Multiple sequence alignment - TraesCS7D01G361000

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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 TraesCS7D01G361000 chr7D 100.000 8221 0 0 688 8908 463877929 463886149 0.000000e+00 15182.0
1 TraesCS7D01G361000 chr7D 100.000 400 0 0 1 400 463877242 463877641 0.000000e+00 739.0
2 TraesCS7D01G361000 chr2D 98.681 2578 29 2 3801 6376 106330120 106332694 0.000000e+00 4567.0
3 TraesCS7D01G361000 chr7A 98.642 2577 33 2 3801 6376 109349378 109351953 0.000000e+00 4564.0
4 TraesCS7D01G361000 chr7A 98.487 2578 36 2 3801 6376 232386599 232384023 0.000000e+00 4542.0
5 TraesCS7D01G361000 chr7A 92.227 3165 149 36 688 3782 536521129 536517992 0.000000e+00 4392.0
6 TraesCS7D01G361000 chr7A 94.803 2001 56 15 6372 8356 536518007 536516039 0.000000e+00 3075.0
7 TraesCS7D01G361000 chr7A 93.711 318 17 2 8591 8908 536515903 536515589 2.910000e-129 473.0
8 TraesCS7D01G361000 chr7A 86.296 270 17 16 140 400 536521461 536521203 8.810000e-70 276.0
9 TraesCS7D01G361000 chr7A 85.417 144 21 0 3284 3427 193560953 193560810 5.570000e-32 150.0
10 TraesCS7D01G361000 chr7A 83.815 173 7 9 8388 8545 228298117 228298283 2.590000e-30 145.0
11 TraesCS7D01G361000 chr7A 88.000 125 6 5 8394 8515 92634949 92634831 1.210000e-28 139.0
12 TraesCS7D01G361000 chr7A 87.500 128 7 5 8391 8515 731343484 731343363 1.210000e-28 139.0
13 TraesCS7D01G361000 chr5D 98.410 2578 39 1 3801 6376 166629264 166631841 0.000000e+00 4532.0
14 TraesCS7D01G361000 chr5A 98.410 2578 36 2 3801 6376 23606399 23608973 0.000000e+00 4529.0
15 TraesCS7D01G361000 chr1D 98.374 2583 30 4 3801 6376 94053238 94050661 0.000000e+00 4527.0
16 TraesCS7D01G361000 chr1A 98.371 2578 37 2 3801 6376 112938264 112940838 0.000000e+00 4523.0
17 TraesCS7D01G361000 chr1A 88.281 128 6 5 8391 8515 557978777 557978656 2.590000e-30 145.0
18 TraesCS7D01G361000 chr1A 95.000 40 2 0 8468 8507 30579103 30579064 7.470000e-06 63.9
19 TraesCS7D01G361000 chr4D 98.332 2578 41 1 3801 6376 48071048 48073625 0.000000e+00 4521.0
20 TraesCS7D01G361000 chr1B 98.295 2581 42 1 3801 6379 69843199 69840619 0.000000e+00 4521.0
21 TraesCS7D01G361000 chr1B 88.800 125 4 5 8391 8511 378403157 378403039 2.590000e-30 145.0
22 TraesCS7D01G361000 chr7B 91.344 3177 170 39 688 3782 487815114 487811961 0.000000e+00 4246.0
23 TraesCS7D01G361000 chr7B 92.933 1882 81 27 6487 8356 487811777 487809936 0.000000e+00 2691.0
24 TraesCS7D01G361000 chr7B 89.404 453 23 13 8460 8908 487809899 487809468 1.690000e-151 547.0
25 TraesCS7D01G361000 chr7B 91.444 374 20 5 33 400 487815551 487815184 3.710000e-138 503.0
26 TraesCS7D01G361000 chr7B 98.319 119 2 0 6372 6490 487811976 487811858 9.060000e-50 209.0
27 TraesCS7D01G361000 chr7B 81.618 136 7 6 8440 8558 529145399 529145265 7.360000e-16 97.1
28 TraesCS7D01G361000 chr2A 84.237 590 73 16 3045 3620 753810623 753811206 2.810000e-154 556.0
29 TraesCS7D01G361000 chr2A 89.602 327 31 2 2715 3039 753798041 753798366 6.440000e-111 412.0
30 TraesCS7D01G361000 chr6B 88.811 143 16 0 3285 3427 300720899 300720757 9.190000e-40 176.0
31 TraesCS7D01G361000 chr6B 89.394 132 14 0 2414 2545 300722204 300722073 5.530000e-37 167.0
32 TraesCS7D01G361000 chr6A 86.709 158 21 0 3270 3427 221345770 221345927 9.190000e-40 176.0
33 TraesCS7D01G361000 chr6A 89.922 129 13 0 2411 2539 221344472 221344600 5.530000e-37 167.0
34 TraesCS7D01G361000 chr6A 83.041 171 7 8 8391 8545 595269447 595269283 1.560000e-27 135.0
35 TraesCS7D01G361000 chr6A 80.537 149 7 10 8413 8545 77839003 77838861 2.650000e-15 95.3
36 TraesCS7D01G361000 chr6D 88.112 143 17 0 3285 3427 161975062 161975204 4.280000e-38 171.0
37 TraesCS7D01G361000 chr6D 88.372 129 15 0 2411 2539 161973750 161973878 1.200000e-33 156.0
38 TraesCS7D01G361000 chrUn 87.879 132 16 0 2414 2545 212095079 212094948 1.200000e-33 156.0
39 TraesCS7D01G361000 chr4A 84.524 168 15 8 8388 8545 115288515 115288681 1.200000e-33 156.0
40 TraesCS7D01G361000 chr4A 81.921 177 10 8 8397 8557 359273961 359273791 7.260000e-26 130.0
41 TraesCS7D01G361000 chr3D 85.417 144 21 0 3284 3427 351126158 351126015 5.570000e-32 150.0
42 TraesCS7D01G361000 chr3D 87.786 131 7 5 8388 8515 66523635 66523759 2.590000e-30 145.0
43 TraesCS7D01G361000 chr3D 87.500 128 7 5 8391 8515 134083935 134083814 1.210000e-28 139.0
44 TraesCS7D01G361000 chr3B 85.417 144 21 0 3284 3427 449810889 449810746 5.570000e-32 150.0
45 TraesCS7D01G361000 chr5B 88.281 128 6 5 8391 8515 506957149 506957028 2.590000e-30 145.0
46 TraesCS7D01G361000 chr2B 82.514 183 9 10 8391 8556 44928301 44928125 1.210000e-28 139.0


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 TraesCS7D01G361000 chr7D 463877242 463886149 8907 False 7960.5 15182 100.00000 1 8908 2 chr7D.!!$F1 8907
1 TraesCS7D01G361000 chr2D 106330120 106332694 2574 False 4567.0 4567 98.68100 3801 6376 1 chr2D.!!$F1 2575
2 TraesCS7D01G361000 chr7A 109349378 109351953 2575 False 4564.0 4564 98.64200 3801 6376 1 chr7A.!!$F1 2575
3 TraesCS7D01G361000 chr7A 232384023 232386599 2576 True 4542.0 4542 98.48700 3801 6376 1 chr7A.!!$R3 2575
4 TraesCS7D01G361000 chr7A 536515589 536521461 5872 True 2054.0 4392 91.75925 140 8908 4 chr7A.!!$R5 8768
5 TraesCS7D01G361000 chr5D 166629264 166631841 2577 False 4532.0 4532 98.41000 3801 6376 1 chr5D.!!$F1 2575
6 TraesCS7D01G361000 chr5A 23606399 23608973 2574 False 4529.0 4529 98.41000 3801 6376 1 chr5A.!!$F1 2575
7 TraesCS7D01G361000 chr1D 94050661 94053238 2577 True 4527.0 4527 98.37400 3801 6376 1 chr1D.!!$R1 2575
8 TraesCS7D01G361000 chr1A 112938264 112940838 2574 False 4523.0 4523 98.37100 3801 6376 1 chr1A.!!$F1 2575
9 TraesCS7D01G361000 chr4D 48071048 48073625 2577 False 4521.0 4521 98.33200 3801 6376 1 chr4D.!!$F1 2575
10 TraesCS7D01G361000 chr1B 69840619 69843199 2580 True 4521.0 4521 98.29500 3801 6379 1 chr1B.!!$R1 2578
11 TraesCS7D01G361000 chr7B 487809468 487815551 6083 True 1639.2 4246 92.68880 33 8908 5 chr7B.!!$R2 8875
12 TraesCS7D01G361000 chr2A 753810623 753811206 583 False 556.0 556 84.23700 3045 3620 1 chr2A.!!$F2 575

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
215 216 0.474184 ATTCGGTATTCCTGCAGGGG 59.526 55.000 32.23 9.58 35.41 4.79 F
859 875 0.677731 CTGAATTTGGAGCTGCGGGA 60.678 55.000 0.00 0.00 0.00 5.14 F
2110 2194 0.601558 TCAGTTCACAGGCGAGGTAC 59.398 55.000 0.00 0.00 0.00 3.34 F
2901 2993 0.622665 AAAGCATGCAGAGGTAGCCT 59.377 50.000 21.98 0.00 36.03 4.58 F
3509 3614 2.027653 AGCTCTTCCTTGGAGTACTTGC 60.028 50.000 0.00 0.00 33.73 4.01 F
4180 4305 0.106519 AGCTGGTGGTTGCTGACTTT 60.107 50.000 0.00 0.00 38.21 2.66 F
5694 5824 0.610687 GTGTGAGGAGGAGGAGGTTG 59.389 60.000 0.00 0.00 0.00 3.77 F
6134 6264 0.250209 CAGAAGCTCCAGTGCACAGT 60.250 55.000 21.04 0.00 34.99 3.55 F
7877 8110 1.376037 CCCTGCGAAGACCTTGGAC 60.376 63.158 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1148 1181 1.377987 GCAATGGCAGTTACCCGGA 60.378 57.895 0.73 0.0 40.72 5.14 R
2405 2496 0.610687 GGACCTGTCACAGAAGGAGG 59.389 60.000 6.30 0.0 37.01 4.30 R
3508 3613 0.037975 CACTGGCAAAACATCAGGGC 60.038 55.000 0.00 0.0 33.19 5.19 R
3788 3908 0.117140 TCCCTCTTCCAGGCTTCTCA 59.883 55.000 0.00 0.0 41.80 3.27 R
5139 5266 3.443037 CAAACTGATTTTTGGTCACGCA 58.557 40.909 0.00 0.0 33.53 5.24 R
6131 6261 1.374252 ACGCTTTAGCCGTCCACTG 60.374 57.895 0.00 0.0 37.91 3.66 R
7271 7503 2.232452 CACCTTCATCAACCGAGAGAGT 59.768 50.000 0.00 0.0 0.00 3.24 R
7895 8128 0.957395 ACAAAGATCAGTGGGCAGCG 60.957 55.000 0.00 0.0 0.00 5.18 R
8863 9114 3.435105 TTGTGCAGCTACAAAACCAAG 57.565 42.857 0.00 0.0 37.60 3.61 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
29 30 6.048073 GTTGCAAACTCAAAAGAAAATCCC 57.952 37.500 0.00 0.00 45.32 3.85
30 31 4.702831 TGCAAACTCAAAAGAAAATCCCC 58.297 39.130 0.00 0.00 0.00 4.81
31 32 3.740832 GCAAACTCAAAAGAAAATCCCCG 59.259 43.478 0.00 0.00 0.00 5.73
36 37 4.141824 ACTCAAAAGAAAATCCCCGCAAAA 60.142 37.500 0.00 0.00 0.00 2.44
48 49 5.476091 TCCCCGCAAAAGAAAATGTAATT 57.524 34.783 0.00 0.00 38.98 1.40
74 75 4.883759 TCATCCTCCTATTCTTGAGTCCA 58.116 43.478 0.00 0.00 0.00 4.02
88 89 5.721480 TCTTGAGTCCAGATTAGAATCCACA 59.279 40.000 0.00 0.00 36.04 4.17
112 113 1.408969 AAAAACGGCCACACAGGAAT 58.591 45.000 2.24 0.00 41.22 3.01
121 122 3.877508 GGCCACACAGGAATACAGTATTC 59.122 47.826 21.06 21.06 42.94 1.75
125 126 6.183360 GCCACACAGGAATACAGTATTCTTTC 60.183 42.308 25.88 13.95 43.15 2.62
126 127 7.106239 CCACACAGGAATACAGTATTCTTTCT 58.894 38.462 25.88 15.58 43.15 2.52
127 128 7.607991 CCACACAGGAATACAGTATTCTTTCTT 59.392 37.037 25.88 10.71 43.15 2.52
129 130 8.375506 ACACAGGAATACAGTATTCTTTCTTGA 58.624 33.333 25.88 0.00 43.15 3.02
132 133 9.442047 CAGGAATACAGTATTCTTTCTTGAAGT 57.558 33.333 25.88 0.00 43.15 3.01
133 134 9.442047 AGGAATACAGTATTCTTTCTTGAAGTG 57.558 33.333 25.88 0.00 43.15 3.16
150 151 5.681880 TGAAGTGTAAAATTTTAGACGCGG 58.318 37.500 24.42 0.00 40.60 6.46
151 152 4.673534 AGTGTAAAATTTTAGACGCGGG 57.326 40.909 24.42 0.00 40.60 6.13
152 153 3.120095 AGTGTAAAATTTTAGACGCGGGC 60.120 43.478 24.42 1.16 40.60 6.13
153 154 3.075884 TGTAAAATTTTAGACGCGGGCT 58.924 40.909 12.47 10.27 0.00 5.19
215 216 0.474184 ATTCGGTATTCCTGCAGGGG 59.526 55.000 32.23 9.58 35.41 4.79
241 247 1.714899 CGCAAAAGCGGTATCCCCTG 61.715 60.000 1.34 0.00 0.00 4.45
282 288 2.684881 CTGCATTAATTTCCCGTCTGCT 59.315 45.455 0.00 0.00 0.00 4.24
807 823 1.931635 CTAGATCTGGGTCTAGGGGC 58.068 60.000 5.18 0.00 42.50 5.80
809 825 1.237458 GATCTGGGTCTAGGGGCCT 59.763 63.158 0.84 0.00 0.00 5.19
853 869 2.401766 CGCGCCTGAATTTGGAGCT 61.402 57.895 19.03 0.00 45.95 4.09
859 875 0.677731 CTGAATTTGGAGCTGCGGGA 60.678 55.000 0.00 0.00 0.00 5.14
878 894 1.427020 GCGATTGGCAGACAGCTTC 59.573 57.895 0.00 0.00 44.79 3.86
896 917 3.668656 GCTTCCTGTATTTGTTTTGTCGC 59.331 43.478 0.00 0.00 0.00 5.19
897 918 4.556699 GCTTCCTGTATTTGTTTTGTCGCT 60.557 41.667 0.00 0.00 0.00 4.93
921 944 2.100631 CGGGGTGATCTGCGTTGTC 61.101 63.158 0.00 0.00 0.00 3.18
929 952 2.037121 TGATCTGCGTTGTCTGGAGAAA 59.963 45.455 0.00 0.00 37.35 2.52
939 965 1.878522 CTGGAGAAACGCGGATCGG 60.879 63.158 12.47 0.00 43.86 4.18
958 991 0.863119 GTTTGATTCTGATGGCGCGC 60.863 55.000 25.94 25.94 0.00 6.86
1096 1129 5.877012 ACGTCTCGTTTAGTGTCTCCTTATA 59.123 40.000 0.00 0.00 36.35 0.98
1116 1149 2.597455 ACTTTAGCTTTGTGTGCCCAT 58.403 42.857 0.00 0.00 0.00 4.00
1148 1181 2.629656 GCGCCATTGCCTGTTGTCT 61.630 57.895 0.00 0.00 0.00 3.41
1149 1182 1.503542 CGCCATTGCCTGTTGTCTC 59.496 57.895 0.00 0.00 0.00 3.36
1228 1261 3.124297 GGAAGTTTGAGATGCTGACTTCG 59.876 47.826 8.04 0.00 44.32 3.79
1229 1262 3.667497 AGTTTGAGATGCTGACTTCGA 57.333 42.857 0.00 0.00 0.00 3.71
1305 1355 2.380084 TGCTGGAAATCCGTAGTGTC 57.620 50.000 0.00 0.00 39.43 3.67
1337 1387 9.391227 AGAGAGGGATCTAATCAAATTGTAGAT 57.609 33.333 6.00 6.00 37.31 1.98
1339 1389 8.381636 AGAGGGATCTAATCAAATTGTAGATGG 58.618 37.037 9.84 0.00 35.26 3.51
1414 1464 5.785639 TCCTTCAGGTCTTGCACTATGCG 62.786 52.174 0.00 0.00 40.63 4.73
1427 1477 5.162000 GCACTATGCGAATTCTTTTAGCT 57.838 39.130 3.52 0.00 31.71 3.32
1430 1480 7.186804 GCACTATGCGAATTCTTTTAGCTTAA 58.813 34.615 3.52 0.00 31.71 1.85
1531 1594 1.200020 GCATAGGGTCAAAGTGCACAC 59.800 52.381 21.04 8.13 35.93 3.82
1559 1628 6.176183 AGTACTGCTGCTACATTCTTTTCAT 58.824 36.000 0.00 0.00 0.00 2.57
1562 1631 5.939883 ACTGCTGCTACATTCTTTTCATACA 59.060 36.000 0.00 0.00 0.00 2.29
1706 1776 4.023707 GCATCTGTTAGCATATTCCCACAC 60.024 45.833 0.00 0.00 0.00 3.82
1715 1785 5.329399 AGCATATTCCCACACTTTTTACCA 58.671 37.500 0.00 0.00 0.00 3.25
1885 1955 7.763985 GGCTGTTGTGCAGGTTAATTAATATTT 59.236 33.333 0.31 0.00 45.14 1.40
1886 1956 9.150348 GCTGTTGTGCAGGTTAATTAATATTTT 57.850 29.630 0.31 0.00 45.14 1.82
2032 2108 9.516314 CTGTCGTTATCTATGTTTATCTGAACA 57.484 33.333 0.00 0.00 43.08 3.18
2058 2142 6.599638 GCTTGATTATACAGGTCTTTGAAGGT 59.400 38.462 0.00 0.00 0.00 3.50
2110 2194 0.601558 TCAGTTCACAGGCGAGGTAC 59.398 55.000 0.00 0.00 0.00 3.34
2140 2224 6.656693 CCATTATCCACAACTCTCTTCTTGTT 59.343 38.462 0.00 0.00 0.00 2.83
2193 2277 1.806247 GCTTTTGGTTGGCCACTGTTC 60.806 52.381 3.88 0.00 46.01 3.18
2217 2303 6.210185 TCGTATGATGAACTGATGATGAGGAT 59.790 38.462 0.00 0.00 0.00 3.24
2250 2336 8.400947 TCTTGAAAATGCTAAGTCATGCTTATC 58.599 33.333 9.18 6.84 38.82 1.75
2251 2337 7.031226 TGAAAATGCTAAGTCATGCTTATCC 57.969 36.000 9.18 5.82 38.82 2.59
2294 2381 2.158623 TGCATACCACTGGAATGGGATC 60.159 50.000 0.71 0.00 39.28 3.36
2296 2383 3.499202 GCATACCACTGGAATGGGATCAT 60.499 47.826 0.71 0.00 39.28 2.45
2298 2385 1.325355 CCACTGGAATGGGATCATGC 58.675 55.000 0.00 0.00 35.95 4.06
2305 2392 2.023673 GAATGGGATCATGCGGACAAA 58.976 47.619 0.00 0.00 33.18 2.83
2405 2496 5.576774 GCCACTTTTTGTTGCTTATGGTATC 59.423 40.000 0.00 0.00 34.83 2.24
2408 2499 7.029563 CACTTTTTGTTGCTTATGGTATCCTC 58.970 38.462 0.00 0.00 0.00 3.71
2471 2562 3.814283 TGCTTGGACGTATTTTTAACGGT 59.186 39.130 0.00 0.00 44.48 4.83
2573 2664 8.429641 AGTTCAAGGACACTGTTATTTAAGAGA 58.570 33.333 1.87 0.00 31.66 3.10
2681 2773 9.962783 ACTTCCGATAGTTATGTATTGTTACTC 57.037 33.333 0.00 0.00 0.00 2.59
2690 2782 9.396022 AGTTATGTATTGTTACTCATTTCAGGG 57.604 33.333 0.00 0.00 0.00 4.45
2873 2965 1.276421 GCTGGTCTTGTCAAGAGGCTA 59.724 52.381 15.71 2.63 38.41 3.93
2898 2990 2.706339 AGGAAAGCATGCAGAGGTAG 57.294 50.000 21.98 0.00 0.00 3.18
2901 2993 0.622665 AAAGCATGCAGAGGTAGCCT 59.377 50.000 21.98 0.00 36.03 4.58
3117 3209 6.007703 CACCCTTTTCCTGAACTTGGTATTA 58.992 40.000 0.00 0.00 0.00 0.98
3127 3219 8.044908 TCCTGAACTTGGTATTAACATTCTACC 58.955 37.037 0.00 0.00 36.30 3.18
3156 3248 3.139077 CAGACTTTTTCCTACCGCAAGT 58.861 45.455 0.00 0.00 0.00 3.16
3233 3338 6.826668 TGTCTCCTAAACAAGATTTGACTCA 58.173 36.000 0.00 0.00 0.00 3.41
3508 3613 3.971245 AGCTCTTCCTTGGAGTACTTG 57.029 47.619 0.00 0.00 33.73 3.16
3509 3614 2.027653 AGCTCTTCCTTGGAGTACTTGC 60.028 50.000 0.00 0.00 33.73 4.01
3603 3711 6.128282 CCTTATTGCACACTAAAATGTCGTCT 60.128 38.462 0.00 0.00 0.00 4.18
3609 3717 7.489160 TGCACACTAAAATGTCGTCTATCTAT 58.511 34.615 0.00 0.00 0.00 1.98
3694 3802 4.423625 ACTGAAGTAGCAGAGTTTGGTT 57.576 40.909 0.00 0.00 39.20 3.67
3718 3827 7.381766 TGTGATCTGGTGTTGAAATATCTTG 57.618 36.000 0.00 0.00 0.00 3.02
3724 3833 8.870160 TCTGGTGTTGAAATATCTTGTTTTTG 57.130 30.769 0.00 0.00 0.00 2.44
3738 3858 8.721019 ATCTTGTTTTTGTTTGTTCATCACAT 57.279 26.923 0.00 0.00 34.43 3.21
3766 3886 4.448210 CCAAACGGCCATATAGTGTTAGT 58.552 43.478 2.24 0.00 0.00 2.24
3767 3887 4.272504 CCAAACGGCCATATAGTGTTAGTG 59.727 45.833 2.24 0.00 0.00 2.74
3768 3888 4.748277 AACGGCCATATAGTGTTAGTGT 57.252 40.909 2.24 0.00 0.00 3.55
3769 3889 4.748277 ACGGCCATATAGTGTTAGTGTT 57.252 40.909 2.24 0.00 0.00 3.32
3770 3890 4.439057 ACGGCCATATAGTGTTAGTGTTG 58.561 43.478 2.24 0.00 0.00 3.33
3771 3891 4.160814 ACGGCCATATAGTGTTAGTGTTGA 59.839 41.667 2.24 0.00 0.00 3.18
3772 3892 5.113383 CGGCCATATAGTGTTAGTGTTGAA 58.887 41.667 2.24 0.00 0.00 2.69
3773 3893 5.583061 CGGCCATATAGTGTTAGTGTTGAAA 59.417 40.000 2.24 0.00 0.00 2.69
3774 3894 6.092944 CGGCCATATAGTGTTAGTGTTGAAAA 59.907 38.462 2.24 0.00 0.00 2.29
3798 3918 2.772739 CCGATTGGTGAGAAGCCTG 58.227 57.895 0.00 0.00 0.00 4.85
3799 3919 0.745845 CCGATTGGTGAGAAGCCTGG 60.746 60.000 0.00 0.00 0.00 4.45
4111 4236 2.099921 GAGAAGAGAAGATAGGCGTGCA 59.900 50.000 0.00 0.00 0.00 4.57
4180 4305 0.106519 AGCTGGTGGTTGCTGACTTT 60.107 50.000 0.00 0.00 38.21 2.66
4239 4364 2.430465 AGTCGCTAGAACGAAGTGGTA 58.570 47.619 0.00 0.00 45.00 3.25
4443 4568 3.524789 TGGAATGATGATGTCCAGAAGGT 59.475 43.478 0.00 0.00 36.51 3.50
4842 4967 2.125106 GCGGCGAATCCAGGAGTT 60.125 61.111 12.98 0.00 34.01 3.01
4999 5124 3.213249 GCAAACAAGATGCCAGAAGAG 57.787 47.619 0.00 0.00 37.85 2.85
5067 5192 8.038944 GGATGTTCAGAGTTGTACTAATTACCA 58.961 37.037 0.00 0.00 0.00 3.25
5139 5266 3.375299 GCACCGCTTAAGAAGAATGACAT 59.625 43.478 6.67 0.00 0.00 3.06
5354 5481 4.949856 CCAGCAAAGTACATTACCCTCATT 59.050 41.667 0.00 0.00 0.00 2.57
5446 5573 1.771255 GATAGGACTGCATCAGGGGTT 59.229 52.381 0.00 0.00 35.51 4.11
5694 5824 0.610687 GTGTGAGGAGGAGGAGGTTG 59.389 60.000 0.00 0.00 0.00 3.77
6131 6261 0.673022 CTCCAGAAGCTCCAGTGCAC 60.673 60.000 9.40 9.40 34.99 4.57
6134 6264 0.250209 CAGAAGCTCCAGTGCACAGT 60.250 55.000 21.04 0.00 34.99 3.55
6441 6571 8.773404 TTTGTAGTTTTCTCTATCCAGTAAGC 57.227 34.615 0.00 0.00 0.00 3.09
6553 6767 4.772886 ACAAGTCAGTAACCCACTTCTT 57.227 40.909 0.00 0.00 34.26 2.52
6744 6958 5.557891 AGTGAATTGCTTGCTCTGTATTC 57.442 39.130 0.00 0.00 0.00 1.75
6746 6960 4.397417 GTGAATTGCTTGCTCTGTATTCCT 59.603 41.667 0.00 0.00 0.00 3.36
6747 6961 5.012239 TGAATTGCTTGCTCTGTATTCCTT 58.988 37.500 0.00 0.00 0.00 3.36
6748 6962 6.094048 GTGAATTGCTTGCTCTGTATTCCTTA 59.906 38.462 0.00 0.00 0.00 2.69
6749 6963 6.094048 TGAATTGCTTGCTCTGTATTCCTTAC 59.906 38.462 0.00 0.00 0.00 2.34
6750 6964 4.551702 TGCTTGCTCTGTATTCCTTACA 57.448 40.909 0.00 0.00 38.50 2.41
6764 6978 9.375974 TGTATTCCTTACAGTTATATAGCACCT 57.624 33.333 0.00 0.00 35.86 4.00
6831 7057 6.631971 TTAAAATCAGCATGTTGTCTGTCA 57.368 33.333 9.54 0.00 37.40 3.58
6832 7058 4.761235 AAATCAGCATGTTGTCTGTCAG 57.239 40.909 9.54 0.00 37.40 3.51
6833 7059 2.916702 TCAGCATGTTGTCTGTCAGT 57.083 45.000 9.54 0.00 37.40 3.41
6834 7060 2.486918 TCAGCATGTTGTCTGTCAGTG 58.513 47.619 9.54 0.00 37.40 3.66
6835 7061 2.158914 TCAGCATGTTGTCTGTCAGTGT 60.159 45.455 9.54 0.00 37.40 3.55
6836 7062 2.615447 CAGCATGTTGTCTGTCAGTGTT 59.385 45.455 0.65 0.00 0.00 3.32
6837 7063 3.065786 CAGCATGTTGTCTGTCAGTGTTT 59.934 43.478 0.65 0.00 0.00 2.83
6838 7064 3.065786 AGCATGTTGTCTGTCAGTGTTTG 59.934 43.478 0.00 0.00 0.00 2.93
6839 7065 3.065233 GCATGTTGTCTGTCAGTGTTTGA 59.935 43.478 0.00 0.00 0.00 2.69
6850 7076 4.734398 TCAGTGTTTGACCATTTTGCTT 57.266 36.364 0.00 0.00 0.00 3.91
6882 7108 4.571984 GTGTGATACAATCTAGCATGTGCA 59.428 41.667 7.83 6.01 45.16 4.57
6886 7112 2.362736 ACAATCTAGCATGTGCACCAG 58.637 47.619 15.69 7.88 45.16 4.00
6894 7120 1.812235 CATGTGCACCAGTCTAGCAA 58.188 50.000 15.69 0.00 40.35 3.91
6961 7187 5.881923 ATCTGATTGCATTTAGGCCAATT 57.118 34.783 5.01 0.00 0.00 2.32
7196 7427 7.932491 AGAACCTGTAGTAGTTTCTTTTCCTTC 59.068 37.037 0.00 0.00 34.86 3.46
7197 7428 7.376335 ACCTGTAGTAGTTTCTTTTCCTTCT 57.624 36.000 0.00 0.00 0.00 2.85
7198 7429 7.803131 ACCTGTAGTAGTTTCTTTTCCTTCTT 58.197 34.615 0.00 0.00 0.00 2.52
7271 7503 2.582172 ACCCATCAATGTCCTTCCATCA 59.418 45.455 0.00 0.00 0.00 3.07
7350 7582 7.719633 GGGTCCATTACTTTAAGATGCTATCAA 59.280 37.037 0.00 0.00 0.00 2.57
7450 7682 5.360999 TCGAGACCATTCAGATGTGTCTAAT 59.639 40.000 9.14 0.00 40.62 1.73
7468 7700 7.272948 GTGTCTAATCAGGTACTTACTTGAACG 59.727 40.741 5.42 0.00 43.93 3.95
7471 7703 4.170292 TCAGGTACTTACTTGAACGCTC 57.830 45.455 0.00 0.00 39.02 5.03
7510 7742 7.336931 CCTTTCTAGCCAATTGTAACATACAGT 59.663 37.037 4.43 0.00 40.24 3.55
7733 7966 4.792528 GCTTGTGCAGCTTTATCTAGAG 57.207 45.455 0.00 0.00 46.27 2.43
7877 8110 1.376037 CCCTGCGAAGACCTTGGAC 60.376 63.158 0.00 0.00 0.00 4.02
7895 8128 0.109689 ACGCGTTCTACAGCAGAGAC 60.110 55.000 5.58 0.00 33.83 3.36
7982 8220 5.681179 GCAGTTCAAACTTCTGGCCTTTTTA 60.681 40.000 3.32 0.00 37.08 1.52
8021 8259 6.830873 AGTCAGATCCCATTCTTTTTGAAG 57.169 37.500 0.00 0.00 38.18 3.02
8129 8374 0.110056 GAACCAACGCACATGAGCTG 60.110 55.000 13.36 9.09 0.00 4.24
8303 8548 3.764972 GGTTCTGTCTGTAACCTCTAGCT 59.235 47.826 0.00 0.00 41.63 3.32
8341 8586 8.701895 TCTCTTGGTACTTCTTTACTTTTCTGA 58.298 33.333 0.00 0.00 0.00 3.27
8356 8601 0.901124 TCTGAGAAGAGGAGCCTTGC 59.099 55.000 0.00 0.00 0.00 4.01
8357 8602 0.107752 CTGAGAAGAGGAGCCTTGCC 60.108 60.000 0.00 0.00 0.00 4.52
8358 8603 0.546267 TGAGAAGAGGAGCCTTGCCT 60.546 55.000 0.00 0.00 38.81 4.75
8359 8604 0.617935 GAGAAGAGGAGCCTTGCCTT 59.382 55.000 0.00 0.00 35.44 4.35
8360 8605 1.004161 GAGAAGAGGAGCCTTGCCTTT 59.996 52.381 0.00 0.00 35.44 3.11
8361 8606 1.426983 AGAAGAGGAGCCTTGCCTTTT 59.573 47.619 0.00 0.00 35.44 2.27
8362 8607 2.158400 AGAAGAGGAGCCTTGCCTTTTT 60.158 45.455 0.00 0.00 35.44 1.94
8382 8627 2.561478 TTTGTGTGGGTAAGAGGAGC 57.439 50.000 0.00 0.00 0.00 4.70
8383 8628 0.690762 TTGTGTGGGTAAGAGGAGCC 59.309 55.000 0.00 0.00 37.51 4.70
8384 8629 0.178903 TGTGTGGGTAAGAGGAGCCT 60.179 55.000 0.00 0.00 37.88 4.58
8385 8630 0.984995 GTGTGGGTAAGAGGAGCCTT 59.015 55.000 0.00 0.00 37.88 4.35
8386 8631 0.984230 TGTGGGTAAGAGGAGCCTTG 59.016 55.000 0.00 0.00 37.88 3.61
8387 8632 0.253327 GTGGGTAAGAGGAGCCTTGG 59.747 60.000 0.00 0.00 37.88 3.61
8388 8633 1.224870 GGGTAAGAGGAGCCTTGGC 59.775 63.158 2.97 2.97 33.97 4.52
8389 8634 1.153349 GGTAAGAGGAGCCTTGGCG 60.153 63.158 5.95 0.00 0.00 5.69
8390 8635 1.597461 GTAAGAGGAGCCTTGGCGT 59.403 57.895 5.95 0.00 0.00 5.68
8391 8636 0.036294 GTAAGAGGAGCCTTGGCGTT 60.036 55.000 5.95 0.00 0.00 4.84
8437 8682 1.266178 TGACCATGTCACGGACTCAT 58.734 50.000 0.00 0.00 37.67 2.90
8438 8683 1.066929 TGACCATGTCACGGACTCATG 60.067 52.381 0.00 0.00 37.67 3.07
8440 8685 3.070076 CATGTCACGGACTCATGGG 57.930 57.895 0.00 0.00 36.36 4.00
8442 8687 0.984230 ATGTCACGGACTCATGGGTT 59.016 50.000 0.00 0.00 33.15 4.11
8443 8688 0.320374 TGTCACGGACTCATGGGTTC 59.680 55.000 0.00 0.00 33.15 3.62
8444 8689 0.320374 GTCACGGACTCATGGGTTCA 59.680 55.000 4.50 0.00 0.00 3.18
8445 8690 1.052617 TCACGGACTCATGGGTTCAA 58.947 50.000 4.50 0.00 0.00 2.69
8446 8691 1.001974 TCACGGACTCATGGGTTCAAG 59.998 52.381 4.50 0.00 0.00 3.02
8447 8692 1.056660 ACGGACTCATGGGTTCAAGT 58.943 50.000 4.50 0.00 0.00 3.16
8448 8693 1.002087 ACGGACTCATGGGTTCAAGTC 59.998 52.381 4.50 3.16 37.90 3.01
8451 8696 2.704572 GACTCATGGGTTCAAGTCCTG 58.295 52.381 0.00 0.00 33.58 3.86
8452 8697 2.303022 GACTCATGGGTTCAAGTCCTGA 59.697 50.000 0.00 0.00 33.58 3.86
8474 8724 8.141268 CCTGAAAAACAGCCTCTTAAAATGTAA 58.859 33.333 0.00 0.00 44.52 2.41
8507 8757 4.320870 CGTACAATAGACCCAAAGTGGTT 58.679 43.478 0.00 0.00 39.24 3.67
8561 8811 4.161377 TGGGCTGTCTTTGCTTTACTTTTT 59.839 37.500 0.00 0.00 0.00 1.94
8712 8962 3.787105 CGAACTAAGCGTAGAGAAAGAGC 59.213 47.826 13.91 0.00 0.00 4.09
8739 8989 4.037446 GTGTAGTCATTTTGGTTTGCCTCA 59.963 41.667 0.00 0.00 35.27 3.86
8749 8999 7.546778 TTTTGGTTTGCCTCATCTTTTTAAC 57.453 32.000 0.00 0.00 35.27 2.01
8752 9002 4.915667 GGTTTGCCTCATCTTTTTAACGTC 59.084 41.667 0.00 0.00 0.00 4.34
8754 9004 2.158841 TGCCTCATCTTTTTAACGTCGC 59.841 45.455 0.00 0.00 0.00 5.19
8821 9071 4.855340 ACTTGGTTTGGTACTGGGATATG 58.145 43.478 0.00 0.00 0.00 1.78
8855 9106 7.648142 TCATTAGTGCCTTTCTGTTAACTTTG 58.352 34.615 7.22 0.00 0.00 2.77
8863 9114 7.440255 TGCCTTTCTGTTAACTTTGTAGAGTAC 59.560 37.037 7.22 0.00 0.00 2.73
8879 9130 4.065789 AGAGTACTTGGTTTTGTAGCTGC 58.934 43.478 0.00 0.00 0.00 5.25
8882 9133 2.374184 ACTTGGTTTTGTAGCTGCACA 58.626 42.857 3.11 0.00 0.00 4.57
8895 9146 4.871993 AGCTGCACAATAGATTCTTTCG 57.128 40.909 1.02 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.641020 GGATTTTCTTTTGAGTTTGCAACAATG 59.359 33.333 0.00 0.00 0.00 2.82
3 4 7.201723 GGGATTTTCTTTTGAGTTTGCAACAAT 60.202 33.333 0.00 0.00 0.00 2.71
4 5 6.093357 GGGATTTTCTTTTGAGTTTGCAACAA 59.907 34.615 0.00 0.00 0.00 2.83
5 6 5.584251 GGGATTTTCTTTTGAGTTTGCAACA 59.416 36.000 0.00 0.00 0.00 3.33
6 7 5.007626 GGGGATTTTCTTTTGAGTTTGCAAC 59.992 40.000 0.00 0.00 0.00 4.17
7 8 5.122519 GGGGATTTTCTTTTGAGTTTGCAA 58.877 37.500 0.00 0.00 0.00 4.08
8 9 4.702831 GGGGATTTTCTTTTGAGTTTGCA 58.297 39.130 0.00 0.00 0.00 4.08
9 10 3.740832 CGGGGATTTTCTTTTGAGTTTGC 59.259 43.478 0.00 0.00 0.00 3.68
10 11 3.740832 GCGGGGATTTTCTTTTGAGTTTG 59.259 43.478 0.00 0.00 0.00 2.93
11 12 3.386402 TGCGGGGATTTTCTTTTGAGTTT 59.614 39.130 0.00 0.00 0.00 2.66
12 13 2.962421 TGCGGGGATTTTCTTTTGAGTT 59.038 40.909 0.00 0.00 0.00 3.01
13 14 2.593026 TGCGGGGATTTTCTTTTGAGT 58.407 42.857 0.00 0.00 0.00 3.41
14 15 3.658757 TTGCGGGGATTTTCTTTTGAG 57.341 42.857 0.00 0.00 0.00 3.02
15 16 4.100189 TCTTTTGCGGGGATTTTCTTTTGA 59.900 37.500 0.00 0.00 0.00 2.69
16 17 4.376146 TCTTTTGCGGGGATTTTCTTTTG 58.624 39.130 0.00 0.00 0.00 2.44
17 18 4.681074 TCTTTTGCGGGGATTTTCTTTT 57.319 36.364 0.00 0.00 0.00 2.27
18 19 4.681074 TTCTTTTGCGGGGATTTTCTTT 57.319 36.364 0.00 0.00 0.00 2.52
19 20 4.681074 TTTCTTTTGCGGGGATTTTCTT 57.319 36.364 0.00 0.00 0.00 2.52
20 21 4.681074 TTTTCTTTTGCGGGGATTTTCT 57.319 36.364 0.00 0.00 0.00 2.52
21 22 4.754618 ACATTTTCTTTTGCGGGGATTTTC 59.245 37.500 0.00 0.00 0.00 2.29
22 23 4.713553 ACATTTTCTTTTGCGGGGATTTT 58.286 34.783 0.00 0.00 0.00 1.82
23 24 4.350368 ACATTTTCTTTTGCGGGGATTT 57.650 36.364 0.00 0.00 0.00 2.17
24 25 5.476091 TTACATTTTCTTTTGCGGGGATT 57.524 34.783 0.00 0.00 0.00 3.01
25 26 5.675684 ATTACATTTTCTTTTGCGGGGAT 57.324 34.783 0.00 0.00 0.00 3.85
26 27 5.476091 AATTACATTTTCTTTTGCGGGGA 57.524 34.783 0.00 0.00 0.00 4.81
27 28 6.552859 AAAATTACATTTTCTTTTGCGGGG 57.447 33.333 0.00 0.00 37.96 5.73
48 49 6.098982 GGACTCAAGAATAGGAGGATGAGAAA 59.901 42.308 7.51 0.00 38.10 2.52
55 56 4.609866 TCTGGACTCAAGAATAGGAGGA 57.390 45.455 0.00 0.00 35.45 3.71
99 100 3.560636 ATACTGTATTCCTGTGTGGCC 57.439 47.619 0.00 0.00 35.26 5.36
125 126 6.302313 CCGCGTCTAAAATTTTACACTTCAAG 59.698 38.462 4.92 1.89 0.00 3.02
126 127 6.137415 CCGCGTCTAAAATTTTACACTTCAA 58.863 36.000 4.92 0.00 0.00 2.69
127 128 5.334260 CCCGCGTCTAAAATTTTACACTTCA 60.334 40.000 4.92 0.00 0.00 3.02
129 130 4.614306 GCCCGCGTCTAAAATTTTACACTT 60.614 41.667 4.92 0.00 0.00 3.16
132 133 3.075884 AGCCCGCGTCTAAAATTTTACA 58.924 40.909 4.92 0.00 0.00 2.41
133 134 3.422655 CAGCCCGCGTCTAAAATTTTAC 58.577 45.455 4.92 0.42 0.00 2.01
150 151 0.106819 AGACATGAATCAGCCCAGCC 60.107 55.000 0.00 0.00 0.00 4.85
151 152 1.022735 CAGACATGAATCAGCCCAGC 58.977 55.000 0.00 0.00 0.00 4.85
152 153 2.704464 TCAGACATGAATCAGCCCAG 57.296 50.000 0.00 0.00 30.61 4.45
153 154 2.158711 GGATCAGACATGAATCAGCCCA 60.159 50.000 0.00 0.00 39.39 5.36
241 247 0.526211 GGAAACCCAATCGTTGAGGC 59.474 55.000 0.15 0.00 0.00 4.70
282 288 1.850345 GAAGAGGAGGAGAGAGGAGGA 59.150 57.143 0.00 0.00 0.00 3.71
740 756 0.171007 TCGGATTCGACACCCGTAAC 59.829 55.000 15.89 0.00 43.40 2.50
741 757 0.452987 CTCGGATTCGACACCCGTAA 59.547 55.000 15.89 1.41 43.40 3.18
823 839 4.719369 GGCGCGACAACCGAGACT 62.719 66.667 12.10 0.00 43.08 3.24
859 875 1.002868 AAGCTGTCTGCCAATCGCT 60.003 52.632 0.00 0.00 44.23 4.93
878 894 3.564511 CCAGCGACAAAACAAATACAGG 58.435 45.455 0.00 0.00 0.00 4.00
883 899 2.095263 CGATCCCAGCGACAAAACAAAT 60.095 45.455 0.00 0.00 0.00 2.32
887 908 1.644786 CCCGATCCCAGCGACAAAAC 61.645 60.000 0.00 0.00 0.00 2.43
913 934 2.600388 CGTTTCTCCAGACAACGCA 58.400 52.632 9.52 0.00 34.55 5.24
921 944 1.878522 CCGATCCGCGTTTCTCCAG 60.879 63.158 4.92 0.00 38.67 3.86
929 952 0.108329 AGAATCAAACCGATCCGCGT 60.108 50.000 4.92 0.00 38.67 6.01
939 965 0.863119 GCGCGCCATCAGAATCAAAC 60.863 55.000 23.24 0.00 0.00 2.93
1096 1129 2.065899 TGGGCACACAAAGCTAAAGT 57.934 45.000 0.00 0.00 0.00 2.66
1116 1149 2.477176 GGCGCAACACAACCACTGA 61.477 57.895 10.83 0.00 0.00 3.41
1148 1181 1.377987 GCAATGGCAGTTACCCGGA 60.378 57.895 0.73 0.00 40.72 5.14
1149 1182 3.196648 GCAATGGCAGTTACCCGG 58.803 61.111 0.00 0.00 40.72 5.73
1298 1348 3.912248 TCCCTCTCTATTGGGACACTAC 58.088 50.000 0.00 0.00 46.69 2.73
1305 1355 6.942163 TTGATTAGATCCCTCTCTATTGGG 57.058 41.667 0.00 0.00 44.66 4.12
1320 1370 8.677300 GCAAACTCCATCTACAATTTGATTAGA 58.323 33.333 2.79 1.55 30.35 2.10
1337 1387 5.108517 CAAAGCTACAAAAAGCAAACTCCA 58.891 37.500 0.00 0.00 45.30 3.86
1339 1389 4.566360 TGCAAAGCTACAAAAAGCAAACTC 59.434 37.500 0.00 0.00 45.30 3.01
1378 1428 2.668457 CTGAAGGAACATACTGTCGCAC 59.332 50.000 0.00 0.00 0.00 5.34
1382 1432 4.810191 AGACCTGAAGGAACATACTGTC 57.190 45.455 2.62 0.00 38.94 3.51
1386 1436 3.437049 GTGCAAGACCTGAAGGAACATAC 59.563 47.826 2.62 0.00 38.94 2.39
1427 1477 9.733219 CCAAAAAGGTTAACATTAGAACGTTAA 57.267 29.630 5.85 0.00 33.73 2.01
1430 1480 7.571080 TCCAAAAAGGTTAACATTAGAACGT 57.429 32.000 5.85 0.00 39.02 3.99
1531 1594 5.255710 AGAATGTAGCAGCAGTACTAGTG 57.744 43.478 5.39 0.00 0.00 2.74
1885 1955 3.248363 CGTCACAACAATGCAGAAGAGAA 59.752 43.478 0.00 0.00 0.00 2.87
1886 1956 2.802247 CGTCACAACAATGCAGAAGAGA 59.198 45.455 0.00 0.00 0.00 3.10
2009 2085 8.414003 AGCTGTTCAGATAAACATAGATAACGA 58.586 33.333 3.84 0.00 38.41 3.85
2032 2108 6.825721 CCTTCAAAGACCTGTATAATCAAGCT 59.174 38.462 0.00 0.00 0.00 3.74
2058 2142 9.431887 GTGTATTTGTTGTCTATTCCTGAAGTA 57.568 33.333 0.00 0.00 0.00 2.24
2110 2194 3.559069 AGAGTTGTGGATAATGGGCATG 58.441 45.455 0.00 0.00 0.00 4.06
2146 2230 9.787435 TTCCTTTTAGAGAGCATTTAAACAGTA 57.213 29.630 0.00 0.00 0.00 2.74
2147 2231 8.691661 TTCCTTTTAGAGAGCATTTAAACAGT 57.308 30.769 0.00 0.00 0.00 3.55
2148 2232 7.752686 GCTTCCTTTTAGAGAGCATTTAAACAG 59.247 37.037 0.00 0.00 33.68 3.16
2193 2277 5.776744 TCCTCATCATCAGTTCATCATACG 58.223 41.667 0.00 0.00 0.00 3.06
2251 2337 5.174395 CAGTTGTGATCCTCCTTACTCAAG 58.826 45.833 0.00 0.00 0.00 3.02
2294 2381 3.756802 TGTGGGTTTGTCCGCATG 58.243 55.556 0.00 0.00 41.81 4.06
2298 2385 1.953686 AGTTCAATGTGGGTTTGTCCG 59.046 47.619 0.00 0.00 37.00 4.79
2305 2392 6.065976 TCATTCTCATAGTTCAATGTGGGT 57.934 37.500 0.00 0.00 0.00 4.51
2405 2496 0.610687 GGACCTGTCACAGAAGGAGG 59.389 60.000 6.30 0.00 37.01 4.30
2408 2499 1.342074 TCAGGACCTGTCACAGAAGG 58.658 55.000 21.06 0.00 39.65 3.46
2471 2562 6.323739 GGCCATTATCAATAGGTTTTCCAGAA 59.676 38.462 0.00 0.00 43.73 3.02
2681 2773 6.423182 TGGGTTAATAGAACTCCCTGAAATG 58.577 40.000 0.00 0.00 38.95 2.32
2690 2782 7.171630 TCTCTCACTTGGGTTAATAGAACTC 57.828 40.000 0.00 0.00 0.00 3.01
2873 2965 3.345414 CTCTGCATGCTTTCCTTTCTCT 58.655 45.455 20.33 0.00 0.00 3.10
3263 3368 5.221048 GCCTAAAAGACAAACAAGAGCAGAA 60.221 40.000 0.00 0.00 0.00 3.02
3508 3613 0.037975 CACTGGCAAAACATCAGGGC 60.038 55.000 0.00 0.00 33.19 5.19
3509 3614 1.270550 GTCACTGGCAAAACATCAGGG 59.729 52.381 0.00 0.00 33.53 4.45
3609 3717 7.783090 TCATTCAAGCAGTAATTTTTGCAAA 57.217 28.000 8.05 8.05 42.67 3.68
3681 3789 3.144506 CAGATCACAACCAAACTCTGCT 58.855 45.455 0.00 0.00 0.00 4.24
3694 3802 6.942005 ACAAGATATTTCAACACCAGATCACA 59.058 34.615 0.00 0.00 0.00 3.58
3718 3827 7.393327 CAGTGATGTGATGAACAAACAAAAAC 58.607 34.615 0.00 0.00 43.61 2.43
3724 3833 3.004629 TGGCAGTGATGTGATGAACAAAC 59.995 43.478 0.00 0.00 43.61 2.93
3766 3886 3.697045 ACCAATCGGTTCTGTTTTCAACA 59.303 39.130 0.00 0.00 46.31 3.33
3767 3887 4.041723 CACCAATCGGTTCTGTTTTCAAC 58.958 43.478 0.00 0.00 46.31 3.18
3768 3888 3.948473 TCACCAATCGGTTCTGTTTTCAA 59.052 39.130 0.00 0.00 46.31 2.69
3769 3889 3.546724 TCACCAATCGGTTCTGTTTTCA 58.453 40.909 0.00 0.00 46.31 2.69
3770 3890 3.813166 TCTCACCAATCGGTTCTGTTTTC 59.187 43.478 0.00 0.00 46.31 2.29
3771 3891 3.815809 TCTCACCAATCGGTTCTGTTTT 58.184 40.909 0.00 0.00 46.31 2.43
3772 3892 3.485463 TCTCACCAATCGGTTCTGTTT 57.515 42.857 0.00 0.00 46.31 2.83
3773 3893 3.403038 CTTCTCACCAATCGGTTCTGTT 58.597 45.455 0.00 0.00 46.31 3.16
3774 3894 2.872038 GCTTCTCACCAATCGGTTCTGT 60.872 50.000 0.00 0.00 46.31 3.41
3775 3895 1.734465 GCTTCTCACCAATCGGTTCTG 59.266 52.381 0.00 0.00 46.31 3.02
3776 3896 1.339151 GGCTTCTCACCAATCGGTTCT 60.339 52.381 0.00 0.00 46.31 3.01
3777 3897 1.087501 GGCTTCTCACCAATCGGTTC 58.912 55.000 0.00 0.00 46.31 3.62
3778 3898 0.693049 AGGCTTCTCACCAATCGGTT 59.307 50.000 0.00 0.00 46.31 4.44
3780 3900 0.745845 CCAGGCTTCTCACCAATCGG 60.746 60.000 0.00 0.00 38.77 4.18
3781 3901 0.250234 TCCAGGCTTCTCACCAATCG 59.750 55.000 0.00 0.00 0.00 3.34
3782 3902 2.026822 TCTTCCAGGCTTCTCACCAATC 60.027 50.000 0.00 0.00 0.00 2.67
3783 3903 1.988107 TCTTCCAGGCTTCTCACCAAT 59.012 47.619 0.00 0.00 0.00 3.16
3784 3904 1.349026 CTCTTCCAGGCTTCTCACCAA 59.651 52.381 0.00 0.00 0.00 3.67
3785 3905 0.979665 CTCTTCCAGGCTTCTCACCA 59.020 55.000 0.00 0.00 0.00 4.17
3786 3906 0.251634 CCTCTTCCAGGCTTCTCACC 59.748 60.000 0.00 0.00 34.56 4.02
3787 3907 0.251634 CCCTCTTCCAGGCTTCTCAC 59.748 60.000 0.00 0.00 41.80 3.51
3788 3908 0.117140 TCCCTCTTCCAGGCTTCTCA 59.883 55.000 0.00 0.00 41.80 3.27
3789 3909 0.829990 CTCCCTCTTCCAGGCTTCTC 59.170 60.000 0.00 0.00 41.80 2.87
3790 3910 0.118144 ACTCCCTCTTCCAGGCTTCT 59.882 55.000 0.00 0.00 41.80 2.85
3791 3911 0.988063 AACTCCCTCTTCCAGGCTTC 59.012 55.000 0.00 0.00 41.80 3.86
3792 3912 0.988063 GAACTCCCTCTTCCAGGCTT 59.012 55.000 0.00 0.00 41.80 4.35
3793 3913 0.118144 AGAACTCCCTCTTCCAGGCT 59.882 55.000 0.00 0.00 41.80 4.58
3794 3914 0.251634 CAGAACTCCCTCTTCCAGGC 59.748 60.000 0.00 0.00 41.80 4.85
3795 3915 0.908198 CCAGAACTCCCTCTTCCAGG 59.092 60.000 0.00 0.00 43.01 4.45
3796 3916 0.908198 CCCAGAACTCCCTCTTCCAG 59.092 60.000 0.00 0.00 0.00 3.86
3797 3917 0.491823 TCCCAGAACTCCCTCTTCCA 59.508 55.000 0.00 0.00 0.00 3.53
3798 3918 1.557371 CTTCCCAGAACTCCCTCTTCC 59.443 57.143 0.00 0.00 0.00 3.46
3799 3919 1.557371 CCTTCCCAGAACTCCCTCTTC 59.443 57.143 0.00 0.00 0.00 2.87
4111 4236 4.589374 GGTATCACCTTACAGTCTAGGCAT 59.411 45.833 0.00 0.00 34.73 4.40
4180 4305 0.734942 GGACACGAATCCGAAAGCGA 60.735 55.000 0.00 0.00 40.82 4.93
4239 4364 0.417841 TACCTCCCCCTTGAGCTTCT 59.582 55.000 0.00 0.00 0.00 2.85
4390 4515 6.544650 AGTATCCTTATCTTCGCTTCTCCTA 58.455 40.000 0.00 0.00 0.00 2.94
4443 4568 9.288576 TGAAGCAATCTTTCTTCTCTTTAATCA 57.711 29.630 4.42 0.00 39.41 2.57
4842 4967 4.447138 TTTAAAGCCTCCTTCACCTCAA 57.553 40.909 0.00 0.00 0.00 3.02
4999 5124 6.000219 TGGTACTAATATACTCCGTCTCCAC 59.000 44.000 0.00 0.00 0.00 4.02
5067 5192 4.174704 TGGCTCATCAGCTTAATTCCAT 57.825 40.909 0.00 0.00 46.03 3.41
5139 5266 3.443037 CAAACTGATTTTTGGTCACGCA 58.557 40.909 0.00 0.00 33.53 5.24
5354 5481 7.490079 GTCACAACATTATCGTACATGTCCTTA 59.510 37.037 0.00 0.00 32.21 2.69
5446 5573 5.105756 GCAAAAAGATAAGGGCTCAAAGCTA 60.106 40.000 0.00 0.00 41.99 3.32
6131 6261 1.374252 ACGCTTTAGCCGTCCACTG 60.374 57.895 0.00 0.00 37.91 3.66
6134 6264 2.740826 GCACGCTTTAGCCGTCCA 60.741 61.111 0.00 0.00 37.91 4.02
6441 6571 5.805728 ACTACCAAGGTGGAAATCTTACAG 58.194 41.667 9.75 0.00 40.96 2.74
6553 6767 4.039245 GGCTGCTGATACCTACACATAAGA 59.961 45.833 0.00 0.00 0.00 2.10
6744 6958 5.853936 TGCAGGTGCTATATAACTGTAAGG 58.146 41.667 3.18 0.00 42.66 2.69
6746 6960 7.773224 ACAATTGCAGGTGCTATATAACTGTAA 59.227 33.333 5.05 7.72 42.66 2.41
6747 6961 7.226523 CACAATTGCAGGTGCTATATAACTGTA 59.773 37.037 5.05 0.00 42.66 2.74
6748 6962 6.038603 CACAATTGCAGGTGCTATATAACTGT 59.961 38.462 5.05 0.00 42.66 3.55
6749 6963 6.038603 ACACAATTGCAGGTGCTATATAACTG 59.961 38.462 5.05 0.00 42.66 3.16
6750 6964 6.122277 ACACAATTGCAGGTGCTATATAACT 58.878 36.000 5.05 0.00 42.66 2.24
6751 6965 6.377327 ACACAATTGCAGGTGCTATATAAC 57.623 37.500 5.05 0.00 42.66 1.89
6764 6978 5.136816 AGCATGTTCATAACACAATTGCA 57.863 34.783 5.05 0.00 45.50 4.08
6831 7057 5.221244 GGACTAAGCAAAATGGTCAAACACT 60.221 40.000 0.00 0.00 0.00 3.55
6832 7058 4.982295 GGACTAAGCAAAATGGTCAAACAC 59.018 41.667 0.00 0.00 0.00 3.32
6833 7059 4.892934 AGGACTAAGCAAAATGGTCAAACA 59.107 37.500 0.00 0.00 0.00 2.83
6834 7060 5.009610 TCAGGACTAAGCAAAATGGTCAAAC 59.990 40.000 0.00 0.00 0.00 2.93
6835 7061 5.136828 TCAGGACTAAGCAAAATGGTCAAA 58.863 37.500 0.00 0.00 0.00 2.69
6836 7062 4.724399 TCAGGACTAAGCAAAATGGTCAA 58.276 39.130 0.00 0.00 0.00 3.18
6837 7063 4.202461 ACTCAGGACTAAGCAAAATGGTCA 60.202 41.667 0.00 0.00 0.00 4.02
6838 7064 4.154918 CACTCAGGACTAAGCAAAATGGTC 59.845 45.833 0.00 0.00 0.00 4.02
6839 7065 4.074970 CACTCAGGACTAAGCAAAATGGT 58.925 43.478 0.00 0.00 0.00 3.55
6840 7066 4.074970 ACACTCAGGACTAAGCAAAATGG 58.925 43.478 0.00 0.00 0.00 3.16
6841 7067 4.756642 TCACACTCAGGACTAAGCAAAATG 59.243 41.667 0.00 0.00 0.00 2.32
6850 7076 6.263392 GCTAGATTGTATCACACTCAGGACTA 59.737 42.308 0.00 0.00 31.10 2.59
6882 7108 4.861196 TCAGATACTCTTGCTAGACTGGT 58.139 43.478 11.59 4.36 0.00 4.00
6886 7112 6.202516 AGTGTTCAGATACTCTTGCTAGAC 57.797 41.667 0.00 0.00 0.00 2.59
6961 7187 8.178964 GTCAATAAAACGGAATGTGCAGTAATA 58.821 33.333 0.00 0.00 0.00 0.98
7219 7450 9.803507 ATATCTGAAACAATACCATGATCATGT 57.196 29.630 29.23 20.57 37.11 3.21
7222 7453 9.725019 GGTATATCTGAAACAATACCATGATCA 57.275 33.333 0.00 0.00 42.23 2.92
7223 7454 9.167311 GGGTATATCTGAAACAATACCATGATC 57.833 37.037 16.76 0.00 43.74 2.92
7224 7455 8.668653 TGGGTATATCTGAAACAATACCATGAT 58.331 33.333 16.76 0.00 43.74 2.45
7271 7503 2.232452 CACCTTCATCAACCGAGAGAGT 59.768 50.000 0.00 0.00 0.00 3.24
7305 7537 3.751698 ACCCAGTTTTGTAAAGCTCGATC 59.248 43.478 0.00 0.00 0.00 3.69
7450 7682 3.825014 AGAGCGTTCAAGTAAGTACCTGA 59.175 43.478 1.01 0.00 0.00 3.86
7510 7742 2.885135 AAGCAGGATGTGTGATTCCA 57.115 45.000 0.00 0.00 39.31 3.53
7733 7966 6.391227 TTCCTCTCAAATTTGTCAAGGAAC 57.609 37.500 28.17 0.00 36.86 3.62
7877 8110 1.128724 CGTCTCTGCTGTAGAACGCG 61.129 60.000 3.53 3.53 35.13 6.01
7895 8128 0.957395 ACAAAGATCAGTGGGCAGCG 60.957 55.000 0.00 0.00 0.00 5.18
8020 8258 3.244009 ACAGATAACATATGCTCGCTGCT 60.244 43.478 1.58 0.00 43.37 4.24
8021 8259 3.062763 ACAGATAACATATGCTCGCTGC 58.937 45.455 1.58 0.00 43.25 5.25
8052 8290 1.174078 TACAGAAGACGCCGTGACCA 61.174 55.000 0.00 0.00 0.00 4.02
8341 8586 1.071434 AAAGGCAAGGCTCCTCTTCT 58.929 50.000 0.00 0.00 32.45 2.85
8361 8606 3.219281 GCTCCTCTTACCCACACAAAAA 58.781 45.455 0.00 0.00 0.00 1.94
8362 8607 2.488347 GGCTCCTCTTACCCACACAAAA 60.488 50.000 0.00 0.00 0.00 2.44
8363 8608 1.073284 GGCTCCTCTTACCCACACAAA 59.927 52.381 0.00 0.00 0.00 2.83
8364 8609 0.690762 GGCTCCTCTTACCCACACAA 59.309 55.000 0.00 0.00 0.00 3.33
8365 8610 0.178903 AGGCTCCTCTTACCCACACA 60.179 55.000 0.00 0.00 0.00 3.72
8366 8611 0.984995 AAGGCTCCTCTTACCCACAC 59.015 55.000 0.00 0.00 0.00 3.82
8367 8612 0.984230 CAAGGCTCCTCTTACCCACA 59.016 55.000 0.00 0.00 0.00 4.17
8368 8613 0.253327 CCAAGGCTCCTCTTACCCAC 59.747 60.000 0.00 0.00 0.00 4.61
8369 8614 1.562672 GCCAAGGCTCCTCTTACCCA 61.563 60.000 3.29 0.00 38.26 4.51
8370 8615 1.224870 GCCAAGGCTCCTCTTACCC 59.775 63.158 3.29 0.00 38.26 3.69
8371 8616 1.153349 CGCCAAGGCTCCTCTTACC 60.153 63.158 9.73 0.00 39.32 2.85
8372 8617 0.036294 AACGCCAAGGCTCCTCTTAC 60.036 55.000 9.73 0.00 39.32 2.34
8373 8618 0.036388 CAACGCCAAGGCTCCTCTTA 60.036 55.000 9.73 0.00 39.32 2.10
8374 8619 1.302832 CAACGCCAAGGCTCCTCTT 60.303 57.895 9.73 0.00 39.32 2.85
8375 8620 2.348998 CAACGCCAAGGCTCCTCT 59.651 61.111 9.73 0.00 39.32 3.69
8376 8621 2.747855 CCAACGCCAAGGCTCCTC 60.748 66.667 9.73 0.00 39.32 3.71
8388 8633 0.179200 GATTTACCACTGCGCCAACG 60.179 55.000 4.18 0.00 44.07 4.10
8389 8634 1.135689 CAGATTTACCACTGCGCCAAC 60.136 52.381 4.18 0.00 0.00 3.77
8390 8635 1.164411 CAGATTTACCACTGCGCCAA 58.836 50.000 4.18 0.00 0.00 4.52
8391 8636 2.853159 CAGATTTACCACTGCGCCA 58.147 52.632 4.18 0.00 0.00 5.69
8432 8677 2.338809 TCAGGACTTGAACCCATGAGT 58.661 47.619 0.00 0.00 31.34 3.41
8433 8678 3.423539 TTCAGGACTTGAACCCATGAG 57.576 47.619 0.00 0.00 40.82 2.90
8435 8680 4.099266 TGTTTTTCAGGACTTGAACCCATG 59.901 41.667 0.00 0.00 45.22 3.66
8437 8682 3.699038 CTGTTTTTCAGGACTTGAACCCA 59.301 43.478 0.00 0.00 45.22 4.51
8438 8683 3.490933 GCTGTTTTTCAGGACTTGAACCC 60.491 47.826 0.00 0.00 45.22 4.11
8439 8684 3.490933 GGCTGTTTTTCAGGACTTGAACC 60.491 47.826 0.00 0.00 45.22 3.62
8440 8685 3.381590 AGGCTGTTTTTCAGGACTTGAAC 59.618 43.478 0.00 0.00 45.22 3.18
8442 8687 3.117888 AGAGGCTGTTTTTCAGGACTTGA 60.118 43.478 0.00 0.00 43.78 3.02
8443 8688 3.217626 AGAGGCTGTTTTTCAGGACTTG 58.782 45.455 0.00 0.00 43.78 3.16
8444 8689 3.584733 AGAGGCTGTTTTTCAGGACTT 57.415 42.857 0.00 0.00 43.78 3.01
8445 8690 3.584733 AAGAGGCTGTTTTTCAGGACT 57.415 42.857 0.00 0.00 43.78 3.85
8446 8691 5.767816 TTTAAGAGGCTGTTTTTCAGGAC 57.232 39.130 0.90 0.00 43.78 3.85
8447 8692 6.323739 ACATTTTAAGAGGCTGTTTTTCAGGA 59.676 34.615 0.90 0.00 43.78 3.86
8448 8693 6.515832 ACATTTTAAGAGGCTGTTTTTCAGG 58.484 36.000 0.90 0.00 43.78 3.86
8449 8694 9.185192 CTTACATTTTAAGAGGCTGTTTTTCAG 57.815 33.333 0.90 0.00 46.12 3.02
8450 8695 8.141268 CCTTACATTTTAAGAGGCTGTTTTTCA 58.859 33.333 0.90 0.00 0.00 2.69
8451 8696 8.357402 TCCTTACATTTTAAGAGGCTGTTTTTC 58.643 33.333 0.90 0.00 0.00 2.29
8452 8697 8.245195 TCCTTACATTTTAAGAGGCTGTTTTT 57.755 30.769 0.90 0.00 0.00 1.94
8474 8724 2.434336 TCTATTGTACGCAGCCATTCCT 59.566 45.455 0.00 0.00 0.00 3.36
8510 8760 4.711949 CTCCCGCTTGTGCAGGCT 62.712 66.667 4.85 0.00 36.71 4.58
8538 8788 2.656947 AGTAAAGCAAAGACAGCCCA 57.343 45.000 0.00 0.00 0.00 5.36
8712 8962 5.234116 GGCAAACCAAAATGACTACACTTTG 59.766 40.000 0.00 0.00 41.12 2.77
8749 8999 7.725199 TTCAAAGTCAATGAAACGAGCGACG 62.725 44.000 0.00 4.95 38.65 5.12
8752 9002 3.519908 TCAAAGTCAATGAAACGAGCG 57.480 42.857 0.00 0.00 0.00 5.03
8754 9004 6.463890 CGATCATTCAAAGTCAATGAAACGAG 59.536 38.462 14.41 0.00 42.23 4.18
8821 9071 7.814587 ACAGAAAGGCACTAATGAAATTTAAGC 59.185 33.333 0.00 0.00 38.49 3.09
8855 9106 5.120363 GCAGCTACAAAACCAAGTACTCTAC 59.880 44.000 0.00 0.00 0.00 2.59
8863 9114 3.435105 TTGTGCAGCTACAAAACCAAG 57.565 42.857 0.00 0.00 37.60 3.61
8879 9130 5.004821 CACTCGGTCGAAAGAATCTATTGTG 59.995 44.000 0.00 0.00 45.01 3.33
8882 9133 5.326200 ACACTCGGTCGAAAGAATCTATT 57.674 39.130 0.00 0.00 45.01 1.73


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

AutoCloner maintained by Alex Coulton.