Multiple sequence alignment - TraesCS4A01G123600

Loading Multiple Alignment...

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 TraesCS4A01G123600 chr4A 100.000 5401 0 0 1 5401 155811685 155806285 0.000000e+00 9974.0
1 TraesCS4A01G123600 chr4A 91.082 527 45 2 59 585 585264716 585265240 0.000000e+00 712.0
2 TraesCS4A01G123600 chr4A 96.471 85 2 1 5028 5112 428159886 428159969 7.290000e-29 139.0
3 TraesCS4A01G123600 chr4A 91.489 94 6 2 5019 5112 379041043 379040952 1.580000e-25 128.0
4 TraesCS4A01G123600 chr4A 91.549 71 5 1 4936 5006 155806680 155806611 4.450000e-16 97.1
5 TraesCS4A01G123600 chr4B 94.772 1358 53 8 1811 3166 395733732 395732391 0.000000e+00 2098.0
6 TraesCS4A01G123600 chr4B 96.646 984 30 3 3737 4720 395732394 395731414 0.000000e+00 1631.0
7 TraesCS4A01G123600 chr4B 93.908 952 31 5 863 1794 395734664 395733720 0.000000e+00 1411.0
8 TraesCS4A01G123600 chr4B 90.260 308 27 3 575 880 395816163 395815857 3.030000e-107 399.0
9 TraesCS4A01G123600 chr4B 92.653 245 7 3 5142 5375 395731126 395730882 5.180000e-90 342.0
10 TraesCS4A01G123600 chr4B 91.603 131 10 1 1 131 315606122 315606251 4.300000e-41 180.0
11 TraesCS4A01G123600 chr4B 95.495 111 5 0 4852 4962 395731386 395731276 1.550000e-40 178.0
12 TraesCS4A01G123600 chr4B 89.706 136 11 3 2 136 315628803 315628936 2.590000e-38 171.0
13 TraesCS4A01G123600 chr4B 93.750 96 6 0 575 670 395816529 395816434 1.570000e-30 145.0
14 TraesCS4A01G123600 chr4B 96.970 33 1 0 5142 5174 395731165 395731133 7.560000e-04 56.5
15 TraesCS4A01G123600 chr4B 94.444 36 2 0 5147 5182 395731198 395731163 7.560000e-04 56.5
16 TraesCS4A01G123600 chr4D 94.541 1209 49 6 575 1782 318492528 318491336 0.000000e+00 1851.0
17 TraesCS4A01G123600 chr4D 96.957 986 26 2 3735 4720 318490674 318489693 0.000000e+00 1652.0
18 TraesCS4A01G123600 chr4D 97.644 679 14 2 2496 3173 318491343 318490666 0.000000e+00 1164.0
19 TraesCS4A01G123600 chr4D 92.925 212 13 2 1 211 76894448 76894238 1.890000e-79 307.0
20 TraesCS4A01G123600 chr4D 92.754 207 14 1 4757 4962 318489682 318489476 1.140000e-76 298.0
21 TraesCS4A01G123600 chr4D 88.636 220 8 7 5143 5346 318489366 318489148 8.980000e-63 252.0
22 TraesCS4A01G123600 chr4D 95.588 68 3 0 2652 2719 22644821 22644888 5.720000e-20 110.0
23 TraesCS4A01G123600 chr4D 95.588 68 3 0 2652 2719 123413556 123413623 5.720000e-20 110.0
24 TraesCS4A01G123600 chr4D 95.588 68 3 0 2652 2719 123538578 123538645 5.720000e-20 110.0
25 TraesCS4A01G123600 chr4D 95.588 68 3 0 2652 2719 134998133 134998066 5.720000e-20 110.0
26 TraesCS4A01G123600 chr4D 95.588 68 3 0 2652 2719 241123224 241123157 5.720000e-20 110.0
27 TraesCS4A01G123600 chr4D 98.276 58 1 0 5343 5400 318489009 318488952 9.570000e-18 102.0
28 TraesCS4A01G123600 chr4D 100.000 28 0 0 5147 5174 318489400 318489373 1.000000e-02 52.8
29 TraesCS4A01G123600 chr2A 96.497 571 18 2 3168 3736 139042856 139042286 0.000000e+00 942.0
30 TraesCS4A01G123600 chr2A 96.649 567 17 2 3170 3735 419090691 419091256 0.000000e+00 941.0
31 TraesCS4A01G123600 chr2A 95.958 569 21 2 3173 3740 721493514 721492947 0.000000e+00 922.0
32 TraesCS4A01G123600 chr1A 96.473 567 18 2 3170 3734 507540524 507539958 0.000000e+00 935.0
33 TraesCS4A01G123600 chr1A 95.353 581 24 3 3163 3741 562083035 562082456 0.000000e+00 920.0
34 TraesCS4A01G123600 chr1A 92.857 98 2 5 5018 5112 389064629 389064534 2.620000e-28 137.0
35 TraesCS4A01G123600 chr7A 96.000 575 22 1 3168 3741 471052574 471052000 0.000000e+00 933.0
36 TraesCS4A01G123600 chr3A 96.466 566 19 1 3170 3734 467348717 467349282 0.000000e+00 933.0
37 TraesCS4A01G123600 chr3A 95.189 582 23 5 3164 3743 191959674 191960252 0.000000e+00 915.0
38 TraesCS4A01G123600 chr3A 95.026 583 26 3 3159 3740 554089596 554089016 0.000000e+00 913.0
39 TraesCS4A01G123600 chr3A 79.675 246 20 16 1811 2051 11413584 11413364 3.370000e-32 150.0
40 TraesCS4A01G123600 chr3A 88.073 109 10 3 5006 5112 725517052 725517159 5.680000e-25 126.0
41 TraesCS4A01G123600 chr1D 86.555 357 31 7 198 539 422865604 422865958 1.420000e-100 377.0
42 TraesCS4A01G123600 chr1D 92.391 92 6 1 5021 5112 462985052 462985142 4.390000e-26 130.0
43 TraesCS4A01G123600 chr1D 95.588 68 3 0 2652 2719 141320936 141320869 5.720000e-20 110.0
44 TraesCS4A01G123600 chr1D 97.297 37 1 0 149 185 422865572 422865608 4.520000e-06 63.9
45 TraesCS4A01G123600 chr5D 93.925 214 11 2 1 213 178425800 178425588 6.750000e-84 322.0
46 TraesCS4A01G123600 chr5D 89.020 255 24 3 1 253 178375907 178375655 4.060000e-81 313.0
47 TraesCS4A01G123600 chr5D 94.309 123 4 1 2719 2841 503255223 503255342 9.240000e-43 185.0
48 TraesCS4A01G123600 chr5D 93.258 89 5 1 5024 5112 128577581 128577668 4.390000e-26 130.0
49 TraesCS4A01G123600 chr7B 87.008 254 30 3 1 252 164392026 164391774 3.180000e-72 283.0
50 TraesCS4A01G123600 chr6A 86.500 200 15 5 5142 5332 572333987 572333791 5.480000e-50 209.0
51 TraesCS4A01G123600 chr6D 91.781 146 11 1 3 147 77478499 77478354 9.170000e-48 202.0
52 TraesCS4A01G123600 chr5B 87.647 170 20 1 179 348 386469984 386470152 4.270000e-46 196.0
53 TraesCS4A01G123600 chrUn 94.309 123 4 1 2719 2841 341018768 341018649 9.240000e-43 185.0
54 TraesCS4A01G123600 chrUn 94.309 123 4 1 2719 2841 355919994 355919875 9.240000e-43 185.0
55 TraesCS4A01G123600 chrUn 94.309 123 4 1 2719 2841 362350442 362350323 9.240000e-43 185.0
56 TraesCS4A01G123600 chrUn 94.309 123 4 1 2719 2841 454067254 454067135 9.240000e-43 185.0
57 TraesCS4A01G123600 chrUn 95.588 68 3 0 2652 2719 189393203 189393270 5.720000e-20 110.0
58 TraesCS4A01G123600 chr3D 94.309 123 4 1 2719 2841 589250611 589250730 9.240000e-43 185.0
59 TraesCS4A01G123600 chr2D 94.309 123 4 1 2719 2841 591995233 591995114 9.240000e-43 185.0
60 TraesCS4A01G123600 chr3B 93.333 90 5 1 5024 5112 2308904 2308993 1.220000e-26 132.0
61 TraesCS4A01G123600 chr3B 92.473 93 5 2 5021 5112 62307973 62308064 1.220000e-26 132.0
62 TraesCS4A01G123600 chr6B 87.850 107 9 4 5007 5112 415874852 415874749 7.350000e-24 122.0


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 TraesCS4A01G123600 chr4A 155806285 155811685 5400 True 9974.000000 9974 100.000 1 5401 1 chr4A.!!$R1 5400
1 TraesCS4A01G123600 chr4A 585264716 585265240 524 False 712.000000 712 91.082 59 585 1 chr4A.!!$F2 526
2 TraesCS4A01G123600 chr4B 395730882 395734664 3782 True 824.714286 2098 94.984 863 5375 7 chr4B.!!$R1 4512
3 TraesCS4A01G123600 chr4B 395815857 395816529 672 True 272.000000 399 92.005 575 880 2 chr4B.!!$R2 305
4 TraesCS4A01G123600 chr4D 318488952 318492528 3576 True 767.400000 1851 95.544 575 5400 7 chr4D.!!$R4 4825
5 TraesCS4A01G123600 chr2A 139042286 139042856 570 True 942.000000 942 96.497 3168 3736 1 chr2A.!!$R1 568
6 TraesCS4A01G123600 chr2A 419090691 419091256 565 False 941.000000 941 96.649 3170 3735 1 chr2A.!!$F1 565
7 TraesCS4A01G123600 chr2A 721492947 721493514 567 True 922.000000 922 95.958 3173 3740 1 chr2A.!!$R2 567
8 TraesCS4A01G123600 chr1A 507539958 507540524 566 True 935.000000 935 96.473 3170 3734 1 chr1A.!!$R2 564
9 TraesCS4A01G123600 chr1A 562082456 562083035 579 True 920.000000 920 95.353 3163 3741 1 chr1A.!!$R3 578
10 TraesCS4A01G123600 chr7A 471052000 471052574 574 True 933.000000 933 96.000 3168 3741 1 chr7A.!!$R1 573
11 TraesCS4A01G123600 chr3A 467348717 467349282 565 False 933.000000 933 96.466 3170 3734 1 chr3A.!!$F2 564
12 TraesCS4A01G123600 chr3A 191959674 191960252 578 False 915.000000 915 95.189 3164 3743 1 chr3A.!!$F1 579
13 TraesCS4A01G123600 chr3A 554089016 554089596 580 True 913.000000 913 95.026 3159 3740 1 chr3A.!!$R2 581

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
152 153 0.322456 TCAGTGTGCATTAGTGGGGC 60.322 55.000 8.38 0.00 0.00 5.80 F
296 297 0.660300 CGTTGGAAAACTGCCGAAGC 60.660 55.000 0.00 0.00 40.48 3.86 F
1925 2315 0.320596 AACGTTTGGGCATGCCAATG 60.321 50.000 36.56 28.15 37.98 2.82 F
2132 2522 0.318441 TCCAGTTCAGGAGCTCAACG 59.682 55.000 17.19 2.80 32.77 4.10 F
2194 2584 1.702401 TCCCATTAGGAACAGTGCACA 59.298 47.619 21.04 0.00 43.78 4.57 F
3482 3875 1.024271 GGCCGCACATATCATTGTGT 58.976 50.000 6.46 0.00 46.93 3.72 F
3893 4287 1.601903 GTGTTTCATCACTGGTTCGCA 59.398 47.619 0.00 0.00 35.68 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1176 1566 0.676184 TAGAGCCCGATGAGCACATC 59.324 55.000 13.51 13.51 46.50 3.06 R
2070 2460 1.473257 GCATAGCAATCCACCGTGAGA 60.473 52.381 0.00 0.00 0.00 3.27 R
2879 3270 1.476891 TCAGCCGAACTACCTTGCTAG 59.523 52.381 0.00 0.00 0.00 3.42 R
3248 3640 1.599542 GTGTCTAATGAAGCGATGGCC 59.400 52.381 0.00 0.00 41.24 5.36 R
4081 4475 2.487805 GGATCCCACTCTGCAATGCATA 60.488 50.000 8.91 0.00 38.13 3.14 R
4314 4708 1.000163 AGTCTCAACTACACACTGCGG 60.000 52.381 0.00 0.00 32.59 5.69 R
4816 5211 2.367241 TGCTAGCAGTTTCTACCACACA 59.633 45.455 14.93 0.00 0.00 3.72 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
17 18 4.032356 CAGTTGACTGCTGACGCA 57.968 55.556 0.00 0.00 45.60 5.24
30 31 1.713597 TGACGCAGCAGTCAATAGTG 58.286 50.000 15.00 0.00 46.81 2.74
31 32 1.002366 GACGCAGCAGTCAATAGTGG 58.998 55.000 11.14 0.00 40.65 4.00
32 33 0.608130 ACGCAGCAGTCAATAGTGGA 59.392 50.000 0.00 0.00 0.00 4.02
33 34 1.002366 CGCAGCAGTCAATAGTGGAC 58.998 55.000 0.00 0.00 35.50 4.02
34 35 1.373570 GCAGCAGTCAATAGTGGACC 58.626 55.000 0.00 0.00 35.89 4.46
35 36 1.339055 GCAGCAGTCAATAGTGGACCA 60.339 52.381 0.00 0.00 35.89 4.02
36 37 2.681976 GCAGCAGTCAATAGTGGACCAT 60.682 50.000 0.00 0.00 35.89 3.55
37 38 3.614092 CAGCAGTCAATAGTGGACCATT 58.386 45.455 0.00 0.00 35.89 3.16
38 39 3.376234 CAGCAGTCAATAGTGGACCATTG 59.624 47.826 0.00 0.00 35.89 2.82
39 40 3.264193 AGCAGTCAATAGTGGACCATTGA 59.736 43.478 0.00 0.55 38.50 2.57
57 58 4.366684 CTGGTCAACAGGGCCCCC 62.367 72.222 21.43 12.43 43.70 5.40
99 100 9.729281 TGAGACGTTTATTTTAAAATAGAGGGT 57.271 29.630 23.83 17.96 32.87 4.34
142 143 2.510411 CCCAGTGGTCAGTGTGCA 59.490 61.111 8.74 0.00 0.00 4.57
152 153 0.322456 TCAGTGTGCATTAGTGGGGC 60.322 55.000 8.38 0.00 0.00 5.80
286 287 2.915137 GCTGGGCCCGTTGGAAAA 60.915 61.111 19.37 0.00 0.00 2.29
296 297 0.660300 CGTTGGAAAACTGCCGAAGC 60.660 55.000 0.00 0.00 40.48 3.86
348 349 2.829458 GAGGACTCTAGCGGCGGT 60.829 66.667 18.21 18.21 0.00 5.68
351 352 4.874977 GACTCTAGCGGCGGTGGC 62.875 72.222 23.33 2.87 38.90 5.01
370 371 4.681978 GTGACCTGAAGCGGCGGT 62.682 66.667 5.44 5.44 0.00 5.68
387 388 2.606213 TGGAGGTCACGGCCATGA 60.606 61.111 0.00 0.00 0.00 3.07
388 389 2.125106 GGAGGTCACGGCCATGAC 60.125 66.667 23.61 23.61 46.95 3.06
481 482 3.546714 AAAAGCGTGGACGGAGGGG 62.547 63.158 0.71 0.00 40.23 4.79
521 522 4.030452 GCAATATCGGGCAGCGGC 62.030 66.667 0.00 0.00 40.13 6.53
572 573 4.314440 AGCAACGGAGCGGCTCAA 62.314 61.111 29.33 0.00 35.24 3.02
597 598 2.421619 GAGAGAGCCCAAACACTTCAG 58.578 52.381 0.00 0.00 0.00 3.02
602 603 0.668535 GCCCAAACACTTCAGGACAC 59.331 55.000 0.00 0.00 0.00 3.67
626 627 2.288763 TGCAATTGAGTAGCGAGTGACA 60.289 45.455 10.34 0.00 0.00 3.58
629 630 1.617322 TTGAGTAGCGAGTGACACCT 58.383 50.000 0.84 0.00 0.00 4.00
670 671 1.290009 GCACAAACATGGGAGGTGC 59.710 57.895 15.02 15.02 46.53 5.01
705 1072 3.003480 GTGAGGAACATCACTAGTTGGC 58.997 50.000 11.48 0.00 45.03 4.52
719 1086 3.405823 AGTTGGCAATGAATGTTTGGG 57.594 42.857 1.92 0.00 0.00 4.12
722 1089 1.419012 TGGCAATGAATGTTTGGGCAA 59.581 42.857 0.00 0.00 0.00 4.52
723 1090 2.040012 TGGCAATGAATGTTTGGGCAAT 59.960 40.909 0.00 0.00 0.00 3.56
750 1117 6.603201 TCCATGCGAAAATAGAGAGGATTTTT 59.397 34.615 0.00 0.00 36.78 1.94
887 1256 2.568090 CCCAGACGGCAATGCAAC 59.432 61.111 7.79 0.00 0.00 4.17
888 1257 2.267351 CCCAGACGGCAATGCAACA 61.267 57.895 7.79 0.00 0.00 3.33
889 1258 1.597797 CCCAGACGGCAATGCAACAT 61.598 55.000 7.79 0.00 0.00 2.71
1028 1418 4.991776 TCACCAGAGAGAAAGAGAGAGAA 58.008 43.478 0.00 0.00 0.00 2.87
1082 1472 1.143183 GTTTCTGCGGCGGATCCTA 59.857 57.895 13.08 0.00 0.00 2.94
1163 1553 2.342648 GTGGGTCTGGACGTGGTC 59.657 66.667 0.00 0.00 0.00 4.02
1164 1554 2.200370 TGGGTCTGGACGTGGTCT 59.800 61.111 0.00 0.00 32.47 3.85
1272 1662 2.282958 TCGAGTCCTTCACCCGCT 60.283 61.111 0.00 0.00 0.00 5.52
1376 1766 3.453679 GAGGCCGAGGACGAGCTT 61.454 66.667 0.00 0.00 42.66 3.74
1430 1820 0.986527 ACGATTACCCGTTCCCCTTT 59.013 50.000 0.00 0.00 40.17 3.11
1454 1844 5.182380 TCTTTGCCCCGATTAGTTACTTTTG 59.818 40.000 0.00 0.00 0.00 2.44
1524 1914 1.254026 GGGGAGTAGTTTGTTTGCCC 58.746 55.000 0.00 0.00 33.90 5.36
1547 1937 4.332819 CGTTTGGTGATAAGGGATGTCTTC 59.667 45.833 0.00 0.00 0.00 2.87
1567 1957 5.880332 TCTTCTCTTTTGATACGGGGAAATG 59.120 40.000 0.00 0.00 0.00 2.32
1590 1980 3.126879 TTGCCTGCGGATTGCTCG 61.127 61.111 0.00 0.00 46.63 5.03
1634 2024 4.575885 TCTTCACCTAGTGCAAATGGTAC 58.424 43.478 5.60 0.00 32.98 3.34
1708 2098 2.361757 TGGCAACCTTTGTCAACAGATG 59.638 45.455 0.00 0.00 43.24 2.90
1712 2102 4.441356 GCAACCTTTGTCAACAGATGGAAA 60.441 41.667 0.00 0.00 0.00 3.13
1764 2154 7.425577 TCAAACATTGAGATACACAAGACTG 57.574 36.000 0.00 0.00 34.08 3.51
1773 2163 5.907207 AGATACACAAGACTGCGTGATTAT 58.093 37.500 11.27 1.69 36.91 1.28
1780 2170 4.465632 AGACTGCGTGATTATTGGTGTA 57.534 40.909 0.00 0.00 0.00 2.90
1784 2174 5.914033 ACTGCGTGATTATTGGTGTACTAT 58.086 37.500 0.00 0.00 0.00 2.12
1794 2184 9.569122 GATTATTGGTGTACTATGGGTATGTTT 57.431 33.333 0.00 0.00 32.56 2.83
1795 2185 9.930158 ATTATTGGTGTACTATGGGTATGTTTT 57.070 29.630 0.00 0.00 32.56 2.43
1796 2186 9.756571 TTATTGGTGTACTATGGGTATGTTTTT 57.243 29.630 0.00 0.00 32.56 1.94
1833 2223 2.175202 TGGGTATGTTTGGATTGCCAC 58.825 47.619 0.00 0.00 45.94 5.01
1837 2227 2.837532 ATGTTTGGATTGCCACCAAC 57.162 45.000 0.00 0.00 45.94 3.77
1838 2228 1.489481 TGTTTGGATTGCCACCAACA 58.511 45.000 0.00 0.00 45.94 3.33
1842 2232 4.101585 TGTTTGGATTGCCACCAACATTTA 59.898 37.500 0.00 0.00 45.94 1.40
1843 2233 5.221803 TGTTTGGATTGCCACCAACATTTAT 60.222 36.000 0.00 0.00 45.94 1.40
1925 2315 0.320596 AACGTTTGGGCATGCCAATG 60.321 50.000 36.56 28.15 37.98 2.82
1937 2327 3.777478 CATGCCAATGCTTCTTTGGTAG 58.223 45.455 11.48 1.64 44.52 3.18
1942 2332 4.843728 CCAATGCTTCTTTGGTAGTCCTA 58.156 43.478 4.00 0.00 39.05 2.94
1943 2333 4.878397 CCAATGCTTCTTTGGTAGTCCTAG 59.122 45.833 4.00 0.00 39.05 3.02
1950 2340 6.092807 GCTTCTTTGGTAGTCCTAGTTCATTG 59.907 42.308 0.00 0.00 34.23 2.82
1983 2373 2.879907 CCAACTCATGGGCAAGCG 59.120 61.111 0.00 0.00 46.27 4.68
1984 2374 1.675310 CCAACTCATGGGCAAGCGA 60.675 57.895 0.00 0.00 46.27 4.93
1992 2382 0.618458 ATGGGCAAGCGAAACCTCTA 59.382 50.000 0.00 0.00 0.00 2.43
1993 2383 0.398696 TGGGCAAGCGAAACCTCTAA 59.601 50.000 0.00 0.00 0.00 2.10
1994 2384 1.004277 TGGGCAAGCGAAACCTCTAAT 59.996 47.619 0.00 0.00 0.00 1.73
1995 2385 2.092323 GGGCAAGCGAAACCTCTAATT 58.908 47.619 0.00 0.00 0.00 1.40
1996 2386 2.492088 GGGCAAGCGAAACCTCTAATTT 59.508 45.455 0.00 0.00 0.00 1.82
1997 2387 3.056821 GGGCAAGCGAAACCTCTAATTTT 60.057 43.478 0.00 0.00 0.00 1.82
1998 2388 3.920412 GGCAAGCGAAACCTCTAATTTTG 59.080 43.478 0.00 0.00 0.00 2.44
1999 2389 3.920412 GCAAGCGAAACCTCTAATTTTGG 59.080 43.478 0.00 0.00 0.00 3.28
2000 2390 3.850122 AGCGAAACCTCTAATTTTGGC 57.150 42.857 0.00 0.00 36.87 4.52
2001 2391 3.421844 AGCGAAACCTCTAATTTTGGCT 58.578 40.909 0.00 0.00 40.62 4.75
2002 2392 4.585879 AGCGAAACCTCTAATTTTGGCTA 58.414 39.130 2.25 0.00 42.72 3.93
2003 2393 4.636206 AGCGAAACCTCTAATTTTGGCTAG 59.364 41.667 2.25 0.00 42.72 3.42
2004 2394 4.730903 GCGAAACCTCTAATTTTGGCTAGC 60.731 45.833 6.04 6.04 34.62 3.42
2005 2395 4.201920 CGAAACCTCTAATTTTGGCTAGCC 60.202 45.833 27.71 27.71 0.00 3.93
2006 2396 4.316025 AACCTCTAATTTTGGCTAGCCA 57.684 40.909 32.88 32.88 45.63 4.75
2050 2440 3.018149 GACACAAACCAAACACACCCTA 58.982 45.455 0.00 0.00 0.00 3.53
2053 2443 4.825085 ACACAAACCAAACACACCCTATAG 59.175 41.667 0.00 0.00 0.00 1.31
2054 2444 4.825085 CACAAACCAAACACACCCTATAGT 59.175 41.667 0.00 0.00 0.00 2.12
2055 2445 5.048991 CACAAACCAAACACACCCTATAGTC 60.049 44.000 0.00 0.00 0.00 2.59
2059 2449 5.557866 ACCAAACACACCCTATAGTCTTTC 58.442 41.667 0.00 0.00 0.00 2.62
2070 2460 8.047310 CACCCTATAGTCTTTCATAGTTTTGGT 58.953 37.037 0.00 0.00 0.00 3.67
2089 2479 2.205074 GTCTCACGGTGGATTGCTATG 58.795 52.381 8.50 0.00 0.00 2.23
2092 2482 1.152963 ACGGTGGATTGCTATGCCC 60.153 57.895 0.00 0.00 0.00 5.36
2131 2521 2.777832 ATCCAGTTCAGGAGCTCAAC 57.222 50.000 17.19 11.53 41.90 3.18
2132 2522 0.318441 TCCAGTTCAGGAGCTCAACG 59.682 55.000 17.19 2.80 32.77 4.10
2171 2561 7.301868 AAATGTCCATTTCTGGTAACATTGT 57.698 32.000 10.64 0.00 43.75 2.71
2193 2583 2.359900 CTCCCATTAGGAACAGTGCAC 58.640 52.381 9.40 9.40 46.94 4.57
2194 2584 1.702401 TCCCATTAGGAACAGTGCACA 59.298 47.619 21.04 0.00 43.78 4.57
2255 2645 3.807561 GCAGCTTTAGCCTATCCCCTTAC 60.808 52.174 0.00 0.00 43.38 2.34
2329 2719 7.795431 TTCGTCAAATTCAGATTAAATGCAC 57.205 32.000 0.00 0.00 0.00 4.57
2375 2765 9.780413 GAGATAATCTTGGAAGAAACAATCAAC 57.220 33.333 0.00 0.00 38.77 3.18
2459 2849 4.045783 GGGTCGGTGTTAAACATTTTGTG 58.954 43.478 0.00 0.00 0.00 3.33
2677 3068 3.329386 ACAAGACGACAGATCAATGTGG 58.671 45.455 0.00 0.00 35.29 4.17
2891 3282 7.507277 TCTCATTGATATCACTAGCAAGGTAGT 59.493 37.037 4.48 6.14 36.73 2.73
2980 3371 5.545063 TCCAATCTTCTCCGCACATTATA 57.455 39.130 0.00 0.00 0.00 0.98
3164 3555 6.186957 TCAAGGCAACCATCATAGTTACATT 58.813 36.000 0.00 0.00 37.17 2.71
3165 3556 6.663093 TCAAGGCAACCATCATAGTTACATTT 59.337 34.615 0.00 0.00 37.17 2.32
3166 3557 6.699575 AGGCAACCATCATAGTTACATTTC 57.300 37.500 0.00 0.00 37.17 2.17
3167 3558 6.426587 AGGCAACCATCATAGTTACATTTCT 58.573 36.000 0.00 0.00 37.17 2.52
3168 3559 6.891908 AGGCAACCATCATAGTTACATTTCTT 59.108 34.615 0.00 0.00 37.17 2.52
3200 3591 4.757019 TTATCAGTTATGCCACCGGTTA 57.243 40.909 2.97 0.00 0.00 2.85
3248 3640 8.749499 CACTAGAAATTTCAACTGCTCAAAAAG 58.251 33.333 19.99 0.00 0.00 2.27
3398 3791 5.308759 TCACTACAATAAAGTATAGGGCCCC 59.691 44.000 21.43 1.95 0.00 5.80
3467 3860 3.612247 CTCCTGACAAGTGGGGCCG 62.612 68.421 0.00 0.00 0.00 6.13
3482 3875 1.024271 GGCCGCACATATCATTGTGT 58.976 50.000 6.46 0.00 46.93 3.72
3521 3914 5.652452 ACATGTGGGTCTAGGCTTATTTTTC 59.348 40.000 0.00 0.00 0.00 2.29
3663 4057 5.988310 TCTCACAGATTGATGGCATTTTT 57.012 34.783 0.00 0.00 32.17 1.94
3868 4262 3.185594 TGTTGAATACGAAAGCTGAACCG 59.814 43.478 0.00 0.00 0.00 4.44
3893 4287 1.601903 GTGTTTCATCACTGGTTCGCA 59.398 47.619 0.00 0.00 35.68 5.10
3923 4317 6.913170 ACTTTTGCCATAACACTTGATACAG 58.087 36.000 0.00 0.00 0.00 2.74
3986 4380 2.203070 GACTGTGCCTATGCCCGG 60.203 66.667 0.00 0.00 36.33 5.73
4314 4708 4.119442 AGATGCATCATTTTTCACCTGC 57.881 40.909 27.81 0.00 0.00 4.85
4315 4709 2.747396 TGCATCATTTTTCACCTGCC 57.253 45.000 0.00 0.00 0.00 4.85
4374 4768 1.406539 CTGCAGTTTGCTTGTTGTCCT 59.593 47.619 5.25 0.00 45.31 3.85
4502 4896 8.986477 AGATCAAATGCTGGTTTGTTTTATAC 57.014 30.769 0.00 0.00 39.50 1.47
4503 4897 8.806146 AGATCAAATGCTGGTTTGTTTTATACT 58.194 29.630 0.00 0.00 39.50 2.12
4572 4966 2.289565 GCCTAGTGATTACCTGCAACC 58.710 52.381 0.00 0.00 0.00 3.77
4644 5038 4.846779 TTTGACAAATGTTCCTGTAGGC 57.153 40.909 0.00 0.00 34.44 3.93
4647 5041 3.758023 TGACAAATGTTCCTGTAGGCATG 59.242 43.478 0.00 0.00 34.44 4.06
4660 5054 5.440610 CTGTAGGCATGGTATTTCTTTCCT 58.559 41.667 0.00 0.00 0.00 3.36
4703 5097 5.712152 TTTTCAAGAAAGGATGGCTCTTC 57.288 39.130 0.00 0.00 0.00 2.87
4707 5101 2.273619 AGAAAGGATGGCTCTTCAGGT 58.726 47.619 0.00 0.00 0.00 4.00
4711 5105 1.566298 GGATGGCTCTTCAGGTGGGT 61.566 60.000 0.00 0.00 0.00 4.51
4725 5119 4.167597 GGGTTGCCCGTCTTGAAA 57.832 55.556 0.00 0.00 32.13 2.69
4726 5120 1.658114 GGGTTGCCCGTCTTGAAAC 59.342 57.895 0.00 0.00 32.13 2.78
4727 5121 0.822121 GGGTTGCCCGTCTTGAAACT 60.822 55.000 0.00 0.00 32.13 2.66
4728 5122 1.543871 GGGTTGCCCGTCTTGAAACTA 60.544 52.381 0.00 0.00 32.13 2.24
4729 5123 2.223745 GGTTGCCCGTCTTGAAACTAA 58.776 47.619 0.00 0.00 0.00 2.24
4730 5124 2.619646 GGTTGCCCGTCTTGAAACTAAA 59.380 45.455 0.00 0.00 0.00 1.85
4731 5125 3.067040 GGTTGCCCGTCTTGAAACTAAAA 59.933 43.478 0.00 0.00 0.00 1.52
4732 5126 3.974871 TGCCCGTCTTGAAACTAAAAC 57.025 42.857 0.00 0.00 0.00 2.43
4733 5127 2.619646 TGCCCGTCTTGAAACTAAAACC 59.380 45.455 0.00 0.00 0.00 3.27
4734 5128 2.882761 GCCCGTCTTGAAACTAAAACCT 59.117 45.455 0.00 0.00 0.00 3.50
4735 5129 4.067192 GCCCGTCTTGAAACTAAAACCTA 58.933 43.478 0.00 0.00 0.00 3.08
4736 5130 4.516321 GCCCGTCTTGAAACTAAAACCTAA 59.484 41.667 0.00 0.00 0.00 2.69
4737 5131 5.561532 GCCCGTCTTGAAACTAAAACCTAAC 60.562 44.000 0.00 0.00 0.00 2.34
4738 5132 5.049198 CCCGTCTTGAAACTAAAACCTAACC 60.049 44.000 0.00 0.00 0.00 2.85
4739 5133 5.333568 CCGTCTTGAAACTAAAACCTAACCG 60.334 44.000 0.00 0.00 0.00 4.44
4740 5134 5.234972 CGTCTTGAAACTAAAACCTAACCGT 59.765 40.000 0.00 0.00 0.00 4.83
4741 5135 6.424683 GTCTTGAAACTAAAACCTAACCGTG 58.575 40.000 0.00 0.00 0.00 4.94
4742 5136 6.258507 GTCTTGAAACTAAAACCTAACCGTGA 59.741 38.462 0.00 0.00 0.00 4.35
4743 5137 6.993902 TCTTGAAACTAAAACCTAACCGTGAT 59.006 34.615 0.00 0.00 0.00 3.06
4744 5138 7.499895 TCTTGAAACTAAAACCTAACCGTGATT 59.500 33.333 0.00 0.00 0.00 2.57
4745 5139 8.674263 TTGAAACTAAAACCTAACCGTGATTA 57.326 30.769 0.00 0.00 0.00 1.75
4746 5140 8.674263 TGAAACTAAAACCTAACCGTGATTAA 57.326 30.769 0.00 0.00 0.00 1.40
4747 5141 9.118300 TGAAACTAAAACCTAACCGTGATTAAA 57.882 29.630 0.00 0.00 0.00 1.52
4748 5142 9.949174 GAAACTAAAACCTAACCGTGATTAAAA 57.051 29.630 0.00 0.00 0.00 1.52
4800 5194 0.322098 TTGCAACGGGATACACTGGG 60.322 55.000 0.00 0.00 39.74 4.45
4816 5211 2.025321 ACTGGGGCGAAATTGGACTATT 60.025 45.455 0.00 0.00 0.00 1.73
4830 5225 5.818678 TGGACTATTGTGTGGTAGAAACT 57.181 39.130 0.00 0.00 0.00 2.66
4831 5226 5.547465 TGGACTATTGTGTGGTAGAAACTG 58.453 41.667 0.00 0.00 0.00 3.16
4835 5230 6.398918 ACTATTGTGTGGTAGAAACTGCTAG 58.601 40.000 0.00 0.00 0.00 3.42
4860 5255 2.032550 AGCAGCATCAATGTATCGTTGC 59.967 45.455 0.00 0.00 31.18 4.17
4879 5274 8.700722 TCGTTGCGGTAGAAAATTATTAGTTA 57.299 30.769 0.00 0.00 0.00 2.24
5057 5452 9.785982 ACTTCCTCCATAAAGAAATATAAGAGC 57.214 33.333 0.00 0.00 0.00 4.09
5058 5453 8.833231 TTCCTCCATAAAGAAATATAAGAGCG 57.167 34.615 0.00 0.00 0.00 5.03
5059 5454 7.963532 TCCTCCATAAAGAAATATAAGAGCGT 58.036 34.615 0.00 0.00 0.00 5.07
5060 5455 8.429641 TCCTCCATAAAGAAATATAAGAGCGTT 58.570 33.333 0.00 0.00 0.00 4.84
5061 5456 9.057089 CCTCCATAAAGAAATATAAGAGCGTTT 57.943 33.333 0.00 0.00 0.00 3.60
5078 5473 9.654663 AAGAGCGTTTAGATCACTATTTTTAGT 57.345 29.630 0.00 0.00 37.82 2.24
5079 5474 9.088512 AGAGCGTTTAGATCACTATTTTTAGTG 57.911 33.333 6.78 6.78 46.52 2.74
5093 5488 9.654663 ACTATTTTTAGTGATCTAAACGCTCTT 57.345 29.630 0.00 0.00 43.20 2.85
5102 5497 9.601217 AGTGATCTAAACGCTCTTATATTTGTT 57.399 29.630 0.00 0.00 0.00 2.83
5110 5505 7.772332 ACGCTCTTATATTTGTTTACAGAGG 57.228 36.000 0.00 0.00 0.00 3.69
5111 5506 6.761714 ACGCTCTTATATTTGTTTACAGAGGG 59.238 38.462 8.36 8.36 38.95 4.30
5140 5575 5.309323 TGGCTTACTTACATGATGCAAAC 57.691 39.130 0.00 0.00 0.00 2.93
5309 5824 5.598830 TGCCACCCACTTAAAAAGTTATTCA 59.401 36.000 0.00 0.00 40.46 2.57
5328 5843 9.284594 GTTATTCAGATCTCGATACAGATTAGC 57.715 37.037 0.00 0.00 32.94 3.09
5400 6057 4.655186 CCTCTCATGATTCCTCTCTTTCCT 59.345 45.833 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.657594 CACTATTGACTGCTGCGTCAG 59.342 52.381 20.34 14.55 44.02 3.51
12 13 1.002366 CCACTATTGACTGCTGCGTC 58.998 55.000 14.64 14.64 34.52 5.19
14 15 1.002366 GTCCACTATTGACTGCTGCG 58.998 55.000 0.00 0.00 0.00 5.18
15 16 1.339055 TGGTCCACTATTGACTGCTGC 60.339 52.381 0.00 0.00 33.22 5.25
16 17 2.768253 TGGTCCACTATTGACTGCTG 57.232 50.000 0.00 0.00 33.22 4.41
17 18 3.264193 TCAATGGTCCACTATTGACTGCT 59.736 43.478 12.94 0.00 45.01 4.24
18 19 3.609853 TCAATGGTCCACTATTGACTGC 58.390 45.455 12.94 0.00 45.01 4.40
22 23 4.220693 CCAGTCAATGGTCCACTATTGA 57.779 45.455 12.94 12.94 46.77 2.57
36 37 1.150536 GGCCCTGTTGACCAGTCAA 59.849 57.895 9.12 9.12 46.27 3.18
37 38 2.829384 GGGCCCTGTTGACCAGTCA 61.829 63.158 17.04 0.00 39.74 3.41
38 39 2.034221 GGGCCCTGTTGACCAGTC 59.966 66.667 17.04 0.00 39.74 3.51
39 40 3.580319 GGGGCCCTGTTGACCAGT 61.580 66.667 24.38 0.00 39.74 4.00
40 41 4.366684 GGGGGCCCTGTTGACCAG 62.367 72.222 24.38 0.00 41.15 4.00
55 56 3.583882 AATGACAAGTGGGCCCGGG 62.584 63.158 19.09 19.09 0.00 5.73
56 57 2.035626 AATGACAAGTGGGCCCGG 59.964 61.111 19.37 9.27 0.00 5.73
57 58 1.303236 TCAATGACAAGTGGGCCCG 60.303 57.895 19.37 4.81 0.00 6.13
92 93 8.871629 TGCTAACAAAAATGATTAACCCTCTA 57.128 30.769 0.00 0.00 0.00 2.43
95 96 7.378181 CACTGCTAACAAAAATGATTAACCCT 58.622 34.615 0.00 0.00 0.00 4.34
99 100 6.295575 CCCCCACTGCTAACAAAAATGATTAA 60.296 38.462 0.00 0.00 0.00 1.40
152 153 5.694006 AGCGCTAATGACTCTGCTAATTAAG 59.306 40.000 8.99 0.00 0.00 1.85
167 168 2.796032 GGCTTTGCCTTTAGCGCTAATG 60.796 50.000 29.17 28.23 46.69 1.90
228 229 1.080093 GTCGACCGAACAGCCATCA 60.080 57.895 3.51 0.00 0.00 3.07
231 232 2.649034 GAGTCGACCGAACAGCCA 59.351 61.111 13.01 0.00 0.00 4.75
348 349 4.680237 CGCTTCAGGTCACCGCCA 62.680 66.667 0.00 0.00 0.00 5.69
370 371 2.606213 TCATGGCCGTGACCTCCA 60.606 61.111 24.15 0.00 0.00 3.86
497 498 2.912624 GCCCGATATTGCTGCTGCC 61.913 63.158 13.47 0.00 38.71 4.85
597 598 1.394917 CTACTCAATTGCAGCGTGTCC 59.605 52.381 0.00 0.00 0.00 4.02
626 627 1.078426 GGCGCTCCACACAATAGGT 60.078 57.895 7.64 0.00 0.00 3.08
670 671 0.464373 CCTCACCATCGGAACATGGG 60.464 60.000 5.90 0.00 46.98 4.00
705 1072 4.186159 GGAGATTGCCCAAACATTCATTG 58.814 43.478 0.00 0.00 0.00 2.82
719 1086 4.512944 TCTCTATTTTCGCATGGAGATTGC 59.487 41.667 0.00 0.00 36.23 3.56
722 1089 4.590647 TCCTCTCTATTTTCGCATGGAGAT 59.409 41.667 0.00 0.00 39.35 2.75
723 1090 3.960755 TCCTCTCTATTTTCGCATGGAGA 59.039 43.478 0.00 5.46 38.19 3.71
810 1179 5.931146 CCATTTCTCTCTATTTGATCCTCGG 59.069 44.000 0.00 0.00 0.00 4.63
883 1252 4.700213 AGGAAAGTGGTGTGTATATGTTGC 59.300 41.667 0.00 0.00 0.00 4.17
884 1253 5.937540 TGAGGAAAGTGGTGTGTATATGTTG 59.062 40.000 0.00 0.00 0.00 3.33
885 1254 6.121776 TGAGGAAAGTGGTGTGTATATGTT 57.878 37.500 0.00 0.00 0.00 2.71
886 1255 5.755409 TGAGGAAAGTGGTGTGTATATGT 57.245 39.130 0.00 0.00 0.00 2.29
887 1256 6.586344 AGATGAGGAAAGTGGTGTGTATATG 58.414 40.000 0.00 0.00 0.00 1.78
888 1257 6.814954 AGATGAGGAAAGTGGTGTGTATAT 57.185 37.500 0.00 0.00 0.00 0.86
889 1258 7.727578 TTAGATGAGGAAAGTGGTGTGTATA 57.272 36.000 0.00 0.00 0.00 1.47
1028 1418 3.992943 TCTTCTTCGGACTCTCTCTCT 57.007 47.619 0.00 0.00 0.00 3.10
1176 1566 0.676184 TAGAGCCCGATGAGCACATC 59.324 55.000 13.51 13.51 46.50 3.06
1272 1662 2.134287 GGCAGATCTGGAGGCGGTA 61.134 63.158 23.89 0.00 0.00 4.02
1430 1820 4.563140 AAGTAACTAATCGGGGCAAAGA 57.437 40.909 0.00 0.00 0.00 2.52
1454 1844 8.420374 TCGATCAGACAAGGATAATAAAACAC 57.580 34.615 0.00 0.00 0.00 3.32
1481 1871 2.309755 ACATCCATCGATTGCCCCATAT 59.690 45.455 0.00 0.00 0.00 1.78
1524 1914 3.873910 AGACATCCCTTATCACCAAACG 58.126 45.455 0.00 0.00 0.00 3.60
1547 1937 3.242739 CGCATTTCCCCGTATCAAAAGAG 60.243 47.826 0.00 0.00 0.00 2.85
1590 1980 5.240403 AGAGCAGAAAGGACATTTTCTCAAC 59.760 40.000 10.70 2.76 43.62 3.18
1634 2024 2.981859 ACTCCTATGCAACCCTAACG 57.018 50.000 0.00 0.00 0.00 3.18
1742 2132 5.106948 CGCAGTCTTGTGTATCTCAATGTTT 60.107 40.000 0.00 0.00 0.00 2.83
1750 2140 3.876274 ATCACGCAGTCTTGTGTATCT 57.124 42.857 2.73 0.00 45.85 1.98
1755 2145 3.436704 ACCAATAATCACGCAGTCTTGTG 59.563 43.478 0.00 0.00 41.61 3.33
1756 2146 3.436704 CACCAATAATCACGCAGTCTTGT 59.563 43.478 0.00 0.00 41.61 3.16
1764 2154 4.451096 CCCATAGTACACCAATAATCACGC 59.549 45.833 0.00 0.00 0.00 5.34
1804 2194 8.254508 GCAATCCAAACATACCCATAGTAAAAA 58.745 33.333 0.00 0.00 33.70 1.94
1805 2195 7.147811 GGCAATCCAAACATACCCATAGTAAAA 60.148 37.037 0.00 0.00 33.70 1.52
1806 2196 6.322712 GGCAATCCAAACATACCCATAGTAAA 59.677 38.462 0.00 0.00 33.70 2.01
1807 2197 5.830991 GGCAATCCAAACATACCCATAGTAA 59.169 40.000 0.00 0.00 33.70 2.24
1808 2198 5.103898 TGGCAATCCAAACATACCCATAGTA 60.104 40.000 0.00 0.00 39.99 1.82
1809 2199 4.215109 GGCAATCCAAACATACCCATAGT 58.785 43.478 0.00 0.00 0.00 2.12
1810 2200 4.037923 GTGGCAATCCAAACATACCCATAG 59.962 45.833 0.00 0.00 45.53 2.23
1811 2201 3.957497 GTGGCAATCCAAACATACCCATA 59.043 43.478 0.00 0.00 45.53 2.74
1812 2202 2.765699 GTGGCAATCCAAACATACCCAT 59.234 45.455 0.00 0.00 45.53 4.00
1813 2203 2.175202 GTGGCAATCCAAACATACCCA 58.825 47.619 0.00 0.00 45.53 4.51
1814 2204 1.480545 GGTGGCAATCCAAACATACCC 59.519 52.381 0.00 0.00 45.53 3.69
1815 2205 2.175202 TGGTGGCAATCCAAACATACC 58.825 47.619 0.00 0.00 45.53 2.73
1816 2206 3.006323 TGTTGGTGGCAATCCAAACATAC 59.994 43.478 10.79 0.87 45.53 2.39
1817 2207 3.234353 TGTTGGTGGCAATCCAAACATA 58.766 40.909 10.79 0.00 45.53 2.29
1818 2208 2.045524 TGTTGGTGGCAATCCAAACAT 58.954 42.857 10.79 0.00 45.53 2.71
1819 2209 1.489481 TGTTGGTGGCAATCCAAACA 58.511 45.000 10.79 8.88 45.53 2.83
1820 2210 2.837532 ATGTTGGTGGCAATCCAAAC 57.162 45.000 10.79 6.77 45.53 2.93
1821 2211 3.853355 AAATGTTGGTGGCAATCCAAA 57.147 38.095 10.79 3.46 45.53 3.28
1822 2212 4.081198 GGATAAATGTTGGTGGCAATCCAA 60.081 41.667 5.52 5.52 45.53 3.53
1823 2213 3.450457 GGATAAATGTTGGTGGCAATCCA 59.550 43.478 4.58 0.00 40.85 3.41
1861 2251 6.594159 ACCGATGTTTTAGACTTTAGGTCATG 59.406 38.462 0.00 0.00 46.72 3.07
1865 2255 5.012354 TGGACCGATGTTTTAGACTTTAGGT 59.988 40.000 0.00 0.00 33.00 3.08
1868 2258 6.469410 ACATGGACCGATGTTTTAGACTTTA 58.531 36.000 0.00 0.00 32.38 1.85
1883 2273 2.480073 GCAATCATCCAAACATGGACCG 60.480 50.000 0.00 0.00 41.33 4.79
1925 2315 5.148651 TGAACTAGGACTACCAAAGAAGC 57.851 43.478 0.00 0.00 38.94 3.86
1937 2327 4.737855 TGGCTAGACAATGAACTAGGAC 57.262 45.455 0.00 5.50 37.25 3.85
1983 2373 4.705023 TGGCTAGCCAAAATTAGAGGTTTC 59.295 41.667 34.27 1.11 44.12 2.78
1984 2374 4.672899 TGGCTAGCCAAAATTAGAGGTTT 58.327 39.130 34.27 0.00 44.12 3.27
2005 2395 5.448904 CCAAGTTTGTCCTGCCAAAATTTTG 60.449 40.000 21.65 21.65 39.70 2.44
2006 2396 4.639755 CCAAGTTTGTCCTGCCAAAATTTT 59.360 37.500 0.00 0.00 39.70 1.82
2007 2397 4.080638 TCCAAGTTTGTCCTGCCAAAATTT 60.081 37.500 0.00 0.00 39.70 1.82
2050 2440 7.545965 CGTGAGACCAAAACTATGAAAGACTAT 59.454 37.037 0.00 0.00 0.00 2.12
2053 2443 5.107065 CCGTGAGACCAAAACTATGAAAGAC 60.107 44.000 0.00 0.00 0.00 3.01
2054 2444 4.994852 CCGTGAGACCAAAACTATGAAAGA 59.005 41.667 0.00 0.00 0.00 2.52
2055 2445 4.755123 ACCGTGAGACCAAAACTATGAAAG 59.245 41.667 0.00 0.00 0.00 2.62
2059 2449 2.742053 CCACCGTGAGACCAAAACTATG 59.258 50.000 0.00 0.00 0.00 2.23
2070 2460 1.473257 GCATAGCAATCCACCGTGAGA 60.473 52.381 0.00 0.00 0.00 3.27
2089 2479 2.166254 CTGGGTCAACAATGTTATGGGC 59.834 50.000 0.00 0.00 0.00 5.36
2092 2482 5.418524 TGGATTCTGGGTCAACAATGTTATG 59.581 40.000 0.00 0.00 0.00 1.90
2131 2521 3.009723 ACATTTTCTGATGTAGCACCCG 58.990 45.455 0.00 0.00 38.43 5.28
2132 2522 3.378427 GGACATTTTCTGATGTAGCACCC 59.622 47.826 0.00 0.00 40.21 4.61
2171 2561 1.559682 GCACTGTTCCTAATGGGAGGA 59.440 52.381 0.00 0.00 46.01 3.71
2193 2583 4.148891 GTCTAGCAACGTTTCGGAAAATG 58.851 43.478 4.46 6.32 37.40 2.32
2194 2584 3.187842 GGTCTAGCAACGTTTCGGAAAAT 59.812 43.478 4.46 0.00 0.00 1.82
2318 2708 7.530426 AAATGGGATAGAGGTGCATTTAATC 57.470 36.000 0.00 0.00 0.00 1.75
2459 2849 0.905357 TAAGAGGTGAAGAGCAGGCC 59.095 55.000 0.00 0.00 0.00 5.19
2677 3068 5.049405 CACCCGAGATATTGTAGAAATTGGC 60.049 44.000 0.00 0.00 0.00 4.52
2806 3197 2.771943 TGGAGCTAGTAACCAATCCCAG 59.228 50.000 0.00 0.00 0.00 4.45
2879 3270 1.476891 TCAGCCGAACTACCTTGCTAG 59.523 52.381 0.00 0.00 0.00 3.42
2891 3282 9.549078 TTAATACATGTATTGTAATCAGCCGAA 57.451 29.630 32.16 16.18 43.84 4.30
2980 3371 8.667076 AAACGAACCATAGTACTAAACAAAGT 57.333 30.769 6.70 1.55 0.00 2.66
3166 3557 9.313118 GGCATAACTGATAAAAACCCATTAAAG 57.687 33.333 0.00 0.00 0.00 1.85
3167 3558 8.816894 TGGCATAACTGATAAAAACCCATTAAA 58.183 29.630 0.00 0.00 0.00 1.52
3168 3559 8.254508 GTGGCATAACTGATAAAAACCCATTAA 58.745 33.333 0.00 0.00 0.00 1.40
3200 3591 3.412386 GCAAAACTGAGTAGTGGGACAT 58.588 45.455 0.00 0.00 44.52 3.06
3248 3640 1.599542 GTGTCTAATGAAGCGATGGCC 59.400 52.381 0.00 0.00 41.24 5.36
3398 3791 2.504367 AGAACGTTGTTGGGATCAAGG 58.496 47.619 5.00 0.00 36.93 3.61
3482 3875 3.509184 CCACATGTCAGTTCTCTCTCTCA 59.491 47.826 0.00 0.00 0.00 3.27
3485 3878 2.564947 ACCCACATGTCAGTTCTCTCTC 59.435 50.000 0.00 0.00 0.00 3.20
3521 3914 3.198068 CCCGTTGACCATGTTCTATGAG 58.802 50.000 0.00 0.00 0.00 2.90
3663 4057 4.695455 GCCATTAGAAGTTACAACTGCTCA 59.305 41.667 5.86 0.00 41.10 4.26
3710 4104 4.439563 GGGTTTTTATCAGTTATGCCACCG 60.440 45.833 0.00 0.00 0.00 4.94
3711 4105 4.709886 AGGGTTTTTATCAGTTATGCCACC 59.290 41.667 0.00 0.00 0.00 4.61
3868 4262 4.499040 CGAACCAGTGATGAAACACAAAAC 59.501 41.667 0.00 0.00 42.45 2.43
3893 4287 7.777095 TCAAGTGTTATGGCAAAAGTAACTTT 58.223 30.769 9.41 0.00 34.94 2.66
4081 4475 2.487805 GGATCCCACTCTGCAATGCATA 60.488 50.000 8.91 0.00 38.13 3.14
4314 4708 1.000163 AGTCTCAACTACACACTGCGG 60.000 52.381 0.00 0.00 32.59 5.69
4315 4709 2.423926 AGTCTCAACTACACACTGCG 57.576 50.000 0.00 0.00 32.59 5.18
4502 4896 9.107367 GTTCTTGAAGTACATGAATCGAAAAAG 57.893 33.333 0.00 0.00 42.00 2.27
4503 4897 8.073768 GGTTCTTGAAGTACATGAATCGAAAAA 58.926 33.333 0.00 0.00 42.00 1.94
4513 4907 3.189287 GTGCAGGGTTCTTGAAGTACATG 59.811 47.826 4.39 3.75 0.00 3.21
4523 4917 4.793201 ACTTAAAGAAGTGCAGGGTTCTT 58.207 39.130 11.23 11.23 44.50 2.52
4644 5038 6.884295 TGTGGTAGAAGGAAAGAAATACCATG 59.116 38.462 5.28 0.00 43.20 3.66
4647 5041 7.610305 TGAATGTGGTAGAAGGAAAGAAATACC 59.390 37.037 0.00 0.00 34.54 2.73
4711 5105 3.067040 GGTTTTAGTTTCAAGACGGGCAA 59.933 43.478 0.00 0.00 0.00 4.52
4717 5111 6.258507 TCACGGTTAGGTTTTAGTTTCAAGAC 59.741 38.462 0.00 0.00 0.00 3.01
4720 5114 7.571080 AATCACGGTTAGGTTTTAGTTTCAA 57.429 32.000 0.00 0.00 0.00 2.69
4721 5115 8.674263 TTAATCACGGTTAGGTTTTAGTTTCA 57.326 30.769 0.00 0.00 0.00 2.69
4754 5148 8.382130 CGCACCGTAATGTAGTTTTAGAATTTA 58.618 33.333 0.00 0.00 0.00 1.40
4755 5149 7.095102 ACGCACCGTAATGTAGTTTTAGAATTT 60.095 33.333 0.00 0.00 38.73 1.82
4762 5156 3.607542 GCAACGCACCGTAATGTAGTTTT 60.608 43.478 0.00 0.00 39.99 2.43
4800 5194 3.427503 CCACACAATAGTCCAATTTCGCC 60.428 47.826 0.00 0.00 0.00 5.54
4816 5211 2.367241 TGCTAGCAGTTTCTACCACACA 59.633 45.455 14.93 0.00 0.00 3.72
4835 5230 3.434641 ACGATACATTGATGCTGCTATGC 59.565 43.478 0.00 0.00 0.00 3.14
4850 5245 7.542534 AATAATTTTCTACCGCAACGATACA 57.457 32.000 0.00 0.00 0.00 2.29
4910 5305 7.399523 ACATGATATTTTAAAGAACGAGCGAC 58.600 34.615 0.00 0.00 0.00 5.19
5031 5426 9.785982 GCTCTTATATTTCTTTATGGAGGAAGT 57.214 33.333 0.00 0.00 0.00 3.01
5032 5427 8.930760 CGCTCTTATATTTCTTTATGGAGGAAG 58.069 37.037 0.00 0.00 0.00 3.46
5033 5428 8.429641 ACGCTCTTATATTTCTTTATGGAGGAA 58.570 33.333 0.00 0.00 0.00 3.36
5034 5429 7.963532 ACGCTCTTATATTTCTTTATGGAGGA 58.036 34.615 0.00 0.00 0.00 3.71
5035 5430 8.608844 AACGCTCTTATATTTCTTTATGGAGG 57.391 34.615 0.00 0.00 0.00 4.30
5052 5447 9.654663 ACTAAAAATAGTGATCTAAACGCTCTT 57.345 29.630 0.00 0.00 0.00 2.85
5066 5461 9.088512 AGAGCGTTTAGATCACTAAAAATAGTG 57.911 33.333 9.22 9.22 45.97 2.74
5067 5462 9.654663 AAGAGCGTTTAGATCACTAAAAATAGT 57.345 29.630 0.00 0.00 45.97 2.12
5076 5471 9.601217 AACAAATATAAGAGCGTTTAGATCACT 57.399 29.630 0.00 0.00 37.82 3.41
5084 5479 8.665685 CCTCTGTAAACAAATATAAGAGCGTTT 58.334 33.333 0.00 0.00 0.00 3.60
5085 5480 7.280205 CCCTCTGTAAACAAATATAAGAGCGTT 59.720 37.037 0.00 0.00 0.00 4.84
5086 5481 6.761714 CCCTCTGTAAACAAATATAAGAGCGT 59.238 38.462 0.00 0.00 0.00 5.07
5087 5482 6.292919 GCCCTCTGTAAACAAATATAAGAGCG 60.293 42.308 0.00 0.00 0.00 5.03
5088 5483 6.017026 GGCCCTCTGTAAACAAATATAAGAGC 60.017 42.308 0.00 0.00 0.00 4.09
5089 5484 7.227512 CAGGCCCTCTGTAAACAAATATAAGAG 59.772 40.741 0.00 0.00 38.64 2.85
5090 5485 7.054124 CAGGCCCTCTGTAAACAAATATAAGA 58.946 38.462 0.00 0.00 38.64 2.10
5091 5486 7.264373 CAGGCCCTCTGTAAACAAATATAAG 57.736 40.000 0.00 0.00 38.64 1.73
5125 5560 8.242085 TGCATAAAAAGTTTGCATCATGTAAG 57.758 30.769 0.00 0.00 41.18 2.34
5194 5693 9.384764 CAGAAGTATATAGAGATCGATGGTGTA 57.615 37.037 0.54 0.00 0.00 2.90
5309 5824 4.328536 ACCGCTAATCTGTATCGAGATCT 58.671 43.478 0.00 0.00 31.07 2.75
5319 5834 8.191534 AGGTATAATTCTTACCGCTAATCTGT 57.808 34.615 10.37 0.00 43.25 3.41


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

AutoCloner maintained by Alex Coulton.