Multiple sequence alignment - TraesCS1D01G405800

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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 TraesCS1D01G405800 chr1D 100.000 4995 0 0 1 4995 470070490 470075484 0.000000e+00 9225.0
1 TraesCS1D01G405800 chr1D 96.421 475 12 2 1 470 354747446 354747920 0.000000e+00 778.0
2 TraesCS1D01G405800 chr1D 97.778 180 4 0 291 470 135062860 135063039 1.350000e-80 311.0
3 TraesCS1D01G405800 chr1D 84.706 85 7 4 2903 2984 21462049 21461968 4.150000e-11 80.5
4 TraesCS1D01G405800 chr1A 95.212 3070 106 7 27 3055 563679821 563682890 0.000000e+00 4817.0
5 TraesCS1D01G405800 chr1A 97.810 1187 21 3 3158 4344 563682888 563684069 0.000000e+00 2043.0
6 TraesCS1D01G405800 chr1A 87.879 627 41 16 4364 4978 563684059 563684662 0.000000e+00 704.0
7 TraesCS1D01G405800 chr1B 94.812 2236 99 10 87 2308 652452939 652455171 0.000000e+00 3470.0
8 TraesCS1D01G405800 chr1B 94.176 1202 45 16 3158 4344 652455969 652457160 0.000000e+00 1808.0
9 TraesCS1D01G405800 chr1B 95.890 876 31 4 2182 3055 652455099 652455971 0.000000e+00 1413.0
10 TraesCS1D01G405800 chr1B 87.601 621 22 13 4364 4978 652457150 652457721 0.000000e+00 669.0
11 TraesCS1D01G405800 chr3D 96.421 475 12 2 1 470 549966001 549966475 0.000000e+00 778.0
12 TraesCS1D01G405800 chr3D 96.000 475 14 2 1 470 550030463 550029989 0.000000e+00 767.0
13 TraesCS1D01G405800 chr3D 95.902 122 5 0 3052 3173 128992639 128992760 1.100000e-46 198.0
14 TraesCS1D01G405800 chr3D 94.872 39 2 0 3298 3336 339850947 339850909 1.500000e-05 62.1
15 TraesCS1D01G405800 chr5D 96.414 474 12 2 2 470 563497566 563497093 0.000000e+00 776.0
16 TraesCS1D01G405800 chr5D 98.230 113 2 0 3048 3160 339105063 339105175 1.100000e-46 198.0
17 TraesCS1D01G405800 chr2D 95.158 475 18 2 1 470 496894486 496894960 0.000000e+00 745.0
18 TraesCS1D01G405800 chr7B 87.712 236 26 3 206 440 78680687 78680920 6.370000e-69 272.0
19 TraesCS1D01G405800 chr7B 86.452 155 21 0 8 162 78680536 78680690 2.390000e-38 171.0
20 TraesCS1D01G405800 chr3A 83.529 255 34 6 2707 2958 25376777 25377026 1.080000e-56 231.0
21 TraesCS1D01G405800 chr3A 81.443 291 32 12 2707 2991 25378593 25378867 8.420000e-53 219.0
22 TraesCS1D01G405800 chr3A 81.443 291 32 12 2707 2991 25391314 25391588 8.420000e-53 219.0
23 TraesCS1D01G405800 chr3A 81.443 291 32 12 2707 2991 25393748 25394022 8.420000e-53 219.0
24 TraesCS1D01G405800 chr3A 94.872 39 2 0 3298 3336 464910653 464910691 1.500000e-05 62.1
25 TraesCS1D01G405800 chr7D 90.123 162 16 0 1 162 134508390 134508551 1.410000e-50 211.0
26 TraesCS1D01G405800 chr7D 98.261 115 1 1 3050 3163 568753476 568753362 3.050000e-47 200.0
27 TraesCS1D01G405800 chr5B 97.521 121 2 1 3043 3162 394273082 394272962 6.550000e-49 206.0
28 TraesCS1D01G405800 chr2B 99.107 112 1 0 3052 3163 171459974 171460085 8.480000e-48 202.0
29 TraesCS1D01G405800 chr6D 98.214 112 2 0 3048 3159 112344487 112344376 3.940000e-46 196.0
30 TraesCS1D01G405800 chr4A 96.639 119 2 2 3045 3161 96321200 96321318 3.940000e-46 196.0
31 TraesCS1D01G405800 chr4D 96.581 117 4 0 3051 3167 160742369 160742253 1.420000e-45 195.0
32 TraesCS1D01G405800 chr5A 93.077 130 6 2 3045 3172 339754815 339754687 2.370000e-43 187.0
33 TraesCS1D01G405800 chr5A 93.750 96 6 0 206 301 296678722 296678817 1.450000e-30 145.0
34 TraesCS1D01G405800 chr6B 85.263 95 13 1 4400 4494 4295810 4295717 4.120000e-16 97.1
35 TraesCS1D01G405800 chr3B 94.872 39 2 0 3298 3336 438542726 438542688 1.500000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G405800 chr1D 470070490 470075484 4994 False 9225.000000 9225 100.000000 1 4995 1 chr1D.!!$F3 4994
1 TraesCS1D01G405800 chr1A 563679821 563684662 4841 False 2521.333333 4817 93.633667 27 4978 3 chr1A.!!$F1 4951
2 TraesCS1D01G405800 chr1B 652452939 652457721 4782 False 1840.000000 3470 93.119750 87 4978 4 chr1B.!!$F1 4891
3 TraesCS1D01G405800 chr3A 25376777 25378867 2090 False 225.000000 231 82.486000 2707 2991 2 chr3A.!!$F2 284
4 TraesCS1D01G405800 chr3A 25391314 25394022 2708 False 219.000000 219 81.443000 2707 2991 2 chr3A.!!$F3 284

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
715 723 1.827344 CTGGCACTAGATCTGTGTCCA 59.173 52.381 23.20 23.20 39.07 4.02 F
1687 1711 0.323633 TCACATGGTCCAGGGCAATG 60.324 55.000 6.91 6.91 0.00 2.82 F
2279 2358 1.901833 GGAATGGTGCAAGGTCCAAAT 59.098 47.619 0.00 0.00 37.27 2.32 F
3068 3161 0.329261 TTCTACTCCCTCCGTTCGGA 59.671 55.000 13.34 13.34 0.00 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2369 2448 0.107508 ATGCATGAACTGGAGGTCCG 60.108 55.000 0.00 0.00 39.43 4.79 R
3060 3153 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44 R
3756 4131 0.953960 GATCGTGACAAAGGGGCGTT 60.954 55.000 0.00 0.00 0.00 4.84 R
4370 4995 1.822371 ACCGAAACTGCAAAACCAAGT 59.178 42.857 0.00 0.00 0.00 3.16 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
18 19 4.880537 CCGCTAGAGTGGCCTGCG 62.881 72.222 3.32 10.26 45.22 5.18
19 20 4.880537 CGCTAGAGTGGCCTGCGG 62.881 72.222 3.32 0.00 42.46 5.69
20 21 4.537433 GCTAGAGTGGCCTGCGGG 62.537 72.222 7.41 7.41 0.00 6.13
21 22 3.077556 CTAGAGTGGCCTGCGGGT 61.078 66.667 14.55 0.00 34.45 5.28
22 23 3.075005 TAGAGTGGCCTGCGGGTC 61.075 66.667 10.01 10.01 37.81 4.46
23 24 3.602075 TAGAGTGGCCTGCGGGTCT 62.602 63.158 19.02 12.55 38.23 3.85
24 25 4.459089 GAGTGGCCTGCGGGTCTC 62.459 72.222 19.02 14.55 38.23 3.36
124 127 1.861575 GCGTGCTGGCTTAGATTAGTC 59.138 52.381 0.00 0.00 0.00 2.59
142 145 7.984050 AGATTAGTCACTGATGAACTAACATGG 59.016 37.037 0.00 0.00 36.31 3.66
184 187 3.338250 GGGGGATGTGCCTGGACA 61.338 66.667 0.00 0.00 36.66 4.02
191 194 3.426568 GTGCCTGGACAAGCGAGC 61.427 66.667 0.00 0.00 0.00 5.03
239 242 4.067896 TGTTTTTGGCTTTTTGCAGTGAA 58.932 34.783 0.00 0.00 45.15 3.18
241 244 3.325293 TTTGGCTTTTTGCAGTGAACA 57.675 38.095 0.00 0.00 45.15 3.18
268 271 5.068198 CGGTACAGGGTAGAACTGCTTAATA 59.932 44.000 0.00 0.00 39.55 0.98
337 343 3.902150 TCTTCGTCTAAGTGACAGCAAG 58.098 45.455 0.00 0.00 45.60 4.01
368 374 3.853831 TGCCAATTGCTGTATGTTCTG 57.146 42.857 0.00 0.00 42.00 3.02
369 375 3.419943 TGCCAATTGCTGTATGTTCTGA 58.580 40.909 0.00 0.00 42.00 3.27
609 615 6.620678 TCTGCAAACTATTCCAAAATGCTAC 58.379 36.000 0.00 0.00 33.66 3.58
635 641 9.478019 CGAGATTAAAACATGTGAAACTCATAC 57.522 33.333 17.93 0.00 38.04 2.39
641 647 3.007506 ACATGTGAAACTCATACGTCCCA 59.992 43.478 0.00 0.00 38.04 4.37
715 723 1.827344 CTGGCACTAGATCTGTGTCCA 59.173 52.381 23.20 23.20 39.07 4.02
847 867 4.396790 TGTGAAGTTTTTGTCCTGTACCAC 59.603 41.667 0.00 0.00 0.00 4.16
1082 1103 4.217118 ACAAGCTCAGCCTGAAAATTACAG 59.783 41.667 1.07 5.82 35.43 2.74
1173 1194 2.093106 ACTAGTGATGGAGTCCGTGAC 58.907 52.381 12.70 12.70 0.00 3.67
1399 1423 3.131933 CACAGGAACTAGGGATGAGAGTG 59.868 52.174 0.00 0.00 36.02 3.51
1445 1469 3.383825 GCTGCCAGAGAATCCATGAAAAT 59.616 43.478 0.00 0.00 33.66 1.82
1461 1485 5.643379 TGAAAATGAGGAATGCTGTAACC 57.357 39.130 0.00 0.00 0.00 2.85
1599 1623 0.809241 GCTCTTCTGCTGATGGACCG 60.809 60.000 6.64 0.00 0.00 4.79
1606 1630 1.450312 GCTGATGGACCGAACAGGG 60.450 63.158 12.17 0.00 46.96 4.45
1637 1661 1.379642 GCTACTCACCCAGCATTGGC 61.380 60.000 0.00 0.00 43.58 4.52
1676 1700 0.478072 TTTCCAGCTGGTCACATGGT 59.522 50.000 31.58 0.00 36.34 3.55
1687 1711 0.323633 TCACATGGTCCAGGGCAATG 60.324 55.000 6.91 6.91 0.00 2.82
1711 1735 2.640332 TGGACTACACACCCTGCAAATA 59.360 45.455 0.00 0.00 0.00 1.40
1981 2006 3.195825 AGATGTGGAGAGGTAACCGAAAG 59.804 47.826 0.00 0.00 37.17 2.62
1983 2008 3.499338 TGTGGAGAGGTAACCGAAAGTA 58.501 45.455 0.00 0.00 37.17 2.24
2051 2076 4.072131 TGCCAAATGGTAGTCTTCAAGAC 58.928 43.478 9.78 9.78 40.50 3.01
2112 2137 4.338879 ACCTCATTTCAACCAGATTCCTG 58.661 43.478 0.00 0.00 40.09 3.86
2174 2199 2.435586 CAAGGGCCTCAGCGTCAG 60.436 66.667 6.46 0.00 41.24 3.51
2279 2358 1.901833 GGAATGGTGCAAGGTCCAAAT 59.098 47.619 0.00 0.00 37.27 2.32
2369 2448 5.916661 TCTCCAGTTCTGGACATACTAAC 57.083 43.478 16.47 0.00 33.77 2.34
2485 2565 4.458295 GGAATGATAGCATGCATGTAGCTT 59.542 41.667 26.79 15.11 45.94 3.74
2557 2638 2.755650 CGTCTACCTGCTGTTTCTTGT 58.244 47.619 0.00 0.00 0.00 3.16
2646 2727 5.063944 GGATACGCATGCTTCATACTTATGG 59.936 44.000 17.13 0.00 34.50 2.74
2678 2759 9.233232 ACACAATTTCGTTTTCAAAGAGTAATC 57.767 29.630 0.00 0.00 0.00 1.75
3057 3150 9.134055 ACCTCACTAATACTGTATTTCTACTCC 57.866 37.037 17.39 0.00 0.00 3.85
3058 3151 8.578151 CCTCACTAATACTGTATTTCTACTCCC 58.422 40.741 17.39 0.00 0.00 4.30
3059 3152 9.357161 CTCACTAATACTGTATTTCTACTCCCT 57.643 37.037 17.39 0.00 0.00 4.20
3060 3153 9.352191 TCACTAATACTGTATTTCTACTCCCTC 57.648 37.037 17.39 0.00 0.00 4.30
3061 3154 8.578151 CACTAATACTGTATTTCTACTCCCTCC 58.422 40.741 17.39 0.00 0.00 4.30
3062 3155 6.651975 AATACTGTATTTCTACTCCCTCCG 57.348 41.667 7.22 0.00 0.00 4.63
3063 3156 3.978610 ACTGTATTTCTACTCCCTCCGT 58.021 45.455 0.00 0.00 0.00 4.69
3064 3157 4.351127 ACTGTATTTCTACTCCCTCCGTT 58.649 43.478 0.00 0.00 0.00 4.44
3065 3158 4.401837 ACTGTATTTCTACTCCCTCCGTTC 59.598 45.833 0.00 0.00 0.00 3.95
3066 3159 3.379372 TGTATTTCTACTCCCTCCGTTCG 59.621 47.826 0.00 0.00 0.00 3.95
3067 3160 1.180029 TTTCTACTCCCTCCGTTCGG 58.820 55.000 4.74 4.74 0.00 4.30
3068 3161 0.329261 TTCTACTCCCTCCGTTCGGA 59.671 55.000 13.34 13.34 0.00 4.55
3069 3162 0.329261 TCTACTCCCTCCGTTCGGAA 59.671 55.000 14.79 0.04 33.41 4.30
3070 3163 1.064166 TCTACTCCCTCCGTTCGGAAT 60.064 52.381 14.79 2.09 33.41 3.01
3071 3164 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
3072 3165 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3073 3166 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3074 3167 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
3075 3168 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3076 3169 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3077 3170 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
3078 3171 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
3079 3172 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
3080 3173 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
3081 3174 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
3082 3175 2.222508 CGTTCGGAATTACTTGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
3083 3176 2.991190 GTTCGGAATTACTTGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
3084 3177 3.306917 TCGGAATTACTTGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
3085 3178 3.655486 TCGGAATTACTTGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
3086 3179 4.250464 TCGGAATTACTTGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
3087 3180 4.092821 TCGGAATTACTTGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
3088 3181 4.662145 GGAATTACTTGTCGCAGAAATGG 58.338 43.478 0.00 0.00 39.69 3.16
3089 3182 4.394920 GGAATTACTTGTCGCAGAAATGGA 59.605 41.667 0.00 0.00 39.69 3.41
3090 3183 4.946784 ATTACTTGTCGCAGAAATGGAC 57.053 40.909 0.00 0.00 39.69 4.02
3091 3184 1.148310 ACTTGTCGCAGAAATGGACG 58.852 50.000 0.00 0.00 39.69 4.79
3092 3185 1.148310 CTTGTCGCAGAAATGGACGT 58.852 50.000 0.00 0.00 39.69 4.34
3093 3186 2.288579 ACTTGTCGCAGAAATGGACGTA 60.289 45.455 0.00 0.00 39.69 3.57
3094 3187 2.665649 TGTCGCAGAAATGGACGTAT 57.334 45.000 0.00 0.00 39.69 3.06
3095 3188 2.536365 TGTCGCAGAAATGGACGTATC 58.464 47.619 0.00 0.00 39.69 2.24
3096 3189 2.165641 TGTCGCAGAAATGGACGTATCT 59.834 45.455 0.00 0.00 39.69 1.98
3097 3190 3.379057 TGTCGCAGAAATGGACGTATCTA 59.621 43.478 0.00 0.00 39.69 1.98
3098 3191 3.975670 GTCGCAGAAATGGACGTATCTAG 59.024 47.826 0.00 0.00 39.69 2.43
3099 3192 3.881089 TCGCAGAAATGGACGTATCTAGA 59.119 43.478 0.00 0.00 0.00 2.43
3100 3193 3.975670 CGCAGAAATGGACGTATCTAGAC 59.024 47.826 0.00 0.00 0.00 2.59
3130 3223 9.542462 TTTTAGTTCTAGATACATCCATTTCCG 57.458 33.333 0.00 0.00 0.00 4.30
3131 3224 6.978674 AGTTCTAGATACATCCATTTCCGA 57.021 37.500 0.00 0.00 0.00 4.55
3132 3225 6.987386 AGTTCTAGATACATCCATTTCCGAG 58.013 40.000 0.00 0.00 0.00 4.63
3133 3226 6.778069 AGTTCTAGATACATCCATTTCCGAGA 59.222 38.462 0.00 0.00 0.00 4.04
3134 3227 6.576662 TCTAGATACATCCATTTCCGAGAC 57.423 41.667 0.00 0.00 0.00 3.36
3135 3228 6.068670 TCTAGATACATCCATTTCCGAGACA 58.931 40.000 0.00 0.00 0.00 3.41
3136 3229 5.614324 AGATACATCCATTTCCGAGACAA 57.386 39.130 0.00 0.00 0.00 3.18
3137 3230 5.605534 AGATACATCCATTTCCGAGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
3138 3231 3.703001 ACATCCATTTCCGAGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
3139 3232 4.819105 ACATCCATTTCCGAGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
3140 3233 5.160607 ACATCCATTTCCGAGACAAGTAA 57.839 39.130 0.00 0.00 0.00 2.24
3141 3234 5.745227 ACATCCATTTCCGAGACAAGTAAT 58.255 37.500 0.00 0.00 0.00 1.89
3142 3235 6.180472 ACATCCATTTCCGAGACAAGTAATT 58.820 36.000 0.00 0.00 0.00 1.40
3143 3236 6.316390 ACATCCATTTCCGAGACAAGTAATTC 59.684 38.462 0.00 0.00 0.00 2.17
3144 3237 5.183228 TCCATTTCCGAGACAAGTAATTCC 58.817 41.667 0.00 0.00 0.00 3.01
3145 3238 4.034048 CCATTTCCGAGACAAGTAATTCCG 59.966 45.833 0.00 0.00 0.00 4.30
3146 3239 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
3147 3240 4.524316 TTCCGAGACAAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
3148 3241 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
3149 3242 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
3150 3243 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
3151 3244 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
3152 3245 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
3153 3246 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
3154 3247 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3155 3248 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
3156 3249 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
3157 3250 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
3158 3251 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
3159 3252 2.083628 ATTCCGAACGGAGGGAGTAT 57.916 50.000 15.34 3.38 46.06 2.12
3582 3957 1.674962 GTGGAGAAGGATGCTTGCATC 59.325 52.381 22.99 22.99 0.00 3.91
3756 4131 7.119262 GCAGCTTATTTACCTAGAACAGTCAAA 59.881 37.037 0.00 0.00 0.00 2.69
4021 4399 1.135939 GTGACCGGCGCCAATAAAC 59.864 57.895 28.98 13.71 0.00 2.01
4187 4571 6.458232 TCATTTCCTAGACTGCTCTTAGAC 57.542 41.667 0.00 0.00 0.00 2.59
4188 4572 5.361285 TCATTTCCTAGACTGCTCTTAGACC 59.639 44.000 0.00 0.00 0.00 3.85
4343 4968 9.401058 CTTCTGGATGTTCTATATGGTTTTCTT 57.599 33.333 0.00 0.00 0.00 2.52
4344 4969 9.753674 TTCTGGATGTTCTATATGGTTTTCTTT 57.246 29.630 0.00 0.00 0.00 2.52
4345 4970 9.396022 TCTGGATGTTCTATATGGTTTTCTTTC 57.604 33.333 0.00 0.00 0.00 2.62
4346 4971 8.519799 TGGATGTTCTATATGGTTTTCTTTCC 57.480 34.615 0.00 0.00 0.00 3.13
4347 4972 7.282224 TGGATGTTCTATATGGTTTTCTTTCCG 59.718 37.037 0.00 0.00 0.00 4.30
4348 4973 7.282450 GGATGTTCTATATGGTTTTCTTTCCGT 59.718 37.037 0.00 0.00 0.00 4.69
4349 4974 7.989416 TGTTCTATATGGTTTTCTTTCCGTT 57.011 32.000 0.00 0.00 0.00 4.44
4350 4975 8.398878 TGTTCTATATGGTTTTCTTTCCGTTT 57.601 30.769 0.00 0.00 0.00 3.60
4351 4976 8.508875 TGTTCTATATGGTTTTCTTTCCGTTTC 58.491 33.333 0.00 0.00 0.00 2.78
4352 4977 7.298507 TCTATATGGTTTTCTTTCCGTTTCG 57.701 36.000 0.00 0.00 0.00 3.46
4353 4978 7.098477 TCTATATGGTTTTCTTTCCGTTTCGA 58.902 34.615 0.00 0.00 0.00 3.71
4354 4979 4.904253 ATGGTTTTCTTTCCGTTTCGAA 57.096 36.364 0.00 0.00 0.00 3.71
4355 4980 4.698583 TGGTTTTCTTTCCGTTTCGAAA 57.301 36.364 6.47 6.47 0.00 3.46
4356 4981 5.056894 TGGTTTTCTTTCCGTTTCGAAAA 57.943 34.783 13.10 0.00 34.18 2.29
4357 4982 5.467705 TGGTTTTCTTTCCGTTTCGAAAAA 58.532 33.333 13.10 0.28 37.18 1.94
4393 5018 2.882324 TGGTTTTGCAGTTTCGGTTTC 58.118 42.857 0.00 0.00 0.00 2.78
4394 5019 2.494073 TGGTTTTGCAGTTTCGGTTTCT 59.506 40.909 0.00 0.00 0.00 2.52
4400 5025 2.035704 TGCAGTTTCGGTTTCTACGGTA 59.964 45.455 0.00 0.00 0.00 4.02
4498 5132 0.752054 TGGCTTTGGCTTTTGACTGG 59.248 50.000 0.00 0.00 38.73 4.00
4529 5163 7.068103 TGTTACATGATGGTATAAGCCAAAAGG 59.932 37.037 0.00 0.00 42.48 3.11
4530 5164 4.342092 ACATGATGGTATAAGCCAAAAGGC 59.658 41.667 0.00 0.00 42.48 4.35
4531 5165 3.974719 TGATGGTATAAGCCAAAAGGCA 58.025 40.909 9.42 0.00 42.48 4.75
4532 5166 4.348486 TGATGGTATAAGCCAAAAGGCAA 58.652 39.130 9.42 0.00 42.48 4.52
4533 5167 4.774726 TGATGGTATAAGCCAAAAGGCAAA 59.225 37.500 9.42 0.00 42.48 3.68
4534 5168 4.799564 TGGTATAAGCCAAAAGGCAAAG 57.200 40.909 9.42 0.00 35.25 2.77
4535 5169 3.056179 TGGTATAAGCCAAAAGGCAAAGC 60.056 43.478 9.42 1.69 35.25 3.51
4536 5170 6.132279 TGGTATAAGCCAAAAGGCAAAGCC 62.132 45.833 9.42 0.00 41.70 4.35
4669 6358 2.673775 TGATGGGAGTCAGCCAAAAA 57.326 45.000 0.00 0.00 0.00 1.94
4726 6416 3.303990 CCTGAACGAAATGGAACTGTGTG 60.304 47.826 0.00 0.00 0.00 3.82
4751 6444 6.305272 ACAATCAGACTCAGGAATACACAT 57.695 37.500 0.00 0.00 0.00 3.21
4815 6509 1.132453 TCGCGATAACCTCACTCACAG 59.868 52.381 3.71 0.00 0.00 3.66
4846 6540 6.382919 TCCCTAAACTATACCAGCAAAAGT 57.617 37.500 0.00 0.00 0.00 2.66
4869 6563 7.383687 AGTTGTAGTCCTGAACGAATCAAATA 58.616 34.615 0.00 0.00 37.67 1.40
4906 6600 6.332630 CAAAATGAACACTGGGATATGGTTC 58.667 40.000 0.00 0.00 38.59 3.62
4970 6664 2.455163 AGTGCCCTCCCCTACAGTATAT 59.545 50.000 0.00 0.00 0.00 0.86
4971 6665 3.666116 AGTGCCCTCCCCTACAGTATATA 59.334 47.826 0.00 0.00 0.00 0.86
4973 6667 4.466726 GTGCCCTCCCCTACAGTATATAAG 59.533 50.000 0.00 0.00 0.00 1.73
4974 6668 4.358918 TGCCCTCCCCTACAGTATATAAGA 59.641 45.833 0.00 0.00 0.00 2.10
4975 6669 5.017431 TGCCCTCCCCTACAGTATATAAGAT 59.983 44.000 0.00 0.00 0.00 2.40
4976 6670 5.364157 GCCCTCCCCTACAGTATATAAGATG 59.636 48.000 0.00 0.00 0.00 2.90
4977 6671 5.364157 CCCTCCCCTACAGTATATAAGATGC 59.636 48.000 0.00 0.00 0.00 3.91
4978 6672 6.198639 CCTCCCCTACAGTATATAAGATGCT 58.801 44.000 0.00 0.00 0.00 3.79
4979 6673 6.670027 CCTCCCCTACAGTATATAAGATGCTT 59.330 42.308 0.00 0.00 0.00 3.91
4980 6674 7.364232 CCTCCCCTACAGTATATAAGATGCTTG 60.364 44.444 0.00 0.00 0.00 4.01
4981 6675 7.246027 TCCCCTACAGTATATAAGATGCTTGA 58.754 38.462 0.00 0.00 0.00 3.02
4982 6676 7.397476 TCCCCTACAGTATATAAGATGCTTGAG 59.603 40.741 0.00 0.00 0.00 3.02
4983 6677 7.038659 CCCTACAGTATATAAGATGCTTGAGC 58.961 42.308 0.00 0.00 42.50 4.26
4984 6678 7.093552 CCCTACAGTATATAAGATGCTTGAGCT 60.094 40.741 4.44 0.00 42.66 4.09
4985 6679 8.961634 CCTACAGTATATAAGATGCTTGAGCTA 58.038 37.037 4.44 0.00 42.66 3.32
4988 6682 9.083422 ACAGTATATAAGATGCTTGAGCTAAGA 57.917 33.333 4.44 0.00 42.66 2.10
4989 6683 9.352784 CAGTATATAAGATGCTTGAGCTAAGAC 57.647 37.037 4.44 1.14 42.66 3.01
4990 6684 8.240682 AGTATATAAGATGCTTGAGCTAAGACG 58.759 37.037 4.44 0.00 42.66 4.18
4991 6685 3.876274 AAGATGCTTGAGCTAAGACGA 57.124 42.857 4.44 0.00 42.66 4.20
4992 6686 3.876274 AGATGCTTGAGCTAAGACGAA 57.124 42.857 4.44 0.00 42.66 3.85
4993 6687 3.516615 AGATGCTTGAGCTAAGACGAAC 58.483 45.455 4.44 0.00 42.66 3.95
4994 6688 2.812358 TGCTTGAGCTAAGACGAACA 57.188 45.000 4.44 0.00 42.66 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.880537 CGCAGGCCACTCTAGCGG 62.881 72.222 5.01 0.00 44.20 5.52
2 3 4.880537 CCGCAGGCCACTCTAGCG 62.881 72.222 5.01 10.53 46.14 4.26
14 15 1.734465 GAAATCAACAGAGACCCGCAG 59.266 52.381 0.00 0.00 0.00 5.18
15 16 1.347707 AGAAATCAACAGAGACCCGCA 59.652 47.619 0.00 0.00 0.00 5.69
16 17 1.734465 CAGAAATCAACAGAGACCCGC 59.266 52.381 0.00 0.00 0.00 6.13
17 18 1.734465 GCAGAAATCAACAGAGACCCG 59.266 52.381 0.00 0.00 0.00 5.28
18 19 2.783135 TGCAGAAATCAACAGAGACCC 58.217 47.619 0.00 0.00 0.00 4.46
19 20 3.057946 GGTTGCAGAAATCAACAGAGACC 60.058 47.826 7.95 0.00 44.02 3.85
20 21 3.364366 CGGTTGCAGAAATCAACAGAGAC 60.364 47.826 7.95 0.00 44.02 3.36
21 22 2.807967 CGGTTGCAGAAATCAACAGAGA 59.192 45.455 7.95 0.00 44.02 3.10
22 23 2.549754 ACGGTTGCAGAAATCAACAGAG 59.450 45.455 11.65 4.19 44.02 3.35
23 24 2.290367 CACGGTTGCAGAAATCAACAGA 59.710 45.455 11.65 0.00 44.02 3.41
24 25 2.605338 CCACGGTTGCAGAAATCAACAG 60.605 50.000 7.95 6.38 44.02 3.16
25 26 1.336440 CCACGGTTGCAGAAATCAACA 59.664 47.619 7.95 0.00 44.02 3.33
124 127 6.818142 TCATACACCATGTTAGTTCATCAGTG 59.182 38.462 0.00 0.00 36.26 3.66
142 145 5.470098 ACCCGAATAATCTGCATTCATACAC 59.530 40.000 0.00 0.00 32.92 2.90
184 187 4.043037 AGCTAATTAACTACGCTCGCTT 57.957 40.909 0.00 0.00 0.00 4.68
191 194 8.926710 AGCAGCATTAATAGCTAATTAACTACG 58.073 33.333 0.00 0.00 41.66 3.51
239 242 2.165998 GTTCTACCCTGTACCGACTGT 58.834 52.381 0.00 0.00 0.00 3.55
241 244 2.444421 CAGTTCTACCCTGTACCGACT 58.556 52.381 0.00 0.00 0.00 4.18
368 374 8.632679 TGCAATAATAAAATCAAGATGAGGGTC 58.367 33.333 0.00 0.00 0.00 4.46
369 375 8.537728 TGCAATAATAAAATCAAGATGAGGGT 57.462 30.769 0.00 0.00 0.00 4.34
404 410 2.576191 TGGGTCTTGGTAATCTTCCAGG 59.424 50.000 0.00 0.00 36.28 4.45
508 514 8.274322 AGACAAGGATCAACCATAACATCATTA 58.726 33.333 0.00 0.00 42.04 1.90
609 615 9.478019 GTATGAGTTTCACATGTTTTAATCTCG 57.522 33.333 0.00 0.00 0.00 4.04
635 641 8.647143 AGCATTAAATGAATAAAATTGGGACG 57.353 30.769 0.00 0.00 0.00 4.79
1082 1103 0.328258 ACTCCCAGTGCCACCATTAC 59.672 55.000 0.00 0.00 0.00 1.89
1173 1194 2.034812 GCTCTCATAGTAACCCCGTGAG 59.965 54.545 0.00 0.00 38.07 3.51
1399 1423 0.242017 CCAAAACTGCTACTGCTGCC 59.758 55.000 0.00 0.00 41.07 4.85
1426 1450 4.037684 CCTCATTTTCATGGATTCTCTGGC 59.962 45.833 0.00 0.00 0.00 4.85
1445 1469 2.166459 CTCTCGGTTACAGCATTCCTCA 59.834 50.000 0.00 0.00 0.00 3.86
1461 1485 2.358957 TCAAAATGATGGCCACTCTCG 58.641 47.619 8.16 0.00 0.00 4.04
1599 1623 0.318120 CCATTGGTGTTGCCCTGTTC 59.682 55.000 0.00 0.00 36.04 3.18
1606 1630 1.200020 GTGAGTAGCCATTGGTGTTGC 59.800 52.381 4.26 0.00 0.00 4.17
1637 1661 5.107607 GGAAATACATAGTTACCATGACGCG 60.108 44.000 3.53 3.53 0.00 6.01
1676 1700 1.380246 GTCCATGCATTGCCCTGGA 60.380 57.895 20.31 20.31 37.14 3.86
1687 1711 3.159298 CAGGGTGTGTAGTCCATGC 57.841 57.895 0.00 0.00 0.00 4.06
1711 1735 1.837439 TGGGACTCCGTCAGCAATAAT 59.163 47.619 0.00 0.00 33.68 1.28
1753 1777 4.559862 ACTTACCTGAAGGATTGTGGAG 57.440 45.455 2.62 0.00 39.74 3.86
1909 1934 7.255486 GCCAGGCCATAACTTATAAAAGGTTAG 60.255 40.741 5.01 0.00 37.01 2.34
2051 2076 1.964552 CAGAAGGGCCAGCTTGATAG 58.035 55.000 6.18 0.00 0.00 2.08
2054 2079 1.200760 TAGCAGAAGGGCCAGCTTGA 61.201 55.000 15.98 0.00 38.47 3.02
2174 2199 1.135575 GCACCTTGCACTACATTGCTC 60.136 52.381 0.00 0.00 44.26 4.26
2279 2358 0.609957 CTTGCACCATTCCAGCAGGA 60.610 55.000 0.00 0.00 43.93 3.86
2369 2448 0.107508 ATGCATGAACTGGAGGTCCG 60.108 55.000 0.00 0.00 39.43 4.79
2557 2638 5.047306 CGGGTAATACATCTTCTATGCCTCA 60.047 44.000 0.00 0.00 0.00 3.86
2646 2727 6.396459 TTGAAAACGAAATTGTGTTTCCAC 57.604 33.333 8.30 0.00 37.31 4.02
2953 3038 8.509690 CAAGACAACAGAAACATGATAATCACT 58.490 33.333 0.00 0.00 0.00 3.41
3024 3117 7.684937 ATACAGTATTAGTGAGGTACGGATC 57.315 40.000 5.52 0.00 0.00 3.36
3055 3148 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
3056 3149 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3057 3150 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
3058 3151 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
3059 3152 2.598589 CGACAAGTAATTCCGAACGGA 58.401 47.619 12.04 12.04 43.52 4.69
3060 3153 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
3061 3154 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
3062 3155 2.991190 TCTGCGACAAGTAATTCCGAAC 59.009 45.455 0.00 0.00 0.00 3.95
3063 3156 3.306917 TCTGCGACAAGTAATTCCGAA 57.693 42.857 0.00 0.00 0.00 4.30
3064 3157 3.306917 TTCTGCGACAAGTAATTCCGA 57.693 42.857 0.00 0.00 0.00 4.55
3065 3158 4.334443 CATTTCTGCGACAAGTAATTCCG 58.666 43.478 0.00 0.00 0.00 4.30
3066 3159 4.394920 TCCATTTCTGCGACAAGTAATTCC 59.605 41.667 0.00 0.00 0.00 3.01
3067 3160 5.324697 GTCCATTTCTGCGACAAGTAATTC 58.675 41.667 0.00 0.00 0.00 2.17
3068 3161 4.142902 CGTCCATTTCTGCGACAAGTAATT 60.143 41.667 0.00 0.00 0.00 1.40
3069 3162 3.370978 CGTCCATTTCTGCGACAAGTAAT 59.629 43.478 0.00 0.00 0.00 1.89
3070 3163 2.734606 CGTCCATTTCTGCGACAAGTAA 59.265 45.455 0.00 0.00 0.00 2.24
3071 3164 2.288579 ACGTCCATTTCTGCGACAAGTA 60.289 45.455 0.00 0.00 0.00 2.24
3072 3165 1.148310 CGTCCATTTCTGCGACAAGT 58.852 50.000 0.00 0.00 0.00 3.16
3073 3166 1.148310 ACGTCCATTTCTGCGACAAG 58.852 50.000 0.00 0.00 0.00 3.16
3074 3167 2.442212 TACGTCCATTTCTGCGACAA 57.558 45.000 0.00 0.00 0.00 3.18
3075 3168 2.165641 AGATACGTCCATTTCTGCGACA 59.834 45.455 0.00 0.00 0.00 4.35
3076 3169 2.810650 AGATACGTCCATTTCTGCGAC 58.189 47.619 0.00 0.00 0.00 5.19
3077 3170 3.881089 TCTAGATACGTCCATTTCTGCGA 59.119 43.478 0.00 0.00 0.00 5.10
3078 3171 3.975670 GTCTAGATACGTCCATTTCTGCG 59.024 47.826 0.00 0.00 0.00 5.18
3079 3172 3.975670 CGTCTAGATACGTCCATTTCTGC 59.024 47.826 0.00 0.00 38.07 4.26
3104 3197 9.542462 CGGAAATGGATGTATCTAGAACTAAAA 57.458 33.333 0.00 0.00 0.00 1.52
3105 3198 8.920174 TCGGAAATGGATGTATCTAGAACTAAA 58.080 33.333 0.00 0.00 0.00 1.85
3106 3199 8.473358 TCGGAAATGGATGTATCTAGAACTAA 57.527 34.615 0.00 0.00 0.00 2.24
3107 3200 7.942894 TCTCGGAAATGGATGTATCTAGAACTA 59.057 37.037 0.00 0.00 0.00 2.24
3108 3201 6.778069 TCTCGGAAATGGATGTATCTAGAACT 59.222 38.462 0.00 0.00 0.00 3.01
3109 3202 6.864165 GTCTCGGAAATGGATGTATCTAGAAC 59.136 42.308 0.00 0.00 0.00 3.01
3110 3203 6.549736 TGTCTCGGAAATGGATGTATCTAGAA 59.450 38.462 0.00 0.00 0.00 2.10
3111 3204 6.068670 TGTCTCGGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
3112 3205 6.332735 TGTCTCGGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
3113 3206 6.323996 ACTTGTCTCGGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
3114 3207 5.129485 ACTTGTCTCGGAAATGGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
3115 3208 5.360591 ACTTGTCTCGGAAATGGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
3116 3209 5.359194 ACTTGTCTCGGAAATGGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
3117 3210 4.819105 ACTTGTCTCGGAAATGGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
3118 3211 3.703001 ACTTGTCTCGGAAATGGATGT 57.297 42.857 0.00 0.00 0.00 3.06
3119 3212 6.238484 GGAATTACTTGTCTCGGAAATGGATG 60.238 42.308 0.00 0.00 0.00 3.51
3120 3213 5.823045 GGAATTACTTGTCTCGGAAATGGAT 59.177 40.000 0.00 0.00 0.00 3.41
3121 3214 5.183228 GGAATTACTTGTCTCGGAAATGGA 58.817 41.667 0.00 0.00 0.00 3.41
3122 3215 4.034048 CGGAATTACTTGTCTCGGAAATGG 59.966 45.833 0.00 0.00 0.00 3.16
3123 3216 4.868171 TCGGAATTACTTGTCTCGGAAATG 59.132 41.667 0.00 0.00 0.00 2.32
3124 3217 5.080969 TCGGAATTACTTGTCTCGGAAAT 57.919 39.130 0.00 0.00 0.00 2.17
3125 3218 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
3126 3219 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
3127 3220 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
3128 3221 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
3129 3222 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
3130 3223 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
3131 3224 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
3132 3225 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
3133 3226 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
3134 3227 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3135 3228 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
3136 3229 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
3137 3230 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
3138 3231 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
3139 3232 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
3140 3233 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
3141 3234 2.734755 TATACTCCCTCCGTTCGGAA 57.265 50.000 14.79 0.00 33.41 4.30
3142 3235 2.107031 TCATATACTCCCTCCGTTCGGA 59.893 50.000 13.34 13.34 0.00 4.55
3143 3236 2.228343 GTCATATACTCCCTCCGTTCGG 59.772 54.545 4.74 4.74 0.00 4.30
3144 3237 3.058155 CAGTCATATACTCCCTCCGTTCG 60.058 52.174 0.00 0.00 35.76 3.95
3145 3238 3.256136 CCAGTCATATACTCCCTCCGTTC 59.744 52.174 0.00 0.00 35.76 3.95
3146 3239 3.231818 CCAGTCATATACTCCCTCCGTT 58.768 50.000 0.00 0.00 35.76 4.44
3147 3240 2.491086 CCCAGTCATATACTCCCTCCGT 60.491 54.545 0.00 0.00 35.76 4.69
3148 3241 2.171840 CCCAGTCATATACTCCCTCCG 58.828 57.143 0.00 0.00 35.76 4.63
3149 3242 1.903183 GCCCAGTCATATACTCCCTCC 59.097 57.143 0.00 0.00 35.76 4.30
3150 3243 2.896039 AGCCCAGTCATATACTCCCTC 58.104 52.381 0.00 0.00 35.76 4.30
3151 3244 3.352611 AAGCCCAGTCATATACTCCCT 57.647 47.619 0.00 0.00 35.76 4.20
3152 3245 4.161102 AGTAAGCCCAGTCATATACTCCC 58.839 47.826 0.00 0.00 35.76 4.30
3153 3246 5.810080 AAGTAAGCCCAGTCATATACTCC 57.190 43.478 0.00 0.00 35.76 3.85
3154 3247 9.780186 ATAAAAAGTAAGCCCAGTCATATACTC 57.220 33.333 0.00 0.00 35.76 2.59
3155 3248 9.561069 CATAAAAAGTAAGCCCAGTCATATACT 57.439 33.333 0.00 0.00 39.81 2.12
3156 3249 9.555727 TCATAAAAAGTAAGCCCAGTCATATAC 57.444 33.333 0.00 0.00 0.00 1.47
3157 3250 9.778741 CTCATAAAAAGTAAGCCCAGTCATATA 57.221 33.333 0.00 0.00 0.00 0.86
3158 3251 8.275040 ACTCATAAAAAGTAAGCCCAGTCATAT 58.725 33.333 0.00 0.00 0.00 1.78
3159 3252 7.552687 CACTCATAAAAAGTAAGCCCAGTCATA 59.447 37.037 0.00 0.00 0.00 2.15
3582 3957 6.016276 GTGTAAGGGAAAATACCTGGCATATG 60.016 42.308 0.00 0.00 38.63 1.78
3626 4001 7.923414 AGAAATTAAGATCCAGTGGTGTTAC 57.077 36.000 9.54 0.00 0.00 2.50
3756 4131 0.953960 GATCGTGACAAAGGGGCGTT 60.954 55.000 0.00 0.00 0.00 4.84
4359 4984 6.657117 ACTGCAAAACCAAGTAAACCATTTTT 59.343 30.769 0.00 0.00 0.00 1.94
4360 4985 6.176896 ACTGCAAAACCAAGTAAACCATTTT 58.823 32.000 0.00 0.00 0.00 1.82
4361 4986 5.739959 ACTGCAAAACCAAGTAAACCATTT 58.260 33.333 0.00 0.00 0.00 2.32
4362 4987 5.351948 ACTGCAAAACCAAGTAAACCATT 57.648 34.783 0.00 0.00 0.00 3.16
4363 4988 5.351948 AACTGCAAAACCAAGTAAACCAT 57.648 34.783 0.00 0.00 0.00 3.55
4364 4989 4.810191 AACTGCAAAACCAAGTAAACCA 57.190 36.364 0.00 0.00 0.00 3.67
4365 4990 4.266739 CGAAACTGCAAAACCAAGTAAACC 59.733 41.667 0.00 0.00 0.00 3.27
4366 4991 4.266739 CCGAAACTGCAAAACCAAGTAAAC 59.733 41.667 0.00 0.00 0.00 2.01
4367 4992 4.082136 ACCGAAACTGCAAAACCAAGTAAA 60.082 37.500 0.00 0.00 0.00 2.01
4368 4993 3.444388 ACCGAAACTGCAAAACCAAGTAA 59.556 39.130 0.00 0.00 0.00 2.24
4369 4994 3.018149 ACCGAAACTGCAAAACCAAGTA 58.982 40.909 0.00 0.00 0.00 2.24
4370 4995 1.822371 ACCGAAACTGCAAAACCAAGT 59.178 42.857 0.00 0.00 0.00 3.16
4393 5018 2.767960 ACCAAACACCCCTATACCGTAG 59.232 50.000 0.00 0.00 0.00 3.51
4394 5019 2.831565 ACCAAACACCCCTATACCGTA 58.168 47.619 0.00 0.00 0.00 4.02
4400 5025 2.284770 AGCCTAACCAAACACCCCTAT 58.715 47.619 0.00 0.00 0.00 2.57
4498 5132 8.094548 TGGCTTATACCATCATGTAACAGTATC 58.905 37.037 0.00 0.00 33.75 2.24
4529 5163 4.556942 ATTTTTCTGCTTTTGGCTTTGC 57.443 36.364 0.00 0.00 42.39 3.68
4530 5164 8.538409 AGTATATTTTTCTGCTTTTGGCTTTG 57.462 30.769 0.00 0.00 42.39 2.77
4532 5166 9.807649 CATAGTATATTTTTCTGCTTTTGGCTT 57.192 29.630 0.00 0.00 42.39 4.35
4533 5167 8.971073 ACATAGTATATTTTTCTGCTTTTGGCT 58.029 29.630 0.00 0.00 42.39 4.75
4534 5168 9.586435 AACATAGTATATTTTTCTGCTTTTGGC 57.414 29.630 0.00 0.00 42.22 4.52
4690 6379 3.054434 TCGTTCAGGGGATTTGTCATGAT 60.054 43.478 0.00 0.00 0.00 2.45
4726 6416 6.166279 TGTGTATTCCTGAGTCTGATTGTTC 58.834 40.000 0.00 0.00 0.00 3.18
4751 6444 6.884472 TGGATGTTTTCTACCTCTTGGATA 57.116 37.500 0.00 0.00 37.04 2.59
4815 6509 7.338449 TGCTGGTATAGTTTAGGGATTTGAAAC 59.662 37.037 0.00 0.00 34.05 2.78
4869 6563 7.332430 CAGTGTTCATTTTGCCATGTTTGATAT 59.668 33.333 0.00 0.00 0.00 1.63
4906 6600 2.110990 CGTTTGTATTCATGCGCCATG 58.889 47.619 4.18 9.25 42.60 3.66
4970 6664 4.983671 TCGTCTTAGCTCAAGCATCTTA 57.016 40.909 4.59 0.00 45.16 2.10
4971 6665 3.876274 TCGTCTTAGCTCAAGCATCTT 57.124 42.857 4.59 0.00 45.16 2.40
4973 6667 3.254060 TGTTCGTCTTAGCTCAAGCATC 58.746 45.455 4.59 0.00 45.16 3.91
4974 6668 3.319137 TGTTCGTCTTAGCTCAAGCAT 57.681 42.857 4.59 0.00 45.16 3.79
4975 6669 2.812358 TGTTCGTCTTAGCTCAAGCA 57.188 45.000 4.59 0.00 45.16 3.91


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

AutoCloner maintained by Alex Coulton.