Multiple sequence alignment - TraesCS7A01G278900

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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 TraesCS7A01G278900 chr7A 100.000 2609 0 0 1 2609 295211623 295214231 0.000000e+00 4819.0
1 TraesCS7A01G278900 chr7B 95.172 1885 52 18 738 2609 272750112 272748254 0.000000e+00 2940.0
2 TraesCS7A01G278900 chr7D 92.948 1886 77 23 738 2609 268836449 268838292 0.000000e+00 2695.0
3 TraesCS7A01G278900 chr1A 88.123 261 26 4 1090 1349 554933696 554933952 3.260000e-79 305.0
4 TraesCS7A01G278900 chr2B 76.562 576 114 16 21 580 550936845 550937415 1.960000e-76 296.0
5 TraesCS7A01G278900 chr2B 100.000 29 0 0 1439 1467 775588459 775588487 1.000000e-03 54.7
6 TraesCS7A01G278900 chr6D 78.076 447 92 6 21 464 174404493 174404050 7.110000e-71 278.0
7 TraesCS7A01G278900 chr6B 84.942 259 27 8 1090 1348 558930467 558930713 4.310000e-63 252.0
8 TraesCS7A01G278900 chr3D 84.158 101 10 2 1113 1213 594957092 594956998 2.760000e-15 93.5
9 TraesCS7A01G278900 chr2D 96.970 33 0 1 1436 1467 632078166 632078134 1.000000e-03 54.7
10 TraesCS7A01G278900 chr2A 96.970 33 0 1 1436 1467 759693264 759693232 1.000000e-03 54.7


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 TraesCS7A01G278900 chr7A 295211623 295214231 2608 False 4819 4819 100.000 1 2609 1 chr7A.!!$F1 2608
1 TraesCS7A01G278900 chr7B 272748254 272750112 1858 True 2940 2940 95.172 738 2609 1 chr7B.!!$R1 1871
2 TraesCS7A01G278900 chr7D 268836449 268838292 1843 False 2695 2695 92.948 738 2609 1 chr7D.!!$F1 1871
3 TraesCS7A01G278900 chr2B 550936845 550937415 570 False 296 296 76.562 21 580 1 chr2B.!!$F1 559

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
556 568 0.031449 CGATTTTTGCCGGTTGTGGT 59.969 50.0 1.9 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2536 2586 1.129998 CTGAAGAGCAAGCATCCAACG 59.87 52.381 0.0 0.0 0.0 4.1 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
51 53 3.712187 AGGTTTTTATGTGGTTTGTGCG 58.288 40.909 0.00 0.00 0.00 5.34
55 57 2.871182 TTATGTGGTTTGTGCGCAAA 57.129 40.000 21.05 21.05 41.77 3.68
56 58 2.414058 TATGTGGTTTGTGCGCAAAG 57.586 45.000 24.99 0.00 44.27 2.77
59 61 1.199624 GTGGTTTGTGCGCAAAGAAG 58.800 50.000 24.99 0.00 44.27 2.85
67 69 4.560136 TGTGCGCAAAGAAGTGATTTTA 57.440 36.364 14.00 0.00 0.00 1.52
73 75 6.635239 TGCGCAAAGAAGTGATTTTAACTAAC 59.365 34.615 8.16 0.00 0.00 2.34
76 78 8.469125 CGCAAAGAAGTGATTTTAACTAACAAC 58.531 33.333 0.00 0.00 0.00 3.32
91 93 5.729510 ACTAACAACAACTTGGCAAAACAT 58.270 33.333 0.00 0.00 0.00 2.71
93 95 6.978080 ACTAACAACAACTTGGCAAAACATAG 59.022 34.615 0.00 0.00 0.00 2.23
96 98 6.868622 ACAACAACTTGGCAAAACATAGTTA 58.131 32.000 0.00 0.00 0.00 2.24
98 100 6.084326 ACAACTTGGCAAAACATAGTTAGG 57.916 37.500 0.00 0.00 0.00 2.69
103 105 2.688446 GGCAAAACATAGTTAGGAGGGC 59.312 50.000 0.00 0.00 0.00 5.19
105 107 3.128764 GCAAAACATAGTTAGGAGGGCAC 59.871 47.826 0.00 0.00 0.00 5.01
109 111 6.382919 AAACATAGTTAGGAGGGCACTAAA 57.617 37.500 0.00 0.00 32.68 1.85
111 113 4.142004 ACATAGTTAGGAGGGCACTAAACG 60.142 45.833 0.00 0.00 32.68 3.60
114 116 4.284178 AGTTAGGAGGGCACTAAACGATA 58.716 43.478 0.00 0.00 32.68 2.92
118 120 3.139077 GGAGGGCACTAAACGATATTGG 58.861 50.000 0.00 0.00 0.00 3.16
125 127 5.157781 GCACTAAACGATATTGGTTTTGCA 58.842 37.500 16.75 0.00 39.30 4.08
128 130 7.462724 GCACTAAACGATATTGGTTTTGCAATC 60.463 37.037 16.75 0.00 39.30 2.67
135 137 6.974048 CGATATTGGTTTTGCAATCAAGATGA 59.026 34.615 16.82 5.40 35.49 2.92
148 150 6.749118 GCAATCAAGATGAAACTATCCAACAC 59.251 38.462 0.00 0.00 0.00 3.32
149 151 7.362401 GCAATCAAGATGAAACTATCCAACACT 60.362 37.037 0.00 0.00 0.00 3.55
150 152 8.517878 CAATCAAGATGAAACTATCCAACACTT 58.482 33.333 0.00 0.00 0.00 3.16
151 153 7.439157 TCAAGATGAAACTATCCAACACTTG 57.561 36.000 0.00 0.00 34.38 3.16
152 154 6.998074 TCAAGATGAAACTATCCAACACTTGT 59.002 34.615 0.00 0.00 34.60 3.16
157 159 7.259290 TGAAACTATCCAACACTTGTTTCTC 57.741 36.000 14.55 0.00 41.86 2.87
161 163 7.264373 ACTATCCAACACTTGTTTCTCAAAG 57.736 36.000 0.00 0.00 35.83 2.77
169 171 3.117663 ACTTGTTTCTCAAAGGCCCACTA 60.118 43.478 0.00 0.00 35.48 2.74
184 186 3.744530 GCCCACTAGCCAAGTTACTATGG 60.745 52.174 8.52 8.52 35.76 2.74
196 198 6.183360 CCAAGTTACTATGGCCTACACTACAT 60.183 42.308 3.32 0.00 0.00 2.29
212 214 2.995466 ACATGTGGCTTTCAATGTCG 57.005 45.000 0.00 0.00 0.00 4.35
217 219 0.400213 TGGCTTTCAATGTCGGTCCT 59.600 50.000 0.00 0.00 0.00 3.85
220 222 1.339151 GCTTTCAATGTCGGTCCTCCT 60.339 52.381 0.00 0.00 0.00 3.69
229 231 3.305720 TGTCGGTCCTCCTAATAGCATT 58.694 45.455 0.00 0.00 0.00 3.56
231 233 3.321111 GTCGGTCCTCCTAATAGCATTGA 59.679 47.826 0.00 0.00 0.00 2.57
235 237 4.051922 GTCCTCCTAATAGCATTGACACG 58.948 47.826 0.00 0.00 0.00 4.49
244 246 3.848272 AGCATTGACACGTTATTTGGG 57.152 42.857 0.00 0.00 0.00 4.12
246 248 3.190535 AGCATTGACACGTTATTTGGGAC 59.809 43.478 0.00 0.00 0.00 4.46
247 249 3.057876 GCATTGACACGTTATTTGGGACA 60.058 43.478 0.00 0.00 0.00 4.02
263 265 4.588899 TGGGACAATGACTAAATGGAGTG 58.411 43.478 0.00 0.00 31.92 3.51
264 266 4.288366 TGGGACAATGACTAAATGGAGTGA 59.712 41.667 0.00 0.00 31.92 3.41
276 278 9.174166 GACTAAATGGAGTGAAGCCTAAAATAA 57.826 33.333 0.00 0.00 0.00 1.40
280 282 4.020039 TGGAGTGAAGCCTAAAATAACGGA 60.020 41.667 0.00 0.00 0.00 4.69
289 291 6.296026 AGCCTAAAATAACGGAGCATATTCA 58.704 36.000 0.00 0.00 0.00 2.57
291 293 7.041098 AGCCTAAAATAACGGAGCATATTCAAG 60.041 37.037 0.00 0.00 0.00 3.02
293 295 8.621286 CCTAAAATAACGGAGCATATTCAAGTT 58.379 33.333 0.00 0.00 0.00 2.66
322 325 7.209475 GTGTGTGCATTAATTTGGGCTATATT 58.791 34.615 0.00 0.00 0.00 1.28
323 326 7.169645 GTGTGTGCATTAATTTGGGCTATATTG 59.830 37.037 0.00 0.00 0.00 1.90
324 327 7.147759 TGTGTGCATTAATTTGGGCTATATTGT 60.148 33.333 0.00 0.00 0.00 2.71
329 332 8.576442 GCATTAATTTGGGCTATATTGTACTGT 58.424 33.333 0.00 0.00 0.00 3.55
333 336 3.568443 TGGGCTATATTGTACTGTCGGA 58.432 45.455 0.00 0.00 0.00 4.55
388 391 6.830324 ACAAATATTGTGCAGGTCATCTACAT 59.170 34.615 0.00 0.00 43.48 2.29
398 401 4.033709 AGGTCATCTACATAGCAACTGGT 58.966 43.478 0.00 0.00 0.00 4.00
401 404 5.419542 GTCATCTACATAGCAACTGGTTGA 58.580 41.667 16.41 0.00 42.93 3.18
405 408 5.428253 TCTACATAGCAACTGGTTGAATCC 58.572 41.667 16.41 0.09 42.93 3.01
409 412 2.423577 AGCAACTGGTTGAATCCGTAC 58.576 47.619 16.41 0.00 42.93 3.67
412 415 2.074547 ACTGGTTGAATCCGTACGTG 57.925 50.000 15.21 5.96 0.00 4.49
413 416 1.614903 ACTGGTTGAATCCGTACGTGA 59.385 47.619 15.21 11.46 0.00 4.35
416 419 2.231721 TGGTTGAATCCGTACGTGATCA 59.768 45.455 15.21 11.72 0.00 2.92
421 424 2.795175 ATCCGTACGTGATCATCACC 57.205 50.000 15.21 0.00 44.20 4.02
435 439 0.615331 ATCACCCAGTCATGCGAAGT 59.385 50.000 0.00 0.00 0.00 3.01
438 442 0.615331 ACCCAGTCATGCGAAGTCAT 59.385 50.000 0.00 0.00 0.00 3.06
439 443 1.831106 ACCCAGTCATGCGAAGTCATA 59.169 47.619 0.00 0.00 0.00 2.15
444 448 2.692557 AGTCATGCGAAGTCATAGAGCT 59.307 45.455 0.00 0.00 0.00 4.09
450 454 2.734079 GCGAAGTCATAGAGCTTATGGC 59.266 50.000 10.63 10.63 42.19 4.40
464 468 2.816777 TATGGCTTATGGGTGCAACA 57.183 45.000 3.06 0.00 39.98 3.33
468 472 2.224892 TGGCTTATGGGTGCAACAGTTA 60.225 45.455 3.06 0.00 39.98 2.24
469 473 2.823154 GGCTTATGGGTGCAACAGTTAA 59.177 45.455 3.06 0.00 39.98 2.01
473 477 2.270352 TGGGTGCAACAGTTAAGAGG 57.730 50.000 3.06 0.00 39.98 3.69
474 478 0.881796 GGGTGCAACAGTTAAGAGGC 59.118 55.000 3.06 0.00 39.98 4.70
476 480 0.517316 GTGCAACAGTTAAGAGGCGG 59.483 55.000 0.00 0.00 36.32 6.13
478 482 1.235724 GCAACAGTTAAGAGGCGGTT 58.764 50.000 0.00 0.00 0.00 4.44
483 487 0.605589 AGTTAAGAGGCGGTTGCACC 60.606 55.000 0.00 0.00 45.35 5.01
501 513 1.283613 ACCGGATAAGTTTGGATGGCA 59.716 47.619 9.46 0.00 0.00 4.92
508 520 5.297029 GGATAAGTTTGGATGGCAGTCTAAC 59.703 44.000 0.00 1.35 0.00 2.34
513 525 5.882557 AGTTTGGATGGCAGTCTAACAATAG 59.117 40.000 15.13 0.00 0.00 1.73
518 530 6.014242 TGGATGGCAGTCTAACAATAGGATAG 60.014 42.308 0.00 0.00 0.00 2.08
519 531 5.808366 TGGCAGTCTAACAATAGGATAGG 57.192 43.478 0.00 0.00 0.00 2.57
527 539 9.710818 AGTCTAACAATAGGATAGGTGTTTAGA 57.289 33.333 0.00 0.00 35.28 2.10
533 545 8.993424 ACAATAGGATAGGTGTTTAGACATCTT 58.007 33.333 4.26 0.00 44.84 2.40
538 550 8.361139 AGGATAGGTGTTTAGACATCTTATTCG 58.639 37.037 4.26 0.00 44.84 3.34
543 555 9.449719 AGGTGTTTAGACATCTTATTCGATTTT 57.550 29.630 0.00 0.00 44.84 1.82
547 559 9.010366 GTTTAGACATCTTATTCGATTTTTGCC 57.990 33.333 0.00 0.00 0.00 4.52
549 561 4.920376 ACATCTTATTCGATTTTTGCCGG 58.080 39.130 0.00 0.00 0.00 6.13
556 568 0.031449 CGATTTTTGCCGGTTGTGGT 59.969 50.000 1.90 0.00 0.00 4.16
560 572 0.681564 TTTTGCCGGTTGTGGTGAGT 60.682 50.000 1.90 0.00 0.00 3.41
563 575 1.358759 GCCGGTTGTGGTGAGTTTG 59.641 57.895 1.90 0.00 0.00 2.93
564 576 1.098712 GCCGGTTGTGGTGAGTTTGA 61.099 55.000 1.90 0.00 0.00 2.69
570 585 4.439426 CGGTTGTGGTGAGTTTGATTTTGA 60.439 41.667 0.00 0.00 0.00 2.69
572 587 6.514212 CGGTTGTGGTGAGTTTGATTTTGATA 60.514 38.462 0.00 0.00 0.00 2.15
588 603 9.961265 TGATTTTGATATTCATTTCAGCTCATC 57.039 29.630 0.00 0.00 0.00 2.92
593 608 8.302965 TGATATTCATTTCAGCTCATCTTACG 57.697 34.615 0.00 0.00 0.00 3.18
594 609 8.143835 TGATATTCATTTCAGCTCATCTTACGA 58.856 33.333 0.00 0.00 0.00 3.43
595 610 6.841443 ATTCATTTCAGCTCATCTTACGAG 57.159 37.500 0.00 0.00 0.00 4.18
604 619 3.364062 CTCATCTTACGAGCTTGTACCG 58.636 50.000 13.64 8.10 0.00 4.02
605 620 2.098607 TCATCTTACGAGCTTGTACCGG 59.901 50.000 13.64 0.00 0.00 5.28
606 621 1.825090 TCTTACGAGCTTGTACCGGA 58.175 50.000 13.64 9.39 0.00 5.14
607 622 1.470098 TCTTACGAGCTTGTACCGGAC 59.530 52.381 13.64 2.18 0.00 4.79
608 623 1.471684 CTTACGAGCTTGTACCGGACT 59.528 52.381 13.64 0.00 0.00 3.85
609 624 2.401583 TACGAGCTTGTACCGGACTA 57.598 50.000 9.46 0.00 0.00 2.59
610 625 0.807496 ACGAGCTTGTACCGGACTAC 59.193 55.000 9.46 0.84 0.00 2.73
611 626 1.093159 CGAGCTTGTACCGGACTACT 58.907 55.000 9.46 0.00 0.00 2.57
612 627 1.471684 CGAGCTTGTACCGGACTACTT 59.528 52.381 9.46 0.00 0.00 2.24
613 628 2.679837 CGAGCTTGTACCGGACTACTTA 59.320 50.000 9.46 0.00 0.00 2.24
614 629 3.486542 CGAGCTTGTACCGGACTACTTAC 60.487 52.174 9.46 0.00 0.00 2.34
615 630 2.421424 AGCTTGTACCGGACTACTTACG 59.579 50.000 9.46 0.00 0.00 3.18
616 631 2.162408 GCTTGTACCGGACTACTTACGT 59.838 50.000 9.46 0.00 0.00 3.57
617 632 3.751621 CTTGTACCGGACTACTTACGTG 58.248 50.000 9.46 0.00 0.00 4.49
618 633 1.468520 TGTACCGGACTACTTACGTGC 59.531 52.381 9.46 0.00 0.00 5.34
619 634 1.740025 GTACCGGACTACTTACGTGCT 59.260 52.381 9.46 0.00 0.00 4.40
620 635 1.251251 ACCGGACTACTTACGTGCTT 58.749 50.000 9.46 0.00 0.00 3.91
621 636 1.068055 ACCGGACTACTTACGTGCTTG 60.068 52.381 9.46 0.00 0.00 4.01
622 637 1.068055 CCGGACTACTTACGTGCTTGT 60.068 52.381 0.00 0.00 0.00 3.16
623 638 2.608752 CCGGACTACTTACGTGCTTGTT 60.609 50.000 0.00 0.00 0.00 2.83
624 639 3.054878 CGGACTACTTACGTGCTTGTTT 58.945 45.455 0.00 0.00 0.00 2.83
625 640 3.492011 CGGACTACTTACGTGCTTGTTTT 59.508 43.478 0.00 0.00 0.00 2.43
626 641 4.681025 CGGACTACTTACGTGCTTGTTTTA 59.319 41.667 0.00 0.00 0.00 1.52
627 642 5.346822 CGGACTACTTACGTGCTTGTTTTAT 59.653 40.000 0.00 0.00 0.00 1.40
628 643 6.128742 CGGACTACTTACGTGCTTGTTTTATT 60.129 38.462 0.00 0.00 0.00 1.40
629 644 7.062138 CGGACTACTTACGTGCTTGTTTTATTA 59.938 37.037 0.00 0.00 0.00 0.98
630 645 8.711457 GGACTACTTACGTGCTTGTTTTATTAA 58.289 33.333 0.00 0.00 0.00 1.40
639 654 9.072294 ACGTGCTTGTTTTATTAATAAGATTGC 57.928 29.630 7.91 10.23 0.00 3.56
640 655 9.071221 CGTGCTTGTTTTATTAATAAGATTGCA 57.929 29.630 7.91 12.17 0.00 4.08
643 658 9.853921 GCTTGTTTTATTAATAAGATTGCATGC 57.146 29.630 11.82 11.82 0.00 4.06
664 679 5.861491 GCATCATTTTAATGCAGAAGTCG 57.139 39.130 3.35 0.00 46.93 4.18
665 680 5.572211 GCATCATTTTAATGCAGAAGTCGA 58.428 37.500 3.35 0.00 46.93 4.20
666 681 6.029607 GCATCATTTTAATGCAGAAGTCGAA 58.970 36.000 3.35 0.00 46.93 3.71
667 682 6.021153 GCATCATTTTAATGCAGAAGTCGAAC 60.021 38.462 3.35 0.00 46.93 3.95
668 683 5.938322 TCATTTTAATGCAGAAGTCGAACC 58.062 37.500 0.00 0.00 36.36 3.62
669 684 5.471797 TCATTTTAATGCAGAAGTCGAACCA 59.528 36.000 0.00 0.00 36.36 3.67
670 685 4.742438 TTTAATGCAGAAGTCGAACCAC 57.258 40.909 0.00 0.00 0.00 4.16
671 686 2.550830 AATGCAGAAGTCGAACCACT 57.449 45.000 0.00 0.00 0.00 4.00
672 687 1.800805 ATGCAGAAGTCGAACCACTG 58.199 50.000 0.00 0.00 0.00 3.66
673 688 0.249868 TGCAGAAGTCGAACCACTGG 60.250 55.000 10.52 0.00 0.00 4.00
674 689 0.033504 GCAGAAGTCGAACCACTGGA 59.966 55.000 0.71 0.00 0.00 3.86
675 690 1.338200 GCAGAAGTCGAACCACTGGAT 60.338 52.381 0.71 0.00 0.00 3.41
676 691 2.094182 GCAGAAGTCGAACCACTGGATA 60.094 50.000 0.71 0.00 0.00 2.59
677 692 3.616560 GCAGAAGTCGAACCACTGGATAA 60.617 47.826 0.71 0.00 0.00 1.75
678 693 4.566004 CAGAAGTCGAACCACTGGATAAA 58.434 43.478 0.71 0.00 0.00 1.40
679 694 5.178797 CAGAAGTCGAACCACTGGATAAAT 58.821 41.667 0.71 0.00 0.00 1.40
680 695 6.338146 CAGAAGTCGAACCACTGGATAAATA 58.662 40.000 0.71 0.00 0.00 1.40
681 696 6.816640 CAGAAGTCGAACCACTGGATAAATAA 59.183 38.462 0.71 0.00 0.00 1.40
682 697 7.495934 CAGAAGTCGAACCACTGGATAAATAAT 59.504 37.037 0.71 0.00 0.00 1.28
683 698 8.701895 AGAAGTCGAACCACTGGATAAATAATA 58.298 33.333 0.71 0.00 0.00 0.98
684 699 9.321562 GAAGTCGAACCACTGGATAAATAATAA 57.678 33.333 0.71 0.00 0.00 1.40
685 700 9.675464 AAGTCGAACCACTGGATAAATAATAAA 57.325 29.630 0.71 0.00 0.00 1.40
686 701 9.675464 AGTCGAACCACTGGATAAATAATAAAA 57.325 29.630 0.71 0.00 0.00 1.52
689 704 9.511144 CGAACCACTGGATAAATAATAAAAACC 57.489 33.333 0.71 0.00 0.00 3.27
690 705 9.811995 GAACCACTGGATAAATAATAAAAACCC 57.188 33.333 0.71 0.00 0.00 4.11
691 706 9.555411 AACCACTGGATAAATAATAAAAACCCT 57.445 29.630 0.71 0.00 0.00 4.34
692 707 9.555411 ACCACTGGATAAATAATAAAAACCCTT 57.445 29.630 0.71 0.00 0.00 3.95
708 723 8.862325 AAAAACCCTTTCTGAAAAATGTTTCT 57.138 26.923 17.28 7.69 43.13 2.52
709 724 7.848223 AAACCCTTTCTGAAAAATGTTTCTG 57.152 32.000 9.75 9.12 43.13 3.02
710 725 6.544928 ACCCTTTCTGAAAAATGTTTCTGT 57.455 33.333 9.75 0.00 43.13 3.41
711 726 6.573434 ACCCTTTCTGAAAAATGTTTCTGTC 58.427 36.000 9.75 0.00 43.13 3.51
712 727 5.687285 CCCTTTCTGAAAAATGTTTCTGTCG 59.313 40.000 9.75 3.16 43.13 4.35
713 728 5.687285 CCTTTCTGAAAAATGTTTCTGTCGG 59.313 40.000 9.75 7.55 43.13 4.79
714 729 5.828299 TTCTGAAAAATGTTTCTGTCGGT 57.172 34.783 9.75 0.00 43.13 4.69
715 730 5.828299 TCTGAAAAATGTTTCTGTCGGTT 57.172 34.783 9.75 0.00 43.13 4.44
716 731 5.816919 TCTGAAAAATGTTTCTGTCGGTTC 58.183 37.500 9.75 0.00 43.13 3.62
717 732 4.927422 TGAAAAATGTTTCTGTCGGTTCC 58.073 39.130 9.75 0.00 43.13 3.62
718 733 3.619233 AAAATGTTTCTGTCGGTTCCG 57.381 42.857 4.74 4.74 0.00 4.30
719 734 2.536761 AATGTTTCTGTCGGTTCCGA 57.463 45.000 10.00 10.00 36.02 4.55
720 735 2.762535 ATGTTTCTGTCGGTTCCGAT 57.237 45.000 16.87 0.00 40.65 4.18
721 736 2.536761 TGTTTCTGTCGGTTCCGATT 57.463 45.000 16.87 0.00 40.65 3.34
722 737 2.841215 TGTTTCTGTCGGTTCCGATTT 58.159 42.857 16.87 0.00 40.65 2.17
723 738 3.207778 TGTTTCTGTCGGTTCCGATTTT 58.792 40.909 16.87 0.00 40.65 1.82
724 739 3.628487 TGTTTCTGTCGGTTCCGATTTTT 59.372 39.130 16.87 0.00 40.65 1.94
725 740 4.815308 TGTTTCTGTCGGTTCCGATTTTTA 59.185 37.500 16.87 1.46 40.65 1.52
726 741 4.996062 TTCTGTCGGTTCCGATTTTTAC 57.004 40.909 16.87 4.60 40.65 2.01
727 742 3.992643 TCTGTCGGTTCCGATTTTTACA 58.007 40.909 16.87 8.76 40.65 2.41
728 743 4.571919 TCTGTCGGTTCCGATTTTTACAT 58.428 39.130 16.87 0.00 40.65 2.29
729 744 4.998672 TCTGTCGGTTCCGATTTTTACATT 59.001 37.500 16.87 0.00 40.65 2.71
730 745 5.121142 TCTGTCGGTTCCGATTTTTACATTC 59.879 40.000 16.87 1.33 40.65 2.67
731 746 4.755629 TGTCGGTTCCGATTTTTACATTCA 59.244 37.500 16.87 3.84 40.65 2.57
732 747 5.238868 TGTCGGTTCCGATTTTTACATTCAA 59.761 36.000 16.87 0.00 40.65 2.69
733 748 5.566395 GTCGGTTCCGATTTTTACATTCAAC 59.434 40.000 16.87 0.00 40.65 3.18
734 749 5.470777 TCGGTTCCGATTTTTACATTCAACT 59.529 36.000 10.00 0.00 33.26 3.16
735 750 6.649973 TCGGTTCCGATTTTTACATTCAACTA 59.350 34.615 10.00 0.00 33.26 2.24
736 751 6.959311 CGGTTCCGATTTTTACATTCAACTAG 59.041 38.462 5.19 0.00 0.00 2.57
744 759 9.262472 GATTTTTACATTCAACTAGCGTAACAG 57.738 33.333 0.00 0.00 0.00 3.16
754 769 2.726832 AGCGTAACAGTCAGAACCTC 57.273 50.000 0.00 0.00 0.00 3.85
755 770 1.961394 AGCGTAACAGTCAGAACCTCA 59.039 47.619 0.00 0.00 0.00 3.86
800 815 3.307906 CCGTTCCTCGTGGGTCCA 61.308 66.667 3.23 0.00 37.94 4.02
823 838 6.861055 CCAAATAGTGACAAAATGTTAGCGTT 59.139 34.615 0.00 0.00 0.00 4.84
837 852 3.710722 CGTTCCAGCCCAGCTCCT 61.711 66.667 0.00 0.00 36.40 3.69
844 859 0.393537 CAGCCCAGCTCCTAACCTTG 60.394 60.000 0.00 0.00 36.40 3.61
845 860 0.547712 AGCCCAGCTCCTAACCTTGA 60.548 55.000 0.00 0.00 30.62 3.02
846 861 0.548510 GCCCAGCTCCTAACCTTGAT 59.451 55.000 0.00 0.00 0.00 2.57
847 862 1.748591 GCCCAGCTCCTAACCTTGATG 60.749 57.143 0.00 0.00 0.00 3.07
849 864 2.025887 CCCAGCTCCTAACCTTGATGTT 60.026 50.000 0.00 0.00 0.00 2.71
850 865 3.562176 CCCAGCTCCTAACCTTGATGTTT 60.562 47.826 0.00 0.00 0.00 2.83
851 866 3.691609 CCAGCTCCTAACCTTGATGTTTC 59.308 47.826 0.00 0.00 0.00 2.78
852 867 3.691609 CAGCTCCTAACCTTGATGTTTCC 59.308 47.826 0.00 0.00 0.00 3.13
853 868 3.330701 AGCTCCTAACCTTGATGTTTCCA 59.669 43.478 0.00 0.00 0.00 3.53
854 869 3.440522 GCTCCTAACCTTGATGTTTCCAC 59.559 47.826 0.00 0.00 0.00 4.02
855 870 4.651778 CTCCTAACCTTGATGTTTCCACA 58.348 43.478 0.00 0.00 37.31 4.17
867 882 4.084011 TGTTTCCACATCATCAGACACA 57.916 40.909 0.00 0.00 0.00 3.72
868 883 3.814842 TGTTTCCACATCATCAGACACAC 59.185 43.478 0.00 0.00 0.00 3.82
869 884 2.768253 TCCACATCATCAGACACACC 57.232 50.000 0.00 0.00 0.00 4.16
876 901 0.686789 CATCAGACACACCCCACTGA 59.313 55.000 0.00 0.00 42.26 3.41
895 920 2.038557 TGAAAGTGAAGAGCCCACTACC 59.961 50.000 0.00 0.00 43.42 3.18
906 931 1.351350 GCCCACTACCTCCAAAAGACT 59.649 52.381 0.00 0.00 0.00 3.24
937 974 4.492604 GCCCAACAGCCTAACACA 57.507 55.556 0.00 0.00 0.00 3.72
938 975 2.727103 GCCCAACAGCCTAACACAA 58.273 52.632 0.00 0.00 0.00 3.33
939 976 1.036707 GCCCAACAGCCTAACACAAA 58.963 50.000 0.00 0.00 0.00 2.83
940 977 1.410882 GCCCAACAGCCTAACACAAAA 59.589 47.619 0.00 0.00 0.00 2.44
941 978 2.545742 GCCCAACAGCCTAACACAAAAG 60.546 50.000 0.00 0.00 0.00 2.27
942 979 2.693074 CCCAACAGCCTAACACAAAAGT 59.307 45.455 0.00 0.00 0.00 2.66
943 980 3.490761 CCCAACAGCCTAACACAAAAGTG 60.491 47.826 0.00 0.00 0.00 3.16
944 981 3.490761 CCAACAGCCTAACACAAAAGTGG 60.491 47.826 0.38 0.00 0.00 4.00
945 982 1.681264 ACAGCCTAACACAAAAGTGGC 59.319 47.619 0.38 0.00 40.54 5.01
946 983 1.680735 CAGCCTAACACAAAAGTGGCA 59.319 47.619 0.00 0.00 42.46 4.92
1183 1221 2.770802 CTCATCTCCATGAACCTGTCCT 59.229 50.000 0.00 0.00 38.63 3.85
1537 1575 1.810853 CGCATCGACAGCCACATCA 60.811 57.895 6.14 0.00 0.00 3.07
1751 1797 1.205655 TCTCTCAAGCTCCAATGTCCG 59.794 52.381 0.00 0.00 0.00 4.79
1752 1798 1.205655 CTCTCAAGCTCCAATGTCCGA 59.794 52.381 0.00 0.00 0.00 4.55
1797 1843 1.202568 TCTGCGGCTCCACATTATCAG 60.203 52.381 0.00 0.00 0.00 2.90
1845 1891 2.827921 AGGAATGTGAAAGACAATGGGC 59.172 45.455 0.00 0.00 38.36 5.36
1850 1897 0.322456 TGAAAGACAATGGGCGAGGG 60.322 55.000 0.00 0.00 0.00 4.30
1859 1906 2.368875 CAATGGGCGAGGGTAAGATAGT 59.631 50.000 0.00 0.00 0.00 2.12
2039 2088 3.255888 TCGATTCATAGGGATGGTTCTCG 59.744 47.826 0.00 0.00 33.49 4.04
2090 2139 1.297378 CGCTCGCAACGACTCGATA 60.297 57.895 5.20 0.00 33.98 2.92
2218 2268 2.107041 TACACACTGGACTTGGGGCG 62.107 60.000 0.00 0.00 0.00 6.13
2434 2484 1.903404 GGCAAAGGGGGACACACAG 60.903 63.158 0.00 0.00 0.00 3.66
2464 2514 2.896685 CGAGATTAGATGGGGAGCTCTT 59.103 50.000 14.64 0.00 0.00 2.85
2536 2586 5.099042 TCCTGGAGTATTTCTTTGCTACC 57.901 43.478 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 53 9.296400 TGTTGTTAGTTAAAATCACTTCTTTGC 57.704 29.630 0.00 0.00 0.00 3.68
59 61 7.489757 TGCCAAGTTGTTGTTAGTTAAAATCAC 59.510 33.333 1.45 0.00 30.95 3.06
67 69 5.542779 TGTTTTGCCAAGTTGTTGTTAGTT 58.457 33.333 1.45 0.00 30.95 2.24
73 75 6.420604 CCTAACTATGTTTTGCCAAGTTGTTG 59.579 38.462 1.45 0.00 32.85 3.33
76 78 6.325919 TCCTAACTATGTTTTGCCAAGTTG 57.674 37.500 0.00 0.00 32.85 3.16
91 93 3.700538 TCGTTTAGTGCCCTCCTAACTA 58.299 45.455 0.00 0.00 0.00 2.24
93 95 3.538634 ATCGTTTAGTGCCCTCCTAAC 57.461 47.619 0.00 0.00 0.00 2.34
96 98 3.181454 CCAATATCGTTTAGTGCCCTCCT 60.181 47.826 0.00 0.00 0.00 3.69
98 100 3.805207 ACCAATATCGTTTAGTGCCCTC 58.195 45.455 0.00 0.00 0.00 4.30
103 105 7.540400 TGATTGCAAAACCAATATCGTTTAGTG 59.460 33.333 1.71 0.71 35.67 2.74
105 107 8.459521 TTGATTGCAAAACCAATATCGTTTAG 57.540 30.769 1.71 0.00 35.67 1.85
109 111 6.266168 TCTTGATTGCAAAACCAATATCGT 57.734 33.333 1.71 0.00 35.67 3.73
111 113 8.706492 TTCATCTTGATTGCAAAACCAATATC 57.294 30.769 1.71 0.00 35.67 1.63
114 116 6.993902 AGTTTCATCTTGATTGCAAAACCAAT 59.006 30.769 1.71 0.00 38.09 3.16
118 120 7.814107 TGGATAGTTTCATCTTGATTGCAAAAC 59.186 33.333 1.71 0.00 32.73 2.43
125 127 8.517878 CAAGTGTTGGATAGTTTCATCTTGATT 58.482 33.333 0.00 0.00 33.00 2.57
128 130 7.206981 ACAAGTGTTGGATAGTTTCATCTTG 57.793 36.000 0.00 0.00 35.96 3.02
135 137 7.639113 TTGAGAAACAAGTGTTGGATAGTTT 57.361 32.000 0.00 0.00 38.44 2.66
148 150 2.310538 AGTGGGCCTTTGAGAAACAAG 58.689 47.619 4.53 0.00 39.77 3.16
149 151 2.452600 AGTGGGCCTTTGAGAAACAA 57.547 45.000 4.53 0.00 36.65 2.83
150 152 2.814097 GCTAGTGGGCCTTTGAGAAACA 60.814 50.000 4.53 0.00 0.00 2.83
151 153 1.813178 GCTAGTGGGCCTTTGAGAAAC 59.187 52.381 4.53 0.00 0.00 2.78
152 154 2.200373 GCTAGTGGGCCTTTGAGAAA 57.800 50.000 4.53 0.00 0.00 2.52
173 175 6.383147 ACATGTAGTGTAGGCCATAGTAACTT 59.617 38.462 5.01 0.00 39.91 2.66
174 176 5.897824 ACATGTAGTGTAGGCCATAGTAACT 59.102 40.000 5.01 1.99 39.91 2.24
175 177 5.983720 CACATGTAGTGTAGGCCATAGTAAC 59.016 44.000 5.01 0.00 43.40 2.50
176 178 6.156748 CACATGTAGTGTAGGCCATAGTAA 57.843 41.667 5.01 0.00 43.40 2.24
181 183 3.491950 AGCCACATGTAGTGTAGGCCAT 61.492 50.000 16.63 0.00 46.88 4.40
191 193 3.181507 CCGACATTGAAAGCCACATGTAG 60.182 47.826 0.00 0.00 31.46 2.74
196 198 1.234821 GACCGACATTGAAAGCCACA 58.765 50.000 0.00 0.00 0.00 4.17
199 201 1.087501 GAGGACCGACATTGAAAGCC 58.912 55.000 0.00 0.00 0.00 4.35
200 202 1.087501 GGAGGACCGACATTGAAAGC 58.912 55.000 0.00 0.00 0.00 3.51
202 204 4.837093 ATTAGGAGGACCGACATTGAAA 57.163 40.909 0.00 0.00 41.83 2.69
209 211 3.321111 TCAATGCTATTAGGAGGACCGAC 59.679 47.826 0.00 0.00 41.83 4.79
212 214 4.381411 GTGTCAATGCTATTAGGAGGACC 58.619 47.826 13.52 0.00 0.00 4.46
217 219 7.011950 CCAAATAACGTGTCAATGCTATTAGGA 59.988 37.037 0.00 0.00 0.00 2.94
220 222 6.824196 TCCCAAATAACGTGTCAATGCTATTA 59.176 34.615 0.00 0.00 0.00 0.98
229 231 4.214545 GTCATTGTCCCAAATAACGTGTCA 59.785 41.667 0.00 0.00 0.00 3.58
231 233 4.394729 AGTCATTGTCCCAAATAACGTGT 58.605 39.130 0.00 0.00 0.00 4.49
235 237 8.062065 TCCATTTAGTCATTGTCCCAAATAAC 57.938 34.615 0.00 0.00 0.00 1.89
244 246 5.163713 GGCTTCACTCCATTTAGTCATTGTC 60.164 44.000 0.00 0.00 0.00 3.18
246 248 4.946157 AGGCTTCACTCCATTTAGTCATTG 59.054 41.667 0.00 0.00 0.00 2.82
247 249 5.184892 AGGCTTCACTCCATTTAGTCATT 57.815 39.130 0.00 0.00 0.00 2.57
248 250 4.851639 AGGCTTCACTCCATTTAGTCAT 57.148 40.909 0.00 0.00 0.00 3.06
251 253 8.957466 GTTATTTTAGGCTTCACTCCATTTAGT 58.043 33.333 0.00 0.00 0.00 2.24
258 260 4.510571 TCCGTTATTTTAGGCTTCACTCC 58.489 43.478 0.00 0.00 0.00 3.85
260 262 3.939592 GCTCCGTTATTTTAGGCTTCACT 59.060 43.478 0.00 0.00 0.00 3.41
261 263 3.687698 TGCTCCGTTATTTTAGGCTTCAC 59.312 43.478 0.00 0.00 0.00 3.18
263 265 6.803154 ATATGCTCCGTTATTTTAGGCTTC 57.197 37.500 0.00 0.00 0.00 3.86
264 266 6.770785 TGAATATGCTCCGTTATTTTAGGCTT 59.229 34.615 0.00 0.00 0.00 4.35
276 278 2.643551 CCCAACTTGAATATGCTCCGT 58.356 47.619 0.00 0.00 0.00 4.69
280 282 3.091545 CACACCCCAACTTGAATATGCT 58.908 45.455 0.00 0.00 0.00 3.79
289 291 2.373335 TAATGCACACACCCCAACTT 57.627 45.000 0.00 0.00 0.00 2.66
291 293 3.676291 AATTAATGCACACACCCCAAC 57.324 42.857 0.00 0.00 0.00 3.77
293 295 2.301296 CCAAATTAATGCACACACCCCA 59.699 45.455 0.00 0.00 0.00 4.96
322 325 1.068125 CCACGTCATTCCGACAGTACA 60.068 52.381 0.00 0.00 45.70 2.90
323 326 1.068055 ACCACGTCATTCCGACAGTAC 60.068 52.381 0.00 0.00 45.70 2.73
324 327 1.200716 GACCACGTCATTCCGACAGTA 59.799 52.381 0.00 0.00 45.70 2.74
329 332 3.663995 TTAAAGACCACGTCATTCCGA 57.336 42.857 0.00 0.00 34.60 4.55
330 333 5.345702 TCTATTAAAGACCACGTCATTCCG 58.654 41.667 0.00 0.00 34.60 4.30
364 367 6.682423 TGTAGATGACCTGCACAATATTTG 57.318 37.500 0.00 0.00 32.40 2.32
368 371 5.070313 TGCTATGTAGATGACCTGCACAATA 59.930 40.000 0.00 0.00 40.29 1.90
370 373 3.197549 TGCTATGTAGATGACCTGCACAA 59.802 43.478 0.00 0.00 40.29 3.33
372 375 3.459232 TGCTATGTAGATGACCTGCAC 57.541 47.619 0.00 0.00 40.29 4.57
381 384 6.058183 GGATTCAACCAGTTGCTATGTAGAT 58.942 40.000 5.63 0.00 40.24 1.98
383 386 4.271049 CGGATTCAACCAGTTGCTATGTAG 59.729 45.833 5.63 0.00 40.24 2.74
388 391 2.851263 ACGGATTCAACCAGTTGCTA 57.149 45.000 5.63 0.00 40.24 3.49
398 401 4.109766 GTGATGATCACGTACGGATTCAA 58.890 43.478 21.06 9.41 37.67 2.69
412 415 1.202568 TCGCATGACTGGGTGATGATC 60.203 52.381 0.00 0.00 36.72 2.92
413 416 0.832626 TCGCATGACTGGGTGATGAT 59.167 50.000 0.00 0.00 36.72 2.45
416 419 0.615331 ACTTCGCATGACTGGGTGAT 59.385 50.000 0.00 0.00 36.72 3.06
421 424 3.379240 CTCTATGACTTCGCATGACTGG 58.621 50.000 0.00 0.00 0.00 4.00
444 448 3.023119 CTGTTGCACCCATAAGCCATAA 58.977 45.455 0.00 0.00 0.00 1.90
450 454 4.396166 CCTCTTAACTGTTGCACCCATAAG 59.604 45.833 2.69 0.00 0.00 1.73
453 457 2.795329 CCTCTTAACTGTTGCACCCAT 58.205 47.619 2.69 0.00 0.00 4.00
464 468 2.928416 GTGCAACCGCCTCTTAACT 58.072 52.632 0.00 0.00 37.32 2.24
476 480 2.156098 TCCAAACTTATCCGGTGCAAC 58.844 47.619 0.00 0.00 0.00 4.17
478 482 2.364632 CATCCAAACTTATCCGGTGCA 58.635 47.619 0.00 0.00 0.00 4.57
483 487 2.614057 GACTGCCATCCAAACTTATCCG 59.386 50.000 0.00 0.00 0.00 4.18
484 488 3.891049 AGACTGCCATCCAAACTTATCC 58.109 45.455 0.00 0.00 0.00 2.59
485 489 5.880332 TGTTAGACTGCCATCCAAACTTATC 59.120 40.000 0.00 0.00 0.00 1.75
489 493 3.788227 TGTTAGACTGCCATCCAAACT 57.212 42.857 0.00 0.00 0.00 2.66
490 494 5.066505 CCTATTGTTAGACTGCCATCCAAAC 59.933 44.000 0.00 0.00 0.00 2.93
501 513 9.710818 TCTAAACACCTATCCTATTGTTAGACT 57.289 33.333 0.00 0.00 31.92 3.24
513 525 8.358148 TCGAATAAGATGTCTAAACACCTATCC 58.642 37.037 0.00 0.00 38.48 2.59
527 539 4.398044 ACCGGCAAAAATCGAATAAGATGT 59.602 37.500 0.00 0.00 0.00 3.06
533 545 3.366476 CCACAACCGGCAAAAATCGAATA 60.366 43.478 0.00 0.00 0.00 1.75
534 546 2.609244 CCACAACCGGCAAAAATCGAAT 60.609 45.455 0.00 0.00 0.00 3.34
537 549 0.031449 ACCACAACCGGCAAAAATCG 59.969 50.000 0.00 0.00 0.00 3.34
538 550 1.067821 TCACCACAACCGGCAAAAATC 59.932 47.619 0.00 0.00 0.00 2.17
543 555 0.681564 AAACTCACCACAACCGGCAA 60.682 50.000 0.00 0.00 0.00 4.52
547 559 3.708563 AAATCAAACTCACCACAACCG 57.291 42.857 0.00 0.00 0.00 4.44
549 561 8.816640 AATATCAAAATCAAACTCACCACAAC 57.183 30.769 0.00 0.00 0.00 3.32
588 603 1.471684 AGTCCGGTACAAGCTCGTAAG 59.528 52.381 0.00 0.00 0.00 2.34
589 604 1.538047 AGTCCGGTACAAGCTCGTAA 58.462 50.000 0.00 0.00 0.00 3.18
590 605 2.009774 GTAGTCCGGTACAAGCTCGTA 58.990 52.381 0.00 0.00 0.00 3.43
591 606 0.807496 GTAGTCCGGTACAAGCTCGT 59.193 55.000 0.00 0.00 0.00 4.18
592 607 1.093159 AGTAGTCCGGTACAAGCTCG 58.907 55.000 0.00 0.00 0.00 5.03
593 608 3.486542 CGTAAGTAGTCCGGTACAAGCTC 60.487 52.174 0.00 0.00 0.00 4.09
594 609 2.421424 CGTAAGTAGTCCGGTACAAGCT 59.579 50.000 0.00 0.00 0.00 3.74
595 610 2.790387 CGTAAGTAGTCCGGTACAAGC 58.210 52.381 0.00 0.00 0.00 4.01
613 628 9.072294 GCAATCTTATTAATAAAACAAGCACGT 57.928 29.630 9.15 0.00 0.00 4.49
614 629 9.071221 TGCAATCTTATTAATAAAACAAGCACG 57.929 29.630 9.15 0.00 0.00 5.34
617 632 9.853921 GCATGCAATCTTATTAATAAAACAAGC 57.146 29.630 14.21 9.76 0.00 4.01
630 645 8.717821 GCATTAAAATGATGCATGCAATCTTAT 58.282 29.630 26.68 6.72 46.96 1.73
631 646 8.078959 GCATTAAAATGATGCATGCAATCTTA 57.921 30.769 26.68 9.22 46.96 2.10
632 647 6.954944 GCATTAAAATGATGCATGCAATCTT 58.045 32.000 26.68 14.73 46.96 2.40
633 648 6.539649 GCATTAAAATGATGCATGCAATCT 57.460 33.333 26.68 8.52 46.96 2.40
643 658 6.470235 GGTTCGACTTCTGCATTAAAATGATG 59.530 38.462 6.87 0.00 38.70 3.07
644 659 6.150976 TGGTTCGACTTCTGCATTAAAATGAT 59.849 34.615 6.87 0.00 38.70 2.45
645 660 5.471797 TGGTTCGACTTCTGCATTAAAATGA 59.528 36.000 6.87 0.00 38.70 2.57
646 661 5.569059 GTGGTTCGACTTCTGCATTAAAATG 59.431 40.000 0.00 0.00 39.40 2.32
647 662 5.473504 AGTGGTTCGACTTCTGCATTAAAAT 59.526 36.000 0.00 0.00 0.00 1.82
648 663 4.819630 AGTGGTTCGACTTCTGCATTAAAA 59.180 37.500 0.00 0.00 0.00 1.52
649 664 4.213270 CAGTGGTTCGACTTCTGCATTAAA 59.787 41.667 0.00 0.00 0.00 1.52
650 665 3.745975 CAGTGGTTCGACTTCTGCATTAA 59.254 43.478 0.00 0.00 0.00 1.40
651 666 3.325870 CAGTGGTTCGACTTCTGCATTA 58.674 45.455 0.00 0.00 0.00 1.90
652 667 2.146342 CAGTGGTTCGACTTCTGCATT 58.854 47.619 0.00 0.00 0.00 3.56
653 668 1.609061 CCAGTGGTTCGACTTCTGCAT 60.609 52.381 0.00 0.00 0.00 3.96
654 669 0.249868 CCAGTGGTTCGACTTCTGCA 60.250 55.000 0.00 0.00 0.00 4.41
655 670 0.033504 TCCAGTGGTTCGACTTCTGC 59.966 55.000 9.54 0.00 0.00 4.26
656 671 2.751166 ATCCAGTGGTTCGACTTCTG 57.249 50.000 9.54 0.00 0.00 3.02
657 672 4.884668 TTTATCCAGTGGTTCGACTTCT 57.115 40.909 9.54 0.00 0.00 2.85
658 673 7.787725 ATTATTTATCCAGTGGTTCGACTTC 57.212 36.000 9.54 0.00 0.00 3.01
659 674 9.675464 TTTATTATTTATCCAGTGGTTCGACTT 57.325 29.630 9.54 0.00 0.00 3.01
660 675 9.675464 TTTTATTATTTATCCAGTGGTTCGACT 57.325 29.630 9.54 0.00 0.00 4.18
663 678 9.511144 GGTTTTTATTATTTATCCAGTGGTTCG 57.489 33.333 9.54 0.00 0.00 3.95
664 679 9.811995 GGGTTTTTATTATTTATCCAGTGGTTC 57.188 33.333 9.54 0.00 0.00 3.62
665 680 9.555411 AGGGTTTTTATTATTTATCCAGTGGTT 57.445 29.630 9.54 3.07 0.00 3.67
666 681 9.555411 AAGGGTTTTTATTATTTATCCAGTGGT 57.445 29.630 9.54 0.00 0.00 4.16
682 697 9.952030 AGAAACATTTTTCAGAAAGGGTTTTTA 57.048 25.926 16.40 0.00 43.29 1.52
683 698 8.729756 CAGAAACATTTTTCAGAAAGGGTTTTT 58.270 29.630 16.40 11.49 43.29 1.94
684 699 7.882791 ACAGAAACATTTTTCAGAAAGGGTTTT 59.117 29.630 16.40 7.99 43.29 2.43
685 700 7.394016 ACAGAAACATTTTTCAGAAAGGGTTT 58.606 30.769 15.74 15.74 43.29 3.27
686 701 6.946340 ACAGAAACATTTTTCAGAAAGGGTT 58.054 32.000 7.08 0.22 43.29 4.11
687 702 6.544928 ACAGAAACATTTTTCAGAAAGGGT 57.455 33.333 7.08 0.00 43.29 4.34
688 703 5.687285 CGACAGAAACATTTTTCAGAAAGGG 59.313 40.000 7.08 0.00 43.29 3.95
689 704 5.687285 CCGACAGAAACATTTTTCAGAAAGG 59.313 40.000 7.08 2.55 43.29 3.11
690 705 6.265577 ACCGACAGAAACATTTTTCAGAAAG 58.734 36.000 7.08 0.00 43.29 2.62
691 706 6.202516 ACCGACAGAAACATTTTTCAGAAA 57.797 33.333 7.08 0.00 43.29 2.52
692 707 5.828299 ACCGACAGAAACATTTTTCAGAA 57.172 34.783 7.08 0.00 43.29 3.02
693 708 5.220970 GGAACCGACAGAAACATTTTTCAGA 60.221 40.000 7.08 0.00 43.29 3.27
694 709 4.976116 GGAACCGACAGAAACATTTTTCAG 59.024 41.667 7.08 1.50 43.29 3.02
695 710 4.496673 CGGAACCGACAGAAACATTTTTCA 60.497 41.667 7.53 0.00 41.75 2.69
696 711 3.972502 CGGAACCGACAGAAACATTTTTC 59.027 43.478 7.53 0.00 42.83 2.29
697 712 3.628487 TCGGAACCGACAGAAACATTTTT 59.372 39.130 12.04 0.00 44.01 1.94
698 713 3.207778 TCGGAACCGACAGAAACATTTT 58.792 40.909 12.04 0.00 44.01 1.82
699 714 2.841215 TCGGAACCGACAGAAACATTT 58.159 42.857 12.04 0.00 44.01 2.32
700 715 2.536761 TCGGAACCGACAGAAACATT 57.463 45.000 12.04 0.00 44.01 2.71
711 726 5.695818 AGTTGAATGTAAAAATCGGAACCG 58.304 37.500 6.94 6.94 41.35 4.44
712 727 6.745907 GCTAGTTGAATGTAAAAATCGGAACC 59.254 38.462 0.00 0.00 0.00 3.62
713 728 6.464834 CGCTAGTTGAATGTAAAAATCGGAAC 59.535 38.462 0.00 0.00 0.00 3.62
714 729 6.148150 ACGCTAGTTGAATGTAAAAATCGGAA 59.852 34.615 0.00 0.00 0.00 4.30
715 730 5.640357 ACGCTAGTTGAATGTAAAAATCGGA 59.360 36.000 0.00 0.00 0.00 4.55
716 731 5.864986 ACGCTAGTTGAATGTAAAAATCGG 58.135 37.500 0.00 0.00 0.00 4.18
717 732 7.953173 TGTTACGCTAGTTGAATGTAAAAATCG 59.047 33.333 0.00 0.00 0.00 3.34
718 733 9.262472 CTGTTACGCTAGTTGAATGTAAAAATC 57.738 33.333 0.00 0.00 0.00 2.17
719 734 8.780249 ACTGTTACGCTAGTTGAATGTAAAAAT 58.220 29.630 0.00 0.00 0.00 1.82
720 735 8.145316 ACTGTTACGCTAGTTGAATGTAAAAA 57.855 30.769 0.00 0.00 0.00 1.94
721 736 7.438757 TGACTGTTACGCTAGTTGAATGTAAAA 59.561 33.333 0.00 0.00 0.00 1.52
722 737 6.924612 TGACTGTTACGCTAGTTGAATGTAAA 59.075 34.615 0.00 0.00 0.00 2.01
723 738 6.448852 TGACTGTTACGCTAGTTGAATGTAA 58.551 36.000 0.00 0.00 0.00 2.41
724 739 6.016213 TGACTGTTACGCTAGTTGAATGTA 57.984 37.500 0.00 0.00 0.00 2.29
725 740 4.878439 TGACTGTTACGCTAGTTGAATGT 58.122 39.130 0.00 0.00 0.00 2.71
726 741 5.161358 TCTGACTGTTACGCTAGTTGAATG 58.839 41.667 0.00 0.00 0.00 2.67
727 742 5.386958 TCTGACTGTTACGCTAGTTGAAT 57.613 39.130 0.00 0.00 0.00 2.57
728 743 4.841443 TCTGACTGTTACGCTAGTTGAA 57.159 40.909 0.00 0.00 0.00 2.69
729 744 4.543692 GTTCTGACTGTTACGCTAGTTGA 58.456 43.478 0.00 0.00 0.00 3.18
730 745 3.673809 GGTTCTGACTGTTACGCTAGTTG 59.326 47.826 0.00 0.00 0.00 3.16
731 746 3.573110 AGGTTCTGACTGTTACGCTAGTT 59.427 43.478 0.00 0.00 0.00 2.24
732 747 3.155501 AGGTTCTGACTGTTACGCTAGT 58.844 45.455 0.00 0.00 0.00 2.57
733 748 3.190744 TGAGGTTCTGACTGTTACGCTAG 59.809 47.826 0.00 0.00 0.00 3.42
734 749 3.151554 TGAGGTTCTGACTGTTACGCTA 58.848 45.455 0.00 0.00 0.00 4.26
735 750 1.961394 TGAGGTTCTGACTGTTACGCT 59.039 47.619 0.00 0.00 0.00 5.07
736 751 2.433868 TGAGGTTCTGACTGTTACGC 57.566 50.000 0.00 0.00 0.00 4.42
744 759 3.677424 CGAGGGAATCTTGAGGTTCTGAC 60.677 52.174 4.18 0.00 0.00 3.51
754 769 3.488384 CGACTTCTCTCGAGGGAATCTTG 60.488 52.174 27.36 17.84 35.58 3.02
755 770 2.685897 CGACTTCTCTCGAGGGAATCTT 59.314 50.000 27.36 14.97 35.58 2.40
781 796 4.754667 GACCCACGAGGAACGGGC 62.755 72.222 0.00 0.00 44.90 6.13
797 812 6.205853 ACGCTAACATTTTGTCACTATTTGGA 59.794 34.615 0.00 0.00 0.00 3.53
800 815 7.081976 GGAACGCTAACATTTTGTCACTATTT 58.918 34.615 0.00 0.00 0.00 1.40
823 838 1.995626 GGTTAGGAGCTGGGCTGGA 60.996 63.158 0.00 0.00 39.88 3.86
844 859 4.696877 TGTGTCTGATGATGTGGAAACATC 59.303 41.667 11.10 11.10 46.14 3.06
845 860 4.456911 GTGTGTCTGATGATGTGGAAACAT 59.543 41.667 0.00 0.00 46.14 2.71
846 861 3.814842 GTGTGTCTGATGATGTGGAAACA 59.185 43.478 0.00 0.00 38.70 2.83
847 862 3.189287 GGTGTGTCTGATGATGTGGAAAC 59.811 47.826 0.00 0.00 0.00 2.78
849 864 2.290260 GGGTGTGTCTGATGATGTGGAA 60.290 50.000 0.00 0.00 0.00 3.53
850 865 1.278985 GGGTGTGTCTGATGATGTGGA 59.721 52.381 0.00 0.00 0.00 4.02
851 866 1.679944 GGGGTGTGTCTGATGATGTGG 60.680 57.143 0.00 0.00 0.00 4.17
852 867 1.003464 TGGGGTGTGTCTGATGATGTG 59.997 52.381 0.00 0.00 0.00 3.21
853 868 1.003580 GTGGGGTGTGTCTGATGATGT 59.996 52.381 0.00 0.00 0.00 3.06
854 869 1.280133 AGTGGGGTGTGTCTGATGATG 59.720 52.381 0.00 0.00 0.00 3.07
855 870 1.280133 CAGTGGGGTGTGTCTGATGAT 59.720 52.381 0.00 0.00 0.00 2.45
856 871 0.686789 CAGTGGGGTGTGTCTGATGA 59.313 55.000 0.00 0.00 0.00 2.92
857 872 0.686789 TCAGTGGGGTGTGTCTGATG 59.313 55.000 0.00 0.00 32.95 3.07
859 874 1.140852 CTTTCAGTGGGGTGTGTCTGA 59.859 52.381 0.00 0.00 35.54 3.27
860 875 1.134098 ACTTTCAGTGGGGTGTGTCTG 60.134 52.381 0.00 0.00 0.00 3.51
861 876 1.134098 CACTTTCAGTGGGGTGTGTCT 60.134 52.381 0.00 0.00 42.35 3.41
862 877 1.134220 TCACTTTCAGTGGGGTGTGTC 60.134 52.381 4.09 0.00 45.94 3.67
863 878 0.916086 TCACTTTCAGTGGGGTGTGT 59.084 50.000 4.09 0.00 45.94 3.72
865 880 1.843851 TCTTCACTTTCAGTGGGGTGT 59.156 47.619 4.09 0.00 45.94 4.16
866 881 2.498167 CTCTTCACTTTCAGTGGGGTG 58.502 52.381 4.09 0.00 45.94 4.61
867 882 1.202818 GCTCTTCACTTTCAGTGGGGT 60.203 52.381 4.09 0.00 45.94 4.95
868 883 1.528129 GCTCTTCACTTTCAGTGGGG 58.472 55.000 4.09 0.00 45.94 4.96
869 884 1.528129 GGCTCTTCACTTTCAGTGGG 58.472 55.000 4.09 0.00 45.94 4.61
876 901 2.303311 GAGGTAGTGGGCTCTTCACTTT 59.697 50.000 1.99 0.00 42.17 2.66
895 920 3.815809 TGGGTGTTGTAGTCTTTTGGAG 58.184 45.455 0.00 0.00 0.00 3.86
906 931 0.188587 TTGGGCCATTGGGTGTTGTA 59.811 50.000 7.26 0.00 36.17 2.41
946 983 0.254178 ATGAATCAGGCTCTTGGCGT 59.746 50.000 0.00 0.00 44.18 5.68
1183 1221 3.702048 CGGCCGGAAGTGGAAGGA 61.702 66.667 20.10 0.00 0.00 3.36
1537 1575 2.413142 GGAAGACGGGGTCGACGAT 61.413 63.158 9.92 0.00 37.67 3.73
1584 1622 2.962421 GGTTAGGTAGAGCTGCATCTCT 59.038 50.000 22.65 22.65 44.88 3.10
1766 1812 3.133901 TGGAGCCGCAGAATATTCTTGTA 59.866 43.478 15.49 0.00 34.74 2.41
1776 1822 1.209261 TGATAATGTGGAGCCGCAGAA 59.791 47.619 8.87 0.00 39.95 3.02
1797 1843 8.108782 GCTAGAACGTAGTATCAATTTGTTGTC 58.891 37.037 0.00 0.00 45.00 3.18
1816 1862 4.997395 TGTCTTTCACATTCCTGCTAGAAC 59.003 41.667 0.00 0.00 0.00 3.01
1845 1891 3.566523 GATGCGAACTATCTTACCCTCG 58.433 50.000 0.00 0.00 0.00 4.63
1850 1897 4.054780 TGTGGGATGCGAACTATCTTAC 57.945 45.455 0.00 0.00 0.00 2.34
1859 1906 2.163412 GCTATGTTTTGTGGGATGCGAA 59.837 45.455 0.00 0.00 0.00 4.70
1912 1961 7.495606 TGTGCAGTGTAATCTTATTAGGACATG 59.504 37.037 0.00 0.00 0.00 3.21
1953 2002 3.248602 GCGACACTCAACTGAGAAACAAT 59.751 43.478 13.61 0.00 44.74 2.71
2090 2139 2.032681 GTCCCGAGCAAAGGCACT 59.967 61.111 0.00 0.00 44.61 4.40
2218 2268 2.125766 AACCGTCCTCTTTCCCCAGC 62.126 60.000 0.00 0.00 0.00 4.85
2434 2484 4.054671 CCCATCTAATCTCGACTTGCTTC 58.945 47.826 0.00 0.00 0.00 3.86
2464 2514 9.230122 TCAACATGACTGCTTATTCAATAAGAA 57.770 29.630 19.66 9.35 43.85 2.52
2536 2586 1.129998 CTGAAGAGCAAGCATCCAACG 59.870 52.381 0.00 0.00 0.00 4.10


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

AutoCloner maintained by Alex Coulton.