Multiple sequence alignment - TraesCS4A01G064800

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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 TraesCS4A01G064800 chr4A 100.000 3504 0 0 1 3504 61619037 61615534 0.000000e+00 6471.0
1 TraesCS4A01G064800 chr4A 100.000 815 0 0 3664 4478 61615374 61614560 0.000000e+00 1506.0
2 TraesCS4A01G064800 chr4A 95.238 42 2 0 1437 1478 465547924 465547883 2.890000e-07 67.6
3 TraesCS4A01G064800 chr4B 96.830 2713 74 6 799 3504 500871046 500868339 0.000000e+00 4523.0
4 TraesCS4A01G064800 chr4B 83.099 568 83 10 3 566 500873266 500872708 5.170000e-139 505.0
5 TraesCS4A01G064800 chr4B 82.752 487 64 12 4000 4478 500867869 500867395 2.490000e-112 416.0
6 TraesCS4A01G064800 chr4B 95.238 42 2 0 1437 1478 172377818 172377859 2.890000e-07 67.6
7 TraesCS4A01G064800 chr4B 92.857 42 3 0 1437 1478 630482113 630482154 1.340000e-05 62.1
8 TraesCS4A01G064800 chr4D 96.199 2710 89 8 806 3504 404113618 404110912 0.000000e+00 4421.0
9 TraesCS4A01G064800 chr4D 82.132 666 79 18 3822 4478 404110875 404110241 6.590000e-148 534.0
10 TraesCS4A01G064800 chr3B 79.516 620 102 21 2522 3124 673170831 673170220 6.930000e-113 418.0
11 TraesCS4A01G064800 chr3A 78.333 660 116 22 2474 3115 647613098 647613748 6.980000e-108 401.0
12 TraesCS4A01G064800 chr7D 77.570 535 103 10 2594 3124 566015597 566016118 1.560000e-79 307.0
13 TraesCS4A01G064800 chr7D 74.583 539 114 17 2593 3124 565645263 565645785 9.760000e-52 215.0
14 TraesCS4A01G064800 chr7B 75.161 620 133 14 2511 3124 616821758 616821154 5.710000e-69 272.0
15 TraesCS4A01G064800 chr7A 76.306 536 110 10 2593 3124 652288062 652288584 2.050000e-68 270.0
16 TraesCS4A01G064800 chr7A 78.125 320 70 0 2805 3124 652339794 652340113 2.110000e-48 204.0
17 TraesCS4A01G064800 chr6A 81.818 187 31 3 4294 4478 91368352 91368537 2.160000e-33 154.0


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 TraesCS4A01G064800 chr4A 61614560 61619037 4477 True 3988.500000 6471 100.000000 1 4478 2 chr4A.!!$R2 4477
1 TraesCS4A01G064800 chr4B 500867395 500873266 5871 True 1814.666667 4523 87.560333 3 4478 3 chr4B.!!$R1 4475
2 TraesCS4A01G064800 chr4D 404110241 404113618 3377 True 2477.500000 4421 89.165500 806 4478 2 chr4D.!!$R1 3672
3 TraesCS4A01G064800 chr3B 673170220 673170831 611 True 418.000000 418 79.516000 2522 3124 1 chr3B.!!$R1 602
4 TraesCS4A01G064800 chr3A 647613098 647613748 650 False 401.000000 401 78.333000 2474 3115 1 chr3A.!!$F1 641
5 TraesCS4A01G064800 chr7D 566015597 566016118 521 False 307.000000 307 77.570000 2594 3124 1 chr7D.!!$F2 530
6 TraesCS4A01G064800 chr7D 565645263 565645785 522 False 215.000000 215 74.583000 2593 3124 1 chr7D.!!$F1 531
7 TraesCS4A01G064800 chr7B 616821154 616821758 604 True 272.000000 272 75.161000 2511 3124 1 chr7B.!!$R1 613
8 TraesCS4A01G064800 chr7A 652288062 652288584 522 False 270.000000 270 76.306000 2593 3124 1 chr7A.!!$F1 531

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
124 125 0.178987 TCCTCTCCTAGCCCGACATC 60.179 60.000 0.00 0.0 0.00 3.06 F
129 130 0.259065 TCCTAGCCCGACATCAGTCT 59.741 55.000 0.00 0.0 42.73 3.24 F
522 524 0.323725 GAAGGGAGATTGCCAAGCCA 60.324 55.000 0.00 0.0 0.00 4.75 F
1016 2459 1.074623 CCATGCTCCTCCTCCTCCT 60.075 63.158 0.00 0.0 0.00 3.69 F
1017 2460 1.120795 CCATGCTCCTCCTCCTCCTC 61.121 65.000 0.00 0.0 0.00 3.71 F
2226 3669 0.685097 AGCTCGTTAACTTGAGGGCA 59.315 50.000 11.13 0.0 32.78 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1014 2457 0.032217 AGAAGAGCAGGAGGAGGAGG 60.032 60.000 0.00 0.0 0.00 4.30 R
1016 2459 0.032615 GGAGAAGAGCAGGAGGAGGA 60.033 60.000 0.00 0.0 0.00 3.71 R
1972 3415 0.832135 TTCCACTCTTGCTCCGACCT 60.832 55.000 0.00 0.0 0.00 3.85 R
2226 3669 1.276421 CCACCTTGGTCAATCGAGAGT 59.724 52.381 0.00 0.0 31.35 3.24 R
2271 3714 3.554692 GCGACGCGGAGGTGAATG 61.555 66.667 12.47 0.0 0.00 2.67 R
3851 5311 0.038159 ACTGCTCCTTCGAACTTCCG 60.038 55.000 0.00 0.0 0.00 4.30 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
45 46 4.506255 CCCGGGCATCCTTGTCCC 62.506 72.222 8.08 0.00 45.40 4.46
90 91 1.597027 GACACACCAACCCCGACAG 60.597 63.158 0.00 0.00 0.00 3.51
94 95 0.838608 ACACCAACCCCGACAGTAAA 59.161 50.000 0.00 0.00 0.00 2.01
97 98 1.770061 ACCAACCCCGACAGTAAAAGA 59.230 47.619 0.00 0.00 0.00 2.52
108 109 4.715713 GACAGTAAAAGACCAACCTTCCT 58.284 43.478 0.00 0.00 0.00 3.36
119 120 0.688087 AACCTTCCTCTCCTAGCCCG 60.688 60.000 0.00 0.00 0.00 6.13
124 125 0.178987 TCCTCTCCTAGCCCGACATC 60.179 60.000 0.00 0.00 0.00 3.06
129 130 0.259065 TCCTAGCCCGACATCAGTCT 59.741 55.000 0.00 0.00 42.73 3.24
144 145 0.396417 AGTCTCCGGATCTGGGTCAG 60.396 60.000 20.82 10.85 0.00 3.51
153 154 0.842030 ATCTGGGTCAGCACCTCCAA 60.842 55.000 0.00 0.00 43.22 3.53
154 155 1.302832 CTGGGTCAGCACCTCCAAC 60.303 63.158 0.00 0.00 43.22 3.77
158 159 0.389948 GGTCAGCACCTCCAACGTAG 60.390 60.000 0.00 0.00 40.00 3.51
169 170 0.872388 CCAACGTAGGAGGCAACAAC 59.128 55.000 0.00 0.00 41.41 3.32
182 183 1.304381 AACAACGCATGCATCCCCT 60.304 52.632 19.57 0.00 0.00 4.79
185 186 1.152963 AACGCATGCATCCCCTACC 60.153 57.895 19.57 0.00 0.00 3.18
193 194 1.075525 CATCCCCTACCAGTCCCGA 60.076 63.158 0.00 0.00 0.00 5.14
194 195 1.075450 ATCCCCTACCAGTCCCGAC 60.075 63.158 0.00 0.00 0.00 4.79
195 196 2.600735 ATCCCCTACCAGTCCCGACC 62.601 65.000 0.00 0.00 0.00 4.79
201 202 2.430704 TACCAGTCCCGACCGACCTT 62.431 60.000 0.00 0.00 32.91 3.50
223 224 1.448013 GACACGACCCTAAGCCTGC 60.448 63.158 0.00 0.00 0.00 4.85
225 226 2.606519 ACGACCCTAAGCCTGCCA 60.607 61.111 0.00 0.00 0.00 4.92
264 265 2.162408 GAGCTTGCACAATACCAAGTCC 59.838 50.000 0.00 0.00 40.34 3.85
265 266 1.885887 GCTTGCACAATACCAAGTCCA 59.114 47.619 0.00 0.00 40.34 4.02
291 292 3.660111 GGTGCCACACCGCAAGAC 61.660 66.667 0.15 0.00 44.95 3.01
302 303 2.040544 CGCAAGACGGGGAAGCATT 61.041 57.895 0.00 0.00 43.02 3.56
305 306 0.804989 CAAGACGGGGAAGCATTGTC 59.195 55.000 0.00 0.00 0.00 3.18
323 324 1.528309 CAGGACAACCACCACACCC 60.528 63.158 0.00 0.00 38.94 4.61
342 343 0.933047 CGCGAAGACAACACTCACGA 60.933 55.000 0.00 0.00 0.00 4.35
346 347 2.408050 GAAGACAACACTCACGAGCAT 58.592 47.619 0.00 0.00 0.00 3.79
373 374 3.458163 CGAGCCCAACCTCGCCTA 61.458 66.667 0.00 0.00 46.69 3.93
375 376 2.284699 AGCCCAACCTCGCCTACT 60.285 61.111 0.00 0.00 0.00 2.57
377 378 2.656069 GCCCAACCTCGCCTACTCA 61.656 63.158 0.00 0.00 0.00 3.41
390 391 1.683917 CCTACTCAGAGAATCCACCCG 59.316 57.143 3.79 0.00 33.66 5.28
391 392 2.656002 CTACTCAGAGAATCCACCCGA 58.344 52.381 3.79 0.00 33.66 5.14
392 393 2.166907 ACTCAGAGAATCCACCCGAT 57.833 50.000 3.79 0.00 33.66 4.18
393 394 2.035632 ACTCAGAGAATCCACCCGATC 58.964 52.381 3.79 0.00 33.66 3.69
394 395 2.315176 CTCAGAGAATCCACCCGATCT 58.685 52.381 0.00 0.00 33.66 2.75
395 396 2.034878 TCAGAGAATCCACCCGATCTG 58.965 52.381 0.00 0.00 33.66 2.90
396 397 0.755686 AGAGAATCCACCCGATCTGC 59.244 55.000 0.00 0.00 33.66 4.26
398 399 0.692419 AGAATCCACCCGATCTGCCT 60.692 55.000 0.00 0.00 0.00 4.75
400 401 2.032860 AATCCACCCGATCTGCCTCG 62.033 60.000 0.00 0.00 38.37 4.63
424 426 2.832201 GATCTGGCCTGCCCAAGC 60.832 66.667 3.32 0.00 44.81 4.01
445 447 4.020128 AGCACAAACCCTAGGTTAGAGAAG 60.020 45.833 8.29 0.00 46.20 2.85
447 449 4.020128 CACAAACCCTAGGTTAGAGAAGCT 60.020 45.833 8.29 0.00 46.20 3.74
449 451 2.112190 ACCCTAGGTTAGAGAAGCTGC 58.888 52.381 8.29 0.00 43.25 5.25
451 453 2.111384 CCTAGGTTAGAGAAGCTGCCA 58.889 52.381 0.00 0.00 43.25 4.92
452 454 2.703007 CCTAGGTTAGAGAAGCTGCCAT 59.297 50.000 0.00 0.00 43.25 4.40
453 455 3.135530 CCTAGGTTAGAGAAGCTGCCATT 59.864 47.826 0.00 0.00 43.25 3.16
454 456 2.996631 AGGTTAGAGAAGCTGCCATTG 58.003 47.619 0.00 0.00 41.84 2.82
459 461 2.505557 GAAGCTGCCATTGTGCGC 60.506 61.111 0.00 0.00 0.00 6.09
463 465 2.400798 CTGCCATTGTGCGCGTAG 59.599 61.111 8.43 0.00 0.00 3.51
495 497 1.807981 CGCACGCTACCAATTCCGA 60.808 57.895 0.00 0.00 0.00 4.55
496 498 1.713830 GCACGCTACCAATTCCGAC 59.286 57.895 0.00 0.00 0.00 4.79
518 520 1.340017 CGGAAGAAGGGAGATTGCCAA 60.340 52.381 0.00 0.00 0.00 4.52
522 524 0.323725 GAAGGGAGATTGCCAAGCCA 60.324 55.000 0.00 0.00 0.00 4.75
526 528 3.056313 GAGATTGCCAAGCCACCGC 62.056 63.158 0.00 0.00 0.00 5.68
581 610 2.656646 CCGTAGTCAGCACCAGCA 59.343 61.111 0.00 0.00 45.49 4.41
582 611 1.738099 CCGTAGTCAGCACCAGCAC 60.738 63.158 0.00 0.00 45.49 4.40
584 613 2.048222 TAGTCAGCACCAGCACGC 60.048 61.111 0.00 0.00 45.49 5.34
601 630 4.807039 CACCGCCGTCCTAACCCG 62.807 72.222 0.00 0.00 0.00 5.28
619 648 1.379309 GTTGCGGCCCCCAAGATAA 60.379 57.895 0.00 0.00 0.00 1.75
621 650 1.858739 TTGCGGCCCCCAAGATAACT 61.859 55.000 0.00 0.00 0.00 2.24
623 652 1.607612 CGGCCCCCAAGATAACTGT 59.392 57.895 0.00 0.00 0.00 3.55
633 662 1.883084 GATAACTGTCCGCGGCCAG 60.883 63.158 32.91 32.91 34.82 4.85
661 1909 4.680237 TGCCGCCGTTCCTCAGTG 62.680 66.667 0.00 0.00 0.00 3.66
683 1931 2.386661 TCTGCTTCAATCCGGTCTTC 57.613 50.000 0.00 0.00 0.00 2.87
699 1947 5.292101 CCGGTCTTCATTCATTTGTAGAGTC 59.708 44.000 0.00 0.00 0.00 3.36
704 1952 8.868916 GTCTTCATTCATTTGTAGAGTCTTCTC 58.131 37.037 0.00 0.00 40.70 2.87
726 1974 7.004086 TCTCTGTAACTGGAATTTTGTGGATT 58.996 34.615 0.00 0.00 0.00 3.01
774 2022 2.017049 GGAGGAATTGACATCCAACGG 58.983 52.381 0.00 0.00 40.01 4.44
790 2038 3.372954 CAACGGTCCTGATAGAATCGAC 58.627 50.000 0.00 0.00 0.00 4.20
846 2278 7.512992 TCCTTAGGCATTCCAAAAATGAAAAA 58.487 30.769 0.00 0.00 33.74 1.94
863 2299 9.904198 AAATGAAAAATATAGATTTTGGTGGGG 57.096 29.630 8.74 0.00 43.10 4.96
926 2369 1.270358 CCCAGGCTCGGCTACTTATTC 60.270 57.143 0.00 0.00 0.00 1.75
932 2375 2.329379 CTCGGCTACTTATTCATCGGC 58.671 52.381 0.00 0.00 0.00 5.54
963 2406 3.758554 AGTGCAGACAAACCAATCATACC 59.241 43.478 0.00 0.00 0.00 2.73
1014 2457 1.694133 CCACCATGCTCCTCCTCCTC 61.694 65.000 0.00 0.00 0.00 3.71
1015 2458 1.383803 ACCATGCTCCTCCTCCTCC 60.384 63.158 0.00 0.00 0.00 4.30
1016 2459 1.074623 CCATGCTCCTCCTCCTCCT 60.075 63.158 0.00 0.00 0.00 3.69
1017 2460 1.120795 CCATGCTCCTCCTCCTCCTC 61.121 65.000 0.00 0.00 0.00 3.71
1138 2581 3.631127 GCGAATTCGAGCTCGGCC 61.631 66.667 33.98 19.11 43.02 6.13
1290 2733 4.521062 ATCCACGGCGAGCTGCTC 62.521 66.667 19.53 19.53 45.43 4.26
1301 2744 1.381056 AGCTGCTCCTCCTCACGAT 60.381 57.895 0.00 0.00 0.00 3.73
1941 3384 4.954970 AGCAACACCACCAGCCCG 62.955 66.667 0.00 0.00 0.00 6.13
2094 3537 2.586245 CAGCTCCCGAATGGCTCA 59.414 61.111 0.00 0.00 33.74 4.26
2161 3604 1.467035 GCTTGAAAGATTGCTCCTGCG 60.467 52.381 0.00 0.00 43.34 5.18
2226 3669 0.685097 AGCTCGTTAACTTGAGGGCA 59.315 50.000 11.13 0.00 32.78 5.36
2498 3941 0.038251 CTGCTGCTGTTCGACTACCA 60.038 55.000 0.00 0.00 0.00 3.25
2544 3987 2.035155 TCGGAGAAGCTCGGTGGA 59.965 61.111 0.00 0.00 33.47 4.02
3441 4901 6.051717 AGGTGAACAGGATGAATTCTATTCG 58.948 40.000 7.05 0.00 39.69 3.34
3692 5152 9.369904 GTGAATATGAAATGCTTGTATGGTTTT 57.630 29.630 0.00 0.00 0.00 2.43
3693 5153 9.941325 TGAATATGAAATGCTTGTATGGTTTTT 57.059 25.926 0.00 0.00 0.00 1.94
3716 5176 8.658840 TTTTTAGGGGAATGCTTGTATAGTTT 57.341 30.769 0.00 0.00 0.00 2.66
3717 5177 7.639113 TTTAGGGGAATGCTTGTATAGTTTG 57.361 36.000 0.00 0.00 0.00 2.93
3718 5178 5.450818 AGGGGAATGCTTGTATAGTTTGA 57.549 39.130 0.00 0.00 0.00 2.69
3719 5179 5.826643 AGGGGAATGCTTGTATAGTTTGAA 58.173 37.500 0.00 0.00 0.00 2.69
3720 5180 5.888161 AGGGGAATGCTTGTATAGTTTGAAG 59.112 40.000 0.00 0.00 0.00 3.02
3721 5181 5.067805 GGGGAATGCTTGTATAGTTTGAAGG 59.932 44.000 0.00 0.00 0.00 3.46
3722 5182 5.652452 GGGAATGCTTGTATAGTTTGAAGGT 59.348 40.000 0.00 0.00 0.00 3.50
3723 5183 6.826741 GGGAATGCTTGTATAGTTTGAAGGTA 59.173 38.462 0.00 0.00 0.00 3.08
3724 5184 7.201705 GGGAATGCTTGTATAGTTTGAAGGTAC 60.202 40.741 0.00 0.00 0.00 3.34
3726 5186 8.494016 AATGCTTGTATAGTTTGAAGGTACTC 57.506 34.615 0.00 0.00 38.49 2.59
3727 5187 6.403878 TGCTTGTATAGTTTGAAGGTACTCC 58.596 40.000 0.00 0.00 38.49 3.85
3728 5188 5.816258 GCTTGTATAGTTTGAAGGTACTCCC 59.184 44.000 0.00 0.00 38.49 4.30
3730 5190 6.786967 TGTATAGTTTGAAGGTACTCCCTC 57.213 41.667 0.00 0.00 45.47 4.30
3731 5191 6.500336 TGTATAGTTTGAAGGTACTCCCTCT 58.500 40.000 0.00 0.00 45.47 3.69
3732 5192 5.941555 ATAGTTTGAAGGTACTCCCTCTG 57.058 43.478 0.00 0.00 45.47 3.35
3733 5193 3.588569 AGTTTGAAGGTACTCCCTCTGT 58.411 45.455 0.00 0.00 45.47 3.41
3734 5194 4.748701 AGTTTGAAGGTACTCCCTCTGTA 58.251 43.478 0.00 0.00 45.47 2.74
3735 5195 4.773149 AGTTTGAAGGTACTCCCTCTGTAG 59.227 45.833 0.00 0.00 45.47 2.74
3736 5196 4.669866 TTGAAGGTACTCCCTCTGTAGA 57.330 45.455 0.00 0.00 45.47 2.59
3737 5197 4.237976 TGAAGGTACTCCCTCTGTAGAG 57.762 50.000 1.86 1.86 45.47 2.43
3738 5198 3.850774 TGAAGGTACTCCCTCTGTAGAGA 59.149 47.826 10.40 0.00 45.47 3.10
3739 5199 4.291513 TGAAGGTACTCCCTCTGTAGAGAA 59.708 45.833 10.40 0.00 45.47 2.87
3740 5200 4.949966 AGGTACTCCCTCTGTAGAGAAA 57.050 45.455 10.40 0.00 40.71 2.52
3741 5201 5.475398 AGGTACTCCCTCTGTAGAGAAAT 57.525 43.478 10.40 0.00 40.71 2.17
3742 5202 6.593759 AGGTACTCCCTCTGTAGAGAAATA 57.406 41.667 10.40 0.00 40.71 1.40
3743 5203 7.169287 AGGTACTCCCTCTGTAGAGAAATAT 57.831 40.000 10.40 0.00 40.71 1.28
3744 5204 8.290463 AGGTACTCCCTCTGTAGAGAAATATA 57.710 38.462 10.40 0.00 40.71 0.86
3745 5205 8.907050 AGGTACTCCCTCTGTAGAGAAATATAT 58.093 37.037 10.40 0.00 40.71 0.86
3803 5263 6.396450 ACAGAGAGTAGTTAATTTTCGACCC 58.604 40.000 0.00 0.00 0.00 4.46
3804 5264 5.515626 CAGAGAGTAGTTAATTTTCGACCCG 59.484 44.000 0.00 0.00 0.00 5.28
3805 5265 4.179298 AGAGTAGTTAATTTTCGACCCGC 58.821 43.478 0.00 0.00 0.00 6.13
3806 5266 3.928375 GAGTAGTTAATTTTCGACCCGCA 59.072 43.478 0.00 0.00 0.00 5.69
3807 5267 4.317488 AGTAGTTAATTTTCGACCCGCAA 58.683 39.130 0.00 0.00 0.00 4.85
3808 5268 4.756135 AGTAGTTAATTTTCGACCCGCAAA 59.244 37.500 0.00 0.00 0.00 3.68
3809 5269 4.571372 AGTTAATTTTCGACCCGCAAAA 57.429 36.364 0.00 0.00 0.00 2.44
3810 5270 4.934515 AGTTAATTTTCGACCCGCAAAAA 58.065 34.783 0.00 0.00 0.00 1.94
3851 5311 1.491563 GTTGTGTGCGTCGGATCAC 59.508 57.895 10.79 10.79 0.00 3.06
3886 5346 2.835027 GCAGTGCCCTGGTAGTAATAC 58.165 52.381 2.85 0.00 39.22 1.89
3887 5347 2.434702 GCAGTGCCCTGGTAGTAATACT 59.565 50.000 2.85 0.00 39.22 2.12
3888 5348 3.492829 GCAGTGCCCTGGTAGTAATACTC 60.493 52.174 2.85 0.00 39.22 2.59
3894 5354 5.010314 TGCCCTGGTAGTAATACTCGTATTG 59.990 44.000 11.51 0.00 36.52 1.90
3927 5388 8.387813 TGGAGTACTATGTTGAATTTTTAGGGT 58.612 33.333 0.00 0.00 0.00 4.34
3928 5389 8.674607 GGAGTACTATGTTGAATTTTTAGGGTG 58.325 37.037 0.00 0.00 0.00 4.61
3930 5391 9.582648 AGTACTATGTTGAATTTTTAGGGTGTT 57.417 29.630 0.00 0.00 0.00 3.32
3932 5393 8.245195 ACTATGTTGAATTTTTAGGGTGTTGT 57.755 30.769 0.00 0.00 0.00 3.32
3933 5394 8.141268 ACTATGTTGAATTTTTAGGGTGTTGTG 58.859 33.333 0.00 0.00 0.00 3.33
3934 5395 5.665459 TGTTGAATTTTTAGGGTGTTGTGG 58.335 37.500 0.00 0.00 0.00 4.17
3935 5396 5.422331 TGTTGAATTTTTAGGGTGTTGTGGA 59.578 36.000 0.00 0.00 0.00 4.02
3936 5397 5.782893 TGAATTTTTAGGGTGTTGTGGAG 57.217 39.130 0.00 0.00 0.00 3.86
3937 5398 5.450453 TGAATTTTTAGGGTGTTGTGGAGA 58.550 37.500 0.00 0.00 0.00 3.71
3938 5399 6.074648 TGAATTTTTAGGGTGTTGTGGAGAT 58.925 36.000 0.00 0.00 0.00 2.75
3939 5400 6.553100 TGAATTTTTAGGGTGTTGTGGAGATT 59.447 34.615 0.00 0.00 0.00 2.40
3940 5401 6.590234 ATTTTTAGGGTGTTGTGGAGATTC 57.410 37.500 0.00 0.00 0.00 2.52
3941 5402 3.713826 TTAGGGTGTTGTGGAGATTCC 57.286 47.619 0.00 0.00 36.96 3.01
3942 5403 1.747444 AGGGTGTTGTGGAGATTCCT 58.253 50.000 0.00 0.00 37.46 3.36
3943 5404 1.352352 AGGGTGTTGTGGAGATTCCTG 59.648 52.381 0.00 0.00 37.46 3.86
3944 5405 1.351017 GGGTGTTGTGGAGATTCCTGA 59.649 52.381 0.00 0.00 37.46 3.86
3984 5445 4.666512 ACTGCATTACATTTCCTTGGTCT 58.333 39.130 0.00 0.00 0.00 3.85
3991 5452 7.095649 GCATTACATTTCCTTGGTCTTGTTTTC 60.096 37.037 0.00 0.00 0.00 2.29
3998 5459 3.119849 CCTTGGTCTTGTTTTCATAGGCG 60.120 47.826 0.00 0.00 0.00 5.52
4049 5784 4.273318 GAGCATCTACAATCAAACCCCTT 58.727 43.478 0.00 0.00 0.00 3.95
4057 5792 5.023514 ACAATCAAACCCCTTAAATCCCT 57.976 39.130 0.00 0.00 0.00 4.20
4064 5799 6.860480 TCAAACCCCTTAAATCCCTCCTATAT 59.140 38.462 0.00 0.00 0.00 0.86
4069 5804 4.384208 CCTTAAATCCCTCCTATATGGCCG 60.384 50.000 0.00 0.00 35.26 6.13
4071 5806 0.983378 ATCCCTCCTATATGGCCGGC 60.983 60.000 21.18 21.18 35.26 6.13
4073 5808 1.613630 CCTCCTATATGGCCGGCCT 60.614 63.158 43.34 30.54 36.94 5.19
4074 5809 1.617947 CCTCCTATATGGCCGGCCTC 61.618 65.000 43.34 21.51 36.94 4.70
4075 5810 1.949847 CTCCTATATGGCCGGCCTCG 61.950 65.000 43.34 25.72 36.94 4.63
4076 5811 2.283529 CCTATATGGCCGGCCTCGT 61.284 63.158 43.34 30.52 36.94 4.18
4078 5813 2.543687 CTATATGGCCGGCCTCGTCG 62.544 65.000 43.34 25.53 36.94 5.12
4088 5825 4.813526 CCTCGTCGCCGTGACTCG 62.814 72.222 10.27 0.00 45.87 4.18
4103 5840 4.458829 TCGGTCAGAGCCCCGGAT 62.459 66.667 0.73 0.00 44.32 4.18
4119 5859 4.508128 ATGCCGCCGTACGTCCTG 62.508 66.667 15.21 0.00 41.42 3.86
4134 5874 0.188587 TCCTGCTCCTCCGGTCATAT 59.811 55.000 0.00 0.00 0.00 1.78
4146 5886 2.457366 GGTCATATACCTTGCCCTCG 57.543 55.000 0.00 0.00 45.75 4.63
4154 5894 0.182775 ACCTTGCCCTCGAAGTGTTT 59.817 50.000 0.00 0.00 0.00 2.83
4155 5895 0.875059 CCTTGCCCTCGAAGTGTTTC 59.125 55.000 0.00 0.00 0.00 2.78
4222 5964 9.552114 CAATGAATTTGTCAGATGAGTAGTTTC 57.448 33.333 0.00 0.00 40.43 2.78
4227 5969 9.512588 AATTTGTCAGATGAGTAGTTTCAGAAT 57.487 29.630 0.00 0.00 0.00 2.40
4274 6016 0.989890 GAGTTTGTCGATTCGTCGGG 59.010 55.000 5.89 0.00 0.00 5.14
4276 6018 0.712222 GTTTGTCGATTCGTCGGGTC 59.288 55.000 5.89 0.00 0.00 4.46
4283 6025 1.399440 CGATTCGTCGGGTCAAGAGTA 59.601 52.381 0.00 0.00 0.00 2.59
4336 6078 6.599638 GTGGAGCATATTCTAAACTTCAAGGT 59.400 38.462 0.00 0.00 0.00 3.50
4340 6082 7.752695 AGCATATTCTAAACTTCAAGGTTTCG 58.247 34.615 0.00 0.00 39.66 3.46
4349 6091 2.631160 TCAAGGTTTCGCTCAAAGGA 57.369 45.000 0.00 0.00 0.00 3.36
4350 6092 2.494059 TCAAGGTTTCGCTCAAAGGAG 58.506 47.619 0.00 0.00 44.33 3.69
4372 6114 6.674419 GGAGGGAGAATTATACACCAGGATAT 59.326 42.308 0.00 0.00 0.00 1.63
4375 6117 7.739444 AGGGAGAATTATACACCAGGATATGAA 59.261 37.037 0.00 0.00 0.00 2.57
4378 6120 6.874134 AGAATTATACACCAGGATATGAACGC 59.126 38.462 0.00 0.00 0.00 4.84
4386 6128 1.230635 GGATATGAACGCTGGCGCAT 61.231 55.000 10.83 12.88 44.19 4.73
4388 6130 2.121564 ATATGAACGCTGGCGCATGC 62.122 55.000 10.83 7.91 44.19 4.06
4405 6147 0.035317 TGCCTGCTGTACAAGGACTG 59.965 55.000 16.40 0.00 0.00 3.51
4415 6157 2.736670 ACAAGGACTGCTTTCAACCT 57.263 45.000 0.00 0.00 32.85 3.50
4416 6158 2.301346 ACAAGGACTGCTTTCAACCTG 58.699 47.619 0.00 0.00 32.21 4.00
4418 6160 2.551459 CAAGGACTGCTTTCAACCTGAG 59.449 50.000 0.00 0.00 32.21 3.35
4420 6162 0.877743 GACTGCTTTCAACCTGAGCC 59.122 55.000 0.00 0.00 35.59 4.70
4424 6166 2.101249 CTGCTTTCAACCTGAGCCAAAA 59.899 45.455 0.00 0.00 35.59 2.44
4437 6179 2.767960 GAGCCAAAATTCCATGATGGGT 59.232 45.455 12.26 0.00 44.01 4.51
4438 6180 3.183801 AGCCAAAATTCCATGATGGGTT 58.816 40.909 12.26 4.45 38.66 4.11
4444 6186 4.470334 AATTCCATGATGGGTTTTTCCG 57.530 40.909 12.26 0.00 38.32 4.30
4445 6187 2.889170 TCCATGATGGGTTTTTCCGA 57.111 45.000 12.26 0.00 38.32 4.55
4450 6192 1.202663 TGATGGGTTTTTCCGACGTCA 60.203 47.619 17.16 0.00 37.00 4.35
4455 6197 2.207590 GGTTTTTCCGACGTCACTTCT 58.792 47.619 17.16 0.00 0.00 2.85
4462 6204 1.618861 CGACGTCACTTCTGGATGAC 58.381 55.000 17.16 0.00 41.54 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.740822 ACAAGGATGCCCGGGTGC 62.741 66.667 24.63 8.70 37.58 5.01
26 27 2.438434 GACAAGGATGCCCGGGTG 60.438 66.667 24.63 14.02 37.58 4.61
27 28 3.728373 GGACAAGGATGCCCGGGT 61.728 66.667 24.63 1.57 37.58 5.28
31 32 2.190578 CTCGGGACAAGGATGCCC 59.809 66.667 0.00 0.00 38.67 5.36
33 34 4.522971 GTCTCGGGACAAGGATGC 57.477 61.111 11.49 0.00 41.75 3.91
45 46 4.082523 ATGGGTGGCGGTGTCTCG 62.083 66.667 0.00 0.00 0.00 4.04
46 47 2.125106 GATGGGTGGCGGTGTCTC 60.125 66.667 0.00 0.00 0.00 3.36
53 54 3.716195 TGAGGTGGATGGGTGGCG 61.716 66.667 0.00 0.00 0.00 5.69
90 91 4.041815 AGGAGAGGAAGGTTGGTCTTTTAC 59.958 45.833 0.00 0.00 0.00 2.01
94 95 2.424684 AGGAGAGGAAGGTTGGTCTT 57.575 50.000 0.00 0.00 0.00 3.01
97 98 1.574263 GCTAGGAGAGGAAGGTTGGT 58.426 55.000 0.00 0.00 0.00 3.67
108 109 0.259065 ACTGATGTCGGGCTAGGAGA 59.741 55.000 0.00 0.00 0.00 3.71
119 120 1.339610 CCAGATCCGGAGACTGATGTC 59.660 57.143 30.45 14.37 43.22 3.06
124 125 0.684479 TGACCCAGATCCGGAGACTG 60.684 60.000 25.26 25.26 0.00 3.51
129 130 2.038813 TGCTGACCCAGATCCGGA 59.961 61.111 6.61 6.61 32.44 5.14
153 154 1.666872 GCGTTGTTGCCTCCTACGT 60.667 57.895 0.00 0.00 34.89 3.57
154 155 1.019278 ATGCGTTGTTGCCTCCTACG 61.019 55.000 0.00 0.00 35.48 3.51
158 159 2.126346 GCATGCGTTGTTGCCTCC 60.126 61.111 0.00 0.00 32.66 4.30
162 163 1.806758 GGGATGCATGCGTTGTTGC 60.807 57.895 14.88 0.00 39.33 4.17
163 164 1.153784 GGGGATGCATGCGTTGTTG 60.154 57.895 14.88 0.00 0.00 3.33
164 165 0.034574 TAGGGGATGCATGCGTTGTT 60.035 50.000 14.88 3.34 0.00 2.83
169 170 1.598962 CTGGTAGGGGATGCATGCG 60.599 63.158 14.09 0.00 0.00 4.73
182 183 2.361610 GGTCGGTCGGGACTGGTA 60.362 66.667 7.74 0.00 38.23 3.25
185 186 2.261671 CAAGGTCGGTCGGGACTG 59.738 66.667 1.11 1.11 37.12 3.51
193 194 3.622826 CGTGTCCCCAAGGTCGGT 61.623 66.667 0.00 0.00 0.00 4.69
194 195 3.307906 TCGTGTCCCCAAGGTCGG 61.308 66.667 0.00 0.00 0.00 4.79
195 196 2.048503 GTCGTGTCCCCAAGGTCG 60.049 66.667 0.00 0.00 0.00 4.79
241 242 3.221771 ACTTGGTATTGTGCAAGCTCAA 58.778 40.909 11.34 11.34 34.58 3.02
264 265 1.377072 TGTGGCACCGATGACCATG 60.377 57.895 16.26 0.00 35.40 3.66
265 266 1.377202 GTGTGGCACCGATGACCAT 60.377 57.895 16.26 0.00 35.40 3.55
291 292 1.026718 GTCCTGACAATGCTTCCCCG 61.027 60.000 0.00 0.00 0.00 5.73
302 303 0.107410 GTGTGGTGGTTGTCCTGACA 60.107 55.000 0.00 0.00 39.98 3.58
305 306 1.528309 GGGTGTGGTGGTTGTCCTG 60.528 63.158 0.00 0.00 34.23 3.86
323 324 0.933047 TCGTGAGTGTTGTCTTCGCG 60.933 55.000 0.00 0.00 35.91 5.87
326 327 1.852942 TGCTCGTGAGTGTTGTCTTC 58.147 50.000 0.00 0.00 0.00 2.87
369 370 1.414550 GGGTGGATTCTCTGAGTAGGC 59.585 57.143 4.32 0.00 0.00 3.93
371 372 2.656002 TCGGGTGGATTCTCTGAGTAG 58.344 52.381 4.32 0.00 0.00 2.57
373 374 2.035632 GATCGGGTGGATTCTCTGAGT 58.964 52.381 4.32 0.00 34.82 3.41
375 376 2.034878 CAGATCGGGTGGATTCTCTGA 58.965 52.381 0.00 0.00 33.14 3.27
377 378 0.755686 GCAGATCGGGTGGATTCTCT 59.244 55.000 0.00 0.00 34.82 3.10
390 391 1.118356 ATCTGGACCCGAGGCAGATC 61.118 60.000 0.00 0.00 30.45 2.75
391 392 1.074926 ATCTGGACCCGAGGCAGAT 60.075 57.895 0.00 0.00 31.09 2.90
392 393 1.758514 GATCTGGACCCGAGGCAGA 60.759 63.158 0.00 0.00 0.00 4.26
393 394 1.760086 AGATCTGGACCCGAGGCAG 60.760 63.158 0.00 0.00 0.00 4.85
394 395 2.060383 CAGATCTGGACCCGAGGCA 61.060 63.158 15.38 0.00 0.00 4.75
395 396 2.818132 CAGATCTGGACCCGAGGC 59.182 66.667 15.38 0.00 0.00 4.70
424 426 4.020128 AGCTTCTCTAACCTAGGGTTTGTG 60.020 45.833 14.81 4.60 44.33 3.33
438 440 1.742761 GCACAATGGCAGCTTCTCTA 58.257 50.000 0.00 0.00 0.00 2.43
445 447 3.723364 CTACGCGCACAATGGCAGC 62.723 63.158 5.73 0.00 0.00 5.25
447 449 3.798650 GCTACGCGCACAATGGCA 61.799 61.111 5.73 0.00 38.92 4.92
449 451 4.222589 CGGCTACGCGCACAATGG 62.223 66.667 5.73 0.00 41.67 3.16
451 453 3.186047 GTCGGCTACGCGCACAAT 61.186 61.111 5.73 0.00 41.67 2.71
452 454 4.649310 TGTCGGCTACGCGCACAA 62.649 61.111 5.73 0.00 41.67 3.33
459 461 4.814294 GGGCTGGTGTCGGCTACG 62.814 72.222 0.00 0.00 44.44 3.51
481 483 1.881252 CGGGTCGGAATTGGTAGCG 60.881 63.158 0.00 0.00 0.00 4.26
495 497 0.912486 CAATCTCCCTTCTTCCGGGT 59.088 55.000 0.00 0.00 42.56 5.28
496 498 0.464554 GCAATCTCCCTTCTTCCGGG 60.465 60.000 0.00 0.00 43.38 5.73
566 595 2.383527 GCGTGCTGGTGCTGACTAC 61.384 63.158 0.00 0.00 40.48 2.73
581 610 4.729856 GTTAGGACGGCGGTGCGT 62.730 66.667 13.24 4.46 39.82 5.24
584 613 4.807039 CGGGTTAGGACGGCGGTG 62.807 72.222 13.24 0.00 0.00 4.94
587 616 2.812178 CAACGGGTTAGGACGGCG 60.812 66.667 4.80 4.80 0.00 6.46
589 618 2.812178 CGCAACGGGTTAGGACGG 60.812 66.667 0.00 0.00 0.00 4.79
601 630 1.379309 TTATCTTGGGGGCCGCAAC 60.379 57.895 29.82 5.57 33.00 4.17
602 631 1.379309 GTTATCTTGGGGGCCGCAA 60.379 57.895 30.96 30.96 35.16 4.85
615 644 1.883084 CTGGCCGCGGACAGTTATC 60.883 63.158 46.00 19.26 45.74 1.75
616 645 2.186903 CTGGCCGCGGACAGTTAT 59.813 61.111 46.00 0.00 45.74 1.89
644 673 4.680237 CACTGAGGAACGGCGGCA 62.680 66.667 13.24 0.00 0.00 5.69
658 687 1.134280 CCGGATTGAAGCAGATCCACT 60.134 52.381 0.00 0.00 41.55 4.00
661 1909 1.139853 AGACCGGATTGAAGCAGATCC 59.860 52.381 9.46 0.00 38.75 3.36
699 1947 6.486657 TCCACAAAATTCCAGTTACAGAGAAG 59.513 38.462 0.00 0.00 0.00 2.85
704 1952 8.661352 AAAAATCCACAAAATTCCAGTTACAG 57.339 30.769 0.00 0.00 0.00 2.74
739 1987 2.247358 TCCTCCCAATTTTCAGGCAAC 58.753 47.619 0.00 0.00 0.00 4.17
743 1991 4.527816 TGTCAATTCCTCCCAATTTTCAGG 59.472 41.667 0.00 0.00 0.00 3.86
751 1999 3.430453 GTTGGATGTCAATTCCTCCCAA 58.570 45.455 0.00 0.00 37.73 4.12
774 2022 4.612943 GTTCCAGTCGATTCTATCAGGAC 58.387 47.826 0.00 0.00 0.00 3.85
790 2038 2.400399 TGAAAGCGACTTACGTTCCAG 58.600 47.619 0.00 0.00 44.60 3.86
802 2050 2.274437 GATCATGCTGACTGAAAGCGA 58.726 47.619 0.00 0.00 43.88 4.93
803 2051 1.329906 GGATCATGCTGACTGAAAGCG 59.670 52.381 0.00 0.00 43.88 4.68
846 2278 8.852671 TTCATTTTCCCCACCAAAATCTATAT 57.147 30.769 0.00 0.00 32.25 0.86
860 2296 0.530744 GCCCTCGTTTCATTTTCCCC 59.469 55.000 0.00 0.00 0.00 4.81
863 2299 8.926715 AATAATTTAGCCCTCGTTTCATTTTC 57.073 30.769 0.00 0.00 0.00 2.29
926 2369 2.104859 CACTCTGCTGGTGCCGATG 61.105 63.158 0.00 0.00 38.71 3.84
932 2375 0.533531 TTGTCTGCACTCTGCTGGTG 60.534 55.000 7.52 7.52 45.31 4.17
963 2406 3.134458 GGAGGATTTTGCTACGATCTGG 58.866 50.000 0.00 0.00 0.00 3.86
1014 2457 0.032217 AGAAGAGCAGGAGGAGGAGG 60.032 60.000 0.00 0.00 0.00 4.30
1015 2458 1.402787 GAGAAGAGCAGGAGGAGGAG 58.597 60.000 0.00 0.00 0.00 3.69
1016 2459 0.032615 GGAGAAGAGCAGGAGGAGGA 60.033 60.000 0.00 0.00 0.00 3.71
1017 2460 0.325110 TGGAGAAGAGCAGGAGGAGG 60.325 60.000 0.00 0.00 0.00 4.30
1138 2581 2.245438 GAGTTGCCGGGGGAGAAGAG 62.245 65.000 2.18 0.00 0.00 2.85
1301 2744 4.980805 GCAAGGTGTCCGACGGCA 62.981 66.667 9.66 8.02 0.00 5.69
1628 3071 3.760035 AGTACTGGCGGTGCTCGG 61.760 66.667 11.59 0.00 36.10 4.63
1972 3415 0.832135 TTCCACTCTTGCTCCGACCT 60.832 55.000 0.00 0.00 0.00 3.85
2226 3669 1.276421 CCACCTTGGTCAATCGAGAGT 59.724 52.381 0.00 0.00 31.35 3.24
2271 3714 3.554692 GCGACGCGGAGGTGAATG 61.555 66.667 12.47 0.00 0.00 2.67
3126 4586 2.210144 CTCCCTTTTCCGATGGGGCA 62.210 60.000 0.00 0.00 41.92 5.36
3132 4592 0.464452 CGTAGCCTCCCTTTTCCGAT 59.536 55.000 0.00 0.00 0.00 4.18
3441 4901 2.924290 CGCTAGTTTGTTACTGCTCTCC 59.076 50.000 0.00 0.00 37.73 3.71
3663 5123 7.073883 CCATACAAGCATTTCATATTCACTCG 58.926 38.462 0.00 0.00 0.00 4.18
3664 5124 7.934457 ACCATACAAGCATTTCATATTCACTC 58.066 34.615 0.00 0.00 0.00 3.51
3665 5125 7.886629 ACCATACAAGCATTTCATATTCACT 57.113 32.000 0.00 0.00 0.00 3.41
3666 5126 8.931385 AAACCATACAAGCATTTCATATTCAC 57.069 30.769 0.00 0.00 0.00 3.18
3667 5127 9.941325 AAAAACCATACAAGCATTTCATATTCA 57.059 25.926 0.00 0.00 0.00 2.57
3692 5152 7.891183 TCAAACTATACAAGCATTCCCCTAAAA 59.109 33.333 0.00 0.00 0.00 1.52
3693 5153 7.406916 TCAAACTATACAAGCATTCCCCTAAA 58.593 34.615 0.00 0.00 0.00 1.85
3694 5154 6.964464 TCAAACTATACAAGCATTCCCCTAA 58.036 36.000 0.00 0.00 0.00 2.69
3695 5155 6.569127 TCAAACTATACAAGCATTCCCCTA 57.431 37.500 0.00 0.00 0.00 3.53
3696 5156 5.450818 TCAAACTATACAAGCATTCCCCT 57.549 39.130 0.00 0.00 0.00 4.79
3697 5157 5.067805 CCTTCAAACTATACAAGCATTCCCC 59.932 44.000 0.00 0.00 0.00 4.81
3698 5158 5.652452 ACCTTCAAACTATACAAGCATTCCC 59.348 40.000 0.00 0.00 0.00 3.97
3699 5159 6.759497 ACCTTCAAACTATACAAGCATTCC 57.241 37.500 0.00 0.00 0.00 3.01
3700 5160 8.494016 AGTACCTTCAAACTATACAAGCATTC 57.506 34.615 0.00 0.00 0.00 2.67
3701 5161 7.553044 GGAGTACCTTCAAACTATACAAGCATT 59.447 37.037 0.00 0.00 0.00 3.56
3702 5162 7.048512 GGAGTACCTTCAAACTATACAAGCAT 58.951 38.462 0.00 0.00 0.00 3.79
3703 5163 6.403878 GGAGTACCTTCAAACTATACAAGCA 58.596 40.000 0.00 0.00 0.00 3.91
3704 5164 5.816258 GGGAGTACCTTCAAACTATACAAGC 59.184 44.000 0.00 0.00 35.85 4.01
3777 5237 8.196103 GGGTCGAAAATTAACTACTCTCTGTAT 58.804 37.037 0.00 0.00 0.00 2.29
3778 5238 7.542025 GGGTCGAAAATTAACTACTCTCTGTA 58.458 38.462 0.00 0.00 0.00 2.74
3779 5239 6.396450 GGGTCGAAAATTAACTACTCTCTGT 58.604 40.000 0.00 0.00 0.00 3.41
3780 5240 5.515626 CGGGTCGAAAATTAACTACTCTCTG 59.484 44.000 0.00 0.00 0.00 3.35
3781 5241 5.648572 CGGGTCGAAAATTAACTACTCTCT 58.351 41.667 0.00 0.00 0.00 3.10
3782 5242 4.267214 GCGGGTCGAAAATTAACTACTCTC 59.733 45.833 0.00 0.00 0.00 3.20
3783 5243 4.179298 GCGGGTCGAAAATTAACTACTCT 58.821 43.478 0.00 0.00 0.00 3.24
3784 5244 3.928375 TGCGGGTCGAAAATTAACTACTC 59.072 43.478 0.00 0.00 0.00 2.59
3785 5245 3.929094 TGCGGGTCGAAAATTAACTACT 58.071 40.909 0.00 0.00 0.00 2.57
3786 5246 4.666928 TTGCGGGTCGAAAATTAACTAC 57.333 40.909 0.00 0.00 0.00 2.73
3787 5247 5.686159 TTTTGCGGGTCGAAAATTAACTA 57.314 34.783 0.00 0.00 34.18 2.24
3788 5248 4.571372 TTTTGCGGGTCGAAAATTAACT 57.429 36.364 0.00 0.00 34.18 2.24
3813 5273 9.623000 ACACAACCAAAATTAACTAGTACTCTT 57.377 29.630 0.00 0.00 0.00 2.85
3814 5274 9.052759 CACACAACCAAAATTAACTAGTACTCT 57.947 33.333 0.00 0.00 0.00 3.24
3815 5275 7.801783 GCACACAACCAAAATTAACTAGTACTC 59.198 37.037 0.00 0.00 0.00 2.59
3816 5276 7.519328 CGCACACAACCAAAATTAACTAGTACT 60.519 37.037 0.00 0.00 0.00 2.73
3817 5277 6.575942 CGCACACAACCAAAATTAACTAGTAC 59.424 38.462 0.00 0.00 0.00 2.73
3818 5278 6.260493 ACGCACACAACCAAAATTAACTAGTA 59.740 34.615 0.00 0.00 0.00 1.82
3819 5279 5.066764 ACGCACACAACCAAAATTAACTAGT 59.933 36.000 0.00 0.00 0.00 2.57
3820 5280 5.516090 ACGCACACAACCAAAATTAACTAG 58.484 37.500 0.00 0.00 0.00 2.57
3832 5292 1.666553 TGATCCGACGCACACAACC 60.667 57.895 0.00 0.00 0.00 3.77
3833 5293 1.491563 GTGATCCGACGCACACAAC 59.508 57.895 10.65 0.00 35.19 3.32
3851 5311 0.038159 ACTGCTCCTTCGAACTTCCG 60.038 55.000 0.00 0.00 0.00 4.30
3884 5344 8.478066 TAGTACTCCACTAACTCAATACGAGTA 58.522 37.037 0.00 0.00 45.57 2.59
3885 5345 7.334090 TAGTACTCCACTAACTCAATACGAGT 58.666 38.462 0.00 0.00 46.99 4.18
3886 5346 6.680874 AGTACTCCACTAACTCAATACGAG 57.319 41.667 0.00 0.00 41.08 4.18
3887 5347 7.772292 ACATAGTACTCCACTAACTCAATACGA 59.228 37.037 0.00 0.00 43.00 3.43
3888 5348 7.928103 ACATAGTACTCCACTAACTCAATACG 58.072 38.462 0.00 0.00 43.00 3.06
3894 5354 9.654663 AAATTCAACATAGTACTCCACTAACTC 57.345 33.333 0.00 0.00 43.00 3.01
3902 5362 8.674607 CACCCTAAAAATTCAACATAGTACTCC 58.325 37.037 0.00 0.00 0.00 3.85
3903 5363 9.227777 ACACCCTAAAAATTCAACATAGTACTC 57.772 33.333 0.00 0.00 0.00 2.59
3940 5401 9.780413 GCAGTTCTAAATTTTTCTAGATTCAGG 57.220 33.333 0.00 0.00 0.00 3.86
3976 5437 3.119849 CGCCTATGAAAACAAGACCAAGG 60.120 47.826 0.00 0.00 0.00 3.61
4020 5755 7.439655 GGGTTTGATTGTAGATGCTCTAAGTAG 59.560 40.741 0.00 0.00 29.58 2.57
4039 5774 3.274383 AGGAGGGATTTAAGGGGTTTGA 58.726 45.455 0.00 0.00 0.00 2.69
4040 5775 3.757947 AGGAGGGATTTAAGGGGTTTG 57.242 47.619 0.00 0.00 0.00 2.93
4041 5776 6.046762 CCATATAGGAGGGATTTAAGGGGTTT 59.953 42.308 0.00 0.00 41.22 3.27
4049 5784 3.112263 CCGGCCATATAGGAGGGATTTA 58.888 50.000 2.24 0.00 41.22 1.40
4057 5792 1.982395 CGAGGCCGGCCATATAGGA 60.982 63.158 45.13 0.00 41.22 2.94
4081 5818 2.574399 GGGCTCTGACCGAGTCAC 59.426 66.667 0.76 0.00 46.34 3.67
4088 5825 4.554036 GCATCCGGGGCTCTGACC 62.554 72.222 0.00 0.00 0.00 4.02
4107 5844 3.412879 GAGGAGCAGGACGTACGGC 62.413 68.421 21.06 17.96 0.00 5.68
4134 5874 1.053424 AACACTTCGAGGGCAAGGTA 58.947 50.000 0.00 0.00 0.00 3.08
4154 5894 4.734398 AAACAGCTTGGACATTTTGTGA 57.266 36.364 0.00 0.00 0.00 3.58
4155 5895 5.799681 AAAAACAGCTTGGACATTTTGTG 57.200 34.783 0.00 0.00 0.00 3.33
4197 5939 9.288576 TGAAACTACTCATCTGACAAATTCATT 57.711 29.630 0.00 0.00 32.17 2.57
4205 5947 9.591792 CATTATTCTGAAACTACTCATCTGACA 57.408 33.333 0.00 0.00 0.00 3.58
4234 5976 8.086522 AAACTCTTGTTGGATGAATTCATCAAG 58.913 33.333 36.93 31.32 43.59 3.02
4235 5977 7.868922 CAAACTCTTGTTGGATGAATTCATCAA 59.131 33.333 36.93 29.42 43.59 2.57
4236 5978 7.014518 ACAAACTCTTGTTGGATGAATTCATCA 59.985 33.333 36.93 25.05 46.79 3.07
4237 5979 7.373493 ACAAACTCTTGTTGGATGAATTCATC 58.627 34.615 31.88 31.88 45.62 2.92
4238 5980 7.294017 ACAAACTCTTGTTGGATGAATTCAT 57.706 32.000 20.85 20.85 43.45 2.57
4239 5981 6.513230 CGACAAACTCTTGTTGGATGAATTCA 60.513 38.462 11.26 11.26 45.98 2.57
4240 5982 5.853282 CGACAAACTCTTGTTGGATGAATTC 59.147 40.000 0.00 0.00 45.98 2.17
4241 5983 5.530915 TCGACAAACTCTTGTTGGATGAATT 59.469 36.000 5.60 0.00 45.98 2.17
4242 5984 5.063204 TCGACAAACTCTTGTTGGATGAAT 58.937 37.500 5.60 0.00 45.98 2.57
4243 5985 4.447290 TCGACAAACTCTTGTTGGATGAA 58.553 39.130 5.60 0.00 45.98 2.57
4274 6016 8.429493 TTTCATCATCATCATGTACTCTTGAC 57.571 34.615 0.00 0.00 32.07 3.18
4276 6018 8.290325 CCATTTCATCATCATCATGTACTCTTG 58.710 37.037 0.00 0.00 0.00 3.02
4283 6025 6.490381 CCTTCTCCATTTCATCATCATCATGT 59.510 38.462 0.00 0.00 0.00 3.21
4336 6078 1.348064 TCTCCCTCCTTTGAGCGAAA 58.652 50.000 0.00 0.00 37.29 3.46
4340 6082 5.760743 GTGTATAATTCTCCCTCCTTTGAGC 59.239 44.000 0.00 0.00 37.29 4.26
4349 6091 7.256399 TCATATCCTGGTGTATAATTCTCCCT 58.744 38.462 0.00 0.00 0.00 4.20
4350 6092 7.496346 TCATATCCTGGTGTATAATTCTCCC 57.504 40.000 0.00 0.00 0.00 4.30
4386 6128 0.035317 CAGTCCTTGTACAGCAGGCA 59.965 55.000 8.52 0.00 0.00 4.75
4388 6130 0.322975 AGCAGTCCTTGTACAGCAGG 59.677 55.000 7.21 7.21 34.59 4.85
4391 6133 2.494059 TGAAAGCAGTCCTTGTACAGC 58.506 47.619 0.00 0.00 33.01 4.40
4392 6134 3.251004 GGTTGAAAGCAGTCCTTGTACAG 59.749 47.826 0.00 0.00 33.01 2.74
4405 6147 2.888834 TTTTGGCTCAGGTTGAAAGC 57.111 45.000 0.00 0.00 35.27 3.51
4415 6157 2.767394 CCCATCATGGAATTTTGGCTCA 59.233 45.455 4.75 0.00 40.96 4.26
4416 6158 2.767960 ACCCATCATGGAATTTTGGCTC 59.232 45.455 4.75 0.00 40.96 4.70
4418 6160 3.632643 AACCCATCATGGAATTTTGGC 57.367 42.857 4.75 0.00 40.96 4.52
4420 6162 5.122082 CGGAAAAACCCATCATGGAATTTTG 59.878 40.000 18.72 6.86 40.96 2.44
4424 6166 3.447229 GTCGGAAAAACCCATCATGGAAT 59.553 43.478 4.75 0.00 40.96 3.01
4437 6179 2.159071 TCCAGAAGTGACGTCGGAAAAA 60.159 45.455 11.62 0.00 0.00 1.94
4438 6180 1.409790 TCCAGAAGTGACGTCGGAAAA 59.590 47.619 11.62 0.00 0.00 2.29
4444 6186 1.272490 TGGTCATCCAGAAGTGACGTC 59.728 52.381 9.11 9.11 44.32 4.34
4445 6187 1.338107 TGGTCATCCAGAAGTGACGT 58.662 50.000 0.00 0.00 44.32 4.34
4450 6192 2.065799 AGGGTTTGGTCATCCAGAAGT 58.934 47.619 0.00 0.00 45.22 3.01
4455 6197 2.765689 AACAAGGGTTTGGTCATCCA 57.234 45.000 0.00 0.00 42.66 3.41


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

AutoCloner maintained by Alex Coulton.