Multiple sequence alignment - TraesCS1D01G439600

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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 TraesCS1D01G439600 chr1D 100.000 7868 0 0 1 7868 485564447 485556580 0.000000e+00 14530.0
1 TraesCS1D01G439600 chr1D 85.556 180 24 2 4181 4360 279508266 279508089 3.750000e-43 187.0
2 TraesCS1D01G439600 chr1A 97.691 3161 61 7 3240 6396 582868758 582865606 0.000000e+00 5422.0
3 TraesCS1D01G439600 chr1A 91.672 3422 160 54 1 3403 582872070 582868755 0.000000e+00 4625.0
4 TraesCS1D01G439600 chr1A 95.556 1395 47 8 6435 7824 582865603 582864219 0.000000e+00 2218.0
5 TraesCS1D01G439600 chr1A 87.006 177 22 1 4181 4357 276180190 276180365 1.730000e-46 198.0
6 TraesCS1D01G439600 chr1A 78.571 154 22 7 6878 7029 30577351 30577207 3.020000e-14 91.6
7 TraesCS1D01G439600 chr1B 90.379 3430 183 57 1 3403 676084429 676081120 0.000000e+00 4370.0
8 TraesCS1D01G439600 chr1B 95.469 2604 101 9 3240 5834 676081123 676078528 0.000000e+00 4139.0
9 TraesCS1D01G439600 chr1B 94.767 2064 70 14 5831 7868 676078314 676076263 0.000000e+00 3179.0
10 TraesCS1D01G439600 chr1B 78.571 154 22 7 6878 7029 673986796 673986652 3.020000e-14 91.6
11 TraesCS1D01G439600 chr7B 92.835 321 21 2 3737 4056 579515130 579515449 1.550000e-126 464.0
12 TraesCS1D01G439600 chr7B 78.571 154 22 7 6878 7029 674015786 674015642 3.020000e-14 91.6
13 TraesCS1D01G439600 chr4B 92.500 320 22 2 3737 4055 562621176 562621494 2.590000e-124 457.0
14 TraesCS1D01G439600 chr4B 78.571 154 22 7 6878 7029 298685027 298684883 3.020000e-14 91.6
15 TraesCS1D01G439600 chr2B 92.788 208 14 1 3737 3943 450427807 450427600 4.610000e-77 300.0
16 TraesCS1D01G439600 chr2B 78.571 154 22 7 6878 7029 732555660 732555516 3.020000e-14 91.6
17 TraesCS1D01G439600 chr5D 93.007 143 10 0 3914 4056 228506479 228506337 8.000000e-50 209.0
18 TraesCS1D01G439600 chr5D 87.571 177 21 1 4181 4357 286972630 286972805 3.720000e-48 204.0
19 TraesCS1D01G439600 chr5D 94.175 103 5 1 3737 3838 228521965 228521863 1.060000e-33 156.0
20 TraesCS1D01G439600 chr7D 87.571 177 21 1 4181 4357 530932469 530932644 3.720000e-48 204.0
21 TraesCS1D01G439600 chr6A 86.932 176 22 1 4181 4356 163284628 163284802 6.230000e-46 196.0
22 TraesCS1D01G439600 chr5A 85.635 181 24 2 4181 4360 417569674 417569495 1.040000e-43 189.0
23 TraesCS1D01G439600 chr2D 85.556 180 24 2 4181 4360 467336565 467336388 3.750000e-43 187.0
24 TraesCS1D01G439600 chr3A 82.051 156 20 7 6878 7029 156075258 156075107 8.290000e-25 126.0
25 TraesCS1D01G439600 chr7A 78.125 160 24 7 6872 7029 692939836 692939986 3.020000e-14 91.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G439600 chr1D 485556580 485564447 7867 True 14530.000000 14530 100.000000 1 7868 1 chr1D.!!$R2 7867
1 TraesCS1D01G439600 chr1A 582864219 582872070 7851 True 4088.333333 5422 94.973000 1 7824 3 chr1A.!!$R2 7823
2 TraesCS1D01G439600 chr1B 676076263 676084429 8166 True 3896.000000 4370 93.538333 1 7868 3 chr1B.!!$R2 7867

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
470 489 0.250513 CCTCCAGACACTAACCCTGC 59.749 60.000 0.00 0.00 0.00 4.85 F
1148 1171 0.455633 GCCAAACTTGCTGATGCTCG 60.456 55.000 0.00 0.00 40.48 5.03 F
2634 2662 1.279271 ACCTCCCGAGACAAAATCAGG 59.721 52.381 0.00 0.00 0.00 3.86 F
3219 3252 1.369625 ATCAAGGAATCGCGTCCAAC 58.630 50.000 17.08 0.97 40.48 3.77 F
3563 3759 0.814010 GTTGTGTTCAGCGTGAGGGT 60.814 55.000 0.00 0.00 0.00 4.34 F
5036 5236 0.947244 CAAGCAGCGTCTTTGTTCCT 59.053 50.000 0.00 0.00 0.00 3.36 F
5226 5426 1.219773 ACATGCCCATCCATCTGTCT 58.780 50.000 0.00 0.00 0.00 3.41 F
6008 6427 3.669949 ACTCAGTATGGGAAGGCCTAAT 58.330 45.455 5.16 0.00 41.11 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1406 2.507471 TGATTGGGCAACAAGGGTTTTT 59.493 40.909 0.00 0.0 43.48 1.94 R
2716 2744 2.224079 CAGAACACCAGAAATGTCACCG 59.776 50.000 0.00 0.0 0.00 4.94 R
3473 3669 0.524862 CCTGCATGAGAAGGTGCAAC 59.475 55.000 0.00 0.0 35.61 4.17 R
5006 5206 1.159285 CGCTGCTTGATGTTTCCTGA 58.841 50.000 0.00 0.0 0.00 3.86 R
5226 5426 0.611618 GGATGGGCATGTTGTGGTGA 60.612 55.000 0.00 0.0 0.00 4.02 R
6012 6431 0.975040 CCTGGAGGCTGCAGAGTAGT 60.975 60.000 34.08 0.0 38.14 2.73 R
6503 6938 1.955778 TGAATGCCAACTGAACCACTG 59.044 47.619 0.00 0.0 0.00 3.66 R
7394 7832 0.887933 CCCTTGGGAAATTGGTGACG 59.112 55.000 0.00 0.0 0.00 4.35 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
43 44 4.778534 TTCGTACAGAGTTGAGGTAAGG 57.221 45.455 0.00 0.00 0.00 2.69
44 45 2.490903 TCGTACAGAGTTGAGGTAAGGC 59.509 50.000 0.00 0.00 0.00 4.35
88 89 1.909302 CCTGTCAACTACCCACCTCAT 59.091 52.381 0.00 0.00 0.00 2.90
215 226 2.665000 CTTTGCCGGAGCCTCTCA 59.335 61.111 5.05 0.00 38.69 3.27
235 246 4.796495 GAATCGGGCCGGCCAGTT 62.796 66.667 44.46 33.33 37.98 3.16
236 247 4.360405 AATCGGGCCGGCCAGTTT 62.360 61.111 44.46 36.24 37.98 2.66
276 289 3.739613 GGTGGGTGGGGGTGGATC 61.740 72.222 0.00 0.00 0.00 3.36
277 290 4.109675 GTGGGTGGGGGTGGATCG 62.110 72.222 0.00 0.00 0.00 3.69
408 427 7.970061 TGCTTCATGTTTCTATATTGTTTCTGC 59.030 33.333 0.00 0.00 0.00 4.26
414 433 8.402798 TGTTTCTATATTGTTTCTGCTGGAAA 57.597 30.769 2.25 2.25 41.11 3.13
416 435 9.860898 GTTTCTATATTGTTTCTGCTGGAAATT 57.139 29.630 8.24 2.00 44.46 1.82
418 437 7.999679 TCTATATTGTTTCTGCTGGAAATTGG 58.000 34.615 8.24 0.00 44.46 3.16
419 438 6.855763 ATATTGTTTCTGCTGGAAATTGGA 57.144 33.333 8.24 0.00 44.46 3.53
421 440 5.549742 TTGTTTCTGCTGGAAATTGGATT 57.450 34.783 8.24 0.00 44.46 3.01
423 442 4.248058 GTTTCTGCTGGAAATTGGATTGG 58.752 43.478 8.24 0.00 44.46 3.16
470 489 0.250513 CCTCCAGACACTAACCCTGC 59.749 60.000 0.00 0.00 0.00 4.85
474 493 1.339151 CCAGACACTAACCCTGCTTCC 60.339 57.143 0.00 0.00 0.00 3.46
521 540 3.191371 CCTAGCCTGTTGATGGTTTGAAC 59.809 47.826 0.00 0.00 0.00 3.18
558 577 2.475339 ATGCACCAGGATCTCTCTCT 57.525 50.000 0.00 0.00 0.00 3.10
559 578 1.482954 TGCACCAGGATCTCTCTCTG 58.517 55.000 0.00 0.00 0.00 3.35
600 619 8.045176 AGCCATAGATTCAGTTTTAGTTGTTC 57.955 34.615 0.00 0.00 0.00 3.18
602 621 8.515414 GCCATAGATTCAGTTTTAGTTGTTCTT 58.485 33.333 0.00 0.00 0.00 2.52
607 626 9.574516 AGATTCAGTTTTAGTTGTTCTTATGGT 57.425 29.630 0.00 0.00 0.00 3.55
610 629 8.842358 TCAGTTTTAGTTGTTCTTATGGTAGG 57.158 34.615 0.00 0.00 0.00 3.18
611 630 7.881232 TCAGTTTTAGTTGTTCTTATGGTAGGG 59.119 37.037 0.00 0.00 0.00 3.53
612 631 7.120726 CAGTTTTAGTTGTTCTTATGGTAGGGG 59.879 40.741 0.00 0.00 0.00 4.79
613 632 6.707273 TTTAGTTGTTCTTATGGTAGGGGT 57.293 37.500 0.00 0.00 0.00 4.95
614 633 4.838904 AGTTGTTCTTATGGTAGGGGTC 57.161 45.455 0.00 0.00 0.00 4.46
615 634 3.197116 AGTTGTTCTTATGGTAGGGGTCG 59.803 47.826 0.00 0.00 0.00 4.79
616 635 2.823959 TGTTCTTATGGTAGGGGTCGT 58.176 47.619 0.00 0.00 0.00 4.34
676 695 1.610886 GGTTAACAGCCCTGTGTCTCC 60.611 57.143 8.10 0.12 44.13 3.71
697 716 3.869272 CTCGTCGGCAATGCTGGC 61.869 66.667 14.73 11.91 44.58 4.85
744 766 7.661437 TGATGGCTTATTGTTGGATATGAGTAC 59.339 37.037 0.00 0.00 0.00 2.73
774 797 0.751277 TGGTGCTGTGGTTGGTTCAG 60.751 55.000 0.00 0.00 0.00 3.02
775 798 0.751643 GGTGCTGTGGTTGGTTCAGT 60.752 55.000 0.00 0.00 0.00 3.41
782 805 1.065551 GTGGTTGGTTCAGTGCTTGAC 59.934 52.381 0.00 0.00 34.94 3.18
783 806 1.340502 TGGTTGGTTCAGTGCTTGACA 60.341 47.619 0.00 0.00 34.94 3.58
874 897 6.542852 TGCTTAGTTTATTAAAAGCTGCGAG 58.457 36.000 10.91 0.00 43.69 5.03
899 922 1.626686 TGTGTGGTTATTGCCTTGGG 58.373 50.000 0.00 0.00 0.00 4.12
973 996 7.014711 TCCTTCTGAGATAACATATGTCCTGAC 59.985 40.741 9.23 2.48 0.00 3.51
1023 1046 2.489938 TGGGAACAGAGTGCATAACC 57.510 50.000 0.00 0.00 35.01 2.85
1136 1159 0.779997 ACCCAGAAGGATGCCAAACT 59.220 50.000 0.00 0.00 39.89 2.66
1148 1171 0.455633 GCCAAACTTGCTGATGCTCG 60.456 55.000 0.00 0.00 40.48 5.03
1239 1262 1.337817 CTCAGAGCCGAAACGACACG 61.338 60.000 0.00 0.00 0.00 4.49
1245 1268 2.235016 CCGAAACGACACGCACTGT 61.235 57.895 0.00 0.00 34.96 3.55
1299 1322 2.266055 CGGAACAGGCCTCCAGTC 59.734 66.667 0.00 0.00 32.77 3.51
1302 1325 1.617947 GGAACAGGCCTCCAGTCGAT 61.618 60.000 0.00 0.00 32.77 3.59
1317 1340 1.933853 GTCGATTACAGCCGCTTTGAT 59.066 47.619 0.00 0.00 0.00 2.57
1326 1349 3.494626 ACAGCCGCTTTGATAATATGTCG 59.505 43.478 0.00 0.00 0.00 4.35
1383 1406 7.891561 AGGTTGCACTTGCTAATGTTTTATTA 58.108 30.769 2.33 0.00 42.66 0.98
1389 1412 9.805966 GCACTTGCTAATGTTTTATTAAAAACC 57.194 29.630 10.32 0.00 44.08 3.27
1442 1467 3.847037 TTTTAACGCGTTCTCACAGTC 57.153 42.857 30.28 0.00 0.00 3.51
1471 1496 3.039202 CTTTTGGCAGGCGGCTACG 62.039 63.158 12.74 0.46 44.01 3.51
1569 1595 7.427989 AGGTTCATATTCATTGCCAAATTCT 57.572 32.000 0.00 0.00 0.00 2.40
1728 1755 3.926527 TCTTGTTGCTAACTGCTGTATCG 59.073 43.478 0.00 0.00 43.37 2.92
1736 1763 4.026475 GCTAACTGCTGTATCGTGCTTTAG 60.026 45.833 0.00 0.00 38.95 1.85
1968 1996 4.992319 TCAACATTTTCTACACGGGTACAG 59.008 41.667 0.00 0.00 0.00 2.74
2067 2095 2.498167 TCAGAGCCAGAAGAAAACAGC 58.502 47.619 0.00 0.00 0.00 4.40
2275 2303 6.292811 GGATTTTGTTTACCAAAGCACACATG 60.293 38.462 0.00 0.00 43.63 3.21
2277 2305 4.727507 TGTTTACCAAAGCACACATGTT 57.272 36.364 0.00 0.00 0.00 2.71
2280 2308 5.105554 TGTTTACCAAAGCACACATGTTCTT 60.106 36.000 0.00 0.00 33.09 2.52
2282 2310 4.470334 ACCAAAGCACACATGTTCTTTT 57.530 36.364 6.88 2.86 38.96 2.27
2283 2311 4.432712 ACCAAAGCACACATGTTCTTTTC 58.567 39.130 6.88 0.00 38.96 2.29
2284 2312 4.081752 ACCAAAGCACACATGTTCTTTTCA 60.082 37.500 6.88 0.00 38.96 2.69
2285 2313 4.505191 CCAAAGCACACATGTTCTTTTCAG 59.495 41.667 6.88 0.00 38.96 3.02
2286 2314 5.342433 CAAAGCACACATGTTCTTTTCAGA 58.658 37.500 6.88 0.00 38.96 3.27
2287 2315 5.581126 AAGCACACATGTTCTTTTCAGAA 57.419 34.783 0.00 0.00 36.62 3.02
2309 2337 6.263842 AGAATTTCAGTTCATTGCTCAACTCA 59.736 34.615 0.00 0.00 30.06 3.41
2418 2446 3.751175 GTGTGTTGTGGTGCTGTATATGT 59.249 43.478 0.00 0.00 0.00 2.29
2454 2482 8.037382 GCATCATTGCATGTAGTCTTACATAT 57.963 34.615 0.00 0.00 46.27 1.78
2526 2554 2.345124 TTTGCCCTGCATTTTGCTTT 57.655 40.000 0.75 0.00 45.31 3.51
2546 2574 7.206687 TGCTTTTTAACTTATTGGAAGGTGTG 58.793 34.615 0.00 0.00 0.00 3.82
2620 2648 2.168496 GGCTTTCCAAAGTTACCTCCC 58.832 52.381 1.14 0.00 38.28 4.30
2634 2662 1.279271 ACCTCCCGAGACAAAATCAGG 59.721 52.381 0.00 0.00 0.00 3.86
2716 2744 3.304996 GCTCAGTTCTTTCTTTTGAGGGC 60.305 47.826 2.45 0.00 36.61 5.19
2896 2924 2.080654 ACCCTGAGATCTACTCTGCC 57.919 55.000 0.00 0.00 45.13 4.85
2942 2970 7.649057 TGTCGAAGATCATCATTTATACTCGT 58.351 34.615 0.00 0.00 40.67 4.18
3028 3056 2.639347 TCTGGAGTCTGCAATGAGGAAA 59.361 45.455 0.00 0.00 0.00 3.13
3084 3112 4.876701 TCACAACCTGGTGAGTGC 57.123 55.556 21.40 0.00 42.56 4.40
3098 3128 2.036475 GTGAGTGCTTCTCTTGACTGGA 59.964 50.000 9.94 0.00 43.13 3.86
3142 3175 4.160439 TCCTATGCTGTACAAGAAGGTCTG 59.840 45.833 0.00 0.00 31.73 3.51
3148 3181 4.322349 GCTGTACAAGAAGGTCTGTGATCT 60.322 45.833 0.00 0.00 0.00 2.75
3149 3182 5.788450 CTGTACAAGAAGGTCTGTGATCTT 58.212 41.667 0.00 0.00 35.51 2.40
3154 3187 7.678947 ACAAGAAGGTCTGTGATCTTTATTG 57.321 36.000 13.21 13.21 32.65 1.90
3184 3217 7.809806 CCATCCTTTTCTGACTATGTTTCAAAC 59.190 37.037 0.00 0.00 0.00 2.93
3198 3231 7.986085 ATGTTTCAAACTTGCTATCACTACT 57.014 32.000 1.10 0.00 0.00 2.57
3202 3235 9.974750 GTTTCAAACTTGCTATCACTACTTATC 57.025 33.333 0.00 0.00 0.00 1.75
3203 3236 9.719355 TTTCAAACTTGCTATCACTACTTATCA 57.281 29.630 0.00 0.00 0.00 2.15
3204 3237 9.719355 TTCAAACTTGCTATCACTACTTATCAA 57.281 29.630 0.00 0.00 0.00 2.57
3207 3240 7.661536 ACTTGCTATCACTACTTATCAAGGA 57.338 36.000 0.00 0.00 35.35 3.36
3208 3241 8.079211 ACTTGCTATCACTACTTATCAAGGAA 57.921 34.615 0.00 0.00 35.35 3.36
3209 3242 8.709308 ACTTGCTATCACTACTTATCAAGGAAT 58.291 33.333 0.00 0.00 35.35 3.01
3210 3243 9.202273 CTTGCTATCACTACTTATCAAGGAATC 57.798 37.037 0.00 0.00 0.00 2.52
3211 3244 7.371159 TGCTATCACTACTTATCAAGGAATCG 58.629 38.462 0.00 0.00 0.00 3.34
3212 3245 6.309251 GCTATCACTACTTATCAAGGAATCGC 59.691 42.308 0.00 0.00 0.00 4.58
3213 3246 4.607955 TCACTACTTATCAAGGAATCGCG 58.392 43.478 0.00 0.00 0.00 5.87
3214 3247 4.097437 TCACTACTTATCAAGGAATCGCGT 59.903 41.667 5.77 0.00 0.00 6.01
3215 3248 4.441415 CACTACTTATCAAGGAATCGCGTC 59.559 45.833 5.77 0.00 0.00 5.19
3216 3249 2.822764 ACTTATCAAGGAATCGCGTCC 58.177 47.619 5.77 6.86 38.03 4.79
3217 3250 2.167693 ACTTATCAAGGAATCGCGTCCA 59.832 45.455 17.08 0.00 40.48 4.02
3218 3251 2.971660 TATCAAGGAATCGCGTCCAA 57.028 45.000 17.08 3.73 40.48 3.53
3219 3252 1.369625 ATCAAGGAATCGCGTCCAAC 58.630 50.000 17.08 0.97 40.48 3.77
3227 3261 2.665649 ATCGCGTCCAACTTACATGA 57.334 45.000 5.77 0.00 0.00 3.07
3234 3268 5.348986 GCGTCCAACTTACATGATTCTCTA 58.651 41.667 0.00 0.00 0.00 2.43
3255 3293 7.065563 TCTCTAGAATCTTTCTGCTTTGCATTC 59.934 37.037 0.00 0.00 40.94 2.67
3262 3300 2.229792 TCTGCTTTGCATTCGTTCCTT 58.770 42.857 0.00 0.00 38.13 3.36
3290 3486 4.468095 AACACTAAAACGTGCTCACATC 57.532 40.909 0.00 0.00 38.45 3.06
3293 3489 4.515191 ACACTAAAACGTGCTCACATCAAT 59.485 37.500 0.00 0.00 38.45 2.57
3302 3498 4.595116 GTGCTCACATCAATAGAACATGC 58.405 43.478 0.00 0.00 0.00 4.06
3320 3516 7.448469 AGAACATGCATGTAAGGTAGTTTCTTT 59.552 33.333 31.55 11.50 40.80 2.52
3321 3517 6.913170 ACATGCATGTAAGGTAGTTTCTTTG 58.087 36.000 30.50 0.00 39.68 2.77
3322 3518 6.714810 ACATGCATGTAAGGTAGTTTCTTTGA 59.285 34.615 30.50 0.00 39.68 2.69
3323 3519 6.801539 TGCATGTAAGGTAGTTTCTTTGAG 57.198 37.500 0.00 0.00 0.00 3.02
3325 3521 6.995686 TGCATGTAAGGTAGTTTCTTTGAGAA 59.004 34.615 0.00 0.00 31.28 2.87
3326 3522 7.173218 TGCATGTAAGGTAGTTTCTTTGAGAAG 59.827 37.037 0.00 0.00 35.37 2.85
3327 3523 7.173390 GCATGTAAGGTAGTTTCTTTGAGAAGT 59.827 37.037 0.00 0.00 35.37 3.01
3328 3524 8.713271 CATGTAAGGTAGTTTCTTTGAGAAGTC 58.287 37.037 0.00 0.00 35.37 3.01
3329 3525 7.788026 TGTAAGGTAGTTTCTTTGAGAAGTCA 58.212 34.615 0.00 0.00 35.37 3.41
3330 3526 8.429641 TGTAAGGTAGTTTCTTTGAGAAGTCAT 58.570 33.333 0.00 0.00 35.37 3.06
3331 3527 7.971183 AAGGTAGTTTCTTTGAGAAGTCATC 57.029 36.000 0.00 0.00 35.37 2.92
3332 3528 7.309770 AGGTAGTTTCTTTGAGAAGTCATCT 57.690 36.000 0.00 0.00 42.61 2.90
3333 3529 8.423906 AGGTAGTTTCTTTGAGAAGTCATCTA 57.576 34.615 0.00 0.00 38.96 1.98
3334 3530 8.527810 AGGTAGTTTCTTTGAGAAGTCATCTAG 58.472 37.037 0.00 0.00 38.96 2.43
3335 3531 8.524487 GGTAGTTTCTTTGAGAAGTCATCTAGA 58.476 37.037 0.00 0.00 38.96 2.43
3369 3565 2.169352 AGGCAGCACTACAGATAGTTGG 59.831 50.000 0.00 0.00 39.80 3.77
3393 3589 2.019156 GCCAGCTCATGTTAGAACCCC 61.019 57.143 0.00 0.00 0.00 4.95
3449 3645 6.553852 CCTAGTCCTAGGTATCCTTTGCTTTA 59.446 42.308 9.08 0.00 45.93 1.85
3450 3646 6.886178 AGTCCTAGGTATCCTTTGCTTTAA 57.114 37.500 9.08 0.00 34.61 1.52
3473 3669 9.706691 TTAAGTAAGGTGATCTTTTAGTGACAG 57.293 33.333 0.00 0.00 36.93 3.51
3479 3675 5.444122 GTGATCTTTTAGTGACAGTTGCAC 58.556 41.667 0.00 0.00 36.53 4.57
3512 3708 5.631026 CAGGTTACTCAATTTTCACCATCG 58.369 41.667 0.00 0.00 0.00 3.84
3533 3729 4.159693 TCGCTGCTAAAATCTGAAGGAGTA 59.840 41.667 0.00 0.00 31.91 2.59
3539 3735 5.065346 GCTAAAATCTGAAGGAGTACAAGCC 59.935 44.000 0.00 0.00 0.00 4.35
3563 3759 0.814010 GTTGTGTTCAGCGTGAGGGT 60.814 55.000 0.00 0.00 0.00 4.34
3620 3816 2.102252 TGGGTTCAATTGTGGCTTCAAC 59.898 45.455 5.13 0.51 0.00 3.18
3699 3895 5.220303 GCTGTAGAGCTTTATCGTGAACAAG 60.220 44.000 4.27 0.00 42.52 3.16
3729 3925 8.749354 GGAAAATAACTGTTTCCCATGATAAGT 58.251 33.333 0.00 0.00 45.62 2.24
4163 4360 7.241628 ACTGGGACAAAAGATTCTTCCTATTT 58.758 34.615 0.00 0.00 38.70 1.40
4460 4657 1.888018 CAATGCCTGCCCTTCTGTG 59.112 57.895 0.00 0.00 0.00 3.66
4776 4976 3.264193 TGAGCATCATAACAGGTCACCTT 59.736 43.478 0.00 0.00 42.56 3.50
4832 5032 6.183360 CCAGTTTAGATAGCTCAAACACTTCG 60.183 42.308 12.75 0.00 35.17 3.79
4917 5117 6.384305 ACTTATAACACCAGAGACTAATGCCT 59.616 38.462 0.00 0.00 0.00 4.75
5013 5213 2.917933 CACCAAGTGTGTCTCAGGAAA 58.082 47.619 0.00 0.00 40.26 3.13
5024 5224 2.161211 GTCTCAGGAAACATCAAGCAGC 59.839 50.000 0.00 0.00 0.00 5.25
5036 5236 0.947244 CAAGCAGCGTCTTTGTTCCT 59.053 50.000 0.00 0.00 0.00 3.36
5058 5258 6.834451 TCCTATAGACCCTTCTAGTGTTCAAG 59.166 42.308 0.00 0.00 37.77 3.02
5226 5426 1.219773 ACATGCCCATCCATCTGTCT 58.780 50.000 0.00 0.00 0.00 3.41
6008 6427 3.669949 ACTCAGTATGGGAAGGCCTAAT 58.330 45.455 5.16 0.00 41.11 1.73
6012 6431 4.972568 TCAGTATGGGAAGGCCTAATGTTA 59.027 41.667 5.16 0.00 36.16 2.41
6356 6788 3.840124 AACAATCCTATCGGGGTTCTC 57.160 47.619 0.00 0.00 35.99 2.87
6396 6828 8.870879 GTCTTAACAAACAGTGTAGGTGATATC 58.129 37.037 0.00 0.00 40.60 1.63
6417 6849 9.970395 GATATCTCAGGCTCTTCTATGATAATG 57.030 37.037 0.00 0.00 0.00 1.90
6468 6900 7.354312 ACTATAAACCCAATTCAGGTGCTAAT 58.646 34.615 0.00 0.00 37.78 1.73
6469 6901 6.715347 ATAAACCCAATTCAGGTGCTAATC 57.285 37.500 0.00 0.00 37.78 1.75
6475 6907 5.361857 CCCAATTCAGGTGCTAATCTTTCAT 59.638 40.000 0.00 0.00 0.00 2.57
6479 6911 6.688637 TTCAGGTGCTAATCTTTCATGATG 57.311 37.500 0.00 0.00 0.00 3.07
6503 6938 4.269363 GCTTAATTTGCATGAATGGCACTC 59.731 41.667 0.00 0.00 41.75 3.51
6937 7372 5.886960 TTCTAGAAGGCAGAGCAAATTTC 57.113 39.130 0.00 0.00 0.00 2.17
7000 7435 4.080129 ACAACTGGACATGGCATATCTCTT 60.080 41.667 5.64 0.00 0.00 2.85
7047 7482 2.672961 TCTGTACTGGCCATCTTTCG 57.327 50.000 5.51 0.00 0.00 3.46
7223 7659 2.632996 CTGGTTCCAGTCTGTACCTTGA 59.367 50.000 17.57 0.00 0.00 3.02
7224 7660 3.042682 TGGTTCCAGTCTGTACCTTGAA 58.957 45.455 17.57 3.70 0.00 2.69
7225 7661 3.071023 TGGTTCCAGTCTGTACCTTGAAG 59.929 47.826 17.57 0.00 0.00 3.02
7226 7662 3.557264 GGTTCCAGTCTGTACCTTGAAGG 60.557 52.174 10.24 10.24 42.49 3.46
7227 7663 1.623811 TCCAGTCTGTACCTTGAAGGC 59.376 52.381 11.96 0.00 39.63 4.35
7228 7664 1.625818 CCAGTCTGTACCTTGAAGGCT 59.374 52.381 11.96 1.25 39.63 4.58
7229 7665 2.039084 CCAGTCTGTACCTTGAAGGCTT 59.961 50.000 11.96 0.00 39.63 4.35
7230 7666 3.070018 CAGTCTGTACCTTGAAGGCTTG 58.930 50.000 11.96 0.00 39.63 4.01
7303 7739 3.670627 GCAGTTTCTCTTTTGTATGCCCG 60.671 47.826 0.00 0.00 0.00 6.13
7319 7755 2.094957 TGCCCGTTTGCTGCTTTTATAC 60.095 45.455 0.00 0.00 0.00 1.47
7398 7836 1.647346 CTGGGCGCTTAATTACGTCA 58.353 50.000 7.64 0.00 35.09 4.35
7456 7894 8.817100 TCTTTCTATATGTAACTGCATGTTTCG 58.183 33.333 6.82 0.00 39.89 3.46
7470 7908 6.734137 TGCATGTTTCGTTATCTTGAAGTTT 58.266 32.000 0.00 0.00 0.00 2.66
7471 7909 6.636447 TGCATGTTTCGTTATCTTGAAGTTTG 59.364 34.615 0.00 0.00 0.00 2.93
7498 7936 8.536175 TCTTTAAATTTTGTTCCACAAGAGGTT 58.464 29.630 0.00 0.00 39.53 3.50
7499 7937 9.161629 CTTTAAATTTTGTTCCACAAGAGGTTT 57.838 29.630 0.00 0.00 39.53 3.27
7627 8066 2.989166 GCTTAAATGCTGCAACTTGTCC 59.011 45.455 6.36 0.00 0.00 4.02
7746 8190 6.403418 GCAGCTTATGATCTAATCTGGCAATC 60.403 42.308 13.10 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.832129 CCTGCCTTACCTCAACTCTGTA 59.168 50.000 0.00 0.00 0.00 2.74
41 42 3.334054 GGTTCTCCCTGCCTGCCT 61.334 66.667 0.00 0.00 0.00 4.75
42 43 4.785453 CGGTTCTCCCTGCCTGCC 62.785 72.222 0.00 0.00 0.00 4.85
44 45 4.785453 GGCGGTTCTCCCTGCCTG 62.785 72.222 3.78 0.00 44.53 4.85
198 209 1.449246 CTGAGAGGCTCCGGCAAAG 60.449 63.158 11.71 0.00 40.87 2.77
209 220 2.279784 GCCCGATTCGCTGAGAGG 60.280 66.667 0.00 0.00 0.00 3.69
235 246 1.490490 CTTCAATCCAGATCGGGGGAA 59.510 52.381 12.28 11.88 36.62 3.97
236 247 1.131638 CTTCAATCCAGATCGGGGGA 58.868 55.000 12.28 9.01 37.64 4.81
408 427 2.391678 CCCCTCCAATCCAATTTCCAG 58.608 52.381 0.00 0.00 0.00 3.86
414 433 0.925720 TCTGCCCCCTCCAATCCAAT 60.926 55.000 0.00 0.00 0.00 3.16
416 435 1.309013 ATCTGCCCCCTCCAATCCA 60.309 57.895 0.00 0.00 0.00 3.41
418 437 1.152368 CCATCTGCCCCCTCCAATC 59.848 63.158 0.00 0.00 0.00 2.67
419 438 3.078843 GCCATCTGCCCCCTCCAAT 62.079 63.158 0.00 0.00 0.00 3.16
423 442 2.408880 GATCTGCCATCTGCCCCCTC 62.409 65.000 0.00 0.00 40.16 4.30
474 493 6.128742 GCAGATTTACTTTCCACAAAGCAATG 60.129 38.462 0.00 0.00 42.66 2.82
540 559 1.272928 ACAGAGAGAGATCCTGGTGCA 60.273 52.381 0.00 0.00 32.52 4.57
558 577 1.207089 GGCTACTGATGGCTACACACA 59.793 52.381 0.00 0.00 31.71 3.72
559 578 1.207089 TGGCTACTGATGGCTACACAC 59.793 52.381 0.00 0.00 31.71 3.82
600 619 3.644738 ACCATAACGACCCCTACCATAAG 59.355 47.826 0.00 0.00 0.00 1.73
602 621 3.117016 AGACCATAACGACCCCTACCATA 60.117 47.826 0.00 0.00 0.00 2.74
603 622 2.044758 GACCATAACGACCCCTACCAT 58.955 52.381 0.00 0.00 0.00 3.55
604 623 1.007479 AGACCATAACGACCCCTACCA 59.993 52.381 0.00 0.00 0.00 3.25
605 624 1.785647 AGACCATAACGACCCCTACC 58.214 55.000 0.00 0.00 0.00 3.18
606 625 3.893813 ACATAGACCATAACGACCCCTAC 59.106 47.826 0.00 0.00 0.00 3.18
607 626 4.188937 ACATAGACCATAACGACCCCTA 57.811 45.455 0.00 0.00 0.00 3.53
608 627 3.042059 ACATAGACCATAACGACCCCT 57.958 47.619 0.00 0.00 0.00 4.79
609 628 3.463944 CAACATAGACCATAACGACCCC 58.536 50.000 0.00 0.00 0.00 4.95
610 629 2.870411 GCAACATAGACCATAACGACCC 59.130 50.000 0.00 0.00 0.00 4.46
611 630 2.538449 CGCAACATAGACCATAACGACC 59.462 50.000 0.00 0.00 0.00 4.79
612 631 3.000078 CACGCAACATAGACCATAACGAC 60.000 47.826 0.00 0.00 0.00 4.34
613 632 3.183754 CACGCAACATAGACCATAACGA 58.816 45.455 0.00 0.00 0.00 3.85
614 633 2.927477 ACACGCAACATAGACCATAACG 59.073 45.455 0.00 0.00 0.00 3.18
615 634 4.032900 CAGACACGCAACATAGACCATAAC 59.967 45.833 0.00 0.00 0.00 1.89
616 635 4.180817 CAGACACGCAACATAGACCATAA 58.819 43.478 0.00 0.00 0.00 1.90
676 695 3.869272 GCATTGCCGACGAGCAGG 61.869 66.667 10.21 8.59 45.13 4.85
744 766 3.006110 ACCACAGCACCATGAAAAATCAG 59.994 43.478 0.00 0.00 0.00 2.90
774 797 1.880027 CCCAGTTAAGGTGTCAAGCAC 59.120 52.381 0.00 0.00 46.97 4.40
775 798 1.817740 GCCCAGTTAAGGTGTCAAGCA 60.818 52.381 0.00 0.00 0.00 3.91
782 805 1.726853 CGAGAAGCCCAGTTAAGGTG 58.273 55.000 0.00 0.00 0.00 4.00
783 806 0.036294 GCGAGAAGCCCAGTTAAGGT 60.036 55.000 0.00 0.00 40.81 3.50
784 807 2.768834 GCGAGAAGCCCAGTTAAGG 58.231 57.895 0.00 0.00 40.81 2.69
874 897 2.890945 AGGCAATAACCACACAAGAACC 59.109 45.455 0.00 0.00 0.00 3.62
899 922 1.412343 ACAATGCCCACCAAGAACAAC 59.588 47.619 0.00 0.00 0.00 3.32
973 996 7.325338 CACTGCATCAAAAGAAATACACTTGAG 59.675 37.037 0.00 0.00 30.10 3.02
1136 1159 1.135139 GACTAGGACGAGCATCAGCAA 59.865 52.381 0.00 0.00 45.49 3.91
1148 1171 1.896465 ACACTTGAGCAGGACTAGGAC 59.104 52.381 0.00 0.00 0.00 3.85
1239 1262 1.134560 CTCCCGGAAGTACTACAGTGC 59.865 57.143 0.73 0.00 0.00 4.40
1245 1268 2.590821 GTATGGCTCCCGGAAGTACTA 58.409 52.381 0.73 0.00 0.00 1.82
1299 1322 4.732285 ATTATCAAAGCGGCTGTAATCG 57.268 40.909 1.81 0.00 0.00 3.34
1302 1325 5.176774 CGACATATTATCAAAGCGGCTGTAA 59.823 40.000 1.81 1.70 0.00 2.41
1326 1349 3.371102 TCGACATCGGAATCTTCATCC 57.629 47.619 0.73 0.00 40.29 3.51
1383 1406 2.507471 TGATTGGGCAACAAGGGTTTTT 59.493 40.909 0.00 0.00 43.48 1.94
1442 1467 5.455392 CGCCTGCCAAAAGAATATTATGAG 58.545 41.667 0.00 0.00 0.00 2.90
1471 1496 3.238441 CTGTCTGCGTCTCACTAAACTC 58.762 50.000 0.00 0.00 0.00 3.01
1569 1595 8.200792 AGCCACAATTTCATAAAAGTAACACAA 58.799 29.630 0.00 0.00 0.00 3.33
1728 1755 4.246458 AGCAACAGTACTAGCTAAAGCAC 58.754 43.478 13.19 0.00 45.16 4.40
1787 1815 9.426534 CCTGATACACCAGAGGATATTATATCA 57.573 37.037 13.45 0.00 36.29 2.15
1788 1816 9.647918 TCCTGATACACCAGAGGATATTATATC 57.352 37.037 3.74 3.74 36.29 1.63
1791 1819 8.923838 ATTCCTGATACACCAGAGGATATTAT 57.076 34.615 0.00 0.00 34.53 1.28
1792 1820 8.742125 AATTCCTGATACACCAGAGGATATTA 57.258 34.615 0.00 0.00 34.53 0.98
1793 1821 7.293299 TGAATTCCTGATACACCAGAGGATATT 59.707 37.037 2.27 0.00 34.53 1.28
1968 1996 4.112634 GGTTTTGAAGCTTGTCAACCTTC 58.887 43.478 17.47 12.06 37.24 3.46
2067 2095 5.477984 TCCAGGTTCAAATCCAAATCTCTTG 59.522 40.000 0.00 0.00 0.00 3.02
2275 2303 8.271487 GCAATGAACTGAAATTCTGAAAAGAAC 58.729 33.333 6.87 0.00 0.00 3.01
2277 2305 7.719483 AGCAATGAACTGAAATTCTGAAAAGA 58.281 30.769 6.87 0.00 0.00 2.52
2280 2308 7.041635 TGAGCAATGAACTGAAATTCTGAAA 57.958 32.000 6.87 0.00 0.00 2.69
2282 2310 6.263842 AGTTGAGCAATGAACTGAAATTCTGA 59.736 34.615 6.87 0.00 31.09 3.27
2283 2311 6.444633 AGTTGAGCAATGAACTGAAATTCTG 58.555 36.000 0.00 0.00 31.09 3.02
2284 2312 6.263842 TGAGTTGAGCAATGAACTGAAATTCT 59.736 34.615 0.00 0.00 32.47 2.40
2285 2313 6.441274 TGAGTTGAGCAATGAACTGAAATTC 58.559 36.000 0.00 0.00 32.47 2.17
2286 2314 6.395426 TGAGTTGAGCAATGAACTGAAATT 57.605 33.333 0.00 0.00 32.47 1.82
2287 2315 6.395426 TTGAGTTGAGCAATGAACTGAAAT 57.605 33.333 0.00 0.00 32.47 2.17
2309 2337 5.818857 ACAGCATGCAAATTTTCTGAAGTTT 59.181 32.000 21.98 0.00 42.53 2.66
2526 2554 7.916450 CGAAAACACACCTTCCAATAAGTTAAA 59.084 33.333 0.00 0.00 0.00 1.52
2546 2574 3.855950 CCGTAGATCACCTACACGAAAAC 59.144 47.826 0.00 0.00 46.32 2.43
2620 2648 3.187227 CCTCAACACCTGATTTTGTCTCG 59.813 47.826 0.00 0.00 32.14 4.04
2634 2662 6.540189 AGATTGTGCATACTTATCCTCAACAC 59.460 38.462 0.00 0.00 0.00 3.32
2716 2744 2.224079 CAGAACACCAGAAATGTCACCG 59.776 50.000 0.00 0.00 0.00 4.94
2896 2924 6.560068 CGACATGCTGTTTAAAACACAACATG 60.560 38.462 15.64 15.64 42.25 3.21
2942 2970 3.257127 GCACCCCAATGCAAGTAGTTTAA 59.743 43.478 0.00 0.00 45.39 1.52
3028 3056 4.593206 TCCTCAAACAAGTCAGGTAGATGT 59.407 41.667 0.00 0.00 0.00 3.06
3120 3153 4.081420 ACAGACCTTCTTGTACAGCATAGG 60.081 45.833 11.58 11.58 0.00 2.57
3123 3156 3.324846 TCACAGACCTTCTTGTACAGCAT 59.675 43.478 0.00 0.00 0.00 3.79
3126 3159 5.398603 AGATCACAGACCTTCTTGTACAG 57.601 43.478 0.00 0.00 0.00 2.74
3154 3187 8.738645 AAACATAGTCAGAAAAGGATGGATAC 57.261 34.615 0.00 0.00 0.00 2.24
3184 3217 9.202273 GATTCCTTGATAAGTAGTGATAGCAAG 57.798 37.037 4.33 4.33 42.34 4.01
3198 3231 2.933906 GTTGGACGCGATTCCTTGATAA 59.066 45.455 15.93 0.00 36.51 1.75
3202 3235 1.156736 AAGTTGGACGCGATTCCTTG 58.843 50.000 15.93 0.00 36.51 3.61
3203 3236 2.289195 TGTAAGTTGGACGCGATTCCTT 60.289 45.455 15.93 10.37 36.51 3.36
3204 3237 1.274167 TGTAAGTTGGACGCGATTCCT 59.726 47.619 15.93 0.00 36.51 3.36
3207 3240 2.967362 TCATGTAAGTTGGACGCGATT 58.033 42.857 15.93 0.00 0.00 3.34
3208 3241 2.665649 TCATGTAAGTTGGACGCGAT 57.334 45.000 15.93 0.00 0.00 4.58
3209 3242 2.665649 ATCATGTAAGTTGGACGCGA 57.334 45.000 15.93 0.00 0.00 5.87
3210 3243 2.930040 AGAATCATGTAAGTTGGACGCG 59.070 45.455 3.53 3.53 0.00 6.01
3211 3244 4.184629 AGAGAATCATGTAAGTTGGACGC 58.815 43.478 0.00 0.00 37.82 5.19
3212 3245 6.796426 TCTAGAGAATCATGTAAGTTGGACG 58.204 40.000 0.00 0.00 37.82 4.79
3227 3261 6.883217 TGCAAAGCAGAAAGATTCTAGAGAAT 59.117 34.615 4.42 4.42 39.54 2.40
3234 3268 4.217118 ACGAATGCAAAGCAGAAAGATTCT 59.783 37.500 0.00 0.00 43.65 2.40
3247 3285 4.902443 TTACACAAGGAACGAATGCAAA 57.098 36.364 0.00 0.00 0.00 3.68
3250 3288 4.602995 TGTTTTACACAAGGAACGAATGC 58.397 39.130 0.00 0.00 29.87 3.56
3278 3316 3.925379 TGTTCTATTGATGTGAGCACGT 58.075 40.909 0.00 0.00 0.00 4.49
3279 3317 4.784394 GCATGTTCTATTGATGTGAGCACG 60.784 45.833 0.00 0.00 0.00 5.34
3280 3318 4.095334 TGCATGTTCTATTGATGTGAGCAC 59.905 41.667 0.00 0.00 0.00 4.40
3281 3319 4.263435 TGCATGTTCTATTGATGTGAGCA 58.737 39.130 0.00 0.00 0.00 4.26
3282 3320 4.888038 TGCATGTTCTATTGATGTGAGC 57.112 40.909 0.00 0.00 0.00 4.26
3283 3321 6.373186 ACATGCATGTTCTATTGATGTGAG 57.627 37.500 26.61 0.00 37.90 3.51
3284 3322 7.012610 CCTTACATGCATGTTCTATTGATGTGA 59.987 37.037 35.45 11.61 41.97 3.58
3290 3486 7.792374 ACTACCTTACATGCATGTTCTATTG 57.208 36.000 35.45 22.67 41.97 1.90
3293 3489 7.620880 AGAAACTACCTTACATGCATGTTCTA 58.379 34.615 35.45 16.93 41.97 2.10
3302 3498 8.608844 ACTTCTCAAAGAAACTACCTTACATG 57.391 34.615 0.00 0.00 33.19 3.21
3320 3516 6.310941 CCCCTAGAATCTAGATGACTTCTCA 58.689 44.000 18.25 0.00 35.79 3.27
3321 3517 5.185056 GCCCCTAGAATCTAGATGACTTCTC 59.815 48.000 18.25 0.00 35.79 2.87
3322 3518 5.083821 GCCCCTAGAATCTAGATGACTTCT 58.916 45.833 18.25 8.65 38.57 2.85
3323 3519 5.083821 AGCCCCTAGAATCTAGATGACTTC 58.916 45.833 18.25 0.59 0.00 3.01
3325 3521 4.757997 AGCCCCTAGAATCTAGATGACT 57.242 45.455 18.25 11.31 0.00 3.41
3326 3522 5.420739 CCTAAGCCCCTAGAATCTAGATGAC 59.579 48.000 18.25 4.12 0.00 3.06
3327 3523 5.584913 CCTAAGCCCCTAGAATCTAGATGA 58.415 45.833 18.25 0.00 0.00 2.92
3328 3524 4.161377 GCCTAAGCCCCTAGAATCTAGATG 59.839 50.000 18.25 9.69 0.00 2.90
3329 3525 4.202836 TGCCTAAGCCCCTAGAATCTAGAT 60.203 45.833 18.25 0.00 38.69 1.98
3330 3526 3.142217 TGCCTAAGCCCCTAGAATCTAGA 59.858 47.826 18.25 0.00 38.69 2.43
3331 3527 3.511477 TGCCTAAGCCCCTAGAATCTAG 58.489 50.000 10.25 10.25 38.69 2.43
3332 3528 3.511477 CTGCCTAAGCCCCTAGAATCTA 58.489 50.000 0.00 0.00 38.69 1.98
3333 3529 2.334023 CTGCCTAAGCCCCTAGAATCT 58.666 52.381 0.00 0.00 38.69 2.40
3334 3530 2.849294 CTGCCTAAGCCCCTAGAATC 57.151 55.000 0.00 0.00 38.69 2.52
3357 3553 2.365617 GCTGGCTAGCCAACTATCTGTA 59.634 50.000 35.07 10.31 46.63 2.74
3381 3577 6.707273 TTAAAGTAGTGGGGGTTCTAACAT 57.293 37.500 0.00 0.00 0.00 2.71
3393 3589 4.221482 AGGTACCGGACTTTAAAGTAGTGG 59.779 45.833 20.58 21.56 39.88 4.00
3449 3645 7.736893 ACTGTCACTAAAAGATCACCTTACTT 58.263 34.615 0.00 0.00 34.00 2.24
3450 3646 7.304497 ACTGTCACTAAAAGATCACCTTACT 57.696 36.000 0.00 0.00 34.00 2.24
3473 3669 0.524862 CCTGCATGAGAAGGTGCAAC 59.475 55.000 0.00 0.00 35.61 4.17
3512 3708 5.178797 TGTACTCCTTCAGATTTTAGCAGC 58.821 41.667 0.00 0.00 0.00 5.25
3533 3729 3.067106 CTGAACACAACGATAGGCTTGT 58.933 45.455 0.00 0.00 43.77 3.16
3539 3735 2.324860 TCACGCTGAACACAACGATAG 58.675 47.619 0.00 0.00 46.19 2.08
3563 3759 2.549992 CGGGAATGTCAGGACAAAGTCA 60.550 50.000 6.17 0.00 45.41 3.41
3566 3762 0.804989 GCGGGAATGTCAGGACAAAG 59.195 55.000 6.17 0.00 45.41 2.77
3620 3816 3.365666 CCACATTAACAGCTTCTGCACAG 60.366 47.826 0.00 0.00 42.74 3.66
3729 3925 1.684386 CTTGCAGCCCCCAACAACAA 61.684 55.000 0.00 0.00 0.00 2.83
3933 4130 2.223829 CCGTCTCAATTCGTGCCTAGAT 60.224 50.000 0.00 0.00 0.00 1.98
4163 4360 3.740631 AGCTCATTGACATCATAGCGA 57.259 42.857 0.00 0.00 34.04 4.93
4460 4657 2.496899 TTCCCAGTTTCATCTGCTCC 57.503 50.000 0.00 0.00 34.47 4.70
4776 4976 5.116180 GTTGGTTCCGTCATGAATCATAGA 58.884 41.667 0.00 0.00 35.41 1.98
4917 5117 5.243507 TGTTGCCTTTCTCAAGCATTATTGA 59.756 36.000 0.00 0.00 37.60 2.57
5006 5206 1.159285 CGCTGCTTGATGTTTCCTGA 58.841 50.000 0.00 0.00 0.00 3.86
5013 5213 1.597742 ACAAAGACGCTGCTTGATGT 58.402 45.000 6.38 0.00 0.00 3.06
5024 5224 5.127356 AGAAGGGTCTATAGGAACAAAGACG 59.873 44.000 0.00 0.00 39.39 4.18
5036 5236 7.506261 GGATCTTGAACACTAGAAGGGTCTATA 59.494 40.741 0.00 0.00 35.76 1.31
5058 5258 1.500396 GAAAACGCCCGTGTGGATC 59.500 57.895 0.00 0.00 37.49 3.36
5226 5426 0.611618 GGATGGGCATGTTGTGGTGA 60.612 55.000 0.00 0.00 0.00 4.02
5624 5825 9.905713 AACTGCCTAAGAAAGAAATCATATACA 57.094 29.630 0.00 0.00 0.00 2.29
6008 6427 1.825474 GGAGGCTGCAGAGTAGTAACA 59.175 52.381 20.43 0.00 0.00 2.41
6012 6431 0.975040 CCTGGAGGCTGCAGAGTAGT 60.975 60.000 34.08 0.00 38.14 2.73
6356 6788 8.861101 TGTTTGTTAAGACATTTGTTTTTACGG 58.139 29.630 0.00 0.00 35.29 4.02
6396 6828 5.791666 TGCATTATCATAGAAGAGCCTGAG 58.208 41.667 0.00 0.00 0.00 3.35
6468 6900 6.283544 TGCAAATTAAGCCATCATGAAAGA 57.716 33.333 0.00 0.00 0.00 2.52
6469 6901 6.759356 TCATGCAAATTAAGCCATCATGAAAG 59.241 34.615 0.00 0.00 36.79 2.62
6475 6907 5.361427 CCATTCATGCAAATTAAGCCATCA 58.639 37.500 0.00 0.00 0.00 3.07
6479 6911 3.310501 GTGCCATTCATGCAAATTAAGCC 59.689 43.478 0.00 0.00 41.06 4.35
6503 6938 1.955778 TGAATGCCAACTGAACCACTG 59.044 47.619 0.00 0.00 0.00 3.66
7000 7435 6.560003 TCTTATACATCAGGAAGAGGCAAA 57.440 37.500 0.00 0.00 0.00 3.68
7047 7482 6.628185 AGAATTCTCATGCCATTTCAACTTC 58.372 36.000 0.88 0.00 0.00 3.01
7223 7659 2.514458 AATCCGATGGTTCAAGCCTT 57.486 45.000 0.00 0.00 0.00 4.35
7224 7660 2.514458 AAATCCGATGGTTCAAGCCT 57.486 45.000 0.00 0.00 0.00 4.58
7225 7661 4.261614 GGATAAAATCCGATGGTTCAAGCC 60.262 45.833 0.00 0.00 40.13 4.35
7226 7662 4.860072 GGATAAAATCCGATGGTTCAAGC 58.140 43.478 0.00 0.00 40.13 4.01
7266 7702 5.802465 AGAAACTGCAAGAGATCAGAATCA 58.198 37.500 0.00 0.00 37.43 2.57
7303 7739 9.285770 GTATGTAAAGGTATAAAAGCAGCAAAC 57.714 33.333 0.00 0.00 0.00 2.93
7319 7755 7.321745 GGAAACCAGATCTTGTATGTAAAGG 57.678 40.000 0.00 0.00 0.00 3.11
7394 7832 0.887933 CCCTTGGGAAATTGGTGACG 59.112 55.000 0.00 0.00 0.00 4.35
7398 7836 5.747545 GCAAAATTACCCTTGGGAAATTGGT 60.748 40.000 13.39 0.00 31.34 3.67
7627 8066 1.369625 GCGGTGATACCAGAAACCAG 58.630 55.000 0.00 0.00 38.47 4.00
7717 8156 5.180868 CCAGATTAGATCATAAGCTGCCAAC 59.819 44.000 17.52 0.00 39.00 3.77
7746 8190 6.316140 TGCCAATACATAAACAGCTGAGTTAG 59.684 38.462 23.35 9.59 0.00 2.34


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

AutoCloner maintained by Alex Coulton.