Multiple sequence alignment - TraesCS2B01G216400

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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 TraesCS2B01G216400 chr2B 100.000 5330 0 0 1 5330 202481266 202486595 0.000000e+00 9843.0
1 TraesCS2B01G216400 chr2B 100.000 40 0 0 1 40 157957195 157957234 2.060000e-09 75.0
2 TraesCS2B01G216400 chr2D 92.705 4085 210 41 1262 5321 144442269 144446290 0.000000e+00 5812.0
3 TraesCS2B01G216400 chr2D 90.797 1217 45 25 40 1226 144441012 144442191 0.000000e+00 1565.0
4 TraesCS2B01G216400 chr2A 90.936 3045 135 58 166 3156 157472967 157470010 0.000000e+00 3964.0
5 TraesCS2B01G216400 chr2A 91.323 1406 81 17 3380 4747 157469560 157468158 0.000000e+00 1882.0
6 TraesCS2B01G216400 chr2A 86.258 473 64 1 4858 5330 157457349 157456878 3.680000e-141 512.0
7 TraesCS2B01G216400 chr2A 94.958 238 10 1 3147 3384 157469860 157469625 6.520000e-99 372.0
8 TraesCS2B01G216400 chrUn 87.685 203 25 0 4638 4840 126930779 126930577 2.480000e-58 237.0
9 TraesCS2B01G216400 chrUn 100.000 31 0 0 9 39 451399234 451399264 2.070000e-04 58.4
10 TraesCS2B01G216400 chr3B 86.432 199 26 1 4643 4840 445200775 445200577 3.230000e-52 217.0
11 TraesCS2B01G216400 chr7D 86.000 200 26 2 4643 4840 56293652 56293453 4.180000e-51 213.0
12 TraesCS2B01G216400 chr4B 85.437 206 24 5 4640 4840 189811822 189812026 5.410000e-50 209.0
13 TraesCS2B01G216400 chr4B 84.653 202 30 1 4640 4840 450474529 450474730 3.260000e-47 200.0
14 TraesCS2B01G216400 chr4A 85.859 198 27 1 4643 4840 713515570 713515374 5.410000e-50 209.0
15 TraesCS2B01G216400 chr6B 85.222 203 29 1 4639 4840 264750341 264750543 1.950000e-49 207.0


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 TraesCS2B01G216400 chr2B 202481266 202486595 5329 False 9843.000000 9843 100.000000 1 5330 1 chr2B.!!$F2 5329
1 TraesCS2B01G216400 chr2D 144441012 144446290 5278 False 3688.500000 5812 91.751000 40 5321 2 chr2D.!!$F1 5281
2 TraesCS2B01G216400 chr2A 157468158 157472967 4809 True 2072.666667 3964 92.405667 166 4747 3 chr2A.!!$R2 4581

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
667 699 1.024579 ATTAGGCGCACGAGGTTTGG 61.025 55.000 10.83 0.0 0.00 3.28 F
923 960 1.066143 GCTTAGTGGCTAACCTGCAGA 60.066 52.381 17.39 0.0 36.63 4.26 F
2121 2227 1.077501 GGGCAAGCTGCTGGTATCA 60.078 57.895 1.35 0.0 44.28 2.15 F
2934 3044 0.034896 TTCTCAGTTTCACGGGAGGC 59.965 55.000 0.00 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 1816 1.002990 CCTCCTGTGTGCATGCTGA 60.003 57.895 20.33 1.72 0.00 4.26 R
2919 3029 0.174845 TATCGCCTCCCGTGAAACTG 59.825 55.000 0.00 0.00 38.35 3.16 R
3573 3922 0.321653 ATTGACCTTCTCCACCACGC 60.322 55.000 0.00 0.00 0.00 5.34 R
4655 5042 0.456142 TCGTCAGAATTCGAGTGGCG 60.456 55.000 12.47 12.47 40.62 5.69 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
20 21 3.290948 GGGCCCAAGACACAATATACA 57.709 47.619 19.95 0.00 0.00 2.29
21 22 3.832527 GGGCCCAAGACACAATATACAT 58.167 45.455 19.95 0.00 0.00 2.29
22 23 4.980573 GGGCCCAAGACACAATATACATA 58.019 43.478 19.95 0.00 0.00 2.29
23 24 4.760204 GGGCCCAAGACACAATATACATAC 59.240 45.833 19.95 0.00 0.00 2.39
24 25 5.373222 GGCCCAAGACACAATATACATACA 58.627 41.667 0.00 0.00 0.00 2.29
25 26 5.238650 GGCCCAAGACACAATATACATACAC 59.761 44.000 0.00 0.00 0.00 2.90
26 27 5.820423 GCCCAAGACACAATATACATACACA 59.180 40.000 0.00 0.00 0.00 3.72
27 28 6.317642 GCCCAAGACACAATATACATACACAA 59.682 38.462 0.00 0.00 0.00 3.33
28 29 7.013274 GCCCAAGACACAATATACATACACAAT 59.987 37.037 0.00 0.00 0.00 2.71
29 30 9.554395 CCCAAGACACAATATACATACACAATA 57.446 33.333 0.00 0.00 0.00 1.90
60 61 4.345271 TTCTCAAACATGTGATGCATCG 57.655 40.909 21.34 9.75 35.19 3.84
99 100 5.858581 GGTCTGCAATTGTACTGTTCAATTC 59.141 40.000 18.62 14.54 41.58 2.17
103 104 6.215121 TGCAATTGTACTGTTCAATTCCAAG 58.785 36.000 18.62 11.12 41.58 3.61
153 154 4.710528 CGCAAGTCGTTATATTTCCTCC 57.289 45.455 0.00 0.00 0.00 4.30
232 264 1.966451 CACCTCTTTCCCGCACCAC 60.966 63.158 0.00 0.00 0.00 4.16
605 637 2.855514 GCCAAGTCCAAAGCCGCAA 61.856 57.895 0.00 0.00 0.00 4.85
667 699 1.024579 ATTAGGCGCACGAGGTTTGG 61.025 55.000 10.83 0.00 0.00 3.28
691 728 1.204856 GCGTCGCGTGGTACTATTCC 61.205 60.000 5.77 0.00 0.00 3.01
698 735 2.540515 CGTGGTACTATTCCTGCAGTG 58.459 52.381 13.81 4.33 0.00 3.66
846 883 4.240103 ACAGCTGCACCACTCGCA 62.240 61.111 15.27 0.00 37.88 5.10
923 960 1.066143 GCTTAGTGGCTAACCTGCAGA 60.066 52.381 17.39 0.00 36.63 4.26
970 1012 1.370293 CACACACCGCACGTACGTA 60.370 57.895 22.34 0.00 0.00 3.57
991 1033 5.463724 CGTACACTTGCTTCTTCTTCTTCTT 59.536 40.000 0.00 0.00 0.00 2.52
992 1034 6.346199 CGTACACTTGCTTCTTCTTCTTCTTC 60.346 42.308 0.00 0.00 0.00 2.87
993 1035 5.679601 ACACTTGCTTCTTCTTCTTCTTCT 58.320 37.500 0.00 0.00 0.00 2.85
1113 1161 2.264794 GTCGCCATCGTCAACCCT 59.735 61.111 0.00 0.00 36.96 4.34
1158 1206 3.367743 CAAGGTGCATGCCACGCT 61.368 61.111 16.68 9.66 45.62 5.07
1159 1207 2.598394 AAGGTGCATGCCACGCTT 60.598 55.556 16.68 14.26 45.62 4.68
1160 1208 2.922950 AAGGTGCATGCCACGCTTG 61.923 57.895 16.68 0.00 45.62 4.01
1178 1226 1.188219 TGACGCTTGCTCCTCCTCTT 61.188 55.000 0.00 0.00 0.00 2.85
1183 1235 2.612972 CGCTTGCTCCTCCTCTTGTTTA 60.613 50.000 0.00 0.00 0.00 2.01
1210 1262 3.050275 GCCACGAGAACCCAGCAC 61.050 66.667 0.00 0.00 0.00 4.40
1258 1341 2.125753 GTGAGCAGAGTGAGCCCG 60.126 66.667 0.00 0.00 0.00 6.13
1289 1391 2.512057 GCTCTGCTCTGCTGCCTC 60.512 66.667 0.00 0.00 0.00 4.70
1298 1400 2.008329 CTCTGCTGCCTCAAGTGATTC 58.992 52.381 0.00 0.00 0.00 2.52
1349 1451 6.033196 TCGTCGTTGAAATCTTTCGATACTTC 59.967 38.462 0.00 0.00 40.01 3.01
1439 1545 3.611549 GGAGTACGAAAGAATTGACCGAC 59.388 47.826 0.00 0.00 0.00 4.79
1504 1610 5.922544 CCAATTGAATGAACTTGGTGAGAAC 59.077 40.000 7.12 0.00 34.69 3.01
1550 1656 5.357257 TGGAACCTGACTTATAATTCGCTC 58.643 41.667 0.00 0.00 0.00 5.03
1592 1698 1.686110 GAGACGGAGGTCCCATGGT 60.686 63.158 11.73 0.00 44.54 3.55
1634 1740 6.688637 TGAGAAAGAATCCATGTAGCATTG 57.311 37.500 0.00 0.00 0.00 2.82
1668 1774 4.039245 TCGTATGACAAGATCCAGATTCCC 59.961 45.833 0.00 0.00 0.00 3.97
1697 1803 6.258507 ACTTTTGTTGCTGATGAATTTGGTTC 59.741 34.615 0.00 0.00 37.35 3.62
1770 1876 2.281761 CCAAGGTGGCGCAGAAGT 60.282 61.111 10.83 0.00 0.00 3.01
1927 2033 1.451207 TCACCAGCGTTTGCACTGT 60.451 52.632 1.85 0.00 46.23 3.55
1953 2059 3.196685 TGTGGCCCCTTATAATTTGTTGC 59.803 43.478 0.00 0.00 0.00 4.17
1954 2060 3.450817 GTGGCCCCTTATAATTTGTTGCT 59.549 43.478 0.00 0.00 0.00 3.91
1955 2061 3.450457 TGGCCCCTTATAATTTGTTGCTG 59.550 43.478 0.00 0.00 0.00 4.41
1956 2062 3.450817 GGCCCCTTATAATTTGTTGCTGT 59.549 43.478 0.00 0.00 0.00 4.40
1957 2063 4.432712 GCCCCTTATAATTTGTTGCTGTG 58.567 43.478 0.00 0.00 0.00 3.66
1958 2064 4.680440 GCCCCTTATAATTTGTTGCTGTGG 60.680 45.833 0.00 0.00 0.00 4.17
1959 2065 4.709397 CCCCTTATAATTTGTTGCTGTGGA 59.291 41.667 0.00 0.00 0.00 4.02
1960 2066 5.394115 CCCCTTATAATTTGTTGCTGTGGAC 60.394 44.000 0.00 0.00 0.00 4.02
1993 2099 7.610865 TGAAAATTGTGGTTGTTCTTCTTCTT 58.389 30.769 0.00 0.00 0.00 2.52
1994 2100 7.759433 TGAAAATTGTGGTTGTTCTTCTTCTTC 59.241 33.333 0.00 0.00 0.00 2.87
2013 2119 8.753133 TCTTCTTCTGATGCTAAGAGACAATTA 58.247 33.333 0.00 0.00 33.49 1.40
2035 2141 1.606668 GAGATGCGTGGTTTGGTTTGA 59.393 47.619 0.00 0.00 0.00 2.69
2049 2155 2.218603 GGTTTGATATAGGTGGTGCGG 58.781 52.381 0.00 0.00 0.00 5.69
2121 2227 1.077501 GGGCAAGCTGCTGGTATCA 60.078 57.895 1.35 0.00 44.28 2.15
2189 2295 3.412386 AGGTACACCTGCATTTCAGTTC 58.588 45.455 0.00 0.00 46.55 3.01
2200 2306 3.003275 GCATTTCAGTTCTTTCACACGGA 59.997 43.478 0.00 0.00 0.00 4.69
2260 2366 2.310233 ATGCGAGACGTGTGTGTGC 61.310 57.895 0.00 0.00 0.00 4.57
2261 2367 4.046998 GCGAGACGTGTGTGTGCG 62.047 66.667 0.00 0.00 0.00 5.34
2262 2368 4.046998 CGAGACGTGTGTGTGCGC 62.047 66.667 0.00 0.00 0.00 6.09
2263 2369 2.658593 GAGACGTGTGTGTGCGCT 60.659 61.111 9.73 0.00 0.00 5.92
2300 2407 5.597806 ACTGTTGATCTGTTCTCGTTTACA 58.402 37.500 0.00 0.00 0.00 2.41
2375 2485 7.719633 TCCTATAAATTGTCTGAATGTAAGGCC 59.280 37.037 0.00 0.00 0.00 5.19
2387 2497 5.425539 TGAATGTAAGGCCTAAGCTTCTACT 59.574 40.000 5.16 0.00 39.73 2.57
2388 2498 4.737855 TGTAAGGCCTAAGCTTCTACTG 57.262 45.455 5.16 0.00 39.73 2.74
2389 2499 4.094476 TGTAAGGCCTAAGCTTCTACTGT 58.906 43.478 5.16 0.00 39.73 3.55
2390 2500 5.266788 TGTAAGGCCTAAGCTTCTACTGTA 58.733 41.667 5.16 0.00 39.73 2.74
2391 2501 4.739587 AAGGCCTAAGCTTCTACTGTAC 57.260 45.455 5.16 0.00 39.73 2.90
2392 2502 3.709587 AGGCCTAAGCTTCTACTGTACA 58.290 45.455 1.29 0.00 39.73 2.90
2393 2503 4.290942 AGGCCTAAGCTTCTACTGTACAT 58.709 43.478 1.29 0.00 39.73 2.29
2441 2551 9.778741 TGTATCAAATTCCCTACACTAATGATC 57.221 33.333 0.00 0.00 0.00 2.92
2449 2559 4.698780 CCCTACACTAATGATCCGTCGATA 59.301 45.833 0.00 0.00 0.00 2.92
2450 2560 5.391736 CCCTACACTAATGATCCGTCGATAC 60.392 48.000 0.00 0.00 0.00 2.24
2452 2562 5.109662 ACACTAATGATCCGTCGATACTG 57.890 43.478 0.00 0.00 0.00 2.74
2454 2564 5.067413 ACACTAATGATCCGTCGATACTGTT 59.933 40.000 0.00 0.00 0.00 3.16
2458 2568 4.182693 TGATCCGTCGATACTGTTTTGT 57.817 40.909 0.00 0.00 0.00 2.83
2655 2765 9.128107 ACTTATTTCGTTACTGCATTTTCATTG 57.872 29.630 0.00 0.00 0.00 2.82
2663 2773 7.589587 CGTTACTGCATTTTCATTGTACTGAAA 59.410 33.333 6.26 6.26 41.97 2.69
2890 3000 4.065088 AGCATTCGTGCTTTTTACAGAGA 58.935 39.130 0.00 0.00 43.52 3.10
2934 3044 0.034896 TTCTCAGTTTCACGGGAGGC 59.965 55.000 0.00 0.00 0.00 4.70
2991 3101 0.397114 TCCCGCTTCAGATGGAGCTA 60.397 55.000 11.25 0.00 0.00 3.32
3116 3229 6.872585 AATTGATTGGGTGGTGTTTCATAT 57.127 33.333 0.00 0.00 0.00 1.78
3117 3230 7.969690 AATTGATTGGGTGGTGTTTCATATA 57.030 32.000 0.00 0.00 0.00 0.86
3118 3231 8.551682 AATTGATTGGGTGGTGTTTCATATAT 57.448 30.769 0.00 0.00 0.00 0.86
3119 3232 9.653516 AATTGATTGGGTGGTGTTTCATATATA 57.346 29.630 0.00 0.00 0.00 0.86
3120 3233 8.690203 TTGATTGGGTGGTGTTTCATATATAG 57.310 34.615 0.00 0.00 0.00 1.31
3121 3234 7.230747 TGATTGGGTGGTGTTTCATATATAGG 58.769 38.462 0.00 0.00 0.00 2.57
3122 3235 4.980573 TGGGTGGTGTTTCATATATAGGC 58.019 43.478 0.00 0.00 0.00 3.93
3123 3236 4.202524 TGGGTGGTGTTTCATATATAGGCC 60.203 45.833 0.00 0.00 0.00 5.19
3125 3238 4.202524 GGTGGTGTTTCATATATAGGCCCA 60.203 45.833 0.00 0.00 0.00 5.36
3126 3239 5.381757 GTGGTGTTTCATATATAGGCCCAA 58.618 41.667 0.00 0.00 0.00 4.12
3127 3240 5.830991 GTGGTGTTTCATATATAGGCCCAAA 59.169 40.000 0.00 0.00 0.00 3.28
3128 3241 5.830991 TGGTGTTTCATATATAGGCCCAAAC 59.169 40.000 0.00 4.22 0.00 2.93
3129 3242 5.243060 GGTGTTTCATATATAGGCCCAAACC 59.757 44.000 0.00 1.27 0.00 3.27
3130 3243 5.830991 GTGTTTCATATATAGGCCCAAACCA 59.169 40.000 0.00 0.00 0.00 3.67
3135 3248 3.971468 ATATAGGCCCAAACCACACAT 57.029 42.857 0.00 0.00 0.00 3.21
3218 3491 3.993081 CCTTAGAGAGTCACAAGCAACAG 59.007 47.826 0.00 0.00 0.00 3.16
3320 3593 6.886459 ACAGATAGTGGTGTCATATGCTTTTT 59.114 34.615 0.00 0.00 0.00 1.94
3370 3646 6.872547 CCATCCTCATGTCATAACTCATACTG 59.127 42.308 0.00 0.00 0.00 2.74
3371 3647 7.440198 CATCCTCATGTCATAACTCATACTGT 58.560 38.462 0.00 0.00 0.00 3.55
3372 3648 7.423844 TCCTCATGTCATAACTCATACTGTT 57.576 36.000 0.00 0.00 0.00 3.16
3387 3663 9.944376 ACTCATACTGTTTATTGTGAGTATTGT 57.056 29.630 4.19 0.00 43.02 2.71
3399 3744 4.821260 TGTGAGTATTGTTGAGCATTGTGT 59.179 37.500 0.00 0.00 0.00 3.72
3416 3761 7.276438 AGCATTGTGTCTTTTTCTTTCAGTTTC 59.724 33.333 0.00 0.00 0.00 2.78
3430 3775 2.358898 TCAGTTTCTGCTTGTGCTTTCC 59.641 45.455 0.00 0.00 40.48 3.13
3431 3776 1.683385 AGTTTCTGCTTGTGCTTTCCC 59.317 47.619 0.00 0.00 40.48 3.97
3432 3777 1.683385 GTTTCTGCTTGTGCTTTCCCT 59.317 47.619 0.00 0.00 40.48 4.20
3433 3778 1.609208 TTCTGCTTGTGCTTTCCCTC 58.391 50.000 0.00 0.00 40.48 4.30
3436 3781 1.538950 CTGCTTGTGCTTTCCCTCTTC 59.461 52.381 0.00 0.00 40.48 2.87
3443 3788 4.620723 TGTGCTTTCCCTCTTCCTATCTA 58.379 43.478 0.00 0.00 0.00 1.98
3447 3792 5.777732 TGCTTTCCCTCTTCCTATCTATCTC 59.222 44.000 0.00 0.00 0.00 2.75
3453 3798 7.181361 TCCCTCTTCCTATCTATCTCATCTTG 58.819 42.308 0.00 0.00 0.00 3.02
3538 3887 2.656646 CAGAGGTGCACTGCCGTA 59.343 61.111 17.98 0.00 0.00 4.02
3622 3971 0.318955 CAAAGCTGAAAGTTGGCCCG 60.319 55.000 0.00 0.00 35.30 6.13
3625 3974 3.373565 CTGAAAGTTGGCCCGCCC 61.374 66.667 0.00 0.00 34.56 6.13
3764 4113 1.821216 CAACCTTATCTGGCCGTTGT 58.179 50.000 0.00 0.00 31.36 3.32
4135 4513 2.669229 TACCGTGTCCGCGACTCA 60.669 61.111 8.23 0.00 33.15 3.41
4180 4558 1.461127 CAAGCTCGTTTTCTCCTTCCG 59.539 52.381 0.00 0.00 0.00 4.30
4196 4574 3.997021 CCTTCCGGTTGCTATATGATGTC 59.003 47.826 0.00 0.00 0.00 3.06
4514 4901 1.600164 GCAAGCACGAATCTTGTTGCA 60.600 47.619 15.97 0.00 42.06 4.08
4555 4942 2.292569 CTCCTTGATGATGAAATGCCGG 59.707 50.000 0.00 0.00 0.00 6.13
4562 4949 2.358957 TGATGAAATGCCGGAGAACTG 58.641 47.619 5.05 0.00 0.00 3.16
4593 4980 4.765339 AGGCCAATCAAAACTGTACTTACC 59.235 41.667 5.01 0.00 0.00 2.85
4607 4994 6.210784 ACTGTACTTACCTGCTGATGAAACTA 59.789 38.462 0.00 0.00 0.00 2.24
4641 5028 4.098196 CCGGGAAACACACTTTTAAAAGGA 59.902 41.667 27.23 0.00 40.31 3.36
4677 5064 2.029728 GCCACTCGAATTCTGACGATTG 59.970 50.000 3.52 0.00 38.34 2.67
4691 5078 0.729116 CGATTGCGAGAAATGCCACT 59.271 50.000 0.00 0.00 40.82 4.00
4707 5094 5.016051 TGCCACTGCAATTTTCAAACTTA 57.984 34.783 0.00 0.00 46.66 2.24
4712 5099 7.218014 GCCACTGCAATTTTCAAACTTAAAAAC 59.782 33.333 0.00 0.00 37.47 2.43
4716 5103 9.771915 CTGCAATTTTCAAACTTAAAAACATGT 57.228 25.926 0.00 0.00 30.20 3.21
4747 5134 3.492011 GTGGCATTTTTCAAAGTCTGCAG 59.508 43.478 7.63 7.63 0.00 4.41
4750 5137 4.362279 GCATTTTTCAAAGTCTGCAGTGA 58.638 39.130 14.67 7.16 0.00 3.41
4751 5138 4.207841 GCATTTTTCAAAGTCTGCAGTGAC 59.792 41.667 14.67 5.73 37.23 3.67
4754 5141 1.570813 TCAAAGTCTGCAGTGACGTG 58.429 50.000 14.67 9.57 41.47 4.49
4759 5146 1.134818 AGTCTGCAGTGACGTGTTTCA 60.135 47.619 14.67 0.00 41.47 2.69
4767 5154 3.300590 CAGTGACGTGTTTCAAAGTTTGC 59.699 43.478 10.90 0.00 0.00 3.68
4796 5184 6.592798 ATGCAGTGACATTTTCAAAGTTTG 57.407 33.333 9.44 9.44 35.39 2.93
4797 5185 5.718146 TGCAGTGACATTTTCAAAGTTTGA 58.282 33.333 14.35 14.35 35.39 2.69
4812 5200 1.070643 GTTTGAAAATTGCAGTGGCGC 60.071 47.619 0.00 0.00 45.35 6.53
4817 5205 0.675633 AAATTGCAGTGGCGCTTCTT 59.324 45.000 7.64 0.00 45.35 2.52
4819 5207 1.870055 ATTGCAGTGGCGCTTCTTGG 61.870 55.000 7.64 0.00 45.35 3.61
4887 5275 5.506708 AGTAACTATAACAGCCTTTTGGGG 58.493 41.667 0.00 0.00 40.82 4.96
4900 5288 3.217626 CTTTTGGGGCATATGGTCTCTC 58.782 50.000 4.56 0.00 0.00 3.20
4901 5289 1.891933 TTGGGGCATATGGTCTCTCA 58.108 50.000 4.56 0.00 0.00 3.27
4911 5299 0.615331 TGGTCTCTCATGAACCCTGC 59.385 55.000 11.68 0.00 0.00 4.85
4912 5300 0.615331 GGTCTCTCATGAACCCTGCA 59.385 55.000 3.96 0.00 0.00 4.41
4921 5309 2.198827 TGAACCCTGCATGGTAGTTG 57.801 50.000 14.55 0.00 37.76 3.16
4938 5326 5.811100 GGTAGTTGTATCTGTAAAGTCAGGC 59.189 44.000 0.00 0.00 36.25 4.85
4943 5331 4.460034 TGTATCTGTAAAGTCAGGCGTACA 59.540 41.667 0.00 0.00 36.25 2.90
4944 5332 4.530710 ATCTGTAAAGTCAGGCGTACAA 57.469 40.909 0.00 0.00 36.25 2.41
4958 5346 6.263617 TCAGGCGTACAACTTTCCTTTAAAAT 59.736 34.615 0.00 0.00 0.00 1.82
5004 5392 0.825410 TGCCGACTCCCGCTATAAAA 59.175 50.000 0.00 0.00 36.84 1.52
5006 5394 1.202498 GCCGACTCCCGCTATAAAACT 60.202 52.381 0.00 0.00 36.84 2.66
5010 5398 3.797256 CGACTCCCGCTATAAAACTTCTG 59.203 47.826 0.00 0.00 0.00 3.02
5030 5418 0.389166 CTCGGGAGCTATGATTCGGC 60.389 60.000 0.00 0.00 0.00 5.54
5031 5419 1.112916 TCGGGAGCTATGATTCGGCA 61.113 55.000 0.00 0.00 0.00 5.69
5092 5486 1.131303 TCCTGTCCGTTTGGGTCCAT 61.131 55.000 0.00 0.00 37.00 3.41
5104 5498 6.378582 CGTTTGGGTCCATACATATAAATGC 58.621 40.000 10.34 0.00 36.50 3.56
5117 5511 1.954362 TAAATGCCATGGCCCAACGC 61.954 55.000 33.44 7.62 41.09 4.84
5130 5524 0.233848 CCAACGCGTGGTCTTTGTAC 59.766 55.000 14.98 0.00 43.20 2.90
5138 5532 3.623863 CGTGGTCTTTGTACGCAAAATT 58.376 40.909 0.00 0.00 43.17 1.82
5139 5533 4.039032 CGTGGTCTTTGTACGCAAAATTT 58.961 39.130 0.00 0.00 43.17 1.82
5142 5536 5.289917 GTGGTCTTTGTACGCAAAATTTGTT 59.710 36.000 7.60 0.00 43.17 2.83
5153 5547 3.596319 CAAAATTTGTTTGCTGCGTGTC 58.404 40.909 0.00 0.00 0.00 3.67
5160 5554 3.858868 TTGCTGCGTGTCCGTCTCC 62.859 63.158 0.00 0.00 36.15 3.71
5167 5561 1.805945 GTGTCCGTCTCCACGCATC 60.806 63.158 0.00 0.00 45.29 3.91
5169 5563 1.226717 GTCCGTCTCCACGCATCTC 60.227 63.158 0.00 0.00 45.29 2.75
5174 5568 4.147449 CTCCACGCATCTCCGGCA 62.147 66.667 0.00 0.00 0.00 5.69
5179 5573 2.325082 ACGCATCTCCGGCACAAAC 61.325 57.895 0.00 0.00 0.00 2.93
5188 5582 1.388065 CCGGCACAAACTTGGGTTGA 61.388 55.000 2.17 0.00 35.63 3.18
5193 5587 4.698575 GGCACAAACTTGGGTTGAATTTA 58.301 39.130 2.17 0.00 35.63 1.40
5198 5592 5.358725 ACAAACTTGGGTTGAATTTACGTCT 59.641 36.000 0.00 0.00 35.63 4.18
5202 5596 5.930569 ACTTGGGTTGAATTTACGTCTAGAC 59.069 40.000 13.18 13.18 0.00 2.59
5223 5617 4.696172 CGTTGAACGGACGTGCGC 62.696 66.667 29.80 14.68 38.08 6.09
5255 5649 4.257654 TTCGCCCTCCGCCAACAA 62.258 61.111 0.00 0.00 36.73 2.83
5260 5654 1.672356 CCCTCCGCCAACAAGTCAG 60.672 63.158 0.00 0.00 0.00 3.51
5266 5660 1.891919 GCCAACAAGTCAGTCGGCA 60.892 57.895 0.00 0.00 39.38 5.69
5277 5671 2.997897 GTCGGCAGACCACCTCCT 60.998 66.667 5.60 0.00 41.41 3.69
5278 5672 1.681327 GTCGGCAGACCACCTCCTA 60.681 63.158 5.60 0.00 41.41 2.94
5279 5673 1.681327 TCGGCAGACCACCTCCTAC 60.681 63.158 0.00 0.00 34.57 3.18
5287 5681 1.616628 CCACCTCCTACCAAGCCCT 60.617 63.158 0.00 0.00 0.00 5.19
5299 5693 2.567169 ACCAAGCCCTTTTAATCCAAGC 59.433 45.455 0.00 0.00 0.00 4.01
5321 5715 3.140814 GGAAAGGGCCCGCATGTC 61.141 66.667 18.44 10.31 0.00 3.06
5322 5716 3.140814 GAAAGGGCCCGCATGTCC 61.141 66.667 18.44 0.00 0.00 4.02
5326 5720 4.476752 GGGCCCGCATGTCCGTTA 62.477 66.667 5.69 0.00 0.00 3.18
5327 5721 3.199891 GGCCCGCATGTCCGTTAC 61.200 66.667 0.00 0.00 0.00 2.50
5328 5722 3.199891 GCCCGCATGTCCGTTACC 61.200 66.667 0.00 0.00 0.00 2.85
5329 5723 2.512974 CCCGCATGTCCGTTACCC 60.513 66.667 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.290948 TGTATATTGTGTCTTGGGCCC 57.709 47.619 17.59 17.59 0.00 5.80
1 2 5.238650 GTGTATGTATATTGTGTCTTGGGCC 59.761 44.000 0.00 0.00 0.00 5.80
2 3 5.820423 TGTGTATGTATATTGTGTCTTGGGC 59.180 40.000 0.00 0.00 0.00 5.36
3 4 7.857734 TTGTGTATGTATATTGTGTCTTGGG 57.142 36.000 0.00 0.00 0.00 4.12
29 30 9.797556 CATCACATGTTTGAGAATGTTGAATAT 57.202 29.630 0.00 0.00 34.81 1.28
30 31 7.756272 GCATCACATGTTTGAGAATGTTGAATA 59.244 33.333 9.26 0.00 34.81 1.75
31 32 6.588756 GCATCACATGTTTGAGAATGTTGAAT 59.411 34.615 9.26 0.00 34.81 2.57
32 33 5.921976 GCATCACATGTTTGAGAATGTTGAA 59.078 36.000 9.26 0.00 34.81 2.69
33 34 5.009811 TGCATCACATGTTTGAGAATGTTGA 59.990 36.000 9.26 0.00 34.81 3.18
34 35 5.224135 TGCATCACATGTTTGAGAATGTTG 58.776 37.500 9.26 0.00 34.81 3.33
35 36 5.456548 TGCATCACATGTTTGAGAATGTT 57.543 34.783 9.26 0.00 34.81 2.71
36 37 5.647589 GATGCATCACATGTTTGAGAATGT 58.352 37.500 21.92 0.00 39.84 2.71
37 38 4.733405 CGATGCATCACATGTTTGAGAATG 59.267 41.667 25.70 0.36 39.84 2.67
38 39 4.637091 TCGATGCATCACATGTTTGAGAAT 59.363 37.500 25.70 0.00 39.84 2.40
60 61 2.688507 CAGACCCCACATATACGCATC 58.311 52.381 0.00 0.00 0.00 3.91
138 139 6.342906 ACATGAAACGGAGGAAATATAACGA 58.657 36.000 0.00 0.00 0.00 3.85
143 144 5.054477 CGGTACATGAAACGGAGGAAATAT 58.946 41.667 0.00 0.00 0.00 1.28
145 146 3.055675 TCGGTACATGAAACGGAGGAAAT 60.056 43.478 0.00 0.00 0.00 2.17
150 151 3.116300 CTGATCGGTACATGAAACGGAG 58.884 50.000 0.00 0.00 30.90 4.63
152 153 3.159353 TCTGATCGGTACATGAAACGG 57.841 47.619 0.00 1.96 0.00 4.44
153 154 4.085568 CGAATCTGATCGGTACATGAAACG 60.086 45.833 0.00 0.03 39.12 3.60
382 414 2.574212 CGGCGTCCACGTACGTAC 60.574 66.667 22.34 15.69 44.64 3.67
383 415 4.459331 GCGGCGTCCACGTACGTA 62.459 66.667 22.34 3.16 44.64 3.57
421 453 2.587194 CAGCTCCATTCGCCGAGG 60.587 66.667 0.00 0.00 0.00 4.63
480 512 3.361977 CAGTTTGAACGCCCGGGG 61.362 66.667 25.28 15.33 0.00 5.73
547 579 7.444183 TCAATGGTAACTCGGAAAATATCATCC 59.556 37.037 0.00 0.00 37.61 3.51
550 582 6.256975 CGTCAATGGTAACTCGGAAAATATCA 59.743 38.462 0.00 0.00 37.61 2.15
552 584 5.526111 CCGTCAATGGTAACTCGGAAAATAT 59.474 40.000 0.00 0.00 40.29 1.28
553 585 4.871557 CCGTCAATGGTAACTCGGAAAATA 59.128 41.667 0.00 0.00 40.29 1.40
634 666 1.680860 GCCTAATACGGGTGGCAGTTT 60.681 52.381 0.00 0.00 44.34 2.66
691 728 0.868406 GACGGAAGAAACCACTGCAG 59.132 55.000 13.48 13.48 0.00 4.41
698 735 0.870393 GGAAACGGACGGAAGAAACC 59.130 55.000 0.00 0.00 0.00 3.27
846 883 1.228552 GGTTGGTGCTGATGGGTGT 60.229 57.895 0.00 0.00 0.00 4.16
970 1012 5.679601 AGAAGAAGAAGAAGAAGCAAGTGT 58.320 37.500 0.00 0.00 0.00 3.55
1157 1205 0.739112 GAGGAGGAGCAAGCGTCAAG 60.739 60.000 0.00 0.00 0.00 3.02
1158 1206 1.188219 AGAGGAGGAGCAAGCGTCAA 61.188 55.000 0.00 0.00 0.00 3.18
1159 1207 1.188219 AAGAGGAGGAGCAAGCGTCA 61.188 55.000 0.00 0.00 0.00 4.35
1160 1208 0.739112 CAAGAGGAGGAGCAAGCGTC 60.739 60.000 0.00 0.00 0.00 5.19
1168 1216 5.582665 CGGAAAGAATAAACAAGAGGAGGAG 59.417 44.000 0.00 0.00 0.00 3.69
1178 1226 1.807742 CGTGGCCGGAAAGAATAAACA 59.192 47.619 5.05 0.00 0.00 2.83
1183 1235 0.323629 TTCTCGTGGCCGGAAAGAAT 59.676 50.000 5.05 0.00 33.95 2.40
1228 1309 2.734723 CTCACACAGCCGGTCACG 60.735 66.667 1.90 0.00 40.55 4.35
1253 1336 1.992277 AATCTCAGACCAGCGGGCT 60.992 57.895 1.46 0.00 45.50 5.19
1258 1341 1.654317 CAGAGCAATCTCAGACCAGC 58.346 55.000 0.00 0.00 41.81 4.85
1349 1451 4.788100 CGATGAAACTTATGTTTGCTTCGG 59.212 41.667 11.15 5.14 45.36 4.30
1504 1610 8.359642 TCCAAAGTTGATTTCTACCATGAAAAG 58.640 33.333 0.00 0.00 39.08 2.27
1550 1656 2.485426 ACGATTTCTGACCACATTGCTG 59.515 45.455 0.00 0.00 0.00 4.41
1592 1698 5.762279 TCTCATATGGTATATGCGGTCCTA 58.238 41.667 2.13 0.00 0.00 2.94
1634 1740 2.727777 TGTCATACGATTCTACGCAGC 58.272 47.619 0.00 0.00 36.70 5.25
1668 1774 7.342194 CAAATTCATCAGCAACAAAAGTTCTG 58.658 34.615 0.00 0.00 0.00 3.02
1710 1816 1.002990 CCTCCTGTGTGCATGCTGA 60.003 57.895 20.33 1.72 0.00 4.26
1927 2033 4.222336 CAAATTATAAGGGGCCACATGGA 58.778 43.478 8.31 0.00 37.39 3.41
1953 2059 2.051334 TTTCAACCACAGGTCCACAG 57.949 50.000 0.00 0.00 33.12 3.66
1954 2060 2.516227 TTTTCAACCACAGGTCCACA 57.484 45.000 0.00 0.00 33.12 4.17
1955 2061 3.132111 ACAATTTTCAACCACAGGTCCAC 59.868 43.478 0.00 0.00 33.12 4.02
1956 2062 3.131933 CACAATTTTCAACCACAGGTCCA 59.868 43.478 0.00 0.00 33.12 4.02
1957 2063 3.492482 CCACAATTTTCAACCACAGGTCC 60.492 47.826 0.00 0.00 33.12 4.46
1958 2064 3.132111 ACCACAATTTTCAACCACAGGTC 59.868 43.478 0.00 0.00 33.12 3.85
1959 2065 3.103742 ACCACAATTTTCAACCACAGGT 58.896 40.909 0.00 0.00 37.65 4.00
1960 2066 3.817709 ACCACAATTTTCAACCACAGG 57.182 42.857 0.00 0.00 0.00 4.00
1993 2099 8.298729 TCTCTTAATTGTCTCTTAGCATCAGA 57.701 34.615 0.00 0.00 0.00 3.27
1994 2100 8.980610 CATCTCTTAATTGTCTCTTAGCATCAG 58.019 37.037 0.00 0.00 0.00 2.90
2013 2119 1.981256 AACCAAACCACGCATCTCTT 58.019 45.000 0.00 0.00 0.00 2.85
2035 2141 1.469335 CCGGACCGCACCACCTATAT 61.469 60.000 8.86 0.00 0.00 0.86
2049 2155 1.024579 ATGACACCAAATCGCCGGAC 61.025 55.000 5.05 0.00 0.00 4.79
2121 2227 2.900546 CTCATTACCGGGGAAGCTATCT 59.099 50.000 6.32 0.00 0.00 1.98
2189 2295 1.194547 CCACAACGATCCGTGTGAAAG 59.805 52.381 19.97 4.96 39.99 2.62
2200 2306 6.040054 GGGCTAATAAAATTACCCACAACGAT 59.960 38.462 0.00 0.00 37.30 3.73
2260 2366 1.135257 CAGTTGTGGGACTAGAGAGCG 60.135 57.143 0.00 0.00 0.00 5.03
2261 2367 1.896465 ACAGTTGTGGGACTAGAGAGC 59.104 52.381 0.00 0.00 0.00 4.09
2262 2368 3.574396 TCAACAGTTGTGGGACTAGAGAG 59.426 47.826 13.14 0.00 0.00 3.20
2263 2369 3.572642 TCAACAGTTGTGGGACTAGAGA 58.427 45.455 13.14 0.00 0.00 3.10
2368 2476 4.739587 ACAGTAGAAGCTTAGGCCTTAC 57.260 45.455 12.58 5.34 39.73 2.34
2387 2497 4.288626 AGGGAACAAGGAAGCTTATGTACA 59.711 41.667 0.00 0.00 0.00 2.90
2388 2498 4.636206 CAGGGAACAAGGAAGCTTATGTAC 59.364 45.833 0.00 2.77 0.00 2.90
2389 2499 4.534500 TCAGGGAACAAGGAAGCTTATGTA 59.466 41.667 0.00 0.00 0.00 2.29
2390 2500 3.330701 TCAGGGAACAAGGAAGCTTATGT 59.669 43.478 0.00 2.28 0.00 2.29
2391 2501 3.955471 TCAGGGAACAAGGAAGCTTATG 58.045 45.455 0.00 1.56 0.00 1.90
2392 2502 4.657814 TTCAGGGAACAAGGAAGCTTAT 57.342 40.909 0.00 0.00 0.00 1.73
2393 2503 4.657814 ATTCAGGGAACAAGGAAGCTTA 57.342 40.909 0.00 0.00 0.00 3.09
2441 2551 3.423123 GCAGAACAAAACAGTATCGACGG 60.423 47.826 0.00 0.00 0.00 4.79
2449 2559 5.117355 CATGAGATGCAGAACAAAACAGT 57.883 39.130 0.00 0.00 0.00 3.55
2476 2586 7.037586 ACTCCAAGAGGTACCTTTATGAATGAA 60.038 37.037 17.53 0.00 33.35 2.57
2629 2739 9.128107 CAATGAAAATGCAGTAACGAAATAAGT 57.872 29.630 0.00 0.00 0.00 2.24
2637 2747 6.598525 TCAGTACAATGAAAATGCAGTAACG 58.401 36.000 0.00 0.00 0.00 3.18
2919 3029 0.174845 TATCGCCTCCCGTGAAACTG 59.825 55.000 0.00 0.00 38.35 3.16
2934 3044 4.182693 TGAAATGGCTATACCGGTATCG 57.817 45.455 30.04 24.19 43.94 2.92
2943 3053 3.882888 CGGCCTTCTTTGAAATGGCTATA 59.117 43.478 0.00 0.00 42.84 1.31
2991 3101 0.700564 TGCAGGCATCTTTTCCTCCT 59.299 50.000 0.00 0.00 0.00 3.69
3116 3229 2.310349 ACATGTGTGGTTTGGGCCTATA 59.690 45.455 4.53 0.00 0.00 1.31
3117 3230 1.077005 ACATGTGTGGTTTGGGCCTAT 59.923 47.619 4.53 0.00 0.00 2.57
3118 3231 0.480690 ACATGTGTGGTTTGGGCCTA 59.519 50.000 4.53 0.00 0.00 3.93
3119 3232 0.827507 GACATGTGTGGTTTGGGCCT 60.828 55.000 1.15 0.00 0.00 5.19
3120 3233 0.827507 AGACATGTGTGGTTTGGGCC 60.828 55.000 1.15 0.00 0.00 5.80
3121 3234 1.000274 GAAGACATGTGTGGTTTGGGC 60.000 52.381 1.15 0.00 0.00 5.36
3122 3235 1.613437 GGAAGACATGTGTGGTTTGGG 59.387 52.381 1.15 0.00 0.00 4.12
3123 3236 2.305928 TGGAAGACATGTGTGGTTTGG 58.694 47.619 1.15 0.00 0.00 3.28
3125 3238 3.751175 CGTATGGAAGACATGTGTGGTTT 59.249 43.478 1.15 0.00 40.82 3.27
3126 3239 3.007506 TCGTATGGAAGACATGTGTGGTT 59.992 43.478 1.15 0.00 40.82 3.67
3127 3240 2.565391 TCGTATGGAAGACATGTGTGGT 59.435 45.455 1.15 0.00 40.82 4.16
3128 3241 3.245518 TCGTATGGAAGACATGTGTGG 57.754 47.619 1.15 0.00 40.82 4.17
3129 3242 5.351189 TCAAATCGTATGGAAGACATGTGTG 59.649 40.000 1.15 0.00 40.82 3.82
3130 3243 5.487433 TCAAATCGTATGGAAGACATGTGT 58.513 37.500 1.15 0.00 40.82 3.72
3135 3248 5.351948 TGGATCAAATCGTATGGAAGACA 57.648 39.130 0.00 0.00 0.00 3.41
3218 3491 9.807649 ATACAGACATTTTTATTCATTTCCAGC 57.192 29.630 0.00 0.00 0.00 4.85
3320 3593 4.403752 AGCATGTGACTATGTGAGCTAAGA 59.596 41.667 0.00 0.00 0.00 2.10
3370 3646 8.853345 CAATGCTCAACAATACTCACAATAAAC 58.147 33.333 0.00 0.00 0.00 2.01
3371 3647 8.575589 ACAATGCTCAACAATACTCACAATAAA 58.424 29.630 0.00 0.00 0.00 1.40
3372 3648 8.022550 CACAATGCTCAACAATACTCACAATAA 58.977 33.333 0.00 0.00 0.00 1.40
3381 3657 7.649306 AGAAAAAGACACAATGCTCAACAATAC 59.351 33.333 0.00 0.00 0.00 1.89
3384 3660 5.964758 AGAAAAAGACACAATGCTCAACAA 58.035 33.333 0.00 0.00 0.00 2.83
3385 3661 5.581126 AGAAAAAGACACAATGCTCAACA 57.419 34.783 0.00 0.00 0.00 3.33
3386 3662 6.531240 TGAAAGAAAAAGACACAATGCTCAAC 59.469 34.615 0.00 0.00 0.00 3.18
3387 3663 6.629128 TGAAAGAAAAAGACACAATGCTCAA 58.371 32.000 0.00 0.00 0.00 3.02
3388 3664 6.127647 ACTGAAAGAAAAAGACACAATGCTCA 60.128 34.615 0.00 0.00 37.43 4.26
3389 3665 6.268566 ACTGAAAGAAAAAGACACAATGCTC 58.731 36.000 0.00 0.00 37.43 4.26
3399 3744 6.808212 CACAAGCAGAAACTGAAAGAAAAAGA 59.192 34.615 2.81 0.00 37.43 2.52
3416 3761 1.538950 GAAGAGGGAAAGCACAAGCAG 59.461 52.381 0.00 0.00 45.49 4.24
3430 3775 8.421249 AACAAGATGAGATAGATAGGAAGAGG 57.579 38.462 0.00 0.00 0.00 3.69
3431 3776 9.695526 CAAACAAGATGAGATAGATAGGAAGAG 57.304 37.037 0.00 0.00 0.00 2.85
3432 3777 8.147058 GCAAACAAGATGAGATAGATAGGAAGA 58.853 37.037 0.00 0.00 0.00 2.87
3433 3778 7.930325 TGCAAACAAGATGAGATAGATAGGAAG 59.070 37.037 0.00 0.00 0.00 3.46
3436 3781 6.426328 GGTGCAAACAAGATGAGATAGATAGG 59.574 42.308 0.00 0.00 0.00 2.57
3443 3788 3.159213 TGGGTGCAAACAAGATGAGAT 57.841 42.857 0.00 0.00 0.00 2.75
3447 3792 1.619827 ACCATGGGTGCAAACAAGATG 59.380 47.619 18.09 0.00 32.98 2.90
3535 3884 4.935205 TCCATGATCAGAACCACTTTTACG 59.065 41.667 0.09 0.00 0.00 3.18
3538 3887 4.219288 GCTTCCATGATCAGAACCACTTTT 59.781 41.667 0.09 0.00 0.00 2.27
3573 3922 0.321653 ATTGACCTTCTCCACCACGC 60.322 55.000 0.00 0.00 0.00 5.34
3622 3971 1.040646 TATCACAGTCATCCTCGGGC 58.959 55.000 0.00 0.00 0.00 6.13
4180 4558 6.462500 AGAGACATGACATCATATAGCAACC 58.538 40.000 0.00 0.00 34.26 3.77
4196 4574 2.562635 CCTGCAATCCAGAGAGACATG 58.437 52.381 0.00 0.00 44.64 3.21
4514 4901 2.232452 AGAAGCGTGCAGAACAGTAGAT 59.768 45.455 0.00 0.00 0.00 1.98
4555 4942 0.957888 GGCCTCCTTGCACAGTTCTC 60.958 60.000 0.00 0.00 0.00 2.87
4562 4949 0.968405 TTTGATTGGCCTCCTTGCAC 59.032 50.000 3.32 0.00 0.00 4.57
4593 4980 5.152097 CAAAGTTGCTAGTTTCATCAGCAG 58.848 41.667 0.00 0.00 45.39 4.24
4641 5028 8.603242 ATTCGAGTGGCGTTTATCTAATTAAT 57.397 30.769 0.00 0.00 41.80 1.40
4648 5035 3.865745 CAGAATTCGAGTGGCGTTTATCT 59.134 43.478 0.00 0.00 41.80 1.98
4655 5042 0.456142 TCGTCAGAATTCGAGTGGCG 60.456 55.000 12.47 12.47 40.62 5.69
4691 5078 9.766277 GACATGTTTTTAAGTTTGAAAATTGCA 57.234 25.926 0.00 0.00 30.11 4.08
4699 5086 9.311916 CTGGAAATGACATGTTTTTAAGTTTGA 57.688 29.630 0.00 0.00 0.00 2.69
4707 5094 4.141756 TGCCACTGGAAATGACATGTTTTT 60.142 37.500 0.00 3.50 0.00 1.94
4712 5099 3.880047 AATGCCACTGGAAATGACATG 57.120 42.857 0.00 0.00 0.00 3.21
4716 5103 4.952071 TGAAAAATGCCACTGGAAATGA 57.048 36.364 0.00 0.00 0.00 2.57
4747 5134 3.238441 TGCAAACTTTGAAACACGTCAC 58.762 40.909 5.65 0.00 0.00 3.67
4750 5137 5.659048 TTTTTGCAAACTTTGAAACACGT 57.341 30.435 12.39 0.00 0.00 4.49
4773 5160 6.339730 TCAAACTTTGAAAATGTCACTGCAT 58.660 32.000 1.47 0.00 36.59 3.96
4796 5184 1.063031 GAAGCGCCACTGCAATTTTC 58.937 50.000 2.29 0.00 37.32 2.29
4797 5185 0.675633 AGAAGCGCCACTGCAATTTT 59.324 45.000 2.29 0.00 37.32 1.82
4817 5205 2.228582 CACTTGAATTGTGGCGATTCCA 59.771 45.455 6.63 0.00 44.18 3.53
4819 5207 2.867429 CCACTTGAATTGTGGCGATTC 58.133 47.619 0.85 2.92 46.73 2.52
4887 5275 3.072184 AGGGTTCATGAGAGACCATATGC 59.928 47.826 15.35 0.12 0.00 3.14
4889 5277 3.072184 GCAGGGTTCATGAGAGACCATAT 59.928 47.826 15.35 0.44 0.00 1.78
4900 5288 2.424601 CAACTACCATGCAGGGTTCATG 59.575 50.000 30.28 19.72 43.89 3.07
4901 5289 2.041620 ACAACTACCATGCAGGGTTCAT 59.958 45.455 30.28 11.74 43.89 2.57
4911 5299 7.492669 CCTGACTTTACAGATACAACTACCATG 59.507 40.741 0.00 0.00 39.94 3.66
4912 5300 7.556844 CCTGACTTTACAGATACAACTACCAT 58.443 38.462 0.00 0.00 39.94 3.55
4921 5309 4.990257 TGTACGCCTGACTTTACAGATAC 58.010 43.478 0.00 0.00 39.94 2.24
4958 5346 3.901844 CCCCTATAGGCTGCTACAGTTAA 59.098 47.826 13.85 0.00 33.43 2.01
4964 5352 4.833390 CAATAACCCCTATAGGCTGCTAC 58.167 47.826 13.85 0.00 0.00 3.58
5092 5486 4.394797 TGGGCCATGGCATTTATATGTA 57.605 40.909 36.56 8.08 44.11 2.29
5117 5511 2.741122 TTTTGCGTACAAAGACCACG 57.259 45.000 0.00 0.00 46.08 4.94
5122 5516 5.790547 GCAAACAAATTTTGCGTACAAAGA 58.209 33.333 9.04 0.00 46.08 2.52
5138 5532 2.042520 GACGGACACGCAGCAAACAA 62.043 55.000 0.00 0.00 46.04 2.83
5139 5533 2.512745 ACGGACACGCAGCAAACA 60.513 55.556 0.00 0.00 46.04 2.83
5142 5536 2.355837 GAGACGGACACGCAGCAA 60.356 61.111 0.00 0.00 46.04 3.91
5153 5547 2.105128 GGAGATGCGTGGAGACGG 59.895 66.667 0.00 0.00 46.20 4.79
5160 5554 2.324330 TTTGTGCCGGAGATGCGTG 61.324 57.895 5.05 0.00 0.00 5.34
5167 5561 1.106944 AACCCAAGTTTGTGCCGGAG 61.107 55.000 5.05 0.00 29.61 4.63
5169 5563 1.067250 CAACCCAAGTTTGTGCCGG 59.933 57.895 0.00 0.00 32.45 6.13
5174 5568 5.358725 AGACGTAAATTCAACCCAAGTTTGT 59.641 36.000 0.00 0.00 32.45 2.83
5179 5573 5.929992 TGTCTAGACGTAAATTCAACCCAAG 59.070 40.000 17.85 0.00 0.00 3.61
5198 5592 1.069703 CGTCCGTTCAACGTCTGTCTA 60.070 52.381 9.52 0.00 40.58 2.59
5207 5601 4.696172 CGCGCACGTCCGTTCAAC 62.696 66.667 8.75 0.00 33.53 3.18
5222 5616 0.163788 CGAACACCAAGATGACACGC 59.836 55.000 0.00 0.00 0.00 5.34
5223 5617 0.163788 GCGAACACCAAGATGACACG 59.836 55.000 0.00 0.00 0.00 4.49
5252 5646 1.367840 GGTCTGCCGACTGACTTGT 59.632 57.895 8.25 0.00 42.61 3.16
5254 5648 1.367840 GTGGTCTGCCGACTGACTT 59.632 57.895 8.25 0.00 42.61 3.01
5255 5649 2.574955 GGTGGTCTGCCGACTGACT 61.575 63.158 8.25 0.00 42.61 3.41
5260 5654 1.681327 TAGGAGGTGGTCTGCCGAC 60.681 63.158 0.00 0.00 39.49 4.79
5266 5660 0.910088 GGCTTGGTAGGAGGTGGTCT 60.910 60.000 0.00 0.00 0.00 3.85
5277 5671 3.767131 GCTTGGATTAAAAGGGCTTGGTA 59.233 43.478 0.00 0.00 0.00 3.25
5278 5672 2.567169 GCTTGGATTAAAAGGGCTTGGT 59.433 45.455 0.00 0.00 0.00 3.67
5279 5673 2.417243 CGCTTGGATTAAAAGGGCTTGG 60.417 50.000 0.00 0.00 31.85 3.61
5287 5681 1.524848 TCCACGCGCTTGGATTAAAA 58.475 45.000 29.88 8.59 41.00 1.52


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

AutoCloner maintained by Alex Coulton.