Multiple sequence alignment - TraesCS7D01G303500

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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 TraesCS7D01G303500 chr7D 100.000 8498 0 0 1 8498 384937306 384945803 0.000000e+00 15693
1 TraesCS7D01G303500 chr7D 85.410 891 98 20 3566 4447 548814423 548813556 0.000000e+00 896
2 TraesCS7D01G303500 chr7D 94.318 88 4 1 8388 8474 384945611 384945698 5.350000e-27 134
3 TraesCS7D01G303500 chr7D 94.318 88 4 1 8306 8393 384945693 384945779 5.350000e-27 134
4 TraesCS7D01G303500 chr7B 92.914 3542 179 33 78 3578 379409765 379413275 0.000000e+00 5084
5 TraesCS7D01G303500 chr7B 94.489 3339 88 39 5082 8373 379413260 379416549 0.000000e+00 5059
6 TraesCS7D01G303500 chr7B 90.090 111 9 2 8283 8393 379416576 379416684 8.890000e-30 143
7 TraesCS7D01G303500 chr7B 94.805 77 4 0 1 77 379408797 379408873 4.170000e-23 121
8 TraesCS7D01G303500 chr7A 95.059 2955 98 19 646 3578 432971665 432974593 0.000000e+00 4604
9 TraesCS7D01G303500 chr7A 93.505 2248 71 34 6148 8373 432975729 432977923 0.000000e+00 3273
10 TraesCS7D01G303500 chr7A 98.694 1072 12 2 5082 6151 432974578 432975649 0.000000e+00 1901
11 TraesCS7D01G303500 chr7A 85.232 1510 189 21 3584 5075 50574785 50576278 0.000000e+00 1522
12 TraesCS7D01G303500 chr7A 90.236 594 31 8 1 568 432969527 432970119 0.000000e+00 750
13 TraesCS7D01G303500 chr7A 95.139 144 4 3 603 743 432971536 432971679 3.090000e-54 224
14 TraesCS7D01G303500 chr7A 97.101 69 1 1 8387 8454 432977855 432977923 1.940000e-21 115
15 TraesCS7D01G303500 chr1D 89.211 1520 128 19 3582 5081 192736986 192735483 0.000000e+00 1866
16 TraesCS7D01G303500 chr1D 85.375 1518 184 24 3579 5081 484200353 484198859 0.000000e+00 1539
17 TraesCS7D01G303500 chr1A 87.632 1520 154 17 3581 5081 207220822 207219318 0.000000e+00 1735
18 TraesCS7D01G303500 chr6D 86.373 1519 175 23 3578 5081 344721368 344719867 0.000000e+00 1629
19 TraesCS7D01G303500 chrUn 86.184 1520 179 23 3577 5081 27119310 27117807 0.000000e+00 1615
20 TraesCS7D01G303500 chrUn 84.656 1512 199 22 3579 5075 43651424 43652917 0.000000e+00 1476
21 TraesCS7D01G303500 chr5D 86.291 1510 175 23 3582 5075 502656886 502658379 0.000000e+00 1613
22 TraesCS7D01G303500 chr6A 86.205 1515 161 33 3582 5081 599192718 599191237 0.000000e+00 1596
23 TraesCS7D01G303500 chr2B 88.955 335 31 6 3579 3911 794754715 794754385 7.940000e-110 409
24 TraesCS7D01G303500 chr6B 92.181 243 15 2 3579 3818 544668518 544668759 2.940000e-89 340
25 TraesCS7D01G303500 chr1B 91.736 242 16 2 3580 3818 113824311 113824551 4.920000e-87 333
26 TraesCS7D01G303500 chr3D 88.281 256 28 2 3580 3834 191167424 191167170 1.070000e-78 305


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 TraesCS7D01G303500 chr7D 384937306 384945803 8497 False 5320.333333 15693 96.212000 1 8498 3 chr7D.!!$F1 8497
1 TraesCS7D01G303500 chr7D 548813556 548814423 867 True 896.000000 896 85.410000 3566 4447 1 chr7D.!!$R1 881
2 TraesCS7D01G303500 chr7B 379408797 379416684 7887 False 2601.750000 5084 93.074500 1 8393 4 chr7B.!!$F1 8392
3 TraesCS7D01G303500 chr7A 432969527 432977923 8396 False 1811.166667 4604 94.955667 1 8454 6 chr7A.!!$F2 8453
4 TraesCS7D01G303500 chr7A 50574785 50576278 1493 False 1522.000000 1522 85.232000 3584 5075 1 chr7A.!!$F1 1491
5 TraesCS7D01G303500 chr1D 192735483 192736986 1503 True 1866.000000 1866 89.211000 3582 5081 1 chr1D.!!$R1 1499
6 TraesCS7D01G303500 chr1D 484198859 484200353 1494 True 1539.000000 1539 85.375000 3579 5081 1 chr1D.!!$R2 1502
7 TraesCS7D01G303500 chr1A 207219318 207220822 1504 True 1735.000000 1735 87.632000 3581 5081 1 chr1A.!!$R1 1500
8 TraesCS7D01G303500 chr6D 344719867 344721368 1501 True 1629.000000 1629 86.373000 3578 5081 1 chr6D.!!$R1 1503
9 TraesCS7D01G303500 chrUn 27117807 27119310 1503 True 1615.000000 1615 86.184000 3577 5081 1 chrUn.!!$R1 1504
10 TraesCS7D01G303500 chrUn 43651424 43652917 1493 False 1476.000000 1476 84.656000 3579 5075 1 chrUn.!!$F1 1496
11 TraesCS7D01G303500 chr5D 502656886 502658379 1493 False 1613.000000 1613 86.291000 3582 5075 1 chr5D.!!$F1 1493
12 TraesCS7D01G303500 chr6A 599191237 599192718 1481 True 1596.000000 1596 86.205000 3582 5081 1 chr6A.!!$R1 1499

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
284 1191 0.107410 TGTTTGTCCAGCGGTTGAGT 60.107 50.000 0.00 0.0 0.00 3.41 F
1389 3791 0.036732 TGCTGCGGTTTCTCATCCTT 59.963 50.000 0.00 0.0 0.00 3.36 F
1493 3895 1.410517 TCGATTCTCCATCAGAGGTGC 59.589 52.381 0.00 0.0 43.44 5.01 F
1494 3896 1.411977 CGATTCTCCATCAGAGGTGCT 59.588 52.381 0.00 0.0 43.44 4.40 F
1878 4288 1.515519 GTGCCATGTGCTGATTGCG 60.516 57.895 7.54 0.0 46.63 4.85 F
2989 5425 2.846206 TCACTACCTCCTGAATGCCATT 59.154 45.455 0.00 0.0 0.00 3.16 F
3924 6399 0.871722 CCAGGCAAAATGTCGAACGA 59.128 50.000 0.00 0.0 0.00 3.85 F
4293 6775 0.977395 AGTCAGTTCCCAGCACTACC 59.023 55.000 0.00 0.0 0.00 3.18 F
4945 7438 1.267121 TACCTGGCTCTCACCAAGTC 58.733 55.000 0.00 0.0 39.86 3.01 F
5159 7652 1.373570 AAGCTTCTGCACTTATCGCC 58.626 50.000 0.00 0.0 42.74 5.54 F
5951 8445 1.135083 CAGGCTAATCGTCGTGTCCTT 60.135 52.381 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1705 4115 0.611618 GTTGGCCACATGGACCATGA 60.612 55.000 35.91 14.39 44.80 3.07 R
2621 5057 1.000385 CGGCAGACCAAAAATCAGCAA 60.000 47.619 0.00 0.00 34.57 3.91 R
2972 5408 4.141482 GGAGTAAATGGCATTCAGGAGGTA 60.141 45.833 14.04 0.00 0.00 3.08 R
3018 5454 5.069648 TCAGGAATTTTGTTGTACCATTGCA 59.930 36.000 0.00 0.00 0.00 4.08 R
3656 6092 1.082690 CTCGCTGCCTTTCTTTCCTC 58.917 55.000 0.00 0.00 0.00 3.71 R
4365 6850 0.179018 ACCCTGTGTGTTCCTTCTGC 60.179 55.000 0.00 0.00 0.00 4.26 R
4770 7255 0.333993 ACTCAATTGATGGGCTGCCT 59.666 50.000 19.68 0.00 30.00 4.75 R
5150 7643 2.289444 CCATATGAACGGGGCGATAAGT 60.289 50.000 3.65 0.00 0.00 2.24 R
5951 8445 3.181451 CCCTTAGCCATTCATCAGTAGCA 60.181 47.826 0.00 0.00 0.00 3.49 R
7109 9688 0.950116 GCAATCAGGTATGAGCAGCC 59.050 55.000 0.00 0.00 39.29 4.85 R
7558 10152 0.474184 ACAGACTTGGGTGGAAGGTG 59.526 55.000 0.00 0.00 0.00 4.00 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
33 34 2.737932 GAAGCCGTTGTTGCTGCCTG 62.738 60.000 0.00 0.00 39.48 4.85
38 39 1.066257 GTTGTTGCTGCCTGTGTGG 59.934 57.895 0.00 0.00 39.35 4.17
106 998 4.596585 CAGGCCACCAAACGGGGT 62.597 66.667 5.01 0.00 43.56 4.95
221 1122 4.891037 GGATCCAGCCAGCCAGCC 62.891 72.222 6.95 0.00 0.00 4.85
241 1142 0.742990 CTTTGTAGGATTCGCCGCCA 60.743 55.000 0.00 0.00 43.43 5.69
284 1191 0.107410 TGTTTGTCCAGCGGTTGAGT 60.107 50.000 0.00 0.00 0.00 3.41
397 1314 4.687483 CCAGTAGTACTGTTTTTACCACGG 59.313 45.833 25.09 5.24 44.50 4.94
430 1347 2.047274 CTGCCGTTGATGACCGGT 60.047 61.111 6.92 6.92 45.91 5.28
431 1352 1.216977 CTGCCGTTGATGACCGGTA 59.783 57.895 7.34 0.00 45.91 4.02
439 1360 4.426416 CGTTGATGACCGGTATTTCACTA 58.574 43.478 7.34 0.00 0.00 2.74
591 1527 0.387622 GACGAACCATGAACCGACGA 60.388 55.000 0.00 0.00 0.00 4.20
687 3078 1.061735 GGGAGGAAGGAGGGAGAGAAT 60.062 57.143 0.00 0.00 0.00 2.40
762 3154 1.068474 GAACTGACGACCCATGTTCG 58.932 55.000 11.37 11.37 0.00 3.95
799 3191 1.696314 ACCAGTCACACCAACCCCT 60.696 57.895 0.00 0.00 0.00 4.79
914 3307 4.226384 AGGTGGCCATTTCTTTTCTTCTT 58.774 39.130 9.72 0.00 0.00 2.52
915 3308 4.281941 AGGTGGCCATTTCTTTTCTTCTTC 59.718 41.667 9.72 0.00 0.00 2.87
916 3309 4.560128 GTGGCCATTTCTTTTCTTCTTCC 58.440 43.478 9.72 0.00 0.00 3.46
918 3311 3.055819 GGCCATTTCTTTTCTTCTTCCCC 60.056 47.826 0.00 0.00 0.00 4.81
919 3312 3.834813 GCCATTTCTTTTCTTCTTCCCCT 59.165 43.478 0.00 0.00 0.00 4.79
920 3313 4.322273 GCCATTTCTTTTCTTCTTCCCCTG 60.322 45.833 0.00 0.00 0.00 4.45
921 3314 4.322273 CCATTTCTTTTCTTCTTCCCCTGC 60.322 45.833 0.00 0.00 0.00 4.85
922 3315 3.884037 TTCTTTTCTTCTTCCCCTGCT 57.116 42.857 0.00 0.00 0.00 4.24
923 3316 4.993705 TTCTTTTCTTCTTCCCCTGCTA 57.006 40.909 0.00 0.00 0.00 3.49
924 3317 4.287766 TCTTTTCTTCTTCCCCTGCTAC 57.712 45.455 0.00 0.00 0.00 3.58
925 3318 3.910627 TCTTTTCTTCTTCCCCTGCTACT 59.089 43.478 0.00 0.00 0.00 2.57
926 3319 3.703001 TTTCTTCTTCCCCTGCTACTG 57.297 47.619 0.00 0.00 0.00 2.74
927 3320 0.905357 TCTTCTTCCCCTGCTACTGC 59.095 55.000 0.00 0.00 40.20 4.40
945 3340 2.688446 CTGCTAGTACGTTCCAGGATCA 59.312 50.000 0.00 0.00 0.00 2.92
1213 3608 2.657237 GTGTGGCCGCTAGACTGT 59.343 61.111 18.96 0.00 0.00 3.55
1233 3628 2.574212 CAGCATTTTCGCGGTCGC 60.574 61.111 6.13 5.16 36.85 5.19
1235 3630 3.799755 GCATTTTCGCGGTCGCCT 61.800 61.111 6.13 0.00 37.98 5.52
1298 3693 5.243426 TCTCGGGTTTTCTTTTCTTTGTG 57.757 39.130 0.00 0.00 0.00 3.33
1389 3791 0.036732 TGCTGCGGTTTCTCATCCTT 59.963 50.000 0.00 0.00 0.00 3.36
1453 3855 2.579207 TTAACGGGATTCAGAGCTCG 57.421 50.000 8.37 3.55 0.00 5.03
1491 3893 3.843422 AGATCGATTCTCCATCAGAGGT 58.157 45.455 0.00 0.00 43.44 3.85
1492 3894 3.573538 AGATCGATTCTCCATCAGAGGTG 59.426 47.826 0.00 0.00 43.44 4.00
1493 3895 1.410517 TCGATTCTCCATCAGAGGTGC 59.589 52.381 0.00 0.00 43.44 5.01
1494 3896 1.411977 CGATTCTCCATCAGAGGTGCT 59.588 52.381 0.00 0.00 43.44 4.40
1526 3929 9.466497 TTTACCAGATTTCAGAATGCTAGAAAT 57.534 29.630 9.57 9.57 42.74 2.17
1661 4070 3.489047 GCTACTTCTCGAATCTGATGTGC 59.511 47.826 0.00 0.00 0.00 4.57
1705 4115 4.060900 CGTATGCCTGCTGAATATTCTGT 58.939 43.478 19.75 5.50 0.00 3.41
1878 4288 1.515519 GTGCCATGTGCTGATTGCG 60.516 57.895 7.54 0.00 46.63 4.85
1906 4316 7.539034 TTATATGTGCTATTGGACTGCTAGA 57.461 36.000 0.00 0.00 35.45 2.43
1969 4380 7.122650 TCCTTGATTGTCTTGGTTAATGATTCC 59.877 37.037 0.00 0.00 0.00 3.01
1993 4405 5.558653 CGCTGCAACATGCTTTTTATTTGTT 60.559 36.000 0.00 0.00 45.31 2.83
2091 4519 3.868757 AGTAGTCTTGCGCTGTGATTA 57.131 42.857 9.73 2.59 0.00 1.75
2213 4641 4.982241 TGGTTCCTTCACAGAAGAAGAT 57.018 40.909 8.26 0.00 46.18 2.40
2350 4779 9.030301 CCTTGTCTTGATCATTTTAACGTTTTT 57.970 29.630 5.91 0.00 0.00 1.94
2385 4814 7.810658 AGTGATGTAATTCAGTTGCAACTTAG 58.189 34.615 29.23 18.88 37.08 2.18
2536 4972 3.821033 GGTGGCTTCAAAGTAGAACACAT 59.179 43.478 0.00 0.00 30.43 3.21
2569 5005 8.632679 GGTCATTTAAGATGGCTGAATAATTCA 58.367 33.333 0.00 0.00 38.17 2.57
2579 5015 6.924111 TGGCTGAATAATTCAAAGAACTTCC 58.076 36.000 0.00 0.00 39.58 3.46
2621 5057 3.490348 ACAGCTGTCCTATTTGCAAACT 58.510 40.909 15.25 6.68 0.00 2.66
2989 5425 2.846206 TCACTACCTCCTGAATGCCATT 59.154 45.455 0.00 0.00 0.00 3.16
3021 5457 4.213564 ACTGGAATGGTTTGTTTTTGCA 57.786 36.364 0.00 0.00 0.00 4.08
3082 5518 4.989875 AGACCTATCTTGAATCCCCATG 57.010 45.455 0.00 0.00 0.00 3.66
3202 5638 5.188327 TGTGCCAAATGAATTAACGTTCA 57.812 34.783 2.82 0.00 41.88 3.18
3517 5953 9.998106 AATCTGCTTTATTTATATACACGTCCT 57.002 29.630 0.00 0.00 0.00 3.85
3518 5954 8.812147 TCTGCTTTATTTATATACACGTCCTG 57.188 34.615 0.00 0.00 0.00 3.86
3519 5955 7.384115 TCTGCTTTATTTATATACACGTCCTGC 59.616 37.037 0.00 0.00 0.00 4.85
3563 5999 7.393551 GTTCAAACCATTCAGTTATGTTGTG 57.606 36.000 0.00 0.00 0.00 3.33
3564 6000 6.707440 TCAAACCATTCAGTTATGTTGTGT 57.293 33.333 0.00 0.00 0.00 3.72
3656 6092 4.585162 AGTATCCGATACAACCAGGAAGAG 59.415 45.833 18.67 0.00 38.21 2.85
3704 6140 0.890996 CTGCCAGGAAACCCACTGTC 60.891 60.000 0.00 0.00 32.90 3.51
3771 6207 6.183361 ACAGCACCTACTTAGTTCAAACCTAA 60.183 38.462 0.00 0.00 0.00 2.69
3791 6227 6.070366 ACCTAACTATTACAAACCAGGGAGAC 60.070 42.308 0.00 0.00 0.00 3.36
3793 6229 5.161943 ACTATTACAAACCAGGGAGACAC 57.838 43.478 0.00 0.00 0.00 3.67
3794 6230 4.595781 ACTATTACAAACCAGGGAGACACA 59.404 41.667 0.00 0.00 0.00 3.72
3803 6244 2.643551 CAGGGAGACACACACAAAAGT 58.356 47.619 0.00 0.00 0.00 2.66
3820 6262 5.070313 ACAAAAGTGGTGCCAGATAACAAAT 59.930 36.000 0.00 0.00 0.00 2.32
3821 6263 5.391312 AAAGTGGTGCCAGATAACAAATC 57.609 39.130 0.00 0.00 0.00 2.17
3822 6264 3.356290 AGTGGTGCCAGATAACAAATCC 58.644 45.455 0.00 0.00 0.00 3.01
3824 6266 3.378427 GTGGTGCCAGATAACAAATCCTC 59.622 47.826 0.00 0.00 0.00 3.71
3825 6267 3.010027 TGGTGCCAGATAACAAATCCTCA 59.990 43.478 0.00 0.00 0.00 3.86
3827 6269 4.462483 GGTGCCAGATAACAAATCCTCAAA 59.538 41.667 0.00 0.00 0.00 2.69
3828 6270 5.402398 GTGCCAGATAACAAATCCTCAAAC 58.598 41.667 0.00 0.00 0.00 2.93
3829 6271 5.183904 GTGCCAGATAACAAATCCTCAAACT 59.816 40.000 0.00 0.00 0.00 2.66
3830 6272 5.415701 TGCCAGATAACAAATCCTCAAACTC 59.584 40.000 0.00 0.00 0.00 3.01
3831 6273 5.415701 GCCAGATAACAAATCCTCAAACTCA 59.584 40.000 0.00 0.00 0.00 3.41
3832 6274 6.404074 GCCAGATAACAAATCCTCAAACTCAG 60.404 42.308 0.00 0.00 0.00 3.35
3833 6275 6.881065 CCAGATAACAAATCCTCAAACTCAGA 59.119 38.462 0.00 0.00 0.00 3.27
3834 6276 7.391554 CCAGATAACAAATCCTCAAACTCAGAA 59.608 37.037 0.00 0.00 0.00 3.02
3835 6277 8.954350 CAGATAACAAATCCTCAAACTCAGAAT 58.046 33.333 0.00 0.00 0.00 2.40
3836 6278 8.954350 AGATAACAAATCCTCAAACTCAGAATG 58.046 33.333 0.00 0.00 37.54 2.67
3860 6307 4.019771 AGCCAGTTTCAAAAGTTCCCAAAA 60.020 37.500 0.00 0.00 0.00 2.44
3879 6327 4.799564 AAAGTGAAGCCTGAGACTAGAG 57.200 45.455 0.00 0.00 0.00 2.43
3899 6347 2.109799 CAGCACATCGCCCCCTAG 59.890 66.667 0.00 0.00 44.04 3.02
3918 6393 1.615392 AGCTCAACCAGGCAAAATGTC 59.385 47.619 0.00 0.00 0.00 3.06
3921 6396 2.293122 CTCAACCAGGCAAAATGTCGAA 59.707 45.455 0.00 0.00 0.00 3.71
3924 6399 0.871722 CCAGGCAAAATGTCGAACGA 59.128 50.000 0.00 0.00 0.00 3.85
4019 6501 2.333417 CCTGGCTGTGCTTGCTCTG 61.333 63.158 0.00 0.00 0.00 3.35
4043 6525 2.154854 TCTCAGTTTCCTTGTCGCAG 57.845 50.000 0.00 0.00 0.00 5.18
4068 6550 3.435186 GCTTCTTCCACCGGCTGC 61.435 66.667 0.00 0.00 0.00 5.25
4105 6587 3.753294 AGAGAAAAGAACAAGCCGAGA 57.247 42.857 0.00 0.00 0.00 4.04
4117 6599 2.376808 AGCCGAGAACACAATCTCAG 57.623 50.000 5.29 0.00 44.98 3.35
4146 6628 8.758715 GGAGATTTGATCAACTGTTTTTCAAAG 58.241 33.333 21.98 1.25 39.04 2.77
4164 6646 2.631984 GTAGCCTTATTGCGCGCC 59.368 61.111 30.77 11.28 36.02 6.53
4188 6670 2.097466 CCAAATAGCCCAAGTTACTGCG 59.903 50.000 0.00 0.00 0.00 5.18
4216 6698 7.367285 CAGACCAACAGTATAGAATCTAGCTC 58.633 42.308 0.00 0.00 0.00 4.09
4221 6703 8.807118 CCAACAGTATAGAATCTAGCTCCATTA 58.193 37.037 0.00 0.00 0.00 1.90
4257 6739 2.230992 GCACCACACATAGAATTGCCAA 59.769 45.455 0.00 0.00 0.00 4.52
4281 6763 6.010219 AGTGTTATTTGGGCATAAGTCAGTT 58.990 36.000 0.00 0.00 0.00 3.16
4286 6768 1.281867 TGGGCATAAGTCAGTTCCCAG 59.718 52.381 0.00 0.00 38.72 4.45
4290 6772 2.616510 GCATAAGTCAGTTCCCAGCACT 60.617 50.000 0.00 0.00 0.00 4.40
4293 6775 0.977395 AGTCAGTTCCCAGCACTACC 59.023 55.000 0.00 0.00 0.00 3.18
4344 6829 3.613193 CGGGACACGTAAAGAACAGATGA 60.613 47.826 0.00 0.00 37.93 2.92
4347 6832 5.411781 GGACACGTAAAGAACAGATGAGAT 58.588 41.667 0.00 0.00 0.00 2.75
4350 6835 4.033358 CACGTAAAGAACAGATGAGATGCC 59.967 45.833 0.00 0.00 0.00 4.40
4358 6843 2.744202 ACAGATGAGATGCCGTTTCAAC 59.256 45.455 0.00 0.00 0.00 3.18
4419 6904 2.386661 TCCTTTTCATCACCGCTCTC 57.613 50.000 0.00 0.00 0.00 3.20
4422 6907 2.416836 CCTTTTCATCACCGCTCTCGTA 60.417 50.000 0.00 0.00 0.00 3.43
4434 6919 2.879462 CTCGTAAGCACCGCGTCC 60.879 66.667 4.92 0.00 37.18 4.79
4437 6922 3.488090 GTAAGCACCGCGTCCTGC 61.488 66.667 4.92 9.02 41.47 4.85
4461 6946 4.325119 CCATCTGCCATAAGAAGATCTGG 58.675 47.826 0.00 0.00 0.00 3.86
4505 6990 4.492646 TCCCAGATCCATCTATAGTTGCA 58.507 43.478 5.42 0.00 34.85 4.08
4511 6996 7.147602 CCAGATCCATCTATAGTTGCATCCATA 60.148 40.741 10.03 0.00 34.85 2.74
4512 6997 8.430431 CAGATCCATCTATAGTTGCATCCATAT 58.570 37.037 10.03 0.00 34.85 1.78
4584 7069 3.955551 TCTTACTCAAACCCCAAAACACC 59.044 43.478 0.00 0.00 0.00 4.16
4592 7077 2.758130 ACCCCAAAACACCACATCTTT 58.242 42.857 0.00 0.00 0.00 2.52
4593 7078 3.917300 ACCCCAAAACACCACATCTTTA 58.083 40.909 0.00 0.00 0.00 1.85
4605 7090 4.081087 ACCACATCTTTATCGGCTGTAGTT 60.081 41.667 0.00 0.00 0.00 2.24
4608 7093 6.456988 CCACATCTTTATCGGCTGTAGTTTTC 60.457 42.308 0.00 0.00 0.00 2.29
4620 7105 4.843728 CTGTAGTTTTCAGCCCCAAGATA 58.156 43.478 0.00 0.00 0.00 1.98
4622 7107 5.192927 TGTAGTTTTCAGCCCCAAGATATG 58.807 41.667 0.00 0.00 0.00 1.78
4625 7110 2.645838 TTCAGCCCCAAGATATGCTC 57.354 50.000 0.00 0.00 30.08 4.26
4641 7126 1.486310 TGCTCTCGCAACTTATCCCAT 59.514 47.619 0.00 0.00 44.62 4.00
4645 7130 1.334869 CTCGCAACTTATCCCATTGCC 59.665 52.381 2.83 0.00 44.71 4.52
4647 7132 1.484038 GCAACTTATCCCATTGCCCA 58.516 50.000 0.00 0.00 42.32 5.36
4649 7134 1.405105 CAACTTATCCCATTGCCCACG 59.595 52.381 0.00 0.00 0.00 4.94
4656 7141 1.312371 CCCATTGCCCACGTAGGTTG 61.312 60.000 0.97 0.00 34.66 3.77
4710 7195 4.280929 GCCTCTACCCTGTCAAATTTTTGT 59.719 41.667 3.18 0.00 39.18 2.83
4719 7204 7.138736 CCCTGTCAAATTTTTGTACTGTACAG 58.861 38.462 21.44 21.44 40.24 2.74
4818 7304 2.357517 CTGGTCAGGTCGCCACAC 60.358 66.667 0.00 0.00 0.00 3.82
4882 7370 3.072915 TCAGAAGAGCTTTCCAACATGGA 59.927 43.478 0.00 0.00 46.61 3.41
4895 7388 3.515502 CCAACATGGAGAGTTGTCTAGGA 59.484 47.826 0.00 0.00 43.61 2.94
4897 7390 5.338708 CCAACATGGAGAGTTGTCTAGGATT 60.339 44.000 0.00 0.00 43.61 3.01
4906 7399 4.899502 AGTTGTCTAGGATTCACAGTTGG 58.100 43.478 0.00 0.00 0.00 3.77
4921 7414 4.754618 CACAGTTGGCACAGACTTGTTATA 59.245 41.667 0.00 0.00 42.39 0.98
4928 7421 8.979574 GTTGGCACAGACTTGTTATATAGATAC 58.020 37.037 0.00 0.00 42.39 2.24
4945 7438 1.267121 TACCTGGCTCTCACCAAGTC 58.733 55.000 0.00 0.00 39.86 3.01
4954 7447 3.152341 CTCTCACCAAGTCTTGCCAAAT 58.848 45.455 7.09 0.00 0.00 2.32
4961 7454 2.206576 AGTCTTGCCAAATCCCAGTC 57.793 50.000 0.00 0.00 0.00 3.51
4985 7478 3.257375 GGGTTTCTAATTTCCACCACCAC 59.743 47.826 0.00 0.00 0.00 4.16
5063 7556 2.496470 GTCCTTCGATCTACACACCCTT 59.504 50.000 0.00 0.00 0.00 3.95
5150 7643 6.935741 TTTAGTTGTTTCTAAGCTTCTGCA 57.064 33.333 0.00 0.00 42.74 4.41
5159 7652 1.373570 AAGCTTCTGCACTTATCGCC 58.626 50.000 0.00 0.00 42.74 5.54
5879 8373 3.123050 CCTTTTTCTTTTGGAGTTGGCG 58.877 45.455 0.00 0.00 0.00 5.69
5951 8445 1.135083 CAGGCTAATCGTCGTGTCCTT 60.135 52.381 0.00 0.00 0.00 3.36
6474 9052 6.240894 TGCAGACAAAGATAAATCTGGAACT 58.759 36.000 2.56 0.00 36.70 3.01
6561 9139 5.065731 GCTATACATGAAGAGCAAGCAACTT 59.934 40.000 0.00 0.00 34.96 2.66
6777 9355 8.420189 CACTTCAGTTAAAATTCATCGCTTTTC 58.580 33.333 0.00 0.00 0.00 2.29
6929 9507 1.328279 GTTTCAACCCCTTCAGGTGG 58.672 55.000 0.00 0.00 40.05 4.61
7024 9603 7.254455 GCACTGTAGTTATTCATGCGAAGTAAT 60.254 37.037 0.00 0.00 33.74 1.89
7523 10117 7.814107 GTCAAAGGAGATATGATTTTGTTTGCA 59.186 33.333 0.00 0.00 32.22 4.08
7525 10119 5.899299 AGGAGATATGATTTTGTTTGCAGC 58.101 37.500 0.00 0.00 0.00 5.25
7535 10129 7.600960 TGATTTTGTTTGCAGCATATACAGAA 58.399 30.769 0.00 3.78 0.00 3.02
7542 10136 4.060900 TGCAGCATATACAGAAGCTAAGC 58.939 43.478 0.00 0.00 35.19 3.09
7543 10137 4.202295 TGCAGCATATACAGAAGCTAAGCT 60.202 41.667 0.00 0.00 42.56 3.74
7544 10138 5.011023 TGCAGCATATACAGAAGCTAAGCTA 59.989 40.000 0.00 0.00 38.25 3.32
7545 10139 5.928839 GCAGCATATACAGAAGCTAAGCTAA 59.071 40.000 0.00 0.00 38.25 3.09
7546 10140 6.090628 GCAGCATATACAGAAGCTAAGCTAAG 59.909 42.308 0.00 0.00 38.25 2.18
7728 10323 6.236941 CGCAAACTCGCAGATTAATTTTGTAC 60.237 38.462 7.83 0.00 33.89 2.90
7729 10324 6.236941 GCAAACTCGCAGATTAATTTTGTACG 60.237 38.462 7.83 0.00 33.89 3.67
7730 10325 6.476243 AACTCGCAGATTAATTTTGTACGT 57.524 33.333 0.00 0.00 33.89 3.57
7731 10326 7.585286 AACTCGCAGATTAATTTTGTACGTA 57.415 32.000 0.00 0.00 33.89 3.57
7814 10409 0.392461 GTTTGTGCGGAGGCCTGATA 60.392 55.000 12.00 0.00 38.85 2.15
7866 10461 3.701040 ACCAGATTTTGTGCTGTGAAACT 59.299 39.130 0.00 0.00 38.04 2.66
7867 10462 4.160252 ACCAGATTTTGTGCTGTGAAACTT 59.840 37.500 0.00 0.00 38.04 2.66
7868 10463 5.111293 CCAGATTTTGTGCTGTGAAACTTT 58.889 37.500 0.00 0.00 38.04 2.66
7869 10464 5.581874 CCAGATTTTGTGCTGTGAAACTTTT 59.418 36.000 0.00 0.00 38.04 2.27
7870 10465 6.092533 CCAGATTTTGTGCTGTGAAACTTTTT 59.907 34.615 0.00 0.00 38.04 1.94
7900 10495 6.701400 GGTGAAAATGCTGTGAAACTGTTTAT 59.299 34.615 5.64 0.00 38.15 1.40
7907 10502 6.437928 TGCTGTGAAACTGTTTATGTGAATC 58.562 36.000 5.64 0.00 38.15 2.52
7940 10537 1.974236 AGCAACTTCTACTGGCTCTGT 59.026 47.619 0.00 0.00 0.00 3.41
7948 10545 4.737855 TCTACTGGCTCTGTATGTTTCC 57.262 45.455 0.00 0.00 0.00 3.13
7966 10563 2.110006 GGCCTCGATCTGCCCTTC 59.890 66.667 9.05 0.00 41.97 3.46
8021 10620 7.339721 TGACTGGAGTAGTAGTAAAGATGAAGG 59.660 40.741 0.00 0.00 40.53 3.46
8042 10644 4.220602 AGGAAAGTTGAGTGTTGTTTTGCT 59.779 37.500 0.00 0.00 0.00 3.91
8054 10656 2.980586 TGTTTTGCTGTTGACGAATCG 58.019 42.857 0.00 0.00 0.00 3.34
8065 10667 0.801067 GACGAATCGGGAGTGTTCCG 60.801 60.000 7.80 0.00 45.04 4.30
8081 10683 7.008021 AGTGTTCCGGTCTATAAAGGTTTAA 57.992 36.000 0.00 0.00 0.00 1.52
8103 10705 3.118261 AGCTCTTGAGTTGTTCCAGTTCA 60.118 43.478 0.00 0.00 0.00 3.18
8192 10818 7.671455 ACTGTTTAGTTGGTACATGGAACACG 61.671 42.308 0.00 0.00 35.12 4.49
8222 10848 2.729194 TGGTGGATAAACAATTCCCCG 58.271 47.619 0.00 0.00 0.00 5.73
8230 10856 6.322712 TGGATAAACAATTCCCCGGAATAAAG 59.677 38.462 0.73 5.84 43.26 1.85
8231 10857 6.239204 GGATAAACAATTCCCCGGAATAAAGG 60.239 42.308 0.73 0.00 43.26 3.11
8232 10858 3.026707 ACAATTCCCCGGAATAAAGGG 57.973 47.619 0.73 0.00 43.26 3.95
8233 10859 1.686587 CAATTCCCCGGAATAAAGGGC 59.313 52.381 0.73 0.00 46.24 5.19
8234 10860 0.930726 ATTCCCCGGAATAAAGGGCA 59.069 50.000 0.73 0.00 46.24 5.36
8235 10861 0.705253 TTCCCCGGAATAAAGGGCAA 59.295 50.000 0.73 0.00 46.24 4.52
8236 10862 0.705253 TCCCCGGAATAAAGGGCAAA 59.295 50.000 0.73 0.00 46.24 3.68
8237 10863 0.821517 CCCCGGAATAAAGGGCAAAC 59.178 55.000 0.73 0.00 46.24 2.93
8238 10864 1.551452 CCCGGAATAAAGGGCAAACA 58.449 50.000 0.73 0.00 41.34 2.83
8239 10865 2.107366 CCCGGAATAAAGGGCAAACAT 58.893 47.619 0.73 0.00 41.34 2.71
8240 10866 2.499693 CCCGGAATAAAGGGCAAACATT 59.500 45.455 0.73 0.00 41.34 2.71
8241 10867 3.520569 CCGGAATAAAGGGCAAACATTG 58.479 45.455 0.00 0.00 0.00 2.82
8242 10868 3.194542 CCGGAATAAAGGGCAAACATTGA 59.805 43.478 0.00 0.00 0.00 2.57
8243 10869 4.141959 CCGGAATAAAGGGCAAACATTGAT 60.142 41.667 0.00 0.00 0.00 2.57
8249 10875 0.542805 GGGCAAACATTGATGGGCAT 59.457 50.000 0.00 0.00 0.00 4.40
8261 10887 5.628797 TTGATGGGCATACTGAATAGACA 57.371 39.130 0.00 0.00 0.00 3.41
8270 10896 5.464722 GCATACTGAATAGACACAGTCCATG 59.535 44.000 0.00 0.00 44.59 3.66
8293 10919 2.543777 TAAGGACCGCAATATCTGGC 57.456 50.000 0.00 0.00 0.00 4.85
8294 10920 0.839946 AAGGACCGCAATATCTGGCT 59.160 50.000 0.00 0.00 0.00 4.75
8304 10930 4.319766 CGCAATATCTGGCTAATGTTCACC 60.320 45.833 0.00 0.00 0.00 4.02
8323 10949 1.272258 CCGGGAAGGGTTGGTATTTGT 60.272 52.381 0.00 0.00 35.97 2.83
8361 10987 4.040706 ACGAGTTTAGTTGTATGGGGTTGA 59.959 41.667 0.00 0.00 0.00 3.18
8365 11012 4.986054 TTAGTTGTATGGGGTTGACAGT 57.014 40.909 0.00 0.00 0.00 3.55
8378 11025 4.304110 GGTTGACAGTCAGAAACGTATGA 58.696 43.478 2.82 0.00 0.00 2.15
8392 11039 7.114811 CAGAAACGTATGACAATTTTTGGGAAG 59.885 37.037 0.00 0.00 34.12 3.46
8396 11043 6.490721 ACGTATGACAATTTTTGGGAAGGTTA 59.509 34.615 0.00 0.00 34.12 2.85
8404 11064 7.659799 ACAATTTTTGGGAAGGTTAGTATTTGC 59.340 33.333 0.00 0.00 34.12 3.68
8421 11081 6.795114 AGTATTTGCAAACGTTTTAGATGACG 59.205 34.615 15.41 0.00 44.34 4.35
8449 11109 0.327924 TGTATGGGGTTGGCAGTCAG 59.672 55.000 0.00 0.00 0.00 3.51
8457 11117 1.529865 GGTTGGCAGTCAGAAACGTAC 59.470 52.381 0.00 0.00 0.00 3.67
8458 11118 1.191647 GTTGGCAGTCAGAAACGTACG 59.808 52.381 15.01 15.01 0.00 3.67
8459 11119 0.669619 TGGCAGTCAGAAACGTACGA 59.330 50.000 24.41 0.00 0.00 3.43
8474 11134 4.128643 ACGTACGACAATTTTTGGGAAGA 58.871 39.130 24.41 0.00 34.12 2.87
8475 11135 4.575645 ACGTACGACAATTTTTGGGAAGAA 59.424 37.500 24.41 0.00 34.12 2.52
8476 11136 5.144359 CGTACGACAATTTTTGGGAAGAAG 58.856 41.667 10.44 0.00 34.12 2.85
8477 11137 5.049954 CGTACGACAATTTTTGGGAAGAAGA 60.050 40.000 10.44 0.00 34.12 2.87
8478 11138 5.845391 ACGACAATTTTTGGGAAGAAGAA 57.155 34.783 0.00 0.00 34.12 2.52
8479 11139 6.405278 ACGACAATTTTTGGGAAGAAGAAT 57.595 33.333 0.00 0.00 34.12 2.40
8480 11140 6.816136 ACGACAATTTTTGGGAAGAAGAATT 58.184 32.000 0.00 0.00 34.12 2.17
8481 11141 7.272244 ACGACAATTTTTGGGAAGAAGAATTT 58.728 30.769 0.00 0.00 34.12 1.82
8482 11142 7.768582 ACGACAATTTTTGGGAAGAAGAATTTT 59.231 29.630 0.00 0.00 34.12 1.82
8483 11143 9.255304 CGACAATTTTTGGGAAGAAGAATTTTA 57.745 29.630 0.00 0.00 34.12 1.52
8485 11145 9.898152 ACAATTTTTGGGAAGAAGAATTTTACA 57.102 25.926 0.00 0.00 34.12 2.41
8488 11148 9.898152 ATTTTTGGGAAGAAGAATTTTACAACA 57.102 25.926 0.00 0.00 0.00 3.33
8489 11149 9.726438 TTTTTGGGAAGAAGAATTTTACAACAA 57.274 25.926 0.00 0.00 0.00 2.83
8490 11150 9.726438 TTTTGGGAAGAAGAATTTTACAACAAA 57.274 25.926 0.00 0.00 0.00 2.83
8491 11151 9.726438 TTTGGGAAGAAGAATTTTACAACAAAA 57.274 25.926 0.00 0.00 0.00 2.44
8492 11152 8.940768 TGGGAAGAAGAATTTTACAACAAAAG 57.059 30.769 0.00 0.00 0.00 2.27
8493 11153 8.754080 TGGGAAGAAGAATTTTACAACAAAAGA 58.246 29.630 0.00 0.00 0.00 2.52
8494 11154 9.764363 GGGAAGAAGAATTTTACAACAAAAGAT 57.236 29.630 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
221 1122 1.436983 GGCGGCGAATCCTACAAAGG 61.437 60.000 12.98 0.00 45.21 3.11
223 1124 0.742990 CTGGCGGCGAATCCTACAAA 60.743 55.000 12.98 0.00 0.00 2.83
241 1142 1.817941 GCGGAGAGAGAGAGACGCT 60.818 63.158 0.00 0.00 43.24 5.07
430 1347 5.574055 CACTTACGCGAAAGGTAGTGAAATA 59.426 40.000 15.93 0.00 0.00 1.40
431 1352 4.387862 CACTTACGCGAAAGGTAGTGAAAT 59.612 41.667 15.93 0.00 0.00 2.17
439 1360 0.249741 ACTGCACTTACGCGAAAGGT 60.250 50.000 15.93 3.81 33.35 3.50
475 1397 7.358770 TCTGTTTGGATTTTTCATTTCTCCA 57.641 32.000 0.00 0.00 34.27 3.86
836 3228 3.311966 GGTACGCGTCTACACTTTTTCT 58.688 45.455 18.63 0.00 0.00 2.52
914 3307 1.749635 CGTACTAGCAGTAGCAGGGGA 60.750 57.143 0.00 0.00 45.49 4.81
915 3308 0.669077 CGTACTAGCAGTAGCAGGGG 59.331 60.000 0.00 0.00 45.49 4.79
916 3309 1.390565 ACGTACTAGCAGTAGCAGGG 58.609 55.000 0.00 0.00 45.49 4.45
918 3311 2.422479 TGGAACGTACTAGCAGTAGCAG 59.578 50.000 0.00 0.00 45.49 4.24
919 3312 2.422479 CTGGAACGTACTAGCAGTAGCA 59.578 50.000 0.00 0.00 45.49 3.49
920 3313 2.223525 CCTGGAACGTACTAGCAGTAGC 60.224 54.545 0.00 0.00 42.56 3.58
921 3314 3.276857 TCCTGGAACGTACTAGCAGTAG 58.723 50.000 0.00 0.00 30.12 2.57
922 3315 3.354948 TCCTGGAACGTACTAGCAGTA 57.645 47.619 0.00 0.00 0.00 2.74
923 3316 2.211250 TCCTGGAACGTACTAGCAGT 57.789 50.000 0.00 0.00 0.00 4.40
924 3317 2.688446 TGATCCTGGAACGTACTAGCAG 59.312 50.000 0.00 0.00 0.00 4.24
925 3318 2.426024 GTGATCCTGGAACGTACTAGCA 59.574 50.000 0.00 0.00 0.00 3.49
926 3319 2.223758 GGTGATCCTGGAACGTACTAGC 60.224 54.545 0.00 0.00 0.00 3.42
927 3320 2.033049 CGGTGATCCTGGAACGTACTAG 59.967 54.545 0.00 0.00 0.00 2.57
958 3353 0.642800 CGCTACGCTTTGCTCTTCTC 59.357 55.000 0.00 0.00 0.00 2.87
959 3354 0.737715 CCGCTACGCTTTGCTCTTCT 60.738 55.000 0.00 0.00 0.00 2.85
992 3387 1.028905 CGTCCACCTCATCTCTCTCC 58.971 60.000 0.00 0.00 0.00 3.71
1162 3557 1.869767 GCAGCAGATCCGATCGAAATT 59.130 47.619 18.66 0.00 0.00 1.82
1184 3579 2.809601 CCACACGAGGTACGCAGC 60.810 66.667 0.00 0.00 46.94 5.25
1189 3584 2.609183 CTAGCGGCCACACGAGGTAC 62.609 65.000 2.24 0.00 35.47 3.34
1213 3608 1.692148 CGACCGCGAAAATGCTGCTA 61.692 55.000 8.23 0.00 40.82 3.49
1233 3628 0.958091 TTCGTGCCCAACATTTGAGG 59.042 50.000 0.00 0.00 0.00 3.86
1235 3630 3.742433 AAATTCGTGCCCAACATTTGA 57.258 38.095 0.00 0.00 0.00 2.69
1389 3791 1.021202 CAACAGTTTCGGTGGCTCAA 58.979 50.000 0.00 0.00 0.00 3.02
1453 3855 5.430007 TCGATCTAGGTAGAGCTATTAGGC 58.570 45.833 1.10 0.00 36.63 3.93
1565 3968 8.059798 ACTATTTTCTTCCCATTTCATCAGTG 57.940 34.615 0.00 0.00 0.00 3.66
1666 4075 2.509336 GAGGTCCACCGCGATGTG 60.509 66.667 8.23 8.30 42.08 3.21
1674 4083 1.144057 CAGGCATACGAGGTCCACC 59.856 63.158 0.00 0.00 0.00 4.61
1705 4115 0.611618 GTTGGCCACATGGACCATGA 60.612 55.000 35.91 14.39 44.80 3.07
1878 4288 8.103948 AGCAGTCCAATAGCACATATAAAATC 57.896 34.615 0.00 0.00 0.00 2.17
1906 4316 7.611467 TGTATTATTCAGAAGTCCAGCATTTGT 59.389 33.333 0.00 0.00 0.00 2.83
1952 4363 3.487544 GCAGCGGAATCATTAACCAAGAC 60.488 47.826 0.00 0.00 0.00 3.01
2187 4615 5.560722 TCTTCTGTGAAGGAACCAATGTA 57.439 39.130 7.37 0.00 0.00 2.29
2213 4641 3.202818 AGCCCAATCATCTACCATTGTCA 59.797 43.478 0.00 0.00 0.00 3.58
2385 4814 7.224949 AGCTACCGCTTACTGAAAAATATTCTC 59.775 37.037 0.00 0.00 46.47 2.87
2442 4871 8.441312 TTCGGAACTCATAACACTAACTTTTT 57.559 30.769 0.00 0.00 0.00 1.94
2621 5057 1.000385 CGGCAGACCAAAAATCAGCAA 60.000 47.619 0.00 0.00 34.57 3.91
2972 5408 4.141482 GGAGTAAATGGCATTCAGGAGGTA 60.141 45.833 14.04 0.00 0.00 3.08
3018 5454 5.069648 TCAGGAATTTTGTTGTACCATTGCA 59.930 36.000 0.00 0.00 0.00 4.08
3021 5457 5.838521 AGGTCAGGAATTTTGTTGTACCATT 59.161 36.000 0.00 0.00 0.00 3.16
3079 5515 6.590292 ACTTGTAGATAACGAACTTCACCATG 59.410 38.462 0.00 0.00 0.00 3.66
3082 5518 7.170320 TCAAACTTGTAGATAACGAACTTCACC 59.830 37.037 0.00 0.00 0.00 4.02
3202 5638 8.043710 CCACCTTTCTGTCAGAGTATTAAGAAT 58.956 37.037 11.29 0.00 0.00 2.40
3516 5952 3.057736 CAGGTTCATTCCTTTGTCAGCAG 60.058 47.826 0.00 0.00 35.37 4.24
3517 5953 2.886523 CAGGTTCATTCCTTTGTCAGCA 59.113 45.455 0.00 0.00 35.37 4.41
3518 5954 2.229784 CCAGGTTCATTCCTTTGTCAGC 59.770 50.000 0.00 0.00 35.37 4.26
3519 5955 3.490348 ACCAGGTTCATTCCTTTGTCAG 58.510 45.455 0.00 0.00 35.37 3.51
3636 6072 3.639094 CTCTCTTCCTGGTTGTATCGGAT 59.361 47.826 0.00 0.00 0.00 4.18
3656 6092 1.082690 CTCGCTGCCTTTCTTTCCTC 58.917 55.000 0.00 0.00 0.00 3.71
3704 6140 4.830765 TTTCGATGGCGGGCGAGG 62.831 66.667 0.00 0.00 37.85 4.63
3771 6207 4.595781 TGTGTCTCCCTGGTTTGTAATAGT 59.404 41.667 0.00 0.00 0.00 2.12
3803 6244 3.010027 TGAGGATTTGTTATCTGGCACCA 59.990 43.478 0.00 0.00 0.00 4.17
3820 6262 2.639347 TGGCTCATTCTGAGTTTGAGGA 59.361 45.455 13.41 0.00 45.94 3.71
3821 6263 3.008330 CTGGCTCATTCTGAGTTTGAGG 58.992 50.000 13.41 0.00 45.94 3.86
3822 6264 3.672808 ACTGGCTCATTCTGAGTTTGAG 58.327 45.455 6.06 9.12 45.94 3.02
3824 6266 4.276678 TGAAACTGGCTCATTCTGAGTTTG 59.723 41.667 0.00 0.12 45.94 2.93
3825 6267 4.464008 TGAAACTGGCTCATTCTGAGTTT 58.536 39.130 6.06 0.00 45.94 2.66
3827 6269 3.777106 TGAAACTGGCTCATTCTGAGT 57.223 42.857 6.06 0.00 45.94 3.41
3828 6270 5.009410 ACTTTTGAAACTGGCTCATTCTGAG 59.991 40.000 0.00 0.00 46.90 3.35
3829 6271 4.889409 ACTTTTGAAACTGGCTCATTCTGA 59.111 37.500 0.00 0.00 0.00 3.27
3830 6272 5.192327 ACTTTTGAAACTGGCTCATTCTG 57.808 39.130 0.00 0.00 0.00 3.02
3831 6273 5.221322 GGAACTTTTGAAACTGGCTCATTCT 60.221 40.000 0.00 0.00 0.00 2.40
3832 6274 4.984785 GGAACTTTTGAAACTGGCTCATTC 59.015 41.667 0.00 0.00 0.00 2.67
3833 6275 4.202253 GGGAACTTTTGAAACTGGCTCATT 60.202 41.667 0.00 0.00 0.00 2.57
3834 6276 3.321968 GGGAACTTTTGAAACTGGCTCAT 59.678 43.478 0.00 0.00 0.00 2.90
3835 6277 2.693074 GGGAACTTTTGAAACTGGCTCA 59.307 45.455 0.00 0.00 0.00 4.26
3836 6278 2.693074 TGGGAACTTTTGAAACTGGCTC 59.307 45.455 0.00 0.00 0.00 4.70
3837 6279 2.745968 TGGGAACTTTTGAAACTGGCT 58.254 42.857 0.00 0.00 0.00 4.75
3838 6280 3.535280 TTGGGAACTTTTGAAACTGGC 57.465 42.857 0.00 0.00 0.00 4.85
3839 6281 5.351189 CACTTTTGGGAACTTTTGAAACTGG 59.649 40.000 0.00 0.00 0.00 4.00
3840 6282 6.162777 TCACTTTTGGGAACTTTTGAAACTG 58.837 36.000 0.00 0.00 0.00 3.16
3841 6283 6.353404 TCACTTTTGGGAACTTTTGAAACT 57.647 33.333 0.00 0.00 0.00 2.66
3842 6284 6.402118 GCTTCACTTTTGGGAACTTTTGAAAC 60.402 38.462 0.00 0.00 36.84 2.78
3860 6307 2.099405 GCTCTAGTCTCAGGCTTCACT 58.901 52.381 0.00 0.00 0.00 3.41
3899 6347 1.666888 CGACATTTTGCCTGGTTGAGC 60.667 52.381 0.00 0.00 0.00 4.26
3918 6393 0.932399 TGATGATGCTGCATCGTTCG 59.068 50.000 31.44 0.00 45.93 3.95
3921 6396 0.816825 GGGTGATGATGCTGCATCGT 60.817 55.000 31.42 31.42 45.93 3.73
3924 6399 0.549469 TCTGGGTGATGATGCTGCAT 59.451 50.000 16.20 16.20 0.00 3.96
3982 6464 3.695556 CAGGTTGATGGCAATGTGTGATA 59.304 43.478 0.00 0.00 36.22 2.15
4006 6488 2.867368 GAGATGATCAGAGCAAGCACAG 59.133 50.000 0.09 0.00 0.00 3.66
4019 6501 3.308323 GCGACAAGGAAACTGAGATGATC 59.692 47.826 0.00 0.00 42.68 2.92
4030 6512 0.944386 GCAAGACTGCGACAAGGAAA 59.056 50.000 0.00 0.00 39.20 3.13
4043 6525 1.578206 GGTGGAAGAAGCGGCAAGAC 61.578 60.000 1.45 0.00 0.00 3.01
4068 6550 4.963318 TCTCTTATATTGGGCAGGTCTG 57.037 45.455 0.00 0.00 0.00 3.51
4117 6599 8.137437 TGAAAAACAGTTGATCAAATCTCCTTC 58.863 33.333 10.35 9.45 0.00 3.46
4134 6616 6.366061 GCAATAAGGCTACCTTTGAAAAACAG 59.634 38.462 3.85 0.00 41.69 3.16
4146 6628 2.631984 GCGCGCAATAAGGCTACC 59.368 61.111 29.10 0.00 0.00 3.18
4164 6646 3.129287 CAGTAACTTGGGCTATTTGGCTG 59.871 47.826 0.00 0.00 41.48 4.85
4188 6670 3.906720 TTCTATACTGTTGGTCTGGCC 57.093 47.619 0.00 0.00 37.90 5.36
4216 6698 6.545666 TGGTGCAATATGTTCTTACCTAATGG 59.454 38.462 0.00 0.00 39.83 3.16
4221 6703 4.700213 GTGTGGTGCAATATGTTCTTACCT 59.300 41.667 0.00 0.00 0.00 3.08
4257 6739 5.570320 ACTGACTTATGCCCAAATAACACT 58.430 37.500 0.00 0.00 0.00 3.55
4281 6763 1.151899 AGTTGGGGTAGTGCTGGGA 60.152 57.895 0.00 0.00 0.00 4.37
4286 6768 2.361230 GGGCAGTTGGGGTAGTGC 60.361 66.667 0.00 0.00 42.47 4.40
4290 6772 1.923395 CTGGAGGGCAGTTGGGGTA 60.923 63.158 0.00 0.00 0.00 3.69
4323 6808 3.921677 TCATCTGTTCTTTACGTGTCCC 58.078 45.455 0.00 0.00 0.00 4.46
4358 6843 1.400142 TGTGTTCCTTCTGCAACAACG 59.600 47.619 0.00 0.00 34.33 4.10
4365 6850 0.179018 ACCCTGTGTGTTCCTTCTGC 60.179 55.000 0.00 0.00 0.00 4.26
4404 6889 2.876091 CTTACGAGAGCGGTGATGAAA 58.124 47.619 0.00 0.00 43.17 2.69
4405 6890 1.469251 GCTTACGAGAGCGGTGATGAA 60.469 52.381 0.00 0.00 43.17 2.57
4419 6904 3.179265 CAGGACGCGGTGCTTACG 61.179 66.667 12.47 0.00 30.21 3.18
4434 6919 0.533531 TCTTATGGCAGATGGCGCAG 60.534 55.000 10.83 0.00 46.16 5.18
4437 6922 2.245159 TCTTCTTATGGCAGATGGCG 57.755 50.000 1.68 0.00 46.16 5.69
4584 7069 6.092122 TGAAAACTACAGCCGATAAAGATGTG 59.908 38.462 0.00 0.00 0.00 3.21
4605 7090 2.511218 AGAGCATATCTTGGGGCTGAAA 59.489 45.455 0.00 0.00 36.59 2.69
4608 7093 1.607509 CGAGAGCATATCTTGGGGCTG 60.608 57.143 0.00 0.00 38.84 4.85
4625 7110 1.334869 GGCAATGGGATAAGTTGCGAG 59.665 52.381 3.60 0.00 46.82 5.03
4631 7116 0.623723 ACGTGGGCAATGGGATAAGT 59.376 50.000 0.00 0.00 0.00 2.24
4645 7130 0.179056 CTATGCCCCAACCTACGTGG 60.179 60.000 0.00 0.00 42.93 4.94
4647 7132 0.828677 GTCTATGCCCCAACCTACGT 59.171 55.000 0.00 0.00 0.00 3.57
4649 7134 0.532196 GCGTCTATGCCCCAACCTAC 60.532 60.000 0.00 0.00 0.00 3.18
4710 7195 3.520691 ACAGACCAGGACTGTACAGTA 57.479 47.619 27.98 0.00 45.10 2.74
4719 7204 3.357203 TGAGATCTGTACAGACCAGGAC 58.643 50.000 27.41 15.16 40.75 3.85
4770 7255 0.333993 ACTCAATTGATGGGCTGCCT 59.666 50.000 19.68 0.00 30.00 4.75
4811 7297 3.261981 AGATTAAACTAGGGTGTGGCG 57.738 47.619 0.00 0.00 0.00 5.69
4818 7304 5.886474 GGTGGGAAGAAAGATTAAACTAGGG 59.114 44.000 0.00 0.00 0.00 3.53
4882 7370 5.279708 CCAACTGTGAATCCTAGACAACTCT 60.280 44.000 0.00 0.00 0.00 3.24
4895 7388 2.620115 CAAGTCTGTGCCAACTGTGAAT 59.380 45.455 0.00 0.00 0.00 2.57
4897 7390 1.065491 ACAAGTCTGTGCCAACTGTGA 60.065 47.619 0.00 0.00 33.30 3.58
4906 7399 7.815068 CCAGGTATCTATATAACAAGTCTGTGC 59.185 40.741 0.00 0.00 35.37 4.57
4921 7414 3.619900 TGGTGAGAGCCAGGTATCTAT 57.380 47.619 0.00 0.00 33.97 1.98
4928 7421 0.689623 AAGACTTGGTGAGAGCCAGG 59.310 55.000 0.00 0.00 40.01 4.45
4945 7438 1.180029 CCAGACTGGGATTTGGCAAG 58.820 55.000 14.26 0.00 32.67 4.01
4961 7454 3.509967 GGTGGTGGAAATTAGAAACCCAG 59.490 47.826 0.00 0.00 0.00 4.45
5150 7643 2.289444 CCATATGAACGGGGCGATAAGT 60.289 50.000 3.65 0.00 0.00 2.24
5159 7652 8.482943 TGAATATAATAGGACCATATGAACGGG 58.517 37.037 3.65 0.00 0.00 5.28
5626 8120 7.197703 TGGTAATTCTTTTGTCGAACCTTTTC 58.802 34.615 0.00 0.00 0.00 2.29
5879 8373 4.808364 GCTGAACTGACAGAAGGATACATC 59.192 45.833 10.08 0.00 39.94 3.06
5951 8445 3.181451 CCCTTAGCCATTCATCAGTAGCA 60.181 47.826 0.00 0.00 0.00 3.49
6237 8815 7.380065 CAGTTCAAGTATCCTAGCGAAAGTATC 59.620 40.741 0.00 0.00 0.00 2.24
6327 8905 8.918116 AGTCACTATGATGTATTGACATGTAGT 58.082 33.333 0.00 2.04 46.64 2.73
6474 9052 6.376864 TGTCTTGGATTTCTTTCACAGTCAAA 59.623 34.615 0.00 0.00 0.00 2.69
6528 9106 7.331026 TGCTCTTCATGTATAGCTTTACTTGT 58.669 34.615 21.38 6.09 35.95 3.16
6561 9139 9.997482 GTTCTTATTAAATCTGCAATTCCGTTA 57.003 29.630 0.00 0.00 0.00 3.18
6716 9294 7.307337 GGAACTTTGTGCATTGTAAAATTCCAG 60.307 37.037 16.74 0.00 32.69 3.86
6929 9507 5.335127 AGCTGACGAATGATGCAAAATAAC 58.665 37.500 0.00 0.00 0.00 1.89
7024 9603 8.132995 CAGATTCAACATAATCATTGCTAGCAA 58.867 33.333 31.05 31.05 38.16 3.91
7089 9668 8.633561 AGCAGCCTAAAAATTATTCTGTTATCC 58.366 33.333 0.00 0.00 0.00 2.59
7106 9685 3.745480 GCAATCAGGTATGAGCAGCCTAA 60.745 47.826 0.00 0.00 39.29 2.69
7107 9686 2.224378 GCAATCAGGTATGAGCAGCCTA 60.224 50.000 0.00 0.00 39.29 3.93
7108 9687 1.476471 GCAATCAGGTATGAGCAGCCT 60.476 52.381 0.00 0.00 39.29 4.58
7109 9688 0.950116 GCAATCAGGTATGAGCAGCC 59.050 55.000 0.00 0.00 39.29 4.85
7110 9689 0.950116 GGCAATCAGGTATGAGCAGC 59.050 55.000 0.00 0.00 39.29 5.25
7523 10117 6.696411 CCTTAGCTTAGCTTCTGTATATGCT 58.304 40.000 13.44 0.00 40.44 3.79
7525 10119 5.872070 GGCCTTAGCTTAGCTTCTGTATATG 59.128 44.000 13.44 0.00 40.44 1.78
7535 10129 2.432510 CACTACTGGCCTTAGCTTAGCT 59.567 50.000 12.67 12.67 43.41 3.32
7558 10152 0.474184 ACAGACTTGGGTGGAAGGTG 59.526 55.000 0.00 0.00 0.00 4.00
7607 10201 5.715279 GCAGGGTTACTTTTATTCTTTCCCT 59.285 40.000 0.00 0.00 42.75 4.20
7728 10323 7.465513 GCATATCTTTGTGGTAAAAGGACTACG 60.466 40.741 0.00 0.00 37.67 3.51
7729 10324 7.335924 TGCATATCTTTGTGGTAAAAGGACTAC 59.664 37.037 0.00 0.00 37.67 2.73
7730 10325 7.398829 TGCATATCTTTGTGGTAAAAGGACTA 58.601 34.615 0.00 0.00 37.67 2.59
7731 10326 6.245408 TGCATATCTTTGTGGTAAAAGGACT 58.755 36.000 0.00 0.00 37.67 3.85
7814 10409 3.057386 TCAACAGCATTTCGCATGACAAT 60.057 39.130 0.00 0.00 46.13 2.71
7870 10465 5.936956 AGTTTCACAGCATTTTCACCAAAAA 59.063 32.000 0.00 0.00 40.98 1.94
7871 10466 5.350914 CAGTTTCACAGCATTTTCACCAAAA 59.649 36.000 0.00 0.00 35.92 2.44
7872 10467 4.869297 CAGTTTCACAGCATTTTCACCAAA 59.131 37.500 0.00 0.00 0.00 3.28
7873 10468 4.081752 ACAGTTTCACAGCATTTTCACCAA 60.082 37.500 0.00 0.00 0.00 3.67
7874 10469 3.446873 ACAGTTTCACAGCATTTTCACCA 59.553 39.130 0.00 0.00 0.00 4.17
7875 10470 4.045636 ACAGTTTCACAGCATTTTCACC 57.954 40.909 0.00 0.00 0.00 4.02
7876 10471 7.222611 ACATAAACAGTTTCACAGCATTTTCAC 59.777 33.333 0.48 0.00 0.00 3.18
7877 10472 7.222417 CACATAAACAGTTTCACAGCATTTTCA 59.778 33.333 0.48 0.00 0.00 2.69
7878 10473 7.434897 TCACATAAACAGTTTCACAGCATTTTC 59.565 33.333 0.48 0.00 0.00 2.29
7879 10474 7.264221 TCACATAAACAGTTTCACAGCATTTT 58.736 30.769 0.48 0.00 0.00 1.82
7880 10475 6.804677 TCACATAAACAGTTTCACAGCATTT 58.195 32.000 0.48 0.00 0.00 2.32
7881 10476 6.389830 TCACATAAACAGTTTCACAGCATT 57.610 33.333 0.48 0.00 0.00 3.56
7882 10477 6.389830 TTCACATAAACAGTTTCACAGCAT 57.610 33.333 0.48 0.00 0.00 3.79
7883 10478 5.826601 TTCACATAAACAGTTTCACAGCA 57.173 34.783 0.48 0.00 0.00 4.41
7884 10479 6.437928 TGATTCACATAAACAGTTTCACAGC 58.562 36.000 0.48 0.00 0.00 4.40
7885 10480 8.077991 ACATGATTCACATAAACAGTTTCACAG 58.922 33.333 0.48 0.00 37.46 3.66
7886 10481 7.939782 ACATGATTCACATAAACAGTTTCACA 58.060 30.769 0.48 0.00 37.46 3.58
7887 10482 8.801715 AACATGATTCACATAAACAGTTTCAC 57.198 30.769 0.48 0.00 37.46 3.18
7888 10483 9.247126 CAAACATGATTCACATAAACAGTTTCA 57.753 29.630 0.48 0.00 37.46 2.69
7889 10484 9.248291 ACAAACATGATTCACATAAACAGTTTC 57.752 29.630 0.48 0.00 37.46 2.78
7890 10485 9.033481 CACAAACATGATTCACATAAACAGTTT 57.967 29.630 0.00 3.49 37.46 2.66
7891 10486 7.652909 CCACAAACATGATTCACATAAACAGTT 59.347 33.333 0.00 0.00 37.46 3.16
7900 10495 3.191162 GCTAGCCACAAACATGATTCACA 59.809 43.478 2.29 0.00 0.00 3.58
7907 10502 3.254166 AGAAGTTGCTAGCCACAAACATG 59.746 43.478 20.04 0.00 0.00 3.21
7940 10537 1.068588 CAGATCGAGGCCGGAAACATA 59.931 52.381 5.05 0.00 36.24 2.29
7966 10563 3.815401 CACCCACTTAACCAGAACTTGAG 59.185 47.826 0.00 0.00 0.00 3.02
8021 10620 4.923281 ACAGCAAAACAACACTCAACTTTC 59.077 37.500 0.00 0.00 0.00 2.62
8042 10644 0.677288 ACACTCCCGATTCGTCAACA 59.323 50.000 5.20 0.00 0.00 3.33
8054 10656 3.181468 CCTTTATAGACCGGAACACTCCC 60.181 52.174 9.46 0.00 38.71 4.30
8065 10667 8.041919 ACTCAAGAGCTTAAACCTTTATAGACC 58.958 37.037 0.00 0.00 0.00 3.85
8081 10683 3.118261 TGAACTGGAACAACTCAAGAGCT 60.118 43.478 0.00 0.00 38.70 4.09
8103 10705 4.159693 GCAGGTTTTCGAAGGGGATATTTT 59.840 41.667 0.00 0.00 0.00 1.82
8222 10848 5.118286 CCATCAATGTTTGCCCTTTATTCC 58.882 41.667 0.00 0.00 0.00 3.01
8230 10856 0.542805 ATGCCCATCAATGTTTGCCC 59.457 50.000 0.00 0.00 0.00 5.36
8231 10857 2.431782 AGTATGCCCATCAATGTTTGCC 59.568 45.455 0.00 0.00 0.00 4.52
8232 10858 3.130869 TCAGTATGCCCATCAATGTTTGC 59.869 43.478 0.00 0.00 34.76 3.68
8233 10859 4.987408 TCAGTATGCCCATCAATGTTTG 57.013 40.909 0.00 0.00 34.76 2.93
8234 10860 7.013655 GTCTATTCAGTATGCCCATCAATGTTT 59.986 37.037 0.00 0.00 34.76 2.83
8235 10861 6.488006 GTCTATTCAGTATGCCCATCAATGTT 59.512 38.462 0.00 0.00 34.76 2.71
8236 10862 6.000219 GTCTATTCAGTATGCCCATCAATGT 59.000 40.000 0.00 0.00 34.76 2.71
8237 10863 5.999600 TGTCTATTCAGTATGCCCATCAATG 59.000 40.000 0.00 0.00 34.76 2.82
8238 10864 6.000219 GTGTCTATTCAGTATGCCCATCAAT 59.000 40.000 0.00 0.00 34.76 2.57
8239 10865 5.104569 TGTGTCTATTCAGTATGCCCATCAA 60.105 40.000 0.00 0.00 34.76 2.57
8240 10866 4.408596 TGTGTCTATTCAGTATGCCCATCA 59.591 41.667 0.00 0.00 34.76 3.07
8241 10867 4.960938 TGTGTCTATTCAGTATGCCCATC 58.039 43.478 0.00 0.00 34.76 3.51
8242 10868 4.410228 ACTGTGTCTATTCAGTATGCCCAT 59.590 41.667 0.00 0.00 42.13 4.00
8243 10869 3.774766 ACTGTGTCTATTCAGTATGCCCA 59.225 43.478 0.00 0.00 42.13 5.36
8249 10875 5.952347 ACTCATGGACTGTGTCTATTCAGTA 59.048 40.000 0.00 0.00 43.64 2.74
8261 10887 2.233922 CGGTCCTTAACTCATGGACTGT 59.766 50.000 10.96 0.00 46.11 3.55
8270 10896 4.058817 CCAGATATTGCGGTCCTTAACTC 58.941 47.826 0.00 0.00 0.00 3.01
8293 10919 1.280998 ACCCTTCCCGGTGAACATTAG 59.719 52.381 0.00 0.00 33.77 1.73
8294 10920 1.364269 ACCCTTCCCGGTGAACATTA 58.636 50.000 0.00 0.00 33.77 1.90
8304 10930 2.209690 ACAAATACCAACCCTTCCCG 57.790 50.000 0.00 0.00 0.00 5.14
8323 10949 8.801715 ACTAAACTCGTCATCTAAAACGTTTA 57.198 30.769 15.03 0.00 39.78 2.01
8361 10987 6.861065 AAATTGTCATACGTTTCTGACTGT 57.139 33.333 19.69 10.22 41.83 3.55
8365 11012 6.263392 TCCCAAAAATTGTCATACGTTTCTGA 59.737 34.615 0.00 0.00 0.00 3.27
8378 11025 7.659799 GCAAATACTAACCTTCCCAAAAATTGT 59.340 33.333 0.00 0.00 0.00 2.71
8392 11039 8.846607 CATCTAAAACGTTTGCAAATACTAACC 58.153 33.333 16.21 0.00 0.00 2.85
8396 11043 6.795114 CGTCATCTAAAACGTTTGCAAATACT 59.205 34.615 16.21 0.00 34.30 2.12
8404 11064 7.561556 ACTAAACTCGTCATCTAAAACGTTTG 58.438 34.615 15.46 2.92 39.78 2.93
8421 11081 3.442625 GCCAACCCCATACAACTAAACTC 59.557 47.826 0.00 0.00 0.00 3.01
8449 11109 4.846509 TCCCAAAAATTGTCGTACGTTTC 58.153 39.130 16.05 7.91 0.00 2.78
8457 11117 7.713764 AAATTCTTCTTCCCAAAAATTGTCG 57.286 32.000 0.00 0.00 0.00 4.35
8459 11119 9.898152 TGTAAAATTCTTCTTCCCAAAAATTGT 57.102 25.926 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.