Multiple sequence alignment - TraesCS3D01G411400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G411400 chr3D 100.000 3430 0 0 1 3430 523838463 523841892 0.000000e+00 6335.0
1 TraesCS3D01G411400 chr3D 95.760 283 8 3 3151 3430 523896752 523897033 1.450000e-123 453.0
2 TraesCS3D01G411400 chr3D 91.266 229 12 4 2927 3147 523896611 523896839 4.300000e-79 305.0
3 TraesCS3D01G411400 chr3D 93.846 130 3 4 3107 3235 523841528 523841653 1.260000e-44 191.0
4 TraesCS3D01G411400 chr3D 93.846 130 3 4 3066 3191 523841569 523841697 1.260000e-44 191.0
5 TraesCS3D01G411400 chr3D 91.860 86 3 3 3151 3236 523841528 523841609 2.160000e-22 117.0
6 TraesCS3D01G411400 chr3D 91.860 86 3 3 3066 3147 523841613 523841698 2.160000e-22 117.0
7 TraesCS3D01G411400 chr3A 91.121 1160 59 20 2020 3142 658750428 658751580 0.000000e+00 1531.0
8 TraesCS3D01G411400 chr3A 90.428 888 50 10 668 1548 658743970 658744829 0.000000e+00 1136.0
9 TraesCS3D01G411400 chr3A 90.508 453 31 4 1583 2024 658744824 658745275 3.810000e-164 588.0
10 TraesCS3D01G411400 chr3A 91.319 288 10 9 3151 3430 658751504 658751784 2.500000e-101 379.0
11 TraesCS3D01G411400 chr3B 91.277 1112 50 18 602 1696 691351066 691352147 0.000000e+00 1472.0
12 TraesCS3D01G411400 chr3B 89.047 703 62 12 2188 2884 691355145 691355838 0.000000e+00 857.0
13 TraesCS3D01G411400 chr3B 86.846 631 48 18 1 601 691346093 691346718 0.000000e+00 673.0
14 TraesCS3D01G411400 chr3B 88.037 326 24 8 1692 2012 691354176 691354491 4.180000e-99 372.0
15 TraesCS3D01G411400 chr3B 87.050 278 17 9 2882 3143 691355927 691356201 2.590000e-76 296.0
16 TraesCS3D01G411400 chr3B 81.924 343 52 8 1 335 804145137 804144797 7.250000e-72 281.0
17 TraesCS3D01G411400 chr3B 81.690 284 28 15 3151 3430 691356125 691356388 7.460000e-52 215.0
18 TraesCS3D01G411400 chr3B 97.333 75 2 0 2123 2197 691354492 691354566 9.990000e-26 128.0
19 TraesCS3D01G411400 chr7D 81.442 652 104 11 1806 2446 220508069 220508714 5.070000e-143 518.0
20 TraesCS3D01G411400 chr7A 81.077 650 109 9 1806 2446 232743073 232743717 1.100000e-139 507.0
21 TraesCS3D01G411400 chr7B 80.526 647 112 12 1809 2446 178419304 178418663 5.150000e-133 484.0
22 TraesCS3D01G411400 chr7B 77.358 371 70 10 15 374 57270645 57270278 1.250000e-49 207.0
23 TraesCS3D01G411400 chr7B 88.525 61 5 2 216 275 384026853 384026912 4.750000e-09 73.1
24 TraesCS3D01G411400 chr2B 80.051 391 62 15 2 380 710279176 710279562 3.370000e-70 276.0
25 TraesCS3D01G411400 chr1A 79.300 343 52 10 8 334 449845771 449845432 4.460000e-54 222.0
26 TraesCS3D01G411400 chr4D 77.333 375 70 15 2 366 87927557 87927188 1.250000e-49 207.0
27 TraesCS3D01G411400 chr5D 80.139 287 42 9 15 286 327532216 327531930 2.090000e-47 200.0
28 TraesCS3D01G411400 chr6B 77.663 291 46 8 15 297 120155849 120155570 3.540000e-35 159.0
29 TraesCS3D01G411400 chr2A 74.474 333 67 16 15 335 712980371 712980697 9.990000e-26 128.0


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 TraesCS3D01G411400 chr3D 523838463 523841892 3429 False 1390.200000 6335 94.282400 1 3430 5 chr3D.!!$F1 3429
1 TraesCS3D01G411400 chr3A 658750428 658751784 1356 False 955.000000 1531 91.220000 2020 3430 2 chr3A.!!$F2 1410
2 TraesCS3D01G411400 chr3A 658743970 658745275 1305 False 862.000000 1136 90.468000 668 2024 2 chr3A.!!$F1 1356
3 TraesCS3D01G411400 chr3B 691346093 691346718 625 False 673.000000 673 86.846000 1 601 1 chr3B.!!$F1 600
4 TraesCS3D01G411400 chr3B 691351066 691356388 5322 False 556.666667 1472 89.072333 602 3430 6 chr3B.!!$F2 2828
5 TraesCS3D01G411400 chr7D 220508069 220508714 645 False 518.000000 518 81.442000 1806 2446 1 chr7D.!!$F1 640
6 TraesCS3D01G411400 chr7A 232743073 232743717 644 False 507.000000 507 81.077000 1806 2446 1 chr7A.!!$F1 640
7 TraesCS3D01G411400 chr7B 178418663 178419304 641 True 484.000000 484 80.526000 1809 2446 1 chr7B.!!$R2 637

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
222 226 0.320421 GCCGCACTTGTGAGGACTAA 60.320 55.0 23.94 0.00 0.00 2.24 F
1376 1392 0.040425 AACAAGACGGATGCGTTTGC 60.040 50.0 23.59 10.57 43.20 3.68 F
1936 4014 0.036294 AGGCGCTCTTCCTGTTTACC 60.036 55.0 7.64 0.00 31.53 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1379 1395 0.323178 AATTCCACCTCTGCAGGCTG 60.323 55.0 15.13 10.94 45.05 4.85 R
2367 5054 0.613260 TCGGCACAATCCAAGCTACT 59.387 50.0 0.00 0.00 0.00 2.57 R
2863 5565 1.223187 ACCCGTTTGTGTTCTTAGCG 58.777 50.0 0.00 0.00 0.00 4.26 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
18 19 2.832931 ACAGTCATCGCTGCTGAAC 58.167 52.632 14.60 0.00 39.96 3.18
24 25 2.042831 ATCGCTGCTGAACCCTTGC 61.043 57.895 0.00 0.00 0.00 4.01
29 30 1.679944 GCTGCTGAACCCTTGCATAGA 60.680 52.381 0.00 0.00 36.07 1.98
40 41 4.402474 ACCCTTGCATAGATTTAAAGCACC 59.598 41.667 6.19 0.00 34.56 5.01
52 53 7.899973 AGATTTAAAGCACCTGACATCAAATT 58.100 30.769 6.19 0.00 0.00 1.82
106 110 2.700897 CCCCAAGGAGACGACAATCTAT 59.299 50.000 0.00 0.00 33.47 1.98
177 181 1.546476 AGCTCGGAAGACAAACTCGAT 59.454 47.619 0.00 0.00 35.39 3.59
179 183 2.671351 GCTCGGAAGACAAACTCGATGA 60.671 50.000 0.00 0.00 35.39 2.92
180 184 3.575630 CTCGGAAGACAAACTCGATGAA 58.424 45.455 0.00 0.00 35.39 2.57
181 185 3.985008 TCGGAAGACAAACTCGATGAAA 58.015 40.909 0.00 0.00 33.31 2.69
213 217 3.683937 GCCCAATGCCGCACTTGT 61.684 61.111 0.00 0.00 0.00 3.16
222 226 0.320421 GCCGCACTTGTGAGGACTAA 60.320 55.000 23.94 0.00 0.00 2.24
225 229 3.074412 CCGCACTTGTGAGGACTAAAAT 58.926 45.455 16.69 0.00 0.00 1.82
228 232 5.354234 CCGCACTTGTGAGGACTAAAATAAT 59.646 40.000 16.69 0.00 0.00 1.28
231 235 6.599638 GCACTTGTGAGGACTAAAATAATCCT 59.400 38.462 4.79 0.00 45.84 3.24
234 238 9.668497 ACTTGTGAGGACTAAAATAATCCTAAC 57.332 33.333 0.62 0.62 43.12 2.34
252 256 4.277921 CCTAACCTAAACTACTAGCCGGAG 59.722 50.000 5.05 0.00 0.00 4.63
253 257 2.030371 ACCTAAACTACTAGCCGGAGC 58.970 52.381 5.05 0.00 40.32 4.70
255 259 2.429610 CCTAAACTACTAGCCGGAGCAA 59.570 50.000 5.05 0.00 43.56 3.91
286 290 2.987431 TTACCTTCCCCACCACCGGT 62.987 60.000 0.00 0.00 35.62 5.28
347 354 1.544825 CGTGAAGCCTGGAGGGAGAA 61.545 60.000 0.00 0.00 37.23 2.87
392 400 9.626045 GTTAGGGAAGAAAAGTTGTATTCAATG 57.374 33.333 2.95 0.00 35.92 2.82
455 463 8.873186 AAAAAGGAATTATTAGGAAGACGGAA 57.127 30.769 0.00 0.00 0.00 4.30
456 464 8.507524 AAAAGGAATTATTAGGAAGACGGAAG 57.492 34.615 0.00 0.00 0.00 3.46
457 465 6.176014 AGGAATTATTAGGAAGACGGAAGG 57.824 41.667 0.00 0.00 0.00 3.46
458 466 5.903589 AGGAATTATTAGGAAGACGGAAGGA 59.096 40.000 0.00 0.00 0.00 3.36
459 467 5.990386 GGAATTATTAGGAAGACGGAAGGAC 59.010 44.000 0.00 0.00 0.00 3.85
460 468 4.644103 TTATTAGGAAGACGGAAGGACG 57.356 45.455 0.00 0.00 40.31 4.79
461 469 2.205022 TTAGGAAGACGGAAGGACGA 57.795 50.000 0.00 0.00 37.61 4.20
462 470 1.747709 TAGGAAGACGGAAGGACGAG 58.252 55.000 0.00 0.00 37.61 4.18
463 471 1.153804 GGAAGACGGAAGGACGAGC 60.154 63.158 0.00 0.00 37.61 5.03
464 472 1.514443 GAAGACGGAAGGACGAGCG 60.514 63.158 0.00 0.00 37.61 5.03
465 473 1.919956 GAAGACGGAAGGACGAGCGA 61.920 60.000 0.00 0.00 37.61 4.93
466 474 1.313812 AAGACGGAAGGACGAGCGAT 61.314 55.000 0.00 0.00 37.61 4.58
467 475 1.139095 GACGGAAGGACGAGCGATT 59.861 57.895 0.00 0.00 37.61 3.34
468 476 0.458025 GACGGAAGGACGAGCGATTT 60.458 55.000 0.00 0.00 37.61 2.17
469 477 0.813184 ACGGAAGGACGAGCGATTTA 59.187 50.000 0.00 0.00 37.61 1.40
470 478 1.407979 ACGGAAGGACGAGCGATTTAT 59.592 47.619 0.00 0.00 37.61 1.40
471 479 2.159142 ACGGAAGGACGAGCGATTTATT 60.159 45.455 0.00 0.00 37.61 1.40
472 480 3.067180 ACGGAAGGACGAGCGATTTATTA 59.933 43.478 0.00 0.00 37.61 0.98
473 481 3.424529 CGGAAGGACGAGCGATTTATTAC 59.575 47.826 0.00 0.00 35.47 1.89
474 482 4.365723 GGAAGGACGAGCGATTTATTACA 58.634 43.478 0.00 0.00 0.00 2.41
475 483 4.208666 GGAAGGACGAGCGATTTATTACAC 59.791 45.833 0.00 0.00 0.00 2.90
476 484 3.714391 AGGACGAGCGATTTATTACACC 58.286 45.455 0.00 0.00 0.00 4.16
477 485 2.798847 GGACGAGCGATTTATTACACCC 59.201 50.000 0.00 0.00 0.00 4.61
478 486 3.492137 GGACGAGCGATTTATTACACCCT 60.492 47.826 0.00 0.00 0.00 4.34
479 487 3.454375 ACGAGCGATTTATTACACCCTG 58.546 45.455 0.00 0.00 0.00 4.45
480 488 2.800544 CGAGCGATTTATTACACCCTGG 59.199 50.000 0.00 0.00 0.00 4.45
481 489 3.491964 CGAGCGATTTATTACACCCTGGA 60.492 47.826 0.00 0.00 0.00 3.86
482 490 4.448210 GAGCGATTTATTACACCCTGGAA 58.552 43.478 0.00 0.00 0.00 3.53
483 491 5.048846 AGCGATTTATTACACCCTGGAAT 57.951 39.130 0.00 0.00 34.73 3.01
484 492 6.182507 AGCGATTTATTACACCCTGGAATA 57.817 37.500 0.00 0.00 32.21 1.75
485 493 5.995897 AGCGATTTATTACACCCTGGAATAC 59.004 40.000 0.00 0.00 33.16 1.89
486 494 5.180680 GCGATTTATTACACCCTGGAATACC 59.819 44.000 0.00 0.00 33.16 2.73
487 495 6.531021 CGATTTATTACACCCTGGAATACCT 58.469 40.000 0.00 0.00 33.16 3.08
488 496 6.649557 CGATTTATTACACCCTGGAATACCTC 59.350 42.308 0.00 0.00 33.16 3.85
489 497 7.472945 CGATTTATTACACCCTGGAATACCTCT 60.473 40.741 0.00 0.00 33.16 3.69
490 498 7.519347 TTTATTACACCCTGGAATACCTCTT 57.481 36.000 0.00 0.00 33.16 2.85
491 499 4.837093 TTACACCCTGGAATACCTCTTG 57.163 45.455 0.00 0.00 37.04 3.02
492 500 2.915869 ACACCCTGGAATACCTCTTGA 58.084 47.619 0.00 0.00 37.04 3.02
493 501 3.256704 ACACCCTGGAATACCTCTTGAA 58.743 45.455 0.00 0.00 37.04 2.69
494 502 3.655777 ACACCCTGGAATACCTCTTGAAA 59.344 43.478 0.00 0.00 37.04 2.69
495 503 4.292306 ACACCCTGGAATACCTCTTGAAAT 59.708 41.667 0.00 0.00 37.04 2.17
496 504 4.641989 CACCCTGGAATACCTCTTGAAATG 59.358 45.833 0.00 0.00 37.04 2.32
497 505 4.210331 CCCTGGAATACCTCTTGAAATGG 58.790 47.826 0.00 0.00 37.04 3.16
498 506 3.633986 CCTGGAATACCTCTTGAAATGGC 59.366 47.826 0.00 0.00 37.04 4.40
499 507 3.278574 TGGAATACCTCTTGAAATGGCG 58.721 45.455 0.00 0.00 37.04 5.69
500 508 3.054728 TGGAATACCTCTTGAAATGGCGA 60.055 43.478 0.00 0.00 37.04 5.54
501 509 3.312697 GGAATACCTCTTGAAATGGCGAC 59.687 47.826 0.00 0.00 0.00 5.19
502 510 2.004583 TACCTCTTGAAATGGCGACG 57.995 50.000 0.00 0.00 0.00 5.12
503 511 0.673644 ACCTCTTGAAATGGCGACGG 60.674 55.000 0.00 0.00 0.00 4.79
504 512 1.425428 CTCTTGAAATGGCGACGGC 59.575 57.895 15.43 15.43 38.90 5.68
505 513 2.098298 CTTGAAATGGCGACGGCG 59.902 61.111 17.16 6.12 41.24 6.46
528 536 2.185867 GGTATCCCGCTGCGTTGA 59.814 61.111 21.59 16.73 0.00 3.18
529 537 2.171725 GGTATCCCGCTGCGTTGAC 61.172 63.158 21.59 12.38 0.00 3.18
530 538 1.153628 GTATCCCGCTGCGTTGACT 60.154 57.895 21.59 9.36 0.00 3.41
531 539 0.739813 GTATCCCGCTGCGTTGACTT 60.740 55.000 21.59 5.83 0.00 3.01
532 540 0.739462 TATCCCGCTGCGTTGACTTG 60.739 55.000 21.59 3.19 0.00 3.16
533 541 2.449031 ATCCCGCTGCGTTGACTTGA 62.449 55.000 21.59 5.88 0.00 3.02
534 542 2.551270 CCGCTGCGTTGACTTGAC 59.449 61.111 21.59 0.00 0.00 3.18
535 543 2.551270 CGCTGCGTTGACTTGACC 59.449 61.111 14.93 0.00 0.00 4.02
536 544 2.551270 GCTGCGTTGACTTGACCG 59.449 61.111 0.00 0.00 0.00 4.79
537 545 2.551270 CTGCGTTGACTTGACCGC 59.449 61.111 0.00 0.00 45.92 5.68
538 546 1.956170 CTGCGTTGACTTGACCGCT 60.956 57.895 0.00 0.00 45.90 5.52
539 547 2.162921 CTGCGTTGACTTGACCGCTG 62.163 60.000 0.00 0.00 45.90 5.18
540 548 2.551270 CGTTGACTTGACCGCTGC 59.449 61.111 0.00 0.00 0.00 5.25
541 549 2.946762 GTTGACTTGACCGCTGCC 59.053 61.111 0.00 0.00 0.00 4.85
542 550 2.664851 TTGACTTGACCGCTGCCG 60.665 61.111 0.00 0.00 0.00 5.69
554 562 4.680237 CTGCCGGCGAGTTGACCA 62.680 66.667 23.90 0.00 0.00 4.02
555 563 4.680237 TGCCGGCGAGTTGACCAG 62.680 66.667 23.90 0.00 0.00 4.00
556 564 4.373116 GCCGGCGAGTTGACCAGA 62.373 66.667 12.58 0.00 0.00 3.86
557 565 2.579201 CCGGCGAGTTGACCAGAT 59.421 61.111 9.30 0.00 0.00 2.90
558 566 1.811266 CCGGCGAGTTGACCAGATG 60.811 63.158 9.30 0.00 0.00 2.90
559 567 1.811266 CGGCGAGTTGACCAGATGG 60.811 63.158 0.00 0.00 42.17 3.51
560 568 2.109126 GGCGAGTTGACCAGATGGC 61.109 63.158 0.00 0.00 39.32 4.40
561 569 2.109126 GCGAGTTGACCAGATGGCC 61.109 63.158 0.00 0.00 39.32 5.36
562 570 1.296392 CGAGTTGACCAGATGGCCA 59.704 57.895 8.56 8.56 39.32 5.36
563 571 1.021390 CGAGTTGACCAGATGGCCAC 61.021 60.000 8.16 1.58 39.32 5.01
564 572 0.678048 GAGTTGACCAGATGGCCACC 60.678 60.000 8.16 0.00 39.32 4.61
565 573 1.136329 AGTTGACCAGATGGCCACCT 61.136 55.000 8.16 0.00 39.32 4.00
566 574 0.678048 GTTGACCAGATGGCCACCTC 60.678 60.000 8.16 1.78 39.32 3.85
567 575 1.852157 TTGACCAGATGGCCACCTCC 61.852 60.000 8.16 0.00 39.32 4.30
568 576 1.997874 GACCAGATGGCCACCTCCT 60.998 63.158 8.16 0.00 39.32 3.69
569 577 1.977293 GACCAGATGGCCACCTCCTC 61.977 65.000 8.16 0.00 39.32 3.71
570 578 2.750657 CCAGATGGCCACCTCCTCC 61.751 68.421 8.16 0.00 0.00 4.30
571 579 2.367512 AGATGGCCACCTCCTCCC 60.368 66.667 8.16 0.00 0.00 4.30
572 580 3.493303 GATGGCCACCTCCTCCCC 61.493 72.222 8.16 0.00 0.00 4.81
586 594 4.564110 CCCCCGCCCCTTTCGATC 62.564 72.222 0.00 0.00 0.00 3.69
587 595 4.564110 CCCCGCCCCTTTCGATCC 62.564 72.222 0.00 0.00 0.00 3.36
588 596 3.480133 CCCGCCCCTTTCGATCCT 61.480 66.667 0.00 0.00 0.00 3.24
589 597 2.203070 CCGCCCCTTTCGATCCTG 60.203 66.667 0.00 0.00 0.00 3.86
590 598 2.897350 CGCCCCTTTCGATCCTGC 60.897 66.667 0.00 0.00 0.00 4.85
591 599 2.592308 GCCCCTTTCGATCCTGCT 59.408 61.111 0.00 0.00 0.00 4.24
592 600 1.524849 GCCCCTTTCGATCCTGCTC 60.525 63.158 0.00 0.00 0.00 4.26
593 601 1.147153 CCCCTTTCGATCCTGCTCC 59.853 63.158 0.00 0.00 0.00 4.70
594 602 1.147153 CCCTTTCGATCCTGCTCCC 59.853 63.158 0.00 0.00 0.00 4.30
595 603 1.147153 CCTTTCGATCCTGCTCCCC 59.853 63.158 0.00 0.00 0.00 4.81
596 604 1.147153 CTTTCGATCCTGCTCCCCC 59.853 63.158 0.00 0.00 0.00 5.40
597 605 1.306997 TTTCGATCCTGCTCCCCCT 60.307 57.895 0.00 0.00 0.00 4.79
598 606 1.338136 TTTCGATCCTGCTCCCCCTC 61.338 60.000 0.00 0.00 0.00 4.30
599 607 2.123077 CGATCCTGCTCCCCCTCT 60.123 66.667 0.00 0.00 0.00 3.69
600 608 2.206536 CGATCCTGCTCCCCCTCTC 61.207 68.421 0.00 0.00 0.00 3.20
612 620 1.394151 CCCTCTCTCCACCTCCCTT 59.606 63.158 0.00 0.00 0.00 3.95
711 719 3.527775 CTATGAGGAGGGCGCTGGC 62.528 68.421 8.56 0.00 38.90 4.85
774 782 2.997897 GGCGAGTGGTCAGGAGGT 60.998 66.667 0.00 0.00 0.00 3.85
811 819 2.450502 AAGGGGTGGGAGTGCAGT 60.451 61.111 0.00 0.00 0.00 4.40
863 871 1.302511 GACTTCTTCAAGGCCCGCA 60.303 57.895 0.00 0.00 30.14 5.69
864 872 1.578206 GACTTCTTCAAGGCCCGCAC 61.578 60.000 0.00 0.00 30.14 5.34
865 873 1.302832 CTTCTTCAAGGCCCGCACT 60.303 57.895 0.00 0.00 0.00 4.40
888 897 4.847444 GAGCTCTTCCCCAGGCGC 62.847 72.222 6.43 0.00 0.00 6.53
926 935 2.202932 CGCCGGATTCTGGGACTG 60.203 66.667 5.05 0.00 0.00 3.51
927 936 2.190578 GCCGGATTCTGGGACTGG 59.809 66.667 5.05 0.00 0.00 4.00
928 937 2.911143 CCGGATTCTGGGACTGGG 59.089 66.667 0.00 0.00 0.00 4.45
929 938 1.689233 CCGGATTCTGGGACTGGGA 60.689 63.158 0.00 0.00 0.00 4.37
930 939 1.522569 CGGATTCTGGGACTGGGAC 59.477 63.158 0.00 0.00 0.00 4.46
931 940 1.915983 GGATTCTGGGACTGGGACC 59.084 63.158 0.00 0.00 0.00 4.46
1013 1022 3.083997 GGAGATGGGCGTCAGGGT 61.084 66.667 0.00 0.00 0.00 4.34
1067 1076 0.608582 ACCTCGTGTACGCTTCTCCT 60.609 55.000 4.67 0.00 39.60 3.69
1071 1080 0.798771 CGTGTACGCTTCTCCTCTGC 60.799 60.000 4.67 0.00 0.00 4.26
1097 1106 4.000988 GACTCTGGTTCGCCTTAATTTGA 58.999 43.478 0.00 0.00 38.36 2.69
1131 1140 0.465705 TCTCCTGAATGCTAAGCCGG 59.534 55.000 0.00 0.00 0.00 6.13
1132 1141 1.153168 TCCTGAATGCTAAGCCGGC 60.153 57.895 21.89 21.89 0.00 6.13
1174 1183 5.257082 TGCTATAAACATACTCGAGCACA 57.743 39.130 13.61 0.00 33.73 4.57
1203 1218 6.423302 CAGGCAAACAGTATAGAGATGCTTAG 59.577 42.308 0.00 0.00 33.09 2.18
1209 1224 3.513515 AGTATAGAGATGCTTAGGCTGCC 59.486 47.826 11.65 11.65 39.59 4.85
1237 1252 5.879223 AGGATATGCAGAGAAAGTTGACAAG 59.121 40.000 0.00 0.00 0.00 3.16
1246 1261 6.203530 CAGAGAAAGTTGACAAGCATAGACAA 59.796 38.462 0.00 0.00 0.00 3.18
1261 1277 7.444299 AGCATAGACAAACCATCACAAATTTT 58.556 30.769 0.00 0.00 0.00 1.82
1355 1371 6.573434 TGATGAGTGACACATATAACAGGTC 58.427 40.000 8.59 0.00 0.00 3.85
1376 1392 0.040425 AACAAGACGGATGCGTTTGC 60.040 50.000 23.59 10.57 43.20 3.68
1377 1393 0.884704 ACAAGACGGATGCGTTTGCT 60.885 50.000 23.59 12.35 43.34 3.91
1378 1394 0.453282 CAAGACGGATGCGTTTGCTG 60.453 55.000 15.15 5.38 43.34 4.41
1379 1395 2.187599 AAGACGGATGCGTTTGCTGC 62.188 55.000 15.15 0.00 43.34 5.25
1381 1397 2.202388 CGGATGCGTTTGCTGCAG 60.202 61.111 10.11 10.11 46.98 4.41
1382 1398 2.505557 GGATGCGTTTGCTGCAGC 60.506 61.111 31.89 31.89 46.98 5.25
1421 1437 2.769893 ACCAAATTTTGCATGACAGCC 58.230 42.857 0.00 0.00 0.00 4.85
1427 1443 0.109179 TTTGCATGACAGCCGAATGC 60.109 50.000 0.00 5.69 45.51 3.56
1532 1548 6.483307 TGATGTGGCATGCTAATTACTACTTC 59.517 38.462 18.92 6.14 0.00 3.01
1576 1592 8.834465 CATCAGAATAGTTCCTTATCCAGTTTG 58.166 37.037 0.00 0.00 0.00 2.93
1621 1637 7.557719 TCTTCATAAGAATGTGGGAAGGATTTC 59.442 37.037 0.00 0.00 33.83 2.17
1622 1638 6.973642 TCATAAGAATGTGGGAAGGATTTCT 58.026 36.000 0.00 0.00 34.50 2.52
1624 1640 3.359950 AGAATGTGGGAAGGATTTCTGC 58.640 45.455 0.00 0.00 33.68 4.26
1807 3877 5.399013 GTGGACGTTTTTATCCAAATCCAG 58.601 41.667 0.00 0.00 32.38 3.86
1857 3927 5.132648 TGAAATGAGCCCATACCAGAACTAT 59.867 40.000 0.00 0.00 31.59 2.12
1879 3949 1.878975 TGCGACGACAGCAACGAAA 60.879 52.632 0.00 0.00 42.18 3.46
1888 3958 3.421826 CGACAGCAACGAAATATATCGCC 60.422 47.826 0.00 0.00 46.51 5.54
1936 4014 0.036294 AGGCGCTCTTCCTGTTTACC 60.036 55.000 7.64 0.00 31.53 2.85
1956 4035 1.628340 CGGTCAGGCCAATATATCCCA 59.372 52.381 5.01 0.00 36.97 4.37
1969 4048 7.689313 GCCAATATATCCCACTCTCTGTTGTTA 60.689 40.741 0.00 0.00 0.00 2.41
1978 4057 7.453752 TCCCACTCTCTGTTGTTATTAAGTACT 59.546 37.037 0.00 0.00 0.00 2.73
1979 4058 7.760340 CCCACTCTCTGTTGTTATTAAGTACTC 59.240 40.741 0.00 0.00 0.00 2.59
1981 4060 9.692749 CACTCTCTGTTGTTATTAAGTACTCAA 57.307 33.333 0.00 0.00 0.00 3.02
2268 4955 2.435422 TGAACATCATGCGTGGTGATT 58.565 42.857 25.79 15.10 38.83 2.57
2305 4992 4.594920 AGGGTTCACCGATGAGATGAATAT 59.405 41.667 0.00 0.00 46.96 1.28
2367 5054 3.776969 AGTTAATCATGAGCACTCTGGGA 59.223 43.478 0.09 0.00 0.00 4.37
2387 5074 1.210478 AGTAGCTTGGATTGTGCCGAT 59.790 47.619 0.00 0.00 0.00 4.18
2473 5161 4.892126 ATCCATGGATGTGCCCTTTGCA 62.892 50.000 26.78 0.00 39.68 4.08
2490 5186 3.264998 TGCATTTGAGATCGACCATCA 57.735 42.857 0.00 0.00 33.29 3.07
2492 5188 3.118665 TGCATTTGAGATCGACCATCAGA 60.119 43.478 0.00 0.00 33.29 3.27
2497 5193 3.625853 TGAGATCGACCATCAGACTTCT 58.374 45.455 0.00 0.00 33.29 2.85
2500 5196 3.380004 AGATCGACCATCAGACTTCTCAC 59.620 47.826 0.00 0.00 33.29 3.51
2512 5208 5.828328 TCAGACTTCTCACACTGTAGAAAGA 59.172 40.000 0.00 0.00 31.61 2.52
2517 5213 6.703607 ACTTCTCACACTGTAGAAAGAATGTG 59.296 38.462 0.00 0.00 39.00 3.21
2522 5218 5.178252 CACACTGTAGAAAGAATGTGTCTGG 59.822 44.000 0.00 0.00 36.40 3.86
2568 5264 4.768968 AGCTGGGAATATTATCATTGTGGC 59.231 41.667 0.00 0.00 0.00 5.01
2754 5455 1.909700 TTGCCTTGCTACTTTCCTGG 58.090 50.000 0.00 0.00 0.00 4.45
2791 5492 8.778358 AGAACTTTCTGAATATTCTGTGTGTTC 58.222 33.333 25.65 25.65 35.89 3.18
2858 5560 9.328845 TGGAGTACGTTTAGAAAACAGTTTTAT 57.671 29.630 11.38 10.98 31.94 1.40
2891 5684 4.224370 AGAACACAAACGGGTAGATGGTAT 59.776 41.667 0.00 0.00 0.00 2.73
2896 5689 5.926542 CACAAACGGGTAGATGGTATGATAG 59.073 44.000 0.00 0.00 0.00 2.08
2918 5715 2.432444 TGGTTCTTGCAGAATTACGGG 58.568 47.619 2.61 0.00 36.50 5.28
2927 5724 2.548480 GCAGAATTACGGGCAGGTATTC 59.452 50.000 6.08 6.08 0.00 1.75
3013 5827 3.374988 CCTAGTGCATCATTTTTGCGAGA 59.625 43.478 0.00 0.00 43.10 4.04
3084 5898 9.677567 GCTCTGTTTTTGATGATACAGTAAAAA 57.322 29.630 0.00 0.00 39.16 1.94
3106 5920 7.974482 AAAAGATAACCACGTAGTTTTAGCT 57.026 32.000 4.33 0.00 41.61 3.32
3107 5921 7.974482 AAAGATAACCACGTAGTTTTAGCTT 57.026 32.000 4.33 0.00 41.21 3.74
3108 5922 7.974482 AAGATAACCACGTAGTTTTAGCTTT 57.026 32.000 4.33 0.00 41.61 3.51
3109 5923 7.974482 AGATAACCACGTAGTTTTAGCTTTT 57.026 32.000 4.33 0.00 41.61 2.27
3110 5924 7.803724 AGATAACCACGTAGTTTTAGCTTTTG 58.196 34.615 4.33 0.00 41.61 2.44
3111 5925 7.658575 AGATAACCACGTAGTTTTAGCTTTTGA 59.341 33.333 4.33 0.00 41.61 2.69
3112 5926 6.628919 AACCACGTAGTTTTAGCTTTTGAT 57.371 33.333 0.00 0.00 41.61 2.57
3113 5927 5.997385 ACCACGTAGTTTTAGCTTTTGATG 58.003 37.500 0.00 0.00 41.61 3.07
3114 5928 5.761234 ACCACGTAGTTTTAGCTTTTGATGA 59.239 36.000 0.00 0.00 41.61 2.92
3115 5929 6.073222 ACCACGTAGTTTTAGCTTTTGATGAG 60.073 38.462 0.00 0.00 41.61 2.90
3116 5930 6.147164 CCACGTAGTTTTAGCTTTTGATGAGA 59.853 38.462 0.00 0.00 41.61 3.27
3117 5931 7.010023 CACGTAGTTTTAGCTTTTGATGAGAC 58.990 38.462 0.00 0.00 41.61 3.36
3118 5932 6.929606 ACGTAGTTTTAGCTTTTGATGAGACT 59.070 34.615 0.00 0.00 37.78 3.24
3119 5933 8.086522 ACGTAGTTTTAGCTTTTGATGAGACTA 58.913 33.333 0.00 0.00 37.78 2.59
3120 5934 8.373992 CGTAGTTTTAGCTTTTGATGAGACTAC 58.626 37.037 0.00 0.00 34.96 2.73
3121 5935 9.204570 GTAGTTTTAGCTTTTGATGAGACTACA 57.795 33.333 0.00 0.00 37.04 2.74
3122 5936 8.316640 AGTTTTAGCTTTTGATGAGACTACAG 57.683 34.615 0.00 0.00 0.00 2.74
3123 5937 7.934120 AGTTTTAGCTTTTGATGAGACTACAGT 59.066 33.333 0.00 0.00 0.00 3.55
3124 5938 9.204570 GTTTTAGCTTTTGATGAGACTACAGTA 57.795 33.333 0.00 0.00 0.00 2.74
3125 5939 9.772973 TTTTAGCTTTTGATGAGACTACAGTAA 57.227 29.630 0.00 0.00 0.00 2.24
3126 5940 9.772973 TTTAGCTTTTGATGAGACTACAGTAAA 57.227 29.630 0.00 0.00 0.00 2.01
3127 5941 9.772973 TTAGCTTTTGATGAGACTACAGTAAAA 57.227 29.630 0.00 0.00 0.00 1.52
3128 5942 8.677148 AGCTTTTGATGAGACTACAGTAAAAA 57.323 30.769 0.00 0.00 0.00 1.94
3150 5964 7.974482 AAAAGATAACCACGTAGTTTTAGCT 57.026 32.000 4.33 0.00 41.61 3.32
3151 5965 7.974482 AAAGATAACCACGTAGTTTTAGCTT 57.026 32.000 4.33 0.00 41.21 3.74
3152 5966 7.974482 AAGATAACCACGTAGTTTTAGCTTT 57.026 32.000 4.33 0.00 41.61 3.51
3153 5967 7.974482 AGATAACCACGTAGTTTTAGCTTTT 57.026 32.000 4.33 0.00 41.61 2.27
3154 5968 7.803724 AGATAACCACGTAGTTTTAGCTTTTG 58.196 34.615 4.33 0.00 41.61 2.44
3155 5969 7.658575 AGATAACCACGTAGTTTTAGCTTTTGA 59.341 33.333 4.33 0.00 41.61 2.69
3156 5970 6.628919 AACCACGTAGTTTTAGCTTTTGAT 57.371 33.333 0.00 0.00 41.61 2.57
3157 5971 5.997385 ACCACGTAGTTTTAGCTTTTGATG 58.003 37.500 0.00 0.00 41.61 3.07
3158 5972 5.761234 ACCACGTAGTTTTAGCTTTTGATGA 59.239 36.000 0.00 0.00 41.61 2.92
3159 5973 6.073222 ACCACGTAGTTTTAGCTTTTGATGAG 60.073 38.462 0.00 0.00 41.61 2.90
3160 5974 6.147164 CCACGTAGTTTTAGCTTTTGATGAGA 59.853 38.462 0.00 0.00 41.61 3.27
3161 5975 7.010023 CACGTAGTTTTAGCTTTTGATGAGAC 58.990 38.462 0.00 0.00 41.61 3.36
3162 5976 6.929606 ACGTAGTTTTAGCTTTTGATGAGACT 59.070 34.615 0.00 0.00 37.78 3.24
3163 5977 8.086522 ACGTAGTTTTAGCTTTTGATGAGACTA 58.913 33.333 0.00 0.00 37.78 2.59
3164 5978 8.373992 CGTAGTTTTAGCTTTTGATGAGACTAC 58.626 37.037 0.00 0.00 34.96 2.73
3165 5979 9.204570 GTAGTTTTAGCTTTTGATGAGACTACA 57.795 33.333 0.00 0.00 37.04 2.74
3166 5980 8.316640 AGTTTTAGCTTTTGATGAGACTACAG 57.683 34.615 0.00 0.00 0.00 2.74
3167 5981 7.934120 AGTTTTAGCTTTTGATGAGACTACAGT 59.066 33.333 0.00 0.00 0.00 3.55
3168 5982 9.204570 GTTTTAGCTTTTGATGAGACTACAGTA 57.795 33.333 0.00 0.00 0.00 2.74
3169 5983 9.772973 TTTTAGCTTTTGATGAGACTACAGTAA 57.227 29.630 0.00 0.00 0.00 2.24
3172 5986 8.677148 AGCTTTTGATGAGACTACAGTAAAAA 57.323 30.769 0.00 0.00 0.00 1.94
3204 6018 4.926238 ACGTAGTCTTGAGCTTTTGATGAG 59.074 41.667 0.00 0.00 29.74 2.90
3205 6019 5.164233 CGTAGTCTTGAGCTTTTGATGAGA 58.836 41.667 0.00 0.00 0.00 3.27
3206 6020 5.061560 CGTAGTCTTGAGCTTTTGATGAGAC 59.938 44.000 0.00 0.00 31.67 3.36
3258 6076 7.543947 TTGATTATTGCTATCTGATATGGCG 57.456 36.000 0.00 0.00 0.00 5.69
3350 6172 9.595823 GAATCAAATCTCATGACATGGAAAAAT 57.404 29.630 15.37 0.38 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.370840 AATCTATGCAAGGGTTCAGCA 57.629 42.857 0.00 0.00 43.14 4.41
13 14 6.127647 TGCTTTAAATCTATGCAAGGGTTCAG 60.128 38.462 0.00 0.00 0.00 3.02
18 19 4.646492 AGGTGCTTTAAATCTATGCAAGGG 59.354 41.667 0.00 0.00 35.34 3.95
24 25 7.558161 TGATGTCAGGTGCTTTAAATCTATG 57.442 36.000 0.00 0.00 0.00 2.23
29 30 8.776470 CAAAATTTGATGTCAGGTGCTTTAAAT 58.224 29.630 0.00 0.00 0.00 1.40
40 41 5.119588 GTCATGTGGCAAAATTTGATGTCAG 59.880 40.000 10.26 0.00 30.67 3.51
52 53 2.548057 GACTTTCTCGTCATGTGGCAAA 59.452 45.455 0.00 0.00 34.11 3.68
135 139 2.163815 TCGATCCTTCTCGAGTTTGTCC 59.836 50.000 13.13 0.00 42.38 4.02
136 140 3.489180 TCGATCCTTCTCGAGTTTGTC 57.511 47.619 13.13 5.11 42.38 3.18
158 162 1.656095 CATCGAGTTTGTCTTCCGAGC 59.344 52.381 0.00 0.00 32.60 5.03
161 165 4.725556 TTTTCATCGAGTTTGTCTTCCG 57.274 40.909 0.00 0.00 0.00 4.30
177 181 0.897863 CGGATGGTGGGGCTTTTTCA 60.898 55.000 0.00 0.00 0.00 2.69
179 183 2.282783 GCGGATGGTGGGGCTTTTT 61.283 57.895 0.00 0.00 0.00 1.94
180 184 2.679996 GCGGATGGTGGGGCTTTT 60.680 61.111 0.00 0.00 0.00 2.27
181 185 4.759205 GGCGGATGGTGGGGCTTT 62.759 66.667 0.00 0.00 0.00 3.51
210 214 8.832735 AGGTTAGGATTATTTTAGTCCTCACAA 58.167 33.333 10.64 0.00 43.06 3.33
225 229 6.491403 CCGGCTAGTAGTTTAGGTTAGGATTA 59.509 42.308 0.00 0.00 0.00 1.75
228 232 4.079787 TCCGGCTAGTAGTTTAGGTTAGGA 60.080 45.833 0.00 0.00 0.00 2.94
231 235 3.633986 GCTCCGGCTAGTAGTTTAGGTTA 59.366 47.826 0.00 0.00 35.22 2.85
234 238 2.029623 TGCTCCGGCTAGTAGTTTAGG 58.970 52.381 0.00 0.00 39.59 2.69
252 256 0.817654 GGTAATCCTGGTGCCTTTGC 59.182 55.000 0.00 0.00 38.26 3.68
253 257 2.514458 AGGTAATCCTGGTGCCTTTG 57.486 50.000 0.00 0.00 43.33 2.77
255 259 1.285078 GGAAGGTAATCCTGGTGCCTT 59.715 52.381 6.42 6.42 44.35 4.35
286 290 2.599281 TCCTTGCCACTCCGACGA 60.599 61.111 0.00 0.00 0.00 4.20
290 294 4.101448 CCCCTCCTTGCCACTCCG 62.101 72.222 0.00 0.00 0.00 4.63
295 299 3.003173 CGTCTCCCCTCCTTGCCA 61.003 66.667 0.00 0.00 0.00 4.92
372 380 9.897744 TCACATCATTGAATACAACTTTTCTTC 57.102 29.630 0.00 0.00 38.90 2.87
430 438 8.873186 TTCCGTCTTCCTAATAATTCCTTTTT 57.127 30.769 0.00 0.00 0.00 1.94
431 439 7.556635 CCTTCCGTCTTCCTAATAATTCCTTTT 59.443 37.037 0.00 0.00 0.00 2.27
432 440 7.054751 CCTTCCGTCTTCCTAATAATTCCTTT 58.945 38.462 0.00 0.00 0.00 3.11
433 441 6.386050 TCCTTCCGTCTTCCTAATAATTCCTT 59.614 38.462 0.00 0.00 0.00 3.36
434 442 5.903589 TCCTTCCGTCTTCCTAATAATTCCT 59.096 40.000 0.00 0.00 0.00 3.36
435 443 5.990386 GTCCTTCCGTCTTCCTAATAATTCC 59.010 44.000 0.00 0.00 0.00 3.01
436 444 5.690857 CGTCCTTCCGTCTTCCTAATAATTC 59.309 44.000 0.00 0.00 0.00 2.17
437 445 5.361857 TCGTCCTTCCGTCTTCCTAATAATT 59.638 40.000 0.00 0.00 0.00 1.40
438 446 4.891756 TCGTCCTTCCGTCTTCCTAATAAT 59.108 41.667 0.00 0.00 0.00 1.28
439 447 4.272489 TCGTCCTTCCGTCTTCCTAATAA 58.728 43.478 0.00 0.00 0.00 1.40
440 448 3.881688 CTCGTCCTTCCGTCTTCCTAATA 59.118 47.826 0.00 0.00 0.00 0.98
441 449 2.688958 CTCGTCCTTCCGTCTTCCTAAT 59.311 50.000 0.00 0.00 0.00 1.73
442 450 2.089980 CTCGTCCTTCCGTCTTCCTAA 58.910 52.381 0.00 0.00 0.00 2.69
443 451 1.747709 CTCGTCCTTCCGTCTTCCTA 58.252 55.000 0.00 0.00 0.00 2.94
444 452 1.596895 GCTCGTCCTTCCGTCTTCCT 61.597 60.000 0.00 0.00 0.00 3.36
445 453 1.153804 GCTCGTCCTTCCGTCTTCC 60.154 63.158 0.00 0.00 0.00 3.46
446 454 1.514443 CGCTCGTCCTTCCGTCTTC 60.514 63.158 0.00 0.00 0.00 2.87
447 455 1.313812 ATCGCTCGTCCTTCCGTCTT 61.314 55.000 0.00 0.00 0.00 3.01
448 456 1.313812 AATCGCTCGTCCTTCCGTCT 61.314 55.000 0.00 0.00 0.00 4.18
449 457 0.458025 AAATCGCTCGTCCTTCCGTC 60.458 55.000 0.00 0.00 0.00 4.79
450 458 0.813184 TAAATCGCTCGTCCTTCCGT 59.187 50.000 0.00 0.00 0.00 4.69
451 459 2.135664 ATAAATCGCTCGTCCTTCCG 57.864 50.000 0.00 0.00 0.00 4.30
452 460 4.208666 GTGTAATAAATCGCTCGTCCTTCC 59.791 45.833 0.00 0.00 0.00 3.46
453 461 4.208666 GGTGTAATAAATCGCTCGTCCTTC 59.791 45.833 0.00 0.00 0.00 3.46
454 462 4.117685 GGTGTAATAAATCGCTCGTCCTT 58.882 43.478 0.00 0.00 0.00 3.36
455 463 3.492137 GGGTGTAATAAATCGCTCGTCCT 60.492 47.826 0.00 0.00 0.00 3.85
456 464 2.798847 GGGTGTAATAAATCGCTCGTCC 59.201 50.000 0.00 0.00 0.00 4.79
457 465 3.489785 CAGGGTGTAATAAATCGCTCGTC 59.510 47.826 0.00 0.00 0.00 4.20
458 466 3.454375 CAGGGTGTAATAAATCGCTCGT 58.546 45.455 0.00 0.00 0.00 4.18
459 467 2.800544 CCAGGGTGTAATAAATCGCTCG 59.199 50.000 0.00 0.00 0.00 5.03
460 468 4.067972 TCCAGGGTGTAATAAATCGCTC 57.932 45.455 0.00 0.00 0.00 5.03
461 469 4.497291 TTCCAGGGTGTAATAAATCGCT 57.503 40.909 0.00 0.00 0.00 4.93
462 470 5.180680 GGTATTCCAGGGTGTAATAAATCGC 59.819 44.000 0.00 0.00 0.00 4.58
463 471 6.531021 AGGTATTCCAGGGTGTAATAAATCG 58.469 40.000 0.00 0.00 35.89 3.34
464 472 7.746703 AGAGGTATTCCAGGGTGTAATAAATC 58.253 38.462 0.00 0.00 35.89 2.17
465 473 7.707467 AGAGGTATTCCAGGGTGTAATAAAT 57.293 36.000 0.00 0.00 35.89 1.40
466 474 7.183112 TCAAGAGGTATTCCAGGGTGTAATAAA 59.817 37.037 0.00 0.00 35.89 1.40
467 475 6.674861 TCAAGAGGTATTCCAGGGTGTAATAA 59.325 38.462 0.00 0.00 35.89 1.40
468 476 6.206787 TCAAGAGGTATTCCAGGGTGTAATA 58.793 40.000 0.00 0.00 35.89 0.98
469 477 5.036916 TCAAGAGGTATTCCAGGGTGTAAT 58.963 41.667 0.00 0.00 35.89 1.89
470 478 4.431378 TCAAGAGGTATTCCAGGGTGTAA 58.569 43.478 0.00 0.00 35.89 2.41
471 479 4.069312 TCAAGAGGTATTCCAGGGTGTA 57.931 45.455 0.00 0.00 35.89 2.90
472 480 2.915869 TCAAGAGGTATTCCAGGGTGT 58.084 47.619 0.00 0.00 35.89 4.16
473 481 4.301072 TTTCAAGAGGTATTCCAGGGTG 57.699 45.455 0.00 0.00 35.89 4.61
474 482 4.325344 CCATTTCAAGAGGTATTCCAGGGT 60.325 45.833 0.00 0.00 35.89 4.34
475 483 4.210331 CCATTTCAAGAGGTATTCCAGGG 58.790 47.826 0.00 0.00 35.89 4.45
476 484 3.633986 GCCATTTCAAGAGGTATTCCAGG 59.366 47.826 0.00 0.00 35.89 4.45
477 485 3.313526 CGCCATTTCAAGAGGTATTCCAG 59.686 47.826 0.00 0.00 35.89 3.86
478 486 3.054728 TCGCCATTTCAAGAGGTATTCCA 60.055 43.478 0.00 0.00 35.89 3.53
479 487 3.312697 GTCGCCATTTCAAGAGGTATTCC 59.687 47.826 0.00 0.00 0.00 3.01
480 488 3.001330 CGTCGCCATTTCAAGAGGTATTC 59.999 47.826 0.00 0.00 0.00 1.75
481 489 2.936498 CGTCGCCATTTCAAGAGGTATT 59.064 45.455 0.00 0.00 0.00 1.89
482 490 2.550978 CGTCGCCATTTCAAGAGGTAT 58.449 47.619 0.00 0.00 0.00 2.73
483 491 1.404986 CCGTCGCCATTTCAAGAGGTA 60.405 52.381 0.00 0.00 0.00 3.08
484 492 0.673644 CCGTCGCCATTTCAAGAGGT 60.674 55.000 0.00 0.00 0.00 3.85
485 493 1.982073 GCCGTCGCCATTTCAAGAGG 61.982 60.000 0.00 0.00 0.00 3.69
486 494 1.425428 GCCGTCGCCATTTCAAGAG 59.575 57.895 0.00 0.00 0.00 2.85
487 495 2.387445 CGCCGTCGCCATTTCAAGA 61.387 57.895 0.00 0.00 0.00 3.02
488 496 2.098298 CGCCGTCGCCATTTCAAG 59.902 61.111 0.00 0.00 0.00 3.02
512 520 0.739813 AAGTCAACGCAGCGGGATAC 60.740 55.000 21.15 11.41 0.00 2.24
513 521 0.739462 CAAGTCAACGCAGCGGGATA 60.739 55.000 21.15 0.00 0.00 2.59
514 522 2.034879 CAAGTCAACGCAGCGGGAT 61.035 57.895 21.15 1.44 0.00 3.85
515 523 2.664851 CAAGTCAACGCAGCGGGA 60.665 61.111 21.15 13.60 0.00 5.14
516 524 2.664851 TCAAGTCAACGCAGCGGG 60.665 61.111 21.15 11.21 0.00 6.13
517 525 2.551270 GTCAAGTCAACGCAGCGG 59.449 61.111 21.15 1.60 0.00 5.52
518 526 2.551270 GGTCAAGTCAACGCAGCG 59.449 61.111 14.82 14.82 0.00 5.18
519 527 2.551270 CGGTCAAGTCAACGCAGC 59.449 61.111 0.00 0.00 0.00 5.25
523 531 2.551270 GCAGCGGTCAAGTCAACG 59.449 61.111 0.00 0.00 0.00 4.10
524 532 2.946762 GGCAGCGGTCAAGTCAAC 59.053 61.111 0.00 0.00 0.00 3.18
525 533 2.664851 CGGCAGCGGTCAAGTCAA 60.665 61.111 0.00 0.00 0.00 3.18
526 534 4.680237 CCGGCAGCGGTCAAGTCA 62.680 66.667 0.00 0.00 0.00 3.41
537 545 4.680237 TGGTCAACTCGCCGGCAG 62.680 66.667 28.98 23.74 0.00 4.85
538 546 4.680237 CTGGTCAACTCGCCGGCA 62.680 66.667 28.98 12.94 0.00 5.69
539 547 3.665675 ATCTGGTCAACTCGCCGGC 62.666 63.158 19.07 19.07 0.00 6.13
540 548 1.811266 CATCTGGTCAACTCGCCGG 60.811 63.158 0.00 0.00 0.00 6.13
541 549 1.811266 CCATCTGGTCAACTCGCCG 60.811 63.158 0.00 0.00 0.00 6.46
542 550 2.109126 GCCATCTGGTCAACTCGCC 61.109 63.158 0.00 0.00 37.57 5.54
543 551 2.109126 GGCCATCTGGTCAACTCGC 61.109 63.158 0.00 0.00 40.23 5.03
544 552 4.208632 GGCCATCTGGTCAACTCG 57.791 61.111 0.00 0.00 40.23 4.18
550 558 1.977293 GAGGAGGTGGCCATCTGGTC 61.977 65.000 27.08 15.95 41.09 4.02
551 559 1.997874 GAGGAGGTGGCCATCTGGT 60.998 63.158 27.08 10.31 37.57 4.00
552 560 2.750657 GGAGGAGGTGGCCATCTGG 61.751 68.421 27.08 0.00 38.53 3.86
553 561 2.750657 GGGAGGAGGTGGCCATCTG 61.751 68.421 27.08 0.00 0.00 2.90
554 562 2.367512 GGGAGGAGGTGGCCATCT 60.368 66.667 21.46 21.46 0.00 2.90
555 563 3.493303 GGGGAGGAGGTGGCCATC 61.493 72.222 9.72 9.02 0.00 3.51
569 577 4.564110 GATCGAAAGGGGCGGGGG 62.564 72.222 0.00 0.00 0.00 5.40
570 578 4.564110 GGATCGAAAGGGGCGGGG 62.564 72.222 0.00 0.00 0.00 5.73
571 579 3.480133 AGGATCGAAAGGGGCGGG 61.480 66.667 0.00 0.00 0.00 6.13
572 580 2.203070 CAGGATCGAAAGGGGCGG 60.203 66.667 0.00 0.00 0.00 6.13
573 581 2.897350 GCAGGATCGAAAGGGGCG 60.897 66.667 0.00 0.00 0.00 6.13
574 582 1.524849 GAGCAGGATCGAAAGGGGC 60.525 63.158 0.00 0.00 0.00 5.80
575 583 1.147153 GGAGCAGGATCGAAAGGGG 59.853 63.158 0.00 0.00 0.00 4.79
576 584 1.147153 GGGAGCAGGATCGAAAGGG 59.853 63.158 0.00 0.00 0.00 3.95
577 585 1.147153 GGGGAGCAGGATCGAAAGG 59.853 63.158 0.00 0.00 0.00 3.11
578 586 1.147153 GGGGGAGCAGGATCGAAAG 59.853 63.158 0.00 0.00 0.00 2.62
579 587 1.306997 AGGGGGAGCAGGATCGAAA 60.307 57.895 0.00 0.00 0.00 3.46
580 588 1.762460 GAGGGGGAGCAGGATCGAA 60.762 63.158 0.00 0.00 0.00 3.71
581 589 2.123251 GAGGGGGAGCAGGATCGA 60.123 66.667 0.00 0.00 0.00 3.59
582 590 2.123077 AGAGGGGGAGCAGGATCG 60.123 66.667 0.00 0.00 0.00 3.69
583 591 0.831711 GAGAGAGGGGGAGCAGGATC 60.832 65.000 0.00 0.00 0.00 3.36
584 592 1.235696 GAGAGAGGGGGAGCAGGAT 59.764 63.158 0.00 0.00 0.00 3.24
585 593 2.693017 GAGAGAGGGGGAGCAGGA 59.307 66.667 0.00 0.00 0.00 3.86
586 594 2.445654 GGAGAGAGGGGGAGCAGG 60.446 72.222 0.00 0.00 0.00 4.85
587 595 2.063378 GTGGAGAGAGGGGGAGCAG 61.063 68.421 0.00 0.00 0.00 4.24
588 596 2.039624 GTGGAGAGAGGGGGAGCA 59.960 66.667 0.00 0.00 0.00 4.26
589 597 2.766229 GGTGGAGAGAGGGGGAGC 60.766 72.222 0.00 0.00 0.00 4.70
590 598 1.075600 GAGGTGGAGAGAGGGGGAG 60.076 68.421 0.00 0.00 0.00 4.30
591 599 2.637640 GGAGGTGGAGAGAGGGGGA 61.638 68.421 0.00 0.00 0.00 4.81
592 600 2.041405 GGAGGTGGAGAGAGGGGG 60.041 72.222 0.00 0.00 0.00 5.40
593 601 2.041405 GGGAGGTGGAGAGAGGGG 60.041 72.222 0.00 0.00 0.00 4.79
594 602 0.980231 CAAGGGAGGTGGAGAGAGGG 60.980 65.000 0.00 0.00 0.00 4.30
595 603 1.621672 GCAAGGGAGGTGGAGAGAGG 61.622 65.000 0.00 0.00 0.00 3.69
596 604 1.621672 GGCAAGGGAGGTGGAGAGAG 61.622 65.000 0.00 0.00 0.00 3.20
597 605 1.613630 GGCAAGGGAGGTGGAGAGA 60.614 63.158 0.00 0.00 0.00 3.10
598 606 2.993853 GGCAAGGGAGGTGGAGAG 59.006 66.667 0.00 0.00 0.00 3.20
599 607 3.003173 CGGCAAGGGAGGTGGAGA 61.003 66.667 0.00 0.00 0.00 3.71
600 608 4.785453 GCGGCAAGGGAGGTGGAG 62.785 72.222 0.00 0.00 0.00 3.86
630 638 0.611714 AAATAGGCGACGGGTCAACT 59.388 50.000 0.00 0.00 0.00 3.16
694 702 3.550431 GCCAGCGCCCTCCTCATA 61.550 66.667 2.29 0.00 0.00 2.15
832 840 1.810030 GAAGTCGGTGATGGTCCGC 60.810 63.158 0.00 0.00 46.49 5.54
863 871 0.973496 GGGGAAGAGCTCCTCGAAGT 60.973 60.000 10.93 0.00 44.68 3.01
864 872 1.819905 GGGGAAGAGCTCCTCGAAG 59.180 63.158 10.93 0.00 44.68 3.79
865 873 4.035843 GGGGAAGAGCTCCTCGAA 57.964 61.111 10.93 0.00 44.68 3.71
927 936 3.699134 GATGAAGGCCGGGTGGTCC 62.699 68.421 2.18 0.00 42.57 4.46
928 937 2.124695 GATGAAGGCCGGGTGGTC 60.125 66.667 2.18 0.00 41.57 4.02
929 938 4.096003 CGATGAAGGCCGGGTGGT 62.096 66.667 2.18 0.00 37.67 4.16
1067 1076 2.203788 AACCAGAGTCGGGGCAGA 60.204 61.111 14.22 0.00 0.00 4.26
1071 1080 4.452733 GGCGAACCAGAGTCGGGG 62.453 72.222 14.22 8.23 35.26 5.73
1131 1140 0.861837 CAATTAGACTGATCCCGCGC 59.138 55.000 0.00 0.00 0.00 6.86
1132 1141 0.861837 GCAATTAGACTGATCCCGCG 59.138 55.000 0.00 0.00 0.00 6.46
1174 1183 3.838317 TCTCTATACTGTTTGCCTGTGGT 59.162 43.478 0.00 0.00 0.00 4.16
1203 1218 2.089980 CTGCATATCCTATTGGCAGCC 58.910 52.381 3.66 3.66 44.45 4.85
1209 1224 7.496920 TGTCAACTTTCTCTGCATATCCTATTG 59.503 37.037 0.00 0.00 0.00 1.90
1237 1252 7.656707 AAAATTTGTGATGGTTTGTCTATGC 57.343 32.000 0.00 0.00 0.00 3.14
1246 1261 4.937015 GGCATGCTAAAATTTGTGATGGTT 59.063 37.500 18.92 0.00 0.00 3.67
1261 1277 2.530460 AAATCCTGTTGGGCATGCTA 57.470 45.000 18.92 4.21 34.39 3.49
1324 1340 3.126001 TGTGTCACTCATCAACTTCCC 57.874 47.619 4.27 0.00 0.00 3.97
1378 1394 2.833604 ATTCCACCTCTGCAGGCTGC 62.834 60.000 31.91 31.91 45.05 5.25
1379 1395 0.323178 AATTCCACCTCTGCAGGCTG 60.323 55.000 15.13 10.94 45.05 4.85
1380 1396 0.323178 CAATTCCACCTCTGCAGGCT 60.323 55.000 15.13 0.00 45.05 4.58
1381 1397 0.610232 ACAATTCCACCTCTGCAGGC 60.610 55.000 15.13 0.00 45.05 4.85
1382 1398 2.359900 GTACAATTCCACCTCTGCAGG 58.640 52.381 15.13 1.31 46.87 4.85
1421 1437 5.557136 CGCCTCTATCTTTTAACAGCATTCG 60.557 44.000 0.00 0.00 0.00 3.34
1427 1443 6.043411 AGCTTACGCCTCTATCTTTTAACAG 58.957 40.000 0.00 0.00 36.60 3.16
1532 1548 5.887598 TCTGATGAAATGTTATTCCAGTGGG 59.112 40.000 9.92 0.00 0.00 4.61
1576 1592 5.008613 TGAAGAACTGCACATGTTAAGTTCC 59.991 40.000 29.74 21.71 46.26 3.62
1608 1624 4.541973 AATTTGCAGAAATCCTTCCCAC 57.458 40.909 0.00 0.00 30.02 4.61
1656 1689 9.859427 ACAATCACAATACCTTAAACAATGATG 57.141 29.630 0.00 0.00 0.00 3.07
1776 3846 1.687563 AAAAACGTCCACCTGAAGGG 58.312 50.000 0.56 0.00 40.27 3.95
1807 3877 0.323360 TAGCAAAGACCCCATGCCAC 60.323 55.000 0.00 0.00 40.93 5.01
1879 3949 2.156917 TCCTTCGACACGGCGATATAT 58.843 47.619 16.62 0.00 40.35 0.86
1936 4014 1.628340 TGGGATATATTGGCCTGACCG 59.372 52.381 3.32 0.00 43.94 4.79
1978 4057 6.303903 TCCAGAATCATCTCTGTTGATTGA 57.696 37.500 3.80 0.00 42.38 2.57
1979 4058 6.598457 AGTTCCAGAATCATCTCTGTTGATTG 59.402 38.462 3.80 0.00 42.38 2.67
1981 4060 6.114089 CAGTTCCAGAATCATCTCTGTTGAT 58.886 40.000 0.35 0.00 41.15 2.57
1986 4065 4.139859 AGCAGTTCCAGAATCATCTCTG 57.860 45.455 0.00 0.00 42.19 3.35
2070 4168 1.673665 GCAACTCTGGGTGGCTCAG 60.674 63.158 0.00 0.00 41.49 3.35
2268 4955 4.147449 CCCTCGACCGCAGATGCA 62.147 66.667 5.55 0.00 42.21 3.96
2325 5012 3.392616 ACTCCCATCAAGCCGAGATAATT 59.607 43.478 0.00 0.00 0.00 1.40
2367 5054 0.613260 TCGGCACAATCCAAGCTACT 59.387 50.000 0.00 0.00 0.00 2.57
2387 5074 2.169769 GGACGGATTGAATACCACCTGA 59.830 50.000 0.00 0.00 0.00 3.86
2473 5161 5.128499 AGAAGTCTGATGGTCGATCTCAAAT 59.872 40.000 0.00 0.00 31.55 2.32
2490 5186 6.716934 TTCTTTCTACAGTGTGAGAAGTCT 57.283 37.500 5.88 0.00 33.38 3.24
2492 5188 6.703607 CACATTCTTTCTACAGTGTGAGAAGT 59.296 38.462 5.88 7.55 39.30 3.01
2497 5193 5.985530 CAGACACATTCTTTCTACAGTGTGA 59.014 40.000 5.88 0.00 39.98 3.58
2500 5196 5.541845 TCCAGACACATTCTTTCTACAGTG 58.458 41.667 0.00 0.00 28.96 3.66
2512 5208 6.798427 ATACTGTACAGATCCAGACACATT 57.202 37.500 29.30 4.50 32.93 2.71
2517 5213 9.522804 CTTAAAGAATACTGTACAGATCCAGAC 57.477 37.037 29.30 12.47 32.93 3.51
2522 5218 7.708752 AGCTGCTTAAAGAATACTGTACAGATC 59.291 37.037 29.30 21.10 0.00 2.75
2568 5264 1.492176 ACCAAGAGATAGGTGGCATGG 59.508 52.381 0.00 0.00 36.60 3.66
2575 5271 8.095452 AGAAAATCACATACCAAGAGATAGGT 57.905 34.615 0.00 0.00 41.89 3.08
2754 5455 2.097142 CAGAAAGTTCTGCAGCCATAGC 59.903 50.000 9.47 0.00 46.97 2.97
2791 5492 4.454847 ACACAGCATTGACAGAATTCAGAG 59.545 41.667 8.44 0.00 0.00 3.35
2858 5560 3.737266 CCGTTTGTGTTCTTAGCGTTCTA 59.263 43.478 0.00 0.00 0.00 2.10
2859 5561 2.542595 CCGTTTGTGTTCTTAGCGTTCT 59.457 45.455 0.00 0.00 0.00 3.01
2863 5565 1.223187 ACCCGTTTGTGTTCTTAGCG 58.777 50.000 0.00 0.00 0.00 4.26
2871 5573 3.516300 TCATACCATCTACCCGTTTGTGT 59.484 43.478 0.00 0.00 0.00 3.72
2927 5724 3.663176 CGGTGCACAAGGCTGGTG 61.663 66.667 17.98 17.98 45.15 4.17
2934 5731 1.648720 CCAACTGACGGTGCACAAG 59.351 57.895 20.43 14.42 0.00 3.16
2935 5732 1.821759 CCCAACTGACGGTGCACAA 60.822 57.895 20.43 0.00 0.00 3.33
2991 5805 3.374988 TCTCGCAAAAATGATGCACTAGG 59.625 43.478 0.00 0.00 44.01 3.02
3013 5827 4.165565 TCAGATTCAGCTGGAAGGAATCAT 59.834 41.667 20.84 8.56 45.82 2.45
3084 5898 7.974482 AAAGCTAAAACTACGTGGTTATCTT 57.026 32.000 18.16 14.21 0.00 2.40
3086 5900 7.799784 TCAAAAGCTAAAACTACGTGGTTATC 58.200 34.615 18.16 7.43 0.00 1.75
3088 5902 7.441760 TCATCAAAAGCTAAAACTACGTGGTTA 59.558 33.333 18.16 2.30 0.00 2.85
3090 5904 5.761234 TCATCAAAAGCTAAAACTACGTGGT 59.239 36.000 0.00 0.00 0.00 4.16
3091 5905 6.147164 TCTCATCAAAAGCTAAAACTACGTGG 59.853 38.462 0.00 0.00 0.00 4.94
3092 5906 7.010023 GTCTCATCAAAAGCTAAAACTACGTG 58.990 38.462 0.00 0.00 0.00 4.49
3093 5907 6.929606 AGTCTCATCAAAAGCTAAAACTACGT 59.070 34.615 0.00 0.00 0.00 3.57
3094 5908 7.352719 AGTCTCATCAAAAGCTAAAACTACG 57.647 36.000 0.00 0.00 0.00 3.51
3095 5909 9.204570 TGTAGTCTCATCAAAAGCTAAAACTAC 57.795 33.333 0.00 0.00 37.14 2.73
3096 5910 9.424319 CTGTAGTCTCATCAAAAGCTAAAACTA 57.576 33.333 0.00 0.00 0.00 2.24
3097 5911 7.934120 ACTGTAGTCTCATCAAAAGCTAAAACT 59.066 33.333 0.00 0.00 0.00 2.66
3098 5912 8.089115 ACTGTAGTCTCATCAAAAGCTAAAAC 57.911 34.615 0.00 0.00 0.00 2.43
3099 5913 9.772973 TTACTGTAGTCTCATCAAAAGCTAAAA 57.227 29.630 0.00 0.00 0.00 1.52
3100 5914 9.772973 TTTACTGTAGTCTCATCAAAAGCTAAA 57.227 29.630 0.00 0.00 0.00 1.85
3101 5915 9.772973 TTTTACTGTAGTCTCATCAAAAGCTAA 57.227 29.630 0.00 0.00 0.00 3.09
3102 5916 9.772973 TTTTTACTGTAGTCTCATCAAAAGCTA 57.227 29.630 0.00 0.00 0.00 3.32
3103 5917 8.677148 TTTTTACTGTAGTCTCATCAAAAGCT 57.323 30.769 0.00 0.00 0.00 3.74
3125 5939 8.387190 AGCTAAAACTACGTGGTTATCTTTTT 57.613 30.769 18.16 9.71 0.00 1.94
3126 5940 7.974482 AGCTAAAACTACGTGGTTATCTTTT 57.026 32.000 18.16 10.41 0.00 2.27
3127 5941 7.974482 AAGCTAAAACTACGTGGTTATCTTT 57.026 32.000 18.16 10.76 0.00 2.52
3128 5942 7.974482 AAAGCTAAAACTACGTGGTTATCTT 57.026 32.000 18.16 14.21 0.00 2.40
3129 5943 7.658575 TCAAAAGCTAAAACTACGTGGTTATCT 59.341 33.333 18.16 9.44 0.00 1.98
3130 5944 7.799784 TCAAAAGCTAAAACTACGTGGTTATC 58.200 34.615 18.16 7.43 0.00 1.75
3131 5945 7.733402 TCAAAAGCTAAAACTACGTGGTTAT 57.267 32.000 18.16 5.77 0.00 1.89
3132 5946 7.441760 TCATCAAAAGCTAAAACTACGTGGTTA 59.558 33.333 18.16 2.30 0.00 2.85
3133 5947 6.261381 TCATCAAAAGCTAAAACTACGTGGTT 59.739 34.615 11.96 11.96 0.00 3.67
3134 5948 5.761234 TCATCAAAAGCTAAAACTACGTGGT 59.239 36.000 0.00 0.00 0.00 4.16
3135 5949 6.147164 TCTCATCAAAAGCTAAAACTACGTGG 59.853 38.462 0.00 0.00 0.00 4.94
3136 5950 7.010023 GTCTCATCAAAAGCTAAAACTACGTG 58.990 38.462 0.00 0.00 0.00 4.49
3137 5951 6.929606 AGTCTCATCAAAAGCTAAAACTACGT 59.070 34.615 0.00 0.00 0.00 3.57
3138 5952 7.352719 AGTCTCATCAAAAGCTAAAACTACG 57.647 36.000 0.00 0.00 0.00 3.51
3139 5953 9.204570 TGTAGTCTCATCAAAAGCTAAAACTAC 57.795 33.333 0.00 0.00 37.14 2.73
3140 5954 9.424319 CTGTAGTCTCATCAAAAGCTAAAACTA 57.576 33.333 0.00 0.00 0.00 2.24
3141 5955 7.934120 ACTGTAGTCTCATCAAAAGCTAAAACT 59.066 33.333 0.00 0.00 0.00 2.66
3142 5956 8.089115 ACTGTAGTCTCATCAAAAGCTAAAAC 57.911 34.615 0.00 0.00 0.00 2.43
3143 5957 9.772973 TTACTGTAGTCTCATCAAAAGCTAAAA 57.227 29.630 0.00 0.00 0.00 1.52
3144 5958 9.772973 TTTACTGTAGTCTCATCAAAAGCTAAA 57.227 29.630 0.00 0.00 0.00 1.85
3145 5959 9.772973 TTTTACTGTAGTCTCATCAAAAGCTAA 57.227 29.630 0.00 0.00 0.00 3.09
3146 5960 9.772973 TTTTTACTGTAGTCTCATCAAAAGCTA 57.227 29.630 0.00 0.00 0.00 3.32
3147 5961 8.677148 TTTTTACTGTAGTCTCATCAAAAGCT 57.323 30.769 0.00 0.00 0.00 3.74
3169 5983 8.305317 AGCTCAAGACTACGTAGTTATCTTTTT 58.695 33.333 27.96 11.72 37.78 1.94
3172 5986 7.393841 AAGCTCAAGACTACGTAGTTATCTT 57.606 36.000 27.96 22.21 37.78 2.40
3225 6039 7.169813 TCAGATAGCAATAATCAAAGCTACGTG 59.830 37.037 0.00 0.00 41.80 4.49
3226 6040 7.210174 TCAGATAGCAATAATCAAAGCTACGT 58.790 34.615 0.00 0.00 41.80 3.57
3258 6076 4.612712 TACAGCAGTAATGTTTTGCGAAGC 60.613 41.667 0.00 0.00 42.84 3.86
3350 6172 6.263842 GCATCAAGATTGGATCTGTTTCCATA 59.736 38.462 0.00 0.00 45.08 2.74
3371 6193 5.450965 CCTGTAATTGGTGAAGATTGGCATC 60.451 44.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.