Multiple sequence alignment - TraesCS6D01G250000

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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 TraesCS6D01G250000 chr6D 100.000 8584 0 0 1 8584 353345406 353353989 0.000000e+00 15852.0
1 TraesCS6D01G250000 chr6B 93.932 7515 283 74 540 7957 525118479 525111041 0.000000e+00 11191.0
2 TraesCS6D01G250000 chr6B 94.712 208 9 2 8378 8584 525110790 525110584 1.070000e-83 322.0
3 TraesCS6D01G250000 chr6B 95.139 144 4 2 8233 8376 525110960 525110820 3.120000e-54 224.0
4 TraesCS6D01G250000 chr6A 93.449 5511 217 49 2931 8378 489230506 489225077 0.000000e+00 8045.0
5 TraesCS6D01G250000 chr6A 93.982 2393 78 27 541 2887 489233044 489230672 0.000000e+00 3561.0
6 TraesCS6D01G250000 chr6A 97.585 207 5 0 8378 8584 489225049 489224843 1.060000e-93 355.0
7 TraesCS6D01G250000 chr5D 91.611 298 21 4 1 296 496975782 496976077 8.020000e-110 409.0
8 TraesCS6D01G250000 chr5D 94.030 67 3 1 2783 2849 546024161 546024096 5.480000e-17 100.0
9 TraesCS6D01G250000 chr2B 91.525 295 24 1 4664 4957 672635278 672635572 1.040000e-108 405.0
10 TraesCS6D01G250000 chr2B 80.732 410 77 2 7017 7425 746322465 746322873 1.390000e-82 318.0
11 TraesCS6D01G250000 chr2B 97.222 36 1 0 7922 7957 777643648 777643683 2.590000e-05 62.1
12 TraesCS6D01G250000 chr2B 97.143 35 1 0 7923 7957 311896397 311896363 9.310000e-05 60.2
13 TraesCS6D01G250000 chr7D 91.468 293 21 3 9 298 520799594 520799303 4.830000e-107 399.0
14 TraesCS6D01G250000 chr7D 90.785 293 24 3 6 296 33545014 33544723 1.040000e-103 388.0
15 TraesCS6D01G250000 chr7D 85.837 233 26 5 312 542 520799318 520799091 3.100000e-59 241.0
16 TraesCS6D01G250000 chr7D 88.571 70 8 0 4776 4845 298511406 298511475 1.540000e-12 86.1
17 TraesCS6D01G250000 chr3A 90.970 299 24 3 1 298 163452086 163452382 4.830000e-107 399.0
18 TraesCS6D01G250000 chr3A 88.018 217 16 8 312 525 1746818 1747027 1.850000e-61 248.0
19 TraesCS6D01G250000 chr3A 84.181 177 24 4 7204 7378 87782445 87782619 1.480000e-37 169.0
20 TraesCS6D01G250000 chr3D 90.492 305 24 3 1 301 151442103 151442406 1.740000e-106 398.0
21 TraesCS6D01G250000 chr3D 81.333 225 36 6 7204 7425 74451690 74451911 2.460000e-40 178.0
22 TraesCS6D01G250000 chr3D 94.872 39 1 1 3453 3491 545173800 545173837 9.310000e-05 60.2
23 TraesCS6D01G250000 chr2A 90.940 298 23 4 4 298 767584471 767584175 1.740000e-106 398.0
24 TraesCS6D01G250000 chr4D 81.356 531 58 17 1 525 93195092 93195587 2.250000e-105 394.0
25 TraesCS6D01G250000 chr2D 90.635 299 25 2 1 298 180494570 180494274 2.250000e-105 394.0
26 TraesCS6D01G250000 chr2D 89.967 299 26 3 3 298 197526437 197526140 4.860000e-102 383.0
27 TraesCS6D01G250000 chr2D 80.482 415 79 2 7012 7425 611898085 611898498 5.000000e-82 316.0
28 TraesCS6D01G250000 chr2D 97.436 39 1 0 3453 3491 596264757 596264719 5.560000e-07 67.6
29 TraesCS6D01G250000 chrUn 90.268 298 23 6 4 298 36183936 36183642 1.350000e-102 385.0
30 TraesCS6D01G250000 chrUn 85.532 235 24 8 312 545 395014310 395014535 4.010000e-58 237.0
31 TraesCS6D01G250000 chr4A 85.957 235 23 8 312 545 591518944 591518719 8.610000e-60 243.0
32 TraesCS6D01G250000 chr4A 85.957 235 23 8 312 545 592525361 592525586 8.610000e-60 243.0
33 TraesCS6D01G250000 chr4A 85.532 235 24 8 312 545 592811656 592811881 4.010000e-58 237.0
34 TraesCS6D01G250000 chr4A 85.106 235 24 7 312 545 593091916 593092140 6.700000e-56 230.0
35 TraesCS6D01G250000 chr4A 76.224 286 64 4 4952 5235 4591303 4591020 1.930000e-31 148.0
36 TraesCS6D01G250000 chr4A 97.297 37 1 0 7921 7957 700022080 700022044 7.190000e-06 63.9
37 TraesCS6D01G250000 chr3B 86.574 216 24 3 313 525 805133156 805133369 5.180000e-57 233.0
38 TraesCS6D01G250000 chr3B 97.143 35 1 0 7923 7957 669724797 669724763 9.310000e-05 60.2
39 TraesCS6D01G250000 chr3B 100.000 29 0 0 8001 8029 188436184 188436212 4.000000e-03 54.7
40 TraesCS6D01G250000 chr4B 77.612 268 57 3 4952 5218 583478095 583478360 8.920000e-35 159.0
41 TraesCS6D01G250000 chr4B 97.143 35 1 0 7923 7957 254413249 254413283 9.310000e-05 60.2
42 TraesCS6D01G250000 chr7B 88.571 70 8 0 4776 4845 277207154 277207223 1.540000e-12 86.1
43 TraesCS6D01G250000 chr7A 88.571 70 8 0 4776 4845 325713950 325713881 1.540000e-12 86.1


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 TraesCS6D01G250000 chr6D 353345406 353353989 8583 False 15852.000000 15852 100.000000 1 8584 1 chr6D.!!$F1 8583
1 TraesCS6D01G250000 chr6B 525110584 525118479 7895 True 3912.333333 11191 94.594333 540 8584 3 chr6B.!!$R1 8044
2 TraesCS6D01G250000 chr6A 489224843 489233044 8201 True 3987.000000 8045 95.005333 541 8584 3 chr6A.!!$R1 8043
3 TraesCS6D01G250000 chr7D 520799091 520799594 503 True 320.000000 399 88.652500 9 542 2 chr7D.!!$R2 533

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
436 439 0.451783 ATCATCTTTGTTTCGGCCGC 59.548 50.000 23.51 7.40 0.00 6.53 F
452 455 1.071605 CCGCAGCTACAAAGTCTCAC 58.928 55.000 0.00 0.00 0.00 3.51 F
1443 1460 1.153429 GTACCTGGGCGTGGTCATC 60.153 63.158 3.30 0.00 38.88 2.92 F
1893 1937 1.188219 TGGTGAGCTCACTCCAGTCC 61.188 60.000 38.17 24.38 45.73 3.85 F
3042 3228 0.981943 ACAAGGGGTTAGAAGTCCGG 59.018 55.000 0.00 0.00 0.00 5.14 F
3801 4022 0.179040 TTGACCGGTCAAGTTCACCC 60.179 55.000 39.59 10.71 43.90 4.61 F
4863 5102 2.100197 ACATACTCTACGGCAAGAGCA 58.900 47.619 12.46 2.14 45.81 4.26 F
5361 5600 1.275010 ACGTGTCTGTACATGGCATCA 59.725 47.619 0.00 0.00 45.34 3.07 F
6462 6719 0.403271 AGAAACACAGCCCAGCTCAT 59.597 50.000 0.00 0.00 36.40 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 2037 0.248134 CTACACGACGGAGCTGTAGC 60.248 60.000 9.55 0.0 42.49 3.58 R
1996 2041 1.550065 CAATCTACACGACGGAGCTG 58.450 55.000 0.00 0.0 0.00 4.24 R
2972 3158 1.033574 CGGGGCAAAACCACTAAACA 58.966 50.000 0.00 0.0 41.20 2.83 R
3218 3407 1.164411 TTCCGCATAACTTGGTGCAG 58.836 50.000 0.00 0.0 41.32 4.41 R
4060 4281 1.153349 GTTGCCGATCACCTCCTCC 60.153 63.158 0.00 0.0 0.00 4.30 R
5300 5539 0.249280 TCGTGCTGTGCGAGAAAGAA 60.249 50.000 0.00 0.0 34.11 2.52 R
6443 6700 0.403271 ATGAGCTGGGCTGTGTTTCT 59.597 50.000 0.00 0.0 39.88 2.52 R
6878 7135 1.025812 CGTAGAAGCGGAGGATGAGT 58.974 55.000 0.00 0.0 0.00 3.41 R
8130 8451 0.107831 TTCGGGCTGTTTGCTGTAGT 59.892 50.000 0.00 0.0 42.39 2.73 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
30 31 9.803315 GGAGACCATATAAAAATGTTCTTTTCC 57.197 33.333 0.00 0.00 29.68 3.13
176 179 5.298276 TGGCGATTCTTAAACTGAAAACTGT 59.702 36.000 0.00 0.00 0.00 3.55
179 182 6.910433 GCGATTCTTAAACTGAAAACTGTCAA 59.090 34.615 0.00 0.00 0.00 3.18
187 190 5.117355 ACTGAAAACTGTCAATGATGCAG 57.883 39.130 0.00 0.04 37.00 4.41
196 199 5.088680 TGTCAATGATGCAGACATGTCTA 57.911 39.130 27.44 14.26 37.98 2.59
197 200 5.677567 TGTCAATGATGCAGACATGTCTAT 58.322 37.500 27.44 18.44 37.98 1.98
215 218 9.481340 CATGTCTATGTAGTGTGCTAATATGTT 57.519 33.333 0.00 0.00 0.00 2.71
250 253 4.138290 TGTCATTTTTCTTTACTCGCCCA 58.862 39.130 0.00 0.00 0.00 5.36
258 261 4.274602 TCTTTACTCGCCCATAACAACA 57.725 40.909 0.00 0.00 0.00 3.33
342 345 4.112634 TCACTTGCCCCTTTCTTTGTAT 57.887 40.909 0.00 0.00 0.00 2.29
343 346 3.826157 TCACTTGCCCCTTTCTTTGTATG 59.174 43.478 0.00 0.00 0.00 2.39
363 366 8.978874 TGTATGGATTAAATCTACATGCAAGT 57.021 30.769 0.00 0.00 32.60 3.16
365 368 9.056005 GTATGGATTAAATCTACATGCAAGTCA 57.944 33.333 0.00 0.00 0.00 3.41
401 404 5.865085 ACACCTGTAGAATCTTAAACTGCA 58.135 37.500 0.00 0.00 0.00 4.41
402 405 5.701290 ACACCTGTAGAATCTTAAACTGCAC 59.299 40.000 0.00 0.00 0.00 4.57
436 439 0.451783 ATCATCTTTGTTTCGGCCGC 59.548 50.000 23.51 7.40 0.00 6.53
446 449 1.573829 TTTCGGCCGCAGCTACAAAG 61.574 55.000 23.51 0.00 39.73 2.77
452 455 1.071605 CCGCAGCTACAAAGTCTCAC 58.928 55.000 0.00 0.00 0.00 3.51
459 462 6.255670 CGCAGCTACAAAGTCTCACATTATAA 59.744 38.462 0.00 0.00 0.00 0.98
461 464 7.905493 GCAGCTACAAAGTCTCACATTATAAAC 59.095 37.037 0.00 0.00 0.00 2.01
462 465 9.155975 CAGCTACAAAGTCTCACATTATAAACT 57.844 33.333 0.00 0.00 0.00 2.66
511 516 2.861462 TTTTTCTCCAGTTGCAACGG 57.139 45.000 25.17 25.17 0.00 4.44
515 520 1.594293 CTCCAGTTGCAACGGACGT 60.594 57.895 28.12 6.88 31.63 4.34
517 522 2.631428 CAGTTGCAACGGACGTGG 59.369 61.111 23.20 5.25 0.00 4.94
519 524 3.276846 GTTGCAACGGACGTGGCT 61.277 61.111 22.90 0.00 44.91 4.75
520 525 2.515057 TTGCAACGGACGTGGCTT 60.515 55.556 22.90 0.00 44.91 4.35
521 526 2.115911 TTGCAACGGACGTGGCTTT 61.116 52.632 22.90 0.00 44.91 3.51
522 527 1.658686 TTGCAACGGACGTGGCTTTT 61.659 50.000 22.90 0.00 44.91 2.27
618 623 2.533916 TCTGAAGCTCTGACATGAGGT 58.466 47.619 0.00 0.00 45.36 3.85
693 698 4.711949 CAGCTTGGGCCTGACGCT 62.712 66.667 4.53 4.27 39.73 5.07
1314 1324 1.459158 TGCCCCCATGCACAAACTT 60.459 52.632 0.00 0.00 36.04 2.66
1332 1345 2.901839 ACTTGCATTGATTGGCTCCTTT 59.098 40.909 0.00 0.00 0.00 3.11
1334 1347 4.159135 ACTTGCATTGATTGGCTCCTTTAG 59.841 41.667 0.00 0.00 0.00 1.85
1338 1351 5.893255 TGCATTGATTGGCTCCTTTAGTTAT 59.107 36.000 0.00 0.00 0.00 1.89
1403 1420 1.437573 CGGCCGTCGTTTTCGTTTC 60.438 57.895 19.50 0.00 44.46 2.78
1443 1460 1.153429 GTACCTGGGCGTGGTCATC 60.153 63.158 3.30 0.00 38.88 2.92
1546 1563 6.842163 AGGAGACAAATACGCAAAATGTTAG 58.158 36.000 0.00 0.00 0.00 2.34
1775 1797 1.227089 CGCCATCTCCGAGAAGGTG 60.227 63.158 18.62 17.62 37.27 4.00
1893 1937 1.188219 TGGTGAGCTCACTCCAGTCC 61.188 60.000 38.17 24.38 45.73 3.85
1992 2037 4.083961 AGTCATCGATCGAACCACTATACG 60.084 45.833 23.50 1.12 0.00 3.06
1996 2041 3.185188 TCGATCGAACCACTATACGCTAC 59.815 47.826 16.99 0.00 0.00 3.58
2065 2110 1.534729 GAATTCCACCCGTCTTTGCT 58.465 50.000 0.00 0.00 0.00 3.91
2144 2189 2.512515 GGCACACGCATCTCTCCC 60.513 66.667 0.00 0.00 41.24 4.30
2147 2192 2.039624 ACACGCATCTCTCCCCCT 59.960 61.111 0.00 0.00 0.00 4.79
2148 2193 2.060980 ACACGCATCTCTCCCCCTC 61.061 63.158 0.00 0.00 0.00 4.30
2149 2194 2.444895 ACGCATCTCTCCCCCTCC 60.445 66.667 0.00 0.00 0.00 4.30
2155 2200 2.728007 CATCTCTCCCCCTCCAAAAAC 58.272 52.381 0.00 0.00 0.00 2.43
2156 2201 1.827792 TCTCTCCCCCTCCAAAAACA 58.172 50.000 0.00 0.00 0.00 2.83
2157 2202 2.140224 TCTCTCCCCCTCCAAAAACAA 58.860 47.619 0.00 0.00 0.00 2.83
2158 2203 2.108250 TCTCTCCCCCTCCAAAAACAAG 59.892 50.000 0.00 0.00 0.00 3.16
2159 2204 1.856920 TCTCCCCCTCCAAAAACAAGT 59.143 47.619 0.00 0.00 0.00 3.16
2160 2205 2.246327 TCTCCCCCTCCAAAAACAAGTT 59.754 45.455 0.00 0.00 0.00 2.66
2165 2210 4.211920 CCCCTCCAAAAACAAGTTGTAGA 58.788 43.478 9.37 1.22 0.00 2.59
2166 2211 4.832823 CCCCTCCAAAAACAAGTTGTAGAT 59.167 41.667 9.37 0.00 0.00 1.98
2168 2213 5.534654 CCCTCCAAAAACAAGTTGTAGATGA 59.465 40.000 9.37 2.40 0.00 2.92
2191 2241 8.362860 TGAAAGATTTTCAAAATCAAATGCGA 57.637 26.923 22.21 0.13 0.00 5.10
2195 2245 5.903764 TTTTCAAAATCAAATGCGACTGG 57.096 34.783 0.00 0.00 0.00 4.00
2208 2258 4.902443 TGCGACTGGTTTGTCATTAAAA 57.098 36.364 0.00 0.00 36.82 1.52
2367 2417 1.792006 ACGGGAAACTCGTTGCTTAG 58.208 50.000 0.00 0.00 37.61 2.18
2373 2423 3.925299 GGAAACTCGTTGCTTAGTCTACC 59.075 47.826 0.00 0.00 0.00 3.18
2689 2739 7.883217 TCTCAACTCTTTTCTACAGTCGTATT 58.117 34.615 0.00 0.00 0.00 1.89
2720 2772 7.597743 ACTCTAGCCATAAATAAAATCGTACGG 59.402 37.037 16.52 0.00 0.00 4.02
2776 2828 5.185828 TCAAGTAGAAAGAGCACTGCTATGA 59.814 40.000 2.71 0.00 39.88 2.15
2777 2829 5.667539 AGTAGAAAGAGCACTGCTATGAA 57.332 39.130 2.71 0.00 39.88 2.57
2778 2830 6.042638 AGTAGAAAGAGCACTGCTATGAAA 57.957 37.500 2.71 0.00 39.88 2.69
2779 2831 6.648192 AGTAGAAAGAGCACTGCTATGAAAT 58.352 36.000 2.71 0.00 39.88 2.17
2780 2832 7.108847 AGTAGAAAGAGCACTGCTATGAAATT 58.891 34.615 2.71 0.00 39.88 1.82
2781 2833 6.434018 AGAAAGAGCACTGCTATGAAATTC 57.566 37.500 2.71 1.78 39.88 2.17
2782 2834 5.356470 AGAAAGAGCACTGCTATGAAATTCC 59.644 40.000 2.71 0.00 39.88 3.01
2783 2835 4.500499 AGAGCACTGCTATGAAATTCCT 57.500 40.909 2.71 0.00 39.88 3.36
2784 2836 5.620738 AGAGCACTGCTATGAAATTCCTA 57.379 39.130 2.71 0.00 39.88 2.94
2785 2837 6.185114 AGAGCACTGCTATGAAATTCCTAT 57.815 37.500 2.71 0.00 39.88 2.57
2839 2891 4.082026 CGACAGCATATATCACATCCTCCA 60.082 45.833 0.00 0.00 0.00 3.86
2927 2980 1.593209 TCCGCACAACAGTTCCGAC 60.593 57.895 0.00 0.00 0.00 4.79
2991 3177 1.033574 TGTTTAGTGGTTTTGCCCCG 58.966 50.000 0.00 0.00 36.04 5.73
3042 3228 0.981943 ACAAGGGGTTAGAAGTCCGG 59.018 55.000 0.00 0.00 0.00 5.14
3066 3252 6.383415 GTCCTGTCATAAGATCGGACTAATC 58.617 44.000 9.89 0.00 40.20 1.75
3068 3254 7.390996 GTCCTGTCATAAGATCGGACTAATCTA 59.609 40.741 9.89 0.00 40.20 1.98
3088 3274 8.594881 AATCTAGAAAATCAAATAGTCGCGAT 57.405 30.769 14.06 3.98 0.00 4.58
3135 3324 9.665719 GGATTCTCAGAAGTTCTAGAAAGAAAT 57.334 33.333 19.61 7.56 43.30 2.17
3166 3355 6.899393 AAATCCAAGCAAAGACATAGAACA 57.101 33.333 0.00 0.00 0.00 3.18
3218 3407 9.538508 TTCAGAGGTTTCTAAGTTACAAACTAC 57.461 33.333 11.89 7.65 41.91 2.73
3285 3474 7.601073 TTTGTTCATTTTGTGCACATAACAA 57.399 28.000 22.39 24.16 33.98 2.83
3287 3476 5.752472 TGTTCATTTTGTGCACATAACAAGG 59.248 36.000 22.39 12.77 38.67 3.61
3317 3506 1.693467 TACTTGTGTGCGACGACATC 58.307 50.000 0.00 0.00 0.00 3.06
3395 3587 6.653989 TGTAATTCTTTTTCTTTTGGGGCAA 58.346 32.000 0.00 0.00 0.00 4.52
3441 3633 9.241919 ACTGTTCATGGTAATTGTAATTCATGA 57.758 29.630 13.40 13.40 37.61 3.07
3563 3773 4.124851 AGTGGTCATCCTGATAAACGTC 57.875 45.455 0.00 0.00 34.23 4.34
3564 3774 2.858344 GTGGTCATCCTGATAAACGTCG 59.142 50.000 0.00 0.00 34.23 5.12
3583 3793 1.252779 CGCACGTACATGTCGATCTTG 59.747 52.381 19.74 11.10 0.00 3.02
3584 3794 2.259618 GCACGTACATGTCGATCTTGT 58.740 47.619 19.74 0.21 37.94 3.16
3585 3795 2.666508 GCACGTACATGTCGATCTTGTT 59.333 45.455 19.74 0.00 36.20 2.83
3667 3877 3.385577 GCTCACCGTCAGATCTTAATCC 58.614 50.000 0.00 0.00 31.78 3.01
3801 4022 0.179040 TTGACCGGTCAAGTTCACCC 60.179 55.000 39.59 10.71 43.90 4.61
4363 4584 5.186021 CACTACAGTACAGACCTTCATTCCT 59.814 44.000 0.00 0.00 0.00 3.36
4366 4587 5.084519 ACAGTACAGACCTTCATTCCTACA 58.915 41.667 0.00 0.00 0.00 2.74
4422 4643 2.159393 GGCAATCATGTGCAATGTACGT 60.159 45.455 10.16 0.00 46.81 3.57
4863 5102 2.100197 ACATACTCTACGGCAAGAGCA 58.900 47.619 12.46 2.14 45.81 4.26
4874 5113 4.927782 AAGAGCAACGCCACCGCA 62.928 61.111 0.00 0.00 38.22 5.69
5361 5600 1.275010 ACGTGTCTGTACATGGCATCA 59.725 47.619 0.00 0.00 45.34 3.07
5372 5611 3.929094 ACATGGCATCAACATTGTTTCC 58.071 40.909 0.00 0.33 0.00 3.13
5426 5665 8.181904 AGTCATTTTAACATGGTTTCATCAGT 57.818 30.769 0.00 0.00 0.00 3.41
5438 5677 7.815840 TGGTTTCATCAGTTTCAAGTATTCA 57.184 32.000 0.00 0.00 0.00 2.57
5742 5981 2.897641 GATCGCCACGCTCTTCTGCT 62.898 60.000 0.00 0.00 0.00 4.24
6124 6364 6.602803 TCTTAATTTTCATCAGCTGCCACATA 59.397 34.615 9.47 0.00 0.00 2.29
6205 6462 2.872858 GTTCATGAAAGGATACGGAGGC 59.127 50.000 10.35 0.00 46.39 4.70
6232 6489 1.405526 GGCAAGTCGTATCTGAAGGCA 60.406 52.381 0.00 0.00 0.00 4.75
6443 6700 9.298250 TGGCTTTATGGTAAGTAAATTGTTACA 57.702 29.630 7.53 0.00 41.88 2.41
6462 6719 0.403271 AGAAACACAGCCCAGCTCAT 59.597 50.000 0.00 0.00 36.40 2.90
6473 6730 3.201708 AGCCCAGCTCATTCTAAATCTGT 59.798 43.478 0.00 0.00 30.62 3.41
6527 6784 1.435577 ATTTCAGGTACGGTTCGCAC 58.564 50.000 0.00 0.00 0.00 5.34
6878 7135 0.944386 GCAAGAGCACCGTTCTTTCA 59.056 50.000 0.00 0.00 41.58 2.69
6902 7159 0.183014 TCCTCCGCTTCTACGATCCT 59.817 55.000 0.00 0.00 34.06 3.24
6917 7174 2.405172 GATCCTATCGCCGGAAAAGTC 58.595 52.381 5.05 0.00 33.55 3.01
6940 7197 6.257849 GTCTTGATCGATGGTATTTTGCTGTA 59.742 38.462 0.54 0.00 0.00 2.74
6962 7219 6.917477 TGTACAAATTTCAAACATGACAGCTC 59.083 34.615 0.00 0.00 0.00 4.09
7022 7279 2.368548 GGGTTTTGCAGGAAAGGACATT 59.631 45.455 0.00 0.00 0.00 2.71
7193 7450 0.671472 CGCACACCTTCATCAGCTCA 60.671 55.000 0.00 0.00 0.00 4.26
7319 7576 3.385384 CTGCTCCTGGACGAGGCA 61.385 66.667 7.94 7.94 42.47 4.75
7394 7651 1.002087 GTGATGAAGAACCGGACCACT 59.998 52.381 9.46 0.00 0.00 4.00
7493 7750 2.592308 GGGGATCACCAGCACCTC 59.408 66.667 9.87 0.00 42.91 3.85
7499 7756 0.904649 ATCACCAGCACCTCATCGAA 59.095 50.000 0.00 0.00 0.00 3.71
7511 7768 4.216257 CACCTCATCGAAAACAAGAATGGT 59.784 41.667 0.00 0.00 0.00 3.55
7540 7797 0.815213 AAGCTCGTCAACTTGCAGCA 60.815 50.000 0.00 0.00 32.17 4.41
7541 7798 1.206072 GCTCGTCAACTTGCAGCAG 59.794 57.895 0.00 0.00 0.00 4.24
7542 7799 1.206072 CTCGTCAACTTGCAGCAGC 59.794 57.895 0.00 0.00 42.57 5.25
7601 7862 0.174617 GAGCTCCCTGGAGAAGAACG 59.825 60.000 17.38 0.00 44.53 3.95
7621 7882 2.216898 GATGTGCTTCTGTATCCAGCC 58.783 52.381 0.00 0.00 38.66 4.85
7623 7884 0.108138 GTGCTTCTGTATCCAGCCGT 60.108 55.000 0.00 0.00 38.66 5.68
7672 7933 4.816392 TCGAATGTAAAAGCTGTGCTCTA 58.184 39.130 0.00 0.00 38.25 2.43
7673 7934 4.625742 TCGAATGTAAAAGCTGTGCTCTAC 59.374 41.667 0.00 0.00 38.25 2.59
7726 7989 5.295950 CATTATACAGGGAGAAGTGCTCTG 58.704 45.833 0.00 0.00 43.43 3.35
7815 8101 4.846779 TGTTGCTGGGTGATAAAAGTTC 57.153 40.909 0.00 0.00 0.00 3.01
7816 8102 3.572255 TGTTGCTGGGTGATAAAAGTTCC 59.428 43.478 0.00 0.00 0.00 3.62
7820 8106 4.898861 TGCTGGGTGATAAAAGTTCCTTTT 59.101 37.500 7.10 7.10 44.46 2.27
7867 8153 2.749076 TCCATTCAATTGAAGCGAGTGG 59.251 45.455 24.17 23.66 37.48 4.00
7949 8235 4.568359 CACTCCATCTGGAAATACTTGTCG 59.432 45.833 0.00 0.00 44.91 4.35
7970 8291 6.183360 TGTCGGAGAAATATTTCCAGAGAGAG 60.183 42.308 21.86 7.74 39.69 3.20
7971 8292 5.303078 TCGGAGAAATATTTCCAGAGAGAGG 59.697 44.000 21.86 4.75 37.92 3.69
8045 8366 7.039011 ACCATCAAGTATCTTACAGACAACTGA 60.039 37.037 0.00 0.00 46.03 3.41
8091 8412 3.399440 ACAGCAGCATAGAATCCTAGC 57.601 47.619 0.00 0.00 0.00 3.42
8093 8414 3.065655 CAGCAGCATAGAATCCTAGCAC 58.934 50.000 0.00 0.00 0.00 4.40
8140 8461 4.111916 GCTTTTCAGCAAACTACAGCAAA 58.888 39.130 0.00 0.00 46.49 3.68
8141 8462 4.026558 GCTTTTCAGCAAACTACAGCAAAC 60.027 41.667 0.00 0.00 46.49 2.93
8142 8463 4.710423 TTTCAGCAAACTACAGCAAACA 57.290 36.364 0.00 0.00 0.00 2.83
8159 8480 4.226761 CAAACAGCCCGAATAAACTTGAC 58.773 43.478 0.00 0.00 0.00 3.18
8193 8514 6.699575 AATTCTGTAATATGGTGAACAGGC 57.300 37.500 0.00 0.00 39.80 4.85
8211 8532 5.130350 ACAGGCTTTGTTCTTTGCTACTTA 58.870 37.500 0.00 0.00 36.31 2.24
8222 8543 9.561069 TGTTCTTTGCTACTTATCTCTTTTTCT 57.439 29.630 0.00 0.00 0.00 2.52
8267 8588 6.533723 CCCAGGAAAAGAAACAAAGTTTGTAC 59.466 38.462 21.14 17.06 44.59 2.90
8283 8604 0.107848 GTACCGGTGCAGCCTGTATT 60.108 55.000 19.93 0.00 38.81 1.89
8293 8614 2.086869 CAGCCTGTATTTGACTGGTGG 58.913 52.381 3.05 0.00 46.40 4.61
8491 8841 8.722394 AGAAAAGAAAATCTTAGCCTAAACTCG 58.278 33.333 0.00 0.00 35.27 4.18
8492 8842 6.424176 AAGAAAATCTTAGCCTAAACTCGC 57.576 37.500 0.00 0.00 34.42 5.03
8529 8879 4.141041 TCCTGAGTTGATCCCCAAGAAAAA 60.141 41.667 0.00 0.00 35.03 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
129 132 6.710744 CCAACTTATGGTAACTCTTGAACACT 59.289 38.462 0.00 0.00 44.85 3.55
146 149 7.681939 TTCAGTTTAAGAATCGCCAACTTAT 57.318 32.000 0.00 0.00 0.00 1.73
155 158 8.895845 CATTGACAGTTTTCAGTTTAAGAATCG 58.104 33.333 0.00 0.00 0.00 3.34
176 179 5.677567 ACATAGACATGTCTGCATCATTGA 58.322 37.500 33.76 14.28 41.75 2.57
179 182 6.183360 ACACTACATAGACATGTCTGCATCAT 60.183 38.462 33.76 18.55 44.42 2.45
187 190 9.133627 CATATTAGCACACTACATAGACATGTC 57.866 37.037 18.47 18.47 44.42 3.06
197 200 9.620660 CATACGATAACATATTAGCACACTACA 57.379 33.333 0.00 0.00 0.00 2.74
221 224 8.539674 GCGAGTAAAGAAAAATGACAAAAACAT 58.460 29.630 0.00 0.00 0.00 2.71
232 235 6.827586 TGTTATGGGCGAGTAAAGAAAAAT 57.172 33.333 0.00 0.00 0.00 1.82
250 253 5.878406 TGTTTGGAATGGGTTGTTGTTAT 57.122 34.783 0.00 0.00 0.00 1.89
258 261 4.158786 TCATGTCATGTTTGGAATGGGTT 58.841 39.130 12.54 0.00 0.00 4.11
298 301 6.927936 TGATCATGCATTTCCTTTTCGAAAAA 59.072 30.769 22.67 9.71 35.47 1.94
299 302 6.365789 GTGATCATGCATTTCCTTTTCGAAAA 59.634 34.615 21.35 21.35 35.47 2.29
300 303 5.863397 GTGATCATGCATTTCCTTTTCGAAA 59.137 36.000 6.47 6.47 36.24 3.46
301 304 5.183713 AGTGATCATGCATTTCCTTTTCGAA 59.816 36.000 0.00 0.00 0.00 3.71
302 305 4.701651 AGTGATCATGCATTTCCTTTTCGA 59.298 37.500 0.00 0.00 0.00 3.71
303 306 4.990257 AGTGATCATGCATTTCCTTTTCG 58.010 39.130 0.00 0.00 0.00 3.46
304 307 5.063060 GCAAGTGATCATGCATTTCCTTTTC 59.937 40.000 14.95 0.00 42.12 2.29
305 308 4.933400 GCAAGTGATCATGCATTTCCTTTT 59.067 37.500 14.95 0.00 42.12 2.27
306 309 4.501071 GCAAGTGATCATGCATTTCCTTT 58.499 39.130 14.95 0.00 42.12 3.11
307 310 3.118884 GGCAAGTGATCATGCATTTCCTT 60.119 43.478 20.02 4.66 44.32 3.36
308 311 2.429610 GGCAAGTGATCATGCATTTCCT 59.570 45.455 20.02 0.00 44.32 3.36
309 312 2.482490 GGGCAAGTGATCATGCATTTCC 60.482 50.000 20.02 10.09 44.32 3.13
310 313 2.482490 GGGGCAAGTGATCATGCATTTC 60.482 50.000 20.02 5.46 44.32 2.17
311 314 1.483415 GGGGCAAGTGATCATGCATTT 59.517 47.619 20.02 0.00 44.32 2.32
312 315 1.117150 GGGGCAAGTGATCATGCATT 58.883 50.000 20.02 2.33 44.32 3.56
313 316 0.260816 AGGGGCAAGTGATCATGCAT 59.739 50.000 20.02 0.00 44.32 3.96
314 317 0.040058 AAGGGGCAAGTGATCATGCA 59.960 50.000 20.02 0.00 44.32 3.96
315 318 1.135721 GAAAGGGGCAAGTGATCATGC 59.864 52.381 12.04 12.04 41.82 4.06
316 319 2.731572 AGAAAGGGGCAAGTGATCATG 58.268 47.619 0.00 0.00 0.00 3.07
317 320 3.463048 AAGAAAGGGGCAAGTGATCAT 57.537 42.857 0.00 0.00 0.00 2.45
318 321 2.892852 CAAAGAAAGGGGCAAGTGATCA 59.107 45.455 0.00 0.00 0.00 2.92
319 322 2.893489 ACAAAGAAAGGGGCAAGTGATC 59.107 45.455 0.00 0.00 0.00 2.92
363 366 8.684386 TCTACAGGTGTTTTATTTCAACATGA 57.316 30.769 0.00 0.00 36.54 3.07
376 379 6.770785 TGCAGTTTAAGATTCTACAGGTGTTT 59.229 34.615 0.00 0.00 0.00 2.83
379 382 5.934625 AGTGCAGTTTAAGATTCTACAGGTG 59.065 40.000 0.00 0.00 0.00 4.00
397 400 9.553064 AGATGATCTTAACCTATAAAAGTGCAG 57.447 33.333 0.00 0.00 0.00 4.41
418 421 0.886938 TGCGGCCGAAACAAAGATGA 60.887 50.000 33.48 0.00 0.00 2.92
430 433 2.740714 GACTTTGTAGCTGCGGCCG 61.741 63.158 24.05 24.05 39.73 6.13
431 434 1.362406 GAGACTTTGTAGCTGCGGCC 61.362 60.000 15.55 0.00 39.73 6.13
436 439 9.155975 AGTTTATAATGTGAGACTTTGTAGCTG 57.844 33.333 0.00 0.00 0.00 4.24
501 506 3.276846 GCCACGTCCGTTGCAACT 61.277 61.111 26.09 5.20 36.85 3.16
502 507 2.331019 AAAGCCACGTCCGTTGCAAC 62.331 55.000 19.89 19.89 38.96 4.17
528 533 6.655062 TGCGTGCATTTTTATGTATACTAGC 58.345 36.000 4.17 0.00 0.00 3.42
618 623 4.152759 CGTTGGATTCGGCTACAAAGTTAA 59.847 41.667 0.00 0.00 0.00 2.01
693 698 2.041922 ATCGCTCCTAGGGCCACA 60.042 61.111 9.46 0.00 0.00 4.17
1089 1099 0.687354 GCACCTTCTCCACCTTCTCA 59.313 55.000 0.00 0.00 0.00 3.27
1314 1324 3.700538 ACTAAAGGAGCCAATCAATGCA 58.299 40.909 0.00 0.00 0.00 3.96
1321 1334 3.747708 GCCGGATAACTAAAGGAGCCAAT 60.748 47.826 5.05 0.00 0.00 3.16
1332 1345 1.737816 GTCGCTGGCCGGATAACTA 59.262 57.895 18.31 0.00 37.59 2.24
1334 1347 2.960129 CGTCGCTGGCCGGATAAC 60.960 66.667 18.31 8.57 37.59 1.89
1403 1420 0.798771 GAAGTCCAGCGAGTACTGCG 60.799 60.000 0.00 5.20 36.29 5.18
1443 1460 1.507174 GGTCCACGACGAGAAGAGG 59.493 63.158 0.00 0.00 32.65 3.69
1477 1494 2.089854 CCGGCTCGGTTTCATTGAG 58.910 57.895 5.56 0.00 42.73 3.02
1521 1538 5.705609 ACATTTTGCGTATTTGTCTCCTT 57.294 34.783 0.00 0.00 0.00 3.36
1546 1563 3.427243 GTGTGATGAGAGCACGTACTAC 58.573 50.000 0.00 0.00 39.07 2.73
1775 1797 2.102553 GAGTGGAGGAGCGTACGC 59.897 66.667 32.17 32.17 42.33 4.42
1893 1937 3.580458 CTCTCATAACTCCCCACCCTATG 59.420 52.174 0.00 0.00 0.00 2.23
1992 2037 0.248134 CTACACGACGGAGCTGTAGC 60.248 60.000 9.55 0.00 42.49 3.58
1996 2041 1.550065 CAATCTACACGACGGAGCTG 58.450 55.000 0.00 0.00 0.00 4.24
2065 2110 3.557054 CGTGAAATTCAGTTGGAGGGAGA 60.557 47.826 0.00 0.00 0.00 3.71
2144 2189 5.534654 TCATCTACAACTTGTTTTTGGAGGG 59.465 40.000 0.00 0.00 35.82 4.30
2147 2192 8.287439 TCTTTCATCTACAACTTGTTTTTGGA 57.713 30.769 0.00 0.00 0.00 3.53
2148 2193 9.533253 AATCTTTCATCTACAACTTGTTTTTGG 57.467 29.630 0.00 0.00 0.00 3.28
2165 2210 8.991026 TCGCATTTGATTTTGAAAATCTTTCAT 58.009 25.926 25.61 12.75 0.00 2.57
2166 2211 8.274939 GTCGCATTTGATTTTGAAAATCTTTCA 58.725 29.630 25.61 9.36 0.00 2.69
2168 2213 8.277713 CAGTCGCATTTGATTTTGAAAATCTTT 58.722 29.630 25.61 11.67 0.00 2.52
2191 2241 7.095691 CGATGCAAATTTTAATGACAAACCAGT 60.096 33.333 0.00 0.00 0.00 4.00
2195 2245 7.116061 ACCGATGCAAATTTTAATGACAAAC 57.884 32.000 0.00 0.00 0.00 2.93
2208 2258 2.282701 ACGTACGTACCGATGCAAAT 57.717 45.000 21.41 0.00 0.00 2.32
2720 2772 2.554893 TCATTTTTGCCCTTGGTACGAC 59.445 45.455 0.00 0.00 0.00 4.34
2776 2828 7.072177 CACAATGTCGTGTGTATAGGAATTT 57.928 36.000 0.00 0.00 43.26 1.82
2777 2829 6.662414 CACAATGTCGTGTGTATAGGAATT 57.338 37.500 0.00 0.00 43.26 2.17
2839 2891 4.178540 GCTTGCACTTTGATACATGCATT 58.821 39.130 0.00 0.00 46.75 3.56
2875 2927 4.664677 GACAGCTGCACGACGGGT 62.665 66.667 15.27 0.00 35.09 5.28
2907 2960 1.885388 CGGAACTGTTGTGCGGACA 60.885 57.895 5.33 5.33 0.00 4.02
2972 3158 1.033574 CGGGGCAAAACCACTAAACA 58.966 50.000 0.00 0.00 41.20 2.83
2980 3166 2.823924 AATGTTAACGGGGCAAAACC 57.176 45.000 0.26 0.00 37.93 3.27
3042 3228 5.769484 TTAGTCCGATCTTATGACAGGAC 57.231 43.478 18.79 18.79 44.95 3.85
3106 3292 6.783708 TTCTAGAACTTCTGAGAATCCTCC 57.216 41.667 0.00 0.00 38.66 4.30
3107 3293 8.062065 TCTTTCTAGAACTTCTGAGAATCCTC 57.938 38.462 4.18 0.00 39.86 3.71
3166 3355 8.497910 AATGTATCACATGTTAGAGAGGGTAT 57.502 34.615 0.00 0.00 37.97 2.73
3218 3407 1.164411 TTCCGCATAACTTGGTGCAG 58.836 50.000 0.00 0.00 41.32 4.41
3252 3441 7.009999 GTGCACAAAATGAACAAATGACTACAA 59.990 33.333 13.17 0.00 36.75 2.41
3253 3442 6.475076 GTGCACAAAATGAACAAATGACTACA 59.525 34.615 13.17 0.00 36.75 2.74
3254 3443 6.475076 TGTGCACAAAATGAACAAATGACTAC 59.525 34.615 19.28 0.00 44.58 2.73
3257 3446 5.715429 TGTGCACAAAATGAACAAATGAC 57.285 34.783 19.28 0.00 44.58 3.06
3264 3453 5.333263 GCCTTGTTATGTGCACAAAATGAAC 60.333 40.000 25.72 20.57 37.38 3.18
3265 3454 4.749099 GCCTTGTTATGTGCACAAAATGAA 59.251 37.500 25.72 11.91 33.74 2.57
3317 3506 4.141855 AGCTTGTTGATTAAACCGAACG 57.858 40.909 0.00 0.00 38.06 3.95
3323 3512 9.158233 TGTAGTACCATAGCTTGTTGATTAAAC 57.842 33.333 0.00 0.00 39.41 2.01
3409 3601 5.630121 ACAATTACCATGAACAGTCCTTGA 58.370 37.500 0.00 0.00 0.00 3.02
3452 3644 6.271391 ACAATTAATATGGACCGGATGGAGTA 59.729 38.462 9.46 0.00 39.21 2.59
3563 3773 1.252779 CAAGATCGACATGTACGTGCG 59.747 52.381 15.12 17.66 0.00 5.34
3564 3774 2.259618 ACAAGATCGACATGTACGTGC 58.740 47.619 15.12 0.00 0.00 5.34
3583 3793 2.945668 AGTCCACAAGAACAGAAGCAAC 59.054 45.455 0.00 0.00 0.00 4.17
3584 3794 3.118261 AGAGTCCACAAGAACAGAAGCAA 60.118 43.478 0.00 0.00 0.00 3.91
3585 3795 2.435805 AGAGTCCACAAGAACAGAAGCA 59.564 45.455 0.00 0.00 0.00 3.91
3667 3877 2.743928 GTCTGCAGAAGGCCGTGG 60.744 66.667 20.19 0.00 43.89 4.94
3705 3915 2.607134 AGCAGCTGGTCAGGCTCT 60.607 61.111 13.85 0.00 38.03 4.09
3748 3966 2.035421 CAGCAGCTGGTCTTGCAAA 58.965 52.632 17.16 0.00 0.00 3.68
3749 3967 2.558286 GCAGCAGCTGGTCTTGCAA 61.558 57.895 24.13 0.00 37.91 4.08
3750 3968 2.981909 GCAGCAGCTGGTCTTGCA 60.982 61.111 24.13 0.00 37.91 4.08
3801 4022 1.800805 ATGTTCACCGAGACTGCAAG 58.199 50.000 0.00 0.00 42.29 4.01
3946 4167 4.796231 ACGATGGCGAGCGTGACC 62.796 66.667 12.19 0.00 44.03 4.02
4060 4281 1.153349 GTTGCCGATCACCTCCTCC 60.153 63.158 0.00 0.00 0.00 4.30
4087 4308 4.680237 CCGACGAAGGCCTGCACA 62.680 66.667 12.53 0.00 0.00 4.57
4338 4559 5.047235 GGAATGAAGGTCTGTACTGTAGTGT 60.047 44.000 0.00 0.00 0.00 3.55
4339 4560 5.186021 AGGAATGAAGGTCTGTACTGTAGTG 59.814 44.000 0.00 0.00 0.00 2.74
4340 4561 5.334421 AGGAATGAAGGTCTGTACTGTAGT 58.666 41.667 0.00 0.00 0.00 2.73
4342 4563 6.250711 TGTAGGAATGAAGGTCTGTACTGTA 58.749 40.000 0.00 0.00 0.00 2.74
4343 4564 5.084519 TGTAGGAATGAAGGTCTGTACTGT 58.915 41.667 0.00 0.00 0.00 3.55
4344 4565 5.661056 TGTAGGAATGAAGGTCTGTACTG 57.339 43.478 0.00 0.00 0.00 2.74
4345 4566 5.364157 GGATGTAGGAATGAAGGTCTGTACT 59.636 44.000 0.00 0.00 0.00 2.73
4346 4567 5.128827 TGGATGTAGGAATGAAGGTCTGTAC 59.871 44.000 0.00 0.00 0.00 2.90
4347 4568 5.277250 TGGATGTAGGAATGAAGGTCTGTA 58.723 41.667 0.00 0.00 0.00 2.74
4348 4569 4.104086 TGGATGTAGGAATGAAGGTCTGT 58.896 43.478 0.00 0.00 0.00 3.41
4396 4617 1.875420 TTGCACATGATTGCCACCCG 61.875 55.000 0.00 0.00 42.25 5.28
4399 4620 2.373540 ACATTGCACATGATTGCCAC 57.626 45.000 13.53 0.00 42.25 5.01
4874 5113 2.792599 GCGTGGTCGATCTCGTCT 59.207 61.111 19.96 0.00 40.80 4.18
4958 5197 3.850095 GAGCTGTATCCCGCGCTCC 62.850 68.421 5.56 0.00 42.20 4.70
5150 5389 1.450312 GGCGTTCCTGATGGTGGAG 60.450 63.158 0.00 0.00 34.76 3.86
5287 5526 0.807496 GAAAGAAGGCTTGCGCTGAT 59.193 50.000 9.73 0.00 33.79 2.90
5300 5539 0.249280 TCGTGCTGTGCGAGAAAGAA 60.249 50.000 0.00 0.00 34.11 2.52
5361 5600 1.688197 CCACCTGCAGGAAACAATGTT 59.312 47.619 39.19 10.61 38.94 2.71
5372 5611 3.046087 CACGCTGACCACCTGCAG 61.046 66.667 6.78 6.78 39.38 4.41
5410 5649 6.469782 ACTTGAAACTGATGAAACCATGTT 57.530 33.333 0.00 0.00 0.00 2.71
5412 5651 8.298854 TGAATACTTGAAACTGATGAAACCATG 58.701 33.333 0.00 0.00 0.00 3.66
5413 5652 8.408043 TGAATACTTGAAACTGATGAAACCAT 57.592 30.769 0.00 0.00 0.00 3.55
5414 5653 7.815840 TGAATACTTGAAACTGATGAAACCA 57.184 32.000 0.00 0.00 0.00 3.67
5415 5654 7.809806 CCTTGAATACTTGAAACTGATGAAACC 59.190 37.037 0.00 0.00 0.00 3.27
5417 5656 7.723616 TCCCTTGAATACTTGAAACTGATGAAA 59.276 33.333 0.00 0.00 0.00 2.69
5420 5659 6.404074 GCTCCCTTGAATACTTGAAACTGATG 60.404 42.308 0.00 0.00 0.00 3.07
5421 5660 5.649831 GCTCCCTTGAATACTTGAAACTGAT 59.350 40.000 0.00 0.00 0.00 2.90
5426 5665 4.985538 ACAGCTCCCTTGAATACTTGAAA 58.014 39.130 0.00 0.00 0.00 2.69
5438 5677 0.832135 TCGTCCTTGACAGCTCCCTT 60.832 55.000 0.00 0.00 32.09 3.95
5512 5751 2.257371 CTTCGTCGTTCGCCTCCA 59.743 61.111 0.00 0.00 39.67 3.86
6205 6462 1.135083 AGATACGACTTGCCGAGGTTG 60.135 52.381 0.00 0.00 0.00 3.77
6283 6540 1.004560 CACCTTCTCCTCTGCGCAA 60.005 57.895 13.05 1.37 0.00 4.85
6289 6546 4.619679 AGAGCTTTATCACCTTCTCCTCT 58.380 43.478 0.00 0.00 0.00 3.69
6443 6700 0.403271 ATGAGCTGGGCTGTGTTTCT 59.597 50.000 0.00 0.00 39.88 2.52
6462 6719 6.874134 GCTCTTGGAGTACAACAGATTTAGAA 59.126 38.462 0.00 0.00 34.76 2.10
6473 6730 2.438021 ACCAGTTGCTCTTGGAGTACAA 59.562 45.455 7.75 0.00 37.55 2.41
6527 6784 1.747709 CCAACTCCTTGCTCATCAGG 58.252 55.000 0.00 0.00 0.00 3.86
6878 7135 1.025812 CGTAGAAGCGGAGGATGAGT 58.974 55.000 0.00 0.00 0.00 3.41
6902 7159 3.454375 GATCAAGACTTTTCCGGCGATA 58.546 45.455 9.30 0.00 0.00 2.92
6917 7174 5.490139 ACAGCAAAATACCATCGATCAAG 57.510 39.130 0.00 0.00 0.00 3.02
6940 7197 5.069516 AGGAGCTGTCATGTTTGAAATTTGT 59.930 36.000 0.00 0.00 32.48 2.83
7193 7450 4.326227 TGGTACCCCTCCGGCAGT 62.326 66.667 10.07 0.00 33.26 4.40
7247 7504 4.728110 ATGCGCTGCTTCTGCCCA 62.728 61.111 9.73 0.00 38.71 5.36
7319 7576 4.742201 ATGTCCAGCGCGCTCGTT 62.742 61.111 34.28 7.98 38.14 3.85
7335 7592 4.498520 CACGCGCTCCGACTCCAT 62.499 66.667 5.73 0.00 41.02 3.41
7364 7621 2.303022 GTTCTTCATCACCCTGTCCAGA 59.697 50.000 0.00 0.00 0.00 3.86
7418 7675 1.342082 CGTCGGCGTTCTTGATCGTT 61.342 55.000 6.85 0.00 0.00 3.85
7493 7750 3.057315 AGGCACCATTCTTGTTTTCGATG 60.057 43.478 0.00 0.00 0.00 3.84
7511 7768 1.292223 GACGAGCTTGTGGTAGGCA 59.708 57.895 12.53 0.00 33.01 4.75
7542 7799 2.255554 CTGTTGCTGCTGCTGCTG 59.744 61.111 27.67 16.73 40.48 4.41
7567 7824 3.644719 CTCATGAGCTCTGGCCCT 58.355 61.111 16.19 0.00 39.73 5.19
7621 7882 1.065854 AGGGAAGCCATGAAAGAGACG 60.066 52.381 0.00 0.00 0.00 4.18
7623 7884 2.269023 TGAGGGAAGCCATGAAAGAGA 58.731 47.619 0.00 0.00 0.00 3.10
7672 7933 7.544217 ACACGCACTTTAAGAAAAAGAAAATGT 59.456 29.630 0.00 1.89 0.00 2.71
7673 7934 7.894847 ACACGCACTTTAAGAAAAAGAAAATG 58.105 30.769 0.00 1.39 0.00 2.32
7694 7957 4.119862 CTCCCTGTATAATGGTGAACACG 58.880 47.826 0.00 0.00 0.00 4.49
7726 7989 8.256611 TCTACTGCTACAAAGAAATCAACATC 57.743 34.615 0.00 0.00 0.00 3.06
7815 8101 8.462016 GGGCTGTGATGCTATATAATTAAAAGG 58.538 37.037 0.00 0.00 0.00 3.11
7816 8102 8.462016 GGGGCTGTGATGCTATATAATTAAAAG 58.538 37.037 0.00 0.00 0.00 2.27
7820 8106 6.653020 CAGGGGCTGTGATGCTATATAATTA 58.347 40.000 0.00 0.00 0.00 1.40
7949 8235 5.604650 TCCCTCTCTCTGGAAATATTTCTCC 59.395 44.000 23.85 12.65 37.35 3.71
8130 8451 0.107831 TTCGGGCTGTTTGCTGTAGT 59.892 50.000 0.00 0.00 42.39 2.73
8132 8453 2.772077 TATTCGGGCTGTTTGCTGTA 57.228 45.000 0.00 0.00 42.39 2.74
8133 8454 1.904287 TTATTCGGGCTGTTTGCTGT 58.096 45.000 0.00 0.00 42.39 4.40
8134 8455 2.228822 AGTTTATTCGGGCTGTTTGCTG 59.771 45.455 0.00 0.00 42.39 4.41
8135 8456 2.514803 AGTTTATTCGGGCTGTTTGCT 58.485 42.857 0.00 0.00 42.39 3.91
8136 8457 2.986479 CAAGTTTATTCGGGCTGTTTGC 59.014 45.455 0.00 0.00 41.94 3.68
8137 8458 4.023193 AGTCAAGTTTATTCGGGCTGTTTG 60.023 41.667 0.00 0.00 0.00 2.93
8140 8461 3.074412 CAGTCAAGTTTATTCGGGCTGT 58.926 45.455 0.00 0.00 0.00 4.40
8141 8462 2.420022 CCAGTCAAGTTTATTCGGGCTG 59.580 50.000 0.00 0.00 0.00 4.85
8142 8463 2.304761 TCCAGTCAAGTTTATTCGGGCT 59.695 45.455 0.00 0.00 0.00 5.19
8146 8467 4.631377 TCTGCATCCAGTCAAGTTTATTCG 59.369 41.667 0.00 0.00 40.09 3.34
8222 8543 5.575157 TGGGCAAAAATACTGATTACTGGA 58.425 37.500 0.00 0.00 0.00 3.86
8267 8588 0.676466 TCAAATACAGGCTGCACCGG 60.676 55.000 15.89 0.00 46.52 5.28
8283 8604 4.002906 GACAGTGTAATCCACCAGTCAA 57.997 45.455 0.00 0.00 45.74 3.18
8492 8842 3.806380 ACTCAGGATGCAATAGAGCTTG 58.194 45.455 0.00 0.00 34.76 4.01
8529 8879 4.468510 TGTACGTAGTTTCCAATCCATCCT 59.531 41.667 0.00 0.00 37.78 3.24


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

AutoCloner maintained by Alex Coulton.