Multiple sequence alignment - TraesCS5A01G267000

Loading Multiple Alignment...

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 TraesCS5A01G267000 chr5A 100.000 4919 0 0 1 4919 478326982 478322064 0.000000e+00 9084
1 TraesCS5A01G267000 chr5B 93.098 2463 109 31 1 2445 450846843 450844424 0.000000e+00 3550
2 TraesCS5A01G267000 chr5B 92.244 851 42 13 2438 3277 450844357 450843520 0.000000e+00 1184
3 TraesCS5A01G267000 chr5B 90.620 693 29 12 3595 4276 450843290 450842623 0.000000e+00 887
4 TraesCS5A01G267000 chr5B 90.737 475 23 10 4452 4919 450842475 450842015 9.050000e-172 614
5 TraesCS5A01G267000 chr5D 92.417 2453 91 29 1 2445 377539214 377536849 0.000000e+00 3411
6 TraesCS5A01G267000 chr5D 90.158 1077 57 10 2438 3511 377536802 377535772 0.000000e+00 1356
7 TraesCS5A01G267000 chr5D 91.429 700 30 16 3583 4266 377535767 377535082 0.000000e+00 933
8 TraesCS5A01G267000 chr5D 86.050 638 47 26 4298 4919 377535101 377534490 0.000000e+00 647
9 TraesCS5A01G267000 chr7A 93.269 104 7 0 4816 4919 229143261 229143158 2.370000e-33 154
10 TraesCS5A01G267000 chr7D 91.667 108 9 0 4812 4919 216082336 216082229 3.070000e-32 150
11 TraesCS5A01G267000 chr7B 90.435 115 9 2 4807 4919 184299349 184299463 3.070000e-32 150
12 TraesCS5A01G267000 chr3A 94.792 96 5 0 4824 4919 17533080 17532985 3.070000e-32 150


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 TraesCS5A01G267000 chr5A 478322064 478326982 4918 True 9084.00 9084 100.00000 1 4919 1 chr5A.!!$R1 4918
1 TraesCS5A01G267000 chr5B 450842015 450846843 4828 True 1558.75 3550 91.67475 1 4919 4 chr5B.!!$R1 4918
2 TraesCS5A01G267000 chr5D 377534490 377539214 4724 True 1586.75 3411 90.01350 1 4919 4 chr5D.!!$R1 4918

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
863 882 1.006758 TCCCACTCGTCCCAAGATACT 59.993 52.381 0.00 0.00 0.00 2.12 F
1985 2007 0.250038 ATGTGTCGCACTGCTTCTGT 60.250 50.000 10.54 0.00 35.11 3.41 F
2355 2386 0.316841 ATGGCGCCATTTCAAACGTT 59.683 45.000 36.10 11.49 31.82 3.99 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 2021 1.131126 GAGCATGATCAAACACACCCG 59.869 52.381 5.98 0.0 0.0 5.28 R
2982 3099 0.398318 AAACCCAGGAGACAGACAGC 59.602 55.000 0.00 0.0 0.0 4.40 R
4144 4324 0.039256 CCACCGGTTAAACTCGACGA 60.039 55.000 2.97 0.0 0.0 4.20 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
262 273 3.565063 TCACTTACCTGCCCGTTTTTAAC 59.435 43.478 0.00 0.00 0.00 2.01
295 313 7.094805 GGCACAAATTTAATCCCTTTCTTTTCC 60.095 37.037 0.00 0.00 0.00 3.13
296 314 7.661437 GCACAAATTTAATCCCTTTCTTTTCCT 59.339 33.333 0.00 0.00 0.00 3.36
448 466 1.037579 CCAAATTTCTCGCCCCCTCC 61.038 60.000 0.00 0.00 0.00 4.30
588 607 1.136695 TGCTGCTTTTGTGTTTCCTGG 59.863 47.619 0.00 0.00 0.00 4.45
770 789 3.245048 CCCGCATTATTTTTCCATTTCGC 59.755 43.478 0.00 0.00 0.00 4.70
773 792 4.207019 CGCATTATTTTTCCATTTCGCTCC 59.793 41.667 0.00 0.00 0.00 4.70
811 830 3.484649 GCTCCCGTTTTCTTTTCGTTTTC 59.515 43.478 0.00 0.00 0.00 2.29
822 841 8.996024 TTTCTTTTCGTTTTCTCCTCATTTTT 57.004 26.923 0.00 0.00 0.00 1.94
863 882 1.006758 TCCCACTCGTCCCAAGATACT 59.993 52.381 0.00 0.00 0.00 2.12
864 883 1.137086 CCCACTCGTCCCAAGATACTG 59.863 57.143 0.00 0.00 0.00 2.74
865 884 1.825474 CCACTCGTCCCAAGATACTGT 59.175 52.381 0.00 0.00 0.00 3.55
866 885 2.417379 CCACTCGTCCCAAGATACTGTG 60.417 54.545 0.00 0.00 0.00 3.66
993 1013 2.579541 GAGCTTCGCTTCTGCTTTTTC 58.420 47.619 0.00 0.00 39.88 2.29
1050 1071 4.880426 GGAGGGATGGCCGGGAGA 62.880 72.222 2.18 0.00 33.83 3.71
1414 1435 2.675423 GTGGTTCCGGGGCTTTCC 60.675 66.667 0.00 0.00 0.00 3.13
1581 1602 6.783708 TCTCTCTCTAACCTTCTCCATTTC 57.216 41.667 0.00 0.00 0.00 2.17
1640 1662 6.841781 TTAGAGGAATTATTTACCTGCCCT 57.158 37.500 0.00 0.00 33.89 5.19
1641 1663 5.734031 AGAGGAATTATTTACCTGCCCTT 57.266 39.130 0.00 0.00 33.89 3.95
1642 1664 6.092346 AGAGGAATTATTTACCTGCCCTTT 57.908 37.500 0.00 0.00 33.89 3.11
1643 1665 7.220890 AGAGGAATTATTTACCTGCCCTTTA 57.779 36.000 0.00 0.00 33.89 1.85
1708 1730 3.505386 CCTAGCCTCTGGACATACTGAT 58.495 50.000 0.00 0.00 0.00 2.90
1810 1832 6.927381 TCAAACTGTAGCCTCTTTACTGTAAC 59.073 38.462 0.00 0.00 33.72 2.50
1843 1865 6.759827 CAGGCAAGCTTAATTGAATAATTGCT 59.240 34.615 0.00 0.00 37.22 3.91
1867 1889 9.173939 GCTGTGATATTTGAAATAATGTGTAGC 57.826 33.333 1.27 4.63 0.00 3.58
1975 1997 5.065346 TGACTGAAGTTTAAAATGTGTCGCA 59.935 36.000 0.00 0.00 0.00 5.10
1984 2006 0.870393 AATGTGTCGCACTGCTTCTG 59.130 50.000 10.54 0.00 35.11 3.02
1985 2007 0.250038 ATGTGTCGCACTGCTTCTGT 60.250 50.000 10.54 0.00 35.11 3.41
1994 2016 2.672381 GCACTGCTTCTGTTGAGATCTC 59.328 50.000 16.21 16.21 0.00 2.75
1997 2019 5.681954 GCACTGCTTCTGTTGAGATCTCTAT 60.682 44.000 22.95 0.00 0.00 1.98
1999 2021 6.917477 CACTGCTTCTGTTGAGATCTCTATAC 59.083 42.308 22.95 17.24 0.00 1.47
2000 2022 6.066054 TGCTTCTGTTGAGATCTCTATACG 57.934 41.667 22.95 13.45 0.00 3.06
2001 2023 5.009110 TGCTTCTGTTGAGATCTCTATACGG 59.991 44.000 22.95 20.13 0.00 4.02
2002 2024 5.563867 GCTTCTGTTGAGATCTCTATACGGG 60.564 48.000 22.95 13.80 0.00 5.28
2003 2025 5.050126 TCTGTTGAGATCTCTATACGGGT 57.950 43.478 22.95 0.00 0.00 5.28
2017 2039 0.881118 ACGGGTGTGTTTGATCATGC 59.119 50.000 0.00 0.00 0.00 4.06
2029 2051 5.244402 TGTTTGATCATGCTCTTGGTGAAAT 59.756 36.000 0.00 0.00 0.00 2.17
2123 2145 5.952347 AGTAAAAATTCCTCCTCAATCCCAC 59.048 40.000 0.00 0.00 0.00 4.61
2142 2164 3.495193 CACATTCACATTGTAGCAGTGC 58.505 45.455 7.13 7.13 33.44 4.40
2216 2246 6.088085 GCTGTGCATTTTCACATTGTAACTAC 59.912 38.462 0.00 0.00 44.88 2.73
2217 2247 7.032377 TGTGCATTTTCACATTGTAACTACA 57.968 32.000 0.00 0.00 41.57 2.74
2218 2248 7.484140 TGTGCATTTTCACATTGTAACTACAA 58.516 30.769 4.84 4.84 41.57 2.41
2219 2249 7.976175 TGTGCATTTTCACATTGTAACTACAAA 59.024 29.630 6.40 0.00 40.94 2.83
2322 2353 1.069703 CATGGAGTTCGTGCAGTTGTG 60.070 52.381 0.00 0.00 0.00 3.33
2355 2386 0.316841 ATGGCGCCATTTCAAACGTT 59.683 45.000 36.10 11.49 31.82 3.99
2438 2469 9.400638 GAATTCGAGATAATACATCTCTTTCGT 57.599 33.333 11.38 0.00 41.68 3.85
2448 2479 8.553459 AATACATCTCTTTCGTTGAAATCACT 57.447 30.769 0.00 0.00 30.85 3.41
2449 2480 6.473397 ACATCTCTTTCGTTGAAATCACTC 57.527 37.500 0.00 0.00 30.85 3.51
2451 2482 7.378966 ACATCTCTTTCGTTGAAATCACTCTA 58.621 34.615 0.00 0.00 30.85 2.43
2454 2559 7.658261 TCTCTTTCGTTGAAATCACTCTAGAA 58.342 34.615 0.00 0.00 30.85 2.10
2459 2565 5.417894 TCGTTGAAATCACTCTAGAAGGCTA 59.582 40.000 0.00 0.00 0.00 3.93
2465 2571 8.001875 TGAAATCACTCTAGAAGGCTAGTCTAT 58.998 37.037 0.00 0.00 43.72 1.98
2496 2605 7.547722 GGTTTGTAAGTGATGGTTCTTGTTTTT 59.452 33.333 0.00 0.00 0.00 1.94
2502 2611 3.960102 TGATGGTTCTTGTTTTTCTGCCT 59.040 39.130 0.00 0.00 0.00 4.75
2538 2647 4.604156 AGATACTGTCACTGTCTGGATCA 58.396 43.478 7.70 0.00 30.05 2.92
2736 2845 4.082625 TGCAGCCATAGTTTCACTTTCATG 60.083 41.667 0.00 0.00 0.00 3.07
2820 2937 4.331968 TCTTTGCATATTTTCGTCCCAGT 58.668 39.130 0.00 0.00 0.00 4.00
2847 2964 7.803659 GTGTTAGCATTCTTCAGTTTCTTTACC 59.196 37.037 0.00 0.00 0.00 2.85
2849 2966 5.063880 AGCATTCTTCAGTTTCTTTACCGT 58.936 37.500 0.00 0.00 0.00 4.83
2961 3078 5.895636 TTCTGTGCATAATTCGGTTTCAT 57.104 34.783 0.00 0.00 0.00 2.57
2965 3082 4.028383 GTGCATAATTCGGTTTCATCGTG 58.972 43.478 0.00 0.00 0.00 4.35
3028 3145 6.320164 GGTTTATGATGTGTATGTAAAGGCCA 59.680 38.462 5.01 0.00 0.00 5.36
3029 3146 7.014230 GGTTTATGATGTGTATGTAAAGGCCAT 59.986 37.037 5.01 0.00 0.00 4.40
3099 3216 5.179742 GCTGCTTCATGATTCTATTCCTCAG 59.820 44.000 0.00 0.00 0.00 3.35
3103 3220 7.070447 TGCTTCATGATTCTATTCCTCAGTAGT 59.930 37.037 0.00 0.00 0.00 2.73
3105 3222 7.531857 TCATGATTCTATTCCTCAGTAGTCC 57.468 40.000 0.00 0.00 0.00 3.85
3219 3337 7.087007 TGCATAATTTCGTTTTGAGTGCATTA 58.913 30.769 0.00 0.00 35.41 1.90
3220 3338 7.273164 TGCATAATTTCGTTTTGAGTGCATTAG 59.727 33.333 0.00 0.00 35.41 1.73
3221 3339 7.603515 CATAATTTCGTTTTGAGTGCATTAGC 58.396 34.615 0.00 0.00 42.57 3.09
3289 3407 3.436359 TGTACATGTGTAGCTTGTGCATG 59.564 43.478 9.11 14.47 40.76 4.06
3299 3417 4.303086 AGCTTGTGCATGATAATTGCTC 57.697 40.909 0.00 0.00 42.74 4.26
3370 3508 6.524734 TCTTCAGTTTCTTCACTGCTTCATA 58.475 36.000 0.00 0.00 43.51 2.15
3371 3509 6.992123 TCTTCAGTTTCTTCACTGCTTCATAA 59.008 34.615 0.00 0.00 43.51 1.90
3400 3538 5.587844 GGATGTTAGCACAATGATCTGTCTT 59.412 40.000 0.00 0.00 36.16 3.01
3419 3557 5.762711 TGTCTTCTGGATTTTCGTTTCATGA 59.237 36.000 0.00 0.00 0.00 3.07
3440 3579 1.767681 TGTTTTGAAAAGGGCATGCCT 59.232 42.857 34.70 16.75 36.10 4.75
3460 3599 3.370315 CCTCTCTGACTGAAATTCTGGGG 60.370 52.174 4.93 0.00 0.00 4.96
3462 3601 3.261897 TCTCTGACTGAAATTCTGGGGAC 59.738 47.826 4.93 0.00 0.00 4.46
3463 3602 2.978978 TCTGACTGAAATTCTGGGGACA 59.021 45.455 4.93 0.00 39.59 4.02
3464 3603 3.077359 CTGACTGAAATTCTGGGGACAC 58.923 50.000 4.93 0.00 35.60 3.67
3465 3604 2.711009 TGACTGAAATTCTGGGGACACT 59.289 45.455 4.93 0.00 35.60 3.55
3466 3605 3.077359 GACTGAAATTCTGGGGACACTG 58.923 50.000 4.93 0.00 35.60 3.66
3467 3606 2.443255 ACTGAAATTCTGGGGACACTGT 59.557 45.455 4.93 0.00 35.60 3.55
3468 3607 3.117512 ACTGAAATTCTGGGGACACTGTT 60.118 43.478 4.93 0.00 35.60 3.16
3469 3608 3.221771 TGAAATTCTGGGGACACTGTTG 58.778 45.455 0.00 0.00 35.60 3.33
3482 3621 4.819630 GGACACTGTTGAAACCTGAATGTA 59.180 41.667 0.00 0.00 0.00 2.29
3484 3623 4.275936 ACACTGTTGAAACCTGAATGTAGC 59.724 41.667 0.00 0.00 0.00 3.58
3510 3649 8.806429 TTCATGATTTTATTTCTCACTAGCCA 57.194 30.769 0.00 0.00 0.00 4.75
3512 3651 8.267183 TCATGATTTTATTTCTCACTAGCCAGA 58.733 33.333 0.00 0.00 0.00 3.86
3514 3653 7.624549 TGATTTTATTTCTCACTAGCCAGACT 58.375 34.615 0.00 0.00 0.00 3.24
3515 3654 7.550551 TGATTTTATTTCTCACTAGCCAGACTG 59.449 37.037 0.00 0.00 0.00 3.51
3519 3658 6.552445 ATTTCTCACTAGCCAGACTGTTAT 57.448 37.500 0.93 0.00 0.00 1.89
3520 3659 4.991153 TCTCACTAGCCAGACTGTTATG 57.009 45.455 0.93 0.00 0.00 1.90
3521 3660 4.344978 TCTCACTAGCCAGACTGTTATGT 58.655 43.478 0.93 0.00 0.00 2.29
3522 3661 4.399618 TCTCACTAGCCAGACTGTTATGTC 59.600 45.833 0.93 0.00 37.23 3.06
3526 3665 3.059352 AGCCAGACTGTTATGTCCAAC 57.941 47.619 0.93 0.00 37.66 3.77
3553 3692 5.604758 TTCCTAGACTCTCCACATCATTG 57.395 43.478 0.00 0.00 0.00 2.82
3554 3693 3.963374 TCCTAGACTCTCCACATCATTGG 59.037 47.826 0.00 0.00 38.10 3.16
3555 3694 2.706339 AGACTCTCCACATCATTGGC 57.294 50.000 0.00 0.00 36.48 4.52
3556 3695 1.911357 AGACTCTCCACATCATTGGCA 59.089 47.619 0.00 0.00 36.48 4.92
3557 3696 2.508716 AGACTCTCCACATCATTGGCAT 59.491 45.455 0.00 0.00 36.48 4.40
3558 3697 2.877168 GACTCTCCACATCATTGGCATC 59.123 50.000 0.00 0.00 36.48 3.91
3561 3700 1.679680 CTCCACATCATTGGCATCCAC 59.320 52.381 0.00 0.00 36.48 4.02
3562 3701 1.285667 TCCACATCATTGGCATCCACT 59.714 47.619 0.00 0.00 36.48 4.00
3571 3728 5.754782 TCATTGGCATCCACTTGTATTAGT 58.245 37.500 0.00 0.00 30.78 2.24
3572 3729 6.894682 TCATTGGCATCCACTTGTATTAGTA 58.105 36.000 0.00 0.00 30.78 1.82
3579 3736 7.499232 GGCATCCACTTGTATTAGTAAGTCATT 59.501 37.037 0.00 0.00 35.08 2.57
3580 3737 9.542462 GCATCCACTTGTATTAGTAAGTCATTA 57.458 33.333 0.00 0.00 35.08 1.90
3843 4013 4.200283 CTGAGCGAGTCCTCCGGC 62.200 72.222 0.00 0.00 0.00 6.13
3977 4157 4.856487 CGTAGAACTCTGAAGCAGAAGAAG 59.144 45.833 0.00 0.00 40.18 2.85
3978 4158 5.335269 CGTAGAACTCTGAAGCAGAAGAAGA 60.335 44.000 0.00 0.00 40.18 2.87
3979 4159 5.543507 AGAACTCTGAAGCAGAAGAAGAA 57.456 39.130 0.00 0.00 40.18 2.52
4010 4190 2.492484 ACCTGAACTAGATGTCACCGTC 59.508 50.000 0.00 0.00 0.00 4.79
4012 4192 2.156917 TGAACTAGATGTCACCGTCGT 58.843 47.619 0.00 0.00 0.00 4.34
4070 4250 3.728718 GGCGTTGAACTGTTTAATGTGTG 59.271 43.478 15.77 1.45 0.00 3.82
4071 4251 4.347813 GCGTTGAACTGTTTAATGTGTGT 58.652 39.130 15.77 0.00 0.00 3.72
4072 4252 4.436523 GCGTTGAACTGTTTAATGTGTGTC 59.563 41.667 15.77 0.00 0.00 3.67
4073 4253 5.564768 CGTTGAACTGTTTAATGTGTGTCA 58.435 37.500 8.60 0.00 0.00 3.58
4084 4264 3.953712 ATGTGTGTCAGTCGTGGATTA 57.046 42.857 0.00 0.00 0.00 1.75
4099 4279 3.502211 GTGGATTATTGTTAGCCCGGATG 59.498 47.826 0.73 0.00 0.00 3.51
4100 4280 3.081804 GGATTATTGTTAGCCCGGATGG 58.918 50.000 0.73 0.00 37.09 3.51
4101 4281 3.244770 GGATTATTGTTAGCCCGGATGGA 60.245 47.826 0.73 0.00 37.49 3.41
4102 4282 4.567747 GGATTATTGTTAGCCCGGATGGAT 60.568 45.833 0.73 0.00 37.49 3.41
4144 4324 1.344226 TATCGTCGTGTCGTCGTCGT 61.344 55.000 1.33 6.94 41.28 4.34
4145 4325 2.539972 ATCGTCGTGTCGTCGTCGTC 62.540 60.000 1.33 0.00 41.28 4.20
4146 4326 2.857992 GTCGTGTCGTCGTCGTCG 60.858 66.667 5.50 5.50 38.33 5.12
4234 4415 0.454600 GGCTGTGATGCTGATGGTTG 59.545 55.000 0.00 0.00 0.00 3.77
4249 4430 6.128035 GCTGATGGTTGTTCTTTTTGGTTTTT 60.128 34.615 0.00 0.00 0.00 1.94
4257 4438 7.685532 TGTTCTTTTTGGTTTTTGTTTTTGC 57.314 28.000 0.00 0.00 0.00 3.68
4258 4439 7.257722 TGTTCTTTTTGGTTTTTGTTTTTGCA 58.742 26.923 0.00 0.00 0.00 4.08
4259 4440 7.759433 TGTTCTTTTTGGTTTTTGTTTTTGCAA 59.241 25.926 0.00 0.00 0.00 4.08
4260 4441 7.920908 TCTTTTTGGTTTTTGTTTTTGCAAG 57.079 28.000 0.00 0.00 0.00 4.01
4261 4442 6.419116 TCTTTTTGGTTTTTGTTTTTGCAAGC 59.581 30.769 0.00 0.00 0.00 4.01
4262 4443 5.444663 TTTGGTTTTTGTTTTTGCAAGCT 57.555 30.435 0.00 0.00 0.00 3.74
4263 4444 5.444663 TTGGTTTTTGTTTTTGCAAGCTT 57.555 30.435 0.00 0.00 0.00 3.74
4264 4445 5.444663 TGGTTTTTGTTTTTGCAAGCTTT 57.555 30.435 0.00 0.00 0.00 3.51
4265 4446 5.836347 TGGTTTTTGTTTTTGCAAGCTTTT 58.164 29.167 0.00 0.00 0.00 2.27
4266 4447 6.276091 TGGTTTTTGTTTTTGCAAGCTTTTT 58.724 28.000 0.00 0.00 0.00 1.94
4267 4448 6.199719 TGGTTTTTGTTTTTGCAAGCTTTTTG 59.800 30.769 0.00 0.00 0.00 2.44
4268 4449 5.819270 TTTTGTTTTTGCAAGCTTTTTGC 57.181 30.435 0.00 0.00 45.11 3.68
4277 4458 3.428163 GCAAGCTTTTTGCAAGTTTTGG 58.572 40.909 0.00 0.00 45.94 3.28
4278 4459 3.119884 GCAAGCTTTTTGCAAGTTTTGGT 60.120 39.130 0.00 0.00 45.94 3.67
4279 4460 4.405196 CAAGCTTTTTGCAAGTTTTGGTG 58.595 39.130 0.00 0.00 45.94 4.17
4280 4461 3.673902 AGCTTTTTGCAAGTTTTGGTGT 58.326 36.364 0.00 0.00 45.94 4.16
4281 4462 4.071423 AGCTTTTTGCAAGTTTTGGTGTT 58.929 34.783 0.00 0.00 45.94 3.32
4282 4463 4.154015 AGCTTTTTGCAAGTTTTGGTGTTC 59.846 37.500 0.00 0.00 45.94 3.18
4283 4464 4.154015 GCTTTTTGCAAGTTTTGGTGTTCT 59.846 37.500 0.00 0.00 42.31 3.01
4284 4465 5.334802 GCTTTTTGCAAGTTTTGGTGTTCTT 60.335 36.000 0.00 0.00 42.31 2.52
4285 4466 6.625873 TTTTTGCAAGTTTTGGTGTTCTTT 57.374 29.167 0.00 0.00 0.00 2.52
4286 4467 5.604010 TTTGCAAGTTTTGGTGTTCTTTG 57.396 34.783 0.00 0.00 0.00 2.77
4287 4468 4.264460 TGCAAGTTTTGGTGTTCTTTGT 57.736 36.364 0.00 0.00 0.00 2.83
4288 4469 3.993081 TGCAAGTTTTGGTGTTCTTTGTG 59.007 39.130 0.00 0.00 0.00 3.33
4289 4470 3.370672 GCAAGTTTTGGTGTTCTTTGTGG 59.629 43.478 0.00 0.00 0.00 4.17
4290 4471 4.815269 CAAGTTTTGGTGTTCTTTGTGGA 58.185 39.130 0.00 0.00 0.00 4.02
4291 4472 5.418676 CAAGTTTTGGTGTTCTTTGTGGAT 58.581 37.500 0.00 0.00 0.00 3.41
4292 4473 5.675684 AGTTTTGGTGTTCTTTGTGGATT 57.324 34.783 0.00 0.00 0.00 3.01
4293 4474 6.048732 AGTTTTGGTGTTCTTTGTGGATTT 57.951 33.333 0.00 0.00 0.00 2.17
4294 4475 6.472016 AGTTTTGGTGTTCTTTGTGGATTTT 58.528 32.000 0.00 0.00 0.00 1.82
4295 4476 6.939730 AGTTTTGGTGTTCTTTGTGGATTTTT 59.060 30.769 0.00 0.00 0.00 1.94
4296 4477 6.976636 TTTGGTGTTCTTTGTGGATTTTTC 57.023 33.333 0.00 0.00 0.00 2.29
4297 4478 5.930837 TGGTGTTCTTTGTGGATTTTTCT 57.069 34.783 0.00 0.00 0.00 2.52
4298 4479 6.293004 TGGTGTTCTTTGTGGATTTTTCTT 57.707 33.333 0.00 0.00 0.00 2.52
4299 4480 6.706295 TGGTGTTCTTTGTGGATTTTTCTTT 58.294 32.000 0.00 0.00 0.00 2.52
4300 4481 7.841956 TGGTGTTCTTTGTGGATTTTTCTTTA 58.158 30.769 0.00 0.00 0.00 1.85
4301 4482 8.482128 TGGTGTTCTTTGTGGATTTTTCTTTAT 58.518 29.630 0.00 0.00 0.00 1.40
4302 4483 9.325198 GGTGTTCTTTGTGGATTTTTCTTTATT 57.675 29.630 0.00 0.00 0.00 1.40
4327 4508 5.421212 TTTTGCAAATTTTCCTGTGATGC 57.579 34.783 13.65 0.00 0.00 3.91
4335 4516 4.707030 TTTTCCTGTGATGCTGCTAATG 57.293 40.909 0.00 0.00 0.00 1.90
4344 4525 3.376234 TGATGCTGCTAATGTTTCTGCTC 59.624 43.478 0.00 0.00 0.00 4.26
4345 4526 2.086869 TGCTGCTAATGTTTCTGCTCC 58.913 47.619 0.00 0.00 0.00 4.70
4346 4527 2.290514 TGCTGCTAATGTTTCTGCTCCT 60.291 45.455 0.00 0.00 0.00 3.69
4347 4528 3.055167 TGCTGCTAATGTTTCTGCTCCTA 60.055 43.478 0.00 0.00 0.00 2.94
4348 4529 3.559242 GCTGCTAATGTTTCTGCTCCTAG 59.441 47.826 0.00 0.00 0.00 3.02
4349 4530 3.535561 TGCTAATGTTTCTGCTCCTAGC 58.464 45.455 0.00 0.00 42.82 3.42
4350 4531 3.198635 TGCTAATGTTTCTGCTCCTAGCT 59.801 43.478 0.00 0.00 42.97 3.32
4351 4532 3.807071 GCTAATGTTTCTGCTCCTAGCTC 59.193 47.826 0.00 0.00 42.97 4.09
4357 4538 2.759973 TGCTCCTAGCTCCCGTGG 60.760 66.667 0.00 0.00 42.97 4.94
4382 4575 4.687483 GCTGATGGTTTTTCTGTTTGGATG 59.313 41.667 0.00 0.00 0.00 3.51
4412 4610 1.500108 TTGCGCAATTTTTCCTGCTG 58.500 45.000 21.02 0.00 0.00 4.41
4415 4613 1.065358 CGCAATTTTTCCTGCTGCTG 58.935 50.000 0.00 0.00 0.00 4.41
4418 4616 2.409975 CAATTTTTCCTGCTGCTGGTG 58.590 47.619 22.62 10.56 0.00 4.17
4421 4619 0.746063 TTTTCCTGCTGCTGGTGTTG 59.254 50.000 22.62 0.00 0.00 3.33
4422 4620 0.106769 TTTCCTGCTGCTGGTGTTGA 60.107 50.000 22.62 2.87 0.00 3.18
4425 4623 1.310933 CCTGCTGCTGGTGTTGATCC 61.311 60.000 16.56 0.00 0.00 3.36
4426 4624 1.642037 CTGCTGCTGGTGTTGATCCG 61.642 60.000 0.00 0.00 0.00 4.18
4428 4626 0.391130 GCTGCTGGTGTTGATCCGTA 60.391 55.000 0.00 0.00 0.00 4.02
4431 4629 1.277842 TGCTGGTGTTGATCCGTATGT 59.722 47.619 0.00 0.00 0.00 2.29
4434 4632 3.595173 CTGGTGTTGATCCGTATGTTGA 58.405 45.455 0.00 0.00 0.00 3.18
4435 4633 4.191544 CTGGTGTTGATCCGTATGTTGAT 58.808 43.478 0.00 0.00 0.00 2.57
4439 4637 5.583061 GGTGTTGATCCGTATGTTGATGTTA 59.417 40.000 0.00 0.00 0.00 2.41
4442 4640 6.312672 TGTTGATCCGTATGTTGATGTTACTG 59.687 38.462 0.00 0.00 0.00 2.74
4447 4645 4.094294 CCGTATGTTGATGTTACTGGGTTG 59.906 45.833 0.00 0.00 0.00 3.77
4448 4646 4.436852 CGTATGTTGATGTTACTGGGTTGC 60.437 45.833 0.00 0.00 0.00 4.17
4449 4647 3.222173 TGTTGATGTTACTGGGTTGCT 57.778 42.857 0.00 0.00 0.00 3.91
4450 4648 2.884012 TGTTGATGTTACTGGGTTGCTG 59.116 45.455 0.00 0.00 0.00 4.41
4455 4657 2.331166 TGTTACTGGGTTGCTGGAGTA 58.669 47.619 0.00 0.00 0.00 2.59
4467 4669 2.270275 CTGGAGTACGTCTTCAGCTG 57.730 55.000 7.63 7.63 42.13 4.24
4469 4671 2.229062 CTGGAGTACGTCTTCAGCTGAA 59.771 50.000 26.87 26.87 42.13 3.02
4488 4690 2.262423 AGTTGACTGGCTTTGGAGAC 57.738 50.000 0.00 0.00 0.00 3.36
4490 4692 2.147150 GTTGACTGGCTTTGGAGACTC 58.853 52.381 0.00 0.00 0.00 3.36
4515 4717 1.446272 CAGGAGAAGGCGACGGTTC 60.446 63.158 0.00 0.00 0.00 3.62
4525 4727 1.134530 GCGACGGTTCAGAGATCACG 61.135 60.000 0.00 0.00 0.00 4.35
4595 4797 0.604780 CTCTTCCACACAGCACAGGG 60.605 60.000 0.00 0.00 0.00 4.45
4632 4834 1.548269 AGAAGACGGCCAAGAGAAGAG 59.452 52.381 2.24 0.00 0.00 2.85
4633 4835 1.546476 GAAGACGGCCAAGAGAAGAGA 59.454 52.381 2.24 0.00 0.00 3.10
4634 4836 1.633774 AGACGGCCAAGAGAAGAGAA 58.366 50.000 2.24 0.00 0.00 2.87
4635 4837 1.548269 AGACGGCCAAGAGAAGAGAAG 59.452 52.381 2.24 0.00 0.00 2.85
4636 4838 1.546476 GACGGCCAAGAGAAGAGAAGA 59.454 52.381 2.24 0.00 0.00 2.87
4707 4909 4.871910 CTAGCCAGCCAGCCAGCC 62.872 72.222 0.00 0.00 0.00 4.85
4760 4973 2.691779 GGGAGACGAGAGGGGGAGA 61.692 68.421 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
295 313 3.306166 CCCGCTGTCACGTAATCTTTTAG 59.694 47.826 0.00 0.00 0.00 1.85
296 314 3.255725 CCCGCTGTCACGTAATCTTTTA 58.744 45.455 0.00 0.00 0.00 1.52
311 329 1.278127 TCTTTCTAAACTCCCCCGCTG 59.722 52.381 0.00 0.00 0.00 5.18
550 569 1.903404 AACAAAGCCAAGCCCTCGG 60.903 57.895 0.00 0.00 0.00 4.63
551 570 1.286880 CAACAAAGCCAAGCCCTCG 59.713 57.895 0.00 0.00 0.00 4.63
552 571 1.005748 GCAACAAAGCCAAGCCCTC 60.006 57.895 0.00 0.00 0.00 4.30
553 572 1.458209 AGCAACAAAGCCAAGCCCT 60.458 52.632 0.00 0.00 34.23 5.19
554 573 1.301165 CAGCAACAAAGCCAAGCCC 60.301 57.895 0.00 0.00 34.23 5.19
555 574 1.957695 GCAGCAACAAAGCCAAGCC 60.958 57.895 0.00 0.00 34.23 4.35
560 579 1.328374 CACAAAAGCAGCAACAAAGCC 59.672 47.619 0.00 0.00 34.23 4.35
588 607 8.703336 GGACAAAAGACAAAGAAAATAATCAGC 58.297 33.333 0.00 0.00 0.00 4.26
714 733 4.610714 GCCCCGGCGAGAGGATTC 62.611 72.222 9.30 0.00 0.00 2.52
863 882 0.459899 ACGAACAGAGCTCACACACA 59.540 50.000 17.77 0.00 0.00 3.72
864 883 1.132588 GACGAACAGAGCTCACACAC 58.867 55.000 17.77 2.35 0.00 3.82
865 884 0.317854 CGACGAACAGAGCTCACACA 60.318 55.000 17.77 0.00 0.00 3.72
866 885 0.317938 ACGACGAACAGAGCTCACAC 60.318 55.000 17.77 3.43 0.00 3.82
916 935 6.321435 GCAGCTATAAGAAAACCATAAACCCT 59.679 38.462 0.00 0.00 0.00 4.34
993 1013 2.104451 CCTCACCTCCATCATTCCTCAG 59.896 54.545 0.00 0.00 0.00 3.35
1050 1071 4.070552 GGCAGTCCGAACGGCTCT 62.071 66.667 8.48 6.66 44.79 4.09
1336 1357 2.616330 CCAATGCCAGCGACGTGTT 61.616 57.895 0.00 0.00 0.00 3.32
1337 1358 3.049674 CCAATGCCAGCGACGTGT 61.050 61.111 0.00 0.00 0.00 4.49
1386 1407 4.947147 GAACCACAGGGCGCCACA 62.947 66.667 30.85 0.00 37.90 4.17
1396 1417 2.114411 GAAAGCCCCGGAACCACA 59.886 61.111 0.73 0.00 0.00 4.17
1417 1438 3.726517 CGGTTTGACGGCAGGCTG 61.727 66.667 10.94 10.94 0.00 4.85
1466 1487 2.203070 CCCGCTTCTTCATCCCCG 60.203 66.667 0.00 0.00 0.00 5.73
1491 1512 1.181098 CCTTGTTGGTGGAGCCCTTG 61.181 60.000 0.00 0.00 36.04 3.61
1660 1682 8.289618 CAGTAAATTTCGAATTTCTCAACAGGA 58.710 33.333 0.00 0.00 0.00 3.86
1667 1689 6.907748 GCTAGGCAGTAAATTTCGAATTTCTC 59.092 38.462 0.00 0.00 0.00 2.87
1708 1730 4.162320 CACCCCAGATCTAGTCAAAGCTAA 59.838 45.833 0.00 0.00 0.00 3.09
1810 1832 2.363788 TAAGCTTGCCTGTACGACAG 57.636 50.000 9.86 7.72 45.53 3.51
1866 1888 2.911552 AGGGATCCCTAGCTAGTAGC 57.088 55.000 33.08 14.62 46.14 3.58
1975 1997 6.238621 CGTATAGAGATCTCAACAGAAGCAGT 60.239 42.308 24.39 1.90 30.24 4.40
1984 2006 4.338682 ACACACCCGTATAGAGATCTCAAC 59.661 45.833 24.39 16.81 0.00 3.18
1985 2007 4.533815 ACACACCCGTATAGAGATCTCAA 58.466 43.478 24.39 6.91 0.00 3.02
1994 2016 4.024893 GCATGATCAAACACACCCGTATAG 60.025 45.833 0.00 0.00 0.00 1.31
1997 2019 2.080693 GCATGATCAAACACACCCGTA 58.919 47.619 0.00 0.00 0.00 4.02
1999 2021 1.131126 GAGCATGATCAAACACACCCG 59.869 52.381 5.98 0.00 0.00 5.28
2000 2022 2.440409 AGAGCATGATCAAACACACCC 58.560 47.619 14.38 0.00 0.00 4.61
2001 2023 3.366679 CCAAGAGCATGATCAAACACACC 60.367 47.826 14.38 0.00 0.00 4.16
2002 2024 3.254166 ACCAAGAGCATGATCAAACACAC 59.746 43.478 14.38 0.00 0.00 3.82
2003 2025 3.253921 CACCAAGAGCATGATCAAACACA 59.746 43.478 14.38 0.00 0.00 3.72
2123 2145 2.751259 AGGCACTGCTACAATGTGAATG 59.249 45.455 0.00 0.00 37.18 2.67
2216 2246 5.984926 AGTGCTGTGGACAATTTGTTATTTG 59.015 36.000 3.08 0.00 0.00 2.32
2217 2247 6.160576 AGTGCTGTGGACAATTTGTTATTT 57.839 33.333 3.08 0.00 0.00 1.40
2218 2248 5.789643 AGTGCTGTGGACAATTTGTTATT 57.210 34.783 3.08 0.00 0.00 1.40
2219 2249 5.068987 ACAAGTGCTGTGGACAATTTGTTAT 59.931 36.000 3.08 0.00 36.69 1.89
2220 2250 4.400884 ACAAGTGCTGTGGACAATTTGTTA 59.599 37.500 3.08 0.00 36.69 2.41
2221 2251 3.195396 ACAAGTGCTGTGGACAATTTGTT 59.805 39.130 3.08 0.00 36.69 2.83
2222 2252 2.760092 ACAAGTGCTGTGGACAATTTGT 59.240 40.909 0.63 0.63 36.69 2.83
2322 2353 1.701704 CGCCATTTGCTGAAAGAACC 58.298 50.000 0.00 0.00 38.05 3.62
2412 2443 9.400638 ACGAAAGAGATGTATTATCTCGAATTC 57.599 33.333 10.31 13.31 46.74 2.17
2413 2444 9.751542 AACGAAAGAGATGTATTATCTCGAATT 57.248 29.630 10.31 7.82 46.74 2.17
2438 2469 6.665680 AGACTAGCCTTCTAGAGTGATTTCAA 59.334 38.462 6.36 0.00 43.95 2.69
2445 2476 6.058833 TGTCATAGACTAGCCTTCTAGAGTG 58.941 44.000 6.36 0.00 43.95 3.51
2446 2477 6.255294 TGTCATAGACTAGCCTTCTAGAGT 57.745 41.667 6.36 0.00 43.95 3.24
2448 2479 5.132985 ACCTGTCATAGACTAGCCTTCTAGA 59.867 44.000 6.36 0.00 43.95 2.43
2449 2480 5.381757 ACCTGTCATAGACTAGCCTTCTAG 58.618 45.833 0.00 0.00 46.06 2.43
2451 2482 4.258457 ACCTGTCATAGACTAGCCTTCT 57.742 45.455 0.00 0.00 33.15 2.85
2454 2559 4.097418 ACAAACCTGTCATAGACTAGCCT 58.903 43.478 0.00 0.00 33.15 4.58
2459 2565 6.665992 TCACTTACAAACCTGTCATAGACT 57.334 37.500 0.00 0.00 36.96 3.24
2465 2571 4.431416 ACCATCACTTACAAACCTGTCA 57.569 40.909 0.00 0.00 36.96 3.58
2502 2611 2.103094 CAGTATCTCAAATCGGCCCTGA 59.897 50.000 0.00 0.00 0.00 3.86
2538 2647 1.609061 CCAGTCTCTTGCACGGTGAAT 60.609 52.381 13.29 0.00 0.00 2.57
2736 2845 7.710896 AGAAAGTTTCATTAGGAATGCTATGC 58.289 34.615 17.65 0.00 38.77 3.14
2820 2937 6.942532 AAGAAACTGAAGAATGCTAACACA 57.057 33.333 0.00 0.00 0.00 3.72
2961 3078 3.511699 CTGTGCTAGAATGCTAACACGA 58.488 45.455 9.28 0.00 43.40 4.35
2965 3082 3.265791 ACAGCTGTGCTAGAATGCTAAC 58.734 45.455 20.97 0.00 36.40 2.34
2982 3099 0.398318 AAACCCAGGAGACAGACAGC 59.602 55.000 0.00 0.00 0.00 4.40
3028 3145 2.509166 TATCCGTCGGAGAGGCATAT 57.491 50.000 20.50 2.42 41.61 1.78
3029 3146 2.509166 ATATCCGTCGGAGAGGCATA 57.491 50.000 20.50 6.30 41.61 3.14
3039 3156 1.588404 GTGTGCACAGAATATCCGTCG 59.412 52.381 22.40 0.00 0.00 5.12
3099 3216 5.246145 ACTGTAAATAGCAGTCGGACTAC 57.754 43.478 10.87 5.16 42.90 2.73
3103 3220 5.909621 ACTAACTGTAAATAGCAGTCGGA 57.090 39.130 0.00 0.00 45.36 4.55
3105 3222 5.519206 GGGAACTAACTGTAAATAGCAGTCG 59.481 44.000 0.00 0.00 45.36 4.18
3219 3337 6.822676 CAGTAAAGAAGAATCAGAGGAATGCT 59.177 38.462 0.00 0.00 0.00 3.79
3220 3338 6.458070 GCAGTAAAGAAGAATCAGAGGAATGC 60.458 42.308 0.00 0.00 0.00 3.56
3221 3339 6.596888 TGCAGTAAAGAAGAATCAGAGGAATG 59.403 38.462 0.00 0.00 0.00 2.67
3222 3340 6.715280 TGCAGTAAAGAAGAATCAGAGGAAT 58.285 36.000 0.00 0.00 0.00 3.01
3224 3342 5.728471 CTGCAGTAAAGAAGAATCAGAGGA 58.272 41.667 5.25 0.00 0.00 3.71
3225 3343 4.332268 GCTGCAGTAAAGAAGAATCAGAGG 59.668 45.833 16.64 0.00 0.00 3.69
3226 3344 4.934001 TGCTGCAGTAAAGAAGAATCAGAG 59.066 41.667 16.64 0.00 0.00 3.35
3227 3345 4.898320 TGCTGCAGTAAAGAAGAATCAGA 58.102 39.130 16.64 0.00 0.00 3.27
3228 3346 5.618056 TTGCTGCAGTAAAGAAGAATCAG 57.382 39.130 15.35 0.00 0.00 2.90
3229 3347 5.163824 CGATTGCTGCAGTAAAGAAGAATCA 60.164 40.000 21.35 0.00 0.00 2.57
3230 3348 5.163814 ACGATTGCTGCAGTAAAGAAGAATC 60.164 40.000 21.35 11.06 0.00 2.52
3231 3349 4.697352 ACGATTGCTGCAGTAAAGAAGAAT 59.303 37.500 21.35 2.65 0.00 2.40
3232 3350 4.065088 ACGATTGCTGCAGTAAAGAAGAA 58.935 39.130 21.35 0.00 0.00 2.52
3233 3351 3.664107 ACGATTGCTGCAGTAAAGAAGA 58.336 40.909 21.35 0.00 0.00 2.87
3289 3407 5.414144 GGGCTAGGAAAGATGAGCAATTATC 59.586 44.000 0.00 0.00 36.63 1.75
3299 3417 3.955471 TCACTTTGGGCTAGGAAAGATG 58.045 45.455 0.00 0.00 34.02 2.90
3370 3508 4.406456 TCATTGTGCTAACATCCTTGGTT 58.594 39.130 0.00 0.00 35.83 3.67
3371 3509 4.032960 TCATTGTGCTAACATCCTTGGT 57.967 40.909 0.00 0.00 35.83 3.67
3400 3538 6.573664 AACATCATGAAACGAAAATCCAGA 57.426 33.333 0.00 0.00 0.00 3.86
3419 3557 2.372837 AGGCATGCCCTTTTCAAAACAT 59.627 40.909 33.14 6.79 43.06 2.71
3440 3579 3.261897 GTCCCCAGAATTTCAGTCAGAGA 59.738 47.826 0.00 0.00 0.00 3.10
3460 3599 4.900635 ACATTCAGGTTTCAACAGTGTC 57.099 40.909 0.00 0.00 0.00 3.67
3462 3601 4.516698 AGCTACATTCAGGTTTCAACAGTG 59.483 41.667 0.00 0.00 0.00 3.66
3463 3602 4.718961 AGCTACATTCAGGTTTCAACAGT 58.281 39.130 0.00 0.00 0.00 3.55
3464 3603 5.239306 TGAAGCTACATTCAGGTTTCAACAG 59.761 40.000 0.00 0.00 36.42 3.16
3465 3604 5.129634 TGAAGCTACATTCAGGTTTCAACA 58.870 37.500 0.00 0.00 36.42 3.33
3466 3605 5.689383 TGAAGCTACATTCAGGTTTCAAC 57.311 39.130 0.00 0.00 36.42 3.18
3467 3606 6.003326 TCATGAAGCTACATTCAGGTTTCAA 58.997 36.000 0.00 0.00 42.20 2.69
3468 3607 5.559770 TCATGAAGCTACATTCAGGTTTCA 58.440 37.500 0.00 0.00 42.20 2.69
3469 3608 6.690194 ATCATGAAGCTACATTCAGGTTTC 57.310 37.500 0.00 0.00 42.20 2.78
3482 3621 8.619546 GCTAGTGAGAAATAAAATCATGAAGCT 58.380 33.333 0.00 0.00 0.00 3.74
3484 3623 8.896744 TGGCTAGTGAGAAATAAAATCATGAAG 58.103 33.333 0.00 0.00 0.00 3.02
3510 3649 6.270231 AGGAAAGTAGTTGGACATAACAGTCT 59.730 38.462 0.00 0.00 38.57 3.24
3512 3651 6.435292 AGGAAAGTAGTTGGACATAACAGT 57.565 37.500 0.00 0.00 33.02 3.55
3514 3653 7.453752 AGTCTAGGAAAGTAGTTGGACATAACA 59.546 37.037 0.00 0.00 33.02 2.41
3515 3654 7.838884 AGTCTAGGAAAGTAGTTGGACATAAC 58.161 38.462 0.00 0.00 0.00 1.89
3519 3658 5.642165 AGAGTCTAGGAAAGTAGTTGGACA 58.358 41.667 0.00 0.00 0.00 4.02
3520 3659 5.125900 GGAGAGTCTAGGAAAGTAGTTGGAC 59.874 48.000 0.00 0.00 0.00 4.02
3521 3660 5.222275 TGGAGAGTCTAGGAAAGTAGTTGGA 60.222 44.000 0.00 0.00 0.00 3.53
3522 3661 5.017490 TGGAGAGTCTAGGAAAGTAGTTGG 58.983 45.833 0.00 0.00 0.00 3.77
3526 3665 5.888724 TGATGTGGAGAGTCTAGGAAAGTAG 59.111 44.000 0.00 0.00 0.00 2.57
3553 3692 6.346096 TGACTTACTAATACAAGTGGATGCC 58.654 40.000 0.00 0.00 35.17 4.40
3554 3693 8.438676 AATGACTTACTAATACAAGTGGATGC 57.561 34.615 0.00 0.00 35.17 3.91
3557 3696 9.865321 GTGTAATGACTTACTAATACAAGTGGA 57.135 33.333 0.00 0.00 38.44 4.02
3558 3697 9.647797 TGTGTAATGACTTACTAATACAAGTGG 57.352 33.333 0.00 0.00 38.44 4.00
3571 3728 9.856488 GTCATTTCTCTAGTGTGTAATGACTTA 57.144 33.333 23.69 7.09 43.26 2.24
3572 3729 8.764524 GTCATTTCTCTAGTGTGTAATGACTT 57.235 34.615 23.69 0.00 43.26 3.01
3579 3736 7.450634 ACTGGTTAGTCATTTCTCTAGTGTGTA 59.549 37.037 0.00 0.00 28.79 2.90
3580 3737 6.267928 ACTGGTTAGTCATTTCTCTAGTGTGT 59.732 38.462 0.00 0.00 28.79 3.72
3581 3738 6.587990 CACTGGTTAGTCATTTCTCTAGTGTG 59.412 42.308 0.00 0.00 34.07 3.82
3621 3788 1.602605 GGTACCCACCACAACCTGC 60.603 63.158 0.00 0.00 45.04 4.85
3636 3803 1.071814 GGCCACGGTGTTGAAGGTA 59.928 57.895 7.45 0.00 0.00 3.08
3843 4013 2.043652 CCCTGGTTCATGGGGCTG 60.044 66.667 0.00 0.00 39.76 4.85
3849 4019 1.221840 CGGGACTCCCTGGTTCATG 59.778 63.158 12.62 0.00 42.67 3.07
4004 4184 2.184385 ATTACGCTAAGACGACGGTG 57.816 50.000 0.00 0.00 36.70 4.94
4010 4190 2.919229 ACCACGAAATTACGCTAAGACG 59.081 45.455 0.00 0.00 36.70 4.18
4012 4192 3.119884 TCGACCACGAAATTACGCTAAGA 60.120 43.478 0.00 0.00 45.74 2.10
4070 4250 4.270325 GGCTAACAATAATCCACGACTGAC 59.730 45.833 0.00 0.00 0.00 3.51
4071 4251 4.439057 GGCTAACAATAATCCACGACTGA 58.561 43.478 0.00 0.00 0.00 3.41
4072 4252 3.560068 GGGCTAACAATAATCCACGACTG 59.440 47.826 0.00 0.00 0.00 3.51
4073 4253 3.740141 CGGGCTAACAATAATCCACGACT 60.740 47.826 0.00 0.00 0.00 4.18
4084 4264 1.494721 ACATCCATCCGGGCTAACAAT 59.505 47.619 0.00 0.00 36.21 2.71
4099 4279 3.245284 CGACACATTAATCCACGACATCC 59.755 47.826 0.00 0.00 0.00 3.51
4100 4280 3.245284 CCGACACATTAATCCACGACATC 59.755 47.826 0.00 0.00 0.00 3.06
4101 4281 3.118920 TCCGACACATTAATCCACGACAT 60.119 43.478 0.00 0.00 0.00 3.06
4102 4282 2.231721 TCCGACACATTAATCCACGACA 59.768 45.455 0.00 0.00 0.00 4.35
4144 4324 0.039256 CCACCGGTTAAACTCGACGA 60.039 55.000 2.97 0.00 0.00 4.20
4145 4325 0.318955 ACCACCGGTTAAACTCGACG 60.319 55.000 2.97 0.00 27.29 5.12
4146 4326 1.869774 AACCACCGGTTAAACTCGAC 58.130 50.000 2.97 0.00 44.94 4.20
4234 4415 7.685532 TGCAAAAACAAAAACCAAAAAGAAC 57.314 28.000 0.00 0.00 0.00 3.01
4257 4438 4.083377 ACACCAAAACTTGCAAAAAGCTTG 60.083 37.500 0.00 0.42 45.94 4.01
4258 4439 4.071423 ACACCAAAACTTGCAAAAAGCTT 58.929 34.783 0.00 0.00 45.94 3.74
4259 4440 3.673902 ACACCAAAACTTGCAAAAAGCT 58.326 36.364 0.00 0.00 45.94 3.74
4260 4441 4.154015 AGAACACCAAAACTTGCAAAAAGC 59.846 37.500 0.00 0.00 45.96 3.51
4261 4442 5.861222 AGAACACCAAAACTTGCAAAAAG 57.139 34.783 0.00 0.00 0.00 2.27
4262 4443 6.038714 ACAAAGAACACCAAAACTTGCAAAAA 59.961 30.769 0.00 0.00 0.00 1.94
4263 4444 5.529060 ACAAAGAACACCAAAACTTGCAAAA 59.471 32.000 0.00 0.00 0.00 2.44
4264 4445 5.049818 CACAAAGAACACCAAAACTTGCAAA 60.050 36.000 0.00 0.00 0.00 3.68
4265 4446 4.450419 CACAAAGAACACCAAAACTTGCAA 59.550 37.500 0.00 0.00 0.00 4.08
4266 4447 3.993081 CACAAAGAACACCAAAACTTGCA 59.007 39.130 0.00 0.00 0.00 4.08
4267 4448 3.370672 CCACAAAGAACACCAAAACTTGC 59.629 43.478 0.00 0.00 0.00 4.01
4268 4449 4.815269 TCCACAAAGAACACCAAAACTTG 58.185 39.130 0.00 0.00 0.00 3.16
4269 4450 5.675684 ATCCACAAAGAACACCAAAACTT 57.324 34.783 0.00 0.00 0.00 2.66
4270 4451 5.675684 AATCCACAAAGAACACCAAAACT 57.324 34.783 0.00 0.00 0.00 2.66
4271 4452 6.735678 AAAATCCACAAAGAACACCAAAAC 57.264 33.333 0.00 0.00 0.00 2.43
4272 4453 7.164803 AGAAAAATCCACAAAGAACACCAAAA 58.835 30.769 0.00 0.00 0.00 2.44
4273 4454 6.706295 AGAAAAATCCACAAAGAACACCAAA 58.294 32.000 0.00 0.00 0.00 3.28
4274 4455 6.293004 AGAAAAATCCACAAAGAACACCAA 57.707 33.333 0.00 0.00 0.00 3.67
4275 4456 5.930837 AGAAAAATCCACAAAGAACACCA 57.069 34.783 0.00 0.00 0.00 4.17
4276 4457 8.887036 ATAAAGAAAAATCCACAAAGAACACC 57.113 30.769 0.00 0.00 0.00 4.16
4313 4494 4.708421 ACATTAGCAGCATCACAGGAAAAT 59.292 37.500 0.00 0.00 0.00 1.82
4324 4505 2.686915 GGAGCAGAAACATTAGCAGCAT 59.313 45.455 0.00 0.00 0.00 3.79
4326 4507 2.363683 AGGAGCAGAAACATTAGCAGC 58.636 47.619 0.00 0.00 0.00 5.25
4327 4508 3.559242 GCTAGGAGCAGAAACATTAGCAG 59.441 47.826 0.00 0.00 41.89 4.24
4335 4516 0.179097 CGGGAGCTAGGAGCAGAAAC 60.179 60.000 0.64 0.00 45.56 2.78
4348 4529 2.821366 CATCAGCACCACGGGAGC 60.821 66.667 4.59 4.59 39.54 4.70
4349 4530 2.124983 CCATCAGCACCACGGGAG 60.125 66.667 0.00 0.00 0.00 4.30
4350 4531 2.063015 AAACCATCAGCACCACGGGA 62.063 55.000 0.00 0.00 0.00 5.14
4351 4532 1.178534 AAAACCATCAGCACCACGGG 61.179 55.000 0.00 0.00 0.00 5.28
4357 4538 3.803778 CCAAACAGAAAAACCATCAGCAC 59.196 43.478 0.00 0.00 0.00 4.40
4395 4588 0.668401 AGCAGCAGGAAAAATTGCGC 60.668 50.000 0.00 0.00 44.80 6.09
4396 4589 1.065358 CAGCAGCAGGAAAAATTGCG 58.935 50.000 0.00 0.00 44.80 4.85
4412 4610 2.024176 ACATACGGATCAACACCAGC 57.976 50.000 0.00 0.00 0.00 4.85
4415 4613 3.938963 ACATCAACATACGGATCAACACC 59.061 43.478 0.00 0.00 0.00 4.16
4418 4616 6.238103 CCAGTAACATCAACATACGGATCAAC 60.238 42.308 0.00 0.00 0.00 3.18
4421 4619 4.750098 CCCAGTAACATCAACATACGGATC 59.250 45.833 0.00 0.00 0.00 3.36
4422 4620 4.163458 ACCCAGTAACATCAACATACGGAT 59.837 41.667 0.00 0.00 0.00 4.18
4425 4623 4.436852 GCAACCCAGTAACATCAACATACG 60.437 45.833 0.00 0.00 0.00 3.06
4426 4624 4.700213 AGCAACCCAGTAACATCAACATAC 59.300 41.667 0.00 0.00 0.00 2.39
4428 4626 3.507233 CAGCAACCCAGTAACATCAACAT 59.493 43.478 0.00 0.00 0.00 2.71
4431 4629 2.107378 TCCAGCAACCCAGTAACATCAA 59.893 45.455 0.00 0.00 0.00 2.57
4434 4632 1.705186 ACTCCAGCAACCCAGTAACAT 59.295 47.619 0.00 0.00 0.00 2.71
4435 4633 1.136828 ACTCCAGCAACCCAGTAACA 58.863 50.000 0.00 0.00 0.00 2.41
4439 4637 1.119574 ACGTACTCCAGCAACCCAGT 61.120 55.000 0.00 0.00 0.00 4.00
4442 4640 0.320697 AAGACGTACTCCAGCAACCC 59.679 55.000 0.00 0.00 0.00 4.11
4447 4645 3.037485 GCTGAAGACGTACTCCAGC 57.963 57.895 9.62 9.62 42.52 4.85
4448 4646 1.813178 TCAGCTGAAGACGTACTCCAG 59.187 52.381 15.67 0.00 0.00 3.86
4449 4647 1.905637 TCAGCTGAAGACGTACTCCA 58.094 50.000 15.67 0.00 0.00 3.86
4467 4669 2.550180 GTCTCCAAAGCCAGTCAACTTC 59.450 50.000 0.00 0.00 0.00 3.01
4469 4671 1.771255 AGTCTCCAAAGCCAGTCAACT 59.229 47.619 0.00 0.00 0.00 3.16
4473 4675 0.390472 CGGAGTCTCCAAAGCCAGTC 60.390 60.000 19.15 0.00 35.91 3.51
4476 4678 3.885814 ACGGAGTCTCCAAAGCCA 58.114 55.556 19.15 0.00 29.74 4.75
4515 4717 2.415010 CGCCTCCCGTGATCTCTG 59.585 66.667 0.00 0.00 0.00 3.35
4557 4759 0.393537 GAAGATGTGGGACCCAGCAG 60.394 60.000 15.52 0.00 32.34 4.24
4632 4834 2.434185 TGCGCCGATGGTGTCTTC 60.434 61.111 4.18 0.00 35.34 2.87
4633 4835 2.742372 GTGCGCCGATGGTGTCTT 60.742 61.111 4.18 0.00 35.34 3.01
4704 4906 3.866582 GCGATACCCAGGCTGGCT 61.867 66.667 28.51 17.72 35.79 4.75
4707 4909 4.609018 CCGGCGATACCCAGGCTG 62.609 72.222 9.30 7.75 33.26 4.85
4755 4968 1.819905 CTTCCGCTCTCCTTCTCCC 59.180 63.158 0.00 0.00 0.00 4.30
4760 4973 2.283529 TTCCGCTTCCGCTCTCCTT 61.284 57.895 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.