Multiple sequence alignment - TraesCS6B01G015400

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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 TraesCS6B01G015400 chr6B 100.000 4417 0 0 1 4417 9098832 9094416 0.000000e+00 8157
1 TraesCS6B01G015400 chr6B 83.929 336 36 7 109 442 196481389 196481708 5.550000e-79 305
2 TraesCS6B01G015400 chr6B 83.631 336 37 10 109 442 375644334 375644015 2.580000e-77 300
3 TraesCS6B01G015400 chr6B 83.631 336 37 7 109 442 393068877 393069196 2.580000e-77 300
4 TraesCS6B01G015400 chr6A 91.015 3617 153 69 1 3522 3689348 3692887 0.000000e+00 4721
5 TraesCS6B01G015400 chr6A 93.229 576 34 3 3604 4178 3692888 3693459 0.000000e+00 843
6 TraesCS6B01G015400 chr6A 83.333 240 13 12 4204 4417 3698888 3699126 3.490000e-46 196
7 TraesCS6B01G015400 chr6A 86.179 123 15 2 410 531 1816274 1816153 9.970000e-27 132
8 TraesCS6B01G015400 chr6A 93.407 91 3 3 259 349 1816390 1816303 9.970000e-27 132
9 TraesCS6B01G015400 chr6D 93.349 2947 98 29 1 2899 3819421 3816525 0.000000e+00 4266
10 TraesCS6B01G015400 chr6D 85.123 894 62 28 2689 3522 3813614 3812732 0.000000e+00 848
11 TraesCS6B01G015400 chr6D 86.888 633 60 12 3604 4233 3815962 3815350 0.000000e+00 688
12 TraesCS6B01G015400 chr6D 86.441 590 37 23 2945 3522 3816519 3815961 1.360000e-169 606
13 TraesCS6B01G015400 chr6D 83.161 677 69 25 144 812 2834643 2834004 1.070000e-160 577
14 TraesCS6B01G015400 chr4D 91.997 1562 76 21 1056 2607 266757768 266756246 0.000000e+00 2146
15 TraesCS6B01G015400 chr5D 93.106 1407 55 18 1206 2607 30064178 30062809 0.000000e+00 2023
16 TraesCS6B01G015400 chr1B 84.273 337 34 11 109 442 586552723 586553043 1.190000e-80 311
17 TraesCS6B01G015400 chrUn 83.333 240 13 12 4204 4417 231619682 231619920 3.490000e-46 196
18 TraesCS6B01G015400 chr2B 83.186 226 22 8 109 334 706089537 706089746 4.510000e-45 193
19 TraesCS6B01G015400 chr7A 97.778 90 1 1 3516 3605 78824051 78824139 2.130000e-33 154
20 TraesCS6B01G015400 chr4B 98.837 86 1 0 3520 3605 54567190 54567105 2.130000e-33 154
21 TraesCS6B01G015400 chr4A 95.699 93 3 1 3518 3610 270628627 270628718 9.900000e-32 148
22 TraesCS6B01G015400 chr3A 95.652 92 3 1 3521 3612 600920364 600920454 3.560000e-31 147
23 TraesCS6B01G015400 chr3A 92.157 102 7 1 3512 3612 436662055 436662156 4.610000e-30 143
24 TraesCS6B01G015400 chr5B 93.814 97 4 2 3513 3609 6678941 6678847 1.280000e-30 145
25 TraesCS6B01G015400 chr5B 94.624 93 5 0 3520 3612 591589359 591589451 1.280000e-30 145
26 TraesCS6B01G015400 chr3D 93.684 95 4 2 3520 3614 219572180 219572272 1.660000e-29 141
27 TraesCS6B01G015400 chr2D 92.929 99 4 3 3517 3615 178776542 178776447 1.660000e-29 141


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 TraesCS6B01G015400 chr6B 9094416 9098832 4416 True 8157 8157 100.00000 1 4417 1 chr6B.!!$R1 4416
1 TraesCS6B01G015400 chr6A 3689348 3693459 4111 False 2782 4721 92.12200 1 4178 2 chr6A.!!$F2 4177
2 TraesCS6B01G015400 chr6D 3812732 3819421 6689 True 1602 4266 87.95025 1 4233 4 chr6D.!!$R2 4232
3 TraesCS6B01G015400 chr6D 2834004 2834643 639 True 577 577 83.16100 144 812 1 chr6D.!!$R1 668
4 TraesCS6B01G015400 chr4D 266756246 266757768 1522 True 2146 2146 91.99700 1056 2607 1 chr4D.!!$R1 1551
5 TraesCS6B01G015400 chr5D 30062809 30064178 1369 True 2023 2023 93.10600 1206 2607 1 chr5D.!!$R1 1401

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
67 68 0.557238 TATGAGCAACATGGCCCCAT 59.443 50.000 0.0 0.0 39.77 4.00 F
1544 1558 1.074889 GGCACCAGAAAAGGTAAGGGA 59.925 52.381 0.0 0.0 40.77 4.20 F
3164 3244 0.613012 ATGCCTCCCTGTCCTTTTGC 60.613 55.000 0.0 0.0 0.00 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1976 2010 1.000896 CGGGGCAAGGAAGATGGTT 60.001 57.895 0.0 0.0 0.0 3.67 R
3391 3517 0.111089 CTTGTCGTCAGCTTGTTCGC 60.111 55.000 0.0 0.0 0.0 4.70 R
4037 4168 0.394899 GCATAGCTCAGCCCCAACTT 60.395 55.000 0.0 0.0 0.0 2.66 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
53 54 6.990798 TCTTCATGGCTCTGATAGTTATGAG 58.009 40.000 0.00 0.00 33.87 2.90
67 68 0.557238 TATGAGCAACATGGCCCCAT 59.443 50.000 0.00 0.00 39.77 4.00
119 121 9.346725 GGCAAAGAATTGTAAATTCAGTTAGAG 57.653 33.333 13.58 0.70 38.85 2.43
130 132 9.914131 GTAAATTCAGTTAGAGCAGGAATTTTT 57.086 29.630 13.70 0.00 42.37 1.94
139 141 5.976458 AGAGCAGGAATTTTTGACACAAAA 58.024 33.333 5.70 5.70 0.00 2.44
141 143 6.536224 AGAGCAGGAATTTTTGACACAAAAAG 59.464 34.615 21.03 12.08 33.28 2.27
142 144 5.585844 AGCAGGAATTTTTGACACAAAAAGG 59.414 36.000 21.03 12.33 33.28 3.11
152 154 3.053544 TGACACAAAAAGGGGTTCAGGTA 60.054 43.478 0.00 0.00 0.00 3.08
399 406 1.465777 TGCATGACAGAGAAATGTGCG 59.534 47.619 0.00 0.00 32.25 5.34
508 516 5.825679 AGTCTAGTACAGATCATGTGTCCTC 59.174 44.000 0.00 0.00 43.80 3.71
549 557 9.917887 ATCTCTGAAATAAATTTCTGATCCAGT 57.082 29.630 19.15 7.07 46.43 4.00
559 567 6.668541 ATTTCTGATCCAGTTATCGTTGTG 57.331 37.500 0.00 0.00 32.61 3.33
610 620 6.727824 AGGACTAAGAATTGACATGTTTCG 57.272 37.500 0.00 0.00 0.00 3.46
611 621 6.464222 AGGACTAAGAATTGACATGTTTCGA 58.536 36.000 0.00 0.00 0.00 3.71
674 684 2.803956 ACCAACGGACTAACAATTGACG 59.196 45.455 13.59 8.79 0.00 4.35
727 738 5.447144 GCCAAACAACAACTTTGCTTTAAGG 60.447 40.000 0.00 0.00 0.00 2.69
730 741 4.180817 ACAACAACTTTGCTTTAAGGCAC 58.819 39.130 12.36 0.00 42.27 5.01
888 900 5.882557 TGCCATTTTATCAGAGAAAGGACTC 59.117 40.000 0.95 0.00 37.19 3.36
943 955 7.769044 TGTGAAGTATAGAAAGGGCATTCTTAC 59.231 37.037 9.63 10.99 40.13 2.34
1144 1156 8.908903 ACAGTGTACCAAATGATTACAGAAAAA 58.091 29.630 0.00 0.00 0.00 1.94
1189 1202 4.067192 GCCTTCATTGGAATGCAAAACTT 58.933 39.130 0.00 0.00 42.22 2.66
1338 1351 3.018856 TCAAGGATAGCATTGCTGGTTG 58.981 45.455 21.31 16.57 40.10 3.77
1339 1352 2.756760 CAAGGATAGCATTGCTGGTTGT 59.243 45.455 21.31 1.01 40.10 3.32
1340 1353 3.091633 AGGATAGCATTGCTGGTTGTT 57.908 42.857 21.31 0.00 40.10 2.83
1392 1406 9.969001 ACTAATGGCAAGTATTAGGTTCTTTTA 57.031 29.630 9.65 0.00 40.66 1.52
1395 1409 9.700831 AATGGCAAGTATTAGGTTCTTTTAGAT 57.299 29.630 0.00 0.00 0.00 1.98
1397 1411 7.067008 TGGCAAGTATTAGGTTCTTTTAGATGC 59.933 37.037 0.00 0.00 0.00 3.91
1403 1417 9.788960 GTATTAGGTTCTTTTAGATGCTTTTGG 57.211 33.333 0.00 0.00 0.00 3.28
1404 1418 8.650143 ATTAGGTTCTTTTAGATGCTTTTGGA 57.350 30.769 0.00 0.00 0.00 3.53
1405 1419 6.976934 AGGTTCTTTTAGATGCTTTTGGAA 57.023 33.333 0.00 0.00 0.00 3.53
1406 1420 6.986250 AGGTTCTTTTAGATGCTTTTGGAAG 58.014 36.000 0.00 0.00 35.92 3.46
1422 1436 7.707774 TTTTGGAAGCACTTTTAATGTTAGC 57.292 32.000 0.00 0.00 0.00 3.09
1431 1445 6.798959 GCACTTTTAATGTTAGCAAGTGAGAG 59.201 38.462 20.25 0.00 44.76 3.20
1493 1507 1.157585 GCTTCCGTCTTTTCTCCACC 58.842 55.000 0.00 0.00 0.00 4.61
1498 1512 2.299297 TCCGTCTTTTCTCCACCTTCTC 59.701 50.000 0.00 0.00 0.00 2.87
1515 1529 6.260936 CACCTTCTCGGCATCTTATGTAATTT 59.739 38.462 0.00 0.00 35.61 1.82
1544 1558 1.074889 GGCACCAGAAAAGGTAAGGGA 59.925 52.381 0.00 0.00 40.77 4.20
1547 1561 3.008704 GCACCAGAAAAGGTAAGGGACTA 59.991 47.826 0.00 0.00 40.77 2.59
1556 1570 6.910259 AAAGGTAAGGGACTAAATCAGGAT 57.090 37.500 0.00 0.00 38.49 3.24
1810 1844 4.933330 TCAGACAGTTAATGAGCGTATCC 58.067 43.478 0.00 0.00 0.00 2.59
1994 2028 1.000896 AACCATCTTCCTTGCCCCG 60.001 57.895 0.00 0.00 0.00 5.73
2038 2072 2.000429 GCAAACACATGCATCCTTCC 58.000 50.000 0.00 0.00 45.70 3.46
2039 2073 1.547372 GCAAACACATGCATCCTTCCT 59.453 47.619 0.00 0.00 45.70 3.36
2040 2074 2.028748 GCAAACACATGCATCCTTCCTT 60.029 45.455 0.00 0.00 45.70 3.36
2041 2075 3.581755 CAAACACATGCATCCTTCCTTG 58.418 45.455 0.00 0.00 0.00 3.61
2042 2076 2.592102 ACACATGCATCCTTCCTTGT 57.408 45.000 0.00 0.00 0.00 3.16
2043 2077 3.719268 ACACATGCATCCTTCCTTGTA 57.281 42.857 0.00 0.00 0.00 2.41
2044 2078 3.347216 ACACATGCATCCTTCCTTGTAC 58.653 45.455 0.00 0.00 0.00 2.90
2045 2079 3.244875 ACACATGCATCCTTCCTTGTACA 60.245 43.478 0.00 0.00 0.00 2.90
2070 2104 1.463674 ACAATCTGCGTTCATTCCCC 58.536 50.000 0.00 0.00 0.00 4.81
2077 2111 1.449601 CGTTCATTCCCCGGGTGAG 60.450 63.158 21.85 3.89 0.00 3.51
2078 2112 1.895020 CGTTCATTCCCCGGGTGAGA 61.895 60.000 21.85 6.81 0.00 3.27
2097 2131 1.349627 CTGAAACTGCATAGCGCCG 59.650 57.895 2.29 0.00 41.33 6.46
2107 2141 3.106986 ATAGCGCCGTGGCATTCCT 62.107 57.895 12.06 3.91 42.06 3.36
2260 2294 4.455606 CCATAACCTTCATCAACCTCTCC 58.544 47.826 0.00 0.00 0.00 3.71
2350 2384 0.953471 CCGCAAAGATCACCGGAACA 60.953 55.000 9.46 0.00 43.20 3.18
2395 2429 2.451490 CTGCTGAGTCTCTACAAGGGA 58.549 52.381 0.65 0.00 0.00 4.20
2441 2487 2.673523 CACCTAGCCCAGCTGCTT 59.326 61.111 8.66 0.00 42.75 3.91
2572 2618 1.729586 AGCTGACCAAGAAGTACCCA 58.270 50.000 0.00 0.00 0.00 4.51
2581 2627 3.392616 CCAAGAAGTACCCAGCCATCTAT 59.607 47.826 0.00 0.00 0.00 1.98
2584 2630 4.298626 AGAAGTACCCAGCCATCTATTCA 58.701 43.478 0.00 0.00 0.00 2.57
2614 2660 3.242641 CCATCATGTTCTTCATCAGCACG 60.243 47.826 0.00 0.00 34.09 5.34
2749 2815 3.380479 TCTTGACTTGTACCACCTTCG 57.620 47.619 0.00 0.00 0.00 3.79
2753 2819 1.798813 GACTTGTACCACCTTCGCAAG 59.201 52.381 0.00 0.00 41.40 4.01
2789 2857 2.001076 ACTTCTCCAAAAGGGGCAAG 57.999 50.000 0.00 0.00 37.22 4.01
2891 2968 8.527810 ACTTGAACAACTGAAACCAAAAATAGA 58.472 29.630 0.00 0.00 0.00 1.98
2941 3018 5.742063 GGTAAGTACCCAACTGCTTAATCT 58.258 41.667 0.00 0.00 40.53 2.40
2943 3020 6.093633 GGTAAGTACCCAACTGCTTAATCTTG 59.906 42.308 0.00 0.00 40.53 3.02
3164 3244 0.613012 ATGCCTCCCTGTCCTTTTGC 60.613 55.000 0.00 0.00 0.00 3.68
3179 3259 4.641541 TCCTTTTGCGATGATCATTGTCAT 59.358 37.500 21.57 0.00 41.36 3.06
3197 3299 1.200716 CATCGCTGCCAACTGAATTGT 59.799 47.619 0.00 0.00 36.47 2.71
3199 3301 2.499197 TCGCTGCCAACTGAATTGTTA 58.501 42.857 0.00 0.00 36.47 2.41
3203 3305 4.559153 GCTGCCAACTGAATTGTTATTGT 58.441 39.130 0.00 0.00 36.47 2.71
3205 3307 5.107375 GCTGCCAACTGAATTGTTATTGTTG 60.107 40.000 0.00 0.00 36.47 3.33
3219 3321 6.245408 TGTTATTGTTGGCTGGAGATAAACT 58.755 36.000 0.00 0.00 0.00 2.66
3228 3330 8.398665 GTTGGCTGGAGATAAACTAAGTTAATG 58.601 37.037 0.00 0.00 0.00 1.90
3241 3343 7.759489 ACTAAGTTAATGGTTTCAGCAATCA 57.241 32.000 0.00 0.00 0.00 2.57
3243 3345 8.637986 ACTAAGTTAATGGTTTCAGCAATCAAA 58.362 29.630 0.00 0.00 0.00 2.69
3336 3450 4.529769 TGATGATACTGGGGCTCTATCTTG 59.470 45.833 0.00 0.00 0.00 3.02
3366 3480 3.277715 GGAAAGAAGAGGGATGAAGCAG 58.722 50.000 0.00 0.00 0.00 4.24
3378 3504 3.637229 GGATGAAGCAGCTACTACCACTA 59.363 47.826 0.00 0.00 0.00 2.74
3391 3517 1.878953 ACCACTAACAAGCAAGTCGG 58.121 50.000 0.00 0.00 0.00 4.79
3421 3547 0.507358 GACGACAAGCCGTGAAACTC 59.493 55.000 0.00 0.00 43.49 3.01
3422 3548 0.104304 ACGACAAGCCGTGAAACTCT 59.896 50.000 0.00 0.00 41.70 3.24
3431 3557 6.127310 ACAAGCCGTGAAACTCTAGAGATTAT 60.127 38.462 26.57 8.70 31.75 1.28
3432 3558 7.068348 ACAAGCCGTGAAACTCTAGAGATTATA 59.932 37.037 26.57 10.39 31.75 0.98
3437 3563 7.201794 CCGTGAAACTCTAGAGATTATACACCA 60.202 40.741 26.57 10.54 31.75 4.17
3452 3578 2.643551 ACACCATTGGATTCGGTCATC 58.356 47.619 10.37 0.00 0.00 2.92
3518 3646 2.911594 GCTGGATGCAGCTAGCTAC 58.088 57.895 30.10 13.19 45.94 3.58
3520 3648 1.270732 GCTGGATGCAGCTAGCTACAT 60.271 52.381 30.10 27.05 45.94 2.29
3521 3649 2.028658 GCTGGATGCAGCTAGCTACATA 60.029 50.000 30.10 13.90 45.94 2.29
3522 3650 3.583806 CTGGATGCAGCTAGCTACATAC 58.416 50.000 27.30 27.30 45.94 2.39
3523 3651 3.234353 TGGATGCAGCTAGCTACATACT 58.766 45.455 31.45 14.13 45.94 2.12
3524 3652 3.256879 TGGATGCAGCTAGCTACATACTC 59.743 47.826 31.45 20.36 45.94 2.59
3525 3653 3.367910 GGATGCAGCTAGCTACATACTCC 60.368 52.174 26.90 21.68 45.94 3.85
3526 3654 1.964223 TGCAGCTAGCTACATACTCCC 59.036 52.381 18.86 0.00 45.94 4.30
3527 3655 2.243810 GCAGCTAGCTACATACTCCCT 58.756 52.381 18.86 0.00 41.15 4.20
3528 3656 2.230266 GCAGCTAGCTACATACTCCCTC 59.770 54.545 18.86 0.00 41.15 4.30
3529 3657 2.823154 CAGCTAGCTACATACTCCCTCC 59.177 54.545 18.86 0.00 0.00 4.30
3530 3658 1.813786 GCTAGCTACATACTCCCTCCG 59.186 57.143 7.70 0.00 0.00 4.63
3531 3659 2.814842 GCTAGCTACATACTCCCTCCGT 60.815 54.545 7.70 0.00 0.00 4.69
3532 3660 1.984066 AGCTACATACTCCCTCCGTC 58.016 55.000 0.00 0.00 0.00 4.79
3533 3661 0.960286 GCTACATACTCCCTCCGTCC 59.040 60.000 0.00 0.00 0.00 4.79
3534 3662 1.618487 CTACATACTCCCTCCGTCCC 58.382 60.000 0.00 0.00 0.00 4.46
3535 3663 0.928505 TACATACTCCCTCCGTCCCA 59.071 55.000 0.00 0.00 0.00 4.37
3536 3664 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
3537 3665 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
3538 3666 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
3539 3667 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3540 3668 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3541 3669 2.488836 ACTCCCTCCGTCCCAAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
3542 3670 3.660959 ACTCCCTCCGTCCCAAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
3543 3671 4.042174 ACTCCCTCCGTCCCAAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
3544 3672 4.102681 ACTCCCTCCGTCCCAAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
3545 3673 4.300345 TCCCTCCGTCCCAAAATATAAGA 58.700 43.478 0.00 0.00 0.00 2.10
3546 3674 4.722781 TCCCTCCGTCCCAAAATATAAGAA 59.277 41.667 0.00 0.00 0.00 2.52
3547 3675 4.820173 CCCTCCGTCCCAAAATATAAGAAC 59.180 45.833 0.00 0.00 0.00 3.01
3548 3676 4.510340 CCTCCGTCCCAAAATATAAGAACG 59.490 45.833 0.00 0.00 0.00 3.95
3549 3677 3.872771 TCCGTCCCAAAATATAAGAACGC 59.127 43.478 0.00 0.00 0.00 4.84
3550 3678 3.875134 CCGTCCCAAAATATAAGAACGCT 59.125 43.478 0.00 0.00 0.00 5.07
3551 3679 4.334481 CCGTCCCAAAATATAAGAACGCTT 59.666 41.667 0.00 0.00 38.15 4.68
3552 3680 5.163693 CCGTCCCAAAATATAAGAACGCTTT 60.164 40.000 0.00 0.00 35.56 3.51
3553 3681 6.319399 CGTCCCAAAATATAAGAACGCTTTT 58.681 36.000 0.00 0.00 35.56 2.27
3554 3682 7.414319 CCGTCCCAAAATATAAGAACGCTTTTA 60.414 37.037 0.00 0.00 35.56 1.52
3555 3683 7.964011 CGTCCCAAAATATAAGAACGCTTTTAA 59.036 33.333 0.00 0.00 35.56 1.52
3556 3684 9.069078 GTCCCAAAATATAAGAACGCTTTTAAC 57.931 33.333 0.00 0.00 35.56 2.01
3557 3685 8.794553 TCCCAAAATATAAGAACGCTTTTAACA 58.205 29.630 0.00 0.00 35.56 2.41
3558 3686 8.856247 CCCAAAATATAAGAACGCTTTTAACAC 58.144 33.333 0.00 0.00 35.56 3.32
3559 3687 9.620660 CCAAAATATAAGAACGCTTTTAACACT 57.379 29.630 0.00 0.00 35.56 3.55
3564 3692 7.958053 ATAAGAACGCTTTTAACACTACACT 57.042 32.000 0.00 0.00 35.56 3.55
3566 3694 7.404139 AAGAACGCTTTTAACACTACACTAG 57.596 36.000 0.00 0.00 0.00 2.57
3567 3695 6.510536 AGAACGCTTTTAACACTACACTAGT 58.489 36.000 0.00 0.00 40.28 2.57
3580 3708 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
3581 3709 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
3582 3710 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
3583 3711 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
3584 3712 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
3585 3713 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
3586 3714 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
3591 3719 9.458374 AGTGTCAAAAACGTTCTTATATTTTGG 57.542 29.630 15.53 0.00 39.94 3.28
3592 3720 8.696175 GTGTCAAAAACGTTCTTATATTTTGGG 58.304 33.333 15.53 0.00 39.94 4.12
3593 3721 8.630917 TGTCAAAAACGTTCTTATATTTTGGGA 58.369 29.630 15.53 4.35 39.94 4.37
3594 3722 8.908678 GTCAAAAACGTTCTTATATTTTGGGAC 58.091 33.333 15.53 7.20 39.94 4.46
3595 3723 7.804129 TCAAAAACGTTCTTATATTTTGGGACG 59.196 33.333 15.53 0.00 39.94 4.79
3596 3724 5.806366 AACGTTCTTATATTTTGGGACGG 57.194 39.130 0.00 0.00 0.00 4.79
3597 3725 5.088680 ACGTTCTTATATTTTGGGACGGA 57.911 39.130 0.00 0.00 0.00 4.69
3598 3726 5.114081 ACGTTCTTATATTTTGGGACGGAG 58.886 41.667 0.00 0.00 0.00 4.63
3599 3727 4.510340 CGTTCTTATATTTTGGGACGGAGG 59.490 45.833 0.00 0.00 0.00 4.30
3600 3728 4.699925 TCTTATATTTTGGGACGGAGGG 57.300 45.455 0.00 0.00 0.00 4.30
3601 3729 4.300345 TCTTATATTTTGGGACGGAGGGA 58.700 43.478 0.00 0.00 0.00 4.20
3602 3730 4.347000 TCTTATATTTTGGGACGGAGGGAG 59.653 45.833 0.00 0.00 0.00 4.30
3652 3780 5.674525 CTGGTACTGTTGACATATGTCCAT 58.325 41.667 28.64 14.18 44.15 3.41
3793 3923 6.887002 ACTTCTTCCTTCTCAAGAACTTTGTT 59.113 34.615 0.00 0.00 35.40 2.83
3806 3936 9.528018 TCAAGAACTTTGTTATTTTGGACATTC 57.472 29.630 0.00 0.00 0.00 2.67
3816 3946 8.359642 TGTTATTTTGGACATTCTCTTTTCCTG 58.640 33.333 0.00 0.00 0.00 3.86
3841 3971 1.650153 CGATGCCTTGCAATTTCGTTG 59.350 47.619 0.00 0.00 43.62 4.10
3873 4003 4.865925 TCGAAAAATTCTCGGCGATCTTAA 59.134 37.500 11.27 3.20 36.93 1.85
3913 4043 6.398234 TGGCAAAGACAGCAAAGTAATAAA 57.602 33.333 0.00 0.00 0.00 1.40
3947 4077 8.533657 TGTACCGTTATATTTCTTCTCCAAGAA 58.466 33.333 0.00 0.00 45.30 2.52
4037 4168 1.202817 CATATTGTGCTTGTGCTGGCA 59.797 47.619 0.00 0.00 40.48 4.92
4043 4174 1.300388 GCTTGTGCTGGCAAGTTGG 60.300 57.895 4.75 0.00 45.47 3.77
4098 4229 1.538419 GCTAACTAGCCATCACGGTCC 60.538 57.143 0.00 0.00 43.39 4.46
4106 4237 1.406887 GCCATCACGGTCCAAGTACAT 60.407 52.381 0.00 0.00 36.97 2.29
4111 4242 5.390613 CATCACGGTCCAAGTACATTTTTC 58.609 41.667 0.00 0.00 0.00 2.29
4113 4244 3.818773 CACGGTCCAAGTACATTTTTCCT 59.181 43.478 0.00 0.00 0.00 3.36
4114 4245 4.070009 ACGGTCCAAGTACATTTTTCCTC 58.930 43.478 0.00 0.00 0.00 3.71
4115 4246 4.202430 ACGGTCCAAGTACATTTTTCCTCT 60.202 41.667 0.00 0.00 0.00 3.69
4116 4247 5.012354 ACGGTCCAAGTACATTTTTCCTCTA 59.988 40.000 0.00 0.00 0.00 2.43
4117 4248 5.935789 CGGTCCAAGTACATTTTTCCTCTAA 59.064 40.000 0.00 0.00 0.00 2.10
4119 4250 7.414098 CGGTCCAAGTACATTTTTCCTCTAATG 60.414 40.741 0.00 0.00 37.67 1.90
4120 4251 7.393515 GGTCCAAGTACATTTTTCCTCTAATGT 59.606 37.037 0.00 0.00 44.63 2.71
4121 4252 9.444600 GTCCAAGTACATTTTTCCTCTAATGTA 57.555 33.333 0.00 0.00 41.74 2.29
4146 4277 7.851228 ACTATATGGACAGATTGTGTTCTCAA 58.149 34.615 0.00 0.00 40.56 3.02
4152 4283 5.916883 GGACAGATTGTGTTCTCAAATTGTG 59.083 40.000 0.00 0.00 40.56 3.33
4221 4352 2.961741 TCCTACTGAATGGAGCTAGCTG 59.038 50.000 24.99 8.30 0.00 4.24
4230 4361 6.577103 TGAATGGAGCTAGCTGTATATATGC 58.423 40.000 24.99 3.61 0.00 3.14
4233 4364 4.142071 TGGAGCTAGCTGTATATATGCTGC 60.142 45.833 24.99 20.16 37.62 5.25
4234 4365 4.099266 GGAGCTAGCTGTATATATGCTGCT 59.901 45.833 28.63 28.63 45.99 4.24
4235 4366 5.300539 GGAGCTAGCTGTATATATGCTGCTA 59.699 44.000 28.04 28.04 43.46 3.49
4236 4367 6.142818 AGCTAGCTGTATATATGCTGCTAC 57.857 41.667 27.03 23.29 43.46 3.58
4238 4369 6.379703 AGCTAGCTGTATATATGCTGCTACTT 59.620 38.462 27.03 18.93 43.46 2.24
4252 4406 3.239449 TGCTACTTTTCTCTCCTGTCCA 58.761 45.455 0.00 0.00 0.00 4.02
4253 4407 3.646162 TGCTACTTTTCTCTCCTGTCCAA 59.354 43.478 0.00 0.00 0.00 3.53
4254 4408 4.102524 TGCTACTTTTCTCTCCTGTCCAAA 59.897 41.667 0.00 0.00 0.00 3.28
4255 4409 5.221925 TGCTACTTTTCTCTCCTGTCCAAAT 60.222 40.000 0.00 0.00 0.00 2.32
4257 4411 6.879458 GCTACTTTTCTCTCCTGTCCAAATTA 59.121 38.462 0.00 0.00 0.00 1.40
4258 4412 7.148390 GCTACTTTTCTCTCCTGTCCAAATTAC 60.148 40.741 0.00 0.00 0.00 1.89
4259 4413 6.004574 ACTTTTCTCTCCTGTCCAAATTACC 58.995 40.000 0.00 0.00 0.00 2.85
4260 4414 5.576563 TTTCTCTCCTGTCCAAATTACCA 57.423 39.130 0.00 0.00 0.00 3.25
4261 4415 5.576563 TTCTCTCCTGTCCAAATTACCAA 57.423 39.130 0.00 0.00 0.00 3.67
4263 4417 6.139679 TCTCTCCTGTCCAAATTACCAAAT 57.860 37.500 0.00 0.00 0.00 2.32
4265 4419 7.872138 TCTCTCCTGTCCAAATTACCAAATAT 58.128 34.615 0.00 0.00 0.00 1.28
4266 4420 7.775093 TCTCTCCTGTCCAAATTACCAAATATG 59.225 37.037 0.00 0.00 0.00 1.78
4267 4421 7.638444 TCTCCTGTCCAAATTACCAAATATGA 58.362 34.615 0.00 0.00 0.00 2.15
4270 4424 8.912988 TCCTGTCCAAATTACCAAATATGATTC 58.087 33.333 0.00 0.00 0.00 2.52
4271 4425 8.694540 CCTGTCCAAATTACCAAATATGATTCA 58.305 33.333 0.00 0.00 0.00 2.57
4272 4426 9.740239 CTGTCCAAATTACCAAATATGATTCAG 57.260 33.333 0.00 0.00 0.00 3.02
4273 4427 9.253832 TGTCCAAATTACCAAATATGATTCAGT 57.746 29.630 0.00 0.00 0.00 3.41
4282 4436 8.523915 ACCAAATATGATTCAGTAAATGAGCA 57.476 30.769 0.00 0.00 39.68 4.26
4283 4437 8.627403 ACCAAATATGATTCAGTAAATGAGCAG 58.373 33.333 0.00 0.00 39.68 4.24
4285 4439 9.880064 CAAATATGATTCAGTAAATGAGCAGAG 57.120 33.333 0.00 0.00 39.68 3.35
4286 4440 9.842775 AAATATGATTCAGTAAATGAGCAGAGA 57.157 29.630 0.00 0.00 39.68 3.10
4287 4441 9.491675 AATATGATTCAGTAAATGAGCAGAGAG 57.508 33.333 0.00 0.00 39.68 3.20
4288 4442 5.114780 TGATTCAGTAAATGAGCAGAGAGC 58.885 41.667 0.00 0.00 39.68 4.09
4299 4453 2.659731 GCAGAGAGCGTATGATTTGC 57.340 50.000 0.00 0.00 0.00 3.68
4300 4454 1.935873 GCAGAGAGCGTATGATTTGCA 59.064 47.619 0.00 0.00 0.00 4.08
4301 4455 2.352651 GCAGAGAGCGTATGATTTGCAA 59.647 45.455 0.00 0.00 0.00 4.08
4302 4456 3.003068 GCAGAGAGCGTATGATTTGCAAT 59.997 43.478 0.00 0.00 0.00 3.56
4303 4457 4.497006 GCAGAGAGCGTATGATTTGCAATT 60.497 41.667 0.00 0.00 0.00 2.32
4304 4458 5.575957 CAGAGAGCGTATGATTTGCAATTT 58.424 37.500 0.00 0.00 0.00 1.82
4305 4459 6.032094 CAGAGAGCGTATGATTTGCAATTTT 58.968 36.000 0.00 0.00 0.00 1.82
4306 4460 6.020916 CAGAGAGCGTATGATTTGCAATTTTG 60.021 38.462 0.00 0.00 0.00 2.44
4345 4499 8.918202 TGGTTGATAGAGACAACAAAGTTATT 57.082 30.769 0.00 0.00 46.16 1.40
4363 4918 8.891671 AAGTTATTAAGACTTTGTTCGTGGTA 57.108 30.769 0.00 0.00 33.76 3.25
4364 4919 8.891671 AGTTATTAAGACTTTGTTCGTGGTAA 57.108 30.769 0.00 0.00 0.00 2.85
4374 4929 9.916397 GACTTTGTTCGTGGTAATATTATTCTG 57.084 33.333 0.00 0.00 0.00 3.02
4406 4961 9.559958 AGCAATTTAAAAACGTATTCTCTCATG 57.440 29.630 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 4.223700 AGATCAAGGCATGTGTCTAACTCA 59.776 41.667 0.00 0.00 0.00 3.41
119 121 5.220835 CCCTTTTTGTGTCAAAAATTCCTGC 60.221 40.000 16.87 0.00 0.00 4.85
130 132 2.291930 ACCTGAACCCCTTTTTGTGTCA 60.292 45.455 0.00 0.00 0.00 3.58
139 141 1.125711 ACGCTGTACCTGAACCCCTT 61.126 55.000 0.00 0.00 0.00 3.95
141 143 0.609662 TTACGCTGTACCTGAACCCC 59.390 55.000 0.00 0.00 0.00 4.95
142 144 2.277084 CATTACGCTGTACCTGAACCC 58.723 52.381 0.00 0.00 0.00 4.11
459 466 7.647907 TTGAGAAAGTAAACGGCTAACTTAG 57.352 36.000 0.00 0.00 33.24 2.18
537 545 4.391830 GCACAACGATAACTGGATCAGAAA 59.608 41.667 1.59 0.00 35.18 2.52
549 557 6.309494 GTCATAGTACAAGTGCACAACGATAA 59.691 38.462 21.04 0.00 0.00 1.75
559 567 6.574350 AGGTGATAAGTCATAGTACAAGTGC 58.426 40.000 0.00 0.00 36.60 4.40
610 620 9.040939 AGGTATTTTTACACTTGCAACATTTTC 57.959 29.630 0.00 0.00 0.00 2.29
611 621 8.956533 AGGTATTTTTACACTTGCAACATTTT 57.043 26.923 0.00 0.00 0.00 1.82
646 656 2.696707 TGTTAGTCCGTTGGTGAGAGTT 59.303 45.455 0.00 0.00 0.00 3.01
674 684 5.347907 AGTTCTGTACGCAACTTAGCAATAC 59.652 40.000 3.90 0.00 27.81 1.89
727 738 1.202245 TGTTTTGCCGAAGTTCTGTGC 60.202 47.619 0.56 1.94 0.00 4.57
730 741 3.108144 CTGTTGTTTTGCCGAAGTTCTG 58.892 45.455 0.56 0.00 0.00 3.02
888 900 4.399618 TCCTGTGTCTCCTTATCTTCTTCG 59.600 45.833 0.00 0.00 0.00 3.79
943 955 5.677319 TTCTTGACATCCCCACTAACTAG 57.323 43.478 0.00 0.00 0.00 2.57
1144 1156 2.928642 AAAACCCGCCGACGAGTGTT 62.929 55.000 0.00 0.00 43.93 3.32
1145 1157 2.086251 TAAAACCCGCCGACGAGTGT 62.086 55.000 0.00 0.00 43.93 3.55
1189 1202 4.952071 TTTTCAATGACAAATCAGGGCA 57.048 36.364 0.00 0.00 38.57 5.36
1261 1274 3.804036 TCAACTCAAACACCACTACTGG 58.196 45.455 0.00 0.00 44.26 4.00
1338 1351 6.743575 AAAAGTGAGCTGGTATATGTCAAC 57.256 37.500 0.00 0.00 0.00 3.18
1397 1411 7.437862 TGCTAACATTAAAAGTGCTTCCAAAAG 59.562 33.333 0.00 0.00 35.47 2.27
1401 1415 6.040391 ACTTGCTAACATTAAAAGTGCTTCCA 59.960 34.615 0.00 0.00 30.17 3.53
1402 1416 6.363357 CACTTGCTAACATTAAAAGTGCTTCC 59.637 38.462 11.20 0.00 40.71 3.46
1403 1417 7.138736 TCACTTGCTAACATTAAAAGTGCTTC 58.861 34.615 15.61 0.00 44.65 3.86
1404 1418 7.013274 TCTCACTTGCTAACATTAAAAGTGCTT 59.987 33.333 15.61 0.00 44.65 3.91
1405 1419 6.486657 TCTCACTTGCTAACATTAAAAGTGCT 59.513 34.615 15.61 0.00 44.65 4.40
1406 1420 6.668323 TCTCACTTGCTAACATTAAAAGTGC 58.332 36.000 15.61 0.00 44.65 4.40
1407 1421 7.173218 TCCTCTCACTTGCTAACATTAAAAGTG 59.827 37.037 14.86 14.86 45.77 3.16
1408 1422 7.173390 GTCCTCTCACTTGCTAACATTAAAAGT 59.827 37.037 0.00 0.00 0.00 2.66
1409 1423 7.389053 AGTCCTCTCACTTGCTAACATTAAAAG 59.611 37.037 0.00 0.00 0.00 2.27
1410 1424 7.224297 AGTCCTCTCACTTGCTAACATTAAAA 58.776 34.615 0.00 0.00 0.00 1.52
1411 1425 6.769512 AGTCCTCTCACTTGCTAACATTAAA 58.230 36.000 0.00 0.00 0.00 1.52
1414 1428 4.899352 AGTCCTCTCACTTGCTAACATT 57.101 40.909 0.00 0.00 0.00 2.71
1493 1507 7.645340 CCAAAAATTACATAAGATGCCGAGAAG 59.355 37.037 0.00 0.00 0.00 2.85
1498 1512 5.681105 CGACCAAAAATTACATAAGATGCCG 59.319 40.000 0.00 0.00 0.00 5.69
1515 1529 2.285889 TTTCTGGTGCCCCGACCAAA 62.286 55.000 0.00 0.00 45.60 3.28
1636 1650 9.224267 ACAACTTACTCGTACTACTGAAGATTA 57.776 33.333 0.00 0.00 0.00 1.75
1755 1769 2.005451 GCAATGCTACTCACTGACCAG 58.995 52.381 0.00 0.00 0.00 4.00
1810 1844 1.258982 GATTGCCGCTACAAGATGACG 59.741 52.381 0.00 0.00 31.96 4.35
1976 2010 1.000896 CGGGGCAAGGAAGATGGTT 60.001 57.895 0.00 0.00 0.00 3.67
1994 2028 5.372547 ACCGTTCTTTGAAAAAGGCTATC 57.627 39.130 0.00 0.00 0.00 2.08
2037 2071 5.753438 ACGCAGATTGTATGTATGTACAAGG 59.247 40.000 0.00 0.65 44.92 3.61
2038 2072 6.828502 ACGCAGATTGTATGTATGTACAAG 57.171 37.500 0.00 0.00 44.92 3.16
2039 2073 6.814146 TGAACGCAGATTGTATGTATGTACAA 59.186 34.615 0.00 2.41 45.55 2.41
2040 2074 6.334202 TGAACGCAGATTGTATGTATGTACA 58.666 36.000 0.00 0.00 40.98 2.90
2041 2075 6.822073 TGAACGCAGATTGTATGTATGTAC 57.178 37.500 0.00 0.00 0.00 2.90
2042 2076 7.170828 GGAATGAACGCAGATTGTATGTATGTA 59.829 37.037 0.00 0.00 0.00 2.29
2043 2077 6.017934 GGAATGAACGCAGATTGTATGTATGT 60.018 38.462 0.00 0.00 0.00 2.29
2044 2078 6.365839 GGAATGAACGCAGATTGTATGTATG 58.634 40.000 0.00 0.00 0.00 2.39
2045 2079 5.470098 GGGAATGAACGCAGATTGTATGTAT 59.530 40.000 0.00 0.00 0.00 2.29
2070 2104 0.249868 TGCAGTTTCAGTCTCACCCG 60.250 55.000 0.00 0.00 0.00 5.28
2077 2111 3.885777 GCGCTATGCAGTTTCAGTC 57.114 52.632 0.00 0.00 45.45 3.51
2260 2294 1.298014 GAGGAAGGTGAGCACAGGG 59.702 63.158 2.75 0.00 0.00 4.45
2420 2454 4.106925 AGCTGGGCTAGGTGCAGC 62.107 66.667 8.11 8.11 45.15 5.25
2441 2487 2.189191 GAGGGTGCTGCATGGTGAGA 62.189 60.000 5.27 0.00 0.00 3.27
2494 2540 1.106351 TGAACAGCAACGCCATGGTT 61.106 50.000 14.67 0.00 0.00 3.67
2572 2618 1.959042 CGGTGCTTGAATAGATGGCT 58.041 50.000 0.00 0.00 0.00 4.75
2581 2627 0.608856 ACATGATGGCGGTGCTTGAA 60.609 50.000 0.00 0.00 0.00 2.69
2584 2630 0.322816 AGAACATGATGGCGGTGCTT 60.323 50.000 0.00 0.00 0.00 3.91
2764 2830 3.576861 CCCCTTTTGGAGAAGTTCCTTT 58.423 45.455 0.00 0.00 46.92 3.11
2766 2832 1.203063 GCCCCTTTTGGAGAAGTTCCT 60.203 52.381 0.00 0.00 46.92 3.36
2768 2834 1.995376 TGCCCCTTTTGGAGAAGTTC 58.005 50.000 0.00 0.00 44.07 3.01
2770 2836 1.217942 ACTTGCCCCTTTTGGAGAAGT 59.782 47.619 0.00 0.00 44.07 3.01
2774 2842 2.586648 AGTACTTGCCCCTTTTGGAG 57.413 50.000 0.00 0.00 44.07 3.86
2904 2981 8.024145 TGGGTACTTACCTACTAGTCTACTAC 57.976 42.308 0.00 0.00 45.72 2.73
2905 2982 8.487028 GTTGGGTACTTACCTACTAGTCTACTA 58.513 40.741 0.00 0.00 45.72 1.82
2907 2984 7.281999 CAGTTGGGTACTTACCTACTAGTCTAC 59.718 44.444 0.00 0.00 45.72 2.59
2908 2985 7.341805 CAGTTGGGTACTTACCTACTAGTCTA 58.658 42.308 0.00 0.00 45.72 2.59
2910 2987 5.163571 GCAGTTGGGTACTTACCTACTAGTC 60.164 48.000 0.00 0.84 45.72 2.59
2912 2989 4.954826 AGCAGTTGGGTACTTACCTACTAG 59.045 45.833 5.41 0.00 45.72 2.57
2913 2990 4.939255 AGCAGTTGGGTACTTACCTACTA 58.061 43.478 5.41 0.00 45.72 1.82
2914 2991 3.787742 AGCAGTTGGGTACTTACCTACT 58.212 45.455 5.41 6.65 45.72 2.57
2915 2992 4.548451 AAGCAGTTGGGTACTTACCTAC 57.452 45.455 5.41 4.68 45.72 3.18
2917 2994 5.487845 AGATTAAGCAGTTGGGTACTTACCT 59.512 40.000 5.41 0.00 45.72 3.08
2918 2995 5.742063 AGATTAAGCAGTTGGGTACTTACC 58.258 41.667 0.00 0.00 45.71 2.85
2919 2996 6.403309 GCAAGATTAAGCAGTTGGGTACTTAC 60.403 42.308 0.00 0.00 33.85 2.34
2920 2997 5.646360 GCAAGATTAAGCAGTTGGGTACTTA 59.354 40.000 0.00 0.00 33.85 2.24
2921 2998 4.459337 GCAAGATTAAGCAGTTGGGTACTT 59.541 41.667 0.00 0.00 33.85 2.24
2923 3000 3.756434 TGCAAGATTAAGCAGTTGGGTAC 59.244 43.478 0.00 0.00 35.51 3.34
2925 3002 2.875296 TGCAAGATTAAGCAGTTGGGT 58.125 42.857 0.00 0.00 35.51 4.51
2926 3003 3.940209 TTGCAAGATTAAGCAGTTGGG 57.060 42.857 0.00 0.00 42.39 4.12
2927 3004 5.063180 TCATTGCAAGATTAAGCAGTTGG 57.937 39.130 4.94 0.00 42.39 3.77
2930 3007 8.306038 TGTAATTTCATTGCAAGATTAAGCAGT 58.694 29.630 4.94 0.00 42.39 4.40
2931 3008 8.692110 TGTAATTTCATTGCAAGATTAAGCAG 57.308 30.769 4.94 0.00 42.39 4.24
2933 3010 9.090692 ACATGTAATTTCATTGCAAGATTAAGC 57.909 29.630 4.94 0.00 38.34 3.09
2941 3018 4.930405 CCTGCACATGTAATTTCATTGCAA 59.070 37.500 22.28 0.00 39.12 4.08
2943 3020 3.866910 CCCTGCACATGTAATTTCATTGC 59.133 43.478 17.23 17.23 35.08 3.56
3011 3091 3.372554 GACCGGGCCCTTCTTCTCG 62.373 68.421 22.43 3.11 0.00 4.04
3127 3207 5.241662 AGGCATGAAACTGAGAAGAACTAC 58.758 41.667 0.00 0.00 0.00 2.73
3179 3259 1.317613 AACAATTCAGTTGGCAGCGA 58.682 45.000 0.00 0.00 42.28 4.93
3180 3260 2.987413 TAACAATTCAGTTGGCAGCG 57.013 45.000 0.00 0.00 42.28 5.18
3197 3299 8.107095 ACTTAGTTTATCTCCAGCCAACAATAA 58.893 33.333 0.00 0.00 0.00 1.40
3199 3301 6.485171 ACTTAGTTTATCTCCAGCCAACAAT 58.515 36.000 0.00 0.00 0.00 2.71
3203 3305 7.556275 CCATTAACTTAGTTTATCTCCAGCCAA 59.444 37.037 1.94 0.00 0.00 4.52
3205 3307 7.054751 ACCATTAACTTAGTTTATCTCCAGCC 58.945 38.462 1.94 0.00 0.00 4.85
3219 3321 9.995003 AATTTGATTGCTGAAACCATTAACTTA 57.005 25.926 0.00 0.00 0.00 2.24
3228 3330 7.384660 TGTCATTACAATTTGATTGCTGAAACC 59.615 33.333 2.79 0.00 43.98 3.27
3263 3365 2.032550 CGCCCATGATTAACAAGCAGAG 59.967 50.000 0.00 0.00 0.00 3.35
3280 3394 3.864686 CGCTGTACATGCACGCCC 61.865 66.667 14.77 0.00 0.00 6.13
3336 3450 1.528129 CTCTTCTTTCCCCACAGCAC 58.472 55.000 0.00 0.00 0.00 4.40
3366 3480 4.566987 ACTTGCTTGTTAGTGGTAGTAGC 58.433 43.478 0.00 0.00 0.00 3.58
3378 3504 1.092921 TGTTCGCCGACTTGCTTGTT 61.093 50.000 0.00 0.00 0.00 2.83
3391 3517 0.111089 CTTGTCGTCAGCTTGTTCGC 60.111 55.000 0.00 0.00 0.00 4.70
3421 3547 7.761704 CCGAATCCAATGGTGTATAATCTCTAG 59.238 40.741 0.00 0.00 0.00 2.43
3422 3548 7.234782 ACCGAATCCAATGGTGTATAATCTCTA 59.765 37.037 0.00 0.00 33.91 2.43
3431 3557 3.739830 CGATGACCGAATCCAATGGTGTA 60.740 47.826 0.00 0.00 41.76 2.90
3432 3558 2.643551 GATGACCGAATCCAATGGTGT 58.356 47.619 0.00 0.00 35.75 4.16
3437 3563 2.036958 TTGCGATGACCGAATCCAAT 57.963 45.000 0.00 0.00 41.76 3.16
3452 3578 6.429624 ACTACATATTATGTGTTGCATTGCG 58.570 36.000 17.68 0.00 44.60 4.85
3518 3646 1.200519 TTTGGGACGGAGGGAGTATG 58.799 55.000 0.00 0.00 0.00 2.39
3520 3648 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
3521 3649 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
3522 3650 4.347000 TCTTATATTTTGGGACGGAGGGAG 59.653 45.833 0.00 0.00 0.00 4.30
3523 3651 4.300345 TCTTATATTTTGGGACGGAGGGA 58.700 43.478 0.00 0.00 0.00 4.20
3524 3652 4.699925 TCTTATATTTTGGGACGGAGGG 57.300 45.455 0.00 0.00 0.00 4.30
3525 3653 4.510340 CGTTCTTATATTTTGGGACGGAGG 59.490 45.833 0.00 0.00 0.00 4.30
3526 3654 4.025145 GCGTTCTTATATTTTGGGACGGAG 60.025 45.833 0.00 0.00 0.00 4.63
3527 3655 3.872771 GCGTTCTTATATTTTGGGACGGA 59.127 43.478 0.00 0.00 0.00 4.69
3528 3656 3.875134 AGCGTTCTTATATTTTGGGACGG 59.125 43.478 0.00 0.00 0.00 4.79
3529 3657 5.479716 AAGCGTTCTTATATTTTGGGACG 57.520 39.130 0.00 0.00 0.00 4.79
3530 3658 9.069078 GTTAAAAGCGTTCTTATATTTTGGGAC 57.931 33.333 0.00 0.00 31.02 4.46
3531 3659 8.794553 TGTTAAAAGCGTTCTTATATTTTGGGA 58.205 29.630 0.00 0.00 31.02 4.37
3532 3660 8.856247 GTGTTAAAAGCGTTCTTATATTTTGGG 58.144 33.333 0.00 0.00 31.02 4.12
3533 3661 9.620660 AGTGTTAAAAGCGTTCTTATATTTTGG 57.379 29.630 0.00 0.00 31.02 3.28
3538 3666 9.649167 AGTGTAGTGTTAAAAGCGTTCTTATAT 57.351 29.630 0.00 0.00 31.02 0.86
3540 3668 7.958053 AGTGTAGTGTTAAAAGCGTTCTTAT 57.042 32.000 0.00 0.00 31.02 1.73
3541 3669 8.137437 ACTAGTGTAGTGTTAAAAGCGTTCTTA 58.863 33.333 0.00 0.00 37.69 2.10
3542 3670 6.982724 ACTAGTGTAGTGTTAAAAGCGTTCTT 59.017 34.615 0.00 0.00 37.69 2.52
3543 3671 6.510536 ACTAGTGTAGTGTTAAAAGCGTTCT 58.489 36.000 0.00 0.00 37.69 3.01
3544 3672 6.760161 ACTAGTGTAGTGTTAAAAGCGTTC 57.240 37.500 0.00 0.00 37.69 3.95
3557 3685 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
3558 3686 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
3559 3687 8.876275 ATAAGAACGTTTTTGACACTAGTGTA 57.124 30.769 27.98 11.50 45.05 2.90
3565 3693 9.458374 CCAAAATATAAGAACGTTTTTGACACT 57.542 29.630 13.87 0.00 38.79 3.55
3566 3694 8.696175 CCCAAAATATAAGAACGTTTTTGACAC 58.304 33.333 13.87 0.00 38.79 3.67
3567 3695 8.630917 TCCCAAAATATAAGAACGTTTTTGACA 58.369 29.630 13.87 0.01 38.79 3.58
3568 3696 8.908678 GTCCCAAAATATAAGAACGTTTTTGAC 58.091 33.333 13.87 5.89 38.79 3.18
3569 3697 7.804129 CGTCCCAAAATATAAGAACGTTTTTGA 59.196 33.333 13.87 2.81 38.79 2.69
3570 3698 7.061326 CCGTCCCAAAATATAAGAACGTTTTTG 59.939 37.037 13.87 12.16 37.14 2.44
3571 3699 7.040548 TCCGTCCCAAAATATAAGAACGTTTTT 60.041 33.333 9.22 9.22 0.00 1.94
3572 3700 6.430616 TCCGTCCCAAAATATAAGAACGTTTT 59.569 34.615 0.46 0.00 0.00 2.43
3573 3701 5.939296 TCCGTCCCAAAATATAAGAACGTTT 59.061 36.000 0.46 0.00 0.00 3.60
3574 3702 5.490159 TCCGTCCCAAAATATAAGAACGTT 58.510 37.500 0.00 0.00 0.00 3.99
3575 3703 5.088680 TCCGTCCCAAAATATAAGAACGT 57.911 39.130 0.00 0.00 0.00 3.99
3576 3704 4.510340 CCTCCGTCCCAAAATATAAGAACG 59.490 45.833 0.00 0.00 0.00 3.95
3577 3705 4.820173 CCCTCCGTCCCAAAATATAAGAAC 59.180 45.833 0.00 0.00 0.00 3.01
3578 3706 4.722781 TCCCTCCGTCCCAAAATATAAGAA 59.277 41.667 0.00 0.00 0.00 2.52
3579 3707 4.300345 TCCCTCCGTCCCAAAATATAAGA 58.700 43.478 0.00 0.00 0.00 2.10
3580 3708 4.102681 ACTCCCTCCGTCCCAAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
3581 3709 4.042174 ACTCCCTCCGTCCCAAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
3582 3710 3.660959 ACTCCCTCCGTCCCAAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
3583 3711 2.488836 ACTCCCTCCGTCCCAAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
3584 3712 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3585 3713 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3586 3714 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
3587 3715 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
3588 3716 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
3589 3717 0.042131 AACATACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
3590 3718 2.077687 TAACATACTCCCTCCGTCCC 57.922 55.000 0.00 0.00 0.00 4.46
3591 3719 8.757982 TTATATATAACATACTCCCTCCGTCC 57.242 38.462 0.81 0.00 0.00 4.79
3592 3720 8.848182 CCTTATATATAACATACTCCCTCCGTC 58.152 40.741 0.81 0.00 0.00 4.79
3593 3721 8.342270 ACCTTATATATAACATACTCCCTCCGT 58.658 37.037 0.81 0.00 0.00 4.69
3594 3722 8.763984 ACCTTATATATAACATACTCCCTCCG 57.236 38.462 0.81 0.00 0.00 4.63
3652 3780 7.195374 ACTAAATCCCACTATTTCAGTAGCA 57.805 36.000 0.00 0.00 34.98 3.49
3703 3831 1.139095 GAAGAGCATTGGCAGCTGC 59.861 57.895 30.88 30.88 43.58 5.25
3793 3923 7.010160 ACCAGGAAAAGAGAATGTCCAAAATA 58.990 34.615 0.00 0.00 32.19 1.40
3806 3936 2.280628 GCATCGGTACCAGGAAAAGAG 58.719 52.381 13.54 0.00 0.00 2.85
3816 3946 1.102978 AATTGCAAGGCATCGGTACC 58.897 50.000 4.94 0.16 38.76 3.34
3841 3971 4.500477 CCGAGAATTTTTCGATGAAATGCC 59.500 41.667 10.60 4.61 40.36 4.40
4037 4168 0.394899 GCATAGCTCAGCCCCAACTT 60.395 55.000 0.00 0.00 0.00 2.66
4043 4174 1.607628 CAGAATTGCATAGCTCAGCCC 59.392 52.381 7.73 0.00 0.00 5.19
4094 4225 7.393515 ACATTAGAGGAAAAATGTACTTGGACC 59.606 37.037 0.00 0.00 42.87 4.46
4116 4247 9.547753 GAACACAATCTGTCCATATAGTACATT 57.452 33.333 0.00 0.00 30.29 2.71
4117 4248 8.928448 AGAACACAATCTGTCCATATAGTACAT 58.072 33.333 0.00 0.00 30.29 2.29
4119 4250 8.414003 TGAGAACACAATCTGTCCATATAGTAC 58.586 37.037 0.00 0.00 30.29 2.73
4120 4251 8.533569 TGAGAACACAATCTGTCCATATAGTA 57.466 34.615 0.00 0.00 30.29 1.82
4121 4252 7.423844 TGAGAACACAATCTGTCCATATAGT 57.576 36.000 0.00 0.00 30.29 2.12
4122 4253 8.722480 TTTGAGAACACAATCTGTCCATATAG 57.278 34.615 0.00 0.00 30.29 1.31
4141 4272 4.819630 GTGTTCCACTACCACAATTTGAGA 59.180 41.667 2.79 0.00 0.00 3.27
4146 4277 8.871629 TTATTATGTGTTCCACTACCACAATT 57.128 30.769 0.00 0.00 41.91 2.32
4208 4339 6.580788 CAGCATATATACAGCTAGCTCCATT 58.419 40.000 16.15 2.69 36.73 3.16
4209 4340 5.453057 GCAGCATATATACAGCTAGCTCCAT 60.453 44.000 16.15 13.19 36.73 3.41
4221 4352 8.527810 AGGAGAGAAAAGTAGCAGCATATATAC 58.472 37.037 0.00 0.00 0.00 1.47
4230 4361 3.259374 TGGACAGGAGAGAAAAGTAGCAG 59.741 47.826 0.00 0.00 0.00 4.24
4233 4364 7.334671 GGTAATTTGGACAGGAGAGAAAAGTAG 59.665 40.741 0.00 0.00 0.00 2.57
4234 4365 7.166167 GGTAATTTGGACAGGAGAGAAAAGTA 58.834 38.462 0.00 0.00 0.00 2.24
4235 4366 6.004574 GGTAATTTGGACAGGAGAGAAAAGT 58.995 40.000 0.00 0.00 0.00 2.66
4236 4367 6.003950 TGGTAATTTGGACAGGAGAGAAAAG 58.996 40.000 0.00 0.00 0.00 2.27
4238 4369 5.576563 TGGTAATTTGGACAGGAGAGAAA 57.423 39.130 0.00 0.00 0.00 2.52
4257 4411 8.523915 TGCTCATTTACTGAATCATATTTGGT 57.476 30.769 0.00 0.00 32.14 3.67
4258 4412 8.843262 TCTGCTCATTTACTGAATCATATTTGG 58.157 33.333 0.00 0.00 32.14 3.28
4259 4413 9.880064 CTCTGCTCATTTACTGAATCATATTTG 57.120 33.333 0.00 0.00 32.14 2.32
4260 4414 9.842775 TCTCTGCTCATTTACTGAATCATATTT 57.157 29.630 0.00 0.00 32.14 1.40
4261 4415 9.491675 CTCTCTGCTCATTTACTGAATCATATT 57.508 33.333 0.00 0.00 32.14 1.28
4263 4417 6.927936 GCTCTCTGCTCATTTACTGAATCATA 59.072 38.462 0.00 0.00 38.95 2.15
4265 4419 5.114780 GCTCTCTGCTCATTTACTGAATCA 58.885 41.667 0.00 0.00 38.95 2.57
4266 4420 4.208873 CGCTCTCTGCTCATTTACTGAATC 59.791 45.833 0.00 0.00 40.11 2.52
4267 4421 4.118410 CGCTCTCTGCTCATTTACTGAAT 58.882 43.478 0.00 0.00 40.11 2.57
4270 4424 2.886081 ACGCTCTCTGCTCATTTACTG 58.114 47.619 0.00 0.00 40.11 2.74
4271 4425 4.339530 TCATACGCTCTCTGCTCATTTACT 59.660 41.667 0.00 0.00 40.11 2.24
4272 4426 4.611943 TCATACGCTCTCTGCTCATTTAC 58.388 43.478 0.00 0.00 40.11 2.01
4273 4427 4.918810 TCATACGCTCTCTGCTCATTTA 57.081 40.909 0.00 0.00 40.11 1.40
4275 4429 4.333913 AATCATACGCTCTCTGCTCATT 57.666 40.909 0.00 0.00 40.11 2.57
4276 4430 4.056740 CAAATCATACGCTCTCTGCTCAT 58.943 43.478 0.00 0.00 40.11 2.90
4278 4432 2.220593 GCAAATCATACGCTCTCTGCTC 59.779 50.000 0.00 0.00 40.11 4.26
4279 4433 2.208431 GCAAATCATACGCTCTCTGCT 58.792 47.619 0.00 0.00 40.11 4.24
4280 4434 1.935873 TGCAAATCATACGCTCTCTGC 59.064 47.619 0.00 0.00 38.57 4.26
4281 4435 4.808077 ATTGCAAATCATACGCTCTCTG 57.192 40.909 1.71 0.00 0.00 3.35
4282 4436 5.824904 AAATTGCAAATCATACGCTCTCT 57.175 34.783 1.71 0.00 0.00 3.10
4283 4437 6.252036 CAAAATTGCAAATCATACGCTCTC 57.748 37.500 1.71 0.00 0.00 3.20
4299 4453 5.141568 CCAAAGAGCAAAATCGCAAAATTG 58.858 37.500 0.00 0.00 0.00 2.32
4300 4454 4.815846 ACCAAAGAGCAAAATCGCAAAATT 59.184 33.333 0.00 0.00 0.00 1.82
4301 4455 4.379652 ACCAAAGAGCAAAATCGCAAAAT 58.620 34.783 0.00 0.00 0.00 1.82
4302 4456 3.791245 ACCAAAGAGCAAAATCGCAAAA 58.209 36.364 0.00 0.00 0.00 2.44
4303 4457 3.451141 ACCAAAGAGCAAAATCGCAAA 57.549 38.095 0.00 0.00 0.00 3.68
4304 4458 3.122297 CAACCAAAGAGCAAAATCGCAA 58.878 40.909 0.00 0.00 0.00 4.85
4305 4459 2.360483 TCAACCAAAGAGCAAAATCGCA 59.640 40.909 0.00 0.00 0.00 5.10
4306 4460 3.011949 TCAACCAAAGAGCAAAATCGC 57.988 42.857 0.00 0.00 0.00 4.58
4307 4461 6.092670 TCTCTATCAACCAAAGAGCAAAATCG 59.907 38.462 0.00 0.00 37.31 3.34
4308 4462 7.094634 TGTCTCTATCAACCAAAGAGCAAAATC 60.095 37.037 0.00 0.00 37.31 2.17
4309 4463 6.716628 TGTCTCTATCAACCAAAGAGCAAAAT 59.283 34.615 0.00 0.00 37.31 1.82
4310 4464 6.061441 TGTCTCTATCAACCAAAGAGCAAAA 58.939 36.000 0.00 0.00 37.31 2.44
4311 4465 5.620206 TGTCTCTATCAACCAAAGAGCAAA 58.380 37.500 0.00 0.00 37.31 3.68
4312 4466 5.227569 TGTCTCTATCAACCAAAGAGCAA 57.772 39.130 0.00 0.00 37.31 3.91
4313 4467 4.890158 TGTCTCTATCAACCAAAGAGCA 57.110 40.909 0.00 0.00 37.31 4.26
4314 4468 4.997395 TGTTGTCTCTATCAACCAAAGAGC 59.003 41.667 6.38 0.00 42.82 4.09
4315 4469 7.227512 ACTTTGTTGTCTCTATCAACCAAAGAG 59.772 37.037 23.03 0.00 42.82 2.85
4316 4470 7.054124 ACTTTGTTGTCTCTATCAACCAAAGA 58.946 34.615 23.03 3.09 42.82 2.52
4317 4471 7.264373 ACTTTGTTGTCTCTATCAACCAAAG 57.736 36.000 19.12 19.12 42.82 2.77
4357 4912 8.394877 TGCTTTTCACAGAATAATATTACCACG 58.605 33.333 0.00 0.00 0.00 4.94
4381 4936 9.554724 TCATGAGAGAATACGTTTTTAAATTGC 57.445 29.630 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.