Multiple sequence alignment - TraesCS4A01G490800

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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 TraesCS4A01G490800 chr4A 100.000 4833 0 0 1 4833 740655701 740660533 0.000000e+00 8925
1 TraesCS4A01G490800 chr4A 94.680 2575 123 7 2117 4681 741886095 741883525 0.000000e+00 3984
2 TraesCS4A01G490800 chr4A 88.241 2194 233 20 2655 4833 740867717 740865534 0.000000e+00 2599
3 TraesCS4A01G490800 chr4A 88.139 2192 240 14 2655 4833 733927124 733924940 0.000000e+00 2590
4 TraesCS4A01G490800 chr4A 88.333 2160 231 17 2655 4800 739833335 739835487 0.000000e+00 2573
5 TraesCS4A01G490800 chr4A 87.774 2192 248 15 2655 4833 739808621 739810805 0.000000e+00 2545
6 TraesCS4A01G490800 chr4A 96.412 1087 26 8 999 2076 741887172 741886090 0.000000e+00 1779
7 TraesCS4A01G490800 chr4A 100.000 384 0 0 5064 5447 740660764 740661147 0.000000e+00 710
8 TraesCS4A01G490800 chr4A 88.547 358 38 3 2148 2503 739832905 739833261 1.080000e-116 431
9 TraesCS4A01G490800 chr4A 88.187 364 40 3 2148 2508 742270100 742269737 1.080000e-116 431
10 TraesCS4A01G490800 chr4A 88.154 363 40 3 2148 2508 740061706 740061345 3.900000e-116 429
11 TraesCS4A01G490800 chr4A 82.268 485 66 13 2025 2508 740868251 740867786 8.500000e-108 401
12 TraesCS4A01G490800 chr4A 90.809 272 15 8 5180 5447 741883471 741883206 6.710000e-94 355
13 TraesCS4A01G490800 chr7A 90.461 2191 191 12 2655 4833 3381649 3383833 0.000000e+00 2872
14 TraesCS4A01G490800 chr7A 89.848 2039 191 8 2655 4681 3583366 3585400 0.000000e+00 2604
15 TraesCS4A01G490800 chr7A 87.901 2182 238 20 2669 4833 3001958 2999786 0.000000e+00 2543
16 TraesCS4A01G490800 chr7A 80.527 873 108 37 1675 2505 3582442 3583294 1.000000e-171 614
17 TraesCS4A01G490800 chr7A 80.259 851 115 35 1675 2491 3002850 3002019 4.700000e-165 592
18 TraesCS4A01G490800 chr7A 89.315 365 33 3 999 1361 3380286 3380646 2.310000e-123 453
19 TraesCS4A01G490800 chr7A 89.668 271 19 6 5180 5447 3585455 3585719 2.430000e-88 337
20 TraesCS4A01G490800 chr7A 83.200 125 14 5 5178 5300 13337372 13337253 2.070000e-19 108
21 TraesCS4A01G490800 chr7D 87.358 2294 253 27 2556 4833 2429945 2432217 0.000000e+00 2595
22 TraesCS4A01G490800 chr7D 82.640 553 69 16 1979 2505 3699143 3699694 1.070000e-126 464
23 TraesCS4A01G490800 chr7D 88.485 330 37 1 2148 2476 3583327 3583656 1.100000e-106 398
24 TraesCS4A01G490800 chr7D 84.594 357 48 4 999 1352 3439190 3439542 1.120000e-91 348
25 TraesCS4A01G490800 chr7D 83.511 376 47 9 999 1363 2427928 2428299 2.430000e-88 337
26 TraesCS4A01G490800 chr7D 89.011 273 22 6 5177 5447 3701842 3702108 1.130000e-86 331
27 TraesCS4A01G490800 chr7D 85.827 254 29 3 1096 1342 3582468 3582721 4.180000e-66 263
28 TraesCS4A01G490800 chr7D 89.773 88 7 1 999 1084 2420935 2421022 1.600000e-20 111
29 TraesCS4A01G490800 chr5B 97.206 1002 27 1 1 1002 706273145 706274145 0.000000e+00 1694
30 TraesCS4A01G490800 chr5B 96.510 1003 32 3 1 1002 676851917 676852917 0.000000e+00 1655
31 TraesCS4A01G490800 chr5B 96.123 1006 33 6 1 1002 545074639 545075642 0.000000e+00 1637
32 TraesCS4A01G490800 chr3B 96.710 1003 31 2 1 1002 811247997 811246996 0.000000e+00 1668
33 TraesCS4A01G490800 chr3B 96.610 1003 32 2 1 1002 31833056 31832055 0.000000e+00 1663
34 TraesCS4A01G490800 chr3B 96.226 1007 32 3 1 1002 761423994 761424999 0.000000e+00 1644
35 TraesCS4A01G490800 chr3B 96.108 1002 35 3 1 1002 751262587 751263584 0.000000e+00 1631
36 TraesCS4A01G490800 chr6B 96.407 1002 35 1 1 1002 24871070 24872070 0.000000e+00 1650
37 TraesCS4A01G490800 chr4B 95.929 1007 35 3 1 1002 106009325 106010330 0.000000e+00 1628


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 TraesCS4A01G490800 chr4A 740655701 740661147 5446 False 4817.500000 8925 100.0000 1 5447 2 chr4A.!!$F3 5446
1 TraesCS4A01G490800 chr4A 733924940 733927124 2184 True 2590.000000 2590 88.1390 2655 4833 1 chr4A.!!$R1 2178
2 TraesCS4A01G490800 chr4A 739808621 739810805 2184 False 2545.000000 2545 87.7740 2655 4833 1 chr4A.!!$F1 2178
3 TraesCS4A01G490800 chr4A 741883206 741887172 3966 True 2039.333333 3984 93.9670 999 5447 3 chr4A.!!$R5 4448
4 TraesCS4A01G490800 chr4A 739832905 739835487 2582 False 1502.000000 2573 88.4400 2148 4800 2 chr4A.!!$F2 2652
5 TraesCS4A01G490800 chr4A 740865534 740868251 2717 True 1500.000000 2599 85.2545 2025 4833 2 chr4A.!!$R4 2808
6 TraesCS4A01G490800 chr7A 3380286 3383833 3547 False 1662.500000 2872 89.8880 999 4833 2 chr7A.!!$F1 3834
7 TraesCS4A01G490800 chr7A 2999786 3002850 3064 True 1567.500000 2543 84.0800 1675 4833 2 chr7A.!!$R2 3158
8 TraesCS4A01G490800 chr7A 3582442 3585719 3277 False 1185.000000 2604 86.6810 1675 5447 3 chr7A.!!$F2 3772
9 TraesCS4A01G490800 chr7D 2427928 2432217 4289 False 1466.000000 2595 85.4345 999 4833 2 chr7D.!!$F3 3834
10 TraesCS4A01G490800 chr7D 3699143 3702108 2965 False 397.500000 464 85.8255 1979 5447 2 chr7D.!!$F5 3468
11 TraesCS4A01G490800 chr7D 3582468 3583656 1188 False 330.500000 398 87.1560 1096 2476 2 chr7D.!!$F4 1380
12 TraesCS4A01G490800 chr5B 706273145 706274145 1000 False 1694.000000 1694 97.2060 1 1002 1 chr5B.!!$F3 1001
13 TraesCS4A01G490800 chr5B 676851917 676852917 1000 False 1655.000000 1655 96.5100 1 1002 1 chr5B.!!$F2 1001
14 TraesCS4A01G490800 chr5B 545074639 545075642 1003 False 1637.000000 1637 96.1230 1 1002 1 chr5B.!!$F1 1001
15 TraesCS4A01G490800 chr3B 811246996 811247997 1001 True 1668.000000 1668 96.7100 1 1002 1 chr3B.!!$R2 1001
16 TraesCS4A01G490800 chr3B 31832055 31833056 1001 True 1663.000000 1663 96.6100 1 1002 1 chr3B.!!$R1 1001
17 TraesCS4A01G490800 chr3B 761423994 761424999 1005 False 1644.000000 1644 96.2260 1 1002 1 chr3B.!!$F2 1001
18 TraesCS4A01G490800 chr3B 751262587 751263584 997 False 1631.000000 1631 96.1080 1 1002 1 chr3B.!!$F1 1001
19 TraesCS4A01G490800 chr6B 24871070 24872070 1000 False 1650.000000 1650 96.4070 1 1002 1 chr6B.!!$F1 1001
20 TraesCS4A01G490800 chr4B 106009325 106010330 1005 False 1628.000000 1628 95.9290 1 1002 1 chr4B.!!$F1 1001

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
154 155 0.891904 ACATACCGGGCAAAGCGTTT 60.892 50.000 6.32 0.0 0.00 3.60 F
486 489 1.002033 CTTGCGCAGTTTCTCTTTGCT 60.002 47.619 11.31 0.0 35.73 3.91 F
1871 2650 0.891904 GGGCGAACAACCTAAAGCCA 60.892 55.000 6.61 0.0 45.79 4.75 F
2499 3404 0.838122 CTGTTGGTCCTGGGTCCTCT 60.838 60.000 9.47 0.0 0.00 3.69 F
4165 5126 0.041238 TCCACCTGGAGGATTCGAGT 59.959 55.000 8.95 0.0 39.78 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 2650 1.668419 GGCGATTACATTGTGGCTCT 58.332 50.0 0.00 0.0 0.00 4.09 R
2475 3380 0.991355 ACCCAGGACCAACAGGTTGA 60.991 55.0 13.47 0.0 42.93 3.18 R
3012 3971 0.600557 CGACTTCCTCTGCACTCAGT 59.399 55.0 0.00 0.0 41.10 3.41 R
4414 5375 0.178953 ATCTTTGGCCACTTGCTGGT 60.179 50.0 3.88 0.0 42.99 4.00 R
5083 6060 0.176680 CACTAGGCGATGCTTCCAGT 59.823 55.0 0.00 0.0 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
72 73 3.160269 CACCTTGGCAGGAATCTTCTTT 58.840 45.455 9.53 0.00 44.19 2.52
75 76 4.289672 ACCTTGGCAGGAATCTTCTTTCTA 59.710 41.667 9.53 0.00 44.19 2.10
148 149 1.974343 GCACCACATACCGGGCAAA 60.974 57.895 6.32 0.00 0.00 3.68
154 155 0.891904 ACATACCGGGCAAAGCGTTT 60.892 50.000 6.32 0.00 0.00 3.60
332 333 5.833131 AGCAACTTTCTAAATCCCTTGTCAA 59.167 36.000 0.00 0.00 0.00 3.18
352 353 5.183904 GTCAAATACACCATTCTCTGCCTTT 59.816 40.000 0.00 0.00 0.00 3.11
486 489 1.002033 CTTGCGCAGTTTCTCTTTGCT 60.002 47.619 11.31 0.00 35.73 3.91
555 558 1.277842 TCTTCAGCTTGTTCCCGCATA 59.722 47.619 0.00 0.00 0.00 3.14
630 633 3.366396 ACCAGGATAGATGTCGTTGTCT 58.634 45.455 0.00 0.00 0.00 3.41
802 806 3.099141 CAAGGCATAAAACCATCCACCT 58.901 45.455 0.00 0.00 0.00 4.00
862 866 2.172717 CCATTAATGAACCCGGGAGAGT 59.827 50.000 32.02 12.03 0.00 3.24
1049 1063 4.172505 CAGTCTCAGAACTTCGATGAAGG 58.827 47.826 10.95 0.00 43.25 3.46
1268 1297 8.357402 ACAAAGTAAGATACAAACAATGAACCC 58.643 33.333 0.00 0.00 0.00 4.11
1632 2162 8.301730 AGATTAATTGTTGTGCAACTTTCATG 57.698 30.769 14.97 0.00 41.67 3.07
1687 2458 1.331756 GTGCCAGTTGTTGAGTCTGTG 59.668 52.381 0.00 0.00 0.00 3.66
1688 2459 1.065491 TGCCAGTTGTTGAGTCTGTGT 60.065 47.619 0.00 0.00 0.00 3.72
1729 2500 3.067833 GGTTACTCTTGGACTGTTGAGC 58.932 50.000 0.00 0.00 0.00 4.26
1735 2506 1.466167 CTTGGACTGTTGAGCGGAATG 59.534 52.381 0.00 0.00 0.00 2.67
1871 2650 0.891904 GGGCGAACAACCTAAAGCCA 60.892 55.000 6.61 0.00 45.79 4.75
2084 2933 3.060479 AGGAATATGTGAGGGCCTACA 57.940 47.619 5.73 12.11 0.00 2.74
2095 2944 5.012046 TGTGAGGGCCTACATATTGTATCAG 59.988 44.000 5.73 0.00 31.66 2.90
2102 2952 6.591834 GGCCTACATATTGTATCAGTAAGCAG 59.408 42.308 0.00 0.00 31.66 4.24
2446 3351 3.884693 TGTTTCTGAATCTCAAAGCAGCA 59.115 39.130 0.00 0.00 0.00 4.41
2475 3380 5.934781 AGTGAAAGAAAGGACACAAGATCT 58.065 37.500 0.00 0.00 35.97 2.75
2479 3384 6.260936 TGAAAGAAAGGACACAAGATCTCAAC 59.739 38.462 0.00 0.00 0.00 3.18
2499 3404 0.838122 CTGTTGGTCCTGGGTCCTCT 60.838 60.000 9.47 0.00 0.00 3.69
2513 3418 1.978580 GTCCTCTGAAGGGGAAGTTGA 59.021 52.381 0.00 0.00 43.56 3.18
2522 3427 1.103398 GGGGAAGTTGATGCCGATGG 61.103 60.000 0.00 0.00 0.00 3.51
2556 3461 9.791820 CTGTTTAATGATCATATTTCAGTTGCA 57.208 29.630 9.04 0.00 0.00 4.08
2632 3549 1.456518 TCCTCTGAGCGGGATGGAG 60.457 63.158 0.00 0.00 0.00 3.86
2818 3777 3.411446 TGGAGTAACATTTGCAGGTCAG 58.589 45.455 0.00 0.00 0.00 3.51
3012 3971 1.256812 TCGTCACTGAGAAGCATGGA 58.743 50.000 0.00 0.00 0.00 3.41
3242 4201 1.265635 CCGTCGACTTTCCATGCAAAA 59.734 47.619 14.70 0.00 0.00 2.44
3344 4303 0.676782 CGACGGCTCCCTTTCCATTT 60.677 55.000 0.00 0.00 0.00 2.32
3453 4412 3.754965 TGTGCTGAAGTATTTGAGCCTT 58.245 40.909 6.95 0.00 34.12 4.35
3546 4507 3.891049 GGAGACCAATATTCAGGTGCTT 58.109 45.455 2.30 0.00 38.50 3.91
3672 4633 2.846039 AAGCACTCCGTATACTGTCG 57.154 50.000 0.56 0.00 0.00 4.35
3819 4780 1.107114 CCATCGAGTACCTCTGCAGT 58.893 55.000 14.67 0.00 0.00 4.40
3889 4850 2.057922 ACTCCTTGGACACCATGTCTT 58.942 47.619 8.75 0.00 46.19 3.01
3963 4924 5.022787 CCCCCAAAGTGGATCAAAAATCTA 58.977 41.667 0.00 0.00 40.96 1.98
3979 4940 8.871125 TCAAAAATCTAGAGAACCTCTACAAGT 58.129 33.333 0.00 0.00 41.50 3.16
4003 4964 4.407621 TGACCCTTTCTGTGACAGTTCTTA 59.592 41.667 12.93 0.00 32.61 2.10
4029 4990 5.809001 ACTGATACTTTCAAGCTCATCCAA 58.191 37.500 0.00 0.00 32.78 3.53
4030 4991 6.240894 ACTGATACTTTCAAGCTCATCCAAA 58.759 36.000 0.00 0.00 32.78 3.28
4032 4993 7.094463 ACTGATACTTTCAAGCTCATCCAAAAG 60.094 37.037 0.00 0.00 32.78 2.27
4036 4997 5.127682 ACTTTCAAGCTCATCCAAAAGTTGT 59.872 36.000 0.00 0.00 34.28 3.32
4048 5009 7.609532 TCATCCAAAAGTTGTCCAAATTGTTTT 59.390 29.630 0.00 0.00 0.00 2.43
4067 5028 5.815740 TGTTTTCTCTCACCTTTACACTCAC 59.184 40.000 0.00 0.00 0.00 3.51
4072 5033 6.010850 TCTCTCACCTTTACACTCACTGTAT 58.989 40.000 0.00 0.00 35.18 2.29
4074 5035 5.055642 TCACCTTTACACTCACTGTATCG 57.944 43.478 0.00 0.00 35.18 2.92
4083 5044 4.646945 ACACTCACTGTATCGAAGGATGAT 59.353 41.667 0.00 0.00 34.00 2.45
4084 5045 5.828328 ACACTCACTGTATCGAAGGATGATA 59.172 40.000 0.00 0.00 34.00 2.15
4085 5046 6.016693 ACACTCACTGTATCGAAGGATGATAG 60.017 42.308 0.00 0.00 34.00 2.08
4130 5091 7.575720 CCTTGAGGAAAATAAACAGCTTACTGG 60.576 40.741 0.00 0.00 42.58 4.00
4162 5123 3.838244 TTATTCCACCTGGAGGATTCG 57.162 47.619 13.86 0.00 46.36 3.34
4165 5126 0.041238 TCCACCTGGAGGATTCGAGT 59.959 55.000 8.95 0.00 39.78 4.18
4182 5143 1.996191 GAGTGTCTAAAGCTGCTTCGG 59.004 52.381 16.28 11.27 0.00 4.30
4191 5152 1.441016 GCTGCTTCGGTTCTTTGCG 60.441 57.895 0.00 0.00 0.00 4.85
4197 5158 2.925306 GCTTCGGTTCTTTGCGACTCTA 60.925 50.000 0.00 0.00 0.00 2.43
4203 5164 0.109272 TCTTTGCGACTCTAGTGCCG 60.109 55.000 0.00 0.00 0.00 5.69
4221 5182 1.633852 CGAGGCTGAGCTTTGCAGTC 61.634 60.000 3.72 5.89 38.23 3.51
4302 5263 2.039084 AGGGATTTATGGCATCGAGACC 59.961 50.000 1.65 2.62 0.00 3.85
4306 5267 2.620251 TTATGGCATCGAGACCCTTG 57.380 50.000 1.65 0.00 0.00 3.61
4329 5290 3.473147 CCTCCAAGAGGTGCATCTG 57.527 57.895 2.86 0.00 44.25 2.90
4332 5293 0.251354 TCCAAGAGGTGCATCTGAGC 59.749 55.000 2.86 0.00 35.89 4.26
4353 5314 2.285220 CGTTGGTAATCAAGCGGATGAG 59.715 50.000 0.00 0.00 36.02 2.90
4496 5458 8.593679 TCTTTCAGTTGACCTACAAATCATCTA 58.406 33.333 0.00 0.00 40.36 1.98
4536 5506 3.181475 GGAGACTATTCCAATCTGCGTCA 60.181 47.826 0.00 0.00 37.20 4.35
4544 5516 1.734465 CCAATCTGCGTCACCTTCTTC 59.266 52.381 0.00 0.00 0.00 2.87
4569 5541 6.488006 CAGGGCTAAATAAACATACTGCATCT 59.512 38.462 0.00 0.00 0.00 2.90
4570 5542 7.013655 CAGGGCTAAATAAACATACTGCATCTT 59.986 37.037 0.00 0.00 0.00 2.40
4638 5610 9.661563 TCCGTTACTGATTCTTGTAATTTGTAT 57.338 29.630 6.27 0.00 32.32 2.29
4690 5664 9.677567 TTGAAGTTTTTGAACTTACATCTATGC 57.322 29.630 4.67 0.00 42.57 3.14
4710 5684 8.436778 TCTATGCTTGGTTGTGGTATGTATATT 58.563 33.333 0.00 0.00 0.00 1.28
4711 5685 6.935741 TGCTTGGTTGTGGTATGTATATTC 57.064 37.500 0.00 0.00 0.00 1.75
4713 5687 5.825679 GCTTGGTTGTGGTATGTATATTCCA 59.174 40.000 0.00 0.00 32.05 3.53
4714 5688 6.320164 GCTTGGTTGTGGTATGTATATTCCAA 59.680 38.462 0.00 0.00 35.78 3.53
4716 5690 7.873719 TGGTTGTGGTATGTATATTCCAAAG 57.126 36.000 0.00 0.00 35.78 2.77
4717 5691 6.320164 TGGTTGTGGTATGTATATTCCAAAGC 59.680 38.462 0.00 7.13 35.78 3.51
4718 5692 6.320164 GGTTGTGGTATGTATATTCCAAAGCA 59.680 38.462 0.00 0.00 35.78 3.91
4719 5693 6.935741 TGTGGTATGTATATTCCAAAGCAC 57.064 37.500 0.00 0.00 35.78 4.40
4738 5713 7.416154 AAGCACATGTTTTGATTGAGATTTG 57.584 32.000 0.00 0.00 0.00 2.32
4740 5715 7.660112 AGCACATGTTTTGATTGAGATTTGTA 58.340 30.769 0.00 0.00 0.00 2.41
4794 5771 4.289672 AGATTCAGTTGGTGTATGGAGGTT 59.710 41.667 0.00 0.00 0.00 3.50
4800 5777 3.433306 TGGTGTATGGAGGTTTCTTGG 57.567 47.619 0.00 0.00 0.00 3.61
4811 5788 1.269778 GGTTTCTTGGCCAAAGTGCTC 60.270 52.381 20.91 7.92 37.18 4.26
4812 5789 1.408702 GTTTCTTGGCCAAAGTGCTCA 59.591 47.619 20.91 0.00 37.18 4.26
4815 5792 0.316204 CTTGGCCAAAGTGCTCAAGG 59.684 55.000 20.91 0.00 36.61 3.61
4820 5797 2.562738 GGCCAAAGTGCTCAAGGTTTAT 59.437 45.455 0.00 0.00 0.00 1.40
4824 5801 5.222631 CCAAAGTGCTCAAGGTTTATGAAC 58.777 41.667 0.00 0.00 34.96 3.18
4825 5802 5.010012 CCAAAGTGCTCAAGGTTTATGAACT 59.990 40.000 0.00 0.00 36.03 3.01
4826 5803 6.206634 CCAAAGTGCTCAAGGTTTATGAACTA 59.793 38.462 0.00 0.00 36.03 2.24
4827 5804 7.301054 CAAAGTGCTCAAGGTTTATGAACTAG 58.699 38.462 0.00 0.00 36.03 2.57
4828 5805 6.360370 AGTGCTCAAGGTTTATGAACTAGA 57.640 37.500 0.00 0.00 36.03 2.43
4829 5806 6.951971 AGTGCTCAAGGTTTATGAACTAGAT 58.048 36.000 0.00 0.00 36.03 1.98
4831 5808 7.335422 AGTGCTCAAGGTTTATGAACTAGATTG 59.665 37.037 0.00 2.16 36.03 2.67
4832 5809 6.094048 TGCTCAAGGTTTATGAACTAGATTGC 59.906 38.462 0.00 0.45 36.03 3.56
5096 6073 4.625800 AGGAACTGGAAGCATCGC 57.374 55.556 0.00 0.00 37.18 4.58
5097 6074 1.078143 AGGAACTGGAAGCATCGCC 60.078 57.895 0.00 0.00 37.18 5.54
5098 6075 1.078143 GGAACTGGAAGCATCGCCT 60.078 57.895 0.00 0.00 37.60 5.52
5099 6076 0.178068 GGAACTGGAAGCATCGCCTA 59.822 55.000 0.00 0.00 37.60 3.93
5100 6077 1.576356 GAACTGGAAGCATCGCCTAG 58.424 55.000 0.00 0.00 37.60 3.02
5101 6078 0.905357 AACTGGAAGCATCGCCTAGT 59.095 50.000 0.00 0.00 37.60 2.57
5102 6079 0.176680 ACTGGAAGCATCGCCTAGTG 59.823 55.000 0.00 0.00 37.60 2.74
5103 6080 0.461548 CTGGAAGCATCGCCTAGTGA 59.538 55.000 0.00 0.00 0.00 3.41
5104 6081 0.901827 TGGAAGCATCGCCTAGTGAA 59.098 50.000 0.00 0.00 0.00 3.18
5105 6082 1.277842 TGGAAGCATCGCCTAGTGAAA 59.722 47.619 0.00 0.00 0.00 2.69
5106 6083 1.666189 GGAAGCATCGCCTAGTGAAAC 59.334 52.381 0.00 0.00 0.00 2.78
5107 6084 2.346803 GAAGCATCGCCTAGTGAAACA 58.653 47.619 0.00 0.00 41.43 2.83
5108 6085 2.472695 AGCATCGCCTAGTGAAACAA 57.527 45.000 0.00 0.00 41.43 2.83
5109 6086 2.778299 AGCATCGCCTAGTGAAACAAA 58.222 42.857 0.00 0.00 41.43 2.83
5110 6087 2.744202 AGCATCGCCTAGTGAAACAAAG 59.256 45.455 0.00 0.00 41.43 2.77
5111 6088 2.159517 GCATCGCCTAGTGAAACAAAGG 60.160 50.000 0.00 0.00 43.05 3.11
5112 6089 3.334691 CATCGCCTAGTGAAACAAAGGA 58.665 45.455 0.00 0.00 42.89 3.36
5113 6090 3.478857 TCGCCTAGTGAAACAAAGGAA 57.521 42.857 0.00 0.00 42.89 3.36
5114 6091 3.811083 TCGCCTAGTGAAACAAAGGAAA 58.189 40.909 0.00 0.00 42.89 3.13
5115 6092 4.200874 TCGCCTAGTGAAACAAAGGAAAA 58.799 39.130 0.00 0.00 42.89 2.29
5116 6093 4.274950 TCGCCTAGTGAAACAAAGGAAAAG 59.725 41.667 0.00 0.00 42.89 2.27
5117 6094 4.274950 CGCCTAGTGAAACAAAGGAAAAGA 59.725 41.667 0.00 0.00 42.89 2.52
5118 6095 5.220970 CGCCTAGTGAAACAAAGGAAAAGAA 60.221 40.000 0.00 0.00 42.89 2.52
5119 6096 5.977725 GCCTAGTGAAACAAAGGAAAAGAAC 59.022 40.000 0.00 0.00 42.89 3.01
5120 6097 6.405397 GCCTAGTGAAACAAAGGAAAAGAACA 60.405 38.462 0.00 0.00 42.89 3.18
5121 6098 7.684428 GCCTAGTGAAACAAAGGAAAAGAACAT 60.684 37.037 0.00 0.00 42.89 2.71
5122 6099 7.862873 CCTAGTGAAACAAAGGAAAAGAACATC 59.137 37.037 0.00 0.00 42.89 3.06
5123 6100 7.410120 AGTGAAACAAAGGAAAAGAACATCT 57.590 32.000 0.00 0.00 41.43 2.90
5124 6101 7.840931 AGTGAAACAAAGGAAAAGAACATCTT 58.159 30.769 0.00 0.00 41.43 2.40
5125 6102 7.976175 AGTGAAACAAAGGAAAAGAACATCTTC 59.024 33.333 0.00 0.00 41.43 2.87
5126 6103 6.972328 TGAAACAAAGGAAAAGAACATCTTCG 59.028 34.615 0.00 0.00 35.27 3.79
5127 6104 6.451064 AACAAAGGAAAAGAACATCTTCGT 57.549 33.333 0.00 0.00 35.27 3.85
5128 6105 6.451064 ACAAAGGAAAAGAACATCTTCGTT 57.549 33.333 0.00 0.00 35.27 3.85
5129 6106 6.265577 ACAAAGGAAAAGAACATCTTCGTTG 58.734 36.000 0.00 0.21 35.27 4.10
5130 6107 5.438761 AAGGAAAAGAACATCTTCGTTGG 57.561 39.130 0.00 0.00 35.27 3.77
5131 6108 3.821033 AGGAAAAGAACATCTTCGTTGGG 59.179 43.478 0.00 0.00 35.27 4.12
5132 6109 3.818773 GGAAAAGAACATCTTCGTTGGGA 59.181 43.478 0.00 0.00 35.27 4.37
5133 6110 4.277423 GGAAAAGAACATCTTCGTTGGGAA 59.723 41.667 0.00 0.00 35.27 3.97
5134 6111 4.830826 AAAGAACATCTTCGTTGGGAAC 57.169 40.909 0.00 0.00 35.27 3.62
5135 6112 3.485463 AGAACATCTTCGTTGGGAACA 57.515 42.857 0.00 0.00 39.83 3.18
5136 6113 4.204012 AAGAACATCTTCGTTGGGAACAA 58.796 39.130 0.00 0.00 39.38 2.83
5137 6114 4.642885 AAGAACATCTTCGTTGGGAACAAA 59.357 37.500 0.00 0.00 42.09 2.83
5138 6115 5.449999 AAGAACATCTTCGTTGGGAACAAAC 60.450 40.000 0.00 0.00 42.09 2.93
5139 6116 8.340321 AAGAACATCTTCGTTGGGAACAAACC 62.340 42.308 0.00 0.00 42.09 3.27
5146 6123 4.191243 GGGAACAAACCCCCTGTG 57.809 61.111 0.00 0.00 43.81 3.66
5147 6124 1.231928 GGGAACAAACCCCCTGTGT 59.768 57.895 0.00 0.00 43.81 3.72
5148 6125 0.479378 GGGAACAAACCCCCTGTGTA 59.521 55.000 0.00 0.00 43.81 2.90
5149 6126 1.076513 GGGAACAAACCCCCTGTGTAT 59.923 52.381 0.00 0.00 43.81 2.29
5150 6127 2.309458 GGGAACAAACCCCCTGTGTATA 59.691 50.000 0.00 0.00 43.81 1.47
5151 6128 3.053170 GGGAACAAACCCCCTGTGTATAT 60.053 47.826 0.00 0.00 43.81 0.86
5152 6129 4.204799 GGAACAAACCCCCTGTGTATATC 58.795 47.826 0.00 0.00 0.00 1.63
5160 6137 3.072915 CCCCCTGTGTATATCAATGCTCA 59.927 47.826 0.00 0.00 0.00 4.26
5167 6144 8.288208 CCTGTGTATATCAATGCTCAAAGATTC 58.712 37.037 0.00 0.00 0.00 2.52
5173 6150 6.600882 ATCAATGCTCAAAGATTCCTTGTT 57.399 33.333 0.00 0.00 31.91 2.83
5193 6191 6.702972 TGTTTGAGACATGTTTTGTGTTTG 57.297 33.333 0.00 0.00 39.18 2.93
5194 6192 5.636965 TGTTTGAGACATGTTTTGTGTTTGG 59.363 36.000 0.00 0.00 39.18 3.28
5218 6216 4.677673 AAAAGCAATTTTCAGTCCAGCT 57.322 36.364 0.00 0.00 0.00 4.24
5219 6217 5.789643 AAAAGCAATTTTCAGTCCAGCTA 57.210 34.783 0.00 0.00 0.00 3.32
5220 6218 4.773323 AAGCAATTTTCAGTCCAGCTAC 57.227 40.909 0.00 0.00 0.00 3.58
5221 6219 3.084786 AGCAATTTTCAGTCCAGCTACC 58.915 45.455 0.00 0.00 0.00 3.18
5222 6220 2.159517 GCAATTTTCAGTCCAGCTACCG 60.160 50.000 0.00 0.00 0.00 4.02
5313 6315 9.287373 AGTTTGATATTACCGGTGAAAGTTTTA 57.713 29.630 19.93 0.00 0.00 1.52
5342 6346 4.323569 TGGCCCTGTATACATCCAAAAA 57.676 40.909 5.91 0.00 0.00 1.94
5361 6365 6.405842 CCAAAAAGTAAGGTTTCAGACAGCTT 60.406 38.462 6.29 6.29 36.05 3.74
5362 6366 5.757850 AAAGTAAGGTTTCAGACAGCTTG 57.242 39.130 10.68 0.00 33.96 4.01
5364 6368 1.986882 AAGGTTTCAGACAGCTTGGG 58.013 50.000 0.07 0.00 30.74 4.12
5383 6387 3.117093 TGGGGGAAATGGTTGTTGAACTA 60.117 43.478 0.00 0.00 32.15 2.24
5405 6409 0.541998 GAACAAACCAGGGGAAGGGG 60.542 60.000 0.00 0.00 0.00 4.79
5437 6441 1.027357 GTACCTTATCTCGGCCGACA 58.973 55.000 27.28 16.50 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 155 0.526096 GCGGTGCGTACGAGGATTTA 60.526 55.000 21.65 0.00 0.00 1.40
233 234 5.106712 CGTATGAAGCAAAGAAGGCTGTTTA 60.107 40.000 0.00 0.00 41.66 2.01
306 307 5.385198 ACAAGGGATTTAGAAAGTTGCTGA 58.615 37.500 0.00 0.00 0.00 4.26
318 319 7.893302 AGAATGGTGTATTTGACAAGGGATTTA 59.107 33.333 0.00 0.00 40.66 1.40
332 333 4.922206 TGAAAGGCAGAGAATGGTGTATT 58.078 39.130 0.00 0.00 0.00 1.89
352 353 2.029739 CACACTGGAATTGCTGCAATGA 60.030 45.455 26.87 13.71 34.04 2.57
394 397 1.802365 GTTGTACCCGAATTGCGAAGT 59.198 47.619 0.00 0.00 44.57 3.01
609 612 3.366396 AGACAACGACATCTATCCTGGT 58.634 45.455 0.00 0.00 0.00 4.00
630 633 7.226441 TGATGGAAGACAATGAAGAAGAAGAA 58.774 34.615 0.00 0.00 0.00 2.52
802 806 2.554636 CCGCTGAGGCAAACAAGCA 61.555 57.895 0.00 0.00 38.60 3.91
862 866 6.358974 ACAATGGATGTATGATGACCGATA 57.641 37.500 0.00 0.00 41.63 2.92
1615 2096 3.693578 TCAGTCATGAAAGTTGCACAACA 59.306 39.130 15.40 0.00 36.78 3.33
1632 2162 6.431198 TTGGTTACAACTTGAAGTTCAGTC 57.569 37.500 7.75 0.11 36.03 3.51
1729 2500 5.402270 GGATCTTGTCAAAAACAACATTCCG 59.598 40.000 0.00 0.00 42.95 4.30
1735 2506 6.863126 CCATACAGGATCTTGTCAAAAACAAC 59.137 38.462 14.50 0.00 40.66 3.32
1834 2613 1.901833 CCCTTTATGCCAGGCTTTTGT 59.098 47.619 14.15 0.00 0.00 2.83
1871 2650 1.668419 GGCGATTACATTGTGGCTCT 58.332 50.000 0.00 0.00 0.00 4.09
1941 2720 2.231964 TCCTGATGCATGGTCTTTTTGC 59.768 45.455 2.46 0.00 36.91 3.68
1996 2811 7.286087 TGAACTTTACCTCTAGTGTAACAGTCA 59.714 37.037 6.99 7.67 41.43 3.41
2078 2927 7.378966 TCTGCTTACTGATACAATATGTAGGC 58.621 38.462 0.00 0.00 36.14 3.93
2079 2928 9.764363 TTTCTGCTTACTGATACAATATGTAGG 57.236 33.333 0.00 0.00 36.14 3.18
2095 2944 8.303876 TCCCATTTGAAGTTTATTTCTGCTTAC 58.696 33.333 0.00 0.00 0.00 2.34
2102 2952 7.657336 TCTGTGTCCCATTTGAAGTTTATTTC 58.343 34.615 0.00 0.00 0.00 2.17
2111 2961 4.728772 ACAAGATCTGTGTCCCATTTGAA 58.271 39.130 0.00 0.00 36.69 2.69
2315 3218 3.058293 CGCACCAACAGCTTGAAATCTTA 60.058 43.478 0.00 0.00 0.00 2.10
2343 3246 4.751767 ATCAGTTCCATCTCTTCCTGAC 57.248 45.455 0.00 0.00 32.32 3.51
2446 3351 6.834168 TGTGTCCTTTCTTTCACTTTCTTT 57.166 33.333 0.00 0.00 0.00 2.52
2475 3380 0.991355 ACCCAGGACCAACAGGTTGA 60.991 55.000 13.47 0.00 42.93 3.18
2479 3384 1.842381 GAGGACCCAGGACCAACAGG 61.842 65.000 7.93 0.00 32.53 4.00
2499 3404 0.322456 CGGCATCAACTTCCCCTTCA 60.322 55.000 0.00 0.00 0.00 3.02
2556 3461 3.502191 TCGTTTTCTTTGCTGCTTTGT 57.498 38.095 0.00 0.00 0.00 2.83
2632 3549 6.259608 ACACTAGCTGAATGCAGATGATTTAC 59.740 38.462 4.31 0.00 45.17 2.01
2818 3777 1.095807 GCCACCTGCTCGGGAAATAC 61.096 60.000 1.01 0.00 36.97 1.89
2844 3803 2.597455 CTTGTGACCCCATCCAAAGTT 58.403 47.619 0.00 0.00 0.00 2.66
3012 3971 0.600557 CGACTTCCTCTGCACTCAGT 59.399 55.000 0.00 0.00 41.10 3.41
3144 4103 1.138069 TCTTCGCTTGACTTGGACACA 59.862 47.619 0.00 0.00 0.00 3.72
3242 4201 1.490490 TCTCTTGCTTGGAACCACTGT 59.510 47.619 0.00 0.00 0.00 3.55
3453 4412 2.417339 CAGAAACCTCTGTTCGACGA 57.583 50.000 0.00 0.00 43.64 4.20
3546 4507 1.406860 GGTGGCCAAAAGCTTTGGGA 61.407 55.000 33.02 13.02 43.05 4.37
3628 4589 6.122277 TCATCGGCTCCTTATTTTTCTCATT 58.878 36.000 0.00 0.00 0.00 2.57
3672 4633 2.028567 GTCCTCATCGATCTCAATCCCC 60.029 54.545 0.00 0.00 0.00 4.81
3819 4780 1.065491 ACAAGTGTCTGCAGACCACAA 60.065 47.619 37.23 20.61 44.15 3.33
3889 4850 4.202398 GCCAATGATGTATCTTGGAGGAGA 60.202 45.833 18.76 0.00 37.31 3.71
3963 4924 3.579151 GGGTCAACTTGTAGAGGTTCTCT 59.421 47.826 2.85 2.85 43.83 3.10
3979 4940 3.199946 AGAACTGTCACAGAAAGGGTCAA 59.800 43.478 13.14 0.00 35.18 3.18
4003 4964 6.112058 GGATGAGCTTGAAAGTATCAGTCTT 58.888 40.000 0.00 0.00 39.77 3.01
4029 4990 7.545615 GTGAGAGAAAACAATTTGGACAACTTT 59.454 33.333 0.78 0.00 0.00 2.66
4030 4991 7.035612 GTGAGAGAAAACAATTTGGACAACTT 58.964 34.615 0.78 0.00 0.00 2.66
4032 4993 5.748630 GGTGAGAGAAAACAATTTGGACAAC 59.251 40.000 0.78 0.00 0.00 3.32
4036 4997 6.790232 AAAGGTGAGAGAAAACAATTTGGA 57.210 33.333 0.78 0.00 0.00 3.53
4048 5009 4.215908 ACAGTGAGTGTAAAGGTGAGAGA 58.784 43.478 0.00 0.00 37.75 3.10
4067 5028 6.094325 GTCCCTACTATCATCCTTCGATACAG 59.906 46.154 0.00 0.00 0.00 2.74
4072 5033 4.448720 TGTCCCTACTATCATCCTTCGA 57.551 45.455 0.00 0.00 0.00 3.71
4074 5035 6.153680 CCACTATGTCCCTACTATCATCCTTC 59.846 46.154 0.00 0.00 0.00 3.46
4083 5044 4.419200 AGGATGTCCACTATGTCCCTACTA 59.581 45.833 1.30 0.00 38.89 1.82
4084 5045 3.207777 AGGATGTCCACTATGTCCCTACT 59.792 47.826 1.30 0.00 38.89 2.57
4085 5046 3.577919 AGGATGTCCACTATGTCCCTAC 58.422 50.000 1.30 0.00 38.89 3.18
4130 5091 5.280215 CCAGGTGGAATAATGATCTCCCTAC 60.280 48.000 0.00 0.00 37.39 3.18
4162 5123 1.996191 CCGAAGCAGCTTTAGACACTC 59.004 52.381 9.62 0.00 0.00 3.51
4165 5126 2.037251 AGAACCGAAGCAGCTTTAGACA 59.963 45.455 9.62 0.00 0.00 3.41
4182 5143 1.727335 GGCACTAGAGTCGCAAAGAAC 59.273 52.381 0.00 0.00 0.00 3.01
4191 5152 1.032657 TCAGCCTCGGCACTAGAGTC 61.033 60.000 11.02 0.00 44.88 3.36
4197 5158 2.888447 AAAGCTCAGCCTCGGCACT 61.888 57.895 11.02 0.00 44.88 4.40
4203 5164 0.604780 TGACTGCAAAGCTCAGCCTC 60.605 55.000 7.76 3.78 35.04 4.70
4221 5182 2.237143 TGGCATTACCTCTTCTCCTGTG 59.763 50.000 0.00 0.00 40.22 3.66
4302 5263 1.831580 CCTCTTGGAGGCTTTCAAGG 58.168 55.000 16.30 7.53 43.29 3.61
4329 5290 0.373716 CCGCTTGATTACCAACGCTC 59.626 55.000 0.00 0.00 32.17 5.03
4332 5293 2.276201 TCATCCGCTTGATTACCAACG 58.724 47.619 0.00 0.00 32.80 4.10
4412 5373 2.704342 CTTTGGCCACTTGCTGGTGC 62.704 60.000 3.88 0.00 42.99 5.01
4414 5375 0.178953 ATCTTTGGCCACTTGCTGGT 60.179 50.000 3.88 0.00 42.99 4.00
4536 5506 5.887754 TGTTTATTTAGCCCTGAAGAAGGT 58.112 37.500 0.00 0.00 45.78 3.50
4544 5516 6.488006 AGATGCAGTATGTTTATTTAGCCCTG 59.512 38.462 0.00 0.00 39.31 4.45
4669 5643 8.082242 ACCAAGCATAGATGTAAGTTCAAAAAC 58.918 33.333 0.00 0.00 35.50 2.43
4683 5657 5.116084 ACATACCACAACCAAGCATAGAT 57.884 39.130 0.00 0.00 0.00 1.98
4686 5660 7.663905 GGAATATACATACCACAACCAAGCATA 59.336 37.037 0.00 0.00 0.00 3.14
4687 5661 6.490040 GGAATATACATACCACAACCAAGCAT 59.510 38.462 0.00 0.00 0.00 3.79
4690 5664 7.873719 TTGGAATATACATACCACAACCAAG 57.126 36.000 0.00 0.00 31.87 3.61
4710 5684 5.068855 TCTCAATCAAAACATGTGCTTTGGA 59.931 36.000 18.43 5.87 33.33 3.53
4711 5685 5.291178 TCTCAATCAAAACATGTGCTTTGG 58.709 37.500 18.43 7.09 33.33 3.28
4713 5687 7.496591 ACAAATCTCAATCAAAACATGTGCTTT 59.503 29.630 0.00 0.00 0.00 3.51
4714 5688 6.987992 ACAAATCTCAATCAAAACATGTGCTT 59.012 30.769 0.00 0.00 0.00 3.91
4716 5690 6.774354 ACAAATCTCAATCAAAACATGTGC 57.226 33.333 0.00 0.00 0.00 4.57
4719 5693 9.520204 GGGTATACAAATCTCAATCAAAACATG 57.480 33.333 5.01 0.00 0.00 3.21
4761 5738 6.119536 ACACCAACTGAATCTTGAAACTACA 58.880 36.000 0.00 0.00 0.00 2.74
4763 5740 7.390440 CCATACACCAACTGAATCTTGAAACTA 59.610 37.037 0.00 0.00 0.00 2.24
4767 5744 5.875224 TCCATACACCAACTGAATCTTGAA 58.125 37.500 0.00 0.00 0.00 2.69
4768 5745 5.491070 CTCCATACACCAACTGAATCTTGA 58.509 41.667 0.00 0.00 0.00 3.02
4771 5748 3.846588 ACCTCCATACACCAACTGAATCT 59.153 43.478 0.00 0.00 0.00 2.40
4773 5750 4.657814 AACCTCCATACACCAACTGAAT 57.342 40.909 0.00 0.00 0.00 2.57
4794 5771 1.682854 CTTGAGCACTTTGGCCAAGAA 59.317 47.619 19.48 3.65 40.97 2.52
4800 5777 3.255642 TCATAAACCTTGAGCACTTTGGC 59.744 43.478 0.00 0.00 0.00 4.52
5069 6046 3.243201 GCTTCCAGTTCCTGACAAAACAG 60.243 47.826 0.00 0.00 37.61 3.16
5070 6047 2.687935 GCTTCCAGTTCCTGACAAAACA 59.312 45.455 3.88 0.00 32.44 2.83
5071 6048 2.687935 TGCTTCCAGTTCCTGACAAAAC 59.312 45.455 0.00 0.00 32.44 2.43
5072 6049 3.011566 TGCTTCCAGTTCCTGACAAAA 57.988 42.857 0.00 0.00 32.44 2.44
5073 6050 2.727123 TGCTTCCAGTTCCTGACAAA 57.273 45.000 0.00 0.00 32.44 2.83
5074 6051 2.783135 GATGCTTCCAGTTCCTGACAA 58.217 47.619 0.00 0.00 32.44 3.18
5075 6052 1.338105 CGATGCTTCCAGTTCCTGACA 60.338 52.381 0.00 0.00 32.44 3.58
5076 6053 1.363744 CGATGCTTCCAGTTCCTGAC 58.636 55.000 0.00 0.00 32.44 3.51
5077 6054 0.391661 GCGATGCTTCCAGTTCCTGA 60.392 55.000 0.00 0.00 32.44 3.86
5078 6055 1.372087 GGCGATGCTTCCAGTTCCTG 61.372 60.000 0.00 0.00 0.00 3.86
5079 6056 1.078143 GGCGATGCTTCCAGTTCCT 60.078 57.895 0.00 0.00 0.00 3.36
5080 6057 0.178068 TAGGCGATGCTTCCAGTTCC 59.822 55.000 0.00 0.00 0.00 3.62
5081 6058 1.134670 ACTAGGCGATGCTTCCAGTTC 60.135 52.381 0.00 0.00 0.00 3.01
5082 6059 0.905357 ACTAGGCGATGCTTCCAGTT 59.095 50.000 0.00 0.00 0.00 3.16
5083 6060 0.176680 CACTAGGCGATGCTTCCAGT 59.823 55.000 0.00 0.00 0.00 4.00
5084 6061 0.461548 TCACTAGGCGATGCTTCCAG 59.538 55.000 0.00 0.00 0.00 3.86
5085 6062 0.901827 TTCACTAGGCGATGCTTCCA 59.098 50.000 0.00 0.00 0.00 3.53
5086 6063 1.666189 GTTTCACTAGGCGATGCTTCC 59.334 52.381 0.00 0.00 0.00 3.46
5087 6064 2.346803 TGTTTCACTAGGCGATGCTTC 58.653 47.619 0.00 0.00 0.00 3.86
5088 6065 2.472695 TGTTTCACTAGGCGATGCTT 57.527 45.000 0.00 0.00 0.00 3.91
5089 6066 2.472695 TTGTTTCACTAGGCGATGCT 57.527 45.000 0.00 0.00 0.00 3.79
5090 6067 2.159517 CCTTTGTTTCACTAGGCGATGC 60.160 50.000 0.00 0.00 0.00 3.91
5091 6068 3.334691 TCCTTTGTTTCACTAGGCGATG 58.665 45.455 0.00 0.00 0.00 3.84
5092 6069 3.695830 TCCTTTGTTTCACTAGGCGAT 57.304 42.857 0.00 0.00 0.00 4.58
5093 6070 3.478857 TTCCTTTGTTTCACTAGGCGA 57.521 42.857 0.00 0.00 0.00 5.54
5094 6071 4.274950 TCTTTTCCTTTGTTTCACTAGGCG 59.725 41.667 0.00 0.00 0.00 5.52
5095 6072 5.767816 TCTTTTCCTTTGTTTCACTAGGC 57.232 39.130 0.00 0.00 0.00 3.93
5096 6073 7.095695 TGTTCTTTTCCTTTGTTTCACTAGG 57.904 36.000 0.00 0.00 0.00 3.02
5097 6074 8.624776 AGATGTTCTTTTCCTTTGTTTCACTAG 58.375 33.333 0.00 0.00 0.00 2.57
5098 6075 8.519799 AGATGTTCTTTTCCTTTGTTTCACTA 57.480 30.769 0.00 0.00 0.00 2.74
5099 6076 7.410120 AGATGTTCTTTTCCTTTGTTTCACT 57.590 32.000 0.00 0.00 0.00 3.41
5100 6077 7.044052 CGAAGATGTTCTTTTCCTTTGTTTCAC 60.044 37.037 0.66 0.00 36.73 3.18
5101 6078 6.972328 CGAAGATGTTCTTTTCCTTTGTTTCA 59.028 34.615 0.66 0.00 36.73 2.69
5102 6079 6.972901 ACGAAGATGTTCTTTTCCTTTGTTTC 59.027 34.615 0.66 0.00 36.73 2.78
5103 6080 6.863275 ACGAAGATGTTCTTTTCCTTTGTTT 58.137 32.000 0.66 0.00 36.73 2.83
5104 6081 6.451064 ACGAAGATGTTCTTTTCCTTTGTT 57.549 33.333 0.66 0.00 36.73 2.83
5105 6082 6.265577 CAACGAAGATGTTCTTTTCCTTTGT 58.734 36.000 0.66 0.00 36.73 2.83
5106 6083 5.687285 CCAACGAAGATGTTCTTTTCCTTTG 59.313 40.000 0.66 0.00 36.73 2.77
5107 6084 5.221244 CCCAACGAAGATGTTCTTTTCCTTT 60.221 40.000 0.66 0.00 36.73 3.11
5108 6085 4.278419 CCCAACGAAGATGTTCTTTTCCTT 59.722 41.667 0.66 0.00 36.73 3.36
5109 6086 3.821033 CCCAACGAAGATGTTCTTTTCCT 59.179 43.478 0.66 0.00 36.73 3.36
5110 6087 3.818773 TCCCAACGAAGATGTTCTTTTCC 59.181 43.478 0.66 0.00 36.73 3.13
5111 6088 5.212934 GTTCCCAACGAAGATGTTCTTTTC 58.787 41.667 0.66 0.00 36.73 2.29
5112 6089 4.642885 TGTTCCCAACGAAGATGTTCTTTT 59.357 37.500 0.66 0.00 36.73 2.27
5113 6090 4.204012 TGTTCCCAACGAAGATGTTCTTT 58.796 39.130 0.66 0.00 36.73 2.52
5114 6091 3.815809 TGTTCCCAACGAAGATGTTCTT 58.184 40.909 0.66 0.00 39.87 2.52
5115 6092 3.485463 TGTTCCCAACGAAGATGTTCT 57.515 42.857 0.66 0.00 0.00 3.01
5116 6093 4.287720 GTTTGTTCCCAACGAAGATGTTC 58.712 43.478 0.00 0.00 35.52 3.18
5117 6094 3.067601 GGTTTGTTCCCAACGAAGATGTT 59.932 43.478 0.00 0.00 35.52 2.71
5118 6095 2.621526 GGTTTGTTCCCAACGAAGATGT 59.378 45.455 0.00 0.00 35.52 3.06
5119 6096 2.030274 GGGTTTGTTCCCAACGAAGATG 60.030 50.000 0.00 0.00 46.30 2.90
5120 6097 2.235891 GGGTTTGTTCCCAACGAAGAT 58.764 47.619 0.00 0.00 46.30 2.40
5121 6098 1.682740 GGGTTTGTTCCCAACGAAGA 58.317 50.000 0.00 0.00 46.30 2.87
5129 6106 0.479378 TACACAGGGGGTTTGTTCCC 59.521 55.000 0.00 0.00 46.31 3.97
5130 6107 2.597578 ATACACAGGGGGTTTGTTCC 57.402 50.000 0.00 0.00 0.00 3.62
5131 6108 4.850680 TGATATACACAGGGGGTTTGTTC 58.149 43.478 0.00 0.00 0.00 3.18
5132 6109 4.938575 TGATATACACAGGGGGTTTGTT 57.061 40.909 0.00 0.00 0.00 2.83
5133 6110 4.938575 TTGATATACACAGGGGGTTTGT 57.061 40.909 0.00 0.00 0.00 2.83
5134 6111 4.037923 GCATTGATATACACAGGGGGTTTG 59.962 45.833 0.00 0.00 0.00 2.93
5135 6112 4.079212 AGCATTGATATACACAGGGGGTTT 60.079 41.667 0.00 0.00 0.00 3.27
5136 6113 3.463329 AGCATTGATATACACAGGGGGTT 59.537 43.478 0.00 0.00 0.00 4.11
5137 6114 3.056080 AGCATTGATATACACAGGGGGT 58.944 45.455 0.00 0.00 0.00 4.95
5138 6115 3.072915 TGAGCATTGATATACACAGGGGG 59.927 47.826 0.00 0.00 0.00 5.40
5139 6116 4.356405 TGAGCATTGATATACACAGGGG 57.644 45.455 0.00 0.00 0.00 4.79
5140 6117 6.057533 TCTTTGAGCATTGATATACACAGGG 58.942 40.000 0.00 0.00 0.00 4.45
5141 6118 7.741027 ATCTTTGAGCATTGATATACACAGG 57.259 36.000 0.00 0.00 0.00 4.00
5142 6119 8.288208 GGAATCTTTGAGCATTGATATACACAG 58.712 37.037 0.00 0.00 0.00 3.66
5143 6120 7.994911 AGGAATCTTTGAGCATTGATATACACA 59.005 33.333 0.00 0.00 0.00 3.72
5144 6121 8.388484 AGGAATCTTTGAGCATTGATATACAC 57.612 34.615 0.00 0.00 0.00 2.90
5145 6122 8.843262 CAAGGAATCTTTGAGCATTGATATACA 58.157 33.333 0.00 0.00 0.00 2.29
5146 6123 8.844244 ACAAGGAATCTTTGAGCATTGATATAC 58.156 33.333 12.13 0.00 0.00 1.47
5147 6124 8.985315 ACAAGGAATCTTTGAGCATTGATATA 57.015 30.769 12.13 0.00 0.00 0.86
5148 6125 7.893124 ACAAGGAATCTTTGAGCATTGATAT 57.107 32.000 12.13 0.00 0.00 1.63
5149 6126 7.707624 AACAAGGAATCTTTGAGCATTGATA 57.292 32.000 12.13 0.00 0.00 2.15
5150 6127 6.600882 AACAAGGAATCTTTGAGCATTGAT 57.399 33.333 12.13 0.00 0.00 2.57
5151 6128 6.040729 TCAAACAAGGAATCTTTGAGCATTGA 59.959 34.615 12.13 12.16 31.72 2.57
5152 6129 6.218019 TCAAACAAGGAATCTTTGAGCATTG 58.782 36.000 12.13 10.41 31.72 2.82
5160 6137 6.966534 ACATGTCTCAAACAAGGAATCTTT 57.033 33.333 0.00 0.00 42.37 2.52
5167 6144 5.410067 ACACAAAACATGTCTCAAACAAGG 58.590 37.500 0.00 0.00 41.46 3.61
5173 6150 5.651387 TCCAAACACAAAACATGTCTCAA 57.349 34.783 0.00 0.00 41.46 3.02
5200 6198 3.084786 GGTAGCTGGACTGAAAATTGCT 58.915 45.455 0.00 0.00 0.00 3.91
5201 6199 2.159517 CGGTAGCTGGACTGAAAATTGC 60.160 50.000 0.00 0.00 0.00 3.56
5209 6207 1.544691 AGTTGTACGGTAGCTGGACTG 59.455 52.381 0.00 0.00 0.00 3.51
5218 6216 6.699366 TGTCAATATCCAAAGTTGTACGGTA 58.301 36.000 0.00 0.00 0.00 4.02
5219 6217 5.553123 TGTCAATATCCAAAGTTGTACGGT 58.447 37.500 0.00 0.00 0.00 4.83
5220 6218 6.072948 TGTTGTCAATATCCAAAGTTGTACGG 60.073 38.462 0.00 0.00 0.00 4.02
5221 6219 6.893759 TGTTGTCAATATCCAAAGTTGTACG 58.106 36.000 0.00 0.00 0.00 3.67
5222 6220 9.522804 TTTTGTTGTCAATATCCAAAGTTGTAC 57.477 29.630 0.00 0.00 33.32 2.90
5342 6346 3.496870 CCCAAGCTGTCTGAAACCTTACT 60.497 47.826 0.00 0.00 0.00 2.24
5361 6365 2.043227 GTTCAACAACCATTTCCCCCA 58.957 47.619 0.00 0.00 0.00 4.96
5362 6366 2.325484 AGTTCAACAACCATTTCCCCC 58.675 47.619 0.00 0.00 32.22 5.40
5364 6368 6.399639 TCTTTAGTTCAACAACCATTTCCC 57.600 37.500 0.00 0.00 32.22 3.97
5383 6387 2.677914 CCTTCCCCTGGTTTGTTCTTT 58.322 47.619 0.00 0.00 0.00 2.52
5405 6409 1.954035 AAGGTACCCTGTTCTCTCCC 58.046 55.000 8.74 0.00 32.13 4.30
5425 6429 3.893763 CGCTCTGTCGGCCGAGAT 61.894 66.667 31.97 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.