Multiple sequence alignment - TraesCS5A01G279200

Loading Multiple Alignment...

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 TraesCS5A01G279200 chr5A 100.000 4189 0 0 1 4189 488265591 488261403 0.000000e+00 7736
1 TraesCS5A01G279200 chr5B 88.993 3516 206 91 644 4064 464330071 464326642 0.000000e+00 4181
2 TraesCS5A01G279200 chr5D 91.455 2797 137 40 643 3392 386654740 386651999 0.000000e+00 3747
3 TraesCS5A01G279200 chr5D 85.565 672 55 21 3394 4060 386651892 386651258 0.000000e+00 665
4 TraesCS5A01G279200 chr2B 98.346 544 5 2 1 543 39425635 39425095 0.000000e+00 952
5 TraesCS5A01G279200 chr2B 97.959 98 2 0 548 645 461096846 461096749 2.000000e-38 171
6 TraesCS5A01G279200 chr2B 98.947 95 1 0 548 642 689374633 689374727 2.000000e-38 171
7 TraesCS5A01G279200 chr4A 98.158 543 7 1 1 543 377592359 377591820 0.000000e+00 944
8 TraesCS5A01G279200 chr4A 97.794 544 8 2 1 543 537234094 537234634 0.000000e+00 935
9 TraesCS5A01G279200 chr4A 97.959 98 2 0 548 645 377591883 377591786 2.000000e-38 171
10 TraesCS5A01G279200 chr7A 97.978 544 7 2 1 543 121045802 121045262 0.000000e+00 941
11 TraesCS5A01G279200 chr7A 97.959 98 2 0 548 645 652192750 652192653 2.000000e-38 171
12 TraesCS5A01G279200 chr1A 97.974 543 8 1 1 543 449181351 449180812 0.000000e+00 939
13 TraesCS5A01G279200 chr1A 97.610 544 9 2 1 543 58179137 58178597 0.000000e+00 929
14 TraesCS5A01G279200 chr1A 98.947 95 1 0 548 642 58178660 58178566 2.000000e-38 171
15 TraesCS5A01G279200 chr4B 97.794 544 8 2 1 543 489024698 489025238 0.000000e+00 935
16 TraesCS5A01G279200 chr4B 98.947 95 1 0 548 642 489025175 489025269 2.000000e-38 171
17 TraesCS5A01G279200 chr2A 97.798 545 7 5 1 543 145437286 145437827 0.000000e+00 935
18 TraesCS5A01G279200 chr2A 97.000 100 3 0 548 647 100131197 100131098 7.200000e-38 169
19 TraesCS5A01G279200 chr7B 97.610 544 9 2 1 543 253904068 253903528 0.000000e+00 929
20 TraesCS5A01G279200 chr6B 97.959 98 2 0 548 645 135851991 135851894 2.000000e-38 171
21 TraesCS5A01G279200 chr1B 98.947 95 1 0 548 642 439510920 439511014 2.000000e-38 171


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 TraesCS5A01G279200 chr5A 488261403 488265591 4188 True 7736.0 7736 100.0000 1 4189 1 chr5A.!!$R1 4188
1 TraesCS5A01G279200 chr5B 464326642 464330071 3429 True 4181.0 4181 88.9930 644 4064 1 chr5B.!!$R1 3420
2 TraesCS5A01G279200 chr5D 386651258 386654740 3482 True 2206.0 3747 88.5100 643 4060 2 chr5D.!!$R1 3417
3 TraesCS5A01G279200 chr2B 39425095 39425635 540 True 952.0 952 98.3460 1 543 1 chr2B.!!$R1 542
4 TraesCS5A01G279200 chr4A 537234094 537234634 540 False 935.0 935 97.7940 1 543 1 chr4A.!!$F1 542
5 TraesCS5A01G279200 chr4A 377591786 377592359 573 True 557.5 944 98.0585 1 645 2 chr4A.!!$R1 644
6 TraesCS5A01G279200 chr7A 121045262 121045802 540 True 941.0 941 97.9780 1 543 1 chr7A.!!$R1 542
7 TraesCS5A01G279200 chr1A 449180812 449181351 539 True 939.0 939 97.9740 1 543 1 chr1A.!!$R1 542
8 TraesCS5A01G279200 chr1A 58178566 58179137 571 True 550.0 929 98.2785 1 642 2 chr1A.!!$R2 641
9 TraesCS5A01G279200 chr4B 489024698 489025269 571 False 553.0 935 98.3705 1 642 2 chr4B.!!$F1 641
10 TraesCS5A01G279200 chr2A 145437286 145437827 541 False 935.0 935 97.7980 1 543 1 chr2A.!!$F1 542
11 TraesCS5A01G279200 chr7B 253903528 253904068 540 True 929.0 929 97.6100 1 543 1 chr7B.!!$R1 542


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
553 556 0.101219 GTGATTTGAATCTGGGCGCC 59.899 55.000 21.18 21.18 36.39 6.53 F
1146 1198 0.246086 CGGTCTCTTCTGCTTCTGCT 59.754 55.000 0.00 0.00 40.48 4.24 F
1626 1703 0.377203 GATGACGCCGGAATTTGGTC 59.623 55.000 5.05 2.32 0.00 4.02 F
1664 1741 1.511768 GGGTCCCGACTCGAAGAAG 59.488 63.158 0.00 0.00 34.09 2.85 F
2947 3075 1.099689 AACAGGTTTGTGTGGTTCGG 58.900 50.000 0.00 0.00 37.67 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2159 2246 0.099436 GCGCTTTGCCAATCACCTAG 59.901 55.0 0.0 0.0 37.76 3.02 R
2589 2678 0.105039 GGTTCTCCATAGCACCCGAG 59.895 60.0 0.0 0.0 33.30 4.63 R
2883 3002 0.248377 GCAGCAAGCAACGATCCATC 60.248 55.0 0.0 0.0 44.79 3.51 R
3151 3279 0.398098 TTCTAGTGTCCCCGATCCCC 60.398 60.0 0.0 0.0 0.00 4.81 R
3934 4205 0.036671 AACCACCGGCTGTAACTAGC 60.037 55.0 0.0 0.0 42.94 3.42 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
173 174 2.718609 AGGATGGATTGGGGATCGAATT 59.281 45.455 0.00 0.00 35.49 2.17
543 546 5.417266 TGAACAGGTCAGTTTGTGATTTGAA 59.583 36.000 0.00 0.00 37.56 2.69
544 547 6.096705 TGAACAGGTCAGTTTGTGATTTGAAT 59.903 34.615 0.00 0.00 37.56 2.57
545 548 6.076981 ACAGGTCAGTTTGTGATTTGAATC 57.923 37.500 0.00 0.00 37.56 2.52
546 549 5.829924 ACAGGTCAGTTTGTGATTTGAATCT 59.170 36.000 5.42 0.00 37.56 2.40
547 550 6.147581 CAGGTCAGTTTGTGATTTGAATCTG 58.852 40.000 5.42 0.00 37.56 2.90
548 551 5.242393 AGGTCAGTTTGTGATTTGAATCTGG 59.758 40.000 5.42 0.00 37.56 3.86
549 552 5.464168 GTCAGTTTGTGATTTGAATCTGGG 58.536 41.667 5.42 0.00 37.56 4.45
550 553 4.022068 TCAGTTTGTGATTTGAATCTGGGC 60.022 41.667 5.42 0.00 36.39 5.36
551 554 3.057315 AGTTTGTGATTTGAATCTGGGCG 60.057 43.478 5.42 0.00 36.39 6.13
552 555 0.810648 TGTGATTTGAATCTGGGCGC 59.189 50.000 0.00 0.00 36.39 6.53
553 556 0.101219 GTGATTTGAATCTGGGCGCC 59.899 55.000 21.18 21.18 36.39 6.53
554 557 1.356624 GATTTGAATCTGGGCGCCG 59.643 57.895 22.54 7.85 32.66 6.46
555 558 2.668261 GATTTGAATCTGGGCGCCGC 62.668 60.000 22.54 14.37 32.66 6.53
556 559 4.713735 TTGAATCTGGGCGCCGCA 62.714 61.111 22.54 18.43 0.00 5.69
575 578 2.938354 CCAAAGGGTCAGCAGAGTG 58.062 57.895 0.00 0.00 0.00 3.51
576 579 0.397941 CCAAAGGGTCAGCAGAGTGA 59.602 55.000 0.00 0.00 0.00 3.41
577 580 1.202806 CCAAAGGGTCAGCAGAGTGAA 60.203 52.381 0.00 0.00 0.00 3.18
578 581 2.575532 CAAAGGGTCAGCAGAGTGAAA 58.424 47.619 0.00 0.00 0.00 2.69
579 582 3.152341 CAAAGGGTCAGCAGAGTGAAAT 58.848 45.455 0.00 0.00 0.00 2.17
580 583 3.515602 AAGGGTCAGCAGAGTGAAATT 57.484 42.857 0.00 0.00 0.00 1.82
581 584 3.515602 AGGGTCAGCAGAGTGAAATTT 57.484 42.857 0.00 0.00 0.00 1.82
582 585 3.837355 AGGGTCAGCAGAGTGAAATTTT 58.163 40.909 0.00 0.00 0.00 1.82
583 586 4.218312 AGGGTCAGCAGAGTGAAATTTTT 58.782 39.130 0.00 0.00 0.00 1.94
609 612 5.247507 TGAACAGGTCAGTTTGTGATTTG 57.752 39.130 0.00 0.00 37.56 2.32
610 613 4.946772 TGAACAGGTCAGTTTGTGATTTGA 59.053 37.500 0.00 0.00 37.56 2.69
650 653 6.506500 AATCTGTGATTTCTGGCTTTACAG 57.493 37.500 0.00 0.00 39.84 2.74
677 680 4.353737 CATCCGTGATTTTGGCAGTAATG 58.646 43.478 2.18 0.00 0.00 1.90
741 758 0.609662 TCGACCGGGGGTAAAAGAAG 59.390 55.000 6.32 0.00 35.25 2.85
743 760 1.002315 CGACCGGGGGTAAAAGAAGAA 59.998 52.381 6.32 0.00 35.25 2.52
744 761 2.708051 GACCGGGGGTAAAAGAAGAAG 58.292 52.381 6.32 0.00 35.25 2.85
745 762 2.303890 GACCGGGGGTAAAAGAAGAAGA 59.696 50.000 6.32 0.00 35.25 2.87
746 763 2.305052 ACCGGGGGTAAAAGAAGAAGAG 59.695 50.000 6.32 0.00 32.11 2.85
747 764 2.355818 CCGGGGGTAAAAGAAGAAGAGG 60.356 54.545 0.00 0.00 0.00 3.69
752 769 5.477291 GGGGGTAAAAGAAGAAGAGGAAAAG 59.523 44.000 0.00 0.00 0.00 2.27
777 794 2.433491 TGAAACCCATCGCCGTCG 60.433 61.111 0.00 0.00 0.00 5.12
852 870 1.755783 CTACGGGCGAGGTTACCCT 60.756 63.158 0.00 0.00 44.63 4.34
924 965 3.512516 GCCGCAAGCATCTCCACC 61.513 66.667 0.00 0.00 42.97 4.61
1016 1062 2.605601 ACACCCACCTACCGTCCC 60.606 66.667 0.00 0.00 0.00 4.46
1017 1063 2.284405 CACCCACCTACCGTCCCT 60.284 66.667 0.00 0.00 0.00 4.20
1020 1066 2.762875 CCACCTACCGTCCCTCCC 60.763 72.222 0.00 0.00 0.00 4.30
1021 1067 2.363361 CACCTACCGTCCCTCCCT 59.637 66.667 0.00 0.00 0.00 4.20
1022 1068 1.757340 CACCTACCGTCCCTCCCTC 60.757 68.421 0.00 0.00 0.00 4.30
1023 1069 2.123382 CCTACCGTCCCTCCCTCC 60.123 72.222 0.00 0.00 0.00 4.30
1024 1070 2.123382 CTACCGTCCCTCCCTCCC 60.123 72.222 0.00 0.00 0.00 4.30
1025 1071 3.752816 CTACCGTCCCTCCCTCCCC 62.753 73.684 0.00 0.00 0.00 4.81
1087 1133 3.700350 CTCACCCTCCCCCTCCCT 61.700 72.222 0.00 0.00 0.00 4.20
1088 1134 3.216371 TCACCCTCCCCCTCCCTT 61.216 66.667 0.00 0.00 0.00 3.95
1089 1135 2.692741 CACCCTCCCCCTCCCTTC 60.693 72.222 0.00 0.00 0.00 3.46
1090 1136 4.040198 ACCCTCCCCCTCCCTTCC 62.040 72.222 0.00 0.00 0.00 3.46
1092 1138 4.416601 CCTCCCCCTCCCTTCCGT 62.417 72.222 0.00 0.00 0.00 4.69
1093 1139 2.764547 CTCCCCCTCCCTTCCGTC 60.765 72.222 0.00 0.00 0.00 4.79
1099 1145 3.391382 CTCCCTTCCGTCCGCCTT 61.391 66.667 0.00 0.00 0.00 4.35
1141 1193 2.665603 GGCCGGTCTCTTCTGCTT 59.334 61.111 1.90 0.00 0.00 3.91
1144 1196 0.739112 GCCGGTCTCTTCTGCTTCTG 60.739 60.000 1.90 0.00 0.00 3.02
1145 1197 0.739112 CCGGTCTCTTCTGCTTCTGC 60.739 60.000 0.00 0.00 40.20 4.26
1146 1198 0.246086 CGGTCTCTTCTGCTTCTGCT 59.754 55.000 0.00 0.00 40.48 4.24
1148 1200 1.405391 GGTCTCTTCTGCTTCTGCTCC 60.405 57.143 0.00 0.00 40.48 4.70
1149 1201 0.529833 TCTCTTCTGCTTCTGCTCCG 59.470 55.000 0.00 0.00 40.48 4.63
1150 1202 0.459934 CTCTTCTGCTTCTGCTCCGG 60.460 60.000 0.00 0.00 40.48 5.14
1151 1203 1.449246 CTTCTGCTTCTGCTCCGGG 60.449 63.158 0.00 0.00 40.48 5.73
1152 1204 1.892819 CTTCTGCTTCTGCTCCGGGA 61.893 60.000 0.00 0.00 40.48 5.14
1153 1205 1.892819 TTCTGCTTCTGCTCCGGGAG 61.893 60.000 19.95 19.95 40.48 4.30
1154 1206 3.382803 CTGCTTCTGCTCCGGGAGG 62.383 68.421 24.81 9.89 44.51 4.30
1502 1572 4.033776 CCGGCAAGGGCAAGGAGA 62.034 66.667 0.00 0.00 43.71 3.71
1527 1597 0.534203 TCCTGTTTCGCCAAGGTGAC 60.534 55.000 1.04 0.00 34.07 3.67
1590 1667 2.409870 GCCGTGCATTAGCCTGCTT 61.410 57.895 0.00 0.00 42.75 3.91
1592 1669 1.226491 CGTGCATTAGCCTGCTTGC 60.226 57.895 8.51 8.51 42.75 4.01
1626 1703 0.377203 GATGACGCCGGAATTTGGTC 59.623 55.000 5.05 2.32 0.00 4.02
1664 1741 1.511768 GGGTCCCGACTCGAAGAAG 59.488 63.158 0.00 0.00 34.09 2.85
1685 1762 2.095718 GTGCAAAATTGAGGACGAGACC 60.096 50.000 0.00 0.00 0.00 3.85
1713 1790 4.787280 AGGTGGAGGAGGAGGCGG 62.787 72.222 0.00 0.00 0.00 6.13
1921 2004 1.884579 ACTCTCGCCGTCTCTTTTACA 59.115 47.619 0.00 0.00 0.00 2.41
1946 2029 5.239306 TGCCTGAATGAAAAGTTGTCAGTAG 59.761 40.000 1.51 0.34 35.07 2.57
1947 2030 5.239525 GCCTGAATGAAAAGTTGTCAGTAGT 59.760 40.000 1.51 0.00 35.07 2.73
1948 2031 6.426937 GCCTGAATGAAAAGTTGTCAGTAGTA 59.573 38.462 1.51 0.00 35.07 1.82
1949 2032 7.571428 GCCTGAATGAAAAGTTGTCAGTAGTAC 60.571 40.741 1.51 0.00 35.07 2.73
1950 2033 7.441157 CCTGAATGAAAAGTTGTCAGTAGTACA 59.559 37.037 1.51 0.00 35.07 2.90
2097 2182 7.056635 CCATCTAGACTGGGAACATAACATTT 58.943 38.462 11.39 0.00 41.51 2.32
2159 2246 9.927668 TGTCTAATTTGAAGAAATTCCCATTTC 57.072 29.630 0.00 0.22 46.20 2.17
2239 2326 1.997669 CAGCAAGTCGAGGTTAGACC 58.002 55.000 0.00 0.00 39.31 3.85
2252 2339 3.143728 GGTTAGACCCGACACACAATTT 58.856 45.455 0.00 0.00 30.04 1.82
2270 2357 5.154932 CAATTTGTCGCGGTACCAAAATAA 58.845 37.500 13.54 0.00 32.39 1.40
2284 2371 5.880341 ACCAAAATAATTTGTAGCTCTCGC 58.120 37.500 2.71 0.00 43.59 5.03
2303 2390 4.369182 TCGCCGAATTCTCTAATCCTTTC 58.631 43.478 3.52 0.00 0.00 2.62
2316 2403 6.698380 TCTAATCCTTTCGCTGTTTTACTCT 58.302 36.000 0.00 0.00 0.00 3.24
2417 2505 3.510388 TGTGAGCTCCAGTTTATCTCG 57.490 47.619 12.15 0.00 0.00 4.04
2418 2506 2.197577 GTGAGCTCCAGTTTATCTCGC 58.802 52.381 12.15 0.00 0.00 5.03
2421 2509 3.056304 GAGCTCCAGTTTATCTCGCATC 58.944 50.000 0.87 0.00 0.00 3.91
2423 2511 3.133721 AGCTCCAGTTTATCTCGCATCTT 59.866 43.478 0.00 0.00 0.00 2.40
2424 2512 3.492756 GCTCCAGTTTATCTCGCATCTTC 59.507 47.826 0.00 0.00 0.00 2.87
2426 2514 4.938080 TCCAGTTTATCTCGCATCTTCTC 58.062 43.478 0.00 0.00 0.00 2.87
2427 2515 3.733224 CCAGTTTATCTCGCATCTTCTCG 59.267 47.826 0.00 0.00 0.00 4.04
2428 2516 3.181377 CAGTTTATCTCGCATCTTCTCGC 59.819 47.826 0.00 0.00 0.00 5.03
2481 2570 8.486210 TCTAACATGCTGTTTCCTCTGTATATT 58.514 33.333 6.82 0.00 41.45 1.28
2499 2588 6.763135 TGTATATTCAGATGAACCAAGCACTC 59.237 38.462 0.00 0.00 36.80 3.51
2589 2678 2.303311 AGACCTTTACCAGTCCTTCAGC 59.697 50.000 0.00 0.00 33.29 4.26
2678 2767 4.465632 ACCCTTTTCAAAAACAGGTGAC 57.534 40.909 4.98 0.00 31.44 3.67
2697 2786 3.068024 TGACTGTTGATTGCCTGGAAAAC 59.932 43.478 0.00 0.00 0.00 2.43
2754 2873 5.608449 TGCATCTGATCCTGATACTCTTTG 58.392 41.667 0.00 0.00 0.00 2.77
2756 2875 4.679373 TCTGATCCTGATACTCTTTGCC 57.321 45.455 0.00 0.00 0.00 4.52
2757 2876 4.293494 TCTGATCCTGATACTCTTTGCCT 58.707 43.478 0.00 0.00 0.00 4.75
2760 2879 4.718774 TGATCCTGATACTCTTTGCCTCTT 59.281 41.667 0.00 0.00 0.00 2.85
2763 2882 5.880901 TCCTGATACTCTTTGCCTCTTTTT 58.119 37.500 0.00 0.00 0.00 1.94
2851 2970 3.564027 GAGAATGCGGGTTCGGCG 61.564 66.667 0.00 0.00 36.79 6.46
2875 2994 4.980434 CCGAATTTCGATGGTTCGTATAGT 59.020 41.667 19.91 0.00 43.74 2.12
2877 2996 5.684184 CGAATTTCGATGGTTCGTATAGTGA 59.316 40.000 13.45 0.00 43.74 3.41
2879 2998 6.823678 ATTTCGATGGTTCGTATAGTGAAC 57.176 37.500 8.60 8.60 45.65 3.18
2880 2999 4.968812 TCGATGGTTCGTATAGTGAACA 57.031 40.909 15.84 6.37 45.86 3.18
2883 3002 5.746721 TCGATGGTTCGTATAGTGAACAATG 59.253 40.000 15.84 8.20 45.86 2.82
2891 3010 6.149633 TCGTATAGTGAACAATGATGGATCG 58.850 40.000 0.00 0.00 0.00 3.69
2933 3052 4.636206 GGTAATTCAGCTTGGACTAACAGG 59.364 45.833 0.00 0.00 0.00 4.00
2947 3075 1.099689 AACAGGTTTGTGTGGTTCGG 58.900 50.000 0.00 0.00 37.67 4.30
2962 3090 1.812686 TTCGGCTTACGCAGGTCAGT 61.813 55.000 0.00 0.00 43.86 3.41
3151 3279 1.418342 CGAATGGTACCAAGACGGCG 61.418 60.000 20.76 4.80 39.03 6.46
3171 3299 1.718280 GGGATCGGGGACACTAGAAT 58.282 55.000 0.00 0.00 0.00 2.40
3179 3307 2.777692 GGGGACACTAGAATGAATCCCA 59.222 50.000 9.26 0.00 46.58 4.37
3196 3324 1.139853 CCCAGCTGAACTACCATCCTC 59.860 57.143 17.39 0.00 0.00 3.71
3197 3325 2.114616 CCAGCTGAACTACCATCCTCT 58.885 52.381 17.39 0.00 0.00 3.69
3198 3326 2.102252 CCAGCTGAACTACCATCCTCTC 59.898 54.545 17.39 0.00 0.00 3.20
3216 3344 4.322349 CCTCTCCTTGATTCTTCTCGTGTT 60.322 45.833 0.00 0.00 0.00 3.32
3382 3513 4.013050 TGTCGTGGAAATGGCAATTATGA 58.987 39.130 0.00 0.00 0.00 2.15
3389 3520 8.296000 CGTGGAAATGGCAATTATGAACATATA 58.704 33.333 0.00 0.00 0.00 0.86
3443 3679 8.028354 TGTATTGTTTTACAGCTCAATGATTGG 58.972 33.333 5.20 0.00 33.48 3.16
3471 3707 5.699839 CCAAATTACAGTTAAGTGGTGCTC 58.300 41.667 14.69 0.00 0.00 4.26
3502 3738 3.402110 TCATCAATCACAGCGAACAGTT 58.598 40.909 0.00 0.00 0.00 3.16
3507 3743 4.211164 TCAATCACAGCGAACAGTTACTTG 59.789 41.667 0.00 0.00 0.00 3.16
3551 3788 4.919168 TGTTCACTCATTTCGGTACTTACG 59.081 41.667 0.00 0.00 0.00 3.18
3587 3825 5.529581 TCACAGTGAACAGTGACTTATCA 57.470 39.130 15.25 0.00 37.44 2.15
3602 3840 6.504398 TGACTTATCACCAGCTATAAGTTCG 58.496 40.000 16.90 0.00 44.81 3.95
3611 3849 8.297426 TCACCAGCTATAAGTTCGTAATAGATG 58.703 37.037 2.85 2.85 38.64 2.90
3629 3872 4.768583 AGATGCTCTCTCCTTTCAACATC 58.231 43.478 0.00 0.00 34.32 3.06
3765 4010 0.396811 AAACAGTGAACGGAGGGAGG 59.603 55.000 0.00 0.00 0.00 4.30
3766 4011 1.481056 AACAGTGAACGGAGGGAGGG 61.481 60.000 0.00 0.00 0.00 4.30
3767 4012 1.913762 CAGTGAACGGAGGGAGGGT 60.914 63.158 0.00 0.00 0.00 4.34
3768 4013 0.613853 CAGTGAACGGAGGGAGGGTA 60.614 60.000 0.00 0.00 0.00 3.69
3769 4014 0.324460 AGTGAACGGAGGGAGGGTAG 60.324 60.000 0.00 0.00 0.00 3.18
3771 4016 1.002069 TGAACGGAGGGAGGGTAGTA 58.998 55.000 0.00 0.00 0.00 1.82
3774 4019 0.469518 ACGGAGGGAGGGTAGTATGC 60.470 60.000 0.00 0.00 0.00 3.14
3804 4055 6.183360 TGCAGTTGTTGGAACCTTTTAATCAT 60.183 34.615 0.00 0.00 0.00 2.45
3805 4056 6.366061 GCAGTTGTTGGAACCTTTTAATCATC 59.634 38.462 0.00 0.00 0.00 2.92
3806 4057 7.432869 CAGTTGTTGGAACCTTTTAATCATCA 58.567 34.615 0.00 0.00 0.00 3.07
3807 4058 8.090214 CAGTTGTTGGAACCTTTTAATCATCAT 58.910 33.333 0.00 0.00 0.00 2.45
3808 4059 8.306761 AGTTGTTGGAACCTTTTAATCATCATC 58.693 33.333 0.00 0.00 0.00 2.92
3809 4060 7.773489 TGTTGGAACCTTTTAATCATCATCA 57.227 32.000 0.00 0.00 0.00 3.07
3810 4061 8.365060 TGTTGGAACCTTTTAATCATCATCAT 57.635 30.769 0.00 0.00 0.00 2.45
3811 4062 8.469200 TGTTGGAACCTTTTAATCATCATCATC 58.531 33.333 0.00 0.00 0.00 2.92
3812 4063 8.469200 GTTGGAACCTTTTAATCATCATCATCA 58.531 33.333 0.00 0.00 0.00 3.07
3840 4110 6.298361 TCAGAAACTCTCATTTCACCATCAA 58.702 36.000 1.47 0.00 40.43 2.57
3843 4113 6.718454 AGAAACTCTCATTTCACCATCAACAT 59.282 34.615 1.47 0.00 40.43 2.71
3845 4115 5.563592 ACTCTCATTTCACCATCAACATCA 58.436 37.500 0.00 0.00 0.00 3.07
3846 4116 5.413833 ACTCTCATTTCACCATCAACATCAC 59.586 40.000 0.00 0.00 0.00 3.06
3847 4117 4.701651 TCTCATTTCACCATCAACATCACC 59.298 41.667 0.00 0.00 0.00 4.02
3848 4118 4.405548 TCATTTCACCATCAACATCACCA 58.594 39.130 0.00 0.00 0.00 4.17
3849 4119 5.018149 TCATTTCACCATCAACATCACCAT 58.982 37.500 0.00 0.00 0.00 3.55
3850 4120 5.481122 TCATTTCACCATCAACATCACCATT 59.519 36.000 0.00 0.00 0.00 3.16
3851 4121 5.389859 TTTCACCATCAACATCACCATTC 57.610 39.130 0.00 0.00 0.00 2.67
3852 4122 4.031636 TCACCATCAACATCACCATTCA 57.968 40.909 0.00 0.00 0.00 2.57
3853 4123 3.758023 TCACCATCAACATCACCATTCAC 59.242 43.478 0.00 0.00 0.00 3.18
3854 4124 3.091545 ACCATCAACATCACCATTCACC 58.908 45.455 0.00 0.00 0.00 4.02
3855 4125 3.090790 CCATCAACATCACCATTCACCA 58.909 45.455 0.00 0.00 0.00 4.17
3856 4126 3.129813 CCATCAACATCACCATTCACCAG 59.870 47.826 0.00 0.00 0.00 4.00
3857 4127 2.161855 TCAACATCACCATTCACCAGC 58.838 47.619 0.00 0.00 0.00 4.85
3858 4128 1.887854 CAACATCACCATTCACCAGCA 59.112 47.619 0.00 0.00 0.00 4.41
3859 4129 1.830279 ACATCACCATTCACCAGCAG 58.170 50.000 0.00 0.00 0.00 4.24
3860 4130 0.454600 CATCACCATTCACCAGCAGC 59.545 55.000 0.00 0.00 0.00 5.25
3861 4131 0.330604 ATCACCATTCACCAGCAGCT 59.669 50.000 0.00 0.00 0.00 4.24
3885 4156 4.226846 AGCATCCCTTCTTTTCTGAGATGA 59.773 41.667 0.00 0.00 33.16 2.92
3886 4157 4.575645 GCATCCCTTCTTTTCTGAGATGAG 59.424 45.833 0.00 0.00 33.16 2.90
3887 4158 5.628666 GCATCCCTTCTTTTCTGAGATGAGA 60.629 44.000 0.00 0.00 33.16 3.27
3888 4159 6.593807 CATCCCTTCTTTTCTGAGATGAGAT 58.406 40.000 0.00 0.00 33.16 2.75
3889 4160 5.987098 TCCCTTCTTTTCTGAGATGAGATG 58.013 41.667 0.00 0.00 0.00 2.90
3890 4161 5.104610 TCCCTTCTTTTCTGAGATGAGATGG 60.105 44.000 15.01 15.01 33.68 3.51
3891 4162 5.104610 CCCTTCTTTTCTGAGATGAGATGGA 60.105 44.000 19.90 0.03 35.04 3.41
3917 4188 2.030893 CACATCACATTTTCACCTGCGT 60.031 45.455 0.00 0.00 0.00 5.24
3919 4190 3.818210 ACATCACATTTTCACCTGCGTAA 59.182 39.130 0.00 0.00 0.00 3.18
3934 4205 2.900122 CGTAAGCAGAAATGGTGGTG 57.100 50.000 0.00 0.00 0.00 4.17
3943 4214 4.323417 CAGAAATGGTGGTGCTAGTTACA 58.677 43.478 0.00 0.00 0.00 2.41
3944 4215 4.393062 CAGAAATGGTGGTGCTAGTTACAG 59.607 45.833 0.00 0.00 0.00 2.74
3946 4217 0.323629 TGGTGGTGCTAGTTACAGCC 59.676 55.000 8.61 6.81 41.04 4.85
3947 4218 0.739813 GGTGGTGCTAGTTACAGCCG 60.740 60.000 4.82 0.00 41.04 5.52
3948 4219 0.739813 GTGGTGCTAGTTACAGCCGG 60.740 60.000 0.00 0.00 41.04 6.13
3949 4220 1.189524 TGGTGCTAGTTACAGCCGGT 61.190 55.000 1.90 0.00 41.04 5.28
3950 4221 0.739813 GGTGCTAGTTACAGCCGGTG 60.740 60.000 1.90 2.53 41.04 4.94
3963 4234 1.007502 CCGGTGGTTGTTGCATGTG 60.008 57.895 0.00 0.00 0.00 3.21
3964 4235 1.007502 CGGTGGTTGTTGCATGTGG 60.008 57.895 0.00 0.00 0.00 4.17
4060 4331 2.753296 CTCTCCGCTGGATCTCATTTC 58.247 52.381 0.00 0.00 0.00 2.17
4064 4335 2.628178 TCCGCTGGATCTCATTTCGTAT 59.372 45.455 0.00 0.00 0.00 3.06
4065 4336 2.989840 CCGCTGGATCTCATTTCGTATC 59.010 50.000 0.00 0.00 0.00 2.24
4066 4337 2.989840 CGCTGGATCTCATTTCGTATCC 59.010 50.000 0.00 0.00 38.71 2.59
4067 4338 2.989840 GCTGGATCTCATTTCGTATCCG 59.010 50.000 0.00 0.00 40.71 4.18
4068 4339 3.553096 GCTGGATCTCATTTCGTATCCGT 60.553 47.826 0.00 0.00 40.71 4.69
4069 4340 4.230657 CTGGATCTCATTTCGTATCCGTC 58.769 47.826 0.00 0.00 40.71 4.79
4070 4341 3.005472 TGGATCTCATTTCGTATCCGTCC 59.995 47.826 0.00 0.00 40.71 4.79
4071 4342 3.005472 GGATCTCATTTCGTATCCGTCCA 59.995 47.826 0.00 0.00 35.01 4.02
4072 4343 4.322049 GGATCTCATTTCGTATCCGTCCAT 60.322 45.833 0.00 0.00 35.01 3.41
4073 4344 3.977427 TCTCATTTCGTATCCGTCCATG 58.023 45.455 0.00 0.00 35.01 3.66
4074 4345 3.634910 TCTCATTTCGTATCCGTCCATGA 59.365 43.478 0.00 0.00 35.01 3.07
4075 4346 3.713288 TCATTTCGTATCCGTCCATGAC 58.287 45.455 0.00 0.00 35.01 3.06
4076 4347 2.589798 TTTCGTATCCGTCCATGACC 57.410 50.000 0.00 0.00 35.01 4.02
4077 4348 1.476477 TTCGTATCCGTCCATGACCA 58.524 50.000 0.00 0.00 35.01 4.02
4078 4349 1.699730 TCGTATCCGTCCATGACCAT 58.300 50.000 0.00 0.00 35.01 3.55
4079 4350 1.339929 TCGTATCCGTCCATGACCATG 59.660 52.381 0.00 3.11 35.59 3.66
4080 4351 1.068588 CGTATCCGTCCATGACCATGT 59.931 52.381 8.93 0.00 37.11 3.21
4081 4352 2.755650 GTATCCGTCCATGACCATGTC 58.244 52.381 8.93 0.00 37.11 3.06
4082 4353 1.203237 ATCCGTCCATGACCATGTCA 58.797 50.000 8.93 0.00 46.90 3.58
4091 4362 0.541392 TGACCATGTCATCCCTTCCG 59.459 55.000 0.00 0.00 37.67 4.30
4092 4363 0.815615 GACCATGTCATCCCTTCCGC 60.816 60.000 0.00 0.00 32.09 5.54
4093 4364 1.526917 CCATGTCATCCCTTCCGCC 60.527 63.158 0.00 0.00 0.00 6.13
4094 4365 1.889105 CATGTCATCCCTTCCGCCG 60.889 63.158 0.00 0.00 0.00 6.46
4095 4366 3.757248 ATGTCATCCCTTCCGCCGC 62.757 63.158 0.00 0.00 0.00 6.53
4110 4381 3.490759 CGCGCCACCTTGCAGTAG 61.491 66.667 0.00 0.00 0.00 2.57
4111 4382 2.358737 GCGCCACCTTGCAGTAGT 60.359 61.111 0.00 0.00 0.00 2.73
4112 4383 1.079405 GCGCCACCTTGCAGTAGTA 60.079 57.895 0.00 0.00 0.00 1.82
4113 4384 1.084370 GCGCCACCTTGCAGTAGTAG 61.084 60.000 0.00 0.00 0.00 2.57
4114 4385 0.246635 CGCCACCTTGCAGTAGTAGT 59.753 55.000 0.00 0.00 0.00 2.73
4115 4386 1.726853 GCCACCTTGCAGTAGTAGTG 58.273 55.000 0.17 0.17 0.00 2.74
4116 4387 1.002087 GCCACCTTGCAGTAGTAGTGT 59.998 52.381 6.84 0.00 0.00 3.55
4117 4388 2.931320 GCCACCTTGCAGTAGTAGTGTC 60.931 54.545 6.84 0.54 0.00 3.67
4118 4389 2.353803 CCACCTTGCAGTAGTAGTGTCC 60.354 54.545 6.84 0.00 0.00 4.02
4119 4390 2.299013 CACCTTGCAGTAGTAGTGTCCA 59.701 50.000 6.84 0.00 0.00 4.02
4120 4391 2.563179 ACCTTGCAGTAGTAGTGTCCAG 59.437 50.000 6.84 1.16 0.00 3.86
4121 4392 2.611518 CTTGCAGTAGTAGTGTCCAGC 58.388 52.381 6.84 0.00 0.00 4.85
4122 4393 1.924731 TGCAGTAGTAGTGTCCAGCT 58.075 50.000 6.84 0.00 0.00 4.24
4123 4394 2.248248 TGCAGTAGTAGTGTCCAGCTT 58.752 47.619 6.84 0.00 0.00 3.74
4124 4395 2.632996 TGCAGTAGTAGTGTCCAGCTTT 59.367 45.455 6.84 0.00 0.00 3.51
4125 4396 3.071023 TGCAGTAGTAGTGTCCAGCTTTT 59.929 43.478 6.84 0.00 0.00 2.27
4126 4397 3.433615 GCAGTAGTAGTGTCCAGCTTTTG 59.566 47.826 6.84 0.00 0.00 2.44
4127 4398 4.632153 CAGTAGTAGTGTCCAGCTTTTGT 58.368 43.478 0.00 0.00 0.00 2.83
4128 4399 5.057149 CAGTAGTAGTGTCCAGCTTTTGTT 58.943 41.667 0.00 0.00 0.00 2.83
4129 4400 6.220930 CAGTAGTAGTGTCCAGCTTTTGTTA 58.779 40.000 0.00 0.00 0.00 2.41
4130 4401 6.704493 CAGTAGTAGTGTCCAGCTTTTGTTAA 59.296 38.462 0.00 0.00 0.00 2.01
4131 4402 7.225931 CAGTAGTAGTGTCCAGCTTTTGTTAAA 59.774 37.037 0.00 0.00 0.00 1.52
4132 4403 7.771826 AGTAGTAGTGTCCAGCTTTTGTTAAAA 59.228 33.333 0.00 0.00 0.00 1.52
4133 4404 7.582667 AGTAGTGTCCAGCTTTTGTTAAAAT 57.417 32.000 0.00 0.00 0.00 1.82
4134 4405 8.685838 AGTAGTGTCCAGCTTTTGTTAAAATA 57.314 30.769 0.00 0.00 0.00 1.40
4135 4406 9.127277 AGTAGTGTCCAGCTTTTGTTAAAATAA 57.873 29.630 0.00 0.00 0.00 1.40
4136 4407 9.908152 GTAGTGTCCAGCTTTTGTTAAAATAAT 57.092 29.630 0.00 0.00 0.00 1.28
4173 4444 9.939802 TCTTCATAAAGTTTAGTTTCTACTCCC 57.060 33.333 1.21 0.00 33.57 4.30
4174 4445 9.945904 CTTCATAAAGTTTAGTTTCTACTCCCT 57.054 33.333 1.21 0.00 35.78 4.20
4175 4446 9.939802 TTCATAAAGTTTAGTTTCTACTCCCTC 57.060 33.333 1.21 0.00 35.78 4.30
4176 4447 8.537858 TCATAAAGTTTAGTTTCTACTCCCTCC 58.462 37.037 1.21 0.00 35.78 4.30
4177 4448 5.402997 AAGTTTAGTTTCTACTCCCTCCG 57.597 43.478 0.00 0.00 35.78 4.63
4178 4449 4.414677 AGTTTAGTTTCTACTCCCTCCGT 58.585 43.478 0.00 0.00 35.78 4.69
4179 4450 4.462132 AGTTTAGTTTCTACTCCCTCCGTC 59.538 45.833 0.00 0.00 35.78 4.79
4180 4451 1.849977 AGTTTCTACTCCCTCCGTCC 58.150 55.000 0.00 0.00 0.00 4.79
4181 4452 0.822811 GTTTCTACTCCCTCCGTCCC 59.177 60.000 0.00 0.00 0.00 4.46
4182 4453 0.410663 TTTCTACTCCCTCCGTCCCA 59.589 55.000 0.00 0.00 0.00 4.37
4183 4454 0.635009 TTCTACTCCCTCCGTCCCAT 59.365 55.000 0.00 0.00 0.00 4.00
4184 4455 1.526315 TCTACTCCCTCCGTCCCATA 58.474 55.000 0.00 0.00 0.00 2.74
4185 4456 1.424302 TCTACTCCCTCCGTCCCATAG 59.576 57.143 0.00 0.00 0.00 2.23
4186 4457 0.178970 TACTCCCTCCGTCCCATAGC 60.179 60.000 0.00 0.00 0.00 2.97
4187 4458 2.520982 TCCCTCCGTCCCATAGCG 60.521 66.667 0.00 0.00 0.00 4.26
4188 4459 2.838225 CCCTCCGTCCCATAGCGT 60.838 66.667 0.00 0.00 0.00 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 174 5.127682 TCAGATCTGAAGATTTGATCCGTGA 59.872 40.000 23.17 0.00 39.71 4.35
557 560 0.397941 TCACTCTGCTGACCCTTTGG 59.602 55.000 0.00 0.00 37.80 3.28
558 561 2.260844 TTCACTCTGCTGACCCTTTG 57.739 50.000 0.00 0.00 0.00 2.77
559 562 3.515602 ATTTCACTCTGCTGACCCTTT 57.484 42.857 0.00 0.00 0.00 3.11
560 563 3.515602 AATTTCACTCTGCTGACCCTT 57.484 42.857 0.00 0.00 0.00 3.95
561 564 3.515602 AAATTTCACTCTGCTGACCCT 57.484 42.857 0.00 0.00 0.00 4.34
562 565 4.590850 AAAAATTTCACTCTGCTGACCC 57.409 40.909 0.00 0.00 0.00 4.46
587 590 4.946772 TCAAATCACAAACTGACCTGTTCA 59.053 37.500 0.00 0.00 0.00 3.18
588 591 5.499139 TCAAATCACAAACTGACCTGTTC 57.501 39.130 0.00 0.00 0.00 3.18
589 592 6.469782 AATCAAATCACAAACTGACCTGTT 57.530 33.333 0.00 0.00 0.00 3.16
590 593 6.322201 AGAAATCAAATCACAAACTGACCTGT 59.678 34.615 0.00 0.00 0.00 4.00
591 594 6.639686 CAGAAATCAAATCACAAACTGACCTG 59.360 38.462 0.00 0.00 0.00 4.00
592 595 6.736794 GCAGAAATCAAATCACAAACTGACCT 60.737 38.462 0.00 0.00 0.00 3.85
593 596 5.403466 GCAGAAATCAAATCACAAACTGACC 59.597 40.000 0.00 0.00 0.00 4.02
594 597 5.403466 GGCAGAAATCAAATCACAAACTGAC 59.597 40.000 0.00 0.00 0.00 3.51
595 598 5.302568 AGGCAGAAATCAAATCACAAACTGA 59.697 36.000 0.00 0.00 0.00 3.41
596 599 5.535333 AGGCAGAAATCAAATCACAAACTG 58.465 37.500 0.00 0.00 0.00 3.16
597 600 5.302568 TGAGGCAGAAATCAAATCACAAACT 59.697 36.000 0.00 0.00 0.00 2.66
598 601 5.531634 TGAGGCAGAAATCAAATCACAAAC 58.468 37.500 0.00 0.00 0.00 2.93
599 602 5.279106 CCTGAGGCAGAAATCAAATCACAAA 60.279 40.000 0.00 0.00 32.44 2.83
600 603 4.219070 CCTGAGGCAGAAATCAAATCACAA 59.781 41.667 0.00 0.00 32.44 3.33
601 604 3.760151 CCTGAGGCAGAAATCAAATCACA 59.240 43.478 0.00 0.00 32.44 3.58
602 605 3.760684 ACCTGAGGCAGAAATCAAATCAC 59.239 43.478 0.00 0.00 32.44 3.06
603 606 4.012374 GACCTGAGGCAGAAATCAAATCA 58.988 43.478 0.00 0.00 32.44 2.57
604 607 4.012374 TGACCTGAGGCAGAAATCAAATC 58.988 43.478 0.00 0.00 32.44 2.17
605 608 4.038271 TGACCTGAGGCAGAAATCAAAT 57.962 40.909 0.00 0.00 32.44 2.32
606 609 3.507162 TGACCTGAGGCAGAAATCAAA 57.493 42.857 0.00 0.00 32.44 2.69
607 610 3.507162 TTGACCTGAGGCAGAAATCAA 57.493 42.857 0.00 0.00 32.44 2.57
608 611 3.507162 TTTGACCTGAGGCAGAAATCA 57.493 42.857 0.00 0.00 32.44 2.57
609 612 4.096081 CAGATTTGACCTGAGGCAGAAATC 59.904 45.833 16.71 16.71 34.90 2.17
610 613 4.015084 CAGATTTGACCTGAGGCAGAAAT 58.985 43.478 0.00 0.18 32.44 2.17
650 653 1.102978 CCAAAATCACGGATGGGGTC 58.897 55.000 0.00 0.00 0.00 4.46
726 743 2.355818 CCTCTTCTTCTTTTACCCCCGG 60.356 54.545 0.00 0.00 0.00 5.73
741 758 3.991367 TCACGGTTCTCTTTTCCTCTTC 58.009 45.455 0.00 0.00 0.00 2.87
743 760 4.127907 GTTTCACGGTTCTCTTTTCCTCT 58.872 43.478 0.00 0.00 0.00 3.69
744 761 3.250280 GGTTTCACGGTTCTCTTTTCCTC 59.750 47.826 0.00 0.00 0.00 3.71
745 762 3.211865 GGTTTCACGGTTCTCTTTTCCT 58.788 45.455 0.00 0.00 0.00 3.36
746 763 2.292569 GGGTTTCACGGTTCTCTTTTCC 59.707 50.000 0.00 0.00 0.00 3.13
747 764 2.946990 TGGGTTTCACGGTTCTCTTTTC 59.053 45.455 0.00 0.00 0.00 2.29
752 769 1.076332 CGATGGGTTTCACGGTTCTC 58.924 55.000 0.00 0.00 0.00 2.87
1087 1133 2.358247 GAAGCAAGGCGGACGGAA 60.358 61.111 0.00 0.00 0.00 4.30
1088 1134 4.388499 GGAAGCAAGGCGGACGGA 62.388 66.667 0.00 0.00 0.00 4.69
1089 1135 3.901797 AAGGAAGCAAGGCGGACGG 62.902 63.158 0.00 0.00 0.00 4.79
1090 1136 2.358737 AAGGAAGCAAGGCGGACG 60.359 61.111 0.00 0.00 0.00 4.79
1091 1137 2.041115 GGAAGGAAGCAAGGCGGAC 61.041 63.158 0.00 0.00 0.00 4.79
1092 1138 2.224159 AGGAAGGAAGCAAGGCGGA 61.224 57.895 0.00 0.00 0.00 5.54
1093 1139 2.042831 CAGGAAGGAAGCAAGGCGG 61.043 63.158 0.00 0.00 0.00 6.13
1096 1142 2.694760 GCGCAGGAAGGAAGCAAGG 61.695 63.158 0.30 0.00 0.00 3.61
1098 1144 0.895100 ATTGCGCAGGAAGGAAGCAA 60.895 50.000 11.31 3.64 44.16 3.91
1099 1145 1.303561 ATTGCGCAGGAAGGAAGCA 60.304 52.632 11.31 0.00 44.16 3.91
1527 1597 5.593679 ATTGAAATCCATGGAGCAAGAAG 57.406 39.130 21.33 0.00 0.00 2.85
1586 1663 1.375908 CGGCTAGAACCAGCAAGCA 60.376 57.895 0.00 0.00 43.67 3.91
1590 1667 1.134699 CATCTTCGGCTAGAACCAGCA 60.135 52.381 0.00 0.00 43.67 4.41
1592 1669 2.796383 CGTCATCTTCGGCTAGAACCAG 60.796 54.545 0.00 0.00 34.66 4.00
1626 1703 2.108566 CGGCTCTCCCATCTGCAG 59.891 66.667 7.63 7.63 0.00 4.41
1664 1741 2.095718 GGTCTCGTCCTCAATTTTGCAC 60.096 50.000 0.00 0.00 0.00 4.57
1685 1762 3.612247 CTCCACCTTGGGCCTCACG 62.612 68.421 4.53 0.00 38.32 4.35
1921 2004 4.586001 ACTGACAACTTTTCATTCAGGCAT 59.414 37.500 0.00 0.00 38.42 4.40
1959 2042 0.110056 CACAATTGAGGACAGCGTGC 60.110 55.000 13.59 0.00 0.00 5.34
2077 2160 7.504238 ACACAAAAATGTTATGTTCCCAGTCTA 59.496 33.333 0.00 0.00 0.00 2.59
2159 2246 0.099436 GCGCTTTGCCAATCACCTAG 59.901 55.000 0.00 0.00 37.76 3.02
2252 2339 4.215827 ACAAATTATTTTGGTACCGCGACA 59.784 37.500 8.23 0.00 45.34 4.35
2256 2343 5.886992 AGCTACAAATTATTTTGGTACCGC 58.113 37.500 7.57 0.00 45.34 5.68
2284 2371 4.210120 CAGCGAAAGGATTAGAGAATTCGG 59.790 45.833 0.00 0.00 39.81 4.30
2303 2390 6.049263 AGAACTGAAAAGAGTAAAACAGCG 57.951 37.500 0.00 0.00 0.00 5.18
2316 2403 4.889409 AGCTTCATGGACAAGAACTGAAAA 59.111 37.500 0.00 0.00 0.00 2.29
2406 2494 3.181377 GCGAGAAGATGCGAGATAAACTG 59.819 47.826 0.00 0.00 0.00 3.16
2417 2505 1.061570 CCAAAGCGCGAGAAGATGC 59.938 57.895 12.10 0.00 0.00 3.91
2418 2506 1.061570 GCCAAAGCGCGAGAAGATG 59.938 57.895 12.10 0.00 0.00 2.90
2421 2509 0.458543 TAGAGCCAAAGCGCGAGAAG 60.459 55.000 12.10 0.00 44.54 2.85
2423 2511 0.528466 CATAGAGCCAAAGCGCGAGA 60.528 55.000 12.10 0.00 44.54 4.04
2424 2512 0.528466 TCATAGAGCCAAAGCGCGAG 60.528 55.000 12.10 0.00 44.54 5.03
2426 2514 0.726827 TTTCATAGAGCCAAAGCGCG 59.273 50.000 0.00 0.00 44.54 6.86
2427 2515 1.468520 TGTTTCATAGAGCCAAAGCGC 59.531 47.619 0.00 0.00 46.67 5.92
2428 2516 3.829886 TTGTTTCATAGAGCCAAAGCG 57.170 42.857 0.00 0.00 46.67 4.68
2481 2570 1.338105 CCGAGTGCTTGGTTCATCTGA 60.338 52.381 0.00 0.00 0.00 3.27
2589 2678 0.105039 GGTTCTCCATAGCACCCGAG 59.895 60.000 0.00 0.00 33.30 4.63
2678 2767 3.645884 CAGTTTTCCAGGCAATCAACAG 58.354 45.455 0.00 0.00 0.00 3.16
2763 2882 3.822735 CCAGAAATCCTGTTGCTGAGAAA 59.177 43.478 0.00 0.00 41.33 2.52
2773 2892 0.909610 TCGCCTCCCAGAAATCCTGT 60.910 55.000 0.00 0.00 41.33 4.00
2806 2925 0.882042 GCTCGTGGTCCATATGCAGG 60.882 60.000 0.00 0.00 0.00 4.85
2875 2994 3.346315 AGCAACGATCCATCATTGTTCA 58.654 40.909 0.00 0.00 37.03 3.18
2877 2996 3.674138 GCAAGCAACGATCCATCATTGTT 60.674 43.478 0.00 0.00 39.43 2.83
2879 2998 2.098607 AGCAAGCAACGATCCATCATTG 59.901 45.455 0.00 0.00 33.51 2.82
2880 2999 2.098607 CAGCAAGCAACGATCCATCATT 59.901 45.455 0.00 0.00 0.00 2.57
2883 3002 0.248377 GCAGCAAGCAACGATCCATC 60.248 55.000 0.00 0.00 44.79 3.51
2933 3052 1.333435 CGTAAGCCGAACCACACAAAC 60.333 52.381 0.00 0.00 39.56 2.93
2962 3090 3.198417 TCTGGATGATCTGCTGCTTGTAA 59.802 43.478 0.00 0.00 0.00 2.41
3151 3279 0.398098 TTCTAGTGTCCCCGATCCCC 60.398 60.000 0.00 0.00 0.00 4.81
3171 3299 2.265367 TGGTAGTTCAGCTGGGATTCA 58.735 47.619 15.13 3.30 0.00 2.57
3179 3307 2.023501 AGGAGAGGATGGTAGTTCAGCT 60.024 50.000 0.00 0.00 0.00 4.24
3196 3324 4.560128 TCAACACGAGAAGAATCAAGGAG 58.440 43.478 0.00 0.00 0.00 3.69
3197 3325 4.600692 TCAACACGAGAAGAATCAAGGA 57.399 40.909 0.00 0.00 0.00 3.36
3198 3326 4.931601 TCATCAACACGAGAAGAATCAAGG 59.068 41.667 0.00 0.00 0.00 3.61
3294 3424 3.195661 GCCGAGTTCTTACACATTAGGG 58.804 50.000 0.00 0.00 0.00 3.53
3433 3669 1.304796 TTGGCGGCCCAATCATTGA 60.305 52.632 17.97 0.00 46.01 2.57
3443 3679 2.490509 ACTTAACTGTAATTTGGCGGCC 59.509 45.455 13.32 13.32 0.00 6.13
3502 3738 3.676172 CGCTAAACCGTGATTGACAAGTA 59.324 43.478 0.00 0.00 0.00 2.24
3551 3788 2.163010 CACTGTGATTGGTGAGCATTCC 59.837 50.000 0.32 0.00 35.69 3.01
3587 3825 7.039644 AGCATCTATTACGAACTTATAGCTGGT 60.040 37.037 0.00 0.00 29.15 4.00
3611 3849 6.344500 TCTTATGATGTTGAAAGGAGAGAGC 58.656 40.000 0.00 0.00 0.00 4.09
3652 3896 9.042008 GCGTCTATATACTTTCAATTCAGGAAA 57.958 33.333 0.00 0.00 33.52 3.13
3653 3897 7.381408 CGCGTCTATATACTTTCAATTCAGGAA 59.619 37.037 0.00 0.00 0.00 3.36
3654 3898 6.861572 CGCGTCTATATACTTTCAATTCAGGA 59.138 38.462 0.00 0.00 0.00 3.86
3655 3899 6.641314 ACGCGTCTATATACTTTCAATTCAGG 59.359 38.462 5.58 0.00 0.00 3.86
3732 3977 5.728351 TCACTGTTTAAAGACGTTTCAGG 57.272 39.130 0.00 0.00 0.00 3.86
3745 3990 1.621814 CCTCCCTCCGTTCACTGTTTA 59.378 52.381 0.00 0.00 0.00 2.01
3784 4035 8.187913 TGATGATGATTAAAAGGTTCCAACAA 57.812 30.769 0.00 0.00 0.00 2.83
3804 4055 7.120923 TGAGAGTTTCTGATGATGATGATGA 57.879 36.000 0.00 0.00 0.00 2.92
3805 4056 7.971183 ATGAGAGTTTCTGATGATGATGATG 57.029 36.000 0.00 0.00 0.00 3.07
3806 4057 8.982091 AAATGAGAGTTTCTGATGATGATGAT 57.018 30.769 0.00 0.00 0.00 2.45
3807 4058 8.044908 TGAAATGAGAGTTTCTGATGATGATGA 58.955 33.333 0.00 0.00 38.58 2.92
3808 4059 8.123575 GTGAAATGAGAGTTTCTGATGATGATG 58.876 37.037 0.00 0.00 38.58 3.07
3809 4060 7.282675 GGTGAAATGAGAGTTTCTGATGATGAT 59.717 37.037 0.00 0.00 38.58 2.45
3810 4061 6.596888 GGTGAAATGAGAGTTTCTGATGATGA 59.403 38.462 0.00 0.00 38.58 2.92
3811 4062 6.373495 TGGTGAAATGAGAGTTTCTGATGATG 59.627 38.462 0.00 0.00 38.58 3.07
3812 4063 6.479006 TGGTGAAATGAGAGTTTCTGATGAT 58.521 36.000 0.00 0.00 38.58 2.45
3840 4110 1.830279 CTGCTGGTGAATGGTGATGT 58.170 50.000 0.00 0.00 0.00 3.06
3843 4113 0.983467 TAGCTGCTGGTGAATGGTGA 59.017 50.000 13.43 0.00 0.00 4.02
3845 4115 0.393537 GCTAGCTGCTGGTGAATGGT 60.394 55.000 13.43 0.00 38.95 3.55
3846 4116 0.393402 TGCTAGCTGCTGGTGAATGG 60.393 55.000 17.23 0.00 43.37 3.16
3847 4117 1.602851 GATGCTAGCTGCTGGTGAATG 59.397 52.381 17.23 0.00 43.37 2.67
3848 4118 1.476471 GGATGCTAGCTGCTGGTGAAT 60.476 52.381 17.23 5.12 43.37 2.57
3849 4119 0.107508 GGATGCTAGCTGCTGGTGAA 60.108 55.000 17.23 0.00 43.37 3.18
3850 4120 1.524002 GGATGCTAGCTGCTGGTGA 59.476 57.895 17.23 0.62 43.37 4.02
3851 4121 1.525535 GGGATGCTAGCTGCTGGTG 60.526 63.158 17.23 3.64 43.37 4.17
3852 4122 1.277580 AAGGGATGCTAGCTGCTGGT 61.278 55.000 17.23 0.00 43.37 4.00
3853 4123 0.534652 GAAGGGATGCTAGCTGCTGG 60.535 60.000 17.23 11.05 43.37 4.85
3854 4124 0.469070 AGAAGGGATGCTAGCTGCTG 59.531 55.000 17.23 3.55 43.37 4.41
3855 4125 1.211456 AAGAAGGGATGCTAGCTGCT 58.789 50.000 17.23 7.57 43.37 4.24
3856 4126 2.049888 AAAGAAGGGATGCTAGCTGC 57.950 50.000 17.23 7.56 43.25 5.25
3857 4127 3.626670 CAGAAAAGAAGGGATGCTAGCTG 59.373 47.826 17.23 0.00 0.00 4.24
3858 4128 3.521126 TCAGAAAAGAAGGGATGCTAGCT 59.479 43.478 17.23 0.83 0.00 3.32
3859 4129 3.876320 CTCAGAAAAGAAGGGATGCTAGC 59.124 47.826 8.10 8.10 0.00 3.42
3860 4130 5.350504 TCTCAGAAAAGAAGGGATGCTAG 57.649 43.478 0.00 0.00 0.00 3.42
3861 4131 5.426509 TCATCTCAGAAAAGAAGGGATGCTA 59.573 40.000 0.00 0.00 32.03 3.49
3867 4137 5.104610 TCCATCTCATCTCAGAAAAGAAGGG 60.105 44.000 9.78 7.38 0.00 3.95
3888 4159 4.278170 GTGAAAATGTGATGTGGAGTTCCA 59.722 41.667 0.00 0.00 45.30 3.53
3889 4160 4.321230 GGTGAAAATGTGATGTGGAGTTCC 60.321 45.833 0.00 0.00 0.00 3.62
3890 4161 4.520492 AGGTGAAAATGTGATGTGGAGTTC 59.480 41.667 0.00 0.00 0.00 3.01
3891 4162 4.279169 CAGGTGAAAATGTGATGTGGAGTT 59.721 41.667 0.00 0.00 0.00 3.01
3917 4188 2.584835 AGCACCACCATTTCTGCTTA 57.415 45.000 0.00 0.00 36.57 3.09
3919 4190 1.352352 ACTAGCACCACCATTTCTGCT 59.648 47.619 0.00 0.00 42.60 4.24
3931 4202 0.739813 CACCGGCTGTAACTAGCACC 60.740 60.000 0.00 0.00 45.46 5.01
3934 4205 0.036671 AACCACCGGCTGTAACTAGC 60.037 55.000 0.00 0.00 42.94 3.42
3936 4207 1.050204 ACAACCACCGGCTGTAACTA 58.950 50.000 0.00 0.00 29.45 2.24
3943 4214 2.203480 ATGCAACAACCACCGGCT 60.203 55.556 0.00 0.00 0.00 5.52
3944 4215 2.049248 CATGCAACAACCACCGGC 60.049 61.111 0.00 0.00 0.00 6.13
3946 4217 1.007502 CCACATGCAACAACCACCG 60.008 57.895 0.00 0.00 0.00 4.94
3947 4218 1.367102 CCCACATGCAACAACCACC 59.633 57.895 0.00 0.00 0.00 4.61
3948 4219 0.249405 CACCCACATGCAACAACCAC 60.249 55.000 0.00 0.00 0.00 4.16
3949 4220 1.398174 CCACCCACATGCAACAACCA 61.398 55.000 0.00 0.00 0.00 3.67
3950 4221 1.367102 CCACCCACATGCAACAACC 59.633 57.895 0.00 0.00 0.00 3.77
3963 4234 1.823169 TTCTCCTACGTGCACCACCC 61.823 60.000 12.15 0.00 0.00 4.61
3964 4235 0.389948 CTTCTCCTACGTGCACCACC 60.390 60.000 12.15 0.00 0.00 4.61
4064 4335 2.677508 TGACATGGTCATGGACGGA 58.322 52.632 14.49 0.00 42.91 4.69
4072 4343 0.541392 CGGAAGGGATGACATGGTCA 59.459 55.000 1.05 1.05 46.90 4.02
4073 4344 0.815615 GCGGAAGGGATGACATGGTC 60.816 60.000 0.00 0.00 0.00 4.02
4074 4345 1.224592 GCGGAAGGGATGACATGGT 59.775 57.895 0.00 0.00 0.00 3.55
4075 4346 1.526917 GGCGGAAGGGATGACATGG 60.527 63.158 0.00 0.00 0.00 3.66
4076 4347 1.889105 CGGCGGAAGGGATGACATG 60.889 63.158 0.00 0.00 0.00 3.21
4077 4348 2.505982 CGGCGGAAGGGATGACAT 59.494 61.111 0.00 0.00 0.00 3.06
4078 4349 4.467084 GCGGCGGAAGGGATGACA 62.467 66.667 9.78 0.00 0.00 3.58
4093 4364 2.829043 TACTACTGCAAGGTGGCGCG 62.829 60.000 0.00 0.00 39.30 6.86
4094 4365 1.079405 TACTACTGCAAGGTGGCGC 60.079 57.895 0.00 0.00 39.30 6.53
4095 4366 0.246635 ACTACTACTGCAAGGTGGCG 59.753 55.000 0.00 0.00 39.30 5.69
4096 4367 1.002087 ACACTACTACTGCAAGGTGGC 59.998 52.381 0.00 0.00 39.30 5.01
4097 4368 2.353803 GGACACTACTACTGCAAGGTGG 60.354 54.545 0.00 0.00 39.30 4.61
4098 4369 2.299013 TGGACACTACTACTGCAAGGTG 59.701 50.000 0.00 0.00 39.30 4.00
4099 4370 2.563179 CTGGACACTACTACTGCAAGGT 59.437 50.000 0.00 0.00 39.30 3.50
4100 4371 2.675317 GCTGGACACTACTACTGCAAGG 60.675 54.545 0.00 0.00 39.30 3.61
4101 4372 2.232452 AGCTGGACACTACTACTGCAAG 59.768 50.000 0.00 0.00 42.29 4.01
4102 4373 2.248248 AGCTGGACACTACTACTGCAA 58.752 47.619 0.00 0.00 0.00 4.08
4103 4374 1.924731 AGCTGGACACTACTACTGCA 58.075 50.000 0.00 0.00 0.00 4.41
4104 4375 3.320673 AAAGCTGGACACTACTACTGC 57.679 47.619 0.00 0.00 0.00 4.40
4105 4376 4.632153 ACAAAAGCTGGACACTACTACTG 58.368 43.478 0.00 0.00 0.00 2.74
4106 4377 4.957684 ACAAAAGCTGGACACTACTACT 57.042 40.909 0.00 0.00 0.00 2.57
4107 4378 7.486802 TTTAACAAAAGCTGGACACTACTAC 57.513 36.000 0.00 0.00 0.00 2.73
4108 4379 8.685838 ATTTTAACAAAAGCTGGACACTACTA 57.314 30.769 0.00 0.00 33.22 1.82
4109 4380 7.582667 ATTTTAACAAAAGCTGGACACTACT 57.417 32.000 0.00 0.00 33.22 2.57
4110 4381 9.908152 ATTATTTTAACAAAAGCTGGACACTAC 57.092 29.630 0.00 0.00 33.22 2.73
4147 4418 9.939802 GGGAGTAGAAACTAAACTTTATGAAGA 57.060 33.333 3.94 0.00 35.56 2.87
4148 4419 9.945904 AGGGAGTAGAAACTAAACTTTATGAAG 57.054 33.333 0.00 0.00 35.56 3.02
4149 4420 9.939802 GAGGGAGTAGAAACTAAACTTTATGAA 57.060 33.333 0.00 0.00 35.56 2.57
4150 4421 8.537858 GGAGGGAGTAGAAACTAAACTTTATGA 58.462 37.037 0.00 0.00 35.56 2.15
4151 4422 7.491696 CGGAGGGAGTAGAAACTAAACTTTATG 59.508 40.741 0.00 0.00 35.56 1.90
4152 4423 7.179872 ACGGAGGGAGTAGAAACTAAACTTTAT 59.820 37.037 0.00 0.00 35.56 1.40
4153 4424 6.494835 ACGGAGGGAGTAGAAACTAAACTTTA 59.505 38.462 0.00 0.00 35.56 1.85
4154 4425 5.306419 ACGGAGGGAGTAGAAACTAAACTTT 59.694 40.000 0.00 0.00 35.56 2.66
4155 4426 4.837298 ACGGAGGGAGTAGAAACTAAACTT 59.163 41.667 0.00 0.00 35.56 2.66
4156 4427 4.414677 ACGGAGGGAGTAGAAACTAAACT 58.585 43.478 0.00 0.00 35.56 2.66
4157 4428 4.381398 GGACGGAGGGAGTAGAAACTAAAC 60.381 50.000 0.00 0.00 35.56 2.01
4158 4429 3.766051 GGACGGAGGGAGTAGAAACTAAA 59.234 47.826 0.00 0.00 35.56 1.85
4159 4430 3.359950 GGACGGAGGGAGTAGAAACTAA 58.640 50.000 0.00 0.00 35.56 2.24
4160 4431 2.357569 GGGACGGAGGGAGTAGAAACTA 60.358 54.545 0.00 0.00 35.56 2.24
4161 4432 1.619160 GGGACGGAGGGAGTAGAAACT 60.619 57.143 0.00 0.00 39.21 2.66
4162 4433 0.822811 GGGACGGAGGGAGTAGAAAC 59.177 60.000 0.00 0.00 0.00 2.78
4163 4434 0.410663 TGGGACGGAGGGAGTAGAAA 59.589 55.000 0.00 0.00 0.00 2.52
4164 4435 0.635009 ATGGGACGGAGGGAGTAGAA 59.365 55.000 0.00 0.00 0.00 2.10
4165 4436 1.424302 CTATGGGACGGAGGGAGTAGA 59.576 57.143 0.00 0.00 0.00 2.59
4166 4437 1.912417 CTATGGGACGGAGGGAGTAG 58.088 60.000 0.00 0.00 0.00 2.57
4167 4438 0.178970 GCTATGGGACGGAGGGAGTA 60.179 60.000 0.00 0.00 0.00 2.59
4168 4439 1.457831 GCTATGGGACGGAGGGAGT 60.458 63.158 0.00 0.00 0.00 3.85
4169 4440 2.565645 CGCTATGGGACGGAGGGAG 61.566 68.421 0.00 0.00 0.00 4.30
4170 4441 2.520982 CGCTATGGGACGGAGGGA 60.521 66.667 0.00 0.00 0.00 4.20
4171 4442 2.838225 ACGCTATGGGACGGAGGG 60.838 66.667 0.00 0.00 0.00 4.30



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

AutoCloner maintained by Alex Coulton.