Multiple sequence alignment - TraesCS7A01G109000

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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 TraesCS7A01G109000 chr7A 100.000 3762 0 0 1 3762 66231775 66235536 0.000000e+00 6948.0
1 TraesCS7A01G109000 chr7A 100.000 30 0 0 4059 4088 66235833 66235862 5.710000e-04 56.5
2 TraesCS7A01G109000 chr7D 96.637 2349 68 4 860 3197 63442305 63444653 0.000000e+00 3890.0
3 TraesCS7A01G109000 chr7D 91.958 572 35 6 3200 3760 63444703 63445274 0.000000e+00 791.0
4 TraesCS7A01G109000 chr7D 88.588 517 26 4 1 516 63441845 63442329 7.560000e-167 597.0
5 TraesCS7A01G109000 chr7D 83.368 481 33 22 3207 3674 63451377 63451823 6.360000e-108 401.0
6 TraesCS7A01G109000 chr7D 92.800 125 9 0 2225 2349 63451248 63451372 9.030000e-42 182.0
7 TraesCS7A01G109000 chr7B 96.369 2341 82 3 860 3197 3846795 3849135 0.000000e+00 3849.0
8 TraesCS7A01G109000 chr7B 96.092 563 20 1 3200 3762 3849185 3849745 0.000000e+00 917.0
9 TraesCS7A01G109000 chr7B 92.353 340 25 1 178 516 3846480 3846819 2.210000e-132 483.0
10 TraesCS7A01G109000 chr7B 94.737 133 7 0 3 135 3798832 3798964 1.490000e-49 207.0
11 TraesCS7A01G109000 chr6B 93.611 360 23 0 514 873 33490222 33490581 4.650000e-149 538.0
12 TraesCS7A01G109000 chr2B 93.056 360 25 0 517 876 507912949 507913308 1.010000e-145 527.0
13 TraesCS7A01G109000 chr6A 94.186 344 16 4 534 873 523216708 523217051 4.680000e-144 521.0
14 TraesCS7A01G109000 chr4A 94.186 344 15 5 534 873 485278085 485277743 1.680000e-143 520.0
15 TraesCS7A01G109000 chr4A 91.736 363 25 1 517 874 656800809 656801171 2.190000e-137 499.0
16 TraesCS7A01G109000 chr1A 94.186 344 15 5 534 873 571547776 571547434 1.680000e-143 520.0
17 TraesCS7A01G109000 chr1A 92.287 363 23 1 516 873 461378265 461377903 1.010000e-140 510.0
18 TraesCS7A01G109000 chr2A 93.895 344 16 5 534 873 731260927 731261269 7.840000e-142 514.0
19 TraesCS7A01G109000 chrUn 91.736 363 25 1 517 874 241404952 241405314 2.190000e-137 499.0
20 TraesCS7A01G109000 chr3D 83.951 81 13 0 151 231 254607852 254607772 1.220000e-10 78.7


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 TraesCS7A01G109000 chr7A 66231775 66235862 4087 False 3502.250000 6948 100.000000 1 4088 2 chr7A.!!$F1 4087
1 TraesCS7A01G109000 chr7D 63441845 63445274 3429 False 1759.333333 3890 92.394333 1 3760 3 chr7D.!!$F1 3759
2 TraesCS7A01G109000 chr7D 63451248 63451823 575 False 291.500000 401 88.084000 2225 3674 2 chr7D.!!$F2 1449
3 TraesCS7A01G109000 chr7B 3846480 3849745 3265 False 1749.666667 3849 94.938000 178 3762 3 chr7B.!!$F2 3584

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
773 782 0.035056 CGGGCTTGATTTCAGGGAGT 60.035 55.0 0.00 0.00 0.0 3.85 F
1890 1907 0.163788 CGCCAGATGTTGTGACGTTC 59.836 55.0 0.00 0.00 0.0 3.95 F
2199 2216 0.318784 GAGTGAAGCCTGACGTCGTT 60.319 55.0 11.62 1.41 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2421 2438 0.462375 TGCAATGGCCATCAATCAGC 59.538 50.000 21.08 15.99 40.13 4.26 R
3012 3029 0.038526 CAGCGTCCACGTTACCTTCT 60.039 55.000 0.36 0.00 42.22 2.85 R
3444 3509 3.377253 AGCTGGGATCAATGTGTCAAT 57.623 42.857 0.00 0.00 0.00 2.57 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
28 29 3.922240 TCGTCTCTAACATTTAACGGTGC 59.078 43.478 0.00 0.00 0.00 5.01
90 91 6.154203 TCTTGTATTCTAGCATGTCCTCAG 57.846 41.667 0.00 0.00 0.00 3.35
123 124 6.427242 GCCTTTCTTTAGATAGGATTTACCGG 59.573 42.308 17.23 0.00 43.29 5.28
124 125 7.506971 CCTTTCTTTAGATAGGATTTACCGGT 58.493 38.462 13.98 13.98 43.29 5.28
125 126 7.656542 CCTTTCTTTAGATAGGATTTACCGGTC 59.343 40.741 12.40 0.00 43.29 4.79
126 127 7.909485 TTCTTTAGATAGGATTTACCGGTCT 57.091 36.000 12.40 3.65 44.74 3.85
127 128 7.521871 TCTTTAGATAGGATTTACCGGTCTC 57.478 40.000 12.40 6.80 44.74 3.36
128 129 6.492772 TCTTTAGATAGGATTTACCGGTCTCC 59.507 42.308 12.40 16.54 44.74 3.71
129 130 4.472690 AGATAGGATTTACCGGTCTCCT 57.527 45.455 27.13 27.13 44.74 3.69
130 131 4.409187 AGATAGGATTTACCGGTCTCCTC 58.591 47.826 27.58 18.39 44.74 3.71
131 132 1.400737 AGGATTTACCGGTCTCCTCG 58.599 55.000 21.66 0.00 44.74 4.63
139 140 3.097461 CGGTCTCCTCGGATGTACT 57.903 57.895 0.00 0.00 0.00 2.73
140 141 2.251409 CGGTCTCCTCGGATGTACTA 57.749 55.000 0.00 0.00 0.00 1.82
141 142 2.144730 CGGTCTCCTCGGATGTACTAG 58.855 57.143 0.00 0.00 0.00 2.57
142 143 2.485124 CGGTCTCCTCGGATGTACTAGT 60.485 54.545 0.00 0.00 0.00 2.57
143 144 3.553904 GGTCTCCTCGGATGTACTAGTT 58.446 50.000 0.00 0.00 0.00 2.24
144 145 3.315749 GGTCTCCTCGGATGTACTAGTTG 59.684 52.174 0.00 0.00 0.00 3.16
145 146 3.315749 GTCTCCTCGGATGTACTAGTTGG 59.684 52.174 0.00 0.00 0.00 3.77
146 147 2.623889 CTCCTCGGATGTACTAGTTGGG 59.376 54.545 0.00 0.00 0.00 4.12
147 148 1.068741 CCTCGGATGTACTAGTTGGGC 59.931 57.143 0.00 0.00 0.00 5.36
165 166 1.445410 CACGGTTTCGGCTCGATCA 60.445 57.895 0.00 0.00 41.39 2.92
244 245 5.721960 ACAATGGTATTCTGTACTCCTGACT 59.278 40.000 0.00 0.00 0.00 3.41
253 254 5.247084 TCTGTACTCCTGACTAGTGACTTC 58.753 45.833 0.00 0.00 0.00 3.01
266 267 9.020731 TGACTAGTGACTTCTATGTAACAATCA 57.979 33.333 0.00 0.00 0.00 2.57
287 288 3.004734 CAGTTTCTTTTGCCGTGAATCCT 59.995 43.478 0.00 0.00 0.00 3.24
291 292 3.486383 TCTTTTGCCGTGAATCCTTCTT 58.514 40.909 0.00 0.00 0.00 2.52
292 293 3.253188 TCTTTTGCCGTGAATCCTTCTTG 59.747 43.478 0.00 0.00 0.00 3.02
414 423 4.038271 TCAGCATGGACTTGGAAGAAAT 57.962 40.909 0.00 0.00 36.16 2.17
415 424 4.012374 TCAGCATGGACTTGGAAGAAATC 58.988 43.478 0.00 0.00 36.16 2.17
416 425 4.015084 CAGCATGGACTTGGAAGAAATCT 58.985 43.478 0.00 0.00 0.00 2.40
417 426 4.461781 CAGCATGGACTTGGAAGAAATCTT 59.538 41.667 0.00 0.00 39.23 2.40
418 427 7.521377 TCAGCATGGACTTGGAAGAAATCTTC 61.521 42.308 13.56 13.56 43.61 2.87
419 428 9.806305 TCAGCATGGACTTGGAAGAAATCTTCA 62.806 40.741 21.23 7.95 44.97 3.02
433 442 8.964476 AAGAAATCTTCAAAAGTAGTGTCAGA 57.036 30.769 0.00 0.00 0.00 3.27
508 517 0.676736 TTTTTGGCCCAGCGTTAAGG 59.323 50.000 0.00 0.00 0.00 2.69
509 518 0.468400 TTTTGGCCCAGCGTTAAGGT 60.468 50.000 0.00 0.00 0.00 3.50
510 519 0.891904 TTTGGCCCAGCGTTAAGGTC 60.892 55.000 0.00 0.00 0.00 3.85
511 520 2.058125 TTGGCCCAGCGTTAAGGTCA 62.058 55.000 0.00 0.00 32.20 4.02
512 521 1.302993 GGCCCAGCGTTAAGGTCAA 60.303 57.895 0.00 0.00 0.00 3.18
513 522 0.891904 GGCCCAGCGTTAAGGTCAAA 60.892 55.000 0.00 0.00 0.00 2.69
514 523 0.955905 GCCCAGCGTTAAGGTCAAAA 59.044 50.000 0.00 0.00 0.00 2.44
515 524 1.335597 GCCCAGCGTTAAGGTCAAAAC 60.336 52.381 0.00 0.00 0.00 2.43
516 525 2.227194 CCCAGCGTTAAGGTCAAAACT 58.773 47.619 0.00 0.00 0.00 2.66
517 526 3.404899 CCCAGCGTTAAGGTCAAAACTA 58.595 45.455 0.00 0.00 0.00 2.24
518 527 3.816523 CCCAGCGTTAAGGTCAAAACTAA 59.183 43.478 0.00 0.00 0.00 2.24
519 528 4.276431 CCCAGCGTTAAGGTCAAAACTAAA 59.724 41.667 0.00 0.00 0.00 1.85
520 529 5.209977 CCAGCGTTAAGGTCAAAACTAAAC 58.790 41.667 0.00 0.00 0.00 2.01
521 530 5.209977 CAGCGTTAAGGTCAAAACTAAACC 58.790 41.667 0.00 0.00 0.00 3.27
522 531 4.276678 AGCGTTAAGGTCAAAACTAAACCC 59.723 41.667 0.00 0.00 33.33 4.11
523 532 4.775664 CGTTAAGGTCAAAACTAAACCCG 58.224 43.478 0.00 0.00 33.33 5.28
524 533 4.319694 CGTTAAGGTCAAAACTAAACCCGG 60.320 45.833 0.00 0.00 33.33 5.73
525 534 2.281539 AGGTCAAAACTAAACCCGGG 57.718 50.000 22.25 22.25 33.33 5.73
526 535 0.599558 GGTCAAAACTAAACCCGGGC 59.400 55.000 24.08 0.00 0.00 6.13
527 536 1.320507 GTCAAAACTAAACCCGGGCA 58.679 50.000 24.08 4.89 0.00 5.36
528 537 1.890489 GTCAAAACTAAACCCGGGCAT 59.110 47.619 24.08 12.83 0.00 4.40
529 538 1.889829 TCAAAACTAAACCCGGGCATG 59.110 47.619 24.08 11.30 0.00 4.06
530 539 1.067213 CAAAACTAAACCCGGGCATGG 60.067 52.381 24.08 14.58 0.00 3.66
597 606 2.983592 CGGGCTCGGGCTTTGTTT 60.984 61.111 7.48 0.00 38.73 2.83
598 607 2.561037 CGGGCTCGGGCTTTGTTTT 61.561 57.895 7.48 0.00 38.73 2.43
599 608 1.006220 GGGCTCGGGCTTTGTTTTG 60.006 57.895 7.48 0.00 38.73 2.44
600 609 1.664649 GGCTCGGGCTTTGTTTTGC 60.665 57.895 7.48 0.00 38.73 3.68
601 610 1.067250 GCTCGGGCTTTGTTTTGCA 59.933 52.632 0.00 0.00 35.22 4.08
602 611 0.940991 GCTCGGGCTTTGTTTTGCAG 60.941 55.000 0.00 0.00 35.22 4.41
603 612 0.940991 CTCGGGCTTTGTTTTGCAGC 60.941 55.000 0.00 0.00 0.00 5.25
604 613 1.955663 CGGGCTTTGTTTTGCAGCC 60.956 57.895 2.37 2.37 44.31 4.85
605 614 4.047834 GGCTTTGTTTTGCAGCCC 57.952 55.556 0.00 0.00 39.57 5.19
606 615 1.955663 GGCTTTGTTTTGCAGCCCG 60.956 57.895 0.00 0.00 39.57 6.13
607 616 1.067250 GCTTTGTTTTGCAGCCCGA 59.933 52.632 0.00 0.00 0.00 5.14
608 617 0.529555 GCTTTGTTTTGCAGCCCGAA 60.530 50.000 0.00 0.00 0.00 4.30
609 618 1.933247 CTTTGTTTTGCAGCCCGAAA 58.067 45.000 0.00 0.00 0.00 3.46
610 619 1.860326 CTTTGTTTTGCAGCCCGAAAG 59.140 47.619 0.00 0.00 0.00 2.62
623 632 2.168054 CGAAAGGTAGTTTGGGCCG 58.832 57.895 0.00 0.00 0.00 6.13
624 633 1.303091 CGAAAGGTAGTTTGGGCCGG 61.303 60.000 0.00 0.00 0.00 6.13
625 634 0.963856 GAAAGGTAGTTTGGGCCGGG 60.964 60.000 2.18 0.00 0.00 5.73
626 635 3.578968 AAGGTAGTTTGGGCCGGGC 62.579 63.158 22.00 22.00 0.00 6.13
627 636 4.043100 GGTAGTTTGGGCCGGGCT 62.043 66.667 28.80 10.22 0.00 5.19
628 637 2.437895 GTAGTTTGGGCCGGGCTC 60.438 66.667 28.80 16.93 0.00 4.70
629 638 4.090588 TAGTTTGGGCCGGGCTCG 62.091 66.667 28.80 0.00 0.00 5.03
639 648 4.394712 CGGGCTCGGGCTTGTCTT 62.395 66.667 7.48 0.00 38.73 3.01
640 649 2.034221 GGGCTCGGGCTTGTCTTT 59.966 61.111 7.48 0.00 38.73 2.52
641 650 1.603739 GGGCTCGGGCTTGTCTTTT 60.604 57.895 7.48 0.00 38.73 2.27
642 651 1.179174 GGGCTCGGGCTTGTCTTTTT 61.179 55.000 7.48 0.00 38.73 1.94
643 652 0.241213 GGCTCGGGCTTGTCTTTTTC 59.759 55.000 7.48 0.00 38.73 2.29
644 653 1.239347 GCTCGGGCTTGTCTTTTTCT 58.761 50.000 0.00 0.00 35.22 2.52
645 654 2.423577 GCTCGGGCTTGTCTTTTTCTA 58.576 47.619 0.00 0.00 35.22 2.10
646 655 3.010420 GCTCGGGCTTGTCTTTTTCTAT 58.990 45.455 0.00 0.00 35.22 1.98
647 656 3.440522 GCTCGGGCTTGTCTTTTTCTATT 59.559 43.478 0.00 0.00 35.22 1.73
648 657 4.082733 GCTCGGGCTTGTCTTTTTCTATTT 60.083 41.667 0.00 0.00 35.22 1.40
649 658 5.564848 GCTCGGGCTTGTCTTTTTCTATTTT 60.565 40.000 0.00 0.00 35.22 1.82
650 659 6.399639 TCGGGCTTGTCTTTTTCTATTTTT 57.600 33.333 0.00 0.00 0.00 1.94
651 660 6.443792 TCGGGCTTGTCTTTTTCTATTTTTC 58.556 36.000 0.00 0.00 0.00 2.29
652 661 5.342259 CGGGCTTGTCTTTTTCTATTTTTCG 59.658 40.000 0.00 0.00 0.00 3.46
653 662 5.633601 GGGCTTGTCTTTTTCTATTTTTCGG 59.366 40.000 0.00 0.00 0.00 4.30
654 663 5.633601 GGCTTGTCTTTTTCTATTTTTCGGG 59.366 40.000 0.00 0.00 0.00 5.14
655 664 5.118664 GCTTGTCTTTTTCTATTTTTCGGGC 59.881 40.000 0.00 0.00 0.00 6.13
656 665 5.128992 TGTCTTTTTCTATTTTTCGGGCC 57.871 39.130 0.00 0.00 0.00 5.80
657 666 4.163552 GTCTTTTTCTATTTTTCGGGCCG 58.836 43.478 22.51 22.51 0.00 6.13
658 667 3.191791 TCTTTTTCTATTTTTCGGGCCGG 59.808 43.478 27.98 8.04 0.00 6.13
659 668 1.465794 TTTCTATTTTTCGGGCCGGG 58.534 50.000 27.98 7.82 0.00 5.73
660 669 1.033202 TTCTATTTTTCGGGCCGGGC 61.033 55.000 27.98 22.00 0.00 6.13
661 670 1.453197 CTATTTTTCGGGCCGGGCT 60.453 57.895 28.80 8.57 0.00 5.19
662 671 1.000646 TATTTTTCGGGCCGGGCTT 60.001 52.632 28.80 10.17 0.00 4.35
663 672 0.612453 TATTTTTCGGGCCGGGCTTT 60.612 50.000 28.80 11.29 0.00 3.51
664 673 1.884075 ATTTTTCGGGCCGGGCTTTC 61.884 55.000 28.80 10.53 0.00 2.62
716 725 2.725641 AAAAACAGCGTTCGGGCC 59.274 55.556 0.00 0.00 0.00 5.80
717 726 3.189010 AAAAACAGCGTTCGGGCCG 62.189 57.895 22.51 22.51 0.00 6.13
744 753 4.319133 GCTTCGGGCCTGATTTCA 57.681 55.556 16.96 0.00 34.27 2.69
745 754 2.101700 GCTTCGGGCCTGATTTCAG 58.898 57.895 16.96 11.04 43.40 3.02
753 762 2.273449 CTGATTTCAGGCCGGGCT 59.727 61.111 27.45 27.45 40.20 5.19
754 763 1.821332 CTGATTTCAGGCCGGGCTC 60.821 63.158 30.43 17.57 40.20 4.70
755 764 2.897350 GATTTCAGGCCGGGCTCG 60.897 66.667 30.43 22.69 0.00 5.03
765 774 2.438434 CGGGCTCGGGCTTGATTT 60.438 61.111 7.48 0.00 38.73 2.17
766 775 2.472909 CGGGCTCGGGCTTGATTTC 61.473 63.158 7.48 0.00 38.73 2.17
767 776 1.378514 GGGCTCGGGCTTGATTTCA 60.379 57.895 7.48 0.00 38.73 2.69
768 777 1.379642 GGGCTCGGGCTTGATTTCAG 61.380 60.000 7.48 0.00 38.73 3.02
769 778 1.379642 GGCTCGGGCTTGATTTCAGG 61.380 60.000 7.48 0.00 38.73 3.86
770 779 1.379642 GCTCGGGCTTGATTTCAGGG 61.380 60.000 0.00 0.00 35.22 4.45
771 780 0.253044 CTCGGGCTTGATTTCAGGGA 59.747 55.000 0.00 0.00 0.00 4.20
772 781 0.253044 TCGGGCTTGATTTCAGGGAG 59.747 55.000 0.00 0.00 0.00 4.30
773 782 0.035056 CGGGCTTGATTTCAGGGAGT 60.035 55.000 0.00 0.00 0.00 3.85
774 783 1.209504 CGGGCTTGATTTCAGGGAGTA 59.790 52.381 0.00 0.00 0.00 2.59
775 784 2.158755 CGGGCTTGATTTCAGGGAGTAT 60.159 50.000 0.00 0.00 0.00 2.12
776 785 3.685550 CGGGCTTGATTTCAGGGAGTATT 60.686 47.826 0.00 0.00 0.00 1.89
777 786 4.281657 GGGCTTGATTTCAGGGAGTATTT 58.718 43.478 0.00 0.00 0.00 1.40
778 787 4.339530 GGGCTTGATTTCAGGGAGTATTTC 59.660 45.833 0.00 0.00 0.00 2.17
779 788 4.035675 GGCTTGATTTCAGGGAGTATTTCG 59.964 45.833 0.00 0.00 0.00 3.46
780 789 4.035675 GCTTGATTTCAGGGAGTATTTCGG 59.964 45.833 0.00 0.00 0.00 4.30
781 790 4.150897 TGATTTCAGGGAGTATTTCGGG 57.849 45.455 0.00 0.00 0.00 5.14
782 791 2.413310 TTTCAGGGAGTATTTCGGGC 57.587 50.000 0.00 0.00 0.00 6.13
783 792 1.580059 TTCAGGGAGTATTTCGGGCT 58.420 50.000 0.00 0.00 0.00 5.19
784 793 1.580059 TCAGGGAGTATTTCGGGCTT 58.420 50.000 0.00 0.00 0.00 4.35
785 794 1.485066 TCAGGGAGTATTTCGGGCTTC 59.515 52.381 0.00 0.00 0.00 3.86
786 795 0.464452 AGGGAGTATTTCGGGCTTCG 59.536 55.000 0.00 0.00 40.90 3.79
787 796 0.532196 GGGAGTATTTCGGGCTTCGG 60.532 60.000 0.75 0.00 39.77 4.30
788 797 0.532196 GGAGTATTTCGGGCTTCGGG 60.532 60.000 0.75 0.00 39.77 5.14
789 798 1.153229 AGTATTTCGGGCTTCGGGC 60.153 57.895 0.75 0.00 39.77 6.13
807 816 4.082523 CGGGCTCGGGCTTGAGAA 62.083 66.667 7.48 0.00 38.28 2.87
808 817 2.351276 GGGCTCGGGCTTGAGAAA 59.649 61.111 7.48 0.00 38.28 2.52
809 818 1.077429 GGGCTCGGGCTTGAGAAAT 60.077 57.895 7.48 0.00 38.28 2.17
810 819 1.379642 GGGCTCGGGCTTGAGAAATG 61.380 60.000 7.48 0.00 38.28 2.32
811 820 0.392998 GGCTCGGGCTTGAGAAATGA 60.393 55.000 7.48 0.00 38.28 2.57
812 821 1.453155 GCTCGGGCTTGAGAAATGAA 58.547 50.000 0.00 0.00 38.28 2.57
813 822 1.399791 GCTCGGGCTTGAGAAATGAAG 59.600 52.381 0.00 0.00 38.28 3.02
814 823 2.012673 CTCGGGCTTGAGAAATGAAGG 58.987 52.381 1.75 0.00 38.28 3.46
815 824 1.351017 TCGGGCTTGAGAAATGAAGGT 59.649 47.619 0.00 0.00 0.00 3.50
816 825 1.740025 CGGGCTTGAGAAATGAAGGTC 59.260 52.381 0.00 0.00 0.00 3.85
817 826 1.740025 GGGCTTGAGAAATGAAGGTCG 59.260 52.381 0.00 0.00 0.00 4.79
818 827 1.740025 GGCTTGAGAAATGAAGGTCGG 59.260 52.381 0.00 0.00 0.00 4.79
819 828 1.740025 GCTTGAGAAATGAAGGTCGGG 59.260 52.381 0.00 0.00 0.00 5.14
820 829 1.740025 CTTGAGAAATGAAGGTCGGGC 59.260 52.381 0.00 0.00 0.00 6.13
821 830 0.984230 TGAGAAATGAAGGTCGGGCT 59.016 50.000 0.00 0.00 0.00 5.19
822 831 1.351017 TGAGAAATGAAGGTCGGGCTT 59.649 47.619 0.00 0.00 0.00 4.35
823 832 2.224769 TGAGAAATGAAGGTCGGGCTTT 60.225 45.455 0.00 0.00 0.00 3.51
824 833 2.820197 GAGAAATGAAGGTCGGGCTTTT 59.180 45.455 0.00 0.00 0.00 2.27
825 834 4.007659 GAGAAATGAAGGTCGGGCTTTTA 58.992 43.478 0.00 0.00 0.00 1.52
826 835 3.756963 AGAAATGAAGGTCGGGCTTTTAC 59.243 43.478 0.00 0.00 0.00 2.01
827 836 2.871096 ATGAAGGTCGGGCTTTTACA 57.129 45.000 0.00 0.00 0.00 2.41
828 837 2.642154 TGAAGGTCGGGCTTTTACAA 57.358 45.000 0.00 0.00 0.00 2.41
829 838 2.500229 TGAAGGTCGGGCTTTTACAAG 58.500 47.619 0.00 0.00 0.00 3.16
837 846 3.284336 CTTTTACAAGCCCGGCCC 58.716 61.111 5.55 0.00 0.00 5.80
838 847 2.673687 TTTTACAAGCCCGGCCCG 60.674 61.111 5.55 0.00 0.00 6.13
839 848 3.193469 TTTTACAAGCCCGGCCCGA 62.193 57.895 3.71 0.00 0.00 5.14
840 849 2.693896 TTTTACAAGCCCGGCCCGAA 62.694 55.000 3.71 0.00 0.00 4.30
841 850 2.693896 TTTACAAGCCCGGCCCGAAA 62.694 55.000 3.71 0.00 0.00 3.46
842 851 3.905437 TACAAGCCCGGCCCGAAAC 62.905 63.158 3.71 0.00 0.00 2.78
869 878 4.636435 CCCGACGTTTGCCCAGGT 62.636 66.667 0.00 0.00 0.00 4.00
870 879 2.593436 CCGACGTTTGCCCAGGTT 60.593 61.111 0.00 0.00 0.00 3.50
871 880 2.190841 CCGACGTTTGCCCAGGTTT 61.191 57.895 0.00 0.00 0.00 3.27
872 881 0.885596 CCGACGTTTGCCCAGGTTTA 60.886 55.000 0.00 0.00 0.00 2.01
1212 1229 3.898509 CTCCTCGCCCTGCTCTCG 61.899 72.222 0.00 0.00 0.00 4.04
1434 1451 3.157252 GAGGGCTCCATGCTCCGA 61.157 66.667 0.00 0.00 45.11 4.55
1890 1907 0.163788 CGCCAGATGTTGTGACGTTC 59.836 55.000 0.00 0.00 0.00 3.95
1905 1922 0.638746 CGTTCACGTCGCTTATCCAC 59.361 55.000 0.00 0.00 34.11 4.02
1941 1958 1.600916 GAACTTGGAGCGGGCAGTT 60.601 57.895 0.00 0.00 32.02 3.16
2070 2087 1.138661 GCACTGAAGGAGATGAGGGAG 59.861 57.143 0.00 0.00 0.00 4.30
2149 2166 2.409948 AGGAAGAATGGAAGAAGCGG 57.590 50.000 0.00 0.00 0.00 5.52
2152 2169 0.681243 AAGAATGGAAGAAGCGGGGC 60.681 55.000 0.00 0.00 0.00 5.80
2157 2174 1.298667 GGAAGAAGCGGGGCAGTTA 59.701 57.895 0.00 0.00 0.00 2.24
2199 2216 0.318784 GAGTGAAGCCTGACGTCGTT 60.319 55.000 11.62 1.41 0.00 3.85
2275 2292 5.390779 GCATTTGAATTGAACCGGAAAATGG 60.391 40.000 9.46 0.00 35.24 3.16
2345 2362 2.227194 GGGTCTTTGCGAGGAGAAAAA 58.773 47.619 0.00 0.00 0.00 1.94
2388 2405 5.700373 ACTCTTTGAGAAGATGCTTCAACTC 59.300 40.000 9.56 14.48 40.93 3.01
2420 2437 8.893727 ACAGCCTGATGAATTTACTTATACAAC 58.106 33.333 0.00 0.00 0.00 3.32
2421 2438 8.064222 CAGCCTGATGAATTTACTTATACAACG 58.936 37.037 0.00 0.00 0.00 4.10
2583 2600 2.876550 GGAAGCACAACGGTTACTCTTT 59.123 45.455 0.00 0.00 34.82 2.52
2667 2684 3.120025 GCAGGAAAGCTGAGTTTAAGAGC 60.120 47.826 0.00 0.00 0.00 4.09
2880 2897 3.686016 TCCTCCTAATTCAACAAGCACC 58.314 45.455 0.00 0.00 0.00 5.01
2922 2939 3.703001 TTTGAAGAGGGGATGACTGTC 57.297 47.619 0.00 0.00 0.00 3.51
2928 2945 1.519455 GGGGATGACTGTCGAAGCG 60.519 63.158 2.98 0.00 0.00 4.68
3012 3029 5.760253 GGCTCTTATTGATCTCAATCGGAAA 59.240 40.000 8.63 0.00 44.67 3.13
3143 3160 4.333926 GGAGCACTGAATTAACTGATGACC 59.666 45.833 0.00 0.00 0.00 4.02
3146 3163 5.948162 AGCACTGAATTAACTGATGACCATT 59.052 36.000 0.00 0.00 0.00 3.16
3147 3164 6.032094 GCACTGAATTAACTGATGACCATTG 58.968 40.000 0.00 0.00 0.00 2.82
3197 3214 3.312421 GCCTTGCTGAGCGTTATTAATGA 59.688 43.478 0.00 0.00 0.00 2.57
3198 3215 4.023707 GCCTTGCTGAGCGTTATTAATGAT 60.024 41.667 0.00 0.00 0.00 2.45
3209 3273 9.803315 GAGCGTTATTAATGATACAGGATGATA 57.197 33.333 0.00 0.00 39.69 2.15
3218 3282 6.423776 TGATACAGGATGATATGCAGTGAA 57.576 37.500 0.00 0.00 39.69 3.18
3272 3336 8.862325 TCCTATCATGTGAATACAAGTTGTTT 57.138 30.769 14.90 3.08 40.84 2.83
3350 3415 6.985188 TTGCTGTTATCAGGTTAAGACATC 57.015 37.500 3.05 0.00 41.57 3.06
3444 3509 3.968649 TGTACCCTGGTCTCAGTTAACAA 59.031 43.478 8.61 0.00 39.31 2.83
3485 3554 6.209589 CAGCTAGCACCTCTATTGGTCTATTA 59.790 42.308 18.83 0.00 38.45 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.242434 ACATGCACCGTTAAATGTTAGAGA 58.758 37.500 0.00 0.00 28.99 3.10
22 23 0.744414 GCACCATAGACATGCACCGT 60.744 55.000 0.00 0.00 39.23 4.83
28 29 5.878332 TGTTGTTAAGCACCATAGACATG 57.122 39.130 0.00 0.00 0.00 3.21
90 91 2.423577 TCTAAAGAAAGGCTTGCGGTC 58.576 47.619 0.00 0.00 36.80 4.79
123 124 3.315749 CCAACTAGTACATCCGAGGAGAC 59.684 52.174 0.00 0.00 0.00 3.36
124 125 3.552875 CCAACTAGTACATCCGAGGAGA 58.447 50.000 0.00 0.00 0.00 3.71
125 126 2.623889 CCCAACTAGTACATCCGAGGAG 59.376 54.545 0.00 0.00 0.00 3.69
126 127 2.662866 CCCAACTAGTACATCCGAGGA 58.337 52.381 0.00 0.00 0.00 3.71
127 128 1.068741 GCCCAACTAGTACATCCGAGG 59.931 57.143 0.00 0.00 0.00 4.63
128 129 1.754803 TGCCCAACTAGTACATCCGAG 59.245 52.381 0.00 0.00 0.00 4.63
129 130 1.479323 GTGCCCAACTAGTACATCCGA 59.521 52.381 0.00 0.00 0.00 4.55
130 131 1.801395 CGTGCCCAACTAGTACATCCG 60.801 57.143 0.00 0.00 0.00 4.18
131 132 1.472728 CCGTGCCCAACTAGTACATCC 60.473 57.143 0.00 0.00 0.00 3.51
132 133 1.206371 ACCGTGCCCAACTAGTACATC 59.794 52.381 0.00 0.00 0.00 3.06
133 134 1.272807 ACCGTGCCCAACTAGTACAT 58.727 50.000 0.00 0.00 0.00 2.29
134 135 1.050204 AACCGTGCCCAACTAGTACA 58.950 50.000 0.00 0.00 0.00 2.90
135 136 2.071540 GAAACCGTGCCCAACTAGTAC 58.928 52.381 0.00 0.00 0.00 2.73
136 137 1.337074 CGAAACCGTGCCCAACTAGTA 60.337 52.381 0.00 0.00 0.00 1.82
137 138 0.601841 CGAAACCGTGCCCAACTAGT 60.602 55.000 0.00 0.00 0.00 2.57
138 139 1.296056 CCGAAACCGTGCCCAACTAG 61.296 60.000 0.00 0.00 0.00 2.57
139 140 1.301874 CCGAAACCGTGCCCAACTA 60.302 57.895 0.00 0.00 0.00 2.24
140 141 2.593436 CCGAAACCGTGCCCAACT 60.593 61.111 0.00 0.00 0.00 3.16
141 142 4.337060 GCCGAAACCGTGCCCAAC 62.337 66.667 0.00 0.00 0.00 3.77
142 143 4.572571 AGCCGAAACCGTGCCCAA 62.573 61.111 0.00 0.00 0.00 4.12
146 147 2.799540 GATCGAGCCGAAACCGTGC 61.800 63.158 1.44 0.00 39.99 5.34
147 148 1.445410 TGATCGAGCCGAAACCGTG 60.445 57.895 0.00 0.00 39.99 4.94
160 161 0.583438 CGGCATGCTTAAGGTGATCG 59.417 55.000 18.92 4.38 0.00 3.69
165 166 2.046285 GTGGCGGCATGCTTAAGGT 61.046 57.895 17.19 0.00 45.43 3.50
253 254 7.271223 CGGCAAAAGAAACTGATTGTTACATAG 59.729 37.037 0.00 0.00 38.03 2.23
266 267 3.222603 AGGATTCACGGCAAAAGAAACT 58.777 40.909 0.00 0.00 0.00 2.66
287 288 8.887393 AGGGTTAGAGTTAGGATTTTACAAGAA 58.113 33.333 0.00 0.00 0.00 2.52
291 292 7.902941 ACCTAGGGTTAGAGTTAGGATTTTACA 59.097 37.037 14.81 0.00 36.88 2.41
292 293 8.316497 ACCTAGGGTTAGAGTTAGGATTTTAC 57.684 38.462 14.81 0.00 36.88 2.01
352 354 6.921486 TTGTGATGTGTACTAACCCTTAGA 57.079 37.500 0.00 0.00 36.73 2.10
414 423 5.069119 TGAGCTCTGACACTACTTTTGAAGA 59.931 40.000 16.19 0.00 0.00 2.87
415 424 5.176590 GTGAGCTCTGACACTACTTTTGAAG 59.823 44.000 16.19 0.00 34.65 3.02
416 425 5.050490 GTGAGCTCTGACACTACTTTTGAA 58.950 41.667 16.19 0.00 34.65 2.69
417 426 4.099419 TGTGAGCTCTGACACTACTTTTGA 59.901 41.667 16.19 0.00 37.81 2.69
418 427 4.371786 TGTGAGCTCTGACACTACTTTTG 58.628 43.478 16.19 0.00 37.81 2.44
419 428 4.672587 TGTGAGCTCTGACACTACTTTT 57.327 40.909 16.19 0.00 37.81 2.27
420 429 4.881019 ATGTGAGCTCTGACACTACTTT 57.119 40.909 16.19 0.00 37.81 2.66
423 432 7.421530 TTTTTAATGTGAGCTCTGACACTAC 57.578 36.000 16.19 3.09 37.81 2.73
427 436 5.335897 GGCATTTTTAATGTGAGCTCTGACA 60.336 40.000 16.19 12.34 0.00 3.58
433 442 5.664294 TGATGGCATTTTTAATGTGAGCT 57.336 34.783 0.00 0.00 0.00 4.09
489 498 0.676736 CCTTAACGCTGGGCCAAAAA 59.323 50.000 8.04 0.00 0.00 1.94
490 499 0.468400 ACCTTAACGCTGGGCCAAAA 60.468 50.000 8.04 0.00 0.00 2.44
508 517 1.320507 TGCCCGGGTTTAGTTTTGAC 58.679 50.000 24.63 0.09 0.00 3.18
509 518 1.889829 CATGCCCGGGTTTAGTTTTGA 59.110 47.619 24.63 0.00 0.00 2.69
510 519 1.067213 CCATGCCCGGGTTTAGTTTTG 60.067 52.381 24.63 8.10 0.00 2.44
511 520 1.262417 CCATGCCCGGGTTTAGTTTT 58.738 50.000 24.63 0.00 0.00 2.43
512 521 0.613572 CCCATGCCCGGGTTTAGTTT 60.614 55.000 24.63 0.00 41.83 2.66
513 522 1.000145 CCCATGCCCGGGTTTAGTT 60.000 57.895 24.63 0.00 41.83 2.24
514 523 2.680965 CCCATGCCCGGGTTTAGT 59.319 61.111 24.63 0.35 41.83 2.24
580 589 2.561037 AAAACAAAGCCCGAGCCCG 61.561 57.895 0.00 0.00 41.25 6.13
581 590 1.006220 CAAAACAAAGCCCGAGCCC 60.006 57.895 0.00 0.00 41.25 5.19
582 591 1.664649 GCAAAACAAAGCCCGAGCC 60.665 57.895 0.00 0.00 41.25 4.70
583 592 0.940991 CTGCAAAACAAAGCCCGAGC 60.941 55.000 0.00 0.00 40.32 5.03
584 593 0.940991 GCTGCAAAACAAAGCCCGAG 60.941 55.000 0.00 0.00 0.00 4.63
585 594 1.067250 GCTGCAAAACAAAGCCCGA 59.933 52.632 0.00 0.00 0.00 5.14
586 595 3.628958 GCTGCAAAACAAAGCCCG 58.371 55.556 0.00 0.00 0.00 6.13
589 598 0.529555 TTCGGGCTGCAAAACAAAGC 60.530 50.000 0.50 0.00 36.17 3.51
590 599 1.860326 CTTTCGGGCTGCAAAACAAAG 59.140 47.619 0.50 0.00 0.00 2.77
591 600 1.472376 CCTTTCGGGCTGCAAAACAAA 60.472 47.619 0.50 0.00 0.00 2.83
592 601 0.103937 CCTTTCGGGCTGCAAAACAA 59.896 50.000 0.50 0.00 0.00 2.83
593 602 1.040339 ACCTTTCGGGCTGCAAAACA 61.040 50.000 0.50 0.00 39.10 2.83
594 603 0.955905 TACCTTTCGGGCTGCAAAAC 59.044 50.000 0.50 0.00 39.10 2.43
595 604 1.243902 CTACCTTTCGGGCTGCAAAA 58.756 50.000 0.50 0.00 39.10 2.44
596 605 0.109723 ACTACCTTTCGGGCTGCAAA 59.890 50.000 0.50 0.00 39.10 3.68
597 606 0.109723 AACTACCTTTCGGGCTGCAA 59.890 50.000 0.50 0.00 39.10 4.08
598 607 0.109723 AAACTACCTTTCGGGCTGCA 59.890 50.000 0.50 0.00 39.10 4.41
599 608 0.521735 CAAACTACCTTTCGGGCTGC 59.478 55.000 0.00 0.00 39.10 5.25
600 609 1.165270 CCAAACTACCTTTCGGGCTG 58.835 55.000 0.00 0.00 39.10 4.85
601 610 0.037734 CCCAAACTACCTTTCGGGCT 59.962 55.000 0.00 0.00 39.10 5.19
602 611 1.592400 GCCCAAACTACCTTTCGGGC 61.592 60.000 0.78 0.78 43.25 6.13
603 612 0.963856 GGCCCAAACTACCTTTCGGG 60.964 60.000 0.00 0.00 41.89 5.14
604 613 1.303091 CGGCCCAAACTACCTTTCGG 61.303 60.000 0.00 0.00 0.00 4.30
605 614 1.303091 CCGGCCCAAACTACCTTTCG 61.303 60.000 0.00 0.00 0.00 3.46
606 615 0.963856 CCCGGCCCAAACTACCTTTC 60.964 60.000 0.00 0.00 0.00 2.62
607 616 1.076014 CCCGGCCCAAACTACCTTT 59.924 57.895 0.00 0.00 0.00 3.11
608 617 2.761160 CCCGGCCCAAACTACCTT 59.239 61.111 0.00 0.00 0.00 3.50
609 618 4.043100 GCCCGGCCCAAACTACCT 62.043 66.667 0.00 0.00 0.00 3.08
610 619 3.989838 GAGCCCGGCCCAAACTACC 62.990 68.421 5.55 0.00 0.00 3.18
611 620 2.437895 GAGCCCGGCCCAAACTAC 60.438 66.667 5.55 0.00 0.00 2.73
612 621 4.090588 CGAGCCCGGCCCAAACTA 62.091 66.667 5.55 0.00 0.00 2.24
622 631 3.901797 AAAGACAAGCCCGAGCCCG 62.902 63.158 0.00 0.00 41.25 6.13
623 632 1.179174 AAAAAGACAAGCCCGAGCCC 61.179 55.000 0.00 0.00 41.25 5.19
624 633 0.241213 GAAAAAGACAAGCCCGAGCC 59.759 55.000 0.00 0.00 41.25 4.70
625 634 1.239347 AGAAAAAGACAAGCCCGAGC 58.761 50.000 0.00 0.00 40.32 5.03
626 635 5.629079 AAATAGAAAAAGACAAGCCCGAG 57.371 39.130 0.00 0.00 0.00 4.63
627 636 6.399639 AAAAATAGAAAAAGACAAGCCCGA 57.600 33.333 0.00 0.00 0.00 5.14
628 637 5.342259 CGAAAAATAGAAAAAGACAAGCCCG 59.658 40.000 0.00 0.00 0.00 6.13
629 638 5.633601 CCGAAAAATAGAAAAAGACAAGCCC 59.366 40.000 0.00 0.00 0.00 5.19
630 639 5.633601 CCCGAAAAATAGAAAAAGACAAGCC 59.366 40.000 0.00 0.00 0.00 4.35
631 640 5.118664 GCCCGAAAAATAGAAAAAGACAAGC 59.881 40.000 0.00 0.00 0.00 4.01
632 641 5.633601 GGCCCGAAAAATAGAAAAAGACAAG 59.366 40.000 0.00 0.00 0.00 3.16
633 642 5.534407 GGCCCGAAAAATAGAAAAAGACAA 58.466 37.500 0.00 0.00 0.00 3.18
634 643 4.320641 CGGCCCGAAAAATAGAAAAAGACA 60.321 41.667 0.00 0.00 0.00 3.41
635 644 4.163552 CGGCCCGAAAAATAGAAAAAGAC 58.836 43.478 0.00 0.00 0.00 3.01
636 645 3.191791 CCGGCCCGAAAAATAGAAAAAGA 59.808 43.478 3.71 0.00 0.00 2.52
637 646 3.507786 CCGGCCCGAAAAATAGAAAAAG 58.492 45.455 3.71 0.00 0.00 2.27
638 647 2.231721 CCCGGCCCGAAAAATAGAAAAA 59.768 45.455 3.71 0.00 0.00 1.94
639 648 1.819903 CCCGGCCCGAAAAATAGAAAA 59.180 47.619 3.71 0.00 0.00 2.29
640 649 1.465794 CCCGGCCCGAAAAATAGAAA 58.534 50.000 3.71 0.00 0.00 2.52
641 650 1.033202 GCCCGGCCCGAAAAATAGAA 61.033 55.000 3.71 0.00 0.00 2.10
642 651 1.452470 GCCCGGCCCGAAAAATAGA 60.452 57.895 3.71 0.00 0.00 1.98
643 652 1.035385 AAGCCCGGCCCGAAAAATAG 61.035 55.000 3.71 0.00 0.00 1.73
644 653 0.612453 AAAGCCCGGCCCGAAAAATA 60.612 50.000 3.71 0.00 0.00 1.40
645 654 1.884075 GAAAGCCCGGCCCGAAAAAT 61.884 55.000 3.71 0.00 0.00 1.82
646 655 2.522193 AAAGCCCGGCCCGAAAAA 60.522 55.556 3.71 0.00 0.00 1.94
647 656 2.986979 GAAAGCCCGGCCCGAAAA 60.987 61.111 3.71 0.00 0.00 2.29
699 708 2.725641 GGCCCGAACGCTGTTTTT 59.274 55.556 0.00 0.00 0.00 1.94
700 709 3.656045 CGGCCCGAACGCTGTTTT 61.656 61.111 0.00 0.00 0.00 2.43
727 736 2.101700 CTGAAATCAGGCCCGAAGC 58.898 57.895 0.00 0.00 40.20 3.86
736 745 1.821332 GAGCCCGGCCTGAAATCAG 60.821 63.158 5.55 3.37 43.40 2.90
737 746 2.272146 GAGCCCGGCCTGAAATCA 59.728 61.111 5.55 0.00 0.00 2.57
738 747 2.897350 CGAGCCCGGCCTGAAATC 60.897 66.667 5.55 0.00 0.00 2.17
748 757 2.438434 AAATCAAGCCCGAGCCCG 60.438 61.111 0.00 0.00 41.25 6.13
749 758 1.378514 TGAAATCAAGCCCGAGCCC 60.379 57.895 0.00 0.00 41.25 5.19
750 759 1.379642 CCTGAAATCAAGCCCGAGCC 61.380 60.000 0.00 0.00 41.25 4.70
751 760 1.379642 CCCTGAAATCAAGCCCGAGC 61.380 60.000 0.00 0.00 40.32 5.03
752 761 0.253044 TCCCTGAAATCAAGCCCGAG 59.747 55.000 0.00 0.00 0.00 4.63
753 762 0.253044 CTCCCTGAAATCAAGCCCGA 59.747 55.000 0.00 0.00 0.00 5.14
754 763 0.035056 ACTCCCTGAAATCAAGCCCG 60.035 55.000 0.00 0.00 0.00 6.13
755 764 3.584733 ATACTCCCTGAAATCAAGCCC 57.415 47.619 0.00 0.00 0.00 5.19
756 765 4.035675 CGAAATACTCCCTGAAATCAAGCC 59.964 45.833 0.00 0.00 0.00 4.35
757 766 4.035675 CCGAAATACTCCCTGAAATCAAGC 59.964 45.833 0.00 0.00 0.00 4.01
758 767 4.576463 CCCGAAATACTCCCTGAAATCAAG 59.424 45.833 0.00 0.00 0.00 3.02
759 768 4.523083 CCCGAAATACTCCCTGAAATCAA 58.477 43.478 0.00 0.00 0.00 2.57
760 769 3.684413 GCCCGAAATACTCCCTGAAATCA 60.684 47.826 0.00 0.00 0.00 2.57
761 770 2.879026 GCCCGAAATACTCCCTGAAATC 59.121 50.000 0.00 0.00 0.00 2.17
762 771 2.509964 AGCCCGAAATACTCCCTGAAAT 59.490 45.455 0.00 0.00 0.00 2.17
763 772 1.913419 AGCCCGAAATACTCCCTGAAA 59.087 47.619 0.00 0.00 0.00 2.69
764 773 1.580059 AGCCCGAAATACTCCCTGAA 58.420 50.000 0.00 0.00 0.00 3.02
765 774 1.485066 GAAGCCCGAAATACTCCCTGA 59.515 52.381 0.00 0.00 0.00 3.86
766 775 1.806623 CGAAGCCCGAAATACTCCCTG 60.807 57.143 0.00 0.00 41.76 4.45
767 776 0.464452 CGAAGCCCGAAATACTCCCT 59.536 55.000 0.00 0.00 41.76 4.20
768 777 0.532196 CCGAAGCCCGAAATACTCCC 60.532 60.000 0.00 0.00 41.76 4.30
769 778 0.532196 CCCGAAGCCCGAAATACTCC 60.532 60.000 0.00 0.00 41.76 3.85
770 779 1.158484 GCCCGAAGCCCGAAATACTC 61.158 60.000 0.00 0.00 41.76 2.59
771 780 1.153229 GCCCGAAGCCCGAAATACT 60.153 57.895 0.00 0.00 41.76 2.12
772 781 3.417601 GCCCGAAGCCCGAAATAC 58.582 61.111 0.00 0.00 41.76 1.89
790 799 2.876368 ATTTCTCAAGCCCGAGCCCG 62.876 60.000 0.00 0.00 41.25 6.13
791 800 1.077429 ATTTCTCAAGCCCGAGCCC 60.077 57.895 0.00 0.00 41.25 5.19
792 801 0.392998 TCATTTCTCAAGCCCGAGCC 60.393 55.000 0.00 0.00 41.25 4.70
793 802 1.399791 CTTCATTTCTCAAGCCCGAGC 59.600 52.381 0.00 0.00 40.32 5.03
794 803 2.012673 CCTTCATTTCTCAAGCCCGAG 58.987 52.381 0.00 0.00 0.00 4.63
795 804 1.351017 ACCTTCATTTCTCAAGCCCGA 59.649 47.619 0.00 0.00 0.00 5.14
796 805 1.740025 GACCTTCATTTCTCAAGCCCG 59.260 52.381 0.00 0.00 0.00 6.13
797 806 1.740025 CGACCTTCATTTCTCAAGCCC 59.260 52.381 0.00 0.00 0.00 5.19
798 807 1.740025 CCGACCTTCATTTCTCAAGCC 59.260 52.381 0.00 0.00 0.00 4.35
799 808 1.740025 CCCGACCTTCATTTCTCAAGC 59.260 52.381 0.00 0.00 0.00 4.01
800 809 1.740025 GCCCGACCTTCATTTCTCAAG 59.260 52.381 0.00 0.00 0.00 3.02
801 810 1.351017 AGCCCGACCTTCATTTCTCAA 59.649 47.619 0.00 0.00 0.00 3.02
802 811 0.984230 AGCCCGACCTTCATTTCTCA 59.016 50.000 0.00 0.00 0.00 3.27
803 812 2.115343 AAGCCCGACCTTCATTTCTC 57.885 50.000 0.00 0.00 0.00 2.87
804 813 2.586648 AAAGCCCGACCTTCATTTCT 57.413 45.000 0.00 0.00 0.00 2.52
805 814 3.504520 TGTAAAAGCCCGACCTTCATTTC 59.495 43.478 0.00 0.00 0.00 2.17
806 815 3.492337 TGTAAAAGCCCGACCTTCATTT 58.508 40.909 0.00 0.00 0.00 2.32
807 816 3.149005 TGTAAAAGCCCGACCTTCATT 57.851 42.857 0.00 0.00 0.00 2.57
808 817 2.871096 TGTAAAAGCCCGACCTTCAT 57.129 45.000 0.00 0.00 0.00 2.57
809 818 2.500229 CTTGTAAAAGCCCGACCTTCA 58.500 47.619 0.00 0.00 0.00 3.02
810 819 1.199327 GCTTGTAAAAGCCCGACCTTC 59.801 52.381 6.34 0.00 39.81 3.46
811 820 1.244816 GCTTGTAAAAGCCCGACCTT 58.755 50.000 6.34 0.00 39.81 3.50
812 821 2.942641 GCTTGTAAAAGCCCGACCT 58.057 52.632 6.34 0.00 39.81 3.85
819 828 2.571757 GGCCGGGCTTGTAAAAGC 59.428 61.111 22.87 9.32 44.76 3.51
820 829 2.696759 CGGGCCGGGCTTGTAAAAG 61.697 63.158 28.80 5.53 0.00 2.27
821 830 2.673687 CGGGCCGGGCTTGTAAAA 60.674 61.111 28.80 0.00 0.00 1.52
822 831 2.693896 TTTCGGGCCGGGCTTGTAAA 62.694 55.000 28.80 18.44 0.00 2.01
823 832 3.193469 TTTCGGGCCGGGCTTGTAA 62.193 57.895 28.80 16.98 0.00 2.41
824 833 3.638316 TTTCGGGCCGGGCTTGTA 61.638 61.111 28.80 11.81 0.00 2.41
852 861 4.636435 ACCTGGGCAAACGTCGGG 62.636 66.667 0.00 0.00 0.00 5.14
853 862 0.885596 TAAACCTGGGCAAACGTCGG 60.886 55.000 0.00 0.00 0.00 4.79
854 863 0.515564 CTAAACCTGGGCAAACGTCG 59.484 55.000 0.00 0.00 0.00 5.12
855 864 1.534163 GACTAAACCTGGGCAAACGTC 59.466 52.381 0.00 0.00 0.00 4.34
856 865 1.134037 TGACTAAACCTGGGCAAACGT 60.134 47.619 0.00 0.00 0.00 3.99
857 866 1.600023 TGACTAAACCTGGGCAAACG 58.400 50.000 0.00 0.00 0.00 3.60
858 867 4.116961 GTTTTGACTAAACCTGGGCAAAC 58.883 43.478 0.00 0.00 40.21 2.93
859 868 3.181485 CGTTTTGACTAAACCTGGGCAAA 60.181 43.478 6.88 0.00 42.57 3.68
860 869 2.359531 CGTTTTGACTAAACCTGGGCAA 59.640 45.455 6.88 0.00 42.57 4.52
861 870 1.950909 CGTTTTGACTAAACCTGGGCA 59.049 47.619 6.88 0.00 42.57 5.36
862 871 1.268625 CCGTTTTGACTAAACCTGGGC 59.731 52.381 6.88 0.00 42.57 5.36
863 872 2.292292 CACCGTTTTGACTAAACCTGGG 59.708 50.000 6.88 5.48 42.57 4.45
864 873 3.207778 TCACCGTTTTGACTAAACCTGG 58.792 45.455 6.88 6.06 42.57 4.45
865 874 4.886247 TTCACCGTTTTGACTAAACCTG 57.114 40.909 6.88 3.61 42.57 4.00
866 875 6.270064 CAAATTCACCGTTTTGACTAAACCT 58.730 36.000 6.88 0.00 42.57 3.50
867 876 5.460748 CCAAATTCACCGTTTTGACTAAACC 59.539 40.000 6.88 0.00 42.57 3.27
868 877 5.051307 GCCAAATTCACCGTTTTGACTAAAC 60.051 40.000 2.82 2.82 42.20 2.01
869 878 5.044558 GCCAAATTCACCGTTTTGACTAAA 58.955 37.500 0.00 0.00 35.34 1.85
870 879 4.500035 GGCCAAATTCACCGTTTTGACTAA 60.500 41.667 0.00 0.00 35.34 2.24
871 880 3.004944 GGCCAAATTCACCGTTTTGACTA 59.995 43.478 0.00 0.00 35.34 2.59
872 881 2.223947 GGCCAAATTCACCGTTTTGACT 60.224 45.455 0.00 0.00 35.34 3.41
1257 1274 2.763710 TAGGCCCTGATGAGCGCA 60.764 61.111 11.47 0.00 0.00 6.09
1905 1922 4.156622 CCAGCACTGCACATCGCG 62.157 66.667 0.00 0.00 46.97 5.87
1917 1934 2.032528 CGCTCCAAGTTCCCAGCA 59.967 61.111 0.00 0.00 0.00 4.41
1950 1967 0.693767 CCCTCTCCTTCATCTGCCCT 60.694 60.000 0.00 0.00 0.00 5.19
2070 2087 1.372087 CCGAAGGCTTGATCCTGCAC 61.372 60.000 3.46 0.00 46.14 4.57
2142 2159 1.597461 GACTAACTGCCCCGCTTCT 59.403 57.895 0.00 0.00 0.00 2.85
2149 2166 2.614057 CCATTTCATCGACTAACTGCCC 59.386 50.000 0.00 0.00 0.00 5.36
2152 2169 3.557595 GCCTCCATTTCATCGACTAACTG 59.442 47.826 0.00 0.00 0.00 3.16
2157 2174 4.446371 CTTTAGCCTCCATTTCATCGACT 58.554 43.478 0.00 0.00 0.00 4.18
2199 2216 8.777578 ACCCACTGAGAATTGTACTATATGTA 57.222 34.615 0.00 0.00 0.00 2.29
2290 2307 3.873952 GAGTAGGTGATTGCATCTGGAAC 59.126 47.826 0.00 0.00 35.86 3.62
2345 2362 3.225104 AGTTCACATGCATCACCAAGTT 58.775 40.909 0.00 0.00 0.00 2.66
2349 2366 2.865119 AGAGTTCACATGCATCACCA 57.135 45.000 0.00 0.00 0.00 4.17
2350 2367 3.503363 TCAAAGAGTTCACATGCATCACC 59.497 43.478 0.00 0.00 0.00 4.02
2420 2437 0.596600 GCAATGGCCATCAATCAGCG 60.597 55.000 21.08 1.58 0.00 5.18
2421 2438 0.462375 TGCAATGGCCATCAATCAGC 59.538 50.000 21.08 15.99 40.13 4.26
2583 2600 3.693085 CAGGGTCTTCGTAGTACAGCTTA 59.307 47.826 0.38 0.00 0.00 3.09
2667 2684 1.676014 CCCTTAAGAAGAGCCACCACG 60.676 57.143 3.36 0.00 0.00 4.94
2880 2897 2.750814 AGGCCCCTAACCAATGAAATG 58.249 47.619 0.00 0.00 0.00 2.32
2928 2945 3.458189 CAACTCCTGAATCACGGTATCC 58.542 50.000 0.00 0.00 0.00 2.59
3012 3029 0.038526 CAGCGTCCACGTTACCTTCT 60.039 55.000 0.36 0.00 42.22 2.85
3143 3160 4.942483 AGAAGTGCTCCAAAGAGATCAATG 59.058 41.667 0.00 0.00 43.39 2.82
3146 3163 4.321718 CAAGAAGTGCTCCAAAGAGATCA 58.678 43.478 0.00 0.00 43.39 2.92
3147 3164 3.688673 CCAAGAAGTGCTCCAAAGAGATC 59.311 47.826 0.00 0.00 43.39 2.75
3197 3214 6.178607 TGTTCACTGCATATCATCCTGTAT 57.821 37.500 0.00 0.00 0.00 2.29
3198 3215 5.612725 TGTTCACTGCATATCATCCTGTA 57.387 39.130 0.00 0.00 0.00 2.74
3313 3378 8.579850 TGATAACAGCAATAACCATTCTTCTT 57.420 30.769 0.00 0.00 0.00 2.52
3444 3509 3.377253 AGCTGGGATCAATGTGTCAAT 57.623 42.857 0.00 0.00 0.00 2.57
3485 3554 9.367160 TGGAAGAAGAAAAGAAGGAATTATGTT 57.633 29.630 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.