Multiple sequence alignment - TraesCS2D01G525000

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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 TraesCS2D01G525000 chr2D 100.000 3959 0 0 1 3959 613321322 613325280 0.000000e+00 7312.0
1 TraesCS2D01G525000 chr2D 86.237 574 68 7 3393 3959 613235144 613234575 2.620000e-171 612.0
2 TraesCS2D01G525000 chr2D 81.890 635 80 19 3037 3653 613238237 613237620 1.640000e-138 503.0
3 TraesCS2D01G525000 chr2D 88.279 401 28 7 2596 2989 613235933 613235545 2.790000e-126 462.0
4 TraesCS2D01G525000 chr2D 86.735 294 17 8 2679 2962 613238702 613238421 1.380000e-79 307.0
5 TraesCS2D01G525000 chr2D 86.194 268 32 5 3366 3631 613308148 613307884 6.480000e-73 285.0
6 TraesCS2D01G525000 chr2D 76.520 592 92 25 3372 3940 613224906 613224339 3.010000e-71 279.0
7 TraesCS2D01G525000 chr2A 93.128 1848 118 5 1138 2982 744979932 744981773 0.000000e+00 2700.0
8 TraesCS2D01G525000 chr2A 87.708 1082 83 19 1 1073 744978890 744979930 0.000000e+00 1216.0
9 TraesCS2D01G525000 chr2A 81.257 939 110 30 3033 3959 744994292 744995176 0.000000e+00 699.0
10 TraesCS2D01G525000 chr2A 87.455 550 61 5 3417 3959 744905479 744904931 9.340000e-176 627.0
11 TraesCS2D01G525000 chr2A 77.394 637 99 23 3319 3944 744902946 744902344 1.760000e-88 337.0
12 TraesCS2D01G525000 chr2A 97.802 91 2 0 3494 3584 744981889 744981979 1.470000e-34 158.0
13 TraesCS2D01G525000 chr2A 92.405 79 6 0 3863 3941 744927842 744927764 3.230000e-21 113.0
14 TraesCS2D01G525000 chr2A 96.774 62 2 0 3613 3674 744981977 744982038 1.950000e-18 104.0
15 TraesCS2D01G525000 chr2B 92.333 1852 121 7 1138 2980 748701044 748702883 0.000000e+00 2614.0
16 TraesCS2D01G525000 chr2B 87.465 1085 88 22 1 1073 748699994 748701042 0.000000e+00 1206.0
17 TraesCS2D01G525000 chr2B 91.842 760 42 7 3146 3904 748703127 748703867 0.000000e+00 1042.0
18 TraesCS2D01G525000 chr2B 86.678 593 61 14 3381 3959 748588940 748588352 3.340000e-180 641.0
19 TraesCS2D01G525000 chr2B 87.000 400 31 5 2599 2989 748589660 748589273 7.860000e-117 431.0
20 TraesCS2D01G525000 chr2B 77.532 632 103 20 3319 3940 748573449 748572847 1.050000e-90 344.0
21 TraesCS2D01G525000 chr2B 82.569 109 12 4 3025 3133 748580970 748580869 5.450000e-14 89.8
22 TraesCS2D01G525000 chr2B 100.000 32 0 0 3055 3086 748703046 748703077 4.270000e-05 60.2
23 TraesCS2D01G525000 chr5D 75.337 519 95 25 3438 3941 410381922 410382422 6.660000e-53 219.0
24 TraesCS2D01G525000 chr5A 75.337 519 95 25 3438 3941 521859734 521860234 6.660000e-53 219.0
25 TraesCS2D01G525000 chr5A 82.692 208 32 4 3435 3640 521768588 521768793 8.740000e-42 182.0


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 TraesCS2D01G525000 chr2D 613321322 613325280 3958 False 7312.00 7312 100.00000 1 3959 1 chr2D.!!$F1 3958
1 TraesCS2D01G525000 chr2D 613234575 613238702 4127 True 471.00 612 85.78525 2596 3959 4 chr2D.!!$R3 1363
2 TraesCS2D01G525000 chr2D 613224339 613224906 567 True 279.00 279 76.52000 3372 3940 1 chr2D.!!$R1 568
3 TraesCS2D01G525000 chr2A 744978890 744982038 3148 False 1044.50 2700 93.85300 1 3674 4 chr2A.!!$F2 3673
4 TraesCS2D01G525000 chr2A 744994292 744995176 884 False 699.00 699 81.25700 3033 3959 1 chr2A.!!$F1 926
5 TraesCS2D01G525000 chr2A 744902344 744905479 3135 True 482.00 627 82.42450 3319 3959 2 chr2A.!!$R2 640
6 TraesCS2D01G525000 chr2B 748699994 748703867 3873 False 1230.55 2614 92.91000 1 3904 4 chr2B.!!$F1 3903
7 TraesCS2D01G525000 chr2B 748588352 748589660 1308 True 536.00 641 86.83900 2599 3959 2 chr2B.!!$R3 1360
8 TraesCS2D01G525000 chr2B 748572847 748573449 602 True 344.00 344 77.53200 3319 3940 1 chr2B.!!$R1 621
9 TraesCS2D01G525000 chr5D 410381922 410382422 500 False 219.00 219 75.33700 3438 3941 1 chr5D.!!$F1 503
10 TraesCS2D01G525000 chr5A 521859734 521860234 500 False 219.00 219 75.33700 3438 3941 1 chr5A.!!$F2 503

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
283 290 1.135915 GCAAACACCATGTGAACACCA 59.864 47.619 0.49 0.0 36.96 4.17 F
1079 1107 0.884704 TCTCAAGTTGAACCCGCTGC 60.885 55.000 7.06 0.0 0.00 5.25 F
1106 1134 0.252239 TGCAGGAGTGAAGCCCTAGA 60.252 55.000 0.00 0.0 0.00 2.43 F
1629 1657 0.460987 CTCTTGATCAGCACGGGGTC 60.461 60.000 0.00 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1087 1115 0.252239 TCTAGGGCTTCACTCCTGCA 60.252 55.0 0.0 0.0 34.75 4.41 R
2583 2614 0.685458 CCATGCTTAGGCCCTGCTTT 60.685 55.0 0.0 0.0 37.74 3.51 R
2627 2802 1.077123 CGAGGAAGAAGAGACGACGA 58.923 55.0 0.0 0.0 0.00 4.20 R
3316 3678 1.525804 GCACGGTCGTTTTCGTTTGC 61.526 55.0 0.0 0.0 44.46 3.68 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
39 40 8.709308 AGTTTCTCAATTCACCTATAGCATACT 58.291 33.333 0.00 0.00 0.00 2.12
79 84 5.054477 TGTTTCCCTAAGAAGTCGAAACTG 58.946 41.667 11.07 0.00 39.04 3.16
90 95 6.281405 AGAAGTCGAAACTGTAGATGTTGTT 58.719 36.000 0.00 0.00 35.36 2.83
223 230 6.801862 GCTGTATTGGTTTTAAAGTAGCACTG 59.198 38.462 0.00 0.00 0.00 3.66
225 232 8.228035 TGTATTGGTTTTAAAGTAGCACTGTT 57.772 30.769 0.00 0.00 0.00 3.16
226 233 9.339850 TGTATTGGTTTTAAAGTAGCACTGTTA 57.660 29.630 0.00 0.00 0.00 2.41
274 281 2.507484 TCCTCTCAAGCAAACACCATG 58.493 47.619 0.00 0.00 0.00 3.66
275 282 2.158623 TCCTCTCAAGCAAACACCATGT 60.159 45.455 0.00 0.00 0.00 3.21
276 283 2.030540 CCTCTCAAGCAAACACCATGTG 60.031 50.000 0.00 0.00 39.75 3.21
277 284 2.880268 CTCTCAAGCAAACACCATGTGA 59.120 45.455 0.49 0.00 36.96 3.58
278 285 3.286353 TCTCAAGCAAACACCATGTGAA 58.714 40.909 0.49 0.00 36.96 3.18
279 286 3.066621 TCTCAAGCAAACACCATGTGAAC 59.933 43.478 0.49 0.00 36.96 3.18
280 287 2.757314 TCAAGCAAACACCATGTGAACA 59.243 40.909 0.49 0.00 36.96 3.18
282 289 1.408702 AGCAAACACCATGTGAACACC 59.591 47.619 0.49 0.00 36.96 4.16
283 290 1.135915 GCAAACACCATGTGAACACCA 59.864 47.619 0.49 0.00 36.96 4.17
285 292 3.005261 GCAAACACCATGTGAACACCATA 59.995 43.478 0.49 0.00 36.96 2.74
286 293 4.797471 CAAACACCATGTGAACACCATAG 58.203 43.478 0.49 0.00 36.96 2.23
287 294 3.788227 ACACCATGTGAACACCATAGT 57.212 42.857 0.49 0.00 36.96 2.12
288 295 3.411446 ACACCATGTGAACACCATAGTG 58.589 45.455 0.49 7.46 42.36 2.74
289 296 2.162208 CACCATGTGAACACCATAGTGC 59.838 50.000 2.46 0.00 40.93 4.40
326 333 5.882000 TGATTCACCATTTCCTCATGTACAG 59.118 40.000 0.33 0.00 0.00 2.74
332 339 6.038603 CACCATTTCCTCATGTACAGTAATGG 59.961 42.308 20.36 20.36 43.89 3.16
395 403 9.844790 TTGATGTATTTCTTTAGCATTTCTGTG 57.155 29.630 0.00 0.00 0.00 3.66
410 418 5.963176 TTTCTGTGCAAGCTCATATGAAA 57.037 34.783 6.90 2.48 0.00 2.69
423 431 9.632638 AAGCTCATATGAAATGGTACTTGTTAT 57.367 29.630 6.90 0.00 0.00 1.89
449 457 7.786030 TCTCATACTTCTGGATTTCCTTACAG 58.214 38.462 0.00 0.00 36.82 2.74
451 459 3.956744 ACTTCTGGATTTCCTTACAGGC 58.043 45.455 0.00 0.00 34.61 4.85
453 461 3.914426 TCTGGATTTCCTTACAGGCTC 57.086 47.619 0.00 0.00 34.61 4.70
469 477 6.506500 ACAGGCTCTTGAATCACTTTATTG 57.493 37.500 0.00 0.00 0.00 1.90
476 484 9.630098 GCTCTTGAATCACTTTATTGATTTCAA 57.370 29.630 0.15 0.00 44.59 2.69
493 501 5.560966 TTTCAACTGTGGTTCTTGTTCTC 57.439 39.130 0.00 0.00 32.73 2.87
536 544 5.455326 GGTTGTGGATGAGTAGGCTTGATAT 60.455 44.000 0.00 0.00 0.00 1.63
556 565 9.540538 TTGATATTTAATCTTTTGGGTTCTCCA 57.459 29.630 0.00 0.00 45.43 3.86
602 611 5.577835 TCAGTCGGTTGTTTTCTTTTGATG 58.422 37.500 0.00 0.00 0.00 3.07
657 666 3.064900 ACCTGACTTTCTTGCAGATCC 57.935 47.619 0.00 0.00 0.00 3.36
695 704 3.125146 TGCGTGATATGAAGTCTGTTTGC 59.875 43.478 0.00 0.00 0.00 3.68
703 712 3.476552 TGAAGTCTGTTTGCGGATTCTT 58.523 40.909 0.00 0.00 31.86 2.52
873 882 5.234757 TGACGTGTACTTCCATTTTGTGTAC 59.765 40.000 0.00 0.00 35.43 2.90
915 924 4.202080 GGTGAAGTTGTTAAACTGGGGTTC 60.202 45.833 0.00 0.00 46.15 3.62
922 931 4.148838 TGTTAAACTGGGGTTCTGATTGG 58.851 43.478 0.00 0.00 34.14 3.16
925 934 1.444933 ACTGGGGTTCTGATTGGTCA 58.555 50.000 0.00 0.00 0.00 4.02
947 969 1.227674 GAAGCTATCGGCCACTGGG 60.228 63.158 2.24 0.00 43.05 4.45
964 986 1.589716 GGGCAGCGCTCAAGTCATTT 61.590 55.000 7.13 0.00 0.00 2.32
1044 1072 3.390003 TGTTCGTGGGAAGGAACAC 57.610 52.632 9.27 0.00 45.38 3.32
1050 1078 1.066143 CGTGGGAAGGAACACATAGCT 60.066 52.381 0.00 0.00 37.45 3.32
1067 1095 3.699411 AGCTGCTTCATTCTCTCAAGT 57.301 42.857 0.00 0.00 0.00 3.16
1073 1101 4.516698 TGCTTCATTCTCTCAAGTTGAACC 59.483 41.667 7.06 0.00 0.00 3.62
1074 1102 4.083057 GCTTCATTCTCTCAAGTTGAACCC 60.083 45.833 7.06 0.00 0.00 4.11
1075 1103 3.664107 TCATTCTCTCAAGTTGAACCCG 58.336 45.455 7.06 0.00 0.00 5.28
1076 1104 1.878953 TTCTCTCAAGTTGAACCCGC 58.121 50.000 7.06 0.00 0.00 6.13
1077 1105 1.048601 TCTCTCAAGTTGAACCCGCT 58.951 50.000 7.06 0.00 0.00 5.52
1078 1106 1.151668 CTCTCAAGTTGAACCCGCTG 58.848 55.000 7.06 0.00 0.00 5.18
1079 1107 0.884704 TCTCAAGTTGAACCCGCTGC 60.885 55.000 7.06 0.00 0.00 5.25
1080 1108 1.856265 CTCAAGTTGAACCCGCTGCC 61.856 60.000 7.06 0.00 0.00 4.85
1081 1109 2.978010 AAGTTGAACCCGCTGCCG 60.978 61.111 0.00 0.00 0.00 5.69
1086 1114 3.747976 GAACCCGCTGCCGCAAAT 61.748 61.111 0.00 0.00 35.30 2.32
1087 1115 3.281359 GAACCCGCTGCCGCAAATT 62.281 57.895 0.00 0.00 35.30 1.82
1088 1116 3.572196 AACCCGCTGCCGCAAATTG 62.572 57.895 0.00 0.00 35.30 2.32
1090 1118 4.721111 CCGCTGCCGCAAATTGCA 62.721 61.111 18.65 0.00 45.36 4.08
1094 1122 2.964174 TGCCGCAAATTGCAGGAG 59.036 55.556 24.94 10.40 45.36 3.69
1095 1123 1.902918 TGCCGCAAATTGCAGGAGT 60.903 52.632 24.94 0.00 45.36 3.85
1097 1125 1.865788 GCCGCAAATTGCAGGAGTGA 61.866 55.000 24.94 0.00 45.36 3.41
1098 1126 0.597568 CCGCAAATTGCAGGAGTGAA 59.402 50.000 18.65 0.00 45.36 3.18
1099 1127 1.401931 CCGCAAATTGCAGGAGTGAAG 60.402 52.381 18.65 0.00 45.36 3.02
1100 1128 1.706443 GCAAATTGCAGGAGTGAAGC 58.294 50.000 13.73 0.00 44.26 3.86
1102 1130 1.067354 CAAATTGCAGGAGTGAAGCCC 60.067 52.381 0.00 0.00 0.00 5.19
1103 1131 0.407139 AATTGCAGGAGTGAAGCCCT 59.593 50.000 0.00 0.00 0.00 5.19
1104 1132 1.289160 ATTGCAGGAGTGAAGCCCTA 58.711 50.000 0.00 0.00 0.00 3.53
1106 1134 0.252239 TGCAGGAGTGAAGCCCTAGA 60.252 55.000 0.00 0.00 0.00 2.43
1107 1135 1.127343 GCAGGAGTGAAGCCCTAGAT 58.873 55.000 0.00 0.00 0.00 1.98
1108 1136 1.202627 GCAGGAGTGAAGCCCTAGATG 60.203 57.143 0.00 0.00 0.00 2.90
1109 1137 2.114616 CAGGAGTGAAGCCCTAGATGT 58.885 52.381 0.00 0.00 0.00 3.06
1110 1138 3.300388 CAGGAGTGAAGCCCTAGATGTA 58.700 50.000 0.00 0.00 0.00 2.29
1111 1139 3.320541 CAGGAGTGAAGCCCTAGATGTAG 59.679 52.174 0.00 0.00 0.00 2.74
1113 1141 2.695666 GAGTGAAGCCCTAGATGTAGCA 59.304 50.000 0.00 0.00 0.00 3.49
1114 1142 3.312890 AGTGAAGCCCTAGATGTAGCAT 58.687 45.455 0.00 0.00 0.00 3.79
1117 1145 3.323115 TGAAGCCCTAGATGTAGCATCAG 59.677 47.826 11.12 6.71 0.00 2.90
1118 1146 2.969628 AGCCCTAGATGTAGCATCAGT 58.030 47.619 11.12 0.00 0.00 3.41
1119 1147 3.312890 AGCCCTAGATGTAGCATCAGTT 58.687 45.455 11.12 0.00 0.00 3.16
1120 1148 4.483950 AGCCCTAGATGTAGCATCAGTTA 58.516 43.478 11.12 0.00 0.00 2.24
1121 1149 4.901849 AGCCCTAGATGTAGCATCAGTTAA 59.098 41.667 11.12 0.00 0.00 2.01
1123 1151 5.698545 GCCCTAGATGTAGCATCAGTTAAAG 59.301 44.000 11.12 0.48 0.00 1.85
1124 1152 6.686632 GCCCTAGATGTAGCATCAGTTAAAGT 60.687 42.308 11.12 0.00 0.00 2.66
1125 1153 7.275920 CCCTAGATGTAGCATCAGTTAAAGTT 58.724 38.462 11.12 0.00 0.00 2.66
1126 1154 7.225538 CCCTAGATGTAGCATCAGTTAAAGTTG 59.774 40.741 11.12 0.00 0.00 3.16
1127 1155 6.992063 AGATGTAGCATCAGTTAAAGTTGG 57.008 37.500 11.12 0.00 0.00 3.77
1128 1156 6.476378 AGATGTAGCATCAGTTAAAGTTGGT 58.524 36.000 11.12 0.00 0.00 3.67
1129 1157 6.942576 AGATGTAGCATCAGTTAAAGTTGGTT 59.057 34.615 11.12 0.00 0.00 3.67
1130 1158 6.312399 TGTAGCATCAGTTAAAGTTGGTTG 57.688 37.500 0.00 0.00 0.00 3.77
1131 1159 4.243007 AGCATCAGTTAAAGTTGGTTGC 57.757 40.909 0.00 0.00 0.00 4.17
1132 1160 3.005791 AGCATCAGTTAAAGTTGGTTGCC 59.994 43.478 0.00 0.00 0.00 4.52
1133 1161 3.005791 GCATCAGTTAAAGTTGGTTGCCT 59.994 43.478 0.00 0.00 0.00 4.75
1134 1162 4.798574 CATCAGTTAAAGTTGGTTGCCTC 58.201 43.478 0.00 0.00 0.00 4.70
1135 1163 2.875933 TCAGTTAAAGTTGGTTGCCTCG 59.124 45.455 0.00 0.00 0.00 4.63
1136 1164 2.031157 CAGTTAAAGTTGGTTGCCTCGG 60.031 50.000 0.00 0.00 0.00 4.63
1143 1171 4.821589 GGTTGCCTCGGGAGCTCG 62.822 72.222 7.83 0.00 0.00 5.03
1173 1201 7.465781 GCAGCTGAGACTTCTAGAAAATCATTC 60.466 40.741 20.43 8.18 0.00 2.67
1182 1210 6.456795 TCTAGAAAATCATTCGAGCAGAGA 57.543 37.500 0.00 0.00 0.00 3.10
1263 1291 3.691118 TGCCAAATCTGTATTCTGCTGAC 59.309 43.478 0.00 0.00 0.00 3.51
1275 1303 4.548451 TTCTGCTGACAGTCAATCATCT 57.452 40.909 4.41 0.00 44.77 2.90
1286 1314 3.012518 GTCAATCATCTGGTGGGAACAG 58.987 50.000 0.00 0.00 44.46 3.16
1301 1329 7.110155 GGTGGGAACAGAGTTAAATTATCTGA 58.890 38.462 9.78 0.00 44.46 3.27
1304 1332 9.010029 TGGGAACAGAGTTAAATTATCTGAAAC 57.990 33.333 9.78 2.65 42.48 2.78
1326 1354 4.578928 ACTTTGTTCACTCCACATTGTACC 59.421 41.667 0.00 0.00 0.00 3.34
1336 1364 2.487762 CCACATTGTACCGCAAGTGATT 59.512 45.455 0.00 0.00 40.86 2.57
1341 1369 1.621317 TGTACCGCAAGTGATTCTGGA 59.379 47.619 0.00 0.00 0.00 3.86
1348 1376 3.935203 CGCAAGTGATTCTGGATTAGTGT 59.065 43.478 0.00 0.00 0.00 3.55
1352 1380 4.265073 AGTGATTCTGGATTAGTGTTGGC 58.735 43.478 0.00 0.00 0.00 4.52
1354 1382 2.107950 TTCTGGATTAGTGTTGGCGG 57.892 50.000 0.00 0.00 0.00 6.13
1389 1417 3.558505 CTCAAGAAATTTGCAGTCCACG 58.441 45.455 0.00 0.00 0.00 4.94
1391 1419 3.820467 TCAAGAAATTTGCAGTCCACGAT 59.180 39.130 0.00 0.00 0.00 3.73
1425 1453 4.427312 GCAAGGAGCATTCACATAAAAGG 58.573 43.478 0.00 0.00 44.79 3.11
1440 1468 9.703892 TCACATAAAAGGAAAAATGGTATTGTG 57.296 29.630 0.00 0.00 0.00 3.33
1448 1476 5.011635 GGAAAAATGGTATTGTGTTCCCACT 59.988 40.000 0.00 0.00 42.34 4.00
1454 1482 5.882040 TGGTATTGTGTTCCCACTTATTGA 58.118 37.500 0.00 0.00 42.34 2.57
1455 1483 6.489603 TGGTATTGTGTTCCCACTTATTGAT 58.510 36.000 0.00 0.00 42.34 2.57
1482 1510 3.576078 TCAACTTCAGCCAAAAGGAGA 57.424 42.857 0.00 0.00 0.00 3.71
1508 1536 4.128925 GTGATTATGAGCTGTCACCTCA 57.871 45.455 0.00 0.30 42.91 3.86
1629 1657 0.460987 CTCTTGATCAGCACGGGGTC 60.461 60.000 0.00 0.00 0.00 4.46
1680 1708 1.587946 GGTTGTTCTTTTGCTGCAACG 59.412 47.619 15.72 9.42 39.95 4.10
1686 1714 1.330521 TCTTTTGCTGCAACGTCAGAC 59.669 47.619 15.72 0.00 36.19 3.51
1707 1735 6.915300 CAGACACACTAGATAGCACTGATAAC 59.085 42.308 0.00 0.00 0.00 1.89
1926 1954 3.599792 CTGCACCAAAAGCGCCGAG 62.600 63.158 2.29 0.00 33.85 4.63
1953 1981 1.078848 AGAGTTCTGCATCGCCCAC 60.079 57.895 0.00 0.00 0.00 4.61
2013 2041 2.190578 GCACGGGGAAGATCAGGG 59.809 66.667 0.00 0.00 0.00 4.45
2126 2154 3.542676 TGGTCGCCGGTGTCAGTT 61.543 61.111 16.01 0.00 0.00 3.16
2181 2209 0.895100 TGTTCTGCAAGTCCCATGGC 60.895 55.000 6.09 0.00 33.76 4.40
2436 2464 0.804989 GTGGCAAGCGCTGTAAATCT 59.195 50.000 12.58 0.00 38.60 2.40
2553 2584 3.028098 AGGGGGAGGAGCGGTCTA 61.028 66.667 15.18 0.00 0.00 2.59
2583 2614 1.488705 ATGGAAACCTGACGGCCTCA 61.489 55.000 0.00 2.72 0.00 3.86
2595 2626 2.677228 GCCTCAAAGCAGGGCCTA 59.323 61.111 5.28 0.00 39.96 3.93
2596 2627 1.000896 GCCTCAAAGCAGGGCCTAA 60.001 57.895 5.28 0.00 39.96 2.69
2597 2628 1.034292 GCCTCAAAGCAGGGCCTAAG 61.034 60.000 5.28 0.00 39.96 2.18
2602 2777 0.685458 AAAGCAGGGCCTAAGCATGG 60.685 55.000 17.20 0.00 42.56 3.66
2627 2802 2.688666 TGGCCTCTTCAGCGGGAT 60.689 61.111 3.32 0.00 0.00 3.85
2628 2803 2.110006 GGCCTCTTCAGCGGGATC 59.890 66.667 0.00 0.00 0.00 3.36
2629 2804 2.279784 GCCTCTTCAGCGGGATCG 60.280 66.667 0.00 0.00 39.81 3.69
2731 2913 1.300697 GGCGAGTCGTTGGAACACT 60.301 57.895 15.08 0.00 39.29 3.55
2807 2991 2.691927 ACCATCGTCTTCGTTTAACCC 58.308 47.619 0.00 0.00 38.33 4.11
2843 3027 2.188817 AGAAGAAGAAGGTGGCGGTAT 58.811 47.619 0.00 0.00 0.00 2.73
2964 3151 4.270008 ACAACCCGGAATCCTGAAAATAG 58.730 43.478 0.73 0.00 0.00 1.73
2989 3176 4.516698 ACATCTTCTGTGTGTGCTTTAAGG 59.483 41.667 0.00 0.00 36.48 2.69
2990 3177 3.476552 TCTTCTGTGTGTGCTTTAAGGG 58.523 45.455 0.00 0.00 0.00 3.95
2997 3319 2.158682 TGTGTGCTTTAAGGGAGCTTCA 60.159 45.455 0.00 0.00 40.75 3.02
3007 3329 1.002544 AGGGAGCTTCAGTGTACTTGC 59.997 52.381 0.00 0.00 0.00 4.01
3009 3331 2.072298 GGAGCTTCAGTGTACTTGCTG 58.928 52.381 8.13 0.53 0.00 4.41
3010 3332 2.548920 GGAGCTTCAGTGTACTTGCTGT 60.549 50.000 8.13 0.00 34.57 4.40
3011 3333 3.306088 GGAGCTTCAGTGTACTTGCTGTA 60.306 47.826 8.13 3.49 34.57 2.74
3012 3334 4.499183 GAGCTTCAGTGTACTTGCTGTAT 58.501 43.478 8.13 0.00 34.57 2.29
3013 3335 4.899502 AGCTTCAGTGTACTTGCTGTATT 58.100 39.130 10.71 0.00 34.57 1.89
3014 3336 6.037786 AGCTTCAGTGTACTTGCTGTATTA 57.962 37.500 10.71 0.00 34.57 0.98
3015 3337 6.644347 AGCTTCAGTGTACTTGCTGTATTAT 58.356 36.000 10.71 0.00 34.57 1.28
3016 3338 7.782049 AGCTTCAGTGTACTTGCTGTATTATA 58.218 34.615 10.71 0.00 34.57 0.98
3017 3339 8.424918 AGCTTCAGTGTACTTGCTGTATTATAT 58.575 33.333 10.71 0.00 34.57 0.86
3018 3340 8.491152 GCTTCAGTGTACTTGCTGTATTATATG 58.509 37.037 10.71 0.00 34.57 1.78
3019 3341 9.750125 CTTCAGTGTACTTGCTGTATTATATGA 57.250 33.333 10.71 0.00 34.57 2.15
3028 3350 8.099537 ACTTGCTGTATTATATGATTCTGAGGG 58.900 37.037 0.00 0.00 0.00 4.30
3029 3351 7.797121 TGCTGTATTATATGATTCTGAGGGA 57.203 36.000 0.00 0.00 0.00 4.20
3030 3352 7.845037 TGCTGTATTATATGATTCTGAGGGAG 58.155 38.462 0.00 0.00 0.00 4.30
3031 3353 7.455953 TGCTGTATTATATGATTCTGAGGGAGT 59.544 37.037 0.00 0.00 0.00 3.85
3044 3366 7.406031 TTCTGAGGGAGTAGTAAATACTGTG 57.594 40.000 3.36 0.00 45.06 3.66
3093 3430 5.468540 TCAGTGTACTTGTTCAGCTGTAT 57.531 39.130 14.67 0.00 0.00 2.29
3094 3431 5.853936 TCAGTGTACTTGTTCAGCTGTATT 58.146 37.500 14.67 0.00 0.00 1.89
3095 3432 6.288294 TCAGTGTACTTGTTCAGCTGTATTT 58.712 36.000 14.67 0.00 0.00 1.40
3096 3433 6.423905 TCAGTGTACTTGTTCAGCTGTATTTC 59.576 38.462 14.67 1.90 0.00 2.17
3097 3434 6.202762 CAGTGTACTTGTTCAGCTGTATTTCA 59.797 38.462 14.67 4.48 0.00 2.69
3098 3435 6.936900 AGTGTACTTGTTCAGCTGTATTTCAT 59.063 34.615 14.67 0.00 0.00 2.57
3105 3442 7.275888 TGTTCAGCTGTATTTCATTTGAACT 57.724 32.000 14.67 0.00 42.72 3.01
3138 3480 8.903570 AAACGAAATTGCATTATCATAAACGA 57.096 26.923 0.00 0.00 0.00 3.85
3139 3481 8.903570 AACGAAATTGCATTATCATAAACGAA 57.096 26.923 0.00 0.00 0.00 3.85
3140 3482 8.903570 ACGAAATTGCATTATCATAAACGAAA 57.096 26.923 0.00 0.00 0.00 3.46
3141 3483 9.515020 ACGAAATTGCATTATCATAAACGAAAT 57.485 25.926 0.00 0.00 0.00 2.17
3172 3527 8.814235 GTCGTTGAAATTCCGAAATCTTCTATA 58.186 33.333 0.00 0.00 31.68 1.31
3174 3529 8.818057 CGTTGAAATTCCGAAATCTTCTATACT 58.182 33.333 0.00 0.00 0.00 2.12
3177 3532 8.612619 TGAAATTCCGAAATCTTCTATACTTGC 58.387 33.333 0.00 0.00 0.00 4.01
3183 3538 8.421784 TCCGAAATCTTCTATACTTGCTGTATT 58.578 33.333 7.92 0.00 41.64 1.89
3184 3539 9.046296 CCGAAATCTTCTATACTTGCTGTATTT 57.954 33.333 7.92 0.00 41.64 1.40
3185 3540 9.855361 CGAAATCTTCTATACTTGCTGTATTTG 57.145 33.333 7.92 3.79 41.64 2.32
3220 3575 4.123497 TCCGATTTCATCACGTTCTCAT 57.877 40.909 0.00 0.00 0.00 2.90
3221 3576 5.257082 TCCGATTTCATCACGTTCTCATA 57.743 39.130 0.00 0.00 0.00 2.15
3236 3591 5.470098 CGTTCTCATATATTCCCACCAAAGG 59.530 44.000 0.00 0.00 0.00 3.11
3354 3716 4.903010 AAGGCAACGCGTCGTGGT 62.903 61.111 14.44 0.00 39.99 4.16
3361 3723 2.027628 AACGCGTCGTGGTGAACAAC 62.028 55.000 14.44 0.00 39.99 3.32
3411 3773 0.395586 TAGATTGCACCCATGGCCAC 60.396 55.000 8.16 0.00 0.00 5.01
3461 3830 0.970937 GGACGTCCTGGTGGAGATCA 60.971 60.000 27.64 0.00 44.16 2.92
3468 3837 0.180642 CTGGTGGAGATCATGCTGCT 59.819 55.000 0.00 0.00 0.00 4.24
3543 3912 0.458543 GTCATCGACGAGCACACCAT 60.459 55.000 3.01 0.00 0.00 3.55
3686 4065 1.147376 GTACCATACATGCGCCCCA 59.853 57.895 4.18 0.00 0.00 4.96
3731 4140 1.818642 GTGCAATGGTCTTCTCTGCT 58.181 50.000 0.00 0.00 34.10 4.24
3844 4258 1.966451 CTCGTTTTTCCCGCCTGCT 60.966 57.895 0.00 0.00 0.00 4.24
3943 4364 2.703798 GCACGTCCCATGCAGCATT 61.704 57.895 4.69 0.00 42.88 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 108 8.899306 TGGGACAAGTGGAAGAAGACTTCATAT 61.899 40.741 17.34 3.14 44.77 1.78
105 110 6.930433 TGGGACAAGTGGAAGAAGACTTCAT 61.930 44.000 17.34 5.22 44.77 2.57
106 111 5.671038 TGGGACAAGTGGAAGAAGACTTCA 61.671 45.833 17.34 0.00 44.77 3.02
107 112 3.181454 TGGGACAAGTGGAAGAAGACTTC 60.181 47.826 7.14 7.14 43.34 3.01
108 113 2.777692 TGGGACAAGTGGAAGAAGACTT 59.222 45.455 0.00 0.00 35.13 3.01
109 114 2.104963 GTGGGACAAGTGGAAGAAGACT 59.895 50.000 0.00 0.00 44.16 3.24
110 115 2.104963 AGTGGGACAAGTGGAAGAAGAC 59.895 50.000 0.00 0.00 44.16 3.01
111 116 2.408565 AGTGGGACAAGTGGAAGAAGA 58.591 47.619 0.00 0.00 44.16 2.87
112 117 2.938956 AGTGGGACAAGTGGAAGAAG 57.061 50.000 0.00 0.00 44.16 2.85
242 249 5.809001 TGCTTGAGAGGAACATGAATTAGT 58.191 37.500 0.00 0.00 0.00 2.24
256 263 2.880268 TCACATGGTGTTTGCTTGAGAG 59.120 45.455 0.00 0.00 34.79 3.20
274 281 7.843490 TTAGAATTAGCACTATGGTGTTCAC 57.157 36.000 11.18 0.00 44.65 3.18
275 282 8.264347 TGATTAGAATTAGCACTATGGTGTTCA 58.736 33.333 11.18 0.00 44.65 3.18
276 283 8.662781 TGATTAGAATTAGCACTATGGTGTTC 57.337 34.615 11.18 6.62 44.65 3.18
277 284 9.060347 CATGATTAGAATTAGCACTATGGTGTT 57.940 33.333 11.18 7.46 44.65 3.32
278 285 8.432013 TCATGATTAGAATTAGCACTATGGTGT 58.568 33.333 11.18 0.72 44.65 4.16
279 286 8.837788 TCATGATTAGAATTAGCACTATGGTG 57.162 34.615 4.57 4.57 45.53 4.17
285 292 7.994911 TGGTGAATCATGATTAGAATTAGCACT 59.005 33.333 20.75 0.00 0.00 4.40
286 293 8.158169 TGGTGAATCATGATTAGAATTAGCAC 57.842 34.615 20.75 18.92 0.00 4.40
287 294 8.929260 ATGGTGAATCATGATTAGAATTAGCA 57.071 30.769 20.75 16.49 0.00 3.49
341 348 1.065491 TCTGATTAGCCGGTGCATGTT 60.065 47.619 1.90 0.00 41.13 2.71
391 399 4.097437 ACCATTTCATATGAGCTTGCACAG 59.903 41.667 5.39 0.00 0.00 3.66
395 403 6.183360 ACAAGTACCATTTCATATGAGCTTGC 60.183 38.462 5.39 0.00 34.68 4.01
410 418 9.823647 CAGAAGTATGAGAATAACAAGTACCAT 57.176 33.333 0.00 0.00 0.00 3.55
423 431 8.146053 TGTAAGGAAATCCAGAAGTATGAGAA 57.854 34.615 1.67 0.00 38.89 2.87
449 457 8.246180 TGAAATCAATAAAGTGATTCAAGAGCC 58.754 33.333 6.15 0.00 45.42 4.70
469 477 6.038714 AGAGAACAAGAACCACAGTTGAAATC 59.961 38.462 0.00 0.00 35.94 2.17
476 484 4.843728 TGAAAGAGAACAAGAACCACAGT 58.156 39.130 0.00 0.00 0.00 3.55
493 501 7.222611 CCACAACCAACTTAATGTTTCTGAAAG 59.777 37.037 2.48 0.00 36.63 2.62
581 590 5.357032 ACTCATCAAAAGAAAACAACCGACT 59.643 36.000 0.00 0.00 0.00 4.18
657 666 3.689161 TCACGCAATTAAATGTCCTCTGG 59.311 43.478 0.00 0.00 0.00 3.86
717 726 2.156891 GCAAAAATCATGTGCACTGCAG 59.843 45.455 19.41 13.48 40.08 4.41
873 882 6.387041 TCACCACCGAGAAAGTATATAGTG 57.613 41.667 0.00 0.00 0.00 2.74
926 935 1.144936 AGTGGCCGATAGCTTCTGC 59.855 57.895 0.00 0.00 43.05 4.26
928 937 1.690219 CCCAGTGGCCGATAGCTTCT 61.690 60.000 2.61 0.00 43.05 2.85
930 939 2.911143 CCCAGTGGCCGATAGCTT 59.089 61.111 2.61 0.00 43.05 3.74
947 969 1.198637 AGAAAATGACTTGAGCGCTGC 59.801 47.619 18.48 7.36 0.00 5.25
956 978 7.182930 AGGTAGGATTAGGACAGAAAATGACTT 59.817 37.037 0.00 0.00 0.00 3.01
993 1021 4.841246 GTCATAGTAAGGTCCATCCCAGAT 59.159 45.833 0.00 0.00 36.75 2.90
994 1022 4.223953 GTCATAGTAAGGTCCATCCCAGA 58.776 47.826 0.00 0.00 36.75 3.86
1027 1055 1.892209 ATGTGTTCCTTCCCACGAAC 58.108 50.000 0.00 0.00 39.07 3.95
1044 1072 5.117584 ACTTGAGAGAATGAAGCAGCTATG 58.882 41.667 0.00 0.00 0.00 2.23
1050 1078 4.516698 GGTTCAACTTGAGAGAATGAAGCA 59.483 41.667 10.16 0.00 42.80 3.91
1081 1109 1.670967 GGCTTCACTCCTGCAATTTGC 60.671 52.381 14.49 14.49 45.29 3.68
1082 1110 1.067354 GGGCTTCACTCCTGCAATTTG 60.067 52.381 0.00 0.00 0.00 2.32
1083 1111 1.203100 AGGGCTTCACTCCTGCAATTT 60.203 47.619 0.00 0.00 31.11 1.82
1084 1112 0.407139 AGGGCTTCACTCCTGCAATT 59.593 50.000 0.00 0.00 31.11 2.32
1085 1113 1.211457 CTAGGGCTTCACTCCTGCAAT 59.789 52.381 0.00 0.00 34.75 3.56
1086 1114 0.615331 CTAGGGCTTCACTCCTGCAA 59.385 55.000 0.00 0.00 34.75 4.08
1087 1115 0.252239 TCTAGGGCTTCACTCCTGCA 60.252 55.000 0.00 0.00 34.75 4.41
1088 1116 1.127343 ATCTAGGGCTTCACTCCTGC 58.873 55.000 0.00 0.00 34.75 4.85
1089 1117 2.114616 ACATCTAGGGCTTCACTCCTG 58.885 52.381 0.00 0.00 34.75 3.86
1090 1118 2.559381 ACATCTAGGGCTTCACTCCT 57.441 50.000 0.00 0.00 37.18 3.69
1091 1119 2.036604 GCTACATCTAGGGCTTCACTCC 59.963 54.545 0.00 0.00 0.00 3.85
1092 1120 2.695666 TGCTACATCTAGGGCTTCACTC 59.304 50.000 0.00 0.00 0.00 3.51
1094 1122 3.070159 TGATGCTACATCTAGGGCTTCAC 59.930 47.826 8.87 0.00 35.17 3.18
1095 1123 3.308401 TGATGCTACATCTAGGGCTTCA 58.692 45.455 8.87 0.00 36.82 3.02
1097 1125 3.312890 ACTGATGCTACATCTAGGGCTT 58.687 45.455 8.87 0.00 0.00 4.35
1098 1126 2.969628 ACTGATGCTACATCTAGGGCT 58.030 47.619 8.87 0.00 0.00 5.19
1099 1127 3.760580 AACTGATGCTACATCTAGGGC 57.239 47.619 8.87 0.00 0.00 5.19
1100 1128 6.821388 ACTTTAACTGATGCTACATCTAGGG 58.179 40.000 8.87 0.69 0.00 3.53
1102 1130 7.766278 ACCAACTTTAACTGATGCTACATCTAG 59.234 37.037 8.87 7.14 0.00 2.43
1103 1131 7.620880 ACCAACTTTAACTGATGCTACATCTA 58.379 34.615 8.87 0.00 0.00 1.98
1104 1132 6.476378 ACCAACTTTAACTGATGCTACATCT 58.524 36.000 8.87 0.00 0.00 2.90
1106 1134 6.570378 GCAACCAACTTTAACTGATGCTACAT 60.570 38.462 0.00 0.00 0.00 2.29
1107 1135 5.278266 GCAACCAACTTTAACTGATGCTACA 60.278 40.000 0.00 0.00 0.00 2.74
1108 1136 5.154222 GCAACCAACTTTAACTGATGCTAC 58.846 41.667 0.00 0.00 0.00 3.58
1109 1137 4.217550 GGCAACCAACTTTAACTGATGCTA 59.782 41.667 0.00 0.00 0.00 3.49
1110 1138 3.005791 GGCAACCAACTTTAACTGATGCT 59.994 43.478 0.00 0.00 0.00 3.79
1111 1139 3.005791 AGGCAACCAACTTTAACTGATGC 59.994 43.478 0.00 0.00 37.17 3.91
1113 1141 3.502211 CGAGGCAACCAACTTTAACTGAT 59.498 43.478 0.00 0.00 37.17 2.90
1114 1142 2.875933 CGAGGCAACCAACTTTAACTGA 59.124 45.455 0.00 0.00 37.17 3.41
1117 1145 1.268625 CCCGAGGCAACCAACTTTAAC 59.731 52.381 0.00 0.00 37.17 2.01
1118 1146 1.143277 TCCCGAGGCAACCAACTTTAA 59.857 47.619 0.00 0.00 37.17 1.52
1119 1147 0.766131 TCCCGAGGCAACCAACTTTA 59.234 50.000 0.00 0.00 37.17 1.85
1120 1148 0.537371 CTCCCGAGGCAACCAACTTT 60.537 55.000 0.00 0.00 37.17 2.66
1121 1149 1.073199 CTCCCGAGGCAACCAACTT 59.927 57.895 0.00 0.00 37.17 2.66
1123 1151 3.056328 GCTCCCGAGGCAACCAAC 61.056 66.667 0.00 0.00 37.17 3.77
1124 1152 3.249189 AGCTCCCGAGGCAACCAA 61.249 61.111 0.00 0.00 37.17 3.67
1125 1153 3.706373 GAGCTCCCGAGGCAACCA 61.706 66.667 0.87 0.00 37.17 3.67
1126 1154 4.821589 CGAGCTCCCGAGGCAACC 62.822 72.222 8.47 0.00 37.17 3.77
1127 1155 4.821589 CCGAGCTCCCGAGGCAAC 62.822 72.222 8.47 0.00 0.00 4.17
1130 1158 4.214327 CTTCCGAGCTCCCGAGGC 62.214 72.222 8.47 0.00 0.00 4.70
1131 1159 4.214327 GCTTCCGAGCTCCCGAGG 62.214 72.222 8.47 3.34 45.65 4.63
1143 1171 2.757868 TCTAGAAGTCTCAGCTGCTTCC 59.242 50.000 21.77 9.83 39.36 3.46
1173 1201 2.339728 AACTTCGACTTCTCTGCTCG 57.660 50.000 0.00 0.00 0.00 5.03
1182 1210 2.438392 AGGAACAGGGAAACTTCGACTT 59.562 45.455 0.00 0.00 0.00 3.01
1263 1291 3.012518 GTTCCCACCAGATGATTGACTG 58.987 50.000 0.00 0.00 0.00 3.51
1275 1303 6.884295 CAGATAATTTAACTCTGTTCCCACCA 59.116 38.462 0.00 0.00 33.34 4.17
1301 1329 5.659440 ACAATGTGGAGTGAACAAAGTTT 57.341 34.783 0.00 0.00 0.00 2.66
1304 1332 4.319477 CGGTACAATGTGGAGTGAACAAAG 60.319 45.833 0.00 0.00 0.00 2.77
1314 1342 1.070914 TCACTTGCGGTACAATGTGGA 59.929 47.619 0.00 0.00 37.72 4.02
1316 1344 3.436704 AGAATCACTTGCGGTACAATGTG 59.563 43.478 0.00 0.00 37.72 3.21
1326 1354 3.935203 ACACTAATCCAGAATCACTTGCG 59.065 43.478 0.00 0.00 0.00 4.85
1336 1364 0.392461 GCCGCCAACACTAATCCAGA 60.392 55.000 0.00 0.00 0.00 3.86
1341 1369 1.812571 CTTGAAGCCGCCAACACTAAT 59.187 47.619 0.00 0.00 0.00 1.73
1348 1376 2.672996 GCCTCTTGAAGCCGCCAA 60.673 61.111 0.00 0.00 0.00 4.52
1352 1380 2.046507 AGCTGCCTCTTGAAGCCG 60.047 61.111 0.00 0.00 37.68 5.52
1354 1382 0.803740 CTTGAGCTGCCTCTTGAAGC 59.196 55.000 0.00 0.00 38.93 3.86
1389 1417 2.124736 TTGCGGCCAGGCACTATC 60.125 61.111 15.19 0.00 43.82 2.08
1391 1419 4.408821 CCTTGCGGCCAGGCACTA 62.409 66.667 15.19 0.36 43.82 2.74
1440 1468 4.503714 TCCCTCATCAATAAGTGGGAAC 57.496 45.455 0.00 0.00 40.39 3.62
1454 1482 1.918262 TGGCTGAAGTTGATCCCTCAT 59.082 47.619 0.00 0.00 0.00 2.90
1455 1483 1.361204 TGGCTGAAGTTGATCCCTCA 58.639 50.000 0.00 0.00 0.00 3.86
1482 1510 4.701765 GTGACAGCTCATAATCACCTGAT 58.298 43.478 0.00 0.00 36.31 2.90
1508 1536 4.298103 ACATCTGATCTTGGAGCAAACT 57.702 40.909 0.00 0.00 0.00 2.66
1601 1629 5.050499 CCGTGCTGATCAAGAGATAAATCAC 60.050 44.000 0.00 0.00 33.72 3.06
1629 1657 4.593864 GGCTCGGGGCTAAGCTCG 62.594 72.222 0.00 0.00 41.46 5.03
1680 1708 4.396478 TCAGTGCTATCTAGTGTGTCTGAC 59.604 45.833 0.00 0.00 0.00 3.51
1686 1714 5.215903 CCGTTATCAGTGCTATCTAGTGTG 58.784 45.833 0.00 0.00 0.00 3.82
1707 1735 2.357009 CTGATGATTTTTCTGCTCCCCG 59.643 50.000 0.00 0.00 0.00 5.73
1824 1852 1.538849 CCTTTGTTGCAACCTGGCTTC 60.539 52.381 26.14 0.00 34.04 3.86
1926 1954 0.687354 TGCAGAACTCTGTCTTCCCC 59.313 55.000 8.46 0.00 45.45 4.81
1998 2026 1.208165 AAAGCCCTGATCTTCCCCGT 61.208 55.000 0.00 0.00 0.00 5.28
2013 2041 0.707822 CGCCGTGTTTTATGCAAAGC 59.292 50.000 0.00 0.00 0.00 3.51
2126 2154 4.020617 CCTTGCTGCAGTCCGGGA 62.021 66.667 16.64 0.00 0.00 5.14
2361 2389 2.674380 CTCTTGGTGCACCCTGGC 60.674 66.667 32.62 8.33 34.29 4.85
2430 2458 3.055458 TCTTGTCGCACCCATCAGATTTA 60.055 43.478 0.00 0.00 0.00 1.40
2436 2464 1.375908 GCTCTTGTCGCACCCATCA 60.376 57.895 0.00 0.00 0.00 3.07
2553 2584 1.284198 AGGTTTCCATGAGCAGAGCAT 59.716 47.619 0.00 0.00 0.00 3.79
2583 2614 0.685458 CCATGCTTAGGCCCTGCTTT 60.685 55.000 0.00 0.00 37.74 3.51
2595 2626 4.431131 CCAGGCCCGACCATGCTT 62.431 66.667 0.00 0.00 43.14 3.91
2627 2802 1.077123 CGAGGAAGAAGAGACGACGA 58.923 55.000 0.00 0.00 0.00 4.20
2628 2803 1.077123 TCGAGGAAGAAGAGACGACG 58.923 55.000 0.00 0.00 0.00 5.12
2629 2804 2.530832 GTCGAGGAAGAAGAGACGAC 57.469 55.000 0.00 0.00 41.84 4.34
2731 2913 2.033141 GAGCCTGCCACTCTGCAA 59.967 61.111 0.00 0.00 41.51 4.08
2843 3027 2.646175 CCGAAGCTCTGGTTCCGGA 61.646 63.158 0.00 0.00 36.81 5.14
2983 3170 5.305585 CAAGTACACTGAAGCTCCCTTAAA 58.694 41.667 0.00 0.00 0.00 1.52
2986 3173 2.551071 GCAAGTACACTGAAGCTCCCTT 60.551 50.000 0.00 0.00 0.00 3.95
2989 3176 2.072298 CAGCAAGTACACTGAAGCTCC 58.928 52.381 4.97 0.00 35.90 4.70
2990 3177 2.760374 ACAGCAAGTACACTGAAGCTC 58.240 47.619 15.06 0.00 37.35 4.09
3016 3338 8.865090 CAGTATTTACTACTCCCTCAGAATCAT 58.135 37.037 0.00 0.00 38.68 2.45
3017 3339 7.839705 ACAGTATTTACTACTCCCTCAGAATCA 59.160 37.037 0.00 0.00 38.68 2.57
3018 3340 8.138712 CACAGTATTTACTACTCCCTCAGAATC 58.861 40.741 0.00 0.00 38.68 2.52
3019 3341 7.839705 TCACAGTATTTACTACTCCCTCAGAAT 59.160 37.037 0.00 0.00 38.68 2.40
3020 3342 7.179966 TCACAGTATTTACTACTCCCTCAGAA 58.820 38.462 0.00 0.00 38.68 3.02
3021 3343 6.728411 TCACAGTATTTACTACTCCCTCAGA 58.272 40.000 0.00 0.00 38.68 3.27
3022 3344 6.460399 GCTCACAGTATTTACTACTCCCTCAG 60.460 46.154 0.00 0.00 38.68 3.35
3023 3345 5.360144 GCTCACAGTATTTACTACTCCCTCA 59.640 44.000 0.00 0.00 38.68 3.86
3024 3346 5.505985 CGCTCACAGTATTTACTACTCCCTC 60.506 48.000 0.00 0.00 38.68 4.30
3025 3347 4.338682 CGCTCACAGTATTTACTACTCCCT 59.661 45.833 0.00 0.00 38.68 4.20
3026 3348 4.097589 ACGCTCACAGTATTTACTACTCCC 59.902 45.833 0.00 0.00 38.68 4.30
3027 3349 5.035443 CACGCTCACAGTATTTACTACTCC 58.965 45.833 0.00 0.00 38.68 3.85
3028 3350 5.638783 ACACGCTCACAGTATTTACTACTC 58.361 41.667 0.00 0.00 38.68 2.59
3029 3351 5.640189 ACACGCTCACAGTATTTACTACT 57.360 39.130 0.00 0.00 41.53 2.57
3030 3352 6.549952 ACTACACGCTCACAGTATTTACTAC 58.450 40.000 0.00 0.00 34.13 2.73
3031 3353 6.183360 GGACTACACGCTCACAGTATTTACTA 60.183 42.308 0.00 0.00 34.13 1.82
3035 3357 3.510360 AGGACTACACGCTCACAGTATTT 59.490 43.478 0.00 0.00 0.00 1.40
3044 3366 2.030540 TGTACACAAGGACTACACGCTC 60.031 50.000 0.00 0.00 0.00 5.03
3093 3430 6.016693 TCGTTTATGGAGCAGTTCAAATGAAA 60.017 34.615 0.00 0.00 35.58 2.69
3094 3431 5.471797 TCGTTTATGGAGCAGTTCAAATGAA 59.528 36.000 0.00 0.00 0.00 2.57
3095 3432 5.000591 TCGTTTATGGAGCAGTTCAAATGA 58.999 37.500 0.00 0.00 0.00 2.57
3096 3433 5.295431 TCGTTTATGGAGCAGTTCAAATG 57.705 39.130 0.00 0.00 0.00 2.32
3097 3434 5.957842 TTCGTTTATGGAGCAGTTCAAAT 57.042 34.783 0.00 0.00 0.00 2.32
3098 3435 5.759506 TTTCGTTTATGGAGCAGTTCAAA 57.240 34.783 0.00 0.00 0.00 2.69
3105 3442 4.717233 ATGCAATTTCGTTTATGGAGCA 57.283 36.364 0.00 0.00 0.00 4.26
3137 3479 6.595794 TCGGAATTTCAACGACTGTAATTTC 58.404 36.000 0.00 0.00 35.75 2.17
3138 3480 6.548441 TCGGAATTTCAACGACTGTAATTT 57.452 33.333 0.00 0.00 35.75 1.82
3139 3481 6.548441 TTCGGAATTTCAACGACTGTAATT 57.452 33.333 0.00 0.00 37.63 1.40
3140 3482 6.548441 TTTCGGAATTTCAACGACTGTAAT 57.452 33.333 0.00 0.00 36.24 1.89
3141 3483 5.987777 TTTCGGAATTTCAACGACTGTAA 57.012 34.783 0.00 0.00 36.24 2.41
3144 3497 5.283060 AGATTTCGGAATTTCAACGACTG 57.717 39.130 0.00 0.00 36.24 3.51
3158 3511 8.594881 AATACAGCAAGTATAGAAGATTTCGG 57.405 34.615 2.73 0.00 42.56 4.30
3172 3527 8.413229 ACAGTTTTTGATACAAATACAGCAAGT 58.587 29.630 15.65 0.00 0.00 3.16
3174 3529 9.243637 GAACAGTTTTTGATACAAATACAGCAA 57.756 29.630 15.65 0.00 0.00 3.91
3177 3532 8.286800 TCGGAACAGTTTTTGATACAAATACAG 58.713 33.333 15.65 11.80 0.00 2.74
3183 3538 7.708051 TGAAATCGGAACAGTTTTTGATACAA 58.292 30.769 0.00 0.00 0.00 2.41
3184 3539 7.265647 TGAAATCGGAACAGTTTTTGATACA 57.734 32.000 0.00 0.00 0.00 2.29
3185 3540 8.382003 GATGAAATCGGAACAGTTTTTGATAC 57.618 34.615 0.00 0.00 31.13 2.24
3220 3575 6.192044 GGAAAGTTCCTTTGGTGGGAATATA 58.808 40.000 2.65 0.00 43.57 0.86
3221 3576 5.023452 GGAAAGTTCCTTTGGTGGGAATAT 58.977 41.667 2.65 0.00 43.57 1.28
3272 3634 3.773418 TTGATTCCGACTTGGTAACCA 57.227 42.857 0.00 0.00 39.52 3.67
3316 3678 1.525804 GCACGGTCGTTTTCGTTTGC 61.526 55.000 0.00 0.00 44.46 3.68
3354 3716 3.167921 TCTCGTTTTCTCGGTTGTTCA 57.832 42.857 0.00 0.00 0.00 3.18
3356 3718 4.729746 GCTTTTCTCGTTTTCTCGGTTGTT 60.730 41.667 0.00 0.00 0.00 2.83
3361 3723 3.247648 TCTTGCTTTTCTCGTTTTCTCGG 59.752 43.478 0.00 0.00 0.00 4.63
3363 3725 5.208503 CCTTCTTGCTTTTCTCGTTTTCTC 58.791 41.667 0.00 0.00 0.00 2.87
3368 3730 3.208747 TCCCTTCTTGCTTTTCTCGTT 57.791 42.857 0.00 0.00 0.00 3.85
3370 3732 3.565902 ACTTTCCCTTCTTGCTTTTCTCG 59.434 43.478 0.00 0.00 0.00 4.04
3543 3912 4.519437 CGCGGCTCTGCATCTCCA 62.519 66.667 0.00 0.00 34.15 3.86
3731 4140 2.010670 CCGTCTTGTTGTCGCACAA 58.989 52.632 0.00 0.00 35.42 3.33


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

AutoCloner maintained by Alex Coulton.