Multiple sequence alignment - TraesCS1A01G311800

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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 TraesCS1A01G311800 chr1A 100.000 6016 0 0 1 6016 503367735 503373750 0.000000e+00 11110.0
1 TraesCS1A01G311800 chr1B 94.940 1838 80 6 2931 4757 548535540 548537375 0.000000e+00 2867.0
2 TraesCS1A01G311800 chr1B 88.532 933 53 16 2037 2935 548534549 548535461 0.000000e+00 1081.0
3 TraesCS1A01G311800 chr1B 92.778 540 39 0 1486 2025 548532846 548533385 0.000000e+00 782.0
4 TraesCS1A01G311800 chr1B 91.594 571 35 4 5385 5946 548538201 548538767 0.000000e+00 776.0
5 TraesCS1A01G311800 chr1B 91.337 531 27 5 4763 5277 548537415 548537942 0.000000e+00 708.0
6 TraesCS1A01G311800 chr1B 83.460 659 39 20 668 1297 548531908 548532525 3.170000e-152 549.0
7 TraesCS1A01G311800 chr1B 86.473 414 43 9 278 688 548531486 548531889 5.530000e-120 442.0
8 TraesCS1A01G311800 chr1B 81.019 216 36 5 3820 4033 343121465 343121253 3.730000e-37 167.0
9 TraesCS1A01G311800 chr1B 87.500 104 11 2 2874 2976 134429648 134429750 1.060000e-22 119.0
10 TraesCS1A01G311800 chr1B 86.139 101 9 4 5276 5375 548537993 548538089 2.970000e-18 104.0
11 TraesCS1A01G311800 chr1D 94.281 1731 75 14 1973 3701 407872444 407874152 0.000000e+00 2627.0
12 TraesCS1A01G311800 chr1D 94.909 1041 37 7 3730 4757 407874151 407875188 0.000000e+00 1615.0
13 TraesCS1A01G311800 chr1D 88.113 1304 111 26 653 1944 407871173 407872444 0.000000e+00 1509.0
14 TraesCS1A01G311800 chr1D 90.164 671 52 6 1 669 407870500 407871158 0.000000e+00 861.0
15 TraesCS1A01G311800 chr1D 90.097 616 42 10 5376 5976 407875980 407876591 0.000000e+00 782.0
16 TraesCS1A01G311800 chr1D 92.814 501 27 9 4780 5277 407875239 407875733 0.000000e+00 717.0
17 TraesCS1A01G311800 chr1D 100.000 41 0 0 5318 5358 407875804 407875844 6.470000e-10 76.8
18 TraesCS1A01G311800 chr4B 81.567 217 33 7 3820 4033 445971362 445971574 8.020000e-39 172.0
19 TraesCS1A01G311800 chr7B 80.930 215 38 3 3820 4033 136967726 136967514 3.730000e-37 167.0
20 TraesCS1A01G311800 chr7B 81.019 216 36 5 3820 4033 368357096 368357308 3.730000e-37 167.0
21 TraesCS1A01G311800 chr7B 88.000 100 11 1 2874 2973 168361397 168361495 3.810000e-22 117.0
22 TraesCS1A01G311800 chr6A 81.019 216 35 6 3820 4033 169859908 169860119 3.730000e-37 167.0
23 TraesCS1A01G311800 chr5B 80.176 227 39 6 3810 4033 113728829 113728606 1.340000e-36 165.0
24 TraesCS1A01G311800 chr2D 80.263 228 36 9 3810 4033 465439884 465440106 4.820000e-36 163.0
25 TraesCS1A01G311800 chr2A 88.542 96 10 1 2874 2969 147477777 147477683 1.370000e-21 115.0
26 TraesCS1A01G311800 chr7D 87.755 98 11 1 2874 2971 391585530 391585434 4.930000e-21 113.0
27 TraesCS1A01G311800 chr3D 86.408 103 13 1 2874 2976 394765702 394765601 1.770000e-20 111.0
28 TraesCS1A01G311800 chr3D 86.598 97 12 1 2874 2970 21002465 21002560 8.250000e-19 106.0
29 TraesCS1A01G311800 chr4A 84.348 115 11 7 2874 2985 455925549 455925439 8.250000e-19 106.0


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 TraesCS1A01G311800 chr1A 503367735 503373750 6015 False 11110.000000 11110 100.000000 1 6016 1 chr1A.!!$F1 6015
1 TraesCS1A01G311800 chr1B 548531486 548538767 7281 False 913.625000 2867 89.406625 278 5946 8 chr1B.!!$F2 5668
2 TraesCS1A01G311800 chr1D 407870500 407876591 6091 False 1169.685714 2627 92.911143 1 5976 7 chr1D.!!$F1 5975

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
879 957 0.107214 CTCTCTCTCTCGCTGGACCT 60.107 60.000 0.0 0.0 0.00 3.85 F
880 958 0.107410 TCTCTCTCTCGCTGGACCTC 60.107 60.000 0.0 0.0 0.00 3.85 F
2388 3838 0.313672 TGGTGAGAATGCCAAAACGC 59.686 50.000 0.0 0.0 0.00 4.84 F
2897 4358 0.245539 CTCCGTCCCAAAGTAAGCGA 59.754 55.000 0.0 0.0 0.00 4.93 F
3335 4881 0.325933 CTGTCAGGATGGACCAAGCA 59.674 55.000 0.0 0.0 42.04 3.91 F
3338 4884 1.379044 CAGGATGGACCAAGCACCC 60.379 63.158 0.0 0.0 42.04 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2569 4023 0.466189 AACAGACAACCAGTGGCAGG 60.466 55.000 9.78 0.91 37.96 4.85 R
2872 4333 1.296715 CTTTGGGACGGAGGGAGTG 59.703 63.158 0.00 0.00 0.00 3.51 R
3354 4900 0.038526 CCTTTCACGTCGGTACTGCT 60.039 55.000 0.00 0.00 0.00 4.24 R
4823 6417 1.078848 CTGCCTGTACTCCCTGTGC 60.079 63.158 0.00 0.00 0.00 4.57 R
4967 6561 0.877071 CAGCAAAATCTGTGCCGTCT 59.123 50.000 0.00 0.00 43.27 4.18 R
5285 6893 0.981277 CGGGTCCCTGTCCAAGGTAT 60.981 60.000 6.29 0.00 45.78 2.73 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
25 26 7.004555 TGTAGCTTCAAATAAGAGGAGTGAA 57.995 36.000 0.00 0.00 0.00 3.18
27 28 7.766278 TGTAGCTTCAAATAAGAGGAGTGAATC 59.234 37.037 0.00 0.00 0.00 2.52
37 38 1.204704 AGGAGTGAATCATCGCGAACA 59.795 47.619 15.24 2.00 41.06 3.18
50 51 1.674817 CGCGAACAAGAGGTGGGTTAT 60.675 52.381 0.00 0.00 0.00 1.89
76 77 3.207677 GCCATAGGCGTGATCTGAG 57.792 57.895 0.00 0.00 39.62 3.35
83 84 1.591703 GCGTGATCTGAGTCCCACA 59.408 57.895 0.00 0.00 0.00 4.17
118 119 1.470979 CCTCCACCCGATGAAGTAACG 60.471 57.143 0.00 0.00 0.00 3.18
143 144 1.779061 AACCTCTCCCCGCACACAAT 61.779 55.000 0.00 0.00 0.00 2.71
164 165 7.872993 CACAATAGGAACATGTACGAGGATATT 59.127 37.037 0.00 0.00 0.00 1.28
186 187 1.214992 ATCCCCTTGACCAAGACCCC 61.215 60.000 11.06 0.00 40.79 4.95
200 201 4.489771 CCCCGGCATGAGACCACC 62.490 72.222 0.00 0.00 0.00 4.61
214 215 1.141019 CCACCGTCTCCGTGTATGG 59.859 63.158 0.00 0.00 0.00 2.74
236 237 6.116806 TGGTGTGTACACTTTGAACTTATGT 58.883 36.000 25.60 0.00 45.73 2.29
266 267 5.895534 ACATCTAATGCATTTGGAGGTCAAT 59.104 36.000 18.75 0.36 35.24 2.57
267 268 6.040166 ACATCTAATGCATTTGGAGGTCAATC 59.960 38.462 18.75 0.00 35.24 2.67
275 276 5.591877 GCATTTGGAGGTCAATCTCACTAAT 59.408 40.000 0.00 0.00 34.98 1.73
276 277 6.459298 GCATTTGGAGGTCAATCTCACTAATG 60.459 42.308 9.39 9.39 34.98 1.90
283 284 7.147811 GGAGGTCAATCTCACTAATGTTACTCT 60.148 40.741 0.00 0.00 35.58 3.24
291 292 5.091552 TCACTAATGTTACTCTGGAACCCT 58.908 41.667 0.00 0.00 0.00 4.34
311 312 3.506067 CCTAACCGCAACAAAATCCTCTT 59.494 43.478 0.00 0.00 0.00 2.85
314 315 2.554032 ACCGCAACAAAATCCTCTTCAG 59.446 45.455 0.00 0.00 0.00 3.02
319 320 5.748152 CGCAACAAAATCCTCTTCAGAAAAA 59.252 36.000 0.00 0.00 0.00 1.94
320 321 6.291796 CGCAACAAAATCCTCTTCAGAAAAAC 60.292 38.462 0.00 0.00 0.00 2.43
321 322 6.534793 GCAACAAAATCCTCTTCAGAAAAACA 59.465 34.615 0.00 0.00 0.00 2.83
322 323 7.064490 GCAACAAAATCCTCTTCAGAAAAACAA 59.936 33.333 0.00 0.00 0.00 2.83
335 336 6.754193 TCAGAAAAACAAACAAACTCCACTT 58.246 32.000 0.00 0.00 0.00 3.16
336 337 6.644592 TCAGAAAAACAAACAAACTCCACTTG 59.355 34.615 0.00 0.00 0.00 3.16
337 338 5.931724 AGAAAAACAAACAAACTCCACTTGG 59.068 36.000 0.00 0.00 0.00 3.61
351 352 0.240411 ACTTGGCGTAGTCGTGACTC 59.760 55.000 5.66 0.00 42.54 3.36
380 381 3.394674 TGCTTATGTCAAACGTGAGGA 57.605 42.857 0.00 0.00 33.27 3.71
390 391 1.213094 AACGTGAGGACTGCGAAACG 61.213 55.000 0.00 0.00 37.09 3.60
409 410 1.373497 CGCACCACTCGAGCTCTTT 60.373 57.895 13.61 0.00 0.00 2.52
420 421 4.750598 ACTCGAGCTCTTTTGTTTTAGGAC 59.249 41.667 13.61 0.00 0.00 3.85
421 422 3.739300 TCGAGCTCTTTTGTTTTAGGACG 59.261 43.478 12.85 0.00 0.00 4.79
422 423 3.120649 CGAGCTCTTTTGTTTTAGGACGG 60.121 47.826 12.85 0.00 0.00 4.79
503 506 9.837525 GCACTTTGATTATTTGATATGATCTCC 57.162 33.333 0.00 0.00 0.00 3.71
506 509 7.615582 TTGATTATTTGATATGATCTCCCGC 57.384 36.000 0.00 0.00 0.00 6.13
519 522 2.632377 TCTCCCGCATGATGAACTTTC 58.368 47.619 0.00 0.00 0.00 2.62
629 632 3.047115 AGATGGCCAGATGTTGATCTCT 58.953 45.455 13.05 1.32 36.75 3.10
709 779 3.421567 GGAACTTGTCCAGCCAGTT 57.578 52.632 0.00 0.00 46.97 3.16
725 795 2.203480 TTGTGCAGGCCCAACTCC 60.203 61.111 0.00 0.00 0.00 3.85
789 867 2.038837 GGCCAGTCGCTTTACCCAC 61.039 63.158 0.00 0.00 37.74 4.61
800 878 0.887387 TTTACCCACTTGTGCGGCTC 60.887 55.000 0.00 0.00 0.00 4.70
801 879 2.046009 TTACCCACTTGTGCGGCTCA 62.046 55.000 0.00 0.00 0.00 4.26
869 947 1.546923 TGACTCGTCGTCTCTCTCTCT 59.453 52.381 8.58 0.00 43.25 3.10
871 949 1.197055 CTCGTCGTCTCTCTCTCTCG 58.803 60.000 0.00 0.00 0.00 4.04
874 952 0.650512 GTCGTCTCTCTCTCTCGCTG 59.349 60.000 0.00 0.00 0.00 5.18
876 954 0.461163 CGTCTCTCTCTCTCGCTGGA 60.461 60.000 0.00 0.00 0.00 3.86
877 955 1.014352 GTCTCTCTCTCTCGCTGGAC 58.986 60.000 0.00 0.00 0.00 4.02
879 957 0.107214 CTCTCTCTCTCGCTGGACCT 60.107 60.000 0.00 0.00 0.00 3.85
880 958 0.107410 TCTCTCTCTCGCTGGACCTC 60.107 60.000 0.00 0.00 0.00 3.85
881 959 1.436195 CTCTCTCTCGCTGGACCTCG 61.436 65.000 0.00 0.00 0.00 4.63
882 960 1.450491 CTCTCTCGCTGGACCTCGA 60.450 63.158 8.67 8.67 0.00 4.04
883 961 1.711060 CTCTCTCGCTGGACCTCGAC 61.711 65.000 5.51 0.00 0.00 4.20
884 962 3.102107 CTCTCGCTGGACCTCGACG 62.102 68.421 5.51 0.00 0.00 5.12
885 963 3.432588 CTCGCTGGACCTCGACGT 61.433 66.667 5.51 0.00 0.00 4.34
886 964 3.384014 CTCGCTGGACCTCGACGTC 62.384 68.421 5.18 5.18 0.00 4.34
945 1024 3.141488 GGAAGAGAGGCGAGGCGA 61.141 66.667 0.00 0.00 0.00 5.54
947 1026 1.215647 GAAGAGAGGCGAGGCGAAA 59.784 57.895 0.00 0.00 0.00 3.46
985 1064 1.383525 TGGATTCCCGGTCCTACCC 60.384 63.158 10.68 0.20 36.68 3.69
987 1066 1.074699 GATTCCCGGTCCTACCCCT 60.075 63.158 0.00 0.00 33.75 4.79
1089 1168 3.827898 CCCTCGCTCGTCAGGTCC 61.828 72.222 0.00 0.00 0.00 4.46
1095 1174 2.760385 CTCGTCAGGTCCCCTCCC 60.760 72.222 0.00 0.00 0.00 4.30
1096 1175 3.273654 TCGTCAGGTCCCCTCCCT 61.274 66.667 0.00 0.00 0.00 4.20
1097 1176 2.284699 CGTCAGGTCCCCTCCCTT 60.285 66.667 0.00 0.00 0.00 3.95
1122 1228 2.790791 CCGCCTCCCTGCTAGAGTG 61.791 68.421 0.00 0.00 0.00 3.51
1130 1236 1.226916 CTGCTAGAGTGCTGCCTCG 60.227 63.158 10.93 2.22 36.56 4.63
1134 1240 1.733402 CTAGAGTGCTGCCTCGGGAG 61.733 65.000 10.93 0.00 36.56 4.30
1155 1261 4.297207 GGATCCCTTCCGCCTACT 57.703 61.111 0.00 0.00 33.93 2.57
1171 1277 4.675029 CTCGGTTTCCACGGCCGT 62.675 66.667 28.70 28.70 45.11 5.68
1229 1335 0.689623 CCTAGCTAGCAAGATGGGGG 59.310 60.000 18.83 3.01 36.19 5.40
1230 1336 1.428869 CTAGCTAGCAAGATGGGGGT 58.571 55.000 18.83 0.00 0.00 4.95
1272 1378 2.813908 GTTCGGTGCGTAGGCCTG 60.814 66.667 17.99 0.00 38.85 4.85
1296 1402 0.548989 TACTGGGTGTTTGGTGCTGT 59.451 50.000 0.00 0.00 0.00 4.40
1311 1420 1.720894 CTGTTGTGCGCACTGTGAA 59.279 52.632 37.59 22.76 0.00 3.18
1316 1425 3.276091 TGCGCACTGTGAAACCGG 61.276 61.111 5.66 0.00 34.36 5.28
1331 1440 2.813908 CGGGTTCGCTACTGTGCC 60.814 66.667 0.00 0.00 0.00 5.01
1357 1466 2.761208 CTCGAGTAGAGGGTGGAACATT 59.239 50.000 3.62 0.00 41.85 2.71
1359 1468 2.233922 CGAGTAGAGGGTGGAACATTGT 59.766 50.000 0.00 0.00 44.52 2.71
1383 1492 9.513906 TGTAGTGTTCTAATTTGATTTCATGGA 57.486 29.630 0.00 0.00 0.00 3.41
1392 1501 5.873179 TTTGATTTCATGGAAGTACCGAC 57.127 39.130 0.00 0.00 42.61 4.79
1405 1514 4.516365 AGTACCGACTTACAGTTTCCTG 57.484 45.455 0.00 0.00 37.39 3.86
1408 1517 1.270625 CCGACTTACAGTTTCCTGCCA 60.271 52.381 0.00 0.00 42.81 4.92
1410 1519 2.875933 CGACTTACAGTTTCCTGCCAAA 59.124 45.455 0.00 0.00 42.81 3.28
1414 1523 5.140454 ACTTACAGTTTCCTGCCAAATTCT 58.860 37.500 0.00 0.00 42.81 2.40
1415 1524 5.241728 ACTTACAGTTTCCTGCCAAATTCTC 59.758 40.000 0.00 0.00 42.81 2.87
1417 1526 3.571401 ACAGTTTCCTGCCAAATTCTCTG 59.429 43.478 0.00 0.00 42.81 3.35
1418 1527 3.571401 CAGTTTCCTGCCAAATTCTCTGT 59.429 43.478 0.00 0.00 0.00 3.41
1420 1529 1.538047 TCCTGCCAAATTCTCTGTGC 58.462 50.000 0.00 0.00 0.00 4.57
1421 1530 1.202915 TCCTGCCAAATTCTCTGTGCA 60.203 47.619 0.00 0.00 0.00 4.57
1435 1545 3.734463 TCTGTGCATTCGAACCTTGTAA 58.266 40.909 0.00 0.00 0.00 2.41
1440 1550 3.185594 TGCATTCGAACCTTGTAAAGTCG 59.814 43.478 0.00 0.00 44.25 4.18
1442 1552 4.386652 GCATTCGAACCTTGTAAAGTCGTA 59.613 41.667 0.00 0.00 44.25 3.43
1448 1558 6.582295 TCGAACCTTGTAAAGTCGTATGTTAC 59.418 38.462 0.00 0.00 44.25 2.50
1452 1562 7.088905 ACCTTGTAAAGTCGTATGTTACTCTG 58.911 38.462 0.00 0.00 44.25 3.35
1455 1565 4.803098 AAAGTCGTATGTTACTCTGGCT 57.197 40.909 0.00 0.00 0.00 4.75
1467 1577 3.636153 ACTCTGGCTCCCTTTCATTAC 57.364 47.619 0.00 0.00 0.00 1.89
1504 1778 6.060028 TGCTTATTTGCTTAGCTAAATCCG 57.940 37.500 7.74 0.00 35.93 4.18
1505 1779 5.008613 TGCTTATTTGCTTAGCTAAATCCGG 59.991 40.000 7.74 0.00 35.93 5.14
1506 1780 5.562890 GCTTATTTGCTTAGCTAAATCCGGG 60.563 44.000 7.74 0.00 32.26 5.73
1510 1784 2.210961 GCTTAGCTAAATCCGGGTGAC 58.789 52.381 7.74 0.00 0.00 3.67
1511 1785 2.158943 GCTTAGCTAAATCCGGGTGACT 60.159 50.000 7.74 0.00 0.00 3.41
1517 1791 3.694566 GCTAAATCCGGGTGACTTGAATT 59.305 43.478 0.00 0.00 0.00 2.17
1520 1794 4.519540 AATCCGGGTGACTTGAATTTTG 57.480 40.909 0.00 0.00 0.00 2.44
1583 1857 5.655488 AGCAATAGCAGTATCTAATAGCCG 58.345 41.667 0.00 0.00 45.49 5.52
1592 1866 4.997395 AGTATCTAATAGCCGGTTGCATTG 59.003 41.667 1.90 0.00 44.83 2.82
1633 1907 5.046087 TGAATATGATCAGCCCATCTGTAGG 60.046 44.000 0.09 0.00 43.32 3.18
1747 2021 8.883731 CCATGTTAGTGTTTACTGAATAAGGAG 58.116 37.037 0.00 0.00 37.78 3.69
1885 2159 8.458573 TGTCATGTTGTTTGGTAGTTATTCTT 57.541 30.769 0.00 0.00 0.00 2.52
1966 2240 7.148188 TGCAGTTTATTGATAGAAAAGCTCTGG 60.148 37.037 0.00 0.00 35.41 3.86
1968 2242 8.180267 CAGTTTATTGATAGAAAAGCTCTGGTG 58.820 37.037 0.00 0.00 35.41 4.17
2014 2288 6.763303 AATAACTCATTTTTCGTGGTTTGC 57.237 33.333 0.00 0.00 0.00 3.68
2038 3466 6.650390 GCTGATAACCATGGTGTTTCATTTTT 59.350 34.615 20.60 0.17 0.00 1.94
2142 3592 4.406648 TGTATTGTAGCCATCTGACTGG 57.593 45.455 2.84 2.84 39.45 4.00
2198 3648 8.819974 CATTCTTTGTGAGCTGTGTTAATTTTT 58.180 29.630 0.00 0.00 0.00 1.94
2225 3675 1.555967 TTATGGTCCAGGCAAAAGCC 58.444 50.000 0.00 0.00 0.00 4.35
2228 3678 2.985847 GTCCAGGCAAAAGCCGCT 60.986 61.111 0.19 0.00 34.52 5.52
2387 3837 2.228582 TGATGGTGAGAATGCCAAAACG 59.771 45.455 0.00 0.00 38.38 3.60
2388 3838 0.313672 TGGTGAGAATGCCAAAACGC 59.686 50.000 0.00 0.00 0.00 4.84
2391 3841 1.215382 GAGAATGCCAAAACGCCCC 59.785 57.895 0.00 0.00 0.00 5.80
2442 3892 8.691661 ATTCATAGTGTAAACTGAACTTGGTT 57.308 30.769 0.00 0.00 31.00 3.67
2456 3906 6.403878 TGAACTTGGTTAGCCTTGTCTATAC 58.596 40.000 0.00 0.00 35.27 1.47
2457 3907 6.212791 TGAACTTGGTTAGCCTTGTCTATACT 59.787 38.462 0.00 0.00 35.27 2.12
2458 3908 6.622427 ACTTGGTTAGCCTTGTCTATACTT 57.378 37.500 0.00 0.00 35.27 2.24
2494 3944 5.414360 TGTATTCTGCTCTGTGTCATCTTC 58.586 41.667 0.00 0.00 0.00 2.87
2506 3956 4.709397 TGTGTCATCTTCCTTTGTTTGGTT 59.291 37.500 0.00 0.00 0.00 3.67
2569 4023 6.089954 GCTCACATCTAATTTCTTGTTTTGGC 59.910 38.462 0.00 0.00 0.00 4.52
2595 4049 4.323417 CCACTGGTTGTCTGTTATGCTTA 58.677 43.478 0.00 0.00 0.00 3.09
2640 4094 8.093307 CCAAGATAGTCAGATAGCATGTTGTAT 58.907 37.037 0.00 0.00 0.00 2.29
2694 4154 2.683362 GCTAGACCAAGCAATTACCCAC 59.317 50.000 0.00 0.00 42.30 4.61
2857 4318 6.100134 TCCTGGCTATACCTAATAACCGTTTT 59.900 38.462 0.00 0.00 40.22 2.43
2872 4333 5.977171 ACCGTTTTTCTTACAAAATTGCC 57.023 34.783 0.00 0.00 0.00 4.52
2890 4351 1.296715 CACTCCCTCCGTCCCAAAG 59.703 63.158 0.00 0.00 0.00 2.77
2895 4356 0.392595 CCCTCCGTCCCAAAGTAAGC 60.393 60.000 0.00 0.00 0.00 3.09
2897 4358 0.245539 CTCCGTCCCAAAGTAAGCGA 59.754 55.000 0.00 0.00 0.00 4.93
2899 4360 1.349259 CCGTCCCAAAGTAAGCGACG 61.349 60.000 0.00 0.00 44.41 5.12
2900 4361 1.785951 GTCCCAAAGTAAGCGACGC 59.214 57.895 13.03 13.03 0.00 5.19
2909 4370 0.863144 GTAAGCGACGCCAACTTTCA 59.137 50.000 17.79 0.00 0.00 2.69
2960 4504 7.776030 TGAAGTTAAGACACTTATTTTGGGACA 59.224 33.333 0.00 0.00 37.11 4.02
2966 4510 3.245264 ACACTTATTTTGGGACAGAGGGG 60.245 47.826 0.00 0.00 42.39 4.79
3146 4691 6.422100 CCTGCTAGCAGTATTATGTTGTAGTG 59.578 42.308 36.14 15.93 42.15 2.74
3153 4698 6.280643 CAGTATTATGTTGTAGTGGCAGCTA 58.719 40.000 0.00 0.00 0.00 3.32
3259 4805 2.897969 GTTCTGAGGGAAGGTCTGTACA 59.102 50.000 0.00 0.00 34.23 2.90
3335 4881 0.325933 CTGTCAGGATGGACCAAGCA 59.674 55.000 0.00 0.00 42.04 3.91
3338 4884 1.379044 CAGGATGGACCAAGCACCC 60.379 63.158 0.00 0.00 42.04 4.61
3470 5016 4.878878 CCCAATAGGACTTCGGGC 57.121 61.111 0.00 0.00 38.24 6.13
3543 5089 4.217767 TCTTCGATAGCAGTAACACACAGT 59.782 41.667 0.00 0.00 0.00 3.55
3548 5094 1.762957 AGCAGTAACACACAGTCCAGT 59.237 47.619 0.00 0.00 0.00 4.00
3701 5247 8.608844 ACATCAAGTAAGGTTTCTTCACTAAG 57.391 34.615 0.00 0.00 34.59 2.18
3728 5274 3.199727 TGCAAGTGTATTGCCTCTCCATA 59.800 43.478 9.86 0.00 44.32 2.74
3764 5311 2.363306 TGCAGTCCTGTTGTTTCCAT 57.637 45.000 0.00 0.00 0.00 3.41
3958 5505 4.696479 TGCCAAAACAATGGTAACCAAT 57.304 36.364 0.00 0.00 42.75 3.16
4041 5588 4.717279 TCCAAACATACCCTTATAGGCC 57.283 45.455 0.00 0.00 32.73 5.19
4160 5713 2.873472 ACCATGTTGCATTTTTGCACAG 59.127 40.909 0.00 0.00 45.32 3.66
4183 5736 4.142469 GGTGCTGTCAAGTTACAAAACTGT 60.142 41.667 0.00 0.00 45.37 3.55
4266 5819 7.173390 GCTTCTGTACCATAAACTCTTCTGTTT 59.827 37.037 0.00 0.00 42.10 2.83
4287 5840 6.382570 TGTTTTTAAATGGATGGATGGGTAGG 59.617 38.462 0.00 0.00 0.00 3.18
4456 6015 7.044641 CGTAAGATCTGTATTCAGTTCGACTTG 60.045 40.741 0.00 0.00 42.15 3.16
4458 6017 6.925211 AGATCTGTATTCAGTTCGACTTGAA 58.075 36.000 11.82 11.82 42.15 2.69
4502 6061 8.908786 TCTCATCTGAAACATGTTAAACTTCT 57.091 30.769 12.39 0.00 0.00 2.85
4591 6150 3.358118 CTCGAAGAAGAGGAGGTTAGGT 58.642 50.000 0.00 0.00 34.09 3.08
4684 6243 2.704464 TGTAGATTGATGCTGCTGCT 57.296 45.000 17.00 2.26 40.48 4.24
4735 6294 8.079211 AGCAAGAGTATGTTCCTTTCTACATA 57.921 34.615 0.00 0.00 36.46 2.29
4757 6316 9.288576 ACATATTGTTCTGTTCATATACCCATG 57.711 33.333 0.00 0.00 0.00 3.66
4758 6317 6.639632 ATTGTTCTGTTCATATACCCATGC 57.360 37.500 0.00 0.00 0.00 4.06
4761 6320 6.894682 TGTTCTGTTCATATACCCATGCTTA 58.105 36.000 0.00 0.00 0.00 3.09
4778 6371 6.309737 CCATGCTTAGCAAAGTGAAGATTTTC 59.690 38.462 12.08 0.00 43.62 2.29
4808 6401 5.596268 TTTTCTGTCGTCAACTCATCATG 57.404 39.130 0.00 0.00 0.00 3.07
4823 6417 9.394477 CAACTCATCATGCATTATTTATCTGTG 57.606 33.333 0.00 0.00 0.00 3.66
4898 6492 3.188786 GCCGCACGGACTGCTAAG 61.189 66.667 14.43 0.00 44.64 2.18
4967 6561 3.247046 TCGAGCGACGACGAAGAA 58.753 55.556 12.29 0.00 46.45 2.52
4970 6564 1.121281 CGAGCGACGACGAAGAAGAC 61.121 60.000 12.29 0.00 45.77 3.01
5004 6598 1.005630 GTTGACTGGAGAGCGCAGT 60.006 57.895 11.47 2.88 0.00 4.40
5051 6645 2.060326 TCGCTACCGTGAACAAGAAG 57.940 50.000 0.00 0.00 35.54 2.85
5064 6658 2.317040 ACAAGAAGTCGGTTCTCCAGA 58.683 47.619 1.97 0.00 45.44 3.86
5065 6659 2.900546 ACAAGAAGTCGGTTCTCCAGAT 59.099 45.455 1.97 0.00 45.44 2.90
5069 6663 4.319177 AGAAGTCGGTTCTCCAGATTTTG 58.681 43.478 0.00 0.00 42.26 2.44
5070 6664 2.427506 AGTCGGTTCTCCAGATTTTGC 58.572 47.619 0.00 0.00 0.00 3.68
5071 6665 2.151202 GTCGGTTCTCCAGATTTTGCA 58.849 47.619 0.00 0.00 0.00 4.08
5072 6666 2.749621 GTCGGTTCTCCAGATTTTGCAT 59.250 45.455 0.00 0.00 0.00 3.96
5073 6667 2.749076 TCGGTTCTCCAGATTTTGCATG 59.251 45.455 0.00 0.00 0.00 4.06
5076 6670 4.673580 CGGTTCTCCAGATTTTGCATGAAG 60.674 45.833 0.00 0.00 0.00 3.02
5120 6714 5.096849 GTCCTTTTACTTTGAAAACGCACA 58.903 37.500 0.00 0.00 0.00 4.57
5182 6776 8.211629 GGTTACTCATTAATGTGAATAGTCCCT 58.788 37.037 21.18 1.72 0.00 4.20
5282 6890 8.747538 ACCAAGAACTATTATATGTTCAACCC 57.252 34.615 13.08 0.00 43.38 4.11
5283 6891 7.778382 ACCAAGAACTATTATATGTTCAACCCC 59.222 37.037 13.08 0.00 43.38 4.95
5306 6967 2.663196 CTTGGACAGGGACCCGTC 59.337 66.667 20.76 20.76 0.00 4.79
5358 7019 1.669999 GGCCAGTGTTGATCCATGCC 61.670 60.000 0.00 0.00 0.00 4.40
5359 7020 0.966875 GCCAGTGTTGATCCATGCCA 60.967 55.000 0.00 0.00 0.00 4.92
5360 7021 1.548081 CCAGTGTTGATCCATGCCAA 58.452 50.000 0.00 0.00 0.00 4.52
5361 7022 1.894466 CCAGTGTTGATCCATGCCAAA 59.106 47.619 0.00 0.00 0.00 3.28
5362 7023 2.299582 CCAGTGTTGATCCATGCCAAAA 59.700 45.455 0.00 0.00 0.00 2.44
5363 7024 3.581755 CAGTGTTGATCCATGCCAAAAG 58.418 45.455 0.00 0.00 0.00 2.27
5365 7026 3.642848 AGTGTTGATCCATGCCAAAAGTT 59.357 39.130 0.00 0.00 0.00 2.66
5366 7027 4.101430 AGTGTTGATCCATGCCAAAAGTTT 59.899 37.500 0.00 0.00 0.00 2.66
5369 7030 2.289569 TGATCCATGCCAAAAGTTTGCC 60.290 45.455 0.00 0.00 36.86 4.52
5370 7031 1.422531 TCCATGCCAAAAGTTTGCCT 58.577 45.000 0.00 0.00 36.86 4.75
5371 7032 1.344114 TCCATGCCAAAAGTTTGCCTC 59.656 47.619 0.00 0.00 36.86 4.70
5372 7033 1.070445 CCATGCCAAAAGTTTGCCTCA 59.930 47.619 0.00 0.00 36.86 3.86
5373 7034 2.485124 CCATGCCAAAAGTTTGCCTCAA 60.485 45.455 0.00 0.00 36.86 3.02
5374 7035 3.204526 CATGCCAAAAGTTTGCCTCAAA 58.795 40.909 0.00 0.00 36.86 2.69
5417 7210 3.513515 TCCTTGTGCTCAACCAACTTTTT 59.486 39.130 0.00 0.00 0.00 1.94
5426 7219 5.681179 GCTCAACCAACTTTTTGAAGCCTAA 60.681 40.000 0.00 0.00 34.24 2.69
5471 7265 9.323985 ACAAGATCTCTATTAGAAGTTGATTGC 57.676 33.333 0.00 0.00 37.89 3.56
5508 7302 1.688197 CACAGTGGCATTCCAAAGGTT 59.312 47.619 0.00 0.00 45.53 3.50
5509 7303 1.688197 ACAGTGGCATTCCAAAGGTTG 59.312 47.619 0.00 0.00 45.53 3.77
5555 7349 3.201290 CCTCATTGTGGTGAGATGTAGC 58.799 50.000 5.53 0.00 46.77 3.58
5560 7354 6.108687 TCATTGTGGTGAGATGTAGCTTAAG 58.891 40.000 0.00 0.00 0.00 1.85
5561 7355 5.738619 TTGTGGTGAGATGTAGCTTAAGA 57.261 39.130 6.67 0.00 0.00 2.10
5732 7531 7.518161 TCTTTTCTGTTTAATCATGTAGCGTG 58.482 34.615 0.00 0.00 0.00 5.34
5760 7559 6.250739 CGAATGAAATCTGAGTTGCAATTGAG 59.749 38.462 10.34 1.36 0.00 3.02
5764 7563 6.039605 TGAAATCTGAGTTGCAATTGAGAACA 59.960 34.615 14.56 11.94 0.00 3.18
5781 7581 0.603569 ACAAGAGGACTCGCGACAAT 59.396 50.000 3.71 0.00 34.09 2.71
5823 7623 1.741732 CGAGATGAAAGGGAGTGGCTG 60.742 57.143 0.00 0.00 0.00 4.85
5843 7643 2.707849 CCAATGACCAGCCTGCAGC 61.708 63.158 8.66 3.91 44.25 5.25
5866 7666 4.498894 TCTGGAGCTGTCAATGATGAAT 57.501 40.909 0.00 0.00 37.30 2.57
5868 7668 2.686405 TGGAGCTGTCAATGATGAATGC 59.314 45.455 0.00 0.00 37.30 3.56
5952 7752 5.704978 GCTTTCAGGGAAAAATAAATGGCAA 59.295 36.000 0.00 0.00 30.84 4.52
5971 7771 3.777478 CAAATGCTGCTTTAGATGGTGG 58.223 45.455 0.00 0.00 0.00 4.61
5976 7776 1.741706 CTGCTTTAGATGGTGGTGCAG 59.258 52.381 0.00 0.00 39.98 4.41
5977 7777 0.453390 GCTTTAGATGGTGGTGCAGC 59.547 55.000 9.47 9.47 0.00 5.25
5978 7778 1.952367 GCTTTAGATGGTGGTGCAGCT 60.952 52.381 18.08 0.00 32.61 4.24
5979 7779 1.741706 CTTTAGATGGTGGTGCAGCTG 59.258 52.381 18.08 10.11 32.61 4.24
5980 7780 0.692476 TTAGATGGTGGTGCAGCTGT 59.308 50.000 18.08 0.00 32.61 4.40
5981 7781 0.692476 TAGATGGTGGTGCAGCTGTT 59.308 50.000 18.08 0.00 32.61 3.16
5982 7782 0.892358 AGATGGTGGTGCAGCTGTTG 60.892 55.000 18.08 0.00 32.61 3.33
5983 7783 0.890542 GATGGTGGTGCAGCTGTTGA 60.891 55.000 18.08 0.00 32.61 3.18
5984 7784 0.251474 ATGGTGGTGCAGCTGTTGAT 60.251 50.000 18.08 0.00 32.61 2.57
5985 7785 1.174078 TGGTGGTGCAGCTGTTGATG 61.174 55.000 18.08 0.00 32.61 3.07
5986 7786 1.582968 GTGGTGCAGCTGTTGATGG 59.417 57.895 18.08 0.00 0.00 3.51
5987 7787 0.890542 GTGGTGCAGCTGTTGATGGA 60.891 55.000 18.08 0.00 0.00 3.41
5989 7789 2.938354 GTGCAGCTGTTGATGGACT 58.062 52.632 16.64 0.00 45.33 3.85
5990 7790 1.242076 GTGCAGCTGTTGATGGACTT 58.758 50.000 16.64 0.00 45.33 3.01
5991 7791 1.068748 GTGCAGCTGTTGATGGACTTG 60.069 52.381 16.64 0.00 45.33 3.16
5992 7792 0.524862 GCAGCTGTTGATGGACTTGG 59.475 55.000 16.64 0.00 0.00 3.61
5993 7793 0.524862 CAGCTGTTGATGGACTTGGC 59.475 55.000 5.25 0.00 0.00 4.52
5994 7794 0.111061 AGCTGTTGATGGACTTGGCA 59.889 50.000 0.00 0.00 0.00 4.92
5995 7795 1.180029 GCTGTTGATGGACTTGGCAT 58.820 50.000 0.00 0.00 0.00 4.40
5996 7796 1.547372 GCTGTTGATGGACTTGGCATT 59.453 47.619 0.00 0.00 0.00 3.56
5997 7797 2.673043 GCTGTTGATGGACTTGGCATTG 60.673 50.000 0.00 0.00 0.00 2.82
5998 7798 1.273048 TGTTGATGGACTTGGCATTGC 59.727 47.619 0.00 0.00 0.00 3.56
5999 7799 1.273048 GTTGATGGACTTGGCATTGCA 59.727 47.619 11.39 0.00 0.00 4.08
6000 7800 1.630223 TGATGGACTTGGCATTGCAA 58.370 45.000 11.39 0.00 0.00 4.08
6001 7801 1.273048 TGATGGACTTGGCATTGCAAC 59.727 47.619 11.39 0.00 0.00 4.17
6002 7802 1.273048 GATGGACTTGGCATTGCAACA 59.727 47.619 11.39 0.00 0.00 3.33
6003 7803 0.675083 TGGACTTGGCATTGCAACAG 59.325 50.000 11.39 5.29 0.00 3.16
6004 7804 0.675633 GGACTTGGCATTGCAACAGT 59.324 50.000 11.39 8.51 0.00 3.55
6005 7805 1.603678 GGACTTGGCATTGCAACAGTG 60.604 52.381 11.39 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.570125 TCGCGATGATTCACTCCTCTTAT 59.430 43.478 3.71 0.00 0.00 1.73
15 16 1.393603 TCGCGATGATTCACTCCTCT 58.606 50.000 3.71 0.00 0.00 3.69
17 18 1.204704 TGTTCGCGATGATTCACTCCT 59.795 47.619 10.88 0.00 0.00 3.69
25 26 1.645034 CACCTCTTGTTCGCGATGAT 58.355 50.000 10.88 0.00 0.00 2.45
27 28 1.361668 CCCACCTCTTGTTCGCGATG 61.362 60.000 10.88 1.69 0.00 3.84
37 38 3.327439 CCCCTATGATAACCCACCTCTT 58.673 50.000 0.00 0.00 0.00 2.85
72 73 1.673033 GGACGATTGTGTGGGACTCAG 60.673 57.143 0.00 0.00 30.26 3.35
76 77 1.298859 GCAGGACGATTGTGTGGGAC 61.299 60.000 0.00 0.00 0.00 4.46
83 84 0.321653 GGAGGTTGCAGGACGATTGT 60.322 55.000 0.00 0.00 0.00 2.71
118 119 1.523938 GCGGGGAGAGGTTATGTGC 60.524 63.158 0.00 0.00 0.00 4.57
143 144 6.072649 TCCAATATCCTCGTACATGTTCCTA 58.927 40.000 2.30 0.00 0.00 2.94
164 165 0.991920 GTCTTGGTCAAGGGGATCCA 59.008 55.000 15.23 0.00 38.88 3.41
214 215 7.011828 ACACATAAGTTCAAAGTGTACACAC 57.988 36.000 27.06 15.84 46.77 3.82
236 237 5.008980 TCCAAATGCATTAGATGTGTGACA 58.991 37.500 13.39 0.00 0.00 3.58
248 249 4.159135 GTGAGATTGACCTCCAAATGCATT 59.841 41.667 5.99 5.99 38.43 3.56
266 267 5.187186 GGGTTCCAGAGTAACATTAGTGAGA 59.813 44.000 0.00 0.00 0.00 3.27
267 268 5.187967 AGGGTTCCAGAGTAACATTAGTGAG 59.812 44.000 0.00 0.00 0.00 3.51
275 276 2.564062 CGGTTAGGGTTCCAGAGTAACA 59.436 50.000 0.00 0.00 0.00 2.41
276 277 2.676176 GCGGTTAGGGTTCCAGAGTAAC 60.676 54.545 0.00 0.00 0.00 2.50
283 284 0.183014 TTGTTGCGGTTAGGGTTCCA 59.817 50.000 0.00 0.00 0.00 3.53
291 292 4.138290 TGAAGAGGATTTTGTTGCGGTTA 58.862 39.130 0.00 0.00 0.00 2.85
311 312 6.339587 AGTGGAGTTTGTTTGTTTTTCTGA 57.660 33.333 0.00 0.00 0.00 3.27
314 315 5.390461 GCCAAGTGGAGTTTGTTTGTTTTTC 60.390 40.000 0.18 0.00 37.39 2.29
319 320 1.134175 CGCCAAGTGGAGTTTGTTTGT 59.866 47.619 0.18 0.00 37.39 2.83
320 321 1.134175 ACGCCAAGTGGAGTTTGTTTG 59.866 47.619 0.18 0.00 46.20 2.93
321 322 1.470051 ACGCCAAGTGGAGTTTGTTT 58.530 45.000 0.18 0.00 46.20 2.83
322 323 2.218603 CTACGCCAAGTGGAGTTTGTT 58.781 47.619 12.13 0.00 46.20 2.83
335 336 0.670239 TACGAGTCACGACTACGCCA 60.670 55.000 14.64 5.17 42.66 5.69
336 337 0.443869 TTACGAGTCACGACTACGCC 59.556 55.000 14.64 0.00 42.66 5.68
337 338 1.795536 CTTACGAGTCACGACTACGC 58.204 55.000 14.64 0.00 42.66 4.42
390 391 3.923563 AAGAGCTCGAGTGGTGCGC 62.924 63.158 15.13 0.00 40.04 6.09
399 400 3.739300 CGTCCTAAAACAAAAGAGCTCGA 59.261 43.478 8.37 0.00 0.00 4.04
400 401 3.120649 CCGTCCTAAAACAAAAGAGCTCG 60.121 47.826 8.37 0.00 0.00 5.03
409 410 1.353022 AGATGCCCCGTCCTAAAACAA 59.647 47.619 0.00 0.00 0.00 2.83
420 421 2.658593 CGCTTACGAGATGCCCCG 60.659 66.667 0.00 0.00 43.93 5.73
421 422 2.812499 TCGCTTACGAGATGCCCC 59.188 61.111 0.00 0.00 45.12 5.80
442 445 6.239430 GGTGAGGCTTATCTCAGATAACATCA 60.239 42.308 14.83 14.83 43.54 3.07
482 485 7.167535 TGCGGGAGATCATATCAAATAATCAA 58.832 34.615 0.00 0.00 0.00 2.57
503 506 2.086869 AGGTGAAAGTTCATCATGCGG 58.913 47.619 7.05 0.00 40.76 5.69
506 509 5.125900 TGCCAATAGGTGAAAGTTCATCATG 59.874 40.000 7.05 3.25 40.76 3.07
519 522 2.428171 CCAAGGTCATTGCCAATAGGTG 59.572 50.000 0.00 0.00 37.60 4.00
608 611 3.047115 AGAGATCAACATCTGGCCATCT 58.953 45.455 5.51 2.70 39.71 2.90
645 649 2.676342 CCGGGAAATAAACTTGAGGTCG 59.324 50.000 0.00 0.00 0.00 4.79
648 652 3.632145 CCATCCGGGAAATAAACTTGAGG 59.368 47.826 0.00 0.00 40.01 3.86
709 779 4.284550 GGGAGTTGGGCCTGCACA 62.285 66.667 4.53 0.00 0.00 4.57
776 854 0.237498 GCACAAGTGGGTAAAGCGAC 59.763 55.000 2.00 0.00 0.00 5.19
800 878 2.742372 CGAGGGGCCGAACTTGTG 60.742 66.667 0.00 0.00 0.00 3.33
801 879 4.016706 CCGAGGGGCCGAACTTGT 62.017 66.667 0.00 0.00 0.00 3.16
851 929 1.468565 CGAGAGAGAGAGACGACGAGT 60.469 57.143 0.00 0.00 0.00 4.18
869 947 3.429141 GACGTCGAGGTCCAGCGA 61.429 66.667 24.23 3.05 0.00 4.93
908 986 6.378848 TCTTCCTTCTAGAACCTTCTTAGCTC 59.621 42.308 0.00 0.00 38.70 4.09
924 1003 1.326951 GCCTCGCCTCTCTTCCTTCT 61.327 60.000 0.00 0.00 0.00 2.85
965 1044 1.408453 GGTAGGACCGGGAATCCAGG 61.408 65.000 17.02 17.02 38.86 4.45
1106 1185 2.063378 AGCACTCTAGCAGGGAGGC 61.063 63.158 5.78 6.02 36.85 4.70
1171 1277 4.374584 CCCCGGCCCAAACCATCA 62.375 66.667 0.00 0.00 0.00 3.07
1258 1364 1.024579 AATTTCAGGCCTACGCACCG 61.025 55.000 3.98 0.00 36.38 4.94
1272 1378 3.320826 AGCACCAAACACCCAGTAATTTC 59.679 43.478 0.00 0.00 0.00 2.17
1296 1402 1.431440 GGTTTCACAGTGCGCACAA 59.569 52.632 39.21 23.46 0.00 3.33
1311 1420 1.005394 CACAGTAGCGAACCCGGTT 60.005 57.895 1.22 1.22 44.97 4.44
1316 1425 2.391389 GCAGGCACAGTAGCGAACC 61.391 63.158 0.00 0.00 34.64 3.62
1357 1466 9.513906 TCCATGAAATCAAATTAGAACACTACA 57.486 29.630 0.00 0.00 0.00 2.74
1366 1475 8.122952 GTCGGTACTTCCATGAAATCAAATTAG 58.877 37.037 0.00 0.00 35.57 1.73
1367 1476 7.827236 AGTCGGTACTTCCATGAAATCAAATTA 59.173 33.333 0.00 0.00 35.57 1.40
1369 1478 6.180472 AGTCGGTACTTCCATGAAATCAAAT 58.820 36.000 0.00 0.00 35.57 2.32
1377 1486 4.713824 CTGTAAGTCGGTACTTCCATGA 57.286 45.455 0.00 0.00 42.42 3.07
1401 1510 1.202915 TGCACAGAGAATTTGGCAGGA 60.203 47.619 0.00 0.00 0.00 3.86
1405 1514 2.162208 TCGAATGCACAGAGAATTTGGC 59.838 45.455 0.00 0.00 0.00 4.52
1408 1517 4.074970 AGGTTCGAATGCACAGAGAATTT 58.925 39.130 0.00 0.00 0.00 1.82
1410 1519 3.340814 AGGTTCGAATGCACAGAGAAT 57.659 42.857 0.00 0.00 0.00 2.40
1414 1523 2.254546 ACAAGGTTCGAATGCACAGA 57.745 45.000 0.00 0.00 0.00 3.41
1415 1524 4.024048 ACTTTACAAGGTTCGAATGCACAG 60.024 41.667 0.00 0.00 0.00 3.66
1417 1526 4.464112 GACTTTACAAGGTTCGAATGCAC 58.536 43.478 0.00 0.00 0.00 4.57
1418 1527 3.185594 CGACTTTACAAGGTTCGAATGCA 59.814 43.478 0.00 0.00 31.04 3.96
1420 1529 4.985044 ACGACTTTACAAGGTTCGAATG 57.015 40.909 0.00 0.00 33.02 2.67
1421 1530 6.161381 ACATACGACTTTACAAGGTTCGAAT 58.839 36.000 0.00 0.00 33.02 3.34
1435 1545 3.130693 GGAGCCAGAGTAACATACGACTT 59.869 47.826 0.00 0.00 0.00 3.01
1440 1550 4.081087 TGAAAGGGAGCCAGAGTAACATAC 60.081 45.833 0.00 0.00 0.00 2.39
1442 1552 2.912956 TGAAAGGGAGCCAGAGTAACAT 59.087 45.455 0.00 0.00 0.00 2.71
1448 1558 2.422093 GGGTAATGAAAGGGAGCCAGAG 60.422 54.545 0.00 0.00 0.00 3.35
1452 1562 0.106167 GGGGGTAATGAAAGGGAGCC 60.106 60.000 0.00 0.00 0.00 4.70
1477 1587 7.383300 GGATTTAGCTAAGCAAATAAGCAATGG 59.617 37.037 6.24 0.00 38.75 3.16
1504 1778 4.099419 ACTGGTTCAAAATTCAAGTCACCC 59.901 41.667 0.00 0.00 0.00 4.61
1505 1779 5.262588 ACTGGTTCAAAATTCAAGTCACC 57.737 39.130 0.00 0.00 0.00 4.02
1506 1780 6.329496 TCAACTGGTTCAAAATTCAAGTCAC 58.671 36.000 0.00 0.00 0.00 3.67
1510 1784 6.254157 CACACTCAACTGGTTCAAAATTCAAG 59.746 38.462 0.00 0.00 0.00 3.02
1511 1785 6.071672 TCACACTCAACTGGTTCAAAATTCAA 60.072 34.615 0.00 0.00 0.00 2.69
1517 1791 4.522114 TGATCACACTCAACTGGTTCAAA 58.478 39.130 0.00 0.00 0.00 2.69
1520 1794 2.481952 GCTGATCACACTCAACTGGTTC 59.518 50.000 0.00 0.00 0.00 3.62
1567 1841 2.737252 GCAACCGGCTATTAGATACTGC 59.263 50.000 0.00 0.00 40.25 4.40
1592 1866 9.664332 ATCATATTCATTATACCTGCAGAAGAC 57.336 33.333 17.39 0.00 0.00 3.01
1747 2021 4.913924 ACGTTTCTGTCGTACATACAGTTC 59.086 41.667 19.46 12.44 43.88 3.01
1759 2033 1.194547 CCCACATTCACGTTTCTGTCG 59.805 52.381 0.00 0.00 0.00 4.35
1885 2159 8.565780 TGCTATGGGGTCATATATTCATATCA 57.434 34.615 0.00 0.00 35.53 2.15
1893 2167 6.891908 GTCCAATTTGCTATGGGGTCATATAT 59.108 38.462 0.00 0.00 37.31 0.86
1904 2178 4.789012 AGTGGTTGTCCAATTTGCTATG 57.211 40.909 0.00 0.00 46.15 2.23
1905 2179 5.418840 CCTTAGTGGTTGTCCAATTTGCTAT 59.581 40.000 0.00 0.00 46.15 2.97
1966 2240 5.957842 TGATACCCAACATGTTTCTTCAC 57.042 39.130 8.77 0.83 0.00 3.18
1997 2271 4.582701 ATCAGCAAACCACGAAAAATGA 57.417 36.364 0.00 0.00 0.00 2.57
2065 3493 4.494855 GCATGCAGCTTAACAGTAAGTAGC 60.495 45.833 14.21 0.00 39.23 3.58
2132 3582 5.178996 GCAGCAAATATACTCCAGTCAGATG 59.821 44.000 0.00 0.00 0.00 2.90
2142 3592 3.871594 ACACCTTCGCAGCAAATATACTC 59.128 43.478 0.00 0.00 0.00 2.59
2198 3648 2.025793 TGCCTGGACCATAAATCGGAAA 60.026 45.455 0.00 0.00 0.00 3.13
2199 3649 1.562008 TGCCTGGACCATAAATCGGAA 59.438 47.619 0.00 0.00 0.00 4.30
2200 3650 1.208706 TGCCTGGACCATAAATCGGA 58.791 50.000 0.00 0.00 0.00 4.55
2225 3675 1.358725 TAACTTTAGCGGCTGCAGCG 61.359 55.000 31.19 25.60 46.23 5.18
2228 3678 1.153353 GTGTAACTTTAGCGGCTGCA 58.847 50.000 21.93 2.54 46.23 4.41
2391 3841 3.579451 TTGTGGGGAGGAGGGAGGG 62.579 68.421 0.00 0.00 0.00 4.30
2393 3843 2.674220 GCTTGTGGGGAGGAGGGAG 61.674 68.421 0.00 0.00 0.00 4.30
2394 3844 1.821966 TAGCTTGTGGGGAGGAGGGA 61.822 60.000 0.00 0.00 0.00 4.20
2398 3848 2.038863 TCTTTAGCTTGTGGGGAGGA 57.961 50.000 0.00 0.00 0.00 3.71
2404 3854 6.992063 ACACTATGAATCTTTAGCTTGTGG 57.008 37.500 0.00 0.00 0.00 4.17
2406 3856 9.726438 AGTTTACACTATGAATCTTTAGCTTGT 57.274 29.630 0.00 0.00 0.00 3.16
2442 3892 8.946085 CAAACAAATGAAGTATAGACAAGGCTA 58.054 33.333 0.00 0.00 0.00 3.93
2456 3906 8.752766 AGCAGAATACAATCAAACAAATGAAG 57.247 30.769 0.00 0.00 32.06 3.02
2457 3907 8.579006 AGAGCAGAATACAATCAAACAAATGAA 58.421 29.630 0.00 0.00 32.06 2.57
2458 3908 8.024865 CAGAGCAGAATACAATCAAACAAATGA 58.975 33.333 0.00 0.00 0.00 2.57
2494 3944 8.631480 ATTTACCTAGACTAACCAAACAAAGG 57.369 34.615 0.00 0.00 0.00 3.11
2569 4023 0.466189 AACAGACAACCAGTGGCAGG 60.466 55.000 9.78 0.91 37.96 4.85
2595 4049 6.484288 TCTTGGTGAGAATACAATCAATGGT 58.516 36.000 0.00 0.00 0.00 3.55
2640 4094 9.481340 CAAATGTGCTCTATTATTACTGCTCTA 57.519 33.333 0.00 0.00 0.00 2.43
2857 4318 4.479158 AGGGAGTGGCAATTTTGTAAGAA 58.521 39.130 0.00 0.00 0.00 2.52
2872 4333 1.296715 CTTTGGGACGGAGGGAGTG 59.703 63.158 0.00 0.00 0.00 3.51
2890 4351 0.863144 TGAAAGTTGGCGTCGCTTAC 59.137 50.000 18.11 14.71 0.00 2.34
2895 4356 2.542595 AGTTAGTTGAAAGTTGGCGTCG 59.457 45.455 0.00 0.00 0.00 5.12
2897 4358 4.976224 AAAGTTAGTTGAAAGTTGGCGT 57.024 36.364 0.00 0.00 0.00 5.68
2899 4360 7.922837 TGTACTAAAGTTAGTTGAAAGTTGGC 58.077 34.615 8.92 0.00 40.96 4.52
2935 4396 8.161699 TGTCCCAAAATAAGTGTCTTAACTTC 57.838 34.615 0.00 0.00 40.77 3.01
2960 4504 4.726825 TCTTGCTTAAATGATACCCCCTCT 59.273 41.667 0.00 0.00 0.00 3.69
3146 4691 3.553105 GCTAAATGCACATTTTAGCTGCC 59.447 43.478 25.57 6.85 40.99 4.85
3259 4805 4.160642 TGAGCATTAGCCACTTGATGAT 57.839 40.909 0.00 0.00 43.56 2.45
3338 4884 7.066525 TCGGTACTGCTTTTATTCCCTTTATTG 59.933 37.037 0.00 0.00 0.00 1.90
3349 4895 3.581024 TCACGTCGGTACTGCTTTTAT 57.419 42.857 0.00 0.00 0.00 1.40
3354 4900 0.038526 CCTTTCACGTCGGTACTGCT 60.039 55.000 0.00 0.00 0.00 4.24
3402 4948 6.183360 GGAACTTCATCTTCATCTTCTTCTGC 60.183 42.308 0.00 0.00 0.00 4.26
3470 5016 2.107366 GGATTGGGGTTGGTGGTATTG 58.893 52.381 0.00 0.00 0.00 1.90
3543 5089 1.877680 CGATGCACTGGTTTCACTGGA 60.878 52.381 0.00 0.00 0.00 3.86
3548 5094 1.069978 TGAGACGATGCACTGGTTTCA 59.930 47.619 0.00 0.00 0.00 2.69
3647 5193 2.398036 GGTTGAATACCGCGTGCG 59.602 61.111 4.92 7.38 37.12 5.34
3701 5247 3.944015 AGAGGCAATACACTTGCAAGATC 59.056 43.478 32.50 14.06 46.58 2.75
3926 5473 4.669206 TTGTTTTGGCATGTCAATGTCT 57.331 36.364 14.57 0.00 39.28 3.41
4041 5588 4.321230 GGCTCCTTACACATCCAAACAAAG 60.321 45.833 0.00 0.00 0.00 2.77
4160 5713 4.142469 ACAGTTTTGTAACTTGACAGCACC 60.142 41.667 0.00 0.00 41.85 5.01
4183 5736 6.202331 TGATTATTGACCCTTCCAGACTCTA 58.798 40.000 0.00 0.00 0.00 2.43
4266 5819 5.435041 AGTCCTACCCATCCATCCATTTAAA 59.565 40.000 0.00 0.00 0.00 1.52
4287 5840 4.519540 TTTTAGCAAAATGGCAGGAGTC 57.480 40.909 0.00 0.00 35.83 3.36
4297 5850 9.396938 GCATAAAAGCATTGTTTTTAGCAAAAT 57.603 25.926 18.95 4.75 34.54 1.82
4410 5969 5.358298 ACGTAAAGATCCAAAGAAGCAAC 57.642 39.130 0.00 0.00 0.00 4.17
4458 6017 9.902684 AGATGAGAATATCAGTCACAGAAAAAT 57.097 29.630 0.00 0.00 42.53 1.82
4512 6071 8.954950 TTTCCTTTTCAAATTCTTTGTATGCA 57.045 26.923 0.00 0.00 41.36 3.96
4591 6150 8.764558 TGCAAGGTAATAATGTAGAGAGGTTAA 58.235 33.333 0.00 0.00 0.00 2.01
4658 6217 2.031314 CAGCATCAATCTACAAGGCACG 59.969 50.000 0.00 0.00 0.00 5.34
4684 6243 3.076182 AGGTCAAGTACTCTTCCCTCTCA 59.924 47.826 0.00 0.00 30.68 3.27
4735 6294 6.367983 AGCATGGGTATATGAACAGAACAAT 58.632 36.000 0.00 0.00 0.00 2.71
4749 6308 4.235079 TCACTTTGCTAAGCATGGGTAT 57.765 40.909 7.87 0.00 38.76 2.73
4752 6311 3.084039 TCTTCACTTTGCTAAGCATGGG 58.916 45.455 7.87 0.00 38.76 4.00
4757 6316 7.936950 AAAGAAAATCTTCACTTTGCTAAGC 57.063 32.000 7.87 0.00 35.27 3.09
4794 6387 8.501580 AGATAAATAATGCATGATGAGTTGACG 58.498 33.333 0.00 0.00 0.00 4.35
4808 6401 4.580167 TCCCTGTGCACAGATAAATAATGC 59.420 41.667 41.50 0.96 46.59 3.56
4823 6417 1.078848 CTGCCTGTACTCCCTGTGC 60.079 63.158 0.00 0.00 0.00 4.57
4898 6492 1.212751 GATGGGTTTGCTGTTCGCC 59.787 57.895 0.00 0.00 38.05 5.54
4967 6561 0.877071 CAGCAAAATCTGTGCCGTCT 59.123 50.000 0.00 0.00 43.27 4.18
4970 6564 1.001487 TCAACAGCAAAATCTGTGCCG 60.001 47.619 0.00 0.00 45.77 5.69
5031 6625 2.223876 ACTTCTTGTTCACGGTAGCGAA 60.224 45.455 22.88 2.41 0.00 4.70
5051 6645 2.151202 TGCAAAATCTGGAGAACCGAC 58.849 47.619 0.00 0.00 39.42 4.79
5064 6658 6.008960 AGAAAGACCTCTCTTCATGCAAAAT 58.991 36.000 0.00 0.00 35.52 1.82
5065 6659 5.380043 AGAAAGACCTCTCTTCATGCAAAA 58.620 37.500 0.00 0.00 35.52 2.44
5069 6663 3.530535 GGAGAAAGACCTCTCTTCATGC 58.469 50.000 0.99 0.00 41.45 4.06
5070 6664 3.194542 ACGGAGAAAGACCTCTCTTCATG 59.805 47.826 0.99 0.00 41.45 3.07
5071 6665 3.436243 ACGGAGAAAGACCTCTCTTCAT 58.564 45.455 0.99 0.00 41.45 2.57
5072 6666 2.877866 ACGGAGAAAGACCTCTCTTCA 58.122 47.619 0.99 0.00 41.45 3.02
5073 6667 3.367600 GGAACGGAGAAAGACCTCTCTTC 60.368 52.174 0.99 0.00 41.45 2.87
5076 6670 2.094442 CAGGAACGGAGAAAGACCTCTC 60.094 54.545 0.00 0.00 41.06 3.20
5120 6714 2.348218 CGCGTTAGTTCAAAAGTCGCTT 60.348 45.455 0.00 0.00 39.99 4.68
5182 6776 8.431910 AGGGAATTTGTCAGTACTTAAGACTA 57.568 34.615 10.09 3.40 33.56 2.59
5191 6785 3.010420 GGCAGAGGGAATTTGTCAGTAC 58.990 50.000 0.00 0.00 0.00 2.73
5270 6878 5.914716 TCCAAGGTATAGGGGTTGAACATAT 59.085 40.000 0.00 0.00 0.00 1.78
5277 6885 2.172717 CCTGTCCAAGGTATAGGGGTTG 59.827 54.545 0.00 0.00 41.74 3.77
5278 6886 2.488836 CCTGTCCAAGGTATAGGGGTT 58.511 52.381 0.00 0.00 41.74 4.11
5279 6887 1.345112 CCCTGTCCAAGGTATAGGGGT 60.345 57.143 13.61 0.00 45.78 4.95
5281 6889 2.047830 GTCCCTGTCCAAGGTATAGGG 58.952 57.143 14.65 14.65 45.78 3.53
5282 6890 2.047830 GGTCCCTGTCCAAGGTATAGG 58.952 57.143 0.00 0.00 45.78 2.57
5283 6891 2.047830 GGGTCCCTGTCCAAGGTATAG 58.952 57.143 0.00 0.00 45.78 1.31
5285 6893 0.981277 CGGGTCCCTGTCCAAGGTAT 60.981 60.000 6.29 0.00 45.78 2.73
5287 6895 2.928396 CGGGTCCCTGTCCAAGGT 60.928 66.667 6.29 0.00 45.78 3.50
5288 6896 2.928396 ACGGGTCCCTGTCCAAGG 60.928 66.667 6.29 0.00 46.94 3.61
5289 6897 2.663196 GACGGGTCCCTGTCCAAG 59.337 66.667 17.36 0.00 44.27 3.61
5300 6961 1.475392 CGAGGACTATCAGAGACGGGT 60.475 57.143 0.00 0.00 0.00 5.28
5306 6967 3.629855 ACATCACACGAGGACTATCAGAG 59.370 47.826 0.00 0.00 0.00 3.35
5313 6974 2.932622 GCATCAACATCACACGAGGACT 60.933 50.000 0.00 0.00 0.00 3.85
5358 7019 7.224362 TCACATGTAATTTGAGGCAAACTTTTG 59.776 33.333 0.00 0.00 36.13 2.44
5359 7020 7.271511 TCACATGTAATTTGAGGCAAACTTTT 58.728 30.769 0.00 0.00 36.13 2.27
5360 7021 6.815089 TCACATGTAATTTGAGGCAAACTTT 58.185 32.000 0.00 0.00 36.13 2.66
5361 7022 6.403866 TCACATGTAATTTGAGGCAAACTT 57.596 33.333 0.00 0.00 36.13 2.66
5362 7023 6.017400 CTCACATGTAATTTGAGGCAAACT 57.983 37.500 0.00 0.00 45.14 2.66
5370 7031 9.142515 GAAATCATTTGCTCACATGTAATTTGA 57.857 29.630 0.00 0.00 31.23 2.69
5371 7032 8.385111 GGAAATCATTTGCTCACATGTAATTTG 58.615 33.333 0.00 0.00 0.00 2.32
5372 7033 8.316214 AGGAAATCATTTGCTCACATGTAATTT 58.684 29.630 0.00 0.00 36.54 1.82
5373 7034 7.844009 AGGAAATCATTTGCTCACATGTAATT 58.156 30.769 0.00 0.00 36.54 1.40
5374 7035 7.414222 AGGAAATCATTTGCTCACATGTAAT 57.586 32.000 0.00 0.00 36.54 1.89
5417 7210 4.671831 TCCACATTCCAAATTAGGCTTCA 58.328 39.130 0.00 0.00 0.00 3.02
5426 7219 8.599624 ATCTTGTAAATCTCCACATTCCAAAT 57.400 30.769 0.00 0.00 0.00 2.32
5471 7265 3.006323 ACTGTGAGACTAACTTGGCAGAG 59.994 47.826 0.00 0.00 0.00 3.35
5508 7302 1.695813 CGCGTGAAATTTCATTGGCA 58.304 45.000 26.86 6.73 39.73 4.92
5509 7303 0.366534 GCGCGTGAAATTTCATTGGC 59.633 50.000 23.05 22.39 39.73 4.52
5555 7349 5.883673 TGATGGGGACGGTATTTTTCTTAAG 59.116 40.000 0.00 0.00 0.00 1.85
5560 7354 2.357952 GCTGATGGGGACGGTATTTTTC 59.642 50.000 0.00 0.00 0.00 2.29
5561 7355 2.375146 GCTGATGGGGACGGTATTTTT 58.625 47.619 0.00 0.00 0.00 1.94
5600 7397 2.043411 CAATCCTGACGTTGTTTTGCG 58.957 47.619 0.00 0.00 0.00 4.85
5713 7510 4.334443 GTGCACGCTACATGATTAAACAG 58.666 43.478 0.00 0.00 0.00 3.16
5732 7531 3.166657 GCAACTCAGATTTCATTCGTGC 58.833 45.455 0.00 0.00 0.00 5.34
5760 7559 0.039437 TGTCGCGAGTCCTCTTGTTC 60.039 55.000 10.24 0.00 0.00 3.18
5764 7563 1.202313 GCTATTGTCGCGAGTCCTCTT 60.202 52.381 10.24 0.00 0.00 2.85
5823 7623 3.455469 GCAGGCTGGTCATTGGCC 61.455 66.667 17.64 0.00 45.57 5.36
5843 7643 3.870274 TCATCATTGACAGCTCCAGAAG 58.130 45.455 0.00 0.00 0.00 2.85
5847 7647 2.686405 GCATTCATCATTGACAGCTCCA 59.314 45.455 0.00 0.00 32.11 3.86
5850 7650 5.768164 TGATATGCATTCATCATTGACAGCT 59.232 36.000 3.54 0.00 34.56 4.24
5952 7752 2.756760 CACCACCATCTAAAGCAGCATT 59.243 45.455 0.00 0.00 0.00 3.56
5961 7761 0.692476 ACAGCTGCACCACCATCTAA 59.308 50.000 15.27 0.00 0.00 2.10
5971 7771 1.068748 CAAGTCCATCAACAGCTGCAC 60.069 52.381 15.27 0.00 0.00 4.57
5976 7776 1.180029 ATGCCAAGTCCATCAACAGC 58.820 50.000 0.00 0.00 0.00 4.40
5977 7777 2.673043 GCAATGCCAAGTCCATCAACAG 60.673 50.000 0.00 0.00 0.00 3.16
5978 7778 1.273048 GCAATGCCAAGTCCATCAACA 59.727 47.619 0.00 0.00 0.00 3.33
5979 7779 1.273048 TGCAATGCCAAGTCCATCAAC 59.727 47.619 1.53 0.00 0.00 3.18
5980 7780 1.630223 TGCAATGCCAAGTCCATCAA 58.370 45.000 1.53 0.00 0.00 2.57
5981 7781 1.273048 GTTGCAATGCCAAGTCCATCA 59.727 47.619 0.59 0.00 0.00 3.07
5982 7782 1.273048 TGTTGCAATGCCAAGTCCATC 59.727 47.619 0.59 0.00 0.00 3.51
5983 7783 1.274167 CTGTTGCAATGCCAAGTCCAT 59.726 47.619 0.59 0.00 0.00 3.41
5984 7784 0.675083 CTGTTGCAATGCCAAGTCCA 59.325 50.000 0.59 0.00 0.00 4.02
5985 7785 0.675633 ACTGTTGCAATGCCAAGTCC 59.324 50.000 0.59 0.00 0.00 3.85
5986 7786 1.774639 CACTGTTGCAATGCCAAGTC 58.225 50.000 0.59 0.00 0.00 3.01
5987 7787 3.972107 CACTGTTGCAATGCCAAGT 57.028 47.368 0.59 0.42 0.00 3.16


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

AutoCloner maintained by Alex Coulton.