Multiple sequence alignment - TraesCS7A01G457200

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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 TraesCS7A01G457200 chr7A 100.000 9107 0 0 1 9107 652712234 652703128 0.000000e+00 16818.0
1 TraesCS7A01G457200 chr7D 97.103 2900 60 14 4477 7363 566526215 566523327 0.000000e+00 4868.0
2 TraesCS7A01G457200 chr7D 95.038 1693 63 11 7415 9107 566523328 566521657 0.000000e+00 2641.0
3 TraesCS7A01G457200 chr7D 95.366 1489 43 14 1659 3140 566529101 566527632 0.000000e+00 2344.0
4 TraesCS7A01G457200 chr7D 94.831 1335 45 8 3141 4474 566527601 566526290 0.000000e+00 2061.0
5 TraesCS7A01G457200 chr7D 96.811 784 19 4 862 1644 566529864 566529086 0.000000e+00 1304.0
6 TraesCS7A01G457200 chr7D 91.856 835 64 3 1 834 566530698 566529867 0.000000e+00 1162.0
7 TraesCS7A01G457200 chr7D 93.023 86 3 2 5867 5950 427001142 427001226 1.240000e-23 122.0
8 TraesCS7A01G457200 chr7D 100.000 34 0 0 3580 3613 566527131 566527098 7.630000e-06 63.9
9 TraesCS7A01G457200 chr7B 97.080 2877 66 13 4497 7363 620672706 620675574 0.000000e+00 4831.0
10 TraesCS7A01G457200 chr7B 94.012 1620 80 12 31 1644 620668034 620669642 0.000000e+00 2438.0
11 TraesCS7A01G457200 chr7B 95.976 1491 49 8 1659 3140 620669627 620671115 0.000000e+00 2410.0
12 TraesCS7A01G457200 chr7B 96.507 1231 38 1 3143 4373 620671174 620672399 0.000000e+00 2030.0
13 TraesCS7A01G457200 chr7B 93.198 1235 43 11 7415 8631 620675573 620676784 0.000000e+00 1777.0
14 TraesCS7A01G457200 chr7B 88.492 504 29 12 8630 9107 620676830 620677330 4.740000e-162 582.0
15 TraesCS7A01G457200 chr7B 90.698 86 8 0 5864 5949 716959442 716959357 2.080000e-21 115.0
16 TraesCS7A01G457200 chr7B 92.188 64 5 0 7361 7424 504476549 504476612 3.500000e-14 91.6
17 TraesCS7A01G457200 chr7B 97.297 37 1 0 3577 3613 620671639 620671675 7.630000e-06 63.9
18 TraesCS7A01G457200 chr6B 84.349 607 71 16 5978 6570 143439212 143439808 2.850000e-159 573.0
19 TraesCS7A01G457200 chr6B 84.385 301 28 13 8818 9107 718595870 718596162 2.500000e-70 278.0
20 TraesCS7A01G457200 chr6B 90.588 85 7 1 5867 5951 435585464 435585547 2.690000e-20 111.0
21 TraesCS7A01G457200 chr5D 83.333 372 43 11 4722 5090 14119118 14118763 8.820000e-85 326.0
22 TraesCS7A01G457200 chr5D 92.941 85 4 2 5867 5949 281024790 281024874 1.240000e-23 122.0
23 TraesCS7A01G457200 chr5B 80.815 417 58 13 4694 5090 13430545 13430131 3.190000e-79 307.0
24 TraesCS7A01G457200 chr5B 82.779 331 45 11 3221 3545 13433695 13433371 1.500000e-72 285.0
25 TraesCS7A01G457200 chr5B 81.773 203 36 1 2501 2702 13434354 13434152 1.570000e-37 169.0
26 TraesCS7A01G457200 chr5B 96.296 54 1 1 7379 7432 612333473 612333525 4.530000e-13 87.9
27 TraesCS7A01G457200 chr5A 79.335 421 58 17 4694 5090 11062898 11062483 1.510000e-67 268.0
28 TraesCS7A01G457200 chr1B 90.361 83 6 2 5875 5955 656151981 656151899 3.480000e-19 108.0
29 TraesCS7A01G457200 chr2B 86.047 86 8 3 5867 5949 52655394 52655478 1.260000e-13 89.8
30 TraesCS7A01G457200 chr2B 92.308 65 2 2 7356 7417 779050009 779049945 1.260000e-13 89.8
31 TraesCS7A01G457200 chr2B 90.625 64 1 1 7359 7417 668383652 668383715 7.580000e-11 80.5
32 TraesCS7A01G457200 chr6D 93.103 58 2 1 7362 7419 81756153 81756098 5.860000e-12 84.2
33 TraesCS7A01G457200 chr3A 91.525 59 3 1 7359 7417 15787277 15787333 7.580000e-11 80.5
34 TraesCS7A01G457200 chr1D 91.525 59 3 2 7358 7416 222915216 222915160 7.580000e-11 80.5
35 TraesCS7A01G457200 chr4B 89.394 66 1 2 7362 7421 10507472 10507537 2.730000e-10 78.7
36 TraesCS7A01G457200 chr2D 83.721 86 11 1 7341 7423 595165404 595165489 2.730000e-10 78.7
37 TraesCS7A01G457200 chr3D 100.000 30 0 0 5864 5893 276579206 276579235 1.000000e-03 56.5


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 TraesCS7A01G457200 chr7A 652703128 652712234 9106 True 16818.000000 16818 100.000000 1 9107 1 chr7A.!!$R1 9106
1 TraesCS7A01G457200 chr7D 566521657 566530698 9041 True 2063.414286 4868 95.857857 1 9107 7 chr7D.!!$R1 9106
2 TraesCS7A01G457200 chr7B 620668034 620677330 9296 False 2018.842857 4831 94.651714 31 9107 7 chr7B.!!$F2 9076
3 TraesCS7A01G457200 chr6B 143439212 143439808 596 False 573.000000 573 84.349000 5978 6570 1 chr6B.!!$F1 592
4 TraesCS7A01G457200 chr5B 13430131 13434354 4223 True 253.666667 307 81.789000 2501 5090 3 chr5B.!!$R1 2589

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
211 212 0.099436 GTGAGCGGATCAAATGCCAC 59.901 55.000 0.00 0.69 40.43 5.01 F
276 278 0.753867 TGGTGACAACGAGCCAAGTA 59.246 50.000 0.00 0.00 37.44 2.24 F
478 480 1.002857 AAATAGGTGAGCAGCCCCTT 58.997 50.000 1.43 0.00 0.00 3.95 F
1642 1648 1.021202 CGAGTTGTCTTTGGGCAACA 58.979 50.000 14.40 0.00 45.16 3.33 F
3270 3428 1.053835 TCCTGTCACTGCCCTTGTGA 61.054 55.000 0.00 0.00 41.48 3.58 F
3660 3830 3.947868 AGCTGTGTATCAGTTGCAGATT 58.052 40.909 0.00 0.00 45.23 2.40 F
4325 6261 0.108186 GCACACACTCATCCCGATGA 60.108 55.000 7.17 7.17 44.83 2.92 F
4474 6421 3.315191 TGTGGTAGTTTGCTCAAAGAAGC 59.685 43.478 0.00 0.00 42.82 3.86 F
4772 7188 4.500035 GGTTTGGATTTTACCGTGAAAGCA 60.500 41.667 6.40 0.00 0.00 3.91 F
5873 8309 1.287146 GGTGTCTCCCTACTACTCCCA 59.713 57.143 0.00 0.00 0.00 4.37 F
6852 9313 1.324383 TCAACTAGTGTCGTGAGCCA 58.676 50.000 0.00 0.00 0.00 4.75 F
7867 10329 0.178873 TCTGGCTGGTAAAGGGGAGT 60.179 55.000 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2021 2029 0.249398 AAAGATACGCCCGCTTCAGT 59.751 50.000 0.00 0.00 0.00 3.41 R
2116 2124 4.415881 TTATGGAAGTGTGACACTGTGT 57.584 40.909 20.19 14.23 44.62 3.72 R
2387 2396 3.731652 CAACAAAAGGAGGTTGCATGA 57.268 42.857 0.00 0.00 38.08 3.07 R
3619 3777 3.922850 GCTAAAAATTCTGAGGCTGCAAC 59.077 43.478 0.50 0.00 0.00 4.17 R
4202 6138 1.609061 CCAAGCTGACCGAACATCAGT 60.609 52.381 4.10 0.00 44.60 3.41 R
4955 7380 2.092968 TCTGCAACGAATTGGGATAGCT 60.093 45.455 0.00 0.00 36.23 3.32 R
5677 8113 0.756294 TGAGAGCTTGGGTCGTTTCA 59.244 50.000 0.00 0.00 35.00 2.69 R
5768 8204 4.019411 TGTCCCACACTCATGATACAATGT 60.019 41.667 0.00 0.00 0.00 2.71 R
6220 8674 4.336993 TCTTGACACCAGTTAAACGCAAAT 59.663 37.500 0.00 0.00 0.00 2.32 R
7081 9543 1.421268 ACAAAGCAGGATGACAGGTGA 59.579 47.619 0.00 0.00 39.69 4.02 R
7981 10443 0.474660 AGTGTCCTCTTGGAGCCCTT 60.475 55.000 0.00 0.00 44.16 3.95 R
8956 11509 0.935898 CACCAGAGATCGATTGCTGC 59.064 55.000 17.97 0.00 0.00 5.25 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
19 20 1.843368 ACGAACCCTAGGTCGATTGA 58.157 50.000 24.18 0.00 33.12 2.57
25 26 0.249073 CCTAGGTCGATTGAGCCGTG 60.249 60.000 8.57 0.00 43.71 4.94
28 29 3.554692 GTCGATTGAGCCGTGCCG 61.555 66.667 0.00 0.00 0.00 5.69
41 42 1.299976 GTGCCGGGGATTCTGTTCT 59.700 57.895 2.18 0.00 0.00 3.01
57 58 0.392461 TTCTGGAATTTCCCTCGCCG 60.392 55.000 12.90 0.00 35.03 6.46
103 104 0.967380 GCTGGTGGCAGGCTGTTATT 60.967 55.000 17.16 0.00 41.35 1.40
110 111 3.928375 GTGGCAGGCTGTTATTCATTTTG 59.072 43.478 17.16 0.00 0.00 2.44
161 162 2.927553 AGCCATCGAAGCATTTGTTC 57.072 45.000 12.70 0.00 0.00 3.18
171 172 2.595386 AGCATTTGTTCGCCGAAATTC 58.405 42.857 0.00 0.00 0.00 2.17
183 184 1.661617 CCGAAATTCGTGGCGTGATTA 59.338 47.619 14.58 0.00 38.40 1.75
211 212 0.099436 GTGAGCGGATCAAATGCCAC 59.901 55.000 0.00 0.69 40.43 5.01
213 214 1.728490 GAGCGGATCAAATGCCACCC 61.728 60.000 0.00 0.00 0.00 4.61
238 240 2.546494 GGCGAATGGAGCCGAATGG 61.546 63.158 0.00 0.00 45.58 3.16
276 278 0.753867 TGGTGACAACGAGCCAAGTA 59.246 50.000 0.00 0.00 37.44 2.24
277 279 1.346395 TGGTGACAACGAGCCAAGTAT 59.654 47.619 0.00 0.00 37.44 2.12
347 349 1.202475 GGTAGCAGTGCTAGAAGGCTC 60.202 57.143 25.09 11.19 42.11 4.70
389 391 1.456287 GAGGGCGGGCTATCCATTT 59.544 57.895 0.26 0.00 34.36 2.32
406 408 9.354673 CTATCCATTTCCACCAAAGTAACATAT 57.645 33.333 0.00 0.00 0.00 1.78
415 417 8.744652 TCCACCAAAGTAACATATTTGTAATGG 58.255 33.333 0.00 0.00 34.06 3.16
440 442 6.489603 ACTAATGGTATCACAATGGTTTCCA 58.510 36.000 0.00 0.00 38.19 3.53
478 480 1.002857 AAATAGGTGAGCAGCCCCTT 58.997 50.000 1.43 0.00 0.00 3.95
486 488 2.294512 GTGAGCAGCCCCTTAATATTGC 59.705 50.000 0.00 0.00 0.00 3.56
527 532 2.996249 TCTCCTTCACTCATGATGCC 57.004 50.000 0.00 0.00 33.85 4.40
529 534 1.211212 CTCCTTCACTCATGATGCCCA 59.789 52.381 0.00 0.00 33.85 5.36
648 653 6.319658 ACTGGCAAGATGGTTATTTATGACTG 59.680 38.462 0.00 0.00 0.00 3.51
657 662 4.157656 GGTTATTTATGACTGTGCTTGGCA 59.842 41.667 0.00 0.00 35.60 4.92
762 767 1.312371 TTTCGGCCATACCTTGCTGC 61.312 55.000 2.24 0.00 35.61 5.25
928 933 4.638865 GGGTTAATAAACTAGCACCACCAG 59.361 45.833 0.00 0.00 35.81 4.00
934 939 1.645710 ACTAGCACCACCAGCTTAGT 58.354 50.000 0.00 0.00 43.25 2.24
1102 1107 7.865707 AGTACAACTTGCTCATTCTTTACTTG 58.134 34.615 0.00 0.00 0.00 3.16
1219 1224 2.162408 CCATCCACTTCGCTTCCTTTTC 59.838 50.000 0.00 0.00 0.00 2.29
1353 1358 2.466846 AGACGTTTAACTGACGGTGTG 58.533 47.619 3.47 0.00 44.34 3.82
1488 1494 3.118531 ACAGAATTAGCCATCCCTGTCT 58.881 45.455 0.00 0.00 29.93 3.41
1489 1495 3.525199 ACAGAATTAGCCATCCCTGTCTT 59.475 43.478 0.00 0.00 29.93 3.01
1490 1496 4.018050 ACAGAATTAGCCATCCCTGTCTTT 60.018 41.667 0.00 0.00 29.93 2.52
1532 1538 4.062991 CACCAGACAAGGTTAGGTACAAC 58.937 47.826 0.00 0.00 40.77 3.32
1586 1592 4.266976 GCATGTTCTCAGCACAAATAATGC 59.733 41.667 0.00 0.00 43.74 3.56
1636 1642 6.727824 ATATTCTGTTCGAGTTGTCTTTGG 57.272 37.500 0.00 0.00 0.00 3.28
1637 1643 2.833794 TCTGTTCGAGTTGTCTTTGGG 58.166 47.619 0.00 0.00 0.00 4.12
1638 1644 1.264288 CTGTTCGAGTTGTCTTTGGGC 59.736 52.381 0.00 0.00 0.00 5.36
1639 1645 1.305201 GTTCGAGTTGTCTTTGGGCA 58.695 50.000 0.00 0.00 0.00 5.36
1640 1646 1.673920 GTTCGAGTTGTCTTTGGGCAA 59.326 47.619 0.00 0.00 0.00 4.52
1641 1647 1.305201 TCGAGTTGTCTTTGGGCAAC 58.695 50.000 5.48 5.48 43.63 4.17
1642 1648 1.021202 CGAGTTGTCTTTGGGCAACA 58.979 50.000 14.40 0.00 45.16 3.33
1643 1649 1.608590 CGAGTTGTCTTTGGGCAACAT 59.391 47.619 14.40 1.88 45.16 2.71
1644 1650 2.034558 CGAGTTGTCTTTGGGCAACATT 59.965 45.455 14.40 0.00 45.16 2.71
1645 1651 3.490761 CGAGTTGTCTTTGGGCAACATTT 60.491 43.478 14.40 0.00 45.16 2.32
1646 1652 4.441792 GAGTTGTCTTTGGGCAACATTTT 58.558 39.130 14.40 0.00 45.16 1.82
1647 1653 4.842574 AGTTGTCTTTGGGCAACATTTTT 58.157 34.783 14.40 0.00 45.16 1.94
1687 1693 3.181487 GGGCAACATCATACACATGGTTC 60.181 47.826 0.00 0.00 39.74 3.62
1734 1741 1.980765 TGGCCCACAAAAATTATGCCA 59.019 42.857 0.00 0.00 44.55 4.92
1867 1875 5.952033 AGATCTAACTGTTGAACTACCGAC 58.048 41.667 2.69 0.00 0.00 4.79
2021 2029 8.616076 CCAAAATTTGCATTACCAACAGTTTTA 58.384 29.630 0.00 0.00 0.00 1.52
2116 2124 7.047271 TGCATGAAAGTGATGCTTACTATACA 58.953 34.615 0.00 0.00 45.45 2.29
2117 2125 7.011389 TGCATGAAAGTGATGCTTACTATACAC 59.989 37.037 0.00 0.00 45.45 2.90
2155 2164 7.118496 TCCATAATGTTTGTTGTGAACCTTT 57.882 32.000 0.00 0.00 0.00 3.11
2270 2279 4.449068 AGTCAAACTATTTCGAGTGTGCTG 59.551 41.667 0.00 0.00 35.02 4.41
2457 2466 7.667043 ATATATTTTGTGCCGGTACTGTATG 57.333 36.000 23.67 0.00 0.00 2.39
2886 2939 4.022935 TCAGATGATTTGTTCAGTGGTTGC 60.023 41.667 0.00 0.00 37.89 4.17
2892 2945 3.552132 TTGTTCAGTGGTTGCTCACTA 57.448 42.857 7.41 0.00 45.24 2.74
2917 2970 4.954092 ACTCTTATTGCACTTGCTAAGC 57.046 40.909 2.33 0.00 42.66 3.09
3089 3164 8.506168 TGGAACTTACCTTTATGATTGATGAC 57.494 34.615 0.00 0.00 0.00 3.06
3178 3309 8.640063 ACCATCTTATATGCAAATGCTAATCA 57.360 30.769 6.97 0.00 42.66 2.57
3214 3345 8.343366 CGACTTCCTATTTTAATAGCCCTTTTC 58.657 37.037 4.33 0.00 37.61 2.29
3270 3428 1.053835 TCCTGTCACTGCCCTTGTGA 61.054 55.000 0.00 0.00 41.48 3.58
3357 3515 5.527582 AGAAACCGTATTGATGTATGCTTCC 59.472 40.000 0.00 0.00 0.00 3.46
3482 3640 5.510861 CCCCACATACCTAATTTCTAGGTCG 60.511 48.000 6.73 3.35 44.10 4.79
3619 3777 6.656945 CCTCAGAATTTTTAGCTGATCGATG 58.343 40.000 0.54 0.00 37.95 3.84
3660 3830 3.947868 AGCTGTGTATCAGTTGCAGATT 58.052 40.909 0.00 0.00 45.23 2.40
3661 3831 4.330250 AGCTGTGTATCAGTTGCAGATTT 58.670 39.130 0.00 0.00 45.23 2.17
3662 3832 4.763793 AGCTGTGTATCAGTTGCAGATTTT 59.236 37.500 0.00 0.00 45.23 1.82
3663 3833 5.091431 GCTGTGTATCAGTTGCAGATTTTC 58.909 41.667 0.00 0.00 45.23 2.29
3664 3834 5.627499 TGTGTATCAGTTGCAGATTTTCC 57.373 39.130 0.00 0.00 0.00 3.13
3665 3835 5.316167 TGTGTATCAGTTGCAGATTTTCCT 58.684 37.500 0.00 0.00 0.00 3.36
3666 3836 5.769662 TGTGTATCAGTTGCAGATTTTCCTT 59.230 36.000 0.00 0.00 0.00 3.36
3667 3837 6.265196 TGTGTATCAGTTGCAGATTTTCCTTT 59.735 34.615 0.00 0.00 0.00 3.11
3668 3838 7.147976 GTGTATCAGTTGCAGATTTTCCTTTT 58.852 34.615 0.00 0.00 0.00 2.27
3669 3839 7.653311 GTGTATCAGTTGCAGATTTTCCTTTTT 59.347 33.333 0.00 0.00 0.00 1.94
3670 3840 8.855110 TGTATCAGTTGCAGATTTTCCTTTTTA 58.145 29.630 0.00 0.00 0.00 1.52
3671 3841 9.860898 GTATCAGTTGCAGATTTTCCTTTTTAT 57.139 29.630 0.00 0.00 0.00 1.40
3864 4034 7.809806 GCTTGCTGATTGTTTGATAGTTAGTTT 59.190 33.333 0.00 0.00 0.00 2.66
3889 4896 7.934855 AATGAATCAGCATTTCACTAGAGTT 57.065 32.000 0.00 0.00 35.01 3.01
4202 6138 3.856206 ACCTTTAGCCTTTAGGGAATCCA 59.144 43.478 0.09 0.00 37.23 3.41
4280 6216 6.384305 AGGTATGCAACTTGATTAGGTACTCT 59.616 38.462 0.00 0.00 41.75 3.24
4311 6247 5.883661 AGAATTATGCATACACAAGCACAC 58.116 37.500 5.74 0.00 44.49 3.82
4325 6261 0.108186 GCACACACTCATCCCGATGA 60.108 55.000 7.17 7.17 44.83 2.92
4386 6322 4.263639 TGCATCCCTTCTCTCAGTTTTCAT 60.264 41.667 0.00 0.00 0.00 2.57
4394 6330 6.313411 CCTTCTCTCAGTTTTCATGTCTCATC 59.687 42.308 0.00 0.00 0.00 2.92
4395 6331 6.350629 TCTCTCAGTTTTCATGTCTCATCA 57.649 37.500 0.00 0.00 0.00 3.07
4396 6332 6.762333 TCTCTCAGTTTTCATGTCTCATCAA 58.238 36.000 0.00 0.00 0.00 2.57
4397 6333 7.219322 TCTCTCAGTTTTCATGTCTCATCAAA 58.781 34.615 0.00 0.00 0.00 2.69
4398 6334 7.716560 TCTCTCAGTTTTCATGTCTCATCAAAA 59.283 33.333 0.00 0.00 0.00 2.44
4399 6335 8.400184 TCTCAGTTTTCATGTCTCATCAAAAT 57.600 30.769 0.00 0.00 0.00 1.82
4400 6336 8.509690 TCTCAGTTTTCATGTCTCATCAAAATC 58.490 33.333 0.00 0.00 0.00 2.17
4401 6337 8.400184 TCAGTTTTCATGTCTCATCAAAATCT 57.600 30.769 0.00 0.00 0.00 2.40
4402 6338 8.853126 TCAGTTTTCATGTCTCATCAAAATCTT 58.147 29.630 0.00 0.00 0.00 2.40
4403 6339 9.472361 CAGTTTTCATGTCTCATCAAAATCTTT 57.528 29.630 0.00 0.00 0.00 2.52
4474 6421 3.315191 TGTGGTAGTTTGCTCAAAGAAGC 59.685 43.478 0.00 0.00 42.82 3.86
4621 6960 8.298854 TGAATTGAACTCTGTTAATGTGATTGG 58.701 33.333 0.00 0.00 0.00 3.16
4772 7188 4.500035 GGTTTGGATTTTACCGTGAAAGCA 60.500 41.667 6.40 0.00 0.00 3.91
5152 7588 9.979578 ATGCTGTTCTGTTTGTTTCATTTTATA 57.020 25.926 0.00 0.00 0.00 0.98
5296 7732 7.623089 GCTTCATCTTGTCATCACACTAACTTC 60.623 40.741 0.00 0.00 29.76 3.01
5566 8002 4.705023 GGTAACCTAACTGTAACCGGTCTA 59.295 45.833 8.04 0.00 0.00 2.59
5650 8086 7.436673 CAGAATATAGAACAACAGAGGCTACAC 59.563 40.741 0.00 0.00 0.00 2.90
5768 8204 2.625314 TGCATGATCACCCGTTTTGAAA 59.375 40.909 0.00 0.00 0.00 2.69
5873 8309 1.287146 GGTGTCTCCCTACTACTCCCA 59.713 57.143 0.00 0.00 0.00 4.37
6155 8609 9.442062 TTTTATGGAAGATGGATGTAGGTAGTA 57.558 33.333 0.00 0.00 0.00 1.82
6220 8674 8.846943 TCTATTTTCACATCTACTTTCTTGCA 57.153 30.769 0.00 0.00 0.00 4.08
6246 8700 4.336993 TGCGTTTAACTGGTGTCAAGATTT 59.663 37.500 0.00 0.00 0.00 2.17
6375 8833 6.478512 AAGGTTGGTATCATTTTGTTGTGT 57.521 33.333 0.00 0.00 0.00 3.72
6461 8919 8.958060 ATGTCCAGGTAACATATCTGTATAGT 57.042 34.615 0.00 0.00 35.10 2.12
6688 9149 6.737254 ACTTATGGAAACCAGTGATAAACG 57.263 37.500 0.00 0.00 36.75 3.60
6852 9313 1.324383 TCAACTAGTGTCGTGAGCCA 58.676 50.000 0.00 0.00 0.00 4.75
7035 9497 3.152341 CCTTGCTGATCTGTTTGGTTCT 58.848 45.455 1.27 0.00 0.00 3.01
7081 9543 0.467290 ATGGGGACGTTGCAGTTGTT 60.467 50.000 0.00 0.00 0.00 2.83
7082 9544 1.098712 TGGGGACGTTGCAGTTGTTC 61.099 55.000 0.00 0.00 0.00 3.18
7136 9598 5.221441 ACCCTGAGCCTTAAATTTGAAACAC 60.221 40.000 0.00 0.00 0.00 3.32
7203 9665 3.084786 CCAAATGAGTTCTGAACCCCTC 58.915 50.000 16.48 8.81 0.00 4.30
7299 9761 9.185192 GAGTTCTTTCATTTTGTTTGTAGATGG 57.815 33.333 0.00 0.00 0.00 3.51
7367 9829 9.516314 GTGTTTATTTTATCAGCATTTACTCCC 57.484 33.333 0.00 0.00 0.00 4.30
7368 9830 9.474313 TGTTTATTTTATCAGCATTTACTCCCT 57.526 29.630 0.00 0.00 0.00 4.20
7369 9831 9.952188 GTTTATTTTATCAGCATTTACTCCCTC 57.048 33.333 0.00 0.00 0.00 4.30
7370 9832 8.691661 TTATTTTATCAGCATTTACTCCCTCC 57.308 34.615 0.00 0.00 0.00 4.30
7371 9833 2.918712 ATCAGCATTTACTCCCTCCG 57.081 50.000 0.00 0.00 0.00 4.63
7372 9834 1.568504 TCAGCATTTACTCCCTCCGT 58.431 50.000 0.00 0.00 0.00 4.69
7373 9835 1.906574 TCAGCATTTACTCCCTCCGTT 59.093 47.619 0.00 0.00 0.00 4.44
7374 9836 2.093658 TCAGCATTTACTCCCTCCGTTC 60.094 50.000 0.00 0.00 0.00 3.95
7375 9837 1.209747 AGCATTTACTCCCTCCGTTCC 59.790 52.381 0.00 0.00 0.00 3.62
7376 9838 1.065709 GCATTTACTCCCTCCGTTCCA 60.066 52.381 0.00 0.00 0.00 3.53
7377 9839 2.617021 GCATTTACTCCCTCCGTTCCAA 60.617 50.000 0.00 0.00 0.00 3.53
7378 9840 3.886123 CATTTACTCCCTCCGTTCCAAT 58.114 45.455 0.00 0.00 0.00 3.16
7379 9841 4.685030 GCATTTACTCCCTCCGTTCCAATA 60.685 45.833 0.00 0.00 0.00 1.90
7380 9842 4.476628 TTTACTCCCTCCGTTCCAATAC 57.523 45.455 0.00 0.00 0.00 1.89
7381 9843 1.946984 ACTCCCTCCGTTCCAATACA 58.053 50.000 0.00 0.00 0.00 2.29
7382 9844 2.262637 ACTCCCTCCGTTCCAATACAA 58.737 47.619 0.00 0.00 0.00 2.41
7383 9845 2.640826 ACTCCCTCCGTTCCAATACAAA 59.359 45.455 0.00 0.00 0.00 2.83
7384 9846 3.270877 CTCCCTCCGTTCCAATACAAAG 58.729 50.000 0.00 0.00 0.00 2.77
7385 9847 2.640826 TCCCTCCGTTCCAATACAAAGT 59.359 45.455 0.00 0.00 0.00 2.66
7386 9848 3.073356 TCCCTCCGTTCCAATACAAAGTT 59.927 43.478 0.00 0.00 0.00 2.66
7387 9849 3.190535 CCCTCCGTTCCAATACAAAGTTG 59.809 47.826 0.00 0.00 0.00 3.16
7388 9850 4.069304 CCTCCGTTCCAATACAAAGTTGA 58.931 43.478 0.00 0.00 0.00 3.18
7389 9851 4.154195 CCTCCGTTCCAATACAAAGTTGAG 59.846 45.833 0.00 0.00 0.00 3.02
7390 9852 4.710324 TCCGTTCCAATACAAAGTTGAGT 58.290 39.130 0.00 0.00 0.00 3.41
7391 9853 4.753107 TCCGTTCCAATACAAAGTTGAGTC 59.247 41.667 0.00 0.00 0.00 3.36
7392 9854 4.513692 CCGTTCCAATACAAAGTTGAGTCA 59.486 41.667 0.00 0.00 0.00 3.41
7393 9855 5.181245 CCGTTCCAATACAAAGTTGAGTCAT 59.819 40.000 0.00 0.00 0.00 3.06
7394 9856 6.307155 CGTTCCAATACAAAGTTGAGTCATC 58.693 40.000 0.00 0.00 0.00 2.92
7395 9857 6.147821 CGTTCCAATACAAAGTTGAGTCATCT 59.852 38.462 0.00 0.00 0.00 2.90
7396 9858 7.330946 CGTTCCAATACAAAGTTGAGTCATCTA 59.669 37.037 4.14 0.00 0.00 1.98
7397 9859 9.167311 GTTCCAATACAAAGTTGAGTCATCTAT 57.833 33.333 4.14 0.00 0.00 1.98
7398 9860 9.739276 TTCCAATACAAAGTTGAGTCATCTATT 57.261 29.630 4.14 0.00 0.00 1.73
7399 9861 9.739276 TCCAATACAAAGTTGAGTCATCTATTT 57.261 29.630 4.14 0.00 0.00 1.40
7403 9865 9.739276 ATACAAAGTTGAGTCATCTATTTTGGA 57.261 29.630 14.35 9.09 40.00 3.53
7404 9866 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
7405 9867 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
7406 9868 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
7407 9869 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
7408 9870 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
7409 9871 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
7410 9872 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
7411 9873 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
7412 9874 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
7413 9875 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
7414 9876 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
7415 9877 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
7425 9887 4.456662 ACGGAGGGAGTAGATATCACTT 57.543 45.455 5.32 0.00 28.03 3.16
7427 9889 3.508012 CGGAGGGAGTAGATATCACTTGG 59.492 52.174 5.32 0.00 28.03 3.61
7434 9896 6.127026 GGGAGTAGATATCACTTGGAACACTT 60.127 42.308 5.32 0.00 39.29 3.16
7485 9947 3.288092 ACAGGAGGAAGTTTTGTTGGAC 58.712 45.455 0.00 0.00 0.00 4.02
7551 10013 1.269166 CTCGAACGGTCCAGAAATCG 58.731 55.000 0.00 0.00 0.00 3.34
7600 10062 4.689062 TCCTTTTGGAGAGGAGATGTACT 58.311 43.478 0.00 0.00 45.19 2.73
7805 10267 2.224523 TGGTGTCAGAAGATGGTCCAAC 60.225 50.000 0.00 0.00 0.00 3.77
7867 10329 0.178873 TCTGGCTGGTAAAGGGGAGT 60.179 55.000 0.00 0.00 0.00 3.85
7887 10349 3.147595 CGAGGATCCGAGGCCACA 61.148 66.667 5.01 0.00 0.00 4.17
7981 10443 4.202419 ACATTGTTCTGGGTGTAGCACTTA 60.202 41.667 0.00 0.00 34.40 2.24
7983 10445 4.002906 TGTTCTGGGTGTAGCACTTAAG 57.997 45.455 0.00 0.00 34.40 1.85
8015 10477 1.275291 GACACTCCCCATCGAACAAGA 59.725 52.381 0.00 0.00 0.00 3.02
8099 10561 6.731467 AGGATAAGAAAGGTCAAAGCCATAA 58.269 36.000 0.00 0.00 0.00 1.90
8251 10713 1.016627 TGCAAATGCTATCTGTCGCC 58.983 50.000 6.97 0.00 42.66 5.54
8252 10714 0.308993 GCAAATGCTATCTGTCGCCC 59.691 55.000 0.00 0.00 38.21 6.13
8254 10716 0.179018 AAATGCTATCTGTCGCCCCC 60.179 55.000 0.00 0.00 0.00 5.40
8257 10719 1.271840 TGCTATCTGTCGCCCCCTTT 61.272 55.000 0.00 0.00 0.00 3.11
8258 10720 0.533085 GCTATCTGTCGCCCCCTTTC 60.533 60.000 0.00 0.00 0.00 2.62
8259 10721 1.123928 CTATCTGTCGCCCCCTTTCT 58.876 55.000 0.00 0.00 0.00 2.52
8260 10722 1.486726 CTATCTGTCGCCCCCTTTCTT 59.513 52.381 0.00 0.00 0.00 2.52
8261 10723 0.698818 ATCTGTCGCCCCCTTTCTTT 59.301 50.000 0.00 0.00 0.00 2.52
8262 10724 0.476771 TCTGTCGCCCCCTTTCTTTT 59.523 50.000 0.00 0.00 0.00 2.27
8263 10725 1.133606 TCTGTCGCCCCCTTTCTTTTT 60.134 47.619 0.00 0.00 0.00 1.94
8264 10726 1.269723 CTGTCGCCCCCTTTCTTTTTC 59.730 52.381 0.00 0.00 0.00 2.29
8265 10727 0.601558 GTCGCCCCCTTTCTTTTTCC 59.398 55.000 0.00 0.00 0.00 3.13
8266 10728 0.481128 TCGCCCCCTTTCTTTTTCCT 59.519 50.000 0.00 0.00 0.00 3.36
8267 10729 1.133294 TCGCCCCCTTTCTTTTTCCTT 60.133 47.619 0.00 0.00 0.00 3.36
8268 10730 1.691976 CGCCCCCTTTCTTTTTCCTTT 59.308 47.619 0.00 0.00 0.00 3.11
8269 10731 2.104111 CGCCCCCTTTCTTTTTCCTTTT 59.896 45.455 0.00 0.00 0.00 2.27
8270 10732 3.740115 GCCCCCTTTCTTTTTCCTTTTC 58.260 45.455 0.00 0.00 0.00 2.29
8271 10733 3.391296 GCCCCCTTTCTTTTTCCTTTTCT 59.609 43.478 0.00 0.00 0.00 2.52
8275 10737 6.542370 CCCCCTTTCTTTTTCCTTTTCTTTTC 59.458 38.462 0.00 0.00 0.00 2.29
8355 10817 6.992063 AAAATGTAGCCTAGTCATTGACTG 57.008 37.500 26.01 16.32 43.30 3.51
8363 10825 1.356124 AGTCATTGACTGTGCTCCCT 58.644 50.000 18.35 0.00 41.76 4.20
8369 10831 1.257750 TGACTGTGCTCCCTGCGTAT 61.258 55.000 0.00 0.00 46.63 3.06
8460 10940 1.817357 TCTGTGCTGCTTCATTCTGG 58.183 50.000 0.00 0.00 0.00 3.86
8497 10977 0.527565 AGGCATGTTCGAAATGGTGC 59.472 50.000 16.66 15.22 0.00 5.01
8499 10979 1.067635 GGCATGTTCGAAATGGTGCTT 60.068 47.619 18.48 0.00 33.38 3.91
8500 10980 1.987770 GCATGTTCGAAATGGTGCTTG 59.012 47.619 16.66 7.29 0.00 4.01
8523 11003 2.224606 CACCAGCATTGTGTTCTGAGT 58.775 47.619 0.00 0.00 0.00 3.41
8575 11055 3.257873 TGTTTGGCATAAGTGGGTGATTG 59.742 43.478 0.00 0.00 0.00 2.67
8592 11072 2.908940 GCTTGGCCGGATCATGGG 60.909 66.667 5.05 0.00 0.00 4.00
8675 11202 6.127083 TGCCTATGTGTCTGATTTGAGATGTA 60.127 38.462 0.00 0.00 0.00 2.29
8782 11312 7.622081 TCATATCCTCTGGTTTCCTGTAAACTA 59.378 37.037 0.00 0.00 45.70 2.24
8783 11313 5.479124 TCCTCTGGTTTCCTGTAAACTAC 57.521 43.478 0.00 0.00 45.70 2.73
8805 11335 0.892755 AGGCACCAACATGCTCATTG 59.107 50.000 0.00 0.00 45.38 2.82
8930 11483 1.610038 TGTCCATGCACTCAAAGCTTG 59.390 47.619 0.00 0.00 37.03 4.01
8965 11518 2.948093 CCGAAATTGGCAGCAATCG 58.052 52.632 0.00 6.96 0.00 3.34
8972 11525 1.660167 TTGGCAGCAATCGATCTCTG 58.340 50.000 17.60 17.60 0.00 3.35
9035 11588 1.067635 GGGCACAGCTACAACATTTGG 60.068 52.381 0.00 0.00 34.12 3.28
9038 11591 2.669391 GCACAGCTACAACATTTGGCTC 60.669 50.000 0.00 0.00 34.12 4.70
9085 11638 1.381056 TCAAATGGGAATGGGCCGG 60.381 57.895 0.00 0.00 0.00 6.13
9103 11656 1.183549 GGCCGAGGAGAACACTAAGA 58.816 55.000 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.452108 CCAGAACAGAATCCCCGGC 60.452 63.158 0.00 0.00 0.00 6.13
28 29 3.701542 GGAAATTCCAGAACAGAATCCCC 59.298 47.826 7.23 0.00 36.28 4.81
32 33 4.265073 CGAGGGAAATTCCAGAACAGAAT 58.735 43.478 14.68 0.00 38.64 2.40
33 34 3.674997 CGAGGGAAATTCCAGAACAGAA 58.325 45.455 14.68 0.00 38.64 3.02
41 42 2.437716 GCGGCGAGGGAAATTCCA 60.438 61.111 12.98 0.00 38.64 3.53
57 58 3.287520 GGCGGGGATTTGGATCGC 61.288 66.667 0.00 0.00 44.80 4.58
103 104 2.485479 GGAGGATCTAGCCGCAAAATGA 60.485 50.000 0.00 0.00 33.73 2.57
110 111 2.203714 AGGGGAGGATCTAGCCGC 60.204 66.667 0.00 0.47 33.73 6.53
171 172 1.436195 CCCCACATAATCACGCCACG 61.436 60.000 0.00 0.00 0.00 4.94
177 178 1.299541 CTCACGCCCCACATAATCAC 58.700 55.000 0.00 0.00 0.00 3.06
231 232 1.152777 TAATGCCCTGGCCATTCGG 60.153 57.895 5.51 7.69 41.09 4.30
233 234 2.508526 CTAGTAATGCCCTGGCCATTC 58.491 52.381 5.51 0.00 41.09 2.67
238 240 1.228276 GCCCTAGTAATGCCCTGGC 60.228 63.158 0.00 0.00 42.35 4.85
276 278 4.895297 CCCCATTACAAACTGAGGCAATAT 59.105 41.667 0.00 0.00 0.00 1.28
277 279 4.017958 TCCCCATTACAAACTGAGGCAATA 60.018 41.667 0.00 0.00 0.00 1.90
347 349 4.932200 GCCCCTCATATCGTCTAATTCAAG 59.068 45.833 0.00 0.00 0.00 3.02
389 391 8.744652 CCATTACAAATATGTTACTTTGGTGGA 58.255 33.333 9.21 0.00 41.05 4.02
406 408 9.693739 ATTGTGATACCATTAGTCCATTACAAA 57.306 29.630 0.00 0.00 0.00 2.83
415 417 6.601613 TGGAAACCATTGTGATACCATTAGTC 59.398 38.462 0.00 0.00 0.00 2.59
446 448 7.962441 TGCTCACCTATTTACAGCTATATTGA 58.038 34.615 0.00 0.00 0.00 2.57
478 480 4.215399 GCTGCAACCTATTCCGCAATATTA 59.785 41.667 0.00 0.00 33.21 0.98
486 488 1.401905 GAAAGGCTGCAACCTATTCCG 59.598 52.381 9.58 0.00 39.93 4.30
527 532 2.270047 CCGGCATTAAAACAAGCATGG 58.730 47.619 0.00 0.00 0.00 3.66
529 534 1.899142 ACCCGGCATTAAAACAAGCAT 59.101 42.857 0.00 0.00 0.00 3.79
531 536 1.708822 CACCCGGCATTAAAACAAGC 58.291 50.000 0.00 0.00 0.00 4.01
642 647 1.965643 ACAAATGCCAAGCACAGTCAT 59.034 42.857 0.00 0.00 43.04 3.06
648 653 2.514205 ACTCAACAAATGCCAAGCAC 57.486 45.000 0.00 0.00 43.04 4.40
657 662 1.688197 CCCACAGCCAACTCAACAAAT 59.312 47.619 0.00 0.00 0.00 2.32
742 747 1.392589 CAGCAAGGTATGGCCGAAAT 58.607 50.000 0.00 0.00 43.70 2.17
854 859 3.780804 TTTGTGGCAGGCTAACTCTTA 57.219 42.857 0.00 0.00 0.00 2.10
855 860 2.623416 GTTTTGTGGCAGGCTAACTCTT 59.377 45.455 0.00 0.00 0.00 2.85
860 865 1.953686 GTGAGTTTTGTGGCAGGCTAA 59.046 47.619 0.00 0.00 0.00 3.09
928 933 1.971357 TGCTATCAGGCCCTACTAAGC 59.029 52.381 0.00 1.91 0.00 3.09
934 939 0.105504 TGAGCTGCTATCAGGCCCTA 60.106 55.000 0.15 0.00 40.65 3.53
1039 1044 3.181465 TGGCTAAATCTGCTGGTAGTAGC 60.181 47.826 9.67 9.67 43.95 3.58
1128 1133 3.817647 AGGAGAGCAAACACTGATGAAAC 59.182 43.478 0.00 0.00 0.00 2.78
1219 1224 5.440610 AGGAAGGAACCATACATAAGCAAG 58.559 41.667 0.00 0.00 0.00 4.01
1498 1504 1.623311 TGTCTGGTGTGTCTATGTGGG 59.377 52.381 0.00 0.00 0.00 4.61
1647 1653 3.708631 TGCCCAAAGACATTCCTCAAAAA 59.291 39.130 0.00 0.00 0.00 1.94
1648 1654 3.303938 TGCCCAAAGACATTCCTCAAAA 58.696 40.909 0.00 0.00 0.00 2.44
1649 1655 2.956132 TGCCCAAAGACATTCCTCAAA 58.044 42.857 0.00 0.00 0.00 2.69
1650 1656 2.627699 GTTGCCCAAAGACATTCCTCAA 59.372 45.455 0.00 0.00 0.00 3.02
1651 1657 2.238521 GTTGCCCAAAGACATTCCTCA 58.761 47.619 0.00 0.00 0.00 3.86
1652 1658 2.238521 TGTTGCCCAAAGACATTCCTC 58.761 47.619 0.00 0.00 0.00 3.71
1653 1659 2.380064 TGTTGCCCAAAGACATTCCT 57.620 45.000 0.00 0.00 0.00 3.36
1654 1660 2.562298 TGATGTTGCCCAAAGACATTCC 59.438 45.455 0.00 0.00 34.38 3.01
1655 1661 3.940209 TGATGTTGCCCAAAGACATTC 57.060 42.857 0.00 0.00 34.38 2.67
1656 1662 4.771577 TGTATGATGTTGCCCAAAGACATT 59.228 37.500 0.00 0.00 34.38 2.71
1657 1663 4.158394 GTGTATGATGTTGCCCAAAGACAT 59.842 41.667 0.00 0.00 36.76 3.06
1658 1664 3.505680 GTGTATGATGTTGCCCAAAGACA 59.494 43.478 0.00 0.00 0.00 3.41
1659 1665 3.505680 TGTGTATGATGTTGCCCAAAGAC 59.494 43.478 0.00 0.00 0.00 3.01
1660 1666 3.760738 TGTGTATGATGTTGCCCAAAGA 58.239 40.909 0.00 0.00 0.00 2.52
1661 1667 4.426416 CATGTGTATGATGTTGCCCAAAG 58.574 43.478 0.00 0.00 36.36 2.77
1662 1668 3.195182 CCATGTGTATGATGTTGCCCAAA 59.805 43.478 0.00 0.00 36.36 3.28
1663 1669 2.759535 CCATGTGTATGATGTTGCCCAA 59.240 45.455 0.00 0.00 36.36 4.12
1664 1670 2.291475 ACCATGTGTATGATGTTGCCCA 60.291 45.455 0.00 0.00 36.36 5.36
1665 1671 2.378038 ACCATGTGTATGATGTTGCCC 58.622 47.619 0.00 0.00 36.36 5.36
1867 1875 2.100216 GCGCATACTTGCCCGTTG 59.900 61.111 0.30 0.00 46.57 4.10
1994 2002 5.923204 ACTGTTGGTAATGCAAATTTTGGA 58.077 33.333 10.96 8.49 34.77 3.53
2002 2010 6.701145 TCAGTAAAACTGTTGGTAATGCAA 57.299 33.333 6.93 0.00 46.03 4.08
2021 2029 0.249398 AAAGATACGCCCGCTTCAGT 59.751 50.000 0.00 0.00 0.00 3.41
2116 2124 4.415881 TTATGGAAGTGTGACACTGTGT 57.584 40.909 20.19 14.23 44.62 3.72
2117 2125 4.756642 ACATTATGGAAGTGTGACACTGTG 59.243 41.667 20.19 6.19 44.62 3.66
2270 2279 7.174080 GGAATTTCAAGATAGGGATAAGCAGAC 59.826 40.741 0.00 0.00 0.00 3.51
2387 2396 3.731652 CAACAAAAGGAGGTTGCATGA 57.268 42.857 0.00 0.00 38.08 3.07
2457 2466 4.642466 ACTAGGGGATATTGCTTAAGGC 57.358 45.455 4.29 0.00 42.22 4.35
2886 2939 6.142818 AGTGCAATAAGAGTAGCTAGTGAG 57.857 41.667 5.62 0.00 0.00 3.51
2892 2945 4.213564 AGCAAGTGCAATAAGAGTAGCT 57.786 40.909 6.00 0.00 45.16 3.32
2917 2970 6.763610 ACTGAGTTGAAGAAGTTACTGAAAGG 59.236 38.462 0.00 0.00 39.30 3.11
3101 3176 7.118723 TGAATTGGCTACAGAATTTATCCAGT 58.881 34.615 0.00 0.00 0.00 4.00
3270 3428 4.151883 ACAATTATTCCAACTGCAGGTGT 58.848 39.130 29.22 14.47 0.00 4.16
3482 3640 5.281727 CAAAGAAGCAAAGGTTGAAGGTAC 58.718 41.667 0.00 0.00 0.00 3.34
3619 3777 3.922850 GCTAAAAATTCTGAGGCTGCAAC 59.077 43.478 0.50 0.00 0.00 4.17
3660 3830 9.313118 GAGCAAAGAACAGAAATAAAAAGGAAA 57.687 29.630 0.00 0.00 0.00 3.13
3661 3831 8.474025 TGAGCAAAGAACAGAAATAAAAAGGAA 58.526 29.630 0.00 0.00 0.00 3.36
3662 3832 7.920682 GTGAGCAAAGAACAGAAATAAAAAGGA 59.079 33.333 0.00 0.00 0.00 3.36
3663 3833 7.706179 TGTGAGCAAAGAACAGAAATAAAAAGG 59.294 33.333 0.00 0.00 0.00 3.11
3664 3834 8.534778 GTGTGAGCAAAGAACAGAAATAAAAAG 58.465 33.333 0.00 0.00 0.00 2.27
3665 3835 8.031864 TGTGTGAGCAAAGAACAGAAATAAAAA 58.968 29.630 0.00 0.00 0.00 1.94
3666 3836 7.487829 GTGTGTGAGCAAAGAACAGAAATAAAA 59.512 33.333 0.00 0.00 0.00 1.52
3667 3837 6.972328 GTGTGTGAGCAAAGAACAGAAATAAA 59.028 34.615 0.00 0.00 0.00 1.40
3668 3838 6.494842 GTGTGTGAGCAAAGAACAGAAATAA 58.505 36.000 0.00 0.00 0.00 1.40
3669 3839 5.277297 CGTGTGTGAGCAAAGAACAGAAATA 60.277 40.000 0.00 0.00 0.00 1.40
3670 3840 4.496341 CGTGTGTGAGCAAAGAACAGAAAT 60.496 41.667 0.00 0.00 0.00 2.17
3671 3841 3.181511 CGTGTGTGAGCAAAGAACAGAAA 60.182 43.478 0.00 0.00 0.00 2.52
3889 4896 6.616577 AGTACTTCCCAGGGTTTTTCATTTA 58.383 36.000 5.01 0.00 0.00 1.40
3900 4907 2.844348 ACCATGTTAGTACTTCCCAGGG 59.156 50.000 14.51 14.51 33.43 4.45
4202 6138 1.609061 CCAAGCTGACCGAACATCAGT 60.609 52.381 4.10 0.00 44.60 3.41
4280 6216 9.313118 CTTGTGTATGCATAATTCTAGTGTACA 57.687 33.333 8.28 0.00 0.00 2.90
4474 6421 7.525688 ACACTATTTCACGATCATAACACAG 57.474 36.000 0.00 0.00 0.00 3.66
4561 6805 4.018490 ACATGCTGTTGCCATCAGATTTA 58.982 39.130 6.96 0.00 38.71 1.40
4772 7188 6.015688 CAGCAATCCAAATGCCAGTATAGATT 60.016 38.462 0.00 0.00 44.91 2.40
4955 7380 2.092968 TCTGCAACGAATTGGGATAGCT 60.093 45.455 0.00 0.00 36.23 3.32
4956 7381 2.288666 TCTGCAACGAATTGGGATAGC 58.711 47.619 0.00 0.00 36.23 2.97
4957 7382 5.505173 AAATCTGCAACGAATTGGGATAG 57.495 39.130 0.00 0.00 36.23 2.08
4960 7385 3.571828 TCAAAATCTGCAACGAATTGGGA 59.428 39.130 0.00 0.00 36.23 4.37
5152 7588 9.325198 TCAGATGACTATTGTTTAAATACGCAT 57.675 29.630 0.00 0.00 0.00 4.73
5192 7628 3.756434 ACAAAACCATGTATCGTGGAAGG 59.244 43.478 13.94 4.34 42.73 3.46
5296 7732 6.991485 ACACGCTGAAAATCAAATTAGTTG 57.009 33.333 0.00 0.00 38.71 3.16
5555 7991 5.082251 AGGAAAACAGATAGACCGGTTAC 57.918 43.478 9.42 0.00 0.00 2.50
5566 8002 7.038799 ACAATTATCTGCCAAAGGAAAACAGAT 60.039 33.333 8.66 8.66 41.33 2.90
5677 8113 0.756294 TGAGAGCTTGGGTCGTTTCA 59.244 50.000 0.00 0.00 35.00 2.69
5768 8204 4.019411 TGTCCCACACTCATGATACAATGT 60.019 41.667 0.00 0.00 0.00 2.71
5873 8309 8.814235 CAAGAACGTCTTATATTTTGATACGGT 58.186 33.333 0.00 0.00 33.78 4.83
5956 8395 5.006386 CAGGGTTTTGATCAGTTTCTAGCT 58.994 41.667 0.00 0.00 0.00 3.32
5962 8401 7.781324 ATTATCACAGGGTTTTGATCAGTTT 57.219 32.000 0.00 0.00 34.28 2.66
6100 8548 9.227777 GGACAACTTACATGTTAGGAGTTTAAT 57.772 33.333 15.77 5.01 0.00 1.40
6220 8674 4.336993 TCTTGACACCAGTTAAACGCAAAT 59.663 37.500 0.00 0.00 0.00 2.32
6375 8833 7.262772 CAGGATACGTAAATCTACAGGACAAA 58.737 38.462 0.00 0.00 46.39 2.83
6461 8919 8.850156 TCTATTGCGAGCAGAATATATAGCATA 58.150 33.333 0.00 0.00 33.21 3.14
7035 9497 2.107552 CCAAACTTTACAGGGAGGACCA 59.892 50.000 0.00 0.00 43.89 4.02
7081 9543 1.421268 ACAAAGCAGGATGACAGGTGA 59.579 47.619 0.00 0.00 39.69 4.02
7082 9544 1.538512 CACAAAGCAGGATGACAGGTG 59.461 52.381 0.00 0.00 39.69 4.00
7136 9598 6.340962 AGATTCATGCAAATATCATGTGGG 57.659 37.500 0.00 0.00 41.40 4.61
7203 9665 7.101652 AGTAGTACCACATAGTGAACAGATG 57.898 40.000 0.00 0.00 35.23 2.90
7299 9761 5.078411 TCTATGCTTCTCCTGTCAAACTC 57.922 43.478 0.00 0.00 0.00 3.01
7363 9825 3.270877 CTTTGTATTGGAACGGAGGGAG 58.729 50.000 0.00 0.00 0.00 4.30
7364 9826 2.640826 ACTTTGTATTGGAACGGAGGGA 59.359 45.455 0.00 0.00 0.00 4.20
7365 9827 3.067684 ACTTTGTATTGGAACGGAGGG 57.932 47.619 0.00 0.00 0.00 4.30
7366 9828 4.069304 TCAACTTTGTATTGGAACGGAGG 58.931 43.478 0.00 0.00 0.00 4.30
7367 9829 4.755123 ACTCAACTTTGTATTGGAACGGAG 59.245 41.667 0.00 0.00 0.00 4.63
7368 9830 4.710324 ACTCAACTTTGTATTGGAACGGA 58.290 39.130 0.00 0.00 0.00 4.69
7369 9831 4.513692 TGACTCAACTTTGTATTGGAACGG 59.486 41.667 0.00 0.00 0.00 4.44
7370 9832 5.666969 TGACTCAACTTTGTATTGGAACG 57.333 39.130 0.00 0.00 0.00 3.95
7371 9833 7.440523 AGATGACTCAACTTTGTATTGGAAC 57.559 36.000 0.00 0.00 0.00 3.62
7372 9834 9.739276 AATAGATGACTCAACTTTGTATTGGAA 57.261 29.630 0.00 0.00 0.00 3.53
7373 9835 9.739276 AAATAGATGACTCAACTTTGTATTGGA 57.261 29.630 0.00 0.00 0.00 3.53
7377 9839 9.739276 TCCAAAATAGATGACTCAACTTTGTAT 57.261 29.630 0.00 0.00 0.00 2.29
7378 9840 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
7379 9841 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
7380 9842 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
7381 9843 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
7382 9844 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
7383 9845 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
7384 9846 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
7385 9847 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
7386 9848 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
7387 9849 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
7388 9850 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
7389 9851 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
7390 9852 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
7391 9853 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
7392 9854 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
7393 9855 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
7394 9856 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
7395 9857 4.355549 TCTACTCCCTCCGTTCCAAAATA 58.644 43.478 0.00 0.00 0.00 1.40
7396 9858 3.178865 TCTACTCCCTCCGTTCCAAAAT 58.821 45.455 0.00 0.00 0.00 1.82
7397 9859 2.612000 TCTACTCCCTCCGTTCCAAAA 58.388 47.619 0.00 0.00 0.00 2.44
7398 9860 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
7399 9861 2.544844 ATCTACTCCCTCCGTTCCAA 57.455 50.000 0.00 0.00 0.00 3.53
7400 9862 3.139584 TGATATCTACTCCCTCCGTTCCA 59.860 47.826 3.98 0.00 0.00 3.53
7401 9863 3.506844 GTGATATCTACTCCCTCCGTTCC 59.493 52.174 3.98 0.00 0.00 3.62
7402 9864 4.400120 AGTGATATCTACTCCCTCCGTTC 58.600 47.826 3.98 0.00 0.00 3.95
7403 9865 4.456662 AGTGATATCTACTCCCTCCGTT 57.543 45.455 3.98 0.00 0.00 4.44
7404 9866 4.145807 CAAGTGATATCTACTCCCTCCGT 58.854 47.826 3.98 0.00 0.00 4.69
7405 9867 3.508012 CCAAGTGATATCTACTCCCTCCG 59.492 52.174 3.98 0.00 0.00 4.63
7406 9868 4.742012 TCCAAGTGATATCTACTCCCTCC 58.258 47.826 3.98 0.00 0.00 4.30
7407 9869 5.598830 TGTTCCAAGTGATATCTACTCCCTC 59.401 44.000 3.98 0.00 0.00 4.30
7408 9870 5.364157 GTGTTCCAAGTGATATCTACTCCCT 59.636 44.000 3.98 0.00 0.00 4.20
7409 9871 5.364157 AGTGTTCCAAGTGATATCTACTCCC 59.636 44.000 3.98 0.00 0.00 4.30
7410 9872 6.472686 AGTGTTCCAAGTGATATCTACTCC 57.527 41.667 3.98 0.00 0.00 3.85
7438 9900 8.954950 TGTGTATTGGAACATCAAAAACATTT 57.045 26.923 0.00 0.00 39.30 2.32
7485 9947 7.999679 TGTGATGGCCAATTATTCTAAGAAAG 58.000 34.615 10.96 0.00 0.00 2.62
7551 10013 2.821546 TCTATGTCTGCGTTGCCATAC 58.178 47.619 0.00 0.00 0.00 2.39
7761 10223 6.264067 CCATCTTTTTCTGTTCCTTCTTGTCT 59.736 38.462 0.00 0.00 0.00 3.41
7805 10267 6.348295 CCCATGATCATTCTTGCTATTCTTCG 60.348 42.308 5.16 0.00 0.00 3.79
7887 10349 0.616111 ACCCATCTCCTTGTCGCTCT 60.616 55.000 0.00 0.00 0.00 4.09
7981 10443 0.474660 AGTGTCCTCTTGGAGCCCTT 60.475 55.000 0.00 0.00 44.16 3.95
7983 10445 1.599576 GAGTGTCCTCTTGGAGCCC 59.400 63.158 0.00 0.00 44.16 5.19
8015 10477 2.171237 TCGGATGCATGAGGATCTGTTT 59.829 45.455 2.46 0.00 45.94 2.83
8115 10577 4.202202 CGGCCTTCTCTAGATGACTTGATT 60.202 45.833 0.00 0.00 0.00 2.57
8251 10713 7.338710 AGAAAAGAAAAGGAAAAAGAAAGGGG 58.661 34.615 0.00 0.00 0.00 4.79
8252 10714 8.792830 AAGAAAAGAAAAGGAAAAAGAAAGGG 57.207 30.769 0.00 0.00 0.00 3.95
8355 10817 0.679505 TATCCATACGCAGGGAGCAC 59.320 55.000 0.00 0.00 46.13 4.40
8363 10825 4.841443 ACGTACAAGATATCCATACGCA 57.159 40.909 21.70 0.00 41.72 5.24
8369 10831 6.718522 TTCACCATACGTACAAGATATCCA 57.281 37.500 0.00 0.00 0.00 3.41
8460 10940 2.732282 GCCTAAGATTGTTCCGCAAAGC 60.732 50.000 0.00 0.00 40.91 3.51
8497 10977 1.731613 CACAATGCTGGTGCGCAAG 60.732 57.895 14.00 8.52 44.06 4.01
8499 10979 2.405061 GAACACAATGCTGGTGCGCA 62.405 55.000 5.66 5.66 45.10 6.09
8500 10980 1.730547 GAACACAATGCTGGTGCGC 60.731 57.895 0.00 0.00 43.34 6.09
8523 11003 2.029918 CACTGCACTACACTCTACAGCA 60.030 50.000 0.00 0.00 0.00 4.41
8575 11055 2.908940 CCCATGATCCGGCCAAGC 60.909 66.667 2.24 0.00 0.00 4.01
8592 11072 1.067582 GACCGATCATCGACACCCC 59.932 63.158 9.16 0.00 43.74 4.95
8675 11202 5.481615 TTATCCCTTCCTGCCCTATTTTT 57.518 39.130 0.00 0.00 0.00 1.94
8782 11312 1.152694 AGCATGTTGGTGCCTGTGT 60.153 52.632 0.00 0.00 46.19 3.72
8783 11313 1.174078 TGAGCATGTTGGTGCCTGTG 61.174 55.000 0.00 0.00 46.19 3.66
8788 11318 2.745728 GCAATGAGCATGTTGGTGC 58.254 52.632 0.00 0.00 44.79 5.01
8805 11335 3.380320 AGGTACGCAATTAATTCCAAGGC 59.620 43.478 0.00 0.00 0.00 4.35
8930 11483 2.761195 GGCGACGAAAAGATGGGGC 61.761 63.158 0.00 0.00 0.00 5.80
8956 11509 0.935898 CACCAGAGATCGATTGCTGC 59.064 55.000 17.97 0.00 0.00 5.25
9035 11588 2.064014 GTGCTTGGAATTTTGCAGAGC 58.936 47.619 10.00 10.00 36.03 4.09
9038 11591 1.000385 TCGGTGCTTGGAATTTTGCAG 60.000 47.619 0.00 0.00 36.03 4.41
9085 11638 2.608268 GTTCTTAGTGTTCTCCTCGGC 58.392 52.381 0.00 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.