Multiple sequence alignment - TraesCS1D01G098300

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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 TraesCS1D01G098300 chr1D 100.000 5340 0 0 1 5340 85177850 85183189 0.000000e+00 9862.0
1 TraesCS1D01G098300 chr1D 93.557 776 45 4 1 772 319517419 319516645 0.000000e+00 1151.0
2 TraesCS1D01G098300 chr1D 92.645 775 53 4 1 772 279519179 279519952 0.000000e+00 1112.0
3 TraesCS1D01G098300 chr1A 94.546 2677 70 30 1112 3763 79166463 79169088 0.000000e+00 4065.0
4 TraesCS1D01G098300 chr1A 92.377 774 56 3 1 772 522194383 522195155 0.000000e+00 1099.0
5 TraesCS1D01G098300 chr1A 83.631 727 103 9 4618 5337 79172442 79173159 0.000000e+00 669.0
6 TraesCS1D01G098300 chr1A 84.029 551 70 9 4183 4725 79171922 79172462 1.030000e-141 514.0
7 TraesCS1D01G098300 chr1A 89.286 336 32 3 782 1117 79147379 79147710 8.270000e-113 418.0
8 TraesCS1D01G098300 chr1A 80.738 244 26 12 3773 4007 79169127 79169358 2.560000e-38 171.0
9 TraesCS1D01G098300 chr1B 96.815 1036 30 1 2201 3236 137625025 137626057 0.000000e+00 1727.0
10 TraesCS1D01G098300 chr1B 84.193 1474 118 50 782 2184 137623541 137624970 0.000000e+00 1325.0
11 TraesCS1D01G098300 chr1B 96.230 504 17 2 3262 3763 137626113 137626616 0.000000e+00 824.0
12 TraesCS1D01G098300 chr1B 88.837 215 19 3 4176 4390 137627947 137628156 5.310000e-65 259.0
13 TraesCS1D01G098300 chr1B 79.602 402 46 18 3773 4163 137626655 137627031 6.860000e-64 255.0
14 TraesCS1D01G098300 chr1B 80.292 274 43 7 3893 4160 137628400 137628668 4.220000e-46 196.0
15 TraesCS1D01G098300 chr3D 93.540 774 48 2 1 772 378028868 378029641 0.000000e+00 1151.0
16 TraesCS1D01G098300 chr3D 92.903 775 52 3 1 772 327438014 327438788 0.000000e+00 1123.0
17 TraesCS1D01G098300 chr3D 92.387 775 54 5 1 772 603976667 603977439 0.000000e+00 1099.0
18 TraesCS1D01G098300 chr5D 93.032 775 51 3 1 772 389374426 389375200 0.000000e+00 1129.0
19 TraesCS1D01G098300 chr7D 92.912 776 51 3 1 772 117521341 117520566 0.000000e+00 1125.0
20 TraesCS1D01G098300 chr7D 76.216 185 34 9 2694 2876 415682957 415682781 7.370000e-14 89.8
21 TraesCS1D01G098300 chr7A 92.367 773 57 2 1 772 53898323 53899094 0.000000e+00 1099.0
22 TraesCS1D01G098300 chr7A 76.216 185 34 9 2694 2876 477809657 477809481 7.370000e-14 89.8
23 TraesCS1D01G098300 chr7A 96.970 33 1 0 2844 2876 511695960 511695928 7.470000e-04 56.5
24 TraesCS1D01G098300 chr7B 76.216 185 34 9 2694 2876 429267874 429267698 7.370000e-14 89.8


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 TraesCS1D01G098300 chr1D 85177850 85183189 5339 False 9862.000000 9862 100.0000 1 5340 1 chr1D.!!$F1 5339
1 TraesCS1D01G098300 chr1D 319516645 319517419 774 True 1151.000000 1151 93.5570 1 772 1 chr1D.!!$R1 771
2 TraesCS1D01G098300 chr1D 279519179 279519952 773 False 1112.000000 1112 92.6450 1 772 1 chr1D.!!$F2 771
3 TraesCS1D01G098300 chr1A 79166463 79173159 6696 False 1354.750000 4065 85.7360 1112 5337 4 chr1A.!!$F3 4225
4 TraesCS1D01G098300 chr1A 522194383 522195155 772 False 1099.000000 1099 92.3770 1 772 1 chr1A.!!$F2 771
5 TraesCS1D01G098300 chr1B 137623541 137628668 5127 False 764.333333 1727 87.6615 782 4390 6 chr1B.!!$F1 3608
6 TraesCS1D01G098300 chr3D 378028868 378029641 773 False 1151.000000 1151 93.5400 1 772 1 chr3D.!!$F2 771
7 TraesCS1D01G098300 chr3D 327438014 327438788 774 False 1123.000000 1123 92.9030 1 772 1 chr3D.!!$F1 771
8 TraesCS1D01G098300 chr3D 603976667 603977439 772 False 1099.000000 1099 92.3870 1 772 1 chr3D.!!$F3 771
9 TraesCS1D01G098300 chr5D 389374426 389375200 774 False 1129.000000 1129 93.0320 1 772 1 chr5D.!!$F1 771
10 TraesCS1D01G098300 chr7D 117520566 117521341 775 True 1125.000000 1125 92.9120 1 772 1 chr7D.!!$R1 771
11 TraesCS1D01G098300 chr7A 53898323 53899094 771 False 1099.000000 1099 92.3670 1 772 1 chr7A.!!$F1 771

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
838 844 0.320771 AGCTGGTTCATCGGTGTGAC 60.321 55.0 0.00 0.00 0.0 3.67 F
1706 1767 0.178903 TGTGGTTGGAGCCTAGGACT 60.179 55.0 14.75 9.37 0.0 3.85 F
3034 3154 0.250124 CCTGCAACGACACCAACCTA 60.250 55.0 0.00 0.00 0.0 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2386 2506 0.189822 GGAGGCAGGAGAGGTAGGAT 59.810 60.0 0.0 0.0 0.00 3.24 R
3133 3253 0.622665 CCTCCTCCCAGTTCTGCATT 59.377 55.0 0.0 0.0 0.00 3.56 R
4527 7193 0.101219 GATGGGGATTGTTTCGCTGC 59.899 55.0 0.0 0.0 37.45 5.25 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
23 24 2.520982 TATGAGGCCGCCGTAGCT 60.521 61.111 3.22 0.00 36.60 3.32
73 74 1.073763 ACTGTTGCATCTACCTTGCCA 59.926 47.619 0.00 0.00 39.39 4.92
112 113 1.667830 CACCACGACGCCAGACAAT 60.668 57.895 0.00 0.00 0.00 2.71
114 115 1.667830 CCACGACGCCAGACAATGT 60.668 57.895 0.00 0.00 0.00 2.71
130 131 1.902765 ATGTCACCATCCTGCGCTCA 61.903 55.000 9.73 0.00 0.00 4.26
144 145 1.944032 CGCTCATCCATCATCACACA 58.056 50.000 0.00 0.00 0.00 3.72
153 154 1.488705 ATCATCACACACCCACCGGT 61.489 55.000 0.00 0.00 46.31 5.28
331 332 3.399952 TCTTAGGATTTCTCCCGGAGT 57.600 47.619 14.36 0.00 43.21 3.85
395 396 1.896220 AGGTAACGACGTAGACACCA 58.104 50.000 19.33 0.00 46.39 4.17
678 683 3.519579 GGCCATATCAGATCTCATCACG 58.480 50.000 0.00 0.00 0.00 4.35
698 704 0.383231 GCCAAATCTCATCCGCCAAG 59.617 55.000 0.00 0.00 0.00 3.61
772 778 2.444895 GGAGGGAGATGGACGCCT 60.445 66.667 0.00 0.00 38.52 5.52
773 779 1.152525 GGAGGGAGATGGACGCCTA 60.153 63.158 0.00 0.00 38.52 3.93
774 780 1.465200 GGAGGGAGATGGACGCCTAC 61.465 65.000 0.00 0.00 38.52 3.18
775 781 1.457831 AGGGAGATGGACGCCTACC 60.458 63.158 0.00 0.00 38.52 3.18
776 782 1.760875 GGGAGATGGACGCCTACCA 60.761 63.158 0.00 0.00 41.83 3.25
777 783 1.442148 GGAGATGGACGCCTACCAC 59.558 63.158 0.00 0.00 40.36 4.16
778 784 1.442148 GAGATGGACGCCTACCACC 59.558 63.158 0.00 0.00 40.36 4.61
779 785 2.106332 GATGGACGCCTACCACCG 59.894 66.667 0.00 0.00 40.36 4.94
780 786 3.441011 GATGGACGCCTACCACCGG 62.441 68.421 0.00 0.00 40.36 5.28
799 805 3.511540 CCGGAAGATGATGGTCTATAGCA 59.488 47.826 0.00 0.00 37.55 3.49
822 828 0.530744 TCGTATTTGAGGCGACAGCT 59.469 50.000 0.00 0.00 44.37 4.24
833 839 1.079819 CGACAGCTGGTTCATCGGT 60.080 57.895 19.93 0.00 0.00 4.69
838 844 0.320771 AGCTGGTTCATCGGTGTGAC 60.321 55.000 0.00 0.00 0.00 3.67
852 858 1.276844 GTGACTGCGTGCTGTTGTC 59.723 57.895 5.84 3.98 0.00 3.18
853 859 1.143838 TGACTGCGTGCTGTTGTCT 59.856 52.632 5.84 0.00 0.00 3.41
869 875 2.615391 TGTCTGGGTACAACAGGATGA 58.385 47.619 14.49 0.00 39.69 2.92
872 878 2.505407 TCTGGGTACAACAGGATGATGG 59.495 50.000 14.49 0.00 43.92 3.51
940 946 3.055719 CATGGTGGGTGCACGTCC 61.056 66.667 11.45 13.03 0.00 4.79
981 991 2.159028 AGCAGCGTCTTCTTCCCTAATC 60.159 50.000 0.00 0.00 0.00 1.75
1017 1036 0.746659 GGATGTTGGTAGGGCAATGC 59.253 55.000 0.00 0.00 0.00 3.56
1020 1039 2.889170 TGTTGGTAGGGCAATGCTTA 57.111 45.000 4.82 0.00 0.00 3.09
1022 1041 1.749063 GTTGGTAGGGCAATGCTTACC 59.251 52.381 22.99 22.99 38.34 2.85
1049 1069 3.146066 TCCTTCCTTGGACAATGTTTCG 58.854 45.455 0.00 0.00 0.00 3.46
1050 1070 3.146066 CCTTCCTTGGACAATGTTTCGA 58.854 45.455 0.00 0.00 0.00 3.71
1051 1071 3.189287 CCTTCCTTGGACAATGTTTCGAG 59.811 47.826 0.00 0.00 0.00 4.04
1058 1078 3.003480 GGACAATGTTTCGAGAAGGAGG 58.997 50.000 0.00 0.00 0.00 4.30
1061 1081 4.508662 ACAATGTTTCGAGAAGGAGGATC 58.491 43.478 0.00 0.00 0.00 3.36
1064 1084 3.926616 TGTTTCGAGAAGGAGGATCAAC 58.073 45.455 0.00 0.00 36.25 3.18
1080 1100 2.876091 TCAACCTTAACGCAGATCTCG 58.124 47.619 11.44 11.44 0.00 4.04
1084 1104 1.629013 CTTAACGCAGATCTCGTGCA 58.371 50.000 17.10 8.66 41.26 4.57
1085 1105 2.196749 CTTAACGCAGATCTCGTGCAT 58.803 47.619 17.10 7.80 41.26 3.96
1086 1106 1.559831 TAACGCAGATCTCGTGCATG 58.440 50.000 17.10 0.00 41.26 4.06
1087 1107 0.390340 AACGCAGATCTCGTGCATGT 60.390 50.000 17.10 1.76 41.26 3.21
1088 1108 0.390340 ACGCAGATCTCGTGCATGTT 60.390 50.000 16.09 0.00 41.26 2.71
1089 1109 1.135112 ACGCAGATCTCGTGCATGTTA 60.135 47.619 16.09 0.00 41.26 2.41
1090 1110 2.130395 CGCAGATCTCGTGCATGTTAT 58.870 47.619 5.68 0.60 41.26 1.89
1091 1111 2.097056 CGCAGATCTCGTGCATGTTATG 60.097 50.000 5.68 1.68 41.26 1.90
1105 1125 5.408204 CATGTTATGCGTTCTTGCTATCA 57.592 39.130 0.00 0.00 35.36 2.15
1121 1141 4.202524 TGCTATCAAGTTGGTTGGTACCTT 60.203 41.667 14.36 0.00 45.27 3.50
1164 1184 5.755849 CCATATTAGGTTCCACAGTTTCCT 58.244 41.667 0.00 0.00 0.00 3.36
1176 1196 1.630369 CAGTTTCCTCCCACCATCAGA 59.370 52.381 0.00 0.00 0.00 3.27
1364 1400 4.228210 AGGATTGGATAGCTGGAACAAGAA 59.772 41.667 0.00 0.00 38.70 2.52
1404 1440 3.074412 GCCTCGATCTGTTCCTTTTTCA 58.926 45.455 0.00 0.00 0.00 2.69
1405 1441 3.502211 GCCTCGATCTGTTCCTTTTTCAA 59.498 43.478 0.00 0.00 0.00 2.69
1565 1607 6.969828 AAGAAACTACTGATAAAGAAGGCG 57.030 37.500 0.00 0.00 0.00 5.52
1568 1610 2.158943 ACTACTGATAAAGAAGGCGGGC 60.159 50.000 0.00 0.00 0.00 6.13
1706 1767 0.178903 TGTGGTTGGAGCCTAGGACT 60.179 55.000 14.75 9.37 0.00 3.85
1833 1902 1.272092 TGCACAATTTGAGGGGAGGAG 60.272 52.381 2.79 0.00 0.00 3.69
1839 1908 1.071314 TTTGAGGGGAGGAGGCCAAA 61.071 55.000 5.01 0.00 0.00 3.28
2122 2201 6.018832 CGTTGATTCTTGCATTTCTTGGTTTT 60.019 34.615 0.00 0.00 0.00 2.43
2155 2234 3.457234 CCTGTGAATCGGATCGAATTGA 58.543 45.455 0.00 0.00 39.99 2.57
2182 2261 2.739293 TCTCGAGATTGATCACGACG 57.261 50.000 12.08 0.00 43.11 5.12
2183 2262 2.277084 TCTCGAGATTGATCACGACGA 58.723 47.619 12.08 4.22 43.11 4.20
2184 2263 2.030579 TCTCGAGATTGATCACGACGAC 59.969 50.000 12.08 0.00 43.11 4.34
2193 2272 1.983605 GATCACGACGACGAACAATGT 59.016 47.619 15.32 0.00 42.66 2.71
2209 2329 7.069569 CGAACAATGTCGATTTCTTTAGTGTT 58.930 34.615 0.00 0.00 43.86 3.32
2833 2953 4.619227 ACCACCCGCGACCACTTG 62.619 66.667 8.23 0.00 0.00 3.16
3034 3154 0.250124 CCTGCAACGACACCAACCTA 60.250 55.000 0.00 0.00 0.00 3.08
3133 3253 4.064388 TCGAGCTGAACAATCACATTTGA 58.936 39.130 0.00 0.00 35.73 2.69
3248 3376 3.326006 TCTCTATCCAAGCATCCATCCAC 59.674 47.826 0.00 0.00 0.00 4.02
3275 3433 2.298593 GGCGGCTAACGTCTTGATC 58.701 57.895 0.00 0.00 45.50 2.92
3646 3806 2.932234 CGCACTCGTCCCAAGAGGT 61.932 63.158 0.00 0.00 39.90 3.85
3656 3816 4.379243 CAAGAGGTCTGCGCCGGT 62.379 66.667 4.18 0.00 0.00 5.28
3765 3925 2.180769 CGTCCGACGGCTGATCAA 59.819 61.111 13.29 0.00 38.08 2.57
3766 3926 1.226974 CGTCCGACGGCTGATCAAT 60.227 57.895 13.29 0.00 38.08 2.57
3767 3927 1.482621 CGTCCGACGGCTGATCAATG 61.483 60.000 13.29 0.00 38.08 2.82
3768 3928 1.521457 TCCGACGGCTGATCAATGC 60.521 57.895 9.66 0.00 0.00 3.56
3770 3930 1.368345 CCGACGGCTGATCAATGCAA 61.368 55.000 0.00 0.00 0.00 4.08
3771 3931 0.027194 CGACGGCTGATCAATGCAAG 59.973 55.000 0.00 5.07 0.00 4.01
3785 3974 2.993471 GCAAGTCAATGCGGGGTGG 61.993 63.158 0.00 0.00 36.45 4.61
3788 3977 1.488705 AAGTCAATGCGGGGTGGAGA 61.489 55.000 0.00 0.00 0.00 3.71
3795 3984 2.202932 CGGGGTGGAGATTGAGCG 60.203 66.667 0.00 0.00 0.00 5.03
3853 4042 0.101759 GGATGCGCCGACTTGTACTA 59.898 55.000 4.18 0.00 0.00 1.82
3854 4043 1.197910 GATGCGCCGACTTGTACTAC 58.802 55.000 4.18 0.00 0.00 2.73
3857 4046 1.131126 TGCGCCGACTTGTACTACTAC 59.869 52.381 4.18 0.00 0.00 2.73
3858 4047 1.399791 GCGCCGACTTGTACTACTACT 59.600 52.381 0.00 0.00 0.00 2.57
3881 4073 3.535561 CCATTATCAGGGATGATACGCC 58.464 50.000 0.00 0.00 31.24 5.68
3905 4097 2.125147 CGGGGCTGATTTGCGAGA 60.125 61.111 0.00 0.00 0.00 4.04
3906 4098 1.524621 CGGGGCTGATTTGCGAGAT 60.525 57.895 0.00 0.00 0.00 2.75
3908 4100 0.665298 GGGGCTGATTTGCGAGATTC 59.335 55.000 0.00 0.00 0.00 2.52
3909 4101 1.673168 GGGCTGATTTGCGAGATTCT 58.327 50.000 0.00 0.00 0.00 2.40
3910 4102 2.019984 GGGCTGATTTGCGAGATTCTT 58.980 47.619 0.00 0.00 0.00 2.52
3912 4104 3.627577 GGGCTGATTTGCGAGATTCTTTA 59.372 43.478 0.00 0.00 0.00 1.85
3914 4106 4.278058 GCTGATTTGCGAGATTCTTTAGC 58.722 43.478 0.00 0.00 0.00 3.09
3962 4163 1.831726 GGGGTAGCGGTAGAGGGAC 60.832 68.421 0.00 0.00 0.00 4.46
3990 4191 5.887035 AGTGTAGTGGAGTGGTACTAATCTC 59.113 44.000 6.64 0.00 31.74 2.75
4026 4227 9.643693 CAATTTTGATTTTGGATTAGCTACTGT 57.356 29.630 0.00 0.00 0.00 3.55
4066 4267 3.627577 ACCTAAATGATAAGTGCCTTGCG 59.372 43.478 0.00 0.00 0.00 4.85
4067 4268 3.876914 CCTAAATGATAAGTGCCTTGCGA 59.123 43.478 0.00 0.00 0.00 5.10
4068 4269 4.024556 CCTAAATGATAAGTGCCTTGCGAG 60.025 45.833 0.00 0.00 0.00 5.03
4069 4270 2.988010 ATGATAAGTGCCTTGCGAGA 57.012 45.000 1.22 0.00 0.00 4.04
4070 4271 2.299993 TGATAAGTGCCTTGCGAGAG 57.700 50.000 1.22 0.00 0.00 3.20
4071 4272 1.824852 TGATAAGTGCCTTGCGAGAGA 59.175 47.619 1.22 0.00 0.00 3.10
4072 4273 2.233676 TGATAAGTGCCTTGCGAGAGAA 59.766 45.455 1.22 0.00 0.00 2.87
4073 4274 2.831685 TAAGTGCCTTGCGAGAGAAA 57.168 45.000 1.22 0.00 0.00 2.52
4074 4275 1.967319 AAGTGCCTTGCGAGAGAAAA 58.033 45.000 1.22 0.00 0.00 2.29
4076 4277 1.202698 AGTGCCTTGCGAGAGAAAAGT 60.203 47.619 1.22 0.00 0.00 2.66
4078 4279 0.519077 GCCTTGCGAGAGAAAAGTGG 59.481 55.000 1.22 0.00 0.00 4.00
4080 4281 1.160137 CTTGCGAGAGAAAAGTGGGG 58.840 55.000 0.00 0.00 0.00 4.96
4088 4289 4.338400 CGAGAGAAAAGTGGGGAAAAAGTT 59.662 41.667 0.00 0.00 0.00 2.66
4093 4294 6.170506 AGAAAAGTGGGGAAAAAGTTTGAAC 58.829 36.000 0.00 0.00 0.00 3.18
4105 4307 7.359347 GGAAAAAGTTTGAACGCTTTGTGTTTA 60.359 33.333 0.00 0.00 36.34 2.01
4106 4308 7.409465 AAAAGTTTGAACGCTTTGTGTTTAA 57.591 28.000 0.00 0.00 36.34 1.52
4133 4335 8.428063 TGAACAAGGTGATTCCATTTATTTTGT 58.572 29.630 0.00 0.00 39.02 2.83
4159 4361 7.350110 TCTTTTTGAAGCAAAACTGAACAAG 57.650 32.000 4.94 0.00 42.02 3.16
4161 4363 4.799564 TTGAAGCAAAACTGAACAAGGT 57.200 36.364 0.00 0.00 0.00 3.50
4162 4364 4.108699 TGAAGCAAAACTGAACAAGGTG 57.891 40.909 0.00 0.00 0.00 4.00
4164 4366 2.456577 AGCAAAACTGAACAAGGTGGT 58.543 42.857 0.00 0.00 0.00 4.16
4165 4367 3.626930 AGCAAAACTGAACAAGGTGGTA 58.373 40.909 0.00 0.00 0.00 3.25
4166 4368 4.020543 AGCAAAACTGAACAAGGTGGTAA 58.979 39.130 0.00 0.00 0.00 2.85
4167 4369 4.464597 AGCAAAACTGAACAAGGTGGTAAA 59.535 37.500 0.00 0.00 0.00 2.01
4168 4370 5.128663 AGCAAAACTGAACAAGGTGGTAAAT 59.871 36.000 0.00 0.00 0.00 1.40
4169 4371 6.322712 AGCAAAACTGAACAAGGTGGTAAATA 59.677 34.615 0.00 0.00 0.00 1.40
4171 4373 7.655732 GCAAAACTGAACAAGGTGGTAAATAAT 59.344 33.333 0.00 0.00 0.00 1.28
4173 4375 6.267496 ACTGAACAAGGTGGTAAATAATGC 57.733 37.500 0.00 0.00 0.00 3.56
4174 4376 5.772672 ACTGAACAAGGTGGTAAATAATGCA 59.227 36.000 0.00 0.00 0.00 3.96
4206 6868 2.243221 ACTAGGCAGATGGGCAGAAATT 59.757 45.455 0.00 0.00 46.44 1.82
4254 6916 0.537188 CGCCTTCCATGGTCTAGTGT 59.463 55.000 12.58 0.00 0.00 3.55
4278 6940 4.309099 TCATCTTCCTTTTGTGCATTTGC 58.691 39.130 0.00 0.00 42.50 3.68
4291 6953 3.674753 GTGCATTTGCTGGTGTTGTAATC 59.325 43.478 3.94 0.00 42.66 1.75
4300 6962 5.105554 TGCTGGTGTTGTAATCAGTTTTTGT 60.106 36.000 0.00 0.00 0.00 2.83
4310 6972 5.852282 AATCAGTTTTTGTAGCTGTGGTT 57.148 34.783 0.00 0.00 0.00 3.67
4312 6974 6.560253 ATCAGTTTTTGTAGCTGTGGTTAG 57.440 37.500 0.00 0.00 0.00 2.34
4335 6997 0.885196 TTTCGGTTGTTGGGCTATGC 59.115 50.000 0.00 0.00 0.00 3.14
4348 7010 0.105039 GCTATGCGGAGTAGCTGGTT 59.895 55.000 0.00 0.00 41.00 3.67
4351 7014 3.555168 GCTATGCGGAGTAGCTGGTTATT 60.555 47.826 0.00 0.00 41.00 1.40
4381 7044 5.907866 AAACTCCTTTCGAGAAAACCAAA 57.092 34.783 0.00 0.00 41.63 3.28
4418 7084 3.424703 CTCTGCCATTCTTCAAAGGGAA 58.575 45.455 0.00 0.00 0.00 3.97
4422 7088 2.926586 GCCATTCTTCAAAGGGAAACGC 60.927 50.000 0.00 0.00 34.44 4.84
4438 7104 4.002797 GCTTTGAATCAGCGGGGT 57.997 55.556 0.00 0.00 0.00 4.95
4448 7114 2.125106 AGCGGGGTCGATTTCAGC 60.125 61.111 0.00 0.00 39.00 4.26
4459 7125 1.622232 GATTTCAGCAAAGCTTCCGC 58.378 50.000 11.83 11.83 36.40 5.54
4460 7126 0.244721 ATTTCAGCAAAGCTTCCGCC 59.755 50.000 15.21 0.00 36.40 6.13
4479 7145 3.274586 CCTCCATCGCATGCCACG 61.275 66.667 13.15 0.00 0.00 4.94
4527 7193 2.480555 GTGCTCAACAATCGCCCG 59.519 61.111 0.00 0.00 0.00 6.13
4530 7196 2.787249 CTCAACAATCGCCCGCAG 59.213 61.111 0.00 0.00 0.00 5.18
4542 7208 2.485122 CCGCAGCGAAACAATCCC 59.515 61.111 18.75 0.00 0.00 3.85
4556 7225 1.592223 AATCCCCATCCATGGCCACA 61.592 55.000 8.16 0.00 46.70 4.17
4561 7230 1.690209 CCCATCCATGGCCACATTCTT 60.690 52.381 8.16 0.00 46.70 2.52
4565 7234 2.726821 TCCATGGCCACATTCTTCTTC 58.273 47.619 8.16 0.00 34.35 2.87
4567 7236 2.622452 CCATGGCCACATTCTTCTTCCT 60.622 50.000 8.16 0.00 34.35 3.36
4596 7265 6.257423 CAGGGAAAGATTTTTGCAACAAAAC 58.743 36.000 0.00 2.75 36.45 2.43
4640 7310 3.058639 GCAACAAAGCTCCTGTTACAGAG 60.059 47.826 14.66 10.19 35.26 3.35
4648 7318 3.119459 GCTCCTGTTACAGAGATCGAACA 60.119 47.826 14.66 0.00 32.44 3.18
4649 7319 4.618460 GCTCCTGTTACAGAGATCGAACAA 60.618 45.833 14.66 0.00 32.44 2.83
4650 7320 5.462530 TCCTGTTACAGAGATCGAACAAA 57.537 39.130 14.66 0.00 32.44 2.83
4651 7321 5.849510 TCCTGTTACAGAGATCGAACAAAA 58.150 37.500 14.66 0.00 32.44 2.44
4675 7345 5.524511 AAAACGGTTTGAAAAAGTTCTGC 57.475 34.783 6.92 0.00 34.60 4.26
4678 7348 4.561105 ACGGTTTGAAAAAGTTCTGCAAA 58.439 34.783 0.00 0.00 34.60 3.68
4693 7363 1.728971 TGCAAAAAGGTTGTTGTTGCG 59.271 42.857 7.87 0.00 45.89 4.85
4694 7364 1.061857 GCAAAAAGGTTGTTGTTGCGG 59.938 47.619 0.00 0.00 35.69 5.69
4699 7369 1.021968 AGGTTGTTGTTGCGGAAGAC 58.978 50.000 0.00 0.00 0.00 3.01
4702 7372 1.021202 TTGTTGTTGCGGAAGACTGG 58.979 50.000 0.00 0.00 0.00 4.00
4713 7383 0.954452 GAAGACTGGGTGCAACAAGG 59.046 55.000 11.79 0.00 39.98 3.61
4716 7386 0.250727 GACTGGGTGCAACAAGGCTA 60.251 55.000 11.79 0.00 39.98 3.93
4767 7521 1.468914 GGTCCGAGAAAGATTGCAACC 59.531 52.381 0.00 0.00 0.00 3.77
4770 7524 2.038426 TCCGAGAAAGATTGCAACCAGA 59.962 45.455 0.00 0.00 0.00 3.86
4794 7548 0.738762 TGTTGCAGAGAGATGAGCGC 60.739 55.000 0.00 0.00 0.00 5.92
4798 7552 1.658102 CAGAGAGATGAGCGCGCTC 60.658 63.158 45.38 45.38 43.01 5.03
4800 7554 3.131196 GAGAGATGAGCGCGCTCCA 62.131 63.158 46.98 36.53 42.09 3.86
4836 7590 2.325583 ACGTCCTTGTTTCAGAAGCA 57.674 45.000 0.00 0.00 0.00 3.91
4839 7593 2.807967 CGTCCTTGTTTCAGAAGCATGA 59.192 45.455 12.77 5.38 0.00 3.07
4857 7611 2.046892 GCGCAAGAAGGCTCCAGA 60.047 61.111 0.30 0.00 43.02 3.86
4869 7623 4.581309 AGGCTCCAGATGAAGAAATCAA 57.419 40.909 0.00 0.00 42.54 2.57
4870 7624 4.927049 AGGCTCCAGATGAAGAAATCAAA 58.073 39.130 0.00 0.00 42.54 2.69
4871 7625 4.948621 AGGCTCCAGATGAAGAAATCAAAG 59.051 41.667 0.00 0.00 42.54 2.77
4872 7626 4.946157 GGCTCCAGATGAAGAAATCAAAGA 59.054 41.667 0.00 0.00 42.54 2.52
4873 7627 5.163673 GGCTCCAGATGAAGAAATCAAAGAC 60.164 44.000 0.00 0.00 42.54 3.01
4874 7628 5.447010 GCTCCAGATGAAGAAATCAAAGACG 60.447 44.000 0.00 0.00 42.54 4.18
4875 7629 5.793817 TCCAGATGAAGAAATCAAAGACGA 58.206 37.500 0.00 0.00 42.54 4.20
4907 7661 3.499918 CCGAGAAAGATTGCAACAAGACT 59.500 43.478 0.00 0.00 0.00 3.24
4909 7663 4.225208 GAGAAAGATTGCAACAAGACTGC 58.775 43.478 0.00 0.00 40.35 4.40
4918 7678 3.072944 GCAACAAGACTGCAGAGAGATT 58.927 45.455 23.35 6.09 39.69 2.40
4930 7690 3.853676 GCAGAGAGATTAGCGCGACATTA 60.854 47.826 12.10 0.00 0.00 1.90
4940 7700 1.136085 GCGCGACATTAAGCTTGTTGA 60.136 47.619 12.10 0.00 31.27 3.18
4948 7708 6.091305 CGACATTAAGCTTGTTGAAGAGATCA 59.909 38.462 9.86 0.00 35.85 2.92
4960 7720 0.539051 AGAGATCAACGGCTCCTTGG 59.461 55.000 0.00 0.00 0.00 3.61
4964 7724 2.129555 ATCAACGGCTCCTTGGCACT 62.130 55.000 0.00 0.00 41.89 4.40
4966 7726 3.553095 AACGGCTCCTTGGCACTCC 62.553 63.158 0.00 0.00 41.89 3.85
4973 7733 0.038166 TCCTTGGCACTCCATCCAAC 59.962 55.000 0.00 0.00 43.05 3.77
4974 7734 1.308069 CCTTGGCACTCCATCCAACG 61.308 60.000 0.00 0.00 43.05 4.10
4981 7741 1.942657 CACTCCATCCAACGGCTATTG 59.057 52.381 0.00 0.00 0.00 1.90
4992 7752 4.787871 GCTATTGAGGCAGCGGAT 57.212 55.556 0.00 0.00 0.00 4.18
4993 7753 2.537863 GCTATTGAGGCAGCGGATC 58.462 57.895 0.00 0.00 0.00 3.36
5000 7760 1.065199 TGAGGCAGCGGATCTTTTCAT 60.065 47.619 0.00 0.00 0.00 2.57
5008 7768 5.412594 GCAGCGGATCTTTTCATATTATCCA 59.587 40.000 0.00 0.00 36.68 3.41
5009 7769 6.402983 GCAGCGGATCTTTTCATATTATCCAG 60.403 42.308 0.00 0.00 36.68 3.86
5020 7780 2.395988 ATTATCCAGCGGCCGATGCA 62.396 55.000 36.87 26.05 40.13 3.96
5043 7803 1.000717 GCGCTGCCCTTTTTCAAACTA 60.001 47.619 0.00 0.00 0.00 2.24
5069 7829 3.507786 ACACGTTCTTTTGCCAAGAAAC 58.492 40.909 9.21 4.68 37.93 2.78
5070 7830 2.529894 CACGTTCTTTTGCCAAGAAACG 59.470 45.455 15.08 15.08 37.93 3.60
5077 7837 0.665835 TTGCCAAGAAACGCGTTCAT 59.334 45.000 26.77 14.11 38.86 2.57
5108 7873 5.790593 TCTCTTTGGTTTGTATTAGAGCGT 58.209 37.500 0.00 0.00 31.48 5.07
5111 7876 7.544566 TCTCTTTGGTTTGTATTAGAGCGTTAG 59.455 37.037 0.00 0.00 31.48 2.34
5123 7888 3.924238 GCGTTAGCACCCATGAATG 57.076 52.632 0.00 0.00 44.35 2.67
5174 7939 6.742109 AGGTGAAGATGTTCAAAATTGTGAG 58.258 36.000 6.89 0.00 44.44 3.51
5212 7977 2.545946 GACTGCAGGAACTCAGAAACAC 59.454 50.000 19.93 0.00 34.60 3.32
5216 7981 0.250338 AGGAACTCAGAAACACGCCC 60.250 55.000 0.00 0.00 0.00 6.13
5296 8061 1.275291 CCCGCTACTTCTCCTTTGTCA 59.725 52.381 0.00 0.00 0.00 3.58
5300 8065 4.142138 CCGCTACTTCTCCTTTGTCAGTAT 60.142 45.833 0.00 0.00 0.00 2.12
5312 8077 4.910585 CAGTATGTCGCCGCCCCC 62.911 72.222 0.00 0.00 0.00 5.40
5339 8104 3.161450 GGCTCTATGGGCGTGGGA 61.161 66.667 0.00 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.524802 AAAGATGGATTGATGGCAGGTA 57.475 40.909 0.00 0.00 0.00 3.08
73 74 2.045242 TCGACGGCAGCTAGACCT 60.045 61.111 0.00 0.00 0.00 3.85
114 115 1.144716 GATGAGCGCAGGATGGTGA 59.855 57.895 11.47 0.00 35.86 4.02
130 131 1.064463 GGTGGGTGTGTGATGATGGAT 60.064 52.381 0.00 0.00 0.00 3.41
194 195 3.175240 CGTGCCTTCTCTCGCGTG 61.175 66.667 5.77 3.13 0.00 5.34
331 332 2.280797 GTCAACCTGCTCGTGCCA 60.281 61.111 7.05 0.00 38.71 4.92
395 396 4.856801 GTCATGGCGGGCGATGGT 62.857 66.667 14.34 0.00 33.79 3.55
417 418 3.562635 GGTGAAAACCGAGCCGAG 58.437 61.111 0.00 0.00 0.00 4.63
436 437 2.100989 GAGTTGGGGAGACATAGTCGT 58.899 52.381 0.00 0.00 37.67 4.34
512 513 1.975327 CTGCCTTCTCCACCGAAGA 59.025 57.895 2.34 0.00 42.29 2.87
607 611 2.254350 CGCCTCGTCTCGACAACA 59.746 61.111 0.00 0.00 0.00 3.33
655 659 2.842496 TGATGAGATCTGATATGGCCCC 59.158 50.000 0.00 0.00 0.00 5.80
661 665 3.168292 TGGCCGTGATGAGATCTGATAT 58.832 45.455 0.00 0.00 0.00 1.63
662 666 2.597455 TGGCCGTGATGAGATCTGATA 58.403 47.619 0.00 0.00 0.00 2.15
678 683 1.037030 TTGGCGGATGAGATTTGGCC 61.037 55.000 0.00 0.00 40.88 5.36
772 778 1.760613 GACCATCATCTTCCGGTGGTA 59.239 52.381 10.38 0.00 42.87 3.25
773 779 0.541863 GACCATCATCTTCCGGTGGT 59.458 55.000 10.21 10.21 45.32 4.16
774 780 0.833287 AGACCATCATCTTCCGGTGG 59.167 55.000 0.00 1.68 36.06 4.61
775 781 4.619394 GCTATAGACCATCATCTTCCGGTG 60.619 50.000 3.21 0.00 0.00 4.94
776 782 3.511934 GCTATAGACCATCATCTTCCGGT 59.488 47.826 3.21 0.00 0.00 5.28
777 783 3.511540 TGCTATAGACCATCATCTTCCGG 59.488 47.826 3.21 0.00 0.00 5.14
778 784 4.460731 TCTGCTATAGACCATCATCTTCCG 59.539 45.833 3.21 0.00 0.00 4.30
779 785 5.991933 TCTGCTATAGACCATCATCTTCC 57.008 43.478 3.21 0.00 0.00 3.46
799 805 1.816835 TGTCGCCTCAAATACGAGTCT 59.183 47.619 0.00 0.00 36.34 3.24
805 811 1.009829 CCAGCTGTCGCCTCAAATAC 58.990 55.000 13.81 0.00 36.60 1.89
817 823 0.603707 CACACCGATGAACCAGCTGT 60.604 55.000 13.81 0.00 0.00 4.40
822 828 0.602638 GCAGTCACACCGATGAACCA 60.603 55.000 0.00 0.00 0.00 3.67
833 839 1.428370 GACAACAGCACGCAGTCACA 61.428 55.000 0.00 0.00 41.61 3.58
838 844 2.610694 CCCAGACAACAGCACGCAG 61.611 63.158 0.00 0.00 0.00 5.18
852 858 2.239654 ACCATCATCCTGTTGTACCCAG 59.760 50.000 3.29 3.29 0.00 4.45
853 859 2.238646 GACCATCATCCTGTTGTACCCA 59.761 50.000 0.00 0.00 0.00 4.51
892 898 2.087344 GGAAAACTCGCATCCGACC 58.913 57.895 0.00 0.00 38.82 4.79
911 917 3.333029 CCCACCATGAATTTTGGGTTC 57.667 47.619 11.73 0.00 43.44 3.62
940 946 2.138596 AGCGCAAGTCCACAAAATTG 57.861 45.000 11.47 0.00 41.68 2.32
981 991 8.853126 ACCAACATCCAATCAAGAACATATATG 58.147 33.333 11.29 11.29 0.00 1.78
1042 1062 4.508662 GTTGATCCTCCTTCTCGAAACAT 58.491 43.478 0.00 0.00 0.00 2.71
1044 1064 3.055747 AGGTTGATCCTCCTTCTCGAAAC 60.056 47.826 0.63 0.00 44.42 2.78
1046 1066 2.821437 AGGTTGATCCTCCTTCTCGAA 58.179 47.619 0.63 0.00 44.42 3.71
1058 1078 3.487574 CGAGATCTGCGTTAAGGTTGATC 59.512 47.826 0.00 17.00 0.00 2.92
1061 1081 2.345641 CACGAGATCTGCGTTAAGGTTG 59.654 50.000 14.78 2.61 40.44 3.77
1064 1084 0.924090 GCACGAGATCTGCGTTAAGG 59.076 55.000 14.78 7.54 40.44 2.69
1071 1091 3.516681 CATAACATGCACGAGATCTGC 57.483 47.619 0.00 0.00 35.03 4.26
1097 1117 4.076394 GGTACCAACCAACTTGATAGCAA 58.924 43.478 7.15 0.00 45.98 3.91
1098 1118 3.681593 GGTACCAACCAACTTGATAGCA 58.318 45.455 7.15 0.00 45.98 3.49
1111 1131 2.227149 CGTTAAGGGCAAAGGTACCAAC 59.773 50.000 15.94 5.32 0.00 3.77
1121 1141 1.816074 CAGGCTAACGTTAAGGGCAA 58.184 50.000 19.00 0.00 0.00 4.52
1164 1184 0.547471 TGGAGCTTCTGATGGTGGGA 60.547 55.000 0.00 0.00 0.00 4.37
1176 1196 1.066143 CGGGTCAACATAGTGGAGCTT 60.066 52.381 4.01 0.00 34.72 3.74
1322 1358 2.767445 CATGACGCCCATGCTGTGG 61.767 63.158 5.60 2.12 45.25 4.17
1364 1400 1.915141 CTCAAATGGGTGCCAGAACT 58.085 50.000 0.00 0.00 36.75 3.01
1565 1607 0.397114 CCAAAGGGAAGGGTATGCCC 60.397 60.000 11.65 11.65 46.57 5.36
1588 1630 1.127343 GGGAGAGATGGAGTCTTGGG 58.873 60.000 0.00 0.00 37.29 4.12
1591 1633 4.352298 ACAAAAAGGGAGAGATGGAGTCTT 59.648 41.667 0.00 0.00 37.29 3.01
1592 1634 3.913163 ACAAAAAGGGAGAGATGGAGTCT 59.087 43.478 0.00 0.00 40.81 3.24
1672 1716 9.726438 GCTCCAACCACATTAAGTTATCTATAT 57.274 33.333 0.00 0.00 0.00 0.86
1673 1717 8.154856 GGCTCCAACCACATTAAGTTATCTATA 58.845 37.037 0.00 0.00 0.00 1.31
1674 1718 6.998673 GGCTCCAACCACATTAAGTTATCTAT 59.001 38.462 0.00 0.00 0.00 1.98
1675 1719 6.157994 AGGCTCCAACCACATTAAGTTATCTA 59.842 38.462 0.00 0.00 0.00 1.98
1678 1739 5.193099 AGGCTCCAACCACATTAAGTTAT 57.807 39.130 0.00 0.00 0.00 1.89
1682 1743 3.199946 TCCTAGGCTCCAACCACATTAAG 59.800 47.826 2.96 0.00 0.00 1.85
1839 1908 3.144506 CTGATAAGATCCTGCGCCATTT 58.855 45.455 4.18 0.00 0.00 2.32
2155 2234 6.423905 TCGTGATCAATCTCGAGAAAACTTTT 59.576 34.615 20.91 4.94 44.60 2.27
2182 2261 6.732392 CACTAAAGAAATCGACATTGTTCGTC 59.268 38.462 0.00 0.00 40.07 4.20
2183 2262 6.202188 ACACTAAAGAAATCGACATTGTTCGT 59.798 34.615 0.00 0.00 40.07 3.85
2184 2263 6.590357 ACACTAAAGAAATCGACATTGTTCG 58.410 36.000 0.00 0.00 40.53 3.95
2193 2272 5.471797 TGGATGCAAACACTAAAGAAATCGA 59.528 36.000 0.00 0.00 0.00 3.59
2204 2324 0.249699 TCGACGTGGATGCAAACACT 60.250 50.000 18.26 8.48 35.51 3.55
2209 2329 1.018752 CACCATCGACGTGGATGCAA 61.019 55.000 28.93 0.00 41.95 4.08
2386 2506 0.189822 GGAGGCAGGAGAGGTAGGAT 59.810 60.000 0.00 0.00 0.00 3.24
3034 3154 1.005275 CATGATCTCGGCTCGCCAT 60.005 57.895 8.87 0.00 35.37 4.40
3133 3253 0.622665 CCTCCTCCCAGTTCTGCATT 59.377 55.000 0.00 0.00 0.00 3.56
3209 3329 3.280295 AGAGATAGAAGACGAAGGCGAA 58.720 45.455 0.00 0.00 41.64 4.70
3269 3427 1.825191 CCGCCACCCCATGATCAAG 60.825 63.158 0.00 0.00 0.00 3.02
3272 3430 2.516930 CACCGCCACCCCATGATC 60.517 66.667 0.00 0.00 0.00 2.92
3656 3816 4.742201 GCGAGGCAGAGCACGGAA 62.742 66.667 9.06 0.00 32.77 4.30
3763 3923 0.458889 CCCCGCATTGACTTGCATTG 60.459 55.000 0.00 0.00 42.91 2.82
3765 3925 1.304381 ACCCCGCATTGACTTGCAT 60.304 52.632 0.00 0.00 42.91 3.96
3766 3926 2.115052 ACCCCGCATTGACTTGCA 59.885 55.556 0.00 0.00 42.91 4.08
3767 3927 2.568090 CACCCCGCATTGACTTGC 59.432 61.111 0.00 0.00 39.29 4.01
3768 3928 1.303236 TCCACCCCGCATTGACTTG 60.303 57.895 0.00 0.00 0.00 3.16
3770 3930 1.274703 ATCTCCACCCCGCATTGACT 61.275 55.000 0.00 0.00 0.00 3.41
3771 3931 0.394352 AATCTCCACCCCGCATTGAC 60.394 55.000 0.00 0.00 0.00 3.18
3781 3970 1.519455 CGGACGCTCAATCTCCACC 60.519 63.158 0.00 0.00 0.00 4.61
3785 3974 2.508891 CGCACGGACGCTCAATCTC 61.509 63.158 0.00 0.00 0.00 2.75
3788 3977 2.809601 GACGCACGGACGCTCAAT 60.810 61.111 0.00 0.00 36.19 2.57
3795 3984 2.476534 TTTACCCTCGACGCACGGAC 62.477 60.000 3.02 0.00 42.82 4.79
3806 3995 0.392461 TCGCATGCACCTTTACCCTC 60.392 55.000 19.57 0.00 0.00 4.30
3838 4027 1.399791 AGTAGTAGTACAAGTCGGCGC 59.600 52.381 10.33 0.00 0.00 6.53
3839 4028 2.790468 GCAGTAGTAGTACAAGTCGGCG 60.790 54.545 10.33 0.00 0.00 6.46
3840 4029 2.479219 GGCAGTAGTAGTACAAGTCGGC 60.479 54.545 10.33 3.92 0.00 5.54
3841 4030 2.751259 TGGCAGTAGTAGTACAAGTCGG 59.249 50.000 10.33 0.00 0.00 4.79
3842 4031 4.634184 ATGGCAGTAGTAGTACAAGTCG 57.366 45.455 10.33 0.00 0.00 4.18
3853 4042 4.234550 TCATCCCTGATAATGGCAGTAGT 58.765 43.478 0.00 0.00 0.00 2.73
3854 4043 4.897509 TCATCCCTGATAATGGCAGTAG 57.102 45.455 0.00 0.00 0.00 2.57
3857 4046 4.186926 CGTATCATCCCTGATAATGGCAG 58.813 47.826 0.00 0.00 44.07 4.85
3858 4047 3.619733 GCGTATCATCCCTGATAATGGCA 60.620 47.826 0.00 0.00 44.07 4.92
3890 4082 1.673168 AGAATCTCGCAAATCAGCCC 58.327 50.000 0.00 0.00 0.00 5.19
3901 4093 4.097135 TCACTCTCAGGCTAAAGAATCTCG 59.903 45.833 0.00 0.00 0.00 4.04
3902 4094 5.359576 TCTCACTCTCAGGCTAAAGAATCTC 59.640 44.000 0.00 0.00 0.00 2.75
3905 4097 4.405358 CCTCTCACTCTCAGGCTAAAGAAT 59.595 45.833 0.00 0.00 0.00 2.40
3906 4098 3.766591 CCTCTCACTCTCAGGCTAAAGAA 59.233 47.826 0.00 0.00 0.00 2.52
3908 4100 2.430332 CCCTCTCACTCTCAGGCTAAAG 59.570 54.545 0.00 0.00 0.00 1.85
3909 4101 2.461695 CCCTCTCACTCTCAGGCTAAA 58.538 52.381 0.00 0.00 0.00 1.85
3910 4102 1.342474 CCCCTCTCACTCTCAGGCTAA 60.342 57.143 0.00 0.00 0.00 3.09
3912 4104 1.001503 CCCCTCTCACTCTCAGGCT 59.998 63.158 0.00 0.00 0.00 4.58
3914 4106 0.975040 CACCCCCTCTCACTCTCAGG 60.975 65.000 0.00 0.00 0.00 3.86
3974 4175 2.029623 TGCCGAGATTAGTACCACTCC 58.970 52.381 0.00 0.00 0.00 3.85
3975 4176 2.541178 CGTGCCGAGATTAGTACCACTC 60.541 54.545 0.00 0.00 0.00 3.51
3976 4177 1.404391 CGTGCCGAGATTAGTACCACT 59.596 52.381 0.00 0.00 0.00 4.00
3977 4178 1.133790 ACGTGCCGAGATTAGTACCAC 59.866 52.381 1.50 0.00 0.00 4.16
3978 4179 1.402968 GACGTGCCGAGATTAGTACCA 59.597 52.381 0.00 0.00 0.00 3.25
3979 4180 1.402968 TGACGTGCCGAGATTAGTACC 59.597 52.381 0.00 0.00 0.00 3.34
3980 4181 2.159476 TGTGACGTGCCGAGATTAGTAC 60.159 50.000 0.00 0.00 0.00 2.73
3981 4182 2.086094 TGTGACGTGCCGAGATTAGTA 58.914 47.619 0.00 0.00 0.00 1.82
3982 4183 0.885879 TGTGACGTGCCGAGATTAGT 59.114 50.000 0.00 0.00 0.00 2.24
3990 4191 2.330231 ATCAAAATTGTGACGTGCCG 57.670 45.000 0.00 0.00 0.00 5.69
4002 4203 9.643693 CAACAGTAGCTAATCCAAAATCAAAAT 57.356 29.630 0.00 0.00 0.00 1.82
4057 4258 1.069636 CACTTTTCTCTCGCAAGGCAC 60.070 52.381 0.00 0.00 38.47 5.01
4059 4260 0.519077 CCACTTTTCTCTCGCAAGGC 59.481 55.000 0.00 0.00 38.47 4.35
4060 4261 1.160137 CCCACTTTTCTCTCGCAAGG 58.840 55.000 0.00 0.00 38.47 3.61
4061 4262 1.160137 CCCCACTTTTCTCTCGCAAG 58.840 55.000 0.00 0.00 0.00 4.01
4063 4264 0.762418 TTCCCCACTTTTCTCTCGCA 59.238 50.000 0.00 0.00 0.00 5.10
4064 4265 1.892209 TTTCCCCACTTTTCTCTCGC 58.108 50.000 0.00 0.00 0.00 5.03
4066 4267 5.854010 AACTTTTTCCCCACTTTTCTCTC 57.146 39.130 0.00 0.00 0.00 3.20
4067 4268 5.719563 TCAAACTTTTTCCCCACTTTTCTCT 59.280 36.000 0.00 0.00 0.00 3.10
4068 4269 5.972935 TCAAACTTTTTCCCCACTTTTCTC 58.027 37.500 0.00 0.00 0.00 2.87
4069 4270 6.170506 GTTCAAACTTTTTCCCCACTTTTCT 58.829 36.000 0.00 0.00 0.00 2.52
4070 4271 5.062934 CGTTCAAACTTTTTCCCCACTTTTC 59.937 40.000 0.00 0.00 0.00 2.29
4071 4272 4.932799 CGTTCAAACTTTTTCCCCACTTTT 59.067 37.500 0.00 0.00 0.00 2.27
4072 4273 4.500127 CGTTCAAACTTTTTCCCCACTTT 58.500 39.130 0.00 0.00 0.00 2.66
4073 4274 3.677700 GCGTTCAAACTTTTTCCCCACTT 60.678 43.478 0.00 0.00 0.00 3.16
4074 4275 2.159156 GCGTTCAAACTTTTTCCCCACT 60.159 45.455 0.00 0.00 0.00 4.00
4076 4277 2.104170 AGCGTTCAAACTTTTTCCCCA 58.896 42.857 0.00 0.00 0.00 4.96
4078 4279 3.930229 ACAAAGCGTTCAAACTTTTTCCC 59.070 39.130 0.00 0.00 33.92 3.97
4080 4281 5.509605 ACACAAAGCGTTCAAACTTTTTC 57.490 34.783 0.00 0.00 33.92 2.29
4088 4289 6.093404 TGTTCATTAAACACAAAGCGTTCAA 58.907 32.000 0.00 0.00 42.95 2.69
4106 4308 9.439500 CAAAATAAATGGAATCACCTTGTTCAT 57.561 29.630 0.00 0.00 39.86 2.57
4133 4335 7.721286 TGTTCAGTTTTGCTTCAAAAAGAAA 57.279 28.000 15.94 6.50 43.50 2.52
4159 4361 2.223479 CGCACCTGCATTATTTACCACC 60.223 50.000 0.00 0.00 42.21 4.61
4161 4363 1.403679 GCGCACCTGCATTATTTACCA 59.596 47.619 0.30 0.00 42.21 3.25
4162 4364 1.269051 GGCGCACCTGCATTATTTACC 60.269 52.381 10.83 0.00 42.21 2.85
4206 6868 1.211703 TGACAACTCTCCACCAAAGCA 59.788 47.619 0.00 0.00 0.00 3.91
4254 6916 5.775686 CAAATGCACAAAAGGAAGATGAGA 58.224 37.500 0.00 0.00 0.00 3.27
4278 6940 6.636850 GCTACAAAAACTGATTACAACACCAG 59.363 38.462 0.00 0.00 0.00 4.00
4291 6953 5.751243 ACTAACCACAGCTACAAAAACTG 57.249 39.130 0.00 0.00 37.45 3.16
4300 6962 5.410355 ACCGAAATAACTAACCACAGCTA 57.590 39.130 0.00 0.00 0.00 3.32
4310 6972 4.023726 AGCCCAACAACCGAAATAACTA 57.976 40.909 0.00 0.00 0.00 2.24
4312 6974 4.668289 CATAGCCCAACAACCGAAATAAC 58.332 43.478 0.00 0.00 0.00 1.89
4335 6997 7.548196 TTTTCATTAATAACCAGCTACTCCG 57.452 36.000 0.00 0.00 0.00 4.63
4377 7040 5.464389 CAGAGCCTTGACTTTGAAAATTTGG 59.536 40.000 0.00 0.00 0.00 3.28
4381 7044 3.006217 GGCAGAGCCTTGACTTTGAAAAT 59.994 43.478 0.00 0.00 46.69 1.82
4422 7088 0.391130 TCGACCCCGCTGATTCAAAG 60.391 55.000 0.00 0.00 35.37 2.77
4427 7093 0.251916 TGAAATCGACCCCGCTGATT 59.748 50.000 0.00 0.00 33.94 2.57
4434 7100 0.171231 GCTTTGCTGAAATCGACCCC 59.829 55.000 0.00 0.00 0.00 4.95
4435 7101 1.168714 AGCTTTGCTGAAATCGACCC 58.831 50.000 0.00 0.00 37.57 4.46
4437 7103 2.726066 CGGAAGCTTTGCTGAAATCGAC 60.726 50.000 0.00 0.00 39.62 4.20
4438 7104 1.464608 CGGAAGCTTTGCTGAAATCGA 59.535 47.619 0.00 0.00 39.62 3.59
4479 7145 1.080025 GTGTAGGACCACTGGACGC 60.080 63.158 0.71 0.00 32.50 5.19
4527 7193 0.101219 GATGGGGATTGTTTCGCTGC 59.899 55.000 0.00 0.00 37.45 5.25
4530 7196 1.067516 CATGGATGGGGATTGTTTCGC 59.932 52.381 0.00 0.00 36.58 4.70
4551 7220 2.352127 GCAACAGGAAGAAGAATGTGGC 60.352 50.000 0.00 0.00 35.59 5.01
4567 7236 3.118482 TGCAAAAATCTTTCCCTGCAACA 60.118 39.130 0.00 0.00 0.00 3.33
4605 7274 4.337555 AGCTTTGTTGCATAGAGCCTTATG 59.662 41.667 9.49 1.66 44.83 1.90
4606 7275 4.530875 AGCTTTGTTGCATAGAGCCTTAT 58.469 39.130 9.49 0.00 44.83 1.73
4607 7276 3.941483 GAGCTTTGTTGCATAGAGCCTTA 59.059 43.478 9.49 0.00 44.83 2.69
4626 7296 3.119459 TGTTCGATCTCTGTAACAGGAGC 60.119 47.826 0.00 0.00 31.51 4.70
4657 7327 5.523013 TTTTGCAGAACTTTTTCAAACCG 57.477 34.783 0.00 0.00 33.72 4.44
4661 7331 6.484977 ACAACCTTTTTGCAGAACTTTTTCAA 59.515 30.769 0.00 0.00 33.72 2.69
4663 7333 6.480524 ACAACCTTTTTGCAGAACTTTTTC 57.519 33.333 0.00 0.00 0.00 2.29
4668 7338 4.535526 ACAACAACCTTTTTGCAGAACT 57.464 36.364 0.00 0.00 0.00 3.01
4673 7343 1.728971 CGCAACAACAACCTTTTTGCA 59.271 42.857 5.55 0.00 42.18 4.08
4675 7345 2.611518 TCCGCAACAACAACCTTTTTG 58.388 42.857 0.00 0.00 0.00 2.44
4678 7348 2.096248 TCTTCCGCAACAACAACCTTT 58.904 42.857 0.00 0.00 0.00 3.11
4693 7363 0.954452 CTTGTTGCACCCAGTCTTCC 59.046 55.000 0.00 0.00 0.00 3.46
4694 7364 0.954452 CCTTGTTGCACCCAGTCTTC 59.046 55.000 0.00 0.00 0.00 2.87
4699 7369 1.203052 CATTAGCCTTGTTGCACCCAG 59.797 52.381 0.00 0.00 0.00 4.45
4702 7372 2.676076 CAACATTAGCCTTGTTGCACC 58.324 47.619 10.05 0.00 45.10 5.01
4739 7492 5.335976 GCAATCTTTCTCGGACCATCTTTTT 60.336 40.000 0.00 0.00 0.00 1.94
4744 7497 2.632377 TGCAATCTTTCTCGGACCATC 58.368 47.619 0.00 0.00 0.00 3.51
4745 7498 2.749621 GTTGCAATCTTTCTCGGACCAT 59.250 45.455 0.59 0.00 0.00 3.55
4746 7499 2.151202 GTTGCAATCTTTCTCGGACCA 58.849 47.619 0.59 0.00 0.00 4.02
4752 7506 2.160417 CGGTCTGGTTGCAATCTTTCTC 59.840 50.000 11.73 0.00 0.00 2.87
4767 7521 1.143305 CTCTCTGCAACAACGGTCTG 58.857 55.000 0.00 0.00 0.00 3.51
4770 7524 1.344438 TCATCTCTCTGCAACAACGGT 59.656 47.619 0.00 0.00 0.00 4.83
4810 7564 3.185594 TCTGAAACAAGGACGTTATTGCG 59.814 43.478 12.13 0.00 37.94 4.85
4815 7569 3.799366 TGCTTCTGAAACAAGGACGTTA 58.201 40.909 0.00 0.00 0.00 3.18
4839 7593 1.908340 ATCTGGAGCCTTCTTGCGCT 61.908 55.000 9.73 0.00 38.27 5.92
4846 7600 4.521146 TGATTTCTTCATCTGGAGCCTTC 58.479 43.478 0.00 0.00 0.00 3.46
4881 7635 2.807967 TGTTGCAATCTTTCTCGGACTG 59.192 45.455 0.59 0.00 0.00 3.51
4882 7636 3.126001 TGTTGCAATCTTTCTCGGACT 57.874 42.857 0.59 0.00 0.00 3.85
4907 7661 0.248661 GTCGCGCTAATCTCTCTGCA 60.249 55.000 5.56 0.00 0.00 4.41
4909 7663 2.414058 ATGTCGCGCTAATCTCTCTG 57.586 50.000 5.56 0.00 0.00 3.35
4918 7678 2.004583 ACAAGCTTAATGTCGCGCTA 57.995 45.000 5.56 0.00 31.48 4.26
4940 7700 1.065854 CCAAGGAGCCGTTGATCTCTT 60.066 52.381 8.57 0.00 0.00 2.85
4948 7708 2.032681 GAGTGCCAAGGAGCCGTT 59.967 61.111 0.00 0.00 0.00 4.44
4960 7720 0.179045 ATAGCCGTTGGATGGAGTGC 60.179 55.000 0.00 0.00 0.00 4.40
4964 7724 1.140852 CCTCAATAGCCGTTGGATGGA 59.859 52.381 0.00 0.00 0.00 3.41
4966 7726 0.947244 GCCTCAATAGCCGTTGGATG 59.053 55.000 0.00 0.00 0.00 3.51
4973 7733 2.721971 ATCCGCTGCCTCAATAGCCG 62.722 60.000 0.00 0.00 36.60 5.52
4974 7734 0.952984 GATCCGCTGCCTCAATAGCC 60.953 60.000 0.00 0.00 36.60 3.93
4981 7741 1.673168 ATGAAAAGATCCGCTGCCTC 58.327 50.000 0.00 0.00 0.00 4.70
4986 7746 5.645497 GCTGGATAATATGAAAAGATCCGCT 59.355 40.000 0.00 0.00 39.19 5.52
4987 7747 5.446473 CGCTGGATAATATGAAAAGATCCGC 60.446 44.000 0.00 0.00 39.19 5.54
4992 7752 4.072131 GGCCGCTGGATAATATGAAAAGA 58.928 43.478 0.00 0.00 0.00 2.52
4993 7753 3.120199 CGGCCGCTGGATAATATGAAAAG 60.120 47.826 14.67 0.00 0.00 2.27
5000 7760 0.391130 GCATCGGCCGCTGGATAATA 60.391 55.000 28.53 5.41 0.00 0.98
5020 7780 1.544724 TTGAAAAAGGGCAGCGCTAT 58.455 45.000 10.99 1.95 0.00 2.97
5043 7803 4.396790 TCTTGGCAAAAGAACGTGTTTAGT 59.603 37.500 0.00 0.00 0.00 2.24
5069 7829 2.600731 AGAGAGTGAAAGATGAACGCG 58.399 47.619 3.53 3.53 0.00 6.01
5070 7830 4.377841 CCAAAGAGAGTGAAAGATGAACGC 60.378 45.833 0.00 0.00 0.00 4.84
5077 7837 9.273016 CTAATACAAACCAAAGAGAGTGAAAGA 57.727 33.333 0.00 0.00 0.00 2.52
5115 7880 9.081204 TCTTGTATAAATGATTCCCATTCATGG 57.919 33.333 0.00 0.00 44.28 3.66
5138 7903 7.944554 TGAACATCTTCACCTAATTTCCTTCTT 59.055 33.333 0.00 0.00 31.00 2.52
5195 7960 0.235926 GCGTGTTTCTGAGTTCCTGC 59.764 55.000 0.00 0.00 0.00 4.85
5212 7977 4.798682 ACTAGGGAGGGTGGGGCG 62.799 72.222 0.00 0.00 0.00 6.13
5216 7981 0.752376 GAGACGACTAGGGAGGGTGG 60.752 65.000 0.00 0.00 0.00 4.61
5275 8040 1.549170 GACAAAGGAGAAGTAGCGGGA 59.451 52.381 0.00 0.00 0.00 5.14
5276 8041 1.275291 TGACAAAGGAGAAGTAGCGGG 59.725 52.381 0.00 0.00 0.00 6.13
5281 8046 5.621555 GCGACATACTGACAAAGGAGAAGTA 60.622 44.000 0.00 0.00 0.00 2.24
5312 8077 2.598985 ATAGAGCCGCCCGAGGAG 60.599 66.667 0.00 0.00 0.00 3.69
5322 8087 3.161450 TCCCACGCCCATAGAGCC 61.161 66.667 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.