Multiple sequence alignment - TraesCS5A01G178900

Loading Multiple Alignment...

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 TraesCS5A01G178900 chr5A 100.000 4436 0 0 1 4436 376995591 376991156 0.000000e+00 8192.0
1 TraesCS5A01G178900 chr5D 94.295 2086 83 14 60 2134 285134570 285132510 0.000000e+00 3160.0
2 TraesCS5A01G178900 chr5D 90.221 1943 117 28 2132 4041 285132480 285130578 0.000000e+00 2468.0
3 TraesCS5A01G178900 chr5D 91.743 327 16 5 4115 4436 285130020 285129700 1.130000e-120 444.0
4 TraesCS5A01G178900 chr5D 100.000 57 0 0 1 57 285134604 285134548 6.070000e-19 106.0
5 TraesCS5A01G178900 chr5B 92.649 2095 112 18 60 2134 322556708 322554636 0.000000e+00 2977.0
6 TraesCS5A01G178900 chr5B 92.000 1675 95 24 2132 3789 322554606 322552954 0.000000e+00 2314.0
7 TraesCS5A01G178900 chr5B 92.661 327 13 5 4115 4436 322552536 322552216 1.120000e-125 460.0
8 TraesCS5A01G178900 chr5B 100.000 37 0 0 2 38 322556741 322556705 7.960000e-08 69.4
9 TraesCS5A01G178900 chr4B 79.137 278 32 16 3671 3945 302736558 302736812 7.630000e-38 169.0
10 TraesCS5A01G178900 chr3B 78.777 278 32 17 3671 3945 153628090 153627837 1.280000e-35 161.0


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 TraesCS5A01G178900 chr5A 376991156 376995591 4435 True 8192.0 8192 100.00000 1 4436 1 chr5A.!!$R1 4435
1 TraesCS5A01G178900 chr5D 285129700 285134604 4904 True 1544.5 3160 94.06475 1 4436 4 chr5D.!!$R1 4435
2 TraesCS5A01G178900 chr5B 322552216 322556741 4525 True 1455.1 2977 94.32750 2 4436 4 chr5B.!!$R1 4434

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
399 400 0.249868 TCCGTGTCAGTCTTTGGCTG 60.250 55.000 0.00 0.00 35.43 4.85 F
402 403 1.261619 CGTGTCAGTCTTTGGCTGTTC 59.738 52.381 0.00 0.00 35.60 3.18 F
1775 1791 0.042281 GTGGTGGTAGGGGTAGAGGT 59.958 60.000 0.00 0.00 0.00 3.85 F
2586 2641 0.459899 TAAGTCGCATCGTGCATCCT 59.540 50.000 9.95 0.82 45.36 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1685 1701 0.744281 AAACACCACGGAAGGCAAAG 59.256 50.0 0.00 0.0 0.00 2.77 R
2155 2207 0.758123 CCACCAAAACAGCCACCAAT 59.242 50.0 0.00 0.0 0.00 3.16 R
2599 2654 0.458543 CACTACTGCTACACTGGGCG 60.459 60.0 0.00 0.0 0.00 6.13 R
4104 4189 0.039798 AACAAGATGCAGCAACGCAG 60.040 50.0 4.07 0.0 46.99 5.18 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
253 254 1.507140 TTACGGGATTCCTGCCTCAT 58.493 50.000 11.65 0.00 32.02 2.90
339 340 3.332034 CCGGTCAAGTTTTTATCGAGGT 58.668 45.455 0.00 0.00 0.00 3.85
369 370 2.029290 GTGATCCAGTTGTAGTCACGGT 60.029 50.000 0.00 0.00 31.15 4.83
373 374 2.132762 CCAGTTGTAGTCACGGTGTTC 58.867 52.381 8.17 3.26 0.00 3.18
399 400 0.249868 TCCGTGTCAGTCTTTGGCTG 60.250 55.000 0.00 0.00 35.43 4.85
402 403 1.261619 CGTGTCAGTCTTTGGCTGTTC 59.738 52.381 0.00 0.00 35.60 3.18
426 427 2.488153 GCCCGACTAATTTTTCAGCTGT 59.512 45.455 14.67 0.00 0.00 4.40
439 440 6.851222 TTTTCAGCTGTTTGTTGTTTGAAA 57.149 29.167 14.67 0.00 32.94 2.69
440 441 7.432350 TTTTCAGCTGTTTGTTGTTTGAAAT 57.568 28.000 14.67 0.00 34.31 2.17
441 442 6.406093 TTCAGCTGTTTGTTGTTTGAAATG 57.594 33.333 14.67 0.00 0.00 2.32
443 444 5.931146 TCAGCTGTTTGTTGTTTGAAATGTT 59.069 32.000 14.67 0.00 0.00 2.71
444 445 6.016718 CAGCTGTTTGTTGTTTGAAATGTTG 58.983 36.000 5.25 0.00 0.00 3.33
445 446 4.787591 GCTGTTTGTTGTTTGAAATGTTGC 59.212 37.500 0.00 0.00 0.00 4.17
446 447 4.950926 TGTTTGTTGTTTGAAATGTTGCG 58.049 34.783 0.00 0.00 0.00 4.85
447 448 3.648179 TTGTTGTTTGAAATGTTGCGC 57.352 38.095 0.00 0.00 0.00 6.09
448 449 2.886081 TGTTGTTTGAAATGTTGCGCT 58.114 38.095 9.73 0.00 0.00 5.92
449 450 2.602211 TGTTGTTTGAAATGTTGCGCTG 59.398 40.909 9.73 0.00 0.00 5.18
555 559 4.148348 GCATTTACCGCTGATAAGTAGACG 59.852 45.833 0.00 0.00 0.00 4.18
609 622 7.199541 CATCTTGAAATGGTGATGGAGTATC 57.800 40.000 0.00 0.00 34.40 2.24
689 702 8.715191 TGTGTCAATTTTTGCAACTAAGAATT 57.285 26.923 0.00 0.00 0.00 2.17
697 710 9.783081 ATTTTTGCAACTAAGAATTCCTTCATT 57.217 25.926 0.00 0.00 36.34 2.57
804 817 5.585500 TGAACAGTCACTTAACATTACGC 57.415 39.130 0.00 0.00 0.00 4.42
877 893 3.314553 TCTTCTTCCTGTTTTACTCGCG 58.685 45.455 0.00 0.00 0.00 5.87
896 912 2.158943 GCGGGCCTACTCTGTTATTCTT 60.159 50.000 0.84 0.00 0.00 2.52
1143 1159 5.707495 TGGGTCTTACCAGGTAACATTTTT 58.293 37.500 8.09 0.00 41.02 1.94
1178 1194 6.096141 TGCAAGTTCTTGAATGGTCTTGTAAA 59.904 34.615 15.52 0.27 35.96 2.01
1512 1528 1.337118 GATCAGGCAGAGGTAGAGGG 58.663 60.000 0.00 0.00 0.00 4.30
1604 1620 3.003689 ACGATTGGTGAGCAACTTTTCTG 59.996 43.478 0.00 0.00 0.00 3.02
1611 1627 4.485163 GTGAGCAACTTTTCTGTTGTTGT 58.515 39.130 8.78 0.00 46.33 3.32
1620 1636 7.448748 ACTTTTCTGTTGTTGTTGACTAGTT 57.551 32.000 0.00 0.00 0.00 2.24
1635 1651 7.386848 TGTTGACTAGTTTGGTCTTTACTATGC 59.613 37.037 0.00 0.00 35.04 3.14
1685 1701 3.641437 TTCAGCTGTGGCAATGTAAAC 57.359 42.857 14.67 0.00 41.70 2.01
1748 1764 1.556911 CCTGCTGGTGTTAGTGGATCT 59.443 52.381 0.51 0.00 0.00 2.75
1775 1791 0.042281 GTGGTGGTAGGGGTAGAGGT 59.958 60.000 0.00 0.00 0.00 3.85
1829 1845 2.985847 GCTGCTGTTGGTGGTCCC 60.986 66.667 0.00 0.00 0.00 4.46
1918 1934 6.779049 TCCATTGCTTTGATATGCCTCTTTAT 59.221 34.615 0.00 0.00 0.00 1.40
1928 1948 9.905713 TTGATATGCCTCTTTATTACTTTGTCT 57.094 29.630 0.00 0.00 0.00 3.41
1935 1955 8.235226 GCCTCTTTATTACTTTGTCTTTACACC 58.765 37.037 0.00 0.00 34.61 4.16
1964 1984 3.660669 TGTACTCCCTCCTTCCCAAAATT 59.339 43.478 0.00 0.00 0.00 1.82
1965 1985 4.853276 TGTACTCCCTCCTTCCCAAAATTA 59.147 41.667 0.00 0.00 0.00 1.40
1966 1986 5.313772 TGTACTCCCTCCTTCCCAAAATTAA 59.686 40.000 0.00 0.00 0.00 1.40
1967 1987 5.552430 ACTCCCTCCTTCCCAAAATTAAT 57.448 39.130 0.00 0.00 0.00 1.40
1969 1989 5.222547 ACTCCCTCCTTCCCAAAATTAATGT 60.223 40.000 0.00 0.00 0.00 2.71
1970 1990 5.269189 TCCCTCCTTCCCAAAATTAATGTC 58.731 41.667 0.00 0.00 0.00 3.06
1972 1992 5.272402 CCTCCTTCCCAAAATTAATGTCCT 58.728 41.667 0.00 0.00 0.00 3.85
1973 1993 5.127682 CCTCCTTCCCAAAATTAATGTCCTG 59.872 44.000 0.00 0.00 0.00 3.86
1975 1995 5.951747 TCCTTCCCAAAATTAATGTCCTGAG 59.048 40.000 0.00 0.00 0.00 3.35
1976 1996 5.716703 CCTTCCCAAAATTAATGTCCTGAGT 59.283 40.000 0.00 0.00 0.00 3.41
1978 1998 6.588719 TCCCAAAATTAATGTCCTGAGTTG 57.411 37.500 0.00 0.00 0.00 3.16
1979 1999 6.074648 TCCCAAAATTAATGTCCTGAGTTGT 58.925 36.000 0.00 0.00 0.00 3.32
1980 2000 6.553100 TCCCAAAATTAATGTCCTGAGTTGTT 59.447 34.615 0.00 0.00 0.00 2.83
1983 2003 9.757227 CCAAAATTAATGTCCTGAGTTGTTTTA 57.243 29.630 0.00 0.00 0.00 1.52
2097 2117 5.308825 ACTTGGTCATTTGACTTAGGACAG 58.691 41.667 10.32 0.62 44.20 3.51
2127 2147 9.853555 TTATGTGCCTTATATTTTGTGAAACTG 57.146 29.630 0.00 0.00 38.04 3.16
2188 2241 6.586344 TGTTTTGGTGGCAAATGATTTTAGA 58.414 32.000 0.00 0.00 0.00 2.10
2194 2247 6.172630 GGTGGCAAATGATTTTAGAATGGTT 58.827 36.000 0.00 0.00 0.00 3.67
2267 2320 7.459795 TTGTAATTGCTATTGTCCATTGTCA 57.540 32.000 3.49 0.00 0.00 3.58
2268 2321 7.643569 TGTAATTGCTATTGTCCATTGTCAT 57.356 32.000 3.49 0.00 0.00 3.06
2269 2322 7.706159 TGTAATTGCTATTGTCCATTGTCATC 58.294 34.615 3.49 0.00 0.00 2.92
2296 2349 4.592485 ATTGTATAGACCTCGCAAGGAG 57.408 45.455 0.00 0.00 46.67 3.69
2322 2375 8.760735 GGATACCCTCTTTCTAGTCTTACTTTT 58.239 37.037 0.00 0.00 0.00 2.27
2324 2377 6.770542 ACCCTCTTTCTAGTCTTACTTTTGG 58.229 40.000 0.00 0.00 0.00 3.28
2327 2380 6.182507 TCTTTCTAGTCTTACTTTTGGCCA 57.817 37.500 0.00 0.00 0.00 5.36
2340 2393 8.655651 TTACTTTTGGCCAATTAAAGTTCTTG 57.344 30.769 29.69 9.53 41.12 3.02
2341 2394 6.883744 ACTTTTGGCCAATTAAAGTTCTTGA 58.116 32.000 22.77 1.26 38.56 3.02
2342 2395 6.986231 ACTTTTGGCCAATTAAAGTTCTTGAG 59.014 34.615 22.77 4.17 38.56 3.02
2384 2439 7.535139 TGTTTTGTAATGTTCTATAAGGCTGC 58.465 34.615 0.00 0.00 0.00 5.25
2393 2448 8.601047 ATGTTCTATAAGGCTGCTATCTGATA 57.399 34.615 0.00 0.00 0.00 2.15
2396 2451 8.690884 GTTCTATAAGGCTGCTATCTGATATGA 58.309 37.037 0.00 0.00 0.00 2.15
2406 2461 9.007901 GCTGCTATCTGATATGAAACCTATTTT 57.992 33.333 0.00 0.00 0.00 1.82
2449 2504 1.904287 ATGTAAACTGGGCAAAGCGA 58.096 45.000 0.00 0.00 0.00 4.93
2518 2573 6.437755 AGGTGGTGTGAGGTACTACATATTA 58.562 40.000 0.00 0.00 41.55 0.98
2586 2641 0.459899 TAAGTCGCATCGTGCATCCT 59.540 50.000 9.95 0.82 45.36 3.24
2588 2643 0.807667 AGTCGCATCGTGCATCCTTC 60.808 55.000 9.95 0.00 45.36 3.46
2592 2647 2.009108 CATCGTGCATCCTTCACCG 58.991 57.895 0.00 0.00 0.00 4.94
2599 2654 1.134699 TGCATCCTTCACCGATCTGAC 60.135 52.381 0.00 0.00 0.00 3.51
2605 2660 2.202797 CACCGATCTGACGCCCAG 60.203 66.667 0.00 0.00 44.27 4.45
2609 2664 1.663379 CCGATCTGACGCCCAGTGTA 61.663 60.000 5.48 0.00 43.38 2.90
2621 2676 2.171840 CCCAGTGTAGCAGTAGTGTCT 58.828 52.381 0.00 0.00 0.00 3.41
2634 2689 6.378564 AGCAGTAGTGTCTACAGTGTTATGAT 59.621 38.462 0.00 0.00 0.00 2.45
2635 2690 6.693545 GCAGTAGTGTCTACAGTGTTATGATC 59.306 42.308 0.00 0.00 0.00 2.92
2704 2774 8.695284 GCTTTGTATCTGATTACTTACATCGAG 58.305 37.037 0.00 0.00 0.00 4.04
2725 2795 6.153170 TCGAGGGTACATATTTGTGTCTTACA 59.847 38.462 0.00 0.00 36.53 2.41
2779 2849 3.131478 CGGGGTGGCGGCTTTAAG 61.131 66.667 11.43 0.00 0.00 1.85
2855 2925 3.129462 GGAGGTAGGATGCTTTCTTTTGC 59.871 47.826 0.00 0.00 0.00 3.68
2891 2965 6.667661 TGTGTCATGATATTGGGTTTCCATA 58.332 36.000 0.00 0.00 43.63 2.74
2893 2967 7.448161 TGTGTCATGATATTGGGTTTCCATATC 59.552 37.037 0.00 0.00 43.63 1.63
2972 3046 6.575162 AAAAGAAGTTCCGTGCTAAATCAT 57.425 33.333 0.00 0.00 0.00 2.45
2987 3061 9.534565 GTGCTAAATCATATCAAACTGAGAGTA 57.465 33.333 0.00 0.00 0.00 2.59
2993 3067 6.867550 TCATATCAAACTGAGAGTACACCAG 58.132 40.000 0.00 1.67 0.00 4.00
3077 3151 6.763303 TTTTTCTTCGCTTTTAAGGCATTC 57.237 33.333 0.00 0.00 0.00 2.67
3080 3154 3.370978 TCTTCGCTTTTAAGGCATTCTCG 59.629 43.478 0.00 0.00 0.00 4.04
3101 3175 6.142798 TCTCGTTTGATTAAGTCGTGTGTTAC 59.857 38.462 0.00 0.00 0.00 2.50
3104 3178 7.010367 TCGTTTGATTAAGTCGTGTGTTACTTT 59.990 33.333 0.00 0.00 37.19 2.66
3106 3180 7.773864 TTGATTAAGTCGTGTGTTACTTTCA 57.226 32.000 0.00 0.00 37.19 2.69
3110 3184 9.136952 GATTAAGTCGTGTGTTACTTTCATAGT 57.863 33.333 0.00 0.00 41.04 2.12
3112 3186 7.404139 AAGTCGTGTGTTACTTTCATAGTTC 57.596 36.000 0.00 0.00 38.33 3.01
3113 3187 6.746120 AGTCGTGTGTTACTTTCATAGTTCT 58.254 36.000 0.00 0.00 38.33 3.01
3114 3188 7.208080 AGTCGTGTGTTACTTTCATAGTTCTT 58.792 34.615 0.00 0.00 38.33 2.52
3115 3189 7.169308 AGTCGTGTGTTACTTTCATAGTTCTTG 59.831 37.037 0.00 0.00 38.33 3.02
3116 3190 6.982141 TCGTGTGTTACTTTCATAGTTCTTGT 59.018 34.615 0.00 0.00 38.33 3.16
3117 3191 7.168637 TCGTGTGTTACTTTCATAGTTCTTGTC 59.831 37.037 0.00 0.00 38.33 3.18
3120 3194 8.773645 TGTGTTACTTTCATAGTTCTTGTCATG 58.226 33.333 0.00 0.00 38.33 3.07
3173 3254 6.449698 ACTAGAGTTTTCCATTTTGCATGTG 58.550 36.000 0.00 0.00 0.00 3.21
3178 3259 2.442212 TCCATTTTGCATGTGCTGTG 57.558 45.000 6.55 0.59 42.66 3.66
3195 3276 3.829948 CTGTGCATGAACTGGTGATTTC 58.170 45.455 5.18 0.00 0.00 2.17
3542 3623 5.651576 TCACATTGCCATTAGACATGCTTAA 59.348 36.000 0.00 0.00 0.00 1.85
3543 3624 6.321945 TCACATTGCCATTAGACATGCTTAAT 59.678 34.615 0.00 0.00 0.00 1.40
3544 3625 6.982141 CACATTGCCATTAGACATGCTTAATT 59.018 34.615 0.00 0.00 0.00 1.40
3545 3626 8.136800 CACATTGCCATTAGACATGCTTAATTA 58.863 33.333 0.00 0.00 0.00 1.40
3575 3656 3.232279 TGGGTTTTGGGTTCCCAAG 57.768 52.632 20.54 0.00 46.78 3.61
3585 3666 2.445145 TGGGTTCCCAAGAAACTGATCA 59.555 45.455 8.26 0.00 39.82 2.92
3588 3669 4.398319 GGTTCCCAAGAAACTGATCAGAA 58.602 43.478 29.27 6.93 36.71 3.02
3592 3673 6.131972 TCCCAAGAAACTGATCAGAAGAAT 57.868 37.500 29.27 9.61 0.00 2.40
3631 3712 2.092211 GGTACAACAGAATTGACGAGCG 59.908 50.000 0.00 0.00 0.00 5.03
3695 3776 3.123804 GACGAACCAGGCATAGTACATG 58.876 50.000 0.00 0.00 0.00 3.21
3696 3777 2.764010 ACGAACCAGGCATAGTACATGA 59.236 45.455 0.00 0.00 0.00 3.07
3698 3779 3.181475 CGAACCAGGCATAGTACATGACT 60.181 47.826 0.00 7.58 42.69 3.41
3708 3789 2.846193 AGTACATGACTTGTTGCGGTT 58.154 42.857 0.00 0.00 39.87 4.44
3767 3850 1.473677 GCCATGTCTGCTATGTTTGCA 59.526 47.619 0.00 0.00 38.81 4.08
3827 3910 5.929992 AGTTGACATTTGATTTGATGGCTTG 59.070 36.000 0.00 0.00 32.40 4.01
3848 3931 2.673200 ATCATGGTGCAGGCGTCCT 61.673 57.895 0.00 0.00 0.00 3.85
3866 3949 6.857964 GGCGTCCTTTACAAATCATTATCATG 59.142 38.462 0.00 0.00 0.00 3.07
3867 3950 7.255104 GGCGTCCTTTACAAATCATTATCATGA 60.255 37.037 0.00 0.00 43.85 3.07
3881 3964 9.797556 ATCATTATCATGATTATCGGCAATTTG 57.202 29.630 14.65 0.00 46.45 2.32
3882 3965 9.012161 TCATTATCATGATTATCGGCAATTTGA 57.988 29.630 14.65 0.00 34.22 2.69
3883 3966 9.797556 CATTATCATGATTATCGGCAATTTGAT 57.202 29.630 14.65 10.82 31.07 2.57
3889 3972 9.414295 CATGATTATCGGCAATTTGATATTTGT 57.586 29.630 0.00 0.00 0.00 2.83
3890 3973 8.800231 TGATTATCGGCAATTTGATATTTGTG 57.200 30.769 0.00 0.00 0.00 3.33
3905 3988 9.906660 TTGATATTTGTGTTATTTGTCTGAACC 57.093 29.630 0.00 0.00 0.00 3.62
3972 4057 1.141657 GGGCACTCCATCAGCTATCAA 59.858 52.381 0.00 0.00 35.00 2.57
4013 4098 2.525750 ATACGTTTGCATCAACAGCG 57.474 45.000 0.00 0.00 33.85 5.18
4022 4107 3.403968 TGCATCAACAGCGTAGGTAAAA 58.596 40.909 0.00 0.00 35.08 1.52
4041 4126 5.876651 AAAATTTCTGGAATATCAGGGCC 57.123 39.130 0.00 0.00 35.58 5.80
4043 4128 3.582998 TTTCTGGAATATCAGGGCCTG 57.417 47.619 28.01 28.01 35.58 4.85
4044 4129 0.767375 TCTGGAATATCAGGGCCTGC 59.233 55.000 29.02 13.95 35.58 4.85
4045 4130 0.769873 CTGGAATATCAGGGCCTGCT 59.230 55.000 29.02 22.07 0.00 4.24
4046 4131 0.767375 TGGAATATCAGGGCCTGCTC 59.233 55.000 29.02 19.65 0.00 4.26
4047 4132 1.063183 GGAATATCAGGGCCTGCTCT 58.937 55.000 29.02 17.16 0.00 4.09
4050 4135 0.767446 ATATCAGGGCCTGCTCTGCT 60.767 55.000 29.02 7.37 43.87 4.24
4051 4136 1.406065 TATCAGGGCCTGCTCTGCTC 61.406 60.000 29.02 0.00 43.87 4.26
4053 4138 2.610233 AGGGCCTGCTCTGCTCTT 60.610 61.111 4.50 0.00 35.56 2.85
4054 4139 2.229928 AGGGCCTGCTCTGCTCTTT 61.230 57.895 4.50 0.00 35.56 2.52
4056 4141 0.897401 GGGCCTGCTCTGCTCTTTTT 60.897 55.000 0.84 0.00 0.00 1.94
4076 4161 4.647424 TTTTGTTTGAAAGATCCAGCGT 57.353 36.364 0.00 0.00 0.00 5.07
4077 4162 4.647424 TTTGTTTGAAAGATCCAGCGTT 57.353 36.364 0.00 0.00 0.00 4.84
4078 4163 3.624326 TGTTTGAAAGATCCAGCGTTG 57.376 42.857 0.00 0.00 0.00 4.10
4080 4165 1.896220 TTGAAAGATCCAGCGTTGCT 58.104 45.000 0.00 0.00 40.77 3.91
4089 4174 3.352222 AGCGTTGCTGCTGCTGTC 61.352 61.111 17.00 6.21 45.28 3.51
4090 4175 4.395583 GCGTTGCTGCTGCTGTCC 62.396 66.667 17.00 1.33 40.48 4.02
4091 4176 2.667536 CGTTGCTGCTGCTGTCCT 60.668 61.111 17.00 0.00 40.48 3.85
4092 4177 2.256591 CGTTGCTGCTGCTGTCCTT 61.257 57.895 17.00 0.00 40.48 3.36
4093 4178 1.789078 CGTTGCTGCTGCTGTCCTTT 61.789 55.000 17.00 0.00 40.48 3.11
4094 4179 0.318445 GTTGCTGCTGCTGTCCTTTG 60.318 55.000 17.00 0.00 40.48 2.77
4097 4182 0.886563 GCTGCTGCTGTCCTTTGATT 59.113 50.000 8.53 0.00 36.03 2.57
4098 4183 1.402456 GCTGCTGCTGTCCTTTGATTG 60.402 52.381 8.53 0.00 36.03 2.67
4101 4186 2.751259 TGCTGCTGTCCTTTGATTGATC 59.249 45.455 0.00 0.00 0.00 2.92
4103 4188 3.380637 GCTGCTGTCCTTTGATTGATCAT 59.619 43.478 0.00 0.00 36.56 2.45
4104 4189 4.497674 GCTGCTGTCCTTTGATTGATCATC 60.498 45.833 0.00 0.00 36.56 2.92
4105 4190 4.851843 TGCTGTCCTTTGATTGATCATCT 58.148 39.130 0.00 0.00 36.56 2.90
4106 4191 4.638865 TGCTGTCCTTTGATTGATCATCTG 59.361 41.667 0.00 0.00 36.56 2.90
4109 4194 3.624861 GTCCTTTGATTGATCATCTGCGT 59.375 43.478 0.00 0.00 36.56 5.24
4110 4195 4.095483 GTCCTTTGATTGATCATCTGCGTT 59.905 41.667 0.00 0.00 36.56 4.84
4111 4196 4.095334 TCCTTTGATTGATCATCTGCGTTG 59.905 41.667 0.00 0.00 36.56 4.10
4112 4197 3.409851 TTGATTGATCATCTGCGTTGC 57.590 42.857 0.00 0.00 36.56 4.17
4113 4198 2.635714 TGATTGATCATCTGCGTTGCT 58.364 42.857 0.00 0.00 32.34 3.91
4187 5036 1.147824 AAGCAGGAGCATGGATCGG 59.852 57.895 0.00 0.00 45.49 4.18
4203 5052 0.392998 TCGGATGCCTTTCTTCCAGC 60.393 55.000 0.00 0.00 38.55 4.85
4259 5108 0.321122 GAGGTGGTTGACTCCTGCTG 60.321 60.000 0.00 0.00 42.94 4.41
4260 5109 1.968540 GGTGGTTGACTCCTGCTGC 60.969 63.158 0.00 0.00 0.00 5.25
4261 5110 1.968540 GTGGTTGACTCCTGCTGCC 60.969 63.158 0.00 0.00 0.00 4.85
4277 5126 3.322466 CCCTGCCACTCGTCCCTT 61.322 66.667 0.00 0.00 0.00 3.95
4299 5148 0.768622 TTTCATGGAGGAACACCCGT 59.231 50.000 0.00 0.00 38.71 5.28
4374 5227 6.821160 TGCTCCATACAAAAACTCGAATATGA 59.179 34.615 0.00 0.00 0.00 2.15
4385 5239 5.661056 ACTCGAATATGAGGTCAACTTCA 57.339 39.130 0.00 0.00 40.39 3.02
4392 5246 7.693951 CGAATATGAGGTCAACTTCATGTTTTC 59.306 37.037 15.65 13.67 41.37 2.29
4410 5264 1.118965 TCCGTGAAGCACCTGAAGGA 61.119 55.000 2.62 0.00 38.94 3.36
4411 5265 0.250295 CCGTGAAGCACCTGAAGGAA 60.250 55.000 2.62 0.00 38.94 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 128 1.945394 GTACCGAGAGTATGCGAGGAA 59.055 52.381 0.00 0.00 32.28 3.36
225 226 3.560068 CAGGAATCCCGTAAATTTCCTCG 59.440 47.826 0.00 0.00 44.73 4.63
253 254 2.684881 GACGTAACTAGAACCCCATCGA 59.315 50.000 0.00 0.00 0.00 3.59
292 293 3.756434 CAGAAATCCAACGGGTAACACAT 59.244 43.478 0.00 0.00 39.74 3.21
298 299 1.673626 GCGTCAGAAATCCAACGGGTA 60.674 52.381 7.13 0.00 35.74 3.69
369 370 0.678950 TGACACGGAGCATCAGAACA 59.321 50.000 0.00 0.00 36.25 3.18
373 374 0.529833 AGACTGACACGGAGCATCAG 59.470 55.000 0.00 0.00 45.09 2.90
399 400 3.058777 TGAAAAATTAGTCGGGCGTGAAC 60.059 43.478 0.00 0.00 0.00 3.18
402 403 2.727916 GCTGAAAAATTAGTCGGGCGTG 60.728 50.000 0.65 0.00 0.00 5.34
426 427 3.681897 AGCGCAACATTTCAAACAACAAA 59.318 34.783 11.47 0.00 0.00 2.83
439 440 2.983229 AGATCTCTTTCAGCGCAACAT 58.017 42.857 11.47 0.00 0.00 2.71
440 441 2.462456 AGATCTCTTTCAGCGCAACA 57.538 45.000 11.47 0.00 0.00 3.33
441 442 4.784710 GCAATAGATCTCTTTCAGCGCAAC 60.785 45.833 11.47 0.00 0.00 4.17
443 444 2.868583 GCAATAGATCTCTTTCAGCGCA 59.131 45.455 11.47 0.00 0.00 6.09
444 445 3.059733 CAGCAATAGATCTCTTTCAGCGC 60.060 47.826 0.00 0.00 0.00 5.92
445 446 4.118410 ACAGCAATAGATCTCTTTCAGCG 58.882 43.478 0.00 0.00 0.00 5.18
446 447 7.279758 AGTTAACAGCAATAGATCTCTTTCAGC 59.720 37.037 8.61 0.00 0.00 4.26
447 448 8.715191 AGTTAACAGCAATAGATCTCTTTCAG 57.285 34.615 8.61 0.00 0.00 3.02
448 449 9.507329 AAAGTTAACAGCAATAGATCTCTTTCA 57.493 29.630 8.61 0.00 0.00 2.69
449 450 9.766277 CAAAGTTAACAGCAATAGATCTCTTTC 57.234 33.333 8.61 0.00 0.00 2.62
555 559 5.182001 ACATCAAGAGCTACCAATTTGACAC 59.818 40.000 0.00 0.00 31.34 3.67
609 622 4.094590 CAGCAGAAAACTTGCAGAGGATAG 59.905 45.833 0.00 0.00 43.92 2.08
618 631 3.183775 CAGCATTTCAGCAGAAAACTTGC 59.816 43.478 16.49 16.49 46.06 4.01
689 702 5.451242 GCACACAACAGGTAAAAATGAAGGA 60.451 40.000 0.00 0.00 0.00 3.36
697 710 3.056536 TGCTTTGCACACAACAGGTAAAA 60.057 39.130 0.00 0.00 34.87 1.52
753 766 4.330620 GTGAACTTAAGTGTCGAACAACCA 59.669 41.667 9.34 0.00 0.00 3.67
804 817 2.422276 AAGCTTGCAAAAAGGCTACG 57.578 45.000 10.91 0.00 34.40 3.51
877 893 4.489306 ACAAGAATAACAGAGTAGGCCC 57.511 45.455 0.00 0.00 0.00 5.80
896 912 3.129871 GCAAATGCCAAAACTAGCAACA 58.870 40.909 0.00 0.00 43.36 3.33
1178 1194 7.738437 ATCATGAAATGGAATTAACAAGGGT 57.262 32.000 0.00 0.00 46.73 4.34
1512 1528 3.127533 GCTGGACCATCACCACGC 61.128 66.667 0.00 0.00 33.57 5.34
1604 1620 5.813080 AGACCAAACTAGTCAACAACAAC 57.187 39.130 0.00 0.00 36.68 3.32
1611 1627 7.446769 TGCATAGTAAAGACCAAACTAGTCAA 58.553 34.615 0.00 0.00 36.68 3.18
1620 1636 6.611642 AGGATAGACTGCATAGTAAAGACCAA 59.388 38.462 0.00 0.00 37.25 3.67
1663 1679 4.099266 AGTTTACATTGCCACAGCTGAAAA 59.901 37.500 23.35 9.05 40.80 2.29
1685 1701 0.744281 AAACACCACGGAAGGCAAAG 59.256 50.000 0.00 0.00 0.00 2.77
1748 1764 2.150719 CCTACCACCACCACCACCA 61.151 63.158 0.00 0.00 0.00 4.17
1775 1791 2.495669 TCTTGCATCATCACTACCACGA 59.504 45.455 0.00 0.00 0.00 4.35
1829 1845 1.497309 TAGGACCAAACAGCCCAGGG 61.497 60.000 0.00 0.00 0.00 4.45
1899 1915 9.455847 CAAAGTAATAAAGAGGCATATCAAAGC 57.544 33.333 0.00 0.00 0.00 3.51
1910 1926 9.503399 AGGTGTAAAGACAAAGTAATAAAGAGG 57.497 33.333 0.00 0.00 37.31 3.69
1918 1934 7.558444 ACAAATGGAGGTGTAAAGACAAAGTAA 59.442 33.333 0.00 0.00 37.31 2.24
1928 1948 4.600111 AGGGAGTACAAATGGAGGTGTAAA 59.400 41.667 0.00 0.00 32.23 2.01
1935 1955 3.118223 GGAAGGAGGGAGTACAAATGGAG 60.118 52.174 0.00 0.00 0.00 3.86
2069 2089 5.929992 CCTAAGTCAAATGACCAAGTTCGTA 59.070 40.000 9.84 0.00 45.85 3.43
2072 2092 5.763204 TGTCCTAAGTCAAATGACCAAGTTC 59.237 40.000 9.84 4.51 45.85 3.01
2073 2093 5.690865 TGTCCTAAGTCAAATGACCAAGTT 58.309 37.500 9.84 1.15 45.85 2.66
2074 2094 5.304686 TGTCCTAAGTCAAATGACCAAGT 57.695 39.130 9.84 0.00 45.85 3.16
2075 2095 4.154918 GCTGTCCTAAGTCAAATGACCAAG 59.845 45.833 9.84 7.64 45.85 3.61
2097 2117 8.870160 TCACAAAATATAAGGCACATAAATGC 57.130 30.769 0.00 0.00 45.34 3.56
2155 2207 0.758123 CCACCAAAACAGCCACCAAT 59.242 50.000 0.00 0.00 0.00 3.16
2157 2209 2.430610 GCCACCAAAACAGCCACCA 61.431 57.895 0.00 0.00 0.00 4.17
2205 2258 9.969001 AAACTTAGCCTGTAACAAGGATAATAA 57.031 29.630 1.73 0.00 44.85 1.40
2209 2262 5.646360 GCAAACTTAGCCTGTAACAAGGATA 59.354 40.000 0.00 0.00 40.02 2.59
2212 2265 3.821033 AGCAAACTTAGCCTGTAACAAGG 59.179 43.478 0.00 0.00 40.63 3.61
2267 2320 5.538813 TGCGAGGTCTATACAATACTTGGAT 59.461 40.000 0.00 0.00 38.02 3.41
2268 2321 4.891168 TGCGAGGTCTATACAATACTTGGA 59.109 41.667 0.00 0.00 34.12 3.53
2269 2322 5.196341 TGCGAGGTCTATACAATACTTGG 57.804 43.478 0.00 0.00 34.12 3.61
2296 2349 7.901283 AAGTAAGACTAGAAAGAGGGTATCC 57.099 40.000 0.00 0.00 0.00 2.59
2309 2362 8.793592 ACTTTAATTGGCCAAAAGTAAGACTAG 58.206 33.333 25.69 17.52 40.65 2.57
2316 2369 8.012957 TCAAGAACTTTAATTGGCCAAAAGTA 57.987 30.769 26.64 15.89 41.36 2.24
2317 2370 6.883744 TCAAGAACTTTAATTGGCCAAAAGT 58.116 32.000 24.71 23.53 43.43 2.66
2318 2371 7.209475 TCTCAAGAACTTTAATTGGCCAAAAG 58.791 34.615 24.71 22.85 36.51 2.27
2322 2375 5.385198 ACTCTCAAGAACTTTAATTGGCCA 58.615 37.500 0.00 0.00 0.00 5.36
2340 2393 9.167311 ACAAAACAATGTCCATCTATTACTCTC 57.833 33.333 0.00 0.00 0.00 3.20
2368 2423 6.924913 TCAGATAGCAGCCTTATAGAACAT 57.075 37.500 0.00 0.00 0.00 2.71
2396 2451 8.576442 CCTGAAACACACATAGAAAATAGGTTT 58.424 33.333 0.00 0.00 0.00 3.27
2406 2461 3.738982 CCACACCTGAAACACACATAGA 58.261 45.455 0.00 0.00 0.00 1.98
2449 2504 6.775629 AGGTGTTACAGACATTACATTTGGTT 59.224 34.615 0.00 0.00 41.10 3.67
2586 2641 2.225791 CTGGGCGTCAGATCGGTGAA 62.226 60.000 2.41 0.00 46.18 3.18
2588 2643 2.202797 CTGGGCGTCAGATCGGTG 60.203 66.667 2.41 0.00 46.18 4.94
2592 2647 0.528684 GCTACACTGGGCGTCAGATC 60.529 60.000 13.38 0.00 46.18 2.75
2599 2654 0.458543 CACTACTGCTACACTGGGCG 60.459 60.000 0.00 0.00 0.00 6.13
2605 2660 4.215827 ACACTGTAGACACTACTGCTACAC 59.784 45.833 13.05 0.00 39.46 2.90
2609 2664 5.710567 TCATAACACTGTAGACACTACTGCT 59.289 40.000 13.05 4.41 0.00 4.24
2621 2676 3.841255 TGTGGGTGGATCATAACACTGTA 59.159 43.478 0.00 0.00 37.72 2.74
2653 2708 6.414732 TGCTTAGCTTTGACCATAACATAGT 58.585 36.000 5.60 0.00 0.00 2.12
2654 2709 6.512415 GCTGCTTAGCTTTGACCATAACATAG 60.512 42.308 5.60 0.00 0.00 2.23
2725 2795 9.918630 CAAAGACAATAATTGATGAGAAAAGGT 57.081 29.630 0.00 0.00 0.00 3.50
2726 2796 8.866956 GCAAAGACAATAATTGATGAGAAAAGG 58.133 33.333 0.00 0.00 0.00 3.11
2734 2804 6.750501 CACCTCTGCAAAGACAATAATTGATG 59.249 38.462 0.00 0.00 0.00 3.07
2735 2805 6.127535 CCACCTCTGCAAAGACAATAATTGAT 60.128 38.462 0.00 0.00 0.00 2.57
2745 2815 2.328099 CGGCCACCTCTGCAAAGAC 61.328 63.158 2.24 0.00 0.00 3.01
2779 2849 8.091449 TCTTCTAGTTCTTCTTCATCAAGTTCC 58.909 37.037 0.00 0.00 0.00 3.62
2800 2870 1.511768 GCGCCTCCGTACTTCTTCT 59.488 57.895 0.00 0.00 36.67 2.85
2898 2972 8.704849 TTCTCCATCATCCTACAAAAAGAAAA 57.295 30.769 0.00 0.00 0.00 2.29
2899 2973 8.704849 TTTCTCCATCATCCTACAAAAAGAAA 57.295 30.769 0.00 0.00 0.00 2.52
2972 3046 4.772624 AGCTGGTGTACTCTCAGTTTGATA 59.227 41.667 12.13 0.00 0.00 2.15
2987 3061 1.462238 ACCCAGGAAGAGCTGGTGT 60.462 57.895 0.00 0.00 39.00 4.16
2993 3067 1.599576 GTCCAGACCCAGGAAGAGC 59.400 63.158 0.00 0.00 36.80 4.09
3057 3131 4.142902 CGAGAATGCCTTAAAAGCGAAGAA 60.143 41.667 0.00 0.00 0.00 2.52
3058 3132 3.370978 CGAGAATGCCTTAAAAGCGAAGA 59.629 43.478 0.00 0.00 0.00 2.87
3065 3139 8.573035 ACTTAATCAAACGAGAATGCCTTAAAA 58.427 29.630 0.00 0.00 0.00 1.52
3068 3142 6.035650 CGACTTAATCAAACGAGAATGCCTTA 59.964 38.462 0.00 0.00 0.00 2.69
3072 3146 5.015733 CACGACTTAATCAAACGAGAATGC 58.984 41.667 0.00 0.00 0.00 3.56
3074 3148 5.694910 ACACACGACTTAATCAAACGAGAAT 59.305 36.000 0.00 0.00 0.00 2.40
3077 3151 4.966850 ACACACGACTTAATCAAACGAG 57.033 40.909 0.00 0.00 0.00 4.18
3080 3154 8.117988 TGAAAGTAACACACGACTTAATCAAAC 58.882 33.333 0.00 0.00 34.81 2.93
3101 3175 6.149973 TGCTTCCATGACAAGAACTATGAAAG 59.850 38.462 8.20 0.00 0.00 2.62
3104 3178 4.937620 GTGCTTCCATGACAAGAACTATGA 59.062 41.667 8.20 0.00 0.00 2.15
3106 3180 5.171339 AGTGCTTCCATGACAAGAACTAT 57.829 39.130 13.73 0.00 37.90 2.12
3110 3184 6.707440 TTTAAAGTGCTTCCATGACAAGAA 57.293 33.333 8.20 0.00 0.00 2.52
3112 3186 7.327761 CAGAATTTAAAGTGCTTCCATGACAAG 59.672 37.037 0.00 0.00 0.00 3.16
3113 3187 7.147312 CAGAATTTAAAGTGCTTCCATGACAA 58.853 34.615 0.00 0.00 0.00 3.18
3114 3188 6.265196 ACAGAATTTAAAGTGCTTCCATGACA 59.735 34.615 0.00 0.00 0.00 3.58
3115 3189 6.681777 ACAGAATTTAAAGTGCTTCCATGAC 58.318 36.000 0.00 0.00 0.00 3.06
3116 3190 6.899393 ACAGAATTTAAAGTGCTTCCATGA 57.101 33.333 0.00 0.00 0.00 3.07
3120 3194 9.774742 CAGTATTACAGAATTTAAAGTGCTTCC 57.225 33.333 0.00 0.00 0.00 3.46
3173 3254 1.171308 ATCACCAGTTCATGCACAGC 58.829 50.000 0.00 0.00 0.00 4.40
3178 3259 1.470098 AGCGAAATCACCAGTTCATGC 59.530 47.619 0.00 0.00 0.00 4.06
3195 3276 1.816835 TCAGTGGAACCTACAGTAGCG 59.183 52.381 1.50 0.00 37.80 4.26
3369 3450 2.360726 TCGCTGCCACGGTCTCTA 60.361 61.111 0.00 0.00 0.00 2.43
3383 3464 2.202864 GCTCCCAGCTTCTCTCGC 60.203 66.667 0.00 0.00 38.45 5.03
3491 3572 2.676839 CACAGCTCTCCAACAGCATAAG 59.323 50.000 0.00 0.00 39.56 1.73
3575 3656 4.397417 CCACCCATTCTTCTGATCAGTTTC 59.603 45.833 21.92 0.00 0.00 2.78
3585 3666 3.184628 TGATCTGACCACCCATTCTTCT 58.815 45.455 0.00 0.00 0.00 2.85
3588 3669 4.042560 CCATATGATCTGACCACCCATTCT 59.957 45.833 3.65 0.00 0.00 2.40
3592 3673 2.775418 ACCATATGATCTGACCACCCA 58.225 47.619 3.65 0.00 0.00 4.51
3631 3712 1.751351 TGTCAGGTCTCGATGGTCATC 59.249 52.381 1.08 1.08 34.56 2.92
3663 3744 3.005554 CCTGGTTCGTCGAGTCTACTAA 58.994 50.000 0.00 0.00 0.00 2.24
3695 3776 2.918131 GCATCAGAAACCGCAACAAGTC 60.918 50.000 0.00 0.00 0.00 3.01
3696 3777 1.001378 GCATCAGAAACCGCAACAAGT 60.001 47.619 0.00 0.00 0.00 3.16
3698 3779 1.028130 TGCATCAGAAACCGCAACAA 58.972 45.000 0.00 0.00 0.00 2.83
3756 3839 9.178427 GATAAATCAGAGAAATGCAAACATAGC 57.822 33.333 0.00 0.00 34.62 2.97
3827 3910 1.709147 GACGCCTGCACCATGATGTC 61.709 60.000 0.00 0.00 0.00 3.06
3866 3949 8.801715 ACACAAATATCAAATTGCCGATAATC 57.198 30.769 0.00 0.00 0.00 1.75
3870 3953 9.598517 AAATAACACAAATATCAAATTGCCGAT 57.401 25.926 0.00 0.00 0.00 4.18
3871 3954 8.867935 CAAATAACACAAATATCAAATTGCCGA 58.132 29.630 0.00 0.00 0.00 5.54
3872 3955 8.655092 ACAAATAACACAAATATCAAATTGCCG 58.345 29.630 0.00 0.00 0.00 5.69
3873 3956 9.971744 GACAAATAACACAAATATCAAATTGCC 57.028 29.630 0.00 0.00 0.00 4.52
3879 3962 9.906660 GGTTCAGACAAATAACACAAATATCAA 57.093 29.630 0.00 0.00 0.00 2.57
3880 3963 9.072375 TGGTTCAGACAAATAACACAAATATCA 57.928 29.630 0.00 0.00 0.00 2.15
3881 3964 9.559958 CTGGTTCAGACAAATAACACAAATATC 57.440 33.333 0.00 0.00 32.44 1.63
3882 3965 9.077885 ACTGGTTCAGACAAATAACACAAATAT 57.922 29.630 1.59 0.00 35.18 1.28
3883 3966 8.458573 ACTGGTTCAGACAAATAACACAAATA 57.541 30.769 1.59 0.00 35.18 1.40
3915 3998 6.091076 TGGGGATGGAAAGATATTTCTTGT 57.909 37.500 12.28 0.00 41.42 3.16
3916 3999 8.710749 TTATGGGGATGGAAAGATATTTCTTG 57.289 34.615 12.28 0.00 41.42 3.02
3917 4000 9.903190 ATTTATGGGGATGGAAAGATATTTCTT 57.097 29.630 12.28 1.24 44.20 2.52
3954 4037 4.337555 ACAATTTGATAGCTGATGGAGTGC 59.662 41.667 2.79 0.00 0.00 4.40
3972 4057 3.671008 TCACCAGTACACGCTACAATT 57.329 42.857 0.00 0.00 0.00 2.32
4013 4098 9.067986 CCCTGATATTCCAGAAATTTTACCTAC 57.932 37.037 0.00 0.00 36.29 3.18
4022 4107 3.753193 GCAGGCCCTGATATTCCAGAAAT 60.753 47.826 16.85 0.00 36.29 2.17
4054 4139 5.004922 ACGCTGGATCTTTCAAACAAAAA 57.995 34.783 0.00 0.00 0.00 1.94
4056 4141 4.358851 CAACGCTGGATCTTTCAAACAAA 58.641 39.130 0.00 0.00 0.00 2.83
4057 4142 3.795150 GCAACGCTGGATCTTTCAAACAA 60.795 43.478 0.00 0.00 0.00 2.83
4058 4143 2.287547 GCAACGCTGGATCTTTCAAACA 60.288 45.455 0.00 0.00 0.00 2.83
4059 4144 2.030805 AGCAACGCTGGATCTTTCAAAC 60.031 45.455 0.00 0.00 37.57 2.93
4060 4145 2.229792 AGCAACGCTGGATCTTTCAAA 58.770 42.857 0.00 0.00 37.57 2.69
4061 4146 1.896220 AGCAACGCTGGATCTTTCAA 58.104 45.000 0.00 0.00 37.57 2.69
4062 4147 3.631453 AGCAACGCTGGATCTTTCA 57.369 47.368 0.00 0.00 37.57 2.69
4072 4157 3.352222 GACAGCAGCAGCAACGCT 61.352 61.111 3.17 0.00 45.49 5.07
4073 4158 4.395583 GGACAGCAGCAGCAACGC 62.396 66.667 3.17 0.00 45.49 4.84
4074 4159 1.789078 AAAGGACAGCAGCAGCAACG 61.789 55.000 3.17 0.00 45.49 4.10
4076 4161 0.466007 TCAAAGGACAGCAGCAGCAA 60.466 50.000 3.17 0.00 45.49 3.91
4077 4162 0.251033 ATCAAAGGACAGCAGCAGCA 60.251 50.000 3.17 0.00 45.49 4.41
4078 4163 0.886563 AATCAAAGGACAGCAGCAGC 59.113 50.000 0.00 0.00 42.56 5.25
4080 4165 2.275134 TCAATCAAAGGACAGCAGCA 57.725 45.000 0.00 0.00 0.00 4.41
4082 4167 4.882427 AGATGATCAATCAAAGGACAGCAG 59.118 41.667 0.00 0.00 40.69 4.24
4083 4168 4.638865 CAGATGATCAATCAAAGGACAGCA 59.361 41.667 0.00 0.00 40.69 4.41
4084 4169 4.497674 GCAGATGATCAATCAAAGGACAGC 60.498 45.833 0.00 0.00 40.69 4.40
4085 4170 4.260661 CGCAGATGATCAATCAAAGGACAG 60.261 45.833 0.00 0.00 40.69 3.51
4086 4171 3.624410 CGCAGATGATCAATCAAAGGACA 59.376 43.478 0.00 0.00 40.69 4.02
4087 4172 3.624861 ACGCAGATGATCAATCAAAGGAC 59.375 43.478 0.00 0.00 40.69 3.85
4088 4173 3.877559 ACGCAGATGATCAATCAAAGGA 58.122 40.909 0.00 0.00 40.69 3.36
4089 4174 4.348656 CAACGCAGATGATCAATCAAAGG 58.651 43.478 0.00 0.00 40.69 3.11
4090 4175 3.789756 GCAACGCAGATGATCAATCAAAG 59.210 43.478 0.00 0.00 40.69 2.77
4091 4176 3.441222 AGCAACGCAGATGATCAATCAAA 59.559 39.130 0.00 0.00 40.69 2.69
4092 4177 3.011818 AGCAACGCAGATGATCAATCAA 58.988 40.909 0.00 0.00 40.69 2.57
4093 4178 2.353579 CAGCAACGCAGATGATCAATCA 59.646 45.455 0.00 0.00 41.70 2.57
4094 4179 2.853662 GCAGCAACGCAGATGATCAATC 60.854 50.000 0.00 0.00 35.29 2.67
4097 4182 0.674269 TGCAGCAACGCAGATGATCA 60.674 50.000 0.00 0.00 36.86 2.92
4098 4183 0.661552 ATGCAGCAACGCAGATGATC 59.338 50.000 0.00 0.00 46.99 2.92
4101 4186 0.450583 AAGATGCAGCAACGCAGATG 59.549 50.000 4.07 0.00 46.99 2.90
4103 4188 0.886043 ACAAGATGCAGCAACGCAGA 60.886 50.000 4.07 0.00 46.99 4.26
4104 4189 0.039798 AACAAGATGCAGCAACGCAG 60.040 50.000 4.07 0.00 46.99 5.18
4106 4191 1.490621 AAAACAAGATGCAGCAACGC 58.509 45.000 4.07 0.00 0.00 4.84
4109 4194 3.551082 CGTTCAAAAACAAGATGCAGCAA 59.449 39.130 4.07 0.00 34.93 3.91
4110 4195 3.114809 CGTTCAAAAACAAGATGCAGCA 58.885 40.909 4.07 0.00 34.93 4.41
4111 4196 3.061006 CACGTTCAAAAACAAGATGCAGC 60.061 43.478 0.00 0.00 34.93 5.25
4112 4197 4.104776 ACACGTTCAAAAACAAGATGCAG 58.895 39.130 0.00 0.00 34.93 4.41
4113 4198 4.103365 ACACGTTCAAAAACAAGATGCA 57.897 36.364 0.00 0.00 34.93 3.96
4187 5036 3.271250 TGGCTGGAAGAAAGGCATC 57.729 52.632 0.00 0.00 44.44 3.91
4203 5052 0.103026 TCGATGCGACTGATCCTTGG 59.897 55.000 0.00 0.00 0.00 3.61
4260 5109 3.322466 AAGGGACGAGTGGCAGGG 61.322 66.667 0.00 0.00 0.00 4.45
4261 5110 2.046892 CAAGGGACGAGTGGCAGG 60.047 66.667 0.00 0.00 0.00 4.85
4277 5126 1.203001 GGGTGTTCCTCCATGAAACCA 60.203 52.381 0.00 0.00 32.10 3.67
4299 5148 3.244318 TGTGATTTTGAGAGCAGAGCAGA 60.244 43.478 0.00 0.00 0.00 4.26
4374 5227 3.315191 CACGGAAAACATGAAGTTGACCT 59.685 43.478 0.00 0.00 41.19 3.85
4385 5239 1.608590 CAGGTGCTTCACGGAAAACAT 59.391 47.619 0.00 0.00 34.83 2.71
4392 5246 0.250295 TTCCTTCAGGTGCTTCACGG 60.250 55.000 0.00 0.00 34.83 4.94
4410 5264 6.959639 TCAAACTAGACTTTTTGGAGCATT 57.040 33.333 0.00 0.00 34.14 3.56
4411 5265 6.959639 TTCAAACTAGACTTTTTGGAGCAT 57.040 33.333 0.00 0.00 34.14 3.79


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

AutoCloner maintained by Alex Coulton.