Multiple sequence alignment - TraesCS7A01G209600

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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 TraesCS7A01G209600 chr7A 100.000 4897 0 0 933 5829 172243493 172238597 0.000000e+00 9044.0
1 TraesCS7A01G209600 chr7A 100.000 472 0 0 1 472 172244425 172243954 0.000000e+00 872.0
2 TraesCS7A01G209600 chr7B 89.211 2586 151 53 2314 4825 135043425 135040894 0.000000e+00 3112.0
3 TraesCS7A01G209600 chr7B 89.857 838 40 13 945 1752 135045011 135044189 0.000000e+00 1035.0
4 TraesCS7A01G209600 chr7B 92.674 546 19 7 1762 2287 135043966 135043422 0.000000e+00 767.0
5 TraesCS7A01G209600 chr7B 92.500 120 3 4 209 327 135045408 135045294 3.610000e-37 167.0
6 TraesCS7A01G209600 chr7B 93.548 62 1 1 4862 4920 135040882 135040821 8.050000e-14 89.8
7 TraesCS7A01G209600 chr7D 90.847 2054 99 35 2555 4553 169543368 169541349 0.000000e+00 2669.0
8 TraesCS7A01G209600 chr7D 90.898 1593 75 25 945 2485 169545046 169543472 0.000000e+00 2074.0
9 TraesCS7A01G209600 chr7D 86.943 314 28 5 4607 4919 169541352 169541051 2.010000e-89 340.0
10 TraesCS7A01G209600 chr7D 83.030 330 35 14 4 325 169545629 169545313 4.450000e-71 279.0
11 TraesCS7A01G209600 chr7D 93.651 63 3 1 4767 4829 169023704 169023765 6.220000e-15 93.5
12 TraesCS7A01G209600 chr7D 100.000 45 0 0 363 407 169545318 169545274 3.740000e-12 84.2
13 TraesCS7A01G209600 chr3A 95.871 775 31 1 5055 5829 699616583 699615810 0.000000e+00 1253.0
14 TraesCS7A01G209600 chr3A 95.161 124 6 0 4932 5055 699616807 699616684 4.610000e-46 196.0
15 TraesCS7A01G209600 chr3D 93.535 495 29 3 5336 5829 365299685 365299193 0.000000e+00 734.0
16 TraesCS7A01G209600 chr3D 93.388 121 8 0 4935 5055 365325824 365325704 4.640000e-41 180.0
17 TraesCS7A01G209600 chr5A 93.722 446 26 2 5385 5829 205030714 205031158 0.000000e+00 667.0
18 TraesCS7A01G209600 chr5A 92.836 335 23 1 5055 5389 205021715 205022048 8.780000e-133 484.0
19 TraesCS7A01G209600 chr5A 92.623 122 9 0 4934 5055 205021493 205021614 6.000000e-40 176.0
20 TraesCS7A01G209600 chr6A 81.295 278 40 9 2066 2341 523128989 523128722 1.270000e-51 215.0
21 TraesCS7A01G209600 chr6A 76.119 335 68 10 3751 4078 523126748 523126419 1.300000e-36 165.0
22 TraesCS7A01G209600 chr6D 80.935 278 41 9 2066 2341 381555004 381554737 5.920000e-50 209.0
23 TraesCS7A01G209600 chr6D 76.833 341 55 15 3751 4078 381552766 381552437 2.790000e-38 171.0
24 TraesCS7A01G209600 chr6B 86.082 194 27 0 2066 2259 570155858 570155665 5.920000e-50 209.0
25 TraesCS7A01G209600 chr6B 75.821 335 69 10 3751 4078 570153819 570153490 6.050000e-35 159.0
26 TraesCS7A01G209600 chr5B 95.935 123 5 0 4933 5055 15267809 15267931 3.560000e-47 200.0
27 TraesCS7A01G209600 chr5B 100.000 28 0 0 5055 5082 15268032 15268059 1.100000e-02 52.8


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 TraesCS7A01G209600 chr7A 172238597 172244425 5828 True 4958.00 9044 100.0000 1 5829 2 chr7A.!!$R1 5828
1 TraesCS7A01G209600 chr7B 135040821 135045408 4587 True 1034.16 3112 91.5580 209 4920 5 chr7B.!!$R1 4711
2 TraesCS7A01G209600 chr7D 169541051 169545629 4578 True 1089.24 2669 90.3436 4 4919 5 chr7D.!!$R1 4915
3 TraesCS7A01G209600 chr3A 699615810 699616807 997 True 724.50 1253 95.5160 4932 5829 2 chr3A.!!$R1 897
4 TraesCS7A01G209600 chr5A 205021493 205022048 555 False 330.00 484 92.7295 4934 5389 2 chr5A.!!$F2 455

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
458 483 0.033991 TTCCACTCTCTCTCCCTCGG 60.034 60.0 0.00 0.00 0.00 4.63 F
1173 1216 0.383949 TTGGTTTTCTTGCGGCTGAC 59.616 50.0 0.00 0.00 0.00 3.51 F
1563 1613 0.536006 GTGAGCATGCCCCCATACTC 60.536 60.0 15.66 2.97 40.69 2.59 F
3385 3760 0.539438 CTGGCAGCAAGGGTTGGTAA 60.539 55.0 0.00 0.00 39.79 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2294 2602 0.327480 ACATGGGATGCTAGGGACCA 60.327 55.0 0.0 0.0 35.39 4.02 R
2295 2603 0.846693 AACATGGGATGCTAGGGACC 59.153 55.0 0.0 0.0 0.00 4.46 R
3440 3824 0.034896 ACCCAAGGCTGACTGTAACG 59.965 55.0 0.0 0.0 0.00 3.18 R
4830 5270 0.038744 CCAAGACCAGTCAAGCCCAT 59.961 55.0 0.0 0.0 0.00 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.340697 GGGAGCCCAACCTTACGAATT 60.341 52.381 0.00 0.00 35.81 2.17
35 36 2.490509 CCCAACCTTACGAATTGAACCC 59.509 50.000 0.00 0.00 0.00 4.11
42 43 1.296056 ACGAATTGAACCCGAAGCCG 61.296 55.000 0.00 0.00 0.00 5.52
62 64 0.958822 GCACCGGAACCAACTCAAAT 59.041 50.000 9.46 0.00 0.00 2.32
66 68 4.578928 GCACCGGAACCAACTCAAATATAT 59.421 41.667 9.46 0.00 0.00 0.86
67 69 5.067283 GCACCGGAACCAACTCAAATATATT 59.933 40.000 9.46 0.00 0.00 1.28
161 173 8.579850 AAATGTGCACTATCTCTTTATTTGGA 57.420 30.769 19.41 0.00 0.00 3.53
162 174 8.757982 AATGTGCACTATCTCTTTATTTGGAT 57.242 30.769 19.41 0.00 0.00 3.41
163 175 8.757982 ATGTGCACTATCTCTTTATTTGGATT 57.242 30.769 19.41 0.00 0.00 3.01
164 176 7.988737 TGTGCACTATCTCTTTATTTGGATTG 58.011 34.615 19.41 0.00 0.00 2.67
213 226 3.747976 GCCCGACCCAACACATGC 61.748 66.667 0.00 0.00 0.00 4.06
223 236 0.322816 CAACACATGCCCAGGCTAGT 60.323 55.000 10.58 5.52 42.51 2.57
231 244 4.153957 CCAGGCTAGTCCAGGGTT 57.846 61.111 6.71 0.00 37.83 4.11
232 245 1.604378 CCAGGCTAGTCCAGGGTTG 59.396 63.158 6.71 0.00 37.83 3.77
305 319 3.181491 CCAAAAGAAAGGCAACAAGACGA 60.181 43.478 0.00 0.00 41.41 4.20
324 338 4.175599 CGAGCAGCAGTGTACCAG 57.824 61.111 0.00 0.00 0.00 4.00
325 339 2.097038 CGAGCAGCAGTGTACCAGC 61.097 63.158 0.00 0.00 0.00 4.85
326 340 1.004560 GAGCAGCAGTGTACCAGCA 60.005 57.895 0.00 0.00 0.00 4.41
327 341 0.392193 GAGCAGCAGTGTACCAGCAT 60.392 55.000 0.00 0.00 0.00 3.79
328 342 0.037303 AGCAGCAGTGTACCAGCATT 59.963 50.000 0.00 0.00 0.00 3.56
329 343 0.169672 GCAGCAGTGTACCAGCATTG 59.830 55.000 4.45 0.00 0.00 2.82
330 344 1.527034 CAGCAGTGTACCAGCATTGT 58.473 50.000 4.45 0.00 0.00 2.71
331 345 1.466167 CAGCAGTGTACCAGCATTGTC 59.534 52.381 4.45 0.00 0.00 3.18
332 346 1.349026 AGCAGTGTACCAGCATTGTCT 59.651 47.619 4.45 0.00 0.00 3.41
333 347 1.734465 GCAGTGTACCAGCATTGTCTC 59.266 52.381 0.00 0.00 0.00 3.36
334 348 2.871637 GCAGTGTACCAGCATTGTCTCA 60.872 50.000 0.00 0.00 0.00 3.27
335 349 3.402110 CAGTGTACCAGCATTGTCTCAA 58.598 45.455 0.00 0.00 0.00 3.02
336 350 3.814842 CAGTGTACCAGCATTGTCTCAAA 59.185 43.478 0.00 0.00 0.00 2.69
337 351 4.275689 CAGTGTACCAGCATTGTCTCAAAA 59.724 41.667 0.00 0.00 0.00 2.44
338 352 4.887071 AGTGTACCAGCATTGTCTCAAAAA 59.113 37.500 0.00 0.00 0.00 1.94
408 422 3.314331 CGAGCTCCACCACCACCT 61.314 66.667 8.47 0.00 0.00 4.00
409 423 2.665603 GAGCTCCACCACCACCTC 59.334 66.667 0.87 0.00 0.00 3.85
410 424 2.930562 AGCTCCACCACCACCTCC 60.931 66.667 0.00 0.00 0.00 4.30
411 425 3.249189 GCTCCACCACCACCTCCA 61.249 66.667 0.00 0.00 0.00 3.86
412 426 2.750350 CTCCACCACCACCTCCAC 59.250 66.667 0.00 0.00 0.00 4.02
413 427 2.852075 TCCACCACCACCTCCACC 60.852 66.667 0.00 0.00 0.00 4.61
422 436 2.367648 ACCTCCACCACCACCACA 60.368 61.111 0.00 0.00 0.00 4.17
450 464 3.192633 GTCTCTTCCACTTCCACTCTCTC 59.807 52.174 0.00 0.00 0.00 3.20
457 482 1.340600 ACTTCCACTCTCTCTCCCTCG 60.341 57.143 0.00 0.00 0.00 4.63
458 483 0.033991 TTCCACTCTCTCTCCCTCGG 60.034 60.000 0.00 0.00 0.00 4.63
949 974 2.774351 CACCTCCCCCATCTCCCC 60.774 72.222 0.00 0.00 0.00 4.81
950 975 2.967014 ACCTCCCCCATCTCCCCT 60.967 66.667 0.00 0.00 0.00 4.79
951 976 2.449322 CCTCCCCCATCTCCCCTG 60.449 72.222 0.00 0.00 0.00 4.45
953 978 4.843331 TCCCCCATCTCCCCTGCC 62.843 72.222 0.00 0.00 0.00 4.85
955 980 3.496160 CCCCATCTCCCCTGCCAG 61.496 72.222 0.00 0.00 0.00 4.85
957 982 3.095163 CCATCTCCCCTGCCAGCT 61.095 66.667 0.00 0.00 0.00 4.24
958 983 2.509916 CATCTCCCCTGCCAGCTC 59.490 66.667 0.00 0.00 0.00 4.09
959 984 2.071262 CATCTCCCCTGCCAGCTCT 61.071 63.158 0.00 0.00 0.00 4.09
960 985 2.071262 ATCTCCCCTGCCAGCTCTG 61.071 63.158 0.00 0.00 0.00 3.35
961 986 4.486503 CTCCCCTGCCAGCTCTGC 62.487 72.222 0.00 0.00 0.00 4.26
998 1030 3.749064 TCCACGAGAGGAGCACGC 61.749 66.667 0.00 0.00 33.70 5.34
1005 1048 2.583593 GAGGAGCACGCGATGGAC 60.584 66.667 15.93 0.00 0.00 4.02
1173 1216 0.383949 TTGGTTTTCTTGCGGCTGAC 59.616 50.000 0.00 0.00 0.00 3.51
1187 1230 2.359850 TGACTGATTGGTGCCCGC 60.360 61.111 0.00 0.00 0.00 6.13
1339 1382 7.967178 TCGGTTTCTTATAAACGGAATCTTTC 58.033 34.615 8.00 0.00 38.69 2.62
1533 1583 3.376935 CTACAGGGTCCAGCTGCCG 62.377 68.421 8.66 3.93 0.00 5.69
1563 1613 0.536006 GTGAGCATGCCCCCATACTC 60.536 60.000 15.66 2.97 40.69 2.59
1577 1627 3.012518 CCATACTCCCAACTGCTTCTTG 58.987 50.000 0.00 0.00 0.00 3.02
1582 1632 2.746362 CTCCCAACTGCTTCTTGATGTC 59.254 50.000 0.00 0.00 0.00 3.06
1584 1634 2.553904 CCCAACTGCTTCTTGATGTCCT 60.554 50.000 0.00 0.00 0.00 3.85
1601 1651 3.513515 TGTCCTTTTTCAGGTTTTGCTGT 59.486 39.130 0.00 0.00 44.37 4.40
1602 1652 4.112634 GTCCTTTTTCAGGTTTTGCTGTC 58.887 43.478 0.00 0.00 44.37 3.51
1635 1692 3.519107 TGCTCAGTCATCATGGGTTTCTA 59.481 43.478 0.00 0.00 0.00 2.10
1645 1702 9.561069 GTCATCATGGGTTTCTACTAAATATGT 57.439 33.333 0.00 0.00 0.00 2.29
1738 1813 3.507233 GGTCAGGCATGTTTCTTGATTGA 59.493 43.478 0.00 0.00 0.00 2.57
1835 2123 3.315470 GGTCACTTTCACTTCCCTTGTTC 59.685 47.826 0.00 0.00 0.00 3.18
1854 2142 3.793797 TCAGAAGTTGAAGACACACGA 57.206 42.857 0.00 0.00 31.34 4.35
1949 2237 4.571176 CCATGTCTGATGTGAAGATCTGTG 59.429 45.833 0.00 0.00 0.00 3.66
1991 2298 4.923871 TCTGTTCTAAAGTGATGAAGTCGC 59.076 41.667 0.00 0.00 37.62 5.19
2023 2330 6.932400 TCTCTATAGTAGCTACTGTTCAGCTC 59.068 42.308 32.21 0.00 46.37 4.09
2129 2437 4.763793 GGATTATCTGGTCATGTTGATGGG 59.236 45.833 0.00 0.00 0.00 4.00
2306 2614 5.904984 TTGTAATGTATGGTCCCTAGCAT 57.095 39.130 0.00 0.00 45.54 3.79
2328 2636 5.096443 TCCCATGTTTGCTCTTTGTTTTT 57.904 34.783 0.00 0.00 0.00 1.94
2342 2650 6.866480 TCTTTGTTTTTGATTGAGCTTCTGT 58.134 32.000 0.00 0.00 0.00 3.41
2565 2875 2.496070 TGTGGGAGAAATCAGTAGTCCG 59.504 50.000 0.00 0.00 0.00 4.79
2569 2879 3.385111 GGGAGAAATCAGTAGTCCGTGAT 59.615 47.826 0.00 0.00 34.79 3.06
2579 2922 7.576861 TCAGTAGTCCGTGATACATAATTGA 57.423 36.000 0.00 0.00 0.00 2.57
2611 2954 7.166307 CAGATTGTATGTGTTTTGAGTGTGTTG 59.834 37.037 0.00 0.00 0.00 3.33
2620 2963 7.867909 TGTGTTTTGAGTGTGTTGAATTAAACA 59.132 29.630 4.09 4.09 37.71 2.83
2630 2973 8.931775 GTGTGTTGAATTAAACAAAGGAGTTTT 58.068 29.630 10.07 0.00 41.52 2.43
2720 3063 3.614870 GCCCAGCCATTTTAACTTCACAG 60.615 47.826 0.00 0.00 0.00 3.66
2724 3067 5.691754 CCAGCCATTTTAACTTCACAGTTTC 59.308 40.000 0.00 0.00 40.66 2.78
2808 3155 2.833244 TTTTTGTGGGGCTTCAGGG 58.167 52.632 0.00 0.00 0.00 4.45
2830 3177 7.443575 CAGGGAACATCTAGAATAAATGTCCTG 59.556 40.741 12.95 12.95 38.23 3.86
2831 3178 7.348274 AGGGAACATCTAGAATAAATGTCCTGA 59.652 37.037 0.00 0.00 32.63 3.86
2832 3179 7.993183 GGGAACATCTAGAATAAATGTCCTGAA 59.007 37.037 0.00 0.00 32.63 3.02
2836 3183 7.923344 ACATCTAGAATAAATGTCCTGAACTCG 59.077 37.037 0.00 0.00 0.00 4.18
2866 3213 8.999431 TGAATTTGTAAGTGGTAATGAAGAGAC 58.001 33.333 0.00 0.00 0.00 3.36
2935 3282 2.659428 GGGAAATCAATGAGAGGTGGG 58.341 52.381 0.00 0.00 0.00 4.61
3112 3484 4.654724 GCTGGTTTCCCTCTAGGTACTATT 59.345 45.833 0.00 0.00 41.70 1.73
3119 3491 5.206587 TCCCTCTAGGTACTATTTCACCAC 58.793 45.833 0.00 0.00 41.70 4.16
3120 3492 4.960469 CCCTCTAGGTACTATTTCACCACA 59.040 45.833 0.00 0.00 41.70 4.17
3123 3495 6.039941 CCTCTAGGTACTATTTCACCACAGAG 59.960 46.154 12.17 12.17 41.70 3.35
3128 3500 6.153000 AGGTACTATTTCACCACAGAGTACTG 59.847 42.308 0.00 0.00 43.74 2.74
3147 3519 4.319177 ACTGTTCTTGTCTGAAGCCATAC 58.681 43.478 0.00 0.00 0.00 2.39
3324 3699 2.228822 AGCAACAGAGGTAATTTTGCCG 59.771 45.455 5.39 0.00 42.91 5.69
3382 3757 3.688159 GCTGGCAGCAAGGGTTGG 61.688 66.667 33.33 0.00 41.89 3.77
3383 3758 2.203538 CTGGCAGCAAGGGTTGGT 60.204 61.111 0.00 0.00 43.12 3.67
3384 3759 1.074775 CTGGCAGCAAGGGTTGGTA 59.925 57.895 0.00 0.00 39.79 3.25
3385 3760 0.539438 CTGGCAGCAAGGGTTGGTAA 60.539 55.000 0.00 0.00 39.79 2.85
3403 3778 0.551396 AATGGTAACTAGGGCAGGGC 59.449 55.000 0.00 0.00 37.61 5.19
3427 3802 6.516718 CCTATACTGGACCATGTTTCTACAG 58.483 44.000 0.00 0.00 37.77 2.74
3428 3803 3.703001 ACTGGACCATGTTTCTACAGG 57.297 47.619 0.00 0.00 37.77 4.00
3440 3824 7.225538 CCATGTTTCTACAGGTCTCATGAATAC 59.774 40.741 0.00 0.00 37.77 1.89
3456 3840 4.242475 TGAATACGTTACAGTCAGCCTTG 58.758 43.478 0.00 0.00 0.00 3.61
3473 3857 0.036765 TTGGGTCACGTAGATGTGGC 60.037 55.000 2.15 0.00 43.66 5.01
3505 3890 0.395586 TTTGCCACAGCCTGTTCACT 60.396 50.000 0.00 0.00 38.69 3.41
3540 3925 9.461312 AGTGGTGCTATGAATTCACTTTATTAA 57.539 29.630 11.07 0.00 32.34 1.40
3606 3991 4.129380 CGGAGTCCATGCATATTCTTCAA 58.871 43.478 10.49 0.00 0.00 2.69
3615 4000 9.679661 TCCATGCATATTCTTCAAAACTACTTA 57.320 29.630 0.00 0.00 0.00 2.24
3682 4067 1.293062 ACCATGCAGGAACCTCAGAT 58.707 50.000 0.00 0.00 41.22 2.90
3695 4080 0.907486 CTCAGATGCCTCCAAGACCA 59.093 55.000 0.00 0.00 0.00 4.02
3792 4177 3.119291 CTGATCCCGAATGAAGACGAAG 58.881 50.000 0.00 0.00 0.00 3.79
3793 4178 1.861575 GATCCCGAATGAAGACGAAGC 59.138 52.381 0.00 0.00 0.00 3.86
3794 4179 0.895530 TCCCGAATGAAGACGAAGCT 59.104 50.000 0.00 0.00 0.00 3.74
3795 4180 1.002366 CCCGAATGAAGACGAAGCTG 58.998 55.000 0.00 0.00 0.00 4.24
3796 4181 1.002366 CCGAATGAAGACGAAGCTGG 58.998 55.000 0.00 0.00 0.00 4.85
3797 4182 1.002366 CGAATGAAGACGAAGCTGGG 58.998 55.000 0.00 0.00 0.00 4.45
3798 4183 1.404181 CGAATGAAGACGAAGCTGGGA 60.404 52.381 0.00 0.00 0.00 4.37
3799 4184 2.699954 GAATGAAGACGAAGCTGGGAA 58.300 47.619 0.00 0.00 0.00 3.97
3800 4185 2.859165 ATGAAGACGAAGCTGGGAAA 57.141 45.000 0.00 0.00 0.00 3.13
3801 4186 1.878953 TGAAGACGAAGCTGGGAAAC 58.121 50.000 0.00 0.00 0.00 2.78
3802 4187 1.140052 TGAAGACGAAGCTGGGAAACA 59.860 47.619 0.00 0.00 0.00 2.83
3803 4188 2.224523 TGAAGACGAAGCTGGGAAACAT 60.225 45.455 0.00 0.00 0.00 2.71
3804 4189 1.813513 AGACGAAGCTGGGAAACATG 58.186 50.000 0.00 0.00 0.00 3.21
3805 4190 1.347707 AGACGAAGCTGGGAAACATGA 59.652 47.619 0.00 0.00 0.00 3.07
3806 4191 2.151202 GACGAAGCTGGGAAACATGAA 58.849 47.619 0.00 0.00 0.00 2.57
3896 4296 4.752879 TCCCGAAAGAAGCGCCCG 62.753 66.667 2.29 0.00 0.00 6.13
3917 4317 0.520404 CAAGACAGCACCATCAGCAC 59.480 55.000 0.00 0.00 0.00 4.40
3927 4327 2.360852 ATCAGCACCACCAGCAGC 60.361 61.111 0.00 0.00 0.00 5.25
3928 4328 3.933048 ATCAGCACCACCAGCAGCC 62.933 63.158 0.00 0.00 0.00 4.85
3932 4332 2.113774 CACCACCAGCAGCCAAGA 59.886 61.111 0.00 0.00 0.00 3.02
3934 4334 2.360852 CCACCAGCAGCCAAGAGG 60.361 66.667 0.00 0.00 38.23 3.69
3940 4340 1.920325 AGCAGCCAAGAGGTAGCCA 60.920 57.895 0.00 0.00 37.47 4.75
3980 4380 4.899239 GCCATCCCGCACGAGGAG 62.899 72.222 0.00 0.00 36.67 3.69
4030 4430 1.558233 ACCCCTCAGAAGAACTACGG 58.442 55.000 0.00 0.00 0.00 4.02
4148 4557 1.136961 TGTATCCCCACCACCAGCAA 61.137 55.000 0.00 0.00 0.00 3.91
4156 4565 2.908428 CCACCAGCAACAGCAGCA 60.908 61.111 0.00 0.00 0.00 4.41
4199 4614 3.121030 GTGTACCGGCAGCAGCAG 61.121 66.667 0.00 0.00 44.61 4.24
4202 4617 4.765449 TACCGGCAGCAGCAGCAG 62.765 66.667 12.41 7.58 45.49 4.24
4245 4660 3.121030 CGTACCACCTGCAGCAGC 61.121 66.667 17.81 0.93 42.57 5.25
4530 4949 1.210478 CTGACGATCCACCCTTCCATT 59.790 52.381 0.00 0.00 0.00 3.16
4537 4957 4.036734 CGATCCACCCTTCCATTTACATTG 59.963 45.833 0.00 0.00 0.00 2.82
4543 4963 5.016831 ACCCTTCCATTTACATTGTCCTTC 58.983 41.667 0.00 0.00 0.00 3.46
4553 4973 8.717821 CATTTACATTGTCCTTCTTCGTTTCTA 58.282 33.333 0.00 0.00 0.00 2.10
4568 4988 6.072112 TCGTTTCTATTGCTCTTTTGCTTT 57.928 33.333 0.00 0.00 0.00 3.51
4571 4991 7.043458 TCGTTTCTATTGCTCTTTTGCTTTTTG 60.043 33.333 0.00 0.00 0.00 2.44
4572 4992 7.254084 CGTTTCTATTGCTCTTTTGCTTTTTGT 60.254 33.333 0.00 0.00 0.00 2.83
4573 4993 7.698836 TTCTATTGCTCTTTTGCTTTTTGTC 57.301 32.000 0.00 0.00 0.00 3.18
4574 4994 6.804677 TCTATTGCTCTTTTGCTTTTTGTCA 58.195 32.000 0.00 0.00 0.00 3.58
4575 4995 5.978934 ATTGCTCTTTTGCTTTTTGTCAG 57.021 34.783 0.00 0.00 0.00 3.51
4576 4996 4.454728 TGCTCTTTTGCTTTTTGTCAGT 57.545 36.364 0.00 0.00 0.00 3.41
4577 4997 5.574891 TGCTCTTTTGCTTTTTGTCAGTA 57.425 34.783 0.00 0.00 0.00 2.74
4578 4998 5.581605 TGCTCTTTTGCTTTTTGTCAGTAG 58.418 37.500 0.00 0.00 0.00 2.57
4579 4999 5.125417 TGCTCTTTTGCTTTTTGTCAGTAGT 59.875 36.000 0.00 0.00 0.00 2.73
4580 5000 6.317642 TGCTCTTTTGCTTTTTGTCAGTAGTA 59.682 34.615 0.00 0.00 0.00 1.82
4581 5001 6.633234 GCTCTTTTGCTTTTTGTCAGTAGTAC 59.367 38.462 0.00 0.00 0.00 2.73
4582 5002 7.618502 TCTTTTGCTTTTTGTCAGTAGTACA 57.381 32.000 2.52 0.00 0.00 2.90
4583 5003 8.220755 TCTTTTGCTTTTTGTCAGTAGTACAT 57.779 30.769 2.52 0.00 0.00 2.29
4584 5004 8.128582 TCTTTTGCTTTTTGTCAGTAGTACATG 58.871 33.333 2.52 0.00 0.00 3.21
4585 5005 5.940192 TGCTTTTTGTCAGTAGTACATGG 57.060 39.130 2.52 0.00 0.00 3.66
4586 5006 5.373222 TGCTTTTTGTCAGTAGTACATGGT 58.627 37.500 2.52 0.00 0.00 3.55
4587 5007 5.468746 TGCTTTTTGTCAGTAGTACATGGTC 59.531 40.000 2.52 0.00 0.00 4.02
4588 5008 5.389516 GCTTTTTGTCAGTAGTACATGGTCG 60.390 44.000 2.52 0.00 0.00 4.79
4589 5009 3.861276 TTGTCAGTAGTACATGGTCGG 57.139 47.619 2.52 0.00 0.00 4.79
4590 5010 2.799017 TGTCAGTAGTACATGGTCGGT 58.201 47.619 2.52 0.00 0.00 4.69
4613 5033 8.350238 GGTTAGATTTACCGCTAGTTCTTAAG 57.650 38.462 0.00 0.00 0.00 1.85
4623 5043 4.082136 CGCTAGTTCTTAAGTCCCTTGTCT 60.082 45.833 1.63 0.00 0.00 3.41
4626 5046 6.295405 GCTAGTTCTTAAGTCCCTTGTCTTCT 60.295 42.308 1.63 0.00 0.00 2.85
4628 5048 6.292150 AGTTCTTAAGTCCCTTGTCTTCTTG 58.708 40.000 1.63 0.00 0.00 3.02
4636 5056 2.417719 CCTTGTCTTCTTGGTTCCTCG 58.582 52.381 0.00 0.00 0.00 4.63
4639 5059 1.618837 TGTCTTCTTGGTTCCTCGAGG 59.381 52.381 26.32 26.32 0.00 4.63
4655 5075 2.771943 TCGAGGGCTCAAGGAATGTAAT 59.228 45.455 0.00 0.00 0.00 1.89
4657 5077 2.620585 GAGGGCTCAAGGAATGTAATGC 59.379 50.000 0.00 0.00 0.00 3.56
4658 5078 2.025037 AGGGCTCAAGGAATGTAATGCA 60.025 45.455 0.00 0.00 0.00 3.96
4660 5080 3.429410 GGGCTCAAGGAATGTAATGCAAC 60.429 47.826 0.00 0.00 0.00 4.17
4661 5081 3.429085 GCTCAAGGAATGTAATGCAACG 58.571 45.455 0.00 0.00 0.00 4.10
4662 5082 3.731867 GCTCAAGGAATGTAATGCAACGG 60.732 47.826 0.00 0.00 0.00 4.44
4663 5083 2.752354 TCAAGGAATGTAATGCAACGGG 59.248 45.455 0.00 0.00 0.00 5.28
4664 5084 2.752354 CAAGGAATGTAATGCAACGGGA 59.248 45.455 0.00 0.00 0.00 5.14
4665 5085 2.643551 AGGAATGTAATGCAACGGGAG 58.356 47.619 0.00 0.00 0.00 4.30
4685 5105 6.486056 GGGAGGAAAAGAGGAAGTAGAAATT 58.514 40.000 0.00 0.00 0.00 1.82
4702 5138 4.946157 AGAAATTGGTAGTCTCATGCCTTG 59.054 41.667 0.00 0.00 0.00 3.61
4703 5139 2.113860 TTGGTAGTCTCATGCCTTGC 57.886 50.000 0.00 0.00 0.00 4.01
4704 5140 1.279496 TGGTAGTCTCATGCCTTGCT 58.721 50.000 0.00 0.00 0.00 3.91
4705 5141 1.630369 TGGTAGTCTCATGCCTTGCTT 59.370 47.619 0.00 0.00 0.00 3.91
4720 5156 3.429822 CCTTGCTTAGATTGTGCAATGGG 60.430 47.826 1.77 0.00 44.20 4.00
4722 5158 3.429492 TGCTTAGATTGTGCAATGGGAA 58.571 40.909 1.77 0.00 33.48 3.97
4739 5175 2.536066 GGAAAGCTGGGGTTTTGGTAT 58.464 47.619 0.00 0.00 33.25 2.73
4745 5181 3.158676 GCTGGGGTTTTGGTATTGTACA 58.841 45.455 0.00 0.00 0.00 2.90
4756 5192 7.389803 TTTGGTATTGTACACTGATGAATGG 57.610 36.000 0.00 0.00 0.00 3.16
4813 5250 1.712401 CACTCAAGTCTCAGCTGCTC 58.288 55.000 9.47 1.54 0.00 4.26
4829 5269 3.027412 CTGCTCTGGTGAGTAGTATGGT 58.973 50.000 3.55 0.00 44.51 3.55
4830 5270 4.207955 CTGCTCTGGTGAGTAGTATGGTA 58.792 47.826 3.55 0.00 44.51 3.25
4835 5275 2.969950 TGGTGAGTAGTATGGTATGGGC 59.030 50.000 0.00 0.00 0.00 5.36
4836 5276 3.240302 GGTGAGTAGTATGGTATGGGCT 58.760 50.000 0.00 0.00 0.00 5.19
4837 5277 3.646637 GGTGAGTAGTATGGTATGGGCTT 59.353 47.826 0.00 0.00 0.00 4.35
4838 5278 4.503296 GGTGAGTAGTATGGTATGGGCTTG 60.503 50.000 0.00 0.00 0.00 4.01
4839 5279 4.344102 GTGAGTAGTATGGTATGGGCTTGA 59.656 45.833 0.00 0.00 0.00 3.02
4849 5289 0.038744 ATGGGCTTGACTGGTCTTGG 59.961 55.000 2.38 0.00 0.00 3.61
4920 5363 3.999663 CCACTTGACTCCATTCTGACTTC 59.000 47.826 0.00 0.00 0.00 3.01
4921 5364 3.999663 CACTTGACTCCATTCTGACTTCC 59.000 47.826 0.00 0.00 0.00 3.46
4922 5365 3.008485 ACTTGACTCCATTCTGACTTCCC 59.992 47.826 0.00 0.00 0.00 3.97
4923 5366 2.907892 TGACTCCATTCTGACTTCCCT 58.092 47.619 0.00 0.00 0.00 4.20
4924 5367 4.061131 TGACTCCATTCTGACTTCCCTA 57.939 45.455 0.00 0.00 0.00 3.53
4925 5368 4.425772 TGACTCCATTCTGACTTCCCTAA 58.574 43.478 0.00 0.00 0.00 2.69
4926 5369 4.844085 TGACTCCATTCTGACTTCCCTAAA 59.156 41.667 0.00 0.00 0.00 1.85
4927 5370 5.309543 TGACTCCATTCTGACTTCCCTAAAA 59.690 40.000 0.00 0.00 0.00 1.52
4928 5371 6.183361 TGACTCCATTCTGACTTCCCTAAAAA 60.183 38.462 0.00 0.00 0.00 1.94
4951 5394 8.753497 AAAAAGACTGTCCAACTAGAAGAAAT 57.247 30.769 3.76 0.00 0.00 2.17
4987 5430 7.636150 AATTGAAATTAGCTAGCACATGAGT 57.364 32.000 18.83 0.00 0.00 3.41
5019 5462 3.245284 ACACGAGCGATAACAATGCATAC 59.755 43.478 0.00 0.00 0.00 2.39
5205 5749 0.467384 ATGTTGCTCCTGATCCCTCG 59.533 55.000 0.00 0.00 0.00 4.63
5221 5765 2.612972 CCCTCGTCAGCAAAGAAAGCTA 60.613 50.000 0.00 0.00 41.14 3.32
5240 5784 9.362539 GAAAGCTACATCAACATTCAATTTCAT 57.637 29.630 0.00 0.00 0.00 2.57
5275 5819 2.158430 GGTTTAACCCACCTCCTTTCCA 60.158 50.000 2.04 0.00 30.04 3.53
5299 5843 7.713507 CCATGTCTCCACTCGGTTTATAATTAA 59.286 37.037 0.00 0.00 0.00 1.40
5307 5851 7.767198 CCACTCGGTTTATAATTAACTTCCTGA 59.233 37.037 0.00 0.00 0.00 3.86
5344 5888 2.954318 GCCAAGACTGACATATGCCATT 59.046 45.455 1.58 0.00 0.00 3.16
5369 5913 0.257905 GGGGGTGAAGGGTTACCATC 59.742 60.000 2.98 1.39 38.74 3.51
5396 5940 1.990563 GTGTTGACGTCTAATCCACCG 59.009 52.381 17.92 0.00 0.00 4.94
5420 5964 0.616111 AACCAACAGCCCACCACAAA 60.616 50.000 0.00 0.00 0.00 2.83
5496 6040 2.983433 GAGGTGCTCCATGATCACG 58.017 57.895 7.70 0.00 30.53 4.35
5502 6046 1.971505 GCTCCATGATCACGGACCCA 61.972 60.000 6.38 0.00 0.00 4.51
5531 6075 5.456921 TCTATTTCCTTTGCCTCTTCCAT 57.543 39.130 0.00 0.00 0.00 3.41
5552 6096 1.134907 CAAATCTGCAATGCCCAGGTC 60.135 52.381 1.53 0.00 0.00 3.85
5557 6101 2.048603 GCAATGCCCAGGTCACTCC 61.049 63.158 0.00 0.00 0.00 3.85
5596 6140 5.239306 TGATCACAATCAAACAAGAGGTGTC 59.761 40.000 0.00 0.00 38.97 3.67
5661 6205 5.428253 TCTGAACCAATGTGCCTATTAGTC 58.572 41.667 0.00 0.00 0.00 2.59
5688 6232 4.764050 TGACTTTAGCGGGATAATTCCA 57.236 40.909 0.00 0.00 44.60 3.53
5772 6316 9.783256 GTACTCCATATTTTTGGTGTATTTGAC 57.217 33.333 8.21 0.00 43.68 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.490509 GGGTTCAATTCGTAAGGTTGGG 59.509 50.000 0.00 0.00 35.20 4.12
18 19 3.332034 CTTCGGGTTCAATTCGTAAGGT 58.668 45.455 0.00 0.00 38.47 3.50
22 23 1.729284 GGCTTCGGGTTCAATTCGTA 58.271 50.000 0.00 0.00 0.00 3.43
24 25 1.423845 CGGCTTCGGGTTCAATTCG 59.576 57.895 0.00 0.00 0.00 3.34
42 43 1.104577 TTTGAGTTGGTTCCGGTGCC 61.105 55.000 0.00 5.66 0.00 5.01
43 44 0.958822 ATTTGAGTTGGTTCCGGTGC 59.041 50.000 0.00 0.00 0.00 5.01
47 49 8.458843 AGAAACAATATATTTGAGTTGGTTCCG 58.541 33.333 10.17 0.00 44.99 4.30
134 146 9.643693 CCAAATAAAGAGATAGTGCACATTTTT 57.356 29.630 21.04 11.41 0.00 1.94
139 151 7.067372 CCAATCCAAATAAAGAGATAGTGCACA 59.933 37.037 21.04 5.47 0.00 4.57
149 161 2.362077 CCGGCCCAATCCAAATAAAGAG 59.638 50.000 0.00 0.00 0.00 2.85
230 243 1.114722 CCAAGCTCAAACAGGCCCAA 61.115 55.000 0.00 0.00 0.00 4.12
231 244 1.531365 CCAAGCTCAAACAGGCCCA 60.531 57.895 0.00 0.00 0.00 5.36
232 245 0.613012 ATCCAAGCTCAAACAGGCCC 60.613 55.000 0.00 0.00 0.00 5.80
305 319 2.262915 GGTACACTGCTGCTCGCT 59.737 61.111 0.00 0.00 40.11 4.93
343 357 4.890581 TGGTATTGCTGGTACACTGTTTTT 59.109 37.500 0.00 0.00 0.00 1.94
344 358 4.465886 TGGTATTGCTGGTACACTGTTTT 58.534 39.130 0.00 0.00 0.00 2.43
345 359 4.072131 CTGGTATTGCTGGTACACTGTTT 58.928 43.478 0.00 0.00 0.00 2.83
346 360 3.326588 TCTGGTATTGCTGGTACACTGTT 59.673 43.478 0.00 0.00 0.00 3.16
347 361 2.903784 TCTGGTATTGCTGGTACACTGT 59.096 45.455 0.00 0.00 0.00 3.55
348 362 3.525537 CTCTGGTATTGCTGGTACACTG 58.474 50.000 0.00 0.00 0.00 3.66
349 363 2.501723 CCTCTGGTATTGCTGGTACACT 59.498 50.000 0.00 0.00 0.00 3.55
350 364 2.906354 CCTCTGGTATTGCTGGTACAC 58.094 52.381 0.00 0.00 0.00 2.90
351 365 1.209504 GCCTCTGGTATTGCTGGTACA 59.790 52.381 0.00 0.00 0.00 2.90
408 422 1.567208 AACAGTGTGGTGGTGGTGGA 61.567 55.000 0.00 0.00 0.00 4.02
409 423 1.077068 AACAGTGTGGTGGTGGTGG 60.077 57.895 0.00 0.00 0.00 4.61
410 424 0.679640 ACAACAGTGTGGTGGTGGTG 60.680 55.000 1.37 0.00 39.97 4.17
411 425 0.393808 GACAACAGTGTGGTGGTGGT 60.394 55.000 8.39 0.00 39.97 4.16
412 426 0.107214 AGACAACAGTGTGGTGGTGG 60.107 55.000 8.39 0.00 39.97 4.61
413 427 1.134401 AGAGACAACAGTGTGGTGGTG 60.134 52.381 8.39 0.00 39.97 4.17
422 436 2.771943 TGGAAGTGGAAGAGACAACAGT 59.228 45.455 0.00 0.00 0.00 3.55
450 464 1.152567 AGATCAGAGGCCGAGGGAG 60.153 63.158 0.00 0.00 0.00 4.30
932 957 2.774351 GGGGAGATGGGGGAGGTG 60.774 72.222 0.00 0.00 0.00 4.00
933 958 2.967014 AGGGGAGATGGGGGAGGT 60.967 66.667 0.00 0.00 0.00 3.85
953 978 2.046507 AAGAAGCGGGCAGAGCTG 60.047 61.111 0.00 0.00 45.31 4.24
955 980 3.130160 CCAAGAAGCGGGCAGAGC 61.130 66.667 0.00 0.00 0.00 4.09
961 986 1.878775 CAAAGAGCCAAGAAGCGGG 59.121 57.895 0.00 0.00 38.01 6.13
1161 1204 0.674581 CCAATCAGTCAGCCGCAAGA 60.675 55.000 0.00 0.00 43.02 3.02
1162 1205 0.957395 ACCAATCAGTCAGCCGCAAG 60.957 55.000 0.00 0.00 0.00 4.01
1322 1365 5.292589 GCCGACAGAAAGATTCCGTTTATAA 59.707 40.000 0.00 0.00 0.00 0.98
1324 1367 3.621715 GCCGACAGAAAGATTCCGTTTAT 59.378 43.478 0.00 0.00 0.00 1.40
1325 1368 2.997986 GCCGACAGAAAGATTCCGTTTA 59.002 45.455 0.00 0.00 0.00 2.01
1326 1369 1.804748 GCCGACAGAAAGATTCCGTTT 59.195 47.619 0.00 0.00 0.00 3.60
1369 1419 4.570663 CATCGACCTCCCGGACGC 62.571 72.222 0.73 0.00 45.84 5.19
1371 1421 2.758737 ACCATCGACCTCCCGGAC 60.759 66.667 0.73 0.00 0.00 4.79
1533 1583 1.153289 ATGCTCACATCGGGACAGC 60.153 57.895 0.00 0.00 0.00 4.40
1534 1584 1.434622 GCATGCTCACATCGGGACAG 61.435 60.000 11.37 0.00 32.87 3.51
1563 1613 1.815003 GGACATCAAGAAGCAGTTGGG 59.185 52.381 0.00 0.00 0.00 4.12
1584 1634 5.596836 AGATGACAGCAAAACCTGAAAAA 57.403 34.783 0.00 0.00 36.67 1.94
1601 1651 3.165071 TGACTGAGCACTACCAAGATGA 58.835 45.455 0.00 0.00 0.00 2.92
1602 1652 3.599730 TGACTGAGCACTACCAAGATG 57.400 47.619 0.00 0.00 0.00 2.90
1645 1702 5.376756 ACCACCCAAACTTAGTTAACAGA 57.623 39.130 8.61 0.00 0.00 3.41
1758 1833 7.064253 GGAACTCATAATTGCAAACTAGTACGT 59.936 37.037 1.71 0.00 0.00 3.57
1835 2123 3.186909 TGTCGTGTGTCTTCAACTTCTG 58.813 45.455 0.00 0.00 0.00 3.02
1854 2142 6.639563 ACAAAACTTTCAGGCAAATACTTGT 58.360 32.000 0.00 0.00 34.79 3.16
1901 2189 7.382218 GGAAGATTTTGATAATAATTGTGGCCG 59.618 37.037 0.00 0.00 0.00 6.13
1991 2298 8.145316 ACAGTAGCTACTATAGAGAAAAGACG 57.855 38.462 25.63 10.75 34.13 4.18
2023 2330 8.944029 CAAGAGATGCAAGGGAAATAGTATATG 58.056 37.037 0.00 0.00 0.00 1.78
2174 2482 2.307496 AAATGTTGCCCCTGTCATCA 57.693 45.000 0.00 0.00 0.00 3.07
2177 2485 3.168035 ACATAAATGTTGCCCCTGTCA 57.832 42.857 0.00 0.00 37.90 3.58
2292 2600 2.269023 CATGGGATGCTAGGGACCATA 58.731 52.381 0.00 0.00 39.78 2.74
2293 2601 1.070604 CATGGGATGCTAGGGACCAT 58.929 55.000 0.00 0.00 42.36 3.55
2294 2602 0.327480 ACATGGGATGCTAGGGACCA 60.327 55.000 0.00 0.00 35.39 4.02
2295 2603 0.846693 AACATGGGATGCTAGGGACC 59.153 55.000 0.00 0.00 0.00 4.46
2296 2604 2.301346 CAAACATGGGATGCTAGGGAC 58.699 52.381 0.00 0.00 0.00 4.46
2297 2605 1.410083 GCAAACATGGGATGCTAGGGA 60.410 52.381 11.09 0.00 37.12 4.20
2306 2614 4.751767 AAAACAAAGAGCAAACATGGGA 57.248 36.364 0.00 0.00 0.00 4.37
2328 2636 4.623932 AAGTACCACAGAAGCTCAATCA 57.376 40.909 0.00 0.00 0.00 2.57
2342 2650 5.883673 ACACAAGTGCTAAGAAAAAGTACCA 59.116 36.000 0.00 0.00 30.71 3.25
2390 2698 3.521560 CGCATCCACTCTTACAGCTTAA 58.478 45.455 0.00 0.00 0.00 1.85
2527 2835 5.508567 TCCCACAGCTTTTCAATATCATGA 58.491 37.500 0.00 0.00 0.00 3.07
2536 2844 3.822735 CTGATTTCTCCCACAGCTTTTCA 59.177 43.478 0.00 0.00 0.00 2.69
2579 2922 9.017509 ACTCAAAACACATACAATCTGAATGAT 57.982 29.630 0.00 0.00 36.89 2.45
2611 2954 7.115663 TGCGCATAAAACTCCTTTGTTTAATTC 59.884 33.333 5.66 0.00 38.98 2.17
2620 2963 3.243704 TGCTTTGCGCATAAAACTCCTTT 60.244 39.130 12.75 0.00 45.47 3.11
2668 3011 8.248117 TCGAAGCAATCATATCAATGACATAG 57.752 34.615 0.00 0.00 44.79 2.23
2673 3016 7.412063 CAAACTCGAAGCAATCATATCAATGA 58.588 34.615 0.00 0.00 46.01 2.57
2674 3017 6.141844 GCAAACTCGAAGCAATCATATCAATG 59.858 38.462 0.00 0.00 0.00 2.82
2675 3018 6.204359 GCAAACTCGAAGCAATCATATCAAT 58.796 36.000 0.00 0.00 0.00 2.57
2676 3019 5.449041 GGCAAACTCGAAGCAATCATATCAA 60.449 40.000 0.00 0.00 0.00 2.57
2799 3146 3.914426 TTCTAGATGTTCCCTGAAGCC 57.086 47.619 0.00 0.00 0.00 4.35
2800 3147 7.500559 ACATTTATTCTAGATGTTCCCTGAAGC 59.499 37.037 0.00 0.00 30.22 3.86
2804 3151 7.443575 CAGGACATTTATTCTAGATGTTCCCTG 59.556 40.741 12.95 12.95 38.40 4.45
2806 3153 7.509546 TCAGGACATTTATTCTAGATGTTCCC 58.490 38.462 0.00 0.00 34.38 3.97
2808 3155 9.606631 AGTTCAGGACATTTATTCTAGATGTTC 57.393 33.333 0.00 0.00 34.38 3.18
2830 3177 7.803724 ACCACTTACAAATTCATAACGAGTTC 58.196 34.615 0.00 0.00 0.00 3.01
2831 3178 7.739498 ACCACTTACAAATTCATAACGAGTT 57.261 32.000 0.00 0.00 0.00 3.01
2832 3179 8.836268 TTACCACTTACAAATTCATAACGAGT 57.164 30.769 0.00 0.00 0.00 4.18
2861 3208 2.455557 CTCACCCTGTCATGAGTCTCT 58.544 52.381 0.00 0.00 38.03 3.10
2866 3213 2.414994 ATTGCTCACCCTGTCATGAG 57.585 50.000 0.00 0.00 44.37 2.90
2935 3282 2.123428 GCTGGGTCCATCCATGTGC 61.123 63.158 0.00 0.00 36.05 4.57
3119 3491 4.683781 GCTTCAGACAAGAACAGTACTCTG 59.316 45.833 0.00 0.00 46.18 3.35
3120 3492 4.262249 GGCTTCAGACAAGAACAGTACTCT 60.262 45.833 0.00 0.00 0.00 3.24
3123 3495 3.728845 TGGCTTCAGACAAGAACAGTAC 58.271 45.455 0.00 0.00 0.00 2.73
3128 3500 6.341316 TGATAGTATGGCTTCAGACAAGAAC 58.659 40.000 0.00 0.00 36.16 3.01
3147 3519 3.805971 TGTGAGCAGCGAATTCATGATAG 59.194 43.478 6.22 0.00 0.00 2.08
3324 3699 9.581099 TTTTCCTCAGAATAACAAAAACAGTTC 57.419 29.630 0.00 0.00 0.00 3.01
3375 3750 3.784202 CCCTAGTTACCATTACCAACCCT 59.216 47.826 0.00 0.00 0.00 4.34
3378 3753 4.196971 CTGCCCTAGTTACCATTACCAAC 58.803 47.826 0.00 0.00 0.00 3.77
3380 3755 2.775384 CCTGCCCTAGTTACCATTACCA 59.225 50.000 0.00 0.00 0.00 3.25
3381 3756 2.105993 CCCTGCCCTAGTTACCATTACC 59.894 54.545 0.00 0.00 0.00 2.85
3382 3757 2.486727 GCCCTGCCCTAGTTACCATTAC 60.487 54.545 0.00 0.00 0.00 1.89
3383 3758 1.772453 GCCCTGCCCTAGTTACCATTA 59.228 52.381 0.00 0.00 0.00 1.90
3384 3759 0.551396 GCCCTGCCCTAGTTACCATT 59.449 55.000 0.00 0.00 0.00 3.16
3385 3760 1.353394 GGCCCTGCCCTAGTTACCAT 61.353 60.000 0.00 0.00 44.06 3.55
3403 3778 6.463049 CCTGTAGAAACATGGTCCAGTATAGG 60.463 46.154 0.00 0.00 34.37 2.57
3419 3794 6.525578 ACGTATTCATGAGACCTGTAGAAA 57.474 37.500 0.00 0.00 0.00 2.52
3427 3802 5.647589 TGACTGTAACGTATTCATGAGACC 58.352 41.667 0.00 0.00 0.00 3.85
3428 3803 5.230306 GCTGACTGTAACGTATTCATGAGAC 59.770 44.000 0.00 0.00 0.00 3.36
3440 3824 0.034896 ACCCAAGGCTGACTGTAACG 59.965 55.000 0.00 0.00 0.00 3.18
3456 3840 1.518572 CGCCACATCTACGTGACCC 60.519 63.158 0.00 0.00 39.34 4.46
3505 3890 4.758773 TCATAGCACCACTGATGAATGA 57.241 40.909 0.00 0.00 0.00 2.57
3540 3925 1.000486 TAGGCTCGCTCTTGAGGGT 60.000 57.895 13.14 0.00 36.47 4.34
3615 4000 7.331687 GGTCACTGTAAATTTGCTGCATAAAAT 59.668 33.333 1.84 0.00 0.00 1.82
3616 4001 6.644592 GGTCACTGTAAATTTGCTGCATAAAA 59.355 34.615 1.84 0.00 0.00 1.52
3682 4067 0.112995 ATTGCTTGGTCTTGGAGGCA 59.887 50.000 0.00 0.00 0.00 4.75
3695 4080 0.822164 GAGGGATGCTTGCATTGCTT 59.178 50.000 10.49 6.96 0.00 3.91
3779 4164 2.386661 TCCCAGCTTCGTCTTCATTC 57.613 50.000 0.00 0.00 0.00 2.67
3792 4177 1.538047 TCAGCTTCATGTTTCCCAGC 58.462 50.000 0.00 0.00 0.00 4.85
3793 4178 3.415212 TCTTCAGCTTCATGTTTCCCAG 58.585 45.455 0.00 0.00 0.00 4.45
3794 4179 3.415212 CTCTTCAGCTTCATGTTTCCCA 58.585 45.455 0.00 0.00 0.00 4.37
3795 4180 2.751806 CCTCTTCAGCTTCATGTTTCCC 59.248 50.000 0.00 0.00 0.00 3.97
3796 4181 2.751806 CCCTCTTCAGCTTCATGTTTCC 59.248 50.000 0.00 0.00 0.00 3.13
3797 4182 3.679389 TCCCTCTTCAGCTTCATGTTTC 58.321 45.455 0.00 0.00 0.00 2.78
3798 4183 3.795688 TCCCTCTTCAGCTTCATGTTT 57.204 42.857 0.00 0.00 0.00 2.83
3799 4184 4.018597 AGAATCCCTCTTCAGCTTCATGTT 60.019 41.667 0.00 0.00 0.00 2.71
3800 4185 3.522750 AGAATCCCTCTTCAGCTTCATGT 59.477 43.478 0.00 0.00 0.00 3.21
3801 4186 4.153673 AGAATCCCTCTTCAGCTTCATG 57.846 45.455 0.00 0.00 0.00 3.07
3802 4187 4.858965 AAGAATCCCTCTTCAGCTTCAT 57.141 40.909 0.00 0.00 40.61 2.57
3896 4296 1.930908 GCTGATGGTGCTGTCTTGCC 61.931 60.000 0.00 0.00 0.00 4.52
3917 4317 1.841302 TACCTCTTGGCTGCTGGTGG 61.841 60.000 0.00 3.48 36.63 4.61
3927 4327 2.799176 GCCAATGGCTACCTCTTGG 58.201 57.895 18.47 11.80 46.69 3.61
3940 4340 0.319405 GCTTTCTTGCACTGGCCAAT 59.681 50.000 7.01 0.00 40.13 3.16
4030 4430 2.668280 GGCTCCGTCGTCACAAAGC 61.668 63.158 0.00 0.00 0.00 3.51
4115 4515 2.420547 GGGATACACTTGCTGCTGATGA 60.421 50.000 0.00 0.00 39.74 2.92
4117 4517 1.133976 GGGGATACACTTGCTGCTGAT 60.134 52.381 0.00 0.00 36.63 2.90
4118 4518 0.253044 GGGGATACACTTGCTGCTGA 59.747 55.000 0.00 0.00 36.63 4.26
4148 4557 1.597302 CTGTCTGTGCTGCTGCTGT 60.597 57.895 17.00 0.00 40.48 4.40
4156 4565 2.032223 CCAGCTGCTGTCTGTGCT 59.968 61.111 26.41 0.00 36.04 4.40
4245 4660 2.359602 CCTCTGCTGGTGCTGGTG 60.360 66.667 0.00 0.00 40.48 4.17
4246 4661 4.341783 GCCTCTGCTGGTGCTGGT 62.342 66.667 0.00 0.00 40.48 4.00
4530 4949 8.717821 CAATAGAAACGAAGAAGGACAATGTAA 58.282 33.333 0.00 0.00 0.00 2.41
4537 4957 5.172205 AGAGCAATAGAAACGAAGAAGGAC 58.828 41.667 0.00 0.00 0.00 3.85
4543 4963 5.693814 AGCAAAAGAGCAATAGAAACGAAG 58.306 37.500 0.00 0.00 36.85 3.79
4553 4973 5.422145 ACTGACAAAAAGCAAAAGAGCAAT 58.578 33.333 0.00 0.00 36.85 3.56
4568 4988 3.575256 ACCGACCATGTACTACTGACAAA 59.425 43.478 0.00 0.00 0.00 2.83
4571 4991 3.863142 AACCGACCATGTACTACTGAC 57.137 47.619 0.00 0.00 0.00 3.51
4572 4992 4.847198 TCTAACCGACCATGTACTACTGA 58.153 43.478 0.00 0.00 0.00 3.41
4573 4993 5.769484 ATCTAACCGACCATGTACTACTG 57.231 43.478 0.00 0.00 0.00 2.74
4574 4994 6.786967 AAATCTAACCGACCATGTACTACT 57.213 37.500 0.00 0.00 0.00 2.57
4575 4995 6.920210 GGTAAATCTAACCGACCATGTACTAC 59.080 42.308 0.00 0.00 0.00 2.73
4576 4996 7.042797 GGTAAATCTAACCGACCATGTACTA 57.957 40.000 0.00 0.00 0.00 1.82
4577 4997 5.910614 GGTAAATCTAACCGACCATGTACT 58.089 41.667 0.00 0.00 0.00 2.73
4588 5008 7.978414 ACTTAAGAACTAGCGGTAAATCTAACC 59.022 37.037 10.09 0.00 0.00 2.85
4589 5009 8.923609 ACTTAAGAACTAGCGGTAAATCTAAC 57.076 34.615 10.09 0.00 0.00 2.34
4590 5010 8.193438 GGACTTAAGAACTAGCGGTAAATCTAA 58.807 37.037 10.09 4.71 0.00 2.10
4613 5033 2.106684 AGGAACCAAGAAGACAAGGGAC 59.893 50.000 0.00 0.00 0.00 4.46
4623 5043 0.836400 AGCCCTCGAGGAACCAAGAA 60.836 55.000 33.39 0.00 38.24 2.52
4626 5046 1.125093 TTGAGCCCTCGAGGAACCAA 61.125 55.000 33.39 25.64 38.24 3.67
4628 5048 1.219393 CTTGAGCCCTCGAGGAACC 59.781 63.158 33.39 19.28 37.44 3.62
4636 5056 2.620585 GCATTACATTCCTTGAGCCCTC 59.379 50.000 0.00 0.00 0.00 4.30
4639 5059 3.731867 CGTTGCATTACATTCCTTGAGCC 60.732 47.826 0.00 0.00 0.00 4.70
4655 5075 0.250727 CCTCTTTTCCTCCCGTTGCA 60.251 55.000 0.00 0.00 0.00 4.08
4657 5077 2.224548 ACTTCCTCTTTTCCTCCCGTTG 60.225 50.000 0.00 0.00 0.00 4.10
4658 5078 2.055579 ACTTCCTCTTTTCCTCCCGTT 58.944 47.619 0.00 0.00 0.00 4.44
4660 5080 3.097614 TCTACTTCCTCTTTTCCTCCCG 58.902 50.000 0.00 0.00 0.00 5.14
4661 5081 5.500546 TTTCTACTTCCTCTTTTCCTCCC 57.499 43.478 0.00 0.00 0.00 4.30
4662 5082 6.375736 CCAATTTCTACTTCCTCTTTTCCTCC 59.624 42.308 0.00 0.00 0.00 4.30
4663 5083 6.943146 ACCAATTTCTACTTCCTCTTTTCCTC 59.057 38.462 0.00 0.00 0.00 3.71
4664 5084 6.853490 ACCAATTTCTACTTCCTCTTTTCCT 58.147 36.000 0.00 0.00 0.00 3.36
4665 5085 7.883833 ACTACCAATTTCTACTTCCTCTTTTCC 59.116 37.037 0.00 0.00 0.00 3.13
4685 5105 1.279496 AGCAAGGCATGAGACTACCA 58.721 50.000 0.00 0.00 27.97 3.25
4702 5138 4.427312 CTTTCCCATTGCACAATCTAAGC 58.573 43.478 0.00 0.00 0.00 3.09
4703 5139 4.159135 AGCTTTCCCATTGCACAATCTAAG 59.841 41.667 0.00 0.00 0.00 2.18
4704 5140 4.082081 CAGCTTTCCCATTGCACAATCTAA 60.082 41.667 0.00 0.00 0.00 2.10
4705 5141 3.444742 CAGCTTTCCCATTGCACAATCTA 59.555 43.478 0.00 0.00 0.00 1.98
4720 5156 3.323691 ACAATACCAAAACCCCAGCTTTC 59.676 43.478 0.00 0.00 0.00 2.62
4722 5158 2.970987 ACAATACCAAAACCCCAGCTT 58.029 42.857 0.00 0.00 0.00 3.74
4739 5175 5.643348 GTGATCACCATTCATCAGTGTACAA 59.357 40.000 15.31 0.00 33.21 2.41
4745 5181 4.831674 TCTGTGATCACCATTCATCAGT 57.168 40.909 22.85 0.00 29.46 3.41
4756 5192 2.996631 AGGCCAGAAATCTGTGATCAC 58.003 47.619 19.27 19.27 42.27 3.06
4813 5250 3.006967 GCCCATACCATACTACTCACCAG 59.993 52.174 0.00 0.00 0.00 4.00
4829 5269 1.281867 CCAAGACCAGTCAAGCCCATA 59.718 52.381 0.00 0.00 0.00 2.74
4830 5270 0.038744 CCAAGACCAGTCAAGCCCAT 59.961 55.000 0.00 0.00 0.00 4.00
4835 5275 4.271696 TGTATCACCAAGACCAGTCAAG 57.728 45.455 0.00 0.00 0.00 3.02
4836 5276 4.908601 ATGTATCACCAAGACCAGTCAA 57.091 40.909 0.00 0.00 0.00 3.18
4837 5277 4.323485 GGAATGTATCACCAAGACCAGTCA 60.323 45.833 0.00 0.00 31.09 3.41
4838 5278 4.080863 AGGAATGTATCACCAAGACCAGTC 60.081 45.833 0.00 0.00 0.00 3.51
4839 5279 3.846588 AGGAATGTATCACCAAGACCAGT 59.153 43.478 0.00 0.00 0.00 4.00
4849 5289 3.750130 CAGCCATGCTAGGAATGTATCAC 59.250 47.826 0.00 0.00 36.40 3.06
4926 5369 8.753497 ATTTCTTCTAGTTGGACAGTCTTTTT 57.247 30.769 0.00 0.00 0.00 1.94
4927 5370 8.214364 AGATTTCTTCTAGTTGGACAGTCTTTT 58.786 33.333 0.00 0.00 30.96 2.27
4928 5371 7.740805 AGATTTCTTCTAGTTGGACAGTCTTT 58.259 34.615 0.00 0.00 30.96 2.52
4929 5372 7.309770 AGATTTCTTCTAGTTGGACAGTCTT 57.690 36.000 0.00 0.00 30.96 3.01
4930 5373 6.926630 AGATTTCTTCTAGTTGGACAGTCT 57.073 37.500 0.00 0.00 30.96 3.24
4965 5408 5.291858 CGACTCATGTGCTAGCTAATTTCAA 59.708 40.000 17.23 0.00 0.00 2.69
5019 5462 3.447586 TCTTCTATCGGGAAGGTTGTCTG 59.552 47.826 11.56 0.00 41.94 3.51
5205 5749 5.149977 GTTGATGTAGCTTTCTTTGCTGAC 58.850 41.667 0.00 0.00 41.32 3.51
5221 5765 8.585471 AGGTCTATGAAATTGAATGTTGATGT 57.415 30.769 0.00 0.00 27.90 3.06
5275 5819 8.483758 AGTTAATTATAAACCGAGTGGAGACAT 58.516 33.333 0.00 0.00 46.14 3.06
5299 5843 7.226523 GGCAATTACAAACAATTTTCAGGAAGT 59.773 33.333 0.00 0.00 0.00 3.01
5307 5851 7.768120 TCAGTCTTGGCAATTACAAACAATTTT 59.232 29.630 0.00 0.00 0.00 1.82
5354 5898 3.440173 CACACATGATGGTAACCCTTCAC 59.560 47.826 0.00 0.00 44.91 3.18
5357 5901 3.181434 ACACACACATGATGGTAACCCTT 60.181 43.478 0.00 0.00 0.00 3.95
5369 5913 4.143115 GGATTAGACGTCAACACACACATG 60.143 45.833 19.50 0.00 0.00 3.21
5396 5940 1.244816 GGTGGGCTGTTGGTTCTTAC 58.755 55.000 0.00 0.00 0.00 2.34
5420 5964 7.444299 ACCAAATTTGAACATCAAGCAAGTAT 58.556 30.769 19.86 0.00 37.70 2.12
5491 6035 6.688073 AATAGATAAATCTGGGTCCGTGAT 57.312 37.500 2.66 0.00 37.76 3.06
5496 6040 7.255625 GCAAAGGAAATAGATAAATCTGGGTCC 60.256 40.741 2.66 6.23 37.76 4.46
5502 6046 9.348476 GAAGAGGCAAAGGAAATAGATAAATCT 57.652 33.333 0.00 0.00 40.86 2.40
5531 6075 1.187974 CCTGGGCATTGCAGATTTGA 58.812 50.000 11.39 0.00 0.00 2.69
5552 6096 0.795085 CGCAAAAGAGCTCTGGAGTG 59.205 55.000 19.06 13.63 0.00 3.51
5557 6101 2.071540 TGATCACGCAAAAGAGCTCTG 58.928 47.619 19.06 7.08 0.00 3.35
5596 6140 2.897436 TCAAGATGCAGAGGACATTCG 58.103 47.619 0.00 0.00 0.00 3.34
5661 6205 6.867662 ATTATCCCGCTAAAGTCAATCTTG 57.132 37.500 0.00 0.00 36.40 3.02
5688 6232 3.383620 TTTTGTTGGCGCATTCTTCAT 57.616 38.095 10.83 0.00 0.00 2.57
5782 6326 1.813896 CGTGCAAATGTATTGGCTCG 58.186 50.000 12.27 12.27 44.01 5.03
5784 6328 0.817013 CCCGTGCAAATGTATTGGCT 59.183 50.000 5.63 0.00 37.60 4.75


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

AutoCloner maintained by Alex Coulton.