Multiple sequence alignment - TraesCS6B01G150300

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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 TraesCS6B01G150300 chr6B 100.000 6231 0 0 1 6231 151371462 151377692 0.000000e+00 11507.0
1 TraesCS6B01G150300 chr6B 86.848 441 42 5 5762 6187 151304856 151304417 4.370000e-131 479.0
2 TraesCS6B01G150300 chr6B 86.377 345 47 0 1078 1422 603147873 603147529 1.640000e-100 377.0
3 TraesCS6B01G150300 chr6B 87.736 212 23 2 1556 1767 603146885 603146677 1.740000e-60 244.0
4 TraesCS6B01G150300 chr6D 91.010 2625 96 63 93 2670 78751777 78754308 0.000000e+00 3411.0
5 TraesCS6B01G150300 chr6D 91.130 1274 45 35 4113 5330 78755968 78757229 0.000000e+00 1664.0
6 TraesCS6B01G150300 chr6D 91.538 1040 53 14 3024 4052 78754675 78755690 0.000000e+00 1400.0
7 TraesCS6B01G150300 chr6D 92.971 882 26 12 5361 6226 78757225 78758086 0.000000e+00 1253.0
8 TraesCS6B01G150300 chr6D 86.067 445 44 8 5760 6187 78546116 78545673 4.400000e-126 462.0
9 TraesCS6B01G150300 chr6D 93.728 287 8 4 2723 3001 78754328 78754612 7.470000e-114 422.0
10 TraesCS6B01G150300 chr6D 86.782 348 40 5 1078 1422 402353271 402352927 3.520000e-102 383.0
11 TraesCS6B01G150300 chr6D 88.152 211 22 2 1556 1766 402352399 402352192 1.340000e-61 248.0
12 TraesCS6B01G150300 chr6D 98.214 56 1 0 4234 4289 78756027 78756082 1.430000e-16 99.0
13 TraesCS6B01G150300 chr6A 90.047 2130 120 44 4113 6205 94230001 94232075 0.000000e+00 2675.0
14 TraesCS6B01G150300 chr6A 87.925 2294 95 67 396 2614 94226350 94228536 0.000000e+00 2534.0
15 TraesCS6B01G150300 chr6A 86.753 1087 80 28 3033 4099 94228978 94230020 0.000000e+00 1151.0
16 TraesCS6B01G150300 chr6A 84.746 590 51 22 5627 6187 94212395 94211816 7.060000e-154 555.0
17 TraesCS6B01G150300 chr6A 87.861 346 40 2 1078 1422 549045515 549045171 7.520000e-109 405.0
18 TraesCS6B01G150300 chr6A 93.103 232 4 2 2765 2984 94228663 94228894 4.660000e-86 329.0
19 TraesCS6B01G150300 chr6A 86.508 252 16 12 5 243 94225786 94226032 1.720000e-65 261.0
20 TraesCS6B01G150300 chr6A 88.208 212 22 2 1556 1767 549044642 549044434 3.730000e-62 250.0
21 TraesCS6B01G150300 chr6A 92.857 56 3 1 4234 4289 94230065 94230119 5.180000e-11 80.5
22 TraesCS6B01G150300 chr5A 90.373 322 29 2 1082 1402 410203610 410203290 7.470000e-114 422.0
23 TraesCS6B01G150300 chr5A 82.143 280 45 5 2085 2362 410202814 410202538 1.040000e-57 235.0
24 TraesCS6B01G150300 chr5D 90.221 317 29 2 1082 1397 315485498 315485183 4.490000e-111 412.0
25 TraesCS6B01G150300 chr5B 90.000 310 29 2 1094 1402 363669759 363669451 3.500000e-107 399.0
26 TraesCS6B01G150300 chr5B 81.579 266 45 4 2085 2348 363668968 363668705 3.780000e-52 217.0
27 TraesCS6B01G150300 chr5B 82.028 217 35 3 1557 1773 363669246 363669034 1.380000e-41 182.0
28 TraesCS6B01G150300 chr7B 82.331 266 43 4 2088 2351 45641346 45641083 1.750000e-55 228.0
29 TraesCS6B01G150300 chr7B 82.510 263 42 4 2088 2348 45848789 45849049 1.750000e-55 228.0
30 TraesCS6B01G150300 chr7B 85.714 217 29 2 1207 1422 120586996 120587211 1.750000e-55 228.0
31 TraesCS6B01G150300 chr7B 85.646 209 27 2 1557 1765 120587634 120587839 3.780000e-52 217.0
32 TraesCS6B01G150300 chr7B 77.011 348 76 4 4839 5184 120589022 120589367 4.930000e-46 196.0
33 TraesCS6B01G150300 chr7D 85.646 209 27 2 1557 1765 159737274 159737479 3.780000e-52 217.0
34 TraesCS6B01G150300 chr7D 77.586 348 74 4 4839 5184 159738667 159739012 2.280000e-49 207.0
35 TraesCS6B01G150300 chr7A 85.646 209 27 2 1557 1765 158395916 158396121 3.780000e-52 217.0
36 TraesCS6B01G150300 chr7A 77.586 348 74 4 4839 5184 158397281 158397626 2.280000e-49 207.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G150300 chr6B 151371462 151377692 6230 False 11507.000000 11507 100.000000 1 6231 1 chr6B.!!$F1 6230
1 TraesCS6B01G150300 chr6B 603146677 603147873 1196 True 310.500000 377 87.056500 1078 1767 2 chr6B.!!$R2 689
2 TraesCS6B01G150300 chr6D 78751777 78758086 6309 False 1374.833333 3411 93.098500 93 6226 6 chr6D.!!$F1 6133
3 TraesCS6B01G150300 chr6D 402352192 402353271 1079 True 315.500000 383 87.467000 1078 1766 2 chr6D.!!$R2 688
4 TraesCS6B01G150300 chr6A 94225786 94232075 6289 False 1171.750000 2675 89.532167 5 6205 6 chr6A.!!$F1 6200
5 TraesCS6B01G150300 chr6A 94211816 94212395 579 True 555.000000 555 84.746000 5627 6187 1 chr6A.!!$R1 560
6 TraesCS6B01G150300 chr6A 549044434 549045515 1081 True 327.500000 405 88.034500 1078 1767 2 chr6A.!!$R2 689
7 TraesCS6B01G150300 chr5A 410202538 410203610 1072 True 328.500000 422 86.258000 1082 2362 2 chr5A.!!$R1 1280
8 TraesCS6B01G150300 chr5B 363668705 363669759 1054 True 266.000000 399 84.535667 1094 2348 3 chr5B.!!$R1 1254
9 TraesCS6B01G150300 chr7B 120586996 120589367 2371 False 213.666667 228 82.790333 1207 5184 3 chr7B.!!$F2 3977
10 TraesCS6B01G150300 chr7D 159737274 159739012 1738 False 212.000000 217 81.616000 1557 5184 2 chr7D.!!$F1 3627
11 TraesCS6B01G150300 chr7A 158395916 158397626 1710 False 212.000000 217 81.616000 1557 5184 2 chr7A.!!$F1 3627

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
744 981 0.105709 GGGAGGAGGAGAAGGAGGAG 60.106 65.0 0.00 0.00 0.00 3.69 F
1536 2362 0.109458 TTTCTGACCCGATCGACGTG 60.109 55.0 18.66 4.52 40.78 4.49 F
2354 4047 0.251653 TCGCCTCCAAGGTCAGTAGT 60.252 55.0 0.00 0.00 37.80 2.73 F
3077 4871 0.035598 TTGATTTTCGTCGAGGGGCA 59.964 50.0 5.12 0.00 0.00 5.36 F
3184 4987 0.107312 CTCAGCCCACCAAGAGGATG 60.107 60.0 0.00 0.00 40.99 3.51 F
3416 5225 0.319728 CTGGACTGTCTGTGAGGGTG 59.680 60.0 7.85 0.00 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1922 3305 1.200760 ACATACCAGACCCAGCTGCA 61.201 55.000 8.66 0.0 34.56 4.41 R
3017 4766 0.584396 TGCAACGTACCGCAAGAAAG 59.416 50.000 4.89 0.0 43.02 2.62 R
4104 6165 0.250124 ACATCAACTCACCCGCGAAA 60.250 50.000 8.23 0.0 0.00 3.46 R
4714 6857 0.252284 AGTGGACGGTGAGGAGGAAT 60.252 55.000 0.00 0.0 0.00 3.01 R
4885 7028 3.000819 TCCATCGGGTTCGTGCCT 61.001 61.111 0.00 0.0 37.69 4.75 R
5342 7493 0.399806 TCCACCCATCCATCCATCGA 60.400 55.000 0.00 0.0 0.00 3.59 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
33 34 7.262772 TGTAAGTACGCTACTTCTATGCATTT 58.737 34.615 3.54 0.00 45.38 2.32
35 36 6.150396 AGTACGCTACTTCTATGCATTTCT 57.850 37.500 3.54 0.00 34.86 2.52
36 37 6.574350 AGTACGCTACTTCTATGCATTTCTT 58.426 36.000 3.54 0.00 34.86 2.52
37 38 5.975410 ACGCTACTTCTATGCATTTCTTC 57.025 39.130 3.54 0.00 0.00 2.87
38 39 5.665459 ACGCTACTTCTATGCATTTCTTCT 58.335 37.500 3.54 0.00 0.00 2.85
51 52 5.066893 TGCATTTCTTCTCATATCACTTGCC 59.933 40.000 0.00 0.00 0.00 4.52
56 57 2.481441 TCTCATATCACTTGCCCCACT 58.519 47.619 0.00 0.00 0.00 4.00
59 60 4.284490 TCTCATATCACTTGCCCCACTATC 59.716 45.833 0.00 0.00 0.00 2.08
61 62 1.898863 ATCACTTGCCCCACTATCCT 58.101 50.000 0.00 0.00 0.00 3.24
66 67 1.478105 CTTGCCCCACTATCCTTTTGC 59.522 52.381 0.00 0.00 0.00 3.68
79 80 2.229690 CTTTTGCATTGGCTCCGGGG 62.230 60.000 0.00 0.00 41.91 5.73
139 140 3.214123 TAGACCGGGGCGATCGTG 61.214 66.667 17.81 4.48 0.00 4.35
255 279 1.044231 GGACCAACCCCCAAAAACGT 61.044 55.000 0.00 0.00 0.00 3.99
259 283 0.963225 CAACCCCCAAAAACGTAGGG 59.037 55.000 8.00 8.00 43.88 3.53
350 381 3.272581 AGTAGCTCGTACTGACTTCTCC 58.727 50.000 0.00 0.00 40.76 3.71
574 795 2.544844 ATTGTCGAGGAGGGTTAGGA 57.455 50.000 0.00 0.00 0.00 2.94
575 796 1.848652 TTGTCGAGGAGGGTTAGGAG 58.151 55.000 0.00 0.00 0.00 3.69
580 801 0.935194 GAGGAGGGTTAGGAGGAGGA 59.065 60.000 0.00 0.00 0.00 3.71
581 802 1.291335 GAGGAGGGTTAGGAGGAGGAA 59.709 57.143 0.00 0.00 0.00 3.36
582 803 1.292546 AGGAGGGTTAGGAGGAGGAAG 59.707 57.143 0.00 0.00 0.00 3.46
583 804 1.291335 GGAGGGTTAGGAGGAGGAAGA 59.709 57.143 0.00 0.00 0.00 2.87
584 805 2.673258 GAGGGTTAGGAGGAGGAAGAG 58.327 57.143 0.00 0.00 0.00 2.85
585 806 1.292546 AGGGTTAGGAGGAGGAAGAGG 59.707 57.143 0.00 0.00 0.00 3.69
586 807 1.291335 GGGTTAGGAGGAGGAAGAGGA 59.709 57.143 0.00 0.00 0.00 3.71
587 808 2.673258 GGTTAGGAGGAGGAAGAGGAG 58.327 57.143 0.00 0.00 0.00 3.69
588 809 2.673258 GTTAGGAGGAGGAAGAGGAGG 58.327 57.143 0.00 0.00 0.00 4.30
690 915 4.690122 CCAATTACTCCGTCGGTTATCTT 58.310 43.478 11.88 0.00 0.00 2.40
716 941 2.132762 TCAGTTTCCGTTTCGAGCTTC 58.867 47.619 0.00 0.00 0.00 3.86
736 961 2.317900 TCAATTACCAGGGAGGAGGAGA 59.682 50.000 0.00 0.00 41.22 3.71
743 980 0.556380 AGGGAGGAGGAGAAGGAGGA 60.556 60.000 0.00 0.00 0.00 3.71
744 981 0.105709 GGGAGGAGGAGAAGGAGGAG 60.106 65.000 0.00 0.00 0.00 3.69
745 982 0.105709 GGAGGAGGAGAAGGAGGAGG 60.106 65.000 0.00 0.00 0.00 4.30
746 983 0.759060 GAGGAGGAGAAGGAGGAGGC 60.759 65.000 0.00 0.00 0.00 4.70
747 984 2.131067 GGAGGAGAAGGAGGAGGCG 61.131 68.421 0.00 0.00 0.00 5.52
748 985 2.762043 AGGAGAAGGAGGAGGCGC 60.762 66.667 0.00 0.00 0.00 6.53
749 986 3.077556 GGAGAAGGAGGAGGCGCA 61.078 66.667 10.83 0.00 0.00 6.09
750 987 2.498726 GAGAAGGAGGAGGCGCAG 59.501 66.667 10.83 0.00 0.00 5.18
751 988 3.080121 AGAAGGAGGAGGCGCAGG 61.080 66.667 10.83 0.00 0.00 4.85
802 1039 1.574702 CCGTTCTTGGAAGCCCGTTC 61.575 60.000 0.00 0.00 34.29 3.95
856 1093 2.088178 GCCATTTCTGTTTGCGGCG 61.088 57.895 0.51 0.51 0.00 6.46
857 1094 1.444212 CCATTTCTGTTTGCGGCGG 60.444 57.895 9.78 0.00 0.00 6.13
858 1095 1.444212 CATTTCTGTTTGCGGCGGG 60.444 57.895 9.78 0.00 0.00 6.13
859 1096 1.602323 ATTTCTGTTTGCGGCGGGA 60.602 52.632 9.78 0.00 0.00 5.14
860 1097 1.175983 ATTTCTGTTTGCGGCGGGAA 61.176 50.000 9.78 0.00 0.00 3.97
862 1099 1.582610 TTCTGTTTGCGGCGGGAATC 61.583 55.000 9.78 0.00 0.00 2.52
863 1100 3.381169 CTGTTTGCGGCGGGAATCG 62.381 63.158 9.78 0.00 42.76 3.34
864 1101 3.122323 GTTTGCGGCGGGAATCGA 61.122 61.111 9.78 0.00 42.43 3.59
865 1102 2.124901 TTTGCGGCGGGAATCGAT 60.125 55.556 9.78 0.00 42.43 3.59
866 1103 2.177580 TTTGCGGCGGGAATCGATC 61.178 57.895 9.78 0.00 42.43 3.69
867 1104 4.942481 TGCGGCGGGAATCGATCG 62.942 66.667 9.36 9.36 42.43 3.69
907 1144 3.454573 AAGGTCGGTCGCGCCATA 61.455 61.111 17.57 4.41 36.97 2.74
1158 1396 2.048597 CTGCCGTACAACCAGCGA 60.049 61.111 0.00 0.00 0.00 4.93
1308 1546 1.746517 GTGGGCCGTCCTCGAATAT 59.253 57.895 0.00 0.00 39.71 1.28
1489 2315 6.196571 GCAGAATGTAAAGTGTAAACACGTT 58.803 36.000 16.54 16.54 45.18 3.99
1490 2316 7.346695 GCAGAATGTAAAGTGTAAACACGTTA 58.653 34.615 14.83 14.83 45.18 3.18
1508 2334 3.422993 CGTTACTACGTAGCGTACACACA 60.423 47.826 22.40 0.00 42.72 3.72
1530 2356 2.611292 CTGCATCTTTTCTGACCCGATC 59.389 50.000 0.00 0.00 0.00 3.69
1531 2357 1.594862 GCATCTTTTCTGACCCGATCG 59.405 52.381 8.51 8.51 0.00 3.69
1532 2358 2.738643 GCATCTTTTCTGACCCGATCGA 60.739 50.000 18.66 0.00 0.00 3.59
1533 2359 2.649331 TCTTTTCTGACCCGATCGAC 57.351 50.000 18.66 8.26 0.00 4.20
1534 2360 1.135489 TCTTTTCTGACCCGATCGACG 60.135 52.381 18.66 8.71 42.18 5.12
1535 2361 0.599558 TTTTCTGACCCGATCGACGT 59.400 50.000 18.66 12.25 40.78 4.34
1536 2362 0.109458 TTTCTGACCCGATCGACGTG 60.109 55.000 18.66 4.52 40.78 4.49
1537 2363 1.239296 TTCTGACCCGATCGACGTGT 61.239 55.000 18.66 7.97 40.78 4.49
1538 2364 1.514228 CTGACCCGATCGACGTGTG 60.514 63.158 18.66 0.00 40.78 3.82
1540 2366 4.430765 ACCCGATCGACGTGTGGC 62.431 66.667 18.66 0.00 40.78 5.01
1799 3174 7.380602 ACGTAGTACATACTTGTCACAGAAAAC 59.619 37.037 0.38 0.00 41.94 2.43
1817 3198 9.463443 ACAGAAAACTAATCAAACATAAAGCAC 57.537 29.630 0.00 0.00 0.00 4.40
1922 3305 1.018148 CGACACTCGATCCACTAGCT 58.982 55.000 0.00 0.00 43.74 3.32
1939 3322 1.910722 CTGCAGCTGGGTCTGGTAT 59.089 57.895 17.12 0.00 34.74 2.73
1949 3332 0.460284 GGTCTGGTATGTGACAGCGG 60.460 60.000 0.00 0.00 35.11 5.52
2001 3395 1.638467 GCTTGACGCTTCGGCTATG 59.362 57.895 0.00 0.00 35.04 2.23
2013 3407 4.382160 GCTTCGGCTATGTCGTAGTATTTC 59.618 45.833 1.09 0.00 38.08 2.17
2014 3408 5.759963 CTTCGGCTATGTCGTAGTATTTCT 58.240 41.667 1.09 0.00 32.72 2.52
2353 4046 0.457851 CTCGCCTCCAAGGTCAGTAG 59.542 60.000 0.00 0.00 37.80 2.57
2354 4047 0.251653 TCGCCTCCAAGGTCAGTAGT 60.252 55.000 0.00 0.00 37.80 2.73
2357 4050 1.481363 GCCTCCAAGGTCAGTAGTACC 59.519 57.143 0.00 0.00 37.80 3.34
2359 4052 3.025262 CCTCCAAGGTCAGTAGTACCTC 58.975 54.545 0.00 0.00 46.85 3.85
2360 4053 2.683867 CTCCAAGGTCAGTAGTACCTCG 59.316 54.545 0.00 0.00 46.85 4.63
2361 4054 2.306805 TCCAAGGTCAGTAGTACCTCGA 59.693 50.000 0.00 0.00 46.85 4.04
2362 4055 3.053842 TCCAAGGTCAGTAGTACCTCGAT 60.054 47.826 0.00 0.00 46.85 3.59
2364 4057 3.928005 AGGTCAGTAGTACCTCGATCA 57.072 47.619 0.00 0.00 44.20 2.92
2365 4058 3.811083 AGGTCAGTAGTACCTCGATCAG 58.189 50.000 0.00 0.00 44.20 2.90
2366 4059 3.200385 AGGTCAGTAGTACCTCGATCAGT 59.800 47.826 0.00 0.00 44.20 3.41
2367 4060 3.312973 GGTCAGTAGTACCTCGATCAGTG 59.687 52.174 0.00 0.00 33.97 3.66
2369 4062 4.817464 GTCAGTAGTACCTCGATCAGTGAT 59.183 45.833 4.98 4.98 0.00 3.06
2370 4063 5.049954 GTCAGTAGTACCTCGATCAGTGATC 60.050 48.000 21.22 21.22 35.88 2.92
2371 4064 4.816925 CAGTAGTACCTCGATCAGTGATCA 59.183 45.833 28.20 16.35 38.84 2.92
2373 4066 3.892284 AGTACCTCGATCAGTGATCACT 58.108 45.455 28.20 22.89 43.61 3.41
2389 4084 5.129634 TGATCACTGATCAGTACCTCTCTC 58.870 45.833 27.44 15.38 43.11 3.20
2419 4114 4.388080 GCTGACGCATGCACGCAA 62.388 61.111 19.57 0.00 36.19 4.85
2602 4318 9.784680 CATACGTCAATTACTACTCACTAGTTT 57.215 33.333 0.00 0.00 36.95 2.66
2643 4359 9.953565 AAATTACTATCAGTAGTTAGTTGGCAA 57.046 29.630 0.00 0.00 41.35 4.52
2644 4360 9.953565 AATTACTATCAGTAGTTAGTTGGCAAA 57.046 29.630 0.00 0.00 41.35 3.68
2645 4361 9.953565 ATTACTATCAGTAGTTAGTTGGCAAAA 57.046 29.630 0.00 0.00 41.35 2.44
2768 4484 8.601047 TGGGATCAATATGGTTAATTTTGACA 57.399 30.769 0.00 0.00 38.52 3.58
2769 4485 8.694540 TGGGATCAATATGGTTAATTTTGACAG 58.305 33.333 0.00 0.00 38.52 3.51
2770 4486 8.912988 GGGATCAATATGGTTAATTTTGACAGA 58.087 33.333 0.00 0.00 38.52 3.41
2771 4487 9.736023 GGATCAATATGGTTAATTTTGACAGAC 57.264 33.333 0.00 0.00 38.52 3.51
2924 4669 4.101741 CCTACCTTACCTAGCATGCTTTCT 59.898 45.833 28.02 10.61 0.00 2.52
3001 4750 3.739519 CGCCCCATCTCTTCTACTTCTTG 60.740 52.174 0.00 0.00 0.00 3.02
3002 4751 3.452627 GCCCCATCTCTTCTACTTCTTGA 59.547 47.826 0.00 0.00 0.00 3.02
3005 4754 5.508825 CCCCATCTCTTCTACTTCTTGATCG 60.509 48.000 0.00 0.00 0.00 3.69
3006 4755 5.068460 CCCATCTCTTCTACTTCTTGATCGT 59.932 44.000 0.00 0.00 0.00 3.73
3007 4756 6.205784 CCATCTCTTCTACTTCTTGATCGTC 58.794 44.000 0.00 0.00 0.00 4.20
3008 4757 6.039270 CCATCTCTTCTACTTCTTGATCGTCT 59.961 42.308 0.00 0.00 0.00 4.18
3010 4759 7.542534 TCTCTTCTACTTCTTGATCGTCTAC 57.457 40.000 0.00 0.00 0.00 2.59
3011 4760 6.539464 TCTCTTCTACTTCTTGATCGTCTACC 59.461 42.308 0.00 0.00 0.00 3.18
3012 4761 5.589452 TCTTCTACTTCTTGATCGTCTACCC 59.411 44.000 0.00 0.00 0.00 3.69
3013 4762 4.205587 TCTACTTCTTGATCGTCTACCCC 58.794 47.826 0.00 0.00 0.00 4.95
3014 4763 3.103080 ACTTCTTGATCGTCTACCCCT 57.897 47.619 0.00 0.00 0.00 4.79
3015 4764 4.246712 ACTTCTTGATCGTCTACCCCTA 57.753 45.455 0.00 0.00 0.00 3.53
3017 4766 4.401837 ACTTCTTGATCGTCTACCCCTAAC 59.598 45.833 0.00 0.00 0.00 2.34
3018 4767 4.246712 TCTTGATCGTCTACCCCTAACT 57.753 45.455 0.00 0.00 0.00 2.24
3020 4769 5.021458 TCTTGATCGTCTACCCCTAACTTT 58.979 41.667 0.00 0.00 0.00 2.66
3022 4771 4.607239 TGATCGTCTACCCCTAACTTTCT 58.393 43.478 0.00 0.00 0.00 2.52
3077 4871 0.035598 TTGATTTTCGTCGAGGGGCA 59.964 50.000 5.12 0.00 0.00 5.36
3101 4899 4.079253 CCATGTGCAAACCCTAGTTAAGT 58.921 43.478 0.00 0.00 34.19 2.24
3102 4900 4.082787 CCATGTGCAAACCCTAGTTAAGTG 60.083 45.833 0.00 0.00 34.19 3.16
3112 4910 7.380423 AACCCTAGTTAAGTGAGCATATGAT 57.620 36.000 6.97 0.00 33.27 2.45
3182 4985 2.596851 GCTCAGCCCACCAAGAGGA 61.597 63.158 0.00 0.00 38.69 3.71
3184 4987 0.107312 CTCAGCCCACCAAGAGGATG 60.107 60.000 0.00 0.00 40.99 3.51
3292 5101 0.890996 CCACCTGTGCCTTTGTCCTC 60.891 60.000 0.00 0.00 0.00 3.71
3294 5103 0.846693 ACCTGTGCCTTTGTCCTCTT 59.153 50.000 0.00 0.00 0.00 2.85
3313 5122 5.652014 CCTCTTGGTAACCATTTCTAATGCA 59.348 40.000 0.00 0.00 31.53 3.96
3332 5141 2.490903 GCATTCCTTTCACATGTGCTCT 59.509 45.455 21.38 0.00 0.00 4.09
3333 5142 3.691118 GCATTCCTTTCACATGTGCTCTA 59.309 43.478 21.38 0.31 0.00 2.43
3334 5143 4.337555 GCATTCCTTTCACATGTGCTCTAT 59.662 41.667 21.38 6.58 0.00 1.98
3335 5144 5.505324 GCATTCCTTTCACATGTGCTCTATC 60.505 44.000 21.38 1.13 0.00 2.08
3411 5220 2.248248 CTAACCCTGGACTGTCTGTGA 58.752 52.381 7.85 0.00 0.00 3.58
3412 5221 1.051812 AACCCTGGACTGTCTGTGAG 58.948 55.000 7.85 0.00 0.00 3.51
3413 5222 0.833834 ACCCTGGACTGTCTGTGAGG 60.834 60.000 7.85 7.97 0.00 3.86
3415 5224 0.833834 CCTGGACTGTCTGTGAGGGT 60.834 60.000 7.85 0.00 0.00 4.34
3416 5225 0.319728 CTGGACTGTCTGTGAGGGTG 59.680 60.000 7.85 0.00 0.00 4.61
3423 5232 1.305297 TCTGTGAGGGTGAGGCGAT 60.305 57.895 0.00 0.00 0.00 4.58
3475 5284 5.912149 ATGGACTGCCTTCCTAATCATAA 57.088 39.130 2.58 0.00 36.51 1.90
3487 5296 6.884472 TCCTAATCATAACTCCTTTGACCA 57.116 37.500 0.00 0.00 0.00 4.02
3494 5303 2.348411 ACTCCTTTGACCACACCTTG 57.652 50.000 0.00 0.00 0.00 3.61
3499 5308 2.099098 CCTTTGACCACACCTTGTGTTC 59.901 50.000 5.62 1.51 45.08 3.18
3579 5388 1.809271 GCTCATCGATCACATGCCTGT 60.809 52.381 0.00 0.00 35.44 4.00
3620 5429 3.548587 CTGTTTTTGTCTCTGTCATGCG 58.451 45.455 0.00 0.00 0.00 4.73
3717 5527 1.509548 CCCAAGTGGAATGGAGGGGT 61.510 60.000 0.00 0.00 40.56 4.95
3732 5542 0.613777 GGGGTCGAGTGGTCATTTCT 59.386 55.000 0.00 0.00 0.00 2.52
3763 5573 6.200665 TGTTTAATGAAAAACACATCAGCAGC 59.799 34.615 0.00 0.00 42.78 5.25
3779 5589 3.369147 CAGCAGCTGTTACTGATGTGTAC 59.631 47.826 16.64 0.00 46.42 2.90
3901 5711 5.654901 ATAGAGTACATGTCTGGGAGAGA 57.345 43.478 0.00 0.00 0.00 3.10
3904 5714 3.370104 AGTACATGTCTGGGAGAGAAGG 58.630 50.000 0.00 0.00 30.26 3.46
4067 6128 3.837213 CATAACGATGGATGCCATTCC 57.163 47.619 0.00 0.00 45.26 3.01
4094 6155 1.778334 CGTCTGTCCGTTGATGTCAA 58.222 50.000 0.00 0.00 0.00 3.18
4095 6156 1.721389 CGTCTGTCCGTTGATGTCAAG 59.279 52.381 0.00 0.00 36.39 3.02
4096 6157 2.607038 CGTCTGTCCGTTGATGTCAAGA 60.607 50.000 0.00 0.00 36.39 3.02
4097 6158 3.589988 GTCTGTCCGTTGATGTCAAGAT 58.410 45.455 0.00 0.00 36.39 2.40
4098 6159 3.997021 GTCTGTCCGTTGATGTCAAGATT 59.003 43.478 0.00 0.00 36.39 2.40
4099 6160 4.452455 GTCTGTCCGTTGATGTCAAGATTT 59.548 41.667 0.00 0.00 36.39 2.17
4100 6161 5.049405 GTCTGTCCGTTGATGTCAAGATTTT 60.049 40.000 0.00 0.00 36.39 1.82
4101 6162 5.530915 TCTGTCCGTTGATGTCAAGATTTTT 59.469 36.000 0.00 0.00 36.39 1.94
4120 6181 3.082165 TTTTTCGCGGGTGAGTTGA 57.918 47.368 6.13 0.00 0.00 3.18
4122 6183 0.871722 TTTTCGCGGGTGAGTTGATG 59.128 50.000 6.13 0.00 0.00 3.07
4139 6200 3.256558 TGATGTCAAGATTCTGCACTCG 58.743 45.455 0.00 0.00 0.00 4.18
4140 6201 2.820059 TGTCAAGATTCTGCACTCGT 57.180 45.000 0.00 0.00 0.00 4.18
4146 6207 7.712797 TGTCAAGATTCTGCACTCGTATATAA 58.287 34.615 0.00 0.00 0.00 0.98
4159 6220 7.961827 GCACTCGTATATAATAGTACCAGACAC 59.038 40.741 0.00 0.00 0.00 3.67
4193 6254 2.135139 TGACAACGATCACTGCTCAAC 58.865 47.619 0.00 0.00 0.00 3.18
4241 6302 4.159693 ACATAGTTTGACTACCAGCGATCA 59.840 41.667 0.00 0.00 32.84 2.92
4299 6364 6.210784 ACATAGTTTGACTACTAGAAGGTGCA 59.789 38.462 0.00 0.00 32.84 4.57
4300 6365 5.140747 AGTTTGACTACTAGAAGGTGCAG 57.859 43.478 0.00 0.00 0.00 4.41
4302 6367 5.482175 AGTTTGACTACTAGAAGGTGCAGAT 59.518 40.000 0.00 0.00 0.00 2.90
4303 6368 5.584253 TTGACTACTAGAAGGTGCAGATC 57.416 43.478 0.00 0.00 0.00 2.75
4304 6369 4.600062 TGACTACTAGAAGGTGCAGATCA 58.400 43.478 0.00 0.00 0.00 2.92
4305 6370 4.399618 TGACTACTAGAAGGTGCAGATCAC 59.600 45.833 0.00 0.00 44.90 3.06
4432 6554 2.022195 AGCCATGCATCAGCTGTTTAG 58.978 47.619 17.81 3.45 42.74 1.85
4433 6555 1.066605 GCCATGCATCAGCTGTTTAGG 59.933 52.381 14.67 10.47 42.74 2.69
4434 6556 1.679680 CCATGCATCAGCTGTTTAGGG 59.320 52.381 14.67 6.47 42.74 3.53
4435 6557 1.066605 CATGCATCAGCTGTTTAGGGC 59.933 52.381 14.67 9.86 42.74 5.19
4436 6558 0.329261 TGCATCAGCTGTTTAGGGCT 59.671 50.000 14.67 0.00 42.74 5.19
4437 6559 1.020437 GCATCAGCTGTTTAGGGCTC 58.980 55.000 14.67 0.00 36.59 4.70
4441 6563 3.439857 TCAGCTGTTTAGGGCTCATTT 57.560 42.857 14.67 0.00 36.59 2.32
4442 6564 3.766545 TCAGCTGTTTAGGGCTCATTTT 58.233 40.909 14.67 0.00 36.59 1.82
4443 6565 4.151883 TCAGCTGTTTAGGGCTCATTTTT 58.848 39.130 14.67 0.00 36.59 1.94
4463 6585 6.567687 TTTTTCTTGCGATCCTGTTGATTA 57.432 33.333 0.00 0.00 32.41 1.75
4465 6587 3.198068 TCTTGCGATCCTGTTGATTAGC 58.802 45.455 0.00 0.00 37.69 3.09
4466 6588 2.689553 TGCGATCCTGTTGATTAGCA 57.310 45.000 0.00 0.00 41.75 3.49
4467 6589 3.198409 TGCGATCCTGTTGATTAGCAT 57.802 42.857 0.00 0.00 40.27 3.79
4513 6656 2.579860 ACATTTCTCTCTCTGGGCCATT 59.420 45.455 6.72 0.00 0.00 3.16
4575 6718 2.357517 CGCGGTGCTGGAGAAGTT 60.358 61.111 0.00 0.00 0.00 2.66
4885 7028 1.452953 CGCAGGCGGACTACATCCTA 61.453 60.000 5.63 0.00 46.69 2.94
5259 7408 3.660111 GCCGGCCGGTGAATATGC 61.660 66.667 42.53 23.54 37.65 3.14
5272 7421 4.305769 GTGAATATGCTCAGCTGTAGGAG 58.694 47.826 14.67 4.56 0.00 3.69
5319 7470 4.708177 TGTGAGAAAAGAAAGAGTGGGAG 58.292 43.478 0.00 0.00 0.00 4.30
5325 7476 0.610687 AGAAAGAGTGGGAGAAGGCG 59.389 55.000 0.00 0.00 0.00 5.52
5326 7477 0.608640 GAAAGAGTGGGAGAAGGCGA 59.391 55.000 0.00 0.00 0.00 5.54
5327 7478 1.208293 GAAAGAGTGGGAGAAGGCGAT 59.792 52.381 0.00 0.00 0.00 4.58
5328 7479 1.280457 AAGAGTGGGAGAAGGCGATT 58.720 50.000 0.00 0.00 0.00 3.34
5329 7480 1.280457 AGAGTGGGAGAAGGCGATTT 58.720 50.000 0.00 0.00 0.00 2.17
5330 7481 1.630878 AGAGTGGGAGAAGGCGATTTT 59.369 47.619 0.00 0.00 0.00 1.82
5331 7482 2.040412 AGAGTGGGAGAAGGCGATTTTT 59.960 45.455 0.00 0.00 0.00 1.94
5437 7588 6.827641 TCGTGTAGGAATGAAATTTCGAAAG 58.172 36.000 16.80 0.00 36.73 2.62
5525 7686 6.089249 GAAAGGTTTTTCCATCACTGACAT 57.911 37.500 0.00 0.00 37.34 3.06
5639 7800 2.437359 AGAAGCAGTGCCCGATGC 60.437 61.111 12.58 0.00 42.87 3.91
5683 7844 3.503363 GCTAGCGCTGCCAACCTG 61.503 66.667 22.90 0.86 0.00 4.00
5684 7845 3.503363 CTAGCGCTGCCAACCTGC 61.503 66.667 22.90 0.00 35.29 4.85
5688 7849 4.124351 CGCTGCCAACCTGCCATG 62.124 66.667 0.00 0.00 35.20 3.66
5689 7850 3.766691 GCTGCCAACCTGCCATGG 61.767 66.667 7.63 7.63 39.80 3.66
5690 7851 2.283388 CTGCCAACCTGCCATGGT 60.283 61.111 14.67 0.00 43.11 3.55
5691 7852 2.283101 TGCCAACCTGCCATGGTC 60.283 61.111 14.67 6.41 39.83 4.02
5692 7853 3.443045 GCCAACCTGCCATGGTCG 61.443 66.667 14.67 4.46 39.83 4.79
5693 7854 3.443045 CCAACCTGCCATGGTCGC 61.443 66.667 14.67 0.00 39.83 5.19
5694 7855 3.803082 CAACCTGCCATGGTCGCG 61.803 66.667 14.67 0.00 39.83 5.87
5981 8163 2.203153 GGTGCGGTGGTGTCTTGT 60.203 61.111 0.00 0.00 0.00 3.16
6197 8394 3.748048 TGAAAAATCAGGACTTCTCTGCG 59.252 43.478 0.00 0.00 32.63 5.18
6217 8414 5.482908 TGCGGTAATGCCAATTGTTAAAAT 58.517 33.333 4.43 0.00 36.97 1.82
6228 8425 9.717942 TGCCAATTGTTAAAATTATTAACTGCT 57.282 25.926 4.43 6.21 36.23 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.526010 AGTAGCGTACTTACAATGCAAAC 57.474 39.130 0.00 0.00 34.86 2.93
13 14 6.697892 AGAAGAAATGCATAGAAGTAGCGTAC 59.302 38.462 0.00 0.00 0.00 3.67
33 34 3.114606 TGGGGCAAGTGATATGAGAAGA 58.885 45.455 0.00 0.00 0.00 2.87
35 36 2.846206 AGTGGGGCAAGTGATATGAGAA 59.154 45.455 0.00 0.00 0.00 2.87
36 37 2.481441 AGTGGGGCAAGTGATATGAGA 58.519 47.619 0.00 0.00 0.00 3.27
37 38 4.564406 GGATAGTGGGGCAAGTGATATGAG 60.564 50.000 0.00 0.00 0.00 2.90
38 39 3.327757 GGATAGTGGGGCAAGTGATATGA 59.672 47.826 0.00 0.00 0.00 2.15
51 52 2.159057 GCCAATGCAAAAGGATAGTGGG 60.159 50.000 6.62 0.00 37.47 4.61
56 57 2.023673 CGGAGCCAATGCAAAAGGATA 58.976 47.619 6.62 0.00 41.13 2.59
59 60 1.216178 CCGGAGCCAATGCAAAAGG 59.784 57.895 0.00 0.00 41.13 3.11
61 62 2.282039 CCCCGGAGCCAATGCAAAA 61.282 57.895 0.73 0.00 41.13 2.44
66 67 4.431131 ACTGCCCCGGAGCCAATG 62.431 66.667 5.13 0.00 0.00 2.82
255 279 1.666888 GCGAGTTCGTTTCGTTCCCTA 60.667 52.381 3.27 0.00 42.22 3.53
259 283 1.504450 GCGCGAGTTCGTTTCGTTC 60.504 57.895 12.10 0.00 42.22 3.95
285 313 4.302455 TCTTCTTCTTCTTGCTCAACTCG 58.698 43.478 0.00 0.00 0.00 4.18
391 594 4.854924 TGGCGATGGATGGCGGTG 62.855 66.667 0.00 0.00 31.82 4.94
392 595 3.877450 ATGGCGATGGATGGCGGT 61.877 61.111 0.00 0.00 31.82 5.68
393 596 3.359523 CATGGCGATGGATGGCGG 61.360 66.667 0.00 0.00 31.82 6.13
394 597 4.034258 GCATGGCGATGGATGGCG 62.034 66.667 10.93 0.00 31.82 5.69
395 598 2.273179 ATGCATGGCGATGGATGGC 61.273 57.895 14.71 0.00 39.06 4.40
396 599 4.090723 ATGCATGGCGATGGATGG 57.909 55.556 14.71 0.00 39.06 3.51
574 795 0.933700 CTCCTCCTCCTCTTCCTCCT 59.066 60.000 0.00 0.00 0.00 3.69
575 796 0.105709 CCTCCTCCTCCTCTTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
580 801 1.308326 CGGACCTCCTCCTCCTCTT 59.692 63.158 0.00 0.00 36.80 2.85
581 802 3.011885 CGGACCTCCTCCTCCTCT 58.988 66.667 0.00 0.00 36.80 3.69
582 803 2.835895 GCGGACCTCCTCCTCCTC 60.836 72.222 0.00 0.00 36.80 3.71
583 804 4.467107 GGCGGACCTCCTCCTCCT 62.467 72.222 0.00 0.00 40.50 3.69
588 809 2.630592 CTTTAGCGGCGGACCTCCTC 62.631 65.000 9.78 0.00 0.00 3.71
690 915 5.067413 AGCTCGAAACGGAAACTGATAGATA 59.933 40.000 0.00 0.00 0.00 1.98
716 941 2.764269 TCTCCTCCTCCCTGGTAATTG 58.236 52.381 0.00 0.00 37.07 2.32
736 961 2.930562 AACCTGCGCCTCCTCCTT 60.931 61.111 4.18 0.00 0.00 3.36
743 980 1.507141 CGAAAAGTGAACCTGCGCCT 61.507 55.000 4.18 0.00 0.00 5.52
744 981 1.082104 CGAAAAGTGAACCTGCGCC 60.082 57.895 4.18 0.00 0.00 6.53
745 982 1.082104 CCGAAAAGTGAACCTGCGC 60.082 57.895 0.00 0.00 0.00 6.09
746 983 0.512952 CTCCGAAAAGTGAACCTGCG 59.487 55.000 0.00 0.00 0.00 5.18
747 984 0.875059 CCTCCGAAAAGTGAACCTGC 59.125 55.000 0.00 0.00 0.00 4.85
748 985 0.875059 GCCTCCGAAAAGTGAACCTG 59.125 55.000 0.00 0.00 0.00 4.00
749 986 0.602905 CGCCTCCGAAAAGTGAACCT 60.603 55.000 0.00 0.00 36.29 3.50
750 987 1.574702 CCGCCTCCGAAAAGTGAACC 61.575 60.000 0.00 0.00 36.29 3.62
751 988 1.866925 CCGCCTCCGAAAAGTGAAC 59.133 57.895 0.00 0.00 36.29 3.18
845 1082 2.485122 GATTCCCGCCGCAAACAG 59.515 61.111 0.00 0.00 0.00 3.16
856 1093 4.681978 CCCGGCCGATCGATTCCC 62.682 72.222 30.73 10.08 0.00 3.97
902 1139 1.139520 CAAACCAAGCGCCTATGGC 59.860 57.895 20.69 0.00 46.75 4.40
905 1142 0.328258 ACTCCAAACCAAGCGCCTAT 59.672 50.000 2.29 0.00 0.00 2.57
907 1144 0.755327 AAACTCCAAACCAAGCGCCT 60.755 50.000 2.29 0.00 0.00 5.52
1489 2315 3.123453 CAGTGTGTGTACGCTACGTAGTA 59.877 47.826 22.98 7.47 45.46 1.82
1490 2316 2.096069 CAGTGTGTGTACGCTACGTAGT 60.096 50.000 22.98 8.49 45.46 2.73
1491 2317 2.502876 CAGTGTGTGTACGCTACGTAG 58.497 52.381 18.47 18.47 45.46 3.51
1492 2318 1.400113 GCAGTGTGTGTACGCTACGTA 60.400 52.381 8.10 0.00 45.46 3.57
1502 2328 3.313526 GTCAGAAAAGATGCAGTGTGTGT 59.686 43.478 0.00 0.00 0.00 3.72
1508 2334 1.347707 TCGGGTCAGAAAAGATGCAGT 59.652 47.619 0.00 0.00 0.00 4.40
1817 3198 7.615582 TGGTGCTAATCTAGTCTGATTTTTG 57.384 36.000 0.00 0.00 37.73 2.44
1871 3252 4.610605 TCGTGAATTCTGTGTAAAGGGA 57.389 40.909 7.05 0.00 0.00 4.20
1922 3305 1.200760 ACATACCAGACCCAGCTGCA 61.201 55.000 8.66 0.00 34.56 4.41
1949 3332 2.456119 CGATGGACGTTGAGCTGCC 61.456 63.158 0.00 0.00 37.22 4.85
2013 3407 8.705239 AATACGACGACATCTATACGTAAAAG 57.295 34.615 0.00 0.24 40.29 2.27
2364 4057 4.865905 AGAGGTACTGATCAGTGATCACT 58.134 43.478 33.76 22.89 43.11 3.41
2365 4058 4.887071 AGAGAGGTACTGATCAGTGATCAC 59.113 45.833 33.76 24.09 43.11 3.06
2366 4059 5.104151 AGAGAGAGGTACTGATCAGTGATCA 60.104 44.000 33.76 29.39 45.35 2.92
2367 4060 5.239306 CAGAGAGAGGTACTGATCAGTGATC 59.761 48.000 33.76 26.23 41.55 2.92
2369 4062 4.018870 ACAGAGAGAGGTACTGATCAGTGA 60.019 45.833 33.76 17.34 41.55 3.41
2370 4063 4.269183 ACAGAGAGAGGTACTGATCAGTG 58.731 47.826 33.76 17.52 41.55 3.66
2371 4064 4.227300 AGACAGAGAGAGGTACTGATCAGT 59.773 45.833 30.11 30.11 41.55 3.41
2373 4066 4.473196 AGAGACAGAGAGAGGTACTGATCA 59.527 45.833 0.00 0.00 41.55 2.92
2374 4067 5.036117 AGAGACAGAGAGAGGTACTGATC 57.964 47.826 0.00 0.00 41.55 2.92
2375 4068 4.141482 GGAGAGACAGAGAGAGGTACTGAT 60.141 50.000 0.00 0.00 41.55 2.90
2376 4069 3.199071 GGAGAGACAGAGAGAGGTACTGA 59.801 52.174 0.00 0.00 41.55 3.41
2377 4070 3.054728 TGGAGAGACAGAGAGAGGTACTG 60.055 52.174 0.00 0.00 41.55 2.74
2381 4074 3.364549 CAATGGAGAGACAGAGAGAGGT 58.635 50.000 0.00 0.00 0.00 3.85
2382 4075 2.101249 GCAATGGAGAGACAGAGAGAGG 59.899 54.545 0.00 0.00 0.00 3.69
2389 4084 1.638133 CGTCAGCAATGGAGAGACAG 58.362 55.000 0.00 0.00 0.00 3.51
2525 4220 2.814336 GGCGGTGGAATGATCCTATTTC 59.186 50.000 0.00 0.00 46.70 2.17
2707 4423 9.205513 CCCCTACTATTTAGTTACTCCAGTAAA 57.794 37.037 0.62 0.00 41.58 2.01
2708 4424 7.786464 CCCCCTACTATTTAGTTACTCCAGTAA 59.214 40.741 0.00 0.00 38.10 2.24
2709 4425 7.091353 ACCCCCTACTATTTAGTTACTCCAGTA 60.091 40.741 0.00 0.00 37.73 2.74
2710 4426 6.141790 CCCCCTACTATTTAGTTACTCCAGT 58.858 44.000 0.00 0.00 37.73 4.00
2711 4427 6.141790 ACCCCCTACTATTTAGTTACTCCAG 58.858 44.000 0.00 0.00 37.73 3.86
2712 4428 6.108983 ACCCCCTACTATTTAGTTACTCCA 57.891 41.667 0.00 0.00 37.73 3.86
2713 4429 7.015682 GGTAACCCCCTACTATTTAGTTACTCC 59.984 44.444 0.00 0.00 38.59 3.85
2714 4430 7.565029 TGGTAACCCCCTACTATTTAGTTACTC 59.435 40.741 0.00 0.00 38.59 2.59
2715 4431 7.430007 TGGTAACCCCCTACTATTTAGTTACT 58.570 38.462 0.00 0.00 38.59 2.24
2716 4432 7.675161 TGGTAACCCCCTACTATTTAGTTAC 57.325 40.000 0.00 0.00 38.09 2.50
2718 4434 8.887393 CATATGGTAACCCCCTACTATTTAGTT 58.113 37.037 0.00 0.00 37.73 2.24
2719 4435 7.460082 CCATATGGTAACCCCCTACTATTTAGT 59.540 40.741 14.09 0.00 40.24 2.24
2720 4436 7.092578 CCCATATGGTAACCCCCTACTATTTAG 60.093 44.444 20.46 0.00 0.00 1.85
2721 4437 6.736655 CCCATATGGTAACCCCCTACTATTTA 59.263 42.308 20.46 0.00 0.00 1.40
2763 4479 6.080648 ACAAAGTCATACTACGTCTGTCAA 57.919 37.500 0.00 0.00 0.00 3.18
2764 4480 5.700722 ACAAAGTCATACTACGTCTGTCA 57.299 39.130 0.00 0.00 0.00 3.58
2765 4481 6.147581 TCAACAAAGTCATACTACGTCTGTC 58.852 40.000 0.00 0.00 0.00 3.51
2768 4484 7.117812 CCAAATCAACAAAGTCATACTACGTCT 59.882 37.037 0.00 0.00 0.00 4.18
2769 4485 7.095355 ACCAAATCAACAAAGTCATACTACGTC 60.095 37.037 0.00 0.00 0.00 4.34
2770 4486 6.708949 ACCAAATCAACAAAGTCATACTACGT 59.291 34.615 0.00 0.00 0.00 3.57
2771 4487 7.129109 ACCAAATCAACAAAGTCATACTACG 57.871 36.000 0.00 0.00 0.00 3.51
2924 4669 2.203422 CCAACGGAAGCACCCCAA 60.203 61.111 0.00 0.00 34.64 4.12
3001 4750 5.349809 CAAGAAAGTTAGGGGTAGACGATC 58.650 45.833 0.00 0.00 0.00 3.69
3002 4751 4.382793 GCAAGAAAGTTAGGGGTAGACGAT 60.383 45.833 0.00 0.00 0.00 3.73
3005 4754 3.259902 CGCAAGAAAGTTAGGGGTAGAC 58.740 50.000 0.00 0.00 43.02 2.59
3006 4755 2.235402 CCGCAAGAAAGTTAGGGGTAGA 59.765 50.000 0.00 0.00 43.02 2.59
3007 4756 2.027469 ACCGCAAGAAAGTTAGGGGTAG 60.027 50.000 0.00 0.00 44.27 3.18
3008 4757 1.980036 ACCGCAAGAAAGTTAGGGGTA 59.020 47.619 0.00 0.00 44.27 3.69
3010 4759 2.353323 GTACCGCAAGAAAGTTAGGGG 58.647 52.381 0.00 0.00 43.02 4.79
3011 4760 1.997606 CGTACCGCAAGAAAGTTAGGG 59.002 52.381 0.00 0.00 43.02 3.53
3012 4761 2.680577 ACGTACCGCAAGAAAGTTAGG 58.319 47.619 0.00 0.00 43.02 2.69
3013 4762 3.663493 GCAACGTACCGCAAGAAAGTTAG 60.663 47.826 0.00 0.00 43.02 2.34
3014 4763 2.221517 GCAACGTACCGCAAGAAAGTTA 59.778 45.455 0.00 0.00 43.02 2.24
3015 4764 1.003223 GCAACGTACCGCAAGAAAGTT 60.003 47.619 0.00 0.00 43.02 2.66
3017 4766 0.584396 TGCAACGTACCGCAAGAAAG 59.416 50.000 4.89 0.00 43.02 2.62
3018 4767 1.015109 TTGCAACGTACCGCAAGAAA 58.985 45.000 13.95 0.00 42.93 2.52
3020 4769 4.440181 TTGCAACGTACCGCAAGA 57.560 50.000 13.95 0.00 42.93 3.02
3022 4771 2.627004 CGTTGCAACGTACCGCAA 59.373 55.556 37.16 13.95 46.63 4.85
3042 4836 2.922740 TCAACCTCTACGCAAAACCT 57.077 45.000 0.00 0.00 0.00 3.50
3044 4838 4.611366 CGAAAATCAACCTCTACGCAAAAC 59.389 41.667 0.00 0.00 0.00 2.43
3077 4871 0.777446 ACTAGGGTTTGCACATGGGT 59.223 50.000 0.00 0.00 0.00 4.51
3182 4985 4.263639 TGGGCATCTCTCAACTTTCTTCAT 60.264 41.667 0.00 0.00 0.00 2.57
3184 4987 3.679389 TGGGCATCTCTCAACTTTCTTC 58.321 45.455 0.00 0.00 0.00 2.87
3223 5026 2.045731 CCGGCCCCGTGTTTGTAT 60.046 61.111 5.93 0.00 37.81 2.29
3292 5101 6.980397 GGAATGCATTAGAAATGGTTACCAAG 59.020 38.462 12.97 0.00 36.95 3.61
3294 5103 6.194235 AGGAATGCATTAGAAATGGTTACCA 58.806 36.000 12.97 6.53 38.19 3.25
3313 5122 5.104193 AGGATAGAGCACATGTGAAAGGAAT 60.104 40.000 29.80 13.27 0.00 3.01
3332 5141 3.234349 GCAGCTGCCAGGAGGATA 58.766 61.111 28.76 0.00 36.89 2.59
3411 5220 3.790437 CAGCCATCGCCTCACCCT 61.790 66.667 0.00 0.00 34.57 4.34
3413 5222 4.783621 TGCAGCCATCGCCTCACC 62.784 66.667 0.00 0.00 34.57 4.02
3415 5224 3.709633 AGTGCAGCCATCGCCTCA 61.710 61.111 0.00 0.00 34.57 3.86
3416 5225 3.200593 CAGTGCAGCCATCGCCTC 61.201 66.667 0.00 0.00 34.57 4.70
3423 5232 1.070275 CTCAGTGACAGTGCAGCCA 59.930 57.895 5.33 0.00 0.00 4.75
3475 5284 1.564348 ACAAGGTGTGGTCAAAGGAGT 59.436 47.619 0.00 0.00 0.00 3.85
3487 5296 3.769792 GCATATGCCGAACACAAGGTGT 61.770 50.000 17.26 0.00 41.10 4.16
3494 5303 3.302480 CGTTCTAAGCATATGCCGAACAC 60.302 47.826 31.98 21.63 43.38 3.32
3497 5306 1.864711 GCGTTCTAAGCATATGCCGAA 59.135 47.619 23.96 19.41 43.38 4.30
3499 5308 1.217001 TGCGTTCTAAGCATATGCCG 58.783 50.000 23.96 18.79 43.38 5.69
3620 5429 3.420893 TCAAACATCACATCCCAAGGAC 58.579 45.455 0.00 0.00 32.98 3.85
3717 5527 4.058124 CAACTGAAGAAATGACCACTCGA 58.942 43.478 0.00 0.00 0.00 4.04
3732 5542 9.645059 TGATGTGTTTTTCATTAAACAACTGAA 57.355 25.926 3.75 0.00 46.27 3.02
3763 5573 4.193826 AGCCTGTACACATCAGTAACAG 57.806 45.455 0.00 0.00 39.14 3.16
3779 5589 3.592059 CCATCACCAATTGAAAAGCCTG 58.408 45.455 7.12 0.00 37.92 4.85
3844 5654 3.671008 AACATGCAACTACTGTCGGTA 57.329 42.857 0.00 0.00 0.00 4.02
3869 5679 9.613428 CCAGACATGTACTCTATTTAATCCAAA 57.387 33.333 0.00 0.00 0.00 3.28
3901 5711 2.338809 TGTGATCCAACCACTCTCCTT 58.661 47.619 0.00 0.00 35.66 3.36
3924 5734 3.324846 TCAGTTACCAGTGCTCAACTCAT 59.675 43.478 0.72 0.00 36.83 2.90
3925 5735 2.698274 TCAGTTACCAGTGCTCAACTCA 59.302 45.455 0.72 0.00 36.83 3.41
3926 5736 3.321497 CTCAGTTACCAGTGCTCAACTC 58.679 50.000 0.72 0.00 36.83 3.01
3927 5737 2.548920 GCTCAGTTACCAGTGCTCAACT 60.549 50.000 0.00 0.00 40.93 3.16
3928 5738 1.801178 GCTCAGTTACCAGTGCTCAAC 59.199 52.381 0.00 0.00 0.00 3.18
4024 5836 4.142752 GGAACTTAATTTCAGTGCCGTACC 60.143 45.833 7.73 0.00 29.67 3.34
4026 5838 4.643463 TGGAACTTAATTTCAGTGCCGTA 58.357 39.130 7.73 0.00 42.57 4.02
4102 6163 1.265635 CATCAACTCACCCGCGAAAAA 59.734 47.619 8.23 0.00 0.00 1.94
4103 6164 0.871722 CATCAACTCACCCGCGAAAA 59.128 50.000 8.23 0.00 0.00 2.29
4104 6165 0.250124 ACATCAACTCACCCGCGAAA 60.250 50.000 8.23 0.00 0.00 3.46
4105 6166 0.669318 GACATCAACTCACCCGCGAA 60.669 55.000 8.23 0.00 0.00 4.70
4106 6167 1.080093 GACATCAACTCACCCGCGA 60.080 57.895 8.23 0.00 0.00 5.87
4107 6168 0.948623 TTGACATCAACTCACCCGCG 60.949 55.000 0.00 0.00 0.00 6.46
4108 6169 0.798776 CTTGACATCAACTCACCCGC 59.201 55.000 0.00 0.00 0.00 6.13
4109 6170 2.455674 TCTTGACATCAACTCACCCG 57.544 50.000 0.00 0.00 0.00 5.28
4110 6171 4.394300 CAGAATCTTGACATCAACTCACCC 59.606 45.833 0.00 0.00 0.00 4.61
4111 6172 4.142730 GCAGAATCTTGACATCAACTCACC 60.143 45.833 0.00 0.00 0.00 4.02
4112 6173 4.453478 TGCAGAATCTTGACATCAACTCAC 59.547 41.667 0.00 0.00 0.00 3.51
4113 6174 4.453478 GTGCAGAATCTTGACATCAACTCA 59.547 41.667 0.00 0.00 0.00 3.41
4114 6175 4.694509 AGTGCAGAATCTTGACATCAACTC 59.305 41.667 0.00 0.00 0.00 3.01
4115 6176 4.649692 AGTGCAGAATCTTGACATCAACT 58.350 39.130 0.00 0.00 0.00 3.16
4116 6177 4.435253 CGAGTGCAGAATCTTGACATCAAC 60.435 45.833 0.00 0.00 0.00 3.18
4117 6178 3.681417 CGAGTGCAGAATCTTGACATCAA 59.319 43.478 0.00 0.00 0.00 2.57
4118 6179 3.256558 CGAGTGCAGAATCTTGACATCA 58.743 45.455 0.00 0.00 0.00 3.07
4119 6180 3.257393 ACGAGTGCAGAATCTTGACATC 58.743 45.455 0.00 0.00 0.00 3.06
4120 6181 3.325293 ACGAGTGCAGAATCTTGACAT 57.675 42.857 0.00 0.00 0.00 3.06
4122 6183 8.749841 ATTATATACGAGTGCAGAATCTTGAC 57.250 34.615 0.00 0.00 0.00 3.18
4140 6201 9.475620 CCTCCATGTGTCTGGTACTATTATATA 57.524 37.037 0.00 0.00 37.57 0.86
4146 6207 3.961408 GTCCTCCATGTGTCTGGTACTAT 59.039 47.826 0.00 0.00 37.57 2.12
4159 6220 2.154462 GTTGTCAACCTGTCCTCCATG 58.846 52.381 4.21 0.00 0.00 3.66
4193 6254 5.622233 GCCAAACTTAAATAGCAGGGTTGAG 60.622 44.000 0.00 0.00 0.00 3.02
4241 6302 0.536006 GCAGGGTTGACTTGAGCAGT 60.536 55.000 0.00 0.00 39.07 4.40
4299 6364 3.099905 TCGACCAGGAAGATTGTGATCT 58.900 45.455 0.00 0.00 44.51 2.75
4300 6365 3.190874 GTCGACCAGGAAGATTGTGATC 58.809 50.000 3.51 0.00 0.00 2.92
4302 6367 1.967779 TGTCGACCAGGAAGATTGTGA 59.032 47.619 14.12 0.00 0.00 3.58
4303 6368 2.455674 TGTCGACCAGGAAGATTGTG 57.544 50.000 14.12 0.00 0.00 3.33
4304 6369 2.936993 GCATGTCGACCAGGAAGATTGT 60.937 50.000 14.12 0.00 0.00 2.71
4305 6370 1.667724 GCATGTCGACCAGGAAGATTG 59.332 52.381 14.12 0.00 0.00 2.67
4306 6371 1.278985 TGCATGTCGACCAGGAAGATT 59.721 47.619 14.12 0.00 0.00 2.40
4307 6372 0.904649 TGCATGTCGACCAGGAAGAT 59.095 50.000 14.12 0.00 0.00 2.40
4445 6567 2.938451 TGCTAATCAACAGGATCGCAAG 59.062 45.455 0.00 0.00 38.56 4.01
4448 6570 4.310769 ACTATGCTAATCAACAGGATCGC 58.689 43.478 0.00 0.00 34.28 4.58
4449 6571 6.258727 ACAAACTATGCTAATCAACAGGATCG 59.741 38.462 0.00 0.00 34.28 3.69
4450 6572 7.559590 ACAAACTATGCTAATCAACAGGATC 57.440 36.000 0.00 0.00 34.28 3.36
4451 6573 7.944729 AACAAACTATGCTAATCAACAGGAT 57.055 32.000 0.00 0.00 38.05 3.24
4452 6574 7.759489 AAACAAACTATGCTAATCAACAGGA 57.241 32.000 0.00 0.00 0.00 3.86
4453 6575 8.081633 TCAAAACAAACTATGCTAATCAACAGG 58.918 33.333 0.00 0.00 0.00 4.00
4454 6576 9.630098 ATCAAAACAAACTATGCTAATCAACAG 57.370 29.630 0.00 0.00 0.00 3.16
4457 6579 7.967854 CGGATCAAAACAAACTATGCTAATCAA 59.032 33.333 0.00 0.00 0.00 2.57
4458 6580 7.120579 ACGGATCAAAACAAACTATGCTAATCA 59.879 33.333 0.00 0.00 0.00 2.57
4459 6581 7.429340 CACGGATCAAAACAAACTATGCTAATC 59.571 37.037 0.00 0.00 0.00 1.75
4460 6582 7.094377 ACACGGATCAAAACAAACTATGCTAAT 60.094 33.333 0.00 0.00 0.00 1.73
4461 6583 6.205853 ACACGGATCAAAACAAACTATGCTAA 59.794 34.615 0.00 0.00 0.00 3.09
4463 6585 4.518970 ACACGGATCAAAACAAACTATGCT 59.481 37.500 0.00 0.00 0.00 3.79
4465 6587 5.996219 TCACACGGATCAAAACAAACTATG 58.004 37.500 0.00 0.00 0.00 2.23
4466 6588 6.817765 ATCACACGGATCAAAACAAACTAT 57.182 33.333 0.00 0.00 0.00 2.12
4467 6589 6.627395 AATCACACGGATCAAAACAAACTA 57.373 33.333 0.00 0.00 34.28 2.24
4579 6722 1.449778 GTAGAACTCGGCCTTGGCC 60.450 63.158 20.15 20.15 0.00 5.36
4714 6857 0.252284 AGTGGACGGTGAGGAGGAAT 60.252 55.000 0.00 0.00 0.00 3.01
4885 7028 3.000819 TCCATCGGGTTCGTGCCT 61.001 61.111 0.00 0.00 37.69 4.75
5259 7408 5.724328 TCAATTAACACTCCTACAGCTGAG 58.276 41.667 23.35 13.13 34.73 3.35
5330 7481 7.611467 CCATCCATCCATCGATCCTAATAAAAA 59.389 37.037 0.00 0.00 0.00 1.94
5331 7482 7.112122 CCATCCATCCATCGATCCTAATAAAA 58.888 38.462 0.00 0.00 0.00 1.52
5335 7486 3.457380 CCCATCCATCCATCGATCCTAAT 59.543 47.826 0.00 0.00 0.00 1.73
5342 7493 0.399806 TCCACCCATCCATCCATCGA 60.400 55.000 0.00 0.00 0.00 3.59
5345 7496 2.248160 ACAAATCCACCCATCCATCCAT 59.752 45.455 0.00 0.00 0.00 3.41
5476 7630 2.930826 TCCCTCTTGGTCAACTCAAC 57.069 50.000 0.00 0.00 34.77 3.18
5593 7754 2.930562 ACCACCAGCACCCTCTCC 60.931 66.667 0.00 0.00 0.00 3.71
5603 7764 0.249120 TCGAGCATTACCACCACCAG 59.751 55.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.