Multiple sequence alignment - TraesCS4B01G236500

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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 TraesCS4B01G236500 chr4B 100.000 5013 0 0 1 5013 494590061 494585049 0.000000e+00 9258.0
1 TraesCS4B01G236500 chr4A 90.711 3068 233 29 1144 4176 58223324 58220274 0.000000e+00 4039.0
2 TraesCS4B01G236500 chr4A 86.595 1119 101 29 1 1084 58224459 58223355 0.000000e+00 1190.0
3 TraesCS4B01G236500 chr4A 84.434 212 25 5 4228 4432 58220093 58219883 8.510000e-48 202.0
4 TraesCS4B01G236500 chr4D 91.801 2110 120 12 1121 3205 399972407 399970326 0.000000e+00 2889.0
5 TraesCS4B01G236500 chr4D 89.111 1249 88 17 3240 4469 399970324 399969105 0.000000e+00 1509.0
6 TraesCS4B01G236500 chr4D 91.545 343 12 8 754 1084 399972747 399972410 1.640000e-124 457.0
7 TraesCS4B01G236500 chr4D 92.683 41 3 0 133 173 503151155 503151195 5.420000e-05 60.2
8 TraesCS4B01G236500 chr7A 93.086 405 21 1 4476 4880 619560355 619559958 2.010000e-163 586.0
9 TraesCS4B01G236500 chr7A 92.099 405 25 1 4476 4880 60701598 60701201 9.420000e-157 564.0
10 TraesCS4B01G236500 chr7A 91.892 111 9 0 4903 5013 60701207 60701097 6.720000e-34 156.0
11 TraesCS4B01G236500 chr7A 90.991 111 10 0 4903 5013 619559964 619559854 3.130000e-32 150.0
12 TraesCS4B01G236500 chr5A 92.500 400 23 1 4481 4880 44926692 44926300 2.620000e-157 566.0
13 TraesCS4B01G236500 chr5A 92.793 111 8 0 4903 5013 44926306 44926196 1.440000e-35 161.0
14 TraesCS4B01G236500 chr6A 92.099 405 25 2 4476 4880 270781633 270781236 9.420000e-157 564.0
15 TraesCS4B01G236500 chr6A 91.892 111 9 0 4903 5013 270781242 270781132 6.720000e-34 156.0
16 TraesCS4B01G236500 chr3A 91.870 246 17 2 4677 4920 686076937 686076693 1.730000e-89 340.0
17 TraesCS4B01G236500 chr3A 94.764 191 9 1 4485 4674 686077239 686077049 3.790000e-76 296.0
18 TraesCS4B01G236500 chr2A 84.362 243 19 11 4681 4923 21142369 21142592 2.350000e-53 220.0
19 TraesCS4B01G236500 chr2A 92.424 132 10 0 4478 4609 21129856 21129987 6.630000e-44 189.0
20 TraesCS4B01G236500 chr1D 86.243 189 20 3 1341 1524 340323192 340323005 3.060000e-47 200.0
21 TraesCS4B01G236500 chr2D 84.574 188 23 4 1341 1523 324042508 324042694 1.110000e-41 182.0
22 TraesCS4B01G236500 chr2D 86.957 92 12 0 1618 1709 324042699 324042790 2.470000e-18 104.0
23 TraesCS4B01G236500 chr2B 84.000 175 25 1 2686 2857 403423931 403424105 1.120000e-36 165.0
24 TraesCS4B01G236500 chr2B 93.182 88 6 0 2317 2404 403423827 403423914 4.070000e-26 130.0
25 TraesCS4B01G236500 chr7B 96.341 82 3 0 4677 4758 54550126 54550207 8.750000e-28 135.0
26 TraesCS4B01G236500 chr6B 90.909 88 8 0 2317 2404 322066716 322066629 8.820000e-23 119.0


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 TraesCS4B01G236500 chr4B 494585049 494590061 5012 True 9258.000000 9258 100.000000 1 5013 1 chr4B.!!$R1 5012
1 TraesCS4B01G236500 chr4A 58219883 58224459 4576 True 1810.333333 4039 87.246667 1 4432 3 chr4A.!!$R1 4431
2 TraesCS4B01G236500 chr4D 399969105 399972747 3642 True 1618.333333 2889 90.819000 754 4469 3 chr4D.!!$R1 3715
3 TraesCS4B01G236500 chr7A 619559854 619560355 501 True 368.000000 586 92.038500 4476 5013 2 chr7A.!!$R2 537
4 TraesCS4B01G236500 chr7A 60701097 60701598 501 True 360.000000 564 91.995500 4476 5013 2 chr7A.!!$R1 537
5 TraesCS4B01G236500 chr6A 270781132 270781633 501 True 360.000000 564 91.995500 4476 5013 2 chr6A.!!$R1 537
6 TraesCS4B01G236500 chr3A 686076693 686077239 546 True 318.000000 340 93.317000 4485 4920 2 chr3A.!!$R1 435

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
259 261 0.105964 TGCTACGTTCTGCACAAGGT 59.894 50.0 5.41 5.41 33.94 3.50 F
1091 1130 0.248784 GGTACGTACCATCCTCGCAC 60.249 60.0 34.65 7.61 45.73 5.34 F
2218 2270 0.242825 CTGCCATGGAACTGCAACAG 59.757 55.0 18.40 6.64 37.52 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1160 1204 0.179043 TTGTAGTTCAACCAGCCGCA 60.179 50.0 0.00 0.0 0.00 5.69 R
2536 2609 0.172578 TTGCCCTATCTGACGACACG 59.827 55.0 0.00 0.0 0.00 4.49 R
4110 4200 0.102300 ACAAGTGGGCGTTTTCTTGC 59.898 50.0 10.59 0.0 40.29 4.01 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
100 101 2.060326 TAGAGAAGGTTTGTCGTGCG 57.940 50.000 0.00 0.00 0.00 5.34
102 103 0.232303 GAGAAGGTTTGTCGTGCGTG 59.768 55.000 0.00 0.00 0.00 5.34
118 119 4.142773 CGTGCGTGTTAAAATAATCACCCT 60.143 41.667 0.00 0.00 0.00 4.34
119 120 5.092781 GTGCGTGTTAAAATAATCACCCTG 58.907 41.667 0.00 0.00 0.00 4.45
229 231 2.159653 GGAACTTGCATGTGACGCTTAG 60.160 50.000 5.94 0.00 0.00 2.18
242 244 3.204811 GCTTAGTGCGTCGAAATGC 57.795 52.632 0.00 0.00 37.95 3.56
249 251 0.711670 TGCGTCGAAATGCTACGTTC 59.288 50.000 0.00 0.00 37.91 3.95
257 259 3.482786 GAAATGCTACGTTCTGCACAAG 58.517 45.455 11.64 0.00 42.26 3.16
259 261 0.105964 TGCTACGTTCTGCACAAGGT 59.894 50.000 5.41 5.41 33.94 3.50
274 276 0.698818 AAGGTTGCCCTCTAACTGGG 59.301 55.000 0.00 0.00 41.56 4.45
304 306 0.727398 GGCGCAGAAATGTAGTGACC 59.273 55.000 10.83 0.00 0.00 4.02
306 308 0.999406 CGCAGAAATGTAGTGACCCG 59.001 55.000 0.00 0.00 0.00 5.28
342 345 5.874810 TCTCTGTTGCAGAAAAGCGTATATT 59.125 36.000 0.37 0.00 40.18 1.28
360 363 8.580431 GCGTATATTTTTCAAGCGTTTTATTGT 58.420 29.630 0.00 0.00 0.00 2.71
365 368 8.641499 ATTTTTCAAGCGTTTTATTGTCTTCA 57.359 26.923 0.00 0.00 0.00 3.02
369 372 4.647291 AGCGTTTTATTGTCTTCAGTCG 57.353 40.909 0.00 0.00 0.00 4.18
370 373 3.432252 AGCGTTTTATTGTCTTCAGTCGG 59.568 43.478 0.00 0.00 0.00 4.79
373 376 4.377022 CGTTTTATTGTCTTCAGTCGGGTG 60.377 45.833 0.00 0.00 0.00 4.61
376 379 2.234300 TTGTCTTCAGTCGGGTGTTC 57.766 50.000 0.00 0.00 0.00 3.18
390 393 3.469739 GGGTGTTCCGTTCAGTTTTCTA 58.530 45.455 0.00 0.00 33.83 2.10
391 394 3.878699 GGGTGTTCCGTTCAGTTTTCTAA 59.121 43.478 0.00 0.00 33.83 2.10
501 505 7.607250 TGAAACTTTAGTTGGAAGCTGAAAAA 58.393 30.769 0.00 0.00 38.44 1.94
525 534 9.921637 AAAACATTAACTTCTGAAAAACTGTGA 57.078 25.926 0.00 0.00 0.00 3.58
527 536 8.911247 ACATTAACTTCTGAAAAACTGTGAAC 57.089 30.769 0.00 0.00 0.00 3.18
531 557 9.921637 TTAACTTCTGAAAAACTGTGAACATTT 57.078 25.926 0.00 0.00 0.00 2.32
533 559 9.921637 AACTTCTGAAAAACTGTGAACATTTTA 57.078 25.926 0.00 0.00 30.14 1.52
602 628 5.760193 TGCATATTCAAAAACATTGCGAC 57.240 34.783 0.00 0.00 0.00 5.19
617 643 7.881643 ACATTGCGACTATTTTATTTTTGCA 57.118 28.000 0.00 0.00 0.00 4.08
618 644 8.477984 ACATTGCGACTATTTTATTTTTGCAT 57.522 26.923 0.00 0.00 0.00 3.96
619 645 9.579768 ACATTGCGACTATTTTATTTTTGCATA 57.420 25.926 0.00 0.00 0.00 3.14
650 676 9.934190 ATTTTAAAAATGTGAACATCTGTTTGC 57.066 25.926 4.44 0.00 38.56 3.68
659 685 9.979578 ATGTGAACATCTGTTTGCTTTATTTTA 57.020 25.926 0.00 0.00 38.56 1.52
715 741 6.859017 ACAAAAAGCATACCCGTAATAAAGG 58.141 36.000 0.00 0.00 0.00 3.11
760 787 1.915952 AAAACCCAACGTGAAAAGCG 58.084 45.000 0.00 0.00 0.00 4.68
772 799 6.449448 ACGTGAAAAGCGTTTTGTTTTAAA 57.551 29.167 0.00 0.00 39.79 1.52
926 957 1.360820 GCACGTAGCTTTCCTTCCTC 58.639 55.000 0.00 0.00 41.15 3.71
962 993 0.914417 TGTCAACCCATCTCTCCCCC 60.914 60.000 0.00 0.00 0.00 5.40
989 1024 4.383552 CCTCTTTCCCTCAGGTACATTCAG 60.384 50.000 0.00 0.00 0.00 3.02
990 1025 3.055094 TCTTTCCCTCAGGTACATTCAGC 60.055 47.826 0.00 0.00 0.00 4.26
1090 1129 2.109431 GGTACGTACCATCCTCGCA 58.891 57.895 34.65 0.00 45.73 5.10
1091 1130 0.248784 GGTACGTACCATCCTCGCAC 60.249 60.000 34.65 7.61 45.73 5.34
1092 1131 0.590732 GTACGTACCATCCTCGCACG 60.591 60.000 15.00 0.00 38.52 5.34
1093 1132 1.026182 TACGTACCATCCTCGCACGT 61.026 55.000 3.46 3.46 46.49 4.49
1094 1133 1.026182 ACGTACCATCCTCGCACGTA 61.026 55.000 0.00 0.00 43.39 3.57
1095 1134 0.309922 CGTACCATCCTCGCACGTAT 59.690 55.000 0.00 0.00 0.00 3.06
1096 1135 1.662309 CGTACCATCCTCGCACGTATC 60.662 57.143 0.00 0.00 0.00 2.24
1097 1136 1.607628 GTACCATCCTCGCACGTATCT 59.392 52.381 0.00 0.00 0.00 1.98
1098 1137 1.977056 ACCATCCTCGCACGTATCTA 58.023 50.000 0.00 0.00 0.00 1.98
1099 1138 1.880675 ACCATCCTCGCACGTATCTAG 59.119 52.381 0.00 0.00 0.00 2.43
1100 1139 1.880675 CCATCCTCGCACGTATCTAGT 59.119 52.381 0.00 0.00 0.00 2.57
1101 1140 2.293677 CCATCCTCGCACGTATCTAGTT 59.706 50.000 0.00 0.00 0.00 2.24
1102 1141 3.243434 CCATCCTCGCACGTATCTAGTTT 60.243 47.826 0.00 0.00 0.00 2.66
1103 1142 4.360563 CATCCTCGCACGTATCTAGTTTT 58.639 43.478 0.00 0.00 0.00 2.43
1104 1143 3.766151 TCCTCGCACGTATCTAGTTTTG 58.234 45.455 0.00 0.00 0.00 2.44
1105 1144 2.858344 CCTCGCACGTATCTAGTTTTGG 59.142 50.000 0.00 0.00 0.00 3.28
1106 1145 2.858344 CTCGCACGTATCTAGTTTTGGG 59.142 50.000 0.00 0.00 0.00 4.12
1107 1146 1.326548 CGCACGTATCTAGTTTTGGGC 59.673 52.381 0.00 0.00 0.00 5.36
1108 1147 2.629051 GCACGTATCTAGTTTTGGGCT 58.371 47.619 0.00 0.00 0.00 5.19
1109 1148 3.007635 GCACGTATCTAGTTTTGGGCTT 58.992 45.455 0.00 0.00 0.00 4.35
1110 1149 3.181510 GCACGTATCTAGTTTTGGGCTTG 60.182 47.826 0.00 0.00 0.00 4.01
1111 1150 4.000988 CACGTATCTAGTTTTGGGCTTGT 58.999 43.478 0.00 0.00 0.00 3.16
1112 1151 5.172934 CACGTATCTAGTTTTGGGCTTGTA 58.827 41.667 0.00 0.00 0.00 2.41
1113 1152 5.291128 CACGTATCTAGTTTTGGGCTTGTAG 59.709 44.000 0.00 0.00 0.00 2.74
1114 1153 4.270325 CGTATCTAGTTTTGGGCTTGTAGC 59.730 45.833 0.00 0.00 41.46 3.58
1115 1154 4.576330 ATCTAGTTTTGGGCTTGTAGCT 57.424 40.909 0.00 0.00 41.99 3.32
1116 1155 3.674997 TCTAGTTTTGGGCTTGTAGCTG 58.325 45.455 0.00 0.00 41.99 4.24
1117 1156 1.620822 AGTTTTGGGCTTGTAGCTGG 58.379 50.000 0.00 0.00 41.99 4.85
1118 1157 1.144913 AGTTTTGGGCTTGTAGCTGGA 59.855 47.619 0.00 0.00 41.99 3.86
1119 1158 1.541588 GTTTTGGGCTTGTAGCTGGAG 59.458 52.381 0.00 0.00 41.99 3.86
1129 1168 5.118990 GCTTGTAGCTGGAGATCACAATAA 58.881 41.667 0.00 0.00 38.45 1.40
1132 1171 4.962362 TGTAGCTGGAGATCACAATAAGGA 59.038 41.667 0.00 0.00 0.00 3.36
1147 1186 8.048534 CACAATAAGGATTTTGTGTCTGAGAT 57.951 34.615 7.45 0.00 44.79 2.75
1157 1201 6.541934 TTTGTGTCTGAGATGAGAGATCAT 57.458 37.500 0.00 0.00 0.00 2.45
1160 1204 7.836479 TGTGTCTGAGATGAGAGATCATAAT 57.164 36.000 0.00 0.00 0.00 1.28
1161 1205 7.659186 TGTGTCTGAGATGAGAGATCATAATG 58.341 38.462 0.00 0.00 0.00 1.90
1169 1213 1.696336 AGAGATCATAATGCGGCTGGT 59.304 47.619 0.00 0.00 0.00 4.00
1177 1221 1.165270 AATGCGGCTGGTTGAACTAC 58.835 50.000 0.00 0.00 0.00 2.73
1218 1262 2.092968 TGAACAGTGTTCAACTCCTGCT 60.093 45.455 31.49 0.00 36.83 4.24
1229 1273 0.965866 ACTCCTGCTTGTCGATCGGA 60.966 55.000 16.41 0.00 0.00 4.55
1455 1499 2.020016 CAAAGATCCGCGCGTTCG 59.980 61.111 29.95 14.04 39.07 3.95
1526 1570 4.819761 ATGCACTGCGACGGCGAT 62.820 61.111 18.90 0.00 44.10 4.58
1832 1876 1.964373 GCCGGTTGTTCGTGTCCAT 60.964 57.895 1.90 0.00 0.00 3.41
1957 2001 2.202987 CAGCTCCGTGGATGCTCC 60.203 66.667 9.10 0.00 34.51 4.70
1986 2030 9.645128 AATAATGGTCTCATGAATGGTGATTTA 57.355 29.630 0.00 0.00 33.18 1.40
2030 2082 7.490962 TGGATATTTGTCTTAATTACAGGCG 57.509 36.000 0.00 0.00 0.00 5.52
2136 2188 1.066645 ACGAGCAGATCATGTTCAGCA 60.067 47.619 19.53 0.00 38.97 4.41
2176 2228 2.870372 GCAGTCCAACATGACGGC 59.130 61.111 0.00 0.87 46.26 5.68
2218 2270 0.242825 CTGCCATGGAACTGCAACAG 59.757 55.000 18.40 6.64 37.52 3.16
2229 2281 4.522789 GGAACTGCAACAGGGAGAAATTTA 59.477 41.667 0.00 0.00 38.52 1.40
2276 2328 3.269178 CATTCTCTCCTCAAAGCCTGTC 58.731 50.000 0.00 0.00 0.00 3.51
2320 2393 8.181573 CAGTTTATAAGTGTTTGCGTAATGGAT 58.818 33.333 0.00 0.00 0.00 3.41
2338 2411 3.513119 TGGATCAGGTGTTCTTCTCAGAG 59.487 47.826 0.00 0.00 0.00 3.35
2392 2465 0.908198 AGAGCGAGCTTTCCTCCATT 59.092 50.000 0.00 0.00 37.27 3.16
2452 2525 6.590068 ACTGATCGAGGATTCAGATTTTGAT 58.410 36.000 18.22 0.00 35.27 2.57
2455 2528 6.704937 TGATCGAGGATTCAGATTTTGATCAG 59.295 38.462 0.00 0.00 35.93 2.90
2456 2529 6.225981 TCGAGGATTCAGATTTTGATCAGA 57.774 37.500 0.00 0.00 35.27 3.27
2458 2531 6.536582 TCGAGGATTCAGATTTTGATCAGAAC 59.463 38.462 0.00 0.00 35.27 3.01
2461 2534 6.538021 AGGATTCAGATTTTGATCAGAACGAG 59.462 38.462 0.00 0.00 35.27 4.18
2536 2609 1.668419 ACACAGAGCACAGTGAAACC 58.332 50.000 13.31 0.00 37.80 3.27
2537 2610 0.583438 CACAGAGCACAGTGAAACCG 59.417 55.000 4.15 0.00 37.80 4.44
2538 2611 0.178068 ACAGAGCACAGTGAAACCGT 59.822 50.000 4.15 0.00 37.80 4.83
2539 2612 0.583438 CAGAGCACAGTGAAACCGTG 59.417 55.000 4.15 0.00 37.80 4.94
2542 2615 1.151777 AGCACAGTGAAACCGTGTCG 61.152 55.000 4.15 0.00 37.80 4.35
2551 2624 2.094906 TGAAACCGTGTCGTCAGATAGG 60.095 50.000 0.00 0.00 0.00 2.57
2611 2684 1.730902 CGGGTCATCAGATAGCGCG 60.731 63.158 0.00 0.00 0.00 6.86
2629 2702 2.602878 GCGAGTAACGGTTCAGATGAA 58.397 47.619 0.00 0.00 42.83 2.57
2650 2723 2.403252 AGGGAAACATTAGCACCGAG 57.597 50.000 0.00 0.00 0.00 4.63
2673 2746 2.115427 TGAGGCCGAGTTTATCCATGA 58.885 47.619 0.00 0.00 0.00 3.07
2704 2777 7.660208 GGAGTTGATGTTACTAGAGAAACCAAA 59.340 37.037 0.00 0.00 0.00 3.28
2707 2780 8.713271 GTTGATGTTACTAGAGAAACCAAAGAG 58.287 37.037 0.00 0.00 0.00 2.85
2710 2783 3.704800 ACTAGAGAAACCAAAGAGCCC 57.295 47.619 0.00 0.00 0.00 5.19
2781 2854 0.887933 GCACCAATCGTTCCCACAAT 59.112 50.000 0.00 0.00 0.00 2.71
2785 2858 3.128589 CACCAATCGTTCCCACAATAAGG 59.871 47.826 0.00 0.00 0.00 2.69
2813 2886 5.831702 AAATGAAGAGATGCCAACAGATC 57.168 39.130 0.00 0.00 0.00 2.75
2822 2895 3.063510 TGCCAACAGATCTCCAAGAAG 57.936 47.619 0.00 0.00 0.00 2.85
2829 2902 5.815233 ACAGATCTCCAAGAAGACAGAAA 57.185 39.130 0.00 0.00 0.00 2.52
2935 3011 1.002069 TCCCAGCAGTTCCCATCATT 58.998 50.000 0.00 0.00 0.00 2.57
2966 3045 1.596895 GAGGAGACCAGACACCGGAC 61.597 65.000 9.46 0.00 0.00 4.79
3061 3140 5.775701 AGCTTCTAGTTCTTCCAGTAACAGA 59.224 40.000 0.00 0.00 0.00 3.41
3081 3160 4.458295 CAGAACATCTCAAGCAAGGACAAT 59.542 41.667 0.00 0.00 0.00 2.71
3096 3175 3.199508 AGGACAATTCCATCTCCTCACAG 59.800 47.826 0.00 0.00 45.72 3.66
3105 3184 3.307269 CCATCTCCTCACAGACAACATGT 60.307 47.826 0.00 0.00 0.00 3.21
3166 3245 6.207614 AGGCAATAAGAGTTTCTTCAAACCTC 59.792 38.462 0.00 0.00 42.72 3.85
3186 3265 1.532868 CTCCAAAGAACACCTGAAGCG 59.467 52.381 0.00 0.00 0.00 4.68
3423 3502 5.075493 TGAAAAACCGAGGAGTAGTAGAGT 58.925 41.667 0.00 0.00 0.00 3.24
3424 3503 6.240894 TGAAAAACCGAGGAGTAGTAGAGTA 58.759 40.000 0.00 0.00 0.00 2.59
3427 3506 2.102252 ACCGAGGAGTAGTAGAGTACCG 59.898 54.545 0.00 0.00 0.00 4.02
3439 3518 5.638783 AGTAGAGTACCGAAACAAGAATCG 58.361 41.667 0.00 0.00 38.74 3.34
3444 3523 1.226018 CGAAACAAGAATCGCCGGC 60.226 57.895 19.07 19.07 31.71 6.13
3537 3622 1.822506 GTTTCTTCCCCGGGAAAGAG 58.177 55.000 22.49 13.32 41.54 2.85
3542 3627 0.619543 TTCCCCGGGAAAGAGTAGGG 60.620 60.000 26.32 0.00 38.93 3.53
3544 3629 2.743179 CCCGGGAAAGAGTAGGGCC 61.743 68.421 18.48 0.00 35.09 5.80
3545 3630 2.743179 CCGGGAAAGAGTAGGGCCC 61.743 68.421 16.46 16.46 35.40 5.80
3546 3631 1.689582 CGGGAAAGAGTAGGGCCCT 60.690 63.158 31.35 31.35 36.62 5.19
3553 3638 0.413832 AGAGTAGGGCCCTGACTTCA 59.586 55.000 35.81 10.69 0.00 3.02
3561 3646 1.298014 CCCTGACTTCACTCCCTGC 59.702 63.158 0.00 0.00 0.00 4.85
3586 3671 1.588674 AGACATCTCGTCCTAGCTCG 58.411 55.000 0.00 0.00 46.69 5.03
3623 3708 1.139947 CCTTCTTCCTCGCCTCGAC 59.860 63.158 0.00 0.00 0.00 4.20
3697 3782 0.809241 GTCCCAGATTCAGCAGAGCG 60.809 60.000 0.00 0.00 0.00 5.03
3807 3892 1.892862 TAGCGACCTCTAGAGCGGC 60.893 63.158 14.73 15.43 34.34 6.53
3873 3958 0.371645 CATCGAGAAGGCGTGAAAGC 59.628 55.000 0.00 0.00 0.00 3.51
3874 3959 0.037326 ATCGAGAAGGCGTGAAAGCA 60.037 50.000 0.00 0.00 39.27 3.91
4079 4167 6.399639 TTGAACCTTTGGTAGAATGGAAAC 57.600 37.500 0.00 0.00 33.12 2.78
4104 4194 6.223852 CAGTGGTCACAATACTACTTCAGTT 58.776 40.000 3.82 0.00 38.95 3.16
4110 4200 5.103000 CACAATACTACTTCAGTTCCCTCG 58.897 45.833 0.00 0.00 38.80 4.63
4142 4232 2.113774 CTTGTGGGCCTGCAGACA 59.886 61.111 17.39 8.75 0.00 3.41
4189 4279 1.608590 ACTCCGCTTGTTGTTCCATTG 59.391 47.619 0.00 0.00 0.00 2.82
4190 4280 1.608590 CTCCGCTTGTTGTTCCATTGT 59.391 47.619 0.00 0.00 0.00 2.71
4217 4307 5.730550 ACTACTGATTACGAATTGGCTTGA 58.269 37.500 0.00 0.00 0.00 3.02
4225 4315 6.811253 TTACGAATTGGCTTGATTGTTAGT 57.189 33.333 0.00 0.00 0.00 2.24
4229 4319 6.430000 ACGAATTGGCTTGATTGTTAGTAAGT 59.570 34.615 0.00 0.00 0.00 2.24
4235 4474 9.953565 TTGGCTTGATTGTTAGTAAGTTATACT 57.046 29.630 0.00 0.00 0.00 2.12
4272 4511 3.371063 CCAGCCCTTGCAGCACTG 61.371 66.667 0.00 0.00 41.13 3.66
4273 4512 2.596631 CAGCCCTTGCAGCACTGT 60.597 61.111 0.00 0.00 41.13 3.55
4274 4513 2.596631 AGCCCTTGCAGCACTGTG 60.597 61.111 2.76 2.76 41.13 3.66
4275 4514 4.353437 GCCCTTGCAGCACTGTGC 62.353 66.667 24.59 24.59 45.46 4.57
4291 4538 4.336433 CACTGTGCTTTCTTCCTTTCTTCA 59.664 41.667 0.00 0.00 0.00 3.02
4293 4540 3.885297 TGTGCTTTCTTCCTTTCTTCAGG 59.115 43.478 0.00 0.00 34.86 3.86
4311 4558 3.289834 CTTGCAACAGTGGCGGCT 61.290 61.111 11.43 0.00 0.00 5.52
4372 4632 1.669779 CAGCACTCAATCTGCTTAGCC 59.330 52.381 0.29 0.00 42.54 3.93
4375 4635 2.286872 CACTCAATCTGCTTAGCCAGG 58.713 52.381 0.29 0.00 33.64 4.45
4425 4685 0.889994 CCCAGCTTGCAGCAACAATA 59.110 50.000 2.83 0.00 45.56 1.90
4439 4699 6.732154 CAGCAACAATAGGATTTCACTATGG 58.268 40.000 0.00 0.00 31.81 2.74
4445 4705 7.595488 ACAATAGGATTTCACTATGGGGATTT 58.405 34.615 0.00 0.00 31.81 2.17
4451 4711 6.204882 GGATTTCACTATGGGGATTTCTTACG 59.795 42.308 0.00 0.00 0.00 3.18
4457 4717 7.289317 TCACTATGGGGATTTCTTACGACTATT 59.711 37.037 0.00 0.00 0.00 1.73
4463 4723 7.093201 TGGGGATTTCTTACGACTATTGTAGTT 60.093 37.037 0.00 0.00 39.59 2.24
4469 4729 1.203994 ACGACTATTGTAGTTGGCGCT 59.796 47.619 7.64 0.00 43.16 5.92
4470 4730 2.424601 ACGACTATTGTAGTTGGCGCTA 59.575 45.455 7.64 0.00 43.16 4.26
4471 4731 3.119388 ACGACTATTGTAGTTGGCGCTAA 60.119 43.478 7.64 4.03 43.16 3.09
4472 4732 3.861113 CGACTATTGTAGTTGGCGCTAAA 59.139 43.478 8.12 0.00 39.59 1.85
4473 4733 4.506654 CGACTATTGTAGTTGGCGCTAAAT 59.493 41.667 11.98 11.98 39.59 1.40
4474 4734 5.006358 CGACTATTGTAGTTGGCGCTAAATT 59.994 40.000 12.63 4.35 39.59 1.82
4475 4735 6.199531 CGACTATTGTAGTTGGCGCTAAATTA 59.800 38.462 12.63 3.31 39.59 1.40
4476 4736 7.095774 CGACTATTGTAGTTGGCGCTAAATTAT 60.096 37.037 12.63 6.47 39.59 1.28
4477 4737 8.446599 ACTATTGTAGTTGGCGCTAAATTATT 57.553 30.769 12.63 1.77 34.86 1.40
4478 4738 9.550406 ACTATTGTAGTTGGCGCTAAATTATTA 57.450 29.630 12.63 2.78 34.86 0.98
4483 4743 8.819974 TGTAGTTGGCGCTAAATTATTAGTAAC 58.180 33.333 12.63 2.02 40.59 2.50
4558 4818 1.850640 ACGAATGCGACAACGTCAC 59.149 52.632 0.00 0.00 41.64 3.67
4609 4869 4.336993 CACCAAGCCTAACTACAACAACAA 59.663 41.667 0.00 0.00 0.00 2.83
4641 4901 5.244851 TCCTTACATGCCAAACAAATAGCAA 59.755 36.000 0.00 0.00 38.99 3.91
4663 4923 6.585702 GCAACAATGTTAATGTTCATGCACTA 59.414 34.615 0.00 0.00 38.90 2.74
4664 4924 7.410728 GCAACAATGTTAATGTTCATGCACTAC 60.411 37.037 0.00 0.00 38.90 2.73
4665 4925 7.452880 ACAATGTTAATGTTCATGCACTACT 57.547 32.000 0.00 0.00 0.00 2.57
4666 4926 7.885297 ACAATGTTAATGTTCATGCACTACTT 58.115 30.769 0.00 0.00 0.00 2.24
4667 4927 9.008965 ACAATGTTAATGTTCATGCACTACTTA 57.991 29.630 0.00 0.00 0.00 2.24
4668 4928 9.838975 CAATGTTAATGTTCATGCACTACTTAA 57.161 29.630 0.00 0.00 0.00 1.85
4840 5219 2.553602 CAACACACAGCCACACATGTAT 59.446 45.455 0.00 0.00 0.00 2.29
4855 5234 8.200120 CCACACATGTATCTTGATTTCTCTCTA 58.800 37.037 0.00 0.00 0.00 2.43
4873 5252 3.759086 CTCTAAACTTCCCAGGCTTTTCC 59.241 47.826 0.00 0.00 0.00 3.13
4874 5253 2.470057 AAACTTCCCAGGCTTTTCCA 57.530 45.000 0.00 0.00 37.29 3.53
4875 5254 2.702270 AACTTCCCAGGCTTTTCCAT 57.298 45.000 0.00 0.00 37.29 3.41
4876 5255 2.702270 ACTTCCCAGGCTTTTCCATT 57.298 45.000 0.00 0.00 37.29 3.16
4877 5256 2.250924 ACTTCCCAGGCTTTTCCATTG 58.749 47.619 0.00 0.00 37.29 2.82
4878 5257 2.158325 ACTTCCCAGGCTTTTCCATTGA 60.158 45.455 0.00 0.00 37.29 2.57
4879 5258 2.925966 TCCCAGGCTTTTCCATTGAT 57.074 45.000 0.00 0.00 37.29 2.57
4880 5259 2.459644 TCCCAGGCTTTTCCATTGATG 58.540 47.619 0.00 0.00 37.29 3.07
4881 5260 1.134610 CCCAGGCTTTTCCATTGATGC 60.135 52.381 0.00 0.00 37.29 3.91
4882 5261 1.829222 CCAGGCTTTTCCATTGATGCT 59.171 47.619 0.00 0.00 37.29 3.79
4883 5262 2.418197 CCAGGCTTTTCCATTGATGCTG 60.418 50.000 0.00 0.00 37.29 4.41
4884 5263 2.494471 CAGGCTTTTCCATTGATGCTGA 59.506 45.455 0.00 0.00 37.29 4.26
4885 5264 3.132289 CAGGCTTTTCCATTGATGCTGAT 59.868 43.478 0.00 0.00 37.29 2.90
4886 5265 3.773119 AGGCTTTTCCATTGATGCTGATT 59.227 39.130 0.00 0.00 37.29 2.57
4887 5266 3.869246 GGCTTTTCCATTGATGCTGATTG 59.131 43.478 0.00 0.00 34.01 2.67
4888 5267 4.382254 GGCTTTTCCATTGATGCTGATTGA 60.382 41.667 0.00 0.00 34.01 2.57
4889 5268 4.565564 GCTTTTCCATTGATGCTGATTGAC 59.434 41.667 0.00 0.00 0.00 3.18
4890 5269 4.724074 TTTCCATTGATGCTGATTGACC 57.276 40.909 0.00 0.00 0.00 4.02
4891 5270 2.658285 TCCATTGATGCTGATTGACCC 58.342 47.619 0.00 0.00 0.00 4.46
4892 5271 1.684983 CCATTGATGCTGATTGACCCC 59.315 52.381 0.00 0.00 0.00 4.95
4893 5272 2.662866 CATTGATGCTGATTGACCCCT 58.337 47.619 0.00 0.00 0.00 4.79
4894 5273 3.435457 CCATTGATGCTGATTGACCCCTA 60.435 47.826 0.00 0.00 0.00 3.53
4895 5274 4.404640 CATTGATGCTGATTGACCCCTAT 58.595 43.478 0.00 0.00 0.00 2.57
4896 5275 5.515359 CCATTGATGCTGATTGACCCCTATA 60.515 44.000 0.00 0.00 0.00 1.31
4897 5276 5.848286 TTGATGCTGATTGACCCCTATAT 57.152 39.130 0.00 0.00 0.00 0.86
4898 5277 5.169992 TGATGCTGATTGACCCCTATATG 57.830 43.478 0.00 0.00 0.00 1.78
4899 5278 4.845796 TGATGCTGATTGACCCCTATATGA 59.154 41.667 0.00 0.00 0.00 2.15
4900 5279 5.489997 TGATGCTGATTGACCCCTATATGAT 59.510 40.000 0.00 0.00 0.00 2.45
4901 5280 5.848286 TGCTGATTGACCCCTATATGATT 57.152 39.130 0.00 0.00 0.00 2.57
4922 5301 5.604758 TTCACTGATCTACTGAAGGGATG 57.395 43.478 0.00 0.00 0.00 3.51
4966 5345 3.835810 CCAATGAGGGGAATCAGGG 57.164 57.895 0.00 0.00 31.44 4.45
4970 5349 1.686236 ATGAGGGGAATCAGGGTTGT 58.314 50.000 0.00 0.00 31.44 3.32
4975 5354 1.005450 GGGGAATCAGGGTTGTTAGCA 59.995 52.381 0.00 0.00 0.00 3.49
4976 5355 2.358195 GGGGAATCAGGGTTGTTAGCAT 60.358 50.000 0.00 0.00 0.00 3.79
4980 5359 0.392461 TCAGGGTTGTTAGCATCCGC 60.392 55.000 1.11 0.00 35.76 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 6.304882 GCACGACAAACCTTCTCTAAAATAC 58.695 40.000 0.00 0.00 0.00 1.89
175 177 8.697846 AAGATATTTCTGAAATACACGACGAA 57.302 30.769 21.51 2.58 36.27 3.85
181 183 8.276325 CCGCACTAAGATATTTCTGAAATACAC 58.724 37.037 21.51 17.92 36.27 2.90
204 206 1.971167 TCACATGCAAGTTCCCCGC 60.971 57.895 0.00 0.00 0.00 6.13
229 231 0.437295 AACGTAGCATTTCGACGCAC 59.563 50.000 0.00 0.22 45.72 5.34
233 235 1.724623 TGCAGAACGTAGCATTTCGAC 59.275 47.619 6.20 0.00 35.51 4.20
234 236 1.724623 GTGCAGAACGTAGCATTTCGA 59.275 47.619 12.44 0.00 43.44 3.71
235 237 1.459209 TGTGCAGAACGTAGCATTTCG 59.541 47.619 12.44 0.00 43.44 3.46
242 244 1.069906 GCAACCTTGTGCAGAACGTAG 60.070 52.381 0.00 0.00 44.29 3.51
327 330 6.523201 ACGCTTGAAAAATATACGCTTTTCTG 59.477 34.615 10.27 6.05 40.58 3.02
329 332 6.848470 ACGCTTGAAAAATATACGCTTTTC 57.152 33.333 4.17 4.17 40.43 2.29
334 337 8.580431 ACAATAAAACGCTTGAAAAATATACGC 58.420 29.630 0.00 0.00 0.00 4.42
342 345 7.254852 ACTGAAGACAATAAAACGCTTGAAAA 58.745 30.769 0.00 0.00 0.00 2.29
369 372 2.294979 AGAAAACTGAACGGAACACCC 58.705 47.619 0.00 0.00 0.00 4.61
370 373 5.488645 TTTAGAAAACTGAACGGAACACC 57.511 39.130 0.00 0.00 0.00 4.16
473 477 7.346751 TCAGCTTCCAACTAAAGTTTCAATT 57.653 32.000 0.00 0.00 35.83 2.32
475 479 6.767524 TTCAGCTTCCAACTAAAGTTTCAA 57.232 33.333 0.00 0.00 35.83 2.69
476 480 6.767524 TTTCAGCTTCCAACTAAAGTTTCA 57.232 33.333 0.00 0.00 35.83 2.69
501 505 9.353999 GTTCACAGTTTTTCAGAAGTTAATGTT 57.646 29.630 0.00 0.00 0.00 2.71
503 507 8.909708 TGTTCACAGTTTTTCAGAAGTTAATG 57.090 30.769 0.00 0.00 0.00 1.90
506 510 9.921637 AAAATGTTCACAGTTTTTCAGAAGTTA 57.078 25.926 0.00 0.00 40.67 2.24
581 607 7.684062 ATAGTCGCAATGTTTTTGAATATGC 57.316 32.000 0.00 0.00 0.00 3.14
627 653 8.715191 AAGCAAACAGATGTTCACATTTTTAA 57.285 26.923 0.00 0.00 37.25 1.52
628 654 8.715191 AAAGCAAACAGATGTTCACATTTTTA 57.285 26.923 0.00 0.00 37.25 1.52
691 717 6.660094 TCCTTTATTACGGGTATGCTTTTTGT 59.340 34.615 0.00 0.00 0.00 2.83
693 719 7.706100 TTCCTTTATTACGGGTATGCTTTTT 57.294 32.000 0.00 0.00 0.00 1.94
772 799 1.859998 GCTCACGAAGCGCAAGTTTTT 60.860 47.619 11.47 0.00 42.39 1.94
856 887 1.271054 ACTTCTCCATGAGCTGCGTTT 60.271 47.619 0.00 0.00 0.00 3.60
962 993 0.252927 ACCTGAGGGAAAGAGGGAGG 60.253 60.000 2.38 0.00 36.25 4.30
1084 1123 2.858344 CCAAAACTAGATACGTGCGAGG 59.142 50.000 0.00 0.00 0.00 4.63
1086 1125 2.883574 CCCAAAACTAGATACGTGCGA 58.116 47.619 0.00 0.00 0.00 5.10
1087 1126 1.326548 GCCCAAAACTAGATACGTGCG 59.673 52.381 0.00 0.00 0.00 5.34
1088 1127 2.629051 AGCCCAAAACTAGATACGTGC 58.371 47.619 0.00 0.00 0.00 5.34
1089 1128 4.000988 ACAAGCCCAAAACTAGATACGTG 58.999 43.478 0.00 0.00 0.00 4.49
1090 1129 4.281898 ACAAGCCCAAAACTAGATACGT 57.718 40.909 0.00 0.00 0.00 3.57
1091 1130 4.270325 GCTACAAGCCCAAAACTAGATACG 59.730 45.833 0.00 0.00 34.48 3.06
1092 1131 5.294552 CAGCTACAAGCCCAAAACTAGATAC 59.705 44.000 0.00 0.00 43.77 2.24
1093 1132 5.428253 CAGCTACAAGCCCAAAACTAGATA 58.572 41.667 0.00 0.00 43.77 1.98
1094 1133 4.265073 CAGCTACAAGCCCAAAACTAGAT 58.735 43.478 0.00 0.00 43.77 1.98
1095 1134 3.559171 CCAGCTACAAGCCCAAAACTAGA 60.559 47.826 0.00 0.00 43.77 2.43
1096 1135 2.749621 CCAGCTACAAGCCCAAAACTAG 59.250 50.000 0.00 0.00 43.77 2.57
1097 1136 2.373836 TCCAGCTACAAGCCCAAAACTA 59.626 45.455 0.00 0.00 43.77 2.24
1098 1137 1.144913 TCCAGCTACAAGCCCAAAACT 59.855 47.619 0.00 0.00 43.77 2.66
1099 1138 1.541588 CTCCAGCTACAAGCCCAAAAC 59.458 52.381 0.00 0.00 43.77 2.43
1100 1139 1.423541 TCTCCAGCTACAAGCCCAAAA 59.576 47.619 0.00 0.00 43.77 2.44
1101 1140 1.064003 TCTCCAGCTACAAGCCCAAA 58.936 50.000 0.00 0.00 43.77 3.28
1102 1141 1.210478 GATCTCCAGCTACAAGCCCAA 59.790 52.381 0.00 0.00 43.77 4.12
1103 1142 0.833287 GATCTCCAGCTACAAGCCCA 59.167 55.000 0.00 0.00 43.77 5.36
1104 1143 0.833287 TGATCTCCAGCTACAAGCCC 59.167 55.000 0.00 0.00 43.77 5.19
1105 1144 1.208052 TGTGATCTCCAGCTACAAGCC 59.792 52.381 0.00 0.00 43.77 4.35
1106 1145 2.680312 TGTGATCTCCAGCTACAAGC 57.320 50.000 0.00 0.00 42.84 4.01
1107 1146 5.757320 CCTTATTGTGATCTCCAGCTACAAG 59.243 44.000 2.74 0.00 35.08 3.16
1108 1147 5.425217 TCCTTATTGTGATCTCCAGCTACAA 59.575 40.000 0.00 0.00 35.93 2.41
1109 1148 4.962362 TCCTTATTGTGATCTCCAGCTACA 59.038 41.667 0.00 0.00 0.00 2.74
1110 1149 5.537300 TCCTTATTGTGATCTCCAGCTAC 57.463 43.478 0.00 0.00 0.00 3.58
1111 1150 6.753913 AATCCTTATTGTGATCTCCAGCTA 57.246 37.500 0.00 0.00 0.00 3.32
1112 1151 5.643421 AATCCTTATTGTGATCTCCAGCT 57.357 39.130 0.00 0.00 0.00 4.24
1113 1152 6.096001 ACAAAATCCTTATTGTGATCTCCAGC 59.904 38.462 0.00 0.00 38.29 4.85
1114 1153 7.636150 ACAAAATCCTTATTGTGATCTCCAG 57.364 36.000 0.00 0.00 38.29 3.86
1129 1168 5.483231 TCTCTCATCTCAGACACAAAATCCT 59.517 40.000 0.00 0.00 0.00 3.24
1132 1171 6.944096 TGATCTCTCATCTCAGACACAAAAT 58.056 36.000 0.00 0.00 0.00 1.82
1139 1178 5.801444 CGCATTATGATCTCTCATCTCAGAC 59.199 44.000 0.00 0.00 41.29 3.51
1147 1186 2.289257 CCAGCCGCATTATGATCTCTCA 60.289 50.000 0.00 0.00 35.41 3.27
1157 1201 2.289756 TGTAGTTCAACCAGCCGCATTA 60.290 45.455 0.00 0.00 0.00 1.90
1160 1204 0.179043 TTGTAGTTCAACCAGCCGCA 60.179 50.000 0.00 0.00 0.00 5.69
1161 1205 2.624169 TTGTAGTTCAACCAGCCGC 58.376 52.632 0.00 0.00 0.00 6.53
1169 1213 2.036733 CTCCGGGTGAGTTGTAGTTCAA 59.963 50.000 0.00 0.00 36.27 2.69
1182 1226 2.290641 CTGTTCAAAGAAACTCCGGGTG 59.709 50.000 0.00 0.00 0.00 4.61
1184 1228 2.290641 CACTGTTCAAAGAAACTCCGGG 59.709 50.000 0.00 0.00 0.00 5.73
1193 1237 4.635765 CAGGAGTTGAACACTGTTCAAAGA 59.364 41.667 30.21 13.21 39.76 2.52
1218 1262 2.771639 CGAGGGCTCCGATCGACAA 61.772 63.158 18.66 0.28 38.72 3.18
1242 1286 2.021380 GTAATCCTTGTGCGCGCG 59.979 61.111 28.44 28.44 0.00 6.86
1256 1300 1.357137 TGATGGTGCTGGTCAGGTAA 58.643 50.000 0.00 0.00 0.00 2.85
1304 1348 0.317160 AGTTGACGACCATGAGCGAA 59.683 50.000 12.95 0.26 0.00 4.70
1352 1396 2.037367 CCGAGGAGGGAGTGGACA 59.963 66.667 0.00 0.00 35.97 4.02
1439 1483 2.431942 ACGAACGCGCGGATCTTT 60.432 55.556 35.22 19.06 42.48 2.52
1610 1654 0.248661 CTCTCCCATACACTGCGTCG 60.249 60.000 0.00 0.00 0.00 5.12
1616 1660 2.786495 CGGCGCTCTCCCATACACT 61.786 63.158 7.64 0.00 0.00 3.55
1853 1897 0.736325 CCGTCGAAGAAACATCGGCT 60.736 55.000 0.00 0.00 42.44 5.52
1986 2030 5.273208 TCCAAGGTAGAAGAGAGCATTACT 58.727 41.667 0.00 0.00 0.00 2.24
2030 2082 0.804989 CCTTGATCACCGTGCTTTCC 59.195 55.000 0.00 0.00 0.00 3.13
2176 2228 4.277515 TCAATGTCCTCCAGAGTGAAAG 57.722 45.455 0.00 0.00 0.00 2.62
2218 2270 5.816682 TGAAGTCCTCCTTAAATTTCTCCC 58.183 41.667 0.00 0.00 32.03 4.30
2229 2281 2.763448 CCTCGATCTTGAAGTCCTCCTT 59.237 50.000 0.00 0.00 35.59 3.36
2276 2328 2.093973 ACTGTATCAGTTCAAGGGAGCG 60.094 50.000 0.00 0.00 42.59 5.03
2309 2361 2.236146 AGAACACCTGATCCATTACGCA 59.764 45.455 0.00 0.00 0.00 5.24
2320 2393 2.630098 CACCTCTGAGAAGAACACCTGA 59.370 50.000 6.17 0.00 0.00 3.86
2338 2411 0.320247 CTGTGTCTGACAGCTCCACC 60.320 60.000 11.41 0.00 45.72 4.61
2392 2465 0.976641 AGAACTCATCTGCGTTCCCA 59.023 50.000 8.92 0.00 39.76 4.37
2452 2525 3.015799 CGATTCACGCTCGTTCTGA 57.984 52.632 0.00 0.00 34.51 3.27
2480 2553 4.424626 TCATAGTGATCTTGTCGTGAAGC 58.575 43.478 0.00 0.00 0.00 3.86
2488 2561 5.426689 TTGGCTCTTCATAGTGATCTTGT 57.573 39.130 0.00 0.00 0.00 3.16
2536 2609 0.172578 TTGCCCTATCTGACGACACG 59.827 55.000 0.00 0.00 0.00 4.49
2537 2610 1.204941 ACTTGCCCTATCTGACGACAC 59.795 52.381 0.00 0.00 0.00 3.67
2538 2611 1.557099 ACTTGCCCTATCTGACGACA 58.443 50.000 0.00 0.00 0.00 4.35
2539 2612 3.119245 TGTTACTTGCCCTATCTGACGAC 60.119 47.826 0.00 0.00 0.00 4.34
2542 2615 4.473477 ACTGTTACTTGCCCTATCTGAC 57.527 45.455 0.00 0.00 0.00 3.51
2551 2624 2.494059 TCTGCTGAACTGTTACTTGCC 58.506 47.619 0.00 0.00 0.00 4.52
2599 2672 1.069159 CCGTTACTCGCGCTATCTGAT 60.069 52.381 5.56 0.00 38.35 2.90
2611 2684 4.392138 CCCTTTTCATCTGAACCGTTACTC 59.608 45.833 0.00 0.00 33.13 2.59
2629 2702 3.081804 CTCGGTGCTAATGTTTCCCTTT 58.918 45.455 0.00 0.00 0.00 3.11
2650 2723 1.416401 TGGATAAACTCGGCCTCATCC 59.584 52.381 0.00 4.32 33.92 3.51
2673 2746 7.962995 TCTCTAGTAACATCAACTCCATCTT 57.037 36.000 0.00 0.00 0.00 2.40
2693 2766 2.057922 TCTGGGCTCTTTGGTTTCTCT 58.942 47.619 0.00 0.00 0.00 3.10
2704 2777 1.847088 GTTTCCCCTAATCTGGGCTCT 59.153 52.381 0.00 0.00 45.78 4.09
2707 2780 2.379005 CTTGTTTCCCCTAATCTGGGC 58.621 52.381 0.00 0.00 45.78 5.36
2710 2783 5.934781 AGATAGCTTGTTTCCCCTAATCTG 58.065 41.667 0.00 0.00 0.00 2.90
2781 2854 8.218423 TGGCATCTCTTCATTTATATCCCTTA 57.782 34.615 0.00 0.00 0.00 2.69
2785 2858 7.663081 TCTGTTGGCATCTCTTCATTTATATCC 59.337 37.037 0.00 0.00 0.00 2.59
2786 2859 8.613060 TCTGTTGGCATCTCTTCATTTATATC 57.387 34.615 0.00 0.00 0.00 1.63
2804 2877 4.020751 TCTGTCTTCTTGGAGATCTGTTGG 60.021 45.833 0.00 0.00 0.00 3.77
2813 2886 5.353678 GTCCATCATTTCTGTCTTCTTGGAG 59.646 44.000 0.00 0.00 31.77 3.86
2846 2922 1.228245 TCTGGCCACCTTCTTGCAC 60.228 57.895 0.00 0.00 0.00 4.57
2880 2956 1.173043 CTGCCTGGTTTTCCGCATAA 58.827 50.000 0.00 0.00 44.36 1.90
2935 3011 4.230733 TCTGGTCTCCTCATCTTCTTCCTA 59.769 45.833 0.00 0.00 0.00 2.94
2966 3045 1.093159 GCAGGCTTCTTGTCATCTGG 58.907 55.000 0.00 0.00 0.00 3.86
3061 3140 4.219288 GGAATTGTCCTTGCTTGAGATGTT 59.781 41.667 0.00 0.00 41.24 2.71
3081 3160 2.972021 TGTTGTCTGTGAGGAGATGGAA 59.028 45.455 0.00 0.00 0.00 3.53
3096 3175 0.517316 GCTCGGAACCACATGTTGTC 59.483 55.000 2.61 0.00 37.29 3.18
3105 3184 2.454832 CTTGAGCCTGCTCGGAACCA 62.455 60.000 13.98 0.00 45.48 3.67
3166 3245 1.532868 CGCTTCAGGTGTTCTTTGGAG 59.467 52.381 0.00 0.00 0.00 3.86
3186 3265 0.164647 CGCTTGTTGCTGTGAGCTAC 59.835 55.000 3.59 3.59 45.06 3.58
3205 3284 2.920384 GCCTCCGGATCTCCTCCC 60.920 72.222 3.57 0.00 41.49 4.30
3206 3285 1.906333 GAGCCTCCGGATCTCCTCC 60.906 68.421 18.26 0.23 41.07 4.30
3219 3298 1.375268 GCAGAGTGCTTTCGAGCCT 60.375 57.895 0.00 0.00 40.96 4.58
3423 3502 1.352114 CGGCGATTCTTGTTTCGGTA 58.648 50.000 0.00 0.00 35.93 4.02
3424 3503 1.296056 CCGGCGATTCTTGTTTCGGT 61.296 55.000 9.30 0.00 35.93 4.69
3427 3506 1.136774 GGCCGGCGATTCTTGTTTC 59.863 57.895 22.54 0.00 0.00 2.78
3444 3523 2.806237 GACGAGGGGCTTCTACGG 59.194 66.667 0.00 0.00 0.00 4.02
3537 3622 0.537653 GAGTGAAGTCAGGGCCCTAC 59.462 60.000 28.13 22.10 0.00 3.18
3542 3627 1.298014 CAGGGAGTGAAGTCAGGGC 59.702 63.158 0.00 0.00 0.00 5.19
3544 3629 1.079543 CGCAGGGAGTGAAGTCAGG 60.080 63.158 0.00 0.00 0.00 3.86
3545 3630 4.586618 CGCAGGGAGTGAAGTCAG 57.413 61.111 0.00 0.00 0.00 3.51
3586 3671 1.383523 GAGAAGCTATGTGCAACCCC 58.616 55.000 0.00 0.00 45.94 4.95
3623 3708 1.063327 TCACGCTGTGTTTTTGCCG 59.937 52.632 8.22 0.00 34.79 5.69
3697 3782 2.749441 GGCTGAGAAGCTGGCACC 60.749 66.667 0.00 0.00 40.17 5.01
3807 3892 1.395670 CGATACAGCGTGTACATCGG 58.604 55.000 16.04 7.90 36.02 4.18
3873 3958 0.595095 GGACAAGCTTCTGCCACTTG 59.405 55.000 0.00 0.00 44.98 3.16
3874 3959 0.538287 GGGACAAGCTTCTGCCACTT 60.538 55.000 7.40 0.00 40.80 3.16
4049 4137 7.362920 CCATTCTACCAAAGGTTCAATTCGAAT 60.363 37.037 4.39 4.39 37.09 3.34
4079 4167 5.147330 TGAAGTAGTATTGTGACCACTGG 57.853 43.478 1.62 0.00 0.00 4.00
4104 4194 1.964373 GGCGTTTTCTTGCGAGGGA 60.964 57.895 0.00 0.00 0.00 4.20
4110 4200 0.102300 ACAAGTGGGCGTTTTCTTGC 59.898 50.000 10.59 0.00 40.29 4.01
4142 4232 5.754890 GCTGTTCCAAATTCAACATTCAACT 59.245 36.000 0.00 0.00 32.13 3.16
4189 4279 7.971455 AGCCAATTCGTAATCAGTAGTTTAAC 58.029 34.615 0.00 0.00 0.00 2.01
4190 4280 8.447833 CAAGCCAATTCGTAATCAGTAGTTTAA 58.552 33.333 0.00 0.00 0.00 1.52
4225 4315 6.216569 GCTGCTGCATGTCTAGTATAACTTA 58.783 40.000 11.11 0.00 39.41 2.24
4229 4319 3.642705 CGCTGCTGCATGTCTAGTATAA 58.357 45.455 16.29 0.00 39.64 0.98
4235 4474 2.512286 GGCGCTGCTGCATGTCTA 60.512 61.111 16.29 0.00 39.64 2.59
4270 4509 4.023365 CCTGAAGAAAGGAAGAAAGCACAG 60.023 45.833 0.00 0.00 40.02 3.66
4272 4511 3.304996 GCCTGAAGAAAGGAAGAAAGCAC 60.305 47.826 0.00 0.00 40.02 4.40
4273 4512 2.887152 GCCTGAAGAAAGGAAGAAAGCA 59.113 45.455 0.00 0.00 40.02 3.91
4274 4513 3.153130 AGCCTGAAGAAAGGAAGAAAGC 58.847 45.455 0.00 0.00 40.02 3.51
4275 4514 4.558296 GCAAGCCTGAAGAAAGGAAGAAAG 60.558 45.833 0.00 0.00 40.02 2.62
4276 4515 3.319122 GCAAGCCTGAAGAAAGGAAGAAA 59.681 43.478 0.00 0.00 40.02 2.52
4277 4516 2.887152 GCAAGCCTGAAGAAAGGAAGAA 59.113 45.455 0.00 0.00 40.02 2.52
4278 4517 2.158623 TGCAAGCCTGAAGAAAGGAAGA 60.159 45.455 0.00 0.00 40.02 2.87
4279 4518 2.233271 TGCAAGCCTGAAGAAAGGAAG 58.767 47.619 0.00 0.00 40.02 3.46
4282 4521 1.682854 TGTTGCAAGCCTGAAGAAAGG 59.317 47.619 0.00 0.00 40.63 3.11
4291 4538 3.289834 CGCCACTGTTGCAAGCCT 61.290 61.111 0.00 0.00 0.00 4.58
4311 4558 1.531128 TTGCAAGCCAGGACATGCA 60.531 52.632 9.50 9.50 46.21 3.96
4372 4632 1.679680 CAATGGCCAGCTATTGTCCTG 59.320 52.381 13.05 0.00 39.19 3.86
4375 4635 1.066605 CTGCAATGGCCAGCTATTGTC 59.933 52.381 23.98 17.91 43.72 3.18
4389 4649 3.673484 GGTGTGTGGCGCTGCAAT 61.673 61.111 7.64 0.00 0.00 3.56
4398 4658 3.297620 GCAAGCTGGGGTGTGTGG 61.298 66.667 0.00 0.00 0.00 4.17
4425 4685 6.347061 AAGAAATCCCCATAGTGAAATCCT 57.653 37.500 0.00 0.00 0.00 3.24
4451 4711 5.986004 ATTTAGCGCCAACTACAATAGTC 57.014 39.130 2.29 0.00 38.26 2.59
4457 4717 8.819974 GTTACTAATAATTTAGCGCCAACTACA 58.180 33.333 2.29 0.00 38.74 2.74
4463 4723 6.259167 CACCAGTTACTAATAATTTAGCGCCA 59.741 38.462 2.29 0.00 38.74 5.69
4483 4743 7.819900 GGGAAGCACTATAAATACTATCACCAG 59.180 40.741 0.00 0.00 0.00 4.00
4558 4818 2.586079 CGTACATGGCTGAGGCGG 60.586 66.667 0.35 0.00 39.81 6.13
4609 4869 3.788227 TGGCATGTAAGGACTGAAGTT 57.212 42.857 0.00 0.00 0.00 2.66
4641 4901 7.452880 AGTAGTGCATGAACATTAACATTGT 57.547 32.000 6.60 0.00 0.00 2.71
4840 5219 7.316393 TGGGAAGTTTAGAGAGAAATCAAGA 57.684 36.000 0.00 0.00 0.00 3.02
4855 5234 2.470057 TGGAAAAGCCTGGGAAGTTT 57.530 45.000 0.00 0.00 37.63 2.66
4873 5252 2.662866 AGGGGTCAATCAGCATCAATG 58.337 47.619 0.00 0.00 0.00 2.82
4874 5253 4.736611 ATAGGGGTCAATCAGCATCAAT 57.263 40.909 0.00 0.00 0.00 2.57
4875 5254 5.310331 TCATATAGGGGTCAATCAGCATCAA 59.690 40.000 0.00 0.00 0.00 2.57
4876 5255 4.845796 TCATATAGGGGTCAATCAGCATCA 59.154 41.667 0.00 0.00 0.00 3.07
4877 5256 5.426689 TCATATAGGGGTCAATCAGCATC 57.573 43.478 0.00 0.00 0.00 3.91
4878 5257 6.012245 TGAATCATATAGGGGTCAATCAGCAT 60.012 38.462 0.00 0.00 0.00 3.79
4879 5258 5.310331 TGAATCATATAGGGGTCAATCAGCA 59.690 40.000 0.00 0.00 0.00 4.41
4880 5259 5.645497 GTGAATCATATAGGGGTCAATCAGC 59.355 44.000 0.00 0.00 0.00 4.26
4881 5260 6.877855 CAGTGAATCATATAGGGGTCAATCAG 59.122 42.308 0.00 0.00 0.00 2.90
4882 5261 6.558394 TCAGTGAATCATATAGGGGTCAATCA 59.442 38.462 0.00 0.00 0.00 2.57
4883 5262 7.009179 TCAGTGAATCATATAGGGGTCAATC 57.991 40.000 0.00 0.00 0.00 2.67
4884 5263 7.460402 AGATCAGTGAATCATATAGGGGTCAAT 59.540 37.037 0.00 0.00 0.00 2.57
4885 5264 6.789457 AGATCAGTGAATCATATAGGGGTCAA 59.211 38.462 0.00 0.00 0.00 3.18
4886 5265 6.326161 AGATCAGTGAATCATATAGGGGTCA 58.674 40.000 0.00 0.00 0.00 4.02
4887 5266 6.865834 AGATCAGTGAATCATATAGGGGTC 57.134 41.667 0.00 0.00 0.00 4.46
4888 5267 7.398618 CAGTAGATCAGTGAATCATATAGGGGT 59.601 40.741 0.00 0.00 0.00 4.95
4889 5268 7.617329 TCAGTAGATCAGTGAATCATATAGGGG 59.383 40.741 0.00 0.00 33.49 4.79
4890 5269 8.586879 TCAGTAGATCAGTGAATCATATAGGG 57.413 38.462 0.00 0.00 33.49 3.53
4893 5272 9.029368 CCCTTCAGTAGATCAGTGAATCATATA 57.971 37.037 12.73 0.00 43.94 0.86
4894 5273 7.732140 TCCCTTCAGTAGATCAGTGAATCATAT 59.268 37.037 12.73 0.00 43.94 1.78
4895 5274 7.069344 TCCCTTCAGTAGATCAGTGAATCATA 58.931 38.462 12.73 0.00 43.94 2.15
4896 5275 5.901853 TCCCTTCAGTAGATCAGTGAATCAT 59.098 40.000 12.73 0.00 43.94 2.45
4897 5276 5.272402 TCCCTTCAGTAGATCAGTGAATCA 58.728 41.667 12.73 0.00 43.94 2.57
4898 5277 5.860941 TCCCTTCAGTAGATCAGTGAATC 57.139 43.478 12.73 0.00 43.94 2.52
4899 5278 5.664908 ACATCCCTTCAGTAGATCAGTGAAT 59.335 40.000 12.73 0.00 43.94 2.57
4900 5279 5.026121 ACATCCCTTCAGTAGATCAGTGAA 58.974 41.667 0.00 12.11 43.00 3.18
4901 5280 4.403752 CACATCCCTTCAGTAGATCAGTGA 59.596 45.833 0.00 0.00 34.66 3.41
4966 5345 2.076863 AGAGTTGCGGATGCTAACAAC 58.923 47.619 6.54 6.54 43.34 3.32
4970 5349 3.407698 TGAAAAGAGTTGCGGATGCTAA 58.592 40.909 0.00 0.00 43.34 3.09
4975 5354 3.126001 TGACTGAAAAGAGTTGCGGAT 57.874 42.857 0.00 0.00 0.00 4.18
4976 5355 2.613026 TGACTGAAAAGAGTTGCGGA 57.387 45.000 0.00 0.00 0.00 5.54
4980 5359 5.407995 GGAGACTGATGACTGAAAAGAGTTG 59.592 44.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.