Multiple sequence alignment - TraesCS5A01G187300

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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 TraesCS5A01G187300 chr5A 100.000 3932 0 0 1 3932 389069723 389073654 0.000000e+00 7262.0
1 TraesCS5A01G187300 chr5D 90.697 2010 99 31 1418 3381 309006059 309004092 0.000000e+00 2595.0
2 TraesCS5A01G187300 chr5D 90.801 1435 68 27 4 1415 309007490 309006097 0.000000e+00 1860.0
3 TraesCS5A01G187300 chr5B 90.447 1612 96 18 1799 3369 354240637 354239043 0.000000e+00 2071.0
4 TraesCS5A01G187300 chr5B 89.387 1093 55 27 351 1415 354242158 354241099 0.000000e+00 1319.0
5 TraesCS5A01G187300 chr5B 92.394 355 17 4 1 347 354242549 354242197 7.590000e-137 497.0
6 TraesCS5A01G187300 chr5B 88.378 413 45 3 3522 3932 354239043 354238632 9.820000e-136 494.0
7 TraesCS5A01G187300 chr5B 89.456 294 12 9 1513 1805 354240969 354240694 1.740000e-93 353.0
8 TraesCS5A01G187300 chr2D 94.340 477 23 3 1195 1671 118801112 118800640 0.000000e+00 728.0
9 TraesCS5A01G187300 chr4A 95.116 430 19 1 1195 1624 198002155 198001728 0.000000e+00 676.0
10 TraesCS5A01G187300 chr4A 93.056 72 5 0 1036 1107 198002371 198002300 5.370000e-19 106.0
11 TraesCS5A01G187300 chr7B 95.082 427 19 1 1195 1621 374717260 374717684 0.000000e+00 671.0
12 TraesCS5A01G187300 chr7B 94.419 430 22 1 1195 1624 705711796 705711369 0.000000e+00 660.0
13 TraesCS5A01G187300 chr7B 88.976 127 9 2 1036 1162 705711977 705711856 6.810000e-33 152.0
14 TraesCS5A01G187300 chr7B 88.189 127 10 2 1036 1162 244641435 244641556 3.170000e-31 147.0
15 TraesCS5A01G187300 chr7B 93.056 72 5 0 1036 1107 374717044 374717115 5.370000e-19 106.0
16 TraesCS5A01G187300 chr6B 94.884 430 20 1 1195 1624 255097101 255096674 0.000000e+00 671.0
17 TraesCS5A01G187300 chr6B 94.186 430 23 1 1195 1624 87322256 87321829 0.000000e+00 654.0
18 TraesCS5A01G187300 chr6B 88.095 126 10 2 1037 1162 255097282 255097162 1.140000e-30 145.0
19 TraesCS5A01G187300 chr6B 93.056 72 5 0 1036 1107 87322472 87322401 5.370000e-19 106.0
20 TraesCS5A01G187300 chr6B 87.671 73 5 4 2482 2552 460209800 460209870 9.060000e-12 82.4
21 TraesCS5A01G187300 chr7A 94.379 427 22 1 1195 1621 133317101 133317525 0.000000e+00 654.0
22 TraesCS5A01G187300 chr7A 93.056 72 5 0 1036 1107 133316885 133316956 5.370000e-19 106.0
23 TraesCS5A01G187300 chr6D 87.671 73 5 4 2482 2552 296824531 296824461 9.060000e-12 82.4
24 TraesCS5A01G187300 chr6A 87.671 73 5 4 2482 2552 423533556 423533486 9.060000e-12 82.4
25 TraesCS5A01G187300 chr1B 86.765 68 7 2 3418 3484 604326880 604326814 1.520000e-09 75.0
26 TraesCS5A01G187300 chr1B 100.000 29 0 0 3453 3481 112744834 112744862 2.000000e-03 54.7
27 TraesCS5A01G187300 chr7D 100.000 29 0 0 3454 3482 195306083 195306055 2.000000e-03 54.7
28 TraesCS5A01G187300 chr1D 100.000 29 0 0 3453 3481 71280092 71280120 2.000000e-03 54.7


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 TraesCS5A01G187300 chr5A 389069723 389073654 3931 False 7262.0 7262 100.0000 1 3932 1 chr5A.!!$F1 3931
1 TraesCS5A01G187300 chr5D 309004092 309007490 3398 True 2227.5 2595 90.7490 4 3381 2 chr5D.!!$R1 3377
2 TraesCS5A01G187300 chr5B 354238632 354242549 3917 True 946.8 2071 90.0124 1 3932 5 chr5B.!!$R1 3931
3 TraesCS5A01G187300 chr4A 198001728 198002371 643 True 391.0 676 94.0860 1036 1624 2 chr4A.!!$R1 588
4 TraesCS5A01G187300 chr7B 705711369 705711977 608 True 406.0 660 91.6975 1036 1624 2 chr7B.!!$R1 588
5 TraesCS5A01G187300 chr7B 374717044 374717684 640 False 388.5 671 94.0690 1036 1621 2 chr7B.!!$F2 585
6 TraesCS5A01G187300 chr6B 255096674 255097282 608 True 408.0 671 91.4895 1037 1624 2 chr6B.!!$R2 587
7 TraesCS5A01G187300 chr6B 87321829 87322472 643 True 380.0 654 93.6210 1036 1624 2 chr6B.!!$R1 588
8 TraesCS5A01G187300 chr7A 133316885 133317525 640 False 380.0 654 93.7175 1036 1621 2 chr7A.!!$F1 585

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
755 815 0.101219 GTGGCGCTGGGATTGATTTC 59.899 55.0 7.64 0.0 0.00 2.17 F
1095 1207 0.250901 GCAGCCCTCTGTTTCCTTCA 60.251 55.0 0.00 0.0 42.29 3.02 F
2278 2552 0.179936 CCAGCAACATCCTCCTCTCC 59.820 60.0 0.00 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 2155 0.035739 TAGTTGGACCGAAACCAGGC 59.964 55.0 0.00 0.0 38.70 4.85 R
2462 2747 0.105039 ACGCGAGATGGAAGAATCCC 59.895 55.0 15.93 0.0 45.95 3.85 R
3711 4036 0.234884 GAACACGCTTCAAGTTCGGG 59.765 55.0 0.00 0.0 33.24 5.14 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
26 27 4.380678 CACACACGCAAATGAAGATTTCTG 59.619 41.667 0.00 0.00 28.65 3.02
29 30 2.179589 CGCAAATGAAGATTTCTGCGG 58.820 47.619 12.99 0.00 38.96 5.69
46 47 1.544759 GCGGGTTCAGAAGGGAGAAAA 60.545 52.381 0.00 0.00 0.00 2.29
106 114 2.435120 TACCACCGCTCCTCAGTCCA 62.435 60.000 0.00 0.00 0.00 4.02
143 152 1.079336 CCGTTTCTTCCTCCCCGAC 60.079 63.158 0.00 0.00 0.00 4.79
174 183 0.991920 TCACCATCCCTCCAAGTTCC 59.008 55.000 0.00 0.00 0.00 3.62
209 218 1.270947 CCTTTGCAATGCACCAACCAT 60.271 47.619 7.72 0.00 38.71 3.55
221 230 4.244862 GCACCAACCATTTAACCAATGAG 58.755 43.478 0.00 0.00 44.78 2.90
250 259 1.001181 CCAATCCACCAAACTGCAAGG 59.999 52.381 0.00 0.00 39.30 3.61
325 334 1.326852 GCTGATCGCAATCTCACACTG 59.673 52.381 4.93 0.00 38.92 3.66
358 402 2.978452 GATCACTGGCCCATCGTCCG 62.978 65.000 0.00 0.00 0.00 4.79
473 517 0.386113 CCAACGCTAGTAGGAGCCTC 59.614 60.000 0.00 0.00 39.43 4.70
518 562 2.457598 ACGTAGCTCCCAAGAGATCAA 58.542 47.619 0.00 0.00 43.39 2.57
521 565 1.661463 AGCTCCCAAGAGATCAACCA 58.339 50.000 0.00 0.00 43.39 3.67
522 566 2.203584 AGCTCCCAAGAGATCAACCAT 58.796 47.619 0.00 0.00 43.39 3.55
523 567 2.172293 AGCTCCCAAGAGATCAACCATC 59.828 50.000 0.00 0.00 43.39 3.51
525 569 3.371380 GCTCCCAAGAGATCAACCATCTT 60.371 47.826 0.00 0.00 42.48 2.40
526 570 4.141620 GCTCCCAAGAGATCAACCATCTTA 60.142 45.833 0.00 0.00 42.48 2.10
527 571 5.455899 GCTCCCAAGAGATCAACCATCTTAT 60.456 44.000 0.00 0.00 42.48 1.73
528 572 6.179906 TCCCAAGAGATCAACCATCTTATC 57.820 41.667 0.00 0.00 42.48 1.75
529 573 4.993584 CCCAAGAGATCAACCATCTTATCG 59.006 45.833 0.00 0.00 42.48 2.92
577 621 4.021631 CACGCCTGTGCTGCACTG 62.022 66.667 30.43 28.44 39.67 3.66
590 634 2.906897 CACTGCACGCACCCCTTT 60.907 61.111 0.00 0.00 0.00 3.11
595 639 2.617274 GCACGCACCCCTTTGTCTC 61.617 63.158 0.00 0.00 0.00 3.36
605 649 1.551452 CCTTTGTCTCGTCCTCTCCT 58.449 55.000 0.00 0.00 0.00 3.69
609 653 0.253610 TGTCTCGTCCTCTCCTCCTC 59.746 60.000 0.00 0.00 0.00 3.71
633 685 1.038130 CCTCTTCATCTCCGTCCGGT 61.038 60.000 0.00 0.00 36.47 5.28
694 754 2.031163 GGTGCAGCCTTGTCTCGT 59.969 61.111 4.03 0.00 0.00 4.18
700 760 0.861837 CAGCCTTGTCTCGTGTGTTC 59.138 55.000 0.00 0.00 0.00 3.18
704 764 1.539065 CCTTGTCTCGTGTGTTCTGCT 60.539 52.381 0.00 0.00 0.00 4.24
719 779 2.416747 TCTGCTTTGTCCTGTTCATCG 58.583 47.619 0.00 0.00 0.00 3.84
722 782 1.400242 GCTTTGTCCTGTTCATCGTGC 60.400 52.381 0.00 0.00 0.00 5.34
755 815 0.101219 GTGGCGCTGGGATTGATTTC 59.899 55.000 7.64 0.00 0.00 2.17
760 820 1.332997 CGCTGGGATTGATTTCTCTGC 59.667 52.381 0.00 0.00 37.61 4.26
762 822 2.947243 GCTGGGATTGATTTCTCTGCCA 60.947 50.000 0.00 0.00 35.63 4.92
805 865 1.377725 AGTGGCAGCCATTCTTCCG 60.378 57.895 19.75 0.00 35.28 4.30
916 977 9.135189 TGATCAAGGAAAGGTATATTGGAATTG 57.865 33.333 0.00 0.00 0.00 2.32
927 988 8.386264 AGGTATATTGGAATTGGATACTTCTGG 58.614 37.037 0.00 0.00 37.61 3.86
935 996 6.183360 GGAATTGGATACTTCTGGTTACAAGC 60.183 42.308 0.00 0.00 37.61 4.01
983 1044 1.968540 GCAGACCGCAGAAAGCCTT 60.969 57.895 0.00 0.00 41.38 4.35
1023 1095 3.978855 TGTTCAACAACATAGTCTCGACG 59.021 43.478 0.00 0.00 37.61 5.12
1095 1207 0.250901 GCAGCCCTCTGTTTCCTTCA 60.251 55.000 0.00 0.00 42.29 3.02
1109 1221 5.221342 TGTTTCCTTCACACTTTGTTGTTGT 60.221 36.000 0.00 0.00 0.00 3.32
1110 1222 4.695217 TCCTTCACACTTTGTTGTTGTC 57.305 40.909 0.00 0.00 0.00 3.18
1111 1223 3.126171 TCCTTCACACTTTGTTGTTGTCG 59.874 43.478 0.00 0.00 0.00 4.35
1115 1229 1.132262 ACACTTTGTTGTTGTCGGCAG 59.868 47.619 0.00 0.00 0.00 4.85
1131 1245 2.498167 GGCAGAGTCATTTGTCACTGT 58.502 47.619 0.00 0.00 0.00 3.55
1132 1246 3.664107 GGCAGAGTCATTTGTCACTGTA 58.336 45.455 0.00 0.00 0.00 2.74
1162 1276 3.844577 ATGTTTCTTCAGTGCAGCATC 57.155 42.857 0.00 0.00 0.00 3.91
1172 1320 0.737219 GTGCAGCATCTAAGGCTTGG 59.263 55.000 10.69 7.23 40.23 3.61
1187 1335 2.433239 GGCTTGGCATGAGGAATTTGAT 59.567 45.455 4.32 0.00 0.00 2.57
1188 1336 3.492137 GGCTTGGCATGAGGAATTTGATC 60.492 47.826 4.32 0.00 0.00 2.92
1189 1337 3.131577 GCTTGGCATGAGGAATTTGATCA 59.868 43.478 4.32 0.00 0.00 2.92
1190 1338 4.202223 GCTTGGCATGAGGAATTTGATCAT 60.202 41.667 4.32 0.00 34.02 2.45
1191 1339 5.524971 TTGGCATGAGGAATTTGATCATC 57.475 39.130 0.00 0.00 31.38 2.92
1490 1699 1.490490 TGGGCAGAGTCTGAACACTTT 59.510 47.619 24.55 0.00 32.44 2.66
1559 1768 8.795786 TGTCATTTAGCTTTTTATGTGTGTTC 57.204 30.769 0.00 0.00 0.00 3.18
1569 1778 9.118236 GCTTTTTATGTGTGTTCTTCAGATTAC 57.882 33.333 0.00 0.00 0.00 1.89
1624 1834 3.729966 AGAACTTCCTCTTTGGTTCGAC 58.270 45.455 0.00 0.00 41.72 4.20
1732 1942 2.481952 GAGTGGTGTGACATTTGCTCTC 59.518 50.000 0.00 0.00 0.00 3.20
1845 2119 2.632377 TGCGATGTTTCATTCTCCCTC 58.368 47.619 0.00 0.00 0.00 4.30
1865 2139 4.455877 CCTCCCAGTTTGTAAATCTGTCAC 59.544 45.833 0.00 0.00 41.03 3.67
1880 2154 1.006281 TGTCACCACCTACCTCGGTAT 59.994 52.381 0.00 0.00 34.94 2.73
1881 2155 1.407979 GTCACCACCTACCTCGGTATG 59.592 57.143 0.00 0.00 34.94 2.39
1891 2165 0.810031 CCTCGGTATGCCTGGTTTCG 60.810 60.000 0.00 0.00 0.00 3.46
1904 2178 2.156098 TGGTTTCGGTCCAACTAATGC 58.844 47.619 0.00 0.00 31.50 3.56
1912 2186 2.414161 GGTCCAACTAATGCGTTCTTGC 60.414 50.000 0.00 0.00 0.00 4.01
2018 2292 0.316841 GGAGATCGACATCCTGAGCC 59.683 60.000 9.92 0.00 32.51 4.70
2053 2327 2.573869 CTGGTGACGCTGATCGGT 59.426 61.111 2.89 0.00 43.86 4.69
2278 2552 0.179936 CCAGCAACATCCTCCTCTCC 59.820 60.000 0.00 0.00 0.00 3.71
2302 2576 0.827368 ACTTCGAGGCCAAGATCTCC 59.173 55.000 5.01 0.00 0.00 3.71
2408 2682 1.808234 CGAGTACGCGCTGGTAATGC 61.808 60.000 5.73 0.00 0.00 3.56
2452 2737 4.760047 CTGGTCGGGTTCCTGGCG 62.760 72.222 0.00 0.00 0.00 5.69
2462 2747 1.369625 GTTCCTGGCGACACTAATGG 58.630 55.000 0.00 0.00 35.60 3.16
2480 2769 0.601311 GGGGATTCTTCCATCTCGCG 60.601 60.000 0.00 0.00 44.60 5.87
2620 2919 4.193090 TCATCGTCAAGGTACTCTCTCTC 58.807 47.826 0.00 0.00 38.49 3.20
2621 2920 3.985019 TCGTCAAGGTACTCTCTCTCT 57.015 47.619 0.00 0.00 38.49 3.10
2622 2921 3.864243 TCGTCAAGGTACTCTCTCTCTC 58.136 50.000 0.00 0.00 38.49 3.20
2623 2922 3.516300 TCGTCAAGGTACTCTCTCTCTCT 59.484 47.826 0.00 0.00 38.49 3.10
2624 2923 3.869246 CGTCAAGGTACTCTCTCTCTCTC 59.131 52.174 0.00 0.00 38.49 3.20
2625 2924 4.382685 CGTCAAGGTACTCTCTCTCTCTCT 60.383 50.000 0.00 0.00 38.49 3.10
2626 2925 5.116882 GTCAAGGTACTCTCTCTCTCTCTC 58.883 50.000 0.00 0.00 38.49 3.20
2627 2926 4.163458 TCAAGGTACTCTCTCTCTCTCTCC 59.837 50.000 0.00 0.00 38.49 3.71
2628 2927 3.046374 AGGTACTCTCTCTCTCTCTCCC 58.954 54.545 0.00 0.00 0.00 4.30
2629 2928 3.046374 GGTACTCTCTCTCTCTCTCCCT 58.954 54.545 0.00 0.00 0.00 4.20
2630 2929 3.071167 GGTACTCTCTCTCTCTCTCCCTC 59.929 56.522 0.00 0.00 0.00 4.30
2631 2930 3.136641 ACTCTCTCTCTCTCTCCCTCT 57.863 52.381 0.00 0.00 0.00 3.69
2632 2931 3.041946 ACTCTCTCTCTCTCTCCCTCTC 58.958 54.545 0.00 0.00 0.00 3.20
2633 2932 3.310954 ACTCTCTCTCTCTCTCCCTCTCT 60.311 52.174 0.00 0.00 0.00 3.10
2705 3004 2.903357 GCCCTCGGCTGATTCTGA 59.097 61.111 0.00 0.00 46.69 3.27
2776 3075 4.182433 TGCGCAAGGTGGTGGACA 62.182 61.111 8.16 0.00 38.28 4.02
2933 3232 3.470709 ACGCCAACATGAAGATATGAGG 58.529 45.455 0.00 0.00 33.26 3.86
2969 3290 7.795482 TTCAGTCTTGGAATTTTTACTCGAA 57.205 32.000 0.00 0.00 0.00 3.71
2972 3293 7.713507 TCAGTCTTGGAATTTTTACTCGAAGAA 59.286 33.333 0.00 0.00 37.90 2.52
2973 3294 8.012241 CAGTCTTGGAATTTTTACTCGAAGAAG 58.988 37.037 0.00 0.00 37.90 2.85
2974 3295 7.931948 AGTCTTGGAATTTTTACTCGAAGAAGA 59.068 33.333 0.00 0.00 37.90 2.87
3015 3336 8.493547 GCGAAACTTGTACAGAATTTTAGTACT 58.506 33.333 0.00 0.00 39.02 2.73
3020 3341 9.708092 ACTTGTACAGAATTTTAGTACTCTTCC 57.292 33.333 0.00 0.00 39.02 3.46
3021 3342 8.752766 TTGTACAGAATTTTAGTACTCTTCCG 57.247 34.615 0.00 0.00 39.02 4.30
3042 3364 3.618594 CGATCCATATTAATCGTGGCTGG 59.381 47.826 12.71 4.03 39.83 4.85
3055 3377 2.751259 CGTGGCTGGTCTAGTACAACTA 59.249 50.000 0.00 0.00 0.00 2.24
3063 3385 9.165035 GGCTGGTCTAGTACAACTATATACTAG 57.835 40.741 10.79 10.79 46.62 2.57
3112 3434 0.589708 AGTAACTTTTCGTTGCGCCC 59.410 50.000 4.18 0.00 42.25 6.13
3115 3437 1.512156 AACTTTTCGTTGCGCCCGAT 61.512 50.000 18.15 2.83 33.72 4.18
3120 3442 3.418913 CGTTGCGCCCGATGTTCA 61.419 61.111 4.18 0.00 0.00 3.18
3125 3448 2.404789 CGCCCGATGTTCATGTGC 59.595 61.111 0.00 0.00 0.00 4.57
3128 3451 1.308047 GCCCGATGTTCATGTGCATA 58.692 50.000 0.00 0.00 0.00 3.14
3134 3457 3.242511 CGATGTTCATGTGCATAGTGGTG 60.243 47.826 0.00 0.00 0.00 4.17
3151 3474 2.962421 TGGTGGGATTGTTTCAAAGTCC 59.038 45.455 0.00 0.00 0.00 3.85
3169 3492 2.028385 GTCCTGAAACGAGAGGGCTTAA 60.028 50.000 0.00 0.00 30.69 1.85
3185 3508 5.047092 AGGGCTTAATTTGTGATGTCCAAAG 60.047 40.000 0.00 0.00 35.45 2.77
3186 3509 5.047377 GGGCTTAATTTGTGATGTCCAAAGA 60.047 40.000 0.00 0.00 35.45 2.52
3197 3520 4.280677 TGATGTCCAAAGAAAATGGTGTCC 59.719 41.667 0.00 0.00 39.09 4.02
3202 3525 3.244181 CCAAAGAAAATGGTGTCCCAAGG 60.244 47.826 0.00 0.00 46.04 3.61
3239 3562 2.676750 CGTCAACGATTGATGGAGGGAA 60.677 50.000 0.00 0.00 42.47 3.97
3251 3574 2.661718 TGGAGGGAACAAGTGGTTTTC 58.338 47.619 0.00 0.00 40.63 2.29
3254 3577 4.079672 TGGAGGGAACAAGTGGTTTTCTTA 60.080 41.667 0.00 0.00 40.63 2.10
3263 3586 9.581099 GAACAAGTGGTTTTCTTATTCTTTTGA 57.419 29.630 0.00 0.00 40.63 2.69
3381 3705 3.060363 CGCGGCGAACCATTATAAGATAC 59.940 47.826 19.16 0.00 34.57 2.24
3382 3706 4.243270 GCGGCGAACCATTATAAGATACT 58.757 43.478 12.98 0.00 34.57 2.12
3383 3707 4.326548 GCGGCGAACCATTATAAGATACTC 59.673 45.833 12.98 0.00 34.57 2.59
3384 3708 4.863131 CGGCGAACCATTATAAGATACTCC 59.137 45.833 0.00 0.00 34.57 3.85
3385 3709 5.176592 GGCGAACCATTATAAGATACTCCC 58.823 45.833 0.00 0.00 35.26 4.30
3386 3710 5.046520 GGCGAACCATTATAAGATACTCCCT 60.047 44.000 0.00 0.00 35.26 4.20
3387 3711 6.465084 GCGAACCATTATAAGATACTCCCTT 58.535 40.000 0.00 0.00 0.00 3.95
3388 3712 6.369065 GCGAACCATTATAAGATACTCCCTTG 59.631 42.308 0.00 0.00 0.00 3.61
3389 3713 6.369065 CGAACCATTATAAGATACTCCCTTGC 59.631 42.308 0.00 0.00 0.00 4.01
3390 3714 7.394144 AACCATTATAAGATACTCCCTTGCT 57.606 36.000 0.00 0.00 0.00 3.91
3391 3715 7.394144 ACCATTATAAGATACTCCCTTGCTT 57.606 36.000 0.00 0.00 0.00 3.91
3392 3716 7.454225 ACCATTATAAGATACTCCCTTGCTTC 58.546 38.462 0.00 0.00 0.00 3.86
3393 3717 6.881602 CCATTATAAGATACTCCCTTGCTTCC 59.118 42.308 0.00 0.00 0.00 3.46
3394 3718 2.990066 AAGATACTCCCTTGCTTCCG 57.010 50.000 0.00 0.00 0.00 4.30
3395 3719 1.867363 AGATACTCCCTTGCTTCCGT 58.133 50.000 0.00 0.00 0.00 4.69
3396 3720 1.757699 AGATACTCCCTTGCTTCCGTC 59.242 52.381 0.00 0.00 0.00 4.79
3397 3721 0.460311 ATACTCCCTTGCTTCCGTCG 59.540 55.000 0.00 0.00 0.00 5.12
3398 3722 2.221906 TACTCCCTTGCTTCCGTCGC 62.222 60.000 0.00 0.00 0.00 5.19
3399 3723 3.589654 CTCCCTTGCTTCCGTCGCA 62.590 63.158 0.00 0.00 35.22 5.10
3400 3724 3.121030 CCCTTGCTTCCGTCGCAG 61.121 66.667 0.00 0.00 38.80 5.18
3401 3725 2.357517 CCTTGCTTCCGTCGCAGT 60.358 61.111 0.00 0.00 38.80 4.40
3402 3726 2.383527 CCTTGCTTCCGTCGCAGTC 61.384 63.158 0.00 0.00 38.80 3.51
3403 3727 2.720758 CTTGCTTCCGTCGCAGTCG 61.721 63.158 0.00 0.00 38.80 4.18
3404 3728 3.493830 TTGCTTCCGTCGCAGTCGT 62.494 57.895 0.00 0.00 38.80 4.34
3405 3729 3.173240 GCTTCCGTCGCAGTCGTC 61.173 66.667 0.00 0.00 37.35 4.20
3406 3730 2.504244 CTTCCGTCGCAGTCGTCC 60.504 66.667 0.00 0.00 37.35 4.79
3407 3731 3.263503 CTTCCGTCGCAGTCGTCCA 62.264 63.158 0.00 0.00 37.35 4.02
3408 3732 2.543687 CTTCCGTCGCAGTCGTCCAT 62.544 60.000 0.00 0.00 37.35 3.41
3409 3733 1.307355 TTCCGTCGCAGTCGTCCATA 61.307 55.000 0.00 0.00 37.35 2.74
3410 3734 1.099295 TCCGTCGCAGTCGTCCATAT 61.099 55.000 0.00 0.00 37.35 1.78
3411 3735 0.248907 CCGTCGCAGTCGTCCATATT 60.249 55.000 0.00 0.00 37.35 1.28
3412 3736 0.846401 CGTCGCAGTCGTCCATATTG 59.154 55.000 0.00 0.00 33.83 1.90
3413 3737 1.209128 GTCGCAGTCGTCCATATTGG 58.791 55.000 0.00 0.00 39.43 3.16
3414 3738 0.821517 TCGCAGTCGTCCATATTGGT 59.178 50.000 0.00 0.00 39.03 3.67
3415 3739 1.206132 TCGCAGTCGTCCATATTGGTT 59.794 47.619 0.00 0.00 39.03 3.67
3416 3740 2.427812 TCGCAGTCGTCCATATTGGTTA 59.572 45.455 0.00 0.00 39.03 2.85
3417 3741 3.119065 TCGCAGTCGTCCATATTGGTTAA 60.119 43.478 0.00 0.00 39.03 2.01
3418 3742 3.619483 CGCAGTCGTCCATATTGGTTAAA 59.381 43.478 0.00 0.00 39.03 1.52
3419 3743 4.272504 CGCAGTCGTCCATATTGGTTAAAT 59.727 41.667 0.00 0.00 39.03 1.40
3420 3744 5.220777 CGCAGTCGTCCATATTGGTTAAATT 60.221 40.000 0.00 0.00 39.03 1.82
3421 3745 6.560711 GCAGTCGTCCATATTGGTTAAATTT 58.439 36.000 0.00 0.00 39.03 1.82
3422 3746 7.466185 CGCAGTCGTCCATATTGGTTAAATTTA 60.466 37.037 0.00 0.00 39.03 1.40
3423 3747 8.349983 GCAGTCGTCCATATTGGTTAAATTTAT 58.650 33.333 0.00 0.00 39.03 1.40
3455 3779 8.523523 AACTTAAATATTAAAAACACGGGTGC 57.476 30.769 0.00 0.00 0.00 5.01
3456 3780 7.659186 ACTTAAATATTAAAAACACGGGTGCA 58.341 30.769 0.00 0.00 0.00 4.57
3457 3781 7.595875 ACTTAAATATTAAAAACACGGGTGCAC 59.404 33.333 8.80 8.80 0.00 4.57
3458 3782 5.715434 AATATTAAAAACACGGGTGCACT 57.285 34.783 17.98 0.00 0.00 4.40
3459 3783 6.821031 AATATTAAAAACACGGGTGCACTA 57.179 33.333 17.98 0.00 0.00 2.74
3460 3784 3.967203 TTAAAAACACGGGTGCACTAC 57.033 42.857 17.98 9.36 0.00 2.73
3461 3785 1.752683 AAAAACACGGGTGCACTACA 58.247 45.000 17.98 0.00 0.00 2.74
3462 3786 1.975660 AAAACACGGGTGCACTACAT 58.024 45.000 17.98 0.00 0.00 2.29
3463 3787 1.975660 AAACACGGGTGCACTACATT 58.024 45.000 17.98 2.54 0.00 2.71
3464 3788 2.843401 AACACGGGTGCACTACATTA 57.157 45.000 17.98 0.00 0.00 1.90
3465 3789 3.343941 AACACGGGTGCACTACATTAT 57.656 42.857 17.98 0.00 0.00 1.28
3466 3790 2.627945 ACACGGGTGCACTACATTATG 58.372 47.619 17.98 8.28 0.00 1.90
3467 3791 2.235155 ACACGGGTGCACTACATTATGA 59.765 45.455 17.98 0.00 0.00 2.15
3468 3792 3.266636 CACGGGTGCACTACATTATGAA 58.733 45.455 17.98 0.00 0.00 2.57
3469 3793 3.687212 CACGGGTGCACTACATTATGAAA 59.313 43.478 17.98 0.00 0.00 2.69
3470 3794 4.335315 CACGGGTGCACTACATTATGAAAT 59.665 41.667 17.98 0.00 0.00 2.17
3471 3795 5.525745 CACGGGTGCACTACATTATGAAATA 59.474 40.000 17.98 0.00 0.00 1.40
3472 3796 6.037720 CACGGGTGCACTACATTATGAAATAA 59.962 38.462 17.98 0.00 44.01 1.40
3473 3797 6.600032 ACGGGTGCACTACATTATGAAATAAA 59.400 34.615 17.98 0.00 42.96 1.40
3474 3798 7.132213 CGGGTGCACTACATTATGAAATAAAG 58.868 38.462 17.98 0.00 42.96 1.85
3475 3799 7.425606 GGGTGCACTACATTATGAAATAAAGG 58.574 38.462 17.98 0.00 42.96 3.11
3476 3800 7.425606 GGTGCACTACATTATGAAATAAAGGG 58.574 38.462 17.98 0.00 42.96 3.95
3477 3801 7.284489 GGTGCACTACATTATGAAATAAAGGGA 59.716 37.037 17.98 0.00 42.96 4.20
3478 3802 8.345565 GTGCACTACATTATGAAATAAAGGGAG 58.654 37.037 10.32 0.00 42.96 4.30
3479 3803 8.052748 TGCACTACATTATGAAATAAAGGGAGT 58.947 33.333 0.00 0.00 42.96 3.85
3480 3804 9.555727 GCACTACATTATGAAATAAAGGGAGTA 57.444 33.333 0.00 0.00 42.96 2.59
3517 3841 8.421673 AATGTAACTAAATCTACTTCTTCCGC 57.578 34.615 0.00 0.00 0.00 5.54
3518 3842 6.927416 TGTAACTAAATCTACTTCTTCCGCA 58.073 36.000 0.00 0.00 0.00 5.69
3519 3843 7.380536 TGTAACTAAATCTACTTCTTCCGCAA 58.619 34.615 0.00 0.00 0.00 4.85
3520 3844 6.723131 AACTAAATCTACTTCTTCCGCAAC 57.277 37.500 0.00 0.00 0.00 4.17
3538 3862 4.498009 CGCAACCAACACTTTCAAGAAGAT 60.498 41.667 0.00 0.00 0.00 2.40
3548 3872 8.252964 ACACTTTCAAGAAGATATAAACGTCC 57.747 34.615 0.00 0.00 0.00 4.79
3550 3874 8.383619 CACTTTCAAGAAGATATAAACGTCCTG 58.616 37.037 0.00 0.00 0.00 3.86
3552 3876 5.357257 TCAAGAAGATATAAACGTCCTGGC 58.643 41.667 0.00 0.00 0.00 4.85
3553 3877 5.105106 TCAAGAAGATATAAACGTCCTGGCA 60.105 40.000 0.00 0.00 0.00 4.92
3559 3883 5.538813 AGATATAAACGTCCTGGCACTATCA 59.461 40.000 0.00 0.00 0.00 2.15
3562 3886 4.481368 AAACGTCCTGGCACTATCATTA 57.519 40.909 0.00 0.00 0.00 1.90
3566 3890 3.990469 CGTCCTGGCACTATCATTATCAC 59.010 47.826 0.00 0.00 0.00 3.06
3572 3896 6.015095 CCTGGCACTATCATTATCACAGTCTA 60.015 42.308 0.00 0.00 0.00 2.59
3609 3933 7.063593 TCATCCTAGTTGTAGAGACTAGCAAT 58.936 38.462 5.91 0.62 43.28 3.56
3638 3962 3.612860 CGACACAATAGCAAGTAGACACC 59.387 47.826 0.00 0.00 0.00 4.16
3639 3963 4.618460 CGACACAATAGCAAGTAGACACCT 60.618 45.833 0.00 0.00 0.00 4.00
3640 3964 4.822026 ACACAATAGCAAGTAGACACCTC 58.178 43.478 0.00 0.00 0.00 3.85
3669 3994 2.873472 AGGTAACAACGCAAATTCGTCA 59.127 40.909 0.00 0.00 42.46 4.35
3673 3998 1.082366 AACGCAAATTCGTCACGGC 60.082 52.632 0.00 0.00 42.46 5.68
3678 4003 0.179215 CAAATTCGTCACGGCTGAGC 60.179 55.000 0.00 0.00 0.00 4.26
3738 4063 5.344207 ACTTGAAGCGTGTTCTAATCAAC 57.656 39.130 0.00 0.00 0.00 3.18
3754 4079 3.401033 TCAACACACCGATGACAGATT 57.599 42.857 0.00 0.00 0.00 2.40
3755 4080 3.066380 TCAACACACCGATGACAGATTG 58.934 45.455 0.00 0.00 0.00 2.67
3762 4087 4.142249 ACACCGATGACAGATTGTTCGATA 60.142 41.667 5.21 0.00 33.76 2.92
3766 4091 4.377153 CGATGACAGATTGTTCGATAGTCG 59.623 45.833 0.00 0.00 42.10 4.18
3775 4100 0.317854 TTCGATAGTCGCATCCGCTG 60.318 55.000 0.00 0.00 40.21 5.18
3779 4104 2.104572 ATAGTCGCATCCGCTGGCAT 62.105 55.000 0.00 0.00 35.30 4.40
3786 4111 1.105167 CATCCGCTGGCATTCCATGT 61.105 55.000 0.00 0.00 42.51 3.21
3794 4119 3.803021 GCTGGCATTCCATGTCAAAACAA 60.803 43.478 0.00 0.00 45.38 2.83
3806 4131 6.765512 CCATGTCAAAACAAAAGGGTACAAAT 59.234 34.615 0.00 0.00 39.30 2.32
3859 4184 1.378646 GCCACTGGCTTTAGGGGTC 60.379 63.158 13.28 0.00 46.69 4.46
3860 4185 1.853250 GCCACTGGCTTTAGGGGTCT 61.853 60.000 13.28 0.00 46.69 3.85
3861 4186 0.035056 CCACTGGCTTTAGGGGTCTG 60.035 60.000 0.00 0.00 36.46 3.51
3863 4188 0.984995 ACTGGCTTTAGGGGTCTGTC 59.015 55.000 0.00 0.00 0.00 3.51
3877 4202 0.603065 TCTGTCCATGTCTCGGTGTG 59.397 55.000 0.00 0.00 0.00 3.82
3878 4203 0.390340 CTGTCCATGTCTCGGTGTGG 60.390 60.000 0.00 0.00 0.00 4.17
3882 4207 0.673644 CCATGTCTCGGTGTGGAACC 60.674 60.000 0.00 0.00 46.60 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.094545 ACCCGCAGAAATCTTCATTTGC 60.095 45.455 0.00 0.00 31.94 3.68
26 27 0.036306 TTTCTCCCTTCTGAACCCGC 59.964 55.000 0.00 0.00 0.00 6.13
29 30 3.147553 AGCTTTTCTCCCTTCTGAACC 57.852 47.619 0.00 0.00 0.00 3.62
39 40 3.384668 GTTGCCAAAGAAGCTTTTCTCC 58.615 45.455 0.00 0.00 0.00 3.71
46 47 0.250727 TAGCCGTTGCCAAAGAAGCT 60.251 50.000 0.00 0.00 38.69 3.74
143 152 1.656652 GATGGTGAGTGATTGGGACG 58.343 55.000 0.00 0.00 0.00 4.79
174 183 1.067635 CAAAGGGGAAATGGTTGAGCG 60.068 52.381 0.00 0.00 0.00 5.03
209 218 3.563479 GGAAGGAGGGCTCATTGGTTAAA 60.563 47.826 0.00 0.00 33.38 1.52
221 230 1.076705 GGTGGATTGGAAGGAGGGC 60.077 63.158 0.00 0.00 0.00 5.19
250 259 1.202698 AGAGCTGGGTGTCAGTTGTTC 60.203 52.381 0.00 0.00 45.08 3.18
306 315 1.326852 GCAGTGTGAGATTGCGATCAG 59.673 52.381 16.42 0.00 34.60 2.90
325 334 1.144716 TGATCACTGGCCGATCAGC 59.855 57.895 15.47 0.00 43.30 4.26
347 356 1.436983 GATCCAAACGGACGATGGGC 61.437 60.000 16.65 9.05 34.62 5.36
358 402 1.474330 AGAAATGCCCGGATCCAAAC 58.526 50.000 13.41 0.00 0.00 2.93
366 410 1.606885 ATGTGCCAAGAAATGCCCGG 61.607 55.000 0.00 0.00 0.00 5.73
436 480 4.917415 CGTTGGCAAAGAAGTAAAGGAATG 59.083 41.667 7.42 0.00 0.00 2.67
473 517 3.127352 GAGGAGACGCGCCACCTAG 62.127 68.421 11.91 0.00 32.53 3.02
518 562 2.400467 ACCTAGGGCGATAAGATGGT 57.600 50.000 14.81 0.00 0.00 3.55
521 565 6.257586 AGATAAGAACCTAGGGCGATAAGAT 58.742 40.000 14.81 0.00 0.00 2.40
522 566 5.642165 AGATAAGAACCTAGGGCGATAAGA 58.358 41.667 14.81 0.00 0.00 2.10
523 567 5.712917 AGAGATAAGAACCTAGGGCGATAAG 59.287 44.000 14.81 0.00 0.00 1.73
525 569 5.010933 CAGAGATAAGAACCTAGGGCGATA 58.989 45.833 14.81 1.37 0.00 2.92
526 570 3.829601 CAGAGATAAGAACCTAGGGCGAT 59.170 47.826 14.81 4.13 0.00 4.58
527 571 3.117625 TCAGAGATAAGAACCTAGGGCGA 60.118 47.826 14.81 0.00 0.00 5.54
528 572 3.223435 TCAGAGATAAGAACCTAGGGCG 58.777 50.000 14.81 0.00 0.00 6.13
529 573 5.279758 GGATTCAGAGATAAGAACCTAGGGC 60.280 48.000 14.81 4.64 0.00 5.19
576 620 2.904866 GACAAAGGGGTGCGTGCA 60.905 61.111 0.00 0.00 0.00 4.57
577 621 2.594592 AGACAAAGGGGTGCGTGC 60.595 61.111 0.00 0.00 0.00 5.34
578 622 2.317609 CGAGACAAAGGGGTGCGTG 61.318 63.158 0.00 0.00 0.00 5.34
579 623 2.030562 CGAGACAAAGGGGTGCGT 59.969 61.111 0.00 0.00 0.00 5.24
580 624 2.027625 GACGAGACAAAGGGGTGCG 61.028 63.158 0.00 0.00 0.00 5.34
585 629 0.533032 GGAGAGGACGAGACAAAGGG 59.467 60.000 0.00 0.00 0.00 3.95
590 634 0.253610 GAGGAGGAGAGGACGAGACA 59.746 60.000 0.00 0.00 0.00 3.41
595 639 0.750182 GACAGGAGGAGGAGAGGACG 60.750 65.000 0.00 0.00 0.00 4.79
605 649 2.358721 GGAGATGAAGAGGACAGGAGGA 60.359 54.545 0.00 0.00 0.00 3.71
609 653 1.407258 GACGGAGATGAAGAGGACAGG 59.593 57.143 0.00 0.00 0.00 4.00
693 753 2.017049 ACAGGACAAAGCAGAACACAC 58.983 47.619 0.00 0.00 0.00 3.82
694 754 2.418368 ACAGGACAAAGCAGAACACA 57.582 45.000 0.00 0.00 0.00 3.72
700 760 2.096069 CACGATGAACAGGACAAAGCAG 60.096 50.000 0.00 0.00 0.00 4.24
704 764 0.865111 CGCACGATGAACAGGACAAA 59.135 50.000 0.00 0.00 0.00 2.83
719 779 1.408422 CACCTAAAAGCAAAGCGCAC 58.592 50.000 11.47 0.00 46.13 5.34
722 782 0.729140 CGCCACCTAAAAGCAAAGCG 60.729 55.000 0.00 0.00 36.06 4.68
755 815 4.015084 AGAAATTCAGAACCATGGCAGAG 58.985 43.478 13.04 0.00 0.00 3.35
760 820 7.478322 CAAGTATCAGAAATTCAGAACCATGG 58.522 38.462 11.19 11.19 0.00 3.66
762 822 6.660521 TGCAAGTATCAGAAATTCAGAACCAT 59.339 34.615 0.00 0.00 0.00 3.55
916 977 6.569179 TTTTGCTTGTAACCAGAAGTATCC 57.431 37.500 0.00 0.00 0.00 2.59
983 1044 6.358974 TGAACATCTTGAGATTACTGTCCA 57.641 37.500 0.00 0.00 31.21 4.02
1020 1092 0.966920 TCCTCCTCTTGTTCCACGTC 59.033 55.000 0.00 0.00 0.00 4.34
1023 1095 2.614229 GCTTCTCCTCCTCTTGTTCCAC 60.614 54.545 0.00 0.00 0.00 4.02
1095 1207 1.132262 CTGCCGACAACAACAAAGTGT 59.868 47.619 0.00 0.00 0.00 3.55
1109 1221 1.344438 AGTGACAAATGACTCTGCCGA 59.656 47.619 0.00 0.00 0.00 5.54
1110 1222 1.462283 CAGTGACAAATGACTCTGCCG 59.538 52.381 2.96 0.00 0.00 5.69
1111 1223 2.498167 ACAGTGACAAATGACTCTGCC 58.502 47.619 12.49 0.00 35.73 4.85
1115 1229 8.877808 TGATCATATACAGTGACAAATGACTC 57.122 34.615 0.00 2.42 0.00 3.36
1132 1246 8.913487 TGCACTGAAGAAACATATGATCATAT 57.087 30.769 20.42 20.42 34.50 1.78
1142 1256 3.418995 AGATGCTGCACTGAAGAAACAT 58.581 40.909 3.57 0.00 0.00 2.71
1162 1276 2.425143 TTCCTCATGCCAAGCCTTAG 57.575 50.000 0.00 0.00 0.00 2.18
1172 1320 6.431543 AGATGAGATGATCAAATTCCTCATGC 59.568 38.462 21.58 15.93 42.53 4.06
1187 1335 6.049790 CAGAAGCAGAAATCAGATGAGATGA 58.950 40.000 0.00 0.00 0.00 2.92
1188 1336 5.277586 GCAGAAGCAGAAATCAGATGAGATG 60.278 44.000 0.00 0.00 41.58 2.90
1189 1337 4.817464 GCAGAAGCAGAAATCAGATGAGAT 59.183 41.667 0.00 0.00 41.58 2.75
1190 1338 4.190001 GCAGAAGCAGAAATCAGATGAGA 58.810 43.478 0.00 0.00 41.58 3.27
1191 1339 4.539509 GCAGAAGCAGAAATCAGATGAG 57.460 45.455 0.00 0.00 41.58 2.90
1275 1438 2.042831 ATGGAGCAGTTGCGCTTCC 61.043 57.895 9.73 6.81 44.01 3.46
1490 1699 2.176045 TGAGGGACGTATCTGCTTTCA 58.824 47.619 0.00 0.00 0.00 2.69
1559 1768 7.549134 TGGTGCTAACACTAATGTAATCTGAAG 59.451 37.037 0.00 0.00 46.57 3.02
1732 1942 2.733227 GCTTTTCTTGACATGGATGCCG 60.733 50.000 0.00 0.00 0.00 5.69
1845 2119 4.023193 GTGGTGACAGATTTACAAACTGGG 60.023 45.833 0.00 0.00 44.46 4.45
1865 2139 0.759436 AGGCATACCGAGGTAGGTGG 60.759 60.000 14.34 3.11 45.54 4.61
1880 2154 1.527380 GTTGGACCGAAACCAGGCA 60.527 57.895 0.00 0.00 38.70 4.75
1881 2155 0.035739 TAGTTGGACCGAAACCAGGC 59.964 55.000 0.00 0.00 38.70 4.85
1891 2165 2.414161 GCAAGAACGCATTAGTTGGACC 60.414 50.000 0.00 0.00 34.00 4.46
1904 2178 1.400629 CCATTCACAGCAGCAAGAACG 60.401 52.381 0.00 0.00 0.00 3.95
1912 2186 3.247886 CGATCTTCATCCATTCACAGCAG 59.752 47.826 0.00 0.00 0.00 4.24
2053 2327 3.636313 CTTCCCGTCGGCGCAGTAA 62.636 63.158 10.83 0.00 36.67 2.24
2302 2576 4.735132 TTGGCGAGCCCGAAGTCG 62.735 66.667 12.05 0.00 38.22 4.18
2323 2597 4.100084 TCCAGGTCCTGCGGCATG 62.100 66.667 13.99 0.00 0.00 4.06
2408 2682 2.607771 CGAGTTCTGCAAAAATGGTGGG 60.608 50.000 0.00 0.00 0.00 4.61
2452 2737 4.503714 TGGAAGAATCCCCATTAGTGTC 57.496 45.455 0.00 0.00 45.95 3.67
2453 2738 4.728860 AGATGGAAGAATCCCCATTAGTGT 59.271 41.667 6.29 0.00 45.95 3.55
2462 2747 0.105039 ACGCGAGATGGAAGAATCCC 59.895 55.000 15.93 0.00 45.95 3.85
2480 2769 2.743928 CAGCTTCCCCGTCTGCAC 60.744 66.667 0.00 0.00 0.00 4.57
2587 2876 1.924731 TGACGATGAGGTTCTGGTCT 58.075 50.000 0.00 0.00 0.00 3.85
2620 2919 1.827789 CCGGCAGAGAGGGAGAGAG 60.828 68.421 0.00 0.00 0.00 3.20
2621 2920 2.277072 CCGGCAGAGAGGGAGAGA 59.723 66.667 0.00 0.00 0.00 3.10
2622 2921 3.535962 GCCGGCAGAGAGGGAGAG 61.536 72.222 24.80 0.00 0.00 3.20
2623 2922 4.067512 AGCCGGCAGAGAGGGAGA 62.068 66.667 31.54 0.00 0.00 3.71
2624 2923 3.847602 CAGCCGGCAGAGAGGGAG 61.848 72.222 31.54 2.29 0.00 4.30
2705 3004 4.057428 GAGCACGAGCCGGACAGT 62.057 66.667 5.05 0.00 43.56 3.55
2776 3075 3.350163 CCCCTTGCCCATGTCCCT 61.350 66.667 0.00 0.00 0.00 4.20
2933 3232 4.750098 TCCAAGACTGAATCTCAAAACGTC 59.250 41.667 0.00 0.00 36.27 4.34
2969 3290 3.118811 CGCCATCTTCTTCCTCTTCTTCT 60.119 47.826 0.00 0.00 0.00 2.85
2972 3293 2.461695 TCGCCATCTTCTTCCTCTTCT 58.538 47.619 0.00 0.00 0.00 2.85
2973 3294 2.969628 TCGCCATCTTCTTCCTCTTC 57.030 50.000 0.00 0.00 0.00 2.87
2974 3295 3.008485 AGTTTCGCCATCTTCTTCCTCTT 59.992 43.478 0.00 0.00 0.00 2.85
3015 3336 5.720202 CCACGATTAATATGGATCGGAAGA 58.280 41.667 19.21 0.00 46.90 2.87
3017 3338 4.020573 AGCCACGATTAATATGGATCGGAA 60.021 41.667 18.40 0.00 46.90 4.30
3018 3339 3.513912 AGCCACGATTAATATGGATCGGA 59.486 43.478 18.40 0.00 46.90 4.55
3019 3340 3.618594 CAGCCACGATTAATATGGATCGG 59.381 47.826 18.40 11.33 46.90 4.18
3021 3342 4.579869 ACCAGCCACGATTAATATGGATC 58.420 43.478 18.40 5.47 35.33 3.36
3034 3356 1.544691 AGTTGTACTAGACCAGCCACG 59.455 52.381 0.00 0.00 0.00 4.94
3083 3405 6.677913 CAACGAAAAGTTACTCCCATCAATT 58.322 36.000 0.00 0.00 42.02 2.32
3089 3411 1.868498 CGCAACGAAAAGTTACTCCCA 59.132 47.619 0.00 0.00 42.02 4.37
3112 3434 2.938451 ACCACTATGCACATGAACATCG 59.062 45.455 0.00 1.29 0.00 3.84
3115 3437 2.435422 CCACCACTATGCACATGAACA 58.565 47.619 0.00 0.00 0.00 3.18
3120 3442 2.025037 ACAATCCCACCACTATGCACAT 60.025 45.455 0.00 0.00 0.00 3.21
3125 3448 5.243730 ACTTTGAAACAATCCCACCACTATG 59.756 40.000 0.00 0.00 0.00 2.23
3128 3451 3.636764 GACTTTGAAACAATCCCACCACT 59.363 43.478 0.00 0.00 0.00 4.00
3134 3457 5.529581 TTTCAGGACTTTGAAACAATCCC 57.470 39.130 0.00 0.00 40.95 3.85
3151 3474 4.455877 ACAAATTAAGCCCTCTCGTTTCAG 59.544 41.667 0.00 0.00 0.00 3.02
3157 3480 3.941483 ACATCACAAATTAAGCCCTCTCG 59.059 43.478 0.00 0.00 0.00 4.04
3169 3492 6.707161 CACCATTTTCTTTGGACATCACAAAT 59.293 34.615 0.00 0.00 37.22 2.32
3197 3520 1.005215 ACAGGGCAGATTTCTCCTTGG 59.995 52.381 10.58 0.00 32.02 3.61
3202 3525 1.066858 TGACGACAGGGCAGATTTCTC 60.067 52.381 0.00 0.00 0.00 2.87
3228 3551 1.444933 ACCACTTGTTCCCTCCATCA 58.555 50.000 0.00 0.00 0.00 3.07
3263 3586 8.328758 TCAGGATTCTAACCATCTGTACAAATT 58.671 33.333 0.00 0.00 0.00 1.82
3340 3664 6.423862 GCCGCGATTGACTTTATTTTGTATA 58.576 36.000 8.23 0.00 0.00 1.47
3344 3668 2.525891 CGCCGCGATTGACTTTATTTTG 59.474 45.455 8.23 0.00 0.00 2.44
3360 3684 4.243270 AGTATCTTATAATGGTTCGCCGC 58.757 43.478 0.00 0.00 41.18 6.53
3381 3705 2.815647 GCGACGGAAGCAAGGGAG 60.816 66.667 0.00 0.00 34.19 4.30
3382 3706 3.589654 CTGCGACGGAAGCAAGGGA 62.590 63.158 0.00 0.00 44.67 4.20
3383 3707 3.121030 CTGCGACGGAAGCAAGGG 61.121 66.667 0.00 0.00 44.67 3.95
3384 3708 2.357517 ACTGCGACGGAAGCAAGG 60.358 61.111 0.00 0.00 44.67 3.61
3385 3709 2.720758 CGACTGCGACGGAAGCAAG 61.721 63.158 0.00 1.59 44.67 4.01
3386 3710 2.733218 CGACTGCGACGGAAGCAA 60.733 61.111 0.00 0.00 44.67 3.91
3387 3711 3.891586 GACGACTGCGACGGAAGCA 62.892 63.158 0.00 2.04 42.99 3.91
3388 3712 3.173240 GACGACTGCGACGGAAGC 61.173 66.667 0.00 0.00 41.64 3.86
3389 3713 2.504244 GGACGACTGCGACGGAAG 60.504 66.667 0.00 0.00 41.64 3.46
3390 3714 1.307355 TATGGACGACTGCGACGGAA 61.307 55.000 0.00 0.00 41.64 4.30
3391 3715 1.099295 ATATGGACGACTGCGACGGA 61.099 55.000 0.00 0.00 41.64 4.69
3392 3716 0.248907 AATATGGACGACTGCGACGG 60.249 55.000 0.00 0.00 41.64 4.79
3393 3717 0.846401 CAATATGGACGACTGCGACG 59.154 55.000 0.00 0.00 41.64 5.12
3394 3718 1.209128 CCAATATGGACGACTGCGAC 58.791 55.000 0.00 0.00 40.96 5.19
3395 3719 0.821517 ACCAATATGGACGACTGCGA 59.178 50.000 2.85 0.00 40.96 5.10
3396 3720 1.651987 AACCAATATGGACGACTGCG 58.348 50.000 2.85 0.00 40.96 5.18
3397 3721 5.751243 ATTTAACCAATATGGACGACTGC 57.249 39.130 2.85 0.00 40.96 4.40
3429 3753 8.980610 GCACCCGTGTTTTTAATATTTAAGTTT 58.019 29.630 0.00 0.00 0.00 2.66
3430 3754 8.142551 TGCACCCGTGTTTTTAATATTTAAGTT 58.857 29.630 0.00 0.00 0.00 2.66
3431 3755 7.595875 GTGCACCCGTGTTTTTAATATTTAAGT 59.404 33.333 5.22 0.00 0.00 2.24
3432 3756 7.810759 AGTGCACCCGTGTTTTTAATATTTAAG 59.189 33.333 14.63 0.00 0.00 1.85
3433 3757 7.659186 AGTGCACCCGTGTTTTTAATATTTAA 58.341 30.769 14.63 0.00 0.00 1.52
3434 3758 7.216973 AGTGCACCCGTGTTTTTAATATTTA 57.783 32.000 14.63 0.00 0.00 1.40
3435 3759 6.091718 AGTGCACCCGTGTTTTTAATATTT 57.908 33.333 14.63 0.00 0.00 1.40
3436 3760 5.715434 AGTGCACCCGTGTTTTTAATATT 57.285 34.783 14.63 0.00 0.00 1.28
3437 3761 5.706369 TGTAGTGCACCCGTGTTTTTAATAT 59.294 36.000 14.63 0.00 0.00 1.28
3438 3762 5.061853 TGTAGTGCACCCGTGTTTTTAATA 58.938 37.500 14.63 0.00 0.00 0.98
3439 3763 3.884091 TGTAGTGCACCCGTGTTTTTAAT 59.116 39.130 14.63 0.00 0.00 1.40
3440 3764 3.276857 TGTAGTGCACCCGTGTTTTTAA 58.723 40.909 14.63 0.00 0.00 1.52
3441 3765 2.915349 TGTAGTGCACCCGTGTTTTTA 58.085 42.857 14.63 0.00 0.00 1.52
3442 3766 1.752683 TGTAGTGCACCCGTGTTTTT 58.247 45.000 14.63 0.00 0.00 1.94
3443 3767 1.975660 ATGTAGTGCACCCGTGTTTT 58.024 45.000 14.63 0.00 0.00 2.43
3444 3768 1.975660 AATGTAGTGCACCCGTGTTT 58.024 45.000 14.63 0.00 0.00 2.83
3445 3769 2.843401 TAATGTAGTGCACCCGTGTT 57.157 45.000 14.63 5.33 0.00 3.32
3446 3770 2.235155 TCATAATGTAGTGCACCCGTGT 59.765 45.455 14.63 0.00 0.00 4.49
3447 3771 2.899976 TCATAATGTAGTGCACCCGTG 58.100 47.619 14.63 3.57 0.00 4.94
3448 3772 3.620427 TTCATAATGTAGTGCACCCGT 57.380 42.857 14.63 2.81 0.00 5.28
3449 3773 6.612247 TTATTTCATAATGTAGTGCACCCG 57.388 37.500 14.63 0.00 0.00 5.28
3450 3774 7.425606 CCTTTATTTCATAATGTAGTGCACCC 58.574 38.462 14.63 5.07 0.00 4.61
3451 3775 7.284489 TCCCTTTATTTCATAATGTAGTGCACC 59.716 37.037 14.63 0.00 0.00 5.01
3452 3776 8.220755 TCCCTTTATTTCATAATGTAGTGCAC 57.779 34.615 9.40 9.40 0.00 4.57
3453 3777 8.052748 ACTCCCTTTATTTCATAATGTAGTGCA 58.947 33.333 0.00 0.00 0.00 4.57
3454 3778 8.451908 ACTCCCTTTATTTCATAATGTAGTGC 57.548 34.615 0.00 0.00 0.00 4.40
3491 3815 8.880750 GCGGAAGAAGTAGATTTAGTTACATTT 58.119 33.333 0.00 0.00 0.00 2.32
3492 3816 8.038944 TGCGGAAGAAGTAGATTTAGTTACATT 58.961 33.333 0.00 0.00 0.00 2.71
3493 3817 7.553334 TGCGGAAGAAGTAGATTTAGTTACAT 58.447 34.615 0.00 0.00 0.00 2.29
3494 3818 6.927416 TGCGGAAGAAGTAGATTTAGTTACA 58.073 36.000 0.00 0.00 0.00 2.41
3495 3819 7.201504 GGTTGCGGAAGAAGTAGATTTAGTTAC 60.202 40.741 0.00 0.00 0.00 2.50
3496 3820 6.815142 GGTTGCGGAAGAAGTAGATTTAGTTA 59.185 38.462 0.00 0.00 0.00 2.24
3497 3821 5.642491 GGTTGCGGAAGAAGTAGATTTAGTT 59.358 40.000 0.00 0.00 0.00 2.24
3498 3822 5.176592 GGTTGCGGAAGAAGTAGATTTAGT 58.823 41.667 0.00 0.00 0.00 2.24
3499 3823 5.175859 TGGTTGCGGAAGAAGTAGATTTAG 58.824 41.667 0.00 0.00 0.00 1.85
3500 3824 5.155278 TGGTTGCGGAAGAAGTAGATTTA 57.845 39.130 0.00 0.00 0.00 1.40
3501 3825 4.015872 TGGTTGCGGAAGAAGTAGATTT 57.984 40.909 0.00 0.00 0.00 2.17
3502 3826 3.695830 TGGTTGCGGAAGAAGTAGATT 57.304 42.857 0.00 0.00 0.00 2.40
3503 3827 3.244422 TGTTGGTTGCGGAAGAAGTAGAT 60.244 43.478 0.00 0.00 0.00 1.98
3504 3828 2.103432 TGTTGGTTGCGGAAGAAGTAGA 59.897 45.455 0.00 0.00 0.00 2.59
3505 3829 2.223377 GTGTTGGTTGCGGAAGAAGTAG 59.777 50.000 0.00 0.00 0.00 2.57
3506 3830 2.158871 AGTGTTGGTTGCGGAAGAAGTA 60.159 45.455 0.00 0.00 0.00 2.24
3507 3831 1.021968 GTGTTGGTTGCGGAAGAAGT 58.978 50.000 0.00 0.00 0.00 3.01
3508 3832 1.308998 AGTGTTGGTTGCGGAAGAAG 58.691 50.000 0.00 0.00 0.00 2.85
3509 3833 1.757682 AAGTGTTGGTTGCGGAAGAA 58.242 45.000 0.00 0.00 0.00 2.52
3510 3834 1.673920 GAAAGTGTTGGTTGCGGAAGA 59.326 47.619 0.00 0.00 0.00 2.87
3511 3835 1.403679 TGAAAGTGTTGGTTGCGGAAG 59.596 47.619 0.00 0.00 0.00 3.46
3512 3836 1.464734 TGAAAGTGTTGGTTGCGGAA 58.535 45.000 0.00 0.00 0.00 4.30
3513 3837 1.403679 CTTGAAAGTGTTGGTTGCGGA 59.596 47.619 0.00 0.00 0.00 5.54
3514 3838 1.403679 TCTTGAAAGTGTTGGTTGCGG 59.596 47.619 0.00 0.00 0.00 5.69
3515 3839 2.842208 TCTTGAAAGTGTTGGTTGCG 57.158 45.000 0.00 0.00 0.00 4.85
3516 3840 4.370364 TCTTCTTGAAAGTGTTGGTTGC 57.630 40.909 0.00 0.00 0.00 4.17
3519 3843 8.504005 CGTTTATATCTTCTTGAAAGTGTTGGT 58.496 33.333 0.00 0.00 0.00 3.67
3520 3844 8.504005 ACGTTTATATCTTCTTGAAAGTGTTGG 58.496 33.333 0.00 0.00 0.00 3.77
3538 3862 5.801531 ATGATAGTGCCAGGACGTTTATA 57.198 39.130 0.00 0.00 0.00 0.98
3544 3868 3.990469 GTGATAATGATAGTGCCAGGACG 59.010 47.826 0.00 0.00 0.00 4.79
3548 3872 5.851720 AGACTGTGATAATGATAGTGCCAG 58.148 41.667 0.00 0.00 0.00 4.85
3550 3874 7.087639 GTCTAGACTGTGATAATGATAGTGCC 58.912 42.308 15.91 0.00 0.00 5.01
3562 3886 9.160496 GATGAAAATCTTTGTCTAGACTGTGAT 57.840 33.333 23.01 18.08 0.00 3.06
3566 3890 9.311916 CTAGGATGAAAATCTTTGTCTAGACTG 57.688 37.037 23.01 13.19 0.00 3.51
3572 3896 9.442047 CTACAACTAGGATGAAAATCTTTGTCT 57.558 33.333 4.95 0.00 0.00 3.41
3580 3904 8.417884 GCTAGTCTCTACAACTAGGATGAAAAT 58.582 37.037 11.18 0.00 44.17 1.82
3583 3907 6.424032 TGCTAGTCTCTACAACTAGGATGAA 58.576 40.000 11.18 0.00 44.17 2.57
3597 3921 6.039829 TGTGTCGATATTCATTGCTAGTCTCT 59.960 38.462 0.00 0.00 0.00 3.10
3609 3933 7.648112 GTCTACTTGCTATTGTGTCGATATTCA 59.352 37.037 0.00 0.00 0.00 2.57
3638 3962 3.311322 TGCGTTGTTACCTTGTTGAAGAG 59.689 43.478 0.00 0.00 0.00 2.85
3639 3963 3.271729 TGCGTTGTTACCTTGTTGAAGA 58.728 40.909 0.00 0.00 0.00 2.87
3640 3964 3.684103 TGCGTTGTTACCTTGTTGAAG 57.316 42.857 0.00 0.00 0.00 3.02
3673 3998 2.821991 CCTTTATAGGTCGGGCTCAG 57.178 55.000 0.00 0.00 36.74 3.35
3697 4022 5.699458 TCAAGTTCGGGTGAAAACTCTTATC 59.301 40.000 0.00 0.00 34.71 1.75
3708 4033 0.878523 CACGCTTCAAGTTCGGGTGA 60.879 55.000 0.00 0.00 42.16 4.02
3710 4035 0.463116 AACACGCTTCAAGTTCGGGT 60.463 50.000 0.00 0.00 42.11 5.28
3711 4036 0.234884 GAACACGCTTCAAGTTCGGG 59.765 55.000 0.00 0.00 33.24 5.14
3738 4063 2.092681 CGAACAATCTGTCATCGGTGTG 59.907 50.000 0.00 0.00 29.72 3.82
3740 4065 2.606108 TCGAACAATCTGTCATCGGTG 58.394 47.619 0.00 0.00 33.03 4.94
3742 4067 4.611943 ACTATCGAACAATCTGTCATCGG 58.388 43.478 0.00 0.00 33.03 4.18
3744 4069 4.147306 GCGACTATCGAACAATCTGTCATC 59.853 45.833 1.69 0.00 43.74 2.92
3754 4079 0.594028 GCGGATGCGACTATCGAACA 60.594 55.000 12.10 0.00 43.74 3.18
3755 4080 2.134098 GCGGATGCGACTATCGAAC 58.866 57.895 12.10 0.00 43.74 3.95
3766 4091 2.829914 TGGAATGCCAGCGGATGC 60.830 61.111 0.00 0.00 39.92 3.91
3779 4104 5.422331 TGTACCCTTTTGTTTTGACATGGAA 59.578 36.000 0.00 0.00 0.00 3.53
3786 4111 9.757227 CAATCTATTTGTACCCTTTTGTTTTGA 57.243 29.630 0.00 0.00 0.00 2.69
3794 4119 5.015817 TCCCACCAATCTATTTGTACCCTTT 59.984 40.000 0.00 0.00 33.15 3.11
3806 4131 3.849574 TGGAAAGATGTCCCACCAATCTA 59.150 43.478 0.00 0.00 36.80 1.98
3859 4184 0.390340 CCACACCGAGACATGGACAG 60.390 60.000 0.00 0.00 33.80 3.51
3860 4185 0.830023 TCCACACCGAGACATGGACA 60.830 55.000 0.00 0.00 36.30 4.02
3861 4186 0.320374 TTCCACACCGAGACATGGAC 59.680 55.000 0.00 0.00 40.96 4.02
3863 4188 0.673644 GGTTCCACACCGAGACATGG 60.674 60.000 0.00 0.00 35.12 3.66
3877 4202 1.406477 GGAATGGTAGTGGTCGGTTCC 60.406 57.143 0.00 0.00 0.00 3.62
3878 4203 1.276989 TGGAATGGTAGTGGTCGGTTC 59.723 52.381 0.00 0.00 0.00 3.62
3882 4207 1.674817 GGTGTGGAATGGTAGTGGTCG 60.675 57.143 0.00 0.00 0.00 4.79
3890 4215 2.282180 GTGCCGGTGTGGAATGGT 60.282 61.111 1.90 0.00 42.00 3.55


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

AutoCloner maintained by Alex Coulton.