Multiple sequence alignment - TraesCS2B01G124700

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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 TraesCS2B01G124700 chr2B 100.000 5747 0 0 1 5747 93120922 93126668 0.000000e+00 10613
1 TraesCS2B01G124700 chr2A 99.492 5318 25 2 1 5316 171835033 171840350 0.000000e+00 9670
2 TraesCS2B01G124700 chr4B 99.061 4793 41 2 525 5316 445328200 445332989 0.000000e+00 8599
3 TraesCS2B01G124700 chr4B 98.936 4795 46 5 525 5317 622887439 622882648 0.000000e+00 8567
4 TraesCS2B01G124700 chr4B 99.622 529 2 0 1 529 622889354 622888826 0.000000e+00 966
5 TraesCS2B01G124700 chr4B 99.244 529 4 0 1 529 445326285 445326813 0.000000e+00 955
6 TraesCS2B01G124700 chr4B 95.134 411 18 1 5322 5730 650785793 650786203 0.000000e+00 647
7 TraesCS2B01G124700 chr6A 99.041 4795 41 5 525 5317 46109085 46113876 0.000000e+00 8595
8 TraesCS2B01G124700 chr6A 98.927 932 9 1 4386 5317 46114727 46115657 0.000000e+00 1664
9 TraesCS2B01G124700 chr6A 99.434 530 2 1 1 529 46107169 46107698 0.000000e+00 961
10 TraesCS2B01G124700 chr6A 99.434 530 2 1 1 529 46138085 46138614 0.000000e+00 961
11 TraesCS2B01G124700 chr3B 98.938 4801 46 4 525 5323 777040297 777035500 0.000000e+00 8578
12 TraesCS2B01G124700 chr3B 99.244 529 4 0 1 529 777042213 777041685 0.000000e+00 955
13 TraesCS2B01G124700 chr3B 89.344 244 26 0 5315 5558 755984501 755984258 2.010000e-79 307
14 TraesCS2B01G124700 chrUn 98.128 4167 74 4 1151 5316 269555825 269559988 0.000000e+00 7260
15 TraesCS2B01G124700 chrUn 90.068 292 26 2 5317 5605 19786964 19787255 5.440000e-100 375
16 TraesCS2B01G124700 chr5A 99.010 3737 35 2 1583 5317 617311019 617307283 0.000000e+00 6695
17 TraesCS2B01G124700 chr6D 96.650 3045 84 14 1680 4716 360751640 360748606 0.000000e+00 5042
18 TraesCS2B01G124700 chr6D 97.465 1144 29 0 525 1668 360745736 360746879 0.000000e+00 1953
19 TraesCS2B01G124700 chr1D 95.992 3044 107 7 1680 4716 485426288 485423253 0.000000e+00 4931
20 TraesCS2B01G124700 chr1D 97.220 1151 25 4 525 1675 42043820 42042677 0.000000e+00 1941
21 TraesCS2B01G124700 chr1D 96.186 603 23 0 4714 5316 485423217 485422615 0.000000e+00 987
22 TraesCS2B01G124700 chr1D 99.055 529 5 0 1 529 485428129 485427601 0.000000e+00 950
23 TraesCS2B01G124700 chr1D 98.866 529 6 0 1 529 42045734 42045206 0.000000e+00 944
24 TraesCS2B01G124700 chr1D 98.299 529 9 0 1 529 162592642 162593170 0.000000e+00 928
25 TraesCS2B01G124700 chr7D 97.220 1151 27 2 525 1675 346629610 346628465 0.000000e+00 1943
26 TraesCS2B01G124700 chr5B 95.673 416 16 1 5317 5730 572742101 572742516 0.000000e+00 667
27 TraesCS2B01G124700 chr4D 89.619 289 26 3 5320 5605 296723651 296723364 1.180000e-96 364
28 TraesCS2B01G124700 chr2D 89.273 289 27 3 5320 5605 373763538 373763251 5.480000e-95 359
29 TraesCS2B01G124700 chr5D 88.581 289 30 2 5320 5605 41883387 41883099 1.190000e-91 348
30 TraesCS2B01G124700 chr5D 89.668 271 25 2 5338 5605 546661955 546661685 5.510000e-90 342
31 TraesCS2B01G124700 chr7A 87.586 290 32 3 5320 5605 69490274 69489985 3.320000e-87 333


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 TraesCS2B01G124700 chr2B 93120922 93126668 5746 False 10613.000000 10613 100.000000 1 5747 1 chr2B.!!$F1 5746
1 TraesCS2B01G124700 chr2A 171835033 171840350 5317 False 9670.000000 9670 99.492000 1 5316 1 chr2A.!!$F1 5315
2 TraesCS2B01G124700 chr4B 445326285 445332989 6704 False 4777.000000 8599 99.152500 1 5316 2 chr4B.!!$F2 5315
3 TraesCS2B01G124700 chr4B 622882648 622889354 6706 True 4766.500000 8567 99.279000 1 5317 2 chr4B.!!$R1 5316
4 TraesCS2B01G124700 chr6A 46107169 46115657 8488 False 3740.000000 8595 99.134000 1 5317 3 chr6A.!!$F2 5316
5 TraesCS2B01G124700 chr6A 46138085 46138614 529 False 961.000000 961 99.434000 1 529 1 chr6A.!!$F1 528
6 TraesCS2B01G124700 chr3B 777035500 777042213 6713 True 4766.500000 8578 99.091000 1 5323 2 chr3B.!!$R2 5322
7 TraesCS2B01G124700 chrUn 269555825 269559988 4163 False 7260.000000 7260 98.128000 1151 5316 1 chrUn.!!$F2 4165
8 TraesCS2B01G124700 chr5A 617307283 617311019 3736 True 6695.000000 6695 99.010000 1583 5317 1 chr5A.!!$R1 3734
9 TraesCS2B01G124700 chr6D 360748606 360751640 3034 True 5042.000000 5042 96.650000 1680 4716 1 chr6D.!!$R1 3036
10 TraesCS2B01G124700 chr6D 360745736 360746879 1143 False 1953.000000 1953 97.465000 525 1668 1 chr6D.!!$F1 1143
11 TraesCS2B01G124700 chr1D 485422615 485428129 5514 True 2289.333333 4931 97.077667 1 5316 3 chr1D.!!$R2 5315
12 TraesCS2B01G124700 chr1D 42042677 42045734 3057 True 1442.500000 1941 98.043000 1 1675 2 chr1D.!!$R1 1674
13 TraesCS2B01G124700 chr1D 162592642 162593170 528 False 928.000000 928 98.299000 1 529 1 chr1D.!!$F1 528
14 TraesCS2B01G124700 chr7D 346628465 346629610 1145 True 1943.000000 1943 97.220000 525 1675 1 chr7D.!!$R1 1150

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
628 2022 5.044179 TGAATATTTCCAGGAAGGTGGTCAT 60.044 40.000 1.07 0.0 38.88 3.06 F
1497 2896 0.331616 GGGAAAGGCACCCATACAGT 59.668 55.000 9.05 0.0 46.05 3.55 F
2192 3656 2.617308 GGCGTCTACTATGTGAGCACTA 59.383 50.000 1.99 0.0 0.00 2.74 F
2928 4394 7.831753 TCTCTTGTAAATTAGAGTCTGAGTGG 58.168 38.462 1.86 0.0 0.00 4.00 F
3288 4755 4.641989 AGAGAGAATTTGTGTGTGCAAGTT 59.358 37.500 0.00 0.0 32.28 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 2896 0.460109 CCGTTGATGGATCACGAGCA 60.460 55.000 4.26 0.00 36.36 4.26 R
2860 4326 0.458543 GCTCAATGCCTCGAAGACGA 60.459 55.000 0.00 0.00 45.93 4.20 R
3288 4755 4.704540 CCATGACCAAAAATACTGCACCTA 59.295 41.667 0.00 0.00 0.00 3.08 R
4515 5991 7.915397 ACAACTACATTTTGACATGACTTGAAC 59.085 33.333 0.00 0.00 0.00 3.18 R
5056 8350 3.118519 ACATTTATAGCCGACGGTTCCTT 60.119 43.478 16.73 0.92 0.00 3.36 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
628 2022 5.044179 TGAATATTTCCAGGAAGGTGGTCAT 60.044 40.000 1.07 0.00 38.88 3.06
1497 2896 0.331616 GGGAAAGGCACCCATACAGT 59.668 55.000 9.05 0.00 46.05 3.55
2192 3656 2.617308 GGCGTCTACTATGTGAGCACTA 59.383 50.000 1.99 0.00 0.00 2.74
2860 4326 8.302515 ACAAATATTTGAAGCAGGAGATCAAT 57.697 30.769 30.18 3.50 40.55 2.57
2928 4394 7.831753 TCTCTTGTAAATTAGAGTCTGAGTGG 58.168 38.462 1.86 0.00 0.00 4.00
3288 4755 4.641989 AGAGAGAATTTGTGTGTGCAAGTT 59.358 37.500 0.00 0.00 32.28 2.66
4771 8065 3.051341 AGGGGTGAGTAATGACCTATGGA 60.051 47.826 0.00 0.00 32.33 3.41
5056 8350 2.089201 TCGGAGAGTAAATGCTCGACA 58.911 47.619 0.00 0.00 40.26 4.35
5172 8466 5.163478 GGTGACAATATTACCCGACTGTACT 60.163 44.000 0.00 0.00 0.00 2.73
5329 8623 9.712305 ATATCTAGTAGTGAATATGGTTGCAAC 57.288 33.333 21.59 21.59 0.00 4.17
5330 8624 7.182817 TCTAGTAGTGAATATGGTTGCAACT 57.817 36.000 27.64 12.75 0.00 3.16
5331 8625 7.041721 TCTAGTAGTGAATATGGTTGCAACTG 58.958 38.462 27.64 0.58 0.00 3.16
5332 8626 4.943705 AGTAGTGAATATGGTTGCAACTGG 59.056 41.667 27.64 0.00 0.00 4.00
5333 8627 4.032960 AGTGAATATGGTTGCAACTGGA 57.967 40.909 27.64 13.87 0.00 3.86
5334 8628 3.758554 AGTGAATATGGTTGCAACTGGAC 59.241 43.478 27.64 12.57 0.00 4.02
5335 8629 3.088532 TGAATATGGTTGCAACTGGACC 58.911 45.455 27.64 13.42 0.00 4.46
5336 8630 3.245229 TGAATATGGTTGCAACTGGACCT 60.245 43.478 27.64 9.55 34.52 3.85
5337 8631 2.969821 TATGGTTGCAACTGGACCTT 57.030 45.000 27.64 13.00 34.52 3.50
5338 8632 2.086610 ATGGTTGCAACTGGACCTTT 57.913 45.000 27.64 2.46 34.52 3.11
5339 8633 1.110442 TGGTTGCAACTGGACCTTTG 58.890 50.000 27.64 0.00 34.52 2.77
5340 8634 1.111277 GGTTGCAACTGGACCTTTGT 58.889 50.000 27.64 0.00 0.00 2.83
5341 8635 1.480545 GGTTGCAACTGGACCTTTGTT 59.519 47.619 27.64 1.53 0.00 2.83
5342 8636 2.093711 GGTTGCAACTGGACCTTTGTTT 60.094 45.455 27.64 0.00 0.00 2.83
5343 8637 3.595173 GTTGCAACTGGACCTTTGTTTT 58.405 40.909 22.36 0.00 0.00 2.43
5344 8638 3.244033 TGCAACTGGACCTTTGTTTTG 57.756 42.857 7.87 0.00 0.00 2.44
5345 8639 2.564947 TGCAACTGGACCTTTGTTTTGT 59.435 40.909 7.87 0.00 0.00 2.83
5346 8640 3.186909 GCAACTGGACCTTTGTTTTGTC 58.813 45.455 7.87 0.00 0.00 3.18
5347 8641 3.434637 CAACTGGACCTTTGTTTTGTCG 58.565 45.455 0.00 0.00 0.00 4.35
5348 8642 2.021457 ACTGGACCTTTGTTTTGTCGG 58.979 47.619 0.00 0.00 0.00 4.79
5349 8643 2.294074 CTGGACCTTTGTTTTGTCGGA 58.706 47.619 0.00 0.00 0.00 4.55
5350 8644 2.290641 CTGGACCTTTGTTTTGTCGGAG 59.709 50.000 0.00 0.00 0.00 4.63
5351 8645 1.607148 GGACCTTTGTTTTGTCGGAGG 59.393 52.381 0.00 0.00 0.00 4.30
5352 8646 1.607148 GACCTTTGTTTTGTCGGAGGG 59.393 52.381 0.00 0.00 0.00 4.30
5353 8647 0.958822 CCTTTGTTTTGTCGGAGGGG 59.041 55.000 0.00 0.00 0.00 4.79
5354 8648 0.958822 CTTTGTTTTGTCGGAGGGGG 59.041 55.000 0.00 0.00 0.00 5.40
5355 8649 1.110518 TTTGTTTTGTCGGAGGGGGC 61.111 55.000 0.00 0.00 0.00 5.80
5356 8650 3.053896 GTTTTGTCGGAGGGGGCG 61.054 66.667 0.00 0.00 0.00 6.13
5357 8651 4.338710 TTTTGTCGGAGGGGGCGG 62.339 66.667 0.00 0.00 0.00 6.13
5375 8669 2.760385 CGAGAGAGGGGGTGGGTC 60.760 72.222 0.00 0.00 0.00 4.46
5376 8670 2.450243 GAGAGAGGGGGTGGGTCA 59.550 66.667 0.00 0.00 0.00 4.02
5377 8671 1.687493 GAGAGAGGGGGTGGGTCAG 60.687 68.421 0.00 0.00 0.00 3.51
5378 8672 2.122954 GAGAGGGGGTGGGTCAGT 59.877 66.667 0.00 0.00 0.00 3.41
5379 8673 1.539124 GAGAGGGGGTGGGTCAGTT 60.539 63.158 0.00 0.00 0.00 3.16
5380 8674 1.842381 GAGAGGGGGTGGGTCAGTTG 61.842 65.000 0.00 0.00 0.00 3.16
5381 8675 3.569200 GAGGGGGTGGGTCAGTTGC 62.569 68.421 0.00 0.00 0.00 4.17
5382 8676 3.897122 GGGGGTGGGTCAGTTGCA 61.897 66.667 0.00 0.00 0.00 4.08
5383 8677 2.440599 GGGGTGGGTCAGTTGCAT 59.559 61.111 0.00 0.00 0.00 3.96
5384 8678 1.978617 GGGGTGGGTCAGTTGCATG 60.979 63.158 0.00 0.00 0.00 4.06
5385 8679 1.228552 GGGTGGGTCAGTTGCATGT 60.229 57.895 0.00 0.00 0.00 3.21
5386 8680 1.244019 GGGTGGGTCAGTTGCATGTC 61.244 60.000 0.00 0.00 0.00 3.06
5387 8681 1.244019 GGTGGGTCAGTTGCATGTCC 61.244 60.000 0.00 0.00 0.00 4.02
5388 8682 1.302431 TGGGTCAGTTGCATGTCCG 60.302 57.895 0.00 0.00 30.13 4.79
5389 8683 1.003839 GGGTCAGTTGCATGTCCGA 60.004 57.895 0.00 0.00 30.13 4.55
5390 8684 1.298859 GGGTCAGTTGCATGTCCGAC 61.299 60.000 0.00 0.00 30.13 4.79
5391 8685 0.602638 GGTCAGTTGCATGTCCGACA 60.603 55.000 3.10 3.10 0.00 4.35
5392 8686 0.512952 GTCAGTTGCATGTCCGACAC 59.487 55.000 2.57 0.00 0.00 3.67
5393 8687 0.392706 TCAGTTGCATGTCCGACACT 59.607 50.000 2.57 0.00 0.00 3.55
5394 8688 1.616374 TCAGTTGCATGTCCGACACTA 59.384 47.619 2.57 0.00 0.00 2.74
5395 8689 1.995484 CAGTTGCATGTCCGACACTAG 59.005 52.381 2.57 0.00 0.00 2.57
5396 8690 1.893137 AGTTGCATGTCCGACACTAGA 59.107 47.619 2.57 0.00 0.00 2.43
5397 8691 1.993370 GTTGCATGTCCGACACTAGAC 59.007 52.381 2.57 0.00 0.00 2.59
5398 8692 1.253100 TGCATGTCCGACACTAGACA 58.747 50.000 2.57 0.00 46.39 3.41
5402 8696 1.253100 TGTCCGACACTAGACATGCA 58.747 50.000 0.00 0.00 38.07 3.96
5403 8697 1.616374 TGTCCGACACTAGACATGCAA 59.384 47.619 0.00 0.00 38.07 4.08
5404 8698 1.993370 GTCCGACACTAGACATGCAAC 59.007 52.381 0.00 0.00 33.08 4.17
5405 8699 1.893137 TCCGACACTAGACATGCAACT 59.107 47.619 0.00 0.00 0.00 3.16
5406 8700 1.995484 CCGACACTAGACATGCAACTG 59.005 52.381 0.00 0.00 0.00 3.16
5407 8701 1.391485 CGACACTAGACATGCAACTGC 59.609 52.381 0.00 0.00 42.50 4.40
5421 8715 3.716006 CTGCAAGTGTCGCACCCG 61.716 66.667 6.39 0.60 34.49 5.28
5422 8716 4.228567 TGCAAGTGTCGCACCCGA 62.229 61.111 6.39 0.00 42.01 5.14
5434 8728 4.329545 ACCCGACCGCAACTGCAT 62.330 61.111 2.12 0.00 42.21 3.96
5435 8729 3.803082 CCCGACCGCAACTGCATG 61.803 66.667 2.12 0.00 42.21 4.06
5436 8730 3.049674 CCGACCGCAACTGCATGT 61.050 61.111 2.12 0.00 42.21 3.21
5437 8731 2.476051 CGACCGCAACTGCATGTC 59.524 61.111 2.12 6.86 42.21 3.06
5438 8732 2.029288 CGACCGCAACTGCATGTCT 61.029 57.895 15.34 0.00 42.21 3.41
5439 8733 1.568612 CGACCGCAACTGCATGTCTT 61.569 55.000 15.34 0.00 42.21 3.01
5440 8734 0.166814 GACCGCAACTGCATGTCTTC 59.833 55.000 11.93 0.00 42.21 2.87
5441 8735 0.250467 ACCGCAACTGCATGTCTTCT 60.250 50.000 2.12 0.00 42.21 2.85
5442 8736 1.001974 ACCGCAACTGCATGTCTTCTA 59.998 47.619 2.12 0.00 42.21 2.10
5443 8737 1.662629 CCGCAACTGCATGTCTTCTAG 59.337 52.381 2.12 0.00 42.21 2.43
5444 8738 1.061711 CGCAACTGCATGTCTTCTAGC 59.938 52.381 2.12 0.00 42.21 3.42
5445 8739 1.399791 GCAACTGCATGTCTTCTAGCC 59.600 52.381 0.00 0.00 41.59 3.93
5446 8740 2.012673 CAACTGCATGTCTTCTAGCCC 58.987 52.381 0.00 0.00 0.00 5.19
5447 8741 0.176680 ACTGCATGTCTTCTAGCCCG 59.823 55.000 0.00 0.00 0.00 6.13
5448 8742 0.461548 CTGCATGTCTTCTAGCCCGA 59.538 55.000 0.00 0.00 0.00 5.14
5449 8743 0.175760 TGCATGTCTTCTAGCCCGAC 59.824 55.000 0.00 0.00 0.00 4.79
5450 8744 0.530870 GCATGTCTTCTAGCCCGACC 60.531 60.000 0.00 0.00 0.00 4.79
5451 8745 0.249073 CATGTCTTCTAGCCCGACCG 60.249 60.000 0.00 0.00 0.00 4.79
5452 8746 2.017559 ATGTCTTCTAGCCCGACCGC 62.018 60.000 0.00 0.00 0.00 5.68
5453 8747 2.361992 TCTTCTAGCCCGACCGCA 60.362 61.111 0.00 0.00 0.00 5.69
5454 8748 1.980232 TCTTCTAGCCCGACCGCAA 60.980 57.895 0.00 0.00 0.00 4.85
5455 8749 1.144057 CTTCTAGCCCGACCGCAAT 59.856 57.895 0.00 0.00 0.00 3.56
5456 8750 0.462047 CTTCTAGCCCGACCGCAATT 60.462 55.000 0.00 0.00 0.00 2.32
5457 8751 0.742990 TTCTAGCCCGACCGCAATTG 60.743 55.000 0.00 0.00 0.00 2.32
5458 8752 2.124901 TAGCCCGACCGCAATTGG 60.125 61.111 7.72 0.00 0.00 3.16
5459 8753 3.690685 TAGCCCGACCGCAATTGGG 62.691 63.158 15.23 15.23 45.47 4.12
5462 8756 3.061848 CCGACCGCAATTGGGCTT 61.062 61.111 16.63 5.82 33.52 4.35
5463 8757 2.635443 CCGACCGCAATTGGGCTTT 61.635 57.895 16.63 3.33 33.52 3.51
5464 8758 1.288752 CGACCGCAATTGGGCTTTT 59.711 52.632 16.63 0.88 33.52 2.27
5465 8759 0.319469 CGACCGCAATTGGGCTTTTT 60.319 50.000 16.63 0.00 33.52 1.94
5482 8776 2.080654 TTTTGTTCTGTGGAAGGGGG 57.919 50.000 0.00 0.00 31.46 5.40
5483 8777 0.469144 TTTGTTCTGTGGAAGGGGGC 60.469 55.000 0.00 0.00 31.46 5.80
5484 8778 2.359975 GTTCTGTGGAAGGGGGCG 60.360 66.667 0.00 0.00 31.46 6.13
5485 8779 4.344865 TTCTGTGGAAGGGGGCGC 62.345 66.667 0.00 0.00 0.00 6.53
5498 8792 4.910585 GGCGCCGGTAGATGGGTG 62.911 72.222 12.58 0.00 36.89 4.61
5499 8793 4.910585 GCGCCGGTAGATGGGTGG 62.911 72.222 1.90 0.00 34.39 4.61
5500 8794 4.235762 CGCCGGTAGATGGGTGGG 62.236 72.222 1.90 0.00 0.00 4.61
5501 8795 4.564110 GCCGGTAGATGGGTGGGC 62.564 72.222 1.90 0.00 0.00 5.36
5502 8796 3.873812 CCGGTAGATGGGTGGGCC 61.874 72.222 0.00 0.00 0.00 5.80
5503 8797 3.087253 CGGTAGATGGGTGGGCCA 61.087 66.667 0.00 0.00 36.17 5.36
5504 8798 2.675242 CGGTAGATGGGTGGGCCAA 61.675 63.158 8.40 0.00 36.17 4.52
5505 8799 1.930520 GGTAGATGGGTGGGCCAAT 59.069 57.895 8.40 0.00 36.17 3.16
5506 8800 0.261696 GGTAGATGGGTGGGCCAATT 59.738 55.000 8.40 0.00 36.17 2.32
5507 8801 1.402787 GTAGATGGGTGGGCCAATTG 58.597 55.000 8.40 0.00 36.17 2.32
5508 8802 0.396974 TAGATGGGTGGGCCAATTGC 60.397 55.000 8.40 0.00 40.16 3.56
5509 8803 1.988956 GATGGGTGGGCCAATTGCA 60.989 57.895 8.40 0.00 43.89 4.08
5510 8804 1.538382 ATGGGTGGGCCAATTGCAA 60.538 52.632 8.40 0.00 43.89 4.08
5511 8805 1.555477 ATGGGTGGGCCAATTGCAAG 61.555 55.000 8.40 0.00 43.89 4.01
5512 8806 2.046988 GGTGGGCCAATTGCAAGC 60.047 61.111 8.40 2.55 43.89 4.01
5513 8807 2.046988 GTGGGCCAATTGCAAGCC 60.047 61.111 17.60 17.60 46.37 4.35
5516 8810 3.381136 GGCCAATTGCAAGCCCGA 61.381 61.111 15.53 0.00 43.89 5.14
5517 8811 2.182537 GCCAATTGCAAGCCCGAG 59.817 61.111 4.94 0.00 40.77 4.63
5518 8812 2.342650 GCCAATTGCAAGCCCGAGA 61.343 57.895 4.94 0.00 40.77 4.04
5519 8813 1.876497 GCCAATTGCAAGCCCGAGAA 61.876 55.000 4.94 0.00 40.77 2.87
5520 8814 0.109132 CCAATTGCAAGCCCGAGAAC 60.109 55.000 4.94 0.00 0.00 3.01
5521 8815 0.597568 CAATTGCAAGCCCGAGAACA 59.402 50.000 4.94 0.00 0.00 3.18
5522 8816 1.203052 CAATTGCAAGCCCGAGAACAT 59.797 47.619 4.94 0.00 0.00 2.71
5523 8817 1.098050 ATTGCAAGCCCGAGAACATC 58.902 50.000 4.94 0.00 0.00 3.06
5524 8818 0.960364 TTGCAAGCCCGAGAACATCC 60.960 55.000 0.00 0.00 0.00 3.51
5525 8819 2.115291 GCAAGCCCGAGAACATCCC 61.115 63.158 0.00 0.00 0.00 3.85
5526 8820 1.452108 CAAGCCCGAGAACATCCCC 60.452 63.158 0.00 0.00 0.00 4.81
5527 8821 3.031417 AAGCCCGAGAACATCCCCG 62.031 63.158 0.00 0.00 0.00 5.73
5529 8823 3.781307 CCCGAGAACATCCCCGCA 61.781 66.667 0.00 0.00 0.00 5.69
5530 8824 2.267642 CCGAGAACATCCCCGCAA 59.732 61.111 0.00 0.00 0.00 4.85
5531 8825 2.106683 CCGAGAACATCCCCGCAAC 61.107 63.158 0.00 0.00 0.00 4.17
5532 8826 1.079127 CGAGAACATCCCCGCAACT 60.079 57.895 0.00 0.00 0.00 3.16
5533 8827 1.361668 CGAGAACATCCCCGCAACTG 61.362 60.000 0.00 0.00 0.00 3.16
5534 8828 1.648467 GAGAACATCCCCGCAACTGC 61.648 60.000 0.00 0.00 37.78 4.40
5535 8829 1.971167 GAACATCCCCGCAACTGCA 60.971 57.895 2.12 0.00 42.21 4.41
5536 8830 1.523154 GAACATCCCCGCAACTGCAA 61.523 55.000 2.12 0.00 42.21 4.08
5537 8831 1.526575 AACATCCCCGCAACTGCAAG 61.527 55.000 2.12 0.00 42.21 4.01
5538 8832 3.064324 ATCCCCGCAACTGCAAGC 61.064 61.111 2.12 0.00 42.21 4.01
5544 8838 4.312231 GCAACTGCAAGCGTCGCA 62.312 61.111 21.09 0.00 41.59 5.10
5545 8839 2.425773 CAACTGCAAGCGTCGCAC 60.426 61.111 21.09 8.97 37.60 5.34
5546 8840 3.649986 AACTGCAAGCGTCGCACC 61.650 61.111 21.09 7.40 37.60 5.01
5547 8841 4.609018 ACTGCAAGCGTCGCACCT 62.609 61.111 21.09 0.00 37.60 4.00
5548 8842 4.081030 CTGCAAGCGTCGCACCTG 62.081 66.667 21.09 14.11 35.08 4.00
5549 8843 4.600576 TGCAAGCGTCGCACCTGA 62.601 61.111 21.09 0.00 33.55 3.86
5550 8844 3.121030 GCAAGCGTCGCACCTGAT 61.121 61.111 21.09 0.00 0.00 2.90
5551 8845 3.084579 CAAGCGTCGCACCTGATC 58.915 61.111 21.09 0.00 0.00 2.92
5552 8846 2.507102 AAGCGTCGCACCTGATCG 60.507 61.111 21.09 0.00 0.00 3.69
5555 8849 2.809174 CGTCGCACCTGATCGCAA 60.809 61.111 0.00 0.00 0.00 4.85
5556 8850 2.778679 GTCGCACCTGATCGCAAC 59.221 61.111 0.00 0.00 0.00 4.17
5557 8851 1.738099 GTCGCACCTGATCGCAACT 60.738 57.895 0.00 0.00 0.00 3.16
5558 8852 0.457853 GTCGCACCTGATCGCAACTA 60.458 55.000 0.00 0.00 0.00 2.24
5559 8853 0.457853 TCGCACCTGATCGCAACTAC 60.458 55.000 0.00 0.00 0.00 2.73
5560 8854 1.742900 CGCACCTGATCGCAACTACG 61.743 60.000 0.00 0.00 0.00 3.51
5561 8855 0.736325 GCACCTGATCGCAACTACGT 60.736 55.000 0.00 0.00 0.00 3.57
5562 8856 1.269166 CACCTGATCGCAACTACGTC 58.731 55.000 0.00 0.00 0.00 4.34
5563 8857 0.172803 ACCTGATCGCAACTACGTCC 59.827 55.000 0.00 0.00 0.00 4.79
5564 8858 0.172578 CCTGATCGCAACTACGTCCA 59.827 55.000 0.00 0.00 0.00 4.02
5565 8859 1.403647 CCTGATCGCAACTACGTCCAA 60.404 52.381 0.00 0.00 0.00 3.53
5566 8860 1.654105 CTGATCGCAACTACGTCCAAC 59.346 52.381 0.00 0.00 0.00 3.77
5567 8861 1.271379 TGATCGCAACTACGTCCAACT 59.729 47.619 0.00 0.00 0.00 3.16
5568 8862 1.654105 GATCGCAACTACGTCCAACTG 59.346 52.381 0.00 0.00 0.00 3.16
5569 8863 0.386476 TCGCAACTACGTCCAACTGT 59.614 50.000 0.00 0.00 0.00 3.55
5570 8864 1.608109 TCGCAACTACGTCCAACTGTA 59.392 47.619 0.00 0.00 0.00 2.74
5571 8865 1.983605 CGCAACTACGTCCAACTGTAG 59.016 52.381 0.00 0.00 42.91 2.74
5576 8870 4.436242 ACTACGTCCAACTGTAGTCATG 57.564 45.455 0.00 0.00 46.15 3.07
5577 8871 2.080286 ACGTCCAACTGTAGTCATGC 57.920 50.000 0.00 0.00 0.00 4.06
5578 8872 1.343142 ACGTCCAACTGTAGTCATGCA 59.657 47.619 0.00 0.00 0.00 3.96
5579 8873 2.224185 ACGTCCAACTGTAGTCATGCAA 60.224 45.455 0.00 0.00 0.00 4.08
5580 8874 2.157668 CGTCCAACTGTAGTCATGCAAC 59.842 50.000 0.00 0.00 0.00 4.17
5581 8875 3.403038 GTCCAACTGTAGTCATGCAACT 58.597 45.455 0.00 0.00 0.00 3.16
5582 8876 3.187227 GTCCAACTGTAGTCATGCAACTG 59.813 47.826 1.14 0.00 0.00 3.16
5583 8877 3.141398 CCAACTGTAGTCATGCAACTGT 58.859 45.455 1.14 0.00 0.00 3.55
5584 8878 4.039852 TCCAACTGTAGTCATGCAACTGTA 59.960 41.667 1.14 0.00 0.00 2.74
5585 8879 4.937620 CCAACTGTAGTCATGCAACTGTAT 59.062 41.667 1.14 0.00 0.00 2.29
5586 8880 5.163824 CCAACTGTAGTCATGCAACTGTATG 60.164 44.000 1.14 1.71 39.12 2.39
5587 8881 5.152623 ACTGTAGTCATGCAACTGTATGT 57.847 39.130 7.52 0.00 38.89 2.29
5588 8882 5.171476 ACTGTAGTCATGCAACTGTATGTC 58.829 41.667 7.52 2.95 38.89 3.06
5589 8883 5.047021 ACTGTAGTCATGCAACTGTATGTCT 60.047 40.000 11.00 11.00 39.07 3.41
5590 8884 5.410924 TGTAGTCATGCAACTGTATGTCTC 58.589 41.667 9.90 4.98 37.57 3.36
5591 8885 4.815533 AGTCATGCAACTGTATGTCTCT 57.184 40.909 7.52 3.51 38.89 3.10
5592 8886 4.753233 AGTCATGCAACTGTATGTCTCTC 58.247 43.478 7.52 0.00 38.89 3.20
5593 8887 4.465660 AGTCATGCAACTGTATGTCTCTCT 59.534 41.667 7.52 0.00 38.89 3.10
5594 8888 5.654209 AGTCATGCAACTGTATGTCTCTCTA 59.346 40.000 7.52 0.00 38.89 2.43
5595 8889 6.153510 AGTCATGCAACTGTATGTCTCTCTAA 59.846 38.462 7.52 0.00 38.89 2.10
5596 8890 6.254589 GTCATGCAACTGTATGTCTCTCTAAC 59.745 42.308 7.52 0.00 38.89 2.34
5597 8891 5.984695 TGCAACTGTATGTCTCTCTAACT 57.015 39.130 0.00 0.00 0.00 2.24
5598 8892 6.346477 TGCAACTGTATGTCTCTCTAACTT 57.654 37.500 0.00 0.00 0.00 2.66
5599 8893 6.159293 TGCAACTGTATGTCTCTCTAACTTG 58.841 40.000 0.00 0.00 0.00 3.16
5600 8894 5.578727 GCAACTGTATGTCTCTCTAACTTGG 59.421 44.000 0.00 0.00 0.00 3.61
5601 8895 5.923733 ACTGTATGTCTCTCTAACTTGGG 57.076 43.478 0.00 0.00 0.00 4.12
5602 8896 5.334421 ACTGTATGTCTCTCTAACTTGGGT 58.666 41.667 0.00 0.00 0.00 4.51
5603 8897 5.186021 ACTGTATGTCTCTCTAACTTGGGTG 59.814 44.000 0.00 0.00 0.00 4.61
5604 8898 3.618690 ATGTCTCTCTAACTTGGGTGC 57.381 47.619 0.00 0.00 0.00 5.01
5605 8899 1.272490 TGTCTCTCTAACTTGGGTGCG 59.728 52.381 0.00 0.00 0.00 5.34
5606 8900 0.895530 TCTCTCTAACTTGGGTGCGG 59.104 55.000 0.00 0.00 0.00 5.69
5607 8901 0.108138 CTCTCTAACTTGGGTGCGGG 60.108 60.000 0.00 0.00 0.00 6.13
5608 8902 1.745489 CTCTAACTTGGGTGCGGGC 60.745 63.158 0.00 0.00 0.00 6.13
5609 8903 3.124921 CTAACTTGGGTGCGGGCG 61.125 66.667 0.00 0.00 0.00 6.13
5610 8904 4.708386 TAACTTGGGTGCGGGCGG 62.708 66.667 0.00 0.00 0.00 6.13
5628 8922 4.179599 GGGGAGGGCCTAGGAGCT 62.180 72.222 14.75 0.00 0.00 4.09
5629 8923 2.040359 GGGAGGGCCTAGGAGCTT 60.040 66.667 14.75 0.00 0.00 3.74
5630 8924 2.447714 GGGAGGGCCTAGGAGCTTG 61.448 68.421 14.75 0.00 0.00 4.01
5631 8925 2.447714 GGAGGGCCTAGGAGCTTGG 61.448 68.421 14.75 0.00 0.00 3.61
5632 8926 2.367512 AGGGCCTAGGAGCTTGGG 60.368 66.667 14.75 0.00 0.00 4.12
5633 8927 2.692741 GGGCCTAGGAGCTTGGGT 60.693 66.667 14.75 0.00 0.00 4.51
5634 8928 2.592308 GGCCTAGGAGCTTGGGTG 59.408 66.667 14.75 0.00 0.00 4.61
5635 8929 2.301738 GGCCTAGGAGCTTGGGTGT 61.302 63.158 14.75 0.00 0.00 4.16
5636 8930 1.222113 GCCTAGGAGCTTGGGTGTC 59.778 63.158 14.75 0.00 0.00 3.67
5637 8931 1.908483 CCTAGGAGCTTGGGTGTCC 59.092 63.158 1.05 0.00 0.00 4.02
5638 8932 1.627297 CCTAGGAGCTTGGGTGTCCC 61.627 65.000 1.05 0.00 45.71 4.46
5650 8944 3.366052 GGGTGTCCCAGTATGTGAATT 57.634 47.619 0.00 0.00 44.65 2.17
5651 8945 3.697166 GGGTGTCCCAGTATGTGAATTT 58.303 45.455 0.00 0.00 44.65 1.82
5652 8946 4.850680 GGGTGTCCCAGTATGTGAATTTA 58.149 43.478 0.00 0.00 44.65 1.40
5653 8947 5.445964 GGGTGTCCCAGTATGTGAATTTAT 58.554 41.667 0.00 0.00 44.65 1.40
5654 8948 5.891551 GGGTGTCCCAGTATGTGAATTTATT 59.108 40.000 0.00 0.00 44.65 1.40
5655 8949 6.379988 GGGTGTCCCAGTATGTGAATTTATTT 59.620 38.462 0.00 0.00 44.65 1.40
5656 8950 7.093509 GGGTGTCCCAGTATGTGAATTTATTTT 60.094 37.037 0.00 0.00 44.65 1.82
5657 8951 8.311109 GGTGTCCCAGTATGTGAATTTATTTTT 58.689 33.333 0.00 0.00 0.00 1.94
5658 8952 9.353999 GTGTCCCAGTATGTGAATTTATTTTTC 57.646 33.333 0.00 0.00 0.00 2.29
5659 8953 9.083422 TGTCCCAGTATGTGAATTTATTTTTCA 57.917 29.630 0.00 0.00 0.00 2.69
5719 9013 9.751542 TCTTTCTATTTATTTTTGCGTTTTGGA 57.248 25.926 0.00 0.00 0.00 3.53
5725 9019 8.779603 ATTTATTTTTGCGTTTTGGATTTGTG 57.220 26.923 0.00 0.00 0.00 3.33
5726 9020 5.809719 ATTTTTGCGTTTTGGATTTGTGT 57.190 30.435 0.00 0.00 0.00 3.72
5727 9021 5.613358 TTTTTGCGTTTTGGATTTGTGTT 57.387 30.435 0.00 0.00 0.00 3.32
5728 9022 6.721571 TTTTTGCGTTTTGGATTTGTGTTA 57.278 29.167 0.00 0.00 0.00 2.41
5729 9023 6.910536 TTTTGCGTTTTGGATTTGTGTTAT 57.089 29.167 0.00 0.00 0.00 1.89
5730 9024 5.896922 TTGCGTTTTGGATTTGTGTTATG 57.103 34.783 0.00 0.00 0.00 1.90
5731 9025 3.738282 TGCGTTTTGGATTTGTGTTATGC 59.262 39.130 0.00 0.00 0.00 3.14
5732 9026 3.738282 GCGTTTTGGATTTGTGTTATGCA 59.262 39.130 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
628 2022 5.546499 ACCATCTACAGAAAAACTACCCAGA 59.454 40.000 0.00 0.00 0.00 3.86
1336 2735 0.328592 TCTAGTCTGAGACCGGCTGT 59.671 55.000 9.33 0.00 32.18 4.40
1497 2896 0.460109 CCGTTGATGGATCACGAGCA 60.460 55.000 4.26 0.00 36.36 4.26
2192 3656 9.939424 ATAACCCTCTAAATTCAGTACTACTCT 57.061 33.333 0.00 0.00 0.00 3.24
2238 3702 2.167693 CGTGTCCCCATTAGCAAGTCTA 59.832 50.000 0.00 0.00 0.00 2.59
2860 4326 0.458543 GCTCAATGCCTCGAAGACGA 60.459 55.000 0.00 0.00 45.93 4.20
2928 4394 3.744942 CAGCATGTCAGCACATACCTATC 59.255 47.826 0.00 0.00 41.69 2.08
3288 4755 4.704540 CCATGACCAAAAATACTGCACCTA 59.295 41.667 0.00 0.00 0.00 3.08
4515 5991 7.915397 ACAACTACATTTTGACATGACTTGAAC 59.085 33.333 0.00 0.00 0.00 3.18
4771 8065 8.707796 TCTCTATAACCGAGACATATTTTCCT 57.292 34.615 0.00 0.00 32.86 3.36
5056 8350 3.118519 ACATTTATAGCCGACGGTTCCTT 60.119 43.478 16.73 0.92 0.00 3.36
5320 8614 1.110442 CAAAGGTCCAGTTGCAACCA 58.890 50.000 25.62 7.67 35.43 3.67
5323 8617 3.007398 ACAAAACAAAGGTCCAGTTGCAA 59.993 39.130 0.00 0.00 0.00 4.08
5324 8618 2.564947 ACAAAACAAAGGTCCAGTTGCA 59.435 40.909 5.45 0.00 0.00 4.08
5325 8619 3.186909 GACAAAACAAAGGTCCAGTTGC 58.813 45.455 5.45 0.00 0.00 4.17
5326 8620 3.434637 CGACAAAACAAAGGTCCAGTTG 58.565 45.455 4.23 4.23 0.00 3.16
5327 8621 2.425668 CCGACAAAACAAAGGTCCAGTT 59.574 45.455 0.00 0.00 0.00 3.16
5328 8622 2.021457 CCGACAAAACAAAGGTCCAGT 58.979 47.619 0.00 0.00 0.00 4.00
5329 8623 2.290641 CTCCGACAAAACAAAGGTCCAG 59.709 50.000 0.00 0.00 0.00 3.86
5330 8624 2.294074 CTCCGACAAAACAAAGGTCCA 58.706 47.619 0.00 0.00 0.00 4.02
5331 8625 1.607148 CCTCCGACAAAACAAAGGTCC 59.393 52.381 0.00 0.00 0.00 4.46
5332 8626 1.607148 CCCTCCGACAAAACAAAGGTC 59.393 52.381 0.00 0.00 0.00 3.85
5333 8627 1.687563 CCCTCCGACAAAACAAAGGT 58.312 50.000 0.00 0.00 0.00 3.50
5334 8628 0.958822 CCCCTCCGACAAAACAAAGG 59.041 55.000 0.00 0.00 0.00 3.11
5335 8629 0.958822 CCCCCTCCGACAAAACAAAG 59.041 55.000 0.00 0.00 0.00 2.77
5336 8630 1.110518 GCCCCCTCCGACAAAACAAA 61.111 55.000 0.00 0.00 0.00 2.83
5337 8631 1.529713 GCCCCCTCCGACAAAACAA 60.530 57.895 0.00 0.00 0.00 2.83
5338 8632 2.114411 GCCCCCTCCGACAAAACA 59.886 61.111 0.00 0.00 0.00 2.83
5339 8633 3.053896 CGCCCCCTCCGACAAAAC 61.054 66.667 0.00 0.00 0.00 2.43
5340 8634 4.338710 CCGCCCCCTCCGACAAAA 62.339 66.667 0.00 0.00 0.00 2.44
5358 8652 2.760385 GACCCACCCCCTCTCTCG 60.760 72.222 0.00 0.00 0.00 4.04
5359 8653 1.687493 CTGACCCACCCCCTCTCTC 60.687 68.421 0.00 0.00 0.00 3.20
5360 8654 2.049792 AACTGACCCACCCCCTCTCT 62.050 60.000 0.00 0.00 0.00 3.10
5361 8655 1.539124 AACTGACCCACCCCCTCTC 60.539 63.158 0.00 0.00 0.00 3.20
5362 8656 1.847968 CAACTGACCCACCCCCTCT 60.848 63.158 0.00 0.00 0.00 3.69
5363 8657 2.757077 CAACTGACCCACCCCCTC 59.243 66.667 0.00 0.00 0.00 4.30
5364 8658 3.580319 GCAACTGACCCACCCCCT 61.580 66.667 0.00 0.00 0.00 4.79
5365 8659 3.224007 ATGCAACTGACCCACCCCC 62.224 63.158 0.00 0.00 0.00 5.40
5366 8660 1.978617 CATGCAACTGACCCACCCC 60.979 63.158 0.00 0.00 0.00 4.95
5367 8661 1.228552 ACATGCAACTGACCCACCC 60.229 57.895 0.00 0.00 0.00 4.61
5368 8662 1.244019 GGACATGCAACTGACCCACC 61.244 60.000 0.00 0.00 0.00 4.61
5369 8663 1.577328 CGGACATGCAACTGACCCAC 61.577 60.000 0.00 0.00 0.00 4.61
5370 8664 1.302431 CGGACATGCAACTGACCCA 60.302 57.895 0.00 0.00 0.00 4.51
5371 8665 1.003839 TCGGACATGCAACTGACCC 60.004 57.895 0.00 0.00 0.00 4.46
5372 8666 0.602638 TGTCGGACATGCAACTGACC 60.603 55.000 20.24 11.78 40.43 4.02
5373 8667 0.512952 GTGTCGGACATGCAACTGAC 59.487 55.000 14.78 17.88 41.21 3.51
5374 8668 0.392706 AGTGTCGGACATGCAACTGA 59.607 50.000 14.78 0.00 0.00 3.41
5375 8669 1.995484 CTAGTGTCGGACATGCAACTG 59.005 52.381 14.78 0.00 0.00 3.16
5376 8670 1.893137 TCTAGTGTCGGACATGCAACT 59.107 47.619 14.78 8.63 0.00 3.16
5377 8671 1.993370 GTCTAGTGTCGGACATGCAAC 59.007 52.381 14.78 7.40 33.19 4.17
5378 8672 1.616374 TGTCTAGTGTCGGACATGCAA 59.384 47.619 14.78 0.00 37.52 4.08
5379 8673 1.253100 TGTCTAGTGTCGGACATGCA 58.747 50.000 14.78 6.54 37.52 3.96
5383 8677 1.253100 TGCATGTCTAGTGTCGGACA 58.747 50.000 6.76 6.76 44.84 4.02
5384 8678 1.993370 GTTGCATGTCTAGTGTCGGAC 59.007 52.381 0.00 0.00 0.00 4.79
5385 8679 1.893137 AGTTGCATGTCTAGTGTCGGA 59.107 47.619 0.00 0.00 0.00 4.55
5386 8680 1.995484 CAGTTGCATGTCTAGTGTCGG 59.005 52.381 0.00 0.00 0.00 4.79
5387 8681 1.391485 GCAGTTGCATGTCTAGTGTCG 59.609 52.381 0.00 0.00 41.59 4.35
5400 8694 1.655350 GTGCGACACTTGCAGTTGC 60.655 57.895 9.34 9.34 44.21 4.17
5401 8695 1.009675 GGTGCGACACTTGCAGTTG 60.010 57.895 9.31 0.00 44.21 3.16
5402 8696 2.186826 GGGTGCGACACTTGCAGTT 61.187 57.895 9.31 0.00 44.21 3.16
5403 8697 2.591715 GGGTGCGACACTTGCAGT 60.592 61.111 9.31 0.00 44.21 4.40
5404 8698 3.716006 CGGGTGCGACACTTGCAG 61.716 66.667 9.31 0.00 44.21 4.41
5405 8699 4.228567 TCGGGTGCGACACTTGCA 62.229 61.111 9.31 0.00 40.70 4.08
5406 8700 3.712881 GTCGGGTGCGACACTTGC 61.713 66.667 0.00 0.00 38.62 4.01
5407 8701 3.041940 GGTCGGGTGCGACACTTG 61.042 66.667 0.00 3.76 40.34 3.16
5408 8702 4.657824 CGGTCGGGTGCGACACTT 62.658 66.667 0.00 0.00 40.34 3.16
5417 8711 4.329545 ATGCAGTTGCGGTCGGGT 62.330 61.111 0.00 0.00 45.83 5.28
5418 8712 3.803082 CATGCAGTTGCGGTCGGG 61.803 66.667 0.00 0.00 45.83 5.14
5419 8713 3.027170 GACATGCAGTTGCGGTCGG 62.027 63.158 11.28 0.00 45.83 4.79
5420 8714 1.568612 AAGACATGCAGTTGCGGTCG 61.569 55.000 17.35 2.93 46.06 4.79
5421 8715 0.166814 GAAGACATGCAGTTGCGGTC 59.833 55.000 16.30 16.30 45.83 4.79
5422 8716 0.250467 AGAAGACATGCAGTTGCGGT 60.250 50.000 0.00 0.41 45.83 5.68
5423 8717 1.662629 CTAGAAGACATGCAGTTGCGG 59.337 52.381 0.00 0.00 45.83 5.69
5424 8718 1.061711 GCTAGAAGACATGCAGTTGCG 59.938 52.381 0.00 0.00 45.83 4.85
5425 8719 1.399791 GGCTAGAAGACATGCAGTTGC 59.600 52.381 0.00 0.00 42.50 4.17
5426 8720 2.012673 GGGCTAGAAGACATGCAGTTG 58.987 52.381 0.00 0.00 0.00 3.16
5427 8721 1.406069 CGGGCTAGAAGACATGCAGTT 60.406 52.381 0.00 0.00 0.00 3.16
5428 8722 0.176680 CGGGCTAGAAGACATGCAGT 59.823 55.000 0.00 0.00 0.00 4.40
5429 8723 0.461548 TCGGGCTAGAAGACATGCAG 59.538 55.000 0.00 0.00 0.00 4.41
5430 8724 0.175760 GTCGGGCTAGAAGACATGCA 59.824 55.000 0.00 0.00 35.19 3.96
5431 8725 0.530870 GGTCGGGCTAGAAGACATGC 60.531 60.000 12.51 0.00 36.68 4.06
5432 8726 0.249073 CGGTCGGGCTAGAAGACATG 60.249 60.000 12.51 0.00 36.68 3.21
5433 8727 2.017559 GCGGTCGGGCTAGAAGACAT 62.018 60.000 12.51 0.00 36.68 3.06
5434 8728 2.707849 GCGGTCGGGCTAGAAGACA 61.708 63.158 12.51 0.00 36.68 3.41
5435 8729 2.104530 GCGGTCGGGCTAGAAGAC 59.895 66.667 0.00 0.00 0.00 3.01
5436 8730 1.327690 ATTGCGGTCGGGCTAGAAGA 61.328 55.000 0.00 0.00 0.00 2.87
5437 8731 0.462047 AATTGCGGTCGGGCTAGAAG 60.462 55.000 0.00 0.00 0.00 2.85
5438 8732 0.742990 CAATTGCGGTCGGGCTAGAA 60.743 55.000 0.00 0.00 0.00 2.10
5439 8733 1.153449 CAATTGCGGTCGGGCTAGA 60.153 57.895 0.00 0.00 0.00 2.43
5440 8734 2.180204 CCAATTGCGGTCGGGCTAG 61.180 63.158 0.00 0.00 0.00 3.42
5441 8735 2.124901 CCAATTGCGGTCGGGCTA 60.125 61.111 0.00 0.00 0.00 3.93
5445 8739 2.153547 AAAAGCCCAATTGCGGTCGG 62.154 55.000 12.71 4.49 36.02 4.79
5446 8740 0.319469 AAAAAGCCCAATTGCGGTCG 60.319 50.000 12.71 0.00 36.02 4.79
5447 8741 3.605013 AAAAAGCCCAATTGCGGTC 57.395 47.368 12.71 6.92 36.02 4.79
5462 8756 2.393646 CCCCCTTCCACAGAACAAAAA 58.606 47.619 0.00 0.00 0.00 1.94
5463 8757 2.032151 GCCCCCTTCCACAGAACAAAA 61.032 52.381 0.00 0.00 0.00 2.44
5464 8758 0.469144 GCCCCCTTCCACAGAACAAA 60.469 55.000 0.00 0.00 0.00 2.83
5465 8759 1.152830 GCCCCCTTCCACAGAACAA 59.847 57.895 0.00 0.00 0.00 2.83
5466 8760 2.843545 GCCCCCTTCCACAGAACA 59.156 61.111 0.00 0.00 0.00 3.18
5467 8761 2.359975 CGCCCCCTTCCACAGAAC 60.360 66.667 0.00 0.00 0.00 3.01
5468 8762 4.344865 GCGCCCCCTTCCACAGAA 62.345 66.667 0.00 0.00 0.00 3.02
5481 8775 4.910585 CACCCATCTACCGGCGCC 62.911 72.222 19.07 19.07 0.00 6.53
5482 8776 4.910585 CCACCCATCTACCGGCGC 62.911 72.222 0.00 0.00 0.00 6.53
5483 8777 4.235762 CCCACCCATCTACCGGCG 62.236 72.222 0.00 0.00 0.00 6.46
5484 8778 4.564110 GCCCACCCATCTACCGGC 62.564 72.222 0.00 0.00 0.00 6.13
5485 8779 3.873812 GGCCCACCCATCTACCGG 61.874 72.222 0.00 0.00 0.00 5.28
5486 8780 1.994885 ATTGGCCCACCCATCTACCG 61.995 60.000 0.00 0.00 44.89 4.02
5487 8781 0.261696 AATTGGCCCACCCATCTACC 59.738 55.000 0.00 0.00 44.89 3.18
5488 8782 1.402787 CAATTGGCCCACCCATCTAC 58.597 55.000 0.00 0.00 44.89 2.59
5489 8783 0.396974 GCAATTGGCCCACCCATCTA 60.397 55.000 7.72 0.00 44.89 1.98
5490 8784 1.686800 GCAATTGGCCCACCCATCT 60.687 57.895 7.72 0.00 44.89 2.90
5491 8785 1.551908 TTGCAATTGGCCCACCCATC 61.552 55.000 7.72 0.00 44.89 3.51
5492 8786 1.538382 TTGCAATTGGCCCACCCAT 60.538 52.632 7.72 0.00 44.89 4.00
5493 8787 2.122681 TTGCAATTGGCCCACCCA 60.123 55.556 7.72 0.00 43.89 4.51
5494 8788 2.664398 CTTGCAATTGGCCCACCC 59.336 61.111 7.72 0.00 43.89 4.61
5495 8789 2.046988 GCTTGCAATTGGCCCACC 60.047 61.111 7.72 0.00 43.89 4.61
5496 8790 2.046988 GGCTTGCAATTGGCCCAC 60.047 61.111 15.53 0.00 43.89 4.61
5499 8793 3.360956 CTCGGGCTTGCAATTGGCC 62.361 63.158 17.60 17.60 43.89 5.36
5500 8794 1.876497 TTCTCGGGCTTGCAATTGGC 61.876 55.000 7.72 0.90 45.13 4.52
5501 8795 0.109132 GTTCTCGGGCTTGCAATTGG 60.109 55.000 7.72 0.00 0.00 3.16
5502 8796 0.597568 TGTTCTCGGGCTTGCAATTG 59.402 50.000 0.00 0.00 0.00 2.32
5503 8797 1.474077 GATGTTCTCGGGCTTGCAATT 59.526 47.619 0.00 0.00 0.00 2.32
5504 8798 1.098050 GATGTTCTCGGGCTTGCAAT 58.902 50.000 0.00 0.00 0.00 3.56
5505 8799 0.960364 GGATGTTCTCGGGCTTGCAA 60.960 55.000 0.00 0.00 0.00 4.08
5506 8800 1.377202 GGATGTTCTCGGGCTTGCA 60.377 57.895 0.00 0.00 0.00 4.08
5507 8801 2.115291 GGGATGTTCTCGGGCTTGC 61.115 63.158 0.00 0.00 0.00 4.01
5508 8802 1.452108 GGGGATGTTCTCGGGCTTG 60.452 63.158 0.00 0.00 0.00 4.01
5509 8803 2.998949 GGGGATGTTCTCGGGCTT 59.001 61.111 0.00 0.00 0.00 4.35
5510 8804 3.470888 CGGGGATGTTCTCGGGCT 61.471 66.667 0.00 0.00 0.00 5.19
5512 8806 3.323758 TTGCGGGGATGTTCTCGGG 62.324 63.158 0.00 0.00 0.00 5.14
5513 8807 2.106683 GTTGCGGGGATGTTCTCGG 61.107 63.158 0.00 0.00 0.00 4.63
5514 8808 1.079127 AGTTGCGGGGATGTTCTCG 60.079 57.895 0.00 0.00 0.00 4.04
5515 8809 1.648467 GCAGTTGCGGGGATGTTCTC 61.648 60.000 0.00 0.00 0.00 2.87
5516 8810 1.675641 GCAGTTGCGGGGATGTTCT 60.676 57.895 0.00 0.00 0.00 3.01
5517 8811 1.523154 TTGCAGTTGCGGGGATGTTC 61.523 55.000 0.00 0.00 45.83 3.18
5518 8812 1.526575 CTTGCAGTTGCGGGGATGTT 61.527 55.000 0.00 0.00 45.83 2.71
5519 8813 1.973281 CTTGCAGTTGCGGGGATGT 60.973 57.895 0.00 0.00 45.83 3.06
5520 8814 2.879907 CTTGCAGTTGCGGGGATG 59.120 61.111 0.00 0.00 45.83 3.51
5521 8815 3.064324 GCTTGCAGTTGCGGGGAT 61.064 61.111 0.00 0.00 45.83 3.85
5527 8821 4.312231 TGCGACGCTTGCAGTTGC 62.312 61.111 22.08 16.74 46.38 4.17
5528 8822 2.425773 GTGCGACGCTTGCAGTTG 60.426 61.111 22.08 0.00 44.21 3.16
5529 8823 3.649986 GGTGCGACGCTTGCAGTT 61.650 61.111 22.08 0.00 44.21 3.16
5530 8824 4.609018 AGGTGCGACGCTTGCAGT 62.609 61.111 22.08 0.00 44.21 4.40
5531 8825 4.081030 CAGGTGCGACGCTTGCAG 62.081 66.667 22.08 3.51 44.21 4.41
5532 8826 3.881952 ATCAGGTGCGACGCTTGCA 62.882 57.895 22.08 0.00 40.70 4.08
5533 8827 3.088500 GATCAGGTGCGACGCTTGC 62.089 63.158 22.08 10.89 0.00 4.01
5534 8828 2.792290 CGATCAGGTGCGACGCTTG 61.792 63.158 22.08 15.93 0.00 4.01
5535 8829 2.507102 CGATCAGGTGCGACGCTT 60.507 61.111 22.08 3.74 0.00 4.68
5538 8832 2.809174 TTGCGATCAGGTGCGACG 60.809 61.111 0.00 0.00 0.00 5.12
5539 8833 0.457853 TAGTTGCGATCAGGTGCGAC 60.458 55.000 3.25 3.25 44.23 5.19
5540 8834 0.457853 GTAGTTGCGATCAGGTGCGA 60.458 55.000 0.00 0.00 0.00 5.10
5541 8835 1.742900 CGTAGTTGCGATCAGGTGCG 61.743 60.000 0.00 0.00 0.00 5.34
5542 8836 0.736325 ACGTAGTTGCGATCAGGTGC 60.736 55.000 0.00 0.00 37.78 5.01
5543 8837 3.418675 ACGTAGTTGCGATCAGGTG 57.581 52.632 0.00 0.00 37.78 4.00
5549 8843 7.823647 GACTACAGTTGGACGTAGTTGCGAT 62.824 48.000 13.02 0.00 46.36 4.58
5550 8844 6.607977 GACTACAGTTGGACGTAGTTGCGA 62.608 50.000 13.02 0.00 46.36 5.10
5551 8845 4.449644 GACTACAGTTGGACGTAGTTGCG 61.450 52.174 13.02 0.00 46.36 4.85
5552 8846 2.985139 GACTACAGTTGGACGTAGTTGC 59.015 50.000 13.02 0.00 46.36 4.17
5553 8847 4.233123 TGACTACAGTTGGACGTAGTTG 57.767 45.455 13.02 0.00 46.36 3.16
5554 8848 4.806330 CATGACTACAGTTGGACGTAGTT 58.194 43.478 13.02 2.08 46.36 2.24
5556 8850 3.179830 GCATGACTACAGTTGGACGTAG 58.820 50.000 0.00 0.00 40.77 3.51
5557 8851 2.559231 TGCATGACTACAGTTGGACGTA 59.441 45.455 0.00 0.00 0.00 3.57
5558 8852 1.343142 TGCATGACTACAGTTGGACGT 59.657 47.619 0.00 0.00 0.00 4.34
5559 8853 2.078849 TGCATGACTACAGTTGGACG 57.921 50.000 0.00 0.00 0.00 4.79
5560 8854 3.187227 CAGTTGCATGACTACAGTTGGAC 59.813 47.826 0.00 0.00 0.00 4.02
5561 8855 3.181455 ACAGTTGCATGACTACAGTTGGA 60.181 43.478 0.00 0.00 0.00 3.53
5562 8856 3.141398 ACAGTTGCATGACTACAGTTGG 58.859 45.455 0.00 0.00 0.00 3.77
5563 8857 5.409520 ACATACAGTTGCATGACTACAGTTG 59.590 40.000 0.00 3.45 0.00 3.16
5564 8858 5.551233 ACATACAGTTGCATGACTACAGTT 58.449 37.500 0.00 0.00 0.00 3.16
5565 8859 5.047021 AGACATACAGTTGCATGACTACAGT 60.047 40.000 0.00 1.30 0.00 3.55
5566 8860 5.414360 AGACATACAGTTGCATGACTACAG 58.586 41.667 0.00 0.00 0.00 2.74
5567 8861 5.185828 AGAGACATACAGTTGCATGACTACA 59.814 40.000 0.00 0.00 29.36 2.74
5568 8862 5.655488 AGAGACATACAGTTGCATGACTAC 58.345 41.667 0.00 0.00 29.36 2.73
5569 8863 5.654209 AGAGAGACATACAGTTGCATGACTA 59.346 40.000 0.00 0.00 29.36 2.59
5570 8864 4.465660 AGAGAGACATACAGTTGCATGACT 59.534 41.667 0.00 0.00 31.37 3.41
5571 8865 4.753233 AGAGAGACATACAGTTGCATGAC 58.247 43.478 0.00 0.00 0.00 3.06
5572 8866 6.153510 AGTTAGAGAGACATACAGTTGCATGA 59.846 38.462 0.00 0.00 0.00 3.07
5573 8867 6.336566 AGTTAGAGAGACATACAGTTGCATG 58.663 40.000 0.00 0.00 0.00 4.06
5574 8868 6.537453 AGTTAGAGAGACATACAGTTGCAT 57.463 37.500 0.00 0.00 0.00 3.96
5575 8869 5.984695 AGTTAGAGAGACATACAGTTGCA 57.015 39.130 0.00 0.00 0.00 4.08
5576 8870 5.578727 CCAAGTTAGAGAGACATACAGTTGC 59.421 44.000 0.00 0.00 0.00 4.17
5577 8871 6.102663 CCCAAGTTAGAGAGACATACAGTTG 58.897 44.000 0.00 0.00 0.00 3.16
5578 8872 5.780793 ACCCAAGTTAGAGAGACATACAGTT 59.219 40.000 0.00 0.00 0.00 3.16
5579 8873 5.186021 CACCCAAGTTAGAGAGACATACAGT 59.814 44.000 0.00 0.00 0.00 3.55
5580 8874 5.655488 CACCCAAGTTAGAGAGACATACAG 58.345 45.833 0.00 0.00 0.00 2.74
5581 8875 4.081642 GCACCCAAGTTAGAGAGACATACA 60.082 45.833 0.00 0.00 0.00 2.29
5582 8876 4.434520 GCACCCAAGTTAGAGAGACATAC 58.565 47.826 0.00 0.00 0.00 2.39
5583 8877 3.130516 CGCACCCAAGTTAGAGAGACATA 59.869 47.826 0.00 0.00 0.00 2.29
5584 8878 2.093973 CGCACCCAAGTTAGAGAGACAT 60.094 50.000 0.00 0.00 0.00 3.06
5585 8879 1.272490 CGCACCCAAGTTAGAGAGACA 59.728 52.381 0.00 0.00 0.00 3.41
5586 8880 1.404315 CCGCACCCAAGTTAGAGAGAC 60.404 57.143 0.00 0.00 0.00 3.36
5587 8881 0.895530 CCGCACCCAAGTTAGAGAGA 59.104 55.000 0.00 0.00 0.00 3.10
5588 8882 0.108138 CCCGCACCCAAGTTAGAGAG 60.108 60.000 0.00 0.00 0.00 3.20
5589 8883 1.980052 CCCGCACCCAAGTTAGAGA 59.020 57.895 0.00 0.00 0.00 3.10
5590 8884 1.745489 GCCCGCACCCAAGTTAGAG 60.745 63.158 0.00 0.00 0.00 2.43
5591 8885 2.349755 GCCCGCACCCAAGTTAGA 59.650 61.111 0.00 0.00 0.00 2.10
5592 8886 3.124921 CGCCCGCACCCAAGTTAG 61.125 66.667 0.00 0.00 0.00 2.34
5593 8887 4.708386 CCGCCCGCACCCAAGTTA 62.708 66.667 0.00 0.00 0.00 2.24
5611 8905 3.722951 AAGCTCCTAGGCCCTCCCC 62.723 68.421 2.96 0.00 0.00 4.81
5612 8906 2.040359 AAGCTCCTAGGCCCTCCC 60.040 66.667 2.96 0.00 0.00 4.30
5613 8907 2.447714 CCAAGCTCCTAGGCCCTCC 61.448 68.421 2.96 0.00 0.00 4.30
5614 8908 2.447714 CCCAAGCTCCTAGGCCCTC 61.448 68.421 2.96 0.00 0.00 4.30
5615 8909 2.367512 CCCAAGCTCCTAGGCCCT 60.368 66.667 2.96 0.00 0.00 5.19
5616 8910 2.692741 ACCCAAGCTCCTAGGCCC 60.693 66.667 2.96 0.00 0.00 5.80
5617 8911 2.258748 GACACCCAAGCTCCTAGGCC 62.259 65.000 2.96 0.00 0.00 5.19
5618 8912 1.222113 GACACCCAAGCTCCTAGGC 59.778 63.158 2.96 0.00 0.00 3.93
5619 8913 1.627297 GGGACACCCAAGCTCCTAGG 61.627 65.000 0.82 0.82 44.65 3.02
5620 8914 1.908483 GGGACACCCAAGCTCCTAG 59.092 63.158 1.54 0.00 44.65 3.02
5621 8915 4.147135 GGGACACCCAAGCTCCTA 57.853 61.111 1.54 0.00 44.65 2.94
5630 8924 3.366052 AATTCACATACTGGGACACCC 57.634 47.619 0.00 0.00 45.71 4.61
5631 8925 7.404671 AAATAAATTCACATACTGGGACACC 57.595 36.000 0.00 0.00 37.24 4.16
5632 8926 9.353999 GAAAAATAAATTCACATACTGGGACAC 57.646 33.333 0.00 0.00 23.46 3.67
5633 8927 9.083422 TGAAAAATAAATTCACATACTGGGACA 57.917 29.630 0.00 0.00 32.10 4.02
5693 8987 9.751542 TCCAAAACGCAAAAATAAATAGAAAGA 57.248 25.926 0.00 0.00 0.00 2.52
5699 8993 9.869844 CACAAATCCAAAACGCAAAAATAAATA 57.130 25.926 0.00 0.00 0.00 1.40
5700 8994 8.401709 ACACAAATCCAAAACGCAAAAATAAAT 58.598 25.926 0.00 0.00 0.00 1.40
5701 8995 7.752695 ACACAAATCCAAAACGCAAAAATAAA 58.247 26.923 0.00 0.00 0.00 1.40
5702 8996 7.308782 ACACAAATCCAAAACGCAAAAATAA 57.691 28.000 0.00 0.00 0.00 1.40
5703 8997 6.910536 ACACAAATCCAAAACGCAAAAATA 57.089 29.167 0.00 0.00 0.00 1.40
5704 8998 5.809719 ACACAAATCCAAAACGCAAAAAT 57.190 30.435 0.00 0.00 0.00 1.82
5705 8999 5.613358 AACACAAATCCAAAACGCAAAAA 57.387 30.435 0.00 0.00 0.00 1.94
5706 9000 6.709643 CATAACACAAATCCAAAACGCAAAA 58.290 32.000 0.00 0.00 0.00 2.44
5707 9001 5.277058 GCATAACACAAATCCAAAACGCAAA 60.277 36.000 0.00 0.00 0.00 3.68
5708 9002 4.210120 GCATAACACAAATCCAAAACGCAA 59.790 37.500 0.00 0.00 0.00 4.85
5709 9003 3.738282 GCATAACACAAATCCAAAACGCA 59.262 39.130 0.00 0.00 0.00 5.24
5710 9004 3.738282 TGCATAACACAAATCCAAAACGC 59.262 39.130 0.00 0.00 0.00 4.84
5724 9018 0.887247 GCCCATGTGTGTGCATAACA 59.113 50.000 1.34 1.34 36.04 2.41
5725 9019 1.135315 CAGCCCATGTGTGTGCATAAC 60.135 52.381 0.00 0.00 30.44 1.89
5726 9020 1.175654 CAGCCCATGTGTGTGCATAA 58.824 50.000 0.00 0.00 30.44 1.90
5727 9021 1.314534 GCAGCCCATGTGTGTGCATA 61.315 55.000 0.00 0.00 34.18 3.14
5728 9022 2.642254 GCAGCCCATGTGTGTGCAT 61.642 57.895 0.00 0.00 34.18 3.96
5729 9023 3.296836 GCAGCCCATGTGTGTGCA 61.297 61.111 0.00 0.00 34.18 4.57


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

AutoCloner maintained by Alex Coulton.