAATACGA 57.486 30.769 0.00 0.00 0.00 3.43
1870 2006 7.552687 TCCAAGTAGTTTGAATATAGTTGCAGG 59.447 37.037 0.00 0.00 39.21 4.85
2035 5066 4.440525 GCATTCCATTGACAATCGACCAAT 60.441 41.667 0.00 0.00 0.00 3.16
2108 5318 9.892444 TCCATGACCTACTTCCTTCTAATTATA 57.108 33.333 0.00 0.00 0.00 0.98
2159 5369 7.259882 GTGTCTGAATTCCATTAATCATGCAA 58.740 34.615 2.27 0.00 0.00 4.08
2179 5389 4.192429 TGTGTCATGAATGATCGTGTCT 57.808 40.909 0.00 0.00 42.22 3.41
2184 5394 4.034742 TGAGCAATGTGTCATGAATGATCG 59.965 41.667 0.00 0.00 39.30 3.69
2198 5408 4.216257 GGAACATGTACTTGTGAGCAATGT 59.784 41.667 14.52 0.00 33.65 2.71
2290 5500 3.791973 TGGATTGTTGCGTTTCACTTT 57.208 38.095 0.00 0.00 0.00 2.66
2299 5509 3.847542 TCAAATGGATTGGATTGTTGCG 58.152 40.909 0.00 0.00 39.62 4.85
2516 5852 8.348285 TGACCAAGAAAATTAAGTGGATAAGG 57.652 34.615 0.00 0.00 33.39 2.69
2661 5997 6.039382 AGCCGACAATAATATCCAGTTTTTCC 59.961 38.462 0.00 0.00 0.00 3.13
2697 6033 9.511272 AGTTGAATATGAATAAGCATCATAGCA 57.489 29.630 3.07 1.69 41.62 3.49
2698 6034 9.985318 GAGTTGAATATGAATAAGCATCATAGC 57.015 33.333 3.07 0.00 41.62 2.97
3557 6977 6.358974 TCATGAACCTTCACAGAGTTATGA 57.641 37.500 0.00 0.00 40.49 2.15
3595 7137 8.865590 TTTCGAATGAAGAACGTATCATGATA 57.134 30.769 11.49 11.49 36.44 2.15
3778 7323 4.613622 CGTCCCATTAAAAAGCAGTGTCAG 60.614 45.833 0.00 0.00 0.00 3.51
3807 7354 2.442413 TCGTCCCCATGGAAAATCAAC 58.558 47.619 15.22 0.00 44.07 3.18
3969 7539 1.369625 GCAGAACATTACCAGTCCCG 58.630 55.000 0.00 0.00 0.00 5.14
3972 7542 3.526534 GAGAGGCAGAACATTACCAGTC 58.473 50.000 0.00 0.00 0.00 3.51
4032 7602 3.342719 TGTGCCGAGAGATTAATTTGCA 58.657 40.909 0.00 0.00 0.00 4.08
4279 7873 4.640805 ACGCATAAACAACAGTACTTCG 57.359 40.909 0.00 0.00 0.00 3.79
4286 7880 5.220662 CCTGGAAGATACGCATAAACAACAG 60.221 44.000 0.00 0.00 34.07 3.16
4298 7892 2.672961 TCTGCAACCTGGAAGATACG 57.327 50.000 0.00 0.00 34.07 3.06
4525 8130 3.110358 CGTATCGAACGTATCTGCCAAA 58.890 45.455 10.63 0.00 46.72 3.28
4684 8289 7.841956 AGCAGAAAGTATAACTAGCTCAGAAA 58.158 34.615 0.00 0.00 0.00 2.52
4697 8302 3.024547 AGCACCGAGAGCAGAAAGTATA 58.975 45.455 0.00 0.00 0.00 1.47
4729 8390 2.751837 AAAAGCGGCCAGGCTAGC 60.752 61.111 20.34 20.34 43.93 3.42
4730 8391 2.409870 CCAAAAGCGGCCAGGCTAG 61.410 63.158 12.43 7.26 43.93 3.42
4731 8392 2.361104 CCAAAAGCGGCCAGGCTA 60.361 61.111 12.43 0.00 43.93 3.93
4734 8395 3.373565 GACCCAAAAGCGGCCAGG 61.374 66.667 2.24 0.00 0.00 4.45
4735 8396 3.373565 GGACCCAAAAGCGGCCAG 61.374 66.667 2.24 0.00 0.00 4.85
4736 8397 4.211330 TGGACCCAAAAGCGGCCA 62.211 61.111 2.24 0.00 0.00 5.36
4737 8398 3.373565 CTGGACCCAAAAGCGGCC 61.374 66.667 0.00 0.00 0.00 6.13
4832 9635 1.426983 AGCTTCTGGAGGCCTTCTTTT 59.573 47.619 13.68 0.00 33.44 2.27
4933 9763 9.214957 AGCATATAATTTTATCCAATCGAACGA 57.785 29.630 0.00 0.00 0.00 3.85
4934 9764 9.265938 CAGCATATAATTTTATCCAATCGAACG 57.734 33.333 0.00 0.00 0.00 3.95
4951 9782 3.181470 TGCACGTAGAAGGCAGCATATAA 60.181 43.478 0.00 0.00 32.95 0.98
4952 9783 2.364002 TGCACGTAGAAGGCAGCATATA 59.636 45.455 0.00 0.00 32.95 0.86
5097 10105 0.773644 ACATGAGGTTCACCAAGCCT 59.226 50.000 0.00 0.00 38.89 4.58
5185 10195 2.541588 GCGTGTGTTTGCTTCTTGACAT 60.542 45.455 0.00 0.00 0.00 3.06
5420 10436 2.449525 GCGACACACACACACACGT 61.450 57.895 0.00 0.00 0.00 4.49
5422 10438 1.348250 CAGCGACACACACACACAC 59.652 57.895 0.00 0.00 0.00 3.82
5423 10439 2.460275 GCAGCGACACACACACACA 61.460 57.895 0.00 0.00 0.00 3.72
5424 10440 2.324477 GCAGCGACACACACACAC 59.676 61.111 0.00 0.00 0.00 3.82
5425 10441 2.894879 GGCAGCGACACACACACA 60.895 61.111 0.00 0.00 0.00 3.72
5486 10502 1.067212 CGGACGCAGCTTCCTATAACT 59.933 52.381 15.64 0.00 0.00 2.24
5569 10585 1.939980 AAGGGGATCTAGGATACGCC 58.060 55.000 3.66 0.00 46.39 5.68
5572 10588 4.494591 AGGACAAAGGGGATCTAGGATAC 58.505 47.826 0.00 0.00 0.00 2.24
5580 10596 3.441500 AGAACAAGGACAAAGGGGATC 57.558 47.619 0.00 0.00 0.00 3.36
5584 10600 2.887152 CAGGAAGAACAAGGACAAAGGG 59.113 50.000 0.00 0.00 0.00 3.95
5590 10606 1.611936 GGAGGCAGGAAGAACAAGGAC 60.612 57.143 0.00 0.00 0.00 3.85
5607 10623 0.689412 GGGAAGGAGGAGGAGTGGAG 60.689 65.000 0.00 0.00 0.00 3.86
5643 10659 2.238898 GGGCCTAATACCACTTGTCACT 59.761 50.000 0.84 0.00 0.00 3.41
5644 10660 2.640184 GGGCCTAATACCACTTGTCAC 58.360 52.381 0.84 0.00 0.00 3.67
5645 10661 1.208535 CGGGCCTAATACCACTTGTCA 59.791 52.381 0.84 0.00 0.00 3.58
5646 10662 1.208776 ACGGGCCTAATACCACTTGTC 59.791 52.381 0.84 0.00 0.00 3.18
5647 10663 1.065709 CACGGGCCTAATACCACTTGT 60.066 52.381 0.84 0.00 0.00 3.16
5648 10664 1.208535 TCACGGGCCTAATACCACTTG 59.791 52.381 0.84 0.00 0.00 3.16
5649 10665 1.208776 GTCACGGGCCTAATACCACTT 59.791 52.381 0.84 0.00 0.00 3.16
5650 10666 0.828677 GTCACGGGCCTAATACCACT 59.171 55.000 0.84 0.00 0.00 4.00
5651 10667 0.538118 TGTCACGGGCCTAATACCAC 59.462 55.000 0.84 0.00 0.00 4.16
5652 10668 1.208535 CTTGTCACGGGCCTAATACCA 59.791 52.381 0.84 0.00 0.00 3.25
5653 10669 1.208776 ACTTGTCACGGGCCTAATACC 59.791 52.381 0.84 0.00 0.00 2.73
5654 10670 2.277084 CACTTGTCACGGGCCTAATAC 58.723 52.381 0.84 0.00 0.00 1.89
5655 10671 1.208535 CCACTTGTCACGGGCCTAATA 59.791 52.381 0.84 0.00 0.00 0.98
5656 10672 0.035439 CCACTTGTCACGGGCCTAAT 60.035 55.000 0.84 0.00 0.00 1.73
5657 10673 1.373435 CCACTTGTCACGGGCCTAA 59.627 57.895 0.84 0.00 0.00 2.69
5658 10674 0.542467 TACCACTTGTCACGGGCCTA 60.542 55.000 0.84 0.00 0.00 3.93
5659 10675 1.198759 ATACCACTTGTCACGGGCCT 61.199 55.000 0.84 0.00 0.00 5.19
5660 10676 0.743345 GATACCACTTGTCACGGGCC 60.743 60.000 0.00 0.00 0.00 5.80
5661 10677 0.036765 TGATACCACTTGTCACGGGC 60.037 55.000 0.00 0.00 0.00 6.13
5662 10678 1.548719 TCTGATACCACTTGTCACGGG 59.451 52.381 0.00 0.00 0.00 5.28
5663 10679 2.417379 CCTCTGATACCACTTGTCACGG 60.417 54.545 0.00 0.00 0.00 4.94
5686 10702 5.541868 TGGTAGATTGAATCCAGGATCTCTC 59.458 44.000 1.11 0.00 31.71 3.20
5704 10720 1.380524 GTAGCTCAGTCGCTGGTAGA 58.619 55.000 0.00 0.00 41.12 2.59
5716 10732 2.810400 GCTTGTTTGGTCTGGTAGCTCA 60.810 50.000 0.00 0.00 0.00 4.26
5718 10734 1.421646 AGCTTGTTTGGTCTGGTAGCT 59.578 47.619 0.00 0.00 33.00 3.32
5728 10744 4.950744 CTTGGCGAGCTTGTTTGG 57.049 55.556 2.14 0.00 0.00 3.28
5762 10778 2.894387 GCCAGAGCGGTGATCTGC 60.894 66.667 6.55 0.00 43.67 4.26
5776 10792 2.355363 CGTTGACCGTCTTCGCCA 60.355 61.111 0.00 0.00 35.54 5.69
5777 10793 2.049802 TCGTTGACCGTCTTCGCC 60.050 61.111 0.00 0.00 37.94 5.54
5779 10795 2.078914 CCGTCGTTGACCGTCTTCG 61.079 63.158 0.00 5.04 37.94 3.79
5888 10904 2.280797 GTCTGGGTGCGCAACTCA 60.281 61.111 26.96 19.86 36.72 3.41
5891 10907 4.947147 TGGGTCTGGGTGCGCAAC 62.947 66.667 19.53 19.53 0.00 4.17
5892 10908 4.641645 CTGGGTCTGGGTGCGCAA 62.642 66.667 14.00 0.00 0.00 4.85
5895 10911 4.704833 CACCTGGGTCTGGGTGCG 62.705 72.222 0.00 0.00 44.94 5.34
5935 10951 0.038021 TACTGGAGCCAATGCAAGCA 59.962 50.000 9.12 0.00 41.13 3.91
5936 10952 1.176527 TTACTGGAGCCAATGCAAGC 58.823 50.000 0.00 0.00 41.13 4.01
5979 10995 2.044352 TGGATCTGTCGGCCGAGA 60.044 61.111 31.97 28.16 0.00 4.04
6034 11050 0.173481 CCCAGTGTCGATGATGACGT 59.827 55.000 0.00 0.00 41.87 4.34
6037 11053 0.617535 ACCCCCAGTGTCGATGATGA 60.618 55.000 0.00 0.00 0.00 2.92
6038 11054 0.253044 AACCCCCAGTGTCGATGATG 59.747 55.000 0.00 0.00 0.00 3.07
6054 11070 2.983592 CACCCCGTGAGCCAAACC 60.984 66.667 0.00 0.00 35.23 3.27
6055 11071 2.983592 CCACCCCGTGAGCCAAAC 60.984 66.667 0.00 0.00 35.23 2.93
6095 11111 1.669440 GGTAGACGCACCCTTGACA 59.331 57.895 0.00 0.00 31.91 3.58
6100 11116 1.076923 AGATCGGTAGACGCACCCT 60.077 57.895 0.00 0.00 43.86 4.34
6106 11122 1.954382 TGGGATTGAGATCGGTAGACG 59.046 52.381 0.00 0.00 46.11 4.18


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

AutoCloner maintained by Alex Coulton.