Multiple sequence alignment - TraesCS3B01G217400

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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 TraesCS3B01G217400 chr3B 100.000 8339 0 0 806 9144 259858832 259850494 0.000000e+00 15400.0
1 TraesCS3B01G217400 chr3B 100.000 486 0 0 1 486 259859637 259859152 0.000000e+00 898.0
2 TraesCS3B01G217400 chr3D 94.765 7488 242 71 806 8269 181571743 181564382 0.000000e+00 11518.0
3 TraesCS3B01G217400 chr3D 97.125 487 13 1 1 486 181572313 181571827 0.000000e+00 821.0
4 TraesCS3B01G217400 chr3D 88.756 418 40 5 8727 9144 181563780 181563370 1.060000e-138 505.0
5 TraesCS3B01G217400 chr3D 94.326 141 8 0 6204 6344 422517646 422517786 5.560000e-52 217.0
6 TraesCS3B01G217400 chr3D 82.836 134 17 5 8437 8566 611068409 611068278 2.090000e-21 115.0
7 TraesCS3B01G217400 chr3A 95.512 4144 158 22 806 4936 227408131 227412259 0.000000e+00 6597.0
8 TraesCS3B01G217400 chr3A 93.502 3832 154 41 4934 8712 227412385 227416174 0.000000e+00 5609.0
9 TraesCS3B01G217400 chr3A 96.933 489 12 1 1 486 227407560 227408048 0.000000e+00 817.0
10 TraesCS3B01G217400 chr3A 88.267 375 32 6 8771 9144 227416186 227416549 1.090000e-118 438.0
11 TraesCS3B01G217400 chr5D 96.657 359 8 2 1 358 35981603 35981248 2.200000e-165 593.0
12 TraesCS3B01G217400 chr5D 94.326 141 8 0 6204 6344 69904768 69904628 5.560000e-52 217.0
13 TraesCS3B01G217400 chr5A 83.046 348 54 3 8749 9096 552742720 552742378 2.480000e-80 311.0
14 TraesCS3B01G217400 chr5A 80.583 309 43 10 8392 8694 552743024 552742727 1.200000e-53 222.0
15 TraesCS3B01G217400 chr4D 81.433 307 40 8 8346 8636 337088747 337088442 1.530000e-57 235.0
16 TraesCS3B01G217400 chr4D 94.326 141 8 0 6204 6344 428723806 428723946 5.560000e-52 217.0
17 TraesCS3B01G217400 chr2D 95.035 141 7 0 6204 6344 273951092 273950952 1.200000e-53 222.0
18 TraesCS3B01G217400 chr1D 95.035 141 7 0 6204 6344 341039736 341039596 1.200000e-53 222.0
19 TraesCS3B01G217400 chr1D 84.431 167 22 4 8478 8644 476201003 476201165 2.640000e-35 161.0
20 TraesCS3B01G217400 chr7D 95.035 141 5 2 6204 6344 139849749 139849611 4.300000e-53 220.0
21 TraesCS3B01G217400 chr5B 94.326 141 8 0 6204 6344 474459402 474459542 5.560000e-52 217.0
22 TraesCS3B01G217400 chr5B 84.865 185 25 3 8446 8629 278863040 278862858 5.640000e-42 183.0
23 TraesCS3B01G217400 chr4B 80.743 296 41 7 8346 8626 416248067 416247773 5.560000e-52 217.0
24 TraesCS3B01G217400 chr7B 82.836 134 19 3 8440 8573 68655858 68655729 5.800000e-22 117.0
25 TraesCS3B01G217400 chr7A 85.185 108 14 2 8466 8573 115311558 115311453 9.710000e-20 110.0
26 TraesCS3B01G217400 chr6A 85.185 81 11 1 1748 1827 351827532 351827612 2.120000e-11 82.4


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 TraesCS3B01G217400 chr3B 259850494 259859637 9143 True 8149.000000 15400 100.000000 1 9144 2 chr3B.!!$R1 9143
1 TraesCS3B01G217400 chr3D 181563370 181572313 8943 True 4281.333333 11518 93.548667 1 9144 3 chr3D.!!$R2 9143
2 TraesCS3B01G217400 chr3A 227407560 227416549 8989 False 3365.250000 6597 93.553500 1 9144 4 chr3A.!!$F1 9143
3 TraesCS3B01G217400 chr5A 552742378 552743024 646 True 266.500000 311 81.814500 8392 9096 2 chr5A.!!$R1 704

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
913 919 0.835941 ATGCCTAGCCTCCAGACTTG 59.164 55.000 0.00 0.00 0.00 3.16 F
1254 1260 0.036732 CCTGCACAAAGGTAGGCTCA 59.963 55.000 0.00 0.00 33.82 4.26 F
1267 1273 1.251251 AGGCTCAATCAAGCAACCAC 58.749 50.000 0.00 0.00 44.35 4.16 F
1291 1297 1.530419 AAACATGGCCGTGCTTCCA 60.530 52.632 25.30 0.00 36.70 3.53 F
3212 3225 1.939980 ACTCAGGGGGTCAAGTAGAC 58.060 55.000 0.00 0.00 46.83 2.59 F
4619 4659 1.625818 CATGCCTATGACCCTAGGGAC 59.374 57.143 35.38 28.30 41.39 4.46 F
6357 6535 0.035056 CGGGCTTCTGGGATTGTCTT 60.035 55.000 0.00 0.00 0.00 3.01 F
6516 6698 0.172578 CACTGCATGGCAATGACCAG 59.827 55.000 4.87 6.21 44.71 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2824 2836 2.040178 AGGGACCCATTCGTGATAGAC 58.960 52.381 14.60 0.00 0.00 2.59 R
3250 3285 1.416030 TGCAACCTGCTTGACAGTAGA 59.584 47.619 0.00 0.00 45.68 2.59 R
3271 3306 5.912892 AGCAGAGAAGTAAATAGAAGAGGC 58.087 41.667 0.00 0.00 0.00 4.70 R
3330 3365 3.896888 ACACACATTATTGGCCCCATATG 59.103 43.478 0.00 1.62 0.00 1.78 R
5096 5265 1.337384 ACCTGAGTGCGGCATATGGA 61.337 55.000 5.72 0.00 0.00 3.41 R
6498 6680 0.251474 ACTGGTCATTGCCATGCAGT 60.251 50.000 5.54 5.54 40.61 4.40 R
7786 7981 0.170561 TAGCAAGCGAAGAGGACGAC 59.829 55.000 0.00 0.00 0.00 4.34 R
8448 8823 0.037590 CCGTGGTTTGAAGGATCCCA 59.962 55.000 8.55 0.00 0.00 4.37 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
57 58 1.765074 ACCGGTGGTGGTTAGCATT 59.235 52.632 6.12 0.00 39.99 3.56
139 140 2.548057 GACAAGGACGATTTCAGCACAA 59.452 45.455 0.00 0.00 0.00 3.33
192 197 9.132521 GAATACAAAACATCAGATTCCACAAAG 57.867 33.333 0.00 0.00 0.00 2.77
296 301 2.161486 CAGCACTACGCCGAGAAGC 61.161 63.158 0.00 0.00 44.04 3.86
874 879 6.071108 GCTCATGATACCTCCTCTTGCTTATA 60.071 42.308 0.00 0.00 0.00 0.98
913 919 0.835941 ATGCCTAGCCTCCAGACTTG 59.164 55.000 0.00 0.00 0.00 3.16
1037 1043 2.740981 CAGCTTGCAGATTTCTCTCGTT 59.259 45.455 0.00 0.00 0.00 3.85
1085 1091 4.794278 TCGTTATGGAGTCTGCTTTGTA 57.206 40.909 0.00 0.00 0.00 2.41
1104 1110 1.077086 TGCCCATTCATGGTGCACT 59.923 52.632 17.98 0.00 46.65 4.40
1150 1156 1.136336 CGGCGTTTAAGCAGAAGACAC 60.136 52.381 0.00 0.00 39.27 3.67
1254 1260 0.036732 CCTGCACAAAGGTAGGCTCA 59.963 55.000 0.00 0.00 33.82 4.26
1267 1273 1.251251 AGGCTCAATCAAGCAACCAC 58.749 50.000 0.00 0.00 44.35 4.16
1291 1297 1.530419 AAACATGGCCGTGCTTCCA 60.530 52.632 25.30 0.00 36.70 3.53
1512 1518 2.191128 ACACAACCATCCTTGCTCTC 57.809 50.000 0.00 0.00 0.00 3.20
1922 1932 9.557338 CCGTTTTTACAACATAAATAAATCCGA 57.443 29.630 0.00 0.00 0.00 4.55
1942 1952 9.675464 AATCCGATTTACTTCCATTACTTGTAA 57.325 29.630 0.00 0.00 0.00 2.41
2002 2013 7.170489 GTGACTTTAGTACAACCAGAACTTACC 59.830 40.741 0.00 0.00 0.00 2.85
2021 2032 4.336889 ACCGATGTTGAGAAAAGACAGA 57.663 40.909 0.00 0.00 0.00 3.41
2117 2128 8.559536 CACTAGTTGCATACCCAATGTTATAAG 58.440 37.037 0.00 0.00 37.93 1.73
2128 2139 5.221303 CCCAATGTTATAAGTGGAGCAATGG 60.221 44.000 10.16 5.39 32.54 3.16
2160 2171 8.732746 TTAATTCCTGCTAGTTAAGGCTAAAG 57.267 34.615 0.00 0.00 33.25 1.85
2161 2172 4.138487 TCCTGCTAGTTAAGGCTAAAGC 57.862 45.455 0.00 0.00 41.14 3.51
2183 2194 6.392354 AGCAATGTCCAGAATTTGTGTAATG 58.608 36.000 0.00 0.00 0.00 1.90
2328 2340 6.191534 CGTGATACGATTCAGAATGAACTC 57.808 41.667 0.00 0.00 46.66 3.01
2353 2365 5.311265 TCAATCCTATCCAGCAAAGCATAG 58.689 41.667 0.00 0.00 0.00 2.23
2356 2368 4.903054 TCCTATCCAGCAAAGCATAGATG 58.097 43.478 0.00 0.00 0.00 2.90
2389 2401 6.148480 GTCAAGTGAAATAGACTTCTGCATGT 59.852 38.462 0.00 0.00 31.05 3.21
2420 2432 6.007936 TGCAAACAAATTAGTCGCTGTTAT 57.992 33.333 0.00 0.00 31.90 1.89
2428 2440 4.577687 TTAGTCGCTGTTATGCTTTTCG 57.422 40.909 0.00 0.00 0.00 3.46
2459 2471 4.635699 TTTTCCCTCTTGTAAGACTCCC 57.364 45.455 0.00 0.00 0.00 4.30
2508 2520 5.363580 ACTGCCCATTCAAGAAAAGAAGAAA 59.636 36.000 0.00 0.00 0.00 2.52
2509 2521 5.846203 TGCCCATTCAAGAAAAGAAGAAAG 58.154 37.500 0.00 0.00 0.00 2.62
2511 2523 5.923114 GCCCATTCAAGAAAAGAAGAAAGTC 59.077 40.000 0.00 0.00 0.00 3.01
2626 2638 6.245115 TCAGCTATGAACAACATTTCACAG 57.755 37.500 0.00 0.00 38.31 3.66
2846 2858 3.256136 GTCTATCACGAATGGGTCCCTAG 59.744 52.174 10.00 0.00 0.00 3.02
2881 2893 5.128008 AGAACTTCAGCCTCTAAGGTATGAC 59.872 44.000 3.46 0.00 37.80 3.06
2909 2921 4.818546 CACAACTCAACTTCATCCTCTTGT 59.181 41.667 0.00 0.00 0.00 3.16
2934 2946 9.226345 GTATGCTTGTAATATCTTGCTCAAAAC 57.774 33.333 0.00 0.00 0.00 2.43
3004 3016 4.515191 TGACTATTTGTTGTGGCTGACTTC 59.485 41.667 0.00 0.00 0.00 3.01
3015 3027 6.048732 TGTGGCTGACTTCAAATATAGTGA 57.951 37.500 0.00 0.00 0.00 3.41
3060 3073 9.133627 CAATATGTAGATAATCTGGTGAAGACG 57.866 37.037 0.00 0.00 37.88 4.18
3077 3090 7.921214 GGTGAAGACGTCATATTTGATCTTAGA 59.079 37.037 19.50 0.00 38.90 2.10
3205 3218 5.853572 AGTAAAAATAACTCAGGGGGTCA 57.146 39.130 0.00 0.00 0.00 4.02
3210 3223 5.437191 AAATAACTCAGGGGGTCAAGTAG 57.563 43.478 0.00 0.00 0.00 2.57
3211 3224 2.715763 AACTCAGGGGGTCAAGTAGA 57.284 50.000 0.00 0.00 0.00 2.59
3212 3225 1.939980 ACTCAGGGGGTCAAGTAGAC 58.060 55.000 0.00 0.00 46.83 2.59
3330 3365 8.628882 AAATTCTAATACAAGGTTAAATGCGC 57.371 30.769 0.00 0.00 0.00 6.09
3490 3527 6.266131 TGGTAGAATAAAGGGCTGATGATT 57.734 37.500 0.00 0.00 0.00 2.57
3548 3585 5.059833 ACAGTGTTTTTGAAGTTTTGGCAA 58.940 33.333 0.00 0.00 0.00 4.52
3631 3668 8.165239 ACAGAAATCACACTATTTGCAACTTA 57.835 30.769 0.00 0.00 0.00 2.24
3665 3702 8.686334 ACTACTACCATGGCTTCAAATAAAATG 58.314 33.333 13.04 0.00 0.00 2.32
3867 3906 5.590663 CCTACCCTAGAAGGAAAAGATTTGC 59.409 44.000 0.00 0.00 37.67 3.68
3870 3909 5.222130 ACCCTAGAAGGAAAAGATTTGCTCA 60.222 40.000 0.00 0.00 37.67 4.26
3954 3993 5.617252 TCAAACGTATTCCTCCAACTTTCT 58.383 37.500 0.00 0.00 0.00 2.52
3981 4020 9.694137 GTAACATAGTTTCTACCCATATCTCAC 57.306 37.037 0.00 0.00 0.00 3.51
4107 4146 8.716646 TTTGATATACTGTTGATGTACACCAG 57.283 34.615 0.00 4.97 43.23 4.00
4215 4254 4.654091 ATGGAGTGAACAAACAACCAAG 57.346 40.909 0.00 0.00 34.37 3.61
4367 4406 2.747446 AGCTAACAAGGCAACATTACCG 59.253 45.455 0.00 0.00 41.41 4.02
4408 4447 7.589574 TTTCAAAGGTGAACTTGCTTTTTAC 57.410 32.000 0.00 0.00 43.52 2.01
4449 4488 5.730550 TGGTGTGTTCCTGATAACTATGAC 58.269 41.667 0.00 0.00 0.00 3.06
4468 4507 4.571919 TGACGGTTCCAAGTTAACCATAG 58.428 43.478 0.88 0.00 45.59 2.23
4516 4555 6.183309 AGTTGAACAGAAACTGACAACTTC 57.817 37.500 24.88 13.20 46.78 3.01
4519 4558 6.182039 TGAACAGAAACTGACAACTTCAAG 57.818 37.500 5.76 0.00 35.18 3.02
4520 4559 4.622701 ACAGAAACTGACAACTTCAAGC 57.377 40.909 5.76 0.00 35.18 4.01
4521 4560 4.265073 ACAGAAACTGACAACTTCAAGCT 58.735 39.130 5.76 0.00 35.18 3.74
4522 4561 4.702131 ACAGAAACTGACAACTTCAAGCTT 59.298 37.500 5.76 0.00 35.18 3.74
4523 4562 5.163713 ACAGAAACTGACAACTTCAAGCTTC 60.164 40.000 0.00 0.00 35.18 3.86
4603 4643 9.376075 AGCTATTGTAGTATGATTATGTCATGC 57.624 33.333 0.00 4.80 46.85 4.06
4619 4659 1.625818 CATGCCTATGACCCTAGGGAC 59.374 57.143 35.38 28.30 41.39 4.46
4748 4788 4.230502 AGTGGAAGTGGGATAAACATGGAT 59.769 41.667 0.00 0.00 0.00 3.41
4809 4849 8.051535 AGTTCAACAGGATGAATCTAATGATGT 58.948 33.333 0.00 0.00 41.09 3.06
4885 4925 7.027874 TCCAAAATATACAGGTGGAAACTCT 57.972 36.000 0.00 0.00 35.45 3.24
5006 5175 6.147864 TGAATTGTTCTTGGAGTTGAAAGG 57.852 37.500 0.00 0.00 0.00 3.11
5076 5245 6.017109 GTCCTTCAAGTAAAGTGAATCAGCAA 60.017 38.462 0.00 0.00 34.59 3.91
5096 5265 9.120538 TCAGCAACAATAAACTCTTCTTTAAGT 57.879 29.630 0.00 0.00 34.13 2.24
5221 5390 8.578308 TGCATGTAATCTTTTTCTGAACAAAG 57.422 30.769 13.87 13.87 0.00 2.77
5233 5402 8.610248 TTTTCTGAACAAAGTACCAATCGATA 57.390 30.769 0.00 0.00 0.00 2.92
5382 5552 2.816087 CTGACCATGCAAAAGTAGCAGT 59.184 45.455 0.00 0.00 46.36 4.40
5505 5675 8.260818 TCATTTTGGTCCAAGTCAACAAAATAA 58.739 29.630 4.09 0.00 44.95 1.40
5839 6009 6.037172 CACTTTTCCTCATAACAGATAACGGG 59.963 42.308 0.00 0.00 0.00 5.28
5860 6030 8.502105 ACGGGTTAACTTTGGAATATCTAAAG 57.498 34.615 12.78 12.78 46.34 1.85
5899 6069 5.049818 GCTATGGCTAAGACATGAACACATC 60.050 44.000 0.00 0.00 31.56 3.06
6162 6332 3.921677 TCACGGTAGAAGTCCAAACATC 58.078 45.455 0.00 0.00 0.00 3.06
6202 6372 3.449746 TTGTCTTGTTATGGAAGGGGG 57.550 47.619 0.00 0.00 0.00 5.40
6216 6386 2.445155 GGGGGCCTTGTGACCATT 59.555 61.111 0.84 0.00 0.00 3.16
6269 6447 6.576442 GCCTCTTACAGAAATGTAGGGAAAGA 60.576 42.308 0.00 0.00 0.00 2.52
6290 6468 2.616842 ACTGCGTACAAAAGACCCAAAG 59.383 45.455 0.00 0.00 0.00 2.77
6313 6491 4.735599 GGACCCTTCCCCGGACCT 62.736 72.222 0.73 0.00 35.57 3.85
6314 6492 2.365764 GACCCTTCCCCGGACCTA 59.634 66.667 0.73 0.00 0.00 3.08
6346 6524 3.296709 CTACGTGCACCGGGCTTCT 62.297 63.158 12.15 0.00 45.15 2.85
6357 6535 0.035056 CGGGCTTCTGGGATTGTCTT 60.035 55.000 0.00 0.00 0.00 3.01
6358 6536 1.209504 CGGGCTTCTGGGATTGTCTTA 59.790 52.381 0.00 0.00 0.00 2.10
6404 6582 6.470235 GTGCACTTTCATACAAGATATTGCAC 59.530 38.462 10.32 11.59 43.16 4.57
6484 6663 0.174845 CAAAGTCCCGCGTATCTCCA 59.825 55.000 4.92 0.00 0.00 3.86
6485 6664 0.899720 AAAGTCCCGCGTATCTCCAA 59.100 50.000 4.92 0.00 0.00 3.53
6489 6668 2.093128 AGTCCCGCGTATCTCCAAAAAT 60.093 45.455 4.92 0.00 0.00 1.82
6498 6680 6.378582 GCGTATCTCCAAAAATGAAAAGACA 58.621 36.000 0.00 0.00 0.00 3.41
6516 6698 0.172578 CACTGCATGGCAATGACCAG 59.827 55.000 4.87 6.21 44.71 4.00
6543 6726 8.296713 TGAGCAATAGTTTTTCTGTTTCCATAC 58.703 33.333 0.00 0.00 0.00 2.39
6546 6729 7.806014 GCAATAGTTTTTCTGTTTCCATACGAA 59.194 33.333 0.00 0.00 0.00 3.85
6614 6801 6.018669 GCATGCATTAACCTAGAGTACAGAAC 60.019 42.308 14.21 0.00 0.00 3.01
6785 6973 5.316987 GGCAATTACTTGGTAGATATGGCT 58.683 41.667 0.00 0.00 32.72 4.75
6786 6974 5.182001 GGCAATTACTTGGTAGATATGGCTG 59.818 44.000 0.00 0.00 32.72 4.85
6802 6990 8.571336 AGATATGGCTGATGCAATAGTTTTAAC 58.429 33.333 0.00 0.00 38.38 2.01
6803 6991 5.973899 TGGCTGATGCAATAGTTTTAACA 57.026 34.783 0.00 0.00 41.91 2.41
6804 6992 5.708948 TGGCTGATGCAATAGTTTTAACAC 58.291 37.500 0.00 0.00 41.91 3.32
6982 7172 7.399674 AAAAGGAGGAGGCTAATGATTATCT 57.600 36.000 0.00 0.00 0.00 1.98
7041 7233 6.644592 GTGCTCTGCTCTCAATATAGTTTAGG 59.355 42.308 0.00 0.00 0.00 2.69
7384 7579 2.360980 CCTCTCTCCCTCACCGGT 59.639 66.667 0.00 0.00 0.00 5.28
7736 7931 2.215478 CTGCGACGAAAAGGTCAGCG 62.215 60.000 0.00 0.00 38.43 5.18
7738 7933 2.470286 GACGAAAAGGTCAGCGCG 59.530 61.111 0.00 0.00 36.91 6.86
7762 7957 2.589157 CCAACACCTCGGCACCCTA 61.589 63.158 0.00 0.00 0.00 3.53
7765 7960 1.412453 AACACCTCGGCACCCTACAA 61.412 55.000 0.00 0.00 0.00 2.41
7786 7981 3.027170 GACTGCGGCGGTGTCATTG 62.027 63.158 20.97 0.00 0.00 2.82
7808 8003 1.400846 CGTCCTCTTCGCTTGCTACTA 59.599 52.381 0.00 0.00 0.00 1.82
7809 8004 2.791849 CGTCCTCTTCGCTTGCTACTAC 60.792 54.545 0.00 0.00 0.00 2.73
7811 8006 3.626670 GTCCTCTTCGCTTGCTACTACTA 59.373 47.826 0.00 0.00 0.00 1.82
7812 8007 3.626670 TCCTCTTCGCTTGCTACTACTAC 59.373 47.826 0.00 0.00 0.00 2.73
7813 8008 3.628487 CCTCTTCGCTTGCTACTACTACT 59.372 47.826 0.00 0.00 0.00 2.57
7814 8009 4.815308 CCTCTTCGCTTGCTACTACTACTA 59.185 45.833 0.00 0.00 0.00 1.82
7815 8010 5.277442 CCTCTTCGCTTGCTACTACTACTAC 60.277 48.000 0.00 0.00 0.00 2.73
7816 8011 5.426504 TCTTCGCTTGCTACTACTACTACT 58.573 41.667 0.00 0.00 0.00 2.57
7819 8014 6.595772 TCGCTTGCTACTACTACTACTTAC 57.404 41.667 0.00 0.00 0.00 2.34
7945 8140 2.818274 GACGGCCGGGTAAGCAAG 60.818 66.667 31.76 0.00 0.00 4.01
8278 8475 2.159327 GTGGCTAACGTACACCTTGT 57.841 50.000 0.00 0.00 0.00 3.16
8314 8675 6.740110 CAGAGGCTACCTATGTAGTACAAAG 58.260 44.000 7.16 1.75 45.24 2.77
8319 8680 6.103997 GCTACCTATGTAGTACAAAGCACAA 58.896 40.000 7.16 0.00 45.24 3.33
8324 8685 8.974238 ACCTATGTAGTACAAAGCACAATAGTA 58.026 33.333 7.16 0.00 0.00 1.82
8325 8686 9.245962 CCTATGTAGTACAAAGCACAATAGTAC 57.754 37.037 7.16 0.00 36.26 2.73
8361 8722 2.515854 TGTACATCTCTAGCGGATCCC 58.484 52.381 6.06 0.00 0.00 3.85
8389 8750 2.375146 GGGCCATCCGACAAAATAACT 58.625 47.619 4.39 0.00 0.00 2.24
8404 8775 4.933505 AATAACTAGGACGGAGGCTAAC 57.066 45.455 0.00 0.00 0.00 2.34
8420 8791 0.887387 TAACTTGCCGGCTGGAACAC 60.887 55.000 29.70 0.00 37.49 3.32
8438 8813 6.287107 GAACACATCCAGTATATTTGTCCG 57.713 41.667 0.00 0.00 0.00 4.79
8440 8815 4.407621 ACACATCCAGTATATTTGTCCGGA 59.592 41.667 0.00 0.00 0.00 5.14
8441 8816 5.071788 ACACATCCAGTATATTTGTCCGGAT 59.928 40.000 7.81 0.00 31.99 4.18
8444 8819 6.486657 ACATCCAGTATATTTGTCCGGATTTG 59.513 38.462 7.81 0.00 29.34 2.32
8448 8823 7.394923 TCCAGTATATTTGTCCGGATTTGTTTT 59.605 33.333 7.81 0.00 0.00 2.43
8471 8846 2.075355 ATCCTTCAAACCACGGCCCA 62.075 55.000 0.00 0.00 0.00 5.36
8575 8952 3.727258 CCGCCATGGTCTTCCCCA 61.727 66.667 14.67 0.00 39.27 4.96
8576 8953 2.597340 CGCCATGGTCTTCCCCAT 59.403 61.111 14.67 0.00 46.28 4.00
8624 9001 2.589157 CGGCCACCACCAGACCTTA 61.589 63.158 2.24 0.00 0.00 2.69
8625 9002 1.299976 GGCCACCACCAGACCTTAG 59.700 63.158 0.00 0.00 0.00 2.18
8626 9003 1.198759 GGCCACCACCAGACCTTAGA 61.199 60.000 0.00 0.00 0.00 2.10
8627 9004 0.912486 GCCACCACCAGACCTTAGAT 59.088 55.000 0.00 0.00 0.00 1.98
8628 9005 1.407437 GCCACCACCAGACCTTAGATG 60.407 57.143 0.00 0.00 0.00 2.90
8629 9006 1.407437 CCACCACCAGACCTTAGATGC 60.407 57.143 0.00 0.00 0.00 3.91
8630 9007 0.912486 ACCACCAGACCTTAGATGCC 59.088 55.000 0.00 0.00 0.00 4.40
8631 9008 1.207791 CCACCAGACCTTAGATGCCT 58.792 55.000 0.00 0.00 0.00 4.75
8632 9009 1.139853 CCACCAGACCTTAGATGCCTC 59.860 57.143 0.00 0.00 0.00 4.70
8633 9010 1.139853 CACCAGACCTTAGATGCCTCC 59.860 57.143 0.00 0.00 0.00 4.30
8634 9011 1.273838 ACCAGACCTTAGATGCCTCCA 60.274 52.381 0.00 0.00 0.00 3.86
8635 9012 1.139853 CCAGACCTTAGATGCCTCCAC 59.860 57.143 0.00 0.00 0.00 4.02
8636 9013 1.115467 AGACCTTAGATGCCTCCACG 58.885 55.000 0.00 0.00 0.00 4.94
8637 9014 0.530870 GACCTTAGATGCCTCCACGC 60.531 60.000 0.00 0.00 0.00 5.34
8638 9015 1.592669 CCTTAGATGCCTCCACGCG 60.593 63.158 3.53 3.53 0.00 6.01
8717 9109 2.781300 GCTAGTTGCTGCTGCGTC 59.219 61.111 11.21 6.42 43.34 5.19
8718 9110 1.739562 GCTAGTTGCTGCTGCGTCT 60.740 57.895 11.21 13.05 43.34 4.18
8719 9111 1.691215 GCTAGTTGCTGCTGCGTCTC 61.691 60.000 11.21 1.61 43.34 3.36
8720 9112 0.108898 CTAGTTGCTGCTGCGTCTCT 60.109 55.000 11.21 8.55 43.34 3.10
8721 9113 0.109086 TAGTTGCTGCTGCGTCTCTC 60.109 55.000 11.21 0.00 43.34 3.20
8722 9114 2.431430 TTGCTGCTGCGTCTCTCG 60.431 61.111 11.21 0.00 43.34 4.04
8790 9182 1.185618 TGCTGCTTACTCCTCGTGGT 61.186 55.000 2.99 0.00 34.23 4.16
8882 9274 4.314440 AGCTCGTTCGCCCAAGCA 62.314 61.111 6.44 0.00 39.83 3.91
8901 9293 4.925861 GGAGGGGATGCAGCGAGC 62.926 72.222 0.00 0.00 45.96 5.03
8926 9318 7.147915 GCAAGATGGACCCAATTGTAATTTAGA 60.148 37.037 4.43 0.00 32.66 2.10
8954 9347 2.611225 TTTGGTGGGTTTGTGCAATC 57.389 45.000 0.00 0.00 0.00 2.67
8981 9374 3.506067 CGGGGCCATGAAATATTCTTACC 59.494 47.826 4.39 0.00 0.00 2.85
8982 9375 4.479158 GGGGCCATGAAATATTCTTACCA 58.521 43.478 4.39 0.00 0.00 3.25
8992 9385 8.964476 TGAAATATTCTTACCAGATCTGTTCC 57.036 34.615 21.11 0.00 0.00 3.62
9051 9444 4.999311 GGTATCCTGTAAACCGACTTTTGT 59.001 41.667 0.00 0.00 0.00 2.83
9061 9454 0.240945 CGACTTTTGTGGGATGGTGC 59.759 55.000 0.00 0.00 0.00 5.01
9109 9502 1.597854 CAGCTGACGCCAAACCAGA 60.598 57.895 8.42 0.00 36.60 3.86
9116 9509 0.823356 ACGCCAAACCAGACAATGCT 60.823 50.000 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 2.104451 TGTCCATTTGCAACTTGCCAAT 59.896 40.909 11.29 9.06 44.23 3.16
57 58 1.117994 TGTCCATTTGCAACTTGCCA 58.882 45.000 11.29 0.00 44.23 4.92
139 140 4.344102 TGGATGGAATAAAGCTAGTACGCT 59.656 41.667 0.00 0.00 43.31 5.07
171 176 5.535333 AGCTTTGTGGAATCTGATGTTTTG 58.465 37.500 0.00 0.00 0.00 2.44
192 197 6.913170 TCTTGAATGTTTCTATTGGACAAGC 58.087 36.000 0.00 0.00 34.31 4.01
296 301 0.038343 CCCCCACACATTTTTCAGCG 60.038 55.000 0.00 0.00 0.00 5.18
874 879 6.874288 GCATCATGAGCCTTTTATCTAAGT 57.126 37.500 0.09 0.00 0.00 2.24
913 919 1.360911 GCGATCCTCGGAGAAGACC 59.639 63.158 6.58 0.00 40.84 3.85
938 944 2.176798 AGAGCCTGTCCTCTATAGCTGT 59.823 50.000 0.00 0.00 40.30 4.40
1104 1110 2.297895 CCTCGGGTTGGGATGTGGA 61.298 63.158 0.00 0.00 0.00 4.02
1133 1139 6.467723 ACTTATGTGTCTTCTGCTTAAACG 57.532 37.500 0.00 0.00 0.00 3.60
1150 1156 5.174037 TCCTGGTACTCCCAAAACTTATG 57.826 43.478 0.00 0.00 44.65 1.90
1254 1260 3.540314 TTGCTTTGTGGTTGCTTGATT 57.460 38.095 0.00 0.00 0.00 2.57
1267 1273 1.559149 GCACGGCCATGTTTGCTTTG 61.559 55.000 2.24 0.00 32.00 2.77
1291 1297 5.530915 CAGTATCCTTCTCTTGACTCGAGAT 59.469 44.000 21.68 2.93 37.37 2.75
1321 1327 3.652057 TCTTTTCCTTATGGGCAGGAG 57.348 47.619 0.00 0.00 41.66 3.69
1512 1518 1.745264 GAGGATTCCAGCCTCGGAG 59.255 63.158 5.29 0.00 42.22 4.63
1633 1639 2.393271 AGGGTGATCTTTGCGAGAAG 57.607 50.000 0.00 0.00 38.06 2.85
1634 1640 2.426522 CAAGGGTGATCTTTGCGAGAA 58.573 47.619 0.00 0.00 38.06 2.87
1721 1727 3.322828 TCGGGCATAAAGTATCACCTACC 59.677 47.826 0.00 0.00 0.00 3.18
1942 1952 6.475402 GGTTTTGTTTCGAATGACACAATCTT 59.525 34.615 12.53 0.00 42.57 2.40
1967 1977 8.301720 TGGTTGTACTAAAGTCACTACATACAG 58.698 37.037 0.00 0.00 0.00 2.74
2002 2013 4.560128 TCCTCTGTCTTTTCTCAACATCG 58.440 43.478 0.00 0.00 0.00 3.84
2021 2032 4.805140 TCACTCTCCATGACTATCTCCT 57.195 45.455 0.00 0.00 0.00 3.69
2117 2128 5.859205 ATTAATTTCCTCCATTGCTCCAC 57.141 39.130 0.00 0.00 0.00 4.02
2149 2160 4.917385 TCTGGACATTGCTTTAGCCTTAA 58.083 39.130 0.00 0.00 41.18 1.85
2160 2171 6.089820 CACATTACACAAATTCTGGACATTGC 59.910 38.462 0.00 0.00 0.00 3.56
2161 2172 7.147312 ACACATTACACAAATTCTGGACATTG 58.853 34.615 0.00 0.00 0.00 2.82
2198 2209 7.013559 CAGTCTAATCATAATTCCATTGGTGCA 59.986 37.037 1.86 0.00 0.00 4.57
2240 2252 8.432805 AGAATGACCTGAAGTCTTTTTAGAAGA 58.567 33.333 0.00 0.00 46.46 2.87
2305 2317 5.743872 TGAGTTCATTCTGAATCGTATCACG 59.256 40.000 0.00 0.00 38.79 4.35
2328 2340 3.887110 TGCTTTGCTGGATAGGATTGATG 59.113 43.478 0.00 0.00 0.00 3.07
2332 2344 5.573380 TCTATGCTTTGCTGGATAGGATT 57.427 39.130 0.00 0.00 38.41 3.01
2353 2365 8.855279 GTCTATTTCACTTGACGATATAGCATC 58.145 37.037 0.00 0.00 29.54 3.91
2356 2368 8.804688 AAGTCTATTTCACTTGACGATATAGC 57.195 34.615 0.00 0.00 32.65 2.97
2389 2401 6.580791 GCGACTAATTTGTTTGCAACTGAATA 59.419 34.615 0.00 0.00 33.82 1.75
2420 2432 2.943449 AAACCGAAAACCGAAAAGCA 57.057 40.000 0.00 0.00 41.76 3.91
2428 2440 3.131577 ACAAGAGGGAAAAACCGAAAACC 59.868 43.478 0.00 0.00 40.11 3.27
2508 2520 5.269505 AGAGTGAAAGCATAATAGCGACT 57.730 39.130 0.00 0.00 40.15 4.18
2509 2521 7.644986 ATTAGAGTGAAAGCATAATAGCGAC 57.355 36.000 0.00 0.00 40.15 5.19
2511 2523 8.749841 ACTATTAGAGTGAAAGCATAATAGCG 57.250 34.615 9.19 0.00 38.86 4.26
2626 2638 3.753294 TTGTGTCTTCTCTCCAAGGTC 57.247 47.619 0.00 0.00 0.00 3.85
2824 2836 2.040178 AGGGACCCATTCGTGATAGAC 58.960 52.381 14.60 0.00 0.00 2.59
2846 2858 2.545946 GCTGAAGTTCTGTGACCTCAAC 59.454 50.000 10.96 0.00 0.00 3.18
2881 2893 3.188048 GGATGAAGTTGAGTTGTGCTGAG 59.812 47.826 0.00 0.00 0.00 3.35
2909 2921 9.177608 AGTTTTGAGCAAGATATTACAAGCATA 57.822 29.630 0.00 0.00 0.00 3.14
2934 2946 8.807581 GTTTCTTTTCTGTGGTTTACATTTGAG 58.192 33.333 0.00 0.00 38.92 3.02
2940 2952 5.017490 TGGGTTTCTTTTCTGTGGTTTACA 58.983 37.500 0.00 0.00 37.78 2.41
3034 3046 9.133627 CGTCTTCACCAGATTATCTACATATTG 57.866 37.037 0.00 0.00 32.60 1.90
3103 3116 8.908903 TGATTTTTGTGTGTAAATACCACTTCT 58.091 29.630 11.08 0.00 32.36 2.85
3152 3165 1.873591 GGGTCCAGCACATAAATAGCG 59.126 52.381 0.00 0.00 0.00 4.26
3154 3167 3.884895 TGTGGGTCCAGCACATAAATAG 58.115 45.455 0.00 0.00 30.45 1.73
3210 3223 9.609950 GACTCACAGTATTATAATAGGAACGTC 57.390 37.037 5.39 5.54 0.00 4.34
3211 3224 9.128404 TGACTCACAGTATTATAATAGGAACGT 57.872 33.333 5.39 0.40 0.00 3.99
3212 3225 9.395707 GTGACTCACAGTATTATAATAGGAACG 57.604 37.037 5.39 0.00 34.08 3.95
3229 3242 5.084519 AGACCTTTATACCTGTGACTCACA 58.915 41.667 11.44 11.44 42.45 3.58
3230 3243 5.662674 AGACCTTTATACCTGTGACTCAC 57.337 43.478 1.86 1.86 34.56 3.51
3231 3244 6.377429 CAGTAGACCTTTATACCTGTGACTCA 59.623 42.308 0.00 0.00 0.00 3.41
3250 3285 1.416030 TGCAACCTGCTTGACAGTAGA 59.584 47.619 0.00 0.00 45.68 2.59
3271 3306 5.912892 AGCAGAGAAGTAAATAGAAGAGGC 58.087 41.667 0.00 0.00 0.00 4.70
3330 3365 3.896888 ACACACATTATTGGCCCCATATG 59.103 43.478 0.00 1.62 0.00 1.78
3344 3379 8.579850 ACATAACTAATGATGGAACACACATT 57.420 30.769 0.00 0.00 45.29 2.71
3459 3496 4.728772 CCCTTTATTCTACCATGCCATCA 58.271 43.478 0.00 0.00 0.00 3.07
3515 3552 6.876257 ACTTCAAAAACACTGTTGGCATTTTA 59.124 30.769 0.00 0.00 0.00 1.52
3607 3644 9.630098 AATAAGTTGCAAATAGTGTGATTTCTG 57.370 29.630 0.00 0.00 0.00 3.02
3631 3668 7.573710 TGAAGCCATGGTAGTAGTGATAAAAT 58.426 34.615 14.67 0.00 0.00 1.82
3665 3702 3.628942 TGCATCAGTAGCATTCAACCATC 59.371 43.478 0.00 0.00 37.02 3.51
3712 3749 9.306777 GATATATATGATACATCTGCTCCTGGA 57.693 37.037 0.00 0.00 0.00 3.86
3741 3778 2.352421 CCTGGTCTTGCATTTTCAGCAG 60.352 50.000 0.00 0.00 43.75 4.24
3826 3863 3.181430 GGTAGGTTGAAAAGGTACCCCAA 60.181 47.826 8.74 5.45 31.88 4.12
3867 3906 4.153835 GGAGCAAATTGAGACTTCACTGAG 59.846 45.833 0.00 0.00 31.71 3.35
3870 3909 4.363991 AGGAGCAAATTGAGACTTCACT 57.636 40.909 0.00 0.00 31.71 3.41
3954 3993 9.429109 TGAGATATGGGTAGAAACTATGTTACA 57.571 33.333 0.00 0.00 0.00 2.41
3981 4020 7.438459 CCTCCTAGTTATGTTTAATGGAACGAG 59.562 40.741 0.00 0.00 32.18 4.18
4100 4139 2.261729 TCCCATGTTAGCACTGGTGTA 58.738 47.619 2.64 0.00 0.00 2.90
4107 4146 3.885297 ACTGCATTATCCCATGTTAGCAC 59.115 43.478 0.00 0.00 0.00 4.40
4215 4254 2.126467 GATGAGCTCAGCGAGACATTC 58.874 52.381 22.96 7.48 32.22 2.67
4326 4365 5.667466 AGCTTTGATCCAGCAATAAATTGG 58.333 37.500 14.67 0.00 39.99 3.16
4399 4438 4.920640 TGTTCCCAAATCGTAAAAAGCA 57.079 36.364 0.00 0.00 0.00 3.91
4408 4447 6.039270 ACACACCATATATTGTTCCCAAATCG 59.961 38.462 0.00 0.00 33.44 3.34
4468 4507 2.749076 TGGATGATACTTGTTGCACTGC 59.251 45.455 0.00 0.00 0.00 4.40
4508 4547 3.743396 AGTCGATGAAGCTTGAAGTTGTC 59.257 43.478 2.10 0.00 0.00 3.18
4603 4643 2.447429 TCAGAGTCCCTAGGGTCATAGG 59.553 54.545 27.58 13.65 41.85 2.57
4899 4939 8.675705 TCAGTCACAAAAGAATAAAGATGTCA 57.324 30.769 0.00 0.00 0.00 3.58
4981 5150 6.476706 CCTTTCAACTCCAAGAACAATTCAAC 59.523 38.462 0.00 0.00 0.00 3.18
5096 5265 1.337384 ACCTGAGTGCGGCATATGGA 61.337 55.000 5.72 0.00 0.00 3.41
5221 5390 9.740239 TGTAGTAAGAATTGTATCGATTGGTAC 57.260 33.333 1.71 0.00 0.00 3.34
5257 5427 9.106070 GTCAACTTAGTTTCTTCTTGGAACTTA 57.894 33.333 0.00 0.00 0.00 2.24
5382 5552 5.708697 TGAATCTGTAGACCTCGAACACTTA 59.291 40.000 0.00 0.00 0.00 2.24
5505 5675 4.892934 TGTTTGGCACTTTCCTTCTTATGT 59.107 37.500 0.00 0.00 0.00 2.29
5722 5892 5.718146 TCAGTTTCATCACTCTCATGACTC 58.282 41.667 0.00 0.00 29.70 3.36
5860 6030 2.159198 CCATAGCCAAACACCATTGCTC 60.159 50.000 0.00 0.00 0.00 4.26
5899 6069 1.003580 AGTGTACCCTTCATGCCTGTG 59.996 52.381 0.00 0.00 0.00 3.66
6023 6193 0.955919 GCAACCTGTCTTCCCTTCCG 60.956 60.000 0.00 0.00 0.00 4.30
6202 6372 3.978876 ACCTAATGGTCACAAGGCC 57.021 52.632 0.00 0.00 44.78 5.19
6216 6386 1.006758 AGGACTCGAACCCATGACCTA 59.993 52.381 0.00 0.00 0.00 3.08
6290 6468 3.714001 GGGGAAGGGTCCGACCAC 61.714 72.222 19.43 8.70 46.04 4.16
6313 6491 3.144871 TAGCTCCCGCTTGCGCTA 61.145 61.111 9.73 0.00 46.47 4.26
6314 6492 4.821589 GTAGCTCCCGCTTGCGCT 62.822 66.667 9.73 3.88 46.47 5.92
6404 6582 6.015688 AGGTGCATGCATTTAATCTTGGATAG 60.016 38.462 25.64 0.00 0.00 2.08
6457 6636 2.359975 CGGGACTTTGGGCAGGAC 60.360 66.667 0.00 0.00 0.00 3.85
6484 6663 4.512571 GCCATGCAGTGTCTTTTCATTTTT 59.487 37.500 0.00 0.00 0.00 1.94
6485 6664 4.060205 GCCATGCAGTGTCTTTTCATTTT 58.940 39.130 0.00 0.00 0.00 1.82
6489 6668 1.689984 TGCCATGCAGTGTCTTTTCA 58.310 45.000 0.00 0.00 33.32 2.69
6498 6680 0.251474 ACTGGTCATTGCCATGCAGT 60.251 50.000 5.54 5.54 40.61 4.40
6516 6698 6.503524 TGGAAACAGAAAAACTATTGCTCAC 58.496 36.000 0.00 0.00 35.01 3.51
6543 6726 8.955061 TTGAGCAGAAGATTCTTAATTTTTCG 57.045 30.769 0.00 0.00 34.74 3.46
6553 6736 7.571919 TGGAATTATCTTGAGCAGAAGATTCT 58.428 34.615 13.62 0.00 41.82 2.40
6563 6746 8.534333 TTCGTATACATGGAATTATCTTGAGC 57.466 34.615 3.32 0.00 0.00 4.26
6761 6948 4.154195 GCCATATCTACCAAGTAATTGCCG 59.846 45.833 0.00 0.00 0.00 5.69
6762 6949 5.182001 CAGCCATATCTACCAAGTAATTGCC 59.818 44.000 0.00 0.00 0.00 4.52
6785 6973 9.190858 GATTTGTGTGTTAAAACTATTGCATCA 57.809 29.630 0.00 0.00 0.00 3.07
6786 6974 9.190858 TGATTTGTGTGTTAAAACTATTGCATC 57.809 29.630 0.00 0.00 0.00 3.91
6802 6990 5.723492 TTGAGATATCGCTGATTTGTGTG 57.277 39.130 8.00 0.00 0.00 3.82
6803 6991 6.372659 ACTTTTGAGATATCGCTGATTTGTGT 59.627 34.615 8.00 0.00 0.00 3.72
6804 6992 6.685828 CACTTTTGAGATATCGCTGATTTGTG 59.314 38.462 8.00 5.96 0.00 3.33
7092 7285 7.859325 TTAAGACAAGTCAAAGCAACTTAGT 57.141 32.000 2.72 0.00 35.25 2.24
7097 7290 9.730420 TCTATTTTTAAGACAAGTCAAAGCAAC 57.270 29.630 2.72 0.00 0.00 4.17
7099 7292 9.950680 CTTCTATTTTTAAGACAAGTCAAAGCA 57.049 29.630 2.72 0.00 0.00 3.91
7100 7293 9.952188 ACTTCTATTTTTAAGACAAGTCAAAGC 57.048 29.630 2.72 0.00 0.00 3.51
7128 7323 3.454082 TGCCACCTGAAAAGGTTTGAAAT 59.546 39.130 0.00 0.00 40.85 2.17
7132 7327 3.132925 CAATGCCACCTGAAAAGGTTTG 58.867 45.455 0.00 0.00 40.85 2.93
7265 7460 8.983789 TGTAATTCTGTTATACTGGTACATCCA 58.016 33.333 0.00 0.00 45.01 3.41
7358 7553 2.829458 GGAGAGAGGGGACGGTCG 60.829 72.222 1.43 0.00 0.00 4.79
7360 7555 2.947785 AGGGAGAGAGGGGACGGT 60.948 66.667 0.00 0.00 0.00 4.83
7384 7579 3.879295 GCTCGGAAATCATGAAGATGGAA 59.121 43.478 0.00 0.00 36.96 3.53
7736 7931 2.335011 GAGGTGTTGGTTTGCCGC 59.665 61.111 0.00 0.00 37.67 6.53
7738 7933 3.039134 CCGAGGTGTTGGTTTGCC 58.961 61.111 0.00 0.00 0.00 4.52
7762 7957 4.235762 ACCGCCGCAGTCAGTTGT 62.236 61.111 0.00 0.00 0.00 3.32
7765 7960 4.664677 GACACCGCCGCAGTCAGT 62.665 66.667 2.86 0.00 32.68 3.41
7786 7981 0.170561 TAGCAAGCGAAGAGGACGAC 59.829 55.000 0.00 0.00 0.00 4.34
7811 8006 7.068716 CCCCGTTACCAATTACTAGTAAGTAGT 59.931 40.741 19.58 17.81 44.69 2.73
7812 8007 7.068716 ACCCCGTTACCAATTACTAGTAAGTAG 59.931 40.741 19.58 13.21 39.36 2.57
7813 8008 6.895204 ACCCCGTTACCAATTACTAGTAAGTA 59.105 38.462 19.58 13.48 37.15 2.24
7814 8009 5.721480 ACCCCGTTACCAATTACTAGTAAGT 59.279 40.000 19.58 14.95 39.91 2.24
7815 8010 6.225981 ACCCCGTTACCAATTACTAGTAAG 57.774 41.667 19.58 9.62 0.00 2.34
7816 8011 5.163561 CGACCCCGTTACCAATTACTAGTAA 60.164 44.000 17.41 17.41 0.00 2.24
7819 8014 3.709987 CGACCCCGTTACCAATTACTAG 58.290 50.000 0.00 0.00 0.00 2.57
7945 8140 2.032681 ACCGTGAGCCTTGCCTTC 59.967 61.111 0.00 0.00 0.00 3.46
8199 8394 2.035617 ATCTTGCGCGTATGCCGTTG 62.036 55.000 8.43 0.00 39.32 4.10
8239 8434 5.589192 CCACGACTAATCAGGTAGGTAAAG 58.411 45.833 0.00 0.00 0.00 1.85
8314 8675 5.779806 AACTTGATCACGTACTATTGTGC 57.220 39.130 5.13 0.00 36.06 4.57
8319 8680 9.136952 GTACAAGAAAACTTGATCACGTACTAT 57.863 33.333 15.32 2.13 37.72 2.12
8324 8685 6.706270 AGATGTACAAGAAAACTTGATCACGT 59.294 34.615 15.32 0.00 37.72 4.49
8325 8686 7.116948 AGAGATGTACAAGAAAACTTGATCACG 59.883 37.037 15.32 0.00 37.72 4.35
8344 8705 2.647356 CGGGATCCGCTAGAGATGT 58.353 57.895 5.45 0.00 41.17 3.06
8389 8750 0.822164 GCAAGTTAGCCTCCGTCCTA 59.178 55.000 0.00 0.00 0.00 2.94
8404 8775 1.926511 GATGTGTTCCAGCCGGCAAG 61.927 60.000 31.54 20.72 0.00 4.01
8420 8791 6.486657 ACAAATCCGGACAAATATACTGGATG 59.513 38.462 6.12 0.00 45.50 3.51
8438 8813 5.482163 TTGAAGGATCCCAAAACAAATCC 57.518 39.130 8.55 0.00 38.37 3.01
8440 8815 5.131809 TGGTTTGAAGGATCCCAAAACAAAT 59.868 36.000 23.92 0.00 44.15 2.32
8441 8816 4.471386 TGGTTTGAAGGATCCCAAAACAAA 59.529 37.500 23.92 17.85 44.15 2.83
8444 8819 3.552068 CGTGGTTTGAAGGATCCCAAAAC 60.552 47.826 19.26 19.26 39.64 2.43
8448 8823 0.037590 CCGTGGTTTGAAGGATCCCA 59.962 55.000 8.55 0.00 0.00 4.37
8617 8994 1.115467 CGTGGAGGCATCTAAGGTCT 58.885 55.000 0.00 0.00 0.00 3.85
8622 8999 1.437573 CTCGCGTGGAGGCATCTAA 59.562 57.895 5.77 0.00 39.22 2.10
8624 9001 4.521062 GCTCGCGTGGAGGCATCT 62.521 66.667 5.77 0.00 43.36 2.90
8625 9002 4.521062 AGCTCGCGTGGAGGCATC 62.521 66.667 5.77 0.00 43.36 3.91
8626 9003 4.827087 CAGCTCGCGTGGAGGCAT 62.827 66.667 5.77 0.00 43.36 4.40
8700 9092 1.691215 GAGACGCAGCAGCAACTAGC 61.691 60.000 0.82 0.00 42.27 3.42
8701 9093 0.108898 AGAGACGCAGCAGCAACTAG 60.109 55.000 0.82 0.00 42.27 2.57
8702 9094 0.109086 GAGAGACGCAGCAGCAACTA 60.109 55.000 0.82 0.00 42.27 2.24
8703 9095 1.373999 GAGAGACGCAGCAGCAACT 60.374 57.895 0.82 0.00 42.27 3.16
8704 9096 2.724708 CGAGAGACGCAGCAGCAAC 61.725 63.158 0.82 0.00 42.27 4.17
8705 9097 2.431430 CGAGAGACGCAGCAGCAA 60.431 61.111 0.82 0.00 42.27 3.91
8714 9106 2.052590 GCTAGCGAGCGAGAGACG 60.053 66.667 2.13 0.00 39.39 4.18
8769 9161 0.244994 CACGAGGAGTAAGCAGCAGT 59.755 55.000 0.00 0.00 0.00 4.40
8770 9162 0.459237 CCACGAGGAGTAAGCAGCAG 60.459 60.000 0.00 0.00 36.89 4.24
8771 9163 1.185618 ACCACGAGGAGTAAGCAGCA 61.186 55.000 5.68 0.00 38.69 4.41
8777 9169 2.872557 CGCGACCACGAGGAGTAA 59.127 61.111 5.68 0.00 42.66 2.24
8862 9254 3.626680 CTTGGGCGAACGAGCTCGA 62.627 63.158 40.58 15.39 41.40 4.04
8901 9293 8.292444 TCTAAATTACAATTGGGTCCATCTTG 57.708 34.615 10.83 9.76 0.00 3.02
8937 9330 1.411977 CAAGATTGCACAAACCCACCA 59.588 47.619 0.00 0.00 0.00 4.17
8954 9347 0.754957 TATTTCATGGCCCCGGCAAG 60.755 55.000 8.23 0.00 42.43 4.01
8963 9356 7.446625 ACAGATCTGGTAAGAATATTTCATGGC 59.553 37.037 26.08 0.00 35.59 4.40
8981 9374 1.227089 CTCCGGCGGAACAGATCTG 60.227 63.158 30.59 21.37 37.49 2.90
8982 9375 3.082579 GCTCCGGCGGAACAGATCT 62.083 63.158 30.59 0.00 0.00 2.75
8992 9385 0.373716 GTATGACTTTTGCTCCGGCG 59.626 55.000 0.00 0.00 42.25 6.46
9045 9438 2.166254 GGTATGCACCATCCCACAAAAG 59.834 50.000 0.00 0.00 45.04 2.27
9051 9444 1.059584 ATCCGGTATGCACCATCCCA 61.060 55.000 0.00 0.00 46.14 4.37
9061 9454 4.887748 ACATTTCTAGCAGATCCGGTATG 58.112 43.478 0.00 0.00 0.00 2.39
9105 9498 2.096069 CGTGAACAGAAGCATTGTCTGG 60.096 50.000 8.61 0.00 45.66 3.86
9109 9502 2.254546 TCCGTGAACAGAAGCATTGT 57.745 45.000 0.00 0.00 0.00 2.71
9116 9509 1.946984 ACCCCTATCCGTGAACAGAA 58.053 50.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.