Multiple sequence alignment - TraesCS4B01G251400

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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 TraesCS4B01G251400 chr4B 100.000 2451 0 0 1 2451 517619852 517617402 0.000000e+00 4527.0
1 TraesCS4B01G251400 chr4B 90.909 44 1 2 1784 1826 668868370 668868411 3.400000e-04 56.5
2 TraesCS4B01G251400 chr4B 86.957 46 6 0 1781 1826 190166667 190166712 4.000000e-03 52.8
3 TraesCS4B01G251400 chr4A 89.967 907 54 14 899 1784 45109001 45109891 0.000000e+00 1136.0
4 TraesCS4B01G251400 chr4A 86.233 523 57 8 120 638 45108400 45108911 9.900000e-154 553.0
5 TraesCS4B01G251400 chr4A 88.636 88 10 0 769 856 45108905 45108992 9.270000e-20 108.0
6 TraesCS4B01G251400 chr4D 92.145 662 45 4 828 1483 419458936 419458276 0.000000e+00 928.0
7 TraesCS4B01G251400 chr4D 93.396 212 6 5 1580 1784 419458292 419458082 8.510000e-80 307.0
8 TraesCS4B01G251400 chr6D 88.650 652 65 9 1780 2428 245260572 245261217 0.000000e+00 785.0
9 TraesCS4B01G251400 chr6D 75.460 163 28 9 1784 1940 457585674 457585830 4.370000e-08 69.4
10 TraesCS4B01G251400 chr5B 88.024 668 55 13 1809 2451 527942684 527942017 0.000000e+00 767.0
11 TraesCS4B01G251400 chr5B 87.224 634 70 9 1821 2451 470199039 470199664 0.000000e+00 712.0
12 TraesCS4B01G251400 chr5B 86.874 579 49 19 1886 2451 661285016 661285580 7.440000e-175 623.0
13 TraesCS4B01G251400 chr5B 78.788 165 24 10 1782 1940 221206867 221206708 1.550000e-17 100.0
14 TraesCS4B01G251400 chr5B 88.679 53 3 3 1776 1826 325548362 325548413 7.320000e-06 62.1
15 TraesCS4B01G251400 chr6A 86.510 682 71 15 1771 2450 61724573 61725235 0.000000e+00 730.0
16 TraesCS4B01G251400 chr2A 90.079 504 42 6 1954 2451 775086695 775086194 0.000000e+00 647.0
17 TraesCS4B01G251400 chr7B 86.851 578 52 15 1886 2451 721492157 721492722 2.070000e-175 625.0
18 TraesCS4B01G251400 chr7B 86.505 578 54 14 1886 2451 721469170 721469735 4.480000e-172 614.0
19 TraesCS4B01G251400 chr5D 89.307 505 44 3 1957 2451 461576347 461575843 2.070000e-175 625.0
20 TraesCS4B01G251400 chr2B 88.454 511 45 6 1954 2451 235165157 235165666 2.700000e-169 604.0
21 TraesCS4B01G251400 chr6B 85.921 554 55 14 1886 2428 37329220 37329761 9.830000e-159 569.0
22 TraesCS4B01G251400 chr1A 78.889 180 29 7 1774 1948 78545385 78545210 1.990000e-21 113.0
23 TraesCS4B01G251400 chr1D 79.070 172 24 9 1781 1947 246077763 246077927 9.270000e-20 108.0
24 TraesCS4B01G251400 chr3B 89.091 55 6 0 2397 2451 532905894 532905840 4.370000e-08 69.4


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 TraesCS4B01G251400 chr4B 517617402 517619852 2450 True 4527.0 4527 100.000000 1 2451 1 chr4B.!!$R1 2450
1 TraesCS4B01G251400 chr4A 45108400 45109891 1491 False 599.0 1136 88.278667 120 1784 3 chr4A.!!$F1 1664
2 TraesCS4B01G251400 chr4D 419458082 419458936 854 True 617.5 928 92.770500 828 1784 2 chr4D.!!$R1 956
3 TraesCS4B01G251400 chr6D 245260572 245261217 645 False 785.0 785 88.650000 1780 2428 1 chr6D.!!$F1 648
4 TraesCS4B01G251400 chr5B 527942017 527942684 667 True 767.0 767 88.024000 1809 2451 1 chr5B.!!$R2 642
5 TraesCS4B01G251400 chr5B 470199039 470199664 625 False 712.0 712 87.224000 1821 2451 1 chr5B.!!$F2 630
6 TraesCS4B01G251400 chr5B 661285016 661285580 564 False 623.0 623 86.874000 1886 2451 1 chr5B.!!$F3 565
7 TraesCS4B01G251400 chr6A 61724573 61725235 662 False 730.0 730 86.510000 1771 2450 1 chr6A.!!$F1 679
8 TraesCS4B01G251400 chr2A 775086194 775086695 501 True 647.0 647 90.079000 1954 2451 1 chr2A.!!$R1 497
9 TraesCS4B01G251400 chr7B 721492157 721492722 565 False 625.0 625 86.851000 1886 2451 1 chr7B.!!$F2 565
10 TraesCS4B01G251400 chr7B 721469170 721469735 565 False 614.0 614 86.505000 1886 2451 1 chr7B.!!$F1 565
11 TraesCS4B01G251400 chr5D 461575843 461576347 504 True 625.0 625 89.307000 1957 2451 1 chr5D.!!$R1 494
12 TraesCS4B01G251400 chr2B 235165157 235165666 509 False 604.0 604 88.454000 1954 2451 1 chr2B.!!$F1 497
13 TraesCS4B01G251400 chr6B 37329220 37329761 541 False 569.0 569 85.921000 1886 2428 1 chr6B.!!$F1 542

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
734 739 0.039074 CGAGTTGGTTCTCTGCTCGT 60.039 55.0 0.0 0.0 42.54 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 2206 0.886043 GCAGTGCCATGACAGTGTGA 60.886 55.0 16.91 0.0 42.01 3.58 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
17 18 3.527641 GTGACCTCGGAGGCTAGG 58.472 66.667 23.84 0.94 39.63 3.02
18 19 2.128507 GTGACCTCGGAGGCTAGGG 61.129 68.421 23.84 0.15 39.63 3.53
19 20 2.279408 GACCTCGGAGGCTAGGGT 59.721 66.667 23.84 3.84 39.63 4.34
20 21 2.042843 ACCTCGGAGGCTAGGGTG 60.043 66.667 23.84 0.00 39.63 4.61
21 22 2.840102 CCTCGGAGGCTAGGGTGG 60.840 72.222 11.83 0.00 0.00 4.61
22 23 3.541713 CTCGGAGGCTAGGGTGGC 61.542 72.222 0.00 0.00 0.00 5.01
25 26 3.851128 GGAGGCTAGGGTGGCGAC 61.851 72.222 0.00 0.00 37.59 5.19
26 27 3.851128 GAGGCTAGGGTGGCGACC 61.851 72.222 9.83 9.83 42.27 4.79
51 52 8.807948 CCTGGTGGTGGGATATTTATATAAAG 57.192 38.462 13.15 0.00 0.00 1.85
52 53 8.611257 CCTGGTGGTGGGATATTTATATAAAGA 58.389 37.037 13.15 9.28 0.00 2.52
54 55 9.973661 TGGTGGTGGGATATTTATATAAAGATG 57.026 33.333 17.77 0.00 28.28 2.90
55 56 9.408648 GGTGGTGGGATATTTATATAAAGATGG 57.591 37.037 17.77 0.00 28.28 3.51
58 59 9.853177 GGTGGGATATTTATATAAAGATGGAGG 57.147 37.037 17.77 0.00 28.28 4.30
74 75 9.981460 AAAGATGGAGGTATGTTCTATTCTTTT 57.019 29.630 0.00 0.00 0.00 2.27
75 76 9.620259 AAGATGGAGGTATGTTCTATTCTTTTC 57.380 33.333 0.00 0.00 0.00 2.29
76 77 8.214364 AGATGGAGGTATGTTCTATTCTTTTCC 58.786 37.037 0.00 0.00 0.00 3.13
77 78 7.510675 TGGAGGTATGTTCTATTCTTTTCCT 57.489 36.000 0.00 0.00 0.00 3.36
78 79 7.928873 TGGAGGTATGTTCTATTCTTTTCCTT 58.071 34.615 0.00 0.00 0.00 3.36
79 80 8.390921 TGGAGGTATGTTCTATTCTTTTCCTTT 58.609 33.333 0.00 0.00 0.00 3.11
80 81 8.678199 GGAGGTATGTTCTATTCTTTTCCTTTG 58.322 37.037 0.00 0.00 0.00 2.77
81 82 9.232473 GAGGTATGTTCTATTCTTTTCCTTTGT 57.768 33.333 0.00 0.00 0.00 2.83
82 83 9.588096 AGGTATGTTCTATTCTTTTCCTTTGTT 57.412 29.630 0.00 0.00 0.00 2.83
95 96 9.744468 TCTTTTCCTTTGTTTTATTAAGTGCTC 57.256 29.630 0.00 0.00 0.00 4.26
96 97 9.528018 CTTTTCCTTTGTTTTATTAAGTGCTCA 57.472 29.630 0.00 0.00 0.00 4.26
98 99 9.474920 TTTCCTTTGTTTTATTAAGTGCTCATG 57.525 29.630 0.00 0.00 0.00 3.07
99 100 8.402798 TCCTTTGTTTTATTAAGTGCTCATGA 57.597 30.769 0.00 0.00 0.00 3.07
100 101 8.296713 TCCTTTGTTTTATTAAGTGCTCATGAC 58.703 33.333 0.00 0.00 0.00 3.06
101 102 7.271223 CCTTTGTTTTATTAAGTGCTCATGACG 59.729 37.037 0.00 0.00 0.00 4.35
102 103 6.176975 TGTTTTATTAAGTGCTCATGACGG 57.823 37.500 0.00 0.00 0.00 4.79
103 104 5.935206 TGTTTTATTAAGTGCTCATGACGGA 59.065 36.000 0.00 0.00 0.00 4.69
104 105 6.092122 TGTTTTATTAAGTGCTCATGACGGAG 59.908 38.462 0.00 0.00 37.97 4.63
110 111 4.391539 CTCATGACGGAGCTCACG 57.608 61.111 17.19 18.28 37.36 4.35
111 112 1.875813 CTCATGACGGAGCTCACGC 60.876 63.158 17.19 12.55 34.00 5.34
128 129 1.066257 GCTTTACCATGGCCATGCG 59.934 57.895 36.08 29.55 37.49 4.73
129 130 1.735360 CTTTACCATGGCCATGCGG 59.265 57.895 36.08 27.10 37.49 5.69
150 151 2.332654 GGCATGGTGGTCGGTGTTC 61.333 63.158 0.00 0.00 0.00 3.18
154 155 1.768684 ATGGTGGTCGGTGTTCTGCT 61.769 55.000 0.00 0.00 0.00 4.24
170 171 0.687920 TGCTTTCGATGGTGGTGGTA 59.312 50.000 0.00 0.00 0.00 3.25
172 173 1.355971 CTTTCGATGGTGGTGGTACG 58.644 55.000 0.00 0.00 0.00 3.67
180 181 0.319297 GGTGGTGGTACGACTGTGTC 60.319 60.000 7.99 0.00 0.00 3.67
184 185 1.604693 GGTGGTACGACTGTGTCCTTG 60.605 57.143 7.99 0.00 0.00 3.61
223 224 1.311651 TGAGAGGCTGAGAGTGCTCG 61.312 60.000 0.00 0.00 44.33 5.03
224 225 2.202730 GAGGCTGAGAGTGCTCGC 60.203 66.667 0.00 0.00 44.33 5.03
228 229 3.753434 CTGAGAGTGCTCGCCGGT 61.753 66.667 1.90 0.00 44.33 5.28
232 233 4.148825 GAGTGCTCGCCGGTGGAT 62.149 66.667 16.49 0.00 0.00 3.41
237 238 2.178235 GCTCGCCGGTGGATAAACC 61.178 63.158 16.49 0.00 36.82 3.27
273 274 4.235762 ACTGGTGTCGGCAGCGTT 62.236 61.111 15.24 0.02 45.36 4.84
293 294 2.599281 TGGGCGTCGTCTCCTTCA 60.599 61.111 0.00 0.00 0.00 3.02
295 296 1.519455 GGGCGTCGTCTCCTTCATG 60.519 63.158 0.00 0.00 0.00 3.07
297 298 0.108804 GGCGTCGTCTCCTTCATGAA 60.109 55.000 8.12 8.12 0.00 2.57
298 299 1.272781 GCGTCGTCTCCTTCATGAAG 58.727 55.000 25.75 25.75 38.14 3.02
299 300 1.135373 GCGTCGTCTCCTTCATGAAGA 60.135 52.381 32.49 18.78 40.79 2.87
300 301 2.520979 CGTCGTCTCCTTCATGAAGAC 58.479 52.381 32.49 22.64 40.79 3.01
302 303 1.272781 CGTCTCCTTCATGAAGACGC 58.727 55.000 32.49 18.82 44.08 5.19
312 313 1.163420 ATGAAGACGCCGTTGTTGCA 61.163 50.000 0.00 0.00 0.00 4.08
330 331 2.833943 TGCAGCTATTCTCTGGTCTTCA 59.166 45.455 0.00 0.00 32.41 3.02
332 333 3.808726 GCAGCTATTCTCTGGTCTTCATG 59.191 47.826 0.00 0.00 32.41 3.07
333 334 4.682859 GCAGCTATTCTCTGGTCTTCATGT 60.683 45.833 0.00 0.00 32.41 3.21
339 340 3.668447 TCTCTGGTCTTCATGTTGCTTC 58.332 45.455 0.00 0.00 0.00 3.86
350 351 5.681337 TCATGTTGCTTCGTGTGAAAATA 57.319 34.783 0.00 0.00 32.66 1.40
378 379 0.327924 TTGGATCAGACAATGGCGGT 59.672 50.000 0.00 0.00 0.00 5.68
385 386 0.534203 AGACAATGGCGGTGTTTCGT 60.534 50.000 0.00 0.00 0.00 3.85
386 387 0.385473 GACAATGGCGGTGTTTCGTG 60.385 55.000 0.00 0.00 0.00 4.35
387 388 1.098712 ACAATGGCGGTGTTTCGTGT 61.099 50.000 0.00 0.00 0.00 4.49
388 389 0.385473 CAATGGCGGTGTTTCGTGTC 60.385 55.000 0.00 0.00 0.00 3.67
389 390 1.837538 AATGGCGGTGTTTCGTGTCG 61.838 55.000 0.00 0.00 0.00 4.35
390 391 2.963320 GGCGGTGTTTCGTGTCGT 60.963 61.111 0.00 0.00 0.00 4.34
391 392 1.661197 GGCGGTGTTTCGTGTCGTA 60.661 57.895 0.00 0.00 0.00 3.43
392 393 1.484232 GCGGTGTTTCGTGTCGTAC 59.516 57.895 0.00 0.00 0.00 3.67
393 394 1.879562 GCGGTGTTTCGTGTCGTACC 61.880 60.000 0.00 0.00 0.00 3.34
394 395 0.318107 CGGTGTTTCGTGTCGTACCT 60.318 55.000 0.00 0.00 0.00 3.08
395 396 1.856802 GGTGTTTCGTGTCGTACCTT 58.143 50.000 0.00 0.00 0.00 3.50
396 397 1.788886 GGTGTTTCGTGTCGTACCTTC 59.211 52.381 0.00 0.00 0.00 3.46
397 398 1.788886 GTGTTTCGTGTCGTACCTTCC 59.211 52.381 0.00 0.00 0.00 3.46
398 399 1.269726 TGTTTCGTGTCGTACCTTCCC 60.270 52.381 0.00 0.00 0.00 3.97
399 400 0.039256 TTTCGTGTCGTACCTTCCCG 60.039 55.000 0.00 0.00 0.00 5.14
400 401 0.888736 TTCGTGTCGTACCTTCCCGA 60.889 55.000 0.00 0.00 0.00 5.14
401 402 0.888736 TCGTGTCGTACCTTCCCGAA 60.889 55.000 0.00 0.00 34.47 4.30
402 403 0.455633 CGTGTCGTACCTTCCCGAAG 60.456 60.000 0.00 0.00 38.14 3.79
418 421 3.161557 AGGCGCTTCCTTGGAGTT 58.838 55.556 7.64 0.00 44.75 3.01
421 424 1.578206 GGCGCTTCCTTGGAGTTCAC 61.578 60.000 7.64 0.00 0.00 3.18
451 454 1.447838 CGGGGACTTGGTCACGATG 60.448 63.158 0.00 0.00 36.73 3.84
452 455 1.078426 GGGGACTTGGTCACGATGG 60.078 63.158 0.00 0.00 36.73 3.51
453 456 1.550130 GGGGACTTGGTCACGATGGA 61.550 60.000 0.00 0.00 36.73 3.41
460 463 1.348064 TGGTCACGATGGAGGACTTT 58.652 50.000 0.00 0.00 0.00 2.66
487 490 4.962155 ACTTCAAGGAGTACTCTTGTTGG 58.038 43.478 21.88 16.86 41.52 3.77
488 491 4.409247 ACTTCAAGGAGTACTCTTGTTGGT 59.591 41.667 21.88 17.31 41.52 3.67
489 492 5.104485 ACTTCAAGGAGTACTCTTGTTGGTT 60.104 40.000 21.88 8.70 41.52 3.67
490 493 4.703897 TCAAGGAGTACTCTTGTTGGTTG 58.296 43.478 21.88 9.01 41.52 3.77
495 498 3.412386 AGTACTCTTGTTGGTTGCCATC 58.588 45.455 0.00 0.00 31.53 3.51
505 508 4.141756 TGTTGGTTGCCATCTTTTGATTGT 60.142 37.500 0.00 0.00 36.97 2.71
514 517 5.509501 GCCATCTTTTGATTGTTTGGAGTGA 60.510 40.000 0.00 0.00 36.97 3.41
521 524 6.713762 TTGATTGTTTGGAGTGATTTGAGT 57.286 33.333 0.00 0.00 0.00 3.41
522 525 7.815840 TTGATTGTTTGGAGTGATTTGAGTA 57.184 32.000 0.00 0.00 0.00 2.59
562 566 1.286354 CGTTGTATCGTGCGTTGGGT 61.286 55.000 0.00 0.00 0.00 4.51
563 567 0.165079 GTTGTATCGTGCGTTGGGTG 59.835 55.000 0.00 0.00 0.00 4.61
589 594 8.484799 GTGTATGATATGGTAACGTGTTGTATG 58.515 37.037 0.00 0.00 42.51 2.39
590 595 5.977171 TGATATGGTAACGTGTTGTATGC 57.023 39.130 0.00 0.00 42.51 3.14
598 603 1.557832 ACGTGTTGTATGCTATGGGGT 59.442 47.619 0.00 0.00 0.00 4.95
599 604 2.767394 ACGTGTTGTATGCTATGGGGTA 59.233 45.455 0.00 0.00 0.00 3.69
607 612 4.719773 TGTATGCTATGGGGTATATGGTCC 59.280 45.833 0.00 0.00 0.00 4.46
619 624 5.012768 GGGTATATGGTCCTTGCTTTAGCTA 59.987 44.000 3.10 0.00 42.66 3.32
623 628 4.844349 TGGTCCTTGCTTTAGCTATTCT 57.156 40.909 3.10 0.00 42.66 2.40
631 636 7.014230 TCCTTGCTTTAGCTATTCTTTTTGTGT 59.986 33.333 3.10 0.00 42.66 3.72
632 637 8.296713 CCTTGCTTTAGCTATTCTTTTTGTGTA 58.703 33.333 3.10 0.00 42.66 2.90
633 638 9.677567 CTTGCTTTAGCTATTCTTTTTGTGTAA 57.322 29.630 3.10 0.00 42.66 2.41
634 639 9.677567 TTGCTTTAGCTATTCTTTTTGTGTAAG 57.322 29.630 3.10 0.00 42.66 2.34
635 640 9.062524 TGCTTTAGCTATTCTTTTTGTGTAAGA 57.937 29.630 3.10 0.00 42.66 2.10
641 646 9.401058 AGCTATTCTTTTTGTGTAAGATATGCT 57.599 29.630 0.00 0.00 32.09 3.79
707 712 8.958043 CATTTTTACTTCAGTTTACTTGTGAGC 58.042 33.333 0.00 0.00 0.00 4.26
708 713 5.900339 TTACTTCAGTTTACTTGTGAGCG 57.100 39.130 0.00 0.00 0.00 5.03
709 714 3.793559 ACTTCAGTTTACTTGTGAGCGT 58.206 40.909 0.00 0.00 0.00 5.07
710 715 3.802685 ACTTCAGTTTACTTGTGAGCGTC 59.197 43.478 0.00 0.00 0.00 5.19
711 716 2.390938 TCAGTTTACTTGTGAGCGTCG 58.609 47.619 0.00 0.00 0.00 5.12
712 717 1.455786 CAGTTTACTTGTGAGCGTCGG 59.544 52.381 0.00 0.00 0.00 4.79
713 718 1.338973 AGTTTACTTGTGAGCGTCGGA 59.661 47.619 0.00 0.00 0.00 4.55
714 719 2.029290 AGTTTACTTGTGAGCGTCGGAT 60.029 45.455 0.00 0.00 0.00 4.18
715 720 2.273370 TTACTTGTGAGCGTCGGATC 57.727 50.000 0.00 0.00 0.00 3.36
716 721 0.098200 TACTTGTGAGCGTCGGATCG 59.902 55.000 0.00 0.00 0.00 3.69
717 722 1.136774 CTTGTGAGCGTCGGATCGA 59.863 57.895 0.00 0.00 0.00 3.59
718 723 0.863538 CTTGTGAGCGTCGGATCGAG 60.864 60.000 0.00 0.00 36.23 4.04
719 724 1.583495 TTGTGAGCGTCGGATCGAGT 61.583 55.000 0.00 0.00 36.23 4.18
720 725 1.136984 GTGAGCGTCGGATCGAGTT 59.863 57.895 0.00 0.00 36.23 3.01
721 726 1.134530 GTGAGCGTCGGATCGAGTTG 61.135 60.000 0.00 0.00 36.23 3.16
722 727 1.586564 GAGCGTCGGATCGAGTTGG 60.587 63.158 0.00 0.00 36.23 3.77
723 728 2.181021 GCGTCGGATCGAGTTGGT 59.819 61.111 0.00 0.00 36.23 3.67
724 729 1.445582 GCGTCGGATCGAGTTGGTT 60.446 57.895 0.00 0.00 36.23 3.67
725 730 1.411493 GCGTCGGATCGAGTTGGTTC 61.411 60.000 0.00 0.00 36.23 3.62
726 731 0.170561 CGTCGGATCGAGTTGGTTCT 59.829 55.000 0.00 0.00 36.23 3.01
727 732 1.794437 CGTCGGATCGAGTTGGTTCTC 60.794 57.143 0.00 0.00 36.23 2.87
728 733 1.473278 GTCGGATCGAGTTGGTTCTCT 59.527 52.381 0.00 0.00 36.23 3.10
729 734 1.472878 TCGGATCGAGTTGGTTCTCTG 59.527 52.381 0.00 0.00 32.83 3.35
730 735 1.646189 GGATCGAGTTGGTTCTCTGC 58.354 55.000 0.00 0.00 32.83 4.26
731 736 1.205893 GGATCGAGTTGGTTCTCTGCT 59.794 52.381 0.00 0.00 32.83 4.24
732 737 2.535331 GATCGAGTTGGTTCTCTGCTC 58.465 52.381 0.00 0.00 32.83 4.26
733 738 0.241213 TCGAGTTGGTTCTCTGCTCG 59.759 55.000 5.99 5.99 46.97 5.03
734 739 0.039074 CGAGTTGGTTCTCTGCTCGT 60.039 55.000 0.00 0.00 42.54 4.18
735 740 1.704070 GAGTTGGTTCTCTGCTCGTC 58.296 55.000 0.00 0.00 0.00 4.20
736 741 0.039074 AGTTGGTTCTCTGCTCGTCG 60.039 55.000 0.00 0.00 0.00 5.12
737 742 0.039437 GTTGGTTCTCTGCTCGTCGA 60.039 55.000 0.00 0.00 0.00 4.20
738 743 0.888619 TTGGTTCTCTGCTCGTCGAT 59.111 50.000 0.00 0.00 0.00 3.59
739 744 0.888619 TGGTTCTCTGCTCGTCGATT 59.111 50.000 0.00 0.00 0.00 3.34
740 745 1.135373 TGGTTCTCTGCTCGTCGATTC 60.135 52.381 0.00 0.00 0.00 2.52
741 746 1.135373 GGTTCTCTGCTCGTCGATTCA 60.135 52.381 0.00 0.00 0.00 2.57
742 747 2.480416 GGTTCTCTGCTCGTCGATTCAT 60.480 50.000 0.00 0.00 0.00 2.57
743 748 3.182967 GTTCTCTGCTCGTCGATTCATT 58.817 45.455 0.00 0.00 0.00 2.57
744 749 3.510388 TCTCTGCTCGTCGATTCATTT 57.490 42.857 0.00 0.00 0.00 2.32
745 750 3.182182 TCTCTGCTCGTCGATTCATTTG 58.818 45.455 0.00 0.00 0.00 2.32
746 751 1.660607 TCTGCTCGTCGATTCATTTGC 59.339 47.619 0.00 0.00 0.00 3.68
747 752 0.726827 TGCTCGTCGATTCATTTGCC 59.273 50.000 0.00 0.00 0.00 4.52
748 753 0.726827 GCTCGTCGATTCATTTGCCA 59.273 50.000 0.00 0.00 0.00 4.92
749 754 1.267732 GCTCGTCGATTCATTTGCCAG 60.268 52.381 0.00 0.00 0.00 4.85
750 755 1.328680 CTCGTCGATTCATTTGCCAGG 59.671 52.381 0.00 0.00 0.00 4.45
751 756 1.086696 CGTCGATTCATTTGCCAGGT 58.913 50.000 0.00 0.00 0.00 4.00
752 757 1.468520 CGTCGATTCATTTGCCAGGTT 59.531 47.619 0.00 0.00 0.00 3.50
753 758 2.476185 CGTCGATTCATTTGCCAGGTTC 60.476 50.000 0.00 0.00 0.00 3.62
754 759 2.091541 TCGATTCATTTGCCAGGTTCC 58.908 47.619 0.00 0.00 0.00 3.62
755 760 2.094675 CGATTCATTTGCCAGGTTCCT 58.905 47.619 0.00 0.00 0.00 3.36
756 761 2.159338 CGATTCATTTGCCAGGTTCCTG 60.159 50.000 11.52 11.52 0.00 3.86
757 762 2.380064 TTCATTTGCCAGGTTCCTGT 57.620 45.000 16.33 0.00 32.56 4.00
758 763 3.517296 TTCATTTGCCAGGTTCCTGTA 57.483 42.857 16.33 3.98 32.56 2.74
759 764 3.737559 TCATTTGCCAGGTTCCTGTAT 57.262 42.857 16.33 3.50 32.56 2.29
760 765 3.620488 TCATTTGCCAGGTTCCTGTATC 58.380 45.455 16.33 6.98 32.56 2.24
761 766 2.507407 TTTGCCAGGTTCCTGTATCC 57.493 50.000 16.33 4.26 32.56 2.59
762 767 1.367346 TTGCCAGGTTCCTGTATCCA 58.633 50.000 16.33 6.43 32.56 3.41
763 768 1.367346 TGCCAGGTTCCTGTATCCAA 58.633 50.000 16.33 0.00 32.56 3.53
764 769 1.922447 TGCCAGGTTCCTGTATCCAAT 59.078 47.619 16.33 0.00 32.56 3.16
765 770 2.301346 GCCAGGTTCCTGTATCCAATG 58.699 52.381 16.33 1.56 32.56 2.82
766 771 2.301346 CCAGGTTCCTGTATCCAATGC 58.699 52.381 16.33 0.00 32.56 3.56
767 772 2.357050 CCAGGTTCCTGTATCCAATGCA 60.357 50.000 16.33 0.00 32.56 3.96
786 791 7.656948 CCAATGCATAAAATAATAACCTGTGGG 59.343 37.037 0.00 0.00 38.88 4.61
793 798 5.396057 AATAATAACCTGTGGGCCATACA 57.604 39.130 10.70 8.63 35.63 2.29
797 802 1.304282 CCTGTGGGCCATACAAGCT 59.696 57.895 10.70 0.00 0.00 3.74
798 803 0.546122 CCTGTGGGCCATACAAGCTA 59.454 55.000 10.70 0.00 0.00 3.32
799 804 1.064758 CCTGTGGGCCATACAAGCTAA 60.065 52.381 10.70 0.00 0.00 3.09
800 805 2.620367 CCTGTGGGCCATACAAGCTAAA 60.620 50.000 10.70 0.00 0.00 1.85
801 806 2.684881 CTGTGGGCCATACAAGCTAAAG 59.315 50.000 10.70 0.00 0.00 1.85
808 813 4.098501 GGCCATACAAGCTAAAGAAAGCAT 59.901 41.667 0.00 0.00 45.30 3.79
837 842 1.105457 ACTTCAGCTGCTGCAACAAA 58.895 45.000 24.38 12.08 42.74 2.83
859 864 2.012673 CAGCAGGTCATACAAAGGAGC 58.987 52.381 0.00 0.00 34.21 4.70
860 865 1.912043 AGCAGGTCATACAAAGGAGCT 59.088 47.619 0.00 0.00 44.51 4.09
863 868 3.902881 AGGTCATACAAAGGAGCTGAG 57.097 47.619 0.00 0.00 42.26 3.35
864 869 3.177228 AGGTCATACAAAGGAGCTGAGT 58.823 45.455 0.00 0.00 42.26 3.41
866 871 4.160626 AGGTCATACAAAGGAGCTGAGTAC 59.839 45.833 0.00 0.00 42.26 2.73
868 873 5.337652 GGTCATACAAAGGAGCTGAGTACTT 60.338 44.000 0.00 0.00 31.43 2.24
869 874 6.166982 GTCATACAAAGGAGCTGAGTACTTT 58.833 40.000 0.00 0.00 33.76 2.66
881 889 0.328258 AGTACTTTTCATGCGGGGCT 59.672 50.000 0.00 0.00 0.00 5.19
899 907 3.715097 GCCAGCCAGCCAGACTCT 61.715 66.667 0.00 0.00 0.00 3.24
900 908 2.583520 CCAGCCAGCCAGACTCTC 59.416 66.667 0.00 0.00 0.00 3.20
922 930 2.086054 AAGCGTTCACAGTCAGATCC 57.914 50.000 0.00 0.00 0.00 3.36
934 942 0.337773 TCAGATCCAGCTCCACCTCT 59.662 55.000 0.00 0.00 0.00 3.69
937 945 0.753479 GATCCAGCTCCACCTCTCGA 60.753 60.000 0.00 0.00 0.00 4.04
977 985 3.312697 ACGAGAAAGAAACCTGAGCAAAC 59.687 43.478 0.00 0.00 0.00 2.93
978 986 3.312421 CGAGAAAGAAACCTGAGCAAACA 59.688 43.478 0.00 0.00 0.00 2.83
1117 1125 2.804090 GCAGCAGCGCAAAGAAGC 60.804 61.111 11.47 1.45 0.00 3.86
1136 1144 2.914289 CCCCCAGGATGCAGAGTC 59.086 66.667 0.00 0.00 33.47 3.36
1138 1146 1.565390 CCCCCAGGATGCAGAGTCAA 61.565 60.000 0.00 0.00 33.47 3.18
1140 1148 0.617413 CCCAGGATGCAGAGTCAAGT 59.383 55.000 0.00 0.00 31.97 3.16
1148 1156 1.002868 CAGAGTCAAGTGGGGGCAG 60.003 63.158 0.00 0.00 0.00 4.85
1250 1258 4.403137 CGACGCCGGGTACGTGAA 62.403 66.667 10.42 0.00 45.24 3.18
1285 1295 1.730902 CGGCTCGCACGGATCATAG 60.731 63.158 0.00 0.00 0.00 2.23
1357 1367 1.296392 CGCCATCTCCAAGGACACA 59.704 57.895 0.00 0.00 0.00 3.72
1477 1498 1.524355 CGAGAGCTGCATACCATTTCG 59.476 52.381 1.02 0.00 0.00 3.46
1478 1499 2.555199 GAGAGCTGCATACCATTTCGT 58.445 47.619 1.02 0.00 0.00 3.85
1479 1500 3.717707 GAGAGCTGCATACCATTTCGTA 58.282 45.455 1.02 0.00 0.00 3.43
1480 1501 4.310769 GAGAGCTGCATACCATTTCGTAT 58.689 43.478 1.02 0.00 0.00 3.06
1481 1502 4.708177 AGAGCTGCATACCATTTCGTATT 58.292 39.130 1.02 0.00 0.00 1.89
1482 1503 4.752101 AGAGCTGCATACCATTTCGTATTC 59.248 41.667 1.02 0.00 0.00 1.75
1486 1507 5.611844 GCTGCATACCATTTCGTATTCGTAC 60.612 44.000 0.00 0.00 38.33 3.67
1488 1509 6.737118 TGCATACCATTTCGTATTCGTACTA 58.263 36.000 0.00 0.00 38.33 1.82
1502 1523 8.965172 CGTATTCGTACTACTTGCTTATTCATT 58.035 33.333 0.00 0.00 0.00 2.57
1507 1531 7.970061 TCGTACTACTTGCTTATTCATTTACGT 59.030 33.333 0.00 0.00 31.68 3.57
1512 1536 6.599437 ACTTGCTTATTCATTTACGTGTCAC 58.401 36.000 0.00 0.00 0.00 3.67
1519 1543 8.836268 TTATTCATTTACGTGTCACTACCTTT 57.164 30.769 0.00 0.00 0.00 3.11
1523 1547 2.814280 ACGTGTCACTACCTTTCTGG 57.186 50.000 0.65 0.00 42.93 3.86
1525 1549 2.897969 ACGTGTCACTACCTTTCTGGAT 59.102 45.455 0.65 0.00 39.71 3.41
1560 1584 1.347320 GGTAGACGACGCTTTTGAGG 58.653 55.000 0.00 0.00 0.00 3.86
1604 1630 4.193826 TGGTTCTGTATTCTGCTCACTC 57.806 45.455 0.00 0.00 0.00 3.51
1605 1631 3.834813 TGGTTCTGTATTCTGCTCACTCT 59.165 43.478 0.00 0.00 0.00 3.24
1637 1670 1.285023 CTGCAAACTGCTGAGTGCC 59.715 57.895 16.20 4.39 45.31 5.01
1664 1697 0.252558 TTTTAGAGGAGCGGGGAGGT 60.253 55.000 0.00 0.00 0.00 3.85
1762 1803 0.875908 CCTGCACGGATCCATACACG 60.876 60.000 13.41 0.00 33.16 4.49
1884 1925 0.179134 GACAAGTCTCCCGATCCACG 60.179 60.000 0.00 0.00 42.18 4.94
1912 1953 4.555747 GCGTTCGTTGTTTTTCTTTCTTGA 59.444 37.500 0.00 0.00 0.00 3.02
1950 1991 1.026718 CCCATCACGAGCTGTTTCCC 61.027 60.000 0.00 0.00 0.00 3.97
1951 1992 0.321564 CCATCACGAGCTGTTTCCCA 60.322 55.000 0.00 0.00 0.00 4.37
1980 2044 4.656112 TCCTCACCCTTTCTCATATCTTCC 59.344 45.833 0.00 0.00 0.00 3.46
2000 2070 4.035102 GTGTGAGGAGGCACCCCC 62.035 72.222 0.00 0.00 40.05 5.40
2135 2206 1.825191 GTGCGACCATGGCCATGAT 60.825 57.895 41.32 30.75 41.20 2.45
2262 2334 4.323417 ACGATTTTTGCTACATCCACTCA 58.677 39.130 0.00 0.00 0.00 3.41
2314 2386 0.884704 ACGATTTGCTGCAACCGTCT 60.885 50.000 26.01 12.38 0.00 4.18
2318 2390 2.248280 TTTGCTGCAACCGTCTTCTA 57.752 45.000 15.72 0.00 0.00 2.10
2319 2391 1.508632 TTGCTGCAACCGTCTTCTAC 58.491 50.000 11.69 0.00 0.00 2.59
2329 2403 4.595762 ACCGTCTTCTACTTTTGCTACA 57.404 40.909 0.00 0.00 0.00 2.74
2362 2436 6.608405 AGGAAATTTGCTACATCCATTCATGA 59.392 34.615 10.87 0.00 32.47 3.07
2395 2483 3.384532 GGGAGGTGGCGACGGTTA 61.385 66.667 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.128507 CCCTAGCCTCCGAGGTCAC 61.129 68.421 16.09 0.00 37.80 3.67
2 3 2.128507 CACCCTAGCCTCCGAGGTC 61.129 68.421 16.09 8.34 37.80 3.85
4 5 2.840102 CCACCCTAGCCTCCGAGG 60.840 72.222 10.41 10.41 38.80 4.63
5 6 3.541713 GCCACCCTAGCCTCCGAG 61.542 72.222 0.00 0.00 0.00 4.63
8 9 3.851128 GTCGCCACCCTAGCCTCC 61.851 72.222 0.00 0.00 0.00 4.30
9 10 3.851128 GGTCGCCACCCTAGCCTC 61.851 72.222 0.00 0.00 36.54 4.70
26 27 8.611257 TCTTTATATAAATATCCCACCACCAGG 58.389 37.037 8.34 0.00 42.21 4.45
28 29 9.973661 CATCTTTATATAAATATCCCACCACCA 57.026 33.333 8.34 0.00 0.00 4.17
29 30 9.408648 CCATCTTTATATAAATATCCCACCACC 57.591 37.037 8.34 0.00 0.00 4.61
32 33 9.853177 CCTCCATCTTTATATAAATATCCCACC 57.147 37.037 8.34 0.00 0.00 4.61
48 49 9.981460 AAAAGAATAGAACATACCTCCATCTTT 57.019 29.630 0.00 0.00 35.56 2.52
49 50 9.620259 GAAAAGAATAGAACATACCTCCATCTT 57.380 33.333 0.00 0.00 0.00 2.40
50 51 8.214364 GGAAAAGAATAGAACATACCTCCATCT 58.786 37.037 0.00 0.00 0.00 2.90
51 52 8.214364 AGGAAAAGAATAGAACATACCTCCATC 58.786 37.037 0.00 0.00 0.00 3.51
52 53 8.107196 AGGAAAAGAATAGAACATACCTCCAT 57.893 34.615 0.00 0.00 0.00 3.41
53 54 7.510675 AGGAAAAGAATAGAACATACCTCCA 57.489 36.000 0.00 0.00 0.00 3.86
54 55 8.678199 CAAAGGAAAAGAATAGAACATACCTCC 58.322 37.037 0.00 0.00 0.00 4.30
55 56 9.232473 ACAAAGGAAAAGAATAGAACATACCTC 57.768 33.333 0.00 0.00 0.00 3.85
56 57 9.588096 AACAAAGGAAAAGAATAGAACATACCT 57.412 29.630 0.00 0.00 0.00 3.08
69 70 9.744468 GAGCACTTAATAAAACAAAGGAAAAGA 57.256 29.630 0.00 0.00 0.00 2.52
70 71 9.528018 TGAGCACTTAATAAAACAAAGGAAAAG 57.472 29.630 0.00 0.00 0.00 2.27
72 73 9.474920 CATGAGCACTTAATAAAACAAAGGAAA 57.525 29.630 0.00 0.00 0.00 3.13
73 74 8.855110 TCATGAGCACTTAATAAAACAAAGGAA 58.145 29.630 0.00 0.00 0.00 3.36
74 75 8.296713 GTCATGAGCACTTAATAAAACAAAGGA 58.703 33.333 0.00 0.00 0.00 3.36
75 76 7.271223 CGTCATGAGCACTTAATAAAACAAAGG 59.729 37.037 0.00 0.00 0.00 3.11
76 77 7.271223 CCGTCATGAGCACTTAATAAAACAAAG 59.729 37.037 0.00 0.00 0.00 2.77
77 78 7.041030 TCCGTCATGAGCACTTAATAAAACAAA 60.041 33.333 0.00 0.00 0.00 2.83
78 79 6.428465 TCCGTCATGAGCACTTAATAAAACAA 59.572 34.615 0.00 0.00 0.00 2.83
79 80 5.935206 TCCGTCATGAGCACTTAATAAAACA 59.065 36.000 0.00 0.00 0.00 2.83
80 81 6.417191 TCCGTCATGAGCACTTAATAAAAC 57.583 37.500 0.00 0.00 0.00 2.43
81 82 6.662414 CTCCGTCATGAGCACTTAATAAAA 57.338 37.500 0.00 0.00 0.00 1.52
93 94 4.391539 CGTGAGCTCCGTCATGAG 57.608 61.111 12.15 0.00 35.75 2.90
105 106 0.676466 TGGCCATGGTAAAGCGTGAG 60.676 55.000 14.67 0.00 0.00 3.51
106 107 0.034574 ATGGCCATGGTAAAGCGTGA 60.035 50.000 20.04 0.00 0.00 4.35
107 108 0.101040 CATGGCCATGGTAAAGCGTG 59.899 55.000 34.31 9.56 35.24 5.34
108 109 1.666209 GCATGGCCATGGTAAAGCGT 61.666 55.000 39.72 4.97 39.16 5.07
109 110 1.066257 GCATGGCCATGGTAAAGCG 59.934 57.895 39.72 18.02 39.16 4.68
110 111 1.066257 CGCATGGCCATGGTAAAGC 59.934 57.895 39.72 26.33 39.16 3.51
111 112 1.735360 CCGCATGGCCATGGTAAAG 59.265 57.895 39.72 19.44 39.16 1.85
112 113 1.756172 CCCGCATGGCCATGGTAAA 60.756 57.895 39.72 3.07 39.16 2.01
113 114 2.123939 CCCGCATGGCCATGGTAA 60.124 61.111 39.72 3.93 39.16 2.85
133 134 1.302511 AGAACACCGACCACCATGC 60.303 57.895 0.00 0.00 0.00 4.06
134 135 1.577328 GCAGAACACCGACCACCATG 61.577 60.000 0.00 0.00 0.00 3.66
142 143 1.428448 CATCGAAAGCAGAACACCGA 58.572 50.000 0.00 0.00 0.00 4.69
150 151 0.606401 ACCACCACCATCGAAAGCAG 60.606 55.000 0.00 0.00 0.00 4.24
154 155 0.967662 TCGTACCACCACCATCGAAA 59.032 50.000 0.00 0.00 0.00 3.46
170 171 1.299926 GTCGCAAGGACACAGTCGT 60.300 57.895 0.00 0.00 45.36 4.34
232 233 3.118905 GCCAAAGCCAAACATGGTTTA 57.881 42.857 0.00 0.00 35.34 2.01
255 256 4.664677 ACGCTGCCGACACCAGTC 62.665 66.667 0.00 0.00 41.46 3.51
260 261 4.059459 CACGAACGCTGCCGACAC 62.059 66.667 3.87 0.00 38.29 3.67
270 271 4.695231 AGACGACGCCCACGAACG 62.695 66.667 0.00 0.73 43.93 3.95
271 272 2.804090 GAGACGACGCCCACGAAC 60.804 66.667 0.00 0.00 43.93 3.95
293 294 1.163420 TGCAACAACGGCGTCTTCAT 61.163 50.000 15.17 0.00 0.00 2.57
295 296 1.082756 CTGCAACAACGGCGTCTTC 60.083 57.895 15.17 1.73 0.00 2.87
297 298 2.709125 TAGCTGCAACAACGGCGTCT 62.709 55.000 15.17 5.87 46.91 4.18
298 299 1.635663 ATAGCTGCAACAACGGCGTC 61.636 55.000 15.17 0.00 46.91 5.19
299 300 1.234615 AATAGCTGCAACAACGGCGT 61.235 50.000 6.77 6.77 46.91 5.68
300 301 0.521242 GAATAGCTGCAACAACGGCG 60.521 55.000 4.80 4.80 46.91 6.46
301 302 0.804989 AGAATAGCTGCAACAACGGC 59.195 50.000 1.02 0.00 42.55 5.68
302 303 2.094894 CAGAGAATAGCTGCAACAACGG 59.905 50.000 1.02 0.00 0.00 4.44
312 313 5.426504 CAACATGAAGACCAGAGAATAGCT 58.573 41.667 0.00 0.00 0.00 3.32
330 331 6.676950 TCATTATTTTCACACGAAGCAACAT 58.323 32.000 0.00 0.00 31.28 2.71
332 333 6.251376 GGATCATTATTTTCACACGAAGCAAC 59.749 38.462 0.00 0.00 31.28 4.17
333 334 6.150976 AGGATCATTATTTTCACACGAAGCAA 59.849 34.615 0.00 0.00 31.28 3.91
339 340 6.851609 TCCAAAGGATCATTATTTTCACACG 58.148 36.000 0.00 0.00 0.00 4.49
368 369 1.098712 ACACGAAACACCGCCATTGT 61.099 50.000 0.00 0.00 0.00 2.71
378 379 1.269726 GGGAAGGTACGACACGAAACA 60.270 52.381 0.00 0.00 0.00 2.83
393 394 2.820037 GGAAGCGCCTTCGGGAAG 60.820 66.667 2.29 1.38 40.99 3.46
402 403 1.302511 TGAACTCCAAGGAAGCGCC 60.303 57.895 2.29 0.00 0.00 6.53
403 404 1.869690 GTGAACTCCAAGGAAGCGC 59.130 57.895 0.00 0.00 0.00 5.92
404 405 1.291877 CCGTGAACTCCAAGGAAGCG 61.292 60.000 0.00 0.00 45.72 4.68
405 406 0.250338 ACCGTGAACTCCAAGGAAGC 60.250 55.000 4.14 0.00 45.72 3.86
407 408 1.539496 CGAACCGTGAACTCCAAGGAA 60.539 52.381 4.14 0.00 45.72 3.36
408 409 0.032952 CGAACCGTGAACTCCAAGGA 59.967 55.000 4.14 0.00 45.72 3.36
410 411 1.578583 AACGAACCGTGAACTCCAAG 58.421 50.000 0.00 0.00 39.99 3.61
411 412 1.666700 CAAACGAACCGTGAACTCCAA 59.333 47.619 0.00 0.00 39.99 3.53
414 417 0.041576 GCCAAACGAACCGTGAACTC 60.042 55.000 0.00 0.00 39.99 3.01
451 454 2.814280 TGAAGTCGTCAAAGTCCTCC 57.186 50.000 0.00 0.00 31.51 4.30
452 455 3.060602 CCTTGAAGTCGTCAAAGTCCTC 58.939 50.000 2.79 0.00 45.67 3.71
453 456 2.698797 TCCTTGAAGTCGTCAAAGTCCT 59.301 45.455 2.79 0.00 45.67 3.85
460 463 3.752665 AGAGTACTCCTTGAAGTCGTCA 58.247 45.455 19.38 0.00 0.00 4.35
487 490 5.055812 TCCAAACAATCAAAAGATGGCAAC 58.944 37.500 0.00 0.00 0.00 4.17
488 491 5.163322 ACTCCAAACAATCAAAAGATGGCAA 60.163 36.000 0.00 0.00 0.00 4.52
489 492 4.344679 ACTCCAAACAATCAAAAGATGGCA 59.655 37.500 0.00 0.00 0.00 4.92
490 493 4.687483 CACTCCAAACAATCAAAAGATGGC 59.313 41.667 0.00 0.00 0.00 4.40
495 498 7.707893 ACTCAAATCACTCCAAACAATCAAAAG 59.292 33.333 0.00 0.00 0.00 2.27
505 508 5.932303 GCTACACTACTCAAATCACTCCAAA 59.068 40.000 0.00 0.00 0.00 3.28
514 517 7.332182 GCTAAAGAACAGCTACACTACTCAAAT 59.668 37.037 0.00 0.00 36.07 2.32
521 524 5.105877 ACGATGCTAAAGAACAGCTACACTA 60.106 40.000 0.00 0.00 39.83 2.74
522 525 4.177026 CGATGCTAAAGAACAGCTACACT 58.823 43.478 0.00 0.00 39.83 3.55
562 566 6.399743 ACAACACGTTACCATATCATACACA 58.600 36.000 0.00 0.00 0.00 3.72
563 567 6.897259 ACAACACGTTACCATATCATACAC 57.103 37.500 0.00 0.00 0.00 2.90
589 594 3.622455 GCAAGGACCATATACCCCATAGC 60.622 52.174 0.00 0.00 0.00 2.97
590 595 3.846588 AGCAAGGACCATATACCCCATAG 59.153 47.826 0.00 0.00 0.00 2.23
598 603 8.207350 AGAATAGCTAAAGCAAGGACCATATA 57.793 34.615 4.54 0.00 45.16 0.86
599 604 7.084268 AGAATAGCTAAAGCAAGGACCATAT 57.916 36.000 4.54 0.00 45.16 1.78
607 612 9.677567 TTACACAAAAAGAATAGCTAAAGCAAG 57.322 29.630 4.54 0.00 45.16 4.01
681 686 8.958043 GCTCACAAGTAAACTGAAGTAAAAATG 58.042 33.333 0.00 0.00 0.00 2.32
682 687 7.855904 CGCTCACAAGTAAACTGAAGTAAAAAT 59.144 33.333 0.00 0.00 0.00 1.82
683 688 7.148373 ACGCTCACAAGTAAACTGAAGTAAAAA 60.148 33.333 0.00 0.00 0.00 1.94
684 689 6.314400 ACGCTCACAAGTAAACTGAAGTAAAA 59.686 34.615 0.00 0.00 0.00 1.52
685 690 5.813672 ACGCTCACAAGTAAACTGAAGTAAA 59.186 36.000 0.00 0.00 0.00 2.01
686 691 5.353938 ACGCTCACAAGTAAACTGAAGTAA 58.646 37.500 0.00 0.00 0.00 2.24
687 692 4.940463 ACGCTCACAAGTAAACTGAAGTA 58.060 39.130 0.00 0.00 0.00 2.24
688 693 3.793559 ACGCTCACAAGTAAACTGAAGT 58.206 40.909 0.00 0.00 0.00 3.01
689 694 3.121328 CGACGCTCACAAGTAAACTGAAG 60.121 47.826 0.00 0.00 0.00 3.02
690 695 2.792674 CGACGCTCACAAGTAAACTGAA 59.207 45.455 0.00 0.00 0.00 3.02
691 696 2.390938 CGACGCTCACAAGTAAACTGA 58.609 47.619 0.00 0.00 0.00 3.41
692 697 1.455786 CCGACGCTCACAAGTAAACTG 59.544 52.381 0.00 0.00 0.00 3.16
693 698 1.338973 TCCGACGCTCACAAGTAAACT 59.661 47.619 0.00 0.00 0.00 2.66
694 699 1.774639 TCCGACGCTCACAAGTAAAC 58.225 50.000 0.00 0.00 0.00 2.01
695 700 2.602878 GATCCGACGCTCACAAGTAAA 58.397 47.619 0.00 0.00 0.00 2.01
696 701 1.466866 CGATCCGACGCTCACAAGTAA 60.467 52.381 0.00 0.00 0.00 2.24
697 702 0.098200 CGATCCGACGCTCACAAGTA 59.902 55.000 0.00 0.00 0.00 2.24
698 703 1.154016 CGATCCGACGCTCACAAGT 60.154 57.895 0.00 0.00 0.00 3.16
699 704 0.863538 CTCGATCCGACGCTCACAAG 60.864 60.000 0.00 0.00 0.00 3.16
700 705 1.136774 CTCGATCCGACGCTCACAA 59.863 57.895 0.00 0.00 0.00 3.33
701 706 1.583495 AACTCGATCCGACGCTCACA 61.583 55.000 0.00 0.00 0.00 3.58
702 707 1.134530 CAACTCGATCCGACGCTCAC 61.135 60.000 0.00 0.00 0.00 3.51
703 708 1.136774 CAACTCGATCCGACGCTCA 59.863 57.895 0.00 0.00 0.00 4.26
704 709 1.586564 CCAACTCGATCCGACGCTC 60.587 63.158 0.00 0.00 0.00 5.03
705 710 1.874345 AACCAACTCGATCCGACGCT 61.874 55.000 0.00 0.00 0.00 5.07
706 711 1.411493 GAACCAACTCGATCCGACGC 61.411 60.000 0.00 0.00 0.00 5.19
707 712 0.170561 AGAACCAACTCGATCCGACG 59.829 55.000 0.00 0.00 0.00 5.12
708 713 1.473278 AGAGAACCAACTCGATCCGAC 59.527 52.381 0.00 0.00 41.25 4.79
709 714 1.472878 CAGAGAACCAACTCGATCCGA 59.527 52.381 0.00 0.00 41.25 4.55
710 715 1.914634 CAGAGAACCAACTCGATCCG 58.085 55.000 0.00 0.00 41.25 4.18
711 716 1.205893 AGCAGAGAACCAACTCGATCC 59.794 52.381 0.00 0.00 41.25 3.36
712 717 2.535331 GAGCAGAGAACCAACTCGATC 58.465 52.381 0.00 0.00 41.25 3.69
713 718 2.663826 GAGCAGAGAACCAACTCGAT 57.336 50.000 0.00 0.00 41.25 3.59
715 720 2.730626 CGAGCAGAGAACCAACTCG 58.269 57.895 0.00 0.00 43.46 4.18
716 721 1.704070 GACGAGCAGAGAACCAACTC 58.296 55.000 0.00 0.00 37.19 3.01
717 722 0.039074 CGACGAGCAGAGAACCAACT 60.039 55.000 0.00 0.00 0.00 3.16
718 723 0.039437 TCGACGAGCAGAGAACCAAC 60.039 55.000 0.00 0.00 0.00 3.77
719 724 0.888619 ATCGACGAGCAGAGAACCAA 59.111 50.000 3.01 0.00 0.00 3.67
720 725 0.888619 AATCGACGAGCAGAGAACCA 59.111 50.000 3.01 0.00 0.00 3.67
721 726 1.135373 TGAATCGACGAGCAGAGAACC 60.135 52.381 3.01 0.00 0.00 3.62
722 727 2.264109 TGAATCGACGAGCAGAGAAC 57.736 50.000 3.01 0.00 0.00 3.01
723 728 3.510388 AATGAATCGACGAGCAGAGAA 57.490 42.857 3.01 0.00 0.00 2.87
724 729 3.182182 CAAATGAATCGACGAGCAGAGA 58.818 45.455 3.01 0.00 0.00 3.10
725 730 2.285486 GCAAATGAATCGACGAGCAGAG 60.285 50.000 3.01 0.48 0.00 3.35
726 731 1.660607 GCAAATGAATCGACGAGCAGA 59.339 47.619 3.01 0.00 0.00 4.26
727 732 1.267732 GGCAAATGAATCGACGAGCAG 60.268 52.381 3.01 0.00 0.00 4.24
728 733 0.726827 GGCAAATGAATCGACGAGCA 59.273 50.000 3.01 4.63 0.00 4.26
729 734 0.726827 TGGCAAATGAATCGACGAGC 59.273 50.000 3.01 0.00 0.00 5.03
730 735 1.328680 CCTGGCAAATGAATCGACGAG 59.671 52.381 3.01 0.00 0.00 4.18
731 736 1.338674 ACCTGGCAAATGAATCGACGA 60.339 47.619 0.00 0.00 0.00 4.20
732 737 1.086696 ACCTGGCAAATGAATCGACG 58.913 50.000 0.00 0.00 0.00 5.12
733 738 2.159379 GGAACCTGGCAAATGAATCGAC 60.159 50.000 0.00 0.00 0.00 4.20
734 739 2.091541 GGAACCTGGCAAATGAATCGA 58.908 47.619 0.00 0.00 0.00 3.59
735 740 2.094675 AGGAACCTGGCAAATGAATCG 58.905 47.619 0.00 0.00 0.00 3.34
736 741 3.515330 CAGGAACCTGGCAAATGAATC 57.485 47.619 12.54 0.00 40.17 2.52
758 763 9.985730 CACAGGTTATTATTTTATGCATTGGAT 57.014 29.630 3.54 0.00 0.00 3.41
759 764 8.420222 CCACAGGTTATTATTTTATGCATTGGA 58.580 33.333 3.54 0.00 0.00 3.53
760 765 7.656948 CCCACAGGTTATTATTTTATGCATTGG 59.343 37.037 3.54 0.00 0.00 3.16
761 766 7.171337 GCCCACAGGTTATTATTTTATGCATTG 59.829 37.037 3.54 0.00 34.57 2.82
762 767 7.216494 GCCCACAGGTTATTATTTTATGCATT 58.784 34.615 3.54 0.00 34.57 3.56
763 768 6.239572 GGCCCACAGGTTATTATTTTATGCAT 60.240 38.462 3.79 3.79 34.57 3.96
764 769 5.069781 GGCCCACAGGTTATTATTTTATGCA 59.930 40.000 0.00 0.00 34.57 3.96
765 770 5.069781 TGGCCCACAGGTTATTATTTTATGC 59.930 40.000 0.00 0.00 34.57 3.14
766 771 6.723298 TGGCCCACAGGTTATTATTTTATG 57.277 37.500 0.00 0.00 34.57 1.90
767 772 8.007742 TGTATGGCCCACAGGTTATTATTTTAT 58.992 33.333 0.00 0.00 34.57 1.40
786 791 4.701956 TGCTTTCTTTAGCTTGTATGGC 57.298 40.909 0.00 0.00 41.76 4.40
799 804 8.619546 GCTGAAGTGAGATAATAATGCTTTCTT 58.380 33.333 0.00 0.00 0.00 2.52
800 805 7.992033 AGCTGAAGTGAGATAATAATGCTTTCT 59.008 33.333 0.00 0.00 0.00 2.52
801 806 8.068977 CAGCTGAAGTGAGATAATAATGCTTTC 58.931 37.037 8.42 0.00 0.00 2.62
808 813 4.813161 GCAGCAGCTGAAGTGAGATAATAA 59.187 41.667 27.39 0.00 37.91 1.40
837 842 3.683847 GCTCCTTTGTATGACCTGCTGAT 60.684 47.826 0.00 0.00 0.00 2.90
859 864 2.009774 CCCCGCATGAAAAGTACTCAG 58.990 52.381 0.00 0.00 0.00 3.35
860 865 1.948611 GCCCCGCATGAAAAGTACTCA 60.949 52.381 0.00 0.00 0.00 3.41
862 867 0.328258 AGCCCCGCATGAAAAGTACT 59.672 50.000 0.00 0.00 0.00 2.73
863 868 0.451783 CAGCCCCGCATGAAAAGTAC 59.548 55.000 0.00 0.00 0.00 2.73
864 869 1.312371 GCAGCCCCGCATGAAAAGTA 61.312 55.000 0.00 0.00 0.00 2.24
866 871 2.182537 GCAGCCCCGCATGAAAAG 59.817 61.111 0.00 0.00 0.00 2.27
868 873 4.675161 TGGCAGCCCCGCATGAAA 62.675 61.111 9.64 0.00 35.87 2.69
890 898 0.667792 AACGCTTTCGAGAGTCTGGC 60.668 55.000 0.00 0.00 39.41 4.85
891 899 1.335964 TGAACGCTTTCGAGAGTCTGG 60.336 52.381 0.00 0.00 39.41 3.86
892 900 1.716581 GTGAACGCTTTCGAGAGTCTG 59.283 52.381 0.00 0.00 39.41 3.51
893 901 1.337071 TGTGAACGCTTTCGAGAGTCT 59.663 47.619 4.73 0.00 39.41 3.24
894 902 1.716581 CTGTGAACGCTTTCGAGAGTC 59.283 52.381 4.73 0.00 39.41 3.36
895 903 1.067212 ACTGTGAACGCTTTCGAGAGT 59.933 47.619 4.73 4.73 39.41 3.24
899 907 1.066454 TCTGACTGTGAACGCTTTCGA 59.934 47.619 0.00 0.00 39.41 3.71
900 908 1.487482 TCTGACTGTGAACGCTTTCG 58.513 50.000 0.00 0.00 42.43 3.46
922 930 2.487428 CGTCGAGAGGTGGAGCTG 59.513 66.667 0.00 0.00 0.00 4.24
934 942 0.931202 CACACGTGTGTTAGCGTCGA 60.931 55.000 35.03 0.00 42.83 4.20
937 945 0.872881 GTCCACACGTGTGTTAGCGT 60.873 55.000 38.40 6.58 42.83 5.07
977 985 1.082300 CTGCTTGTTGTGCGCTCTG 60.082 57.895 9.73 0.00 0.00 3.35
978 986 1.226686 CTCTGCTTGTTGTGCGCTCT 61.227 55.000 9.73 0.00 0.00 4.09
1128 1136 3.160585 CCCCCACTTGACTCTGCA 58.839 61.111 0.00 0.00 0.00 4.41
1250 1258 2.261671 GGCCGACGTGATGTGAGT 59.738 61.111 0.00 0.00 0.00 3.41
1271 1281 3.251487 TCGTTTATCTATGATCCGTGCGA 59.749 43.478 0.00 0.00 0.00 5.10
1434 1444 2.832129 TCTTCCTAAGATTCACTGCCGT 59.168 45.455 0.00 0.00 31.20 5.68
1474 1495 8.183536 TGAATAAGCAAGTAGTACGAATACGAA 58.816 33.333 0.00 0.00 42.66 3.85
1475 1496 7.696755 TGAATAAGCAAGTAGTACGAATACGA 58.303 34.615 0.00 0.00 42.66 3.43
1476 1497 7.903452 TGAATAAGCAAGTAGTACGAATACG 57.097 36.000 0.00 0.00 45.75 3.06
1480 1501 8.800972 CGTAAATGAATAAGCAAGTAGTACGAA 58.199 33.333 0.00 0.00 33.21 3.85
1481 1502 7.970061 ACGTAAATGAATAAGCAAGTAGTACGA 59.030 33.333 0.00 0.00 34.93 3.43
1482 1503 8.048436 CACGTAAATGAATAAGCAAGTAGTACG 58.952 37.037 0.00 0.00 36.45 3.67
1486 1507 7.898309 GTGACACGTAAATGAATAAGCAAGTAG 59.102 37.037 0.00 0.00 0.00 2.57
1488 1509 6.426937 AGTGACACGTAAATGAATAAGCAAGT 59.573 34.615 0.00 0.00 0.00 3.16
1502 1523 3.890756 TCCAGAAAGGTAGTGACACGTAA 59.109 43.478 0.00 0.00 39.02 3.18
1507 1531 3.072330 TGCAATCCAGAAAGGTAGTGACA 59.928 43.478 0.00 0.00 39.02 3.58
1523 1547 1.930100 CGCTCACTCGGATGCAATC 59.070 57.895 0.00 0.00 44.55 2.67
1560 1584 6.309737 CCATGGTTAAACACTCTCGTACTTAC 59.690 42.308 2.57 0.00 0.00 2.34
1577 1603 5.045942 TGAGCAGAATACAGAACCATGGTTA 60.046 40.000 29.89 15.11 38.60 2.85
1637 1670 2.520979 CGCTCCTCTAAAACTCTGTCG 58.479 52.381 0.00 0.00 0.00 4.35
1664 1697 5.885912 AGAAACACTGCTGAAGTTCCTAAAA 59.114 36.000 0.00 0.00 36.83 1.52
1762 1803 4.335315 TCCATATGAAAATTCACGAGGCAC 59.665 41.667 3.65 0.00 40.49 5.01
1843 1884 0.933097 AGTTAGATTGCTGCGCGATG 59.067 50.000 12.10 1.46 32.11 3.84
1849 1890 2.113860 TGTCCCAGTTAGATTGCTGC 57.886 50.000 0.00 0.00 0.00 5.25
1884 1925 4.555718 AGAAAAACAACGAACGCAAAAC 57.444 36.364 0.00 0.00 0.00 2.43
1894 1935 4.561213 GTGGGTCAAGAAAGAAAAACAACG 59.439 41.667 0.00 0.00 0.00 4.10
1950 1991 1.827969 AGAAAGGGTGAGGACGAGATG 59.172 52.381 0.00 0.00 0.00 2.90
1951 1992 2.104170 GAGAAAGGGTGAGGACGAGAT 58.896 52.381 0.00 0.00 0.00 2.75
1980 2044 2.262915 GGTGCCTCCTCACACGAG 59.737 66.667 0.00 0.00 38.66 4.18
2000 2070 3.931578 AGATGAAGGTTGAAGAAGACCG 58.068 45.455 0.00 0.00 40.89 4.79
2135 2206 0.886043 GCAGTGCCATGACAGTGTGA 60.886 55.000 16.91 0.00 42.01 3.58
2262 2334 2.442272 AGGTCGTAGCTCCGCCAT 60.442 61.111 12.97 0.00 0.00 4.40
2314 2386 5.593968 TCGTCAGTTGTAGCAAAAGTAGAA 58.406 37.500 0.00 0.00 0.00 2.10
2318 2390 3.131396 CCTCGTCAGTTGTAGCAAAAGT 58.869 45.455 0.00 0.00 0.00 2.66
2319 2391 3.390135 TCCTCGTCAGTTGTAGCAAAAG 58.610 45.455 0.00 0.00 0.00 2.27
2329 2403 4.385825 TGTAGCAAATTTCCTCGTCAGTT 58.614 39.130 0.00 0.00 0.00 3.16
2381 2469 1.743995 GCAATAACCGTCGCCACCT 60.744 57.895 0.00 0.00 0.00 4.00
2395 2483 1.282570 CAACGACGGTTGCAGCAAT 59.717 52.632 11.96 0.00 46.22 3.56


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

AutoCloner maintained by Alex Coulton.