Multiple sequence alignment - TraesCS3A01G343100

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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 TraesCS3A01G343100 chr3A 100.000 6927 0 0 1 6927 590229585 590236511 0.000000e+00 12792.0
1 TraesCS3A01G343100 chr3A 84.797 296 36 6 6154 6443 747055289 747055581 8.790000e-74 289.0
2 TraesCS3A01G343100 chr3D 92.099 2620 122 34 4378 6926 448867652 448870257 0.000000e+00 3613.0
3 TraesCS3A01G343100 chr3D 91.155 1956 102 28 1543 3448 448865018 448866952 0.000000e+00 2588.0
4 TraesCS3A01G343100 chr3D 91.454 1451 86 18 104 1520 448863511 448864957 0.000000e+00 1958.0
5 TraesCS3A01G343100 chr3D 88.645 502 48 6 3445 3945 448866993 448867486 2.760000e-168 603.0
6 TraesCS3A01G343100 chr3D 86.102 295 36 1 6154 6443 532808897 532808603 5.220000e-81 313.0
7 TraesCS3A01G343100 chr3D 84.746 295 40 3 6154 6443 507634215 507633921 2.440000e-74 291.0
8 TraesCS3A01G343100 chr3D 91.000 100 7 2 4271 4369 448867509 448867607 4.360000e-27 134.0
9 TraesCS3A01G343100 chr3D 85.849 106 6 7 4 108 448863387 448863484 3.420000e-18 104.0
10 TraesCS3A01G343100 chr3B 92.192 1934 120 15 1543 3448 589543693 589545623 0.000000e+00 2706.0
11 TraesCS3A01G343100 chr3B 92.674 1911 81 22 4366 6226 589548384 589550285 0.000000e+00 2699.0
12 TraesCS3A01G343100 chr3B 90.305 1114 73 17 104 1183 589542151 589543263 0.000000e+00 1426.0
13 TraesCS3A01G343100 chr3B 91.144 813 58 7 3445 4250 589545664 589546469 0.000000e+00 1090.0
14 TraesCS3A01G343100 chr3B 89.274 634 46 14 6308 6926 589550634 589551260 0.000000e+00 774.0
15 TraesCS3A01G343100 chr3B 92.775 346 19 5 1179 1520 589543289 589543632 4.830000e-136 496.0
16 TraesCS3A01G343100 chr4D 86.195 297 33 4 6154 6443 389492677 389492382 1.450000e-81 315.0
17 TraesCS3A01G343100 chr4D 92.593 81 6 0 5193 5273 14438068 14438148 4.390000e-22 117.0
18 TraesCS3A01G343100 chr2D 86.195 297 33 4 6154 6443 628171295 628171000 1.450000e-81 315.0
19 TraesCS3A01G343100 chr2D 92.500 80 6 0 5198 5277 14768254 14768333 1.580000e-21 115.0
20 TraesCS3A01G343100 chr1D 85.085 295 39 3 6154 6443 28220435 28220729 5.250000e-76 296.0
21 TraesCS3A01G343100 chr5B 84.746 295 40 1 6154 6443 12073379 12073673 2.440000e-74 291.0
22 TraesCS3A01G343100 chr5B 91.011 89 8 0 5189 5277 328105890 328105802 3.390000e-23 121.0
23 TraesCS3A01G343100 chr5B 88.235 85 10 0 5193 5277 571174103 571174019 1.230000e-17 102.0
24 TraesCS3A01G343100 chr5A 90.217 92 8 1 5193 5283 558960322 558960231 1.220000e-22 119.0
25 TraesCS3A01G343100 chr4B 89.655 87 9 0 5191 5277 316295873 316295959 2.040000e-20 111.0
26 TraesCS3A01G343100 chr6D 81.818 143 15 7 5193 5327 429012232 429012093 7.350000e-20 110.0
27 TraesCS3A01G343100 chr1B 90.361 83 8 0 5193 5275 519505613 519505695 7.350000e-20 110.0
28 TraesCS3A01G343100 chr1B 90.361 83 8 0 5193 5275 519518094 519518176 7.350000e-20 110.0
29 TraesCS3A01G343100 chr1B 87.805 82 9 1 5197 5277 437601021 437601102 2.060000e-15 95.3
30 TraesCS3A01G343100 chr4A 81.333 150 11 8 5193 5325 136431373 136431522 9.500000e-19 106.0
31 TraesCS3A01G343100 chr4A 88.235 85 10 0 5193 5277 476341522 476341606 1.230000e-17 102.0
32 TraesCS3A01G343100 chr7D 87.209 86 11 0 5192 5277 436459624 436459709 1.590000e-16 99.0
33 TraesCS3A01G343100 chr2A 87.059 85 11 0 5193 5277 176673418 176673334 5.720000e-16 97.1
34 TraesCS3A01G343100 chr7A 86.207 87 11 1 5192 5277 113028383 113028297 7.400000e-15 93.5
35 TraesCS3A01G343100 chr6A 79.618 157 11 9 5192 5328 118284203 118284358 7.400000e-15 93.5


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 TraesCS3A01G343100 chr3A 590229585 590236511 6926 False 12792.000000 12792 100.000000 1 6927 1 chr3A.!!$F1 6926
1 TraesCS3A01G343100 chr3D 448863387 448870257 6870 False 1500.000000 3613 90.033667 4 6926 6 chr3D.!!$F1 6922
2 TraesCS3A01G343100 chr3B 589542151 589551260 9109 False 1531.833333 2706 91.394000 104 6926 6 chr3B.!!$F1 6822

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
143 176 0.326808 TCCCATTTAGCTACCCCCGT 60.327 55.000 0.00 0.00 0.00 5.28 F
477 542 0.548682 ACCCATCTTCTGTGCCTCCT 60.549 55.000 0.00 0.00 0.00 3.69 F
1264 1364 0.165295 GCTTTCTCCCGTTTGTACGC 59.835 55.000 0.00 0.00 46.27 4.42 F
1793 1941 1.065102 CCTCCTTTGATGAAGCATGCG 59.935 52.381 13.01 0.00 33.84 4.73 F
2623 2797 1.204146 GAGTACCAAGGGATGCAGGA 58.796 55.000 0.00 0.00 0.00 3.86 F
3416 3617 0.039035 AGGCGACTCTTGAGACTCCT 59.961 55.000 4.49 5.33 32.90 3.69 F
3970 4259 0.114954 ATTGGCCTTGTCACCACCAT 59.885 50.000 3.32 0.00 35.10 3.55 F
4203 4492 0.609662 AATGCCTCCATTGTGGTTGC 59.390 50.000 0.00 1.41 40.09 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1240 1340 1.134220 ACAAACGGGAGAAAGCTCACA 60.134 47.619 0.00 0.00 45.13 3.58 R
2299 2452 0.036022 GGAGAAGTTCCTGCTGCACT 59.964 55.000 0.00 0.00 43.16 4.40 R
3252 3449 0.325577 ATTCCAAGGCCAATGGGTCC 60.326 55.000 23.19 0.00 40.78 4.46 R
3378 3579 0.250295 TTTGACGACCCAGAAGGCAG 60.250 55.000 0.00 0.00 40.58 4.85 R
3485 3774 0.449388 CAATGGAAGACGAGCAAGGC 59.551 55.000 0.00 0.00 0.00 4.35 R
5363 7520 1.925229 ATTGCCGTTTACATGCATGC 58.075 45.000 26.53 11.82 34.51 4.06 R
5533 7690 3.071206 AGCTCGGCCACGACATCT 61.071 61.111 2.24 0.00 45.59 2.90 R
6173 8336 0.486879 TGATTTTTGTCCTGGGCCCT 59.513 50.000 25.70 0.00 0.00 5.19 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
38 39 9.865321 ATACAACTAATACATGAACAAGTACGT 57.135 29.630 0.00 0.00 0.00 3.57
40 41 9.132521 ACAACTAATACATGAACAAGTACGTAC 57.867 33.333 18.10 18.10 0.00 3.67
41 42 8.589629 CAACTAATACATGAACAAGTACGTACC 58.410 37.037 21.80 7.01 0.00 3.34
42 43 7.829725 ACTAATACATGAACAAGTACGTACCA 58.170 34.615 21.80 12.52 0.00 3.25
43 44 8.472413 ACTAATACATGAACAAGTACGTACCAT 58.528 33.333 21.80 14.18 0.00 3.55
44 45 9.955208 CTAATACATGAACAAGTACGTACCATA 57.045 33.333 21.80 4.77 0.00 2.74
53 54 6.558009 ACAAGTACGTACCATATACTGTGTG 58.442 40.000 21.80 2.00 0.00 3.82
135 168 3.782523 TGGACTGAATCTCCCATTTAGCT 59.217 43.478 0.00 0.00 0.00 3.32
139 172 4.103311 ACTGAATCTCCCATTTAGCTACCC 59.897 45.833 0.00 0.00 0.00 3.69
140 173 3.394606 TGAATCTCCCATTTAGCTACCCC 59.605 47.826 0.00 0.00 0.00 4.95
142 175 0.396811 CTCCCATTTAGCTACCCCCG 59.603 60.000 0.00 0.00 0.00 5.73
143 176 0.326808 TCCCATTTAGCTACCCCCGT 60.327 55.000 0.00 0.00 0.00 5.28
144 177 1.062275 TCCCATTTAGCTACCCCCGTA 60.062 52.381 0.00 0.00 0.00 4.02
145 178 1.982958 CCCATTTAGCTACCCCCGTAT 59.017 52.381 0.00 0.00 0.00 3.06
147 180 3.558533 CCCATTTAGCTACCCCCGTATTC 60.559 52.174 0.00 0.00 0.00 1.75
148 181 3.071892 CCATTTAGCTACCCCCGTATTCA 59.928 47.826 0.00 0.00 0.00 2.57
149 182 3.825143 TTTAGCTACCCCCGTATTCAC 57.175 47.619 0.00 0.00 0.00 3.18
151 184 1.068585 GCTACCCCCGTATTCACCG 59.931 63.158 0.00 0.00 0.00 4.94
175 209 8.427276 CCGGAACTATAAATCTACCCTTAACTT 58.573 37.037 0.00 0.00 0.00 2.66
238 272 3.741476 GCTCTGCTGGCCCGTTTG 61.741 66.667 0.00 0.00 0.00 2.93
426 491 3.802948 ACAACGGCCTCACTAATCTAG 57.197 47.619 0.00 0.00 0.00 2.43
439 504 3.844211 ACTAATCTAGTCCCAACTGGCAA 59.156 43.478 0.00 0.00 36.92 4.52
464 529 0.886490 CTAATCGGCTGGCACCCATC 60.886 60.000 1.08 0.00 30.82 3.51
477 542 0.548682 ACCCATCTTCTGTGCCTCCT 60.549 55.000 0.00 0.00 0.00 3.69
588 653 5.241064 GGAACCGAGCTCAATCATAGTACTA 59.759 44.000 15.40 4.77 0.00 1.82
628 694 8.094798 AGAAAACAAACGCTATTTATCACAGA 57.905 30.769 0.00 0.00 0.00 3.41
704 771 1.901591 ATCCATAATTGGCGGCAGAG 58.098 50.000 12.87 1.54 43.29 3.35
729 796 7.041030 AGTCATCGTCTCGAATCTATTATGTGT 60.041 37.037 0.00 0.00 39.99 3.72
762 829 6.418057 AAACATATGAAAAGACCCTGCAAA 57.582 33.333 10.38 0.00 0.00 3.68
773 840 1.318158 CCCTGCAAAGCCTCATGACC 61.318 60.000 0.00 0.00 0.00 4.02
863 932 4.562789 CGCTGCCTCCTAAAAATTTAAAGC 59.437 41.667 0.00 0.00 0.00 3.51
919 988 3.730116 TGGCTACCCCATCTTCTCA 57.270 52.632 0.00 0.00 39.18 3.27
1167 1236 3.957591 AAGAGAAGGTACGGAAACTCC 57.042 47.619 0.00 0.00 0.00 3.85
1240 1340 1.299541 CACTCTTTGTGTTGCTCGGT 58.700 50.000 0.00 0.00 41.53 4.69
1258 1358 1.594331 GTGTGAGCTTTCTCCCGTTT 58.406 50.000 0.00 0.00 38.58 3.60
1264 1364 0.165295 GCTTTCTCCCGTTTGTACGC 59.835 55.000 0.00 0.00 46.27 4.42
1310 1410 3.059352 ACTCATTTCTGTACTGTGCCC 57.941 47.619 0.00 0.00 0.00 5.36
1343 1443 8.421002 GTTGTATGCCAATATGGGTAAGATTTT 58.579 33.333 0.00 0.00 38.19 1.82
1493 1597 6.127814 GGTTTACTGCAGGTTAATAAACTCCC 60.128 42.308 24.50 12.84 36.45 4.30
1514 1618 4.380233 CCCAAAACACTGATGATTGAGAGC 60.380 45.833 0.00 0.00 31.85 4.09
1520 1624 4.340666 ACACTGATGATTGAGAGCGATAGT 59.659 41.667 0.00 0.00 39.35 2.12
1521 1625 5.163468 ACACTGATGATTGAGAGCGATAGTT 60.163 40.000 0.00 0.00 39.35 2.24
1545 1661 8.837389 GTTGAACCTAGACTAAAACAACATTCT 58.163 33.333 0.00 0.00 37.10 2.40
1546 1662 8.378172 TGAACCTAGACTAAAACAACATTCTG 57.622 34.615 0.00 0.00 0.00 3.02
1547 1663 7.444183 TGAACCTAGACTAAAACAACATTCTGG 59.556 37.037 0.00 0.00 0.00 3.86
1570 1712 4.872691 GGTCGAGCTATATTTCATGGGATG 59.127 45.833 7.51 0.00 0.00 3.51
1572 1714 6.166279 GTCGAGCTATATTTCATGGGATGAA 58.834 40.000 0.00 0.00 46.77 2.57
1617 1759 9.167311 GATTATTATGGTAGCCATTACTGGAAG 57.833 37.037 2.72 0.00 42.23 3.46
1619 1761 7.626999 ATTATGGTAGCCATTACTGGAAGTA 57.373 36.000 2.72 0.00 44.42 2.24
1657 1799 6.671614 TCTGTTTACTTCTTTTCTTTCGCA 57.328 33.333 0.00 0.00 0.00 5.10
1671 1813 6.493449 TTCTTTCGCATTTGTACATCATCA 57.507 33.333 0.00 0.00 0.00 3.07
1731 1873 5.066893 TGGAATGCTGCTGTATTCATTCTTC 59.933 40.000 26.98 14.31 43.85 2.87
1780 1928 5.104817 CCCAAAAATATGCACATCCTCCTTT 60.105 40.000 0.00 0.00 0.00 3.11
1793 1941 1.065102 CCTCCTTTGATGAAGCATGCG 59.935 52.381 13.01 0.00 33.84 4.73
1861 2009 5.371115 TGATTTGCTTTACCTGTGCTTAC 57.629 39.130 0.00 0.00 0.00 2.34
1868 2016 5.534654 TGCTTTACCTGTGCTTACATCTTTT 59.465 36.000 0.00 0.00 0.00 2.27
1904 2052 5.707764 GGTTCCATTTTCTTGAGAAGCTACT 59.292 40.000 0.00 0.00 35.21 2.57
1905 2053 6.348868 GGTTCCATTTTCTTGAGAAGCTACTG 60.349 42.308 0.00 0.00 35.21 2.74
1923 2071 7.167831 GCTACTGCTATTACTAAACTGAAGC 57.832 40.000 0.00 0.00 36.03 3.86
1992 2145 1.967319 ACAGTCACAACACATGGTCC 58.033 50.000 0.00 0.00 0.00 4.46
2162 2315 6.879400 AGTGGTTCTCATTTCTCATACTACC 58.121 40.000 0.00 0.00 0.00 3.18
2166 2319 7.110155 GGTTCTCATTTCTCATACTACCCAAA 58.890 38.462 0.00 0.00 0.00 3.28
2260 2413 4.396357 ACCCAATAAATCAGTTGGTGGA 57.604 40.909 3.73 0.00 42.62 4.02
2299 2452 8.112822 TGGTGATCCATTCCTTTATTCTAAACA 58.887 33.333 0.00 0.00 39.03 2.83
2439 2609 8.435931 TTCATAGCCACACATAGATATAAGGT 57.564 34.615 0.00 0.00 0.00 3.50
2489 2659 4.090761 TGAGGCTTCTTGTCTTGTTGAT 57.909 40.909 0.00 0.00 0.00 2.57
2492 2662 4.464008 AGGCTTCTTGTCTTGTTGATCAA 58.536 39.130 3.38 3.38 34.61 2.57
2556 2726 6.791867 AACACACAAGAGCATAGTAGGATA 57.208 37.500 0.00 0.00 0.00 2.59
2562 2732 6.151312 CACAAGAGCATAGTAGGATATACCGT 59.849 42.308 0.00 0.00 44.74 4.83
2565 2735 5.652891 AGAGCATAGTAGGATATACCGTTGG 59.347 44.000 0.00 0.00 44.74 3.77
2574 2744 5.425630 AGGATATACCGTTGGTTCACTTTC 58.574 41.667 0.00 0.00 44.74 2.62
2623 2797 1.204146 GAGTACCAAGGGATGCAGGA 58.796 55.000 0.00 0.00 0.00 3.86
2781 2955 2.363795 CGGCAGACCCAGTCCCTA 60.364 66.667 0.00 0.00 32.18 3.53
2876 3050 1.227853 GCCATATGGTCCGACCCAC 60.228 63.158 22.79 0.00 37.50 4.61
2877 3051 1.978455 GCCATATGGTCCGACCCACA 61.978 60.000 22.79 0.32 37.50 4.17
2925 3099 6.385649 AACAAGAATCGGTTACACAACAAT 57.614 33.333 0.00 0.00 36.29 2.71
2926 3100 5.757886 ACAAGAATCGGTTACACAACAATG 58.242 37.500 0.00 0.00 36.29 2.82
2930 3118 4.742438 ATCGGTTACACAACAATGTCAC 57.258 40.909 0.00 0.00 37.82 3.67
3172 3368 6.249035 ACATATTACAAACCTTGACAACCG 57.751 37.500 0.00 0.00 0.00 4.44
3178 3374 4.678622 ACAAACCTTGACAACCGAAAATC 58.321 39.130 0.00 0.00 0.00 2.17
3197 3393 1.908793 GGCCGAGCCTCTAGCCATA 60.909 63.158 15.53 0.00 46.69 2.74
3215 3411 3.454447 CCATAATGGACCAGTGGTGACTA 59.546 47.826 22.50 4.25 40.96 2.59
3252 3449 1.604604 TTCAAGAAGCCGACCCAAAG 58.395 50.000 0.00 0.00 0.00 2.77
3327 3524 5.226803 TCATCCCATTCCCATCTTTAGAGA 58.773 41.667 0.00 0.00 36.09 3.10
3351 3548 4.941263 AGCCGCAAAGTCATAGTTAAATGA 59.059 37.500 0.00 0.00 33.48 2.57
3378 3579 5.621193 TCTAGGTAAAAATAGATGGCTGCC 58.379 41.667 12.87 12.87 0.00 4.85
3396 3597 1.371183 CTGCCTTCTGGGTCGTCAA 59.629 57.895 0.00 0.00 37.43 3.18
3411 3612 1.335964 CGTCAAAGGCGACTCTTGAGA 60.336 52.381 13.86 0.00 42.68 3.27
3416 3617 0.039035 AGGCGACTCTTGAGACTCCT 59.961 55.000 4.49 5.33 32.90 3.69
3417 3618 0.172352 GGCGACTCTTGAGACTCCTG 59.828 60.000 4.49 0.00 0.00 3.86
3485 3774 0.684479 GGCCCCTTTCTAGCCCAAAG 60.684 60.000 0.00 0.00 41.00 2.77
3508 3797 1.377202 GCTCGTCTTCCATTGCCCA 60.377 57.895 0.00 0.00 0.00 5.36
3513 3802 1.679944 CGTCTTCCATTGCCCATGTCT 60.680 52.381 0.00 0.00 0.00 3.41
3514 3803 2.019984 GTCTTCCATTGCCCATGTCTC 58.980 52.381 0.00 0.00 0.00 3.36
3515 3804 1.064463 TCTTCCATTGCCCATGTCTCC 60.064 52.381 0.00 0.00 0.00 3.71
3516 3805 1.002069 TTCCATTGCCCATGTCTCCT 58.998 50.000 0.00 0.00 0.00 3.69
3626 3915 1.415659 CTCTGGGCTTGGAGATGGTAG 59.584 57.143 0.00 0.00 0.00 3.18
3630 3919 0.833287 GGCTTGGAGATGGTAGCTGA 59.167 55.000 0.00 0.00 34.16 4.26
3642 3931 4.991789 TGGTAGCTGATTGGCCATATTA 57.008 40.909 6.09 0.00 0.00 0.98
3645 3934 5.073008 TGGTAGCTGATTGGCCATATTAGAA 59.927 40.000 6.09 0.00 0.00 2.10
3647 3936 7.037658 TGGTAGCTGATTGGCCATATTAGAATA 60.038 37.037 6.09 4.13 0.00 1.75
3648 3937 7.995488 GGTAGCTGATTGGCCATATTAGAATAT 59.005 37.037 6.09 0.00 31.93 1.28
3703 3992 8.549731 CCTACTACTATCAGGTATGGATGAGTA 58.450 40.741 0.00 0.00 0.00 2.59
3712 4001 8.211030 TCAGGTATGGATGAGTATTGATTGAT 57.789 34.615 0.00 0.00 0.00 2.57
3817 4106 1.337118 GGCAACATCTTCCACCCAAA 58.663 50.000 0.00 0.00 0.00 3.28
3819 4108 1.686052 GCAACATCTTCCACCCAAACA 59.314 47.619 0.00 0.00 0.00 2.83
3820 4109 2.299867 GCAACATCTTCCACCCAAACAT 59.700 45.455 0.00 0.00 0.00 2.71
3828 4117 6.463995 TCTTCCACCCAAACATATTATTGC 57.536 37.500 0.00 0.00 0.00 3.56
3829 4118 4.909696 TCCACCCAAACATATTATTGCG 57.090 40.909 0.00 0.00 0.00 4.85
3842 4131 9.847706 AACATATTATTGCGTTGTGTTGAAATA 57.152 25.926 0.00 0.00 0.00 1.40
3860 4149 8.616076 GTTGAAATAACAATGTCATCCTAGAGG 58.384 37.037 0.00 0.00 32.36 3.69
3868 4157 1.834263 GTCATCCTAGAGGCACCTTGT 59.166 52.381 0.00 0.00 34.44 3.16
3880 4169 2.436417 GCACCTTGTCTTGATTGGCTA 58.564 47.619 0.00 0.00 0.00 3.93
3886 4175 7.420800 CACCTTGTCTTGATTGGCTAATATTC 58.579 38.462 0.00 0.00 0.00 1.75
3888 4177 6.483307 CCTTGTCTTGATTGGCTAATATTCGA 59.517 38.462 0.00 0.00 0.00 3.71
3970 4259 0.114954 ATTGGCCTTGTCACCACCAT 59.885 50.000 3.32 0.00 35.10 3.55
3990 4279 1.021968 GTTGGTGTGGTGTGTCTTCC 58.978 55.000 0.00 0.00 0.00 3.46
3995 4284 2.550208 GGTGTGGTGTGTCTTCCCTTAG 60.550 54.545 0.00 0.00 0.00 2.18
4039 4328 9.315525 GTCATTCTTTCCCTACTACAGTTTATC 57.684 37.037 0.00 0.00 0.00 1.75
4059 4348 3.587498 TCTAGGTTGGATAGGATGGTGG 58.413 50.000 0.00 0.00 0.00 4.61
4069 4358 2.203070 GATGGTGGTGCGGGCTAG 60.203 66.667 0.00 0.00 0.00 3.42
4084 4373 3.393472 CTAGGCAAGCTGGGATGTC 57.607 57.895 0.00 0.00 0.00 3.06
4141 4430 5.974751 CGAGAACCTATTCTTGAGCTCTTAC 59.025 44.000 16.19 0.00 45.95 2.34
4203 4492 0.609662 AATGCCTCCATTGTGGTTGC 59.390 50.000 0.00 1.41 40.09 4.17
4223 4519 7.148154 TGGTTGCAATGACCAACTGTATATTAC 60.148 37.037 6.27 0.00 43.87 1.89
4250 4546 6.393171 TGATCGGTGCATCAATATTCTAGAG 58.607 40.000 0.00 0.00 29.41 2.43
4269 6307 6.895756 TCTAGAGTCCATTTCCAGTTAAGCTA 59.104 38.462 0.00 0.00 0.00 3.32
4309 6347 5.304357 TGCTCTGCTAGTTATTACAGGCATA 59.696 40.000 3.10 0.00 34.00 3.14
4384 6488 5.585047 ACGTTATTTTTGTCCTAGATCTGCC 59.415 40.000 5.18 0.00 0.00 4.85
4385 6489 5.584649 CGTTATTTTTGTCCTAGATCTGCCA 59.415 40.000 5.18 0.00 0.00 4.92
4454 6558 6.202570 GCTTCATGCTTTACAAATTTTGGACA 59.797 34.615 13.42 0.35 38.95 4.02
4476 6580 8.739972 GGACAATTTACAAGTCTACCATGAATT 58.260 33.333 0.00 0.00 32.98 2.17
4613 6717 2.233922 CGGTCACCTGTGGAGAAAGTAT 59.766 50.000 0.00 0.00 0.00 2.12
4693 6797 9.745880 GATTACCATCTAACGTCTGAGAATTTA 57.254 33.333 0.00 0.00 0.00 1.40
4730 6835 2.019249 CTGAATGGATGTCCGTGCATT 58.981 47.619 6.01 6.01 39.78 3.56
4807 6912 2.747446 ACAAATTACCACGACAGATGGC 59.253 45.455 0.00 0.00 41.31 4.40
4871 6987 5.407407 ACATCAACTAATTCTCAGTCGGT 57.593 39.130 0.00 0.00 0.00 4.69
4900 7016 9.086336 ACACAACATTGTAGACAAATGAAAAAG 57.914 29.630 0.00 0.00 39.91 2.27
4980 7103 8.827177 TTAGTTAATTCTTTGTCGACTGTGAT 57.173 30.769 17.92 1.90 0.00 3.06
5085 7209 9.780186 GAAGTTATATAGGGCATCAACTAAACT 57.220 33.333 0.00 0.00 0.00 2.66
5097 7221 6.634436 GCATCAACTAAACTGAAGAAACTGTG 59.366 38.462 0.00 0.00 0.00 3.66
5122 7250 1.822371 AGGTTTTGTGGTTGGTGTGAC 59.178 47.619 0.00 0.00 0.00 3.67
5196 7334 1.596496 AGGCCCTTGCTATGGTACTT 58.404 50.000 0.00 0.00 37.74 2.24
5224 7362 9.490663 CTCCGTTCACAAATATAAGATGTTTTC 57.509 33.333 0.00 0.00 0.00 2.29
5225 7363 9.004717 TCCGTTCACAAATATAAGATGTTTTCA 57.995 29.630 0.00 0.00 0.00 2.69
5277 7415 7.041780 AGTGAAATGAATGAACAGACACACTAC 60.042 37.037 0.00 0.00 33.10 2.73
5278 7416 6.204688 TGAAATGAATGAACAGACACACTACC 59.795 38.462 0.00 0.00 0.00 3.18
5279 7417 4.955811 TGAATGAACAGACACACTACCT 57.044 40.909 0.00 0.00 0.00 3.08
5280 7418 4.631131 TGAATGAACAGACACACTACCTG 58.369 43.478 0.00 0.00 0.00 4.00
5281 7419 4.100963 TGAATGAACAGACACACTACCTGT 59.899 41.667 0.00 0.00 42.34 4.00
5285 7423 3.735237 ACAGACACACTACCTGTTCAG 57.265 47.619 0.00 0.00 37.86 3.02
5286 7424 3.296854 ACAGACACACTACCTGTTCAGA 58.703 45.455 1.00 0.00 37.86 3.27
5335 7492 2.612672 GCGGAGGGAGTACAAATTAAGC 59.387 50.000 0.00 0.00 0.00 3.09
5363 7520 6.090358 ACTTTCACTACCATCGAAATAACACG 59.910 38.462 0.00 0.00 0.00 4.49
5578 7735 2.736995 GCAACTGGCGACGCACTA 60.737 61.111 23.09 6.34 0.00 2.74
5593 7750 3.119101 ACGCACTATTTCTGAGGTTCGAT 60.119 43.478 0.00 0.00 0.00 3.59
5879 8042 2.030412 ATGTGCACTTCGGCGACA 59.970 55.556 19.41 3.76 36.28 4.35
6091 8254 8.914011 TCACTAGCTTGAGTGTGTTATATATGT 58.086 33.333 14.77 0.00 45.88 2.29
6163 8326 2.757077 CCTTTTGGGGCCGTCTCT 59.243 61.111 0.00 0.00 35.46 3.10
6173 8336 2.093128 GGGGCCGTCTCTAGAAATTTGA 60.093 50.000 0.00 0.00 0.00 2.69
6180 8343 3.054361 GTCTCTAGAAATTTGAGGGCCCA 60.054 47.826 27.56 2.25 30.73 5.36
6261 8426 8.951541 AGTAAAGCATACCCCCACTTAATTATA 58.048 33.333 0.00 0.00 0.00 0.98
6377 8808 8.871629 TTTATAAACTGGCCTCATTTTCTACA 57.128 30.769 3.32 0.00 30.19 2.74
6413 8844 7.066284 CACCCTTCGAGTATTTCTTGAAATGAT 59.934 37.037 16.22 6.69 43.51 2.45
6543 8974 4.440826 TTTACTTGGGCTAACAACCAGA 57.559 40.909 0.00 0.00 38.16 3.86
6563 9003 8.319057 ACCAGACTAACATTACCATTGATAGA 57.681 34.615 0.00 0.00 0.00 1.98
6571 9011 8.561738 AACATTACCATTGATAGACTTTTCGT 57.438 30.769 0.00 0.00 0.00 3.85
6592 9032 6.688578 TCGTTGACATAGAGCTAGAAAAGTT 58.311 36.000 0.00 0.00 0.00 2.66
6620 9060 1.550524 CACTAGCCTCTTGTACTGCCA 59.449 52.381 0.00 0.00 0.00 4.92
6689 9129 5.070580 GGCTTAGGGAGACAAGCTAAATCTA 59.929 44.000 6.30 0.00 45.20 1.98
6690 9130 6.408206 GGCTTAGGGAGACAAGCTAAATCTAA 60.408 42.308 6.30 0.00 45.20 2.10
6696 9136 8.862085 AGGGAGACAAGCTAAATCTAATAGTAC 58.138 37.037 0.00 0.00 0.00 2.73
6734 9179 4.038402 GGTGGCTCCATAGGAATGATTTTG 59.962 45.833 0.00 0.00 34.84 2.44
6817 9262 4.202567 TGGCAAGACAAAATTAGGAGTCCT 60.203 41.667 17.78 17.78 37.71 3.85
6918 9363 6.106648 TGATAGATTAGATGTCAAGGCTGG 57.893 41.667 0.00 0.00 0.00 4.85
6926 9371 2.024176 TGTCAAGGCTGGAACCTCTA 57.976 50.000 0.00 0.00 39.93 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.865321 ACGTACTTGTTCATGTATTAGTTGTAT 57.135 29.630 0.00 0.00 0.00 2.29
26 27 7.094248 ACACAGTATATGGTACGTACTTGTTCA 60.094 37.037 24.07 13.91 0.00 3.18
27 28 7.219535 CACACAGTATATGGTACGTACTTGTTC 59.780 40.741 24.07 8.64 0.00 3.18
37 38 6.461110 ACACTACCACACAGTATATGGTAC 57.539 41.667 6.48 0.00 45.04 3.34
38 39 9.865152 TTATACACTACCACACAGTATATGGTA 57.135 33.333 9.25 9.25 45.04 3.25
40 41 8.635328 TGTTATACACTACCACACAGTATATGG 58.365 37.037 0.00 0.00 39.57 2.74
44 45 8.755028 TGATTGTTATACACTACCACACAGTAT 58.245 33.333 0.00 0.00 0.00 2.12
45 46 8.124808 TGATTGTTATACACTACCACACAGTA 57.875 34.615 0.00 0.00 0.00 2.74
89 90 1.726853 CTCCTTAGGACTTTGCACCG 58.273 55.000 0.00 0.00 0.00 4.94
142 175 7.816513 GGGTAGATTTATAGTTCCGGTGAATAC 59.183 40.741 0.00 0.00 31.98 1.89
143 176 7.731688 AGGGTAGATTTATAGTTCCGGTGAATA 59.268 37.037 0.00 0.00 31.98 1.75
144 177 6.557633 AGGGTAGATTTATAGTTCCGGTGAAT 59.442 38.462 0.00 0.00 31.98 2.57
145 178 5.901276 AGGGTAGATTTATAGTTCCGGTGAA 59.099 40.000 0.00 0.00 0.00 3.18
147 180 5.803237 AGGGTAGATTTATAGTTCCGGTG 57.197 43.478 0.00 0.00 0.00 4.94
148 181 7.566509 AGTTAAGGGTAGATTTATAGTTCCGGT 59.433 37.037 0.00 0.00 0.00 5.28
149 182 7.960262 AGTTAAGGGTAGATTTATAGTTCCGG 58.040 38.462 0.00 0.00 0.00 5.14
175 209 4.075682 CCTCTTGTCTGACTGACTGTCTA 58.924 47.826 9.51 0.11 45.54 2.59
197 231 6.019318 GCATTAAATGGATGCATCTTCACAAC 60.019 38.462 25.28 8.17 46.96 3.32
198 232 6.044046 GCATTAAATGGATGCATCTTCACAA 58.956 36.000 25.28 14.48 46.96 3.33
199 233 5.593968 GCATTAAATGGATGCATCTTCACA 58.406 37.500 25.28 15.27 46.96 3.58
238 272 2.564504 AGCAGAGCAATTCTTTTTCCCC 59.435 45.455 0.00 0.00 32.41 4.81
241 275 2.991866 GCCAGCAGAGCAATTCTTTTTC 59.008 45.455 0.00 0.00 32.41 2.29
246 280 1.340697 TGATGCCAGCAGAGCAATTCT 60.341 47.619 0.00 0.00 44.83 2.40
247 281 1.065701 CTGATGCCAGCAGAGCAATTC 59.934 52.381 3.29 0.00 44.83 2.17
250 284 0.255033 ATCTGATGCCAGCAGAGCAA 59.745 50.000 18.47 0.00 44.75 3.91
331 395 5.277442 GCAGTTTGTAACAATTTGCTGCAAT 60.277 36.000 16.77 3.15 44.97 3.56
347 411 0.098025 CACGTTTCGGTGCAGTTTGT 59.902 50.000 0.00 0.00 0.00 2.83
426 491 3.004752 AGATGTATTGCCAGTTGGGAC 57.995 47.619 0.00 0.00 40.01 4.46
439 504 2.289694 GGTGCCAGCCGATTAGATGTAT 60.290 50.000 0.00 0.00 0.00 2.29
464 529 0.879765 CAGCAAAGGAGGCACAGAAG 59.120 55.000 0.00 0.00 0.00 2.85
522 587 0.892755 TCAATCTTACGTGGGCGAGT 59.107 50.000 0.00 0.00 42.00 4.18
523 588 1.860950 CATCAATCTTACGTGGGCGAG 59.139 52.381 0.00 0.00 42.00 5.03
569 634 8.858003 TTTCTTTAGTACTATGATTGAGCTCG 57.142 34.615 9.64 0.00 0.00 5.03
588 653 9.592720 CGTTTGTTTTCTTCAAATGTTTTCTTT 57.407 25.926 0.00 0.00 37.16 2.52
654 720 5.938125 TGGGCTTATTTTTCTCAGTACTGAC 59.062 40.000 21.74 7.76 35.46 3.51
655 721 6.121776 TGGGCTTATTTTTCTCAGTACTGA 57.878 37.500 23.80 23.80 38.06 3.41
704 771 7.060059 CACACATAATAGATTCGAGACGATGAC 59.940 40.741 0.00 0.00 35.23 3.06
729 796 9.921637 GGTCTTTTCATATGTTTAATGTTTCCA 57.078 29.630 1.90 0.00 0.00 3.53
762 829 3.329889 TTGCGGGGTCATGAGGCT 61.330 61.111 0.00 0.00 0.00 4.58
773 840 1.065851 ACGGTTTAGTTTTGTTGCGGG 59.934 47.619 0.00 0.00 0.00 6.13
886 955 1.722011 AGCCACCTATGTCGTTTTCG 58.278 50.000 0.00 0.00 45.64 3.46
919 988 3.685550 GCAGCAGGTATATGTGGGAAACT 60.686 47.826 0.00 0.00 0.00 2.66
1068 1137 3.057548 TAGGACGCGGACGCAGAA 61.058 61.111 17.35 0.00 45.53 3.02
1098 1167 4.516195 GAGAGGCCGAAGACGCCC 62.516 72.222 0.00 0.00 37.29 6.13
1140 1209 1.747355 CCGTACCTTCTCTTTCGGCTA 59.253 52.381 0.00 0.00 0.00 3.93
1167 1236 5.757320 CAGAATGAACACTTGCTATAGAGGG 59.243 44.000 3.21 0.00 39.69 4.30
1240 1340 1.134220 ACAAACGGGAGAAAGCTCACA 60.134 47.619 0.00 0.00 45.13 3.58
1258 1358 4.099380 TGACAGATTCAATACGCGTACA 57.901 40.909 23.19 7.96 0.00 2.90
1310 1410 2.332063 ATTGGCATACAACCGAGGAG 57.668 50.000 0.00 0.00 42.94 3.69
1343 1443 8.167392 TCAATGTTCCCTCTCCTTAATTTTACA 58.833 33.333 0.00 0.00 0.00 2.41
1464 1567 9.523168 AGTTTATTAACCTGCAGTAAACCATTA 57.477 29.630 23.09 6.59 36.44 1.90
1489 1592 5.005740 TCTCAATCATCAGTGTTTTGGGAG 58.994 41.667 0.00 0.00 30.82 4.30
1493 1597 4.152938 TCGCTCTCAATCATCAGTGTTTTG 59.847 41.667 0.00 0.00 0.00 2.44
1514 1618 8.645487 GTTGTTTTAGTCTAGGTTCAACTATCG 58.355 37.037 0.00 0.00 33.57 2.92
1520 1624 8.836413 CAGAATGTTGTTTTAGTCTAGGTTCAA 58.164 33.333 0.00 0.00 0.00 2.69
1521 1625 7.444183 CCAGAATGTTGTTTTAGTCTAGGTTCA 59.556 37.037 0.00 0.00 0.00 3.18
1545 1661 3.007940 CCCATGAAATATAGCTCGACCCA 59.992 47.826 0.00 0.00 0.00 4.51
1546 1662 3.260884 TCCCATGAAATATAGCTCGACCC 59.739 47.826 0.00 0.00 0.00 4.46
1547 1663 4.537135 TCCCATGAAATATAGCTCGACC 57.463 45.455 0.00 0.00 0.00 4.79
1570 1712 1.949525 TGGTTCAGCTTTCAGCAGTTC 59.050 47.619 0.00 0.00 45.56 3.01
1572 1714 1.141657 TCTGGTTCAGCTTTCAGCAGT 59.858 47.619 12.99 0.00 45.56 4.40
1649 1791 6.682423 ATGATGATGTACAAATGCGAAAGA 57.318 33.333 0.00 0.00 0.00 2.52
1689 1831 8.950210 AGCATTCCACTGCATGTATTTATATAC 58.050 33.333 0.00 0.00 44.77 1.47
1731 1873 9.557061 GGGAATATGGAGTTACTAGTAAAAAGG 57.443 37.037 16.82 0.00 0.00 3.11
1743 1885 7.786943 TGCATATTTTTGGGGAATATGGAGTTA 59.213 33.333 14.93 0.00 43.10 2.24
1756 1900 3.962718 AGGAGGATGTGCATATTTTTGGG 59.037 43.478 0.00 0.00 0.00 4.12
1780 1928 3.779271 TTAAATGCGCATGCTTCATCA 57.221 38.095 26.09 6.06 43.34 3.07
1793 1941 4.092821 GCCCGAAGTTTCCAAATTAAATGC 59.907 41.667 0.00 0.00 0.00 3.56
1882 2030 5.182001 GCAGTAGCTTCTCAAGAAAATGGAA 59.818 40.000 0.00 0.00 37.91 3.53
1904 2052 4.755411 AGCGCTTCAGTTTAGTAATAGCA 58.245 39.130 2.64 0.00 0.00 3.49
1905 2053 5.720261 AAGCGCTTCAGTTTAGTAATAGC 57.280 39.130 18.98 0.00 0.00 2.97
1923 2071 9.301238 ATGCTTAAAATGTGCATGCATAAAGCG 62.301 37.037 29.93 16.61 44.48 4.68
1951 2099 9.593134 ACTGTAGTCATTGTTTTCTCTCATATC 57.407 33.333 0.00 0.00 0.00 1.63
1992 2145 4.634883 ACAGTGCTGCAATATCAGAAAGAG 59.365 41.667 2.77 0.00 36.19 2.85
2230 2383 7.341769 CCAACTGATTTATTGGGTAATGAAGGA 59.658 37.037 0.00 0.00 41.52 3.36
2260 2413 5.762179 TGGATCACCAAGATTCACTAAGT 57.238 39.130 0.00 0.00 43.91 2.24
2299 2452 0.036022 GGAGAAGTTCCTGCTGCACT 59.964 55.000 0.00 0.00 43.16 4.40
2439 2609 0.995803 TGGGCACAAGCATACCCTAA 59.004 50.000 0.00 0.00 43.25 2.69
2556 2726 1.802365 GCGAAAGTGAACCAACGGTAT 59.198 47.619 0.00 0.00 33.12 2.73
2562 2732 0.395862 TTGGGGCGAAAGTGAACCAA 60.396 50.000 0.00 0.00 35.78 3.67
2565 2735 0.958822 ATGTTGGGGCGAAAGTGAAC 59.041 50.000 0.00 0.00 0.00 3.18
2574 2744 4.156922 TCAAACTTTGTATATGTTGGGGCG 59.843 41.667 1.44 0.00 0.00 6.13
2781 2955 1.695597 CAGAGGAGAGGGGGCCAAT 60.696 63.158 4.39 0.00 0.00 3.16
2925 3099 6.601332 AGGAAATTCTGGTTTCTAAGTGACA 58.399 36.000 0.00 0.00 38.02 3.58
2926 3100 7.148390 GCTAGGAAATTCTGGTTTCTAAGTGAC 60.148 40.741 0.00 0.00 38.02 3.67
2930 3118 7.391833 ACTTGCTAGGAAATTCTGGTTTCTAAG 59.608 37.037 0.00 0.00 38.02 2.18
3197 3393 2.979678 AGTTAGTCACCACTGGTCCATT 59.020 45.455 0.00 0.00 31.02 3.16
3215 3411 2.445525 TGAAAACTAGGGCAAGGGAGTT 59.554 45.455 0.00 0.00 33.60 3.01
3252 3449 0.325577 ATTCCAAGGCCAATGGGTCC 60.326 55.000 23.19 0.00 40.78 4.46
3307 3504 4.141390 GCTTCTCTAAAGATGGGAATGGGA 60.141 45.833 0.00 0.00 0.00 4.37
3327 3524 5.414454 TCATTTAACTATGACTTTGCGGCTT 59.586 36.000 0.00 0.00 29.82 4.35
3351 3548 8.633561 GCAGCCATCTATTTTTACCTAGATTTT 58.366 33.333 0.00 0.00 33.45 1.82
3374 3575 2.045536 GACCCAGAAGGCAGGCAG 60.046 66.667 0.00 0.00 40.58 4.85
3378 3579 0.250295 TTTGACGACCCAGAAGGCAG 60.250 55.000 0.00 0.00 40.58 4.85
3396 3597 0.892063 GGAGTCTCAAGAGTCGCCTT 59.108 55.000 9.15 0.00 43.64 4.35
3411 3612 1.694696 GTGGTGGAAGAAGTCAGGAGT 59.305 52.381 0.00 0.00 0.00 3.85
3416 3617 1.070786 GCGGTGGTGGAAGAAGTCA 59.929 57.895 0.00 0.00 0.00 3.41
3417 3618 0.951040 CTGCGGTGGTGGAAGAAGTC 60.951 60.000 0.00 0.00 0.00 3.01
3480 3769 0.519077 GAAGACGAGCAAGGCTTTGG 59.481 55.000 10.89 0.00 40.07 3.28
3485 3774 0.449388 CAATGGAAGACGAGCAAGGC 59.551 55.000 0.00 0.00 0.00 4.35
3508 3797 5.635120 ACTTTTGCTAAAGGAAGGAGACAT 58.365 37.500 21.83 0.00 44.10 3.06
3513 3802 4.760204 GTGCTACTTTTGCTAAAGGAAGGA 59.240 41.667 21.83 16.74 44.10 3.36
3514 3803 4.762251 AGTGCTACTTTTGCTAAAGGAAGG 59.238 41.667 21.83 6.66 44.10 3.46
3515 3804 5.335191 CCAGTGCTACTTTTGCTAAAGGAAG 60.335 44.000 21.83 18.46 44.10 3.46
3516 3805 4.518970 CCAGTGCTACTTTTGCTAAAGGAA 59.481 41.667 21.83 10.58 44.10 3.36
3626 3915 6.017605 CGGATATTCTAATATGGCCAATCAGC 60.018 42.308 10.96 0.00 31.96 4.26
3630 3919 5.193728 ACCCGGATATTCTAATATGGCCAAT 59.806 40.000 10.96 1.41 31.96 3.16
3680 3969 9.249053 CAATACTCATCCATACCTGATAGTAGT 57.751 37.037 0.00 0.00 0.00 2.73
3703 3992 1.883638 CGGGATCCGCCATCAATCAAT 60.884 52.381 5.45 0.00 41.17 2.57
3739 4028 8.948631 TCACCATGAATGTCTATTAAGAGAAC 57.051 34.615 0.38 0.00 30.45 3.01
3749 4038 2.892374 CGCACTCACCATGAATGTCTA 58.108 47.619 0.00 0.00 0.00 2.59
3750 4039 1.730501 CGCACTCACCATGAATGTCT 58.269 50.000 0.00 0.00 0.00 3.41
3817 4106 9.847706 TTATTTCAACACAACGCAATAATATGT 57.152 25.926 0.00 0.00 0.00 2.29
3819 4108 9.847706 TGTTATTTCAACACAACGCAATAATAT 57.152 25.926 0.00 0.00 0.00 1.28
3820 4109 9.678941 TTGTTATTTCAACACAACGCAATAATA 57.321 25.926 0.00 0.00 0.00 0.98
3828 4117 7.148983 GGATGACATTGTTATTTCAACACAACG 60.149 37.037 0.00 0.00 33.33 4.10
3829 4118 7.867403 AGGATGACATTGTTATTTCAACACAAC 59.133 33.333 0.00 0.00 33.33 3.32
3842 4131 3.370953 GGTGCCTCTAGGATGACATTGTT 60.371 47.826 0.00 0.00 37.39 2.83
3860 4149 1.251251 AGCCAATCAAGACAAGGTGC 58.749 50.000 0.00 0.00 0.00 5.01
3868 4157 6.591935 AGGTTCGAATATTAGCCAATCAAGA 58.408 36.000 0.00 0.00 0.00 3.02
3880 4169 7.339212 TCCAATGATCACAAAGGTTCGAATATT 59.661 33.333 0.00 0.00 0.00 1.28
3886 4175 4.764679 TTCCAATGATCACAAAGGTTCG 57.235 40.909 0.00 0.00 0.00 3.95
3888 4177 5.336102 AGGATTCCAATGATCACAAAGGTT 58.664 37.500 5.29 0.00 0.00 3.50
3926 4215 2.022195 CCTCATACTCGAGTTTCCCGA 58.978 52.381 25.44 11.89 34.61 5.14
3970 4259 1.680555 GGAAGACACACCACACCAACA 60.681 52.381 0.00 0.00 0.00 3.33
3990 4279 0.526662 AGAGCCGACAACGACTAAGG 59.473 55.000 0.00 0.00 42.66 2.69
3995 4284 0.935196 ACAAAAGAGCCGACAACGAC 59.065 50.000 0.00 0.00 42.66 4.34
4007 4296 7.741785 TGTAGTAGGGAAAGAATGACAAAAGA 58.258 34.615 0.00 0.00 0.00 2.52
4039 4328 3.071602 CACCACCATCCTATCCAACCTAG 59.928 52.174 0.00 0.00 0.00 3.02
4042 4331 1.750682 GCACCACCATCCTATCCAACC 60.751 57.143 0.00 0.00 0.00 3.77
4069 4358 0.895100 TGTTGACATCCCAGCTTGCC 60.895 55.000 0.00 0.00 0.00 4.52
4084 4373 3.864583 CCAAATTGTAATGCCCGATGTTG 59.135 43.478 0.00 0.00 0.00 3.33
4141 4430 2.555123 CCAATCTGGGGTGTTCACG 58.445 57.895 0.00 0.00 32.67 4.35
4202 4491 8.620416 TCAATGTAATATACAGTTGGTCATTGC 58.380 33.333 0.00 0.00 42.77 3.56
4215 4504 7.595311 TGATGCACCGATCAATGTAATATAC 57.405 36.000 0.00 0.00 29.11 1.47
4250 4546 7.499232 ACATATGTAGCTTAACTGGAAATGGAC 59.501 37.037 6.56 0.00 0.00 4.02
4269 6307 9.265901 CTAGCAGAGCAAACTTTATACATATGT 57.734 33.333 13.93 13.93 0.00 2.29
4287 6325 8.715998 CAAATATGCCTGTAATAACTAGCAGAG 58.284 37.037 0.00 0.00 37.62 3.35
4289 6327 8.383318 ACAAATATGCCTGTAATAACTAGCAG 57.617 34.615 0.00 0.00 37.62 4.24
4301 6339 7.469181 GCTTTATGCTAGAACAAATATGCCTGT 60.469 37.037 0.00 0.00 38.95 4.00
4309 6347 6.660949 ACAGAAGGCTTTATGCTAGAACAAAT 59.339 34.615 0.00 0.00 42.39 2.32
4331 6370 2.771943 ACACATACCCTCCCACATACAG 59.228 50.000 0.00 0.00 0.00 2.74
4613 6717 2.627699 GTCCTTGATGTTTTTCTGGCCA 59.372 45.455 4.71 4.71 0.00 5.36
4663 6767 8.459911 TCTCAGACGTTAGATGGTAATCAATA 57.540 34.615 0.00 0.00 35.03 1.90
4807 6912 6.780706 TTACTCTAAGAAAAAGGCTGTTCG 57.219 37.500 0.00 0.00 0.00 3.95
4850 6955 4.500837 CGACCGACTGAGAATTAGTTGATG 59.499 45.833 0.00 0.00 32.37 3.07
4871 6987 5.755861 TCATTTGTCTACAATGTTGTGTCGA 59.244 36.000 8.57 0.57 42.31 4.20
4968 7091 5.057819 GGAGAGTCTATATCACAGTCGACA 58.942 45.833 19.50 0.00 0.00 4.35
5085 7209 6.657541 ACAAAACCTAAGTCACAGTTTCTTCA 59.342 34.615 0.00 0.00 31.47 3.02
5097 7221 3.697542 ACACCAACCACAAAACCTAAGTC 59.302 43.478 0.00 0.00 0.00 3.01
5122 7250 9.755064 CAGTTTTACAGATAGGAAAATACAACG 57.245 33.333 0.00 0.00 0.00 4.10
5196 7334 6.884832 ACATCTTATATTTGTGAACGGAGGA 58.115 36.000 0.00 0.00 0.00 3.71
5250 7388 6.319658 AGTGTGTCTGTTCATTCATTTCACTT 59.680 34.615 0.00 0.00 0.00 3.16
5254 7392 6.428159 AGGTAGTGTGTCTGTTCATTCATTTC 59.572 38.462 0.00 0.00 0.00 2.17
5292 7447 7.766738 TCCGCACAAATATAAGATGTTCTAACA 59.233 33.333 0.00 0.00 44.06 2.41
5335 7492 9.146984 TGTTATTTCGATGGTAGTGAAAGTTAG 57.853 33.333 0.00 0.00 35.31 2.34
5363 7520 1.925229 ATTGCCGTTTACATGCATGC 58.075 45.000 26.53 11.82 34.51 4.06
5533 7690 3.071206 AGCTCGGCCACGACATCT 61.071 61.111 2.24 0.00 45.59 2.90
5575 7732 5.420409 GTGGAATCGAACCTCAGAAATAGT 58.580 41.667 12.11 0.00 0.00 2.12
5578 7735 3.610911 GGTGGAATCGAACCTCAGAAAT 58.389 45.455 12.11 0.00 33.40 2.17
5879 8042 4.261801 CCACTGTTTGGGAGATACGAATT 58.738 43.478 0.00 0.00 42.54 2.17
6003 8166 3.823873 TGTGCACATACCCTAAACAAAGG 59.176 43.478 17.42 0.00 36.30 3.11
6011 8174 2.164827 CAGTACGTGTGCACATACCCTA 59.835 50.000 24.69 5.39 30.99 3.53
6128 8291 0.541764 GGGTTTTGACCATGGCTCCA 60.542 55.000 13.04 4.68 0.00 3.86
6163 8326 2.025321 GTCCTGGGCCCTCAAATTTCTA 60.025 50.000 25.70 0.00 0.00 2.10
6173 8336 0.486879 TGATTTTTGTCCTGGGCCCT 59.513 50.000 25.70 0.00 0.00 5.19
6413 8844 6.918067 ATTATGAAGATGTGACCGGAGATA 57.082 37.500 9.46 0.00 0.00 1.98
6418 8849 7.657354 TCAGATTAATTATGAAGATGTGACCGG 59.343 37.037 0.00 0.00 0.00 5.28
6501 8932 9.661954 AGTAAATATCCTAGAAGAGGTGAATGA 57.338 33.333 0.00 0.00 46.76 2.57
6520 8951 5.941647 GTCTGGTTGTTAGCCCAAGTAAATA 59.058 40.000 0.00 0.00 0.00 1.40
6563 9003 6.268825 TCTAGCTCTATGTCAACGAAAAGT 57.731 37.500 0.00 0.00 0.00 2.66
6599 9039 1.825474 GGCAGTACAAGAGGCTAGTGA 59.175 52.381 4.05 0.00 0.00 3.41
6601 9041 1.938585 TGGCAGTACAAGAGGCTAGT 58.061 50.000 0.00 0.00 0.00 2.57
6689 9129 7.176690 CCACCATTTCTCAAACTTGGTACTATT 59.823 37.037 0.00 0.00 38.61 1.73
6690 9130 6.659242 CCACCATTTCTCAAACTTGGTACTAT 59.341 38.462 0.00 0.00 38.61 2.12
6696 9136 2.629617 AGCCACCATTTCTCAAACTTGG 59.370 45.455 0.00 0.00 0.00 3.61
6743 9188 4.093743 GGAGCCTTCCAAATTTTCCCTAA 58.906 43.478 0.00 0.00 43.45 2.69
6747 9192 2.354103 GCAGGAGCCTTCCAAATTTTCC 60.354 50.000 0.00 0.00 46.64 3.13
6840 9285 6.701841 CCTAAGTTCAGCTTCTATATCGCAAA 59.298 38.462 0.00 0.00 38.57 3.68


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

AutoCloner maintained by Alex Coulton.