Multiple sequence alignment - TraesCS2A01G077800

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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 TraesCS2A01G077800 chr2A 100.000 8358 0 0 1 8358 35499995 35491638 0.000000e+00 15435.0
1 TraesCS2A01G077800 chr2B 93.691 3392 165 22 3388 6773 53468900 53465552 0.000000e+00 5033.0
2 TraesCS2A01G077800 chr2B 95.146 2390 89 17 889 3262 53471641 53469263 0.000000e+00 3746.0
3 TraesCS2A01G077800 chr2B 94.372 764 26 10 1 761 53472698 53471949 0.000000e+00 1157.0
4 TraesCS2A01G077800 chr2B 82.805 1105 94 46 6782 7841 53465489 53464436 0.000000e+00 900.0
5 TraesCS2A01G077800 chr2B 82.408 955 124 21 6942 7874 53415449 53414517 0.000000e+00 793.0
6 TraesCS2A01G077800 chr2B 87.927 381 35 4 7338 7709 53453100 53452722 9.960000e-119 438.0
7 TraesCS2A01G077800 chr2B 85.286 367 37 10 7704 8062 53445954 53445597 6.170000e-96 363.0
8 TraesCS2A01G077800 chr2B 84.653 202 21 4 7868 8062 53403035 53402837 8.560000e-45 193.0
9 TraesCS2A01G077800 chr2B 92.793 111 6 1 3248 3356 53469248 53469138 8.680000e-35 159.0
10 TraesCS2A01G077800 chr2B 87.156 109 12 2 7577 7684 53197488 53197381 1.140000e-23 122.0
11 TraesCS2A01G077800 chr2B 87.156 109 12 2 7577 7684 53219465 53219358 1.140000e-23 122.0
12 TraesCS2A01G077800 chr2B 92.683 82 6 0 8213 8294 53441974 53441893 1.470000e-22 119.0
13 TraesCS2A01G077800 chr2B 86.111 108 11 3 7577 7683 53060284 53060180 6.860000e-21 113.0
14 TraesCS2A01G077800 chr2B 93.750 64 4 0 8047 8110 53414168 53414105 6.910000e-16 97.1
15 TraesCS2A01G077800 chr2D 94.212 3231 123 28 1 3184 32480532 32477319 0.000000e+00 4872.0
16 TraesCS2A01G077800 chr2D 93.457 2583 121 18 3419 5977 32477025 32474467 0.000000e+00 3790.0
17 TraesCS2A01G077800 chr2D 94.905 2316 60 8 5976 8272 32474305 32472029 0.000000e+00 3570.0
18 TraesCS2A01G077800 chr2D 93.125 160 8 2 3231 3388 32477320 32477162 1.810000e-56 231.0
19 TraesCS2A01G077800 chr2D 81.395 172 24 8 7586 7754 32434611 32434445 5.260000e-27 134.0
20 TraesCS2A01G077800 chr2D 88.073 109 11 2 7577 7684 32416285 32416178 2.450000e-25 128.0
21 TraesCS2A01G077800 chr2D 100.000 30 0 0 8329 8358 394051977 394052006 1.000000e-03 56.5
22 TraesCS2A01G077800 chr2D 100.000 30 0 0 8329 8358 558198856 558198885 1.000000e-03 56.5
23 TraesCS2A01G077800 chr3A 100.000 31 0 0 8328 8358 15457835 15457805 3.260000e-04 58.4
24 TraesCS2A01G077800 chr7D 100.000 30 0 0 8329 8358 53429349 53429320 1.000000e-03 56.5
25 TraesCS2A01G077800 chr5D 100.000 30 0 0 8329 8358 330900425 330900396 1.000000e-03 56.5
26 TraesCS2A01G077800 chr4B 100.000 30 0 0 8329 8358 28960863 28960834 1.000000e-03 56.5
27 TraesCS2A01G077800 chr4A 100.000 30 0 0 8329 8358 596787555 596787526 1.000000e-03 56.5
28 TraesCS2A01G077800 chr3D 100.000 30 0 0 8329 8358 5869285 5869256 1.000000e-03 56.5
29 TraesCS2A01G077800 chr1D 100.000 30 0 0 8329 8358 58567865 58567836 1.000000e-03 56.5


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 TraesCS2A01G077800 chr2A 35491638 35499995 8357 True 15435.00 15435 100.00000 1 8358 1 chr2A.!!$R1 8357
1 TraesCS2A01G077800 chr2B 53464436 53472698 8262 True 2199.00 5033 91.76140 1 7841 5 chr2B.!!$R8 7840
2 TraesCS2A01G077800 chr2B 53414105 53415449 1344 True 445.05 793 88.07900 6942 8110 2 chr2B.!!$R6 1168
3 TraesCS2A01G077800 chr2B 53441893 53445954 4061 True 241.00 363 88.98450 7704 8294 2 chr2B.!!$R7 590
4 TraesCS2A01G077800 chr2D 32472029 32480532 8503 True 3115.75 4872 93.92475 1 8272 4 chr2D.!!$R3 8271

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
579 585 1.396996 CTTGTCGGGCCTACAATTTCG 59.603 52.381 22.18 8.52 36.33 3.46 F
1308 1562 0.512518 TCGATGCTTGACTGCAAACG 59.487 50.000 10.97 10.97 46.61 3.60 F
2154 2417 0.323999 AGCTGGCTGAATTGCATGGA 60.324 50.000 0.00 0.00 34.04 3.41 F
3824 4405 0.105760 ACCAAGATGGGCAACAACCA 60.106 50.000 0.87 0.00 43.37 3.67 F
4772 5357 0.034896 AGACGCCGTCAGACCATTTT 59.965 50.000 20.65 0.00 34.60 1.82 F
5314 5911 0.331278 TGGGCTTGTGGATAAGGTGG 59.669 55.000 0.00 0.00 0.00 4.61 F
7229 8070 0.380733 TATCAGGTACGACGCTGCAG 59.619 55.000 10.11 10.11 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 1990 3.340814 AGCAAGTCATTGGTAGTGGAG 57.659 47.619 0.00 0.0 45.07 3.86 R
2589 2854 0.469705 TTTGTGGGCACTGAGGCAAT 60.470 50.000 0.65 0.0 46.44 3.56 R
3952 4533 0.973632 TGCACAGACTGGTATCGGTT 59.026 50.000 7.51 0.0 31.54 4.44 R
5375 5972 0.944386 GCAATGACCTGTGTTGACGT 59.056 50.000 0.00 0.0 0.00 4.34 R
5757 6354 3.426695 GCTGTCCAATGATAGTTGCACAC 60.427 47.826 0.00 0.0 32.67 3.82 R
7236 8077 0.044855 ACCCTTAGGATCAGCCACCT 59.955 55.000 0.00 0.0 40.02 4.00 R
8313 12884 0.385751 ATACGAGCTGGATCACCGTG 59.614 55.000 1.44 0.0 39.42 4.94 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.329267 TGGAGAACCTCAAGAAGAGCA 58.671 47.619 0.00 0.00 43.31 4.26
143 144 1.916181 TCCTCCAAGGGAAGGTTGATC 59.084 52.381 0.00 0.00 35.59 2.92
201 204 1.404851 GCTCAGGCTGTAAGTGACCTC 60.405 57.143 15.27 0.00 35.30 3.85
250 253 8.996024 TTTTGTTAGGCTAATTATTTCTTGCC 57.004 30.769 10.65 3.55 40.54 4.52
404 410 8.312564 GGAGAAGTTGTGGTTAGTAAGTTCTAT 58.687 37.037 0.00 0.00 41.60 1.98
459 465 2.763448 TGAAAGAACCAGTGTTTTGGGG 59.237 45.455 0.00 0.00 42.76 4.96
495 501 5.590145 ACTGCATTGCAAAATTATATCGCA 58.410 33.333 13.18 0.89 38.41 5.10
501 507 7.116090 GCATTGCAAAATTATATCGCATTACCA 59.884 33.333 1.71 0.00 31.67 3.25
579 585 1.396996 CTTGTCGGGCCTACAATTTCG 59.603 52.381 22.18 8.52 36.33 3.46
588 594 2.580589 CCTACAATTTCGTTGGTTGCG 58.419 47.619 0.00 0.00 42.28 4.85
761 783 6.944234 AAAGTGTTTAGAGAACAGGGAAAG 57.056 37.500 0.00 0.00 0.00 2.62
773 795 4.917906 ACAGGGAAAGCTAACTTCAGAT 57.082 40.909 0.00 0.00 34.05 2.90
812 834 2.154462 AGGGCGTTTTCTGATGTTGAG 58.846 47.619 0.00 0.00 0.00 3.02
821 843 3.703001 TCTGATGTTGAGGAGAAACCC 57.297 47.619 0.00 0.00 40.05 4.11
854 876 7.440556 TGAAACCATTATTGTCAACAATTGTGG 59.559 33.333 23.58 23.58 43.48 4.17
929 1182 7.441890 TGTAAAATTCCGTGTTATGACATGT 57.558 32.000 0.00 0.00 40.47 3.21
1241 1495 5.425539 AGGTAGGCTCTGTTGCTTCTTATTA 59.574 40.000 0.00 0.00 0.00 0.98
1261 1515 3.979501 ATTATGGTTCCCTTCCATGCT 57.020 42.857 7.58 0.00 44.26 3.79
1269 1523 4.526970 GTTCCCTTCCATGCTTGAATCTA 58.473 43.478 0.22 0.00 0.00 1.98
1308 1562 0.512518 TCGATGCTTGACTGCAAACG 59.487 50.000 10.97 10.97 46.61 3.60
1319 1573 7.065204 TGCTTGACTGCAAACGTGATATATTTA 59.935 33.333 0.00 0.00 40.29 1.40
1320 1574 8.070171 GCTTGACTGCAAACGTGATATATTTAT 58.930 33.333 0.00 0.00 32.73 1.40
1350 1605 6.882610 TGAGTGCAGTCTATTTCATGTTTT 57.117 33.333 21.79 0.00 0.00 2.43
1422 1677 4.643334 GGTACCCCCAAAAGCTTTATGTAG 59.357 45.833 13.10 4.61 0.00 2.74
1445 1700 6.852664 AGTTATGCAGTTTTACCATGTTAGC 58.147 36.000 0.00 0.00 0.00 3.09
1512 1773 7.864379 GGTGCTAGATTTCATGATAAACCATTG 59.136 37.037 0.00 0.00 0.00 2.82
1715 1976 7.346471 ACTGAATGTACTGTATATGGGCTTTT 58.654 34.615 0.00 0.00 0.00 2.27
1729 1990 3.572255 TGGGCTTTTTATTGGTGTCTGTC 59.428 43.478 0.00 0.00 0.00 3.51
1858 2121 8.943909 ATTATAAGGTCAACTCTTAGGAAACG 57.056 34.615 0.00 0.00 31.26 3.60
2036 2299 6.579292 TCGTAAACAAATTGCTTCATTTACCG 59.421 34.615 9.21 6.32 31.73 4.02
2154 2417 0.323999 AGCTGGCTGAATTGCATGGA 60.324 50.000 0.00 0.00 34.04 3.41
2189 2452 2.102578 GGTCTGCCCATGCTGTAAAAT 58.897 47.619 0.00 0.00 38.71 1.82
2196 2459 3.066760 GCCCATGCTGTAAAATGGAGTAC 59.933 47.826 3.24 0.00 45.29 2.73
2212 2475 5.448654 TGGAGTACGCTTTATCTTACCCTA 58.551 41.667 0.00 0.00 0.00 3.53
2242 2506 3.503800 ACTTTCTTAGGGGAACACCAC 57.496 47.619 0.00 0.00 42.91 4.16
2465 2730 5.365403 TTTTTCATCTCGGCGTGTTTTAT 57.635 34.783 6.85 0.00 0.00 1.40
2479 2744 6.584563 GGCGTGTTTTATCAAGAAAATGCTTA 59.415 34.615 0.00 0.00 31.29 3.09
2489 2754 7.621832 TCAAGAAAATGCTTATTTGTGAACG 57.378 32.000 0.00 0.00 0.00 3.95
2626 2898 7.337167 CCCACAAATATCCCATTTTGAAATCA 58.663 34.615 2.69 0.00 36.54 2.57
2638 2910 9.709495 CCCATTTTGAAATCAATCACTAAAGAA 57.291 29.630 0.00 0.00 35.55 2.52
2672 2944 7.094805 CCTCAAAATTACCTTCGAGATTCACAA 60.095 37.037 0.00 0.00 0.00 3.33
3011 3285 6.402983 CCTCACACAATAGATGCAGTTTTCTC 60.403 42.308 0.00 0.00 0.00 2.87
3012 3286 6.233434 TCACACAATAGATGCAGTTTTCTCT 58.767 36.000 0.00 0.00 0.00 3.10
3013 3287 6.712095 TCACACAATAGATGCAGTTTTCTCTT 59.288 34.615 0.00 0.00 0.00 2.85
3069 3343 5.590663 TGTCACTTGCCAACAAATGTTACTA 59.409 36.000 0.00 0.00 34.65 1.82
3155 3429 3.705072 GAGGGGTGCATACTTACTGTAGT 59.295 47.826 0.00 0.00 34.24 2.73
3216 3496 3.622163 TGCCATTTGCTTCAAACTGTTTG 59.378 39.130 23.72 23.72 42.00 2.93
3218 3498 3.622163 CCATTTGCTTCAAACTGTTTGCA 59.378 39.130 24.62 17.79 40.43 4.08
3294 3606 8.694394 GGAAAAATCAATTGCTCGATTAATAGC 58.306 33.333 0.00 3.64 39.25 2.97
3316 3630 4.932200 GCTGTACAAAAGTCTGTAGATGCT 59.068 41.667 0.00 0.00 32.49 3.79
3334 3648 7.368480 AGATGCTTCAAAATTTAAATGCACC 57.632 32.000 9.90 2.33 31.92 5.01
3430 3983 2.159382 GATCCCTGTTTCTTTGCCGAA 58.841 47.619 0.00 0.00 0.00 4.30
3441 3995 0.383949 TTTGCCGAAGTGCTTGGAAC 59.616 50.000 0.00 0.00 0.00 3.62
3447 4001 1.680338 GAAGTGCTTGGAACAGTGGT 58.320 50.000 0.00 0.00 42.39 4.16
3457 4011 4.223556 TGGAACAGTGGTTTTGTGTAGA 57.776 40.909 0.00 0.00 37.36 2.59
3460 4014 4.819630 GGAACAGTGGTTTTGTGTAGATCA 59.180 41.667 0.00 0.00 37.36 2.92
3479 4033 3.609853 TCATCCTTTCGTGGAAATCTGG 58.390 45.455 0.00 0.00 39.85 3.86
3505 4059 3.137446 GGATTGATCCTGAGGATGGTG 57.863 52.381 20.60 0.00 43.27 4.17
3506 4060 2.502295 GATTGATCCTGAGGATGGTGC 58.498 52.381 20.60 4.74 43.27 5.01
3507 4061 1.288188 TTGATCCTGAGGATGGTGCA 58.712 50.000 20.60 7.65 43.27 4.57
3508 4062 1.288188 TGATCCTGAGGATGGTGCAA 58.712 50.000 20.60 0.00 43.27 4.08
3509 4063 1.211212 TGATCCTGAGGATGGTGCAAG 59.789 52.381 20.60 0.00 43.27 4.01
3510 4064 1.487976 GATCCTGAGGATGGTGCAAGA 59.512 52.381 20.60 0.00 43.27 3.02
3511 4065 0.615331 TCCTGAGGATGGTGCAAGAC 59.385 55.000 0.00 0.00 0.00 3.01
3512 4066 0.617413 CCTGAGGATGGTGCAAGACT 59.383 55.000 0.00 0.00 0.00 3.24
3513 4067 1.833630 CCTGAGGATGGTGCAAGACTA 59.166 52.381 0.00 0.00 0.00 2.59
3514 4068 2.437281 CCTGAGGATGGTGCAAGACTAT 59.563 50.000 0.00 0.00 0.00 2.12
3515 4069 3.118112 CCTGAGGATGGTGCAAGACTATT 60.118 47.826 0.00 0.00 0.00 1.73
3516 4070 3.875727 CTGAGGATGGTGCAAGACTATTG 59.124 47.826 0.00 0.00 0.00 1.90
3517 4071 3.209410 GAGGATGGTGCAAGACTATTGG 58.791 50.000 0.00 0.00 0.00 3.16
3518 4072 1.678101 GGATGGTGCAAGACTATTGGC 59.322 52.381 0.00 0.00 0.00 4.52
3519 4073 2.648059 GATGGTGCAAGACTATTGGCT 58.352 47.619 0.00 0.00 0.00 4.75
3520 4074 2.584835 TGGTGCAAGACTATTGGCTT 57.415 45.000 0.00 0.00 0.00 4.35
3521 4075 2.875296 TGGTGCAAGACTATTGGCTTT 58.125 42.857 0.00 0.00 0.00 3.51
3530 4110 4.575885 AGACTATTGGCTTTAGCAAACGA 58.424 39.130 3.88 0.00 44.36 3.85
3545 4125 3.906008 GCAAACGATCACATGTACAACAC 59.094 43.478 0.00 0.00 0.00 3.32
3666 4246 5.053978 AGATGGGAAGTGAGAAAAACAGT 57.946 39.130 0.00 0.00 0.00 3.55
3717 4297 4.183101 CCAACTGTGTCAAAAATGCTTGT 58.817 39.130 0.00 0.00 0.00 3.16
3824 4405 0.105760 ACCAAGATGGGCAACAACCA 60.106 50.000 0.87 0.00 43.37 3.67
3839 4420 5.982516 GCAACAACCAGAATGAAATACACAA 59.017 36.000 0.00 0.00 39.69 3.33
3841 4422 7.516627 GCAACAACCAGAATGAAATACACAAAC 60.517 37.037 0.00 0.00 39.69 2.93
3854 4435 7.925483 TGAAATACACAAACCTTTCAAGAATGG 59.075 33.333 11.84 11.84 40.36 3.16
3892 4473 2.031245 CCGTTGTATGTTGAAGCTGCAA 60.031 45.455 1.85 1.85 0.00 4.08
3952 4533 2.484947 CCTAAGCTGCTGCATGAGATCA 60.485 50.000 18.42 0.00 42.74 2.92
3994 4575 3.442977 TCCCTAGTTCTACTTCAACGAGC 59.557 47.826 0.00 0.00 0.00 5.03
4047 4628 4.946157 AGCTTTGATCTGGATGAAACGATT 59.054 37.500 0.00 0.00 0.00 3.34
4050 4631 6.183360 GCTTTGATCTGGATGAAACGATTGTA 60.183 38.462 0.00 0.00 0.00 2.41
4219 4800 1.081892 CTGTGCATGGACTGTGCTAC 58.918 55.000 18.75 0.00 42.92 3.58
4340 4921 6.984740 TCTGTTTGTTCATTGTTAATTCGC 57.015 33.333 0.00 0.00 0.00 4.70
4359 4940 2.676750 CGCAGGTAGCAGGTTGAACATA 60.677 50.000 0.00 0.00 46.13 2.29
4394 4975 8.786826 AATAACGAACCATGATTCTGTTCTTA 57.213 30.769 11.63 8.59 36.97 2.10
4671 5254 3.542712 ATGCTACGTCTGCACTTTTTG 57.457 42.857 16.58 0.00 43.59 2.44
4757 5342 4.703645 TTACCTCTGAATGACTGAGACG 57.296 45.455 0.00 0.00 43.97 4.18
4772 5357 0.034896 AGACGCCGTCAGACCATTTT 59.965 50.000 20.65 0.00 34.60 1.82
4782 5367 6.645003 GCCGTCAGACCATTTTTAGAAATTTT 59.355 34.615 0.00 0.00 33.25 1.82
4833 5418 8.700439 TTAGGCCTTACTAAACTTTGTGATTT 57.300 30.769 12.58 0.00 30.43 2.17
4948 5533 5.885465 AGAACTTGGATTCCTGATTCAGTT 58.115 37.500 12.54 3.12 0.00 3.16
4961 5546 5.242393 CCTGATTCAGTTCAAAGGTGTGAAT 59.758 40.000 12.54 0.00 39.61 2.57
4991 5576 9.075678 AGGAGATGATTTTCCATGTTTATGATC 57.924 33.333 0.00 0.00 36.36 2.92
5134 5720 9.979578 ATAATGATTGAAACACTGTTTGCTTAA 57.020 25.926 11.97 3.06 0.00 1.85
5212 5808 7.180051 ACTTTCTAATGGCATTTGATAAACCCA 59.820 33.333 21.76 5.70 32.01 4.51
5314 5911 0.331278 TGGGCTTGTGGATAAGGTGG 59.669 55.000 0.00 0.00 0.00 4.61
5363 5960 9.442047 GTTGCTATTATATGTCTCCTTGCTATT 57.558 33.333 0.00 0.00 0.00 1.73
5375 5972 7.885922 TGTCTCCTTGCTATTGTAATTTAACCA 59.114 33.333 0.00 0.00 0.00 3.67
5417 6014 3.244665 TGGAGTGATGTGCATTCTGAGTT 60.245 43.478 0.00 0.00 34.02 3.01
5476 6073 1.528586 CTTCTTCTTCGGCACACAGTG 59.471 52.381 0.00 0.00 36.51 3.66
5488 6085 2.949644 GCACACAGTGAAAAGTAGGGTT 59.050 45.455 7.81 0.00 35.23 4.11
5511 6108 8.023706 GGTTGTCTCACCATTTCTTAAATCTTC 58.976 37.037 0.00 0.00 36.73 2.87
5530 6127 4.890581 TCTTCATCCTTACCTAGCTCTGTC 59.109 45.833 0.00 0.00 0.00 3.51
5622 6219 5.803967 GCCTCATTAACAAGATTTTGAGCAG 59.196 40.000 2.48 0.00 37.73 4.24
5936 6533 5.106157 ACCATTGTCATTTCTTCGGTCAATC 60.106 40.000 0.00 0.00 0.00 2.67
5969 6566 9.859427 ATTCAAAATAATATGTCCACACTGTTG 57.141 29.630 0.00 0.00 0.00 3.33
6156 6923 3.599730 TCTGACATGAAGCCTGTAGTG 57.400 47.619 0.00 0.00 0.00 2.74
6238 7005 0.606130 ATGTGCCAACTGATCACGCA 60.606 50.000 0.00 0.00 33.69 5.24
6239 7006 1.229975 TGTGCCAACTGATCACGCAG 61.230 55.000 0.00 0.00 41.63 5.18
6240 7007 0.950555 GTGCCAACTGATCACGCAGA 60.951 55.000 0.00 0.00 39.20 4.26
6241 7008 0.671472 TGCCAACTGATCACGCAGAG 60.671 55.000 0.00 0.00 39.20 3.35
6421 7192 5.418840 CCATGTTAATTTCCAGGTTAGCAGT 59.581 40.000 0.00 0.00 0.00 4.40
6514 7285 1.553690 GGAGCAGGAGGTGTTAGGCA 61.554 60.000 0.00 0.00 0.00 4.75
6622 7393 3.116551 AGCCATCCTATCCCTCACTTACT 60.117 47.826 0.00 0.00 0.00 2.24
6925 7750 8.246180 GTGTGTGAAATGATCAAATGAACCTAT 58.754 33.333 0.00 0.00 40.50 2.57
7190 8031 3.194542 GCCAAGAGCCGAGACATCTATAT 59.805 47.826 0.00 0.00 34.35 0.86
7227 8068 1.787155 CATTATCAGGTACGACGCTGC 59.213 52.381 0.00 0.00 0.00 5.25
7229 8070 0.380733 TATCAGGTACGACGCTGCAG 59.619 55.000 10.11 10.11 0.00 4.41
7230 8071 1.313091 ATCAGGTACGACGCTGCAGA 61.313 55.000 20.43 0.00 0.00 4.26
7231 8072 1.139734 CAGGTACGACGCTGCAGAT 59.860 57.895 20.43 3.79 0.00 2.90
7232 8073 0.867753 CAGGTACGACGCTGCAGATC 60.868 60.000 20.43 13.11 0.00 2.75
7233 8074 1.032657 AGGTACGACGCTGCAGATCT 61.033 55.000 20.43 0.00 0.00 2.75
7234 8075 0.592754 GGTACGACGCTGCAGATCTC 60.593 60.000 20.43 6.77 0.00 2.75
7235 8076 0.098905 GTACGACGCTGCAGATCTCA 59.901 55.000 20.43 1.53 0.00 3.27
7236 8077 0.808755 TACGACGCTGCAGATCTCAA 59.191 50.000 20.43 0.00 0.00 3.02
7237 8078 0.457509 ACGACGCTGCAGATCTCAAG 60.458 55.000 20.43 3.67 0.00 3.02
7238 8079 1.144565 CGACGCTGCAGATCTCAAGG 61.145 60.000 20.43 0.00 0.00 3.61
7239 8080 0.108424 GACGCTGCAGATCTCAAGGT 60.108 55.000 20.43 0.87 0.00 3.50
7240 8081 0.390866 ACGCTGCAGATCTCAAGGTG 60.391 55.000 20.43 0.00 0.00 4.00
7241 8082 1.088340 CGCTGCAGATCTCAAGGTGG 61.088 60.000 20.43 0.00 0.00 4.61
7242 8083 1.375098 GCTGCAGATCTCAAGGTGGC 61.375 60.000 20.43 0.00 0.00 5.01
7243 8084 0.252479 CTGCAGATCTCAAGGTGGCT 59.748 55.000 8.42 0.00 0.00 4.75
7469 8334 3.137533 GCAGAGAGTTAGATGAATGGGC 58.862 50.000 0.00 0.00 0.00 5.36
7649 8533 4.944930 CAGGTTAATGGTACCGGATGAAAA 59.055 41.667 9.46 0.00 40.69 2.29
7696 8580 7.024340 GTGAGCATACATCACTTGATCATTT 57.976 36.000 0.00 0.00 43.03 2.32
7698 8582 6.038936 TGAGCATACATCACTTGATCATTTGG 59.961 38.462 0.00 0.00 31.43 3.28
7754 8638 1.273327 GCTTGGTGGAATTCTTGTGGG 59.727 52.381 5.23 0.00 0.00 4.61
7786 8671 2.568090 GCCCAACTTGTCATGGCG 59.432 61.111 0.00 0.00 35.28 5.69
7867 8752 2.042104 ACTTCGGTGTCGTAGTTTCG 57.958 50.000 0.00 0.00 42.83 3.46
7956 9055 2.099141 TCATCTCCCGTGAAGCAAAG 57.901 50.000 0.00 0.00 0.00 2.77
7959 9058 2.743636 TCTCCCGTGAAGCAAAGTAG 57.256 50.000 0.00 0.00 0.00 2.57
7981 9080 4.997395 AGTTGATGCTTACTCGATTGTGTT 59.003 37.500 0.00 0.00 0.00 3.32
8006 9105 6.316140 TGTTCTAATCCCGAGATCAAACAATG 59.684 38.462 0.00 0.00 30.97 2.82
8020 9119 1.838913 ACAATGCAAACTTCACGCAC 58.161 45.000 0.00 0.00 38.73 5.34
8141 11362 1.075659 GGCCCTGAGGACTTTTGCT 59.924 57.895 0.00 0.00 38.67 3.91
8169 11390 7.172019 CAGCCATAAGAAAACTTGCAAATTCTT 59.828 33.333 25.33 25.33 42.82 2.52
8172 11393 9.264719 CCATAAGAAAACTTGCAAATTCTTCTT 57.735 29.630 25.58 23.76 41.15 2.52
8178 11399 6.581171 AACTTGCAAATTCTTCTTCCCTAG 57.419 37.500 0.00 0.00 0.00 3.02
8179 11400 5.635120 ACTTGCAAATTCTTCTTCCCTAGT 58.365 37.500 0.00 0.00 0.00 2.57
8182 11403 5.003804 TGCAAATTCTTCTTCCCTAGTGTC 58.996 41.667 0.00 0.00 0.00 3.67
8192 11415 9.268282 TCTTCTTCCCTAGTGTCATAAACTTAT 57.732 33.333 0.00 0.00 0.00 1.73
8197 11420 7.719483 TCCCTAGTGTCATAAACTTATAACGG 58.281 38.462 0.00 0.00 0.00 4.44
8203 11426 7.124750 AGTGTCATAAACTTATAACGGTACCCT 59.875 37.037 6.25 0.00 0.00 4.34
8294 12865 2.643551 ACGCATGGTTATCCTTCCAAG 58.356 47.619 0.00 0.00 37.27 3.61
8295 12866 1.334869 CGCATGGTTATCCTTCCAAGC 59.665 52.381 0.00 0.00 42.58 4.01
8296 12867 2.659428 GCATGGTTATCCTTCCAAGCT 58.341 47.619 0.00 0.00 42.67 3.74
8297 12868 2.620585 GCATGGTTATCCTTCCAAGCTC 59.379 50.000 0.00 0.00 42.67 4.09
8298 12869 3.217626 CATGGTTATCCTTCCAAGCTCC 58.782 50.000 0.00 0.00 37.27 4.70
8299 12870 2.274542 TGGTTATCCTTCCAAGCTCCA 58.725 47.619 0.00 0.00 34.23 3.86
8300 12871 2.239654 TGGTTATCCTTCCAAGCTCCAG 59.760 50.000 0.00 0.00 34.23 3.86
8301 12872 2.293170 GTTATCCTTCCAAGCTCCAGC 58.707 52.381 0.00 0.00 42.49 4.85
8302 12873 0.839946 TATCCTTCCAAGCTCCAGCC 59.160 55.000 0.00 0.00 43.38 4.85
8303 12874 1.210204 ATCCTTCCAAGCTCCAGCCA 61.210 55.000 0.00 0.00 43.38 4.75
8304 12875 1.210204 TCCTTCCAAGCTCCAGCCAT 61.210 55.000 0.00 0.00 43.38 4.40
8305 12876 0.548031 CCTTCCAAGCTCCAGCCATA 59.452 55.000 0.00 0.00 43.38 2.74
8306 12877 1.673168 CTTCCAAGCTCCAGCCATAC 58.327 55.000 0.00 0.00 43.38 2.39
8307 12878 0.107703 TTCCAAGCTCCAGCCATACG 60.108 55.000 0.00 0.00 43.38 3.06
8308 12879 1.221840 CCAAGCTCCAGCCATACGT 59.778 57.895 0.00 0.00 43.38 3.57
8309 12880 1.091771 CCAAGCTCCAGCCATACGTG 61.092 60.000 0.00 0.00 43.38 4.49
8310 12881 0.108186 CAAGCTCCAGCCATACGTGA 60.108 55.000 0.00 0.00 43.38 4.35
8311 12882 0.176680 AAGCTCCAGCCATACGTGAG 59.823 55.000 0.00 0.00 43.38 3.51
8312 12883 1.227380 GCTCCAGCCATACGTGAGG 60.227 63.158 0.00 0.04 34.31 3.86
8324 12895 2.662596 GTGAGGCACGGTGATCCA 59.337 61.111 13.29 2.57 0.00 3.41
8325 12896 1.448540 GTGAGGCACGGTGATCCAG 60.449 63.158 13.29 0.00 0.00 3.86
8326 12897 2.512515 GAGGCACGGTGATCCAGC 60.513 66.667 13.29 0.00 34.84 4.85
8327 12898 3.005539 AGGCACGGTGATCCAGCT 61.006 61.111 13.29 0.00 35.58 4.24
8328 12899 2.512515 GGCACGGTGATCCAGCTC 60.513 66.667 13.29 0.00 35.58 4.09
8329 12900 2.887568 GCACGGTGATCCAGCTCG 60.888 66.667 13.29 0.00 33.46 5.03
8330 12901 2.573869 CACGGTGATCCAGCTCGT 59.426 61.111 0.74 0.00 34.19 4.18
8331 12902 1.807226 CACGGTGATCCAGCTCGTA 59.193 57.895 0.74 0.00 32.56 3.43
8332 12903 0.385751 CACGGTGATCCAGCTCGTAT 59.614 55.000 0.74 0.00 32.56 3.06
8333 12904 1.112113 ACGGTGATCCAGCTCGTATT 58.888 50.000 0.00 0.00 32.03 1.89
8334 12905 1.480954 ACGGTGATCCAGCTCGTATTT 59.519 47.619 0.00 0.00 32.03 1.40
8335 12906 2.128035 CGGTGATCCAGCTCGTATTTC 58.872 52.381 0.00 0.00 0.00 2.17
8336 12907 2.128035 GGTGATCCAGCTCGTATTTCG 58.872 52.381 0.00 0.00 41.41 3.46
8337 12908 2.481449 GGTGATCCAGCTCGTATTTCGT 60.481 50.000 0.00 0.00 40.80 3.85
8338 12909 2.789893 GTGATCCAGCTCGTATTTCGTC 59.210 50.000 0.00 0.00 40.80 4.20
8339 12910 2.223735 TGATCCAGCTCGTATTTCGTCC 60.224 50.000 0.00 0.00 40.80 4.79
8340 12911 1.471119 TCCAGCTCGTATTTCGTCCT 58.529 50.000 0.00 0.00 40.80 3.85
8341 12912 1.134367 TCCAGCTCGTATTTCGTCCTG 59.866 52.381 0.00 0.00 40.80 3.86
8342 12913 1.134367 CCAGCTCGTATTTCGTCCTGA 59.866 52.381 0.00 0.00 39.22 3.86
8343 12914 2.416836 CCAGCTCGTATTTCGTCCTGAA 60.417 50.000 0.00 0.00 39.22 3.02
8355 12926 6.687081 TTTCGTCCTGAAAATTTACACACT 57.313 33.333 0.00 0.00 43.46 3.55
8356 12927 6.687081 TTCGTCCTGAAAATTTACACACTT 57.313 33.333 0.00 0.00 32.37 3.16
8357 12928 6.055231 TCGTCCTGAAAATTTACACACTTG 57.945 37.500 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.940994 TAGCCTAGCGACATCTCTCT 57.059 50.000 0.00 0.00 0.00 3.10
143 144 3.578282 AGGGTTTGGAAGTAGGCAAAATG 59.422 43.478 0.00 0.00 0.00 2.32
172 173 4.342092 ACTTACAGCCTGAGCAAACAAAAT 59.658 37.500 0.00 0.00 43.56 1.82
459 465 3.308323 GCAATGCAGTAGCTACTCAGTTC 59.692 47.826 23.68 13.71 42.74 3.01
579 585 1.001048 GTTAGAAACCCCGCAACCAAC 60.001 52.381 0.00 0.00 0.00 3.77
641 663 4.882842 TGCACTACAGACCATACTGAAA 57.117 40.909 0.00 0.00 40.63 2.69
773 795 6.207810 ACGCCCTTGTAAAAATAACAATGAGA 59.792 34.615 0.00 0.00 36.33 3.27
790 812 2.293122 TCAACATCAGAAAACGCCCTTG 59.707 45.455 0.00 0.00 0.00 3.61
812 834 2.826128 GTTTCAATCTGGGGGTTTCTCC 59.174 50.000 0.00 0.00 0.00 3.71
821 843 6.528537 TGACAATAATGGTTTCAATCTGGG 57.471 37.500 0.00 0.00 0.00 4.45
878 900 1.995376 AGGACAAAATCACCACCCAC 58.005 50.000 0.00 0.00 0.00 4.61
1289 1543 0.512518 CGTTTGCAGTCAAGCATCGA 59.487 50.000 0.00 0.00 45.19 3.59
1319 1573 6.712095 TGAAATAGACTGCACTCAAGTCAAAT 59.288 34.615 5.90 0.00 35.23 2.32
1320 1574 6.054941 TGAAATAGACTGCACTCAAGTCAAA 58.945 36.000 5.90 0.00 35.23 2.69
1350 1605 9.836864 ACTAACTGATCTACAAATCATGCATTA 57.163 29.630 0.00 0.00 35.21 1.90
1422 1677 5.737290 CGCTAACATGGTAAAACTGCATAAC 59.263 40.000 0.00 0.00 0.00 1.89
1445 1700 9.745880 AACTACTACATGAATAAGTATGGTTCG 57.254 33.333 0.00 0.00 0.00 3.95
1715 1976 4.222145 GGTAGTGGAGACAGACACCAATAA 59.778 45.833 0.00 0.00 44.46 1.40
1729 1990 3.340814 AGCAAGTCATTGGTAGTGGAG 57.659 47.619 0.00 0.00 45.07 3.86
2015 2278 5.053145 TGCGGTAAATGAAGCAATTTGTTT 58.947 33.333 0.00 0.00 36.60 2.83
2036 2299 7.076842 ACATGGATAGCATAAATACGATTGC 57.923 36.000 0.00 0.00 35.34 3.56
2154 2417 3.829026 GGCAGACCTCCTTGAAAGAATTT 59.171 43.478 0.00 0.00 43.98 1.82
2189 2452 4.284178 AGGGTAAGATAAAGCGTACTCCA 58.716 43.478 0.00 0.00 0.00 3.86
2234 2498 7.489160 AGAAAAAGGAACTATTTGTGGTGTTC 58.511 34.615 0.00 0.00 38.49 3.18
2242 2506 8.197439 ACCAACAGAAGAAAAAGGAACTATTTG 58.803 33.333 0.00 0.00 38.49 2.32
2455 2720 6.452244 AAGCATTTTCTTGATAAAACACGC 57.548 33.333 0.00 0.00 31.50 5.34
2465 2730 7.421599 TCGTTCACAAATAAGCATTTTCTTGA 58.578 30.769 0.00 0.00 31.82 3.02
2479 2744 9.233232 GTCTAACAGAATTTTTCGTTCACAAAT 57.767 29.630 0.00 0.00 32.04 2.32
2483 2748 8.782533 ATTGTCTAACAGAATTTTTCGTTCAC 57.217 30.769 0.00 0.00 32.04 3.18
2589 2854 0.469705 TTTGTGGGCACTGAGGCAAT 60.470 50.000 0.65 0.00 46.44 3.56
2638 2910 9.379791 CTCGAAGGTAATTTTGAGGTAATACTT 57.620 33.333 0.00 0.00 35.71 2.24
2672 2944 8.993424 AGTAAATTCACCAAGTATCATCCTAGT 58.007 33.333 0.00 0.00 0.00 2.57
2730 3003 9.575783 TTTATTTTGAGAACACAACACCTAAAC 57.424 29.630 0.00 0.00 0.00 2.01
2765 3039 6.156256 AGCATGACATAAGTACCTTTCCACTA 59.844 38.462 0.00 0.00 0.00 2.74
2778 3052 2.158856 TGCCTGGAGAGCATGACATAAG 60.159 50.000 0.00 0.00 34.69 1.73
3011 3285 7.693969 ACCATAATGAAGAAGGAAACTGAAG 57.306 36.000 0.00 0.00 42.68 3.02
3012 3286 9.010029 GTAACCATAATGAAGAAGGAAACTGAA 57.990 33.333 0.00 0.00 42.68 3.02
3013 3287 8.160765 TGTAACCATAATGAAGAAGGAAACTGA 58.839 33.333 0.00 0.00 42.68 3.41
3116 3390 1.949525 CCTCGTTATTTGCCTCCATGG 59.050 52.381 4.97 4.97 39.35 3.66
3216 3496 6.415798 AAAAACTGTTTGTTGGTGTATTGC 57.584 33.333 6.53 0.00 39.13 3.56
3263 3546 6.713762 TCGAGCAATTGATTTTTCCCATAT 57.286 33.333 10.34 0.00 0.00 1.78
3265 3548 5.603170 ATCGAGCAATTGATTTTTCCCAT 57.397 34.783 10.34 0.00 0.00 4.00
3294 3606 6.646653 TGAAGCATCTACAGACTTTTGTACAG 59.353 38.462 0.00 0.00 32.56 2.74
3360 3802 1.696063 ACTTGCAGTTTCTGGCATGT 58.304 45.000 0.00 0.00 41.70 3.21
3388 3830 8.136165 GGATCGTAAGTTCTAACACTATGACAT 58.864 37.037 0.00 0.00 36.33 3.06
3389 3831 7.415989 GGGATCGTAAGTTCTAACACTATGACA 60.416 40.741 0.00 0.00 36.33 3.58
3390 3832 6.916932 GGGATCGTAAGTTCTAACACTATGAC 59.083 42.308 0.00 0.00 36.33 3.06
3393 3835 6.606395 ACAGGGATCGTAAGTTCTAACACTAT 59.394 38.462 0.00 0.00 36.33 2.12
3394 3836 5.948162 ACAGGGATCGTAAGTTCTAACACTA 59.052 40.000 0.00 0.00 36.33 2.74
3395 3837 4.771054 ACAGGGATCGTAAGTTCTAACACT 59.229 41.667 0.00 0.00 36.33 3.55
3396 3838 5.069501 ACAGGGATCGTAAGTTCTAACAC 57.930 43.478 0.00 0.00 36.33 3.32
3397 3839 5.733620 AACAGGGATCGTAAGTTCTAACA 57.266 39.130 0.00 0.00 36.33 2.41
3430 3983 2.143876 AAACCACTGTTCCAAGCACT 57.856 45.000 0.00 0.00 32.15 4.40
3441 3995 5.248640 AGGATGATCTACACAAAACCACTG 58.751 41.667 0.00 0.00 0.00 3.66
3447 4001 5.411361 CCACGAAAGGATGATCTACACAAAA 59.589 40.000 0.00 0.00 0.00 2.44
3457 4011 4.202441 CCAGATTTCCACGAAAGGATGAT 58.798 43.478 0.00 0.00 37.56 2.45
3460 4014 2.369394 GCCAGATTTCCACGAAAGGAT 58.631 47.619 0.00 0.00 37.56 3.24
3495 4049 3.370846 CCAATAGTCTTGCACCATCCTCA 60.371 47.826 0.00 0.00 0.00 3.86
3504 4058 3.684908 TGCTAAAGCCAATAGTCTTGCA 58.315 40.909 0.00 0.00 41.18 4.08
3505 4059 4.701956 TTGCTAAAGCCAATAGTCTTGC 57.298 40.909 0.00 0.00 41.18 4.01
3506 4060 5.088739 CGTTTGCTAAAGCCAATAGTCTTG 58.911 41.667 0.00 0.00 41.18 3.02
3507 4061 5.001232 TCGTTTGCTAAAGCCAATAGTCTT 58.999 37.500 0.00 0.00 41.18 3.01
3508 4062 4.575885 TCGTTTGCTAAAGCCAATAGTCT 58.424 39.130 0.00 0.00 41.18 3.24
3509 4063 4.939509 TCGTTTGCTAAAGCCAATAGTC 57.060 40.909 0.00 0.00 41.18 2.59
3510 4064 4.941263 TGATCGTTTGCTAAAGCCAATAGT 59.059 37.500 0.00 0.00 41.18 2.12
3511 4065 5.163764 TGTGATCGTTTGCTAAAGCCAATAG 60.164 40.000 0.00 0.00 41.18 1.73
3512 4066 4.697828 TGTGATCGTTTGCTAAAGCCAATA 59.302 37.500 0.00 0.00 41.18 1.90
3513 4067 3.505680 TGTGATCGTTTGCTAAAGCCAAT 59.494 39.130 0.00 0.00 41.18 3.16
3514 4068 2.881513 TGTGATCGTTTGCTAAAGCCAA 59.118 40.909 0.00 0.00 41.18 4.52
3515 4069 2.499197 TGTGATCGTTTGCTAAAGCCA 58.501 42.857 0.00 0.00 41.18 4.75
3516 4070 3.119849 ACATGTGATCGTTTGCTAAAGCC 60.120 43.478 0.00 0.00 41.18 4.35
3517 4071 4.083581 ACATGTGATCGTTTGCTAAAGC 57.916 40.909 0.00 0.00 42.50 3.51
3518 4072 6.164408 TGTACATGTGATCGTTTGCTAAAG 57.836 37.500 9.11 0.00 0.00 1.85
3519 4073 6.017852 TGTTGTACATGTGATCGTTTGCTAAA 60.018 34.615 9.11 0.00 0.00 1.85
3520 4074 5.467063 TGTTGTACATGTGATCGTTTGCTAA 59.533 36.000 9.11 0.00 0.00 3.09
3521 4075 4.991687 TGTTGTACATGTGATCGTTTGCTA 59.008 37.500 9.11 0.00 0.00 3.49
3530 4110 1.804151 GGTGCGTGTTGTACATGTGAT 59.196 47.619 9.11 0.00 37.43 3.06
3545 4125 1.066143 ACTTAGGTGAAGGATGGTGCG 60.066 52.381 0.00 0.00 39.74 5.34
3666 4246 3.168035 ACAACCATGCCCACTGAATTA 57.832 42.857 0.00 0.00 0.00 1.40
3737 4318 3.885484 TTTTGCGCTTTCTCAAGAGAG 57.115 42.857 9.73 0.00 43.48 3.20
3765 4346 6.782494 TCCTTACCTATCTATGCATCAAGACA 59.218 38.462 0.19 0.00 0.00 3.41
3824 4405 8.912988 TCTTGAAAGGTTTGTGTATTTCATTCT 58.087 29.630 0.56 0.00 40.32 2.40
3841 4422 8.837788 ATTAAAAGCTTTCCATTCTTGAAAGG 57.162 30.769 13.10 0.00 45.60 3.11
3854 4435 3.850122 ACGGCCTGATTAAAAGCTTTC 57.150 42.857 13.10 0.00 0.00 2.62
3952 4533 0.973632 TGCACAGACTGGTATCGGTT 59.026 50.000 7.51 0.00 31.54 4.44
3994 4575 3.810310 AAAGGAGCAAGGACTAGATCG 57.190 47.619 0.00 0.00 0.00 3.69
4219 4800 7.969536 ACAACCAAGTATATAGCAATAGCAG 57.030 36.000 0.00 0.00 45.49 4.24
4340 4921 6.515272 AAAATATGTTCAACCTGCTACCTG 57.485 37.500 0.00 0.00 0.00 4.00
4535 5116 9.635404 TCTCTTTGGTCCATACTTAAAAGAAAA 57.365 29.630 0.00 0.00 33.37 2.29
4757 5342 4.759516 TTTCTAAAAATGGTCTGACGGC 57.240 40.909 1.07 0.00 0.00 5.68
4782 5367 7.548097 TGAAACAGCCAAATAAACAACACTTA 58.452 30.769 0.00 0.00 0.00 2.24
4799 5384 6.374613 AGTTTAGTAAGGCCTAATGAAACAGC 59.625 38.462 24.13 7.89 0.00 4.40
4948 5533 5.047566 TCTCCTTCAATTCACACCTTTGA 57.952 39.130 0.00 0.00 0.00 2.69
4961 5546 7.543359 AAACATGGAAAATCATCTCCTTCAA 57.457 32.000 0.00 0.00 32.51 2.69
4991 5576 3.077359 CTGCAAAACCAGTTCCTAGGAG 58.923 50.000 12.26 2.65 0.00 3.69
5133 5719 3.857010 GCGCTGGTGTTCTTTAAATGCTT 60.857 43.478 0.00 0.00 0.00 3.91
5134 5720 2.351738 GCGCTGGTGTTCTTTAAATGCT 60.352 45.455 0.00 0.00 0.00 3.79
5139 5725 4.142491 CCATATTGCGCTGGTGTTCTTTAA 60.142 41.667 9.73 0.00 0.00 1.52
5314 5911 4.639135 AAGGAAACTGAACAGAAACAGC 57.361 40.909 8.87 0.00 42.68 4.40
5363 5960 5.007823 CCTGTGTTGACGTGGTTAAATTACA 59.992 40.000 0.00 0.00 0.00 2.41
5375 5972 0.944386 GCAATGACCTGTGTTGACGT 59.056 50.000 0.00 0.00 0.00 4.34
5417 6014 4.180817 CGTATATATGGAGGAATGCGCAA 58.819 43.478 17.11 0.00 0.00 4.85
5476 6073 4.081322 TGGTGAGACAACCCTACTTTTC 57.919 45.455 0.00 0.00 39.70 2.29
5488 6085 8.868522 ATGAAGATTTAAGAAATGGTGAGACA 57.131 30.769 0.00 0.00 0.00 3.41
5511 6108 5.344743 TTTGACAGAGCTAGGTAAGGATG 57.655 43.478 0.00 0.00 0.00 3.51
5622 6219 8.470040 TTGCAAAGAATTTTATCATCTTCAGC 57.530 30.769 0.00 0.00 35.03 4.26
5757 6354 3.426695 GCTGTCCAATGATAGTTGCACAC 60.427 47.826 0.00 0.00 32.67 3.82
5936 6533 9.878599 GTGGACATATTATTTTGAATAACCTCG 57.121 33.333 0.00 0.00 0.00 4.63
5968 6565 9.268268 GGCATAAAATAAGCATACTAGTACACA 57.732 33.333 4.31 0.00 0.00 3.72
5969 6566 9.268268 TGGCATAAAATAAGCATACTAGTACAC 57.732 33.333 4.31 0.07 0.00 2.90
6171 6938 7.336931 TCTCCAATATACCTCTGCAAAGAAAAC 59.663 37.037 0.00 0.00 0.00 2.43
6427 7198 8.512138 GCAGCAAAGTTAGAAGATAAAGGTTTA 58.488 33.333 0.00 0.00 0.00 2.01
6514 7285 7.524717 AAACAAAGGCACTATCACATTAACT 57.475 32.000 0.00 0.00 38.49 2.24
6622 7393 3.866703 TCCCTAAACACATGTCCACAA 57.133 42.857 0.00 0.00 0.00 3.33
6925 7750 6.436532 AGAGAGGTACCAAGTATCGAGAAAAA 59.563 38.462 15.94 0.00 0.00 1.94
7190 8031 1.584175 ATGTTGGTCACAAACGCGTA 58.416 45.000 14.46 0.00 39.50 4.42
7227 8068 2.485124 GGATCAGCCACCTTGAGATCTG 60.485 54.545 0.00 0.00 36.30 2.90
7229 8070 1.767681 AGGATCAGCCACCTTGAGATC 59.232 52.381 0.00 0.00 40.02 2.75
7230 8071 1.890552 AGGATCAGCCACCTTGAGAT 58.109 50.000 0.00 0.00 40.02 2.75
7231 8072 2.550277 TAGGATCAGCCACCTTGAGA 57.450 50.000 0.00 0.00 40.02 3.27
7232 8073 2.158842 CCTTAGGATCAGCCACCTTGAG 60.159 54.545 0.00 0.00 40.02 3.02
7233 8074 1.839994 CCTTAGGATCAGCCACCTTGA 59.160 52.381 0.00 0.00 40.02 3.02
7234 8075 1.133976 CCCTTAGGATCAGCCACCTTG 60.134 57.143 0.00 0.00 40.02 3.61
7235 8076 1.216990 CCCTTAGGATCAGCCACCTT 58.783 55.000 0.00 0.00 40.02 3.50
7236 8077 0.044855 ACCCTTAGGATCAGCCACCT 59.955 55.000 0.00 0.00 40.02 4.00
7237 8078 1.694696 CTACCCTTAGGATCAGCCACC 59.305 57.143 0.00 0.00 40.02 4.61
7238 8079 2.399580 ACTACCCTTAGGATCAGCCAC 58.600 52.381 0.00 0.00 40.02 5.01
7239 8080 2.771943 CAACTACCCTTAGGATCAGCCA 59.228 50.000 0.00 0.00 40.02 4.75
7240 8081 2.104963 CCAACTACCCTTAGGATCAGCC 59.895 54.545 0.00 0.00 36.73 4.85
7241 8082 3.039011 TCCAACTACCCTTAGGATCAGC 58.961 50.000 0.00 0.00 36.73 4.26
7242 8083 4.901849 TCATCCAACTACCCTTAGGATCAG 59.098 45.833 0.00 0.00 36.99 2.90
7243 8084 4.890988 TCATCCAACTACCCTTAGGATCA 58.109 43.478 0.00 0.00 36.99 2.92
7469 8334 1.279271 AGATGTTCCACCTTCCCTTCG 59.721 52.381 0.00 0.00 0.00 3.79
7649 8533 4.792068 TGGGACTGTTCTGAAAATTCTGT 58.208 39.130 0.00 0.00 0.00 3.41
7696 8580 3.599343 CAGTGCTGACTAGTTAATGCCA 58.401 45.455 0.00 0.00 0.00 4.92
7698 8582 3.265791 AGCAGTGCTGACTAGTTAATGC 58.734 45.455 18.98 5.83 37.57 3.56
7754 8638 3.656264 AGTTGGGCCTATAGGGGATAAAC 59.344 47.826 20.58 1.42 35.18 2.01
7770 8654 1.973281 AGCGCCATGACAAGTTGGG 60.973 57.895 2.29 0.00 33.40 4.12
7786 8671 6.037830 TGGAACTAAAAACACAGAACTACAGC 59.962 38.462 0.00 0.00 0.00 4.40
7824 8709 3.290948 AGAAACCACAACAGGCTTGTA 57.709 42.857 0.22 0.00 36.23 2.41
7867 8752 2.926838 GACTGAATCTTTCTCGGTCAGC 59.073 50.000 6.87 0.00 45.03 4.26
7956 9055 5.577164 ACACAATCGAGTAAGCATCAACTAC 59.423 40.000 0.00 0.00 0.00 2.73
7959 9058 4.928661 ACACAATCGAGTAAGCATCAAC 57.071 40.909 0.00 0.00 0.00 3.18
7981 9080 5.414789 TGTTTGATCTCGGGATTAGAACA 57.585 39.130 14.32 14.32 31.98 3.18
8006 9105 0.522495 ACAACGTGCGTGAAGTTTGC 60.522 50.000 0.00 0.00 0.00 3.68
8102 11323 1.378531 TGCGAATGATGTAAGGTGGC 58.621 50.000 0.00 0.00 0.00 5.01
8141 11362 3.495331 TGCAAGTTTTCTTATGGCTGGA 58.505 40.909 0.00 0.00 38.17 3.86
8172 11393 7.342799 ACCGTTATAAGTTTATGACACTAGGGA 59.657 37.037 0.00 0.00 31.32 4.20
8178 11399 7.468922 GGGTACCGTTATAAGTTTATGACAC 57.531 40.000 5.65 0.04 40.86 3.67
8197 11420 6.657541 TCAAATATGTGGAACTTCAAGGGTAC 59.342 38.462 0.00 0.00 38.04 3.34
8203 11426 6.660521 AGCATCTCAAATATGTGGAACTTCAA 59.339 34.615 0.00 0.00 38.04 2.69
8281 12852 2.293170 GCTGGAGCTTGGAAGGATAAC 58.707 52.381 0.00 0.00 38.21 1.89
8294 12865 1.227380 CCTCACGTATGGCTGGAGC 60.227 63.158 0.00 0.00 41.14 4.70
8295 12866 1.227380 GCCTCACGTATGGCTGGAG 60.227 63.158 19.77 6.76 45.26 3.86
8296 12867 2.900273 GCCTCACGTATGGCTGGA 59.100 61.111 19.77 0.00 45.26 3.86
8307 12878 1.448540 CTGGATCACCGTGCCTCAC 60.449 63.158 0.00 0.00 39.42 3.51
8308 12879 2.981302 CTGGATCACCGTGCCTCA 59.019 61.111 0.00 0.00 39.42 3.86
8309 12880 2.512515 GCTGGATCACCGTGCCTC 60.513 66.667 0.00 0.00 39.42 4.70
8310 12881 3.005539 AGCTGGATCACCGTGCCT 61.006 61.111 0.00 0.00 38.40 4.75
8311 12882 2.512515 GAGCTGGATCACCGTGCC 60.513 66.667 0.00 0.00 38.40 5.01
8312 12883 2.279502 TACGAGCTGGATCACCGTGC 62.280 60.000 1.44 0.00 39.42 5.34
8313 12884 0.385751 ATACGAGCTGGATCACCGTG 59.614 55.000 1.44 0.00 39.42 4.94
8314 12885 1.112113 AATACGAGCTGGATCACCGT 58.888 50.000 1.44 0.59 39.42 4.83
8315 12886 2.128035 GAAATACGAGCTGGATCACCG 58.872 52.381 1.44 0.00 39.42 4.94
8316 12887 2.128035 CGAAATACGAGCTGGATCACC 58.872 52.381 1.44 0.00 45.77 4.02
8317 12888 2.789893 GACGAAATACGAGCTGGATCAC 59.210 50.000 1.44 0.00 45.77 3.06
8318 12889 2.223735 GGACGAAATACGAGCTGGATCA 60.224 50.000 1.44 0.00 45.77 2.92
8319 12890 2.034812 AGGACGAAATACGAGCTGGATC 59.965 50.000 1.44 0.00 45.77 3.36
8320 12891 2.032620 AGGACGAAATACGAGCTGGAT 58.967 47.619 1.44 0.00 45.77 3.41
8321 12892 1.134367 CAGGACGAAATACGAGCTGGA 59.866 52.381 1.44 0.00 45.77 3.86
8322 12893 1.134367 TCAGGACGAAATACGAGCTGG 59.866 52.381 0.00 0.00 45.77 4.85
8323 12894 2.561733 TCAGGACGAAATACGAGCTG 57.438 50.000 0.00 0.00 45.77 4.24
8324 12895 3.587797 TTTCAGGACGAAATACGAGCT 57.412 42.857 0.00 0.00 45.77 4.09
8325 12896 4.859629 ATTTTCAGGACGAAATACGAGC 57.140 40.909 0.00 0.00 43.12 5.03
8326 12897 7.686938 GTGTAAATTTTCAGGACGAAATACGAG 59.313 37.037 0.00 0.00 43.12 4.18
8327 12898 7.171167 TGTGTAAATTTTCAGGACGAAATACGA 59.829 33.333 0.00 0.00 43.12 3.43
8328 12899 7.267600 GTGTGTAAATTTTCAGGACGAAATACG 59.732 37.037 0.00 0.00 43.12 3.06
8329 12900 8.287503 AGTGTGTAAATTTTCAGGACGAAATAC 58.712 33.333 0.00 0.00 43.12 1.89
8330 12901 8.385898 AGTGTGTAAATTTTCAGGACGAAATA 57.614 30.769 0.00 0.00 43.12 1.40
8331 12902 7.272037 AGTGTGTAAATTTTCAGGACGAAAT 57.728 32.000 0.00 0.00 43.12 2.17
8332 12903 6.687081 AGTGTGTAAATTTTCAGGACGAAA 57.313 33.333 0.00 0.00 41.95 3.46
8333 12904 6.491394 CAAGTGTGTAAATTTTCAGGACGAA 58.509 36.000 0.00 0.00 0.00 3.85
8334 12905 6.055231 CAAGTGTGTAAATTTTCAGGACGA 57.945 37.500 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.