Multiple sequence alignment - TraesCS6A01G180600

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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 TraesCS6A01G180600 chr6A 100.000 7579 0 0 1 7579 204745755 204738177 0.000000e+00 13996.0
1 TraesCS6A01G180600 chr6D 93.427 3271 131 37 3808 7038 143644676 143647902 0.000000e+00 4772.0
2 TraesCS6A01G180600 chr6D 93.591 2668 99 21 789 3420 143641396 143644027 0.000000e+00 3914.0
3 TraesCS6A01G180600 chr6D 92.091 746 48 8 3 739 422576601 422575858 0.000000e+00 1040.0
4 TraesCS6A01G180600 chr6D 89.355 620 48 13 181 789 413015462 413014850 0.000000e+00 763.0
5 TraesCS6A01G180600 chr6D 92.407 540 31 7 1 537 24386702 24386170 0.000000e+00 761.0
6 TraesCS6A01G180600 chr6D 87.884 619 57 12 181 789 457629276 457629886 0.000000e+00 712.0
7 TraesCS6A01G180600 chr6D 91.799 378 22 4 3405 3781 143644234 143644603 1.130000e-142 518.0
8 TraesCS6A01G180600 chr6D 95.349 43 0 2 4703 4745 376907717 376907757 4.910000e-07 67.6
9 TraesCS6A01G180600 chr6D 100.000 36 0 0 4710 4745 376915715 376915750 4.910000e-07 67.6
10 TraesCS6A01G180600 chr6B 92.999 2928 109 38 789 3671 255665306 255668182 0.000000e+00 4183.0
11 TraesCS6A01G180600 chr6B 91.483 2090 94 35 4761 6846 255671297 255673306 0.000000e+00 2796.0
12 TraesCS6A01G180600 chr6B 87.189 804 43 21 3780 4549 255670395 255671172 0.000000e+00 859.0
13 TraesCS6A01G180600 chr6B 92.661 109 7 1 4586 4693 255671178 255671286 1.020000e-33 156.0
14 TraesCS6A01G180600 chr3D 92.211 796 47 9 3 790 506168598 506169386 0.000000e+00 1112.0
15 TraesCS6A01G180600 chr3D 80.000 205 29 9 2713 2911 459465100 459465298 2.850000e-29 141.0
16 TraesCS6A01G180600 chr4A 92.539 764 45 8 1 752 640915390 640914627 0.000000e+00 1085.0
17 TraesCS6A01G180600 chr4A 83.688 141 22 1 65 204 49206000 49206140 1.720000e-26 132.0
18 TraesCS6A01G180600 chr4A 94.118 68 4 0 4 71 606589278 606589345 3.740000e-18 104.0
19 TraesCS6A01G180600 chr4A 100.000 37 0 0 4709 4745 718955926 718955890 1.360000e-07 69.4
20 TraesCS6A01G180600 chr2D 94.796 538 28 0 7039 7576 106365198 106365735 0.000000e+00 839.0
21 TraesCS6A01G180600 chr2D 95.455 44 2 0 4702 4745 42718051 42718094 3.790000e-08 71.3
22 TraesCS6A01G180600 chr2D 100.000 37 0 0 4709 4745 8087051 8087015 1.360000e-07 69.4
23 TraesCS6A01G180600 chr5A 94.195 534 30 1 7039 7572 14259542 14260074 0.000000e+00 813.0
24 TraesCS6A01G180600 chr5A 82.998 547 77 13 7038 7576 10913628 10914166 1.480000e-131 481.0
25 TraesCS6A01G180600 chr5A 82.998 547 77 13 7039 7576 685434280 685434819 1.480000e-131 481.0
26 TraesCS6A01G180600 chr5A 90.426 282 27 0 2629 2910 427067764 427068045 9.290000e-99 372.0
27 TraesCS6A01G180600 chr5A 94.012 167 10 0 1711 1877 427066704 427066870 3.510000e-63 254.0
28 TraesCS6A01G180600 chr5A 74.928 690 104 46 1000 1635 427065910 427066584 1.260000e-62 252.0
29 TraesCS6A01G180600 chr5A 77.340 406 83 4 2907 3303 427068373 427068778 1.640000e-56 231.0
30 TraesCS6A01G180600 chr7D 88.728 621 49 14 181 789 514347530 514346919 0.000000e+00 739.0
31 TraesCS6A01G180600 chr7D 86.613 620 61 15 181 787 569416686 569416076 0.000000e+00 665.0
32 TraesCS6A01G180600 chr7D 95.789 380 15 1 7201 7579 194497142 194496763 5.030000e-171 612.0
33 TraesCS6A01G180600 chr7D 93.333 165 11 0 7039 7203 194497146 194497310 2.110000e-60 244.0
34 TraesCS6A01G180600 chr7D 94.366 71 4 0 1 71 23558264 23558194 8.040000e-20 110.0
35 TraesCS6A01G180600 chr7D 100.000 37 0 0 4709 4745 627234079 627234115 1.360000e-07 69.4
36 TraesCS6A01G180600 chr2A 86.907 611 62 14 188 789 753473675 753473074 0.000000e+00 669.0
37 TraesCS6A01G180600 chr2A 83.846 260 18 3 3 262 44087783 44087548 7.650000e-55 226.0
38 TraesCS6A01G180600 chr5D 95.641 390 17 0 7187 7576 510920420 510920809 1.800000e-175 627.0
39 TraesCS6A01G180600 chr5D 91.166 283 23 2 2629 2910 329617526 329617245 4.290000e-102 383.0
40 TraesCS6A01G180600 chr5D 93.413 167 11 0 1711 1877 329618623 329618457 1.630000e-61 248.0
41 TraesCS6A01G180600 chr5D 93.960 149 8 1 7038 7185 510920226 510920374 2.750000e-54 224.0
42 TraesCS6A01G180600 chr5D 76.790 405 83 8 2910 3304 329616842 329616439 4.610000e-52 217.0
43 TraesCS6A01G180600 chr5D 78.521 284 38 17 1000 1273 329619410 329619140 1.690000e-36 165.0
44 TraesCS6A01G180600 chr5B 82.278 553 66 21 7039 7579 22044317 22043785 4.170000e-122 449.0
45 TraesCS6A01G180600 chr5B 91.135 282 25 0 2629 2910 382777031 382776750 4.290000e-102 383.0
46 TraesCS6A01G180600 chr5B 94.611 167 9 0 1711 1877 382778148 382777982 7.540000e-65 259.0
47 TraesCS6A01G180600 chr5B 76.647 501 73 26 1178 1638 382778772 382778276 3.540000e-58 237.0
48 TraesCS6A01G180600 chr5B 77.284 405 83 4 2910 3305 382776167 382775763 5.920000e-56 230.0
49 TraesCS6A01G180600 chr5B 92.000 125 9 1 2233 2356 382777506 382777382 2.810000e-39 174.0
50 TraesCS6A01G180600 chr3B 90.952 210 17 2 7244 7452 807541985 807542193 1.610000e-71 281.0
51 TraesCS6A01G180600 chr3B 79.512 205 30 9 2713 2911 607381914 607382112 1.330000e-27 135.0
52 TraesCS6A01G180600 chr3B 92.105 38 3 0 6261 6298 607384049 607384086 4.000000e-03 54.7
53 TraesCS6A01G180600 chr2B 83.969 262 17 10 1 262 752853204 752852968 2.130000e-55 228.0
54 TraesCS6A01G180600 chr2B 84.173 139 20 2 68 204 711870175 711870037 4.770000e-27 134.0
55 TraesCS6A01G180600 chr2B 86.667 105 14 0 90 194 507926795 507926691 4.800000e-22 117.0
56 TraesCS6A01G180600 chr3A 79.147 211 32 9 2713 2917 601558984 601558780 1.330000e-27 135.0
57 TraesCS6A01G180600 chr7A 94.030 67 4 0 4 70 85598879 85598945 1.350000e-17 102.0
58 TraesCS6A01G180600 chrUn 97.619 42 1 0 4710 4751 325244142 325244101 1.050000e-08 73.1
59 TraesCS6A01G180600 chrUn 97.619 42 1 0 4710 4751 338391327 338391286 1.050000e-08 73.1
60 TraesCS6A01G180600 chr7B 93.333 45 3 0 7035 7079 215968702 215968658 4.910000e-07 67.6


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 TraesCS6A01G180600 chr6A 204738177 204745755 7578 True 13996.00 13996 100.0000 1 7579 1 chr6A.!!$R1 7578
1 TraesCS6A01G180600 chr6D 143641396 143647902 6506 False 3068.00 4772 92.9390 789 7038 3 chr6D.!!$F4 6249
2 TraesCS6A01G180600 chr6D 422575858 422576601 743 True 1040.00 1040 92.0910 3 739 1 chr6D.!!$R3 736
3 TraesCS6A01G180600 chr6D 413014850 413015462 612 True 763.00 763 89.3550 181 789 1 chr6D.!!$R2 608
4 TraesCS6A01G180600 chr6D 24386170 24386702 532 True 761.00 761 92.4070 1 537 1 chr6D.!!$R1 536
5 TraesCS6A01G180600 chr6D 457629276 457629886 610 False 712.00 712 87.8840 181 789 1 chr6D.!!$F3 608
6 TraesCS6A01G180600 chr6B 255665306 255673306 8000 False 1998.50 4183 91.0830 789 6846 4 chr6B.!!$F1 6057
7 TraesCS6A01G180600 chr3D 506168598 506169386 788 False 1112.00 1112 92.2110 3 790 1 chr3D.!!$F2 787
8 TraesCS6A01G180600 chr4A 640914627 640915390 763 True 1085.00 1085 92.5390 1 752 1 chr4A.!!$R1 751
9 TraesCS6A01G180600 chr2D 106365198 106365735 537 False 839.00 839 94.7960 7039 7576 1 chr2D.!!$F2 537
10 TraesCS6A01G180600 chr5A 14259542 14260074 532 False 813.00 813 94.1950 7039 7572 1 chr5A.!!$F2 533
11 TraesCS6A01G180600 chr5A 10913628 10914166 538 False 481.00 481 82.9980 7038 7576 1 chr5A.!!$F1 538
12 TraesCS6A01G180600 chr5A 685434280 685434819 539 False 481.00 481 82.9980 7039 7576 1 chr5A.!!$F3 537
13 TraesCS6A01G180600 chr5A 427065910 427068778 2868 False 277.25 372 84.1765 1000 3303 4 chr5A.!!$F4 2303
14 TraesCS6A01G180600 chr7D 514346919 514347530 611 True 739.00 739 88.7280 181 789 1 chr7D.!!$R3 608
15 TraesCS6A01G180600 chr7D 569416076 569416686 610 True 665.00 665 86.6130 181 787 1 chr7D.!!$R4 606
16 TraesCS6A01G180600 chr2A 753473074 753473675 601 True 669.00 669 86.9070 188 789 1 chr2A.!!$R2 601
17 TraesCS6A01G180600 chr5D 510920226 510920809 583 False 425.50 627 94.8005 7038 7576 2 chr5D.!!$F1 538
18 TraesCS6A01G180600 chr5D 329616439 329619410 2971 True 253.25 383 84.9725 1000 3304 4 chr5D.!!$R1 2304
19 TraesCS6A01G180600 chr5B 22043785 22044317 532 True 449.00 449 82.2780 7039 7579 1 chr5B.!!$R1 540
20 TraesCS6A01G180600 chr5B 382775763 382778772 3009 True 256.60 383 86.3354 1178 3305 5 chr5B.!!$R2 2127

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
636 653 0.462047 CTGTTATGGCCCTCGTCCAC 60.462 60.0 0.00 0.0 36.26 4.02 F
2026 2241 0.825840 GGAGGATCACGAGGGAGGAG 60.826 65.0 0.00 0.0 36.25 3.69 F
2193 2411 0.184933 TTACTGCTTGGTTGCCCAGT 59.815 50.0 0.00 0.0 43.15 4.00 F
2194 2412 1.060729 TACTGCTTGGTTGCCCAGTA 58.939 50.0 0.00 0.0 43.15 2.74 F
2195 2413 0.184933 ACTGCTTGGTTGCCCAGTAA 59.815 50.0 0.00 0.0 43.15 2.24 F
3621 4951 0.745845 CTTGAGATCCAAGCCACCCG 60.746 60.0 9.94 0.0 44.90 5.28 F
4935 8431 0.615331 AGGCGAACACATCCTCATGT 59.385 50.0 0.00 0.0 44.72 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2131 2349 0.959372 AGGCATCAGCAGTTCAGCAC 60.959 55.000 0.0 0.0 44.61 4.40 R
3620 4950 0.179174 GGAAATAAGTTGCCGGTGCG 60.179 55.000 1.9 0.0 41.78 5.34 R
3621 4951 1.173913 AGGAAATAAGTTGCCGGTGC 58.826 50.000 1.9 0.0 38.26 5.01 R
3877 7321 1.409427 CGGGATTCTGTGAGTAGGGAC 59.591 57.143 0.0 0.0 0.00 4.46 R
4096 7563 3.594603 ATTCTGGTTGATTCGTCTCGT 57.405 42.857 0.0 0.0 0.00 4.18 R
5419 8915 0.172127 TGCAGCAGAGACGAGACATC 59.828 55.000 0.0 0.0 0.00 3.06 R
6661 10169 0.251341 AAATGGCGAAGAGGGCAAGT 60.251 50.000 0.0 0.0 46.16 3.16 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
51 52 7.939039 AGTGAAATATGAAACTGACTGAAAGGA 59.061 33.333 0.00 0.00 39.30 3.36
167 171 4.753107 GGTGAAGTATGTTTTCTCAACCGA 59.247 41.667 0.00 0.00 0.00 4.69
228 232 6.578023 TCCATACACATGACACATATTTCGA 58.422 36.000 0.00 0.00 33.67 3.71
311 316 6.439599 TGTAAATGGGTGTAATGTGTTTTCG 58.560 36.000 0.00 0.00 0.00 3.46
316 321 4.585162 TGGGTGTAATGTGTTTTCGGAATT 59.415 37.500 0.00 0.00 0.00 2.17
328 333 8.622157 TGTGTTTTCGGAATTTAGTGAAATGTA 58.378 29.630 0.00 0.00 35.38 2.29
426 432 6.263617 ACGGTTAAATTCAAACTAGCCAAAGA 59.736 34.615 0.00 0.00 0.00 2.52
622 639 4.203226 TGACATGACAAAAGGTGCTGTTA 58.797 39.130 0.00 0.00 0.00 2.41
636 653 0.462047 CTGTTATGGCCCTCGTCCAC 60.462 60.000 0.00 0.00 36.26 4.02
705 726 4.803329 AATAAAGCATGATGGGTCTCCT 57.197 40.909 0.00 0.00 0.00 3.69
729 750 3.686241 CCAGATCAATCTCAAAGCAACGA 59.314 43.478 0.00 0.00 34.22 3.85
735 756 5.938322 TCAATCTCAAAGCAACGATTAACC 58.062 37.500 0.00 0.00 0.00 2.85
802 823 6.823678 AACTTTTTCGAGCATATACCTACG 57.176 37.500 0.00 0.00 0.00 3.51
860 882 3.758425 ACCACGCCAGGTAAAATAAACT 58.242 40.909 0.00 0.00 40.98 2.66
861 883 4.909001 ACCACGCCAGGTAAAATAAACTA 58.091 39.130 0.00 0.00 40.98 2.24
862 884 4.696877 ACCACGCCAGGTAAAATAAACTAC 59.303 41.667 0.00 0.00 40.98 2.73
922 944 2.839098 AGCCCACAGGTGAACCAG 59.161 61.111 1.62 0.00 38.89 4.00
1520 1605 2.989639 CCTCCGGTTCATCAGCCA 59.010 61.111 0.00 0.00 0.00 4.75
1664 1752 1.671054 ATGCCACTTCGGTTCACGG 60.671 57.895 0.00 0.00 44.45 4.94
1684 1772 3.774959 ATGATCGCGAGTCGGCACC 62.775 63.158 16.66 0.00 39.05 5.01
1978 2134 2.293955 GCTGCCATTGCCAAAACAAATT 59.706 40.909 0.00 0.00 36.33 1.82
1979 2135 3.243468 GCTGCCATTGCCAAAACAAATTT 60.243 39.130 0.00 0.00 36.33 1.82
1980 2136 4.538917 CTGCCATTGCCAAAACAAATTTC 58.461 39.130 0.00 0.00 36.33 2.17
1981 2137 4.205587 TGCCATTGCCAAAACAAATTTCT 58.794 34.783 0.00 0.00 36.33 2.52
2026 2241 0.825840 GGAGGATCACGAGGGAGGAG 60.826 65.000 0.00 0.00 36.25 3.69
2077 2292 8.258708 ACTAAAACGAATCTGCTCCTTATTACT 58.741 33.333 0.00 0.00 0.00 2.24
2099 2317 7.601705 ACTGTACCACTAGTAGTTTAAACCA 57.398 36.000 14.72 0.00 0.00 3.67
2184 2402 2.545526 CTGCCGACATATTACTGCTTGG 59.454 50.000 0.00 0.00 0.00 3.61
2187 2405 3.242739 GCCGACATATTACTGCTTGGTTG 60.243 47.826 0.00 0.00 0.00 3.77
2189 2407 3.242739 CGACATATTACTGCTTGGTTGCC 60.243 47.826 0.00 0.00 0.00 4.52
2190 2408 3.023832 ACATATTACTGCTTGGTTGCCC 58.976 45.455 0.00 0.00 0.00 5.36
2191 2409 2.889170 TATTACTGCTTGGTTGCCCA 57.111 45.000 0.00 0.00 39.65 5.36
2192 2410 1.549203 ATTACTGCTTGGTTGCCCAG 58.451 50.000 0.00 0.00 43.15 4.45
2193 2411 0.184933 TTACTGCTTGGTTGCCCAGT 59.815 50.000 0.00 0.00 43.15 4.00
2194 2412 1.060729 TACTGCTTGGTTGCCCAGTA 58.939 50.000 0.00 0.00 43.15 2.74
2195 2413 0.184933 ACTGCTTGGTTGCCCAGTAA 59.815 50.000 0.00 0.00 43.15 2.24
2196 2414 1.203050 ACTGCTTGGTTGCCCAGTAAT 60.203 47.619 0.00 0.00 43.15 1.89
2197 2415 1.203052 CTGCTTGGTTGCCCAGTAATG 59.797 52.381 0.00 0.00 43.15 1.90
2199 2417 1.474077 GCTTGGTTGCCCAGTAATGAG 59.526 52.381 0.00 0.00 43.15 2.90
2200 2418 2.879756 GCTTGGTTGCCCAGTAATGAGA 60.880 50.000 0.00 0.00 43.15 3.27
2202 2420 3.737559 TGGTTGCCCAGTAATGAGATT 57.262 42.857 0.00 0.00 35.17 2.40
2203 2421 4.046286 TGGTTGCCCAGTAATGAGATTT 57.954 40.909 0.00 0.00 35.17 2.17
2204 2422 3.763360 TGGTTGCCCAGTAATGAGATTTG 59.237 43.478 0.00 0.00 35.17 2.32
2205 2423 4.016444 GGTTGCCCAGTAATGAGATTTGA 58.984 43.478 0.00 0.00 0.00 2.69
2206 2424 4.646492 GGTTGCCCAGTAATGAGATTTGAT 59.354 41.667 0.00 0.00 0.00 2.57
2275 2640 2.095252 GTCGGCGAACAAGCTCTCC 61.095 63.158 12.92 0.00 37.29 3.71
2320 2685 2.175621 CGCGCTGCTCATCATGGAA 61.176 57.895 5.56 0.00 0.00 3.53
2736 3209 4.487412 CAGTACCGCCGGTCCGTC 62.487 72.222 14.44 2.00 37.09 4.79
2811 3284 1.154093 CAAGCTCAACATGGCGCTG 60.154 57.895 7.64 0.00 32.22 5.18
3336 4431 1.697982 ACCACCACTAGTTCCTTCACC 59.302 52.381 0.00 0.00 0.00 4.02
3345 4440 5.927115 CACTAGTTCCTTCACCTTTCTGTAC 59.073 44.000 0.00 0.00 0.00 2.90
3351 4451 5.751586 TCCTTCACCTTTCTGTACACTTTT 58.248 37.500 0.00 0.00 0.00 2.27
3378 4486 4.691860 ATCTTCACTGCATTGTTACTGC 57.308 40.909 3.77 0.00 40.10 4.40
3379 4487 3.475575 TCTTCACTGCATTGTTACTGCA 58.524 40.909 3.77 0.00 46.82 4.41
3461 4791 9.221775 CTAATTTTATTTCATGACGCTAACACC 57.778 33.333 0.00 0.00 0.00 4.16
3493 4823 2.483876 GGCCTTCCAAAAGAAAAGCAC 58.516 47.619 0.00 0.00 36.15 4.40
3588 4918 6.970613 GGAAAGACAATGTAGTTCAAACGTTT 59.029 34.615 7.96 7.96 0.00 3.60
3620 4950 3.181526 CTTGAGATCCAAGCCACCC 57.818 57.895 9.94 0.00 44.90 4.61
3621 4951 0.745845 CTTGAGATCCAAGCCACCCG 60.746 60.000 9.94 0.00 44.90 5.28
3622 4952 2.514824 GAGATCCAAGCCACCCGC 60.515 66.667 0.00 0.00 37.98 6.13
3623 4953 3.329542 GAGATCCAAGCCACCCGCA 62.330 63.158 0.00 0.00 41.38 5.69
3624 4954 3.134127 GATCCAAGCCACCCGCAC 61.134 66.667 0.00 0.00 41.38 5.34
3625 4955 4.740822 ATCCAAGCCACCCGCACC 62.741 66.667 0.00 0.00 41.38 5.01
3657 4987 5.616488 TTTCCTTTACGTGCTTTGGATAC 57.384 39.130 0.00 0.00 0.00 2.24
3743 7134 6.595326 CAGCTGAGAACATTAATGTCCACTTA 59.405 38.462 21.02 15.00 40.80 2.24
3781 7173 6.344500 CATGTCCATCCAATATAGGTAGAGC 58.656 44.000 0.00 0.00 0.00 4.09
3783 7175 5.481824 TGTCCATCCAATATAGGTAGAGCAG 59.518 44.000 0.00 0.00 0.00 4.24
3785 7177 5.481824 TCCATCCAATATAGGTAGAGCAGTG 59.518 44.000 0.00 0.00 0.00 3.66
3786 7178 5.481824 CCATCCAATATAGGTAGAGCAGTGA 59.518 44.000 0.00 0.00 0.00 3.41
3787 7179 6.350864 CCATCCAATATAGGTAGAGCAGTGAG 60.351 46.154 0.00 0.00 0.00 3.51
3788 7180 5.706447 TCCAATATAGGTAGAGCAGTGAGT 58.294 41.667 0.00 0.00 0.00 3.41
3789 7181 6.136857 TCCAATATAGGTAGAGCAGTGAGTT 58.863 40.000 0.00 0.00 0.00 3.01
3790 7182 7.295340 TCCAATATAGGTAGAGCAGTGAGTTA 58.705 38.462 0.00 0.00 0.00 2.24
3795 7187 3.131933 AGGTAGAGCAGTGAGTTATGCAG 59.868 47.826 0.00 0.00 45.01 4.41
3797 7189 3.969287 AGAGCAGTGAGTTATGCAGAA 57.031 42.857 0.00 0.00 45.01 3.02
3798 7190 4.484537 AGAGCAGTGAGTTATGCAGAAT 57.515 40.909 0.00 0.00 45.01 2.40
3799 7191 5.604758 AGAGCAGTGAGTTATGCAGAATA 57.395 39.130 0.00 0.00 45.01 1.75
3800 7192 6.172136 AGAGCAGTGAGTTATGCAGAATAT 57.828 37.500 0.00 0.00 45.01 1.28
3801 7193 5.990386 AGAGCAGTGAGTTATGCAGAATATG 59.010 40.000 0.00 0.00 45.01 1.78
3803 7195 6.820335 AGCAGTGAGTTATGCAGAATATGTA 58.180 36.000 0.00 0.00 45.01 2.29
3804 7196 7.448420 AGCAGTGAGTTATGCAGAATATGTAT 58.552 34.615 0.00 0.00 45.01 2.29
3805 7197 8.588472 AGCAGTGAGTTATGCAGAATATGTATA 58.412 33.333 0.00 0.00 45.01 1.47
3877 7321 2.023318 CGTACGTGAGGCTCCCTAG 58.977 63.158 12.86 3.14 31.76 3.02
3895 7339 3.892588 CCTAGTCCCTACTCACAGAATCC 59.107 52.174 0.00 0.00 37.15 3.01
3900 7344 1.471676 CCTACTCACAGAATCCCGTGC 60.472 57.143 0.00 0.00 33.03 5.34
3906 7350 2.436646 AGAATCCCGTGCTTGGCG 60.437 61.111 0.00 0.00 0.00 5.69
4096 7563 4.889856 CCCGTGCGCCGATGATGA 62.890 66.667 17.96 0.00 39.56 2.92
4150 7617 1.449601 CCACCACCGTACCATCAGC 60.450 63.158 0.00 0.00 0.00 4.26
4152 7619 1.019278 CACCACCGTACCATCAGCAC 61.019 60.000 0.00 0.00 0.00 4.40
4159 7634 1.134699 CGTACCATCAGCACTCACCAT 60.135 52.381 0.00 0.00 0.00 3.55
4160 7635 2.283298 GTACCATCAGCACTCACCATG 58.717 52.381 0.00 0.00 0.00 3.66
4161 7636 0.679002 ACCATCAGCACTCACCATGC 60.679 55.000 0.00 0.00 43.74 4.06
4187 7665 6.162777 GCTTATCTCAGATACAATGGACCTC 58.837 44.000 0.00 0.00 0.00 3.85
4191 7669 5.462240 TCTCAGATACAATGGACCTCTGAT 58.538 41.667 8.79 0.00 40.94 2.90
4192 7670 6.614657 TCTCAGATACAATGGACCTCTGATA 58.385 40.000 8.79 1.09 40.94 2.15
4193 7671 6.491745 TCTCAGATACAATGGACCTCTGATAC 59.508 42.308 8.79 0.00 40.94 2.24
4194 7672 6.136155 TCAGATACAATGGACCTCTGATACA 58.864 40.000 5.07 0.00 37.89 2.29
4195 7673 6.784473 TCAGATACAATGGACCTCTGATACAT 59.216 38.462 5.07 0.00 37.89 2.29
4196 7674 7.950124 TCAGATACAATGGACCTCTGATACATA 59.050 37.037 5.07 0.00 37.89 2.29
4197 7675 8.031864 CAGATACAATGGACCTCTGATACATAC 58.968 40.741 0.84 0.00 36.32 2.39
4198 7676 7.730332 AGATACAATGGACCTCTGATACATACA 59.270 37.037 0.00 0.00 0.00 2.29
4199 7677 6.166984 ACAATGGACCTCTGATACATACAG 57.833 41.667 0.00 0.00 36.80 2.74
4200 7678 5.663106 ACAATGGACCTCTGATACATACAGT 59.337 40.000 0.00 0.00 36.81 3.55
4202 7680 7.014711 ACAATGGACCTCTGATACATACAGTAG 59.985 40.741 0.00 0.00 35.85 2.57
4203 7681 6.262056 TGGACCTCTGATACATACAGTAGA 57.738 41.667 0.00 0.00 35.85 2.59
4204 7682 6.669631 TGGACCTCTGATACATACAGTAGAA 58.330 40.000 0.00 0.00 35.85 2.10
4205 7683 6.546403 TGGACCTCTGATACATACAGTAGAAC 59.454 42.308 0.00 0.00 35.85 3.01
4206 7684 6.773685 GGACCTCTGATACATACAGTAGAACT 59.226 42.308 0.00 0.00 35.85 3.01
4248 7726 3.629398 CCTGCCTGTCAAGTGATTTATCC 59.371 47.826 0.00 0.00 0.00 2.59
4392 7874 2.181975 TCCTCAAGGTAAGGTAACCGG 58.818 52.381 0.00 0.00 44.77 5.28
4444 7929 9.729023 TGAACGCCAAACATTAATATTAATCAG 57.271 29.630 16.25 9.98 31.28 2.90
4534 8023 6.825213 TGATTAGGTCTTGTGATCCATTTCTG 59.175 38.462 0.00 0.00 0.00 3.02
4555 8044 1.676615 CCCTGCCATGCCAAATCAAAC 60.677 52.381 0.00 0.00 0.00 2.93
4579 8068 5.051641 CGGAAGCACTAAGAATGATACGAAC 60.052 44.000 0.00 0.00 0.00 3.95
4705 8195 2.440817 GGTCATGGGGGTAGGTCCG 61.441 68.421 0.00 0.00 37.00 4.79
4841 8336 1.629043 AACTGAGTAACTGGCCGAGA 58.371 50.000 8.91 0.00 0.00 4.04
4906 8402 2.922740 TTTCCTTACCAGCGTGAAGT 57.077 45.000 0.00 0.00 0.00 3.01
4920 8416 3.241995 GCGTGAAGTAATGAAACTAGGCG 60.242 47.826 0.00 0.00 0.00 5.52
4928 8424 4.946784 AATGAAACTAGGCGAACACATC 57.053 40.909 0.00 0.00 0.00 3.06
4935 8431 0.615331 AGGCGAACACATCCTCATGT 59.385 50.000 0.00 0.00 44.72 3.21
4953 8449 9.177608 TCCTCATGTTCTTACTTAATTTGATGG 57.822 33.333 0.00 0.00 0.00 3.51
5012 8508 2.355756 CCATAACGATGTCAAAGCCCTG 59.644 50.000 0.00 0.00 0.00 4.45
5016 8512 1.377202 GATGTCAAAGCCCTGCGGA 60.377 57.895 0.00 0.00 0.00 5.54
5174 8670 1.341080 CATTGTTCAGGCACCCCTTT 58.659 50.000 0.00 0.00 40.33 3.11
5231 8727 1.421646 GTTCATATCCAGACCAGGGGG 59.578 57.143 0.00 0.00 41.29 5.40
5264 8760 1.392853 GAGCTCAAGCACATCTTCGTG 59.607 52.381 9.40 0.00 45.16 4.35
5374 8870 2.040145 TCCTTGTCAATGTCATGCCTGA 59.960 45.455 0.00 0.00 0.00 3.86
5396 8892 3.808728 TCCACTGTCAGTTCCTTCTTTG 58.191 45.455 1.67 0.00 0.00 2.77
5401 8897 5.463724 CACTGTCAGTTCCTTCTTTGACTAC 59.536 44.000 1.67 0.00 40.36 2.73
5402 8898 4.957296 TGTCAGTTCCTTCTTTGACTACC 58.043 43.478 5.25 0.00 40.36 3.18
5405 8901 4.899457 TCAGTTCCTTCTTTGACTACCTGA 59.101 41.667 0.00 0.00 0.00 3.86
5406 8902 5.365605 TCAGTTCCTTCTTTGACTACCTGAA 59.634 40.000 0.00 0.00 0.00 3.02
5407 8903 5.698545 CAGTTCCTTCTTTGACTACCTGAAG 59.301 44.000 0.00 0.00 35.31 3.02
5409 8905 3.944087 CCTTCTTTGACTACCTGAAGGG 58.056 50.000 11.08 0.00 45.84 3.95
5419 8915 3.217242 CCTGAAGGGTCACTGAACG 57.783 57.895 0.00 0.00 0.00 3.95
5645 9141 2.100631 GTTCAGTGCCGATGACCCG 61.101 63.158 0.00 0.00 0.00 5.28
5646 9142 3.950794 TTCAGTGCCGATGACCCGC 62.951 63.158 0.00 0.00 0.00 6.13
5649 9145 3.845259 GTGCCGATGACCCGCCTA 61.845 66.667 0.00 0.00 0.00 3.93
5650 9146 3.078196 TGCCGATGACCCGCCTAA 61.078 61.111 0.00 0.00 0.00 2.69
5651 9147 2.188469 GCCGATGACCCGCCTAAA 59.812 61.111 0.00 0.00 0.00 1.85
5652 9148 2.178235 GCCGATGACCCGCCTAAAC 61.178 63.158 0.00 0.00 0.00 2.01
5653 9149 1.523032 CCGATGACCCGCCTAAACC 60.523 63.158 0.00 0.00 0.00 3.27
5654 9150 1.523032 CGATGACCCGCCTAAACCC 60.523 63.158 0.00 0.00 0.00 4.11
5655 9151 1.912971 GATGACCCGCCTAAACCCT 59.087 57.895 0.00 0.00 0.00 4.34
5656 9152 1.125633 GATGACCCGCCTAAACCCTA 58.874 55.000 0.00 0.00 0.00 3.53
5657 9153 1.487558 GATGACCCGCCTAAACCCTAA 59.512 52.381 0.00 0.00 0.00 2.69
5658 9154 1.360185 TGACCCGCCTAAACCCTAAA 58.640 50.000 0.00 0.00 0.00 1.85
5659 9155 1.003464 TGACCCGCCTAAACCCTAAAC 59.997 52.381 0.00 0.00 0.00 2.01
5660 9156 0.329261 ACCCGCCTAAACCCTAAACC 59.671 55.000 0.00 0.00 0.00 3.27
5664 9160 3.117776 CCCGCCTAAACCCTAAACCTAAT 60.118 47.826 0.00 0.00 0.00 1.73
5739 9235 1.436195 GCAACACCTTCAGCGTGTCA 61.436 55.000 0.00 0.00 43.56 3.58
5874 9370 4.943705 GCTGAAATGGACAAGAAGGTGATA 59.056 41.667 0.00 0.00 0.00 2.15
5907 9403 2.281692 TTCTGCATGTGCCGCTGT 60.282 55.556 2.07 0.00 41.18 4.40
5917 9413 1.600356 TGCCGCTGTTCATCTTGCA 60.600 52.632 0.00 0.00 0.00 4.08
5932 9428 5.181811 TCATCTTGCAATGTTGGTTACTGAG 59.818 40.000 0.00 0.00 0.00 3.35
6309 9811 4.019771 AGGGAAGAGTTCACAAGAATCTCC 60.020 45.833 0.00 0.00 34.83 3.71
6340 9842 1.730064 CCGGTTCGACAGTTGGTAATG 59.270 52.381 0.00 0.00 0.00 1.90
6429 9931 4.490035 GCGTTGAGCTTTTATCAATTGC 57.510 40.909 0.00 0.00 44.04 3.56
6503 10009 1.373570 GCAAGCCCACACTAGCTAAG 58.626 55.000 0.00 0.00 38.74 2.18
6506 10012 1.490574 AGCCCACACTAGCTAAGGAG 58.509 55.000 0.00 0.00 37.64 3.69
6610 10116 8.883954 AGAATAGAATACACACACATCTGATG 57.116 34.615 15.83 15.83 0.00 3.07
6624 10130 6.818644 ACACATCTGATGACCATAGTAACAAC 59.181 38.462 23.59 0.00 0.00 3.32
6674 10182 2.226674 GGAAGAAAACTTGCCCTCTTCG 59.773 50.000 4.98 0.00 43.06 3.79
6908 10418 1.132500 ACCCTCTACCAAGGCATAGC 58.868 55.000 0.00 0.00 34.88 2.97
6940 10450 0.109723 TGGCTTTGCTCTTTACCGGT 59.890 50.000 13.98 13.98 0.00 5.28
6943 10453 2.419667 GCTTTGCTCTTTACCGGTGTA 58.580 47.619 19.93 1.41 0.00 2.90
6955 10465 3.756933 ACCGGTGTAATAGTGTGTGTT 57.243 42.857 6.12 0.00 0.00 3.32
6957 10467 3.810941 ACCGGTGTAATAGTGTGTGTTTG 59.189 43.478 6.12 0.00 0.00 2.93
6970 10480 5.701750 AGTGTGTGTTTGTGTGTTACTGTTA 59.298 36.000 0.00 0.00 0.00 2.41
6984 10494 5.767665 TGTTACTGTTAATTGTGTGCATCCT 59.232 36.000 0.00 0.00 0.00 3.24
6987 10497 6.254281 ACTGTTAATTGTGTGCATCCTAAC 57.746 37.500 0.00 0.00 0.00 2.34
6997 10507 2.703416 TGCATCCTAACTGTGCAGAAG 58.297 47.619 6.17 3.28 43.30 2.85
7009 10519 1.594862 GTGCAGAAGTCGGATATGTGC 59.405 52.381 7.78 7.78 34.27 4.57
7079 10589 4.037208 CCTAAATGAATGTGAGCCATCCAC 59.963 45.833 0.00 0.00 31.75 4.02
7095 10605 4.141413 CCATCCACCCATCTTAATCTGACA 60.141 45.833 0.00 0.00 0.00 3.58
7478 11039 2.378038 GGTTATGCACCCATGATGTGT 58.622 47.619 14.32 0.00 40.19 3.72
7491 11052 5.011586 CCATGATGTGTATATCAATGGCCA 58.988 41.667 8.56 8.56 40.21 5.36
7576 11139 1.836166 CATGGATGTGTGAGGAGGAGT 59.164 52.381 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 7.000472 TCAGAAATCCTTTCAGTCAGTTTCAT 59.000 34.615 2.76 0.00 42.10 2.57
141 145 5.300792 GGTTGAGAAAACATACTTCACCCAA 59.699 40.000 0.00 0.00 0.00 4.12
144 148 4.753107 TCGGTTGAGAAAACATACTTCACC 59.247 41.667 0.00 0.00 0.00 4.02
194 198 7.651304 TGTGTCATGTGTATGGAAAACAAATTC 59.349 33.333 0.00 0.00 34.97 2.17
328 333 6.834168 TCAGAAAACCTTTCAGTCAGTTTT 57.166 33.333 0.00 0.00 43.20 2.43
586 601 2.082231 CATGTCAGGGTGAGAGCAAAG 58.918 52.381 0.00 0.00 0.00 2.77
622 639 1.903877 CTTCAGTGGACGAGGGCCAT 61.904 60.000 6.18 0.00 37.81 4.40
675 694 7.099120 ACCCATCATGCTTTATTTTTGTCTTC 58.901 34.615 0.00 0.00 0.00 2.87
705 726 3.076079 TGCTTTGAGATTGATCTGGCA 57.924 42.857 0.00 1.79 37.25 4.92
780 801 5.899299 ACGTAGGTATATGCTCGAAAAAGT 58.101 37.500 0.00 0.00 0.00 2.66
781 802 5.115171 CGACGTAGGTATATGCTCGAAAAAG 59.885 44.000 0.00 0.00 0.00 2.27
786 807 3.030668 TCGACGTAGGTATATGCTCGA 57.969 47.619 0.00 4.84 32.79 4.04
787 808 3.186001 AGTTCGACGTAGGTATATGCTCG 59.814 47.826 0.00 0.00 0.00 5.03
802 823 1.000163 TGAAGCTGAGGTGAGTTCGAC 60.000 52.381 0.00 0.00 0.00 4.20
860 882 6.392911 TTCACCTTGGTACTAGGAGTAGTA 57.607 41.667 17.81 0.00 40.23 1.82
861 883 4.942363 TCACCTTGGTACTAGGAGTAGT 57.058 45.455 17.81 0.00 42.49 2.73
862 884 4.098196 GCTTCACCTTGGTACTAGGAGTAG 59.902 50.000 17.81 14.13 36.58 2.57
903 925 2.282462 GGTTCACCTGTGGGCTGG 60.282 66.667 0.00 0.00 39.33 4.85
922 944 0.741927 CCGTCCACGAAACATACCCC 60.742 60.000 0.00 0.00 43.02 4.95
972 994 1.609501 CCGGTCTCCCAACTCCTCA 60.610 63.158 0.00 0.00 0.00 3.86
997 1019 2.202743 CGACGGCGTCCACATGAT 60.203 61.111 31.86 0.00 0.00 2.45
1664 1752 3.696426 GCCGACTCGCGATCATGC 61.696 66.667 10.36 7.20 44.57 4.06
1891 2047 4.104143 CGTGATCGTTAGGTGGCC 57.896 61.111 0.00 0.00 0.00 5.36
2077 2292 6.516527 CGGTGGTTTAAACTACTAGTGGTACA 60.517 42.308 27.40 7.82 39.92 2.90
2099 2317 1.941975 CCAAACTTGTTACCGTTCGGT 59.058 47.619 20.39 20.39 41.93 4.69
2131 2349 0.959372 AGGCATCAGCAGTTCAGCAC 60.959 55.000 0.00 0.00 44.61 4.40
2184 2402 5.841957 ATCAAATCTCATTACTGGGCAAC 57.158 39.130 0.00 0.00 0.00 4.17
2187 2405 5.827797 TGGTAATCAAATCTCATTACTGGGC 59.172 40.000 0.00 0.00 36.24 5.36
2189 2407 9.740239 CAAATGGTAATCAAATCTCATTACTGG 57.260 33.333 0.00 0.00 36.24 4.00
2205 2423 8.121305 TCAAGCAGTGATTAACAAATGGTAAT 57.879 30.769 3.43 3.43 40.37 1.89
2206 2424 7.517614 TCAAGCAGTGATTAACAAATGGTAA 57.482 32.000 0.00 0.00 31.21 2.85
2320 2685 4.824515 CCCTCCGGGTCGAGCTCT 62.825 72.222 15.18 0.00 38.25 4.09
2401 2766 2.560119 GCCCACGTGCCATGTCAAA 61.560 57.895 10.91 0.00 0.00 2.69
2733 3206 2.202440 ATCACCTCGAACGCGACG 60.202 61.111 15.93 18.45 42.51 5.12
2736 3209 2.885644 CCCATCACCTCGAACGCG 60.886 66.667 3.53 3.53 39.35 6.01
2811 3284 3.775654 CAGACGGGGAGGAGCACC 61.776 72.222 0.00 0.00 36.39 5.01
3310 4405 5.244626 TGAAGGAACTAGTGGTGGTAAGTAC 59.755 44.000 0.00 0.00 38.49 2.73
3312 4407 4.040095 GTGAAGGAACTAGTGGTGGTAAGT 59.960 45.833 0.00 0.00 38.49 2.24
3313 4408 4.562963 GGTGAAGGAACTAGTGGTGGTAAG 60.563 50.000 0.00 0.00 38.49 2.34
3314 4409 3.325716 GGTGAAGGAACTAGTGGTGGTAA 59.674 47.826 0.00 0.00 38.49 2.85
3315 4410 2.901839 GGTGAAGGAACTAGTGGTGGTA 59.098 50.000 0.00 0.00 38.49 3.25
3316 4411 1.697982 GGTGAAGGAACTAGTGGTGGT 59.302 52.381 0.00 0.00 38.49 4.16
3317 4412 1.978580 AGGTGAAGGAACTAGTGGTGG 59.021 52.381 0.00 0.00 38.49 4.61
3318 4413 3.771577 AAGGTGAAGGAACTAGTGGTG 57.228 47.619 0.00 0.00 38.49 4.17
3345 4440 7.935338 ATGCAGTGAAGATAAACAAAAAGTG 57.065 32.000 0.00 0.00 0.00 3.16
3351 4451 8.075574 CAGTAACAATGCAGTGAAGATAAACAA 58.924 33.333 22.73 0.00 0.00 2.83
3378 4486 0.519519 TAAAAACAGACCGCGGCATG 59.480 50.000 28.58 25.97 0.00 4.06
3379 4487 0.802494 CTAAAAACAGACCGCGGCAT 59.198 50.000 28.58 11.77 0.00 4.40
3380 4488 0.533308 ACTAAAAACAGACCGCGGCA 60.533 50.000 28.58 0.00 0.00 5.69
3381 4489 0.589708 AACTAAAAACAGACCGCGGC 59.410 50.000 28.58 18.62 0.00 6.53
3382 4490 1.600485 ACAACTAAAAACAGACCGCGG 59.400 47.619 26.86 26.86 0.00 6.46
3456 4786 1.620822 GCCCAAATCAGACAGGTGTT 58.379 50.000 0.00 0.00 0.00 3.32
3461 4791 1.272092 TGGAAGGCCCAAATCAGACAG 60.272 52.381 0.00 0.00 43.29 3.51
3588 4918 4.323028 GGATCTCAAGAATATCATGGGCGA 60.323 45.833 0.00 0.00 0.00 5.54
3620 4950 0.179174 GGAAATAAGTTGCCGGTGCG 60.179 55.000 1.90 0.00 41.78 5.34
3621 4951 1.173913 AGGAAATAAGTTGCCGGTGC 58.826 50.000 1.90 0.00 38.26 5.01
3622 4952 3.934457 AAAGGAAATAAGTTGCCGGTG 57.066 42.857 1.90 0.00 0.00 4.94
3623 4953 3.437741 CGTAAAGGAAATAAGTTGCCGGT 59.562 43.478 1.90 0.00 0.00 5.28
3624 4954 3.437741 ACGTAAAGGAAATAAGTTGCCGG 59.562 43.478 0.00 0.00 0.00 6.13
3625 4955 4.399978 CACGTAAAGGAAATAAGTTGCCG 58.600 43.478 0.00 0.00 0.00 5.69
3630 4960 5.766174 TCCAAAGCACGTAAAGGAAATAAGT 59.234 36.000 0.00 0.00 0.00 2.24
3751 7142 6.792473 ACCTATATTGGATGGACATGGTTCTA 59.208 38.462 10.38 0.00 0.00 2.10
3755 7147 6.331032 TCTACCTATATTGGATGGACATGGT 58.669 40.000 10.38 0.00 0.00 3.55
3757 7149 6.070596 TGCTCTACCTATATTGGATGGACATG 60.071 42.308 10.38 0.00 0.00 3.21
3766 7158 6.412362 AACTCACTGCTCTACCTATATTGG 57.588 41.667 1.22 1.22 0.00 3.16
3769 7161 6.721668 TGCATAACTCACTGCTCTACCTATAT 59.278 38.462 0.00 0.00 39.16 0.86
3781 7173 8.854312 CGTATACATATTCTGCATAACTCACTG 58.146 37.037 3.32 0.00 0.00 3.66
3783 7175 8.744008 ACGTATACATATTCTGCATAACTCAC 57.256 34.615 3.32 0.00 0.00 3.51
3787 7179 9.933175 CGTTTACGTATACATATTCTGCATAAC 57.067 33.333 15.09 2.18 34.11 1.89
3788 7180 9.896263 TCGTTTACGTATACATATTCTGCATAA 57.104 29.630 15.09 0.00 40.80 1.90
3789 7181 9.550811 CTCGTTTACGTATACATATTCTGCATA 57.449 33.333 15.09 0.00 40.80 3.14
3790 7182 8.080417 ACTCGTTTACGTATACATATTCTGCAT 58.920 33.333 15.09 0.00 40.80 3.96
3797 7189 9.357652 ACAAACAACTCGTTTACGTATACATAT 57.642 29.630 15.09 0.00 46.27 1.78
3798 7190 8.637704 CACAAACAACTCGTTTACGTATACATA 58.362 33.333 15.09 3.27 46.27 2.29
3799 7191 7.381948 TCACAAACAACTCGTTTACGTATACAT 59.618 33.333 15.09 0.00 46.27 2.29
3800 7192 6.694844 TCACAAACAACTCGTTTACGTATACA 59.305 34.615 15.09 3.44 46.27 2.29
3801 7193 7.092710 TCACAAACAACTCGTTTACGTATAC 57.907 36.000 6.13 6.13 46.27 1.47
3803 7195 6.256321 ACTTCACAAACAACTCGTTTACGTAT 59.744 34.615 0.00 0.00 46.27 3.06
3804 7196 5.576384 ACTTCACAAACAACTCGTTTACGTA 59.424 36.000 1.88 0.00 46.27 3.57
3805 7197 4.389687 ACTTCACAAACAACTCGTTTACGT 59.610 37.500 1.88 0.00 46.27 3.57
3873 7317 3.892588 GGATTCTGTGAGTAGGGACTAGG 59.107 52.174 0.00 0.00 44.14 3.02
3877 7321 1.409427 CGGGATTCTGTGAGTAGGGAC 59.591 57.143 0.00 0.00 0.00 4.46
4096 7563 3.594603 ATTCTGGTTGATTCGTCTCGT 57.405 42.857 0.00 0.00 0.00 4.18
4159 7634 5.070847 TCCATTGTATCTGAGATAAGCAGCA 59.929 40.000 3.31 0.00 33.45 4.41
4160 7635 5.407995 GTCCATTGTATCTGAGATAAGCAGC 59.592 44.000 3.31 0.00 33.45 5.25
4161 7636 5.931146 GGTCCATTGTATCTGAGATAAGCAG 59.069 44.000 3.31 0.00 34.71 4.24
4200 7678 6.719829 TCCAAGTGTAGAAGATCACAGTTCTA 59.280 38.462 0.00 0.00 36.42 2.10
4202 7680 5.635700 GTCCAAGTGTAGAAGATCACAGTTC 59.364 44.000 0.00 0.00 36.42 3.01
4203 7681 5.511545 GGTCCAAGTGTAGAAGATCACAGTT 60.512 44.000 0.00 0.00 38.53 3.16
4204 7682 4.021016 GGTCCAAGTGTAGAAGATCACAGT 60.021 45.833 0.00 0.00 37.07 3.55
4205 7683 4.221703 AGGTCCAAGTGTAGAAGATCACAG 59.778 45.833 0.00 0.00 37.07 3.66
4206 7684 4.021104 CAGGTCCAAGTGTAGAAGATCACA 60.021 45.833 0.00 0.00 37.07 3.58
4208 7686 3.055819 GCAGGTCCAAGTGTAGAAGATCA 60.056 47.826 0.00 0.00 0.00 2.92
4209 7687 3.526534 GCAGGTCCAAGTGTAGAAGATC 58.473 50.000 0.00 0.00 0.00 2.75
4210 7688 2.237392 GGCAGGTCCAAGTGTAGAAGAT 59.763 50.000 0.00 0.00 34.01 2.40
4211 7689 1.623811 GGCAGGTCCAAGTGTAGAAGA 59.376 52.381 0.00 0.00 34.01 2.87
4212 7690 1.625818 AGGCAGGTCCAAGTGTAGAAG 59.374 52.381 0.00 0.00 37.29 2.85
4213 7691 1.347707 CAGGCAGGTCCAAGTGTAGAA 59.652 52.381 0.00 0.00 37.29 2.10
4214 7692 0.976641 CAGGCAGGTCCAAGTGTAGA 59.023 55.000 0.00 0.00 37.29 2.59
4215 7693 0.687354 ACAGGCAGGTCCAAGTGTAG 59.313 55.000 0.00 0.00 37.29 2.74
4216 7694 0.685097 GACAGGCAGGTCCAAGTGTA 59.315 55.000 0.00 0.00 37.29 2.90
4217 7695 1.344953 TGACAGGCAGGTCCAAGTGT 61.345 55.000 6.83 0.00 36.97 3.55
4218 7696 0.179020 TTGACAGGCAGGTCCAAGTG 60.179 55.000 6.83 0.00 36.97 3.16
4219 7697 0.109342 CTTGACAGGCAGGTCCAAGT 59.891 55.000 6.83 0.00 36.97 3.16
4248 7726 4.083324 ACAAAGATCACAATGTTAGCACCG 60.083 41.667 0.00 0.00 0.00 4.94
4313 7795 4.117372 CGTTCGCCGACGTGAAGC 62.117 66.667 0.00 0.00 39.13 3.86
4392 7874 5.067805 ACACTGAACTTTGGTTTCAGATTCC 59.932 40.000 16.88 0.00 35.83 3.01
4444 7929 7.689953 TCTTTATTTTATCTACGCGGAGTTC 57.310 36.000 19.83 0.00 0.00 3.01
4534 8023 1.901654 TTGATTTGGCATGGCAGGGC 61.902 55.000 22.17 19.44 0.00 5.19
4555 8044 4.607955 TCGTATCATTCTTAGTGCTTCCG 58.392 43.478 0.00 0.00 0.00 4.30
4705 8195 9.463443 GAAAGCCACATAAATATCCAACAATAC 57.537 33.333 0.00 0.00 0.00 1.89
4816 8311 1.807142 GCCAGTTACTCAGTTTCTGCC 59.193 52.381 4.09 0.00 0.00 4.85
4906 8402 4.873827 GGATGTGTTCGCCTAGTTTCATTA 59.126 41.667 0.00 0.00 0.00 1.90
4928 8424 8.960591 ACCATCAAATTAAGTAAGAACATGAGG 58.039 33.333 0.00 0.00 0.00 3.86
5012 8508 3.126831 CCACTTCTGTATCTGAATCCGC 58.873 50.000 0.00 0.00 0.00 5.54
5016 8512 8.489489 ACATATTGTCCACTTCTGTATCTGAAT 58.511 33.333 0.00 0.00 0.00 2.57
5121 8617 7.024340 TCAATACAGTAGTACAATCCGAGAC 57.976 40.000 2.52 0.00 31.96 3.36
5174 8670 0.329261 CAGGGGCTGAAGTGATGGAA 59.671 55.000 0.00 0.00 32.44 3.53
5231 8727 0.681733 TGAGCTCTTGTGTCCAGTCC 59.318 55.000 16.19 0.00 0.00 3.85
5374 8870 4.103153 TCAAAGAAGGAACTGACAGTGGAT 59.897 41.667 9.33 0.00 40.86 3.41
5401 8897 0.679505 TCGTTCAGTGACCCTTCAGG 59.320 55.000 0.00 0.00 43.78 3.86
5402 8898 2.289072 ACATCGTTCAGTGACCCTTCAG 60.289 50.000 0.00 0.00 30.10 3.02
5405 8901 1.971357 AGACATCGTTCAGTGACCCTT 59.029 47.619 0.00 0.00 0.00 3.95
5406 8902 1.546476 GAGACATCGTTCAGTGACCCT 59.454 52.381 0.00 0.00 0.00 4.34
5407 8903 1.732732 CGAGACATCGTTCAGTGACCC 60.733 57.143 0.00 0.00 44.09 4.46
5419 8915 0.172127 TGCAGCAGAGACGAGACATC 59.828 55.000 0.00 0.00 0.00 3.06
5467 8963 4.529219 TGCGCCGGAGCACCATAG 62.529 66.667 30.00 0.00 42.92 2.23
5645 9141 5.384145 AGGATTAGGTTTAGGGTTTAGGC 57.616 43.478 0.00 0.00 0.00 3.93
5646 9142 7.672660 ACAAAAGGATTAGGTTTAGGGTTTAGG 59.327 37.037 0.00 0.00 0.00 2.69
5647 9143 8.645814 ACAAAAGGATTAGGTTTAGGGTTTAG 57.354 34.615 0.00 0.00 0.00 1.85
5675 9171 7.091993 TGGTCTCCATTGATAGGTCCTAAAAAT 60.092 37.037 1.78 3.37 0.00 1.82
5709 9205 1.072159 GGTGTTGCTGCTGTCCTCT 59.928 57.895 0.00 0.00 0.00 3.69
5739 9235 2.896801 CTTGTTGCTGCTCGCCGTT 61.897 57.895 0.00 0.00 38.05 4.44
5874 9370 2.765699 GCAGAAGGAAGGATGAGAGACT 59.234 50.000 0.00 0.00 0.00 3.24
5907 9403 5.534278 TCAGTAACCAACATTGCAAGATGAA 59.466 36.000 4.94 0.00 0.00 2.57
5917 9413 4.641989 GCATCATCCTCAGTAACCAACATT 59.358 41.667 0.00 0.00 0.00 2.71
5932 9428 4.397103 TGAGAACAACATCAAGCATCATCC 59.603 41.667 0.00 0.00 0.00 3.51
6382 9884 7.179269 TGGGTACTTTTAGATGCCTATTTGTT 58.821 34.615 0.00 0.00 0.00 2.83
6383 9885 6.727394 TGGGTACTTTTAGATGCCTATTTGT 58.273 36.000 0.00 0.00 0.00 2.83
6387 9889 4.503296 CGCTGGGTACTTTTAGATGCCTAT 60.503 45.833 0.00 0.00 0.00 2.57
6426 9928 6.335471 ACTTCAGTGATCAAAATGATGCAA 57.665 33.333 0.00 0.00 37.20 4.08
6429 9931 9.218359 CGAATAACTTCAGTGATCAAAATGATG 57.782 33.333 0.00 7.46 37.20 3.07
6503 10009 5.482908 TCAAGTGATAGTTTCTTCAGCTCC 58.517 41.667 0.00 0.00 0.00 4.70
6506 10012 6.815641 TCATCTCAAGTGATAGTTTCTTCAGC 59.184 38.462 0.00 0.00 0.00 4.26
6585 10091 8.699130 TCATCAGATGTGTGTGTATTCTATTCT 58.301 33.333 10.34 0.00 0.00 2.40
6586 10092 8.759641 GTCATCAGATGTGTGTGTATTCTATTC 58.240 37.037 10.34 0.00 0.00 1.75
6587 10093 7.712639 GGTCATCAGATGTGTGTGTATTCTATT 59.287 37.037 10.34 0.00 0.00 1.73
6588 10094 7.147672 TGGTCATCAGATGTGTGTGTATTCTAT 60.148 37.037 10.34 0.00 0.00 1.98
6589 10095 6.154363 TGGTCATCAGATGTGTGTGTATTCTA 59.846 38.462 10.34 0.00 0.00 2.10
6598 10104 6.340522 TGTTACTATGGTCATCAGATGTGTG 58.659 40.000 10.34 0.01 0.00 3.82
6661 10169 0.251341 AAATGGCGAAGAGGGCAAGT 60.251 50.000 0.00 0.00 46.16 3.16
6896 10406 1.378762 ACCAACGCTATGCCTTGGT 59.621 52.632 16.25 16.25 47.00 3.67
6908 10418 2.668279 GCAAAGCCATACAAGACCAACG 60.668 50.000 0.00 0.00 0.00 4.10
6940 10450 6.745159 AACACACAAACACACACTATTACA 57.255 33.333 0.00 0.00 0.00 2.41
6943 10453 6.373216 ACAGTAACACACAAACACACACTATT 59.627 34.615 0.00 0.00 0.00 1.73
6955 10465 6.030849 GCACACAATTAACAGTAACACACAA 58.969 36.000 0.00 0.00 0.00 3.33
6957 10467 5.574082 TGCACACAATTAACAGTAACACAC 58.426 37.500 0.00 0.00 0.00 3.82
6970 10480 3.057315 GCACAGTTAGGATGCACACAATT 60.057 43.478 0.00 0.00 39.23 2.32
6984 10494 4.159693 ACATATCCGACTTCTGCACAGTTA 59.840 41.667 0.00 0.00 0.00 2.24
6987 10497 2.862536 CACATATCCGACTTCTGCACAG 59.137 50.000 0.00 0.00 0.00 3.66
6997 10507 5.734855 AACACAATAAGCACATATCCGAC 57.265 39.130 0.00 0.00 0.00 4.79
7079 10589 6.767456 AGATTAGCTGTCAGATTAAGATGGG 58.233 40.000 3.32 0.00 0.00 4.00
7095 10605 6.808321 TTGGAGTACCATGTAAGATTAGCT 57.192 37.500 0.00 0.00 46.34 3.32
7121 10631 5.970289 TGAGATAGTACTCCCCATGATCTT 58.030 41.667 0.00 0.00 36.22 2.40
7470 11031 5.012239 GGTGGCCATTGATATACACATCAT 58.988 41.667 9.72 0.00 34.95 2.45
7478 11039 1.271325 CCAGCGGTGGCCATTGATATA 60.271 52.381 22.48 0.00 41.24 0.86
7538 11101 1.146041 GATGCGCCAGTATCCCACA 59.854 57.895 4.18 0.00 34.04 4.17


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

AutoCloner maintained by Alex Coulton.