Multiple sequence alignment - TraesCS6A01G102400

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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 TraesCS6A01G102400 chr6A 100.000 3953 0 0 783 4735 71454318 71450366 0.000000e+00 7300.0
1 TraesCS6A01G102400 chr6A 100.000 412 0 0 1 412 71455100 71454689 0.000000e+00 761.0
2 TraesCS6A01G102400 chr6B 91.075 2252 123 29 783 2998 127329155 127326946 0.000000e+00 2974.0
3 TraesCS6A01G102400 chr6B 94.730 1651 86 1 3084 4733 127326904 127325254 0.000000e+00 2566.0
4 TraesCS6A01G102400 chr6B 89.791 382 21 7 31 412 127329538 127329175 1.540000e-129 473.0
5 TraesCS6A01G102400 chr6D 88.463 2271 131 53 783 2993 56853173 56850974 0.000000e+00 2621.0
6 TraesCS6A01G102400 chr6D 95.218 1652 74 3 3084 4730 56850928 56849277 0.000000e+00 2608.0
7 TraesCS6A01G102400 chr6D 88.259 247 19 6 167 412 56853430 56853193 2.160000e-73 287.0
8 TraesCS6A01G102400 chr6D 78.981 157 19 10 1 150 13036431 13036580 1.400000e-15 95.3
9 TraesCS6A01G102400 chr2D 81.132 159 19 9 1 150 646367797 646367953 2.990000e-22 117.0
10 TraesCS6A01G102400 chr5A 81.944 144 17 6 9 144 552661759 552661901 3.870000e-21 113.0
11 TraesCS6A01G102400 chr4D 80.132 151 19 8 1 142 394409435 394409287 8.380000e-18 102.0
12 TraesCS6A01G102400 chr2A 85.556 90 11 2 53 141 615339806 615339718 5.050000e-15 93.5


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 TraesCS6A01G102400 chr6A 71450366 71455100 4734 True 4030.500000 7300 100.000000 1 4735 2 chr6A.!!$R1 4734
1 TraesCS6A01G102400 chr6B 127325254 127329538 4284 True 2004.333333 2974 91.865333 31 4733 3 chr6B.!!$R1 4702
2 TraesCS6A01G102400 chr6D 56849277 56853430 4153 True 1838.666667 2621 90.646667 167 4730 3 chr6D.!!$R1 4563

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
270 272 0.036164 ACGGCAAGAACCATGTAGCA 59.964 50.0 0.00 0.0 0.00 3.49 F
987 1012 0.400213 TCTGGGTAGCTGGTTTGTGG 59.600 55.0 0.00 0.0 0.00 4.17 F
2050 2141 0.035458 ACTTCCGAAGCCACCTCTTG 59.965 55.0 8.11 0.0 0.00 3.02 F
2681 2780 0.250252 TTCTTGCCGATGCTGACACA 60.250 50.0 0.00 0.0 38.71 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 2120 0.035458 AGAGGTGGCTTCGGAAGTTG 59.965 55.0 18.32 0.0 0.00 3.16 R
2852 2954 0.255318 ATCCTTGCAGCTCCTTGAGG 59.745 55.0 0.00 0.0 0.00 3.86 R
3024 3127 1.045407 TTCGATATGGGTAGCGGCTT 58.955 50.0 8.26 0.0 39.98 4.35 R
4159 4266 0.392998 ACTTGCCGTGGAATAGCAGG 60.393 55.0 0.00 0.0 37.89 4.85 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
21 22 4.946784 ACACCGCATATCTTTCAGAAAC 57.053 40.909 0.00 0.00 0.00 2.78
22 23 4.323417 ACACCGCATATCTTTCAGAAACA 58.677 39.130 0.00 0.00 0.00 2.83
23 24 4.943705 ACACCGCATATCTTTCAGAAACAT 59.056 37.500 0.00 0.00 0.00 2.71
24 25 6.112734 ACACCGCATATCTTTCAGAAACATA 58.887 36.000 0.00 0.00 0.00 2.29
25 26 6.258727 ACACCGCATATCTTTCAGAAACATAG 59.741 38.462 0.00 0.00 0.00 2.23
26 27 5.237344 ACCGCATATCTTTCAGAAACATAGC 59.763 40.000 0.00 0.00 0.00 2.97
27 28 5.334414 CCGCATATCTTTCAGAAACATAGCC 60.334 44.000 0.00 0.00 0.00 3.93
28 29 5.468072 CGCATATCTTTCAGAAACATAGCCT 59.532 40.000 0.00 0.00 0.00 4.58
29 30 6.017605 CGCATATCTTTCAGAAACATAGCCTT 60.018 38.462 0.00 0.00 0.00 4.35
45 46 2.353376 TTTGTTGCAGAAGCGCGC 60.353 55.556 26.66 26.66 46.23 6.86
67 68 1.134401 CGGCAGTATGTGAACCCTCAT 60.134 52.381 0.00 0.00 39.31 2.90
154 155 9.140286 GTAAGCTTTTCCCAAAATCAAACTATC 57.860 33.333 3.20 0.00 0.00 2.08
219 221 7.014711 CAGCTCTCACATAAGATAACCTTCCTA 59.985 40.741 0.00 0.00 36.34 2.94
269 271 0.447801 CACGGCAAGAACCATGTAGC 59.552 55.000 0.00 0.00 0.00 3.58
270 272 0.036164 ACGGCAAGAACCATGTAGCA 59.964 50.000 0.00 0.00 0.00 3.49
271 273 0.447801 CGGCAAGAACCATGTAGCAC 59.552 55.000 0.00 0.00 0.00 4.40
272 274 0.811281 GGCAAGAACCATGTAGCACC 59.189 55.000 0.00 0.00 0.00 5.01
273 275 1.533625 GCAAGAACCATGTAGCACCA 58.466 50.000 0.00 0.00 0.00 4.17
274 276 1.200020 GCAAGAACCATGTAGCACCAC 59.800 52.381 0.00 0.00 0.00 4.16
275 277 2.503331 CAAGAACCATGTAGCACCACA 58.497 47.619 0.00 0.00 0.00 4.17
276 278 2.479566 AGAACCATGTAGCACCACAG 57.520 50.000 0.00 0.00 0.00 3.66
326 336 4.992951 GCAAAAGTCCAAATGAATGAAGCT 59.007 37.500 0.00 0.00 0.00 3.74
329 339 2.163010 AGTCCAAATGAATGAAGCTGCG 59.837 45.455 0.00 0.00 0.00 5.18
369 379 5.294552 GGGCGATGATAATAACCTGATAAGC 59.705 44.000 0.00 0.00 0.00 3.09
800 810 2.676471 GGCACATTCCCAACGCCT 60.676 61.111 0.00 0.00 39.73 5.52
985 1010 2.441750 TCTTTCTGGGTAGCTGGTTTGT 59.558 45.455 0.00 0.00 0.00 2.83
986 1011 2.270352 TTCTGGGTAGCTGGTTTGTG 57.730 50.000 0.00 0.00 0.00 3.33
987 1012 0.400213 TCTGGGTAGCTGGTTTGTGG 59.600 55.000 0.00 0.00 0.00 4.17
989 1014 0.553819 TGGGTAGCTGGTTTGTGGTT 59.446 50.000 0.00 0.00 0.00 3.67
991 1016 1.339929 GGGTAGCTGGTTTGTGGTTTG 59.660 52.381 0.00 0.00 0.00 2.93
992 1017 2.028876 GGTAGCTGGTTTGTGGTTTGT 58.971 47.619 0.00 0.00 0.00 2.83
1031 1062 3.785859 GGAGGCCGACATGGAGCA 61.786 66.667 0.00 0.00 42.00 4.26
1032 1063 2.268920 GAGGCCGACATGGAGCAA 59.731 61.111 0.00 0.00 42.00 3.91
1038 1069 1.813513 CCGACATGGAGCAAGTTCTT 58.186 50.000 0.00 0.00 42.00 2.52
1066 1097 2.583593 GCCTCCAGCTAAGCGACG 60.584 66.667 0.00 0.00 38.99 5.12
1074 1105 4.925576 CTAAGCGACGGCGGCGAT 62.926 66.667 41.98 34.21 46.35 4.58
1082 1113 2.335011 CGGCGGCGATAGTGATGA 59.665 61.111 29.19 0.00 39.35 2.92
1646 1695 2.673523 CAAGGCCCTCCAGGTCAG 59.326 66.667 0.00 0.00 45.84 3.51
1656 1705 0.970937 TCCAGGTCAGACATCCGTCC 60.971 60.000 2.17 0.00 43.73 4.79
1657 1706 1.139734 CAGGTCAGACATCCGTCCG 59.860 63.158 2.17 0.00 43.73 4.79
1664 1713 0.748729 AGACATCCGTCCGTCTCTCC 60.749 60.000 0.00 0.00 43.73 3.71
1699 1750 0.459585 GCATTCTCGCTCCACCGTAA 60.460 55.000 0.00 0.00 0.00 3.18
1702 1753 2.529780 TTCTCGCTCCACCGTAAAAA 57.470 45.000 0.00 0.00 0.00 1.94
1720 1771 7.540055 CCGTAAAAACTACTACTACTCCTTGTG 59.460 40.741 0.00 0.00 0.00 3.33
1721 1772 7.061557 CGTAAAAACTACTACTACTCCTTGTGC 59.938 40.741 0.00 0.00 0.00 4.57
1722 1773 6.415206 AAAACTACTACTACTCCTTGTGCA 57.585 37.500 0.00 0.00 0.00 4.57
1723 1774 6.607004 AAACTACTACTACTCCTTGTGCAT 57.393 37.500 0.00 0.00 0.00 3.96
1724 1775 7.713734 AAACTACTACTACTCCTTGTGCATA 57.286 36.000 0.00 0.00 0.00 3.14
1725 1776 7.713734 AACTACTACTACTCCTTGTGCATAA 57.286 36.000 0.00 0.00 0.00 1.90
1746 1829 1.337074 ACAGCCGCCATGAAATGTTTG 60.337 47.619 0.00 0.00 44.81 2.93
1769 1852 1.056700 AGGTAGCCGCCATGAATCCT 61.057 55.000 0.00 0.00 0.00 3.24
1779 1862 3.629398 CGCCATGAATCCTAAAAGCTTCT 59.371 43.478 0.00 0.00 0.00 2.85
1781 1864 5.277538 CGCCATGAATCCTAAAAGCTTCTAC 60.278 44.000 0.00 0.00 0.00 2.59
1822 1905 3.051479 TGCATGCAGGCAGTGTCG 61.051 61.111 24.07 0.00 39.25 4.35
1955 2045 5.164620 TGGTGCATCAAACTCAATAGAGA 57.835 39.130 0.00 0.00 44.98 3.10
1956 2046 5.181009 TGGTGCATCAAACTCAATAGAGAG 58.819 41.667 0.00 0.00 44.98 3.20
1970 2060 2.231215 AGAGAGGCGTAATCACATGC 57.769 50.000 0.00 0.00 0.00 4.06
2025 2116 4.123497 TCCATTCGTGTTCATCTACCAG 57.877 45.455 0.00 0.00 0.00 4.00
2028 2119 2.913777 TCGTGTTCATCTACCAGTCG 57.086 50.000 0.00 0.00 0.00 4.18
2029 2120 1.135489 TCGTGTTCATCTACCAGTCGC 60.135 52.381 0.00 0.00 0.00 5.19
2030 2121 1.402325 CGTGTTCATCTACCAGTCGCA 60.402 52.381 0.00 0.00 0.00 5.10
2031 2122 2.683968 GTGTTCATCTACCAGTCGCAA 58.316 47.619 0.00 0.00 0.00 4.85
2032 2123 2.412089 GTGTTCATCTACCAGTCGCAAC 59.588 50.000 0.00 0.00 0.00 4.17
2033 2124 2.299013 TGTTCATCTACCAGTCGCAACT 59.701 45.455 0.00 0.00 35.60 3.16
2050 2141 0.035458 ACTTCCGAAGCCACCTCTTG 59.965 55.000 8.11 0.00 0.00 3.02
2053 2144 0.984230 TCCGAAGCCACCTCTTGATT 59.016 50.000 0.00 0.00 0.00 2.57
2061 2152 5.121380 AGCCACCTCTTGATTATGAACAT 57.879 39.130 0.00 0.00 0.00 2.71
2062 2153 4.885907 AGCCACCTCTTGATTATGAACATG 59.114 41.667 0.00 0.00 0.00 3.21
2107 2203 2.045926 GACTCAGGCGGCCATGTT 60.046 61.111 23.09 1.92 0.00 2.71
2500 2599 4.189188 CGACGACGGCCAGGTAGG 62.189 72.222 2.24 0.00 41.84 3.18
2658 2757 3.507162 TGCAAGATTTGTCCTTGGAGA 57.493 42.857 0.00 0.00 40.85 3.71
2659 2758 3.831323 TGCAAGATTTGTCCTTGGAGAA 58.169 40.909 0.00 0.00 40.85 2.87
2681 2780 0.250252 TTCTTGCCGATGCTGACACA 60.250 50.000 0.00 0.00 38.71 3.72
2741 2840 0.323542 ATTCAGACGAGGAGGACGGT 60.324 55.000 0.00 0.00 34.93 4.83
2852 2954 2.435059 GCCGGAAGACCTGTCAGC 60.435 66.667 5.05 0.00 0.00 4.26
2855 2957 1.216710 CGGAAGACCTGTCAGCCTC 59.783 63.158 0.00 0.00 0.00 4.70
2958 3061 6.721208 AGATTAACCAAGATGAACACCACAAT 59.279 34.615 0.00 0.00 0.00 2.71
2964 3067 5.636121 CCAAGATGAACACCACAATGAATTG 59.364 40.000 1.45 1.45 43.26 2.32
2968 3071 5.437289 TGAACACCACAATGAATTGACTC 57.563 39.130 9.94 0.00 40.14 3.36
2969 3072 4.278170 TGAACACCACAATGAATTGACTCC 59.722 41.667 9.94 0.00 40.14 3.85
2970 3073 3.157087 ACACCACAATGAATTGACTCCC 58.843 45.455 9.94 0.00 40.14 4.30
2975 3078 3.573538 CACAATGAATTGACTCCCAACCA 59.426 43.478 9.94 0.00 40.14 3.67
2978 3081 3.593442 TGAATTGACTCCCAACCAAGT 57.407 42.857 0.00 0.00 37.63 3.16
2983 3086 3.593442 TGACTCCCAACCAAGTTCATT 57.407 42.857 0.00 0.00 0.00 2.57
2998 3101 6.475076 CCAAGTTCATTGAAACATGTCGAAAA 59.525 34.615 0.00 0.00 41.83 2.29
3000 3103 7.858052 AGTTCATTGAAACATGTCGAAAATC 57.142 32.000 0.00 0.00 0.00 2.17
3001 3104 7.651808 AGTTCATTGAAACATGTCGAAAATCT 58.348 30.769 0.00 0.00 0.00 2.40
3003 3106 6.380995 TCATTGAAACATGTCGAAAATCTGG 58.619 36.000 0.00 0.00 0.00 3.86
3004 3107 5.766150 TTGAAACATGTCGAAAATCTGGT 57.234 34.783 0.00 0.00 0.00 4.00
3005 3108 6.869315 TTGAAACATGTCGAAAATCTGGTA 57.131 33.333 0.00 0.00 0.00 3.25
3006 3109 6.236017 TGAAACATGTCGAAAATCTGGTAC 57.764 37.500 0.00 0.00 0.00 3.34
3007 3110 5.995282 TGAAACATGTCGAAAATCTGGTACT 59.005 36.000 0.00 0.00 0.00 2.73
3008 3111 6.485313 TGAAACATGTCGAAAATCTGGTACTT 59.515 34.615 0.00 0.00 0.00 2.24
3009 3112 5.862924 ACATGTCGAAAATCTGGTACTTG 57.137 39.130 0.00 0.00 0.00 3.16
3010 3113 4.695455 ACATGTCGAAAATCTGGTACTTGG 59.305 41.667 0.00 0.00 0.00 3.61
3011 3114 4.345859 TGTCGAAAATCTGGTACTTGGT 57.654 40.909 0.00 0.00 0.00 3.67
3012 3115 4.710324 TGTCGAAAATCTGGTACTTGGTT 58.290 39.130 0.00 0.00 0.00 3.67
3013 3116 5.127491 TGTCGAAAATCTGGTACTTGGTTT 58.873 37.500 0.00 0.00 0.00 3.27
3014 3117 5.008217 TGTCGAAAATCTGGTACTTGGTTTG 59.992 40.000 0.00 0.00 0.00 2.93
3015 3118 4.023536 TCGAAAATCTGGTACTTGGTTTGC 60.024 41.667 0.00 0.00 0.00 3.68
3016 3119 4.261405 CGAAAATCTGGTACTTGGTTTGCA 60.261 41.667 0.00 0.00 0.00 4.08
3017 3120 5.564651 CGAAAATCTGGTACTTGGTTTGCAT 60.565 40.000 0.00 0.00 0.00 3.96
3018 3121 5.806654 AAATCTGGTACTTGGTTTGCATT 57.193 34.783 0.00 0.00 0.00 3.56
3019 3122 5.391312 AATCTGGTACTTGGTTTGCATTC 57.609 39.130 0.00 0.00 0.00 2.67
3020 3123 2.811431 TCTGGTACTTGGTTTGCATTCG 59.189 45.455 0.00 0.00 0.00 3.34
3021 3124 2.552315 CTGGTACTTGGTTTGCATTCGT 59.448 45.455 0.00 0.00 0.00 3.85
3022 3125 3.741249 TGGTACTTGGTTTGCATTCGTA 58.259 40.909 0.00 0.00 0.00 3.43
3023 3126 4.328536 TGGTACTTGGTTTGCATTCGTAT 58.671 39.130 0.00 0.00 0.00 3.06
3024 3127 5.489249 TGGTACTTGGTTTGCATTCGTATA 58.511 37.500 0.00 0.00 0.00 1.47
3025 3128 5.938710 TGGTACTTGGTTTGCATTCGTATAA 59.061 36.000 0.00 0.00 0.00 0.98
3026 3129 6.092944 TGGTACTTGGTTTGCATTCGTATAAG 59.907 38.462 0.00 0.00 0.00 1.73
3027 3130 4.981794 ACTTGGTTTGCATTCGTATAAGC 58.018 39.130 0.00 0.00 0.00 3.09
3028 3131 4.142469 ACTTGGTTTGCATTCGTATAAGCC 60.142 41.667 0.00 0.00 0.00 4.35
3029 3132 2.353269 TGGTTTGCATTCGTATAAGCCG 59.647 45.455 0.00 0.00 0.00 5.52
3030 3133 2.372350 GTTTGCATTCGTATAAGCCGC 58.628 47.619 0.00 0.00 0.00 6.53
3031 3134 1.948104 TTGCATTCGTATAAGCCGCT 58.052 45.000 0.00 0.00 0.00 5.52
3032 3135 2.804697 TGCATTCGTATAAGCCGCTA 57.195 45.000 0.00 0.00 0.00 4.26
3033 3136 2.400399 TGCATTCGTATAAGCCGCTAC 58.600 47.619 0.00 0.00 0.00 3.58
3034 3137 1.725164 GCATTCGTATAAGCCGCTACC 59.275 52.381 0.00 0.00 0.00 3.18
3035 3138 2.334838 CATTCGTATAAGCCGCTACCC 58.665 52.381 0.00 0.00 0.00 3.69
3036 3139 1.401761 TTCGTATAAGCCGCTACCCA 58.598 50.000 0.00 0.00 0.00 4.51
3037 3140 1.624336 TCGTATAAGCCGCTACCCAT 58.376 50.000 0.00 0.00 0.00 4.00
3038 3141 2.794103 TCGTATAAGCCGCTACCCATA 58.206 47.619 0.00 0.00 0.00 2.74
3039 3142 3.359033 TCGTATAAGCCGCTACCCATAT 58.641 45.455 0.00 0.00 0.00 1.78
3040 3143 3.379372 TCGTATAAGCCGCTACCCATATC 59.621 47.826 0.00 0.00 0.00 1.63
3041 3144 2.961526 ATAAGCCGCTACCCATATCG 57.038 50.000 0.00 0.00 0.00 2.92
3042 3145 1.913778 TAAGCCGCTACCCATATCGA 58.086 50.000 0.00 0.00 0.00 3.59
3043 3146 1.045407 AAGCCGCTACCCATATCGAA 58.955 50.000 0.00 0.00 0.00 3.71
3047 3150 2.032290 GCCGCTACCCATATCGAAAAAC 60.032 50.000 0.00 0.00 0.00 2.43
3048 3151 2.546789 CCGCTACCCATATCGAAAAACC 59.453 50.000 0.00 0.00 0.00 3.27
3054 3157 6.203338 GCTACCCATATCGAAAAACCGAAATA 59.797 38.462 0.00 0.00 42.22 1.40
3059 3163 9.389570 CCCATATCGAAAAACCGAAATATTTAC 57.610 33.333 0.00 0.00 42.22 2.01
3062 3166 7.964545 ATCGAAAAACCGAAATATTTACTGC 57.035 32.000 0.00 0.00 42.22 4.40
3067 3171 9.301153 GAAAAACCGAAATATTTACTGCATGAT 57.699 29.630 0.00 0.00 0.00 2.45
3069 3173 7.566760 AACCGAAATATTTACTGCATGATGA 57.433 32.000 0.00 0.00 0.00 2.92
3070 3174 7.194607 ACCGAAATATTTACTGCATGATGAG 57.805 36.000 0.00 0.00 0.00 2.90
3071 3175 6.205464 ACCGAAATATTTACTGCATGATGAGG 59.795 38.462 0.00 0.00 0.00 3.86
3072 3176 6.082338 CGAAATATTTACTGCATGATGAGGC 58.918 40.000 0.00 0.00 0.00 4.70
3073 3177 6.293571 CGAAATATTTACTGCATGATGAGGCA 60.294 38.462 0.00 0.00 36.28 4.75
3074 3178 6.964807 AATATTTACTGCATGATGAGGCAA 57.035 33.333 0.00 0.00 38.69 4.52
3075 3179 4.644103 ATTTACTGCATGATGAGGCAAC 57.356 40.909 0.00 0.00 38.69 4.17
3116 3220 2.137425 CTACAGTGTGCCCGACGACA 62.137 60.000 5.88 0.00 0.00 4.35
3291 3395 2.203451 CCCCTCATCTGCCATGCC 60.203 66.667 0.00 0.00 0.00 4.40
3464 3568 1.133181 TCATCAGGTTCAGGGTGCCA 61.133 55.000 0.00 0.00 0.00 4.92
3555 3659 2.156917 ACATCAAGTACCTCGACGACA 58.843 47.619 0.00 0.00 0.00 4.35
3698 3805 0.837272 TAATGGTGCAGGAGGTAGCC 59.163 55.000 0.00 0.00 0.00 3.93
3716 3823 1.066787 GCCGATAACCATAGGAGCTCC 60.067 57.143 26.22 26.22 0.00 4.70
3742 3849 5.535406 GTGGTAGCTCAGATTAGCCTTACTA 59.465 44.000 0.00 0.00 43.86 1.82
3743 3850 6.040616 GTGGTAGCTCAGATTAGCCTTACTAA 59.959 42.308 0.00 0.00 44.87 2.24
3744 3851 6.610020 TGGTAGCTCAGATTAGCCTTACTAAA 59.390 38.462 0.00 0.00 43.99 1.85
3894 4001 8.917088 ACATTGTTTGAATAATGATAGAAGGGG 58.083 33.333 16.72 0.00 39.11 4.79
3898 4005 5.582950 TGAATAATGATAGAAGGGGTGGG 57.417 43.478 0.00 0.00 0.00 4.61
3947 4054 6.959361 ACATGCAGTAACAGTTTCAAACTAG 58.041 36.000 1.43 0.50 40.46 2.57
4089 4196 3.364621 GCTTTGCATTTCATACAACACGG 59.635 43.478 0.00 0.00 0.00 4.94
4097 4204 2.967362 TCATACAACACGGATTTCGCT 58.033 42.857 0.00 0.00 43.89 4.93
4099 4206 0.793861 TACAACACGGATTTCGCTGC 59.206 50.000 0.00 0.00 43.89 5.25
4102 4209 1.577328 AACACGGATTTCGCTGCAGG 61.577 55.000 17.12 5.82 43.89 4.85
4129 4236 6.918473 ACCCATGGTAGTAATCTGGTACAGC 61.918 48.000 11.73 0.00 46.24 4.40
4159 4266 2.628178 AGTTCTAAGGGGCAGCAAAAAC 59.372 45.455 0.00 0.00 0.00 2.43
4173 4280 2.671070 GCAAAAACCTGCTATTCCACGG 60.671 50.000 0.00 0.00 39.34 4.94
4175 4282 0.037590 AAACCTGCTATTCCACGGCA 59.962 50.000 0.00 0.00 34.66 5.69
4290 4397 7.922278 AGCTTTATTATGCACACAAACATATGG 59.078 33.333 7.80 0.00 0.00 2.74
4322 4429 1.491670 TAATGAATCAGAGCGAGCGC 58.508 50.000 6.78 6.78 42.33 5.92
4441 4549 0.322726 CACCATGTGACCAGCCATCA 60.323 55.000 0.00 0.00 35.23 3.07
4500 4608 7.234661 TGTATACACATGGTGAGTAAGAACA 57.765 36.000 0.08 0.00 36.96 3.18
4501 4609 7.847096 TGTATACACATGGTGAGTAAGAACAT 58.153 34.615 0.08 0.00 36.96 2.71
4533 4641 3.328931 AGAATGAGGACAAAAGCAGAGGA 59.671 43.478 0.00 0.00 0.00 3.71
4582 4691 7.701539 ATGGACAAATATAACAGTGCAAGAA 57.298 32.000 0.00 0.00 35.97 2.52
4587 4696 9.543018 GACAAATATAACAGTGCAAGAAGTTAC 57.457 33.333 0.00 0.00 30.19 2.50
4652 4762 1.586154 CCAACCCAATGGACAGCGAC 61.586 60.000 0.00 0.00 43.54 5.19
4674 4784 5.071370 ACTTCTCGAGGTCTTAAAGACTCA 58.929 41.667 13.56 0.00 44.46 3.41
4733 4843 1.608590 TGCAGGAAAGCAAACACTAGC 59.391 47.619 0.00 0.00 42.46 3.42
4734 4844 1.608590 GCAGGAAAGCAAACACTAGCA 59.391 47.619 0.00 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.323417 TGTTTCTGAAAGATATGCGGTGT 58.677 39.130 2.48 0.00 46.36 4.16
1 2 4.944962 TGTTTCTGAAAGATATGCGGTG 57.055 40.909 2.48 0.00 46.36 4.94
2 3 5.237344 GCTATGTTTCTGAAAGATATGCGGT 59.763 40.000 17.17 0.00 46.36 5.68
3 4 5.334414 GGCTATGTTTCTGAAAGATATGCGG 60.334 44.000 17.17 9.17 46.36 5.69
4 5 5.468072 AGGCTATGTTTCTGAAAGATATGCG 59.532 40.000 17.17 9.45 46.36 4.73
5 6 6.874288 AGGCTATGTTTCTGAAAGATATGC 57.126 37.500 17.17 19.15 46.36 3.14
6 7 8.680903 ACAAAGGCTATGTTTCTGAAAGATATG 58.319 33.333 17.17 14.59 46.36 1.78
7 8 8.814038 ACAAAGGCTATGTTTCTGAAAGATAT 57.186 30.769 17.17 9.15 46.36 1.63
8 9 8.514594 CAACAAAGGCTATGTTTCTGAAAGATA 58.485 33.333 16.27 16.27 46.36 1.98
9 10 7.373493 CAACAAAGGCTATGTTTCTGAAAGAT 58.627 34.615 15.80 15.80 46.36 2.40
10 11 6.735694 GCAACAAAGGCTATGTTTCTGAAAGA 60.736 38.462 2.48 2.36 44.68 2.52
11 12 5.403466 GCAACAAAGGCTATGTTTCTGAAAG 59.597 40.000 2.48 0.00 38.90 2.62
12 13 5.163468 TGCAACAAAGGCTATGTTTCTGAAA 60.163 36.000 0.00 0.00 38.90 2.69
13 14 4.340666 TGCAACAAAGGCTATGTTTCTGAA 59.659 37.500 0.00 0.00 38.90 3.02
14 15 3.888323 TGCAACAAAGGCTATGTTTCTGA 59.112 39.130 0.00 0.00 38.90 3.27
15 16 4.022935 TCTGCAACAAAGGCTATGTTTCTG 60.023 41.667 0.00 1.57 38.90 3.02
16 17 4.144297 TCTGCAACAAAGGCTATGTTTCT 58.856 39.130 0.00 0.00 38.90 2.52
17 18 4.503741 TCTGCAACAAAGGCTATGTTTC 57.496 40.909 0.00 0.00 38.90 2.78
18 19 4.797275 GCTTCTGCAACAAAGGCTATGTTT 60.797 41.667 0.00 0.00 38.90 2.83
19 20 3.305608 GCTTCTGCAACAAAGGCTATGTT 60.306 43.478 0.00 0.00 41.50 2.71
20 21 2.229784 GCTTCTGCAACAAAGGCTATGT 59.770 45.455 0.00 0.00 39.41 2.29
21 22 2.730090 CGCTTCTGCAACAAAGGCTATG 60.730 50.000 0.00 0.00 39.64 2.23
22 23 1.470098 CGCTTCTGCAACAAAGGCTAT 59.530 47.619 0.00 0.00 39.64 2.97
23 24 0.874390 CGCTTCTGCAACAAAGGCTA 59.126 50.000 0.00 0.00 39.64 3.93
24 25 1.656441 CGCTTCTGCAACAAAGGCT 59.344 52.632 5.58 0.00 39.64 4.58
25 26 2.018324 GCGCTTCTGCAACAAAGGC 61.018 57.895 0.00 4.13 39.64 4.35
26 27 1.727022 CGCGCTTCTGCAACAAAGG 60.727 57.895 5.56 0.00 39.64 3.11
27 28 2.359791 GCGCGCTTCTGCAACAAAG 61.360 57.895 26.67 0.00 39.64 2.77
28 29 2.353376 GCGCGCTTCTGCAACAAA 60.353 55.556 26.67 0.00 39.64 2.83
29 30 3.240606 GAGCGCGCTTCTGCAACAA 62.241 57.895 36.87 0.00 39.64 2.83
45 46 0.537188 AGGGTTCACATACTGCCGAG 59.463 55.000 0.00 0.00 0.00 4.63
57 58 2.103432 ACACGTGTACAATGAGGGTTCA 59.897 45.455 21.98 0.00 37.81 3.18
67 68 1.507562 CCTGCATGACACGTGTACAA 58.492 50.000 23.44 11.00 0.00 2.41
116 117 2.516225 GCTTACCATCACCCCGGC 60.516 66.667 0.00 0.00 0.00 6.13
119 120 2.100197 GGAAAAGCTTACCATCACCCC 58.900 52.381 15.03 0.00 0.00 4.95
154 155 7.112984 GTGCTTTAAAAGATACAAACTGTTCGG 59.887 37.037 0.00 0.00 0.00 4.30
165 166 9.615295 TTTATTTGGACGTGCTTTAAAAGATAC 57.385 29.630 8.99 0.00 0.00 2.24
219 221 2.503765 CAAAGGGGTTGGTTTTGAAGGT 59.496 45.455 0.00 0.00 34.55 3.50
269 271 0.105224 TGTTCCGTGGTACTGTGGTG 59.895 55.000 0.00 0.00 0.00 4.17
270 272 1.053424 ATGTTCCGTGGTACTGTGGT 58.947 50.000 0.00 0.00 0.00 4.16
271 273 1.270625 ACATGTTCCGTGGTACTGTGG 60.271 52.381 0.00 0.00 0.00 4.17
272 274 2.066262 GACATGTTCCGTGGTACTGTG 58.934 52.381 0.00 3.94 0.00 3.66
273 275 1.001633 GGACATGTTCCGTGGTACTGT 59.998 52.381 0.00 0.17 33.46 3.55
274 276 1.722011 GGACATGTTCCGTGGTACTG 58.278 55.000 0.00 0.00 33.46 2.74
800 810 0.314935 GGGCCGGAATATTACGACGA 59.685 55.000 21.78 0.00 36.35 4.20
908 923 1.834263 AGCTTCGCAGATCCTAGGTTT 59.166 47.619 9.08 0.00 35.04 3.27
985 1010 1.836158 CCATGCCCACCACAAACCA 60.836 57.895 0.00 0.00 0.00 3.67
986 1011 1.836604 ACCATGCCCACCACAAACC 60.837 57.895 0.00 0.00 0.00 3.27
987 1012 1.112315 TCACCATGCCCACCACAAAC 61.112 55.000 0.00 0.00 0.00 2.93
989 1014 0.899253 CATCACCATGCCCACCACAA 60.899 55.000 0.00 0.00 0.00 3.33
991 1016 2.053865 CCATCACCATGCCCACCAC 61.054 63.158 0.00 0.00 0.00 4.16
992 1017 2.214122 CTCCATCACCATGCCCACCA 62.214 60.000 0.00 0.00 0.00 4.17
1031 1062 1.518903 GCTGAAGCCGCCAAGAACTT 61.519 55.000 0.00 0.00 34.31 2.66
1032 1063 1.968540 GCTGAAGCCGCCAAGAACT 60.969 57.895 0.00 0.00 34.31 3.01
1059 1090 4.925576 CTATCGCCGCCGTCGCTT 62.926 66.667 0.00 0.00 35.54 4.68
1066 1097 0.387878 CTCTCATCACTATCGCCGCC 60.388 60.000 0.00 0.00 0.00 6.13
1070 1101 1.006314 GCCGCTCTCATCACTATCGC 61.006 60.000 0.00 0.00 0.00 4.58
1074 1105 3.120105 CCGCCGCTCTCATCACTA 58.880 61.111 0.00 0.00 0.00 2.74
1646 1695 0.748729 AGGAGAGACGGACGGATGTC 60.749 60.000 0.00 0.00 44.72 3.06
1656 1705 2.218603 GAGGAAGCTAGAGGAGAGACG 58.781 57.143 0.00 0.00 0.00 4.18
1657 1706 2.174854 AGGAGGAAGCTAGAGGAGAGAC 59.825 54.545 0.00 0.00 0.00 3.36
1664 1713 3.134442 AGAATGCAAGGAGGAAGCTAGAG 59.866 47.826 0.00 0.00 0.00 2.43
1699 1750 6.415206 TGCACAAGGAGTAGTAGTAGTTTT 57.585 37.500 0.00 0.00 0.00 2.43
1702 1753 7.177921 TGTTTATGCACAAGGAGTAGTAGTAGT 59.822 37.037 0.00 0.00 0.00 2.73
1720 1771 0.455410 TTCATGGCGGCTGTTTATGC 59.545 50.000 11.43 0.00 0.00 3.14
1721 1772 2.937469 TTTCATGGCGGCTGTTTATG 57.063 45.000 11.43 5.13 0.00 1.90
1722 1773 2.760092 ACATTTCATGGCGGCTGTTTAT 59.240 40.909 11.43 0.00 33.60 1.40
1723 1774 2.166829 ACATTTCATGGCGGCTGTTTA 58.833 42.857 11.43 0.00 33.60 2.01
1724 1775 0.968405 ACATTTCATGGCGGCTGTTT 59.032 45.000 11.43 0.00 33.60 2.83
1725 1776 0.968405 AACATTTCATGGCGGCTGTT 59.032 45.000 11.43 8.41 33.60 3.16
1779 1862 7.624360 AGAATGGCAGAAAATGTTAATCGTA 57.376 32.000 0.00 0.00 0.00 3.43
1781 1864 7.113965 GCATAGAATGGCAGAAAATGTTAATCG 59.886 37.037 0.00 0.00 0.00 3.34
1816 1899 1.581954 CGAGCCTCTCAACGACACT 59.418 57.895 0.00 0.00 0.00 3.55
1822 1905 1.066908 CAGATCTCCGAGCCTCTCAAC 59.933 57.143 0.00 0.00 0.00 3.18
1925 2008 4.523558 TGAGTTTGATGCACCAATCAATCA 59.476 37.500 4.69 0.00 44.04 2.57
1927 2010 5.471556 TTGAGTTTGATGCACCAATCAAT 57.528 34.783 5.84 0.00 44.04 2.57
1928 2011 4.933505 TTGAGTTTGATGCACCAATCAA 57.066 36.364 5.84 5.84 43.20 2.57
1955 2045 2.113860 AAGTGCATGTGATTACGCCT 57.886 45.000 0.00 0.00 0.00 5.52
1956 2046 2.518949 CAAAGTGCATGTGATTACGCC 58.481 47.619 0.00 0.00 0.00 5.68
2001 2092 6.127168 ACTGGTAGATGAACACGAATGGATTA 60.127 38.462 0.00 0.00 0.00 1.75
2011 2102 2.363788 TGCGACTGGTAGATGAACAC 57.636 50.000 0.00 0.00 0.00 3.32
2025 2116 1.959226 TGGCTTCGGAAGTTGCGAC 60.959 57.895 19.64 8.84 40.66 5.19
2028 2119 1.578206 GAGGTGGCTTCGGAAGTTGC 61.578 60.000 18.32 5.82 0.00 4.17
2029 2120 0.035458 AGAGGTGGCTTCGGAAGTTG 59.965 55.000 18.32 0.00 0.00 3.16
2030 2121 0.765510 AAGAGGTGGCTTCGGAAGTT 59.234 50.000 18.32 1.13 0.00 2.66
2031 2122 0.035458 CAAGAGGTGGCTTCGGAAGT 59.965 55.000 18.32 0.00 0.00 3.01
2032 2123 0.321671 TCAAGAGGTGGCTTCGGAAG 59.678 55.000 13.39 13.39 0.00 3.46
2033 2124 0.984230 ATCAAGAGGTGGCTTCGGAA 59.016 50.000 0.00 0.00 0.00 4.30
2050 2141 6.367686 TCTGCACATCACATGTTCATAATC 57.632 37.500 0.00 0.00 42.70 1.75
2053 2144 7.429636 CATATCTGCACATCACATGTTCATA 57.570 36.000 0.00 0.00 42.70 2.15
2215 2311 1.372087 CGTCAGGGAGAAATGCTGGC 61.372 60.000 0.00 0.00 0.00 4.85
2500 2599 3.134127 GCACCACGCATTCCTCCC 61.134 66.667 0.00 0.00 41.79 4.30
2588 2687 2.478831 GAGCATTCCTTCCTGATCGTC 58.521 52.381 0.00 0.00 0.00 4.20
2658 2757 0.602638 TCAGCATCGGCAAGAACGTT 60.603 50.000 0.00 0.00 44.61 3.99
2659 2758 1.005037 TCAGCATCGGCAAGAACGT 60.005 52.632 0.00 0.00 44.61 3.99
2681 2780 1.740380 CGATCGTTCAGTTCATGGGCT 60.740 52.381 7.03 0.00 0.00 5.19
2741 2840 1.219124 GACGCCTCCTGCTTGATCA 59.781 57.895 0.00 0.00 38.05 2.92
2792 2891 4.065281 GTCTCCGGTGGTGGTCCG 62.065 72.222 0.00 0.00 46.49 4.79
2794 2893 2.488087 CTTCGTCTCCGGTGGTGGTC 62.488 65.000 0.00 0.00 33.95 4.02
2818 2920 0.833949 GGCCTTCCTTCCGATCTTCT 59.166 55.000 0.00 0.00 0.00 2.85
2819 2921 3.388272 GGCCTTCCTTCCGATCTTC 57.612 57.895 0.00 0.00 0.00 2.87
2852 2954 0.255318 ATCCTTGCAGCTCCTTGAGG 59.745 55.000 0.00 0.00 0.00 3.86
2855 2957 2.706339 AGTATCCTTGCAGCTCCTTG 57.294 50.000 0.00 0.00 0.00 3.61
2958 3061 3.593442 ACTTGGTTGGGAGTCAATTCA 57.407 42.857 0.00 0.00 37.73 2.57
2964 3067 3.486383 TCAATGAACTTGGTTGGGAGTC 58.514 45.455 0.00 0.00 35.43 3.36
2968 3071 4.399004 TGTTTCAATGAACTTGGTTGGG 57.601 40.909 0.00 0.00 35.43 4.12
2969 3072 5.358922 ACATGTTTCAATGAACTTGGTTGG 58.641 37.500 0.00 0.00 38.36 3.77
2970 3073 5.173673 CGACATGTTTCAATGAACTTGGTTG 59.826 40.000 0.00 0.00 38.36 3.77
2975 3078 8.137437 AGATTTTCGACATGTTTCAATGAACTT 58.863 29.630 0.00 0.00 0.00 2.66
2978 3081 6.862608 CCAGATTTTCGACATGTTTCAATGAA 59.137 34.615 0.00 0.00 0.00 2.57
2983 3086 5.995282 AGTACCAGATTTTCGACATGTTTCA 59.005 36.000 0.00 0.00 0.00 2.69
2998 3101 3.440173 CGAATGCAAACCAAGTACCAGAT 59.560 43.478 0.00 0.00 0.00 2.90
3000 3103 2.552315 ACGAATGCAAACCAAGTACCAG 59.448 45.455 0.00 0.00 0.00 4.00
3001 3104 2.577700 ACGAATGCAAACCAAGTACCA 58.422 42.857 0.00 0.00 0.00 3.25
3003 3106 5.963586 GCTTATACGAATGCAAACCAAGTAC 59.036 40.000 0.00 0.00 0.00 2.73
3004 3107 5.065474 GGCTTATACGAATGCAAACCAAGTA 59.935 40.000 0.00 0.00 0.00 2.24
3005 3108 4.142469 GGCTTATACGAATGCAAACCAAGT 60.142 41.667 0.00 0.00 0.00 3.16
3006 3109 4.351192 GGCTTATACGAATGCAAACCAAG 58.649 43.478 0.00 0.00 0.00 3.61
3007 3110 3.181505 CGGCTTATACGAATGCAAACCAA 60.182 43.478 0.00 0.00 0.00 3.67
3008 3111 2.353269 CGGCTTATACGAATGCAAACCA 59.647 45.455 0.00 0.00 0.00 3.67
3009 3112 2.853281 GCGGCTTATACGAATGCAAACC 60.853 50.000 0.00 0.00 0.00 3.27
3010 3113 2.031683 AGCGGCTTATACGAATGCAAAC 59.968 45.455 0.00 0.00 0.00 2.93
3011 3114 2.285083 AGCGGCTTATACGAATGCAAA 58.715 42.857 0.00 0.00 0.00 3.68
3012 3115 1.948104 AGCGGCTTATACGAATGCAA 58.052 45.000 0.00 0.00 0.00 4.08
3013 3116 2.400399 GTAGCGGCTTATACGAATGCA 58.600 47.619 8.26 0.00 0.00 3.96
3014 3117 1.725164 GGTAGCGGCTTATACGAATGC 59.275 52.381 8.26 0.00 0.00 3.56
3015 3118 2.288579 TGGGTAGCGGCTTATACGAATG 60.289 50.000 8.26 0.00 0.00 2.67
3016 3119 1.965643 TGGGTAGCGGCTTATACGAAT 59.034 47.619 8.26 0.00 0.00 3.34
3017 3120 1.401761 TGGGTAGCGGCTTATACGAA 58.598 50.000 8.26 0.00 0.00 3.85
3018 3121 1.624336 ATGGGTAGCGGCTTATACGA 58.376 50.000 8.26 0.00 0.00 3.43
3019 3122 3.703420 GATATGGGTAGCGGCTTATACG 58.297 50.000 8.26 0.00 0.00 3.06
3020 3123 3.379372 TCGATATGGGTAGCGGCTTATAC 59.621 47.826 8.26 0.00 39.98 1.47
3021 3124 3.623703 TCGATATGGGTAGCGGCTTATA 58.376 45.455 8.26 3.29 39.98 0.98
3022 3125 2.453521 TCGATATGGGTAGCGGCTTAT 58.546 47.619 8.26 0.00 39.98 1.73
3023 3126 1.913778 TCGATATGGGTAGCGGCTTA 58.086 50.000 8.26 0.00 39.98 3.09
3024 3127 1.045407 TTCGATATGGGTAGCGGCTT 58.955 50.000 8.26 0.00 39.98 4.35
3025 3128 1.045407 TTTCGATATGGGTAGCGGCT 58.955 50.000 7.98 7.98 39.98 5.52
3026 3129 1.873698 TTTTCGATATGGGTAGCGGC 58.126 50.000 0.00 0.00 39.98 6.53
3027 3130 2.546789 GGTTTTTCGATATGGGTAGCGG 59.453 50.000 0.00 0.00 39.98 5.52
3028 3131 2.220133 CGGTTTTTCGATATGGGTAGCG 59.780 50.000 0.00 0.00 40.86 4.26
3029 3132 3.460103 TCGGTTTTTCGATATGGGTAGC 58.540 45.455 0.00 0.00 33.92 3.58
3030 3133 6.613755 ATTTCGGTTTTTCGATATGGGTAG 57.386 37.500 0.00 0.00 39.03 3.18
3031 3134 8.680039 AATATTTCGGTTTTTCGATATGGGTA 57.320 30.769 0.00 0.00 39.03 3.69
3032 3135 7.576861 AATATTTCGGTTTTTCGATATGGGT 57.423 32.000 0.00 0.00 39.03 4.51
3033 3136 9.389570 GTAAATATTTCGGTTTTTCGATATGGG 57.610 33.333 3.39 0.00 39.03 4.00
3036 3139 9.659830 GCAGTAAATATTTCGGTTTTTCGATAT 57.340 29.630 3.39 0.00 39.03 1.63
3037 3140 8.666573 TGCAGTAAATATTTCGGTTTTTCGATA 58.333 29.630 3.39 0.00 39.03 2.92
3038 3141 7.531716 TGCAGTAAATATTTCGGTTTTTCGAT 58.468 30.769 3.39 0.00 39.03 3.59
3039 3142 6.900189 TGCAGTAAATATTTCGGTTTTTCGA 58.100 32.000 3.39 0.00 37.38 3.71
3040 3143 7.483375 TCATGCAGTAAATATTTCGGTTTTTCG 59.517 33.333 3.39 0.00 0.00 3.46
3041 3144 8.682128 TCATGCAGTAAATATTTCGGTTTTTC 57.318 30.769 3.39 0.00 0.00 2.29
3042 3145 9.086336 CATCATGCAGTAAATATTTCGGTTTTT 57.914 29.630 3.39 0.00 0.00 1.94
3043 3146 8.465999 TCATCATGCAGTAAATATTTCGGTTTT 58.534 29.630 3.39 0.00 0.00 2.43
3047 3150 6.605849 CCTCATCATGCAGTAAATATTTCGG 58.394 40.000 3.39 0.00 0.00 4.30
3048 3151 6.082338 GCCTCATCATGCAGTAAATATTTCG 58.918 40.000 3.39 0.00 0.00 3.46
3054 3157 4.097437 CAGTTGCCTCATCATGCAGTAAAT 59.903 41.667 0.00 0.00 38.95 1.40
3059 3163 1.671328 CTCAGTTGCCTCATCATGCAG 59.329 52.381 0.00 0.00 38.95 4.41
3062 3166 3.118702 AGACTCTCAGTTGCCTCATCATG 60.119 47.826 0.00 0.00 0.00 3.07
3067 3171 2.001076 TCAGACTCTCAGTTGCCTCA 57.999 50.000 0.00 0.00 0.00 3.86
3069 3173 2.703007 AGTTTCAGACTCTCAGTTGCCT 59.297 45.455 0.00 0.00 31.20 4.75
3070 3174 3.118905 AGTTTCAGACTCTCAGTTGCC 57.881 47.619 0.00 0.00 31.20 4.52
3080 3184 6.127310 ACACTGTAGAACAAGAGTTTCAGACT 60.127 38.462 12.33 0.00 42.70 3.24
3081 3185 6.019479 CACACTGTAGAACAAGAGTTTCAGAC 60.019 42.308 12.33 0.00 38.30 3.51
3082 3186 6.042777 CACACTGTAGAACAAGAGTTTCAGA 58.957 40.000 12.33 0.00 38.30 3.27
3116 3220 2.001361 GCCTGCAGATGCGCTTCATT 62.001 55.000 23.42 2.75 45.83 2.57
3291 3395 3.761218 TCTTCTCCTAGAGCACTTGACAG 59.239 47.826 0.00 0.00 0.00 3.51
3482 3586 1.280457 CCACCTCCTCCTTTACTGCT 58.720 55.000 0.00 0.00 0.00 4.24
3570 3674 2.512515 GGCATCGCAGGACAGGAC 60.513 66.667 0.00 0.00 0.00 3.85
3668 3772 1.202867 TGCACCATTAGCCTGACAACA 60.203 47.619 0.00 0.00 0.00 3.33
3698 3805 2.894126 ACAGGAGCTCCTATGGTTATCG 59.106 50.000 34.67 20.56 46.65 2.92
3716 3823 2.697751 AGGCTAATCTGAGCTACCACAG 59.302 50.000 0.00 0.00 42.43 3.66
3742 3849 3.131046 GCTGTATGGTTAAGGCATGCTTT 59.869 43.478 19.67 19.67 0.00 3.51
3743 3850 2.689983 GCTGTATGGTTAAGGCATGCTT 59.310 45.455 18.92 7.19 0.00 3.91
3744 3851 2.092212 AGCTGTATGGTTAAGGCATGCT 60.092 45.455 18.92 0.24 0.00 3.79
3947 4054 2.977914 TGTGCTAGGAGCTGATCAAAC 58.022 47.619 0.00 0.00 42.97 2.93
3956 4063 2.627515 TGAATCCATGTGCTAGGAGC 57.372 50.000 0.00 0.00 42.82 4.70
3963 4070 3.067742 CCTTCTTCCATGAATCCATGTGC 59.932 47.826 0.00 0.00 46.68 4.57
4089 4196 1.648467 GGGTGTCCTGCAGCGAAATC 61.648 60.000 8.66 2.56 45.88 2.17
4097 4204 0.840288 ACTACCATGGGTGTCCTGCA 60.840 55.000 18.09 0.00 36.19 4.41
4099 4206 3.711704 AGATTACTACCATGGGTGTCCTG 59.288 47.826 18.09 0.26 36.19 3.86
4102 4209 3.454812 ACCAGATTACTACCATGGGTGTC 59.545 47.826 18.09 8.20 36.19 3.67
4129 4236 3.714798 TGCCCCTTAGAACTGTATTAGGG 59.285 47.826 9.09 9.09 41.63 3.53
4159 4266 0.392998 ACTTGCCGTGGAATAGCAGG 60.393 55.000 0.00 0.00 37.89 4.85
4173 4280 6.363357 GGATTGACACAGAACAATAAACTTGC 59.637 38.462 0.00 0.00 36.94 4.01
4175 4282 6.777580 AGGGATTGACACAGAACAATAAACTT 59.222 34.615 0.00 0.00 36.94 2.66
4322 4429 2.816958 AGTTCTGCGATGCTGCCG 60.817 61.111 0.00 0.00 0.00 5.69
4441 4549 2.166254 CGTGCAAATTATGGGCTCCTTT 59.834 45.455 0.00 0.00 0.00 3.11
4500 4608 7.707624 TTTGTCCTCATTCTCATTTTGCTAT 57.292 32.000 0.00 0.00 0.00 2.97
4501 4609 7.523293 TTTTGTCCTCATTCTCATTTTGCTA 57.477 32.000 0.00 0.00 0.00 3.49
4559 4668 6.714810 ACTTCTTGCACTGTTATATTTGTCCA 59.285 34.615 0.00 0.00 0.00 4.02
4611 4720 3.514645 CATGGCTGAGGTAAACAAATGC 58.485 45.455 0.00 0.00 0.00 3.56
4652 4762 5.630661 TGAGTCTTTAAGACCTCGAGAAG 57.369 43.478 20.05 8.48 46.18 2.85


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

AutoCloner maintained by Alex Coulton.