Multiple sequence alignment - TraesCS2B01G530500

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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 TraesCS2B01G530500 chr2B 100.000 6967 0 0 877 7843 725966383 725959417 0.000000e+00 12866
1 TraesCS2B01G530500 chr2B 100.000 473 0 0 1 473 725967259 725966787 0.000000e+00 874
2 TraesCS2B01G530500 chr2B 97.546 163 4 0 2992 3154 664125038 664125200 5.990000e-71 279
3 TraesCS2B01G530500 chr2B 95.294 170 8 0 2985 3154 713695966 713695797 3.610000e-68 270
4 TraesCS2B01G530500 chr2D 96.946 3995 86 12 3305 7284 596915216 596911243 0.000000e+00 6669
5 TraesCS2B01G530500 chr2D 91.382 2170 116 24 877 2993 596917577 596915426 0.000000e+00 2905
6 TraesCS2B01G530500 chr2D 93.658 473 16 7 1 466 596918460 596917995 0.000000e+00 695
7 TraesCS2B01G530500 chr2D 90.414 459 19 11 7397 7843 596911045 596910600 1.470000e-161 580
8 TraesCS2B01G530500 chr2D 93.671 158 9 1 3153 3309 596915427 596915270 1.320000e-57 235
9 TraesCS2B01G530500 chr2A 95.615 3991 122 28 3306 7284 731160468 731156519 0.000000e+00 6351
10 TraesCS2B01G530500 chr2A 91.235 2179 109 40 880 2993 731162841 731160680 0.000000e+00 2891
11 TraesCS2B01G530500 chr2A 91.304 483 24 8 1 469 731163546 731163068 1.840000e-180 643
12 TraesCS2B01G530500 chr2A 88.558 437 23 12 7397 7819 731156339 731155916 9.080000e-139 505
13 TraesCS2B01G530500 chr2A 93.038 158 8 3 3153 3309 731160681 731160526 2.200000e-55 228
14 TraesCS2B01G530500 chr3B 98.160 163 3 0 2992 3154 539941568 539941730 1.290000e-72 285
15 TraesCS2B01G530500 chr7D 97.024 168 5 0 2992 3159 416628415 416628248 4.630000e-72 283
16 TraesCS2B01G530500 chr7D 95.322 171 8 0 2984 3154 573953284 573953114 1.000000e-68 272
17 TraesCS2B01G530500 chr6A 78.913 460 66 14 6483 6937 614862483 614862050 4.630000e-72 283
18 TraesCS2B01G530500 chr7B 97.546 163 4 0 2992 3154 497576786 497576624 5.990000e-71 279
19 TraesCS2B01G530500 chr5B 96.988 166 5 0 2992 3157 701551649 701551814 5.990000e-71 279
20 TraesCS2B01G530500 chr5B 92.857 182 13 0 2978 3159 467382702 467382521 1.680000e-66 265
21 TraesCS2B01G530500 chrUn 96.386 166 6 0 2992 3157 65533276 65533111 2.790000e-69 274
22 TraesCS2B01G530500 chr1A 84.211 247 33 4 2629 2872 450096398 450096155 1.320000e-57 235
23 TraesCS2B01G530500 chr1D 83.401 247 35 4 2629 2872 349794642 349794399 2.850000e-54 224


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 TraesCS2B01G530500 chr2B 725959417 725967259 7842 True 6870.0 12866 100.0000 1 7843 2 chr2B.!!$R2 7842
1 TraesCS2B01G530500 chr2D 596910600 596918460 7860 True 2216.8 6669 93.2142 1 7843 5 chr2D.!!$R1 7842
2 TraesCS2B01G530500 chr2A 731155916 731163546 7630 True 2123.6 6351 91.9500 1 7819 5 chr2A.!!$R1 7818

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
919 967 0.944311 CGTTGGTGCGTGCTAGAGTT 60.944 55.000 0.0 0.0 0.00 3.01 F
1177 1241 0.099082 GATCTCTCGACACACGGGTC 59.901 60.000 0.0 0.0 43.73 4.46 F
2875 3004 0.178990 ACCCAAGACAAAGGTGAGCC 60.179 55.000 0.0 0.0 30.97 4.70 F
3006 3135 1.006758 TGATGTACTCCCTCCGTTCCT 59.993 52.381 0.0 0.0 0.00 3.36 F
3674 3863 1.476488 GTTGACAGCACCAACCAAGTT 59.524 47.619 0.0 0.0 38.28 2.66 F
5078 5267 2.159544 GCTGCAAGAGAAGAAGCACATC 60.160 50.000 0.0 0.0 34.07 3.06 F
6098 6288 1.061546 TGGTTACCGCCTTCCTTCTT 58.938 50.000 0.0 0.0 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2856 2985 0.178990 GGCTCACCTTTGTCTTGGGT 60.179 55.000 0.00 0.00 0.00 4.51 R
3138 3267 1.358445 ACTTCTACTCCCTCCGTTCCT 59.642 52.381 0.00 0.00 0.00 3.36 R
3722 3911 0.527600 CGATTCCCACTGCGATCGAA 60.528 55.000 21.57 7.71 42.82 3.71 R
4888 5077 2.771943 AGGAAGTGACTCAAGTGAACCA 59.228 45.455 0.00 0.00 0.00 3.67 R
5596 5785 0.177141 TTGGCCGTAGTACCTGCATC 59.823 55.000 0.00 0.00 0.00 3.91 R
6424 6614 1.064166 AGGGTCATCATTTGCTCCAGG 60.064 52.381 0.00 0.00 0.00 4.45 R
7357 7638 0.682852 ACCACAACCAGCTACGCTTA 59.317 50.000 0.00 0.00 36.40 3.09 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
40 41 2.574212 CGTCCGCACCGTACGTAC 60.574 66.667 15.90 15.90 32.16 3.67
65 66 4.161295 CCCCATCCGCTCGCAGAA 62.161 66.667 0.00 0.00 34.09 3.02
67 68 2.464459 CCCATCCGCTCGCAGAAAC 61.464 63.158 0.00 0.00 34.09 2.78
469 503 2.258591 GGCACGCGAACAGAGAGA 59.741 61.111 15.93 0.00 0.00 3.10
471 505 1.210413 GCACGCGAACAGAGAGAGA 59.790 57.895 15.93 0.00 0.00 3.10
918 966 1.372997 CGTTGGTGCGTGCTAGAGT 60.373 57.895 0.00 0.00 0.00 3.24
919 967 0.944311 CGTTGGTGCGTGCTAGAGTT 60.944 55.000 0.00 0.00 0.00 3.01
970 1018 1.216710 CTCTCTTCCCGTGCTGGTC 59.783 63.158 0.00 0.00 35.15 4.02
1060 1108 3.760035 TGAGAACCGCTCCCGCTC 61.760 66.667 0.00 0.00 43.26 5.03
1083 1140 1.821332 CCTTCTCTTGCGATGCCCC 60.821 63.158 0.00 0.00 0.00 5.80
1093 1150 4.593864 GATGCCCCGTCTCTCGCC 62.594 72.222 0.00 0.00 38.35 5.54
1113 1170 0.166814 GTGATGCTTGGTTCACGCTC 59.833 55.000 0.00 0.00 33.57 5.03
1116 1173 1.661112 GATGCTTGGTTCACGCTCTAC 59.339 52.381 0.00 0.00 29.82 2.59
1117 1174 0.391228 TGCTTGGTTCACGCTCTACA 59.609 50.000 0.00 0.00 29.82 2.74
1118 1175 0.790814 GCTTGGTTCACGCTCTACAC 59.209 55.000 0.00 0.00 0.00 2.90
1177 1241 0.099082 GATCTCTCGACACACGGGTC 59.901 60.000 0.00 0.00 43.73 4.46
1178 1242 0.608308 ATCTCTCGACACACGGGTCA 60.608 55.000 0.00 0.00 43.73 4.02
1182 1246 0.387367 CTCGACACACGGGTCAAGAG 60.387 60.000 0.00 0.00 42.82 2.85
1209 1273 5.282510 CACGAACTGTGGTAGGATAGATTC 58.717 45.833 0.00 0.00 45.21 2.52
1213 1277 6.015856 CGAACTGTGGTAGGATAGATTCATCT 60.016 42.308 0.00 0.00 40.86 2.90
1216 1280 4.284490 TGTGGTAGGATAGATTCATCTGCC 59.716 45.833 0.00 1.68 37.76 4.85
1219 1283 2.614259 AGGATAGATTCATCTGCCGGT 58.386 47.619 1.90 0.00 37.60 5.28
1242 1309 3.471680 GTTTCACCTGCTGTTCTTCTCT 58.528 45.455 0.00 0.00 0.00 3.10
1264 1331 9.998752 TCTCTTTTTGGGGAATTATTATTACCA 57.001 29.630 7.97 2.67 45.38 3.25
1316 1383 7.653783 CGTAGCTTTTAATTTTTCCATTCACG 58.346 34.615 0.00 0.00 0.00 4.35
1396 1467 2.084546 AGTAAACTTTCCATGCGAGGC 58.915 47.619 0.00 0.00 0.00 4.70
1397 1468 2.084546 GTAAACTTTCCATGCGAGGCT 58.915 47.619 0.00 0.00 0.00 4.58
1456 1527 2.686835 GGAGAGGGCCAGCTGTCT 60.687 66.667 13.81 8.71 0.00 3.41
1477 1548 2.464459 GGCCATGTAGCGCAGACAC 61.464 63.158 16.27 5.98 0.00 3.67
1524 1601 4.406173 GCTGTGCTGCTGCTGCTG 62.406 66.667 27.67 16.73 40.48 4.41
1545 1622 3.834373 CCGCGCCGAAACGTACAG 61.834 66.667 0.00 0.00 34.88 2.74
1546 1623 3.834373 CGCGCCGAAACGTACAGG 61.834 66.667 0.00 0.00 34.88 4.00
1692 1781 9.098355 GCATAATTTCTTCCCCAGTTTTTATTC 57.902 33.333 0.00 0.00 0.00 1.75
1747 1836 8.831550 GCTAAGAATAAATGGAGATTTTCGAGT 58.168 33.333 0.00 0.00 33.63 4.18
1757 1856 7.884816 TGGAGATTTTCGAGTAGTTTTAGTG 57.115 36.000 0.00 0.00 0.00 2.74
1759 1858 6.313164 GGAGATTTTCGAGTAGTTTTAGTGGG 59.687 42.308 0.00 0.00 0.00 4.61
1784 1883 1.128200 TGGGATGGGAGTACGGATTG 58.872 55.000 0.00 0.00 0.00 2.67
2193 2320 1.361668 CCACGCCTCCTTCGTTGATG 61.362 60.000 0.00 0.00 38.19 3.07
2217 2344 1.219393 CCGCTTGGACTCTTCCCTC 59.781 63.158 0.00 0.00 42.01 4.30
2260 2387 2.365635 TCTGGTAGAGGCTGGCCC 60.366 66.667 8.11 0.20 36.58 5.80
2309 2436 3.173668 TCTGTACAACGAGCTGTGTTT 57.826 42.857 0.00 0.00 0.00 2.83
2414 2541 3.246619 TGGTTTGTTTCGCTTGTGTTTC 58.753 40.909 0.00 0.00 0.00 2.78
2516 2643 2.036556 CGCAGCGTGTTGAAATCTTT 57.963 45.000 6.65 0.00 0.00 2.52
2519 2646 2.543653 GCAGCGTGTTGAAATCTTTGGT 60.544 45.455 0.00 0.00 0.00 3.67
2551 2678 1.355005 GAAGAGAAGAAGGTGAGCGC 58.645 55.000 0.00 0.00 0.00 5.92
2553 2680 1.188219 AGAGAAGAAGGTGAGCGCCA 61.188 55.000 2.29 0.00 0.00 5.69
2596 2723 0.752658 GGTGCCTGTTTTCTTGCCTT 59.247 50.000 0.00 0.00 0.00 4.35
2601 2728 2.287849 GCCTGTTTTCTTGCCTTGTCTC 60.288 50.000 0.00 0.00 0.00 3.36
2608 2735 2.867624 TCTTGCCTTGTCTCAATTGCT 58.132 42.857 0.00 0.00 0.00 3.91
2697 2826 1.351080 CCTGGGTCATGGAGATGGCT 61.351 60.000 0.00 0.00 34.34 4.75
2760 2889 0.657840 CGGATTGGCAGGATTTCGTC 59.342 55.000 0.00 0.00 0.00 4.20
2856 2985 2.277591 GCTCATGGCCAACCTTGCA 61.278 57.895 10.96 0.00 40.21 4.08
2875 3004 0.178990 ACCCAAGACAAAGGTGAGCC 60.179 55.000 0.00 0.00 30.97 4.70
2939 3068 8.067751 TCCATAGTACAGTAGCCATGATATTC 57.932 38.462 0.00 0.00 0.00 1.75
2956 3085 7.083062 TGATATTCTATTGGTCTGCTTCCAT 57.917 36.000 0.00 0.00 34.75 3.41
2971 3100 9.384764 GTCTGCTTCCATTATACTTTTCTAGTT 57.615 33.333 0.00 0.00 38.33 2.24
2974 3103 7.773690 TGCTTCCATTATACTTTTCTAGTTCCC 59.226 37.037 0.00 0.00 38.33 3.97
2985 3114 4.877378 TTCTAGTTCCCGCTTTCAACTA 57.123 40.909 0.00 0.00 32.56 2.24
2990 3119 3.941483 AGTTCCCGCTTTCAACTATGATG 59.059 43.478 0.00 0.00 34.96 3.07
2993 3122 4.439057 TCCCGCTTTCAACTATGATGTAC 58.561 43.478 0.00 0.00 34.96 2.90
2994 3123 4.161565 TCCCGCTTTCAACTATGATGTACT 59.838 41.667 0.00 0.00 34.96 2.73
2995 3124 4.508124 CCCGCTTTCAACTATGATGTACTC 59.492 45.833 0.00 0.00 34.96 2.59
2996 3125 4.508124 CCGCTTTCAACTATGATGTACTCC 59.492 45.833 0.00 0.00 34.96 3.85
2997 3126 4.508124 CGCTTTCAACTATGATGTACTCCC 59.492 45.833 0.00 0.00 34.96 4.30
2998 3127 5.675538 GCTTTCAACTATGATGTACTCCCT 58.324 41.667 0.00 0.00 34.96 4.20
2999 3128 5.755861 GCTTTCAACTATGATGTACTCCCTC 59.244 44.000 0.00 0.00 34.96 4.30
3000 3129 5.871396 TTCAACTATGATGTACTCCCTCC 57.129 43.478 0.00 0.00 34.96 4.30
3001 3130 3.889538 TCAACTATGATGTACTCCCTCCG 59.110 47.826 0.00 0.00 0.00 4.63
3002 3131 3.596940 ACTATGATGTACTCCCTCCGT 57.403 47.619 0.00 0.00 0.00 4.69
3003 3132 3.912248 ACTATGATGTACTCCCTCCGTT 58.088 45.455 0.00 0.00 0.00 4.44
3004 3133 3.890147 ACTATGATGTACTCCCTCCGTTC 59.110 47.826 0.00 0.00 0.00 3.95
3005 3134 1.481871 TGATGTACTCCCTCCGTTCC 58.518 55.000 0.00 0.00 0.00 3.62
3006 3135 1.006758 TGATGTACTCCCTCCGTTCCT 59.993 52.381 0.00 0.00 0.00 3.36
3007 3136 2.242965 TGATGTACTCCCTCCGTTCCTA 59.757 50.000 0.00 0.00 0.00 2.94
3008 3137 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
3009 3138 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
3010 3139 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
3011 3140 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
3012 3141 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
3013 3142 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
3014 3143 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
3015 3144 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3016 3145 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3017 3146 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3018 3147 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3019 3148 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3020 3149 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3021 3150 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
3022 3151 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
3050 3179 9.357652 GAGATTCTACTAGGTAGACTACATACG 57.642 40.741 14.48 8.15 43.65 3.06
3051 3180 8.313292 AGATTCTACTAGGTAGACTACATACGG 58.687 40.741 14.48 3.88 43.65 4.02
3052 3181 7.603180 TTCTACTAGGTAGACTACATACGGA 57.397 40.000 14.48 5.33 43.65 4.69
3053 3182 7.225784 TCTACTAGGTAGACTACATACGGAG 57.774 44.000 14.48 10.89 39.81 4.63
3054 3183 4.640364 ACTAGGTAGACTACATACGGAGC 58.360 47.826 14.48 0.00 0.00 4.70
3055 3184 3.572632 AGGTAGACTACATACGGAGCA 57.427 47.619 14.48 0.00 0.00 4.26
3056 3185 3.478509 AGGTAGACTACATACGGAGCAG 58.521 50.000 14.48 0.00 0.00 4.24
3057 3186 3.136077 AGGTAGACTACATACGGAGCAGA 59.864 47.826 14.48 0.00 0.00 4.26
3058 3187 3.881688 GGTAGACTACATACGGAGCAGAA 59.118 47.826 14.48 0.00 0.00 3.02
3059 3188 4.261114 GGTAGACTACATACGGAGCAGAAC 60.261 50.000 14.48 0.00 0.00 3.01
3060 3189 2.355132 AGACTACATACGGAGCAGAACG 59.645 50.000 0.00 0.00 0.00 3.95
3061 3190 2.353889 GACTACATACGGAGCAGAACGA 59.646 50.000 0.00 0.00 0.00 3.85
3062 3191 2.751259 ACTACATACGGAGCAGAACGAA 59.249 45.455 0.00 0.00 0.00 3.85
3063 3192 2.961526 ACATACGGAGCAGAACGAAT 57.038 45.000 0.00 0.00 0.00 3.34
3064 3193 2.540515 ACATACGGAGCAGAACGAATG 58.459 47.619 0.00 0.00 0.00 2.67
3065 3194 2.165641 ACATACGGAGCAGAACGAATGA 59.834 45.455 0.00 0.00 0.00 2.57
3066 3195 3.186909 CATACGGAGCAGAACGAATGAA 58.813 45.455 0.00 0.00 0.00 2.57
3067 3196 2.386661 ACGGAGCAGAACGAATGAAT 57.613 45.000 0.00 0.00 0.00 2.57
3068 3197 2.271800 ACGGAGCAGAACGAATGAATC 58.728 47.619 0.00 0.00 0.00 2.52
3069 3198 2.093973 ACGGAGCAGAACGAATGAATCT 60.094 45.455 0.00 0.00 0.00 2.40
3070 3199 3.130516 ACGGAGCAGAACGAATGAATCTA 59.869 43.478 0.00 0.00 0.00 1.98
3071 3200 4.112634 CGGAGCAGAACGAATGAATCTAA 58.887 43.478 0.00 0.00 0.00 2.10
3072 3201 4.566759 CGGAGCAGAACGAATGAATCTAAA 59.433 41.667 0.00 0.00 0.00 1.85
3073 3202 5.500931 CGGAGCAGAACGAATGAATCTAAAC 60.501 44.000 0.00 0.00 0.00 2.01
3074 3203 5.582665 GGAGCAGAACGAATGAATCTAAACT 59.417 40.000 0.00 0.00 0.00 2.66
3075 3204 6.092807 GGAGCAGAACGAATGAATCTAAACTT 59.907 38.462 0.00 0.00 0.00 2.66
3076 3205 7.277981 GGAGCAGAACGAATGAATCTAAACTTA 59.722 37.037 0.00 0.00 0.00 2.24
3077 3206 8.547967 AGCAGAACGAATGAATCTAAACTTAA 57.452 30.769 0.00 0.00 0.00 1.85
3078 3207 8.999431 AGCAGAACGAATGAATCTAAACTTAAA 58.001 29.630 0.00 0.00 0.00 1.52
3079 3208 9.607285 GCAGAACGAATGAATCTAAACTTAAAA 57.393 29.630 0.00 0.00 0.00 1.52
3083 3212 9.906660 AACGAATGAATCTAAACTTAAAATGCA 57.093 25.926 0.00 0.00 0.00 3.96
3098 3227 9.944376 ACTTAAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
3102 3231 7.953158 AATGCATCTATATACATCCGTATGC 57.047 36.000 0.00 0.00 38.79 3.14
3103 3232 5.519722 TGCATCTATATACATCCGTATGCG 58.480 41.667 0.00 0.00 38.79 4.73
3118 3247 5.511088 CGTATGCGGTTTATAGTGGAATC 57.489 43.478 0.00 0.00 0.00 2.52
3119 3248 5.227908 CGTATGCGGTTTATAGTGGAATCT 58.772 41.667 0.00 0.00 0.00 2.40
3120 3249 5.345202 CGTATGCGGTTTATAGTGGAATCTC 59.655 44.000 0.00 0.00 0.00 2.75
3121 3250 5.552870 ATGCGGTTTATAGTGGAATCTCT 57.447 39.130 0.00 0.00 0.00 3.10
3122 3251 6.665992 ATGCGGTTTATAGTGGAATCTCTA 57.334 37.500 0.00 0.00 0.00 2.43
3123 3252 5.839621 TGCGGTTTATAGTGGAATCTCTAC 58.160 41.667 0.00 0.00 0.00 2.59
3124 3253 5.361571 TGCGGTTTATAGTGGAATCTCTACA 59.638 40.000 0.00 0.00 29.47 2.74
3125 3254 6.127281 TGCGGTTTATAGTGGAATCTCTACAA 60.127 38.462 0.00 0.00 29.47 2.41
3126 3255 6.759827 GCGGTTTATAGTGGAATCTCTACAAA 59.240 38.462 0.00 0.00 29.47 2.83
3127 3256 7.042658 GCGGTTTATAGTGGAATCTCTACAAAG 60.043 40.741 0.00 0.00 29.47 2.77
3128 3257 8.195436 CGGTTTATAGTGGAATCTCTACAAAGA 58.805 37.037 0.00 0.00 29.47 2.52
3129 3258 9.315525 GGTTTATAGTGGAATCTCTACAAAGAC 57.684 37.037 0.00 0.00 29.47 3.01
3134 3263 7.540474 AGTGGAATCTCTACAAAGACTTACA 57.460 36.000 0.00 0.00 29.47 2.41
3135 3264 8.140112 AGTGGAATCTCTACAAAGACTTACAT 57.860 34.615 0.00 0.00 29.47 2.29
3136 3265 8.598041 AGTGGAATCTCTACAAAGACTTACATT 58.402 33.333 0.00 0.00 29.47 2.71
3137 3266 9.220767 GTGGAATCTCTACAAAGACTTACATTT 57.779 33.333 0.00 0.00 0.00 2.32
3143 3272 9.924650 TCTCTACAAAGACTTACATTTAGGAAC 57.075 33.333 0.00 0.00 0.00 3.62
3144 3273 8.752766 TCTACAAAGACTTACATTTAGGAACG 57.247 34.615 0.00 0.00 0.00 3.95
3145 3274 6.796705 ACAAAGACTTACATTTAGGAACGG 57.203 37.500 0.00 0.00 0.00 4.44
3146 3275 6.527423 ACAAAGACTTACATTTAGGAACGGA 58.473 36.000 0.00 0.00 0.00 4.69
3147 3276 6.649557 ACAAAGACTTACATTTAGGAACGGAG 59.350 38.462 0.00 0.00 0.00 4.63
3148 3277 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
3149 3278 4.161754 AGACTTACATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
3150 3279 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
3151 3280 4.161754 ACTTACATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
3152 3281 2.547990 ACATTTAGGAACGGAGGGAGT 58.452 47.619 0.00 0.00 0.00 3.85
3153 3282 3.716431 ACATTTAGGAACGGAGGGAGTA 58.284 45.455 0.00 0.00 0.00 2.59
3154 3283 3.705072 ACATTTAGGAACGGAGGGAGTAG 59.295 47.826 0.00 0.00 0.00 2.57
3155 3284 3.744940 TTTAGGAACGGAGGGAGTAGA 57.255 47.619 0.00 0.00 0.00 2.59
3156 3285 3.744940 TTAGGAACGGAGGGAGTAGAA 57.255 47.619 0.00 0.00 0.00 2.10
3157 3286 2.146920 AGGAACGGAGGGAGTAGAAG 57.853 55.000 0.00 0.00 0.00 2.85
3171 3300 7.746703 AGGGAGTAGAAGTAAGTTTTGAATGT 58.253 34.615 0.00 0.00 0.00 2.71
3245 3374 8.211116 TGGATTAGCAATTGCAATTTATTTGG 57.789 30.769 30.89 10.81 45.16 3.28
3252 3381 9.398538 AGCAATTGCAATTTATTTGGACATAAT 57.601 25.926 30.89 1.40 45.16 1.28
3354 3543 5.798125 TGCCCATTCTTTTTGTAACATGA 57.202 34.783 0.00 0.00 0.00 3.07
3367 3556 9.593134 TTTTTGTAACATGAATTACTGTTGCTT 57.407 25.926 16.30 0.00 38.36 3.91
3674 3863 1.476488 GTTGACAGCACCAACCAAGTT 59.524 47.619 0.00 0.00 38.28 2.66
3722 3911 2.163818 TCGGAAACTTCTGCATCGTT 57.836 45.000 0.00 0.00 33.56 3.85
4271 4460 2.863809 CCTGAGCAGGTTGGTAAAACT 58.136 47.619 8.38 0.00 43.61 2.66
4365 4554 6.824305 ATGAAGACTTGGTATGAAACTTGG 57.176 37.500 0.00 0.00 0.00 3.61
4525 4714 2.463589 TTTCGGCTGTAGTGGCTGGG 62.464 60.000 0.00 0.00 36.77 4.45
4544 4733 3.269381 TGGGGAGTCAATTTCTAATGCCT 59.731 43.478 0.00 0.00 0.00 4.75
5022 5211 3.873952 TGCATTTTGTTAACCTGGTTTGC 59.126 39.130 18.58 18.54 0.00 3.68
5078 5267 2.159544 GCTGCAAGAGAAGAAGCACATC 60.160 50.000 0.00 0.00 34.07 3.06
5341 5530 5.797051 TGATCACATCACATTCAGACTCAA 58.203 37.500 0.00 0.00 33.59 3.02
5416 5605 4.400251 TCCGTATTGTGGTAAGTACCTCAG 59.600 45.833 11.08 2.29 46.63 3.35
5417 5606 4.110482 CGTATTGTGGTAAGTACCTCAGC 58.890 47.826 11.08 6.59 46.63 4.26
5437 5626 2.811873 GCGATATTTCTGCCCCACTGAT 60.812 50.000 0.00 0.00 0.00 2.90
5554 5743 4.401022 TCATGGTCCTTATCATTGCCATC 58.599 43.478 0.00 0.00 34.84 3.51
5596 5785 4.693566 TCTTTTGTTGTCCATTAGTAGCCG 59.306 41.667 0.00 0.00 0.00 5.52
5609 5798 1.955080 AGTAGCCGATGCAGGTACTAC 59.045 52.381 12.96 11.54 41.13 2.73
5913 6103 5.972107 ATTTCAGTGGGATGTTCTTTCTG 57.028 39.130 0.00 0.00 0.00 3.02
6098 6288 1.061546 TGGTTACCGCCTTCCTTCTT 58.938 50.000 0.00 0.00 0.00 2.52
6117 6307 3.249799 TCTTGCACAATTGGTACGTGAAG 59.750 43.478 10.83 5.06 32.23 3.02
6155 6345 6.088616 GCAAAGAAAGAAATTCAGGACAATCG 59.911 38.462 0.00 0.00 40.72 3.34
6418 6608 6.148150 TCAGCACCTTTATTTTTAGGTACACG 59.852 38.462 0.00 0.00 42.81 4.49
6424 6614 9.154847 ACCTTTATTTTTAGGTACACGTACATC 57.845 33.333 9.43 0.00 42.87 3.06
6425 6615 8.606602 CCTTTATTTTTAGGTACACGTACATCC 58.393 37.037 9.43 0.00 37.78 3.51
6426 6616 9.374838 CTTTATTTTTAGGTACACGTACATCCT 57.625 33.333 9.43 0.00 37.78 3.24
6665 6867 9.851686 TGAGATTGCAAGGTATATTATCTTTGT 57.148 29.630 4.94 0.00 0.00 2.83
6675 6877 8.903820 AGGTATATTATCTTTGTGCTTCCAAAC 58.096 33.333 0.00 0.00 31.38 2.93
6726 6929 3.509575 TCGTTGATTGCTAATGCCCTTTT 59.490 39.130 0.00 0.00 38.71 2.27
6727 6930 4.021544 TCGTTGATTGCTAATGCCCTTTTT 60.022 37.500 0.00 0.00 38.71 1.94
7173 7377 1.849116 CCCCATGCTTGCTATCCCT 59.151 57.895 0.00 0.00 0.00 4.20
7300 7542 3.034721 ACAAGCACAATTTGGCATGAG 57.965 42.857 16.52 6.04 33.34 2.90
7307 7549 3.081061 ACAATTTGGCATGAGCTTACGA 58.919 40.909 0.00 0.00 41.70 3.43
7309 7551 4.158394 ACAATTTGGCATGAGCTTACGATT 59.842 37.500 0.00 0.00 41.70 3.34
7313 7555 3.342719 TGGCATGAGCTTACGATTGAAA 58.657 40.909 0.00 0.00 41.70 2.69
7314 7556 3.947196 TGGCATGAGCTTACGATTGAAAT 59.053 39.130 0.00 0.00 41.70 2.17
7315 7557 4.201940 TGGCATGAGCTTACGATTGAAATG 60.202 41.667 0.00 0.00 41.70 2.32
7317 7559 5.335127 GCATGAGCTTACGATTGAAATGTT 58.665 37.500 0.00 0.00 37.91 2.71
7318 7560 5.801947 GCATGAGCTTACGATTGAAATGTTT 59.198 36.000 0.00 0.00 37.91 2.83
7319 7561 6.966632 GCATGAGCTTACGATTGAAATGTTTA 59.033 34.615 0.00 0.00 37.91 2.01
7337 7579 7.709269 ATGTTTATATGTGGTTAGCTACACG 57.291 36.000 9.26 0.00 38.90 4.49
7338 7580 6.044046 TGTTTATATGTGGTTAGCTACACGG 58.956 40.000 9.26 0.00 38.90 4.94
7339 7581 6.127394 TGTTTATATGTGGTTAGCTACACGGA 60.127 38.462 9.26 1.71 38.90 4.69
7340 7582 2.961526 ATGTGGTTAGCTACACGGAG 57.038 50.000 9.26 0.00 38.90 4.63
7342 7584 0.175073 GTGGTTAGCTACACGGAGGG 59.825 60.000 0.00 0.00 0.00 4.30
7343 7585 0.040058 TGGTTAGCTACACGGAGGGA 59.960 55.000 0.00 0.00 0.00 4.20
7357 7638 5.183228 CACGGAGGGAGTAATTGTGTAAAT 58.817 41.667 0.00 0.00 0.00 1.40
7358 7639 6.070653 ACACGGAGGGAGTAATTGTGTAAATA 60.071 38.462 0.00 0.00 37.32 1.40
7359 7640 6.819649 CACGGAGGGAGTAATTGTGTAAATAA 59.180 38.462 0.00 0.00 0.00 1.40
7360 7641 7.011109 CACGGAGGGAGTAATTGTGTAAATAAG 59.989 40.741 0.00 0.00 0.00 1.73
7361 7642 6.018180 CGGAGGGAGTAATTGTGTAAATAAGC 60.018 42.308 0.00 0.00 0.00 3.09
7378 7659 3.253955 CGTAGCTGGTTGTGGTGC 58.746 61.111 0.00 0.00 0.00 5.01
7379 7660 2.667318 CGTAGCTGGTTGTGGTGCG 61.667 63.158 0.00 0.00 35.18 5.34
7391 7672 3.568000 TGGTGCGCCAATCATACTT 57.432 47.368 18.77 0.00 42.83 2.24
7392 7673 1.093972 TGGTGCGCCAATCATACTTG 58.906 50.000 18.77 0.00 42.83 3.16
7394 7675 1.094785 GTGCGCCAATCATACTTGGT 58.905 50.000 4.18 0.00 46.19 3.67
7494 7803 5.077134 AGATAAATTGTTCCTTGCAAGGC 57.923 39.130 36.24 24.89 46.06 4.35
7558 7867 7.656137 GGAAGCAATAATACCGACTATTCTTCA 59.344 37.037 0.00 0.00 31.67 3.02
7559 7868 7.948278 AGCAATAATACCGACTATTCTTCAC 57.052 36.000 0.00 0.00 0.00 3.18
7560 7869 7.497595 AGCAATAATACCGACTATTCTTCACA 58.502 34.615 0.00 0.00 0.00 3.58
7577 7890 1.534595 CACAGCACAGAAAGCTCTTCC 59.465 52.381 0.00 0.00 41.14 3.46
7579 7892 1.805345 CAGCACAGAAAGCTCTTCCTG 59.195 52.381 0.00 0.00 41.14 3.86
7589 7902 1.994507 CTCTTCCTGCTGCCCTCCT 60.995 63.158 0.00 0.00 0.00 3.69
7597 7910 3.160585 CTGCCCTCCTCCACACAA 58.839 61.111 0.00 0.00 0.00 3.33
7601 7914 1.133199 TGCCCTCCTCCACACAATTTT 60.133 47.619 0.00 0.00 0.00 1.82
7632 7945 7.565398 ACAATACAGTACTCTCTACATCCCAAT 59.435 37.037 0.00 0.00 0.00 3.16
7726 8040 3.124921 CACCCACGGTCGCCATTC 61.125 66.667 0.00 0.00 31.02 2.67
7729 8043 4.402528 CCACGGTCGCCATTCCCA 62.403 66.667 0.00 0.00 0.00 4.37
7730 8044 3.124921 CACGGTCGCCATTCCCAC 61.125 66.667 0.00 0.00 0.00 4.61
7731 8045 3.632080 ACGGTCGCCATTCCCACA 61.632 61.111 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 0.536460 ATTCCGCTCCACCGTTGTTT 60.536 50.000 0.00 0.00 0.00 2.83
65 66 1.072505 ATTCCGCTCCACCGTTGTT 59.927 52.632 0.00 0.00 0.00 2.83
67 68 2.398554 CCATTCCGCTCCACCGTTG 61.399 63.158 0.00 0.00 0.00 4.10
105 125 3.147132 CTGGGTTGGGTTTTGGCC 58.853 61.111 0.00 0.00 0.00 5.36
109 129 2.523168 CGGGCTGGGTTGGGTTTT 60.523 61.111 0.00 0.00 0.00 2.43
372 401 1.039785 AGATAGCGAGCACAGGCAGA 61.040 55.000 0.00 0.00 44.61 4.26
378 407 2.025719 CGGAGAGATAGCGAGCACA 58.974 57.895 0.00 0.00 0.00 4.57
425 459 3.691297 TTAGGCCGTCCCTCCCTCC 62.691 68.421 0.00 0.00 44.96 4.30
899 947 2.730672 CTCTAGCACGCACCAACGC 61.731 63.158 0.00 0.00 36.19 4.84
900 948 0.944311 AACTCTAGCACGCACCAACG 60.944 55.000 0.00 0.00 39.50 4.10
901 949 0.512952 CAACTCTAGCACGCACCAAC 59.487 55.000 0.00 0.00 0.00 3.77
902 950 0.602638 CCAACTCTAGCACGCACCAA 60.603 55.000 0.00 0.00 0.00 3.67
1074 1131 4.933064 CGAGAGACGGGGCATCGC 62.933 72.222 0.00 0.00 38.46 4.58
1117 1174 2.667318 CGAAACGAGCACCGCATGT 61.667 57.895 0.00 0.00 43.32 3.21
1118 1175 1.896339 TTCGAAACGAGCACCGCATG 61.896 55.000 0.00 0.00 43.32 4.06
1124 1181 0.111089 CAGCAGTTCGAAACGAGCAC 60.111 55.000 0.00 0.26 39.43 4.40
1125 1182 0.529773 ACAGCAGTTCGAAACGAGCA 60.530 50.000 0.00 0.00 39.43 4.26
1170 1227 2.022129 GTGCGACTCTTGACCCGTG 61.022 63.158 0.00 0.00 0.00 4.94
1172 1229 2.742710 TTCGTGCGACTCTTGACCCG 62.743 60.000 0.00 0.00 0.00 5.28
1177 1241 0.504384 CACAGTTCGTGCGACTCTTG 59.496 55.000 0.00 0.00 39.19 3.02
1178 1242 0.597637 CCACAGTTCGTGCGACTCTT 60.598 55.000 0.00 0.00 44.91 2.85
1182 1246 1.007336 CCTACCACAGTTCGTGCGAC 61.007 60.000 0.00 0.00 44.91 5.19
1209 1273 1.635663 GGTGAAACGACCGGCAGATG 61.636 60.000 0.00 0.00 38.12 2.90
1213 1277 2.280524 CAGGTGAAACGACCGGCA 60.281 61.111 0.00 0.00 41.35 5.69
1216 1280 1.157870 AACAGCAGGTGAAACGACCG 61.158 55.000 6.61 0.00 41.35 4.79
1219 1283 2.158957 AGAAGAACAGCAGGTGAAACGA 60.159 45.455 6.61 0.00 38.12 3.85
1242 1309 7.418025 CCGCTGGTAATAATAATTCCCCAAAAA 60.418 37.037 0.00 0.00 30.15 1.94
1396 1467 1.495878 GCTCACATGGCGAGATACAG 58.504 55.000 16.26 0.00 31.84 2.74
1397 1468 3.667448 GCTCACATGGCGAGATACA 57.333 52.632 16.26 0.00 31.84 2.29
1456 1527 0.249868 GTCTGCGCTACATGGCCATA 60.250 55.000 20.30 2.28 0.00 2.74
1477 1548 1.635487 TCAGAGGAAGAAACATGGGGG 59.365 52.381 0.00 0.00 0.00 5.40
1532 1609 1.743995 ATGCCCTGTACGTTTCGGC 60.744 57.895 0.00 0.29 40.16 5.54
1628 1705 0.179194 GCTCGTATCCCGCTCGTATC 60.179 60.000 0.00 0.00 36.19 2.24
1630 1707 1.524393 TGCTCGTATCCCGCTCGTA 60.524 57.895 0.00 0.00 36.19 3.43
1631 1708 2.827190 TGCTCGTATCCCGCTCGT 60.827 61.111 0.00 0.00 36.19 4.18
1633 1710 2.027751 GGTGCTCGTATCCCGCTC 59.972 66.667 0.00 0.00 36.19 5.03
1634 1711 3.900892 CGGTGCTCGTATCCCGCT 61.901 66.667 0.00 0.00 36.19 5.52
1635 1712 2.694829 ATTCGGTGCTCGTATCCCGC 62.695 60.000 0.00 0.00 40.23 6.13
1692 1781 7.837202 TTAGTAGTCATTTATTTGTGGACGG 57.163 36.000 0.00 0.00 33.84 4.79
1747 1836 6.126594 CCATCCCACTAATCCCACTAAAACTA 60.127 42.308 0.00 0.00 0.00 2.24
1757 1856 1.821088 ACTCCCATCCCACTAATCCC 58.179 55.000 0.00 0.00 0.00 3.85
1759 1858 2.299297 CCGTACTCCCATCCCACTAATC 59.701 54.545 0.00 0.00 0.00 1.75
1784 1883 4.336280 ACTATCTTTTGACTTCAAGCCCC 58.664 43.478 0.00 0.00 37.15 5.80
2003 2102 3.055719 CAAGATGCGCACCCCGTT 61.056 61.111 14.90 0.00 39.71 4.44
2193 2320 2.514824 GAGTCCAAGCGGGCATCC 60.515 66.667 0.00 0.00 40.51 3.51
2217 2344 0.613260 TGGGGTCAGAACATCCGAAG 59.387 55.000 0.00 0.00 0.00 3.79
2276 2403 4.492611 GTTGTACAGAACAGTAGCTACCC 58.507 47.826 20.31 7.55 39.87 3.69
2279 2406 4.379186 GCTCGTTGTACAGAACAGTAGCTA 60.379 45.833 0.00 0.00 39.87 3.32
2309 2436 5.277974 GCTAGAACAGACAAATCAAACAGCA 60.278 40.000 0.00 0.00 0.00 4.41
2384 2511 3.820467 AGCGAAACAAACCATTGATGAGA 59.180 39.130 0.00 0.00 38.94 3.27
2414 2541 3.217626 GGGGATGTTCTCCTGCAAATAG 58.782 50.000 0.00 0.00 44.28 1.73
2516 2643 1.686587 TCTTCGAGCTTGTTGAGACCA 59.313 47.619 0.00 0.00 0.00 4.02
2519 2646 3.570125 TCTTCTCTTCGAGCTTGTTGAGA 59.430 43.478 18.15 18.15 0.00 3.27
2553 2680 4.357918 ACTTGCATCAGAAACCAGTAGT 57.642 40.909 0.00 0.00 0.00 2.73
2596 2723 2.886523 CCACAAGGAAGCAATTGAGACA 59.113 45.455 10.34 0.00 36.89 3.41
2601 2728 2.229784 GAGACCCACAAGGAAGCAATTG 59.770 50.000 0.00 0.00 39.89 2.32
2608 2735 2.778299 CAAATCGAGACCCACAAGGAA 58.222 47.619 0.00 0.00 39.89 3.36
2670 2799 2.284625 ATGACCCAGGACAGCGGA 60.285 61.111 0.00 0.00 0.00 5.54
2673 2802 1.222936 CTCCATGACCCAGGACAGC 59.777 63.158 0.00 0.00 0.00 4.40
2676 2805 0.471617 CCATCTCCATGACCCAGGAC 59.528 60.000 0.00 0.00 30.57 3.85
2760 2889 1.137086 ACCAGGAGAACGATGATTCCG 59.863 52.381 0.00 0.00 34.87 4.30
2856 2985 0.178990 GGCTCACCTTTGTCTTGGGT 60.179 55.000 0.00 0.00 0.00 4.51
2914 3043 7.895962 AGAATATCATGGCTACTGTACTATGGA 59.104 37.037 0.00 0.00 0.00 3.41
2923 3052 7.548427 CAGACCAATAGAATATCATGGCTACTG 59.452 40.741 0.00 0.00 34.45 2.74
2925 3054 6.314896 GCAGACCAATAGAATATCATGGCTAC 59.685 42.308 0.00 0.00 34.45 3.58
2939 3068 8.682936 AAAGTATAATGGAAGCAGACCAATAG 57.317 34.615 0.00 0.00 40.93 1.73
2956 3085 7.388437 TGAAAGCGGGAACTAGAAAAGTATAA 58.612 34.615 0.00 0.00 37.50 0.98
2971 3100 3.627395 ACATCATAGTTGAAAGCGGGA 57.373 42.857 0.00 0.00 34.96 5.14
2974 3103 4.508124 GGGAGTACATCATAGTTGAAAGCG 59.492 45.833 0.00 0.00 34.96 4.68
2985 3114 2.040178 GGAACGGAGGGAGTACATCAT 58.960 52.381 0.00 0.00 0.00 2.45
2990 3119 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
2993 3122 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2994 3123 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2995 3124 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2996 3125 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
2997 3126 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
3024 3153 9.357652 CGTATGTAGTCTACCTAGTAGAATCTC 57.642 40.741 7.89 4.76 45.12 2.75
3025 3154 8.313292 CCGTATGTAGTCTACCTAGTAGAATCT 58.687 40.741 7.89 4.53 45.12 2.40
3026 3155 8.310382 TCCGTATGTAGTCTACCTAGTAGAATC 58.690 40.741 7.89 2.56 45.12 2.52
3027 3156 8.200024 TCCGTATGTAGTCTACCTAGTAGAAT 57.800 38.462 7.56 9.39 45.12 2.40
3028 3157 7.603180 TCCGTATGTAGTCTACCTAGTAGAA 57.397 40.000 7.56 0.00 45.12 2.10
3029 3158 6.295011 GCTCCGTATGTAGTCTACCTAGTAGA 60.295 46.154 7.56 0.32 42.04 2.59
3030 3159 5.868801 GCTCCGTATGTAGTCTACCTAGTAG 59.131 48.000 7.56 0.00 37.47 2.57
3031 3160 5.305386 TGCTCCGTATGTAGTCTACCTAGTA 59.695 44.000 7.56 0.00 0.00 1.82
3032 3161 4.102210 TGCTCCGTATGTAGTCTACCTAGT 59.898 45.833 7.56 0.00 0.00 2.57
3033 3162 4.639334 TGCTCCGTATGTAGTCTACCTAG 58.361 47.826 7.56 0.00 0.00 3.02
3034 3163 4.346127 TCTGCTCCGTATGTAGTCTACCTA 59.654 45.833 7.56 0.00 0.00 3.08
3035 3164 3.136077 TCTGCTCCGTATGTAGTCTACCT 59.864 47.826 7.56 0.35 0.00 3.08
3036 3165 3.474600 TCTGCTCCGTATGTAGTCTACC 58.525 50.000 7.56 0.00 0.00 3.18
3037 3166 4.552378 CGTTCTGCTCCGTATGTAGTCTAC 60.552 50.000 2.81 2.81 0.00 2.59
3038 3167 3.558829 CGTTCTGCTCCGTATGTAGTCTA 59.441 47.826 0.00 0.00 0.00 2.59
3039 3168 2.355132 CGTTCTGCTCCGTATGTAGTCT 59.645 50.000 0.00 0.00 0.00 3.24
3040 3169 2.353889 TCGTTCTGCTCCGTATGTAGTC 59.646 50.000 0.00 0.00 0.00 2.59
3041 3170 2.362736 TCGTTCTGCTCCGTATGTAGT 58.637 47.619 0.00 0.00 0.00 2.73
3042 3171 3.416119 TTCGTTCTGCTCCGTATGTAG 57.584 47.619 0.00 0.00 0.00 2.74
3043 3172 3.379057 TCATTCGTTCTGCTCCGTATGTA 59.621 43.478 0.00 0.00 34.67 2.29
3044 3173 2.165641 TCATTCGTTCTGCTCCGTATGT 59.834 45.455 0.00 0.00 34.67 2.29
3045 3174 2.809446 TCATTCGTTCTGCTCCGTATG 58.191 47.619 0.00 0.00 34.46 2.39
3046 3175 3.520290 TTCATTCGTTCTGCTCCGTAT 57.480 42.857 0.00 0.00 0.00 3.06
3047 3176 3.130516 AGATTCATTCGTTCTGCTCCGTA 59.869 43.478 0.00 0.00 0.00 4.02
3048 3177 2.093973 AGATTCATTCGTTCTGCTCCGT 60.094 45.455 0.00 0.00 0.00 4.69
3049 3178 2.544685 AGATTCATTCGTTCTGCTCCG 58.455 47.619 0.00 0.00 0.00 4.63
3050 3179 5.582665 AGTTTAGATTCATTCGTTCTGCTCC 59.417 40.000 0.00 0.00 0.00 4.70
3051 3180 6.654793 AGTTTAGATTCATTCGTTCTGCTC 57.345 37.500 0.00 0.00 0.00 4.26
3052 3181 8.547967 TTAAGTTTAGATTCATTCGTTCTGCT 57.452 30.769 0.00 0.00 0.00 4.24
3053 3182 9.607285 TTTTAAGTTTAGATTCATTCGTTCTGC 57.393 29.630 0.00 0.00 0.00 4.26
3057 3186 9.906660 TGCATTTTAAGTTTAGATTCATTCGTT 57.093 25.926 0.00 0.00 0.00 3.85
3072 3201 9.944376 ACGGATGTATATAGATGCATTTTAAGT 57.056 29.630 11.19 0.00 38.38 2.24
3076 3205 8.830580 GCATACGGATGTATATAGATGCATTTT 58.169 33.333 9.90 0.00 38.38 1.82
3077 3206 7.169813 CGCATACGGATGTATATAGATGCATTT 59.830 37.037 9.90 0.00 38.38 2.32
3078 3207 6.642540 CGCATACGGATGTATATAGATGCATT 59.357 38.462 9.90 1.23 38.38 3.56
3079 3208 6.152379 CGCATACGGATGTATATAGATGCAT 58.848 40.000 9.90 0.00 40.68 3.96
3080 3209 5.519722 CGCATACGGATGTATATAGATGCA 58.480 41.667 9.90 0.00 39.28 3.96
3096 3225 5.227908 AGATTCCACTATAAACCGCATACG 58.772 41.667 0.00 0.00 39.67 3.06
3097 3226 6.456501 AGAGATTCCACTATAAACCGCATAC 58.543 40.000 0.00 0.00 0.00 2.39
3098 3227 6.665992 AGAGATTCCACTATAAACCGCATA 57.334 37.500 0.00 0.00 0.00 3.14
3099 3228 5.552870 AGAGATTCCACTATAAACCGCAT 57.447 39.130 0.00 0.00 0.00 4.73
3100 3229 5.361571 TGTAGAGATTCCACTATAAACCGCA 59.638 40.000 0.00 0.00 0.00 5.69
3101 3230 5.839621 TGTAGAGATTCCACTATAAACCGC 58.160 41.667 0.00 0.00 0.00 5.68
3102 3231 8.195436 TCTTTGTAGAGATTCCACTATAAACCG 58.805 37.037 0.00 0.00 30.73 4.44
3103 3232 9.315525 GTCTTTGTAGAGATTCCACTATAAACC 57.684 37.037 0.00 0.00 30.73 3.27
3108 3237 9.256228 TGTAAGTCTTTGTAGAGATTCCACTAT 57.744 33.333 0.00 0.00 0.00 2.12
3109 3238 8.645814 TGTAAGTCTTTGTAGAGATTCCACTA 57.354 34.615 0.00 0.00 0.00 2.74
3110 3239 7.540474 TGTAAGTCTTTGTAGAGATTCCACT 57.460 36.000 0.00 0.00 0.00 4.00
3111 3240 8.779354 AATGTAAGTCTTTGTAGAGATTCCAC 57.221 34.615 0.00 0.00 0.00 4.02
3117 3246 9.924650 GTTCCTAAATGTAAGTCTTTGTAGAGA 57.075 33.333 0.00 0.00 0.00 3.10
3118 3247 8.861101 CGTTCCTAAATGTAAGTCTTTGTAGAG 58.139 37.037 0.00 0.00 0.00 2.43
3119 3248 7.816031 CCGTTCCTAAATGTAAGTCTTTGTAGA 59.184 37.037 0.00 0.00 0.00 2.59
3120 3249 7.816031 TCCGTTCCTAAATGTAAGTCTTTGTAG 59.184 37.037 0.00 0.00 0.00 2.74
3121 3250 7.669427 TCCGTTCCTAAATGTAAGTCTTTGTA 58.331 34.615 0.00 0.00 0.00 2.41
3122 3251 6.527423 TCCGTTCCTAAATGTAAGTCTTTGT 58.473 36.000 0.00 0.00 0.00 2.83
3123 3252 6.092259 CCTCCGTTCCTAAATGTAAGTCTTTG 59.908 42.308 0.00 0.00 0.00 2.77
3124 3253 6.171213 CCTCCGTTCCTAAATGTAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
3125 3254 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
3126 3255 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
3127 3256 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
3128 3257 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
3129 3258 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
3130 3259 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
3131 3260 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
3132 3261 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
3133 3262 3.958798 TCTACTCCCTCCGTTCCTAAATG 59.041 47.826 0.00 0.00 0.00 2.32
3134 3263 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
3135 3264 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
3136 3265 3.011032 ACTTCTACTCCCTCCGTTCCTAA 59.989 47.826 0.00 0.00 0.00 2.69
3137 3266 2.579860 ACTTCTACTCCCTCCGTTCCTA 59.420 50.000 0.00 0.00 0.00 2.94
3138 3267 1.358445 ACTTCTACTCCCTCCGTTCCT 59.642 52.381 0.00 0.00 0.00 3.36
3139 3268 1.849977 ACTTCTACTCCCTCCGTTCC 58.150 55.000 0.00 0.00 0.00 3.62
3140 3269 4.015764 ACTTACTTCTACTCCCTCCGTTC 58.984 47.826 0.00 0.00 0.00 3.95
3141 3270 4.044946 ACTTACTTCTACTCCCTCCGTT 57.955 45.455 0.00 0.00 0.00 4.44
3142 3271 3.735720 ACTTACTTCTACTCCCTCCGT 57.264 47.619 0.00 0.00 0.00 4.69
3143 3272 5.047519 TCAAAACTTACTTCTACTCCCTCCG 60.048 44.000 0.00 0.00 0.00 4.63
3144 3273 6.356186 TCAAAACTTACTTCTACTCCCTCC 57.644 41.667 0.00 0.00 0.00 4.30
3145 3274 7.878644 ACATTCAAAACTTACTTCTACTCCCTC 59.121 37.037 0.00 0.00 0.00 4.30
3146 3275 7.746703 ACATTCAAAACTTACTTCTACTCCCT 58.253 34.615 0.00 0.00 0.00 4.20
3147 3276 7.981102 ACATTCAAAACTTACTTCTACTCCC 57.019 36.000 0.00 0.00 0.00 4.30
3171 3300 8.592529 TTCTTTCATGATGGTGGAATTTGATA 57.407 30.769 0.00 0.00 0.00 2.15
3215 3344 4.888326 TTGCAATTGCTAATCCAGGTTT 57.112 36.364 29.37 0.00 42.66 3.27
3223 3352 8.789825 TGTCCAAATAAATTGCAATTGCTAAT 57.210 26.923 29.37 22.36 42.66 1.73
3282 3411 3.194062 GCTGGAGCTTGACTATCAGTTC 58.806 50.000 0.00 0.00 38.21 3.01
3309 3438 7.064016 GGCAAACAAACAAACAGAACTCAATTA 59.936 33.333 0.00 0.00 0.00 1.40
3310 3439 6.128309 GGCAAACAAACAAACAGAACTCAATT 60.128 34.615 0.00 0.00 0.00 2.32
3319 3508 4.190772 AGAATGGGCAAACAAACAAACAG 58.809 39.130 0.00 0.00 0.00 3.16
3354 3543 5.105756 GCACCTGGAATAAGCAACAGTAATT 60.106 40.000 0.00 0.00 0.00 1.40
3367 3556 2.711009 CCATCCCTAAGCACCTGGAATA 59.289 50.000 0.00 0.00 0.00 1.75
3410 3599 3.117701 TGTCACCAGGAACCAAGATTGAA 60.118 43.478 0.00 0.00 0.00 2.69
3536 3725 1.715019 CCCCAGGGTTCTTGGTCACA 61.715 60.000 4.22 0.00 0.00 3.58
3674 3863 3.177884 ACCTGCTGGAAGTGCCCA 61.178 61.111 17.64 0.00 35.30 5.36
3722 3911 0.527600 CGATTCCCACTGCGATCGAA 60.528 55.000 21.57 7.71 42.82 3.71
4365 4554 5.648092 AGTTGCACAGGGTAATAATCTGTTC 59.352 40.000 0.00 0.00 39.43 3.18
4496 4685 5.393027 CCACTACAGCCGAAATAGCATTTTT 60.393 40.000 0.00 0.00 0.00 1.94
4497 4686 4.096382 CCACTACAGCCGAAATAGCATTTT 59.904 41.667 0.00 0.00 0.00 1.82
4525 4714 6.349300 TCACTAGGCATTAGAAATTGACTCC 58.651 40.000 0.00 0.00 32.22 3.85
4888 5077 2.771943 AGGAAGTGACTCAAGTGAACCA 59.228 45.455 0.00 0.00 0.00 3.67
5007 5196 3.304794 GCATAACGCAAACCAGGTTAACA 60.305 43.478 4.87 0.00 41.79 2.41
5022 5211 3.865164 TCATACTTGTGCTCTGCATAACG 59.135 43.478 0.00 0.00 41.91 3.18
5078 5267 2.168521 ACCATCTCCAGTCATACCAACG 59.831 50.000 0.00 0.00 0.00 4.10
5341 5530 5.779529 AACACATGACAGAAAAAGAGCAT 57.220 34.783 0.00 0.00 0.00 3.79
5416 5605 0.947244 CAGTGGGGCAGAAATATCGC 59.053 55.000 0.00 0.00 0.00 4.58
5417 5606 2.620251 TCAGTGGGGCAGAAATATCG 57.380 50.000 0.00 0.00 0.00 2.92
5527 5716 4.147321 CAATGATAAGGACCATGAAGGGG 58.853 47.826 0.00 0.00 43.89 4.79
5554 5743 8.906867 ACAAAAGAATACATACCATCATTGAGG 58.093 33.333 0.00 0.00 0.00 3.86
5596 5785 0.177141 TTGGCCGTAGTACCTGCATC 59.823 55.000 0.00 0.00 0.00 3.91
5859 6049 6.313905 ACCAGAAGTTTAGATGCAAAGATACG 59.686 38.462 0.00 0.00 0.00 3.06
5913 6103 7.985634 TGTTCTGCACAAAGAAATTTAAGTC 57.014 32.000 0.00 0.00 37.90 3.01
6098 6288 2.839975 TCTTCACGTACCAATTGTGCA 58.160 42.857 4.43 0.00 33.69 4.57
6136 6326 6.660949 AGGATTCGATTGTCCTGAATTTCTTT 59.339 34.615 12.23 0.00 43.11 2.52
6155 6345 5.491982 TCAAGAAGGTTCAGCTAAGGATTC 58.508 41.667 0.00 0.00 0.00 2.52
6418 6608 4.274459 GTCATCATTTGCTCCAGGATGTAC 59.726 45.833 0.00 0.00 37.29 2.90
6424 6614 1.064166 AGGGTCATCATTTGCTCCAGG 60.064 52.381 0.00 0.00 0.00 4.45
6425 6615 2.092538 AGAGGGTCATCATTTGCTCCAG 60.093 50.000 0.00 0.00 0.00 3.86
6426 6616 1.918262 AGAGGGTCATCATTTGCTCCA 59.082 47.619 0.00 0.00 0.00 3.86
6664 6866 5.586243 TGATCTATTAGCAGTTTGGAAGCAC 59.414 40.000 0.00 0.00 0.00 4.40
6665 6867 5.744171 TGATCTATTAGCAGTTTGGAAGCA 58.256 37.500 0.00 0.00 0.00 3.91
6666 6868 6.018343 GTCTGATCTATTAGCAGTTTGGAAGC 60.018 42.308 0.00 0.00 42.45 3.86
6675 6877 5.334802 CCTGACTCGTCTGATCTATTAGCAG 60.335 48.000 5.63 0.00 43.24 4.24
6726 6929 5.104402 TCAACCTGCAGATAATCATCAGGAA 60.104 40.000 17.39 6.06 45.31 3.36
6727 6930 4.409901 TCAACCTGCAGATAATCATCAGGA 59.590 41.667 17.39 2.80 45.31 3.86
7173 7377 7.883391 TTGTCTTTGTATAAACCCAAGTGAA 57.117 32.000 0.00 0.00 0.00 3.18
7223 7427 3.981211 TGAAACTCCATTGCAGAAAAGC 58.019 40.909 0.00 0.00 0.00 3.51
7256 7461 5.961396 AATATGTACTCCTAGTGCGGTAG 57.039 43.478 0.00 0.00 33.27 3.18
7300 7542 9.169468 CCACATATAAACATTTCAATCGTAAGC 57.831 33.333 0.00 0.00 37.18 3.09
7309 7551 9.674068 TGTAGCTAACCACATATAAACATTTCA 57.326 29.630 0.00 0.00 0.00 2.69
7313 7555 6.704493 CCGTGTAGCTAACCACATATAAACAT 59.296 38.462 13.22 0.00 0.00 2.71
7314 7556 6.044046 CCGTGTAGCTAACCACATATAAACA 58.956 40.000 13.22 0.00 0.00 2.83
7315 7557 6.275335 TCCGTGTAGCTAACCACATATAAAC 58.725 40.000 13.22 0.00 0.00 2.01
7317 7559 5.010314 CCTCCGTGTAGCTAACCACATATAA 59.990 44.000 13.22 0.00 0.00 0.98
7318 7560 4.521639 CCTCCGTGTAGCTAACCACATATA 59.478 45.833 13.22 0.00 0.00 0.86
7319 7561 3.321111 CCTCCGTGTAGCTAACCACATAT 59.679 47.826 13.22 0.00 0.00 1.78
7332 7574 3.167485 ACACAATTACTCCCTCCGTGTA 58.833 45.455 0.00 0.00 34.55 2.90
7337 7579 6.018180 CGCTTATTTACACAATTACTCCCTCC 60.018 42.308 0.00 0.00 0.00 4.30
7338 7580 6.537660 ACGCTTATTTACACAATTACTCCCTC 59.462 38.462 0.00 0.00 0.00 4.30
7339 7581 6.412214 ACGCTTATTTACACAATTACTCCCT 58.588 36.000 0.00 0.00 0.00 4.20
7340 7582 6.673154 ACGCTTATTTACACAATTACTCCC 57.327 37.500 0.00 0.00 0.00 4.30
7342 7584 8.056571 CAGCTACGCTTATTTACACAATTACTC 58.943 37.037 0.00 0.00 36.40 2.59
7343 7585 7.011109 CCAGCTACGCTTATTTACACAATTACT 59.989 37.037 0.00 0.00 36.40 2.24
7357 7638 0.682852 ACCACAACCAGCTACGCTTA 59.317 50.000 0.00 0.00 36.40 3.09
7358 7639 0.884704 CACCACAACCAGCTACGCTT 60.885 55.000 0.00 0.00 36.40 4.68
7359 7640 1.301716 CACCACAACCAGCTACGCT 60.302 57.895 0.00 0.00 40.77 5.07
7360 7641 2.966309 GCACCACAACCAGCTACGC 61.966 63.158 0.00 0.00 0.00 4.42
7361 7642 2.667318 CGCACCACAACCAGCTACG 61.667 63.158 0.00 0.00 0.00 3.51
7381 7662 7.148573 GGCGTATAGAATCACCAAGTATGATTG 60.149 40.741 5.01 0.00 44.85 2.67
7382 7663 6.874134 GGCGTATAGAATCACCAAGTATGATT 59.126 38.462 0.00 0.00 46.93 2.57
7383 7664 6.014584 TGGCGTATAGAATCACCAAGTATGAT 60.015 38.462 0.00 0.00 38.47 2.45
7385 7666 5.538118 TGGCGTATAGAATCACCAAGTATG 58.462 41.667 0.00 0.00 0.00 2.39
7386 7667 5.538813 TCTGGCGTATAGAATCACCAAGTAT 59.461 40.000 0.00 0.00 0.00 2.12
7387 7668 4.891168 TCTGGCGTATAGAATCACCAAGTA 59.109 41.667 0.00 0.00 0.00 2.24
7388 7669 3.704566 TCTGGCGTATAGAATCACCAAGT 59.295 43.478 0.00 0.00 0.00 3.16
7389 7670 4.051922 GTCTGGCGTATAGAATCACCAAG 58.948 47.826 0.00 0.00 0.00 3.61
7390 7671 3.490249 CGTCTGGCGTATAGAATCACCAA 60.490 47.826 0.00 0.00 35.54 3.67
7391 7672 2.034179 CGTCTGGCGTATAGAATCACCA 59.966 50.000 0.00 0.00 35.54 4.17
7392 7673 2.292569 TCGTCTGGCGTATAGAATCACC 59.707 50.000 0.09 0.00 42.13 4.02
7394 7675 2.552743 CCTCGTCTGGCGTATAGAATCA 59.447 50.000 0.09 0.00 42.13 2.57
7395 7676 2.812591 TCCTCGTCTGGCGTATAGAATC 59.187 50.000 0.09 0.00 42.13 2.52
7436 7740 1.376683 CGCTTTGTTCGGGGGATGA 60.377 57.895 0.00 0.00 0.00 2.92
7437 7741 2.406616 CCGCTTTGTTCGGGGGATG 61.407 63.158 0.00 0.00 42.99 3.51
7438 7742 2.045340 CCGCTTTGTTCGGGGGAT 60.045 61.111 0.00 0.00 42.99 3.85
7465 7772 6.434028 TGCAAGGAACAATTTATCTACAGCTT 59.566 34.615 0.00 0.00 0.00 3.74
7508 7817 2.096496 GCATTTTGTGAGGATGACGAGG 59.904 50.000 0.00 0.00 0.00 4.63
7510 7819 3.057969 AGCATTTTGTGAGGATGACGA 57.942 42.857 0.00 0.00 0.00 4.20
7558 7867 1.419387 AGGAAGAGCTTTCTGTGCTGT 59.581 47.619 0.00 0.00 41.30 4.40
7559 7868 1.805345 CAGGAAGAGCTTTCTGTGCTG 59.195 52.381 9.86 0.00 40.48 4.41
7560 7869 1.881498 GCAGGAAGAGCTTTCTGTGCT 60.881 52.381 17.42 0.00 45.71 4.40
7577 7890 3.324930 TGTGGAGGAGGGCAGCAG 61.325 66.667 0.00 0.00 0.00 4.24
7579 7892 2.490270 ATTGTGTGGAGGAGGGCAGC 62.490 60.000 0.00 0.00 0.00 5.25
7589 7902 9.290988 ACTGTATTGTGTATAAAATTGTGTGGA 57.709 29.630 0.00 0.00 0.00 4.02
7632 7945 2.111384 CCTCGGAAAGATTCTCCTCCA 58.889 52.381 12.78 3.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.