Multiple sequence alignment - TraesCS2B01G333300

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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 TraesCS2B01G333300 chr2B 100.000 5520 0 0 1 5520 476556425 476561944 0.000000e+00 10194.0
1 TraesCS2B01G333300 chr2B 96.078 153 5 1 3056 3207 548773606 548773758 1.190000e-61 248.0
2 TraesCS2B01G333300 chr2B 93.590 156 8 1 3057 3210 421092144 421092299 1.200000e-56 231.0
3 TraesCS2B01G333300 chr2B 93.082 159 10 1 3056 3213 494282758 494282916 1.200000e-56 231.0
4 TraesCS2B01G333300 chr2B 86.486 74 9 1 473 545 64113760 64113687 4.580000e-11 80.5
5 TraesCS2B01G333300 chr2D 95.869 3074 99 16 1 3057 402708959 402712021 0.000000e+00 4948.0
6 TraesCS2B01G333300 chr2D 93.333 1560 66 21 3211 4747 402712007 402713551 0.000000e+00 2270.0
7 TraesCS2B01G333300 chr2D 90.781 640 43 13 4885 5520 402713831 402714458 0.000000e+00 841.0
8 TraesCS2B01G333300 chr2A 92.276 2900 154 29 1 2856 539963861 539966734 0.000000e+00 4050.0
9 TraesCS2B01G333300 chr2A 93.157 1476 62 20 3211 4664 539966876 539968334 0.000000e+00 2130.0
10 TraesCS2B01G333300 chr2A 83.384 662 46 28 4866 5520 539970368 539970972 6.250000e-154 555.0
11 TraesCS2B01G333300 chr2A 96.795 156 5 0 2902 3057 539966735 539966890 1.530000e-65 261.0
12 TraesCS2B01G333300 chr2A 77.841 176 26 8 4695 4860 539968337 539968509 4.550000e-16 97.1
13 TraesCS2B01G333300 chrUn 83.212 274 41 5 1732 2003 449424837 449424567 4.270000e-61 246.0
14 TraesCS2B01G333300 chr7D 83.032 277 42 5 1729 2003 624087726 624087999 4.270000e-61 246.0
15 TraesCS2B01G333300 chr7D 83.032 277 42 5 1729 2003 624415531 624415804 4.270000e-61 246.0
16 TraesCS2B01G333300 chr7D 82.671 277 43 5 1729 2003 624184576 624184849 1.990000e-59 241.0
17 TraesCS2B01G333300 chr7D 82.671 277 43 5 1729 2003 624313839 624314112 1.990000e-59 241.0
18 TraesCS2B01G333300 chr7D 82.671 277 43 5 1729 2003 624657878 624658151 1.990000e-59 241.0
19 TraesCS2B01G333300 chr7D 82.310 277 44 5 1729 2003 624387068 624387341 9.240000e-58 235.0
20 TraesCS2B01G333300 chr1B 94.937 158 6 1 3055 3210 1847488 1847331 4.270000e-61 246.0
21 TraesCS2B01G333300 chr1B 95.270 148 7 0 3057 3204 657167797 657167650 9.240000e-58 235.0
22 TraesCS2B01G333300 chr6B 94.268 157 8 1 3051 3206 561645202 561645358 7.150000e-59 239.0
23 TraesCS2B01G333300 chr4B 93.210 162 9 2 3057 3217 346758954 346759114 2.570000e-58 237.0
24 TraesCS2B01G333300 chr5B 93.590 156 9 1 3054 3208 360936446 360936601 1.200000e-56 231.0
25 TraesCS2B01G333300 chr5D 90.055 181 12 5 3036 3212 216062858 216063036 4.300000e-56 230.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G333300 chr2B 476556425 476561944 5519 False 10194.000000 10194 100.000000 1 5520 1 chr2B.!!$F2 5519
1 TraesCS2B01G333300 chr2D 402708959 402714458 5499 False 2686.333333 4948 93.327667 1 5520 3 chr2D.!!$F1 5519
2 TraesCS2B01G333300 chr2A 539963861 539970972 7111 False 1418.620000 4050 88.690600 1 5520 5 chr2A.!!$F1 5519

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
497 499 2.619074 GGCTCCCTCAATGCTTGTAGTT 60.619 50.0 0.0 0.0 0.0 2.24 F
1371 1414 0.542805 GGGTTCCTGGTTGCGGTATA 59.457 55.0 0.0 0.0 0.0 1.47 F
3127 3171 0.035458 CTCAAGTTCAAGTCCCGGCT 59.965 55.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1403 1446 0.588252 CTGCGTTGTCCACCAAGAAG 59.412 55.0 0.00 0.0 32.51 2.85 R
3136 3180 0.033504 GAGAAACTCCGTGAGCACCA 59.966 55.0 1.36 0.0 32.04 4.17 R
5088 7158 0.387239 AAAATCCGAGCGCAAACAGC 60.387 50.0 11.47 0.0 40.87 4.40 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
60 62 7.556844 TCTGCAAATAAAAAGGTGGTTAACAA 58.443 30.769 8.10 0.00 0.00 2.83
180 182 6.837568 ACGATAAGGGTTTATTAGGTCTCTCA 59.162 38.462 0.00 0.00 29.67 3.27
189 191 8.077386 GGTTTATTAGGTCTCTCAGTCGAATAG 58.923 40.741 0.00 0.00 0.00 1.73
275 277 6.896860 TGACCATTCCCATCACTATTTCAATT 59.103 34.615 0.00 0.00 0.00 2.32
497 499 2.619074 GGCTCCCTCAATGCTTGTAGTT 60.619 50.000 0.00 0.00 0.00 2.24
516 518 4.801891 AGTTGTCGCTAAATTGTCTACGA 58.198 39.130 0.00 0.00 0.00 3.43
530 532 6.778834 TTGTCTACGAACCTGGATGTAATA 57.221 37.500 0.00 0.00 0.00 0.98
562 565 5.994054 TCTGATGTTCTTTGTTCTCTCTTGG 59.006 40.000 0.00 0.00 0.00 3.61
630 634 6.993175 AGAAGCTTTCTCGCAAAATAAAAC 57.007 33.333 0.00 0.00 34.07 2.43
1130 1168 3.254903 GTCTTCGTTTTGGGGTAAGCATT 59.745 43.478 0.00 0.00 0.00 3.56
1170 1208 1.419922 CGCCGTCAATTTCTCCGTG 59.580 57.895 0.00 0.00 0.00 4.94
1189 1227 3.004419 CGTGTTCTCCCTTTTCCTTTTCC 59.996 47.826 0.00 0.00 0.00 3.13
1200 1238 6.665248 CCCTTTTCCTTTTCCATGTCTAATCT 59.335 38.462 0.00 0.00 0.00 2.40
1236 1279 4.329545 GGTGCGGAGGTGAAGCCA 62.330 66.667 0.00 0.00 40.61 4.75
1328 1371 2.096980 CGCCCTTAACTTTCGATTTCCC 59.903 50.000 0.00 0.00 0.00 3.97
1350 1393 3.865745 CCTGTTAATGTCACGAGATGGTC 59.134 47.826 0.00 0.00 0.00 4.02
1366 1409 4.323477 TCGGGGTTCCTGGTTGCG 62.323 66.667 0.00 0.00 0.00 4.85
1369 1412 2.751688 GGGTTCCTGGTTGCGGTA 59.248 61.111 0.00 0.00 0.00 4.02
1370 1413 1.301954 GGGTTCCTGGTTGCGGTAT 59.698 57.895 0.00 0.00 0.00 2.73
1371 1414 0.542805 GGGTTCCTGGTTGCGGTATA 59.457 55.000 0.00 0.00 0.00 1.47
1372 1415 1.065272 GGGTTCCTGGTTGCGGTATAA 60.065 52.381 0.00 0.00 0.00 0.98
1374 1417 2.876550 GGTTCCTGGTTGCGGTATAATC 59.123 50.000 0.00 0.00 0.00 1.75
1375 1418 3.537580 GTTCCTGGTTGCGGTATAATCA 58.462 45.455 0.00 0.00 0.00 2.57
1376 1419 3.188159 TCCTGGTTGCGGTATAATCAC 57.812 47.619 0.00 0.00 0.00 3.06
1377 1420 2.769663 TCCTGGTTGCGGTATAATCACT 59.230 45.455 0.00 0.00 0.00 3.41
1389 1432 6.718388 CGGTATAATCACTCTACGTTGTGTA 58.282 40.000 4.48 0.00 35.82 2.90
1397 1440 3.181487 ACTCTACGTTGTGTAACCGTGTT 60.181 43.478 2.91 0.00 34.36 3.32
1398 1441 3.114809 TCTACGTTGTGTAACCGTGTTG 58.885 45.455 0.00 0.00 34.36 3.33
1403 1446 3.605231 CGTTGTGTAACCGTGTTGGATTC 60.605 47.826 0.23 0.00 42.00 2.52
1405 1448 3.811083 TGTGTAACCGTGTTGGATTCTT 58.189 40.909 0.23 0.00 42.00 2.52
1406 1449 3.810941 TGTGTAACCGTGTTGGATTCTTC 59.189 43.478 0.23 0.00 42.00 2.87
1408 1451 4.514066 GTGTAACCGTGTTGGATTCTTCTT 59.486 41.667 0.23 0.00 42.00 2.52
1410 1453 2.504367 ACCGTGTTGGATTCTTCTTGG 58.496 47.619 0.00 0.00 42.00 3.61
1509 1552 1.271217 ACCGTTAAGAACAAGGAGCCC 60.271 52.381 0.00 0.00 0.00 5.19
1614 1657 2.657237 CTTGGGTCGAGGAGCGTT 59.343 61.111 0.00 0.00 41.80 4.84
1633 1676 4.500887 GCGTTCACTTGGCTGGATACTATA 60.501 45.833 0.00 0.00 37.61 1.31
1721 1764 8.336235 TGATTACTGGGATTATTTTCTCTGGTT 58.664 33.333 0.00 0.00 0.00 3.67
1786 1829 5.047590 TGTTAGTGATGTGTACGAGGACATT 60.048 40.000 0.00 0.00 32.85 2.71
1852 1895 6.068670 TGATGATTTCTTGGCATCTGATGAT 58.931 36.000 21.30 3.78 39.24 2.45
1997 2040 6.343716 AGCGAAGATGATTCAGACTATGAT 57.656 37.500 0.00 0.00 37.89 2.45
2006 2049 7.517614 TGATTCAGACTATGATGAGGACTAC 57.482 40.000 0.00 0.00 37.89 2.73
2042 2085 6.244654 TGATGAGGATTTGATGTACAACCAA 58.755 36.000 0.00 4.77 38.29 3.67
2121 2164 8.761575 TTTCCATGATGTAAGCAATTTCTTTC 57.238 30.769 0.00 0.00 33.49 2.62
2122 2165 7.465353 TCCATGATGTAAGCAATTTCTTTCA 57.535 32.000 0.00 0.00 33.49 2.69
2165 2208 7.012138 GGAGAACTATTGTACATAGTCAGTCGA 59.988 40.741 14.40 0.00 34.04 4.20
2199 2242 1.683943 AGTGCTTGTCTGCATGTGTT 58.316 45.000 0.00 0.00 45.23 3.32
2220 2263 6.017440 GTGTTTATCAGGTTGAAGTTAGCACA 60.017 38.462 0.00 0.00 0.00 4.57
2230 2273 7.766278 AGGTTGAAGTTAGCACAGATTAGTATG 59.234 37.037 0.00 0.00 0.00 2.39
2355 2398 7.372451 TGTTAATTCTGTCCTTATTTGTCCG 57.628 36.000 0.00 0.00 0.00 4.79
2387 2430 6.839124 AATAGAAGTCATGTTGCCATTTGA 57.161 33.333 0.00 0.00 0.00 2.69
2389 2432 3.057033 AGAAGTCATGTTGCCATTTGAGC 60.057 43.478 0.00 0.00 0.00 4.26
2402 2445 6.688276 GCCATTTGAGCTATTGGCGTTGAA 62.688 45.833 11.52 0.00 44.58 2.69
2550 2594 0.326264 CAGCTTGCTGTTAGGACCCT 59.674 55.000 13.89 0.00 0.00 4.34
2584 2628 3.433615 CCGTGGAAAGTGAAGATGAAGAC 59.566 47.826 0.00 0.00 0.00 3.01
2777 2821 7.872163 TTGTTTAATCATGATGAAGCAACAC 57.128 32.000 23.97 12.38 30.47 3.32
3046 3090 7.864686 ACGTACGTATGTTAAGCTGTCATATA 58.135 34.615 21.41 0.00 0.00 0.86
3047 3091 8.509690 ACGTACGTATGTTAAGCTGTCATATAT 58.490 33.333 21.41 0.00 0.00 0.86
3048 3092 9.338291 CGTACGTATGTTAAGCTGTCATATATT 57.662 33.333 7.22 1.81 0.00 1.28
3051 3095 8.978539 ACGTATGTTAAGCTGTCATATATTGTG 58.021 33.333 8.34 0.00 0.00 3.33
3052 3096 8.978539 CGTATGTTAAGCTGTCATATATTGTGT 58.021 33.333 8.34 0.00 0.00 3.72
3055 3099 8.424274 TGTTAAGCTGTCATATATTGTGTCTG 57.576 34.615 0.00 0.00 0.00 3.51
3056 3100 7.495606 TGTTAAGCTGTCATATATTGTGTCTGG 59.504 37.037 0.00 0.00 0.00 3.86
3057 3101 5.876651 AGCTGTCATATATTGTGTCTGGA 57.123 39.130 0.00 0.00 0.00 3.86
3058 3102 5.851720 AGCTGTCATATATTGTGTCTGGAG 58.148 41.667 0.00 0.00 0.00 3.86
3059 3103 4.993584 GCTGTCATATATTGTGTCTGGAGG 59.006 45.833 0.00 0.00 0.00 4.30
3060 3104 5.221521 GCTGTCATATATTGTGTCTGGAGGA 60.222 44.000 0.00 0.00 0.00 3.71
3061 3105 6.161855 TGTCATATATTGTGTCTGGAGGAC 57.838 41.667 0.00 0.00 44.70 3.85
3082 3126 4.424566 GCGTCGACCCGTTGGCTA 62.425 66.667 10.58 0.00 33.59 3.93
3083 3127 2.202570 CGTCGACCCGTTGGCTAG 60.203 66.667 10.58 0.00 33.59 3.42
3084 3128 2.183555 GTCGACCCGTTGGCTAGG 59.816 66.667 3.51 0.00 33.59 3.02
3085 3129 3.766691 TCGACCCGTTGGCTAGGC 61.767 66.667 9.85 9.85 33.59 3.93
3086 3130 4.077184 CGACCCGTTGGCTAGGCA 62.077 66.667 16.16 16.16 33.59 4.75
3087 3131 2.125106 GACCCGTTGGCTAGGCAG 60.125 66.667 19.32 10.25 33.59 4.85
3096 3140 4.215349 GCTAGGCAGCTGAGGTTG 57.785 61.111 20.43 3.83 44.93 3.77
3097 3141 2.111582 GCTAGGCAGCTGAGGTTGC 61.112 63.158 20.43 10.49 46.58 4.17
3098 3142 1.601171 CTAGGCAGCTGAGGTTGCT 59.399 57.895 20.43 0.00 46.51 3.91
3103 3147 2.033757 AGCTGAGGTTGCTGCCAG 59.966 61.111 0.00 0.00 39.56 4.85
3104 3148 3.745803 GCTGAGGTTGCTGCCAGC 61.746 66.667 10.45 10.45 44.00 4.85
3105 3149 3.060615 CTGAGGTTGCTGCCAGCC 61.061 66.667 15.29 0.00 41.51 4.85
3106 3150 4.666253 TGAGGTTGCTGCCAGCCC 62.666 66.667 15.29 9.16 42.79 5.19
3107 3151 4.666253 GAGGTTGCTGCCAGCCCA 62.666 66.667 15.29 0.00 42.79 5.36
3108 3152 4.982701 AGGTTGCTGCCAGCCCAC 62.983 66.667 15.29 10.81 42.79 4.61
3109 3153 4.982701 GGTTGCTGCCAGCCCACT 62.983 66.667 15.29 0.00 41.51 4.00
3110 3154 3.368571 GTTGCTGCCAGCCCACTC 61.369 66.667 15.29 0.00 41.51 3.51
3111 3155 3.888460 TTGCTGCCAGCCCACTCA 61.888 61.111 15.29 0.00 41.51 3.41
3112 3156 3.433984 TTGCTGCCAGCCCACTCAA 62.434 57.895 15.29 0.00 41.51 3.02
3113 3157 3.060615 GCTGCCAGCCCACTCAAG 61.061 66.667 5.06 0.00 34.48 3.02
3114 3158 2.433446 CTGCCAGCCCACTCAAGT 59.567 61.111 0.00 0.00 0.00 3.16
3115 3159 1.228367 CTGCCAGCCCACTCAAGTT 60.228 57.895 0.00 0.00 0.00 2.66
3116 3160 1.228245 TGCCAGCCCACTCAAGTTC 60.228 57.895 0.00 0.00 0.00 3.01
3117 3161 1.228245 GCCAGCCCACTCAAGTTCA 60.228 57.895 0.00 0.00 0.00 3.18
3118 3162 0.823356 GCCAGCCCACTCAAGTTCAA 60.823 55.000 0.00 0.00 0.00 2.69
3119 3163 1.242076 CCAGCCCACTCAAGTTCAAG 58.758 55.000 0.00 0.00 0.00 3.02
3120 3164 1.477558 CCAGCCCACTCAAGTTCAAGT 60.478 52.381 0.00 0.00 0.00 3.16
3121 3165 1.876156 CAGCCCACTCAAGTTCAAGTC 59.124 52.381 0.00 0.00 0.00 3.01
3122 3166 1.202818 AGCCCACTCAAGTTCAAGTCC 60.203 52.381 0.00 0.00 0.00 3.85
3123 3167 1.897560 CCCACTCAAGTTCAAGTCCC 58.102 55.000 0.00 0.00 0.00 4.46
3124 3168 1.512926 CCACTCAAGTTCAAGTCCCG 58.487 55.000 0.00 0.00 0.00 5.14
3125 3169 1.512926 CACTCAAGTTCAAGTCCCGG 58.487 55.000 0.00 0.00 0.00 5.73
3126 3170 0.250338 ACTCAAGTTCAAGTCCCGGC 60.250 55.000 0.00 0.00 0.00 6.13
3127 3171 0.035458 CTCAAGTTCAAGTCCCGGCT 59.965 55.000 0.00 0.00 0.00 5.52
3128 3172 0.472471 TCAAGTTCAAGTCCCGGCTT 59.528 50.000 0.00 0.00 0.00 4.35
3129 3173 0.593128 CAAGTTCAAGTCCCGGCTTG 59.407 55.000 13.87 13.87 45.18 4.01
3130 3174 0.537371 AAGTTCAAGTCCCGGCTTGG 60.537 55.000 18.28 4.22 44.26 3.61
3131 3175 1.072505 GTTCAAGTCCCGGCTTGGA 59.927 57.895 18.28 9.78 44.26 3.53
3132 3176 0.322546 GTTCAAGTCCCGGCTTGGAT 60.323 55.000 18.28 0.00 44.26 3.41
3133 3177 0.322456 TTCAAGTCCCGGCTTGGATG 60.322 55.000 18.28 3.52 44.26 3.51
3134 3178 2.044946 AAGTCCCGGCTTGGATGC 60.045 61.111 0.00 0.00 42.00 3.91
3135 3179 3.976701 AAGTCCCGGCTTGGATGCG 62.977 63.158 0.00 0.00 42.00 4.73
3136 3180 4.778143 GTCCCGGCTTGGATGCGT 62.778 66.667 0.00 0.00 42.00 5.24
3137 3181 4.776322 TCCCGGCTTGGATGCGTG 62.776 66.667 0.00 0.00 42.00 5.34
3140 3184 3.803082 CGGCTTGGATGCGTGGTG 61.803 66.667 0.00 0.00 0.00 4.17
3141 3185 4.120331 GGCTTGGATGCGTGGTGC 62.120 66.667 0.00 0.00 46.70 5.01
3142 3186 3.058160 GCTTGGATGCGTGGTGCT 61.058 61.111 0.00 0.00 46.63 4.40
3143 3187 3.044059 GCTTGGATGCGTGGTGCTC 62.044 63.158 0.00 0.00 46.63 4.26
3144 3188 1.672030 CTTGGATGCGTGGTGCTCA 60.672 57.895 0.00 0.00 46.63 4.26
3145 3189 1.915614 CTTGGATGCGTGGTGCTCAC 61.916 60.000 0.00 1.50 46.63 3.51
3152 3196 4.456806 GTGGTGCTCACGGAGTTT 57.543 55.556 3.38 0.00 41.61 2.66
3153 3197 2.235546 GTGGTGCTCACGGAGTTTC 58.764 57.895 3.38 0.00 41.61 2.78
3154 3198 0.249911 GTGGTGCTCACGGAGTTTCT 60.250 55.000 3.38 0.00 41.61 2.52
3155 3199 0.033504 TGGTGCTCACGGAGTTTCTC 59.966 55.000 3.38 0.00 41.61 2.87
3156 3200 0.670854 GGTGCTCACGGAGTTTCTCC 60.671 60.000 5.79 5.79 46.44 3.71
3171 3215 8.691661 GGAGTTTCTCCTATAAATAAATGCCA 57.308 34.615 8.38 0.00 46.41 4.92
3172 3216 9.131791 GGAGTTTCTCCTATAAATAAATGCCAA 57.868 33.333 8.38 0.00 46.41 4.52
3173 3217 9.952188 GAGTTTCTCCTATAAATAAATGCCAAC 57.048 33.333 0.00 0.00 0.00 3.77
3174 3218 8.621286 AGTTTCTCCTATAAATAAATGCCAACG 58.379 33.333 0.00 0.00 0.00 4.10
3175 3219 8.617809 GTTTCTCCTATAAATAAATGCCAACGA 58.382 33.333 0.00 0.00 0.00 3.85
3176 3220 7.962964 TCTCCTATAAATAAATGCCAACGAG 57.037 36.000 0.00 0.00 0.00 4.18
3177 3221 6.934645 TCTCCTATAAATAAATGCCAACGAGG 59.065 38.462 0.00 0.00 41.84 4.63
3178 3222 6.001460 TCCTATAAATAAATGCCAACGAGGG 58.999 40.000 0.00 0.00 38.09 4.30
3179 3223 5.768164 CCTATAAATAAATGCCAACGAGGGT 59.232 40.000 0.00 0.00 38.09 4.34
3180 3224 6.264518 CCTATAAATAAATGCCAACGAGGGTT 59.735 38.462 0.00 0.00 38.09 4.11
3181 3225 7.446013 CCTATAAATAAATGCCAACGAGGGTTA 59.554 37.037 0.00 0.00 38.09 2.85
3182 3226 5.576447 AAATAAATGCCAACGAGGGTTAG 57.424 39.130 0.00 0.00 38.09 2.34
3183 3227 1.173913 AAATGCCAACGAGGGTTAGC 58.826 50.000 0.00 0.00 40.57 3.09
3184 3228 0.679960 AATGCCAACGAGGGTTAGCC 60.680 55.000 0.00 0.00 39.61 3.93
3194 3238 4.434483 GGTTAGCCCTTGGGTTGG 57.566 61.111 7.61 0.00 34.28 3.77
3195 3239 1.463375 GGTTAGCCCTTGGGTTGGT 59.537 57.895 7.61 0.00 34.28 3.67
3196 3240 0.611062 GGTTAGCCCTTGGGTTGGTC 60.611 60.000 7.61 0.00 34.28 4.02
3197 3241 0.404426 GTTAGCCCTTGGGTTGGTCT 59.596 55.000 7.61 0.00 34.28 3.85
3198 3242 1.154430 TTAGCCCTTGGGTTGGTCTT 58.846 50.000 7.61 0.00 34.28 3.01
3199 3243 1.154430 TAGCCCTTGGGTTGGTCTTT 58.846 50.000 7.61 0.00 34.28 2.52
3200 3244 0.264657 AGCCCTTGGGTTGGTCTTTT 59.735 50.000 7.61 0.00 0.00 2.27
3201 3245 1.128200 GCCCTTGGGTTGGTCTTTTT 58.872 50.000 7.61 0.00 0.00 1.94
3298 3342 3.640967 GAGACAATGATGAGGAGCCTAGT 59.359 47.826 0.00 0.00 0.00 2.57
3592 3636 6.882610 ACTTTCAATGCTCAGTGTAATCAA 57.117 33.333 0.00 0.00 0.00 2.57
3605 3649 6.478673 TCAGTGTAATCAATATGTACTTGCCG 59.521 38.462 0.00 0.00 0.00 5.69
3607 3651 6.479001 AGTGTAATCAATATGTACTTGCCGTC 59.521 38.462 0.00 0.00 0.00 4.79
3629 3673 7.044966 CCGTCGCATTGTTCTAATTAATTTGAC 60.045 37.037 11.20 8.03 0.00 3.18
3634 3678 7.462724 GCATTGTTCTAATTAATTTGACCACGC 60.463 37.037 11.20 11.50 0.00 5.34
3880 3924 0.250901 ATGCAGGTGTTGGACAGGTC 60.251 55.000 0.00 0.00 0.00 3.85
3927 3971 9.834628 TGTCAACGGTATTTAATTTCTCAAATC 57.165 29.630 0.00 0.00 0.00 2.17
3971 4018 4.152402 GGCTATTGCATATGTTGTACTCCG 59.848 45.833 4.29 0.00 41.91 4.63
3985 4032 4.529897 TGTACTCCGTACCTGATACATGT 58.470 43.478 2.69 2.69 38.14 3.21
3997 4044 6.721318 ACCTGATACATGTGGTTAGTTCATT 58.279 36.000 9.11 0.00 0.00 2.57
4064 4111 3.904717 TGGGGACAAAAGAAAGCTTACA 58.095 40.909 0.00 0.00 37.44 2.41
4149 4196 5.214417 TGCTTGTTTCGATTCTGATTTGTG 58.786 37.500 0.00 0.00 0.00 3.33
4151 4198 4.827304 TGTTTCGATTCTGATTTGTGCA 57.173 36.364 0.00 0.00 0.00 4.57
4186 4233 2.420466 GAAACCAGAAGGCCGGGGAA 62.420 60.000 2.18 0.00 39.06 3.97
4241 4288 4.106197 GGAGCTAATGAACGTACAGTGAG 58.894 47.826 0.00 0.00 0.00 3.51
4288 4337 0.586802 GGACAAACTGAGACGGTTGC 59.413 55.000 0.00 0.00 32.82 4.17
4293 4342 1.092921 AACTGAGACGGTTGCGCAAA 61.093 50.000 26.87 6.30 31.12 3.68
4295 4344 0.179215 CTGAGACGGTTGCGCAAATC 60.179 55.000 26.87 21.47 0.00 2.17
4354 4403 5.290493 TCAGTCAACAACATCCTACAGTT 57.710 39.130 0.00 0.00 0.00 3.16
4395 4444 6.732531 TTTTTCATCAGCTCTACATGTCAG 57.267 37.500 0.00 0.27 0.00 3.51
4398 4447 3.065925 TCATCAGCTCTACATGTCAGACG 59.934 47.826 0.00 0.00 0.00 4.18
4455 4504 0.321919 CTGGGCTGCAACTGAGCTTA 60.322 55.000 0.50 0.00 36.63 3.09
4491 4542 3.394674 TGTGGCTCGTTGACATTCTTA 57.605 42.857 0.00 0.00 35.31 2.10
4501 4552 5.290885 TCGTTGACATTCTTATGGAATCACG 59.709 40.000 0.00 0.00 42.20 4.35
4504 4555 5.912892 TGACATTCTTATGGAATCACGCTA 58.087 37.500 0.00 0.00 42.20 4.26
4505 4556 6.524734 TGACATTCTTATGGAATCACGCTAT 58.475 36.000 0.00 0.00 42.20 2.97
4506 4557 7.666623 TGACATTCTTATGGAATCACGCTATA 58.333 34.615 0.00 0.00 42.20 1.31
4517 4568 6.755141 TGGAATCACGCTATAAGACTTGTTAC 59.245 38.462 0.00 0.00 0.00 2.50
4530 4581 6.380079 AGACTTGTTACTGAAGGAATGGAT 57.620 37.500 0.00 0.00 0.00 3.41
4558 4609 6.590292 CACAGTTTTGAACTATCGTAGGACAT 59.410 38.462 0.00 0.00 40.46 3.06
4559 4610 6.590292 ACAGTTTTGAACTATCGTAGGACATG 59.410 38.462 0.00 0.00 40.46 3.21
4560 4611 6.590292 CAGTTTTGAACTATCGTAGGACATGT 59.410 38.462 0.00 0.00 40.46 3.21
4561 4612 6.812160 AGTTTTGAACTATCGTAGGACATGTC 59.188 38.462 17.91 17.91 40.69 3.06
4562 4613 5.907866 TTGAACTATCGTAGGACATGTCA 57.092 39.130 26.47 6.73 0.00 3.58
4581 4632 8.046708 ACATGTCATACTAGTTGCTCCATTTTA 58.953 33.333 0.00 0.00 0.00 1.52
4591 4654 9.309516 CTAGTTGCTCCATTTTACGTTATCTTA 57.690 33.333 0.00 0.00 0.00 2.10
4610 4673 4.782691 TCTTAGTTGGATCCCATTGTCTGA 59.217 41.667 9.90 0.00 31.53 3.27
4620 4683 4.018490 TCCCATTGTCTGATGGTTGAATG 58.982 43.478 3.47 0.00 44.17 2.67
4622 4685 4.142315 CCCATTGTCTGATGGTTGAATGTC 60.142 45.833 3.47 0.00 44.17 3.06
4624 4687 5.047872 CCATTGTCTGATGGTTGAATGTCAA 60.048 40.000 0.00 0.00 41.37 3.18
4628 4691 7.053316 TGTCTGATGGTTGAATGTCAATTTT 57.947 32.000 0.00 0.00 38.79 1.82
4632 4695 7.014518 TCTGATGGTTGAATGTCAATTTTCACT 59.985 33.333 0.00 0.00 38.79 3.41
4644 4707 6.091986 TGTCAATTTTCACTTTTTGGCTGAAC 59.908 34.615 0.00 0.00 0.00 3.18
4657 4720 0.880278 GCTGAACTCGACTGTTGCCA 60.880 55.000 0.00 0.00 0.00 4.92
4678 4741 2.572104 ACAAATCTAAGGACGCTTCCCT 59.428 45.455 5.45 0.00 44.10 4.20
4680 4743 1.867363 ATCTAAGGACGCTTCCCTGT 58.133 50.000 5.45 0.00 44.10 4.00
4687 4750 1.369625 GACGCTTCCCTGTTGTATGG 58.630 55.000 0.00 0.00 0.00 2.74
4693 4756 4.021102 CTTCCCTGTTGTATGGAAGTGT 57.979 45.455 8.93 0.00 46.53 3.55
4710 4773 5.163332 GGAAGTGTAGGAGAAAATATCCGGT 60.163 44.000 0.00 0.00 42.02 5.28
4730 4797 4.031028 GGTGAGATGCAATTTCGAATTCG 58.969 43.478 21.78 21.78 41.45 3.34
4769 4836 8.915057 AGTGAGAATGTCATTATAATTCAGGG 57.085 34.615 0.00 0.00 37.56 4.45
4771 4838 7.939039 GTGAGAATGTCATTATAATTCAGGGGA 59.061 37.037 0.00 0.00 37.56 4.81
4772 4839 8.159447 TGAGAATGTCATTATAATTCAGGGGAG 58.841 37.037 0.00 0.00 33.61 4.30
4774 4841 9.170890 AGAATGTCATTATAATTCAGGGGAGTA 57.829 33.333 0.00 0.00 33.61 2.59
4783 4850 9.582648 TTATAATTCAGGGGAGTAAATAAAGCC 57.417 33.333 0.00 0.00 0.00 4.35
4784 4851 5.734031 ATTCAGGGGAGTAAATAAAGCCT 57.266 39.130 0.00 0.00 0.00 4.58
4785 4852 4.503714 TCAGGGGAGTAAATAAAGCCTG 57.496 45.455 0.00 0.00 0.00 4.85
4787 4854 4.080526 TCAGGGGAGTAAATAAAGCCTGAC 60.081 45.833 0.00 0.00 0.00 3.51
4788 4855 3.850173 AGGGGAGTAAATAAAGCCTGACA 59.150 43.478 0.00 0.00 0.00 3.58
4789 4856 3.945921 GGGGAGTAAATAAAGCCTGACAC 59.054 47.826 0.00 0.00 0.00 3.67
4790 4857 3.621715 GGGAGTAAATAAAGCCTGACACG 59.378 47.826 0.00 0.00 0.00 4.49
4791 4858 4.501071 GGAGTAAATAAAGCCTGACACGA 58.499 43.478 0.00 0.00 0.00 4.35
4792 4859 4.329256 GGAGTAAATAAAGCCTGACACGAC 59.671 45.833 0.00 0.00 0.00 4.34
4793 4860 4.890088 AGTAAATAAAGCCTGACACGACA 58.110 39.130 0.00 0.00 0.00 4.35
4794 4861 5.488341 AGTAAATAAAGCCTGACACGACAT 58.512 37.500 0.00 0.00 0.00 3.06
4798 4959 3.402628 AAAGCCTGACACGACATTAGT 57.597 42.857 0.00 0.00 0.00 2.24
4839 5000 9.955208 TCATCATTATACATTGCTGAATTTGTC 57.045 29.630 0.00 0.00 0.00 3.18
4840 5001 9.738832 CATCATTATACATTGCTGAATTTGTCA 57.261 29.630 0.00 0.00 34.17 3.58
4882 6914 9.968743 AAAACGATATTTCTAGAACGTCATTTC 57.031 29.630 16.32 7.11 33.59 2.17
4883 6915 7.695869 ACGATATTTCTAGAACGTCATTTCC 57.304 36.000 4.18 0.00 0.00 3.13
4884 6916 7.490000 ACGATATTTCTAGAACGTCATTTCCT 58.510 34.615 4.18 0.00 0.00 3.36
4885 6917 7.980099 ACGATATTTCTAGAACGTCATTTCCTT 59.020 33.333 4.18 0.00 0.00 3.36
4997 7065 1.278985 TGTGATCTGGTTTCAGCGGAT 59.721 47.619 0.00 0.00 43.73 4.18
5006 7074 4.584874 TGGTTTCAGCGGATATTTTCTCA 58.415 39.130 0.00 0.00 0.00 3.27
5010 7078 7.035612 GGTTTCAGCGGATATTTTCTCAAAAT 58.964 34.615 0.23 0.23 43.19 1.82
5011 7079 7.545615 GGTTTCAGCGGATATTTTCTCAAAATT 59.454 33.333 0.00 0.00 41.16 1.82
5012 7080 9.567848 GTTTCAGCGGATATTTTCTCAAAATTA 57.432 29.630 0.00 0.00 41.16 1.40
5013 7081 9.787532 TTTCAGCGGATATTTTCTCAAAATTAG 57.212 29.630 0.00 0.00 41.16 1.73
5014 7082 8.731275 TCAGCGGATATTTTCTCAAAATTAGA 57.269 30.769 0.00 0.00 41.16 2.10
5016 7084 9.956720 CAGCGGATATTTTCTCAAAATTAGAAT 57.043 29.630 0.00 0.00 41.16 2.40
5054 7124 3.058293 TGCGTACTTGCAGAAATTTCAGG 60.058 43.478 19.99 12.34 40.62 3.86
5055 7125 3.058224 GCGTACTTGCAGAAATTTCAGGT 60.058 43.478 19.99 9.23 34.15 4.00
5057 7127 5.334569 GCGTACTTGCAGAAATTTCAGGTAA 60.335 40.000 19.99 14.79 34.15 2.85
5061 7131 5.928264 ACTTGCAGAAATTTCAGGTAATTGC 59.072 36.000 19.99 17.47 0.00 3.56
5062 7132 4.819769 TGCAGAAATTTCAGGTAATTGCC 58.180 39.130 19.99 4.07 0.00 4.52
5065 7135 5.349543 GCAGAAATTTCAGGTAATTGCCTTG 59.650 40.000 19.99 7.26 36.58 3.61
5066 7136 5.870978 CAGAAATTTCAGGTAATTGCCTTGG 59.129 40.000 19.99 2.88 36.58 3.61
5067 7137 5.543790 AGAAATTTCAGGTAATTGCCTTGGT 59.456 36.000 19.99 0.00 36.58 3.67
5069 7139 2.969821 TCAGGTAATTGCCTTGGTGT 57.030 45.000 13.03 0.00 36.58 4.16
5070 7140 3.237268 TCAGGTAATTGCCTTGGTGTT 57.763 42.857 13.03 0.00 36.58 3.32
5071 7141 3.571590 TCAGGTAATTGCCTTGGTGTTT 58.428 40.909 13.03 0.00 36.58 2.83
5072 7142 3.572255 TCAGGTAATTGCCTTGGTGTTTC 59.428 43.478 13.03 0.00 36.58 2.78
5073 7143 3.573967 CAGGTAATTGCCTTGGTGTTTCT 59.426 43.478 13.03 0.00 36.58 2.52
5074 7144 3.826729 AGGTAATTGCCTTGGTGTTTCTC 59.173 43.478 9.62 0.00 34.71 2.87
5075 7145 3.572255 GGTAATTGCCTTGGTGTTTCTCA 59.428 43.478 5.16 0.00 0.00 3.27
5076 7146 4.038642 GGTAATTGCCTTGGTGTTTCTCAA 59.961 41.667 5.16 0.00 0.00 3.02
5077 7147 4.326504 AATTGCCTTGGTGTTTCTCAAG 57.673 40.909 0.00 0.00 39.83 3.02
5084 7154 1.748493 TGGTGTTTCTCAAGGTGCAAC 59.252 47.619 0.00 0.00 0.00 4.17
5088 7158 2.423185 TGTTTCTCAAGGTGCAACTGTG 59.577 45.455 4.19 6.30 36.74 3.66
5114 7184 1.925052 CGCTCGGATTTTCTACGCC 59.075 57.895 0.00 0.00 0.00 5.68
5119 7189 1.134907 TCGGATTTTCTACGCCACTCC 60.135 52.381 0.00 0.00 0.00 3.85
5121 7191 2.706890 GGATTTTCTACGCCACTCCAA 58.293 47.619 0.00 0.00 0.00 3.53
5123 7193 3.065371 GGATTTTCTACGCCACTCCAATG 59.935 47.826 0.00 0.00 0.00 2.82
5125 7195 2.093306 TTCTACGCCACTCCAATGTG 57.907 50.000 0.00 0.00 37.66 3.21
5126 7196 1.262417 TCTACGCCACTCCAATGTGA 58.738 50.000 0.00 0.00 40.12 3.58
5131 7201 2.224426 ACGCCACTCCAATGTGAAGTTA 60.224 45.455 0.00 0.00 40.12 2.24
5133 7203 3.412386 GCCACTCCAATGTGAAGTTAGT 58.588 45.455 0.00 0.00 40.12 2.24
5138 7208 6.128172 CCACTCCAATGTGAAGTTAGTTGATC 60.128 42.308 0.00 0.00 40.12 2.92
5139 7209 6.427853 CACTCCAATGTGAAGTTAGTTGATCA 59.572 38.462 0.00 0.00 40.12 2.92
5140 7210 6.652481 ACTCCAATGTGAAGTTAGTTGATCAG 59.348 38.462 0.00 0.00 0.00 2.90
5141 7211 5.412594 TCCAATGTGAAGTTAGTTGATCAGC 59.587 40.000 0.50 0.50 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 1.600916 GACAACCCGCTGCCTTCTT 60.601 57.895 0.00 0.00 0.00 2.52
16 17 2.032681 GACAACCCGCTGCCTTCT 59.967 61.111 0.00 0.00 0.00 2.85
17 18 1.648467 GATGACAACCCGCTGCCTTC 61.648 60.000 0.00 0.00 0.00 3.46
20 22 2.045926 AGATGACAACCCGCTGCC 60.046 61.111 0.00 0.00 0.00 4.85
60 62 0.324645 GTGGCCCCAACATTCCTGAT 60.325 55.000 0.00 0.00 0.00 2.90
180 182 1.867363 AACCCCAGAGCTATTCGACT 58.133 50.000 0.00 0.00 0.00 4.18
189 191 6.208797 ACTTGAATAGTTTAAAACCCCAGAGC 59.791 38.462 0.00 0.00 31.29 4.09
242 244 2.512692 TGGGAATGGTCAGGTCAATG 57.487 50.000 0.00 0.00 0.00 2.82
275 277 2.575532 CTTGGACTTGCTCAACCTTGA 58.424 47.619 0.00 0.00 35.57 3.02
313 315 3.450457 CAGGCTTGAGTGGACTTATCTCT 59.550 47.826 0.00 0.00 0.00 3.10
497 499 3.922240 GGTTCGTAGACAATTTAGCGACA 59.078 43.478 0.00 0.00 34.32 4.35
562 565 6.644181 AGGTAGTACTTCTCGCAAAAACTTAC 59.356 38.462 0.00 0.00 0.00 2.34
630 634 9.710979 TTACTTTTCTCGTGTACTTGAATTTTG 57.289 29.630 0.00 0.00 0.00 2.44
964 993 0.109919 GCGGCGACAAACCCTAAAAG 60.110 55.000 12.98 0.00 0.00 2.27
992 1021 1.380112 GAGGAGGTGGTAGACGGCT 60.380 63.158 0.00 0.00 0.00 5.52
993 1022 2.772691 CGAGGAGGTGGTAGACGGC 61.773 68.421 0.00 0.00 0.00 5.68
994 1023 0.679002 TTCGAGGAGGTGGTAGACGG 60.679 60.000 0.00 0.00 0.00 4.79
996 1025 0.456628 GCTTCGAGGAGGTGGTAGAC 59.543 60.000 0.00 0.00 0.00 2.59
1148 1186 2.358247 AGAAATTGACGGCGGCGT 60.358 55.556 38.13 38.13 0.00 5.68
1170 1208 4.588951 ACATGGAAAAGGAAAAGGGAGAAC 59.411 41.667 0.00 0.00 0.00 3.01
1189 1227 1.869767 GCGGCCAAGAGATTAGACATG 59.130 52.381 2.24 0.00 0.00 3.21
1200 1238 2.672996 GGAAGCAAGCGGCCAAGA 60.673 61.111 2.24 0.00 46.50 3.02
1221 1264 2.922503 TCTGGCTTCACCTCCGCA 60.923 61.111 0.00 0.00 40.22 5.69
1236 1279 1.185618 TGTGCGTGTAGGGCTTCTCT 61.186 55.000 0.00 0.00 0.00 3.10
1317 1360 5.182380 GTGACATTAACAGGGGAAATCGAAA 59.818 40.000 0.00 0.00 0.00 3.46
1319 1362 4.258543 GTGACATTAACAGGGGAAATCGA 58.741 43.478 0.00 0.00 0.00 3.59
1328 1371 3.861840 ACCATCTCGTGACATTAACAGG 58.138 45.455 0.00 0.00 0.00 4.00
1351 1394 2.206182 ATACCGCAACCAGGAACCCC 62.206 60.000 0.00 0.00 0.00 4.95
1366 1409 7.433425 GGTTACACAACGTAGAGTGATTATACC 59.567 40.741 18.75 13.71 39.47 2.73
1367 1410 7.164826 CGGTTACACAACGTAGAGTGATTATAC 59.835 40.741 18.75 10.18 39.47 1.47
1369 1412 6.032094 CGGTTACACAACGTAGAGTGATTAT 58.968 40.000 18.75 3.28 39.47 1.28
1370 1413 5.048782 ACGGTTACACAACGTAGAGTGATTA 60.049 40.000 18.75 3.35 39.47 1.75
1371 1414 4.232221 CGGTTACACAACGTAGAGTGATT 58.768 43.478 18.75 4.14 39.47 2.57
1372 1415 3.254166 ACGGTTACACAACGTAGAGTGAT 59.746 43.478 18.75 8.52 39.47 3.06
1374 1417 2.722629 CACGGTTACACAACGTAGAGTG 59.277 50.000 12.45 12.45 41.21 3.51
1375 1418 2.358898 ACACGGTTACACAACGTAGAGT 59.641 45.455 0.00 0.00 35.34 3.24
1376 1419 3.004024 ACACGGTTACACAACGTAGAG 57.996 47.619 0.00 0.00 35.34 2.43
1377 1420 3.114809 CAACACGGTTACACAACGTAGA 58.885 45.455 0.00 0.00 35.34 2.59
1389 1432 2.884639 CCAAGAAGAATCCAACACGGTT 59.115 45.455 0.00 0.00 35.57 4.44
1397 1440 3.486383 GTTGTCCACCAAGAAGAATCCA 58.514 45.455 0.00 0.00 32.51 3.41
1398 1441 2.484264 CGTTGTCCACCAAGAAGAATCC 59.516 50.000 0.00 0.00 32.51 3.01
1403 1446 0.588252 CTGCGTTGTCCACCAAGAAG 59.412 55.000 0.00 0.00 32.51 2.85
1405 1448 1.227823 CCTGCGTTGTCCACCAAGA 60.228 57.895 0.00 0.00 32.51 3.02
1406 1449 2.908073 GCCTGCGTTGTCCACCAAG 61.908 63.158 0.00 0.00 32.51 3.61
1410 1453 3.712881 GTCGCCTGCGTTGTCCAC 61.713 66.667 11.68 0.00 40.74 4.02
1491 1534 1.076332 CGGGCTCCTTGTTCTTAACG 58.924 55.000 0.00 0.00 0.00 3.18
1509 1552 1.589993 CAGGGCGCAGAGATACACG 60.590 63.158 10.83 0.00 0.00 4.49
1614 1657 5.013079 CCCAATATAGTATCCAGCCAAGTGA 59.987 44.000 0.00 0.00 0.00 3.41
1633 1676 5.773176 AGAAACGAAACAAAGGATACCCAAT 59.227 36.000 0.00 0.00 33.88 3.16
1721 1764 2.236146 ACCACACTGACAACAACTCTCA 59.764 45.455 0.00 0.00 0.00 3.27
1765 1808 4.142249 CCAATGTCCTCGTACACATCACTA 60.142 45.833 0.00 0.00 31.79 2.74
1786 1829 3.509967 CACTACCAGTATCACTGTCACCA 59.490 47.826 5.65 0.00 44.50 4.17
1934 1977 5.805486 GCTCGTCAGAATCAGTATTACAACA 59.195 40.000 0.00 0.00 0.00 3.33
1941 1984 2.363680 CCAGGCTCGTCAGAATCAGTAT 59.636 50.000 0.00 0.00 0.00 2.12
1997 2040 3.646736 TCCTCTGAATCGTAGTCCTCA 57.353 47.619 0.00 0.00 0.00 3.86
2006 2049 4.804868 ATCCTCATCATCCTCTGAATCG 57.195 45.455 0.00 0.00 37.44 3.34
2042 2085 2.183679 CCTGAACTCTTGCCTCTACCT 58.816 52.381 0.00 0.00 0.00 3.08
2121 2164 3.316029 TCTCCTATGCGCATTTTCCAATG 59.684 43.478 30.42 6.36 42.60 2.82
2122 2165 3.554934 TCTCCTATGCGCATTTTCCAAT 58.445 40.909 30.42 4.34 0.00 3.16
2133 2176 7.594714 ACTATGTACAATAGTTCTCCTATGCG 58.405 38.462 0.00 0.00 36.47 4.73
2165 2208 4.225267 ACAAGCACTTACTAGGCCTACATT 59.775 41.667 8.91 0.00 0.00 2.71
2199 2242 6.109156 TCTGTGCTAACTTCAACCTGATAA 57.891 37.500 0.00 0.00 0.00 1.75
2338 2381 9.504708 TTTATTTTACGGACAAATAAGGACAGA 57.495 29.630 8.02 0.00 37.38 3.41
2387 2430 1.818060 TGCATTTCAACGCCAATAGCT 59.182 42.857 0.00 0.00 40.39 3.32
2389 2432 3.117794 CCATGCATTTCAACGCCAATAG 58.882 45.455 0.00 0.00 0.00 1.73
2550 2594 1.271856 TTCCACGGATTCAGCAGGTA 58.728 50.000 0.00 0.00 0.00 3.08
2584 2628 2.813754 TGATTCAGAAACAGGAAAGCCG 59.186 45.455 0.00 0.00 39.96 5.52
2764 2808 4.884458 TTAAACACGTGTTGCTTCATCA 57.116 36.364 32.89 6.51 38.44 3.07
2777 2821 4.621034 GGATGACAGGCAAAATTAAACACG 59.379 41.667 0.00 0.00 0.00 4.49
3046 3090 1.553690 CCCCGTCCTCCAGACACAAT 61.554 60.000 0.00 0.00 46.69 2.71
3047 3091 2.214216 CCCCGTCCTCCAGACACAA 61.214 63.158 0.00 0.00 46.69 3.33
3048 3092 2.603473 CCCCGTCCTCCAGACACA 60.603 66.667 0.00 0.00 46.69 3.72
3049 3093 4.083862 GCCCCGTCCTCCAGACAC 62.084 72.222 0.00 0.00 46.69 3.67
3065 3109 4.424566 TAGCCAACGGGTCGACGC 62.425 66.667 21.72 21.72 37.37 5.19
3066 3110 2.202570 CTAGCCAACGGGTCGACG 60.203 66.667 9.92 1.01 40.31 5.12
3067 3111 2.183555 CCTAGCCAACGGGTCGAC 59.816 66.667 7.13 7.13 34.28 4.20
3068 3112 3.766691 GCCTAGCCAACGGGTCGA 61.767 66.667 0.00 0.00 34.28 4.20
3069 3113 4.077184 TGCCTAGCCAACGGGTCG 62.077 66.667 0.00 0.00 34.28 4.79
3070 3114 2.125106 CTGCCTAGCCAACGGGTC 60.125 66.667 0.00 0.00 34.28 4.46
3071 3115 4.410400 GCTGCCTAGCCAACGGGT 62.410 66.667 0.00 0.00 44.33 5.28
3080 3124 1.601171 AGCAACCTCAGCTGCCTAG 59.399 57.895 9.47 0.70 41.61 3.02
3081 3125 3.811702 AGCAACCTCAGCTGCCTA 58.188 55.556 9.47 0.00 41.61 3.93
3086 3130 2.033757 CTGGCAGCAACCTCAGCT 59.966 61.111 0.00 0.00 44.62 4.24
3087 3131 3.745803 GCTGGCAGCAACCTCAGC 61.746 66.667 33.33 4.00 44.34 4.26
3088 3132 3.060615 GGCTGGCAGCAACCTCAG 61.061 66.667 37.49 0.50 44.75 3.35
3089 3133 4.666253 GGGCTGGCAGCAACCTCA 62.666 66.667 37.49 0.00 44.75 3.86
3090 3134 4.666253 TGGGCTGGCAGCAACCTC 62.666 66.667 37.49 21.25 44.75 3.85
3091 3135 4.982701 GTGGGCTGGCAGCAACCT 62.983 66.667 37.49 0.00 44.75 3.50
3092 3136 4.982701 AGTGGGCTGGCAGCAACC 62.983 66.667 37.49 29.89 44.75 3.77
3093 3137 3.368571 GAGTGGGCTGGCAGCAAC 61.369 66.667 37.49 32.02 44.75 4.17
3094 3138 3.433984 TTGAGTGGGCTGGCAGCAA 62.434 57.895 37.49 23.99 44.75 3.91
3095 3139 3.855503 CTTGAGTGGGCTGGCAGCA 62.856 63.158 37.49 18.52 44.75 4.41
3096 3140 3.060615 CTTGAGTGGGCTGGCAGC 61.061 66.667 30.93 30.93 41.46 5.25
3097 3141 1.228367 AACTTGAGTGGGCTGGCAG 60.228 57.895 10.94 10.94 0.00 4.85
3098 3142 1.228245 GAACTTGAGTGGGCTGGCA 60.228 57.895 2.88 0.00 0.00 4.92
3099 3143 0.823356 TTGAACTTGAGTGGGCTGGC 60.823 55.000 0.00 0.00 0.00 4.85
3100 3144 1.242076 CTTGAACTTGAGTGGGCTGG 58.758 55.000 0.00 0.00 0.00 4.85
3101 3145 1.876156 GACTTGAACTTGAGTGGGCTG 59.124 52.381 0.00 0.00 0.00 4.85
3102 3146 1.202818 GGACTTGAACTTGAGTGGGCT 60.203 52.381 0.00 0.00 0.00 5.19
3103 3147 1.239347 GGACTTGAACTTGAGTGGGC 58.761 55.000 0.00 0.00 0.00 5.36
3104 3148 1.878102 CGGGACTTGAACTTGAGTGGG 60.878 57.143 0.00 0.00 0.00 4.61
3105 3149 1.512926 CGGGACTTGAACTTGAGTGG 58.487 55.000 0.00 0.00 0.00 4.00
3106 3150 1.512926 CCGGGACTTGAACTTGAGTG 58.487 55.000 0.00 0.00 0.00 3.51
3107 3151 0.250338 GCCGGGACTTGAACTTGAGT 60.250 55.000 2.18 0.00 0.00 3.41
3108 3152 0.035458 AGCCGGGACTTGAACTTGAG 59.965 55.000 2.18 0.00 0.00 3.02
3109 3153 0.472471 AAGCCGGGACTTGAACTTGA 59.528 50.000 2.18 0.00 0.00 3.02
3110 3154 3.021451 AAGCCGGGACTTGAACTTG 57.979 52.632 2.18 0.00 0.00 3.16
3116 3160 2.409870 GCATCCAAGCCGGGACTTG 61.410 63.158 18.45 18.45 45.42 3.16
3117 3161 2.044946 GCATCCAAGCCGGGACTT 60.045 61.111 2.18 0.00 40.44 3.01
3118 3162 4.473520 CGCATCCAAGCCGGGACT 62.474 66.667 2.18 0.00 40.44 3.85
3119 3163 4.778143 ACGCATCCAAGCCGGGAC 62.778 66.667 2.18 0.00 40.44 4.46
3120 3164 4.776322 CACGCATCCAAGCCGGGA 62.776 66.667 2.18 0.00 42.21 5.14
3123 3167 3.803082 CACCACGCATCCAAGCCG 61.803 66.667 0.00 0.00 0.00 5.52
3124 3168 4.120331 GCACCACGCATCCAAGCC 62.120 66.667 0.00 0.00 41.79 4.35
3125 3169 3.044059 GAGCACCACGCATCCAAGC 62.044 63.158 0.00 0.00 46.13 4.01
3126 3170 1.672030 TGAGCACCACGCATCCAAG 60.672 57.895 0.00 0.00 46.13 3.61
3127 3171 1.965930 GTGAGCACCACGCATCCAA 60.966 57.895 0.00 0.00 46.13 3.53
3128 3172 2.358615 GTGAGCACCACGCATCCA 60.359 61.111 0.00 0.00 46.13 3.41
3135 3179 0.249911 AGAAACTCCGTGAGCACCAC 60.250 55.000 1.36 0.00 42.30 4.16
3136 3180 0.033504 GAGAAACTCCGTGAGCACCA 59.966 55.000 1.36 0.00 32.04 4.17
3137 3181 0.670854 GGAGAAACTCCGTGAGCACC 60.671 60.000 1.97 0.00 41.08 5.01
3138 3182 2.828933 GGAGAAACTCCGTGAGCAC 58.171 57.895 1.97 0.00 41.08 4.40
3147 3191 9.952188 GTTGGCATTTATTTATAGGAGAAACTC 57.048 33.333 0.00 0.00 0.00 3.01
3148 3192 8.621286 CGTTGGCATTTATTTATAGGAGAAACT 58.379 33.333 0.00 0.00 0.00 2.66
3149 3193 8.617809 TCGTTGGCATTTATTTATAGGAGAAAC 58.382 33.333 0.00 0.00 0.00 2.78
3150 3194 8.740123 TCGTTGGCATTTATTTATAGGAGAAA 57.260 30.769 0.00 0.00 0.00 2.52
3151 3195 7.444183 CCTCGTTGGCATTTATTTATAGGAGAA 59.556 37.037 0.00 0.00 0.00 2.87
3152 3196 6.934645 CCTCGTTGGCATTTATTTATAGGAGA 59.065 38.462 0.00 0.00 0.00 3.71
3153 3197 6.149474 CCCTCGTTGGCATTTATTTATAGGAG 59.851 42.308 0.00 0.00 0.00 3.69
3154 3198 6.001460 CCCTCGTTGGCATTTATTTATAGGA 58.999 40.000 0.00 0.00 0.00 2.94
3155 3199 5.768164 ACCCTCGTTGGCATTTATTTATAGG 59.232 40.000 0.00 0.00 0.00 2.57
3156 3200 6.877611 ACCCTCGTTGGCATTTATTTATAG 57.122 37.500 0.00 0.00 0.00 1.31
3157 3201 8.385898 CTAACCCTCGTTGGCATTTATTTATA 57.614 34.615 0.00 0.00 33.17 0.98
3158 3202 7.272037 CTAACCCTCGTTGGCATTTATTTAT 57.728 36.000 0.00 0.00 33.17 1.40
3159 3203 6.687081 CTAACCCTCGTTGGCATTTATTTA 57.313 37.500 0.00 0.00 33.17 1.40
3160 3204 5.576447 CTAACCCTCGTTGGCATTTATTT 57.424 39.130 0.00 0.00 33.17 1.40
3177 3221 0.611062 GACCAACCCAAGGGCTAACC 60.611 60.000 4.70 0.00 39.32 2.85
3178 3222 0.404426 AGACCAACCCAAGGGCTAAC 59.596 55.000 4.70 0.00 44.68 2.34
3179 3223 1.154430 AAGACCAACCCAAGGGCTAA 58.846 50.000 4.70 0.00 46.21 3.09
3180 3224 1.154430 AAAGACCAACCCAAGGGCTA 58.846 50.000 4.70 0.00 46.21 3.93
3182 3226 1.128200 AAAAAGACCAACCCAAGGGC 58.872 50.000 4.70 0.00 39.32 5.19
3298 3342 2.777459 TTTTCTTGGCCCCCTGTTTA 57.223 45.000 0.00 0.00 0.00 2.01
3605 3649 7.753132 TGGTCAAATTAATTAGAACAATGCGAC 59.247 33.333 0.01 0.00 0.00 5.19
3607 3651 7.253288 CGTGGTCAAATTAATTAGAACAATGCG 60.253 37.037 0.01 0.00 28.18 4.73
3629 3673 2.159653 GCATACAAAACTCTCTGCGTGG 60.160 50.000 0.00 0.00 0.00 4.94
3634 3678 6.506500 AATCCAAGCATACAAAACTCTCTG 57.493 37.500 0.00 0.00 0.00 3.35
3791 3835 6.043938 AGAGGGTAAAACATCAGAACTTACCA 59.956 38.462 10.54 0.00 42.14 3.25
3880 3924 3.099141 ACCAATGTCCCAGCCTTTAATG 58.901 45.455 0.00 0.00 0.00 1.90
3971 4018 6.636705 TGAACTAACCACATGTATCAGGTAC 58.363 40.000 6.05 0.00 33.15 3.34
3997 4044 7.712639 GCAAACAAGACAGGATCATAAGAGATA 59.287 37.037 0.00 0.00 0.00 1.98
4064 4111 3.657727 CCTACCCCATAGATGGTGGAATT 59.342 47.826 17.92 4.09 46.65 2.17
4149 4196 4.095036 GGTTTCCATAGCTACAAAGAGTGC 59.905 45.833 0.00 0.00 0.00 4.40
4151 4198 5.248477 TCTGGTTTCCATAGCTACAAAGAGT 59.752 40.000 0.00 0.00 30.82 3.24
4186 4233 1.549170 AGAGTTGAGTTCGGCGGTATT 59.451 47.619 7.21 0.00 0.00 1.89
4241 4288 0.397564 TTTGGTAACCGGTCACCTCC 59.602 55.000 27.52 15.70 35.73 4.30
4288 4337 2.791383 TGGTGTTTCTTGGATTTGCG 57.209 45.000 0.00 0.00 0.00 4.85
4293 4342 4.528206 GGAGGAAAATGGTGTTTCTTGGAT 59.472 41.667 0.00 0.00 37.60 3.41
4295 4344 3.305335 CGGAGGAAAATGGTGTTTCTTGG 60.305 47.826 0.00 0.00 37.60 3.61
4413 4462 2.027653 CCAATGTTACGCCCCCAAAATT 60.028 45.455 0.00 0.00 0.00 1.82
4414 4463 1.552792 CCAATGTTACGCCCCCAAAAT 59.447 47.619 0.00 0.00 0.00 1.82
4417 4466 1.979693 GCCAATGTTACGCCCCCAA 60.980 57.895 0.00 0.00 0.00 4.12
4455 4504 4.084287 AGCCACAAAATCATCACAGTGAT 58.916 39.130 10.53 10.53 40.44 3.06
4491 4542 5.918608 ACAAGTCTTATAGCGTGATTCCAT 58.081 37.500 0.00 0.00 0.00 3.41
4501 4552 8.821894 CATTCCTTCAGTAACAAGTCTTATAGC 58.178 37.037 0.00 0.00 0.00 2.97
4504 4555 7.918076 TCCATTCCTTCAGTAACAAGTCTTAT 58.082 34.615 0.00 0.00 0.00 1.73
4505 4556 7.311092 TCCATTCCTTCAGTAACAAGTCTTA 57.689 36.000 0.00 0.00 0.00 2.10
4506 4557 6.187727 TCCATTCCTTCAGTAACAAGTCTT 57.812 37.500 0.00 0.00 0.00 3.01
4517 4568 3.947868 ACTGTGACATCCATTCCTTCAG 58.052 45.455 0.00 0.00 0.00 3.02
4558 4609 6.533723 CGTAAAATGGAGCAACTAGTATGACA 59.466 38.462 0.00 0.00 0.00 3.58
4559 4610 6.534079 ACGTAAAATGGAGCAACTAGTATGAC 59.466 38.462 0.00 0.00 0.00 3.06
4560 4611 6.636705 ACGTAAAATGGAGCAACTAGTATGA 58.363 36.000 0.00 0.00 0.00 2.15
4561 4612 6.903883 ACGTAAAATGGAGCAACTAGTATG 57.096 37.500 0.00 0.00 0.00 2.39
4562 4613 9.257651 GATAACGTAAAATGGAGCAACTAGTAT 57.742 33.333 0.00 0.00 0.00 2.12
4581 4632 5.888982 ATGGGATCCAACTAAGATAACGT 57.111 39.130 15.23 0.00 36.95 3.99
4591 4654 3.372349 CCATCAGACAATGGGATCCAACT 60.372 47.826 15.23 0.00 42.19 3.16
4610 4673 8.735692 AAAAGTGAAAATTGACATTCAACCAT 57.264 26.923 0.00 0.00 39.45 3.55
4620 4683 6.313658 AGTTCAGCCAAAAAGTGAAAATTGAC 59.686 34.615 0.00 0.00 32.15 3.18
4622 4685 6.508404 CGAGTTCAGCCAAAAAGTGAAAATTG 60.508 38.462 0.00 0.00 32.15 2.32
4624 4687 5.043248 CGAGTTCAGCCAAAAAGTGAAAAT 58.957 37.500 0.00 0.00 32.15 1.82
4628 4691 2.612212 GTCGAGTTCAGCCAAAAAGTGA 59.388 45.455 0.00 0.00 0.00 3.41
4632 4695 2.639065 ACAGTCGAGTTCAGCCAAAAA 58.361 42.857 0.00 0.00 0.00 1.94
4657 4720 2.572104 AGGGAAGCGTCCTTAGATTTGT 59.428 45.455 18.54 0.00 44.28 2.83
4678 4741 6.428083 TTTCTCCTACACTTCCATACAACA 57.572 37.500 0.00 0.00 0.00 3.33
4680 4743 9.832445 GATATTTTCTCCTACACTTCCATACAA 57.168 33.333 0.00 0.00 0.00 2.41
4687 4750 5.753921 CACCGGATATTTTCTCCTACACTTC 59.246 44.000 9.46 0.00 0.00 3.01
4691 4754 5.205821 TCTCACCGGATATTTTCTCCTACA 58.794 41.667 9.46 0.00 0.00 2.74
4693 4756 5.279506 GCATCTCACCGGATATTTTCTCCTA 60.280 44.000 9.46 0.00 0.00 2.94
4747 4814 8.160106 ACTCCCCTGAATTATAATGACATTCTC 58.840 37.037 3.36 0.00 0.00 2.87
4748 4815 8.050316 ACTCCCCTGAATTATAATGACATTCT 57.950 34.615 3.36 0.00 0.00 2.40
4749 4816 9.793259 TTACTCCCCTGAATTATAATGACATTC 57.207 33.333 3.36 0.00 0.00 2.67
4758 4825 8.955794 AGGCTTTATTTACTCCCCTGAATTATA 58.044 33.333 0.00 0.00 0.00 0.98
4759 4826 7.725844 CAGGCTTTATTTACTCCCCTGAATTAT 59.274 37.037 0.00 0.00 40.52 1.28
4760 4827 7.060421 CAGGCTTTATTTACTCCCCTGAATTA 58.940 38.462 0.00 0.00 40.52 1.40
4763 4830 4.538490 TCAGGCTTTATTTACTCCCCTGAA 59.462 41.667 4.15 0.00 42.99 3.02
4764 4831 4.080526 GTCAGGCTTTATTTACTCCCCTGA 60.081 45.833 2.57 2.57 43.53 3.86
4765 4832 4.200092 GTCAGGCTTTATTTACTCCCCTG 58.800 47.826 0.00 0.00 39.68 4.45
4767 4834 3.945921 GTGTCAGGCTTTATTTACTCCCC 59.054 47.826 0.00 0.00 0.00 4.81
4768 4835 3.621715 CGTGTCAGGCTTTATTTACTCCC 59.378 47.826 0.00 0.00 0.00 4.30
4769 4836 4.329256 GTCGTGTCAGGCTTTATTTACTCC 59.671 45.833 0.00 0.00 0.00 3.85
4771 4838 4.890088 TGTCGTGTCAGGCTTTATTTACT 58.110 39.130 0.00 0.00 0.00 2.24
4772 4839 5.796350 ATGTCGTGTCAGGCTTTATTTAC 57.204 39.130 0.00 0.00 0.00 2.01
4774 4841 5.938125 ACTAATGTCGTGTCAGGCTTTATTT 59.062 36.000 0.00 0.00 0.00 1.40
4777 4844 4.021807 TCACTAATGTCGTGTCAGGCTTTA 60.022 41.667 0.00 0.00 34.14 1.85
4778 4845 3.067106 CACTAATGTCGTGTCAGGCTTT 58.933 45.455 0.00 0.00 0.00 3.51
4779 4846 2.299013 TCACTAATGTCGTGTCAGGCTT 59.701 45.455 0.00 0.00 34.14 4.35
4780 4847 1.893137 TCACTAATGTCGTGTCAGGCT 59.107 47.619 0.00 0.00 34.14 4.58
4781 4848 2.363788 TCACTAATGTCGTGTCAGGC 57.636 50.000 0.00 0.00 34.14 4.85
4782 4849 5.408299 TCATTTTCACTAATGTCGTGTCAGG 59.592 40.000 0.00 0.00 36.95 3.86
4783 4850 6.466308 TCATTTTCACTAATGTCGTGTCAG 57.534 37.500 0.00 0.00 36.95 3.51
4784 4851 6.852858 TTCATTTTCACTAATGTCGTGTCA 57.147 33.333 0.00 0.00 36.95 3.58
4785 4852 8.728088 ATTTTCATTTTCACTAATGTCGTGTC 57.272 30.769 0.00 0.00 36.95 3.67
4860 5039 7.932120 AGGAAATGACGTTCTAGAAATATCG 57.068 36.000 6.78 9.11 0.00 2.92
4944 7011 8.859090 ACTCAGTGAAATCATGTTTGGAAATTA 58.141 29.630 0.00 0.00 0.00 1.40
4947 7014 6.713762 ACTCAGTGAAATCATGTTTGGAAA 57.286 33.333 0.00 0.00 0.00 3.13
5054 7124 4.846779 TGAGAAACACCAAGGCAATTAC 57.153 40.909 0.00 0.00 0.00 1.89
5055 7125 5.452078 CTTGAGAAACACCAAGGCAATTA 57.548 39.130 0.00 0.00 36.90 1.40
5062 7132 2.023673 TGCACCTTGAGAAACACCAAG 58.976 47.619 0.00 0.00 39.43 3.61
5065 7135 2.024414 AGTTGCACCTTGAGAAACACC 58.976 47.619 0.00 0.00 0.00 4.16
5066 7136 2.423538 ACAGTTGCACCTTGAGAAACAC 59.576 45.455 0.00 0.00 0.00 3.32
5067 7137 2.423185 CACAGTTGCACCTTGAGAAACA 59.577 45.455 0.00 0.00 0.00 2.83
5084 7154 2.127496 CGAGCGCAAACAGCACAG 60.127 61.111 11.47 0.00 46.13 3.66
5088 7158 0.387239 AAAATCCGAGCGCAAACAGC 60.387 50.000 11.47 0.00 40.87 4.40
5089 7159 1.197721 AGAAAATCCGAGCGCAAACAG 59.802 47.619 11.47 0.00 0.00 3.16
5096 7166 0.804544 TGGCGTAGAAAATCCGAGCG 60.805 55.000 0.00 0.00 0.00 5.03
5100 7170 1.287425 GGAGTGGCGTAGAAAATCCG 58.713 55.000 0.00 0.00 0.00 4.18
5114 7184 6.427853 TGATCAACTAACTTCACATTGGAGTG 59.572 38.462 0.00 0.00 40.85 3.51
5119 7189 6.245115 TGCTGATCAACTAACTTCACATTG 57.755 37.500 0.00 0.00 0.00 2.82
5121 7191 4.394300 GCTGCTGATCAACTAACTTCACAT 59.606 41.667 0.00 0.00 0.00 3.21
5123 7193 3.181526 CGCTGCTGATCAACTAACTTCAC 60.182 47.826 0.00 0.00 0.00 3.18
5125 7195 2.349886 CCGCTGCTGATCAACTAACTTC 59.650 50.000 0.00 0.00 0.00 3.01
5126 7196 2.350522 CCGCTGCTGATCAACTAACTT 58.649 47.619 0.00 0.00 0.00 2.66
5131 7201 1.744368 CTGCCGCTGCTGATCAACT 60.744 57.895 0.70 0.00 38.61 3.16
5133 7203 3.129502 GCTGCCGCTGCTGATCAA 61.130 61.111 14.47 0.00 38.61 2.57
5253 7326 1.867487 AGTAGGAGGGAGGGGGTGT 60.867 63.158 0.00 0.00 0.00 4.16


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

AutoCloner maintained by Alex Coulton.