Multiple sequence alignment - TraesCS7D01G055200

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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 TraesCS7D01G055200 chr7D 100.000 3572 0 0 1 3572 29677857 29674286 0.000000e+00 6597.0
1 TraesCS7D01G055200 chr7D 93.612 2802 128 22 790 3572 29698343 29695574 0.000000e+00 4135.0
2 TraesCS7D01G055200 chr7D 88.624 378 41 2 52 427 29699444 29699067 3.250000e-125 459.0
3 TraesCS7D01G055200 chr7D 77.073 205 33 14 2677 2878 49682905 49682712 4.880000e-19 106.0
4 TraesCS7D01G055200 chr7D 80.137 146 18 11 2677 2819 1178866 1179003 8.160000e-17 99.0
5 TraesCS7D01G055200 chr7D 76.500 200 33 14 2680 2876 631029503 631029315 2.940000e-16 97.1
6 TraesCS7D01G055200 chr7D 76.500 200 33 14 2680 2876 631034278 631034090 2.940000e-16 97.1
7 TraesCS7D01G055200 chr7D 76.974 152 27 8 2727 2876 15717356 15717501 2.960000e-11 80.5
8 TraesCS7D01G055200 chr7D 77.612 134 25 5 2744 2876 15722068 15722197 3.820000e-10 76.8
9 TraesCS7D01G055200 chr3A 87.391 1713 169 26 857 2556 81483686 81482008 0.000000e+00 1923.0
10 TraesCS7D01G055200 chr3A 87.259 1711 174 24 857 2556 81662791 81664468 0.000000e+00 1912.0
11 TraesCS7D01G055200 chr3B 87.214 1705 176 23 857 2556 116080761 116082428 0.000000e+00 1903.0
12 TraesCS7D01G055200 chr3B 87.155 1705 177 26 857 2556 116010433 116008766 0.000000e+00 1897.0
13 TraesCS7D01G055200 chr3B 82.353 102 16 2 2105 2205 766178791 766178691 1.770000e-13 87.9
14 TraesCS7D01G055200 chr3D 87.010 1709 177 27 857 2556 70228702 70230374 0.000000e+00 1884.0
15 TraesCS7D01G055200 chr3D 86.249 1709 191 24 857 2552 69907854 69906177 0.000000e+00 1814.0
16 TraesCS7D01G055200 chr3D 82.957 487 48 18 857 1341 69915589 69915136 1.190000e-109 407.0
17 TraesCS7D01G055200 chr4A 80.882 1428 232 32 1167 2578 5348854 5350256 0.000000e+00 1086.0
18 TraesCS7D01G055200 chr5D 86.559 186 21 3 608 792 344567242 344567424 6.050000e-48 202.0
19 TraesCS7D01G055200 chr6A 85.405 185 25 1 608 792 551862600 551862418 1.310000e-44 191.0
20 TraesCS7D01G055200 chr6A 81.183 186 32 2 607 791 54200457 54200640 2.870000e-31 147.0
21 TraesCS7D01G055200 chr5B 87.879 165 15 4 631 794 402740337 402740177 4.710000e-44 189.0
22 TraesCS7D01G055200 chr2D 85.106 188 18 7 609 793 209024691 209024511 2.190000e-42 183.0
23 TraesCS7D01G055200 chr2D 76.961 204 33 14 2677 2877 87823097 87823289 1.750000e-18 104.0
24 TraesCS7D01G055200 chr2D 76.961 204 33 12 2677 2877 87827870 87828062 1.750000e-18 104.0
25 TraesCS7D01G055200 chr7B 84.409 186 24 5 610 793 87456301 87456119 1.020000e-40 178.0
26 TraesCS7D01G055200 chr7A 82.486 177 28 3 617 793 24861278 24861451 6.180000e-33 152.0
27 TraesCS7D01G055200 chr5A 84.459 148 16 5 609 754 23936644 23936502 4.810000e-29 139.0
28 TraesCS7D01G055200 chr1A 83.108 148 17 5 609 751 521979680 521979824 1.040000e-25 128.0


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 TraesCS7D01G055200 chr7D 29674286 29677857 3571 True 6597 6597 100.000 1 3572 1 chr7D.!!$R1 3571
1 TraesCS7D01G055200 chr7D 29695574 29699444 3870 True 2297 4135 91.118 52 3572 2 chr7D.!!$R5 3520
2 TraesCS7D01G055200 chr3A 81482008 81483686 1678 True 1923 1923 87.391 857 2556 1 chr3A.!!$R1 1699
3 TraesCS7D01G055200 chr3A 81662791 81664468 1677 False 1912 1912 87.259 857 2556 1 chr3A.!!$F1 1699
4 TraesCS7D01G055200 chr3B 116080761 116082428 1667 False 1903 1903 87.214 857 2556 1 chr3B.!!$F1 1699
5 TraesCS7D01G055200 chr3B 116008766 116010433 1667 True 1897 1897 87.155 857 2556 1 chr3B.!!$R1 1699
6 TraesCS7D01G055200 chr3D 70228702 70230374 1672 False 1884 1884 87.010 857 2556 1 chr3D.!!$F1 1699
7 TraesCS7D01G055200 chr3D 69906177 69907854 1677 True 1814 1814 86.249 857 2552 1 chr3D.!!$R1 1695
8 TraesCS7D01G055200 chr4A 5348854 5350256 1402 False 1086 1086 80.882 1167 2578 1 chr4A.!!$F1 1411

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
771 774 0.169672 ACATGGTTACGTCTCGGTCG 59.83 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2673 3185 0.388649 ACTAGAGCACGTTTCTGGCG 60.389 55.0 9.11 0.0 0.0 5.69 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
21 22 4.771114 TTTTCTCAGAGGTCTTGGTCAA 57.229 40.909 0.00 0.00 0.00 3.18
22 23 4.771114 TTTCTCAGAGGTCTTGGTCAAA 57.229 40.909 0.00 0.00 0.00 2.69
23 24 4.342862 TTCTCAGAGGTCTTGGTCAAAG 57.657 45.455 0.00 0.00 37.22 2.77
24 25 3.309296 TCTCAGAGGTCTTGGTCAAAGT 58.691 45.455 0.00 0.00 37.18 2.66
25 26 3.711704 TCTCAGAGGTCTTGGTCAAAGTT 59.288 43.478 0.00 0.00 37.18 2.66
26 27 4.164221 TCTCAGAGGTCTTGGTCAAAGTTT 59.836 41.667 0.00 0.00 37.18 2.66
27 28 4.451900 TCAGAGGTCTTGGTCAAAGTTTC 58.548 43.478 0.00 0.00 37.18 2.78
28 29 4.164221 TCAGAGGTCTTGGTCAAAGTTTCT 59.836 41.667 0.00 0.00 37.18 2.52
29 30 4.274459 CAGAGGTCTTGGTCAAAGTTTCTG 59.726 45.833 0.00 4.75 37.18 3.02
30 31 4.164221 AGAGGTCTTGGTCAAAGTTTCTGA 59.836 41.667 0.00 0.00 37.18 3.27
31 32 4.200092 AGGTCTTGGTCAAAGTTTCTGAC 58.800 43.478 0.00 0.00 42.08 3.51
32 33 4.080299 AGGTCTTGGTCAAAGTTTCTGACT 60.080 41.667 7.46 0.00 42.38 3.41
43 44 4.448537 AGTTTCTGACTTCTCTCATCGG 57.551 45.455 0.00 0.00 33.92 4.18
44 45 3.829601 AGTTTCTGACTTCTCTCATCGGT 59.170 43.478 0.00 0.00 33.92 4.69
45 46 5.010933 AGTTTCTGACTTCTCTCATCGGTA 58.989 41.667 0.00 0.00 33.92 4.02
46 47 5.654650 AGTTTCTGACTTCTCTCATCGGTAT 59.345 40.000 0.00 0.00 33.92 2.73
47 48 6.153680 AGTTTCTGACTTCTCTCATCGGTATT 59.846 38.462 0.00 0.00 33.92 1.89
48 49 5.759506 TCTGACTTCTCTCATCGGTATTC 57.240 43.478 0.00 0.00 0.00 1.75
49 50 5.441500 TCTGACTTCTCTCATCGGTATTCT 58.558 41.667 0.00 0.00 0.00 2.40
50 51 5.888724 TCTGACTTCTCTCATCGGTATTCTT 59.111 40.000 0.00 0.00 0.00 2.52
55 56 6.096987 ACTTCTCTCATCGGTATTCTTAGCAA 59.903 38.462 0.00 0.00 0.00 3.91
60 61 7.103641 TCTCATCGGTATTCTTAGCAACTTTT 58.896 34.615 0.00 0.00 0.00 2.27
74 75 3.230976 CAACTTTTAGGACAAGGGGCTT 58.769 45.455 0.00 0.00 0.00 4.35
80 81 1.376649 AGGACAAGGGGCTTGAGATT 58.623 50.000 0.00 0.00 43.42 2.40
87 88 0.750911 GGGGCTTGAGATTGGAGCAG 60.751 60.000 0.00 0.00 38.14 4.24
114 115 7.545965 CCAAGACAACTTTCTTATCGTACTGAT 59.454 37.037 5.71 5.71 33.89 2.90
129 131 7.117241 TCGTACTGATTTCATCAACACTTTC 57.883 36.000 0.00 0.00 39.11 2.62
139 141 5.005740 TCATCAACACTTTCTTCTGGATGG 58.994 41.667 0.00 0.00 33.52 3.51
141 143 4.792068 TCAACACTTTCTTCTGGATGGTT 58.208 39.130 0.00 0.00 0.00 3.67
143 145 5.299279 TCAACACTTTCTTCTGGATGGTTTC 59.701 40.000 0.00 0.00 0.00 2.78
166 168 4.785669 CTCCGAAGCATTTGTATCAGAC 57.214 45.455 0.00 0.00 0.00 3.51
180 182 7.969536 TTGTATCAGACTTTTCCTCAGAAAG 57.030 36.000 0.00 0.00 42.78 2.62
181 183 5.934625 TGTATCAGACTTTTCCTCAGAAAGC 59.065 40.000 0.00 0.00 42.78 3.51
224 226 6.881602 AGACTCAATTGTGGTCTTCTTATTCC 59.118 38.462 21.75 3.99 33.86 3.01
233 235 2.937149 GTCTTCTTATTCCGGTCCTTGC 59.063 50.000 0.00 0.00 0.00 4.01
239 241 5.562635 TCTTATTCCGGTCCTTGCTTTTAA 58.437 37.500 0.00 0.00 0.00 1.52
240 242 5.413523 TCTTATTCCGGTCCTTGCTTTTAAC 59.586 40.000 0.00 0.00 0.00 2.01
241 243 1.900245 TCCGGTCCTTGCTTTTAACC 58.100 50.000 0.00 0.00 0.00 2.85
244 246 2.030274 CCGGTCCTTGCTTTTAACCTTG 60.030 50.000 0.00 0.00 0.00 3.61
253 255 7.225734 TCCTTGCTTTTAACCTTGTAAAAATGC 59.774 33.333 0.00 0.00 33.66 3.56
255 257 6.349300 TGCTTTTAACCTTGTAAAAATGCCA 58.651 32.000 0.00 0.00 33.66 4.92
257 259 7.500559 TGCTTTTAACCTTGTAAAAATGCCATT 59.499 29.630 0.00 0.00 33.66 3.16
279 281 2.034558 GCAAAAAGGAAGTGTAGCAGCA 59.965 45.455 0.00 0.00 0.00 4.41
282 284 0.326264 AAGGAAGTGTAGCAGCAGGG 59.674 55.000 0.00 0.00 0.00 4.45
312 314 7.959175 AGAGTTGTATGTGTCTTAGTTTGGTA 58.041 34.615 0.00 0.00 0.00 3.25
420 423 1.064166 CCAGTGATTTCAGCCCATCCT 60.064 52.381 0.00 0.00 0.00 3.24
421 424 2.022195 CAGTGATTTCAGCCCATCCTG 58.978 52.381 0.00 0.00 0.00 3.86
430 433 4.806640 TCAGCCCATCCTGAAAAATTTC 57.193 40.909 0.00 0.00 38.81 2.17
431 434 3.515104 TCAGCCCATCCTGAAAAATTTCC 59.485 43.478 3.60 0.00 38.81 3.13
432 435 2.497273 AGCCCATCCTGAAAAATTTCCG 59.503 45.455 3.60 0.00 36.36 4.30
438 441 4.799564 TCCTGAAAAATTTCCGGAATGG 57.200 40.909 19.62 10.05 44.25 3.16
465 468 2.292828 AAAGTTGTGGTGAGGATGGG 57.707 50.000 0.00 0.00 0.00 4.00
466 469 0.251341 AAGTTGTGGTGAGGATGGGC 60.251 55.000 0.00 0.00 0.00 5.36
467 470 2.040544 GTTGTGGTGAGGATGGGCG 61.041 63.158 0.00 0.00 0.00 6.13
468 471 2.220586 TTGTGGTGAGGATGGGCGA 61.221 57.895 0.00 0.00 0.00 5.54
469 472 2.125106 GTGGTGAGGATGGGCGAC 60.125 66.667 0.00 0.00 0.00 5.19
470 473 3.770040 TGGTGAGGATGGGCGACG 61.770 66.667 0.00 0.00 0.00 5.12
481 484 3.192922 GGCGACGCCGTTGCTTAT 61.193 61.111 27.02 0.00 42.17 1.73
482 485 2.021380 GCGACGCCGTTGCTTATG 59.979 61.111 21.83 0.00 39.63 1.90
483 486 2.736682 GCGACGCCGTTGCTTATGT 61.737 57.895 21.83 0.00 39.63 2.29
484 487 1.343821 CGACGCCGTTGCTTATGTC 59.656 57.895 0.00 0.00 34.43 3.06
485 488 1.343821 GACGCCGTTGCTTATGTCG 59.656 57.895 0.00 0.00 34.43 4.35
486 489 1.074319 GACGCCGTTGCTTATGTCGA 61.074 55.000 0.00 0.00 34.43 4.20
487 490 0.668096 ACGCCGTTGCTTATGTCGAA 60.668 50.000 0.00 0.00 34.43 3.71
488 491 0.247145 CGCCGTTGCTTATGTCGAAC 60.247 55.000 0.00 0.00 34.43 3.95
492 495 2.159707 CCGTTGCTTATGTCGAACCTTG 60.160 50.000 0.00 0.00 0.00 3.61
542 545 1.001815 GAGCTGTCTCTATGAGCCGAC 60.002 57.143 0.00 0.00 36.42 4.79
545 548 1.402259 CTGTCTCTATGAGCCGACGTT 59.598 52.381 0.00 0.00 0.00 3.99
593 596 2.503356 TCTTGGGTTGCCATGTGTTTTT 59.497 40.909 0.00 0.00 0.00 1.94
594 597 2.611225 TGGGTTGCCATGTGTTTTTC 57.389 45.000 0.00 0.00 0.00 2.29
601 604 2.560542 TGCCATGTGTTTTTCGGCTTAT 59.439 40.909 0.00 0.00 43.38 1.73
603 606 2.923020 CCATGTGTTTTTCGGCTTATGC 59.077 45.455 0.00 0.00 38.76 3.14
615 618 2.262572 GCTTATGCCGGACAGTTTTG 57.737 50.000 5.05 0.00 0.00 2.44
617 620 1.812571 CTTATGCCGGACAGTTTTGCT 59.187 47.619 5.05 0.00 0.00 3.91
619 622 1.904287 ATGCCGGACAGTTTTGCTAA 58.096 45.000 5.05 0.00 0.00 3.09
620 623 1.234821 TGCCGGACAGTTTTGCTAAG 58.765 50.000 5.05 0.00 0.00 2.18
621 624 1.235724 GCCGGACAGTTTTGCTAAGT 58.764 50.000 5.05 0.00 0.00 2.24
622 625 1.197036 GCCGGACAGTTTTGCTAAGTC 59.803 52.381 5.05 0.00 0.00 3.01
623 626 2.767505 CCGGACAGTTTTGCTAAGTCT 58.232 47.619 0.00 0.00 0.00 3.24
625 628 4.504858 CCGGACAGTTTTGCTAAGTCTAT 58.495 43.478 0.00 0.00 0.00 1.98
626 629 4.330074 CCGGACAGTTTTGCTAAGTCTATG 59.670 45.833 0.00 0.00 0.00 2.23
627 630 4.929808 CGGACAGTTTTGCTAAGTCTATGT 59.070 41.667 0.00 0.00 0.00 2.29
628 631 5.062308 CGGACAGTTTTGCTAAGTCTATGTC 59.938 44.000 0.00 0.00 35.07 3.06
632 635 5.864474 CAGTTTTGCTAAGTCTATGTCGACT 59.136 40.000 17.92 4.95 45.73 4.18
646 649 9.011407 GTCTATGTCGACTTAGACTTTGTTATG 57.989 37.037 38.67 16.64 44.04 1.90
647 650 8.737175 TCTATGTCGACTTAGACTTTGTTATGT 58.263 33.333 28.06 0.00 41.47 2.29
648 651 7.813852 ATGTCGACTTAGACTTTGTTATGTC 57.186 36.000 17.92 0.00 41.47 3.06
649 652 6.978338 TGTCGACTTAGACTTTGTTATGTCT 58.022 36.000 17.92 0.00 44.56 3.41
650 653 7.082602 TGTCGACTTAGACTTTGTTATGTCTC 58.917 38.462 17.92 0.00 41.92 3.36
651 654 7.082602 GTCGACTTAGACTTTGTTATGTCTCA 58.917 38.462 8.70 0.00 41.92 3.27
653 656 7.040617 TCGACTTAGACTTTGTTATGTCTCAGT 60.041 37.037 8.97 8.97 45.06 3.41
655 658 8.594881 ACTTAGACTTTGTTATGTCTCAGTTG 57.405 34.615 0.00 0.00 41.91 3.16
656 659 8.421784 ACTTAGACTTTGTTATGTCTCAGTTGA 58.578 33.333 0.00 0.00 41.91 3.18
657 660 9.429359 CTTAGACTTTGTTATGTCTCAGTTGAT 57.571 33.333 0.00 0.00 41.92 2.57
659 662 8.764524 AGACTTTGTTATGTCTCAGTTGATAC 57.235 34.615 0.00 0.00 39.04 2.24
660 663 8.589338 AGACTTTGTTATGTCTCAGTTGATACT 58.411 33.333 0.00 0.00 39.04 2.12
661 664 9.856488 GACTTTGTTATGTCTCAGTTGATACTA 57.144 33.333 0.37 0.00 31.96 1.82
679 682 9.927668 TTGATACTATATTCATTTGATCTCGCA 57.072 29.630 0.00 0.00 0.00 5.10
680 683 9.578439 TGATACTATATTCATTTGATCTCGCAG 57.422 33.333 0.00 0.00 0.00 5.18
681 684 8.939201 ATACTATATTCATTTGATCTCGCAGG 57.061 34.615 0.00 0.00 0.00 4.85
682 685 6.169094 ACTATATTCATTTGATCTCGCAGGG 58.831 40.000 0.00 0.00 0.00 4.45
683 686 3.565764 ATTCATTTGATCTCGCAGGGA 57.434 42.857 0.00 0.00 0.00 4.20
684 687 2.609427 TCATTTGATCTCGCAGGGAG 57.391 50.000 8.23 8.23 44.58 4.30
690 693 4.338815 TCTCGCAGGGAGATTCGT 57.661 55.556 13.11 0.00 46.80 3.85
691 694 3.489391 TCTCGCAGGGAGATTCGTA 57.511 52.632 13.11 0.00 46.80 3.43
692 695 1.022735 TCTCGCAGGGAGATTCGTAC 58.977 55.000 13.11 0.00 46.80 3.67
693 696 0.738975 CTCGCAGGGAGATTCGTACA 59.261 55.000 8.88 0.00 46.23 2.90
694 697 1.134367 CTCGCAGGGAGATTCGTACAA 59.866 52.381 8.88 0.00 46.23 2.41
695 698 1.546923 TCGCAGGGAGATTCGTACAAA 59.453 47.619 0.00 0.00 0.00 2.83
696 699 2.028839 TCGCAGGGAGATTCGTACAAAA 60.029 45.455 0.00 0.00 0.00 2.44
697 700 2.739913 CGCAGGGAGATTCGTACAAAAA 59.260 45.455 0.00 0.00 0.00 1.94
763 766 3.321111 ACTTGACTGAGACATGGTTACGT 59.679 43.478 0.00 0.00 0.00 3.57
764 767 3.570926 TGACTGAGACATGGTTACGTC 57.429 47.619 0.00 0.00 0.00 4.34
765 768 3.154710 TGACTGAGACATGGTTACGTCT 58.845 45.455 0.00 0.00 45.07 4.18
768 771 2.190325 GAGACATGGTTACGTCTCGG 57.810 55.000 0.00 0.00 46.20 4.63
769 772 1.471684 GAGACATGGTTACGTCTCGGT 59.528 52.381 0.00 0.00 46.20 4.69
770 773 1.471684 AGACATGGTTACGTCTCGGTC 59.528 52.381 0.00 0.00 38.03 4.79
771 774 0.169672 ACATGGTTACGTCTCGGTCG 59.830 55.000 0.00 0.00 0.00 4.79
772 775 0.448990 CATGGTTACGTCTCGGTCGA 59.551 55.000 0.00 0.00 0.00 4.20
773 776 0.449388 ATGGTTACGTCTCGGTCGAC 59.551 55.000 7.13 7.13 0.00 4.20
775 778 0.179205 GGTTACGTCTCGGTCGACTG 60.179 60.000 18.66 18.66 0.00 3.51
777 780 2.231745 TTACGTCTCGGTCGACTGCG 62.232 60.000 19.89 18.62 39.35 5.18
786 789 4.707791 TCGACTGCGACCTAGACA 57.292 55.556 0.00 0.00 42.51 3.41
788 791 0.604511 TCGACTGCGACCTAGACACA 60.605 55.000 0.00 0.00 42.51 3.72
791 1273 1.215647 CTGCGACCTAGACACACCC 59.784 63.158 0.00 0.00 0.00 4.61
804 1286 1.003580 ACACACCCTATGCCAGAACAG 59.996 52.381 0.00 0.00 0.00 3.16
835 1317 1.546029 GAGTTTTTCCCATGGTGGCTC 59.454 52.381 11.73 5.72 35.79 4.70
840 1322 1.863155 TTCCCATGGTGGCTCCCTTC 61.863 60.000 11.73 0.00 35.79 3.46
849 1331 1.279025 TGGCTCCCTTCCCATACACC 61.279 60.000 0.00 0.00 0.00 4.16
850 1332 0.988678 GGCTCCCTTCCCATACACCT 60.989 60.000 0.00 0.00 0.00 4.00
854 1336 3.908103 GCTCCCTTCCCATACACCTAATA 59.092 47.826 0.00 0.00 0.00 0.98
880 1363 5.414765 CCAAATCTCTACACCTAACCCAAAC 59.585 44.000 0.00 0.00 0.00 2.93
887 1371 1.146152 CACCTAACCCAAACCCCTCAA 59.854 52.381 0.00 0.00 0.00 3.02
893 1377 0.251341 CCCAAACCCCTCAACTCAGG 60.251 60.000 0.00 0.00 0.00 3.86
895 1379 1.271597 CCAAACCCCTCAACTCAGGAG 60.272 57.143 0.00 0.00 35.20 3.69
936 1420 6.260050 CCTAGCTAGCTCTACATATAGCTCAC 59.740 46.154 23.26 0.00 46.03 3.51
937 1421 5.815581 AGCTAGCTCTACATATAGCTCACT 58.184 41.667 12.68 0.00 46.03 3.41
938 1422 5.880332 AGCTAGCTCTACATATAGCTCACTC 59.120 44.000 12.68 0.00 46.03 3.51
939 1423 5.645929 GCTAGCTCTACATATAGCTCACTCA 59.354 44.000 7.70 0.00 45.92 3.41
1437 1924 4.742201 GCGCTGCTCTTCGACCCA 62.742 66.667 0.00 0.00 0.00 4.51
1780 2267 1.062047 GTGCTCGACGCGTCTATCA 59.938 57.895 33.94 23.36 43.27 2.15
1845 2341 3.379445 AACGCCGACGGGACTGAT 61.379 61.111 17.22 0.00 46.04 2.90
2112 2617 1.342819 GATCTGAAGCGCCTGGTCTAT 59.657 52.381 2.29 0.00 0.00 1.98
2357 2862 1.360820 GAGCCTTCCTACAAGTTCGC 58.639 55.000 0.00 0.00 0.00 4.70
2460 2965 1.374758 GCAGTTCAGGGTCGAGGTG 60.375 63.158 0.00 0.00 0.00 4.00
2499 3007 2.936202 CCGATTCCCAAGATGTCCATT 58.064 47.619 0.00 0.00 0.00 3.16
2535 3043 2.352805 GGGCTCAAGGTGAGGGTG 59.647 66.667 7.34 0.00 44.43 4.61
2547 3055 0.394192 TGAGGGTGCACAAGAGACAG 59.606 55.000 20.43 0.00 0.00 3.51
2581 3093 8.274939 CACTAAGTACAATCTAGAGCTACGTAC 58.725 40.741 0.00 5.41 0.00 3.67
2582 3094 6.616774 AAGTACAATCTAGAGCTACGTACC 57.383 41.667 0.00 0.00 0.00 3.34
2583 3095 5.927819 AGTACAATCTAGAGCTACGTACCT 58.072 41.667 0.00 0.00 0.00 3.08
2584 3096 7.060383 AGTACAATCTAGAGCTACGTACCTA 57.940 40.000 0.00 0.00 0.00 3.08
2586 3098 8.156165 AGTACAATCTAGAGCTACGTACCTATT 58.844 37.037 0.00 0.00 0.00 1.73
2589 3101 4.904241 TCTAGAGCTACGTACCTATTCCC 58.096 47.826 0.00 0.00 0.00 3.97
2591 3103 3.907221 AGAGCTACGTACCTATTCCCAA 58.093 45.455 0.00 0.00 0.00 4.12
2594 3106 2.364647 GCTACGTACCTATTCCCAAGCT 59.635 50.000 0.00 0.00 0.00 3.74
2596 3108 1.761198 ACGTACCTATTCCCAAGCTCC 59.239 52.381 0.00 0.00 0.00 4.70
2607 3119 3.731431 TCCCAAGCTCCCAAGTCTAATA 58.269 45.455 0.00 0.00 0.00 0.98
2609 3121 5.473273 TCCCAAGCTCCCAAGTCTAATATA 58.527 41.667 0.00 0.00 0.00 0.86
2610 3122 5.307196 TCCCAAGCTCCCAAGTCTAATATAC 59.693 44.000 0.00 0.00 0.00 1.47
2616 3128 6.439058 AGCTCCCAAGTCTAATATACTCCATC 59.561 42.308 0.00 0.00 0.00 3.51
2720 3232 1.676014 GCGGCTTTGTCTGAGTGGTAT 60.676 52.381 0.00 0.00 0.00 2.73
2721 3233 2.002586 CGGCTTTGTCTGAGTGGTATG 58.997 52.381 0.00 0.00 0.00 2.39
2722 3234 2.612972 CGGCTTTGTCTGAGTGGTATGT 60.613 50.000 0.00 0.00 0.00 2.29
2723 3235 2.744202 GGCTTTGTCTGAGTGGTATGTG 59.256 50.000 0.00 0.00 0.00 3.21
2727 3239 5.728471 CTTTGTCTGAGTGGTATGTGAGAT 58.272 41.667 0.00 0.00 0.00 2.75
2762 3274 6.822073 AAATTTTCTTTCCTGTAAACGTGC 57.178 33.333 0.00 0.00 0.00 5.34
2813 3325 3.887621 TGGAACAGAAGTAAGGGATCG 57.112 47.619 0.00 0.00 0.00 3.69
2814 3326 3.170717 TGGAACAGAAGTAAGGGATCGT 58.829 45.455 0.00 0.00 0.00 3.73
2815 3327 3.056107 TGGAACAGAAGTAAGGGATCGTG 60.056 47.826 0.00 0.00 0.00 4.35
2816 3328 3.522553 GAACAGAAGTAAGGGATCGTGG 58.477 50.000 0.00 0.00 0.00 4.94
2817 3329 1.831736 ACAGAAGTAAGGGATCGTGGG 59.168 52.381 0.00 0.00 0.00 4.61
2818 3330 0.831307 AGAAGTAAGGGATCGTGGGC 59.169 55.000 0.00 0.00 0.00 5.36
2819 3331 0.529992 GAAGTAAGGGATCGTGGGCG 60.530 60.000 0.00 0.00 39.92 6.13
2845 3357 3.070446 ACTTCGGATGTGGTTGTTACTCA 59.930 43.478 0.00 0.00 0.00 3.41
2849 3361 4.454161 TCGGATGTGGTTGTTACTCAATTG 59.546 41.667 0.00 0.00 38.38 2.32
2881 3393 1.725973 GCCGAAAAGCACGCAAGAC 60.726 57.895 0.00 0.00 43.62 3.01
2888 3400 0.948623 AAGCACGCAAGACATACGCA 60.949 50.000 0.00 0.00 43.62 5.24
2891 3403 0.043907 CACGCAAGACATACGCATCG 60.044 55.000 0.00 0.00 43.62 3.84
2905 3417 2.171567 CGCATCGCAAAAATCTGTCTG 58.828 47.619 0.00 0.00 0.00 3.51
2912 3424 3.183574 CGCAAAAATCTGTCTGTGTACGA 59.816 43.478 0.00 0.00 0.00 3.43
2913 3425 4.664139 CGCAAAAATCTGTCTGTGTACGAG 60.664 45.833 0.00 0.00 0.00 4.18
2914 3426 4.211374 GCAAAAATCTGTCTGTGTACGAGT 59.789 41.667 0.00 0.00 0.00 4.18
2946 3458 0.667487 CTCCTGCATGTGTTCGTCGT 60.667 55.000 0.00 0.00 0.00 4.34
2958 3470 1.128136 GTTCGTCGTGATCGAGTCTCA 59.872 52.381 0.00 0.00 46.96 3.27
2966 3478 1.791103 GATCGAGTCTCAGGCTCCCG 61.791 65.000 0.00 0.00 0.00 5.14
2967 3479 3.522731 CGAGTCTCAGGCTCCCGG 61.523 72.222 0.00 0.00 0.00 5.73
2996 3508 1.552337 CATGGCGGCAGATATAGGAGT 59.448 52.381 19.29 0.00 0.00 3.85
3001 3513 1.751924 CGGCAGATATAGGAGTAGGGC 59.248 57.143 0.00 0.00 0.00 5.19
3015 3527 0.758734 TAGGGCCGGTCATGAGATTG 59.241 55.000 9.07 0.00 0.00 2.67
3042 3555 1.515081 CCGGGCGAAACTAAAACTCA 58.485 50.000 0.00 0.00 0.00 3.41
3095 3609 6.401474 CGTCAACTCAAAGTCACTTATGATGG 60.401 42.308 0.00 0.00 37.14 3.51
3099 3613 5.934625 ACTCAAAGTCACTTATGATGGTGTC 59.065 40.000 0.00 0.00 37.14 3.67
3126 3643 0.398664 ATCCCTCCTCCGGGTTGTAG 60.399 60.000 0.00 0.00 44.95 2.74
3146 3663 1.069378 GAAGGTGAACGTAGACGCCG 61.069 60.000 1.14 0.00 44.43 6.46
3154 3671 4.527157 GTAGACGCCGCGCTACGT 62.527 66.667 22.00 22.00 46.91 3.57
3155 3672 4.525576 TAGACGCCGCGCTACGTG 62.526 66.667 25.86 12.75 43.71 4.49
3172 3689 1.135915 CGTGATCTAGACAGCAAGGCT 59.864 52.381 0.00 0.00 40.77 4.58
3184 3701 2.356313 AAGGCTGTGACTGCGTCG 60.356 61.111 9.96 0.00 34.95 5.12
3197 3714 1.954146 GCGTCGTTCACAAGGAGCA 60.954 57.895 0.00 0.00 0.00 4.26
3204 3721 1.815003 GTTCACAAGGAGCAATGAGGG 59.185 52.381 0.00 0.00 0.00 4.30
3205 3722 1.067295 TCACAAGGAGCAATGAGGGT 58.933 50.000 0.00 0.00 0.00 4.34
3206 3723 1.171308 CACAAGGAGCAATGAGGGTG 58.829 55.000 0.00 0.00 0.00 4.61
3207 3724 1.067295 ACAAGGAGCAATGAGGGTGA 58.933 50.000 0.00 0.00 0.00 4.02
3231 3748 2.040145 TCATGGGAGCATCAAGTGTGAA 59.960 45.455 0.00 0.00 37.30 3.18
3234 3751 2.158623 TGGGAGCATCAAGTGTGAACTT 60.159 45.455 0.00 0.00 37.30 2.66
3237 3754 3.058639 GGAGCATCAAGTGTGAACTTCAC 60.059 47.826 14.10 14.10 42.16 3.18
3239 3756 4.319333 GAGCATCAAGTGTGAACTTCACTG 60.319 45.833 20.18 11.90 44.03 3.66
3267 3784 2.880890 GGGACCTCATTCAATGGAATCG 59.119 50.000 0.00 0.00 41.78 3.34
3276 3793 6.331845 TCATTCAATGGAATCGTTTTGGATG 58.668 36.000 0.00 0.00 41.78 3.51
3285 3802 0.094046 CGTTTTGGATGGCGACGTAC 59.906 55.000 0.00 0.00 0.00 3.67
3288 3805 2.172851 TTTGGATGGCGACGTACTTT 57.827 45.000 0.00 0.00 0.00 2.66
3318 3835 8.672815 GTTCTTATAGTGAGAACCGTTAGTACT 58.327 37.037 0.00 0.00 44.50 2.73
3338 3861 1.552792 TGCCTCCGTGTCATCAATACA 59.447 47.619 0.00 0.00 0.00 2.29
3435 3960 2.169832 ATTATGGCGGTCGAATCCAG 57.830 50.000 7.48 0.00 32.78 3.86
3451 3976 4.525912 ATCCAGCAATTCAAACAAGGAC 57.474 40.909 0.00 0.00 0.00 3.85
3478 4003 6.839124 AAAACAGAAGGATGAATATGCACA 57.161 33.333 0.00 0.00 0.00 4.57
3488 4013 9.976511 AAGGATGAATATGCACATCAATTTTAG 57.023 29.630 14.76 0.00 42.95 1.85
3550 4075 1.228367 CCAGTGTTGCTTCCCTGCT 60.228 57.895 0.00 0.00 0.00 4.24
3556 4081 2.819608 GTGTTGCTTCCCTGCTTGAATA 59.180 45.455 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.771114 TTGACCAAGACCTCTGAGAAAA 57.229 40.909 6.17 0.00 0.00 2.29
1 2 4.164221 ACTTTGACCAAGACCTCTGAGAAA 59.836 41.667 6.17 0.00 36.21 2.52
2 3 3.711704 ACTTTGACCAAGACCTCTGAGAA 59.288 43.478 6.17 0.00 36.21 2.87
3 4 3.309296 ACTTTGACCAAGACCTCTGAGA 58.691 45.455 6.17 0.00 36.21 3.27
4 5 3.760580 ACTTTGACCAAGACCTCTGAG 57.239 47.619 0.00 0.00 36.21 3.35
5 6 4.164221 AGAAACTTTGACCAAGACCTCTGA 59.836 41.667 0.00 0.00 36.21 3.27
6 7 4.274459 CAGAAACTTTGACCAAGACCTCTG 59.726 45.833 0.00 0.00 36.21 3.35
7 8 4.164221 TCAGAAACTTTGACCAAGACCTCT 59.836 41.667 0.00 0.00 36.21 3.69
8 9 4.273724 GTCAGAAACTTTGACCAAGACCTC 59.726 45.833 0.00 0.00 39.17 3.85
9 10 4.080299 AGTCAGAAACTTTGACCAAGACCT 60.080 41.667 2.04 0.00 44.68 3.85
10 11 4.200092 AGTCAGAAACTTTGACCAAGACC 58.800 43.478 2.04 0.00 44.68 3.85
11 12 5.819825 AAGTCAGAAACTTTGACCAAGAC 57.180 39.130 2.04 0.00 46.26 3.01
22 23 3.829601 ACCGATGAGAGAAGTCAGAAACT 59.170 43.478 0.00 0.00 41.10 2.66
23 24 4.181309 ACCGATGAGAGAAGTCAGAAAC 57.819 45.455 0.00 0.00 0.00 2.78
24 25 6.378564 AGAATACCGATGAGAGAAGTCAGAAA 59.621 38.462 0.00 0.00 0.00 2.52
25 26 5.888724 AGAATACCGATGAGAGAAGTCAGAA 59.111 40.000 0.00 0.00 0.00 3.02
26 27 5.441500 AGAATACCGATGAGAGAAGTCAGA 58.558 41.667 0.00 0.00 0.00 3.27
27 28 5.766150 AGAATACCGATGAGAGAAGTCAG 57.234 43.478 0.00 0.00 0.00 3.51
28 29 6.238786 GCTAAGAATACCGATGAGAGAAGTCA 60.239 42.308 0.00 0.00 0.00 3.41
29 30 6.146898 GCTAAGAATACCGATGAGAGAAGTC 58.853 44.000 0.00 0.00 0.00 3.01
30 31 5.594725 TGCTAAGAATACCGATGAGAGAAGT 59.405 40.000 0.00 0.00 0.00 3.01
31 32 6.078202 TGCTAAGAATACCGATGAGAGAAG 57.922 41.667 0.00 0.00 0.00 2.85
32 33 6.096987 AGTTGCTAAGAATACCGATGAGAGAA 59.903 38.462 0.00 0.00 0.00 2.87
33 34 5.594725 AGTTGCTAAGAATACCGATGAGAGA 59.405 40.000 0.00 0.00 0.00 3.10
34 35 5.837437 AGTTGCTAAGAATACCGATGAGAG 58.163 41.667 0.00 0.00 0.00 3.20
35 36 5.854010 AGTTGCTAAGAATACCGATGAGA 57.146 39.130 0.00 0.00 0.00 3.27
36 37 6.910536 AAAGTTGCTAAGAATACCGATGAG 57.089 37.500 0.00 0.00 0.00 2.90
37 38 7.494625 CCTAAAAGTTGCTAAGAATACCGATGA 59.505 37.037 0.00 0.00 0.00 2.92
38 39 7.494625 TCCTAAAAGTTGCTAAGAATACCGATG 59.505 37.037 0.00 0.00 0.00 3.84
39 40 7.494952 GTCCTAAAAGTTGCTAAGAATACCGAT 59.505 37.037 0.00 0.00 0.00 4.18
40 41 6.815142 GTCCTAAAAGTTGCTAAGAATACCGA 59.185 38.462 0.00 0.00 0.00 4.69
41 42 6.592607 TGTCCTAAAAGTTGCTAAGAATACCG 59.407 38.462 0.00 0.00 0.00 4.02
42 43 7.916914 TGTCCTAAAAGTTGCTAAGAATACC 57.083 36.000 0.00 0.00 0.00 2.73
43 44 8.451748 CCTTGTCCTAAAAGTTGCTAAGAATAC 58.548 37.037 0.00 0.00 0.00 1.89
44 45 7.610305 CCCTTGTCCTAAAAGTTGCTAAGAATA 59.390 37.037 0.00 0.00 0.00 1.75
45 46 6.434340 CCCTTGTCCTAAAAGTTGCTAAGAAT 59.566 38.462 0.00 0.00 0.00 2.40
46 47 5.768164 CCCTTGTCCTAAAAGTTGCTAAGAA 59.232 40.000 0.00 0.00 0.00 2.52
47 48 5.313712 CCCTTGTCCTAAAAGTTGCTAAGA 58.686 41.667 0.00 0.00 0.00 2.10
48 49 4.459337 CCCCTTGTCCTAAAAGTTGCTAAG 59.541 45.833 0.00 0.00 0.00 2.18
49 50 4.403734 CCCCTTGTCCTAAAAGTTGCTAA 58.596 43.478 0.00 0.00 0.00 3.09
50 51 3.812882 GCCCCTTGTCCTAAAAGTTGCTA 60.813 47.826 0.00 0.00 0.00 3.49
55 56 2.445525 TCAAGCCCCTTGTCCTAAAAGT 59.554 45.455 5.03 0.00 41.66 2.66
60 61 2.239654 CAATCTCAAGCCCCTTGTCCTA 59.760 50.000 5.03 0.00 41.66 2.94
80 81 0.183492 AAGTTGTCTTGGCTGCTCCA 59.817 50.000 0.00 0.00 44.85 3.86
87 88 5.638234 AGTACGATAAGAAAGTTGTCTTGGC 59.362 40.000 0.00 0.00 38.33 4.52
94 95 9.907576 GATGAAATCAGTACGATAAGAAAGTTG 57.092 33.333 0.00 0.00 44.70 3.16
114 115 6.016024 CCATCCAGAAGAAAGTGTTGATGAAA 60.016 38.462 0.00 0.00 32.17 2.69
129 131 1.373570 GGAGCGAAACCATCCAGAAG 58.626 55.000 0.00 0.00 33.08 2.85
158 160 6.169800 AGCTTTCTGAGGAAAAGTCTGATAC 58.830 40.000 0.00 0.00 40.41 2.24
166 168 7.920160 AGAAGAATAGCTTTCTGAGGAAAAG 57.080 36.000 10.60 0.00 40.41 2.27
205 207 4.918588 ACCGGAATAAGAAGACCACAATT 58.081 39.130 9.46 0.00 0.00 2.32
210 212 2.829023 AGGACCGGAATAAGAAGACCA 58.171 47.619 9.46 0.00 0.00 4.02
213 215 2.838202 AGCAAGGACCGGAATAAGAAGA 59.162 45.455 9.46 0.00 0.00 2.87
224 226 2.621526 ACAAGGTTAAAAGCAAGGACCG 59.378 45.455 0.00 0.00 35.56 4.79
233 235 7.802720 GCAATGGCATTTTTACAAGGTTAAAAG 59.197 33.333 10.65 0.00 40.72 2.27
253 255 3.989817 GCTACACTTCCTTTTTGCAATGG 59.010 43.478 0.00 3.54 0.00 3.16
255 257 4.797275 GCTGCTACACTTCCTTTTTGCAAT 60.797 41.667 0.00 0.00 0.00 3.56
257 259 2.034558 GCTGCTACACTTCCTTTTTGCA 59.965 45.455 0.00 0.00 0.00 4.08
265 267 0.107945 CTCCCTGCTGCTACACTTCC 60.108 60.000 0.00 0.00 0.00 3.46
279 281 3.515901 GACACATACAACTCTTCCTCCCT 59.484 47.826 0.00 0.00 0.00 4.20
282 284 6.926313 ACTAAGACACATACAACTCTTCCTC 58.074 40.000 0.00 0.00 0.00 3.71
348 350 8.960075 CGTCCGTAAGAATAAAACAAAATTTGT 58.040 29.630 5.41 5.41 44.06 2.83
353 355 9.565213 TTTTTCGTCCGTAAGAATAAAACAAAA 57.435 25.926 0.00 0.00 43.02 2.44
402 405 1.918262 TCAGGATGGGCTGAAATCACT 59.082 47.619 0.00 0.00 36.16 3.41
420 423 6.412362 TTTCTCCATTCCGGAAATTTTTCA 57.588 33.333 23.08 0.59 45.75 2.69
421 424 7.722795 TTTTTCTCCATTCCGGAAATTTTTC 57.277 32.000 23.08 0.00 45.75 2.29
447 450 0.251341 GCCCATCCTCACCACAACTT 60.251 55.000 0.00 0.00 0.00 2.66
448 451 1.380302 GCCCATCCTCACCACAACT 59.620 57.895 0.00 0.00 0.00 3.16
449 452 2.040544 CGCCCATCCTCACCACAAC 61.041 63.158 0.00 0.00 0.00 3.32
451 454 2.606213 TCGCCCATCCTCACCACA 60.606 61.111 0.00 0.00 0.00 4.17
452 455 2.125106 GTCGCCCATCCTCACCAC 60.125 66.667 0.00 0.00 0.00 4.16
453 456 3.770040 CGTCGCCCATCCTCACCA 61.770 66.667 0.00 0.00 0.00 4.17
470 473 0.096454 GGTTCGACATAAGCAACGGC 59.904 55.000 0.00 0.00 41.61 5.68
471 474 1.722011 AGGTTCGACATAAGCAACGG 58.278 50.000 0.00 0.00 0.00 4.44
472 475 2.724839 GCAAGGTTCGACATAAGCAACG 60.725 50.000 0.00 0.00 0.00 4.10
473 476 2.225491 TGCAAGGTTCGACATAAGCAAC 59.775 45.455 0.00 0.00 0.00 4.17
474 477 2.499197 TGCAAGGTTCGACATAAGCAA 58.501 42.857 0.00 0.00 0.00 3.91
475 478 2.177394 TGCAAGGTTCGACATAAGCA 57.823 45.000 0.00 0.00 0.00 3.91
476 479 2.420022 ACATGCAAGGTTCGACATAAGC 59.580 45.455 0.00 0.00 0.00 3.09
477 480 5.351465 ACTTACATGCAAGGTTCGACATAAG 59.649 40.000 10.43 0.83 28.09 1.73
478 481 5.121611 CACTTACATGCAAGGTTCGACATAA 59.878 40.000 10.43 0.00 28.09 1.90
479 482 4.629634 CACTTACATGCAAGGTTCGACATA 59.370 41.667 10.43 0.00 28.09 2.29
480 483 3.436704 CACTTACATGCAAGGTTCGACAT 59.563 43.478 10.43 0.00 28.09 3.06
481 484 2.805671 CACTTACATGCAAGGTTCGACA 59.194 45.455 10.43 0.00 28.09 4.35
482 485 2.806244 ACACTTACATGCAAGGTTCGAC 59.194 45.455 10.43 0.00 28.09 4.20
483 486 3.120321 ACACTTACATGCAAGGTTCGA 57.880 42.857 10.43 0.00 28.09 3.71
484 487 3.896648 AACACTTACATGCAAGGTTCG 57.103 42.857 10.43 0.00 28.09 3.95
519 522 1.678627 GGCTCATAGAGACAGCTCGAA 59.321 52.381 0.00 0.00 45.98 3.71
522 525 1.001815 GTCGGCTCATAGAGACAGCTC 60.002 57.143 0.27 0.00 37.60 4.09
527 530 2.563471 AAACGTCGGCTCATAGAGAC 57.437 50.000 0.00 0.00 33.67 3.36
571 574 1.331214 AACACATGGCAACCCAAGAG 58.669 50.000 0.00 0.00 46.14 2.85
577 580 1.496934 CCGAAAAACACATGGCAACC 58.503 50.000 0.00 0.00 0.00 3.77
578 581 0.858583 GCCGAAAAACACATGGCAAC 59.141 50.000 0.00 0.00 45.06 4.17
601 604 1.234821 CTTAGCAAAACTGTCCGGCA 58.765 50.000 0.00 0.00 0.00 5.69
603 606 2.767505 AGACTTAGCAAAACTGTCCGG 58.232 47.619 0.00 0.00 0.00 5.14
605 608 5.062308 CGACATAGACTTAGCAAAACTGTCC 59.938 44.000 0.00 0.00 0.00 4.02
606 609 5.862323 TCGACATAGACTTAGCAAAACTGTC 59.138 40.000 0.00 0.00 0.00 3.51
607 610 5.634020 GTCGACATAGACTTAGCAAAACTGT 59.366 40.000 11.55 0.00 38.09 3.55
608 611 6.083925 GTCGACATAGACTTAGCAAAACTG 57.916 41.667 11.55 0.00 38.09 3.16
620 623 9.011407 CATAACAAAGTCTAAGTCGACATAGAC 57.989 37.037 36.35 36.35 43.59 2.59
621 624 8.737175 ACATAACAAAGTCTAAGTCGACATAGA 58.263 33.333 22.90 22.90 36.38 1.98
622 625 8.912787 ACATAACAAAGTCTAAGTCGACATAG 57.087 34.615 19.29 19.29 36.38 2.23
623 626 8.737175 AGACATAACAAAGTCTAAGTCGACATA 58.263 33.333 19.50 9.54 42.92 2.29
625 628 6.978338 AGACATAACAAAGTCTAAGTCGACA 58.022 36.000 19.50 0.00 42.92 4.35
626 629 7.082602 TGAGACATAACAAAGTCTAAGTCGAC 58.917 38.462 7.70 7.70 44.61 4.20
627 630 7.210718 TGAGACATAACAAAGTCTAAGTCGA 57.789 36.000 0.00 0.00 44.61 4.20
628 631 7.499438 CTGAGACATAACAAAGTCTAAGTCG 57.501 40.000 0.00 0.00 44.61 4.18
653 656 9.927668 TGCGAGATCAAATGAATATAGTATCAA 57.072 29.630 0.00 0.00 0.00 2.57
655 658 9.029243 CCTGCGAGATCAAATGAATATAGTATC 57.971 37.037 0.00 0.00 0.00 2.24
656 659 7.984050 CCCTGCGAGATCAAATGAATATAGTAT 59.016 37.037 0.00 0.00 0.00 2.12
657 660 7.178451 TCCCTGCGAGATCAAATGAATATAGTA 59.822 37.037 0.00 0.00 0.00 1.82
658 661 6.014242 TCCCTGCGAGATCAAATGAATATAGT 60.014 38.462 0.00 0.00 0.00 2.12
659 662 6.401394 TCCCTGCGAGATCAAATGAATATAG 58.599 40.000 0.00 0.00 0.00 1.31
660 663 6.211384 TCTCCCTGCGAGATCAAATGAATATA 59.789 38.462 0.00 0.00 42.97 0.86
661 664 5.012458 TCTCCCTGCGAGATCAAATGAATAT 59.988 40.000 0.00 0.00 42.97 1.28
662 665 4.344968 TCTCCCTGCGAGATCAAATGAATA 59.655 41.667 0.00 0.00 42.97 1.75
665 668 2.110578 TCTCCCTGCGAGATCAAATGA 58.889 47.619 0.00 0.00 42.97 2.57
666 669 2.609427 TCTCCCTGCGAGATCAAATG 57.391 50.000 0.00 0.00 42.97 2.32
674 677 0.738975 TGTACGAATCTCCCTGCGAG 59.261 55.000 0.00 0.00 40.30 5.03
675 678 1.179152 TTGTACGAATCTCCCTGCGA 58.821 50.000 0.00 0.00 0.00 5.10
676 679 2.004583 TTTGTACGAATCTCCCTGCG 57.995 50.000 0.00 0.00 0.00 5.18
731 734 8.801299 CCATGTCTCAGTCAAGTGATATATAGT 58.199 37.037 0.00 0.00 0.00 2.12
732 735 8.801299 ACCATGTCTCAGTCAAGTGATATATAG 58.199 37.037 0.00 0.00 0.00 1.31
733 736 8.712228 ACCATGTCTCAGTCAAGTGATATATA 57.288 34.615 0.00 0.00 0.00 0.86
734 737 7.609097 ACCATGTCTCAGTCAAGTGATATAT 57.391 36.000 0.00 0.00 0.00 0.86
735 738 7.423844 AACCATGTCTCAGTCAAGTGATATA 57.576 36.000 0.00 0.00 0.00 0.86
736 739 5.946942 ACCATGTCTCAGTCAAGTGATAT 57.053 39.130 0.00 0.00 0.00 1.63
737 740 5.745312 AACCATGTCTCAGTCAAGTGATA 57.255 39.130 0.00 0.00 0.00 2.15
738 741 4.630644 AACCATGTCTCAGTCAAGTGAT 57.369 40.909 0.00 0.00 0.00 3.06
739 742 4.558697 CGTAACCATGTCTCAGTCAAGTGA 60.559 45.833 0.00 0.00 0.00 3.41
740 743 3.675225 CGTAACCATGTCTCAGTCAAGTG 59.325 47.826 0.00 0.00 0.00 3.16
741 744 3.321111 ACGTAACCATGTCTCAGTCAAGT 59.679 43.478 0.00 0.00 0.00 3.16
742 745 3.914312 ACGTAACCATGTCTCAGTCAAG 58.086 45.455 0.00 0.00 0.00 3.02
743 746 3.572682 AGACGTAACCATGTCTCAGTCAA 59.427 43.478 0.00 0.00 46.07 3.18
744 747 3.154710 AGACGTAACCATGTCTCAGTCA 58.845 45.455 0.00 0.00 46.07 3.41
745 748 3.851976 AGACGTAACCATGTCTCAGTC 57.148 47.619 0.00 0.00 46.07 3.51
769 772 0.604511 TGTGTCTAGGTCGCAGTCGA 60.605 55.000 0.00 0.00 43.28 4.20
770 773 0.454620 GTGTGTCTAGGTCGCAGTCG 60.455 60.000 0.00 0.00 0.00 4.18
771 774 0.109226 GGTGTGTCTAGGTCGCAGTC 60.109 60.000 0.00 0.00 0.00 3.51
772 775 1.533469 GGGTGTGTCTAGGTCGCAGT 61.533 60.000 0.00 0.00 0.00 4.40
773 776 1.215647 GGGTGTGTCTAGGTCGCAG 59.784 63.158 0.00 0.00 0.00 5.18
775 778 1.067212 CATAGGGTGTGTCTAGGTCGC 59.933 57.143 0.00 0.00 0.00 5.19
777 780 1.413077 GGCATAGGGTGTGTCTAGGTC 59.587 57.143 0.00 0.00 0.00 3.85
781 784 2.500098 GTTCTGGCATAGGGTGTGTCTA 59.500 50.000 0.00 0.00 0.00 2.59
782 785 1.279271 GTTCTGGCATAGGGTGTGTCT 59.721 52.381 0.00 0.00 0.00 3.41
783 786 1.003118 TGTTCTGGCATAGGGTGTGTC 59.997 52.381 0.00 0.00 0.00 3.67
784 787 1.003580 CTGTTCTGGCATAGGGTGTGT 59.996 52.381 0.00 0.00 0.00 3.72
785 788 1.003580 ACTGTTCTGGCATAGGGTGTG 59.996 52.381 0.00 0.00 0.00 3.82
786 789 1.362224 ACTGTTCTGGCATAGGGTGT 58.638 50.000 0.00 0.00 0.00 4.16
788 791 3.115390 ACATACTGTTCTGGCATAGGGT 58.885 45.455 0.00 0.00 0.00 4.34
791 1273 6.986231 TCATGTTACATACTGTTCTGGCATAG 59.014 38.462 0.00 0.00 0.00 2.23
825 1307 1.941403 ATGGGAAGGGAGCCACCATG 61.941 60.000 0.00 0.00 40.24 3.66
835 1317 4.849810 TGGATATTAGGTGTATGGGAAGGG 59.150 45.833 0.00 0.00 0.00 3.95
840 1322 7.922382 AGAGATTTGGATATTAGGTGTATGGG 58.078 38.462 0.00 0.00 0.00 4.00
849 1331 9.930693 GGTTAGGTGTAGAGATTTGGATATTAG 57.069 37.037 0.00 0.00 0.00 1.73
850 1332 8.877195 GGGTTAGGTGTAGAGATTTGGATATTA 58.123 37.037 0.00 0.00 0.00 0.98
854 1336 5.036916 TGGGTTAGGTGTAGAGATTTGGAT 58.963 41.667 0.00 0.00 0.00 3.41
880 1363 1.920325 TGGCTCCTGAGTTGAGGGG 60.920 63.158 0.00 0.00 36.55 4.79
887 1371 6.155393 GGCTTATTATATAGTGGCTCCTGAGT 59.845 42.308 0.00 0.00 0.00 3.41
893 1377 7.354751 AGCTAGGCTTATTATATAGTGGCTC 57.645 40.000 0.00 0.00 33.89 4.70
895 1379 7.014808 AGCTAGCTAGGCTTATTATATAGTGGC 59.985 40.741 17.69 2.04 40.44 5.01
936 1420 6.200286 ACGTGAAGTGTTATTGTACAAGTGAG 59.800 38.462 14.65 0.00 0.00 3.51
937 1421 6.044046 ACGTGAAGTGTTATTGTACAAGTGA 58.956 36.000 14.65 0.00 0.00 3.41
938 1422 6.200286 AGACGTGAAGTGTTATTGTACAAGTG 59.800 38.462 14.65 0.00 0.00 3.16
939 1423 6.278363 AGACGTGAAGTGTTATTGTACAAGT 58.722 36.000 14.65 5.26 0.00 3.16
1212 1699 3.338126 GACGACGTGCGACATCCCT 62.338 63.158 4.58 0.00 44.57 4.20
1437 1924 1.301479 GACGGCAGAACGGAACCTT 60.301 57.895 0.00 0.00 38.39 3.50
1845 2341 2.343758 GTGAGAAGGTCAGCGGCA 59.656 61.111 1.45 0.00 35.13 5.69
2079 2584 2.764128 AGATCGATGGCGGTGGGT 60.764 61.111 0.54 0.00 38.28 4.51
2444 2949 2.584391 GCCACCTCGACCCTGAACT 61.584 63.158 0.00 0.00 0.00 3.01
2479 2984 2.645838 ATGGACATCTTGGGAATCGG 57.354 50.000 0.00 0.00 0.00 4.18
2499 3007 2.963101 CCCGTCCTTCATGTGGAGTATA 59.037 50.000 9.77 0.00 33.78 1.47
2535 3043 1.354040 CATCGTCCTGTCTCTTGTGC 58.646 55.000 0.00 0.00 0.00 4.57
2547 3055 4.683832 AGATTGTACTTAGTGCATCGTCC 58.316 43.478 3.66 0.00 0.00 4.79
2581 3093 1.566231 ACTTGGGAGCTTGGGAATAGG 59.434 52.381 0.00 0.00 0.00 2.57
2582 3094 2.507471 AGACTTGGGAGCTTGGGAATAG 59.493 50.000 0.00 0.00 0.00 1.73
2583 3095 2.562296 AGACTTGGGAGCTTGGGAATA 58.438 47.619 0.00 0.00 0.00 1.75
2584 3096 1.376649 AGACTTGGGAGCTTGGGAAT 58.623 50.000 0.00 0.00 0.00 3.01
2586 3098 2.038863 TTAGACTTGGGAGCTTGGGA 57.961 50.000 0.00 0.00 0.00 4.37
2589 3101 6.042093 TGGAGTATATTAGACTTGGGAGCTTG 59.958 42.308 0.00 0.00 0.00 4.01
2591 3103 5.716979 TGGAGTATATTAGACTTGGGAGCT 58.283 41.667 0.00 0.00 0.00 4.09
2594 3106 6.211584 GCAGATGGAGTATATTAGACTTGGGA 59.788 42.308 0.00 0.00 0.00 4.37
2596 3108 6.997655 TGCAGATGGAGTATATTAGACTTGG 58.002 40.000 0.00 0.00 0.00 3.61
2607 3119 3.181471 GGCGCTATATGCAGATGGAGTAT 60.181 47.826 9.07 0.00 43.06 2.12
2609 3121 1.066573 GGCGCTATATGCAGATGGAGT 60.067 52.381 9.07 0.00 43.06 3.85
2610 3122 1.206610 AGGCGCTATATGCAGATGGAG 59.793 52.381 9.07 6.46 43.06 3.86
2616 3128 1.869774 TGTTCAGGCGCTATATGCAG 58.130 50.000 7.64 0.00 43.06 4.41
2673 3185 0.388649 ACTAGAGCACGTTTCTGGCG 60.389 55.000 9.11 0.00 0.00 5.69
2742 3254 3.622163 TCGCACGTTTACAGGAAAGAAAA 59.378 39.130 0.00 0.00 0.00 2.29
2746 3258 1.459592 CCTCGCACGTTTACAGGAAAG 59.540 52.381 0.00 0.00 0.00 2.62
2762 3274 1.079127 AATCGTGGCCAAGTCCTCG 60.079 57.895 18.61 11.65 42.53 4.63
2787 3299 3.933332 CCCTTACTTCTGTTCCATTCGAC 59.067 47.826 0.00 0.00 0.00 4.20
2819 3331 2.218603 ACAACCACATCCGAAGTGTTC 58.781 47.619 3.25 0.00 35.24 3.18
2820 3332 2.341846 ACAACCACATCCGAAGTGTT 57.658 45.000 3.25 0.00 35.24 3.32
2821 3333 2.341846 AACAACCACATCCGAAGTGT 57.658 45.000 3.25 0.00 35.24 3.55
2822 3334 3.399330 AGTAACAACCACATCCGAAGTG 58.601 45.455 0.00 0.00 36.76 3.16
2823 3335 3.070446 TGAGTAACAACCACATCCGAAGT 59.930 43.478 0.00 0.00 0.00 3.01
2824 3336 3.659786 TGAGTAACAACCACATCCGAAG 58.340 45.455 0.00 0.00 0.00 3.79
2825 3337 3.755112 TGAGTAACAACCACATCCGAA 57.245 42.857 0.00 0.00 0.00 4.30
2826 3338 3.755112 TTGAGTAACAACCACATCCGA 57.245 42.857 0.00 0.00 33.18 4.55
2827 3339 4.454161 TCAATTGAGTAACAACCACATCCG 59.546 41.667 3.38 0.00 41.52 4.18
2828 3340 5.957842 TCAATTGAGTAACAACCACATCC 57.042 39.130 3.38 0.00 41.52 3.51
2829 3341 9.906660 TTTATTCAATTGAGTAACAACCACATC 57.093 29.630 19.58 0.00 41.52 3.06
2831 3343 9.743057 CTTTTATTCAATTGAGTAACAACCACA 57.257 29.630 19.58 4.44 41.52 4.17
2845 3357 9.143631 CTTTTCGGCATTCTCTTTTATTCAATT 57.856 29.630 0.00 0.00 0.00 2.32
2849 3361 6.033937 GTGCTTTTCGGCATTCTCTTTTATTC 59.966 38.462 0.00 0.00 44.34 1.75
2876 3388 2.804421 TTTGCGATGCGTATGTCTTG 57.196 45.000 0.00 0.00 0.00 3.02
2881 3393 3.683989 ACAGATTTTTGCGATGCGTATG 58.316 40.909 0.00 0.00 0.00 2.39
2888 3400 4.143115 CGTACACAGACAGATTTTTGCGAT 60.143 41.667 0.00 0.00 0.00 4.58
2891 3403 4.211374 ACTCGTACACAGACAGATTTTTGC 59.789 41.667 0.00 0.00 0.00 3.68
2912 3424 0.040499 AGGAGGAAGAAGAGCGGACT 59.960 55.000 0.00 0.00 0.00 3.85
2913 3425 0.174617 CAGGAGGAAGAAGAGCGGAC 59.825 60.000 0.00 0.00 0.00 4.79
2914 3426 1.608717 GCAGGAGGAAGAAGAGCGGA 61.609 60.000 0.00 0.00 0.00 5.54
2946 3458 0.753479 GGGAGCCTGAGACTCGATCA 60.753 60.000 0.00 0.00 34.87 2.92
2981 3493 1.751924 GCCCTACTCCTATATCTGCCG 59.248 57.143 0.00 0.00 0.00 5.69
2983 3495 1.751924 CGGCCCTACTCCTATATCTGC 59.248 57.143 0.00 0.00 0.00 4.26
2996 3508 0.758734 CAATCTCATGACCGGCCCTA 59.241 55.000 0.00 0.00 0.00 3.53
3001 3513 1.431488 CGCCACAATCTCATGACCGG 61.431 60.000 0.00 0.00 0.00 5.28
3070 3584 6.401474 CCATCATAAGTGACTTTGAGTTGACG 60.401 42.308 1.97 0.00 37.14 4.35
3095 3609 0.761802 GGAGGGATCCAGGATGACAC 59.238 60.000 15.23 0.00 39.69 3.67
3099 3613 1.190833 CGGAGGAGGGATCCAGGATG 61.191 65.000 15.23 0.00 36.57 3.51
3126 3643 0.735287 GGCGTCTACGTTCACCTTCC 60.735 60.000 0.00 0.00 42.22 3.46
3146 3663 1.922444 GCTGTCTAGATCACGTAGCGC 60.922 57.143 0.00 0.00 0.00 5.92
3177 3694 1.891060 GCTCCTTGTGAACGACGCAG 61.891 60.000 0.00 0.00 40.21 5.18
3178 3695 1.954146 GCTCCTTGTGAACGACGCA 60.954 57.895 0.00 0.00 37.22 5.24
3184 3701 1.815003 CCCTCATTGCTCCTTGTGAAC 59.185 52.381 0.00 0.00 0.00 3.18
3197 3714 3.907221 CTCCCATGAAATCACCCTCATT 58.093 45.455 0.00 0.00 29.69 2.57
3204 3721 3.698040 ACTTGATGCTCCCATGAAATCAC 59.302 43.478 0.00 0.00 0.00 3.06
3205 3722 3.697542 CACTTGATGCTCCCATGAAATCA 59.302 43.478 0.00 0.00 0.00 2.57
3206 3723 3.698040 ACACTTGATGCTCCCATGAAATC 59.302 43.478 0.00 0.00 0.00 2.17
3207 3724 3.446161 CACACTTGATGCTCCCATGAAAT 59.554 43.478 0.00 0.00 0.00 2.17
3231 3748 1.918293 TCCCGGATGCCAGTGAAGT 60.918 57.895 0.73 0.00 0.00 3.01
3234 3751 3.399181 GGTCCCGGATGCCAGTGA 61.399 66.667 0.73 0.00 0.00 3.41
3237 3754 1.987807 AATGAGGTCCCGGATGCCAG 61.988 60.000 0.73 0.00 0.00 4.85
3239 3756 1.227973 GAATGAGGTCCCGGATGCC 60.228 63.158 0.73 1.13 0.00 4.40
3267 3784 1.435577 AGTACGTCGCCATCCAAAAC 58.564 50.000 0.00 0.00 0.00 2.43
3276 3793 0.980525 GAACGAGAAAGTACGTCGCC 59.019 55.000 0.00 0.00 41.87 5.54
3318 3835 1.552792 TGTATTGATGACACGGAGGCA 59.447 47.619 0.00 0.00 0.00 4.75
3428 3953 4.925646 GTCCTTGTTTGAATTGCTGGATTC 59.074 41.667 0.00 0.00 36.73 2.52
3435 3960 6.419413 TGTTTTATCGTCCTTGTTTGAATTGC 59.581 34.615 0.00 0.00 0.00 3.56
3451 3976 7.800380 GTGCATATTCATCCTTCTGTTTTATCG 59.200 37.037 0.00 0.00 0.00 2.92
3508 4033 4.610605 TTTTGGTGATCAGTCGGTAGAA 57.389 40.909 0.00 0.00 0.00 2.10
3510 4035 3.871594 GGATTTTGGTGATCAGTCGGTAG 59.128 47.826 0.00 0.00 0.00 3.18
3515 4040 3.441572 CACTGGGATTTTGGTGATCAGTC 59.558 47.826 0.00 0.00 32.51 3.51
3517 4042 3.424703 ACACTGGGATTTTGGTGATCAG 58.575 45.455 0.00 0.00 34.28 2.90
3525 4050 2.289010 GGGAAGCAACACTGGGATTTTG 60.289 50.000 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.