Multiple sequence alignment - TraesCS7D01G244600

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G244600 chr7D 100.000 5345 0 0 1 5345 213372791 213378135 0.000000e+00 9871.0
1 TraesCS7D01G244600 chr7D 82.906 117 17 3 271 385 588081782 588081897 9.470000e-18 102.0
2 TraesCS7D01G244600 chr7D 82.759 116 19 1 266 380 593035315 593035200 9.470000e-18 102.0
3 TraesCS7D01G244600 chr7B 94.827 4040 138 31 557 4573 188605487 188601496 0.000000e+00 6237.0
4 TraesCS7D01G244600 chr7B 91.501 353 23 6 4572 4923 188601406 188601060 3.740000e-131 479.0
5 TraesCS7D01G244600 chr7B 95.105 286 11 1 285 570 188605786 188605504 1.060000e-121 448.0
6 TraesCS7D01G244600 chr7B 94.718 284 7 3 3 286 188606175 188605900 8.220000e-118 435.0
7 TraesCS7D01G244600 chr7B 95.181 166 8 0 5180 5345 188595069 188594904 4.110000e-66 263.0
8 TraesCS7D01G244600 chr7B 84.034 119 13 6 266 380 72998486 72998370 5.660000e-20 110.0
9 TraesCS7D01G244600 chr7B 93.617 47 3 0 5138 5184 188595138 188595092 2.670000e-08 71.3
10 TraesCS7D01G244600 chr7A 96.996 2197 62 4 1491 3685 224987317 224989511 0.000000e+00 3688.0
11 TraesCS7D01G244600 chr7A 89.960 1006 46 15 3922 4923 224989724 224990678 0.000000e+00 1247.0
12 TraesCS7D01G244600 chr7A 91.124 890 43 16 580 1459 224986453 224987316 0.000000e+00 1173.0
13 TraesCS7D01G244600 chr7A 81.203 399 40 17 61 426 224985918 224986314 6.770000e-74 289.0
14 TraesCS7D01G244600 chr7A 96.988 166 5 0 5180 5345 224990758 224990923 4.080000e-71 279.0
15 TraesCS7D01G244600 chr7A 89.062 192 20 1 4923 5113 267096097 267095906 2.490000e-58 237.0
16 TraesCS7D01G244600 chr7A 95.652 115 5 0 482 596 224986320 224986434 9.140000e-43 185.0
17 TraesCS7D01G244600 chr7A 85.714 154 14 7 3686 3835 224989577 224989726 7.170000e-34 156.0
18 TraesCS7D01G244600 chr7A 82.906 117 17 3 271 385 679957023 679957138 9.470000e-18 102.0
19 TraesCS7D01G244600 chr7A 96.364 55 2 0 5130 5184 224990681 224990735 2.050000e-14 91.6
20 TraesCS7D01G244600 chr5B 80.407 786 146 4 1833 2611 449752506 449751722 4.610000e-165 592.0
21 TraesCS7D01G244600 chr5B 81.513 119 16 6 271 385 243851016 243851132 5.700000e-15 93.5
22 TraesCS7D01G244600 chr5D 79.684 822 156 6 1833 2644 376664380 376663560 2.770000e-162 582.0
23 TraesCS7D01G244600 chr5D 84.211 209 29 4 4917 5122 168559553 168559346 3.260000e-47 200.0
24 TraesCS7D01G244600 chr5A 79.771 786 151 3 1833 2611 477437375 477436591 1.000000e-156 564.0
25 TraesCS7D01G244600 chr3A 90.500 200 18 1 4923 5121 702519326 702519127 4.110000e-66 263.0
26 TraesCS7D01G244600 chr1B 90.104 192 18 1 4923 5113 666849934 666850125 1.150000e-61 248.0
27 TraesCS7D01G244600 chr3D 86.911 191 24 1 4924 5113 604301912 604302102 4.190000e-51 213.0
28 TraesCS7D01G244600 chr3D 85.000 200 26 4 4917 5113 281396659 281396461 3.260000e-47 200.0
29 TraesCS7D01G244600 chr3D 83.028 218 33 4 4908 5122 556429342 556429126 1.520000e-45 195.0
30 TraesCS7D01G244600 chr3D 79.339 121 24 1 266 385 375193910 375193790 3.430000e-12 84.2
31 TraesCS7D01G244600 chr2D 86.082 194 24 3 4922 5113 637830354 637830546 7.020000e-49 206.0
32 TraesCS7D01G244600 chr2D 81.731 104 17 2 283 385 195295020 195294918 9.540000e-13 86.1
33 TraesCS7D01G244600 chr6D 84.500 200 27 4 4917 5113 244681604 244681802 1.520000e-45 195.0
34 TraesCS7D01G244600 chr2A 79.259 135 25 3 256 388 210472160 210472027 2.050000e-14 91.6


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 TraesCS7D01G244600 chr7D 213372791 213378135 5344 False 9871.000 9871 100.000000 1 5345 1 chr7D.!!$F1 5344
1 TraesCS7D01G244600 chr7B 188601060 188606175 5115 True 1899.750 6237 94.037750 3 4923 4 chr7B.!!$R3 4920
2 TraesCS7D01G244600 chr7A 224985918 224990923 5005 False 888.575 3688 91.750125 61 5345 8 chr7A.!!$F2 5284
3 TraesCS7D01G244600 chr5B 449751722 449752506 784 True 592.000 592 80.407000 1833 2611 1 chr5B.!!$R1 778
4 TraesCS7D01G244600 chr5D 376663560 376664380 820 True 582.000 582 79.684000 1833 2644 1 chr5D.!!$R2 811
5 TraesCS7D01G244600 chr5A 477436591 477437375 784 True 564.000 564 79.771000 1833 2611 1 chr5A.!!$R1 778

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
116 147 2.501723 ACGCTTCTCTCTCTCTCTCTCT 59.498 50.000 0.00 0.00 0.00 3.10 F
602 841 2.832838 TCTGGAGGCTTATCTTCACCA 58.167 47.619 0.00 0.00 0.00 4.17 F
1230 1480 2.485122 GGTTTCAGATTGCCGCGG 59.515 61.111 24.05 24.05 0.00 6.46 F
1413 1663 2.887151 AGGATGGTCTTGGTTCCTTG 57.113 50.000 0.00 0.00 34.98 3.61 F
2770 3031 2.167281 AGACGATGTGGGAGTTCATCAG 59.833 50.000 0.00 0.00 39.99 2.90 F
3776 4105 1.001633 GCGAGAGGTGAGGTTGGTTAA 59.998 52.381 0.00 0.00 0.00 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1057 1305 1.325355 ACCTCGTCGAGAAAAGGTCA 58.675 50.000 23.74 0.00 37.59 4.02 R
1775 2027 1.478510 CACATCACCTAGCTCCTTCGT 59.521 52.381 0.00 0.00 0.00 3.85 R
2770 3031 1.645704 CTCTGATGTGCACAGCTGGC 61.646 60.000 32.56 18.37 35.61 4.85 R
3324 3585 0.535102 GGCAGGGACATGGTTATCCG 60.535 60.000 0.00 0.00 35.67 4.18 R
3813 4142 0.035458 CCAACCTCACCTCTCACACC 59.965 60.000 0.00 0.00 0.00 4.16 R
4907 5342 0.035439 GGCTCGAATTTCCTGGGTCA 60.035 55.000 0.00 0.00 0.00 4.02 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
97 98 4.942483 TGGAGGACTTAAGAAGACTAGACG 59.058 45.833 10.09 0.00 0.00 4.18
115 146 2.866762 GACGCTTCTCTCTCTCTCTCTC 59.133 54.545 0.00 0.00 0.00 3.20
116 147 2.501723 ACGCTTCTCTCTCTCTCTCTCT 59.498 50.000 0.00 0.00 0.00 3.10
117 148 3.126831 CGCTTCTCTCTCTCTCTCTCTC 58.873 54.545 0.00 0.00 0.00 3.20
118 149 3.181471 CGCTTCTCTCTCTCTCTCTCTCT 60.181 52.174 0.00 0.00 0.00 3.10
119 150 4.125703 GCTTCTCTCTCTCTCTCTCTCTG 58.874 52.174 0.00 0.00 0.00 3.35
120 151 4.383552 GCTTCTCTCTCTCTCTCTCTCTGT 60.384 50.000 0.00 0.00 0.00 3.41
121 152 4.743057 TCTCTCTCTCTCTCTCTCTGTG 57.257 50.000 0.00 0.00 0.00 3.66
122 153 4.096681 TCTCTCTCTCTCTCTCTCTGTGT 58.903 47.826 0.00 0.00 0.00 3.72
123 154 4.081476 TCTCTCTCTCTCTCTCTCTGTGTG 60.081 50.000 0.00 0.00 0.00 3.82
124 155 3.837731 TCTCTCTCTCTCTCTCTGTGTGA 59.162 47.826 0.00 0.00 0.00 3.58
130 161 5.240623 TCTCTCTCTCTCTGTGTGAAAGAAC 59.759 44.000 0.00 0.00 0.00 3.01
147 178 9.646427 GTGAAAGAACTAGACACTTGATAGAAT 57.354 33.333 0.00 0.00 0.00 2.40
177 208 5.841957 AGGATTGGCAAGATGTGTTTATC 57.158 39.130 5.96 0.00 0.00 1.75
219 250 3.664107 TGATAGAACAGTGTGTTGCTCC 58.336 45.455 0.00 0.00 41.28 4.70
346 520 7.500807 AATTAAAACGAGTGAACAAACACAC 57.499 32.000 0.00 0.00 42.45 3.82
403 577 4.229582 TGTTATACAGAGGGAAAATGGGCT 59.770 41.667 0.00 0.00 0.00 5.19
476 650 6.609237 ATGTCGATTTGTCATCTTGTATGG 57.391 37.500 0.00 0.00 0.00 2.74
477 651 5.729510 TGTCGATTTGTCATCTTGTATGGA 58.270 37.500 0.00 0.00 0.00 3.41
478 652 5.812127 TGTCGATTTGTCATCTTGTATGGAG 59.188 40.000 0.00 0.00 0.00 3.86
531 705 6.034161 AGAAACAGGTGCGTATACTAAACT 57.966 37.500 0.56 0.00 0.00 2.66
544 718 3.764237 ACTAAACTCATGGTCAACGGT 57.236 42.857 0.00 0.00 0.00 4.83
559 733 2.943653 GGTTCACTTTGCCGGACG 59.056 61.111 5.05 0.00 0.00 4.79
602 841 2.832838 TCTGGAGGCTTATCTTCACCA 58.167 47.619 0.00 0.00 0.00 4.17
610 849 3.993081 GGCTTATCTTCACCATCATCGAG 59.007 47.826 0.00 0.00 0.00 4.04
1230 1480 2.485122 GGTTTCAGATTGCCGCGG 59.515 61.111 24.05 24.05 0.00 6.46
1362 1612 2.979240 AGGTCTTCTCGATTGGCTTTC 58.021 47.619 0.00 0.00 0.00 2.62
1413 1663 2.887151 AGGATGGTCTTGGTTCCTTG 57.113 50.000 0.00 0.00 34.98 3.61
1427 1677 4.202243 TGGTTCCTTGCAAATTTTCTCCAG 60.202 41.667 0.00 0.00 0.00 3.86
1469 1719 3.895232 ACATGCTAGGATGTTCTCGTT 57.105 42.857 22.81 0.00 32.38 3.85
1486 1736 6.164408 TCTCGTTACAGTGCACATTATTTG 57.836 37.500 21.04 9.85 0.00 2.32
1489 1739 7.385478 TCTCGTTACAGTGCACATTATTTGTTA 59.615 33.333 21.04 4.42 36.00 2.41
1597 1849 5.643777 GCACTGTATGGTCACAATTCTAAGT 59.356 40.000 0.00 0.00 0.00 2.24
1608 1860 9.366216 GGTCACAATTCTAAGTTTGTTCTTTTT 57.634 29.630 0.00 0.00 33.93 1.94
1735 1987 6.620877 TGAGTAGGGTGATGTTATTGAGTT 57.379 37.500 0.00 0.00 0.00 3.01
1775 2027 9.264653 AGATGATGGATAATCTAGCTATTGTCA 57.735 33.333 7.89 0.00 36.15 3.58
2062 2320 4.910195 TGCTCAAGTTGATGGAAGTATGT 58.090 39.130 5.91 0.00 0.00 2.29
2657 2918 7.284716 ACGGTGTATCAGATACTCATCTTGTTA 59.715 37.037 19.39 0.00 39.62 2.41
2672 2933 4.976864 TCTTGTTAACCTAGGGGACAAAC 58.023 43.478 14.81 9.87 36.25 2.93
2770 3031 2.167281 AGACGATGTGGGAGTTCATCAG 59.833 50.000 0.00 0.00 39.99 2.90
2847 3108 6.506513 CGTCATGATAAACGCTCTACTCAAAC 60.507 42.308 0.00 0.00 31.48 2.93
2848 3109 6.310467 GTCATGATAAACGCTCTACTCAAACA 59.690 38.462 0.00 0.00 0.00 2.83
2944 3205 4.080582 TCTGAGGTTGAAGGAACACAAAGA 60.081 41.667 0.00 0.00 36.12 2.52
2992 3253 3.304659 GCAACGCAATTCCGGATATGAAT 60.305 43.478 18.38 0.47 33.97 2.57
3241 3502 5.185828 GCCTGGAAATACTTTTCAACCAGAT 59.814 40.000 0.00 0.00 42.55 2.90
3320 3581 4.124238 TGCAAAACACTCAGTACCACTAC 58.876 43.478 0.00 0.00 0.00 2.73
3324 3585 5.718724 AAACACTCAGTACCACTACCTAC 57.281 43.478 0.00 0.00 0.00 3.18
3337 3598 4.261909 CCACTACCTACGGATAACCATGTC 60.262 50.000 0.00 0.00 35.59 3.06
3378 3642 5.428253 AGCTTTGAACAGTTCTTACAGTCA 58.572 37.500 14.51 0.00 0.00 3.41
3379 3643 6.058183 AGCTTTGAACAGTTCTTACAGTCAT 58.942 36.000 14.51 0.00 0.00 3.06
3380 3644 6.203723 AGCTTTGAACAGTTCTTACAGTCATC 59.796 38.462 14.51 0.00 0.00 2.92
3430 3694 1.308783 TTGCTGGTGACACGCAACAA 61.309 50.000 14.52 11.10 45.20 2.83
3460 3724 6.321181 TGAGTGATGCTTTTTATATTGACCCC 59.679 38.462 0.00 0.00 0.00 4.95
3628 3892 4.346418 TCCCTGATCTTTCCTAGCTCATTC 59.654 45.833 0.00 0.00 29.22 2.67
3655 3919 5.794894 TCTCAGTTCTTTGGATACTTGGAC 58.205 41.667 0.00 0.00 37.61 4.02
3776 4105 1.001633 GCGAGAGGTGAGGTTGGTTAA 59.998 52.381 0.00 0.00 0.00 2.01
3789 4118 8.135529 GTGAGGTTGGTTAAAGGCAATTATATC 58.864 37.037 0.00 0.00 0.00 1.63
3791 4120 8.838649 AGGTTGGTTAAAGGCAATTATATCTT 57.161 30.769 0.00 0.00 0.00 2.40
3890 4219 4.992951 GCCAGCAAAGAAAGATTGTGATTT 59.007 37.500 0.00 0.00 0.00 2.17
3912 4241 4.314961 TCTCAGCTGAATTCGCAAGTAAA 58.685 39.130 18.85 0.00 39.48 2.01
3967 4299 3.764237 TTCCCAGTGTCTTACAAGTCC 57.236 47.619 0.00 0.00 0.00 3.85
3975 4307 2.749076 TGTCTTACAAGTCCATGCATGC 59.251 45.455 21.69 11.82 0.00 4.06
3989 4321 1.881973 TGCATGCCTTGTTCTCAGTTC 59.118 47.619 16.68 0.00 0.00 3.01
4012 4344 6.524734 TCTGATTTCAGCTCTCTTTGTAACA 58.475 36.000 2.60 0.00 43.46 2.41
4040 4372 1.999648 TTCTGTTGATTGCAGCCCTT 58.000 45.000 0.00 0.00 34.21 3.95
4067 4400 1.740025 GATCGCTGAGAAAAAGGGGTG 59.260 52.381 0.00 0.00 0.00 4.61
4128 4461 3.132289 GTGGTGCTAATCCTGCTACAGTA 59.868 47.826 0.00 0.00 0.00 2.74
4129 4462 3.384789 TGGTGCTAATCCTGCTACAGTAG 59.615 47.826 2.85 2.85 0.00 2.57
4134 4467 4.825085 GCTAATCCTGCTACAGTAGAGAGT 59.175 45.833 12.15 6.37 0.00 3.24
4188 4521 1.181098 AGTGCCCCTTTGACATGTGC 61.181 55.000 1.15 0.00 0.00 4.57
4189 4522 1.152589 TGCCCCTTTGACATGTGCA 60.153 52.632 1.15 1.06 0.00 4.57
4304 4644 7.581213 TTTTTCTTTGTGGCTAAGAGAATCA 57.419 32.000 0.00 0.00 37.82 2.57
4339 4679 0.394762 TGTCATGCCCTCTTGGATGC 60.395 55.000 0.00 0.00 35.39 3.91
4354 4694 0.099436 GATGCCGTCCTGAATGTTGC 59.901 55.000 0.00 0.00 0.00 4.17
4384 4728 1.154093 CTGAATGTTGCTGCTGGCG 60.154 57.895 0.00 0.00 45.43 5.69
4385 4729 2.180017 GAATGTTGCTGCTGGCGG 59.820 61.111 0.00 0.00 45.43 6.13
4404 4748 1.002134 ACACCTGCATGGCTGTACC 60.002 57.895 0.00 0.00 40.22 3.34
4405 4749 1.300963 CACCTGCATGGCTGTACCT 59.699 57.895 0.00 0.00 40.22 3.08
4406 4750 1.028330 CACCTGCATGGCTGTACCTG 61.028 60.000 0.00 0.00 40.22 4.00
4407 4751 1.300963 CCTGCATGGCTGTACCTGT 59.699 57.895 0.00 0.00 40.22 4.00
4435 4779 0.883833 CTTGCCGCAGAATTTCCTGT 59.116 50.000 0.00 0.00 36.57 4.00
4455 4799 3.822735 TGTTCTTTTTCTGCAGGATGAGG 59.177 43.478 15.13 0.00 39.69 3.86
4564 4908 1.680249 GGGCCTTGTCTCTCAATGTCC 60.680 57.143 0.84 0.00 38.73 4.02
4657 5092 6.018433 ACCATGACCAATATTTTAGGCTCT 57.982 37.500 0.00 0.00 0.00 4.09
4660 5095 7.400052 ACCATGACCAATATTTTAGGCTCTTTT 59.600 33.333 0.00 0.00 0.00 2.27
4752 5187 4.785453 CTGCCCTTGCTCCCGTCC 62.785 72.222 0.00 0.00 38.71 4.79
4789 5224 2.037121 TCACTCTCTCGTTGATTTGGCA 59.963 45.455 0.00 0.00 0.00 4.92
4801 5236 1.213926 GATTTGGCAGGACTGAGGGAT 59.786 52.381 3.00 0.00 0.00 3.85
4864 5299 0.249911 GAGTTGTCTTGGCGAGGTGT 60.250 55.000 0.97 0.00 0.00 4.16
4870 5305 1.947456 GTCTTGGCGAGGTGTTTTTCT 59.053 47.619 0.97 0.00 0.00 2.52
4907 5342 3.322466 CCCAGAGTCGCTTGGGGT 61.322 66.667 7.88 0.00 37.92 4.95
4923 5358 3.948735 GGTGACCCAGGAAATTCGA 57.051 52.632 0.00 0.00 0.00 3.71
4924 5359 1.739067 GGTGACCCAGGAAATTCGAG 58.261 55.000 0.00 0.00 0.00 4.04
4925 5360 1.087501 GTGACCCAGGAAATTCGAGC 58.912 55.000 0.00 0.00 0.00 5.03
4926 5361 0.035439 TGACCCAGGAAATTCGAGCC 60.035 55.000 0.00 0.00 0.00 4.70
4927 5362 0.253327 GACCCAGGAAATTCGAGCCT 59.747 55.000 0.00 0.00 0.00 4.58
4928 5363 1.485066 GACCCAGGAAATTCGAGCCTA 59.515 52.381 0.00 0.00 0.00 3.93
4929 5364 1.913419 ACCCAGGAAATTCGAGCCTAA 59.087 47.619 0.00 0.00 0.00 2.69
4930 5365 2.509964 ACCCAGGAAATTCGAGCCTAAT 59.490 45.455 0.00 0.00 0.00 1.73
4931 5366 3.053619 ACCCAGGAAATTCGAGCCTAATT 60.054 43.478 0.00 0.00 0.00 1.40
4932 5367 3.316308 CCCAGGAAATTCGAGCCTAATTG 59.684 47.826 0.00 0.00 0.00 2.32
4933 5368 3.316308 CCAGGAAATTCGAGCCTAATTGG 59.684 47.826 0.00 0.00 39.35 3.16
4934 5369 3.947834 CAGGAAATTCGAGCCTAATTGGT 59.052 43.478 0.00 0.00 38.35 3.67
4935 5370 4.399303 CAGGAAATTCGAGCCTAATTGGTT 59.601 41.667 0.00 0.00 38.35 3.67
4936 5371 5.016831 AGGAAATTCGAGCCTAATTGGTTT 58.983 37.500 0.00 0.00 38.35 3.27
4937 5372 5.102313 GGAAATTCGAGCCTAATTGGTTTG 58.898 41.667 0.00 0.00 38.35 2.93
4938 5373 5.105917 GGAAATTCGAGCCTAATTGGTTTGA 60.106 40.000 0.00 0.00 37.62 2.69
4939 5374 6.405842 GGAAATTCGAGCCTAATTGGTTTGAT 60.406 38.462 0.00 0.00 38.91 2.57
4940 5375 4.963276 TTCGAGCCTAATTGGTTTGATG 57.037 40.909 0.00 0.00 38.91 3.07
4941 5376 2.682856 TCGAGCCTAATTGGTTTGATGC 59.317 45.455 0.00 0.00 34.94 3.91
4942 5377 2.223572 CGAGCCTAATTGGTTTGATGCC 60.224 50.000 0.00 0.00 38.35 4.40
4943 5378 2.760092 GAGCCTAATTGGTTTGATGCCA 59.240 45.455 0.00 0.00 38.35 4.92
4950 5385 2.886862 TGGTTTGATGCCAACAGTTG 57.113 45.000 6.28 6.28 32.29 3.16
4983 5418 3.742433 TTGGCAACTACCAAATGTTGG 57.258 42.857 5.46 5.46 46.65 3.77
4997 5432 6.789262 CCAAATGTTGGCTAGAGATTAGTTG 58.211 40.000 0.00 0.00 45.17 3.16
4998 5433 6.261118 CAAATGTTGGCTAGAGATTAGTTGC 58.739 40.000 0.00 0.00 0.00 4.17
4999 5434 4.551702 TGTTGGCTAGAGATTAGTTGCA 57.448 40.909 0.00 0.00 0.00 4.08
5000 5435 5.102953 TGTTGGCTAGAGATTAGTTGCAT 57.897 39.130 0.00 0.00 0.00 3.96
5001 5436 6.233905 TGTTGGCTAGAGATTAGTTGCATA 57.766 37.500 0.00 0.00 0.00 3.14
5002 5437 6.049149 TGTTGGCTAGAGATTAGTTGCATAC 58.951 40.000 0.00 0.00 0.00 2.39
5003 5438 5.215252 TGGCTAGAGATTAGTTGCATACC 57.785 43.478 0.00 0.00 0.00 2.73
5004 5439 4.653801 TGGCTAGAGATTAGTTGCATACCA 59.346 41.667 0.00 0.00 0.00 3.25
5005 5440 5.130311 TGGCTAGAGATTAGTTGCATACCAA 59.870 40.000 0.00 0.00 0.00 3.67
5006 5441 6.183361 TGGCTAGAGATTAGTTGCATACCAAT 60.183 38.462 0.00 0.00 35.55 3.16
5007 5442 7.016170 TGGCTAGAGATTAGTTGCATACCAATA 59.984 37.037 0.00 0.00 35.55 1.90
5008 5443 8.043710 GGCTAGAGATTAGTTGCATACCAATAT 58.956 37.037 0.00 0.00 35.55 1.28
5009 5444 9.442047 GCTAGAGATTAGTTGCATACCAATATT 57.558 33.333 0.00 0.00 35.55 1.28
5012 5447 9.632638 AGAGATTAGTTGCATACCAATATTTGT 57.367 29.630 0.00 0.00 35.55 2.83
5015 5450 8.647143 ATTAGTTGCATACCAATATTTGTTGC 57.353 30.769 14.39 14.39 35.55 4.17
5016 5451 5.418676 AGTTGCATACCAATATTTGTTGCC 58.581 37.500 16.65 8.35 35.55 4.52
5017 5452 5.046735 AGTTGCATACCAATATTTGTTGCCA 60.047 36.000 16.65 8.91 35.55 4.92
5018 5453 5.411831 TGCATACCAATATTTGTTGCCAA 57.588 34.783 16.65 4.78 0.00 4.52
5019 5454 5.987098 TGCATACCAATATTTGTTGCCAAT 58.013 33.333 16.65 0.00 0.00 3.16
5020 5455 6.047870 TGCATACCAATATTTGTTGCCAATC 58.952 36.000 16.65 0.84 0.00 2.67
5021 5456 6.127111 TGCATACCAATATTTGTTGCCAATCT 60.127 34.615 16.65 0.00 0.00 2.40
5022 5457 6.421801 GCATACCAATATTTGTTGCCAATCTC 59.578 38.462 12.03 0.00 0.00 2.75
5023 5458 5.999205 ACCAATATTTGTTGCCAATCTCA 57.001 34.783 0.00 0.00 0.00 3.27
5024 5459 5.723295 ACCAATATTTGTTGCCAATCTCAC 58.277 37.500 0.00 0.00 0.00 3.51
5025 5460 5.245751 ACCAATATTTGTTGCCAATCTCACA 59.754 36.000 0.00 0.00 0.00 3.58
5026 5461 6.164876 CCAATATTTGTTGCCAATCTCACAA 58.835 36.000 0.00 0.00 0.00 3.33
5027 5462 6.649973 CCAATATTTGTTGCCAATCTCACAAA 59.350 34.615 0.00 0.00 0.00 2.83
5028 5463 7.172875 CCAATATTTGTTGCCAATCTCACAAAA 59.827 33.333 0.80 0.00 32.08 2.44
5029 5464 7.894376 ATATTTGTTGCCAATCTCACAAAAG 57.106 32.000 0.80 0.00 32.08 2.27
5030 5465 3.731652 TGTTGCCAATCTCACAAAAGG 57.268 42.857 0.00 0.00 0.00 3.11
5031 5466 3.030291 TGTTGCCAATCTCACAAAAGGT 58.970 40.909 0.00 0.00 0.00 3.50
5032 5467 3.450457 TGTTGCCAATCTCACAAAAGGTT 59.550 39.130 0.00 0.00 0.00 3.50
5033 5468 3.731652 TGCCAATCTCACAAAAGGTTG 57.268 42.857 0.00 0.00 37.17 3.77
5034 5469 2.224018 TGCCAATCTCACAAAAGGTTGC 60.224 45.455 0.00 0.00 36.28 4.17
5035 5470 2.036346 GCCAATCTCACAAAAGGTTGCT 59.964 45.455 0.00 0.00 36.28 3.91
5036 5471 3.255642 GCCAATCTCACAAAAGGTTGCTA 59.744 43.478 0.00 0.00 36.28 3.49
5037 5472 4.261994 GCCAATCTCACAAAAGGTTGCTAA 60.262 41.667 0.00 0.00 36.28 3.09
5038 5473 5.738783 GCCAATCTCACAAAAGGTTGCTAAA 60.739 40.000 0.00 0.00 36.28 1.85
5039 5474 6.458210 CCAATCTCACAAAAGGTTGCTAAAT 58.542 36.000 0.00 0.00 36.28 1.40
5040 5475 6.366877 CCAATCTCACAAAAGGTTGCTAAATG 59.633 38.462 0.00 0.00 36.28 2.32
5041 5476 6.655078 ATCTCACAAAAGGTTGCTAAATGT 57.345 33.333 0.00 0.00 38.39 2.71
5042 5477 6.463995 TCTCACAAAAGGTTGCTAAATGTT 57.536 33.333 0.00 0.00 38.39 2.71
5043 5478 6.272318 TCTCACAAAAGGTTGCTAAATGTTG 58.728 36.000 0.00 0.00 38.39 3.33
5044 5479 5.355596 TCACAAAAGGTTGCTAAATGTTGG 58.644 37.500 0.00 0.00 38.39 3.77
5045 5480 4.024977 CACAAAAGGTTGCTAAATGTTGGC 60.025 41.667 0.00 0.00 38.39 4.52
5046 5481 4.125703 CAAAAGGTTGCTAAATGTTGGCA 58.874 39.130 0.00 0.00 45.81 4.92
5056 5491 7.507733 TGCTAAATGTTGGCAAATTTTGATT 57.492 28.000 20.92 0.87 44.47 2.57
5057 5492 7.938715 TGCTAAATGTTGGCAAATTTTGATTT 58.061 26.923 20.92 10.90 44.47 2.17
5058 5493 8.411683 TGCTAAATGTTGGCAAATTTTGATTTT 58.588 25.926 20.92 5.38 44.47 1.82
5059 5494 8.692615 GCTAAATGTTGGCAAATTTTGATTTTG 58.307 29.630 20.92 10.41 37.09 2.44
5071 5506 9.733219 CAAATTTTGATTTTGCCAAATGTTAGT 57.267 25.926 2.88 0.00 32.35 2.24
5073 5508 9.733219 AATTTTGATTTTGCCAAATGTTAGTTG 57.267 25.926 0.00 0.00 32.35 3.16
5074 5509 5.921004 TGATTTTGCCAAATGTTAGTTGC 57.079 34.783 0.00 0.00 32.35 4.17
5075 5510 4.754114 TGATTTTGCCAAATGTTAGTTGCC 59.246 37.500 0.00 0.00 32.35 4.52
5076 5511 3.827008 TTTGCCAAATGTTAGTTGCCA 57.173 38.095 0.00 0.00 0.00 4.92
5077 5512 3.827008 TTGCCAAATGTTAGTTGCCAA 57.173 38.095 0.00 0.00 0.00 4.52
5078 5513 3.827008 TGCCAAATGTTAGTTGCCAAA 57.173 38.095 0.00 0.00 0.00 3.28
5079 5514 4.348863 TGCCAAATGTTAGTTGCCAAAT 57.651 36.364 0.00 0.00 0.00 2.32
5080 5515 5.474578 TGCCAAATGTTAGTTGCCAAATA 57.525 34.783 0.00 0.00 0.00 1.40
5081 5516 6.047511 TGCCAAATGTTAGTTGCCAAATAT 57.952 33.333 0.00 0.00 0.00 1.28
5082 5517 6.471146 TGCCAAATGTTAGTTGCCAAATATT 58.529 32.000 0.00 0.00 0.00 1.28
5083 5518 6.370994 TGCCAAATGTTAGTTGCCAAATATTG 59.629 34.615 0.00 0.00 0.00 1.90
5084 5519 6.593382 GCCAAATGTTAGTTGCCAAATATTGA 59.407 34.615 0.00 0.00 0.00 2.57
5085 5520 7.412891 GCCAAATGTTAGTTGCCAAATATTGAC 60.413 37.037 0.00 0.00 0.00 3.18
5086 5521 7.601886 CCAAATGTTAGTTGCCAAATATTGACA 59.398 33.333 0.00 0.00 0.00 3.58
5087 5522 8.986847 CAAATGTTAGTTGCCAAATATTGACAA 58.013 29.630 0.00 0.00 30.37 3.18
5088 5523 9.723601 AAATGTTAGTTGCCAAATATTGACAAT 57.276 25.926 5.87 5.87 35.51 2.71
5089 5524 8.706492 ATGTTAGTTGCCAAATATTGACAATG 57.294 30.769 11.05 0.00 35.51 2.82
5090 5525 6.589523 TGTTAGTTGCCAAATATTGACAATGC 59.410 34.615 11.05 5.78 35.51 3.56
5091 5526 4.506758 AGTTGCCAAATATTGACAATGCC 58.493 39.130 11.05 0.00 35.51 4.40
5092 5527 4.020396 AGTTGCCAAATATTGACAATGCCA 60.020 37.500 11.05 0.00 35.51 4.92
5093 5528 4.548451 TGCCAAATATTGACAATGCCAA 57.452 36.364 11.05 0.00 0.00 4.52
5094 5529 4.903054 TGCCAAATATTGACAATGCCAAA 58.097 34.783 11.05 0.00 0.00 3.28
5095 5530 5.498393 TGCCAAATATTGACAATGCCAAAT 58.502 33.333 11.05 0.00 0.00 2.32
5096 5531 5.354513 TGCCAAATATTGACAATGCCAAATG 59.645 36.000 11.05 2.07 0.00 2.32
5097 5532 5.354792 GCCAAATATTGACAATGCCAAATGT 59.645 36.000 11.05 0.00 0.00 2.71
5098 5533 6.127952 GCCAAATATTGACAATGCCAAATGTT 60.128 34.615 11.05 0.00 0.00 2.71
5099 5534 7.065563 GCCAAATATTGACAATGCCAAATGTTA 59.934 33.333 11.05 0.00 0.00 2.41
5100 5535 8.605746 CCAAATATTGACAATGCCAAATGTTAG 58.394 33.333 11.05 0.00 0.00 2.34
5101 5536 9.153721 CAAATATTGACAATGCCAAATGTTAGT 57.846 29.630 11.05 0.00 0.00 2.24
5104 5539 5.309323 TGACAATGCCAAATGTTAGTAGC 57.691 39.130 0.00 0.00 0.00 3.58
5105 5540 4.764308 TGACAATGCCAAATGTTAGTAGCA 59.236 37.500 0.00 0.00 34.28 3.49
5106 5541 5.242615 TGACAATGCCAAATGTTAGTAGCAA 59.757 36.000 0.00 0.00 33.35 3.91
5107 5542 6.095432 ACAATGCCAAATGTTAGTAGCAAA 57.905 33.333 0.00 0.00 33.35 3.68
5108 5543 5.925969 ACAATGCCAAATGTTAGTAGCAAAC 59.074 36.000 0.00 0.00 33.35 2.93
5109 5544 4.513198 TGCCAAATGTTAGTAGCAAACC 57.487 40.909 0.00 0.00 0.00 3.27
5110 5545 3.891977 TGCCAAATGTTAGTAGCAAACCA 59.108 39.130 0.00 0.00 0.00 3.67
5111 5546 4.342378 TGCCAAATGTTAGTAGCAAACCAA 59.658 37.500 0.00 0.00 0.00 3.67
5112 5547 5.011533 TGCCAAATGTTAGTAGCAAACCAAT 59.988 36.000 0.00 0.00 0.00 3.16
5113 5548 5.576774 GCCAAATGTTAGTAGCAAACCAATC 59.423 40.000 0.00 0.00 0.00 2.67
5114 5549 6.686630 CCAAATGTTAGTAGCAAACCAATCA 58.313 36.000 0.00 0.00 0.00 2.57
5115 5550 6.808212 CCAAATGTTAGTAGCAAACCAATCAG 59.192 38.462 0.00 0.00 0.00 2.90
5116 5551 5.567138 ATGTTAGTAGCAAACCAATCAGC 57.433 39.130 0.00 0.00 0.00 4.26
5117 5552 3.756434 TGTTAGTAGCAAACCAATCAGCC 59.244 43.478 0.00 0.00 0.00 4.85
5118 5553 2.887151 AGTAGCAAACCAATCAGCCT 57.113 45.000 0.00 0.00 0.00 4.58
5119 5554 2.716217 AGTAGCAAACCAATCAGCCTC 58.284 47.619 0.00 0.00 0.00 4.70
5120 5555 2.307098 AGTAGCAAACCAATCAGCCTCT 59.693 45.455 0.00 0.00 0.00 3.69
5121 5556 2.299326 AGCAAACCAATCAGCCTCTT 57.701 45.000 0.00 0.00 0.00 2.85
5122 5557 2.165998 AGCAAACCAATCAGCCTCTTC 58.834 47.619 0.00 0.00 0.00 2.87
5123 5558 1.135575 GCAAACCAATCAGCCTCTTCG 60.136 52.381 0.00 0.00 0.00 3.79
5124 5559 2.154462 CAAACCAATCAGCCTCTTCGT 58.846 47.619 0.00 0.00 0.00 3.85
5125 5560 2.554032 CAAACCAATCAGCCTCTTCGTT 59.446 45.455 0.00 0.00 0.00 3.85
5126 5561 2.100605 ACCAATCAGCCTCTTCGTTC 57.899 50.000 0.00 0.00 0.00 3.95
5127 5562 1.625818 ACCAATCAGCCTCTTCGTTCT 59.374 47.619 0.00 0.00 0.00 3.01
5128 5563 2.275318 CCAATCAGCCTCTTCGTTCTC 58.725 52.381 0.00 0.00 0.00 2.87
5173 5608 6.484364 TCTGAAAGTGATATGTAGATGGCA 57.516 37.500 0.00 0.00 33.76 4.92
5182 5644 0.913934 TGTAGATGGCAGGCCCTGAA 60.914 55.000 16.85 1.23 32.44 3.02
5257 5719 1.202580 ACTTCAGCGATGAGTATGCCC 60.203 52.381 2.57 0.00 0.00 5.36
5303 5765 2.836262 CTCATCTGGAGCACCTTCATC 58.164 52.381 0.71 0.00 36.69 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.170828 CACCTTGGGTAAAAGCAAAATTACTTC 59.829 37.037 0.00 0.00 32.11 3.01
1 2 6.989759 CACCTTGGGTAAAAGCAAAATTACTT 59.010 34.615 0.00 0.00 32.11 2.24
20 21 2.079925 GGCTCTAAGCTTCACACCTTG 58.920 52.381 0.00 0.00 41.99 3.61
97 98 4.125703 CAGAGAGAGAGAGAGAGAGAAGC 58.874 52.174 0.00 0.00 0.00 3.86
115 146 5.837437 AGTGTCTAGTTCTTTCACACAGAG 58.163 41.667 10.24 0.00 39.91 3.35
116 147 5.854010 AGTGTCTAGTTCTTTCACACAGA 57.146 39.130 10.24 0.00 39.91 3.41
117 148 6.042777 TCAAGTGTCTAGTTCTTTCACACAG 58.957 40.000 10.24 4.06 39.91 3.66
118 149 5.972935 TCAAGTGTCTAGTTCTTTCACACA 58.027 37.500 10.24 0.00 39.91 3.72
119 150 8.082852 TCTATCAAGTGTCTAGTTCTTTCACAC 58.917 37.037 1.42 1.42 38.10 3.82
120 151 8.178313 TCTATCAAGTGTCTAGTTCTTTCACA 57.822 34.615 0.00 0.00 0.00 3.58
121 152 9.646427 ATTCTATCAAGTGTCTAGTTCTTTCAC 57.354 33.333 0.00 0.00 0.00 3.18
147 178 6.099701 ACACATCTTGCCAATCCTACATACTA 59.900 38.462 0.00 0.00 0.00 1.82
177 208 4.814234 TCAAATCGGAGGAATTTCATACGG 59.186 41.667 15.00 0.22 0.00 4.02
219 250 3.119245 CCTTGAGGAGCACAATTTCATGG 60.119 47.826 0.00 0.00 37.39 3.66
330 504 4.721977 CGTTTTAGTGTGTTTGTTCACTCG 59.278 41.667 1.08 0.00 42.77 4.18
346 520 6.807708 AGAATGTATGTAGACGCGTTTTAG 57.192 37.500 15.53 0.00 0.00 1.85
403 577 7.487822 AAGACATACTGGATTTTGAGAGAGA 57.512 36.000 0.00 0.00 0.00 3.10
531 705 2.616376 CAAAGTGAACCGTTGACCATGA 59.384 45.455 0.00 0.00 34.86 3.07
544 718 0.672401 GGATCGTCCGGCAAAGTGAA 60.672 55.000 0.00 0.00 0.00 3.18
559 733 8.119226 CAGATTTCTCGTTTTGAATACAGGATC 58.881 37.037 0.00 0.00 0.00 3.36
602 841 3.119708 GCTTGCCTGTTTTTCTCGATGAT 60.120 43.478 0.00 0.00 0.00 2.45
610 849 1.120437 CGTTCGCTTGCCTGTTTTTC 58.880 50.000 0.00 0.00 0.00 2.29
670 909 2.288518 GGATATGCTCTCCACGGAAGAC 60.289 54.545 0.00 0.00 32.72 3.01
1027 1275 4.856801 CGGGATCAGGCGGTTGGG 62.857 72.222 0.00 0.00 0.00 4.12
1057 1305 1.325355 ACCTCGTCGAGAAAAGGTCA 58.675 50.000 23.74 0.00 37.59 4.02
1062 1310 1.815003 GTCCCTACCTCGTCGAGAAAA 59.185 52.381 23.74 7.32 0.00 2.29
1158 1408 2.223340 GGAATCAGGCGCAACAACTATG 60.223 50.000 10.83 0.00 0.00 2.23
1297 1547 4.723789 ACAAGATCAATCTATGTGAGGGGT 59.276 41.667 0.00 0.00 35.76 4.95
1362 1612 4.270808 TGCGCAAGTCATCACTACATTATG 59.729 41.667 8.16 0.00 41.68 1.90
1413 1663 5.232463 TCAGCAATTCTGGAGAAAATTTGC 58.768 37.500 14.33 14.33 42.92 3.68
1427 1677 9.282247 CATGTTACTACAAGATTTCAGCAATTC 57.718 33.333 0.00 0.00 37.91 2.17
1469 1719 9.171877 TGATCATAACAAATAATGTGCACTGTA 57.828 29.630 19.41 10.32 42.99 2.74
1486 1736 6.372659 TGCTTTTCTTCTGACCTGATCATAAC 59.627 38.462 0.00 0.00 36.48 1.89
1489 1739 4.699257 GTGCTTTTCTTCTGACCTGATCAT 59.301 41.667 0.00 0.00 36.48 2.45
1542 1793 5.982516 GCAATATCTACAGAACTGACAGAGG 59.017 44.000 10.08 0.00 32.15 3.69
1545 1796 6.475076 GTGAGCAATATCTACAGAACTGACAG 59.525 42.308 8.87 0.00 0.00 3.51
1597 1849 7.151999 TGCTAGTCAACTGAAAAAGAACAAA 57.848 32.000 0.00 0.00 0.00 2.83
1608 1860 5.241285 TGAAAATGCAATGCTAGTCAACTGA 59.759 36.000 6.82 0.00 0.00 3.41
1735 1987 9.588096 TTATCCATCATCTCTAGTGCTTACTAA 57.412 33.333 0.00 0.00 0.00 2.24
1775 2027 1.478510 CACATCACCTAGCTCCTTCGT 59.521 52.381 0.00 0.00 0.00 3.85
2032 2290 5.316167 TCCATCAACTTGAGCATGTACTTT 58.684 37.500 0.00 0.00 0.00 2.66
2062 2320 5.279708 CCCATAAACAAAACCCTGTGCATTA 60.280 40.000 0.00 0.00 0.00 1.90
2657 2918 3.256704 TCTCATGTTTGTCCCCTAGGTT 58.743 45.455 8.29 0.00 0.00 3.50
2672 2933 3.556365 CAGCTGCTGTATGAACTCTCATG 59.444 47.826 21.21 0.00 42.48 3.07
2732 2993 7.492669 CACATCGTCTTTGGATATTGTAGACTT 59.507 37.037 0.00 0.00 34.51 3.01
2770 3031 1.645704 CTCTGATGTGCACAGCTGGC 61.646 60.000 32.56 18.37 35.61 4.85
2847 3108 5.662674 AGTTTCCTTAGTACTAGGCAGTG 57.337 43.478 6.50 0.00 36.14 3.66
2848 3109 7.787623 TTTAGTTTCCTTAGTACTAGGCAGT 57.212 36.000 6.50 5.28 38.91 4.40
2944 3205 8.537728 TCAAAACCTCTGGCATATTATCATTT 57.462 30.769 0.00 0.00 0.00 2.32
2992 3253 2.435805 GACCACCTCCATCTGATTGCTA 59.564 50.000 0.00 0.00 0.00 3.49
3152 3413 5.049405 GGTCGACCATATAAATGCTTGAAGG 60.049 44.000 29.75 0.00 35.64 3.46
3241 3502 3.266772 AGCCAATAGATCCAAGACCAACA 59.733 43.478 0.00 0.00 0.00 3.33
3324 3585 0.535102 GGCAGGGACATGGTTATCCG 60.535 60.000 0.00 0.00 35.67 4.18
3378 3642 2.990195 TCCCACTACCTGCCATATGAT 58.010 47.619 3.65 0.00 0.00 2.45
3379 3643 2.487746 TCCCACTACCTGCCATATGA 57.512 50.000 3.65 0.00 0.00 2.15
3380 3644 3.795688 ATTCCCACTACCTGCCATATG 57.204 47.619 0.00 0.00 0.00 1.78
3460 3724 8.594881 AAGAACTGCCTATAAACTTATCATCG 57.405 34.615 0.00 0.00 0.00 3.84
3628 3892 7.445402 TCCAAGTATCCAAAGAACTGAGAAAAG 59.555 37.037 0.00 0.00 0.00 2.27
3809 4138 2.741145 ACCTCACCTCTCACACCTATC 58.259 52.381 0.00 0.00 0.00 2.08
3813 4142 0.035458 CCAACCTCACCTCTCACACC 59.965 60.000 0.00 0.00 0.00 4.16
3867 4196 3.648339 TCACAATCTTTCTTTGCTGGC 57.352 42.857 0.00 0.00 0.00 4.85
3890 4219 2.462456 ACTTGCGAATTCAGCTGAGA 57.538 45.000 17.43 8.70 35.28 3.27
3912 4241 6.317391 GGAGTAATTCTTGCAACTAAGCTCAT 59.683 38.462 0.00 0.00 34.99 2.90
3967 4299 1.816835 ACTGAGAACAAGGCATGCATG 59.183 47.619 22.70 22.70 0.00 4.06
3975 4307 5.334724 GCTGAAATCAGAACTGAGAACAAGG 60.335 44.000 14.43 2.08 46.59 3.61
3989 4321 6.128336 CCTGTTACAAAGAGAGCTGAAATCAG 60.128 42.308 6.05 6.05 46.40 2.90
4012 4344 4.081406 TGCAATCAACAGAATAAGCACCT 58.919 39.130 0.00 0.00 0.00 4.00
4040 4372 4.690748 CCTTTTTCTCAGCGATCAACTACA 59.309 41.667 0.00 0.00 0.00 2.74
4128 4461 5.714333 AGAGACACAATACATCACACTCTCT 59.286 40.000 0.00 0.00 0.00 3.10
4129 4462 5.960113 AGAGACACAATACATCACACTCTC 58.040 41.667 0.00 0.00 0.00 3.20
4188 4521 3.272574 ACAGGCTAATGACATGTCCTG 57.727 47.619 22.85 22.05 44.80 3.86
4189 4522 5.435686 TTTACAGGCTAATGACATGTCCT 57.564 39.130 22.85 10.76 0.00 3.85
4197 4530 7.455058 TCTACCAAGTTTTTACAGGCTAATGA 58.545 34.615 0.00 0.00 0.00 2.57
4198 4531 7.681939 TCTACCAAGTTTTTACAGGCTAATG 57.318 36.000 0.00 0.00 0.00 1.90
4304 4644 1.108776 GACAACCAGGCATGCATCAT 58.891 50.000 21.36 0.00 0.00 2.45
4339 4679 3.369546 AAAAAGCAACATTCAGGACGG 57.630 42.857 0.00 0.00 0.00 4.79
4372 4716 4.030452 GTGTCCGCCAGCAGCAAC 62.030 66.667 0.00 0.00 44.04 4.17
4384 4728 1.026718 GTACAGCCATGCAGGTGTCC 61.027 60.000 13.35 0.00 40.61 4.02
4385 4729 1.026718 GGTACAGCCATGCAGGTGTC 61.027 60.000 13.35 6.62 40.61 3.67
4435 4779 3.424703 CCCTCATCCTGCAGAAAAAGAA 58.575 45.455 17.39 0.00 0.00 2.52
4455 4799 1.514553 CTCGTACTCCGTTTCCCCC 59.485 63.158 0.00 0.00 37.94 5.40
4459 4803 2.597748 GCTAAAGCTCGTACTCCGTTTC 59.402 50.000 0.00 0.00 38.21 2.78
4512 4856 3.838795 GTCACGATGCCGCGACAC 61.839 66.667 8.23 0.00 44.56 3.67
4564 4908 0.252197 GTTGCCACAGTAGGGGGTAG 59.748 60.000 0.00 0.00 0.00 3.18
4666 5101 7.543947 AAGAAGAAATTTGAACTTTTGCAGG 57.456 32.000 0.00 0.00 0.00 4.85
4719 5154 1.134946 GGCAGCAGTTGAGTGTTTTGT 59.865 47.619 0.00 0.00 0.00 2.83
4724 5159 0.820891 CAAGGGCAGCAGTTGAGTGT 60.821 55.000 0.00 0.00 0.00 3.55
4752 5187 3.056962 AGAGTGATGCACGCTATATGAGG 60.057 47.826 1.96 0.00 42.25 3.86
4864 5299 1.573829 CTACGCCGCCAGCAGAAAAA 61.574 55.000 0.00 0.00 44.04 1.94
4892 5327 1.374758 GTCACCCCAAGCGACTCTG 60.375 63.158 0.00 0.00 0.00 3.35
4893 5328 2.584391 GGTCACCCCAAGCGACTCT 61.584 63.158 0.00 0.00 0.00 3.24
4907 5342 0.035439 GGCTCGAATTTCCTGGGTCA 60.035 55.000 0.00 0.00 0.00 4.02
4913 5348 4.236527 ACCAATTAGGCTCGAATTTCCT 57.763 40.909 0.00 0.00 43.14 3.36
4923 5358 2.818921 TGGCATCAAACCAATTAGGCT 58.181 42.857 0.00 0.00 43.14 4.58
4924 5359 3.608316 TTGGCATCAAACCAATTAGGC 57.392 42.857 0.00 0.00 42.23 3.93
4930 5365 2.158986 CCAACTGTTGGCATCAAACCAA 60.159 45.455 25.21 0.00 45.17 3.67
4931 5366 1.411977 CCAACTGTTGGCATCAAACCA 59.588 47.619 25.21 0.00 45.17 3.67
4932 5367 2.153366 CCAACTGTTGGCATCAAACC 57.847 50.000 25.21 0.00 45.17 3.27
4963 5398 3.742433 CCAACATTTGGTAGTTGCCAA 57.258 42.857 0.00 0.00 45.93 4.52
4974 5409 6.127925 TGCAACTAATCTCTAGCCAACATTTG 60.128 38.462 0.00 0.00 0.00 2.32
4975 5410 5.945784 TGCAACTAATCTCTAGCCAACATTT 59.054 36.000 0.00 0.00 0.00 2.32
4976 5411 5.500234 TGCAACTAATCTCTAGCCAACATT 58.500 37.500 0.00 0.00 0.00 2.71
4977 5412 5.102953 TGCAACTAATCTCTAGCCAACAT 57.897 39.130 0.00 0.00 0.00 2.71
4978 5413 4.551702 TGCAACTAATCTCTAGCCAACA 57.448 40.909 0.00 0.00 0.00 3.33
4979 5414 5.467063 GGTATGCAACTAATCTCTAGCCAAC 59.533 44.000 0.00 0.00 0.00 3.77
4980 5415 5.130311 TGGTATGCAACTAATCTCTAGCCAA 59.870 40.000 0.00 0.00 0.00 4.52
4981 5416 4.653801 TGGTATGCAACTAATCTCTAGCCA 59.346 41.667 0.00 0.00 0.00 4.75
4982 5417 5.215252 TGGTATGCAACTAATCTCTAGCC 57.785 43.478 0.00 0.00 0.00 3.93
4983 5418 9.442047 AATATTGGTATGCAACTAATCTCTAGC 57.558 33.333 11.72 0.00 39.69 3.42
4986 5421 9.632638 ACAAATATTGGTATGCAACTAATCTCT 57.367 29.630 11.72 0.88 39.69 3.10
4989 5424 8.755018 GCAACAAATATTGGTATGCAACTAATC 58.245 33.333 17.89 0.00 39.69 1.75
4990 5425 7.710475 GGCAACAAATATTGGTATGCAACTAAT 59.290 33.333 21.42 12.57 41.64 1.73
4991 5426 7.038659 GGCAACAAATATTGGTATGCAACTAA 58.961 34.615 21.42 0.00 39.22 2.24
4992 5427 6.568869 GGCAACAAATATTGGTATGCAACTA 58.431 36.000 21.42 0.00 39.22 2.24
4993 5428 5.418676 GGCAACAAATATTGGTATGCAACT 58.581 37.500 21.42 0.00 39.22 3.16
4994 5429 5.717038 GGCAACAAATATTGGTATGCAAC 57.283 39.130 21.42 9.57 39.22 4.17
5011 5446 3.733443 ACCTTTTGTGAGATTGGCAAC 57.267 42.857 0.00 0.00 0.00 4.17
5012 5447 3.740764 GCAACCTTTTGTGAGATTGGCAA 60.741 43.478 0.68 0.68 34.90 4.52
5013 5448 2.224018 GCAACCTTTTGTGAGATTGGCA 60.224 45.455 0.00 0.00 34.90 4.92
5014 5449 2.036346 AGCAACCTTTTGTGAGATTGGC 59.964 45.455 0.00 0.00 34.90 4.52
5015 5450 5.452078 TTAGCAACCTTTTGTGAGATTGG 57.548 39.130 0.00 0.00 34.90 3.16
5016 5451 6.925165 ACATTTAGCAACCTTTTGTGAGATTG 59.075 34.615 0.00 0.00 34.90 2.67
5017 5452 7.054491 ACATTTAGCAACCTTTTGTGAGATT 57.946 32.000 0.00 0.00 34.90 2.40
5018 5453 6.655078 ACATTTAGCAACCTTTTGTGAGAT 57.345 33.333 0.00 0.00 34.90 2.75
5019 5454 6.272318 CAACATTTAGCAACCTTTTGTGAGA 58.728 36.000 0.00 0.00 34.90 3.27
5020 5455 5.463061 CCAACATTTAGCAACCTTTTGTGAG 59.537 40.000 0.00 0.00 34.90 3.51
5021 5456 5.355596 CCAACATTTAGCAACCTTTTGTGA 58.644 37.500 0.00 0.00 34.90 3.58
5022 5457 4.024977 GCCAACATTTAGCAACCTTTTGTG 60.025 41.667 0.00 0.00 34.90 3.33
5023 5458 4.126437 GCCAACATTTAGCAACCTTTTGT 58.874 39.130 0.00 0.00 34.90 2.83
5024 5459 4.125703 TGCCAACATTTAGCAACCTTTTG 58.874 39.130 0.00 0.00 32.56 2.44
5025 5460 4.414337 TGCCAACATTTAGCAACCTTTT 57.586 36.364 0.00 0.00 32.56 2.27
5026 5461 4.414337 TTGCCAACATTTAGCAACCTTT 57.586 36.364 0.00 0.00 41.35 3.11
5027 5462 4.414337 TTTGCCAACATTTAGCAACCTT 57.586 36.364 0.00 0.00 45.57 3.50
5028 5463 4.622260 ATTTGCCAACATTTAGCAACCT 57.378 36.364 0.00 0.00 45.57 3.50
5029 5464 5.687770 AAATTTGCCAACATTTAGCAACC 57.312 34.783 0.00 0.00 45.57 3.77
5030 5465 6.723282 TCAAAATTTGCCAACATTTAGCAAC 58.277 32.000 0.00 0.00 45.57 4.17
5031 5466 6.932356 TCAAAATTTGCCAACATTTAGCAA 57.068 29.167 0.00 0.00 44.32 3.91
5032 5467 7.507733 AATCAAAATTTGCCAACATTTAGCA 57.492 28.000 0.00 0.00 33.97 3.49
5033 5468 8.692615 CAAAATCAAAATTTGCCAACATTTAGC 58.307 29.630 0.00 0.00 35.27 3.09
5045 5480 9.733219 ACTAACATTTGGCAAAATCAAAATTTG 57.267 25.926 17.70 9.58 40.04 2.32
5047 5482 9.733219 CAACTAACATTTGGCAAAATCAAAATT 57.267 25.926 17.70 4.04 37.60 1.82
5048 5483 7.861872 GCAACTAACATTTGGCAAAATCAAAAT 59.138 29.630 17.70 0.00 37.60 1.82
5049 5484 7.192232 GCAACTAACATTTGGCAAAATCAAAA 58.808 30.769 17.70 0.28 37.60 2.44
5050 5485 6.238593 GGCAACTAACATTTGGCAAAATCAAA 60.239 34.615 17.70 1.33 46.16 2.69
5051 5486 5.238214 GGCAACTAACATTTGGCAAAATCAA 59.762 36.000 17.70 2.75 46.16 2.57
5052 5487 4.754114 GGCAACTAACATTTGGCAAAATCA 59.246 37.500 17.70 2.03 46.16 2.57
5053 5488 5.281693 GGCAACTAACATTTGGCAAAATC 57.718 39.130 17.70 0.00 46.16 2.17
5059 5494 6.593382 TCAATATTTGGCAACTAACATTTGGC 59.407 34.615 0.00 1.93 46.86 4.52
5060 5495 7.601886 TGTCAATATTTGGCAACTAACATTTGG 59.398 33.333 0.00 0.00 43.24 3.28
5061 5496 8.531622 TGTCAATATTTGGCAACTAACATTTG 57.468 30.769 0.00 1.07 43.24 2.32
5072 5507 4.548451 TTGGCATTGTCAATATTTGGCA 57.452 36.364 8.74 8.74 44.76 4.92
5073 5508 5.354792 ACATTTGGCATTGTCAATATTTGGC 59.645 36.000 4.24 0.69 35.37 4.52
5074 5509 6.988622 ACATTTGGCATTGTCAATATTTGG 57.011 33.333 4.24 0.00 0.00 3.28
5075 5510 9.153721 ACTAACATTTGGCATTGTCAATATTTG 57.846 29.630 4.24 3.85 0.00 2.32
5078 5513 8.137437 GCTACTAACATTTGGCATTGTCAATAT 58.863 33.333 4.24 0.00 0.00 1.28
5079 5514 7.121907 TGCTACTAACATTTGGCATTGTCAATA 59.878 33.333 4.24 0.00 0.00 1.90
5080 5515 6.071447 TGCTACTAACATTTGGCATTGTCAAT 60.071 34.615 4.24 0.00 0.00 2.57
5081 5516 5.242615 TGCTACTAACATTTGGCATTGTCAA 59.757 36.000 0.00 0.00 0.00 3.18
5082 5517 4.764308 TGCTACTAACATTTGGCATTGTCA 59.236 37.500 4.32 0.00 0.00 3.58
5083 5518 5.309323 TGCTACTAACATTTGGCATTGTC 57.691 39.130 4.32 0.00 0.00 3.18
5084 5519 5.720371 TTGCTACTAACATTTGGCATTGT 57.280 34.783 0.00 0.00 0.00 2.71
5085 5520 5.348451 GGTTTGCTACTAACATTTGGCATTG 59.652 40.000 0.00 0.00 0.00 2.82
5086 5521 5.011533 TGGTTTGCTACTAACATTTGGCATT 59.988 36.000 0.00 0.00 0.00 3.56
5087 5522 4.526262 TGGTTTGCTACTAACATTTGGCAT 59.474 37.500 0.00 0.00 0.00 4.40
5088 5523 3.891977 TGGTTTGCTACTAACATTTGGCA 59.108 39.130 0.00 0.00 0.00 4.92
5089 5524 4.513198 TGGTTTGCTACTAACATTTGGC 57.487 40.909 0.00 0.00 0.00 4.52
5090 5525 6.686630 TGATTGGTTTGCTACTAACATTTGG 58.313 36.000 0.00 0.00 29.31 3.28
5091 5526 6.308766 GCTGATTGGTTTGCTACTAACATTTG 59.691 38.462 0.00 0.00 29.31 2.32
5092 5527 6.389906 GCTGATTGGTTTGCTACTAACATTT 58.610 36.000 0.00 0.00 29.31 2.32
5093 5528 5.105756 GGCTGATTGGTTTGCTACTAACATT 60.106 40.000 0.00 0.00 29.31 2.71
5094 5529 4.399303 GGCTGATTGGTTTGCTACTAACAT 59.601 41.667 0.00 0.00 29.31 2.71
5095 5530 3.756434 GGCTGATTGGTTTGCTACTAACA 59.244 43.478 0.00 0.00 29.31 2.41
5096 5531 4.010349 AGGCTGATTGGTTTGCTACTAAC 58.990 43.478 0.00 0.00 29.31 2.34
5097 5532 4.019321 AGAGGCTGATTGGTTTGCTACTAA 60.019 41.667 0.00 0.00 0.00 2.24
5098 5533 3.519510 AGAGGCTGATTGGTTTGCTACTA 59.480 43.478 0.00 0.00 0.00 1.82
5099 5534 2.307098 AGAGGCTGATTGGTTTGCTACT 59.693 45.455 0.00 0.00 0.00 2.57
5100 5535 2.716217 AGAGGCTGATTGGTTTGCTAC 58.284 47.619 0.00 0.00 0.00 3.58
5101 5536 3.347216 GAAGAGGCTGATTGGTTTGCTA 58.653 45.455 0.00 0.00 0.00 3.49
5102 5537 2.165998 GAAGAGGCTGATTGGTTTGCT 58.834 47.619 0.00 0.00 0.00 3.91
5103 5538 1.135575 CGAAGAGGCTGATTGGTTTGC 60.136 52.381 0.00 0.00 0.00 3.68
5104 5539 2.154462 ACGAAGAGGCTGATTGGTTTG 58.846 47.619 0.00 0.00 0.00 2.93
5105 5540 2.568623 ACGAAGAGGCTGATTGGTTT 57.431 45.000 0.00 0.00 0.00 3.27
5106 5541 2.039084 AGAACGAAGAGGCTGATTGGTT 59.961 45.455 8.54 8.54 31.20 3.67
5107 5542 1.625818 AGAACGAAGAGGCTGATTGGT 59.374 47.619 0.00 0.00 0.00 3.67
5108 5543 2.275318 GAGAACGAAGAGGCTGATTGG 58.725 52.381 0.00 0.00 0.00 3.16
5109 5544 2.093764 AGGAGAACGAAGAGGCTGATTG 60.094 50.000 0.00 0.00 0.00 2.67
5110 5545 2.167487 GAGGAGAACGAAGAGGCTGATT 59.833 50.000 0.00 0.00 0.00 2.57
5111 5546 1.754226 GAGGAGAACGAAGAGGCTGAT 59.246 52.381 0.00 0.00 0.00 2.90
5112 5547 1.178276 GAGGAGAACGAAGAGGCTGA 58.822 55.000 0.00 0.00 0.00 4.26
5113 5548 0.174617 GGAGGAGAACGAAGAGGCTG 59.825 60.000 0.00 0.00 0.00 4.85
5114 5549 0.251832 TGGAGGAGAACGAAGAGGCT 60.252 55.000 0.00 0.00 0.00 4.58
5115 5550 0.608640 TTGGAGGAGAACGAAGAGGC 59.391 55.000 0.00 0.00 0.00 4.70
5116 5551 1.618837 TGTTGGAGGAGAACGAAGAGG 59.381 52.381 0.00 0.00 0.00 3.69
5117 5552 3.005897 TCTTGTTGGAGGAGAACGAAGAG 59.994 47.826 0.00 0.00 0.00 2.85
5118 5553 2.963101 TCTTGTTGGAGGAGAACGAAGA 59.037 45.455 0.00 0.00 0.00 2.87
5119 5554 3.386768 TCTTGTTGGAGGAGAACGAAG 57.613 47.619 0.00 0.00 0.00 3.79
5120 5555 3.728845 CTTCTTGTTGGAGGAGAACGAA 58.271 45.455 0.00 0.00 0.00 3.85
5121 5556 2.548067 GCTTCTTGTTGGAGGAGAACGA 60.548 50.000 0.00 0.00 0.00 3.85
5122 5557 1.801178 GCTTCTTGTTGGAGGAGAACG 59.199 52.381 0.00 0.00 0.00 3.95
5123 5558 3.133141 AGCTTCTTGTTGGAGGAGAAC 57.867 47.619 0.00 0.00 0.00 3.01
5124 5559 5.505181 AATAGCTTCTTGTTGGAGGAGAA 57.495 39.130 0.00 0.00 0.00 2.87
5125 5560 5.221925 ACAAATAGCTTCTTGTTGGAGGAGA 60.222 40.000 7.17 0.00 31.76 3.71
5126 5561 5.006386 ACAAATAGCTTCTTGTTGGAGGAG 58.994 41.667 7.17 0.00 31.76 3.69
5127 5562 4.985538 ACAAATAGCTTCTTGTTGGAGGA 58.014 39.130 7.17 0.00 31.76 3.71
5128 5563 5.474876 AGAACAAATAGCTTCTTGTTGGAGG 59.525 40.000 23.18 0.00 43.88 4.30
5169 5604 1.151760 ATATCATTCAGGGCCTGCCA 58.848 50.000 29.02 17.71 37.98 4.92
5173 5608 2.981784 TGCTACATATCATTCAGGGCCT 59.018 45.455 0.00 0.00 0.00 5.19
5182 5644 4.139786 CCAGCCTTGTTGCTACATATCAT 58.860 43.478 0.81 0.00 40.32 2.45
5301 5763 7.356680 TCCATCAAAATCATTCCACCTAAGAT 58.643 34.615 0.00 0.00 0.00 2.40
5303 5765 6.460676 GCTCCATCAAAATCATTCCACCTAAG 60.461 42.308 0.00 0.00 0.00 2.18
5313 5775 4.646492 GGGTACTTGCTCCATCAAAATCAT 59.354 41.667 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.