Multiple sequence alignment - TraesCS1D01G344000

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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 TraesCS1D01G344000 chr1D 100.000 6791 0 0 1 6791 432790406 432797196 0.000000e+00 12541.0
1 TraesCS1D01G344000 chr1D 100.000 42 0 0 5543 5584 432795906 432795947 2.030000e-10 78.7
2 TraesCS1D01G344000 chr1D 100.000 42 0 0 5501 5542 432795948 432795989 2.030000e-10 78.7
3 TraesCS1D01G344000 chr1A 93.347 2405 99 26 994 3362 531227588 531229967 0.000000e+00 3498.0
4 TraesCS1D01G344000 chr1A 98.062 1290 19 4 3373 4660 531230064 531231349 0.000000e+00 2239.0
5 TraesCS1D01G344000 chr1A 94.304 632 24 4 1 630 531226599 531227220 0.000000e+00 957.0
6 TraesCS1D01G344000 chr1A 94.639 429 20 3 5113 5541 531236925 531237350 0.000000e+00 662.0
7 TraesCS1D01G344000 chr1A 82.670 779 57 45 5907 6648 531237634 531238371 2.690000e-173 619.0
8 TraesCS1D01G344000 chr1A 96.524 374 10 2 4733 5104 531231514 531231886 3.480000e-172 616.0
9 TraesCS1D01G344000 chr1A 91.793 329 19 3 5543 5869 531237311 531237633 1.040000e-122 451.0
10 TraesCS1D01G344000 chr1A 91.083 157 11 2 689 844 531227342 531227496 6.900000e-50 209.0
11 TraesCS1D01G344000 chr1A 95.122 82 4 0 4656 4737 531231389 531231470 5.530000e-26 130.0
12 TraesCS1D01G344000 chr1A 94.000 50 2 1 637 686 531227263 531227311 2.630000e-09 75.0
13 TraesCS1D01G344000 chr1B 94.851 2117 72 16 2571 4660 584147132 584149238 0.000000e+00 3271.0
14 TraesCS1D01G344000 chr1B 95.342 1653 54 12 926 2569 584145450 584147088 0.000000e+00 2604.0
15 TraesCS1D01G344000 chr1B 90.771 1051 67 15 5543 6579 584155984 584157018 0.000000e+00 1376.0
16 TraesCS1D01G344000 chr1B 95.435 460 18 2 5085 5544 584155569 584156025 0.000000e+00 730.0
17 TraesCS1D01G344000 chr1B 83.192 827 53 37 153 935 584144027 584144811 0.000000e+00 678.0
18 TraesCS1D01G344000 chr1B 97.802 364 7 1 4733 5096 584149402 584149764 1.610000e-175 627.0
19 TraesCS1D01G344000 chr1B 97.802 364 7 1 4733 5096 584150111 584150473 1.610000e-175 627.0
20 TraesCS1D01G344000 chr1B 84.884 172 7 8 6584 6737 584157073 584157243 9.120000e-34 156.0
21 TraesCS1D01G344000 chr1B 93.902 82 5 0 4656 4737 584149278 584149359 2.570000e-24 124.0
22 TraesCS1D01G344000 chr1B 93.902 82 5 0 4656 4737 584149987 584150068 2.570000e-24 124.0
23 TraesCS1D01G344000 chr1B 92.424 66 3 2 4597 4660 584149882 584149947 7.250000e-15 93.5
24 TraesCS1D01G344000 chr1B 97.222 36 1 0 4622 4657 584149899 584149864 2.050000e-05 62.1
25 TraesCS1D01G344000 chr7B 95.556 90 3 1 4514 4602 22075113 22075024 7.100000e-30 143.0
26 TraesCS1D01G344000 chr7B 88.764 89 10 0 4514 4602 22265865 22265777 7.200000e-20 110.0
27 TraesCS1D01G344000 chr7D 94.444 90 4 1 4514 4602 75943357 75943268 3.300000e-28 137.0
28 TraesCS1D01G344000 chr2D 97.297 37 1 0 3508 3544 626935287 626935251 5.690000e-06 63.9
29 TraesCS1D01G344000 chr2D 100.000 28 0 0 4613 4640 492711305 492711332 1.200000e-02 52.8


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 TraesCS1D01G344000 chr1D 432790406 432797196 6790 False 4232.800000 12541 100.000000 1 6791 3 chr1D.!!$F1 6790
1 TraesCS1D01G344000 chr1A 531226599 531231886 5287 False 1103.428571 3498 94.634571 1 5104 7 chr1A.!!$F1 5103
2 TraesCS1D01G344000 chr1A 531236925 531238371 1446 False 577.333333 662 89.700667 5113 6648 3 chr1A.!!$F2 1535
3 TraesCS1D01G344000 chr1B 584144027 584150473 6446 False 1018.562500 3271 93.652125 153 5096 8 chr1B.!!$F1 4943
4 TraesCS1D01G344000 chr1B 584155569 584157243 1674 False 754.000000 1376 90.363333 5085 6737 3 chr1B.!!$F2 1652

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
445 456 0.191064 TGGAGAGTTGGAGACCCACT 59.809 55.000 0.0 0.0 43.41 4.00 F
1149 1894 0.030297 AGTGGGAGCAGATGGAGGAT 60.030 55.000 0.0 0.0 0.00 3.24 F
1567 2351 0.518636 CAAACACAGCATCCCTGACG 59.481 55.000 0.0 0.0 44.64 4.35 F
2451 3235 0.616111 TCCAAGCTCCTCCCTCTCAC 60.616 60.000 0.0 0.0 0.00 3.51 F
2607 3435 1.340399 CCACTAGGCTGATGCTCCCA 61.340 60.000 0.0 0.0 39.59 4.37 F
3373 4211 4.875536 TGTTTAGTGCCATGTGTATGCTAG 59.124 41.667 0.0 0.0 32.79 3.42 F
4208 5137 2.816087 TCCTTCTGCAAGTGATTCAAGC 59.184 45.455 0.0 0.0 33.76 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 2646 0.458669 GCATTGGCAAGGTGAGGATG 59.541 55.000 13.90 1.28 40.72 3.51 R
2430 3214 1.002792 AGAGGGAGGAGCTTGGAGG 59.997 63.158 0.00 0.00 0.00 4.30 R
2870 3701 1.803334 AATGTGTAACCGTGCACGAT 58.197 45.000 39.10 27.93 42.79 3.73 R
3345 4176 2.224621 ACACATGGCACTAAACAGCTCT 60.225 45.455 0.00 0.00 0.00 4.09 R
3654 4580 2.277591 ATGTGTGCCATGCCACCAC 61.278 57.895 4.08 3.72 34.85 4.16 R
4615 5551 1.340991 ACACTTTGTCAGGCCACAAGT 60.341 47.619 5.01 5.48 37.57 3.16 R
6101 7850 0.037590 TGCCTTGTTTAGCATCCGGT 59.962 50.000 0.00 0.00 33.08 5.28 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
48 49 2.212869 TGTTTTCGCGTGTAGTGAGT 57.787 45.000 5.77 0.00 40.88 3.41
129 130 3.128764 GCAACCTCTAGCCAAACAATACC 59.871 47.826 0.00 0.00 0.00 2.73
143 145 6.238374 CCAAACAATACCGCGAGATCTAAAAT 60.238 38.462 8.23 0.00 0.00 1.82
147 149 0.508641 CCGCGAGATCTAAAATGGCG 59.491 55.000 8.23 4.61 41.60 5.69
149 151 1.221414 GCGAGATCTAAAATGGCGCT 58.779 50.000 7.64 0.00 39.84 5.92
272 283 2.831333 CTACAGCATGCTTCTAGTGGG 58.169 52.381 19.98 6.67 42.53 4.61
300 311 0.248215 CCTAGCTCGGCAAAAATGCG 60.248 55.000 0.00 0.00 35.24 4.73
432 443 0.534427 ATGTGATGGCGCATGGAGAG 60.534 55.000 10.83 0.00 43.26 3.20
433 444 1.153289 GTGATGGCGCATGGAGAGT 60.153 57.895 10.83 0.00 0.00 3.24
434 445 0.745845 GTGATGGCGCATGGAGAGTT 60.746 55.000 10.83 0.00 0.00 3.01
435 446 0.745486 TGATGGCGCATGGAGAGTTG 60.745 55.000 10.83 0.00 0.00 3.16
436 447 1.442526 GATGGCGCATGGAGAGTTGG 61.443 60.000 10.83 0.00 0.00 3.77
437 448 1.913951 ATGGCGCATGGAGAGTTGGA 61.914 55.000 10.83 0.00 0.00 3.53
438 449 1.817099 GGCGCATGGAGAGTTGGAG 60.817 63.158 10.83 0.00 0.00 3.86
439 450 1.219124 GCGCATGGAGAGTTGGAGA 59.781 57.895 0.30 0.00 0.00 3.71
443 454 1.279496 CATGGAGAGTTGGAGACCCA 58.721 55.000 0.00 0.00 41.64 4.51
444 455 1.065854 CATGGAGAGTTGGAGACCCAC 60.066 57.143 0.00 0.00 43.41 4.61
445 456 0.191064 TGGAGAGTTGGAGACCCACT 59.809 55.000 0.00 0.00 43.41 4.00
446 457 1.353091 GGAGAGTTGGAGACCCACTT 58.647 55.000 0.00 0.00 43.41 3.16
527 540 3.849951 GAGCGAGGGATTGGCGGA 61.850 66.667 0.00 0.00 35.41 5.54
528 541 3.798954 GAGCGAGGGATTGGCGGAG 62.799 68.421 0.00 0.00 35.41 4.63
530 543 3.154473 CGAGGGATTGGCGGAGGA 61.154 66.667 0.00 0.00 0.00 3.71
610 623 4.459089 GTGCCGACCCCTGCTCTC 62.459 72.222 0.00 0.00 0.00 3.20
686 734 0.317103 CAGACGATACGGAGAAGCGG 60.317 60.000 0.00 0.00 0.00 5.52
752 829 2.757917 GACTGAGAGGAGGCCGCT 60.758 66.667 6.40 0.00 36.09 5.52
818 902 0.748005 AGATGTGTAATGGGCCGTGC 60.748 55.000 0.00 0.00 0.00 5.34
833 917 2.108157 TGCACACGTGGACTGGAC 59.892 61.111 21.57 1.31 0.00 4.02
834 918 3.036084 GCACACGTGGACTGGACG 61.036 66.667 21.57 0.00 42.62 4.79
835 919 2.355837 CACACGTGGACTGGACGG 60.356 66.667 21.57 0.00 41.21 4.79
836 920 2.520020 ACACGTGGACTGGACGGA 60.520 61.111 21.57 0.00 41.21 4.69
837 921 2.129146 ACACGTGGACTGGACGGAA 61.129 57.895 21.57 0.00 41.21 4.30
838 922 1.292223 CACGTGGACTGGACGGAAT 59.708 57.895 7.95 0.00 41.21 3.01
839 923 1.014044 CACGTGGACTGGACGGAATG 61.014 60.000 7.95 0.00 41.21 2.67
840 924 1.447838 CGTGGACTGGACGGAATGG 60.448 63.158 0.00 0.00 33.08 3.16
867 951 2.556534 GAGAAGCCTCGCGTAGTTTA 57.443 50.000 5.77 0.00 0.00 2.01
868 952 2.183636 GAGAAGCCTCGCGTAGTTTAC 58.816 52.381 5.77 0.00 0.00 2.01
870 954 1.652619 GAAGCCTCGCGTAGTTTACAC 59.347 52.381 5.77 0.00 0.00 2.90
872 956 0.712222 GCCTCGCGTAGTTTACACAC 59.288 55.000 5.77 0.00 0.00 3.82
873 957 1.931709 GCCTCGCGTAGTTTACACACA 60.932 52.381 5.77 0.00 0.00 3.72
874 958 1.717645 CCTCGCGTAGTTTACACACAC 59.282 52.381 5.77 0.00 0.00 3.82
875 959 1.717645 CTCGCGTAGTTTACACACACC 59.282 52.381 5.77 0.00 0.00 4.16
876 960 1.337703 TCGCGTAGTTTACACACACCT 59.662 47.619 5.77 0.00 0.00 4.00
877 961 2.129607 CGCGTAGTTTACACACACCTT 58.870 47.619 0.00 0.00 0.00 3.50
878 962 2.097104 CGCGTAGTTTACACACACCTTG 60.097 50.000 0.00 0.00 0.00 3.61
879 963 2.222445 GCGTAGTTTACACACACCTTGG 59.778 50.000 0.00 0.00 0.00 3.61
880 964 2.803956 CGTAGTTTACACACACCTTGGG 59.196 50.000 0.00 0.00 33.17 4.12
881 965 2.358322 AGTTTACACACACCTTGGGG 57.642 50.000 0.00 0.00 38.88 4.96
882 966 1.133606 AGTTTACACACACCTTGGGGG 60.134 52.381 0.00 0.00 41.89 5.40
914 998 2.268280 CAGGCAGCCCAGACAGAG 59.732 66.667 8.22 0.00 0.00 3.35
1016 1755 3.083997 GATGGAGGCGGAGTGGGT 61.084 66.667 0.00 0.00 0.00 4.51
1056 1798 4.933064 GACGCCGCGGAGATGGAG 62.933 72.222 35.95 14.83 0.00 3.86
1072 1814 0.974383 GGAGGAGTTCGAAAGGGTGA 59.026 55.000 0.00 0.00 0.00 4.02
1076 1818 1.615107 GAGTTCGAAAGGGTGACGCG 61.615 60.000 3.53 3.53 0.00 6.01
1149 1894 0.030297 AGTGGGAGCAGATGGAGGAT 60.030 55.000 0.00 0.00 0.00 3.24
1251 2011 3.585990 GCCGTAGCCGTAGCCGTA 61.586 66.667 0.00 0.00 41.25 4.02
1368 2128 3.711348 CCGAGAGAGCATTTCGGC 58.289 61.111 7.78 0.00 46.10 5.54
1462 2246 8.922058 ACTCTCGTTTCGCTTATTAAAGATTA 57.078 30.769 0.00 0.00 34.37 1.75
1463 2247 9.530633 ACTCTCGTTTCGCTTATTAAAGATTAT 57.469 29.630 0.00 0.00 34.37 1.28
1500 2284 3.029570 GTCATCCGGACTAAACCCTAGT 58.970 50.000 6.12 0.00 43.46 2.57
1567 2351 0.518636 CAAACACAGCATCCCTGACG 59.481 55.000 0.00 0.00 44.64 4.35
1579 2363 0.744874 CCCTGACGGAAATCTCGCTA 59.255 55.000 0.00 0.00 0.00 4.26
1588 2372 3.253677 CGGAAATCTCGCTATGTAGTCCT 59.746 47.826 0.00 0.00 0.00 3.85
1589 2373 4.551388 GGAAATCTCGCTATGTAGTCCTG 58.449 47.826 0.00 0.00 0.00 3.86
1590 2374 4.278669 GGAAATCTCGCTATGTAGTCCTGA 59.721 45.833 0.00 0.00 0.00 3.86
1591 2375 5.047660 GGAAATCTCGCTATGTAGTCCTGAT 60.048 44.000 0.00 0.00 0.00 2.90
1712 2496 0.958876 GGGAATTCGGCCGTCAAACT 60.959 55.000 27.15 0.75 0.00 2.66
1758 2542 1.496060 ATTATCAGTGCCGACCTCCA 58.504 50.000 0.00 0.00 0.00 3.86
1760 2544 0.752658 TATCAGTGCCGACCTCCATG 59.247 55.000 0.00 0.00 0.00 3.66
1761 2545 2.599645 ATCAGTGCCGACCTCCATGC 62.600 60.000 0.00 0.00 0.00 4.06
1862 2646 4.500716 GCTACTCTCTTAGATGCTGGTTCC 60.501 50.000 0.00 0.00 0.00 3.62
1984 2768 6.696583 CACAGTAATGCTCTTCTATCTCTGTG 59.303 42.308 0.00 0.00 41.39 3.66
2090 2874 2.463752 AGATGCATGGATTGGTGCTTT 58.536 42.857 2.46 0.00 41.78 3.51
2297 3081 8.320617 AGATGCCTTGGCTTTTCAATTAATAAA 58.679 29.630 13.18 0.00 0.00 1.40
2385 3169 1.462791 GTTGTGGTTGAAACGCTTCG 58.537 50.000 0.00 0.00 33.94 3.79
2430 3214 1.418264 GCAATTCTACCTCCTCCTCCC 59.582 57.143 0.00 0.00 0.00 4.30
2451 3235 0.616111 TCCAAGCTCCTCCCTCTCAC 60.616 60.000 0.00 0.00 0.00 3.51
2607 3435 1.340399 CCACTAGGCTGATGCTCCCA 61.340 60.000 0.00 0.00 39.59 4.37
2870 3701 5.600484 ACAATTTGGTATGGTTTGACCTGAA 59.400 36.000 0.78 0.00 39.58 3.02
3306 4137 7.682628 TGATCAATCTCTATGTGCATGGATTA 58.317 34.615 0.00 0.00 0.00 1.75
3373 4211 4.875536 TGTTTAGTGCCATGTGTATGCTAG 59.124 41.667 0.00 0.00 32.79 3.42
3375 4213 5.862678 TTAGTGCCATGTGTATGCTAGTA 57.137 39.130 0.00 0.00 32.79 1.82
3376 4214 4.963318 AGTGCCATGTGTATGCTAGTAT 57.037 40.909 0.00 0.00 32.79 2.12
3377 4215 5.296151 AGTGCCATGTGTATGCTAGTATT 57.704 39.130 0.00 0.00 32.79 1.89
3654 4580 7.985589 AGGGATTAGGGGTTATTAGTTACATG 58.014 38.462 0.00 0.00 0.00 3.21
3938 4864 9.145442 GGTAAGTCTAAGATCTAATTGGGTAGT 57.855 37.037 0.00 0.00 0.00 2.73
3986 4912 3.754965 AGCAGGACAAATGTAGCTTTGA 58.245 40.909 2.92 0.00 38.17 2.69
4189 5115 3.898123 TCAGGCCTAGATTGTGATACTCC 59.102 47.826 3.98 0.00 0.00 3.85
4190 5116 3.900601 CAGGCCTAGATTGTGATACTCCT 59.099 47.826 3.98 0.00 0.00 3.69
4191 5117 4.346418 CAGGCCTAGATTGTGATACTCCTT 59.654 45.833 3.98 0.00 0.00 3.36
4208 5137 2.816087 TCCTTCTGCAAGTGATTCAAGC 59.184 45.455 0.00 0.00 33.76 4.01
4480 5415 9.010029 TCCTATTTCATCAAACTGGTTTCTTAC 57.990 33.333 0.00 0.00 0.00 2.34
4614 5550 1.732941 CGCCACACTTTGCCATACTA 58.267 50.000 0.00 0.00 0.00 1.82
4615 5551 2.080693 CGCCACACTTTGCCATACTAA 58.919 47.619 0.00 0.00 0.00 2.24
4665 5651 6.951778 ACCTTAGTATACCAACCAAATTTGCT 59.048 34.615 12.92 3.84 0.00 3.91
4680 5666 8.367156 ACCAAATTTGCTCTGTGTATATTGTTT 58.633 29.630 12.92 0.00 0.00 2.83
4713 5699 6.884280 AAACATCCTCTCACCAAAGTAAAG 57.116 37.500 0.00 0.00 0.00 1.85
4847 6589 4.360951 AACCAACTTCCAGTATCGGAAA 57.639 40.909 0.00 0.00 44.42 3.13
4884 6626 4.059773 TGCTGGAGATTAATGGGGTTTT 57.940 40.909 0.00 0.00 0.00 2.43
5109 6852 5.996669 TCACAGCATGCTAGATTAACATG 57.003 39.130 22.19 7.32 42.53 3.21
5195 6938 2.033049 GCTGCTTGATGAGTAATGGCAG 59.967 50.000 0.00 0.00 45.48 4.85
5308 7051 7.228507 TGACATGTATGTTAATTATGGCAGTCC 59.771 37.037 0.00 0.00 41.95 3.85
5371 7114 1.277273 GGGCCTCTTGGTACTTACGTT 59.723 52.381 0.84 0.00 35.27 3.99
5418 7161 5.627499 ACGATTACTGTGAACAATGCAAT 57.373 34.783 0.00 0.00 0.00 3.56
5511 7254 5.566826 CGACTCCTTGTTTATCTTCCAGTCA 60.567 44.000 0.00 0.00 0.00 3.41
5526 7269 3.000727 CCAGTCACCTCCGTGTTTATTC 58.999 50.000 0.00 0.00 41.09 1.75
5527 7270 3.306780 CCAGTCACCTCCGTGTTTATTCT 60.307 47.826 0.00 0.00 41.09 2.40
5528 7271 4.315803 CAGTCACCTCCGTGTTTATTCTT 58.684 43.478 0.00 0.00 41.09 2.52
5529 7272 5.475719 CAGTCACCTCCGTGTTTATTCTTA 58.524 41.667 0.00 0.00 41.09 2.10
5530 7273 5.347907 CAGTCACCTCCGTGTTTATTCTTAC 59.652 44.000 0.00 0.00 41.09 2.34
5531 7274 4.325472 GTCACCTCCGTGTTTATTCTTACG 59.675 45.833 0.00 0.00 41.09 3.18
5532 7275 4.218200 TCACCTCCGTGTTTATTCTTACGA 59.782 41.667 0.00 0.00 41.09 3.43
5533 7276 5.105635 TCACCTCCGTGTTTATTCTTACGAT 60.106 40.000 0.00 0.00 41.09 3.73
5534 7277 6.095300 TCACCTCCGTGTTTATTCTTACGATA 59.905 38.462 0.00 0.00 41.09 2.92
5535 7278 6.921857 CACCTCCGTGTTTATTCTTACGATAT 59.078 38.462 0.00 0.00 38.72 1.63
5536 7279 7.437267 CACCTCCGTGTTTATTCTTACGATATT 59.563 37.037 0.00 0.00 38.72 1.28
5537 7280 7.983484 ACCTCCGTGTTTATTCTTACGATATTT 59.017 33.333 0.00 0.00 38.72 1.40
5538 7281 8.273557 CCTCCGTGTTTATTCTTACGATATTTG 58.726 37.037 0.00 0.00 38.72 2.32
5539 7282 8.929827 TCCGTGTTTATTCTTACGATATTTGA 57.070 30.769 0.00 0.00 38.72 2.69
5540 7283 9.368674 TCCGTGTTTATTCTTACGATATTTGAA 57.631 29.630 0.00 0.00 38.72 2.69
5541 7284 9.417284 CCGTGTTTATTCTTACGATATTTGAAC 57.583 33.333 0.00 0.00 38.72 3.18
5542 7285 9.961266 CGTGTTTATTCTTACGATATTTGAACA 57.039 29.630 0.00 0.00 38.72 3.18
5549 7292 9.613428 ATTCTTACGATATTTGAACATCTTCCA 57.387 29.630 0.00 0.00 0.00 3.53
5550 7293 8.648557 TCTTACGATATTTGAACATCTTCCAG 57.351 34.615 0.00 0.00 0.00 3.86
5551 7294 8.258007 TCTTACGATATTTGAACATCTTCCAGT 58.742 33.333 0.00 0.00 0.00 4.00
5552 7295 6.910536 ACGATATTTGAACATCTTCCAGTC 57.089 37.500 0.00 0.00 0.00 3.51
5553 7296 6.406370 ACGATATTTGAACATCTTCCAGTCA 58.594 36.000 0.00 0.00 0.00 3.41
5554 7297 6.313905 ACGATATTTGAACATCTTCCAGTCAC 59.686 38.462 0.00 0.00 0.00 3.67
5555 7298 6.238211 CGATATTTGAACATCTTCCAGTCACC 60.238 42.308 0.00 0.00 0.00 4.02
5556 7299 4.437682 TTTGAACATCTTCCAGTCACCT 57.562 40.909 0.00 0.00 0.00 4.00
5557 7300 3.685139 TGAACATCTTCCAGTCACCTC 57.315 47.619 0.00 0.00 0.00 3.85
5558 7301 2.303022 TGAACATCTTCCAGTCACCTCC 59.697 50.000 0.00 0.00 0.00 4.30
5559 7302 0.898320 ACATCTTCCAGTCACCTCCG 59.102 55.000 0.00 0.00 0.00 4.63
5560 7303 0.898320 CATCTTCCAGTCACCTCCGT 59.102 55.000 0.00 0.00 0.00 4.69
5561 7304 0.898320 ATCTTCCAGTCACCTCCGTG 59.102 55.000 0.00 0.00 41.72 4.94
5562 7305 0.469331 TCTTCCAGTCACCTCCGTGT 60.469 55.000 0.00 0.00 41.09 4.49
5706 7453 0.685097 TCAGTACCACCAAGAGGCAC 59.315 55.000 0.00 0.00 39.06 5.01
5709 7456 0.036294 GTACCACCAAGAGGCACCTC 60.036 60.000 8.74 8.74 43.03 3.85
5748 7495 1.449353 GATCCGCAGCTCCCAGATT 59.551 57.895 0.00 0.00 0.00 2.40
5825 7574 0.468226 ACAGCGAACCCTGTCTTGAA 59.532 50.000 0.00 0.00 42.10 2.69
5873 7622 2.099427 CCGCAGACTTAGAACCTAGACC 59.901 54.545 0.00 0.00 0.00 3.85
5878 7627 4.573201 CAGACTTAGAACCTAGACCGAGAG 59.427 50.000 0.00 0.00 0.00 3.20
5903 7652 3.197790 CCTGCGCCATCCTTGTCG 61.198 66.667 4.18 0.00 0.00 4.35
5941 7690 1.145377 GCCCCATATATACCCGCCG 59.855 63.158 0.00 0.00 0.00 6.46
5945 7694 1.551430 CCCATATATACCCGCCGTTCA 59.449 52.381 0.00 0.00 0.00 3.18
5946 7695 2.169769 CCCATATATACCCGCCGTTCAT 59.830 50.000 0.00 0.00 0.00 2.57
5948 7697 2.925578 TATATACCCGCCGTTCATCG 57.074 50.000 0.00 0.00 39.52 3.84
6005 7754 1.360393 AACCACCCTCTTCTTGGCCA 61.360 55.000 0.00 0.00 33.25 5.36
6021 7770 1.535462 GGCCATGTTGTGTGTACTGTC 59.465 52.381 0.00 0.00 0.00 3.51
6023 7772 2.479837 CCATGTTGTGTGTACTGTCGT 58.520 47.619 0.00 0.00 0.00 4.34
6025 7774 3.311322 CCATGTTGTGTGTACTGTCGTTT 59.689 43.478 0.00 0.00 0.00 3.60
6026 7775 4.270894 CATGTTGTGTGTACTGTCGTTTG 58.729 43.478 0.00 0.00 0.00 2.93
6027 7776 3.327626 TGTTGTGTGTACTGTCGTTTGT 58.672 40.909 0.00 0.00 0.00 2.83
6056 7805 3.060895 GCGTAGTCCGTTTCAGAAATCTG 59.939 47.826 3.99 3.99 41.16 2.90
6068 7817 3.877508 TCAGAAATCTGCTGAGATGCATG 59.122 43.478 2.46 0.00 43.46 4.06
6090 7839 2.747855 GCACACACCTAGGCTGGC 60.748 66.667 9.30 6.71 0.00 4.85
6101 7850 5.427481 ACACCTAGGCTGGCTAATAAGTTTA 59.573 40.000 9.30 0.00 0.00 2.01
6117 7866 5.622770 AAGTTTACCGGATGCTAAACAAG 57.377 39.130 21.02 0.00 35.94 3.16
6149 7902 7.817962 TCTGTGGAAGTCTGTACTTAAATAAGC 59.182 37.037 0.13 0.00 46.09 3.09
6164 7918 9.389570 ACTTAAATAAGCGTGTTATGTTGAAAC 57.610 29.630 0.13 0.00 36.79 2.78
6166 7920 9.731819 TTAAATAAGCGTGTTATGTTGAAACAA 57.268 25.926 0.00 0.00 43.03 2.83
6172 7926 5.051973 GCGTGTTATGTTGAAACAAAAGTCC 60.052 40.000 0.00 0.00 43.03 3.85
6174 7928 6.020995 CGTGTTATGTTGAAACAAAAGTCCAC 60.021 38.462 0.00 2.06 43.03 4.02
6177 7931 4.448537 TGTTGAAACAAAAGTCCACCTG 57.551 40.909 0.00 0.00 35.67 4.00
6207 7971 1.820519 TGATGCTTGGAAATGTGGCTC 59.179 47.619 0.00 0.00 0.00 4.70
6216 7980 3.181434 TGGAAATGTGGCTCCTTTGTAGT 60.181 43.478 0.00 0.00 32.51 2.73
6250 8019 2.671177 CGTGCGGCTTTGTGGAGAG 61.671 63.158 0.00 0.00 0.00 3.20
6258 8027 3.339141 GGCTTTGTGGAGAGGAAAGTAG 58.661 50.000 0.00 0.00 0.00 2.57
6263 8032 5.888982 TTGTGGAGAGGAAAGTAGAAAGT 57.111 39.130 0.00 0.00 0.00 2.66
6264 8033 5.888982 TGTGGAGAGGAAAGTAGAAAGTT 57.111 39.130 0.00 0.00 0.00 2.66
6265 8034 5.611374 TGTGGAGAGGAAAGTAGAAAGTTG 58.389 41.667 0.00 0.00 0.00 3.16
6266 8035 4.452795 GTGGAGAGGAAAGTAGAAAGTTGC 59.547 45.833 0.00 0.00 0.00 4.17
6267 8036 4.102524 TGGAGAGGAAAGTAGAAAGTTGCA 59.897 41.667 0.00 0.00 0.00 4.08
6268 8037 4.452795 GGAGAGGAAAGTAGAAAGTTGCAC 59.547 45.833 0.00 0.00 0.00 4.57
6287 8056 1.633432 ACTTGCACTTGCCATACCCTA 59.367 47.619 0.00 0.00 41.18 3.53
6309 8078 7.201714 CCCTATACGGTAATGCAGTAGAGTATC 60.202 44.444 18.62 0.00 36.04 2.24
6338 8111 1.532238 GGAAGTGGCCCTGATACCC 59.468 63.158 0.00 0.00 0.00 3.69
6355 8128 2.467880 ACCCGAGTGAATGAGTGGTAT 58.532 47.619 0.00 0.00 0.00 2.73
6375 8149 5.696724 GGTATCTCCACAATTTACTCCATCG 59.303 44.000 0.00 0.00 35.97 3.84
6527 8305 2.202837 GTAGCGATTCGGCCGGTT 60.203 61.111 27.83 13.49 38.72 4.44
6574 8358 2.282251 AGACCTGACGCTCACGGA 60.282 61.111 0.00 0.00 46.04 4.69
6644 8487 3.774066 TCTCTGCGTCTGTATGTTGATG 58.226 45.455 0.00 0.00 0.00 3.07
6645 8488 2.270923 TCTGCGTCTGTATGTTGATGC 58.729 47.619 0.00 0.00 43.32 3.91
6648 8491 3.791245 TGCGTCTGTATGTTGATGCATA 58.209 40.909 0.00 0.00 46.30 3.14
6649 8492 4.379652 TGCGTCTGTATGTTGATGCATAT 58.620 39.130 0.00 0.00 46.30 1.78
6650 8493 4.448732 TGCGTCTGTATGTTGATGCATATC 59.551 41.667 0.00 0.00 46.30 1.63
6652 8495 5.389202 GCGTCTGTATGTTGATGCATATCTG 60.389 44.000 0.00 0.00 42.76 2.90
6655 8513 7.543520 CGTCTGTATGTTGATGCATATCTGTAT 59.456 37.037 0.00 0.00 34.35 2.29
6674 8532 1.431195 TTACCTGCCAGCCCTTCCAA 61.431 55.000 0.00 0.00 0.00 3.53
6682 8540 1.117150 CAGCCCTTCCAATTCCATGG 58.883 55.000 4.97 4.97 42.12 3.66
6685 8543 0.826062 CCCTTCCAATTCCATGGTGC 59.174 55.000 12.58 0.00 41.46 5.01
6704 8565 3.999001 GTGCACAGAGATCACTTGATTGA 59.001 43.478 13.17 0.00 34.37 2.57
6709 8570 3.615937 CAGAGATCACTTGATTGACGGTG 59.384 47.826 0.00 0.00 34.37 4.94
6719 8580 8.135529 TCACTTGATTGACGGTGATAATAGTAG 58.864 37.037 0.00 0.00 34.38 2.57
6722 8583 6.213677 TGATTGACGGTGATAATAGTAGTGC 58.786 40.000 0.00 0.00 0.00 4.40
6737 8598 8.859236 AATAGTAGTGCTACGAAGTATGGATA 57.141 34.615 3.99 0.00 44.56 2.59
6738 8599 9.463902 AATAGTAGTGCTACGAAGTATGGATAT 57.536 33.333 3.99 0.00 44.56 1.63
6739 8600 7.147143 AGTAGTGCTACGAAGTATGGATATG 57.853 40.000 3.99 0.00 44.56 1.78
6740 8601 6.715718 AGTAGTGCTACGAAGTATGGATATGT 59.284 38.462 3.99 0.00 44.56 2.29
6741 8602 5.773575 AGTGCTACGAAGTATGGATATGTG 58.226 41.667 0.00 0.00 44.56 3.21
6742 8603 4.386049 GTGCTACGAAGTATGGATATGTGC 59.614 45.833 0.00 0.00 44.56 4.57
6743 8604 4.038642 TGCTACGAAGTATGGATATGTGCA 59.961 41.667 0.00 0.00 44.56 4.57
6744 8605 4.386049 GCTACGAAGTATGGATATGTGCAC 59.614 45.833 10.75 10.75 44.56 4.57
6745 8606 4.400529 ACGAAGTATGGATATGTGCACA 57.599 40.909 24.08 24.08 41.94 4.57
6746 8607 4.960938 ACGAAGTATGGATATGTGCACAT 58.039 39.130 33.20 33.20 41.94 3.21
6747 8608 6.096673 ACGAAGTATGGATATGTGCACATA 57.903 37.500 35.03 35.03 41.94 2.29
6748 8609 6.521162 ACGAAGTATGGATATGTGCACATAA 58.479 36.000 36.12 23.83 41.94 1.90
6749 8610 7.161404 ACGAAGTATGGATATGTGCACATAAT 58.839 34.615 36.12 27.71 41.94 1.28
6750 8611 7.661437 ACGAAGTATGGATATGTGCACATAATT 59.339 33.333 36.12 24.43 41.94 1.40
6751 8612 7.959109 CGAAGTATGGATATGTGCACATAATTG 59.041 37.037 36.12 17.55 41.60 2.32
6752 8613 8.696043 AAGTATGGATATGTGCACATAATTGT 57.304 30.769 36.12 23.43 41.60 2.71
6753 8614 8.696043 AGTATGGATATGTGCACATAATTGTT 57.304 30.769 36.12 23.09 41.60 2.83
6754 8615 9.135189 AGTATGGATATGTGCACATAATTGTTT 57.865 29.630 36.12 22.43 41.60 2.83
6758 8619 9.800433 TGGATATGTGCACATAATTGTTTAAAG 57.200 29.630 36.12 0.00 41.60 1.85
6759 8620 8.755018 GGATATGTGCACATAATTGTTTAAAGC 58.245 33.333 36.12 18.51 41.60 3.51
6760 8621 9.520204 GATATGTGCACATAATTGTTTAAAGCT 57.480 29.630 36.12 19.16 41.60 3.74
6761 8622 7.585286 ATGTGCACATAATTGTTTAAAGCTG 57.415 32.000 30.50 0.00 34.26 4.24
6762 8623 5.404968 TGTGCACATAATTGTTTAAAGCTGC 59.595 36.000 17.42 0.00 32.34 5.25
6763 8624 5.404968 GTGCACATAATTGTTTAAAGCTGCA 59.595 36.000 13.17 0.00 32.34 4.41
6764 8625 5.987953 TGCACATAATTGTTTAAAGCTGCAA 59.012 32.000 1.02 0.00 32.34 4.08
6765 8626 6.649973 TGCACATAATTGTTTAAAGCTGCAAT 59.350 30.769 1.02 0.00 32.34 3.56
6766 8627 7.172875 TGCACATAATTGTTTAAAGCTGCAATT 59.827 29.630 14.98 14.98 42.14 2.32
6767 8628 7.479291 GCACATAATTGTTTAAAGCTGCAATTG 59.521 33.333 17.97 0.00 40.42 2.32
6768 8629 8.497554 CACATAATTGTTTAAAGCTGCAATTGT 58.502 29.630 17.97 12.11 40.42 2.71
6769 8630 8.497554 ACATAATTGTTTAAAGCTGCAATTGTG 58.502 29.630 22.79 22.79 46.27 3.33
6770 8631 5.927954 ATTGTTTAAAGCTGCAATTGTGG 57.072 34.783 7.40 1.53 0.00 4.17
6771 8632 4.399004 TGTTTAAAGCTGCAATTGTGGT 57.601 36.364 7.40 3.52 0.00 4.16
6772 8633 4.118410 TGTTTAAAGCTGCAATTGTGGTG 58.882 39.130 7.40 0.00 0.00 4.17
6773 8634 3.383620 TTAAAGCTGCAATTGTGGTGG 57.616 42.857 7.40 0.00 0.00 4.61
6774 8635 1.412079 AAAGCTGCAATTGTGGTGGA 58.588 45.000 7.40 0.00 0.00 4.02
6775 8636 0.963962 AAGCTGCAATTGTGGTGGAG 59.036 50.000 7.40 0.00 37.49 3.86
6776 8637 0.896940 AGCTGCAATTGTGGTGGAGG 60.897 55.000 7.40 0.00 35.19 4.30
6777 8638 1.181098 GCTGCAATTGTGGTGGAGGT 61.181 55.000 7.40 0.00 35.19 3.85
6778 8639 1.331214 CTGCAATTGTGGTGGAGGTT 58.669 50.000 7.40 0.00 31.32 3.50
6779 8640 1.000060 CTGCAATTGTGGTGGAGGTTG 60.000 52.381 7.40 0.00 31.32 3.77
6780 8641 0.319813 GCAATTGTGGTGGAGGTTGC 60.320 55.000 7.40 0.00 35.74 4.17
6781 8642 1.039068 CAATTGTGGTGGAGGTTGCA 58.961 50.000 0.00 0.00 0.00 4.08
6782 8643 1.039856 AATTGTGGTGGAGGTTGCAC 58.960 50.000 0.00 0.00 38.03 4.57
6783 8644 0.185901 ATTGTGGTGGAGGTTGCACT 59.814 50.000 0.88 0.00 38.83 4.40
6784 8645 0.033601 TTGTGGTGGAGGTTGCACTT 60.034 50.000 0.88 0.00 38.83 3.16
6785 8646 0.751277 TGTGGTGGAGGTTGCACTTG 60.751 55.000 0.88 0.00 38.83 3.16
6786 8647 0.465460 GTGGTGGAGGTTGCACTTGA 60.465 55.000 0.88 0.00 38.83 3.02
6787 8648 0.478072 TGGTGGAGGTTGCACTTGAT 59.522 50.000 0.88 0.00 38.83 2.57
6788 8649 0.883833 GGTGGAGGTTGCACTTGATG 59.116 55.000 0.88 0.00 38.83 3.07
6789 8650 0.883833 GTGGAGGTTGCACTTGATGG 59.116 55.000 0.00 0.00 35.71 3.51
6790 8651 0.478072 TGGAGGTTGCACTTGATGGT 59.522 50.000 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.362556 AAACAAGAATCATCTGAACACCG 57.637 39.130 0.00 0.00 35.59 4.94
48 49 6.436847 TGAAATTATGAGGACAAATGCAAGGA 59.563 34.615 0.00 0.00 0.00 3.36
86 87 3.364964 GCTAATAAATGGGTCGCCAATCG 60.365 47.826 0.00 0.00 40.15 3.34
129 130 0.111089 GCGCCATTTTAGATCTCGCG 60.111 55.000 0.00 0.00 40.97 5.87
143 145 0.034756 ATGCATAATCGGTAGCGCCA 59.965 50.000 9.99 0.00 36.97 5.69
147 149 7.852945 GCTTATTTGATATGCATAATCGGTAGC 59.147 37.037 11.13 10.56 36.32 3.58
149 151 8.785329 TGCTTATTTGATATGCATAATCGGTA 57.215 30.769 11.13 0.00 39.89 4.02
191 193 5.045797 GGTAAATCCAACTAGGGAAGTCACT 60.046 44.000 0.00 0.00 41.12 3.41
272 283 0.595310 GCCGAGCTAGGTTCGTGATC 60.595 60.000 14.88 0.00 34.63 2.92
399 410 2.203070 ACATCAGCCGCGGAATCC 60.203 61.111 33.48 11.55 0.00 3.01
432 443 0.251209 GGGGAAAGTGGGTCTCCAAC 60.251 60.000 0.00 0.00 46.04 3.77
433 444 1.432023 GGGGGAAAGTGGGTCTCCAA 61.432 60.000 0.00 0.00 46.04 3.53
434 445 1.850755 GGGGGAAAGTGGGTCTCCA 60.851 63.158 0.00 0.00 37.38 3.86
435 446 3.087988 GGGGGAAAGTGGGTCTCC 58.912 66.667 0.00 0.00 34.56 3.71
511 524 3.854669 CTCCGCCAATCCCTCGCT 61.855 66.667 0.00 0.00 0.00 4.93
609 622 1.394572 CGCTGATTTGTGCTGATTCGA 59.605 47.619 0.00 0.00 0.00 3.71
610 623 1.129251 ACGCTGATTTGTGCTGATTCG 59.871 47.619 0.00 0.00 0.00 3.34
752 829 3.506096 CGTACGAGCTCCTCCGCA 61.506 66.667 10.44 0.00 0.00 5.69
793 877 0.108585 CCCATTACACATCTCCCCCG 59.891 60.000 0.00 0.00 0.00 5.73
800 884 1.029408 TGCACGGCCCATTACACATC 61.029 55.000 0.00 0.00 0.00 3.06
818 902 2.355837 CCGTCCAGTCCACGTGTG 60.356 66.667 15.65 6.22 35.39 3.82
833 917 2.196749 CTTCTCGTCACATCCATTCCG 58.803 52.381 0.00 0.00 0.00 4.30
834 918 1.936547 GCTTCTCGTCACATCCATTCC 59.063 52.381 0.00 0.00 0.00 3.01
835 919 1.936547 GGCTTCTCGTCACATCCATTC 59.063 52.381 0.00 0.00 0.00 2.67
836 920 1.556911 AGGCTTCTCGTCACATCCATT 59.443 47.619 0.00 0.00 0.00 3.16
837 921 1.137872 GAGGCTTCTCGTCACATCCAT 59.862 52.381 0.00 0.00 0.00 3.41
838 922 0.532573 GAGGCTTCTCGTCACATCCA 59.467 55.000 0.00 0.00 0.00 3.41
839 923 3.354131 GAGGCTTCTCGTCACATCC 57.646 57.895 0.00 0.00 0.00 3.51
861 945 2.106857 CCCCCAAGGTGTGTGTAAACTA 59.893 50.000 0.00 0.00 0.00 2.24
863 947 1.133730 TCCCCCAAGGTGTGTGTAAAC 60.134 52.381 0.00 0.00 36.75 2.01
864 948 1.223501 TCCCCCAAGGTGTGTGTAAA 58.776 50.000 0.00 0.00 36.75 2.01
867 951 0.336737 TTTTCCCCCAAGGTGTGTGT 59.663 50.000 0.00 0.00 36.75 3.72
868 952 1.490574 TTTTTCCCCCAAGGTGTGTG 58.509 50.000 0.00 0.00 36.75 3.82
896 980 3.324930 TCTGTCTGGGCTGCCTGG 61.325 66.667 19.68 11.54 0.00 4.45
914 998 0.603569 TCTCTCCGGCTGTTTCTGTC 59.396 55.000 0.00 0.00 0.00 3.51
1056 1798 1.289800 GCGTCACCCTTTCGAACTCC 61.290 60.000 0.00 0.00 0.00 3.85
1149 1894 1.676678 GCACCTGGCGGTAGATCTCA 61.677 60.000 0.00 0.00 43.24 3.27
1251 2011 4.379243 AGCAAGCACGCTACGGCT 62.379 61.111 6.88 6.88 41.55 5.52
1500 2284 3.174987 CCCCACACACTCCCCACA 61.175 66.667 0.00 0.00 0.00 4.17
1567 2351 4.278669 TCAGGACTACATAGCGAGATTTCC 59.721 45.833 0.00 0.00 0.00 3.13
1579 2363 3.746751 GCAGCCAATCATCAGGACTACAT 60.747 47.826 0.00 0.00 0.00 2.29
1588 2372 0.881600 CGATCCGCAGCCAATCATCA 60.882 55.000 3.29 0.00 0.00 3.07
1589 2373 0.882042 ACGATCCGCAGCCAATCATC 60.882 55.000 0.00 0.00 0.00 2.92
1590 2374 1.146930 ACGATCCGCAGCCAATCAT 59.853 52.632 0.00 0.00 0.00 2.45
1591 2375 1.815003 CACGATCCGCAGCCAATCA 60.815 57.895 0.00 0.00 0.00 2.57
1712 2496 1.611410 CCAAGATAGGTGTGCAGTGCA 60.611 52.381 15.37 15.37 35.60 4.57
1862 2646 0.458669 GCATTGGCAAGGTGAGGATG 59.541 55.000 13.90 1.28 40.72 3.51
2196 2980 7.865889 CCAATTCTAAAGGAAACAACTACCAAC 59.134 37.037 0.00 0.00 37.49 3.77
2321 3105 1.061421 GTCGTCGTTCAGCACAAACAA 59.939 47.619 0.00 0.00 0.00 2.83
2430 3214 1.002792 AGAGGGAGGAGCTTGGAGG 59.997 63.158 0.00 0.00 0.00 4.30
2723 3551 5.176592 ACCTTTTTAGGATTGCTCGTAGAC 58.823 41.667 0.00 0.00 0.00 2.59
2870 3701 1.803334 AATGTGTAACCGTGCACGAT 58.197 45.000 39.10 27.93 42.79 3.73
3139 3970 5.386447 CATGAGAACCTATACATCGAGTCG 58.614 45.833 6.09 6.09 0.00 4.18
3328 4159 5.817816 ACAGCTCTATTGGGAATTTAGAACG 59.182 40.000 0.00 0.00 0.00 3.95
3345 4176 2.224621 ACACATGGCACTAAACAGCTCT 60.225 45.455 0.00 0.00 0.00 4.09
3654 4580 2.277591 ATGTGTGCCATGCCACCAC 61.278 57.895 4.08 3.72 34.85 4.16
3986 4912 7.607991 CACACCTAAGGACAAGAGTAAATGAAT 59.392 37.037 0.00 0.00 0.00 2.57
4049 4975 2.777832 ATGCACCTCTTGGAGTTCTC 57.222 50.000 0.00 0.00 37.04 2.87
4189 5115 3.501062 TGAGCTTGAATCACTTGCAGAAG 59.499 43.478 0.00 0.00 35.07 2.85
4190 5116 3.251729 GTGAGCTTGAATCACTTGCAGAA 59.748 43.478 0.00 0.00 43.03 3.02
4191 5117 2.810274 GTGAGCTTGAATCACTTGCAGA 59.190 45.455 0.00 0.00 43.03 4.26
4208 5137 4.237724 TCGTTGAATTGCTAGACTGTGAG 58.762 43.478 0.00 0.00 0.00 3.51
4480 5415 5.120674 TGACAAGAATGCACTGTAAGATTCG 59.879 40.000 0.00 0.00 37.43 3.34
4584 5520 2.432206 AGTGTGGCGCCAATTTTAAC 57.568 45.000 34.66 21.10 0.00 2.01
4614 5550 1.750778 CACTTTGTCAGGCCACAAGTT 59.249 47.619 5.01 0.00 37.57 2.66
4615 5551 1.340991 ACACTTTGTCAGGCCACAAGT 60.341 47.619 5.01 5.48 37.57 3.16
4680 5666 6.180472 GGTGAGAGGATGTTTTTCCTATGAA 58.820 40.000 0.00 0.00 46.35 2.57
4713 5699 8.392612 CAAAAGGATTTGCACAATTATCATTCC 58.607 33.333 0.00 0.00 39.02 3.01
4847 6589 3.953612 TCCAGCAATTTTTGTCTCACAGT 59.046 39.130 0.00 0.00 0.00 3.55
5003 6745 8.746052 AACCGGATCAACATCAAGATATAAAA 57.254 30.769 9.46 0.00 0.00 1.52
5004 6746 8.746052 AAACCGGATCAACATCAAGATATAAA 57.254 30.769 9.46 0.00 0.00 1.40
5109 6852 4.126437 ACCAAGCCTTGTTGCAAAATAAC 58.874 39.130 0.00 0.00 0.00 1.89
5195 6938 9.908152 ATTAGAAGCAACTTGGTTTTACATTAC 57.092 29.630 7.61 0.00 38.31 1.89
5222 6965 2.826428 AGCTACACATGAGCAATACGG 58.174 47.619 0.00 0.00 42.69 4.02
5267 7010 7.875041 ACATACATGTCAGAATAGAGTAATGGC 59.125 37.037 0.00 0.00 35.87 4.40
5308 7051 3.181826 TCGCTGTGTTTTGCTATTTCG 57.818 42.857 0.00 0.00 0.00 3.46
5371 7114 3.336138 TGCACGTACCCATGATTGTTA 57.664 42.857 0.00 0.00 0.00 2.41
5418 7161 3.393970 CCTCGAGAGCAAGCCCCA 61.394 66.667 15.71 0.00 0.00 4.96
5526 7269 8.425577 ACTGGAAGATGTTCAAATATCGTAAG 57.574 34.615 4.83 0.00 37.43 2.34
5527 7270 8.038351 TGACTGGAAGATGTTCAAATATCGTAA 58.962 33.333 4.83 0.00 37.43 3.18
5528 7271 7.491372 GTGACTGGAAGATGTTCAAATATCGTA 59.509 37.037 4.83 0.00 37.43 3.43
5529 7272 6.313905 GTGACTGGAAGATGTTCAAATATCGT 59.686 38.462 4.83 0.00 37.43 3.73
5530 7273 6.238211 GGTGACTGGAAGATGTTCAAATATCG 60.238 42.308 4.83 0.00 37.43 2.92
5531 7274 6.825721 AGGTGACTGGAAGATGTTCAAATATC 59.174 38.462 4.83 0.00 41.13 1.63
5532 7275 6.725364 AGGTGACTGGAAGATGTTCAAATAT 58.275 36.000 4.83 0.00 41.13 1.28
5533 7276 6.126863 AGGTGACTGGAAGATGTTCAAATA 57.873 37.500 4.83 0.00 41.13 1.40
5534 7277 4.990526 AGGTGACTGGAAGATGTTCAAAT 58.009 39.130 4.83 0.00 41.13 2.32
5535 7278 4.389374 GAGGTGACTGGAAGATGTTCAAA 58.611 43.478 4.83 0.00 44.43 2.69
5536 7279 3.244561 GGAGGTGACTGGAAGATGTTCAA 60.245 47.826 4.83 0.00 44.43 2.69
5537 7280 2.303022 GGAGGTGACTGGAAGATGTTCA 59.697 50.000 4.83 0.00 44.43 3.18
5538 7281 2.675317 CGGAGGTGACTGGAAGATGTTC 60.675 54.545 0.00 0.00 44.43 3.18
5539 7282 1.276421 CGGAGGTGACTGGAAGATGTT 59.724 52.381 0.00 0.00 44.43 2.71
5540 7283 0.898320 CGGAGGTGACTGGAAGATGT 59.102 55.000 0.00 0.00 44.43 3.06
5541 7284 0.898320 ACGGAGGTGACTGGAAGATG 59.102 55.000 0.00 0.00 44.43 2.90
5542 7285 3.383162 ACGGAGGTGACTGGAAGAT 57.617 52.632 0.00 0.00 44.43 2.40
5543 7286 4.945645 ACGGAGGTGACTGGAAGA 57.054 55.556 0.00 0.00 44.43 2.87
5548 7291 7.811759 CGTAAGAATAAACACGGAGGTGACTG 61.812 46.154 0.62 0.00 44.06 3.51
5549 7292 5.848880 CGTAAGAATAAACACGGAGGTGACT 60.849 44.000 0.62 0.00 44.06 3.41
5550 7293 4.325472 CGTAAGAATAAACACGGAGGTGAC 59.675 45.833 0.62 0.00 44.06 3.67
5551 7294 4.218200 TCGTAAGAATAAACACGGAGGTGA 59.782 41.667 0.62 0.00 45.99 4.02
5552 7295 4.835199 CGTAAGAATAAACACGGAGGTG 57.165 45.455 0.00 0.00 46.00 4.00
5621 7368 1.970640 TCCAGGCGTATCTGCACATAT 59.029 47.619 0.00 0.00 36.28 1.78
5622 7369 1.068588 GTCCAGGCGTATCTGCACATA 59.931 52.381 0.00 0.00 36.28 2.29
5623 7370 0.179073 GTCCAGGCGTATCTGCACAT 60.179 55.000 0.00 0.00 36.28 3.21
5624 7371 1.218047 GTCCAGGCGTATCTGCACA 59.782 57.895 0.00 0.00 36.28 4.57
5706 7453 0.912486 AGAAGGATTTCGGGTGGAGG 59.088 55.000 0.00 0.00 38.38 4.30
5709 7456 0.394352 CCCAGAAGGATTTCGGGTGG 60.394 60.000 5.88 0.00 44.33 4.61
5748 7495 4.081917 TGTTCTACATCTACAACATCCGCA 60.082 41.667 0.00 0.00 0.00 5.69
5775 7522 1.134280 CGGCATCATTCTTCCTCCTGT 60.134 52.381 0.00 0.00 0.00 4.00
5825 7574 3.253432 GGAGAAAAAGAAGACGGCACAAT 59.747 43.478 0.00 0.00 0.00 2.71
5903 7652 1.588861 CTAGGCTAAAAACGAGAGCGC 59.411 52.381 0.00 0.00 42.48 5.92
5941 7690 2.531206 GCTACCACTCTGACGATGAAC 58.469 52.381 0.00 0.00 0.00 3.18
5945 7694 1.107114 CTGGCTACCACTCTGACGAT 58.893 55.000 0.00 0.00 0.00 3.73
5946 7695 0.251209 ACTGGCTACCACTCTGACGA 60.251 55.000 0.00 0.00 0.00 4.20
5948 7697 1.257743 TCACTGGCTACCACTCTGAC 58.742 55.000 0.00 0.00 0.00 3.51
6005 7754 3.936453 ACAAACGACAGTACACACAACAT 59.064 39.130 0.00 0.00 0.00 2.71
6021 7770 1.436446 CTACGCGCACACACAAACG 60.436 57.895 5.73 0.00 0.00 3.60
6023 7772 1.492319 GGACTACGCGCACACACAAA 61.492 55.000 5.73 0.00 0.00 2.83
6025 7774 2.355363 GGACTACGCGCACACACA 60.355 61.111 5.73 0.00 0.00 3.72
6026 7775 3.467119 CGGACTACGCGCACACAC 61.467 66.667 5.73 0.00 34.82 3.82
6068 7817 0.608640 AGCCTAGGTGTGTGCACTAC 59.391 55.000 19.41 16.27 44.65 2.73
6101 7850 0.037590 TGCCTTGTTTAGCATCCGGT 59.962 50.000 0.00 0.00 33.08 5.28
6117 7866 1.271054 ACAGACTTCCACAGACATGCC 60.271 52.381 0.00 0.00 0.00 4.40
6149 7902 6.020995 GTGGACTTTTGTTTCAACATAACACG 60.021 38.462 0.00 0.00 38.95 4.49
6164 7918 3.731652 TCAAATGCAGGTGGACTTTTG 57.268 42.857 0.00 0.00 34.16 2.44
6166 7920 4.344679 TCATTTCAAATGCAGGTGGACTTT 59.655 37.500 5.12 0.00 0.00 2.66
6177 7931 5.866335 TTTCCAAGCATCATTTCAAATGC 57.134 34.783 5.12 0.00 46.84 3.56
6207 7971 4.717280 ACTTCCCCAGATCTACTACAAAGG 59.283 45.833 0.00 0.00 0.00 3.11
6216 7980 0.824109 CACGCACTTCCCCAGATCTA 59.176 55.000 0.00 0.00 0.00 1.98
6265 8034 0.109132 GGTATGGCAAGTGCAAGTGC 60.109 55.000 13.24 13.24 44.36 4.40
6266 8035 0.527565 GGGTATGGCAAGTGCAAGTG 59.472 55.000 5.52 0.00 44.36 3.16
6267 8036 0.405585 AGGGTATGGCAAGTGCAAGT 59.594 50.000 5.52 0.00 44.36 3.16
6268 8037 2.418368 TAGGGTATGGCAAGTGCAAG 57.582 50.000 5.52 0.00 44.36 4.01
6287 8056 5.123502 CCGATACTCTACTGCATTACCGTAT 59.876 44.000 0.00 0.00 0.00 3.06
6309 8078 0.106149 GCCACTTCCCCACTATACCG 59.894 60.000 0.00 0.00 0.00 4.02
6338 8111 3.381590 TGGAGATACCACTCATTCACTCG 59.618 47.826 0.00 0.00 44.64 4.18
6355 8128 3.531538 GCGATGGAGTAAATTGTGGAGA 58.468 45.455 0.00 0.00 0.00 3.71
6449 8227 2.658285 GCTCCATATGCATTTGCTTCG 58.342 47.619 3.54 0.00 42.66 3.79
6451 8229 2.026641 ACGCTCCATATGCATTTGCTT 58.973 42.857 3.54 0.06 42.66 3.91
6527 8305 2.096220 TACGAAGGCGGTATTGCAAA 57.904 45.000 1.71 0.00 43.17 3.68
6540 8318 3.119779 AGGTCTCTCTCGCTTTTACGAAG 60.120 47.826 0.00 0.00 42.39 3.79
6574 8358 2.651361 CTCTCGTCCTTGTGCCGT 59.349 61.111 0.00 0.00 0.00 5.68
6644 8487 3.686726 GCTGGCAGGTAATACAGATATGC 59.313 47.826 17.64 0.00 32.86 3.14
6645 8488 4.256920 GGCTGGCAGGTAATACAGATATG 58.743 47.826 17.64 0.00 32.86 1.78
6648 8491 1.421646 GGGCTGGCAGGTAATACAGAT 59.578 52.381 17.64 0.00 32.86 2.90
6649 8492 0.837272 GGGCTGGCAGGTAATACAGA 59.163 55.000 17.64 0.00 32.86 3.41
6650 8493 0.839946 AGGGCTGGCAGGTAATACAG 59.160 55.000 17.64 0.00 0.00 2.74
6652 8495 1.477014 GGAAGGGCTGGCAGGTAATAC 60.477 57.143 17.64 0.00 0.00 1.89
6655 8513 1.431195 TTGGAAGGGCTGGCAGGTAA 61.431 55.000 17.64 0.00 0.00 2.85
6674 8532 2.240414 TGATCTCTGTGCACCATGGAAT 59.760 45.455 21.47 0.00 0.00 3.01
6682 8540 3.999001 TCAATCAAGTGATCTCTGTGCAC 59.001 43.478 10.75 10.75 32.75 4.57
6685 8543 3.615937 CCGTCAATCAAGTGATCTCTGTG 59.384 47.826 0.00 0.27 32.75 3.66
6704 8565 5.059161 TCGTAGCACTACTATTATCACCGT 58.941 41.667 6.28 0.00 34.04 4.83
6709 8570 8.944029 TCCATACTTCGTAGCACTACTATTATC 58.056 37.037 6.28 0.00 34.04 1.75
6719 8580 4.386049 GCACATATCCATACTTCGTAGCAC 59.614 45.833 0.00 0.00 0.00 4.40
6722 8583 5.528870 TGTGCACATATCCATACTTCGTAG 58.471 41.667 17.42 0.00 0.00 3.51
6737 8598 6.091169 GCAGCTTTAAACAATTATGTGCACAT 59.909 34.615 33.20 33.20 40.46 3.21
6738 8599 5.404968 GCAGCTTTAAACAATTATGTGCACA 59.595 36.000 24.08 24.08 40.46 4.57
6739 8600 5.404968 TGCAGCTTTAAACAATTATGTGCAC 59.595 36.000 10.75 10.75 40.46 4.57
6740 8601 5.536260 TGCAGCTTTAAACAATTATGTGCA 58.464 33.333 0.00 0.00 40.46 4.57
6741 8602 6.464895 TTGCAGCTTTAAACAATTATGTGC 57.535 33.333 0.00 0.00 40.46 4.57
6742 8603 8.497554 ACAATTGCAGCTTTAAACAATTATGTG 58.502 29.630 5.05 5.98 39.92 3.21
6743 8604 8.497554 CACAATTGCAGCTTTAAACAATTATGT 58.502 29.630 5.05 7.18 39.92 2.29
6744 8605 7.958567 CCACAATTGCAGCTTTAAACAATTATG 59.041 33.333 5.05 11.32 39.92 1.90
6745 8606 7.661027 ACCACAATTGCAGCTTTAAACAATTAT 59.339 29.630 5.05 2.07 39.92 1.28
6746 8607 6.989169 ACCACAATTGCAGCTTTAAACAATTA 59.011 30.769 5.05 0.00 39.92 1.40
6747 8608 5.821995 ACCACAATTGCAGCTTTAAACAATT 59.178 32.000 5.05 8.09 41.98 2.32
6748 8609 5.236911 CACCACAATTGCAGCTTTAAACAAT 59.763 36.000 5.05 0.00 34.30 2.71
6749 8610 4.569966 CACCACAATTGCAGCTTTAAACAA 59.430 37.500 5.05 0.00 0.00 2.83
6750 8611 4.118410 CACCACAATTGCAGCTTTAAACA 58.882 39.130 5.05 0.00 0.00 2.83
6751 8612 3.494251 CCACCACAATTGCAGCTTTAAAC 59.506 43.478 5.05 0.00 0.00 2.01
6752 8613 3.386078 TCCACCACAATTGCAGCTTTAAA 59.614 39.130 5.05 0.00 0.00 1.52
6753 8614 2.961741 TCCACCACAATTGCAGCTTTAA 59.038 40.909 5.05 0.00 0.00 1.52
6754 8615 2.557924 CTCCACCACAATTGCAGCTTTA 59.442 45.455 5.05 0.00 0.00 1.85
6755 8616 1.342174 CTCCACCACAATTGCAGCTTT 59.658 47.619 5.05 0.00 0.00 3.51
6756 8617 0.963962 CTCCACCACAATTGCAGCTT 59.036 50.000 5.05 0.00 0.00 3.74
6757 8618 0.896940 CCTCCACCACAATTGCAGCT 60.897 55.000 5.05 0.00 0.00 4.24
6758 8619 1.181098 ACCTCCACCACAATTGCAGC 61.181 55.000 5.05 0.00 0.00 5.25
6759 8620 1.000060 CAACCTCCACCACAATTGCAG 60.000 52.381 5.05 0.00 0.00 4.41
6760 8621 1.039068 CAACCTCCACCACAATTGCA 58.961 50.000 5.05 0.00 0.00 4.08
6761 8622 0.319813 GCAACCTCCACCACAATTGC 60.320 55.000 5.05 0.00 36.07 3.56
6762 8623 1.039068 TGCAACCTCCACCACAATTG 58.961 50.000 3.24 3.24 0.00 2.32
6763 8624 1.039856 GTGCAACCTCCACCACAATT 58.960 50.000 0.00 0.00 0.00 2.32
6764 8625 0.185901 AGTGCAACCTCCACCACAAT 59.814 50.000 0.00 0.00 37.80 2.71
6765 8626 0.033601 AAGTGCAACCTCCACCACAA 60.034 50.000 0.00 0.00 37.80 3.33
6766 8627 0.751277 CAAGTGCAACCTCCACCACA 60.751 55.000 0.00 0.00 37.80 4.17
6767 8628 0.465460 TCAAGTGCAACCTCCACCAC 60.465 55.000 0.00 0.00 37.80 4.16
6768 8629 0.478072 ATCAAGTGCAACCTCCACCA 59.522 50.000 0.00 0.00 37.80 4.17
6769 8630 0.883833 CATCAAGTGCAACCTCCACC 59.116 55.000 0.00 0.00 37.80 4.61
6770 8631 0.883833 CCATCAAGTGCAACCTCCAC 59.116 55.000 0.00 0.00 37.80 4.02
6771 8632 0.478072 ACCATCAAGTGCAACCTCCA 59.522 50.000 0.00 0.00 37.80 3.86
6772 8633 3.346426 ACCATCAAGTGCAACCTCC 57.654 52.632 0.00 0.00 37.80 4.30


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

AutoCloner maintained by Alex Coulton.