Multiple sequence alignment - TraesCS6D01G249400

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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 TraesCS6D01G249400 chr6D 100.000 4360 0 0 1 4360 352874202 352878561 0.000000e+00 8052.0
1 TraesCS6D01G249400 chr6D 100.000 3326 0 0 4645 7970 352878846 352882171 0.000000e+00 6143.0
2 TraesCS6D01G249400 chr6D 86.747 249 30 3 7206 7454 291723289 291723534 2.830000e-69 274.0
3 TraesCS6D01G249400 chr6D 90.000 50 3 2 7530 7578 316631900 316631948 6.680000e-06 63.9
4 TraesCS6D01G249400 chr6A 96.427 4142 110 13 1 4126 490474245 490478364 0.000000e+00 6794.0
5 TraesCS6D01G249400 chr6A 95.464 1940 38 15 4645 6542 490478476 490480407 0.000000e+00 3049.0
6 TraesCS6D01G249400 chr6A 97.201 536 15 0 6639 7174 490480835 490481370 0.000000e+00 907.0
7 TraesCS6D01G249400 chr6A 94.375 320 14 2 7175 7492 490481437 490481754 9.300000e-134 488.0
8 TraesCS6D01G249400 chr6A 94.961 258 9 3 7715 7970 490482033 490482288 1.250000e-107 401.0
9 TraesCS6D01G249400 chr6A 94.792 96 5 0 7682 7777 490481935 490482030 4.980000e-32 150.0
10 TraesCS6D01G249400 chr6A 98.630 73 1 0 4288 4360 490478363 490478435 6.490000e-26 130.0
11 TraesCS6D01G249400 chr6B 96.824 2739 77 5 1390 4126 526037480 526034750 0.000000e+00 4567.0
12 TraesCS6D01G249400 chr6B 95.541 1637 49 7 5029 6643 526034161 526032527 0.000000e+00 2597.0
13 TraesCS6D01G249400 chr6B 97.002 1401 28 7 2 1398 526038970 526037580 0.000000e+00 2342.0
14 TraesCS6D01G249400 chr6B 96.468 538 17 1 6639 7174 526032415 526031878 0.000000e+00 887.0
15 TraesCS6D01G249400 chr6B 93.147 394 19 2 4645 5030 526034636 526034243 8.970000e-159 571.0
16 TraesCS6D01G249400 chr6B 95.312 320 11 1 7176 7491 526031809 526031490 9.230000e-139 505.0
17 TraesCS6D01G249400 chr6B 95.016 321 11 2 7175 7491 525995830 525995511 4.290000e-137 499.0
18 TraesCS6D01G249400 chr6B 94.464 289 15 1 7682 7970 525995202 525994915 2.040000e-120 444.0
19 TraesCS6D01G249400 chr6B 93.772 289 17 1 7682 7970 526031180 526030893 4.420000e-117 433.0
20 TraesCS6D01G249400 chr6B 97.661 171 3 1 4125 4294 320412939 320413109 7.820000e-75 292.0
21 TraesCS6D01G249400 chr6B 94.681 94 4 1 7592 7684 526031479 526031386 2.320000e-30 145.0
22 TraesCS6D01G249400 chr6B 93.617 94 5 1 7592 7684 525995500 525995407 1.080000e-28 139.0
23 TraesCS6D01G249400 chr6B 92.105 76 3 2 4288 4360 526034751 526034676 3.930000e-18 104.0
24 TraesCS6D01G249400 chr4B 98.225 169 3 0 4121 4289 71600620 71600788 6.050000e-76 296.0
25 TraesCS6D01G249400 chr4B 98.039 51 1 0 6306 6356 564164149 564164099 1.100000e-13 89.8
26 TraesCS6D01G249400 chr4A 98.204 167 3 0 4125 4291 582530141 582529975 7.820000e-75 292.0
27 TraesCS6D01G249400 chr2D 97.110 173 4 1 4125 4297 516708312 516708483 2.810000e-74 291.0
28 TraesCS6D01G249400 chr2D 96.023 176 5 2 4121 4295 455269178 455269004 1.310000e-72 285.0
29 TraesCS6D01G249400 chr2D 94.545 55 3 0 6306 6360 291859286 291859340 1.430000e-12 86.1
30 TraesCS6D01G249400 chr5A 97.093 172 4 1 4119 4289 651496993 651496822 1.010000e-73 289.0
31 TraesCS6D01G249400 chr5A 90.625 64 3 3 6306 6367 106360345 106360283 1.840000e-11 82.4
32 TraesCS6D01G249400 chr4D 96.552 174 5 1 4125 4298 75782217 75782045 3.640000e-73 287.0
33 TraesCS6D01G249400 chr7D 94.595 185 8 2 4115 4298 202716854 202716671 1.310000e-72 285.0
34 TraesCS6D01G249400 chr7D 95.062 81 3 1 7495 7575 167359525 167359604 8.400000e-25 126.0
35 TraesCS6D01G249400 chr2B 96.023 176 6 1 4124 4299 594833874 594834048 1.310000e-72 285.0
36 TraesCS6D01G249400 chr2B 96.226 53 2 0 6306 6358 656970100 656970048 3.960000e-13 87.9
37 TraesCS6D01G249400 chr7A 95.062 81 4 0 7495 7575 168872253 168872333 2.330000e-25 128.0
38 TraesCS6D01G249400 chr3B 92.683 82 5 1 7495 7575 738379698 738379779 5.050000e-22 117.0
39 TraesCS6D01G249400 chr3B 95.455 44 2 0 7532 7575 256413661 256413704 3.990000e-08 71.3
40 TraesCS6D01G249400 chr2A 90.588 85 5 3 7491 7574 115749921 115749839 8.460000e-20 110.0
41 TraesCS6D01G249400 chr2A 93.333 60 1 3 6296 6352 712316364 712316423 1.430000e-12 86.1
42 TraesCS6D01G249400 chrUn 85.542 83 12 0 7496 7578 49214742 49214824 3.960000e-13 87.9
43 TraesCS6D01G249400 chrUn 85.542 83 12 0 7496 7578 273545134 273545216 3.960000e-13 87.9
44 TraesCS6D01G249400 chr1B 91.935 62 3 2 6306 6365 211323008 211323069 1.430000e-12 86.1
45 TraesCS6D01G249400 chr3A 89.552 67 4 3 6296 6360 528595035 528595100 1.840000e-11 82.4
46 TraesCS6D01G249400 chr5B 96.875 32 0 1 7545 7575 659746741 659746710 1.400000e-02 52.8


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 TraesCS6D01G249400 chr6D 352874202 352882171 7969 False 7097.500000 8052 100.000000 1 7970 2 chr6D.!!$F3 7969
1 TraesCS6D01G249400 chr6A 490474245 490482288 8043 False 1702.714286 6794 95.978571 1 7970 7 chr6A.!!$F1 7969
2 TraesCS6D01G249400 chr6B 526030893 526038970 8077 True 1350.111111 4567 94.983556 2 7970 9 chr6B.!!$R2 7968
3 TraesCS6D01G249400 chr6B 525994915 525995830 915 True 360.666667 499 94.365667 7175 7970 3 chr6B.!!$R1 795

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
932 948 0.035439 TTGTTTGGGATCGGGAGAGC 60.035 55.000 0.00 0.0 45.48 4.09 F
1089 1105 1.732259 CCGTATGTGAAACTGCAGGTC 59.268 52.381 19.93 15.2 38.04 3.85 F
1598 1729 1.978454 CATCCTGCAGGGGAGATTTC 58.022 55.000 32.23 0.0 38.92 2.17 F
2027 2158 2.153645 TCAACAAGCACCAGCAGTATG 58.846 47.619 0.00 0.0 45.49 2.39 F
3353 3486 0.240945 CCAATTTGGCACCAGTCGAC 59.759 55.000 7.70 7.7 0.00 4.20 F
4759 4903 1.053424 TACCCAGGAAGCACGAAACT 58.947 50.000 0.00 0.0 0.00 2.66 F
5329 5558 2.104111 TGTGGCCAATAGGTAATCTCCG 59.896 50.000 7.24 0.0 37.19 4.63 F
5821 6050 0.471211 TTCTGGAGGTGTTCGAGGGT 60.471 55.000 0.00 0.0 32.92 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2685 2816 2.178580 CCCCCTTGCAATGAAGCTAAA 58.821 47.619 0.00 0.00 34.99 1.85 R
2802 2933 2.704572 ACTGCACCTGAATTCACTAGC 58.295 47.619 3.38 8.94 0.00 3.42 R
3299 3432 1.135689 GCAACAGTTAGCAACCATCCG 60.136 52.381 3.63 0.00 0.00 4.18 R
3938 4071 0.119155 ACCCAGATCAGACAAGGGGA 59.881 55.000 0.00 0.00 43.96 4.81 R
5248 5477 0.730265 CACTCTCTACGCTCTTCGCT 59.270 55.000 0.00 0.00 43.23 4.93 R
5818 6047 0.323629 TCATCTCCAACGAACCACCC 59.676 55.000 0.00 0.00 0.00 4.61 R
6426 6674 1.433534 GTCTTTCGAACCAGCAGAGG 58.566 55.000 0.00 0.00 0.00 3.69 R
7529 8245 0.033781 CGTCGGGGAAAACCAGTACA 59.966 55.000 0.00 0.00 42.91 2.90 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
322 335 4.049186 CGGAGAAAAGACAAGACGAAGAA 58.951 43.478 0.00 0.00 0.00 2.52
413 426 3.426695 CCATCAAGAACACGATGCCTTTC 60.427 47.826 0.00 0.00 38.14 2.62
622 635 2.413765 CCATTTCTCGTCTGCTTGCTTG 60.414 50.000 0.00 0.00 0.00 4.01
623 636 0.588252 TTTCTCGTCTGCTTGCTTGC 59.412 50.000 0.00 0.00 0.00 4.01
624 637 0.250038 TTCTCGTCTGCTTGCTTGCT 60.250 50.000 3.47 0.00 0.00 3.91
625 638 0.250038 TCTCGTCTGCTTGCTTGCTT 60.250 50.000 3.47 0.00 0.00 3.91
626 639 0.165511 CTCGTCTGCTTGCTTGCTTC 59.834 55.000 3.47 0.00 0.00 3.86
627 640 0.250038 TCGTCTGCTTGCTTGCTTCT 60.250 50.000 3.47 0.00 0.00 2.85
628 641 0.590195 CGTCTGCTTGCTTGCTTCTT 59.410 50.000 3.47 0.00 0.00 2.52
692 708 1.760029 GTCTGATCTGGTTCTCCTCCC 59.240 57.143 0.00 0.00 34.23 4.30
903 919 2.624364 GGCCCGTTTCTTGGTTCTTTTA 59.376 45.455 0.00 0.00 0.00 1.52
932 948 0.035439 TTGTTTGGGATCGGGAGAGC 60.035 55.000 0.00 0.00 45.48 4.09
1089 1105 1.732259 CCGTATGTGAAACTGCAGGTC 59.268 52.381 19.93 15.20 38.04 3.85
1403 1531 2.030946 GCTCATGGACGTTTGCTATGTC 59.969 50.000 0.00 3.91 41.26 3.06
1458 1587 7.202016 TGGATTCAGTATTTGACTTTGTGAC 57.798 36.000 0.00 0.00 35.64 3.67
1468 1597 4.811555 TGACTTTGTGACATTACAGCAC 57.188 40.909 0.00 0.00 0.00 4.40
1523 1652 6.115446 TCTACAAGGGCATGAATTCTACTTG 58.885 40.000 17.91 17.91 39.60 3.16
1528 1657 6.439636 AGGGCATGAATTCTACTTGCTATA 57.560 37.500 7.05 0.00 38.11 1.31
1550 1679 5.772825 ATAATTGTGCGAAATATGCTGGT 57.227 34.783 0.00 0.00 0.00 4.00
1598 1729 1.978454 CATCCTGCAGGGGAGATTTC 58.022 55.000 32.23 0.00 38.92 2.17
1809 1940 4.292186 TGGAACTGAAATCCCTGAAGAG 57.708 45.455 0.00 0.00 36.04 2.85
1821 1952 2.224867 CCCTGAAGAGGACAAATGTGGT 60.225 50.000 0.00 0.00 42.93 4.16
1834 1965 5.380043 ACAAATGTGGTGAAGTGAGAGATT 58.620 37.500 0.00 0.00 0.00 2.40
1858 1989 5.729229 TCAGAGGACAGGTTTAATGGGATTA 59.271 40.000 0.00 0.00 0.00 1.75
2027 2158 2.153645 TCAACAAGCACCAGCAGTATG 58.846 47.619 0.00 0.00 45.49 2.39
2364 2495 2.307098 AGCTGTAAAGGCAACAGAGGAT 59.693 45.455 15.97 0.00 45.89 3.24
2685 2816 3.387962 TGGATCAGATAAGGAGCAGGTT 58.612 45.455 0.00 0.00 0.00 3.50
2802 2933 5.102020 TGTACATTGGTGTTCATGTTTCG 57.898 39.130 0.00 0.00 39.77 3.46
2903 3034 2.164422 GTGGGCTATTGTTTCTTCAGGC 59.836 50.000 0.00 0.00 0.00 4.85
2960 3091 4.578928 TCAGGCAAGAGAACAAAAAGGTAC 59.421 41.667 0.00 0.00 0.00 3.34
3001 3132 2.356695 TCATCATTTTGCATCTCCAGCG 59.643 45.455 0.00 0.00 33.85 5.18
3353 3486 0.240945 CCAATTTGGCACCAGTCGAC 59.759 55.000 7.70 7.70 0.00 4.20
3526 3659 4.944317 GGAAGATTAACTTGGGAACTCCTG 59.056 45.833 0.00 0.00 39.13 3.86
3582 3715 6.719370 ACACCTGCATCTGGAAACTAAATAAA 59.281 34.615 0.00 0.00 0.00 1.40
3966 4099 2.497675 GTCTGATCTGGGTTACTGCTGA 59.502 50.000 0.00 0.00 0.00 4.26
4126 4259 6.410048 GCGACTTAACACTGTTTTGAACTTAC 59.590 38.462 0.00 0.00 0.00 2.34
4127 4260 7.675637 GCGACTTAACACTGTTTTGAACTTACT 60.676 37.037 0.00 0.00 0.00 2.24
4128 4261 7.844653 CGACTTAACACTGTTTTGAACTTACTC 59.155 37.037 0.00 0.00 0.00 2.59
4129 4262 7.982224 ACTTAACACTGTTTTGAACTTACTCC 58.018 34.615 0.00 0.00 0.00 3.85
4130 4263 5.830000 AACACTGTTTTGAACTTACTCCC 57.170 39.130 0.00 0.00 0.00 4.30
4131 4264 5.112129 ACACTGTTTTGAACTTACTCCCT 57.888 39.130 0.00 0.00 0.00 4.20
4132 4265 5.123936 ACACTGTTTTGAACTTACTCCCTC 58.876 41.667 0.00 0.00 0.00 4.30
4133 4266 4.515567 CACTGTTTTGAACTTACTCCCTCC 59.484 45.833 0.00 0.00 0.00 4.30
4134 4267 3.735591 TGTTTTGAACTTACTCCCTCCG 58.264 45.455 0.00 0.00 0.00 4.63
4135 4268 3.135167 TGTTTTGAACTTACTCCCTCCGT 59.865 43.478 0.00 0.00 0.00 4.69
4136 4269 4.132336 GTTTTGAACTTACTCCCTCCGTT 58.868 43.478 0.00 0.00 0.00 4.44
4137 4270 3.672767 TTGAACTTACTCCCTCCGTTC 57.327 47.619 0.00 0.00 35.69 3.95
4138 4271 1.897802 TGAACTTACTCCCTCCGTTCC 59.102 52.381 0.00 0.00 34.58 3.62
4139 4272 2.177734 GAACTTACTCCCTCCGTTCCT 58.822 52.381 0.00 0.00 0.00 3.36
4140 4273 3.245371 TGAACTTACTCCCTCCGTTCCTA 60.245 47.826 0.00 0.00 34.58 2.94
4141 4274 3.463048 ACTTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
4142 4275 3.782992 ACTTACTCCCTCCGTTCCTAAA 58.217 45.455 0.00 0.00 0.00 1.85
4143 4276 4.359996 ACTTACTCCCTCCGTTCCTAAAT 58.640 43.478 0.00 0.00 0.00 1.40
4144 4277 5.522641 ACTTACTCCCTCCGTTCCTAAATA 58.477 41.667 0.00 0.00 0.00 1.40
4145 4278 6.141790 ACTTACTCCCTCCGTTCCTAAATAT 58.858 40.000 0.00 0.00 0.00 1.28
4146 4279 6.614496 ACTTACTCCCTCCGTTCCTAAATATT 59.386 38.462 0.00 0.00 0.00 1.28
4147 4280 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
4148 4281 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
4149 4282 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
4150 4283 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
4151 4284 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
4152 4285 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
4153 4286 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
4154 4287 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
4155 4288 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
4156 4289 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
4157 4290 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
4158 4291 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
4173 4306 9.559732 TGTCTTTCTAGAGATTTCAACAAATGA 57.440 29.630 0.00 0.00 31.94 2.57
4174 4307 9.818796 GTCTTTCTAGAGATTTCAACAAATGAC 57.181 33.333 0.00 0.00 37.92 3.06
4175 4308 9.784531 TCTTTCTAGAGATTTCAACAAATGACT 57.215 29.630 0.00 0.00 37.92 3.41
4178 4311 9.996554 TTCTAGAGATTTCAACAAATGACTACA 57.003 29.630 0.00 0.00 37.92 2.74
4182 4315 8.873830 AGAGATTTCAACAAATGACTACATACG 58.126 33.333 0.00 0.00 37.92 3.06
4183 4316 8.771920 AGATTTCAACAAATGACTACATACGA 57.228 30.769 0.00 0.00 37.92 3.43
4184 4317 9.214957 AGATTTCAACAAATGACTACATACGAA 57.785 29.630 0.00 0.00 37.92 3.85
4185 4318 9.478019 GATTTCAACAAATGACTACATACGAAG 57.522 33.333 0.00 0.00 37.92 3.79
4186 4319 6.403333 TCAACAAATGACTACATACGAAGC 57.597 37.500 0.00 0.00 35.50 3.86
4187 4320 5.929415 TCAACAAATGACTACATACGAAGCA 59.071 36.000 0.00 0.00 35.50 3.91
4188 4321 6.425417 TCAACAAATGACTACATACGAAGCAA 59.575 34.615 0.00 0.00 35.50 3.91
4189 4322 6.795098 ACAAATGACTACATACGAAGCAAA 57.205 33.333 0.00 0.00 35.50 3.68
4190 4323 7.197071 ACAAATGACTACATACGAAGCAAAA 57.803 32.000 0.00 0.00 35.50 2.44
4191 4324 7.816640 ACAAATGACTACATACGAAGCAAAAT 58.183 30.769 0.00 0.00 35.50 1.82
4192 4325 7.750458 ACAAATGACTACATACGAAGCAAAATG 59.250 33.333 0.00 0.00 35.50 2.32
4193 4326 7.609760 AATGACTACATACGAAGCAAAATGA 57.390 32.000 0.00 0.00 35.50 2.57
4194 4327 6.647212 TGACTACATACGAAGCAAAATGAG 57.353 37.500 0.00 0.00 0.00 2.90
4195 4328 6.163476 TGACTACATACGAAGCAAAATGAGT 58.837 36.000 0.00 0.00 0.00 3.41
4196 4329 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
4197 4330 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
4198 4331 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
4199 4332 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
4200 4333 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
4201 4334 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
4202 4335 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
4203 4336 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
4204 4337 5.700832 ACGAAGCAAAATGAGTGAATCTACA 59.299 36.000 0.00 0.00 0.00 2.74
4205 4338 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
4238 4371 7.956328 ATGTCTATATACATCCGTATGTGGT 57.044 36.000 3.56 0.00 45.99 4.16
4240 4373 8.502105 TGTCTATATACATCCGTATGTGGTAG 57.498 38.462 3.56 3.93 45.99 3.18
4241 4374 8.105197 TGTCTATATACATCCGTATGTGGTAGT 58.895 37.037 3.56 0.00 45.99 2.73
4242 4375 8.610896 GTCTATATACATCCGTATGTGGTAGTC 58.389 40.741 3.56 0.00 45.99 2.59
4243 4376 6.770746 ATATACATCCGTATGTGGTAGTCC 57.229 41.667 3.56 0.00 45.99 3.85
4244 4377 2.742348 ACATCCGTATGTGGTAGTCCA 58.258 47.619 0.00 0.00 44.79 4.02
4245 4378 3.305720 ACATCCGTATGTGGTAGTCCAT 58.694 45.455 0.00 0.00 44.79 3.41
4246 4379 3.709653 ACATCCGTATGTGGTAGTCCATT 59.290 43.478 0.00 0.00 44.79 3.16
4247 4380 4.163458 ACATCCGTATGTGGTAGTCCATTT 59.837 41.667 0.00 0.00 44.79 2.32
4248 4381 4.131649 TCCGTATGTGGTAGTCCATTTG 57.868 45.455 0.00 0.00 46.20 2.32
4249 4382 3.770388 TCCGTATGTGGTAGTCCATTTGA 59.230 43.478 0.00 0.00 46.20 2.69
4250 4383 4.223255 TCCGTATGTGGTAGTCCATTTGAA 59.777 41.667 0.00 0.00 46.20 2.69
4251 4384 4.938832 CCGTATGTGGTAGTCCATTTGAAA 59.061 41.667 0.00 0.00 46.20 2.69
4252 4385 5.588648 CCGTATGTGGTAGTCCATTTGAAAT 59.411 40.000 0.00 0.00 46.20 2.17
4253 4386 6.238374 CCGTATGTGGTAGTCCATTTGAAATC 60.238 42.308 0.00 0.00 46.20 2.17
4254 4387 6.538742 CGTATGTGGTAGTCCATTTGAAATCT 59.461 38.462 0.00 0.00 46.20 2.40
4255 4388 7.254455 CGTATGTGGTAGTCCATTTGAAATCTC 60.254 40.741 0.00 0.00 46.20 2.75
4256 4389 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
4257 4390 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
4258 4391 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
4259 4392 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
4260 4393 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
4261 4394 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
4265 4398 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
4266 4399 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
4283 4416 7.675161 AAAGACAAATATTTAGGAATGGGGG 57.325 36.000 0.00 0.00 0.00 5.40
4328 4464 5.724854 ACTATAGTGTAGAGGAAGGCCAAAA 59.275 40.000 5.01 0.00 36.29 2.44
4759 4903 1.053424 TACCCAGGAAGCACGAAACT 58.947 50.000 0.00 0.00 0.00 2.66
4828 4972 7.121168 TCAGTTACTCTCATAAATGCCTTTTGG 59.879 37.037 0.00 0.00 44.18 3.28
5022 5168 9.779237 CGATTTCAAATAGTACACGAATATCAC 57.221 33.333 0.00 0.00 0.00 3.06
5047 5276 2.403252 TAGCTTGCTAAGGGTTCAGC 57.597 50.000 0.00 0.00 38.31 4.26
5329 5558 2.104111 TGTGGCCAATAGGTAATCTCCG 59.896 50.000 7.24 0.00 37.19 4.63
5378 5607 4.102681 AGCTCCACTAACACCAAACTACTT 59.897 41.667 0.00 0.00 0.00 2.24
5498 5727 7.186268 TCTTGTTATTTTACCCTTGCCCTTAT 58.814 34.615 0.00 0.00 0.00 1.73
5741 5970 4.099266 TGCAACTTTTGGAACTGCTTATGT 59.901 37.500 0.00 0.00 34.10 2.29
5781 6010 7.041780 CCAGATGGTTAACTGAAGTATATGTGC 60.042 40.741 5.42 0.00 36.38 4.57
5818 6047 1.613925 TCACTTCTGGAGGTGTTCGAG 59.386 52.381 11.54 0.00 39.18 4.04
5821 6050 0.471211 TTCTGGAGGTGTTCGAGGGT 60.471 55.000 0.00 0.00 32.92 4.34
5848 6077 4.002982 CGTTGGAGATGAAAGTCATGGAA 58.997 43.478 0.00 0.00 37.20 3.53
5902 6131 3.553828 TGGGAATCAGATAAACCCGAC 57.446 47.619 12.68 0.00 43.04 4.79
6213 6447 4.365514 TGAAAACTAGTTGCATCCCTCA 57.634 40.909 9.34 1.58 0.00 3.86
6214 6448 4.072131 TGAAAACTAGTTGCATCCCTCAC 58.928 43.478 9.34 0.00 0.00 3.51
6215 6449 4.202461 TGAAAACTAGTTGCATCCCTCACT 60.202 41.667 9.34 0.00 0.00 3.41
6216 6450 4.373156 AAACTAGTTGCATCCCTCACTT 57.627 40.909 9.34 0.00 0.00 3.16
6337 6582 3.284617 ACTTGTTTGGGACTAAACGCTT 58.715 40.909 6.77 0.00 42.11 4.68
6338 6583 3.697542 ACTTGTTTGGGACTAAACGCTTT 59.302 39.130 6.77 0.00 42.11 3.51
6339 6584 3.701532 TGTTTGGGACTAAACGCTTTG 57.298 42.857 6.77 0.00 42.11 2.77
6340 6585 3.018149 TGTTTGGGACTAAACGCTTTGT 58.982 40.909 6.77 0.00 42.11 2.83
6381 6629 6.406177 CCCTGTATGGAGGATTTGTTTGATTG 60.406 42.308 0.00 0.00 38.35 2.67
6408 6656 7.492077 AAGGTTAGTACTAAACTACAGGCAT 57.508 36.000 29.01 12.31 41.86 4.40
6493 6761 7.605410 AAACAATGTGAGTATAGGTTTACCG 57.395 36.000 0.00 0.00 42.08 4.02
6561 6829 3.492102 TCTGGGGTTTATATGCAGAGC 57.508 47.619 0.00 0.00 0.00 4.09
6601 6869 1.915141 AGCTTGTCCCTTTGTCCATG 58.085 50.000 0.00 0.00 0.00 3.66
6617 6887 6.312141 TGTCCATGTCCTGATTAAAGATGA 57.688 37.500 0.00 0.00 0.00 2.92
6629 6899 1.247567 AAAGATGAAACCAGGCACGG 58.752 50.000 0.00 0.00 0.00 4.94
6665 7305 0.893270 TTAACGCAGCCCATTGCACT 60.893 50.000 0.00 0.00 44.28 4.40
7032 7672 4.072131 GACCAAAGATTTACTGACCAGCA 58.928 43.478 0.00 0.00 0.00 4.41
7033 7673 3.821033 ACCAAAGATTTACTGACCAGCAC 59.179 43.478 0.00 0.00 0.00 4.40
7069 7709 5.587388 ACATACATTGCTTGATTGAAGGG 57.413 39.130 0.00 0.00 31.56 3.95
7435 8150 1.842052 TGACACTAGACGTATGGCCA 58.158 50.000 8.56 8.56 0.00 5.36
7481 8196 1.412710 ACACTAGCCGTATGACCATGG 59.587 52.381 11.19 11.19 0.00 3.66
7492 8208 4.262207 CGTATGACCATGGTTGCTCTCTAT 60.262 45.833 20.85 6.48 0.00 1.98
7494 8210 2.435805 TGACCATGGTTGCTCTCTATCC 59.564 50.000 20.85 1.54 0.00 2.59
7495 8211 1.771255 ACCATGGTTGCTCTCTATCCC 59.229 52.381 13.00 0.00 0.00 3.85
7496 8212 1.072965 CCATGGTTGCTCTCTATCCCC 59.927 57.143 2.57 0.00 0.00 4.81
7497 8213 2.053244 CATGGTTGCTCTCTATCCCCT 58.947 52.381 0.00 0.00 0.00 4.79
7498 8214 1.794714 TGGTTGCTCTCTATCCCCTC 58.205 55.000 0.00 0.00 0.00 4.30
7499 8215 1.292242 TGGTTGCTCTCTATCCCCTCT 59.708 52.381 0.00 0.00 0.00 3.69
7500 8216 1.691434 GGTTGCTCTCTATCCCCTCTG 59.309 57.143 0.00 0.00 0.00 3.35
7501 8217 2.393646 GTTGCTCTCTATCCCCTCTGT 58.606 52.381 0.00 0.00 0.00 3.41
7502 8218 3.567397 GTTGCTCTCTATCCCCTCTGTA 58.433 50.000 0.00 0.00 0.00 2.74
7503 8219 3.231207 TGCTCTCTATCCCCTCTGTAC 57.769 52.381 0.00 0.00 0.00 2.90
7504 8220 2.158445 TGCTCTCTATCCCCTCTGTACC 60.158 54.545 0.00 0.00 0.00 3.34
7505 8221 2.158445 GCTCTCTATCCCCTCTGTACCA 60.158 54.545 0.00 0.00 0.00 3.25
7506 8222 3.492337 CTCTCTATCCCCTCTGTACCAC 58.508 54.545 0.00 0.00 0.00 4.16
7507 8223 2.856864 TCTCTATCCCCTCTGTACCACA 59.143 50.000 0.00 0.00 0.00 4.17
7508 8224 3.271225 TCTCTATCCCCTCTGTACCACAA 59.729 47.826 0.00 0.00 0.00 3.33
7509 8225 4.078571 TCTCTATCCCCTCTGTACCACAAT 60.079 45.833 0.00 0.00 0.00 2.71
7510 8226 5.135533 TCTCTATCCCCTCTGTACCACAATA 59.864 44.000 0.00 0.00 0.00 1.90
7511 8227 5.145564 TCTATCCCCTCTGTACCACAATAC 58.854 45.833 0.00 0.00 0.00 1.89
7512 8228 3.484953 TCCCCTCTGTACCACAATACT 57.515 47.619 0.00 0.00 0.00 2.12
7513 8229 3.798515 TCCCCTCTGTACCACAATACTT 58.201 45.455 0.00 0.00 0.00 2.24
7514 8230 3.517901 TCCCCTCTGTACCACAATACTTG 59.482 47.826 0.00 0.00 0.00 3.16
7515 8231 3.263425 CCCCTCTGTACCACAATACTTGT 59.737 47.826 0.00 0.00 46.75 3.16
7516 8232 4.504858 CCCTCTGTACCACAATACTTGTC 58.495 47.826 0.00 0.00 43.23 3.18
7517 8233 4.174009 CCTCTGTACCACAATACTTGTCG 58.826 47.826 0.00 0.00 43.23 4.35
7518 8234 4.321750 CCTCTGTACCACAATACTTGTCGT 60.322 45.833 0.00 0.00 43.23 4.34
7519 8235 5.204409 TCTGTACCACAATACTTGTCGTT 57.796 39.130 0.00 0.00 43.23 3.85
7520 8236 6.330004 TCTGTACCACAATACTTGTCGTTA 57.670 37.500 0.00 0.00 43.23 3.18
7521 8237 6.384224 TCTGTACCACAATACTTGTCGTTAG 58.616 40.000 0.00 0.00 43.23 2.34
7522 8238 5.472148 TGTACCACAATACTTGTCGTTAGG 58.528 41.667 0.00 0.00 43.23 2.69
7523 8239 3.934068 ACCACAATACTTGTCGTTAGGG 58.066 45.455 0.00 0.00 43.23 3.53
7524 8240 3.267483 CCACAATACTTGTCGTTAGGGG 58.733 50.000 0.00 0.00 43.23 4.79
7525 8241 3.055675 CCACAATACTTGTCGTTAGGGGA 60.056 47.826 0.00 0.00 43.23 4.81
7526 8242 4.563993 CCACAATACTTGTCGTTAGGGGAA 60.564 45.833 0.00 0.00 43.23 3.97
7527 8243 4.390909 CACAATACTTGTCGTTAGGGGAAC 59.609 45.833 0.00 0.00 43.23 3.62
7545 8261 0.399075 ACCTGTACTGGTTTTCCCCG 59.601 55.000 18.03 0.00 36.89 5.73
7546 8262 0.688487 CCTGTACTGGTTTTCCCCGA 59.312 55.000 10.53 0.00 39.73 5.14
7547 8263 1.609841 CCTGTACTGGTTTTCCCCGAC 60.610 57.143 10.53 0.00 39.73 4.79
7548 8264 0.033781 TGTACTGGTTTTCCCCGACG 59.966 55.000 0.00 0.00 39.73 5.12
7549 8265 0.318120 GTACTGGTTTTCCCCGACGA 59.682 55.000 0.00 0.00 39.73 4.20
7550 8266 0.318120 TACTGGTTTTCCCCGACGAC 59.682 55.000 0.00 0.00 39.73 4.34
7551 8267 1.070105 CTGGTTTTCCCCGACGACA 59.930 57.895 0.00 0.00 39.73 4.35
7552 8268 0.533308 CTGGTTTTCCCCGACGACAA 60.533 55.000 0.00 0.00 39.73 3.18
7553 8269 0.533308 TGGTTTTCCCCGACGACAAG 60.533 55.000 0.00 0.00 39.73 3.16
7554 8270 0.533531 GGTTTTCCCCGACGACAAGT 60.534 55.000 0.00 0.00 0.00 3.16
7555 8271 1.270252 GGTTTTCCCCGACGACAAGTA 60.270 52.381 0.00 0.00 0.00 2.24
7556 8272 2.613725 GGTTTTCCCCGACGACAAGTAT 60.614 50.000 0.00 0.00 0.00 2.12
7557 8273 3.069289 GTTTTCCCCGACGACAAGTATT 58.931 45.455 0.00 0.00 0.00 1.89
7558 8274 3.405823 TTTCCCCGACGACAAGTATTT 57.594 42.857 0.00 0.00 0.00 1.40
7559 8275 2.660189 TCCCCGACGACAAGTATTTC 57.340 50.000 0.00 0.00 0.00 2.17
7560 8276 1.135315 TCCCCGACGACAAGTATTTCG 60.135 52.381 0.00 0.00 41.14 3.46
7561 8277 1.274596 CCCGACGACAAGTATTTCGG 58.725 55.000 0.00 1.29 39.63 4.30
7562 8278 1.403249 CCCGACGACAAGTATTTCGGT 60.403 52.381 7.50 0.00 39.63 4.69
7563 8279 2.159393 CCCGACGACAAGTATTTCGGTA 60.159 50.000 7.50 0.00 39.63 4.02
7564 8280 2.848302 CCGACGACAAGTATTTCGGTAC 59.152 50.000 0.00 0.00 39.63 3.34
7565 8281 3.491356 CGACGACAAGTATTTCGGTACA 58.509 45.455 0.00 0.00 39.63 2.90
7566 8282 3.541130 CGACGACAAGTATTTCGGTACAG 59.459 47.826 0.00 0.00 39.63 2.74
7567 8283 4.669965 CGACGACAAGTATTTCGGTACAGA 60.670 45.833 0.00 0.00 39.63 3.41
7568 8284 4.730657 ACGACAAGTATTTCGGTACAGAG 58.269 43.478 0.00 0.00 39.63 3.35
7569 8285 4.103357 CGACAAGTATTTCGGTACAGAGG 58.897 47.826 0.00 0.00 0.00 3.69
7570 8286 4.430908 GACAAGTATTTCGGTACAGAGGG 58.569 47.826 0.00 0.00 0.00 4.30
7571 8287 4.091549 ACAAGTATTTCGGTACAGAGGGA 58.908 43.478 0.00 0.00 0.00 4.20
7572 8288 4.159879 ACAAGTATTTCGGTACAGAGGGAG 59.840 45.833 0.00 0.00 0.00 4.30
7573 8289 3.978610 AGTATTTCGGTACAGAGGGAGT 58.021 45.455 0.00 0.00 0.00 3.85
7574 8290 5.121380 AGTATTTCGGTACAGAGGGAGTA 57.879 43.478 0.00 0.00 0.00 2.59
7575 8291 5.513233 AGTATTTCGGTACAGAGGGAGTAA 58.487 41.667 0.00 0.00 0.00 2.24
7576 8292 6.134754 AGTATTTCGGTACAGAGGGAGTAAT 58.865 40.000 0.00 0.00 0.00 1.89
7577 8293 5.952347 ATTTCGGTACAGAGGGAGTAATT 57.048 39.130 0.00 0.00 0.00 1.40
7578 8294 4.730949 TTCGGTACAGAGGGAGTAATTG 57.269 45.455 0.00 0.00 0.00 2.32
7579 8295 3.028850 TCGGTACAGAGGGAGTAATTGG 58.971 50.000 0.00 0.00 0.00 3.16
7580 8296 2.483188 CGGTACAGAGGGAGTAATTGGC 60.483 54.545 0.00 0.00 0.00 4.52
7581 8297 2.483188 GGTACAGAGGGAGTAATTGGCG 60.483 54.545 0.00 0.00 0.00 5.69
7582 8298 0.541863 ACAGAGGGAGTAATTGGCGG 59.458 55.000 0.00 0.00 0.00 6.13
7583 8299 0.541863 CAGAGGGAGTAATTGGCGGT 59.458 55.000 0.00 0.00 0.00 5.68
7584 8300 1.065418 CAGAGGGAGTAATTGGCGGTT 60.065 52.381 0.00 0.00 0.00 4.44
7585 8301 1.065418 AGAGGGAGTAATTGGCGGTTG 60.065 52.381 0.00 0.00 0.00 3.77
7586 8302 0.696501 AGGGAGTAATTGGCGGTTGT 59.303 50.000 0.00 0.00 0.00 3.32
7587 8303 1.910671 AGGGAGTAATTGGCGGTTGTA 59.089 47.619 0.00 0.00 0.00 2.41
7588 8304 2.306512 AGGGAGTAATTGGCGGTTGTAA 59.693 45.455 0.00 0.00 0.00 2.41
7589 8305 3.083293 GGGAGTAATTGGCGGTTGTAAA 58.917 45.455 0.00 0.00 0.00 2.01
7659 8376 2.265739 GGCACGCTGAGGTGATCA 59.734 61.111 5.45 0.00 40.38 2.92
7660 8377 1.153289 GGCACGCTGAGGTGATCAT 60.153 57.895 0.00 0.00 40.38 2.45
7661 8378 1.434622 GGCACGCTGAGGTGATCATG 61.435 60.000 0.00 0.00 40.38 3.07
7840 8830 2.891191 TCCCACTAATCAAACCACCC 57.109 50.000 0.00 0.00 0.00 4.61
7877 8868 2.479049 CCCGTAATCTCACGTAGGTGTG 60.479 54.545 14.78 12.58 44.68 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 105 2.094675 GGGTGGTCATGATTGAGTTGG 58.905 52.381 0.00 0.00 30.85 3.77
279 291 2.506438 CTCGTCTCCCCGCGTTTC 60.506 66.667 4.92 0.00 0.00 2.78
622 635 1.815613 GGGGCAAGAAGAAGAAGAAGC 59.184 52.381 0.00 0.00 0.00 3.86
623 636 2.441410 GGGGGCAAGAAGAAGAAGAAG 58.559 52.381 0.00 0.00 0.00 2.85
624 637 2.586648 GGGGGCAAGAAGAAGAAGAA 57.413 50.000 0.00 0.00 0.00 2.52
692 708 1.446099 CTGGATGTGGACGGACACG 60.446 63.158 7.16 0.00 44.21 4.49
766 782 1.199624 GCAAAACAACAAGACTGGCG 58.800 50.000 0.00 0.00 0.00 5.69
768 784 1.535860 CCGGCAAAACAACAAGACTGG 60.536 52.381 0.00 0.00 0.00 4.00
811 827 5.694995 TCAAACTCCCATCACTTCTTTCTT 58.305 37.500 0.00 0.00 0.00 2.52
903 919 1.530655 CCCAAACAAACTCCGCCCT 60.531 57.895 0.00 0.00 0.00 5.19
932 948 2.887360 CCCGGAAATGGCTTGCTG 59.113 61.111 0.73 0.00 0.00 4.41
1089 1105 2.668212 TTGAACCGCTGCTTCCCG 60.668 61.111 0.00 0.00 0.00 5.14
1424 1553 9.241317 GTCAAATACTGAATCCATATGCAAAAG 57.759 33.333 0.00 0.00 35.22 2.27
1523 1652 7.641411 CCAGCATATTTCGCACAATTATATAGC 59.359 37.037 0.00 0.00 0.00 2.97
1528 1657 5.299028 TGACCAGCATATTTCGCACAATTAT 59.701 36.000 0.00 0.00 0.00 1.28
1598 1729 7.909121 CAGCTGTTTCTAAAGATATTGCAAGAG 59.091 37.037 5.25 0.00 0.00 2.85
1809 1940 3.476552 TCTCACTTCACCACATTTGTCC 58.523 45.455 0.00 0.00 0.00 4.02
1821 1952 4.411013 TGTCCTCTGAATCTCTCACTTCA 58.589 43.478 0.00 0.00 0.00 3.02
1834 1965 3.526899 TCCCATTAAACCTGTCCTCTGA 58.473 45.455 0.00 0.00 0.00 3.27
1858 1989 7.103641 TCGGCTTCATTAGAAATTTCAGTAGT 58.896 34.615 19.99 1.71 32.35 2.73
2304 2435 5.878116 TGGTGCAGTTGTATAACTTATCACC 59.122 40.000 25.20 25.20 44.57 4.02
2364 2495 6.425735 TCCATCAGCCTTCAAATAAGATTGA 58.574 36.000 0.00 0.00 37.53 2.57
2685 2816 2.178580 CCCCCTTGCAATGAAGCTAAA 58.821 47.619 0.00 0.00 34.99 1.85
2802 2933 2.704572 ACTGCACCTGAATTCACTAGC 58.295 47.619 3.38 8.94 0.00 3.42
2903 3034 9.075519 ACATGATTTTCTTAAATATGTGTTGCG 57.924 29.630 0.00 0.00 34.16 4.85
2960 3091 8.340618 TGATGAGAAGATAAAAACTGGGAAAG 57.659 34.615 0.00 0.00 0.00 2.62
3001 3132 2.770164 AGAGGTTCAGGTACATGCAC 57.230 50.000 1.79 1.64 0.00 4.57
3221 3354 9.056005 GCCTAACATAATCACATTCATGTCTAA 57.944 33.333 0.00 0.00 39.39 2.10
3299 3432 1.135689 GCAACAGTTAGCAACCATCCG 60.136 52.381 3.63 0.00 0.00 4.18
3353 3486 2.428890 AGGATCAGAGAAACCAGTAGCG 59.571 50.000 0.00 0.00 0.00 4.26
3526 3659 7.865706 TGGCTCCATCTTTTCTACTAAAATC 57.134 36.000 0.00 0.00 0.00 2.17
3938 4071 0.119155 ACCCAGATCAGACAAGGGGA 59.881 55.000 0.00 0.00 43.96 4.81
3966 4099 0.388649 GAGACCGCAACGTCATCTGT 60.389 55.000 0.00 0.00 35.07 3.41
4126 4259 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
4127 4260 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
4128 4261 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
4129 4262 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
4130 4263 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
4131 4264 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
4132 4265 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
4147 4280 9.559732 TCATTTGTTGAAATCTCTAGAAAGACA 57.440 29.630 0.00 0.00 28.65 3.41
4148 4281 9.818796 GTCATTTGTTGAAATCTCTAGAAAGAC 57.181 33.333 0.00 0.00 35.70 3.01
4149 4282 9.784531 AGTCATTTGTTGAAATCTCTAGAAAGA 57.215 29.630 0.00 0.00 35.70 2.52
4152 4285 9.996554 TGTAGTCATTTGTTGAAATCTCTAGAA 57.003 29.630 0.00 0.00 35.70 2.10
4156 4289 8.873830 CGTATGTAGTCATTTGTTGAAATCTCT 58.126 33.333 0.00 0.00 35.70 3.10
4157 4290 8.869897 TCGTATGTAGTCATTTGTTGAAATCTC 58.130 33.333 0.00 0.00 35.70 2.75
4158 4291 8.771920 TCGTATGTAGTCATTTGTTGAAATCT 57.228 30.769 0.00 0.00 35.70 2.40
4159 4292 9.478019 CTTCGTATGTAGTCATTTGTTGAAATC 57.522 33.333 0.00 0.00 35.70 2.17
4160 4293 7.962918 GCTTCGTATGTAGTCATTTGTTGAAAT 59.037 33.333 0.00 0.00 35.70 2.17
4161 4294 7.041712 TGCTTCGTATGTAGTCATTTGTTGAAA 60.042 33.333 0.00 0.00 35.70 2.69
4162 4295 6.425417 TGCTTCGTATGTAGTCATTTGTTGAA 59.575 34.615 0.00 0.00 35.70 2.69
4163 4296 5.929415 TGCTTCGTATGTAGTCATTTGTTGA 59.071 36.000 0.00 0.00 35.70 3.18
4164 4297 6.164408 TGCTTCGTATGTAGTCATTTGTTG 57.836 37.500 0.00 0.00 35.70 3.33
4165 4298 6.795098 TTGCTTCGTATGTAGTCATTTGTT 57.205 33.333 0.00 0.00 35.70 2.83
4166 4299 6.795098 TTTGCTTCGTATGTAGTCATTTGT 57.205 33.333 0.00 0.00 35.70 2.83
4167 4300 7.962373 TCATTTTGCTTCGTATGTAGTCATTTG 59.038 33.333 0.00 0.00 35.70 2.32
4168 4301 8.039603 TCATTTTGCTTCGTATGTAGTCATTT 57.960 30.769 0.00 0.00 35.70 2.32
4169 4302 7.334421 ACTCATTTTGCTTCGTATGTAGTCATT 59.666 33.333 0.00 0.00 35.70 2.57
4170 4303 6.818644 ACTCATTTTGCTTCGTATGTAGTCAT 59.181 34.615 0.00 0.00 38.00 3.06
4171 4304 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
4172 4305 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
4173 4306 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
4174 4307 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
4175 4308 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
4176 4309 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
4177 4310 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
4178 4311 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
4179 4312 6.871492 TGTAGATTCACTCATTTTGCTTCGTA 59.129 34.615 0.00 0.00 0.00 3.43
4180 4313 5.700832 TGTAGATTCACTCATTTTGCTTCGT 59.299 36.000 0.00 0.00 0.00 3.85
4181 4314 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
4182 4315 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
4212 4345 9.642343 ACCACATACGGATGTATATAGACATAT 57.358 33.333 14.23 5.08 44.82 1.78
4214 4347 7.956328 ACCACATACGGATGTATATAGACAT 57.044 36.000 14.23 12.70 44.82 3.06
4215 4348 8.105197 ACTACCACATACGGATGTATATAGACA 58.895 37.037 22.62 2.07 44.82 3.41
4216 4349 8.503458 ACTACCACATACGGATGTATATAGAC 57.497 38.462 22.62 0.00 44.82 2.59
4217 4350 7.772292 GGACTACCACATACGGATGTATATAGA 59.228 40.741 22.62 5.04 44.82 1.98
4218 4351 7.555195 TGGACTACCACATACGGATGTATATAG 59.445 40.741 14.23 16.35 44.82 1.31
4219 4352 7.404481 TGGACTACCACATACGGATGTATATA 58.596 38.462 14.23 5.36 44.82 0.86
4220 4353 6.250711 TGGACTACCACATACGGATGTATAT 58.749 40.000 14.23 4.37 44.82 0.86
4221 4354 5.633117 TGGACTACCACATACGGATGTATA 58.367 41.667 14.23 8.27 44.82 1.47
4222 4355 4.476297 TGGACTACCACATACGGATGTAT 58.524 43.478 14.23 7.46 44.82 2.29
4223 4356 3.900971 TGGACTACCACATACGGATGTA 58.099 45.455 14.23 0.00 44.82 2.29
4239 4372 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
4240 4373 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
4257 4390 8.548025 CCCCCATTCCTAAATATTTGTCTTTTT 58.452 33.333 11.05 0.00 0.00 1.94
4258 4391 8.089625 CCCCCATTCCTAAATATTTGTCTTTT 57.910 34.615 11.05 0.00 0.00 2.27
4259 4392 7.675161 CCCCCATTCCTAAATATTTGTCTTT 57.325 36.000 11.05 0.00 0.00 2.52
4280 4413 3.438183 TCTACTTGTGAACTACTCCCCC 58.562 50.000 0.00 0.00 0.00 5.40
4281 4414 5.678955 AATCTACTTGTGAACTACTCCCC 57.321 43.478 0.00 0.00 0.00 4.81
4282 4415 7.407393 AGTAATCTACTTGTGAACTACTCCC 57.593 40.000 0.00 0.00 34.86 4.30
4328 4464 2.978156 TTTCCCTTCAAGTCATGCCT 57.022 45.000 0.00 0.00 0.00 4.75
4759 4903 5.997746 ACAACTCTGCAAGTTAAGCTTATGA 59.002 36.000 7.08 0.00 46.69 2.15
4838 4982 2.308570 TCAGGCCAGCATCCTTTTAAGA 59.691 45.455 5.01 0.00 0.00 2.10
5022 5168 6.514048 GCTGAACCCTTAGCAAGCTATTTATG 60.514 42.308 2.16 0.00 39.67 1.90
5047 5276 4.836736 AGATGGCCCTGAAATGAATATTGG 59.163 41.667 0.00 0.00 0.00 3.16
5248 5477 0.730265 CACTCTCTACGCTCTTCGCT 59.270 55.000 0.00 0.00 43.23 4.93
5378 5607 6.117488 GGCAGTTGCTATAGGTAAACCTTTA 58.883 40.000 7.04 3.14 43.31 1.85
5741 5970 4.331968 ACCATCTGGCGATTAAAGTTCAA 58.668 39.130 0.00 0.00 39.32 2.69
5781 6010 4.796038 AGTGAATTCATCTGGCAAAAGG 57.204 40.909 12.12 0.00 0.00 3.11
5818 6047 0.323629 TCATCTCCAACGAACCACCC 59.676 55.000 0.00 0.00 0.00 4.61
5821 6050 3.181459 TGACTTTCATCTCCAACGAACCA 60.181 43.478 0.00 0.00 0.00 3.67
5848 6077 5.106157 CGAGTATTTGAGGCATCCAACTTTT 60.106 40.000 0.00 0.00 0.00 2.27
6157 6387 7.726291 TGTTTCTTGAAGTGGTATCCCATTTAA 59.274 33.333 0.00 0.00 44.35 1.52
6213 6447 6.749923 TTTAAAAACAAATGGCAAGCAAGT 57.250 29.167 0.00 0.00 0.00 3.16
6214 6448 8.631676 AAATTTAAAAACAAATGGCAAGCAAG 57.368 26.923 0.00 0.00 0.00 4.01
6215 6449 8.992835 AAAATTTAAAAACAAATGGCAAGCAA 57.007 23.077 0.00 0.00 0.00 3.91
6337 6582 5.174395 CAGGGATTTCAACAACAACAACAA 58.826 37.500 0.00 0.00 0.00 2.83
6338 6583 4.221703 ACAGGGATTTCAACAACAACAACA 59.778 37.500 0.00 0.00 0.00 3.33
6339 6584 4.754322 ACAGGGATTTCAACAACAACAAC 58.246 39.130 0.00 0.00 0.00 3.32
6340 6585 6.462207 CCATACAGGGATTTCAACAACAACAA 60.462 38.462 0.00 0.00 0.00 2.83
6381 6629 7.874528 TGCCTGTAGTTTAGTACTAACCTTTTC 59.125 37.037 16.74 9.39 40.93 2.29
6426 6674 1.433534 GTCTTTCGAACCAGCAGAGG 58.566 55.000 0.00 0.00 0.00 3.69
6493 6761 5.561532 GCAATGCATGTCACATATACCTCAC 60.562 44.000 0.00 0.00 0.00 3.51
6578 6846 2.173782 TGGACAAAGGGACAAGCTACAA 59.826 45.455 0.00 0.00 0.00 2.41
6601 6869 5.163612 GCCTGGTTTCATCTTTAATCAGGAC 60.164 44.000 16.20 5.81 42.06 3.85
6617 6887 1.675641 GAGATGCCGTGCCTGGTTT 60.676 57.895 0.00 0.00 0.00 3.27
6629 6899 4.054671 CGTTAAGATGGAGGAAGAGATGC 58.945 47.826 0.00 0.00 0.00 3.91
6665 7305 8.415950 TTTGAAATATGCAAAGGAGGAACTTA 57.584 30.769 0.00 0.00 32.51 2.24
6795 7435 4.706842 TTGTTTAGGAGCAAGGTCTTCT 57.293 40.909 0.00 0.00 0.00 2.85
7458 8173 1.475280 TGGTCATACGGCTAGTGTCAC 59.525 52.381 0.00 0.00 0.00 3.67
7481 8196 2.393646 ACAGAGGGGATAGAGAGCAAC 58.606 52.381 0.00 0.00 0.00 4.17
7492 8208 3.484953 AGTATTGTGGTACAGAGGGGA 57.515 47.619 0.00 0.00 41.80 4.81
7506 8222 3.937079 GGTTCCCCTAACGACAAGTATTG 59.063 47.826 0.00 0.00 45.23 1.90
7507 8223 3.842436 AGGTTCCCCTAACGACAAGTATT 59.158 43.478 0.00 0.00 40.19 1.89
7508 8224 3.197116 CAGGTTCCCCTAACGACAAGTAT 59.803 47.826 0.00 0.00 39.89 2.12
7509 8225 2.564062 CAGGTTCCCCTAACGACAAGTA 59.436 50.000 0.00 0.00 39.89 2.24
7510 8226 1.346722 CAGGTTCCCCTAACGACAAGT 59.653 52.381 0.00 0.00 39.89 3.16
7511 8227 1.346722 ACAGGTTCCCCTAACGACAAG 59.653 52.381 0.00 0.00 39.89 3.16
7512 8228 1.426751 ACAGGTTCCCCTAACGACAA 58.573 50.000 0.00 0.00 39.89 3.18
7513 8229 1.895131 GTACAGGTTCCCCTAACGACA 59.105 52.381 0.00 0.00 39.89 4.35
7514 8230 2.094338 CAGTACAGGTTCCCCTAACGAC 60.094 54.545 0.00 0.00 39.89 4.34
7515 8231 2.173519 CAGTACAGGTTCCCCTAACGA 58.826 52.381 0.00 0.00 39.89 3.85
7516 8232 1.206371 CCAGTACAGGTTCCCCTAACG 59.794 57.143 0.00 0.00 39.89 3.18
7517 8233 2.263545 ACCAGTACAGGTTCCCCTAAC 58.736 52.381 3.70 0.00 39.89 2.34
7518 8234 2.727429 ACCAGTACAGGTTCCCCTAA 57.273 50.000 3.70 0.00 39.89 2.69
7526 8242 0.399075 CGGGGAAAACCAGTACAGGT 59.601 55.000 3.70 3.70 45.91 4.00
7527 8243 0.688487 TCGGGGAAAACCAGTACAGG 59.312 55.000 2.14 2.14 42.91 4.00
7528 8244 1.804601 GTCGGGGAAAACCAGTACAG 58.195 55.000 0.00 0.00 42.91 2.74
7529 8245 0.033781 CGTCGGGGAAAACCAGTACA 59.966 55.000 0.00 0.00 42.91 2.90
7530 8246 0.318120 TCGTCGGGGAAAACCAGTAC 59.682 55.000 0.00 0.00 42.91 2.73
7531 8247 0.318120 GTCGTCGGGGAAAACCAGTA 59.682 55.000 0.00 0.00 42.91 2.74
7532 8248 1.070275 GTCGTCGGGGAAAACCAGT 59.930 57.895 0.00 0.00 42.91 4.00
7533 8249 0.533308 TTGTCGTCGGGGAAAACCAG 60.533 55.000 0.00 0.00 42.91 4.00
7534 8250 0.533308 CTTGTCGTCGGGGAAAACCA 60.533 55.000 0.00 0.00 42.91 3.67
7535 8251 0.533531 ACTTGTCGTCGGGGAAAACC 60.534 55.000 0.00 0.00 39.11 3.27
7536 8252 2.153366 TACTTGTCGTCGGGGAAAAC 57.847 50.000 0.00 0.00 0.00 2.43
7537 8253 3.405823 AATACTTGTCGTCGGGGAAAA 57.594 42.857 0.00 0.00 0.00 2.29
7538 8254 3.328505 GAAATACTTGTCGTCGGGGAAA 58.671 45.455 0.00 0.00 0.00 3.13
7539 8255 2.671914 CGAAATACTTGTCGTCGGGGAA 60.672 50.000 0.00 0.00 32.61 3.97
7540 8256 1.135315 CGAAATACTTGTCGTCGGGGA 60.135 52.381 0.00 0.00 32.61 4.81
7541 8257 1.274596 CGAAATACTTGTCGTCGGGG 58.725 55.000 0.00 0.00 32.61 5.73
7542 8258 1.274596 CCGAAATACTTGTCGTCGGG 58.725 55.000 2.51 0.00 45.87 5.14
7544 8260 3.491356 TGTACCGAAATACTTGTCGTCG 58.509 45.455 0.00 0.00 35.48 5.12
7545 8261 4.726416 TCTGTACCGAAATACTTGTCGTC 58.274 43.478 0.00 0.00 35.48 4.20
7546 8262 4.380233 CCTCTGTACCGAAATACTTGTCGT 60.380 45.833 0.00 0.00 35.48 4.34
7547 8263 4.103357 CCTCTGTACCGAAATACTTGTCG 58.897 47.826 0.00 0.00 37.01 4.35
7548 8264 4.159135 TCCCTCTGTACCGAAATACTTGTC 59.841 45.833 0.00 0.00 0.00 3.18
7549 8265 4.091549 TCCCTCTGTACCGAAATACTTGT 58.908 43.478 0.00 0.00 0.00 3.16
7550 8266 4.159879 ACTCCCTCTGTACCGAAATACTTG 59.840 45.833 0.00 0.00 0.00 3.16
7551 8267 4.351127 ACTCCCTCTGTACCGAAATACTT 58.649 43.478 0.00 0.00 0.00 2.24
7552 8268 3.978610 ACTCCCTCTGTACCGAAATACT 58.021 45.455 0.00 0.00 0.00 2.12
7553 8269 5.841957 TTACTCCCTCTGTACCGAAATAC 57.158 43.478 0.00 0.00 0.00 1.89
7554 8270 6.183360 CCAATTACTCCCTCTGTACCGAAATA 60.183 42.308 0.00 0.00 0.00 1.40
7555 8271 5.396436 CCAATTACTCCCTCTGTACCGAAAT 60.396 44.000 0.00 0.00 0.00 2.17
7556 8272 4.081309 CCAATTACTCCCTCTGTACCGAAA 60.081 45.833 0.00 0.00 0.00 3.46
7557 8273 3.449737 CCAATTACTCCCTCTGTACCGAA 59.550 47.826 0.00 0.00 0.00 4.30
7558 8274 3.028850 CCAATTACTCCCTCTGTACCGA 58.971 50.000 0.00 0.00 0.00 4.69
7559 8275 2.483188 GCCAATTACTCCCTCTGTACCG 60.483 54.545 0.00 0.00 0.00 4.02
7560 8276 2.483188 CGCCAATTACTCCCTCTGTACC 60.483 54.545 0.00 0.00 0.00 3.34
7561 8277 2.483188 CCGCCAATTACTCCCTCTGTAC 60.483 54.545 0.00 0.00 0.00 2.90
7562 8278 1.760613 CCGCCAATTACTCCCTCTGTA 59.239 52.381 0.00 0.00 0.00 2.74
7563 8279 0.541863 CCGCCAATTACTCCCTCTGT 59.458 55.000 0.00 0.00 0.00 3.41
7564 8280 0.541863 ACCGCCAATTACTCCCTCTG 59.458 55.000 0.00 0.00 0.00 3.35
7565 8281 1.065418 CAACCGCCAATTACTCCCTCT 60.065 52.381 0.00 0.00 0.00 3.69
7566 8282 1.339727 ACAACCGCCAATTACTCCCTC 60.340 52.381 0.00 0.00 0.00 4.30
7567 8283 0.696501 ACAACCGCCAATTACTCCCT 59.303 50.000 0.00 0.00 0.00 4.20
7568 8284 2.406596 TACAACCGCCAATTACTCCC 57.593 50.000 0.00 0.00 0.00 4.30
7569 8285 3.754850 AGTTTACAACCGCCAATTACTCC 59.245 43.478 0.00 0.00 0.00 3.85
7570 8286 5.151389 CAAGTTTACAACCGCCAATTACTC 58.849 41.667 0.00 0.00 0.00 2.59
7571 8287 4.581409 ACAAGTTTACAACCGCCAATTACT 59.419 37.500 0.00 0.00 0.00 2.24
7572 8288 4.862350 ACAAGTTTACAACCGCCAATTAC 58.138 39.130 0.00 0.00 0.00 1.89
7573 8289 6.630444 TTACAAGTTTACAACCGCCAATTA 57.370 33.333 0.00 0.00 0.00 1.40
7574 8290 5.517322 TTACAAGTTTACAACCGCCAATT 57.483 34.783 0.00 0.00 0.00 2.32
7575 8291 5.475564 AGATTACAAGTTTACAACCGCCAAT 59.524 36.000 0.00 0.00 0.00 3.16
7576 8292 4.822896 AGATTACAAGTTTACAACCGCCAA 59.177 37.500 0.00 0.00 0.00 4.52
7577 8293 4.391155 AGATTACAAGTTTACAACCGCCA 58.609 39.130 0.00 0.00 0.00 5.69
7578 8294 5.180680 AGAAGATTACAAGTTTACAACCGCC 59.819 40.000 0.00 0.00 0.00 6.13
7579 8295 6.077838 CAGAAGATTACAAGTTTACAACCGC 58.922 40.000 0.00 0.00 0.00 5.68
7580 8296 6.599437 CCAGAAGATTACAAGTTTACAACCG 58.401 40.000 0.00 0.00 0.00 4.44
7581 8297 6.379386 GCCAGAAGATTACAAGTTTACAACC 58.621 40.000 0.00 0.00 0.00 3.77
7582 8298 6.016610 TGGCCAGAAGATTACAAGTTTACAAC 60.017 38.462 0.00 0.00 0.00 3.32
7583 8299 6.065374 TGGCCAGAAGATTACAAGTTTACAA 58.935 36.000 0.00 0.00 0.00 2.41
7584 8300 5.626142 TGGCCAGAAGATTACAAGTTTACA 58.374 37.500 0.00 0.00 0.00 2.41
7585 8301 6.569179 TTGGCCAGAAGATTACAAGTTTAC 57.431 37.500 5.11 0.00 0.00 2.01
7586 8302 6.775629 AGTTTGGCCAGAAGATTACAAGTTTA 59.224 34.615 5.11 0.00 0.00 2.01
7587 8303 5.598417 AGTTTGGCCAGAAGATTACAAGTTT 59.402 36.000 5.11 0.00 0.00 2.66
7588 8304 5.140454 AGTTTGGCCAGAAGATTACAAGTT 58.860 37.500 5.11 0.00 0.00 2.66
7589 8305 4.729868 AGTTTGGCCAGAAGATTACAAGT 58.270 39.130 5.11 0.00 0.00 3.16
7590 8306 7.253422 CAATAGTTTGGCCAGAAGATTACAAG 58.747 38.462 5.11 0.00 0.00 3.16
7659 8376 2.028385 GGAACGTAGGAAGGTCACACAT 60.028 50.000 0.00 0.00 0.00 3.21
7660 8377 1.342174 GGAACGTAGGAAGGTCACACA 59.658 52.381 0.00 0.00 0.00 3.72
7661 8378 1.617357 AGGAACGTAGGAAGGTCACAC 59.383 52.381 0.00 0.00 0.00 3.82
7799 8789 7.769970 TGGGAAAGGTAATTACGTAGGTTTATG 59.230 37.037 11.01 0.00 0.00 1.90
7840 8830 2.314215 GGGGTCAAGGGGGTTAGGG 61.314 68.421 0.00 0.00 0.00 3.53
7923 8914 1.032014 TGCCACTTTGCACCTTTCTC 58.968 50.000 0.00 0.00 36.04 2.87
7944 8936 2.106683 GGAGAAATGGTGGCGTCCG 61.107 63.158 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.