Multiple sequence alignment - TraesCS2B01G319600

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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 TraesCS2B01G319600 chr2B 100.000 4018 0 0 1 4018 455585951 455589968 0.000000e+00 7420
1 TraesCS2B01G319600 chr2B 93.482 537 30 3 1 536 142551247 142551779 0.000000e+00 793
2 TraesCS2B01G319600 chr2B 93.333 540 31 2 1 539 444527801 444528336 0.000000e+00 793
3 TraesCS2B01G319600 chr2B 93.333 540 31 2 1 539 543175050 543174515 0.000000e+00 793
4 TraesCS2B01G319600 chr2B 93.148 540 32 4 1 539 653895058 653894523 0.000000e+00 787
5 TraesCS2B01G319600 chr2B 83.901 764 93 22 1 743 494261913 494261159 0.000000e+00 702
6 TraesCS2B01G319600 chr2B 89.947 189 16 3 3822 4010 486203670 486203485 1.440000e-59 241
7 TraesCS2B01G319600 chr2D 93.136 1690 54 27 782 2424 384884580 384886254 0.000000e+00 2422
8 TraesCS2B01G319600 chr2D 92.868 673 26 11 2512 3173 384886304 384886965 0.000000e+00 957
9 TraesCS2B01G319600 chr2D 88.361 610 31 12 3236 3823 384887209 384887800 0.000000e+00 697
10 TraesCS2B01G319600 chr2A 92.908 1551 34 20 782 2279 519932209 519933736 0.000000e+00 2185
11 TraesCS2B01G319600 chr2A 87.690 723 40 21 2478 3199 519933932 519934606 0.000000e+00 797
12 TraesCS2B01G319600 chr2A 87.467 383 25 8 3244 3614 519935511 519935882 1.730000e-113 420
13 TraesCS2B01G319600 chr2A 92.754 207 13 1 3617 3823 519937369 519937573 8.440000e-77 298
14 TraesCS2B01G319600 chr2A 90.833 120 11 0 2266 2385 519933756 519933875 1.160000e-35 161
15 TraesCS2B01G319600 chr2A 86.957 138 17 1 606 743 149056689 149056825 1.930000e-33 154
16 TraesCS2B01G319600 chr5D 93.161 541 30 4 1 539 297123251 297122716 0.000000e+00 787
17 TraesCS2B01G319600 chr3B 93.148 540 32 2 1 539 507294735 507295270 0.000000e+00 787
18 TraesCS2B01G319600 chr3B 92.976 541 32 3 1 539 644833883 644833347 0.000000e+00 784
19 TraesCS2B01G319600 chr3B 90.000 190 16 2 3822 4011 265881062 265880876 4.010000e-60 243
20 TraesCS2B01G319600 chr3B 86.290 124 13 3 621 743 697191629 697191749 9.060000e-27 132
21 TraesCS2B01G319600 chr1B 92.976 541 32 3 1 539 394894897 394894361 0.000000e+00 784
22 TraesCS2B01G319600 chr1B 92.072 555 35 5 1 554 643824374 643824920 0.000000e+00 773
23 TraesCS2B01G319600 chr5A 91.133 203 17 1 3817 4018 632278093 632277891 1.420000e-69 274
24 TraesCS2B01G319600 chr5A 89.637 193 18 2 3819 4011 550111698 550111888 1.120000e-60 244
25 TraesCS2B01G319600 chr5A 89.062 192 21 0 3820 4011 287582785 287582976 5.190000e-59 239
26 TraesCS2B01G319600 chr5A 80.488 164 32 0 576 739 509912814 509912651 4.220000e-25 126
27 TraesCS2B01G319600 chr7A 92.632 190 13 1 3822 4011 227229467 227229655 5.120000e-69 272
28 TraesCS2B01G319600 chr7A 92.063 189 14 1 3821 4009 677100401 677100214 8.560000e-67 265
29 TraesCS2B01G319600 chr7D 90.000 190 16 2 3822 4011 496720572 496720758 4.010000e-60 243
30 TraesCS2B01G319600 chr7D 85.294 170 23 2 577 745 269697241 269697073 1.480000e-39 174
31 TraesCS2B01G319600 chr3D 89.474 190 19 1 3822 4011 185496955 185496767 5.190000e-59 239
32 TraesCS2B01G319600 chr1A 83.459 133 18 4 614 744 249129889 249129759 1.960000e-23 121
33 TraesCS2B01G319600 chr6B 81.690 142 20 3 614 749 672369282 672369423 3.280000e-21 113


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 TraesCS2B01G319600 chr2B 455585951 455589968 4017 False 7420.000000 7420 100.0000 1 4018 1 chr2B.!!$F3 4017
1 TraesCS2B01G319600 chr2B 142551247 142551779 532 False 793.000000 793 93.4820 1 536 1 chr2B.!!$F1 535
2 TraesCS2B01G319600 chr2B 444527801 444528336 535 False 793.000000 793 93.3330 1 539 1 chr2B.!!$F2 538
3 TraesCS2B01G319600 chr2B 543174515 543175050 535 True 793.000000 793 93.3330 1 539 1 chr2B.!!$R3 538
4 TraesCS2B01G319600 chr2B 653894523 653895058 535 True 787.000000 787 93.1480 1 539 1 chr2B.!!$R4 538
5 TraesCS2B01G319600 chr2B 494261159 494261913 754 True 702.000000 702 83.9010 1 743 1 chr2B.!!$R2 742
6 TraesCS2B01G319600 chr2D 384884580 384887800 3220 False 1358.666667 2422 91.4550 782 3823 3 chr2D.!!$F1 3041
7 TraesCS2B01G319600 chr2A 519932209 519937573 5364 False 772.200000 2185 90.3304 782 3823 5 chr2A.!!$F2 3041
8 TraesCS2B01G319600 chr5D 297122716 297123251 535 True 787.000000 787 93.1610 1 539 1 chr5D.!!$R1 538
9 TraesCS2B01G319600 chr3B 507294735 507295270 535 False 787.000000 787 93.1480 1 539 1 chr3B.!!$F1 538
10 TraesCS2B01G319600 chr3B 644833347 644833883 536 True 784.000000 784 92.9760 1 539 1 chr3B.!!$R2 538
11 TraesCS2B01G319600 chr1B 394894361 394894897 536 True 784.000000 784 92.9760 1 539 1 chr1B.!!$R1 538
12 TraesCS2B01G319600 chr1B 643824374 643824920 546 False 773.000000 773 92.0720 1 554 1 chr1B.!!$F1 553

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
593 615 0.118144 AAAAATAAGGGGGCCAGGCA 59.882 50.0 15.19 0.0 0.0 4.75 F
2102 2195 0.236187 GCGGTGCATTTACGTCAACA 59.764 50.0 0.00 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2497 2628 0.320771 GCCACAGACAGTCGTTGGAT 60.321 55.0 21.89 0.00 0.00 3.41 R
3440 4463 0.026803 GAAACGGCTCTGCGCATTAG 59.973 55.0 12.24 13.32 41.67 1.73 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
19 20 0.981183 AACAGCCCACCGATGAACTA 59.019 50.000 0.00 0.00 0.00 2.24
31 32 4.397103 ACCGATGAACTATACTGTCAACGA 59.603 41.667 4.43 0.00 0.00 3.85
84 85 2.820787 GACGGTATCTATCCTCAGTGGG 59.179 54.545 0.00 0.00 36.20 4.61
112 113 2.773487 TGTCAAGACAATACCCAACCG 58.227 47.619 0.00 0.00 38.56 4.44
178 179 0.965866 AGGAAGGATGTCGAGCGTGA 60.966 55.000 0.00 0.00 0.00 4.35
208 209 1.031571 TTGCAATCTCGATGGGGCAC 61.032 55.000 0.00 0.00 0.00 5.01
232 233 5.475909 CCGTTCAGTATCCTGCTAATACCTA 59.524 44.000 0.00 0.00 38.66 3.08
287 288 7.662669 ACTGCTTGTGTGATCATGCATAATATA 59.337 33.333 0.00 0.00 43.71 0.86
417 419 6.721208 AGTTCACCCAATTTCATAAGACATGT 59.279 34.615 0.00 0.00 0.00 3.21
426 428 7.943079 ATTTCATAAGACATGTGTGATTGGA 57.057 32.000 1.15 0.00 0.00 3.53
464 466 3.808726 TGCAAAATGATTTGGTTGAGCAC 59.191 39.130 0.00 0.00 44.93 4.40
539 543 7.607607 TGCAAAACTATGTGAGAACTATGTGAT 59.392 33.333 0.00 0.00 0.00 3.06
546 550 9.786105 CTATGTGAGAACTATGTGATAGCTATG 57.214 37.037 11.94 0.00 36.30 2.23
547 551 6.450545 TGTGAGAACTATGTGATAGCTATGC 58.549 40.000 11.94 4.48 36.30 3.14
549 553 7.448469 TGTGAGAACTATGTGATAGCTATGCTA 59.552 37.037 11.94 1.60 45.55 3.49
562 566 5.192327 AGCTATGCTATTTTGAACCATGC 57.808 39.130 0.00 0.00 36.99 4.06
563 567 4.646040 AGCTATGCTATTTTGAACCATGCA 59.354 37.500 0.00 0.00 36.99 3.96
564 568 5.127519 AGCTATGCTATTTTGAACCATGCAA 59.872 36.000 0.00 0.00 36.99 4.08
593 615 0.118144 AAAAATAAGGGGGCCAGGCA 59.882 50.000 15.19 0.00 0.00 4.75
611 633 1.134367 GCAGCCGCTCCGATACATATA 59.866 52.381 0.00 0.00 34.30 0.86
612 634 2.416836 GCAGCCGCTCCGATACATATAA 60.417 50.000 0.00 0.00 34.30 0.98
617 639 3.373130 CCGCTCCGATACATATAAGTCGA 59.627 47.826 0.00 0.00 36.25 4.20
618 640 4.035324 CCGCTCCGATACATATAAGTCGAT 59.965 45.833 0.00 0.00 36.25 3.59
621 643 4.905269 TCCGATACATATAAGTCGATGCG 58.095 43.478 0.00 0.00 36.25 4.73
626 648 4.316205 ACATATAAGTCGATGCGTTGGA 57.684 40.909 0.00 0.00 0.00 3.53
628 650 1.556564 ATAAGTCGATGCGTTGGACG 58.443 50.000 0.00 0.00 45.88 4.79
639 661 4.717629 TTGGACGCTCTGCCGACG 62.718 66.667 0.00 0.00 0.00 5.12
643 665 3.751401 GACGCTCTGCCGACGCATA 62.751 63.158 0.00 0.00 46.11 3.14
644 666 2.355126 CGCTCTGCCGACGCATAT 60.355 61.111 0.00 0.00 46.11 1.78
645 667 2.368105 CGCTCTGCCGACGCATATC 61.368 63.158 0.00 0.00 46.11 1.63
646 668 1.006805 GCTCTGCCGACGCATATCT 60.007 57.895 0.00 0.00 46.11 1.98
717 739 1.223417 ACGAAATCGCCGTCCGTTTT 61.223 50.000 2.15 2.65 44.43 2.43
718 740 0.787908 CGAAATCGCCGTCCGTTTTG 60.788 55.000 6.52 2.18 38.54 2.44
720 742 1.858372 AAATCGCCGTCCGTTTTGGG 61.858 55.000 2.32 0.00 37.44 4.12
721 743 3.540367 ATCGCCGTCCGTTTTGGGT 62.540 57.895 0.00 0.00 38.76 4.51
722 744 3.719144 CGCCGTCCGTTTTGGGTC 61.719 66.667 0.00 0.00 38.76 4.46
724 746 3.719144 CCGTCCGTTTTGGGTCGC 61.719 66.667 0.00 0.00 38.76 5.19
743 765 2.684881 CGCCCATTGAAGTTGCTCTAAT 59.315 45.455 0.00 0.00 0.00 1.73
744 766 3.876914 CGCCCATTGAAGTTGCTCTAATA 59.123 43.478 0.00 0.00 0.00 0.98
745 767 4.335315 CGCCCATTGAAGTTGCTCTAATAA 59.665 41.667 0.00 0.00 0.00 1.40
746 768 5.163663 CGCCCATTGAAGTTGCTCTAATAAA 60.164 40.000 0.00 0.00 0.00 1.40
747 769 6.036470 GCCCATTGAAGTTGCTCTAATAAAC 58.964 40.000 0.00 0.00 0.00 2.01
748 770 6.258160 CCCATTGAAGTTGCTCTAATAAACG 58.742 40.000 0.00 0.00 0.00 3.60
749 771 6.258160 CCATTGAAGTTGCTCTAATAAACGG 58.742 40.000 0.00 0.00 0.00 4.44
750 772 4.939509 TGAAGTTGCTCTAATAAACGGC 57.060 40.909 0.00 0.00 0.00 5.68
751 773 4.575885 TGAAGTTGCTCTAATAAACGGCT 58.424 39.130 0.00 0.00 0.00 5.52
752 774 5.726397 TGAAGTTGCTCTAATAAACGGCTA 58.274 37.500 0.00 0.00 0.00 3.93
753 775 6.167685 TGAAGTTGCTCTAATAAACGGCTAA 58.832 36.000 0.00 0.00 0.00 3.09
754 776 6.651643 TGAAGTTGCTCTAATAAACGGCTAAA 59.348 34.615 0.00 0.00 0.00 1.85
755 777 7.173562 TGAAGTTGCTCTAATAAACGGCTAAAA 59.826 33.333 0.00 0.00 0.00 1.52
756 778 6.839033 AGTTGCTCTAATAAACGGCTAAAAC 58.161 36.000 0.00 0.00 0.00 2.43
757 779 5.806366 TGCTCTAATAAACGGCTAAAACC 57.194 39.130 0.00 0.00 0.00 3.27
758 780 4.637091 TGCTCTAATAAACGGCTAAAACCC 59.363 41.667 0.00 0.00 0.00 4.11
765 787 2.674033 GGCTAAAACCCGCCCGTT 60.674 61.111 0.00 0.00 40.43 4.44
766 788 2.693762 GGCTAAAACCCGCCCGTTC 61.694 63.158 0.00 0.00 40.43 3.95
767 789 3.030763 GCTAAAACCCGCCCGTTCG 62.031 63.158 0.00 0.00 0.00 3.95
780 802 4.047059 GTTCGGAGGCACGGTCGA 62.047 66.667 0.00 0.00 0.00 4.20
800 825 1.291877 CGCCCATCGTTATAGCAGCC 61.292 60.000 0.00 0.00 0.00 4.85
803 828 0.599991 CCATCGTTATAGCAGCCGCA 60.600 55.000 0.00 0.00 42.27 5.69
856 898 3.000819 AAGTCATCCCCGGACGCA 61.001 61.111 0.73 0.00 40.20 5.24
880 922 2.067605 ACACCTCCCAACACGTCCA 61.068 57.895 0.00 0.00 0.00 4.02
949 991 3.887110 AGCACTACTACACAGTACACACA 59.113 43.478 0.00 0.00 36.14 3.72
951 993 4.498513 GCACTACTACACAGTACACACACA 60.499 45.833 0.00 0.00 36.14 3.72
1207 1283 1.684049 CGCCTCCTCCTTCCACTCT 60.684 63.158 0.00 0.00 0.00 3.24
1492 1571 4.452733 AAGGTGCGCTACGGGCTC 62.453 66.667 9.73 0.92 42.10 4.70
1591 1670 2.142239 CGTCTCCGTCAACGTACGC 61.142 63.158 16.72 0.00 41.51 4.42
1597 1676 1.081641 CGTCAACGTACGCACTCCT 60.082 57.895 16.72 0.00 35.87 3.69
1645 1725 3.178618 CGTGATTCGTCTTCTCTTATGCG 59.821 47.826 0.00 0.00 34.52 4.73
1988 2068 2.992124 TGGAGAACAACCGAGTCAAA 57.008 45.000 0.00 0.00 0.00 2.69
1989 2069 3.485463 TGGAGAACAACCGAGTCAAAT 57.515 42.857 0.00 0.00 0.00 2.32
1990 2070 3.399330 TGGAGAACAACCGAGTCAAATC 58.601 45.455 0.00 0.00 0.00 2.17
1991 2071 3.071023 TGGAGAACAACCGAGTCAAATCT 59.929 43.478 0.00 0.00 0.00 2.40
2102 2195 0.236187 GCGGTGCATTTACGTCAACA 59.764 50.000 0.00 0.00 0.00 3.33
2198 2291 2.224314 GTGAACTTTGGACTACAGCTGC 59.776 50.000 15.27 0.00 0.00 5.25
2199 2292 2.158827 TGAACTTTGGACTACAGCTGCA 60.159 45.455 15.27 0.00 0.00 4.41
2200 2293 1.884235 ACTTTGGACTACAGCTGCAC 58.116 50.000 15.27 2.48 0.00 4.57
2201 2294 1.417890 ACTTTGGACTACAGCTGCACT 59.582 47.619 15.27 0.00 0.00 4.40
2285 2412 0.886490 AAAGCAGAGGCCACTGAACG 60.886 55.000 31.50 7.61 42.56 3.95
2289 2416 3.426568 GAGGCCACTGAACGCTGC 61.427 66.667 5.01 0.00 0.00 5.25
2313 2440 2.814280 AAACTCGAACAGGACATCGT 57.186 45.000 0.00 0.00 39.91 3.73
2344 2475 5.121811 AGTTGCTGTCATCCAGTTCATATC 58.878 41.667 0.00 0.00 43.55 1.63
2354 2485 9.566432 GTCATCCAGTTCATATCCTTTATTTCT 57.434 33.333 0.00 0.00 0.00 2.52
2377 2508 4.312052 TTTCCGCGGGAAATCCAG 57.688 55.556 27.83 0.00 45.42 3.86
2386 2517 3.058914 CGCGGGAAATCCAGTTCATATTC 60.059 47.826 0.00 0.00 37.91 1.75
2390 2521 6.498304 CGGGAAATCCAGTTCATATTCTTTG 58.502 40.000 1.22 0.00 37.91 2.77
2399 2530 9.354673 TCCAGTTCATATTCTTTGTTTCTTTCT 57.645 29.630 0.00 0.00 0.00 2.52
2400 2531 9.617975 CCAGTTCATATTCTTTGTTTCTTTCTC 57.382 33.333 0.00 0.00 0.00 2.87
2411 2542 9.103861 TCTTTGTTTCTTTCTCTCTCTTTTCTC 57.896 33.333 0.00 0.00 0.00 2.87
2424 2555 3.999663 CTCTTTTCTCTGCGTGGAAATCT 59.000 43.478 0.00 0.00 32.54 2.40
2425 2556 3.997021 TCTTTTCTCTGCGTGGAAATCTC 59.003 43.478 0.00 0.00 32.54 2.75
2426 2557 3.401033 TTTCTCTGCGTGGAAATCTCA 57.599 42.857 0.00 0.00 0.00 3.27
2427 2558 3.616956 TTCTCTGCGTGGAAATCTCAT 57.383 42.857 0.00 0.00 0.00 2.90
2428 2559 3.616956 TCTCTGCGTGGAAATCTCATT 57.383 42.857 0.00 0.00 0.00 2.57
2429 2560 3.525537 TCTCTGCGTGGAAATCTCATTC 58.474 45.455 0.00 0.00 0.00 2.67
2435 2566 6.203530 TCTGCGTGGAAATCTCATTCATATTC 59.796 38.462 0.00 0.00 0.00 1.75
2457 2588 2.583143 ACTCAAGTTGTAACCTTGGCC 58.417 47.619 2.11 0.00 0.00 5.36
2504 2635 3.338249 AGTTGTGAATCCTGATCCAACG 58.662 45.455 0.00 0.00 35.24 4.10
2506 2637 2.972625 TGTGAATCCTGATCCAACGAC 58.027 47.619 0.00 0.00 0.00 4.34
2507 2638 2.567169 TGTGAATCCTGATCCAACGACT 59.433 45.455 0.00 0.00 0.00 4.18
2508 2639 2.932614 GTGAATCCTGATCCAACGACTG 59.067 50.000 0.00 0.00 0.00 3.51
2509 2640 2.567169 TGAATCCTGATCCAACGACTGT 59.433 45.455 0.00 0.00 0.00 3.55
2813 2944 1.330655 ATCCTGCACCCACGTCTAGG 61.331 60.000 0.00 0.00 0.00 3.02
2814 2945 2.283529 CCTGCACCCACGTCTAGGT 61.284 63.158 0.00 0.00 36.58 3.08
2815 2946 1.215647 CTGCACCCACGTCTAGGTC 59.784 63.158 0.00 0.00 32.72 3.85
2816 2947 1.228769 TGCACCCACGTCTAGGTCT 60.229 57.895 0.00 0.00 32.72 3.85
2817 2948 0.038599 TGCACCCACGTCTAGGTCTA 59.961 55.000 0.00 0.00 32.72 2.59
2818 2949 0.739561 GCACCCACGTCTAGGTCTAG 59.260 60.000 0.00 0.00 32.72 2.43
2819 2950 0.739561 CACCCACGTCTAGGTCTAGC 59.260 60.000 0.00 0.00 32.72 3.42
2820 2951 0.395448 ACCCACGTCTAGGTCTAGCC 60.395 60.000 0.34 0.00 33.32 3.93
2827 2958 1.401199 GTCTAGGTCTAGCCACACGAC 59.599 57.143 6.07 0.00 40.61 4.34
2828 2959 0.739561 CTAGGTCTAGCCACACGACC 59.260 60.000 6.07 0.00 45.88 4.79
2829 2960 0.682209 TAGGTCTAGCCACACGACCC 60.682 60.000 4.20 0.00 46.53 4.46
2830 2961 2.181021 GTCTAGCCACACGACCCG 59.819 66.667 0.00 0.00 0.00 5.28
2831 2962 2.034532 TCTAGCCACACGACCCGA 59.965 61.111 0.00 0.00 0.00 5.14
2832 2963 2.181021 CTAGCCACACGACCCGAC 59.819 66.667 0.00 0.00 0.00 4.79
2833 2964 3.352338 CTAGCCACACGACCCGACC 62.352 68.421 0.00 0.00 0.00 4.79
2834 2965 3.873679 TAGCCACACGACCCGACCT 62.874 63.158 0.00 0.00 0.00 3.85
2878 3012 1.154525 CTTCTCGTTGCTTGCTGCG 60.155 57.895 0.00 0.00 46.63 5.18
2888 3022 1.063912 TGCTTGCTGCGTATGTTATGC 59.936 47.619 0.00 0.00 46.63 3.14
2894 3028 3.494251 TGCTGCGTATGTTATGCTATGTG 59.506 43.478 0.00 0.00 41.24 3.21
2911 3045 5.405269 GCTATGTGATGTGATGTAATGCGTA 59.595 40.000 0.00 0.00 0.00 4.42
2918 3052 6.645003 TGATGTGATGTAATGCGTAGATTACC 59.355 38.462 0.00 0.00 37.82 2.85
2921 3055 6.423604 TGTGATGTAATGCGTAGATTACCATG 59.576 38.462 0.00 0.00 37.82 3.66
2952 3086 3.880846 CGGGAGAAAGCGGCATGC 61.881 66.667 9.90 9.90 46.98 4.06
2965 3102 0.179129 GGCATGCCACTTGTGTATGC 60.179 55.000 32.08 21.33 42.43 3.14
3062 3199 3.084646 TGACGGTGTGGGTGTGGT 61.085 61.111 0.00 0.00 0.00 4.16
3135 3272 1.546476 TGTTGCTTCCGTTTTTGGTGT 59.454 42.857 0.00 0.00 0.00 4.16
3136 3273 2.753452 TGTTGCTTCCGTTTTTGGTGTA 59.247 40.909 0.00 0.00 0.00 2.90
3139 3281 2.614983 TGCTTCCGTTTTTGGTGTAGAC 59.385 45.455 0.00 0.00 0.00 2.59
3146 3288 4.998672 CCGTTTTTGGTGTAGACTGGATTA 59.001 41.667 0.00 0.00 0.00 1.75
3173 3315 2.509336 GCTGTCCCATCACCGTCG 60.509 66.667 0.00 0.00 0.00 5.12
3174 3316 2.509336 CTGTCCCATCACCGTCGC 60.509 66.667 0.00 0.00 0.00 5.19
3199 3341 0.035439 ACTGCTCCCATAAACCGTGG 60.035 55.000 0.00 0.00 36.47 4.94
3200 3342 0.251916 CTGCTCCCATAAACCGTGGA 59.748 55.000 0.00 0.00 39.12 4.02
3201 3343 0.916086 TGCTCCCATAAACCGTGGAT 59.084 50.000 0.00 0.00 39.12 3.41
3202 3344 1.283613 TGCTCCCATAAACCGTGGATT 59.716 47.619 0.00 0.00 39.12 3.01
3203 3345 2.291282 TGCTCCCATAAACCGTGGATTT 60.291 45.455 0.00 0.00 39.12 2.17
3204 3346 2.758423 GCTCCCATAAACCGTGGATTTT 59.242 45.455 0.00 0.00 39.12 1.82
3205 3347 3.181490 GCTCCCATAAACCGTGGATTTTC 60.181 47.826 0.00 0.00 39.12 2.29
3206 3348 3.358118 TCCCATAAACCGTGGATTTTCC 58.642 45.455 0.00 0.00 39.12 3.13
3207 3349 2.429250 CCCATAAACCGTGGATTTTCCC 59.571 50.000 0.00 0.00 39.12 3.97
3208 3350 2.429250 CCATAAACCGTGGATTTTCCCC 59.571 50.000 0.00 0.00 39.12 4.81
3209 3351 2.219080 TAAACCGTGGATTTTCCCCC 57.781 50.000 0.00 0.00 35.03 5.40
3210 3352 0.485543 AAACCGTGGATTTTCCCCCT 59.514 50.000 0.00 0.00 35.03 4.79
3211 3353 0.485543 AACCGTGGATTTTCCCCCTT 59.514 50.000 0.00 0.00 35.03 3.95
3212 3354 0.485543 ACCGTGGATTTTCCCCCTTT 59.514 50.000 0.00 0.00 35.03 3.11
3213 3355 1.182667 CCGTGGATTTTCCCCCTTTC 58.817 55.000 0.00 0.00 35.03 2.62
3214 3356 1.272480 CCGTGGATTTTCCCCCTTTCT 60.272 52.381 0.00 0.00 35.03 2.52
3215 3357 2.525368 CGTGGATTTTCCCCCTTTCTT 58.475 47.619 0.00 0.00 35.03 2.52
3216 3358 2.897326 CGTGGATTTTCCCCCTTTCTTT 59.103 45.455 0.00 0.00 35.03 2.52
3217 3359 3.056821 CGTGGATTTTCCCCCTTTCTTTC 60.057 47.826 0.00 0.00 35.03 2.62
3218 3360 4.160329 GTGGATTTTCCCCCTTTCTTTCT 58.840 43.478 0.00 0.00 35.03 2.52
3219 3361 5.330233 GTGGATTTTCCCCCTTTCTTTCTA 58.670 41.667 0.00 0.00 35.03 2.10
3220 3362 5.185249 GTGGATTTTCCCCCTTTCTTTCTAC 59.815 44.000 0.00 0.00 35.03 2.59
3221 3363 5.162925 TGGATTTTCCCCCTTTCTTTCTACA 60.163 40.000 0.00 0.00 35.03 2.74
3222 3364 5.185249 GGATTTTCCCCCTTTCTTTCTACAC 59.815 44.000 0.00 0.00 0.00 2.90
3223 3365 3.412237 TTCCCCCTTTCTTTCTACACG 57.588 47.619 0.00 0.00 0.00 4.49
3224 3366 1.626825 TCCCCCTTTCTTTCTACACGG 59.373 52.381 0.00 0.00 0.00 4.94
3225 3367 1.626825 CCCCCTTTCTTTCTACACGGA 59.373 52.381 0.00 0.00 0.00 4.69
3226 3368 2.354805 CCCCCTTTCTTTCTACACGGAG 60.355 54.545 0.00 0.00 0.00 4.63
3227 3369 2.354805 CCCCTTTCTTTCTACACGGAGG 60.355 54.545 0.00 0.00 0.00 4.30
3228 3370 2.302157 CCCTTTCTTTCTACACGGAGGT 59.698 50.000 0.00 0.00 0.00 3.85
3229 3371 3.244457 CCCTTTCTTTCTACACGGAGGTT 60.244 47.826 0.00 0.00 0.00 3.50
3230 3372 4.386711 CCTTTCTTTCTACACGGAGGTTT 58.613 43.478 0.00 0.00 0.00 3.27
3231 3373 4.820173 CCTTTCTTTCTACACGGAGGTTTT 59.180 41.667 0.00 0.00 0.00 2.43
3232 3374 5.993441 CCTTTCTTTCTACACGGAGGTTTTA 59.007 40.000 0.00 0.00 0.00 1.52
3233 3375 6.484308 CCTTTCTTTCTACACGGAGGTTTTAA 59.516 38.462 0.00 0.00 0.00 1.52
3234 3376 7.307811 CCTTTCTTTCTACACGGAGGTTTTAAG 60.308 40.741 0.00 0.00 0.00 1.85
3262 4264 0.173935 TACCGTGGTACGCATCCAAG 59.826 55.000 0.00 0.00 40.91 3.61
3272 4274 3.521947 ACGCATCCAAGTAGAGTTACC 57.478 47.619 0.00 0.00 0.00 2.85
3360 4371 1.557099 TAGTTCCACGACTGCTCCAT 58.443 50.000 0.00 0.00 0.00 3.41
3368 4391 3.280920 GACTGCTCCATGTCGATCC 57.719 57.895 0.00 0.00 0.00 3.36
3509 4532 2.348666 GCTGTAATGGTAGAACACTGCG 59.651 50.000 0.00 0.00 0.00 5.18
3510 4533 2.930040 CTGTAATGGTAGAACACTGCGG 59.070 50.000 0.00 0.00 0.00 5.69
3511 4534 2.563620 TGTAATGGTAGAACACTGCGGA 59.436 45.455 0.00 0.00 0.00 5.54
3512 4535 2.851263 AATGGTAGAACACTGCGGAA 57.149 45.000 0.00 0.00 0.00 4.30
3513 4536 2.851263 ATGGTAGAACACTGCGGAAA 57.149 45.000 0.00 0.00 0.00 3.13
3514 4537 2.851263 TGGTAGAACACTGCGGAAAT 57.149 45.000 0.00 0.00 0.00 2.17
3515 4538 2.695359 TGGTAGAACACTGCGGAAATC 58.305 47.619 0.00 0.00 0.00 2.17
3516 4539 2.007608 GGTAGAACACTGCGGAAATCC 58.992 52.381 0.00 0.00 0.00 3.01
3517 4540 2.007608 GTAGAACACTGCGGAAATCCC 58.992 52.381 0.00 0.00 0.00 3.85
3518 4541 0.400213 AGAACACTGCGGAAATCCCA 59.600 50.000 0.00 0.00 34.14 4.37
3519 4542 1.202879 AGAACACTGCGGAAATCCCAA 60.203 47.619 0.00 0.00 34.14 4.12
3520 4543 1.818674 GAACACTGCGGAAATCCCAAT 59.181 47.619 0.00 0.00 34.14 3.16
3521 4544 1.923356 ACACTGCGGAAATCCCAATT 58.077 45.000 0.00 0.00 34.14 2.32
3522 4545 1.818674 ACACTGCGGAAATCCCAATTC 59.181 47.619 0.00 0.00 34.14 2.17
3523 4546 1.094785 ACTGCGGAAATCCCAATTCG 58.905 50.000 0.00 0.00 34.14 3.34
3524 4547 0.381801 CTGCGGAAATCCCAATTCGG 59.618 55.000 0.00 0.00 34.14 4.30
3525 4548 1.065764 GCGGAAATCCCAATTCGGC 59.934 57.895 3.61 3.61 42.97 5.54
3526 4549 1.384222 GCGGAAATCCCAATTCGGCT 61.384 55.000 10.38 0.00 44.76 5.52
3527 4550 1.961793 CGGAAATCCCAATTCGGCTA 58.038 50.000 0.00 0.00 34.14 3.93
3528 4551 1.873591 CGGAAATCCCAATTCGGCTAG 59.126 52.381 0.00 0.00 34.14 3.42
3578 4610 1.804748 GTGAAGGTTTGTGTCGGATCC 59.195 52.381 0.00 0.00 0.00 3.36
3580 4612 2.076863 GAAGGTTTGTGTCGGATCCTG 58.923 52.381 10.75 3.62 0.00 3.86
3602 4634 1.614525 TGTGCTCCCATCTCCTGCT 60.615 57.895 0.00 0.00 0.00 4.24
3713 6230 7.717568 TCCCACGAAAATTTAAATTCAGAACA 58.282 30.769 13.68 0.00 0.00 3.18
3773 6290 6.381481 TTCAGTGATGGTATTGATGATTGC 57.619 37.500 0.00 0.00 0.00 3.56
3784 6301 3.891422 TGATGATTGCCCAATTTGACC 57.109 42.857 0.00 0.00 0.00 4.02
3823 6340 7.954788 AGCTACCACGTACTACTACTATAAC 57.045 40.000 0.00 0.00 0.00 1.89
3824 6341 7.731054 AGCTACCACGTACTACTACTATAACT 58.269 38.462 0.00 0.00 0.00 2.24
3825 6342 8.861086 AGCTACCACGTACTACTACTATAACTA 58.139 37.037 0.00 0.00 0.00 2.24
3826 6343 9.134734 GCTACCACGTACTACTACTATAACTAG 57.865 40.741 0.00 0.00 0.00 2.57
3838 6355 7.890515 ACTACTATAACTAGAAAATACCCCGC 58.109 38.462 0.00 0.00 0.00 6.13
3839 6356 5.776744 ACTATAACTAGAAAATACCCCGCG 58.223 41.667 0.00 0.00 0.00 6.46
3840 6357 1.660167 AACTAGAAAATACCCCGCGC 58.340 50.000 0.00 0.00 0.00 6.86
3841 6358 0.538118 ACTAGAAAATACCCCGCGCA 59.462 50.000 8.75 0.00 0.00 6.09
3842 6359 1.140252 ACTAGAAAATACCCCGCGCAT 59.860 47.619 8.75 0.00 0.00 4.73
3843 6360 2.218603 CTAGAAAATACCCCGCGCATT 58.781 47.619 8.75 0.00 0.00 3.56
3844 6361 0.738389 AGAAAATACCCCGCGCATTG 59.262 50.000 8.75 0.00 0.00 2.82
3845 6362 0.869880 GAAAATACCCCGCGCATTGC 60.870 55.000 8.75 0.00 41.47 3.56
3846 6363 1.319614 AAAATACCCCGCGCATTGCT 61.320 50.000 8.75 0.00 43.27 3.91
3847 6364 2.003658 AAATACCCCGCGCATTGCTG 62.004 55.000 8.75 1.74 43.27 4.41
3860 6377 2.727777 CATTGCTGCAGGAATCGATTG 58.272 47.619 28.33 16.14 33.70 2.67
3861 6378 0.452987 TTGCTGCAGGAATCGATTGC 59.547 50.000 20.76 20.76 38.30 3.56
3862 6379 0.677414 TGCTGCAGGAATCGATTGCA 60.677 50.000 28.21 23.55 44.81 4.08
3863 6380 0.452987 GCTGCAGGAATCGATTGCAA 59.547 50.000 28.21 14.17 46.08 4.08
3864 6381 1.066605 GCTGCAGGAATCGATTGCAAT 59.933 47.619 28.21 12.83 46.08 3.56
3865 6382 2.291465 GCTGCAGGAATCGATTGCAATA 59.709 45.455 28.21 14.05 46.08 1.90
3866 6383 3.057736 GCTGCAGGAATCGATTGCAATAT 60.058 43.478 28.21 7.78 46.08 1.28
3867 6384 4.154737 GCTGCAGGAATCGATTGCAATATA 59.845 41.667 28.21 10.98 46.08 0.86
3868 6385 5.163683 GCTGCAGGAATCGATTGCAATATAT 60.164 40.000 28.21 6.04 46.08 0.86
3869 6386 6.624423 GCTGCAGGAATCGATTGCAATATATT 60.624 38.462 28.21 14.35 46.08 1.28
3870 6387 7.218228 TGCAGGAATCGATTGCAATATATTT 57.782 32.000 28.21 5.29 44.13 1.40
3871 6388 7.307694 TGCAGGAATCGATTGCAATATATTTC 58.692 34.615 28.21 13.16 44.13 2.17
3872 6389 7.040548 TGCAGGAATCGATTGCAATATATTTCA 60.041 33.333 28.21 6.72 44.13 2.69
3873 6390 7.484007 GCAGGAATCGATTGCAATATATTTCAG 59.516 37.037 28.21 11.26 37.75 3.02
3874 6391 8.509690 CAGGAATCGATTGCAATATATTTCAGT 58.490 33.333 28.21 3.20 0.00 3.41
3875 6392 8.509690 AGGAATCGATTGCAATATATTTCAGTG 58.490 33.333 28.21 0.00 0.00 3.66
3876 6393 8.506437 GGAATCGATTGCAATATATTTCAGTGA 58.494 33.333 22.97 0.00 0.00 3.41
3880 6397 9.667989 TCGATTGCAATATATTTCAGTGATTTG 57.332 29.630 12.97 0.00 0.00 2.32
3881 6398 9.667989 CGATTGCAATATATTTCAGTGATTTGA 57.332 29.630 12.97 0.00 0.00 2.69
3892 6409 8.922058 ATTTCAGTGATTTGATTGTATGAAGC 57.078 30.769 0.00 0.00 0.00 3.86
3893 6410 7.692460 TTCAGTGATTTGATTGTATGAAGCT 57.308 32.000 0.00 0.00 0.00 3.74
3894 6411 7.692460 TCAGTGATTTGATTGTATGAAGCTT 57.308 32.000 0.00 0.00 0.00 3.74
3895 6412 8.114331 TCAGTGATTTGATTGTATGAAGCTTT 57.886 30.769 0.00 0.00 0.00 3.51
3896 6413 8.239314 TCAGTGATTTGATTGTATGAAGCTTTC 58.761 33.333 0.00 0.00 0.00 2.62
3897 6414 8.024865 CAGTGATTTGATTGTATGAAGCTTTCA 58.975 33.333 0.00 0.27 45.01 2.69
4006 6523 9.161629 TCGAATATAAGTGGCATAATGTAATGG 57.838 33.333 0.00 0.00 0.00 3.16
4007 6524 9.161629 CGAATATAAGTGGCATAATGTAATGGA 57.838 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.047590 TGTGGTCGTTGACAGTATAGTTCAT 60.048 40.000 0.00 0.00 33.68 2.57
19 20 1.968493 AGGTGTGGTCGTTGACAGTAT 59.032 47.619 0.00 0.00 33.68 2.12
31 32 3.695830 ATCATTTGTCGTAGGTGTGGT 57.304 42.857 0.00 0.00 0.00 4.16
84 85 4.335594 GGGTATTGTCTTGACAATAGTGGC 59.664 45.833 26.81 18.31 41.52 5.01
112 113 5.461032 TCTTTTCCTCTTCTCTCTGACAC 57.539 43.478 0.00 0.00 0.00 3.67
178 179 3.380004 TCGAGATTGCAAAACACCAAAGT 59.620 39.130 1.71 0.00 0.00 2.66
232 233 0.882042 CCACAGTTTCTGCGTGCTCT 60.882 55.000 0.00 0.00 34.37 4.09
305 306 1.471287 CATACAGACAGACGTTCCGGA 59.529 52.381 0.00 0.00 0.00 5.14
318 319 5.762179 ACTGAAACCCTTGATCATACAGA 57.238 39.130 0.00 0.00 0.00 3.41
319 320 6.430925 TGAAACTGAAACCCTTGATCATACAG 59.569 38.462 0.00 0.00 0.00 2.74
320 321 6.303054 TGAAACTGAAACCCTTGATCATACA 58.697 36.000 0.00 0.00 0.00 2.29
321 322 6.127897 CCTGAAACTGAAACCCTTGATCATAC 60.128 42.308 0.00 0.00 0.00 2.39
417 419 2.032799 GCACGTGAGTTTTCCAATCACA 59.967 45.455 22.23 0.00 46.40 3.58
426 428 3.622459 GCAGTTGCACGTGAGTTTT 57.378 47.368 22.23 0.00 46.40 2.43
539 543 5.827267 TGCATGGTTCAAAATAGCATAGCTA 59.173 36.000 0.00 0.00 45.55 3.32
546 550 6.281848 CATGATTGCATGGTTCAAAATAGC 57.718 37.500 0.00 0.00 46.45 2.97
591 613 0.108615 ATATGTATCGGAGCGGCTGC 60.109 55.000 10.33 10.33 43.24 5.25
593 615 3.090037 ACTTATATGTATCGGAGCGGCT 58.910 45.455 0.00 0.00 0.00 5.52
597 619 4.735822 GCATCGACTTATATGTATCGGAGC 59.264 45.833 0.00 5.75 35.31 4.70
599 621 4.393990 ACGCATCGACTTATATGTATCGGA 59.606 41.667 0.00 0.00 35.31 4.55
602 624 6.033619 GTCCAACGCATCGACTTATATGTATC 59.966 42.308 0.00 0.00 0.00 2.24
603 625 5.862323 GTCCAACGCATCGACTTATATGTAT 59.138 40.000 0.00 0.00 0.00 2.29
604 626 5.217393 GTCCAACGCATCGACTTATATGTA 58.783 41.667 0.00 0.00 0.00 2.29
611 633 3.856508 CGTCCAACGCATCGACTT 58.143 55.556 0.00 0.00 33.65 3.01
621 643 3.112709 GTCGGCAGAGCGTCCAAC 61.113 66.667 0.00 0.00 0.00 3.77
639 661 2.548480 GTCCGCCCTGTTTTAGATATGC 59.452 50.000 0.00 0.00 0.00 3.14
640 662 2.800544 CGTCCGCCCTGTTTTAGATATG 59.199 50.000 0.00 0.00 0.00 1.78
641 663 2.805657 GCGTCCGCCCTGTTTTAGATAT 60.806 50.000 0.00 0.00 34.56 1.63
642 664 1.472026 GCGTCCGCCCTGTTTTAGATA 60.472 52.381 0.00 0.00 34.56 1.98
643 665 0.743345 GCGTCCGCCCTGTTTTAGAT 60.743 55.000 0.00 0.00 34.56 1.98
644 666 1.375013 GCGTCCGCCCTGTTTTAGA 60.375 57.895 0.00 0.00 34.56 2.10
645 667 3.174788 GCGTCCGCCCTGTTTTAG 58.825 61.111 0.00 0.00 34.56 1.85
667 689 2.125832 GTTCGAATCGGACGCCCA 60.126 61.111 0.00 0.00 0.00 5.36
720 742 0.169009 GAGCAACTTCAATGGGCGAC 59.831 55.000 0.00 0.00 0.00 5.19
721 743 0.036732 AGAGCAACTTCAATGGGCGA 59.963 50.000 0.00 0.00 0.00 5.54
722 744 1.737838 TAGAGCAACTTCAATGGGCG 58.262 50.000 0.00 0.00 0.00 6.13
724 746 6.258160 CGTTTATTAGAGCAACTTCAATGGG 58.742 40.000 0.00 0.00 0.00 4.00
727 749 5.648092 AGCCGTTTATTAGAGCAACTTCAAT 59.352 36.000 0.00 0.00 0.00 2.57
731 753 7.303261 GTTTTAGCCGTTTATTAGAGCAACTT 58.697 34.615 0.00 0.00 0.00 2.66
749 771 2.872557 GAACGGGCGGGTTTTAGC 59.127 61.111 0.00 0.00 0.00 3.09
750 772 3.171056 CGAACGGGCGGGTTTTAG 58.829 61.111 0.00 0.00 0.00 1.85
763 785 4.047059 TCGACCGTGCCTCCGAAC 62.047 66.667 0.00 0.00 0.00 3.95
764 786 4.047059 GTCGACCGTGCCTCCGAA 62.047 66.667 3.51 0.00 32.60 4.30
856 898 2.426023 GTTGGGAGGTGTGCGTCT 59.574 61.111 0.00 0.00 0.00 4.18
880 922 4.393778 ATCGGGTCGGGGTGGACT 62.394 66.667 0.00 0.00 37.12 3.85
949 991 0.966179 TGTAGTGAGCGTGGATGTGT 59.034 50.000 0.00 0.00 0.00 3.72
951 993 1.893137 TCTTGTAGTGAGCGTGGATGT 59.107 47.619 0.00 0.00 0.00 3.06
1591 1670 2.909662 AGAGGGAAAGGAAAGAGGAGTG 59.090 50.000 0.00 0.00 0.00 3.51
1645 1725 4.768583 AGAGGAATCATCAGTTCTTGCTC 58.231 43.478 0.00 0.00 36.62 4.26
1796 1876 2.586635 ACGTGCACGCCGAAGAAA 60.587 55.556 37.35 0.00 44.43 2.52
1868 1948 3.066621 GCGGGAATGAATGAATGCTTACA 59.933 43.478 0.00 0.00 0.00 2.41
1988 2068 7.560991 TGATTAATTCACAGCCATTTACCAGAT 59.439 33.333 0.00 0.00 0.00 2.90
1989 2069 6.889177 TGATTAATTCACAGCCATTTACCAGA 59.111 34.615 0.00 0.00 0.00 3.86
1990 2070 7.099266 TGATTAATTCACAGCCATTTACCAG 57.901 36.000 0.00 0.00 0.00 4.00
2077 2170 1.065701 ACGTAAATGCACCGCACAAAA 59.934 42.857 0.00 0.00 43.04 2.44
2102 2195 7.228507 TGCAAATGTGTGTTCATAAGACTACTT 59.771 33.333 0.00 0.00 39.81 2.24
2198 2291 1.596603 TGGTCAAGACATGTGCAGTG 58.403 50.000 1.15 0.00 0.00 3.66
2199 2292 2.346766 TTGGTCAAGACATGTGCAGT 57.653 45.000 1.15 0.00 0.00 4.40
2200 2293 3.181488 TGTTTTGGTCAAGACATGTGCAG 60.181 43.478 1.15 0.00 31.57 4.41
2201 2294 2.757314 TGTTTTGGTCAAGACATGTGCA 59.243 40.909 1.15 0.00 31.57 4.57
2202 2295 3.435105 TGTTTTGGTCAAGACATGTGC 57.565 42.857 1.15 0.00 31.57 4.57
2285 2412 2.603173 CCTGTTCGAGTTTTTCAGCAGC 60.603 50.000 0.00 0.00 0.00 5.25
2289 2416 4.376413 CGATGTCCTGTTCGAGTTTTTCAG 60.376 45.833 0.00 0.00 37.55 3.02
2313 2440 0.904649 ATGACAGCAACTCGGGATGA 59.095 50.000 0.00 0.00 0.00 2.92
2344 2475 5.344933 CCGCGGAAAAAGAAAGAAATAAAGG 59.655 40.000 24.07 0.00 0.00 3.11
2386 2517 9.108284 AGAGAAAAGAGAGAGAAAGAAACAAAG 57.892 33.333 0.00 0.00 0.00 2.77
2390 2521 6.346518 CGCAGAGAAAAGAGAGAGAAAGAAAC 60.347 42.308 0.00 0.00 0.00 2.78
2395 2526 4.302455 CACGCAGAGAAAAGAGAGAGAAA 58.698 43.478 0.00 0.00 0.00 2.52
2399 2530 2.239400 TCCACGCAGAGAAAAGAGAGA 58.761 47.619 0.00 0.00 0.00 3.10
2400 2531 2.732412 TCCACGCAGAGAAAAGAGAG 57.268 50.000 0.00 0.00 0.00 3.20
2401 2532 3.469008 TTTCCACGCAGAGAAAAGAGA 57.531 42.857 0.00 0.00 32.47 3.10
2402 2533 3.999663 AGATTTCCACGCAGAGAAAAGAG 59.000 43.478 0.00 0.00 37.03 2.85
2403 2534 3.997021 GAGATTTCCACGCAGAGAAAAGA 59.003 43.478 0.00 0.00 37.03 2.52
2404 2535 3.748048 TGAGATTTCCACGCAGAGAAAAG 59.252 43.478 0.00 0.00 37.03 2.27
2405 2536 3.738982 TGAGATTTCCACGCAGAGAAAA 58.261 40.909 0.00 0.00 37.03 2.29
2409 2540 3.264947 TGAATGAGATTTCCACGCAGAG 58.735 45.455 0.00 0.00 0.00 3.35
2411 2542 5.936686 ATATGAATGAGATTTCCACGCAG 57.063 39.130 0.00 0.00 0.00 5.18
2479 2610 6.761242 CGTTGGATCAGGATTCACAACTATTA 59.239 38.462 16.21 0.00 36.86 0.98
2480 2611 5.586243 CGTTGGATCAGGATTCACAACTATT 59.414 40.000 16.21 0.00 36.86 1.73
2487 2618 2.932614 CAGTCGTTGGATCAGGATTCAC 59.067 50.000 0.00 0.00 0.00 3.18
2497 2628 0.320771 GCCACAGACAGTCGTTGGAT 60.321 55.000 21.89 0.00 0.00 3.41
2499 2630 1.224069 CTGCCACAGACAGTCGTTGG 61.224 60.000 15.91 15.91 32.44 3.77
2504 2635 2.289320 ACTTCATCTGCCACAGACAGTC 60.289 50.000 0.00 0.00 43.63 3.51
2506 2637 2.469274 ACTTCATCTGCCACAGACAG 57.531 50.000 0.00 0.00 43.63 3.51
2507 2638 2.899900 AGTACTTCATCTGCCACAGACA 59.100 45.455 0.00 0.00 43.63 3.41
2508 2639 3.601443 AGTACTTCATCTGCCACAGAC 57.399 47.619 0.00 0.00 43.63 3.51
2509 2640 3.834813 AGAAGTACTTCATCTGCCACAGA 59.165 43.478 31.80 0.00 41.84 3.41
2580 2711 3.788766 CGTACAGCGGCACCTTGC 61.789 66.667 1.45 0.00 44.08 4.01
2813 2944 2.181021 CGGGTCGTGTGGCTAGAC 59.819 66.667 0.00 0.00 0.00 2.59
2814 2945 2.034532 TCGGGTCGTGTGGCTAGA 59.965 61.111 0.00 0.00 0.00 2.43
2815 2946 2.181021 GTCGGGTCGTGTGGCTAG 59.819 66.667 0.00 0.00 0.00 3.42
2816 2947 3.376078 GGTCGGGTCGTGTGGCTA 61.376 66.667 0.00 0.00 0.00 3.93
2818 2949 4.736896 GAGGTCGGGTCGTGTGGC 62.737 72.222 0.00 0.00 0.00 5.01
2819 2950 4.065281 GGAGGTCGGGTCGTGTGG 62.065 72.222 0.00 0.00 0.00 4.17
2820 2951 4.065281 GGGAGGTCGGGTCGTGTG 62.065 72.222 0.00 0.00 0.00 3.82
2839 2970 1.826385 AGAAAGAAAGATGGCGGTGG 58.174 50.000 0.00 0.00 0.00 4.61
2878 3012 8.315391 ACATCACATCACATAGCATAACATAC 57.685 34.615 0.00 0.00 0.00 2.39
2888 3022 5.912360 ACGCATTACATCACATCACATAG 57.088 39.130 0.00 0.00 0.00 2.23
2894 3028 6.645003 TGGTAATCTACGCATTACATCACATC 59.355 38.462 12.19 0.00 39.92 3.06
2911 3045 6.538742 CGTCAAAATGGTACTCATGGTAATCT 59.461 38.462 0.00 0.00 35.99 2.40
2918 3052 3.605634 TCCCGTCAAAATGGTACTCATG 58.394 45.455 0.00 0.00 35.99 3.07
2921 3055 3.604875 TCTCCCGTCAAAATGGTACTC 57.395 47.619 0.00 0.00 0.00 2.59
2965 3102 3.495193 CAGGCGACAAAATTCATCTGTG 58.505 45.455 0.00 0.00 0.00 3.66
3062 3199 0.965866 TCACAAAACCCACGCCACAA 60.966 50.000 0.00 0.00 0.00 3.33
3135 3272 2.048444 ACGTCCGCTAATCCAGTCTA 57.952 50.000 0.00 0.00 0.00 2.59
3136 3273 1.135083 CAACGTCCGCTAATCCAGTCT 60.135 52.381 0.00 0.00 0.00 3.24
3139 3281 0.460284 AGCAACGTCCGCTAATCCAG 60.460 55.000 10.47 0.00 38.15 3.86
3173 3315 3.128764 GGTTTATGGGAGCAGTTTACAGC 59.871 47.826 0.00 0.00 0.00 4.40
3174 3316 3.374058 CGGTTTATGGGAGCAGTTTACAG 59.626 47.826 0.00 0.00 0.00 2.74
3199 3341 5.106277 CGTGTAGAAAGAAAGGGGGAAAATC 60.106 44.000 0.00 0.00 0.00 2.17
3200 3342 4.765339 CGTGTAGAAAGAAAGGGGGAAAAT 59.235 41.667 0.00 0.00 0.00 1.82
3201 3343 4.139038 CGTGTAGAAAGAAAGGGGGAAAA 58.861 43.478 0.00 0.00 0.00 2.29
3202 3344 3.497227 CCGTGTAGAAAGAAAGGGGGAAA 60.497 47.826 0.00 0.00 0.00 3.13
3203 3345 2.039348 CCGTGTAGAAAGAAAGGGGGAA 59.961 50.000 0.00 0.00 0.00 3.97
3204 3346 1.626825 CCGTGTAGAAAGAAAGGGGGA 59.373 52.381 0.00 0.00 0.00 4.81
3205 3347 1.626825 TCCGTGTAGAAAGAAAGGGGG 59.373 52.381 0.00 0.00 0.00 5.40
3206 3348 2.354805 CCTCCGTGTAGAAAGAAAGGGG 60.355 54.545 0.00 0.00 0.00 4.79
3207 3349 2.302157 ACCTCCGTGTAGAAAGAAAGGG 59.698 50.000 0.00 0.00 0.00 3.95
3208 3350 3.679824 ACCTCCGTGTAGAAAGAAAGG 57.320 47.619 0.00 0.00 0.00 3.11
3209 3351 7.486802 TTAAAACCTCCGTGTAGAAAGAAAG 57.513 36.000 0.00 0.00 0.00 2.62
3210 3352 6.017687 GCTTAAAACCTCCGTGTAGAAAGAAA 60.018 38.462 0.00 0.00 0.00 2.52
3211 3353 5.467735 GCTTAAAACCTCCGTGTAGAAAGAA 59.532 40.000 0.00 0.00 0.00 2.52
3212 3354 4.992951 GCTTAAAACCTCCGTGTAGAAAGA 59.007 41.667 0.00 0.00 0.00 2.52
3213 3355 4.995487 AGCTTAAAACCTCCGTGTAGAAAG 59.005 41.667 0.00 0.00 0.00 2.62
3214 3356 4.964593 AGCTTAAAACCTCCGTGTAGAAA 58.035 39.130 0.00 0.00 0.00 2.52
3215 3357 4.612264 AGCTTAAAACCTCCGTGTAGAA 57.388 40.909 0.00 0.00 0.00 2.10
3216 3358 4.312443 CAAGCTTAAAACCTCCGTGTAGA 58.688 43.478 0.00 0.00 0.00 2.59
3217 3359 3.120304 GCAAGCTTAAAACCTCCGTGTAG 60.120 47.826 0.00 0.00 0.00 2.74
3218 3360 2.809696 GCAAGCTTAAAACCTCCGTGTA 59.190 45.455 0.00 0.00 0.00 2.90
3219 3361 1.607148 GCAAGCTTAAAACCTCCGTGT 59.393 47.619 0.00 0.00 0.00 4.49
3220 3362 1.880027 AGCAAGCTTAAAACCTCCGTG 59.120 47.619 0.00 0.00 0.00 4.94
3221 3363 1.880027 CAGCAAGCTTAAAACCTCCGT 59.120 47.619 0.00 0.00 0.00 4.69
3222 3364 1.200020 CCAGCAAGCTTAAAACCTCCG 59.800 52.381 0.00 0.00 0.00 4.63
3223 3365 2.239400 ACCAGCAAGCTTAAAACCTCC 58.761 47.619 0.00 0.00 0.00 4.30
3224 3366 3.190744 GGTACCAGCAAGCTTAAAACCTC 59.809 47.826 7.15 0.00 0.00 3.85
3225 3367 3.154710 GGTACCAGCAAGCTTAAAACCT 58.845 45.455 7.15 0.00 0.00 3.50
3226 3368 2.095415 CGGTACCAGCAAGCTTAAAACC 60.095 50.000 13.54 0.73 0.00 3.27
3227 3369 2.551032 ACGGTACCAGCAAGCTTAAAAC 59.449 45.455 13.54 0.00 0.00 2.43
3228 3370 2.550606 CACGGTACCAGCAAGCTTAAAA 59.449 45.455 13.54 0.00 0.00 1.52
3229 3371 2.147958 CACGGTACCAGCAAGCTTAAA 58.852 47.619 13.54 0.00 0.00 1.52
3230 3372 1.609580 CCACGGTACCAGCAAGCTTAA 60.610 52.381 13.54 0.00 0.00 1.85
3231 3373 0.036765 CCACGGTACCAGCAAGCTTA 60.037 55.000 13.54 0.00 0.00 3.09
3232 3374 1.302511 CCACGGTACCAGCAAGCTT 60.303 57.895 13.54 0.00 0.00 3.74
3233 3375 1.189524 TACCACGGTACCAGCAAGCT 61.190 55.000 13.54 0.00 0.00 3.74
3234 3376 1.017701 GTACCACGGTACCAGCAAGC 61.018 60.000 13.54 0.00 43.60 4.01
3299 4305 1.976045 CCCGCGAAAAGAAAACATTCG 59.024 47.619 8.23 3.02 46.36 3.34
3360 4371 0.673985 GGTCATCCATCGGATCGACA 59.326 55.000 18.68 0.00 40.98 4.35
3394 4417 3.737559 AACCATCAGATTTGGGCAGTA 57.262 42.857 0.00 0.00 38.64 2.74
3401 4424 8.815141 TTTTGTGATTGTAACCATCAGATTTG 57.185 30.769 0.00 0.00 0.00 2.32
3440 4463 0.026803 GAAACGGCTCTGCGCATTAG 59.973 55.000 12.24 13.32 41.67 1.73
3509 4532 2.932261 ACTAGCCGAATTGGGATTTCC 58.068 47.619 11.18 0.00 38.63 3.13
3510 4533 4.704965 ACTACTAGCCGAATTGGGATTTC 58.295 43.478 11.18 0.00 38.63 2.17
3511 4534 4.772886 ACTACTAGCCGAATTGGGATTT 57.227 40.909 11.18 0.00 38.63 2.17
3512 4535 6.435292 AATACTACTAGCCGAATTGGGATT 57.565 37.500 11.18 0.00 38.63 3.01
3513 4536 7.735326 ATAATACTACTAGCCGAATTGGGAT 57.265 36.000 11.18 6.58 38.63 3.85
3514 4537 7.233962 TCAATAATACTACTAGCCGAATTGGGA 59.766 37.037 11.18 0.00 38.63 4.37
3515 4538 7.383687 TCAATAATACTACTAGCCGAATTGGG 58.616 38.462 1.39 1.39 38.63 4.12
3516 4539 8.873830 CATCAATAATACTACTAGCCGAATTGG 58.126 37.037 0.00 0.00 42.50 3.16
3517 4540 9.424319 ACATCAATAATACTACTAGCCGAATTG 57.576 33.333 0.00 0.00 0.00 2.32
3578 4610 0.177604 GAGATGGGAGCACAGGACAG 59.822 60.000 0.00 0.00 0.00 3.51
3580 4612 0.980231 AGGAGATGGGAGCACAGGAC 60.980 60.000 0.00 0.00 0.00 3.85
3602 4634 2.539338 GCGTTTCAGTCGTGGGCAA 61.539 57.895 0.00 0.00 0.00 4.52
3660 6176 5.942236 AGACATACAATGTTGAATCTGTGCT 59.058 36.000 0.00 0.00 45.03 4.40
3713 6230 6.737254 TTTTTCTCTCGAGTTGTGTTTTCT 57.263 33.333 13.13 0.00 0.00 2.52
3773 6290 0.678950 AGTTTGGCGGTCAAATTGGG 59.321 50.000 11.33 0.00 45.79 4.12
3784 6301 3.438781 TGGTAGCTAATTTCAGTTTGGCG 59.561 43.478 0.00 0.00 0.00 5.69
3823 6340 1.878953 ATGCGCGGGGTATTTTCTAG 58.121 50.000 8.83 0.00 0.00 2.43
3824 6341 1.944024 CAATGCGCGGGGTATTTTCTA 59.056 47.619 8.83 0.00 0.00 2.10
3825 6342 0.738389 CAATGCGCGGGGTATTTTCT 59.262 50.000 8.83 0.00 0.00 2.52
3826 6343 0.869880 GCAATGCGCGGGGTATTTTC 60.870 55.000 8.83 0.00 0.00 2.29
3827 6344 1.140804 GCAATGCGCGGGGTATTTT 59.859 52.632 8.83 0.00 0.00 1.82
3828 6345 2.804856 GCAATGCGCGGGGTATTT 59.195 55.556 8.83 0.00 0.00 1.40
3837 6354 1.588139 GATTCCTGCAGCAATGCGC 60.588 57.895 7.83 13.40 42.91 6.09
3838 6355 1.298116 CGATTCCTGCAGCAATGCG 60.298 57.895 7.83 7.62 37.69 4.73
3839 6356 0.666913 ATCGATTCCTGCAGCAATGC 59.333 50.000 7.83 0.00 0.00 3.56
3840 6357 2.727777 CAATCGATTCCTGCAGCAATG 58.272 47.619 7.83 0.66 0.00 2.82
3841 6358 1.066605 GCAATCGATTCCTGCAGCAAT 59.933 47.619 14.23 5.04 36.09 3.56
3842 6359 0.452987 GCAATCGATTCCTGCAGCAA 59.547 50.000 14.23 0.00 36.09 3.91
3843 6360 0.677414 TGCAATCGATTCCTGCAGCA 60.677 50.000 17.14 14.95 41.01 4.41
3844 6361 0.452987 TTGCAATCGATTCCTGCAGC 59.547 50.000 19.43 14.12 46.08 5.25
3845 6362 4.761235 ATATTGCAATCGATTCCTGCAG 57.239 40.909 16.86 6.78 46.08 4.41
3846 6363 6.822667 AATATATTGCAATCGATTCCTGCA 57.177 33.333 16.86 17.14 44.04 4.41
3847 6364 7.307694 TGAAATATATTGCAATCGATTCCTGC 58.692 34.615 16.86 10.68 36.60 4.85
3848 6365 8.509690 ACTGAAATATATTGCAATCGATTCCTG 58.490 33.333 16.86 10.69 0.00 3.86
3849 6366 8.509690 CACTGAAATATATTGCAATCGATTCCT 58.490 33.333 16.86 3.00 0.00 3.36
3850 6367 8.506437 TCACTGAAATATATTGCAATCGATTCC 58.494 33.333 16.86 5.41 0.00 3.01
3854 6371 9.667989 CAAATCACTGAAATATATTGCAATCGA 57.332 29.630 16.86 5.36 0.00 3.59
3855 6372 9.667989 TCAAATCACTGAAATATATTGCAATCG 57.332 29.630 16.86 0.00 0.00 3.34
3867 6384 8.746530 AGCTTCATACAATCAAATCACTGAAAT 58.253 29.630 0.00 0.00 0.00 2.17
3868 6385 8.114331 AGCTTCATACAATCAAATCACTGAAA 57.886 30.769 0.00 0.00 0.00 2.69
3869 6386 7.692460 AGCTTCATACAATCAAATCACTGAA 57.308 32.000 0.00 0.00 0.00 3.02
3870 6387 7.692460 AAGCTTCATACAATCAAATCACTGA 57.308 32.000 0.00 0.00 0.00 3.41
3871 6388 8.024865 TGAAAGCTTCATACAATCAAATCACTG 58.975 33.333 0.00 0.00 34.08 3.66
3872 6389 8.114331 TGAAAGCTTCATACAATCAAATCACT 57.886 30.769 0.00 0.00 34.08 3.41
3980 6497 9.161629 CCATTACATTATGCCACTTATATTCGA 57.838 33.333 0.00 0.00 0.00 3.71
3981 6498 9.161629 TCCATTACATTATGCCACTTATATTCG 57.838 33.333 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.