Multiple sequence alignment - TraesCS5A01G193700

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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 TraesCS5A01G193700 chr5A 100.000 4869 0 0 1 4869 397142683 397147551 0.000000e+00 8992
1 TraesCS5A01G193700 chr5B 94.372 1617 61 12 1625 3214 341052000 341053613 0.000000e+00 2455
2 TraesCS5A01G193700 chr5B 89.692 1397 54 33 3515 4869 341053912 341055260 0.000000e+00 1700
3 TraesCS5A01G193700 chr5B 86.617 1076 67 34 606 1628 341050812 341051863 0.000000e+00 1118
4 TraesCS5A01G193700 chr5B 85.014 367 35 10 1 350 341050082 341050445 5.990000e-94 355
5 TraesCS5A01G193700 chr5B 90.948 232 12 7 362 589 341050429 341050655 2.200000e-78 303
6 TraesCS5A01G193700 chr5B 93.500 200 6 2 3318 3512 341053612 341053809 1.710000e-74 291
7 TraesCS5A01G193700 chr5B 95.798 119 4 1 3201 3319 521817154 521817037 1.790000e-44 191
8 TraesCS5A01G193700 chr5D 93.947 1619 62 11 1625 3214 299811157 299812768 0.000000e+00 2414
9 TraesCS5A01G193700 chr5D 90.169 1597 90 27 3318 4869 299812767 299814341 0.000000e+00 2017
10 TraesCS5A01G193700 chr5D 90.988 1043 58 20 598 1628 299810002 299811020 0.000000e+00 1373
11 TraesCS5A01G193700 chr5D 91.625 597 33 10 1 589 299809263 299809850 0.000000e+00 809
12 TraesCS5A01G193700 chr5D 96.610 118 2 2 3210 3326 547442150 547442034 1.380000e-45 195
13 TraesCS5A01G193700 chr5D 95.763 118 3 2 3211 3328 52741843 52741958 6.430000e-44 189
14 TraesCS5A01G193700 chr1A 85.319 361 28 10 4447 4807 543638592 543638927 2.790000e-92 350
15 TraesCS5A01G193700 chr7A 99.074 108 1 0 3213 3320 25411110 25411003 1.380000e-45 195
16 TraesCS5A01G193700 chr7A 93.548 124 6 2 3209 3331 619359594 619359716 2.990000e-42 183
17 TraesCS5A01G193700 chr2A 97.368 114 3 0 3213 3326 763687569 763687456 1.380000e-45 195
18 TraesCS5A01G193700 chr2A 96.460 113 4 0 3212 3324 138184412 138184300 2.310000e-43 187
19 TraesCS5A01G193700 chr3A 98.182 110 2 0 3210 3319 651627754 651627863 4.970000e-45 193
20 TraesCS5A01G193700 chr3A 97.297 111 2 1 3213 3323 657423037 657423146 2.310000e-43 187
21 TraesCS5A01G193700 chr2D 84.242 165 24 2 1 164 543527347 543527510 5.040000e-35 159
22 TraesCS5A01G193700 chr7B 84.049 163 22 3 1 160 185284278 185284439 2.350000e-33 154
23 TraesCS5A01G193700 chr3B 83.133 166 25 2 1 164 117952933 117952769 1.090000e-31 148
24 TraesCS5A01G193700 chr3B 83.030 165 25 2 1 163 818995156 818994993 3.930000e-31 147
25 TraesCS5A01G193700 chr4A 82.927 164 24 3 4 164 742465721 742465883 1.410000e-30 145
26 TraesCS5A01G193700 chr2B 82.209 163 24 4 5 164 54522992 54522832 8.500000e-28 135
27 TraesCS5A01G193700 chr7D 79.058 191 33 5 1 185 134171395 134171584 1.840000e-24 124


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 TraesCS5A01G193700 chr5A 397142683 397147551 4868 False 8992.00 8992 100.000000 1 4869 1 chr5A.!!$F1 4868
1 TraesCS5A01G193700 chr5B 341050082 341055260 5178 False 1037.00 2455 90.023833 1 4869 6 chr5B.!!$F1 4868
2 TraesCS5A01G193700 chr5D 299809263 299814341 5078 False 1653.25 2414 91.682250 1 4869 4 chr5D.!!$F2 4868

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
29 30 0.036306 AAAAGGGCGTGAGATCGGTT 59.964 50.000 0.0 0.0 0.00 4.44 F
545 568 1.130373 GTCCACTTGTGTGTGTGTGTG 59.870 52.381 0.0 0.0 42.34 3.82 F
1416 1651 0.393077 AGTGGTTTGACGACCTCTGG 59.607 55.000 0.0 0.0 40.85 3.86 F
3228 3640 0.038744 AACTACTCCCTCCGTTCCGA 59.961 55.000 0.0 0.0 0.00 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1249 1469 0.891373 CGGAGCAGGAAGAGACAAGA 59.109 55.000 0.0 0.0 0.00 3.02 R
1466 1703 1.202510 GCAACCCACAACAAATCAGCA 60.203 47.619 0.0 0.0 0.00 4.41 R
3302 3714 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.0 0.0 0.00 3.53 R
4308 4853 0.107654 GGGATAAGTGGCAGAAGCGT 60.108 55.000 0.0 0.0 43.41 5.07 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 0.036306 AAAAGGGCGTGAGATCGGTT 59.964 50.000 0.00 0.00 0.00 4.44
199 216 3.631686 TGCCCTTAATCAATCCAACATCG 59.368 43.478 0.00 0.00 0.00 3.84
207 224 8.568676 TTAATCAATCCAACATCGGTTAGAAA 57.431 30.769 0.00 0.00 34.87 2.52
208 225 6.683974 ATCAATCCAACATCGGTTAGAAAG 57.316 37.500 0.00 0.00 34.87 2.62
324 341 5.074515 ACCTCTTGATGAACTAGGGGAAAAA 59.925 40.000 0.00 0.00 43.07 1.94
421 440 8.907885 AGAATAAACCCTTTTGATTCTCTATGC 58.092 33.333 0.00 0.00 32.67 3.14
427 446 5.278169 CCCTTTTGATTCTCTATGCATTCCG 60.278 44.000 3.54 0.00 0.00 4.30
458 480 7.087409 TCCACATAATGTATGCAACTTTGAG 57.913 36.000 0.00 0.00 39.79 3.02
543 566 1.447945 TGTCCACTTGTGTGTGTGTG 58.552 50.000 0.00 0.00 42.34 3.82
544 567 1.271108 TGTCCACTTGTGTGTGTGTGT 60.271 47.619 0.00 0.00 42.34 3.72
545 568 1.130373 GTCCACTTGTGTGTGTGTGTG 59.870 52.381 0.00 0.00 42.34 3.82
546 569 1.164411 CCACTTGTGTGTGTGTGTGT 58.836 50.000 0.00 0.00 42.34 3.72
547 570 1.135717 CCACTTGTGTGTGTGTGTGTG 60.136 52.381 0.00 0.00 42.34 3.82
740 945 9.533253 AAAAACAATGTCTTCTAAACCAGAATG 57.467 29.630 0.00 0.00 42.44 2.67
741 946 7.823745 AACAATGTCTTCTAAACCAGAATGT 57.176 32.000 0.00 0.00 42.44 2.71
742 947 7.440523 ACAATGTCTTCTAAACCAGAATGTC 57.559 36.000 0.00 0.00 42.44 3.06
743 948 6.998074 ACAATGTCTTCTAAACCAGAATGTCA 59.002 34.615 0.00 0.00 42.44 3.58
1102 1319 1.804748 GCGTTCGTGGGATTTTCTTCT 59.195 47.619 0.00 0.00 0.00 2.85
1103 1320 2.225727 GCGTTCGTGGGATTTTCTTCTT 59.774 45.455 0.00 0.00 0.00 2.52
1131 1349 3.074687 AGCTAGATTCCTCCCGTGAGATA 59.925 47.826 0.00 0.00 41.42 1.98
1141 1359 2.700371 TCCCGTGAGATATGCTGATTGT 59.300 45.455 0.00 0.00 0.00 2.71
1148 1367 4.945543 TGAGATATGCTGATTGTTGTGCTT 59.054 37.500 0.00 0.00 0.00 3.91
1168 1387 1.651461 CTCGCTCGCTGCAGATCTA 59.349 57.895 20.43 0.00 43.06 1.98
1245 1464 3.771160 CGCCGTAAGTGCTCCCCT 61.771 66.667 0.00 0.00 0.00 4.79
1249 1469 1.120530 CCGTAAGTGCTCCCCTACAT 58.879 55.000 0.00 0.00 0.00 2.29
1319 1554 3.917760 CGGTCTGATCCGGGCTCC 61.918 72.222 0.00 0.00 45.88 4.70
1416 1651 0.393077 AGTGGTTTGACGACCTCTGG 59.607 55.000 0.00 0.00 40.85 3.86
1438 1673 2.046604 GGGTAGCGCGAGGGTTTT 60.047 61.111 12.10 0.00 0.00 2.43
1439 1674 1.673337 GGGTAGCGCGAGGGTTTTT 60.673 57.895 12.10 0.00 0.00 1.94
1448 1683 3.528532 CGCGAGGGTTTTTAGATAGGTT 58.471 45.455 0.00 0.00 0.00 3.50
1466 1703 3.071457 AGGTTTTGCTGCTTATGGCTTTT 59.929 39.130 0.00 0.00 42.39 2.27
1482 1719 2.545106 GCTTTTGCTGATTTGTTGTGGG 59.455 45.455 0.00 0.00 43.35 4.61
1502 1742 2.360165 GGTTGCATTTGGGCTGATAGAG 59.640 50.000 0.00 0.00 34.04 2.43
1508 1748 4.261909 GCATTTGGGCTGATAGAGGAATTG 60.262 45.833 0.00 0.00 0.00 2.32
1564 1805 1.457346 ACTCAATGTGCTAGCCTTGC 58.543 50.000 13.29 0.42 0.00 4.01
1568 1809 1.479323 CAATGTGCTAGCCTTGCCATT 59.521 47.619 13.29 9.58 34.29 3.16
1677 2058 2.435805 GTCATCAACATAGGGCTGGAGA 59.564 50.000 0.00 0.00 0.00 3.71
1695 2076 3.196685 GGAGACTGGAGAACAATAGCTGT 59.803 47.826 0.00 0.00 41.27 4.40
1792 2173 3.943137 CTGGGGCTGTAGGTGGGGA 62.943 68.421 0.00 0.00 0.00 4.81
1879 2268 9.959721 TCCAAAAGCTATTCTACTTTATTCTGT 57.040 29.630 0.00 0.00 35.10 3.41
1897 2287 6.702716 TTCTGTCGTTTCCTTATTTTGGTT 57.297 33.333 0.00 0.00 0.00 3.67
1909 2299 0.104725 TTTTGGTTTGGCTGGGGGAT 60.105 50.000 0.00 0.00 0.00 3.85
1922 2312 1.497309 GGGGGATGTGTGGGTTCTGA 61.497 60.000 0.00 0.00 0.00 3.27
1990 2380 4.463539 TGATGCAACTGGATTTATGCTGTT 59.536 37.500 0.00 1.65 39.95 3.16
1997 2387 7.537715 CAACTGGATTTATGCTGTTGTCAATA 58.462 34.615 18.90 0.00 45.73 1.90
2111 2502 5.463392 CAGTGAAATATGATAGTGTCACCGG 59.537 44.000 0.00 0.00 40.28 5.28
2173 2564 2.849880 TTTCTTGTGACAACTGCTGC 57.150 45.000 0.00 0.00 0.00 5.25
2177 2568 3.069289 TCTTGTGACAACTGCTGCTATG 58.931 45.455 0.00 0.00 0.00 2.23
2250 2641 7.264947 TGTCAACCTTTTCTTTGAATTTCTCC 58.735 34.615 0.00 0.00 33.58 3.71
2383 2774 5.698832 CATCGAATGTATGTCTCTCTCTCC 58.301 45.833 0.00 0.00 0.00 3.71
2387 2778 3.201353 TGTATGTCTCTCTCTCCCTCG 57.799 52.381 0.00 0.00 0.00 4.63
2403 2794 7.710907 TCTCTCCCTCGTCAAACATTATAATTG 59.289 37.037 0.00 0.00 0.00 2.32
2551 2942 5.779241 TCAGAAATCTGGAAAGGTGGTAT 57.221 39.130 10.37 0.00 43.91 2.73
2727 3118 2.290464 TCGGAACTAGTGCTCTAGCTC 58.710 52.381 20.12 17.37 45.32 4.09
2813 3204 6.658188 AGCTACACTAACCAGGATCTTATC 57.342 41.667 0.00 0.00 0.00 1.75
2946 3356 6.260493 ACGTGATCTAAACGCTCTTAGAGTAT 59.740 38.462 11.18 0.00 44.80 2.12
2975 3385 9.262358 GTTAATCACTATTTGTCCTATCTCACC 57.738 37.037 0.00 0.00 0.00 4.02
2978 3388 7.825331 TCACTATTTGTCCTATCTCACCTAG 57.175 40.000 0.00 0.00 0.00 3.02
3136 3547 8.531622 TTGTATCATTGCAACCACAAATAAAG 57.468 30.769 0.00 0.00 32.27 1.85
3141 3552 3.976169 TGCAACCACAAATAAAGCTGAC 58.024 40.909 0.00 0.00 0.00 3.51
3171 3582 4.620982 GCAGTTGCTGTGTCCTTTTATTT 58.379 39.130 0.00 0.00 38.21 1.40
3173 3584 5.591099 CAGTTGCTGTGTCCTTTTATTTGT 58.409 37.500 0.00 0.00 0.00 2.83
3214 3626 9.606631 AAATCAGACATATCCTTTCTCAACTAC 57.393 33.333 0.00 0.00 0.00 2.73
3215 3627 7.962995 TCAGACATATCCTTTCTCAACTACT 57.037 36.000 0.00 0.00 0.00 2.57
3216 3628 8.001881 TCAGACATATCCTTTCTCAACTACTC 57.998 38.462 0.00 0.00 0.00 2.59
3217 3629 7.068839 TCAGACATATCCTTTCTCAACTACTCC 59.931 40.741 0.00 0.00 0.00 3.85
3218 3630 6.325286 AGACATATCCTTTCTCAACTACTCCC 59.675 42.308 0.00 0.00 0.00 4.30
3219 3631 6.206042 ACATATCCTTTCTCAACTACTCCCT 58.794 40.000 0.00 0.00 0.00 4.20
3220 3632 6.325286 ACATATCCTTTCTCAACTACTCCCTC 59.675 42.308 0.00 0.00 0.00 4.30
3221 3633 3.442076 TCCTTTCTCAACTACTCCCTCC 58.558 50.000 0.00 0.00 0.00 4.30
3222 3634 2.166664 CCTTTCTCAACTACTCCCTCCG 59.833 54.545 0.00 0.00 0.00 4.63
3223 3635 2.599408 TTCTCAACTACTCCCTCCGT 57.401 50.000 0.00 0.00 0.00 4.69
3224 3636 2.599408 TCTCAACTACTCCCTCCGTT 57.401 50.000 0.00 0.00 0.00 4.44
3225 3637 2.444421 TCTCAACTACTCCCTCCGTTC 58.556 52.381 0.00 0.00 0.00 3.95
3226 3638 1.477295 CTCAACTACTCCCTCCGTTCC 59.523 57.143 0.00 0.00 0.00 3.62
3227 3639 0.172803 CAACTACTCCCTCCGTTCCG 59.827 60.000 0.00 0.00 0.00 4.30
3228 3640 0.038744 AACTACTCCCTCCGTTCCGA 59.961 55.000 0.00 0.00 0.00 4.55
3229 3641 0.038744 ACTACTCCCTCCGTTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
3230 3642 1.341778 ACTACTCCCTCCGTTCCGAAT 60.342 52.381 0.00 0.00 0.00 3.34
3231 3643 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
3232 3644 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
3233 3645 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
3234 3646 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
3235 3647 1.753073 TCCCTCCGTTCCGAATTACTC 59.247 52.381 0.00 0.00 0.00 2.59
3237 3649 1.133790 CCTCCGTTCCGAATTACTCGT 59.866 52.381 0.00 0.00 46.65 4.18
3238 3650 2.448219 CTCCGTTCCGAATTACTCGTC 58.552 52.381 0.00 0.00 46.65 4.20
3239 3651 1.186030 CCGTTCCGAATTACTCGTCG 58.814 55.000 0.00 0.00 46.65 5.12
3240 3652 0.564767 CGTTCCGAATTACTCGTCGC 59.435 55.000 0.00 0.00 46.65 5.19
3241 3653 1.621107 GTTCCGAATTACTCGTCGCA 58.379 50.000 0.00 0.00 46.65 5.10
3242 3654 1.582502 GTTCCGAATTACTCGTCGCAG 59.417 52.381 0.00 0.00 46.65 5.18
3243 3655 1.089112 TCCGAATTACTCGTCGCAGA 58.911 50.000 0.00 0.00 46.65 4.26
3244 3656 1.469703 TCCGAATTACTCGTCGCAGAA 59.530 47.619 0.00 0.00 46.65 3.02
3245 3657 2.095110 TCCGAATTACTCGTCGCAGAAA 60.095 45.455 0.00 0.00 46.65 2.52
3246 3658 2.858344 CCGAATTACTCGTCGCAGAAAT 59.142 45.455 0.00 0.00 46.65 2.17
3247 3659 3.301835 CCGAATTACTCGTCGCAGAAATG 60.302 47.826 0.00 0.00 46.65 2.32
3248 3660 3.301835 CGAATTACTCGTCGCAGAAATGG 60.302 47.826 0.00 0.00 42.89 3.16
3249 3661 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
3250 3662 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
3251 3663 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
3252 3664 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
3253 3665 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
3254 3666 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
3255 3667 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
3256 3668 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
3257 3669 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
3258 3670 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
3259 3671 5.562890 CGTCGCAGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 39.69 2.43
3260 3672 6.393990 GTCGCAGAAATGGATGTATCTAGAT 58.606 40.000 10.73 10.73 39.69 1.98
3261 3673 6.309980 GTCGCAGAAATGGATGTATCTAGATG 59.690 42.308 15.79 0.00 39.69 2.90
3262 3674 6.015095 TCGCAGAAATGGATGTATCTAGATGT 60.015 38.462 15.79 1.25 0.00 3.06
3263 3675 7.176690 TCGCAGAAATGGATGTATCTAGATGTA 59.823 37.037 15.79 4.44 0.00 2.29
3264 3676 7.978414 CGCAGAAATGGATGTATCTAGATGTAT 59.022 37.037 15.79 9.11 0.00 2.29
3265 3677 9.664332 GCAGAAATGGATGTATCTAGATGTATT 57.336 33.333 15.79 4.32 0.00 1.89
3291 3703 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
3292 3704 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
3293 3705 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
3294 3706 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
3295 3707 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
3296 3708 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
3297 3709 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
3298 3710 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
3299 3711 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
3300 3712 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
3301 3713 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
3302 3714 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
3303 3715 5.957842 TCCATTTCTGCGACAAGTAATTT 57.042 34.783 0.00 0.00 0.00 1.82
3304 3716 5.698832 TCCATTTCTGCGACAAGTAATTTG 58.301 37.500 0.00 0.00 42.68 2.32
3305 3717 4.858692 CCATTTCTGCGACAAGTAATTTGG 59.141 41.667 0.00 0.00 41.25 3.28
3306 3718 5.335583 CCATTTCTGCGACAAGTAATTTGGA 60.336 40.000 0.00 0.00 41.25 3.53
3307 3719 5.759506 TTTCTGCGACAAGTAATTTGGAA 57.240 34.783 0.00 0.00 41.25 3.53
3308 3720 4.742438 TCTGCGACAAGTAATTTGGAAC 57.258 40.909 0.00 0.00 41.25 3.62
3309 3721 3.185594 TCTGCGACAAGTAATTTGGAACG 59.814 43.478 0.00 0.00 41.25 3.95
3310 3722 2.224549 TGCGACAAGTAATTTGGAACGG 59.775 45.455 0.00 0.00 41.25 4.44
3311 3723 2.481185 GCGACAAGTAATTTGGAACGGA 59.519 45.455 0.00 0.00 41.25 4.69
3312 3724 3.424433 GCGACAAGTAATTTGGAACGGAG 60.424 47.826 0.00 0.00 41.25 4.63
3313 3725 3.124636 CGACAAGTAATTTGGAACGGAGG 59.875 47.826 0.00 0.00 41.25 4.30
3314 3726 3.418047 ACAAGTAATTTGGAACGGAGGG 58.582 45.455 0.00 0.00 41.25 4.30
3315 3727 3.073356 ACAAGTAATTTGGAACGGAGGGA 59.927 43.478 0.00 0.00 41.25 4.20
3316 3728 3.629142 AGTAATTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
3317 3729 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
3318 3730 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
3352 3764 2.119495 AGTGCCCCTCGAAGAATACAT 58.881 47.619 0.00 0.00 34.09 2.29
3377 3789 8.445275 TGTTGTGAGCTGTTAGATTCTTTAAA 57.555 30.769 0.00 0.00 0.00 1.52
3418 3830 6.835914 AGCTCTTGTTCTGATTTTTATCGTG 58.164 36.000 0.00 0.00 0.00 4.35
3419 3831 6.428159 AGCTCTTGTTCTGATTTTTATCGTGT 59.572 34.615 0.00 0.00 0.00 4.49
3589 4107 0.472734 ACAAGGGAGACAGCCTGACT 60.473 55.000 0.00 0.00 0.00 3.41
3631 4149 0.250901 AGAAATCCGGCACAGCTGTT 60.251 50.000 18.94 0.00 32.22 3.16
3874 4392 0.731417 CTCTCAAGCCTTGATTGCGG 59.269 55.000 7.75 0.00 39.30 5.69
3961 4481 2.095919 GGGTTGACAATACTTCACACGC 60.096 50.000 0.00 0.00 0.00 5.34
4067 4587 0.946221 CTGTCCGTTGAGCCACACTC 60.946 60.000 0.00 0.00 46.45 3.51
4120 4663 5.181811 TGAACTTGATTCAGCATTCGTCAAT 59.818 36.000 0.00 0.00 42.62 2.57
4143 4686 4.561735 TTTTAACTTGCTGTGGTGTAGC 57.438 40.909 0.00 0.00 41.49 3.58
4153 4696 2.301870 CTGTGGTGTAGCCTACTTTCCA 59.698 50.000 3.13 6.67 38.35 3.53
4157 4700 2.355818 GGTGTAGCCTACTTTCCAAGGG 60.356 54.545 3.13 0.00 33.17 3.95
4166 4709 5.104485 GCCTACTTTCCAAGGGAGAAGATAA 60.104 44.000 11.51 0.00 33.17 1.75
4167 4710 6.409810 GCCTACTTTCCAAGGGAGAAGATAAT 60.410 42.308 11.51 0.00 33.17 1.28
4168 4711 6.995091 CCTACTTTCCAAGGGAGAAGATAATG 59.005 42.308 11.51 0.00 31.21 1.90
4169 4712 6.642733 ACTTTCCAAGGGAGAAGATAATGA 57.357 37.500 11.51 0.00 31.21 2.57
4173 4716 6.581388 TCCAAGGGAGAAGATAATGATTGT 57.419 37.500 0.00 0.00 0.00 2.71
4181 4724 6.017275 GGAGAAGATAATGATTGTTGCCTGAG 60.017 42.308 0.00 0.00 0.00 3.35
4187 4730 1.881973 TGATTGTTGCCTGAGTTGAGC 59.118 47.619 0.00 0.00 0.00 4.26
4195 4738 0.103937 CCTGAGTTGAGCCCTCGATC 59.896 60.000 0.00 0.00 0.00 3.69
4196 4739 0.103937 CTGAGTTGAGCCCTCGATCC 59.896 60.000 0.00 0.00 0.00 3.36
4211 4754 5.416083 CCTCGATCCGGCAATAATATACAA 58.584 41.667 0.00 0.00 0.00 2.41
4212 4755 6.049149 CCTCGATCCGGCAATAATATACAAT 58.951 40.000 0.00 0.00 0.00 2.71
4213 4756 6.201044 CCTCGATCCGGCAATAATATACAATC 59.799 42.308 0.00 0.00 0.00 2.67
4214 4757 6.873997 TCGATCCGGCAATAATATACAATCT 58.126 36.000 0.00 0.00 0.00 2.40
4215 4758 8.002984 TCGATCCGGCAATAATATACAATCTA 57.997 34.615 0.00 0.00 0.00 1.98
4435 4982 1.334870 CGCTCGAGATCACATCCTCAG 60.335 57.143 18.75 0.00 0.00 3.35
4436 4983 1.602668 GCTCGAGATCACATCCTCAGC 60.603 57.143 18.75 0.00 31.68 4.26
4437 4984 1.680207 CTCGAGATCACATCCTCAGCA 59.320 52.381 6.58 0.00 0.00 4.41
4438 4985 2.100418 CTCGAGATCACATCCTCAGCAA 59.900 50.000 6.58 0.00 0.00 3.91
4439 4986 2.697229 TCGAGATCACATCCTCAGCAAT 59.303 45.455 0.00 0.00 0.00 3.56
4441 4988 3.740452 CGAGATCACATCCTCAGCAATGT 60.740 47.826 0.00 0.00 36.56 2.71
4442 4989 3.806380 AGATCACATCCTCAGCAATGTC 58.194 45.455 0.00 0.00 33.92 3.06
4445 4992 0.745845 ACATCCTCAGCAATGTCGCC 60.746 55.000 0.00 0.00 30.35 5.54
4446 4993 1.522355 ATCCTCAGCAATGTCGCCG 60.522 57.895 0.00 0.00 0.00 6.46
4447 4994 2.244117 ATCCTCAGCAATGTCGCCGT 62.244 55.000 0.00 0.00 0.00 5.68
4448 4995 2.456119 CCTCAGCAATGTCGCCGTC 61.456 63.158 0.00 0.00 0.00 4.79
4476 5028 2.105466 GTCGTCGCTCTACTCCGGT 61.105 63.158 0.00 0.00 0.00 5.28
4752 5304 0.179111 TCCGCATCGAGGTAGCAAAG 60.179 55.000 0.00 0.00 0.00 2.77
4753 5305 1.638467 CGCATCGAGGTAGCAAAGC 59.362 57.895 0.00 0.00 0.00 3.51
4756 5308 1.737838 CATCGAGGTAGCAAAGCCAA 58.262 50.000 0.00 0.00 0.00 4.52
4758 5310 1.808411 TCGAGGTAGCAAAGCCAAAG 58.192 50.000 0.00 0.00 0.00 2.77
4759 5311 0.169009 CGAGGTAGCAAAGCCAAAGC 59.831 55.000 0.00 0.00 40.32 3.51
4760 5312 1.247567 GAGGTAGCAAAGCCAAAGCA 58.752 50.000 0.00 0.00 43.56 3.91
4762 5314 0.673437 GGTAGCAAAGCCAAAGCACA 59.327 50.000 0.00 0.00 43.56 4.57
4764 5316 2.331194 GTAGCAAAGCCAAAGCACATG 58.669 47.619 0.00 0.00 43.56 3.21
4765 5317 0.754472 AGCAAAGCCAAAGCACATGT 59.246 45.000 0.00 0.00 43.56 3.21
4766 5318 1.142474 GCAAAGCCAAAGCACATGTC 58.858 50.000 0.00 0.00 43.56 3.06
4767 5319 1.787012 CAAAGCCAAAGCACATGTCC 58.213 50.000 0.00 0.00 43.56 4.02
4768 5320 0.681175 AAAGCCAAAGCACATGTCCC 59.319 50.000 0.00 0.00 43.56 4.46
4809 5361 1.263217 GTGGAACTGCGTTTGATCGTT 59.737 47.619 0.00 0.00 0.00 3.85
4810 5362 1.529438 TGGAACTGCGTTTGATCGTTC 59.471 47.619 0.00 0.00 34.70 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.218316 GAACCGATCTCACGCCCTT 59.782 57.895 0.00 0.00 0.00 3.95
199 216 9.814899 GGGTACTACTTTAGATTCTTTCTAACC 57.185 37.037 0.00 0.00 44.71 2.85
259 276 5.630121 TGTATAATTCACATGACATCCCCC 58.370 41.667 0.00 0.00 0.00 5.40
370 389 7.673641 TTTCCAATCATGTGGCCTAAATAAT 57.326 32.000 3.32 0.00 38.68 1.28
418 437 0.911769 TGGAGTCCTTCGGAATGCAT 59.088 50.000 11.33 0.00 42.61 3.96
421 440 2.698855 ATGTGGAGTCCTTCGGAATG 57.301 50.000 11.33 0.00 31.38 2.67
427 446 5.368145 TGCATACATTATGTGGAGTCCTTC 58.632 41.667 11.33 4.40 38.43 3.46
543 566 7.462109 TGTGCAATTTGAGATAAAAACACAC 57.538 32.000 0.00 0.00 31.80 3.82
544 567 7.924947 TCATGTGCAATTTGAGATAAAAACACA 59.075 29.630 0.00 2.29 36.61 3.72
545 568 8.296799 TCATGTGCAATTTGAGATAAAAACAC 57.703 30.769 0.00 0.00 0.00 3.32
546 569 8.883954 TTCATGTGCAATTTGAGATAAAAACA 57.116 26.923 0.00 0.00 0.00 2.83
857 1064 0.036765 AGAAATTCTACGGCGCACCA 60.037 50.000 10.83 0.00 34.57 4.17
858 1065 0.651031 GAGAAATTCTACGGCGCACC 59.349 55.000 10.83 0.00 0.00 5.01
1102 1319 2.588620 GGAGGAATCTAGCTCGGAGAA 58.411 52.381 9.69 0.00 34.09 2.87
1103 1320 1.202952 GGGAGGAATCTAGCTCGGAGA 60.203 57.143 9.69 0.00 0.00 3.71
1131 1349 1.616865 AGCAAGCACAACAATCAGCAT 59.383 42.857 0.00 0.00 0.00 3.79
1141 1359 3.716006 GCGAGCGAGCAAGCACAA 61.716 61.111 6.21 0.00 40.15 3.33
1168 1387 2.557005 GGTCTGGTAGTCCCTGTACAGT 60.557 54.545 21.18 5.57 33.97 3.55
1244 1463 4.441356 GGAGCAGGAAGAGACAAGATGTAG 60.441 50.000 0.00 0.00 0.00 2.74
1245 1464 3.449018 GGAGCAGGAAGAGACAAGATGTA 59.551 47.826 0.00 0.00 0.00 2.29
1249 1469 0.891373 CGGAGCAGGAAGAGACAAGA 59.109 55.000 0.00 0.00 0.00 3.02
1416 1651 4.577246 CCTCGCGCTACCCAGAGC 62.577 72.222 5.56 0.00 43.48 4.09
1438 1673 5.299279 GCCATAAGCAGCAAAACCTATCTAA 59.701 40.000 0.00 0.00 42.97 2.10
1439 1674 4.821805 GCCATAAGCAGCAAAACCTATCTA 59.178 41.667 0.00 0.00 42.97 1.98
1466 1703 1.202510 GCAACCCACAACAAATCAGCA 60.203 47.619 0.00 0.00 0.00 4.41
1482 1719 2.360165 CCTCTATCAGCCCAAATGCAAC 59.640 50.000 0.00 0.00 0.00 4.17
1502 1742 5.946377 AGTCCTAACCAACAGAATCAATTCC 59.054 40.000 0.00 0.00 37.51 3.01
1508 1748 3.933332 CCGAAGTCCTAACCAACAGAATC 59.067 47.826 0.00 0.00 0.00 2.52
1564 1805 2.620115 CCCGATGAATTCAGGACAATGG 59.380 50.000 14.54 7.21 0.00 3.16
1568 1809 1.486310 CTCCCCGATGAATTCAGGACA 59.514 52.381 14.54 0.31 0.00 4.02
1616 1857 5.341872 TGTGCCCTAGTTATTAAGCGTAA 57.658 39.130 0.00 0.00 0.00 3.18
1617 1858 5.535333 GATGTGCCCTAGTTATTAAGCGTA 58.465 41.667 0.00 0.00 0.00 4.42
1677 2058 7.093289 ACAGTAATACAGCTATTGTTCTCCAGT 60.093 37.037 0.00 0.00 41.29 4.00
1766 2147 1.202879 CCTACAGCCCCAGAAAACACA 60.203 52.381 0.00 0.00 0.00 3.72
1767 2148 1.202891 ACCTACAGCCCCAGAAAACAC 60.203 52.381 0.00 0.00 0.00 3.32
1879 2268 4.342665 AGCCAAACCAAAATAAGGAAACGA 59.657 37.500 0.00 0.00 0.00 3.85
1897 2287 2.440147 CACACATCCCCCAGCCAA 59.560 61.111 0.00 0.00 0.00 4.52
1961 2351 2.706339 ATCCAGTTGCATCAGACTCC 57.294 50.000 0.00 0.00 0.00 3.85
2111 2502 3.185246 AGGATATGTACAGCACTGCAC 57.815 47.619 0.33 0.00 0.00 4.57
2173 2564 6.292865 CCGTTACCATAGCAATGTCAACATAG 60.293 42.308 0.00 0.00 35.10 2.23
2177 2568 3.687698 ACCGTTACCATAGCAATGTCAAC 59.312 43.478 0.00 0.00 0.00 3.18
2383 2774 8.450964 ACAGAACAATTATAATGTTTGACGAGG 58.549 33.333 0.00 0.00 40.90 4.63
2403 2794 7.649057 ACTAAAAGCTGGAAATACAACAGAAC 58.351 34.615 0.00 0.00 34.21 3.01
2413 2804 5.412904 GCAGTCAGTACTAAAAGCTGGAAAT 59.587 40.000 0.00 0.00 33.48 2.17
2551 2942 5.789574 AACCATTACATTGAGGGTTAGGA 57.210 39.130 0.00 0.00 39.91 2.94
2727 3118 0.952497 AGCGACACATCAGCACCAAG 60.952 55.000 0.00 0.00 0.00 3.61
2813 3204 0.742281 CTCACAGGTTCAGGGATGCG 60.742 60.000 0.00 0.00 0.00 4.73
2864 3255 7.698130 GCTAAGATTGGCAAAGTAATACTTGTG 59.302 37.037 6.41 8.31 38.66 3.33
2965 3375 6.821388 ACAATAACTTGCTAGGTGAGATAGG 58.179 40.000 0.00 0.00 35.69 2.57
2966 3376 7.981789 TGAACAATAACTTGCTAGGTGAGATAG 59.018 37.037 0.00 0.00 35.69 2.08
2975 3385 7.171508 TGTCTCAACTGAACAATAACTTGCTAG 59.828 37.037 0.00 0.00 35.69 3.42
2978 3388 6.060028 TGTCTCAACTGAACAATAACTTGC 57.940 37.500 0.00 0.00 35.69 4.01
3072 3483 3.383620 TTGCAACTACCAAGCAATTGG 57.616 42.857 7.72 5.48 42.71 3.16
3227 3639 3.863424 TCCATTTCTGCGACGAGTAATTC 59.137 43.478 0.00 0.00 0.00 2.17
3228 3640 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
3229 3641 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
3230 3642 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
3231 3643 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
3232 3644 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
3233 3645 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
3234 3646 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
3235 3647 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
3236 3648 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
3237 3649 6.015095 ACATCTAGATACATCCATTTCTGCGA 60.015 38.462 4.54 0.00 0.00 5.10
3238 3650 6.162079 ACATCTAGATACATCCATTTCTGCG 58.838 40.000 4.54 0.00 0.00 5.18
3239 3651 9.664332 AATACATCTAGATACATCCATTTCTGC 57.336 33.333 4.54 0.00 0.00 4.26
3265 3677 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
3266 3678 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
3267 3679 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
3268 3680 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
3269 3681 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
3270 3682 6.183360 TGTCGCAGAAATGGATGTATCTAGAA 60.183 38.462 0.00 0.00 39.69 2.10
3271 3683 5.301805 TGTCGCAGAAATGGATGTATCTAGA 59.698 40.000 0.00 0.00 39.69 2.43
3272 3684 5.532557 TGTCGCAGAAATGGATGTATCTAG 58.467 41.667 0.00 0.00 39.69 2.43
3273 3685 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
3274 3686 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
3275 3687 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
3276 3688 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
3277 3689 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
3278 3690 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
3279 3691 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
3280 3692 6.324819 CAAATTACTTGTCGCAGAAATGGAT 58.675 36.000 0.00 0.00 39.69 3.41
3281 3693 5.335583 CCAAATTACTTGTCGCAGAAATGGA 60.336 40.000 0.00 0.00 39.69 3.41
3282 3694 4.858692 CCAAATTACTTGTCGCAGAAATGG 59.141 41.667 0.00 0.00 39.69 3.16
3283 3695 5.698832 TCCAAATTACTTGTCGCAGAAATG 58.301 37.500 0.00 0.00 39.69 2.32
3284 3696 5.957842 TCCAAATTACTTGTCGCAGAAAT 57.042 34.783 0.00 0.00 39.69 2.17
3285 3697 5.516090 GTTCCAAATTACTTGTCGCAGAAA 58.484 37.500 0.00 0.00 39.69 2.52
3286 3698 4.319190 CGTTCCAAATTACTTGTCGCAGAA 60.319 41.667 0.00 0.00 39.69 3.02
3287 3699 3.185594 CGTTCCAAATTACTTGTCGCAGA 59.814 43.478 0.00 0.00 32.65 4.26
3288 3700 3.479006 CGTTCCAAATTACTTGTCGCAG 58.521 45.455 0.00 0.00 32.65 5.18
3289 3701 2.224549 CCGTTCCAAATTACTTGTCGCA 59.775 45.455 0.00 0.00 32.65 5.10
3290 3702 2.481185 TCCGTTCCAAATTACTTGTCGC 59.519 45.455 0.00 0.00 32.65 5.19
3291 3703 3.124636 CCTCCGTTCCAAATTACTTGTCG 59.875 47.826 0.00 0.00 32.65 4.35
3292 3704 3.439129 CCCTCCGTTCCAAATTACTTGTC 59.561 47.826 0.00 0.00 32.65 3.18
3293 3705 3.073356 TCCCTCCGTTCCAAATTACTTGT 59.927 43.478 0.00 0.00 32.65 3.16
3294 3706 3.681593 TCCCTCCGTTCCAAATTACTTG 58.318 45.455 0.00 0.00 34.52 3.16
3295 3707 3.329814 ACTCCCTCCGTTCCAAATTACTT 59.670 43.478 0.00 0.00 0.00 2.24
3296 3708 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
3297 3709 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
3298 3710 3.118519 GCTACTCCCTCCGTTCCAAATTA 60.119 47.826 0.00 0.00 0.00 1.40
3299 3711 2.355818 GCTACTCCCTCCGTTCCAAATT 60.356 50.000 0.00 0.00 0.00 1.82
3300 3712 1.209747 GCTACTCCCTCCGTTCCAAAT 59.790 52.381 0.00 0.00 0.00 2.32
3301 3713 0.611714 GCTACTCCCTCCGTTCCAAA 59.388 55.000 0.00 0.00 0.00 3.28
3302 3714 0.252103 AGCTACTCCCTCCGTTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
3303 3715 0.627451 TAGCTACTCCCTCCGTTCCA 59.373 55.000 0.00 0.00 0.00 3.53
3304 3716 1.772836 TTAGCTACTCCCTCCGTTCC 58.227 55.000 0.00 0.00 0.00 3.62
3305 3717 5.243283 TCAATATTAGCTACTCCCTCCGTTC 59.757 44.000 0.00 0.00 0.00 3.95
3306 3718 5.145564 TCAATATTAGCTACTCCCTCCGTT 58.854 41.667 0.00 0.00 0.00 4.44
3307 3719 4.737578 TCAATATTAGCTACTCCCTCCGT 58.262 43.478 0.00 0.00 0.00 4.69
3308 3720 5.419155 TGATCAATATTAGCTACTCCCTCCG 59.581 44.000 0.00 0.00 0.00 4.63
3309 3721 6.439058 ACTGATCAATATTAGCTACTCCCTCC 59.561 42.308 0.00 0.00 0.00 4.30
3310 3722 7.319646 CACTGATCAATATTAGCTACTCCCTC 58.680 42.308 0.00 0.00 0.00 4.30
3311 3723 6.295575 GCACTGATCAATATTAGCTACTCCCT 60.296 42.308 0.00 0.00 0.00 4.20
3312 3724 5.872070 GCACTGATCAATATTAGCTACTCCC 59.128 44.000 0.00 0.00 0.00 4.30
3313 3725 5.872070 GGCACTGATCAATATTAGCTACTCC 59.128 44.000 0.00 0.00 0.00 3.85
3314 3726 5.872070 GGGCACTGATCAATATTAGCTACTC 59.128 44.000 0.00 0.00 0.00 2.59
3315 3727 5.280215 GGGGCACTGATCAATATTAGCTACT 60.280 44.000 0.00 0.00 0.00 2.57
3316 3728 4.938226 GGGGCACTGATCAATATTAGCTAC 59.062 45.833 0.00 0.00 0.00 3.58
3317 3729 4.846367 AGGGGCACTGATCAATATTAGCTA 59.154 41.667 0.00 0.00 0.00 3.32
3318 3730 3.654806 AGGGGCACTGATCAATATTAGCT 59.345 43.478 0.00 0.00 0.00 3.32
3352 3764 8.342634 GTTTAAAGAATCTAACAGCTCACAACA 58.657 33.333 0.00 0.00 0.00 3.33
3377 3789 5.869649 AGAGCTTGTTTAATTGGTTTGGT 57.130 34.783 0.00 0.00 0.00 3.67
3393 3805 7.041098 ACACGATAAAAATCAGAACAAGAGCTT 60.041 33.333 0.00 0.00 0.00 3.74
3443 3856 5.350504 TTCTTCTGAGGATGCTAAAGGAG 57.649 43.478 0.00 0.00 0.00 3.69
3479 3892 0.322975 AGTTCCTCGTGCATCAGCTT 59.677 50.000 0.00 0.00 42.74 3.74
3658 4176 0.106708 TGAGGCTGTTCTCGTTGCTT 59.893 50.000 0.00 0.00 36.61 3.91
3961 4481 4.341502 CAACAACGCGCCCAAGGG 62.342 66.667 5.73 0.00 38.57 3.95
4067 4587 5.973651 TCAGAGCTTGAATTATTACTGCG 57.026 39.130 0.00 0.00 31.34 5.18
4068 4588 9.578439 AATTTTCAGAGCTTGAATTATTACTGC 57.422 29.630 10.72 0.00 44.90 4.40
4125 4668 1.697432 AGGCTACACCACAGCAAGTTA 59.303 47.619 0.00 0.00 43.14 2.24
4140 4683 3.484953 TCTCCCTTGGAAAGTAGGCTA 57.515 47.619 0.00 0.00 44.25 3.93
4141 4684 2.344093 TCTCCCTTGGAAAGTAGGCT 57.656 50.000 0.00 0.00 44.25 4.58
4142 4685 2.572104 TCTTCTCCCTTGGAAAGTAGGC 59.428 50.000 0.00 0.00 44.25 3.93
4143 4686 6.561519 TTATCTTCTCCCTTGGAAAGTAGG 57.438 41.667 0.00 0.00 44.25 3.18
4153 4696 5.595952 GGCAACAATCATTATCTTCTCCCTT 59.404 40.000 0.00 0.00 0.00 3.95
4157 4700 6.541641 ACTCAGGCAACAATCATTATCTTCTC 59.458 38.462 0.00 0.00 41.41 2.87
4166 4709 2.490903 GCTCAACTCAGGCAACAATCAT 59.509 45.455 0.00 0.00 41.41 2.45
4167 4710 1.881973 GCTCAACTCAGGCAACAATCA 59.118 47.619 0.00 0.00 41.41 2.57
4168 4711 1.200948 GGCTCAACTCAGGCAACAATC 59.799 52.381 0.00 0.00 38.83 2.67
4169 4712 1.251251 GGCTCAACTCAGGCAACAAT 58.749 50.000 0.00 0.00 38.83 2.71
4173 4716 1.376466 GAGGGCTCAACTCAGGCAA 59.624 57.895 0.00 0.00 40.79 4.52
4181 4724 2.107141 CCGGATCGAGGGCTCAAC 59.893 66.667 0.00 0.00 0.00 3.18
4187 4730 3.543680 ATATTATTGCCGGATCGAGGG 57.456 47.619 5.05 0.00 0.00 4.30
4211 4754 3.904339 AGCCGTTCATCCCAGTTATAGAT 59.096 43.478 0.00 0.00 0.00 1.98
4212 4755 3.069586 CAGCCGTTCATCCCAGTTATAGA 59.930 47.826 0.00 0.00 0.00 1.98
4213 4756 3.069586 TCAGCCGTTCATCCCAGTTATAG 59.930 47.826 0.00 0.00 0.00 1.31
4214 4757 3.035363 TCAGCCGTTCATCCCAGTTATA 58.965 45.455 0.00 0.00 0.00 0.98
4215 4758 1.837439 TCAGCCGTTCATCCCAGTTAT 59.163 47.619 0.00 0.00 0.00 1.89
4222 4766 0.321653 AACCAGTCAGCCGTTCATCC 60.322 55.000 0.00 0.00 0.00 3.51
4277 4821 4.155733 CCACGTGGCCAGCCGATA 62.156 66.667 24.02 0.00 39.42 2.92
4302 4847 2.770164 AGTGGCAGAAGCGTAAATCT 57.230 45.000 0.00 0.00 43.41 2.40
4305 4850 3.267483 GGATAAGTGGCAGAAGCGTAAA 58.733 45.455 0.00 0.00 43.41 2.01
4306 4851 2.419574 GGGATAAGTGGCAGAAGCGTAA 60.420 50.000 0.00 0.00 43.41 3.18
4308 4853 0.107654 GGGATAAGTGGCAGAAGCGT 60.108 55.000 0.00 0.00 43.41 5.07
4309 4854 0.815615 GGGGATAAGTGGCAGAAGCG 60.816 60.000 0.00 0.00 43.41 4.68
4310 4855 0.255890 TGGGGATAAGTGGCAGAAGC 59.744 55.000 0.00 0.00 41.10 3.86
4312 4857 2.173356 CTCATGGGGATAAGTGGCAGAA 59.827 50.000 0.00 0.00 0.00 3.02
4314 4859 1.770658 TCTCATGGGGATAAGTGGCAG 59.229 52.381 0.00 0.00 0.00 4.85
4452 4999 1.295787 GTAGAGCGACGACGACGAC 60.296 63.158 22.94 14.79 42.66 4.34
4476 5028 4.507916 CGGGAGGAGAGGAGGCGA 62.508 72.222 0.00 0.00 0.00 5.54
4610 5162 1.005037 GTCTCGTGCATGGTCACCA 60.005 57.895 0.00 0.00 38.19 4.17
4752 5304 1.885871 GAGGGACATGTGCTTTGGC 59.114 57.895 17.44 0.00 39.26 4.52
4753 5305 0.606401 ACGAGGGACATGTGCTTTGG 60.606 55.000 18.91 10.00 0.00 3.28
4756 5308 0.396435 TTGACGAGGGACATGTGCTT 59.604 50.000 17.44 9.86 0.00 3.91
4758 5310 0.729116 CATTGACGAGGGACATGTGC 59.271 55.000 9.16 9.16 0.00 4.57
4759 5311 1.372582 CCATTGACGAGGGACATGTG 58.627 55.000 1.15 0.00 0.00 3.21
4760 5312 0.392998 GCCATTGACGAGGGACATGT 60.393 55.000 0.00 0.00 0.00 3.21
4762 5314 1.153369 CGCCATTGACGAGGGACAT 60.153 57.895 0.00 0.00 0.00 3.06
4764 5316 3.195698 GCGCCATTGACGAGGGAC 61.196 66.667 0.00 0.00 0.00 4.46
4765 5317 4.812476 CGCGCCATTGACGAGGGA 62.812 66.667 0.00 0.00 0.00 4.20
4767 5319 3.853330 CACGCGCCATTGACGAGG 61.853 66.667 5.73 0.00 34.45 4.63
4768 5320 3.112075 ACACGCGCCATTGACGAG 61.112 61.111 5.73 0.00 36.35 4.18
4809 5361 3.740832 CGTGCGCATTTTATCCAGATAGA 59.259 43.478 15.91 0.00 0.00 1.98
4810 5362 3.665323 GCGTGCGCATTTTATCCAGATAG 60.665 47.826 15.91 0.00 41.49 2.08
4840 5404 2.443203 TCCCCTCGCTGCCGAATA 60.443 61.111 0.00 0.00 43.87 1.75


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

AutoCloner maintained by Alex Coulton.