Multiple sequence alignment - TraesCS2D01G486800

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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 TraesCS2D01G486800 chr2D 100.000 6160 0 0 609 6768 586962119 586955960 0.000000e+00 11376.0
1 TraesCS2D01G486800 chr2D 86.050 1319 153 20 1051 2355 618333434 618334735 0.000000e+00 1387.0
2 TraesCS2D01G486800 chr2D 85.375 1347 153 23 1018 2354 618143206 618141894 0.000000e+00 1356.0
3 TraesCS2D01G486800 chr2D 82.157 1289 178 28 1116 2370 586846900 586845630 0.000000e+00 1059.0
4 TraesCS2D01G486800 chr2D 80.377 1274 199 37 1106 2353 618660290 618659042 0.000000e+00 920.0
5 TraesCS2D01G486800 chr2D 100.000 229 0 0 1 229 586962727 586962499 2.260000e-114 424.0
6 TraesCS2D01G486800 chr2D 87.755 245 29 1 3852 4096 586843175 586842932 1.110000e-72 285.0
7 TraesCS2D01G486800 chr2D 80.866 277 52 1 4701 4976 618336906 618337182 4.110000e-52 217.0
8 TraesCS2D01G486800 chr2D 90.840 131 10 2 1 130 579206928 579207057 2.510000e-39 174.0
9 TraesCS2D01G486800 chr2D 87.838 148 18 0 3938 4085 586803992 586803845 2.510000e-39 174.0
10 TraesCS2D01G486800 chr2A 94.662 3297 104 17 846 4135 721729773 721726542 0.000000e+00 5048.0
11 TraesCS2D01G486800 chr2A 93.343 2103 107 22 4121 6202 721726481 721724391 0.000000e+00 3077.0
12 TraesCS2D01G486800 chr2A 86.505 1319 147 21 1051 2355 749385158 749386459 0.000000e+00 1421.0
13 TraesCS2D01G486800 chr2A 84.837 1352 160 24 1018 2359 748910525 748909209 0.000000e+00 1319.0
14 TraesCS2D01G486800 chr2A 80.505 277 53 1 4701 4976 749388497 749388773 1.910000e-50 211.0
15 TraesCS2D01G486800 chr2A 85.204 196 29 0 1 196 557301915 557302110 1.150000e-47 202.0
16 TraesCS2D01G486800 chr2A 82.014 139 22 1 2227 2362 748871279 748871141 1.540000e-21 115.0
17 TraesCS2D01G486800 chr2A 95.833 48 2 0 2688 2735 721728122 721728075 2.020000e-10 78.7
18 TraesCS2D01G486800 chr2B 95.615 1528 46 8 846 2362 708716495 708714978 0.000000e+00 2431.0
19 TraesCS2D01G486800 chr2B 94.251 1235 50 9 3117 4342 708712165 708710943 0.000000e+00 1868.0
20 TraesCS2D01G486800 chr2B 92.955 1235 80 4 4552 5786 708710943 708709716 0.000000e+00 1792.0
21 TraesCS2D01G486800 chr2B 86.160 1315 155 14 1051 2355 755150784 755149487 0.000000e+00 1395.0
22 TraesCS2D01G486800 chr2B 85.070 1353 156 30 1018 2359 754654644 754653327 0.000000e+00 1338.0
23 TraesCS2D01G486800 chr2B 92.652 558 41 0 6204 6761 478160666 478161223 0.000000e+00 804.0
24 TraesCS2D01G486800 chr2B 87.785 483 40 8 2604 3085 708714958 708714494 1.280000e-151 547.0
25 TraesCS2D01G486800 chr2B 80.351 285 52 4 4701 4983 755148071 755147789 5.320000e-51 213.0
26 TraesCS2D01G486800 chr2B 90.062 161 14 2 6042 6200 708704292 708704132 2.470000e-49 207.0
27 TraesCS2D01G486800 chr2B 78.648 281 56 4 4705 4983 755032296 755032574 4.170000e-42 183.0
28 TraesCS2D01G486800 chr2B 98.734 79 1 0 5835 5913 708709712 708709634 2.540000e-29 141.0
29 TraesCS2D01G486800 chr7D 95.053 566 27 1 6204 6768 474500939 474501504 0.000000e+00 889.0
30 TraesCS2D01G486800 chr7D 92.266 556 40 2 6204 6758 615562014 615562567 0.000000e+00 785.0
31 TraesCS2D01G486800 chr7D 91.262 103 9 0 1 103 566313114 566313012 2.540000e-29 141.0
32 TraesCS2D01G486800 chr7D 78.802 217 24 19 1 204 4621544 4621751 7.130000e-25 126.0
33 TraesCS2D01G486800 chr5D 93.274 565 37 1 6204 6767 324107272 324107836 0.000000e+00 832.0
34 TraesCS2D01G486800 chr5D 92.091 569 44 1 6200 6767 365346874 365346306 0.000000e+00 800.0
35 TraesCS2D01G486800 chr5D 91.873 566 45 1 6203 6767 491568862 491568297 0.000000e+00 789.0
36 TraesCS2D01G486800 chr5D 83.254 209 23 10 1 198 28955687 28955894 1.500000e-41 182.0
37 TraesCS2D01G486800 chr5D 75.745 235 33 23 1 229 444297836 444298052 5.590000e-16 97.1
38 TraesCS2D01G486800 chr3A 93.250 563 36 2 6205 6767 523540734 523541294 0.000000e+00 828.0
39 TraesCS2D01G486800 chr7A 92.349 562 43 0 6206 6767 138554087 138554648 0.000000e+00 800.0
40 TraesCS2D01G486800 chr7A 85.437 206 29 1 1 205 718424220 718424015 5.320000e-51 213.0
41 TraesCS2D01G486800 chr7A 84.375 64 10 0 663 726 10886477 10886540 5.670000e-06 63.9
42 TraesCS2D01G486800 chr3D 91.166 566 49 1 6203 6767 9592359 9591794 0.000000e+00 767.0
43 TraesCS2D01G486800 chr6B 92.806 139 10 0 15 153 277157284 277157422 1.150000e-47 202.0
44 TraesCS2D01G486800 chr5A 81.938 227 32 5 3 228 565668407 565668625 4.170000e-42 183.0


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 TraesCS2D01G486800 chr2D 586955960 586962727 6767 True 5900.000000 11376 100.000000 1 6768 2 chr2D.!!$R5 6767
1 TraesCS2D01G486800 chr2D 618141894 618143206 1312 True 1356.000000 1356 85.375000 1018 2354 1 chr2D.!!$R2 1336
2 TraesCS2D01G486800 chr2D 618659042 618660290 1248 True 920.000000 920 80.377000 1106 2353 1 chr2D.!!$R3 1247
3 TraesCS2D01G486800 chr2D 618333434 618337182 3748 False 802.000000 1387 83.458000 1051 4976 2 chr2D.!!$F2 3925
4 TraesCS2D01G486800 chr2D 586842932 586846900 3968 True 672.000000 1059 84.956000 1116 4096 2 chr2D.!!$R4 2980
5 TraesCS2D01G486800 chr2A 721724391 721729773 5382 True 2734.566667 5048 94.612667 846 6202 3 chr2A.!!$R3 5356
6 TraesCS2D01G486800 chr2A 748909209 748910525 1316 True 1319.000000 1319 84.837000 1018 2359 1 chr2A.!!$R2 1341
7 TraesCS2D01G486800 chr2A 749385158 749388773 3615 False 816.000000 1421 83.505000 1051 4976 2 chr2A.!!$F2 3925
8 TraesCS2D01G486800 chr2B 708709634 708716495 6861 True 1355.800000 2431 93.868000 846 5913 5 chr2B.!!$R3 5067
9 TraesCS2D01G486800 chr2B 754653327 754654644 1317 True 1338.000000 1338 85.070000 1018 2359 1 chr2B.!!$R2 1341
10 TraesCS2D01G486800 chr2B 478160666 478161223 557 False 804.000000 804 92.652000 6204 6761 1 chr2B.!!$F1 557
11 TraesCS2D01G486800 chr2B 755147789 755150784 2995 True 804.000000 1395 83.255500 1051 4983 2 chr2B.!!$R4 3932
12 TraesCS2D01G486800 chr7D 474500939 474501504 565 False 889.000000 889 95.053000 6204 6768 1 chr7D.!!$F2 564
13 TraesCS2D01G486800 chr7D 615562014 615562567 553 False 785.000000 785 92.266000 6204 6758 1 chr7D.!!$F3 554
14 TraesCS2D01G486800 chr5D 324107272 324107836 564 False 832.000000 832 93.274000 6204 6767 1 chr5D.!!$F2 563
15 TraesCS2D01G486800 chr5D 365346306 365346874 568 True 800.000000 800 92.091000 6200 6767 1 chr5D.!!$R1 567
16 TraesCS2D01G486800 chr5D 491568297 491568862 565 True 789.000000 789 91.873000 6203 6767 1 chr5D.!!$R2 564
17 TraesCS2D01G486800 chr3A 523540734 523541294 560 False 828.000000 828 93.250000 6205 6767 1 chr3A.!!$F1 562
18 TraesCS2D01G486800 chr7A 138554087 138554648 561 False 800.000000 800 92.349000 6206 6767 1 chr7A.!!$F2 561
19 TraesCS2D01G486800 chr3D 9591794 9592359 565 True 767.000000 767 91.166000 6203 6767 1 chr3D.!!$R1 564

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
673 674 0.098200 GCCGCGGTTTTTACATCTCC 59.902 55.000 28.70 0.08 0.00 3.71 F
1004 1005 0.036952 TGAGCTCTACTGTGCAAGGC 60.037 55.000 16.19 0.00 35.37 4.35 F
2030 2102 1.079750 GTCGGCTCAGGAGGTGAAC 60.080 63.158 0.00 0.00 33.60 3.18 F
3298 8794 0.529378 CATGAAACTTCTGGCAGGGC 59.471 55.000 15.73 0.00 0.00 5.19 F
4240 9976 0.759346 CCACTCTTCCCTTATCCCCG 59.241 60.000 0.00 0.00 0.00 5.73 F
5271 11080 0.249911 GTGTTCCGGCACTCAGTCTT 60.250 55.000 5.66 0.00 36.51 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 2229 0.811915 CACTCCTCTAGGGTGACGTG 59.188 60.000 0.00 2.09 38.09 4.49 R
2731 5926 1.276421 AGAAGCTACAGGTGCGACAAT 59.724 47.619 0.00 0.00 35.28 2.71 R
3722 9259 1.066908 CACACACATCACAAACCCCAC 59.933 52.381 0.00 0.00 0.00 4.61 R
4619 10362 2.200373 ACTCCCCTAATTGCACACAC 57.800 50.000 0.00 0.00 0.00 3.82 R
5660 11469 0.519077 GGCTGCAGCAACAACTAGTC 59.481 55.000 37.63 14.35 44.36 2.59 R
6446 12268 2.224892 TGCCTATCTACGGATGCTCTCT 60.225 50.000 0.00 0.00 33.71 3.10 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
25 26 4.735132 CTTCGCCCTCACGCCGAA 62.735 66.667 0.00 0.00 38.49 4.30
26 27 4.735132 TTCGCCCTCACGCCGAAG 62.735 66.667 0.00 0.00 36.23 3.79
28 29 4.735132 CGCCCTCACGCCGAAGAA 62.735 66.667 0.00 0.00 0.00 2.52
29 30 2.358247 GCCCTCACGCCGAAGAAA 60.358 61.111 0.00 0.00 0.00 2.52
30 31 2.677979 GCCCTCACGCCGAAGAAAC 61.678 63.158 0.00 0.00 0.00 2.78
31 32 2.033194 CCCTCACGCCGAAGAAACC 61.033 63.158 0.00 0.00 0.00 3.27
32 33 2.033194 CCTCACGCCGAAGAAACCC 61.033 63.158 0.00 0.00 0.00 4.11
33 34 2.356553 TCACGCCGAAGAAACCCG 60.357 61.111 0.00 0.00 0.00 5.28
34 35 2.356553 CACGCCGAAGAAACCCGA 60.357 61.111 0.00 0.00 0.00 5.14
35 36 2.356673 ACGCCGAAGAAACCCGAC 60.357 61.111 0.00 0.00 0.00 4.79
36 37 2.048503 CGCCGAAGAAACCCGACT 60.049 61.111 0.00 0.00 0.00 4.18
37 38 1.666872 CGCCGAAGAAACCCGACTT 60.667 57.895 0.00 0.00 0.00 3.01
38 39 1.866925 GCCGAAGAAACCCGACTTG 59.133 57.895 0.00 0.00 0.00 3.16
39 40 1.866925 CCGAAGAAACCCGACTTGC 59.133 57.895 0.00 0.00 0.00 4.01
40 41 1.574702 CCGAAGAAACCCGACTTGCC 61.575 60.000 0.00 0.00 0.00 4.52
41 42 1.574702 CGAAGAAACCCGACTTGCCC 61.575 60.000 0.00 0.00 0.00 5.36
42 43 0.250770 GAAGAAACCCGACTTGCCCT 60.251 55.000 0.00 0.00 0.00 5.19
43 44 0.185175 AAGAAACCCGACTTGCCCTT 59.815 50.000 0.00 0.00 0.00 3.95
44 45 0.185175 AGAAACCCGACTTGCCCTTT 59.815 50.000 0.00 0.00 0.00 3.11
45 46 0.313987 GAAACCCGACTTGCCCTTTG 59.686 55.000 0.00 0.00 0.00 2.77
46 47 1.112916 AAACCCGACTTGCCCTTTGG 61.113 55.000 0.00 0.00 0.00 3.28
57 58 2.162716 CCCTTTGGCGTCTTCTTCG 58.837 57.895 0.00 0.00 0.00 3.79
58 59 1.298859 CCCTTTGGCGTCTTCTTCGG 61.299 60.000 0.00 0.00 0.00 4.30
59 60 0.602905 CCTTTGGCGTCTTCTTCGGT 60.603 55.000 0.00 0.00 0.00 4.69
60 61 0.512952 CTTTGGCGTCTTCTTCGGTG 59.487 55.000 0.00 0.00 0.00 4.94
61 62 1.503818 TTTGGCGTCTTCTTCGGTGC 61.504 55.000 0.00 0.00 0.00 5.01
62 63 3.119096 GGCGTCTTCTTCGGTGCC 61.119 66.667 0.00 0.00 35.04 5.01
63 64 2.357034 GCGTCTTCTTCGGTGCCA 60.357 61.111 0.00 0.00 0.00 4.92
64 65 1.741770 GCGTCTTCTTCGGTGCCAT 60.742 57.895 0.00 0.00 0.00 4.40
65 66 1.298859 GCGTCTTCTTCGGTGCCATT 61.299 55.000 0.00 0.00 0.00 3.16
66 67 0.443869 CGTCTTCTTCGGTGCCATTG 59.556 55.000 0.00 0.00 0.00 2.82
67 68 0.804989 GTCTTCTTCGGTGCCATTGG 59.195 55.000 0.00 0.00 0.00 3.16
68 69 0.322456 TCTTCTTCGGTGCCATTGGG 60.322 55.000 4.53 0.00 37.18 4.12
69 70 0.609131 CTTCTTCGGTGCCATTGGGT 60.609 55.000 4.53 0.00 36.17 4.51
70 71 0.893270 TTCTTCGGTGCCATTGGGTG 60.893 55.000 4.53 0.00 36.17 4.61
79 80 3.751246 CATTGGGTGGCTGCGGTG 61.751 66.667 0.00 0.00 0.00 4.94
92 93 4.803426 CGGTGGCTGGAGCGAGTC 62.803 72.222 0.00 0.00 43.26 3.36
93 94 4.803426 GGTGGCTGGAGCGAGTCG 62.803 72.222 8.54 8.54 43.26 4.18
94 95 4.803426 GTGGCTGGAGCGAGTCGG 62.803 72.222 15.52 0.00 43.26 4.79
98 99 3.522731 CTGGAGCGAGTCGGGGAG 61.523 72.222 15.52 0.00 0.00 4.30
118 119 3.462678 GGCGGGTGGAGAGAGGTC 61.463 72.222 0.00 0.00 0.00 3.85
119 120 3.827898 GCGGGTGGAGAGAGGTCG 61.828 72.222 0.00 0.00 0.00 4.79
120 121 3.141488 CGGGTGGAGAGAGGTCGG 61.141 72.222 0.00 0.00 0.00 4.79
121 122 2.760385 GGGTGGAGAGAGGTCGGG 60.760 72.222 0.00 0.00 0.00 5.14
122 123 2.760385 GGTGGAGAGAGGTCGGGG 60.760 72.222 0.00 0.00 0.00 5.73
123 124 3.462678 GTGGAGAGAGGTCGGGGC 61.463 72.222 0.00 0.00 0.00 5.80
125 126 4.816984 GGAGAGAGGTCGGGGCGA 62.817 72.222 0.00 0.00 0.00 5.54
630 631 3.524346 GGGGGTTGGTTGAACTCAA 57.476 52.632 0.00 0.00 36.66 3.02
631 632 1.328279 GGGGGTTGGTTGAACTCAAG 58.672 55.000 0.00 0.00 36.66 3.02
632 633 1.328279 GGGGTTGGTTGAACTCAAGG 58.672 55.000 0.00 0.00 36.66 3.61
633 634 1.133606 GGGGTTGGTTGAACTCAAGGA 60.134 52.381 0.00 0.00 36.66 3.36
634 635 1.954382 GGGTTGGTTGAACTCAAGGAC 59.046 52.381 0.00 0.00 34.80 3.85
635 636 1.602377 GGTTGGTTGAACTCAAGGACG 59.398 52.381 0.00 0.00 36.39 4.79
636 637 1.602377 GTTGGTTGAACTCAAGGACGG 59.398 52.381 0.00 0.00 36.39 4.79
637 638 0.834612 TGGTTGAACTCAAGGACGGT 59.165 50.000 0.00 0.00 36.39 4.83
638 639 1.210967 TGGTTGAACTCAAGGACGGTT 59.789 47.619 0.00 0.00 36.39 4.44
639 640 1.602377 GGTTGAACTCAAGGACGGTTG 59.398 52.381 0.00 0.00 36.39 3.77
640 641 1.602377 GTTGAACTCAAGGACGGTTGG 59.398 52.381 0.00 0.00 36.39 3.77
641 642 0.107831 TGAACTCAAGGACGGTTGGG 59.892 55.000 0.00 0.00 33.75 4.12
642 643 1.228154 AACTCAAGGACGGTTGGGC 60.228 57.895 0.00 0.00 30.21 5.36
643 644 2.742372 CTCAAGGACGGTTGGGCG 60.742 66.667 0.00 0.00 0.00 6.13
644 645 3.530910 CTCAAGGACGGTTGGGCGT 62.531 63.158 0.00 0.00 0.00 5.68
645 646 2.593436 CAAGGACGGTTGGGCGTT 60.593 61.111 0.00 0.00 0.00 4.84
646 647 2.593436 AAGGACGGTTGGGCGTTG 60.593 61.111 0.00 0.00 0.00 4.10
647 648 4.636435 AGGACGGTTGGGCGTTGG 62.636 66.667 0.00 0.00 0.00 3.77
648 649 4.629523 GGACGGTTGGGCGTTGGA 62.630 66.667 0.00 0.00 0.00 3.53
649 650 3.047877 GACGGTTGGGCGTTGGAG 61.048 66.667 0.00 0.00 0.00 3.86
669 670 2.871828 CCGCCGCGGTTTTTACAT 59.128 55.556 28.70 0.00 42.73 2.29
670 671 1.226184 CCGCCGCGGTTTTTACATC 60.226 57.895 28.70 5.16 42.73 3.06
671 672 1.641123 CCGCCGCGGTTTTTACATCT 61.641 55.000 28.70 0.00 42.73 2.90
672 673 0.247537 CGCCGCGGTTTTTACATCTC 60.248 55.000 28.70 3.74 0.00 2.75
673 674 0.098200 GCCGCGGTTTTTACATCTCC 59.902 55.000 28.70 0.08 0.00 3.71
674 675 1.734163 CCGCGGTTTTTACATCTCCT 58.266 50.000 19.50 0.00 0.00 3.69
675 676 1.396996 CCGCGGTTTTTACATCTCCTG 59.603 52.381 19.50 0.00 0.00 3.86
676 677 1.396996 CGCGGTTTTTACATCTCCTGG 59.603 52.381 0.00 0.00 0.00 4.45
677 678 1.132453 GCGGTTTTTACATCTCCTGGC 59.868 52.381 0.00 0.00 0.00 4.85
678 679 2.711542 CGGTTTTTACATCTCCTGGCT 58.288 47.619 0.00 0.00 0.00 4.75
679 680 3.081804 CGGTTTTTACATCTCCTGGCTT 58.918 45.455 0.00 0.00 0.00 4.35
680 681 3.506067 CGGTTTTTACATCTCCTGGCTTT 59.494 43.478 0.00 0.00 0.00 3.51
681 682 4.615912 CGGTTTTTACATCTCCTGGCTTTG 60.616 45.833 0.00 0.00 0.00 2.77
682 683 4.321974 GGTTTTTACATCTCCTGGCTTTGG 60.322 45.833 0.00 0.00 0.00 3.28
683 684 4.380843 TTTTACATCTCCTGGCTTTGGA 57.619 40.909 0.00 0.00 0.00 3.53
693 694 5.456921 TCCTGGCTTTGGAGATCTAAATT 57.543 39.130 0.00 0.00 0.00 1.82
694 695 5.831103 TCCTGGCTTTGGAGATCTAAATTT 58.169 37.500 0.00 0.00 0.00 1.82
695 696 5.653769 TCCTGGCTTTGGAGATCTAAATTTG 59.346 40.000 0.00 0.00 0.00 2.32
696 697 5.329035 TGGCTTTGGAGATCTAAATTTGC 57.671 39.130 0.00 0.00 0.00 3.68
697 698 4.771577 TGGCTTTGGAGATCTAAATTTGCA 59.228 37.500 0.00 0.00 0.00 4.08
698 699 5.422970 TGGCTTTGGAGATCTAAATTTGCAT 59.577 36.000 0.00 0.00 0.00 3.96
699 700 5.981915 GGCTTTGGAGATCTAAATTTGCATC 59.018 40.000 0.00 2.26 0.00 3.91
700 701 5.684626 GCTTTGGAGATCTAAATTTGCATCG 59.315 40.000 0.00 0.00 0.00 3.84
701 702 4.818534 TGGAGATCTAAATTTGCATCGC 57.181 40.909 0.00 3.98 0.00 4.58
702 703 3.248363 TGGAGATCTAAATTTGCATCGCG 59.752 43.478 0.00 0.00 0.00 5.87
703 704 3.494626 GGAGATCTAAATTTGCATCGCGA 59.505 43.478 13.09 13.09 0.00 5.87
704 705 4.376819 GGAGATCTAAATTTGCATCGCGAG 60.377 45.833 16.66 8.11 0.00 5.03
705 706 3.496130 AGATCTAAATTTGCATCGCGAGG 59.504 43.478 17.78 17.78 0.00 4.63
706 707 2.627945 TCTAAATTTGCATCGCGAGGT 58.372 42.857 22.83 3.43 0.00 3.85
708 709 0.881118 AAATTTGCATCGCGAGGTGT 59.119 45.000 22.83 0.00 46.24 4.16
709 710 0.881118 AATTTGCATCGCGAGGTGTT 59.119 45.000 22.83 9.14 46.24 3.32
710 711 0.447801 ATTTGCATCGCGAGGTGTTC 59.552 50.000 22.83 5.88 46.24 3.18
711 712 0.602638 TTTGCATCGCGAGGTGTTCT 60.603 50.000 22.83 0.00 46.24 3.01
712 713 0.245266 TTGCATCGCGAGGTGTTCTA 59.755 50.000 22.83 0.00 46.24 2.10
713 714 0.459899 TGCATCGCGAGGTGTTCTAT 59.540 50.000 22.83 0.00 46.24 1.98
714 715 1.134818 TGCATCGCGAGGTGTTCTATT 60.135 47.619 22.83 0.00 46.24 1.73
715 716 1.933853 GCATCGCGAGGTGTTCTATTT 59.066 47.619 22.83 0.00 46.24 1.40
716 717 2.351726 GCATCGCGAGGTGTTCTATTTT 59.648 45.455 22.83 0.00 46.24 1.82
717 718 3.554324 GCATCGCGAGGTGTTCTATTTTA 59.446 43.478 22.83 0.00 46.24 1.52
718 719 4.550255 GCATCGCGAGGTGTTCTATTTTAC 60.550 45.833 22.83 0.00 46.24 2.01
719 720 4.177165 TCGCGAGGTGTTCTATTTTACA 57.823 40.909 3.71 0.00 0.00 2.41
720 721 4.751060 TCGCGAGGTGTTCTATTTTACAT 58.249 39.130 3.71 0.00 0.00 2.29
721 722 4.802039 TCGCGAGGTGTTCTATTTTACATC 59.198 41.667 3.71 0.00 0.00 3.06
722 723 4.804139 CGCGAGGTGTTCTATTTTACATCT 59.196 41.667 0.00 0.00 38.39 2.90
723 724 5.051641 CGCGAGGTGTTCTATTTTACATCTC 60.052 44.000 0.00 0.00 45.01 2.75
724 725 5.234543 GCGAGGTGTTCTATTTTACATCTCC 59.765 44.000 9.25 0.88 45.45 3.71
725 726 5.459107 CGAGGTGTTCTATTTTACATCTCCG 59.541 44.000 9.25 2.76 45.45 4.63
726 727 5.671493 AGGTGTTCTATTTTACATCTCCGG 58.329 41.667 0.00 0.00 30.00 5.14
727 728 5.424252 AGGTGTTCTATTTTACATCTCCGGA 59.576 40.000 2.93 2.93 30.00 5.14
728 729 6.070424 AGGTGTTCTATTTTACATCTCCGGAA 60.070 38.462 5.23 0.00 30.00 4.30
729 730 6.596497 GGTGTTCTATTTTACATCTCCGGAAA 59.404 38.462 5.23 0.00 0.00 3.13
730 731 7.120138 GGTGTTCTATTTTACATCTCCGGAAAA 59.880 37.037 5.23 1.85 0.00 2.29
731 732 7.961283 GTGTTCTATTTTACATCTCCGGAAAAC 59.039 37.037 5.23 0.00 0.00 2.43
732 733 6.897259 TCTATTTTACATCTCCGGAAAACG 57.103 37.500 5.23 0.00 43.80 3.60
803 804 7.593875 TTTTGTTTCAGAAGTCCAAATGTTG 57.406 32.000 5.88 0.00 0.00 3.33
804 805 6.522625 TTGTTTCAGAAGTCCAAATGTTGA 57.477 33.333 0.00 0.00 0.00 3.18
805 806 6.713762 TGTTTCAGAAGTCCAAATGTTGAT 57.286 33.333 0.00 0.00 0.00 2.57
806 807 7.111247 TGTTTCAGAAGTCCAAATGTTGATT 57.889 32.000 0.00 0.00 0.00 2.57
807 808 8.231692 TGTTTCAGAAGTCCAAATGTTGATTA 57.768 30.769 0.00 0.00 0.00 1.75
808 809 8.859090 TGTTTCAGAAGTCCAAATGTTGATTAT 58.141 29.630 0.00 0.00 0.00 1.28
809 810 9.696917 GTTTCAGAAGTCCAAATGTTGATTATT 57.303 29.630 0.00 0.00 0.00 1.40
825 826 8.132362 TGTTGATTATTTTTACATATGGACCGC 58.868 33.333 7.80 0.00 0.00 5.68
826 827 7.209471 TGATTATTTTTACATATGGACCGCC 57.791 36.000 7.80 0.00 0.00 6.13
827 828 7.001674 TGATTATTTTTACATATGGACCGCCT 58.998 34.615 7.80 0.00 34.31 5.52
828 829 8.158132 TGATTATTTTTACATATGGACCGCCTA 58.842 33.333 7.80 0.00 34.31 3.93
829 830 9.174166 GATTATTTTTACATATGGACCGCCTAT 57.826 33.333 7.80 0.00 34.31 2.57
830 831 8.556213 TTATTTTTACATATGGACCGCCTATC 57.444 34.615 7.80 0.00 34.31 2.08
831 832 3.861276 TTACATATGGACCGCCTATCG 57.139 47.619 7.80 0.00 38.08 2.92
832 833 1.919240 ACATATGGACCGCCTATCGA 58.081 50.000 7.80 0.00 41.67 3.59
833 834 2.244695 ACATATGGACCGCCTATCGAA 58.755 47.619 7.80 0.00 41.67 3.71
834 835 2.231478 ACATATGGACCGCCTATCGAAG 59.769 50.000 7.80 0.00 41.67 3.79
835 836 2.281539 TATGGACCGCCTATCGAAGA 57.718 50.000 0.00 0.00 41.67 2.87
836 837 1.633774 ATGGACCGCCTATCGAAGAT 58.366 50.000 0.00 0.00 41.67 2.40
837 838 0.673985 TGGACCGCCTATCGAAGATG 59.326 55.000 0.00 0.00 41.67 2.90
838 839 0.674534 GGACCGCCTATCGAAGATGT 59.325 55.000 0.00 0.00 45.12 3.06
839 840 1.068741 GGACCGCCTATCGAAGATGTT 59.931 52.381 0.00 0.00 45.12 2.71
840 841 2.395654 GACCGCCTATCGAAGATGTTC 58.604 52.381 0.00 0.00 45.12 3.18
841 842 2.032620 ACCGCCTATCGAAGATGTTCT 58.967 47.619 0.66 0.00 45.12 3.01
842 843 2.431057 ACCGCCTATCGAAGATGTTCTT 59.569 45.455 0.66 0.00 45.12 2.52
843 844 3.635373 ACCGCCTATCGAAGATGTTCTTA 59.365 43.478 0.66 0.00 45.12 2.10
844 845 3.982058 CCGCCTATCGAAGATGTTCTTAC 59.018 47.826 0.66 0.00 45.12 2.34
845 846 4.261656 CCGCCTATCGAAGATGTTCTTACT 60.262 45.833 0.66 0.00 45.12 2.24
846 847 5.282510 CGCCTATCGAAGATGTTCTTACTT 58.717 41.667 0.66 0.00 45.12 2.24
847 848 6.436261 CGCCTATCGAAGATGTTCTTACTTA 58.564 40.000 0.66 0.00 45.12 2.24
848 849 7.085116 CGCCTATCGAAGATGTTCTTACTTAT 58.915 38.462 0.66 0.00 45.12 1.73
849 850 8.235226 CGCCTATCGAAGATGTTCTTACTTATA 58.765 37.037 0.66 0.00 45.12 0.98
1004 1005 0.036952 TGAGCTCTACTGTGCAAGGC 60.037 55.000 16.19 0.00 35.37 4.35
1661 1709 1.163554 GAGACGTCAAGAGGTACCGT 58.836 55.000 19.50 0.00 0.00 4.83
2030 2102 1.079750 GTCGGCTCAGGAGGTGAAC 60.080 63.158 0.00 0.00 33.60 3.18
2459 3171 4.019591 ACTTGATTTACACCTACTGGACCC 60.020 45.833 0.00 0.00 37.04 4.46
2505 3754 3.023119 TCATGTTTGAACTGGTTGCTGT 58.977 40.909 0.00 0.00 0.00 4.40
2869 6064 9.612620 GTTACTGTTATTTCACATGGAGAAAAG 57.387 33.333 16.30 12.38 38.36 2.27
2973 6168 6.151985 TGGGTGACATATAAAACGCTTTGAAT 59.848 34.615 0.00 0.00 0.00 2.57
3093 8573 4.388378 AGTCCATAACCTCGTTAAGAGC 57.612 45.455 0.00 0.00 45.54 4.09
3239 8735 2.254546 ACATGTTCTTGCCGTTCAGA 57.745 45.000 0.00 0.00 0.00 3.27
3298 8794 0.529378 CATGAAACTTCTGGCAGGGC 59.471 55.000 15.73 0.00 0.00 5.19
3365 8865 9.315525 GCTAGATTAGTCTCGTAAAAATCCTTT 57.684 33.333 0.00 0.00 35.87 3.11
3411 8912 7.374272 TGTTTTCTTTTGTCAGTGATTGTTCA 58.626 30.769 0.00 0.00 0.00 3.18
3711 9248 5.127194 AGAGATATGAGCAAAACCTCGTGTA 59.873 40.000 0.00 0.00 34.56 2.90
3722 9259 6.534059 CAAAACCTCGTGTATAAGTGTGATG 58.466 40.000 0.00 0.00 0.00 3.07
3774 9384 3.987868 TGTACTGTTCGAGAAACTCATGC 59.012 43.478 0.00 0.00 38.76 4.06
3775 9385 3.111853 ACTGTTCGAGAAACTCATGCA 57.888 42.857 0.00 0.00 38.76 3.96
3777 9387 3.434641 ACTGTTCGAGAAACTCATGCATG 59.565 43.478 21.07 21.07 38.76 4.06
3880 9503 6.432403 AAATTTCAAAATCAACAGGGGCTA 57.568 33.333 0.00 0.00 0.00 3.93
3899 9522 2.503895 ACTGCCTGAAGGAAGAATGG 57.496 50.000 11.60 0.00 44.07 3.16
4057 9680 8.954834 AGGAGAGAATACTCATCTATGAACAT 57.045 34.615 0.00 0.00 44.79 2.71
4113 9774 4.377897 GGTACACACTGCTACAAGAACTT 58.622 43.478 0.00 0.00 0.00 2.66
4159 9893 7.759886 TCATGAAAACTAGACCGTCTAATTCTG 59.240 37.037 19.22 16.07 0.00 3.02
4170 9904 3.924686 CGTCTAATTCTGGTGTGTGTACC 59.075 47.826 0.00 0.00 41.24 3.34
4236 9970 5.209659 TCCTAAGTCCACTCTTCCCTTATC 58.790 45.833 0.00 0.00 0.00 1.75
4240 9976 0.759346 CCACTCTTCCCTTATCCCCG 59.241 60.000 0.00 0.00 0.00 5.73
4247 9983 3.135895 TCTTCCCTTATCCCCGAATTGTC 59.864 47.826 0.00 0.00 0.00 3.18
4326 10062 5.372343 AACACCATAAGCTATCACATCCA 57.628 39.130 0.00 0.00 0.00 3.41
4331 10067 7.016563 ACACCATAAGCTATCACATCCAAGATA 59.983 37.037 0.00 0.00 0.00 1.98
4393 10129 8.378172 TGGTTACAAAATACAGCTATCTATGC 57.622 34.615 0.00 0.00 0.00 3.14
4394 10130 7.990314 TGGTTACAAAATACAGCTATCTATGCA 59.010 33.333 0.00 0.00 0.00 3.96
4395 10131 8.836413 GGTTACAAAATACAGCTATCTATGCAA 58.164 33.333 0.00 0.00 0.00 4.08
4429 10165 5.848833 ATTAAGTAGGTCCGTTAGGTCAG 57.151 43.478 0.00 0.00 39.05 3.51
4433 10169 2.305858 AGGTCCGTTAGGTCAGAAGT 57.694 50.000 0.00 0.00 39.05 3.01
4436 10172 2.067013 GTCCGTTAGGTCAGAAGTTGC 58.933 52.381 0.00 0.00 39.05 4.17
4440 10176 2.352030 CGTTAGGTCAGAAGTTGCCGTA 60.352 50.000 0.00 0.00 0.00 4.02
4481 10219 9.959721 AATGGTTACTCTTATGTACTTCATGTT 57.040 29.630 0.00 0.00 37.91 2.71
4509 10248 9.490379 AACTAACATATATGATTTTCTCCGGAC 57.510 33.333 19.63 0.00 0.00 4.79
4514 10253 8.840321 ACATATATGATTTTCTCCGGACTTTTG 58.160 33.333 19.63 0.00 0.00 2.44
4515 10254 9.056005 CATATATGATTTTCTCCGGACTTTTGA 57.944 33.333 6.92 0.00 0.00 2.69
4587 10330 1.646447 TCTAGGATGGACAGTCAGGGT 59.354 52.381 2.17 0.00 0.00 4.34
4614 10357 6.509418 AGTGAGCTAGAAACAACTAGAGAG 57.491 41.667 0.00 0.00 41.42 3.20
4619 10362 8.516234 TGAGCTAGAAACAACTAGAGAGTTAAG 58.484 37.037 0.00 0.00 44.39 1.85
4625 10368 7.707035 AGAAACAACTAGAGAGTTAAGTGTGTG 59.293 37.037 0.00 0.00 44.39 3.82
4650 10393 7.093945 TGCAATTAGGGGAGTAAAATGAACTTC 60.094 37.037 0.00 0.00 0.00 3.01
4659 10402 8.512956 GGGAGTAAAATGAACTTCTACCTTTTC 58.487 37.037 0.00 0.00 0.00 2.29
4711 10520 7.446001 AGTAGCCGTGTAGGTATCTAATAAC 57.554 40.000 0.00 0.00 43.70 1.89
5114 10923 5.826208 TGATGTCTATAGCTTCGGAGTTGTA 59.174 40.000 0.00 0.00 0.00 2.41
5188 10997 8.417106 CCTTTCTCATGTAAGCTCAGATACTTA 58.583 37.037 0.00 0.00 0.00 2.24
5271 11080 0.249911 GTGTTCCGGCACTCAGTCTT 60.250 55.000 5.66 0.00 36.51 3.01
5319 11128 4.340666 TGAAGCAAGACATAACTTGGCAAA 59.659 37.500 0.00 0.00 44.87 3.68
5348 11157 1.379916 CAGGCATGGGAACTGTGGA 59.620 57.895 0.00 0.00 0.00 4.02
5426 11235 2.977772 GCCTGAGCTATTGTCTGAGT 57.022 50.000 0.00 0.00 35.50 3.41
5660 11469 4.093703 TGACGTAAATTTCTATTGGGTGCG 59.906 41.667 0.00 0.00 0.00 5.34
5802 11614 3.323403 TGAAGCAAACACTAAAATGGGGG 59.677 43.478 0.00 0.00 0.00 5.40
6189 12010 6.265196 TCCATACCAATGAATATTTGAGTGCC 59.735 38.462 0.00 0.00 34.84 5.01
6202 12023 3.388552 TGAGTGCCAGGAGAGAATAGA 57.611 47.619 0.00 0.00 0.00 1.98
6446 12268 2.027561 AGTGGCCATAAGTTGAACGCTA 60.028 45.455 9.72 0.00 0.00 4.26
6490 12312 1.412710 ACAACGCTTCAGAAGAGTCCA 59.587 47.619 18.69 0.00 40.79 4.02
6542 12364 1.348064 ATAGCCAGCGCCATACCTTA 58.652 50.000 2.29 0.00 34.57 2.69
6602 12424 6.877236 TGCAGTGAAAGACATATCTGTATGA 58.123 36.000 0.00 0.00 40.12 2.15
6622 12445 4.464008 TGATGCAAATAGAATCACCCCTC 58.536 43.478 0.00 0.00 37.37 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.358247 TTTCTTCGGCGTGAGGGC 60.358 61.111 6.85 0.00 37.98 5.19
13 14 2.033194 GGTTTCTTCGGCGTGAGGG 61.033 63.158 6.85 0.00 0.00 4.30
14 15 2.033194 GGGTTTCTTCGGCGTGAGG 61.033 63.158 6.85 0.00 0.00 3.86
15 16 2.380410 CGGGTTTCTTCGGCGTGAG 61.380 63.158 6.85 6.75 0.00 3.51
16 17 2.356553 CGGGTTTCTTCGGCGTGA 60.357 61.111 6.85 3.83 0.00 4.35
17 18 2.356553 TCGGGTTTCTTCGGCGTG 60.357 61.111 6.85 1.06 0.00 5.34
18 19 2.356673 GTCGGGTTTCTTCGGCGT 60.357 61.111 6.85 0.00 0.00 5.68
19 20 1.666872 AAGTCGGGTTTCTTCGGCG 60.667 57.895 0.00 0.00 36.00 6.46
20 21 1.866925 CAAGTCGGGTTTCTTCGGC 59.133 57.895 0.00 0.00 0.00 5.54
21 22 1.574702 GGCAAGTCGGGTTTCTTCGG 61.575 60.000 0.00 0.00 0.00 4.30
22 23 1.574702 GGGCAAGTCGGGTTTCTTCG 61.575 60.000 0.00 0.00 0.00 3.79
23 24 0.250770 AGGGCAAGTCGGGTTTCTTC 60.251 55.000 0.00 0.00 0.00 2.87
24 25 0.185175 AAGGGCAAGTCGGGTTTCTT 59.815 50.000 0.00 0.00 0.00 2.52
25 26 0.185175 AAAGGGCAAGTCGGGTTTCT 59.815 50.000 0.00 0.00 0.00 2.52
26 27 0.313987 CAAAGGGCAAGTCGGGTTTC 59.686 55.000 0.00 0.00 0.00 2.78
27 28 1.112916 CCAAAGGGCAAGTCGGGTTT 61.113 55.000 0.00 0.00 0.00 3.27
28 29 1.530655 CCAAAGGGCAAGTCGGGTT 60.531 57.895 0.00 0.00 0.00 4.11
29 30 2.115266 CCAAAGGGCAAGTCGGGT 59.885 61.111 0.00 0.00 0.00 5.28
39 40 1.298859 CCGAAGAAGACGCCAAAGGG 61.299 60.000 0.00 0.00 37.18 3.95
40 41 0.602905 ACCGAAGAAGACGCCAAAGG 60.603 55.000 0.00 0.00 0.00 3.11
41 42 0.512952 CACCGAAGAAGACGCCAAAG 59.487 55.000 0.00 0.00 0.00 2.77
42 43 1.503818 GCACCGAAGAAGACGCCAAA 61.504 55.000 0.00 0.00 0.00 3.28
43 44 1.959226 GCACCGAAGAAGACGCCAA 60.959 57.895 0.00 0.00 0.00 4.52
44 45 2.357034 GCACCGAAGAAGACGCCA 60.357 61.111 0.00 0.00 0.00 5.69
45 46 3.119096 GGCACCGAAGAAGACGCC 61.119 66.667 0.00 0.00 0.00 5.68
46 47 1.298859 AATGGCACCGAAGAAGACGC 61.299 55.000 0.00 0.00 0.00 5.19
47 48 0.443869 CAATGGCACCGAAGAAGACG 59.556 55.000 0.00 0.00 0.00 4.18
48 49 0.804989 CCAATGGCACCGAAGAAGAC 59.195 55.000 0.00 0.00 0.00 3.01
49 50 0.322456 CCCAATGGCACCGAAGAAGA 60.322 55.000 0.00 0.00 0.00 2.87
50 51 0.609131 ACCCAATGGCACCGAAGAAG 60.609 55.000 0.00 0.00 33.59 2.85
51 52 0.893270 CACCCAATGGCACCGAAGAA 60.893 55.000 0.00 0.00 33.59 2.52
52 53 1.303236 CACCCAATGGCACCGAAGA 60.303 57.895 0.00 0.00 33.59 2.87
53 54 2.342650 CCACCCAATGGCACCGAAG 61.343 63.158 0.00 0.00 43.24 3.79
54 55 2.282816 CCACCCAATGGCACCGAA 60.283 61.111 0.00 0.00 43.24 4.30
62 63 3.751246 CACCGCAGCCACCCAATG 61.751 66.667 0.00 0.00 0.00 2.82
75 76 4.803426 GACTCGCTCCAGCCACCG 62.803 72.222 0.00 0.00 37.91 4.94
76 77 4.803426 CGACTCGCTCCAGCCACC 62.803 72.222 0.00 0.00 37.91 4.61
77 78 4.803426 CCGACTCGCTCCAGCCAC 62.803 72.222 0.00 0.00 37.91 5.01
81 82 3.522731 CTCCCCGACTCGCTCCAG 61.523 72.222 0.00 0.00 0.00 3.86
101 102 3.462678 GACCTCTCTCCACCCGCC 61.463 72.222 0.00 0.00 0.00 6.13
102 103 3.827898 CGACCTCTCTCCACCCGC 61.828 72.222 0.00 0.00 0.00 6.13
103 104 3.141488 CCGACCTCTCTCCACCCG 61.141 72.222 0.00 0.00 0.00 5.28
104 105 2.760385 CCCGACCTCTCTCCACCC 60.760 72.222 0.00 0.00 0.00 4.61
105 106 2.760385 CCCCGACCTCTCTCCACC 60.760 72.222 0.00 0.00 0.00 4.61
106 107 3.462678 GCCCCGACCTCTCTCCAC 61.463 72.222 0.00 0.00 0.00 4.02
108 109 4.816984 TCGCCCCGACCTCTCTCC 62.817 72.222 0.00 0.00 0.00 3.71
612 613 1.328279 CTTGAGTTCAACCAACCCCC 58.672 55.000 0.00 0.00 35.28 5.40
613 614 1.133606 TCCTTGAGTTCAACCAACCCC 60.134 52.381 0.00 0.00 35.28 4.95
614 615 1.954382 GTCCTTGAGTTCAACCAACCC 59.046 52.381 0.00 0.00 35.28 4.11
615 616 1.602377 CGTCCTTGAGTTCAACCAACC 59.398 52.381 0.00 0.00 35.28 3.77
616 617 1.602377 CCGTCCTTGAGTTCAACCAAC 59.398 52.381 0.00 0.00 34.86 3.77
617 618 1.210967 ACCGTCCTTGAGTTCAACCAA 59.789 47.619 0.00 0.00 0.00 3.67
618 619 0.834612 ACCGTCCTTGAGTTCAACCA 59.165 50.000 0.00 0.00 0.00 3.67
619 620 1.602377 CAACCGTCCTTGAGTTCAACC 59.398 52.381 0.00 0.00 0.00 3.77
620 621 1.602377 CCAACCGTCCTTGAGTTCAAC 59.398 52.381 0.00 0.00 0.00 3.18
621 622 1.476110 CCCAACCGTCCTTGAGTTCAA 60.476 52.381 0.00 0.00 0.00 2.69
622 623 0.107831 CCCAACCGTCCTTGAGTTCA 59.892 55.000 0.00 0.00 0.00 3.18
623 624 1.235281 GCCCAACCGTCCTTGAGTTC 61.235 60.000 0.00 0.00 0.00 3.01
624 625 1.228154 GCCCAACCGTCCTTGAGTT 60.228 57.895 0.00 0.00 0.00 3.01
625 626 2.430367 GCCCAACCGTCCTTGAGT 59.570 61.111 0.00 0.00 0.00 3.41
626 627 2.742372 CGCCCAACCGTCCTTGAG 60.742 66.667 0.00 0.00 0.00 3.02
627 628 3.109592 AACGCCCAACCGTCCTTGA 62.110 57.895 0.00 0.00 41.16 3.02
628 629 2.593436 AACGCCCAACCGTCCTTG 60.593 61.111 0.00 0.00 41.16 3.61
629 630 2.593436 CAACGCCCAACCGTCCTT 60.593 61.111 0.00 0.00 41.16 3.36
630 631 4.636435 CCAACGCCCAACCGTCCT 62.636 66.667 0.00 0.00 41.16 3.85
631 632 4.629523 TCCAACGCCCAACCGTCC 62.630 66.667 0.00 0.00 41.16 4.79
632 633 3.047877 CTCCAACGCCCAACCGTC 61.048 66.667 0.00 0.00 41.16 4.79
653 654 0.247537 GAGATGTAAAAACCGCGGCG 60.248 55.000 28.58 16.78 0.00 6.46
654 655 0.098200 GGAGATGTAAAAACCGCGGC 59.902 55.000 28.58 8.37 0.00 6.53
655 656 1.396996 CAGGAGATGTAAAAACCGCGG 59.603 52.381 26.86 26.86 0.00 6.46
656 657 1.396996 CCAGGAGATGTAAAAACCGCG 59.603 52.381 0.00 0.00 0.00 6.46
657 658 1.132453 GCCAGGAGATGTAAAAACCGC 59.868 52.381 0.00 0.00 0.00 5.68
658 659 2.711542 AGCCAGGAGATGTAAAAACCG 58.288 47.619 0.00 0.00 0.00 4.44
659 660 4.321974 CCAAAGCCAGGAGATGTAAAAACC 60.322 45.833 0.00 0.00 0.00 3.27
660 661 4.522789 TCCAAAGCCAGGAGATGTAAAAAC 59.477 41.667 0.00 0.00 0.00 2.43
661 662 4.735369 TCCAAAGCCAGGAGATGTAAAAA 58.265 39.130 0.00 0.00 0.00 1.94
662 663 4.380843 TCCAAAGCCAGGAGATGTAAAA 57.619 40.909 0.00 0.00 0.00 1.52
671 672 5.456921 AATTTAGATCTCCAAAGCCAGGA 57.543 39.130 0.00 0.00 0.00 3.86
672 673 5.680665 GCAAATTTAGATCTCCAAAGCCAGG 60.681 44.000 0.00 0.00 0.00 4.45
673 674 5.105635 TGCAAATTTAGATCTCCAAAGCCAG 60.106 40.000 0.00 0.00 0.00 4.85
674 675 4.771577 TGCAAATTTAGATCTCCAAAGCCA 59.228 37.500 0.00 0.00 0.00 4.75
675 676 5.329035 TGCAAATTTAGATCTCCAAAGCC 57.671 39.130 0.00 0.00 0.00 4.35
676 677 5.684626 CGATGCAAATTTAGATCTCCAAAGC 59.315 40.000 0.00 0.00 0.00 3.51
677 678 5.684626 GCGATGCAAATTTAGATCTCCAAAG 59.315 40.000 0.00 0.00 0.00 2.77
678 679 5.581605 GCGATGCAAATTTAGATCTCCAAA 58.418 37.500 0.00 0.00 0.00 3.28
679 680 4.260743 CGCGATGCAAATTTAGATCTCCAA 60.261 41.667 0.00 0.00 0.00 3.53
680 681 3.248363 CGCGATGCAAATTTAGATCTCCA 59.752 43.478 0.00 0.00 0.00 3.86
681 682 3.494626 TCGCGATGCAAATTTAGATCTCC 59.505 43.478 3.71 0.00 0.00 3.71
682 683 4.376819 CCTCGCGATGCAAATTTAGATCTC 60.377 45.833 10.36 0.00 0.00 2.75
683 684 3.496130 CCTCGCGATGCAAATTTAGATCT 59.504 43.478 10.36 0.00 0.00 2.75
684 685 3.248602 ACCTCGCGATGCAAATTTAGATC 59.751 43.478 10.36 0.00 0.00 2.75
685 686 3.002656 CACCTCGCGATGCAAATTTAGAT 59.997 43.478 10.36 0.00 0.00 1.98
686 687 2.351418 CACCTCGCGATGCAAATTTAGA 59.649 45.455 10.36 0.00 0.00 2.10
687 688 2.095853 ACACCTCGCGATGCAAATTTAG 59.904 45.455 10.36 0.00 0.00 1.85
688 689 2.080693 ACACCTCGCGATGCAAATTTA 58.919 42.857 10.36 0.00 0.00 1.40
689 690 0.881118 ACACCTCGCGATGCAAATTT 59.119 45.000 10.36 0.00 0.00 1.82
690 691 0.881118 AACACCTCGCGATGCAAATT 59.119 45.000 10.36 0.00 0.00 1.82
691 692 0.447801 GAACACCTCGCGATGCAAAT 59.552 50.000 10.36 0.00 0.00 2.32
692 693 0.602638 AGAACACCTCGCGATGCAAA 60.603 50.000 10.36 0.00 0.00 3.68
693 694 0.245266 TAGAACACCTCGCGATGCAA 59.755 50.000 10.36 0.00 0.00 4.08
694 695 0.459899 ATAGAACACCTCGCGATGCA 59.540 50.000 10.36 0.00 0.00 3.96
695 696 1.571919 AATAGAACACCTCGCGATGC 58.428 50.000 10.36 0.00 0.00 3.91
696 697 4.565166 TGTAAAATAGAACACCTCGCGATG 59.435 41.667 10.36 10.15 0.00 3.84
697 698 4.751060 TGTAAAATAGAACACCTCGCGAT 58.249 39.130 10.36 0.00 0.00 4.58
698 699 4.177165 TGTAAAATAGAACACCTCGCGA 57.823 40.909 9.26 9.26 0.00 5.87
699 700 4.804139 AGATGTAAAATAGAACACCTCGCG 59.196 41.667 0.00 0.00 0.00 5.87
700 701 5.234543 GGAGATGTAAAATAGAACACCTCGC 59.765 44.000 0.00 0.00 37.16 5.03
701 702 5.459107 CGGAGATGTAAAATAGAACACCTCG 59.541 44.000 0.00 0.00 37.16 4.63
702 703 5.753921 CCGGAGATGTAAAATAGAACACCTC 59.246 44.000 0.00 0.00 35.79 3.85
703 704 5.424252 TCCGGAGATGTAAAATAGAACACCT 59.576 40.000 0.00 0.00 0.00 4.00
704 705 5.667466 TCCGGAGATGTAAAATAGAACACC 58.333 41.667 0.00 0.00 0.00 4.16
705 706 7.605410 TTTCCGGAGATGTAAAATAGAACAC 57.395 36.000 3.34 0.00 0.00 3.32
706 707 7.148540 CGTTTTCCGGAGATGTAAAATAGAACA 60.149 37.037 3.34 0.00 0.00 3.18
707 708 7.178074 CGTTTTCCGGAGATGTAAAATAGAAC 58.822 38.462 3.34 0.00 0.00 3.01
708 709 7.298507 CGTTTTCCGGAGATGTAAAATAGAA 57.701 36.000 3.34 0.00 0.00 2.10
709 710 6.897259 CGTTTTCCGGAGATGTAAAATAGA 57.103 37.500 3.34 0.00 0.00 1.98
745 746 7.199541 CCAACAAATGGTTCATATGCAAAAA 57.800 32.000 0.00 0.00 44.85 1.94
746 747 6.798315 CCAACAAATGGTTCATATGCAAAA 57.202 33.333 0.00 0.00 44.85 2.44
778 779 7.875041 TCAACATTTGGACTTCTGAAACAAAAA 59.125 29.630 14.37 5.17 35.06 1.94
779 780 7.382110 TCAACATTTGGACTTCTGAAACAAAA 58.618 30.769 14.37 8.21 35.06 2.44
780 781 6.929625 TCAACATTTGGACTTCTGAAACAAA 58.070 32.000 13.36 13.36 35.76 2.83
781 782 6.522625 TCAACATTTGGACTTCTGAAACAA 57.477 33.333 0.00 0.00 0.00 2.83
782 783 6.713762 ATCAACATTTGGACTTCTGAAACA 57.286 33.333 0.00 0.00 0.00 2.83
783 784 9.696917 AATAATCAACATTTGGACTTCTGAAAC 57.303 29.630 0.00 0.00 0.00 2.78
799 800 8.132362 GCGGTCCATATGTAAAAATAATCAACA 58.868 33.333 1.24 0.00 0.00 3.33
800 801 7.593644 GGCGGTCCATATGTAAAAATAATCAAC 59.406 37.037 1.24 0.00 0.00 3.18
801 802 7.504238 AGGCGGTCCATATGTAAAAATAATCAA 59.496 33.333 1.24 0.00 33.74 2.57
802 803 7.001674 AGGCGGTCCATATGTAAAAATAATCA 58.998 34.615 1.24 0.00 33.74 2.57
803 804 7.448748 AGGCGGTCCATATGTAAAAATAATC 57.551 36.000 1.24 0.00 33.74 1.75
804 805 9.174166 GATAGGCGGTCCATATGTAAAAATAAT 57.826 33.333 1.24 0.00 33.74 1.28
805 806 7.332430 CGATAGGCGGTCCATATGTAAAAATAA 59.668 37.037 1.24 0.00 36.03 1.40
806 807 6.814644 CGATAGGCGGTCCATATGTAAAAATA 59.185 38.462 1.24 0.00 36.03 1.40
807 808 5.642063 CGATAGGCGGTCCATATGTAAAAAT 59.358 40.000 1.24 0.00 36.03 1.82
808 809 4.992319 CGATAGGCGGTCCATATGTAAAAA 59.008 41.667 1.24 0.00 36.03 1.94
809 810 4.281435 TCGATAGGCGGTCCATATGTAAAA 59.719 41.667 1.24 0.00 41.33 1.52
810 811 3.827876 TCGATAGGCGGTCCATATGTAAA 59.172 43.478 1.24 0.00 41.33 2.01
811 812 3.423749 TCGATAGGCGGTCCATATGTAA 58.576 45.455 1.24 0.00 41.33 2.41
812 813 3.076079 TCGATAGGCGGTCCATATGTA 57.924 47.619 1.24 0.00 41.33 2.29
813 814 1.919240 TCGATAGGCGGTCCATATGT 58.081 50.000 1.24 0.00 41.33 2.29
814 815 2.492088 TCTTCGATAGGCGGTCCATATG 59.508 50.000 0.00 0.00 41.33 1.78
815 816 2.803956 TCTTCGATAGGCGGTCCATAT 58.196 47.619 0.00 0.00 41.33 1.78
816 817 2.281539 TCTTCGATAGGCGGTCCATA 57.718 50.000 0.00 0.00 41.33 2.74
817 818 1.273606 CATCTTCGATAGGCGGTCCAT 59.726 52.381 0.00 0.00 41.33 3.41
818 819 0.673985 CATCTTCGATAGGCGGTCCA 59.326 55.000 0.00 0.00 41.33 4.02
819 820 0.674534 ACATCTTCGATAGGCGGTCC 59.325 55.000 0.00 0.00 41.33 4.46
820 821 2.034812 AGAACATCTTCGATAGGCGGTC 59.965 50.000 0.00 0.00 41.33 4.79
821 822 2.032620 AGAACATCTTCGATAGGCGGT 58.967 47.619 0.00 0.00 41.33 5.68
822 823 2.802787 AGAACATCTTCGATAGGCGG 57.197 50.000 0.00 0.00 41.33 6.13
823 824 4.861210 AGTAAGAACATCTTCGATAGGCG 58.139 43.478 0.00 0.00 37.89 5.52
824 825 9.344309 GTATAAGTAAGAACATCTTCGATAGGC 57.656 37.037 0.00 0.00 37.89 3.93
825 826 9.843334 GGTATAAGTAAGAACATCTTCGATAGG 57.157 37.037 0.00 0.00 37.89 2.57
828 829 9.530633 GTTGGTATAAGTAAGAACATCTTCGAT 57.469 33.333 0.00 0.00 37.89 3.59
829 830 8.746530 AGTTGGTATAAGTAAGAACATCTTCGA 58.253 33.333 0.00 0.00 37.89 3.71
830 831 8.928270 AGTTGGTATAAGTAAGAACATCTTCG 57.072 34.615 0.00 0.00 37.89 3.79
898 899 3.365969 GGCTTGGACCGAAAACATAACAG 60.366 47.826 0.00 0.00 0.00 3.16
1004 1005 0.245539 CCCTCATTGCTTTGCACTGG 59.754 55.000 9.40 2.46 39.22 4.00
2011 2083 1.228894 TTCACCTCCTGAGCCGACT 60.229 57.895 0.00 0.00 0.00 4.18
2157 2229 0.811915 CACTCCTCTAGGGTGACGTG 59.188 60.000 0.00 2.09 38.09 4.49
2428 2507 7.538678 CAGTAGGTGTAAATCAAGTCAATTTGC 59.461 37.037 0.00 0.00 31.70 3.68
2505 3754 5.514169 ACTCTCTCTGGTCATCTGTTATGA 58.486 41.667 0.00 0.00 0.00 2.15
2731 5926 1.276421 AGAAGCTACAGGTGCGACAAT 59.724 47.619 0.00 0.00 35.28 2.71
2946 6141 4.216411 AGCGTTTTATATGTCACCCACT 57.784 40.909 0.00 0.00 0.00 4.00
3239 8735 9.442047 CTGTTCTAAGAGAAATTGTTCCATAGT 57.558 33.333 0.00 0.00 35.75 2.12
3254 8750 4.569966 CAGCCTATGCAACTGTTCTAAGAG 59.430 45.833 0.00 0.00 41.13 2.85
3411 8912 4.647564 AGTGAGTTGTTGGATCTCCATT 57.352 40.909 0.00 0.00 46.97 3.16
3699 9236 6.147164 CACATCACACTTATACACGAGGTTTT 59.853 38.462 0.00 0.00 0.00 2.43
3711 9248 3.826157 CACAAACCCCACATCACACTTAT 59.174 43.478 0.00 0.00 0.00 1.73
3722 9259 1.066908 CACACACATCACAAACCCCAC 59.933 52.381 0.00 0.00 0.00 4.61
3774 9384 5.554070 TGTGAAGGATATAGTCATGCCATG 58.446 41.667 0.00 0.00 0.00 3.66
3775 9385 5.830799 TGTGAAGGATATAGTCATGCCAT 57.169 39.130 0.00 0.00 0.00 4.40
3777 9387 5.798132 TCATGTGAAGGATATAGTCATGCC 58.202 41.667 0.00 0.00 33.58 4.40
3880 9503 1.707427 ACCATTCTTCCTTCAGGCAGT 59.293 47.619 0.00 0.00 34.44 4.40
3899 9522 2.080286 TTAAGCCTCTTGACAGCGAC 57.920 50.000 0.00 0.00 0.00 5.19
4057 9680 3.338249 GTTCAGGCTCTTGTTCTGCATA 58.662 45.455 0.00 0.00 0.00 3.14
4125 9786 8.029642 ACGGTCTAGTTTTCATGATAAGTTTG 57.970 34.615 10.90 6.02 0.00 2.93
4126 9787 8.095169 AGACGGTCTAGTTTTCATGATAAGTTT 58.905 33.333 9.33 0.00 0.00 2.66
4236 9970 2.275418 CAGGGGGACAATTCGGGG 59.725 66.667 0.00 0.00 0.00 5.73
4247 9983 3.456277 AGTCAAGCTAATAAGTCAGGGGG 59.544 47.826 0.00 0.00 0.00 5.40
4298 10034 4.511826 GTGATAGCTTATGGTGTTAGGTGC 59.488 45.833 0.00 0.00 0.00 5.01
4339 10075 3.830755 ACGTATATACTGACCCCATGACC 59.169 47.826 11.05 0.00 0.00 4.02
4412 10148 3.087781 ACTTCTGACCTAACGGACCTAC 58.912 50.000 0.00 0.00 0.00 3.18
4415 10151 2.685100 CAACTTCTGACCTAACGGACC 58.315 52.381 0.00 0.00 0.00 4.46
4454 10190 9.959721 ACATGAAGTACATAAGAGTAACCATTT 57.040 29.630 0.00 0.00 37.46 2.32
4455 10191 9.959721 AACATGAAGTACATAAGAGTAACCATT 57.040 29.630 0.00 0.00 37.46 3.16
4457 10193 8.590204 TGAACATGAAGTACATAAGAGTAACCA 58.410 33.333 0.00 0.00 37.46 3.67
4458 10194 8.997621 TGAACATGAAGTACATAAGAGTAACC 57.002 34.615 0.00 0.00 37.46 2.85
4481 10219 9.489084 CCGGAGAAAATCATATATGTTAGTTGA 57.511 33.333 12.42 0.00 0.00 3.18
4541 10280 8.592809 AGCACATCACCCTTTAAATATTTTTGA 58.407 29.630 5.91 1.33 0.00 2.69
4542 10281 8.776376 AGCACATCACCCTTTAAATATTTTTG 57.224 30.769 5.91 0.00 0.00 2.44
4543 10282 8.815912 AGAGCACATCACCCTTTAAATATTTTT 58.184 29.630 5.91 0.00 0.00 1.94
4544 10283 8.366359 AGAGCACATCACCCTTTAAATATTTT 57.634 30.769 5.91 0.00 0.00 1.82
4545 10284 7.961326 AGAGCACATCACCCTTTAAATATTT 57.039 32.000 5.89 5.89 0.00 1.40
4546 10285 7.721399 CCTAGAGCACATCACCCTTTAAATATT 59.279 37.037 0.00 0.00 0.00 1.28
4548 10287 6.385759 TCCTAGAGCACATCACCCTTTAAATA 59.614 38.462 0.00 0.00 0.00 1.40
4550 10289 4.534500 TCCTAGAGCACATCACCCTTTAAA 59.466 41.667 0.00 0.00 0.00 1.52
4587 10330 8.857098 TCTCTAGTTGTTTCTAGCTCACTTAAA 58.143 33.333 0.00 0.00 37.78 1.52
4614 10357 4.076394 TCCCCTAATTGCACACACTTAAC 58.924 43.478 0.00 0.00 0.00 2.01
4619 10362 2.200373 ACTCCCCTAATTGCACACAC 57.800 50.000 0.00 0.00 0.00 3.82
4625 10368 6.775594 AGTTCATTTTACTCCCCTAATTGC 57.224 37.500 0.00 0.00 0.00 3.56
4711 10520 3.084039 ACCTGTGAGTGCCAAATATGTG 58.916 45.455 0.00 0.00 0.00 3.21
4992 10801 8.008332 TGTTAGGTATATATCTGGTGGTGAAGA 58.992 37.037 5.73 0.00 0.00 2.87
5029 10838 3.442625 AGCTGCGTATCCCCTTTTTAAAC 59.557 43.478 0.00 0.00 0.00 2.01
5114 10923 2.403378 GCTGAGCGTCTCGAGGAGT 61.403 63.158 13.56 0.00 32.35 3.85
5319 11128 1.279846 CCCATGCCTGCCAAAAAGATT 59.720 47.619 0.00 0.00 0.00 2.40
5364 11173 2.383527 GCGGTGTCAAGAAGCTCCG 61.384 63.158 2.08 2.08 42.48 4.63
5426 11235 5.174395 CCCAATTTGGATGCATCGTTTTAA 58.826 37.500 20.15 9.70 40.96 1.52
5473 11282 0.899717 ACATGGTTGGCCTTTCGCAT 60.900 50.000 3.32 0.00 40.31 4.73
5660 11469 0.519077 GGCTGCAGCAACAACTAGTC 59.481 55.000 37.63 14.35 44.36 2.59
5698 11507 3.066203 ACAAACACAAACCGAGCCTTTAG 59.934 43.478 0.00 0.00 0.00 1.85
5776 11588 4.202202 CCATTTTAGTGTTTGCTTCACCCA 60.202 41.667 0.00 0.00 36.58 4.51
5802 11614 0.761802 TTGCCCAACCAATTTCCACC 59.238 50.000 0.00 0.00 0.00 4.61
5803 11615 2.698803 GATTGCCCAACCAATTTCCAC 58.301 47.619 0.00 0.00 35.67 4.02
5804 11616 1.274728 CGATTGCCCAACCAATTTCCA 59.725 47.619 0.00 0.00 35.67 3.53
5942 11757 6.625873 AAAGAAAGACTGACAGACAAATCC 57.374 37.500 10.08 0.00 0.00 3.01
6051 11870 3.041946 ACTTGACAGTCAAAGAGGACCT 58.958 45.455 16.85 0.00 35.73 3.85
6169 11989 4.403432 CCTGGCACTCAAATATTCATTGGT 59.597 41.667 0.00 0.00 0.00 3.67
6223 12044 8.947055 AACTCTGTGAATTTGCAATAAAACTT 57.053 26.923 0.00 0.00 0.00 2.66
6446 12268 2.224892 TGCCTATCTACGGATGCTCTCT 60.225 50.000 0.00 0.00 33.71 3.10
6490 12312 4.632153 GATGCTCCGGTGATACTACAATT 58.368 43.478 7.92 0.00 0.00 2.32
6542 12364 2.473816 CGGAACTACATGCGATGATGT 58.526 47.619 0.00 0.00 39.87 3.06
6602 12424 3.748668 CGGAGGGGTGATTCTATTTGCAT 60.749 47.826 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.