Multiple sequence alignment - TraesCS5A01G294700

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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 TraesCS5A01G294700 chr5A 100.000 6067 0 0 1 6067 503522880 503528946 0.000000e+00 11204.0
1 TraesCS5A01G294700 chr5D 96.403 3086 84 11 2955 6015 398532890 398535973 0.000000e+00 5059.0
2 TraesCS5A01G294700 chr5D 90.020 3066 178 53 1 2955 398529809 398532857 0.000000e+00 3849.0
3 TraesCS5A01G294700 chr5D 90.643 171 9 4 5900 6065 398535901 398536069 2.850000e-53 220.0
4 TraesCS5A01G294700 chr5D 87.838 74 7 2 5942 6015 398535859 398535930 1.080000e-12 86.1
5 TraesCS5A01G294700 chr5B 96.199 3052 70 14 2955 5972 478484430 478487469 0.000000e+00 4951.0
6 TraesCS5A01G294700 chr5B 87.911 2614 193 52 417 2955 478481832 478484397 0.000000e+00 2963.0
7 TraesCS5A01G294700 chr5B 100.000 93 0 0 5973 6065 478487427 478487519 8.080000e-39 172.0
8 TraesCS5A01G294700 chr6A 87.071 2096 198 37 3071 5145 571853481 571851438 0.000000e+00 2302.0
9 TraesCS5A01G294700 chr6A 81.808 907 109 37 1597 2496 571854833 571853976 0.000000e+00 710.0
10 TraesCS5A01G294700 chr6A 78.218 303 29 19 916 1210 571855480 571855207 6.290000e-35 159.0
11 TraesCS5A01G294700 chr6B 88.418 967 75 21 4152 5105 642976059 642975117 0.000000e+00 1131.0
12 TraesCS5A01G294700 chr6B 80.617 908 106 38 1597 2496 642980985 642980140 6.630000e-179 638.0
13 TraesCS5A01G294700 chr6D 86.216 798 71 19 4316 5105 427130378 427129612 0.000000e+00 828.0
14 TraesCS5A01G294700 chr6D 81.547 905 124 27 1597 2496 427156290 427155424 0.000000e+00 706.0
15 TraesCS5A01G294700 chr6D 87.692 585 58 7 3230 3813 427144418 427143847 0.000000e+00 669.0
16 TraesCS5A01G294700 chr6D 92.457 464 35 0 3857 4320 427143843 427143380 0.000000e+00 664.0
17 TraesCS5A01G294700 chr6D 77.389 314 26 24 916 1210 427156936 427156649 1.760000e-30 145.0
18 TraesCS5A01G294700 chr3D 95.652 115 4 1 2955 3069 426451970 426451857 3.730000e-42 183.0
19 TraesCS5A01G294700 chr3D 94.690 113 5 1 2955 3067 71517789 71517678 2.250000e-39 174.0
20 TraesCS5A01G294700 chr3B 95.536 112 4 1 2955 3066 42630929 42630819 1.740000e-40 178.0
21 TraesCS5A01G294700 chr3B 93.750 112 6 1 2955 3066 556089645 556089755 3.760000e-37 167.0
22 TraesCS5A01G294700 chr3A 94.643 112 5 1 2955 3066 34532560 34532450 8.080000e-39 172.0
23 TraesCS5A01G294700 chr3A 94.643 112 5 1 2955 3066 83748132 83748022 8.080000e-39 172.0
24 TraesCS5A01G294700 chr3A 93.043 115 5 3 2955 3069 562286795 562286684 1.350000e-36 165.0
25 TraesCS5A01G294700 chr4D 83.217 143 19 5 996 1135 1639515 1639375 6.380000e-25 126.0
26 TraesCS5A01G294700 chr4B 93.220 59 2 2 594 651 643147729 643147786 1.080000e-12 86.1
27 TraesCS5A01G294700 chr4B 100.000 36 0 0 985 1020 551239153 551239188 3.920000e-07 67.6


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 TraesCS5A01G294700 chr5A 503522880 503528946 6066 False 11204.000000 11204 100.000000 1 6067 1 chr5A.!!$F1 6066
1 TraesCS5A01G294700 chr5D 398529809 398536069 6260 False 2303.525000 5059 91.226000 1 6065 4 chr5D.!!$F1 6064
2 TraesCS5A01G294700 chr5B 478481832 478487519 5687 False 2695.333333 4951 94.703333 417 6065 3 chr5B.!!$F1 5648
3 TraesCS5A01G294700 chr6A 571851438 571855480 4042 True 1057.000000 2302 82.365667 916 5145 3 chr6A.!!$R1 4229
4 TraesCS5A01G294700 chr6B 642975117 642976059 942 True 1131.000000 1131 88.418000 4152 5105 1 chr6B.!!$R1 953
5 TraesCS5A01G294700 chr6B 642980140 642980985 845 True 638.000000 638 80.617000 1597 2496 1 chr6B.!!$R2 899
6 TraesCS5A01G294700 chr6D 427129612 427130378 766 True 828.000000 828 86.216000 4316 5105 1 chr6D.!!$R1 789
7 TraesCS5A01G294700 chr6D 427143380 427144418 1038 True 666.500000 669 90.074500 3230 4320 2 chr6D.!!$R2 1090
8 TraesCS5A01G294700 chr6D 427155424 427156936 1512 True 425.500000 706 79.468000 916 2496 2 chr6D.!!$R3 1580

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
594 670 0.039708 GAGAAAGGCAAGCACAGCAC 60.040 55.000 0.00 0.00 0.00 4.40 F
1144 1310 0.606673 GCACAAGTTCCCCAGAGACC 60.607 60.000 0.00 0.00 0.00 3.85 F
1939 2276 1.069668 AGCTCATCACTGCGCATCATA 59.930 47.619 12.24 0.00 35.52 2.15 F
2085 2424 1.423450 CGATTGTTCGCGAATGCCA 59.577 52.632 26.23 15.65 38.75 4.92 F
3743 4243 1.136891 CCACAGTCACAGTCACAGTCA 59.863 52.381 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 2276 1.064906 CCCCATGACAAGAGCAGTGAT 60.065 52.381 0.00 0.00 0.00 3.06 R
2931 3386 0.183492 TGTGCCATGCCTATCCTTCC 59.817 55.000 0.00 0.00 0.00 3.46 R
2943 3398 1.134401 CATCGAACCCTACTGTGCCAT 60.134 52.381 0.00 0.00 0.00 4.40 R
3995 4495 1.888512 GAATTGTCCTTGCAAGCCAGA 59.111 47.619 21.43 10.27 0.00 3.86 R
5739 6274 0.605083 TTGGCAACTTTGTGCACACA 59.395 45.000 21.56 13.06 46.81 3.72 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
32 33 4.738124 TGAGAGTTAGAGTCAAATCAGCG 58.262 43.478 0.00 0.00 0.00 5.18
40 41 1.002624 TCAAATCAGCGTGGTCCCC 60.003 57.895 0.00 0.00 0.00 4.81
44 45 0.178975 AATCAGCGTGGTCCCCAAAA 60.179 50.000 0.00 0.00 34.18 2.44
72 73 9.539825 AACTACAGTAAATGAGCAATCAGATAG 57.460 33.333 0.00 0.00 0.00 2.08
89 90 2.130272 TAGATCAGAGCACAGACGGT 57.870 50.000 0.00 0.00 0.00 4.83
131 132 4.209080 TCATGAATTAGCTATGCACGTTCG 59.791 41.667 0.00 0.00 0.00 3.95
144 145 2.222596 GCACGTTCGATTCTTACTGCAG 60.223 50.000 13.48 13.48 0.00 4.41
156 157 2.245159 TACTGCAGATACAGGCATGC 57.755 50.000 23.35 9.90 42.21 4.06
175 202 5.694910 GCATGCCATTTTTCAGGAGATAATG 59.305 40.000 6.36 0.00 0.00 1.90
176 203 6.461927 GCATGCCATTTTTCAGGAGATAATGA 60.462 38.462 6.36 0.00 32.32 2.57
178 205 5.068198 TGCCATTTTTCAGGAGATAATGAGC 59.932 40.000 0.00 0.00 32.32 4.26
182 209 6.500684 TTTTTCAGGAGATAATGAGCACAC 57.499 37.500 0.00 0.00 0.00 3.82
198 225 6.956047 TGAGCACACTATTATCTGTACTACG 58.044 40.000 0.00 0.00 0.00 3.51
199 226 6.541278 TGAGCACACTATTATCTGTACTACGT 59.459 38.462 0.00 0.00 0.00 3.57
200 227 6.957150 AGCACACTATTATCTGTACTACGTC 58.043 40.000 0.00 0.00 0.00 4.34
210 237 1.171308 GTACTACGTCTGCCAGGTCA 58.829 55.000 0.00 0.00 0.00 4.02
220 247 2.328099 GCCAGGTCAGCGGAAACTG 61.328 63.158 11.26 11.26 39.12 3.16
222 249 2.357517 AGGTCAGCGGAAACTGCG 60.358 61.111 0.00 0.00 37.59 5.18
243 270 4.037690 CGTAGGCAAAATCATTTAGCTGC 58.962 43.478 0.00 0.00 0.00 5.25
247 274 4.110482 GGCAAAATCATTTAGCTGCTCTG 58.890 43.478 4.91 2.80 0.00 3.35
251 278 5.814764 AAATCATTTAGCTGCTCTGACTG 57.185 39.130 4.91 0.00 0.00 3.51
278 308 4.278310 ACAATTTAGCCCCAATCCACTAC 58.722 43.478 0.00 0.00 0.00 2.73
288 318 3.195661 CCAATCCACTACCGCTAACTTC 58.804 50.000 0.00 0.00 0.00 3.01
289 319 3.369052 CCAATCCACTACCGCTAACTTCA 60.369 47.826 0.00 0.00 0.00 3.02
290 320 4.250464 CAATCCACTACCGCTAACTTCAA 58.750 43.478 0.00 0.00 0.00 2.69
292 322 3.921677 TCCACTACCGCTAACTTCAAAG 58.078 45.455 0.00 0.00 0.00 2.77
293 323 3.322828 TCCACTACCGCTAACTTCAAAGT 59.677 43.478 0.00 0.00 42.04 2.66
294 324 4.523943 TCCACTACCGCTAACTTCAAAGTA 59.476 41.667 0.00 0.00 38.57 2.24
298 328 5.930569 ACTACCGCTAACTTCAAAGTAAAGG 59.069 40.000 0.00 1.39 38.57 3.11
299 329 4.711399 ACCGCTAACTTCAAAGTAAAGGT 58.289 39.130 0.00 1.95 38.57 3.50
300 330 4.514066 ACCGCTAACTTCAAAGTAAAGGTG 59.486 41.667 9.78 3.06 38.57 4.00
301 331 4.514066 CCGCTAACTTCAAAGTAAAGGTGT 59.486 41.667 0.00 0.00 38.57 4.16
302 332 5.697633 CCGCTAACTTCAAAGTAAAGGTGTA 59.302 40.000 0.00 0.00 38.57 2.90
303 333 6.370718 CCGCTAACTTCAAAGTAAAGGTGTAT 59.629 38.462 0.00 0.00 38.57 2.29
304 334 7.412672 CCGCTAACTTCAAAGTAAAGGTGTATC 60.413 40.741 0.00 0.00 38.57 2.24
305 335 7.453838 GCTAACTTCAAAGTAAAGGTGTATCG 58.546 38.462 0.00 0.00 38.57 2.92
306 336 5.857822 ACTTCAAAGTAAAGGTGTATCGC 57.142 39.130 0.00 0.00 37.52 4.58
310 340 6.476243 TCAAAGTAAAGGTGTATCGCTTTC 57.524 37.500 0.00 0.00 0.00 2.62
311 341 5.992829 TCAAAGTAAAGGTGTATCGCTTTCA 59.007 36.000 0.00 0.00 0.00 2.69
312 342 5.857822 AAGTAAAGGTGTATCGCTTTCAC 57.142 39.130 0.00 0.00 0.00 3.18
313 343 4.890088 AGTAAAGGTGTATCGCTTTCACA 58.110 39.130 0.00 0.00 34.27 3.58
314 344 5.488341 AGTAAAGGTGTATCGCTTTCACAT 58.512 37.500 0.00 0.00 34.27 3.21
315 345 5.938125 AGTAAAGGTGTATCGCTTTCACATT 59.062 36.000 0.00 0.00 37.62 2.71
316 346 4.946784 AAGGTGTATCGCTTTCACATTC 57.053 40.909 0.00 0.00 32.06 2.67
317 347 3.270877 AGGTGTATCGCTTTCACATTCC 58.729 45.455 0.00 0.00 34.27 3.01
318 348 2.354821 GGTGTATCGCTTTCACATTCCC 59.645 50.000 0.00 0.00 34.27 3.97
319 349 3.006940 GTGTATCGCTTTCACATTCCCA 58.993 45.455 0.00 0.00 33.04 4.37
323 372 2.302260 TCGCTTTCACATTCCCAAACA 58.698 42.857 0.00 0.00 0.00 2.83
332 381 2.959707 ACATTCCCAAACAAACGGCTTA 59.040 40.909 0.00 0.00 0.00 3.09
336 385 2.359531 TCCCAAACAAACGGCTTACAAG 59.640 45.455 0.00 0.00 0.00 3.16
338 387 3.368495 CCAAACAAACGGCTTACAAGAC 58.632 45.455 0.00 0.00 0.00 3.01
340 389 3.963383 AACAAACGGCTTACAAGACAG 57.037 42.857 0.00 0.00 31.90 3.51
348 397 3.206964 GGCTTACAAGACAGGATTAGGC 58.793 50.000 0.00 0.00 32.98 3.93
350 399 3.873952 GCTTACAAGACAGGATTAGGCAG 59.126 47.826 0.00 0.00 0.00 4.85
365 414 2.989196 GCAGTTGCATGCCAAACAA 58.011 47.368 16.68 0.00 40.43 2.83
369 418 1.209019 AGTTGCATGCCAAACAACCAA 59.791 42.857 16.68 0.00 43.68 3.67
377 426 2.224402 TGCCAAACAACCAATTAAGGGC 60.224 45.455 0.00 0.00 39.29 5.19
383 432 3.964411 ACAACCAATTAAGGGCCTACTC 58.036 45.455 6.41 0.00 0.00 2.59
384 433 3.288092 CAACCAATTAAGGGCCTACTCC 58.712 50.000 6.41 0.00 0.00 3.85
385 434 2.859951 ACCAATTAAGGGCCTACTCCT 58.140 47.619 6.41 0.00 35.88 3.69
386 435 2.778270 ACCAATTAAGGGCCTACTCCTC 59.222 50.000 6.41 0.00 32.59 3.71
387 436 2.106684 CCAATTAAGGGCCTACTCCTCC 59.893 54.545 6.41 0.00 32.59 4.30
413 462 9.308000 CAAGATACCTATCTATCTTCCTTGAGT 57.692 37.037 0.00 0.00 41.96 3.41
439 488 0.252375 AGAACATGGGCTGGGCATTT 60.252 50.000 0.00 0.00 0.00 2.32
480 529 1.151668 CCAGAAGCTGACCACGAAAG 58.848 55.000 0.00 0.00 32.44 2.62
505 559 1.756538 GGAGAGGAGCAGAGAAGAAGG 59.243 57.143 0.00 0.00 0.00 3.46
521 575 1.760029 GAAGGCTTACAGAGGAGGGAG 59.240 57.143 0.00 0.00 0.00 4.30
523 577 0.325765 GGCTTACAGAGGAGGGAGGT 60.326 60.000 0.00 0.00 0.00 3.85
524 578 0.827368 GCTTACAGAGGAGGGAGGTG 59.173 60.000 0.00 0.00 0.00 4.00
525 579 1.619977 GCTTACAGAGGAGGGAGGTGA 60.620 57.143 0.00 0.00 0.00 4.02
528 582 0.489567 ACAGAGGAGGGAGGTGAAGT 59.510 55.000 0.00 0.00 0.00 3.01
530 584 0.787084 AGAGGAGGGAGGTGAAGTGA 59.213 55.000 0.00 0.00 0.00 3.41
541 617 1.620819 GGTGAAGTGAAGCAGAGAGGA 59.379 52.381 0.00 0.00 0.00 3.71
548 624 3.257127 AGTGAAGCAGAGAGGACTTGTAC 59.743 47.826 0.00 0.00 0.00 2.90
549 625 3.257127 GTGAAGCAGAGAGGACTTGTACT 59.743 47.826 0.00 0.00 0.00 2.73
550 626 4.459685 GTGAAGCAGAGAGGACTTGTACTA 59.540 45.833 0.00 0.00 0.00 1.82
551 627 4.702612 TGAAGCAGAGAGGACTTGTACTAG 59.297 45.833 2.56 2.56 0.00 2.57
552 628 4.310022 AGCAGAGAGGACTTGTACTAGT 57.690 45.455 9.83 9.83 0.00 2.57
553 629 4.266714 AGCAGAGAGGACTTGTACTAGTC 58.733 47.826 23.99 23.99 43.05 2.59
554 630 4.011023 GCAGAGAGGACTTGTACTAGTCA 58.989 47.826 29.93 0.00 45.07 3.41
555 631 4.142556 GCAGAGAGGACTTGTACTAGTCAC 60.143 50.000 29.93 23.66 45.07 3.67
556 632 5.250200 CAGAGAGGACTTGTACTAGTCACT 58.750 45.833 29.93 26.67 45.07 3.41
569 645 5.230323 ACTAGTCACTAGTCAGTCAGTCA 57.770 43.478 12.06 0.00 42.87 3.41
590 666 1.202915 TCCATGAGAAAGGCAAGCACA 60.203 47.619 0.00 0.00 0.00 4.57
592 668 0.886563 ATGAGAAAGGCAAGCACAGC 59.113 50.000 0.00 0.00 0.00 4.40
593 669 0.466007 TGAGAAAGGCAAGCACAGCA 60.466 50.000 0.00 0.00 0.00 4.41
594 670 0.039708 GAGAAAGGCAAGCACAGCAC 60.040 55.000 0.00 0.00 0.00 4.40
598 674 3.292936 GGCAAGCACAGCACAGCT 61.293 61.111 0.00 0.00 44.31 4.24
599 675 1.968017 GGCAAGCACAGCACAGCTA 60.968 57.895 0.00 0.00 40.90 3.32
601 677 1.500844 CAAGCACAGCACAGCTAGC 59.499 57.895 6.62 6.62 40.90 3.42
602 678 0.954449 CAAGCACAGCACAGCTAGCT 60.954 55.000 12.68 12.68 46.09 3.32
603 679 0.673022 AAGCACAGCACAGCTAGCTC 60.673 55.000 16.15 3.70 44.37 4.09
679 774 5.030295 GCAAATAAATCACCATCAGTCACG 58.970 41.667 0.00 0.00 0.00 4.35
693 831 6.367695 CCATCAGTCACGTCAATACAAAACTA 59.632 38.462 0.00 0.00 0.00 2.24
694 832 7.411912 CCATCAGTCACGTCAATACAAAACTAG 60.412 40.741 0.00 0.00 0.00 2.57
696 834 7.204604 TCAGTCACGTCAATACAAAACTAGAA 58.795 34.615 0.00 0.00 0.00 2.10
715 853 8.100508 ACTAGAAAACAGATTAAACAAGGAGC 57.899 34.615 0.00 0.00 0.00 4.70
716 854 6.959639 AGAAAACAGATTAAACAAGGAGCA 57.040 33.333 0.00 0.00 0.00 4.26
717 855 7.346751 AGAAAACAGATTAAACAAGGAGCAA 57.653 32.000 0.00 0.00 0.00 3.91
718 856 7.203218 AGAAAACAGATTAAACAAGGAGCAAC 58.797 34.615 0.00 0.00 0.00 4.17
719 857 5.453567 AACAGATTAAACAAGGAGCAACC 57.546 39.130 0.00 0.00 39.35 3.77
720 858 4.469657 ACAGATTAAACAAGGAGCAACCA 58.530 39.130 2.96 0.00 42.04 3.67
721 859 4.892934 ACAGATTAAACAAGGAGCAACCAA 59.107 37.500 2.96 0.00 42.04 3.67
722 860 5.539955 ACAGATTAAACAAGGAGCAACCAAT 59.460 36.000 2.96 0.00 42.04 3.16
723 861 6.719370 ACAGATTAAACAAGGAGCAACCAATA 59.281 34.615 2.96 0.00 42.04 1.90
724 862 7.029563 CAGATTAAACAAGGAGCAACCAATAC 58.970 38.462 2.96 0.00 42.04 1.89
725 863 6.719370 AGATTAAACAAGGAGCAACCAATACA 59.281 34.615 2.96 0.00 42.04 2.29
726 864 6.716934 TTAAACAAGGAGCAACCAATACAA 57.283 33.333 2.96 0.00 42.04 2.41
727 865 5.806654 AAACAAGGAGCAACCAATACAAT 57.193 34.783 2.96 0.00 42.04 2.71
728 866 6.909550 AAACAAGGAGCAACCAATACAATA 57.090 33.333 2.96 0.00 42.04 1.90
729 867 5.897377 ACAAGGAGCAACCAATACAATAC 57.103 39.130 2.96 0.00 42.04 1.89
730 868 5.321102 ACAAGGAGCAACCAATACAATACA 58.679 37.500 2.96 0.00 42.04 2.29
731 869 5.772672 ACAAGGAGCAACCAATACAATACAA 59.227 36.000 2.96 0.00 42.04 2.41
732 870 6.266558 ACAAGGAGCAACCAATACAATACAAA 59.733 34.615 2.96 0.00 42.04 2.83
733 871 6.909550 AGGAGCAACCAATACAATACAAAA 57.090 33.333 2.96 0.00 42.04 2.44
734 872 6.687604 AGGAGCAACCAATACAATACAAAAC 58.312 36.000 2.96 0.00 42.04 2.43
735 873 6.493458 AGGAGCAACCAATACAATACAAAACT 59.507 34.615 2.96 0.00 42.04 2.66
736 874 7.668052 AGGAGCAACCAATACAATACAAAACTA 59.332 33.333 2.96 0.00 42.04 2.24
737 875 7.753580 GGAGCAACCAATACAATACAAAACTAC 59.246 37.037 0.00 0.00 38.79 2.73
738 876 8.404107 AGCAACCAATACAATACAAAACTACT 57.596 30.769 0.00 0.00 0.00 2.57
739 877 8.512138 AGCAACCAATACAATACAAAACTACTC 58.488 33.333 0.00 0.00 0.00 2.59
740 878 7.753580 GCAACCAATACAATACAAAACTACTCC 59.246 37.037 0.00 0.00 0.00 3.85
741 879 9.010029 CAACCAATACAATACAAAACTACTCCT 57.990 33.333 0.00 0.00 0.00 3.69
743 881 9.662947 ACCAATACAATACAAAACTACTCCTAC 57.337 33.333 0.00 0.00 0.00 3.18
744 882 9.661563 CCAATACAATACAAAACTACTCCTACA 57.338 33.333 0.00 0.00 0.00 2.74
749 887 9.398538 ACAATACAAAACTACTCCTACAAAACA 57.601 29.630 0.00 0.00 0.00 2.83
792 930 4.962836 GCCTGGCAGCAGGTGTGT 62.963 66.667 15.17 0.00 44.07 3.72
804 952 1.066858 CAGGTGTGTGTACTGGCCTAG 60.067 57.143 3.32 2.01 0.00 3.02
863 1011 8.573035 GTCGGAGAAAGATGAGAGAATTACTAT 58.427 37.037 0.00 0.00 39.69 2.12
864 1012 9.794719 TCGGAGAAAGATGAGAGAATTACTATA 57.205 33.333 0.00 0.00 0.00 1.31
884 1032 8.958060 ACTATAGTATAGAATGGTGTGGATGT 57.042 34.615 21.59 0.00 0.00 3.06
911 1059 6.886459 AGAAGCAAGTATAAAAATGCAGAGGA 59.114 34.615 0.00 0.00 41.18 3.71
912 1060 6.690194 AGCAAGTATAAAAATGCAGAGGAG 57.310 37.500 0.00 0.00 41.18 3.69
913 1061 5.067023 AGCAAGTATAAAAATGCAGAGGAGC 59.933 40.000 0.00 0.00 41.18 4.70
914 1062 5.067023 GCAAGTATAAAAATGCAGAGGAGCT 59.933 40.000 0.00 0.00 38.63 4.09
958 1106 2.034687 GCTGGCCTGGCTGAGAAA 59.965 61.111 19.68 0.00 0.00 2.52
1144 1310 0.606673 GCACAAGTTCCCCAGAGACC 60.607 60.000 0.00 0.00 0.00 3.85
1147 1313 1.133809 CAAGTTCCCCAGAGACCCCA 61.134 60.000 0.00 0.00 0.00 4.96
1148 1314 1.134438 AAGTTCCCCAGAGACCCCAC 61.134 60.000 0.00 0.00 0.00 4.61
1332 1503 7.172875 TGCAACAAAATCATTAAATCAACCTGG 59.827 33.333 0.00 0.00 0.00 4.45
1350 1521 1.173913 GGTGATTTTTGGTCCCTCCG 58.826 55.000 0.00 0.00 39.52 4.63
1372 1543 8.251750 TCCGTTTCTTTCTGTAAATCATACTG 57.748 34.615 0.00 0.00 0.00 2.74
1554 1828 8.176365 GTGATGATCAATCAAAGTCTTCTCTTG 58.824 37.037 0.00 0.00 46.90 3.02
1616 1943 7.439655 GGAGAGTAGTAAACTATGGATGCAAAG 59.560 40.741 0.00 0.00 39.07 2.77
1629 1956 4.096231 TGGATGCAAAGATTTATGTGTCCG 59.904 41.667 0.00 0.00 0.00 4.79
1722 2049 3.944015 AGATGGAGCTACAAACAATCAGC 59.056 43.478 0.66 0.00 0.00 4.26
1723 2050 3.138884 TGGAGCTACAAACAATCAGCA 57.861 42.857 0.00 0.00 36.47 4.41
1939 2276 1.069668 AGCTCATCACTGCGCATCATA 59.930 47.619 12.24 0.00 35.52 2.15
1981 2318 2.877168 GCAGCAGCTGATAAGCATTACT 59.123 45.455 27.39 0.00 37.91 2.24
2012 2349 3.788227 ATGTGGGCAAACTTCTGACTA 57.212 42.857 0.00 0.00 0.00 2.59
2026 2363 7.067496 ACTTCTGACTAATCCTTTCAGAACA 57.933 36.000 8.78 0.00 46.55 3.18
2085 2424 1.423450 CGATTGTTCGCGAATGCCA 59.577 52.632 26.23 15.65 38.75 4.92
2187 2526 2.743928 GTGGAACAGCGGGCAGAG 60.744 66.667 0.00 0.00 41.80 3.35
2285 2639 8.345565 GCGGATAATCTTCACTTTTGTTCATAT 58.654 33.333 0.00 0.00 0.00 1.78
2356 2712 3.766591 CTCCCTCTCTGCTTTCTCTACAA 59.233 47.826 0.00 0.00 0.00 2.41
2881 3335 6.815142 CAGGATTTATTTGAGGCTTTCCAAAG 59.185 38.462 6.11 0.00 35.97 2.77
2931 3386 8.748380 TTTCAGTAATATCGAGTATGCTGATG 57.252 34.615 13.01 0.00 36.44 3.07
2943 3398 1.510492 TGCTGATGGAAGGATAGGCA 58.490 50.000 0.00 0.00 0.00 4.75
3018 3506 2.084546 GCTTGCCTCGTACAATCCTTT 58.915 47.619 0.00 0.00 0.00 3.11
3087 3575 9.734984 TCCTTATCGAGTATACTGATGTTGATA 57.265 33.333 10.90 2.81 0.00 2.15
3143 3631 6.058827 GAGCATTATTTGGAAGAAGCTCTC 57.941 41.667 0.00 0.00 42.77 3.20
3247 3747 5.316327 GCTGCCAGCTAATTTTTCTAACT 57.684 39.130 10.04 0.00 38.45 2.24
3620 4120 3.642848 AGGATGCAACCAACAACTTTGAT 59.357 39.130 16.21 0.00 0.00 2.57
3743 4243 1.136891 CCACAGTCACAGTCACAGTCA 59.863 52.381 0.00 0.00 0.00 3.41
3835 4335 7.872483 ACTGGTATTTTGCTGGTTCAAATAAAG 59.128 33.333 0.00 0.00 36.04 1.85
3995 4495 0.620556 ATGGAAGCTTGGATGACCGT 59.379 50.000 2.10 0.00 39.42 4.83
4145 4645 6.311445 TGAAAGCATCGAACATTCTTCTAGAC 59.689 38.462 0.00 0.00 0.00 2.59
4220 4720 0.182775 AGTTCAGGGACACAACCACC 59.817 55.000 0.00 0.00 0.00 4.61
4523 5023 1.523758 ATCGTCCAGACCTGCAAAAC 58.476 50.000 0.00 0.00 0.00 2.43
4765 5270 9.241317 CTAAGCATGTTTGATTAGCCTTAAATG 57.759 33.333 4.89 0.00 42.85 2.32
5362 5878 2.485426 CACTGCTTGATCAACAATCGGT 59.515 45.455 3.38 2.87 42.54 4.69
5443 5975 7.041372 ACAGTTCAAATGTCGCTAATTACAACT 60.041 33.333 0.00 0.00 0.00 3.16
5510 6044 4.292306 AGTCTAATTCCCATCCAACCTGTT 59.708 41.667 0.00 0.00 0.00 3.16
5525 6059 7.685481 TCCAACCTGTTTATTCTGAATGTCTA 58.315 34.615 13.01 0.00 0.00 2.59
5561 6095 7.831193 ACAATAACTGCTCAGAAGGTAAATGAT 59.169 33.333 3.60 0.00 0.00 2.45
5570 6104 7.519649 GCTCAGAAGGTAAATGATGTAGCAATC 60.520 40.741 0.00 0.00 0.00 2.67
5610 6144 1.202651 AGTACGCCTGCTTCTGTTGTT 60.203 47.619 0.00 0.00 0.00 2.83
6065 6654 8.904099 ACCAAGTGCCAAGTATCTAATTATAC 57.096 34.615 0.00 0.00 33.33 1.47
6066 6655 8.491134 ACCAAGTGCCAAGTATCTAATTATACA 58.509 33.333 2.10 0.00 35.23 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.489810 CACGCTGATTTGACTCTAACTCT 58.510 43.478 0.00 0.00 0.00 3.24
19 20 1.079503 GGACCACGCTGATTTGACTC 58.920 55.000 0.00 0.00 0.00 3.36
21 22 2.171635 GGGACCACGCTGATTTGAC 58.828 57.895 0.00 0.00 0.00 3.18
44 45 8.621532 TCTGATTGCTCATTTACTGTAGTTTT 57.378 30.769 0.00 0.00 0.00 2.43
47 48 8.918116 TCTATCTGATTGCTCATTTACTGTAGT 58.082 33.333 0.00 0.00 0.00 2.73
48 49 9.926158 ATCTATCTGATTGCTCATTTACTGTAG 57.074 33.333 0.00 0.00 29.59 2.74
72 73 2.086054 AAACCGTCTGTGCTCTGATC 57.914 50.000 0.00 0.00 0.00 2.92
108 109 4.209080 CGAACGTGCATAGCTAATTCATGA 59.791 41.667 15.13 0.00 0.00 3.07
112 113 4.974103 ATCGAACGTGCATAGCTAATTC 57.026 40.909 0.00 0.00 0.00 2.17
131 132 4.697514 TGCCTGTATCTGCAGTAAGAATC 58.302 43.478 14.67 0.72 34.84 2.52
144 145 4.365723 CTGAAAAATGGCATGCCTGTATC 58.634 43.478 35.53 25.06 36.94 2.24
156 157 6.095860 TGTGCTCATTATCTCCTGAAAAATGG 59.904 38.462 0.00 0.00 33.80 3.16
175 202 6.957150 ACGTAGTACAGATAATAGTGTGCTC 58.043 40.000 0.38 0.00 41.94 4.26
176 203 6.939132 ACGTAGTACAGATAATAGTGTGCT 57.061 37.500 0.38 0.00 41.94 4.40
198 225 2.731691 TTTCCGCTGACCTGGCAGAC 62.732 60.000 17.94 10.29 38.14 3.51
199 226 2.515979 TTTCCGCTGACCTGGCAGA 61.516 57.895 17.94 0.00 38.14 4.26
200 227 2.032528 TTTCCGCTGACCTGGCAG 59.967 61.111 7.75 7.75 38.91 4.85
210 237 2.434359 GCCTACGCAGTTTCCGCT 60.434 61.111 0.00 0.00 37.78 5.52
220 247 4.037690 CAGCTAAATGATTTTGCCTACGC 58.962 43.478 18.10 1.81 41.31 4.42
222 249 5.067023 AGAGCAGCTAAATGATTTTGCCTAC 59.933 40.000 18.10 9.75 41.31 3.18
231 258 4.440880 GTCAGTCAGAGCAGCTAAATGAT 58.559 43.478 0.00 0.00 0.00 2.45
243 270 5.112686 GGCTAAATTGTAGGTCAGTCAGAG 58.887 45.833 0.00 0.00 0.00 3.35
247 274 3.054655 TGGGGCTAAATTGTAGGTCAGTC 60.055 47.826 0.00 0.00 0.00 3.51
251 278 3.889538 GGATTGGGGCTAAATTGTAGGTC 59.110 47.826 0.00 0.00 0.00 3.85
278 308 4.514066 ACACCTTTACTTTGAAGTTAGCGG 59.486 41.667 1.20 1.31 40.37 5.52
288 318 6.077838 GTGAAAGCGATACACCTTTACTTTG 58.922 40.000 0.00 0.00 31.85 2.77
289 319 5.761234 TGTGAAAGCGATACACCTTTACTTT 59.239 36.000 8.09 0.00 31.85 2.66
290 320 5.302360 TGTGAAAGCGATACACCTTTACTT 58.698 37.500 8.09 0.00 31.85 2.24
292 322 5.796350 ATGTGAAAGCGATACACCTTTAC 57.204 39.130 8.09 0.00 31.85 2.01
293 323 5.353123 GGAATGTGAAAGCGATACACCTTTA 59.647 40.000 8.09 0.00 31.85 1.85
294 324 4.156008 GGAATGTGAAAGCGATACACCTTT 59.844 41.667 8.09 3.32 34.22 3.11
298 328 3.006940 TGGGAATGTGAAAGCGATACAC 58.993 45.455 4.38 4.38 35.45 2.90
299 329 3.342377 TGGGAATGTGAAAGCGATACA 57.658 42.857 0.00 0.00 0.00 2.29
300 330 4.083003 TGTTTGGGAATGTGAAAGCGATAC 60.083 41.667 0.00 0.00 0.00 2.24
301 331 4.075682 TGTTTGGGAATGTGAAAGCGATA 58.924 39.130 0.00 0.00 0.00 2.92
302 332 2.890311 TGTTTGGGAATGTGAAAGCGAT 59.110 40.909 0.00 0.00 0.00 4.58
303 333 2.302260 TGTTTGGGAATGTGAAAGCGA 58.698 42.857 0.00 0.00 0.00 4.93
304 334 2.791383 TGTTTGGGAATGTGAAAGCG 57.209 45.000 0.00 0.00 0.00 4.68
305 335 3.245048 CGTTTGTTTGGGAATGTGAAAGC 59.755 43.478 0.00 0.00 0.00 3.51
306 336 3.801594 CCGTTTGTTTGGGAATGTGAAAG 59.198 43.478 0.00 0.00 0.00 2.62
310 340 1.068434 AGCCGTTTGTTTGGGAATGTG 59.932 47.619 0.00 0.00 0.00 3.21
311 341 1.408969 AGCCGTTTGTTTGGGAATGT 58.591 45.000 0.00 0.00 0.00 2.71
312 342 2.524569 AAGCCGTTTGTTTGGGAATG 57.475 45.000 0.00 0.00 0.00 2.67
313 343 2.959707 TGTAAGCCGTTTGTTTGGGAAT 59.040 40.909 0.00 0.00 0.00 3.01
314 344 2.376109 TGTAAGCCGTTTGTTTGGGAA 58.624 42.857 0.00 0.00 0.00 3.97
315 345 2.054232 TGTAAGCCGTTTGTTTGGGA 57.946 45.000 0.00 0.00 0.00 4.37
316 346 2.359531 TCTTGTAAGCCGTTTGTTTGGG 59.640 45.455 0.00 0.00 0.00 4.12
317 347 3.181495 TGTCTTGTAAGCCGTTTGTTTGG 60.181 43.478 0.00 0.00 0.00 3.28
318 348 4.022464 TGTCTTGTAAGCCGTTTGTTTG 57.978 40.909 0.00 0.00 0.00 2.93
319 349 3.066203 CCTGTCTTGTAAGCCGTTTGTTT 59.934 43.478 0.00 0.00 0.00 2.83
323 372 2.922740 TCCTGTCTTGTAAGCCGTTT 57.077 45.000 0.00 0.00 0.00 3.60
332 381 3.679389 CAACTGCCTAATCCTGTCTTGT 58.321 45.455 0.00 0.00 0.00 3.16
336 385 2.113860 TGCAACTGCCTAATCCTGTC 57.886 50.000 0.00 0.00 41.18 3.51
338 387 1.066605 GCATGCAACTGCCTAATCCTG 59.933 52.381 14.21 0.00 41.18 3.86
340 389 3.953201 GCATGCAACTGCCTAATCC 57.047 52.632 14.21 0.00 41.18 3.01
348 397 1.219646 GGTTGTTTGGCATGCAACTG 58.780 50.000 21.36 0.00 41.36 3.16
350 399 1.661341 TTGGTTGTTTGGCATGCAAC 58.339 45.000 21.36 16.41 41.02 4.17
365 414 2.778270 GAGGAGTAGGCCCTTAATTGGT 59.222 50.000 0.00 0.00 33.36 3.67
369 418 2.889522 TGGAGGAGTAGGCCCTTAAT 57.110 50.000 0.00 0.00 33.36 1.40
377 426 6.147437 AGATAGGTATCTTGGAGGAGTAGG 57.853 45.833 0.00 0.00 39.96 3.18
383 432 7.418378 AGGAAGATAGATAGGTATCTTGGAGG 58.582 42.308 10.18 0.00 45.70 4.30
384 433 8.748412 CAAGGAAGATAGATAGGTATCTTGGAG 58.252 40.741 10.18 0.00 45.70 3.86
385 434 8.456940 TCAAGGAAGATAGATAGGTATCTTGGA 58.543 37.037 10.18 2.08 45.70 3.53
386 435 8.657387 TCAAGGAAGATAGATAGGTATCTTGG 57.343 38.462 10.18 0.20 45.70 3.61
387 436 9.308000 ACTCAAGGAAGATAGATAGGTATCTTG 57.692 37.037 10.18 0.00 45.70 3.02
413 462 0.674581 CAGCCCATGTTCTCGCTCAA 60.675 55.000 0.00 0.00 0.00 3.02
439 488 1.999071 GCGCACCACCTGTTTGTTCA 61.999 55.000 0.30 0.00 0.00 3.18
480 529 0.395586 TCTCTGCTCCTCTCCTCTGC 60.396 60.000 0.00 0.00 0.00 4.26
505 559 0.827368 CACCTCCCTCCTCTGTAAGC 59.173 60.000 0.00 0.00 0.00 3.09
521 575 1.620819 TCCTCTCTGCTTCACTTCACC 59.379 52.381 0.00 0.00 0.00 4.02
523 577 2.603021 AGTCCTCTCTGCTTCACTTCA 58.397 47.619 0.00 0.00 0.00 3.02
524 578 3.244044 ACAAGTCCTCTCTGCTTCACTTC 60.244 47.826 0.00 0.00 0.00 3.01
525 579 2.703007 ACAAGTCCTCTCTGCTTCACTT 59.297 45.455 0.00 0.00 0.00 3.16
528 582 3.501349 AGTACAAGTCCTCTCTGCTTCA 58.499 45.455 0.00 0.00 0.00 3.02
530 584 4.668636 ACTAGTACAAGTCCTCTCTGCTT 58.331 43.478 0.00 0.00 0.00 3.91
541 617 6.531923 TGACTGACTAGTGACTAGTACAAGT 58.468 40.000 23.95 23.93 45.90 3.16
548 624 5.295787 GGATGACTGACTGACTAGTGACTAG 59.704 48.000 17.61 17.61 39.72 2.57
549 625 5.186942 GGATGACTGACTGACTAGTGACTA 58.813 45.833 0.00 0.00 37.25 2.59
550 626 4.013728 GGATGACTGACTGACTAGTGACT 58.986 47.826 0.00 0.00 37.25 3.41
551 627 3.759086 TGGATGACTGACTGACTAGTGAC 59.241 47.826 0.00 0.00 37.25 3.67
552 628 4.034285 TGGATGACTGACTGACTAGTGA 57.966 45.455 0.00 0.00 37.25 3.41
553 629 4.400567 TCATGGATGACTGACTGACTAGTG 59.599 45.833 0.00 0.00 37.25 2.74
554 630 4.604156 TCATGGATGACTGACTGACTAGT 58.396 43.478 0.00 0.00 40.66 2.57
555 631 4.886489 TCTCATGGATGACTGACTGACTAG 59.114 45.833 0.00 0.00 32.50 2.57
556 632 4.860022 TCTCATGGATGACTGACTGACTA 58.140 43.478 0.00 0.00 32.50 2.59
569 645 2.097825 GTGCTTGCCTTTCTCATGGAT 58.902 47.619 0.00 0.00 0.00 3.41
590 666 2.583520 GCAGGAGCTAGCTGTGCT 59.416 61.111 29.37 14.90 44.24 4.40
592 668 0.814410 CATGGCAGGAGCTAGCTGTG 60.814 60.000 24.99 19.70 41.70 3.66
593 669 1.525923 CATGGCAGGAGCTAGCTGT 59.474 57.895 24.99 6.11 41.70 4.40
594 670 1.892862 GCATGGCAGGAGCTAGCTG 60.893 63.158 24.99 10.30 41.70 4.24
598 674 1.149854 CATGGCATGGCAGGAGCTA 59.850 57.895 27.79 1.36 41.70 3.32
599 675 2.123854 CATGGCATGGCAGGAGCT 60.124 61.111 27.79 7.33 41.70 4.09
660 755 5.084818 TGACGTGACTGATGGTGATTTAT 57.915 39.130 0.00 0.00 0.00 1.40
661 756 4.529109 TGACGTGACTGATGGTGATTTA 57.471 40.909 0.00 0.00 0.00 1.40
693 831 6.959639 TGCTCCTTGTTTAATCTGTTTTCT 57.040 33.333 0.00 0.00 0.00 2.52
694 832 6.420903 GGTTGCTCCTTGTTTAATCTGTTTTC 59.579 38.462 0.00 0.00 0.00 2.29
696 834 5.362430 TGGTTGCTCCTTGTTTAATCTGTTT 59.638 36.000 0.80 0.00 37.07 2.83
712 850 8.512138 AGTAGTTTTGTATTGTATTGGTTGCTC 58.488 33.333 0.00 0.00 0.00 4.26
713 851 8.404107 AGTAGTTTTGTATTGTATTGGTTGCT 57.596 30.769 0.00 0.00 0.00 3.91
714 852 7.753580 GGAGTAGTTTTGTATTGTATTGGTTGC 59.246 37.037 0.00 0.00 0.00 4.17
715 853 9.010029 AGGAGTAGTTTTGTATTGTATTGGTTG 57.990 33.333 0.00 0.00 0.00 3.77
717 855 9.662947 GTAGGAGTAGTTTTGTATTGTATTGGT 57.337 33.333 0.00 0.00 0.00 3.67
718 856 9.661563 TGTAGGAGTAGTTTTGTATTGTATTGG 57.338 33.333 0.00 0.00 0.00 3.16
723 861 9.398538 TGTTTTGTAGGAGTAGTTTTGTATTGT 57.601 29.630 0.00 0.00 0.00 2.71
726 864 9.063615 CCTTGTTTTGTAGGAGTAGTTTTGTAT 57.936 33.333 0.00 0.00 33.13 2.29
727 865 8.266473 TCCTTGTTTTGTAGGAGTAGTTTTGTA 58.734 33.333 0.00 0.00 35.66 2.41
728 866 7.114095 TCCTTGTTTTGTAGGAGTAGTTTTGT 58.886 34.615 0.00 0.00 35.66 2.83
729 867 7.562454 TCCTTGTTTTGTAGGAGTAGTTTTG 57.438 36.000 0.00 0.00 35.66 2.44
738 876 3.892284 TGTTGCTCCTTGTTTTGTAGGA 58.108 40.909 0.00 0.00 38.22 2.94
739 877 4.097892 ACTTGTTGCTCCTTGTTTTGTAGG 59.902 41.667 0.00 0.00 0.00 3.18
740 878 5.163663 TGACTTGTTGCTCCTTGTTTTGTAG 60.164 40.000 0.00 0.00 0.00 2.74
741 879 4.702612 TGACTTGTTGCTCCTTGTTTTGTA 59.297 37.500 0.00 0.00 0.00 2.41
742 880 3.509575 TGACTTGTTGCTCCTTGTTTTGT 59.490 39.130 0.00 0.00 0.00 2.83
743 881 4.108699 TGACTTGTTGCTCCTTGTTTTG 57.891 40.909 0.00 0.00 0.00 2.44
744 882 4.747810 CTTGACTTGTTGCTCCTTGTTTT 58.252 39.130 0.00 0.00 0.00 2.43
745 883 3.429410 GCTTGACTTGTTGCTCCTTGTTT 60.429 43.478 0.00 0.00 0.00 2.83
746 884 2.099756 GCTTGACTTGTTGCTCCTTGTT 59.900 45.455 0.00 0.00 0.00 2.83
747 885 1.678101 GCTTGACTTGTTGCTCCTTGT 59.322 47.619 0.00 0.00 0.00 3.16
748 886 1.000938 GGCTTGACTTGTTGCTCCTTG 60.001 52.381 0.00 0.00 0.00 3.61
749 887 1.322442 GGCTTGACTTGTTGCTCCTT 58.678 50.000 0.00 0.00 0.00 3.36
750 888 0.886490 CGGCTTGACTTGTTGCTCCT 60.886 55.000 0.00 0.00 0.00 3.69
751 889 1.576421 CGGCTTGACTTGTTGCTCC 59.424 57.895 0.00 0.00 0.00 4.70
863 1011 9.429109 TTCTTACATCCACACCATTCTATACTA 57.571 33.333 0.00 0.00 0.00 1.82
864 1012 7.914427 TCTTACATCCACACCATTCTATACT 57.086 36.000 0.00 0.00 0.00 2.12
884 1032 8.677300 CCTCTGCATTTTTATACTTGCTTCTTA 58.323 33.333 0.00 0.00 36.10 2.10
913 1061 3.785859 TCCCCTGCGCTTGGCTAG 61.786 66.667 9.73 0.00 44.05 3.42
914 1062 4.096003 GTCCCCTGCGCTTGGCTA 62.096 66.667 9.73 0.00 44.05 3.93
958 1106 2.230266 GTCTCTCGTTTCTCTCTTGGCT 59.770 50.000 0.00 0.00 0.00 4.75
1144 1310 4.722700 CAAGGAGGTGGCGGTGGG 62.723 72.222 0.00 0.00 0.00 4.61
1332 1503 1.905637 ACGGAGGGACCAAAAATCAC 58.094 50.000 0.00 0.00 38.90 3.06
1372 1543 7.352739 CCAAATATTTACCGCAGTGAGTTATC 58.647 38.462 0.00 0.00 0.00 1.75
1414 1587 3.069872 GCCCCATAAATTGCATGATGACA 59.930 43.478 0.00 0.00 0.00 3.58
1431 1604 2.156098 GACACTGATTTTTACGCCCCA 58.844 47.619 0.00 0.00 0.00 4.96
1581 1855 3.482722 TTACTACTCTCCGTTGCGAAG 57.517 47.619 0.00 0.00 0.00 3.79
1616 1943 4.332543 TGAACAGCATCGGACACATAAATC 59.667 41.667 0.00 0.00 0.00 2.17
1722 2049 2.810274 CAGGTGTTGATCCAGAGTGTTG 59.190 50.000 0.00 0.00 0.00 3.33
1723 2050 2.811873 GCAGGTGTTGATCCAGAGTGTT 60.812 50.000 0.00 0.00 0.00 3.32
1939 2276 1.064906 CCCCATGACAAGAGCAGTGAT 60.065 52.381 0.00 0.00 0.00 3.06
1981 2318 5.321102 AGTTTGCCCACATACATACTTTGA 58.679 37.500 0.00 0.00 30.88 2.69
2012 2349 7.348815 TCATCCATACATGTTCTGAAAGGATT 58.651 34.615 2.30 0.00 33.20 3.01
2187 2526 3.699038 TGTACCATATTTTGCAGGAAGGC 59.301 43.478 0.00 0.00 0.00 4.35
2285 2639 7.280876 GGAGTTCAGCTACAATGTAATCAATCA 59.719 37.037 0.00 0.00 0.00 2.57
2356 2712 1.645402 AAGGGGCACGGCATTCCTAT 61.645 55.000 0.00 0.00 0.00 2.57
2525 2881 2.956333 TCCATTATCGTCTGATCCACGT 59.044 45.455 12.56 0.00 38.45 4.49
2526 2882 3.643159 TCCATTATCGTCTGATCCACG 57.357 47.619 7.77 7.77 38.67 4.94
2528 2884 4.408921 ACCTTTCCATTATCGTCTGATCCA 59.591 41.667 0.00 0.00 35.99 3.41
2931 3386 0.183492 TGTGCCATGCCTATCCTTCC 59.817 55.000 0.00 0.00 0.00 3.46
2943 3398 1.134401 CATCGAACCCTACTGTGCCAT 60.134 52.381 0.00 0.00 0.00 4.40
3247 3747 9.944376 AGACAAGCTAAATGTGAGAAAGTATTA 57.056 29.630 0.00 0.00 0.00 0.98
3620 4120 5.070981 ACTTTCTCCAATCTTCAGTGAGTGA 59.929 40.000 0.00 0.00 34.41 3.41
3726 4226 2.159184 ACTGTGACTGTGACTGTGACTG 60.159 50.000 14.58 14.58 0.00 3.51
3743 4243 6.774656 AGAATTCAACCTCTTGATTGAACTGT 59.225 34.615 8.44 0.00 45.09 3.55
3995 4495 1.888512 GAATTGTCCTTGCAAGCCAGA 59.111 47.619 21.43 10.27 0.00 3.86
4145 4645 5.065218 ACTGAGCTTTGCTACATTATTTCCG 59.935 40.000 0.00 0.00 39.88 4.30
4220 4720 3.731431 TGGGTGGGTATGCCTATATAGG 58.269 50.000 22.63 22.63 46.42 2.57
4298 4798 6.286758 TCCGAAAGAGTATACGTCAGATAGT 58.713 40.000 0.00 0.00 0.00 2.12
4416 4916 0.178998 CCCCCAGCAGATGAATCCAG 60.179 60.000 0.00 0.00 0.00 3.86
4505 5005 0.878523 CGTTTTGCAGGTCTGGACGA 60.879 55.000 0.00 0.00 0.00 4.20
4523 5023 3.380479 TCAAGTACAGTCCAAACCTCG 57.620 47.619 0.00 0.00 0.00 4.63
4738 5243 8.574251 TTTAAGGCTAATCAAACATGCTTAGA 57.426 30.769 0.00 0.00 0.00 2.10
4765 5270 3.157087 TGGAAAGAACAATTCAGAGGGC 58.843 45.455 0.00 0.00 0.00 5.19
5289 5805 6.891624 AGCATGTAACAGCAATATTATCACG 58.108 36.000 0.00 0.00 0.00 4.35
5362 5878 3.576550 TCAGATGCTAGTACCACAACACA 59.423 43.478 0.00 0.00 0.00 3.72
5397 5913 4.188462 TGTATGCTTCCGTACTTTCCATG 58.812 43.478 0.00 0.00 35.05 3.66
5525 6059 6.712095 TCTGAGCAGTTATTGTTGATTGTTCT 59.288 34.615 0.00 0.00 0.00 3.01
5644 6178 5.922544 CACACATCTTTCAAGGATGGTTTTC 59.077 40.000 13.67 0.00 43.25 2.29
5739 6274 0.605083 TTGGCAACTTTGTGCACACA 59.395 45.000 21.56 13.06 46.81 3.72
5943 6529 6.006449 ACATAATTCTTCCTGTCAAGCTGTT 58.994 36.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.