Multiple sequence alignment - TraesCS5A01G347400

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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 TraesCS5A01G347400 chr5A 100.000 3787 0 0 1 3787 549952172 549955958 0.000000e+00 6994.0
1 TraesCS5A01G347400 chr5A 91.484 411 19 5 1794 2198 550250386 550250786 5.530000e-153 551.0
2 TraesCS5A01G347400 chr5A 85.659 516 36 13 902 1396 550249558 550250056 3.370000e-140 508.0
3 TraesCS5A01G347400 chr5D 88.466 1786 87 56 1545 3245 435933794 435935545 0.000000e+00 2047.0
4 TraesCS5A01G347400 chr5D 87.635 1019 55 34 550 1516 435932797 435933796 0.000000e+00 1118.0
5 TraesCS5A01G347400 chr5D 88.542 96 7 3 356 451 435932684 435932775 3.090000e-21 113.0
6 TraesCS5A01G347400 chr5D 82.105 95 11 6 1103 1194 565703009 565702918 4.060000e-10 76.8
7 TraesCS5A01G347400 chr5B 85.160 1314 78 52 400 1646 529607960 529609223 0.000000e+00 1238.0
8 TraesCS5A01G347400 chr5B 82.903 1240 107 59 994 2198 529987400 529988569 0.000000e+00 1018.0
9 TraesCS5A01G347400 chr5B 82.462 975 91 41 621 1527 529686554 529687516 0.000000e+00 780.0
10 TraesCS5A01G347400 chr5B 89.244 595 34 14 1676 2260 529687607 529688181 0.000000e+00 717.0
11 TraesCS5A01G347400 chr5B 85.190 709 49 26 1734 2406 529609235 529609923 0.000000e+00 676.0
12 TraesCS5A01G347400 chr5B 79.906 851 64 41 2390 3176 529609948 529610755 3.350000e-145 525.0
13 TraesCS5A01G347400 chr5B 82.873 362 31 6 1 335 529607091 529607448 2.860000e-76 296.0
14 TraesCS5A01G347400 chr5B 79.751 321 42 12 2636 2952 529688615 529688916 1.070000e-50 211.0
15 TraesCS5A01G347400 chr5B 93.396 106 4 3 1542 1645 529687504 529687608 1.820000e-33 154.0
16 TraesCS5A01G347400 chr5B 85.149 101 6 5 498 598 529686473 529686564 1.120000e-15 95.3
17 TraesCS5A01G347400 chr3D 75.315 555 111 22 3243 3787 559634936 559635474 3.780000e-60 243.0
18 TraesCS5A01G347400 chr3D 93.182 44 3 0 1153 1196 288113426 288113383 8.780000e-07 65.8
19 TraesCS5A01G347400 chr4A 82.105 95 11 6 1103 1194 607261959 607261868 4.060000e-10 76.8
20 TraesCS5A01G347400 chr3B 93.182 44 3 0 1153 1196 380895259 380895216 8.780000e-07 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G347400 chr5A 549952172 549955958 3786 False 6994.000000 6994 100.000000 1 3787 1 chr5A.!!$F1 3786
1 TraesCS5A01G347400 chr5A 550249558 550250786 1228 False 529.500000 551 88.571500 902 2198 2 chr5A.!!$F2 1296
2 TraesCS5A01G347400 chr5D 435932684 435935545 2861 False 1092.666667 2047 88.214333 356 3245 3 chr5D.!!$F1 2889
3 TraesCS5A01G347400 chr5B 529987400 529988569 1169 False 1018.000000 1018 82.903000 994 2198 1 chr5B.!!$F1 1204
4 TraesCS5A01G347400 chr5B 529607091 529610755 3664 False 683.750000 1238 83.282250 1 3176 4 chr5B.!!$F2 3175
5 TraesCS5A01G347400 chr5B 529686473 529688916 2443 False 391.460000 780 86.000400 498 2952 5 chr5B.!!$F3 2454
6 TraesCS5A01G347400 chr3D 559634936 559635474 538 False 243.000000 243 75.315000 3243 3787 1 chr3D.!!$F1 544

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
740 1268 0.037326 ACACATGCTGGTTCGATCGT 60.037 50.0 15.94 0.0 0.0 3.73 F
1272 1882 0.177141 TAGGTAAGCATGTCGGGCAC 59.823 55.0 0.00 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 2310 0.396001 TGGGGTATGGTGTCGATCGA 60.396 55.0 15.15 15.15 0.0 3.59 R
3258 4335 0.174162 GCCGCTCGTCCTTAGGTAAA 59.826 55.0 0.00 0.00 0.0 2.01 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
32 33 8.894768 ATCCAAACTATATGAGAAGTACTTGC 57.105 34.615 14.14 5.49 0.00 4.01
98 99 0.395586 GCCCATTCCACCACATAGCA 60.396 55.000 0.00 0.00 0.00 3.49
103 104 2.584835 TTCCACCACATAGCAAAGCT 57.415 45.000 0.00 0.00 43.41 3.74
104 105 2.584835 TCCACCACATAGCAAAGCTT 57.415 45.000 0.00 0.00 40.44 3.74
105 106 2.436417 TCCACCACATAGCAAAGCTTC 58.564 47.619 0.00 0.00 40.44 3.86
128 130 4.237349 AGAAACGATTTTGCGACCAAAT 57.763 36.364 0.00 0.00 40.40 2.32
129 131 4.616953 AGAAACGATTTTGCGACCAAATT 58.383 34.783 0.00 0.00 40.40 1.82
130 132 5.764131 AGAAACGATTTTGCGACCAAATTA 58.236 33.333 0.00 0.00 40.40 1.40
131 133 6.210078 AGAAACGATTTTGCGACCAAATTAA 58.790 32.000 0.00 0.00 40.40 1.40
157 159 0.537371 CAAGGAAGGCCAGAACGGTT 60.537 55.000 5.01 0.00 36.97 4.44
158 160 0.250770 AAGGAAGGCCAGAACGGTTC 60.251 55.000 12.91 12.91 36.97 3.62
170 172 4.199310 CAGAACGGTTCAATCATATGGGT 58.801 43.478 21.86 0.00 0.00 4.51
174 176 3.053991 ACGGTTCAATCATATGGGTTCCA 60.054 43.478 2.13 0.00 38.19 3.53
178 180 5.339990 GTTCAATCATATGGGTTCCAAACG 58.660 41.667 2.13 0.00 36.95 3.60
191 193 3.040147 TCCAAACGAACTCACATCCTC 57.960 47.619 0.00 0.00 0.00 3.71
200 202 3.815856 ACTCACATCCTCTGCATACAG 57.184 47.619 0.00 0.00 45.95 2.74
222 250 6.094061 CAGAACTGCTACTACTACAAAGACC 58.906 44.000 0.00 0.00 0.00 3.85
227 255 6.164417 TGCTACTACTACAAAGACCACAAA 57.836 37.500 0.00 0.00 0.00 2.83
240 268 3.751698 AGACCACAAAAGTAAATCCTCGC 59.248 43.478 0.00 0.00 0.00 5.03
243 271 4.023193 ACCACAAAAGTAAATCCTCGCAAG 60.023 41.667 0.00 0.00 0.00 4.01
248 276 2.607187 AGTAAATCCTCGCAAGTGACG 58.393 47.619 0.00 0.00 39.48 4.35
258 286 1.006832 GCAAGTGACGTGACACAGTT 58.993 50.000 8.15 0.00 42.45 3.16
261 289 3.543460 GCAAGTGACGTGACACAGTTTAC 60.543 47.826 8.15 8.11 42.45 2.01
267 295 5.675444 GTGACGTGACACAGTTTACAATTTC 59.325 40.000 6.37 0.00 40.11 2.17
271 299 5.202640 GTGACACAGTTTACAATTTCGTCC 58.797 41.667 0.00 0.00 0.00 4.79
318 346 7.993183 TGACCAGGGAATTGAATTACTAAGATC 59.007 37.037 0.00 0.00 0.00 2.75
320 348 8.336235 ACCAGGGAATTGAATTACTAAGATCAA 58.664 33.333 0.00 0.00 36.35 2.57
369 854 1.134007 TGACAGGAATAGCATGGGCAG 60.134 52.381 0.00 0.00 44.61 4.85
388 873 3.403936 GGCACCATCCCATCTACAC 57.596 57.895 0.00 0.00 0.00 2.90
389 874 0.546122 GGCACCATCCCATCTACACA 59.454 55.000 0.00 0.00 0.00 3.72
390 875 1.143684 GGCACCATCCCATCTACACAT 59.856 52.381 0.00 0.00 0.00 3.21
392 877 2.759191 CACCATCCCATCTACACATCG 58.241 52.381 0.00 0.00 0.00 3.84
393 878 2.365293 CACCATCCCATCTACACATCGA 59.635 50.000 0.00 0.00 0.00 3.59
394 879 2.630098 ACCATCCCATCTACACATCGAG 59.370 50.000 0.00 0.00 0.00 4.04
395 880 2.611473 CCATCCCATCTACACATCGAGC 60.611 54.545 0.00 0.00 0.00 5.03
396 881 1.775385 TCCCATCTACACATCGAGCA 58.225 50.000 0.00 0.00 0.00 4.26
397 882 1.683385 TCCCATCTACACATCGAGCAG 59.317 52.381 0.00 0.00 0.00 4.24
398 883 1.410517 CCCATCTACACATCGAGCAGT 59.589 52.381 0.00 0.00 0.00 4.40
484 984 0.739813 CCTACCACTTGGCTACACGC 60.740 60.000 0.00 0.00 39.32 5.34
486 986 1.475280 CTACCACTTGGCTACACGCTA 59.525 52.381 0.00 0.00 39.32 4.26
490 990 0.249120 ACTTGGCTACACGCTATGCA 59.751 50.000 0.00 0.00 39.13 3.96
496 996 0.863799 CTACACGCTATGCATGCCTG 59.136 55.000 16.68 12.71 0.00 4.85
545 1045 3.128938 GCGTATAGTCAAGTCACTGGAGT 59.871 47.826 0.00 0.00 0.00 3.85
546 1046 4.334759 GCGTATAGTCAAGTCACTGGAGTA 59.665 45.833 0.00 0.00 0.00 2.59
548 1048 5.007823 CGTATAGTCAAGTCACTGGAGTAGG 59.992 48.000 3.06 0.00 0.00 3.18
550 1050 3.426615 AGTCAAGTCACTGGAGTAGGAG 58.573 50.000 0.00 0.00 0.00 3.69
551 1051 3.158676 GTCAAGTCACTGGAGTAGGAGT 58.841 50.000 0.00 0.00 0.00 3.85
552 1052 4.043059 AGTCAAGTCACTGGAGTAGGAGTA 59.957 45.833 0.00 0.00 0.00 2.59
553 1053 4.156373 GTCAAGTCACTGGAGTAGGAGTAC 59.844 50.000 0.00 0.00 0.00 2.73
554 1054 4.043059 TCAAGTCACTGGAGTAGGAGTACT 59.957 45.833 0.00 0.00 42.59 2.73
555 1055 3.958018 AGTCACTGGAGTAGGAGTACTG 58.042 50.000 0.00 0.00 39.78 2.74
597 1097 4.580995 TCAGCTAGGTCATAACAGCTACTC 59.419 45.833 0.00 0.00 42.33 2.59
598 1098 3.892588 AGCTAGGTCATAACAGCTACTCC 59.107 47.826 0.00 0.00 42.41 3.85
599 1099 3.892588 GCTAGGTCATAACAGCTACTCCT 59.107 47.826 0.00 0.00 0.00 3.69
600 1100 5.071370 GCTAGGTCATAACAGCTACTCCTA 58.929 45.833 0.00 0.00 0.00 2.94
730 1258 3.244078 ACCCCACGTATATACACATGCTG 60.244 47.826 13.22 4.65 0.00 4.41
739 1267 1.921243 TACACATGCTGGTTCGATCG 58.079 50.000 9.36 9.36 0.00 3.69
740 1268 0.037326 ACACATGCTGGTTCGATCGT 60.037 50.000 15.94 0.00 0.00 3.73
742 1270 1.061131 CACATGCTGGTTCGATCGTTC 59.939 52.381 15.94 9.18 0.00 3.95
743 1271 1.337728 ACATGCTGGTTCGATCGTTCA 60.338 47.619 15.94 10.73 0.00 3.18
775 1305 3.958704 TGCGGTAAAAGAAACACATGTG 58.041 40.909 24.25 24.25 0.00 3.21
783 1319 2.498167 AGAAACACATGTGCTCCAGTC 58.502 47.619 25.68 13.02 0.00 3.51
784 1320 1.537202 GAAACACATGTGCTCCAGTCC 59.463 52.381 25.68 3.16 0.00 3.85
835 1375 2.280457 GCTAGCTCCCACGCCATC 60.280 66.667 7.70 0.00 0.00 3.51
955 1499 1.018148 CACGGCACCACAACTGTTTA 58.982 50.000 0.00 0.00 0.00 2.01
1199 1796 0.248289 GGCAAGGAGCTGGTACGTAA 59.752 55.000 0.00 0.00 44.79 3.18
1272 1882 0.177141 TAGGTAAGCATGTCGGGCAC 59.823 55.000 0.00 0.00 0.00 5.01
1348 1961 3.813724 GGGCTCATGGGGGAGGTG 61.814 72.222 0.00 0.00 35.41 4.00
1468 2110 7.780008 TCTCTCTCTTATTCTACTCGAAGTG 57.220 40.000 0.00 0.00 34.56 3.16
1527 2169 6.069905 TCCAACTGGCCTAATTAACAGTATCA 60.070 38.462 3.32 3.21 42.85 2.15
1529 2171 7.122055 CCAACTGGCCTAATTAACAGTATCAAA 59.878 37.037 3.32 0.00 42.85 2.69
1530 2172 8.519526 CAACTGGCCTAATTAACAGTATCAAAA 58.480 33.333 3.32 0.00 42.85 2.44
1531 2173 8.644374 ACTGGCCTAATTAACAGTATCAAAAA 57.356 30.769 3.32 0.00 41.95 1.94
1532 2174 9.255029 ACTGGCCTAATTAACAGTATCAAAAAT 57.745 29.630 3.32 0.00 41.95 1.82
1571 2213 1.896220 TCCATGTCCAAGTTGCTCAC 58.104 50.000 0.00 0.00 0.00 3.51
1576 2218 3.726517 CCAAGTTGCTCACCGGCG 61.727 66.667 0.00 0.00 34.52 6.46
1607 2251 2.101082 TGCTTTTCTTTGATGTGCAGCA 59.899 40.909 0.00 0.00 33.69 4.41
1646 2290 1.598701 GGGCAAGGAGGTACGTACGT 61.599 60.000 25.98 25.98 0.00 3.57
1647 2291 0.244721 GGCAAGGAGGTACGTACGTT 59.755 55.000 27.92 8.78 0.00 3.99
1649 2293 1.986698 CAAGGAGGTACGTACGTTGG 58.013 55.000 27.92 0.10 0.00 3.77
1650 2294 1.541147 CAAGGAGGTACGTACGTTGGA 59.459 52.381 27.92 5.61 0.00 3.53
1651 2295 1.457346 AGGAGGTACGTACGTTGGAG 58.543 55.000 27.92 0.00 0.00 3.86
1652 2296 1.003580 AGGAGGTACGTACGTTGGAGA 59.996 52.381 27.92 4.73 0.00 3.71
1723 2396 2.530497 CCATGCATGCAATTGCGGC 61.530 57.895 29.46 29.46 45.77 6.53
1990 2703 6.261118 CAGTTAAGCTCATCAAATAACTGGC 58.739 40.000 18.35 0.00 44.75 4.85
2009 2730 2.696187 GGCCTTAGCTGCTCTAGTTACT 59.304 50.000 4.91 0.00 39.73 2.24
2010 2731 3.133183 GGCCTTAGCTGCTCTAGTTACTT 59.867 47.826 4.91 0.00 39.73 2.24
2011 2732 4.341520 GGCCTTAGCTGCTCTAGTTACTTA 59.658 45.833 4.91 0.00 39.73 2.24
2012 2733 5.508320 GGCCTTAGCTGCTCTAGTTACTTAG 60.508 48.000 4.91 0.00 39.73 2.18
2135 2879 0.396139 GCTTCATCAGGCCATCCCAA 60.396 55.000 5.01 0.00 35.39 4.12
2230 2983 2.035442 GCACCTTCCTTCGTCCTGC 61.035 63.158 0.00 0.00 0.00 4.85
2289 3052 2.588877 CCGTCCGGTCCATGCATC 60.589 66.667 0.00 0.00 0.00 3.91
2304 3067 0.033208 GCATCCACCCTCCAATCCAA 60.033 55.000 0.00 0.00 0.00 3.53
2437 3294 2.464865 CTAGCTAGGTTGCTTGCTACG 58.535 52.381 13.32 0.00 43.74 3.51
2449 3312 2.596452 CTTGCTACGTGTCGAGTTGAT 58.404 47.619 0.00 0.00 0.00 2.57
2501 3370 2.610976 GCTGATCAAAAGTTGCCATGCA 60.611 45.455 0.00 0.00 36.47 3.96
2504 3373 3.258622 TGATCAAAAGTTGCCATGCATGA 59.741 39.130 28.31 6.08 38.76 3.07
2505 3374 3.965379 TCAAAAGTTGCCATGCATGAT 57.035 38.095 28.31 5.45 38.76 2.45
2506 3375 4.274602 TCAAAAGTTGCCATGCATGATT 57.725 36.364 28.31 11.05 38.76 2.57
2507 3376 3.997681 TCAAAAGTTGCCATGCATGATTG 59.002 39.130 28.31 17.75 38.76 2.67
2553 3423 0.514691 GCAGAGCTGGTCTTCGTTTG 59.485 55.000 6.64 0.00 30.64 2.93
2554 3424 0.514691 CAGAGCTGGTCTTCGTTTGC 59.485 55.000 6.64 0.00 30.64 3.68
2555 3425 0.394565 AGAGCTGGTCTTCGTTTGCT 59.605 50.000 3.02 0.00 27.07 3.91
2558 3428 2.413453 GAGCTGGTCTTCGTTTGCTTAG 59.587 50.000 0.00 0.00 0.00 2.18
2577 3474 8.059798 TGCTTAGGTAGTAGTAGAAAAATCGT 57.940 34.615 0.00 0.00 0.00 3.73
2596 3495 2.000447 GTTTGAGTTAGCTAGTGGGCG 59.000 52.381 0.00 0.00 37.29 6.13
2597 3496 0.535335 TTGAGTTAGCTAGTGGGCGG 59.465 55.000 0.00 0.00 37.29 6.13
2746 3761 2.107953 GTGGGAGATCGAGCAGGC 59.892 66.667 2.38 0.00 0.00 4.85
2887 3922 5.555818 GCGCCGCTAGTTGTTAGTTAATTAG 60.556 44.000 0.00 0.00 0.00 1.73
2959 4004 1.962100 GACGGAGGAACGGGATATTCT 59.038 52.381 0.00 0.00 38.39 2.40
2961 4006 3.762823 GACGGAGGAACGGGATATTCTAT 59.237 47.826 0.00 0.00 38.39 1.98
2963 4008 4.220163 ACGGAGGAACGGGATATTCTATTC 59.780 45.833 0.00 0.00 38.39 1.75
2964 4009 4.381718 CGGAGGAACGGGATATTCTATTCC 60.382 50.000 8.16 8.16 36.63 3.01
2965 4010 4.778427 GGAGGAACGGGATATTCTATTCCT 59.222 45.833 15.45 15.45 46.72 3.36
3109 4186 2.917933 TGATTATGTGTAGGTGGCTGC 58.082 47.619 0.00 0.00 0.00 5.25
3128 4205 1.234821 CAACAGTGGTGCGTATGGTT 58.765 50.000 0.00 0.00 0.00 3.67
3133 4210 0.732571 GTGGTGCGTATGGTTCATGG 59.267 55.000 0.00 0.00 0.00 3.66
3137 4214 1.023502 TGCGTATGGTTCATGGCATG 58.976 50.000 21.42 21.42 32.61 4.06
3147 4224 8.959548 GTATGGTTCATGGCATGATTAATCATA 58.040 33.333 29.22 24.62 45.23 2.15
3155 4232 9.836076 CATGGCATGATTAATCATACTTAAGTG 57.164 33.333 26.55 16.20 45.23 3.16
3199 4276 4.215399 TGCACACTACTGGAAATTAACTGC 59.785 41.667 0.00 0.00 0.00 4.40
3207 4284 2.225491 TGGAAATTAACTGCACGCTGAC 59.775 45.455 2.69 0.00 0.00 3.51
3220 4297 2.684843 GCTGACGGCTTGGCTCTTG 61.685 63.158 0.00 0.00 38.06 3.02
3235 4312 1.228124 CTTGGCCGAGGACCAAACA 60.228 57.895 12.81 0.00 46.24 2.83
3237 4314 1.104577 TTGGCCGAGGACCAAACAAC 61.105 55.000 13.12 0.00 44.11 3.32
3257 4334 1.449778 GGCGCTGAGTTTAGTCCCC 60.450 63.158 7.64 0.00 0.00 4.81
3258 4335 1.597461 GCGCTGAGTTTAGTCCCCT 59.403 57.895 0.00 0.00 0.00 4.79
3259 4336 0.036294 GCGCTGAGTTTAGTCCCCTT 60.036 55.000 0.00 0.00 0.00 3.95
3261 4338 2.354403 GCGCTGAGTTTAGTCCCCTTTA 60.354 50.000 0.00 0.00 0.00 1.85
3262 4339 3.259902 CGCTGAGTTTAGTCCCCTTTAC 58.740 50.000 0.00 0.00 0.00 2.01
3277 4355 0.174162 TTTACCTAAGGACGAGCGGC 59.826 55.000 0.00 0.00 0.00 6.53
3278 4356 0.966875 TTACCTAAGGACGAGCGGCA 60.967 55.000 1.45 0.00 0.00 5.69
3279 4357 1.381928 TACCTAAGGACGAGCGGCAG 61.382 60.000 1.45 0.00 0.00 4.85
3281 4359 2.361992 TAAGGACGAGCGGCAGGA 60.362 61.111 1.45 0.00 0.00 3.86
3282 4360 1.945354 CTAAGGACGAGCGGCAGGAA 61.945 60.000 1.45 0.00 0.00 3.36
3283 4361 2.221906 TAAGGACGAGCGGCAGGAAC 62.222 60.000 1.45 0.00 0.00 3.62
3288 4366 2.668550 GAGCGGCAGGAACGGTTT 60.669 61.111 1.45 0.00 42.62 3.27
3291 4369 0.322187 AGCGGCAGGAACGGTTTAAT 60.322 50.000 1.45 0.00 39.19 1.40
3292 4370 1.065998 AGCGGCAGGAACGGTTTAATA 60.066 47.619 1.45 0.00 39.19 0.98
3293 4371 1.329599 GCGGCAGGAACGGTTTAATAG 59.670 52.381 0.00 0.00 0.00 1.73
3294 4372 2.624636 CGGCAGGAACGGTTTAATAGT 58.375 47.619 0.00 0.00 0.00 2.12
3295 4373 2.606272 CGGCAGGAACGGTTTAATAGTC 59.394 50.000 0.00 0.00 0.00 2.59
3296 4374 3.602483 GGCAGGAACGGTTTAATAGTCA 58.398 45.455 0.00 0.00 0.00 3.41
3297 4375 3.621715 GGCAGGAACGGTTTAATAGTCAG 59.378 47.826 0.00 0.00 0.00 3.51
3303 4381 7.980099 CAGGAACGGTTTAATAGTCAGATAGTT 59.020 37.037 0.00 0.00 0.00 2.24
3314 4392 8.526667 AATAGTCAGATAGTTCAGAAGCAGTA 57.473 34.615 0.00 0.00 0.00 2.74
3316 4394 7.233389 AGTCAGATAGTTCAGAAGCAGTAAA 57.767 36.000 0.00 0.00 0.00 2.01
3320 4398 7.815068 TCAGATAGTTCAGAAGCAGTAAACTTC 59.185 37.037 0.00 0.00 43.16 3.01
3379 4457 9.099454 CTGTCACTATAAATCTTTACCTGTTCC 57.901 37.037 0.00 0.00 0.00 3.62
3385 4463 0.323629 TCTTTACCTGTTCCGGGCAG 59.676 55.000 16.65 16.65 32.02 4.85
3393 4471 1.079057 GTTCCGGGCAGAGAAGGTC 60.079 63.158 0.00 0.00 0.00 3.85
3397 4475 1.153289 CGGGCAGAGAAGGTCCATG 60.153 63.158 0.00 0.00 0.00 3.66
3423 4501 9.403583 GGTGACAGTCCATATTCCTAAAAATAA 57.596 33.333 0.00 0.00 0.00 1.40
3434 4512 7.823745 ATTCCTAAAAATAATGACGGATGCT 57.176 32.000 0.00 0.00 0.00 3.79
3435 4513 6.618287 TCCTAAAAATAATGACGGATGCTG 57.382 37.500 0.00 0.00 0.00 4.41
3436 4514 6.353323 TCCTAAAAATAATGACGGATGCTGA 58.647 36.000 0.00 0.00 0.00 4.26
3449 4527 4.393680 ACGGATGCTGACGCTTTTTATTAA 59.606 37.500 0.00 0.00 36.97 1.40
3451 4529 5.621228 CGGATGCTGACGCTTTTTATTAATC 59.379 40.000 0.00 0.00 36.97 1.75
3452 4530 6.511767 CGGATGCTGACGCTTTTTATTAATCT 60.512 38.462 0.00 0.00 36.97 2.40
3453 4531 6.634436 GGATGCTGACGCTTTTTATTAATCTG 59.366 38.462 0.00 0.00 36.97 2.90
3454 4532 5.879237 TGCTGACGCTTTTTATTAATCTGG 58.121 37.500 0.00 0.00 36.97 3.86
3492 4573 5.298527 ACAATCATATGTGTGAGAGCAATGG 59.701 40.000 13.15 0.00 30.82 3.16
3526 4607 5.479716 AAATCCACGGAAAATCATACGAC 57.520 39.130 0.00 0.00 0.00 4.34
3527 4608 2.532235 TCCACGGAAAATCATACGACG 58.468 47.619 0.00 0.00 0.00 5.12
3528 4609 1.005347 CCACGGAAAATCATACGACGC 60.005 52.381 0.00 0.00 0.00 5.19
3537 4618 1.835121 TCATACGACGCTGGAAATCG 58.165 50.000 0.00 0.00 41.60 3.34
3538 4619 0.229753 CATACGACGCTGGAAATCGC 59.770 55.000 0.00 0.00 39.47 4.58
3539 4620 0.102481 ATACGACGCTGGAAATCGCT 59.898 50.000 0.00 0.00 39.47 4.93
3542 4623 2.125106 ACGCTGGAAATCGCTCCC 60.125 61.111 0.00 0.00 34.22 4.30
3543 4624 2.187946 CGCTGGAAATCGCTCCCT 59.812 61.111 0.00 0.00 34.22 4.20
3548 4630 1.486726 CTGGAAATCGCTCCCTTAGGT 59.513 52.381 0.00 0.00 34.22 3.08
3551 4633 1.671328 GAAATCGCTCCCTTAGGTTGC 59.329 52.381 0.00 0.00 0.00 4.17
3558 4640 3.477530 GCTCCCTTAGGTTGCGATAAAT 58.522 45.455 0.00 0.00 0.00 1.40
3565 4647 3.866883 AGGTTGCGATAAATGTTTGGG 57.133 42.857 0.00 0.00 0.00 4.12
3568 4650 1.169577 TGCGATAAATGTTTGGGCGT 58.830 45.000 0.00 0.00 0.00 5.68
3579 4661 1.064357 GTTTGGGCGTGTTTCGAAGAA 59.936 47.619 0.00 0.00 45.90 2.52
3582 4664 1.206831 GGCGTGTTTCGAAGAAGCC 59.793 57.895 16.47 16.47 45.90 4.35
3588 4670 1.157585 GTTTCGAAGAAGCCTCACCC 58.842 55.000 0.00 0.00 45.90 4.61
3604 4686 0.328258 ACCCGAGGCTGCTTGTAAAT 59.672 50.000 0.00 0.00 0.00 1.40
3609 4691 2.599659 GAGGCTGCTTGTAAATTGCAC 58.400 47.619 0.00 0.00 32.91 4.57
3617 4699 4.082625 TGCTTGTAAATTGCACCATCTCTG 60.083 41.667 0.00 0.00 0.00 3.35
3618 4700 4.156556 GCTTGTAAATTGCACCATCTCTGA 59.843 41.667 0.00 0.00 0.00 3.27
3619 4701 5.675575 GCTTGTAAATTGCACCATCTCTGAG 60.676 44.000 0.00 0.00 0.00 3.35
3620 4702 4.264253 TGTAAATTGCACCATCTCTGAGG 58.736 43.478 4.59 0.00 0.00 3.86
3621 4703 3.446442 AAATTGCACCATCTCTGAGGT 57.554 42.857 4.59 0.00 39.10 3.85
3622 4704 4.574674 AAATTGCACCATCTCTGAGGTA 57.425 40.909 4.59 0.00 36.07 3.08
3623 4705 3.834489 ATTGCACCATCTCTGAGGTAG 57.166 47.619 4.59 0.00 36.07 3.18
3624 4706 2.238084 TGCACCATCTCTGAGGTAGT 57.762 50.000 4.59 0.00 36.07 2.73
3625 4707 3.382083 TGCACCATCTCTGAGGTAGTA 57.618 47.619 4.59 0.00 36.07 1.82
3626 4708 3.916035 TGCACCATCTCTGAGGTAGTAT 58.084 45.455 4.59 0.00 36.07 2.12
3629 4711 4.022416 GCACCATCTCTGAGGTAGTATCTG 60.022 50.000 4.59 0.00 36.07 2.90
3635 4717 6.532119 TCTCTGAGGTAGTATCTGGGTATT 57.468 41.667 4.59 0.00 0.00 1.89
3641 4723 6.102762 TGAGGTAGTATCTGGGTATTGAGAGA 59.897 42.308 0.00 0.00 0.00 3.10
3642 4724 6.923670 AGGTAGTATCTGGGTATTGAGAGAA 58.076 40.000 0.00 0.00 0.00 2.87
3651 4733 3.683340 GGGTATTGAGAGAAAACGTGTCC 59.317 47.826 0.00 0.00 0.00 4.02
3652 4734 3.367025 GGTATTGAGAGAAAACGTGTCCG 59.633 47.826 0.00 0.00 40.83 4.79
3666 4748 2.018515 GTGTCCGGTTTGTGAAGGAAA 58.981 47.619 0.00 0.00 34.17 3.13
3667 4749 2.018515 TGTCCGGTTTGTGAAGGAAAC 58.981 47.619 0.00 0.00 34.17 2.78
3669 4751 0.317519 CCGGTTTGTGAAGGAAACGC 60.318 55.000 0.00 0.00 34.67 4.84
3671 4753 0.317519 GGTTTGTGAAGGAAACGCGG 60.318 55.000 12.47 0.00 34.67 6.46
3673 4755 2.065906 TTTGTGAAGGAAACGCGGGC 62.066 55.000 12.47 0.00 0.00 6.13
3685 4767 2.124736 GCGGGCCATGTTGCTCTA 60.125 61.111 4.39 0.00 0.00 2.43
3690 4772 1.410083 GGGCCATGTTGCTCTATTGGA 60.410 52.381 4.39 0.00 0.00 3.53
3693 4775 3.019564 GCCATGTTGCTCTATTGGACTT 58.980 45.455 0.00 0.00 0.00 3.01
3694 4776 3.065925 GCCATGTTGCTCTATTGGACTTC 59.934 47.826 0.00 0.00 0.00 3.01
3700 4782 5.827797 TGTTGCTCTATTGGACTTCAAACTT 59.172 36.000 0.00 0.00 39.05 2.66
3701 4783 6.321181 TGTTGCTCTATTGGACTTCAAACTTT 59.679 34.615 0.00 0.00 39.05 2.66
3706 4788 7.752686 GCTCTATTGGACTTCAAACTTTTCATC 59.247 37.037 0.00 0.00 39.05 2.92
3711 4793 5.765182 TGGACTTCAAACTTTTCATCCTCTC 59.235 40.000 0.00 0.00 0.00 3.20
3713 4795 6.263168 GGACTTCAAACTTTTCATCCTCTCAA 59.737 38.462 0.00 0.00 0.00 3.02
3714 4796 7.201821 GGACTTCAAACTTTTCATCCTCTCAAA 60.202 37.037 0.00 0.00 0.00 2.69
3728 4810 4.277515 CTCTCAAAGGAGACCATCACAA 57.722 45.455 0.00 0.00 45.12 3.33
3744 4826 2.275134 ACAAGACATGTGACATGCCA 57.725 45.000 24.32 0.00 41.93 4.92
3746 4828 2.156917 CAAGACATGTGACATGCCACT 58.843 47.619 24.32 17.47 37.89 4.00
3759 4841 2.121291 TGCCACTGCATTATTCGGAA 57.879 45.000 0.00 0.00 44.23 4.30
3761 4843 2.017049 GCCACTGCATTATTCGGAACT 58.983 47.619 0.00 0.00 37.47 3.01
3766 4848 3.118408 ACTGCATTATTCGGAACTGCCTA 60.118 43.478 15.11 2.35 31.89 3.93
3767 4849 3.202906 TGCATTATTCGGAACTGCCTAC 58.797 45.455 15.11 0.00 31.89 3.18
3775 4857 5.811399 TTCGGAACTGCCTACAATATTTG 57.189 39.130 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.213777 AGTACTTCTCATATAGTTTGGATTCCA 57.786 33.333 0.00 0.00 0.00 3.53
14 15 6.810911 ACACCAGCAAGTACTTCTCATATAG 58.189 40.000 4.77 0.00 0.00 1.31
16 17 5.683876 ACACCAGCAAGTACTTCTCATAT 57.316 39.130 4.77 0.00 0.00 1.78
17 18 6.791867 ATACACCAGCAAGTACTTCTCATA 57.208 37.500 4.77 0.00 0.00 2.15
21 22 4.003648 GCAATACACCAGCAAGTACTTCT 58.996 43.478 4.77 3.55 0.00 2.85
25 26 2.678336 GAGGCAATACACCAGCAAGTAC 59.322 50.000 0.00 0.00 0.00 2.73
30 31 3.248043 GTGAGGCAATACACCAGCA 57.752 52.632 0.00 0.00 0.00 4.41
98 99 5.049680 TCGCAAAATCGTTTCTAGAAGCTTT 60.050 36.000 16.13 8.74 0.00 3.51
103 104 4.059511 TGGTCGCAAAATCGTTTCTAGAA 58.940 39.130 0.00 0.00 0.00 2.10
104 105 3.655486 TGGTCGCAAAATCGTTTCTAGA 58.345 40.909 0.00 0.00 0.00 2.43
105 106 4.398549 TTGGTCGCAAAATCGTTTCTAG 57.601 40.909 0.00 0.00 0.00 2.43
128 130 3.948735 CCTTCCTTGGCTCGGTTAA 57.051 52.632 0.00 0.00 0.00 2.01
157 159 4.849518 TCGTTTGGAACCCATATGATTGA 58.150 39.130 3.65 0.00 31.53 2.57
158 160 5.574891 TTCGTTTGGAACCCATATGATTG 57.425 39.130 3.65 0.00 32.31 2.67
170 172 3.071023 AGAGGATGTGAGTTCGTTTGGAA 59.929 43.478 0.00 0.00 0.00 3.53
174 176 2.224281 TGCAGAGGATGTGAGTTCGTTT 60.224 45.455 0.00 0.00 0.00 3.60
178 180 4.118410 CTGTATGCAGAGGATGTGAGTTC 58.882 47.826 4.57 0.00 45.28 3.01
191 193 5.255710 AGTAGTAGCAGTTCTGTATGCAG 57.744 43.478 4.14 4.14 45.01 4.41
200 202 5.862860 GTGGTCTTTGTAGTAGTAGCAGTTC 59.137 44.000 0.00 0.00 0.00 3.01
212 214 8.166422 AGGATTTACTTTTGTGGTCTTTGTAG 57.834 34.615 0.00 0.00 0.00 2.74
222 250 4.911610 CACTTGCGAGGATTTACTTTTGTG 59.088 41.667 5.79 0.00 0.00 3.33
227 255 2.993899 CGTCACTTGCGAGGATTTACTT 59.006 45.455 5.79 0.00 0.00 2.24
240 268 3.615056 TGTAAACTGTGTCACGTCACTTG 59.385 43.478 8.63 4.74 38.90 3.16
243 271 4.789095 ATTGTAAACTGTGTCACGTCAC 57.211 40.909 0.60 0.60 38.63 3.67
248 276 5.007332 AGGACGAAATTGTAAACTGTGTCAC 59.993 40.000 0.00 0.00 0.00 3.67
261 289 7.965107 CCAGAAGATAAAAAGAGGACGAAATTG 59.035 37.037 0.00 0.00 0.00 2.32
267 295 7.617041 AAATCCAGAAGATAAAAAGAGGACG 57.383 36.000 0.00 0.00 33.66 4.79
271 299 8.796475 TGGTCAAAATCCAGAAGATAAAAAGAG 58.204 33.333 0.00 0.00 33.66 2.85
335 363 7.439655 GCTATTCCTGTCAACTGGAGTTATTAG 59.560 40.741 8.90 3.22 43.41 1.73
337 365 6.116126 GCTATTCCTGTCAACTGGAGTTATT 58.884 40.000 8.90 0.00 43.41 1.40
345 435 2.947652 CCCATGCTATTCCTGTCAACTG 59.052 50.000 0.00 0.00 0.00 3.16
392 877 1.193426 GTGAAACTGCTCGAACTGCTC 59.807 52.381 0.00 0.00 0.00 4.26
393 878 1.221414 GTGAAACTGCTCGAACTGCT 58.779 50.000 0.00 0.00 0.00 4.24
394 879 0.937304 TGTGAAACTGCTCGAACTGC 59.063 50.000 0.00 0.00 38.04 4.40
395 880 2.473816 TCTGTGAAACTGCTCGAACTG 58.526 47.619 0.00 0.00 38.04 3.16
396 881 2.890808 TCTGTGAAACTGCTCGAACT 57.109 45.000 0.00 0.00 38.04 3.01
397 882 4.686554 ACTAATCTGTGAAACTGCTCGAAC 59.313 41.667 0.00 0.00 38.04 3.95
398 883 4.883083 ACTAATCTGTGAAACTGCTCGAA 58.117 39.130 0.00 0.00 38.04 3.71
484 984 0.882042 GTCCGTCCAGGCATGCATAG 60.882 60.000 21.36 5.56 40.77 2.23
486 986 2.124570 GTCCGTCCAGGCATGCAT 60.125 61.111 21.36 10.32 40.77 3.96
496 996 3.562779 TTCAACTCGCCGTCCGTCC 62.563 63.158 0.00 0.00 38.35 4.79
522 1022 2.096980 TCCAGTGACTTGACTATACGCG 59.903 50.000 3.53 3.53 0.00 6.01
530 1030 3.158676 ACTCCTACTCCAGTGACTTGAC 58.841 50.000 0.00 0.00 0.00 3.18
545 1045 1.492176 CCTCCCGTACCAGTACTCCTA 59.508 57.143 6.40 0.00 34.04 2.94
546 1046 0.258194 CCTCCCGTACCAGTACTCCT 59.742 60.000 6.40 0.00 34.04 3.69
548 1048 0.682209 TGCCTCCCGTACCAGTACTC 60.682 60.000 6.40 0.00 34.04 2.59
550 1050 1.673808 CCTGCCTCCCGTACCAGTAC 61.674 65.000 0.00 0.00 0.00 2.73
551 1051 1.380785 CCTGCCTCCCGTACCAGTA 60.381 63.158 0.00 0.00 0.00 2.74
552 1052 2.683933 CCTGCCTCCCGTACCAGT 60.684 66.667 0.00 0.00 0.00 4.00
553 1053 4.162690 GCCTGCCTCCCGTACCAG 62.163 72.222 0.00 0.00 0.00 4.00
555 1055 4.162690 CTGCCTGCCTCCCGTACC 62.163 72.222 0.00 0.00 0.00 3.34
597 1097 0.031449 GCTTCCTCGCAGCTACTAGG 59.969 60.000 0.00 0.00 34.15 3.02
598 1098 0.741326 TGCTTCCTCGCAGCTACTAG 59.259 55.000 0.00 0.00 38.19 2.57
599 1099 1.182667 TTGCTTCCTCGCAGCTACTA 58.817 50.000 0.00 0.00 41.55 1.82
600 1100 0.321671 TTTGCTTCCTCGCAGCTACT 59.678 50.000 0.00 0.00 41.55 2.57
663 1163 0.725117 CGGTCGGTCCAAAATGCTAC 59.275 55.000 0.00 0.00 35.57 3.58
687 1201 6.624741 GGTACGTACCGATGCTATGCATGA 62.625 50.000 28.00 0.00 42.16 3.07
730 1258 2.923605 ACTCTCTGAACGATCGAACC 57.076 50.000 24.34 10.43 0.00 3.62
739 1267 3.027974 ACCGCAGTTAACTCTCTGAAC 57.972 47.619 4.77 0.00 34.02 3.18
740 1268 4.859304 TTACCGCAGTTAACTCTCTGAA 57.141 40.909 4.77 0.00 34.02 3.02
742 1270 5.227908 TCTTTTACCGCAGTTAACTCTCTG 58.772 41.667 4.77 0.00 35.12 3.35
743 1271 5.464030 TCTTTTACCGCAGTTAACTCTCT 57.536 39.130 4.77 0.00 0.00 3.10
775 1305 1.390383 GGTACCCTACGGACTGGAGC 61.390 65.000 0.00 0.00 0.00 4.70
783 1319 1.105457 TGACGAATGGTACCCTACGG 58.895 55.000 19.98 6.21 0.00 4.02
784 1320 1.532505 CGTGACGAATGGTACCCTACG 60.533 57.143 10.07 13.98 0.00 3.51
835 1375 4.030913 AGACGGGTGGATGGGTATATATG 58.969 47.826 0.00 0.00 0.00 1.78
955 1499 3.901797 CTGCCGCGGAAAGGAAGGT 62.902 63.158 33.48 0.00 30.48 3.50
1013 1574 1.075896 GTCTCCTCCATCCCTCCGT 60.076 63.158 0.00 0.00 0.00 4.69
1199 1796 4.157289 ACGTGTGTAATCAACTAGATCGGT 59.843 41.667 0.00 0.00 35.39 4.69
1275 1885 2.848858 GCAACCTGCCACCACACAG 61.849 63.158 0.00 0.00 37.42 3.66
1348 1961 1.374758 CTTGTGGACGGCCTCTGAC 60.375 63.158 9.82 0.00 34.31 3.51
1410 2034 2.874701 CGAGTCCAATAATGCAAGAGGG 59.125 50.000 0.00 0.00 0.00 4.30
1468 2110 1.443802 GACAGAAAGGTGGCTACAGC 58.556 55.000 1.52 0.00 45.24 4.40
1538 2180 9.088987 ACTTGGACATGGATACTGTTAATTTTT 57.911 29.630 0.00 0.00 37.61 1.94
1539 2181 8.650143 ACTTGGACATGGATACTGTTAATTTT 57.350 30.769 0.00 0.00 37.61 1.82
1540 2182 8.522830 CAACTTGGACATGGATACTGTTAATTT 58.477 33.333 0.00 0.00 37.61 1.82
1541 2183 7.362920 GCAACTTGGACATGGATACTGTTAATT 60.363 37.037 0.00 0.00 37.61 1.40
1542 2184 6.095440 GCAACTTGGACATGGATACTGTTAAT 59.905 38.462 0.00 0.00 37.61 1.40
1543 2185 5.414454 GCAACTTGGACATGGATACTGTTAA 59.586 40.000 0.00 0.00 37.61 2.01
1544 2186 4.941263 GCAACTTGGACATGGATACTGTTA 59.059 41.667 0.00 0.00 37.61 2.41
1545 2187 3.758554 GCAACTTGGACATGGATACTGTT 59.241 43.478 0.00 0.00 37.61 3.16
1546 2188 3.009473 AGCAACTTGGACATGGATACTGT 59.991 43.478 0.00 0.00 37.61 3.55
1547 2189 3.614092 AGCAACTTGGACATGGATACTG 58.386 45.455 0.00 0.00 37.61 2.74
1548 2190 3.264193 TGAGCAACTTGGACATGGATACT 59.736 43.478 0.00 0.00 37.61 2.12
1549 2191 3.375299 GTGAGCAACTTGGACATGGATAC 59.625 47.826 0.00 0.00 0.00 2.24
1550 2192 3.609853 GTGAGCAACTTGGACATGGATA 58.390 45.455 0.00 0.00 0.00 2.59
1551 2193 2.440409 GTGAGCAACTTGGACATGGAT 58.560 47.619 0.00 0.00 0.00 3.41
1552 2194 1.545428 GGTGAGCAACTTGGACATGGA 60.545 52.381 0.00 0.00 0.00 3.41
1553 2195 0.883833 GGTGAGCAACTTGGACATGG 59.116 55.000 0.00 0.00 0.00 3.66
1554 2196 0.518636 CGGTGAGCAACTTGGACATG 59.481 55.000 0.00 0.00 0.00 3.21
1555 2197 0.606401 CCGGTGAGCAACTTGGACAT 60.606 55.000 0.00 0.00 0.00 3.06
1556 2198 1.227823 CCGGTGAGCAACTTGGACA 60.228 57.895 0.00 0.00 0.00 4.02
1557 2199 2.617274 GCCGGTGAGCAACTTGGAC 61.617 63.158 1.90 0.00 0.00 4.02
1558 2200 2.281484 GCCGGTGAGCAACTTGGA 60.281 61.111 1.90 0.00 0.00 3.53
1559 2201 3.726517 CGCCGGTGAGCAACTTGG 61.727 66.667 10.20 0.00 0.00 3.61
1560 2202 3.726517 CCGCCGGTGAGCAACTTG 61.727 66.667 18.79 0.00 0.00 3.16
1576 2218 3.064820 TCAAAGAAAAGCAGAACGTGACC 59.935 43.478 0.00 0.00 0.00 4.02
1607 2251 4.163427 CCCATGAGAGTGGTAGGTATGAT 58.837 47.826 0.00 0.00 37.57 2.45
1664 2308 1.067776 GGGGTATGGTGTCGATCGATC 60.068 57.143 22.50 15.68 0.00 3.69
1665 2309 0.966920 GGGGTATGGTGTCGATCGAT 59.033 55.000 22.50 7.28 0.00 3.59
1666 2310 0.396001 TGGGGTATGGTGTCGATCGA 60.396 55.000 15.15 15.15 0.00 3.59
1767 2466 6.979817 TCCATTTTGCATGCATGAATTAGTAC 59.020 34.615 30.64 10.13 0.00 2.73
1770 2469 6.314152 TGTTCCATTTTGCATGCATGAATTAG 59.686 34.615 30.64 16.47 0.00 1.73
1990 2703 6.702716 ACTAAGTAACTAGAGCAGCTAAGG 57.297 41.667 0.00 0.00 0.00 2.69
2135 2879 1.738099 GCTGACGAAGATGTGGCGT 60.738 57.895 0.00 0.00 41.45 5.68
2230 2983 3.733236 CATGCATGCAAGAAGGTGG 57.267 52.632 26.68 3.21 0.00 4.61
2289 3052 2.888212 TCTTTTTGGATTGGAGGGTGG 58.112 47.619 0.00 0.00 0.00 4.61
2437 3294 5.748872 GAGTTCAACTATCAACTCGACAC 57.251 43.478 0.00 0.00 39.28 3.67
2449 3312 6.495181 ACTGATGGAGAAAGAGAGTTCAACTA 59.505 38.462 0.00 0.00 0.00 2.24
2501 3370 3.072211 CACACTGACACTGAGCAATCAT 58.928 45.455 0.00 0.00 0.00 2.45
2504 3373 2.627515 ACACACTGACACTGAGCAAT 57.372 45.000 0.00 0.00 0.00 3.56
2505 3374 3.181466 ACATACACACTGACACTGAGCAA 60.181 43.478 0.00 0.00 0.00 3.91
2506 3375 2.365293 ACATACACACTGACACTGAGCA 59.635 45.455 0.00 0.00 0.00 4.26
2507 3376 3.032017 ACATACACACTGACACTGAGC 57.968 47.619 0.00 0.00 0.00 4.26
2508 3377 5.182190 AGAGTACATACACACTGACACTGAG 59.818 44.000 0.00 0.00 0.00 3.35
2509 3378 5.048713 CAGAGTACATACACACTGACACTGA 60.049 44.000 0.00 0.00 0.00 3.41
2510 3379 5.157067 CAGAGTACATACACACTGACACTG 58.843 45.833 0.00 0.00 0.00 3.66
2511 3380 4.218635 CCAGAGTACATACACACTGACACT 59.781 45.833 0.00 0.00 0.00 3.55
2512 3381 4.486090 CCAGAGTACATACACACTGACAC 58.514 47.826 0.00 0.00 0.00 3.67
2513 3382 3.056821 GCCAGAGTACATACACACTGACA 60.057 47.826 0.00 0.00 0.00 3.58
2514 3383 3.056821 TGCCAGAGTACATACACACTGAC 60.057 47.826 0.00 0.00 0.00 3.51
2553 3423 8.923609 AACGATTTTTCTACTACTACCTAAGC 57.076 34.615 0.00 0.00 0.00 3.09
2558 3428 8.754230 ACTCAAACGATTTTTCTACTACTACC 57.246 34.615 0.00 0.00 0.00 3.18
2577 3474 1.066430 CCGCCCACTAGCTAACTCAAA 60.066 52.381 0.00 0.00 0.00 2.69
2677 3692 2.341101 ACCGCCACGTACTCCTGAG 61.341 63.158 0.00 0.00 0.00 3.35
2678 3693 2.282674 ACCGCCACGTACTCCTGA 60.283 61.111 0.00 0.00 0.00 3.86
2935 3976 4.430765 CCCGTTCCTCCGTCCGTG 62.431 72.222 0.00 0.00 0.00 4.94
3080 4151 8.292448 GCCACCTACACATAATCAAAATAGATG 58.708 37.037 0.00 0.00 0.00 2.90
3109 4186 1.196808 GAACCATACGCACCACTGTTG 59.803 52.381 0.00 0.00 0.00 3.33
3128 4205 9.797642 ACTTAAGTATGATTAATCATGCCATGA 57.202 29.630 32.15 20.56 46.76 3.07
3220 4297 2.613506 CGTTGTTTGGTCCTCGGCC 61.614 63.158 0.00 0.00 0.00 6.13
3224 4301 2.613506 CGCCCGTTGTTTGGTCCTC 61.614 63.158 0.00 0.00 0.00 3.71
3227 4304 3.284449 AGCGCCCGTTGTTTGGTC 61.284 61.111 2.29 0.00 0.00 4.02
3235 4312 0.669625 GACTAAACTCAGCGCCCGTT 60.670 55.000 2.29 1.66 0.00 4.44
3237 4314 1.810030 GGACTAAACTCAGCGCCCG 60.810 63.158 2.29 0.00 0.00 6.13
3257 4334 1.801765 GCCGCTCGTCCTTAGGTAAAG 60.802 57.143 0.00 0.00 34.73 1.85
3258 4335 0.174162 GCCGCTCGTCCTTAGGTAAA 59.826 55.000 0.00 0.00 0.00 2.01
3259 4336 0.966875 TGCCGCTCGTCCTTAGGTAA 60.967 55.000 0.00 0.00 0.00 2.85
3261 4338 2.678934 TGCCGCTCGTCCTTAGGT 60.679 61.111 0.00 0.00 0.00 3.08
3262 4339 2.105128 CTGCCGCTCGTCCTTAGG 59.895 66.667 0.00 0.00 0.00 2.69
3274 4352 2.606272 GACTATTAAACCGTTCCTGCCG 59.394 50.000 0.00 0.00 0.00 5.69
3275 4353 3.602483 TGACTATTAAACCGTTCCTGCC 58.398 45.455 0.00 0.00 0.00 4.85
3277 4355 7.490000 ACTATCTGACTATTAAACCGTTCCTG 58.510 38.462 0.00 0.00 0.00 3.86
3278 4356 7.657023 ACTATCTGACTATTAAACCGTTCCT 57.343 36.000 0.00 0.00 0.00 3.36
3279 4357 7.977853 TGAACTATCTGACTATTAAACCGTTCC 59.022 37.037 0.00 0.00 0.00 3.62
3281 4359 8.746530 TCTGAACTATCTGACTATTAAACCGTT 58.253 33.333 0.00 0.00 0.00 4.44
3282 4360 8.289939 TCTGAACTATCTGACTATTAAACCGT 57.710 34.615 0.00 0.00 0.00 4.83
3283 4361 9.239002 CTTCTGAACTATCTGACTATTAAACCG 57.761 37.037 0.00 0.00 33.78 4.44
3288 4366 8.526667 ACTGCTTCTGAACTATCTGACTATTA 57.473 34.615 0.00 0.00 33.78 0.98
3291 4369 7.939784 TTACTGCTTCTGAACTATCTGACTA 57.060 36.000 0.00 0.00 33.78 2.59
3292 4370 6.842437 TTACTGCTTCTGAACTATCTGACT 57.158 37.500 0.00 0.00 33.78 3.41
3293 4371 7.093992 AGTTTACTGCTTCTGAACTATCTGAC 58.906 38.462 0.00 0.00 33.78 3.51
3294 4372 7.233389 AGTTTACTGCTTCTGAACTATCTGA 57.767 36.000 0.00 0.00 0.00 3.27
3295 4373 7.897575 AAGTTTACTGCTTCTGAACTATCTG 57.102 36.000 0.00 0.00 30.91 2.90
3348 4426 8.993424 AGGTAAAGATTTATAGTGACAGTCCAT 58.007 33.333 0.00 0.00 0.00 3.41
3349 4427 8.258007 CAGGTAAAGATTTATAGTGACAGTCCA 58.742 37.037 0.00 0.00 0.00 4.02
3350 4428 8.258708 ACAGGTAAAGATTTATAGTGACAGTCC 58.741 37.037 0.00 0.00 0.00 3.85
3357 4435 6.482308 CCCGGAACAGGTAAAGATTTATAGTG 59.518 42.308 0.73 0.00 0.00 2.74
3363 4441 2.224917 TGCCCGGAACAGGTAAAGATTT 60.225 45.455 0.73 0.00 0.00 2.17
3370 4448 0.543410 TTCTCTGCCCGGAACAGGTA 60.543 55.000 20.28 9.20 35.78 3.08
3379 4457 1.153289 CATGGACCTTCTCTGCCCG 60.153 63.158 0.00 0.00 0.00 6.13
3385 4463 1.625818 ACTGTCACCATGGACCTTCTC 59.374 52.381 21.47 2.07 36.97 2.87
3393 4471 3.137176 AGGAATATGGACTGTCACCATGG 59.863 47.826 11.19 11.19 46.05 3.66
3397 4475 7.881775 ATTTTTAGGAATATGGACTGTCACC 57.118 36.000 10.38 3.27 0.00 4.02
3407 4485 9.559958 GCATCCGTCATTATTTTTAGGAATATG 57.440 33.333 0.00 0.00 0.00 1.78
3413 4491 6.430451 GTCAGCATCCGTCATTATTTTTAGG 58.570 40.000 0.00 0.00 0.00 2.69
3418 4496 2.287915 GCGTCAGCATCCGTCATTATTT 59.712 45.455 0.00 0.00 44.35 1.40
3432 4510 5.880341 ACCAGATTAATAAAAAGCGTCAGC 58.120 37.500 0.00 0.00 45.58 4.26
3464 4542 7.218228 TGCTCTCACACATATGATTGTTTTT 57.782 32.000 10.38 0.00 0.00 1.94
3465 4543 6.822667 TGCTCTCACACATATGATTGTTTT 57.177 33.333 10.38 0.00 0.00 2.43
3466 4544 6.822667 TTGCTCTCACACATATGATTGTTT 57.177 33.333 10.38 0.00 0.00 2.83
3467 4545 6.183360 CCATTGCTCTCACACATATGATTGTT 60.183 38.462 10.38 0.00 0.00 2.83
3468 4546 5.298527 CCATTGCTCTCACACATATGATTGT 59.701 40.000 10.38 0.96 0.00 2.71
3469 4547 5.298527 ACCATTGCTCTCACACATATGATTG 59.701 40.000 10.38 5.88 0.00 2.67
3470 4548 5.443283 ACCATTGCTCTCACACATATGATT 58.557 37.500 10.38 0.00 0.00 2.57
3471 4549 5.045012 ACCATTGCTCTCACACATATGAT 57.955 39.130 10.38 0.00 0.00 2.45
3473 4551 3.562973 GGACCATTGCTCTCACACATATG 59.437 47.826 0.00 0.00 0.00 1.78
3474 4552 3.200605 TGGACCATTGCTCTCACACATAT 59.799 43.478 0.00 0.00 0.00 1.78
3476 4554 1.352017 TGGACCATTGCTCTCACACAT 59.648 47.619 0.00 0.00 0.00 3.21
3492 4573 3.191735 CGTGGATTTAAACGGTTGGAC 57.808 47.619 0.00 0.00 36.17 4.02
3526 4607 0.179084 TAAGGGAGCGATTTCCAGCG 60.179 55.000 0.00 0.00 39.09 5.18
3527 4608 1.587547 CTAAGGGAGCGATTTCCAGC 58.412 55.000 0.00 0.00 39.09 4.85
3528 4609 1.486726 ACCTAAGGGAGCGATTTCCAG 59.513 52.381 0.00 0.00 39.09 3.86
3537 4618 2.614829 TTATCGCAACCTAAGGGAGC 57.385 50.000 0.00 0.00 36.25 4.70
3538 4619 4.451900 ACATTTATCGCAACCTAAGGGAG 58.548 43.478 0.00 0.00 36.25 4.30
3539 4620 4.497291 ACATTTATCGCAACCTAAGGGA 57.503 40.909 0.00 0.00 36.25 4.20
3542 4623 5.339990 CCCAAACATTTATCGCAACCTAAG 58.660 41.667 0.00 0.00 0.00 2.18
3543 4624 4.381079 GCCCAAACATTTATCGCAACCTAA 60.381 41.667 0.00 0.00 0.00 2.69
3548 4630 1.542030 ACGCCCAAACATTTATCGCAA 59.458 42.857 0.00 0.00 0.00 4.85
3551 4633 2.911819 ACACGCCCAAACATTTATCG 57.088 45.000 0.00 0.00 0.00 2.92
3553 4635 3.253677 TCGAAACACGCCCAAACATTTAT 59.746 39.130 0.00 0.00 42.26 1.40
3558 4640 0.378962 CTTCGAAACACGCCCAAACA 59.621 50.000 0.00 0.00 42.26 2.83
3565 4647 0.164002 GAGGCTTCTTCGAAACACGC 59.836 55.000 0.00 0.00 42.26 5.34
3568 4650 1.542547 GGGTGAGGCTTCTTCGAAACA 60.543 52.381 0.00 0.00 0.00 2.83
3582 4664 1.888436 TACAAGCAGCCTCGGGTGAG 61.888 60.000 18.57 9.60 45.42 3.51
3588 4670 1.199789 TGCAATTTACAAGCAGCCTCG 59.800 47.619 0.00 0.00 33.75 4.63
3594 4676 4.081406 AGAGATGGTGCAATTTACAAGCA 58.919 39.130 0.00 0.00 35.63 3.91
3595 4677 4.156556 TCAGAGATGGTGCAATTTACAAGC 59.843 41.667 0.00 0.00 0.00 4.01
3604 4686 2.540383 ACTACCTCAGAGATGGTGCAA 58.460 47.619 0.00 0.00 37.74 4.08
3609 4691 4.085733 CCCAGATACTACCTCAGAGATGG 58.914 52.174 0.00 0.00 0.00 3.51
3617 4699 6.544650 TCTCTCAATACCCAGATACTACCTC 58.455 44.000 0.00 0.00 0.00 3.85
3618 4700 6.532119 TCTCTCAATACCCAGATACTACCT 57.468 41.667 0.00 0.00 0.00 3.08
3619 4701 7.598759 TTTCTCTCAATACCCAGATACTACC 57.401 40.000 0.00 0.00 0.00 3.18
3620 4702 7.648510 CGTTTTCTCTCAATACCCAGATACTAC 59.351 40.741 0.00 0.00 0.00 2.73
3621 4703 7.341256 ACGTTTTCTCTCAATACCCAGATACTA 59.659 37.037 0.00 0.00 0.00 1.82
3622 4704 6.154706 ACGTTTTCTCTCAATACCCAGATACT 59.845 38.462 0.00 0.00 0.00 2.12
3623 4705 6.255887 CACGTTTTCTCTCAATACCCAGATAC 59.744 42.308 0.00 0.00 0.00 2.24
3624 4706 6.070995 ACACGTTTTCTCTCAATACCCAGATA 60.071 38.462 0.00 0.00 0.00 1.98
3625 4707 5.178797 CACGTTTTCTCTCAATACCCAGAT 58.821 41.667 0.00 0.00 0.00 2.90
3626 4708 4.039973 ACACGTTTTCTCTCAATACCCAGA 59.960 41.667 0.00 0.00 0.00 3.86
3629 4711 3.683340 GGACACGTTTTCTCTCAATACCC 59.317 47.826 0.00 0.00 0.00 3.69
3635 4717 0.748450 ACCGGACACGTTTTCTCTCA 59.252 50.000 9.46 0.00 38.78 3.27
3641 4723 1.451067 TCACAAACCGGACACGTTTT 58.549 45.000 9.46 0.00 34.96 2.43
3642 4724 1.399089 CTTCACAAACCGGACACGTTT 59.601 47.619 9.46 0.00 38.78 3.60
3651 4733 0.656205 CGCGTTTCCTTCACAAACCG 60.656 55.000 0.00 0.00 31.12 4.44
3652 4734 0.317519 CCGCGTTTCCTTCACAAACC 60.318 55.000 4.92 0.00 31.12 3.27
3656 4738 2.975799 GCCCGCGTTTCCTTCACA 60.976 61.111 4.92 0.00 0.00 3.58
3659 4741 2.750237 ATGGCCCGCGTTTCCTTC 60.750 61.111 4.92 0.00 0.00 3.46
3669 4751 0.664761 CAATAGAGCAACATGGCCCG 59.335 55.000 0.00 0.00 0.00 6.13
3671 4753 1.678101 GTCCAATAGAGCAACATGGCC 59.322 52.381 0.00 0.00 0.00 5.36
3673 4755 4.264253 TGAAGTCCAATAGAGCAACATGG 58.736 43.478 0.00 0.00 0.00 3.66
3683 4765 8.115490 AGGATGAAAAGTTTGAAGTCCAATAG 57.885 34.615 10.42 0.00 34.23 1.73
3685 4767 6.779539 AGAGGATGAAAAGTTTGAAGTCCAAT 59.220 34.615 10.42 0.00 34.23 3.16
3690 4772 7.645058 TTTGAGAGGATGAAAAGTTTGAAGT 57.355 32.000 0.00 0.00 0.00 3.01
3711 4793 3.743521 TGTCTTGTGATGGTCTCCTTTG 58.256 45.455 0.00 0.00 0.00 2.77
3713 4795 3.328931 ACATGTCTTGTGATGGTCTCCTT 59.671 43.478 0.00 0.00 37.11 3.36
3714 4796 2.909006 ACATGTCTTGTGATGGTCTCCT 59.091 45.455 0.00 0.00 37.11 3.69
3725 4807 1.881973 GTGGCATGTCACATGTCTTGT 59.118 47.619 25.20 0.00 39.91 3.16
3726 4808 2.095415 CAGTGGCATGTCACATGTCTTG 60.095 50.000 30.70 16.41 39.93 3.02
3728 4810 1.817357 CAGTGGCATGTCACATGTCT 58.183 50.000 30.70 13.62 39.93 3.41
3744 4826 2.017049 GGCAGTTCCGAATAATGCAGT 58.983 47.619 14.27 0.00 38.63 4.40
3746 4828 2.418368 AGGCAGTTCCGAATAATGCA 57.582 45.000 14.27 0.00 40.77 3.96
3752 4834 6.119536 TCAAATATTGTAGGCAGTTCCGAAT 58.880 36.000 0.00 0.00 40.77 3.34
3755 4837 5.006746 GTCTCAAATATTGTAGGCAGTTCCG 59.993 44.000 0.00 0.00 40.77 4.30
3759 4841 7.944729 AAATGTCTCAAATATTGTAGGCAGT 57.055 32.000 9.63 5.29 30.26 4.40


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

AutoCloner maintained by Alex Coulton.