Multiple sequence alignment - TraesCS6A01G131300

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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 TraesCS6A01G131300 chr6A 100.000 6600 0 0 1 6600 103765461 103758862 0.000000e+00 12189.0
1 TraesCS6A01G131300 chr6D 93.852 2391 99 18 1123 3479 86148286 86145910 0.000000e+00 3557.0
2 TraesCS6A01G131300 chr6D 95.165 1634 34 18 3561 5154 86145911 86144283 0.000000e+00 2538.0
3 TraesCS6A01G131300 chr6D 92.045 1433 46 16 5181 6600 86144211 86142834 0.000000e+00 1953.0
4 TraesCS6A01G131300 chr6D 79.333 1050 195 20 62 1101 423002280 423001243 0.000000e+00 717.0
5 TraesCS6A01G131300 chr6D 93.000 100 6 1 3473 3572 114587803 114587705 1.920000e-30 145.0
6 TraesCS6A01G131300 chr6D 88.793 116 11 2 3467 3581 255817387 255817273 2.480000e-29 141.0
7 TraesCS6A01G131300 chr6B 94.572 2174 90 9 1318 3479 163235283 163233126 0.000000e+00 3336.0
8 TraesCS6A01G131300 chr6B 93.754 1617 60 19 3561 5142 163233127 163231517 0.000000e+00 2388.0
9 TraesCS6A01G131300 chr6B 94.641 765 28 5 5181 5936 163231420 163230660 0.000000e+00 1173.0
10 TraesCS6A01G131300 chr6B 91.556 675 11 12 5928 6600 163230635 163230005 0.000000e+00 889.0
11 TraesCS6A01G131300 chr6B 90.244 164 7 3 1121 1284 163235778 163235624 8.680000e-49 206.0
12 TraesCS6A01G131300 chr5A 90.152 985 63 15 4933 5906 323083803 323084764 0.000000e+00 1251.0
13 TraesCS6A01G131300 chr4A 90.164 976 63 11 4933 5898 113485800 113486752 0.000000e+00 1240.0
14 TraesCS6A01G131300 chr1A 88.618 861 97 1 161 1020 520827215 520826355 0.000000e+00 1046.0
15 TraesCS6A01G131300 chr3A 91.712 736 59 2 1 735 46983566 46984300 0.000000e+00 1020.0
16 TraesCS6A01G131300 chr2B 79.126 1030 196 18 84 1101 526402144 526403166 0.000000e+00 693.0
17 TraesCS6A01G131300 chr2B 88.085 235 27 1 1506 1740 613042945 613042712 1.810000e-70 278.0
18 TraesCS6A01G131300 chr3D 89.368 348 31 2 1450 1797 420473709 420473368 3.660000e-117 433.0
19 TraesCS6A01G131300 chr3D 88.596 114 9 3 3451 3563 312907617 312907507 1.150000e-27 135.0
20 TraesCS6A01G131300 chr7B 81.545 466 75 8 3928 4388 594418883 594418424 2.250000e-99 374.0
21 TraesCS6A01G131300 chr7B 86.207 232 31 1 1506 1737 511947404 511947634 3.950000e-62 250.0
22 TraesCS6A01G131300 chr7B 96.774 31 1 0 3443 3473 75793893 75793863 1.200000e-02 52.8
23 TraesCS6A01G131300 chr1B 89.787 235 23 1 1506 1740 113518791 113519024 3.870000e-77 300.0
24 TraesCS6A01G131300 chr5B 88.511 235 26 1 1506 1740 84735462 84735229 3.900000e-72 283.0
25 TraesCS6A01G131300 chr7A 91.713 181 13 2 107 286 672868736 672868915 3.950000e-62 250.0
26 TraesCS6A01G131300 chrUn 73.029 723 184 11 156 873 102571445 102570729 1.840000e-60 244.0
27 TraesCS6A01G131300 chr4D 87.135 171 10 6 1447 1611 24254374 24254210 4.060000e-42 183.0
28 TraesCS6A01G131300 chr5D 96.703 91 3 0 3478 3568 447627018 447626928 1.150000e-32 152.0
29 TraesCS6A01G131300 chr2A 94.898 98 3 2 3474 3570 712971380 712971476 1.150000e-32 152.0
30 TraesCS6A01G131300 chr2A 75.000 176 42 2 138 312 779898775 779898601 5.490000e-11 80.5
31 TraesCS6A01G131300 chr7D 94.792 96 3 2 3469 3562 448931412 448931317 1.480000e-31 148.0
32 TraesCS6A01G131300 chr7D 96.591 88 3 0 3478 3565 22964257 22964344 5.330000e-31 147.0
33 TraesCS6A01G131300 chr7D 95.604 91 3 1 3475 3564 426558895 426558985 1.920000e-30 145.0
34 TraesCS6A01G131300 chr2D 93.069 101 6 1 3478 3577 15682984 15682884 5.330000e-31 147.0


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 TraesCS6A01G131300 chr6A 103758862 103765461 6599 True 12189.000000 12189 100.000000 1 6600 1 chr6A.!!$R1 6599
1 TraesCS6A01G131300 chr6D 86142834 86148286 5452 True 2682.666667 3557 93.687333 1123 6600 3 chr6D.!!$R4 5477
2 TraesCS6A01G131300 chr6D 423001243 423002280 1037 True 717.000000 717 79.333000 62 1101 1 chr6D.!!$R3 1039
3 TraesCS6A01G131300 chr6B 163230005 163235778 5773 True 1598.400000 3336 92.953400 1121 6600 5 chr6B.!!$R1 5479
4 TraesCS6A01G131300 chr5A 323083803 323084764 961 False 1251.000000 1251 90.152000 4933 5906 1 chr5A.!!$F1 973
5 TraesCS6A01G131300 chr4A 113485800 113486752 952 False 1240.000000 1240 90.164000 4933 5898 1 chr4A.!!$F1 965
6 TraesCS6A01G131300 chr1A 520826355 520827215 860 True 1046.000000 1046 88.618000 161 1020 1 chr1A.!!$R1 859
7 TraesCS6A01G131300 chr3A 46983566 46984300 734 False 1020.000000 1020 91.712000 1 735 1 chr3A.!!$F1 734
8 TraesCS6A01G131300 chr2B 526402144 526403166 1022 False 693.000000 693 79.126000 84 1101 1 chr2B.!!$F1 1017
9 TraesCS6A01G131300 chrUn 102570729 102571445 716 True 244.000000 244 73.029000 156 873 1 chrUn.!!$R1 717

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
268 269 0.388659 AATTGCCGCACACAACACAT 59.611 45.0 0.00 0.0 0.00 3.21 F
1209 1234 0.109919 GCCGAACACCGTTTCATTCC 60.110 55.0 0.00 0.0 36.31 3.01 F
1938 2275 0.689080 TTTGCCCACTTTTGCCCTCA 60.689 50.0 0.00 0.0 0.00 3.86 F
2001 2356 1.087202 TGTGACTGTGCGGTGTTGAC 61.087 55.0 0.00 0.0 0.00 3.18 F
3675 4033 1.141645 TTATCACGACGGTGTTGTGC 58.858 50.0 11.60 0.0 44.87 4.57 F
4911 5299 0.896923 TCGCCGGGTAAGTAATGTGT 59.103 50.0 2.18 0.0 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 1951 0.030092 ATCCCCTCCCAATCCTTCGA 60.030 55.000 0.0 0.0 0.00 3.71 R
2178 2533 1.592400 GCAAACACAGCCACAAGCC 60.592 57.895 0.0 0.0 45.47 4.35 R
3547 3903 0.108281 GCAACTACTTCCTCCGTCCC 60.108 60.000 0.0 0.0 0.00 4.46 R
3918 4276 0.471617 GATCCTGACTGATGTGGGGG 59.528 60.000 0.0 0.0 0.00 5.40 R
5051 5451 0.031917 TCCCCATCATTGCAGGCATT 60.032 50.000 0.0 0.0 0.00 3.56 R
6359 6874 0.171455 TTTGTGTGTTTGGTCGGCAC 59.829 50.000 0.0 0.0 0.00 5.01 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
44 45 6.336566 TCTGAATCATACTCTGAGCTTTCAC 58.663 40.000 4.19 0.00 37.28 3.18
46 47 4.991153 ATCATACTCTGAGCTTTCACGA 57.009 40.909 4.19 0.00 37.28 4.35
53 54 0.976641 TGAGCTTTCACGATCCTGGT 59.023 50.000 0.00 0.00 0.00 4.00
60 61 3.973206 TTCACGATCCTGGTTGTACAT 57.027 42.857 0.00 0.00 0.00 2.29
64 65 1.484653 CGATCCTGGTTGTACATGGGA 59.515 52.381 0.00 2.84 0.00 4.37
97 98 1.451567 CGAGCGACCTCCACCTCTA 60.452 63.158 0.00 0.00 34.49 2.43
100 101 1.681327 GCGACCTCCACCTCTACCA 60.681 63.158 0.00 0.00 0.00 3.25
101 102 1.668101 GCGACCTCCACCTCTACCAG 61.668 65.000 0.00 0.00 0.00 4.00
151 152 3.003173 CTGCCTTCTCCCGGTCCA 61.003 66.667 0.00 0.00 0.00 4.02
152 153 2.285368 TGCCTTCTCCCGGTCCAT 60.285 61.111 0.00 0.00 0.00 3.41
263 264 1.068753 CCCAAATTGCCGCACACAA 59.931 52.632 0.00 0.00 0.00 3.33
268 269 0.388659 AATTGCCGCACACAACACAT 59.611 45.000 0.00 0.00 0.00 3.21
289 290 6.147985 CACATCAATCAGGCAATCTCTCATAG 59.852 42.308 0.00 0.00 0.00 2.23
310 311 2.930682 GTTTACCCTGAAGATGACTCGC 59.069 50.000 0.00 0.00 0.00 5.03
370 371 0.882927 TTTTGAGGGGCTTCGTGACG 60.883 55.000 0.00 0.00 0.00 4.35
376 377 0.953960 GGGGCTTCGTGACGTCAATT 60.954 55.000 21.95 0.00 0.00 2.32
391 392 1.375523 AATTCTCACCCGGACACGC 60.376 57.895 0.73 0.00 39.22 5.34
416 417 3.188159 AGTTACCTTCAAAGTCGTGCA 57.812 42.857 0.00 0.00 0.00 4.57
421 422 6.261381 AGTTACCTTCAAAGTCGTGCAATTTA 59.739 34.615 0.00 0.00 0.00 1.40
429 430 3.740115 AGTCGTGCAATTTAGGTTCAGT 58.260 40.909 0.00 0.00 0.00 3.41
494 495 2.941480 GGAAGTATCCGTCTGGTAGGA 58.059 52.381 0.00 0.00 41.30 2.94
582 584 2.597510 GCAAGGACCACCGCCTTT 60.598 61.111 0.00 0.00 42.99 3.11
592 594 2.176045 CCACCGCCTTTCCCTTAAAAT 58.824 47.619 0.00 0.00 0.00 1.82
712 714 3.866582 GATCCCAGGCCACCCTCG 61.867 72.222 5.01 0.00 40.33 4.63
719 721 2.047179 GGCCACCCTCGTGTTCTC 60.047 66.667 0.00 0.00 38.41 2.87
752 754 3.773418 TTGGTTGTAGGATTTGTCGGA 57.227 42.857 0.00 0.00 0.00 4.55
846 848 2.239654 CAGTTCATCCTCCTTAAGCCCA 59.760 50.000 0.00 0.00 0.00 5.36
867 869 1.645455 CTCCGCCATCATTGCTTCG 59.355 57.895 0.00 0.00 0.00 3.79
906 908 1.497991 CCGAACTTGACGCAGAAGAA 58.502 50.000 0.00 0.00 0.00 2.52
907 909 1.192534 CCGAACTTGACGCAGAAGAAC 59.807 52.381 0.00 0.00 0.00 3.01
935 937 0.906775 CCCTAGCCCGAGGTTGTTTA 59.093 55.000 0.00 0.00 34.45 2.01
944 946 1.287425 GAGGTTGTTTAGATCCGCGG 58.713 55.000 22.12 22.12 0.00 6.46
967 969 0.596859 GTATGAACCCTAGCGCCGTC 60.597 60.000 2.29 0.00 0.00 4.79
968 970 2.067091 TATGAACCCTAGCGCCGTCG 62.067 60.000 2.29 0.00 39.07 5.12
985 987 3.782443 GCCAATCCCCCGTCGACT 61.782 66.667 14.70 0.00 0.00 4.18
986 988 2.499685 CCAATCCCCCGTCGACTC 59.500 66.667 14.70 0.00 0.00 3.36
999 1004 2.683933 GACTCCGAGGCCCCAAGA 60.684 66.667 0.00 0.00 0.00 3.02
1000 1005 3.003763 ACTCCGAGGCCCCAAGAC 61.004 66.667 0.00 0.00 0.00 3.01
1001 1006 3.003173 CTCCGAGGCCCCAAGACA 61.003 66.667 0.00 0.00 0.00 3.41
1006 1013 1.152830 GAGGCCCCAAGACACCAAA 59.847 57.895 0.00 0.00 0.00 3.28
1011 1018 1.547675 GCCCCAAGACACCAAAGATCA 60.548 52.381 0.00 0.00 0.00 2.92
1016 1023 1.348064 AGACACCAAAGATCACCGGA 58.652 50.000 9.46 0.00 0.00 5.14
1030 1037 2.363406 CGGAGGGGGTAGAACGGT 60.363 66.667 0.00 0.00 0.00 4.83
1035 1042 1.763655 GGGGGTAGAACGGTAGGGG 60.764 68.421 0.00 0.00 0.00 4.79
1038 1045 0.259938 GGGTAGAACGGTAGGGGAGA 59.740 60.000 0.00 0.00 0.00 3.71
1041 1049 2.357569 GGTAGAACGGTAGGGGAGAGAA 60.358 54.545 0.00 0.00 0.00 2.87
1056 1064 1.026584 GAGAAGTCTCTACGGGAGGC 58.973 60.000 0.87 4.45 46.30 4.70
1080 1088 2.194212 GCCATCGCCGAGAGTAGGA 61.194 63.158 0.00 0.00 0.00 2.94
1104 1112 2.406205 CCTAACGAGAGGGGAGACG 58.594 63.158 0.00 0.00 32.39 4.18
1105 1113 0.394080 CCTAACGAGAGGGGAGACGT 60.394 60.000 0.00 0.00 40.64 4.34
1106 1114 4.515718 AACGAGAGGGGAGACGTT 57.484 55.556 0.00 0.00 42.60 3.99
1107 1115 1.817447 CTAACGAGAGGGGAGACGTTT 59.183 52.381 0.00 0.00 44.46 3.60
1108 1116 0.602060 AACGAGAGGGGAGACGTTTC 59.398 55.000 0.00 0.00 44.46 2.78
1109 1117 0.251253 ACGAGAGGGGAGACGTTTCT 60.251 55.000 6.02 0.00 35.47 2.52
1110 1118 0.889306 CGAGAGGGGAGACGTTTCTT 59.111 55.000 6.02 0.00 29.47 2.52
1111 1119 1.402984 CGAGAGGGGAGACGTTTCTTG 60.403 57.143 6.02 0.00 29.47 3.02
1112 1120 1.893801 GAGAGGGGAGACGTTTCTTGA 59.106 52.381 6.02 0.00 29.47 3.02
1113 1121 2.498078 GAGAGGGGAGACGTTTCTTGAT 59.502 50.000 6.02 0.00 29.47 2.57
1114 1122 2.907042 AGAGGGGAGACGTTTCTTGATT 59.093 45.455 6.02 0.00 29.47 2.57
1115 1123 3.003480 GAGGGGAGACGTTTCTTGATTG 58.997 50.000 6.02 0.00 29.47 2.67
1116 1124 2.372172 AGGGGAGACGTTTCTTGATTGT 59.628 45.455 6.02 0.00 29.47 2.71
1117 1125 3.146847 GGGGAGACGTTTCTTGATTGTT 58.853 45.455 6.02 0.00 29.47 2.83
1118 1126 3.568430 GGGGAGACGTTTCTTGATTGTTT 59.432 43.478 6.02 0.00 29.47 2.83
1119 1127 4.037565 GGGGAGACGTTTCTTGATTGTTTT 59.962 41.667 6.02 0.00 29.47 2.43
1130 1138 4.588106 TCTTGATTGTTTTCATTCAGCCCA 59.412 37.500 0.00 0.00 39.99 5.36
1175 1183 3.185880 ACTGACCTAACAGGCCTTCTA 57.814 47.619 0.00 0.00 39.63 2.10
1200 1208 1.145156 TCATATGGGCCGAACACCG 59.855 57.895 2.13 0.00 38.18 4.94
1209 1234 0.109919 GCCGAACACCGTTTCATTCC 60.110 55.000 0.00 0.00 36.31 3.01
1473 1808 2.517402 CCGACTCGAGGAGGGAGG 60.517 72.222 18.41 6.55 35.82 4.30
1591 1926 1.959226 TGTTCTCGCAACCTTCGCC 60.959 57.895 0.00 0.00 0.00 5.54
1617 1952 3.451894 CACCAGCGCCCCCAAATC 61.452 66.667 2.29 0.00 0.00 2.17
1811 2148 2.644992 GAGTTTTGCCGCTGGTGG 59.355 61.111 0.00 0.00 0.00 4.61
1875 2212 1.016130 CGATTGCTGACTCCAAGCGT 61.016 55.000 3.93 0.00 44.28 5.07
1938 2275 0.689080 TTTGCCCACTTTTGCCCTCA 60.689 50.000 0.00 0.00 0.00 3.86
1979 2334 3.291584 CTGCTGGTAGTAGGAGATGTGA 58.708 50.000 0.00 0.00 38.28 3.58
1980 2335 3.291584 TGCTGGTAGTAGGAGATGTGAG 58.708 50.000 0.00 0.00 0.00 3.51
1981 2336 3.053619 TGCTGGTAGTAGGAGATGTGAGA 60.054 47.826 0.00 0.00 0.00 3.27
1982 2337 4.148838 GCTGGTAGTAGGAGATGTGAGAT 58.851 47.826 0.00 0.00 0.00 2.75
1983 2338 4.022416 GCTGGTAGTAGGAGATGTGAGATG 60.022 50.000 0.00 0.00 0.00 2.90
1984 2339 5.130705 TGGTAGTAGGAGATGTGAGATGT 57.869 43.478 0.00 0.00 0.00 3.06
1985 2340 4.889995 TGGTAGTAGGAGATGTGAGATGTG 59.110 45.833 0.00 0.00 0.00 3.21
2001 2356 1.087202 TGTGACTGTGCGGTGTTGAC 61.087 55.000 0.00 0.00 0.00 3.18
2037 2392 2.292103 ATCTGCAGCTCGTTTCTCTC 57.708 50.000 9.47 0.00 0.00 3.20
2142 2497 4.105486 GCGCCTCATCTGTTTTTATTTCC 58.895 43.478 0.00 0.00 0.00 3.13
2153 2508 5.757886 TGTTTTTATTTCCGCTGAGTTCAG 58.242 37.500 4.77 4.77 46.40 3.02
2178 2533 2.815503 TGTGTGATGTTTGAGCTGGATG 59.184 45.455 0.00 0.00 0.00 3.51
2187 2542 2.362120 AGCTGGATGGCTTGTGGC 60.362 61.111 0.00 0.00 39.86 5.01
2191 2546 1.592400 CTGGATGGCTTGTGGCTGTG 61.592 60.000 0.00 0.00 41.46 3.66
2261 2616 5.418310 TGAACTGCTTGCTGTAAGTTTAC 57.582 39.130 7.33 0.00 38.70 2.01
2262 2617 4.878971 TGAACTGCTTGCTGTAAGTTTACA 59.121 37.500 7.33 4.78 41.06 2.41
2264 2619 5.828299 ACTGCTTGCTGTAAGTTTACAAA 57.172 34.783 7.33 0.00 42.55 2.83
2269 2624 7.708051 TGCTTGCTGTAAGTTTACAAAATGTA 58.292 30.769 7.33 0.00 42.55 2.29
2270 2625 8.356657 TGCTTGCTGTAAGTTTACAAAATGTAT 58.643 29.630 7.33 0.00 42.55 2.29
2284 2639 9.621629 TTACAAAATGTATAGATTACCCTGTGG 57.378 33.333 0.00 0.00 32.20 4.17
2292 2647 3.624777 AGATTACCCTGTGGCATTCAAG 58.375 45.455 0.00 0.00 33.59 3.02
2294 2649 4.227300 AGATTACCCTGTGGCATTCAAGTA 59.773 41.667 0.00 0.00 33.59 2.24
2295 2650 2.969821 ACCCTGTGGCATTCAAGTAA 57.030 45.000 0.00 0.00 33.59 2.24
2418 2773 1.606601 GTCTGCCCCCTTTTCCCAC 60.607 63.158 0.00 0.00 0.00 4.61
2443 2798 9.490379 ACGGTAAATCATGATAATAAAGTCCTC 57.510 33.333 9.04 0.00 0.00 3.71
2596 2951 7.104043 ACTTTGTCATTGCAGCACATATTAT 57.896 32.000 0.00 0.00 0.00 1.28
2817 3172 2.417243 CCGGTTCAATGATTTTGCCTCC 60.417 50.000 0.00 0.00 0.00 4.30
2830 3185 1.288508 TGCCTCCCCATTGCTGGTAT 61.289 55.000 0.00 0.00 41.37 2.73
2848 3203 6.877322 GCTGGTATAGACTTCTGTTTAAACCA 59.123 38.462 15.59 1.58 0.00 3.67
2850 3205 9.449719 CTGGTATAGACTTCTGTTTAAACCATT 57.550 33.333 15.59 0.00 0.00 3.16
2857 3212 7.979537 AGACTTCTGTTTAAACCATTGTTTTCC 59.020 33.333 15.59 0.00 41.92 3.13
2884 3239 8.797350 ATGATTTACAGATCACAATGTTCTCA 57.203 30.769 0.00 0.00 38.75 3.27
2888 3243 4.978099 ACAGATCACAATGTTCTCAACCT 58.022 39.130 0.00 0.00 0.00 3.50
2907 3262 5.972327 ACCTCATCTTCTTTCATCCTGAT 57.028 39.130 0.00 0.00 0.00 2.90
2923 3278 7.341030 TCATCCTGATTGTGTTATTGAGTCAT 58.659 34.615 0.00 0.00 0.00 3.06
3122 3477 6.509418 TTCATTTTTAGCCACACCATCTAC 57.491 37.500 0.00 0.00 0.00 2.59
3479 3835 8.607441 TGTAGCATGATGTGAGGATTTAATAC 57.393 34.615 0.00 0.00 0.00 1.89
3480 3836 8.432013 TGTAGCATGATGTGAGGATTTAATACT 58.568 33.333 0.00 0.00 0.00 2.12
3481 3837 7.976135 AGCATGATGTGAGGATTTAATACTC 57.024 36.000 10.12 10.12 40.81 2.59
3482 3838 6.939163 AGCATGATGTGAGGATTTAATACTCC 59.061 38.462 14.02 6.70 39.62 3.85
3483 3839 6.150140 GCATGATGTGAGGATTTAATACTCCC 59.850 42.308 14.02 3.79 39.62 4.30
3484 3840 7.456725 CATGATGTGAGGATTTAATACTCCCT 58.543 38.462 14.02 0.00 39.62 4.20
3485 3841 7.067496 TGATGTGAGGATTTAATACTCCCTC 57.933 40.000 14.02 8.71 39.62 4.30
3486 3842 5.888982 TGTGAGGATTTAATACTCCCTCC 57.111 43.478 14.02 1.53 39.62 4.30
3487 3843 4.344102 TGTGAGGATTTAATACTCCCTCCG 59.656 45.833 14.02 0.00 39.62 4.63
3488 3844 4.344390 GTGAGGATTTAATACTCCCTCCGT 59.656 45.833 14.02 0.00 39.62 4.69
3489 3845 4.587684 TGAGGATTTAATACTCCCTCCGTC 59.412 45.833 14.02 0.00 39.62 4.79
3490 3846 3.902467 AGGATTTAATACTCCCTCCGTCC 59.098 47.826 0.00 0.00 31.49 4.79
3491 3847 3.007723 GGATTTAATACTCCCTCCGTCCC 59.992 52.174 0.00 0.00 0.00 4.46
3492 3848 2.852714 TTAATACTCCCTCCGTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
3493 3849 3.339713 TTAATACTCCCTCCGTCCCAT 57.660 47.619 0.00 0.00 0.00 4.00
3494 3850 4.474303 TTAATACTCCCTCCGTCCCATA 57.526 45.455 0.00 0.00 0.00 2.74
3495 3851 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
3496 3852 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
3497 3853 4.687262 ATACTCCCTCCGTCCCATAATA 57.313 45.455 0.00 0.00 0.00 0.98
3498 3854 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
3499 3855 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
3500 3856 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
3501 3857 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
3502 3858 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
3503 3859 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
3504 3860 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
3505 3861 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
3506 3862 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
3507 3863 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
3508 3864 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
3509 3865 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
3510 3866 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
3535 3891 9.748708 TTTATACTAGTGTAGTGTCAAAAACGT 57.251 29.630 5.39 0.00 39.81 3.99
3536 3892 9.748708 TTATACTAGTGTAGTGTCAAAAACGTT 57.251 29.630 5.39 0.00 39.81 3.99
3537 3893 6.579491 ACTAGTGTAGTGTCAAAAACGTTC 57.421 37.500 0.00 0.00 37.69 3.95
3538 3894 6.335777 ACTAGTGTAGTGTCAAAAACGTTCT 58.664 36.000 0.00 0.00 37.69 3.01
3539 3895 6.815142 ACTAGTGTAGTGTCAAAAACGTTCTT 59.185 34.615 0.00 0.00 37.69 2.52
3540 3896 7.975616 ACTAGTGTAGTGTCAAAAACGTTCTTA 59.024 33.333 0.00 0.00 37.69 2.10
3541 3897 7.781548 AGTGTAGTGTCAAAAACGTTCTTAT 57.218 32.000 0.00 0.00 0.00 1.73
3542 3898 8.876275 AGTGTAGTGTCAAAAACGTTCTTATA 57.124 30.769 0.00 0.00 0.00 0.98
3543 3899 9.485206 AGTGTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 0.00 0.00 0.00 0.86
3549 3905 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
3550 3906 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
3551 3907 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
3552 3908 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
3553 3909 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
3554 3910 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
3555 3911 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
3556 3912 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
3557 3913 5.184479 CGTTCTTATATTATGGGACGGAGGA 59.816 44.000 0.00 0.00 0.00 3.71
3558 3914 6.294899 CGTTCTTATATTATGGGACGGAGGAA 60.295 42.308 0.00 0.00 0.00 3.36
3559 3915 6.852420 TCTTATATTATGGGACGGAGGAAG 57.148 41.667 0.00 0.00 0.00 3.46
3560 3916 6.320518 TCTTATATTATGGGACGGAGGAAGT 58.679 40.000 0.00 0.00 0.00 3.01
3561 3917 7.472741 TCTTATATTATGGGACGGAGGAAGTA 58.527 38.462 0.00 0.00 0.00 2.24
3675 4033 1.141645 TTATCACGACGGTGTTGTGC 58.858 50.000 11.60 0.00 44.87 4.57
3802 4160 9.337091 ACACGTGTAAAATATTTATGCACTTTC 57.663 29.630 21.98 0.00 0.00 2.62
3871 4229 7.180322 TCAATTTGCATTCCCTATTTGCTTA 57.820 32.000 0.00 0.00 37.28 3.09
3918 4276 9.745018 TTATCCCATTGATCTCTCATATTTTCC 57.255 33.333 0.00 0.00 34.76 3.13
3953 4311 4.161189 TCAGGATCTGATGAAAGGACTGTC 59.839 45.833 0.00 0.00 35.39 3.51
3980 4338 3.367703 GCAATACAATTGCAGTCCAAGCT 60.368 43.478 17.41 0.00 44.34 3.74
4004 4362 6.422333 TGATATGCCTTTCAATGGTCTTACA 58.578 36.000 0.00 0.00 0.00 2.41
4198 4556 1.760029 GGTGAAAAGCAAAGGACCCAA 59.240 47.619 0.00 0.00 0.00 4.12
4606 4966 9.207868 AGTCCTCTTCTCTATAATGCTTTAAGT 57.792 33.333 0.00 0.00 0.00 2.24
4644 5005 2.897969 TCTGGAGACTGAAGGTTGTACC 59.102 50.000 0.00 0.00 35.13 3.34
4645 5006 2.632996 CTGGAGACTGAAGGTTGTACCA 59.367 50.000 0.00 0.00 41.95 3.25
4646 5007 3.042682 TGGAGACTGAAGGTTGTACCAA 58.957 45.455 0.00 0.00 41.95 3.67
4647 5008 3.456644 TGGAGACTGAAGGTTGTACCAAA 59.543 43.478 0.00 0.00 41.95 3.28
4648 5009 4.080243 TGGAGACTGAAGGTTGTACCAAAA 60.080 41.667 0.00 0.00 41.95 2.44
4651 5039 5.445964 AGACTGAAGGTTGTACCAAAATGT 58.554 37.500 0.00 0.00 41.95 2.71
4673 5061 9.807649 AATGTATATTCTTGAAGACCAAAATGC 57.192 29.630 0.00 0.00 33.76 3.56
4908 5296 2.132762 GTGATCGCCGGGTAAGTAATG 58.867 52.381 2.18 0.00 0.00 1.90
4909 5297 1.758280 TGATCGCCGGGTAAGTAATGT 59.242 47.619 2.18 0.00 0.00 2.71
4910 5298 2.132762 GATCGCCGGGTAAGTAATGTG 58.867 52.381 2.18 0.00 0.00 3.21
4911 5299 0.896923 TCGCCGGGTAAGTAATGTGT 59.103 50.000 2.18 0.00 0.00 3.72
4912 5300 1.135024 TCGCCGGGTAAGTAATGTGTC 60.135 52.381 2.18 0.00 0.00 3.67
4915 5303 2.612212 GCCGGGTAAGTAATGTGTCATG 59.388 50.000 2.18 0.00 0.00 3.07
4922 5322 6.238374 GGGTAAGTAATGTGTCATGTGTATGC 60.238 42.308 0.00 0.00 34.21 3.14
4926 5326 7.395190 AGTAATGTGTCATGTGTATGCAATT 57.605 32.000 0.00 0.00 34.21 2.32
5051 5451 0.478072 TTGGCCAGCTGAAGAAGGAA 59.522 50.000 17.39 0.00 0.00 3.36
5173 5618 7.658575 CCAAGATGAAACCAAATGAATTTCAGT 59.341 33.333 5.21 0.00 43.52 3.41
5179 5637 4.805219 ACCAAATGAATTTCAGTTACGCC 58.195 39.130 11.36 0.00 31.77 5.68
5299 5757 3.382832 CGGGCGACTTCCCTGACT 61.383 66.667 0.00 0.00 44.30 3.41
5448 5906 2.271944 ACCCTTACCAGTGAACTTGC 57.728 50.000 0.00 0.00 0.00 4.01
5539 5997 1.307097 GCAAGCATGAGAGACCCATC 58.693 55.000 0.00 0.00 0.00 3.51
5570 6028 0.108662 GTTATGCCTGCCCTTTGTGC 60.109 55.000 0.00 0.00 0.00 4.57
5579 6037 1.006220 CCCTTTGTGCGGGAAAAGC 60.006 57.895 0.00 0.00 44.90 3.51
5598 6056 4.379374 AGCGATAAACGTGTAACACAAC 57.621 40.909 0.00 0.00 44.60 3.32
5608 6066 3.061403 CGTGTAACACAACGTTCAGAGAC 60.061 47.826 0.00 0.00 39.14 3.36
5711 6170 4.951715 TGGTGGGAGAATTCAAGATGAATG 59.048 41.667 8.44 0.00 45.57 2.67
5927 6396 2.207590 GCTTAAAATCCCGTCCCGTAG 58.792 52.381 0.00 0.00 0.00 3.51
6088 6591 2.283298 CCATCCGTCCATCACAGAAAG 58.717 52.381 0.00 0.00 0.00 2.62
6089 6592 2.283298 CATCCGTCCATCACAGAAAGG 58.717 52.381 0.00 0.00 0.00 3.11
6092 6595 1.026718 CGTCCATCACAGAAAGGGGC 61.027 60.000 0.00 0.00 0.00 5.80
6114 6622 2.649531 AAAAATCCGTCCACCAGACA 57.350 45.000 0.00 0.00 46.69 3.41
6115 6623 2.185004 AAAATCCGTCCACCAGACAG 57.815 50.000 0.00 0.00 46.69 3.51
6116 6624 1.348064 AAATCCGTCCACCAGACAGA 58.652 50.000 0.00 0.00 46.69 3.41
6117 6625 0.608640 AATCCGTCCACCAGACAGAC 59.391 55.000 0.00 0.00 46.69 3.51
6273 6787 1.087771 GGACGCGGTCGATTGGAATT 61.088 55.000 12.47 0.00 39.41 2.17
6274 6788 0.026285 GACGCGGTCGATTGGAATTG 59.974 55.000 12.47 0.00 39.41 2.32
6275 6789 1.351707 CGCGGTCGATTGGAATTGG 59.648 57.895 0.00 0.00 38.10 3.16
6276 6790 1.087202 CGCGGTCGATTGGAATTGGA 61.087 55.000 0.00 0.00 38.10 3.53
6277 6791 1.091537 GCGGTCGATTGGAATTGGAA 58.908 50.000 0.00 0.00 0.00 3.53
6278 6792 1.676006 GCGGTCGATTGGAATTGGAAT 59.324 47.619 0.00 0.00 0.00 3.01
6409 6924 3.379445 GTGGAGTCGCCGAGGGAA 61.379 66.667 0.00 0.00 40.66 3.97
6410 6925 3.068691 TGGAGTCGCCGAGGGAAG 61.069 66.667 0.00 0.00 40.66 3.46
6411 6926 3.839432 GGAGTCGCCGAGGGAAGG 61.839 72.222 0.00 0.00 0.00 3.46
6467 6982 4.838486 CGAGGCGAGCGAGACCAC 62.838 72.222 0.00 0.00 0.00 4.16
6468 6983 3.749064 GAGGCGAGCGAGACCACA 61.749 66.667 0.00 0.00 0.00 4.17
6469 6984 3.973267 GAGGCGAGCGAGACCACAC 62.973 68.421 0.00 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 1.484653 TCCCATGTACAACCAGGATCG 59.515 52.381 0.00 0.00 0.00 3.69
46 47 5.930209 ATAATCCCATGTACAACCAGGAT 57.070 39.130 0.00 6.58 35.64 3.24
53 54 6.155910 ACCATGCAAAATAATCCCATGTACAA 59.844 34.615 0.00 0.00 33.29 2.41
60 61 3.625853 TCGACCATGCAAAATAATCCCA 58.374 40.909 0.00 0.00 0.00 4.37
64 65 2.942376 TCGCTCGACCATGCAAAATAAT 59.058 40.909 0.00 0.00 0.00 1.28
263 264 4.197750 GAGAGATTGCCTGATTGATGTGT 58.802 43.478 0.00 0.00 0.00 3.72
268 269 5.883685 ACTATGAGAGATTGCCTGATTGA 57.116 39.130 0.00 0.00 0.00 2.57
289 290 2.930682 GCGAGTCATCTTCAGGGTAAAC 59.069 50.000 0.00 0.00 0.00 2.01
310 311 4.605183 TCAGAAAGAAGGACTCCCTAGAG 58.395 47.826 0.00 0.00 43.48 2.43
370 371 1.439679 GTGTCCGGGTGAGAATTGAC 58.560 55.000 0.00 0.00 0.00 3.18
376 377 3.986006 GTGCGTGTCCGGGTGAGA 61.986 66.667 0.00 0.00 33.68 3.27
421 422 5.531287 GGGCGAATTCATATTTACTGAACCT 59.469 40.000 6.22 0.00 35.57 3.50
429 430 4.509970 CGACAGTGGGCGAATTCATATTTA 59.490 41.667 6.22 0.00 0.00 1.40
582 584 2.645797 AGGACCGTGGAATTTTAAGGGA 59.354 45.455 0.00 0.00 0.00 4.20
592 594 1.278127 GATGGAAGAAGGACCGTGGAA 59.722 52.381 0.00 0.00 0.00 3.53
661 663 2.203126 GATCAGGCCGCTTGAGGG 60.203 66.667 11.21 0.00 0.00 4.30
736 738 4.322198 GGTACACTCCGACAAATCCTACAA 60.322 45.833 0.00 0.00 0.00 2.41
752 754 2.488355 CGATCGCCACGGTACACT 59.512 61.111 0.26 0.00 0.00 3.55
806 808 2.069776 CAGGATGTGGTGGTGGAGT 58.930 57.895 0.00 0.00 0.00 3.85
867 869 1.943340 GGAACAGCCAAATCCGATCTC 59.057 52.381 0.00 0.00 36.34 2.75
906 908 2.464403 GGGCTAGGGCATCATGGGT 61.464 63.158 0.00 0.00 40.87 4.51
907 909 2.437897 GGGCTAGGGCATCATGGG 59.562 66.667 0.00 0.00 40.87 4.00
944 946 1.300697 CGCTAGGGTTCATACCGCC 60.301 63.158 0.00 0.00 46.04 6.13
968 970 3.735037 GAGTCGACGGGGGATTGGC 62.735 68.421 10.46 0.00 0.00 4.52
973 975 4.790962 CTCGGAGTCGACGGGGGA 62.791 72.222 10.46 5.75 40.88 4.81
980 982 4.689549 TTGGGGCCTCGGAGTCGA 62.690 66.667 0.84 0.00 43.86 4.20
982 984 2.683933 TCTTGGGGCCTCGGAGTC 60.684 66.667 0.84 0.00 0.00 3.36
983 985 3.003763 GTCTTGGGGCCTCGGAGT 61.004 66.667 0.84 0.00 0.00 3.85
984 986 3.003173 TGTCTTGGGGCCTCGGAG 61.003 66.667 0.84 0.00 0.00 4.63
985 987 3.319198 GTGTCTTGGGGCCTCGGA 61.319 66.667 0.84 0.00 0.00 4.55
986 988 4.410400 GGTGTCTTGGGGCCTCGG 62.410 72.222 0.84 0.00 0.00 4.63
999 1004 0.324943 CCTCCGGTGATCTTTGGTGT 59.675 55.000 4.76 0.00 0.00 4.16
1000 1005 0.392998 CCCTCCGGTGATCTTTGGTG 60.393 60.000 4.76 0.00 0.00 4.17
1001 1006 1.562672 CCCCTCCGGTGATCTTTGGT 61.563 60.000 4.76 0.00 0.00 3.67
1006 1013 1.233369 CTACCCCCTCCGGTGATCT 59.767 63.158 4.76 0.00 36.56 2.75
1011 1018 2.363406 CGTTCTACCCCCTCCGGT 60.363 66.667 0.00 0.00 40.13 5.28
1016 1023 1.312437 CCCTACCGTTCTACCCCCT 59.688 63.158 0.00 0.00 0.00 4.79
1021 1028 2.725221 TCTCTCCCCTACCGTTCTAC 57.275 55.000 0.00 0.00 0.00 2.59
1023 1030 1.358445 ACTTCTCTCCCCTACCGTTCT 59.642 52.381 0.00 0.00 0.00 3.01
1027 1034 1.682740 GAGACTTCTCTCCCCTACCG 58.317 60.000 0.00 0.00 37.56 4.02
1038 1045 0.396001 GGCCTCCCGTAGAGACTTCT 60.396 60.000 0.00 0.00 46.50 2.85
1041 1049 1.076632 CTGGCCTCCCGTAGAGACT 60.077 63.158 3.32 0.00 46.50 3.24
1101 1109 7.565789 GCTGAATGAAAACAATCAAGAAACGTC 60.566 37.037 0.00 0.00 32.06 4.34
1102 1110 6.198966 GCTGAATGAAAACAATCAAGAAACGT 59.801 34.615 0.00 0.00 32.06 3.99
1103 1111 6.346040 GGCTGAATGAAAACAATCAAGAAACG 60.346 38.462 0.00 0.00 32.06 3.60
1104 1112 6.073602 GGGCTGAATGAAAACAATCAAGAAAC 60.074 38.462 0.00 0.00 32.06 2.78
1105 1113 5.990996 GGGCTGAATGAAAACAATCAAGAAA 59.009 36.000 0.00 0.00 32.06 2.52
1106 1114 5.070180 TGGGCTGAATGAAAACAATCAAGAA 59.930 36.000 0.00 0.00 32.06 2.52
1107 1115 4.588106 TGGGCTGAATGAAAACAATCAAGA 59.412 37.500 0.00 0.00 32.06 3.02
1108 1116 4.885413 TGGGCTGAATGAAAACAATCAAG 58.115 39.130 0.00 0.00 32.06 3.02
1109 1117 4.588106 TCTGGGCTGAATGAAAACAATCAA 59.412 37.500 0.00 0.00 32.06 2.57
1110 1118 4.151121 TCTGGGCTGAATGAAAACAATCA 58.849 39.130 0.00 0.00 0.00 2.57
1111 1119 4.789012 TCTGGGCTGAATGAAAACAATC 57.211 40.909 0.00 0.00 0.00 2.67
1112 1120 4.773674 TCATCTGGGCTGAATGAAAACAAT 59.226 37.500 0.00 0.00 0.00 2.71
1113 1121 4.151121 TCATCTGGGCTGAATGAAAACAA 58.849 39.130 0.00 0.00 0.00 2.83
1114 1122 3.765381 TCATCTGGGCTGAATGAAAACA 58.235 40.909 0.00 0.00 0.00 2.83
1115 1123 4.789012 TTCATCTGGGCTGAATGAAAAC 57.211 40.909 6.53 0.00 0.00 2.43
1116 1124 5.539574 TCTTTTCATCTGGGCTGAATGAAAA 59.460 36.000 21.47 21.47 44.14 2.29
1117 1125 5.078949 TCTTTTCATCTGGGCTGAATGAAA 58.921 37.500 13.67 13.67 38.84 2.69
1118 1126 4.665451 TCTTTTCATCTGGGCTGAATGAA 58.335 39.130 5.33 5.33 32.94 2.57
1119 1127 4.305539 TCTTTTCATCTGGGCTGAATGA 57.694 40.909 0.00 0.00 32.94 2.57
1175 1183 2.628657 GTTCGGCCCATATGACTAGACT 59.371 50.000 3.65 0.00 0.00 3.24
1200 1208 7.201435 GCTCGGAATTATTGTTTGGAATGAAAC 60.201 37.037 0.00 0.00 36.53 2.78
1209 1234 3.425404 CGGTGCTCGGAATTATTGTTTG 58.575 45.455 0.00 0.00 34.75 2.93
1473 1808 2.663188 GCGATCTCCATCCACGGC 60.663 66.667 0.00 0.00 0.00 5.68
1575 1910 2.736995 CGGCGAAGGTTGCGAGAA 60.737 61.111 0.00 0.00 0.00 2.87
1613 1948 1.215423 CCCCTCCCAATCCTTCGATTT 59.785 52.381 0.00 0.00 36.54 2.17
1616 1951 0.030092 ATCCCCTCCCAATCCTTCGA 60.030 55.000 0.00 0.00 0.00 3.71
1617 1952 0.109342 CATCCCCTCCCAATCCTTCG 59.891 60.000 0.00 0.00 0.00 3.79
1618 1953 0.480252 CCATCCCCTCCCAATCCTTC 59.520 60.000 0.00 0.00 0.00 3.46
1811 2148 3.553904 ACGGACTAGTTAGACTCCCATC 58.446 50.000 0.00 0.00 0.00 3.51
1838 2175 2.115291 GCCCAGACCTTGAATCGGC 61.115 63.158 0.00 0.00 0.00 5.54
1839 2176 1.815421 CGCCCAGACCTTGAATCGG 60.815 63.158 0.00 0.00 0.00 4.18
1875 2212 1.684734 GAAGCCGAGGTACCCCTGA 60.685 63.158 8.74 0.00 42.86 3.86
1938 2275 2.431942 CAGACGCGCCTAAACGGT 60.432 61.111 5.73 0.00 34.25 4.83
1979 2334 0.106708 AACACCGCACAGTCACATCT 59.893 50.000 0.00 0.00 0.00 2.90
1980 2335 0.235665 CAACACCGCACAGTCACATC 59.764 55.000 0.00 0.00 0.00 3.06
1981 2336 0.179059 TCAACACCGCACAGTCACAT 60.179 50.000 0.00 0.00 0.00 3.21
1982 2337 1.087202 GTCAACACCGCACAGTCACA 61.087 55.000 0.00 0.00 0.00 3.58
1983 2338 1.641677 GTCAACACCGCACAGTCAC 59.358 57.895 0.00 0.00 0.00 3.67
1984 2339 1.880796 CGTCAACACCGCACAGTCA 60.881 57.895 0.00 0.00 0.00 3.41
1985 2340 2.594962 CCGTCAACACCGCACAGTC 61.595 63.158 0.00 0.00 0.00 3.51
2001 2356 1.531149 AGATTGCAACAGACGAAACCG 59.469 47.619 0.00 0.00 0.00 4.44
2091 2446 2.041620 AGCCCACATCATAACAAGGTGT 59.958 45.455 0.00 0.00 0.00 4.16
2153 2508 1.605710 AGCTCAAACATCACACACAGC 59.394 47.619 0.00 0.00 0.00 4.40
2178 2533 1.592400 GCAAACACAGCCACAAGCC 60.592 57.895 0.00 0.00 45.47 4.35
2187 2542 3.370366 GCTACTCAGATCTGCAAACACAG 59.630 47.826 18.36 10.48 39.12 3.66
2191 2546 3.305629 CGAAGCTACTCAGATCTGCAAAC 59.694 47.826 18.36 6.20 0.00 2.93
2261 2616 6.545666 TGCCACAGGGTAATCTATACATTTTG 59.454 38.462 0.00 0.00 36.17 2.44
2262 2617 6.668645 TGCCACAGGGTAATCTATACATTTT 58.331 36.000 0.00 0.00 36.17 1.82
2264 2619 5.904984 TGCCACAGGGTAATCTATACATT 57.095 39.130 0.00 0.00 36.17 2.71
2269 2624 5.103940 ACTTGAATGCCACAGGGTAATCTAT 60.104 40.000 0.00 0.00 36.17 1.98
2270 2625 4.227300 ACTTGAATGCCACAGGGTAATCTA 59.773 41.667 0.00 0.00 36.17 1.98
2273 2628 3.456380 ACTTGAATGCCACAGGGTAAT 57.544 42.857 0.00 0.00 36.17 1.89
2277 2632 4.806640 AATTTACTTGAATGCCACAGGG 57.193 40.909 0.00 0.00 37.18 4.45
2284 2639 4.993905 AGGCGGTAAATTTACTTGAATGC 58.006 39.130 23.89 17.52 34.16 3.56
2292 2647 4.251268 AGTGTGAGAGGCGGTAAATTTAC 58.749 43.478 18.30 18.30 0.00 2.01
2294 2649 3.418684 AGTGTGAGAGGCGGTAAATTT 57.581 42.857 0.00 0.00 0.00 1.82
2295 2650 4.251268 GTTAGTGTGAGAGGCGGTAAATT 58.749 43.478 0.00 0.00 0.00 1.82
2418 2773 9.712305 AGAGGACTTTATTATCATGATTTACCG 57.288 33.333 14.65 1.67 0.00 4.02
2760 3115 5.613358 AAGGCTTCAGTTTTTCGATGTAG 57.387 39.130 0.00 0.00 0.00 2.74
2817 3172 4.141620 ACAGAAGTCTATACCAGCAATGGG 60.142 45.833 0.00 0.00 0.00 4.00
2850 3205 9.513906 TTGTGATCTGTAAATCATAGGAAAACA 57.486 29.630 0.00 0.00 37.93 2.83
2855 3210 9.330063 GAACATTGTGATCTGTAAATCATAGGA 57.670 33.333 0.00 0.00 37.93 2.94
2884 3239 5.768980 TCAGGATGAAAGAAGATGAGGTT 57.231 39.130 0.00 0.00 45.97 3.50
3122 3477 6.869913 TGTTATAGAGAAACGTACCACCAAAG 59.130 38.462 0.00 0.00 0.00 2.77
3346 3701 7.599998 AGCTGATGTTTTCCAATCAACATAAAC 59.400 33.333 0.00 0.00 42.46 2.01
3479 3835 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
3480 3836 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
3481 3837 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
3482 3838 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
3483 3839 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
3484 3840 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
3485 3841 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
3486 3842 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
3509 3865 9.748708 ACGTTTTTGACACTACACTAGTATAAA 57.251 29.630 0.00 0.00 37.23 1.40
3510 3866 9.748708 AACGTTTTTGACACTACACTAGTATAA 57.251 29.630 0.00 0.00 37.23 0.98
3511 3867 9.398170 GAACGTTTTTGACACTACACTAGTATA 57.602 33.333 0.46 0.00 37.23 1.47
3512 3868 8.139989 AGAACGTTTTTGACACTACACTAGTAT 58.860 33.333 0.46 0.00 37.23 2.12
3513 3869 7.483307 AGAACGTTTTTGACACTACACTAGTA 58.517 34.615 0.46 0.00 37.23 1.82
3514 3870 6.335777 AGAACGTTTTTGACACTACACTAGT 58.664 36.000 0.46 0.00 40.28 2.57
3515 3871 6.823678 AGAACGTTTTTGACACTACACTAG 57.176 37.500 0.46 0.00 0.00 2.57
3516 3872 8.876275 ATAAGAACGTTTTTGACACTACACTA 57.124 30.769 13.87 0.00 0.00 2.74
3517 3873 7.781548 ATAAGAACGTTTTTGACACTACACT 57.218 32.000 13.87 0.00 0.00 3.55
3523 3879 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
3524 3880 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
3525 3881 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
3526 3882 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
3527 3883 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
3528 3884 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
3529 3885 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
3530 3886 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
3531 3887 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
3532 3888 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
3533 3889 5.184479 TCCTCCGTCCCATAATATAAGAACG 59.816 44.000 0.00 0.00 0.00 3.95
3534 3890 6.600882 TCCTCCGTCCCATAATATAAGAAC 57.399 41.667 0.00 0.00 0.00 3.01
3535 3891 6.785963 ACTTCCTCCGTCCCATAATATAAGAA 59.214 38.462 0.00 0.00 0.00 2.52
3536 3892 6.320518 ACTTCCTCCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
3537 3893 6.607004 ACTTCCTCCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
3538 3894 7.243824 ACTACTTCCTCCGTCCCATAATATAA 58.756 38.462 0.00 0.00 0.00 0.98
3539 3895 6.797707 ACTACTTCCTCCGTCCCATAATATA 58.202 40.000 0.00 0.00 0.00 0.86
3540 3896 5.652324 ACTACTTCCTCCGTCCCATAATAT 58.348 41.667 0.00 0.00 0.00 1.28
3541 3897 5.070823 ACTACTTCCTCCGTCCCATAATA 57.929 43.478 0.00 0.00 0.00 0.98
3542 3898 3.924922 ACTACTTCCTCCGTCCCATAAT 58.075 45.455 0.00 0.00 0.00 1.28
3543 3899 3.393426 ACTACTTCCTCCGTCCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
3544 3900 3.028850 CAACTACTTCCTCCGTCCCATA 58.971 50.000 0.00 0.00 0.00 2.74
3545 3901 1.831736 CAACTACTTCCTCCGTCCCAT 59.168 52.381 0.00 0.00 0.00 4.00
3546 3902 1.263356 CAACTACTTCCTCCGTCCCA 58.737 55.000 0.00 0.00 0.00 4.37
3547 3903 0.108281 GCAACTACTTCCTCCGTCCC 60.108 60.000 0.00 0.00 0.00 4.46
3548 3904 0.896226 AGCAACTACTTCCTCCGTCC 59.104 55.000 0.00 0.00 0.00 4.79
3549 3905 2.745515 AAGCAACTACTTCCTCCGTC 57.254 50.000 0.00 0.00 0.00 4.79
3550 3906 3.139077 CAAAAGCAACTACTTCCTCCGT 58.861 45.455 0.00 0.00 0.00 4.69
3551 3907 3.139077 ACAAAAGCAACTACTTCCTCCG 58.861 45.455 0.00 0.00 0.00 4.63
3552 3908 5.299531 AGAAACAAAAGCAACTACTTCCTCC 59.700 40.000 0.00 0.00 0.00 4.30
3553 3909 6.378710 AGAAACAAAAGCAACTACTTCCTC 57.621 37.500 0.00 0.00 0.00 3.71
3554 3910 7.502561 ACATAGAAACAAAAGCAACTACTTCCT 59.497 33.333 0.00 0.00 0.00 3.36
3555 3911 7.649057 ACATAGAAACAAAAGCAACTACTTCC 58.351 34.615 0.00 0.00 0.00 3.46
3556 3912 8.342634 TGACATAGAAACAAAAGCAACTACTTC 58.657 33.333 0.00 0.00 0.00 3.01
3557 3913 8.220755 TGACATAGAAACAAAAGCAACTACTT 57.779 30.769 0.00 0.00 0.00 2.24
3558 3914 7.520614 GCTGACATAGAAACAAAAGCAACTACT 60.521 37.037 0.00 0.00 0.00 2.57
3559 3915 6.578919 GCTGACATAGAAACAAAAGCAACTAC 59.421 38.462 0.00 0.00 0.00 2.73
3560 3916 6.262049 TGCTGACATAGAAACAAAAGCAACTA 59.738 34.615 0.00 0.00 36.54 2.24
3561 3917 5.067674 TGCTGACATAGAAACAAAAGCAACT 59.932 36.000 0.00 0.00 36.54 3.16
3675 4033 6.250819 CCATTGTATTTCAGCAAACTACGAG 58.749 40.000 0.00 0.00 0.00 4.18
3774 4132 7.812648 AGTGCATAAATATTTTACACGTGTGT 58.187 30.769 30.83 15.70 46.87 3.72
3802 4160 3.571401 AGCCACAAATCCTGTCTCAAAAG 59.429 43.478 0.00 0.00 35.47 2.27
3918 4276 0.471617 GATCCTGACTGATGTGGGGG 59.528 60.000 0.00 0.00 0.00 5.40
3953 4311 1.826720 ACTGCAATTGTATTGCCAGGG 59.173 47.619 18.60 10.39 44.32 4.45
3980 4338 6.422333 TGTAAGACCATTGAAAGGCATATCA 58.578 36.000 0.00 0.00 0.00 2.15
4004 4362 0.983467 GGAATGCACCCCCAAATGTT 59.017 50.000 0.00 0.00 0.00 2.71
4198 4556 5.790593 ACACCAGTGAAATCATAACTACGT 58.209 37.500 4.48 0.00 0.00 3.57
4439 4799 2.435372 AATCATGTGTGCCGGGTTAT 57.565 45.000 2.18 0.00 0.00 1.89
4617 4977 5.308237 ACAACCTTCAGTCTCCAGAAGTAAT 59.692 40.000 0.00 0.00 39.61 1.89
4647 5008 9.807649 GCATTTTGGTCTTCAAGAATATACATT 57.192 29.630 0.00 0.00 36.62 2.71
4648 5009 8.970020 TGCATTTTGGTCTTCAAGAATATACAT 58.030 29.630 0.00 0.00 36.62 2.29
4651 5039 8.461222 CACTGCATTTTGGTCTTCAAGAATATA 58.539 33.333 0.00 0.00 36.62 0.86
4908 5296 9.603298 CATATAAGAATTGCATACACATGACAC 57.397 33.333 0.00 0.00 33.67 3.67
4909 5297 8.785946 CCATATAAGAATTGCATACACATGACA 58.214 33.333 0.00 0.00 33.67 3.58
4910 5298 9.002600 TCCATATAAGAATTGCATACACATGAC 57.997 33.333 0.00 0.00 33.67 3.06
4911 5299 9.002600 GTCCATATAAGAATTGCATACACATGA 57.997 33.333 0.00 0.00 33.67 3.07
4912 5300 9.006839 AGTCCATATAAGAATTGCATACACATG 57.993 33.333 0.00 0.00 35.07 3.21
4915 5303 7.041167 TGCAGTCCATATAAGAATTGCATACAC 60.041 37.037 10.22 0.00 33.62 2.90
4922 5322 9.674824 GAAATTCTGCAGTCCATATAAGAATTG 57.325 33.333 14.67 0.00 41.24 2.32
4926 5326 8.985315 ATTGAAATTCTGCAGTCCATATAAGA 57.015 30.769 14.67 0.00 0.00 2.10
5051 5451 0.031917 TCCCCATCATTGCAGGCATT 60.032 50.000 0.00 0.00 0.00 3.56
5130 5530 2.552599 TGGGACGCTGTTTTGTATGA 57.447 45.000 0.00 0.00 0.00 2.15
5173 5618 2.984562 TGAATCAAGATGCAGGCGTAA 58.015 42.857 0.00 0.00 0.00 3.18
5179 5637 6.513180 AGGCAATTTATGAATCAAGATGCAG 58.487 36.000 6.27 0.00 33.14 4.41
5223 5681 1.078918 CTCAGGCGTCAATGGAGCA 60.079 57.895 0.00 0.00 0.00 4.26
5295 5753 1.134128 TGCTTGAAGTGCTCCAAGTCA 60.134 47.619 0.46 0.00 41.21 3.41
5299 5757 0.183492 ACCTGCTTGAAGTGCTCCAA 59.817 50.000 0.00 0.00 0.00 3.53
5539 5997 0.526096 GGCATAACCTTGCACATGCG 60.526 55.000 0.00 0.00 43.72 4.73
5564 6022 1.524848 TATCGCTTTTCCCGCACAAA 58.475 45.000 0.00 0.00 0.00 2.83
5570 6028 1.461897 ACACGTTTATCGCTTTTCCCG 59.538 47.619 0.00 0.00 44.19 5.14
5579 6037 4.359041 ACGTTGTGTTACACGTTTATCG 57.641 40.909 11.07 10.50 46.00 2.92
5598 6056 3.000080 GCCAACGCGTCTCTGAACG 62.000 63.158 14.44 0.00 45.31 3.95
5608 6066 0.310854 AAAAGGAAAGAGCCAACGCG 59.689 50.000 3.53 3.53 41.18 6.01
5711 6170 3.705072 ACACAAGTCCTACTATAGTGCCC 59.295 47.826 15.90 1.11 32.43 5.36
5845 6314 1.378514 CATGGTAAGCAGGCGGGTT 60.379 57.895 7.33 7.33 40.94 4.11
5857 6326 0.388006 CGACACAGCGACACATGGTA 60.388 55.000 0.00 0.00 0.00 3.25
5884 6353 2.205074 ACGATTCGTGGATGAGATTGC 58.795 47.619 11.56 0.00 39.18 3.56
6359 6874 0.171455 TTTGTGTGTTTGGTCGGCAC 59.829 50.000 0.00 0.00 0.00 5.01
6360 6875 0.171455 GTTTGTGTGTTTGGTCGGCA 59.829 50.000 0.00 0.00 0.00 5.69
6361 6876 0.171455 TGTTTGTGTGTTTGGTCGGC 59.829 50.000 0.00 0.00 0.00 5.54
6362 6877 2.525055 CTTGTTTGTGTGTTTGGTCGG 58.475 47.619 0.00 0.00 0.00 4.79
6363 6878 2.525055 CCTTGTTTGTGTGTTTGGTCG 58.475 47.619 0.00 0.00 0.00 4.79
6364 6879 2.267426 GCCTTGTTTGTGTGTTTGGTC 58.733 47.619 0.00 0.00 0.00 4.02
6365 6880 1.403514 CGCCTTGTTTGTGTGTTTGGT 60.404 47.619 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.